# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Ferroplasma_acidarmanus_fer1_uid54095/NC_021592.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Ferroplasma_acidarmanus_fer1_uid54095/NC_021592.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Archaea/Euryarchaeota/Ferroplasma_acidarmanus_fer1_uid54095/NC_021592.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       gi|518651361|ref|YP_008140881.1|  [L=180]
Description: zinc metalloprotease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0016   17.8   0.6      0.003   16.9   0.2    1.6  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.65    9.8   9.4        2.1    8.1   9.0    2.1  2  TatC           Sec-independent protein translocase protein (T


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.2   1.8e+03     144     165 ..      53      74 ..      30      87 .. 0.57
   2 !   16.9   0.2   3.3e-07     0.003       2      29 ..      98     125 ..      97     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.2
                                       XXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 144 ektlkvvvltvkalgklitgkl 165
                                       ++ +++++l+++ ++ +++g++
  gi|518651361|ref|YP_008140881.1|  53 SNKVNLIMLILTLVSTIYVGSI 74 
                                       3445555555555555555555 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 3.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   2 filllgilvvvHElGHflvAklcgvkve 29 
                                       f l l++++ +HE +H++vA++ +v+  
  gi|518651361|ref|YP_008140881.1|  98 FSLPLMFILGIHETAHYIVARRYKVNAS 125
                                       88999******************99873 PP

>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1     0.067     6e+02      73     112 ..      30      69 ..      27      76 .. 0.70
   2 ?    8.1   9.0   0.00024       2.1      65     128 ..      61     144 ..      55     180 .] 0.63

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.067
                                       HHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHH CS
                              TatC  73 sPvilyqlwafvapgLykherrlvlvfliaslllfllGaa 112
                                       +P++++ +  +v+ g++++      ++ ++ l+l+l+  +
  gi|518651361|ref|YP_008140881.1|  30 IPFLVLDVEHYVEVGIRPKASYRSNKVNLIMLILTLVSTI 69 
                                       6888999999999999988766666666666666655444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00024
                                       HHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHH.HHHHHHHH.HHHHTHH.....HHHHHHHT....... CS
                              TatC  65 lvaglvlasPvilyqlwafvapgLykherrlvlvfliasl.llfllGaa.fayfvvl.....plvlkfll....... 127
                                       l++ lv ++ v  +   +fv pg   +e +l++ f+++sl l+f+lG+   a+++v+      ++l f++       
  gi|518651361|ref|YP_008140881.1|  61 LILTLVSTIYVGSIYASSFVHPGTFAEEYKLLYGFVFFSLpLMFILGIHeTAHYIVArrykvNASLPFFIpfpylig 137
                                       566667777777777889*********************86889999963455555422222333335554444444 PP

                                       ......T CS
                              TatC 128 ......s 128
                                             s
  gi|518651361|ref|YP_008140881.1| 138 tfgafvS 144
                                       4444440 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1155.95
//
Query:       gi|518651362|ref|YP_008140882.1|  [L=349]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   0.2    1.6e-29  103.1   0.2    1.3  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   24.1   1.1      0.034   14.1   0.0    2.5  2  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
       0.14   12.2   0.9       0.56   10.3   0.0    2.5  3  HTH_19       Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.2   2.7e-33   1.6e-29       3     213 ..     106     308 ..     104     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 2.7e-33
                         DDE_Tnp_1   3 krevlivDattvrvpgtkedarwgykggkykygyklhiavdtr.sglilsvvitpgnvhdskglkqlldelrpr..k 76 
                                        ++vl++D+t++++  ++   +  y++g++++g+k+h+a  +    l+l++ itp+nvhdsk++++ll+ +++    
  gi|518651362|ref|YP_008140882.1| 106 LYSVLAIDSTFIETMVKG---SGIYQRGERRNGIKIHTAAIASpYPLPLKAIITPANVHDSKVFDDLLEYINEYisG 179
                                       589**********97777...55888***********8754441566**************************9*** PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyy 153
                                       +++++ D GY + + + +l+ekg+++++r+kkn+ +    +e ++ ++ r ++  + +  s   +n+         +
  gi|518651362|ref|YP_008140882.1| 180 NTVLTFDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIKEETFNSKIVRFRNGLELRLVSLDINNR--------KR 248
                                       ***********************************99994444444444444444444444444444........45 PP

                         DDE_Tnp_1 154 vtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                        + t+  +l+   +  +y +Rw+iE +F  +kr +++ +l +r+ln++ +q++++l+++ 
  gi|518651362|ref|YP_008140882.1| 249 EYITDILDLPEIYIYYIYMRRWVIEKIFENMKRILKITHLISRDLNGIINQVFATLISYI 308
                                       667889999************************************************995 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.7e-06     0.034      59     121 ..     151     219 ..     134     236 .. 0.77
   2 !    8.1   0.3   0.00041       2.4     127     150 ..     265     288 ..     240     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                       DDE_Tnp_1_3  59 lavkltpgnvdDrepveelakellgklfa......Dkgyiskklaeelleegielitklrknmkkklls 121
                                       l++ +tp+nv+D +  ++l + + + + +      D gy     + el+e+gi+++++++kn   ++++
  gi|518651362|ref|YP_008140882.1| 151 LKAIITPANVHDSKVFDDLLEYINEYISGntvltfDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIK 219
                                       56789**********9888777665443322222399*************************8877765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00041
                       DDE_Tnp_1_3 127 lLrkrslietvndelknisqieht 150
                                       +  +r +ie +++++k+i +i h 
  gi|518651362|ref|YP_008140882.1| 265 IYMRRWVIEKIFENMKRILKITHL 288
                                       6679******************95 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.3e-05      0.56      15      50 ..      53      88 ..      48      90 .. 0.76
   2 ?   -2.8   0.0       1.1   6.6e+03      28      41 ..     172     184 ..     167     187 .. 0.79
   3 ?   -2.5   0.1       0.9   5.4e+03      26      46 ..     203     224 ..     196     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.3e-05
                            HTH_19 15 qeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      + ++a+++gis+s++s++ n + + +  +++++i++
  gi|518651362|ref|YP_008140882.1| 53 LTDIAYNNGISKSQLSKLNNKRPYSIFEKVFYSILR 88
                                      679***************977554554666677766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                            HTH_19  28 kisaiEngkkdvps 41 
                                       +i+++++g++ v++
  gi|518651362|ref|YP_008140882.1| 172 YINEYISGNT-VLT 184
                                       8999999998.765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.9
                            HTH_19  26 rskisaiEng.kkdvpsaelll 46 
                                       +++ s i ++  + v++ e+++
  gi|518651362|ref|YP_008140882.1| 203 INFVSRIKKNaDYTVIKEETFN 224
                                       6778888888866678777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.34s 00:00:01.03 Elapsed: 00:00:00.58
# Mc/sec: 1826.14
//
Query:       gi|518651363|ref|YP_008140883.1|  [L=81]
Description: hypothetical protein FACI_IFERC00001G0002 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-17   61.6   2.4    7.3e-17   61.3   2.4    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 !   61.3   2.4   4.1e-21   7.3e-17       1      67 [.       1      64 [.       1      67 [. 0.96

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 4.1e-21
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEE CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriyk 67
                                      m+v++vYD+     r ++++k+lk++ ++++Q+SVFege++e+ql+++++ l k  +++ d i iy+
  gi|518651363|ref|YP_008140883.1|  1 MYVIIVYDV--AVDRINNIRKFLKRF-LNWIQNSVFEGEITESQLIRIENYLNKKTEQDYDFIKIYH 64
                                      9********..9**************.******************************9999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 515.56
//
Query:       gi|518651364|ref|YP_008140884.1|  [L=328]
Description: hypothetical protein FACI_IFERC00001G0003 [Ferroplasma acidarmanus fer1]
Scores for complete 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-80  268.5   0.1    6.3e-80  268.3   0.1    1.0  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
       0.13   12.4   2.9       0.69   10.1   0.2    2.4  2  DUF1874   Domain of unknown function (DUF1874)
       0.13   12.2   3.3        0.3   11.1   2.6    1.9  2  RSV_NS2   Respiratory synctial virus non-structural protein N


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 !  268.3   0.1   1.1e-83   6.3e-80       7     283 .]      11     283 ..       6     283 .. 0.98

  Alignments for each domain:
  == domain 1  score: 268.3 bits;  conditional E-value: 1.1e-83
                                       EEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.SSSSTHH CS
                          Cas_Cas1   7 gaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.eesgnve 82 
                                       ++++ ++g+++++e+    k+ ip+e+++s++ ++ vs+s+ +++ +++ gip++f++++g+y ++l+p ++  +++
  gi|518651364|ref|YP_008140884.1|  11 ESTVYVDGGTIIIENSIG-KNAIPVENVRSVYAHKPVSISSGVVSIISKLGIPIHFFNWYGNYEATLWPkSKDISGD 86 
                                       345999*********988.99************************************************9999**** PP

                                       HHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHHHHHHHH CS
                          Cas_Cas1  83 lrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrgiEGeaa 159
                                       + ++Q++ + d ++r+++ak++v+g+l+n  ++l+++  ++    +++  e++++ + +l++a +++e++giEG+  
  gi|518651364|ref|YP_008140884.1|  87 VIIKQAQKYLDIHERINIAKSFVSGALHNFNRILSEYDTET----VKKSREDIKSNIGNLTNAMDITEIMGIEGRSH 159
                                       *************************************9999....9******************************* PP

                                       HHHHHHHHHHCSCGGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HHHHHHHHH CS
                          Cas_Cas1 160 kaYfeafdkllkeefefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsLalDLmEe 236
                                       + Yf+a+d++++e+f++++R rrpp ++ Nal+sfg++l+y+ vl++i+ ++L+P+i++LHe++++r+sL lD++E+
  gi|518651364|ref|YP_008140884.1| 160 NSYFKAMDSVIPEKFRINKRIRRPPGNMGNALISFGNSLVYASVLTEIYFTHLNPTISYLHEPSERRFSLSLDIAEI 236
                                       ***************************************************************************** PP

                                       HHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHHH CS
                          Cas_Cas1 237 fRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafee 283
                                       f+p++  +l l link++++e+dF+++ ++v+L+e+g+k +l+++ee
  gi|518651364|ref|YP_008140884.1| 237 FKPIISHKLFLYLINKKIINENDFDNSLEKVILNEKGKKLYLKNYEE 283
                                       *********************************************96 PP

>> DUF1874  Domain of unknown function (DUF1874)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.2     0.027   1.6e+02      16      59 ..     113     156 ..      87     181 .. 0.78
   2 ?   10.1   0.2   0.00011      0.69       1      51 [.     247     298 ..     247     312 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.027
                                       .....EEEEEEE-HHHHHSSTTEEE----HHHHHHHHHHHT--- CS
                           DUF1874  16 lykiekitieeakellkenneefvsaiGHeataellselldvei 59 
                                       l+++++i  e   e +k++ e+++s iG    a  ++e++++e 
  gi|518651364|ref|YP_008140884.1| 113 LHNFNRILSEYDTETVKKSREDIKSNIGNLTNAMDITEIMGIEG 156
                                       55677777777788889989999999999999999999988765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00011
                                       EEEES---GGB-SE.......EEEEEEE-HH.HHHSSTTEEE----HHHHHHH CS
                           DUF1874   1 vyllNslvltlkeeglykie.kitieeakel.lkenneefvsaiGHeataell 51 
                                       +yl+N  +++ ++    ++e  i  e+ k+l lk+++e++ s + H   ++ +
  gi|518651364|ref|YP_008140884.1| 247 LYLINKKIINENDFD-NSLEkVILNEKGKKLyLKNYEEKLTSTVFHRTLKKNV 298
                                       69********44443.3556155667789999**************9887765 PP

>> RSV_NS2  Respiratory synctial virus non-structural protein NS2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.91   5.4e+03      48      68 ..      55      75 ..      36     100 .. 0.60
   2 ?   11.1   2.6     5e-05       0.3      12      85 ..     218     301 ..     208     326 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.91
                           RSV_NS2 48 ivrklderqatftflvnyemk 68
                                      i+ kl      f +  nye  
  gi|518651364|ref|YP_008140884.1| 55 IISKLGIPIHFFNWYGNYEAT 75
                                      334444444444444444444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5e-05
                           RSV_NS2  12 rlmitdmrplsmdsiitsltkeiithk.fiylinnecivrk.ld........erqatftflvnyemkllhkvgstky 78 
                                        l     r +s+   i+ + k ii+hk f+ylin++ i  + +d        + +    +l nye kl   v     
  gi|518651364|ref|YP_008140884.1| 218 YLHEPSERRFSLSLDIAEIFKPIISHKlFLYLINKKIINENdFDnslekvilNEKGKKLYLKNYEEKLTSTVFHRTL 294
                                       55555667788888899*********9789***99888643133111011112234445777777777777666666 PP

                           RSV_NS2  79 kkyteyn 85 
                                       kk   y+
  gi|518651364|ref|YP_008140884.1| 295 KKNVTYQ 301
                                       6665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2028.78
//
Query:       gi|518651365|ref|YP_008140885.1|  [L=165]
Description: hypothetical protein FACI_IFERC00001G0004 [Ferroplasma acidarmanus fer1]
Scores for 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-50  170.1   8.7    4.5e-50  169.9   8.7    1.0  1  Cas_Cas4  Domain of unknown function DUF83
  ------ inclusion threshold ------
      0.022   15.1   0.7      0.032   14.6   0.7    1.3  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily
      0.069   13.1   1.4      0.094   12.6   1.4    1.4  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> Cas_Cas4  Domain of unknown function DUF83
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   8.7   7.5e-54   4.5e-50       1     162 []       8     165 .]       8     165 .] 0.99

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 7.5e-54
                          Cas_Cas4   1 tgtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskk 77 
                                       tg++++yy+iCk+klwl+sh++++e+++e+v++Gk lh+ +y++e+kev++ ++ik D+++ ++++++++E+Kk +k
  gi|518651365|ref|YP_008140885.1|   8 TGVQMSYYVICKTKLWLHSHKVSMEKENENVKIGKELHDIRYKNERKEVSM-DNIKYDFIR-KGKNIEIHEIKKTDK 82 
                                       699************************************************.*********.9************** PP

                          Cas_Cas4  78 keeaaklQllyYlllLekkgveikeGvleypkekkreevelteelreelekaikeieeiissekppkvkkkkiCkkC 154
                                        e+a+++Q+lyYl+ L+ +g++++ G+l+yp ++k +++ l++e++ e+ k+i++i++iis+ +pp++++k++Ck+C
  gi|518651365|ref|YP_008140885.1|  83 LEKAHTIQVLYYLFRLDLNGIKAT-GFLDYPLTNKHKKIVLEDEDKCEIIKIIENIKKIISN-EPPQPEYKNYCKSC 157
                                       ************************.************************************9.8************* PP

                          Cas_Cas4 155 ayaelCli 162
                                       +y+e+C++
  gi|518651365|ref|YP_008140885.1| 158 SYFEFCWC 165
                                       *******6 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   5.4e-06     0.032      49      97 ..      46      99 ..      25     121 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-06
                          PDDEXK_3 49 pvvYkgkevg...eeyrlDllv..eekvivElKaveelkeeheaqllnYlkltk 97
                                      ++ Yk+++ +   +++  D++   ++  i E+K +++l+++h++q+l Yl  ++
  gi|518651365|ref|YP_008140885.1| 46 DIRYKNERKEvsmDNIKYDFIRkgKNIEIHEIKKTDKLEKAHTIQVLYYLFRLD 99
                                      577776543311133778888864555689*******************96655 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 ?   12.6   1.4   1.6e-05     0.094     134     254 ..      63     163 ..       9     164 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.6e-05
                          PDDEXK_1 134 iDrvddkegelriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkk 210
                                       +D + + ++ ++i + K ++    ++   e ++ +Q+l Yl+ l  +  +     + g l +    p +++++++  
  gi|518651365|ref|YP_008140885.1|  63 YDFIRKGKN-IEIHEIKKTD----KL---EKAHTIQVLYYLFRLDLNGIK-----ATGFLDY----PLTNKHKKIVL 122
                                       566655555.7777777444....22...345667999999888888221.....3444444....44555555555 PP

                          PDDEXK_1 211 malteeeleallqeleelaeeilagefparpskk.CeyCpyksvC 254
                                           +e+  ++ + +e++ ++i + e p  ++k+ C++C+y + C
  gi|518651365|ref|YP_008140885.1| 123 E---DEDKCEIIKIIENI-KKIISNEPPQPEYKNyCKSCSYFEFC 163
                                       5...55555555555554.4444444455555557*******999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1410  (0.0786435); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1082.45
//
Query:       gi|518651366|ref|YP_008140886.1|  [L=746]
Description: CRISPR-associated helicase Cas3 [Ferroplasma acidarmanus fer1]
Scores for 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   45.5   1.1    1.9e-10   40.8   0.0    3.4  4  DEAD        DEAD/DEAH box helicase
    4.8e-09   36.5   1.2    4.8e-09   36.5   1.2    2.8  3  Helicase_C  Helicase conserved C-terminal domain
    2.4e-08   34.2   0.1    2.4e-08   34.2   0.1    3.8  4  ResIII      Type III restriction enzyme, res subunit
    1.4e-07   31.8   0.0    2.4e-07   31.1   0.0    1.3  1  HD_6        HD 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 ?   -0.1   0.0      0.15   6.9e+02     134     167 ..      68     101 ..      63     103 .. 0.84
   2 !   40.8   0.0   4.1e-14   1.9e-10      13     174 ..     258     423 ..     249     425 .. 0.69
   3 ?   -0.4   0.2      0.19   8.6e+02      39      94 ..     463     518 ..     452     538 .. 0.66
   4 ?   -3.1   0.1       1.3   5.7e+03      58      94 ..     588     628 ..     587     652 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.15
                                       HHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEES CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 134 ldqgfsdfinrilnqlpqitcdgklqrqvivlSA 167
                                       ld++f+d in++++q p  + d ++     ++SA
  gi|518651366|ref|YP_008140886.1|  68 LDKSFQDMINKVIQQDPGDKVDIPKALPHALISA 101
                                       6889************999999887766777776 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 4.1e-14
                                       TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST....SEEEEE... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx....xxxxxx... RF
                              DEAD  13 gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.id....lrvlli... 81 
                                       ++++ +++ +TGsGKT+a l+            ++ +++++ Pt    ++++++lk+++   ++       +l+   
  gi|518651366|ref|YP_008140886.1| 258 NNDNYIIQSPTGSGKTEASLLWSK--------YNNGRIVYILPTMVTSNKIFERLKQIFGDiVGiqhsT--SLLlmd 324
                                       56799*************777665........5667************************633344432..322122 PP

                                       ..ETTSSHHHHHHHH....HTT..CSEEEEEHHHHHHHH.....HCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHH CS
                                       ..xxxxxxxxxxxxx....xxx..xxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  82 ..iggvaardqlskl....dng..vdivvgtpgrlddll.....stgklnlsqvrflVlDEadrlldqgfsdfinri 145
                                         i  ++ + +++++     ++    i+v+t ++l+  l     ++  +  s ++ +++DE++ +     s  i+  
  gi|518651366|ref|YP_008140886.1| 325 tdIDADKNNYNHDAFarfyYKTfsSPIMVSTVDQLLYSLfninrWDSVFFNSGISNVIFDEIHAYDPYTTSLIIEY- 400
                                       22444444444444443331336799******999995557754333444888999***********966666666. PP

                                       HHHSHHHCTTSTTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 146 lnqlpqitcdgklqrqvivlSATlpkdvk 174
                                       +n+  +i    +  ++v+++SAT+p+ +k
  gi|518651366|ref|YP_008140886.1| 401 INKA-HI---FN--QRVLIMSATIPDILK 423
                                       5555.22...23..46********96655 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.19
                                       HHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSH..HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                              DEAD  39 vyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaa..rdqlskl 94 
                                       + + k+k+ +k+l+++ t + a+  +++++ + +  d +v+l+ ++ ++  r+++s+l
  gi|518651366|ref|YP_008140886.1| 463 I-K-KHKDIKKILVIANTIKTAKYLYSQIRDIDEIKDKKVVLFHSQFTYndRKEKSEL 518
                                       3.2.577778999999999999999999999998777777777664333113333333 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHTTTST...SEEE.EEETTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx...xxxx.xxxxxxxxxxxxxxx RF
                              DEAD  58 eLaeqtlnnlkkfkkyid...lrvl.liiggvaardqlskl 94 
                                       eL+++t++ ++k+  + +    ++   i+++++++++l++ 
  gi|518651366|ref|YP_008140886.1| 588 ELMKKTFDYFNKYNYKSNtdsKKLInEIYNDNEYKENLKNA 628
                                       67777777776666643322422222445555555555544 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1   4.6e+03      47      47 ..     268     268 ..     196     337 .. 0.57
   2 ?   -0.9   0.0      0.46   2.1e+03      11      51 ..     403     457 ..     394     462 .. 0.53
   3 !   36.5   1.2   1.1e-12   4.8e-09       6     110 ..     459     564 ..     454     565 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                       S CS
                        Helicase_C  47 h 47 
                                       +
  gi|518651366|ref|YP_008140886.1| 268 T 268
                                       1 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.46
                                       HHTTTTSEEEEEESSHHHHHH.........HHHHHHHT.....TSTEEEESTTST CS
                        Helicase_C  11 kleeeggkilifvntidrlek.........vklllekk.....gikvavlhgelp 51 
                                       k +  ++++li++ ti ++ k         ++++ +++      ++v v++g+++
  gi|518651366|ref|YP_008140886.1| 403 KAHIFNQRVLIMSATIPDILKdfikcktkkINFVDKEFdineiRYNVNVIDGDIN 457
                                       5566778888888888844222222221223333333344445677777777665 PP

  == domain 3  score: 36.5 bits;  conditional E-value: 1.1e-12
                                       HHHHHHHTTTTSEEEEEESSHHHHHH....HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek....vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                        ++++k++++ +kil+++nti++++     ++ + e k+ kv+ +h++ + n+r+e  e   k++  + iat+v+e 
  gi|518651366|ref|YP_008140886.1| 459 SIDIIKKHKDIKKILVIANTIKTAKYlysqIRDIDEIKDKKVVLFHSQFTYNDRKEKSELLEKEDNIIAIATQVVEV 535
                                       56778999**************994343333333555599*********************99998899******** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRa 110
                                       ++di + +l+i   +p  ++ +iqr GR+ R 
  gi|518651366|ref|YP_008140886.1| 536 SLDI-DFDLLITQIAP--PDALIQRFGRVNRR 564
                                       ****.68888888887..789********996 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.76   3.4e+03      76     120 ..     152     190 ..     121     237 .. 0.60
   2 !   34.2   0.1   5.3e-12   2.4e-08      21     170 ..     250     419 ..     209     420 .. 0.77
   3 ?    2.6   0.9     0.026   1.2e+02      48     108 ..     463     527 ..     457     550 .. 0.65
   4 ?    4.0   2.0      0.01        46      63     121 ..     586     654 ..     583     714 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.76
                                       GGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH.. CS
                            ResIII  76 kflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadsee 120
                                       +f+s  +ke +++++ d +k+      n++i  + ++++ + +++
  gi|518651366|ref|YP_008140886.1| 152 DFISFVNKEFKEIFNTDPYKF------NININNVDYKKIIKGIHN 190
                                       444444444444444444444......333333333333333333 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 5.3e-12
                                       ........TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EE.EEESSHHHHHHHHHHGGGGTGG........GE CS
                            ResIII  21 s......krdkrglikmaTGtGKTlvaaklierllkkgkeekfl.flvprkslleqtleefkkflseayke....ig 86 
                                       +      +++ +++i+ +TG+GKT    +l ++ +++g++  +l  +v ++++ e++++ f ++   +++       
  gi|518651366|ref|YP_008140886.1| 250 ElqifmqENNDNYIIQSPTGSGKTEA--SLLWSKYNNGRIVYILpTMVTSNKIFERLKQIFGDIVGIQHSTslllMD 324
                                       13335558999*************85..5566666665544333245677799999999998887777766777733 PP

                                       EEESSS-B--..............-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT CS
                            ResIII  87 kkvsgdkkka.......kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilek 156
                                       ++++ dk++        + +++ ++ i+v+t+++l  ++ + ++++  + ++ +  +i+DE H +    +   i+e+
  gi|518651366|ref|YP_008140886.1| 325 TDIDADKNNYnhdafarFYYKTFSSPIMVSTVDQLLYSLFNINRWDSVFFNSGISNVIFDEIHAYDP-YTTSLIIEY 400
                                       334444444344556669999999**********99999888*********************9998.788889999 PP

                                       ---.....SEEEEEESS-S CS
                            ResIII 157 fke.....avllglTATpe 170
                                       +++     + +l ++AT++
  gi|518651366|ref|YP_008140886.1| 401 INKahifnQRVLIMSATIP 419
                                       9877777799999999986 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.026
                                       H-S.....-EEEEESSHHHHHHHHHHGGGGTGG........GEEEESSS-B--.......-SEEE CS
                            ResIII  48 llkkgkeekflflvprkslleqtleefkkflseayke....igkkvsgdkkkakekdstnkkilv 108
                                       ++k+++++k+l+++++++  + ++++++++ + ++k+    +++++ +d+k+++e  +++ +i+ 
  gi|518651366|ref|YP_008140886.1| 463 IKKHKDIKKILVIANTIKTAKYLYSQIRDIDEIKDKKvvlfHSQFTYNDRKEKSELLEKEDNIIA 527
                                       55666777999999998888888877777766666666666555555555544344444444443 PP

  == domain 4  score: 4.0 bits;  conditional E-value: 0.01
                                       SHHHHHHHHHHGGGGTGG........GEEEESSS-B--.............-SEEEEEHHHHHHTH... CS
                            ResIII  63 rkslleqtleefkkflseayke....igkkvsgdkkka......kekdstnkkilvttiqsldadseee 121
                                       +++l+++t + f+k+  + +++    i+++++++++k+      +e +++  +i v+  +s+++ + ee
  gi|518651366|ref|YP_008140886.1| 586 KNELMKKTFDYFNKYNYKSNTDskklINEIYNDNEYKEnlknayTEVKNKIYEIQVEDLKSVYKFNIEE 654
                                       68999*******999999888877887888888888778776666666666666666666666666444 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   5.3e-11   2.4e-07      39     193 ..      42     222 ..      12     225 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 5.3e-11
                                       HHHC.TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH......... CS
                              HD_6  39 arllrgleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle......... 106
                                        ++  +++++++   + + +a HD+GK+ ++Fq + ++ +++  + + +++   + ++H+ ++a+ l          
  gi|518651366|ref|YP_008140886.1|  42 LNKY-NIDNNNFWIHAFYAVAFHDFGKLDKSFQDMINKVIQQDPGDKVDIP---KALPHALISAIALLnfeennylf 114
                                       4444.5666666666778899****************99999999999999...99*******99966677777777 PP

                                       HHHHHHHHHHHTTTS---HHHHHTSS-HHHHTT.HHHHHHHHHHHHHHHHCT-TTS-S................... CS
                              HD_6 107 evarslaaavggHHGkppkeeeekaekkssaae.dweeaqkelleaaaeflgaaaalllelael............. 169
                                       + +     +v+ HH   +++  e++++ s+++  d    +++ ++ + + +++ +++++ + ++             
  gi|518651366|ref|YP_008140886.1| 115 DNIPISSICVLTHHSMLKDNLFERNSNLSNMNLyD----YSDFISFVNKEFKEIFNTDPYKFNIninnvdykkiikg 187
                                       88889999*******88887777766665554342....33444444444444444444443336677888888999 PP

                                       ...........---HHHHHHHHHHHHHHHHHCTSC CS
                              HD_6 170 ...........elskaasvllaGlvvlADWigSne 193
                                                  ++ + + +++  ++ ++DW +S++
  gi|518651366|ref|YP_008140886.1| 188 ihnkiieyyekDKLRIMYIIIENIIHMCDWNASSN 222
                                       9999****998888999999*************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (746 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1549  (0.0863963); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.26s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 5113.32
//
Query:       gi|518651367|ref|YP_008140887.1|  [L=237]
Description: hypothetical protein FACI_IFERC00001G0006 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-08   32.9   0.0    1.1e-07   32.0   0.0    1.5  1  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)


Domain annotation for each model (and alignments):
>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.0   5.9e-12   1.1e-07       7     169 ..      12     155 ..       6     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 5.9e-12
                                       ECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS-..-CCCCTTEEEEEEEEEEEEEEE.TEEEEECT-G CS
                         Cas_Cas5d   7 egplasfgrpsrkveretydvPtkSavlGllaaalGirrddd..leelkpalrwgvrvdrrgellr.gdyhtvagrt 80 
                                       +g + sf+ p+  +  +t+d+P k+ ++G++aaa+G+ rdd+  +e l ++ ++g+   + +++ +   + +++   
  gi|518651367|ref|YP_008140887.1|  12 YGIINSFRIPLHMTIHDTLDLPVKTHIIGMIAAAMGYLRDDKekIESLYKNTSIGIYGTSYSKFYDlIRIYKYK--- 85 
                                       666779999999999***************************99999999999999998888888855554444... PP

                                       GGS--BSSS----CCEEEEEEEEEEEECEEEEEECCSCCHHHHHHHHHHHHHTTSSSSESSSTTSEEEECESETTT. CS
                         Cas_Cas5d  81 lperrkektadrkkraatvlseraYladahfevalegeeegklleelaralrkpvwplyLGrkecivpvepveaekv 157
                                                    k+ +  l++r+  ++  +++ +e+ ++    ee+ + l++pv+ l LG    ++ +  +     
  gi|518651367|ref|YP_008140887.1|  86 ------------GKEVEVSLVNRQINYKNNYTIYIENNNL----EEIYNFLKNPVFALSLGKAHDLINIKDISI--- 143
                                       ............57899******************99977....******************999999998885... PP

                                       CESSHHHCCHSS CS
                         Cas_Cas5d 158 geeegledalke 169
                                       +++  +ed + +
  gi|518651367|ref|YP_008140887.1| 144 INATIVEDDYID 155
                                       777666643333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1445.39
//
Query:       gi|518651368|ref|YP_008140888.1|  [L=302]
Description: CRISPR-associated autoregulator DevR family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   43.4   0.2    9.6e-11   41.3   0.1    1.9  2  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 ?   -0.5   0.0      0.03   5.3e+02      15      49 ..      21      52 ..      15      77 .. 0.79
   2 !   41.3   0.1   5.3e-15   9.6e-11      83     226 ..      67     195 ..      54     209 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.03
                                      -----.-.-----EEEEEE--TT--EEEEEE-THHHH CS
                              DevR 15 desvG.N.ytehrkvpvvlkeeykvrtvpaiSgeslk 49
                                      ++s+G   +  ++k+++      + ++ ++iSg++l+
  gi|518651368|ref|YP_008140888.1| 21 NGSWGeDiISTIKKIRM-----PDSTMRTYISGQALR 52
                                      56666531445677776.....67889999****998 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 5.3e-15
                                       --EEEBTTS.EESS-HHHHHHH-HHHHHH-EEEGGGT....EEE--SEEE--BEE-TTTTTTT-------------- CS
                              DevR  83 fatekklke.kelkvekeiikecvveDvfGfLitekeks..vkRkspvkfsyavpveesekavvdaqfharydllen 156
                                       +a++ ++k+ k+   ++++ ++++  D+ G++ t  + +  ++R spv++s a+++ +++ +  d  + ++ d    
  gi|518651368|ref|YP_008140888.1|  67 SAKDPNVKNdKQPLSTQCDPEKYIDDDLYGYMKTIGKGEkvLTRISPVRVSPAISLFPYYFER-DLGLQNNNDI--- 139
                                       4545555554666667788899***********86554455*******************877.7777777775... PP

                                       ---------------HHHHHSSEEEEEEEEEGGGTTS-TTS--EE---S-HHHHHHHHHHHHHTHHHHHH CS
                              DevR 157 rarkkgeeeekqnifqvEehsalYalsfvlDldriGkpevkkskieyvleeeerkkRikaalkallnlLs 226
                                               +++   ++ E +  +Y++++ +++dr+G+ +        +l+ eerk+Rik+++k++ +l  
  gi|518651368|ref|YP_008140888.1| 140 --------KKDNRFYETEISMNYYVYTVLIEADRVGVFDE------NSLSIEERKERIKTVIKSFQYLWG 195
                                       ........456789***********************999......88999************9998654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2102.56
//
Query:       gi|518651369|ref|YP_008140889.1|  [L=515]
Description: hypothetical protein FACI_IFERC00001G0008 [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   25.8   3.4    3.3e-05   24.0   3.4    2.0  1  Cas_CXXC_CXXC  CRISPR-associated protein (Cas_CXXC_CXXC)
     0.0017   18.4   0.6     0.0073   16.4   0.6    2.2  1  DUF4973        Domain of unknown function (DUF4973)


Domain annotation for each model (and alignments):
>> Cas_CXXC_CXXC  CRISPR-associated protein (Cas_CXXC_CXXC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   3.4   3.7e-09   3.3e-05       3      64 ..     161     216 ..     159     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.7e-09
                     Cas_CXXC_CXXC   3 dkkgnCitCgeRnvkqlkgklsvlsksgivpLlgsegslknyfwngknkadiCpiCklllff 64 
                                       + kg C +Cg  n +++        k++  p+ +s ++  n+++n+k +++iC +C l  f 
  gi|518651369|ref|YP_008140889.1| 161 NRKGHCDFCG-NNDVNIDK-----IKTKYYPFAASLNKYGNFYSNFKSNLNICMYCSLSSFL 216
                                       57999*****.55555555.....488888***************************98775 PP

>> DUF4973  Domain of unknown function (DUF4973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.6   8.1e-07    0.0073      48      83 ..      74     109 ..      38     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-07
                                       ----EEEEEEE-HHHHHHHHHHHHTT-GGGSEEETT CS
                           DUF4973  48 nerdldvkvavDaDtleilnleryaeredlyykele 83 
                                       ++++ dvk++v +Dt+e+++ e +++ + +++k + 
  gi|518651369|ref|YP_008140889.1|  74 KTKNKDVKIDVQNDTMETIDRESFSQLTKFFFKGIL 109
                                       5799****************************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1528  (0.0852251); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3613.61
//
Query:       gi|518651370|ref|YP_008140890.1|  [L=241]
Description: CRISPR-associated Cas6 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-18   67.0   3.3    4.7e-18   66.1   3.3    1.4  1  Cas_Cas6  CRISPR associated protein Cas6
    0.00032   20.8   2.4    0.00044   20.3   2.4    1.2  1  RAMPs     RAMP superfamily
  ------ inclusion threshold ------
       0.83   10.0   4.5        6.2    7.2   1.5    2.9  3  DUF4968   Domain of unknown function (DUF4968)


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   3.3   7.8e-22   4.7e-18       2     145 ..      90     237 ..      89     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 7.8e-22
                                       HHCS-EEEET....TEEEEEEEEEE----S--TCEE.EEESS-BBEEEEEEETTCCEEEEE..-T.TSTTHHHHHHH CS
                          Cas_Cas6   2 llknkeirlg....nnefkveevellkepeitssevvfktlSPivvrstkkengkkktyyl..sp.ddeeFsellke 71 
                                       +lkn+ ++++     ++f  ++++++++ + +s+ v++ tlSPi+++ +  +++k   +    ++ d + + + lk+
  gi|518651370|ref|YP_008140890.1|  90 FLKNPLFEINnngsTTRFATSNMRIIDNYNNKSN-VKLITLSPIILKLK--DENKFLAINSesNDsDIDTWLNTLKY 163
                                       8999******999999**************9888.66**********44..44444444332333588999999*** PP

                                       HHHHHHHHHHSS..SS---EEEEE.EEEE......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EE CS
                          Cas_Cas6  72 nlkkkykalygeekeeklsikpdk.kvkkivvkkketyirGylgrfelegdpellklaydaGlGeknsqGFGmve 145
                                        +k +y  ++++e +++l+ik+dk ++k++ +k k+ +  ++ g+  ++++p+l++++ d+GlG k   GFG++e
  gi|518651370|ref|YP_008140890.1| 164 SIKSRYMYFTNDE-INNLEIKIDKnDFKTKYIKIKNQRYLCSDGTIDISAEPKLIRFINDVGLGMKLKFGFGFME 237
                                       ***********98.9**********************************************************98 PP

>> RAMPs  RAMP superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   2.4   7.4e-08   0.00044      38     213 .]      22     237 ..       4     237 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.4e-08
                                       HHHHHHHHHHHHHHH...................HHHTT-HHHHH.H.............................. CS
                             RAMPs  38 SlkGalRsalekllg..................sekkekkdeysrkkekqrvkkgd..................... 75 
                                       Sl+G++   l+ +                                          +                     
  gi|518651370|ref|YP_008140890.1|  22 SLRGVILEKLRVVNPelskiyhddpkhifnfsqI---------------------Lgrshsnqygihikrgvlfiss 77 
                                       7777777666633222222222222222222220.....................1334444444445555555555 PP

                                       .............HHHHHH.....--S..............SS--SEEEEE.......................... CS
                             RAMPs  76 .............leeaiF.....Gne...........eeskiagrvffeDarpvkipgqileeskqikstpsp... 120
                                                    l + +F     G++           +++ ++++v+++  +p+  +++   + + i+s  +    
  gi|518651370|ref|YP_008140890.1|  78 lekefisniiksfLKNPLFeinnnGSTtrfatsnmriiDNYNNKSNVKLITLSPIILKLKDENKFLAINSESNDsdi 154
                                       55555555555558888998877788888888888888888888888888888888888877777777777777*** PP

                                       ......EEEEEEEEEEEEEEEEE--.SSS-EEEEEE...-TT-EEEEEEEESS..............HHHHHHHHHH CS
                             RAMPs 121 ......klsgselrelldhsterrt.rvaidrktktngkkkgglftleaipaerikfsgrirlenlsdeelgallkl 190
                                              + +++ r++ + ++e+++ +++id+ + +++   +++ + ++++ +               ++  a  kl
  gi|518651370|ref|YP_008140890.1| 155 dtwlntLKYSIKSRYMYFTNDEINNlEIKIDKNDFKTKY--IKIKNQRYLCSD-------------GTIDISAEPKL 216
                                       ******888888888888888876548999999888888..889999999999.............9********** PP

                                       HHHH.HHH---STTTTBTTT-EE CS
                             RAMPs 191 LdlldlhflglGggkplGfGsve 213
                                       ++++  +++glG++  +GfG++e
  gi|518651370|ref|YP_008140890.1| 217 IRFI--NDVGLGMKLKFGFGFME 237
                                       ****..**************986 PP

>> DUF4968  Domain of unknown function (DUF4968)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   7.3e+03      78      90 ..       3      15 ..       2      17 .. 0.82
   2 ?    2.6   0.0     0.029   1.8e+02      43      71 ..      86     114 ..      74     116 .. 0.79
   3 ?    7.2   1.5     0.001       6.2      67      93 ..     178     205 ..     115     206 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                           DUF4968 78 lrisfydkegkll 90
                                      l+i +y+ ++++l
  gi|518651370|ref|YP_008140890.1|  3 LEINIYNIDNNML 15
                                      6799999999998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.029
                           DUF4968  43 vvkkadektefeveekedevvikTekltv 71 
                                       ++k   ++  fe+++++++ +++T+++++
  gi|518651370|ref|YP_008140890.1|  86 IIKSFLKNPLFEINNNGSTTRFATSNMRI 114
                                       5555458889****************997 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.001
                           DUF4968  67 ekltvkieksplrisfyd.kegkllleD 93 
                                       ++l++ki+k++++ ++   k+++ l++D
  gi|518651370|ref|YP_008140890.1| 178 NNLEIKIDKNDFKTKYIKiKNQRYLCSD 205
                                       4799**************9999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1594.83
//
Query:       gi|518651371|ref|YP_008140891.1|  [L=889]
Description: hypothetical protein FACI_IFERC00001G0010 [Ferroplasma acidarmanus fer1]
Scores for complete 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-48  164.7  18.1    2.7e-26   92.8   0.1    3.5  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
    7.4e-37  127.5   8.1    1.3e-20   74.1   0.0    3.1  4  UvrD_C           UvrD-like helicase C-terminal domain
    8.2e-29  100.8   0.0    2.2e-28   99.4   0.0    1.8  1  AAA_19           AAA domain
    1.9e-20   73.9   0.0    3.6e-20   73.0   0.0    1.5  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    1.3e-09   37.7   1.1    0.00014   21.6   0.0    3.0  3  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.2e-08   33.9   4.1    8.9e-08   32.4   4.1    1.8  1  Cas_Cas4         Domain of unknown function DUF83
    6.3e-06   26.1   0.3      0.097   12.4   0.0    4.4  5  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    2.3e-05   24.2   0.0      0.015   15.0   0.0    2.4  2  AAA_30           AAA domain
    6.3e-05   22.4   0.6    0.00011   21.6   0.2    1.6  2  DUF2800          Protein of unknown function (DUF2800)
  ------ inclusion threshold ------
       0.53   10.1   6.8        1.1    9.0   0.0    3.7  4  Dna2             DNA replication factor Dna2


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.1   1.5e-29   2.7e-26       1     110 [.      11     112 ..      11     132 .. 0.91
   2 !   78.7   6.3   2.9e-25   5.3e-22     205     314 ..     168     272 ..     118     273 .. 0.88
   3 ?   -1.0   1.8      0.56     1e+03     245     245 ..     705     705 ..     335     873 .. 0.66

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 1.5e-29
                                       SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCT CS
                     UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqess 77 
                                       l++eq ++++s++  i ++A+AG+GKT vl+ ri++l+ ++   p++i+++TFT kAa+E+k+R+ +++++   +  
  gi|518651371|ref|YP_008140891.1|  11 LSNEQIKPVNSSSRYIKILAGAGAGKTEVLTRRIVNLLLNTDAPPESIVAFTFTDKAAKEMKNRVLKRIQEIAPQ-- 85 
                                       5789***************************************************************99987543.. PP

                                       T-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHG CS
                     UvrD-helicase  78 dderlrlalqnlseanisTlHsfcqkilkkean 110
                                              + +++ ++ i+T+Hsfc+++l+++++
  gi|518651371|ref|YP_008140891.1|  86 ------FNTSSILNMYIGTIHSFCLRLLQEHFD 112
                                       ......4667899*****************986 PP

  == domain 2  score: 78.7 bits;  conditional E-value: 2.9e-25
                                       SCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHT CS
                     UvrD-helicase 205 kasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllas 281
                                       + ++l+  ++++l +y++ +++++++ fs+l++++++  ++n+e      +++k++l+DEyQD nk+Qy+++k + +
  gi|518651371|ref|YP_008140891.1| 168 NINELNPNFIKILDRYENSMNKNKIISFSQLIYFAVNKIKDNKEKI----SNIKYLLVDEYQDINKVQYDLIKQIGE 240
                                       456778899****************************999987744....4689*********************99 PP

                                       TTTTEEEEE-GGG--GGGGTB-THHHHHHHHHS CS
                     UvrD-helicase 282 gheelfmvGDpkQsIYgFRgAdielflkkkkdf 314
                                       +   +f vGDp QsIY++Rg++ + f ++++df
  gi|518651371|ref|YP_008140891.1| 241 NA-SIFAVGDPRQSIYEWRGSNYKYFEEFSNDF 272
                                       87.7**************************998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.56
                                       H CS
                     UvrD-helicase 245 e 245
                                       e
  gi|518651371|ref|YP_008140891.1| 705 E 705
                                       1 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1         1   1.8e+03     124     201 ..     187     211 ..     153     270 .. 0.62
   2 !   57.7   0.0   7.1e-19   1.3e-15       2     116 ..     279     394 ..     278     404 .. 0.88
   3 !   74.1   0.0   7.1e-24   1.3e-20     196     345 ..     438     614 ..     400     618 .. 0.71
   4 ?   -3.0   0.4       2.1   3.7e+03      57      57 ..     827     827 ..     731     883 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 124 ankqdkialkrilkrlvlgigkatveriseelkklglsltDfikedtleygeeFieliraleeknlelllkkiekta 200
                                       +nk+ +i+++ +++  v +i++++                                                     
  gi|518651371|ref|YP_008140891.1| 187 MNKNKIISFSQLIYFAVNKIKDNK----------------------------------------------------- 210
                                       344444444444444444433332..................................................... PP

                                       x RF
                            UvrD_C 201 e 201
                                       e
  gi|518651371|ref|YP_008140891.1| 211 E 211
                                       1 PP

  == domain 2  score: 57.7 bits;  conditional E-value: 7.1e-19
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikalleknekledia 76 
                                       +L++N RStks+++++n++++++ +++ + + +    +ek+  ++ +e e+ + Eae ia++ik   +k++k+++ a
  gi|518651371|ref|YP_008140891.1| 279 TLNENRRSTKSIVNISNTIVKQFPDNPGY-P-DmvPVREKSGDVIATEYENASREAEGIANKIKCEIKKDKKYSKFA 353
                                       69******************776666333.3.24766666667*********************9999********* PP

                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  77 vLvRs.nkdadkiskaLkkegipfnvvdeekfFkreeikdi 116
                                       vL Rs n   d+i +++kk++ip+ v ++  +Fkr e+  +
  gi|518651371|ref|YP_008140891.1| 354 VLLRSvNTSGDLIIDEFKKQKIPYLVAGNAGLFKRGEVLAL 394
                                       *****9*******************************9866 PP

  == domain 3  score: 74.1 bits;  conditional E-value: 7.1e-24
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            UvrD_C 196 iektaeerqalvskyadlfkelaeklaelkekseskrkkee..klenlreLysllkelekkeeeeeveek....... 263
                                       i+   ++ ++ +++y+d+   ++  l+++   +  ++++ +   l n+ ++ ++l ++e+     + +++       
  gi|518651371|ref|YP_008140891.1| 438 IKDDLNHIKSSLNSYGDYRVLYQDVLKRFDYSALDQDNDLDnaILANIGRFTKVLGDYEQSVRYGGGNKNiqkemkd 514
                                       3333334455556666555555555555544444443222256899************9976665655554455555 PP

                                       ...xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                            UvrD_C 264 ...lneileia......tLseseleeskkkekipiiTiHqAKGlEFdvVflagleegtfPsyrskk........... 320
                                          +      +      + +e + e+++k++ ++++TiHq+KGlE+ +Vfl ++ +++fPs++  k           
  gi|518651371|ref|YP_008140891.1| 515 lcwF------IntyanhSYQEAKIEDLSKDNVVTVSTIHQSKGLEWQTVFLPSIINKRFPSLTHFKsnlmidqslye 585
                                       4442......04444447888888888888******************************99999999999999999 PP

                                       ....xxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 321 ....ekrleEEkRlfYVaiTRAkkrLfis 345
                                           e  l+ E RlfYVa+TRAk+   +s
  gi|518651371|ref|YP_008140891.1| 586 ysryETSLDSEYRLFYVAVTRAKNYCLMS 614
                                       999999*****************988777 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 2.1
                                       x RF
                            UvrD_C  57 k 57 
                                       k
  gi|518651371|ref|YP_008140891.1| 827 K 827
                                       1 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.0   1.3e-31   2.2e-28       7     144 ..      20     256 ..      13     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.3e-31
                            AAA_19   7 alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae..............a 69 
                                       +++++ + ++aG+G GKT+vl+ ++  l+ +++ +pe+i++ +ft +Aake+++r+ +  +e              +
  gi|518651371|ref|YP_008140891.1|  20 NSSSRYIKILAGAGAGKTEVLTRRIVNLLLNTDAPPESIVAFTFTDKAAKEMKNRVLKRIQEiapqfntssilnmyI 96 
                                       678899*************************************************966555599************* PP

                            AAA_19  70 tTiHrlal..................................................................... 77 
                                        TiH++ l                                                                     
  gi|518651371|ref|YP_008140891.1|  97 GTIHSFCLrllqehfdygmyktvdqnqemayilqngytyglkqvegstysdkcinfqktldiyygeeiprdnineln 173
                                       ******88********************************************************************* PP

                            AAA_19  78 ...................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrLlkallgekkklllv 135
                                                          + f +l+  a++ ++  ++++k+ + ++l+vDE+qd++++qy L+k++  e++++++v
  gi|518651371|ref|YP_008140891.1| 174 pnfikildryensmnknkiISFSQLIYFAVNKIK--DNKEKISNIKYLLVDEYQDINKVQYDLIKQIG-ENASIFAV 247
                                       ******9999999999998888888888888866..5788897778**********************.6666**** PP

                            AAA_19 136 GDpdQliyv 144
                                       GDp Q+iy+
  gi|518651371|ref|YP_008140891.1| 248 GDPRQSIYE 256
                                       ********7 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0     2e-23   3.6e-20       4     255 .]     661     885 ..     658     885 .. 0.72

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 2e-23
                          PDDEXK_1   4 vsrletfleCplrfflryllglreeeeleap.dlGtlvHaaleefyewkkldke.dleelleeaveelwpellleee 78 
                                       v++l ++++Cp+++ l++  g+  ++ +++   +G+++H +l+ ++e   ++++   e+++e++v+  +   + +  
  gi|518651371|ref|YP_008140891.1| 661 VTSLIDYKRCPYHYKLSKEWGY--TQGVSPFmGYGEALHYILQCLSE-AIINNKqIDEHYIENVVNTKFFLPFAST- 733
                                       79999*****************..99999977***********9999.3333333555666555555555544444. PP

                          PDDEXK_1  79 ilessarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriDrvddkegelriiDyKtgsap 155
                                               ++l ++ k++ +k  + + ++  ++ ++++v++ +ef  e   + G+iD + dk+g ++i DyKt+   
  gi|518651371|ref|YP_008140891.1| 734 --------QFLDNQKKDINKKI-KLIFDTYLKNNKISEVESRIEFPVENAIIDGKIDVIIDKHGNAEIRDYKTSEDV 801
                                       ........44444444444444.43333223333345555555555233559********99999*******99944 PP

                          PDDEXK_1 156 pkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeeleallqeleelaeei 232
                                              + + ++Q llY+  l+ +  +     + ++  +++    +++e++ +++  +++ +++ +++ e l++++
  gi|518651371|ref|YP_008140891.1| 802 ---VT--KEEADMQILLYAEGLRSQ-GYH----VTKVSTISI----KTNEKNEQEI--DDNIISENKKRTEGLINSL 862
                                       ...44..446889************.233....777777777....2244444444..55556999999999***** PP

                          PDDEXK_1 233 lagefparpskkCeyCpyksvCr 255
                                       ++gef+ + sk C++C+y ++C+
  gi|518651371|ref|YP_008140891.1| 863 KNGEFKGKKSKFCDRCEYLEICK 885
                                       **********************6 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   7.7e-08   0.00014       2      25 ..     541     562 ..     540     577 .. 0.84
   2 !   13.4   0.1   2.9e-05     0.052      34      49 ..     596     611 ..     581     614 .. 0.79
   3 ?   -1.6   0.0       1.4   2.5e+03      25      40 ..     668     683 ..     660     683 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 7.7e-08
                          UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdl 25 
                                       ++++tih+++G+e+++V++  p+ 
  gi|518651371|ref|YP_008140891.1| 541 VTVSTIHQSKGLEWQTVFL--PSI 562
                                       689****************..654 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-05
                          UvrD_C_2  34 rrrlLYtavTRArekl 49 
                                         rl+Y+avTRA+  +
  gi|518651371|ref|YP_008140891.1| 596 EYRLFYVAVTRAKNYC 611
                                       58***********877 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.4
                          UvrD_C_2  25 laaarmgelrrrlLYt 40 
                                          ++++ l++++ Yt
  gi|518651371|ref|YP_008140891.1| 668 KRCPYHYKLSKEWGYT 683
                                       445678999******9 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 !   32.4   4.1     5e-11   8.9e-08      48     161 ..     768     885 ..     734     886 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5e-11
                          Cas_Cas4  48 evelse...sikiDvvekekeklvvvEvKkskkk..eeaaklQllyYlllLekkgveikeGvleypkekkreevelt 119
                                       e+ +++    +kiDv+ ++++++++ ++K s+    +e+a +Q+l Y+  L+++g ++++     +k+++++e e++
  gi|518651371|ref|YP_008140891.1| 768 EFPVENaiiDGKIDVIIDKHGNAEIRDYKTSEDVvtKEEADMQILLYAEGLRSQGYHVTKVSTISIKTNEKNEQEID 844
                                       34443367789*********************98657788*******************888888889999999999 PP

                          Cas_Cas4 120 eelreelekaikeieeiissekppkvkkkkiCkkCayaelCl 161
                                       ++  +e +k ++ + + +++ +  k kk+k+C++C+y e+C 
  gi|518651371|ref|YP_008140891.1| 845 DNIISENKKRTEGLINSLKNGE-FKGKKSKFCDRCEYLEICK 885
                                       9887777777666665555544.4678999***********5 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.015        28       4      54 ..      29      80 ..      26      92 .. 0.73
   2 !   12.4   0.0   5.4e-05     0.097      61     121 ..     214     271 ..     197     305 .. 0.80
   3 ?   -3.6   0.0       4.2   7.5e+03      61      75 ..     360     374 ..     336     383 .. 0.68
   4 ?    1.4   0.0      0.12   2.2e+02     171     201 ..     529     559 ..     492     578 .. 0.75
   5 ?    1.4   0.0      0.12   2.2e+02     213     230 ..     595     611 ..     582     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.015
                   Viral_helicase1  4 hGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsfl 54
                                       + +G+GK+ ++ + + +  l+  + +++++++t   + ++  ++r ++ ++
  gi|518651371|ref|YP_008140891.1| 29 LAGAGAGKTEVLTRRIVNLlLNTDAPPESIVAFTFTDKAAKEMKNRVLKRIQ 80
                                      5779********9999887777777888888888888666666666655554 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.4e-05
                   Viral_helicase1  61 tkgkililDEylllhaGyilllaalskaklvilfGDplQipfhsrnasfllahlpsslshr 121
                                        + k+l++DEy+  +  + +l+ ++ +   ++++GDp+Q+ ++ r    ++ +++ ++s+ 
  gi|518651371|ref|YP_008140891.1| 214 SNIKYLLVDEYQDINKVQYDLIKQIGENASIFAVGDPRQSIYEWRG---SNYKYFEEFSND 271
                                       45799***********99999999999999*********9999754...566666666554 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.2
                   Viral_helicase1  61 tkgkililDEylllh 75 
                                        ++  li+DE+ +++
  gi|518651371|ref|YP_008140891.1| 360 NTSGDLIIDEFKKQK 374
                                       347789999998877 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.12
                   Viral_helicase1 171 tftqalkealgvr...evttvhevqGltfdkVtl 201
                                       +++ ++++    +    v+t h+  Gl++++V l
  gi|518651371|ref|YP_008140891.1| 529 EAKIEDLSK---DnvvTVSTIHQSKGLEWQTVFL 559
                                       333333333...245579************9987 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.12
                   Viral_helicase1 213 sesrenllvAlTRhrksl 230
                                       s +   ++vA TR+++ +
  gi|518651371|ref|YP_008140891.1| 595 S-EYRLFYVAVTRAKNYC 611
                                       3.46789*******9865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   8.3e-06     0.015      14      66 ..      20      75 ..      10     111 .. 0.75
   2 !    6.7   0.0     0.003       5.3      82     128 ..     209     253 ..     179     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.3e-06
                            AAA_30 14 ltsgdrvavltGpAGtGKttalka.lreaweaag...grviglAptgkaAkvLaeel 66
                                       +s+ r+  + ++AG+GKt +l+  +++++ +     +++++++ t kaAk++++ +
  gi|518651371|ref|YP_008140891.1| 20 NSSS-RYIKILAGAGAGKTEVLTRrIVNLLLNTDappESIVAFTFTDKAAKEMKNRV 75
                                      3444.57778889*******996515776655534679***************9754 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.003
                            AAA_30  82 grarlepgtllivDEagmvdtkqlaallkaaekagakvilvGDerQl 128
                                       +++++++ + l+vDE   ++  q  +l+k++ + +a++  vGD+rQ 
  gi|518651371|ref|YP_008140891.1| 209 NKEKISNIKYLLVDEYQDINKVQY-DLIKQIGE-NASIFAVGDPRQS 253
                                       4456667799*****999987775.69999999.9**********95 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0         3   5.3e+03      40      91 ..     100     142 ..      70     158 .. 0.59
   2 !   21.6   0.2   6.2e-08   0.00011      30     171 ..     687     834 ..     663     887 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                           DUF2800  40 Helaelklrkaldakekkgvkselkkkeeevteemeeavdeyvdfvlekiee 91 
                                       H+++  +l++++d   +k+v+          ++em+   ++  ++ l+++e 
  gi|518651371|ref|YP_008140891.1| 100 HSFCLRLLQEHFDYGMYKTVD---------QNQEMAYILQNGYTYGLKQVEG 142
                                       444444444444444444444.........4556666555555555555554 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6.2e-08
                           DUF2800  30 SeyAeeGtlaHelaelklrkaldakekkg..vkselkk......keeevteemeeavdeyvdfvlekieeakkdalv 98 
                                       S++   G + H + + + +  +++k+ ++  +++ +++      +++++ ++ ++ +++ ++++ + +   k++++ 
  gi|518651371|ref|YP_008140891.1| 687 SPFMGYGEALHYILQCLSEAIINNKQIDEhyIENVVNTkfflpfASTQFLDNQKKDINKKIKLIFDTYL--KNNKIS 761
                                       666666666666555444444433322221122223335566776777777777788888888888855..479*** PP

                           DUF2800  99 lvEqrvdfskyvpegfGtaDvviiaddvLeviDlKyGkgvkVsaekNpQlalYAlGAleefdllydiktVrlt 171
                                        vE r++f   +    G  Dv+i ++++ e+ D+K  + v  + e   Q+ lYA G  ++  ++ +++t+++ 
  gi|518651371|ref|YP_008140891.1| 762 EVESRIEFPVENAIIDGKIDVIIDKHGNAEIRDYKTSEDVVTKEEADMQILLYAEGLRSQGYHVTKVSTISIK 834
                                       ********999888******************************************99999999999998875 PP

>> Dna2  DNA replication factor Dna2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.6      0.46   8.2e+02     136     191 ..     166     218 ..      53     220 .. 0.60
   2 ?   -3.7   0.1         5   8.9e+03     125     170 ..     244     289 ..     228     297 .. 0.66
   3 ?    2.1   0.0     0.083   1.5e+02     134     180 ..     503     547 ..     457     558 .. 0.62
   4 ?    9.0   0.0   0.00061       1.1      55     157 ..     659     758 ..     624     790 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.46
                              Dna2 136 keeikekleeiekwakkyvkksnkakakvekkkekkeklsiskvldiEEniwspky 191
                                       +++i+e  +++ k++++y ++ nk+k ++    ++   ++++k+ d  E+i   ky
  gi|518651371|ref|YP_008140891.1| 166 RDNINELNPNFIKILDRYENSMNKNKIISF---SQLIYFAVNKIKDNKEKISNIKY 218
                                       445555556666666666666665555543...33446777777777777777766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5
                              Dna2 125 lyalglteeeakeeikekleeiekwakkyvkksnkakakvekkkek 170
                                       ++a+g  ++++ e   ++++ +e++++ + ++++ + +++++++++
  gi|518651371|ref|YP_008140891.1| 244 IFAVGDPRQSIYEWRGSNYKYFEEFSNDFSNAEEFTLNENRRSTKS 289
                                       5666666666666666777888888888888777666665544443 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.083
                              Dna2 134 eakeeikekleeiekwakkyvkksnkakakvekkkekkeklsiskvl 180
                                         +++i+++++++  ++++y ++s +++++++ +k++   +++s ++
  gi|518651371|ref|YP_008140891.1| 503 GGNKNIQKEMKDLCWFINTYANHSYQEAKIEDLSKDN--VVTVSTIH 547
                                       35789***************99998777766555554..56666555 PP

  == domain 4  score: 9.0 bits;  conditional E-value: 0.00061
                              Dna2  55 vsaTsvanslsClRravLqerlkvsgesskamliGtilHelfqkalleeeldkekleel.ldklleknleelyalgl 130
                                       +  Ts+ +  +C+    L++    ++  s  m +G+ lH ++q +l+e  +++++++e+ ++++++++    +a  +
  gi|518651371|ref|YP_008140891.1| 659 IPVTSLIDYKRCPYHYKLSKEWGYTQGVSPFMGYGEALHYILQ-CLSEAIINNKQIDEHyIENVVNTKFFLPFASTQ 734
                                       7789999999************999*****************9.787878888888654156666655554455555 PP

                              Dna2 131 teeeakeeikekleeiekwakkyvkks 157
                                         ++ k++i++k+   + ++++y+k++
  gi|518651371|ref|YP_008140891.1| 735 FLDNQKKDINKKI---KLIFDTYLKNN 758
                                       5555555555544...44455555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (889 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.56
# Mc/sec: 4779.55
//
Query:       gi|518651372|ref|YP_008140892.1|  [L=451]
Description: hypothetical protein FACI_IFERC00001G0011 [Ferroplasma acidarmanus fer1]
Scores for 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-22   78.5   0.4      6e-22   78.5   0.4    2.1  2  ResIII         Type III restriction enzyme, res subunit
    3.5e-11   43.4   1.1    1.4e-10   41.5   0.0    2.4  2  Helicase_C     Helicase conserved C-terminal domain
    8.6e-10   38.7   0.2    3.5e-09   36.7   0.0    2.0  2  DEAD           DEAD/DEAH box helicase
    3.9e-06   25.8   0.1    8.7e-06   24.7   0.1    1.5  1  SNF2_N         SNF2 family N-terminal domain
    7.2e-06   25.4   0.0    1.8e-05   24.1   0.0    1.5  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.9e-05   24.5   0.1      4e-05   23.4   0.1    1.4  1  SWI2_SNF2      SWI2/SNF2 ATPase
     0.0061   16.9   0.1      0.022   15.1   0.0    1.9  2  AAA_19         AAA domain
  ------ inclusion threshold ------
      0.078   12.4   0.0       0.25   10.8   0.0    1.8  2  PhoH           PhoH-like protein


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 !   78.5   0.4   2.7e-25     6e-22       1     171 []       8     170 ..       8     170 .. 0.85
   2 ?   -1.0   0.7      0.67   1.5e+03      59      84 ..     252     284 ..     229     337 .. 0.47

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 2.7e-25
                                       --EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   1 klelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       k+e+r+yQ++a+++++     +++ +g+++maTGtGKT++++  i +l + +++  +++ +p  +ll q+++ ++++
  gi|518651372|ref|YP_008140892.1|   8 KMEIRDYQQDAVNKWK-----NHNMNGIFEMATGTGKTYTSILCINELIQTNEKLLIVIACPYVHLLTQWQKSLNNV 79 
                                       689************8.....8899*************************87755666668999*********9999 PP

                                       TGG.....GEEEESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTH CS
                            ResIII  78 lseayke.igkkvsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswr 151
                                         +   + + +k++++  ++  k + s+++ i++tt ++l +++      +   ++d+ +++i+DE+H +g+ +++r
  gi|518651372|ref|YP_008140892.1|  80 GLTSIFNtNITKWKEKLGQEiiKLRYSSKILIILTTHNTLANNE----FLNILSSSDYPKFLIVDEVHDIGS-AQHR 151
                                       98887656444444444444577999999999999999999999....789999999999************.7777 PP

                                       H.HHHT---SEEEEEESS-S- CS
                            ResIII 152 e.ilekfkeavllglTATper 171
                                         + e+f+  ++lgl+ATp+r
  gi|518651372|ref|YP_008140892.1| 152 LgLSEMFQ--YRLGLSATPQR 170
                                       76899998..*********85 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.67
                                       EEESSHHHHHHHHHHG.......GGGTGG.... CS
                            ResIII  59 flvprkslleqtleef.......kkflseayke 84 
                                       +l  r+++l+ + +++        +f+++++++
  gi|518651372|ref|YP_008140892.1| 252 LLFKRQNILKNATNKYnilniimDNFIKSYNTS 284
                                       444555555555555533333332222222222 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.68   1.5e+03      29      29 ..      92      92 ..      43     139 .. 0.51
   2 !   41.5   0.0     6e-14   1.4e-10       7     109 ..     274     384 ..     266     386 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.68
                                      H CS
                        Helicase_C 29 l 29
                                       
  gi|518651372|ref|YP_008140892.1| 92 W 92
                                      2 PP

  == domain 2  score: 41.5 bits;  conditional E-value: 6e-14
                                       HHHHHHTTTTSEEEEEESSHH..HHHHHHHHHHHT..TSTEEEESTT......STHHHHHHHHHHHHTTSSSEEEES CS
                        Helicase_C   7 lellkleeeggkilifvntid..rlekvklllekk..gikvavlhge......lpqnereeileqfnkgesdvLiat 73 
                                       ++ + ++ +++++li++  ++  +++  +ll ek+  + k++++ g+         +er+ il++f +g +  L+a 
  gi|518651372|ref|YP_008140892.1| 274 MDNFIKSYNTSNTLIYCSPQQidEVQ--NLLSEKNiiNHKFTMIEGTkpdkkyNGLSERDFILHKFSEGAYSTLVAM 348
                                       44434677788889998655444887..9999999999********93333333345788***************** PP

                                       GGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  74 dvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       + + +G+d+p++++ i ++   n+++  qr+GR+ R
  gi|518651372|ref|YP_008140892.1| 349 KCLDEGVDVPSIKNAILMSSSGNLREWYQRMGRILR 384
                                       **********************************99 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.0   1.6e-12   3.5e-09       2     147 ..      13     159 ..      12     174 .. 0.73
   2 ?   -0.8   0.1      0.49   1.1e+03      98     154 ..     267     320 ..     228     333 .. 0.62

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHH.TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplil.gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       d+Q+ a++    ++ + + +++TG+GKT   ++ + + + +  ++++  ++i +P   L  q  + l++++ +   +
  gi|518651372|ref|YP_008140892.1|  13 DYQQDAVNKWKnHNMNGIFEMATGTGKTYTSILCINELI-Q--TNEKLLIVIACPYVHLLTQWQKSLNNVGLTSIFN 86 
                                       789999999884455889***********9666666555.4..899999*********************9963344 PP

                                       EEEEET.TSSHHHHHHHHH..TTCSEEEEEHHHHHHHHHCTSSH....CTTEEEEEEETHHHHHHTTTHHHHHHHHH CS
                                       xxxxxx.xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliig.gvaardqlskld..ngvdivvgtpgrlddllstgkln....lsqvrflVlDEadrlldqgfsdfinriln 147
                                       ++ i++ +++  +++ kl+  +++ i+++t+  l++   ++ ln     +  +fl++DE++ + + + +  ++++++
  gi|518651372|ref|YP_008140892.1|  87 TN-ITKwKEKLGQEIIKLRysSKILIILTTHNTLAN---NEFLNilssSDYPKFLIVDEVHDIGSAQHRLGLSEMFQ 159
                                       44.333366678888888643669999999999998...333443112444499***********988877777654 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.49
                                       CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  98 vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                       ++i+    + +++  +t + +l  ++   +DE+++ll++  ++ in+ ++ ++ ++ 
  gi|518651372|ref|YP_008140892.1| 267 YNILNIIMDNFIKSYNTSN-TLIYCSPQQIDEVQNLLSE--KNIINHKFTMIEGTKP 320
                                       5555555555555444333.4555555557888888887..7777777766654444 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 !   24.7   0.1   3.9e-09   8.7e-06      52     215 ..      23     168 ..      12     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.9e-09
                                       HHTT--EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--H.HHHHHHHHHHHHH..-TTS-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx..xxxxxxx RF
                            SNF2_N  52 kqsvrGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPa.slldqWeneierh..vsssalr 125
                                       k+++ +Gi+   +G GKT +++  i   + +++++k           ++i +P   ll+qW++ +++   +s  +++
  gi|518651372|ref|YP_008140892.1|  23 KNHNMNGIFEMATGTGKTYTSILCIN--ELIQTNEKLL---------IVIACPYvHLLTQWQKSLNNVglTSIFNTN 88 
                                       466789********************..5556666655.........8999***9**********996225555666 PP

                                       E--SSHHHH-----------------EEEE-HHHHHHHT......TTS-S-S.-SEEEES-GGGT--TTSH..HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx..xxxx RF
                            SNF2_N 126 vlvyggqkkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqve.wkrvvlDEghtlknstsk..aaea 199
                                       +  +++    k  ++ ++ ++  +  +++tt ++l+++       + l++ +  k++++DE h +++ + +  ++e+
  gi|518651372|ref|YP_008140892.1|  89 ITKWKE----KLGQEIIKLRYSSKILIILTTHNTLANNE----FLNILSSSDyPKFLIVDEVHDIGSAQHRlgLSEM 157
                                       666666....577789999999**************666....677777776589************9766115666 PP

                                       HHH---S-EEEE-S-- CS
                                       xxxxxxxxxxxxxxxx RF
                            SNF2_N 200 vskLstsnrwiltGTP 215
                                        +     +r+ l++TP
  gi|518651372|ref|YP_008140892.1| 158 FQ-----YRLGLSATP 168
                                       66.....999999999 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   8.2e-09   1.8e-05      92     170 ..     328     400 ..     296     414 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 8.2e-09
                     ERCC3_RAD25_C  92 aerlkilqkfkknpkvntiflskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLv 168
                                       +er  il+kf +  +++t++  k  D+ +D+P+ +  i +ss  g  r   qr+GriLr  k+    + +a+ Y ++
  gi|518651372|ref|YP_008140892.1| 328 SERDFILHKFSEG-AYSTLVAMKCLDEGVDVPSIKNAILMSSS-GNLREWYQRMGRILRRDKN----KDHAYIYDII 398
                                       69999*****876.89999999*************99998875.788899********98776....5678888887 PP

                     ERCC3_RAD25_C 169 sk 170
                                        k
  gi|518651372|ref|YP_008140892.1| 399 VK 400
                                       66 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.8e-08     4e-05       9     183 ..      18     198 ..       9     212 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.8e-08
                         SWI2_SNF2   9 avervkegdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfakageek...pkqaes 82 
                                       av++ k+ ++ +G++   +G GK++t++++ ++l++ + ++  +v+      L +Q +k ++++g ++   ++ ++ 
  gi|518651372|ref|YP_008140892.1|  18 AVNKWKN-HNMNGIFEMATGTGKTYTSILCINELIQ-TNEKLLIVIACPYVHLLTQWQKSLNNVGLTSifnTNITKW 92 
                                       5556665.4899************************.888899999999**************96554110334555 PP

                         SWI2_SNF2  83 rkeLkell.e.kesek..iifttiqKfeeeekeklevlsere.niivlvDEaHRsqygelakklrkalpnaafigFT 154
                                       +++L +++ + + s+k  ii+tt + ++++  e l+ ls+++   +++vDE H   + + +  l ++++   ++g+ 
  gi|518651372|ref|YP_008140892.1|  93 KEKLGQEIiKlRYSSKilIILTTHNTLANN--EFLNILSSSDyPKFLIVDEVHDIGSAQHRLGLSEMFQ--YRLGLS 165
                                       667766665322234411444444444433..235666665535799******8888888888888886..689999 PP

                         SWI2_SNF2 155 GTPilkkdkk.t...kevFgeyidkYtikeave 183
                                        TP    d++ t    + F +++ ++++kea e
  gi|518651372|ref|YP_008140892.1| 166 ATPQRYFDEEgTefiLNYFSGIVYTFSLKEALE 198
                                       999887443324223677888888998888875 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.7e-06     0.022       1     121 [.      15     152 ..      15     164 .. 0.74
   2 ?   -1.8   0.0       1.6   3.5e+03      78      78 ..     265     265 ..     225     306 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.7e-06
                            AAA_19   1 qreave..alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae....... 68 
                                       q++av+  + ++ + +     GtGKT++    +++l+++++     i+++++  +   + +++l+++g+        
  gi|518651372|ref|YP_008140892.1|  15 QQDAVNkwKNHNMNGIFEMATGTGKTYTSILCINELIQTNEK--LLIVIACPYVHLLTQWQKSLNNVGLTsifntni 89 
                                       666774244444455666788*******99999999999966..788999999999999999998888888888888 PP

                            AAA_19  69 ......................atTiHrlalldfddlltealelleeaeeekklqeeellivDEfqdvdelqyrL 121
                                                             + T H+   l++++ l    ++l +    ++    + livDE+ d+   q rL
  gi|518651372|ref|YP_008140892.1|  90 tkwkeklgqeiiklrysskiliILTTHNT--LANNEFL----NILSS----SD--YPKFLIVDEVHDIGSAQHRL 152
                                       88888888888888888888888888866..5444433....33333....12..24489*********999988 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                            AAA_19  78 l 78 
                                        
  gi|518651372|ref|YP_008140892.1| 265 N 265
                                       2 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   0.00011      0.25       8      60 ..      14      67 ..       9     112 .. 0.84
   2 ?   -3.2   0.0       2.1   4.7e+03     121     137 ..     135     151 ..     134     165 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHH-SEEEEE-.-TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S-- CS
                              PhoH  8 eQkeylealkkndivfaiG.paGtGKtylavalavealkkkkvkriiltrpave 60
                                       Q+++++  k++++  ++   +GtGKty ++ +  e+++ ++   i+++ p v+
  gi|518651372|ref|YP_008140892.1| 14 YQQDAVNKWKNHNMNGIFEmATGTGKTYTSILCINELIQTNEKLLIVIACPYVH 67
                                      5888889999888887765167*********99999999888888999888876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                                       EEEEE-SGGG--HHHHH CS
                              PhoH 121 afvilDEAQnttkeqmk 137
                                       +f+i+DE  ++ ++q +
  gi|518651372|ref|YP_008140892.1| 135 KFLIVDEVHDIGSAQHR 151
                                       59999999998888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3233.17
//
Query:       gi|518651373|ref|YP_008140893.1|  [L=67]
Description: hypothetical protein FACI_IFERC00001G0012 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 492.68
//
Query:       gi|518651374|ref|YP_008140894.1|  [L=641]
Description: hypothetical protein FACI_IFERC00001G0013 [Ferroplasma acidarmanus fer1]
Scores for complete 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-17   61.2   8.1    1.2e-16   60.8   8.1    1.2  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.6e-15   58.1  36.3    1.6e-15   58.1  36.3    3.7  1  AAA_23          AAA domain
    3.7e-10   40.1  47.5    3.7e-10   40.1  47.5    3.2  1  AAA_15          AAA ATPase domain
    1.7e-05   24.6   0.0    1.7e-05   24.6   0.0    2.8  3  AAA_27          AAA domain
    3.1e-05   23.6   0.1    7.3e-05   22.4   0.1    1.7  1  AAA_29          P-loop containing region of AAA domain
     0.0047   16.8   6.3     0.0047   16.8   6.3    3.5  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
     0.0052   16.7   0.0      0.014   15.3   0.0    1.9  1  NACHT           NACHT domain
  ------ inclusion threshold ------
       0.01   16.1  11.0       0.11   12.8   1.7    3.2  3  FliJ            Flagellar FliJ protein
      0.011   14.6  32.6      0.026   13.4  13.9    2.9  3  Spc7            Spc7 kinetochore protein
      0.012   15.5   0.8      0.012   15.5   0.8    3.0  2  Med10           Transcription factor subunit Med10 of Mediato
       0.25   11.4  13.6          2    8.5   3.1    3.0  2  DHR10           Designed helical repeat protein 10 domain
       0.33   10.8   6.3          3    7.7   0.5    2.5  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
       0.43   10.1   1.8       0.96    9.0   0.1    2.0  2  DUF885          Bacterial protein of unknown function (DUF885
          3    7.6   5.1        4.1    7.2   0.8    2.7  2  Lectin_N        Hepatic lectin, N-terminal domain
        6.5    6.0  17.7       0.53    9.6   1.8    2.5  2  DUF4407         Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   8.1     1e-19   1.2e-16       1     205 [.       2     610 ..       2     624 .. 0.95

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 1e-19
                                       EEEEEEEESETTEECEEEEEET..TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTT CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   1 vlkrleienFksyagktvilpf..sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvk 75 
                                       ++++++i+nF+ y++ +++ +   +k++ +i+G NG GK+ +l+Ai ++L  +++ +  ++   +li++ +++++ +
  gi|518651374|ref|YP_008140894.1|   2 YINNIIIKNFRLYKNVNIDFNSanNKNIAIIIGDNGKGKTTFLNAIAWCLYGKES-NTSKNIGLSLINNIAKNDNEN 77 
                                       699**********88877766522567889********************87666.677788889****999999** PP

                                       EEEEEEEEEETTEESSSSSSCEEEEEEEETTSE.EEEEETTEEE-HHHHHHHHHCTT-STT................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                             SMC_N  76 kaeveitfdnedkklkiekeevsisrrvkrkge.seykingkevtkkevsellesagiske................ 135
                                       + +v+i++++++k+      +++i r + ++++  ++++  k+  ++e++ +l  +++ ++                
  gi|518651374|ref|YP_008140894.1|  78 EIRVSIIMTDKQKN------KFEIVRALNNTNNrPQFYVLYKSEDSREYQPILDAENFIEKhfpesimhyflfdgem 148
                                       ******98888777......899988887766548999999999************999989*************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518651374|ref|YP_008140894.1| 149 leeyfqndnekikkevynlsnielldkvnthikavltdikyrvrnkniistnkidteieqinqgideqtrslekqkh 225
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518651374|ref|YP_008140894.1| 226 diqdaknnrdnlrkqlqgipsisdkeelidayknelknikkdrdgieielystlikedpyiitmkeskeitedlsnk 302
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518651374|ref|YP_008140894.1| 303 idkgeippmykkdfltnildknvcicgrdldvdsknlltqlynntneetnnsdslsvlyhtlkdfdshvnsfrntiq 379
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518651374|ref|YP_008140894.1| 380 nlhdkdakledkfnstsksmekiqneidgydneqikiwqkelkdydeeiengdikigeinsainqfnkqlpikqkey 456
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518651374|ref|YP_008140894.1| 457 tealksnketegyrkeinfinkiidavklskdnitnnmkkqiekttneifleiiekqqtfkevhisdnysfsvkdin 533
                                       ***************************************************************************** PP

                                       ......CS-HHHHHHHHHHHHHHHHCCS--SE.EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC- CS
                                       ......xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ......lLSgGektLvalaLlfAiqkvkpapl.yllDeidaaLDeknvkkvaellkeksknaQfivislreemleka 205
                                             +LS Ge+  +al+++ A++ +    +  + D +   LD +  +++a+++++  + +Q+i    ++e++ k 
  gi|518651374|ref|YP_008140894.1| 534 deeslgTLSAGERESLALSFIAALNDITEIDVpIIADTLLGRLDPNVKENIANIFDNIFTGTQLILLVTESEFTDKF 610
                                       *************************99987662456999**************************999988887776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1  36.3   1.4e-18   1.6e-15       2     176 ..       6     252 ..       5     307 .. 0.48

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.4e-18
                            AAA_23   2 LkienfrsfrdqeidF....skgltlItGpNGaGKTTildAiklaLygetprlsrks....grgfeksdve.iese. 68 
                                       + i+nfr +++++idF    +k++ +I+G+NG GKTT+l+Ai ++Lyg+ +++s++           + ++   +e 
  gi|518651374|ref|YP_008140894.1|   6 IIIKNFRLYKNVNIDFnsanNKNIAIIIGDNGKGKTTFLNAIAWCLYGKESNTSKNIglslI-----NNIAkNDNEn 77 
                                       89*****************999**************************99988888744331.....3333011111 PP

                            AAA_23  69 ..........gkvkay.veltfenkdgry................................................ 86 
                                                 ++++++ + + ++n+++r                                                 
  gi|518651374|ref|YP_008140894.1|  78 eirvsiimtdKQKNKFeIVRALNNTNNRPqfyvlyksedsreyqpildaenfiekhfpesimhyflfdgemleeyfq 154
                                       11122333322222222222233333333444444444444455555555555555555555555555444444444 PP

                            AAA_23  87 .......trsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgqerfeefelkdkke... 153
                                              +                                                                 e   
  gi|518651374|ref|YP_008140894.1| 155 ndnekikK-----------------------------------------------------------------Evyn 166
                                       44444440.................................................................1444 PP

                            AAA_23 154 ....................................................rleelekeleeledekkllekl... 175
                                                                                            le+ + +++++++ ++ l+k+   
  gi|518651374|ref|YP_008140894.1| 167 lsnielldkvnthikavltdikyrvrnkniistnkidteieqinqgideqtrSLEKQKHDIQDAKNNRDNLRKQlqg 243
                                       55555555555555555555555555555554444444333333333332222222233333333333333333333 PP

                            AAA_23 176 ........e 176
                                               e
  gi|518651374|ref|YP_008140894.1| 244 ipsisdkeE 252
                                       322222111 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1  47.5   3.1e-13   3.7e-10       1     253 [.       1     307 [.       1     331 [. 0.74

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.1e-13
                            AAA_15   1 MkIkkikikNFRslkdveidlsee....ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenise 73 
                                       M+I++i+ikNFR +k+v id+++     + ++iG N+ GK+++l+a+ + l  ke+     ++i  + +++  ++++
  gi|518651374|ref|YP_008140894.1|   1 MYINNIIIKNFRLYKNVNIDFNSAnnknIAIIIGDNGKGKTTFLNAIAWCLYGKESNT--SKNIGLSLINNIAKNDN 75 
                                       **********************99999999**********************995555..45555555555555555 PP

                            AAA_15  74 skdikIdvef.................................................................ae 85 
                                       +++i++ +                                                                   + 
  gi|518651374|ref|YP_008140894.1|  76 ENEIRVSIIMtdkqknkfeivralnntnnrpqfyvlyksedsreyqpildaenfiekhfpesimhyflfdgemleE- 151
                                       5555544444448888888888888888888888888888888888888888888888888888888888775431. PP

                            AAA_15  86 kekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeeklekekeel 162
                                         +++++ek++k+    ++  ll+k ++ +k  ++d k+ + ++++++ ++ + +++++++  +e++ +lek+k ++
  gi|518651374|ref|YP_008140894.1| 152 -YFQNDNEKIKKEVYNLSNIELLDKVNTHIKAVLTDIKYRVRNKNIISTNKIDTEIEQINQGIDEQTRSLEKQKHDI 227
                                       .4455555666666666666788888999999999999999999998888888888888888888888999999999 PP

                            AAA_15 163 kidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..eee 237
                                       +  k++ ++l k+l+ + + ++           k +li a +n  ++ ++  + + ++l++ +++e  +      +e
  gi|518651374|ref|YP_008140894.1| 228 QDAKNNRDNLRKQLQGIPSISD-----------KEELIDAYKNELKNIKKDRDGIEIELYSTLIKEDPY--IitMKE 291
                                       8777777777776665554444...........778888888888888888888888888888887433..234556 PP

                            AAA_15 238 lteklkeiqeklkeid 253
                                       ++e+ +++ +k+++ +
  gi|518651374|ref|YP_008140894.1| 292 SKEITEDLSNKIDKGE 307
                                       6666666666666544 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.4e-08   1.7e-05       1      87 [.       1      98 [.       1     107 [. 0.73
   2 ?   -1.7   0.2       1.5   1.8e+03     158     197 ..     202     241 ..     197     266 .. 0.69
   3 ?   -0.9   0.1      0.83     1e+03     160     198 ..     369     407 ..     361     423 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.4e-08
                            AAA_27  1 MrlerLdLeryGkftdrsldfsa.eeadlhliyGpNEAGKstalrAisdllfGipertkdnflh..........dakkL 68
                                      M ++++ ++ +  +++ ++df++ +++++ +i+G N  GK+t l+Ai   l+G + +t++n             +++++
  gi|518651374|ref|YP_008140894.1|  1 MYINNIIIKNFRLYKNVNIDFNSaNNKNIAIIIGDNGKGKTTFLNAIAWCLYGKESNTSKNIGLslinniakndNENEI 79
                                      778888899999999******9857899*****************************9998532111111111134556 PP

                            AAA_27 69 rigavleeadgeelefaRr 87
                                      r++ ++++++++++e++R 
  gi|518651374|ref|YP_008140894.1| 80 RVSIIMTDKQKNKFEIVRA 98
                                      6666666666666666665 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                            AAA_27 158 lrevleaLeaeadelfkprkskkrainealeeleeakkel 197
                                       + + +e++++  de  ++ +++k+ i++a+++ ++++k+l
  gi|518651374|ref|YP_008140894.1| 202 IDTEIEQINQGIDEQTRSLEKQKHDIQDAKNNRDNLRKQL 241
                                       5555566666666666666666666666666666666665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.83
                            AAA_27 160 evleaLeaeadelfkprkskkrainealeeleeakkelr 198
                                       + ++++++  ++l+++ ++ + ++n + +++e+ ++e+ 
  gi|518651374|ref|YP_008140894.1| 369 SHVNSFRNTIQNLHDKDAKLEDKFNSTSKSMEKIQNEID 407
                                       556677777778888888888788888888888777765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   6.1e-08   7.3e-05       5      50 ..       7      55 ..       3      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.1e-08
                            AAA_29  5 qlvNWgtfdghtieidlkg...atlltGpsGsGKSTllDAiqalLvpak 50
                                       + N   +++  i+++ ++   + +++G++G GK+T+l Ai+  L++++
  gi|518651374|ref|YP_008140894.1|  7 IIKNFRLYKNVNIDFNSANnknIAIIIGDNGKGKTTFLNAIAWCLYGKE 55
                                      5667788888888888776677899*********************998 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   6.3   3.9e-06    0.0047       1      97 [.      29     118 ..      29     240 .. 0.75
   2 ?   -1.5   7.8       1.4   1.7e+03      61     165 ..     274     382 ..     262     563 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.9e-06
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglr 77 
                                       ++++iG+Ng GK+++L a+ +          ++ ++++++   + ++ +  +d e +++ +i+ +++q+++++    
  gi|518651374|ref|YP_008140894.1|  29 IAIIIGDNGKGKTTFLNAIAWCL-------YGKESNTSKNIGLSLINNIAKNDNENEIRVSIIMTDKQKNKFEIVRA 98 
                                       689*******************4.......68888888888899999999999999999999999999999999988 PP

                            AAA_21  78 lersqv...eeklssvetllesg 97 
                                       l++ +        +++ + + s+
  gi|518651374|ref|YP_008140894.1|  99 LNNTNNrpqF---YVLYKSEDSR 118
                                       8888882222...2222222222 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.4
                            AAA_21  61 eieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepnd 137
                                       e++ +l+++  y   ++  +++  e ls++ +++e++++ +k+ l  + ++n +  g + +v+++ l + ++++ n+
  gi|518651374|ref|YP_008140894.1| 274 ELYSTLIKEDPYIITMKESKEIT-EDLSNKIDKGEIPPMYKKDFLTNILDKNVCICGRDLDVDSKNLLTQLYNNTNE 349
                                       55555555555555555555555.88888888888999999999999999999999999999999999999999888 PP

                            AAA_21 138 lqfgka.ltditsrawsllllldglrke....r 165
                                       + ++++ l  +++++ ++ +  +++r+      
  gi|518651374|ref|YP_008140894.1| 350 ETNNSDsLSVLYHTLKDFDSHVNSFRNTiqnlH 382
                                       877665255667777777777777765443330 PP

>> NACHT  NACHT 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     0.014       3      31 ..      30      58 ..      28     165 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS-SCC CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegklpq 31
                                       i+ G++G+GKTt+l  +a ++  ++ + 
  gi|518651374|ref|YP_008140894.1| 30 AIIIGDNGKGKTTFLNAIAWCLYGKESNT 58
                                      589***************98886665554 PP

>> FliJ  Flagellar FliJ protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.9    0.0025         3      47      82 ..     206     241 ..     147     271 .. 0.74
   2 ?   12.8   1.7   8.8e-05      0.11       9      90 ..     387     464 ..     380     473 .. 0.87
   3 ?   -1.8   0.0       2.9   3.5e+03      49      77 ..     471     500 ..     460     513 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0025
                              FliJ  47 lrnyqafisaldeaiaqqkqelaqaekqvekareew 82 
                                       + ++++ i+   + +++qk+++++a++++++ r+++
  gi|518651374|ref|YP_008140894.1| 206 IEQINQGIDEQTRSLEKQKHDIQDAKNNRDNLRKQL 241
                                       334444444444444444444444444444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.8e-05
                              FliJ   9 eaqrelqqaeekleeleqyrqeyqkqlsgeaqglsaaelrnyqafisaldeaiaqqkqelaqaekqvekareewqea 85 
                                       + + ++++  + +e+++++++ y +++ +        el+ y + i++ d +i ++ ++++q +kq+  +++e+ ea
  gi|518651374|ref|YP_008140894.1| 387 KLEDKFNSTSKSMEKIQNEIDGYDNEQIKIW----QKELKDYDEEIENGDIKIGEINSAINQFNKQLPIKQKEYTEA 459
                                       677889999999***********66665555....6***************************************99 PP

                              FliJ  86 rqerk 90 
                                        +  k
  gi|518651374|ref|YP_008140894.1| 460 LKSNK 464
                                       66655 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.9
                              FliJ  49 nyqafisaldeaiaqqkqelaq.aekqvek 77 
                                       +  +fi+++ +a++  k ++++  +kq+ek
  gi|518651374|ref|YP_008140894.1| 471 KEINFINKIIDAVKLSKDNITNnMKKQIEK 500
                                       556788888888888888775415666665 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   8.6    0.0012       1.4     209     302 ..     200     295 ..     149     302 .. 0.82
   2 ?   11.0   1.0   0.00012      0.14     184     251 ..     341     407 ..     336     413 .. 0.88
   3 ?   13.4  13.9   2.2e-05     0.026     144     300 ..     360     523 ..     354     530 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                              Spc7 209 aelkaeieekkkelaelqeqleeleekieelkeqkseleeeiaeaervleeckgws..esevsrlkeevkaleeltg 283
                                       +++++eie+ ++ ++e ++ le+++ +i+++k+++++l+++++   ++ ++++ ++  ++e++++k+  + +e ++ 
  gi|518651374|ref|YP_008140894.1| 200 NKIDTEIEQINQGIDEQTRSLEKQKHDIQDAKNNRDNLRKQLQGIPSISDKEELIDayKNELKNIKKDRDGIEIELY 276
                                       56789999999999999999999999999999999999999999988888887766225799999999999999999 PP

                              Spc7 284 wkivslsgstleltyrsel 302
                                        ++++ ++  ++++  +e+
  gi|518651374|ref|YP_008140894.1| 277 STLIKEDPYIITMKESKEI 295
                                       9999999999998877776 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00012
                              Spc7 184 eklqeaaeelesidkeeLeelreelaelkaeieekkkelaelqeqleeleekieelkeqkseleeeia 251
                                       ++l +  +e e+ ++++L  l ++l++ ++ ++++++ +++l ++ ++le+k+++++++++++++ei 
  gi|518651374|ref|YP_008140894.1| 341 TQLYNNTNE-ETNNSDSLSVLYHTLKDFDSHVNSFRNTIQNLHDKDAKLEDKFNSTSKSMEKIQNEID 407
                                       555555555.667899**************************************************96 PP

  == domain 3  score: 13.4 bits;  conditional E-value: 2.2e-05
                              Spc7 144 leenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeeles....idkeeLeelreelaelkaeie 216
                                       l ++l+++++  +   +  ++l++   +le ++++ ++ +ek+q++ +  ++    i ++eL+ + ee+++ + +i 
  gi|518651374|ref|YP_008140894.1| 360 LYHTLKDFDSHVNSFRNTIQNLHDKDAKLEDKFNSTSKSMEKIQNEIDGYDNeqikIWQKELKDYDEEIENGDIKIG 436
                                       66777777777778888888888888899999999999999999955555554444669999999999999999999 PP

                              Spc7 217 ekkkelaelqeqleeleekieelkeqkse...leeeiaeaervleeckgwsesevsrlkeevkaleeltgwkivsls 290
                                       e +  +++ ++ql  ++++ +e+ ++ +e   +++ei+  ++++++ k ++++  +++k++ ++  ++  ++i++ +
  gi|518651374|ref|YP_008140894.1| 437 EINSAINQFNKQLPIKQKEYTEALKSNKEtegYRKEINFINKIIDAVKLSKDNITNNMKKQIEKTTNEIFLEIIEKQ 513
                                       99999999999998888777665444333123789999999999999999999999999999999999999888887 PP

                              Spc7 291 gstleltyrs 300
                                       ++  e+ + +
  gi|518651374|ref|YP_008140894.1| 514 QTFKEVHISD 523
                                       7766666555 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 ?   15.5   0.8     1e-05     0.012       9      93 ..     215     330 ..     198     351 .. 0.81
   2 ?    0.4   1.1      0.51   6.1e+02      25      49 ..     378     406 ..     335     505 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                       HHHHHHHHHHHS--TT.S-TTHHHHHH.............HHHHHHHHHHHHHHH....................HH CS
                             Med10   9 qsllelgvqvsdydenessqevlaqkl.............ktlvesLqelsktaskl..................lq 54 
                                       ++ + l+ q +d ++++++++ l ++l             ++  ++L++++k ++                    ++
  gi|518651374|ref|YP_008140894.1| 215 EQTRSLEKQKHDIQDAKNNRDNLRKQLqgipsisdkeeliDAYKNELKNIKKDRDGIeielystlikedpyiitmKE 291
                                       45667777788888888777888777767666666665556666666666666665599***************999 PP

                                       --EEEHHHHHHHHTTB-HHHHHHHHHHHHHHHHHHHHHH CS
                             Med10  55 dikiPlelieyvenGrNPdiYtrefvelvrrkNqlmkGk 93 
                                       + +i  +l + +++G+ P +Y ++f+ ++  kN  + G+
  gi|518651374|ref|YP_008140894.1| 292 SKEITEDLSNKIDKGEIPPMYKKDFLTNILDKNVCICGR 330
                                       *********************************887776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.51
                                       .....S-TTHHHHHHHHHHHHHHHHHHHH CS
                             Med10  25 e....ssqevlaqklktlvesLqelskta 49 
                                             ++  l++k +++++s+++++++ 
  gi|518651374|ref|YP_008140894.1| 378 IqnlhDKDAKLEDKFNSTSKSMEKIQNEI 406
                                       23333444455555555555555555443 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.8    0.0038       4.5      36      81 ..     197     242 ..     188     269 .. 0.77
   2 ?    8.5   3.1    0.0017         2      29     101 ..     386     463 ..     339     472 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0038
                             DHR10  36 rsciklleeieaelakleeakkklkelrdaleekeielrelerkee 81 
                                        s+ k+  eie+  +  +e+ + l++++  +++ ++++  l ++ +
  gi|518651374|ref|YP_008140894.1| 197 ISTNKIDTEIEQINQGIDEQTRSLEKQKHDIQDAKNNRDNLRKQLQ 242
                                       5666666777777777777777777777777777777777666654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0017
                             DHR10  29 qvvekdlrsciklleeieaelakleea.....kkklkelrdaleekeielrelerkeerlqrqlenaeeklerlreq 100
                                       +++e  ++s+ k +e+i++e+  ++ +     +k+lk+  +++e+  i+  e+++ + + ++ql  ++++++ + ++
  gi|518651374|ref|YP_008140894.1| 386 AKLEDKFNSTSKSMEKIQNEIDGYDNEqikiwQKELKDYDEEIENGDIKIGEINSAINQFNKQLPIKQKEYTEALKS 462
                                       67899999************998888833333699*****************************7666665555444 PP

                             DHR10 101 a 101
                                        
  gi|518651374|ref|YP_008140894.1| 463 N 463
                                       4 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.8     0.011        13      42     100 ..     180     237 ..     148     266 .. 0.62
   2 ?    7.7   0.5    0.0025         3       4     113 ..     355     465 ..     353     519 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCH CS
                    Apolipoprotein  42 lraeleevrarlepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavy 100
                                       ++a l++ + r+ ++     +++  ++e+++q +++ t+ l ++ ++d++++++  +  
  gi|518651374|ref|YP_008140894.1| 180 IKAVLTDIKYRVRNKNIISTNKIDTEIEQINQGIDEQTRSLEKQ-KHDIQDAKNNRDNL 237
                                       45555555555555555556666666666666666666666663.33333333332222 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                                       HCCCCHHHHHCCHHHCHHCHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHCCCCHHHHHHCCCHHHHHHHHHCCH CS
                    Apolipoprotein   4 esldelkayaeeleeqlaplaqelrdrlskeleelrarl...raeleevrarlepyrdevqeqlgqnleelrqrlap 77 
                                       +sl+ l  +++++ + ++++ ++++++l ++ ++l ++    ++ +e   + +  y +e  + ++++l+++++++++
  gi|518651374|ref|YP_008140894.1| 355 DSLSVLYHTLKDFDSHVNSF-RNTIQNLHDKDAKLEDKFnstSKSMEKIQNEIDGYDNEQIKIWQKELKDYDEEIEN 430
                                       66666777788888888887.6699999999999**99999999********************************* PP

                                       HHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHH CS
                    Apolipoprotein  78 yteelrerlaadaeelqeqlavyaeelrerlerhve 113
                                          ++ e ++ ++++  +ql  +++e+ e l+++ e
  gi|518651374|ref|YP_008140894.1| 431 GDIKIGE-INSAINQFNKQLPIKQKEYTEALKSNKE 465
                                       9999955.9999999999999999999999999944 PP

>> DUF885  Bacterial protein of unknown function (DUF885)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1    0.0008      0.96     105     221 ..     169     282 ..      87     305 .. 0.82
   2 ?    0.3   0.2      0.35   4.1e+02     283     302 ..     432     451 ..     345     538 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0008
                                       HHHHCCCHHHHHHHHHHHHHHHHHTT.-S-HHHHHHHHHHHHHHHGTSSHHCCCHH.CCCCCC...HHHHHHHHHH. CS
                            DUF885 105 ylarlaavpaaldqaranlregaaaglvpprrqvekvieqlrgllagaaaeasalvaplaeleaekealraeleaal 181
                                        +++l++v++ ++++++ ++ +++++ + +   +++ ieq+++ +++++ + ++ ++ ++++++++++lr++l+ + 
  gi|518651374|ref|YP_008140894.1| 169 NIELLDKVNTHIKAVLTDIKYRVRNKNIISTNKIDTEIEQINQGIDEQTRSLEKQKHDIQDAKNNRDNLRKQLQGI- 244
                                       4789*****************************************9877777766678888878889******988. PP

                                       HHHHHHHHHHHHHHHHHCCHHHS-BSS..HH..HHHHHHHHH CS
                            DUF885 182 aeavkpayaeladfleeellpaarkdapdGe..elYarllrs 221
                                           +   +el+d  ++el++  + d  dG   elY +l+++
  gi|518651374|ref|YP_008140894.1| 245 --PSISDKEELIDAYKNELKNIKK-DR-DGIeiELYSTLIKE 282
                                       ..7778889999999999988877.77.75411567777665 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHHHHCCHHHC CS
                            DUF885 283 eellaaaraaiaeldaklpe 302
                                       +  + +++ ai++ +++lp 
  gi|518651374|ref|YP_008140894.1| 432 DIKIGEINSAINQFNKQLPI 451
                                       22222222222222222222 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2      0.23   2.8e+02      59     104 ..     148     228 ..     144     246 .. 0.70
   2 ?    7.2   0.8    0.0034       4.1      57     104 ..     357     407 ..     348     423 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.23
                          Lectin_N  59 tLketfsnfssstlaeiqalss...................................qggslsekvtsleaklekkq 100
                                        L+e f+n  ++++ e+ +ls                                    + +++++ +      lek++
  gi|518651374|ref|YP_008140894.1| 148 MLEEYFQNDNEKIKKEVYNLSNielldkvnthikavltdikyrvrnkniistnkidtEIEQINQGIDEQTRSLEKQK 224
                                       57788888888888888888887777777777777777777777777777777666655566666666666666666 PP

                          Lectin_N 101 qdlk 104
                                       +d++
  gi|518651374|ref|YP_008140894.1| 225 HDIQ 228
                                       5554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0034
                          Lectin_N  57 LetLketfsnfss...stlaeiqalssqggslsekvtsleaklekkqqdlk 104
                                       L+ L +t+++f s   s    iq+l+ ++ +l++k +s +  +ek q++++
  gi|518651374|ref|YP_008140894.1| 357 LSVLYHTLKDFDShvnSFRNTIQNLHDKDAKLEDKFNSTSKSMEKIQNEID 407
                                       455555555555511156789**************************9986 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8   0.00045      0.53     103     208 ..     143     285 ..     138     321 .. 0.55
   2 ?    1.3   8.3      0.15   1.8e+02     107     213 ..     401     499 ..     336     524 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                           DUF4407 103 iFekeIdaelaeeqqeeakelkeqlaaa.....ltaelaeleaqia...................alqaeidaaear 155
                                       +F++e  +e +++++e++k+   +l +       ++ +++  ++i+                   ++++ id++ + 
  gi|518651374|ref|YP_008140894.1| 143 LFDGEMLEEYFQNDNEKIKKEVYNLSNIelldkVNTHIKAVLTDIKyrvrnkniistnkidteieQINQGIDEQTRS 219
                                       57777777777777777777666655446655533333333333333333444444441111111444445444444 PP

                           DUF4407 156 ldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelkakld...............a 208
                                       l++++ + q+  ++   +  ++ +G  p+   k++ +da+++el+++k+++d                
  gi|518651374|ref|YP_008140894.1| 220 LEKQKHDIQDAKNNR-DNLRKQLQGI-PSISDKEELIDAYKNELKNIKKDRDgieielystlikedpY 285
                                       444444444443332.2222334444.67777888888888888888888777766666666654440 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgp 183
                                        I+ e++  ++e++k  +++l+ ++++e+++ + +i +++++i++ +++l  +++e+++ l+ +k      ++G+ +
  gi|518651374|ref|YP_008140894.1| 401 KIQNEIDGYDNEQIKIWQKELK-DYDEEIENGDIKIGEINSAINQFNKQLPIKQKEYTEALKSNKE-----TEGYRK 471
                                       3444444444555555544444.4666666666666677777777777777777777777765332.....234444 PP

                           DUF4407 184 aakekkaqldaaqaelaelkakldatarla 213
                                       +    ++ +da +   ++++++   +++++
  gi|518651374|ref|YP_008140894.1| 472 EINFINKIIDAVKLSKDNITNN--MKKQIE 499
                                       4444444444444444444444..333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2686  (0.149813); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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):              15  [number of targets reported over threshold]
# CPU time: 1.00u 0.34s 00:00:01.34 Elapsed: 00:00:00.52
# Mc/sec: 3712.72
//
Query:       gi|518651375|ref|YP_008140895.1|  [L=142]
Description: hypothetical protein FACI_IFERC00001G0014 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.1   0.0       0.22   11.4   0.0    1.4  1  DUF1317   Protein of unknown function (DUF1317)


Domain annotation for each model (and alignments):
>> DUF1317  Protein of unknown function (DUF1317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   1.2e-05      0.22      30      48 ..      93     111 ..      89     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.2e-05
                           DUF1317  30 kviknPlkAqrlAEEknnk 48 
                                       ++i nPlk + +AEE  n 
  gi|518651375|ref|YP_008140895.1|  93 NIISNPLKYYTIAEEYVNA 111
                                       79*************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 928.97
//
Query:       gi|518651376|ref|YP_008140896.1|  [L=46]
Description: hypothetical protein FACI_IFERC00001G0015 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 329.18
//
Query:       gi|518651377|ref|YP_008140897.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G0016 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.48
# Mc/sec: 336.39
//
Query:       gi|518651378|ref|YP_008140898.1|  [L=510]
Description: hypothetical protein FACI_IFERC00001G0017 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); 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: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3736.19
//
Query:       gi|518651379|ref|YP_008140899.1|  [L=302]
Description: hypothetical protein FACI_IFERC00001G0018 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.16   12.2   3.0        6.8    7.0   0.1    3.2  3  Bac_DNA_binding  Bacterial DNA-binding protein


Domain annotation for each model (and alignments):
>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1   0.00038       6.8      66      90 .]      36      60 ..      33      60 .. 0.88
   2 ?    2.1   0.1     0.013   2.3e+02       7      41 ..     185     219 ..     183     229 .. 0.85
   3 ?    2.0   0.1     0.014   2.5e+02       7      30 ..     240     263 ..     226     267 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00038
                                      --B--B--EEEEEEEE-HHHHHHH. CS
                   Bac_DNA_binding 66 gekvkiparkvvkFkpskelkeavn 90
                                      +e +ki++ ++vk kp+k++ + +n
  gi|518651379|ref|YP_008140899.1| 36 QELYKIQEENKVKMKPGKAVVDFLN 60
                                      6889***************988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.013
                                       HHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-E CS
                   Bac_DNA_binding   7 ieeiaektgltkkdakrvveafldtikeaLkkgek 41 
                                       ++++ ek+++ +++ +++++++l  ike L+ + k
  gi|518651379|ref|YP_008140899.1| 185 LKKMQEKAKCLRNQNSNIFKELLLNIKEPLETNLK 219
                                       67889999999*****************9998755 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.014
                                       HHHHHTT----HHHHHHHHHHHHH CS
                   Bac_DNA_binding   7 ieeiaektgltkkdakrvveafld 30 
                                       ++ei ++ +lt+++++++++ f++
  gi|518651379|ref|YP_008140899.1| 240 LKEIPNNGELTENTVTAIISKFIE 263
                                       355666679***********9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1983.41
//
Query:       gi|518651380|ref|YP_008140900.1|  [L=924]
Description: hypothetical protein FACI_IFERC00001G0019 [Ferroplasma acidarmanus fer1]
Scores for complete 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-51  173.3   0.3    1.5e-47  162.7   0.2    2.8  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    9.9e-34  117.2   0.0    9.4e-17   61.4   0.0    2.7  2  UvrD_C           UvrD-like helicase C-terminal domain
    3.3e-30  105.3   0.0    9.8e-30  103.8   0.0    1.8  2  AAA_19           AAA domain
    6.2e-27   95.1   0.0    1.1e-26   94.3   0.0    1.4  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
    8.6e-12   44.7   1.8    1.1e-09   38.0   0.2    3.2  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    3.2e-08   33.9   0.4    3.2e-08   33.9   0.4    1.8  1  Cas_Cas4         Domain of unknown function DUF83
    2.2e-06   27.6   0.0     0.0041   16.9   0.0    2.3  2  AAA_30           AAA domain
    0.00031   20.1   0.0    0.00057   19.3   0.0    1.4  1  DUF2800          Protein of unknown function (DUF2800)
    0.00057   20.2   0.1        0.2   11.9   0.0    2.6  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.083   12.6   0.1         23    4.6   0.0    3.7  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        0.2   11.4   0.1        2.7    7.7   0.0    2.3  2  DEAD             DEAD/DEAH box helicase


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.7   0.2     9e-51   1.5e-47       1     312 [.       7     273 ..       7     275 .. 0.87
   2 ?   -3.1   0.0       2.7   4.3e+03      49      67 ..     372     390 ..     364     425 .. 0.75

  Alignments for each domain:
  == domain 1  score: 162.7 bits;  conditional E-value: 9e-51
                                       SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCT CS
                     UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqess 77 
                                       l++eq++aia+ +g + v+A +GsGKT v+a r+++lik +  +p+ i+++TFT+kAaeElk+Ri+++l  ++ e+ 
  gi|518651380|ref|YP_008140900.1|   7 LTDEQEKAIAHKSGRLRVIACPGSGKTEVIARRVAKLIKDG-EKPEGIVAITFTEKAAEELKTRIRKILDVECPER- 81 
                                       699**************************************.***************************9998655. PP

                                       T-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHH CS
                     UvrD-helicase  78 dderlrlalqnlseanisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkl 154
                                                + + ++  +T+H+f++ il++      ldp +r++d  +  d+++ + + +    s++ +  +    l
  gi|518651380|ref|YP_008140900.1|  82 ---------ADFGDMFTGTIHGFALDILRE------LDPYYRTFDVLE--DARRVAYVSK----SQNYYRRIGLVRL 137
                                       .........779****************97......677777777777..3333333333....3345555555555 PP

                                       HHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEE CS
                     UvrD-helicase 155 eklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenalD 231
                                       e+              +   + +++ ++ + v+ +  +q++p +l++         k++a+++ +y++ +ke + +D
  gi|518651380|ref|YP_008140900.1| 138 ENA-------------YGLKYYNVISQFLKSVDIMLMEQIDPGNLTN---------KEFAKCFADYMDSLKEDRYFD 192
                                       533.............2233445667777777777777888877776.........89******************* PP

                                       HHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHH CS
                     UvrD-helicase 232 fsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielfl 308
                                       f+ +l++l+  l++n+e  + +  r+++i +DE+QD +k Q ++l+ll+  +e +++vGD++Q IY +Rg d++l++
  gi|518651380|ref|YP_008140900.1| 193 FATILYNLVYELKNNPEKINLITHRVRHIIVDEFQDVDKLQNTLLELLSPVTESICVVGDDDQGIYHWRGTDVGLIM 269
                                       ***************************************************************************** PP

                                       HHHH CS
                     UvrD-helicase 309 kkkk 312
                                       ++++
  gi|518651380|ref|YP_008140900.1| 270 NFSN 273
                                       9975 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.7
                                       EEEESSHHHHHHHHHHHHH CS
                     UvrD-helicase  49 lvvTFTnkAaeElkeRiee 67 
                                        v+T Tnk a+ +  R+ +
  gi|518651380|ref|YP_008140900.1| 372 AVLTRTNKWAKKIIDRLDR 390
                                       68999*******9999987 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   5.8e-20   9.4e-17       2     122 ..     284     418 ..     283     422 .. 0.90
   2 !   52.8   0.0   2.3e-17   3.8e-14     281     347 ..     557     636 ..     503     637 .. 0.81

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 5.8e-20
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                            UvrD_C   2 vLekNyRStksLlkaankflenilnr.ralekek....ktvekgekivvleaeteeeEaekiaatikall....... 66 
                                        L++N+RSt+ +++++ +f+en+ +r +   +e+    ++ e+g+ i+  e+e+e++E ++i+++i +l+       
  gi|518651380|ref|YP_008140900.1| 284 ALNTNFRSTRAVVELSRQFIENNGSRlPKGMTENpglkRKYEEGD-IQSCEFENEKDELDFIVSKIGELVgtdfldr 359
                                       69************************6666677689999999999.*****************************86 PP

                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  67 ...ekneklediavLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkl 122
                                               l+d avL+R+nk a+ki + L +egip + +++e++F+r+e+  +l+ + +
  gi|518651380|ref|YP_008140900.1| 360 nnkPFSLSLSDFAVLTRTNKWAKKIIDRLDREGIPSVAYSGESIFERPEVEFALHSIAY 418
                                       5433344689****************************************999998876 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 2.3e-17
                                       xxxx..xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 281 skkk..ekipiiTiHqAKGlEFdvVflagle..egtfPsyrskk..............ekrleEEkRlfYVaiTRAk 339
                                       ++    + ++i+TiH+AKGlEF+vVf+ +    + ++P     +               ++ e E+R++Y a TR  
  gi|518651380|ref|YP_008140900.1| 557 QDPSiiNAVKILTIHKAKGLEFPVVFVPDFIkpNHRTP-----DrnfvdnvlydseryTGTDEDERRVYYTAFTRSE 628
                                       33334599********************9632255666.....333444677777778889999************* PP

                                       xxxxxxxx RF
                            UvrD_C 340 krLfisys 347
                                       k Lf+++s
  gi|518651380|ref|YP_008140900.1| 629 KYLFMTWS 636
                                       ******98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.8   0.0     6e-33   9.8e-30       1     144 [.      11     259 ..      11     261 .. 0.93
   2 ?   -2.8   0.0       4.4   7.1e+03      43      67 ..     369     393 ..     362     435 .. 0.75

  Alignments for each domain:
  == domain 1  score: 103.8 bits;  conditional E-value: 6e-33
                            AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae......... 68 
                                       q++a+ a+k++ l v+a pG+GKT+v+  +va l++ g+ kpe i++++ft++Aa+el++r+++++           
  gi|518651380|ref|YP_008140900.1|  11 QEKAI-AHKSGRLRVIACPGSGKTEVIARRVAKLIKDGE-KPEGIVAITFTEKAAEELKTRIRKILDVecperadfg 85 
                                       899**.*******************************95.68********************877665799****** PP

                            AAA_19  69 ...atTiHrlal................................................................. 77 
                                          + TiH++al                                                                 
  gi|518651380|ref|YP_008140900.1|  86 dmfTGTIHGFALdilreldpyyrtfdvledarrvayvsksqnyyrriglvrlenayglkyynvisqflksvdimlme 162
                                       ***********9***************************************************************** PP

                            AAA_19  78 ............................ldfddlltealelle.eaeeekklqeee.llivDEfqdvdelqyrLlka 124
                                                                    df ++l + +  l+ + e+ + ++++  ++ivDEfqdvd+lq++Ll+ 
  gi|518651380|ref|YP_008140900.1| 163 qidpgnltnkefakcfadymdslkedryFDFATILYNLVYELKnNPEKINLITHRVrHIIVDEFQDVDKLQNTLLEL 239
                                       ****************99999999988888888887777777764455677778889******************** PP

                            AAA_19 125 llgekkklllvGDpdQliyv 144
                                       l + ++++++vGD+dQ iy 
  gi|518651380|ref|YP_008140900.1| 240 LSPVTESICVVGDDDQGIYH 259
                                       **99999***********96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.4
                            AAA_19  43 eeillvaftgrAakelrerlaalga 67 
                                        ++++++ t++ ak++ +rl+  g 
  gi|518651380|ref|YP_008140900.1| 369 SDFAVLTRTNKWAKKIIDRLDREGI 393
                                       5678999999999999999965544 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 !   94.3   0.0   6.6e-30   1.1e-26       2     254 ..     685     920 ..     684     921 .. 0.83

  Alignments for each domain:
  == domain 1  score: 94.3 bits;  conditional E-value: 6.6e-30
                          PDDEXK_1   2 lSvsrletfleCplrfflryllglreeeeleap.dlGtlvHaaleefyewkkldke...dleelleeaveelwpell 74 
                                        S+s+l  +l+Cp  f lr + g+  +  + a   +Gt +H +l+ +++ + +++e   d +e++ ++v++++  + 
  gi|518651380|ref|YP_008140900.1| 685 TSYSELTSYLRCPNDFLLRNVYGY--NAGVPAGfGYGTNIHNVLNMIHR-DYIRNEkvpDMDEVV-AMVDRMFHLR- 756
                                       69**********************..5555554488*************.444444456888888.7888888773. PP

                          PDDEXK_1  75 leeeilessarlrylaeklkevleklve.rlaeeleakrgfrpvalelefg...gekvrLkGriDrvd..dkeg... 142
                                          +          +++ +k+++e++v+ ++ae  ++k+  r+++ e +f    g +  + G+iD++   +++g   
  gi|518651380|ref|YP_008140900.1| 757 --YAT-------DAMSDNMKKAAERVVRsYVAE--HSKDFSRILETEKRFEfvlG-EALIAGQIDLLKktNPDGslk 821
                                       ..322.......677888888888888856667..77777799999955555464.789*********98778899* PP

                          PDDEXK_1 143 elriiDyKtgsappkskelaelkeglQlllYllalaegeelkeegepagalylrleepkvkdeevvkkmalteeele 219
                                       e++iiD+Kt +  +   +     ++ Ql+ Y+la+++  +lk    p +a+  +l      d   +++++ ++ el+
  gi|518651380|ref|YP_008140900.1| 822 EVEIIDFKTEK-IDGVYS---ADYDRQLRYYALACLKSLNLK----PQKAIVHHL------DDDSITQVDISDVELT 884
                                       ********988.445555...55666************4444....9********......99************** PP

                          PDDEXK_1 220 allqeleelaeeilagefparpskk.CeyCpyksvC 254
                                       ++  e+ +++++il+++fp++p+ k C+ C+y+++C
  gi|518651380|ref|YP_008140900.1| 885 KTVAEVGKTVDNILKKKFPPSPESKkCDGCDYRKLC 920
                                       ***********************888********** PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.93   1.5e+03      22      40 ..     104     122 ..     103     123 .. 0.91
   2 !   38.0   0.2   6.7e-13   1.1e-09       4      51 ..     567     633 ..     564     634 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.93
                          UvrD_C_2  22 dpdlaaarmgelrrrlLYt 40 
                                       dp++ +++  e+ rr +Y+
  gi|518651380|ref|YP_008140900.1| 104 DPYYRTFDVLEDARRVAYV 122
                                       89999***9999******9 PP

  == domain 2  score: 38.0 bits;  conditional E-value: 6.7e-13
                          UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaarmgel.....................rrrlLYtavTRAreklil 51 
                                       +ltihka+G+efp+V+v  pd+  + + +                       rr  Yta+TR+ + l++
  gi|518651380|ref|YP_008140900.1| 567 ILTIHKAKGLEFPVVFV--PDFIKPNHRTPdrnfvdnvlydserytgtdedERRVYYTAFTRSEKYLFM 633
                                       79***************..7777766655577*********************************9975 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 !   33.9   0.4   1.9e-11   3.2e-08      53     160 ..     801     920 ..     756     922 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 1.9e-11
                          Cas_Cas4  53 e...sikiDvvekekeklvv.....vEvKkskkk...eeaaklQllyYll.lLekkgveikeGvleypkekkreeve 117
                                       e    ++iD+++k++ +  +     +++K  k +   + +   Ql yY+l +L++ +++ ++++++ +     ++v 
  gi|518651380|ref|YP_008140900.1| 801 EaliAGQIDLLKKTNPDGSLkeveiIDFKTEKIDgvySADYDRQLRYYALaCLKSLNLKPQKAIVHHLDDDSITQVD 877
                                       2466788999996655544422222444433332654445599*****7649************************* PP

                          Cas_Cas4 118 lte.elreelekaikeieeiissekppkvkkkkiCkkCayaelC 160
                                       +++ el++ + ++ k +++i+++ k p+  ++k+C+ C y++lC
  gi|518651380|ref|YP_008140900.1| 878 ISDvELTKTVAEVGKTVDNILKK-KFPPSPESKKCDGCDYRKLC 920
                                       98736778888999999999999.5666667889********** PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.5e-06    0.0041       2      65 ..       7      69 ..       6      96 .. 0.79
   2 !    8.4   0.0   0.00099       1.6      81     127 ..     205     255 ..     180     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.5e-06
                            AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag...grviglAptgkaAkvLaee 65
                                      l++eQ++a+  +++sg+ +  + + +G+GKt +++  ++ + ++g   + +++++ t+kaA++L++ 
  gi|518651380|ref|YP_008140900.1|  7 LTDEQEKAI--AHKSGR-LR-VIACPGSGKTEVIARRVAKLIKDGekpEGIVAITFTEKAAEELKTR 69
                                      7899**999..466775.44.66899*******98775555555546789**************965 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00099
                            AAA_30  81 k....grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQ 127
                                       k    + + ++++ + +ivDE   vd  q ++ll+ ++    ++ +vGD++Q
  gi|518651380|ref|YP_008140900.1| 205 KnnpeKINLITHRvRHIIVDEFQDVDKLQ-NTLLELLSPVTESICVVGDDDQ 255
                                       4555533345556689*********9765.788899999899*********9 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.5e-07   0.00057       9     161 ..     690     858 ..     684     923 .. 0.66

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.5e-07
                           DUF2800   9 ahrWlkCppSarleeeipdesSeyAe..eGtlaHelaelklrkaldakekkgvkselkk.....keeevteemeeav 78 
                                          +l+Cp    l++ +  +++  A    Gt  H++ ++  r ++ +++  ++++ +       + ++ t+ m++ +
  gi|518651380|ref|YP_008140900.1| 690 LTSYLRCPNDFLLRNVYGYNAGVPAGfgYGTNIHNVLNMIHRDYIRNEKVPDMDEVVAMvdrmfHLRYATDAMSDNM 766
                                       556677777777777766666666642258***********999988888877755555778995555555565555 PP

                           DUF2800  79 deyvdfvl.ekieeakkdalvlvEqrvdfskyvpe..gfGtaDvviia.....ddvLeviDlKyGkgvkV.saekNp 146
                                       +++++ v+ + + e +kd    +E++  f+ + +e    G  D++  +      +++e+iD+K  k   V sa+   
  gi|518651380|ref|YP_008140900.1| 767 KKAAERVVrSYVAEHSKDFSRILETEKRFEFVLGEalIAGQIDLLKKTnpdgsLKEVEIIDFKTEKIDGVySADYDR 843
                                       555543330333333355556666666666667776699******9876644347889******99855527899** PP

                           DUF2800 147 QlalYAlGAleefdl 161
                                       Ql+ YAl+ l++++l
  gi|518651380|ref|YP_008140900.1| 844 QLRYYALACLKSLNL 858
                                       **********99874 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   0.00013       0.2       9      74 ..      23      83 ..      16     122 .. 0.79
   2 ?    5.3   0.1     0.014        22      88     112 ..     215     240 ..     195     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                            AAA_22  9 vvtGesGtGKTtllrrlleqldeeakaee..erpevvfvtlpsstsskdllrellralglelkaerls 74
                                       v++++G+GKT +++r + +l   +k  +  ++ ++v +t +++   ++l +++ ++l++e+ + r++
  gi|518651380|ref|YP_008140900.1| 23 RVIACPGSGKTEVIARRVAKL---IK--DgeKPEGIVAITFTEKA-AEELKTRIRKILDVECPE-RAD 83
                                      599**********99999998...23..34366677788888888.888888888888888887.444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                            AAA_22  88 aravielliiDEaqhlr..seealeeL 112
                                       +++v + +i+DE+q ++  ++++le L
  gi|518651380|ref|YP_008140900.1| 215 THRV-RHIIVDEFQDVDklQNTLLELL 240
                                       4455.89*********76667777776 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.014        23       5      21 ..      26      42 ..      23      83 .. 0.66
   2 ?    1.0   0.0      0.18   2.9e+02      64     107 ..     219     263 ..     209     340 .. 0.76
   3 ?    1.3   0.0      0.15   2.4e+02     185     201 ..     567     583 ..     548     633 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.014
                   Viral_helicase1  5 GvpGcGKStlirkllrt 21
                                      ++pG+GK+ +i + + +
  gi|518651380|ref|YP_008140900.1| 26 ACPGSGKTEVIARRVAK 42
                                      79*********998877 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                   Viral_helicase1  64 kililDEylllhaGyilllaalska.klvilfGDplQipfhsrna 107
                                       + +i+DE++ ++  +  ll  ls + + ++++GD  Q+ +h r  
  gi|518651380|ref|YP_008140900.1| 219 RHIIVDEFQDVDKLQNTLLELLSPVtESICVVGDDDQGIYHWRGT 263
                                       45899999998876666654444441567779******9997655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.15
                   Viral_helicase1 185 vttvhevqGltfdkVtl 201
                                       ++t h + Gl+f++V +
  gi|518651380|ref|YP_008140900.1| 567 ILTIHKAKGLEFPVVFV 583
                                       66667777777766654 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0016       2.7       2      65 ..       9      68 ..       8      88 .. 0.68
   2 ?    1.0   0.1      0.19   3.2e+02     112     135 ..     201     231 ..     143     250 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                                      HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-E.EEEEESSHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                              DEAD  2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpk.alivePtreLaeqtln 65
                                      d Q++ai +    g + v a  GsGKT++ +  v + +    + ++p  ++ ++ t++ ae+  +
  gi|518651380|ref|YP_008140900.1|  9 DEQEKAIAHKS--GRLRVIACPGSGKTEVIARRVAKLIK---DGEKPEgIVAITFTEKAAEELKT 68
                                      66777776654..778899999*************8884...34444404444444444555555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
                                       H.....HCTSSH..CTTEEEEEEETHHHHHH CS
                                       x.....xxxxxx..xxxxxxxxxxxxxxxxx RF
                              DEAD 112 l.....stgkln..lsqvrflVlDEadrlld 135
                                       +     + +k+n  +++vr +++DE + + +
  gi|518651380|ref|YP_008140900.1| 201 VyelknNPEKINliTHRVRHIIVDEFQDVDK 231
                                       233344445555558999*******988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (924 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.52
# Mc/sec: 5314.51
//
Query:       gi|518651381|ref|YP_008140901.1|  [L=1008]
Description: hypothetical protein FACI_IFERC00001G0020 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.12   12.1   1.6       0.25   11.1   1.6    1.5  1  Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
        4.9    7.2   8.8        5.2    7.1   0.4    3.3  3  DUF1160         Protein of unknown function (DUF1160)


Domain annotation for each model (and alignments):
>> Paired_CXXCH_1  Doubled CXXCH motif (Paired_CXXCH_1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.6   2.8e-05      0.25       9      36 ..      15      48 ..      11      48 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.8e-05
                    Paired_CXXCH_1  9 ClsCHnphgsd..npkll....kkakgaalCysC 36
                                      C +CH+ph sd  ++  l    k + ++ +C sC
  gi|518651381|ref|YP_008140901.1| 15 CPDCHEPHNSDevHKSGLplvrKGDGNTFICSSC 48
                                      99********745444447887777778889998 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.005        45      63      98 ..     219     254 ..     177     260 .. 0.73
   2 ?    7.1   0.4   0.00058       5.2      46      97 ..     324     375 ..     286     378 .. 0.76
   3 ?   -2.2   0.2      0.43   3.8e+03      42      68 ..     519     545 ..     502     572 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.005
                           DUF1160  63 vdgikLtkkQidylvkqvyenekiisilqkfvdeqr 98 
                                       +d+ +   +Qi  +++  y n++i silq+  ++++
  gi|518651381|ref|YP_008140901.1| 219 TDSFRSCINQITRFINTNYGNKYIRSILQNKLNKKK 254
                                       578888899*******************99877765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00058
                           DUF1160  46 FiereievediyeiveavdgikLtkkQidylvkqvyenekiisilqkfvdeq 97 
                                        i + +e  +iye ++ ++++ L  + +dy++k +y+  + ++ + ++v+++
  gi|518651381|ref|YP_008140901.1| 324 MIPSTLELSNIYEYIDKINPSFLIIEDVDYFIKDLYSYYTDTEYILNYVKRS 375
                                       47889999****************************9888777777787765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.43
                           DUF1160  42 vlkmFiereievediyeiveavdgikL 68 
                                       +lk  ++++++ve+  ++++  ++i +
  gi|518651381|ref|YP_008140901.1| 519 ILKNILSQNVSVEEYDRLIKIFNSIYM 545
                                       556666666666655555555554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1008 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       889  (0.0495845); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.55
# Mc/sec: 5520.76
//
Query:       gi|518651382|ref|YP_008140902.1|  [L=625]
Description: hypothetical protein FACI_IFERC00001G0021 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-09   37.6   0.0    6.4e-09   36.5   0.0    1.7  1  DUF1998         Domain of unknown function (DUF1998)
  ------ inclusion threshold ------
       0.04   14.1   0.7       0.04   14.1   0.7    1.9  2  Mlp             Mlp lipoprotein family
      0.055   13.3   0.9        1.4    8.8   0.2    2.6  2  Prok-RING_4     Prokaryotic RING finger family 4
       0.13   12.6   0.1        7.6    7.0   0.0    2.9  2  NOD2_WH         NOD2 winged helix domain
       0.19   11.5   3.2        0.2   11.4   0.2    2.3  2  Zn_Tnp_IS1      InsA N-terminal domain
        0.2   12.1   0.5        0.6   10.6   0.5    1.8  1  Zn-C2H2_12      Autophagy receptor zinc finger-C2H2 domain
       0.24   11.4   2.3        5.2    7.1   0.1    2.5  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.25   11.1   2.6        8.4    6.3   0.4    2.8  2  zf-RING_4       RING/Ubox like zinc-binding domain
       0.52   10.4   2.4        6.4    6.9   0.0    2.7  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
          1    9.3   3.7       0.97    9.5   0.2    2.3  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
        1.1    9.0   3.7        4.8    7.1   0.3    2.7  2  PADR1           PADR1 (NUC008) domain
        1.8    8.7   4.7        6.7    6.9   0.4    2.6  2  UPF0547         Uncharacterised protein family UPF0547
        4.1    7.5   7.0        2.1    8.4   2.7    2.5  2  DZR             Double zinc ribbon


Domain annotation for each model (and alignments):
>> DUF1998  Domain of unknown function (DUF1998)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.6e-12   6.4e-09       1      83 []     505     603 ..     505     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.6e-12
                           DUF1998   1 lehalinalplflqcdesdlgteckapedeprkrpariliydavp...gGaGiaekaaellee.....llraaleli 69 
                                       l+ha+in+l+l+ ++++++++++++ ++   ++++ +iliy+++p      G+   +  l+++     +l +a e+i
  gi|518651382|ref|YP_008140902.1| 505 LSHAIINVLSLYSGYSSASMRERIYIDR---NQKNGGILIYTSTPgedA--GM-GGLSGLVTQeklqqILVKAKERI 575
                                       69***********************664...47************6442..44.22444443344444********* PP

                           DUF1998  70 eec.d...Cee..........aGCpaCl 83 
                                       + c +   C +          a+C++C+
  gi|518651382|ref|YP_008140902.1| 576 DICsNdplCLDvskgsksqngAACYSCI 603
                                       999626898669999999999******7 PP

>> Mlp  Mlp lipoprotein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.7   2.9e-05      0.04      39     104 ..     323     382 ..     312     440 .. 0.76
   2 ?   -3.7   0.1       9.3   1.3e+04      96     114 ..     563     581 ..     560     596 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.9e-05
                               Mlp  39 vfkytiekltneiqgcsddnkskcnnfldWLktdiqkqkelaqafkkvykFLeskkekdksfdtyi 104
                                       +++y iekl+  +++ ++  k    nf+d++    q    l+q+ ++ ++F+  k+e +ks+d + 
  gi|518651382|ref|YP_008140902.1| 323 LMEYGIEKLKSSLEKFNNTRKM---NFIDFID---QEFDSLLQGPRNCENFVMGKHEIIKSIDSFP 382
                                       569*************999999...*******...9999**********************99984 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 9.3
                               Mlp  96 kdksfdtyiKseldckkgk 114
                                       k ++++   K+ +d ++++
  gi|518651382|ref|YP_008140902.1| 563 KLQQILVKAKERIDICSND 581
                                       4455555566667766665 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2     0.001       1.4      25      40 ..     133     148 ..     132     154 .. 0.82
   2 ?    2.2   0.0      0.12   1.6e+02      32      44 ..     201     213 ..     193     215 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.001
                       Prok-RING_4  25 fdskdlssCPlCqrri 40 
                                       f+sk+++ CP+Cq+  
  gi|518651382|ref|YP_008140902.1| 133 FNSKNSKKCPVCQNTY 148
                                       89999********875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.12
                       Prok-RING_4  32 sCPlCqrrisksd 44 
                                       +CP Cq+++  +d
  gi|518651382|ref|YP_008140902.1| 201 RCPECQSEVTMND 213
                                       7******998766 PP

>> NOD2_WH  NOD2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0055       7.6      21      39 ..      43      61 ..      38      66 .. 0.91
   2 ?    1.9   0.0       0.2   2.8e+02      11      34 ..     308     333 ..     308     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0055
                           NOD2_WH 21 FseedLkeygldesdlssg 39
                                      Fse+ L++y +d++ l++g
  gi|518651382|ref|YP_008140902.1| 43 FSEGNLEKYEIDNDRLCTG 61
                                      ****************998 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
                           NOD2_WH  11 fegLekgklvFseedLkeygld..es 34 
                                       ++g+++ +++  +  L+eyg++  +s
  gi|518651382|ref|YP_008140902.1| 308 ANGILEETYIIFKNYLMEYGIEklKS 333
                                       6899*****************95555 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 ?   -0.3   0.3      0.66   9.1e+02       7      14 ..     140     147 ..     138     153 .. 0.84
   2 ?   11.4   0.2   0.00015       0.2       2      14 ..     196     208 ..     195     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.66
                        Zn_Tnp_IS1   7 hCPrCsst 14 
                                        CP C+ t
  gi|518651382|ref|YP_008140902.1| 140 KCPVCQNT 147
                                       6****976 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00015
                        Zn_Tnp_IS1   2 AsVsihCPrCsst 14 
                                       As+ i CP C+s+
  gi|518651382|ref|YP_008140902.1| 196 ASIAIRCPECQSE 208
                                       9**********95 PP

>> Zn-C2H2_12  Autophagy receptor zinc finger-C2H2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.5   0.00043       0.6       1      14 [.     139     152 ..     139     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00043
                        Zn-C2H2_12   1 KeCPlCseqFpknv 14 
                                       K+CP+C +++ + v
  gi|518651382|ref|YP_008140902.1| 139 KKCPVCQNTYTSSV 152
                                       9*********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 ?    3.3   0.4      0.06        82      18      40 ..     138     158 ..     133     161 .. 0.64
   2 ?    7.1   0.1    0.0038       5.2      15      40 ..     188     221 ..     186     223 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.06
                     Zn_Tnp_IS1595  18 gfvCPhCgsrkayriktrglfqC 40 
                                          CP C+++  y+ + r+l  C
  gi|518651382|ref|YP_008140902.1| 138 SKKCPVCQNT--YTSSVRFLMAC 158
                                       467*****65..44444445555 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0038
                     Zn_Tnp_IS1595  15 Wpng........fvCPhCgsr.kayriktrglfqC 40 
                                       W++g         +CP C+s+ +   + +  +f C
  gi|518651382|ref|YP_008140902.1| 188 WKAGgvslasiaIRCPECQSEvTMNDVYN-TRFDC 221
                                       77777777777678******998888887.88888 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4    0.0061       8.4      35      47 ..     136     148 ..     111     149 .. 0.63
   2 ?    3.8   0.1     0.036        50      15      46 ..     178     208 ..     173     209 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0061
                         zf-RING_4  35 eeegrCPaCreeY 47 
                                       +++++CP C+++Y
  gi|518651382|ref|YP_008140902.1| 136 KNSKKCPVCQNTY 148
                                       4599*******99 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.036
                         zf-RING_4  15 lkpCeCgyqiClfCyhrileeeegrCPaCree 46 
                                       +k C+ +y ++      +  + + rCP+C++e
  gi|518651382|ref|YP_008140902.1| 178 IKECNPDYYVWKAGGVSLA-SIAIRCPECQSE 208
                                       5566666666666655444.4578*****985 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.6      0.14   1.9e+02       1       6 [.     140     145 ..     140     147 .. 0.84
   2 ?    6.9   0.0    0.0047       6.4       1      10 [.     201     210 ..     201     218 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.14
                    DNA_ligase_ZBD   1 hCPvCG 6  
                                       +CPvC 
  gi|518651382|ref|YP_008140902.1| 140 KCPVCQ 145
                                       6****6 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0047
                    DNA_ligase_ZBD   1 hCPvCGsavv 10 
                                       +CP+C s+v 
  gi|518651382|ref|YP_008140902.1| 201 RCPECQSEVT 210
                                       5*******95 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.4      0.73     1e+03       4      10 ..     140     146 ..     138     158 .. 0.80
   2 ?    9.5   0.2    0.0007      0.97       4      14 ..     201     211 ..     197     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.73
                    PhnA_Zn_Ribbon   4 kCplCaS 10 
                                       kCp C+ 
  gi|518651382|ref|YP_008140902.1| 140 KCPVCQN 146
                                       8999985 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0007
                    PhnA_Zn_Ribbon   4 kCplCaSeytY 14 
                                        Cp+C+Se+t 
  gi|518651382|ref|YP_008140902.1| 201 RCPECQSEVTM 211
                                       5*******985 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.3      0.14   1.9e+02      14      21 ..     139     146 ..     137     162 .. 0.79
   2 ?    7.1   0.3    0.0035       4.8      15      37 ..     201     225 ..     199     230 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.14
                             PADR1  14 ekCpeCke 21 
                                       +kCp C++
  gi|518651382|ref|YP_008140902.1| 139 KKCPVCQN 146
                                       79****96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0035
                             PADR1  15 kCpeCkegqlvfdss...gYkCtGnm 37 
                                       +CpeC+ +++ ++     ++ CtG++
  gi|518651382|ref|YP_008140902.1| 201 RCPECQ-SEVTMNDVyntRFDCTGKY 225
                                       7*****.88887776778******87 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.4       0.1   1.4e+02       1       7 [.     139     145 ..     137     148 .. 0.75
   2 ?    6.9   0.4    0.0048       6.7       2      10 ..     201     209 ..     201     212 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.1
                           UPF0547   1 KvCPeCe 7  
                                       K+CP C+
  gi|518651382|ref|YP_008140902.1| 139 KKCPVCQ 145
                                       7788776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0048
                           UPF0547   2 vCPeCeakv 10 
                                       +CPeC+++v
  gi|518651382|ref|YP_008140902.1| 201 RCPECQSEV 209
                                       6******99 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   2.7    0.0016       2.1      11      42 ..     137     213 ..     116     222 .. 0.80
   2 ?   -3.5   0.1       8.4   1.2e+04      30      34 ..     598     602 ..     589     603 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0016
                               DZR  11 darfCseCgtklkavaa.............................................edrCpsCgekvdpea 42 
                                       +++ C+ C+++  +  +                                             ++rCp+C+++v++++
  gi|518651382|ref|YP_008140902.1| 137 NSKKCPVCQNTYTSSVRflmacrrghldnvkwkwivhknssikecnpdyyvwkaggvslasiAIRCPECQSEVTMND 213
                                       566666666665544445666666666667789999999999999999999999******************99886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8.4
                               DZR  30 rCpsC 34 
                                       +C sC
  gi|518651382|ref|YP_008140902.1| 598 ACYSC 602
                                       44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (625 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.70u 0.30s 00:00:01.00 Elapsed: 00:00:00.52
# Mc/sec: 3612.72
//
Query:       gi|518651383|ref|YP_008140903.1|  [L=1254]
Description: hypothetical protein FACI_IFERC00001G0022 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-07   31.0   0.0    7.8e-07   29.4   0.0    1.9  1  Helicase_C      Helicase conserved C-terminal domain
  ------ inclusion threshold ------
        0.6   10.2   3.4         18    5.5   0.1    2.5  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   8.7e-11   7.8e-07      58     110 ..    1019    1071 ..     984    1072 .. 0.90

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.7e-11
                                        HHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C   58 ileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRa 110 
                                         +e+  +++ d + +t++ ++G+di  ++l+i  + p+++++yiq+ GRtgR 
  gi|518651383|ref|YP_008140903.1| 1019 GIEKSPEDNPDAIFTTSMFGTGVDISHLSLMIVNGQPKTTSQYIQATGRTGRS 1071
                                        556666777789****************************************5 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 ?    4.8   0.6    0.0031        28       1       9 [.     558     566 ..     558     570 .. 0.86
   2 ?    5.5   0.1     0.002        18      17      25 ..     691     699 ..     674     700 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0031
                    DNA_ligase_ZBD   1 hCPvCGsav 9  
                                       +CP+CGs +
  gi|518651383|ref|YP_008140903.1| 558 RCPACGSWL 566
                                       5*****965 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.002
                    DNA_ligase_ZBD  17 iyRCtnlsC 25 
                                        ++Ctn+sC
  gi|518651383|ref|YP_008140903.1| 691 EIYCTNPSC 699
                                       58******* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.92u 0.33s 00:00:01.25 Elapsed: 00:00:00.53
# Mc/sec: 7075.41
//
Query:       gi|518651384|ref|YP_008140904.1|  [L=223]
Description: T/G-specific DNA glycosylase [Ferroplasma acidarmanus fer1]
Scores for complete 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   41.0   0.0    2.9e-10   40.6   0.0    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
    1.2e-05   24.9   0.0    2.1e-05   24.2   0.0    1.4  1  HHH       Helix-hairpin-helix motif
     0.0052   17.1   0.0      0.012   15.9   0.0    1.6  1  HHH_8     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   4.9e-14   2.9e-10       1     101 [.      44     171 ..      44     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.9e-14
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       +++i+  +t+ e +nri+ ++  +   p+  ++ da +  L++ +++lG++ ++   +  lA +++           
  gi|518651384|ref|YP_008140904.1|  44 IAEIMLHRTRAEQVNRIYDSFIMK--YPDIYAIVDAGPHALKNDLKSLGLS-YRGDMLYRLAAQIIekydgnipdni 117
                                       689*********************..59***********************.************************* PP

                                       ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekk 101
                                                           +++ +++  D+++ ri++r+++ik++ + +   k+
  gi|518651384|ref|YP_008140904.1| 118 ndlaslpgigdyaasavmcsAYKSPAPFLDTNTVRIISRVYGIKPT-DSSRRSKE 171
                                       ********************9989*********************8.44444444 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   3.4e-09   2.1e-05       2      29 ..     109     136 ..     108     137 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.4e-09
                                       HHHHHTSSHHHHHTSTT-SHHHHHHHHH CS
                               HHH   2 leglipasreeLlalPGVGpktAeaIls 29 
                                       ++g ip+++ +L++lPG+G + A a+++
  gi|518651384|ref|YP_008140904.1| 109 YDGNIPDNINDLASLPGIGDYAASAVMC 136
                                       8999**********************98 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06     0.012      28      61 ..      99     132 ..      97     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                                       HHHHHCCCCC-SS-HHHH.TTHCTTSTT--HHHHH CS
                             HHH_8  28 YrrAaraiealpeeitsl.eeeltklpgiGkkiaa 61 
                                       Yr Aa+ ie+++  i +    +l +lpgiG+  a 
  gi|518651384|ref|YP_008140904.1|  99 YRLAAQIIEKYDGNIPDNiN-DLASLPGIGDYAAS 132
                                       ****************9744.6********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1374.09
//
Query:       gi|518651385|ref|YP_008140905.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G0024 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-51  175.3   2.1    2.4e-51  175.1   2.1    1.2  1  DNA_methylase  C-5 cytosine-specific DNA methylase


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 !  175.1   2.1   1.3e-55   2.4e-51      56     335 .]      63     381 ..      15     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: 175.1 bits;  conditional E-value: 1.3e-55
                                       -..........GS--...-SEEEE---GGGTECTSE.......E--TTSGGGHHHHHHHHHHHHH--SEEEEEEEGG CS
                     DNA_methylase  56 k..........klpe..diDlLvgGfPCqpfSvaGk.......qkgfedtrgtLffeiiriikekkPkvfllENVkg 113
                                       +          kl++  ++D+++gG+PCq +Sv +        ++  +d+r+ Lf  ++ ++++ +P++f++ENV+g
  gi|518651385|ref|YP_008140905.1|  63 EiiadeitdkmKLKGihKVDVMIGGPPCQTYSVIRRfdskmqgRNWKDDPRNYLFKRYVYFLQKFSPDIFVFENVPG 139
                                       233333334455554425****************9999999889999****************************** PP

                                       GGGGCCSHHHHHHHHHHHHHTEEEEEEEEEGGGTT-SB--EEEEEEEEEGGG---.-------SS---GGG...... CS
                     DNA_methylase 114 LlkhdkgktlkvilekleelGYevsykllnasdyGvpQnReRvfivgirkdleln.vlvkvkefrfpkkkd...... 183
                                       +++ + g+ l +++ + +++GY+++ k+lna+d+ v Q+R+R +i+g +k+++l+ +     ef++ + ++      
  gi|518651385|ref|YP_008140905.1| 140 IKSANGGEFLHNFVTMVNKAGYNITEKILNAKDFMVLQQRKREIIIGWKKGYKLDyP-----EFETVEHNYnvgell 211
                                       ***************************************************987652.....333333332122334 PP

                                       ............TSGGGTTS-EEBTTTB--GGGSSSTT-EE--.......S---H...HHTS--B--TTS...-B-- CS
                     DNA_methylase 184 .......leasktlrdlleekseldeektalsdklvekeekikkttkaseegypk...elsrnridkveelkglsat 250
                                                + + l+++++ +s++ e+    +++ +  + k + ++++++ +y++   e + n ++ +++++ + ++
  gi|518651385|ref|YP_008140905.1| 212 ndlpglePGQGDYLQEYKSGASDYLEKTGIRKHNDILIQHKARYHNERDRRIYRYvinEWNTN-HRHIKYGELPAEL 287
                                       455333345555555555555554444444444444444444446777777777654322222.6666666666666 PP

                                       --S-STT-..........-B-TTS---EEEETTEEE--T.......TTGGG--B-BHHHHHHHHT--TT-----SBH CS
                     DNA_methylase 251 rrksgrge..........klekelaeagklqknkerfkp......viekkriRrLtprEaarlqGfPddfefgskks 311
                                       r   + g+           l+ + + +  l        +        + +++R +t+rEaarlq+fPd+f+f++  s
  gi|518651385|ref|YP_008140905.1| 288 RPYENTGTfsdkfkvvasDLNYSQTITAHLS-------RdghyyiHPDIEQARSITVREAARLQSFPDNFKFEGPVS 357
                                       6666655577766655432222222222222.......1333433567799************************** PP

                                       HHHHHHHTS--HHHHHHHHHHHHH CS
                     DNA_methylase 312 aaykqiGnsVpvpvieaiakeikk 335
                                       a+y+qiGn+Vp+ ++++ia +ikk
  gi|518651385|ref|YP_008140905.1| 358 AQYRQIGNAVPPIMAKSIALKIKK 381
                                       *******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.53
# Mc/sec: 2185.34
//
Query:       gi|518651386|ref|YP_008140906.1|  [L=878]
Description: hypothetical protein FACI_IFERC00001G0025 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (878 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 5607.17
//
Query:       gi|518651387|ref|YP_008140907.1|  [L=193]
Description: hypothetical protein FACI_IFERC00001G0026 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-12   48.5   0.0    1.7e-12   48.1   0.0    1.2  1  NYN       NYN domain


Domain annotation for each model (and alignments):
>> NYN  NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   9.3e-17   1.7e-12       2     132 ..      17     166 ..      16     175 .. 0.72

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 9.3e-17
                               NYN   2 vavfiDgenlpvpak.......gke...vdyrklleeirs...kgelvraraygn..........wedeeqnkfqda 55 
                                       + ++ D++ l+ + k       ++      + k +    +     +   a  y +          ++++e n ++  
  gi|518651387|ref|YP_008140907.1|  17 TVILADISCLFNAVKksynshaNRStinRYIVKYMT---KlkhEHPADKAIGYDSkfpesfknrrKSNNETNILHGE 90 
                                       567777777777777544333211111122333333...25436668888888888888876664444445666688 PP

                               NYN  56 lsstgikvkhkplkkrg.gsgkkavDvelavdalelaydnkydtivLvsgDgDFaplveklrergkrVevllaeeas 131
                                       l+++g++ +  pl  r+ g  +k+vDv+la da+el++   + ++++vsgDgDF p++e + +++ + ++++  +++
  gi|518651387|ref|YP_008140907.1|  91 LKNIGFETVSSPLMYRKqGIFEKGVDVKLAMDATELIHSGIFHRLIIVSGDGDFYPVAELAVRNHLEFIIIF--PGK 165
                                       8*****888999988889999*****************9977*******************99999888777..344 PP

                               NYN 132 t 132
                                       +
  gi|518651387|ref|YP_008140907.1| 166 I 166
                                       4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1322.26
//
Query:       gi|518651388|ref|YP_008140908.1|  [L=283]
Description: hypothetical protein FACI_IFERC00001G0027 [Ferroplasma acidarmanus fer1]
Scores for 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   64.3   0.1    1.6e-17   63.5   0.1    1.4  1  UDPG_MGDP_dh    UDP-glucose/GDP-mannose dehydrogenase family,
    1.4e-15   57.4   0.3    3.6e-14   52.8   0.0    2.7  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
  ------ inclusion threshold ------
      0.029   13.7   0.1      0.099   12.0   0.0    1.8  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.035   14.7   0.4       0.88   10.2   0.1    2.9  4  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.083   13.1   0.3       0.69   10.1   0.0    2.4  3  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy


Domain annotation for each model (and alignments):
>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.1   4.5e-21   1.6e-17       1      79 [.     167     247 ..     167     264 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 4.5e-21
                      UDPG_MGDP_dh   1 etAEliKlaaNaflatkIsfiNelanlcealgidveeVieavgldprigpkf.lkpglG.vGGsclpkDvkaLvala 75 
                                       ++AE+ Kla+Naf atk+sf N ++n++ +   ++++++++v +d+r+ ++  l+p lG +GG+c+pkD+  L+++ 
  gi|518651388|ref|YP_008140908.1| 167 RSAEIGKLAHNAFIATKVSFTNTMENIAARGRGNIDDIMKIVYTDRRVRNMAhLTPHLGaFGGKCVPKDTMELMNAF 243
                                       69*********************************************98866699998769*************998 PP

                      UDPG_MGDP_dh  76 eelg 79 
                                       ++++
  gi|518651388|ref|YP_008140908.1| 244 SSES 247
                                       7765 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.3      0.07   2.5e+02       2      21 ..      14      33 ..      13      45 .. 0.78
   2 !   52.8   0.0   9.9e-18   3.6e-14      73     183 ..      50     149 ..      36     153 .. 0.85
   3 ?   -0.9   0.0      0.28     1e+03      22      57 ..     157     192 ..     149     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.07
                                      EEEEE--STTHHHHHHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlae 21
                                      k+ +iGlG vG      l++
  gi|518651388|ref|YP_008140908.1| 14 KVGIIGLGSVGSALFKHLSN 33
                                      799********987766665 PP

  == domain 2  score: 52.8 bits;  conditional E-value: 9.9e-18
                                       HHHC-SEEEE-----B-TTTTCB-THHHHHHHHHHHHHHHCEEEEEE-S---TTHHHHCHHHHHHHHCSS-TTCEEE CS
                    UDPG_MGDP_dh_N  73 aveeadvifiaVgTPskkkgkaaDlkyvesaarsiaealkkgkvvvvkSTvpvgtaeelvkkileeaskkkgvdfdv 149
                                        + ++ v fi+V TP +++g+  D ++ve++++++a+  +   v+++kST  vg +e++      + +     ++++
  gi|518651388|ref|YP_008140908.1|  50 DILKCPVSFICVQTPGDRNGRL-DCNHVEDTLQKLASS-NYSGVIIIKSTLGVGFMENVT----SKFP-----ELRI 115
                                       57899*************6666.************986.55679999*********9555....4344.....489* PP

                                       EE------TTSHHHHHHS-S-EEEEESSCHHHHH CS
                    UDPG_MGDP_dh_N 150 vsnPEflregsavkdllnpdrvviGveekkaeaa 183
                                       v++PEflre sa++ ++npdr v  ++e++ ++a
  gi|518651388|ref|YP_008140908.1| 116 VYSPEFLREKSALEWTANPDRLVFSGKEDDVREA 149
                                       **********************998877776655 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.28
                                       CTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHH CS
                    UDPG_MGDP_dh_N  22 ighevigvDideekvdklnsgkipiyepgLeelvkk 57 
                                        g+++i+ D  ++ + kl ++ +  +     + +++
  gi|518651388|ref|YP_008140908.1| 157 TGVDIIITDYRSAEIGKLAHNAFIATKVSFTNTMEN 192
                                       689999999999999999988776666666655555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.8e-05     0.099      38      67 ..      14      42 ..       4      51 .. 0.84
   2 ?   -2.5   0.0      0.78   2.8e+03      81      98 ..     241     258 ..     232     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.8e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydr 67
                                      +vGiiGlG++G+a+ k l+ f  +v +yd 
  gi|518651388|ref|YP_008140908.1| 14 KVGIIGLGSVGSALFKHLSNF-YNVSGYDI 42
                                      79****************999.57777775 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.78
                                       EECSHHHHHHH-SEEEE- CS
                      2-Hacid_dh_C  81 elvsleellaesDivslh 98 
                                       +  s e ll ++D+v++ 
  gi|518651388|ref|YP_008140908.1| 241 NAFSSESLLFKADFVVNE 258
                                       456778899999999875 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00025      0.88       1      20 [.      14      33 ..      14      47 .. 0.86
   2 ?    0.8   0.0       0.2   7.3e+02      72      95 ..      74      97 ..      71      99 .. 0.87
   3 ?   -1.5   0.0       1.1   3.9e+03      40      71 ..     147     184 ..     130     201 .. 0.60
   4 ?   -2.5   0.0       2.2     8e+03      31      47 ..     209     225 ..     178     257 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00025
                                      EEEEETTSHHHHHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasglla 20
                                      k+giiG G++g+al + l++
  gi|518651388|ref|YP_008140908.1| 14 KVGIIGLGSVGSALFKHLSN 33
                                      79************999875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                                      HHHHHHHHHCGHHHHTTSEEEEES CS
                     F420_oxidored 72 edveevlselakdalkgklvisvl 95
                                      ++ve++l++la+++ +g ++i  +
  gi|518651388|ref|YP_008140908.1| 74 NHVEDTLQKLASSNYSGVIIIKST 97
                                      689****************99765 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.1
                                       HHHHHHHC......-EEECECHHHHHHH-SEEEE-S-H CS
                     F420_oxidored  40 eelaeelg......vkvtavdneeaaeeadvvvlavkp 71 
                                       +e+ + ++      + +t    +e  + a   ++a k 
  gi|518651388|ref|YP_008140908.1| 147 REALKIYSwatgvdIIITDYRSAEIGKLAHNAFIATKV 184
                                       44444444444433555555555556666666666655 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 2.2
                                       EEESSCCCHHHHHHHHC CS
                     F420_oxidored  31 ansrnpekaeelaeelg 47 
                                        ++r    +++l  +lg
  gi|518651388|ref|YP_008140908.1| 209 YTDRRVRNMAHLTPHLG 225
                                       33444444444444444 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00019      0.69       1      29 [.      14      41 ..      14      53 .. 0.86
   2 ?   -2.4   0.0       1.3   4.6e+03      67      89 ..      74      96 ..      72      98 .. 0.81
   3 ?   -0.2   0.0      0.28   9.9e+02      22      72 ..     158     217 ..     149     232 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE- CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavyn 29
                                      k+g+iGlG  Gs + ++l  + y+v++y+
  gi|518651388|ref|YP_008140908.1| 14 KVGIIGLGSVGSALFKHLS-NFYNVSGYD 41
                                      69***************85.568888887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                      HHHHHHHHSHCCC--TT-EEEE- CS
                     NAD_binding_2 67 kavdeviegllealkkgdilidg 89
                                      ++v++++++l+++  +g i+i +
  gi|518651388|ref|YP_008140908.1| 74 NHVEDTLQKLASSNYSGVIIIKS 96
                                      68999999999988889888876 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.28
                                       T-EEEEE-SSHHHHHHHHHTT.....EEE-SSHHHHHHHC....SEEEE-SSSHHHHHHH CS
                     NAD_binding_2  22 gykvavynrtkekveelvaeg.....akaaesieelvasl....dvvitmvkagkavdev 72 
                                       g ++++ + +++++ +l+++      ++ ++++e+++a+     d ++ +v  ++ v+++
  gi|518651388|ref|YP_008140908.1| 158 GVDIIITDYRSAEIGKLAHNAfiatkVSFTNTMENIAARGrgniDDIMKIVYTDRRVRNM 217
                                       666667776666666666665544446677777777666577778888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 1891.51
//
Query:       gi|518651389|ref|YP_008140909.1|  [L=961]
Description: hypothetical protein FACI_IFERC00001G0028 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-09   38.1   0.0    5.3e-09   36.1   0.0    2.1  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.046   13.6   0.0       0.46   10.3   0.0    2.6  4  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   5.9e-13   5.3e-09      41     131 ..      39     145 ..      27     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 5.9e-13
                                       CHHHHHGGGCH.........C-TTEEEEEESSS-HHHHHHHHHHHH--SS.......EEEEEESSEEE-TTHHHHHH CS
                   Glycos_transf_2  41 etveileelak.........edprvrvirreenvGkagalnaglraatgd.......yilflDaDdepdpdwleklv 101
                                        t  +++++ k         ++ +++ i + + + ++ga+n++l++           +i++lD+Dd+++p++l+  +
  gi|518651389|ref|YP_008140909.1|  39 ATYLVADSWEKldtinipeiNKLQIKKIVNRREKNLSGAINTALSEILNTgydpdntFIAVLDDDDWWEPGYLKNSL 115
                                       4444555555555555566678899999999999************8877789************************ PP

                                       HHHHH.TTCEEEEEEEEEECCCCCCCHC-S CS
                   Glycos_transf_2 102 ealekdgadvvlgqrprifgetdeiernkr 131
                                       +++ +++ad v+ ++ r++ et+e  + + 
  gi|518651389|ref|YP_008140909.1| 116 DKAIEENADWVISGIIRHETETGEGIKLSI 145
                                       ********************9998877654 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 ?   10.3   0.0   5.2e-05      0.46       6     110 ..      11     116 ..       8     133 .. 0.65
   2 ?   -2.6   0.0      0.46   4.1e+03     160     196 ..     161     197 ..     156     207 .. 0.87
   3 ?   -2.8   0.0      0.52   4.7e+03      88     101 ..     400     413 ..     381     480 .. 0.68
   4 ?   -1.9   0.0      0.27   2.4e+03     158     181 ..     569     593 ..     562     597 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 5.2e-05
                   Glyco_tranf_2_3   6 vlVptfneedvlge.vlesllaqeyprvevvvvvde.sdaetlevaeelaaalpdvrvrvvvnarnlgs.tgksral 79 
                                       + +++  ++ ++    l s+++qe  ++ +++v+d  ++ +t++ + e   +  + +++ +vn r+    ++  +al
  gi|518651389|ref|YP_008140909.1|  11 ITITAVTRPGDVSTiSLPSIINQELTPDATYLVADSwEKLDTIN-IPE---IN-KLQIKKIVNRREKNLsGAINTAL 82 
                                       56778888776666589999999987777777775536666665.333...23.33666666755443203444455 PP

                   Glyco_tranf_2_3  80 nealra.vk..sdlvllvDdDtvvePdtlkrllq 110
                                       +e l++ ++   ++++++DdD+ +eP++lk +l 
  gi|518651389|ref|YP_008140909.1|  83 SEILNTgYDpdNTFIAVLDDDDWWEPGYLKNSLD 116
                                       5555553334455****************98776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.46
                   Glyco_tranf_2_3 160 lnGsgslirrevlkelegldplflltdDyelglrlrr 196
                                       + Gs ++ir ++l   +g d++   t D +l+ rl +
  gi|518651389|ref|YP_008140909.1| 161 IQGSNLFIRLSYLLMAGGYDENLPSTTDRDLCIRLLA 197
                                       6799*****************8888899999999876 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.52
                   Glyco_tranf_2_3  88 sdlvllvDdDtvve 101
                                         +++++DdD  ++
  gi|518651389|ref|YP_008140909.1| 400 NPVIWIIDDDIDIS 413
                                       56899999997665 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.27
                   Glyco_tranf_2_3 158 ltlnGsgslirrevlkelegldp.l 181
                                       +t +G+    +revlke+ ++ p +
  gi|518651389|ref|YP_008140909.1| 569 PTRGGNVIILDREVLKEFTDSAPvN 593
                                       455679999*********9888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (961 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 6018.52
//
Query:       gi|518651390|ref|YP_008140910.1|  [L=757]
Description: hypothetical protein FACI_IFERC00001G0029 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-14   53.8   0.2    8.4e-11   42.0   0.1    3.2  3  Glycos_transf_2  Glycosyl transferase family 2
    3.4e-10   40.0   0.0    1.2e-09   38.2   0.0    1.9  2  Methyltransf_23  Methyltransferase domain
    5.2e-07   29.8   0.0    1.1e-05   25.5   0.0    2.3  2  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.3e-05   24.6   0.0    2.5e-05   23.7   0.0    1.4  1  Methyltransf_2   O-methyltransferase domain
    1.9e-05   25.3   0.0      9e-05   23.1   0.0    2.3  1  Methyltransf_25  Methyltransferase domain
    0.00016   22.2   0.0    0.00041   20.9   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
    0.00027   21.6   0.2     0.0049   17.6   0.1    3.1  2  Methyltransf_12  Methyltransferase domain
    0.00062   19.6   1.5      0.024   14.4   1.5    2.8  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.016   14.5   0.0      0.034   13.5   0.0    1.5  1  CMAS             Mycolic acid cyclopropane synthetase
      0.033   13.8   0.0      0.073   12.6   0.0    1.5  1  MTS              Methyltransferase small domain
       0.14   11.8   0.0       0.28   10.8   0.0    1.4  1  MetW             Methionine biosynthesis protein MetW
       0.17   11.7   0.1        1.9    8.4   0.0    2.8  4  CutA1            CutA1 divalent ion tolerance protein


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 ?   -0.9   0.0      0.81   1.2e+03       9      41 ..     249     283 ..     246     291 .. 0.85
   2 !    7.6   0.0     0.002         3      73     142 ..     350     423 ..     300     446 .. 0.70
   3 !   42.0   0.1   5.6e-14   8.4e-11       9     123 ..     535     654 ..     526     688 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.81
                                       -TTTHHHHHHHHHHH..GGCCEEEEEEEEES-SSC CS
                   Glycos_transf_2   9 eektlletlesllaq..dpypdfeiivvDDgStDe 41 
                                       e+ t+   ++ +++q   p + fe ivv D  t +
  gi|518651390|ref|YP_008140910.1| 249 EWRTIDTRIRHIVNQleGPEKFFEKIVVTDKNTSG 283
                                       889999999*******999999**99999987654 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.002
                                       HHHHH--SSEEEEEESSEEE....-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCC CS
                   Glycos_transf_2  73 aglraatgdyilflDaDdep....dpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfke 142
                                        g+++ +++yil lD+D+++     p +l+ l + le++++++ +g + +++   d+   n  +++++ ++f  
  gi|518651390|ref|YP_008140910.1| 350 YGFEQLKTKYILQLDSDCIIgrtpGPSYLKVLKNVLENNDDALTVGFPIYSKTRADFTIGNNYNKWRTEVRFSL 423
                                       499***************86331146666666666666555555554444444444444443335555555544 PP

  == domain 3  score: 42.0 bits;  conditional E-value: 5.6e-14
                                       -.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH..C-TTEEEEEESSS-HHHHHHHHHHHH.--SS CS
                   Glycos_transf_2   9 e.ektlletlesllaqdpypdfeiivvDDgStDetveileelak..edprvrvirreenvGkagalnaglra.atgd 81 
                                          + l+++++sl +q +y++f ii +D +S  + ve l e+a    ++r++ +++ e +  + ++  ++++ ++  
  gi|518651390|ref|YP_008140910.1| 535 VsFQKLRRCIKSLSRQ-DYQNFGIIAIDAASVNGMVEYLYEIAGrlFRDRITTFKNVEPRSSIENIYIAIERiCKNP 610
                                       36789***********.*****************************************************9945555 PP

                                       ..EEEEEESSEEE-TT.HHHHHHHHHHH.TTCEEEEEEEEEECCC CS
                   Glycos_transf_2  82 ..yilflDaDdepdpd.wleklvealekdgadvvlgqrprifget 123
                                         +i+ lDaDd+   d  l+k++e +++ gad+ +g+  r ++e 
  gi|518651390|ref|YP_008140910.1| 611 esIIVMLDADDALIADnALSKIMELYHN-GADLTVGSMLRADKEA 654
                                       ***********999888***********.********99887765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   8.1e-13   1.2e-09      12     122 ..      33     145 ..      24     176 .. 0.79
   2 ?   -2.6   0.0       2.9   4.3e+03      36      69 ..     697     730 ..     694     745 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.1e-13
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiaekakkaqkdqfdeq..........eaae 78 
                                       k+e++l ++  + +vLd+GcGtG  ++ l+++ ++v ++D++  +++      ++++++++ q          ++++
  gi|518651390|ref|YP_008140910.1|  33 KIEEIL-NKIHPDNVLDYGCGTGAIADALSKK-YNVSVFDID--MSG------FYKHHPAPGQpaalkaldmdFIDK 99 
                                       677777.478899****************777.666667765..333......444444444444555555557888 PP

                   Methyltransf_23  79 pqgkfdlIvlrevlehvpd..ppellrqiatllkpgGylllsepla 122
                                       +++ + ++ l++vl++v d  ++  l +i+  + ++G+l++s  + 
  gi|518651390|ref|YP_008140910.1| 100 KKELYHTVLLSQVLCSVNDeeVTDILGKIKGVIHENGNLVVSICNP 145
                                       999***************98899******************98765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.9
                   Methyltransf_23  36 llevlrengfsvtgvDlspeaveiaekakkaqkd 69 
                                       + +v++++ f + +v+ls + v+ia k++ + ++
  gi|518651390|ref|YP_008140910.1| 697 WISVAEDWAFMLRLVELSKNPVNIADKIYYYDPS 730
                                       6677778888888999999999998766655554 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 ?    1.6   0.0      0.14   2.1e+02      82     127 ..     351     401 ..     338     431 .. 0.73
   2 !   25.5   0.0   7.3e-09   1.1e-05      16     117 ..     539     640 ..     526     678 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.14
                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvv....ePdtlkrllqff.ltpkvgavgtpvfll 127
                                       ++++ k++++l +D+D+++    +P +lk+l +++ + +++  vg p +++
  gi|518651390|ref|YP_008140910.1| 351 GFEQLKTKYILQLDSDCIIgrtpGPSYLKVLKNVLeNNDDALTVGFPIYSK 401
                                       78999*************833334666777666666555666666666555 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 7.3e-09
                   Glyco_tranf_2_3  16 vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravk...sd 89 
                                       +l++++ sl++q+y ++ ++ ++  s  + +e + e+a +l + r+++    +n ++++ +++++ a++++      
  gi|518651390|ref|YP_008140910.1| 539 KLRRCIKSLSRQDYQNFGIIAIDAASVNGMVEYLYEIAGRLFRDRITTF---KNVEPRSSIENIYIAIERICknpES 612
                                       799*************************************998799986...77889************85547666 PP

                   Glyco_tranf_2_3  90 lvllvDdDtvv.ePdtlkrllqffltpkv 117
                                       +++++D+D+ +  +++l ++  ++ + ++
  gi|518651390|ref|YP_008140910.1| 613 IIVMLDADDALiADNALSKIMELY-HNGA 640
                                       *******99988*****9999988.4444 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.7e-08   2.5e-05      65     197 ..      45     168 ..       9     179 .. 0.76

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.7e-08
                                       EEEEET-TTSHHHHHHHHH-TT-EEEEEE-..HHHHHHHHHHS-----TTEEEEES-TTTS-----SEEEEESSGGG CS
                    Methyltransf_2  65 slvDvGGGtGalakaivsayPtikvivfDl..peVveaAkehlsageeervefvgGdffkdslPeaDaillkrvlhD 139
                                       +++D G GtGa+a+a +++y   +v+vfD+  +   ++   h  +g+   ++  + df +++      +ll++vl  
  gi|518651390|ref|YP_008140910.1|  45 NVLDYGCGTGAIADALSKKY---NVSVFDIdmSGFYKH---HPAPGQPAALKALDMDFIDKKKELYHTVLLSQVLCS 115
                                       689*****************...455666500444444...445699999*********99999999********** PP

                                       S-HHHHHHHHHHHHHH--TT-EEEEEE----TTS---HHHHHHHHHHHHCSS-----H CS
                    Methyltransf_2 140 wsdekcvklLkrvkkalpagGkvivveavlgadpsgeletelvdlimlvqteGkeRte 197
                                        +de+++ +L ++k  ++++G+++v  +   + +++e++t++      +q++G   ++
  gi|518651390|ref|YP_008140910.1| 116 VNDEEVTDILGKIKGVIHENGNLVVSICNPYNLNNNETQTHI-----KIQPTGDYNSN 168
                                       **********************98866654444444444333.....44555555555 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     6e-08     9e-05       1      97 []      46     136 ..      46     136 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 6e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       vLd GcGtG ++ al+k++   +v  +Di+ +     ++ + + g  + +   d++ ++ +++ ++ v++s++l+ +
  gi|518651390|ref|YP_008140910.1|  46 VLDYGCGTGAIADALSKKY---NVSVFDIDMSG--FYKH-HPAPGQPAALKALDMDFIDKKKELYHTVLLSQVLCSV 116
                                       9***************996...55555554332..3333.33456689999999999999999*******988999* PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +de++ ++l +i+ v+ ++G
  gi|518651390|ref|YP_008140910.1| 117 NDEEVTDILGKIKGVIHENG 136
                                       ************99998887 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.7e-07   0.00041       1      96 []      47     140 ..      47     140 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.7e-07
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-.. CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhv.. 74 
                                       Ld GcGtG++a al k++  +v+ +D+s       ++ a++++    +   d+  +  +++ +  v++s+vl+ v  
  gi|518651390|ref|YP_008140910.1|  47 LDYGCGTGAIADALSKKYnVSVFDIDMSGFYK---HHPAPGQPAA--LKALDMDFIDKKKELYHTVLLSQVLCSVnd 118
                                       89*************99967777777665554...4555555533..3444444445778899************99 PP

                                       CCHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  75 edpekalkeiaRvLkpgGllvi 96 
                                       e++ ++l +i+ v   +G lv+
  gi|518651390|ref|YP_008140910.1| 119 EEVTDILGKIKGVIHENGNLVV 140
                                       9*****************9986 PP

>> Methyltransf_12  Methyltransferase 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    0.0049       1      99 []      47     138 ..      47     138 .. 0.84
   2 ?   -0.1   0.0       1.1   1.6e+03      21      46 ..     722     747 ..     707     753 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.3e-06
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+ GcGtG++++al +k    ++ + Di+ s +       ++  + + + ++  + d +d++++  + +v++s+vl+
  gi|518651390|ref|YP_008140910.1|  47 LDYGCGTGAIADALSKK---YNVSVFDIDMSGF-----YKHHPAPGQPAALKALDMDFIDKKKE-LYHTVLLSQVLC 114
                                       899***********999...99999****9999.....33333334556777777777766655.9*********** PP

                   Methyltransf_12  78 hl..kdirevldnirklLkpgGrl 99 
                                        +  +++ ++l +i+ ++  +G l
  gi|518651390|ref|YP_008140910.1| 115 SVndEEVTDILGKIKGVIHENGNL 138
                                       **9999***************976 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.1
                   Methyltransf_12  21 ieytgvDispsaiedakeklakrenn 46 
                                        +++++D+s++   + +e+l +++++
  gi|518651390|ref|YP_008140910.1| 722 DKIYYYDPSEDKYRRSREELDEIIAR 747
                                       5799*********9999999988765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   1.5   1.6e-05     0.024       6     127 ..      45     153 ..      42     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.6e-05
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       +vlD+GCGtG+++ +l ++   +  v+ iD+s +     + + +  +   ++    d+ +++k    e +  +l  +
  gi|518651390|ref|YP_008140910.1|  45 NVLDYGCGTGAIADALSKKY--NVSVFDIDMSGFY----KHHPAPGQPAALKALDMDFIDKKK----ELYHTVLLSQ 111
                                       8****************653..5789999998764....666666667777777788888554....3466888889 PP

                   Methyltransf_31  83 vlnaladpd..kileeiervlkpggilliedprllaelpakveeesk 127
                                       vl+ ++d +  +il++i+ v++++g l+++ ++     p+++ ++++
  gi|518651390|ref|YP_008140910.1| 112 VLCSVNDEEvtDILGKIKGVIHENGNLVVSICN-----PYNLNNNET 153
                                       997777754338899999999999999999888.....554444444 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.034      50      94 ..      33      74 ..      22     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                      HHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES- CS
                              CMAS 50 KldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlS 94
                                      K++ il+k++    +++Ld GcG G+++    ++y+v+v+ + +S
  gi|518651390|ref|YP_008140910.1| 33 KIEEILNKIH---PDNVLDYGCGTGAIADALSKKYNVSVFDIDMS 74
                                      6666666654...478************************99998 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.9e-05     0.073      26      64 ..      37      72 ..      30      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.9e-05
                                      HCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESB CS
                               MTS 26 tlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvd 64
                                       l+k + ++vlD GcG+G+++ al k+++   v ++d+d
  gi|518651390|ref|YP_008140910.1| 37 ILNKIHPDNVLDYGCGTGAIADALSKKYN---VSVFDID 72
                                      466668889************99998664...4555555 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.28       5      90 ..      35     118 ..      32     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                              MetW   5 eliaelikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvl 81 
                                       e+i++ i+p  +vld GcG G + + l ++ +v+   ++++    ++  a G     + ld d+   + + +  v+l
  gi|518651390|ref|YP_008140910.1|  35 EEILNKIHPD-NVLDYGCGTGAIADALSKKYNVSVFDIDMSGF-YKHHPAPGQPAALKALDMDFIDKKKELYHTVLL 109
                                       6778888875.7***************9998988877766543.344567888888888999988888889999999 PP

                              MetW  82 sqtlqatrn 90 
                                       sq l ++++
  gi|518651390|ref|YP_008140910.1| 110 SQVLCSVND 118
                                       998887754 PP

>> CutA1  CutA1 divalent ion tolerance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2   3.2e+03      53      77 ..      21      46 ..      20      49 .. 0.78
   2 ?   -3.3   0.0       5.8   8.7e+03      51      72 ..     239     260 ..     237     262 .. 0.86
   3 ?    8.4   0.0    0.0013       1.9      46      87 ..     521     564 ..     520     576 .. 0.79
   4 ?   -2.3   0.0       2.7     4e+03      16      55 ..     575     616 ..     567     623 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                      EEEEEEGG.GHHHHHHHHHHHSSSSS CS
                             CutA1 53 lliktree.kveelekrvkelhpyev 77
                                      l ikt+ +  ++++e+ ++++hp +v
  gi|518651390|ref|YP_008140910.1| 21 LSIKTNYQmGITKIEEILNKIHPDNV 46
                                      5678876636899*********9876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.8
                                       EEEEEEEEGGGHHHHHHHHHHH CS
                             CutA1  51 vllliktreekveelekrvkel 72 
                                       v l+ik ++ ++  + +r++++
  gi|518651390|ref|YP_008140910.1| 239 VSLMIKASAMEWRTIDTRIRHI 260
                                       67999*9999999999999875 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0013
                                       EEEEEEEEEEEEEGGGHHHHHHHHHHHS..SSSS-EEEEEEESE CS
                             CutA1  46 eedkEvllliktreekveelekrvkelh..pyevpeiialpiea 87 
                                       e+++E+++++k r+  +++l +++k+l    y+   iia+++ +
  gi|518651390|ref|YP_008140910.1| 521 ERKEEMVIIVKGRNVSFQKLRRCIKSLSrqDYQNFGIIAIDAAS 564
                                       6789*********************9861156666777776654 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 2.7
                                       HHHHHHHTTS-SEEEEEEE..EEEEEEETTEEEEEEEEEEEE CS
                             CutA1  16 laralveeklaACvnilpk..ieSvYrWkgkieedkEvllli 55 
                                       +a +l ++++    n+ p+  ie +Y   ++i+++ E  +++
  gi|518651390|ref|YP_008140910.1| 575 IAGRLFRDRITTFKNVEPRssIENIYIAIERICKNPESIIVM 616
                                       556666666666666655433888999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (757 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 4833.60
//
Query:       gi|518651391|ref|YP_008140911.1|  [L=245]
Description: hypothetical protein FACI_IFERC00001G0030 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.044   13.5   0.0    1.7  1  CheR_N    CheR methyltransferase, all-alpha domain
      0.071   13.4   0.7       0.22   11.8   0.7    1.8  1  DUF1031   Protein of unknown function (DUF1031)


Domain annotation for each model (and alignments):
>> CheR_N  CheR methyltransferase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     5e-06     0.044      23      47 ..      13      37 ..      12      38 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-06
                                      HHHHHTHHHHHHHTTT-SSSHHHHH CS
                            CheR_N 23 rallkrRlsrRmralglksfeeYld 47
                                      + l+ rRl++    +g+++f+eY++
  gi|518651391|ref|YP_008140911.1| 13 KELVIRRLWNIYSFTGFNDFAEYVK 37
                                      579********************86 PP

>> DUF1031  Protein of unknown function (DUF1031)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.7   2.5e-05      0.22      45      76 ..     106     137 ..     100     141 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.5e-05
                           DUF1031  45 lYlDikskynnskdmkWneLykildkeLtkdk 76 
                                        Y +i  k+n   + kW+eLy  l+k L k+k
  gi|518651391|ref|YP_008140911.1| 106 YYINIDAKWNIKLESKWQELYTELNKSLNKKK 137
                                       5999************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1688.75
//
Query:       gi|518651392|ref|YP_008140912.1|  [L=380]
Description: hypothetical protein FACI_IFERC00001G0031 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-30  105.8   0.0      3e-30  105.4   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
    6.5e-05   21.6   0.0    9.3e-05   21.1   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.4   0.0   3.3e-34     3e-30      26     342 ..      13     325 ..       7     344 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.4 bits;  conditional E-value: 3.3e-34
                                       TCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHH.HHHHHHHHCCCC-TTTSEEEEETTSHGGG CS
                       Aminotran_5  26 ynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtte.ainlvalslarslkpgdeivvteaehhan 101
                                        +a+v+ +++ ++ e+++a++   e ++++ +a+++++   + G+++ a++ v+      + +  +i+v++++  + 
  gi|518651392|ref|YP_008140912.1|  13 LSAAVQPNIGFASPEFNSAMKSSLEGLRYITGAADSYTPFILPGSGTvAMESVMSF----IPRNSRILVVSNGVFGD 85 
                                       5667777788889999******************9888888888885466655544....6899************* PP

                                       THHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-T CS
                       Aminotran_5 102 lvpwqelakrtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaa 177
                                       +  w++++ r  + +kv+++++++++ l+++++ ++  ++ +va+t+v+++tG+  +ve+++k +++k  l++vD++
  gi|518651392|ref|YP_008140912.1|  86 R--WEAIMSRYPVAIKVLKAEAGKSVSLEDIDHEVSsRRYFAVAMTQVETSTGVKLDVESVAKTVRNKVDLIIVDGV 160
                                       *..****************************999975999****************************9******** PP

                                       TTTTTS---HHHHTESEEEEETTTTTSS.TT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS.S. CS
                       Aminotran_5 178 qavghipidvkklgvDflafsghKllgP.tGiGvlyvrkellekleplllggemveevsl.eettfaeapskfeaG. 251
                                       +++g  +++ +++g+D++   ++K lg+ +G G+l+++++++ekl+   ++g+      + + + +++  +kf aG 
  gi|518651392|ref|YP_008140912.1| 161 ASIGGENMQAARWGIDVVLTASQKALGAqAGAGLLVASRSAIEKLREESISGY------FaDLRNWSDLMNKFLAGg 231
                                       ************************666537**********************9......336666668888888887 PP

                                       .....S--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHH CS
                       Aminotran_5 252 .....Tpnvagiiglgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaed 323
                                            Tp++  + ++++ + ++++  +ea  k+++  +++ +++++ ++   l  ++++ r+++++ + ++g++  d
  gi|518651392|ref|YP_008140912.1| 232 ggyfaTPPIGTVFSIQKSMALIRSETIEARIKRHEICSQAFRAGISHMGLEIL--ASEKLRSNTVTGVIVDGIDIPD 306
                                       88888*****************************************9988766..4689****************** PP

                                       HHHHHHHTTEEEEEE-TTT CS
                       Aminotran_5 324 vatlLdeegIavrsGhhca 342
                                       + + + ++g++  +G h a
  gi|518651392|ref|YP_008140912.1| 307 FLQRCMKKGVEFGAGVHPA 325
                                       ************9999976 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     1e-08   9.3e-05      74     260 ..      56     269 ..      42     274 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1e-08
                                       SSHHHHHHHHHHTTS-TTEE.EEEESTSSHHHHHHHHHTHHH..TTCEEEEESTTSHHHHHHHCCT....TEEEEEE CS
                   Cys_Met_Meta_PP  74 ssGmaAiaaailallkaGde.ivvsddlYggtqrllkkvlkk..lgievkfvdtsdleelekaike....ntklvyl 143
                                        sG+ A+  ++++++   ++ +vvs+ ++g   + + + ++     ++++     +le++ + +++     + +  +
  gi|518651392|ref|YP_008140912.1|  56 GSGTVAM-ESVMSFIPRNSRiLVVSNGVFGDRWEAIMSRYPVaiKVLKAEAGKSVSLEDIDHEVSSrryfAVAMTQV 131
                                       5888888.677777766555267788899876655444433211223444444566777777777642223444555 PP

                                       ESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT.TTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHH CS
                   Cys_Met_Meta_PP 144 EtptnpllkvvDiekiaklakkagvlvvvDntfasp.llqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeel 219
                                       Et t  +   +D+e++ak+++++  l++vD + + +  ++++ ++g+D+v+ +  K lg +    aG++v++ +   
  gi|518651392|ref|YP_008140912.1| 132 ETSTGVK---LDVESVAKTVRNKVDLIIVDGVASIGgENMQAARWGIDVVLTASQKALGAQAG--AGLLVASRSAIE 203
                                       5555544...699******************9876659********************97755..799997774433 PP

                                       HHHHHHHH..........................HHHT-B--HHHHHHHHHHHTTHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 220 kkelkflq..........................nalGavlspfdawlllrGlkTLslRlerhqenA 260
                                       k + + +                             +G v s +++  l+r  +T++ R++rh+  +
  gi|518651392|ref|YP_008140912.1| 204 KLREESISgyfadlrnwsdlmnkflaggggyfatPPIGTVFSIQKSMALIRS-ETIEARIKRHEICS 269
                                       444444449999999***************9999999*********999995.99999999998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2736.16
//
Query:       gi|518651393|ref|YP_008140913.1|  [L=467]
Description: hypothetical protein FACI_IFERC00001G0032 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-30  103.6  42.3    1.1e-29  103.3  42.3    1.1  1  AA_permease    Amino acid permease
    3.4e-27   95.4  55.4    4.1e-27   95.1  55.4    1.0  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3  42.3   1.3e-33   1.1e-29       4     469 ..      23     459 ..      20     464 .. 0.78

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.3e-33
                       AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                       +++   v +++    l   ++ +  +++ l+++la ++++l  ++ ++++ ++ +sgg++++a+  lg+++G  +G+
  gi|518651393|ref|YP_008140913.1|  23 FQSFSHVAPAAEVAILITGTALVAEGSTPLIFILAPLIVLLWLNTNYQFSGYVASSGGYSAFARAGLGKSAGDITGW 99 
                                       5555556665555666666667777889************************************************* PP

                       AA_permease  81 nylfsw.itvlaleltaasiliqfwel.vtdlpkawvtgavf.lvvlliinlvgvkvygeaefi..lalikiiaiia 152
                                       +++f++ +t+++++l   + ++ +++  +t++p++wv ++++ lv+ +++ + gvk++        ++  ++++i+a
  gi|518651393|ref|YP_008140913.1| 100 LFFFNEfLTYIGFALLSFAAFVYLLSPsITSIPYLWVPILLIpLVFSTAMVYRGVKLSLNYAAYtgFIETAVLTIAA 176
                                       *999862578899999999999999888**********65551666689999*****99844433366677777777 PP

                       AA_permease 153 fiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPe 229
                                       +ii++     + + ++     f+     +f +  +++        f+ +  ++ + + ++ G+++v+++++E+k+P+
  gi|518651393|ref|YP_008140913.1| 177 LIIIF-----KLGSSNT----FY-----VFTAVPVHN-------DFSIIGLGLLFGLYSYGGTGSVVALGEEMKEPK 232
                                       77777.....3333333....22.....233344555.......4999***************************** PP

                       AA_permease 230 ksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssans 306
                                       k i kai++  ++++i   l +++++++++ ++ +++  s ++  +++ +++++g  + + +++av++ + l  +++
  gi|518651393|ref|YP_008140913.1| 233 KVIGKAIIYGWLLVLIPLALNAYALTVGWGLSNISSFGTSPDP--GVIEYFSFLGP-FGGWIFVAVVINSFLDFGIA 306
                                       **************************************99999..**********6.557888899999******** PP

                       AA_permease 307 slysasRvlyslakd.glaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwl 381
                                       +  s +R+ly la+d +l+P +  k + k+g P++ai++++i+s+++ +++++ ++ p v + ++  +a i++++ +
  gi|518651393|ref|YP_008140913.1| 307 INNSLTRMLYYLARDsNLLPrFLTKTHPKYGTPYKAIIAVAIVSFIIAVVSGIIFG-PFVGALVIEGAASIAFMLQH 382
                                       *************98568897778889*****************************.88999999999988888877 PP

                       AA_permease 382 liilsylrfRkalkyqgrsieelgfkaallplg...vilvlaaliiillilalyayltvkkgpkdwgaasfaaayli 455
                                       + ++ +l+f      ++r+ + l+++ ++++     v +++a+l++++ i a+ + l+         + + a ++ +
  gi|518651393|ref|YP_008140913.1| 383 SLATLSLPF------YSRREKHLKVTVHVVIPAislVFIAFAILSTVYPIPAFPLNLP--------AYMVIAWTIAG 445
                                       777777744......3333444555555444430003344555566666666665566........56666666666 PP

                       AA_permease 456 vllfliilvgvklh 469
                                       vll+ ++  ++ ++
  gi|518651393|ref|YP_008140913.1| 446 VLLIALLRQAGRDR 459
                                       66666666665555 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1  55.4   4.5e-31   4.1e-27       1     414 [.      16     434 ..      16     451 .. 0.83

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 4.5e-31
                     AA_permease_2   1 lsllsafalvigsv...igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgk 74 
                                       l+l+  ++ +++ v   + ++i++++ a+ +  ++ l++++a li+ l  l +  ++s+   +sgG + +++a+ gk
  gi|518651393|ref|YP_008140913.1|  16 LGLWHGIFQSFSHVapaAEVAILITGTALVAEGSTPLIFILAPLIV-LLWLNTNYQFSGYVASSGGYSAFARAGLGK 91 
                                       7899999999999977633566666658888889999999999999.7888899999888***************** PP

                     AA_permease_2  75 kvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                        ++ +++w+++f  +++  + + + +++++++l+p+++  ++l++ i  + l++ +++ +rg+k s +++ ++g + 
  gi|518651393|ref|YP_008140913.1|  92 SAGDITGWLFFFNEFLTYIGFALLSFAAFVYLLSPSITSIPYLWVPILLIPLVFSTAMVYRGVKLSLNYAAYTGFIE 168
                                       ****************99888899*************99999999999999************************** PP

                     AA_permease_2 152 illpliiliilglitvdgggfsslstetdtffpngwpg..vllgllivlwsfdGfesaanvseevkk..kdvpkaif 224
                                       + ++ i ++i+ + +++ ++f        t +p  +++  + lgll  l+s++G  s++   ee+k+  k + kai+
  gi|518651393|ref|YP_008140913.1| 169 TAVLTIAALIIIFKLGSSNTFYV----F-TAVPVHNDFsiIGLGLLFGLYSYGGTGSVVALGEEMKEpkKVIGKAII 240
                                       *7666666666666667778873....2.667777887335778888*****************9977468****** PP

                     AA_permease_2 225 igllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlea 301
                                       +g+l+vl+   l + a++ + + ++i++ +++++++ + +  + g+++ +i+v++++ s l  +++   + +r+l+ 
  gi|518651393|ref|YP_008140913.1| 241 YGWLLVLIPLALNAYALTVGWGLSNISSFGTSPDPGVIEYFSFLGPFGGWIFVAVVINSFLDFGIAINNSLTRMLYY 317
                                       ***********************************86666665669******99999999999999999******** PP

                     AA_permease_2 302 lard.gvlPrffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisyllliigalilrk 374
                                       lard + lPrf+ k++ k+g+p+ aii +aivs+i+++++ ++        ++  ++s+++++   l+ +++ ++ +
  gi|518651393|ref|YP_008140913.1| 318 LARDsNLLPRFLTKTHpKYGTPYKAIIAVAIVSFIIAVVSGIIFgpFVGALVIEGAASIAFMLQHSLATLSLPFYSR 394
                                       ****77788**************************999888553112233477788889999999999999999999 PP

                     AA_permease_2 375 krphlkrpgkilvaiigalfllfllvalffppkgpatqss 414
                                       +++hlk    +++ +i+++f+ f++  + +p      + +
  gi|518651393|ref|YP_008140913.1| 395 REKHLKVTVHVVIPAISLVFIAFAILSTVYPIPAFPLNLP 434
                                       9999999767777788888888888766666544443322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.32s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 3016.14
//
Query:       gi|518651394|ref|YP_008140914.1|  [L=79]
Description: hypothetical protein FACI_IFERC00001G0033 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.3   0.2      0.027   14.1   0.2    1.0  1  STD1      STD1/MTH1
       0.13   12.3   0.0        0.2   11.7   0.0    1.4  1  DUF5444   Family of unknown function (DUF5444)


Domain annotation for each model (and alignments):
>> STD1  STD1/MTH1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   3.1e-06     0.027      37      85 ..      26      77 ..       3      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.1e-06
                              STD1 37 sdilledalpkqqkklddmynpeelkksllndellyngrpe......eLiDWelN 85
                                      +di +++  +k   k d++y +ee+ ++l+  e ++n  p       eLi W++N
  gi|518651394|ref|YP_008140914.1| 26 EDIEKQKIAIK---KADELYGVEETNRKLTALESFSNRFPDkkekirELIEWNKN 77
                                      45555555555...9**************9999999999988887877******* PP

>> DUF5444  Family of unknown function (DUF5444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   2.2e-05       0.2      12      42 ..      44      76 ..      37      78 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.2e-05
                           DUF5444 12 vqqGnrelnkL..yeasfPdteeGlkeayeWas 42
                                      v   nr+l  L  +   fPd +e ++e +eW  
  gi|518651394|ref|YP_008140914.1| 44 VEETNRKLTALesFSNRFPDKKEKIRELIEWNK 76
                                      56678888887335566**************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 530.12
//
Query:       gi|518651395|ref|YP_008140915.1|  [L=383]
Description: ATPase [Ferroplasma acidarmanus fer1]
Scores for 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   82.7   2.1    8.3e-23   80.7   1.1    2.4  2  DUF234    Archaea bacterial proteins of unknown function
    4.2e-13   49.8   0.1    8.9e-13   48.7   0.1    1.5  1  ATPase_2  ATPase domain predominantly from Archaea
    0.00029   20.6   0.0    0.00062   19.6   0.0    1.5  1  HTH_5     Bacterial regulatory protein, arsR family
     0.0055   16.9   0.1      0.013   15.7   0.1    1.6  1  UPF0102   Uncharacterised protein family UPF0102
  ------ inclusion threshold ------
       0.01   15.8   0.6      0.031   14.3   0.6    1.9  1  HTH_45    Winged helix-turn-helix
      0.023   14.7   0.1      0.085   12.9   0.1    2.0  1  AAA_14    AAA domain
      0.028   14.4   0.0      0.049   13.6   0.0    1.4  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.69   1.8e+03      22      45 ..      85     109 ..      67     118 .. 0.74
   2 !   80.7   1.1   3.3e-26   8.3e-23       1      95 [.     227     325 ..     227     329 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.69
                            DUF234  22 ekik.eelneyvgkvFEelvrelll 45 
                                       + ik + ++e++   F el++ +++
  gi|518651395|ref|YP_008140915.1|  85 KPIKfRYIKEFINYNFTELCKIYFI 109
                                       66663345999********998875 PP

  == domain 2  score: 80.7 bits;  conditional E-value: 3.3e-26
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwW........kkeee 69 
                                       wfr++ pnr+ ie+ ++ ev +ki++++++++g++FE l+rel++     g l  +ft+v+rwW        k+ ee
  gi|518651395|ref|YP_008140915.1| 227 WFRYILPNRTGIENFNYLEVARKIENDFSQFAGEQFEYLMRELIM----DGILGRTFTTVSRWWgkvgnntgKNIEE 299
                                       *********************************************....7889999*********99999888999* PP

                            DUF234  70 iDivaldeeekkalfgEvKwknseke 95 
                                       iDiva++++ +++lf+E+Kw+n++ +
  gi|518651395|ref|YP_008140915.1| 300 IDIVAYSDTRDEILFCECKWTNKKVS 325
                                       **********************6655 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 !   48.7   0.1   3.5e-16   8.9e-13     116     232 ..      13     119 ..       5     120 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 3.5e-16
                          ATPase_2 116 kgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfie.rvyneselegrhky.ilvd 190
                                       ++kk+ii iDe+++li    +g+++  + ++++++ l+k+ ++++++ +sS +++ + +++++s+l+gr+++ i+++
  gi|518651395|ref|YP_008140915.1|  13 SRKKLIIAIDEFPYLI----EGNRSIPSVFQKIYDLLLKNMNVMLILSGSSITMMENnVLSYKSPLYGRRSGqIKLK 85 
                                       4689************....888*********************************97889**************** PP

                          ATPase_2 191 dldketalnflkegfkeleelskedfeeiyryvGGkPkalve 232
                                       ++++  +++f++  f el         +iy ++GG+P++l +
  gi|518651395|ref|YP_008140915.1|  86 PIKFRYIKEFINYNFTEL--------CKIYFILGGIPEYLLK 119
                                       **9999999998866555........58**********9986 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 !   19.6   0.0   2.4e-07   0.00062       6      47 .]     161     202 ..     157     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                                       HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   6 kILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                        IL++ a g ++v+e+  ++++ +s vS +  +L  + L+++
  gi|518651395|ref|YP_008140915.1| 161 LILRSIAGGYRTVGEINSYTNMDKSMVSKYIDILLSLELISY 202
                                       59*************************************986 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   5.1e-06     0.013      20      60 ..     292     337 ..     281     344 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.1e-06
                                       EEEETTEEEEEEE....TTEEEEEEEEE-.......-------HHH CS
                           UPF0102  20 nwrcragEiDiia....tevlvfvEVKtR.ssekfgspaeavtprK 60 
                                       n   ++ EiDi+a    +++++f+E K+  ++ +++  +e + ++K
  gi|518651395|ref|YP_008140915.1| 292 NTGKNIEEIDIVAysdtRDEILFCECKWTnKKVSYKIIEELIRKSK 337
                                       5555678**********889*******9635555677777777776 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.6   1.2e-05     0.031       9      51 ..     160     202 ..     155     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                            HTH_45   9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikk 51 
                                       + IL++i  g  +  +i    n++ ++++kY+d+L++ +li+ 
  gi|518651395|ref|YP_008140915.1| 160 MLILRSIAGGYRTVGEINSYTNMDKSMVSKYIDILLSLELISY 202
                                       5699***999999****************************43 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   3.3e-05     0.085      60     128 ..      12      90 ..       2      93 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                            AAA_14  60 lkeekktylflDEiqev.......pewekalkslvdegknldvivtGSnskllskeia...tslagrva.eielypl 125
                                       +++ kk ++ +DE  ++       p++++ + +l+ ++ n+ +i++GS+  ++ +++    + l gr + +i+l p+
  gi|518651395|ref|YP_008140915.1|  12 VSR-KKLIIAIDEFPYLiegnrsiPSVFQKIYDLLLKNMNVMLILSGSSITMMENNVLsykSPLYGRRSgQIKLKPI 87 
                                       334.788999****9997887666666666666666888**************998764445666665449999999 PP

                            AAA_14 126 sfa 128
                                       +f+
  gi|518651395|ref|YP_008140915.1|  88 KFR 90 
                                       997 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.9e-05     0.049       5      72 ..     258     335 ..     254     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-05
                                       -TTCHHHHHHHHHHH..HSSS.........EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHH CS
                           Mrr_cat   5 spkeFeklvaellea..lGyk.........eveltgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeli 70 
                                        +++Fe+l++el+    lG +         +v ++ +++ + iD++a +d  + e ++ ++K+ ++kv+ k ++eli
  gi|518651395|ref|YP_008140915.1| 258 AGEQFEYLMRELIMDgiLGRTfttvsrwwgKVGNNTGKNIEEIDIVAYSDTRD-EILFCECKWTNKKVSYKIIEELI 333
                                       677888888887766333444667777777777777888999******99855.999******************98 PP

                                       HH CS
                           Mrr_cat  71 ga 72 
                                         
  gi|518651395|ref|YP_008140915.1| 334 RK 335
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2575.22
//
Query:       gi|518651396|ref|YP_008140916.1|  [L=70]
Description: hypothetical protein FACI_IFERC00001G0035 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-14   52.2   3.3      9e-14   52.0   3.3    1.0  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   3.3     5e-18     9e-14       1      62 [.       3      61 ..       3      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 5e-18
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgil..seeeadeiekask 62
                                      K +s+s  +Y +Lk++K+ +eSFsdvI+rLl+ + k    ++++++gil   ++e+d +e+++ 
  gi|518651396|ref|YP_008140916.1|  3 KMVSLSNKAYAELKDIKNIDESFSDVILRLLK-NTK----DIKQFAGILkdHKSELDLMEESIT 61
                                      789****************************7.444....5********666678899999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); 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:                         1  (5.57756e-05); expected 0.2 (1e-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 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 502.55
//
Query:       gi|518651397|ref|YP_008140917.1|  [L=289]
Description: ATP-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-21   75.6   0.9    3.2e-21   75.6   0.9    1.8  2  DUF234    Archaea bacterial proteins of unknown function
    0.00011   22.2   0.0    0.00026   21.0   0.0    1.7  1  Mrr_cat   Restriction endonuclease


Domain annotation for each model (and alignments):
>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.67     6e+03       5      13 ..      27      35 ..       9      58 .. 0.52
   2 !   75.6   0.9   3.6e-25   3.2e-21       1      92 [.     124     224 ..     124     235 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.67
                            DUF234  5 vypnrseie 13
                                      +++++s + 
  gi|518651397|ref|YP_008140917.1| 27 IFQETSVYA 35
                                      233333333 PP

  == domain 2  score: 75.6 bits;  conditional E-value: 3.6e-25
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnk.agklpfrftkvGrwW........kkee 68 
                                       wf+  yp  ++ elg++e v++++ +++n+ v  +FE++++e+l++ln+ ++ lpf ++k+G+wW        +++e
  gi|518651397|ref|YP_008140917.1| 124 WFSKFYPVINQFELGNYEGVINNLINSINSIVPYKFEDICKEFLVYLNNnSSYLPFSISKIGKWWgknklepnYNQE 200
                                       99999***************************************9776515679***********999998888*** PP

                            DUF234  69 eiDivaldeeekkalfgEvKwkns 92 
                                       eiDi+a+++++ +++f E+Kw+n+
  gi|518651397|ref|YP_008140917.1| 201 EIDIIAINDSTLDIIFSECKWSNK 224
                                       **********************93 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0     3e-08   0.00026       3     114 ..     153     284 ..     151     285 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-08
                                       TT-TTCHHHHHHHHHHHHSSS................EEE---B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-H CS
                           Mrr_cat   3 kmspkeFeklvaellealGyk................eveltgrsgDggiDliakkdplgserilvqaKryknkvgv 63 
                                       ++ p++Fe++++e+l  l  +                + +l +  + + iD+ia  d    + i+ ++K+++++++ 
  gi|518651397|ref|YP_008140917.1| 153 SIVPYKFEDICKEFLVYLNNNssylpfsiskigkwwgKNKLEPNYNQEEIDIIAINDS-TLDIIFSECKWSNKPIDI 228
                                       566888888888888877777677788887777777766788889999*****98876.679*********988887 PP

                                       HHHHHH......HHHCTTS..SEEEEEESS-B-HHHHHHHHTT--EEEE-HHHHHHH CS
                           Mrr_cat  64 keVqel......igalkkrgadkgifvttsdftkaAreeaeelnkieLldgdeLael 114
                                       ++ + l      +++ ++++ ++ i+ + s+ft+  re a+  n+i+L+d  +++e+
  gi|518651397|ref|YP_008140917.1| 229 DVYSNLkrksglVSWNNDKRIEHFILFSKSGFTDRMRETAKL-NNIILFDLVKMQEI 284
                                       776555221111444555889********************9.********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2369.32
//
Query:       gi|518651398|ref|YP_008140918.1|  [L=73]
Description: hypothetical protein FACI_IFERC00001G0037 [Ferroplasma acidarmanus fer1]
Scores for complete 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   22.4   1.5    0.00018   22.2   1.5    1.1  1  VAPB_antitox  Putative antitoxin
  ------ inclusion threshold ------
       0.39   11.5   4.0        1.9    9.3   4.0    1.9  1  DUF4259       Domain of unknown function (DUF4259)


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.5     2e-08   0.00018       2      58 ..       7      62 ..       6      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 2e-08
                      VAPB_antitox  2 tIsIsdevYekLkklKr.egeSFsdvIerLlekkkkgkkkellelfgilseeeadeie 58
                                      tI ++ +v ++Lk++K+ ++e ++++I+ L++  +  + +el  ++ + +e+ ++e+ 
  gi|518651398|ref|YP_008140918.1|  7 TIQLKKSVVNALKEIKKdPRETYNEIILDLIKDAR--ETSELNTFVAKAQESKMKELW 62
                                      8****************99************9666..457899999999999887765 PP

>> DUF4259  Domain of unknown function (DUF4259)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.0   0.00021       1.9      96     135 ..      23      72 ..       2      73 .] 0.60

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00021
                           DUF4259  96 ksdd.......adlrelarrald..rvlaek..sElkelWeeseeleeWke 135
                                       k++         dl++ ar++ +    +a+   s +kelWee  ++  W++
  gi|518651398|ref|YP_008140918.1|  23 KDPRetyneiiLDLIKDARETSElnTFVAKAqeSKMKELWEEG-DYSGWEH 72 
                                       333344444446777777776541133444456*********9.9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 489.83
//
Query:       gi|518651399|ref|YP_008140919.1|  [L=114]
Description: hypothetical protein FACI_IFERC00001G0038 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.3      0.027   14.8   0.3    1.3  1  Dynein_light  Dynein light chain type 1


Domain annotation for each model (and alignments):
>> Dynein_light  Dynein light chain type 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   1.5e-06     0.027      11      56 ..      19      59 ..       9      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHHHHHHHHH-SSHH..HHHHHHHHHHHHHH-S-EEEEE CS
                      Dynein_light 11 eemqeeaielakealekfkkekekdiaayikkeldkkygptWhciV 56
                                      + m +++++++ +      ke+++ + + ik++++ +y + Whc +
  gi|518651399|ref|YP_008140919.1| 19 TLMNDTFLKTVLHLS----KEDKQPVLKTIKEKFE-TYLRKWHCYI 59
                                      455555555554444....344579*********5.5*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       771  (0.043003); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 810.63
//
Query:       gi|518651400|ref|YP_008140920.1|  [L=92]
Description: hypothetical protein FACI_IFERC00001G0039 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.0   0.0      0.031   13.9   0.0    1.2  1  Tenui_NCP  Tenuivirus major non-capsid protein


Domain annotation for each model (and alignments):
>> Tenui_NCP  Tenuivirus major non-capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.7e-06     0.031      73     109 ..      25      61 ..       3      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.7e-06
                         Tenui_NCP  73 hkhipefchsflshllggedddnalidiglffnmlqp 109
                                          + ef+ + l  ll  e+ d+++idig+ +n   p
  gi|518651400|ref|YP_008140920.1|  25 NVTLSEFVETKLRLLLSVEEHDKSFIDIGIKYNYTSP 61 
                                       45689****************************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 679.60
//
Query:       gi|518651401|ref|YP_008140921.1|  [L=79]
Description: hypothetical protein FACI_IFERC00001G0040 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.7   0.1       0.11   12.5   0.1    1.3  1  ENOD93    Early nodulin 93 ENOD93 protein


Domain annotation for each model (and alignments):
>> ENOD93  Early nodulin 93 ENOD93 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   5.9e-06      0.11      51      69 ..      46      64 ..      29      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.9e-06
                            ENOD93 51 aliisaaaiaayFitadKt 69
                                        iis+  i++ FitadK 
  gi|518651401|ref|YP_008140921.1| 46 IHIISSMNISSLFITADKE 64
                                      459***************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 548.54
//
Query:       gi|518651402|ref|YP_008140922.1|  [L=1015]
Description: hypothetical protein FACI_IFERC00001G0041 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-55  188.6   0.0    2.9e-55  187.4   0.0    1.5  2  SNF2_N      SNF2 family N-terminal domain
    6.2e-31  107.1   0.0    1.5e-30  105.9   0.0    1.6  1  DUF3670     SNF2 Helicase protein
    1.2e-18   67.5   0.1      1e-16   61.2   0.0    2.6  2  Helicase_C  Helicase conserved C-terminal domain
    5.3e-08   33.0   0.1    5.2e-07   29.8   0.0    2.2  2  ResIII      Type III restriction enzyme, res subunit
    0.00086   19.3   0.0     0.0073   16.3   0.0    2.1  2  Flavi_DEAD  Flavivirus DEAD domain
  ------ inclusion threshold ------
      0.047   13.4   0.1       0.17   11.5   0.0    2.0  2  SWI2_SNF2   SWI2/SNF2 ATPase


Domain annotation for each model (and alignments):
>> SNF2_N  SNF2 family N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.48   1.4e+03       1       9 [.     541     549 ..     541     556 .. 0.90
   2 !  187.4   0.0   9.7e-59   2.9e-55      56     350 .]     557     821 ..     551     821 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.48
                                       HHHHHHHHH CS
                                       xxxxxxxxx RF
                            SNF2_N   1 yQkeavkwm 9  
                                       yQk++v+w+
  gi|518651402|ref|YP_008140922.1| 541 YQKHGVAWL 549
                                       9*******9 PP

  == domain 2  score: 187.4 bits;  conditional E-value: 9.7e-59
                                       --EEE---TTS--HHHHHHHHH...HHTTTS---.......S-EEEE--HHHHHHHHHHHHHH-TTS-EEE--SSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N  56 rGGiLaDemGLGKTvqvlalilaqrakeekdkekkrkdtlagptLivvPaslldqWeneierhvsssalrvlvyggq 132
                                        G+ LaD+mGLGKT++++a++l     e+               Li++P+s++ +We+ei+++++s   +v++++g+
  gi|518651402|ref|YP_008140922.1| 557 FGCCLADDMGLGKTIEIIAFLL--DRLEN----------NGSTSLILCPTSVISNWEHEIHKFAPSL--NVYIHHGN 619
                                       69********************..22222..........23457********************998..56999998 PP

                                       HH-----------------EEEE-HHHHHHHT......TTS-S-S-SEEEES-GGGT--TTSHHHHHHHH---S-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 133 kkmkkkntkvapklladydvvittYdvlsreaelqkkrsvlkqvewkrvvlDEghtlknstskaaeavskLstsnrw 209
                                       +    k++ ++ +  +dy +v+t+Y+ l+r+       + l+qv+w+ ++ DE++ +kn  +k + a+++L+++ ++
  gi|518651402|ref|YP_008140922.1| 620 S---RKKDDNFIDNITDYKIVLTSYSLLQRDI------KFLSQVNWDGIIADEAQYIKNYSTKQSRAIRSLQGNFKI 687
                                       6...444567888899*************999......9************************************** PP

                                       EE-S--SSS-HHHHHHHHHHH-TTTT--HHHHHHHTHHHHH.HHHHHHHHHHHTT-STTEE---GGGT..--S---E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
                            SNF2_N 210 iltGTPiqnsledlygLlkfLreepfgekqtfdkllqrpie.aqaekgrsrLlqllqrlmlrrakkdv..eknlPpk 283
                                        ltGTPi n l+dl ++++f++++ ++  + f++ ++ pie   +e+ ++ L++l+++++lrr+k+d    ++lP+k
  gi|518651402|ref|YP_008140922.1| 688 ALTGTPIENRLQDLRSIFEFINPGYLSGEKKFRETFSIPIErYGDENAMNALNTLVNPMILRRVKTDKsiIQDLPDK 764
                                       *****************************************667788899****************9954558**** PP

                                       EEEEEEEE--HHHHHHHH....................HHHHHH-HHH-HHHHHHHHHHHHH---XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            SNF2_N 284 teeiiflklskverksYnrllevlrkkalakllkrseaalkssskskekilelllelrqacnhpqlv 350
                                       +e  ++++l+ +++++Y+         a++++l++  +++k++ + k++il+++++l++   hp+lv
  gi|518651402|ref|YP_008140922.1| 765 EEVKVYIPLTGEQASLYE--------AAVNTMLES--VNTKKGIERKSVILSTITKLKRLLDHPSLV 821
                                       ******************........444444444..677778866788**************9985 PP

>> DUF3670  SNF2 Helicase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.9   0.0   4.9e-34   1.5e-30       2     135 ..     368     498 ..     367     499 .. 0.96

  Alignments for each domain:
  == domain 1  score: 105.9 bits;  conditional E-value: 4.9e-34
                           DUF3670   2 vpdalelddeeaaefLkeaaeaLeaaGvgVllPrwlkkrarprltlklavkgpasaakesklgldalldfdwelalG 78 
                                       +pd++ l+dee++++Lk+ +  +e+aG+g+l P+w+ ++++++l++k++vk++ + +++ klg++alld++ +++l+
  gi|518651402|ref|YP_008140922.1| 368 KPDGVYLSDEEVFDLLKTYSSSMEEAGFGILFPEWW-GKKENKLGIKIKVKAG-DINNSVKLGINALLDYSLDIVLN 442
                                       799*********************************.***************9.777889***************** PP

                           DUF3670  79 deeLseeEldrLaeakrpLvrlrgqWvevdpeelrraleflkrreekkltladaLra 135
                                       +e++s+++l++La  k+ Lv++  +Wve+d ++l+++l+ l++ + kk++l ++L +
  gi|518651402|ref|YP_008140922.1| 443 GEPVSKSDLEKLAIMKSHLVQIGKKWVEIDNDQLNKILKLLDKGN-KKMSLPELLTM 498
                                       *******************************************55.5******9987 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 ?    3.5   0.1      0.03        90       5      92 ..     573     671 ..     569     682 .. 0.61
   2 !   61.2   0.0   3.4e-20     1e-16       2     111 .]     834     947 ..     833     947 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.03
                                       HHHHHH.HHTTTTSEEEEEESSHHHHHH.HHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSS.EEEESGGG CS
                        Helicase_C   5 allell.kleeeggkilifvntidrlek.vklllekk..gikvavlhgelpqnereeileqfnkgesd.vLiatdva 76 
                                       ++  ll  le++g+++li ++t    +   ++   k+  +++v ++hg+ + ++ +  +++    +++ vL + + +
  gi|518651402|ref|YP_008140922.1| 573 IIAFLLdRLENNGSTSLILCPTSVISNWeHEIH--KFapSLNVYIHHGN-SRKKDDNFIDNI--TDYKiVLTSYSLL 644
                                       444445778999999*******99443333444..4445999*999995.455556666666..3455355555555 PP

                                       TS...........SSTSTTESEEEESS CS
                        Helicase_C  77 er...........GidipkvnlVinfd 92 
                                       +r           Gi  ++++++ n++
  gi|518651402|ref|YP_008140922.1| 645 QRdikflsqvnwdGIIADEAQYIKNYS 671
                                       555555555555555555555555555 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 3.4e-20
                                       HHHHHHHHH.HHTTTTSEEEEEESSHH..HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHH..TTSSSEEEE CS
                        Helicase_C   2 kleallell.kleeeggkilifvntid..rlek.vklllekkgikvavlhgelpqnereeileqfn..kgesdvLia 72 
                                       kl +l e+l +   +++k+l+f++++d  +     + +l+k g ++++l+g++p + r+ ++e+f+  +g   ++i+
  gi|518651402|ref|YP_008140922.1| 834 KLVRLREMLeEAIDSNQKTLVFTQYTDagK--IiKEEMLKKLGEEALYLNGSTPMSLRQNMVERFQdpDGPKIFIIS 908
                                       666777777777899************553..3334445677***********************98779999**** PP

                                       SGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  73 tdvaerGidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                        ++++ Gi+++ +++Vi+fd ++n++   q+ +R++R+g
  gi|518651402|ref|YP_008140922.1| 909 VKAGGAGINLTAATNVIHFDRWWNPSVEDQATDRAYRIG 947
                                       *************************************97 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.0   1.7e-10   5.2e-07       3     170 ..     537     694 ..     535     695 .. 0.78
   2 ?    0.5   0.0      0.18   5.5e+02      84     121 ..     828     868 ..     778     892 .. 0.62

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 1.7e-10
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       +lr yQ++ +  l+  ++       +++   G GKT+ + a l +rl ++g+    l+l+p+ s+++ +++e+ kf+
  gi|518651402|ref|YP_008140922.1| 537 NLRAYQKHGVAWLK-FMT-GAGFGCCLADDMGLGKTIEIiAFLLDRLENNGS--TSLILCPT-SVISNWEHEIHKFA 608
                                       56777777775554.333.344566799999*****9775788888888766..89999997.78899**9999999 PP

                                       GG......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS..TTTHH CS
                            ResIII  79 seayke..igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak.kswre 152
                                       ++ +    +g++ ++d + +   ++t+ ki++t+++ l++d+       + l++ + d ii DEa  ++   ++  +
  gi|518651402|ref|YP_008140922.1| 609 PSLNVYihHGNSRKKDDNFI--DNITDYKIVLTSYSLLQRDI-------KFLSQVNWDGIIADEAQYIKNYsTKQSR 676
                                       98754455444444444444..79******************.......778888999*******999886336666 PP

                                       HHHT---SEEEEEESS-S CS
                            ResIII 153 ilekfkeavllglTATpe 170
                                       ++++++ +++++lT+Tp 
  gi|518651402|ref|YP_008140922.1| 677 AIRSLQGNFKIALTGTPI 694
                                       8999************96 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                                       ....GEEEESSS-B--.......-SEEEEEHHHHHHTH... CS
                            ResIII  84 e...igkkvsgdkkkakekdstnkkilvttiqsldadseee 121
                                       +    +k v+ ++  ++++ds++k +++t++  + ++++ee
  gi|518651402|ref|YP_008140922.1| 828 RldrSEKLVRLREMLEEAIDSNQKTLVFTQYTDAGKIIKEE 868
                                       23333344444444447888999999999999988888444 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.4e-06    0.0073      14     113 ..     566     673 ..     560     696 .. 0.76
   2 ?   -0.1   0.0      0.27   8.2e+02      22      54 ..     838     874 ..     833     891 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.4e-06
                                       TS-TTTTHHHHHHHHHHHTT--EEEEESSHHHH...HHHHHHTTTS-EEE-----..--------SEE...EEEHHH CS
                        Flavi_DEAD  14 GaGktrkvlpelvkeaierrlrtlvLaPtrvvl...aemeealkglevryktsav..keektgrelvd...vmchat 82 
                                       G Gkt  +++ l+++  ++   +l+L Pt v+    +e+++    l+v  ++     k+++  +++ d   v+    
  gi|518651402|ref|YP_008140922.1| 566 GLGKTIEIIAFLLDRLENNGSTSLILCPTSVISnweHEIHKFAPSLNVYIHHGNSrkKDDNFIDNITDykiVLTSYS 642
                                       89*****************************9733358888888888877765550034445567776444455566 PP

                                       HHHHHHHT------SEEEEETTT--SHHHHH CS
                        Flavi_DEAD  83 ftkrllspvrkknyeliimDeahflDPasia 113
                                       + +r ++   ++n++ ii Dea ++   s  
  gi|518651402|ref|YP_008140922.1| 643 LLQRDIKFLSQVNWDGIIADEAQYIKNYSTK 673
                                       88999999****************9887764 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHTT--EEEEE....SSHHHHHHHHHHTT CS
                        Flavi_DEAD  22 lpelvkeaierrlrtlvLa....Ptrvvlaemeealk 54 
                                       l e+++eai+++++tlv +      +++ +em + l 
  gi|518651402|ref|YP_008140922.1| 838 LREMLEEAIDSNQKTLVFTqytdAGKIIKEEMLKKLG 874
                                       678999***********98222234677777776665 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.7e-05      0.17     117     170 ..     652     706 ..     603     750 .. 0.76
   2 ?   -2.7   0.0       1.3   3.9e+03      93     107 ..     799     813 ..     776     857 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.7e-05
                         SWI2_SNF2 117 sereniivlvDEaHRs.qygelakklrkalpnaafigFTGTPilkkdkktkevFg 170
                                       s+ +   +++DEa    +y++ +++  + l+    i++TGTPi+++ ++ +++F+
  gi|518651402|ref|YP_008140922.1| 652 SQVNWDGIIADEAQYIkNYSTKQSRAIRSLQGNFKIALTGTPIENRLQDLRSIFE 706
                                       4444445899**98752677778888899***************98877777775 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                         SWI2_SNF2  93 esekiifttiqKfee 107
                                       e++++i++ti K+++
  gi|518651402|ref|YP_008140922.1| 799 ERKSVILSTITKLKR 813
                                       356778888888762 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1015 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.48
# Mc/sec: 6353.61
//
Query:       gi|518651403|ref|YP_008140923.1|  [L=280]
Description: hypothetical protein FACI_IFERC00001G0042 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-07   30.1   0.4    5.5e-07   29.1   0.4    1.5  1  SWIM      SWIM zinc finger
  ------ inclusion threshold ------
      0.079   13.0   0.0       0.13   12.3   0.0    1.3  1  DUF2948   Protein of unknown function (DUF2948)


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 !   29.1   0.4   6.2e-11   5.5e-07      16      37 ..     148     166 ..     144     169 .. 0.93

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 6.2e-11
                              SWIM  16 tCsCpefqkngipCkHalAvll 37 
                                       +C+Cp+   + ipCkH++Av++
  gi|518651403|ref|YP_008140923.1| 148 NCTCPD---YAIPCKHIAAVFY 166
                                       6*****...************8 PP

>> DUF2948  Protein of unknown function (DUF2948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.5e-05      0.13      26      79 ..      28      80 ..      24      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.5e-05
                           DUF2948 26 gdiaylkkerrfvlllnRfrwekaeekekkeyeRvrsalrferVlavksrgidr 79
                                      gdi  +  ++rf+ +ln + we++  +++k+y Rv  +l+++  ++v s +++ 
  gi|518651403|ref|YP_008140923.1| 28 GDIGTKWWSKRFIAILNSYGWETRL-QRGKRYARVGQVLSVNIDSNVVSADVQG 80
                                      6666777789**************9.99***********998666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.40
# Mc/sec: 2076.83
//
Query:       gi|518651404|ref|YP_008140924.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G0043 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   78.8   0.2      3e-22   78.6   0.2    1.0  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.2   1.7e-26     3e-22       2      56 .]      11      65 ..      10      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.7e-26
                           DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaIkd 56
                                      +efkC+D+g+dCgf ++a++ +E+++ ++ Hak+aH++tei+pel  k+k+aIk+
  gi|518651404|ref|YP_008140924.1| 11 YEFKCKDIGMDCGFDVKADSVDELIPVIQVHAKNAHNITEITPELFSKVKAAIKQ 65
                                      89***************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.79
# Mc/sec: 250.64
//
Query:       gi|518651405|ref|YP_008140925.1|  [L=200]
Description: hypothetical protein FACI_IFERC00001G0044 [Ferroplasma acidarmanus fer1]
Scores for complete 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   53.2   0.0    2.9e-14   52.6   0.0    1.4  1  HTH_10        HTH DNA binding domain
     0.0038   16.7   0.0     0.0068   15.9   0.0    1.4  1  Sigma70_r4    Sigma-70, region 4
     0.0042   17.1   0.4      0.071   13.2   0.0    2.7  2  HTH_Mga       M protein trans-acting positive regulator (MGA)
  ------ inclusion threshold ------
      0.087   12.5   0.0       0.35   10.6   0.0    2.0  2  Sigma70_r4_2  Sigma-70, region 4
        0.1   12.6   0.0       0.18   11.8   0.0    1.4  1  POP1          Ribonucleases P/MRP protein subunit POP1
       0.44   10.4   4.4        3.3    7.6   0.1    3.5  5  IF2_N         Translation initiation factor IF-2, N-terminal 
       0.72   10.0   3.0        1.2    9.3   0.0    2.6  3  DUF5415       Family of unknown function (DUF5415)


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   1.1e-17   2.9e-14       1      52 [.     141     192 ..     141     193 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.1e-17
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT +q evl +A+++GYF+  R ++l+ LA elGIsk +++  L++ + k++
  gi|518651405|ref|YP_008140925.1| 141 LTLRQKEVLYIAFKNGYFEFQRGINLDGLASELGISKKAVQSDLKRGIDKIV 192
                                       899**********************************************998 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06    0.0068       4      48 ..     140     191 ..     139     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       +L+ r++evl+  f        +g +l  ++ +lgiS+ +V + +kr+++k+
  gi|518651405|ref|YP_008140925.1| 140 ELTLRQKEVLYIAFkngyfefQRGINLDGLASELGISKKAVQSDLKRGIDKI 191
                                       7999****************99***************************996 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 ?    1.1   0.3      0.15     4e+02      16      39 ..      71      95 ..      56     114 .. 0.74
   2 !   13.2   0.0   2.8e-05     0.071      18      41 ..     161     184 ..     142     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.15
                           HTH_Mga 16 eneksltld..elakeLglseltlqs 39
                                      + + +l+++  e++ + +ls +++ s
  gi|518651405|ref|YP_008140925.1| 71 D-KTWLETHscEICRAVALSGSIITS 95
                                      4.678999999999999999888864 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 2.8e-05
                           HTH_Mga  18 eksltldelakeLglseltlqsdi 41 
                                       ++ ++ld la+eLg+s +++qsd+
  gi|518651405|ref|YP_008140925.1| 161 QRGINLDGLASELGISKKAVQSDL 184
                                       6779*******************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 ?   -1.6   0.0       0.9   2.3e+03       9      19 ..     139     149 ..     133     153 .. 0.82
   2 ?   10.6   0.0   0.00014      0.35      33      53 ..     170     190 ..     167     191 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.9
                                       TTS-HHHHHHH CS
                      Sigma70_r4_2   9 aeLperqreif 19 
                                       +eL+ rq+e++
  gi|518651405|ref|YP_008140925.1| 139 EELTLRQKEVL 149
                                       68999999997 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00014
                                       HHHHT--HHHHHHHHHHHHHH CS
                      Sigma70_r4_2  33 AellgisegtVksrlsRArkk 53 
                                       A++lgis ++V+s l+R+  k
  gi|518651405|ref|YP_008140925.1| 170 ASELGISKKAVQSDLKRGIDK 190
                                       99***************9766 PP

>> POP1  Ribonucleases P/MRP protein subunit POP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   7.1e-05      0.18     127     152 ..      54      79 ..      17      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.1e-05
                              POP1 127 klaeppkkkikylkrqkektWLpTHv 152
                                         ++++ +ki    +q++ktWL+TH 
  gi|518651405|ref|YP_008140925.1|  54 IRESIKDDKITIYENQRDKTWLETHS 79 
                                       33556889999999***********6 PP

>> IF2_N  Translation initiation factor IF-2, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       0.8     2e+03      15      29 ..      14      27 ..      10      31 .. 0.74
   2 ?   -2.3   0.0       1.6     4e+03       2       7 ..      61      66 ..      46      67 .. 0.63
   3 ?   -3.2   0.0         3   7.6e+03      18      41 ..     113     121 ..     109     126 .. 0.55
   4 ?    2.1   0.0     0.065   1.7e+02       6      30 ..     134     157 ..     133     159 .. 0.85
   5 ?    7.6   0.1    0.0013       3.3       9      33 ..     169     190 ..     163     194 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.8
                             IF2_N 15 vkskevikkLfkelG 29
                                      ++s +v+kkL   l 
  gi|518651405|ref|YP_008140925.1| 14 KPSCDVLKKLAP-LN 27
                                      678899***944.65 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.6
                             IF2_N  2 skirVy 7 
                                      +ki++y
  gi|518651405|ref|YP_008140925.1| 61 DKITIY 66
                                      456666 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3
                             IF2_N  18 kevikkLfkelGievkshsssLDe 41 
                                       k+ +                +LD+
  gi|518651405|ref|YP_008140925.1| 113 KKAL---------------ETLDQ 121
                                       4444...............44443 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.065
                             IF2_N   6 VyeLAkeLgvkskevikkLfkelGi 30 
                                       V  L +eL ++ kev+  +fk  G+
  gi|518651405|ref|YP_008140925.1| 134 VTKLPEELTLRQKEVLYIAFK-NGY 157
                                       667779**********99999.887 PP

  == domain 5  score: 7.6 bits;  conditional E-value: 0.0013
                             IF2_N   9 LAkeLgvkskevikkLfkelGievk 33 
                                       LA eLg++ k v   L k  Gi+ k
  gi|518651405|ref|YP_008140925.1| 169 LASELGISKKAVQSDL-K-RGID-K 190
                                       9***************.9.9999.4 PP

>> DUF5415  Family of unknown function (DUF5415)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1      0.86   2.2e+03      41      57 ..      56      72 ..      49      79 .. 0.67
   2 ?   -1.0   0.1      0.76     2e+03      33      47 ..     103     117 ..      94     120 .. 0.74
   3 ?    9.3   0.0   0.00046       1.2      33      52 ..     179     198 ..     173     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.86
                           DUF5415 41 Gkdkdleeyiyqrerek 57
                                         kd +  iy  +r+k
  gi|518651405|ref|YP_008140925.1| 56 ESIKDDKITIYENQRDK 72
                                      45566666777777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.76
                           DUF5415  33 kvqfdllrGkdkdle 47 
                                       kvq+ +l    k le
  gi|518651405|ref|YP_008140925.1| 103 KVQYKILLKNKKALE 117
                                       889998887778777 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00046
                           DUF5415  33 kvqfdllrGkdkdleeyiyq 52 
                                        vq dl rG dk ++eyi++
  gi|518651405|ref|YP_008140925.1| 179 AVQSDLKRGIDKIVKEYIFN 198
                                       489***************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       929  (0.0518155); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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 0.26s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1339.78
//
Query:       gi|518651406|ref|YP_008140926.1|  [L=132]
Description: hypothetical protein FACI_IFERC00001G0045 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.50
# Mc/sec: 789.51
//
Query:       gi|518651407|ref|YP_008140927.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G0046 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  116.0   0.2    1.2e-33  116.0   0.2    2.4  3  AAA_14    AAA domain
      2e-08   34.4   2.1    2.5e-08   34.1   0.6    2.2  2  DUF4143   Domain of unknown function (DUF4143)
  ------ inclusion threshold ------
      0.016   15.5   0.1      0.048   14.0   0.1    1.8  1  Dpoe2NT   DNA polymerases epsilon N terminal
       0.03   14.1   0.0         11    5.8   0.0    2.5  2  AAA_29    P-loop containing region of AAA domain
      0.078   13.3   0.0        0.3   11.4   0.0    1.9  2  AAA_22    AAA domain


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.2   3.3e-37   1.2e-33       4     131 .]      40     161 ..      38     161 .. 0.90
   2 ?   -1.7   0.1      0.75   2.7e+03      49      71 ..     267     287 ..     233     297 .. 0.69
   3 ?   -1.8   0.1       0.8   2.9e+03      32      50 ..     320     338 ..     308     388 .. 0.51

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 3.3e-37
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkk..ladpekllelileklkeekktylflDEiqevpe 78 
                                       +++++G+Rr+GK+tll+q+i+ ++   +++ y+n++d r+ +  ++d+ekl+++++e++k  + +y ++DEiq++++
  gi|518651407|ref|YP_008140927.1|  40 AIILSGIRRCGKSTLLHQYIS-NI---DNYYYLNFEDARLNDfdSNDFEKLDDVFKELFK--ECNYYMFDEIQNIDK 110
                                       689*****************5.55...7*********99966215578899999999864..6899*********** PP

                            AAA_14  79 wekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       we ++++ +d + + ++++tGSn++llske+ t+l+gr+ +iel+p+sf+Efl
  gi|518651407|ref|YP_008140927.1| 111 WEVFVRQQLDID-K-RFLITGSNASLLSKELGTKLTGRHINIELFPFSFKEFL 161
                                       **********88.3.8************************************7 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.75
                            AAA_14  49 pekllelileklkeekktylflD 71 
                                       p k++  +++++++ +k++ ++D
  gi|518651407|ref|YP_008140927.1| 267 P-KFDYSFKKQIMN-QKKVYCID 287
                                       2.566667777777.77777777 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.8
                            AAA_14  32 silyinldderdkkladpe 50 
                                       +i+y++ ++e d   ++++
  gi|518651407|ref|YP_008140927.1| 320 EIFYYKGNNECDFIVKEKN 338
                                       4555544444442222111 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.6     7e-12   2.5e-08       1     121 [.     203     348 ..      80     349 .. 0.89
   2 ?   -1.5   0.0      0.75   2.7e+03     101     109 ..     357     365 ..     352     395 .. 0.57

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 7e-12
                                       xxxxxxxxxxxxxxxxxx........................................xxxxxxxxxxxxxxxxxxx RF
                           DUF4143   1 erDirklagvrdpeelrk........................................glverlppwsespnskkrl 37 
                                       erDi   ++ rd + l++                                        +l++ +p++      kk++
  gi|518651407|ref|YP_008140927.1| 203 ERDIVARHQLRDSKLLKNialylltntgnefsynklkktfnlgsvntvisfihyledsYLLFTIPKF--DYSFKKQI 277
                                       56666666666666666688899999999999999999999999999********************..999***** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  38 rkspKlyfvDtGLlvallgldkeelledsenkGallEnlVaqeLlkysekegaklyyyrdkngaEvDfvielkggki 114
                                        ++ K+y +D  L+ a    ++++    s ++G+llEn V+  +++     +++++yy+   ++E+Df++++k++  
  gi|518651407|ref|YP_008140927.1| 278 MNQKKVYCIDNKLILA---NSASF----SMDYGRLLENSVFLFIRR----TYKEIFYYKG--NNECDFIVKEKNNIK 341
                                       *************998...22222....3469**************....7899*****8..79******9999999 PP

                                       xxxxxxx RF
                           DUF4143 115 vpiEvKs 121
                                       ++++v s
  gi|518651407|ref|YP_008140927.1| 342 MAVQVTS 348
                                       9998865 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.75
                                       xxxxxxxxx RF
                           DUF4143 101 aEvDfviel 109
                                       +E+D +ie 
  gi|518651407|ref|YP_008140927.1| 357 REIDGIIEA 365
                                       555555542 PP

>> Dpoe2NT  DNA polymerases epsilon N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.3e-05     0.048      22      61 ..     337     376 ..     330     386 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                           Dpoe2NT  22 seaskylaevllsldeeeledwlekiieavekQpLssnli 61 
                                       +++ k  ++v ++l+ ++ ++ ++ iieav+k +Ls+ li
  gi|518651407|ref|YP_008140927.1| 337 KNNIKMAVQVTSELNVDNKKREIDGIIEAVKKFNLSTGLI 376
                                       56789999*****************************998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0036        13      10      39 ..      24      55 ..      16      60 .. 0.72
   2 ?    5.8   0.0    0.0031        11       8      33 ..     110     133 ..     103     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0036
                            AAA_29 10 gtfdg..htieidlkgatlltGpsGsGKSTll 39
                                      gt ++  ++i++d+  a++l+G    GKSTll
  gi|518651407|ref|YP_008140927.1| 24 GTTREklEDINLDMPYAIILSGIRRCGKSTLL 55
                                      5555524455566555899************8 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0031
                            AAA_29   8 NWgtfdghtieidlkgatlltGpsGs 33 
                                        W  f +++++id k  +l+tG + s
  gi|518651407|ref|YP_008140927.1| 110 KWEVFVRQQLDID-K-RFLITGSNAS 133
                                       5***********9.4.39****9976 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   8.3e-05       0.3       7      63 ..      40      96 ..      36     100 .. 0.89
   2 ?   -2.2   0.0       1.3   4.5e+03      95     105 ..     100     110 ..      84     134 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.3e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellra 63
                                       +++ G   +GK+tll ++ ++ d++++ + e++++  ++ +  ++++d+++el+++
  gi|518651407|ref|YP_008140927.1| 40 AIILSGIRRCGKSTLLHQYISNIDNYYYLNFEDARLNDFDSNDFEKLDDVFKELFKE 96
                                      6899************************99999999999999999999999888875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                            AAA_22  95 liiDEaqhlrs 105
                                        + DE+q++++
  gi|518651407|ref|YP_008140927.1| 100 YMFDEIQNIDK 110
                                       57899999952 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2748.28
//
Query:       gi|518651408|ref|YP_008140928.1|  [L=185]
Description: hypothetical protein FACI_IFERC00001G0047 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-12   46.5   0.0    4.6e-12   46.0   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    9.2e-11   42.0   0.2    1.5e-10   41.4   0.2    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    4.4e-09   36.6   0.0    5.8e-09   36.2   0.0    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00048   20.2   0.0    0.00075   19.6   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.037   14.1   0.0       0.37   10.9   0.0    2.1  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.0   0.0   1.3e-15   4.6e-12      17     108 ..      83     176 ..      69     183 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 1.3e-15
                   Acetyltransf_10  17 ispealrerieegealllvaeeggkivGvi..el..rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.e 88 
                                       +++ ++++ i +++  +lva ++g ivG++  +l  +++ ++  +fV +e rgqG+gk++++  +ee +   +k  +
  gi|518651408|ref|YP_008140928.1|  83 LEASEMKKLIGKSKFNVLVAVVDGGIVGFLrgSLleKNRLYVDDIFVLKELRGQGLGKQMMNLFLEEWK---GKAvS 156
                                       677899****9*******************8844355555*************************9983...33339 PP

                   Acetyltransf_10  89 ltvnaspyavpfYeklGFka 108
                                       + ++ ++  v+ +ek+GFk+
  gi|518651408|ref|YP_008140928.1| 157 VGLHTKDFNVKKFEKMGFKK 176
                                       ******************97 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.2   4.1e-14   1.5e-10       4      76 .]      98     176 ..      95     176 .. 0.74

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 4.1e-14
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHH..TT.SEEEEE.EEEETHHHHHHHHHHTT CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLlea..ae.kgiile.qlelnaekaikfYeklG 73 
                                       +v+Va  dg+ivGf++ sll+    +   ++V++e rg+G+G++++++  +e kg  ++  l++++  ++k +ek+G
  gi|518651408|ref|YP_008140928.1|  98 NVLVAVVDGGIVGFLRGSLLEknrLYVDDIFVLKELRGQGLGKQMMNLflEEwKGKAVSvGLHTKD-FNVKKFEKMG 173
                                       7899************9999765555555******************5453366622223333422.46899***** PP

                                       EEE CS
                    Acetyltransf_7  74 Fee 76 
                                       F++
  gi|518651408|ref|YP_008140928.1| 174 FKK 176
                                       *85 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   1.6e-12   5.8e-09      13     117 .]      76     174 ..      62     174 .. 0.76

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.6e-12
                                       HHHHHHHHHHH.HHHHHHSTTC.EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                    Acetyltransf_1  13 fppnedaseee.feesfsleae.gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealee 87 
                                       fp + d+ e+  +++  +   +   lva  dg ++Gf++++       ++ y+++++V +e rg+GlG+++++  +e
  gi|518651408|ref|YP_008140928.1|  76 FPDWWDCLEASeMKKL-IGKSKfNVLVAVVDGGIVGFLRGSLLEK---NRLYVDDIFVLKELRGQGLGKQMMNLFLE 148
                                       4445555555532333.2233335666999*************99...**************************999 PP

                                       HHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  88 rareegikkivlaveedndaairlYeklGF 117
                                       + + + +    l++ + n   ++ +ek+GF
  gi|518651408|ref|YP_008140928.1| 149 EWKGKAVSV-GLHTKDFN---VKKFEKMGF 174
                                       888886644.88776669...999999998 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00075       7      56 ..     102     153 ..      96     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                   Acetyltransf_CG   7 d..egeevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddaree 56 
                                          +g  v+fl+ +  ++++l ++ ++V +elrG+G++k++++  l++ + +
  gi|518651408|ref|YP_008140928.1| 102 AvvDGGIVGFLRGSLLEKNRLYVDDIFVLKELRGQGLGKQMMNLFLEEWKGK 153
                                       4445778899988889999************************999987765 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001      0.37      75     125 ..     123     174 ..      53     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                       EEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.SSHHHHHTTT- CS
                    Acetyltransf_9  75 gvtgVavapehrgrgvlskLlaraleemreegqplsllfP.ssipiYrrfGy 125
                                       +v ++ v  e rg+g+ +++++ +lee++ + +++ l +  ++++ ++++G+
  gi|518651408|ref|YP_008140928.1| 123 YVDDIFVLKELRGQGLGKQMMNLFLEEWKGKAVSVGLHTKdFNVKKFEKMGF 174
                                       677899999********************76555544433666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.32s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1195.03
//
Query:       gi|518651409|ref|YP_008140929.1|  [L=323]
Description: hypothetical protein FACI_IFERC00001G0048 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2323.63
//
Query:       gi|518651410|ref|YP_008140930.1|  [L=218]
Description: hypothetical protein FACI_IFERC00001G0049 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.6        5.5    6.9   0.1    2.7  2  YL1_C     YL1 nuclear protein C-terminal domain


Domain annotation for each model (and alignments):
>> YL1_C  YL1 nuclear protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0003       5.5      15      28 ..     111     124 ..     108     124 .. 0.88
   2 ?    2.3   0.1    0.0079   1.4e+02      18      29 .]     130     141 ..     127     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0003
                             YL1_C  15 kTgLpYanveaykv 28 
                                       +T+L Y nv ay++
  gi|518651410|ref|YP_008140930.1| 111 VTNLQYTNVFAYEI 124
                                       7***********85 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0079
                             YL1_C  18 LpYanveaykvI 29 
                                       ++Y n e++k++
  gi|518651410|ref|YP_008140930.1| 130 INYKNYEEFKQV 141
                                       68********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 1614.53
//
Query:       gi|518651411|ref|YP_008140931.1|  [L=165]
Description: hypothetical protein FACI_IFERC00001G0050 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1096.73
//
Query:       gi|518651412|ref|YP_008140932.1|  [L=148]
Description: hypothetical protein FACI_IFERC00001G0051 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1093.70
//
Query:       gi|518651413|ref|YP_008140933.1|  [L=422]
Description: hypothetical protein FACI_IFERC00001G0052 [Ferroplasma acidarmanus fer1]
Scores for complete 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-48  163.7  34.9    5.7e-31  107.9   9.5    2.1  2  Sugar_tr  Sugar (and other) transporter
    1.4e-39  136.0  63.7    5.4e-37  127.5  36.7    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.055   13.4   0.7          8    6.4   0.0    3.2  3  DUF5411   Family of unknown function (DUF5411)


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.9   9.5   9.5e-35   5.7e-31       6     204 ..      34     216 ..      29     226 .. 0.89
   2 !   65.4  14.6     7e-22   4.2e-18     251     447 ..     226     413 ..     214     418 .. 0.86

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 9.5e-35
                                       HHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHH CS
                          Sugar_tr   6 alggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksllia 82 
                                       ++g +l gYd+ +i  ++ ++ ++ +f+  ++            ++  + +vG +iG+ ++gll+dr+GRkk++   
  gi|518651413|ref|YP_008140933.1|  34 SMGIFLDGYDLSIITMAILVIPAQLDFTKMEYI-----------FVDISSFVGMLIGAPVLGLLSDRIGRKKIFGLD 99 
                                       566688888888888888888866655544433...........44456789************************* PP

                                       HHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  83 avlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifgl 159
                                        ++fv+ a+  ++++   ++  l+++R+l+Gig+G+ + ++++ ++E++pkk Rg+l      ++ +G +v++++++
  gi|518651413|ref|YP_008140933.1| 100 LIFFVVFAITAGLSN---NFIELFLSRFLMGIGIGGDYPISSTMMAEFSPKKSRGKLLISMVGMYWLGAFVSSFVNY 173
                                       ***************...****************************************99999************** PP

                                       HHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-H CS
                          Sugar_tr 160 glnktsnadgwrillglqlvpallllilllflPESPrylvekgke 204
                                       ++  + +   wr+++ +  ++a+ +++l++ +PESPr+l++k+k+
  gi|518651413|ref|YP_008140933.1| 174 IFVINAY--FWRYTFIIGGLIAIPVILLRFKIPESPRWLLSKEKD 216
                                       **88888..8********************************986 PP

  == domain 2  score: 65.4 bits;  conditional E-value: 7e-22
                                       ...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH....HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHH CS
                          Sugar_tr 251 vrqrlligvvlqifqqltGinaimyysptifenlglsks....llvtiivgvvnfvatfvaiflvdrfGRRtllllG 323
                                        ++ +li v+l++f + +    + +y p+if+ lg++++    ++++++++v  +   ++a++l d++GRR l + G
  gi|518651413|ref|YP_008140933.1| 226 KFYTMLIFVLLAWFVFDVAAYGLGFYYPVIFSALGFKDQfrqiAEISMLISVGGISGYLIALPLADKLGRRFLIIAG 302
                                       6788999999999999999999999****************9999******************************** PP

                                       HHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 324 aagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanf 400
                                       +++m++++++ +    +++ +    +  a+ f++lf +lf+  +g v  ++ +E+f++s+Rs+++ +a+ v+ +  +
  gi|518651413|ref|YP_008140933.1| 303 FFIMSVLLILGS----VIKIT----GLYAVPFYFLF-VLFEQWVGAVTLFYPTEIFDTSIRSSVQGLATSVSRVGAI 370
                                       *****9877665....22222....45555666666.89999*********************************** PP

                                       HHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCC CS
                          Sugar_tr 401 lisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtlee 447
                                          +lfp +      +++  +fa++ vl++++v f  petk+++le+
  gi|518651413|ref|YP_008140933.1| 371 MGIVLFPLFPL----FKSLSIFAAFSVLGLFVVIFLAPETKNKSLEQ 413
                                       **999998643....45678*************************97 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.5  36.7     9e-41   5.4e-37       3     352 ..      35     372 ..      33     373 .. 0.88
   2 !   22.3  19.0   8.8e-09   5.3e-05      40     178 ..     274     409 ..     271     418 .. 0.82

  Alignments for each domain:
  == domain 1  score: 127.5 bits;  conditional E-value: 9e-41
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       +++fl +++ si+++a+   +  +l +++ e+ ++    ++g+++++++lG lsdr+Gr++++ l l++f+++ ++ 
  gi|518651413|ref|YP_008140933.1|  35 MGIFLDGYDLSIITMAIL-VIPAQLDFTKMEYIFVDISSFVGMLIGAPVLGLLSDRIGRKKIFGLDLIFFVVF-AIT 109
                                       689**************9.8999999***********************************************.555 PP

                             MFS_1  80 l.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWrav 153
                                       + + s+ +  l+++r+l+G+g g+ +p++ +++a+ +pk+ rg+ +  + +++ lGa +   +  +++  ++ Wr++
  gi|518651413|ref|YP_008140933.1| 110 AgL-SNNFiELFLSRFLMGIGIGGDYPISSTMMAEFSPKKSRGKLLISMVGMYWLGAFVSSFVNYIFViNAYFWRYT 185
                                       546.78887***********************************************************88888**** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw....illialllfffgfsgl 226
                                       f+i +++++ +++   l +  ++++r+  s++++             k+ +k+p ++    ++l+a+++f ++ +gl
  gi|518651413|ref|YP_008140933.1| 186 FIIGGLIAIPVIL---LRFKIPESPRWLLSKEKD-----------YKKYNKKSPKFYtmliFVLLAWFVFDVAAYGL 248
                                       ***********99...9*****************...........6777778887755345577777777777777* PP

                             MFS_1 227 ltllplylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavl 302
                                        ++ p++  + lg++  + +++ +++l++++g+ + l+a  l+d+lgr   ++l+++++++++++l+l +v++ + l
  gi|518651413|ref|YP_008140933.1| 249 GFYYPVI-FSALGFKdQFRQIAEISMLISVGGISGYLIALPLADKLGR---RFLIIAGFFIMSVLLILGSVIKITGL 321
                                       ******7.********7777777788888888888**********997...66666666666666666666666688 PP

                             MFS_1 303 lllvlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggalg 352
                                       ++++++++ + +   v +  l + ++ + ++ + +++gl+++++ +g+++g
  gi|518651413|ref|YP_008140933.1| 322 YAVPFYFLFVlFEQWVGAVTLFYPTEIFDTSIRSSVQGLATSVSRVGAIMG 372
                                       8887777555599999999999999***********************987 PP

  == domain 2  score: 22.3 bits;  conditional E-value: 8.8e-09
                             MFS_1  40 lyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa..sslwlllvlrvlqGlgagalfpagaaliadw 113
                                       l ++g + + l++ +l+d++Grr ++++g++++++  l+l  ++  ++l + + + +l  l++ ++ ++ + + +++
  gi|518651413|ref|YP_008140933.1| 274 LISVGGISGYLIALPLADKLGRRFLIIAGFFIMSVL-LILGsVIkiTGL-YAVPFYFLFVLFEQWVGAVTLFYPTEI 348
                                       56889999999*************************.666644233333.377778899999999************ PP

                             MFS_1 114 fpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                                       f  + r+++ gl+++ + +Gai+g +l +l+  ++   ++f ++ +++l++++   +l pe++ +
  gi|518651413|ref|YP_008140933.1| 349 FDTSIRSSVQGLATSVSRVGAIMGIVLFPLFP-LFKSLSIFAAFSVLGLFVVI---FLAPETKNK 409
                                       *****************************998.88888888888888888866...565555444 PP

>> DUF5411  Family of unknown function (DUF5411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.0    0.0013         8      66     101 ..     114     149 ..     106     155 .. 0.93
   2 ?    2.1   0.0     0.029   1.7e+02       5      24 ..     181     200 ..     177     216 .. 0.89
   3 ?    0.2   0.8      0.11   6.7e+02       9      27 ..     297     315 ..     292     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0013
                           DUF5411  66 ekfvevfirrfaesvtlskeykidfydiyeePPkvs 101
                                       + f+e f+ rf   + ++ +y i+ + + e  Pk s
  gi|518651413|ref|YP_008140933.1| 114 NNFIELFLSRFLMGIGIGGDYPISSTMMAEFSPKKS 149
                                       68****************************999976 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.029
                           DUF5411   5 lwgylllllGiivvsvlllv 24 
                                       +w y  ++ G+i + v+ll 
  gi|518651413|ref|YP_008140933.1| 181 FWRYTFIIGGLIAIPVILLR 200
                                       69***************995 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.11
                           DUF5411   9 lllllGiivvsvlllvqrl 27 
                                       +l++ G +++svll++ ++
  gi|518651413|ref|YP_008140933.1| 297 FLIIAGFFIMSVLLILGSV 315
                                       68999*********99776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       897  (0.0500307); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3023.41
//
Query:       gi|518651414|ref|YP_008140934.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G0053 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0051   17.2   0.3      0.017   15.6   0.1    1.7  2  CcdA             Post-segregation antitoxin CcdA
  ------ inclusion threshold ------
       0.03   14.2   1.5      0.033   14.1   1.5    1.1  1  NleF_casp_inhib  NleF caspase inhibitor
      0.042   14.2   0.1      0.051   13.9   0.1    1.2  1  Imm57            Immunity protein 57
      0.049   13.7   0.3      0.094   12.8   0.2    1.5  2  P_C10            Protein C10
      0.078   13.2   0.1       0.13   12.4   0.1    1.4  1  CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
       0.11   12.7   1.1       0.11   12.6   1.1    1.0  1  DUF3347          Protein of unknown function (DUF3347)
       0.12   12.6   1.8       0.15   12.3   0.7    1.6  2  Ca_chan_IQ       Voltage gated calcium channel IQ domain


Domain annotation for each model (and alignments):
>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   6.6e-06     0.017       8      48 ..      11      51 ..       3      55 .. 0.84
   2 ?    2.7   0.1      0.07   1.8e+02       9      40 ..      43      74 ..      42      75 .] 0.88

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 6.6e-06
                              CcdA  8 ldsdllaqAralgiNlSatleeaLaeevkeekaerwkeenr 48
                                      ++++  ++ r+lgiN  +++ +a+ +e+k+++  +  e+ +
  gi|518651414|ref|YP_008140934.1| 11 ITKEDREELRKLGINPTEIIRKAIHDEIKRARDNELMEKMK 51
                                      789999***********************999877666555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.07
                              CcdA  9 dsdllaqAralgiNlSatleeaLaeevkeeka 40
                                      d +l+++ +++   lS++  + L + ++e ++
  gi|518651414|ref|YP_008140934.1| 43 DNELMEKMKKVAPVLSKLKMDELVKDIREDRE 74
                                      679999***********999999999998876 PP

>> NleF_casp_inhib  NleF caspase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   1.5   1.3e-05     0.033      71     138 ..       4      69 ..       1      73 [. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.3e-05
                   NleF_casp_inhib  71 kveLkegitaedRdnylkdlvalyq.iknavkekidnakiktikdsvkkvvdeihngkvsvdaklagDl 138
                                        ++L+  it+edR+++ k  ++  + i++a++++i+ a+ +   + +kkv+ +  + k+     l++D+
  gi|518651414|ref|YP_008140934.1|   4 YTTLSAKITKEDREELRKLGINPTEiIRKAIHDEIKRARDNELMEKMKKVAPVLSKLKM---DELVKDI 69 
                                       589*************9988886652799************999999999988877776...5566665 PP

>> Imm57  Immunity protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1     2e-05     0.051      54      99 ..      27      72 ..       5      75 .] 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2e-05
                             Imm57 54 sklmrykidaGlsesytcylldkskkvrtylknlkplelvkdciee 99
                                      ++++r  i   +  +    l++k kkv + l  lk +elvkd  e+
  gi|518651414|ref|YP_008140934.1| 27 TEIIRKAIHDEIKRARDNELMEKMKKVAPVLSKLKMDELVKDIRED 72
                                      57888888888888999999**********************9876 PP

>> P_C10  Protein C10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         1   2.6e+03      70      84 ..       3      17 ..       1      31 [. 0.67
   2 ?   12.8   0.2   3.7e-05     0.094      27      54 ..      36      63 ..      25      68 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
                             P_C10 70 kfaqlvrelekedke 84
                                      k++ l  ++ ked+e
  gi|518651414|ref|YP_008140934.1|  3 KYTTLSAKITKEDRE 17
                                      566666667777754 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.7e-05
                             P_C10 27 eeakesagndmlkvmqlvlPvvvqiqme 54
                                      +e+k++ +n+++  m++v Pv+ +++m+
  gi|518651414|ref|YP_008140934.1| 36 DEIKRARDNELMEKMKKVAPVLSKLKMD 63
                                      78999********************997 PP

>> CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   5.1e-05      0.13      18      38 ..      44      64 ..      42      67 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.1e-05
                   CSN4_RPN5_eIF3a 18 NeliEKIasaePeWmakalee 38
                                      Nel+EK+++++P+  + +++e
  gi|518651414|ref|YP_008140934.1| 44 NELMEKMKKVAPVLSKLKMDE 64
                                      9*************9999998 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.1   4.4e-05      0.11      54     125 ..       1      72 [.       1      75 [] 0.93

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                           DUF3347  54 lesYlklkdALvaddakeakkaakkleeklkavdtsklkekekkelkeiseelkekaekiaeskdieeqRea 125
                                       +++Y  l   ++++d +e +k + + +e +++    ++k+ + +el+e++++++  ++k++  + +++ Re+
  gi|518651414|ref|YP_008140934.1|   1 MNKYTTLSAKITKEDREELRKLGINPTEIIRKAIHDEIKRARDNELMEKMKKVAPVLSKLKMDELVKDIRED 72 
                                       589******************************9**************************999877777764 PP

>> Ca_chan_IQ  Voltage gated calcium channel IQ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.84   2.2e+03      24      31 ..      14      21 ..       4      33 .. 0.56
   2 ?   12.3   0.7   5.9e-05      0.15      19      54 ..      35      71 ..      27      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.84
                        Ca_chan_IQ 24 qadeelrk 31
                                      +  eelrk
  gi|518651414|ref|YP_008140934.1| 14 EDREELRK 21
                                      22334443 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.9e-05
                        Ca_chan_IQ 19 eeeldqa.deelrkeikkiwpslskklldllvppeke 54
                                      ++e+++a d+el + +kk+ p lsk  +d+lv+  +e
  gi|518651414|ref|YP_008140934.1| 35 HDEIKRArDNELMEKMKKVAPVLSKLKMDELVKDIRE 71
                                      35666666************************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1276  (0.0711696); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 615.01
//
Query:       gi|518651415|ref|YP_008140935.1|  [L=127]
Description: hypothetical protein FACI_IFERC00001G0054 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0045   17.5   0.0     0.0068   16.9   0.0    1.2  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   3.8e-07    0.0068       2     120 ..       3     115 ..       3     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-07
                                       EE-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHS...SCHCHHHHHHHHHHHHHHHTSEEEEBCH CS
                               PIN   2 vlDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlar...rkskrekaaelvelllllsalkilpida 75 
                                       +lDTs +++l+r+ + +    ++l++    +t +l+++E+ +vl +   +k ++ k+++      l + ++ ++   
  gi|518651415|ref|YP_008140935.1|   3 ILDTSSIFNLFRRGKYT----EILDN----ATIPLAIYEVGNVLWKnsnVKNTISKEEAKDIGSVLFELINSIEQVI 71 
                                       699*****999777766....78877....999*************7773333333333333333333344444445 PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       + +  ++ +al  gl+ +D   +   +e+g  li t D ++ r+a
  gi|518651415|ref|YP_008140935.1|  72 PTWSSVLSLALTEGLTFYDSSFLGASIERGYGLI-TDDIKLFRIA 115
                                       67888888888889********************.***9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.27s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 948.12
//
Query:       gi|518651416|ref|YP_008140936.1|  [L=50]
Description: hypothetical protein FACI_IFERC00001G0055 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    8.6e-06   25.3   0.0    9.1e-06   25.2   0.0    1.0  1  Thiolase_N  Thiolase, N-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   5.1e-10   9.1e-06       2      42 ..       9      49 ..       8      50 .] 0.96

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 5.1e-10
                                      EEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-G CS
                        Thiolase_N  2 vivsaartpigkfggslkdlsaeeLlaealkallekagvdp 42
                                      +i++++rtpigk +gslkd+  ++Ll ++ ++ l+ +++dp
  gi|518651416|ref|YP_008140936.1|  9 YIIDSKRTPIGKRNGSLKDVHPVDLLGNLTRDTLAINKIDP 49
                                      79************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       177  (0.00987227); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.35
# Mc/sec: 429.35
//
Query:       gi|518651417|ref|YP_008140937.1|  [L=109]
Description: trehalose synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.23   10.5   5.2       0.27   10.2   5.2    1.1  1  COX15-CtaA   Cytochrome oxidase assembly protein
        3.2    7.1  11.9        3.8    6.8  11.9    1.1  1  TssN         Type VI secretion system, TssN
        9.5    6.4   9.5         16    5.6   4.4    2.5  2  Insulin_TMD  Insulin receptor trans-membrane segment


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   5.2   4.6e-05      0.27      88     161 ..      23      94 ..      17     106 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 4.6e-05
                        COX15-CtaA  88 llGllilvpllyflakkrisrelkkllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllall 161
                                       +lG+l++++ +++ +  +   +l++l+++ +ll+++ G++G   + ++   ++  s+y+  +H+lla+ +++  
  gi|518651417|ref|YP_008140937.1|  23 SLGVLLFIMSILSYVYTKNIIRLAHLAIVNILLIVITGIIGSGFIILKT--NSFYSTYIPYLHMLLAIGIISNY 94 
                                       5899999999999999999999**********************99996..8999************9998754 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8  11.9   0.00064       3.8       8      86 ..      25     102 ..      15     108 .. 0.65

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.00064
                              TssN   8 pllavilllilsliakknkllkkkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkf 84 
                                        +l +i++ ils++ +kn       +i+ iLl++++  + + + +lk++     yi +  + l +Gi+  y+++  +
  gi|518651417|ref|YP_008140937.1|  25 GVLLFIMS-ILSYVYTKNIIRLAHLAIVNILLIVITGIIGSGFIILKTNSFYSTYIPYLHMLLAIGIISNYAVMLGI 100
                                       23334444.455555555555555566666666666555566666***********************999777665 PP

                              TssN  85 fk 86 
                                       ++
  gi|518651417|ref|YP_008140937.1| 101 KR 102
                                       55 PP

>> Insulin_TMD  Insulin receptor trans-membrane segment
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.5     0.012        69       3      38 ..       4      38 ..       3      44 .. 0.78
   2 ?    5.6   4.4    0.0027        16      21      40 ..      52      70 ..      35      72 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.012
                       Insulin_TMD  3 FYvadyldpsnivkIvigPviciillllvigavfvv 38
                                      FY+    +p  +  I i  + + +ll ++    +v 
  gi|518651417|ref|YP_008140937.1|  4 FYLSQIANP-ANSEILILHISLGVLLFIMSILSYVY 38
                                      899998999.77888888888888888877777775 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0027
                       Insulin_TMD 21 Pviciillllvigavfvvvk 40
                                        i++i++ ++ig+ f+++k
  gi|518651417|ref|YP_008140937.1| 52 N-ILLIVITGIIGSGFIILK 70
                                      3.56777889999*****99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 749.48
//
Query:       gi|518651418|ref|YP_008140938.1|  [L=515]
Description: hypothetical protein FACI_IFERC00001G0057 [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   75.9   3.6      3e-19   69.9   1.0    2.8  2  ATPase_2       ATPase domain predominantly from Archaea
    6.5e-17   61.8   1.0    6.5e-17   61.8   1.0    2.2  2  DUF234         Archaea bacterial proteins of unknown function
    9.5e-12   45.1   1.2    1.9e-11   44.1   0.2    2.1  2  AAA_14         AAA domain
    1.1e-07   32.1   0.0    2.2e-07   31.2   0.0    1.4  1  AAA_22         AAA domain
    1.4e-06   28.1   0.2    8.5e-06   25.6   0.0    2.3  3  AAA_24         AAA domain
    5.4e-06   26.9   0.0    0.00022   21.7   0.0    2.3  1  AAA_16         AAA ATPase domain
    0.00037   20.0   0.1     0.0012   18.3   0.0    1.8  2  TniB           Bacterial TniB protein
     0.0092   16.0   0.0      0.036   14.2   0.0    2.0  1  LPD11          Large polyvalent protein-associated domain 11
  ------ inclusion threshold ------
      0.024   15.1   0.0      0.063   13.7   0.0    1.7  1  DUF3398        Domain of unknown function (DUF3398)
      0.036   14.0   0.3      0.095   12.6   0.1    1.8  2  TrmB           Sugar-specific transcriptional regulator TrmB
      0.047   13.9   0.0       0.13   12.5   0.0    1.8  1  Roc            Ras of Complex, Roc, domain of DAPkinase
      0.047   13.8   0.1       0.17   12.0   0.1    2.0  1  DUF4143        Domain of unknown function (DUF4143)
      0.055   13.8   0.2        7.1    7.0   0.0    2.9  3  UvrA_DNA-bind  UvrA DNA-binding domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   1.0   2.2e-22     3e-19       1     233 []      63     258 ..      63     258 .. 0.84
   2 ?   -2.8   0.1       3.5   4.9e+03     149     162 ..     286     299 ..     267     352 .. 0.51

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 2.2e-22
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F+dR +el++le + ++++++ ++iYG++++GKt+Ll e+++n+++     +++ + +e  ++++++          
  gi|518651418|ref|YP_008140938.1|  63 FVDRINELQNLEDLSNENRAQLILIYGRRRIGKTTLLYEFLKNKDN---ALFFMADASENILDTFSDI--------- 127
                                       9******************************************944...6777777776666555555......... PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkk..iiiiiDelqklidlglngaellvkeLlnliesl 152
                                       +++    +++            +  f++++++++ +  k k+   i++iDe+q+l    l   ++    L++ +e+ 
  gi|518651418|ref|YP_008140938.1| 128 ASE----KFN------------NVRFQNWDNFFDFLYSKSKEnrFIVVIDEFQYLT-AVL---KSWPTILQRHWEK- 183
                                       222....233............3347899999999988888888************.334...6999999999998. PP

                          ATPase_2 153 tkekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkP 227
                                       +k +++++v+ +s  + + +  + + s l+gr+++ +++++l      nf++ g+    +   +++ +iy ++GG P
  gi|518651418|ref|YP_008140938.1| 184 LKTTKIFLVLSGSLVSSIYRiAMGYGSALYGRKTGeMNIKPL------NFIDTGS--FFNTDINNLVKIYMILGGVP 252
                                       8999*********98888887899******************......9999984..4444667899********** PP

                          ATPase_2 228 kalvel 233
                                       ++l+e+
  gi|518651418|ref|YP_008140938.1| 253 RYLEEF 258
                                       ***985 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.5
                          ATPase_2 149 iesltkekhlcvvi 162
                                       + +  k+    +++
  gi|518651418|ref|YP_008140938.1| 286 LHEEFKDLTSYFAV 299
                                       33333333333332 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       4.6   6.3e+03       8       8 ..     150     150 ..     112     192 .. 0.57
   2 !   61.8   1.0   4.7e-20   6.5e-17       1      92 [.     364     463 ..     364     474 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.6
                            DUF234   8 n 8  
                                       +
  gi|518651418|ref|YP_008140938.1| 150 K 150
                                       1 PP

  == domain 2  score: 61.8 bits;  conditional E-value: 4.7e-20
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwW.........kkee 68 
                                       wf+fvyp rs++e++++e v++kik+e+n+ +g +FE ++r+lll   +++klpf ++ +Gr W         +++ 
  gi|518651418|ref|YP_008140938.1| 364 WFKFVYPFRSLLEMNNEEVVISKIKSEINTLFGHRFEFIARDLLL--HNQDKLPFAISYIGRSWgklknkvgnNSNY 438
                                       *********************************************..55779***************9999977899 PP

                            DUF234  69 eiDivaldeeekkalfgEvKwkn.s 92 
                                       e+D+v  d ++    ++EvK+k+ s
  gi|518651418|ref|YP_008140938.1| 439 EFDVVIQDAKKYYTGIFEVKYKKlS 463
                                       ***********99*********954 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.2   1.4e-14   1.9e-11       3     127 ..      83     227 ..      81     230 .. 0.72
   2 ?   -3.0   0.1       4.9   6.8e+03      22      55 ..     331     363 ..     325     381 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 1.4e-14
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell......vkkesilyinldderdkkladpe.....kllelileklkeekktyl 68 
                                       ++++i G Rr+GKTtll++++k++       +++++ +  ++ d   +k+++ +     ++ +++ +k k e++ ++
  gi|518651418|ref|YP_008140938.1|  83 QLILIYGRRRIGKTTLLYEFLKNKDnalffmADASENILDTFSDIASEKFNNVRfqnwdNFFDFLYSKSK-ENRFIV 158
                                       5789*****************9988666665444444444444444444443223334355666666644.58999* PP

                            AAA_14  69 flDEiqev....pewekalkslvd..egknldvivtGSnskllskeia....tslagrva.eielyplsf 127
                                       ++DE q++    ++w ++l++  +  +++++ ++++GS+ + +++ ia    + l gr + e+++ pl+f
  gi|518651418|ref|YP_008140938.1| 159 VIDEFQYLtavlKSWPTILQRHWEklKTTKIFLVLSGSLVSSIYR-IAmgygSALYGRKTgEMNIKPLNF 227
                                       *******9888899999***9999544478899999*99988876.444555889988876899999988 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.9
                            AAA_14  22 likell.vkkesilyinldderdkkladpekllel 55 
                                       li+ +l +++esi+  n+ + + + ++d+  l ++
  gi|518651418|ref|YP_008140938.1| 331 LIRAELiAREESIIKSNVRNIHSYYIKDN--LFNF 363
                                       56666667788888888888877666644..4444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.0   1.6e-10   2.2e-07       4     129 ..      81     195 ..      77     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-10
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelle 80 
                                       +a++++++G   +GKTtll ++l++          ++  +f+ + +s++  d +++++++  ++     ++ + +++
  gi|518651418|ref|YP_008140938.1|  81 RAQLILIYGRRRIGKTTLLYEFLKN----------KDNALFFMADASENILDTFSDIASEKFNNVRF--QNWDNFFD 145
                                       789*********************9..........78899999999999************999999..9******* PP

                            AAA_22  81 aleqalraravielliiDEaqhlrs..eealeeL..rsllnlsrkgvqliLvG 129
                                        l+  +++ +   +++iDE+q+l +   + + ++  r++ +l+++++ l+L G
  gi|518651418|ref|YP_008140938.1| 146 FLYSKSKENRF--IVVIDEFQYL-TavLKSWPTIlqRHWEKLKTTKIFLVLSG 195
                                       ***********..**********.43444444443444444357777777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   6.2e-09   8.5e-06       4      77 ..      84     166 ..      81     187 .. 0.72
   2 ?   -2.0   0.0       1.9   2.6e+03     151     175 ..     314     339 ..     301     355 .. 0.68
   3 ?   -2.0   0.0       1.8   2.4e+03     151     169 ..     427     445 ..     423     464 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.2e-09
                            AAA_24   4 kiliyGpsgiGKTtlakel...gpkplfidtekGlksldadkfpdie..........swedfldevvelaaeladyk 67 
                                        iliyG   iGKTtl++e+   ++++lf+  +++ + ld   f di           +w++f d++ + ++e++   
  gi|518651418|ref|YP_008140938.1|  84 LILIYGRRRIGKTTLLYEFlknKDNALFFMADASENILD--TFSDIAsekfnnvrfqNWDNFFDFLYSKSKENR--F 156
                                       69***************************6666443333..233333345555547788888888877766666..6 PP

                            AAA_24  68 tlviDtidel 77 
                                       ++viD  + l
  gi|518651418|ref|YP_008140938.1| 157 IVVIDEFQYL 166
                                       7888876655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                            AAA_24 151 klgkkt.anelkeevDlvlranlkre 175
                                       +++++  +n+l + +D+++ra+l   
  gi|518651418|ref|YP_008140938.1| 314 SVKSRIaQNKLSKVLDVLIRAELIAR 339
                                       444444489999999***99998643 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.8
                            AAA_24 151 klgkktanelkeevDlvlr 169
                                       kl++k++n+ ++e+D+v++
  gi|518651418|ref|YP_008140938.1| 427 KLKNKVGNNSNYEFDVVIQ 445
                                       6788999999999999997 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.6e-07   0.00022       5      76 ..      66     124 ..      62     179 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.6e-07
                            AAA_16   5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       R +el+ L+++    +++r +l+l++G + +GK++l+ e+l+  +kd+++f+ +++ ++        +++++
  gi|518651418|ref|YP_008140938.1|  66 RINELQNLEDL---SNENRAQLILIYGRRRIGKTTLLYEFLK--NKDNALFFMADASEN--------ILDTF 124
                                       55555555554...5577779********************8..777799999999999........66666 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.5e-07    0.0012      20      61 ..      67     108 ..      55     123 .. 0.89
   2 ?   -3.7   0.0       4.7   6.5e+03     122     132 ..     157     167 ..     156     169 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.5e-07
                              TniB  20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61 
                                       +++L++L +  +++r + +l++G+  +GKt+++ +F +++ +
  gi|518651418|ref|YP_008140938.1|  67 INELQNLEDLSNENRAQLILIYGRRRIGKTTLLYEFLKNKDN 108
                                       678999*******************************99865 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.7
                              TniB 122 vLiiDEihnll 132
                                       +++iDE++ l 
  gi|518651418|ref|YP_008140938.1| 157 IVVIDEFQYLT 167
                                       689****9775 PP

>> LPD11  Large polyvalent protein-associated domain 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.6e-05     0.036      16      54 ..     449     487 ..     443     491 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                             LPD11  16 eyylgygnrnekhLwagsveeqieemkelynslpedeKP 54 
                                       +yy+g  + + k+L +g+  + i++m+e+yn+++ +  P
  gi|518651418|ref|YP_008140938.1| 449 KYYTGIFEVKYKKLSYGDAYKIIKNMQEIYNNISVNSHP 487
                                       6999999989999*********************99887 PP

>> DUF3398  Domain of unknown function (DUF3398)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.6e-05     0.063      26      96 ..     404     475 ..     400     489 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.6e-05
                           DUF3398  26 relllfPqdDv..evkvlpreirtlqstvPeeaekeldslVreciktYtsdwkvveykyekysgsfrelpkkk 96 
                                       r+lll  qd +   ++++ r++  l++ v ++++ e d  ++++ k+Yt  ++v +yk  +y+  ++ +++++
  gi|518651418|ref|YP_008140938.1| 404 RDLLLHNQDKLpfAISYIGRSWGKLKNKVGNNSNYEFDVVIQDAKKYYTGIFEV-KYKKLSYGDAYKIIKNMQ 475
                                       8899999997522679************************************99.999999999999988877 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   6.9e-05     0.095      13      57 ..     295     342 ..     291     357 .. 0.87
   2 ?   -3.1   0.0       5.7   7.8e+03      34      47 ..     462     475 ..     459     476 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.9e-05
                                       HCHHHH...HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB  13 vYlaLl...klgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57 
                                        Y+a+l    +g  t +ei+ ++ + ++k  +vL  L+++ l+ re++
  gi|518651418|ref|YP_008140938.1| 295 SYFAVLdtiGSGATTFNEISVKSRIAQNKLSKVLDVLIRAELIAREES 342
                                       68888877678999*******************************987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.7
                                       SSCHCHHHHHHHHH CS
                              TrmB  34 vprskvYevLrsLe 47 
                                       +++  +Y++++++ 
  gi|518651418|ref|YP_008140938.1| 462 LSYGDAYKIIKNMQ 475
                                       678899**999985 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.1e-05      0.13       2      62 ..      85     141 ..      84     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                                       EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEE CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWD 62 
                                       +++ G  ++GKt+ll +f+++k +      + +d +++ + +++ +  ++k ++v+++ WD
  gi|518651418|ref|YP_008140938.1|  85 ILIYGRRRIGKTTLLYEFLKNKDNA---LFFMADASENILDTFSDIA-SEKFNNVRFQNWD 141
                                       6788***************887654...4555566565555566654.457899******9 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00012      0.17      66     121 ..     386     459 ..     370     460 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                                       x......xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx..........x.xxxxxxxxxxxxxxxxxx.xxxx RF
                           DUF4143  66 s......enkGallEnlVaqeLlky.sekegaklyyyrdk..........n.gaEvDfvielkggkivpi.EvKs 121
                                       +      +++G+ +E ++a++Ll + ++k    ++y  ++          n ++E D+vi+++++ + +i EvK+
  gi|518651418|ref|YP_008140938.1| 386 KikseinTLFGHRFE-FIARDLLLHnQDKLPFAISYIGRSwgklknkvgnNsNYEFDVVIQDAKKYYTGIfEVKY 459
                                       344455578888888.6666666655888888888888889999*****966*********99888877559998 PP

>> UvrA_DNA-bind  UvrA DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.075     1e+02      30      69 ..     163     202 ..     147     221 .. 0.84
   2 ?    7.0   0.0    0.0052       7.1      22      59 ..     257     294 ..     247     298 .. 0.88
   3 ?   -2.4   0.0       4.3   5.9e+03      57      77 ..     460     480 ..     434     495 .. 0.58

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.075
                                       HHHHHHHHTTTS------------S-THHHHH----.... CS
                     UvrA_DNA-bind  30 rqlleavaehygidldtpfkeLpeeqkdilLyGsgeekik 69 
                                       +q+l av++   + l+  +++L+  +  ++L Gs   +i 
  gi|518651418|ref|YP_008140938.1| 163 FQYLTAVLKSWPTILQRHWEKLKTTKIFLVLSGSLVSSIY 202
                                       7899*****************************9765554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0052
                                       ..TT-HHHHHHHHHHHTTTS------------S-THHH CS
                     UvrA_DNA-bind  22 sskkssyyrqlleavaehygidldtpfkeLpeeqkdil 59 
                                         +++++y++++++++++  +  + p++ L ee kd+ 
  gi|518651418|ref|YP_008140938.1| 257 EFDSGNIYNNIIKKILNKNSFLYNEPLNLLHEEFKDLT 294
                                       56899****************************99975 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.3
                                       HHHHH----............ CS
                     UvrA_DNA-bind  57 dilLyGsgeekikveyksggr 77 
                                       + l yG+  ++ik  ++ +++
  gi|518651418|ref|YP_008140938.1| 460 KKLSYGDAYKIIKNMQEIYNN 480
                                       344455555444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       904  (0.0504211); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3608.55
//
Query:       gi|518651419|ref|YP_008140939.1|  [L=222]
Description: hypothetical protein FACI_IFERC00001G0058 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1552  (0.0865637); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.32s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 1454.31
//
Query:       gi|518651420|ref|YP_008140940.1|  [L=344]
Description: hypothetical protein FACI_IFERC00001G0059 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-31  108.8  41.4      4e-31  108.5  41.4    1.0  1  SLAC1     Voltage-dependent anion channel


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.5  41.4   2.3e-35     4e-31       2     323 ..       9     331 ..       9     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 108.5 bits;  conditional E-value: 2.3e-35
                             SLAC1   2 ftpawFaivMGtgilalllk.alp....arglriislilfllalvlfllllvlyllrfilypeavrkelrhpveslf 73 
                                       f  +wF++v +t +++ ++    +    +  l++ ++++f l++++f+++++l+++r +   ++   ++++ ++  f
  gi|518651420|ref|YP_008140940.1|   9 FGSEWFGMVIATLAVSQVFFlV-SkylvNIDLKYTGEVFFGLGIIMFIVIFILWAIRGLTIHDKKYLHWNNLTRLSF 84 
                                       6779************998430.233332558889************************88887777778888**** PP

                             SLAC1  74 lgtfpmglltilnglllvl.pgewlatlalvllWigvllslltavvvvfllftekeekleeitpawllpvvgllvva 149
                                       ++++p+ l+++  +l+ ++  ++ la+++l+ ++++++l+l++ +++ + l+t++ +  +ei+ a+++p+ ++  + 
  gi|518651420|ref|YP_008140940.1|  85 IALIPIILFIMDHILIDLIgMSKLLAEVSLYNYFFSYFLALVLGILLGYRLYTKEID-KNEINYAIIIPPLSIGTSI 160
                                       *******65555555555556699999****989*****************999977.89***************** PP

                             SLAC1 150 llgallaesqnpslqllgilvvslllwglGlllalvlfvlyl..yrlithklppaelrptlfiplGplgqgalalll 224
                                       +l++ l+ + + +++ +   ++ l+l+glG++++l +f+  +  +  ++    + + +pt ++p+G+ +++++ ll+
  gi|518651420|ref|YP_008140940.1| 161 FLATPLMGYYHGDIAET---IYFLVLMGLGIFFFLYIFIGSIalSGHVS--NKSDSTLPTAMLPVGVSSLIIINLLS 232
                                       ******88888886666...55666666666666555555551044444..468889****************9999 PP

                             SLAC1 225 lgkaapkaaevlkvlall..lalflwglglfwllvavlsvls..lpvrlkfslswWaftFPlgalalatielgkale 297
                                       + +  + +++++  ++ +  ++++l+g+ ++ ++v+++++++          ls Wa+ FPlg +a++ti+l +al+
  gi|518651420|ref|YP_008140940.1| 233 IMSFGKVIGDITLNFGTVefISILLYGFEVWNFIVVFILIFRktT----FGYLSVWAYGFPLGLFATSTIKLESALK 305
                                       988887788888775554448999***********9999999432....468************************* PP

                             SLAC1 298 seafkvlgtillvllvlvwllvlvgt 323
                                        +++  + +++ ++l+++w++ l++t
  gi|518651420|ref|YP_008140940.1| 306 IPFLGDVFIFIWIVLMILWVYALINT 331
                                       ****88888899***********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2424.00
//
Query:       gi|518651421|ref|YP_008140941.1|  [L=86]
Description: TetR family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   40.8   0.3      2e-10   40.3   0.3    1.3  1  TetR_N    Bacterial regulatory proteins, tetR family


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.3   1.1e-14     2e-10       1      45 [.       9      52 ..       9      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.1e-14
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      Il+ A + fa +Gy+ ++++eIA  A+vskg+l+ y++sKe L+ 
  gi|518651421|ref|YP_008140941.1|  9 ILESAIKNFAINGYE-ASMDEIAYDAKVSKGLLFFYYKSKENLII 52
                                      9**************.78************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      199  (0.0110993); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 591.56
//
Query:       gi|518651422|ref|YP_008140942.1|  [L=216]
Description: death-on-curing family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-09   38.8   0.1    5.7e-09   36.8   0.1    2.1  2  Fic       Fic/DOC family
  ------ inclusion threshold ------
      0.056   13.8   0.6       0.19   12.1   0.0    2.0  2  DUF1889   Domain of unknown function (DUF1889)


Domain annotation for each model (and alignments):
>> Fic  Fic/DOC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.1   6.4e-13   5.7e-09       2      97 .]       3      84 ..       2      84 .. 0.68
   2 ?   -2.2   0.0      0.93   8.3e+03      26      26 ..     142     142 ..     112     175 .. 0.46

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 6.4e-13
                                      -SHHHHHHHHCHS-S------TS--SS-ST..EEEE---SCCCHHHHHHHHHHHHCHHT-S-HHHHHHHHHHHHHHH-- CS
                               Fic  2 ltledllelhrlllqdigeeagefrdeevsegklesalappeevpaeleelleylnelekeeplekaaalhyefekiHP 80
                                      +t++ ++e+h+++ +++  +  ++ +  +  + ++s + +  +  +     + y++      +++kaa l+ ++++ HP
  gi|518651422|ref|YP_008140942.1|  3 FTYKNIIEIHEKIAKNYSID-SNYLN--I--NAIKSIVYRMNDNFNN---SDIYPT------IYDKAAVLFMRIIRCHP 67
                                      56777778888887776622.44433..3..3344444443322222...266777......***************** PP

                                      SSS-HHHHHHHHHHHHH CS
                               Fic 81 FaDGNgRtarlllnllL 97
                                      F DGN+Rta++ l+ +L
  gi|518651422|ref|YP_008140942.1| 68 FIDGNKRTALASLSEYL 84
                                      **********9988876 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.93
                                       - CS
                               Fic  26 r 26 
                                       r
  gi|518651422|ref|YP_008140942.1| 142 R 142
                                       1 PP

>> DUF1889  Domain of unknown function (DUF1889)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1      0.18   1.6e+03       3      29 ..      28      56 ..      26      77 .. 0.69
   2 ?   12.1   0.0   2.1e-05      0.19       7      43 ..     144     182 ..     136     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.18
                           DUF1889  3 ikviyslidnmv.nfkdkn.mpavidkal 29
                                      i+ i s++  m  nf++ +  p++ dka 
  gi|518651422|ref|YP_008140942.1| 28 INAIKSIVYRMNdNFNNSDiYPTIYDKAA 56
                                      55666666666435665551588999975 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2.1e-05
                           DUF1889   7 yslidnmvnf.kdknmpavidkaldfigamdvsa.ptps 43 
                                        sli  ++ + k+kn p++idk++d+  a d+    tps
  gi|518651422|ref|YP_008140942.1| 144 LSLIKTIIGVaKNKNRPSMIDKTFDYWYATDIYPyYTPS 182
                                       5888888764399*****************996413554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1536.94
//
Query:       gi|518651423|ref|YP_008140943.1|  [L=34]
Description: hypothetical protein FACI_IFERC00001G0062 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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: 0.36u 0.29s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 236.68
//
Query:       gi|518651424|ref|YP_008140944.1|  [L=399]
Description: major facilitator superfamily MFS_1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-23   81.1 109.1    1.4e-19   70.3  68.4    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0031   16.4  42.9      0.036   12.9   5.7    3.3  3  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3  68.4   1.5e-23   1.4e-19       2     353 .]      12     349 ..      11     349 .. 0.84
   2 !   24.6  32.7   1.2e-09   1.1e-05       6     171 ..     213     383 ..     204     398 .. 0.69

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.5e-23
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++++f ++++++il+p++p  l++++ +  s+i ll+++y+ +++++ l++G+ls +f  ++ l +++ l+++gl+ 
  gi|518651424|ref|YP_008140944.1|  12 WFLLFTIGFGWFILAPLVP-ELSSSFSVGLSSILLLVSTYGYTMVILGLLAGWLSAKFTVKSSLYTAAGLSIIGLIG 87 
                                       7999***************.9*************************************9999************444 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                        ++ s+ +  +lv  +++++++ ++++ +++++  +f++ +   +ig+  ++  lG+++g  +g+ + ++lg r+++
  gi|518651424|ref|YP_008140944.1|  88 RAL-SPDYlSFLVTGIIAAAAYPLAMAPVGSVADSLFHD-RSHTVIGISVGMLFLGMAFGSFFGPGIFTALGLRGAM 162
                                       446.666669****************************9.************************************* PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltll 230
                                       +i  i++++a++   +l+p  +  +   +++ +         + a+++   ++  w ++  +++++ +++g l +++
  gi|518651424|ref|YP_008140944.1| 163 WIPVILAIIAVI---WLVPGIRGYPTSYKGRSL---------RGAFRIGMVKN--W-YIGLAISAMSVMFGsLGSTV 224
                                       *********977...777544444444444333.........22455555555..5.44444444434444233333 PP

                             MFS_1 231 plylqevlgls.glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll. 305
                                        l    ++  + +l ++gll +l++l++a +al++  +  +++r r+ l++ ++l++++ +++ ++++ s++++l+ 
  gi|518651424|ref|YP_008140944.1| 225 LL--LHHMATAqALAYGGLLGGLAFLGSALGALILPPVFEKYNRIRTGLITTGVLMFIFTAVMTVSLSYSTIIILIg 299
                                       33..344444456788888899999999999*************************************677766668 PP

                             MFS_1 306 .vlvliGfglgfvfpsllalasdla.ppeeagtasglfntagslggalgp 353
                                        +++++G+++  +++++++l+++++  p +ag+a++ ++++ +lg a+ p
  gi|518651424|ref|YP_008140944.1| 300 aGYFFFGIFGNAYWSMAMTLTTRYVsDPAQAGFATSMYSVFTNLGVAFIP 349
                                       99999***88889***********9888*****************99987 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.2e-09
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll. 80 
                                       + +++++   +++l  ++a++   + +  gll +l +lg+a+++l+l ++ +++ r r  l+++ +l+++++++++ 
  gi|518651424|ref|YP_008140944.1| 213 MSVMFGSLGSTVLLLHHMATA--QALAYGGLLGGLAFLGSALGALILPPVFEKYNRIRtGLITTGVLMFIFTAVMTv 287
                                       222333333333332244333..345557889999*******************99998777777777777344442 PP

                             MFS_1  81 .fa.sslw.lllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllgg.llasslgWra 152
                                        ++ s++  l+ ++ ++ G+++ a+++++++l+++++++  + g+a++++s++++lG+++ p++ g  + s++  ++
  gi|518651424|ref|YP_008140944.1| 288 sLSySTIIiLIGAGYFFFGIFGNAYWSMAMTLTTRYVSDpAQAGFATSMYSVFTNLGVAFIPVFLGpEFGSLATITV 364
                                       5447888878888899***********************99********************9887754444444444 PP

                             MFS_1 153 vfyilaivsllafvlflll 171
                                          ++ ++ ++a++l+ +l
  gi|518651424|ref|YP_008140944.1| 365 GVSVVLAIEVVAMILAPFL 383
                                       4444444444444444444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.9   2.8    0.0011        10      50     101 ..      45      96 ..      31     105 .. 0.81
   2 !   12.9   5.7     4e-06     0.036      17      92 ..     101     175 ..      94     202 .. 0.77
   3 !    8.8  21.1   6.9e-05      0.62      13     181 ..     204     371 ..     195     396 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0011
                                       HHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS CS
                          Sugar_tr  50 livsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgkns 101
                                       l+vs +    +i +l+ag+l+ +f  k+sl +aa l++ig +  a+++++ s
  gi|518651424|ref|YP_008140944.1|  45 LLVSTYGYTMVILGLLAGWLSAKFTVKSSLYTAAGLSIIGLIGRALSPDYLS 96 
                                       5555555666677899*****************************9996633 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4e-06
                                       HCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  17 gvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavl 92 
                                       g+i+a+++ l+ a    +  s   +++s + +g++v+++++G ++Gs+f+  + + +G + ++ i ++l++i+ + 
  gi|518651424|ref|YP_008140944.1| 101 GIIAAAAYPLAMAPVGSVADSLF-HDRSHTVIGISVGMLFLGMAFGSFFGPGIFTALGLRGAMWIPVILAIIAVIW 175
                                       55555555555444444444443.4447899**********************************99999998775 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 6.9e-05
                                       HHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTH.HHHHHHHHHHHHH CS
                          Sugar_tr  13 gYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGR.kkslliaavlfvi 88 
                                       +Y    i+a++ + + +    l  ++ +++++  + gl+ +++++G+++G+l++ ++ +++ R + +l++++vl++i
  gi|518651424|ref|YP_008140944.1| 204 WYIGLAISAMSVMFGSLGSTVLLLHHMATAQALAYGGLLGGLAFLGSALGALILPPVFEKYNRiRTGLITTGVLMFI 280
                                       5555568888888888888888888888888888899999***********************6678888******* PP

                                       HHHHHH-TTTTSS-TGGG.GGHHHHHH.HHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHH.HHHHHHHHHHH CS
                          Sugar_tr  89 gavlqaaakgknsvevli.vgRvlvGi.gvGlasvlvPmyisEiApkklRgalvslyqlaitfGi.lvaaifglgln 162
                                        ++++ ++ +++++ +li +g ++ Gi g    s+ +++++  ++ ++ +g+ +s+y +++ +G  ++  ++g  + 
  gi|518651424|ref|YP_008140944.1| 281 FTAVMTVSLSYSTIIILIgAGYFFFGIfGNAYWSMAMTLTTRYVSDPAQAGFATSMYSVFTNLGVaFIPVFLGPEFG 357
                                       *********996666666245999997356677899999999999*******************6244444444444 PP

                                       TSS-TTHHHHHHHCCHHHH CS
                          Sugar_tr 163 ktsnadgwrillglqlvpa 181
                                                i++g+++v+a
  gi|518651424|ref|YP_008140944.1| 358 SLAT-----ITVGVSVVLA 371
                                       4444.....5666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      302  (0.0168442); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.48
# Mc/sec: 2491.26
//
Query:       gi|518651425|ref|YP_008140945.1|  [L=163]
Description: hypothetical protein FACI_IFERC00001G0064 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.9e-37  126.9   0.0    4.9e-37  126.6   0.0    1.1  1  AhpC-TSA   AhpC/TSA family
    8.8e-23   80.7   0.0    1.1e-22   80.3   0.0    1.1  1  Redoxin    Redoxin
  ------ inclusion threshold ------
       0.07   13.0   0.0       0.25   11.2   0.0    1.8  1  SCO1-SenC  SCO1/SenC
       0.09   12.3   0.3       0.17   11.3   0.1    1.6  2  DUF1248    Protein of unknown function (DUF1248)
       0.12   12.4   0.1       0.37   10.7   0.0    1.7  2  OST_P2     Oligosaccharyltransferase Peripheral 2 domain


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 !  126.6   0.0   1.4e-40   4.9e-37       1     122 [.       5     125 ..       5     127 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 1.4e-40
                                       TTSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkf 76 
                                       +gdkapdf+++++ g+tvsl+d++g +pvvl+fypk+++p+Ct+e++ ++++++++k +g+ v+gvs+ds+e++k+f
  gi|518651425|ref|YP_008140945.1|   5 IGDKAPDFKANDELGKTVSLADFRGkSPVVLYFYPKAETPGCTAEAKCFRDNWDAIKPLGAIVLGVSSDSEEKQKSF 81 
                                       8**********************9999************************************************** PP

                                       HHH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEE CS
                          AhpC-TSA  77 iekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkir 122
                                       +++++l+f+llsD+++ + +ay++      ++ r t++idk+g+ir
  gi|518651425|ref|YP_008140945.1|  82 KDHYKLQFTLLSDKNKSIREAYDAK--GFLIPARITYIIDKQGIIR 125
                                       *************************..568***************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.0   3.1e-26   1.1e-22       2     141 ..       5     136 ..       4     143 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 3.1e-26
                                       TTSBB---ECCEETTCEEEEEHHHHTTSE.EEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkk.vvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafv 76 
                                        gdkaPdf+  +  + g++vsl++f+gk+ vv++f+p a +P C+ae+  + ++ ++  k  g  v++v++d+++ +
  gi|518651425|ref|YP_008140945.1|   5 IGDKAPDFKAND--ELGKTVSLADFRGKSpVVLYFYPKAETPGCTAEAKcFRDNWDAI-KPLGAIVLGVSSDSEEKQ 78 
                                       69*******877..**************98999****************788888887.****************** PP

                                       HHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG..EEE-EEEEEEETTEEEEEEESSSCHTSTT CS
                           Redoxin  77 kefwgkeglkfpvlsDgsaaftkalGlrleedaseg..lrtpryavidedgkvvylevepepetees 141
                                       k+f + ++l+f++lsD ++++ +a++++       g  + ++ + +id++g ++ +++ ++++  +s
  gi|518651425|ref|YP_008140945.1|  79 KSFKDHYKLQFTLLSDKNKSIREAYDAK-------GflIPARITYIIDKQGIIRGVHNSQMDP--KS 136
                                       **************************77.......4457888899*************99984..44 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0     7e-05      0.25       3     102 ..      11     105 ..       9     120 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7e-05
                         SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdv.CpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkey 78 
                                       +F+  d+ g++v+ +d++gk  +v +++ + ++  C+++ +  ++  da+    +++ +++  v    D+ e+ k++
  gi|518651425|ref|YP_008140945.1|  11 DFKANDELGKTVSLADFRGKSPVVLYFYPKAETPgCTAEAKCFRDNWDAI----KPLGAIVLGV--SSDSEEKQKSF 81 
                                       899*****************999999998877631444444444444444....4445555555..56788888888 PP

                         SCO1-SenC  79 leafdpriigltGskeeiakaake 102
                                        ++++ +++ l++++++i++a+++
  gi|518651425|ref|YP_008140945.1|  82 KDHYKLQFTLLSDKNKSIREAYDA 105
                                       888888888888888888888766 PP

>> DUF1248  Protein of unknown function (DUF1248)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.5   5.5e+03      22      33 ..       5      16 ..       4      18 .. 0.86
   2 ?   11.3   0.1   4.9e-05      0.17      33      60 ..      73     100 ..      71     110 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.5
                           DUF1248 22 hGneRldfkkeD 33
                                      +G++  dfk +D
  gi|518651425|ref|YP_008140945.1|  5 IGDKAPDFKAND 16
                                      6999999**999 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.9e-05
                           DUF1248  33 DiakwkesfkddYrlklvllkgtervia 60 
                                       D ++ ++sfkd+Y+l+++ll + ++ i 
  gi|518651425|ref|YP_008140945.1|  73 DSEEKQKSFKDHYKLQFTLLSDKNKSIR 100
                                       667779*****************99886 PP

>> OST_P2  Oligosaccharyltransferase Peripheral 2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.46   1.6e+03      23      47 ..      66      91 ..      54      95 .. 0.66
   2 ?   10.7   0.0    0.0001      0.37      36      92 ..      98     155 ..      92     162 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                                      S-TT-EEEE.EEEEEESS-EEEEEEE CS
                            OST_P2 23 lkeGqsGel.elkaafrkdytvdlyl 47
                                      +  G s +  e +++f+  y+++++l
  gi|518651425|ref|YP_008140945.1| 66 IVLGVSSDSeEKQKSFKDHYKLQFTL 91
                                      55555555414556888889999987 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0001
                                       EESS-EEEE.EEEEEEEEEEEE-SSSSTT-TT--EEEEEEEEEEEEEEEEEEE-SEEE CS
                            OST_P2  36 afrkdytvd.lylratviylvrknGkdiddkdaalePhmdiityvkvaeglkvkegen 92 
                                       ++r  y+++ + + a ++y++ k+G  +  ++ +++P+  i +++k  ++++ ++++n
  gi|518651425|ref|YP_008140945.1|  98 SIREAYDAKgFLIPARITYIIDKQGIIRGVHNSQMDPKSHIDFAIKTLKEISSTQEKN 155
                                       67788955438889*************************9977776555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1172.29
//
Query:       gi|518651426|ref|YP_008140946.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G0065 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-13   50.8   0.0    3.5e-13   49.7   0.0    1.6  1  DDE_Tnp_1     Transposase DDE domain
      0.006   16.0   0.0      0.009   15.4   0.0    1.2  1  DDE_5         DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.043   12.9   0.0       0.07   12.2   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
      0.093   11.0   0.0        3.9    5.6   0.0    2.0  2  DDE_Tnp_1_4   Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   7.7e-17   3.5e-13      21     214 .]     181     399 ..     160     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 7.7e-17
                         DDE_Tnp_1  21 edarwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       ++  +g++ ++ + + +++ ++++    l++ +++ pg+  d+ ++  ++d++ + ++++++aD+G++sa+++++l+
  gi|518651426|ref|YP_008140946.1| 181 SFLEPGHNSKEiHLPQINVMMLFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGI-EKCVIVADKGFFSADNIKKLK 256
                                       666778887777889999999999998999999999******************9.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrk................................gaeskrrgrlrkhdrnkiltksqkrr 141
                                       +++++yii+l+ n+ l  +                                 +e++r+  +r hd+ ++ + +  + 
  gi|518651426|ref|YP_008140946.1| 257 KRHLSYIIPLRRNSSLVPDtddflgvfmyngkpvkywkpengvymfedpvlKSEEERDYLIRIHDNIRPKSSYYDHS 333
                                       ****************9999999988888877777766665555554444434444444444444444444443333 PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       +           ++++++   ++e + +ly+ R  +E  F   k+++  dr + r+     a+++l ll+l l
  gi|518651426|ref|YP_008140946.1| 334 GD-------FGKLYLLSDINDEPERIYRLYKDREYVEYAFNVYKNDLEADRSYIRDDHMLSAYMFLNLLSLYL 399
                                       33.......4445555555559*********************************************999865 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-06     0.009     167     219 ..     226     277 ..     205     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                             DDE_5 167 lldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdralyppga 219
                                       + + +  ag++  v+vaD g+ +a+ + + l+ + l y++ +r++++l+p  +
  gi|518651426|ref|YP_008140946.1| 226 MANTIDMAGIEKCVIVADKGFFSADNI-KKLKKRHLSYIIPLRRNSSLVPDTD 277
                                       5556666899999**************.********************99765 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 ?   12.2   0.0   1.6e-05      0.07      71     141 ..     190     257 ..     180     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       CCTT-EEEESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH CS
                      ANF_receptor  71 nlfkiPvisygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee 141
                                       ++ ++P+i ++     +s+++  ptf+r+ p + + + A+++++ + g  k +++++++      +++l++
  gi|518651426|ref|YP_008140946.1| 190 KEIHLPQINVMM---LFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGIEKCVIVADKGFFSADNIKKLKK 257
                                       567899996544...8999**************************************99666666666665 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0   0.00087       3.9     217     254 ..     237     274 ..     222     283 .. 0.87
   2 ?    3.2   0.0    0.0049        22     313     354 ..     345     384 ..     329     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00087
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlea 254
                                       k ++ +D +f + + +k +++r+++Y+i l++ns l  
  gi|518651426|ref|YP_008140946.1| 237 KCVIVADKGFFSADNIKKLKKRHLSYIIPLRRNSSLVP 274
                                       567889****************************9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0049
                       DDE_Tnp_1_4 313 laklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfa 354
                                       ++  +pe++y +lY+ R  +E  +   k+dl+adr   ++ +
  gi|518651426|ref|YP_008140946.1| 345 IN-DEPERIY-RLYKDREYVEYAFNVYKNDLEADRSYIRDDH 384
                                       44.799****.***********************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3004.33
//
Query:       gi|518651427|ref|YP_008140947.1|  [L=559]
Description: hypothetical protein FACI_IFERC00001G0066 [Ferroplasma acidarmanus fer1]
Scores for complete 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-78  261.7   0.0    1.1e-77  261.4   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    6.4e-11   43.1   0.0    2.2e-10   41.3   0.0    2.0  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.14   12.1   0.8       0.53   10.3   0.1    2.1  2  Pallilysin     Pallilysin beta barrel domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.4   0.0   1.9e-81   1.1e-77       2     422 ..      33     446 ..      32     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 261.4 bits;  conditional E-value: 1.9e-81
                                       HHHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   2 eeqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       +++a+++  k++l++ ++g+++TY++ d  +n++A  L+s+G kkg+++ai++ nspew++a+++ilkaG+++v++n
  gi|518651427|ref|YP_008140947.1|  33 RKKAEENDRKICLIF-QDGRKYTYAQIDLLSNNIAINLLSRGFKKGNKIAIFALNSPEWILAYFGILKAGCIPVTVN 108
                                       57899999*******.78*********************99************************************ PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS....... CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae....... 148
                                       +++ +e l y ++ ++a  +i   ds+l+++  +++ +l   ++v ++ + + ++++ + + e+ +   +       
  gi|518651427|ref|YP_008140947.1| 109 TSFVKEPLVYNFQMTDALSVI--LDSRLAKNFINVQLSLSNIQSVFIIGNSNEDTNKIEGNVENFS---Nllndnis 180
                                       *********************..8999999999999999999999999876666554444444333...13456788 PP

                                       ...-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHH CS
                       AMP-binding 149 ...kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilell 222
                                          k  + + l+ +d+  +i TSGTTG+ K V+ s  +++a++ ++   +  ++ +d++++++lpl+hi++l l+++
  gi|518651427|ref|YP_008140947.1| 181 kniKI-KLPDLTGKDPSAMILTSGTTGRSKVVVESNSQFIATALDM--IDAGGVASDSRIYVYLPLFHIMALDLAII 254
                                       88644.5557899*****************************8885..66788889********************* PP

                                       HHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHH CS
                       AMP-binding 223 lallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspel 299
                                        ++ls +tv+l++k+++  + +++++i  +++t++++v  ++e+l+++++ +      + + + + +++ +  s+e+
  gi|518651427|ref|YP_008140947.1| 255 SSILSNSTVYLVEKFNP--S-TFWKDIVGYQITHFHAVGPIFEMLIKQNPSA------EEKQHGT-IIAIAYSSREV 321
                                       *************9988..3.35688888******************65444......3344555.4688999**** PP

                                       HHHHHHHHTCEEEEEEEEGGGSSECEE..CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET.. CS
                       AMP-binding 300 lrffralfgeevlegYGlTEttgvvtv..lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp.. 372
                                       ++ ++++fg ++  gYG TE+++ vt    +  +  + +gs+Gk+ p  ev+i+De+ g pv +g  Ge+++r +  
  gi|518651427|ref|YP_008140947.1| 322 WTTAENRFGIKITGGYGGTEAGIPVTSpySEVVNGINPPGSCGKATPPYEVAIIDES-GFPVVTGAIGEIVIRPKlp 397
                                       *************************8777555666678******************9.9**************9866 PP

                                       .TS-SEBTT-HHHHHHHEEETCC.EEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 373 .gvmkgYlkkpeataeafdsegr.wlrTGDlgrldedGyleivgRkkdlikl 422
                                         ++  Y+k +++  +af+   + w++TGDlg++d +Gy+++v+R+kd i +
  gi|518651427|ref|YP_008140947.1| 398 wVTFLEYYKMQKESLQAFT---GlWFHTGDLGKYDNNGYIYFVDRSKDSIRR 446
                                       569*******9*******8...55************************9976 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0         3   1.8e+04      52      68 ..     423     439 ..     410     441 .. 0.84
   2 !   41.3   0.0   3.7e-14   2.2e-10       1      75 [.     455     528 ..     455     529 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3
                                       HHT-TTTS-SEEEE-S- CS
                     AMP-binding_C  52 kelgpyavpkkvvfvde 68 
                                         lg+y  + +++fvd+
  gi|518651427|ref|YP_008140947.1| 423 GDLGKYDNNGYIYFVDR 439
                                       67999999999999996 PP

  == domain 2  score: 41.3 bits;  conditional E-value: 3.7e-14
                                       HHHHHHHSSTTEEEEEEE-----TTS.---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkG.ealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       evE++++++++V e+aV+ vp ++   e++va+     +se+ +e++++++  +++py+ p++++f+d+lpkt +G
  gi|518651427|ref|YP_008140947.1| 455 EVEQTILKMDGVLEVAVYPVPSNLGEdEVMVALSRN--NSELKPENIIEYCLNNMPPYWIPNYIRFLDSLPKTPTG 528
                                       8**********************5556777777666..434457******************************99 PP

>> Pallilysin  Pallilysin beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.27   1.6e+03      48      88 ..     144     187 ..     122     191 .. 0.68
   2 ?   10.3   0.1   8.8e-05      0.53      13      69 ..     410     467 ..     403     476 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.27
                        Pallilysin  48 llddteevyewensslrrnGiylstknks...itnlkrrldiel 88 
                                       +l +++ v+ + ns+   n i  + +n s     n+++ ++i+l
  gi|518651427|ref|YP_008140947.1| 144 SLSNIQSVFIIGNSNEDTNKIEGNVENFSnllNDNISKNIKIKL 187
                                       56788888888888877776655555544211356666666666 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.8e-05
                        Pallilysin  13 esfakflnGLWykasskk..dkkryvffdkeekeiifllddteevyewensslrrnGiy 69 
                                       es+++f +GLW+++ +    d++ y++f  ++k+ i    ++   +e+e++ l+  G++
  gi|518651427|ref|YP_008140947.1| 410 ESLQAF-TGLWFHTGDLGkyDNNGYIYFVDRSKDSIRRRGENISSFEVEQTILKMDGVL 467
                                       455555.8*****98754449*******9999999999999989999999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 3739.44
//
Query:       gi|518651428|ref|YP_008140948.1|  [L=303]
Description: hypothetical protein FACI_IFERC00001G0067 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1866.98
//
Query:       gi|518651429|ref|YP_008140949.1|  [L=231]
Description: hypothetical protein FACI_IFERC00001G0068 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0069   16.4   0.9       0.03   14.3   0.1    2.4  2  HTH_19    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2     0.062   1.1e+03      22      38 ..      24      40 ..      23      42 .. 0.83
   2 !   14.3   0.1   1.7e-06      0.03      13      64 ..      42      93 ..      38      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.062
                            HTH_19 22 lgisrskisaiEngkkd 38
                                      l+i+   is++ n +++
  gi|518651429|ref|YP_008140949.1| 24 LQINSEIISNLKNTNNE 40
                                      68999999***999886 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.7e-06
                            HTH_19 13 ltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgid.leyllqged 64
                                      +t++++a+++g+++s+ s+iE g+  ++ ++++++iae+ +++ ++  lq+ d
  gi|518651429|ref|YP_008140949.1| 42 ITLDDIARNIGFTPSMGSKIEPGRLSKL-SNRVNSIAEKQKLSlPKLNLQLLD 93
                                      69*********************77677.6*********99996666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1455.50
//
Query:       gi|518651430|ref|YP_008140950.1|  [L=511]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-11   42.2   0.2    1.5e-10   40.8   0.2    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.4e-08   33.7   4.3      1e-07   32.2   4.3    1.8  1  OrfB_IS605      Probable transposase
     0.0007   19.9   1.3     0.0017   18.6   1.3    1.7  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.071   12.8   1.6       0.15   11.8   1.6    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.11   12.7   0.1       0.22   11.7   0.1    1.5  1  FYVE            FYVE zinc finger
       0.12   12.4   3.0       0.11   12.6   0.8    2.0  2  DUF1451         Zinc-ribbon containing domain
       0.14   12.1   0.3       0.28   11.2   0.3    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        0.8    9.7   4.6        8.5    6.4   4.6    2.7  1  zinc_ribbon_4   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 !   40.8   0.2   6.7e-14   1.5e-10      16      67 ..     340     392 ..     331     394 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 6.7e-14
                    OrfB_Zn_ribbon  16 Gikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                         ++++++++  T k+Cs+C  k + +l++r +kC+nCgf +drD+n+a+N++
  gi|518651430|ref|YP_008140950.1| 340 ASTLILIDRFIpTTKECSNCHNKYNIKLDERIYKCTNCGFIIDRDYNSALNMI 392
                                       447889999999********9999889************************86 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   4.3   4.7e-11     1e-07      10     104 ..     202     304 ..     185     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 4.7e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn.......ykkasrkla 78 
                                       +++++++k ++ DlGi+n +t+++++     ++k++r  + +++l+++ + ++ + +k k        y k ++kl 
  gi|518651430|ref|YP_008140950.1| 202 EKPVNNQKILSFDLGIKNQLTCSNGSILNyNIPKSKREIRLQRSLSRKARYVEGTNSKNKLsreqsknYYKNKNKLN 278
                                       6788999****************998444599999999999999999999988775554445556666********* PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlk 104
                                       r   k +++rk+ ++k++++l+ +++
  gi|518651430|ref|YP_008140950.1| 279 REQTKTTNKRKDTINKITHYLTFNYD 304
                                       ********************987776 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.3   7.5e-07    0.0017       3      44 ..     338     383 ..     336     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 7.5e-07
                              C1_2   3 Hp.HpLtlskgedssesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                       H+  +L+l  ++    +++Cs C +k     d  +  Y+C+ C f+++ 
  gi|518651430|ref|YP_008140950.1| 338 HKaSTLILI-DRFIPTTKECSNCHNKynikLD--EriYKCTNCGFIIDR 383
                                       777789999.999999**********885443..246*********995 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.6   6.7e-05      0.15       3      25 ..     356     379 ..     355     381 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 6.7e-05
                                       -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpi.RCkeCGh 25 
                                       C +C+++  +k  + i +C++CG+
  gi|518651430|ref|YP_008140950.1| 356 CSNCHNKYNIKLDERIyKCTNCGF 379
                                       **************9989*****8 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   9.7e-05      0.22       9      35 ..     353     381 ..     350     416 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.7e-05
                                       -SB-TTT--B--SS..S--EE-TTT--EE CS
                              FYVE   9 vkkCeiCakkFsll..rrrhhCrlCGkvv 35 
                                       +k+C++C++k+++   +r + C +CG ++
  gi|518651430|ref|YP_008140950.1| 353 TKECSNCHNKYNIKldERIYKCTNCGFII 381
                                       689********76555999*******987 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.1   2.4e+03      22      41 ..     278     297 ..     242     328 .. 0.56
   2 ?   12.6   0.8   4.8e-05      0.11     112     139 ..     351     378 ..     347     380 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                           DUF1451  22 keklseaeeltkeelelvae 41 
                                       +++  ++ +  k+ ++++++
  gi|518651430|ref|YP_008140950.1| 278 NREQTKTTNKRKDTINKITH 297
                                       22222233333344444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 4.8e-05
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C +C+++ ++k  e+i +C +Cg
  gi|518651430|ref|YP_008140950.1| 351 PTTKECSNCHNKYNIKLDERIYKCTNCG 378
                                       66789**********************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 ?   11.2   0.3   0.00013      0.28      16      44 ..     351     378 ..     342     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       p++  C +C+++  +++   + ++C  C+
  gi|518651430|ref|YP_008140950.1| 351 PTTKECSNCHNKYNIKLDE-RIYKCTNCG 378
                                       56678*****998899987.********7 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.6    0.0038       8.5       4      34 ..     355     380 ..     355     382 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0038
                     zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghv 34 
                                       +C +C+ ky+i  +      +  +C++Cg +
  gi|518651430|ref|YP_008140950.1| 355 ECSNCHNKYNIKLD-----ERIYKCTNCGFI 380
                                       6**********873.....677889999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (511 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2192  (0.12226); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3270.36
//
Query:       gi|518651431|ref|YP_008140951.1|  [L=408]
Description: hypothetical protein FACI_IFERC00001G0070 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.5e-15   55.1  36.4    5.5e-15   55.1  36.4    1.7  1  MFS_1       Major Facilitator Superfamily
  ------ inclusion threshold ------
        0.4    9.5  47.3      0.009   14.9  37.1    2.1  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1  36.4   6.1e-19   5.5e-15       1     351 [.       8     346 ..       8     348 .. 0.80

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 6.1e-19
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                       l+l+++++ +a+sil++ +++++ ++ +  +  +g ++ + +++ ++ s ++G ++dr+  ++ ++ l l++++l+l
  gi|518651431|ref|YP_008140951.1|   8 LILSTLIANIASSILYIGITWYVLTSVN-GEILYGSIVLTATITGFAISNFIGKIIDRYNKKKiFIRLHLIVSLLFL 83 
                                       578999999************9999999.555566655555666666666789999*******99999999999995 PP

                             MFS_1  77 llll.fa....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                       l++l ++     ++ +l+v+ ++ ++ + +++ ++++++ ++f+ +e  + ++ + +  ++++++  +++g+++   
  gi|518651431|ref|YP_008140951.1|  84 LIFLlLIrnieFGIATLFVSYMILSVYSMFYWNIILSITQQIFSIKEYKSINSKMEIIGQISSVFS-IIAGFII--- 156
                                       5555343555666777**************************************************.8899999... PP

                             MFS_1 149 gWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg 225
                                        +++ f+++ i++ +af + ++ +   +  ++ k+ +       ++ ++ ++++l+++++l++ll+al++ f+++ +
  gi|518651431|ref|YP_008140951.1| 157 -YSVNFLFIIIACSIAFAISAMTFKKIKIIEAEKNNI------SNSTFS-GFTYLKNNKYLFFLLFALYTPFIAIII 225
                                       .455555555555555444333332222222222222......223444.5********998899999999999999 PP

                             MFS_1 226 lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavl 302
                                         ++ p +++ vl+ +  ++    ++++  + ai+a++++ l+ +++ ++  +l++++++++++g + +++++  ++
  gi|518651431|ref|YP_008140951.1| 226 GNFTQPAFVVNVLNGT-PVI----IGAMESIYAISAVITSLLIPKMNEKNEFVLIVISMIVFSVGTIAMGLIKIVII 297
                                       9999999999999999.344....44555556666889999999****************************88899 PP

                             MFS_1 303 lllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       +l + ++ G g   ++++  +++++ +p++  g+++g   t+++ +++ 
  gi|518651431|ref|YP_008140951.1| 298 FLGLEAIQGYGNPAIRIIRKTIMMKTIPKKFIGRVYGSLETISYMARIA 346
                                       9999999999*****************************9999988875 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 ?   14.9  37.1     1e-06     0.009      37     357 ..      41     339 ..      32     341 .. 0.87
   2 ?    0.1   5.2     0.031   2.8e+02     146     210 ..     331     390 ..     294     400 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-06
                        MFS_1_like  37 giitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeesklevsvaqdvdaektfwi 113
                                       g i+l + +t ++ ++++g + Dr++k+k  ++l l++s++++l++l++               ++ ++++ + f++
  gi|518651431|ref|YP_008140951.1|  41 GSIVLTATITGFAISNFIGKIIDRYNKKKIFIRLHLIVSLLFLLIFLLLI--------------RNIEFGIATLFVS 103
                                       7899999*************************************888777..............789999******* PP

                        MFS_1_like 114 lfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaall 190
                                       +++l v   f ++ il ++  +    ++e +   ++  + G ++  +f++i G++i  +++  l    +++ + + +
  gi|518651431|ref|YP_008140951.1| 104 YMILSVYSMFYWNIILSITQQI--FSIKEYKSINSKMEIIGQIS-SVFSIIAGFIIYSVNF--LF---IIIACSIAF 172
                                       ******************9876..57889999999********9.6899******965555..44...445555556 PP

                        MFS_1_like 191 visllvvlilnetekesklkvtkslqvllnilknpeviifllvalilgmswgiienFlf.lYL.kelgasntllGsl 265
                                        is + + +++  e ++k ++ +s  + +  lkn ++++fll+al   ++  ii+nF +  +  + l+ +  ++G++
  gi|518651431|ref|YP_008140951.1| 173 AISAMTFKKIKIIE-AEKNNISNSTFSGFTYLKNNKYLFFLLFALYTPFIAIIIGNFTQpAFVvNVLNGTPVIIGAM 248
                                       66666655555555.4567788888899*****************************76467778999********* PP

                        MFS_1_like 266 valgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskia 342
                                         + +++ +++ ++  k+ ek  + +l++i+++++ +  + +++i+ + + l +e+++g+   ++  +  + + k +
  gi|518651431|ref|YP_008140951.1| 249 ESIYAISAVITSLLIPKMNEKNEF-VLIVISMIVFSVGTIAMGLIKIVIIFLGLEAIQGYGNPAIRIIRKTIMMKTI 324
                                       *****************9999765.688999*****************************99999999999999999 PP

                        MFS_1_like 343 pksleatgqgllsgl 357
                                       pk+ ++++ g l+++
  gi|518651431|ref|YP_008140951.1| 325 PKKFIGRVYGSLETI 339
                                       999999888766665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.031
                        MFS_1_like 146 d.yGrqrlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklk 210
                                       + yG      +++y+   +++ i+i  ++ +  + s +l+ + +++v+++++v+i    + + k +
  gi|518651431|ref|YP_008140951.1| 331 RvYGSLE---TISYMARIAFLAIFILIIKYT--G-SGILIAIQGIFVLAFVFVVIYSFRKMQIKAQ 390
                                       3344332...478888888888877777764..3.5577777777777777777766666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1486  (0.0828825); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); 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):               2  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.41
# Mc/sec: 3006.44
//
Query:       gi|518651432|ref|YP_008140952.1|  [L=140]
Description: hypothetical protein FACI_IFERC00001G0071 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-15   56.9  26.9    3.4e-15   56.5  26.9    1.2  1  DUF996         Protein of unknown function (DUF996)
     0.0086   16.1   8.7      0.023   14.7   0.1    2.1  2  Sensor         Putative sensor
  ------ inclusion threshold ------
       0.78   10.1   0.0       0.78   10.1   0.0    2.3  2  Comm           Commissureless
        0.9    8.7  13.4        1.1    8.4  13.4    1.1  1  CitMHS         Citrate transporter
        1.4    7.0   4.8        1.5    6.9   4.8    1.2  1  UPF0182        Uncharacterised protein family (UPF0182)
        1.4    8.2  13.1       0.96    8.8  11.7    1.4  1  TMEM43         Transmembrane protein 43
        4.7    6.8  11.6          8    6.1   0.2    2.1  2  DUF4131        Domain of unknown function (DUF4131)
        7.3    6.9  10.6        5.3    7.3   0.5    2.5  2  Glycophorin_A  Glycophorin A


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 !   56.5  26.9   1.5e-18   3.4e-15      30     135 .]       2     109 ..       1     109 [. 0.79

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 1.5e-18
                            DUF996  30 liafilsiialvva...ilalllvlgalatalelpgleeaaslilllllvliiayvlliisavflkksyellgkrtg 103
                                       l+++i +ii  +va    ++ll+ ++ +a+  +++   +  sli+++ll++++++v+  +s +f + +y+ +gk tg
  gi|518651432|ref|YP_008140952.1|   2 LYSLISGIILAIVAgisLFLLLIPIFNSASSTSSTSTFY-VSLISIFLLIVVLVLVPSFVSIIFQYLAYDSVGKLTG 77 
                                       677777777666665443344444444444344443333.359********************************** PP

                            DUF996 104 vklFetagllyfiGaiLtivlvGliilliaei 135
                                       +  F ta+ll++iG iLti+++G+i+++i+ i
  gi|518651432|ref|YP_008140952.1|  78 IHEFHTAALLLLIGIILTIIVIGIILIFIGII 109
                                       ******************************87 PP

>> Sensor  Putative sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   5.3     0.045     1e+02     101     149 ..       4      58 ..       1      65 [. 0.76
   2 !   14.7   0.1     1e-05     0.023       4      49 ..      72     118 ..      69     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.045
                            Sensor 101 glvlfvvavvllalalalltaPlw......tlpeallvavlGlllllvllwvvrg 149
                                       +l+++++++++  ++l+ll++P+       +    + v +++++ll+v+l +v+ 
  gi|518651432|ref|YP_008140952.1|   4 SLISGIILAIVAGISLFLLLIPIFnsasstSSTSTFYVSLISIFLLIVVLVLVPS 58 
                                       5677888889999999999999975666552457778889999999888888775 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1e-05
                            Sensor   4 lglplgvaafvllvtglslglgllvllvGlp.lLalalllarglaav 49 
                                       +g ++g+  f  + ++l++g++l+++++G+  ++++ + l+ ++a++
  gi|518651432|ref|YP_008140952.1|  72 VGKLTGIHEFHTAALLLLIGIILTIIVIGIIlIFIGIIFLIIAFAKL 118
                                       56789999999999***************862567888888888876 PP

>> Comm  Commissureless
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   2.2      0.98   2.2e+03       6      27 ..      43      63 ..      35      72 .. 0.51
   2 ?   10.1   0.0   0.00035      0.78       4      49 ..      82     128 ..      79     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.98
                              Comm  6 iindvwigivltLlilslvFcl 27
                                      +i++ ++ +vl+L + s+v ++
  gi|518651432|ref|YP_008140952.1| 43 LISIFLLIVVLVL-VPSFVSII 63
                                      4444444444443.33333333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                              Comm   4 eriindvwigivltLlilslvFclcs.CflyrkfrtWkkkktardak 49 
                                       ++    ++igi+lt+++++++ + +   fl   f +  +  ++  + 
  gi|518651432|ref|YP_008140952.1|  82 HTAALLLLIGIILTIIVIGIILIFIGiIFLIIAFAKLPGEAKPALND 128
                                       55566789************999887678888887766555554444 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  13.4   0.00049       1.1      79     177 ..       4     119 ..       1     139 [. 0.55

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00049
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                            CitMHS  79 vlltallsafvsndgvvlimipivlslakrlkklppll.liplalaaniggaltpiGtpttraa............. 141
                                       +l+++++ a+v     +l++ipi+ s     + +++ +  ++ ++   +  +l+p + +    +             
  gi|518651432|ref|YP_008140952.1|   4 SLISGIILAIVAGISLFLLLIPIFNSASST-SSTSTFYvSLISIFLLIVVLVLVPSFVS----Iifqylaydsvgkl 75 
                                       567778888887777799999999999986.6666665033333333333334444444....24444888888888 PP

                                       ...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 142 ...........arpglslpnllllalllvgllplvllfmfgvalalp 177
                                                    ++ +++ +++++++l+++ +++l++   ++ +lp
  gi|518651432|ref|YP_008140952.1|  76 tgihefhtaalLLLIGIILTIIVIGIILIFIGIIFLII---AFAKLP 119
                                       88888866655444444444444444444444444444...333333 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.8   0.00067       1.5       4      58 ..      45     103 ..       2     137 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00067
                           UPF0182   4 llavlavlllllellarlytellwfkelg....ylsvfltrlltrlllfvvvflllall 58 
                                        +++l+v+l+l+  +++++ ++l ++++g      +  +  ll+ ++++++++++ ++l
  gi|518651432|ref|YP_008140952.1|  45 SIFLLIVVLVLVPSFVSIIFQYLAYDSVGkltgIHEFHTAALLLLIGIILTIIVIGIIL 103
                                       45556666666777778888888888777322222222222222222222222222222 PP

>> TMEM43  Transmembrane protein 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8  11.7   0.00043      0.96     174     248 ..      26     105 ..      20     107 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00043
                            TMEM43 174 mfakeksenklltwllRllGfllmflglllllsplsvlvslipl..l...gelvglglalvalllslslsllviala 245
                                       +f++++s +++ t  + l++++l+++ l+l+ s +s++++++ +  +    ++ ++ +a + ll++++l+++vi+++
  gi|518651432|ref|YP_008140952.1|  26 IFNSASSTSSTSTFYVSLISIFLLIVVLVLVPSFVSIIFQYLAYdsVgklTGIHEFHTAALLLLIGIILTIIVIGII 102
                                       799************************************9988765644455556677789999***********98 PP

                            TMEM43 246 wll 248
                                        ++
  gi|518651432|ref|YP_008140952.1| 103 LIF 105
                                       776 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   6.0     0.012        27       7      48 ..      10      55 ..       4      67 .. 0.74
   2 ?    6.1   0.2    0.0036         8       8      62 ..      86     131 ..      79     140 .] 0.48

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                           DUF4131  7 lvllalllllllllllllrr....rprrrvllllllllllallgfa 48
                                      ++++++++ l+lll+ ++++      + ++ ++l+ ++ll+++ ++
  gi|518651432|ref|YP_008140952.1| 10 ILAIVAGISLFLLLIPIFNSasstSSTSTFYVSLISIFLLIVVLVL 55
                                      6778888888888888888899876677777777777777776655 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0036
                           DUF4131   8 vllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsql 62 
                                       +ll+++++l+++ +          ++l+++ +++l+ +++ l+   ++a + +++
  gi|518651432|ref|YP_008140952.1|  86 LLLLIGIILTIIVIG---------IILIFIGIIFLIIAFAKLPGEAKPALNDQTF 131
                                       222222222222222.........3555555555555555555555555555555 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.5    0.0024       5.3      60      78 ..       6      24 ..       3      38 .. 0.91
   2 ?    3.4   4.0     0.039        88      59      78 ..      93     112 ..      70     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0024
                                      HHHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A 60 itliifgvmAgvigtilli 78
                                      i +ii++++Ag+ + +lli
  gi|518651432|ref|YP_008140952.1|  6 ISGIILAIVAGISLFLLLI 24
                                      899**************99 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.039
                                       THHHHHHHHHHHHHHHHHHH CS
                     Glycophorin_A  59 vitliifgvmAgvigtilli 78 
                                        +t i++g++   ig+i+li
  gi|518651432|ref|YP_008140952.1|  93 ILTIIVIGIILIFIGIIFLI 112
                                       34566666666677777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1519  (0.0847231); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       125  (0.00697194); 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):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 956.12
//
Query:       gi|518651433|ref|YP_008140953.1|  [L=118]
Description: hypothetical protein FACI_IFERC00001G0072 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 825.24
//
Query:       gi|518651434|ref|YP_008140954.1|  [L=418]
Description: hypothetical protein FACI_IFERC00001G0073 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-25   90.1  38.6    1.3e-13   50.7  17.2    2.1  2  MFS_1       Major Facilitator Superfamily
      3e-07   29.6  23.5    6.9e-07   28.4  23.5    1.6  1  MFS_1_like  MFS_1 like family
  ------ inclusion threshold ------
       0.15   12.3   0.1        1.5    9.1   0.0    2.2  2  DUF1161     Protein of unknown function (DUF1161)


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 !   45.3  13.5   8.8e-16   5.3e-12       7     181 ..      13     185 ..       7     211 .. 0.83
   2 !   50.7  17.2   2.1e-17   1.3e-13       5     166 ..     211     373 ..     207     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 8.8e-16
                             MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.f 81 
                                       ++a++++++++++   ++   g++++e+g+l +    ++ ++++++Gr+sdr+G r+ +l+ g +++a+  ++ll +
  gi|518651434|ref|YP_008140954.1|  13 IIAAGATVAASFVG-VYGVMIGATAAEMGWLQSSSNSLSNLGQILWGRISDRVGKRKpFLVSGSVILAVL-WFLLpY 87 
                                       45555555555555.56666899***********999********************8888888888888.888866 PP

                             MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfy 155
                                        s  +  l+vl  l ++++++++ + +++iad     ergr + l++  +s+G+i+  ++  ++++ +      +f 
  gi|518651434|ref|YP_008140954.1|  88 -SRTPvNLIVLYSLISIFSAMITVNWYSFIADNIIS-ERGRFLTLINDIASAGTIVSLIAMVFILAKYPddVVIPFS 162
                                       .777766***************************99.*************************999888878778899 PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkr 181
                                        +a+ +++++v    ++  +++++k 
  gi|518651434|ref|YP_008140954.1| 163 TAAASYVISAV---TVFKFKESKSKS 185
                                       99999999999...555555555554 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 2.1e-17
                             MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll 80 
                                       + + ++ +s+++p++p+++ +  ++s   +  l+   +l+++++++++G ++d++ r + ++l  + l+++  l+ +
  gi|518651434|ref|YP_008140954.1| 211 TNIQSFFWSMAWPMFPITIVSIMHFSLEIVAVLTISSTLTMLLTQYIIGKFIDKVNRVPiIFLNRIMLSGIP-LMYA 286
                                       567899*************************************************66665555555555555.5555 PP

                             MFS_1  81 fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslgWravfy 155
                                       f  ++  l+++l + +G+ +++ +++  +++ d++p+++++ +i++l++++++ + +g+l gg+l+   l+ + + +
  gi|518651434|ref|YP_008140954.1| 287 F-FNILpLFILLEIYSGFIGSIQNTVTTSYTLDIVPQNNKAEYISILNGFNGMVYFFGALTGGYLLtLFLSIEPLKI 362
                                       5.78888***********************************************************55555555555 PP

                             MFS_1 156 ilaivsllafv 166
                                       +l + +l++f 
  gi|518651434|ref|YP_008140954.1| 363 ALLLSYLIVFA 373
                                       55555555543 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 !   28.4  23.5   1.2e-10   6.9e-07      21     375 ..      24     352 ..      16     358 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 1.2e-10
                        MFS_1_like  21 YltiylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlflsllfippskerqeeskl 97 
                                       ++++y   +g +a+e g + +    +s l++ +wg ++Dr+gkrk+ ++ ++++ avl++   ++p           
  gi|518651434|ref|YP_008140954.1|  24 FVGVYGVMIGATAAEMGWLQSSSNSLSNLGQILWGRISDRVGKRKPFLVSGSVILAVLWF---LLP----------- 86 
                                       77888888999************************************************9...468........... PP

                        MFS_1_like  98 evsvaqdvdaektfwilfllvvlasfflaailvlldaatlkelgedrkdyGr.qrlfGsvGyaifafitGilidhys 173
                                                 + t + l++l +l s+f+a i v   + +  ++ ++r+++   +    s G +++ +++ +++  y 
  gi|518651434|ref|YP_008140954.1|  87 ---------YSRTPVNLIVLYSLISIFSAMITVNWYSFIADNIISERGRFLTlINDIASAGTIVSLIAMVFILAKYP 154
                                       .........999999999999999999999999999*******999999865155799******************9 PP

                        MFS_1_like 174 vnllpysallyvlaallvisllvvlilnetekesklkvtksl.qvllnilknpeviifllvalilgmswgiienFlf 249
                                        ++   +  + ++aa +vis +   +++ +e +sk  +t +l + l+n+ +n      + ++ i  ++w++++  + 
  gi|518651434|ref|YP_008140954.1| 155 DDV---VIPFSTAAASYVISAVT--VFKFKESKSKSVMTRNLyKTLKNLKNNNAFYKYFRATNIQSFFWSMAWPMFP 226
                                       986...45899*********999..55556666666666666255666666777778999999**********9888 PP

                        MFS_1_like 250 lYL.kelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgi 325
                                       + + + + +s +++ +l++  ++  + + ++  k ++k+  v ++++  ++     l+ya+++ + l +++e+ +g+
  gi|518651434|ref|YP_008140954.1| 227 ITIvSIMHFSLEIVAVLTISSTLTMLLTQYIIGKFIDKVNRVPIIFLNRIMLSGIPLMYAFFNILPLFILLEIYSGF 303
                                       87769999****************************************999999999******************** PP

                        MFS_1_like 326 sfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllwd 375
                                          +   + ++y  +i+p++ +a ++++l+g+  g+  ++G+l+GG+l  
  gi|518651434|ref|YP_008140954.1| 304 IGSIQNTVTTSYTLDIVPQNNKAEYISILNGF-NGMVYFFGALTGGYLLT 352
                                       *******************************9.8************9865 PP

>> DUF1161  Protein of unknown function (DUF1161)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.13   7.7e+02      18      27 ..     233     242 ..     228     253 .. 0.81
   2 ?    9.1   0.0   0.00024       1.5      14      30 ..     308     325 ..     306     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.13
                           DUF1161  18 tsytLeiVpn 27 
                                        +++LeiV++
  gi|518651434|ref|YP_008140954.1| 233 MHFSLEIVAV 242
                                       69******87 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00024
                           DUF1161  14 angV.tsytLeiVpndqa 30 
                                       +n V tsytL+iVp+++ 
  gi|518651434|ref|YP_008140954.1| 308 QNTVtTSYTLDIVPQNNK 325
                                       46676*********9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2569.48
//
Query:       gi|518651435|ref|YP_008140955.1|  [L=166]
Description: hypothetical protein FACI_IFERC00001G0074 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.30s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1162.96
//
Query:       gi|518651436|ref|YP_008140956.1|  [L=494]
Description: Acyl-CoA synthetase [Ferroplasma acidarmanus fer1]
Scores for complete 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-94  315.4   0.0    5.4e-94  315.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.6e-18   67.4   0.6    3.6e-18   66.3   0.6    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  315.2   0.0   6.1e-98   5.4e-94      39     421 ..       3     397 ..       1     399 [. 0.84

  Alignments for each domain:
  == domain 1  score: 315.2 bits;  conditional E-value: 6.1e-98
                                       HHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHS CS
                       AMP-binding  39 LrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelayiledseakvliatvdselleklleaaa 115
                                       L +lG++kgdr+a++lpn p+++  ++ai+k+Ga++v +np +t +el++ ++ds+a +li  v ++ ++k+l+  +
  gi|518651436|ref|YP_008140956.1|   3 LGELGITKGDRIAVMLPNIPQYITYFFAIVKLGAIIVQVNPLYTMRELEFEIKDSGANTLI--VMDDFIDKALPLYP 77 
                                       6689*********************************************************..66666444444433 PP

                                       CC-EECEEEEESCCS-HCCHCCCHCCCCSCTT.S.................-TSCCCS-BTTSEEEEEEE--SSSS- CS
                       AMP-binding 116 kleavklvivldadellkeeelkeeeeseeka.e.................kpeeeeelkpddlayiiYTSGTTGkP 174
                                       ++ ++ lv+ ++   ++  ++l++  ++e+k+ +                   +e++   ++d+a+++YT+GTTG P
  gi|518651436|ref|YP_008140956.1|  78 AKLKRILVVKVQYYLPPVVSQLYTLIKKEHKKiPvadniylckvpkksklpS-KEADIDPENDPALLQYTGGTTGLP 153
                                       3333333333333333344456666666665542556788999999999742.34445666**************** PP

                                       EEEEEEHHHHHHHHHHHHHHHC..SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHH CS
                       AMP-binding 175 KGVmlshrnlvanvaslkletr..fklkeddvvlsilplahifglilelllallsGatvvllpkdaaldpkllleli 249
                                       K+++l+h+nl++n++++  e +  +k k++  +ls  p++h++g+++++l++ll+G++++l+p  +++d k+ l+ i
  gi|518651436|ref|YP_008140956.1| 154 KAAILTHKNLISNAYQII-E-YmpDKYKKNISYLSSIPFFHVYGMMTAMLTPLLQGSKIILIP--DPRDIKTALKII 226
                                       ****************84.3.3356677889*******************************9..446777889*** PP

                                       HHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE CS
                       AMP-binding 250 eklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtv 326
                                       +k k+  ++g+P++++ ++  ++ k    ++    ++++++g++pl+ el++ f++ +g  ++egYGl+E+++v+ v
  gi|518651436|ref|YP_008140956.1| 227 DKKKPVAFPGIPTLYHGIITYKDVK----KYHIDNVKICISGASPLPVELQKNFESMTGAILVEGYGLSECSPVANV 299
                                       ******************9965666....446889****************************************55 PP

                                       ....CHCTTTCTSTTS-BEE-TTEEEEEE-TTTS.CBEETTSEEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEE CS
                       AMP-binding 327 ....lpleedkkklgsvGkplpgvevkivDeetg.epvpdgeeGellvrgpgvmkgYlkkpeataeafdsegrwlrT 398
                                            +++e+ ++ gsvG p+ ++  kiv  e+g  ++p +e+Gel+++gp+vmkgY+++p+++a++++  ++wl+T
  gi|518651436|ref|YP_008140956.1| 300 tplvEDDREKYRRFGSVGLPVSNTYEKIVSTEDGvTEMPLNEPGELVIKGPQVMKGYWNRPDENAKTMV--DGWLHT 374
                                       578777789999*****************6655515789*****************************9..57**** PP

                                       EEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 399 GDlgrldedGyleivgRkkdlik 421
                                       GD++++dedGy++iv+R kdli+
  gi|518651436|ref|YP_008140956.1| 375 GDIAKMDEDGYVYIVDREKDLII 397
                                       **********************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.6     4e-22   3.6e-18       1      76 []     407     481 ..     407     481 .. 0.95

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 4e-22
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       evE+++ + p+V+e+aV+Gv+d+ +Ge+++af+v kd  +++++e++ +++++l+ y+vpk ++f delp+t  GK
  gi|518651436|ref|YP_008140956.1| 407 EVEEVIYENPKVSECAVIGVKDAHRGETVKAFIVKKDS-SLTDAEIINFCKERLAVYKVPKIIEFRDELPLTLVGK 481
                                       8*********************************9854.4578*****************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3139.39
//
Query:       gi|518651437|ref|YP_008140957.1|  [L=207]
Description: hypothetical protein FACI_IFERC00001G0076 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1050  (0.0585643); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1355.92
//
Query:       gi|518651438|ref|YP_008140958.1|  [L=447]
Description: hypothetical protein FACI_IFERC00001G0077 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.026   14.9   0.1      0.064   13.6   0.1    1.6  1  Eaf7      Chromatin modification-related protein EAF7
          1    9.9   5.4       0.44   11.1   0.4    3.0  3  Csd3_N    Csd3 N-terminal


Domain annotation for each model (and alignments):
>> Eaf7  Chromatin modification-related protein EAF7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.2e-06     0.064      48     104 ..      12      64 ..       6      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.2e-06
                              Eaf7  48 khtsiediwekLktlYdLkaldelenekeeeeeeeekekeekakeleekkdFeLPed 104
                                        h+++++i+ kL  +Y  ++ d++ +++ ++++       + ++ +  +kdF LPe+
  gi|518651438|ref|YP_008140958.1|  12 GHIEVKKIKGKLYAYYTVNKWDKRTKKEIKKSKYMG----KVKDGRIIQKDFVLPEK 64 
                                       6899********************999554444444....346789999******97 PP

>> Csd3_N  Csd3 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   4.9e-05      0.44      15      81 ..      15      97 ..      10      99 .. 0.86
   2 ?   -2.0   0.1      0.59   5.3e+03      39      62 ..     144     170 ..     133     186 .. 0.54
   3 ?   -2.2   0.1       0.7   6.3e+03       8      25 ..     360     377 ..     357     381 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.9e-05
                            Csd3_N 15 eknnipek..lyynldeedkellseiragvkyyelrd...............dkgellqalipvneelQihifkdkdkY 76
                                      e ++i+ k   yy++++ dk+  +ei+    + +++d               + g++  +l+++n++l i+i +   kY
  gi|518651438|ref|YP_008140958.1| 15 EVKKIKGKlyAYYTVNKWDKRTKKEIKKSKYMGKVKDgriiqkdfvlpekslQYGDI-ALLMDLNKDLVIKILRGFTKY 92
                                      566777772247**********************************99988888886.5899************99999 PP

                            Csd3_N 77 rleii 81
                                      + eii
  gi|518651438|ref|YP_008140958.1| 93 KTEII 97
                                      99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.59
                            Csd3_N  39 ragvkyyelrd...dkgellqalipvn 62 
                                        ++ ++ye +    ++  l+++ i++n
  gi|518651438|ref|YP_008140958.1| 144 SSERNLYESMTvieENMLLMHIEISIN 170
                                       444444433332113444444444433 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.7
                            Csd3_N   8 etllefleknnipeklyy 25 
                                       ++  ++l  n+i  ++y 
  gi|518651438|ref|YP_008140958.1| 360 MSVDGYLILNSIALEMYL 377
                                       566789999****99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.55
# Mc/sec: 2432.08
//
Query:       gi|518651439|ref|YP_008140959.1|  [L=44]
Description: hypothetical protein FACI_IFERC00001G0078 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       176  (0.0098165); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); 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 0.29s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 310.85
//
Query:       gi|518651440|ref|YP_008140960.1|  [L=400]
Description: ATPase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   89.5   3.1    3.8e-25   88.6   3.1    1.5  1  ATPase    KaiC


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   3.1   2.1e-29   3.8e-25       4     226 ..     180     399 ..     177     400 .] 0.92

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.1e-29
                            ATPase   4 gIeglDeilkgGipegrvvlitGepGtGKti.falqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                       gI ++D+il  G+ e++v+ i  +  +G t+ f  +Fl++ga + g++g+++t+  ++e + + a s+G+++++l +
  gi|518651440|ref|YP_008140960.1| 180 GIDEFDNILLYGLEENNVYGIE-TFSSGNTLyFLSKFLMQGALN-GQNGLYITTRYSPEYILKIADSFGINIKQLVN 254
                                       9********************8.567899986889*********.******************************** PP

                            ATPase  80 egklaiidasesaeesaee.....kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvl 151
                                         k++i d  +s e+ +++     k ++ ++++i+e+ ++i ++++kr+viDsi++l+ +       + +r l+++l
  gi|518651440|ref|YP_008140960.1| 255 DKKIFIFDGNSSLEKFQHSesdiwKIRDHISKVISEIGKYITKYNIKRLVIDSIEPLEISP----GEDSIRYLFNEL 327
                                       ********9999888666678999*********************************3333....34677789999* PP

                            ATPase 152 kklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIte.egikv 226
                                       k+l+++++ +       ++++ + +e    +g++ +      ++++ ++ i k  + + s++ ++++It+ ++ ++
  gi|518651440|ref|YP_008140960.1| 328 KNLDCVTMATKY----INNINSNSIEDMYFTGIVEIGTVIDLNSIKNIIVIKKFMIRDNSRRLVEYNITDkNTLEI 399
                                       ********9998....5899*****************99999****************************888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       841  (0.0469072); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3121.68
//
Query:       gi|518651441|ref|YP_008140961.1|  [L=388]
Description: cellulose synthase (UDP-forming) [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   83.9   0.0    1.4e-23   83.9   0.0    1.9  2  Glyco_trans_2_3  Glycosyl transferase family group 2
    1.5e-19   70.4   0.1    2.7e-19   69.6   0.1    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    1.5e-15   57.7   0.0      2e-15   57.3   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.4e-13   50.7   0.0    2.2e-13   50.1   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    9.1e-11   41.0   6.0    2.1e-10   39.8   4.8    1.8  2  Cellulose_synt   Cellulose synthase
  ------ inclusion threshold ------
       0.42   10.6   5.5       0.13   12.2   2.0    1.9  2  DUF5345          Family of unknown function (DUF5345)


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 !   83.9   0.0   4.6e-27   1.4e-23       2     186 ..      61     271 ..      60     282 .. 0.71
   2 ?   -2.9   2.1       1.8   5.3e+03     169     193 ..     353     377 ..     328     386 .. 0.42

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4.6e-27
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelas.pevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       +++ DaD  + +++l e++  +++ ++  i+q p  ++n+++ +++ a   + e ++++i  +++l + ++s Gs++
  gi|518651441|ref|YP_008140961.1|  61 FAVFDADQEPLQEFLTELIPIMEDnDDLSIIQVPQKYVNNNTPVAKGAN-DIQEVFYNFITEGKSLENSMFSCGSNV 136
                                       6899*******************758********999866555555555.37899********************** PP

                   Glyco_trans_2_3  78 flrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.....elekl 149
                                       + r + ++++gg++  e++v+ED+  +++l + Gy+ ++++ +l + + p tl  ++ Q +Rw +G      +   +
  gi|518651441|ref|YP_008140961.1| 137 IYRTETIKSIGGFN--EKNVTEDLATSIKLHESGYHSIYYNRPLAYGEAPQTLNSYFIQQSRWSQGSigiffQ---V 208
                                       **************..**************************************************7554441...2 PP

                   Glyco_trans_2_3 150 il...............lvrllgylgsllwsalplhl.allllfslla..........lalvl 186
                                       i                ++++  +++  +++ l+l + +l++ f++++          +a+++
  gi|518651441|ref|YP_008140961.1| 209 IKllfrrkkltlrqktgYFVSTSWYFVGVVNMLMLVFpLLFIFFNIVSiitpenyifiFAFYI 271
                                       222222233333333332222222222222222222212223333333455555332233333 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                   Glyco_trans_2_3 169 lhlallllfsllalalvllllllla 193
                                        +++ +l+++ l ++l  +++l+++
  gi|518651441|ref|YP_008140961.1| 353 YSVYRYLISGTLEYLLNGIFMLYFF 377
                                       2222222223222333333333332 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 !   69.6   0.1   9.1e-23   2.7e-19      32     168 ..      10     145 ..       9     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 9.1e-23
                                       EEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHHH. CS
                   Glycos_transf_2  32 ivvDDgStDetveileelakedprvrvirreenv.GkagalnaglraatgdyilflDaDdepdpdwleklvealekd 107
                                       +++DD+   +t e +++la  + r+ +i+r++++  kagaln +l+ ++++y++++DaD ep  ++l +l+  +e+ 
  gi|518651441|ref|YP_008140961.1|  10 YILDDSTDKKTIEDIKDLA-LRYRIGYIHRDNRRgYKAGALNDALKITDSKYFAVFDADQEPLQEFLTELIPIMED- 84 
                                       6899999999********7.7*************99****************************************. PP

                                       TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCSTCCCEEEEHHHHH CS
                   Glycos_transf_2 108 gadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfeigsaallrrealee 168
                                       ++d+ + q+p + +++++      +  +e +y+++++++   n++f +gs+ ++r e +++
  gi|518651441|ref|YP_008140961.1|  85 NDDLSIIQVPQKYVNNNTPVAKGANDIQEVFYNFITEGKSLENSMFSCGSNVIYRTETIKS 145
                                       77788888888777777777666679*****************************997766 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   6.8e-19     2e-15      35     228 ..      10     198 ..       8     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 6.8e-19
                   Glyco_tranf_2_3  35 vvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralnealravksdlvllvDdDtvvePdtlkrllqf 111
                                       ++ +d  d++t+e+++ la ++   r+ +++++++  ++ k+ aln+al++++s++ +++D+D     ++l  l ++
  gi|518651441|ref|YP_008140961.1|  10 YILDDSTDKKTIEDIKDLALRY---RIGYIHRDNR--RGYKAGALNDALKITDSKYFAVFDADQEPLQEFLTELIPI 81 
                                       56788899**********9999...899****995..558************************************* PP

                   Glyco_tranf_2_3 112 f.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg.vltlnGsgslirrevlkelegldplfllt 185
                                       +   ++  ++++p+ +++n + +   +++  ++e + +f    ++l   +++ Gs + +r+e  k ++g+ + +++t
  gi|518651441|ref|YP_008140961.1|  82 MeDNDDLSIIQVPQkYVNNNTPVAKGAND--IQEVFYNFITEGKSLEnSMFSCGSNVIYRTETIKSIGGFNE-KNVT 155
                                       *8888******999455555555665566..5577777777788886467777*******************.**** PP

                   Glyco_tranf_2_3 186 dDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwv 228
                                       +D+ ++  l + g+++ y+++++ + + p++l  y+ q  Rw+
  gi|518651441|ref|YP_008140961.1| 156 EDLATSIKLHESGYHSIYYNRPLAYGEAPQTLNSYFIQQSRWS 198
                                       ******************************************7 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 !   50.1   0.0   7.3e-17   2.2e-13      12     172 ..      39     198 ..      29     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 7.3e-17
                   Glyco_transf_21  12 pvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdakglaaaleaaflntl 87 
                                            +K  +l+ al+    +++ + D+d    +++L+el   +ed ++ ++++ +  +++ ++  a+ ++ + + +
  gi|518651441|ref|YP_008140961.1|  39 DNRRGYKAGALNDALKITDSKYFAVFDADQEPLQEFLTELIPIMEDnDDLSIIQVPQKYVNNNTPVAKGANDIQEVF 115
                                       556678999*************************************677888888888******************* PP

                   Glyco_transf_21  88 agvlqa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslr 162
                                       +++++   +l+   f +G+ +++r+e++++iGGf++  +++ eD+a++  l++ G+  +  ++p+a  ++p+  +l 
  gi|518651441|ref|YP_008140961.1| 116 YNFITEgkSLENSMFSCGSNVIYRTETIKSIGGFNE--KNVTEDLATSIKLHESGYHSIYYNRPLAYGEAPQ--TLN 188
                                       *****99888999***********************..****************************999985..9** PP

                   Glyco_transf_21 163 allaRqlrWa 172
                                       +++ +q rW+
  gi|518651441|ref|YP_008140961.1| 189 SYFIQQSRWS 198
                                       *********8 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.069   2.1e+02     158     244 ..      22      97 ..       8     121 .. 0.69
   2 !   39.8   4.8   7.2e-14   2.1e-10     408     575 ..     139     302 ..     100     355 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.069
                    Cellulose_synt 158 edveGnelp.rlvyvsrekrpGydhnkkaGamnalvrvsavlsnapfilnldcdhyinnskalreamcflldrelGk 233
                                       ed++   l  r+ y+ r+ r Gy    kaGa+n  ++    ++++ ++  +d d      + l e + ++ d+   +
  gi|518651441|ref|YP_008140961.1|  22 EDIKDLALRyRIGYIHRDNRRGY----KAGALNDALK----ITDSKYFAVFDADQEPL-QEFLTELIPIMEDN---D 86 
                                       45555444326789999999999....8999998777....56788888888887533.23445555444444...4 PP

                    Cellulose_synt 234 kvcyvqfpqrf 244
                                       +++ +q pq++
  gi|518651441|ref|YP_008140961.1|  87 DLSIIQVPQKY 97 
                                       88888888876 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 7.2e-14
                    Cellulose_synt 408 ktewGkeiG.wiyGsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalf 483
                                       +te  k+iG +    vted+ t  k+h+ G++s+y   +r+   G ap  l   + q  rw+ Gs+ iff     lf
  gi|518651441|ref|YP_008140961.1| 139 RTETIKSIGgFNEKNVTEDLATSIKLHESGYHSIYY--NRPLAYGEAPQTLNSYFIQQSRWSQGSIGIFFQVIKLLF 213
                                       677777776244578********************7..577778**************************9999999 PP

                    Cellulose_synt 484 agykkklkllerlaylnviiypftsifllvycilpalsllsgkfivkelsnlasiyllllflsl..ivlavlelkws 558
                                           kkl l ++  y+ ++ + f  ++ ++  ++p l ++ +   + + +n++ i+ + +++ +  +  +v  ++ s
  gi|518651441|ref|YP_008140961.1| 214 RR--KKLTLRQKTGYFVSTSWYFVGVVNMLMLVFPLLFIFFNIVSIITPENYIFIFAFYIIFNFfaFSSSVYSVEKS 288
                                       88..9***********999999999999999999*999998876666666666555555544440034456666655 PP

                    Cellulose_synt 559 Gvsleewwrneqfwvig 575
                                        +      rn  +  i+
  gi|518651441|ref|YP_008140961.1| 289 IIP---VMRNMSLTFIS 302
                                       444...35665555554 PP

>> DUF5345  Family of unknown function (DUF5345)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.0   4.4e-05      0.13      24      75 ..     207     258 ..     194     259 .. 0.90
   2 ?   -2.8   0.1       2.2   6.6e+03      38      51 ..     338     351 ..     335     356 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.4e-05
                           DUF5345  24 qllaeekerkrkrlrrElllFlliAllilsllllalvqapalfiviQviali 75 
                                       q ++   +rk+  lr+    F++++  +++++ ++++ +p lfi+++++++i
  gi|518651441|ref|YP_008140961.1| 207 QVIKLLFRRKKLTLRQKTGYFVSTSWYFVGVVNMLMLVFPLLFIFFNIVSII 258
                                       5666667899999************************************998 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                           DUF5345  38 rrElllFlliAlli 51 
                                       +  ll+F+++ + +
  gi|518651441|ref|YP_008140961.1| 338 WAQLLIFFITGIGL 351
                                       66788998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2665.82
//
Query:       gi|518651442|ref|YP_008140962.1|  [L=349]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   0.2    1.6e-29  103.1   0.2    1.3  1  DDE_Tnp_1    Transposase DDE domain
      3e-05   24.1   1.1      0.034   14.1   0.0    2.5  2  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
       0.14   12.2   0.9       0.56   10.3   0.0    2.5  3  HTH_19       Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.1   0.2   2.7e-33   1.6e-29       3     213 ..     106     308 ..     104     309 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 2.7e-33
                         DDE_Tnp_1   3 krevlivDattvrvpgtkedarwgykggkykygyklhiavdtr.sglilsvvitpgnvhdskglkqlldelrpr..k 76 
                                        ++vl++D+t++++  ++   +  y++g++++g+k+h+a  +    l+l++ itp+nvhdsk++++ll+ +++    
  gi|518651442|ref|YP_008140962.1| 106 LYSVLAIDSTFIETMVKG---SGIYQRGERRNGIKIHTAAIASpYPLPLKAIITPANVHDSKVFDDLLEYINEYisG 179
                                       589**********97777...55888***********8754441566**************************9*** PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyy 153
                                       +++++ D GY + + + +l+ekg+++++r+kkn+ +    +e ++ ++ r ++  + +  s   +n+         +
  gi|518651442|ref|YP_008140962.1| 180 NTVLTFDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIKEETFNSKIVRFRNGLELRLVSLDINNR--------KR 248
                                       ***********************************99994444444444444444444444444444........45 PP

                         DDE_Tnp_1 154 vtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                        + t+  +l+   +  +y +Rw+iE +F  +kr +++ +l +r+ln++ +q++++l+++ 
  gi|518651442|ref|YP_008140962.1| 249 EYITDILDLPEIYIYYIYMRRWVIEKIFENMKRILKITHLISRDLNGIINQVFATLISYI 308
                                       667889999************************************************995 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   5.7e-06     0.034      59     121 ..     151     219 ..     134     236 .. 0.77
   2 !    8.1   0.3   0.00041       2.4     127     150 ..     265     288 ..     240     293 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-06
                       DDE_Tnp_1_3  59 lavkltpgnvdDrepveelakellgklfa......Dkgyiskklaeelleegielitklrknmkkklls 121
                                       l++ +tp+nv+D +  ++l + + + + +      D gy     + el+e+gi+++++++kn   ++++
  gi|518651442|ref|YP_008140962.1| 151 LKAIITPANVHDSKVFDDLLEYINEYISGntvltfDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIK 219
                                       56789**********9888777665443322222399*************************8877765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00041
                       DDE_Tnp_1_3 127 lLrkrslietvndelknisqieht 150
                                       +  +r +ie +++++k+i +i h 
  gi|518651442|ref|YP_008140962.1| 265 IYMRRWVIEKIFENMKRILKITHL 288
                                       6679******************95 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   9.3e-05      0.56      15      50 ..      53      88 ..      48      90 .. 0.76
   2 ?   -2.8   0.0       1.1   6.6e+03      28      41 ..     172     184 ..     167     187 .. 0.79
   3 ?   -2.5   0.1       0.9   5.4e+03      26      46 ..     203     224 ..     196     232 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.3e-05
                            HTH_19 15 qeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      + ++a+++gis+s++s++ n + + +  +++++i++
  gi|518651442|ref|YP_008140962.1| 53 LTDIAYNNGISKSQLSKLNNKRPYSIFEKVFYSILR 88
                                      679***************977554554666677766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                            HTH_19  28 kisaiEngkkdvps 41 
                                       +i+++++g++ v++
  gi|518651442|ref|YP_008140962.1| 172 YINEYISGNT-VLT 184
                                       8999999998.765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.9
                            HTH_19  26 rskisaiEng.kkdvpsaelll 46 
                                       +++ s i ++  + v++ e+++
  gi|518651442|ref|YP_008140962.1| 203 INFVSRIKKNaDYTVIKEETFN 224
                                       6778888888866678777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2520.64
//
Query:       gi|518651443|ref|YP_008140963.1|  [L=50]
Description: hypothetical protein FACI_IFERC00001G0082 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 328.80
//
Query:       gi|518651444|ref|YP_008140964.1|  [L=466]
Description: hypothetical protein FACI_IFERC00001G0083 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3031.83
//
Query:       gi|518651445|ref|YP_008140965.1|  [L=516]
Description: hypothetical protein FACI_IFERC00001G0084 [Ferroplasma acidarmanus fer1]
Scores for complete 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-19   66.6  15.0    1.8e-05   24.4   0.1    7.9  7  TPR_1            Tetratricopeptide repeat
    7.2e-18   63.2  15.6     0.0068   16.4   0.1    8.0  7  TPR_2            Tetratricopeptide repeat
    6.2e-17   61.9  14.1    9.3e-06   26.1   0.1    7.5  8  TPR_19           Tetratricopeptide repeat
    2.9e-16   58.8   5.8    0.00015   22.3   0.1    8.4  8  TPR_14           Tetratricopeptide repeat
      2e-12   46.3  21.5     0.0026   17.9   0.1    8.7  9  TPR_8            Tetratricopeptide repeat
    9.5e-12   45.4   4.8    0.00027   21.5   0.6    6.1  6  TPR_16           Tetratricopeptide repeat
      1e-11   44.0   8.4      0.046   13.8   0.0    6.4  6  TPR_7            Tetratricopeptide repeat
    2.1e-10   40.2  10.4    8.6e-05   22.7   0.1    6.1  6  TPR_17           Tetratricopeptide repeat
    3.9e-10   39.2  14.9    0.00031   20.3   0.0    6.1  6  TPR_11           TPR repeat
    4.5e-10   39.5   0.5      0.012   15.7   0.1    4.2  6  TPR_9            Tetratricopeptide repeat
    1.8e-08   34.5  16.6      0.028   14.7   2.9    7.2  7  TPR_12           Tetratricopeptide repeat
    1.3e-06   28.6  16.7     0.0069   16.6   0.6    6.7  7  ANAPC3           Anaphase-promoting complex, cyclosome, subun
    1.8e-06   27.4   3.0      0.033   13.4   0.2    3.9  4  TPR_15           Tetratricopeptide repeat
    4.8e-06   27.1   1.4       0.12   12.8   0.9    3.6  2  BTAD             Bacterial transcriptional activator domain
    9.6e-06   25.8   6.0      0.058   13.7   0.1    5.6  7  TPR_20           Tetratricopeptide repeat
    1.7e-05   24.0  18.2    0.00034   19.7   0.0    5.0  6  NARP1            NMDA receptor-regulated protein 1
    1.8e-05   24.5  13.4        3.2    7.8   0.0    7.2  7  TPR_10           Tetratricopeptide repeat
    0.00039   20.8   0.5       0.77   10.6   0.0    4.1  3  TPR_4            Tetratricopeptide repeat
    0.00042   20.8  12.5       0.56   11.0   0.0    6.1  4  TPR_6            Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.019   15.4   0.7          3    8.3   0.0    3.7  4  Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
      0.032   13.9   5.0        4.3    7.1   0.1    4.5  5  SPOB_a           Sensor_kinase_SpoOB-type, alpha-helical doma
      0.053   13.6   6.4       0.31   11.1   0.1    4.7  4  DUF3856          Domain of Unknown Function (DUF3856)
      0.057   12.9   0.1       0.13   11.8   0.1    1.5  1  OAS1_C           2'-5'-oligoadenylate synthetase 1, domain 2,
       0.11   12.5  13.7         23    5.2   0.3    5.7  5  MIT              MIT (microtubule interacting and transport) 
       0.71   10.0   4.3        3.1    7.9   0.0    3.9  4  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat
        1.7    8.4  10.0       0.18   11.6   0.5    3.4  4  DUF5113          Domain of unknown function (DUF5113)


Domain annotation for each model (and alignments):
>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00092      0.64       4      34 .]      12      42 ..       9      42 .. 0.90
   2 ?   -1.4   0.0       3.6   2.5e+03      10      22 ..      52      64 ..      51      75 .. 0.83
   3 !   14.5   0.6   3.3e-05     0.023       9      33 ..      85     109 ..      85     110 .. 0.93
   4 !   24.4   0.1   2.6e-08   1.8e-05       3      34 .]     113     144 ..     112     144 .. 0.96
   5 ?    5.7   0.1      0.02        14       3      22 ..     147     166 ..     145     178 .. 0.82
   6 ?    1.7   0.1      0.38   2.6e+02       6      18 ..     251     263 ..     249     264 .. 0.92
   7 !   13.2   0.0   8.7e-05      0.06      10      30 ..     389     409 ..     388     412 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00092
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALelnPnn 34
                                      l  +++ +f+  ++  Ale+ ++A+++ P n
  gi|518651445|ref|YP_008140965.1| 12 LTEKAQKLFEADDFAGALEAINRAISILPRN 42
                                      66789999*******************9986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.6
                                      HHHHTT-HHHHHH CS
                             TPR_1 10 ayfklgkydeAle 22
                                      ++f+ g+++e ++
  gi|518651445|ref|YP_008140965.1| 52 ILFHSGDFEETIK 64
                                      68999****9886 PP

  == domain 3  score: 14.5 bits;  conditional E-value: 3.3e-05
                                       HHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                       ++y+++g+ ++Ale  +kA++++ +
  gi|518651445|ref|YP_008140965.1|  85 LCYLQMGEDEKALELADKAIKVDND 109
                                       69*******************9966 PP

  == domain 4  score: 24.4 bits;  conditional E-value: 2.6e-08
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                       ++yn++ a+ +lg+ ++A+ +y+  Le nP++
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSLEKNPSD 144
                                       69****************************86 PP

  == domain 5  score: 5.7 bits;  conditional E-value: 0.02
                                       HHHHHHHHHHHTT-HHHHHH CS
                             TPR_1   3 alynlGnayfklgkydeAle 22 
                                        +  l+ +y+  g+y+ A+ 
  gi|518651445|ref|YP_008140965.1| 147 GHRDLAELYLDAGNYKMAER 166
                                       56779*************85 PP

  == domain 6  score: 1.7 bits;  conditional E-value: 0.38
                                       HHHHHHHHTT-HH CS
                             TPR_1   6 nlGnayfklgkyd 18 
                                       nl+ +y+  +kyd
  gi|518651445|ref|YP_008140965.1| 251 NLAKVYYIEQKYD 263
                                       9***********9 PP

  == domain 7  score: 13.2 bits;  conditional E-value: 8.7e-05
                                       HHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  10 ayfklgkydeAleyyekALel 30 
                                       +y ++g yd+A+ey  +A+e 
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEM 409
                                       79****************997 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   0.00021      0.14       5      34 .]      13      42 ..       9      42 .. 0.90
   2 ?    0.5   0.0       1.2   8.4e+02       4      19 ..      46      61 ..      43      67 .. 0.81
   3 !   14.8   0.1   3.3e-05     0.023       6      33 ..      82     109 ..      80     110 .. 0.89
   4 !   16.4   0.1   9.9e-06    0.0068       3      34 .]     113     144 ..     112     144 .. 0.95
   5 !   10.9   0.2   0.00057      0.39       2      33 ..     146     177 ..     145     178 .. 0.87
   6 ?    1.5   0.1      0.61   4.2e+02       6      25 ..     251     270 ..     249     279 .. 0.74
   7 !   10.0   0.0    0.0011      0.77      10      31 ..     389     410 ..     388     413 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                             TPR_2  5 ynlGlayyklgdyeeAleafekAleldPnn 34
                                       + ++ +++++d++ Alea ++A+++ P+n
  gi|518651445|ref|YP_008140965.1| 13 TEKAQKLFEADDFAGALEAINRAISILPRN 42
                                      5678999*******************9987 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                             TPR_2  4 lynlGlayyklgdyee 19
                                      +    ++++++gd+ee
  gi|518651445|ref|YP_008140965.1| 46 HDFKSDILFHSGDFEE 61
                                      5667899*******98 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.3e-05
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                       +  l+y+++g+ e+Ale+ +kA++ d +
  gi|518651445|ref|YP_008140965.1|  82 MESLCYLQMGEDEKALELADKAIKVDND 109
                                       6789********************9976 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 9.9e-06
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPnn 34 
                                        +yn+++a+ +lg+ e+A+ a++ +le +P +
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSLEKNPSD 144
                                       59****************************76 PP

  == domain 5  score: 10.9 bits;  conditional E-value: 0.00057
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++  l+++y+ +g+y+ A++ ++ +l+   n
  gi|518651445|ref|YP_008140965.1| 146 DGHRDLAELYLDAGNYKMAERELKLSLRFRKN 177
                                       68999****************99988886665 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.61
                             TPR_2   6 nlGlayyklgdyeeAleafe 25 
                                       nl+++yy  ++y+     f+
  gi|518651445|ref|YP_008140965.1| 251 NLAKVYYIEQKYDMGNGIFK 270
                                       8***********96555555 PP

  == domain 7  score: 10.0 bits;  conditional E-value: 0.0011
                             TPR_2  10 ayyklgdyeeAleafekAleld 31 
                                       +y+++g y++A+e++ +A+e +
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEME 410
                                       699***************9976 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00015       0.1       1      62 [.      19      81 ..      19      85 .. 0.93
   2 !   14.6   0.1   5.1e-05     0.035       2      66 ..      54     120 ..      53     121 .. 0.90
   3 !   26.1   0.1   1.3e-08   9.3e-06       5      53 ..     125     173 ..     124     184 .. 0.91
   4 ?    4.6   0.3     0.066        45       1      36 [.     222     257 ..     222     289 .. 0.87
   5 ?    2.4   0.1      0.32   2.2e+02       6      61 ..     294     349 ..     289     350 .. 0.89
   6 ?    6.7   0.0     0.014        10      22      57 ..     377     412 ..     365     420 .. 0.82
   7 ?   -2.0   0.0       7.9   5.4e+03      46      66 ..     438     456 ..     436     460 .. 0.78
   8 ?    0.7   0.0       1.1   7.9e+02      34      52 ..     462     480 ..     451     484 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00015
                            TPR_19  1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.arya 62
                                      l+++ d+a Al++  +a++  p n ++     ++l+ +g+++e ++ L+ +   dp d + y+
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEAINRAISILPRNVDLHDFKSDILFHSGDFEETIKELEFIETLDPGDaSHYS 81
                                      7899********************************************999999999877765 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.1e-05
                            TPR_19   2 laegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd.d.aryasLlA 66 
                                       + +gd++e ++ le + + dp++a        ++l++g+ ++A +l d++ + d d + ++y +++A
  gi|518651445|ref|YP_008140965.1|  54 FHSGDFEETIKELEFIETLDPGDASHYSMESLCYLQMGEDEKALELADKAIKVDNDyEfSYYNRAKA 120
                                       66899999999999999999999999998899************************86699998887 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 1.3e-08
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpe 53 
                                       g+ ++A+++++  l+++p +++   +LAe++l +g+++ Ae+ L+  ++
  gi|518651445|ref|YP_008140965.1| 125 GRTEDAISAYRLSLEKNPSDPDGHRDLAELYLDAGNYKMAERELKLSLR 173
                                       7899***************************************987665 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.066
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeall 36 
                                       ll++gd ++A ++ +  +  + +n++ + +LA++++
  gi|518651445|ref|YP_008140965.1| 222 LLDNGDMDNAEKIAKDFYNSALDNLDMASNLAKVYY 257
                                       79**************98888999****9***9997 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.32
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                       +y+ Al++ e+   ++p+ +    +   al + g+ ++A   +++l +++pd+ +y
  gi|518651445|ref|YP_008140965.1| 294 QYDLALSIIEENARKYPEEETFIFYKFYALSEKGEHADALLPIKTLYDKQPDSIQY 349
                                       799999999998899999999999999************99999999999998666 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.014
                            TPR_19  22 pknaearllLAeallalgqldeAealLdalpeedpd 57 
                                        k +e+  ++  ++ ++g +d+A + L ++ e++ d
  gi|518651445|ref|YP_008140965.1| 377 DKGPEIERAYYTVYANMGLYDKAVEYLGRAVEMEDD 412
                                       567888899999****************99999877 PP

  == domain 7  score: -2.0 bits;  conditional E-value: 7.9
                            TPR_19  46 alLdalpeedpddaryasLlA 66 
                                       +lL++lp+++ +   +++L A
  gi|518651445|ref|YP_008140965.1| 438 QLLNTLPDKEEN--IIHALYA 456
                                       899****99998..5555554 PP

  == domain 8  score: 0.7 bits;  conditional E-value: 1.1
                            TPR_19  34 allalgqldeAealLdalp 52 
                                       +l a ++++eA ++L+ + 
  gi|518651445|ref|YP_008140965.1| 462 ILSAVNRTEEATKILEGID 480
                                       5677899*******99775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0    0.0026       1.8      11      38 ..      19      46 ..      12      52 .. 0.87
   2 ?    2.4   0.0      0.54   3.7e+02      10      35 ..      52      77 ..      47      82 .. 0.88
   3 ?    4.5   0.1      0.12        80      11      33 ..      87     109 ..      77     112 .. 0.87
   4 !   22.3   0.1   2.2e-07   0.00015       4      44 .]     114     154 ..     111     154 .. 0.95
   5 !   10.1   0.1    0.0018       1.2       2      34 ..     146     178 ..     145     188 .. 0.82
   6 ?    0.3   0.0       2.5   1.7e+03       9      26 ..     220     237 ..     213     255 .. 0.81
   7 ?   -1.0   0.0       6.8   4.7e+03       9      34 ..     321     346 ..     316     354 .. 0.80
   8 !    8.4   0.0    0.0064       4.4       2      30 ..     381     409 ..     380     416 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0026
                            TPR_14 11 llalGdpdeAiallrralalaPddaeaw 38
                                      l++++d+++A+++ +ra++  P + +++
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEAINRAISILPRNVDLH 46
                                      7899******************998876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.54
                            TPR_14 10 allalGdpdeAiallrralalaPdda 35
                                      +l+++Gd++e i+ l+ +  l+P+da
  gi|518651445|ref|YP_008140965.1| 52 ILFHSGDFEETIKELEFIETLDPGDA 77
                                      799************99998999887 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.12
                            TPR_14  11 llalGdpdeAiallrralalaPd 33 
                                       +l+ G+ ++A++l+++a++ + d
  gi|518651445|ref|YP_008140965.1|  87 YLQMGEDEKALELADKAIKVDND 109
                                       7899*************997765 PP

  == domain 4  score: 22.3 bits;  conditional E-value: 2.2e-07
                            TPR_14   4 llalaeallalGdpdeAiallrralalaPddaeawlllaql 44 
                                       ++ +a+al +lG++++Ai ++r  l+++P+d++ ++ la+l
  gi|518651445|ref|YP_008140965.1| 114 YYNRAKALNNLGRTEDAISAYRLSLEKNPSDPDGHRDLAEL 154
                                       6779**********************************986 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.0018
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPdd 34 
                                       + +++lae++l +G+++ A++ l+  l+   +d
  gi|518651445|ref|YP_008140965.1| 146 DGHRDLAELYLDAGNYKMAERELKLSLRFRKND 178
                                       6689*******************9999876665 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 2.5
                            TPR_14   9 eallalGdpdeAiallrr 26 
                                       ++ll +Gd d A++++++
  gi|518651445|ref|YP_008140965.1| 220 DFLLDNGDMDNAEKIAKD 237
                                       68999*******999887 PP

  == domain 7  score: -1.0 bits;  conditional E-value: 6.8
                            TPR_14   9 eallalGdpdeAiallrralalaPdd 34 
                                        al + G++++A+   + + +++Pd+
  gi|518651445|ref|YP_008140965.1| 321 YALSEKGEHADALLPIKTLYDKQPDS 346
                                       5788999***9998888888888876 PP

  == domain 8  score: 8.4 bits;  conditional E-value: 0.0064
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       e  +a+  ++++ G +d+A+++l ra++ 
  gi|518651445|ref|YP_008140965.1| 381 EIERAYYTVYANMGLYDKAVEYLGRAVEM 409
                                       556788899*****************985 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.9   1.3e+03      13      30 ..      21      38 ..      13      42 .. 0.80
   2 ?    0.7   0.0       1.2   8.3e+02       7      25 ..      49      67 ..      44      76 .. 0.82
   3 !   10.9   0.5   0.00061      0.42       8      33 ..      84     109 ..      80     110 .. 0.89
   4 !   17.9   0.1   3.7e-06    0.0026       3      32 ..     113     142 ..     113     144 .. 0.91
   5 !    7.3   0.3     0.009       6.2       7      33 ..     151     177 ..     150     178 .. 0.89
   6 ?    2.0   0.0      0.44     3e+02      10      24 ..     221     235 ..     213     244 .. 0.82
   7 ?   -1.3   0.2       5.3   3.6e+03       6      29 ..     251     274 ..     247     278 .. 0.71
   8 !   12.9   0.0   0.00015       0.1      10      31 ..     389     410 ..     388     413 .. 0.91
   9 ?    0.4   0.0       1.5     1e+03       7      25 ..     459     477 ..     455     478 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.9
                                      HTT-HHHHHHHHHHHHHH CS
                             TPR_8 13 klgdyeeAkeyyekalel 30
                                      +  d+  A e++++a+++
  gi|518651445|ref|YP_008140965.1| 21 EADDFAGALEAINRAISI 38
                                      556888899999999998 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1.2
                                      HHHHHHHTT-HHHHHHHHH CS
                             TPR_8  7 lgsiylklgdyeeAkeyye 25
                                      +++i++  gd+ee ++ +e
  gi|518651445|ref|YP_008140965.1| 49 KSDILFHSGDFEETIKELE 67
                                      7899*********888776 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00061
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpd 33 
                                       +++yl++g+ e+A e   ka++ d d
  gi|518651445|ref|YP_008140965.1|  84 SLCYLQMGEDEKALELADKAIKVDND 109
                                       789********************987 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 3.7e-06
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +yyn ++++ +lg+ e A+++y+  le +p
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSLEKNP 142
                                       6**********************9998666 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.009
                                       HHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekaleldpd 33 
                                       l+ +yl+ g+y++A+  ++  l+ +++
  gi|518651445|ref|YP_008140965.1| 151 LAELYLDAGNYKMAERELKLSLRFRKN 177
                                       899*************99999988776 PP

  == domain 6  score: 2.0 bits;  conditional E-value: 0.44
                                       HHHHTT-HHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyy 24 
                                        +l+ gd+++A++  
  gi|518651445|ref|YP_008140965.1| 221 FLLDNGDMDNAEKIA 235
                                       67899******9975 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 5.3
                                       HHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekale 29 
                                       nl+++y   ++y++    ++++++
  gi|518651445|ref|YP_008140965.1| 251 NLAKVYYIEQKYDMGNGIFKEYIK 274
                                       789999888888876555666655 PP

  == domain 8  score: 12.9 bits;  conditional E-value: 0.00015
                                       HHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleld 31 
                                       +y ++g y++A+ey+ +a+e++
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEME 410
                                       699*****************97 PP

  == domain 9  score: 0.4 bits;  conditional E-value: 1.5
                                       HHHHHHHTT-HHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyye 25 
                                       +++i++  ++ eeA + +e
  gi|518651445|ref|YP_008140965.1| 459 KACILSAVNRTEEATKILE 477
                                       899***********99886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0022       1.5       3      52 ..      15      61 ..      13      67 .. 0.92
   2 ?    6.3   0.0     0.023        16       7      66 ..      53     109 ..      51     111 .. 0.87
   3 !   21.5   0.6   3.9e-07   0.00027       1      56 [.     115     167 ..     115     178 .. 0.88
   4 ?    1.0   0.0         1   6.9e+02       7      50 ..     222     262 ..     221     263 .. 0.85
   5 ?    2.6   0.0      0.31   2.1e+02      13      67 ..     295     346 ..     289     347 .. 0.74
   6 ?    2.2   0.0      0.44     3e+02       7      27 ..     390     410 ..     388     412 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0022
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlae 52
                                      +a+ +++a d++ A++a ++a+      P++++ + ++ d++++ g+++e
  gi|518651445|ref|YP_008140965.1| 15 KAQKLFEADDFAGALEAINRAISIL---PRNVDLHDFKSDILFHSGDFEE 61
                                      677899*******************...*******************987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.023
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       ++ +gd+++ ++ le    +d   P +a  +    +++l+ g+ ++A++l ++a++ + d
  gi|518651445|ref|YP_008140965.1|  53 LFHSGDFEETIKELEFIETLD---PGDASHYSMESLCYLQMGEDEKALELADKAIKVDND 109
                                       566788888889998889999...*****************************9977665 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 3.9e-07
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaal 56 
                                       +++a+a+ ++g+ +dA+ a++  l+++   P +++ +  l++++l +g+++ A+  
  gi|518651445|ref|YP_008140965.1| 115 YNRAKALNNLGRTEDAISAYRLSLEKN---PSDPDGHRDLAELYLDAGNYKMAERE 167
                                       78999999*******************...66667***************999843 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 1
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrl 50 
                                       +l++gd d A++ ++ +  ++    d+ +++ +l+ +++  + +
  gi|518651445|ref|YP_008140965.1| 222 LLDNGDMDNAEKIAKDFYNSA---LDNLDMASNLAKVYYIEQKY 262
                                       6899*******9999999999...99999999999998876665 PP

  == domain 5  score: 2.6 bits;  conditional E-value: 0.31
                            TPR_16  13 yddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapda 67 
                                       yd A+   e+  +++   P+   + +++  a+ ++g++a+A+  ++ +++  pd+
  gi|518651445|ref|YP_008140965.1| 295 YDLALSIIEENARKY---PEEETFIFYKFYALSEKGEHADALLPIKTLYDKQPDS 346
                                       566666665555666...5655666666678999********9999999999986 PP

  == domain 6  score: 2.2 bits;  conditional E-value: 0.44
                            TPR_16   7 alragdyddAaaaleaalkrd 27 
                                       +++ g yd+A+++l +a+++ 
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAVEME 410
                                       788999**********99876 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.021        14       7      31 ..      84     107 ..      78     111 .. 0.75
   2 !   13.6   0.0   7.6e-05     0.052       1      35 [.     113     145 ..     113     147 .. 0.86
   3 !    9.6   0.1    0.0014      0.97       5      32 ..     151     178 ..     148     181 .. 0.91
   4 ?   -1.1   0.0       3.7   2.6e+03       3      20 ..     216     233 ..     215     236 .. 0.81
   5 !   13.8   0.0   6.6e-05     0.046       8      35 ..     389     416 ..     388     417 .. 0.89
   6 ?   -1.6   0.0       5.4   3.7e+03       6      23 ..     460     477 ..     458     478 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                             TPR_7   7 rl.ysrlGdyeeAielyeqsLaltkd 31 
                                       +l y ++G+ e+A+el  +  a+  d
  gi|518651445|ref|YP_008140965.1|  84 SLcYLQMGEDEKALELADK--AIKVD 107
                                       55599***********999..55443 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 7.6e-05
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +++n a +  +lG++e+Ai+ y+    l+k p+d+
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRL--SLEKNPSDP 145
                                       6999********************..666666654 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0014
                             TPR_7   5 LarlysrlGdyeeAielyeqsLaltkdp 32 
                                       La+ly + G+y+ A++ ++ sL+++k +
  gi|518651445|ref|YP_008140965.1| 151 LAELYLDAGNYKMAERELKLSLRFRKND 178
                                       9*******************99998765 PP

  == domain 4  score: -1.1 bits;  conditional E-value: 3.7
                             TPR_7   3 lnLarlysrlGdyeeAie 20 
                                       +++ +   + Gd+++A++
  gi|518651445|ref|YP_008140965.1| 216 VRITDFLLDNGDMDNAEK 233
                                       5677888899******86 PP

  == domain 5  score: 13.8 bits;  conditional E-value: 6.6e-05
                             TPR_7   8 lysrlGdyeeAielyeqsLaltkdpeda 35 
                                       +y ++G y++A+e++ ++ ++++d ed+
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEMEDDIEDI 416
                                       5999*************99999998876 PP

  == domain 6  score: -1.6 bits;  conditional E-value: 5.4
                             TPR_7   6 arlysrlGdyeeAielye 23 
                                       a + s+++++eeA +++e
  gi|518651445|ref|YP_008140965.1| 460 ACILSAVNRTEEATKILE 477
                                       678999******977766 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         9   6.2e+03       3      16 ..      33      46 ..      31      47 .. 0.86
   2 ?    2.2   0.0      0.41   2.8e+02       8      34 .]      71      98 ..      66      98 .. 0.85
   3 !   16.3   0.3   1.3e-05    0.0092       2      33 ..     100     131 ..      99     132 .. 0.94
   4 !   22.7   0.1   1.2e-07   8.6e-05       2      33 ..     134     165 ..     133     166 .. 0.94
   5 ?   -1.3   0.1       5.6   3.9e+03      17      30 ..     250     263 ..     244     266 .. 0.73
   6 ?   -2.1   0.0       9.9   6.8e+03      17      32 ..     317     332 ..     309     333 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 9
                            TPR_17  3 lkaleldPnnaday 16
                                       +a+ + P n+d++
  gi|518651445|ref|YP_008140965.1| 33 NRAISILPRNVDLH 46
                                      6999999***9975 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.41
                            TPR_17  8 l.dPnnadaynnLAelllknGdlmtArq 34
                                        dP +a +y +   ++l+ G+ ++A++
  gi|518651445|ref|YP_008140965.1| 71 TlDPGDASHYSMESLCYLQMGEDEKALE 98
                                      559*******************999975 PP

  == domain 3  score: 16.3 bits;  conditional E-value: 1.3e-05
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                         ka++ d ++  +y+n+A++l ++G++++A+
  gi|518651445|ref|YP_008140965.1| 100 ADKAIKVDNDYEFSYYNRAKALNNLGRTEDAI 131
                                       689***************************97 PP

  == domain 4  score: 22.7 bits;  conditional E-value: 1.2e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y+ +le++P+++d +  LAel+l +G++++A+
  gi|518651445|ref|YP_008140965.1| 134 YRLSLEKNPSDPDGHRDLAELYLDAGNYKMAE 165
                                       7779***************************8 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 5.6
                            TPR_17  17 nnLAelllknGdlm 30 
                                        nLA++++   +++
  gi|518651445|ref|YP_008140965.1| 250 SNLAKVYYIEQKYD 263
                                       69999999766665 PP

  == domain 6  score: -2.1 bits;  conditional E-value: 9.9
                            TPR_17  17 nnLAelllknGdlmtA 32 
                                       +++ ++l+++G++++A
  gi|518651445|ref|YP_008140965.1| 317 FYKFYALSEKGEHADA 332
                                       677789999**99998 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.013       8.6       4      31 ..      19      46 ..      16      46 .. 0.91
   2 ?    0.2   0.0      0.87     6e+02       2      18 ..      51      67 ..      51      81 .. 0.81
   3 !   18.7   0.9   1.5e-06     0.001       4      42 .]      87     125 ..      86     125 .. 0.95
   4 !   20.3   0.0   4.5e-07   0.00031       4      42 .]     121     159 ..     119     159 .. 0.91
   5 ?   -1.8   0.0       3.8   2.7e+03      32      39 ..     250     257 ..     244     262 .. 0.81
   6 ?    0.6   0.0      0.69   4.8e+02       4      22 ..     390     408 ..     388     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.013
                            TPR_11  4 yyeqGkyeeAieaYkkAlkldPdnaeay 31
                                      ++e  ++ +A+ea ++A+ + P n++++
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEAINRAISILPRNVDLH 46
                                      78888999******************98 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.87
                            TPR_11  2 dayyeqGkyeeAieaYk 18
                                      d+++  G++ee i++++
  gi|518651445|ref|YP_008140965.1| 51 DILFHSGDFEETIKELE 67
                                      78999******999876 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 1.5e-06
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       y + G+ e+A+e   kA+k d+d+   yyn+++a+ ++G
  gi|518651445|ref|YP_008140965.1|  87 YLQMGEDEKALELADKAIKVDNDYEFSYYNRAKALNNLG 125
                                       899*******************************98776 PP

  == domain 4  score: 20.3 bits;  conditional E-value: 4.5e-07
                            TPR_11   4 yyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       +  +G+ e+Ai aY+  l+ +P++++ +  L+++y+  G
  gi|518651445|ref|YP_008140965.1| 121 LNNLGRTEDAISAYRLSLEKNPSDPDGHRDLAELYLDAG 159
                                       6678*******************************8765 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 3.8
                            TPR_11  32 ynLGlayy 39 
                                       +nL+++yy
  gi|518651445|ref|YP_008140965.1| 250 SNLAKVYY 257
                                       68999998 PP

  == domain 6  score: 0.6 bits;  conditional E-value: 0.69
                            TPR_11   4 yyeqGkyeeAieaYkkAlk 22 
                                       y   G y++A+e + +A++
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAVE 408
                                       6667889*****9999987 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0045       3.1      28      65 ..       8      45 ..       4      52 .. 0.76
   2 !   13.0   0.0   0.00013     0.088       6      64 ..      20      78 ..      15      86 .. 0.89
   3 ?    3.9   0.0     0.088        60       5      50 ..      53      98 ..      50     120 .. 0.87
   4 !    8.3   0.0    0.0036       2.5       4      64 ..      86     146 ..      84     146 .. 0.93
   5 !   15.7   0.1   1.8e-05     0.012      10      53 ..     126     169 ..     117     185 .. 0.90
   6 ?    5.1   0.0     0.035        24      38      66 ..     389     417 ..     383     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0045
                             TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                       ++e+ + ++ l++ +++++Al++ ++++++ p + d 
  gi|518651445|ref|YP_008140965.1|  8 NVYELTEKAQKLFEADDFAGALEAINRAISILPRNVDL 45
                                      57888888888888888888888888888888866554 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00013
                             TPR_9  6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64
                                       +++d++ al++++r + + P+ ++++     +l+++G++++ +++Le    l+p ++ 
  gi|518651445|ref|YP_008140965.1| 20 FEADDFAGALEAINRAISILPRNVDLHDFKSDILFHSGDFEETIKELEFIETLDPGDAS 78
                                      5799*******************************************987777776655 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.088
                             TPR_9  5 aireedweralavverllllaPddpeerrdRGlllaqlGclsaAla 50
                                      +  + d+e++++ +e +  l+P d++ +    l++ q+G  ++Al+
  gi|518651445|ref|YP_008140965.1| 53 LFHSGDFEETIKELEFIETLDPGDASHYSMESLCYLQMGEDEKALE 98
                                      56678999999999999999999999999999*******9999986 PP

  == domain 4  score: 8.3 bits;  conditional E-value: 0.0036
                             TPR_9   4 iaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       ++++  + e+al+ ++  + ++ d    ++ R+ +l  lG+++ A+ +    l+++p++pd
  gi|518651445|ref|YP_008140965.1|  86 CYLQMGEDEKALELADKAIKVDNDYEFSYYNRAKALNNLGRTEDAISAYRLSLEKNPSDPD 146
                                       5788888899999*********99999*******************************997 PP

  == domain 5  score: 15.7 bits;  conditional E-value: 1.8e-05
                             TPR_9  10 dweralavverllllaPddpeerrdRGlllaqlGclsaAladLe 53 
                                       + e a+ ++ + l  +P dp+ +rd + l+   G+++ A ++L 
  gi|518651445|ref|YP_008140965.1| 126 RTEDAISAYRLSLEKNPSDPDGHRDLAELYLDAGNYKMAERELK 169
                                       7789999********************************99996 PP

  == domain 6  score: 5.1 bits;  conditional E-value: 0.035
                             TPR_9  38 llaqlGclsaAladLeaylalapdapdae 66 
                                       ++a +G + +A++ L +++++++d +d+ 
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEMEDDIEDIS 417
                                       79*******************99877765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0         2   1.4e+03      55      75 ..      19      39 ..      12      41 .. 0.73
   2 !   11.8   0.0   0.00033      0.22      41      75 ..      73     107 ..      44     109 .. 0.79
   3 !   14.7   2.9     4e-05     0.028       5      76 ..     113     176 ..     109     177 .. 0.88
   4 ?    0.7   0.0      0.94   6.5e+02       5      20 ..     248     263 ..     216     264 .. 0.72
   5 ?    0.8   0.0       0.9   6.2e+02       4      21 ..     247     264 ..     244     271 .. 0.82
   6 !    7.8   0.1    0.0059       4.1      12      32 ..     389     409 ..     383     415 .. 0.89
   7 ?   -0.8   0.0       2.9     2e+03      25      69 ..     432     477 ..     431     477 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2
                            TPR_12 55 yralgryeeAlelleealaia 75
                                      ++++++++ Ale+ ++a+ i+
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEAINRAISIL 39
                                      567778888888888888775 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00033
                            TPR_12  41 hpltattlrnLgrlyralgryeeAlelleealaia 75 
                                        p+ a+ +   + +y+++g+ e+Alel  +a++++
  gi|518651445|ref|YP_008140965.1|  73 DPGDASHYSMESLCYLQMGEDEKALELADKAIKVD 107
                                       5678999***********************99875 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 4e-05
                            TPR_12   5 alnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaiae 76 
                                       +++n+a +l+ lgr ++A++ ++ +le       p  p+     r+L++ly+ +g+y+ A++ l+ +l+ ++
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSLEKN-----PSDPD---GHRDLAELYLDAGNYKMAERELKLSLRFRK 176
                                       578**********************8888.....44444...389********************9999887 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.94
                            TPR_12   5 alnnlaavlrrlgryd 20 
                                       +++nla v++  ++yd
  gi|518651445|ref|YP_008140965.1| 248 MASNLAKVYYIEQKYD 263
                                       4556666666666665 PP

  == domain 5  score: 0.8 bits;  conditional E-value: 0.9
                            TPR_12   4 talnnlaavlrrlgryde 21 
                                        +++nla v++  ++yd 
  gi|518651445|ref|YP_008140965.1| 247 DMASNLAKVYYIEQKYDM 264
                                       577899999999999985 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0059
                            TPR_12  12 vlrrlgrydeAlellekalei 32 
                                       v++ +g yd+A e+l +a+e+
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEM 409
                                       89999*********9999986 PP

  == domain 7  score: -0.8 bits;  conditional E-value: 2.9
                            TPR_12  25 llekaleiarrl.lGpdhpltattlrnLgrlyralgryeeAlelle 69 
                                       ++ek +++ + l   +++   a + +  + +++a +r+eeA ++le
  gi|518651445|ref|YP_008140965.1| 432 YHEKIIQLLNTLpDKEENIIHALYAIEKACILSAVNRTEEATKILE 477
                                       5666666666662223334444444455556677799999877765 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0      0.12        82      21      74 ..       4      61 ..       1      69 [. 0.70
   2 !   16.6   0.6     1e-05    0.0069      20      79 ..      74     134 ..      69     137 .. 0.90
   3 ?    1.0   0.0      0.75   5.2e+02      29      44 ..     151     166 ..     136     177 .. 0.82
   4 !    8.5   0.5    0.0032       2.2       1      75 [.     224     298 ..     224     305 .. 0.74
   5 ?   -0.4   0.1         2   1.4e+03       5      57 ..     295     348 ..     291     355 .. 0.63
   6 ?    1.2   0.0      0.63   4.3e+02      31      49 ..     388     406 ..     369     416 .. 0.76
   7 ?    2.3   0.1      0.29     2e+02      41      81 ..     435     478 ..     429     479 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.12
                                      --HHHHHHH...HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHH CS
                            ANAPC3 21 espedayll...AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyee 74
                                       +++++y l   A+ l+++ ++  A+e +++a  + +++   +  +   l+  + +ee
  gi|518651445|ref|YP_008140965.1|  4 TDNKNVYELtekAQKLFEADDFAGALEAINRAiSILPRNVDLHDFKSDILFHSGDFEE 61
                                      466677776666****************999977776666655555555555555555 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1e-05
                                       H--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3  20 tespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       + ++++  + +lc++++g+ ++A+el++ka k ++  + + y  A++l  L++ e+Ai+a+
  gi|518651445|ref|YP_008140965.1|  74 PGDASHYSMESLCYLQMGEDEKALELADKAiKVDNDYEFSYYNRAKALNNLGRTEDAISAY 134
                                       55666667779*******************99999999********************986 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.75
                                       HHHHHHHTT-HHHHHH CS
                            ANAPC3  29 lAlclylngqykrAye 44 
                                       lA+ ++ +g+yk A +
  gi|518651445|ref|YP_008140965.1| 151 LAELYLDAGNYKMAER 166
                                       7889999999998865 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0032
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeA 75 
                                       d+++ +nA+ +a   +++  ++++ a  lA+++y  ++y+    +++++ ++++++++   + + l+   +y+ A
  gi|518651445|ref|YP_008140965.1| 224 DNGDMDNAEKIAKDFYNSALDNLDMASNLAKVYYIEQKYDMGNGIFKEYIKRNNNIEANEEYIKMLVTTAQYDLA 298
                                       578899**********888888888999*********************55555555544444444444444444 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HH CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslg 57 
                                       y+ A+ ++e    + +e +  ++++ ++l + g++  A+  ++++ ++++ s++
  gi|518651445|ref|YP_008140965.1| 295 YDLALSIIEENARKYPEEETFIFYKFYALSEKGEHADALLPIKTLyDKQPDSIQ 348
                                       455555555444344666666777778888888888888877777666666665 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.63
                                       HHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  31 lclylngqykrAyellrka 49 
                                        ++ ++g y++A e+l +a
  gi|518651445|ref|YP_008140965.1| 388 TVYANMGLYDKAVEYLGRA 406
                                       6888889999999988877 PP

  == domain 7  score: 2.3 bits;  conditional E-value: 0.29
                                       HHHHHHHCT.SHHHC-HHHHHHHHHHHH..HTT-HHHHHHHH-S CS
                            ANAPC3  41 rAyellrka.klnskslgcrylfAqcll..kLkkyeeAiaaLek 81 
                                       + ++ll+++ +++++ + ++y + ++++  + ++ eeA ++Le 
  gi|518651445|ref|YP_008140965.1| 435 KIIQLLNTLpDKEENIIHALYAIEKACIlsAVNRTEEATKILEG 478
                                       55788889988888999999999999976677*******99986 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.49   3.4e+02      12      35 ..      10      36 ..       2      46 .. 0.73
   2 ?    2.8   0.0     0.084        58     133     178 ..      63     109 ..      55     113 .. 0.79
   3 !   10.3   0.2   0.00043       0.3     147     271 ..     112     235 ..     108     241 .. 0.63
   4 !   13.4   0.2   4.7e-05     0.033      29     249 ..     197     414 ..     189     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.49
                            TPR_15 12 lkl...atllykqgdvkkAlevLkeaa 35
                                      ++l   a+ l++ +d+++Ale++++a+
  gi|518651445|ref|YP_008140965.1| 10 YELtekAQKLFEADDFAGALEAINRAI 36
                                      44444599999************7654 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.084
                            TPR_15 133 lksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapd 178
                                       +k+le  e++  ++a  +++ +  y+q g+ ++Al+++ +A++++ d
  gi|518651445|ref|YP_008140965.1|  63 IKELEFIETLDpGDASHYSMESLCYLQMGEDEKALELADKAIKVDND 109
                                       555555555555788889999999*****************999876 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00043
                            TPR_15 147 afllaraelyrqegqtdaAlrdyreAlalapdsselraallWlliDlgrraeLrellk...awkaraesdasLwgpl 220
                                       + ++ ra++  + g+t++A+ +yr  l+++p + +    l  l++D+g+++ + + lk   +++++ +  ++L+  l
  gi|518651445|ref|YP_008140965.1| 112 FSYYNRAKALNNLGRTEDAISAYRLSLEKNPSDPDGHRDLAELYLDAGNYKMAERELKlslRFRKNDKITNDLMVEL 188
                                       66788999999999999999999999999999999999999999999998874444431113344434444444444 PP

                            TPR_15 221 aaAlllLgrpkkA.LeylrkqakenrkdplwllaYADaleqagradeAwrlR 271
                                         A     + +kA L+ +++ a+    d+l++++  D l ++g+ d+A+++ 
  gi|518651445|ref|YP_008140965.1| 189 KLATGGAFEFTKAlLDAFKNTAD---TDYLVRIT--DFLLDNGDMDNAEKIA 235
                                       44333333333330344444333...55555554..7777777777777775 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 4.7e-05
                            TPR_15  29 evLkeaaqkaapskdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliellydaepkeaarlaekgw. 104
                                       e  k+ ++  +  +dt+y+    d   ++ ++d+a+k+++  ++s   +++ +++l + +y ++  + ++   k + 
  gi|518651445|ref|YP_008140965.1| 197 EFTKALLDAFKNTADTDYLVRITDFLLDNGDMDNAEKIAKDFYNSALDNLDMASNLAKVYYIEQKYDMGNGIFKEYi 273
                                       5555555666667899999999999999*******************************776666666666666663 PP

                            TPR_15 105 rrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsse 181
                                       +r  + +  ++++++l  + +yd   +++++  +  ++ ++++f ++   + +++g++++Al  ++   +++pds +
  gi|518651445|ref|YP_008140965.1| 274 KRNNNIEANEEYIKMLVTTAQYDLALSIIEE--NARKYPEEETFIFYKFYALSEKGEHADALLPIKTLYDKQPDSIQ 348
                                       77888999*********************99..9999*************************************888 PP

                            TPR_15 182 lraallWlliDlgrraeLrellkawkaraesdasLwgplaaAlllLgrpkkALeylrkqakenrkdpl 249
                                          ++   l   g ++e   +l +  +  ++ +++  ++ + ++ +g ++kA eyl +  + +++d+ 
  gi|518651445|ref|YP_008140965.1| 349 YGINYAIELSHNGVKDEPVDILNRISKL-DKGPEIERAYYTVYANMGLYDKAVEYLGRAVE-MEDDIE 414
                                       8888877777778888766777666654.999************************99877.777765 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.9   0.00017      0.12       8     120 ..      11     135 ..       4     140 .. 0.67
   2 !    8.9   0.0    0.0027       1.9      60     116 ..     277     333 ..     273     340 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHTT-.-SSTTGGGTT...........STTHHHHHHHHH..HHHHHHHHHHHH CS
                              BTAD   8 alvaagraalaagdpeeaaelleaAlalw.rGpaladlea...........gewleaererle..elrlealealae 70 
                                       +l ++++++ +a+d+++a+e++++A+++  r   l d+++                 ++e+l+  +     +e+l+ 
  gi|518651445|ref|YP_008140965.1|  11 ELTEKAQKLFEADDFAGALEAINRAISILpRNVDLHDFKSdilfhsgdfeeTIKELEFIETLDpgDASHYSMESLCY 87 
                                       55666777777777777777777777644255556666666666655532211111222333311222334455555 PP

                                       HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                              BTAD  71 aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                         l++G+ e+al+ ++++++ ++  E ++    +Al  +Gr+++A+ +Y+
  gi|518651445|ref|YP_008140965.1|  88 --LQMGEDEKALELADKAIKVDNDYEFSYYNRAKALNNLGRTEDAISAYR 135
                                       ..999********************************************8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0027
                                       HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                              BTAD  60 lrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                         +ea e+ ++++++ ++++ al+  e+ ++++P  E++    + Al   G+ a+AL
  gi|518651445|ref|YP_008140965.1| 277 NNIEANEEYIKMLVTTAQYDLALSIIEENARKYPEEETFIFYKFYALSEKGEHADAL 333
                                       678999**************************************************9 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       8.2   5.7e+03      29      45 ..      16      32 ..       4      50 .. 0.60
   2 ?   -1.5   0.0       4.6   3.2e+03       7      45 ..      28      66 ..      24      70 .. 0.76
   3 ?    6.1   0.1      0.02        14      17      57 ..      72     112 ..      55     138 .. 0.72
   4 !   13.7   0.1   8.5e-05     0.058       7      55 ..     130     178 ..     125     217 .. 0.82
   5 ?    4.2   0.1     0.077        53      17      57 ..     241     281 ..     225     305 .. 0.84
   6 ?    0.0   0.0       1.6   1.1e+03      12      56 ..     337     381 ..     328     399 .. 0.85
   7 ?   -2.1   0.0       7.4   5.1e+03      34      55 ..     392     413 ..     364     449 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.2
                            TPR_20 29 AlallaagryeeAleqL 45
                                      A++l++a + + Ale++
  gi|518651445|ref|YP_008140965.1| 16 AQKLFEADDFAGALEAI 32
                                      66666666666655544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.6
                            TPR_20  7 elaeleaalaanpddldarldlAlallaagryeeAleqL 45
                                       l+++ +a+   p ++d++   ++ l++ g+ ee +++L
  gi|518651445|ref|YP_008140965.1| 28 ALEAINRAISILPRNVDLHDFKSDILFHSGDFEETIKEL 66
                                      567777778888888888888888888888888887776 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.02
                            TPR_20  17 anpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                        +p d       +l +l+ g+ e+Ale+  + +k d ++e 
  gi|518651445|ref|YP_008140965.1|  72 LDPGDASHYSMESLCYLQMGEDEKALELADKAIKVDNDYEF 112
                                       5888888888899999***********99999999999854 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 8.5e-05
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrkw 55 
                                        +++ +  l++np+d d + dlA+++l ag+y+ A  +L   l+  +++
  gi|518651445|ref|YP_008140965.1| 130 AISAYRLSLEKNPSDPDGHRDLAELYLDAGNYKMAERELKLSLRFRKND 178
                                       67888999***************************99998888777665 PP

  == domain 5  score: 4.2 bits;  conditional E-value: 0.077
                            TPR_20  17 anpddldarldlAlallaagryeeAleqLleilkrdrkwed 57 
                                       ++ d+ld + +lA++++ +++y+     + e +kr+ + e 
  gi|518651445|ref|YP_008140965.1| 241 SALDNLDMASNLAKVYYIEQKYDMGNGIFKEYIKRNNNIEA 281
                                       556899*****************999999999999998854 PP

  == domain 6  score: 0.0 bits;  conditional E-value: 1.6
                            TPR_20  12 eaalaanpddldarldlAlallaagryeeAleqLleilkrdrkwe 56 
                                       ++ + ++pd ++  +++A  l ++g ++e ++ L +i k d++ e
  gi|518651445|ref|YP_008140965.1| 337 KTLYDKQPDSIQYGINYAIELSHNGVKDEPVDILNRISKLDKGPE 381
                                       55677899*********************9999999988888765 PP

  == domain 7  score: -2.1 bits;  conditional E-value: 7.4
                            TPR_20  34 aagryeeAleqLleilkrdrkw 55 
                                         g y++A+e L + ++ + + 
  gi|518651445|ref|YP_008140965.1| 392 NMGLYDKAVEYLGRAVEMEDDI 413
                                       5555566665555555444433 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0     5e-07   0.00034     203     259 ..      20      76 ..       8      80 .. 0.86
   2 !    9.4   1.0   0.00063      0.44      16      82 ..      89     155 ..      78     201 .. 0.80
   3 ?   -0.2   2.9       0.5   3.4e+02      15      84 ..     223     295 ..     213     343 .. 0.76
   4 ?    0.7   1.2      0.28     2e+02     162     256 ..     286     377 ..     250     379 .. 0.64
   5 ?   -1.7   0.0       1.5     1e+03     202     225 ..     390     413 ..     385     417 .. 0.84
   6 ?    1.0   0.1      0.23   1.6e+02      22      62 ..     438     477 ..     427     494 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5e-07
                                       HHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 203 dklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                        +  +   Ale i++ai+  p  v+l+  K+ il h+Gd+++ ++ +e    lD  D
  gi|518651445|ref|YP_008140965.1|  20 FEADDFAGALEAINRAISILPRNVDLHDFKSDILFHSGDFEETIKELEFIETLDPGD 76 
                                       45556669**************************************99999998665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00063
                                       HHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-CHHHHHHHHHT CS
                             NARP1  16 eagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpenskYyeglekak 82 
                                       + g+ e+Ale  +++ k   D      ++a+ l +Lgr+e+A ++y+  le+np + + +++l +  
  gi|518651445|ref|YP_008140965.1|  89 QMGEDEKALELADKAIKVDNDYEFSYYNRAKALNNLGRTEDAISAYRLSLEKNPSDPDGHRDLAELY 155
                                       6788999999999988888898888999**************************9999999888766 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.5
                                       HHHTHHHHHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT...-CHHHHHHHHHT.. CS
                             NARP1  15 eeagkleeAlehLeekekqivDklavketkaelllkLgrkeeAeatyeaLlernpe...nskYyeglekakkl 84 
                                        + g++++A +  +   ++ +D+l +  + a+++   ++++  + ++++ ++rn +   n++Y + l ++ ++
  gi|518651445|ref|YP_008140965.1| 223 LDNGDMDNAEKIAKDFYNSALDNLDMASNLAKVYYIEQKYDMGNGIFKEYIKRNNNieaNEEYIKMLVTTAQY 295
                                       5678888888888888999999999999999999999999999999999999997533466777776666642 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.28
                                       HHHHHTTTTTSSSSTTGG.GSS----SSHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHH CS
                             NARP1 162 vegyvkslktsgklsesdnedsekepesallwvlyflAqhydklgsrekAleyidkaiehtptlvelyltKarilkh 238
                                       ++ +v++ + +  ls  +++  +   e+++++  ++      + g+   Al  i +  +++p ++++ ++ a  l h
  gi|518651445|ref|YP_008140965.1| 286 IKMLVTTAQYDLALSIIEENARKYPEEETFIFYKFYA---LSEKGEHADALLPIKTLYDKQPDSIQYGINYAIELSH 359
                                       4444444444444443333333333333333333222...3455666788888888888888888888888888888 PP

                                       TT-HHHHHHHHHHHHHCT CS
                             NARP1 239 aGdlkkAaevmeearklD 256
                                        G  ++ ++++++  klD
  gi|518651445|ref|YP_008140965.1| 360 NGVKDEPVDILNRISKLD 377
                                       888888888888888888 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 1.5
                                       HHHHT-SHHHHHHHHHHHHH-TT- CS
                             NARP1 202 ydklgsrekAleyidkaiehtptl 225
                                       y ++g ++kA+ey+ +a+e ++ +
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAVEMEDDI 413
                                       888999************998876 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.23
                                       HHHHHHHHHGGG---HHHHHHHHHHHHHHTT-HHHHHHHHH CS
                             NARP1  22 eAlehLeekekqivDklavketkaelllkLgrkeeAeatye 62 
                                       + l+ L  ke++i+  l   e ka +l +++r+eeA++++e
  gi|518651445|ref|YP_008140965.1| 438 QLLNTLPDKEENIIHALYAIE-KACILSAVNRTEEATKILE 477
                                       568888899999999987766.899************9986 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.028        19      12      30 ..      87     105 ..      86     106 .. 0.93
   2 ?    4.4   0.3     0.052        36       4      29 ..     113     138 ..     112     141 .. 0.76
   3 ?    5.4   0.4     0.025        17       7      33 ..     150     176 ..     149     177 .. 0.91
   4 ?   -0.6   0.0         2   1.4e+03       5      18 ..     249     262 ..     246     263 .. 0.76
   5 ?   -2.5   0.0       7.6   5.3e+03      11      22 ..     322     333 ..     321     338 .. 0.85
   6 !    7.8   0.0    0.0046       3.2      11      31 ..     389     409 ..     388     410 .. 0.94
   7 ?    3.5   0.0     0.098        68       9      26 ..     460     477 ..     456     479 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.028
                            TPR_10  12 lrqrgrydeAealleeala 30 
                                       + q+g+ ++A++l+++a+ 
  gi|518651445|ref|YP_008140965.1|  87 YLQMGEDEKALELADKAIK 105
                                       789**************96 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.052
                            TPR_10   4 slnNLanalrqrgrydeAealleeal 29 
                                       s+ N a al ++gr ++A   ++ +l
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSL 138
                                       57788888888888888887777666 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.025
                            TPR_10   7 NLanalrqrgrydeAealleealairr 33 
                                       +La ++ + g+y+ Ae+ l+ +l+ r+
  gi|518651445|ref|YP_008140965.1| 150 DLAELYLDAGNYKMAERELKLSLRFRK 176
                                       69****************999998876 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2
                            TPR_10   5 lnNLanalrqrgry 18 
                                        +NLa +++  ++y
  gi|518651445|ref|YP_008140965.1| 249 ASNLAKVYYIEQKY 262
                                       79******966665 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 7.6
                            TPR_10  11 alrqrgrydeAe 22 
                                       al++ g++++A+
  gi|518651445|ref|YP_008140965.1| 322 ALSEKGEHADAL 333
                                       78999****997 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0046
                            TPR_10  11 alrqrgrydeAealleealai 31 
                                       ++ ++g yd+A+++l +a+++
  gi|518651445|ref|YP_008140965.1| 389 VYANMGLYDKAVEYLGRAVEM 409
                                       79****************997 PP

  == domain 7  score: 3.5 bits;  conditional E-value: 0.098
                            TPR_10   9 analrqrgrydeAealle 26 
                                       a++l++++r +eA ++le
  gi|518651445|ref|YP_008140965.1| 460 ACILSAVNRTEEATKILE 477
                                       789************998 PP

>> TPR_4  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       8.8   6.1e+03      11      23 ..      19      31 ..      16      34 .. 0.82
   2 ?    5.3   0.0     0.056        39       4      20 ..     114     130 ..     113     135 .. 0.88
   3 !   10.6   0.0    0.0011      0.77       3      24 ..     147     168 ..     145     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 8.8
                             TPR_4 11 llalGdldeAral 23
                                      l+++ d++ A+++
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEA 31
                                      67899*****986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.056
                             TPR_4   4 llaLArallalGdldeA 20 
                                       ++++A al  lG+ ++A
  gi|518651445|ref|YP_008140965.1| 114 YYNRAKALNNLGRTEDA 130
                                       689************99 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0011
                             TPR_4   3 allaLArallalGdldeArall 24 
                                        + +LA+++l++G++  A++ l
  gi|518651445|ref|YP_008140965.1| 147 GHRDLAELYLDAGNYKMAEREL 168
                                       5899***************976 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.7   1.9e+03      11      29 ..      20      38 ..      13      42 .. 0.77
   2 ?    6.8   0.1     0.017        12       8      28 ..      85     105 ..      83     106 .. 0.92
   3 !   11.0   0.0   0.00081      0.56       2      31 ..     113     142 ..     112     144 .. 0.90
   4 ?    5.8   0.0     0.036        25      10      27 ..     390     407 ..     388     409 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.7
                                      HHHHHHHHHHHHHHHHHHH CS
                             TPR_6 11 rklgdtdkAlealerlike 29
                                      ++++d + Alea +r i+ 
  gi|518651445|ref|YP_008140965.1| 20 FEADDFAGALEAINRAISI 38
                                      5567999999999998876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   8 lsyrklgdtdkAlealerlik 28 
                                       l+y+++g+ +kAle+ ++ ik
  gi|518651445|ref|YP_008140965.1|  85 LCYLQMGEDEKALELADKAIK 105
                                       7***************99986 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00081
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-T CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYP 31 
                                       ++y++a+++ +lg+t++A+ a++  +++ P
  gi|518651445|ref|YP_008140965.1| 113 SYYNRAKALNNLGRTEDAISAYRLSLEKNP 142
                                       68*********9**********98888877 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.036
                                       HHHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerli 27 
                                       y ++g +dkA+e+l r +
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAV 407
                                       88899*********9987 PP

>> Alkyl_sulf_dimr  Alkyl sulfatase dimerisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0043         3      71     123 ..      11      63 ..       7      71 .. 0.92
   2 ?    2.2   0.1      0.34   2.3e+02      80     122 ..      88     130 ..      75     139 .. 0.83
   3 ?   -1.7   0.0       5.3   3.7e+03      83     129 ..     226     257 ..     187     279 .. 0.50
   4 ?   -0.9   0.0       2.9     2e+03      50      85 ..     463     498 ..     459     507 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0043
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSH CS
                   Alkyl_sulf_dimr  71 kvlekakealkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesa 123
                                       ++ eka++ ++++d+  a+e +n ++   p+n + ++ k d+l + g ++e+ 
  gi|518651445|ref|YP_008140965.1|  11 ELTEKAQKLFEADDFAGALEAINRAISILPRNVDLHDFKSDILFHSGDFEETI 63 
                                       6789***************************************9999998875 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.34
                                       HHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SS CS
                   Alkyl_sulf_dimr  80 lkegdyrwaaellnhlvfadpenaeakelkadaleqlgyqaes 122
                                       l+ g+ + a+el+++++  d++ +     +a+al++lg+ + +
  gi|518651445|ref|YP_008140965.1|  88 LQMGEDEKALELADKAIKVDNDYEFSYYNRAKALNNLGRTEDA 130
                                       5667788899999999999999999999999999999988765 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 5.3
                                       T-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHHHHH-SSHHHHHHH CS
                   Alkyl_sulf_dimr  83 gdyrwaaellnhlvfadpenaeakelkadaleqlgyqaesatwRniY 129
                                       gd+  a +              ak+   +al++l   + s  ++ +Y
  gi|518651445|ref|YP_008140965.1| 226 GDMDNAEK-------------IAKDFYNSALDNLD--MASNLAKVYY 257
                                       33333333.............33333333333332..2223333333 PP

  == domain 4  score: -0.9 bits;  conditional E-value: 2.9
                                       TS---HHHHHHHHHHHTTSHHHHHHHHHHHHHTT-H CS
                   Alkyl_sulf_dimr  50 LnplppeekakrlvelmGgaekvlekakealkegdy 85 
                                       L  ++++e+a++++e + ++e v+  ++++++ ++ 
  gi|518651445|ref|YP_008140965.1| 463 LSAVNRTEEATKILEGIDSKEDVCMIINQYMDFENS 498
                                       6778999****************9999999986665 PP

>> SPOB_a  Sensor_kinase_SpoOB-type, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.11        73      33      51 ..      87     105 ..      85     107 .. 0.88
   2 ?   -2.0   0.0       4.5   3.1e+03      33      53 ..     222     242 ..     220     252 .. 0.73
   3 ?    2.2   0.1      0.22   1.5e+02      30      56 ..     286     312 ..     277     316 .. 0.78
   4 ?    7.1   0.1    0.0062       4.3      33      60 ..     390     417 ..     388     421 .. 0.79
   5 ?   -3.0   0.0       8.9   6.2e+03      35      47 ..     465     477 ..     463     479 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.11
                            SPOB_a  33 ylqLgkydkaeeyieevvk 51 
                                       ylq+g+ +ka e+ ++++k
  gi|518651445|ref|YP_008140965.1|  87 YLQMGEDEKALELADKAIK 105
                                       9***********9888775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.5
                            SPOB_a  33 ylqLgkydkaeeyieevvkel 53 
                                       +l+ g +d+ae++ ++ ++ +
  gi|518651445|ref|YP_008140965.1| 222 LLDNGDMDNAEKIAKDFYNSA 242
                                       677799999999988877655 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.22
                            SPOB_a  30 IsGylqLgkydkaeeyieevvkelkee 56 
                                       I++++++ +yd a ++iee ++ + ee
  gi|518651445|ref|YP_008140965.1| 286 IKMLVTTAQYDLALSIIEENARKYPEE 312
                                       788888888888888888877666555 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0062
                            SPOB_a  33 ylqLgkydkaeeyieevvkelkeeskil 60 
                                       y  +g ydka+ey+ ++v++  ++++i+
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAVEMEDDIEDIS 417
                                       889*************998755555554 PP

  == domain 5  score: -3.0 bits;  conditional E-value: 8.9
                            SPOB_a  35 qLgkydkaeeyie 47 
                                       + ++ ++a++++e
  gi|518651445|ref|YP_008140965.1| 465 AVNRTEEATKILE 477
                                       5789999999887 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.2   2.2e+03      65      93 ..      19      47 ..      10      56 .. 0.71
   2 ?   11.1   0.1   0.00044      0.31     103     128 ..     114     139 ..      55     141 .. 0.83
   3 ?    0.5   0.0      0.81   5.6e+02      37      68 ..     304     336 ..     288     360 .. 0.70
   4 ?   -1.8   0.0       4.4     3e+03     112     129 ..     392     409 ..     385     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.2
                                      HHHTT-HHHHHHHHHHHHHHHHHH--TTS CS
                           DUF3856 65 laklgrydealesadkalryfnrrGeleq 93
                                      l +  ++  ale++++a+  + r  +l++
  gi|518651445|ref|YP_008140965.1| 19 LFEADDFAGALEAINRAISILPRNVDLHD 47
                                      44456677788888888887777777775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00044
                                       HHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856 103 vfsravaleelGrkdealkafrmage 128
                                        ++ra+al++lGr+++a+ a+r + e
  gi|518651445|ref|YP_008140965.1| 114 YYNRAKALNNLGRTEDAISAYRLSLE 139
                                       589******************98766 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.81
                                       HHHTTS-TTS---HHHHHHHHHHH.HHHHHHHT CS
                           DUF3856  37 evsrtipaeeafdheGfdalchag.lsealakl 68 
                                       e +r  p+ee+f +  f al   g  ++al+ +
  gi|518651445|ref|YP_008140965.1| 304 ENARKYPEEETFIFYKFYALSEKGeHADALLPI 336
                                       457889999999999999988655245666555 PP

  == domain 4  score: -1.8 bits;  conditional E-value: 4.4
                                       HTT-HHHHHHHHHHHHHH CS
                           DUF3856 112 elGrkdealkafrmagem 129
                                       ++G +d+a++++  a+em
  gi|518651445|ref|YP_008140965.1| 392 NMGLYDKAVEYLGRAVEM 409
                                       567777777777777777 PP

>> OAS1_C  2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00018      0.13      73     130 ..     453     510 ..     430     513 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHT-SSS--HHHHHHHHHHHHHTGGG-EE---SS--SSSHHHHHHHHHHHTS CS
                            OAS1_C  73 tvyaWEqgskkekfklaeglrtvleLiqkykqlciyWtvnYdfedetvreflkkqlkk 130
                                       ++ya E+++  ++++ +e  + +le i +++++c+  +++ dfe+++++efl++ ++k
  gi|518651445|ref|YP_008140965.1| 453 ALYAIEKACILSAVNRTEEATKILEGIDSKEDVCMIINQYMDFENSKISEFLEDYFNK 510
                                       68**************************************************988776 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       5.4   3.7e+03       6      32 ..      11      37 ..      10      40 .. 0.72
   2 ?    5.2   0.3     0.033        23       2      19 ..      94     111 ..      94     114 .. 0.87
   3 ?    3.4   0.0      0.12        80       8      32 ..     115     139 ..     112     140 .. 0.87
   4 ?    4.3   0.4     0.062        43      23      64 ..     235     280 ..     227     281 .. 0.76
   5 ?    4.9   0.0     0.039        27      26      42 ..     395     412 ..     391     441 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 5.4
                               MIT  6 elvkkAveeDnagnyeeAlelYkeale 32
                                      el +kA ++ +a +++ Ale+   a+ 
  gi|518651445|ref|YP_008140965.1| 11 ELTEKAQKLFEADDFAGALEAINRAIS 37
                                      677788888888888888887666665 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.033
                               MIT   2 dkAlelvkkAveeDnagn 19 
                                       +kAlel+ kA++ Dn  +
  gi|518651445|ref|YP_008140965.1|  94 EKALELADKAIKVDNDYE 111
                                       69************9765 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.12
                               MIT   8 vkkAveeDnagnyeeAlelYkeale 32 
                                        ++A  + n g  e+A+++Y+ +le
  gi|518651445|ref|YP_008140965.1| 115 YNRAKALNNLGRTEDAISAYRLSLE 139
                                       67899999*************9987 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.062
                               MIT  23 AlelYkealelLlqalk.e...kneerrellrekieeYleRaeeLk 64 
                                       A + Y +al+ L +a +       e++ ++     +eY++R + ++
  gi|518651445|ref|YP_008140965.1| 235 AKDFYNSALDNLDMASNlAkvyYIEQKYDMGNGIFKEYIKRNNNIE 280
                                       7799***********9953344334999999999999999987775 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.039
                               MIT  26 lYkealelLlqalk.ekn 42 
                                       lY +a+e+L  a+  e++
  gi|518651445|ref|YP_008140965.1| 395 LYDKAVEYLGRAVEmEDD 412
                                       899999999999985544 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.8   1.3e+03       9      32 ..      85     108 ..      84     111 .. 0.84
   2 ?   -0.5   0.1       1.9   1.3e+03      15      28 ..     159     172 ..     155     181 .. 0.72
   3 ?   -2.3   0.0       6.9   4.8e+03      15      36 ..     327     348 ..     317     349 .. 0.85
   4 ?    7.9   0.0    0.0045       3.1      11      51 ..     390     431 ..     383     433 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.8
                                       HHHHHHT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C   9 lGhyklgeYseArryvdalLeiEP 32 
                                       l ++ +ge ++A++++d  ++++ 
  gi|518651445|ref|YP_008140965.1|  85 LCYLQMGEDEKALELADKAIKVDN 108
                                       668889999*********999985 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.9
                                       T-HHHHHHHHHHHH CS
                        Fis1_TPR_C  15 geYseArryvdalL 28 
                                       g+Y++A r ++  L
  gi|518651445|ref|YP_008140965.1| 159 GNYKMAERELKLSL 172
                                       77777777776655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 6.9
                                       T-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  15 geYseArryvdalLeiEPenrQ 36 
                                       ge+ +A+  +++l  ++P+  Q
  gi|518651445|ref|YP_008140965.1| 327 GEHADALLPIKTLYDKQPDSIQ 348
                                       7899999999999999998665 PP

  == domain 4  score: 7.9 bits;  conditional E-value: 0.0045
                                       HHHHT-HHHHHHHHHHHHHHTTS-HHHHH.HHHHHHHHHHHT CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaqs.Lkeliedkikke 51 
                                       ++ +g Y++A +y+ +  e+E + +   + L+ +ied i+k 
  gi|518651445|ref|YP_008140965.1| 390 YANMGLYDKAVEYLGRAVEMEDDIEDISDiLNPAIEDSITKN 431
                                       567999******************999876999999999985 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.4e+03      14      45 ..      15      46 ..       8      71 .. 0.75
   2 ?   11.6   0.5   0.00026      0.18       8      56 ..      77     124 ..      75     136 .. 0.86
   3 ?    0.8   0.7      0.56   3.8e+02       8      48 ..     269     312 ..     230     337 .. 0.57
   4 ?   -3.1   0.1       8.6   5.9e+03      20      36 ..     392     408 ..     384     410 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                           DUF5113 14 layylnvegeyeeALeyldsaleylNahyekY 45
                                       a++l+  +++  ALe ++ a+++l +  + +
  gi|518651445|ref|YP_008140965.1| 15 KAQKLFEADDFAGALEAINRAISILPRNVDLH 46
                                      6778889999999********99987665555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00026
                           DUF5113   8 andYanlayylnvegeyeeALeyldsaleylNahyekYakkkadtldkl 56 
                                       a++Y     ++   ge e+ALe++d+a+++ N +  +Y+++++  l++l
  gi|518651445|ref|YP_008140965.1|  77 ASHYSMESLCYLQMGEDEKALELADKAIKVDNDYEFSYYNRAK-ALNNL 124
                                       78899999999999**************************995.77666 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.56
                           DUF5113   8 andYanlayylnvegeyeeALeyl...dsaleylNahyekYakk 48 
                                        ++Y +  +++ +++ey + L +    d al+++ +  +kY ++
  gi|518651445|ref|YP_008140965.1| 269 FKEYIKRNNNIEANEEYIKMLVTTaqyDLALSIIEENARKYPEE 312
                                       34455555555555555555543211144555555555555555 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 8.6
                           DUF5113  20 vegeyeeALeyldsale 36 
                                         g y++A+eyl  a+e
  gi|518651445|ref|YP_008140965.1| 392 NMGLYDKAVEYLGRAVE 408
                                       34788888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (516 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.53
# Mc/sec: 2921.63
//
Query:       gi|518651446|ref|YP_008140966.1|  [L=178]
Description: hypothetical protein FACI_IFERC00001G0085 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-06   28.4   0.0    2.9e-06   27.9   0.0    1.3  1  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 !   27.9   0.0   1.6e-10   2.9e-06       3     129 ..      21     133 ..      19     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.6e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHCCHHHHHHHHHHHHHHHHHHHHHHCHHHHH..CCC.HHHHHHHHH CS
                       Hemerythrin   3 vealdeeHralrallerlraladaaaevhgalrklaelldelvdeleaHhaaEEellfPlle.drpggravldvler 78 
                                       ve+l+ eH ++r  +     ++++        ++l ++ ++l +   +H  +EE+++fPll+  ++     ++ l +
  gi|518651446|ref|YP_008140966.1|  21 VELLMVEHSGIRIIAY--NNILQKG------SAELIDFNKFLLN---IHVNIEETVVFPLLKeNDSSTSKLISTLIA 86 
                                       6677777777777776..5555552......3455555555555...7***************************** PP

                                       HHHHHHHHHHHHHHHCHTCGGSTCHHHHHHHHHHHHHHHHHHHHHHHTHHH CS
                       Hemerythrin  79 eHdeirelleelrellkgleepsaaafaelleeladllreHiakEesilfp 129
                                       +H  i+ l+++l ++  + +      f  +l  +++ l eH+  Ee +lf 
  gi|518651446|ref|YP_008140966.1|  87 DHKLIETLFNNLYKWKLSEN----PLFNVRLPLFYKTLTEHNSNEEILLFS 133
                                       *************8877766....78999*****************88886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1224.15
//
Query:       gi|518651447|ref|YP_008140967.1|  [L=240]
Description: transposon tn10 jemc related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   46.4   0.6    7.9e-12   44.9   0.1    1.9  2  HTH_5     Bacterial regulatory protein, arsR family
    2.1e-06   27.7   0.0    3.9e-06   26.8   0.0    1.5  1  HTH_20    Helix-turn-helix domain
    4.1e-05   23.4   0.0    0.00011   22.1   0.0    1.7  2  TrmB      Sugar-specific transcriptional regulator TrmB
     0.0011   18.8   0.0       0.26   11.2   0.0    2.5  2  HxlR      HxlR-like helix-turn-helix
     0.0075   16.3   0.1      0.017   15.2   0.1    1.6  1  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d
     0.0079   16.3   0.1       0.15   12.3   0.0    2.5  2  HTH_34    Winged helix DNA-binding domain
  ------ inclusion threshold ------
       0.01   15.4   0.5      0.073   12.6   0.1    2.2  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.026   14.3   0.1        1.4    8.7   0.0    2.4  3  DUF4364   Domain of unknown function (DUF4364)
      0.064   13.0   0.0       0.24   11.2   0.0    2.0  1  HTH_DeoR  DeoR-like helix-turn-helix domain
      0.077   13.0   0.1       0.45   10.5   0.0    2.1  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.1   4.4e-15   7.9e-12       1      45 [.      31      75 ..      31      76 .. 0.97
   2 ?   -1.1   0.0         1   1.8e+03       6      15 ..     206     215 ..     205     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 4.4e-15
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      +p Rl+I+ lL++g+l v +l+  +++sq+++S +L++L + G+V
  gi|518651447|ref|YP_008140967.1| 31 NPVRLRIILLLSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIV 75
                                      699*****************************************9 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1
                                       HHHHHHTTSS CS
                             HTH_5   6 kILklLaege 15 
                                       +I+k+L +++
  gi|518651447|ref|YP_008140967.1| 206 EIMKALINQN 215
                                       8999998865 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   2.2e-09   3.9e-06       1      56 [.      23      77 ..      23      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 2.2e-09
                                      HHHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20  1 dqiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvev 56
                                      d++++ L++PvR+ri  +L +++ l +++l  ++ +s+  +s +L +L+  g+v++
  gi|518651447|ref|YP_008140967.1| 23 DRLFYCLSNPVRLRIILLL-SKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIVHG 77
                                      6899***************.********************************9976 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   5.9e-08   0.00011      16      66 ..      39      90 ..      37      92 .. 0.90
   2 ?   -3.6   0.0         6   1.1e+04      42      55 ..     207     220 ..     206     227 .. 0.65

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.9e-08
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES.STTTEEEE-- CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerek.grpklYravd 66
                                       Ll++g+++++++++  +v+++k+   L+ L + G+V+  + gr k+Y+ ++
  gi|518651447|ref|YP_008140967.1| 39 LLLSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIVHGWQvGREKYYKIIP 90
                                      588***********************************98856677888776 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 6
                                       HHHHHHHCTSEEEE CS
                              TrmB  42 vLrsLedkGlVere 55 
                                       +++ L++  ++++ 
  gi|518651447|ref|YP_008140967.1| 207 IMKALINQNYIKIY 220
                                       56777777777654 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0   0.00014      0.26       8      51 ..      35      77 ..      28     109 .. 0.84
   2 ?    5.1   0.0     0.012        21      48      72 ..     143     167 ..     138     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00014
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEE CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglier 51
                                      l i+  l kgk   ++l+ ++ ++sq  ++++L  L++ g+++ 
  gi|518651447|ref|YP_008140967.1| 35 LRIILLLSKGKLNVNQLSSTF-NVSQPKISAQLSILQNYGIVHG 77
                                      679999**************9.*******************984 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.012
                                       SEEEEEESSSS-EEEEEE-TCGGGG CS
                              HxlR  48 lierevypevPpkveYsltekGrsl 72 
                                       l++r+ ++    k eY+lt+ G+ +
  gi|518651447|ref|YP_008140967.1| 143 LLSRKWISIKNDKPEYELTDSGEII 167
                                       788999999999**********976 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   9.4e-06     0.017      21      58 ..      39      76 ..      37      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
                                      HHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                             HTH_9 21 tLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                      +Ll+kg+l +++l+++ ++s  ++   L++L++ ++V 
  gi|518651447|ref|YP_008140967.1| 39 LLLSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIVH 76
                                      69********************************9996 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 !   12.3   0.0   8.2e-05      0.15       1      44 [.      33      75 ..      33      89 .. 0.87
   2 ?    1.2   0.0      0.23   4.2e+02      32      47 ..     205     220 ..     200     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.2e-05
                            HTH_34  1 vRlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYi 44
                                      vRl ++  L+s+ + + ++l+++ ++++ ++s++l++L++ g +
  gi|518651447|ref|YP_008140967.1| 33 VRLRIIL-LLSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIV 75
                                      6888775.667899************************998866 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.23
                            HTH_34  32 svhlkkLekagYievd 47 
                                       s  +k+L +++Yi++ 
  gi|518651447|ref|YP_008140967.1| 205 SEIMKALINQNYIKIY 220
                                       55699********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 ?   12.6   0.1   4.1e-05     0.073       4      47 ..      33      75 ..      30      76 .. 0.90
   2 ?    0.8   0.0      0.21   3.7e+02      36      48 .]     206     218 ..     205     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.1e-05
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                       +++I+ lL k ++++ ++L+   ++S++ ++++l  L++ G++
  gi|518651447|ref|YP_008140967.1| 33 VRLRIILLLSK-GKLNVNQLSSTFNVSQPKISAQLSILQNYGIV 75
                                      56778888887.*****************************998 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.21
                            HTH_24  36 rrlkrLeeeGlIk 48 
                                       + +k L+++ +Ik
  gi|518651447|ref|YP_008140967.1| 206 EIMKALINQNYIK 218
                                       679*********7 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.037        66      38      92 ..      64     118 ..      49     128 .. 0.82
   2 ?    8.7   0.0   0.00077       1.4      40      82 ..     140     180 ..     137     188 .. 0.87
   3 ?   -3.7   0.0       4.9   8.9e+03      40      52 ..     208     220 ..     205     227 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.037
                           DUF4364  38 qalseLvesglieeeekenktlykiTekGketlelfenripksirekideylken 92 
                                         ls L + g ++  +   +++yki ++  e l    ++i+ s+  +    ++++
  gi|518651447|ref|YP_008140967.1|  64 AQLSILQNYGIVHGWQVGREKYYKIIPESIESLTSWLDNIATSVTVDNLPEFDSH 118
                                       5677788888999889999*********************999987666555555 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00077
                           DUF4364  40 lseLvesglieeeekenktlykiTekGketlelfenripksir 82 
                                       l+ L++ + i+   k++k  y++T++G+ +l  +  +ip + +
  gi|518651447|ref|YP_008140967.1| 140 LKLLLSRKWISI--KNDKPEYELTDSGEIILTRLGVNIPVQKK 180
                                       666888999998..6899*********************8876 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 4.9
                           DUF4364  40 lseLvesglieee 52 
                                       ++ L+++++i+  
  gi|518651447|ref|YP_008140967.1| 208 MKALINQNYIKIY 220
                                       4555555555543 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00013      0.24       8      43 ..      39      74 ..      36      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00013
                          HTH_DeoR  8 llkqqgklsveelvellgvSeaTiRRDLneLeeqgl 43
                                      ll ++gkl+v++l+  ++vS+  i   L++L++ g+
  gi|518651447|ref|YP_008140967.1| 39 LLLSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGI 74
                                      7899****************9888777777777777 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.2   2.1e+03      15      50 ..      41      79 ..      35      91 .. 0.69
   2 ?   10.5   0.0   0.00025      0.45      40      69 ..     140     171 ..     135     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.2
                            HTH_45 15 isegeakkTkimykanLsykllnkYLdmLvekgli...k 50
                                      +s+g+ +  ++    n s   ++  L++L++ g++   +
  gi|518651447|ref|YP_008140967.1| 41 LSKGKLNVNQLSSTFNVSQPKISAQLSILQNYGIVhgwQ 79
                                      556777777777778888888888888888888886553 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00025
                            HTH_45  40 LdmLvekgli..kkskekYvlTekGlellekl 69 
                                       L+ L++++ i  k++k +Y+lT+ G+ +l +l
  gi|518651447|ref|YP_008140967.1| 140 LKLLLSRKWIsiKNDKPEYELTDSGEIILTRL 171
                                       788899999766**************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1734.70
//
Query:       gi|518651448|ref|YP_008140968.1|  [L=402]
Description: major facilitator superfamily transporter [Ferroplasma acidarmanus fer1]
Scores for complete 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   60.3  49.6    1.5e-16   60.3  49.6    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3  49.6   8.3e-21   1.5e-16       2     348 ..      22     353 ..      21     356 .. 0.68
   2 !   10.8  18.0   9.6e-06      0.17      65     171 ..     282     391 ..     275     398 .. 0.71

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 8.3e-21
                             MFS_1   2 llaaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +l++f ++  ++i +p++ l a++ ++g    +i  ++++y ++ + + l++G  sd  G +  ++lg+++ ++g +
  gi|518651448|ref|YP_008140968.1|  22 ALLIFAIMVVSNIPTPLYALyAIKFNFG--SLAIAGIFAIYVVFLIPSLLFWGQYSDVKGGKIPIILGIIFEIAG-I 95 
                                       7889999999999999999766666655..5556668**************************************.4 PP

                             MFS_1  78 lll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsa.gfslGailgpllggllasslgWra 152
                                       +++ +a ++  l+++r++qGl++ga+   + al+ +      rg+a ++l++ ++s G+++gpllgg++a++l +++
  gi|518651448|ref|YP_008140968.1|  96 IAFlLAGNISELFLARAFQGLASGAISGPASALLFH-----YRGKAGAILTSvSTSSGTAVGPLLGGVMAEYLPFHL 167
                                       4443568888************99999999888887.....677777777665999***************999665 PP

                             MFS_1 153 v..fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvp...awkallkdpvlwillialllfffgfs 224
                                          +++  i+ ++   ++ +  + +++  kr+s        +++++ +     k l++      + +a++ ++ +++
  gi|518651448|ref|YP_008140968.1| 168 KlvYILSLIIIIIP--VARIAPMINKSIVKRQSNHNV----FEFHFPKldmEEKNLFTLS----AATAFIAWS-ITA 233
                                       41044444444443..333444444444444444444....3333333112223333333....444444444.777 PP

                             MFS_1 225 glltllplylqevlglsglllaglllallalvgail.allagrlsdrlgrrrrlllallllllaalglallavtssa 300
                                       ++++++ply+   lg+s+  ++g  l ++ ++g+++ + +++  s+ +++   ll ++++l++a +++++  +++s 
  gi|518651448|ref|YP_008140968.1| 234 FYMSMSPLYIIRLLGISNIAITG--LIVFLMLGIASiMQILSMKSTIFSS---LLTGIISLIIAIALIVISFPFKSM 305
                                       7****************545666..3333333333312244555555544...444444444444444444444688 PP

                             MFS_1 301 vllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslg 348
                                        +++++ ++ G+g+gf+f+ ++  +    pp ++g +++ + ++ ++g
  gi|518651448|ref|YP_008140968.1| 306 DIFIVATIMTGIGQGFAFTGATREIRTISPPLKMGGVLSNYYIIIYFG 353
                                       888889999***********9999999999988888888777766666 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 9.6e-06
                             MFS_1  65 lllglllfalg.lllll.fa.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgp 138
                                       ll+g+++++++ +l+ + f+  s+ +++v+ +++G+g+g++f+++   i+ ++p+ + g +++ +++ + +G+ +  
  gi|518651448|ref|YP_008140968.1| 282 LLTGIISLIIAiALIVIsFPfKSMDIFIVATIMTGIGQGFAFTGATREIRTISPPLKMGGVLSNYYIIIYFGVGIPT 358
                                       55666666666333333444455558***********************************************9999 PP

                             MFS_1 139 llggllasslg.Wrav.fyilaivsllafvlflll 171
                                       ++ gl+    g ++++ +y   ++ + ++++  ++
  gi|518651448|ref|YP_008140968.1| 359 VILGLIDMISGlFSGIlYYGSSLIICSLIII--IF 391
                                       9999888555555555233333333333222..22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1192  (0.0664845); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2566.76
//
Query:       gi|518651449|ref|YP_008140969.1|  [L=251]
Description: methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-17   64.0   0.0    2.7e-17   63.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.6e-15   56.0   0.0    8.7e-15   55.1   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
    1.8e-14   53.8   0.0    2.8e-14   53.2   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.6e-11   44.8   0.0    3.2e-11   43.8   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    9.9e-09   35.2   0.0    1.3e-08   34.9   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    1.7e-05   24.3   0.0    8.3e-05   22.0   0.0    1.8  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    8.5e-05   22.1   0.0    0.00012   21.6   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00012   21.5   0.0    0.00024   20.5   0.0    1.5  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00013   21.6   0.0    0.00019   21.0   0.0    1.3  1  MTS              Methyltransferase small domain
    0.00017   21.2   0.0    0.00025   20.7   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00055   19.6   0.0    0.00084   19.0   0.0    1.2  1  NodS             Nodulation protein S (NodS)
    0.00068   19.8   0.0      0.001   19.2   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
     0.0058   16.4   0.0     0.0086   15.9   0.0    1.2  1  DUF938           Protein of unknown function (DUF938)
     0.0086   15.8   0.0      0.021   14.6   0.0    1.6  2  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.013   14.6   0.0      0.022   13.8   0.0    1.4  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.018   14.3   0.0      0.022   14.0   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
      0.034   14.1   0.0      0.055   13.4   0.0    1.3  1  LCM              Leucine carboxyl methyltransferase
       0.04   13.1   0.5        1.3    8.2   0.0    2.2  2  DUF43            Branched-chain polyamine synthase A C-termin
      0.046   13.7   0.0      0.073   13.0   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
      0.065   12.9   0.0       0.12   12.0   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.18   11.7   0.0        0.3   11.0   0.0    1.4  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   0.0   3.2e-20   2.7e-17       1      97 []      44     144 ..      44     144 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 3.2e-20
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC..CGBS..SSTTTEEEEEEEST CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda..edlp..fedgsfDlvvssga 73 
                                       +Ld+GcG+  +t +la+r+++a+++ +D+++ +l+ a+++a+  g +v++++ d+  +++   ++d+ fD++vs+ a
  gi|518651449|ref|YP_008140969.1|  44 ILDAGCGPASFTVRLARRFKDARIYSIDYDPVLLALAKSNASIYGSRVKILEYDLkgNAWAkdLADEGFDAIVSTTA 120
                                       8******************99********************99999****999995444433379*********988 PP

                                       GGGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  74 lhhlsdedlekalkeiarvLkpgG 97 
                                       lh++++++l +++++++++Lk+gG
  gi|518651449|ref|YP_008140969.1| 121 LHWIPRNNLSNVYENFYKLLKDGG 144
                                       ***********************9 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.1   0.0     1e-17   8.7e-15       1      95 [.      45     147 ..      45     147 .. 0.91

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1e-17
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC....CTSS-TT-EEEEEEES-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadae....klpfednsfDlvvssevl 71 
                                       Ld+GcG  +++  la+r+  ar++ +D+++ +l+lak++as  g +v++++ d++       ++d+ fD++vs+ +l
  gi|518651449|ref|YP_008140969.1|  45 LDAGCGPASFTVRLARRFkdARIYSIDYDPVLLALAKSNASIYGSRVKILEYDLKgnawAKDLADEGFDAIVSTTAL 121
                                       8**************9999***********************99999996666664322568*************** PP

                                       CC-..CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  72 hhv..edpekalkeiaRvLkpgGllv 95 
                                       h++  ++++ + ++++++Lk gG+++
  gi|518651449|ref|YP_008140969.1| 122 HWIprNNLSNVYENFYKLLKDGGIFM 147
                                       ***999*****************985 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.2   0.0   3.2e-17   2.8e-14       5     119 ..      42     156 ..      40     196 .. 0.75

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 3.2e-17
                   Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.lekl.ledekfDlil 79 
                                       +r+lD+GCG   +t +la + +++a++++iD+++  + lA++na+  g+ +v+  + d    +  + l+de fD i+
  gi|518651449|ref|YP_008140969.1|  42 NRILDAGCGPASFTVRLA-RRFKDARIYSIDYDPVLLALAKSNASIYGS-RVKILEYDLKGnAWAKdLADEGFDAIV 116
                                       589***************.77899*******************998888.69999988777655556999******* PP

                   Methyltransf_31  80 snevl..naladpdkileeiervlkpggilliedprllaelp 119
                                       s  +l     +++ +++e+  ++lk+ggi++  d+   + + 
  gi|518651449|ref|YP_008140969.1| 117 STTALhwIPRNNLSNVYENFYKLLKDGGIFMDGDHF--RSNS 156
                                       *****666667899*****************44433..3333 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.7e-14   3.2e-11       1      99 []      45     146 ..      45     146 .. 0.82

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.7e-14
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.....ssfDlvva 72 
                                       L+ GcG +s++ +l+++++d++++ +D++p  ++ ak   + ++     +v++ + dl   +       + fD++v+
  gi|518651449|ref|YP_008140969.1|  45 LDAGCGPASFTVRLARRFKDARIYSIDYDPVLLALAKSNASIYGS----RVKILEYDLKGNAWAkdladEGFDAIVS 117
                                       89*******************************555555444443....55555555443333366678******** PP

                   Methyltransf_12  73 snvlhhl..kdirevldnirklLkpgGrl 99 
                                         +lh++  +++  v +n++klLk+gG++
  gi|518651449|ref|YP_008140969.1| 118 TTALHWIprNNLSNVYENFYKLLKDGGIF 146
                                       ********99*****************85 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.0   1.5e-11   1.3e-08       3     125 ..      24     177 ..      22     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 1.5e-11
                   Methyltransf_23   3 aqreeelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae................ 61 
                                       ++r+ ++ d +e++    ++ +r+Ld GcG  +++  l+++++   ++ +D +p++ ++a+                
  gi|518651449|ref|YP_008140969.1|  24 EERFSFMMDVIEETH---PEVNRILDAGCGPASFTVRLARRFKdaRIYSIDYDPVLLALAKsnasiygsrvkileyd 97 
                                       677788888888776...699***************9999988779************9977666665554333332 PP

                   Methyltransf_23  62 .kakkaqkdqfdeqeaaepqg..........kfdlIvlrevlehvp..dppellrqiatllkpgGylllseplasl. 124
                                        k                  g           fd Iv++  l+++p  ++  +  ++++llk+gG ++  ++ +s  
  gi|518651449|ref|YP_008140969.1|  98 lK------------------GnawakdladeGFDAIVSTTALHWIPrnNLSNVYENFYKLLKDGGIFMDGDHFRSNs 156
                                       22..................22233333344***************988*******************999988755 PP

                   Methyltransf_23 125 ....................k 125
                                                            
  gi|518651449|ref|YP_008140969.1| 157 dsvylhemyskirnkisalnI 177
                                       566666555555555555541 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   9.7e-08   8.3e-05      38     150 ..      29     147 ..      19     167 .. 0.84
   2 ?   -0.4   0.0      0.72   6.1e+02     186     216 ..     205     235 ..     170     240 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 9.7e-08
                                       HHHHH--S--TT..EEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS..TEEE.EE--TTT CS
                   Ubie_methyltran  38 fveklvavkrga..kvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki..nief.lqanaee 109
                                       f++++  + +++  ++lD  +G + ++++l++  ++  ++  +D+++ +L  ++  +   g     +e+ l++na +
  gi|518651449|ref|YP_008140969.1|  29 FMMDVIEETHPEvnRILDAGCGPASFTVRLARRFKD-ARIYSIDYDPVLLALAKSNASIYGSRvkILEYdLKGNAWA 104
                                       566666666554449*****************9865.69****************99988876546688799***** PP

                                       -TTS-T-EEEEEEES-GGG-S..-HHHHHHHHHHHEEEEEEEE CS
                   Ubie_methyltran 110 LpfeddsfDvvtvsfGlrnvt..DklkaLkeayrvlkpGGrlv 150
                                        +  d+ fD +  +  l  ++  + +++ ++ y+ lk GG+++
  gi|518651449|ref|YP_008140969.1| 105 KDLADEGFDAIVSTTALHWIPrnNLSNVYENFYKLLKDGGIFM 147
                                       **********99888998887224578999**********986 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.72
                                       HHHHHHHHHHHHS--HHHHHHHHHHTTEEEE CS
                   Ubie_methyltran 186 dsyryLvesirafPdqetlkeliedaGfksv 216
                                        s ryL  s  +    e+  +++++aGf+s 
  gi|518651449|ref|YP_008140969.1| 205 RSKRYLSGSHDQNVSLEEHIDILNHAGFSST 235
                                       4679999999999999999999999999875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.4e-07   0.00012     152     257 ..      31     147 ..      28     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.4e-07
                              PrmA 152 lealeklvkegeevlDvGtGSGiLaia.aakLgakkvvavDiDevAvkvakeNaelNkvea.klevalseellk... 223
                                       + ++e++  e +++lD G+G +  ++  a ++  ++++ +D+D+v +  ak+Na++ + +   le  l++++ +   
  gi|518651449|ref|YP_008140969.1|  31 MDVIEETHPEVNRILDAGCGPASFTVRlARRFKDARIYSIDYDPVLLALAKSNASIYGSRVkILEYDLKGNAWAkdl 107
                                       567888888889************99637789************************988873444444444442234 PP

                              PrmA 224 .eekadvivaN.....ILaevlielaedikklvkegglli 257
                                        +e +d iv+      I  + l + +e+++kl+k+gg+++
  gi|518651449|ref|YP_008140969.1| 108 aDEGFDAIVSTtalhwIPRNNLSNVYENFYKLLKDGGIFM 147
                                       4689*****9733333556778899999999999999986 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.8e-07   0.00024      63     164 ..      41     148 ..      10     172 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.8e-07
                                       T-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-...EEEEES-G.GG---.--SEEEE CS
                              CMAS  63 GmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerk...vevklldy.edlde.kvdrvvs 133
                                        +++Ld GcG  s ++r ++r+ d+++ ++       +lak +    +++ k    ++k   + +dl++  +d++vs
  gi|518651449|ref|YP_008140969.1|  41 VNRILDAGCGPASFTVRLARRFkDARIYSIDYDPVLLALAKSNASIYGSRVKileYDLKGNAWaKDLADeGFDAIVS 117
                                       4689*****************97899999988777777777777776644331113344445645776659****** PP

                                       ES-GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 134 vgafehvgkenydtffkklkkllkedGllll 164
                                         a+  +  +n+ + +++++kllk++G+++ 
  gi|518651449|ref|YP_008140969.1| 118 TTALHWIPRNNLSNVYENFYKLLKDGGIFMD 148
                                       ****************************985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.3e-07   0.00019      22     103 ..      29     117 ..      27     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.3e-07
                                       HHHHHCHCC..TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-ST.....TT CS
                               MTS  22 lLletlpke..lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdv.....le 91 
                                       ++++ ++++  + +++lD GcG    ++ la++ ++a++  +d d   l++ak n++  + +v++++ d+      +
  gi|518651449|ref|YP_008140969.1|  29 FMMDVIEEThpEVNRILDAGCGPASFTVRLARRFKDARIYSIDYDPVLLALAKSNASIYGSRVKILEYDLkgnawAK 105
                                       577777777666678******************************************99999888888872222246 PP

                                       TSTTS-EEEEEE CS
                               MTS  92 eveekkfdlivs 103
                                       +++++ fd+ivs
  gi|518651449|ref|YP_008140969.1| 106 DLADEGFDAIVS 117
                                       677888999987 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.9e-07   0.00025       2      52 ..      42      94 ..      41     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.9e-07
                   Methyltransf_15  2 rvilDlfsGaGGnviqfalvfe..kviaieinleklacaqhNaevYgvsdkit 52
                                      + ilD+ +G    ++ +a+ f+  ++++i++++  la+a+ Na +Yg   ki 
  gi|518651449|ref|YP_008140969.1| 42 NRILDAGCGPASFTVRLARRFKdaRIYSIDYDPVLLALAKSNASIYGSRVKIL 94
                                      579*****************96448*********************9888874 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   9.9e-07   0.00084      19     146 ..      12     150 ..       8     160 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 9.9e-07
                              NodS  19 wrldan...efeqerlaqilrlsla.qgsiadalevGcaaGalterlapyck..rltvvdv..veeaiararervke 87 
                                       w+l+ +   e  +er++ ++ +  + + ++  +l+ Gc   ++t+rla   k  r+  +d   v  a+a+++  +  
  gi|518651449|ref|YP_008140969.1|  12 WELQQSaliEMREERFSFMMDVIEEtHPEVNRILDAGCGPASFTVRLARRFKdaRIYSIDYdpVLLALAKSNASIYG 88 
                                       666655111456799999**987651668999****************98773356667653366799999999998 PP

                              NodS  88 sshiswivsdvqqfs.....tdekfdlivvaevlyyiedvaelraavrnlvsllapdgqlvfGs 146
                                        s ++ ++ d++        +de fd iv +  l++i   ++l    +n+ +ll+ +g ++ G 
  gi|518651449|ref|YP_008140969.1|  89 -SRVKILEYDLKGNAwakdlADEGFDAIVSTTALHWIPR-NNLSNVYENFYKLLKDGGIFMDGD 150
                                       .99999999997543222226899*************75.689999*********999988765 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06     0.001      21     110 ..      40     158 ..      19     184 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
                                       TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS........HHH..TTEEEECS-CCCSSHHHHHCHCHHH.. CS
                              FtsJ  21 pgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm........apl..pgvttiqgditdpetiekikealse.. 85 
                                       ++++++D g++P +++  l++r++  ++++++D  p+        a +  ++v++++ d +  + ++ + +   +  
  gi|518651449|ref|YP_008140969.1|  40 EVNRILDAGCGPASFTVRLARRFKD-ARIYSIDYDPVllalaksnASIygSRVKILEYDLKGNAWAKDLADE--Gfd 113
                                       5688******************986.***********99888766555788999995555555444444431..112 PP

                                       ....................SSEEEEEE--S-SS-CHHHHHHHHH CS
                              FtsJ  86 ....................rkvdlvvsDgapdvsgvhdldeylq 110
                                                           + +   + Dg+ ++ g h   +  +
  gi|518651449|ref|YP_008140969.1| 114 aivsttalhwiprnnlsnvyENFYKLLKDGGIFMDGDHFRSNSDS 158
                                       233356666666666666666666666666667777666655555 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     1e-05    0.0086      16     138 ..      32     147 ..      23     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                            DUF938  16 evLksylakttervLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnlkpPleldvtaevapv 92 
                                       +v++++ ++ + r+L+ + G     v +A +++ ++  + d+d+ l  ++a+  +++  s +k  le d + + +  
  gi|518651449|ref|YP_008140969.1|  32 DVIEETHPEVN-RILDAGCGPASFTVRLARRFKDARIYSIDYDPVLL-ALAKSNASIYGSRVK-ILEYDLKGNAWAK 105
                                       56666666666.6*********************************7.555555555555555.4788888876665 PP

                            DUF938  93 ereappapasidailsinllHispwsaveglfagagellkkkavlv 138
                                       +    +a++++dai+s+  lH  p +    +++   +llk++++++
  gi|518651449|ref|YP_008140969.1| 106 D----LADEGFDAIVSTTALHWIPRNNLSNVYENFYKLLKDGGIFM 147
                                       5....68**********************************99875 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   2.4e-05     0.021      64     160 ..      29     129 ..      13     147 .. 0.77
   2 ?   -2.6   0.0       4.6   3.9e+03     108     128 ..     200     220 ..     198     223 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                                       HHHHHTT..--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-..GGGT CS
                              PCMT  64 lalelle..lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgD..GrkG 136
                                       ++++ +e    +++r+L+ G+G    t+ lar +++  r+ si++ + l + ak n    ++ +v++ + D  G+  
  gi|518651449|ref|YP_008140969.1|  29 FMMDVIEetHPEVNRILDAGCGPASFTVRLARRFKDA-RIYSIDYDPVLLALAKSNASIYGS-RVKILEYDlkGNAW 103
                                       67777776555789********************876.6*****************988776.55555555336665 PP

                                       TGGG-..SEEEEEESSBBSS--HHHH CS
                              PCMT 137 yeeka..PYdaihvgaaapeiPeali 160
                                        ++ a   +dai+ + a + iP++ +
  gi|518651449|ref|YP_008140969.1| 104 AKDLAdeGFDAIVSTTALHWIPRNNL 129
                                       555553369****9999999998644 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.6
                                       HHHHHHHHHHHHHCTTCSEEE CS
                              PCMT 108 kelveeakrnlkkldlenviv 128
                                       +el+e++kr l  ++ +nv++
  gi|518651449|ref|YP_008140969.1| 200 EELMERSKRYLSGSHDQNVSL 220
                                       689999999999999999987 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.022      30      85 ..      40      98 ..      15     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                                      TTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S-C CS
                            RrnaAD 30 ekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls.kdeklkvvhqDf 85
                                      e   +l+ g G++ +T++La r+      ++  d++L++l + + s  ++++k+++ D 
  gi|518651449|ref|YP_008140969.1| 40 EVNRILDAGCGPASFTVRLARRFkdARIYSIDYDPVLLALAKSNASiYGSRVKILEYDL 98
                                      5578*******************7667889999**********999999*****99886 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.022      38     131 ..      30     117 ..      24     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                          N6_Mtase  38 ivell...epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvk.ir 110
                                       +++++   +p+ ++ ++D  cG +++ v  ++ +       k+  iy  + ++   +Lak N  + g+ +k ++   
  gi|518651449|ref|YP_008140969.1|  30 MMDVIeetHPEVNR-ILDAGCGPASFTVRLARRF-------KDARIYSIDYDPVLLALAKSNASIYGSRVKILEyDL 98 
                                       55566433666776.***************9987.......5899**************************888556 PP

                          N6_Mtase 111 lgdtlekpkfekdkkfdvvva 131
                                        g++ +k+  +  + fd++v+
  gi|518651449|ref|YP_008140969.1|  99 KGNAWAKDLAD--EGFDAIVS 117
                                       78888888877..99999997 PP

>> LCM  Leucine carboxyl methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.5e-05     0.055      84     165 ..      40     119 ..      12     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.5e-05
                                       TESEEEEET-TT--HHHHHHHTT.TEEEEEEE-HHHHHHHHHHHHHSHHHHHE.ECSEEE--TTSHHHHHHHHHHTT CS
                               LCM  84 girqvViLGAGlDtrayRlpwla.glkvfEvDqpevlefKretlkelgaepka.elryvpvDlrdddwpeaLaaagf 158
                                        ++ +   G+G  ++ +Rl+    + +++ +D+  vl      l++++a++   +++    Dl+ + w++ La++gf
  gi|518651449|ref|YP_008140969.1|  40 EVNRILDAGCGPASFTVRLARRFkDARIYSIDYDPVLL----ALAKSNASIYGsRVKILEYDLKGNAWAKDLADEGF 112
                                       56666667999999*****998889**********996....5777888777526669******************* PP

                                       -TTSEEE CS
                               LCM 159 dpekpta 165
                                       d+ + t+
  gi|518651449|ref|YP_008140969.1| 113 DAIVSTT 119
                                       *877665 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 ?    8.2   0.0    0.0016       1.3      67     117 ..      64     116 ..      52     122 .. 0.82
   2 ?    3.1   0.2     0.056        48     148     203 ..     176     229 ..     167     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0016
                                       -SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TT.S---TTTS.S-BSEEE CS
                             DUF43  67 pkkvvvvDiDeRlikfiervakelglkieaivyDlr.kplpeelk.ekFdvfi 117
                                         ++  +D D+ l+ + +  a  +g  ++++ yDl+ ++++++l  e Fd ++
  gi|518651449|ref|YP_008140969.1|  64 DARIYSIDYDPVLLALAKSNASIYGSRVKILEYDLKgNAWAKDLAdEGFDAIV 116
                                       458999*****************************967788776525688776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.056
                                       EE-TTT--HHHHHHHHHHHHTS--EEEEEEEEEEEB---S-GGGSHHHHHSSS--- CS
                             DUF43 148 gltrressldkWkeiqklllemgvvitdlirnFneYenweykeetraikllpvkkk 203
                                        ++r++    +W+e  + +l+ gv   +l+++ + Y      +++   + + + ++
  gi|518651449|ref|YP_008140969.1| 176 NISREK--AMNWEEWWEYILNSGVFREELMERSKRYLSGSHDQNVSLEEHIDILNH 229
                                       555555..578*************************99888888888888777664 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.6e-05     0.073      11      77 ..      28      90 ..      23     110 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.6e-05
                   Methyltransf_32 11 elvakllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkk 77
                                      ++  ++++e  ++ + ++++D+G+G +  + +la    + +  ++++id    l + a+  a+ +g++
  gi|518651449|ref|YP_008140969.1| 28 SFMMDVIEE--THPEVNRILDAGCGPASFTVRLAR---RfKDARIYSIDYDPVLLALAKSNASIYGSR 90
                                      566677777..578889*****************9...5589********999988888887777655 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.12       9      83 ..      41     115 ..      34     119 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                                       T-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CT..CCHHHHCC..EEEE CS
                   Methyltr_RsmB-F   9 eetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDar..kidkvlggelfDri 83 
                                        ++ilD+ ++P + T  +a    + ++++ +d +   l   ++n +  g + +++le+D++     k+l++e fD i
  gi|518651449|ref|YP_008140969.1|  41 VNRILDAGCGPASFTVRLARR-FKDARIYSIDYDPVLLALAKSNASIYGSR-VKILEYDLKgnAWAKDLADEGFDAI 115
                                       578****************98.56799**********************99.*******872144566777888876 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00035       0.3       8      67 ..      34      93 ..      24     116 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00035
                   Methyltransf_18  8 iaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledki 67
                                      i +  ++ +r++D G+  +  ++ l+++ k  +++ +D  +  l+ ak+n++ +g + ki
  gi|518651449|ref|YP_008140969.1| 34 IEETHPEVNRILDAGCGPASFTVRLARRFKDARIYSIDYDPVLLALAKSNASIYGSRVKI 93
                                      455556778*****************************************9999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1801.07
//
Query:       gi|518651450|ref|YP_008140970.1|  [L=386]
Description: transposase (04) [Ferroplasma acidarmanus fer1]
Scores for complete 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-85  284.9   0.4    1.1e-84  284.5   0.4    1.0  1  Transposase_mut  Transposase, Mutator family
    3.7e-06   27.3   0.0    6.7e-06   26.4   0.0    1.4  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.5   0.4   1.2e-88   1.1e-84      31     368 ..      17     351 ..       3     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 284.5 bits;  conditional E-value: 1.2e-88
                   Transposase_mut  31 ktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspallerykRrekaleav 106
                                         +l++ +++++++ +++e  +  ee+ + +nG+++r+l+T++g++ +l++PrdR+ +F+++++e y+R+   +e+ 
  gi|518651450|ref|YP_008140970.1|  17 DKILKQTIKEKIEKLMEIELNAYLEENPGIKNGKYKRDLKTKYGEIkQLNVPRDRDSNFHTQVIEPYNRSI-GMEDL 92 
                                       3455555666666666666666677888999*************9957*********************86.689** PP

                   Transposase_mut 107 vielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                       ++++y +G+str+++ ++e++ g +++Sks++S+it+ + e+v +f +R+L++  y ++flD+l   +R  g v  +
  gi|518651450|ref|YP_008140970.1|  93 IVSMYSNGISTRRIAGIMEDILG-NKYSKSTISRITDLTIEEVYKFINRPLDKR-YIAVFLDGLFFYLR-RGNVDKE 166
                                       ***********************.66***************************9.**************.788999* PP

                   Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHll 260
                                       +v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L nrGlk+  l+v+D+ k L + + + +p ++ Q C++H++
  gi|518651450|ref|YP_008140970.1| 167 PVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGLKEPLLIVADGIKNLDEEVMEIYPRSEFQLCTIHYA 243
                                       ***************************************************************************** PP

                   Transposase_mut 261 rnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpeqirrkikst 337
                                       r l ++v  k+ d+++ +  +++k  + eea  ++++f  k+ +kypkv    +++  ++l f+++p +ir+++kst
  gi|518651450|ref|YP_008140970.1| 244 RGLKSNVREKDIDEITIDANKMFKCDNKEEAIIRFNDFKYKWKSKYPKVIYNTEKNLGKLLRFYNYPVNIRKSLKST 320
                                       ***************************************************************************** PP

                   Transposase_mut 338 NllErLNkeirRrtrvvgiFPneesilrlvg 368
                                       N++Er N e+rRr++++  FP+e+s++++ +
  gi|518651450|ref|YP_008140970.1| 321 NAIERFNGEVRRRVKTISSFPDEDSAMKVFY 351
                                       ****************************977 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.5e-10   6.7e-06      15      94 ..     166     243 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.5e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ + y+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518651450|ref|YP_008140970.1| 166 EPVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGL--KEPLLIVADGIKNLDEEVMEIYPRSEFQLCTI 240
                                       5677899*******************************99644..6******************************* PP

                              MULE  92 Hia 94 
                                       H a
  gi|518651450|ref|YP_008140970.1| 241 HYA 243
                                       *76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       888  (0.0495287); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2542.57
//
Query:       gi|518651451|ref|YP_008140971.1|  [L=520]
Description: hypothetical protein FACI_IFERC00001G0090 [Ferroplasma acidarmanus fer1]
Scores for complete 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-22   77.7  59.3    7.8e-22   77.7  59.3    1.8  2  AA_permease_2  Amino acid permease
      3e-21   75.6  56.7    5.6e-21   74.7  56.7    1.4  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.7  59.3   8.7e-26   7.8e-22       3     418 ..      20     482 ..      18     490 .. 0.77
   2 !    1.8   0.5    0.0096        86     354     389 ..     476     512 ..     474     513 .. 0.74

  Alignments for each domain:
  == domain 1  score: 77.7 bits;  conditional E-value: 8.7e-26
                     AA_permease_2   3 llsafalvigsv....igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       +++a+a  i+++     +++++v+ +a  +  ++ l+++ia+l + +  + ++  ls ++ + gG y+y ++afg++
  gi|518651451|ref|YP_008140971.1|  20 TWGAIAEEISAMapacDSIAFVVS-SAVFAFFLTPLSFIIATLTM-FLEVNTLYHLSKRHASAGGYYGYIANAFGPV 94 
                                       666666666666443322333333.22224455677777777776.6777788889999****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasi.lsvaasyl....lnalgpdlqgntwltyliaiaililvalinirgikesakiqnil 147
                                       +a  ++ ++ + + +++a+i + va+  l    +++lg  +    w+++ ++ a++i+ ++i i+gi+   k+  + 
  gi|518651451|ref|YP_008140971.1|  95 PAISAGLMYPMYQTVSTAAIpVFVAGVVLpgvvMYFLGVGMP--AWIWIPFILAFIIVPIVIAIVGIRPQMKYIRVA 169
                                       *********555555555551333444445544555554554..57788888999999999999****9999999** PP

                     AA_permease_2 148 gilkillpliiliilglitvdgggfssl.....stetdt...ffpn...gwpgvllgllivlwsfdGfesaanvsee 213
                                       g + i ++l++l ++ +i +  ++ +       +    +   +f+    + +gv lg+   l sf+G+ ++a   ee
  gi|518651451|ref|YP_008140971.1| 170 GFFEI-IFLAVLSAIIIIKAPDNTLNVFnpfawP----QyssWFAPeggVFTGVGLGMIFGLTSFIGYGGSAPLGEE 241
                                       *****.7888888777776655554443544422....23334443355666677788889**************** PP

                     AA_permease_2 214 vkk.kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgain 289
                                       + + k + + + +gl iv+++ + v+ a + + ++  +++ s++g ++ +++ ++ g v+ ++++++++ s++  + 
  gi|518651451|ref|YP_008140971.1| 242 ATNpKAITRSLTFGLFIVGIVMTEVAYAQIVGWGIPLMQTFSSSGIPGIIVATTYTGIVGGVMFALVAFNSAFSDGV 318
                                       ***99********************9999999999999999999878888888888556666666666669999999 PP

                     AA_permease_2 290 tavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfl......................... 340
                                       +  + + rv++a++rdg++P+ff+ ++ k+ +p+ a+i++ +vs+i+++l++                         
  gi|518651451|ref|YP_008140971.1| 319 AMQANAGRVYFAMGRDGIIPKFFSFIHkKYVTPSKALIFVGVVSSIVAVLSTfivamgagvspyalmdnkasdpvii 395
                                       999999*********************9*******************99999******************9999965 PP

                     AA_permease_2 341 ..lassaaynfllsvsslgliisyllliigalilrkkrphlkr.........pgkilvaiigalfllfllvalffpp 406
                                         l  ++ ++fl++++  glii  +ll ++++   ++ +++ +            +l+  i++++++f+l+   +pp
  gi|518651451|ref|YP_008140971.1| 396 kaL--TDTFQFLTTMALAGLIITHILLNTSVMTMFRRLKEKHTgirdivlhmTQHYLFPSIATVIFIFVLYESLVPP 470
                                       532..79999******************9999998888887555556665544449999999*******99999999 PP

                     AA_permease_2 407 kgpatqssliyt 418
                                       + p t+  li+ 
  gi|518651451|ref|YP_008140971.1| 471 VYPITYAILIIG 482
                                       988886555444 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.0096
                     AA_permease_2 354 sslgliisylll.iigalilrkkrphlkrpgkilvai 389
                                       +++++i +y+++ +++al++++k+p+l +++   v+i
  gi|518651451|ref|YP_008140971.1| 476 YAILIIGVYTVFsVVYALYIKYKKPELAKKAGKYVNI 512
                                       5666777777776999***********6655444776 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7  56.7   6.2e-25   5.6e-21      30     477 ..      51     502 ..      21     504 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 6.2e-25
                       AA_permease  30 gallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln.ylfswitvlaleltaasil..... 100
                                        + l++++a++ +fl +++l+ ++    ++gg+y y+++  gp  + + Gl+ ++++ + ++a+ +++a+ +     
  gi|518651451|ref|YP_008140971.1|  51 LTPLSFIIATLTMFLEVNTLYHLSKRHASAGGYYGYIANAFGPVPAISAGLMyPMYQTVSTAAIPVFVAGVVlpgvv 127
                                       579*************************************************77*************9987611111 PP

                       AA_permease 101 iqfwelvtdlpkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg...iillaggkpnkgag 171
                                       + f+     +p aw++   ++ f++v ++i +vg++   +    ++ +++   i+f+ v+   ii+ a +++ +  +
  gi|518651451|ref|YP_008140971.1| 128 MYFL--GVGMP-AWIWipfILAFIIVPIVIAIVGIRPQMK----YIRVAGFFEIIFLAVLsaiIIIKAPDNTLNV-F 196
                                       4444..88899.9999777777777777777777777666....9999999999999999754444455555554.5 PP

                       AA_permease 172 frflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYv 248
                                         f + ++s    ++ p      +g f+++  ++++ + +f G++  a +++E+ +P k+i ++  + +++++i+ +
  gi|518651451|ref|YP_008140971.1| 197 NPFAWPQYS---SWFAPE-----GGVFTGVGLGMIFGLTSFIGYGGSAPLGEEATNP-KAITRSLTFGLFIVGIVMT 264
                                       556676666...778888.....99********************************.79***************** PP

                       AA_permease 249 lsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaP 325
                                        ++++ +++++ +  + +++s  +  +++++++++g+ + ++ +++v + +a+s ++++ + a Rv++++ +dg++P
  gi|518651451|ref|YP_008140971.1| 265 EVAYAQIVGWGIPLMQTFSSSGIP--GIIVATTYTGIVG-GVMFALVAFNSAFSDGVAMQANAGRVYFAMGRDGIIP 338
                                       *******************99977..**********976.7899********************************* PP

                       AA_permease 326 kvlkkv.skrgvPlraillsmiisllal..........................llaslnlaapivfnfllaisali 375
                                       k+++ + +k+  P +a++++ ++s ++                           ++ ++ ++   +f+fl +++ + 
  gi|518651451|ref|YP_008140971.1| 339 KFFSFIhKKYVTPSKALIFVGVVSSIVAvlstfivamgagvspyalmdnkasdpVIIKALTD---TFQFLTTMALAG 412
                                       888866156677******99988888888999*************98888877744444444...7*********** PP

                       AA_permease 376 glivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaa 452
                                        +i+++l ++s + + + lk++   i+++  ++    l++ ++ +++i++l    + ++ +              +a
  gi|518651451|ref|YP_008140971.1| 413 LIITHILLNTSVMTMFRRLKEKHTGIRDIVLHMTQHYLFPSIATVIFIFVLYESLVPPVYP------------ITYA 477
                                       *************888888888888888877777766666666555555554444444444............7899 PP

                       AA_permease 453 ylivllfliilvgvklhvknkrpql 477
                                       +li+ ++ ++ v++ l++k k+p+l
  gi|518651451|ref|YP_008140971.1| 478 ILIIGVYTVFSVVYALYIKYKKPEL 502
                                       9999999999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1114  (0.062134); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 3459.15
//
Query:       gi|518651452|ref|YP_008140972.1|  [L=245]
Description: oligopeptide ABC transporter Dpp1, ATP binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-23   82.9   0.0    4.5e-23   82.3   0.0    1.3  1  ABC_tran     ABC transporter
    5.5e-05   22.7   0.9      0.015   14.7   0.0    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00068   19.8   1.9      0.013   15.7   1.0    2.7  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.001   19.6   0.3     0.0022   18.5   0.3    1.5  1  AAA_23       AAA domain
     0.0014   18.9   0.6      0.011   16.0   0.6    2.0  1  AAA_22       AAA domain
     0.0051   16.7   0.0     0.0084   16.0   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
     0.0067   16.1   0.3      0.014   15.1   0.1    1.7  2  AAA_29       P-loop containing region of AAA domain
     0.0071   16.1   0.0      0.024   14.4   0.0    1.8  1  AAA_30       AAA domain
  ------ inclusion threshold ------
      0.041   14.4   0.0      0.077   13.5   0.0    1.6  1  AAA_18       AAA domain
      0.097   12.7   0.9        1.4    8.9   0.0    2.6  3  AAA_14       AAA domain
      0.098   11.9   1.4        5.7    6.1   0.0    2.1  2  KAP_NTPase   KAP family P-loop domain
       0.13   11.9   0.0        7.2    6.1   0.0    2.1  2  AAA_25       AAA domain
       0.13   12.5   0.3       0.23   11.7   0.3    1.4  1  AAA_28       AAA domain
       0.15   11.0   0.4         12    4.7   0.1    2.1  2  UPF0261      Uncharacterised protein family (UPF0261)
       0.15   11.1   0.1       0.23   10.5   0.1    1.2  1  T2SSE        Type II/IV secretion system protein
       0.17   11.4   0.2        0.3   10.7   0.2    1.4  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.19   11.1   0.7       0.58    9.6   0.1    1.9  2  PhoH         PhoH-like protein
        1.1    9.0   6.7        1.5    8.6   1.2    2.6  3  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.3   0.0   4.5e-26   4.5e-23       1     136 [.      26     164 ..      26     165 .. 0.93

  Alignments for each domain:
  == domain 1  score: 82.3 bits;  conditional E-value: 4.5e-26
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS..--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe..pqlfpelt 75 
                                       l+n+s +++++++ +i+G +G+GK+tL+++++g  ++ +G+il++       +l ++  ++++++q+  ++++p +t
  gi|518651452|ref|YP_008140972.1|  26 LDNISTTFRNNNISGITGASGSGKTTLANIITGYDTDYAGQILYN------SSLVRTLGSVRYVFQDpyTSMNPVKT 96 
                                       79****************************************777......567778**********8888889998 PP

                                       HHHH......HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  76 vren......esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllDEpt 136
                                       v+ +        ++e+++a++kl++ +++ ++ k++  +sLSgG+ q++ala +++ +p++++lDE++
  gi|518651452|ref|YP_008140972.1|  97 VEWHlataasINNVEMSDAIKKLEIAGMDYSIYKDRYgHSLSGGELQKLALAISIIPEPEFIVLDEAF 164
                                       88889**99999999************99999988778****************************97 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.1    0.0037       3.7      19      43 ..      30      55 ..      19      61 .. 0.77
   2 !   14.7   0.0   1.5e-05     0.015     135     212 ..     127     208 ..      66     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0037
                                      EEET.TSSEEEEEESTTSSHHHHHHH CS
                                      xxxx.xxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 19 ilpf.sksftaivGpNGSGKsnlldA 43
                                      ++ f +++++ i+G+ GSGK+ l + 
  gi|518651452|ref|YP_008140972.1| 30 STTFrNNNISGITGASGSGKTTLANI 55
                                      44551467999**********98765 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.5e-05
                                       T........CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCC CS
                                       x........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e........lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemle 203
                                       +        +LSgGe + +ala    i  +    + +lDe  + +D     k  ++lk+ +k+  +i i ++ + ++
  gi|518651452|ref|YP_008140972.1| 127 SiykdryghSLSGGELQKLALA----ISIIPEPEFIVLDEAFSMMDSITLFKTLNFLKQLKKTISIIYIDHDINRIA 199
                                       2555566668****97655544....4445555599*********************************99998888 PP

                                       C-SCEEEEE CS
                                       xxxxxxxxx RF
                             SMC_N 204 kadklvgvt 212
                                        a+  v + 
  gi|518651452|ref|YP_008140972.1| 200 FASDYVYIL 208
                                       887766655 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.7   4.7e+03       8      45 ..      19      56 ..      16      58 .. 0.66
   2 !   15.7   1.0   1.3e-05     0.013      62      89 ..     153     180 ..     118     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.7
                           SbcCD_C  8 nylsfevevrdedgkekelsrssgtlSGGekqflayla 45
                                      +y+++++  +  +  + +  + +++ SG  k +la ++
  gi|518651452|ref|YP_008140972.1| 19 KYHDLYALDNISTTFRNNNISGITGASGSGKTTLANII 56
                                      56666666665555555667788888988887777665 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.3e-05
                           SbcCD_C  62 palrlvfLDEAFsklDeesiatllelle 89 
                                       p +++++LDEAFs +D+ ++ + l++l+
  gi|518651452|ref|YP_008140972.1| 153 PEPEFIVLDEAFSMMDSITLFKTLNFLK 180
                                       6799*************99999999887 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.3   2.2e-06    0.0022      12      40 ..      28      57 ..      15      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                            AAA_23 12 dqeidF.skgltlItGpNGaGKTTildAik 40
                                      + +  F ++++  ItG  G+GKTT+ + i+
  gi|518651452|ref|YP_008140972.1| 28 NISTTFrNNNISGITGASGSGKTTLANIIT 57
                                      444567889*****************9997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.6   1.1e-05     0.011       8     117 ..      39     184 ..      34     200 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee.......................erpevvfvtlpsstsskdllrell 61 
                                         +tG sG+GKTtl++ ++  ++ +a +                         +++++v+  l+   s  ++     
  gi|518651452|ref|YP_008140972.1|  39 SGITGASGSGKTTLANIITGYDTDYAGQILynsslvrtlgsvryvfqdpytsmNPVKTVEWHLATAASINNV----- 110
                                       569*************99998877776666889999888555555555555444444444444444444444..... PP

                            AAA_22  62 ralglelka..................erlsseell.ealeqalrarav...ielliiDEaqhlr.s...eealeeL 112
                                               +                  +    + l    l++ + a +    +e++++DEa  ++ s    + l++L
  gi|518651452|ref|YP_008140972.1| 111 --------EmsdaikkleiagmdysiyKDRYGHSLSgGELQKLALAISIipePEFIVLDEAFSMMdSitlFKTLNFL 179
                                       ........244444555555555888833334444447777777777778889********9977655577777777 PP

                            AAA_22 113 rslln 117
                                       ++l +
  gi|518651452|ref|YP_008140972.1| 180 KQLKK 184
                                       66644 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.5e-06    0.0084      88     125 ..      24      62 ..       8      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.5e-06
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                        +l+++++ +++ ++s + G SG GK+tL n +++ ++ 
  gi|518651452|ref|YP_008140972.1|  24 YALDNISTTFRNnNISGITGASGSGKTTLANIITGYDTD 62 
                                       57888999999889******************9986554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   1.4e-05     0.014      13      38 ..      27      52 ..      17      57 .. 0.79
   2 ?   -3.4   0.0       8.6   8.6e+03       4      14 ..      94     104 ..      92     113 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.4e-05
                            AAA_29 13 dghtieidlkgatlltGpsGsGKSTl 38
                                      d+ + +++ +++  +tG+sGsGK+Tl
  gi|518651452|ref|YP_008140972.1| 27 DNISTTFRNNNISGITGASGSGKTTL 52
                                      55556677677889***********9 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 8.6
                            AAA_29   4 lqlvNWgtfdg 14 
                                       ++ v+W+  + 
  gi|518651452|ref|YP_008140972.1|  94 VKTVEWHLATA 104
                                       56788987765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.4e-05     0.024      17     113 ..      35     180 ..      27     191 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
                            AAA_30  17 gdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa.......eelgi..eastiakllkrlk... 81 
                                       ++ ++ +tG+ G+GKtt+ + ++   ++  g+++  ++  +    ++       +      + +t++  l + +   
  gi|518651452|ref|YP_008140972.1|  35 NNNISGITGASGSGKTTLANIITGYDTDYAGQILYNSSLVRTLGSVRyvfqdpyT---SmnPVKTVEWHLATAAsin 108
                                       445999****************999999977777665555555555433322221...0225555555554444555 PP

                            AAA_30  82 .......................................grarlepg.tllivDEa.gmvdtkqlaallkaae 113
                                                                              +  ++ p+ + ++ DEa +m+d+ +l + l+ ++
  gi|518651452|ref|YP_008140972.1| 109 nvemsdaikkleiagmdysiykdryghslsggelqklalA-ISIIPEpEFIVLDEAfSMMDSITLFKTLNFLK 180
                                       5555666666667777777777777788888888888753.45556668888888767888777766665555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   7.8e-05     0.077       3      18 ..      41      56 ..      40     122 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.8e-05
                            AAA_18  3 ltGtpGvGKttlakeL 18
                                      +tG++G+GKttla+ +
  gi|518651452|ref|YP_008140972.1| 41 ITGASGSGKTTLANII 56
                                      9************988 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0014       1.4       2      23 ..      36      57 ..      35      77 .. 0.76
   2 ?    1.2   0.1      0.35   3.4e+02      61      86 ..     152     179 ..     114     203 .. 0.64
   3 ?   -0.2   0.1      0.93   9.3e+02      20      57 ..     179     208 ..     169     225 .. 0.58

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0014
                            AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                      ++i  itGa  +GKTtl++ + 
  gi|518651452|ref|YP_008140972.1| 36 NNISGITGASGSGKTTLANIIT 57
                                      78999************86554 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.35
                            AAA_14  61 keekktylflDEiqev...pewekalksl 86 
                                        + + ++++lDE+  +    +++k+l+ l
  gi|518651452|ref|YP_008140972.1| 152 IP-EPEFIVLDEAFSMmdsITLFKTLNFL 179
                                       34.77888999987664443333333333 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.93
                            AAA_14  20 kqlikellvkkesilyinldderdkkladpekllelil 57 
                                        + +k    k  si+yi+ d +r + ++d+     +il
  gi|518651452|ref|YP_008140972.1| 179 LKQLK----KTISIIYIDHDINRIAFASDY----VYIL 208
                                       33333....445899998887776544443....3444 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0057       5.7      24      65 ..      40     111 ..      26     120 .. 0.74
   2 ?    4.3   0.8     0.019        19     190     243 ..     169     224 ..     164     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0057
                        KAP_NTPase  24 gLygkWGsGKssllnkledelkefa..............................kpvrflfaefnawsfkg 65 
                                       g++g+ GsGK++l n +  +  + a                              k+v+++ a++ +    +
  gi|518651452|ref|YP_008140972.1|  40 GITGASGSGKTTLANIITGYDTDYAgqilynsslvrtlgsvryvfqdpytsmnpvKTVEWHLATAASINNVE 111
                                       899************998877777777777777777777777777777777777777777777766655555 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.019
                        KAP_NTPase 190 vlqlleavkllfslkpvvfilavDphviakaieansesll..geiaghdYlekiiq 243
                                       +++l++++++l +lk++++i+  D ++   a +  +   l  g+i  ++Y +ki  
  gi|518651452|ref|YP_008140972.1| 169 SITLFKTLNFLKQLKKTISIIYIDHDINRIAFASDYVYILnhGKIIEENYTDKIMN 224
                                       5799********************98876677776666667899999999999976 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0073       7.2      36      50 ..      39      53 ..      27      56 .. 0.84
   2 ?    3.7   0.0     0.041        41     107     155 ..     120     167 ..      94     170 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0073
                            AAA_25 36 allaGapgtGKttla 50
                                      + ++Ga+g+GKttla
  gi|518651452|ref|YP_008140972.1| 39 SGITGASGSGKTTLA 53
                                      5689*********98 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
                            AAA_25 107 dlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsral 155
                                        +ag+ +  +++++ g++l  +++++l+ ai  +++++++v+D   +++
  gi|518651452|ref|YP_008140972.1| 120 EIAGM-DYSIYKDRYGHSLSGGELQKLALAISIIPEPEFIVLDEAFSMM 167
                                       45554.677788888999999**********************876665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   0.00023      0.23       4      20 ..      41      57 ..      40      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                            AAA_28  4 itGgestGKTtlleaLa 20
                                      itG++++GKTtl++ ++
  gi|518651452|ref|YP_008140972.1| 41 ITGASGSGKTTLANIIT 57
                                      8************9876 PP

>> UPF0261  Uncharacterised protein family (UPF0261)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.1     0.012        12      72     108 ..      17      54 ..       7      58 .. 0.76
   2 ?    4.4   0.0     0.015        15     365     397 ..     172     205 ..     159     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.012
                           UPF0261  72 aieamseaaaklvkely.eekidgvislGGsggtslat 108
                                       ++++    a + +++ + +++i+g+ ++ Gsg t+la 
  gi|518651452|ref|YP_008140972.1|  17 YMKYHDLYALDNISTTFrNNNISGITGASGSGKTTLAN 54 
                                       555555556666667774777**************986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.015
                           UPF0261 365 lfeale..eelkeseievvevdahindeeFaeava 397
                                       lf++l+  ++lk++ i+++ +d++in  +Fa++ +
  gi|518651452|ref|YP_008140972.1| 172 LFKTLNflKQLKKT-ISIIYIDHDINRIAFASDYV 205
                                       56665533678888.****************9877 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 ?   10.5   0.1   0.00023      0.23     132     150 ..      39      57 ..      16      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00023
                             T2SSE 132 ilvsGgTgsGKttllyall 150
                                         ++G+ gsGKttl++++ 
  gi|518651452|ref|YP_008140972.1|  39 SGITGASGSGKTTLANIIT 57 
                                       459*************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 ?   10.7   0.2    0.0003       0.3       3      28 ..      39      64 ..      37      73 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0003
                                      EEEEESTTCCHHHHHHHHHCT--SS- CS
                              cobW  3 tvltGflGsGKTtLlnhllenraglk 28
                                      +++tG  GsGKTtL n ++    ++ 
  gi|518651452|ref|YP_008140972.1| 39 SGITGASGSGKTTLANIITGYDTDYA 64
                                      689***********988875555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00058      0.58      14      37 ..      31      54 ..      24      67 .. 0.86
   2 ?   -0.9   0.0      0.94   9.4e+02     121     132 ..     156     167 ..     154     199 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00058
                                      HHHHH-SEEEEE--TTSSTTHHHH CS
                              PhoH 14 ealkkndivfaiGpaGtGKtylav 37
                                      ++ ++n+i  ++G +G+GKt la 
  gi|518651452|ref|YP_008140972.1| 31 TTFRNNNISGITGASGSGKTTLAN 54
                                      556799****************96 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.94
                                       EEEEE-SGGG-- CS
                              PhoH 121 afvilDEAQntt 132
                                        f++lDEA ++ 
  gi|518651452|ref|YP_008140972.1| 156 EFIVLDEAFSMM 167
                                       599999997664 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 ?    8.6   1.2    0.0015       1.5       2      21 ..      39      58 ..      38      85 .. 0.86
   2 ?    2.5   0.0      0.11   1.1e+02     235     265 ..     135     162 ..     124     162 .. 0.90
   3 ?   -1.7   0.1         2     2e+03      14      50 ..     171     196 ..     171     238 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0015
                            AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                       +++G+ gsGK++L  ++ +
  gi|518651452|ref|YP_008140972.1| 39 SGITGASGSGKTTLANIITG 58
                                      689***********999965 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.11
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDE 265
                                       ++lS G ++ lal+ +++  +    ++++DE
  gi|518651452|ref|YP_008140972.1| 135 HSLSGGELQKLALAISIIPEP---EFIVLDE 162
                                       689***************988...99**999 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2
                            AAA_21  14 nLLdaldllarl...drdvegltdelsggggirkipslld 50 
                                       +L+++l +l++l   +              +i+ i++ ++
  gi|518651452|ref|YP_008140972.1| 171 TLFKTLNFLKQLkktI--------------SIIYIDHDIN 196
                                       5777777777654331..............2222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 1803.21
//
Query:       gi|518651453|ref|YP_008140973.1|  [L=300]
Description: oligopeptide ABC transporter Dpp1, ATP binding protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.3   0.0    1.3e-26   93.8   0.0    1.3  1  ABC_tran     ABC transporter
    5.8e-10   39.5   0.0    1.3e-09   38.4   0.0    1.6  1  oligo_HPY    Oligopeptide/dipeptide transporter, C-terminal r
    6.6e-07   29.4   1.5     0.0086   15.9   0.2    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00017   21.1   1.6     0.0036   16.8   1.6    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    0.00063   19.4   0.2      0.016   15.0   0.1    2.4  2  AAA_29       P-loop containing region of AAA domain
    0.00085   18.6   0.5     0.0015   17.8   0.5    1.5  1  NB-ARC       NB-ARC domain
     0.0045   17.5   0.1     0.0096   16.4   0.1    1.6  1  AAA_23       AAA domain
     0.0061   16.5   0.1      0.012   15.5   0.1    1.5  1  NACHT        NACHT domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.035   14.2   0.1    1.7  1  DUF87        Helicase HerA, central domain
      0.017   15.1   0.2      0.029   14.3   0.2    1.3  1  ATPase_2     ATPase domain predominantly from Archaea
      0.021   14.9   0.2      0.067   13.2   0.1    1.9  2  AAA_14       AAA domain
      0.029   13.5   0.0      0.045   12.8   0.0    1.2  1  T2SSE        Type II/IV secretion system protein
       0.03   14.1   0.1        5.6    6.7   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
       0.04   14.3   0.0      0.047   14.1   0.0    1.3  1  AAA_16       AAA ATPase domain
       0.05   13.3   0.0       0.13   11.9   0.0    1.6  2  AAA_30       AAA domain
      0.066   13.8   0.0      0.099   13.2   0.0    1.4  1  AAA_18       AAA domain
       0.12   11.3   0.0       0.17   10.8   0.0    1.1  1  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
       0.15   12.0   0.0       0.25   11.2   0.0    1.3  1  RsgA_GTPase  RsgA GTPase
       0.22    9.0   0.1       0.34    8.4   0.1    1.2  1  DUF3584      Protein of unknown function (DUF3584)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   0.0   1.3e-29   1.3e-26       1     136 [.      21     165 ..      21     166 .. 0.90

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 1.3e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS..--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx..xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqe..pqlfpel 74 
                                       lkn+++++   e+v+++G nG+GK+tL+k ++g     eG++l++gk++ + ++  ++r+   +++q+  ++l+p +
  gi|518651453|ref|YP_008140973.1|  21 LKNINMHVADHEIVGVLGANGSGKTTLMKSIMGDIYASEGDVLYNGKSIYRkENYGKYRRVAIYVKQDsfNSLKPLK 97 
                                       79***********************************************998999999**********999999999 PP

                                       BHHHH......HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren......esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       tv  +      +++ + e ++  ++  +l+ ++ + ++ +LS G++ rv++a+all++p+ll+lDEpt
  gi|518651453|ref|YP_008140973.1|  98 TVNFQigklydWKSFDKEYVRLLFKELNLDPEIFNMKAIQLSDGMRHRVVIAMALLTNPELLVLDEPT 165
                                       987778**988555556666666666667779999999*****************************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 !   38.4   0.0   1.4e-12   1.3e-09       1      65 []     215     273 ..     215     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1.4e-12
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g+ s ++d p HPYT +Ll+ vp   ++++      +  +  ++   GC+F+++C++ ++eC
  gi|518651453|ref|YP_008140973.1| 215 IEDGEYSSILDGPFHPYTDTLLKYVPLYSNRNR------EYIEINNKKYGGCVFINNCRYWTKEC 273
                                       79**************************99999......44445566777*************** 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   0.2   9.1e-06    0.0086       2      36 ..      34      69 ..      33     108 .. 0.72
   2 !   12.8   0.1   7.8e-05     0.074     236     296 ..     137     193 ..      89     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.1e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdvegltdel 36
                                       ++ G+NgsGK++L++ +  + ++    +dv   + + 
  gi|518651453|ref|YP_008140973.1| 34 VGVLGANGSGKTTLMKSI--MGDIyasEGDVLYNGKSI 69
                                      6789************99..555555544444444444 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 7.8e-05
                            AAA_21 236 elSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltT 296
                                       +lSdG+++   ++++ l +++   ll++DEp +gL+   +  ll +lk  ++ +a v++++
  gi|518651453|ref|YP_008140973.1| 137 QLSDGMRHRV-VIAMALLTNP--ELLVLDEPTTGLDSISTYNLLIMLKTIKK-KASVLFSS 193
                                       67******95.5555555555..9***********98777777766644444.46666666 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 !   16.8   1.6   3.8e-06    0.0036      23     209 ..      30     207 ..      15     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.8e-06
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsi 99 
                                       ++++  ++G+NGSGK+ l+ +i   +G+  a++       + i++  +++  k  +v+i++++++ +    k+  ++
  gi|518651453|ref|YP_008140973.1|  30 DHEIVGVLGANGSGKTTLMKSI---MGDIYASEGDVLYNGKSIYR--KENYGKYRRVAIYVKQDSFN--SLKPLKTV 99 
                                       5678899***************...99655544444444444444..45555666777755444433..22222222 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiske.......lLSgGektLvalaLlfAiqkvkpaplyllDeida 169
                                       + ++   g      + k+  k+ v+ l+++ ++++e       +LS G +  v +a+           l +lDe   
  gi|518651453|ref|YP_008140973.1| 100 NFQI---G---KLYDWKSFDKEYVRLLFKELNLDPEifnmkaiQLSDGMRHRVVIAMA----LLTNPELLVLDEPTT 166
                                       2222...2...24556666666666666666666666666666999998765444443....234445889999999 PP

                                       TS-HHHHHHHHHHHHHHCTTSEEEEE-SSHH.HCCC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N 170 aLDeknvkkvaellkeksknaQfivislree.mlekadklv 209
                                        LD   + ++  +lk+ +k+a ++  s + + +++ +d+++
  gi|518651453|ref|YP_008140973.1| 167 GLDSISTYNLLIMLKTIKKKASVLFSSNDVNaLFQVCDRVY 207
                                       99999999999999999999999888876441445556655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.7e-05     0.016      19      55 ..      28      65 ..      19      69 .. 0.73
   2 ?    1.9   0.0      0.19   1.8e+02       5      19 ..     105     119 ..     102     126 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.7e-05
                            AAA_29 19 idlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      +  ++++ + G++GsGK+Tl+ +i+  +++++ +v +N
  gi|518651453|ref|YP_008140973.1| 28 VADHEIVGVLGANGSGKTTLMKSIMGDIYASEgDVLYN 65
                                      3334467799***********99887777766666666 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                            AAA_29   5 qlvNWgtfdghtiei 19 
                                       +l++W +fd++ +++
  gi|518651453|ref|YP_008140973.1| 105 KLYDWKSFDKEYVRL 119
                                       69*******987766 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.5   1.6e-06    0.0015      10      49 ..      22      60 ..      13     208 .. 0.58

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.6e-06
                                      HHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCCCC CS
                            NB-ARC 10 ekLlekdelqslvvalvGmgGvGKttlakqilnksdeveg 49
                                      ++   ++  +  +v++ G  G+GKttl+k+i+ +    eg
  gi|518651453|ref|YP_008140973.1| 22 KNIN-MHVADHEIVGVLGANGSGKTTLMKSIMGDIYASEG 60
                                      4444.4455566*******************998655555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1     1e-05    0.0096      17      40 ..      26      52 ..      10     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1e-05
                            AAA_23 17 F...skgltlItGpNGaGKTTildAik 40
                                          ++ ++ + G NG+GKTT++  i 
  gi|518651453|ref|YP_008140973.1| 26 MhvaDHEIVGVLGANGSGKTTLMKSIM 52
                                      45567889999************9986 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.3e-05     0.012       3      24 ..      34      55 ..      32      64 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.3e-05
                                      EEEEC-TTTCHHHHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqklalaw 24
                                      v + G++GsGKTtL+++++ ++
  gi|518651453|ref|YP_008140973.1| 34 VGVLGANGSGKTTLMKSIMGDI 55
                                      6689**************9876 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   3.7e-05     0.035      26      51 ..      34      58 ..       9      69 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.7e-05
                             DUF87 26 lAilgsTGsGKSntvavLleellekk 51
                                      +++lg  GsGK++++++++  +++  
  gi|518651453|ref|YP_008140973.1| 34 VGVLGANGSGKTTLMKSIMGDIYA-S 58
                                      79*****************99994.3 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   3.1e-05     0.029      20     114 ..      31     125 ..      18     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 3.1e-05
                          ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdkyviyyia..lreesiskldefieeeeekkklekalgiavpkaeleei 94 
                                        ei+ + G  gsGKt+L+k i+     ++ +v+y  +   r+e+  k+++  +   ++++++  +  ++ ++++ ++
  gi|518651453|ref|YP_008140973.1|  31 HEIVGVLGANGSGKTTLMKSIMGDIYASEGDVLYNGKsiYRKENYGKYRRV-AIYVKQDSFNSLKPLKTVNFQIGKL 106
                                       689999******************988888999965422577777777776.4344455566666777777778788 PP

                          ATPase_2  95 lkeksklvfkaielllekik 114
                                       ++ ks + ++++ ll+++++
  gi|518651453|ref|YP_008140973.1| 107 YDWKSFD-KEYVRLLFKELN 125
                                       7766666.677777777765 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.1e-05     0.067       2      35 ..      31      64 ..      30      99 .. 0.79
   2 ?   -2.0   0.0       3.5   3.3e+03      55      72 ..     148     163 ..     102     166 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.1e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesily 35
                                      ++i+ + Ga  +GKTtl+k ++ + ++++ ++ly
  gi|518651453|ref|YP_008140973.1| 31 HEIVGVLGANGSGKTTLMKSIMGDIYASEGDVLY 64
                                      57999*****************998866666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                            AAA_14  55 lileklkeekktylflDE 72 
                                       + ++ l   + ++l+lDE
  gi|518651453|ref|YP_008140973.1| 148 IAMA-LL-TNPELLVLDE 163
                                       1222.22.3567888888 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 ?   12.8   0.0   4.7e-05     0.045     113     157 ..      15      59 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.7e-05
                             T2SSE 113 alkekiaevlrkavrerglilvsGgTgsGKttllyallkeinksd 157
                                       +   +i + ++  v+ + ++ v G+ gsGKttl+ +++  i +s+
  gi|518651453|ref|YP_008140973.1|  15 KKYTEILKNINMHVADHEIVGVLGANGSGKTTLMKSIMGDIYASE 59 
                                       34456667778899*********************9999887765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0059       5.6      33      79 ..      16      63 ..       8      70 .. 0.74
   2 ?    5.2   0.0     0.017        16     102     150 ..     149     196 ..     133     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0059
                         IstB_IS21 33 rkvkeLat.lsfiekkenivllGpsGvGKshlaialgveavraglsvl 79
                                      + ++ L +   +++++e + +lG  G GK+ l  ++  +  +++  vl
  gi|518651453|ref|YP_008140973.1| 16 KYTEILKNiNMHVADHEIVGVLGANGSGKTTLMKSIMGDIYASEGDVL 63
                                      555555441357999****************99887666555555555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.017
                         IstB_IS21 102 alkrllkvdllilDdlgllpldqaeaellfeviekryerrsiiitsnlp 150
                                       a++ l++++ll+lD+   + ld+ ++ +l+ +++   +++s++ +sn  
  gi|518651453|ref|YP_008140973.1| 149 AMALLTNPELLVLDEPT-TGLDSISTYNLLIMLKTIKKKASVLFSSNDV 196
                                       66778999*******75.578999999999999999999****999965 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     5e-05     0.047      16      52 ..      24      59 ..      11     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-05
                            AAA_16 16 lervrsgrpelvllsGesGvGKsslvrellralekdg 52
                                      +++  ++  e+v + G+ G+GK++l+++++  + +++
  gi|518651453|ref|YP_008140973.1| 24 INMHVADH-EIVGVLGANGSGKTTLMKSIMGDIYASE 59
                                      44333333.89*****************998777773 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00014      0.13      17      46 ..      30      60 ..      22      87 .. 0.80
   2 ?   -1.7   0.0       2.1   1.9e+03      83     120 ..     150     190 ..     118     193 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00014
                            AAA_30 17 gdrvavltGpAGtGKttalkal.reaweaag 46
                                      ++ ++ + G+ G+GKtt++k++  ++++++g
  gi|518651453|ref|YP_008140973.1| 30 DHEIVGVLGANGSGKTTLMKSImGDIYASEG 60
                                      44588999*************9555666555 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.1
                            AAA_30  83 rarlepgtllivDEagmv....dtkqlaallkaaekagakvi 120
                                       +a l++ +ll+ DE        +t +l  +lk ++k +a+v+
  gi|518651453|ref|YP_008140973.1| 150 MALLTNPELLVLDEPTTGldsiSTYNLLIMLKTIKK-KASVL 190
                                       445566689999996543233366666666666666.56655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0    0.0001     0.099       1      65 [.      34      94 ..      34     159 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldklldale 65
                                      +++ G+ G+GKttl k +          +dv++++ + +  +++   +++r+ + + +  ++ l+
  gi|518651453|ref|YP_008140973.1| 34 VGVLGANGSGKTTLMKSIMGDI--YASEGDVLYNGKSIYRKENY--GKYRRVAIYVKQDSFNSLK 94
                                      6899**************5554..88889999999999999999..6666666666555555555 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00018      0.17      15      50 ..      17      52 ..       4      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00018
                                      HHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
                              MeaB 15 akellerllakaGraqvvGltGvPGaGkstlvealg 50
                                       +e+l+++  +    + vG+ G  G+Gk tl++ ++
  gi|518651453|ref|YP_008140973.1| 17 YTEILKNINMHVADHEIVGVLGANGSGKTTLMKSIM 52
                                      5799***************************98875 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   0.00027      0.25      84     128 ..      15      60 ..       4      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                                       TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S CS
                       RsgA_GTPase  84 aktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktg 128
                                       +k +e l++++ +++d +++ ++G  G GK+tL+++++++  ++ g
  gi|518651453|ref|YP_008140973.1|  15 KKYTEILKNINMHVADhEIVGVLGANGSGKTTLMKSIMGDIYASEG 60 
                                       455677889999999978999****************998766655 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   0.1   0.00036      0.34      20      36 ..      34      50 ..      23      51 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00036
                           DUF3584 20 tnieGtNaaGKTtLlrL 36
                                      + + G+N++GKTtL++ 
  gi|518651453|ref|YP_008140973.1| 34 VGVLGANGSGKTTLMKS 50
                                      6789***********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                       108  (0.00602376); 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 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 2188.75
//
Query:       gi|518651454|ref|YP_008140974.1|  [L=67]
Description: hypothetical protein FACI_IFERC00001G0093 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); 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: 00:00:00.41
# Mc/sec: 489.55
//
Query:       gi|518651455|ref|YP_008140975.1|  [L=172]
Description: hypothetical protein FACI_IFERC00001G0094 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.5   0.3      0.016   15.5   0.3    2.4  2  DUF3262      Protein of unknown function (DUF3262)
        3.8    7.2  11.4        2.1    8.0   9.6    1.6  1  Tetraspanin  Tetraspanin family


Domain annotation for each model (and alignments):
>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   1.3      0.57   5.1e+03      27      44 ..      25      42 ..       3      46 .. 0.54
   2 ?   15.5   0.3   1.8e-06     0.016      22      75 ..     105     161 ..      98     162 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.57
                           DUF3262 27 illvvllLwaaWalvsvY 44
                                      + +v +l+ a W+ v+v+
  gi|518651455|ref|YP_008140975.1| 25 LDYVHVLFGALWTGVDVF 42
                                      223444445556555555 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.8e-06
                           DUF3262  22 lliagillvvllLwaaWalvsvYkgWaeekiseadllslviR...avvlllvlgflf 75 
                                       ++i +il+vv +   + a++s Y g+++++++e++ + l++R   a+ l +vl +++
  gi|518651455|ref|YP_008140975.1| 105 ITISIILAVVSFAVIVPAIYSIYTGFKSNNVDESRNGKLLMRiakAASLQMVLQIII 161
                                       56777888888999999***************9988777777222567777777665 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   9.6   0.00024       2.1       8      99 ..      25     119 ..      18     168 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00024
                                       XXXXXXXXXXXXXXXXXXXXX.XXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
                                       xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Tetraspanin   8 fnllfwligivllavGvwlrl.khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkclll.tf 82 
                                       + ++ +l+g++  +v v + l      +   ++ +s+ +++ +++ll  + ++ +++ +lG+  a++en++ l  +f
  gi|518651455|ref|YP_008140975.1|  25 LDYVHVLFGALWTGVDVFMGLiFFIVLSGMEDKIRSDISFRLIPMLLYFIPAMSVFTPLLGFTLAMRENIFRLDyLF 101
                                       5566667777777775444445223334455567789999******************************6554134 PP

                                       XXXXXXXXXXXX.XXXXX CS
                                       xxxxxxxxxxxx.xxxxx RF
                       Tetraspanin  83 sllllvlfllel.aagil 99 
                                       + ++++ ++l + +++++
  gi|518651455|ref|YP_008140975.1| 102 IAIITISIILAVvSFAVI 119
                                       433333332222022222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1315.97
//
Query:       gi|518651456|ref|YP_008140976.1|  [L=188]
Description: hypothetical protein FACI_IFERC00001G0095 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1113  (0.0620782); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1512.85
//
Query:       gi|518651457|ref|YP_008140977.1|  [L=303]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   71.3   0.5    1.3e-19   70.7   0.5    1.3  1  DDE_Tnp_1    Transposase DDE domain
    3.2e-11   43.5   0.1    5.6e-11   42.7   0.1    1.4  1  DDE_Tnp_1_3  Transposase DDE domain
    0.00019   21.7   0.3    0.00087   19.6   0.2    2.0  2  DDE_Tnp_1_5  Transposase DDE domain
     0.0034   17.4   0.1     0.0069   16.4   0.1    1.5  1  DUF772       Transposase domain (DUF772)
     0.0075   15.9   0.0      0.016   14.9   0.0    1.6  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.5   3.6e-23   1.3e-19       2     214 .]      94     282 ..      93     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3.6e-23
                         DDE_Tnp_1   2 skrevlivDattvrvpgtk...........edarw..gyk.ggk.ykygyklhiavdtrsglilsvvitpgnvhdsk 63 
                                       s++++ ++D+  + +++++           +d  +  g++ + k + yg+k+h+ +d  s +i+   it gn hds+
  gi|518651457|ref|YP_008140977.1|  94 SVESIAAIDSFIIHTCKHStamrrkvwgnyKD--PvsGWSkTTKgWSYGRKCHMSIDIDSLIIMEWLITKGNMHDSH 168
                                       578999*************8777776665522..25566644446******************************** PP

                         DDE_Tnp_1  64 glkqlldelrprkgklvlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqk 139
                                       + ++++d++r  + +++laD++Y+  +++d++    ++ ++i                ++ r + ++r    +k+ +
  gi|518651457|ref|YP_008140977.1| 169 VSHDMVDSVR--DFSYILADSAYDASDIYDYIFeNTHALPVIDT--------------NKRRGIVDNRLPVNRKIGI 229
                                       **********..9********************44444444422..............3334444444444444444 PP

                         DDE_Tnp_1 140 rrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                         +                      +e+a +y+lRw+iEr+F+ l+  ++ +   y   +   +++ l+++a+nl
  gi|518651457|ref|YP_008140977.1| 230 DLR----------------------KEYASMYPLRWEIERTFSILEEIMKAEYIWYTVNRDYDTAIGLKAIAYNL 282
                                       444......................6************************9999999999999999999999998 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.7   0.1   1.6e-14   5.6e-11       5     108 ..      96     208 ..      93     233 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 1.6e-14
                       DDE_Tnp_1_3   5 tgisfiDstklavChnkrikrhkvfkg....lakrGkssmGWfyGfkLhliin.dkGeilavkltpgnvdDrepvee 76 
                                       + i+ iDs  ++ C+   + r+kv  +    ++ + k++ GW yG k h+ i+ d+  i+++ +t+gn++D +  ++
  gi|518651457|ref|YP_008140977.1|  96 ESIAAIDSFIIHTCKHSTAMRRKVWGNykdpVSGWSKTTKGWSYGRKCHMSIDiDSLIIMEWLITKGNMHDSHVSHD 172
                                       6899********************865222367899**************998355567899*************** PP

                       DDE_Tnp_1_3  77 lakellg..klfaDkgyiskklaeellee..gieli 108
                                       ++ ++ +   ++aD +y + ++ + ++e+  ++ +i
  gi|518651457|ref|YP_008140977.1| 173 MVDSVRDfsYILADSAYDASDIYDYIFENthALPVI 208
                                       **9996522789*********999999873334444 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   2.4e-07   0.00087      29      91 ..      22      86 ..      13     111 .. 0.83
   2 ?   -0.1   0.0      0.32   1.1e+03      59      82 ..      95     118 ..      91     132 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.4e-07
                       DDE_Tnp_1_5 29 rpqvysdaaiqtcltvkvlfklplRqlqGfvqs...llklaglellvpdystlsrraktlevkipv 91
                                      r+++y+d  i  +l+v ++f++++R ++ f++     +++ag+ + +p + tlsrra+ ++++   
  gi|518651457|ref|YP_008140977.1| 22 RKRKYTDRQILKVLIVLQIFNISYRSARIFLTNheeYIRMAGI-TEIPSFQTLSRRARMIDLHAIN 86
                                      7899**************************9752226889998.99************99988744 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                       DDE_Tnp_1_5  59 vqsllklaglellvpdystlsrra 82 
                                       v+s+ ++ ++ + ++++st +rr+
  gi|518651457|ref|YP_008140977.1|  95 VESIAAIDSFIIHTCKHSTAMRRK 118
                                       78999999999999*******997 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.9e-06    0.0069       8      58 ..      29      75 ..      23      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
                            DUF772  8 elmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsr 58
                                      + +lk+l++ +++++S r +   l ++ ++ + +g+     ++p++ tlsr
  gi|518651457|ref|YP_008140977.1| 29 RQILKVLIVLQIFNISYRSARIFLTNHEEYIRMAGI----TEIPSFQTLSR 75
                                      789********************************8....67********9 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   4.4e-06     0.016       2     134 ..     102     238 ..     101     261 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.4e-06
                         DDE_Tnp_4   2 Dgteipiqrpsnleeraqtysnykkkn............tlkvlivvdpngkiifvskgypGsvsDkeilensgllk 66 
                                       D++ i + + s+ ++r++ + nyk               + k+ + +d +  ii+     +G ++D+++ +  ++++
  gi|518651457|ref|YP_008140977.1| 102 DSFIIHTCKHST-AMRRKVWGNYKDPVsgwskttkgwsyGRKCHMSIDIDSLIIMEWLITKGNMHDSHVSH--DMVD 175
                                       666666655443.567777777776666666677777778889999999999998888889*******965..5666 PP

                         DDE_Tnp_4  67 alkeavkpgdvilaDkgFklsekllvpykkkkkkqlseeevefnraiasarihvErvigr.lkgrfril 134
                                        ++      ++ilaD++++ s+ +   +  ++ + l   ++++ r i  +r  v r ig  l++ +  +
  gi|518651457|ref|YP_008140977.1| 176 SVR----DFSYILADSAYDASDIYDYIF--ENTHALPVIDTNKRRGIVDNRLPVNRKIGIdLRKEYASM 238
                                       655....558************554444..489999999999999999999999999985356666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2210.42
//
Query:       gi|518651458|ref|YP_008140978.1|  [L=128]
Description: hypothetical protein FACI_IFERC00001G0097 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-06   27.4  10.6    2.2e-06   27.2  10.6    1.0  1  SLAC1     Voltage-dependent anion channel


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  10.6   1.2e-10   2.2e-06     209     319 ..       1     115 [.       1     123 [. 0.68

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.2e-10
                             SLAC1 209 fiplGplgqgalallllgkaapkaaevlkvlalllalf....lwglglfwllvavlsvlslpvrlkfslswWaftFP 281
                                       +i  G+ ++++++  l+ +++   +++++vl  ++  +     +gl++f++l+++l +++  ++l++++s W+ +FP
  gi|518651458|ref|YP_008140978.1|   1 MIYAGISSLTTVSGTLIIENYGLHGNSFYVLIHWIVTVdyaySVGLSVFLILFSILKIIKNSIDLNYKISIWGAVFP 77 
                                       588899999999999998888666888888555533331100335566666666666666333899*********** PP

                             SLAC1 282 lgalalatielgkaleseafkvlgtillvllvlvwllv 319
                                        g+l+ a++  g+  +   ++ l+++++ +++ ++++ 
  gi|518651458|ref|YP_008140978.1|  78 FGVLSSASYLTGRYNHINILSFLSLFYVSVALSLIIIG 115
                                       ***********855446666777776655555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       876  (0.0488594); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 848.11
//
Query:       gi|518651459|ref|YP_008140979.1|  [L=329]
Description: hypothetical protein FACI_IFERC00001G0098 [Ferroplasma acidarmanus fer1]
Scores for complete 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-100  334.8   1.9    4.9e-69  232.8   0.1    2.0  2  UxuA          D-mannonate dehydratase (UxuA)
    2.5e-13   49.9   0.0    5.5e-13   48.8   0.0    1.6  1  AP_endonuc_2  Xylose isomerase-like TIM barrel


Domain annotation for each model (and alignments):
>> UxuA  D-mannonate dehydratase (UxuA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.2   2.2e-33     2e-29       5     142 ..       7     151 ..       3     154 .. 0.95
   2 !  232.8   0.1   5.5e-73   4.9e-69     172     349 ..     152     327 ..     150     328 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 2.2e-33
                                       EE---T.T-SS-HHHHHHH.T--EEEE--TTS-T.......TS---HHHHHHHHHHHHHTT-EEEEEE-----HHHH CS
                              UxuA   5 lrwygeeddpvsleeirqipGvkgvvsalhdipa.......gevWekeeilklkeeiekagltlevvesvpvhedik 74 
                                       l+++  e++p  +++i +  Gv++ v++l + ++       +e+W++++++k+ ++++++gl+l ++e++p+++ i 
  gi|518651459|ref|YP_008140979.1|   7 LAEIILESKPDRFWKILKQIGVNDAVGVLPRNYNdwrksteDEPWDYYPLMKYMNMLQDSGLNLIAIEDNPPMNGIM 83 
                                       67778889999*****9989***********9999999999************************************ PP

                                       HT-TTHHHHHHHHHHHHHHHHHTT--EEEE---SS--S--SEEEEE-TTS-EEEEE-HHHHHHHHHHT CS
                              UxuA  75 lgteerdryienykqtirnlakiGvkvvCYnfmpvldWtrtdleykledgskalrfdkkeiealelki 142
                                       +g+ +r+++i+++ ++i n++++ +k++CYn+m++ +W+rt+ ++ +++g ++  fd ++i+++e+ +
  gi|518651459|ref|YP_008140979.1|  84 YGNSDREKEIDYISKMIENMGELNIKIWCYNWMAGSGWSRTKSDIIGKNGEYVSGFDYNDIKNIEPPV 151
                                       **************************************************************999865 PP

  == domain 2  score: 232.8 bits;  conditional E-value: 5.5e-73
                                       CTT--HHHHHHHHHHHHHHHHHHHHHHT-EEEE---SSSS-.BTTB--SSSSHHHHHHHHHH--STTEEEEEEHHHH CS
                              UxuA 172 ykkideeklrenlayFlkeiiPvaeevgvklaihPDDPPlp.ifGlpRivstkedlqrlldlvdspangitlCtGsl 247
                                       + ki++++l++nl+yFl++iiPvaee++vkla+hPDDPP+  ++G++Ri++++e++++ll+l++s++ngitlC+G++
  gi|518651459|ref|YP_008140979.1| 152 MGKIGKDELWKNLKYFLDNIIPVAEENDVKLAMHPDDPPIEnFRGIDRIMNSIESYDKLLELNRSKYNGITLCQGNF 228
                                       789*************************************98*********************************** PP

                                       TTSTT--HHHHHHHHGGGEEEEE--EEEE-SSTT-EEEE-TTSSSS-HHHHHHHHHHHHHHH-EE-----B-GGGG- CS
                              UxuA 248 garadndlvemikefadriyFahlRnikreedeksFveaahleGsvdlaevvkalleeeyrrylRpDhgrlllddkk 324
                                       ++++ ++l++ i++f+dri+F+h+R+++ +  + +++e+ + eG +d+a+++ka+ +++y++++R+Dh+++l +d +
  gi|518651459|ref|YP_008140979.1| 229 TLMT-DNLPSAIRHFNDRIFFVHFRDVNGN--KYNYQESLINEGRTDMAACMKAYNDINYNGIMRVDHTPTLEGDIE 302
                                       ****.88********************999..689****************************************** PP

                                       -STT--HHHHHHHHHHHHHHHHHHH CS
                              UxuA 325 lrPGYslidRllgiaylrGlleale 349
                                       l PGYs+ +R+++i+y++Gl ++++
  gi|518651459|ref|YP_008140979.1| 303 LVPGYSYSGRIYSIGYIKGLRDSIS 327
                                       **********************997 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 !   48.8   0.0   6.1e-17   5.5e-13      32     194 ..      58     274 ..       6     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 6.1e-17
                                       HHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSE..EEEEBCC............. CS
                      AP_endonuc_2  32 elrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapl..lvlhpGt............. 93 
                                       ++ ++l++ gl++ +++ ++  ++     ++++re+ +d++ ++ie + +L++++   + ++G+             
  gi|518651459|ref|YP_008140979.1|  58 KYMNMLQDSGLNLIAIEDNPPMNGIMY--GNSDREKEIDYISKMIENMGELNIKIwcYNWMAGSgwsrtksdiigkn 132
                                       455788899999888877777777554..77778899**************9776559999999************* PP

                                       ................GBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC........HHHHH CS
                      AP_endonuc_2  94 ................agagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd........eelar 146
                                                        +  +k +++e w++l   l+ ++++ae+++vkla+++ +++  ++++        e +++
  gi|518651459|ref|YP_008140979.1| 133 geyvsgfdyndikniePPVMGKIGKDELWKNLKYFLDNIIPVAEENDVKLAMHPDDPPIENFRGidrimnsiESYDK 209
                                       ***************98889999**********************************99888889************ PP

                                       HHHHHTTTTEEEEEEHHHHHHHTTTHHHHHHHHHGGEEEEEE.EESS.................T CS
                      AP_endonuc_2 147 lldavdspnvgvclDtgHlliaeedvddalraladrikhvHikDakg.................d 194
                                       ll+  +s+  g++l  g++ ++ +++ +a+r+++dri++vH+ D++g                  
  gi|518651459|ref|YP_008140979.1| 210 LLELNRSKYNGITLCQGNFTLMTDNLPSAIRHFNDRIFFVHFRDVNGnkynyqeslinegrtdmA 274
                                       *********************************************99666666666555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2216.21
//
Query:       gi|518651460|ref|YP_008140980.1|  [L=258]
Description: aldose dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-60  204.3   0.3    2.8e-60  203.8   0.3    1.1  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    4.3e-49  166.6   1.3    6.6e-49  166.0   1.3    1.2  1  adh_short      short chain dehydrogenase
    2.3e-12   47.2   0.7    6.9e-12   45.6   0.7    1.7  1  KR             KR domain
    0.00019   21.0   0.2    0.00035   20.1   0.2    1.6  1  Epimerase      NAD dependent epimerase/dehydratase family
    0.00076   18.7   0.0     0.0011   18.2   0.0    1.2  1  RmlD_sub_bind  RmlD substrate binding domain
     0.0054   15.8   1.4     0.0074   15.3   1.4    1.2  1  3Beta_HSD      3-beta hydroxysteroid dehydrogenase/isomerase 
  ------ inclusion threshold ------
       0.01   15.1   1.3      0.085   12.2   0.2    2.8  2  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
      0.015   14.9   0.3      0.034   13.7   0.0    1.7  2  LDcluster4     SLOG cluster4 family
      0.017   15.0   0.0      0.063   13.1   0.0    1.9  2  DFP            DNA / pantothenate metabolism flavoprotein


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 !  203.8   0.3   1.4e-63   2.8e-60       3     234 .]      16     248 ..      14     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 203.8 bits;  conditional E-value: 1.4e-63
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE---- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagi 79 
                                        +gIG+ai   +a eGa+v+   ++  +  ++++       ++++cDV++ ++v++++e++ +kf+++Dilvnnagi
  gi|518651460|ref|YP_008140980.1|  16 TKGIGKAISLGFAVEGARVISISRHTPE--DTDD-----RITYYNCDVSSSNDVKSTIENILSKFNTIDILVNNAGI 85 
                                       58******************99999997..2222.....2346********************************** PP

                                       -EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                      adh_short_C2  80 apklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtry 154
                                        +   +++ +t++  +dr++d+n++++++++k++++ ++k++ g+i+n+ssv+a+++++n +ay ++K+a+++lt++
  gi|518651460|ref|YP_008140980.1|  86 EEY--ASLDKTDEGMWDRIMDINVKGVYNVSKYCIQeMIKNHgGNIINISSVQANIITKNAAAYVTSKHAIIGLTKS 160
                                       ***..*******************************8666556********************************** PP

                                       HHHHHGGGTEEEEEEEE--BHCTGGGGSTT......HHH...HHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT- CS
                      adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgikg......fde...lleelearaplgrlgtpeevaeaalfLasdeasyi 222
                                       +A +++p +iR+Nav p  i+T+++++++       +++    ++e+  ++plgr+g+peeva+++lfLas+++s+i
  gi|518651460|ref|YP_008140980.1| 161 IALDYAP-EIRCNAVLPATIDTPLVRKAAIlevgnnEEKikeKIREWGLQHPLGRIGKPEEVANTVLFLASNQSSFI 236
                                       *******.9***************77654222444444411144556679*************************** PP

                                       -SEEEEESTTGG CS
                      adh_short_C2 223 tGqtlvvDgGlt 234
                                       tG+ ++vDgGl+
  gi|518651460|ref|YP_008140980.1| 237 TGASIMVDGGLS 248
                                       **********86 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   1.3   3.3e-52   6.6e-49       1     189 [.       8     186 ..       8     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 3.3e-52
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k vlvtG+++GIG+ai+  +a eGa+v+ ++r+        +    + ++++++++Dv+++++v+ ++e++ +k+ +
  gi|518651460|ref|YP_008140980.1|   8 KNVLVTGGTKGIGKAISLGFAVEGARVISISRHTP------ED---TDDRITYYNCDVSSSNDVKSTIENILSKFNT 75 
                                       78***************************988843......23...34579************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       +d+LvnNAGi++ ++  +++e  w+r++++N++gv+++++ ++++m+k+++G+I+n+sSv+++   ++ aaY +sK+
  gi|518651460|ref|YP_008140980.1|  76 IDILVNNAGIEEYASLDKTDEGMWDRIMDINVKGVYNVSKYCIQEMIKNHGGNIINISSVQANIITKNAAAYVTSKH 152
                                       ***********9***************************************************************** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTdmake 189
                                       a++glt+s+a ++ap+ ir+nav P+ +dT+++++
  gi|518651460|ref|YP_008140980.1| 153 AIIGLTKSIALDYAPE-IRCNAVLPATIDTPLVRK 186
                                       ***************8.**************9887 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.7   3.5e-15   6.9e-12       3     151 ..      10     149 ..       9     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.5e-15
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       +l+tGG+ g+G++++   a +gar ++ +sR+ ++d             + +++++++Dvs++++v++++e+i +++
  gi|518651460|ref|YP_008140980.1|  10 VLVTGGTKGIGKAISLGFAVEGAR-VISISRHTPEDT------------DDRITYYNCDVSSSNDVKSTIENILSKF 73 
                                       69********************98.567899944332............34799*********************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaa 151
                                       ++i   ++ Ag+ + + l+++++ ++++++   vkG+ n+ +++ +    ++   ++ +SS+ + + ++  a+Y +
  gi|518651460|ref|YP_008140980.1|  74 NTIDILVNNAGIEEYASLDKTDEGMWDRIMDINVKGVYNVSKYCIQemikNHGGNIINISSVQANIITKNAAAYVT 149
                                       ******************************************9998555455567899999999888888888876 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.2   1.8e-07   0.00035       1     116 [.      10     135 ..      10     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.8e-07
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HH....HHHHHHHHH.T-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrs....alerlfkee.qpdavihlA 72 
                                       +lVtG+t  iG+a+   ++ +g +vi ++r + ++    +++++ +++d+  ++     +e++++++  +d+ ++ A
  gi|518651460|ref|YP_008140980.1|  10 VLVTGGTKGIGKAISLGFAVEGARVISISRHTPED---TDDRITYYNCDVSSSNdvksTIENILSKFnTIDILVNNA 83 
                                       79*****************************5444...455568999**99998444456667777779*******9 PP

                                       S---HHHHHHSHH....HHHHHHTHHHHHHHHHHHHHTCT....EEEEEEEG CS
                         Epimerase  73 avggvaassedpa....dfieknlqgtlnlleaarkagvk....rllflsSs 116
                                       ++  +a   ++ +    +++++n++g++n+ +++ +  +k    +++++sS+
  gi|518651460|ref|YP_008140980.1|  84 GIEEYASLDKTDEgmwdRIMDINVKGVYNVSKYCIQEMIKnhggNIINISSV 135
                                       9555555444444122246679************977666666688888884 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 !   18.2   0.0   5.4e-07    0.0011       2      91 ..       9     119 ..       8     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 5.4e-07
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT............T--TTSHHHHHHHH.....HHH--SEEEE---. CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre............eldltdaeavaell.....keakpdvvvnaAA. 60 
                                       ++lvtG++  +G+++   +a eg+ v++++r+            ++d++ ++ v++++     k +  d++vn A  
  gi|518651460|ref|YP_008140980.1|   9 NVLVTGGTKGIGKAISLGFAVEGARVISISRHtpedtddrityyNCDVSSSNDVKSTIenilsKFNTIDILVNNAGi 85 
                                       69*****************************9******************999999993333333456799999854 PP

                                       ..---HHHHHHS.HHHHHHHHTHHHHHHHHHHHH CS
                     RmlD_sub_bind  61 ..ytavDkaEse.eeaayavnaeavealAeaaaa 91 
                                         y   Dk  +   ++ + +n+++v ++++++ +
  gi|518651460|ref|YP_008140980.1|  86 eeYASLDKTDEGmWDRIMDINVKGVYNVSKYCIQ 119
                                       559999**97765899***************954 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   1.4   3.7e-06    0.0074       2     117 ..      12     135 ..      11     151 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3.7e-06
                         3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealeg.......vdvvi 71 
                                       vtGg+  +G+a+   +  ++     rv+ +  +++      + +++++ ++Dv + ++++  +e+       +d+++
  gi|518651460|ref|YP_008140980.1|  12 VTGGTKGIGKAISLGFAVEGA----RVISISRHTPE----DTDDRITYYNCDVSSSNDVKSTIENilskfntIDILV 80 
                                       777777777777666665553....66665544443....2334556788888887777776654222222279999 PP

                         3Beta_HSD  72 hlaslvdvagklte.....deimkvnvkGTrnvleacvkagvrv....lvYtSsa 117
                                         a++ + a+ +++     d+im++nvkG  nv + c++  ++     ++  Ss+
  gi|518651460|ref|YP_008140980.1|  81 NNAGIEEYASLDKTdegmwDRIMDINVKGVYNVSKYCIQEMIKNhggnIINISSV 135
                                       999999988854441233368******************9997422226666665 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 ?   12.2   0.2   4.3e-05     0.085      33      72 ..       4      43 ..       1     117 [. 0.93
   2 ?   -0.6   0.1      0.36   7.2e+02      45      76 ..     137     168 ..     115     202 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.3e-05
                                      --TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCC CS
                     THF_DHG_CYH_C 33 elegkkvvvvGrsnivgkplallLleknatVtvchsktkd 72
                                      +l+gk+v+v G  + +gk+++l ++ ++a V  + ++t +
  gi|518651460|ref|YP_008140980.1|  4 DLKGKNVLVTGGTKGIGKAISLGFAVEGARVISISRHTPE 43
                                      79********************************999954 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.36
                                       -TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHH CS
                     THF_DHG_CYH_C  45 snivgkplallLleknatVtvchsktkdlaei 76 
                                        ni+ k  a+ +++k+a++ +++s + d a  
  gi|518651460|ref|YP_008140980.1| 137 ANIITKNAAAYVTSKHAIIGLTKSIALDYAPE 168
                                       45555555555555555555555544444444 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.7e-05     0.034      34      72 ..       9      47 ..       6      81 .. 0.79
   2 ?   -3.4   0.1       3.2   6.4e+03      87     102 ..     125     140 ..     115     145 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.7e-05
                        LDcluster4 34 avlltGgrtGvmeaaskGakeagGltvGilpassekehs 72
                                       vl+tGg++G+ +a s G   +g  ++ i++++ e+++ 
  gi|518651460|ref|YP_008140980.1|  9 NVLVTGGTKGIGKAISLGFAVEGARVISISRHTPEDTDD 47
                                      69****************************996555433 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.2
                        LDcluster4  87 agRnlilvlssdvvia 102
                                        g n+i++ s ++ i+
  gi|518651460|ref|YP_008140980.1| 125 HGGNIINISSVQANII 140
                                       4557888888777665 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   2.2e+03       1      12 [.       5      16 ..       5      18 .. 0.86
   2 ?   13.1   0.0   3.2e-05     0.063      32     101 ..      20      94 ..      12     104 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                                      TTT-EEEEEES- CS
                               DFP  1 legkkvlvtaGp 12
                                      l+gk+vlvt+G 
  gi|518651460|ref|YP_008140980.1|  5 LKGKNVLVTGGT 16
                                      689******984 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.2e-05
                                       HHHHHHHHHHTT-EEEEEE-S-SS---TT-..EEEE--SHHHHHHHHHHHHTT-...SEEEE---S--EEES--- CS
                               DFP  32 GyalAeaaaarGaeVtlvsgpvsletpegv..evvkvesaeemleaveealkea...divimaAAvaDyrpkeaa 101
                                       G a+   +a +Ga+V  +s ++  +t +++     +v+s+++ ++++e+ l++    di++  A +  y   +++
  gi|518651460|ref|YP_008140980.1|  20 GKAISLGFAVEGARVISISRHTPEDTDDRItyYNCDVSSSNDVKSTIENILSKFntiDILVNNAGIEEYASLDKT 94 
                                       7899999************99866665555115778******999998776544455********9999876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 1782.59
//
Query:       gi|518651461|ref|YP_008140981.1|  [L=201]
Description: hypothetical protein FACI_IFERC00001G0100 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-38  131.2  30.3    5.1e-38  130.8  30.3    1.1  1  Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family


Domain annotation for each model (and alignments):
>> Gpr1_Fun34_YaaH  GPR1/FUN34/yaaH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8  30.3   2.9e-42   5.1e-38      19     194 ..      15     185 ..      10     192 .. 0.94

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 2.9e-42
                   Gpr1_Fun34_YaaH  19 NPaPlgllafalttfvlslvnlgargite.pnvvvglalfyGGlvqllaGiwefavgntFgatalssYGgFwlsyaa 94 
                                       +PaPlgl++falttf+ls+vn+g  g +  + +++++a++yGG++ql+aG we+  g+ Fg++a+s+YG+Fwl y +
  gi|518651461|ref|YP_008140981.1|  15 DPAPLGLTGFALTTFMLSFVNAGIIGSKGgTGMAISFAFAYGGIAQLIAGQWEMRRGSQFGFVAFSTYGAFWLWYVF 91 
                                       8***********************9998537899*****************************************99 PP

                   Gpr1_Fun34_YaaH  95 ilip.gfgilaaYeedeeelnnalglyllgwfiftfllllatlrstvalfllfffldltflllaigeltgsakvlkA 170
                                       + +   fg+++         n+alg+ l+ w +ft+ +++ ++r ++ l+++f+fl+ltf++l++g+++g   +++ 
  gi|518651461|ref|YP_008140981.1|  92 LEVAaHFGVITVT-------NEALGISLILWGVFTLYMFVTAIRLNMGLMFTFLFLWLTFFFLGAGAMSGVVIITHI 161
                                       9776578887666.......8******************************************************** PP

                   Gpr1_Fun34_YaaH 171 ggvfgiiaaflawYnalaglatke 194
                                       gg++gi+aa +a Y+a+a +++++
  gi|518651461|ref|YP_008140981.1| 162 GGYLGILAAAFAIYTAFAVVTNSN 185
                                       ******************999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       944  (0.0526521); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1345.40
//
Query:       gi|518651462|ref|YP_008140982.1|  [L=639]
Description: hypothetical protein FACI_IFERC00001G0101 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-89  300.3   0.0    2.1e-89  300.1   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      1e-22   80.9   0.1    2.5e-22   79.6   0.1    1.7  1  AMP-binding_C  AMP-binding enzyme C-terminal domain
    3.2e-20   71.8   2.3    7.6e-20   70.6   2.3    1.7  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.1   0.0   3.5e-93   2.1e-89       6     422 ..      79     511 ..      73     512 .. 0.84

  Alignments for each domain:
  == domain 1  score: 300.1 bits;  conditional E-value: 3.5e-93
                                       HHSTTSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   6 aktpdkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       +++++kva+++   +ge + +TY  l++rvn++A+gL++lGvkkgd++ i++p+ +e  +a+la++++Gav  ++ +
  gi|518651462|ref|YP_008140982.1|  79 NEKRNKVAFIWvpeKGEEKVVTYFGLYRRVNAFARGLLNLGVKKGDKITIYMPMILEAPIAMLACARIGAVFNVVFS 155
                                       4455**********999************************************************************ PP

                                       TS-HHHHHHHHHHHTESEEE.........ETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCT CS
                       AMP-binding  80 tltaeelayiledseakvli.........atvdsel.leklleaaakleavklvivldadellkeeelkeeeeseek 146
                                       ++++++la  +++s++k++i              +  l+++ ++a +l      +++ ++   + +++++++  ++ 
  gi|518651462|ref|YP_008140982.1| 156 GFGEQALAERINNSNSKTIItadggyrkgN----IIqLKNIVDKAIDLSNGVDNVIVVKNTHTEIDMEPDRDYYYD- 227
                                       ********************9877654321....222334433333343333333333344444444444443333. PP

                                       TS....-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHH CS
                       AMP-binding 147 ae....kpeeeeelkpddlayiiYTSGTTGkPKGVmlsh.rnlvanvaslkletrfklkeddvvlsilplahifgli 218
                                        +      +e+e+ +++d+++i+YTSGTTGkPKG+ +   ++ v+ + +lk+   f+ k++d++++ +++ +i+g++
  gi|518651462|ref|YP_008140982.1| 228 -DiiedGYVEPEQMDSNDPLFILYTSGTTGKPKGILHANgGYPVWIANTLKW--AFNPKDEDRWWCAADIGWITGHS 301
                                       .1345545577899*************************5555776666542..2444568**************** PP

                                       HHHHHHHHTT-EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHH.CHHHHCCGTT-SEEEEESS CS
                       AMP-binding 219 lelllallsGatvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalk.aakkakdlsslrlvllgge 293
                                       + ++++ll G t v++++  + ++p++++e ie+++v+++++ P++++ l++ g+++     ++dlssl+++ ++ge
  gi|518651462|ref|YP_008140982.1| 302 YIVFAPLLLGLTSVMYEGAIDyPKPDRMWEIIERYGVNLLYTSPTAIRLLMKYGEKYpL---SHDLSSLKTLGTVGE 375
                                       *********************777****************************7777734...67************* PP

                                       -EBHHHHHHHHHHHTC...EEEEEEEEGGGSSECEE..CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEE CS
                       AMP-binding 294 plspellrffralfge...evlegYGlTEttgvvtv..lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeG 365
                                       p++p+++++++++ g+   +++++Y++TEt+g+++   ++l  ++ k+gs+ +p+pg++++i+De+ g+ v++ge+G
  gi|518651462|ref|YP_008140982.1| 376 PINPAAWHWYYEVIGKsrcPIIDTYWQTETGGFTISpsARLGLPDLKPGSATFPMPGIDAEILDEN-GKNVKPGEKG 451
                                       **************99******************66676666667799*****************9.999******* PP

                                       EEEEEET..TS-SEBTT-HHHHHHHEEET.CCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 366 ellvrgp..gvmkgYlkkpeataeafdse.grwlrTGDlgrldedGyleivgRkkdlikl 422
                                        +++++p  g+m    +++++  ++++s+ ++ +  GD +  d+dGy++++gR+++++k+
  gi|518651462|ref|YP_008140982.1| 452 YIVIKKPwpGLMLTVNNDDKRYIDTYFSKfKGKYFMGDYAIQDDDGYYWLLGRSDEVLKV 511
                                       ******9778***************9986778999***********************98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.1   4.2e-26   2.5e-22       1      76 []     520     598 ..     520     598 .. 0.95

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.2e-26
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsea...leeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE  lvs++++aeaaV+G+pd vkG ++vaf +lkdg+e+   l e++k+++r +lgp++vp+++++v+ +pktrs
  gi|518651462|ref|YP_008140982.1| 520 EVEDGLVSMKEIAEAAVFGKPDTVKGDTIVAFATLKDGYEKspeLIENIKKRIRNNLGPIMVPEEIHIVSTVPKTRS 596
                                       8***********************************99522357********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|518651462|ref|YP_008140982.1| 597 GK 598
                                       *9 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   2.3   1.3e-23   7.6e-20       1      55 []      18      72 ..      18      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.3e-23
                                      HHHHHHHHHH-HHHHHHHHHCCS--SB--S-SECSTTTCT-EESTT-EE-HHHHH CS
                            ACAS_N  1 ykelykeSiedpeaFWaeqakeldWekpfdkvldgskgpfikWFeGGklNicyNc 55
                                      y e y++S++d ++FW+e  + +dW+kpfdkvld+sk+pf++WF +Gk+N +yNc
  gi|518651462|ref|YP_008140982.1| 18 YFEEYERSLKDVNGFWNENGRIIDWFKPFDKVLDDSKKPFYRWFINGKTNLSYNC 72
                                      6678*************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (639 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.48
# Mc/sec: 4014.75
//
Query:       gi|518651463|ref|YP_008140983.1|  [L=342]
Description: hypothetical protein FACI_IFERC00001G0102 [Ferroplasma acidarmanus fer1]
Scores for complete 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-62  210.1   0.5    4.3e-62  210.0   0.5    1.0  1  Aldo_ket_red  Aldo/keto reductase family
  ------ inclusion threshold ------
      0.084   12.6   0.1       0.23   11.2   0.1    1.8  1  RPN6_C_helix  26S proteasome subunit RPN6 C-terminal helix do


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 !  210.0   0.5   4.8e-66   4.3e-62       2     292 ..      16     331 ..      15     333 .. 0.94

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 4.8e-66
                                       EEEE-SSS-ST........TS-HHHHHHHHHHHHHTT--EEE--TT-............TTTHHHHHHHHHHHH-TT CS
                      Aldo_ket_red   2 lglGtwqlgsk.......eeiskeealellrraleaGinffDtAevY............gkgqseellGealkksrk 59 
                                       + +Gtw+l +        e +++ee  ++ ++a++ Ginf+DtA++Y             +g se++lG+++k+   
  gi|518651463|ref|YP_008140983.1|  16 VAIGTWHLPGSgqfvnkvESVNEEEFKKIFKKAYDFGINFYDTADIYhgrvennedcieCTGNSERVLGNIIKD--Y 90 
                                       67999999999999999*********************************************************..* PP

                                       TGGG-EEEEEE..--SSSTTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEE CS
                      Aldo_ket_red  60 kreeviiatKv..dlrdaeiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkir 134
                                       +re+++i+tKv  +++ + ++sgls+++i++ ++ sl+rL+tdyvDl+++H+ d ++p + e+l+a+ + v+  + r
  gi|518651463|ref|YP_008140983.1|  91 DRESLVISTKVagPMNYYVNSSGLSRKHIMHGIKSSLERLKTDYVDLYQFHWSDNDTP-LIETLKAMSHIVDLDLSR 166
                                       *************9********************************************.****************** PP

                                       EEEEES--HHHHHHH....HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---S CS
                      Aldo_ket_red 135 aiGvSnfsveqleka....kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedk 207
                                       +iG Sn+++  + +     +k +   +++ q  yn+l++  e+  + +++ ++++l ay pl +G+l gky ++  k
  gi|518651463|ref|YP_008140983.1| 167 YIGMSNVNACDIPEFmnlsEKYNLNNFITMQEAYNILDRKIENDKILYAQRYNLGLLAYIPLDQGILAGKYLNNYGK 243
                                       ********666655558866666777***********88888888889****************************9 PP

                                       SSCCC-------TS-HHHHHHHHHHHHHHHHTT--HHHHHHHHHTTS....TT-SEEEE--SSHHHHHHHHGGGG-- CS
                      Aldo_ket_red 208 edkeprkdlkrdertsknldaaeelselakehgvslaqlalryalsq....pavgivipgasnieqlednldalelk 280
                                       ++  +  + + +++++++l+++++l+e+a e++++l+qla++++l++    + ++i+++g +ni+ l+dn++al+++
  gi|518651463|ref|YP_008140983.1| 244 GSRITYYS-GLQNEIDRTLNTVKKLKEFADENDITLSQLAIAWLLKRgaelNIKIIPLLGITNIKYLDDNINALNVN 319
                                       97766655.4449**********************************99999************************* PP

                                       --HHHHHHHHHH CS
                      Aldo_ket_red 281 lseeevaeldel 292
                                       l++e++++++e+
  gi|518651463|ref|YP_008140983.1| 320 LKDEDMKYINEI 331
                                       **********98 PP

>> RPN6_C_helix  26S proteasome subunit RPN6 C-terminal helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   2.6e-05      0.23       9      21 ..     150     162 ..     150     162 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.6e-05
                      RPN6_C_helix   9 LeTIknmgkVVDs 21 
                                       +eT+k+m+++VD+
  gi|518651463|ref|YP_008140983.1| 150 IETLKAMSHIVDL 162
                                       7***********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2603.82
//
Query:       gi|518651464|ref|YP_008140984.1|  [L=622]
Description: hypothetical protein FACI_IFERC00001G0103 [Ferroplasma acidarmanus fer1]
Scores for 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  172.9   2.5    2.1e-48  165.2   0.1    2.3  3  Glyco_hydro_15  Glycosyl hydrolases family 15
  ------ inclusion threshold ------
      0.048   13.2   0.0       0.62    9.6   0.0    2.3  2  Peptidase_S39   Peptidase S39


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.3   0.3      0.63   5.7e+03     141     167 ..     199     224 ..     193     225 .. 0.78
   2 !  165.2   0.1   2.4e-52   2.1e-48       3     358 ..     236     552 ..     234     559 .. 0.93
   3 !    9.5   0.0   4.2e-05      0.38     399     447 ..     548     596 ..     543     597 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.3 bits;  conditional E-value: 0.63
                                       TTHCHCCCCHHHHTHHHHHHHHHHHTT CS
                    Glyco_hydro_15 141 sglqiistldevafvqnlvdYieaayk 167
                                       ++ ++ s++de+    +l++Y+ +++k
  gi|518651464|ref|YP_008140984.1| 199 TDINHLSNVDEY-KSYKLLEYTRNYWK 224
                                       566778889999.66789999999998 PP

  == domain 2  score: 165.2 bits;  conditional E-value: 2.4e-52
                                       HHHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-H CS
                    Glyco_hydro_15   3 rldlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleq 70 
                                       ++++++r++ +l+ l+++p tG+++A+p+ s+p         DYr+tW+RD +yvi+a+  +   de+ ++ y+l  
  gi|518651464|ref|YP_008140984.1| 236 YHKYIVRSALALKGLFYEP-TGMMVAAPTSSLPesiggernwDYRFTWIRDTAYVIEALSLIRLNDEATKFLYDLLY 311
                                       7899***************.***************************************944466************ PP

                                       CCHHHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCC CS
                    Glyco_hydro_15  71 slvklmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiis 147
                                        +++  +  l++++++++  +      ++k +  ++++++ ++++G+++ ++lQlD+ + ++ a++q+  +g +++ 
  gi|518651464|ref|YP_008140984.1| 312 RINRDQK--LRTIYSIDDSDTT-----DEKIIDYSGYMNSAPVRIGNKAGDQLQLDQFGSIINAIYQFNLAGGMVTI 381
                                       **98666..9*******97222.....2335689**********************************999999999 PP

                                       CCHHHHTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHH CS
                    Glyco_hydro_15 148 tldevafvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnkl 224
                                       +l+ +  v  ++  +++ +k pd+ +WE + + +++++s++ ++ A+ eai + +++g ++  + +++  dei n++
  gi|518651464|ref|YP_008140984.1| 382 QLWDF--VLSILNSLKSIWKYPDSSIWEFRTEPKQYVYSKIISWTAFHEAIIMGKALGYSAPYNEWKQIEDEIKNDI 456
                                       99999..9********************************************************************* PP

                                       HSTTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHH CS
                    Glyco_hydro_15 225 qgkygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyild 301
                                             k gf  + n +++++gs             ++dasll +p   f p +d           r+ +++++i++
  gi|518651464|ref|YP_008140984.1| 457 -----LKNGFNSEINSFTQYYGS------------TNVDASLLRIPLTDFLPVND----------YRITGTLKKIES 506
                                       .....9*****************............********************..........9*********** PP

                                       HHHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 302 sllsegflavgeldplvrRysedvkpdklglsGrpyylctlwtvetlldelyekagk 358
                                       +l+   +l        ++Ry+ed   d+l+++ ++++l ++w +e+l +    k+ k
  gi|518651464|ref|YP_008140984.1| 507 DLMHNNYL--------FKRYNED---DGLKGDDNAFLLLSFWYIEDLIKMKKIKDAK 552
                                       *8888774........9******...68**************999998877766665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHHHHS-TTS---SEE-TTT--EESSTT-HHHHHHHHHHH CS
                    Glyco_hydro_15 399 veeladliveaveednslgvLteevdvylgeliraqpllfsealllrig 447
                                       ++  ++ + ++ + +n+l +++ee+d ++  +++++p++  ++  +r++
  gi|518651464|ref|YP_008140984.1| 548 IKDAKNALETILNLSNHLMLFSEEIDLQTHDFLGNFPQAITHLGVIRAI 596
                                       45555666666666********************************986 PP

>> Peptidase_S39  Peptidase S39
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.039   3.5e+02     113     148 ..     168     203 ..     159     216 .. 0.86
   2 ?    9.6   0.0   6.9e-05      0.62      13      88 ..     400     485 ..     392     491 .. 0.70

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.039
                     Peptidase_S39 113 aslftlskegwssssakivgsegkfvsvlsntkpgh 148
                                       ++ f+l+k+++++++ +i   +g f  ++  t+ +h
  gi|518651464|ref|YP_008140984.1| 168 STNFKLNKNKTMVYNDNIKLNKGSFQWIVISTDINH 203
                                       6789******************99999988888776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 6.9e-05
                     Peptidase_S39  13 ppkksvleishadgshvGyAtcvklldgenalvtaehvlse...........pskvkslrtgekiplaefkkllese 78 
                                       +p++s+ e + ++++ v y   +  +  ++a++  ++ + +           ++k++ l++g  + +++f++ ++s+
  gi|518651464|ref|YP_008140984.1| 400 YPDSSIWEFRTEPKQYV-YSKIISWTAFHEAIIMGKALGYSapynewkqiedEIKNDILKNGFNSEINSFTQYYGST 475
                                       55555555555555555.444455555555555555544444445555566699*********************** PP

                     Peptidase_S39  79 kadllilegp 88 
                                       ++d ++l++p
  gi|518651464|ref|YP_008140984.1| 476 NVDASLLRIP 485
                                       ********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 4287.58
//
Query:       gi|518651465|ref|YP_008140985.1|  [L=386]
Description: multidrug efflux permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.5e-28   99.0  59.0    8.8e-13   47.9  19.6    3.0  3  MFS_1      Major Facilitator Superfamily
    3.1e-07   29.2  13.3    4.3e-05   22.1   7.0    2.1  2  MFS_3      Transmembrane secretion effector
  ------ inclusion threshold ------
      0.016   15.2   0.4      0.016   15.2   0.4    3.2  4  DUF1304    Protein of unknown function (DUF1304)


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 !   40.3  18.8     3e-14   1.8e-10     212     329 ..       9     126 ..       2     130 .. 0.90
   2 !   28.3  18.5   1.4e-10   8.2e-07     121     293 ..     131     285 ..     127     285 .. 0.86
   3 !   47.9  19.6   1.5e-16   8.8e-13       2     172 ..     209     377 ..     208     385 .. 0.87

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 3e-14
                             MFS_1 212 llialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaa 288
                                       +  a+ + +fg+s++ +++ ly+++ l++s ll++g+++ ++++++a + + +g++sdr+g + ++++++++ ++++
  gi|518651465|ref|YP_008140985.1|   9 ITGASTVRGFGYSSIWIYSSLYMHDILHIS-LLYVGIIFTAGGFIAALVNIYGGAISDRVGYKGTMIFSFSISVVIY 84 
                                       4445555599********************.********************************************** PP

                             MFS_1 289 lglallavtssavllllvlvliGf.glgfvfpsllalasdla 329
                                       + l +++  s ++ll+ v +++ + + ++++p+++al+s++ 
  gi|518651465|ref|YP_008140985.1|  85 AVLSFVPGVSLSALLYPVAFIMFMiANAIMSPASNALISRSS 126
                                       *********8888888877777777*************9875 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 1.4e-10
                             MFS_1 121 raigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplv 197
                                       +++++l +g+++G  +gp++gg++ s +g++++f++  i+++++  l++ l++ + +  ++  ++++         +
  gi|518651465|ref|YP_008140985.1| 131 KGFSILRVGNNIGWGFGPAIGGFIESFGGYHLLFVFGLIMGIIS--LGISLFLKNVKYDGKIGKVPL---------T 196
                                       689*****************************************..888*************66666.........4 PP

                             MFS_1 198 pawkallkdpvlw...illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrl 271
                                       +  +        w   + lialllf ++ s+ +++l+ y+   + ++  +++g+++   ++++++l+ ++ ++++++
  gi|518651465|ref|YP_008140985.1| 197 T--SN------TWliqLSLIALLLF-VVQSQETVTLTNYATIFRSIK-IYQLGIVYLTNGIFVIVLQGFIYKIIRKI 263
                                       4..22......34443355555555.588888888888888889999.8**************************** PP

                             MFS_1 272 grrrrlllallllllaalglal 293
                                       g+     ++ ++ +++++++a+
  gi|518651465|ref|YP_008140985.1| 264 GNFSSFAIGSFVYSFGFFSYAF 285
                                       **99999999999999999876 PP

  == domain 3  score: 47.9 bits;  conditional E-value: 1.5e-16
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +l++f++  + +++++++  ++ ++  i   ++g+++ + +++ +v++ ++  ++ ++G  + + +g +++++g++ 
  gi|518651465|ref|YP_008140985.1| 209 ALLLFVVQSQETVTLTNYA-TIFRS--IKIYQLGIVYLTNGIFVIVLQGFIYKIIRKIGNFSSFAIGSFVYSFGFFS 282
                                       6778888888888888888.88888..66999******************************************555 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                        +f +++  ++++ ++  +g+ ++fp+g++++++++++e+ g+ +g+++a+ s+G ++gp lgg+  +++  ++  +
  gi|518651465|ref|YP_008140985.1| 283 YAFDTGIIGMVISTIVLTIGEDFAFPVGYSMVSAVSKPENIGKNMGIYNAFLSVGRAIGPTLGGVAFTLFTVPYEIW 359
                                       556577778**************************************************************999988 PP

                             MFS_1 156 ilaivslla.fvlfllll 172
                                       +++ ++ ++ +++f++ +
  gi|518651465|ref|YP_008140985.1| 360 LFTTFTGFVaCIIFIIKF 377
                                       888777666255544444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   7.0   7.2e-09   4.3e-05      34     178 ..      28     170 ..       8     230 .. 0.80
   2 !   11.1   0.4   1.5e-05      0.09     106     190 ..     292     378 ..     271     385 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 7.2e-09
                             MFS_3  34 sWlmtdi.sasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllal 109
                                       s  m di + s l v ++  a+     l+ i  Ga++D +  +  ++   ++ ++  ++l  +  + l +    +a+
  gi|518651465|ref|YP_008140985.1|  28 SLYMHDIlHISLLYVGIIFTAGGFIAALVNIYGGAISDRVGYKGTMIFSFSISVVIYAVLSFVPGVSLSALLYPVAF 104
                                       5455554378999**********************************998887777777766666666665555565 PP

                             MFS_3 110 tlligiGaalndPaWqAsvgelvkrrdvp.aAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnals 178
                                       +++  i  a+++Pa +A ++     +d++ +   +  vg ni    GPA+gG + ++ G  l f +  + 
  gi|518651465|ref|YP_008140985.1| 105 IMF-MIANAIMSPASNALISRS---SDIQlKGFSILRVGNNIGWGFGPAIGGFIESFGGYHLLFVFGLIM 170
                                       544.5899*********99864...444425677889*******************99999888776554 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.5e-05
                             MFS_3 106 llaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavG.aalafavnals.yl 180
                                       ++++t+++ iG  +  P    +v+ + k +++ + + +    + + R++GP lgGv  +++  +   + +++++ ++
  gi|518651465|ref|YP_008140985.1| 292 MVISTIVLTIGEDFAFPVGYSMVSAVSKPENIGKNMGIYNAFLSVGRAIGPTLGGVAFTLFTvPYEIWLFTTFTgFV 368
                                       688999***************************************************99986366778888876355 PP

                             MFS_3 181 alivallrwk 190
                                       a i+ +++ +
  gi|518651465|ref|YP_008140985.1| 369 ACIIFIIKFR 378
                                       6666666655 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   1.6      0.35   2.1e+03      51      86 ..      51      88 ..      47     110 .. 0.67
   2 ?   -2.4   0.3      0.77   4.6e+03      46      61 ..     158     173 ..     154     184 .. 0.77
   3 ?   -3.6   0.1       1.8   1.1e+04       2      19 ..     207     224 ..     202     232 .. 0.60
   4 ?   15.2   0.4   2.6e-06     0.016      39      86 ..     321     373 ..     309     381 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                           DUF1304 51 fLAa.gliwglll.gseavglalvlfflgcvvvaglyg 86
                                      f+Aa + i+g ++  +  ++ ++++ f ++vv+ ++  
  gi|518651465|ref|YP_008140985.1| 51 FIAAlVNIYGGAIsDRVGYKGTMIFSFSISVVIYAVLS 88
                                      55541457777553555566677777777777777654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.77
                           DUF1304  46 GlYNgfLAagliwgll 61 
                                       G Y +++  gli+g++
  gi|518651465|ref|YP_008140985.1| 158 GGYHLLFVFGLIMGII 173
                                       7788999999999984 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 1.8
                           DUF1304   2 lvallhlyilvlEmflwt 19 
                                       l+all +++   E+++ t
  gi|518651465|ref|YP_008140985.1| 207 LIALLLFVVQSQETVTLT 224
                                       455555555555555544 PP

  == domain 4  score: 15.2 bits;  conditional E-value: 2.6e-06
                           DUF1304  39 kvlaanqGlYNgfLAagliwglll.....gseavglalvlfflgcvvvaglyg 86 
                                       + + +n+G+YN fL++g ++g  l     +  +v ++++lf+++  +va +++
  gi|518651465|ref|YP_008140985.1| 321 ENIGKNMGIYNAFLSVGRAIGPTLggvafTLFTVPYEIWLFTTFTGFVACIIF 373
                                       67889************999986633333334456777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2476.21
//
Query:       gi|518651466|ref|YP_008140986.1|  [L=382]
Description: hypothetical protein FACI_IFERC00001G0105 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-34  119.6   0.0    2.2e-34  118.9   0.0    1.4  1  ABC_tran         ABC transporter
    6.2e-11   42.6   0.0      2e-10   40.9   0.0    1.9  1  GlcV_C_terminal  Glucose ABC transporter C-terminal domain
    2.7e-06   27.4   1.0      0.023   14.5   0.2    2.3  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0071   16.5   0.5      0.031   14.4   0.1    2.0  2  DUF87            Helicase HerA, central domain
     0.0095   16.5   1.5      0.015   15.8   0.4    1.9  2  AAA_23           AAA domain
     0.0098   16.1   0.1       0.19   12.0   0.1    2.3  1  SbcCD_C          Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
      0.015   15.0   0.1      0.031   14.0   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.024   14.1   1.0       0.26   10.7   1.0    2.1  1  SMC_N            RecF/RecN/SMC N terminal domain
       0.16   12.0   0.1       0.64   10.1   0.1    2.0  2  Phage_terminase  Phage terminase small subunit
       0.24   11.3   0.5       0.71    9.8   0.2    1.8  2  NACHT            NACHT domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   1.3e-37   2.2e-34       1     136 [.      23     170 ..      23     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 1.3e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqepqlfpel 74 
                                       l++++l++  ge  +i+G++G+GK+tL++++agl+ pteG++ +d+k++++   + +e+ +++ig+++q+  l p+l
  gi|518651466|ref|YP_008140986.1|  23 LQHINLDIDSGEFFGILGSSGSGKTTLMRIIAGLEIPTEGTVSFDQKPVSKdnkIITEVEDRNIGMVFQNWALYPHL 99 
                                       689**********************************************99999999******************** PP

                                       BHHHH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       t+ en             + +++++++++ l+++e+ +++     ++ SgGq+qrva aral+k+p llllDEp+
  gi|518651466|ref|YP_008140986.1| 100 TNFENiafplrimrlkesAVNRRVKEIAELLDISEVLNKHP----KEASGGQQQRVAYARALVKNPALLLLDEPF 170
                                       ***************99888999*********999888887....*****************************7 PP

>> GlcV_C_terminal  Glucose ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.0   1.1e-13     2e-10       2      61 .]     315     374 ..     314     374 .. 0.97

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.1e-13
                                       TCEEEEEEEEEEEEEETTEEEEEEEETTS---EEEEESS---TT-EEEEEEEGGG-EEEE CS
                   GlcV_C_terminal   2 kyinvGkvkVkvvsYqaGiFkitvspidseeeivvnseepikaGeevllyvrknkiKiFd 61 
                                       ++++ G++ V ++sY  G F++t+s+ ds e ++   + p++ Ge v++y  ++ i +F+
  gi|518651466|ref|YP_008140986.1| 315 GFKECGEAEVAISSYYQGSFRVTLSFKDSSESFFCFHNTPLQPGEKVNIYLNPDLIHLFN 374
                                       6999****************************************************9995 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.2   1.3e-05     0.023       1      56 [.      35      77 ..      35      88 .. 0.67
   2 !   11.4   0.0   0.00011       0.2     171     300 ..     101     204 ..      92     206 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpei 56
                                      + ++ G  gsGK++L++++ +l             + ++ g+ + + ++ ++d +i
  gi|518651466|ref|YP_008140986.1| 35 FFGILGSSGSGKTTLMRIIAGL-------------EIPTEGTVSFDQKPVSKDNKI 77
                                      5789***************999.............444444444444444444444 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                            AAA_21 171 ifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllal 247
                                       +f + +++ ++ rl +  v+++ +  +el d+ e+ +++ ++                        +S G+++  a 
  gi|518651466|ref|YP_008140986.1| 101 NFENIAFPLRIMRLKESAVNRRVKEIAELLDISEVLNKHPKE------------------------ASGGQQQRVAY 153
                                       566666666666777777777777777777776666666543........................48888888666 PP

                            AAA_21 248 ltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpl 300
                                       + al   +   +lll+DEp ++L+  +     +  kel++  g   i+++H+p 
  gi|518651466|ref|YP_008140986.1| 154 ARALVKNP---ALLLLDEPFSNLDATIKDVARKYTKELQNiLGFTAIIVSHDPA 204
                                       66666655...**************77777778889999999999999999995 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.7e-05     0.031      24      43 ..      34      53 ..      18      58 .. 0.83
   2 ?   -0.6   0.0      0.66   1.2e+03     101     151 ..     125     178 ..     111     224 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                             DUF87 24 rHlAilgsTGsGKSntvavL 43
                                      + ++ilgs+GsGK+++++++
  gi|518651466|ref|YP_008140986.1| 34 EFFGILGSSGSGKTTLMRII 53
                                      559**************998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.66
                             DUF87 101 elldllee....ddkpaaav..qrsvleealdqakakeekeklssdepveklleelk 151
                                       e+++ll++    ++ p++a   q++ +++a + +k   +   l  dep+ +l   +k
  gi|518651466|ref|YP_008140986.1| 125 EIAELLDIsevlNKHPKEASggQQQRVAYARALVK---NPALLLLDEPFSNLDATIK 178
                                       44444444433633333333355555555555444...5555555555555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.4   8.4e-06     0.015      13      39 ..      24      53 ..       3      57 .. 0.80
   2 ?   -1.7   0.0         2   3.6e+03     117     117 ..     135     135 ..      60     195 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 8.4e-06
                            AAA_23 13 qeidF...skgltlItGpNGaGKTTildAi 39
                                      q+i++   s  ++ I G  G+GKTT+++ i
  gi|518651466|ref|YP_008140986.1| 24 QHINLdidSGEFFGILGSSGSGKTTLMRII 53
                                      55666666778****************987 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2
                            AAA_23 117 l 117
                                        
  gi|518651466|ref|YP_008140986.1| 135 V 135
                                       1 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00011      0.19      61      84 ..     158     181 ..     120     187 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                           SbcCD_C  61 epalrlvfLDEAFsklDeesiatl 84 
                                        ++++l++LDE Fs+lD++  + +
  gi|518651466|ref|YP_008140986.1| 158 VKNPALLLLDEPFSNLDATIKDVA 181
                                       45699************9866655 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.7e-05     0.031      17      39 ..      28      50 ..      17      68 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                            AAA_29 17 ieidlkgatlltGpsGsGKSTll 39
                                      ++id  +++ + G sGsGK+Tl+
  gi|518651466|ref|YP_008140986.1| 28 LDIDSGEFFGILGSSGSGKTTLM 50
                                      5677555999************8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   0.00014      0.26      25     213 ..      34     217 ..      10     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkk.lkiekeevsi 99 
                                       +f  i+G+ GSGK+ l+  i    G +  ++   +  ++ ++k +k   +v+  ++ ++f+n       ++ e++  
  gi|518651466|ref|YP_008140986.1|  34 EFFGILGSSGSGKTTLMRIIA---GLEIPTEGTVSFDQKPVSKdNKIITEVEDRNIGMVFQNWALYpHLTNFENIAF 107
                                       577899999999999998883...33222222222222223332444556777888888888877745566677888 PP

                                       EEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 100 srrvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknv 176
                                         r++r +es   +n++  + +e+ ++ e  + ++++ SgG+++ va a       vk  +l llDe  ++LD++  
  gi|518651466|ref|YP_008140986.1| 108 PLRIMRLKESA--VNRRVKEIAELLDISEVLNKHPKEASGGQQQRVAYAR----ALVKNPALLLLDEPFSNLDATIK 178
                                       88888888754..5666555566666666666678899*****9888764....45788899***********9999 PP

                                       HHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 177 kkvaellkekskn..aQfivislreemlekadklvgvtk 213
                                           ++ ke ++   +  i++s++   +   ++ vgv  
  gi|518651466|ref|YP_008140986.1| 179 DVARKYTKELQNIlgFTAIIVSHDPADIFSLSRQVGVIN 217
                                       888899999988744667999999888777777777765 PP

>> Phage_terminase  Phage terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.2   5.7e+03      19      35 ..      44      59 ..      43      65 .. 0.74
   2 ?   10.1   0.1   0.00036      0.64      17      36 ..     115     134 ..     111     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.2
                   Phage_terminase 19 sggtlklkdIAkvLdvs 35
                                      sg+t +++ IA  L+++
  gi|518651466|ref|YP_008140986.1| 44 SGKTTLMRIIAG-LEIP 59
                                      799999999985.5665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00036
                   Phage_terminase  17 kEsggtlklkdIAkvLdvse 36 
                                       kEs+ + ++k+IA+ Ld+se
  gi|518651466|ref|YP_008140986.1| 115 KESAVNRRVKEIAELLDISE 134
                                       9******************9 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00039      0.71       5      21 ..      38      54 ..      35      57 .. 0.90
   2 ?   -1.6   0.0       1.2   2.2e+03      52      88 ..     130     167 ..     107     189 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00039
                                      EEC-TTTCHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqkla 21
                                      + G +GsGKTtL++ +a
  gi|518651466|ref|YP_008140986.1| 38 ILGSSGSGKTTLMRIIA 54
                                      78***********9886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                                       .-HCHHHCCCCTS--.SSS-CCHHHHCCSCCCEEEEEE CS
                             NACHT  52 rsladllfsqlpepa.apvsevwavllelperlLlilD 88 
                                       + + ++l ++ +e + +++++v   ++ +++ +Ll+lD
  gi|518651466|ref|YP_008140986.1| 130 LDISEVLNKHPKEASgGQQQRVAYARALVKNPALLLLD 167
                                       55555555555544404445577778888888888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2467.54
//
Query:       gi|518651467|ref|YP_008140987.1|  [L=288]
Description: hypothetical protein FACI_IFERC00001G0106 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-15   55.8  20.9    4.8e-15   55.8  20.9    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 ?   -4.2   9.4      0.66   1.2e+04      13      75 ..      20      91 ..      14      95 .. 0.59
   2 !   55.8  20.9   2.7e-19   4.8e-15       2     182 ..      95     278 ..      94     281 .. 0.82

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 0.66
                      BPD_transp_1 13 nkkldkllrpliivllslPsfv.............laillvlvfvilsilghlilpviillllsaapyvrlirraa 75
                                      +++l +++++l  +++ +P++v               ++lv      s+  h+i+ v+ +l+++++  v++ ++ a
  gi|518651467|ref|YP_008140987.1| 20 RGVLHHVVLVLLAIIWIFPVYVlvvdslkttgsvlTTPILV----PASATLHSIITVFEALITQFFNSVVIAISTA 91
                                      56667777777777777777774444444433333333333....5566667777777777766666666666655 PP

  == domain 2  score: 55.8 bits;  conditional E-value: 2.7e-19
                      BPD_transp_1   2 illGilaa...lnrnkkldkllrpliivllslPsfvlail...lvlvfvilsilghlilpviillllsaapyvrlir 72 
                                       +++G++aa   ++ ++++++++ ++i +   +P+ v  ++   l+    i  +l ++i ++i+ +l++++p+  l++
  gi|518651467|ref|YP_008140987.1|  95 TFIGAMAAyyfYRISSRINDVIFTVIAIATFIPFEVTSVPldkLL----IEIGLFNSIPGLIFSFLIFYLPTGALLM 167
                                       689*********************************777634423....34555666666***************** PP

                      BPD_transp_1  73 raalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgyd 149
                                       + +l +lpk+ +e ar++Ga++w+if kvv+P++ p +i+++i+ ++  +++++l++  +s p   +++  ++l+y 
  gi|518651467|ref|YP_008140987.1| 168 SIFLAVLPKSTIESARIDGANDWTIFSKVVIPLTYPGLISTFIFIMIETWNNFFLPLVATSTPS-VSTISLSLLSYT 243
                                       ************************************************************8875.334444444433 PP

                      BPD_transp_1 150 yseis..nggvlalviavlllnlvadilqrlldpr 182
                                         ++   n +++a++ia +  ++v+ +l r++ + 
  gi|518651467|ref|YP_008140987.1| 244 GGYGVlyNDSFAAALIASIFPLVVFILLGRYFVKG 278
                                       33333565677888888888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 1821.04
//
Query:       gi|518651468|ref|YP_008140988.1|  [L=284]
Description: alpha glucoside ABC transporter permease protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-11   44.3  18.7    1.5e-11   44.3  18.7    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0021   16.4   4.7     0.0047   15.3   4.7    1.5  1  OATP          Organic Anion Transporter Polypeptide (OATP) fa


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   2.7    0.0059        53      26      56 ..       7      38 ..       3      65 .. 0.69
   2 !   44.3  18.7   1.7e-15   1.5e-11       1     174 [.      77     271 ..      77     280 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.0059
                      BPD_transp_1 26 vllslPsfvlaillvlvfvilsilghlilp.v 56
                                      +l+slP + ++ +l++++ ++ ++ +++l+ +
  gi|518651468|ref|YP_008140988.1|  7 ILFSLPALFFGAILIYFLLWNVYFSFTNLSpI 38
                                      789************99988888888877743 PP

  == domain 2  score: 44.3 bits;  conditional E-value: 1.7e-15
                      BPD_transp_1   1 gillGilaa....lnrnkkldkllrpliivllslPsfvlaillvlvf..................vilsilghlilp 55 
                                       g+++Gil a    + +n k + + + l+  +l++ + ++ai++ ++                    +ls++ ++  +
  gi|518651468|ref|YP_008140988.1|  77 GNGMGILFAslifFLKNPKARTVYSSLFLYPLAVAMSAVAIIWSWIYspsegidtllravglpapNWLSSAPQALPS 153
                                       6789999999999*******************************888****************************** PP

                      BPD_transp_1  56 viillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflg 132
                                       +ii++++ + +++ +++ aa+++++++ +e a+++ a+++ i+rk++lP ++  +i + +l ++++l  +++++  +
  gi|518651468|ref|YP_008140988.1| 154 LIIITTWVYSGLAAVFYLAAFQNVNSESIESAKLDVAGPFVILRKILLPESKNAFIVTSALLIIFSLRIFTIPYVAT 230
                                       ***************************************************************************** PP

                      BPD_transp_1 133 swpGlgtllleailgydyseis...nggvlalviavlllnlvadi 174
                                       +     ++++e++  y +++ +   ++ ++a+ i+v+++ +v+ i
  gi|518651468|ref|YP_008140988.1| 231 GI----NPRTETSVLYLFNFYTygyYAEAAAVSIIVIVIAIVVVI 271
                                       44....477777777777777756644444444444444444444 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 !   15.3   4.7   5.2e-07    0.0047     290     381 ..      24     115 ..      15     130 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.2e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 290 llknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGillgGllvkklklsakkla 366
                                       ll n  f ++ ls +  ++ + Gf+t+ +  + + F+ +  +   +tG ++++g ++Gil++ l+   ++++a+++ 
  gi|518651468|ref|YP_008140988.1|  24 LLWNVYFSFTNLSPIHSSYTIVGFATYESVLIRRIFQSTLLRTLEWTGGMFLVGNGMGILFASLIFFLKNPKARTVY 100
                                       88999******************************************************************999988 PP

                                       xxxxxxxxxxxxxxx RF
                              OATP 367 klvlvvsllslllll 381
                                          ++  l  ++  +
  gi|518651468|ref|YP_008140988.1| 101 SSLFLYPLAVAMSAV 115
                                       777766655555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1940.10
//
Query:       gi|518651469|ref|YP_008140989.1|  [L=549]
Description: sugar binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3637.21
//
Query:       gi|518651470|ref|YP_008140990.1|  [L=358]
Description: hypothetical protein FACI_IFERC00001G0109 [Ferroplasma acidarmanus fer1]
Scores for complete 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   79.1   0.0    4.4e-22   78.6   0.0    1.2  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
    1.8e-20   72.8   0.5    3.7e-20   71.8   0.5    1.5  1  ADH_N          Alcohol dehydrogenase GroES-like domain
     0.0012   19.0   0.0     0.0024   18.0   0.0    1.4  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.058   12.7   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.04   13.2   0.0      0.068   12.4   0.0    1.3  1  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.2e-25   4.4e-22       2     208 ..     140     353 ..     139     356 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.2e-25
                       Glu_dehyd_C   2 dvgvLvEPisiveKaielaeasrsafewe.......pesalvlGaGslGLLalalleaeerglervyvlgrrdrpdp 71 
                                       ++++L  P++  eK+++ ++++++++ w+        + alv+G+G++G+L   ll+  + g++ v++ +rr   d+
  gi|518651470|ref|YP_008140990.1| 140 NMAILAQPLADLEKSMDEIINIQKRMIWRcsdntfhCRNALVIGTGTIGVLFSLLLK--TYGFS-VTIANRRYAHDK 213
                                       5899*****************999998862222222579*************77776..589*8.99********** PP

                       Glu_dehyd_C  72 tidlveelGatYvdsretpvdeipeaseemdlvvEaTGs.akhafeaiealapnGvaaLlGvpedsevevdggelhr 147
                                       + ++ +  +  Y +s++    +    ++++dl++Ea Gs a ++ +++  l+ nG+  L G   + e++++  ++ +
  gi|518651470|ref|YP_008140990.1| 214 ESKICNIADIKYYNSATG--YK--FDDNSFDLIIEASGSsADVISQTMGFLKNNGIFGLFGFIRSGELSINS-HMLQ 285
                                       *************98433..23..34689*********735678899***********************96.5668 PP

                       Glu_dehyd_C 148 elvleNkalvGsvNanrrhfeaavdtLaalpesl...ldelvtkvvdldeleeAfe....dddetiKt 208
                                       ++v +  a+vG +N +  hfe+a+d+L + +  +    + l+t+++++++ e+  +    +++++iKt
  gi|518651470|ref|YP_008140990.1| 286 DFVYKSIAMVGLINGQKPHFEMAMDHLMQWKYMYpgiEKLLITDEIKISDREKITTvlteKSKDEIKT 353
                                       99****************************99998834557999998877666543232366677877 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.8   0.5     1e-23   3.7e-20       3     109 .]      24     134 ..      22     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1e-23
                                       EEEEEEEEEEE-HHHHHHHTTSTTTTSSSS.....EE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHH CS
                             ADH_N   3 evlikvkaagiCgsDlhilkggkelevklp.....lilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCk 74 
                                        + ik+   giCg+D +i+kg+   +++ p     lilGHE++G+v e g   + +k+Gd V+      cg+C +C 
  gi|518651470|ref|YP_008140990.1|  24 GIKIKILENGICGTDREIVKGQ-LNSAAIPagsnyLILGHEAIGTVMEDG---TIFKKGDIVMPVNRRGCGKCLNCL 96 
                                       689******************5.555666666777*************88...5689******************** PP

                                       TT-GGG-TTBEETTTS...S-SSSBSEEEECGGGEEEE CS
                             ADH_N  75 egeenlCeeakllgvs...ldGgfaeyvvvpekklvkl 109
                                        g++++Ce+++++ ++   ++G + ey++ +ek+lv++
  gi|518651470|ref|YP_008140990.1|  97 VGRPDFCETGNFVEAGikgMQGFMGEYIYDDEKYLVRV 134
                                       *************9999999*************99875 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.6e-07    0.0024       9      93 ..     173     256 ..     168     259 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.6e-07
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHH..HHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerake..laeelkgeeiealkleelkellaeadvvisat 83 
                                       +++ +++l+iG+G ++ l    L + g+  v++aNR +++ ke  +++  + +   + + + +k   +++d++i a 
  gi|518651470|ref|YP_008140990.1| 173 TFHCRNALVIGTGTIGVLFSLLLKTYGFS-VTIANRRYAHDKEskICNIADIK--YYNSATGYKFDDNSFDLIIEAS 246
                                       567899************99999999998.******99877651144444322..3444555555667888999888 PP

                                       SSSS-SB-HH CS
                      Shikimate_DH  84 aseepileke 93 
                                       +s+  ++++ 
  gi|518651470|ref|YP_008140990.1| 247 GSSADVISQT 256
                                       8888887765 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.6e-05     0.058      29      74 ..     169     214 ..     146     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                                       GSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHC CS
                      2-Hacid_dh_C  29 llgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeee 74 
                                        + ++ + +   +iG+G IG  +  +lk  g+ v++ +r+  +++e
  gi|518651470|ref|YP_008140990.1| 169 CSDNTFHCRNALVIGTGTIGVLFSLLLKTYGFSVTIANRRYAHDKE 214
                                       455667788899************************9999775552 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05     0.068       4      39 ..     179     214 ..     177     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39 
                                        l++G+G  G++ +llL+++G +v++ ++r    ++
  gi|518651470|ref|YP_008140990.1| 179 ALVIGTGTIGVLFSLLLKTYGFSVTIANRRYAHDKE 214
                                       69*************************998766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2539.99
//
Query:       gi|518651471|ref|YP_008140991.1|  [L=404]
Description: hypothetical protein FACI_IFERC00001G0110 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-53  181.4   0.0    2.2e-53  181.1   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    4.1e-09   36.7   0.0    7.9e-09   35.7   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.1   0.0   2.4e-57   2.2e-53       4     219 ..     156     378 ..     153     379 .. 0.95

  Alignments for each domain:
  == domain 1  score: 181.1 bits;  conditional E-value: 2.4e-57
                                       HHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGG. CS
                          MR_MLE_C   4 eearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvarelee. 71 
                                       +ear+ v  +g+ra+K++++g+        ++++ +e ++ v  +v  gd+++++++ +++++++tA++++rele+ 
  gi|518651471|ref|YP_008140991.1| 156 KEARK-VINKGYRALKFDPFGSgsgfleydEFKKSMEIIQIVHGVV--GDKIEMLIEGHGRFNRSTAMKIGRELEKy 229
                                       67877.5557************************************..5577**********************995 PP

                                       GTESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHH CS
                          MR_MLE_C  72 ldllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaea 147
                                        ++ w+EEPv pe d+eg+a+l+ ++ +ipiaagE+l + +df +l++ + v i+qpd+ ++gGi e++k+ a+aea
  gi|518651471|ref|YP_008140991.1| 230 PNIGWFEEPVIPE-DIEGMAMLS-KSlKIPIAAGERLITSYDFTQLFKLNSVSIAQPDLINTGGIIELLKIGAMAEA 304
                                       56**********5.6********.8889************************************************* PP

                                       TT-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH..TSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                          MR_MLE_C 148 fgvpvapHsgsgglglaaslhlaaaipnllileyfldael..leeelleeplevedGrvtvpdgpGlGveldee 219
                                       +++ +apH  +g+l++  +l + a + nl+i+e+f  + +  +  ++++  +ev++G+v++p++pG+Gv l+++
  gi|518651471|ref|YP_008140991.1| 305 NNISMAPHQAEGPLNTFTTLNIDALMNNLKIQEMFDEFAYpaWITDIVDTVPEVKNGYVELPEKPGIGVNLKDK 378
                                       *********88***************************99******************************9976 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   8.8e-13   7.9e-09      27     117 .]      36     130 ..      28     130 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 8.8e-13
                                       EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS......CHHHHHHHH CS
                          MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg......nmsAkaaid 97 
                                       + v+++i t++G  G geat +   + ++  +++d +   +v+kd+ ++++l+++     +       nms +++++
  gi|518651471|ref|YP_008140991.1|  36 KWVFIEIITDNGENGYGEATVYS-GQFSVVNHIKD-IKKFIVNKDPFKVRELVNEWFTSSFNrnrdivNMSLISGVE 110
                                       68*********************.56677777777.9***************9988887777889999********* PP

                                       HHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  98 mAlwDlkakalnlpladLlG 117
                                       +A +Dl +k  +  +++L G
  gi|518651471|ref|YP_008140991.1| 111 SACFDLIGKHFGSTIYNLFG 130
                                       ******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2560.06
//
Query:       gi|518651472|ref|YP_008140992.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G0111 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-16   59.3   0.0    3.6e-16   59.1   0.0    1.0  1  LigB      Catalytic LigB subunit of aromatic ring-opening dio


Domain annotation for each model (and alignments):
>> 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 !   59.1   0.0     2e-20   3.6e-16      27     267 ..      22     250 ..       5     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 2e-20
                              LigB  27 vikgyesireriaek.sPdtiivvsphhltdvnpvfvlgvaeefeaiddfgkflprleyelkgnpeLaekiaealkk 102
                                       ++  ++++ +++ae+ s d++++ sph+++  + ++v++++  f+a  + +     l ++++++ +L+e i+++++ 
  gi|518651472|ref|YP_008140992.1|  22 DSRKLNNALKELAENdSSDVLVILSPHGVNLSKNIAVVNTEY-FKADTQLK--NTYLDFKAQNERKLTEDIIKSTRD 95 
                                       3344677788888888**************444344444443.55555544..66799*****************98 PP

                              LigB 103 sgidlav.....esnsmklDHGtlvPLelmlpdeakvpvikvslntvaypllsferlykLGeAlrkaveeldknvli 174
                                          +l       ++   +lD+G  +PL++  +     + i ++ ++    + +  +l ++G++l + v+ ++k+v i
  gi|518651472|ref|YP_008140992.1|  96 TTEELRFitysgDISVFPLDFGSSIPLSFFKQ-----RNIVLIGQS---RINNRDKLINFGKSLYNSVQAYNKKVSI 164
                                       777766667888888899***********999.....666666666...799************************* PP

                              LigB 175 lgsGglsHqlegdeaakadaqtlllneefdeelldllkegrveelckmskeelsaaagheeeelvplvvalGalsgd 251
                                       + s +  H+ +++ ++++      ++e++ +++   ++ g +eel k+++e ++     + + +  l+v+ G+l+ +
  gi|518651472|ref|YP_008140992.1| 165 IISADQAHTHSDKGPYGYSQ----NAEKYEHTVKHCFETGSFEELYKIEQEIIDTG---KPDSFWNLMVMYGILQAS 234
                                       ****************9998....*************************8888888...5899************88 PP

                              LigB 252 kaelrkelvsyeglpa 267
                                         ++r ++++ e +++
  gi|518651472|ref|YP_008140992.1| 235 GRKMRLDYHYVEIYFG 250
                                       8888888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:01.20
# Mc/sec: 648.91
//
Query:       gi|518651473|ref|YP_008140993.1|  [L=189]
Description: hypothetical protein FACI_IFERC00001G0112 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-21   76.3  25.6    2.6e-21   76.1  25.6    1.0  1  DUF998    Protein of unknown function (DUF998)
  ------ inclusion threshold ------
        5.9    7.0   7.2       0.22   11.6   0.5    1.9  2  DUF4337   Domain of unknown function (DUF4337)


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 !   76.1  25.6   2.9e-25   2.6e-21       2     183 ..      18     179 ..      17     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.1 bits;  conditional E-value: 2.9e-25
                            DUF998   2 aaallalavilaaallrpgydplrhaiSeLgaeggpggwlfnaglvllgllvlalavgllraargragragrlllav 78 
                                       a+a+ +++++l+a +l+p y+++ ++iS+Lg   g ++++fn+  vllg++++  av+l      + +++ r++l++
  gi|518651473|ref|YP_008140993.1|  18 AGAAQFFLLVLIAEALYPHYSVANNYISDLGV--GSTAYIFNTSIVLLGIAIIISAVFL-----LKFSKPLRIVLIL 87 
                                       8999****************************..***********************77.....89*********** PP

                            DUF998  79 aglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllvaalvwlla 155
                                       ag+g++++g+fp+++g+        +H + s+++f++  +a   +        w+l +++++  ++l+++al++l++
  gi|518651473|ref|YP_008140993.1|  88 AGIGAMGVGIFPETTGA--------IHLYSSLLVFFMASIATYFIL-------WRLKNIISVFWAILGTVALIALVL 149
                                       ****************8........******************999.......677777666666666666666666 PP

                            DUF998 156 a..aldgslllGlaerllvlaitawllala 183
                                          +++ +l++G  erl+v+  ++w l ++
  gi|518651473|ref|YP_008140993.1| 150 YamGIYLGLGVGGMERLIVYPDILWALGFG 179
                                       66667777999**************98766 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   2.4e-05      0.22     116     157 ..      53      96 ..      30     100 .. 0.69
   2 ?   -2.1   1.3      0.42   3.7e+03     147     152 ..     140     145 ..     113     162 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           DUF4337 116 k..fdlasalLqiaIvlaaialltkkklllylslvlglvGlvlf 157
                                       +  f+ + +lL iaI+++a+ ll  +k l ++ +++g+  ++++
  gi|518651473|ref|YP_008140993.1|  53 AyiFNTSIVLLGIAIIISAVFLLKFSKPLRIVLILAGIGAMGVG 96 
                                       155999999***********999886666665555554444443 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.42
                           DUF4337 147 lvlglv 152
                                         ++l+
  gi|518651473|ref|YP_008140993.1| 140 GTVALI 145
                                       222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1024  (0.0571142); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1231.50
//
Query:       gi|518651474|ref|YP_008140994.1|  [L=393]
Description: hypothetical protein FACI_IFERC00001G0113 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  103.1  32.2    6.9e-19   68.0   8.6    2.0  2  MFS_1     Major Facilitator Superfamily
      4e-08   32.1   3.3    3.9e-05   22.3   0.1    2.0  2  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
        2.9    8.1   0.0        2.9    8.1   0.0    4.3  4  CD225     Interferon-induced transmembrane protein


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 !   68.0   8.6   1.2e-22   6.9e-19       2     219 ..      20     232 ..      19     237 .. 0.80
   2 !   40.3  19.2     3e-14   1.8e-10      12     171 ..     224     380 ..     213     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.2e-22
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslpl.GrlsdrfGrrrvlllglllfalgll 77 
                                       ++++f + ++ +++++++pl+ +  l+++  eig+l +l    a+++s ++ + l     rr+++++++++++++ l
  gi|518651474|ref|YP_008140994.1|  20 VVITFSTRINNNLILTTIPLISKYYLNFNSLEIGILGALAVGSAGIMSALInSKLCSE-NRRKLFIASIIIYLIF-L 94 
                                       568899999**********999999**********99997777777776665888776.699*************.5 PP

                             MFS_1  78 lll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                        l+ f s+ + ++v+ +++G++ g+++p++++ +  +  k+ r r ++l++++ s + i gpll ++l+ +++   +
  gi|518651474|ref|YP_008140994.1|  95 PLFyF-SNRYSIWVFVIISGFFFGTVMPNIISSTGTIKDKKTRERTVALYTLSLSTSLIAGPLLESYLLLYFNLYQL 170
                                       55558.7766799999************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllf 219
                                       f+++ ++++la+ l +   + e+ +++rk+++    + ++++l+ ++  +  d ++  +li  +++
  gi|518651474|ref|YP_008140994.1| 171 FLFFIPFGILAVALSFKIKFPEENRNERKNKINV-FKNKGFQLS-IFNNISYDTPF--ALILTFGG 232
                                       ***********77544444444444444444444.233334444.48888888866..33333333 PP

  == domain 2  score: 40.3 bits;  conditional E-value: 3e-14
                             MFS_1  12 rsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fasslw 86 
                                       +++++++  ++  +++++  s+i +ll++++++++++ l+l++    f     + ++++ ++++g l+++ f s+  
  gi|518651474|ref|YP_008140994.1| 224 FALILTFGGIFARTEFNAPYSFIEILLAGFFALSFISRLILSYK--HFKKLYfTTIISISITIIG-LIMIyF-SNNL 296
                                       5566666667889****************************998..7755555777777777777.555547.6767 PP

                             MFS_1  87 .lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsl 162
                                        + ++  ++ G+  g+ +p++++++++ f ++e + a+ +++a + l a++ p ++gl++  +g r +f+++a+  +
  gi|518651474|ref|YP_008140994.1| 297 iVYFIIICFLGIPHGLTYPTSLTALSRSFDEDEISIANTYFYAIMMLIAVIVPSISGLMVYTIGLRETFLFFAFPVI 373
                                       69*************************************************************************** PP

                             MFS_1 163 lafvlflll 171
                                       ++f +  + 
  gi|518651474|ref|YP_008140994.1| 374 ILFFI--II 380
                                       **663..33 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   6.5e-09   3.9e-05     227     371 ..      23     166 ..      11     215 .. 0.79
   2 !   10.3   1.0   2.8e-05      0.17      82     187 ..     272     380 ..     242     391 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 6.5e-09
                             MFS_3 227 aalFglsasavlaLLPlvardqldgdalvyGillg.alGvGAilgalllsrLRerlsserlvllaavalAlvllsla 302
                                       ++   +    +l+ +Pl+ +  l+ ++l  Gil + a+G+  i++al++s+L +   + r + +a++ + l+ l l 
  gi|518651474|ref|YP_008140994.1|  23 TFSTRINNNLILTTIPLISKYYLNFNSLEIGILGAlAVGSAGIMSALINSKLCSE--NRRKLFIASIIIYLIFLPLF 97 
                                       45555666779999*****************985446788889*******99875..5566778999999******* PP

                             MFS_3 303 lasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaeals 371
                                         s+++ + + ++++G  + t++ ++ ++  ++  +  + R++a+Y   l+ +l aG ll   +    +
  gi|518651474|ref|YP_008140994.1|  98 YFSNRYSIWVFVIISGFFFGTVMPNIISSTGTIKDKKTRERTVALYTLSLSTSLIAGPLLESYLLLYFN 166
                                       ********************************************************9887665555555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 2.8e-05
                             MFS_3  82 qlllalvsvlltvlaalgl.lspwlll..altlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvG 155
                                         +  + s+ +t++ ++ + +s  l++  ++++++gi   l+ P+   +++   + ++++ A +     + +   + 
  gi|518651474|ref|YP_008140994.1| 272 LYFTTIISISITIIGLIMIyFSNNLIVyfIIICFLGIPHGLTYPTSLTALSRSFDEDEISIANTYFYAIMMLIAVIV 348
                                       344455555555554444313444444114556788999***********************99998888899999* PP

                             MFS_3 156 PAlgGvlvaavGaalafavnalsylalivall 187
                                       P ++G++v ++G   +f + a+  ++l ++++
  gi|518651474|ref|YP_008140994.1| 349 PSISGLMVYTIGLRETFLFFAFPVIILFFIII 380
                                       *****************999998888777665 PP

>> CD225  Interferon-induced transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1       0.3   1.8e+03      43      65 ..      72      94 ..      52      97 .. 0.71
   2 ?    8.1   0.0   0.00048       2.9      13      31 ..     170     188 ..     161     202 .. 0.80
   3 ?   -5.0   5.6         3   1.8e+04      20      28 ..     285     293 ..     272     313 .. 0.61
   4 ?   -3.4   0.4       1.9   1.1e+04       9      24 ..     331     345 ..     330     351 .. 0.48

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.3
                             CD225 43 AqsasstAkllniialvlgiili 65
                                      ++  s++ ++l i+++++ +i++
  gi|518651474|ref|YP_008140994.1| 72 SKLCSENRRKLFIASIIIYLIFL 94
                                      55567777888899999888765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00048
                             CD225  13 tlfcclplGivAlvySvkv 31 
                                        +++++p+Gi+A++ S+k 
  gi|518651474|ref|YP_008140994.1| 170 LFLFFIPFGILAVALSFKI 188
                                       566999**********995 PP

  == domain 3  score: -5.0 bits;  conditional E-value: 3
                             CD225  20 lGivAlvyS 28 
                                       +G++ +++S
  gi|518651474|ref|YP_008140994.1| 285 IGLIMIYFS 293
                                       355555554 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 1.9
                             CD225   9 sifntlf...cclplGivA 24 
                                       si nt f   +     ++A
  gi|518651474|ref|YP_008140994.1| 331 SIANTYFyaiM----MLIA 345
                                       66666663322....2233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.50
# Mc/sec: 2379.97
//
Query:       gi|518651475|ref|YP_008140995.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G0114 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-27   96.2  43.4    4.2e-21   75.3  28.2    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0077   14.7  14.8     0.0044   15.5   7.6    2.1  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.3  28.2   4.7e-25   4.2e-21       2     291 ..      17     298 ..      16     300 .. 0.78
   2 !   23.5  17.2   2.6e-09   2.3e-05      61     176 ..     280     394 ..     248     405 .] 0.79

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 4.7e-25
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslpl.Grl.sdrfGrrrvlllglllfalgl 76 
                                       l +af + ++ ++l++++p + +   ++++ ++gl +tly++ga+va++++ Gr+ +++  +r + ll l++++  +
  gi|518651475|ref|YP_008140995.1|  17 LSVAFTMRTSTNMLMTVVPVFTKYVINADVFFVGLTATLYGIGAMVANVLInGRInIEKT-PRTIALLLLIMTGGIF 92 
                                       67899999***********999999**************************999944554.6665555555555553 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       ++ll +++++ +l+l  ++Gl +g++ p+ ++++  ++p+ +r r+i+ ++a+ sl+ i+g +  gl++ss++ r++
  gi|518651475|ref|YP_008140995.1|  93 FYLL-SNNVYEVLILSTVTGLSMGVVQPLLMTVTNVIAPPGKRDRYIAAYTASLSLSLIFGVVMEGLITSSINVRYA 168
                                       5555.477779****************************************************************** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltll 230
                                       f+i+ ++sl++ vl++ l ++ + + krk+  +      +  l +a  +l+  +    +l+al+++  ++++ ++ll
  gi|518651475|ref|YP_008140995.1| 169 FLIFLFISLISTVLMFSLSTRIKMNMKRKNRLTF-----KEILGKASHSLKQGK----VLFALFGNI-AYAFPFILL 235
                                       *************855555555555555555444.....222222334445555....788888885.888888888 PP

                             MFS_1 231 plylqevlgls.......glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgl 291
                                        +y  + +g           +  +  lal++ v++  +l+++    + ++++ ++ +++++++++l+l
  gi|518651475|ref|YP_008140995.1| 236 ITY-GSIMGKEydginpdI-FFYL--LALFYSVSFLTRLVLSVKNVK-NHEILMYASFAATIIGYLLL 298
                                       888.777777777665633.3333..677777776668888887777.77889999999999988876 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 2.6e-09
                             MFS_1  61 rrrvlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGai 135
                                       +  ++ ++++++++g +lll +  +++ +++ + ++ G+  g+++p++ ++ia  +  e+ + +++++ + + + + 
  gi|518651475|ref|YP_008140995.1| 280 HEILMYASFAATIIG-YLLL-GidAGIIMFIGSLLILGFPHGSIYPTASYYIASSVELEDLNVVYSVFILIMDVIIF 354
                                       455888999999999.4444.3359999************************************************* PP

                             MFS_1 136 lgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                       l p + g++++ ++ r + y+ a+ ++l+++   +++  ++
  gi|518651475|ref|YP_008140995.1| 355 LIPFVFGIISTIYSIRMAIYLTAVPMVLLLL-TSVFFNIKD 394
                                       ****************************966.445554443 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   7.6   4.9e-07    0.0044     220     425 ..      11     218 ..       8     229 .. 0.81
   2 !    3.9   0.6    0.0015        14     345     403 ..     342     400 ..     241     405 .] 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.9e-07
                             MFS_3 220 ikavlvRaalFglsasa..vlaLLPlvardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaaval 294
                                       i+ +++ +++F + +s+   ++++P+  +  +++d  + G+  +  G+GA+++ +l +   ++ ++ r ++l  + +
  gi|518651475|ref|YP_008140995.1|  11 INLIMLLSVAFTMRTSTnmLMTVVPVFTKYVINADVFFVGLTATLYGIGAMVANVLINGRINIEKTPRTIALLLLIM 87 
                                       56678888999887665226899*****************************9988776555555566666666666 PP

                             MFS_3 295 AlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaeals 371
                                          ++   l+++++ +++   ++G +  ++   l +   ++ P   + R +a Y + l+ +l  G ++ G ++++++
  gi|518651475|ref|YP_008140995.1|  88 TGGIFFYLLSNNVYEVLILSTVTGLSMGVVQPLLMTVTNVIAPPGKRDRYIAAYTASLSLSLIFGVVMEGLITSSIN 164
                                       666666779999999999999999999899999999999************************************** PP

                             MFS_3 372 vtlaLlaaaaalllaaaillllklpeleasdlapsnrfeeplvaldlkprrGpv 425
                                       v+ a l+     l+++++++ l  +   +++ + +  f+e l +++ + ++G v
  gi|518651475|ref|YP_008140995.1| 165 VRYAFLIFLFISLISTVLMFSLSTRIKMNMKRKNRLTFKEILGKASHSLKQGKV 218
                                       *****9999988999888888877766666666666677766555555556655 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0015
                             MFS_3 345 lavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklpeleasdl 403
                                        +v++ +++  + +  +++G ++  +s+++a+ ++a+ ++l  ++++++++++ +a ++
  gi|518651475|ref|YP_008140995.1| 342 YSVFILIMDVIIFLIPFVFGIISTIYSIRMAIYLTAVPMVLLLLTSVFFNIKDNKAIKK 400
                                       57788888888888889**********************************99988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1196  (0.0667076); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3009.01
//
Query:       gi|518651476|ref|YP_008140996.1|  [L=694]
Description: hypothetical protein FACI_IFERC00001G0115 [Ferroplasma acidarmanus fer1]
Scores for complete 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-96  323.0   2.5    9.2e-93  311.3   3.4    2.3  2  Glu_synthase     Conserved region in glutamate synthase
    6.2e-16   58.7   0.3    9.4e-06   25.3   0.0    3.2  3  Glu_syn_central  Glutamate synthase central domain
    6.7e-09   35.2   5.4    0.00014   21.0   1.8    4.0  4  FMN_dh           FMN-dependent dehydrogenase
    0.00028   20.0   2.7      0.026   13.5   1.9    2.9  3  IMPDH            IMP dehydrogenase / GMP reductase domain
  ------ inclusion threshold ------
      0.031   13.5   0.2       0.15   11.3   0.1    2.1  3  DHO_dh           Dihydroorotate dehydrogenase


Domain annotation for each model (and alignments):
>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.3   3.4   2.6e-96   9.2e-93      53     368 .]      69     380 ..      36     380 .. 0.94
   2 !    8.5   0.0   0.00027      0.98     256     304 ..     572     621 ..     569     626 .. 0.90

  Alignments for each domain:
  == domain 1  score: 311.3 bits;  conditional E-value: 2.6e-96
                                       --GGGS--HHHHHTTEE---B-TTTS-HHHHHHHHHHHHHHT-B-EETTS---GGGGS-----SEEEE-TT-TT--H CS
                      Glu_synthase  53 ikleevepalkikkriltsamSyGalseeahealakamnrlgtksntGEGGedeerlktakdvaikQvasgrFGvte 129
                                       i+++++   +k++ ++  + mSyGals + ++a+ak+++   t++ tGEGG+    ++  k +  +Q as+rFGv++
  gi|518651476|ref|YP_008140996.1|  69 IQTDTMLAGMKLSVPVYLGDMSYGALSGNPNIAIAKTAEITETMAGTGEGGLYGS-VSGSKRI-FVQWASARFGVSA 143
                                       67778888899****************************************9875.5555666.8************ PP

                                       HHHHH-SEEEEE---TTSTTS--EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEE CS
                      Glu_synthase 130 eyLnnakaleikiaQGakpgeGgqlpgeKvseeiakiRkikpgvdliSPaphhdiysiedlaqliedLkevnkeakv 206
                                       + Ln+++a+ iki+QGakpg+Gg+lpg+Kv+++i+  Rki+++ d+iSPaphhdiysiedl+q ie+Lk ++ +++v
  gi|518651476|ref|YP_008140996.1| 144 SSLNQGAAIVIKIGQGAKPGIGGHLPGSKVTHNISLARKIPENMDAISPAPHHDIYSIEDLTQRIEALKILS-DKPV 219
                                       *********************************************************************998.**** PP

                                       EEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS- CS
                      Glu_synthase 207 svKlvaeagvetiaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGgl 283
                                       +vK++a + +  i +g+a+++a  + idG+  GTGA+p  ++++ G+P+ela+a +d  lk+e+lr++ ++ia+G++
  gi|518651476|ref|YP_008140996.1| 220 FVKVAATNYIPYIVTGIARSGAAGVIIDGHGAGTGAAPVAVRDNMGIPVELAVASADSILKKENLRKNFTIIAAGRV 296
                                       ***************************************************************************** PP

                                       -SHHHHHHHHHHT-SEEE-SHHHHHHTT--S---GGGT--TTSSS---HHHH..TT----HHHHHHHHHHHHHHHHH CS
                      Glu_synthase 284 ktgadvvkalalGAdavgigtaalialgCimarvChtntCpvGvatqdpeLrkrlkveekaervvnyikalaeevre 360
                                         ++d +k  alGAd v++gt  lia+gCim+++C ++ Cpv ++ + ++  k l+++ + +rvvn+i  ++ e++e
  gi|518651476|ref|YP_008140996.1| 297 SNSTDAMKLYALGADVVSLGTSILIAMGCIMVKKCNLGYCPVALTNRTDSS-KSLDIDFAVNRVVNFINGFRSEMAE 372
                                       ******************************************998777665.59*********************** PP

                                       HHHHHT-S CS
                      Glu_synthase 361 llaalgin 368
                                       ++++lgin
  gi|518651476|ref|YP_008140996.1| 373 MMGKLGIN 380
                                       ******86 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00027
                                       HHHHHHHHHHHHHTT-GGG-EEEEE.SS--SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 256 elalaevdqtlkeeglrdrvsliad.GglktgadvvkalalGAdavgigt 304
                                       el ++e++  l +eg+r++ +li +  +++ + d++k lalG d+v +++
  gi|518651476|ref|YP_008140996.1| 572 ELKITEINDILGKEGIRENYDLILEiSRFRNSGDIIKYLALGCDSVILSS 621
                                       78899**************999987479******************9887 PP

>> Glu_syn_central  Glutamate synthase central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.2   4.2e-07    0.0015     164     265 ..     261     383 ..     207     394 .. 0.73
   2 !   25.3   0.0   2.6e-09   9.4e-06      16      72 ..     428     482 ..     419     490 .. 0.89
   3 !   11.6   0.0     4e-05      0.14     173     265 ..     573     663 ..     570     668 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.2e-07
                                       TTEEE--HHHHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHH..HHHHTTTS-... CS
                   Glu_syn_central 164 eervpipslLavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaleti..eklveegal... 235
                                       ++++ ip  Lav++ ++ L +++lr+++ ++  +g + +  +++ l ++Gad v     + ++    +v++ +l   
  gi|518651476|ref|YP_008140996.1| 261 RDNMGIPVELAVASADSILKKENLRKNFTII-AAGRVSNSTDAMKLYALGADVVSLGTSILIAmgCIMVKKCNLgyc 336
                                       58899***********************986.68*******************975443333312123333322333 PP

                                       ...............----HH......HHHHHHHHHHHHHHHHHTT--BHH CS
                   Glu_syn_central 236 ...............aeeele......knyrkavekGllKimskmGistlq 265
                                                           +       n+++++++ +   m k+Gi  ++
  gi|518651476|ref|YP_008140996.1| 337 pvaltnrtdssksldI----DfavnrvVNFINGFRSEMAEMMGKLGINSMK 383
                                       4444444443333331....1344456999999999**********99876 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.6e-09
                                       THHHHHHHSS--EE-S---S--TTT-SS---GGGGEEE----SSS----TTTTGGG- CS
                   Glu_syn_central  16 llepmakegkeaigsmGdDtplavLsekprllydYFkqlfAqVTNPpiDpiREelvm 72 
                                       +l+ ++++g+  ++smG+++p  v  +kp  ++d+++   AqVT P+iDp RE++ +
  gi|518651476|ref|YP_008140996.1| 428 YLNSLINKGEPVMSSMGSNAPPEV--DKPARIIDWLRLDGAQVTRPSIDPYRENINL 482
                                       67889999**************98..9**************************9865 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHHHHTT-GGG-EEEEEESS--SHHHHHHHHHTT-SEEEEHHHHHHHHHHHTTTS-----HHHHHHHHHH CS
                   Glu_syn_central 173 LavgavhhhLvrkglrtkvslvvesgearevhhfavllgyGadavnPylaletieklveegalaeeeleknyrkave 249
                                       L +  ++  L ++g r +  l++e +  r+  +++  l++G+d v   l  +++e+  e++  + +e++ n+  +++
  gi|518651476|ref|YP_008140996.1| 573 LKITEINDILGKEGIRENYDLILEISRFRNSGDIIKYLALGCDSVI--LSSKIFESGLENNYSNLKEKALNFLMGIR 647
                                       667889999**********************************985..4445554445555555566669******* PP

                                       HHHHHHHHHTT--BHH CS
                   Glu_syn_central 250 kGllKimskmGistlq 265
                                       k l      mGis lq
  gi|518651476|ref|YP_008140996.1| 648 KELALLSGAMGISNLQ 663
                                       *************997 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.0    0.0014       5.1      29      90 ..      50     112 ..      30     119 .. 0.76
   2 !   21.0   1.8     4e-08   0.00014     233     308 ..     236     324 ..     201     329 .. 0.79
   3 !    3.3   0.1    0.0095        34     314     342 ..     358     386 ..     355     393 .. 0.88
   4 ?    2.9   0.0     0.013        46     280     300 ..     600     620 ..     575     667 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0014
                                       GGGGEEE---SSSS-SS-B--..EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS- CS
                            FMN_dh  29 aferirlrprvlrdvskvdls..ttllGqklslPvliaPvglaklahpdgelalaraaakagip 90 
                                        +++i +r +  + + ++d++  t l G kls+Pv+++ +++  l   + ++a+a++a+ ++++
  gi|518651476|ref|YP_008140996.1|  50 ILDNIIFRGNKSHAIPNMDIQtdTMLAGMKLSVPVYLGDMSYGALSG-NPNIAIAKTAEITETM 112
                                       567777888888888887665115677***************99986.8899999999877766 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 4e-08
                                       HHHTTESEEEE--GGG..............TSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-S CS
                            FMN_dh 233 aveaGvdgivvSNHGG..............RqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAd 295
                                       +++ G+ g+++  HG+                ++ a+a+ d + +  e++++++++++ g +++ +D++k  alGAd
  gi|518651476|ref|YP_008140996.1| 236 IARSGAAGVIIDGHGAgtgaapvavrdnmgIPVELAVASADSILK-KENLRKNFTIIAAGRVSNSTDAMKLYALGAD 311
                                       567899999999999989999999933333334444444444444.6788889************************ PP

                                       EEEESHHHHHHHH CS
                            FMN_dh 296 avllGRpflygla 308
                                       +v lG  +l ++ 
  gi|518651476|ref|YP_008140996.1| 312 VVSLGTSILIAMG 324
                                       *******999875 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 314 GvervleilraelertmallGvksvaeld 342
                                       +v + ++ +r+e+ + m  lG++s++el+
  gi|518651476|ref|YP_008140996.1| 358 RVVNFINGFRSEMAEMMGKLGINSMKELT 386
                                       67889999*******************97 PP

  == domain 4  score: 2.9 bits;  conditional E-value: 0.013
                                       --SHHHHHHHHHTT-SEEEES CS
                            FMN_dh 280 irrGsDvlkAlalGAdavllG 300
                                       +r+  D++k lalG d v+l 
  gi|518651476|ref|YP_008140996.1| 600 FRNSGDIIKYLALGCDSVILS 620
                                       78999***********99875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.9   7.3e-06     0.026     166     237 ..     240     317 ..     206     323 .. 0.76
   2 ?   -1.6   0.0       0.3   1.1e+03     299     331 ..     359     391 ..     355     398 .. 0.77
   3 !    3.6   0.0    0.0078        28     217     237 ..     601     621 ..     598     632 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 7.3e-06
                                       T-SEEEE...-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT....-EEEEES---SHHHHHHHHHTT-SEEEE CS
                                       xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 166 gadavkv...GiGpGsiCttrvvagvGvpqltAvaevaeaakkag....vpviaDGGikysgdivkAlaaGadavml 235
                                       ga +v +   G G+G+  +  v   +G+p   Ava++ ++ kk +     ++ia G +++s d +k  a+Gad+v l
  gi|518651476|ref|YP_008140996.1| 240 GAAGVIIdghGAGTGAAPV-AVRDNMGIPVELAVASADSILKKENlrknFTIIAAGRVSNSTDAMKLYALGADVVSL 315
                                       5555544422334444333.3446789999999999999888776555599************************** PP

                                       SC CS
                                       xx RF
                             IMPDH 236 Gs 237
                                       G 
  gi|518651476|ref|YP_008140996.1| 316 GT 317
                                       97 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.3
                                       HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 299 vkevveqlvgglrsgmgylGaktieelkekakf 331
                                       v ++++ + +++ + mg+lG ++++el  +  +
  gi|518651476|ref|YP_008140996.1| 359 VVNFINGFRSEMAEMMGKLGINSMKELTGNRDL 391
                                       556677777788888999999999999877665 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.0078
                                       -SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 217 kysgdivkAlaaGadavmlGs 237
                                       ++sgdi+k la+G d+v+l s
  gi|518651476|ref|YP_008140996.1| 601 RNSGDIIKYLALGCDSVILSS 621
                                       79***************9976 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.51   1.8e+03     155     170 ..     209     224 ..     177     241 .. 0.80
   2 ?   11.3   0.1   4.1e-05      0.15     239     278 ..     282     321 ..     269     332 .. 0.84
   3 ?   -3.0   0.0      0.92   3.3e+03      15      40 ..     498     523 ..     493     533 .. 0.60

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.51
                                       HHHHHHHSSEEEEEE- CS
                            DHO_dh 155 kvvkevskvpvlvKla 170
                                       +++k  s++pv+vK+a
  gi|518651476|ref|YP_008140996.1| 209 EALKILSDKPVFVKVA 224
                                       455556699*****98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.1e-05
                                       HHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHH CS
                            DHO_dh 239 krlkkeipiIgvGGiesgeDalekieaGAslvqvytalvf 278
                                       ++l+k+  iI+ G ++ + Da+  +  GA +v ++t +  
  gi|518651476|ref|YP_008140996.1| 282 ENLRKNFTIIAAGRVSNSTDAMKLYALGADVVSLGTSILI 321
                                       57888999****************************8654 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.92
                                       EEE-TTSSTTSSSHHHHHCTTSSEEE CS
                            DHO_dh  15 iglAaGfdkegeeilkllklgfgaie 40 
                                       i++  G dk+ +e+l++  l +g+++
  gi|518651476|ref|YP_008140996.1| 498 IINVNGSDKNVMEALEWASLFIGSVT 523
                                       44555666666666666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (694 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 4599.78
//
Query:       gi|518651477|ref|YP_008140997.1|  [L=631]
Description: hypothetical protein FACI_IFERC00001G0116 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-21   74.4   8.3    1.4e-20   73.7   8.3    1.2  1  GXGXG     GXGXG motif
    3.8e-08   33.6   0.0    2.4e-07   31.0   0.0    2.2  1  GATase_6  Glutamine amidotransferase domain
     0.0002   21.3   0.0    0.00098   19.0   0.0    2.1  2  GATase_7  Glutamine amidotransferase domain
  ------ inclusion threshold ------
      0.035   14.3   0.2       0.12   12.5   0.2    1.9  1  IRK_N     Inward rectifier potassium channel N-terminal


Domain annotation for each model (and alignments):
>> GXGXG  GXGXG motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   8.3   3.1e-24   1.4e-20       3     166 ..     355     520 ..     353     533 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 3.1e-24
                                       E-TT--STTH.....HHHHHHHHHHTTT---.-EEEEEEEEEE-TTTTTT--TTEEEEEEEEE-STTTTT-ESSEEE CS
                             GXGXG   3 irnldrsvgt.....ilsneiakrygeeglpedtikiklkGsaGqslgaflakGltleleGdandyvGkglsgGkiv 74 
                                       ++ l++++ +     +++n+ ++ry   ++p+ + +i+++G+ G+ +   + + ++ ++ G+  d +++++ gG + 
  gi|518651477|ref|YP_008140997.1| 355 YNRLNQAILKgdqaiTINNVAGHRYVGINFPDSEKDITIYGTLGNCFMNLNENNIS-TIYGNVADDCCDSMGGGMVK 430
                                       666777777677777999*****************************999977765.789999999*********** PP

                                       EE--TT-SS-GGGSB-S-SSTTTT--SEEEEESSB--SSTTTT-.....SS-EEEESEB.-SSTTTT-EEEEEEE-S CS
                             GXGXG  75 ikpskeskfkaeeniivGnvvlygatgGklfirgkageRfavrn.....sgatavvegv.gdhgceYmtGGvvvvLg 145
                                       i++++            G+ + ++  gGk+++ g+ag+R+++++     + +++v++g   d+++eYm GG++ vL+
  gi|518651477|ref|YP_008140997.1| 431 IYGDA------------GDILCQALNGGKVYVLGNAGNRACIQMreyvdKSTVVVINGKfDDYLGEYMSGGTLLVLS 495
                                       *****............***************************99999899999999999**************** PP

                                       -B....-SSBTTT--EEEEEEE-SS CS
                             GXGXG 146 kt....grnfaaGmsgGiayvlded 166
                                       +     g+++++Gm gG+++++ + 
  gi|518651477|ref|YP_008140997.1| 496 NSarnfGKYIGSGMIGGTIFIRGKV 520
                                       997777888899*********9443 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   5.3e-11   2.4e-07      11      82 ..     150     223 ..     138     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.3e-11
                          GATase_6  11 edevalaHvRlaivglaeeega.qPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....e 82 
                                       e++++laH+R  ++         +Pf  ++ ++++vhNG+i+ +++ re l++ kg++    +D+ev++ ++    +
  gi|518651477|ref|YP_008140997.1| 150 EADMWLAHTRQPTNSPGYLPYWsHPF--SSFNIAIVHNGDISSFGANREFLKS-KGVNSFVGTDSEVIAYIFrellK 223
                                       45699*******99998777778***..*****************99999999.****889*********9955552 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   2.2e-07   0.00098      22     120 ..     178     299 ..     171     301 .. 0.88
   2 ?   -3.2   0.0       1.6   7.3e+03      21      35 ..     467     481 ..     462     482 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.2e-07
                          GATase_7  22 grlvivfnGeiyNykelreeLeakghrfrtksDtevllallea......................ewgeealerlnG 76 
                                        +++iv+nG i  +   re L++kg++    +D+ev++ ++++                       + ++    l+G
  gi|518651477|ref|YP_008140997.1| 178 FNIAIVHNGDISSFGANREFLKSKGVNSFVGTDSEVIAYIFREllkqydlittvkimagkiedpvMKYKNRGAVLDG 254
                                       4699************************************999***************9999998888888899*** PP

                          GATase_7  77 mfAfaiwdeeek..rlllaRDrlGikPLyygedkgdallfaSelka 120
                                        + ++i  ++ +   ++++ Dr   +P ++ged+g ++++aSe + 
  gi|518651477|ref|YP_008140997.1| 255 PYTLVIGYDDGNdlYMICIADRTKLRPAILGEDDG-NFFIASEESQ 299
                                       *****975555524677899*************86.9999999766 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                          GATase_7  21 dgrlvivfnGeiyNy 35 
                                       d++ v+v+nG+  +y
  gi|518651477|ref|YP_008140997.1| 467 DKSTVVVINGKFDDY 481
                                       78899*****98776 PP

>> IRK_N  Inward rectifier potassium channel N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   2.7e-05      0.12       6      35 ..      53      83 ..      50      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.7e-05
                             IRK_N  6 ahrYSI.VSseEdglklstlalvNGfgnGki 35
                                       ++YSI V  eEd ++l +l  +NGfg  k+
  gi|518651477|ref|YP_008140997.1| 53 NNHYSInVFYEEDEHQLRSLLEQNGFGINKM 83
                                      599***99*******************6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4148.68
//
Query:       gi|518651478|ref|YP_008140998.1|  [L=441]
Description: hypothetical protein FACI_IFERC00001G0117 [Ferroplasma acidarmanus fer1]
Scores for complete 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-121  403.8   0.0   6.9e-121  403.4   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    5.8e-23   80.4   0.1    1.5e-22   79.1   0.1    1.8  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 !  403.4   0.0  7.7e-125  6.9e-121       2     345 .]     104     437 ..     103     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 403.4 bits;  conditional E-value: 7.7e-125
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR++l++++++l++e+ t+++gpElE+flf+++e++e            + +p++ ggyf+ +p+d+a  + +ei
  gi|518651478|ref|YP_008140998.1| 104 GDPRYILEKQVEKLTKENKTYYLGPELEYFLFKQDENGE-----------PTIEPSDYGGYFDKEPLDKAFTVKQEI 169
                                       79*********************************9987...........56779999******************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       ++ le l +  eashhEva +Q+Ei++k++da+++aD+++++K vvke+A+++g++atFmpKp++g nG+gmHvh+S
  gi|518651478|ref|YP_008140998.1| 170 IRKLEGLHYYPEASHHEVAYSQHEIDVKYSDAVTMADRIIMIKSVVKETANEYGYYATFMPKPVKGVNGNGMHVHQS 246
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-T CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipas 232
                                       ++ + ++nlf++e+++y+ls+ a h++gG+l+ + + ++++a+tvnSYkRlvpgyeaPv++aw++rNRsal+Ripa+
  gi|518651478|ref|YP_008140998.1| 247 IF-SGDENLFYNESNKYGLSDYAMHYLGGILNNVSNASLVLASTVNSYKRLVPGYEAPVYIAWANRNRSALVRIPAA 322
                                       **.888*********************************************************************** PP

                                       SGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                        Gln-synt_C 233 kekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                        +k+kr+ElR+pda+ N YL +Aa+l  gldGienk +p+e++ek+++e++ +er  +gi+++P sl +A+e+++++
  gi|518651478|ref|YP_008140998.1| 323 PPKGKRMELRFPDAAGNQYLQFAAILGMGLDGIENKTNPPEAMEKNIFEMDLAERqkNGIKSMPGSLGQAIESFRNS 399
                                       ***************************************************9999999******************* PP

                                       HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 308 ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       el+k+++ge+v+++ l++k++E++e+++ev+dwe+++y
  gi|518651478|ref|YP_008140998.1| 400 ELMKKIFGESVFNNLLRIKENEWNEFRSEVTDWEINKY 437
                                       ***********************************988 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 !   79.1   0.1   1.7e-26   1.5e-22       1      82 [.      15      96 ..      15      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.7e-26
                                      T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvic 78
                                      ev+f++lqFtDi g++k++tip +++ ed++ +gv+FDGSsi g+++ie+SDm  +P+ls+++i+  ++   kt+r++c
  gi|518651478|ref|YP_008140998.1| 15 EVEFLQLQFTDISGSVKSLTIPHNRF-EDVIYNGVMFDGSSIVGYKQIEDSDMKAVPELSSYTILTNENYAgKTVRFVC 92
                                      599***********************.***************************************9998889****** PP

                                      EEE- CS
                        Gln-synt_N 79 dvyd 82
                                      ++++
  gi|518651478|ref|YP_008140998.1| 93 KIFN 96
                                      **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2903.07
//
Query:       gi|518651479|ref|YP_008140999.1|  [L=508]
Description: hypothetical protein FACI_IFERC00001G0118 [Ferroplasma acidarmanus fer1]
Scores for complete 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-188  625.2   2.3   7.2e-188  625.1   2.3    1.0  1  PEPcase_2  Phosphoenolpyruvate carboxylase
  ------ inclusion threshold ------
        1.4    9.1   5.8        1.6    9.0   0.1    3.8  5  Pro_sub2   Prodomain subtilisin 2


Domain annotation for each model (and alignments):
>> PEPcase_2  Phosphoenolpyruvate carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  625.1   2.3    8e-192  7.2e-188       1     494 []       2     508 .]       2     508 .] 0.99

  Alignments for each domain:
  == domain 1  score: 625.1 bits;  conditional E-value: 8e-192
                                       --SEEEE--ST-........SS--B-TTTHHHHHHHHHSS----EEEEE-SSB---TTHHHHHHHHHHC..TT--TT CS
                         PEPcase_2   1 iprtmsTQHPDnakvPef.aeeevisgedEveEAykalselgvdEvMwDfEGKevdehvvrkllseyeeffkekvlG 76 
                                       ip+tmsTQHPDna +Pe+ ++++ i++edE+eEAy a+ +lg++EvMwD+EGK+vd+hv+rkl+ + + ff++ ++G
  gi|518651479|ref|YP_008140999.1|   2 IPKTMSTQHPDNALMPEWsSNKNIITNEDEIEEAYIAYKKLGIQEVMWDAEGKDVDTHVIRKLFAKDRIFFENSKIG 78 
                                       9*****************6677889**************************************************** PP

                                       TSSEEEEE---TTTS-HHHHHHHHHHHHHHHHH.HHHHH...SS-S-SEEEESS--SHHHHHHHHHHHHHHHH.... CS
                         PEPcase_2  77 edvfltlRvPnpkvEkaerkvlaetlesipnsydlaekf..eetkpifevilPmttsaeelievakyyekvvagkee 151
                                       +d+flt+RvPnp +E+aerk+l etl+sip +yd+++++  + ++pifevilP+tt+++++ +v+k+yek v g ++
  gi|518651479|ref|YP_008140999.1|  79 QDIFLTYRVPNPLIEGAERKILNETLNSIPLNYDVSNRIfnNGIAPIFEVILPFTTDYRSMLNVVKFYEKCVVGAQS 155
                                       ***********************************9999856*********************************** PP

                                       ......HHHHH-SS---TTSSEEEEEE-SHHHHHTHHHHHHHHHHHT--SEEEEEEESHHHHHHH-HHHHHHHHHHH CS
                         PEPcase_2 152 lelad.lkvkelvgelkpesievIPLiEdkesllnideiveeyvkekklkelRvflarSDpAlnyGlisavllvkvA 227
                                       ++l+d +++++++ge+ p +i++IPLiEdk+s++ni++iv+ey + ++++++R+f+arSDpA+nyG+i+a+ll+k+A
  gi|518651479|ref|YP_008140999.1| 156 INLYDnVYSRDVTGEVLPGKINLIPLIEDKDSIFNIEHIVKEYHRVISPEYMRIFIARSDPAMNYGMIPATLLAKYA 232
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHT-EEEEEEE-BSSGGGT---TTGHHHHHHHTTT-SEEEE-HHHHHTTHHHHHHHHHHHHHHGGG-- CS
                         PEPcase_2 228 lselykleeelgvkiyPilGvGslpfRGhlspenveevleeYagvkTfTvQSafkYdyeeeevkeairkineaevkk 304
                                        s++ ++++++g+++yPi+G+Gs+pfRG+l p n+++ l+eY +++Tf +QSaf+Ydy+++evk++i+ in+++ +k
  gi|518651479|ref|YP_008140999.1| 233 ASKMGQISDDTGMSVYPIIGAGSSPFRGNLGPANIKRALSEYDQYYTFSIQSAFRYDYNDQEVKDSIKLINKHTPQK 309
                                       ***************************************************************************** PP

                                       -----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---S-B----------EEE--HE---HHHHHHHHHH CS
                         PEPcase_2 305 prelseeeeelllevieklseaYqekiekladvinevaklipkrRaRklhiglfgYsReieevelPRAIsftgalYs 381
                                       ++ ++ e e++++ ++ ++se++q+ ie++a+ in+++ ++pkrR+RklhiglfgYsR++++ +lPRAIsf+galYs
  gi|518651479|ref|YP_008140999.1| 310 AEFIDIETEKIIKGIVGTYSERFQKIIEDIAQPINDITFYLPKRRERKLHIGLFGYSRSTGKASLPRAISFVGALYS 386
                                       ***************************************************************************** PP

                                       TT--GGGTTHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHTT--SS.....TTTTTS-HHHHHHHHHHHHHHHHHTT- CS
                         PEPcase_2 382 iGlPpellgissllelaeeelevllevykalkedlaeaarylnle.....ksklkldeetvkkikedleiveeildl 453
                                       iG+Ppe+lgi+sl++l e++   l+++y+++++d++ +a+y+n+e     k+ +k++++t+ +i+ed+++ve+++++
  gi|518651479|ref|YP_008140999.1| 387 IGVPPEILGIASLSSLPESSQVLLKKLYRYMEQDIKASAQYFNYEsldylKEIWKVSDKTLDMIREDIKYVEDNIGI 463
                                       *************************************************************************9999 PP

                                       -....HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-- CS
                         PEPcase_2 454 k....yeeeeheeltsellkalkekkdeelkelilemaklRkflG 494
                                            y+ ++h+  t+ ll a+k+ k ee+k++i+e++ lRkf+G
  gi|518651479|ref|YP_008140999.1| 464 PtetsYNVQKHNLYTKLLLMAFKNRKFEEVKSYIYELSLLRKFIG 508
                                       88899999************************************9 PP

>> Pro_sub2  Prodomain subtilisin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.46   4.1e+03      20      48 ..      22      50 ..      19      53 .. 0.80
   2 ?   -2.9   0.1      0.91   8.2e+03      27      59 ..     114     146 ..     107     159 .. 0.61
   3 ?    9.0   0.1   0.00018       1.6      16      61 ..     305     351 ..     299     355 .. 0.74
   4 ?   -2.4   0.0      0.61   5.5e+03      61      88 .]     391     418 ..     386     418 .. 0.87
   5 ?   -0.6   0.1      0.17   1.5e+03      33      51 ..     484     502 ..     469     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.46
                          Pro_sub2 20 mktvikeadekfekyikrhfkevdkiryd 48
                                       k++i + de+ e yi  +   ++++++d
  gi|518651479|ref|YP_008140999.1| 22 NKNIITNEDEIEEAYIAYKKLGIQEVMWD 50
                                      58999999999999998887777777776 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.91
                          Pro_sub2  27 adekfekyikrhfkevdkirydisspinflcff 59 
                                       ++++f++ i   f+ +   + d  s +n + f+
  gi|518651479|ref|YP_008140999.1| 114 SNRIFNNGIAPIFEVILPFTTDYRSMLNVVKFY 146
                                       455566666666666666666666666666665 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00018
                          Pro_sub2  16 hskemktvikeadekfekyik.rhfkevdkirydisspinflcffip 61 
                                       h+++    i+   ek+ k i  +  ++++ki  di+ pin + f++p
  gi|518651479|ref|YP_008140999.1| 305 HTPQKAEFIDIETEKIIKGIVgTYSERFQKIIEDIAQPINDITFYLP 351
                                       5555666666555555555550455789*****************99 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 0.61
                          Pro_sub2  61 ptifdmnnlkllkeallilhkelkeyie 88 
                                       p i+ ++ l+ l e+  +l k+l +y+e
  gi|518651479|ref|YP_008140999.1| 391 PEILGIASLSSLPESSQVLLKKLYRYME 418
                                       6788899999999999999999*99997 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 0.17
                          Pro_sub2  33 kyikrhfkevdkirydiss 51 
                                        + +r+f+ev+   y++s 
  gi|518651479|ref|YP_008140999.1| 484 AFKNRKFEEVKSYIYELSL 502
                                       566899999*999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 2955.40
//
Query:       gi|518651480|ref|YP_008141000.1|  [L=465]
Description: hypothetical protein FACI_IFERC00001G0119 [Ferroplasma acidarmanus fer1]
Scores for complete 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  296.7  31.0    2.4e-88  296.5  31.0    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
        8.2    6.7   6.1        4.3    7.6   0.6    2.7  2  HemY_N           HemY protein N-terminus


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  296.5  31.0   2.7e-92   2.4e-88       2     397 ..      27     433 ..      26     435 .. 0.95

  Alignments for each domain:
  == domain 1  score: 296.5 bits;  conditional E-value: 2.7e-92
                                       HHHHHHHHHHHH.HHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCB..SSSSSCE-...... CS
                   Ammonium_transp   2 flllsaalvifm.qagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgksk..gvsgfign...... 69 
                                       ++l ++ lv +m  +g+a+++agl+++k ++n +++ l ++a+v+++++l Gy + fg+s   ++ g+ ++      
  gi|518651480|ref|YP_008141000.1|  27 WMLTASTLVGLMsIPGLAIYYAGLTKRKYMVNAMMMALYAFAAVLIIWILAGYNFGFGTSSllKIDGYYIFgipspa 103
                                       9**********************************************************97777888888799***9 PP

                                       ........TTTTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHHHHS.S CS
                   Ammonium_transp  70 ........lglsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahwvwgeg 138
                                               + +     +  t+++  +++fq++faa++  +  g++ er++f+a+++f  +++ +vy+pva+w ++ g
  gi|518651480|ref|YP_008141000.1| 104 gagsfisgQAIVGPLKDALTIPNSTVMFFQFVFAAITPILLLGGILERMNFKAWMIFVPIWSLIVYSPVAYWLFA-G 179
                                       99988877666666667778888889*************************************************.* PP

                                       SHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTGTTTSS--GSBHHHHHHHHHHHHHHHHHHHHGGGSSS CS
                   Ammonium_transp 139 gwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfegkeeaikghnlpfavlGtllLwfgWfgFNaGsalta 215
                                       gwl++lg++ Df g+ v+Hl +g+ +Laaa+v+g+r +     e+++k  nl +++lG  l+w+gW gFN+G  ++a
  gi|518651480|ref|YP_008141000.1| 180 GWLNQLGAV-DFSGGYVIHLDAGIGALAAAFVIGPRLKD----EMKMKANNLGLVMLGLGLIWLGWDGFNGGDPYGA 251
                                       *********.***************************64....69******************************** PP

                                       SHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 216 nkrararaavtTllAaaagaltallisrlkegkinvlglanGilAGlVAiTaacavvepwgAliiGlvAgvlsvlgv 292
                                       +  a   a+++T++A+a++++t+++++    +k++++g+  G++AGlV+iT+a+++v+++gA++iG+ +g++  + +
  gi|518651480|ref|YP_008141000.1| 252 TIDAGI-AIINTNVATAVSMMTWMFMDLKFFKKPSLIGASVGAIAGLVGITPAAGYVNIYGAMVIGIATGIIPWIFL 327
                                       ****99.*****************************************************************98888 PP

                                       HHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC..SSHSSTTGGGT-CHHHHHHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 293 kklkeklkidDsldvvavHgvgGiwGllavgifaaekvv..askisggllsgegkqlvvqligilvilayafvvtli 367
                                        k++ k+k+dDsl+v++ H+v+G++G+l++g++a++ v   ++    g l+g+  +l++q+++++++++y+f++t+ 
  gi|518651480|ref|YP_008141000.1| 328 YKIEPKFKVDDSLGVFSSHAVAGVVGGLLTGVLADPVVTqyIDPGLRGALYGNFYELGIQAFAAVIVILYVFALTYG 404
                                       88**********************************88898999999****************************** PP

                                       HHHHHHHHTTSB--HHHHHHSHHHHHHSSS CS
                   Ammonium_transp 368 lllllklllgLrvseeeeevglDvaehget 397
                                       ll l++ ++ Lr ++   ++g D+a hge+
  gi|518651480|ref|YP_008141000.1| 405 LLRLIGVFIPLRETNARLKIG-DMAIHGEA 433
                                       ************977766665.78888886 PP

>> HemY_N  HemY protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.6     0.078     7e+02      17      36 ..      57      76 ..      28      86 .. 0.67
   2 ?    7.6   0.6   0.00048       4.3      10      44 ..     382     416 ..     377     423 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.078
                            HemY_N 17 vvavlllvllfvllylllrl 36
                                      v a+++++ +f+++++++ l
  gi|518651480|ref|YP_008141000.1| 57 VNAMMMALYAFAAVLIIWIL 76
                                      44555555555555555544 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00048
                            HemY_N  10 yrietslvvavlllvllfvllylllrllrlllrlp 44 
                                       y++ +   +av++++ +f+l y llrl++ ++ l 
  gi|518651480|ref|YP_008141000.1| 382 YELGIQAFAAVIVILYVFALTYGLLRLIGVFIPLR 416
                                       677788899*******************9998774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3333.01
//
Query:       gi|518651481|ref|YP_008141001.1|  [L=617]
Description: hypothetical protein FACI_IFERC00001G0120 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-58  198.8   0.0    1.9e-58  198.5   0.0    1.1  1  DUF2075          Uncharacterized conserved protein (DUF2075)
  ------ inclusion threshold ------
      0.015   15.6   0.0      0.032   14.6   0.0    1.5  1  AAA_16           AAA ATPase domain
       0.04   13.6   0.0       0.07   12.8   0.0    1.3  1  AAA_30           AAA domain
      0.075   12.8   0.0       0.15   11.7   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.077   13.3   0.0       0.26   11.6   0.0    1.9  1  AAA_22           AAA domain
        0.1   12.0   0.2       0.18   11.1   0.2    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.14   11.9   0.1       0.37   10.5   0.1    1.7  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase


Domain annotation for each model (and alignments):
>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  198.5   0.0   7.3e-62   1.9e-58       4     363 .]     249     590 ..     246     590 .. 0.87

  Alignments for each domain:
  == domain 1  score: 198.5 bits;  conditional E-value: 7.3e-62
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef... 77 
                                       ++++G++G+GK++++lnll +   ++ ++++v+ ++N++ v+ lr+ l++ +         +++s++i+ +s++   
  gi|518651481|ref|YP_008141001.1| 249 YIIHGGPGSGKSLIALNLLLRS--SAMGKQSVLSYRNNRMVASLRKLLDSIS---------TGMSTLIKYYSTGrpg 314
                                       79*******************9..************************8777.........99*********99999 PP

                           DUF2075  78 .kkaeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDegQelntgeigteeelkklakk 153
                                           +e+k   + d++i+DE +r++            +++k+  k a+++v+++D++Q+l t e gt++++ k++++
  gi|518651481|ref|YP_008141001.1| 315 nPGVAEDKFPVHYDIAIFDESQRMTV-----------KNIKNAGKVADISVFFYDDSQILGTREQGTQSNFLKYLEN 380
                                       77888999999***************...........7899***********************9999998885544 PP

                           DUF2075 154 leveleekvhLksqfRvaaseaviewvdalldgkkekakplssqenfdirvfddleelkkalkeknkesgrsrlvat 230
                                        ++e+    +Lk  +R    +++ e+v++ll+g+++  +p    e +d++ f d++ l ++lk+k + +++s+lva+
  gi|518651481|ref|YP_008141001.1| 381 -PHEI----TLKGLYRN--GNEYGEFVNKLLKGESTI-YP----EPYDLQYFPDIKCLINTLKTKIDLGKKSALVAS 445
                                       .4443....8*******..899*********554443.44....69******************************* PP

                           DUF2075 231 ydakrlaekkkkkskekdvkiee..........gd.fklpWnleek.elkkpwaess.dtleevgseytiQGleldy 294
                                       +++ +   ++++ +++++++i+           g    ++W +++k e+   w+  + ++le+++s+y +QG+e+dy
  gi|518651481|ref|YP_008141001.1| 446 FTEAKG--NIHDINSQDNIRIGDripsglnlysGTgIAVRWLMDPKkEYAPFWVGGEsNKLEKCASVYGAQGFEADY 520
                                       ****99..8999999999999886666655555333555******97778899987669****************** PP

                           DUF2075 295 vgviiGpdlvyrkeedrikfrgkksedkeaks...krkk.kkeseekaqkllkNayrVLLtRGrkGlyiyaed 363
                                       +gvi+G+dlv r  +++ ++ g+++ed e k+   k k+ +k+s ++a +ll N+yr+LLtRG++G+yi++ed
  gi|518651481|ref|YP_008141001.1| 521 TGVIWGRDLVRR--DNK-WVLGDNCEDFEIKKlffKGKNgDKTSYDTAIELLVNRYRILLTRGIYGTYIFCED 590
                                       ***********9..333.46666666665544111444479999***************************98 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   1.3e-05     0.032       9      46 ..     231     269 ..     228     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_16   9 leqLlsalervrsgrpelvllsGesGvGKsslv.rellr 46 
                                       le  l++++++ +g+p++ +++G +G+GKs ++ + llr
  gi|518651481|ref|YP_008141001.1| 231 LEPYLEIINNLLTGTPGNYIIHGGPGSGKSLIAlNLLLR 269
                                       4444556669999*******************9555554 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   2.7e-05      0.07       9     174 ..     237     408 ..     229     417 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                            AAA_30   9 avealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae...elgieastiakllkrlk. 81 
                                       ++++llt++    +++G++G+GK+ +   l     a g++ ++   ++++ + L++   ++ +  st+ k+ ++ + 
  gi|518651481|ref|YP_008141001.1| 237 IINNLLTGTPGNYIIHGGPGSGKSLIALNLLLRSSAMGKQSVLSYRNNRMVASLRKlldSISTGMSTLIKYYSTGRp 313
                                       5677788888889***********88666655556667777777777778778886221555666677777766559 PP

                            AAA_30  82 .....grarlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQlasVeaGgvlrdlveaagigtaeLt 152
                                            ++ ++  + ++ i DE+  +  k++++  k a   +++v +  D + l+  e+G + + l   ++++ ++L+
  gi|518651481|ref|YP_008141001.1| 314 gnpgvAEDKFPVHyDIAIFDESQRMTVKNIKNAGKVA---DISVFFYDDSQILGTREQGTQSNFLKYLENPHEITLK 387
                                       ***99556677777***********999999988888...5699999999999999999999999777999999999 PP

                            AAA_30 153 evvRqkeseeraaalalregda 174
                                        ++R  + e+ + +++l +g+ 
  gi|518651481|ref|YP_008141001.1| 388 GLYRNGN-EYGEFVNKLLKGES 408
                                       9999965.77777777777765 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     6e-05      0.15      47      92 ..     246     292 ..     233     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6e-05
                         IstB_IS21  47 kenivllGpsGvGKshlaialgveavrag.lsvlfvrvedLveelkr 92 
                                         n ++ G++G GKs +a  l  +  + g  svl +r +++v++l++
  gi|518651481|ref|YP_008141001.1| 246 PGNYIIHGGPGSGKSLIALNLLLRSSAMGkQSVLSYRNNRMVASLRK 292
                                       5699****************998877755268999********9986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0001      0.26       4      31 ..     245     272 ..     242     387 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqlde 31 
                                       t g  +++G +G+GK++ + +ll +  +
  gi|518651481|ref|YP_008141001.1| 245 TPGNYIIHGGPGSGKSLIALNLLLRSSA 272
                                       56789*****************998743 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2   7.1e-05      0.18      37      64 ..     244     272 ..     236     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.1e-05
                                       GS-.SEEEE--TTSSHHH.HHHHHHHHHH CS
                      FtsK_SpoIIIE  37 kmashllvaGatgsGKSt.alntLilSla 64 
                                       + +++ +++G++gsGKS  aln L+ S a
  gi|518651481|ref|YP_008141001.1| 244 GTPGNYIIHGGPGSGKSLiALNLLLRSSA 272
                                       5679*************635777766655 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 ?   10.5   0.1   0.00014      0.37       2      28 ..     250     284 ..     249     450 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00014
                   Viral_helicase1   2 vvhGvpGcGKStlirkllrts........liltvn 28 
                                       ++hG pG+GKS +  +ll  s        l+ + n
  gi|518651481|ref|YP_008141001.1| 250 IIHGGPGSGKSLIALNLLLRSsamgkqsvLSYRNN 284
                                       79**********99999988556665332222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 3775.18
//
Query:       gi|518651482|ref|YP_008141002.1|  [L=403]
Description: permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-24   85.7  48.1    8.2e-19   67.7  19.9    2.0  2  MFS_1     Major Facilitator Superfamily
    5.6e-20   71.3  36.2    7.4e-20   70.9  36.2    1.1  1  MFS_2     MFS/sugar transport protein
  ------ inclusion threshold ------
      0.011   14.2   7.1      0.026   12.9   7.1    1.5  1  MFS_3     Transmembrane secretion effector
      0.072   13.4   3.5       0.13   12.5   0.9    2.2  2  DUF5503   Family of unknown function (DUF5503)
       0.23   10.3   1.2       0.48    9.2   1.2    1.5  1  DUF5423   Family of unknown function (DUF5423)


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 !   67.7  19.9   2.3e-22   8.2e-19      34     279 ..      37     281 ..       4     282 .. 0.79
   2 !   31.8  20.2     2e-11   7.1e-08      43     164 ..     257     390 ..     252     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 2.3e-22
                             MFS_1  34 igllltlyalgaavaslplGrlsdrf....Grrr.vlllglllfalglllll.fa.sslwlllvlrvlqGlgagalf 103
                                       +g+++ +  +  ++++++ G++sd+f    Grrr ++l+g ++ +++ lll+ ++  ++ ++++  +l  +g+ +++
  gi|518651482|ref|YP_008141002.1|  37 LGIIAFAGIIIGIAFNFLSGSFSDKFhsryGRRRpMILIGSIIVIFS-LLLFiIIkETIVTIFIIYILIEIGSNIAY 112
                                       778888888999************555555****8999999999999.5555234677779**************** PP

                             MFS_1 104 pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperk 180
                                        + + li+d+ p+++r+   g+ + ++ +G+++g +l+g+l+  +  +++ +++ i  + + ++    ++ ++ +  
  gi|518651482|ref|YP_008141002.1| 113 GSYQPLIRDIIPESQRSTSSGVGGFFTLIGSAFGFGLSGVLIGTGRIELATVLILITIAAGSII--TIFTIKREDYI 187
                                       ******************************************9999999988888888888776..55555555555 PP

                             MFS_1 181 rkspkeeekgtgpaplvpawkallkdpvl.willialllfffgfsglltllplylqevlgls.glllaglllallal 255
                                        +s++ +      ++l+ ++k ++ +  + w++++ +++++ g sgl+++   y+   l+l+ ++++++++   + l
  gi|518651482|ref|YP_008141002.1| 188 SNSEIIR------RKLSGVIKNFKQSTKFkWMAIANFFITT-GSSGLVFFEYYYFEYSLDLKdTAIYVAIAGVTILL 257
                                       5444444......4455567788888888799999999996.99999999999889999999955777766777777 PP

                             MFS_1 256 vgailallagrlsdrlgrrrrlll 279
                                       ++a + + +g l+d+++++++ll+
  gi|518651482|ref|YP_008141002.1| 258 ISALSTVGIGILADKINKEIFLLI 281
                                       77777999**********998887 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2e-11
                             MFS_1  43 lgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeer 119
                                       l +a++++ +G l+d++    +ll+  l++++++l+++f++ ++l+lvl  l G+++g +f++ +++++ ++p+   
  gi|518651482|ref|YP_008141002.1| 257 LISALSTVGIGILADKINKEIFLLIFPLISGFSILFISFIHAFYLFLVLGSLIGIAYGNYFTITNSYMSFIVPHGSA 333
                                       5677888888*******888888888888888867777867777********************************* PP

                             MFS_1 120 graigllsagfslGailgpllggllasslg............Wravfyilaivslla 164
                                       g++++++ +++ +Ga++ pl+ gl++ ++              +++fy+++++++l+
  gi|518651482|ref|YP_008141002.1| 334 GKYLSIFLVSTEIGAAFSPLIYGLVLFLFRgmgsaeysrlfeLSSIFYFIGFALILL 390
                                       ***********************9996666699999777777777777777777665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9  36.2   2.1e-23   7.4e-20       7     417 ..       6     392 ..       3     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 2.1e-23
                             MFS_2   7 laanilsvllatylliFytdvl...glsaalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilav 80 
                                       l+ n l++ +   +l+++ + l   +l+ +++g+++++  ++ + +++++G ++dk + r+GrrrP +l++ ii  +
  gi|518651482|ref|YP_008141002.1|   6 LGNNYLWTSFESLFLPYVIELLvpsRLQTIYLGIIAFAGIIIGIAFNFLSGSFSDKFHSRYGRRRPMILIGSIIVIF 82 
                                       56777888888888888888778889***********************************************9985 PP

                             MFS_2  81 siillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafll 157
                                       s +llf+ ++     +++ ++++yil  i  +  + +y  l+  +    ++R++ ++v  f++++g++ +  l ++l
  gi|518651482|ref|YP_008141002.1|  83 S-LLLFIIIK----ETIVTIFIIYILIEIGSNIAYGSYQPLIRDI-IPESQRSTSSGVGGFFTLIGSAFGFGLSGVL 153
                                       5.56677777....69*************9888888888888888.7889******************999999999 PP

                             MFS_2 158 vlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillllfl 234
                                       ++  +       + l+++li   ++++++i+++++ +e+    ++++  +++   +++++k++    +f +++++ +
  gi|518651482|ref|YP_008141002.1| 154 IGTGR-------IELATVLILITIAAGSIITIFTIKREDYI--SNSEIIRRKLSGVIKNFKQS---TKFKWMAIANF 218
                                       66555.......5899999999*********9999998854..45555555555555555555...55555555555 PP

                             MFS_2 235 laalalgvlnglllYyltyvlg.ngsaasvfllvvtisal..lgiplwqplakrlgkkntyllgalltivllvlvll 308
                                       + +++   l     Yy++y l+ +++a+ v  + vti+ +  l+++ +  la +++k    l++ l+  +++ ++++
  gi|518651482|ref|YP_008141002.1| 219 FITTGSSGLVFFEYYYFEYSLDlKDTAIYVAIAGVTILLIsaLSTVGIGILADKINKEIFLLIFPLI--SGFSILFI 293
                                       555555555555689*******8888887777777887778899***********987444444333..33333333 PP

                             MFS_2 309 lqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsaf. 384
                                             +lflvl  ++g+++g  +++  s ++ +v  g        +g + ++++  + ++++++ +++gl+L +f 
  gi|518651482|ref|YP_008141002.1| 294 SFIHAFYLFLVLGSLIGIAYGNYFTITNSYMSFIVPHGS-------AGKYLSIFLVSTEIGAAFSPLIYGLVLFLFr 363
                                       3369*************************9999998887.......9*****************************9 PP

                             MFS_2 385 gyrakasvqspqvvlalrllyavlpavlllval 417
                                       g+  +++++s   ++ l++++  ++ +l+l+ +
  gi|518651482|ref|YP_008141002.1| 364 GM--GSAEYSR--LFELSSIFYFIGFALILLKV 392
                                       99..7777777..99999999999999998866 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   7.1   7.3e-06     0.026      61     366 ..      51     358 ..      37     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                             MFS_3  61 lsilaGalaDnfd....rRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvk 133
                                       +  l+G  +D+f     rR+ ++ + +++++ s+ll ++    +++   + ++ +li+iG+ +   ++q  + ++++
  gi|518651482|ref|YP_008141002.1|  51 FNFLSGSFSDKFHsrygRRRPMILIGSIIVIFSLLLFIIIKETIVT---IFIIYILIEIGSNIAYGSYQPLIRDIIP 124
                                       6678899999764333399*****************9998877765...56667899******************** PP

                             MFS_3 134 rrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGa..alafavnalsylalivallrwkrevrksslprEkllealr 208
                                        ++ ++   +      i  + G  l+Gvl+ +     a++  + +++    i+++  +kre   s+  +E +++ l+
  gi|518651482|ref|YP_008141002.1| 125 ESQRSTSSGVGGFFTLIGSAFGFGLSGVLIGTGRIelATVLILITIA-AGSIITIFTIKREDYISN--SEIIRRKLS 198
                                       **9999999999999999***********986443103333333333.345777777777765553..677777777 PP

                             MFS_3 209 aglRftaasreikavlvRaalFglsasavlaLLPlv.ardqld.gdalvyGillgalGvGAi..lgalllsrLRerl 281
                                         ++  + s++ k  ++ a  F  + s+ l           ld  d+++y   ++++ +  i  l+++   +L +++
  gi|518651482|ref|YP_008141002.1| 199 GVIKNFKQSTKFKW-MAIANFFITTGSSGLVFFEYYyFEYSLDlKDTAIYV-AIAGVTILLIsaLSTVGIGILADKI 273
                                       77888889999876.555667777777777777654144455524555664.4555555444114566678999999 PP

                             MFS_3 282 sserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaa 358
                                       ++e ++l+  +   + +l +++ +  ++ ++   l G a+   ++  n+ +  +vP+   g+ l+++l+ ++ g a 
  gi|518651482|ref|YP_008141002.1| 274 NKEIFLLIFPLISGFSILFISFIHAFYLFLVLGSLIGIAYGNYFTITNSYMSFIVPHGSAGKYLSIFLVSTEIGAAF 350
                                       99999999999999999999999999999888899999999999999999999999999999999999999999999 PP

                             MFS_3 359 GsllWGav 366
                                         l++G v
  gi|518651482|ref|YP_008141002.1| 351 SPLIYGLV 358
                                       88888877 PP

>> DUF5503  Family of unknown function (DUF5503)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   3.7e-05      0.13      23     115 ..     177     268 ..     165     269 .. 0.81
   2 ?    0.5   0.1       0.2   7.3e+02      82     102 ..     368     388 ..     342     397 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                           DUF5503  23 testikqhelvsddaiine.lsselvsclgngkftpisedsklfnmlsefkllhseyfewgdyslwfqdfsiynkig 98 
                                       t  tik+ + +s+  ii   ls  +       kf  ++  +++f       l+  ey+   +ysl ++d +iy  i 
  gi|518651482|ref|YP_008141002.1| 177 TIFTIKREDYISNSEIIRRkLSGVIKNFKQSTKFKWMAI-ANFFITTGSSGLVFFEYYY-FEYSLDLKDTAIYVAIA 251
                                       5579*********99997615555555667788988775.5677777888999999985.58*************** PP

                           DUF5503  99 fimiekirelvthpfgi 115
                                        + i  i  l t  +gi
  gi|518651482|ref|YP_008141002.1| 252 GVTILLISALSTVGIGI 268
                                       ****9999999988887 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                           DUF5503  82 gdyslwfqdfsiynkigfimi 102
                                        +ys  f+  si+  igf +i
  gi|518651482|ref|YP_008141002.1| 368 AEYSRLFELSSIFYFIGFALI 388
                                       58999999999*999999876 PP

>> DUF5423  Family of unknown function (DUF5423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.2   0.00013      0.48      29     144 ..      77     193 ..      54     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00013
                           DUF5423  29 silcivsiilwt..qgsglalfaiapalaig...algv.tllvsdl.aesqkskeiadtvaavslpfiltgtaaglm 98 
                                       si++i s++l+   + + +++f i   + ig   a g    l+ d+  esq+s     t + v   f l g+a g+ 
  gi|518651482|ref|YP_008141002.1|  77 SIIVIFSLLLFIiiKETIVTIFIIYILIEIGsniAYGSyQPLIRDIiPESQRS-----TSSGVGGFFTLIGSAFGFG 148
                                       67777777776422566677788777777773333443134666642588887.....67889999*********** PP

                           DUF5423  99 fsaiavgggavilanplflmgsmtlgfalmslhrvtyqylsnreqw 144
                                       +s + +g g + la  l+l+  ++ g  +  +     +y+sn e  
  gi|518651482|ref|YP_008141002.1| 149 LSGVLIGTGRIELATVLILIT-IAAGSIITIFTIKREDYISNSEII 193
                                       ***************999985.444544433333345678887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1091  (0.0608511); 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:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2656.25
//
Query:       gi|518651483|ref|YP_008141003.1|  [L=392]
Description: hypothetical protein FACI_IFERC00001G0122 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.9e-30  105.0  46.7    1.7e-20   73.2  19.4    2.4  2  MFS_1       Major Facilitator Superfamily
    2.4e-15   56.0  34.8    3.6e-15   55.5  34.8    1.3  1  MFS_2       MFS/sugar transport protein
      3e-06   26.4  14.7      3e-06   26.4  14.7    3.3  3  Sugar_tr    Sugar (and other) transporter
    0.00011   21.3  21.3     0.0091   15.0  21.3    3.0  1  PUCC        PUCC protein
     0.0011   18.0  26.4     0.0054   15.6  24.4    2.5  1  MFS_1_like  MFS_1 like family
     0.0046   16.6   1.8      0.007   16.1   0.4    2.0  2  DUF4325     STAS-like domain of unknown function (DUF4325)


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 !   37.7  22.4   3.8e-13   1.1e-09      18     258 ..      19     255 ..       3     258 .. 0.70
   2 !   73.2  19.4   5.8e-24   1.7e-20      35     170 ..     248     388 ..     242     392 .] 0.90

  Alignments for each domain:
  == domain 1  score: 37.7 bits;  conditional E-value: 3.8e-13
                             MFS_1  18 alplalaedlgispseigllltlyalgaavaslplGrlsdrf....Grrrvlllglllfalglllll...fasslwl 87 
                                       +lp+    +++ s  ++g+++ + +++ ++  l++G lsd++    Grr  ++++ ++f++   ++l   ++++l  
  gi|518651483|ref|YP_008141003.1|  19 ILPI-ELLSYNKSSLFLGIIAFIGTALGVFIGLFFGTLSDKYnfgwGRRGPYIMAGAIFIVL-SMFLnqlLTITLAG 93 
                                       5664.23467789999*************************988888999666666666666.35553533467666 PP

                             MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivslla 164
                                       +l++ ++  + + +++ a + l ad+  +++rg++ g+ +++  lG+++g+++ g+l++    ++v +++++v ++ 
  gi|518651483|ref|YP_008141003.1|  94 VLLGYIMIQISSNVAVGAYQPLYADILGEDQRGKGSGIGGIFRLLGSMMGYGITGFLIDTPYRQYVIVLITVVVVVT 170
                                       999999999999**********************************************7766666666666666666 PP

                             MFS_1 165 fvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsg....lltllpl...y 233
                                       ++l     + ++++   k++k+       +     +  +++ +  +  +++++++ f++fsg         ++   +
  gi|518651483|ref|YP_008141003.1| 171 ALL--STNTIKKSDLIIKRKKPG----ITKL----FMDMFNLKNGLkNYIYVVVGSFMVFSGviglS----FFelyF 233
                                       443..333444444444444444....3333....44444444334679999999999999955433....443444 PP

                             MFS_1 234 lqevlgls..glllaglllallalvga 258
                                       ++  l+++  +    + +++++++v++
  gi|518651483|ref|YP_008141003.1| 234 FKYILHYAnpA----Y-YVSIAGIVVL 255
                                       59999999432....2.2444444443 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 5.8e-24
                             MFS_1  35 gllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fasslwlllvlrvlqGlgagalfpagaal 109
                                       +++  ++ +++a+as+++G+lsd++Gr+++l+   ++ +++ ++l+  f   + ++l+l  + G+ +g++++++ al
  gi|518651483|ref|YP_008141003.1| 248 SIAGIVVLITSAFASFVFGVLSDKIGRKKILVYITVIGGIA-MILIpeF-EKFVYFLILGSIIGMSYGIFMSVSDAL 322
                                       667778999********************************.5666579.9999*********************** PP

                             MFS_1 110 iadwfpkeergraigllsagfslGailgpllggllasslg......Wravfyilaivsllafvlfll 170
                                       ++d++p+ee g+++g+++++++ ++ + pl+ gl++ +++      +r+vfy+++++++++f +f+ 
  gi|518651483|ref|YP_008141003.1| 323 ASDMAPGEETGKYMGYYNMATGGASSVSPLIYGLIL-YFSssyslgFRYVFYAAGGFFFIGFAMFYK 388
                                       *********************************777.444467799***************997654 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5  34.8   1.2e-18   3.6e-15      31     386 ..      30     364 ..       3     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 1.2e-18
                             MFS_2  31 saalvglvllvarlvDaitDpivGtlidktstrwGrrrPwlllsaiilavsiillftppelsqsakfiwllvtyill 107
                                       s  ++g+++++   + +++  ++Gtl+dk ++ wGrr P+++++ai++++s++l   ++    + +++ +l+ yi+ 
  gi|518651483|ref|YP_008141003.1|  30 SSLFLGIIAFIGTALGVFIGLFFGTLSDKYNFGWGRRGPYIMAGAIFIVLSMFL--NQLL---TITLAGVLLGYIMI 101
                                       67899********************************************66544..3333...57889999999999 PP

                             MFS_2 108 rilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailafllvlilgglkserkgylifaliialLmll 184
                                       +i  ++   +y  l + +    d+R + +++  ++ +lg++++  +++ l+  +           +++++i++++++
  gi|518651483|ref|YP_008141003.1| 102 QISSNVAVGAYQPLYADI-LGEDQRGKGSGIGGIFRLLGSMMGYGITGFLIDTPYR--------QYVIVLITVVVVV 169
                                       999988888888887777.7889*************************99877776........6777778888888 PP

                             MFS_2 185 gviivvlgtkervemrkkekteqkeklslleqlkevfrn.raflillllfllaalalgvlnglllYyltyvlg.ngs 259
                                       ++++++ + k+++   k+   ++++ ++l++++ ++ +  + ++ ++++ ++++ ++  l    lY+++y+l  ++ 
  gi|518651483|ref|YP_008141003.1| 170 TALLSTNTIKKSDLIIKR---KKPGITKLFMDMFNLKNGlKNYIYVVVGSFMVFSGVIGLSFFELYFFKYILHyANP 243
                                       888888888888766444...44444554444444444313355555554444454555555569********7554 PP

                             MFS_2 260 aa..svfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaall 334
                                       a+  s+  +vv i ++ +++++ +l  ++g+k++ +  +++  + ++l+  +  ++ + fl+l  i+g+++g+++++
  gi|518651483|ref|YP_008141003.1| 244 AYyvSIAGIVVLITSAFASFVFGVLSDKIGRKKILVYITVIGGIAMILIPEF--EKFVYFLILGSIIGMSYGIFMSV 318
                                       441244555667777899***************9998888888888888777..99********************* PP

                             MFS_2 335 pwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsaf.gy 386
                                        +++ +d++   e       +g +++ + +++  a+ ++ +++gl+L ++  y
  gi|518651483|ref|YP_008141003.1| 319 SDALASDMAPGEE-------TGKYMGYYNMATGGASSVSPLIYGLILYFSsSY 364
                                       ********98888.......999************************987555 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   3.9    0.0076        23      45      90 ..      31      80 ..      13      85 .. 0.70
   2 !    7.2   3.1   0.00066         2      48      97 ..     129     178 ..      85     192 .. 0.71
   3 !   26.4  14.7     1e-09     3e-06      46     175 ..     245     373 ..     200     388 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0076
                                      ..HHHHHHHTHHHHHHHHHHHHHHHHHHT....THHHHHHHHHHHHHHHH CS
                          Sugar_tr 45 svlsglivsiflvGaiiGslfagllgdrf....GRkkslliaavlfviga 90
                                      s+ +g+i+ i  + +++ +lf+g+l+d++    GR+  +++a+++f++ +
  gi|518651483|ref|YP_008141003.1| 31 SLFLGIIAFIGTALGVFIGLFFGTLSDKYnfgwGRRGPYIMAGAIFIVLS 80
                                      4444554444433333445788899999766669********99999865 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00066
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                       sg+   + l+G+++G  ++g+l+d+  R+++++ ++v++v+ a+l+  + 
  gi|518651483|ref|YP_008141003.1| 129 SGIGGIFRLLGSMMGYGITGFLIDTPYRQYVIVLITVVVVVTALLSTNTI 178
                                       4555556689**********************************998776 PP

  == domain 3  score: 26.4 bits;  conditional E-value: 1e-09
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                        ++++   ++l+ +++ s+++g l+d++GRkk+l+    ++vig++ ++++++ +++  +++   ++G++ G++  +
  gi|518651483|ref|YP_008141003.1| 245 YYVSIAGIVVLITSAFASFVFGVLSDKIGRKKILVY---ITVIGGIAMILIPEFEKFVYFLILGSIIGMSYGIFMSV 318
                                       35566666788999******************9876...6678888888888666776666677899********** PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-..TTHHHHHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn..adgwrillg 175
                                       +  ++s +Ap +  g+ +++y++a+     v+  ++  + ++s+  + g+r+ ++
  gi|518651483|ref|YP_008141003.1| 319 SDALASDMAPGEETGKYMGYYNMATGGASSVSPLIYGLILYFSSsySLGFRYVFY 373
                                       **********************987665555554444444444445666666655 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0  21.3   3.1e-06    0.0091      33     397 ..      51     390 ..      33     392 .] 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-06
                              PUCC  33 liGfrSDtkralGw.kRvpyiwlGslalalglaiaplalivlsgkgeaeaaatwaglilaavafllvGlgvslsqTa 108
                                       ++G  SD ++  Gw +R pyi+ G++ ++l +++  l  i l g                 + ++++ ++ ++   a
  gi|518651483|ref|YP_008141003.1|  51 FFGTLSDKYN-FGWgRRGPYIMAGAIFIVLSMFLNQLLTITLAG---------------VLLGYIMIQISSNVAVGA 111
                                       58********.7775789********999988887777777666...............55679999999999999* PP

                              PUCC 109 llALladlaeeeerpkvvgllyvmlligivvsaivvgallkdytearLirvvqgvalitlvlnvlalWkievkskkk 185
                                       +  L ad+  e++r k  g+  +  l+g +++ +++g l+++ + +  i +++ v+++t +l++  + k +   k+k
  gi|518651483|ref|YP_008141003.1| 112 YQPLYADILGEDQRGKGSGIGGIFRLLGSMMGYGITGFLIDTPYRQYVIVLITVVVVVTALLSTNTIKKSDLIIKRK 188
                                       *****************************************999999998988888888888887777776655554 PP

                              PUCC 186 keekeeeepslleawlklvaekq...alaflaflllgtlaffmqdviLEpYgGevlgLtvgeTTkLtalfalGtlvG 259
                                       k   +  ++ + + + + ++ k+   ++   ++++ g++++++ ++    Y      L  ++     ++ ++ +l+ 
  gi|518651483|ref|YP_008141003.1| 189 K---PGITKLFMDMFNLKNGLKNyiyVVVGSFMVFSGVIGLSFFELYFFKY-----ILHYANPAYYVSIAGIVVLIT 257
                                       4...55555555555555533331113334456666666666666655555.....37788899999999999**** PP

                              PUCC 260 lllaglvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeragl 336
                                          a++v +   +k   +++ v +++++ +++il+ ++e+ + ++    ++G+  G+f   + +l+ d+a+ e++g 
  gi|518651483|ref|YP_008141003.1| 258 SAFASFVFGVLSDKIGRKKILVYITVIGGIAMILIPEFEKFVYFLILGSIIGMSYGIFMSVSDALASDMAPGEETGK 334
                                       9****999988888888999999999999***********8888888899*************************** PP

                              PUCC 337 alGaWGaaQaiaaglavllggalrdllkalaandaalayglVfaleavlliisilvlnklv 397
                                        +G + +a   a +++ l+ g ++     +  ++ +l++  Vf +  ++++i  ++  k++
  gi|518651483|ref|YP_008141003.1| 335 YMGYYNMATGGASSVSPLIYGLIL----YFS-SSYSLGFRYVFYAAGGFFFIGFAMFYKIL 390
                                       *****9999999988888888654....344.46889*******************99987 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 !   15.6  24.4   1.8e-06    0.0054     151     374 ..     136     359 ..      20     370 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-06
                        MFS_1_like 151 rlfGsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesklkvtksl...qvllnilkn 224
                                       rl Gs   ++ + itG+lid+ +++++  + + +v+ +  ++s+  + + +   k +k ++tk      +l+n lkn
  gi|518651483|ref|YP_008141003.1| 136 RLLGS---MMGYGITGFLIDTPYRQYVI-VLITVVVVVTALLSTNTIKKSDLIIKRKKPGITKLFmdmFNLKNGLKN 208
                                       44444...4455579999***9998643.222233333333333333444444455555555544666556777999 PP

                        MFS_1_like 225 peviifllvalilgms.wgiienFlflYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallay 300
                                         ++++  ++++ g++  +++e ++f Y+ ++  + + ++++ ++  + +    f+   l +k+G  k+l+   ++ 
  gi|518651483|ref|YP_008141003.1| 209 YIYVVVGSFMVFSGVIgLSFFELYFFKYILHYANPAYYVSIAGIVVLITSAFASFVFGVLSDKIGRKKILVYITVIG 285
                                       99999999999999764799*********9999999****9999999999999999999****************** PP

                        MFS_1_like 301 ilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqgllsglyfglGralGsliGGllw 374
                                        +  +l+  +e+++  l++  + g+s+g++ ++    +s++ap +  ++++g +++++ g+ + +  ++G +l+
  gi|518651483|ref|YP_008141003.1| 286 GIAMILIPEFEKFVYFLILGSIIGMSYGIFMSVSDALASDMAPGEETGKYMGYYNMATGGASSVSPLIYGLILY 359
                                       *********************************************************99998887777764444 PP

>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.51   1.5e+03      25      43 ..     221     237 ..     220     245 .. 0.79
   2 !   16.1   0.4   2.3e-06     0.007      23      58 ..     248     284 ..     232     286 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.51
                           DUF4325  25 dgvesigssFldeaFggli 43 
                                       +gv  ig sF++  F + i
  gi|518651483|ref|YP_008141003.1| 221 SGV--IGLSFFELYFFKYI 237
                                       555..999****9998877 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.3e-06
                           DUF4325  23 DFdg.vesigssFldeaFgglirefgeeeiskklkik 58 
                                       +  g v  i+s+F+  +Fg+l  ++g+++i   ++++
  gi|518651483|ref|YP_008141003.1| 248 SIAGiVVLITSAFASFVFGVLSDKIGRKKILVYITVI 284
                                       556656689******************9999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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):               6  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 2586.16
//
Query:       gi|518651484|ref|YP_008141004.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G0123 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.7e-40  131.8  28.3    2.6e-05   24.0   0.1    9.4  9  TPR_2         Tetratricopeptide repeat
    1.1e-35  119.9  41.9    4.2e-07   29.5   2.3    9.5  9  TPR_1         Tetratricopeptide repeat
    3.3e-27   93.9  34.3    3.8e-08   32.9   2.0    8.5  8  TPR_11        TPR repeat
    5.4e-25   87.8   0.1    5.5e-05   23.7   0.0    5.3  5  TPR_16        Tetratricopeptide repeat
    3.9e-23   79.7  37.1    0.00026   21.0   1.3    9.9 11  TPR_8         Tetratricopeptide repeat
    2.1e-18   66.6   7.0      0.001   19.5   1.9    6.2  7  TPR_19        Tetratricopeptide repeat
      4e-17   62.3  13.5    5.2e-05   23.4   0.5    7.1  6  TPR_12        Tetratricopeptide repeat
    4.3e-16   58.9   5.0    2.8e-05   24.3   0.0    4.5  4  ANAPC3        Anaphase-promoting complex, cyclosome, subunit 
      1e-12   47.1   5.9      0.038   14.0   0.1    7.3  7  TPR_7         Tetratricopeptide repeat
    1.5e-12   47.2   4.1       0.27   12.2   0.2    8.0  8  TPR_14        Tetratricopeptide repeat
    2.1e-11   43.3  14.7    0.00013   22.1   0.0    7.6  8  TPR_17        Tetratricopeptide repeat
      1e-10   41.1  11.5      0.067   13.1   0.2    5.9  5  TPR_10        Tetratricopeptide repeat
    1.9e-10   40.7   0.0     0.0058   16.8   0.0    3.7  3  TPR_9         Tetratricopeptide repeat
      9e-10   38.6  18.3       0.39   11.4   0.1    7.7  7  TPR_6         Tetratricopeptide repeat
    1.6e-09   37.1   1.6        1.7    8.2   0.0    6.1  6  SHNi-TPR      SHNi-TPR
     0.0022   18.0  24.4      0.013   15.6   1.0    6.5  7  MIT           MIT (microtubule interacting and transport) dom
     0.0035   16.3  10.3        0.9    8.4   0.1    3.9  3  NARP1         NMDA receptor-regulated protein 1
  ------ inclusion threshold ------
      0.021   14.1   0.1      0.079   12.2   0.1    2.1  1  FAT           FAT domain
      0.022   14.5   6.9        3.2    7.4   0.4    3.5  4  TPR_21        Tetratricopeptide repeat-like domain
      0.042   13.6   0.1      0.072   12.8   0.1    1.3  1  mRNA_triPase  mRNA capping enzyme, beta chain
        0.1   12.7   3.6        7.3    6.7   0.3    3.7  4  DUF3856       Domain of Unknown Function (DUF3856)
       0.12   12.2   1.0        8.5    6.3   0.2    2.9  2  Prion         Prion/Doppel alpha-helical domain
        2.7    7.8  20.9        1.6    8.5   2.1    5.4  5  DUF5113       Domain of unknown function (DUF5113)


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 !    7.5   0.1    0.0066       5.1       4      34 .]      13      43 ..      10      43 .. 0.91
   2 !   14.0   0.0   5.4e-05     0.042       1      30 [.      44      73 ..      44      76 .. 0.93
   3 !   11.5   0.2   0.00033      0.26       1      34 []      77     110 ..      77     110 .. 0.96
   4 !   10.9   0.0   0.00053      0.41       2      33 ..     112     143 ..     111     144 .. 0.92
   5 !   22.2   0.2   1.3e-07   9.8e-05       3      33 ..     147     177 ..     145     178 .. 0.95
   6 !   21.6   0.1   1.9e-07   0.00015       2      31 ..     180     209 ..     179     211 .. 0.94
   7 !   24.0   0.1   3.3e-08   2.6e-05       6      32 ..     218     244 ..     213     246 .. 0.91
   8 !   22.9   0.6   7.4e-08   5.8e-05       1      33 [.     247     279 ..     247     280 .. 0.93
   9 !   11.4   0.2   0.00035      0.27       6      33 ..     297     324 ..     293     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0066
                             TPR_2  4 lynlGlayyklgdyeeAleafekAleldPnn 34
                                      +yn ++ +++   y++A+  + +A++ld +n
  gi|518651484|ref|YP_008141004.1| 13 YYNEAMKLFNDEIYDKAILPLTRAIKLDNGN 43
                                      9**************************9875 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.4e-05
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAlel 30
                                      +e++  + ++y++ ++ ++A+e+ +kAl++
  gi|518651484|ref|YP_008141004.1| 44 PEYYEKRSWCYIYTDESKKAIEDIDKALSI 73
                                      68999***********************87 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00033
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +e++ + ++a+++ ++  eA  a++ A+  +P+n
  gi|518651484|ref|YP_008141004.1|  77 PEYYIAKAYALINDNNNSEAYTALDTAINMAPGN 110
                                       689*****************************87 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00053
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                       +++   G++++  ++y  Ale ++ A+++ P+
  gi|518651484|ref|YP_008141004.1| 112 DYHSIKGDLLLDDKKYGPALEQYNTAIKILPG 143
                                       688999***********************995 PP

  == domain 5  score: 22.2 bits;  conditional E-value: 1.3e-07
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        +y  ++ay ++ ++ eAle +++++e++Pn
  gi|518651484|ref|YP_008141004.1| 147 FHYGKAMAYSYMEKFPEALEEYNRVIEIEPN 177
                                       69****************************9 PP

  == domain 6  score: 21.6 bits;  conditional E-value: 1.9e-07
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       ea+yn+  +y+ ++++e+A+++ e+A  l+
  gi|518651484|ref|YP_008141004.1| 180 EAYYNRSIIYLDQDKFEDAIRDAERAMDLE 209
                                       89************************9986 PP

  == domain 7  score: 24.0 bits;  conditional E-value: 3.3e-08
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldP 32 
                                        +G++++++ +yeeAl+++ +A+eld 
  gi|518651484|ref|YP_008141004.1| 218 LMGNILAAMEKYEEALKYYGEAIELDS 244
                                       68***********************95 PP

  == domain 8  score: 22.9 bits;  conditional E-value: 7.4e-08
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPn 33 
                                       a a+y +G  y ++++y  A+e ++kA++l  n
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIKLVDN 279
                                       689**************************9765 PP

  == domain 9  score: 11.4 bits;  conditional E-value: 0.00035
                             TPR_2   6 nlGlayyklgdyeeAleafekAleldPn 33 
                                         ++ +y l++ ++A++ +e+A + +P+
  gi|518651484|ref|YP_008141004.1| 297 KKANDLYLLNKADDAIATYEQAFKREPG 324
                                       67999*******************9996 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.2   0.00087      0.68       4      31 ..      13      40 ..      10      43 .. 0.92
   2 !    7.6   0.0    0.0046       3.6      10      30 ..      53      73 ..      52      75 .. 0.91
   3 ?    1.9   0.6      0.28   2.2e+02       2      34 .]      78     110 ..      77     110 .. 0.88
   4 !   10.0   0.0    0.0008      0.63       3      32 ..     113     142 ..     111     143 .. 0.89
   5 !   28.3   0.2   1.3e-09     1e-06       3      34 .]     147     178 ..     145     178 .. 0.95
   6 !   17.3   0.1   3.8e-06    0.0029       2      31 ..     180     209 ..     179     211 .. 0.93
   7 !   27.8   0.5   1.9e-09   1.5e-06       7      33 ..     219     245 ..     218     246 .. 0.94
   8 !   29.5   2.3   5.4e-10   4.2e-07       1      30 [.     247     276 ..     247     280 .. 0.94
   9 !   12.3   0.2   0.00015      0.11       3      32 ..     294     323 ..     292     325 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00087
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1  4 lynlGnayfklgkydeAleyyekALeln 31
                                      +yn ++ +f+ + yd+A+    +A++l+
  gi|518651484|ref|YP_008141004.1| 13 YYNEAMKLFNDEIYDKAILPLTRAIKLD 40
                                      9**************************9 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0046
                                      HHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1 10 ayfklgkydeAleyyekALel 30
                                      +y +  + ++A+e+ +kAL++
  gi|518651484|ref|YP_008141004.1| 53 CYIYTDESKKAIEDIDKALSI 73
                                      88899999***********87 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + +  +++a+ + ++  eA  + + A+   P n
  gi|518651484|ref|YP_008141004.1|  78 EYYIAKAYALINDNNNSEAYTALDTAINMAPGN 110
                                       6688899999999*************9999976 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0008
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                        +  +G +++  +ky  Ale y+ A+++ P
  gi|518651484|ref|YP_008141004.1| 113 YHSIKGDLLLDDKKYGPALEQYNTAIKILP 142
                                       5667899999*****************988 PP

  == domain 5  score: 28.3 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnPnn 34 
                                        +y++++ay +++k+ eAle y++++e++Pn+
  gi|518651484|ref|YP_008141004.1| 147 FHYGKAMAYSYMEKFPEALEEYNRVIEIEPNF 178
                                       69****************************97 PP

  == domain 6  score: 17.3 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALeln 31 
                                       +a+yn+  +y+ + k+++A+ + e+A  l+
  gi|518651484|ref|YP_008141004.1| 180 EAYYNRSIIYLDQDKFEDAIRDAERAMDLE 209
                                       79************************9886 PP

  == domain 7  score: 27.8 bits;  conditional E-value: 1.9e-09
                                       HHHHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   7 lGnayfklgkydeAleyyekALelnPn 33 
                                       +Gn++  ++ky+eAl+yy +A+el+  
  gi|518651484|ref|YP_008141004.1| 219 MGNILAAMEKYEEALKYYGEAIELDSR 245
                                       7***********************975 PP

  == domain 8  score: 29.5 bits;  conditional E-value: 5.4e-10
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1   1 akalynlGnayfklgkydeAleyyekALel 30 
                                       a a+y +G +y ++++y  A+e y+kA++l
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIKL 276
                                       78***************************9 PP

  == domain 9  score: 12.3 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALelnP 32 
                                       a+  ++n ++ l+k d+A++ ye+A + +P
  gi|518651484|ref|YP_008141004.1| 294 AFLKKANDLYLLNKADDAIATYEQAFKREP 323
                                       677899********************9999 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.2   0.00038      0.29      10      33 ..      26      49 ..      25      50 .. 0.94
   2 !    7.2   0.1    0.0051         4       8      37 ..      91     120 ..      84     124 .. 0.84
   3 !   12.3   0.5   0.00014      0.11       1      37 [.     118     154 ..     118     158 .. 0.83
   4 !   26.5   0.9   4.7e-09   3.7e-06       6      41 ..     157     192 ..     152     193 .. 0.89
   5 ?    3.2   0.0     0.095        74       3      28 ..     188     213 ..     187     216 .. 0.87
   6 !   32.9   2.0   4.9e-11   3.8e-08       1      38 [.     220     257 ..     220     261 .. 0.95
   7 !   11.6   1.5   0.00022      0.17       9      26 ..     262     279 ..     257     282 .. 0.87
   8 !   10.9   0.0   0.00036      0.28       2      39 ..     300     337 ..     299     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00038
                            TPR_11 10 yeeAieaYkkAlkldPdnaeayyn 33
                                      y++Ai  + +A+kld+ n+e y +
  gi|518651484|ref|YP_008141004.1| 26 YDKAILPLTRAIKLDNGNPEYYEK 49
                                      99********************87 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0051
                            TPR_11   8 GkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       +++ eA +a+ +A++  P n++ ++  G++
  gi|518651484|ref|YP_008141004.1|  91 NNNSEAYTALDTAINMAPGNPDYHSIKGDL 120
                                       7899********************866665 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 0.00014
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGla 37 
                                       Gd++ +  ky  A+e+Y++A+k+ P    ++y+ + a
  gi|518651484|ref|YP_008141004.1| 118 GDLLLDDKKYGPALEQYNTAIKILPGVYQFHYGKAMA 154
                                       89999999***************88777666666555 PP

  == domain 4  score: 26.5 bits;  conditional E-value: 4.7e-09
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayynLGlayykq 41 
                                          k++eA+e+Y++ +++ P++ eayyn+  +y+ q
  gi|518651484|ref|YP_008141004.1| 157 YMEKFPEALEEYNRVIEIEPNFGEAYYNRSIIYLDQ 192
                                       56799************************9999876 PP

  == domain 5  score: 3.2 bits;  conditional E-value: 0.095
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdna 28 
                                       +y +q k+e+Ai + ++A +l +d +
  gi|518651484|ref|YP_008141004.1| 188 IYLDQDKFEDAIRDAERAMDLESDVP 213
                                       799*********99999988888766 PP

  == domain 6  score: 32.9 bits;  conditional E-value: 4.9e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       G+++ +  kyeeA++ Y +A++ld+ +a ayy +G  y
  gi|518651484|ref|YP_008141004.1| 220 GNILAAMEKYEEALKYYGEAIELDSRFAAAYYDMGIMY 257
                                       9**********************************766 PP

  == domain 7  score: 11.6 bits;  conditional E-value: 0.00022
                            TPR_11   9 kyeeAieaYkkAlkldPd 26 
                                       +y +Aie+Y kA+kl  +
  gi|518651484|ref|YP_008141004.1| 262 NYSNAIENYDKAIKLVDN 279
                                       799***********9765 PP

  == domain 8  score: 10.9 bits;  conditional E-value: 0.00036
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayy 39 
                                       + +y ++k ++Ai+ Y++A k  P ++ +  ++G++++
  gi|518651484|ref|YP_008141004.1| 300 NDLYLLNKADDAIATYEQAFKREPGSVIIPVKMGHILF 337
                                       78999**************9888877777666666665 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0       1.5   1.2e+03       9      45 ..      22      55 ..      14      75 .. 0.62
   2 !   22.9   0.0   1.3e-07    0.0001       2      66 ..      82     143 ..      81     144 .. 0.96
   3 !   23.7   0.0     7e-08   5.5e-05       1      60 [.     149     206 ..     149     214 .. 0.94
   4 !   21.8   0.1   2.9e-07   0.00022       3      62 ..     219     275 ..     218     290 .. 0.93
   5 !   11.8   0.0   0.00037      0.29       1      32 [.     296     324 ..     296     344 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 1.5
                            TPR_16  9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45
                                      +   yd+A+  l++a+k+d     ++e +  + +++ 
  gi|518651484|ref|YP_008141004.1| 22 NDEIYDKAILPLTRAIKLD---NGNPEYYEKRSWCYI 55
                                      5555777777778888888...555557777777665 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.3e-07
                            TPR_16   2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       a+a+a+++ ++  +A  al++a+ ++   P +++ +  +gd++l  + + +A+++y+ a++  p+
  gi|518651484|ref|YP_008141004.1|  82 AKAYALINDNNNSEAYTALDTAINMA---PGNPDYHSIKGDLLLDDKKYGPALEQYNTAIKILPG 143
                                       789***********************...99999*************************999886 PP

  == domain 3  score: 23.7 bits;  conditional E-value: 7e-08
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.alyraa 60 
                                       + +a+a+ +  ++++A++ ++++++     P   eA++++  ++l q  +++A+ ++ ra+
  gi|518651484|ref|YP_008141004.1| 149 YGKAMAYSYMEKFPEALEEYNRVIEIE---PNFGEAYYNRSIIYLDQDKFEDAIrDAERAM 206
                                       67899**********************...************************9988875 PP

  == domain 4  score: 21.8 bits;  conditional E-value: 2.9e-07
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +++++++  +y++A++++ +a+++d   ++ a+A++  g ++   +++  A++ y++a++
  gi|518651484|ref|YP_008141004.1| 219 MGNILAAMEKYEEALKYYGEAIELD---SRFAAAYYDMGIMYDNMKNYSNAIENYDKAIK 275
                                       6899*********************...************************99999875 PP

  == domain 5  score: 11.8 bits;  conditional E-value: 0.00037
                            TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPd 32 
                                       l++a++++ +++ ddA+a +e+a kr    P 
  gi|518651484|ref|YP_008141004.1| 296 LKKANDLYLLNKADDAIATYEQAFKRE---PG 324
                                       6899***********************...54 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1       2.8   2.2e+03      22      30 ..      12      20 ..      11      24 .. 0.61
   2 ?   -1.6   0.0       5.6   4.4e+03      17      32 ..      26      41 ..      25      43 .. 0.79
   3 !   10.6   0.2    0.0007      0.55       2      30 ..      45      73 ..      44      76 .. 0.94
   4 !    9.4   0.2    0.0017       1.4       2      33 ..      78     109 ..      77     110 .. 0.94
   5 ?    4.8   0.0     0.051        40       7      30 ..     117     140 ..     112     142 .. 0.92
   6 !   14.2   0.1   4.7e-05     0.037       2      33 ..     146     177 ..     145     178 .. 0.94
   7 !   14.3   0.1   4.5e-05     0.035       2      32 ..     180     210 ..     179     212 .. 0.94
   8 !   18.0   0.4   2.9e-06    0.0023       6      32 ..     218     244 ..     215     246 .. 0.93
   9 !   21.0   1.3   3.4e-07   0.00026       1      30 [.     247     276 ..     247     277 .. 0.96
  10 !    7.4   0.1    0.0073       5.7      13      32 ..     304     323 ..     292     325 .. 0.83
  11 ?   -2.1   0.0       8.1   6.3e+03       6      17 ..     331     342 ..     330     343 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.8
                                      HHHHHHHHH CS
                             TPR_8 22 eyyekalel 30
                                      +yy++a +l
  gi|518651484|ref|YP_008141004.1| 12 KYYNEAMKL 20
                                      566666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.6
                                      HHHHHHHHHHHHHHHH CS
                             TPR_8 17 yeeAkeyyekaleldp 32
                                      y++A+  + +a++ld 
  gi|518651484|ref|YP_008141004.1| 26 YDKAILPLTRAIKLDN 41
                                      6777777889999996 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0007
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekalel 30
                                      e+y + +++y+ + + ++A+e + kal++
  gi|518651484|ref|YP_008141004.1| 45 EYYEKRSWCYIYTDESKKAIEDIDKALSI 73
                                      789999*********************97 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0017
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       e+y  +++++++ ++  eA  ++  a+ ++p 
  gi|518651484|ref|YP_008141004.1|  78 EYYIAKAYALINDNNNSEAYTALDTAINMAPG 109
                                       79***************************996 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.051
                                       HHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkeyyekalel 30 
                                       +g+++l+ ++y  A e y+ a+++
  gi|518651484|ref|YP_008141004.1| 117 KGDLLLDDKKYGPALEQYNTAIKI 140
                                       89********************98 PP

  == domain 6  score: 14.2 bits;  conditional E-value: 4.7e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       + +y ++++y+ ++++ eA e y++++e++p+
  gi|518651484|ref|YP_008141004.1| 146 QFHYGKAMAYSYMEKFPEALEEYNRVIEIEPN 177
                                       67899**************************8 PP

  == domain 7  score: 14.3 bits;  conditional E-value: 4.5e-05
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldp 32 
                                       eayyn + iyl++ ++e A+   e+a +l+ 
  gi|518651484|ref|YP_008141004.1| 180 EAYYNRSIIYLDQDKFEDAIRDAERAMDLES 210
                                       89************************99976 PP

  == domain 8  score: 18.0 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   6 nlgsiylklgdyeeAkeyyekaleldp 32 
                                       ++g+i+  +++yeeA +yy +a+eld 
  gi|518651484|ref|YP_008141004.1| 218 LMGNILAAMEKYEEALKYYGEAIELDS 244
                                       579**********************96 PP

  == domain 9  score: 21.0 bits;  conditional E-value: 3.4e-07
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekalel 30 
                                       a ayy +g  y+++++y +A+e y ka++l
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIKL 276
                                       579*************************97 PP

  == domain 10  score: 7.4 bits;  conditional E-value: 0.0073
                                       HTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  13 klgdyeeAkeyyekaleldp 32 
                                        l++ + A+++ye+a + +p
  gi|518651484|ref|YP_008141004.1| 304 LLNKADDAIATYEQAFKREP 323
                                       58999***********9988 PP

  == domain 11  score: -2.1 bits;  conditional E-value: 8.1
                                       HHHHHHHHTT-H CS
                             TPR_8   6 nlgsiylklgdy 17 
                                       ++g+i+++l +y
  gi|518651484|ref|YP_008141004.1| 331 KMGHILFELARY 342
                                       689***999887 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.54   4.2e+02       7      62 ..      26      80 ..      20      85 .. 0.80
   2 !   13.7   0.0   8.5e-05     0.066      27      67 ..      79     119 ..      59     120 .. 0.82
   3 ?    0.9   0.0      0.87   6.8e+02       1      35 [.     121     155 ..     121     158 .. 0.82
   4 !   17.9   0.0   4.2e-06    0.0033       4      46 ..     158     200 ..     156     222 .. 0.86
   5 !   19.5   1.9   1.3e-06     0.001       1      51 [.     223     273 ..     223     282 .. 0.91
   6 ?    0.2   0.0       1.4   1.1e+03       6      27 ..     269     292 ..     265     299 .. 0.66
   7 !    9.9   0.0    0.0013         1       6      51 ..     307     352 ..     302     354 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.54
                            TPR_19  7 yaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      y+ A+  l++a++ d++n+e       +++ + + ++A++ +d+++   ++ ++y 
  gi|518651484|ref|YP_008141004.1| 26 YDKAILPLTRAIKLDNGNPEYYEKRSWCYIYTDESKKAIEDIDKALSIVKK-PEYY 80
                                      677777789999999999999888899999999999999888888887777.6555 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.5e-05
                            TPR_19  27 arllLAeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                         ++ A al++ ++  eA  +Ld++ +++p +++y+s ++ 
  gi|518651484|ref|YP_008141004.1|  79 YYIAKAYALINDNNNSEAYTALDTAINMAPGNPDYHSIKGD 119
                                       4455699******************************9875 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.87
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeal 35 
                                       ll++++y  Al+ +  a++  p+     ++ A a+
  gi|518651484|ref|YP_008141004.1| 121 LLDDKKYGPALEQYNTAIKILPGVYQFHYGKAMAY 155
                                       68888999999999999999998888888877776 PP

  == domain 4  score: 17.9 bits;  conditional E-value: 4.2e-06
                            TPR_19   4 egdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       ++++ eAl+ + ++++ +p+ +ea ++  +++l +  +++A++
  gi|518651484|ref|YP_008141004.1| 158 MEKFPEALEEYNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAIR 200
                                       67899************************************87 PP

  == domain 5  score: 19.5 bits;  conditional E-value: 1.3e-06
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       l a+++y+eAl+++ +a++ d   a+a +++ + + +++++  A++  d++
  gi|518651484|ref|YP_008141004.1| 223 LAAMEKYEEALKYYGEAIELDSRFAAAYYDMGIMYDNMKNYSNAIENYDKA 273
                                       5799****************************************9977766 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 1.4
                            TPR_19   6 dyaeAlalleqalqe..dpknaea 27 
                                       +y+ A++l  + ++   +p na++
  gi|518651484|ref|YP_008141004.1| 269 NYDKAIKLVDNYYEGtkSPSNAAI 292
                                       677777777776643336666665 PP

  == domain 7  score: 9.9 bits;  conditional E-value: 0.0013
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdal 51 
                                       + ++A+a +eqa++ +p++  +   +  +l++l ++ +   lL+++
  gi|518651484|ref|YP_008141004.1| 307 KADDAIATYEQAFKREPGSVIIPVKMGHILFELARYSDVVSLLSPI 352
                                       689*******************************999988888765 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.37   2.9e+02      48      76 ..      47      75 ..      26      76 .. 0.77
   2 ?    1.0   0.0       0.7   5.5e+02      15      35 ..      56      76 ..      53      89 .. 0.63
   3 ?    3.0   0.0      0.16   1.3e+02      52      75 ..     118     141 ..      84     143 .. 0.90
   4 !    8.5   0.0    0.0031       2.4      51      74 ..     151     174 ..     146     177 .. 0.78
   5 !   17.0   0.2   7.1e-06    0.0055       8      35 ..     218     245 ..     211     247 .. 0.87
   6 !   23.4   0.5   6.7e-08   5.2e-05       3      73 ..     247     320 ..     245     321 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.37
                            TPR_12 48 lrnLgrlyralgryeeAlelleealaiae 76
                                      +   +++y ++++ ++A+e   +al i +
  gi|518651484|ref|YP_008141004.1| 47 YEKRSWCYIYTDESKKAIEDIDKALSIVK 75
                                      66677888888888888888888887765 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.7
                            TPR_12 15 rlgrydeAlellekaleiarr 35
                                      +  +  +A+e  +kal i+++
  gi|518651484|ref|YP_008141004.1| 56 YTDESKKAIEDIDKALSIVKK 76
                                      555667899999999999943 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.16
                            TPR_12  52 grlyralgryeeAlelleealaia 75 
                                       g+l++  ++y  Ale ++ a++i+
  gi|518651484|ref|YP_008141004.1| 118 GDLLLDDKKYGPALEQYNTAIKIL 141
                                       788889999**********99986 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.0031
                            TPR_12  51 LgrlyralgryeeAlelleealai 74 
                                        +++y++++++ eAle ++++++i
  gi|518651484|ref|YP_008141004.1| 151 KAMAYSYMEKFPEALEEYNRVIEI 174
                                       577888888888888888888876 PP

  == domain 5  score: 17.0 bits;  conditional E-value: 7.1e-06
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarr 35 
                                        ++++l+++++y+eAl+++ +a+e+ +r
  gi|518651484|ref|YP_008141004.1| 218 LMGNILAAMEKYEEALKYYGEAIELDSR 245
                                       5899999************999998765 PP

  == domain 6  score: 23.4 bits;  conditional E-value: 6.7e-08
                            TPR_12   3 atalnnlaavlrrlgrydeAlellekaleiarrl.lGpdhpltat..tlrnLgrlyralgryeeAlelleeala 73 
                                       a+a++ ++ ++  +++y  A+e+++ka+ ++ ++  G+++p  a+  +    +  +++l++ ++A++ +e+a +
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIKLVDNYyEGTKSPSNAAipAFLKKANDLYLLNKADDAIATYEQAFK 320
                                       78999**************************77747777766555227888899999**************975 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.6   0.00049      0.38       5      80 ..      26     101 ..      22     103 .. 0.92
   2 !   12.4   0.1   0.00018      0.14       3      78 ..      91     167 ..      89     171 .. 0.93
   3 !   15.3   0.0   2.2e-05     0.017       8      81 ..     164     238 ..     159     239 .. 0.88
   4 !   24.3   0.0   3.6e-08   2.8e-05       3      80 ..     268     350 ..     259     352 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00049
                                       HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHHHH- CS
                            ANAPC3   5 yknAiflaerllaaetespedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAiaaLe 80 
                                       y++Ai+ + r+ + ++ +pe     + c+  + + k+A+e ++ka +  k +++ + +A +l+  ++  eA++aL+
  gi|518651484|ref|YP_008141004.1|  26 YDKAILPLTRAIKLDNGNPEYYEKRSWCYIYTDESKKAIEDIDKALSIVKKPEYYIAKAYALINDNNNSEAYTALD 101
                                       89999999****9999999998889********************99999999*999*****************97 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00018
                                       T-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3   3 nnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       nn  +A+  ++ + ++ + +p+    ++  l+ +++y  A+e +++a k+ +   + +y +A ++  ++k+ eA+  
  gi|518651484|ref|YP_008141004.1|  91 NNNSEAYTALDTAINMAPGNPDYHSIKGDLLLDDKKYGPALEQYNTAiKILPGVYQFHYGKAMAYSYMEKFPEALEE 167
                                       67789999999999999*********************************************************975 PP

  == domain 3  score: 15.3 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3   8 AiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaLek 81 
                                       A+  ++r+ + e++  e+ y  +  ++ + +++ A++ +++a +l+s  +    l++  l +++kyeeA++ +++
  gi|518651484|ref|YP_008141004.1| 164 ALEEYNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAIRDAERAmDLESDVPDNFDLMGNILAAMEKYEEALKYYGE 238
                                       5666677777778888888888999*********************************************99886 PP

  == domain 4  score: 24.3 bits;  conditional E-value: 3.6e-08
                                       T-HHHHHHHHHHHH.HHH--HHH....HHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HH CS
                            ANAPC3   3 nnyknAiflaerllaaetesped....ayll.AlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkye 73 
                                       +ny++Ai l + ++   t+sp++    a+l+ A  lyl+++ + A+  +++a k ++ s  + + +++ l++L +y 
  gi|518651484|ref|YP_008141004.1| 268 ENYDKAIKLVDNYY-EGTKSPSNaaipAFLKkANDLYLLNKADDAIATYEQAfKREPGSVIIPVKMGHILFELARYS 343
                                       58999999999999.77777777678889967********************************************* PP

                                       HHHHHH- CS
                            ANAPC3  74 eAiaaLe 80 
                                       + +++L+
  gi|518651484|ref|YP_008141004.1| 344 DVVSLLS 350
                                       *999886 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.5   4.2e+03      13      32 ..      58      77 ..      52      78 .. 0.71
   2 ?    1.1   0.0      0.63   4.9e+02       6      29 ..     152     175 ..     149     180 .. 0.82
   3 !    8.6   0.0    0.0026         2       1      32 [.     181     212 ..     181     215 .. 0.85
   4 !   14.0   0.1   4.9e-05     0.038       4      30 ..     218     244 ..     216     247 .. 0.87
   5 !   10.2   0.0    0.0008      0.62       1      29 [.     249     277 ..     249     291 .. 0.82
   6 !    7.4   0.0    0.0065       5.1      13      34 ..     306     325 ..     301     327 .. 0.87
   7 ?   -0.3   0.0       1.8   1.4e+03       5      21 ..     332     348 ..     330     349 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.5
                             TPR_7 13 GdyeeAielyeqsLaltkdp 32
                                       + ++Aie   ++L + k p
  gi|518651484|ref|YP_008141004.1| 58 DESKKAIEDIDKALSIVKKP 77
                                      56789999888877776665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.63
                             TPR_7   6 arlysrlGdyeeAielyeqsLalt 29 
                                       a +ys + ++ eA+e y ++++++
  gi|518651484|ref|YP_008141004.1| 152 AMAYSYMEKFPEALEEYNRVIEIE 175
                                       568999*********999966654 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.0026
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       a++n   +y ++ ++e+Ai+  e+++ l++d 
  gi|518651484|ref|YP_008141004.1| 181 AYYNRSIIYLDQDKFEDAIRDAERAMDLESDV 212
                                       6888889*****************77777775 PP

  == domain 4  score: 14.0 bits;  conditional E-value: 4.9e-05
                             TPR_7   4 nLarlysrlGdyeeAielyeqsLaltk 30 
                                        ++++  ++ +yeeA+++y ++++l++
  gi|518651484|ref|YP_008141004.1| 218 LMGNILAAMEKYEEALKYYGEAIELDS 244
                                       79*******************777765 PP

  == domain 5  score: 10.2 bits;  conditional E-value: 0.0008
                             TPR_7   1 aLlnLarlysrlGdyeeAielyeqsLalt 29 
                                       a++ ++ +y ++ +y++Aie y +++ l 
  gi|518651484|ref|YP_008141004.1| 249 AYYDMGIMYDNMKNYSNAIENYDKAIKLV 277
                                       7899********************66544 PP

  == domain 6  score: 7.4 bits;  conditional E-value: 0.0065
                             TPR_7  13 GdyeeAielyeqsLaltkdped 34 
                                       ++ ++Ai  yeq  a+ ++p+ 
  gi|518651484|ref|YP_008141004.1| 306 NKADDAIATYEQ--AFKREPGS 325
                                       6779********..***99986 PP

  == domain 7  score: -0.3 bits;  conditional E-value: 1.8
                             TPR_7   5 LarlysrlGdyeeAiel 21 
                                       ++++ ++l +y++ ++l
  gi|518651484|ref|YP_008141004.1| 332 MGHILFELARYSDVVSL 348
                                       899*********99987 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       2.4   1.9e+03      17      38 ..      26      47 ..      16      51 .. 0.86
   2 ?    6.4   0.0     0.024        19       2      38 ..      78     114 ..      77     120 .. 0.88
   3 ?    1.5   0.0      0.92   7.2e+02       8      36 ..     118     146 ..     111     152 .. 0.79
   4 ?    7.3   0.0     0.013        10       8      39 ..     152     183 ..     146     186 .. 0.85
   5 ?    5.9   0.1     0.035        27       2      30 ..     180     208 ..     179     218 .. 0.83
   6 !   12.2   0.2   0.00035      0.27       5      42 ..     217     254 ..     213     256 .. 0.90
   7 ?    5.5   0.0     0.047        37       2      30 ..     248     276 ..     247     296 .. 0.87
   8 ?    7.2   0.0     0.014        11       5      34 ..     296     325 ..     292     341 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 2.4
                            TPR_14 17 pdeAiallrralalaPddaeaw 38
                                      +d+Ai  l ra++l+ +++e++
  gi|518651484|ref|YP_008141004.1| 26 YDKAILPLTRAIKLDNGNPEYY 47
                                      689999999****999999887 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.024
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeaw 38 
                                       e + a a al +  +  eA ++l+ a+  aP++++++
  gi|518651484|ref|YP_008141004.1|  78 EYYIAKAYALINDNNNSEAYTALDTAINMAPGNPDYH 114
                                       667788999**********************999875 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.92
                            TPR_14   8 aeallalGdpdeAiallrralalaPddae 36 
                                       +++ll   ++  A++ ++ a++  P+  +
  gi|518651484|ref|YP_008141004.1| 118 GDLLLDDKKYGPALEQYNTAIKILPGVYQ 146
                                       567888889999**********9998555 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.013
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeawl 39 
                                       a a+   +++ eA++ ++r+++  P++ ea++
  gi|518651484|ref|YP_008141004.1| 152 AMAYSYMEKFPEALEEYNRVIEIEPNFGEAYY 183
                                       56777788999***************999986 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.035
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       ea++ +  ++l ++++++Ai+ ++ra +l
  gi|518651484|ref|YP_008141004.1| 180 EAYYNRSIIYLDQDKFEDAIRDAERAMDL 208
                                       68999999****************99554 PP

  == domain 6  score: 12.2 bits;  conditional E-value: 0.00035
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                        +++ +l+a ++++eA++++ +a++l+  +a+a++ ++
  gi|518651484|ref|YP_008141004.1| 217 DLMGNILAAMEKYEEALKYYGEAIELDSRFAAAYYDMG 254
                                       57899**************************9998776 PP

  == domain 7  score: 5.5 bits;  conditional E-value: 0.047
                            TPR_14   2 eallalaeallalGdpdeAiallrralal 30 
                                       +a+++++  + +  ++  Ai+ +++a++l
  gi|518651484|ref|YP_008141004.1| 248 AAYYDMGIMYDNMKNYSNAIENYDKAIKL 276
                                       799******************99999985 PP

  == domain 8  score: 7.2 bits;  conditional E-value: 0.014
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPdd 34 
                                       l+ a  l+ l + d+Aia +++a ++ P++
  gi|518651484|ref|YP_008141004.1| 296 LKKANDLYLLNKADDAIATYEQAFKREPGS 325
                                       6667778888999**************987 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0     0.033        26       3      34 .]      34      65 ..      33      65 .. 0.91
   2 ?    1.2   0.2      0.78   6.1e+02       5      19 ..      86     100 ..      85     100 .. 0.84
   3 ?    2.0   0.0      0.43   3.4e+02       3      33 ..     101     138 ..      99     139 .. 0.77
   4 ?    0.8   0.0         1   7.9e+02       2      33 ..     134     165 ..     133     166 .. 0.85
   5 !   22.1   0.0   1.7e-07   0.00013       2      33 ..     168     199 ..     167     200 .. 0.95
   6 ?    2.8   0.0      0.25   1.9e+02       3      33 ..     203     233 ..     201     234 .. 0.86
   7 !   11.5   0.7    0.0004      0.31       1      33 [.     235     267 ..     235     276 .. 0.90
   8 ?   -2.2   0.0       9.4   7.3e+03       1      13 [.     314     326 ..     314     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.033
                            TPR_17  3 lkaleldPnnadaynnLAelllknGdlmtArq 34
                                      ++a++ld  n++ y  + +++    ++++A++
  gi|518651484|ref|YP_008141004.1| 34 TRAIKLDNGNPEYYEKRSWCYIYTDESKKAIE 65
                                      79*******************99999998875 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.78
                            TPR_17   5 aleldPnnadaynnL 19 
                                       al +d nn++ay+ L
  gi|518651484|ref|YP_008141004.1|  86 ALINDNNNSEAYTAL 100
                                       677899******876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.43
                            TPR_17   3 lkaleldPnnadaynnLAelll.......knGdlmtAr 33 
                                         a+   P n+d +  ++ lll        + ++ tA+
  gi|518651484|ref|YP_008141004.1| 101 DTAINMAPGNPDYHSIKGDLLLddkkygpALEQYNTAI 138
                                       5799999*************996666666666666665 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 1
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y  a+++ P    +++ +A +++   ++ +A+
  gi|518651484|ref|YP_008141004.1| 134 YNTAIKILPGVYQFHYGKAMAYSYMEKFPEAL 165
                                       8899999999999********99887777775 PP

  == domain 5  score: 22.1 bits;  conditional E-value: 1.7e-07
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y +++e++Pn  +ay+n+  ++l + ++++A+
  gi|518651484|ref|YP_008141004.1| 168 YNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAI 199
                                       99**************************9997 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.25
                            TPR_17   3 lkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       ++a++l+ + +d + +++++l+   ++++A+
  gi|518651484|ref|YP_008141004.1| 203 ERAMDLESDVPDNFDLMGNILAAMEKYEEAL 233
                                       7889999888999999999999999999997 PP

  == domain 7  score: 11.5 bits;  conditional E-value: 0.0004
                            TPR_17   1 lylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +y +a+eld   a ay+ ++  + + +++  A+
  gi|518651484|ref|YP_008141004.1| 235 YYGEAIELDSRFAAAYYDMGIMYDNMKNYSNAI 267
                                       5889********************999888776 PP

  == domain 8  score: -2.2 bits;  conditional E-value: 9.4
                            TPR_17   1 lylkaleldPnna 13 
                                       +y++a +++P ++
  gi|518651484|ref|YP_008141004.1| 314 TYEQAFKREPGSV 326
                                       5999999999876 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0     0.008       6.2       9      31 ..     152     174 ..     151     175 .. 0.95
   2 !   10.6   0.1   0.00053      0.41       4      30 ..     181     207 ..     179     209 .. 0.92
   3 !   13.1   0.2   8.6e-05     0.067       8      31 ..     219     242 ..     217     244 .. 0.94
   4 !   11.2   0.2   0.00035      0.27       2      30 ..     247     275 ..     246     276 .. 0.95
   5 ?    2.1   0.0      0.24   1.9e+02      26      38 ..     309     321 ..     299     323 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.008
                            TPR_10   9 analrqrgrydeAealleealai 31 
                                       a+a++ + ++ eA++ + ++++i
  gi|518651484|ref|YP_008141004.1| 152 AMAYSYMEKFPEALEEYNRVIEI 174
                                       89****************99987 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00053
                            TPR_10   4 slnNLanalrqrgrydeAealleeala 30 
                                       ++ N ++++ ++ ++++A +++e+a++
  gi|518651484|ref|YP_008141004.1| 181 AYYNRSIIYLDQDKFEDAIRDAERAMD 207
                                       78899********************86 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 8.6e-05
                            TPR_10   8 LanalrqrgrydeAealleealai 31 
                                       ++n+l ++ +y+eA++++ ea+++
  gi|518651484|ref|YP_008141004.1| 219 MGNILAAMEKYEEALKYYGEAIEL 242
                                       69*******************985 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00035
                            TPR_10   2 AsslnNLanalrqrgrydeAealleeala 30 
                                       A+++ ++++++ ++++y  A + +++a+ 
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIK 275
                                       899************************96 PP

  == domain 5  score: 2.1 bits;  conditional E-value: 0.24
                            TPR_10  26 eealairrrllGp 38 
                                       ++a+a++++++ +
  gi|518651484|ref|YP_008141004.1| 309 DDAIATYEQAFKR 321
                                       5788888887765 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.032        25       6      69 ..      55     117 ..      50     121 .. 0.81
   2 !   16.8   0.0   7.4e-06    0.0058       9      64 ..     159     214 ..     151     219 .. 0.92
   3 !   14.4   0.0     4e-05     0.031       3      57 ..     221     275 ..     219     291 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.032
                             TPR_9   6 ireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapdaeair 69 
                                       i  +++ +a++ ++  l +    pe +   + +l   ++ s+A  +L++++ +ap +pd + i+
  gi|518651484|ref|YP_008141004.1|  55 IYTDESKKAIEDIDKALSIVK-KPEYYIAKAYALINDNNNSEAYTALDTAINMAPGNPDYHSIK 117
                                       556667777777777777754.457788899999999999******************999887 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 7.4e-06
                             TPR_9   9 edweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalapdapd 64 
                                       e++++al+ ++r++ + P+  e ++ R +++  ++ ++ A++d e++++l+ d pd
  gi|518651484|ref|YP_008141004.1| 159 EKFPEALEEYNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAIRDAERAMDLESDVPD 214
                                       8999********************************************99987665 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 4e-05
                             TPR_9   3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeayla 57 
                                       +i++  e++e+al+++   + l+++ +  ++d G+++  + ++s A++  + ++ 
  gi|518651484|ref|YP_008141004.1| 221 NILAAMEKYEEALKYYGEAIELDSRFAAAYYDMGIMYDNMKNYSNAIENYDKAIK 275
                                       6788899*****************************************9998875 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       2.3   1.8e+03       6      22 ..      50      66 ..      47      73 .. 0.77
   2 ?    4.6   0.1     0.074        58       4      31 ..      79     108 ..      78     110 .. 0.82
   3 !    8.8   0.0    0.0035       2.7       4      32 ..     149     177 ..     147     177 .. 0.91
   4 ?    4.3   0.2     0.093        72       1      26 [.     180     205 ..     180     209 .. 0.89
   5 ?    5.0   0.1     0.055        43       6      28 ..     219     241 ..     214     243 .. 0.79
   6 !   11.4   0.1    0.0005      0.39       2      28 ..     249     275 ..     248     279 .. 0.94
   7 !   10.4   0.1    0.0011      0.84       2      33 .]     294     325 ..     293     325 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlea 22
                                      + ++y+ ++++ kA+e 
  gi|518651484|ref|YP_008141004.1| 50 RSWCYIYTDESKKAIED 66
                                      67999999899999985 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.074
                                       HHHHHHHHH.H.HHHHHHHHHHHHHHHH-T CS
                             TPR_6   4 yklalsyrk.l.gdtdkAlealerlikeYP 31 
                                       y++a++y     ++ ++A +al+  i+  P
  gi|518651484|ref|YP_008141004.1|  79 YYIAKAYALiNdNNNSEAYTALDTAINMAP 108
                                       9999999995556888*******9998776 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0035
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   4 yklalsyrklgdtdkAlealerlikeYPd 32 
                                       y  a++y  + +  +Ale ++r+i+  P+
  gi|518651484|ref|YP_008141004.1| 149 YGKAMAYSYMEKFPEALEEYNRVIEIEPN 177
                                       778999**988**************9997 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.093
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   1 dAlyklalsyrklgdtdkAlealerl 26 
                                       +A+y++   y+ +++ ++A++  er 
  gi|518651484|ref|YP_008141004.1| 180 EAYYNRSIIYLDQDKFEDAIRDAERA 205
                                       79***********9*****9988875 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       ++  + ++ ++++Al+++ + i+
  gi|518651484|ref|YP_008141004.1| 219 MGNILAAMEKYEEALKYYGEAIE 241
                                       77788887799999999988876 PP

  == domain 6  score: 11.4 bits;  conditional E-value: 0.0005
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlik 28 
                                       A+y ++  y +++++++A+e +++ ik
  gi|518651484|ref|YP_008141004.1| 249 AYYDMGIMYDNMKNYSNAIENYDKAIK 275
                                       9***********************997 PP

  == domain 7  score: 10.4 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
                             TPR_6   2 AlyklalsyrklgdtdkAlealerlikeYPdS 33 
                                       A++k a  ++ l+++d+A++++e+  k+ P+S
  gi|518651484|ref|YP_008141004.1| 294 AFLKKANDLYLLNKADDAIATYEQAFKREPGS 325
                                       7788887777788***************9998 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.87   6.8e+02      20      30 ..      63      73 ..      61      74 .. 0.90
   2 ?    0.2   0.0      0.68   5.3e+02      12      35 ..     122     145 ..     118     148 .. 0.71
   3 !    7.0   0.0    0.0052       4.1      15      29 ..     159     173 ..     158     175 .. 0.86
   4 !    6.6   0.1    0.0068       5.3      12      30 ..     190     208 ..     188     209 .. 0.87
   5 !    6.8   0.0    0.0056       4.4       4      30 ..     216     242 ..     213     242 .. 0.90
   6 !    8.2   0.0    0.0021       1.7      16      36 ..     262     282 ..     261     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.87
                          SHNi-TPR 20 AveDlrkaLeL 30
                                      A+eD +kaL +
  gi|518651484|ref|YP_008141004.1| 63 AIEDIDKALSI 73
                                      9********87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.68
                          SHNi-TPR  12 lEnenFpqAveDlrkaLeLreqll 35 
                                       l + ++  A+e +++a+++   ++
  gi|518651484|ref|YP_008141004.1| 122 LDDKKYGPALEQYNTAIKILPGVY 145
                                       556688889999999999875555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0052
                          SHNi-TPR  15 enFpqAveDlrkaLe 29 
                                       e+Fp+A+e++++ +e
  gi|518651484|ref|YP_008141004.1| 159 EKFPEALEEYNRVIE 173
                                       9*********98555 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0068
                          SHNi-TPR  12 lEnenFpqAveDlrkaLeL 30 
                                       l +++F++A+ D ++a +L
  gi|518651484|ref|YP_008141004.1| 190 LDQDKFEDAIRDAERAMDL 208
                                       5689***********9876 PP

  == domain 5  score: 6.8 bits;  conditional E-value: 0.0056
                          SHNi-TPR   4 ydlLGEislEnenFpqAveDlrkaLeL 30 
                                       +dl G+i    e++++A++ + +a+eL
  gi|518651484|ref|YP_008141004.1| 216 FDLMGNILAAMEKYEEALKYYGEAIEL 242
                                       78999999999*************998 PP

  == domain 6  score: 8.2 bits;  conditional E-value: 0.0021
                          SHNi-TPR  16 nFpqAveDlrkaLeLreqllp 36 
                                       n++ A+e+++ka++L  ++++
  gi|518651484|ref|YP_008141004.1| 262 NYSNAIENYDKAIKLVDNYYE 282
                                       9**************888887 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.5   1.2e+03       2      17 ..      27      42 ..      26      48 .. 0.83
   2 ?   -2.1   0.0       5.5   4.3e+03       1      10 [.      67      76 ..      61      77 .. 0.74
   3 ?    3.6   0.6     0.088        69      17      34 ..     124     141 ..     121     168 .. 0.86
   4 ?   -0.3   0.1       1.4   1.1e+03      10      29 ..     151     170 ..     147     174 .. 0.78
   5 !    9.1   1.1    0.0017       1.3      18      33 ..     227     242 ..     223     242 .. 0.91
   6 !   15.6   1.0   1.6e-05     0.013       6      35 ..     249     278 ..     246     300 .. 0.83
   7 ?   -1.6   0.1       3.9     3e+03      18      30 ..     306     318 ..     290     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.5
                               MIT  2 dkAlelvkkAveeDna 17
                                      dkA+  +++A+++Dn 
  gi|518651484|ref|YP_008141004.1| 27 DKAILPLTRAIKLDNG 42
                                      7888889999999996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.5
                               MIT  1 ldkAlelvkk 10
                                      +dkAl++vkk
  gi|518651484|ref|YP_008141004.1| 67 IDKALSIVKK 76
                                      5778887775 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.088
                               MIT  17 agnyeeAlelYkealelL 34 
                                        ++y  Ale Y +a+++L
  gi|518651484|ref|YP_008141004.1| 124 DKKYGPALEQYNTAIKIL 141
                                       58999**********998 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 1.4
                               MIT  10 kAveeDnagnyeeAlelYke 29 
                                       kA+ +   ++++eAle Y  
  gi|518651484|ref|YP_008141004.1| 151 KAMAYSYMEKFPEALEEYNR 170
                                       56666667899*****9976 PP

  == domain 5  score: 9.1 bits;  conditional E-value: 0.0017
                               MIT  18 gnyeeAlelYkealel 33 
                                       ++yeeAl++Y ea+el
  gi|518651484|ref|YP_008141004.1| 227 EKYEEALKYYGEAIEL 242
                                       69************96 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 1.6e-05
                               MIT   6 elvkkAveeDnagnyeeAlelYkealelLl 35 
                                       ++  + + +Dn +ny+ A+e+Y +a++l  
  gi|518651484|ref|YP_008141004.1| 249 AYYDMGIMYDNMKNYSNAIENYDKAIKLVD 278
                                       55667899******************9865 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 3.9
                               MIT  18 gnyeeAlelYkea 30 
                                       ++ ++A+  Y++a
  gi|518651484|ref|YP_008141004.1| 306 NKADDAIATYEQA 318
                                       6788899999988 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.4    0.0025         2     195     236 ..      78     121 ..      58     140 .. 0.79
   2 !    8.4   0.1    0.0012       0.9     196     255 ..     149     208 ..     132     216 .. 0.89
   3 ?    4.1   0.9     0.023        18     189     223 ..     244     278 ..     217     286 .. 0.55

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHT-SH..HHHHHHHHHHHH-TT-HHHHHHHHHHH CS
                             NARP1 195 lyflAqhydklgsre..kAleyidkaiehtptlvelyltKaril 236
                                        y++A+ y  +++ +  +A + +d+ai+  p   +++ +K+ +l
  gi|518651484|ref|YP_008141004.1|  78 EYYIAKAYALINDNNnsEAYTALDTAINMAPGNPDYHSIKGDLL 121
                                       69999999999998777899999999999999999999999876 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHC CS
                             NARP1 196 yflAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearkl 255
                                       y  A+ y ++++  +Ale  ++ ie +p++ e y++++ i+  +  +++A++ +e+a  l
  gi|518651484|ref|YP_008141004.1| 149 YGKAMAYSYMEKFPEALEEYNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAIRDAERAMDL 208
                                       456999********************************************9999888766 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.023
                                       SHHHHHHHHHHHHHHHHT-SHHHHHHHHHHHHH-T CS
                             NARP1 189 sallwvlyflAqhydklgsrekAleyidkaiehtp 223
                                       s +  ++y +   yd+++++++A+e  dkai+  +
  gi|518651484|ref|YP_008141004.1| 244 SRFAAAYYDMGIMYDNMKNYSNAIENYDKAIKLVD 278
                                       33333455556666666666666666666666554 PP

>> FAT  FAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1    0.0001     0.079     232     306 ..     200     267 ..      57     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                                       ...........HHHHCCCTCCCCCCCCCCCT.S...-SSCCHHHHCCHHCTCCCHSTTCCCCHHHHHCCHHHHHH CS
                               FAT 232 keptnleeftkllarcylkkGewqealqkldwseekieeilqsysaateidpswykawhtwalfnfevvskeeeq 306
                                       ++++  ++++  +  ++ + G  ++a++k        ee+l++y +a e+d + + a++ ++ +++++ +     
  gi|518651484|ref|YP_008141004.1| 200 RDAERAMDLESDVPDNFDLMGNILAAMEK-------YEEALKYYGEAIELDSRFAAAYYDMGIMYDNMKNYSNAI 267
                                       66777777777777889999999999999.......9******************************99987444 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0052       4.1     123     174 ..      87     139 ..      59     145 .. 0.84
   2 ?    7.3   0.5    0.0046       3.6     122     175 ..     188     242 ..     186     253 .. 0.79
   3 ?    7.4   0.4    0.0041       3.2     121     175 ..     221     276 ..     216     286 .. 0.77
   4 ?    0.9   0.1      0.41   3.2e+02     156     179 ..     303     325 ..     265     336 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0052
                            TPR_21 123 llaekkydeAlktLeakke.eafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       l+++++  eA ++L+++ + +  +  +  ++GD+l+  +k   A + Y+ A++
  gi|518651484|ref|YP_008141004.1|  87 LINDNNNSEAYTALDTAINmAPGNPDYHSIKGDLLLDDKKYGPALEQYNTAIK 139
                                       5666777888888866554145678999***********************97 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0046
                            TPR_21 122 vllaekkydeAlktLeakkeeafaa.lvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       ++l+++k+++A++  e++ + + ++    +l G+il+a++k +eA + Y +A++ 
  gi|518651484|ref|YP_008141004.1| 188 IYLDQDKFEDAIRDAERAMDLESDVpDNFDLMGNILAAMEKYEEALKYYGEAIEL 242
                                       577888888888887777665555414569**********************975 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.0041
                            TPR_21 121 rvllaekkydeAlktL..eakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaa 175
                                       ++l+a++ky+eAlk    + + ++ faa++ ++ G ++ ++++  +A + Y++A++ 
  gi|518651484|ref|YP_008141004.1| 221 NILAAMEKYEEALKYYgeAIELDSRFAAAYYDM-GIMYDNMKNYSNAIENYDKAIKL 276
                                       678888999999998843334578888888887.88888888888888888888875 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.41
                            TPR_21 156 lvaqgkldeAraaYqaAlaaleek 179
                                       +   +k d+A a Y++A+++   +
  gi|518651484|ref|YP_008141004.1| 303 Y-LLNKADDAIATYEQAFKREPGS 325
                                       3.3578999999999999887665 PP

>> mRNA_triPase  mRNA capping enzyme, beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.2e-05     0.072      13     113 ..     158     286 ..     147     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.2e-05
                                       HHHHHHCTCCGGCCEEEEEEEEEEEETTTSSB---SBSS-EEE-TTCTEEEEE-B-HHHHHHHHHHHHHHHH..... CS
                      mRNA_triPase  13 iaaldniksekrsqiEiEaklGlivdkstkeRlklpvsteaivennadskfesgvdedqfkelnnfLnelsrr.... 85 
                                       ++++ ++ +e +  iEiE  +G    +++   l+    ++ai + +  +++es+v  d+f+ + n+L  +++     
  gi|518651484|ref|YP_008141004.1| 158 MEKFPEALEEYNRVIEIEPNFGEAYYNRSIIYLDQDKFEDAIRDAERAMDLESDVP-DNFDLMGNILAAMEKYeeal 233
                                       44455566777899**************9*****************9********8.68***********977999* PP

                                       ..........................HTTCCCTTTEEEEEEEEEEEEEE-S-S CS
                      mRNA_triPase  86 .........................neeenskrekvslkeskevDkfYelkkk 113
                                                                n ++ s+ +    k+ k vD++Ye +k+
  gi|518651484|ref|YP_008141004.1| 234 kyygeaieldsrfaaayydmgimydNMKNYSNAIENYDKAIKLVDNYYEGTKS 286
                                       *********************99987777777777888889999999998743 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       7.3   5.7e+03     105     123 ..      82     100 ..      53     108 .. 0.58
   2 ?   -0.8   0.0       1.9   1.5e+03     107     126 ..     152     171 ..     116     194 .. 0.58
   3 ?    4.4   0.2     0.047        36      20      51 ..     190     219 ..     177     245 .. 0.78
   4 ?    6.7   0.3    0.0093       7.3      55     126 ..     247     318 ..     224     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 7.3
                                       HHHHHHHHTT-HHHHHHHH CS
                           DUF3856 105 sravaleelGrkdealkaf 123
                                        +a al +  +++ea  a+
  gi|518651484|ref|YP_008141004.1|  82 AKAYALINDNNNSEAYTAL 100
                                       3344444444444444444 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                                       HHHHHHTT-HHHHHHHHHHH CS
                           DUF3856 107 avaleelGrkdealkafrma 126
                                       a+a++ + +  eal++++ +
  gi|518651484|ref|YP_008141004.1| 152 AMAYSYMEKFPEALEEYNRV 171
                                       33333333333333333333 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.047
                                       HHHT-HHHHHHHHHHHHHHHTTS-TTS---HH CS
                           DUF3856  20 leegayeeaaasyrkalevsrtipaeeafdhe 51 
                                       l ++++e+a +++++a+++   +p +  fd  
  gi|518651484|ref|YP_008141004.1| 190 LDQDKFEDAIRDAERAMDLESDVPDN--FDLM 219
                                       78899*************99999854..5555 PP

  == domain 4  score: 6.7 bits;  conditional E-value: 0.0093
                                       HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH--TTSTHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                           DUF3856  55 alchaglsealaklgrydealesadkalryfnrrGeleqdeGklWiaavfsravaleelGrkdealkafrma 126
                                       a ++  +   + ++++y +a+e  dka++  +   e  +   +  i a +++a  l  l + d+a+ ++++a
  gi|518651484|ref|YP_008141004.1| 247 AAAYYDMGIMYDNMKNYSNAIENYDKAIKLVDNYYEGTKSPSNAAIPAFLKKANDLYLLNKADDAIATYEQA 318
                                       555666666777889999999999999999999999999999999999999999999999999999999877 PP

>> Prion  Prion/Doppel alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.011       8.5      13      32 ..      10      29 ..       3      54 .. 0.90
   2 ?    3.5   0.0     0.081        63      75     100 ..     358     382 ..     356     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                                      HHHHHHHHGGGSTSCEEES- CS
                             Prion 13 enryyeenyarypdqvyyrk 32
                                       ++yy+e ++ + d++y + 
  gi|518651484|ref|YP_008141004.1| 10 VDKYYNEAMKLFNDEIYDKA 29
                                      579**************875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.081
                                       HHHHHHHHHHHHHCHHHHH-XXXXXX CS
                             Prion  75 rvirelCiekycefslrrgaGlrvll 100
                                       + i+++C+e+ ce   ++ +Gl+ l+
  gi|518651484|ref|YP_008141004.1| 358 KTIKKMCAEDECE-DNHLISGLNDLI 382
                                       679*********9.678889987555 PP

>> DUF5113  Domain of unknown function (DUF5113)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.2     0.031        24       7      49 ..       9      51 ..       4      70 .. 0.76
   2 ?   -0.7   0.1       1.4   1.1e+03       9      37 ..      78     106 ..      67     125 .. 0.79
   3 ?    2.0   0.1       0.2   1.6e+02      21      50 ..     124     153 ..     110     175 .. 0.80
   4 ?    4.6   0.4     0.033        26       9      46 ..     214     251 ..     206     253 .. 0.85
   5 ?    8.5   2.1    0.0021       1.6       7      43 ..     246     282 ..     241     298 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.031
                           DUF5113  7 iandYanlayylnvegeyeeALeyldsaleylNahyekYakkk 49
                                        ++Y n a++l+ ++ y++A+  l+ a+++ N   e Y k++
  gi|518651484|ref|YP_008141004.1|  9 QVDKYYNEAMKLFNDEIYDKAILPLTRAIKLDNGNPEYYEKRS 51
                                      5689*************************99887766555444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.4
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsaley 37 
                                       + Y   ay+l  +++ +eA + ld+a+++
  gi|518651484|ref|YP_008141004.1|  78 EYYIAKAYALINDNNNSEAYTALDTAINM 106
                                       45777777777788888888888888765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.2
                           DUF5113  21 egeyeeALeyldsaleylNahyekYakkka 50 
                                       +++y  ALe  ++a+++l   y+ ++ k+ 
  gi|518651484|ref|YP_008141004.1| 124 DKKYGPALEQYNTAIKILPGVYQFHYGKAM 153
                                       678999************999999998874 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.033
                           DUF5113   9 ndYanlayylnvegeyeeALeyldsaleylNahyekYa 46 
                                       +++  +++ l + ++yeeAL+y  +a+e+  ++   Y+
  gi|518651484|ref|YP_008141004.1| 214 DNFDLMGNILAAMEKYEEALKYYGEAIELDSRFAAAYY 251
                                       5677788999999**************99888888887 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0021
                           DUF5113   7 iandYanlayylnvegeyeeALeyldsaleylNahye 43 
                                        a +Y +++ ++   ++y++A+e  d+a++++ ++ye
  gi|518651484|ref|YP_008141004.1| 246 FAAAYYDMGIMYDNMKNYSNAIENYDKAIKLVDNYYE 282
                                       5789999999999999****************99997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.52
# Mc/sec: 2354.54
//
Query:       gi|518651485|ref|YP_008141005.1|  [L=53]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.5   1.0    1.6e-24   85.3   1.0    1.0  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   9.1e-29   1.6e-24       1      50 []       4      53 .]       4      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.1e-29
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++d+
  gi|518651485|ref|YP_008141005.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITRDE 53
                                      8**********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.30s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 375.95
//
Query:       gi|518651486|ref|YP_008141006.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518651486|ref|YP_008141006.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518651486|ref|YP_008141006.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518651486|ref|YP_008141006.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518651486|ref|YP_008141006.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518651486|ref|YP_008141006.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518651486|ref|YP_008141006.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518651486|ref|YP_008141006.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518651486|ref|YP_008141006.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2465.61
//
Query:       gi|518651487|ref|YP_008141007.1|  [L=598]
Description: hypothetical protein FACI_IFERC00001G0126 [Ferroplasma acidarmanus fer1]
Scores for complete 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-137  456.9   0.4   4.9e-137  456.6   0.4    1.1  1  PEPCK_GTP  Phosphoenolpyruvate carboxykinase C-terminal P-loo
    3.4e-62  209.9   0.0    5.9e-62  209.1   0.0    1.3  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 !  456.6   0.4  5.4e-141  4.9e-137       2     356 ..     242     592 ..     241     594 .. 0.97

  Alignments for each domain:
  == domain 1  score: 456.6 bits;  conditional E-value: 5.4e-141
                                       EEES-EEEEEE-TTS-EEEEEEE-TTTSSHHHHHT---S..STT-EEEEEESS-EEEEE-TTSBEEEE---SEEEEE CS
                         PEPCK_GTP   2 LaEhmlilgvtspegkkkyvaaafpsacGKtnlamlept..legwkvetvgdDiawlkfgedgrlraiNpeaGfFgv 76 
                                       +aEhm+ l+vtsp+g+k+ +++afpsa+GKtnl+m++++  + gw  ++++dDi w++++ +++l+aiNpe+GfFgv
  gi|518651487|ref|YP_008141007.1| 242 MAEHMMALEVTSPSGRKYGISGAFPSASGKTNLSMIRTPtdMAGWDAQLLSDDIIWMHIN-NDSLYAINPEYGFFGV 317
                                       8**********************************99866799****************9.899************* PP

                                       -TT-STTT-HHHHHHTTBS-EEES-EEETTS-EE-TT--------EE-TTSSEE-T.T-SSS-TT-EEEEEGGGSTT CS
                         PEPCK_GTP  77 apgtnektnpnalktlkkntiftNvaltedgdvwWegleeeapaelidwkgkkwtkekekaahpnsrftvpakqlpi 153
                                       apgtn++tnpna+k+++++tiftN alt+dg++wW  l+ + + e++dw+g + t++ ++aahpnsrft+p+k++p 
  gi|518651487|ref|YP_008141007.1| 318 APGTNATTNPNAMKAFNRDTIFTNTALTTDGKPWWYSLDPSVS-EVYDWHG-NLTTDLKNAAHPNSRFTTPIKNYPY 392
                                       **************************************87666.9******.6677799****************** PP

                                       B-TTTT-TT-EEEEEEEEEEB-SSSS-SEEE-SSHHHHHHHHHT-EEE--TTSSS-TT-EEE-GGG-GGG-SS-HHH CS
                         PEPCK_GTP 154 iapewedpeGvpisaiifggrrsetvplvleafdwehGvflgatlesetTaaaegkvgvvrrdPfamlpFlgynlgd 230
                                       +++++ d+eG +i+a++fggrrs+ +plv +a++w++Gv++ga++++etTaa++gkvg +r+dP+am pF+gyn+gd
  gi|518651487|ref|YP_008141007.1| 393 LSSKFYDNEGLKIDAMLFGGRRSDLIPLVRQAKSWAQGVLFGAMIRAETTAATTGKVGILRNDPMAMIPFCGYNIGD 469
                                       ***************************************************************************** PP

                                       HHHHHHHHTTSTT-B--EEEEEES--B-TTSSBSS--GGGHHHHHHHHHHHHTT..S-EEETTEEEE-BTTC--TT- CS
                         PEPCK_GTP 231 YlehwlelgkklekklPkifsvNwfrkdeegkflWPGfgenlrvlkWilkrvegeakavetpiGlvPkkedldlkgl 307
                                       Y++hwl++gk   +++P+if+vNwfrkd++g+f+WPGf+en+rv++Wi +r++ +a+a+etp+Gl+P+  ++   +l
  gi|518651487|ref|YP_008141007.1| 470 YFQHWLDMGKL-VQHRPEIFYVNWFRKDSDGNFIWPGFSENFRVIEWIASRLDAKANAIETPVGLIPDIANFASGNL 545
                                       *********98.9*********************************************************9777777 PP

                                       ..TT--HHHHS---HHHHHHHHHHHHHHHHHTGGGS-HHHHHHHHHHHH CS
                         PEPCK_GTP 308 dlskedleellsvdkeewkeeveeieelfeklgeklPkelleeleelek 356
                                          k++le+l+++d   w++e++eie +f+k+g+++P+el++e++++++
  gi|518651487|ref|YP_008141007.1| 546 --GKNKLEQLFEIDYPGWLKELNEIEPFFKKIGDSFPEELWREFHNMKD 592
                                       ..899**************************************998875 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 !  209.1   0.0   6.6e-66   5.9e-62       4     218 .]      31     237 ..      30     237 .. 0.97

  Alignments for each domain:
  == domain 1  score: 209.1 bits;  conditional E-value: 6.6e-66
                                       HHHHHHH--SEEEE----HHHHHHHHHHHHHTTSEEE-..TTSBS-EEE---TTSSS--GGGEEEE-SSHHHH-SS- CS
                           PEPCK_N   4 eevaelcqPdkvvvcdgseeeneellkelvekgelikl..ekypnsylarsdpkDvARvesrTfictekeedagpln 78 
                                       e+++++++P+++vv+++ +  +++l+ e+ ++ eli+l  + y+nsyl+rs+p+DvAR+e++T+i + +e++ag++n
  gi|518651487|ref|YP_008141007.1|  31 ETFVRMLEPANIVVITDPDFYEKKLVGEMATDHELIELnrKYYSNSYLYRSNPDDVARTEKDTYISSLDEKNAGATN 107
                                       67899*********************************98899********************************** PP

                                       -EE-HHHHHHHHHHHSTTTTTTSEEEEEEEEES-TTSTT-EEEEEEES-HHHHHHHHHHSEESHHHHTT-SS..TSE CS
                           PEPCK_N  79 nwmdpeemkeelkelfkgcmkGrtmyVipfsmGpvgsplskigveiTdsaYVvlsmrimtrvgkkvleklgeeeefv 155
                                       nwm+pe++k+++ +l+kg+mk++tmy++pf++Gp+gs++s+ g++iTd +YVv++   +  vgk++++++++++++v
  gi|518651487|ref|YP_008141007.1| 108 NWMEPEHLKSRIFNLIKGSMKNKTMYIVPFILGPAGSKYSEAGIQITDNPYVVINLIKISLVGKEAINRIENTGKYV 184
                                       ***************************************************************************** PP

                                       EEEEE-S--SS-SS-BTB---GG-EEEEEGGGTEEEEES--SHHHH-TCCHHHHCHHHHHHHH CS
                           PEPCK_N 156 kclHsvgaplegqkdvkWpcnekkyivhfpeereilsvgsgYgGNaLlgKkcfalRiasviar 218
                                        ++H +g+ +   k+       ++yi+hf++e+ i+sv+++YgGNaLl Kk +alRiasv ar
  gi|518651487|ref|YP_008141007.1| 185 VAIHVTGTLD---KN-------NRYIAHFTDEDLIISVNTAYGGNALLTKKGYALRIASVHAR 237
                                       *******733...33.......8*************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 4260.98
//
Query:       gi|518651488|ref|YP_008141008.1|  [L=587]
Description: hypothetical protein FACI_IFERC00001G0127 [Ferroplasma acidarmanus fer1]
Scores for complete 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-48  162.8   0.4    1.2e-47  162.1   0.4    1.3  1  Peptidase_S9   Prolyl oligopeptidase family
    2.9e-12   46.6   0.0    6.8e-12   45.4   0.0    1.6  1  DLH            Dienelactone hydrolase family
    1.5e-10   41.2   0.3    4.8e-05   23.1   0.4    2.2  2  Abhydrolase_1  alpha/beta hydrolase fold
    1.2e-06   28.3   0.2      0.028   14.0   0.3    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
      2e-06   27.3   0.2      0.018   14.3   0.0    2.2  2  Hydrolase_4    Serine aminopeptidase, S33
    7.3e-06   25.9   0.1    0.00033   20.5   0.0    2.4  2  Abhydrolase_2  Phospholipase/Carboxylesterase
    2.3e-05   24.4   0.1      0.022   14.7   0.1    2.4  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
    7.4e-05   22.1   0.3     0.0027   16.9   0.4    2.2  2  DUF2920        Protein of unknown function (DUF2920)
    0.00042   20.2   0.2      0.047   13.6   0.0    2.6  2  Abhydrolase_3  alpha/beta hydrolase fold
     0.0022   18.6   0.0      0.041   14.5   0.0    2.1  2  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.012   14.3   0.3      0.088   11.5   0.3    2.3  1  AXE1           Acetyl xylan esterase (AXE1)
      0.013   15.0   0.1        0.6    9.4   0.0    2.2  2  Peptidase_S10  Serine carboxypeptidase
      0.088   12.9   0.0        0.2   11.8   0.0    1.5  1  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.1   0.4   8.7e-51   1.2e-47       7     208 ..     389     586 ..     382     587 .] 0.94

  Alignments for each domain:
  == domain 1  score: 162.1 bits;  conditional E-value: 8.7e-51
                                       HHHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTTS--GGGEEEEEETHHHHHHHHHHH CS
                      Peptidase_S9   7 lqlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakegyvdserlaitGgSyGGyltgaaln 83 
                                       + +l  +G+ v+ +n+rGs g+G++++++ ++++g  +f+D+i+++ +l k+g ++++r++itGgSyGGy ++ a++
  gi|518651488|ref|YP_008141008.1| 389 TMYL-GAGFSVFLPNYRGSIGMGRQYAESNRGDMGGMDFEDVITGINYLKKQGKIKTDRIYITGGSYGGYISALAIM 464
                                       4445.89********************************************************************** PP

                                       H-GGG-SEEEEESE---CCCHHCSTTSTHH.HCCCC--TTTCHHHHHHHHHH-CGGG-----EEEEEEETT-SSS-T CS
                      Peptidase_S9  84 qrpdlFkaavaevpvvdvlrydsdtdllte.eymewgnpeeneegykelspyspldnvkaypplLlihGlaDdrvpp 159
                                        ++d+Fka v+ ++++d+++++  ++l+++ ++    +  +n ++y+ +s+++  +   +++p+Ll+hG +D  vp+
  gi|518651488|ref|YP_008141008.1| 465 -KSDIFKASVSLYGISDWISFHGVSNLYNWdQVHM-NDDPYNFKKYDGFSAIRMDHD--VKTPVLLMHGVEDPYVPI 537
                                       .***********************99999955544.55559****************..99**************** PP

                                       HHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHHHHHHHHHHHHHHHHH CS
                      Peptidase_S9 160 aealklvaaLqkkgknvlllifpdegHgvgkprakveelarllaFlkea 208
                                        + +++++ L+++gk v+ll++p egHg+ ++++ + +++++ +F++++
  gi|518651488|ref|YP_008141008.1| 538 GQYYEFYRFLKEHGKSVRLLVYPREGHGFTEKDHMITQYKETIDFFNRY 586
                                       **********************************************986 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   4.9e-15   6.8e-12      84     197 ..     431     576 ..     360     586 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.9e-15
                               DLH  84 aavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYG.............................. 130
                                         ++ylk++++ +t+++ ++G   GG ++ l + + + ++a+v+ YG                              
  gi|518651488|ref|YP_008141008.1| 431 TGINYLKKQGKIKTDRIYITGGSYGGYISALAIMKSDIFKASVSLYGisdwisfhgvsnlynwdqvhmnddpynfkk 507
                                       568*********************************************************************98766 PP

                               DLH 131 lspekeleeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFandsre..sy 197
                                           + +  ++++k+p+l ++g eD+ +p ++  ++   lk++++ ++l vYp  gH+F+++++   +y
  gi|518651488|ref|YP_008141008.1| 508 YDGFSAIRMDHDVKTPVLLMHGVEDPYVPIGQYYEFYRFLKEHGKSVRLLVYPREGHGFTEKDHMitQY 576
                                       5555789999**************************************************998764444 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.4   3.5e-08   4.8e-05       1     106 [.     367     477 ..     367     488 .. 0.75
   2 !   15.7   0.0   6.4e-06    0.0089     206     250 ..     515     564 ..     488     568 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.5e-08
                                       SEEEEE-STTTCGGG..GTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB..CHHSHHHHHHHHH...HH..HHH CS
                     Abhydrolase_1   1 pvlvilhGlpgssdv..waerglapaLakdgfdvillDlrGvgySspapacin.ddygtasvaddld...ri..lda 69 
                                       pv+v++hG+p s+ +  ++ r  ++  a  gf v+l++ rG+    +  a+ n  d+g ++++d++    ++  + +
  gi|518651488|ref|YP_008141008.1| 367 PVIVYIHGGPTSFSYpaFIDRTTMYLGA--GFSVFLPNYRGSIGMGRQYAESNrGDMGGMDFEDVITginYLkkQGK 441
                                       79*********88875577777775555..***********955555555555577777778888876557787778 PP

                                       CTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  70 lgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                        + d++++ G+S+GG i++ +  +  +  ka v+l +
  gi|518651488|ref|YP_008141008.1| 442 IKTDRIYITGGSYGGYISALAIMK-SDIFKASVSLYG 477
                                       8999*************9866544.666666666655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.4e-06
                                       C.THHHHSEEEEEEETTCSSSCH.HHHHHHHHCHTS...EEEEEEETCSS CS
                     Abhydrolase_1 206 e.lknvlaptlvisgtsDplvpp.kaledlaqllpk...krlvvisdagH 250
                                       +  ++v+ p+l+++g +Dp+vp+ +++e+++ l  +   +rl+v++ +gH
  gi|518651488|ref|YP_008141008.1| 515 RmDHDVKTPVLLMHGVEDPYVPIgQYYEFYRFLKEHgksVRLLVYPREGH 564
                                       14689******************9*****9999888999*********99 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.3     2e-05     0.028      54     140 ..     392     483 ..     333     501 .. 0.78
   2 !   12.2   0.0   7.2e-05     0.099     219     264 ..     512     560 ..     488     565 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2e-05
                                       HHTT-EEEEEE-TTSTTS-S---TT.....TTTHHHHHHHHHHHHHHC.TTEEEEEEEEEECHHHHHHHHHCTT--T CS
                     Peptidase_S15  54 varGYavVvqdvrGtggSeGeftvg.....dsdeaedgadvidWlakq.pwsnGkVgmtGiSYlGttqllaaatgvp 124
                                       +  G+ v + + rG+ g   ++        +  + ed+   i  l kq +  ++++  tG SY+G+++ la + +++
  gi|518651488|ref|YP_008141008.1| 392 LGAGFSVFLPNYRGSIGMGRQYAESnrgdmGGMDFEDVITGINYLKKQgKIKTDRIYITGGSYGGYISALAIM-KSD 467
                                       55555555555555554333332223433356677888888999999*********************99998.99* PP

                                       TEEEEEEECE-S-TCC CS
                     Peptidase_S15 125 alkaivpeaaisdlyd 140
                                         ka v++ +isd+  
  gi|518651488|ref|YP_008141008.1| 468 IFKASVSLYGISDWIS 483
                                       **************87 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 7.2e-05
                                       -HHHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EEEEEC CS
                     Peptidase_S15 219 nlsedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..klilgp 264
                                       ++ ++ + vk+pvll++G  D  v   + +++y+ lk++g+  +l++ p
  gi|518651488|ref|YP_008141008.1| 512 SAIRMDHDVKTPVLLMHGVEDPYVPiGQYYEFYRFLKEHGKsvRLLVYP 560
                                       3334669**************55559*************9988777655 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00015       0.2       4      96 ..     366     465 ..     363     475 .. 0.69
   2 !   14.3   0.0   1.3e-05     0.018     187     233 ..     517     565 ..     511     570 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                       Hydrolase_4   4 kavvvlvHGlaehsgryaelaea...LaaqGfavyalDhrGh...Grse..gkrghvpsfddyvdDlaafvekvkee 72 
                                       k v+v +HG   +   y  ++++      +Gf+v+  ++rG    Gr+    +rg++  +d   +D+ + ++ +k++
  gi|518651488|ref|YP_008141008.1| 366 KPVIVYIHGGPTSF-SYPAFIDRttmYLGAGFSVFLPNYRGSigmGRQYaeSNRGDMGGMD--FEDVITGINYLKKQ 439
                                       66777777754433.3333333311034689********9752226665667777776666..68888889999988 PP

                       Hydrolase_4  73 hpel..plfllGhSmGGliallyllr 96 
                                        + +  ++++ G S GG+i++l++ +
  gi|518651488|ref|YP_008141008.1| 440 GKIKtdRIYITGGSYGGYISALAIMK 465
                                       877789**************999865 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 1.3e-05
                       Hydrolase_4 187 aakitlPllllhGeaDkvvdpeasrelyerlgsk..dktlklypglyHe 233
                                       ++++++P+ll+hG +D+ v+ ++  e+y+ l+     ++l +yp   H 
  gi|518651488|ref|YP_008141008.1| 517 DHDVKTPVLLMHGVEDPYVPIGQYYEFYRFLKEHgkSVRLLVYPREGHG 565
                                       68899*******************9999988887446677778877775 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.061        84      94     126 ..     433     466 ..     424     503 .. 0.80
   2 !   20.5   0.0   2.4e-07   0.00033     154     203 ..     519     568 ..     510     581 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.061
                                       HHHHHHTT.--GGGEEEEEETHHHHHHHHHHHT- CS
                     Abhydrolase_2  94 idaelkkg.ipssriiigGFSqGaalalylaltl 126
                                       i++  k+g i+ +ri i G S G+ ++  +++++
  gi|518651488|ref|YP_008141008.1| 433 INYLKKQGkIKTDRIYITGGSYGGYISALAIMKS 466
                                       566667779***************9987776665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.4e-07
                                       GGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS--H CS
                     Abhydrolase_2 154 tkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHside 203
                                        +k+p+l++Hg eDp+vp+   ++++ +lk+  k v l +y+  +H   e
  gi|518651488|ref|YP_008141008.1| 519 DVKTPVLLMHGVEDPYVPIGQYYEFYRFLKEHGKSVRLLVYPREGHGFTE 568
                                       479***************************************99997655 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.6e-05     0.022       9     163 ..     432     566 ..     425     572 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                       HHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHHSSSEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE- CS
                            BAAT_C   9 ainyllrhpkvkkdkigllGiSkGgelalllasflkkisavvlingsavvvegklvykdeskvlpelklsmeklkvn 85 
                                       +inyl+++ k+k d+i + G S Gg +  l  ++++  +a v++ g +   +++ v +                ++ 
  gi|518651488|ref|YP_008141008.1| 432 GINYLKKQGKIKTDRIYITGGSYGGYISALAIMKSDIFKASVSLYGISDWISFHGVSNLY--------------NWD 494
                                       688888888888888888888888888877777777778888877776666666655522..............222 PP

                                       TTS-EE-TT-B--TTTGGGCCCB--GGG-.-SEEEEEEETT-SSS-HHHHHHHHHHHHHCTT--.--EEEEETTB-S CS
                            BAAT_C  86 knglldivdvlallkeklaekalipveka.kgpillvvgedDknwpSkesaekaserLkkagkkvevqlltYpkaGH 161
                                       + ++ d+ +++++     +  + i+++   k+p+ll+ g++D  +p  ++  +  + Lk++gk+  v+ll Yp  GH
  gi|518651488|ref|YP_008141008.1| 495 QVHMNDDPYNFKKY----DGFSAIRMDHDvKTPVLLMHGVEDPYVPIGQYY-EFYRFLKEHGKS--VRLLVYPREGH 564
                                       22222333333322....233445555444999***********9999998.889999999999..99999999999 PP

                                       -- CS
                            BAAT_C 162 li 163
                                        +
  gi|518651488|ref|YP_008141008.1| 565 GF 566
                                       65 PP

>> DUF2920  Protein of unknown function (DUF2920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.4     2e-06    0.0027     155     197 ..     421     462 ..     412     471 .. 0.85
   2 ?    2.6   0.0     0.045        62     285     322 ..     521     558 ..     505     563 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2e-06
                           DUF2920 155 fGimaAlDiinalkdlvkrfpkeadlpviliGgsyGGYlalLi 197
                                       +G m   D+i  +++l+k+  +++ + + + GgsyGGY++ L+
  gi|518651488|ref|YP_008141008.1| 421 MGGMDFEDVITGINYLKKQGKIKT-DRIYITGGSYGGYISALA 462
                                       577888899*******99999998.667778*********996 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.045
                           DUF2920 285 ntiyvsyHsekDklapaeeKiqlakilkklgfdvelel 322
                                       +t  + +H  +D+++p+ +  ++++ lk+ g  v+l +
  gi|518651488|ref|YP_008141008.1| 521 KTPVLLMHGVEDPYVPIGQYYEFYRFLKEHGKSVRLLV 558
                                       477899*************************9999865 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       2.4   3.3e+03       1      20 [.     369     388 ..     369     405 .. 0.63
   2 !   13.6   0.0   3.4e-05     0.047      49     209 ..     426     566 ..     423     568 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                                       EEEE--STTTS--TTTTHHH CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldthdal 20 
                                       +vy+HGG   +  ++  d++
  gi|518651488|ref|YP_008141008.1| 369 IVYIHGGPTSFSYPAFIDRT 388
                                       69****97666666665555 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHHHHHHHTHHHHTETTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHH CS
                     Abhydrolase_3  49 vedalaalrwlaeqawelgadpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaee 125
                                       +ed+++ +++l++q    +++++ri++ G S GG ++a + ++  d      ++ v +y   d  ++ + s      
  gi|518651488|ref|YP_008141008.1| 426 FEDVITGINYLKKQG---KIKTDRIYITGGSYGGYISALAIMK-SD----IFKASVSLYGISDWISFHGVSN---LY 491
                                       799999999999995...8*****************9866544.44....3678888888776633333333...11 PP

                                       TTTSSSSCHHHHHHHHHHHSSGGGGGSTTTSGGGC.S-SST---EEEEEETT-TTHHHHHHH..HHHHHHTT--EEE CS
                     Abhydrolase_3 126 ladgplltraaldlfwrlylpeadrddplasplla.edlsglpptlvvvaefDplrdegeay..aerlraagvevel 199
                                       + d+  ++ +     ++ y          +s ++  +d++   p+l++ + +Dp    g+ y  ++ l+++g++v+l
  gi|518651488|ref|YP_008141008.1| 492 NWDQVHMNDDPY--NFKKYD--------GFSAIRMdHDVK--TPVLLMHGVEDPYVPIGQYYefYRFLKEHGKSVRL 556
                                       122111211111..122221........122232312454..77888888888887777665225778888888888 PP

                                       EEETTEETTG CS
                     Abhydrolase_3 200 ieyegmvHgf 209
                                        +y+ + Hgf
  gi|518651488|ref|YP_008141008.1| 557 LVYPREGHGF 566
                                       8888888888 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0     3e-05     0.041       1      82 [.     369     462 ..     369     477 .. 0.66
   2 ?    1.2   0.0      0.34   4.8e+02       1      42 [.     524     569 ..     524     583 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
                                       EEEE--GC.....G.CHHHH...HHHHCCTCEEEEE--TTS.T.........S-GGCS--HHHCHHHHHHHCCTT.. CS
                     Abhydrolase_6   1 vlllHGagssassW.lvapL...aallaagvhvlapDlpGh.G.........rsdpppldledladlaalldelaa. 62 
                                       ++ +HG+++s   + + a++     +l+ag+ v+ p ++G  G         r d    d+ed+ +  ++l + ++ 
  gi|518651488|ref|YP_008141008.1| 369 IVYIHGGPTS---FsYPAFIdrtTMYLGAGFSVFLPNYRGSiGmgrqyaesnRGDMGGMDFEDVITGINYLKKQGKi 442
                                       6889**9965...54223334445577999899******88754455443332244445555555556666666669 PP

                                       .TTSEEEEEETCHHHHHHHH CS
                     Abhydrolase_6  63 gggpvvlvGHSlGGalalaa 82 
                                        ++++++ G S+GG+++++a
  gi|518651488|ref|YP_008141008.1| 443 KTDRIYITGGSYGGYISALA 462
                                       99999**********99984 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.34
                                       EEEE--.......GC.....GCHHHHHHHHCCT...CEEEEE--TTSTS-GG CS
                     Abhydrolase_6   1 vlllHG.......agssassWlvapLaallaag...vhvlapDlpGhGrsdp 42 
                                       vll+HG        g     ++  ++ ++l ++   v+ l++ + GhG+++ 
  gi|518651488|ref|YP_008141008.1| 524 VLLMHGvedpyvpIGQ----YY--EFYRFLKEHgksVRLLVYPREGHGFTEK 569
                                       7899997766655443....54..3333334444558889999999996543 PP

>> AXE1  Acetyl xylan esterase (AXE1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3   6.3e-05     0.088     155     299 ..     426     564 ..     310     580 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                                       HHHHHHHHHHHHTSTTEEEEEEEEEEETHHHHHHHHHHHH-SS-SEEEEES-SSSSHHHHHHH-SSTTCHHHHHHHH CS
                              AXE1 155 flDavrlveivaslpevDeeRvavlGasqGGalalavaalekrikavvadyPfLsdfkRvvelaleeaYdEitrylk 231
                                       f D++  ++ ++   ++  +R+ ++G+s GG ++  +   ++  ka v+ y  +sd+          +++ + + ++
  gi|518651488|ref|YP_008141008.1| 426 FEDVITGINYLKKQGKIKTDRIYITGGSYGGYISALAIMKSDIFKASVSLYG-ISDWI---------SFHGVSNLYN 492
                                       678888899999999999***************9776667777888888775.67764.........4555555555 PP

                                       HSH-C.CHHHHHHHHHHTT-HHHHHCC--S-EEEEEETT-SSS-HHHHHHHHHH--SS.EEEE..EETT-ST CS
                              AXE1 232 ldper.ekeeevletLsYiDvknlAkrvkaevllsvgLeDevcpPstvfaaynklete.keik..vyeefah 299
                                        d+ + + + + +++   +  + + + vk++vll+ g+eD   p    +  y  l+ + k+++  vy+  +h
  gi|518651488|ref|YP_008141008.1| 493 WDQVHmNDDPYNFKKYDGFSAIRMDHDVKTPVLLMHGVEDPYVPIGQYYEFYRFLKEHgKSVRllVYPREGH 564
                                       555441456688999999**********************99988888888887766557766225665555 PP

>> Peptidase_S10  Serine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.038        53      28      58 ..     356     384 ..     335     387 .. 0.76
   2 ?    9.4   0.0   0.00044       0.6     125     153 ..     434     461 ..     426     475 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.038
                                       EEEEE-SSGTTTS-EEEEE--TTTB-THHHH CS
                     Peptidase_S10  28 YwfveseknpeedplvlWLnGGPGCsSldGl 58 
                                       Y f+ se   +e+p+++ + GGP + S  ++
  gi|518651488|ref|YP_008141008.1| 356 YGFFRSEG--SEKPVIVYIHGGPTSFSYPAF 384
                                       77888887..569**********99887665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00044
                                       HHHHHSTCGTTSEEEEEEETTHHHHHHHH CS
                     Peptidase_S10 125 kffekfpeyksrdfyitGESYaGhyvPal 153
                                       ++++k+ + k++ +yitG SY+G y+ al
  gi|518651488|ref|YP_008141008.1| 434 NYLKKQGKIKTDRIYITGGSYGG-YISAL 461
                                       89*******************99.56555 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00014       0.2      32      77 ..     519     568 ..     507     582 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00014
                     Abhydrolase_4  32 kgaapvLllqnerDpaTPyegakklakalgg.a...vlvtvegeGHgala 77 
                                        +++pvLl+ +  Dp +P  +  ++ + l++ +   +l+++  eGHg+ +
  gi|518651488|ref|YP_008141008.1| 519 DVKTPVLLMHGVEDPYVPIGQYYEFYRFLKEhGksvRLLVYPREGHGFTE 568
                                       3469**************999999888888764557999********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 3713.40
//
Query:       gi|518651489|ref|YP_008141009.1|  [L=169]
Description: SAM-dependent methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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   44.1   0.0    3.9e-11   43.5   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    4.5e-11   43.3   0.0    6.2e-11   42.8   0.0    1.2  1  Methyltransf_11  Methyltransferase domain
    1.9e-07   31.0   0.0    2.2e-07   30.9   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    5.6e-06   27.0   0.0    7.8e-06   26.6   0.0    1.2  1  Methyltransf_12  Methyltransferase domain
    1.5e-05   24.5   0.1      2e-05   24.1   0.1    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
     0.0051   16.2   0.0      0.011   15.1   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0058   16.4   0.1      0.014   15.2   0.1    1.7  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.036   13.4   0.1       0.23   10.7   0.0    1.9  2  GidB             rRNA small subunit methyltransferase G
      0.081   11.8   0.0        0.1   11.5   0.0    1.1  1  Methyltransf_9   Protein of unknown function (DUF1698)
      0.081   12.8   0.0       0.14   12.1   0.0    1.5  2  Methyltransf_18  Methyltransferase domain
       0.18   12.3   0.0       0.29   11.6   0.0    1.4  1  NOP5NT           NOP5NT (NUC127) domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.0   2.4e-14   3.9e-11       1      93 [.      22     113 ..      22     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 2.4e-14
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       vLd+G+G G +++al ++ ++ k+t +D+     ++ ++ +  e +  +++++++ ae+lpf d++f   +s ++ h
  gi|518651489|ref|YP_008141009.1|  22 VLDIGTGFGIVIKALINN-KDLKITSIDPETWRFDELKNTFLTEIYenRLKLMNAYAENLPFRDNEFTTTISLFSAH 97 
                                       9***************99.79******************998754477*************************99** PP

                                       GSSHHHHHHHHHHHHHHE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvL 93 
                                       h++  d+ kal+ei rv+
  gi|518651489|ref|YP_008141009.1|  98 HFK--DIIKALDEINRVT 113
                                       *98..999********96 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   3.8e-14   6.2e-11       1      88 [.      23     113 ..      23     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 3.8e-14
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CCC- CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlhhv 74 
                                       Ld+G+G G++ +al ++   +++ +D+ +   +  k+   +e    +++++ a ae+lpf+dn f   +s ++ hh+
  gi|518651489|ref|YP_008141009.1|  23 LDIGTGFGIVIKALINNKdLKITSIDPETWRFDELKNTFLTEIYenRLKLMNAYAENLPFRDNEFTTTISLFSAHHF 99 
                                       8**************77789******8877776666666555557899***************************** PP

                                       CCHHHHHHHHHHHE CS
                   Methyltransf_11  75 edpekalkeiaRvL 88 
                                       +d  kal+ei Rv 
  gi|518651489|ref|YP_008141009.1| 100 KDIIKALDEINRVT 113
                                       ************96 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   1.3e-10   2.2e-07       7     123 ..       4     125 ..       1     159 [. 0.74

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.3e-10
                   Methyltransf_23   7 eelsdklerllpklraggrvLdiGcGtGillevl.rengfsvtgvDlspeaveiae.........kakkaqkdqfde 73 
                                       + +++  e+++p l +g++vLdiG+G Gi+ + l   +  ++t +D+  +  ++++         +    +  ++++
  gi|518651489|ref|YP_008141009.1|   4 RSMDEIMEKISP-LVTGNNVLDIGTGFGIVIKALiNNKDLKITSIDPETWRFDELKntflteiyeN--RLKLMNAYA 77 
                                       567777788887.99*****************99555566*******8775555545555533221..111122223 PP

                   Methyltransf_23  74 qeaaepqgkfdlIvlrevlehvpdppellrqiatllkpgGylllseplas 123
                                       ++ ++ ++ f + ++ ++ +h++d  ++l+ i++ ++  G +++ +++ +
  gi|518651489|ref|YP_008141009.1|  78 ENLPFRDNEFTTTISLFSAHHFKDIIKALDEINRVTS--GTIIIADWGPE 125
                                       45555888**************************877..88888877655 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   4.8e-09   7.8e-06       1      92 [.      23     112 ..      23     115 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 4.8e-09
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakren.nnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L+iG+G G +++al ++ +d+++t +D+ +  ++  k+ +  ++  n+ + ++  a++l  +d    f + ++++  
  gi|518651489|ref|YP_008141009.1|  23 LDIGTGFGIVIKALINN-KDLKITSIDPETWRFDELKNTFLTEIYeNRLKLMNAYAENLPFRDN--EFTTTISLFSA 96 
                                       8***************9.************9996777666665550555666666777666665..9********** PP

                   Methyltransf_12  77 hhlkdirevldnirkl 92 
                                       hh+kdi ++ld+i ++
  gi|518651489|ref|YP_008141009.1|  97 HHFKDIIKALDEINRV 112
                                       *************987 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.2e-08     2e-05      39     143 ..      10     113 ..       3     121 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.2e-08
                                       HHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSS.TEEEEE--TTT-TTS- CS
                   Ubie_methyltran  39 veklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegki.nieflqanaeeLpfed 114
                                       +ek++   +g++vlD+ +G g +  +l +  ++  k++ +D +   +++ ++    e +  ++++++a ae+Lpf d
  gi|518651489|ref|YP_008141009.1|  10 MEKISPLVTGNNVLDIGTGFGIVIKALIN--NKDLKITSIDPETWRFDELKNTFLTEIYEnRLKLMNAYAENLPFRD 84 
                                       567777889*******9999866655554..3456888888888888887777666655559*************** PP

                                       T-EEEEEEES-GGG-S-HHHHHHHHHHHE CS
                   Ubie_methyltran 115 dsfDvvtvsfGlrnvtDklkaLkeayrvl 143
                                       + f +    f    + D+ kaL e+ rv 
  gi|518651489|ref|YP_008141009.1|  85 NEFTTTISLFSAHHFKDIIKALDEINRVT 113
                                       ***8765569*****************95 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   6.5e-06     0.011      51      91 ..       6      47 ..       2      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.5e-06
                                      HHHHHTTTT.--TT-EEEEES-TTSHHHHHHHHHH--EEEEE CS
                              CMAS 51 ldlilekle.lkpGmtlLdiGcGWGslvrraverydvkvvgl 91
                                      +d i+ek++ l  G+++LdiG+G+G +++  +++ d k+ ++
  gi|518651489|ref|YP_008141009.1|  6 MDEIMEKISpLVTGNNVLDIGTGFGIVIKALINNKDLKITSI 47
                                      678888885599********************9999999876 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.6e-06     0.014       4     111 ..      19     121 ..      16     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlil 79 
                                       g++vlD+G+G G  +++l    +++ ++++iD +       ++      ++ ++++  + +e+l+  + d+ f   +
  gi|518651489|ref|YP_008141009.1|  19 GNNVLDIGTGFGIVIKALI--NNKDLKITSIDPETWRFDELKNTFLTEIYEnRLKLMNAYAENLP--FRDNEFTTTI 91 
                                       789****************..57899*********99999999999999998899**********..9*****9999 PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggillied 111
                                       s    ++++d  k+l ei rv +  g ++i+d
  gi|518651489|ref|YP_008141009.1|  92 SLFSAHHFKDIIKALDEINRVTS--GTIIIAD 121
                                       86666*************99987..5555444 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00014      0.23      42      97 ..      14      72 ..       1      86 [. 0.64
   2 ?    0.9   0.0      0.15   2.5e+02      26      50 ..      90     114 ..      66     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                                      GGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHH.....HHHHHHHH.HCT- CS
                              GidB 42 lellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekki.....aFLeevke.elkl 97
                                      ++l++ ++  v+D+G+G G+  i   i +++lk+t ++++  +      +FL+e+ e +lkl
  gi|518651489|ref|YP_008141009.1| 14 SPLVTGNN--VLDIGTGFGI-VIKALINNKDLKITSIDPETWRFdelknTFLTEIYEnRLKL 72
                                      44555555..*******986.233346678999******87765111115666654314444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.15
                                       SHHHHHHHCHHHHHHHGGCS-CCC- CS
                              GidB  26 epeellerhlldslsvlellkekrd 50 
                                       +++ +  +h+ d++++l  +++  +
  gi|518651489|ref|YP_008141009.1|  90 TISLFSAHHFKDIIKALDEINRVTS 114
                                       5566778999999999888877665 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.3e-05       0.1     104     205 ..       6     109 ..       2     123 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.3e-05
                                       HHHHGGGS.--.TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---GGGS-T CS
                    Methyltransf_9 104 Wdrvlphlsdl.kgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgieqlpe 179
                                        d +++ +s+l +g  +ld+G g G  +  ++ ++   +  idP++  +  ++        ++r  l+    e+lp 
  gi|518651489|ref|YP_008141009.1|   6 MDEIMEKISPLvTGNNVLDIGTGFGIVIKALINNKDLKITSIDPETWRFDELKNTFLTEIYENRLKLMNAYAENLPF 82 
                                       578899999985799*****************************988776666554444456777777778899998 PP

                                       .---EEEEEEES-GGG-S-HHHHHHHH CS
                    Methyltransf_9 180 .leafdtvfsmGvlyhrrsPldhllql 205
                                         + f t  s+   +h +  +  l ++
  gi|518651489|ref|YP_008141009.1|  83 rDNEFTTTISLFSAHHFKDIIKALDEI 109
                                       567888888888888887777766665 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   8.6e-05      0.14       5      70 ..      10      73 ..       6     123 .. 0.75
   2 ?   -3.3   0.0       4.7   7.7e+03     128     146 ..     149     161 ..     142     165 .. 0.47

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.6e-05
                   Methyltransf_18  5 LkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievr 70
                                      +++i  lv+ g++v+DiGt  g++  +l++++   k++ +D ++  +++ k++  ++ +e++++++
  gi|518651489|ref|YP_008141009.1| 10 MEKISPLVT-GNNVLDIGTGFGIVIKALINNKDL-KITSIDPETWRFDELKNTFLTEIYENRLKLM 73
                                      678888898.99*************999977766.7888888888888888887777777766665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.7
                   Methyltransf_18 128 lvengfkiedEelvkeegk 146
                                              i+++  vk+++ 
  gi|518651489|ref|YP_008141009.1| 149 G------IKNNYAVKDGSM 161
                                       3......444444444444 PP

>> NOP5NT  NOP5NT (NUC127) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00018      0.29      33      65 .]      84     115 ..      63     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            NOP5NT  33 dlekfsklvkLkaFqkFesaaeALenanaiseG 65 
                                       d ++f  +++L + + F++  +AL+++n ++ G
  gi|518651489|ref|YP_008141009.1|  84 D-NEFTTTISLFSAHHFKDIIKALDEINRVTSG 115
                                       4.7899***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1133.09
//
Query:       gi|518651490|ref|YP_008141010.1|  [L=153]
Description: hypothetical protein FACI_IFERC00001G0129 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); 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 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1169.87
//
Query:       gi|518651491|ref|YP_008141011.1|  [L=675]
Description: zinc metalloprotease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-88  298.4   0.1      2e-88  297.7   0.1    1.3  1  Peptidase_M13_N  Peptidase family M13
    3.7e-64  216.1   0.0    5.6e-64  215.5   0.0    1.2  1  Peptidase_M13    Peptidase family M13
  ------ inclusion threshold ------
       0.13   12.0   0.0       0.25   11.1   0.0    1.4  1  Peptidase_M48    Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M13_N  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  297.7   0.1   3.3e-92     2e-88       1     382 []      45     420 ..      45     420 .. 0.95

  Alignments for each domain:
  == domain 1  score: 297.7 bits;  conditional E-value: 3.3e-92
                   Peptidase_M13_N   1 PCdDFYeyaCGnWlkehpipadkssygtfeelqeelekqlreileekpsskedakavkkaktlYksCmdedaieklg 77 
                                       P +DF  y+ G+W k+hp+p+dk  y++ +el e ++ +l +ile+ + +++++ a++ ++++Y s md+d iek g
  gi|518651491|ref|YP_008141011.1|  45 PMEDFSIYSYGKWVKSHPVPEDKYVYDASTELMEWNNFILGKILESCARNSQNP-AERALGDFYISIMDVDGIEKNG 120
                                       899**********************************88*****9999888666.9********************* PP

                   Peptidase_M13_N  78 lkplldllkelggldsnwkdkfdllellaklrrygidilfslgvdpdpkdpsknvlyldqpglglpdreyylkerde 154
                                       +kp+ ++++ ++ +    ++k ++ e+ ++++ +gi+ lfs++  pd k++s ++ yl+q gl+lp+r+yy+   d+
  gi|518651491|ref|YP_008141011.1| 121 FKPVSRFMEIIDRI----DSKNNIIETFGEFNTMGISGLFSFDSMPDEKNSSVYACYLNQDGLSLPNRDYYF---DD 190
                                       *************9....7899*************************************************6...66 PP

                   Peptidase_M13_N 155 keeeileaykeylakllkllgeea...aelaeevvefekklakitldseerrdpeklynpmtlaelqklapqidwka 228
                                       + +ei+++y +++++++ l+g ++   +++ + v+++e++la  + +++e+rdp+k+yn++++++++k +p +  ++
  gi|518651491|ref|YP_008141011.1| 191 SFKEIRAQYINHIKNMFILYGFDDktsENMGNTVLKIETSLALKSRSPVELRDPDKNYNRFQFNDIEKEFPGLRHRE 267
                                       7999***************987532325566***********99999********************888******* PP

                   Peptidase_M13_N 229 ylsa.llertsssekvivtepeylkklskllaettpkrtlanYllwrlvrelapylsdefrdakfefyk.tlsgree 303
                                       y+s+ +l+     +++i+ +pe++++l++++++   +++++ Y+ w+++++ ap+l  +++ ++f+f + +l g++ 
  gi|518651491|ref|YP_008141011.1| 268 YFSKiGLT---GLDYIIIGQPEFFRDLDSIIQQ-YTLDDWKIYMKWNVLNSAAPFLFGDVEMEHFDFFQrKLLGQQL 340
                                       ****6555...48******************66.777********************************9******5 PP

                   Peptidase_M13_N 304 r.prwkrCvsqvnsllgmalgrlyvkkyfpeeskkdveemvedikeafkerlkeldWmdeetkkkAleKldamklki 379
                                         +rwk++vs ++s++g+alg++yv+k+f e+sk+++++m+ed+ke f er+++l+Wm  etk+kAleK ++++ k+
  gi|518651491|ref|YP_008141011.1| 341 PaKRWKKAVSIIDSFMGEALGKIYVEKQFGEDSKRRMDDMIEDLKEVFIERINNLSWMGRETKEKALEKFSKFRAKV 417
                                       549************************************************************************** PP

                   Peptidase_M13_N 380 gyP 382
                                       gyP
  gi|518651491|ref|YP_008141011.1| 418 GYP 420
                                       **9 PP

>> Peptidase_M13  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.5   0.0   9.5e-68   5.6e-64       1     190 [.     472     660 ..     472     670 .. 0.96

  Alignments for each domain:
  == domain 1  score: 215.5 bits;  conditional E-value: 9.5e-68
                     Peptidase_M13   1 NAyYqpeensivfpaailqppffdleypeavNyggiGaviaHEltHgfddqgvqfdkegnlaswltdedaeefkeka 77 
                                       NAy++p++n+ivfpa+ilqppffd+e+++avNyg++Ga+iaHE++Hgfdd+g ++d +gnl++w+t+ed ++f eka
  gi|518651491|ref|YP_008141011.1| 472 NAYFSPTDNEIVFPAGILQPPFFDPEMDDAVNYGATGATIAHEISHGFDDEGRKYDLNGNLNDWWTPEDDKAFTEKA 548
                                       9**************************************************************************** PP

                     Peptidase_M13  78 kclieqfsevtepektkavngaltlgEniADlggleiAyraykklksakeerlpelenltkdqlfFisyAqiwcekq 154
                                       k ++e ++ ++    + +vng ltlgEniAD gg++iA++a +++ +++ e  + ++++t++q+fF+++Aq+w++  
  gi|518651491|ref|YP_008141011.1| 549 KSVVELYNSIEALPGI-HVNGPLTLGENIADIGGVSIAFEALEHRLKKNPELRKVIDGYTPEQRFFMGWAQSWRTTV 624
                                       ***************9.**************************865555555566********************** PP

                     Peptidase_M13 155 sdeellrqllvdvHspaelRvngvlsnlpaFaeaFn 190
                                       +de+l  q+l dvHsp ++R+  +    p+F+++F 
  gi|518651491|ref|YP_008141011.1| 625 KDEALKWQILNDVHSPEKIRAEIPAYVNPNFQHTFT 660
                                       **********************************96 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   4.2e-05      0.25      23      74 ..     459     517 ..     445     525 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.2e-05
                                       -EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH.........-SSB-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  23 pltkvyvvnspkrNAFalgggknkrivltdgLl.........kqllseeelaaVlGHElGH 74 
                                         +++ ++  p++NA++++    + iv+  g+l          ++++     a ++HE++H
  gi|518651491|ref|YP_008141011.1| 459 VDKELWEMTPPTVNAYFSPTD--NEIVFPAGILqppffdpemDDAVNYGATGATIAHEISH 517
                                       3478899999**********9..79************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 4570.23
//
Query:       gi|518651492|ref|YP_008141012.1|  [L=227]
Description: hypothetical protein FACI_IFERC00001G0131 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-12   46.7  26.6    2.6e-12   46.4  26.6    1.0  1  DUF973        Protein of unknown function (DUF973)
  ------ inclusion threshold ------
       0.14   11.7   0.1       0.25   11.0   0.1    1.4  1  pEK499_p136   HEPN pEK499 p136
       0.26   11.0  13.6       0.49   10.1  13.6    1.4  1  Tetraspanin   Tetraspanin family
        1.8    6.4   5.7        2.4    6.0   5.7    1.1  1  Prominin      Prominin
        2.1    7.4   9.4        3.8    6.6   9.4    1.6  1  Bac_export_2  FlhB HrpN YscU SpaS Family
        3.7    7.9  35.0        6.8    7.0   2.3    3.3  3  DUF996        Protein of unknown function (DUF996)
        4.4    7.5   0.0        4.4    7.5   0.0    3.3  3  S1FA          DNA binding protein S1FA


Domain annotation for each model (and alignments):
>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4  26.6     1e-15   2.6e-12       4     196 ..      12     218 ..       9     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1e-15
                            DUF973   4 gleklregslfliiasllaliliilvlvvlft...aissglsqliqssasilssvlllliaaiiliiiasvllilgl 77 
                                       g+ ++++gs++ ii+++l + l il +++++    +    +++++ + +++ +++  ++   +++++ ++++l +g+
  gi|518651492|ref|YP_008141012.1|  12 GIGYIKRGSIYAIIVAILDIPLYILEFLFISRftgI----INSVTSNGLHMPAGEYYIFYTLMLISLAGLIILTFGI 84 
                                       899*****************9999999888773322....24455565666666666777777799*********** PP

                            DUF973  78 lkirsgfsiLsstgrdvgiGitgltliligaiiiiigvilaivsll..................slilslillgvii 136
                                        + r+gf +++ +    ++    +  +++ +ii ii ++  +++l                   ++ l+l+l++++i
  gi|518651492|ref|YP_008141012.1|  85 ANYREGFRNFKGLDTRFSKPFSYSKYVIMLYIIFIIVYVFILAFLPasnqnihfpalsssstlaHVFLVLLLISALI 161
                                       **********99988888888888888888999999999777665599***************999*********** PP

                            DUF973 137 lligiilaliGqillglsfyklGevYnnglikigGiliiipvidilsfIGyilsyiglgn 196
                                       +li ++lal+G+i + ++ y+   +  +++ ++g il iip   i ++++  l+y++ ++
  gi|518651492|ref|YP_008141012.1| 162 VLIISVLALVGFIYILIGLYRFSGMVHQEVGELGAILYIIP---IANIVSPFLIYVASSR 218
                                       **********************9999999************...9**********99876 PP

>> pEK499_p136  HEPN pEK499 p136
   #    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      51 ..      35      81 ..      31     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 9.6e-05
                       pEK499_p136  6 dfekefieRtlanldqyeeaaelkpaeekyn.lTlllnsllGlivlp 51
                                       +e  fi+R   +++ + +    +pa e y  +Tl+l+sl Gli+l+
  gi|518651492|ref|YP_008141012.1| 35 ILEFLFISRFTGIINSVTSNGLHMPAGEYYIfYTLMLISLAGLIILT 81
                                      67778*************988888888888537************97 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  13.6   0.00019      0.49       3     102 ..      63     171 ..      62     179 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00019
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXX.....................XXXXXX....XXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                       Tetraspanin   3 yllfffnllfwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGv....llfllgflGcigalken 75 
                                       y++f + +l+ l+g+++l +G  +++++ + +++ l ++ ++++++ ++++++  +     +f+l+fl    a ++n
  gi|518651492|ref|YP_008141012.1|  63 YYIFYTLMLISLAGLIILTFG-IANYREGFRNFKGLDTRFSKPFSYSKYVIMLYIIfiivYVFILAFLP---ASNQN 135
                                       99*******************.66676666666666666666666665554444332012445555554...55555 PP

                                       X.........XXXXXXXXXXXXXXXXXXXXXXXXX- CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  76 k.........cllltfsllllvlfllelaagilgfv 102
                                       +         +l  +f++lll+  l+ l++ +l++v
  gi|518651492|ref|YP_008141012.1| 136 IhfpalssssTLAHVFLVLLLISALIVLIISVLALV 171
                                       5555555555*************9999999999987 PP

>> Prominin  Prominin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.7   0.00094       2.4     409     490 ..      99     180 ..      81     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00094
                          Prominin 409 ekyekyrwliglivcs.llllivvililgLlcGilGlsrtatptdrgcskntGasfL..lvgvglsFlffsllmlvv 482
                                        +++k  ++  +++++ ++++iv ++il+ l      +++ + +  ++s+  + +fL  l+  +l+ l++s+l lv+
  gi|518651492|ref|YP_008141012.1|  99 TRFSKPFSYSKYVIMLyIIFIIVYVFILAFL--PAS-NQNIHFPALSSSSTLAHVFLvlLLISALIVLIISVLALVG 172
                                       5666666666666555155566666667766..333.444444477777788888762144557999********** PP

                          Prominin 483 lltFlvGl 490
                                       +++ l+Gl
  gi|518651492|ref|YP_008141012.1| 173 FIYILIGL 180
                                       *******7 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 ?    6.6   9.4    0.0015       3.8     126     209 ..     104     190 ..      19     193 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0015
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2 126 lvellksllkvvlvgavaylvlkseleellalaeld...leaalelllslllkllllvllallviallDlllqrwef 199
                                        +   k ++ + ++++++y+++ + l++  + ++++    +++l++++ +ll + +l++l++ v+al+ +++     
  gi|518651492|ref|YP_008141012.1| 104 PFSYSKYVIMLYIIFIIVYVFILAFLPASNQNIHFPalsSSSTLAHVFLVLLLISALIVLIISVLALVGFIYILIGL 180
                                       34455566666666666666666655555555544400055555555555555555666666666666666666666 PP

                                       XXXXXXXXXX CS
                      Bac_export_2 200 ekklkMtkqE 209
                                        +   M +qE
  gi|518651492|ref|YP_008141012.1| 181 YRFSGMVHQE 190
                                       6666666666 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.6    0.0071        18      69     131 ..      19      81 ..       4      86 .. 0.74
   2 ?    6.9  11.3    0.0028       7.1      26      89 ..     105     168 ..      93     170 .. 0.63
   3 ?    7.0   2.3    0.0027       6.8       1      34 [.     168     201 ..     168     219 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0071
                            DUF996  69 lilllllvliiayvlliisavflkksyellgkrtgvklFetagllyfiGaiLtivlvGliill 131
                                       +    ++v i+ + l+i++ +f+++    +++ t++ l   ag  y++ ++++i l Gliil 
  gi|518651492|ref|YP_008141012.1|  19 GSIYAIIVAILDIPLYILEFLFISRFTGIINSVTSNGLHMPAGEYYIFYTLMLISLAGLIILT 81 
                                       444555666666678888899999999999999999999999999999999999999998875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0028
                            DUF996  26 fsnaliafilsiialvvailalllvlgalatalelpgleeaaslilllllvl.iiayvlliisav 89 
                                       fs+  +  i+ +i ++++++ +l+ l a+   + +p+l+  + l  ++l++l i a+++liis++
  gi|518651492|ref|YP_008141012.1| 105 FSYSKYV-IMLYIIFIIVYVFILAFLPASNQNIHFPALSSSSTLAHVFLVLLlISALIVLIISVL 168
                                       4444444.444444444455555667777778888888887775555555443888899999986 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0027
                            DUF996   1 lsivGliLvlvalkeiskavndekifsnaliafi 34 
                                       l++vG+i +l++l+++s  v +e     a+ ++i
  gi|518651492|ref|YP_008141012.1| 168 LALVGFIYILIGLYRFSGMVHQEVGELGAILYII 201
                                       579***************9887754444433332 PP

>> S1FA  DNA binding protein S1FA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0017       4.4      13      51 ..      70     109 ..      67     113 .. 0.84
   2 ?   -0.9   1.6      0.73   1.9e+03      12      25 ..     116     129 ..     110     136 .. 0.80
   3 ?   -1.7   3.2       1.3   3.2e+03      12      25 ..     152     165 ..     143     183 .. 0.57

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                              S1FA  13 vllvvggl.lllflvgnyvlyvyaqktlPprkkkPvskkk 51 
                                       +l+ ++gl +l+f ++ny       k l  r  kP s  k
  gi|518651492|ref|YP_008141012.1|  70 MLISLAGLiILTFGIANYREGFRNFKGLDTRFSKPFSYSK 109
                                       577777762699*******999999****99999999766 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.73
                              S1FA  12 ivllvvggllllfl 25 
                                       i++++v  ++l fl
  gi|518651492|ref|YP_008141012.1| 116 IIFIIVYVFILAFL 129
                                       77888888888887 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.3
                              S1FA  12 ivllvvggllllfl 25 
                                       +vll++++l++l +
  gi|518651492|ref|YP_008141012.1| 152 LVLLLISALIVLII 165
                                       55555555544322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1269  (0.0707792); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 1449.18
//
Query:       gi|518651493|ref|YP_008141013.1|  [L=225]
Description: hypothetical protein FACI_IFERC00001G0132 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.4   0.1       0.03   14.4   0.1    3.4  3  DUF2892        Protein of unknown function (DUF2892)


Domain annotation for each model (and alignments):
>> DUF2892  Protein of unknown function (DUF2892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.1       0.3   5.3e+03      31      31 ..      25      25 ..       3      56 .. 0.55
   2 ?   -2.9   5.0       0.4   7.1e+03      13      41 ..     100     131 ..      67     156 .. 0.61
   3 ?   14.4   0.1   1.7e-06      0.03      11      61 ..     164     218 ..     160     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.3
                           DUF2892 31 g 31
                                      +
  gi|518651493|ref|YP_008141013.1| 25 S 25
                                      1 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.4
                           DUF2892  13 rivvGlvllllallglsggw...gwllglvGa 41 
                                        i+  ++++++al++  g     g+++g++ +
  gi|518651493|ref|YP_008141013.1| 100 MIISTVFVIVSALISHVGDIvthGVVYGVLPI 131
                                       44444555555555554444555444444444 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.7e-06
                           DUF2892  11 ilrivvGlvllllallglsggw...gwllglvGavllltgltgfCplyallg.in 61 
                                       +l+ivvG++++ +a + +   +   ++ + ++G+ ll+ g++ f +l +l++ +n
  gi|518651493|ref|YP_008141013.1| 164 LLSIVVGVIIVSVAGTLYIVEFpafLYYAEFFGILLLWIGFVDFKVLKSLFKtHN 218
                                       799**************9888799989999**************99999996355 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 1618.41
//
Query:       gi|518651494|ref|YP_008141014.1|  [L=497]
Description: transposase-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.1e-12   47.2   5.0    5.7e-12   45.7   5.0    1.7  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.055   13.6   0.1    1.7  2  GSH-S_N    Prokaryotic glutathione synthetase, N-terminal dom
      0.023   14.8   0.2      0.049   13.8   0.2    1.5  1  DUF809     Protein of unknown function (DUF809)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   5.0   9.5e-16   5.7e-12       8     214 .]     167     433 ..     162     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 9.5e-16
                         DDE_Tnp_1   8 ivDattvrvpgtk.edarwgykggkykygyklhiavdtrsgl..ilsvvitpgnvhdskglkqlldelrprkgklvl 81 
                                        +Da+++++  +  + a++g++ +k++y ++++  + + +    +l  +  pgn hds++++ +++ ++  ++++++
  gi|518651494|ref|YP_008141014.1| 167 FFDASNMYTFMEEnSIAKKGHN-KKHRYDLNQVSYYIASTYDyiPLYGEAYPGNIHDSRTFENIVKNIP--EDSTLI 240
                                       5677777765555333444444.4445666555555444322334444445******************..****** PP

                         DDE_Tnp_1  82 aDaGYasaelldtleekgvdyiirl..kkntklyrk...........gaeskrrgrlrkhdrnkiltksqkrrnk.. 143
                                        D+GY s++++d +   +  yi +l  ++n+ + +            +  + +++r++  + +   t       +  
  gi|518651494|ref|YP_008141014.1| 241 FDRGYNSKDNIDMIS--NRRYIGALkqSDNHSIMEInvkedsyieliRNVYGKDHRIILYHSKSLET-------Rkk 308
                                       ***************..89999999553343333336766655555533333344444444444444.......334 PP

                         DDE_Tnp_1 144 ........................................................skkekgdvyyvtntnsellsa 164
                                                                                               + +  g +  + +tn  + +a
  gi|518651494|ref|YP_008141014.1| 309 nkfmkhlakvmvkakkiidsgdsdsmekariylesehlnetillpsleidgermeyRISMMGKN--AIFTNIIDKDA 383
                                       44555899999999999********************************999997744444444..55566666789 PP

                         DDE_Tnp_1 165 eevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       e ++ely++R+++E+ F+++  k     l++ ++++++ ++++ l+a+++
  gi|518651494|ref|YP_008141014.1| 384 ESIVELYKKRARVEHCFRTINAKGIAFPLYHWTPQKIKVHMFFSLMAYLF 433
                                       **********************7556778888999***********9975 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.7     1e+04      39      70 ..     163     197 ..     149     209 .. 0.58
   2 ?   13.6   0.1   9.2e-06     0.055      10      66 ..     271     326 ..     268     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.7
                           GSH-S_N  39 aadLslregkatararkvevkedked...wyelge 70 
                                       ++d+ ++++++++ +++ ++ ++ ++    y+l++
  gi|518651494|ref|YP_008141014.1| 163 TGDIFFDASNMYTFMEENSIAKKGHNkkhRYDLNQ 197
                                       55666666666666666666443322122455544 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.2e-06
                           GSH-S_N  10 lesikikkDttfalmleaqarghevfvleaadLslr.egkatararkvevkedkedwy 66 
                                       + +i++k+D+ + l++++  ++h++++++ ++L  r ++k + ++ kv vk+  ++++
  gi|518651494|ref|YP_008141014.1| 271 IMEINVKEDSYIELIRNVYGKDHRIILYHSKSLETRkKNKFMKHLAKVMVKA--KKII 326
                                       789********************************95677888889998844..3333 PP

>> DUF809  Protein of unknown function (DUF809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   8.2e-06     0.049      15      80 ..     415     481 ..     405     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.2e-06
                            DUF809  15 ltpteckvsvisffllafllmahiwlswfsnnq..hclrtmrhleklkipyefqygwlgvkitiksnv 80 
                                        tp + kv +  f l+a+l++a i+     n +    + t+ +l+ ++i y ++   +  ki  ks++
  gi|518651494|ref|YP_008141014.1| 415 WTPQKIKVHM-FFSLMAYLFLALIYNEIHRNSKtaSLISTIDYLKDININYAIKGKIVTTKIECKSDI 481
                                       5777777764.47799*********98887766115689**************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3375.20
//
Query:       gi|518651495|ref|YP_008141015.1|  [L=36]
Description: hypothetical protein FACI_IFERC00001G0134 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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 0.24s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 261.54
//
Query:       gi|518651496|ref|YP_008141016.1|  [L=213]
Description: hypothetical protein FACI_IFERC00001G0135 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-17   64.4   0.0    2.1e-17   64.1   0.0    1.0  1  Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
    3.9e-06   27.0   0.0    9.2e-06   25.8   0.0    1.6  1  Lipase_GDSL    GDSL-like Lipase/Acylhydrolase
  ------ inclusion threshold ------
      0.059   13.6   0.8       0.14   12.4   0.3    1.8  2  DUF3760        Protein of unknown function (DUF3760)


Domain annotation for each model (and alignments):
>> Lipase_GDSL_2  GDSL-like Lipase/Acylhydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.1   0.0   3.5e-21   2.1e-17       2     174 ..      12     196 ..      11     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 64.1 bits;  conditional E-value: 3.5e-21
                                       EESHHHHTCTTB.......CCHCHHCCCCCCCHHHTT...-EEEEE.EEHCCH-H..HHHHHHHH.CTGGG-TSEEE CS
                     Lipase_GDSL_2   2 lGDSiTaGygad.......gggrsypaylarllaarl...gldvvnnlgvsGattallrllerlr.dllrlkpdlvt 67 
                                       +GDS T+            g g++y +y+ +ll+  +   + + vn  g+ G+t+  ++l  r++ d+  ++pd+v 
  gi|518651496|ref|YP_008141016.1|  12 IGDSVTDSNRERpvgrypwGLGNGYVSYIDALLGYLYpdiDQKIVN-MGIAGDTI--RDLKYRWNsDVISQNPDWVS 85 
                                       8******655558999999999******999999999986666666.********..******************** PP

                                       EE--CCCCCTT--HHHHHHH..........HHHHHHHHCCC...GEEECEEEEE-TTT-TTSTCCHHHHHHHHHHHH CS
                     Lipase_GDSL_2  68 iliGtNDlgrgvpaaaaaand........nleelidalraaapgarilvlgplpptpeaaadarelnaviaayneal 136
                                       i+iG+ND++r+ +++  +           ++ +li++   + +     ++  + p++  a  ++ +++ + +y+ ++
  gi|518651496|ref|YP_008141016.1|  86 IMIGINDVWRHFDQPSDHLSLispveyatTINTLIKRTIHHVK-----GIILMSPFYIIASLDNVMRQETLYYAHIM 157
                                       ***************999888****555555555554444433.....33456666666666677899********* PP

                                       HHHHHHCT-EEE-H...HHHHHHCCCCCGGBBTTS.SSB-H CS
                     Lipase_GDSL_2 137 revaaeegvpfvDl...hdaladsgerladlladdglHPna 174
                                       +++  +++ +fv +    da  +++   ++l +d+ +HPn+
  gi|518651496|ref|YP_008141016.1| 158 ESISIRYKTRFVHTqawLDAYMSGT-GAKRLSNDG-VHPNP 196
                                       **************98733333333.344555555.****8 PP

>> Lipase_GDSL  GDSL-like Lipase/Acylhydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.5e-09   9.2e-06       1     199 [.       9     205 ..       9     206 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.5e-09
                                       EEEEESHHHH............TTTHHHHHHHCCCCEECCCTTC.GCEEEEEEECTTHHHHHHHCCHECTTTECHHH CS
                                       xxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL   1 ivafGDSltd............Gdgaatlntiqlktpknlnefdlaldrianignkgasdnelqqllnkyplkseql 65 
                                       i+++GDS td            G+g   ++ i    +  ++ +d   + i n g+ g+  + l+ +        ++ 
  gi|518651496|ref|YP_008141016.1|   9 ILMIGDSVTDsnrerpvgrypwGLGNGYVSYIDALLGYLYPDID---QKIVNMGIAGDTIRDLKYRW------NSDV 76 
                                       899**************999999999999999999999999996...57788888888887777777......7778 PP

                                       HHCTTSEEEEE--CTCC.-EECSSCTTT.CEEHHHHHHHHHHHHHHHHHHHHTTEEEEEEE-SSTCHCTCCCCHCCH CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL  66 kalhpdlviislGtNDs.nlgkkstdaa.kkeaeeyiknlreaikelkeegapkaivvlvsppglgpqeekdakklg 140
                                        +  pd+v i++G ND+  +++++ d+    ++ ey + +  +ik   +   ++  ++l+sp  +  +       l 
  gi|518651496|ref|YP_008141016.1|  77 ISQNPDWVSIMIGINDVwRHFDQPSDHLsLISPVEYATTINTLIK---RTIHHVKGIILMSPFYIIAS-------LD 143
                                       8888*************8666666555535577788888888888...34445556666666666663.......55 PP

                                       HHHHHHHHHHHHHHHHHHHHCTEEEECH...HHHHHHTHCCGCHCHTSSSB-HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Lipase_GDSL 141 ekgnefvgeynqrlndlaekdgfavvDl...ydelqglsgieqlkaDglHpsekgyeklael 199
                                       +  ++   +y+ +++++    +  +v      d   + +g+++l++Dg+Hp++  + +la++
  gi|518651496|ref|YP_008141016.1| 144 NVMRQETLYYAHIMESISIRYKTRFVHTqawLDAYMSGTGAKRLSNDGVHPNPLTNMILANA 205
                                       5555666666666666666444444443000222222246788888********99999876 PP

>> DUF3760  Protein of unknown function (DUF3760)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.3e-05      0.14      12      38 ..     101     127 ..      91     164 .. 0.82
   2 ?   -1.9   0.0      0.66     4e+03      19      26 ..     195     202 ..     193     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                           DUF3760  12 ldeLsrlrPltyllLSrfhYksiiPil 38 
                                       +d+Ls ++P++y +   +  k++i+++
  gi|518651496|ref|YP_008141016.1| 101 SDHLSLISPVEYATTINTLIKRTIHHV 127
                                       69***********************98 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                           DUF3760  19 rPltyllL 26 
                                        Plt++ L
  gi|518651496|ref|YP_008141016.1| 195 NPLTNMIL 202
                                       59***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1421.02
//
Query:       gi|518651497|ref|YP_008141017.1|  [L=479]
Description: hypothetical protein FACI_IFERC00001G0136 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-54  184.0  15.6    1.2e-49  169.0   9.2    2.2  2  Glyco_hydro_1    Glycosyl hydrolase family 1
  ------ inclusion threshold ------
      0.073   13.4   0.2        3.1    8.1   0.0    2.4  2  Misat_Tub_SegII  Misato Segment II tubulin-like domain


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.4   4.9e-08   0.00044       5      92 ..       2      92 ..       1     109 [. 0.80
   2 !  169.0   9.2   1.3e-53   1.2e-49      93     452 ..     121     466 ..     114     467 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.9e-08
                                      S-TT-EEEEE--HHHHH--TTSTT---BHHHHHHHHGGGSTTS--.-SS...TT-HHHHHHHHHHHHHHTT-SEEEEE- CS
                     Glyco_hydro_1  5 fpedFlwgaataayqiEGawnedGkgesiwDtftetpgkvlegsn.gdv...acdsYhrykeDvallkelgvkayrfSi 79
                                       p++F +g +   +q E + + +   +s w ++++ + ++ +++  gd+   ++ +++ yk+D +   +l+++a r+ i
  gi|518651497|ref|YP_008141017.1|  2 VPNNFKFGFSECGFQSEMGLS-GTDNNSDWFIWSNDKRNIEKHYVsGDLpqnGVAYWDLYKQDHDNADKLNINAARLGI 79
                                      599**************7765.34456777777777766666655555522278899********************** PP

                                      -HHHHSTTSTT-- CS
                     Glyco_hydro_1 80 sWpRilPkGegei 92
                                       W+Ri+ + + +i
  gi|518651497|ref|YP_008141017.1| 80 EWSRIFTESTENI 92
                                      ******9987666 PP

  == domain 2  score: 169.0 bits;  conditional E-value: 1.3e-53
                                       -HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHHH-GGG-............SHHHHHHHHHHHHHHHHHTTT- CS
                     Glyco_hydro_1  93 nekGlayYerLidelleagieplvTlyHwdlPqaLqdeGgwen............rsiidafkeyaevvfkrfgdkv 157
                                       n++ ++ Y  ++   ++++   ++ lyHw +P++L+d   +++            ++ii +f++y++++ ++f + v
  gi|518651497|ref|YP_008141017.1| 121 NKDAIKRYMDIFKDFKSRNKFLIINLYHWTIPKWLNDPSKFSDndkqraiggcfnNHIIIEFTKYCAYIASKFDNIV 197
                                       8889999****************************9866555555555555555599******************** PP

                                       -EEEEEE-HHHHHHHHHTSS-STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSSHHH CS
                     Glyco_hydro_1 158 klwlTfnEpnvvallgyltgefaPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplseseed 234
                                       ++w T+nEpn+v +   + + +  g +  ++ +        ahara++++k  +++  +gi+++    + ++    d
  gi|518651497|ref|YP_008141017.1| 198 DRWSTMNEPNMVYQGCSVDSSYN-GISARKKKF------AEAHARAYDAIK-LYSQKPVGIIFANGDIQSIDG---D 263
                                       **********9988777777775.555555555......56899***9997.566779****99888777765...4 PP

                                       HHHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...-STT CS
                     Glyco_hydro_1 235 keaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseeasls 311
                                       +  +++a+ f+   f+d +++Gd + +  el ++   +p  t    + +k+k+d+lglnyY+++++k+++ +  ++ 
  gi|518651497|ref|YP_008141017.1| 264 NDIVDKAKFFNRYSFFDSIINGDLSWYH-ELTNDG--KPIKTR---SDMKNKVDWLGLNYYSRDVIKRND-SGWEIL 333
                                       45566777777778*********87553.333333..344444...45789*******************.455555 PP

                                       ---SSGGGGG-SB..SS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH--HHHHHHHHHH CS
                     Glyco_hydro_1 312 kteekkleeevdp..slpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveDdkRidYlkeh 386
                                       k   +   + ++   +   +d+gw+i+peg++++++  +++Y+ +pi iteNGl++ +        D +R +Y+ +h
  gi|518651497|ref|YP_008141017.1| 334 KGYGHYCGDIKNSldNRSVSDTGWEIYPEGIYNIIMDYHNRYK-IPITITENGLADDM--------DRYRSNYILSH 401
                                       5555555554433114456899********************9.**********9877........99********* PP

                                       HHHHHHHHHTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH-SS CS
                     Glyco_hydro_1 387 lnevkkaiedgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviekng 452
                                         ++++ai+dg+ ++gY+ wsl+Dn+ewa+g+sk+fGl+ v+  et+eR+++ Sa  yke+i+++g
  gi|518651497|ref|YP_008141017.1| 402 FYNIERAISDGAIVEGYYHWSLTDNYEWASGFSKKFGLFKVN-METKERYMRPSALIYKEIIDSHG 466
                                       ******************************************.9******************9986 PP

>> Misat_Tub_SegII  Misato Segment II tubulin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.018   1.6e+02       4      28 ..     178     202 ..     176     228 .. 0.80
   2 ?    8.1   0.0   0.00034       3.1      11      23 ..     394     406 ..     393     413 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.018
                   Misat_Tub_SegII   4 vtlqlGnyaNyvgtHfWNtQesyft 28 
                                       + + + +y+ y+++ f N+ +   t
  gi|518651497|ref|YP_008141017.1| 178 IIIEFTKYCAYIASKFDNIVDRWST 202
                                       568999***********99877554 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00034
                   Misat_Tub_SegII  11 yaNyvgtHfWNtQ 23 
                                       ++Ny+ +Hf+N+ 
  gi|518651497|ref|YP_008141017.1| 394 RSNYILSHFYNIE 406
                                       69*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 3105.83
//
Query:       gi|518651498|ref|YP_008141018.1|  [L=338]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-41  141.5   0.3    2.8e-41  141.2   0.3    1.1  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
    3.8e-20   71.5   0.0    7.1e-20   70.7   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.2   0.3   3.1e-45   2.8e-41       1     232 [.     110     335 ..     110     336 .. 0.97

  Alignments for each domain:
  == domain 1  score: 141.2 bits;  conditional E-value: 3.1e-45
                                       -EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S CS
                    Regulator_TrmB   1 avwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvr 77 
                                       ++w vk++++v eri ++I+sA+ne+i++l+   +  +r+ + +a ++g+tV l++++d +++el++    + +++r
  gi|518651498|ref|YP_008141018.1| 110 YIWFVKGNKNVTERIISMIYSAKNEIIMALSHDSFVNVRKFINSALKKGITVALVLFDDTNDNELKTVPPGVILKKR 186
                                       59*************************************************************************** PP

                                       ---S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHH CS
                    Regulator_TrmB  78 rsgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlav 154
                                        +++ ++v+vDr+  + + ++    ++  y+i+ +e++l hvls+yF+  +W +s++i  + ++   +++++i+l++
  gi|518651498|ref|YP_008141018.1| 187 LEKPMEMVLVDRNFILSNLKS--GIENMDYSIYLEEDQLLHVLSYYFFYDIWLPSKYII-YPENFIHYKLNNIWLTC 260
                                       *************98888776..88999*******************************.999999*********** PP

                                       HHHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTT.EEEEEEEETTEEEEEE-TT--SSSEEEEEEEE CS
                    Regulator_TrmB 155 edikkllraglkveaeveGrdtetgeevtieGrvveatlnstpg.vaslvvetedgevtVGGlgAvlEDieaeeitl 230
                                       + i+  l+++ k++a++ G+   +++++ ++ ++++  +++++g +++++v+ ++++++VGG+ A+ EDi+   +t+
  gi|518651498|ref|YP_008141018.1| 261 DIIDYYLTNNIKLKADLNGII--NNKNISLKCEIIK--TERINGvRQTFFVKDDKNTYSVGGKSALREDIKLIDVTI 333
                                       *********************..*************..8988888******************************99 PP

                                       EE CS
                    Regulator_TrmB 231 er 232
                                       +r
  gi|518651498|ref|YP_008141018.1| 334 SR 335
                                       75 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0     8e-24   7.1e-20       1      67 [.       9      75 ..       9      76 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 8e-24
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+ +GLs yE+k+Y++Ll +gp ta+   +++gvp++++Y+  +sLe kG+V+++ g+++lYrav++
  gi|518651498|ref|YP_008141018.1|  9 LKRFGLSNYEIKIYKTLLLKGPNTATGTVKIAGVPQPRIYDLFSSLEGKGFVDTVTGKRHLYRAVPV 75
                                      789**************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2409.76
//
Query:       gi|518651499|ref|YP_008141019.1|  [L=327]
Description: hypothetical protein FACI_IFERC00001G0138 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.4   0.0    1.4e-26   93.6   0.0    1.4  1  ABC_tran         ABC transporter
    1.4e-14   54.3   0.1      3e-14   53.3   0.0    1.6  1  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
     0.0012   18.7   4.5     0.0083   16.0   0.8    2.2  2  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
     0.0017   17.6   0.1      0.023   13.9   0.0    2.0  2  NB-ARC           NB-ARC domain
     0.0025   17.3   4.3      0.017   14.6   4.3    1.9  1  SMC_N            RecF/RecN/SMC N terminal domain
     0.0088   15.8   0.2      0.018   14.7   0.2    1.5  1  AAA_29           P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.029   14.1   0.0    1.3  1  PRK              Phosphoribulokinase / Uridine kinase family
      0.019   14.0   0.4      0.034   13.2   0.1    1.5  2  T2SSE            Type II/IV secretion system protein
      0.023   14.4   0.0      0.038   13.7   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
      0.026   14.9   0.0      0.032   14.6   0.0    1.2  1  AAA_16           AAA ATPase domain
      0.037   14.6   0.6        0.1   13.2   0.6    1.8  1  AAA_18           AAA domain
      0.037   13.0   0.1      0.091   11.7   0.0    1.5  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.043   13.7   0.1       0.12   12.3   0.1    1.7  2  RsgA_GTPase      RsgA GTPase
      0.056   13.2   0.6      0.056   13.2   0.6    2.5  2  Orthopox_B11R    Orthopoxvirus B11R protein
      0.079   12.7   0.3       0.17   11.5   0.3    1.6  1  AAA_24           AAA domain
      0.099   11.9   0.0       0.17   11.1   0.0    1.3  1  Zeta_toxin       Zeta toxin
        0.1   12.7   1.1       0.16   12.0   0.3    1.7  2  DUF87            Helicase HerA, central domain
        0.1   12.5   0.0       0.18   11.7   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.11   12.8   0.7       0.44   10.8   0.7    2.0  1  AAA_22           AAA domain
       0.18   11.7   0.1       0.32   10.9   0.1    1.3  1  NACHT            NACHT domain
       0.43   11.1   2.6       0.38   11.2   0.5    1.8  2  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 !   93.6   0.0   1.6e-29   1.4e-26       1     136 [.      25     181 ..      25     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.6e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxx.. RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp....teGeilldgkdlke....qeleslrkeigvlpqe.. 67 
                                       lkn++++++++ +++i Ge+G+GKStL++ l++ lk     t G+i ++g ++ +    + ++    + +++pq   
  gi|518651499|ref|YP_008141019.1|  25 LKNINFSVQKNIILGIAGESGSGKSTLASSLYNYLKYpgkiTGGNIIFNGINILNakpnDLRKLRGVKYSFIPQAam 101
                                       79*******************************99988999999999999999998885556666679999999988 PP

                                       --S-TTSBHHHH..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxxxxxxxxx..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  68 pqlfpeltvren..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkll 130
                                       + l+p +++r +              e+d++i+++l+ ++l   +++v+++ p++LSgG++qrv++a+al+  p+l+
  gi|518651499|ref|YP_008141019.1| 102 NALNPVKKIRFQfydmmmahninnenEQDRKIDEILKLVRL---NNNVLDNYPHELSGGMRQRVVIAMALILSPELV 175
                                       88888888888899999999999666666677777777775...559****************************** PP

                                       EEESTT CS
                                       xxxxxx RF
                          ABC_tran 131 llDEpt 136
                                       +lDEpt
  gi|518651499|ref|YP_008141019.1| 176 ILDEPT 181
                                       *****9 PP

>> oligo_HPY  Oligopeptide/dipeptide transporter, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   0.0   3.5e-17     3e-14       1      65 []     233     298 ..     233     298 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.5e-17
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerlde.GCpFapRCpfaleeC 65 
                                       vE g+ + l+++p+HPYT  L +s+pr+  +  k   ikg+  +l+++++ GC F++RC +a ++C
  gi|518651499|ref|YP_008141019.1| 233 VESGSYDSLLNSPAHPYTYSLEKSIPRIGMKINKESIIKGSTINLSNRENsGCYFYDRCIYAENQC 298
                                       8******************************************88777777**************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 ?    4.1   0.9      0.04        34       3      25 ..      39      61 ..      37      95 .. 0.72
   2 !   16.0   0.8   9.7e-06    0.0083     158     302 ..      82     217 ..      64     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.04
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl 25
                                      ++ G  gsGKS+L   l+    +
  gi|518651499|ref|YP_008141019.1| 39 GIAGESGSGKSTLASSLYNYLKY 61
                                      789**********9988766544 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 9.7e-06
                            AAA_21 158 ldglrke..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqel 232
                                        ++lrk    +  +  +a+    +++k++++++++     +i+ +++++++ +  +  +r          n++  + 
  gi|518651499|ref|YP_008141019.1|  82 PNDLRKLrgVKYSFIPQAAMNALNPVKKIRFQFYDMMMAHNINNENEQDRKIDEILKLVR---------LNNNVLDN 149
                                       555555555555555566666778888888888888888888888887666666555555.........46677777 PP

                            AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSplll 302
                                        ++elS G+++   ++ al+  l++  l+++DEp +gL+  + + +l ++ k+ ++ g   i+ +H+ ++l
  gi|518651499|ref|YP_008141019.1| 150 YPHELSGGMRQRVVIAMALI--LSP-ELVILDEPTTGLDVVVEHNILvDIKKIQRSLGMTMIFISHDLSIL 217
                                       88999******933333333..333.9*************9999999555566666888999999998876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.7e-05     0.023      19      43 ..      34      58 ..      18      64 .. 0.82
   2 ?    1.7   0.0      0.15   1.2e+02      42     192 ..     105     266 ..      96     277 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                                      CSEEEEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC 19 qslvvalvGmgGvGKttlakqilnk 43
                                      + +++++ G  G+GK+tla++ +n 
  gi|518651499|ref|YP_008141019.1| 34 KNIILGIAGESGSGKSTLASSLYNY 58
                                      4589****************99985 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.15
                                       CSHCCCCC.CBTEEEEEEEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS....HHHHHHHHCCCTTEEEEEE... CS
                            NB-ARC  42 nksdeveg.rFdsvawvvvsktdkseeiletilkeLslseddleekeeves....lkrklvrlLltkrfllvlD... 110
                                       n  ++++   +d+++   + ++ ++ + +++ilk + l+++ l++ +++ s        +  +L+    l++lD   
  gi|518651499|ref|YP_008141019.1| 105 NPVKKIRFqFYDMMMAHNINNENEQDRKIDEILKLVRLNNNVLDNYPHELSggmrQRVVIAMALILSPELVILDept 181
                                       55555555346788888888888888888889999999999999988877788755556777788888999998777 PP

                                       ...EE-SHHH.H.....HHHHCHTTSEEEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHHHHCCTS-GGCHH.. CS
                            NB-ARC 111 ...DVweeed.wdkigvvlparenrlrvllTTRdeevanavsat.sekievelLekdeawellenkvfekkleekes 182
                                          DV+ e++ +  + +   +r+ ++ +++ + d ++  ++s++   +   e+ e      ll++ + + + + ++s
  gi|518651499|ref|YP_008141019.1| 182 tglDVVVEHNiL--VDIKKIQRSLGMTMIFISHDLSILFEISDEmIMMYSGEIVESGSYDSLLNSPAHPYTYSLEKS 256
                                       777777776634..666666778888888888888887777776333333344443333346666666666666666 PP

                                       CHHHHHHHHH CS
                            NB-ARC 183 leevakeive 192
                                       +++++ +i +
  gi|518651499|ref|YP_008141019.1| 257 IPRIGMKINK 266
                                       6666666655 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   4.3     2e-05     0.017      21     212 ..      31     228 ..      19     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-05
                                       ETTSSE.EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSS CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  21 pfsksf.taivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiek 94 
                                        ++k++   i G+ GSGKs l  ++  +L     k    + + + i+    k ++  k   v+  f  + +  +  +
  gi|518651499|ref|YP_008141019.1|  31 SVQKNIiLGIAGESGSGKSTLASSLYNYLKY-PGKITGGNIIFNGINIlnAKPNDLRKLRGVKYSFIPQAAM-NALN 105
                                       44444313578999***********888874.4433333333333333423455555666788888655554.6667 PP

                                       SCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.......CS-HH..HHHHHHHHHHHHHHCCS--SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  95 eevsisrrvkrkgeseykingkevtkkevsellesagiske.......lLSgG..ektLvalaLlfAiqkvkpaply 162
                                       +  +i+ + +      + in+++ + +++ e+l+ ++++ +       +LSgG  ++ ++a+aL+++        l+
  gi|518651499|ref|YP_008141019.1| 106 PVKKIRFQFYDMMM-AHNINNENEQDRKIDEILKLVRLNNNvldnyphELSGGmrQRVVIAMALILSP------ELV 175
                                       77778777776665.99**********************999999999*****666778999999763......388 PP

                                       EECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHH.CCC-SCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxx.xxxxxxxxxxx RF
                             SMC_N 163 llDeidaaLDeknvkkvaellkekskn..aQfivislreem.lekadklvgvt 212
                                       +lDe    LD    +++   +k+ + +  + +i is++  + +e +d+++ ++
  gi|518651499|ref|YP_008141019.1| 176 ILDEPTTGLDVVVEHNILVDIKKIQRSlgMTMIFISHDLSIlFEISDEMIMMY 228
                                       99999999999999888888885554433888888888665144557776666 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 !   14.7   0.2   2.2e-05     0.018      19      39 ..      30      52 ..      20      69 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
                            AAA_29 19 idlkg..atlltGpsGsGKSTll 39
                                      ++++   +  ++G+sGsGKSTl 
  gi|518651499|ref|YP_008141019.1| 30 FSVQKniILGIAGESGSGKSTLA 52
                                      55444445569**********95 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.4e-05     0.029       1      27 [.      37      63 ..      37     104 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.4e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrek 27
                                      ++g+ag+SG+Gk+t+a  l + ++  +
  gi|518651499|ref|YP_008141019.1| 37 ILGIAGESGSGKSTLASSLYNYLKYPG 63
                                      78*****************99998444 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 ?   13.2   0.1     4e-05     0.034     105     154 ..       8      60 ..       2      67 .. 0.69
   2 ?   -3.1   0.0       3.7   3.2e+03      94     124 ..     109     139 ..      87     146 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                             T2SSE 105 lddlgaeealk...ekiaevlrkavrerglilvsGgTgsGKttllyallkein 154
                                       +++l a   ++   +ki + ++ +v+++ ++ ++G  gsGK+tl+ +l ++++
  gi|518651499|ref|YP_008141019.1|   8 VNNLNAGYYMEtgfAKILKNINFSVQKNIILGIAGESGSGKSTLASSLYNYLK 60 
                                       555555555551114555556667777777779************99988876 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.7
                             T2SSE  94 viRkksakeltlddlgaeealkekiaevlrk 124
                                        iR +    +  +++  e++++ ki+e+l+ 
  gi|518651499|ref|YP_008141019.1| 109 KIRFQFYDMMMAHNINNENEQDRKIDEILKL 139
                                       4666666666777777777888888888765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-05     0.038       8      46 ..      21      59 ..      16      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
                                      HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
                   Sigma54_activat  8 lkelleqikkvaktdlsvlitGesGtGKellaraiheas 46
                                      ++++l++i+  +++++ + i GesG+GK++la+++++  
  gi|518651499|ref|YP_008141019.1| 21 FAKILKNINFSVQKNIILGIAGESGSGKSTLASSLYNYL 59
                                      5678888888999999999****************9864 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   3.8e-05     0.032      29      52 ..      40      69 ..      25     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.8e-05
                            AAA_16 29 lsGesGvGKsslvrellralekd......g 52
                                      + GesG+GKs+l+ +l+++l+        +
  gi|518651499|ref|YP_008141019.1| 40 IAGESGSGKSTLASSLYNYLKYPgkitggN 69
                                      89***************9998875555542 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.6   0.00012       0.1       2      55 ..      39     113 ..      38     176 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00012
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.................gvnlrdvakenglllevdpe....aldeskrlded 55 
                                       +++G +G+GK+tla  L + l++                   + +d+ k +g  +++ p+    al++ k+++ +
  gi|518651499|ref|YP_008141019.1|  39 GIAGESGSGKSTLASSLYNYLKYpgkitggniifnginilNAKPNDLRKLRGVKYSFIPQaamnALNPVKKIRFQ 113
                                       599**************9988889888866666665555544445555555555555555555544444444444 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011     0.091      17      57 ..      23      63 ..      16      67 .. 0.88
   2 ?   -2.6   0.0       2.5   2.1e+03     227     255 ..     113     141 ..     104     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      HHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 17 ellerllakaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                      ++l+++  +  +   +G+ G  G+Gkstl + l   l+  G
  gi|518651499|ref|YP_008141019.1| 23 KILKNINFSVQKNIILGIAGESGSGKSTLASSLYNYLKYPG 63
                                      68889999999999******************999887766 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHH CS
                              MeaB 227 ehrevlkktGllekrrrerakeelrelve 255
                                       ++ +++ +    ++++++r+ +e+ +lv+
  gi|518651499|ref|YP_008141019.1| 113 QFYDMMMAHNINNENEQDRKIDEILKLVR 141
                                       67788888888889999999999988885 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   0.00014      0.12      89     121 ..      24      57 ..       7      65 .. 0.78
   2 ?   -2.5   0.0       4.9   4.2e+03      57      85 ..     185     213 ..     181     226 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00014
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                        l++++  +++  +  ++G+SG GKStL  +l +
  gi|518651499|ref|YP_008141019.1|  24 ILKNINFSVQKnIILGIAGESGSGKSTLASSLYN 57 
                                       56777778887345569***********998865 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                                       GG--HHHHHHHHHHHHHHTTSEEEE--TT CS
                       RsgA_GTPase  57 Dlleeeeeleelkeelealgyevllvsak 85 
                                       D++ e++ l ++k+  ++lg++++++s +
  gi|518651499|ref|YP_008141019.1| 185 DVVVEHNILVDIKKIQRSLGMTMIFISHD 213
                                       66667777778889999999999998865 PP

>> Orthopox_B11R  Orthopoxvirus B11R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.64   5.5e+02      20      33 ..      23      36 ..      16      43 .. 0.89
   2 ?   13.2   0.6   6.5e-05     0.056      12      49 ..     127     165 ..     116     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.64
                     Orthopox_B11R 20 eilknveiennkni 33
                                      +ilkn++   +kni
  gi|518651499|ref|YP_008141019.1| 23 KILKNINFSVQKNI 36
                                      69******999998 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 6.5e-05
                     Orthopox_B11R  12 neidrekeeilknveiennkninknhp.sGyirealvin 49 
                                       ne dr+ +eilk v ++nn   n  h  sG +r+ +vi 
  gi|518651499|ref|YP_008141019.1| 127 NEQDRKIDEILKLVRLNNNVLDNYPHElSGGMRQRVVIA 165
                                       899*************99988888775599999999996 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.3    0.0002      0.17       3      26 ..      36      58 ..      34      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                            AAA_24  3 lkiliyGpsgiGKTtlakelgpkp 26
                                      + + i G+sg+GK+tla++l ++ 
  gi|518651499|ref|YP_008141019.1| 36 IILGIAGESGSGKSTLASSL-YNY 58
                                      56789*************99.665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.17       6      41 ..      26      60 ..      22      73 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                        Zeta_toxin  6 kdkkypsqerPklillgGqpGAGKselaellkdele 41
                                      k+++  s ++ +++ ++G +G+GKs+la+ l ++l+
  gi|518651499|ref|YP_008141019.1| 26 KNIN-FSVQKNIILGIAGESGSGKSTLASSLYNYLK 60
                                      5554.56677788889*************9988875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00019      0.16      26      58 ..      38      72 ..      28      73 .. 0.83
   2 ?   -2.6   0.0       5.6   4.8e+03     149     174 ..     113     138 ..      83     156 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00019
                             DUF87 26 lAilgsTGsGKSntvavLleelle..kkgatilil 58
                                      l+i g++GsGKS+++++L + l    k  +  +i+
  gi|518651499|ref|YP_008141019.1| 38 LGIAGESGSGKSTLASSLYNYLKYpgKITGGNIIF 72
                                      6899**************99887655555566665 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.6
                             DUF87 149 elkkekeelrklknqaiarlldkled 174
                                       + ++++  ++ ++++ + r++d + +
  gi|518651499|ref|YP_008141019.1| 113 QFYDMMMAHNINNENEQDRKIDEILK 138
                                       33333333333333333333333333 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   0.00021      0.18       3      31 ..      36      64 ..      34      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT- CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgi 31
                                      +++ ++G sgsGKst+a  l ++L+  g+
  gi|518651499|ref|YP_008141019.1| 36 IILGIAGESGSGKSTLASSLYNYLKYPGK 64
                                      566799****************9987764 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00051      0.44       8      29 ..      38      59 ..      33     216 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00051
                            AAA_22  8 lvvtGesGtGKTtllrrlleql 29
                                      l + GesG+GK+tl+  l + l
  gi|518651499|ref|YP_008141019.1| 38 LGIAGESGSGKSTLASSLYNYL 59
                                      5589***********9987755 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00037      0.32       5      25 ..      40      60 ..      37      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                                      EEC-TTTCHHHHHHHHHHHHC CS
                             NACHT  5 lqGeaGsGKTtLlqklalawa 25
                                      + Ge+GsGK+tL+ +l   ++
  gi|518651499|ref|YP_008141019.1| 40 IAGESGSGKSTLASSLYNYLK 60
                                      78************9987665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00044      0.38      14      36 ..      27      52 ..      19      55 .. 0.77
   2 ?   -1.5   0.1       3.5     3e+03     129     155 ..     109     133 ..      64     153 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00044
                            AAA_23 14 eidF...skgltlItGpNGaGKTTil 36
                                      +i+F   ++ +  I G+ G+GK+T+ 
  gi|518651499|ref|YP_008141019.1| 27 NINFsvqKNIILGIAGESGSGKSTLA 52
                                      5777775556778***********96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.5
                            AAA_23 129 kiilnlilflgqerfeefelkdkkerl 155
                                       ki++++++++ + + +++  +++  ++
  gi|518651499|ref|YP_008141019.1| 109 KIRFQFYDMMMAHNINNE--NEQDRKI 133
                                       444444444333332111..1111122 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                       103  (0.00574488); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2176.36
//
Query:       gi|518651500|ref|YP_008141020.1|  [L=262]
Description: hypothetical protein FACI_IFERC00001G0139 [Ferroplasma acidarmanus fer1]
Scores for complete 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    7.6e-34  117.2   0.0    1.2  1  ABC_tran      ABC transporter
    4.1e-06   26.8   1.9     0.0012   18.8   0.2    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    1.2e-05   24.8   0.0      3e-05   23.6   0.0    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
    4.1e-05   24.2   0.1    6.4e-05   23.6   0.1    1.3  1  AAA_23        AAA domain
    8.2e-05   22.1   0.2      0.011   15.1   0.1    2.2  2  TniB          Bacterial TniB protein
    0.00014   22.3   0.0    0.00024   21.6   0.0    1.4  1  oligo_HPY     Oligopeptide/dipeptide transporter, C-terminal 
    0.00022   20.5   0.0    0.00023   20.5   0.0    1.2  1  G-alpha       G-protein alpha subunit
    0.00039   20.1   0.0    0.00073   19.2   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
    0.00062   20.1   0.4     0.0052   17.1   0.4    2.0  1  AAA_22        AAA domain
    0.00068   19.5   1.1     0.0012   18.7   0.9    1.4  1  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.4   0.2      0.059   13.4   0.0    2.1  3  AAA_14        AAA domain
      0.018   14.8   0.0      0.033   13.9   0.0    1.5  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.05   14.1   0.0        0.1   13.2   0.0    1.6  1  AAA_18        AAA domain
      0.052   13.7   0.0       0.17   12.0   0.0    1.9  2  AAA_33        AAA domain
      0.055   12.6   0.0      0.098   11.8   0.0    1.3  1  NB-ARC        NB-ARC domain
      0.056   13.9   0.1          3    8.3   0.1    2.3  1  AAA           ATPase family associated with various cellular 
      0.089   12.9   0.1       0.22   11.7   0.1    1.6  1  Peripla_BP_7  Periplasmic binding protein domain
       0.13   12.6   0.1       0.19   12.1   0.1    1.4  1  AAA_16        AAA ATPase domain
       0.43    9.2   5.1        3.7    6.1   0.6    2.3  2  AAA_13        AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   8.1e-37   7.6e-34       1     136 [.      28     179 ..      28     180 .. 0.93

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 8.1e-37
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG...B-HHHCCHCEEEE-SS..--S-T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke...qeleslrkeigvlpqe..pqlfp 72 
                                       l+nv+++l+e e+++ivG +G+GKStL+k++  l++pt+G+i ++++++++    +++++rk+i++++q+  ++l+p
  gi|518651500|ref|YP_008141020.1|  28 LDNVNIELNERELIGIVGASGSGKSTLAKIFVLLYRPTSGSIYFNDENITKyksGKIKKYRKNIQMVFQDpyASLDP 104
                                       79***********************************************9999999**************999**** PP

                                       TSBHHHH............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  73 eltvren............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       ++tv+ +            + +e+i+++l+ + l+  +  + ++ p++LSgGq+qrv lar+l+ +pk+l++DEp 
  gi|518651500|ref|YP_008141020.1| 105 NHTVEWHikrplilikykgDINERINQLLNMVTLDPPEYYK-NKFPHQLSGGQRQRVYLARTLAVEPKILIADEPV 179
                                       ****999********99999999999999999999844433.4557*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.2e-06    0.0012       2      48 ..      41      90 ..      40      98 .. 0.82
   2 !    7.7   0.1    0.0028       2.7     234     301 ..     149     214 ..      98     216 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                            AAA_21  2 nvliGpNgsGKSnLLdaldllarl...drdvegltdelsggggirkipsl 48
                                       +++G+ gsGKS+L +++ ll r      +++++++++ ++g+i+k+++ 
  gi|518651500|ref|YP_008141020.1| 41 IGIVGASGSGKSTLAKIFVLLYRPtsgSIYFNDENITKYKSGKIKKYRKN 90
                                      68*******************99999977777777777777777777665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0028
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHSpll 301
                                       +++lS G+++  +l+  l+  +   ++l+ DEp + L+ ++   +l llk  ++  +  +i  TH+   
  gi|518651500|ref|YP_008141020.1| 149 PHQLSGGQRQRVYLARTLAVEP---KILIADEPVSMLDVSVRIDILNLLKTIRDnLNLSIIYITHDLNT 214
                                       4566999999988888888777...99**********************666666789*******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 !   23.6   0.0   3.2e-08     3e-05      23     208 ..      37     222 ..      20     232 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.2e-08
                                       TSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE.SSSSSSCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
                             SMC_N  23 sksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk.lkiekeevs 98 
                                       ++++  ivG+ GSGKs l   i FvL  r ++     + +++ ++++ k +  + +++++f+++ ++  + ++ e+ 
  gi|518651500|ref|YP_008141020.1|  37 ERELIGIVGASGSGKSTLAK-I-FVLLYRPTSGSIYFNDENITKYKSGKIKKYRKNIQMVFQDPYASlDPNHTVEWH 111
                                       456889**********9865.6.999998776555566677777778888888999*****9999882334444566 PP

                                       EEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  99 isrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyllDe 166
                                       i+r ++        i+ k   ++ +++ll+++ +++          +LSgG+++ v la  +A++   p+ + + De
  gi|518651500|ref|YP_008141020.1| 112 IKRPLI-------LIKYKGDINERINQLLNMVTLDPPeyyknkfphQLSGGQRQRVYLARTLAVE---PK-ILIADE 177
                                       666554.......444444455667777777777776677777888*************999975...44.7789** PP

                                       TTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 167 idaaLDeknvkkvaellkekskn..aQfivislreemleka.dkl 208
                                         + LD + +  + +llk+ ++n    +i i+++ ++++   d+l
  gi|518651500|ref|YP_008141020.1| 178 PVSMLDVSVRIDILNLLKTIRDNlnLSIIYITHDLNTVSMItDRL 222
                                       ******************888873366788888888777663444 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   6.7e-08   6.4e-05       3      96 ..      21     114 ..      20     160 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 6.7e-08
                            AAA_23   3 kienfrsfrdqeidF.skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay...v 75 
                                       k +n+  +++++i++ ++ l  I+G  G+GK+T+   i   Ly  t++     +  f+++ ++  ++gk k+y   +
  gi|518651500|ref|YP_008141020.1|  21 KGRNVVALDNVNIELnERELIGIVGASGSGKSTLAK-IFVLLYRPTSG-----SIYFNDENITKYKSGKIKKYrknI 91 
                                       56899999*******888***************987.77889984433.....456666666666666666666557 PP

                            AAA_23  76 eltfenkdgry..trsiererel 96 
                                       ++ f++       + ++e+ +++
  gi|518651500|ref|YP_008141020.1|  92 QMVFQDPYASLdpNHTVEWHIKR 114
                                       77775544333666666665554 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.015        14      38      62 ..      41      65 ..      31      77 .. 0.84
   2 !   15.1   0.1   1.2e-05     0.011     114     160 ..     164     208 ..     113     221 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.015
                              TniB 38 lllvGdsnnGKtmivekFarlhppe 62
                                      + +vG s  GK+++++ F  l++p+
  gi|518651500|ref|YP_008141020.1| 41 IGIVGASGSGKSTLAKIFVLLYRPT 65
                                      569*************998777665 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.2e-05
                              TniB 114 llrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlv 160
                                          ++++++Li DE  ++l   ++ +  +ln+lk++ ++l+++i+++
  gi|518651500|ref|YP_008141020.1| 164 RTLAVEPKILIADEPVSML--DVSVRIDILNLLKTIRDNLNLSIIYI 208
                                       3446889************..6667899****************987 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 !   21.6   0.0   2.5e-07   0.00024       1      29 [.     231     259 ..     231     262 .] 0.93

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.5e-07
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprld 29 
                                       vE+g++++++++p  +YT+ L++s+p + 
  gi|518651500|ref|YP_008141020.1| 231 VEEGNTDNIIKNPVDRYTRELIESAPNPY 259
                                       8*************************875 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.4e-07   0.00023      26      80 ..      41     100 ..      26     242 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.4e-07
                                       EEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHHHHHHHHHHHHHHHH CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg.....fseeelatwraviqlnivrsiktileales 80 
                                       + ++G+s+SGKsT+ k + lly+++     f++e++ ++++  +++  ++i+++++    
  gi|518651500|ref|YP_008141020.1|  41 IGIVGASGSGKSTLAKIFVLLYRPTsgsiyFNDENITKYKSGKIKKYRKNIQMVFQDPYA 100
                                       5589******************************99999998888888888888765433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   7.7e-07   0.00073      12      55 ..      28      72 ..      23      74 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 7.7e-07
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvpak..kvrfN 55
                                      +d+  ie+++++ + ++G+sGsGKSTl   i +lL+ ++  ++ fN
  gi|518651500|ref|YP_008141020.1| 28 LDNVNIELNERELIGIVGASGSGKSTLA-KIFVLLYRPTsgSIYFN 72
                                      567788999888999***********97.44444443333666666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.4   5.5e-06    0.0052       5     128 ..      38     208 ..      34     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.5e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv.....fvtlpsstsskdllrellralglelka...... 70 
                                       + ++ ++G sG+GK+tl++ ++  +          ++ +      +t  +s++ k+ ++++   ++++  +      
  gi|518651500|ref|YP_008141020.1|  38 RELIGIVGASGSGKSTLAKIFVLLYRPT-------SGSIyfndeNITKYKSGKIKKYRKNIQMVFQDPYASldpnht 107
                                       567789*****************99432.......222222443444555556666666666666666555666666 PP

                            AAA_22  71 .....................................erlsseellealeqalrarav............ielliiD 98 
                                                                            +++  ++l           ++            +++li D
  gi|518651500|ref|YP_008141020.1| 108 vewhikrplilikykgdinerinqllnmvtldppeyyKNKFPHQLS--------GGQRqrvylartlavePKILIAD 176
                                       6666666666666666666677777777655555455333333333........22222333333346677888888 PP

                            AAA_22  99 Eaqh.lr...seealeeLrsllnlsrkgvqliLv 128
                                       E    l+   + ++l+ L+++ +    ++++i++
  gi|518651500|ref|YP_008141020.1| 177 EPVSmLDvsvRIDILNLLKTIRD--NLNLSIIYI 208
                                       87775657444888888888888..666666655 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.9   1.2e-06    0.0012      13      80 ..      27      96 ..      20     154 .. 0.61

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.2e-06
                            AAA_15 13 slkdveidlsee.ltvliGkNnsGKSsilealdlFlnnk...ekkn.kkvikiekedleifeniseskdikId 80
                                      +l++v i+l+e  l  ++G+ +sGKS++++++ l+   +    ++n ++ +k ++    + +++ +++++  +
  gi|518651500|ref|YP_008141020.1| 27 ALDNVNIELNEReLIGIVGASGSGKSTLAKIFVLLYRPTsgsIYFNdENITKYKS---GKIKKYRKNIQMVFQ 96
                                      578999****999**********************99883323333322222222...222233444444333 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   6.3e-05     0.059       2      55 ..      38      90 ..      37     114 .. 0.71
   2 ?   -2.2   0.0       4.1   3.9e+03      64      72 ..     169     177 ..     125     210 .. 0.50
   3 ?   -1.7   0.0       2.9   2.7e+03      21      47 ..     195     219 ..     190     239 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 6.3e-05
                            AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllel 55
                                      r+++ i+Ga  +GK+tl+k ++  +  + +  +y+n ++ +++k+ + +k+ + 
  gi|518651500|ref|YP_008141020.1| 38 RELIGIVGASGSGKSTLAKIFVLLY-RPTSGSIYFNDENITKYKSGKIKKYRKN 90
                                      56789************98888444.5999999999999988776655322222 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.1
                            AAA_14  64 kktylflDE 72 
                                       + ++l+ DE
  gi|518651500|ref|YP_008141020.1| 169 EPKILIADE 177
                                       344444454 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.9
                            AAA_14  21 qlikellvkkesilyinldderdkkla 47 
                                       + i+++l  + si+yi+ d ++ ++++
  gi|518651500|ref|YP_008141020.1| 195 KTIRDNL--NLSIIYITHDLNTVSMIT 219
                                       5566666..688999988877665554 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.5e-05     0.033       1      45 [.      40      83 ..      40     114 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                               PRK  1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldrae 45
                                      +Ig+ g+SG+Gk+t+a+ ++ + +  +  + + +   ++++++ +
  gi|518651500|ref|YP_008141020.1| 40 LIGIVGASGSGKSTLAKIFVLLYR-PTSGSIYFNDENITKYKSGK 83
                                      69**************99987766.44444555555555555554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00011       0.1       1      17 [.      41      57 ..      41     107 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                            AAA_18  1 IlltGtpGvGKttlake 17
                                      I++ G++G+GK+tlak 
  gi|518651500|ref|YP_008141020.1| 41 IGIVGASGSGKSTLAKI 57
                                      89*************96 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   0.00018      0.17       2      17 ..      41      56 ..      40      92 .. 0.91
   2 ?   -1.1   0.0         2   1.9e+03      24      45 ..     134     155 ..     125     215 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                            AAA_33  2 vllvGlpGsGKstlae 17
                                      + +vG++GsGKstla+
  gi|518651500|ref|YP_008141020.1| 41 IGIVGASGSGKSTLAK 56
                                      5689**********97 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2
                            AAA_33  24 gavllssdtlrrrlfgtdqqsk 45 
                                        +v+l+ ++++++ f+ +    
  gi|518651500|ref|YP_008141020.1| 134 NMVTLDPPEYYKNKFPHQLSGG 155
                                       4666666666666666322222 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001     0.098      16      38 ..      36      56 ..      24      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
                                      TTSCSEEEEEEESTTSSHHHHHH CS
                            NB-ARC 16 delqslvvalvGmgGvGKttlak 38
                                      +e +  ++++vG  G+GK+tlak
  gi|518651500|ref|YP_008141020.1| 36 NERE--LIGIVGASGSGKSTLAK 56
                                      4556..99*************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 ?    8.3   0.1    0.0031         3       3      52 ..      43      97 ..      41     231 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0031
                                      EESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfke 52
                                      ++G  G GK++lak  +        +++f   + ++  s  +++  k+i+++f++
  gi|518651500|ref|YP_008141020.1| 43 IVGASGSGKSTLAKIFVLLYrptsgSIYFNDENITKYKSGKIKKYRKNIQMVFQD 97
                                      5789999999999988777533333355555555555555666666666666665 PP

>> Peripla_BP_7  Periplasmic binding protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00023      0.22      23      60 ..     193     228 ..     187     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                       HHHHHHHHTTEEEEEEE-BSS-THHHHTTS--GGG-SE CS
                      Peripla_BP_7  23 llkkYkdllnldlevvaGDgqsEssildrlgnlkkyDa 60 
                                       llk+  d lnl++ ++  D ++ s i+drl    ++D+
  gi|518651500|ref|YP_008141020.1| 193 LLKTIRDNLNLSIIYITHDLNTVSMITDRL--YVMHDG 228
                                       89999*************************..556665 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    0.0002      0.19      25      45 ..      39      59 ..      27     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                            AAA_16 25 elvllsGesGvGKsslvrell 45
                                      el+ ++G+sG+GKs+l++ + 
  gi|518651500|ref|YP_008141020.1| 39 ELIGIVGASGSGKSTLAKIFV 59
                                      78889***********97655 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0087       8.2      21      48 ..      43      70 ..      33     135 .. 0.63
   2 ?    6.1   0.6    0.0039       3.7     526     578 ..     169     219 ..     160     242 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0087
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkf 48
                                      i G+ G+GK+tL++++  l +    + +
  gi|518651500|ref|YP_008141020.1| 43 IVGASGSGKSTLAKIFVLLYRPTSGSIY 70
                                      56999**********9998654433333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0039
                            AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevk 578
                                       + ki + D PvS LD  +   + +l+k+   ++ +   ++  TH l+    ++
  gi|518651500|ref|YP_008141020.1| 169 EPKILIADEPVSMLDVSVRIDILNLLKTIR-DNLNL-SIIYITHDLNTVSMIT 219
                                       789*************************95.44444.5666799988766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 1809.52
//
Query:       gi|518651501|ref|YP_008141021.1|  [L=319]
Description: hypothetical protein FACI_IFERC00001G0140 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-12   48.0  24.4    1.2e-12   48.0  24.4    2.1  2  BPD_transp_1  Binding-protein-dependent transport system inne
    8.2e-05   22.5   0.6    8.2e-05   22.5   0.6    3.3  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 ?   -1.6   2.6      0.21   1.8e+03      43      68 ..      50     109 ..      28     114 .. 0.47
   2 !   48.0  24.4   1.3e-16   1.2e-12       2     184 ..     112     301 ..     111     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.21
                      BPD_transp_1  43 f.................................vilsilghlilp.viillllsaapyv 68 
                                       +                                  ++s l +++ p +++ +++++++++
  gi|518651501|ref|YP_008141021.1|  50 LgqffapynpnkyefarsapptyahllgttvygqDVFSQLFYGAAPtLLVGFAVGFMGTF 109
                                       344444444444444444444444444444444433333334444434444444444444 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.3e-16
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilp.viillllsaapyvrlirraal 76 
                                       i++Gi a+ + + +++++++++i+++l +P ++l++l+   f  i  +   + lp ++il+++++a+ +r +r+  l
  gi|518651501|ref|YP_008141021.1| 112 IFVGISAG-FASERVNNIVSGVINIFLIIPGVLLIMLFGSYFlGIHES--LGYLPtILILVITGWAFGARTFRSITL 185
                                       899*****.999*********************888877655344444..4567779******************** PP

                      BPD_transp_1  77 rslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydysei 153
                                       ++  +d++  + + G sr  i+++ ++++++p+i++ +++++++   g +++e+lg    +g+ ll++++g ++ ++
  gi|518651501|ref|YP_008141021.1| 186 SIAKRDFILSSMLIGESRLSIIFRQIIRAIFPVIVSNFFFTAMYGTLGLTFVEYLG----VGN-LLQINWGTMLYWA 257
                                       ********************************************************....774.4566777777766 PP

                      BPD_transp_1 154 s.............nggvlalviavlllnlvadilqrlldprvr 184
                                       +               +++++ i+++ ++l+ + + ++ +p +r
  gi|518651501|ref|YP_008141021.1| 258 InneayltglwwwiLPPSFMISILMFSFILLNFGMDEIGNPSLR 301
                                       66777777779999888888888888888887777777666665 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 !   22.5   0.6   9.1e-09   8.2e-05      15      51 .]      33      70 ..      28      70 .. 0.90
   2 ?   -2.9   1.6      0.77   6.9e+03      26      36 ..     142     152 ..     128     157 .. 0.58
   3 ?   -2.0   0.5      0.42   3.8e+03      16      28 ..     276     288 ..     274     290 .. 0.79

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 9.1e-09
                            OppC_N 15 lAvvglvilllllliaifaPliaPydpqdli.qnllpP 51
                                       A +g+vil+ ++++++++ ++aPy+p+ +  ++ +pP
  gi|518651501|ref|YP_008141021.1| 33 KAKAGFVILVGMIIFSVLGQFFAPYNPNKYEfARSAPP 70
                                      5889***********************88887789999 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.77
                            OppC_N  26 llliaifaPli 36 
                                       +lli +f+ ++
  gi|518651501|ref|YP_008141021.1| 142 VLLIMLFGSYF 152
                                       44455666555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.42
                            OppC_N  16 Avvglvillllll 28 
                                        +++  ++ ++ll
  gi|518651501|ref|YP_008141021.1| 276 FMISILMFSFILL 288
                                       6888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2222.06
//
Query:       gi|518651502|ref|YP_008141022.1|  [L=334]
Description: hypothetical protein FACI_IFERC00001G0141 [Ferroplasma acidarmanus fer1]
Scores for complete 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  139.9  13.2    7.5e-41  139.9  13.2    1.7  3  BPD_transp_1  Binding-protein-dependent transport system inne


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.27   4.8e+03     116     131 ..      13      28 ..       5      44 .. 0.57
   2 ?   -3.9   0.1      0.54   9.8e+03     104     120 ..     104     120 ..     100     123 .. 0.41
   3 !  139.9  13.2   4.2e-45   7.5e-41       1     184 [.     125     330 ..     125     331 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.27
                      BPD_transp_1 116 lafggllggavllefl 131
                                       +af ++l ga+ l fl
  gi|518651502|ref|YP_008141022.1|  13 IAFLAVLYGAITLNFL 28 
                                       3444444444444443 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.54
                      BPD_transp_1 104 Pnalppiitglilafgg 120
                                       + alp ++ ++i ++++
  gi|518651502|ref|YP_008141022.1| 104 REALPWTLYLVISSIAI 120
                                       44444444333333333 PP

  == domain 3  score: 139.9 bits;  conditional E-value: 4.2e-45
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghli 53 
                                       g+ lG +a+ nrn + d  ++ ++ ++ s+P fvla++++ vf                        +i+s+++h+i
  gi|518651502|ref|YP_008141022.1| 125 GNRLGRYAGINRNTVKDLSIDLFSMFMASFPAFVLAFIILDVFsvsggvfpiggaysstvnigfnlpFIISAIYHSI 201
                                       56799************************************************************************ PP

                      BPD_transp_1  54 lpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllef 130
                                       lp+++++l+s++++v+ +r++++ ++++d+++++++lG+++ q + +++++na+ p +tg+ +++g+++ g ++ e 
  gi|518651502|ref|YP_008141022.1| 202 LPILTIVLTSIGGWVLGMRNNIIPNVNSDFIKFSETLGLRKEQ-INRIAYRNAILPNLTGFSMSIGLSVSGVIIEES 277
                                       *******************************************.888****************************** PP

                      BPD_transp_1 131 lgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       ++s+pG+g+ +++ai + dy++i+ g++l+++iavl+ n+++dil+ ++dpr+r
  gi|518651502|ref|YP_008141022.1| 278 IFSYPGVGLYMMTAIDSLDYPLIQ-GIFLMVIIAVLVGNAIVDILYGFFDPRIR 330
                                       ************************.***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2220.35
//
Query:       gi|518651503|ref|YP_008141023.1|  [L=597]
Description: hypothetical protein FACI_IFERC00001G0142 [Ferroplasma acidarmanus fer1]
Scores for complete 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-71  239.7  10.1    7.5e-71  239.1  10.1    1.4  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 !  239.1  10.1   4.2e-75   7.5e-71       2     371 ..      90     454 ..      89     492 .. 0.93

  Alignments for each domain:
  == domain 1  score: 239.1 bits;  conditional E-value: 4.2e-75
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHCTCTEEEEEEEETTEE CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyaslleedqdikkveavddytv 78 
                                        +p+LA++ +++s + + +t++LR++v+Fs+G p+++ Dvv++f   ++  +++g          ik+++av+ ytv
  gi|518651503|ref|YP_008141023.1|  90 TIPWLATN-YTWSHNDTMLTLNLRHNVTFSNGMPFNSTDVVYTFHIQKKLLGQWGH---------IKNITAVNQYTV 156
                                       58******.8**********************************999988888887.........899********* PP

                                       EEEESSETT..TTTTHCHHHHHHHGCCHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTEEEEEE-TTSTTTSCSSSS CS
                         SBP_bac_5  79 rftlkkpna..lfltllaavpasiakkaaekeddkdkdtnekpvgtGPYklkefkpgqkivlernpdYwgggkpkld 153
                                        f++++ ++  lf++    + + +    +++ + ++++  ++p+gtGPY+l +f+  qkivl++np+Yw+ ++p+++
  gi|518651503|ref|YP_008141023.1| 157 DFNFSTIDTqcLFYIGSNFMLPEPL---WVNISSPNSKVVTNPIGTGPYVLSSFSA-QKIVLTANPHYWKSDEPHIK 229
                                       *******997888888888888888...9***************************.************77****** PP

                                       EEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE.EEEEEEEEEEEEEETTTSTGGGSHHHHHHHHH CS
                         SBP_bac_5 154 riefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv.lyespgggvtylafNtkkppfddkrvRqAlsy 229
                                        +++  +++++a  +alq G++  +++ +++++ +l++  + k+ +y++p+g+   l  N +++p++   +RqA+s+
  gi|518651503|ref|YP_008141023.1| 230 NVVYVDYTSASALTLALQEGKV-QWTSAFEPNVSKLFVHYNPKYnHYYFPPGQPSTLITNDAIYPLNLSYFRQAMSM 305
                                       *******6666666666*****.88899999*****9999999999******************************* PP

                                       HS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH.....SHHHHHHHHHHHTT-BCSSTSCEETC...EEE CS
                         SBP_bac_5 230 AiDreeivkavlegyatpansllppsspgadeeykpayka.....ydpekAkklLkeaGykdgdggglrek...klk 298
                                        i+r+ i ++  +gy +pan++   + + ++ + ++a++a     y++++AkklL+++G++ ++g++++++   +++
  gi|518651503|ref|YP_008141023.1| 306 SINRTNICNIGEYGYEKPANAANILQQQLSWLNSTNANEAnklaqYNITEAKKLLAAHGFTIKNGKLYEPNgtkVPS 382
                                       **********************55555555555555544568*********************************** PP

                                       EEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHS CS
                         SBP_bac_5 299 ltlllasgspaekaiaeliqqqlkkiGikvevktvdwaatylervkdgdfdmillgwgadypdpdnflnpfls 371
                                       ltl+ ++g+++++    +i+++lk+iG+++++ t  + at +++  +g+++m+l   +++ p+p + + ++ +
  gi|518651503|ref|YP_008141023.1| 383 LTLISVAGYTDWDTDISIIASDLKEIGLTINIATPTA-ATVEADIASGNYQMALDTVTGIGPNPWYDYTALIG 454
                                       ***********************************99.9*************************999887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       831  (0.0463495); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 4170.48
//
Query:       gi|518651504|ref|YP_008141024.1|  [L=223]
Description: hypothetical protein FACI_IFERC00001G0143 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-22   78.8   0.0    4.9e-22   78.5   0.0    1.1  1  Haem_oxygenas_2  Iron-containing redox enzyme
    8.3e-07   29.0   0.1    1.3e-06   28.4   0.1    1.4  1  TENA_THI-4       TENA/THI-4/PQQC family
    0.00015   21.8   0.0     0.0002   21.3   0.0    1.2  1  DUF3865          Domain of Unknown Function with PDB structur
  ------ inclusion threshold ------
      0.014   15.2   0.1      0.058   13.1   0.1    2.1  1  SHOCT            Short C-terminal domain
       0.16   12.3   2.0       0.67   10.3   0.3    2.5  2  DUF2004          Protein of unknown function (DUF2004)


Domain annotation for each model (and alignments):
>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.5   0.0   1.4e-25   4.9e-22       2     176 ..      40     211 ..      39     213 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.5 bits;  conditional E-value: 1.4e-25
                   Haem_oxygenas_2   2 eflrqrapyklvfgdwlalvhsrltdrevkrallenlsEElGdgdlernHvelyrrllkalGldeeplealpelpet 78 
                                       +f ++++++++ ++ +la ++ ++++++   +l  +l  ElG gd  ++H+ lyrr+l+++G+++e+l   ++l +t
  gi|518651504|ref|YP_008141024.1|  40 RFSIEFYHFTREWPEILAKLLVSTENEDDAYELTGILVSELGSGDSGKRHELLYRRYLRSIGFKPEELVKREQLSTT 116
                                       7899************************************************************************* PP

                   Haem_oxygenas_2  79 lalinlfeavalsrrllgallGallalEllvsletlklaee...lrelgldeeapeyfdlHvtiDnaHaamaleavi 152
                                         +++ +++++ s ++ +  lGa +alE ++ ++++kl+ +   ++e + ++ ++ yf+ H +++  H+  + e++i
  gi|518651504|ref|YP_008141024.1| 117 KGWLDGMREYFSSDHAKA--LGAEFALENMAIPMWDKLLPGlkiMKERKYKDMDILYFTFHRELESTHEDAM-ENII 190
                                       **************9998..*******************99666678999999***************9766.5999 PP

                   Haem_oxygenas_2 153 ellateepeeqedvlegawrrlql 176
                                         +  ++   +e+ + +a+ +l+l
  gi|518651504|ref|YP_008141024.1| 191 GVHSNDQ---KEQFISSAKGMLDL 211
                                       9999988...66666666666655 PP

>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.1   3.5e-10   1.3e-06      16     119 ..      24     133 ..      10     222 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.5e-10
                                       HHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCH.....HHHH.HHHHHHT CS
                        TENA_THI-4  16 FvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgee.....ielh.lrlaeal 86 
                                       F+++ ++G ++ e f+ + i+ y++ ++++  la  l++++++++ +el  ++v  +g+       el+ +r+ ++ 
  gi|518651504|ref|YP_008141024.1|  24 FINRFSRGDITEEEFKRFSIEFYHFTREWPEILAKLLVSTENEDDAYELTGILVSELGSGdsgkrHELLyRRYLRSI 100
                                       99********************************9999999999999*********99999999955545******* PP

                                       T-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HH CS
                        TENA_THI-4  87 Glsreelsktkpspatkayvrylldlarrgsla 119
                                       G ++eel k++ + +tk   + + +  ++++ +
  gi|518651504|ref|YP_008141024.1| 101 GFKPEELVKREQLSTTKGWLDGMREYFSSDHAK 133
                                       ******999999999998777777665555554 PP

>> DUF3865  Domain of Unknown Function with PDB structure (DUF3865)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   5.6e-08    0.0002      72     221 ..      70     219 ..      54     222 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 5.6e-08
                           DUF3865  72 eelqenideelGsgiggishytllaegled.slg.vavksvkPsqatskllesvksvltketeyvlGavyaieassi 146
                                        el   +  elGsg  g  h  l ++ l+  +++ +++++ +   +t+  l+ +++ ++ + +  lGa +a+e  +i
  gi|518651504|ref|YP_008141024.1|  70 YELTGILVSELGSGDSGKRHELLYRRYLRSiGFKpEELVKREQLSTTKGWLDGMREYFSSDHAKALGAEFALENMAI 146
                                       5666777789999999999998888888763443244555555668899**************************** PP

                           DUF3865 147 Pellllrklveylakdevsktldd.ffekhlneieveheadlrnalasyi..kpeeliefeaGfravlevmevWWkd 220
                                       P    l   ++ +++    k++d  +f+ h  e+e  he+ + n +  +   + e++       + +l+  e +W +
  gi|518651504|ref|YP_008141024.1| 147 PMWDKLLPGLKIMKER-KYKDMDIlYFTFH-RELESTHEDAMENIIGVHSndQKEQF---ISSAKGMLDLEEKFWLG 218
                                       *875555444544444.4455554156666.79***********9976531144445...55555577877888877 PP

                           DUF3865 221 l 221
                                       l
  gi|518651504|ref|YP_008141024.1| 219 L 219
                                       6 PP

>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   1.6e-05     0.058       9      22 ..      27      40 ..      26      40 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                             SHOCT  9 LyarGeIteEEFea 22
                                      ++ rG IteEEF +
  gi|518651504|ref|YP_008141024.1| 27 RFSRGDITEEEFKR 40
                                      899*********75 PP

>> DUF2004  Protein of unknown function (DUF2004)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1      0.15   5.2e+02      12      43 ..      32      62 ..      10     119 .. 0.63
   2 ?   10.3   0.3   0.00019      0.67      14      56 ..     159     203 ..     156     209 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.15
                                      HHHHHH.TT---EEEEEEEES--HHHHHHHHHH CS
                           DUF2004 12 dylkne.kdtvtkyidfHvdelgpeieeellek 43
                                      d++++e k+ ++++ +f ++ + pei+++ll +
  gi|518651504|ref|YP_008141024.1| 32 DITEEEfKRFSIEFYHFTRE-W-PEILAKLLVS 62
                                      55666677777777777666.2.2333333333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00019
                                       HHHH..TT---EEEEEEEE..S--HHHHHHHHHHHHHHHS-HHHHHH CS
                           DUF2004  14 lkne..kdtvtkyidfHvd..elgpeieeellekddlsklteeellk 56 
                                       +k++  kd+++ y+ fH++    +++  e++++    s +++e++++
  gi|518651504|ref|YP_008141024.1| 159 MKERkyKDMDILYFTFHREleSTHEDAMENIIGV--HSNDQKEQFIS 203
                                       5555679***********9989999999999999..77777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       471  (0.0262703); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1494.51
//
Query:       gi|518651505|ref|YP_008141025.1|  [L=132]
Description: hypothetical protein FACI_IFERC00001G0144 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.8   2.4      0.016   15.6   0.0    2.2  2  DUF4059   Protein of unknown function (DUF4059)
       0.04   14.2   1.4        0.1   12.9   1.4    1.7  1  DUF5461   Family of unknown function (DUF5461)
       0.05   14.0   7.5      0.063   13.7   7.5    1.1  1  DUF2569   Protein of unknown function (DUF2569)
       0.14   12.4   3.5       0.15   12.4   2.5    1.5  2  DUF3040   Protein of unknown function (DUF3040)
       0.79    9.9   7.2       0.58   10.3   1.7    2.5  3  DUF5326   Family of unknown function (DUF5326)
        7.1    5.6   7.4        8.5    5.3   7.4    1.2  1  PHO4      Phosphate transporter family


Domain annotation for each model (and alignments):
>> DUF4059  Protein of unknown function (DUF4059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6         1   3.1e+03      14      16 ..      44      46 ..      23      60 .. 0.57
   2 ?   15.6   0.0   5.5e-06     0.016      10      43 ..      99     132 .]      97     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                           DUF4059 14 lls 16
                                      +++
  gi|518651505|ref|YP_008141025.1| 44 VIA 46
                                      222 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 5.5e-06
                           DUF4059  10 lqgLllsillvllvsliwillralrkkdKtaker 43 
                                       + +++l ++++++ ++i++  +a + kdK+a+++
  gi|518651505|ref|YP_008141025.1|  99 IDSIILDVIMIIISGAIYFSTKAFKSKDKPANQK 132
                                       568999************************9985 PP

>> DUF5461  Family of unknown function (DUF5461)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.4   3.4e-05       0.1      46      88 ..      18      68 ..       3      71 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                           DUF5461 46 sktyiGivlv.dGvkipfvaevhlnnkid.......iyldprkdfylallv 88
                                      s  ++Gi ++  G+ +p++ +v++   i        iy+  rk+fyl  ++
  gi|518651505|ref|YP_008141025.1| 18 SAIWAGIHMTlLGITLPYIVKVFFGFVIAiaivsamIYVSDRKEFYLPVFI 68
                                      678999977636**********997655322222238**********9987 PP

>> DUF2569  Protein of unknown function (DUF2569)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   7.5   2.1e-05     0.063      32     127 ..      14     111 ..       2     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                           DUF2569  32 alfsleewstlknleslltlllileiitnialvafsilllvlffkrrksfPklyiifllanlvlalidalllspif. 107
                                       +++ ++ w+ ++ +   +tl +i+  +++ +++a++i+ ++++++ rk f   + if+++  vl+l + + ++p+f 
  gi|518651505|ref|YP_008141025.1|  14 GILGSAIWAGIHMTLLGITLPYIV-KVFFGFVIAIAIVSAMIYVSDRKEFYLPVFIFYILDTVLLLESRISIAPVFn 89 
                                       566677788886664455555555.5667788899999999999999999776666666666666666788888855 PP

                           DUF2569 108 ..ekldaqairellqsvlaaai 127
                                           + a ai++++  v+ ++i
  gi|518651505|ref|YP_008141025.1|  90 erLPWTASAIDSIILDVIMIII 111
                                       6788***********9999988 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.5   4.9e-05      0.15      42      82 ..      11      50 ..       2      52 .. 0.81
   2 ?   -3.0   0.0         3   9.1e+03      46      54 ..     103     111 ..      88     117 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.9e-05
                           DUF3040 42 rrlavlavllfvaGllllvlGvaaaavvlgvvGfvvmlagv 82
                                      r+l++l+  +++aG+ + +lG+++  +v +++Gfv+++a v
  gi|518651505|ref|YP_008141025.1| 11 RWLGILG-SAIWAGIHMTLLGITLPYIVKVFFGFVIAIAIV 50
                                      4544444.46689*************9**********9986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3
                           DUF3040  46 vlavllfva 54 
                                       +l v+++++
  gi|518651505|ref|YP_008141025.1| 103 ILDVIMIII 111
                                       333333333 PP

>> DUF5326  Family of unknown function (DUF5326)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7   0.00019      0.58      28      57 ..      28      57 ..      10      63 .. 0.73
   2 ?   -3.2   0.1       3.2   9.4e+03      40      48 ..      68      76 ..      64      85 .. 0.51
   3 ?    2.6   0.0     0.052   1.6e+02      45      61 ..     106     122 ..      86     130 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                           DUF5326 28 liasvvgvligllfkvLvlvalvggliyvv 57
                                      l+   + +++ ++f  ++++a+v+++iyv 
  gi|518651505|ref|YP_008141025.1| 28 LLGITLPYIVKVFFGFVIAIAIVSAMIYVS 57
                                      333445568888999999**********96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.2
                           DUF5326 40 lfkvLvlva 48
                                      +f +L  v 
  gi|518651505|ref|YP_008141025.1| 68 IFYILDTVL 76
                                      333333333 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.052
                           DUF5326  45 vlvalvggliyvvrkft 61 
                                       v++ +++g iy   k  
  gi|518651505|ref|YP_008141025.1| 106 VIMIIISGAIYFSTKAF 122
                                       34455666666655554 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   7.4    0.0029       8.5      97     165 ..      15      79 ..       2     130 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0029
                              PHO4  97 liGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlvt.......i 165
                                       ++G a+ a    +++ ++l+ i l  ++ ++ g++ia++++ ++ ++        ++  +lpv+++ +        
  gi|518651505|ref|YP_008141025.1|  15 ILGSAIWA----GIH-MTLLGITLPYIVKVFFGFVIAIAIVSAMIYV------SDRKEFYLPVFIFYIldtvlllE 79 
                                       44555442....343.569**********************999999......46788899999777634333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.32s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 815.82
//
Query:       gi|518651506|ref|YP_008141026.1|  [L=382]
Description: hypothetical protein FACI_IFERC00001G0145 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   46.6   2.0    2.6e-12   46.2   2.0    1.1  1  HgmA      homogentisate 1,2-dioxygenase
    0.00023   20.8   0.1     0.0033   17.1   0.0    2.5  3  Cupin_2   Cupin domain
  ------ inclusion threshold ------
       0.04   13.6   0.0      0.094   12.4   0.0    1.5  1  Cupin_3   Protein of unknown function (DUF861)


Domain annotation for each model (and alignments):
>> HgmA  homogentisate 1,2-dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.2   2.0   4.4e-16   2.6e-12     135     421 ..     105     379 ..      95     382 .] 0.84

  Alignments for each domain:
  == domain 1  score: 46.2 bits;  conditional E-value: 4.4e-16
                                       ---SEEEEESSEEEEEEEEES-EEEEETTEEEEE-TTEEEEE-TT--EEEE-S.SSEEEEEEEEES--EE--..... CS
                              HgmA 135 smedkafynadGellivpqkGelelvtelGrlkvepgeiaviprGvrfkveledeearGyilevygakfklP..... 206
                                       s  d +f na  + ++  q+G+ ++   +G+lk + g+ + iprG +++  +   e   +      +++ +P     
  gi|518651506|ref|YP_008141026.1| 105 STPDAYFRNALCDEVFYVQSGKGSIESPFGTLKFRKGDFIYIPRGTTYRAVMD--ERSFFFFTISSDHMDIPahymn 179
                                       66788999**99999**********************************8776..4445666777888888833333 PP

                                       --GGGTTS-BS-GGGEEEE-------EE.EEEEEEEEETTEEEEEEEEE-S--EEEEEES---EEEEGGG-B----S CS
                              HgmA 207 dlGPiGanglanprdfkaPvaayedkes.keltviskfqgklfaakldhspldvvaWhGnyvPykydlkkfnvinsv 282
                                       + G i       +rd ++P    e +es  e+++++ +   +   + ++ +ld+ ++ G  +P++ ++ kf++i  v
  gi|518651506|ref|YP_008141026.1| 180 KYGQIKEGMPYYTRDIEIPEFH-ESTESpGEYHIMVDYGSYYLNISRTYPVLDLEGYDGYLYPFTINIDKFAPI--V 253
                                       5699988888899******654.4444459******************************************99..5 PP

                                       SSS---GGGGEEEEEE-SSTT-EEEEEEEE-SE.EE--TTS--S---B--SSE.EEEEEEE-----------TT-EE CS
                              HgmA 283 sfdhpdPsiftvltapsekeGvaivdfvifpPr.WlvaektfrPPyyhrnvms.efmGlieGaydakeeGfvpgGas 357
                                          h+ P ++tv+ a+    G        f Pr +   e++   Pyyh n+ s e++   +G++ ++  G     ++
  gi|518651506|ref|YP_008141026.1| 254 GKLHMPPPVHTVFEAEHFMIGA-------FLPRlFDFHERAIPIPYYHNNIDSdELIFYSSGNFMSR-TGIGEKSIT 322
                                       667***********99988885.......667735688999999*******8746777788999876.688889999 PP

                                       EE-TT--B---HHHHHHHHHS----EEEST-EEEEEEESS--EE-HHHHH-------------- CS
                              HgmA 358 lhslmtahGPdaesfekaskaelkPekiddtlafmfesslvlavtelaaelealdedylecWqg 421
                                       +h     hGP        + ++l  +k d+ +a m es   l+ te a   +  d++y+  W++
  gi|518651506|ref|YP_008141026.1| 323 MHVHGIIHGPQPGV----VGNSLGETKTDE-VAIMVESYKWLMPTEKA--ESVKDKNYMYSWKA 379
                                       9999999***8755....566778888877.9**************99..5567999**99986 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.4   8.3e+03       8      18 ..       7      17 ..       2      21 .. 0.60
   2 !   17.1   0.0   5.5e-07    0.0033      20      56 ..     117     153 ..     109     160 .. 0.88
   3 ?    0.1   0.0      0.11   6.5e+02      13      42 ..     293     324 ..     280     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.4
                                      TEEEEEECSSS CS
                           Cupin_2  8 GesapshrHpg 18
                                       ++ p+ rH++
  gi|518651506|ref|YP_008141026.1|  7 KGKVPEQRHTY 17
                                      34566677766 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 5.5e-07
                                       EEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEE CS
                           Cupin_2  20 deffyVleGegeltvdgeeveleaGdsvyfpagtpHr 56 
                                       de+fyV +G+g ++    + + ++Gd++y+p+gt  r
  gi|518651506|ref|YP_008141026.1| 117 DEVFYVQSGKGSIESPFGTLKFRKGDFIYIPRGTTYR 153
                                       79************66669**************9876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.11
                                       EECSSSEEEEEEEEESE.EEEE.ECTEEEEEE CS
                           Cupin_2  13 shrHpgedeffyVleGe.gelt.vdgeevele 42 
                                        h+  ++de+++  +G  +  t ++++ ++++
  gi|518651506|ref|YP_008141026.1| 293 YHNNIDSDELIFYSSGNfMSRTgIGEKSITMH 324
                                       45555666999999999655566777777776 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05     0.094      26      61 ..     117     151 ..     106     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
                                       EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEE CS
                           Cupin_3  26 dEfcyileGevkvtpeggetvelraGDlvvlpkgls 61 
                                       dE +y+ +G+ +++     t ++r+GD++++p g++
  gi|518651506|ref|YP_008141026.1| 117 DEVFYVQSGKGSIES-PFGTLKFRKGDFIYIPRGTT 151
                                       899***********9.6668**************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (382 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2555.45
//
Query:       gi|518651507|ref|YP_008141027.1|  [L=295]
Description: hypothetical protein FACI_IFERC00001G0146 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-47  160.5   0.0    5.3e-47  160.3   0.0    1.0  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.3   0.0     3e-51   5.3e-47       3     218 .]      75     295 .]      73     295 .] 0.92

  Alignments for each domain:
  == domain 1  score: 160.3 bits;  conditional E-value: 3e-51
                                       EEEEEE--SHHHHHTTT....-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T- CS
                     FAA_hydrolase   3 vcdglnyaehvreagka...aeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevl 76 
                                       v d++++++hv++a+k     + ++++  p+   f++  +  + ++g +i++P++s+ +dyE+E+a+vig ++ +  
  gi|518651507|ref|YP_008141027.1|  75 VRDFYAFEDHVKNARKNkglDMIKEWYDFPV---FYFSCTPNVYPSGYEIKYPEKSKAFDYEMEVAAVIGNRTIDCH 148
                                       789***********99998877788866555...****999******************************888884 PP

                                       -HHHHHTTEEEEEEEEEEE-SBGGG---..HHHHHHTGGGEEEEEE-B--B-.STT---S.....S-EEEEEETTEE CS
                     FAA_hydrolase  77 sveeAedaiaGytllnDvsaRdlqaeek.aplgwflgksfdtftpiGpwivtpdeledpe.....dlelrlrvngee 147
                                         e+ +d i+G+  +nD+s Rd+q+ee+ ++lg+++gk +  +t++Gp++vt+de+ + +     ++el+  vng+ 
  gi|518651507|ref|YP_008141027.1| 149 --EKCMDSIFGFITMNDWSLRDIQKEEMkVMLGPAKGKDY--ATSFGPFLVTKDEILSGSeggkiNIELKGYVNGKL 221
                                       ..9*************************8888***99999..**************9844577779999999***** PP

                                       EEEEEGGGTTTSHHHHHHHHHHHH-B-TT-EEEEEES...........S--EE--TT-EEEEEETTTEEEEEEE. CS
                     FAA_hydrolase 148 vqdsntkdmifspaeliahlsagltLepGdliltGTpsgvga....eeeslkflkdgDeveveieglGelrnrVa 218
                                        ++ n+k+++fs++el++++s+ ++L pGd+i++GT  g g+    + e+  +lk+gDev +e  +lG l nrV+
  gi|518651507|ref|YP_008141027.1| 222 YSHNNLKNIYFSFSELLERASESVPLLPGDVIGSGTF-GTGCilelGPEKYGWLKAGDEVILESPQLGNLVNRVV 295
                                       *************************************.7655666679999**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2229.44
//
Query:       gi|518651508|ref|YP_008141028.1|  [L=359]
Description: hypothetical protein FACI_IFERC00001G0147 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-18   66.5   0.2    7.3e-12   45.6   0.1    2.2  2  Glyoxalase    Glyoxalase/Bleomycin resistance protein/Dioxyge
    5.3e-08   33.1   0.0     0.0018   18.6   0.0    2.6  3  Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxyge
  ------ inclusion threshold ------
      0.055   13.6   0.0        3.5    7.7   0.0    2.3  2  Glyoxalase_3  Glyoxalase-like domain
       0.24   11.7   1.2       0.71   10.2   0.2    2.3  2  Osmo_CC       Osmosensory transporter coiled coil


Domain annotation for each model (and alignments):
>> Glyoxalase  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   2.5e-07    0.0011       1     107 [.      10     114 ..      10     132 .. 0.78
   2 !   45.6   0.1   1.6e-15   7.3e-12       2     128 .]     164     313 ..     163     313 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 2.5e-07
                                       EEEEEEEEESHHHHHHHHHHHHHTSEEEEEEEEEESTEEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC....T CS
                        Glyoxalase   1 gidhvallvgdleksldFYtkvLGfklvkktdnteeteglriaffhaggghielvlneapsgaakhvkkiee....t 73 
                                       +i+h+  +v+ ++ +  F ++ LG++l   ++ +++  g  ++++  g+  i+lv  ++ ++         +    +
  gi|518651508|ref|YP_008141028.1|  10 KINHIEFYVSSAKTWSYFMERGLGLDLKAYSGLETGNRGKSSYVLNKGD--INLVFSSSMEKHSEIN----DsislH 80 
                                       69******************************55444666666665555..5555554444444444....223567 PP

                                       SEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEEC CS
                        Glyoxalase  74 vhhvafialdvedvgkaldrlkeagvkvvaepgr 107
                                       + +v  i l+v+d++ + ++l+++ +kv+ + + 
  gi|518651508|ref|YP_008141028.1|  81 GDGVRDISLEVDDIEFTKKHLESRNIKVSSIKEE 114
                                       9***************************988665 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 1.6e-15
                                       EEEEE..EEESHHHHHHHHHHHHHTSEEEEEEEE.EEST..EEEEEEEEETTTSEEEEEEEECCTTSCTHHCCBSC. CS
                        Glyoxalase   2 idhva..llvgdleksldFYtkvLGfklvkktdn.teet..eglriaffhaggghielvlneapsgaakhvkkiee. 72 
                                       +dhv+  ++ g++++++++Y k ++f  +  +d+ ++ t  + lr+ ++  +++ i +++ne+++g +k++ +  e 
  gi|518651508|ref|YP_008141028.1| 164 VDHVVgnVYEGEMDQWVNYYIKNMNFSQLVTFDDkMIRTdySALRSKVV-KYNDNIVFPINEPAQGLKKSQIQ--Ey 237
                                       7899999999****************99999999855555377777555.56667889999999999999933..35 PP

                                       ....TSEEEEEEEEEHCHHHHHHHHHHHTTGEEEEEEECHHCTEEEEE................EEEETTSEEEEE CS
                        Glyoxalase  73 ....tvhhvafialdvedvgkaldrlkeagvkvvaepgrhyfgalysf................yfrDpdGillei 128
                                           + ++v++ial+++++++++ ++k++g+++ ++p  +y +  + +                + rD dG+ll+i
  gi|518651508|ref|YP_008141028.1| 238 ldyyNSQGVQHIALKTDNIIETVSKMKQNGIQFLQTPASYYDTLTERVgnvdedieelkklnilVDRDDDGYLLQI 313
                                       667889****************************************99*************************997 PP

>> Glyoxalase_4  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   4.7e-05      0.21       2      96 ..      13     111 ..      12     124 .. 0.71
   2 !   18.6   0.0   3.9e-07    0.0018      39      97 ..     210     274 ..     171     282 .. 0.67
   3 ?   -2.9   0.0       1.9   8.3e+03      76      90 ..     285     299 ..     280     302 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                                       EEEEE-S-HHHHHHHHHH.TT-EESS--E.EETTTTEEEEEEEETTEEEEEEEESSTT-THHH....TS-EEEEEEE CS
                      Glyoxalase_4   2 QigivVeDleaavarfsallGvgpwqryrdepqevdlafallgsgsvqieLieplegpeflae....hgeglhhlay 74 
                                       +i++ V + +    ++++ lG++       e  +   +   l++g++ + + +  e+ + +++    hg g+  + +
  gi|518651508|ref|YP_008141028.1|  13 HIEFYVSSAKTWSYFMERGLGLDLKAYSGLETGNRGKSSYVLNKGDINLVFSSSMEKHSEINDsislHGDGVRDISL 89 
                                       6666666666666666666666644333344445555556666667888888888888777777888********** PP

                                       EES-HHHHHHHHCTTTEEEEEE CS
                      Glyoxalase_4  75 wvddldaavarleeqGfevvqk 96 
                                       +vdd++ + ++le++ ++v + 
  gi|518651508|ref|YP_008141028.1|  90 EVDDIEFTKKHLESRNIKVSSI 111
                                       ******************9753 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.9e-07
                                       EEEEEEETTEEEEEEEESSTT..-THHH.....TS-EEEEEEEEES-HHHHHHHHCTTTEEEEEEE CS
                      Glyoxalase_4  39 afallgsgsvqieLieplegp..eflae.....hgeglhhlaywvddldaavarleeqGfevvqkg 97 
                                       +++++++ ++     ep +g   + ++e     +  g++h+a+ +d++ ++v +++++G++++q  
  gi|518651508|ref|YP_008141028.1| 210 KVVKYND-NIVFPINEPAQGLkkSQIQEyldyyNSQGVQHIALKTDNIIETVSKMKQNGIQFLQTP 274
                                       4445555.34444445555435555555666699****************************9975 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.9
                                       ES-HHHHHHHHCTTT CS
                      Glyoxalase_4  76 vddldaavarleeqG 90 
                                       v ++d+++++l++  
  gi|518651508|ref|YP_008141028.1| 285 VGNVDEDIEELKKLN 299
                                       778999999998865 PP

>> Glyoxalase_3  Glyoxalase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.015        68      74     112 ..      80     119 ..      61     155 .. 0.79
   2 ?    7.7   0.0   0.00079       3.5      70     102 ..     239     273 ..     218     301 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.015
                      Glyoxalase_3  74 kgeglhtlalrtddidataarlraaGvd.eagrrvrpdgg 112
                                       +g+g+ ++ l++ddi+ t+++l+++ ++ + +++ + d g
  gi|518651508|ref|YP_008141028.1|  80 HGDGVRDISLEVDDIEFTKKHLESRNIKvSSIKEEKDDNG 119
                                       689********************99988644444444444 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00079
                      Glyoxalase_3  70 drlakgeglhtlalrtddidataarlraaGvd...e 102
                                       d + + +g+ ++al+td+i +t+ +++++G++   +
  gi|518651508|ref|YP_008141028.1| 239 DYY-NSQGVQHIALKTDNIIETVSKMKQNGIQflqT 273
                                       333.479***********************985441 PP

>> Osmo_CC  Osmosensory transporter coiled coil
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.4   6.2e+03      23      36 ..      86      99 ..      83     104 .. 0.56
   2 ?   10.2   0.2   0.00016      0.71      13      33 ..     277     297 ..     275     306 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHH CS
                           Osmo_CC 23 dideeIaaLeekRq 36
                                      di  e+ ++e  ++
  gi|518651508|ref|YP_008141028.1| 86 DISLEVDDIEFTKK 99
                                      66666666555444 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                                       XXTHHHHHHHHHHHHHHHHHH CS
                           Osmo_CC  13 hYdnIEqkvedideeIaaLee 33 
                                       +Yd   ++v+++de+I++L++
  gi|518651508|ref|YP_008141028.1| 277 YYDTLTERVGNVDEDIEELKK 297
                                       79*****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); 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: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2453.94
//
Query:       gi|518651509|ref|YP_008141029.1|  [L=646]
Description: hypothetical protein FACI_IFERC00001G0148 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-45  155.6   0.0    1.9e-45  155.2   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.3e-07   30.6   0.7    6.1e-07   29.3   0.7    1.8  1  ACAS_N         Acetyl-coenzyme A synthetase N-terminus
    1.8e-05   25.6   0.0    3.8e-05   24.6   0.0    1.6  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.2   0.0   3.2e-49   1.9e-45      10     421 ..     100     517 ..      91     519 .. 0.84

  Alignments for each domain:
  == domain 1  score: 155.2 bits;  conditional E-value: 3.2e-49
                                       TSEEEEE...CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding  10 dkvalvd...sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                       +k a+++   +g+ q +TY+ l+++v++lAa+++s G+   d+V  +  n pe v++lla++++Ga+ + ++p+++ 
  gi|518651509|ref|YP_008141029.1| 100 EKAAIISyneEGKEQVITYHSLWQKVSSLAAYFQSNGIAASDTVCAYIGNIPEAVITLLATASIGAIWSSCSPDFGI 176
                                       7888888889889999******************99***************************************** PP

                                       HHHHHHHHHHTESEEE.........ETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TS CS
                       AMP-binding  84 eelayiledseakvli.........atvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpe 151
                                       + +   +++  +kvli         + +d++  e++ ++ ++l++v++ i + ++e+ + +++++  +s+++     
  gi|518651509|ref|YP_008141029.1| 177 KGVIERFSQISPKVLIvspeysyngKLYDRT--ENAIKILKALPEVRIAITTGNKEIHDFTKMNSIPDSRSE---F- 247
                                       *****************99887654233333..455566667777888888887777777666666654433...3. PP

                                       CCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT CS
                       AMP-binding 152 eeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplahifglilelllallsG 228
                                        + +++ ++++ i+Y+SGTTGkPK++++ h+ ++    ++ +  + ++ke++v+ +     +++     l + ll+G
  gi|518651509|ref|YP_008141029.1| 248 VPIKVEFSHPLWILYSSGTTGKPKAIVHGHGGILLEHLKV-IMLHMNIKENSVFTWATTTGWMMW--NVLVGGLLAG 321
                                       4558999***********************9998887775.444677889999999999999987..799******* PP

                                       -EEEE-TTCGC.CHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHH CS
                       AMP-binding 229 atvvllpkdaa.ldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffr 304
                                       +t+ l++++   +d ++l++l ek+++t++ +  + +  l++s+ +k  k++++l +l+++ + g+plsp++ +f++
  gi|518651509|ref|YP_008141029.1| 322 STILLYDGSLSyPDTGILWKLSEKYGITHLGVSAAYIGSLMDSR-IK-IKDHYQLDKLEFIGSTGSPLSPDAFEFVY 396
                                       ***********888***************999999999999974.55.34566999********************* PP

                                       HHHTC..EEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET..TS-SE CS
                       AMP-binding 305 alfge..evlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp..gvmkg 377
                                       +  ++   ++ + G T  + +++ l  ++  ++ g       g+ v+ +D++ g+pv  +e+Gel +  p   +   
  gi|518651509|ref|YP_008141029.1| 397 ENIKGnvWLSSLSGGTDLCSAIC-LGSPTLPVYSGMLQCRGLGAHVEALDPD-GKPV-INEKGELAIMDPmpDMPVF 470
                                       *99997779999**********9.5545554455544455568999999**9.9999.9*********995458888 PP

                                       BTT-HHHHH..HHEEE..TCCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 378 Ylkkpeata..eafds..egrwlrTGDlgrldedGyleivgRkkdlik 421
                                       ++++p++t+  e++ +  + +  r GD   +d++G++ i gR++ +++
  gi|518651509|ref|YP_008141029.1| 471 FWNDPDKTRyyESYYNfyP-GIWRHGDYISIDDEGRVIIYGRSDAILN 517
                                       99***99972244443544.78999*******9***********9876 PP

>> ACAS_N  Acetyl-coenzyme A synthetase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.7     1e-10   6.1e-07       1      52 [.      39      90 ..      39      93 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1e-10
                                      HHHHHHHHHH-HHHHHHHHHCC..S--SB--S-SECSTTTCT-EESTT-EE-HH CS
                            ACAS_N  1 ykelykeSiedpeaFWaeqake..ldWekpfdkvldgskgpfikWFeGGklNic 52
                                      ykel+++S+++pe FW + a+   ld   +++++l++ ++ +++WFeG+++N++
  gi|518651509|ref|YP_008141029.1| 39 YKELWEWSVKNPEIFWISLADFsgLDL-GEYNSILSE-NNVNARWFEGARVNYA 90
                                      9*******************9645776.479999999.888***********98 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   6.4e-09   3.8e-05       4      76 .]     530     605 ..     527     605 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 6.4e-09
                                       HHHHSSTTEEEEEEE-----TTS---EEEEEE---..---...HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   4 salvshpaVaeaaVvGvpdevkGealvafVvlkdg..sea...leeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       s l+  + V++  V+G +d +k  ++  fVvl+ g  + +   l  ++k+++r+ l p  vp+++   +++p t +G
  gi|518651509|ref|YP_008141029.1| 530 SSLNGIEMVDDSIVIGYTDSRKIYRITLFVVLR-GnaK-LddnLIGTIKSKIRDDLSPRHVPDYILQAPSVPYTLNG 604
                                       67888899************************8.5332.2447********************************** PP

                                       - CS
                     AMP-binding_C  76 K 76 
                                       K
  gi|518651509|ref|YP_008141029.1| 605 K 605
                                       9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (646 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 4319.31
//
Query:       gi|518651510|ref|YP_008141030.1|  [L=309]
Description: hypothetical protein FACI_IFERC00001G0149 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-24   85.2   0.0    6.9e-24   84.6   0.0    1.2  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.0   3.8e-28   6.9e-24       2     135 ..      54     244 ..      53     245 .. 0.77

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 3.8e-28
                           Cyclase   2 dLshplsedt...pvwpdp............................islsehtGTHlDapgHfae.....kti... 39 
                                        +sh++++++   p+++ p                            +++++htGTH+Da++H+a      ++i   
  gi|518651510|ref|YP_008141030.1|  54 RMSHTIYNGMadrPTHG-PyffdimlrpydngftekyankygpslgrLEMCDHTGTHFDALSHMAYdgkffNNIpvn 129
                                       68999999885555552.1345567777888999999999999********************95565333222444 PP

                           Cyclase  40 .............delpleelvgpavvldvsaka.aa..edyeiitaedleaalakqgveikpgdivlirTgwskrl 100
                                                    +   + ++++ ++++d +a++ ++  e+ + it+++++++l+++ ++ +pgd+++++Tg+s+ +
  gi|518651510|ref|YP_008141030.1| 130 evitntgykklgvE--NAGPIITGGIMVDAAAASgTDilEGGYPITVKEVKNFLKDNSITPEPGDAMFFHTGASSMF 204
                                       44555555554435..4579**********888433345455578*****************************999 PP

                           Cyclase 101 ..edk.eky..rnpglseeaaewlaekgvkavGvDtlsvD 135
                                         ++k +k+  + pg++++ a++l e +++++G Dt+s +
  gi|518651510|ref|YP_008141030.1| 205 snPGKyDKFydSSPGIGYDLARYLSELKISVTGSDTPSSE 244
                                       7633334445777************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2124.63
//
Query:       gi|518651511|ref|YP_008141031.1|  [L=304]
Description: cell wall biosynthesis glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-17   63.3   0.4    3.5e-17   62.7   0.4    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    1.6e-05   24.9   0.0    2.2e-05   24.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.7   0.4   3.9e-21   3.5e-17       1     112 [.       9     115 ..       9     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 62.7 bits;  conditional E-value: 3.9e-21
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       sv+i++yN+ +++l +l+s  +q   ++ +eii+v++    +  +++ee+     +v+ i  e n+ ++g + +++ 
  gi|518651511|ref|YP_008141031.1|   9 SVIITAYNRRQYVLDALKSTTEQsLSRQLYEIIIVKNFRDTNIDAFAEEY-----NVINIYSE-NETLSGKIIEAIG 79 
                                       8*************************************************.....9******9.88*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEE CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvv 112
                                        a+g++++flD+Dd + +++le +++++++ ++ + 
  gi|518651511|ref|YP_008141031.1|  80 IARGNILCFLDDDDMFYREKLEYVLNKFKESNNLCY 115
                                       ******************************776333 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   2.4e-09   2.2e-05       4     112 ..       8     107 ..       5     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 2.4e-09
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++v+++++n+ +++++ l s+  q+ +r  +e+++v +  d+   ++aee    + +v ++++   +  +  gk   
  gi|518651511|ref|YP_008141031.1|   8 ISVIITAYNRRQYVLDALKSTTEQSLSRqlYEIIIVKNFRDTNIDAFAEE----Y-NV-INIYSENE--TLSGK--- 73 
                                       79**********************986667*************8888887....6.54.78885544..43366... PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff 112
                                       + ea+ ++++ ++ ++DdD+    + l+++l+ f
  gi|518651511|ref|YP_008141031.1|  74 IIEAIGIARGNILCFLDDDDMFYREKLEYVLNKF 107
                                       56******************98888778877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       633  (0.0353059); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2285.62
//
Query:       gi|518651512|ref|YP_008141032.1|  [L=502]
Description: hypothetical protein FACI_IFERC00001G0151 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-14   54.0  24.2    1.8e-14   54.0  24.2    3.6  3  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    1.3e-12   47.7  44.5    1.3e-12   47.7  44.5    2.9  3  Polysacc_synt    Polysaccharide biosynthesis protein
    4.6e-12   45.8  30.7    4.6e-12   45.8  30.7    2.4  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    1.5e-07   30.4  57.4    5.1e-07   28.7  42.3    2.1  2  MurJ             Lipid II flippase MurJ
     0.0046   16.6  19.6     0.0046   16.6  19.6    3.9  4  MatE             MatE


Domain annotation for each model (and alignments):
>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   8.3     0.072   2.6e+02      67     135 ..       2      86 ..       1      91 [. 0.69
   2 !    5.9  22.3    0.0034        12       4     133 ..     107     254 ..     104     264 .. 0.82
   3 !   54.0  24.2   5.1e-18   1.8e-14       3     136 ..     323     451 ..     321     458 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.072
                   Polysacc_synt_C  67 lvvavlnlyalrrllgiklellrrllkpllaalvmgiv.vylllllllglllla.................alalll 125
                                       ++++ l ++++ +ll +++  + ++  +++++ +m++v v++l + +   l+++                 a++++l
  gi|518651512|ref|YP_008141032.1|   2 FISSSLFYFFIAHLLPVSV--VGSISLLYAIMNIMAVVfVFGLSNGVQHYLSYHiarenhsaviklmkqtiAFSIIL 76 
                                       78888999**********9..44554455555555555467777777777777788889999999776655556666 PP

                   Polysacc_synt_C 126 avlvgalvYl 135
                                       a+++ +++Y+
  gi|518651512|ref|YP_008141032.1|  77 ALAAFGFMYF 86 
                                       6666666665 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0034
                   Polysacc_synt_C   4 ilalsiiflslstvlssiLqglgrqkialkalvigalvk..lilnllli...plfgivGaaiatvlallvvavlnly 75 
                                       ++ ++i  +++++v++s+L gl++ k++ ++ ++  ++   + l++l+i     + i G a   +++ ++ +++ + 
  gi|518651512|ref|YP_008141032.1| 107 LIGIAIAGSVMINVSGSMLLGLNQYKKYSLIYIFINIFTyfFPLSMLFItgkSVYLIAGLATINIISAMLFMIFVYK 183
                                       566888889999************998766666555544125688888888778889**999999**999999**** PP

                   Polysacc_synt_C  76 alrrllgikl....ellrrll...kpllaalvmgivvylllllllglllla......alalllavlvgalv 133
                                         +rl g++     e +r+l+    pl+++ +mg  ++++ +++++ + +       ++al++a ++  lv
  gi|518651512|ref|YP_008141032.1| 184 VYNRLSGLQTkavkEPYRNLVyysIPLFFSSIMGTSATYIDRIVVSYFINLsylgiyNFALIIASAATFLV 254
                                       ***********9**8899998888************99999999999998888876666777766655555 PP

  == domain 3  score: 54.0 bits;  conditional E-value: 5.1e-18
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr 79 
                                        i+++++ ++  +tvl+s + ++ +++i+l+++ ++++ +++l+++lip+f+i+Gaaia     +v + + +y++r+
  gi|518651512|ref|YP_008141032.1| 323 IIIMFITSIFIGTTVLASGISSIRKTRIFLYSSGFALASNIVLSVILIPRFNIIGAAIAYSSMNAVNFSIVYYYARK 399
                                       45555555555578999999********************************************************* PP

                   Polysacc_synt_C  80 llgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYll 136
                                           +++ + r++k+ ++a++m++++++++ l++ +     +++++ +l+g l+Yl+
  gi|518651512|ref|YP_008141032.1| 400 FSVNNYD-ISRVIKIWISAIIMFGIIFTIQGLFPYTM----INIFIYILAGLLIYLV 451
                                       8888887.78888************887777777654....499***********97 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7  44.5   3.7e-16   1.3e-12      21     273 ..       7     268 ..       2     269 .. 0.86
   2 ?   -6.3  27.4         5   1.8e+04      83     235 ..     283     447 ..     273     452 .. 0.71
   3 ?   -0.9   5.2      0.23   8.3e+02      72     120 ..     408     447 ..     401     471 .. 0.62

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 3.7e-16
                     Polysacc_synt  21 vtlvylarilgpegfGlvalalaivtllviltdlGlna....alvreiakyrekkelvslillnvllvllvlvllfl 93 
                                       ++++ +a +l+   +G  +l++ai+ ++ +++ +Gl++    +l+ +ia+++   + v +++++++  +++l+l ++
  gi|518651512|ref|YP_008141032.1|   7 LFYFFIAHLLPVSVVGSISLLYAIMNIMAVVFVFGLSNgvqhYLSYHIARENH--SAVIKLMKQTIAFSIILALAAF 81 
                                       788999****************************9987233366666777766..5666666677777777777777 PP

                     Polysacc_synt  94 lllliaa......flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflfl 164
                                        +++++a      f++ +++++ + ++ ++++  v+++   ++l+   +  ky ++  +++  +++ + l+++f+ +
  gi|518651512|ref|YP_008141032.1|  82 GFMYFSAgeiailFFHSSAYVLSIKLIGIAIAGSVMINVSGSMLLGLNQYKKYSLIYIFINIFTYF-FPLSMLFITG 157
                                       77777777************************8888888888888888899999999999987766.7777777777 PP

                     Polysacc_synt 165 divaavlgavlaalvggivslavlrkkfr...prfvilslklvrellsfsapltisslaillytyidsillglllga 238
                                       + v++++g++  +++++ +++++++k ++     +++  ++  r+l+ +s+pl++ss++++  tyid+i+ +++++ 
  gi|518651512|ref|YP_008141032.1| 158 KSVYLIAGLATINIISAMLFMIFVYKVYNrlsGLQTKAVKEPYRNLVYYSIPLFFSSIMGTSATYIDRIVVSYFINL 234
                                       789999999999****************548755555558************************************* PP

                     Polysacc_synt 239 eavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                       + +GiYn+a  +++a++ l++p  +  l+P +s +
  gi|518651512|ref|YP_008141032.1| 235 SYLGIYNFALIIASAATFLVVPVSN-LLVPKLSSF 268
                                       *****************99999999.999999875 PP

  == domain 2  score: -6.3 bits;  conditional E-value: 5
                     Polysacc_synt  83 lvllvlvllfllllliaa........flglpelavly.lilalmll..llvgvasfrrglfqglermkyaavsqvve 148
                                       ++l++++l+++ + l  a         + ++++++ y +++++m+   +++g++ + +g+    ++ + ++ s+   
  gi|518651512|ref|YP_008141032.1| 283 ILLNIVSLIYIPAALGIAalsriilyEFAGSDYTIAYiPLIIIMFItsIFIGTTVLASGIS-SIRKTRIFLYSSGFA 358
                                       5556666666666665555666666666666666544256666666767777777777775.799************ PP

                     Polysacc_synt 149 qlsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr....prfvils..lklvrellsfsapltissl 219
                                         s ++l++i++  f+ i +a++++++ + v+  + +++ rk+           ++  +  +  ++ f++ +ti  l
  gi|518651512|ref|YP_008141032.1| 359 LASNIVLSVILIPRFN-IIGAAIAYSSMNAVNFSIVYYYARKFSVnnydI----SRviKIWISAIIMFGIIFTIQGL 430
                                       ****************.***************999999999555323331....32313477889999999999999 PP

                     Polysacc_synt 220 ailly.tyidsillgll 235
                                       + +   + + +il+gll
  gi|518651512|ref|YP_008141032.1| 431 FPYTMiNIFIYILAGLL 447
                                       86544044444466665 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.23
                     Polysacc_synt  72 elvslillnvllvllvlvllfllllliaaflglpelavlylilalmlll 120
                                       ++v +i++++++++++ +++  l++++          ++++i++l++ll
  gi|518651512|ref|YP_008141032.1| 408 SRVIKIWISAIIMFGIIFTIQGLFPYT---------MINIFIYILAGLL 447
                                       567788888888888888888877777.........3344444444443 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8  30.7   1.3e-15   4.6e-12       3     288 ..      13     315 ..      11     320 .. 0.83
   2 ?   -3.8   5.0       1.6   5.6e+03     117     181 ..     350     414 ..     324     439 .. 0.68

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 1.3e-15
                   Polysacc_synt_3   3 ARLLspedFGvvaialvvislanlfvdmGlssal.......iqkedltee..dlstvftfnlvlgllialvlfllap 70 
                                       A LL  +  G ++++ ++++++ ++  +Gls+ +       i +e+ ++    +++   f+++l+l+++  ++++a 
  gi|518651512|ref|YP_008141032.1|  13 AHLLPVSVVGSISLLYAIMNIMAVVFVFGLSNGVqhylsyhIARENHSAVikLMKQTIAFSIILALAAFGFMYFSAG 89 
                                       667777888999999999999999998888875522212223333222224467788889999999999999***** PP

                   Polysacc_synt_3  71 lias.fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivaivlAll.glgvw...AL 142
                                        ia  f+ +   v  ++++++ +  s +++v+ ++l    ++kk + i ++ ++++ ++ + + ++ g++v+    L
  gi|518651512|ref|YP_008141032.1|  90 EIAIlFFHSSAYVLSIKLIGIAIAGSVMINVSGSMLLGLNQYKKYSLIYIFINIFTYFFPLSMLFItGKSVYliaGL 166
                                       ***97899999999******************************************999999887626787733346 PP

                   Polysacc_synt_3 143 vigtllssllslvllwlaskwr..prlkfslkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsva 217
                                       ++ +++s++l +++++ +++    +++k   +  ++l+ +++ l++s+++ + a+ +d +++ ++++ ++LG+Y+ a
  gi|518651512|ref|YP_008141032.1| 167 ATINIISAMLFMIFVYKVYNRLsgLQTKAVKEPYRNLVYYSIPLFFSSIMGTSATYIDRIVVSYFINLSYLGIYNFA 243
                                       6677777777777777777765556777778999******************************************* PP

                   Polysacc_synt_3 218 krlaslpvaeitsviakVlfPalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqW 288
                                         +as+  + +  ++++ l+P lS++   d+k+ +r++++ +l++++li +P+a g+a++++ ++  + Gs +
  gi|518651512|ref|YP_008141032.1| 244 LIIASA-ATFLVVPVSNLLVPKLSSFfsLDNKEGFRKSIRILLNIVSLIYIPAALGIAALSRIILYEFAGSDY 315
                                       987766.6788899**********98435899*****************************999888888777 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.6
                   Polysacc_synt_3 117 itlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkelfsfg 181
                                       i l ss +++++ ivl +++   + ++   +++s +++v + +++ +  +++++   +++++++ 
  gi|518651512|ref|YP_008141032.1| 350 IFLYSSGFALASNIVLSVILIPRFNIIGAAIAYSSMNAVNFSIVYYYARKFSVNNYDISRVIKIW 414
                                       44566666777777777777777777777777777777777777777777777776666666543 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   8.0   0.00046       1.7     222     311 ..      10      99 ..       1     114 [. 0.82
   2 !   28.7  42.3   1.4e-10   5.1e-07     112     437 ..     116     439 ..     100     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00046
                              MurJ 222 talAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgllv 298
                                       +++A  l  ++v  ++   +i+++   +f+  +s+ +   lS + +++++ +v +l++q+i ++++l++ +  ++ +
  gi|518651512|ref|YP_008141032.1|  10 FFIAHLLPVSVVGSISLLYAIMNIMAVVFVFGLSNGVQHYLSYHIARENHSAVIKLMKQTIAFSIILALAAFGFMYF 86 
                                       6677776666666666666899999999************************************9999877777777 PP

                              MurJ 299 lskpivsllferG 311
                                        + +i  l+f  +
  gi|518651512|ref|YP_008141032.1|  87 SAGEIAILFFHSS 99 
                                       7788887777655 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 1.4e-10
                              MurJ 112 slsavfgavLnarkkFfapafsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkp 188
                                        ++ v+g++L   +++   ++  ++ N+   ++ l +   +g ++++ +a   +i  +  +l++++  k    l+ +
  gi|518651512|ref|YP_008141032.1| 116 VMINVSGSMLLGLNQYKKYSLIYIFINIFTYFFPLSMLFITG-KSVYLIAGLATINIISAMLFMIFVYKVYNRLSGL 191
                                       577899999999999999999999999988888777777777.899999999******************9999999 PP

                              MurJ 189 rfafrdeglkkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrs 265
                                         +  +e  ++++   +p ++++ +   ++++d ++ s+++  s   +++  +i+  +   ++v +s+ l P+lS  
  gi|518651512|ref|YP_008141032.1| 192 QTKAVKEPYRNLVYYSIPLFFSSIMGTSATYIDRIVVSYFINLSYLGIYNFALIIASAATFLVVPVSNLLVPKLSSF 268
                                       9**************************************************************************** PP

                              MurJ 266 akekdedevrdllsqairltllllipvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklll 342
                                       ++ ++++ +r+ ++  + ++ l+ ip++ g+++ls+ i   l+e +  s++ ++++  ++ ++  ++  ++ +++l+
  gi|518651512|ref|YP_008141032.1| 269 FSLDNKEGFRKSIRILLNIVSLIYIPAALGIAALSRII---LYEFAG-SDYTIAYIPLIIIMFITSI--FIGTTVLA 339
                                       ***********************************876...564443.5677889999999999997..689***** PP

                              MurJ 343 rvfYAredtktPvkislislvlnillsllllpplgvvglalatslsaliglvllyvllrkrlk..lteargiktfla 417
                                       +   + + t+  ++ s ++l  ni+ls++l+p++  +g a+a+s  + +++ ++y+++rk  +  ++++r+ik+ + 
  gi|518651512|ref|YP_008141032.1| 340 SGISSIRKTRIFLYSSGFALASNIVLSVILIPRFNIIGAAIAYSSMNAVNFSIVYYYARKFSVnnYDISRVIKIWIS 416
                                       ************************************************************87778999999999988 PP

                              MurJ 418 k...lvvllalaavvilllsslt 437
                                       +     +++++ +   + +++++
  gi|518651512|ref|YP_008141032.1| 417 AiimFGIIFTIQGLFPYTMINIF 439
                                       83322233333344444444444 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  22.6   7.1e-06     0.025      12     152 ..       4     146 ..       1     156 [. 0.81
   2 !   16.6  19.6   1.3e-06    0.0046       1     161 []     209     368 ..     209     368 .. 0.94
   3 ?   -3.0   2.9       1.4   4.9e+03      44      89 ..     380     426 ..     369     442 .. 0.46
   4 ?   -1.4   0.4      0.46   1.7e+03      76     105 ..     434     463 ..     427     471 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.1e-06
                              MatE  12 lslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllslii 86 
                                       +s ++ +++++l + + ++++s+   i +++ v f++gls++++   ++ +  +n  ++ + + q++ ++++l+l++
  gi|518651512|ref|YP_008141032.1|   4 SSSLFYFFIAHLlPVSVVGSISLLYAIMNIMAVvFVFGLSNGVQHYLSYHIARENHSAVIKLMKQTIAFSIILALAA 80 
                                       5667789999999******************999******************************************* PP

                              MatE  87 allvllfseqilslftqdeevlelakrylrililgipal.alqlvlsgilrgagktkvplyislisl 152
                                       + ++++ +  i+ lf ++ +   l+ +++ i+i g + + +   +l g  +  +++ +  +i+++++
  gi|518651512|ref|YP_008141032.1|  81 FGFMYFSAGEIAILFFHSSA-YVLSIKLIGIAIAGSVMInVSGSMLLGLNQYKKYSLIYIFINIFTY 146
                                       ***************99997.5555566666555555550445555566666666666677777766 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-06
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+++++++ ++ + id ++v+++   + l+ +++al i+s  +++++ +s+ l +  + ++   n++++++++r+ l
  gi|518651512|ref|YP_008141032.1| 209 PLFFSSIMGTSATYIDRIVVSYFiNLSYLGIYNFALIIASAATFLVVPVSNLLVPKLSSFFSLDNKEGFRKSIRILL 285
                                       99*************************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                        ++ l+++++al + ++s++il+ f  ++    +a   l i+ + + +++ ++vl++   ++ kt++ ly s ++l 
  gi|518651512|ref|YP_008141032.1| 286 NIVSLIYIPAALGIAALSRIILYEFAGSDY--TIAYIPLIIIMFITSIFIGTTVLASGISSIRKTRIFLYSSGFALA 360
                                       *****************************5..56666667777777777789************************* PP

                              MatE 154 lniplnyl 161
                                        ni+l+++
  gi|518651512|ref|YP_008141032.1| 361 SNIVLSVI 368
                                       ****9875 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.4
                              MatE  44 fllglstalttlvgqalGak.nfkrakealrqglilllllsliiall 89 
                                       ++ + ++a++  + +++  k ++++   + ++ +++++++++ i++ 
  gi|518651512|ref|YP_008141032.1| 380 IAYSSMNAVNFSIVYYYARKfSVNNYDISRVIKIWISAIIMFGIIFT 426
                                       55555555555555555444222223333333344444333333332 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.46
                              MatE  76 lilllllsliiallvllfseqilslftqde 105
                                       +++++++++++ ll++l   + ++l++q+e
  gi|518651512|ref|YP_008141032.1| 434 TMINIFIYILAGLLIYLVEIKVFHLISQEE 463
                                       577888888888888888777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1110  (0.0619109); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.44
# Mc/sec: 3422.70
//
Query:       gi|518651513|ref|YP_008141033.1|  [L=672]
Description: hypothetical protein FACI_IFERC00001G0152 [Ferroplasma acidarmanus fer1]
Scores for complete 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-64  216.3  36.5    9.9e-64  215.9  36.5    1.2  1  DUF2079          Predicted membrane protein (DUF2079)
  ------ inclusion threshold ------
      0.049   14.1   0.5        0.2   12.2   0.1    2.1  2  Cu_amine_oxidN1  Copper amine oxidase N-terminal domain


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9  36.5   1.1e-67   9.9e-64       2     455 ..      45     528 ..      44     529 .. 0.83

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 1.1e-67
                           DUF2079   2 lasLnstayDlGifdQviwntsqGelfysslsgvlhlLgqHfapillllaplyalfPsvltLllvqalllslgglpl 78 
                                        ++Ln+ a DlG+++Q+++++++G+lfys+l+g+ + L++Hf+p+++ l+   +++P ++ Ll++qa+++s+++lpl
  gi|518651513|ref|YP_008141033.1|  45 AYTLNAYAWDLGLYSQAFYSSMHGQLFYSNLLGE-SYLAEHFSPFMFALLGVFYIYPNPYILLIIQAVFISFATLPL 120
                                       589*******************************.****************************************** PP

                           DUF2079  79 yrlarerlls............rrlalliallYllspvvinptlfdFhpevlaiPllll.alllalrrrkwllllvl 142
                                       y++   ++               + +++ia  +llsp++ +p  fdFh + ++ P++++ a++++++ r ++++++l
  gi|518651513|ref|YP_008141033.1| 121 YYISMHIFSRiketypeniknpALYSFIIASAFLLSPLTESPIYFDFHLMIFL-PFFYFmAIYFYIKNRMAWNIVFL 196
                                       *******95599********99999****************************.***97367778888999****** PP

                           DUF2079 143 illlllvredlslvvvilglwlilre......rkrrkiglillllglawvilvtsvliPlfsstksqvfgverysyl 213
                                       +l+++l+  ++ +vv++l + +++ +       +r+k ++  +++  + v+l++ +   +++ +++ + ++  + + 
  gi|518651513|ref|YP_008141033.1| 197 ALIVSLHASFVFIVVMTLIMEMMISRyyfkesGERTK-RMSYIFITSLLVLLIYYTAAGYLKGDIAHSQSILLFASG 272
                                       *****************99999999878877644555.666677766666666666666666666554444433332 PP

                           DUF2079 214 g.....sSlleillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqls 285
                                             +S+++++l+ +++p++ + +++ +   kl +l+l+fl + f   +  p+ L++a+P+l +++ s+y p++ 
  gi|518651513|ref|YP_008141033.1| 273 AtgsasRSITGLVLTFFLHPYRFMTYIIANYQIKLLFLVLAFLAVDFAFYR-FPIGLIPAIPYLVYAMTSSYIPYYF 348
                                       244666*******************99999999**************9999.************************* PP

                           DUF2079 286 lgyqYsllvipflvlaaifglakls.........ssvelrrikriwsvalvlvlvltlflnparslsflvpdsespv 353
                                       +gyqYs++ ip++++aa+fg++k            + ++r +k+ ++v++v++++  +  +p  ++s   + + ++ 
  gi|518651513|ref|YP_008141033.1| 349 IGYQYSMMFIPMIFIAAVFGISKMMefkptpsikTKRAYRNLKNTMVVIAVFAIAAFIVVSPISPVSLEPSGIHNI- 424
                                       *************************997777666555555566666666666655555555555555555555554. PP

                           DUF2079 354 vylstlaqlqas...rellklIpsdasvlatsnLaPhlanRayvylfpeneelydleylleevdyvlld...vafrg 424
                                       v+ st    ++      l ++I  ++s+++ +n++P++      ++fp+n        +   + y+++d    ++  
  gi|518651513|ref|YP_008141033.1| 425 VNDSTGYSAERNhlvYSLENNISMNSSLVTGNNIYPLFYRDLNATAFPYNNIS----SPSVHFKYLIADlndSQTYI 497
                                       3333332222223469999*********************5554577766665....57889*******76644455 PP

                           DUF2079 425 wasrkdrerklidklrnsgrygviaeedgvl 455
                                       ++  + +  +l ++ +nsg+yg+ ae  gv+
  gi|518651513|ref|YP_008141033.1| 498 ENAYNISLANLASDYMNSGSYGILAEGYGVI 528
                                       5666778889999*************99997 PP

>> Cu_amine_oxidN1  Copper amine oxidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.42   3.8e+03      68      81 ..     356     369 ..     351     376 .. 0.80
   2 ?   12.2   0.1   2.2e-05       0.2      29      70 ..     614     655 ..     598     659 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.42
                   Cu_amine_oxidN1  68 tyvPlrfvaealga 81 
                                       +++P+ f+a ++g 
  gi|518651513|ref|YP_008141033.1| 356 MFIPMIFIAAVFGI 369
                                       78999999999885 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
                   Cu_amine_oxidN1  29 Vtikkgdktiklkigsneatvngkeikldvapklinngrtyv 70 
                                       +ti ++++ +  +i+s+++++ng++++ +v+ ++i  g+tyv
  gi|518651513|ref|YP_008141033.1| 614 ITILDNGRVSLYTINSSSYRLNGETLTFNVNSTEIYTGVTYV 655
                                       7888899999999****************99999999****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (672 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1262  (0.0703888); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 4084.56
//
Query:       gi|518651514|ref|YP_008141034.1|  [L=296]
Description: hypothetical protein FACI_IFERC00001G0153 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-34  117.8   0.0    6.9e-34  117.2   0.0    1.2  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    0.00044   20.3   0.0    0.00098   19.2   0.0    1.5  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    0.00064   20.5   0.0     0.0012   19.6   0.0    1.5  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
       0.04   13.5   0.0      0.099   12.2   0.0    1.6  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.2   0.0   1.5e-37   6.9e-34       7     313 ..       6     290 ..       2     292 .. 0.91

  Alignments for each domain:
  == domain 1  score: 117.2 bits;  conditional E-value: 1.5e-37
                                       -HHHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSS CS
                   OCD_Mu_crystall   7 taveveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglp 83 
                                       t+++v+++l++ ++++ + +af+++ +g+ +  pr + + ++    l+ mp   + r+l+g+K +           p
  gi|518651514|ref|YP_008141034.1|   6 TEEDVRSNLKMGECIEELRKAFKSYGNGASDAHPRDRIMNNN--SMLNTMPGVYGDRHLAGLKTYYAG--------P 72 
                                       789***********************************9999..9******************98653........4 PP

                                       SEEEE.EEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEE CS
                   OCD_Mu_crystall  84 tvtal.vvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevri 159
                                       + +++ vv++++e    l +++a+ l ++RT+A +a+a+    ++ +  ++iiG G qae+q +a+k+++++k++ +
  gi|518651514|ref|YP_008141034.1|  73 SGIHFvVVIFNTEKPEDLYILEANTLGQVRTGALAAMATSEVVKEKSINFTIIGSGYQAESQFLAMKEIFNLKHAHV 149
                                       5555416789******************************************************************* PP

                                       E-SSHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHH CS
                   OCD_Mu_crystall 160 ydrdeeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddi 236
                                       y  +++  ++fa++       ++ ++   ++ ++ d+++ +T +++pi+  + + +  hin+ g++ p ++e  +d+
  gi|518651514|ref|YP_008141034.1| 150 YSKNPSHSKAFADKF-----GIESVD-SLDVLKESDVITSITNSNSPIFNYSQLPERYHINLAGSNFPIRREAAPDV 220
                                       ***********9975.....477665.569*********************************************** PP

                                       HHCCEEEE.SHHHH.HHHCCCCHCHHHTTSSTCGGEEEEHHHHH..CTSS-..-STTSEEEEE----HHHHHHHHHH CS
                   OCD_Mu_crystall 237 lkradifv.dseaq.areeGeiqvaiekgvlaedakvaelgevi..aGkkpGRtsdeeitlfdsvGlaveDvaaakl 309
                                       l ++d+++ ++++q  +e+ ei        +++++k+ el + +  +Gk pG +     t+f+s+G++ eDvaa  +
  gi|518651514|ref|YP_008141034.1| 221 LDNSDVVIvENLEQgMKESAEIMG------VQKKEKIVELKDYMinKGKYPGNK-----TIFKSMGIGLEDVAAGYV 286
                                       *****9887888773688888888......999999****99653488888755.....9*************9888 PP

                                       HHHH CS
                   OCD_Mu_crystall 310 vyer 313
                                       +  +
  gi|518651514|ref|YP_008141034.1| 287 ILKN 290
                                       7665 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   2.2e-07   0.00098       7      95 ..     114     197 ..     106     208 .. 0.84
   2 ?   -3.5   0.0       2.3     1e+04      71      81 ..     219     229 ..     215     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.2e-07
                                       HS..TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE- CS
                      Shikimate_DH   7 leslkekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisa 82 
                                       + + k+ + ++iG G  ae  + ++ +  ++k+  v   + ++ k++a++++ e     ++++l+ +l+e+dv+ s 
  gi|518651514|ref|YP_008141034.1| 114 VVKEKSINFTIIGSGYQAESQFLAMKEIfNLKHAHVYSKNPSHSKAFADKFGIE-----SVDSLD-VLKESDVITSI 184
                                       4456677889********9988888876699999*****************655.....666666.889******** PP

                                       SSSSS-SB-HHHH CS
                      Shikimate_DH  83 taseepilekeev 95 
                                       t+s++pi++ +++
  gi|518651514|ref|YP_008141034.1| 185 TNSNSPIFNYSQL 197
                                       ********98876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                                       HHHHT-SEEEE CS
                      Shikimate_DH  71 ellaeadvvis 81 
                                       ++l+++dvvi+
  gi|518651514|ref|YP_008141034.1| 219 DVLDNSDVVIV 229
                                       56788888875 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 !   19.6   0.0   2.7e-07    0.0012       1      61 [.     120     179 ..     120     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESSHHHHHTCT CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysdleelladp 61 
                                       +++ iiG+G+ ++ ++ +++e   +++ +++++++++ ++a+a++fg+e++++l+ l++++
  gi|518651514|ref|YP_008141034.1| 120 INFTIIGSGYQAESQFLAMKEI-FNLKHAHVYSKNPSHSKAFADKFGIESVDSLDVLKESD 179
                                       5899*******99999999999.7779999***********************99888755 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 ?   -4.0   0.0       2.1   9.6e+03      76      91 ..       5      20 ..       4      21 .. 0.83
   2 ?   12.2   0.0   2.2e-05     0.099       5      67 ..     118     184 ..     114     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 2.1
                                      HHHHHTGGG--TT-EE CS
                              IlvN 76 vyeeeiepnlkegkal 91
                                      v ee+++ nlk g+++
  gi|518651514|ref|YP_008141034.1|  5 VTEEDVRSNLKMGECI 20
                                      6789999999999886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
                                       S-E..EEES-SHHHHHHHHHHHHT.T-.-EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE- CS
                              IlvN   5 kki..aviGyGsqGhaqalnlrds.gl.dvvvglregsksvkkAkeegfevltvaeavkkadvvmil 67 
                                       k i  ++iG G q+++q l +++   l +  v  ++ s+s + A + g+e ++  ++ k++dv++ +
  gi|518651514|ref|YP_008141034.1| 118 KSInfTIIGSGYQAESQFLAMKEIfNLkHAHVYSKNPSHSKAFADKFGIESVDSLDVLKESDVITSI 184
                                       554337****************961232455555666678888888899999999********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 2386.99
//
Query:       gi|518651515|ref|YP_008141035.1|  [L=532]
Description: hypothetical protein FACI_IFERC00001G0154 [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   70.8   0.0    6.2e-19   68.2   0.0    2.1  2  B12-binding      B12 binding domain
    3.6e-17   63.3   0.0    1.7e-16   61.1   0.0    2.1  2  Radical_SAM      Radical SAM superfamily
  ------ inclusion threshold ------
       0.13   12.9   0.0       0.79   10.4   0.0    2.3  2  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0     1e-22   6.2e-19      12     120 ..      26     136 ..      15     137 .. 0.89
   2 ?   -0.3   0.0      0.18   1.1e+03      24      47 ..     300     322 ..     287     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 1e-22
                       B12-binding  12 lhplGlavlaaalrd.agfeVqllganven...edivaairaekpdvvglSalltsqleavkelvellkrirprvkv 84 
                                         plGl +la+ +++    +V++++++++n   ++ + +i ++kpd+vg++++ t+ ++++  +++ +k+++p++ +
  gi|518651515|ref|YP_008141035.1|  26 PAPLGLLALAGEIKRiPDSKVKIIDMEADNislDEAIIQILEFKPDLVGITLHATAAHNNAGYIARGIKKAKPDTVL 102
                                       5689999999877774688**************6666669************************************* PP

                       B12-binding  85 vvGGahpsldpeetleaklgiddvvvgegedaleal 120
                                       v+GG+h++++pee++e   g+d+ v+geg++++ ++
  gi|518651515|ref|YP_008141035.1| 103 VAGGHHATFLPEELIE--AGFDISVLGEGDETIYDI 136
                                       *************998..8************98776 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.18
                       B12-binding  24 lrdagfeVqllganvenedivaai 47 
                                         +ag+++++lg++   e+i++++
  gi|518651515|ref|YP_008141035.1| 300 A-KAGMSISFLGVESGSEEILKKM 322
                                       3.469**************99986 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.37   2.2e+03      84     113 ..      53      81 ..      32     116 .. 0.78
   2 !   61.1   0.0   2.8e-20   1.7e-16       2     166 ..     203     367 ..     202     368 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.37
                                       ECSSCHGHHHHHHHHHTT-SEEEEEEBSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaad 113
                                       +  + + +e +  +le  +d v ++l+a+ 
  gi|518651515|ref|YP_008141035.1|  53 ADNISL-DEAIIQILEFKPDLVGITLHATA 81 
                                       444555.88888899999888888888764 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 2.8e-20
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE....SSTGGGSTTHHHHHHHHHHTC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilg....ggepllypdfvellerlakla 74 
                                       +++rgC+++C fC+++ t  ++ ++r++s e+i++e++ + ++ g + ++++      ep++ ++ + l +++ ++ 
  gi|518651515|ref|YP_008141035.1| 203 ETSRGCPYGCDFCSVTPT--WGNTWRNKSNERIIKEMENA-KSYGYNWIFFTddifIVEPNV-KHREALFDMILEKN 275
                                       689**************8..********************.699899999997777778888.55666666666665 PP

                                       .....CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEE CS
                                       .....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 .....vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvv 146
                                               +r+ v++ +    ++ +e+ +++g+    lg+e++++e +lk+m++g+   +  +a+++l +++i ++v
  gi|518651515|ref|YP_008141035.1| 276 lntswIVQMRVDVTSRH----PDLIEKAAKAGMSISFLGVESGSEE-ILKKMHKGEFTPQSAQAVRILSSNDIVVIV 347
                                       67744444444444444....567**********************.*****999999******************* PP

                                       EEEEEBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 147 drivglpGendeeleellel 166
                                        +++g p e  ++l+ ++++
  gi|518651515|ref|YP_008141035.1| 348 GMMIGAPYERYRDLRSTVRF 367
                                       ***************99987 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 ?    1.1   0.0       0.1   6.1e+02      19      54 ..      39      76 ..      36      79 .. 0.84
   2 ?   10.4   0.0   0.00013      0.79      15      87 ..      63     138 ..      57     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.1
                                      HHCTT.TEEEEEEEE.SSTHHHHHHHHHHHT-SEEEES CS
                   DXP_reductoisom 19 eenpd.kfevvalaa.gsnvellaeqakefkpklvava 54
                                      +++pd k +++ + a + ++++++ q+ efkp+lv ++
  gi|518651515|ref|YP_008141035.1| 39 KRIPDsKVKIIDMEAdNISLDEAIIQILEFKPDLVGIT 76
                                      56666588999999988899**************9875 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00013
                                       HHHHHHCTT..TEEEEEEEESSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEE.ESHHHHHHHHC CS
                   DXP_reductoisom  15 Ldvieenpd..kfevvalaagsnvellaeqakefkpklvavadeeaaeelkealkekelktevl.vGeealkelae 87 
                                       ++++e +pd   ++++a aa++n   +a+ +k+ kp++v va  ++a+ l e+l e++++++vl  G+e++ ++a 
  gi|518651515|ref|YP_008141035.1|  63 IQILEFKPDlvGITLHATAAHNNAGYIARGIKKAKPDTVLVAGGHHATFLPEELIEAGFDISVLgEGDETIYDIAM 138
                                       5666666774446788999***********************************9999999988347777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (532 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3485.52
//
Query:       gi|518651516|ref|YP_008141036.1|  [L=127]
Description: hypothetical protein FACI_IFERC00001G0155 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-10   40.3   0.0    3.5e-10   39.4   0.0    1.5  1  GntR       Bacterial regulatory proteins, gntR family
     0.0078   16.2   0.1      0.016   15.1   0.0    1.6  2  HTH_Crp_2  Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.072   12.9   0.0       0.14   12.0   0.0    1.5  1  UBA_3      Fungal ubiquitin-associated domain


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   5.9e-14   3.5e-10       1      55 [.      17      71 ..      17      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 5.9e-14
                                      HHHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  1 lyeqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      ly q+y +++  I++  l+pGd LPs r La+ ++++ +tv++A+++L   g+++
  gi|518651516|ref|YP_008141036.1| 17 LYLQIYNQITYNISTRKLNPGDVLPSSRTLASVLDINFHTVNQAYQKLRNNGIIV 71
                                      699************************************************9986 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.7e-06     0.016      23      54 ..      42      73 ..      20      81 .. 0.86
   2 ?   -2.9   0.1       1.2   6.9e+03      36      44 ..     115     123 ..     114     126 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.7e-06
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSEEET CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkreglisrg 54
                                      + + lAs l ++  tv+++ ++L++ g+i  g
  gi|518651516|ref|YP_008141036.1| 42 SSRTLASVLDINFHTVNQAYQKLRNNGIIVLG 73
                                      6678*************************954 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                                       HHHHHHHHH CS
                         HTH_Crp_2  36 etvsrilse 44 
                                       e+v ri+s 
  gi|518651516|ref|YP_008141036.1| 115 ESVKRIISS 123
                                       899999886 PP

>> UBA_3  Fungal ubiquitin-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.3e-05      0.14       9      33 ..      96     120 ..      90     126 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.3e-05
                                       SHHHHHHHHHHT--HHHHHHHHHHS CS
                             UBA_3   9 drdlVdefvsqGFekdkvievLkrL 33 
                                       ++d+V+e  ++G+  + +ie  kr+
  gi|518651516|ref|YP_008141036.1|  96 EKDMVNEALAMGYTENDIIESVKRI 120
                                       589********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 955.81
//
Query:       gi|518651517|ref|YP_008141037.1|  [L=558]
Description: hypothetical protein FACI_IFERC00001G0156 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-22   78.6  44.9    4.2e-22   78.6  44.9    2.0  2  AA_permease_2  Amino acid permease
    1.5e-12   46.9  43.9    1.5e-12   46.9  43.9    2.1  2  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 !   78.6  44.9   4.6e-26   4.2e-22      15     406 ..      30     438 ..      22     442 .. 0.77
   2 ?   -3.6  13.1      0.39   3.5e+03      85     167 ..     429     516 ..     419     545 .. 0.60

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 4.6e-26
                     AA_permease_2  15 igsgifvkn........laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawf 83 
                                       +g+ + + n        +++ +gp +il +++++ i+s   +l+y+El+ + p  gG   y+ ++ g++   ++a++
  gi|518651517|ref|YP_008141037.1|  30 VGLVGAFGNgalfgtvaMITIAGPEAILAFILGAAIYS-LIGLTYMELGVTYPEAGGPTRYSIYTHGRWTNIINAMS 105
                                       3333333333433336455569999************8.6889*****977**********9988777666555555 PP

                     AA_permease_2  84 n..wfayvp.vlasilsvaasyl..lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillp 155
                                          w+ ++p v +++++++++y+  ++ l+ ++ + t++ + ++ a++++++ +n++gik  +k + ++g +ki++ 
  gi|518651517|ref|YP_008141037.1| 106 DiiWYLFIPpVEVISIIAGINYFdpIF-LAASGAP-TYTGVALGLALMLGLIPFNYYGIKQFGKSTLYTGAVKIFFY 180
                                       444555555155555666777776433.3346666.689999********************************855 PP

                     AA_permease_2 156 liiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk.kdvpkaifiglliv 230
                                       l +   lgl+++ +++++   + +  f p g  +  ++ ++ +++ f+++ ++   +ee  +  ++p+ai ++ll+ 
  gi|518651517|ref|YP_008141037.1| 181 LSMS--LGLVFFAFDYAN---FYKYGFAPYGVAIpLFSIMPYAMYDFGAIRVIPDLAEETNNrSKMPRAIGMVLLFE 252
                                       4444..699999999999...345446666777657999999*****************999468************ PP

                     AA_permease_2 231 lvlyllvniaflgvvpddei.anlsnlgsv......aalffeavggk..vvaiivvilialsllgaintavigssrv 298
                                       +++y+ v++a++++ +++ i   ++n+++v        +ff  +  +  +v+i++vi ++l  +  +  ++ + +rv
  gi|518651517|ref|YP_008141037.1| 253 TLIYISVAFALTMGTNWSLIgVIPGNFLGVqaafhgDNPFFLLSK-PfpFVFIAAVITGVLTPFVTGYIYLGSGTRV 328
                                       ********************5345556666544443245555554.23599999999999999************** PP

                     AA_permease_2 299 lealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrk 374
                                       l++++r g++ + ++++  k+  p+ ++i++a+v ++l+++++ ++ + y+f+ ++++ g+i  ++ +i++++  r 
  gi|518651517|ref|YP_008141037.1| 329 LFSMGRSGYMSNKLKSIEsKHSVPLWSLIIFAVVGVVLVFVTAPVP-SIYTFIDDATAAGYIGLITNPIALMVTRR- 403
                                       ***********************************99887777665.89*************99999995444444. PP

                     AA_permease_2 375 krphlkr....pgkilvaiigalfllfllvalffpp 406
                                        + + k+     g+ ++a +++ ++ ++++++ +p+
  gi|518651517|ref|YP_008141037.1| 404 -QGITKKkdmvRGMSIIAPLATAGSALIVFWTGWPS 438
                                       .34443325656667788888888888888777765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.39
                     AA_permease_2  85 wfayvpvlas.....ilsvaasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilkillp 155
                                       ++ ++ +++s     il++a++ l +al++ ++  ++ l+y+++i++ ++ ++ ++ g       q ++ +  + ++
  gi|518651517|ref|YP_008141037.1| 429 LIVFWTGWPSepyavILIAAGAVLFGALSKvKIGAKNALWYVFFIGFATFMVATSHDGLTSAVFPQYFTYLQGT-II 504
                                       444444444444221344455556666664799999********************999666666655555444.33 PP

                     AA_permease_2 156 liiliilglitv 167
                                        +i+ +++++ +
  gi|518651517|ref|YP_008141037.1| 505 TFIVGLFVIYPL 516
                                       333333333322 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.9  43.9   1.7e-16   1.5e-12       2     419 ..      27     431 ..      26     436 .. 0.81
   2 ?   -5.1   7.3      0.98   8.8e+03      95     157 ..     424     479 ..     412     514 .. 0.60

  Alignments for each domain:
  == domain 1  score: 46.9 bits;  conditional E-value: 1.7e-16
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       +l+  l g++G g ++g+   +  aGp +a+la++l+ +++ l++l+  e+ + +p++gg + y+  ++g++     
  gi|518651517|ref|YP_008141037.1|  27 MLMVGLVGAFGNGALFGTVAMITIAGP-EAILAFILGAAIYSLIGLTYMELGVTYPEAGGPTRYSIYTHGRWTNIIN 102
                                       6899999********************.*************************************999999999988 PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwel.vtdlpkawvt........gavflvvlliinlvgvkvygeaefilalik 146
                                       +++  + +++  ++e++ ++  i++    + +++             g+ +++ l+ +n++g+k +g+  + +  +k
  gi|518651517|ref|YP_008141037.1| 103 AMSDIIWYLFIPPVEVISIIAGINYFDPiFLAASG---AptytgvalGLALMLGLIPFNYYGIKQFGKSTLYTGAVK 176
                                       88877777777888877777777776554555543...134577778888899999999999999999999999999 PP

                       AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                       i   +++ ++++++ ++ +  ++       ++++     + p+      g     +s+++ ++ +f  i  ++ +a+
  gi|518651517|ref|YP_008141037.1| 177 IFFYLSMSLGLVFFAFDYA--NF-------YKYG-----FAPY------GVAIPLFSIMPYAMYDFGAIRVIPDLAE 233
                                       9999999999965555554..66.......5556.....6677......678899********************** PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifi....kesgvsvlaplinavi 296
                                       E+ + + ++P+ai +v++  t++Y+ ++++++++ +++  g++ +     + +  f      ++ ++ ++++++a++
  gi|518651517|ref|YP_008141037.1| 234 ETNN-RSKMPRAIGMVLLFETLIYISVAFALTMGTNWSLIGVIPGNFL--GVQAAFHgdnpFFLLSKPFPFVFIAAV 307
                                       *987.6779**********************************97774..455555433336788999999998888 PP

                       AA_permease 297 ltaals.sanssly..sasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfl. 368
                                       +t +l   + +++y  s++Rvl+s+ ++g++  k  +  sk+ vPl +++++++++++++    +++++p++++f+ 
  gi|518651517|ref|YP_008141037.1| 308 ITGVLTpFVTGYIYlgSGTRVLFSMGRSGYMSnKLKSIESKHSVPLWSLIIFAVVGVVLV---FVTAPVPSIYTFId 381
                                       8888763567777744678*************77777779999******99888888887...56667778999994 PP

                       AA_permease 369 .laisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvl 419
                                         +++++igli+ +++++     R+ + +++  ++ ++++a+l+  g+ l++
  gi|518651517|ref|YP_008141037.1| 382 dATAAGYIGLITNPIALMVTR--RQGITKKKDMVRGMSIIAPLATAGSALIV 431
                                       445667788887777666555..77777777777777777777766666655 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 0.98
                       AA_permease  95 taasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivg 157
                                       ta s li fw  +   ++ ++++++  +++l+  l  vk  ++  ++      + +i+f  + 
  gi|518651517|ref|YP_008141037.1| 424 TAGSALIVFW--TGWPSEPYAVILIAAGAVLFGALSKVKIGAKNALW-----YVFFIGFATFM 479
                                       5566777777..44444446677777777777777788888874444.....44444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); 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:                         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: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 3922.80
//
Query:       gi|518651518|ref|YP_008141038.1|  [L=168]
Description: inorganic pyrophosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-47  161.6   1.2    1.4e-47  161.4   1.2    1.0  1  Pyrophosphatase  Inorganic pyrophosphatase
  ------ inclusion threshold ------
      0.047   13.8   0.0      0.067   13.3   0.0    1.2  1  PglZ             PglZ domain


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 !  161.4   1.2   1.6e-51   1.4e-47       1     155 [.      16     166 ..      16     168 .] 0.97

  Alignments for each domain:
  == domain 1  score: 161.4 bits;  conditional E-value: 1.6e-51
                                       EEEEE-TTCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEE CS
                   Pyrophosphatase   1 vvvEiprgsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkv 77 
                                       v++Eip+g n K+e++ + ++++ldr+lfts+ yp+nYGf+ +T ++     D+DPlDvlv++++p+ +g +v+++ 
  gi|518651518|ref|YP_008141038.1|  16 VFIEIPQGGNTKLEYKFDVENIVLDRILFTSMVYPTNYGFVLNTKAK-----DEDPLDVLVISSVPMPSGAIVKCRA 87 
                                       68*********************************************.....************************* PP

                                       EEEEEEEETTEEEEEEEEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHH CS
                   Pyrophosphatase  78 lGvlamiDegetDdKiiavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvi 152
                                       +G+ +m De++ D+K+iavp +  dp+ k+++di+d+p+ ++++i+hfF++yk+le k+k   ++++k+k+eA+k i
  gi|518651518|ref|YP_008141038.1|  88 IGIAEMSDEEGSDNKVIAVPLDkvDPMSKEYTDIKDVPDAVKDKIKHFFQHYKELE-KGKFMTFHDFKGKDEAIKQI 163
                                       *********************999**88****************************.77888*************** PP

                                       HHH CS
                   Pyrophosphatase 153 eea 155
                                       +e+
  gi|518651518|ref|YP_008141038.1| 164 KES 166
                                       997 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   7.5e-06     0.067     109     151 ..      98     140 ..      74     147 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.5e-06
                              PglZ 109 lkdkevvyivhnkvDalgdkasteqksfeaveeslkelkelvk 151
                                        +d++v+++ ++kvD ++ ++   +++ +av+ ++k++ +  k
  gi|518651518|ref|YP_008141038.1|  98 GSDNKVIAVPLDKVDPMSKEYTDIKDVPDAVKDKIKHFFQHYK 140
                                       478********************************97765554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1161.39
//
Query:       gi|518651519|ref|YP_008141039.1|  [L=414]
Description: 1,3-propanediol dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete 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-93  312.6   0.0    3.7e-93  312.2   0.0    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    2.1e-22   80.0   1.6    6.2e-14   52.3   0.0    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
  ------ inclusion threshold ------
      0.047   12.8   0.0        1.3    8.1   0.0    2.4  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 !  312.2   0.0   6.3e-97   3.7e-93       3     362 ..      21     395 ..      20     397 .. 0.93

  Alignments for each domain:
  == domain 1  score: 312.2 bits;  conditional E-value: 6.3e-97
                                       EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-T CS
                            Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalare 79 
                                       ri+fg+ +  ++ge lk++  k+ livtd++++ k gll+++++sl++ +i+++v+d+++ +pt e++ +a+++ar+
  gi|518651519|ref|YP_008141039.1|  21 RILFGEWQSMRVGEQLKEIEKKNTLIVTDPNVY-KFGLLNDIETSLSKFQIKYEVYDKISNEPTMENIVNAVEFARS 96 
                                       89******************9**********99.*****************************************99 PP

                                       T..--EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  80 eg.advviavGGGsviDtAKaialllanpe.vedyl.gegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       +g +d v+avGGGsv+Dt K++a +++n++ +++yl  ++ + k+++lp i iPTt GtGsev++ +v+ + e+  k
  gi|518651519|ref|YP_008141039.1|  97 NGkFDSVVAVGGGSVLDTSKMVASMVTNKGePAEYLtPVEDKFKNPGLPKILIPTTGGTGSEVSNMSVVINRESMYK 173
                                       966*************************9559999985555668999***************************9** PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedl 230
                                       +  ++ +ll+d+aivDp l +++P+r+taa+g+Dalah +E ++sk+anp+sd++a +a+ li++nl++a++d++++
  gi|518651519|ref|YP_008141039.1| 174 TWAASSNLLADTAIVDPVLNVSAPPRTTAASGMDALAHNIEGLISKEANPISDGMATKAASLIFRNLRTAYNDPSNM 250
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHSS---....HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.... CS
                            Fe-ADH 231 eareqmllastlaglafsnaglg....avHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralgge 303
                                       ear++m + ++l+g+ ++   ++    + H l++a+g ++g+ hg+a++++lp++l+fn++aa++++  lar ++  
  gi|518651519|ref|YP_008141039.1| 251 EARSAMSMSAMLGGMVITFPWVAgpavLGHCLGEAFGPKYGAIHGVAVGMALPYILDFNISAAYNKIGSLARIFNIR 327
                                       ***************999887777778999999999999**********************************9888 PP

                                       .......T--HHHHHHHHHHHHHTT---SHHHHT-TT-HHHHHHHHHT-T.....SGGGGSSS---HH CS
                            Fe-ADH 304 ....sdeeaaeeliealrellkelglptsLselgvdeedldklaeaalkd.....rslannpreltae 362
                                           s+++ a ++  a+++ll++l +pt+L++++++++d++k+ + ++++        + npr+lt+e
  gi|518651519|ref|YP_008141039.1| 328 ykgeSARAVASKIPPAIIQLLEDLEMPTTLKDINFPASDIEKFGDYIFSSrqklyDLPRFNPRRLTKE 395
                                       99*9999*********************************8888888666522244556777777776 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 !   52.3   0.0     1e-17   6.2e-14       9      96 ..      31     120 ..      24     125 .. 0.93
   2 !   27.0   0.3   5.5e-10   3.3e-06     118     250 .]     159     299 ..     141     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.3 bits;  conditional E-value: 1e-17
                          Fe-ADH_2   9 klgellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealre.ketdlvvavG 83 
                                       ++ge lke e k+ l+v+d n++k+ + +++e sl++ +ik ev+++ ++e+++e++ + ve +r+  ++d vvavG
  gi|518651519|ref|YP_008141039.1|  31 RVGEQLKEIEKKNTLIVTDPNVYKFgLLNDIETSLSKFQIKYEVYDKISNEPTMENIVNAVEFARSnGKFDSVVAVG 107
                                       78999********************999**********************************9985379******** PP

                          Fe-ADH_2  84 gGtiiDiakyvsa 96 
                                       gG+++D++k+v++
  gi|518651519|ref|YP_008141039.1| 108 GGSVLDTSKMVAS 120
                                       ***********97 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 5.5e-10
                          Fe-ADH_2 118 gaslvvdgkkrtv.akaaaPlaviaDldvla.....eAPrrllasGvGDllgkytaladwklanevseplaklsaam 188
                                       ++ + v  +++++ ++ aa   ++aD+ ++       AP r +a+   D+l+  +    +k an +s+ +a ++a  
  gi|518651519|ref|YP_008141039.1| 159 VSNMSVVINRESMyKTWAASSNLLADTAIVDpvlnvSAPPRTTAASGMDALAHNIEGLISKEANPISDGMATKAASL 235
                                       333444434455534556677788888877433333899999988888***************************** PP

                          Fe-ADH_2 189 vqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlal..kqalHGeqVG 250
                                       ++ +++++ +d+ ++ea +++ ++ +l+g+ i+ p   +   + H l +++     a+HG  VG
  gi|518651519|ref|YP_008141039.1| 236 IFRNLRTAYNDPSNMEARSAMSMSAMLGGMVITFPWVAGPAVLGHCLGEAFGpkYGAIHGVAVG 299
                                       ************************************999********99987556799***998 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00023       1.3      18      53 ..      86     122 ..      71     126 .. 0.74
   2 ?    2.2   0.0     0.014        86     181     228 ..     278     343 ..     277     374 .. 0.59

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00023
                                       HHHHHH.HHTT--TT-EEEEEESHHHHHHHHHHHHHB CS
                      DHQ_synthase  18 kildal.leakleRksllialGGGvvgDlaGfvAaty 53 
                                       +i++a+ ++++  + + ++a+GGG v+D    vA+++
  gi|518651519|ref|YP_008141039.1|  86 NIVNAVeFARSNGKFDSVVAVGGGSVLDTSKMVASMV 122
                                       44444413334556689*****************986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.014
                                       TTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHH.....................H CS
                      DHQ_synthase 181 lGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeve.....................r 228
                                       lGH +g a+    g     HG aV + + + +++  ++ + k  +++                     +
  gi|518651519|ref|YP_008141039.1| 278 LGHCLGEAFGPKYGA---IHGVAVGMALPYILDFNISAAYNKIGSLArifnirykgesaravaskippA 343
                                       688888887777666...899888877766555554444444444443334444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 2613.49
//
Query:       gi|518651520|ref|YP_008141040.1|  [L=497]
Description: hypothetical protein FACI_IFERC00001G0159 [Ferroplasma acidarmanus fer1]
Scores for complete 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-168  560.2   0.0   3.2e-168  560.0   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  560.0   0.0  1.8e-172  3.2e-168       1     462 []      12     478 ..      12     478 .. 0.99

  Alignments for each domain:
  == domain 1  score: 560.0 bits;  conditional E-value: 1.8e-172
                                       EET-SSSE.EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHH..HHTTS-HHHHHHHHHHHHHHHHHTHHHHHHH CS
                            Aldedh   1 wveseset.ievinPatgeviakvpaataedvdaavaaAkeafk..awaklpaeeRaeiLrkaadlleerkeelael 74 
                                       wves++++ ++v+nP+tg ++a+v++a+++dv +a++aA++ f+   w++ ++ +R+++L k+adl+e+++++++++
  gi|518651520|ref|YP_008141040.1|  12 WVESSENQvLKVLNPSTGLPVASVQSASRDDVGKAIDAARNSFDsgIWSRATPGDRSNVLLKVADLIEKNQDKFIKV 88 
                                       999999777***********************************766****************************** PP

                                       HHHHH---HHHHHH.HHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHH CS
                            Aldedh  75 etletGkplaeara.eveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklap 149
                                       et + Gk++++ ++ ++++++d +r+ a+++++leg++++   ++ ++ +rreP+G +g+ItPWN+Pl++++w + p
  gi|518651520|ref|YP_008141040.1|  89 ETENSGKSIKQISGyDIPYTVDNIRFLAGACRTLEGKAMNEyVADGTSAIRREPIGAIGIITPWNYPLMMVVWRAFP 165
                                       **************************************999779********************************* PP

                                       HHHTT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHH CS
                            Aldedh 150 alaaGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaa 226
                                       ala+GN+vv+KPa+ tpl++l+la +++eag+P+gv+nv+tg+gs+vge++++++++d+++ftGstevg+++   aa
  gi|518651520|ref|YP_008141040.1| 166 ALAMGNSVVVKPASYTPLTTLMLADILKEAGVPDGVFNVITGPGSSVGEEMAKSEKLDMIAFTGSTEVGKRLSVLAA 242
                                       ***************************************************************************** PP

                                       CTTSEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTS CS
                            Aldedh 227 knlkrvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpld 303
                                       +nlk+v+lElGGk+p+iv++da++d+ave+++ g ++n+GQ C + +r ++qe+++d+fv+ l+++++kl++gdp+d
  gi|518651520|ref|YP_008141040.1| 243 SNLKKVSLELGGKAPFIVFKDANIDAAVESAIVGGLVNNGQDCANSTRYYIQEEVFDKFVSLLKKRIQKLRIGDPMD 319
                                       ***************************************************************************** PP

                                       TT-SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT.E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEE CS
                            Aldedh 304 edtdvGPliseaqlekvekyveeakeegaklllGge.reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvik 379
                                       ++td+GPlise q+e+ve+y+e++++eg kll Gge  e +g +kgy+++P ++   ++d++i++eEiFGPV++++k
  gi|518651520|ref|YP_008141040.1| 320 PSTDMGPLISETQRERVEGYIEKGIKEGGKLLSGGErPEIPGHKKGYYINPALIYTENEDSAIVKEEIFGPVFTILK 396
                                       ************************************9999************************************* PP

                                       ESSHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHT CS
                            Aldedh 380 fkdeeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleey 456
                                       fkd ++ai+  Nd  yGL+++v+t+d+++a+r++++l++G+v++N++ ++  e+ p+ G+k+Sg+G+  ++++lee+
  gi|518651520|ref|YP_008141040.1| 397 FKDYNDAIRRSNDVTYGLGSSVWTSDITTAMRATRDLRFGTVWVNEHVVVPSEM-PWAGYKESGHGASLSPYSLEEF 472
                                       ***********************************************8888888.********************** PP

                                       EEEEEE CS
                            Aldedh 457 tevktv 462
                                       t +k+v
  gi|518651520|ref|YP_008141040.1| 473 TYIKHV 478
                                       ****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 3158.98
//
Query:       gi|518651521|ref|YP_008141041.1|  [L=476]
Description: hypothetical protein FACI_IFERC00001G0160 [Ferroplasma acidarmanus fer1]
Scores for complete 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   98.8  46.9    3.2e-28   98.6  46.9    1.1  1  AA_permease    Amino acid permease
    1.2e-22   80.4  51.9    1.5e-22   80.0  51.9    1.2  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6  46.9   3.5e-32   3.2e-28       1     430 [.      23     428 ..      23     463 .. 0.82

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 3.5e-32
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       h++++a   v + g +  l   ++   +++  la+ll++v+++l++++ + ++  ++++gg+y+   + +g   Gf+
  gi|518651521|ref|YP_008141041.1|  23 HAVFQAYTHVAPSGDIGILLTGVALFALGASPLAVLLSWVIYLLMVNTNYRFSQRVSHAGGYYAIGGHGMGGFYGFM 99 
                                       56666666666666666666666666676799********************************************* PP

                       AA_permease  78 iGlnylfswitvla.leltaasiliqfwel.vtdlpkawvt.gavflvvlliinlvgvkvygeaefilalikiiaii 151
                                        G++yl+ + + ++ ++l + +++i +++  ++++p +wv  +++ ++  l++n++g+k +      ++li     +
  gi|518651521|ref|YP_008141041.1| 100 NGWIYLLDEMIIYPsFGLLGFASVIFLLSPaISSIPFIWVPlILIPFATGLLFNYFGIKPSLV----YLLITATVEV 172
                                       ******9876655538999999**9999888999997777689999999999*******9988....8888888888 PP

                       AA_permease 152 afiivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEv 225
                                       +f++ +   i  ++  +p++          +s     ++ +     + ++  fi+++   + a+ G + v+ i++E+
  gi|518651521|ref|YP_008141041.1| 173 IFLLSTswyI--IFTMGPANT---------LS----VFSLS-----GINVIPFIFALLYGIEAYGGLGTVIGISEET 229
                                       9999888544..444444444.........22....34444.....5889999************************ PP

                       AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaals 302
                                       k ++ +iP+ai+ + i+ +   + +++++++ ++ ++ ++ + s ++  +++i  ++ g+++   ++ ++il   + 
  gi|518651521|ref|YP_008141041.1| 230 KQSKLNIPRAIIIAAILAGATLISAMYALTIAWGPTSMTSYATSPDP--GLIIWHRFFGLPG-EIILLFFILNGYIA 303
                                       *************************************9999999988..************9.56778889999999 PP

                       AA_permease 303 sansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaligli 378
                                       + ++  ++ sRv+y++a+dg++P +++  ++k++ P+ra++l++ii+l++ +  s+ ++++++  +  a++++  ++
  gi|518651521|ref|YP_008141041.1| 304 YTVANPIVQSRVIYAMARDGVFPrWFAVTHKKYKTPYRAVILVSIIALIVSMGLSFPFGPFNAAIITGAMAGIGLVS 380
                                       99*********************7677778999******************************************** PP

                       AA_permease 379 vwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillila 430
                                        + +++l+y+r+ ++   +++  + + +k a +pl + ++l+ +ii++    
  gi|518651521|ref|YP_008141041.1| 381 AHAMSSLAYIRYARK--DNKI--KYSIVKDAIIPLASLIILIPIIIFAFDEL 428
                                       **********76666..4444..44667777777777666665555443333 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0  51.9   1.7e-26   1.5e-22      11     405 ..      29     424 ..      19     459 .. 0.75

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.7e-26
                     AA_permease_2  11 igsv..ig.sgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfn 84 
                                       ++ v   g +gi+ +++a+ +  a+ l v+++ +i+ l ++ +   +s + ++ gG y  + +++g + +f+++w++
  gi|518651521|ref|YP_008141041.1|  29 YTHVapSGdIGILLTGVALFALGASPLAVLLSWVIY-LLMVNTNYRFSQRVSHAGGYYAIGGHGMGGFYGFMNGWIY 104
                                       555544445667776633334444455555555555.4455677778888999************************ PP

                     AA_permease_2  85 wfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliilii 161
                                       +++ ++  +s   +++++ +++l+p +   +++++ ++ + +++  l+n++gik s  +  i++++ ++ +l+   +
  gi|518651521|ref|YP_008141041.1| 105 LLDEMIIYPSFGLLGFASVIFLLSPAISSIPFIWVPLILIPFATGLLFNYFGIKPSLVYLLITATVEVI-FLLSTSW 180
                                       *************************9988888888888888899999*********************4.5333333 PP

                     AA_permease_2 162 lglitvdgggfsslstetdtffpn.gwpg..vllgllivlwsfdGfesaanvseevkk.k.dvpkaifigllivlvl 233
                                         ++t   g ++     t ++f+  g +   ++++ll  + +++G  +++++see k+ k ++p+ai+i++++++  
  gi|518651521|ref|YP_008141041.1| 181 YIIFT--MGPAN-----TLSVFSLsGINVipFIFALLYGIEAYGGLGTVIGISEETKQsKlNIPRAIIIAAILAGAT 250
                                       33333..23333.....334333334443244556666899**************9998789*************** PP

                     AA_permease_2 234 yllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlPr 310
                                        +  + a++++ ++ ++++ +++++++ +  ++++g  ++ii+ ++i  + +    +  i +srv++a+ardgv+Pr
  gi|518651521|ref|YP_008141041.1| 251 LISAMYALTIAWGPTSMTSYATSPDPGLIIWHRFFGLPGEIILLFFILNGYIAYTVANPIVQSRVIYAMARDGVFPR 327
                                       ***********************************8899999999999988888888899***************** PP

                     AA_permease_2 311 ffakvn.kfgspiraiiltaivslillllfl..lassaaynfllsvsslgliisyllliigal.ilrkkrphlkrpg 383
                                       +fa ++ k+++p+ra+il+ i++li+++ ++  +++ +a  +  +++ +gl++  ++ +++++ + rk+++++    
  gi|518651521|ref|YP_008141041.1| 328 WFAVTHkKYKTPYRAVILVSIIALIVSMGLSfpFGPFNAAIITGAMAGIGLVSAHAMSSLAYIrYARKDNKIKYS-- 402
                                       ***********************9999888733333444456777888888888887776666344555555433.. PP

                     AA_permease_2 384 kilvaiigalfllfllvalffp 405
                                       ++  aii + +l++l+ +++f 
  gi|518651521|ref|YP_008141041.1| 403 IVKDAIIPLASLIILIPIIIFA 424
                                       2233333333333333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3232.26
//
Query:       gi|518651522|ref|YP_008141042.1|  [L=35]
Description: hypothetical protein FACI_IFERC00001G0161 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        95  (0.00529868); expected 358.6 (0.02)
Passed bias filter:                       92  (0.00513135); expected 358.6 (0.02)
Passed Vit filter:                         1  (5.57756e-05); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 260.57
//
Query:       gi|518651523|ref|YP_008141043.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G0162 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2135.99
//
Query:       gi|518651524|ref|YP_008141044.1|  [L=520]
Description: cell wall biosynthesis glycosyltransferase-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-22   80.5   0.7    1.5e-22   80.5   0.7    2.3  3  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.5e-19   70.1   0.0    3.3e-19   69.7   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.4e-15   57.5   0.1      2e-15   57.0   0.1    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
      1e-12   47.9   0.0    1.6e-12   47.3   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    3.4e-06   25.9   5.5    0.00028   19.5   3.6    2.9  3  Cellulose_synt   Cellulose synthase
  ------ inclusion threshold ------
      0.042   14.3   0.0       0.12   13.0   0.0    1.8  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.048   13.5   0.0       0.11   12.4   0.0    1.5  1  FAM216B          FAM216B protein family
       0.91    9.2   8.8      0.033   13.9   2.0    2.0  2  Claudin_2        PMP-22/EMP/MP20/Claudin tight junction


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 ?   -3.9   1.9       4.8   1.1e+04     156     169 ..      38      51 ..      14      77 .. 0.41
   2 !   80.5   0.7   6.5e-26   1.5e-22       1     184 [.     181     389 ..     181     403 .. 0.75
   3 ?   -3.2   2.7       2.8   6.4e+03     165     185 ..     465     490 ..     416     503 .. 0.56

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 4.8
                   Glyco_trans_2_3 156 lgylgsllwsalpl 169
                                         y +++l ++  +
  gi|518651524|ref|YP_008141044.1|  38 ALYSALVLKNGTTF 51 
                                       22222222222222 PP

  == domain 2  score: 80.5 bits;  conditional E-value: 6.5e-26
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvmnv.anwleelaalffaedhgkdilvre..algrvvpsv 73 
                                       +++++D D  + pd+lre+ a la +p+++++q p ++ n  +++l+e+a +   +++++  + +e  +  ++++s 
  gi|518651524|ref|YP_008141044.1| 181 YVAVIDIDQTPAPDFLRETTAVLAkDPKIGFIQVPQVYSNIdSSILAEIAQA---QQFIFYDILTEgkSVAGTLFSC 254
                                       799******************99978*********99987527777777764...55555555554348889***** PP

                   Glyco_trans_2_3  74 GsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc.el... 146
                                       G +++ +++al++vg++d  e ++ ED   +++++ +G++ ++++  lv+   p t++ +++Q  Rw+yG  +l   
  gi|518651524|ref|YP_008141044.1| 255 GTNVVYNLDALKSVGYFD--ENNIVEDIATSVNMAINGWTGVYYNKKLVFGRAPVTMQGYINQQWRWMYGSlSLmpk 329
                                       ******************..**************************************************8622345 PP

                   Glyco_trans_2_3 147 .eklillvrll......gylgsllwsalplhlallllfslla...............lal 184
                                         k+ill r +       ++++  w  + + ++++ll+++l                la+
  gi|518651524|ref|YP_008141044.1| 330 iVKKILLSRKFspkqklDWFATSTWYIFGWFYLIFLLSPILEivgirvltinsllylLAW 389
                                       555555444444445446666767777777777777777666666655544443222111 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.8
                   Glyco_trans_2_3 165 salplhlallllfs..lla...lalv 185
                                         lpl+ ++l+l+   +++   ++++
  gi|518651524|ref|YP_008141044.1| 465 ILLPLAAIYLILQHntFSYitaFWAF 490
                                       23344444444432111112222111 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 !   69.7   0.0   1.5e-22   3.3e-19       3     230 .]      99     322 ..      97     322 .. 0.83

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 1.5e-22
                   Glyco_tranf_2_3   3 dlavlVptfneed..vlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       ++avlVp fnee+  v    l ++ +++  +++++v +d  + + ++ ++ l ++l   + ++++++++ g   k+ 
  gi|518651524|ref|YP_008141044.1|  99 KVAVLVPIFNEEEemV-ITNLVAIYSNAGEDSDIYVLDDSTRGDSAPIID-LCRKL---GMKYIHRENRNG--YKAG 168
                                       59*********88533.333444445456779*****9888877788886.44445...668****99767..8*** PP

                   Glyco_tranf_2_3  78 alnealravksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaar 152
                                       aln++l++ +  +v+++D D    Pd+l+ +++++ ++pk+g++++p+ +++ +s+ ++       a+ ++    ++
  gi|518651524|ref|YP_008141044.1| 169 ALNNVLKTLEVPYVAVIDIDQTPAPDFLRETTAVLaKDPKIGFIQVPQvYSNIDSSILAEIAQ---AQQFIFYDILT 242
                                       *********************************************999455559998775544...45555444444 PP

                   Glyco_tranf_2_3 153 ...ralgvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnR 226
                                             g+l++ G+ +++  + lk  + +d+ +++++D+ +++ +  +g+  +y+++++v    p + + yi+q  R
  gi|518651524|ref|YP_008141044.1| 243 egkSVAGTLFSCGTNVVYNLDALKSVGYFDE-NNIVEDIATSVNMAINGWTGVYYNKKLVFGRAPVTMQGYINQQWR 318
                                       332455789999*******************.********************************************* PP

                   Glyco_tranf_2_3 227 wvyg 230
                                       w+yg
  gi|518651524|ref|YP_008141044.1| 319 WMYG 322
                                       **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 !   57.0   0.1     9e-19     2e-15       2     169 ..     102     268 ..     101     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 9e-19
                                       EEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglr 76 
                                       v +p++Ne e+++   l ++ ++   +d +i+v+DD+ + +++ i++  +  + + ++i+re+++  kagaln+ l+
  gi|518651524|ref|YP_008141044.1| 102 VLVPIFNEeEEMVITNLVAIYSN-AGEDSDIYVLDDSTRGDSAPIIDLCR--KLGMKYIHRENRNgYKAGALNNVLK 175
                                       89******966666666668888.9***********99888888888776..5************99********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                            y++++D D +p+pd+l+++ + l kd++ ++++ + +++  +  i        + ++y   ++++   ++ f
  gi|518651524|ref|YP_008141044.1| 176 TLEVPYVAVIDIDQTPAPDFLRETTAVLAKDPKIGFIQVPQVYSNIDSSILAEIAQAQQFIFYDILTEGKSVAGTLF 252
                                       ******************************8887777766666666666665555589999999999999999**** PP

                                       CSTCCCEEEEHHHHHC CS
                   Glycos_transf_2 154 eigsaallrrealeel 169
                                        +g++ +++ +al+++
  gi|518651524|ref|YP_008141044.1| 253 SCGTNVVYNLDALKSV 268
                                       *********9999876 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 !   47.3   0.0     7e-16   1.6e-12      14     172 ..     162     320 ..     153     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 7e-16
                   Glyco_transf_21  14 gvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaled.pkvglVtslpvgsdak.glaaaleaaflntla 88 
                                          +K  +l++ l+  + +++ + D d + +pd+L+e  a l++ pk+g+++ + v+s+ + ++ a++++a+  +++
  gi|518651524|ref|YP_008141044.1| 162 RNGYKAGALNNVLKTLEVPYVAVIDIDQTPAPDFLRETTAVLAKdPKIGFIQVPQVYSNIDsSILAEIAQAQQFIFY 238
                                       44579*********************************9999866**************995699***999999999 PP

                   Glyco_transf_21  89 gvlqa..klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrsslra 163
                                        +l+   +++g+ f +G  ++++ +aL+++G f +   ++ eD a++  ++ +G++ v  ++ ++   +p   +++ 
  gi|518651524|ref|YP_008141044.1| 239 DILTEgkSVAGTLFSCGTNVVYNLDALKSVGYFDE--NNIVEDIATSVNMAINGWTGVYYNKKLVFGRAP--VTMQG 311
                                       999998999**************************..************************998876666..599** PP

                   Glyco_transf_21 164 llaRqlrWa 172
                                       + ++q rW+
  gi|518651524|ref|YP_008141044.1| 312 YINQQWRWM 320
                                       ********6 PP

>> Cellulose_synt  Cellulose synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   2.9      0.64   1.4e+03     630     668 ..      22      61 ..      14      70 .. 0.71
   2 !   14.4   0.0   4.6e-06      0.01     168     288 ..     154     265 ..     140     273 .. 0.82
   3 !   19.5   3.6   1.3e-07   0.00028     420     531 ..     274     381 ..     264     408 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.64
                    Cellulose_synt 630 tllivnlvavvvgvsrainsaye.swgkllGklffafwvl 668
                                        + i+ +v +++g+++a++sa   + g  +  +f a++ +
  gi|518651524|ref|YP_008141044.1|  22 IMSILSIVFIIIGIASALYSALVlKNGTTFDYIFTAWFWI 61 
                                       45688899999*******9986426777888888775444 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 4.6e-06
                    Cellulose_synt 168 lvyvsrekrpGydhnkkaGamnalvrvsavlsnapfilnldcdhyinnskalreamcflldrelGkkvcyvqfpqrf 244
                                       + y+ re r Gy    kaGa+n ++++       p++  +d d        lre+   l       k++++q pq +
  gi|518651524|ref|YP_008141044.1| 154 MKYIHRENRNGY----KAGALNNVLKTLE----VPYVAVIDIDQT-PAPDFLRETTAVLAKDP---KIGFIQVPQVY 218
                                       569********9....8********9875....5*********85.567899**998886554...8********** PP

                    Cellulose_synt 245 dGidks...dryanrnvvffdinlraldGiqGpvy.vGtGcvfrrqal 288
                                         id s   +    ++ +f+di   +   + G ++  Gt +v++  al
  gi|518651524|ref|YP_008141044.1| 219 SNIDSSilaEIAQAQQFIFYDILTEG-KSVAGTLFsCGTNVVYNLDAL 265
                                       ****97432445568899***98777.567777763799999998888 PP

  == domain 3  score: 19.5 bits;  conditional E-value: 1.3e-07
                    Cellulose_synt 420 GsvtedvltGfkmharGwrsvycvtkrdafkGsapinlsdrlhqvlrwalGsveiffsrnnalfagykkklkllerl 496
                                         + ed+ t  +m  +Gw  vy   k     G ap+ +   ++q  rw  Gs+ ++      ++ +  +k+   ++l
  gi|518651524|ref|YP_008141044.1| 274 NNIVEDIATSVNMAINGWTGVYYNKK-L-VFGRAPVTMQGYINQQWRWMYGSLSLMPKIVKKILLS--RKFSPKQKL 346
                                       4699******************8654.3.459***********************99999999999..899999999 PP

                    Cellulose_synt 497 aylnviiypftsifllvycilpalsllsgkfivke 531
                                        ++ +  + +   f l++ + p l ++  + +  +
  gi|518651524|ref|YP_008141044.1| 347 DWFATSTWYIFGWFYLIFLLSPILEIVGIRVLTIN 381
                                       99988887777777778887787777665544322 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.1e-05      0.12       2      81 ..     110     188 ..     109     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
                   Glyco_tranf_2_4   2 neadiLpeflahhlalgfd.rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlv 77 
                                       +e+ ++ + +a + ++g d +i+v+d+  + +++ i++   ++ + +++ + +   ++  +l+++l+   e  +v+v
  gi|518651524|ref|YP_008141044.1| 110 EEEMVITNLVAIYSNAGEDsDIYVLDDSTRGDSAPIIDLCRKLGMKYIHRENR-NGYKAGALNNVLKTL-EVPYVAV 184
                                       7999*************9846***************99989988888888654.689999999999885.999**** PP

                   Glyco_tranf_2_4  78 vDaD 81 
                                       +D+D
  gi|518651524|ref|YP_008141044.1| 185 IDID 188
                                       ***9 PP

>> FAM216B  FAM216B protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.8e-05      0.11      11      47 ..     203     241 ..     197     247 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.8e-05
                           FAM216B  11 lwkvpqiqtirvPk..sasdtsllKdLtqGqkRylySiv 47 
                                       l k p+i +i+vP+  s +d+s+l ++ q q+  +y i+
  gi|518651524|ref|YP_008141044.1| 203 LAKDPKIGFIQVPQvySNIDSSILAEIAQAQQFIFYDIL 241
                                       6789*********855789*****************996 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   1.5e-05     0.033      89     158 ..      17      88 ..      11      94 .. 0.81
   2 ?   -2.4   0.7       1.5   3.4e+03     122     147 ..     378     403 ..     355     441 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                         Claudin_2  89 arfvqvlliLslvlivlavvlgllallkqsv.....lllkaagilfllagvlgllavvvfiesvkkvfeesfqqw 158
                                        +fv+++ iLs+v+i++++  +l ++l  +      ++++a    f +a+v++ ++ ++++ s +++ +++++++
  gi|518651524|ref|YP_008141044.1|  17 VIFVNIMSILSIVFIIIGIASALYSALVLKNgttfdYIFTA---WFWIASVFFGIQSITYFLSFHRSVTDYTDTI 88 
                                       689*****************999666665555554344444...47799***************99999999887 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.5
                         Claudin_2 122 lkaagilfllagvlgllavvvfiesv 147
                                       l+ ++ l+lla ++  + +++++  +
  gi|518651524|ref|YP_008141044.1| 378 LTINSLLYLLAWLPYTILLMTTFTLS 403
                                       33333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); 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):               8  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3340.16
//
Query:       gi|518651525|ref|YP_008141045.1|  [L=380]
Description: ATPase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-39  134.1   0.7    7.1e-39  133.5   0.7    1.2  1  ATPase       KaiC
    0.00018   20.8   0.0    0.00031   20.0   0.0    1.3  1  ArsA_ATPase  Anion-transporting ATPase
    0.00045   20.0   0.2    0.00079   19.2   0.2    1.4  1  AAA_24       AAA domain
      0.004   16.5   3.7      0.025   13.9   1.4    3.0  2  DnaB_C       DnaB-like helicase C terminal domain
     0.0061   16.2   0.7      0.053   13.1   0.7    2.0  1  AAA_25       AAA domain
     0.0096   16.3   0.0      0.015   15.6   0.0    1.3  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.044   13.4   0.0      0.074   12.7   0.0    1.4  1  SRP54        SRP54-type protein, GTPase domain
      0.053   14.0   0.3       0.12   12.9   0.3    1.7  1  ABC_tran     ABC transporter
       0.13   12.8   0.7        0.3   11.6   0.7    1.8  1  AAA_18       AAA domain
       0.17   11.8   3.2       0.31   10.9   0.3    2.5  2  AAA_31       AAA domain
       0.23   11.5   0.8       0.51   10.4   0.5    1.9  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding 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 !  133.5   0.7   4.3e-42   7.1e-39       3     225 ..     121     341 ..     119     346 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 4.3e-42
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                        gI+ lD  l+gG+  g v+ i+G+pG GKt+++ +Fl  ga+  ge+g+++ ++  + +++ n++++ + + +  +
  gi|518651525|ref|YP_008141045.1| 121 FGIPILDAKLSGGLRPGYVYMISGKPGVGKTTLSSTFLSYGASI-GEKGLMILTDTFPDQFIDNIRTMNIGFAEAYK 196
                                       59***************************************888.******************************** PP

                            ATPase  80 egklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrv 150
                                         k+ ++++s + +  +++      ++++ + +l++el+++i ++ +krvviD+it l  + ++    + +  l++ 
  gi|518651525|ref|YP_008141045.1| 197 DRKIEVMEISDQIRSMKSDisqgkaDSRKFITKLVTELKKIIISKDIKRVVIDPITLL-IIPDD----DFVNLLLNS 268
                                       **********9998877778889888889999**************************.55555....46899**** PP

                            ATPase 151 lkklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegik 225
                                       ++ +gvT +++s  ++s  + + +g+ee+  +g+i+L+++ +++  +Rt +i+kmRgt+ +++ + f+It +gi+
  gi|518651525|ref|YP_008141045.1| 269 MAIKGVTILITSGLRNS--NLSIFGIEEYYTTGIIKLEYRPQNDISTRTGSIIKMRGTAFDPNPFDFKITADGIV 341
                                       *************8666..99**************************************************9996 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.9e-07   0.00031       4      85 ..     140     228 ..     138     250 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.9e-07
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S..TTTHHHHHHTS--BSS-EEETSSEEEEE--HH.....HHH CS
                       ArsA_ATPase   4 ilvgGKGGVGKttvsaatavklsekgkkvllistD..PAhslsDsfdqklgkeptkvkeNLsavEidpe.....vel 73 
                                        +++GK GVGKtt+s+++  + +  g+k l+i tD  P   +  +   ++g  +   +  ++++Ei  +      ++
  gi|518651525|ref|YP_008141045.1| 140 YMISGKPGVGKTTLSSTFLSYGASIGEKGLMILTDtfPDQFIDNIRTMNIGFAEAYKDRKIEVMEISDQirsmkSDI 216
                                       589*****************************999445555555555566666666668888888877755544445 PP

                                       HHHHCCHHGGGS CS
                       ArsA_ATPase  74 eeakqevqkeee 85 
                                       ++ k +  k+++
  gi|518651525|ref|YP_008141045.1| 217 SQGKADSRKFIT 228
                                       555554444444 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.9e-07   0.00079       3      75 ..     138     252 ..     136     257 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.9e-07
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie.............swedfldevve 58 
                                       + ++i G++g+GKTtl +++       g+k l+i t+    + +d+++  +i                         
  gi|518651525|ref|YP_008141045.1| 138 YVYMISGKPGVGKTTLSSTFlsygasiGEKGLMILTDTfPDQFIDNIRTMNIGfaeaykdrkievmE---------- 204
                                       7889***********************9999999888866777777777777666644444443331.......... PP

                            AAA_24  59 l...............................aaeladyktlviDtid 75 
                                       +                                   +d+k +viD i+
  gi|518651525|ref|YP_008141045.1| 205 IsdqirsmksdisqgkadsrkfitklvtelkkIIISKDIKRVVIDPIT 252
                                       344555556666666777777777778888888888999999999887 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 ?   -1.9   0.0         1   1.6e+03      31      73 ..      49      89 ..      46      97 .. 0.74
   2 !   13.9   1.4   1.5e-05     0.025       9     140 ..     126     253 ..     120     259 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1
                                      SHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C 31 GktalalniaenaavkeklpvavfslemsaeqlvqRllsseae 73
                                      G   +a+++a++  +  ++ ++vf+   ++  +++++l se e
  gi|518651525|ref|YP_008141045.1| 49 GEDKIAVKLANSDIT--TNDIMVFNSQATDAGIARKILISEIE 89
                                      555667777765443..34699999999999999999998865 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       HH.HHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTS CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C   9 LD.kltsGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgkl 84 
                                       LD kl +Gl++g +++i ++p++Gkt+l  ++ +  a   +++ ++   +   +q ++ + +++ +   ++++  k+
  gi|518651525|ref|YP_008141045.1| 126 LDaKLSGGLRPGYVYMISGKPGVGKTTLSSTFLSYGASIGEKGLMIL-TDTFPDQFIDNIRTMNIGFA-EAYKDRKI 200
                                       77456789********************9999887775455454444.34444455554444333321.12222222 PP

                                       XHHHHHHHHHHHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  85 keedweklteaieelseaklfiddtpaltvseirskarrlkkekglgliviDyLql 140
                                          ++ +++++i+++++     +  ++  ++++ ++++++  +k+++ +viD + l
  gi|518651525|ref|YP_008141045.1| 201 ---EVMEISDQIRSMKSDISQGKADSRKFITKLVTELKKIIISKDIKRVVIDPITL 253
                                       ...22333333333332222222333444666666666666666666666666655 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.7   3.3e-05     0.053      26     152 ..     131     252 ..     108     261 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.3e-05
                            AAA_25  26 vkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...r 98 
                                        +gl + g + ++ G pg+GKttl +      a  G+           k l++ ++   d++   +r +   +    
  gi|518651525|ref|YP_008141045.1| 131 SGGL-RPGYVYMISGKPGVGKTTLSSTFLSYGAsIGE-----------KGLMILTDTFPDQFIDNIRTMNIGFaeaY 195
                                       3455.56*****************9988777772233...........77888888888888887777774443333 PP

                            AAA_25  99 ddarllvldlagveslpLfakd.rggtl.....ltadvdaleaaieevegvrlvviDpls 152
                                        d++  v+ + ++  ++ +++d ++g++     +t  v +l + i + ++++ vviDp++
  gi|518651525|ref|YP_008141045.1| 196 KDRKIEVMEISDQ--IRSMKSDiSQGKAdsrkfITKLVTELKKIIIS-KDIKRVVIDPIT 252
                                       4566677776665..44443322333333123566666666666666.888888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   9.5e-06     0.015      27     124 ..     140     235 ..     126     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-06
                            AAA_16  27 vllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesaeleawreklee 103
                                        ++sG +GvGK++l  ++l ++ ++    + +k            l++++  ++++  + ++     +ea++++  e
  gi|518651525|ref|YP_008141045.1| 140 YMISGKPGVGKTTLSSTFL-SYGAS----IGEKGLMI--------LTDTF-PDQFIDNIRTMNIG-FAEAYKDRKIE 201
                                       579****************.66666....55555555........66666.44667777666444.66666666666 PP

                            AAA_16 104 alaavpelagaea.............srllellk 124
                                       ++++++++++ ++             + l  +lk
  gi|518651525|ref|YP_008141045.1| 202 VMEISDQIRSMKSdisqgkadsrkfiTKLVTELK 235
                                       6664444444433332444333333344444444 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.5e-05     0.074       3      61 ..     139     193 ..     137     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvik 61 
                                       v+++ G  G+GKTt  +    +  + g+k l++ +Dtf     +Q   + +++++ + +
  gi|518651525|ref|YP_008141045.1| 139 VYMISGKPGVGKTTLSSTFLSYGASIGEKGLMILTDTFP----DQFIDNIRTMNIGFAE 193
                                       89************************************5....5555555555555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.3   7.3e-05      0.12       4      32 ..     130     158 ..     128     237 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-05
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlklla 32 
                                       +s  l++g ++ i G+ G GK+tL ++++
  gi|518651525|ref|YP_008141045.1| 130 LSGGLRPGYVYMISGKPGVGKTTLSSTFL 158
                                       678899******************98775 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.7   0.00019       0.3       2      17 ..     141     156 ..     141     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                            AAA_18   2 lltGtpGvGKttlake 17 
                                       +++G+pGvGKttl+  
  gi|518651525|ref|YP_008141045.1| 141 MISGKPGVGKTTLSST 156
                                       699**********975 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.43   7.1e+02      86     144 ..      10      69 ..       3     100 .. 0.57
   2 ?   10.9   0.3   0.00019      0.31       6      59 ..     141     200 ..     138     257 .. 0.63

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.43
                            AAA_31  86 ssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcpPsLglltena.Lvasdsvi 144
                                       ++i L++++ ++ +++    +  +  + ++ ++Dyii     ++ + + n+ +++ d ++
  gi|518651525|ref|YP_008141045.1|  10 AQIALQKFQFDIHKVKVVGGMAVQGASGLSYKFDYIIASGEDKIAVKLANSdITTNDIMV 69 
                                       566666666666666666666666666667777777765555555544443133333333 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDp...Q..an.attglgiekneiektl 59 
                                       ++  K GvGKTT s  + +  a+ g+k L++  D+   Q   n  t+++g+ +  +++++
  gi|518651525|ref|YP_008141045.1| 141 MISGKPGVGKTTLSSTFLSYGASIGEKGLMILTDTfpdQfiDNiRTMNIGFAEAYKDRKI 200
                                       677899*******99998888999999999988862222111213445555444444333 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 ?   -2.2   0.0       2.4   3.9e+03      64      85 ..      86     109 ..      14     128 .. 0.69
   2 ?   10.4   0.5   0.00031      0.51       3      33 ..     141     171 ..     139     267 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.4
                                       HHHCHCHHHH....EEEEEEEEES CS
                                       xxxxxxxxxx..xxxxxxxxxxxx RF
                              CbiA  64 ealgkkkall..lkiagvvlnrvd 85 
                                       +++  +  ++   +i g+++  ++
  gi|518651525|ref|YP_008141045.1|  86 SEIELGEYVKkmCNIYGIIISDPR 109
                                       333333333335777888877765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00031
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllv 33 
                                       ++s+k GvGKTtl+ +++ + a  g + l++
  gi|518651525|ref|YP_008141045.1| 141 MISGKPGVGKTTLSSTFLSYGASIGEKGLMI 171
                                       689***********99998887777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 2336.77
//
Query:       gi|518651526|ref|YP_008141046.1|  [L=69]
Description: ferredoxin [Ferroplasma acidarmanus fer1]
Scores for 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   57.8  17.1    5.2e-08   32.4   3.8    2.1  2  Fer4      4Fe-4S binding domain
    3.6e-13   49.9  33.6    3.6e-08   33.9  12.2    1.8  3  Fer4_7    4Fe-4S dicluster domain
    1.2e-10   40.9  16.2    3.8e-07   29.9   4.9    2.1  2  Fer4_6    4Fe-4S binding domain
    1.5e-10   41.1  21.1    5.8e-08   32.8  11.5    1.6  2  Fer4_9    4Fe-4S dicluster domain
      5e-09   37.0   9.0    3.6e-05   24.6   0.6    2.1  2  Fer4_16   4Fe-4S double cluster binding domain
    5.3e-08   32.9  20.7    3.5e-07   30.3  12.0    1.4  2  Fer4_21   4Fe-4S dicluster domain
    2.2e-07   30.6  11.8    0.00025   20.9   2.4    2.2  2  Fer4_2    4Fe-4S binding domain
    4.4e-07   29.9  11.6    0.00045   20.3   2.4    2.1  2  Fer4_10   4Fe-4S dicluster domain
    0.00017   21.9   6.3      0.091   13.2   0.8    2.1  2  Fer4_8    4Fe-4S dicluster domain
     0.0015   18.7  10.6      0.046   13.9   2.5    2.0  2  Fer4_18   4Fe-4S dicluster domain
     0.0016   18.9  10.6       0.09   13.3   1.4    2.1  3  Fer4_17   4Fe-4S dicluster domain
     0.0017   18.7  14.1     0.0081   16.6   3.7    2.2  2  Fer4_4    4Fe-4S binding domain
     0.0024   18.7  17.4      0.076   14.0   5.6    2.2  2  Fer4_3    4Fe-4S binding domain
     0.0027   17.8   2.3      0.003   17.6   2.3    1.2  1  Fer4_11   4Fe-4S dicluster domain
     0.0029   17.7   1.9     0.0032   17.6   1.9    1.1  1  ETF_QO    Electron transfer flavoprotein-ubiquinone oxidoredu
  ------ inclusion threshold ------
      0.024   15.2  14.7       0.61   10.7   4.0    2.7  3  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
      0.046   14.5  15.4       0.21   12.3   4.0    3.1  3  Fer4_15   4Fe-4S single cluster domain
       0.24   12.2   8.7        3.1    8.7   0.4    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 !   32.4   3.8   5.2e-11   5.2e-08       3      23 ..      11      31 ..       9      32 .. 0.94
   2 !   31.7   5.4   8.8e-11   8.8e-08       2      24 .]      39      61 ..      38      61 .. 0.94

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 5.2e-11
                                      EETTTSSS-THHHHHSTTTEE CS
                              Fer4  3 ideekCigCGaCvevCPvgAI 23
                                      +d  +C +CGaCv +CP++AI
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCPTDAI 31
                                      89******************9 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 8.8e-11
                                      EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  2 videekCigCGaCvevCPvgAIt 24
                                       i+e+kCi+C  Cv  CP+gAI+
  gi|518651526|ref|YP_008141046.1| 39 AINEDKCIKCEFCVIGCPTGAIS 61
                                      69********************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   2.9   3.6e-06    0.0035      29      52 .]       7      30 ..       2      30 .. 0.84
   2 !   33.9  12.2   3.6e-11   3.6e-08       2      52 .]      16      59 ..      15      59 .. 0.96
   3 !   20.4   2.9   5.9e-07   0.00059       1      19 [.      44      62 ..      44      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.6e-06
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                       ++++d   C +CgaCv  CPt+a
  gi|518651526|ref|YP_008141046.1|  7 SEMDVDRGLCDYCGACVGMCPTDA 30
                                      578888899************997 PP

  == domain 2  score: 33.9 bits;  conditional E-value: 3.6e-11
                            Fer4_7  2 CigCgaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      C  CgaCv +Cp++ai+lde         ++i+++kC+ C+ Cv  CPtga
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDAINLDET-------VIAINEDKCIKCEFCVIGCPTGA 59
                                      99****************997.......69*******************98 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 5.9e-07
                            Fer4_7  1 rCigCgaCvaaCpvkaiel 19
                                      +Ci+C++Cv  Cp++ai+ 
  gi|518651526|ref|YP_008141046.1| 44 KCIKCEFCVIGCPTGAISA 62
                                      7***************986 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   3.5     4e-06     0.004       4      24 .]      11      31 ..       8      31 .. 0.94
   2 !   29.9   4.9   3.8e-10   3.8e-07       1      24 []      37      60 ..      37      60 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4e-06
                            Fer4_6  4 idpdkCigCgdCvrvCPegai 24
                                      +d+ +C+ Cg+Cv  CP++ai
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCPTDAI 31
                                      8******************98 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 3.8e-10
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      v++i++dkCi C+ Cv+ CP+gai
  gi|518651526|ref|YP_008141046.1| 37 VIAINEDKCIKCEFCVIGCPTGAI 60
                                      699********************8 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   2.0     1e-06     0.001      26      51 .]       9      31 ..       1      31 [. 0.71
   2 !   32.8  11.5   5.8e-11   5.8e-08       2      51 .]      16      60 ..      15      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-06
                            Fer4_9 26 arlraaseeaCigCgaCveaCpkgai 51
                                      + +++     C  CgaCv  Cp++ai
  gi|518651526|ref|YP_008141046.1|  9 MDVDR---GLCDYCGACVGMCPTDAI 31
                                      33322...47*************997 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 5.8e-11
                            Fer4_9  2 CtgCgaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                                      C  CgaCv +Cp+++++ d+    ++ +     +Ci+C+ Cv  Cp+gai
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDAINLDETVIAINED-----KCIKCEFCVIGCPTGAI 60
                                      9*******************99999974.....6**************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 !   24.6   0.6   3.6e-08   3.6e-05       2      29 ..      16      42 ..      15      44 .. 0.89
   2 !   17.1   2.4   8.1e-06    0.0081       1      20 [.      44      63 ..      44      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3.6e-08
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeieare 29
                                      C  Cg+C+ +CPt+ai+ + e++i+++e
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDAINLD-ETVIAINE 42
                                      ******************9.78888776 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8.1e-06
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      +C++C+ C+  CPt+ai+++
  gi|518651526|ref|YP_008141046.1| 44 KCIKCEFCVIGCPTGAISAE 63
                                      6****************986 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.4   7.1e-05      0.07      31      58 ..       6      32 ..       2      33 .. 0.80
   2 !   30.3  12.0   3.5e-10   3.5e-07       3      58 ..      11      61 ..       9      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-05
                           Fer4_21 31 ktvlkvvedeCvGCnlCssvCPvedcie 58
                                      k+ + v    C  C  C+ +CP+ d+i+
  gi|518651526|ref|YP_008141046.1|  6 KSEMDVDRGLCDYCGACVGMCPT-DAIN 32
                                      5567788889999*********6.8886 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 3.5e-10
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCssvCPvedcie 58
                                      +d+  C  Cg C+ +C+   ++ai++d +tv+++ ed+C+ C+ C++ CP+ ++i+
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCP---TDAINLD-ETVIAINEDKCIKCEFCVIGCPT-GAIS 61
                                      7888999**********...6****97.7899******************6.8885 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   2.1   1.6e-05     0.016       5      22 .]      11      28 ..       7      28 .. 0.90
   2 !   20.9   2.4   2.5e-07   0.00025       2      22 .]      37      57 ..      36      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.6e-05
                            Fer4_2  5 vdtdrCigCgaCvsaCPa 22
                                      vd+  C  CgaCv  CP+
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCPT 28
                                      78999************7 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 2.5e-07
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      ++++++d+Ci C+ Cv  CP+
  gi|518651526|ref|YP_008141046.1| 37 VIAINEDKCIKCEFCVIGCPT 57
                                      589*****************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.9   1.2e-05     0.012       4      23 ..      11      30 ..       8      39 .. 0.77
   2 !   20.3   2.4   4.5e-07   0.00045       3      22 ..      39      58 ..      37      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                           Fer4_10  4 idddtCirCgkCvkaCPadl 23
                                      +d+  C  Cg+Cv +CP+d+
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCPTDA 30
                                      57778************944 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 4.5e-07
                           Fer4_10  3 vidddtCirCgkCvkaCPad 22
                                       i++d+Ci+C+ Cv  CP+ 
  gi|518651526|ref|YP_008141046.1| 39 AINEDKCIKCEFCVIGCPTG 58
                                      699***************93 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.5   0.00019      0.19      50      63 ..      15      28 ..       3      37 .. 0.74
   2 !   13.2   0.8   9.2e-05     0.091       3      22 ..      43      62 ..      41      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00019
                            Fer4_8 50 sCttcgaCtevCpv 63
                                       C  cgaC+  Cp+
  gi|518651526|ref|YP_008141046.1| 15 LCDYCGACVGMCPT 28
                                      56666666666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 9.2e-05
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk 22
                                      +kCi+C++C   Cp+   ++
  gi|518651526|ref|YP_008141046.1| 43 DKCIKCEFCVIGCPTGAISA 62
                                      589******99999876655 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   1.4   0.00046      0.45      53      74 ..       8      29 ..       1      41 [. 0.79
   2 !   13.9   2.5   4.6e-05     0.046      55      74 ..      39      58 ..      29      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00046
                           Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                                      + + + g c  c++cv +cPt+
  gi|518651526|ref|YP_008141046.1|  8 EMDVDRGLCDYCGACVGMCPTD 29
                                      44567889************96 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.6e-05
                           Fer4_18 55 ekgagdcidcescvkvcPtg 74
                                      + ++ +ci+ce+cv  cPtg
  gi|518651526|ref|YP_008141046.1| 39 AINEDKCIKCEFCVIGCPTG 58
                                      556789*************8 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   1.4     9e-05      0.09       2      20 ..      16      34 ..      15      43 .. 0.84
   2 !   11.0   1.9   0.00047      0.47      45      58 ..      44      57 ..      34      60 .. 0.67
   3 !   10.5   2.3   0.00069      0.69       1      16 [.      44      59 ..      44      67 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9e-05
                           Fer4_17  2 CiqCgyClpeCpsyeaydn 20
                                      C  Cg+C+ +Cp+ +++ +
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDAINLD 34
                                      99**********9887665 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00047
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      +Ci+C+ C+  CP 
  gi|518651526|ref|YP_008141046.1| 44 KCIKCEFCVIGCPT 57
                                      56666666666654 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00069
                           Fer4_17  1 rCiqCgyClpeCpsye 16
                                      +Ci+C++C+  Cp+++
  gi|518651526|ref|YP_008141046.1| 44 KCIKCEFCVIGCPTGA 59
                                      5888888888888765 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   2.8    0.0055       5.5       4      16 ..      16      28 ..      12      29 .. 0.85
   2 !   16.6   3.7   8.1e-06    0.0081       2      17 .]      43      58 ..      42      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0055
                            Fer4_4  4 CigCgsCvaaCPq 16
                                      C  Cg+Cv  CP+
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPT 28
                                      666*********7 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 8.1e-06
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++Ci C  Cv+ CP+g
  gi|518651526|ref|YP_008141046.1| 43 DKCIKCEFCVIGCPTG 58
                                      89************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 !   14.0   5.6   7.6e-05     0.076       1      15 []      16      30 ..      16      30 .. 0.97
   2 !   10.8   3.9   0.00081      0.81       1      15 []      45      59 ..      45      59 .. 0.97

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.6e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ CgaCv  CP++A
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDA 30
                                      9************98 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00081
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ C+ Cv  CP+gA
  gi|518651526|ref|YP_008141046.1| 45 CIKCEFCVIGCPTGA 59
                                      ****99********9 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.3     3e-06     0.003      10      65 ..      16      66 ..       7      69 .] 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3e-06
                           Fer4_11 10 CrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrkneet 65
                                      C  C   +Cv ++p++ai  de   ++ ++e+++  +++ +v +cP  ++ +++ +
  gi|518651526|ref|YP_008141046.1| 16 CDYC--GACVGMCPTDAINLDE--TVIAINEDKCI-KCEFCVIGCPTGAISAEWFH 66
                                      7777..48*************9..67888889996.9*********9999888765 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 !   17.6   1.9   3.2e-06    0.0032      47      91 ..      16      61 ..       1      67 [. 0.76

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.2e-06
                                      HHH-TTS-EEEEETT.TTSSEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO 47 qryCPagvyeivede.eakekklqinaqnCvhCktCdikdpsqnie 91
                                        yC a v  + +d+ + +e+ + in   C+ C  C i  p+  i+
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPTDAiNLDETVIAINEDKCIKCEFCVIGCPTGAIS 61
                                      3588888888877776778899*******************99885 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.3   0.00091      0.91       1      17 [.      11      27 ..      11      32 .. 0.95
   2 ?   10.7   4.0   0.00061      0.61       1      17 [.      40      56 ..      40      58 .. 0.93
   3 ?    2.9   0.1      0.17   1.7e+02      50      57 ..      54      61 ..      52      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00091
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      VDr  C  cgaCv ++P
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCP 27
                                      89*************** PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00061
                           Fer4_13  1 VDrdtCiacgaCvelaP 17
                                      +++d+Ci c+ Cv  +P
  gi|518651526|ref|YP_008141046.1| 40 INEDKCIKCEFCVIGCP 56
                                      799***********999 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.17
                           Fer4_13 50 aCPvesIg 57
                                      +CP+ +I 
  gi|518651526|ref|YP_008141046.1| 54 GCPTGAIS 61
                                      7*****96 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   4.0   0.00021      0.21       3      26 ..      11      35 ..       9      39 .. 0.80
   2 ?    7.3   2.8    0.0081         8       1      19 [.      38      56 ..      38      58 .. 0.88
   3 ?    1.7   0.0      0.44   4.3e+02      59      65 ..      55      61 ..      53      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00021
                           Fer4_15  3 vDrdaCigcglCvaea.pevfelde 26
                                      vDr +C+ cg+Cv  + ++ + lde
  gi|518651526|ref|YP_008141046.1| 11 VDRGLCDYCGACVGMCpTDAINLDE 35
                                      8***************445666665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0081
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      + +++d+Ci c+ Cv  +p
  gi|518651526|ref|YP_008141046.1| 38 IAINEDKCIKCEFCVIGCP 56
                                      6899***********8887 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.44
                           Fer4_15 59 CPvdAIr 65
                                      CP++AI+
  gi|518651526|ref|YP_008141046.1| 55 CPTGAIS 61
                                      ******6 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0032       3.1       2      14 ..      16      28 ..       3      40 .. 0.71
   2 ?    7.8   2.5    0.0061       6.1       1      15 [.      44      58 ..      44      63 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0032
                           Fer4_22  2 ClsCgaCtlvCpt 14
                                      C  CgaC  +Cpt
  gi|518651526|ref|YP_008141046.1| 16 CDYCGACVGMCPT 28
                                      4456666666655 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0061
                           Fer4_22  1 rClsCgaCtlvCptC 15
                                      +C++C  C + Cpt 
  gi|518651526|ref|YP_008141046.1| 44 KCIKCEFCVIGCPTG 58
                                      7************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 467.36
//
Query:       gi|518651527|ref|YP_008141047.1|  [L=396]
Description: hypothetical protein FACI_IFERC00001G0166 [Ferroplasma acidarmanus fer1]
Scores for complete 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   56.6   0.1    3.5e-14   52.8   0.1    2.4  1  FAD_binding_3   FAD binding domain
    1.2e-12   47.7   1.7    2.7e-06   26.7   0.0    3.2  4  FAD_binding_2   FAD binding domain
    1.1e-11   44.8   0.5      3e-11   43.4   0.2    1.8  2  FAD_oxidored    FAD dependent oxidoreductase
    1.1e-09   37.9   0.1    4.4e-09   36.0   0.0    1.9  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-09   37.5   0.3    4.5e-06   26.5   0.1    2.2  2  DAO             FAD dependent oxidoreductase
    3.9e-09   35.9   0.0    1.1e-05   24.5   0.0    2.1  2  Trp_halogenase  Tryptophan halogenase
    8.3e-08   31.7   0.0    1.6e-05   24.1   0.1    2.2  2  Lycopene_cycl   Lycopene cyclase protein
    1.4e-07   31.7   0.0    3.1e-07   30.5   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.1e-06   28.0   0.2    4.1e-06   26.1   0.2    1.9  1  GIDA            Glucose inhibited division protein A
    9.7e-06   25.0   0.1    3.9e-05   23.0   0.0    1.9  2  Thi4            Thi4 family
      1e-05   24.5   0.5      5e-05   22.2   0.0    2.2  3  HI0933_like     HI0933-like protein
     0.0019   18.7   0.0      0.014   15.9   0.0    2.6  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0028   16.9   0.0      0.045   13.0   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
     0.0037   16.6   0.0     0.0094   15.3   0.0    1.7  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
  ------ inclusion threshold ------
       0.15   11.1   0.0       0.29   10.1   0.0    1.4  1  SE              Squalene epoxidase
       0.19   11.6   2.1        2.3    8.1   0.0    3.0  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.1   3.1e-17   3.5e-14       2     308 ..       4     300 ..       3     305 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.1e-17
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS.--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpr.adglnqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dVl++GaGpaG ++a+  s++G +++lvekr +     r ++g+++  m    ++ ++ +++    + e+ g   y
  gi|518651527|ref|YP_008141047.1|   4 YDVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGSPVRcGEGISKAWMP---EVDIKPEAHWI--SDEVKGARIY 75 
                                       79******************************9987777637889888775...55555554444..4777888888 PP

                                       EECCCCCEEEEEHHCH.HCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlele.sspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetv 153
                                       ++ s+  k ++ l++e ++ e   v+  +++++ ++  a+ +g+++  k    s+ ++++ v      + +gee +v
  gi|518651527|ref|YP_008141047.1|  76 GP-SE--KKPIMLTAEsAGNEVGFVVERDKFDKHIATLAATEGADIWIKSPAMSVIKEGNRVVGAK-IRHNGEEVEV 148
                                       88.44..55555554416677778999************************999999998875443.344699999* PP

                                       EEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC.-SCCCTTCCEEEEECCTTEEEEEECCETEEEEEEE CS
                     FAD_binding_3 154 rakYlvGaDGgrStvrktlgiefegeetvyeagvldvlfda.dlsdiveplvlilsaesrgvmviPlentlerfyvq 229
                                       rak +++aDG+ S   + +g++ +  ++  ++  l+  ++  d ++   + +l   a+ + + v P   ++      
  gi|518651527|ref|YP_008141047.1| 149 RAKMVIAADGFESEFSRWAGLKSPILKKNDIISALEYRMENvDSNEDFTDFYLGSIAPAGYLWVFPKGPHEA----N 221
                                       **********************66666665677777777766776545554555556666669999999444....4 PP

                                       EECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHHH CS
                     FAD_binding_3 230 vearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlNt 306
                                       v ++ +++  +++ + +++ + + +++  +     i+++s     ++v +k++   ++ +GDAa    P +G G+  
  gi|518651527|ref|YP_008141047.1| 222 VGIGVTITMMKDRLDVKNYLDSWIKSHPAYSKGRIIQQISGGVSVNKVKDKMSLPGLLAIGDAARLIDPITGGGIAN 298
                                       55555555666677777777777777777777777788888888889999**********************99866 PP

                                       HH CS
                     FAD_binding_3 307 ai 308
                                       ++
  gi|518651527|ref|YP_008141047.1| 299 GM 300
                                       65 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.4e-09   2.7e-06       1      51 [.       5      54 ..       5      99 .. 0.85
   2 !   17.7   0.1   1.4e-06    0.0015     152     200 ..     112     158 ..     100     173 .. 0.85
   3 ?   -2.6   0.0         2   2.2e+03     387     402 ..     270     285 ..     261     304 .. 0.75
   4 ?    0.3   0.0      0.26   2.9e+02     294     332 ..     309     346 ..     303     369 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.4e-09
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT.. CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlsp 51
                                      Dv+ViG+G AG +AA  a++ Glk+++vek +  g+   + +G   a+  p
  gi|518651527|ref|YP_008141047.1|  5 DVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGSPVRCGEGISKAWM-P 54
                                      9********************************9999999999877777.3 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 1.4e-06
                                       HTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE--- CS
                     FAD_binding_2 152 rkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatg 200
                                          g d++ + +a ++i e++rv+Ga ++  ++g+ev++rak v+ a g
  gi|518651527|ref|YP_008141047.1| 112 ATEGADIWIKSPAMSVIKEGNRVVGAKIR--HNGEEVEVRAKMVIAADG 158
                                       34469************************..***********9987765 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2
                                       TEEESSBTEEE-STCE CS
                     FAD_binding_2 387 adgqpipGLYAaGeva 402
                                       +d+  +pGL A+G +a
  gi|518651527|ref|YP_008141047.1| 270 KDKMSLPGLLAIGDAA 285
                                       5667899999*99998 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.26
                                       HHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHH CS
                     FAD_binding_2 294 vvsrailekeiaeggseanvyldashgldaegleatlea 332
                                       v ++ai e+ ++e+   +n++l++++++++++l++ +++
  gi|518651527|ref|YP_008141047.1| 309 VSKKAIDENDFSEEMM-KNYDLMVKDKFERKHLRNWFAK 346
                                       5678999999*99999.899*************987766 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.4   0.2   2.6e-14     3e-11       1     142 [.       5     156 ..       5     169 .. 0.75
   2 ?   -2.0   0.0       1.6   1.8e+03      63     122 ..     319     380 ..     288     385 .. 0.43

  Alignments for each domain:
  == domain 1  score: 43.4 bits;  conditional E-value: 2.6e-14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG.....Glltsglvatdignkaeeqvvtgiarefl.erlrq.. 69 
                                       Dv+V+G+gpaG  AA  A r G k+lLve+r+ +G     G   s++ ++ +  k     ++ i +e+  +r+    
  gi|518651527|ref|YP_008141047.1|   5 DVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGspvrcGEGISKAWMPEVDIK---PEAHWISDEVKgARIYGps 78 
                                       9*********************************966555555554444444433...3344444444312333332 PP

                      FAD_oxidored  70 rgga.rlkkrskwn....tfepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiD 141
                                       +++   l+++s+ n    ++e + + + +  + a +g +++ ++ + +v+keg+r+ + +++++ ++ ++rAk++i 
  gi|518651527|ref|YP_008141047.1|  79 EKKPiMLTAESAGNevgfVVERDKFDKHIATLAATEGADIWIKSPAMSVIKEGNRVVGAKIRHNGEEVEVRAKMVIA 155
                                       2222333322222245669**************999*************************87768*********96 PP

                      FAD_oxidored 142 A 142
                                       A
  gi|518651527|ref|YP_008141047.1| 156 A 156
                                       6 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                      FAD_oxidored  63 flerlrqrgga..rlk.krskw.ntfepevakavleemlaeagvtvllntrlvevekegkries 122
                                       f e++ ++ +   + k +r++  n f  e + ++ +e l++  v+v+ + +++++ +e+  +++
  gi|518651527|ref|YP_008141047.1| 319 FSEEMMKNYDLmvKDKfERKHLrNWFAKEKLGTLSDETLDK-LVDVVADVKMTSISVEE-ILKG 380
                                       22333221111111111222222356666666666666655.66666666666665553.4555 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 !   36.0   0.0     4e-12   4.4e-09       1     119 [.       4     169 ..       4     198 .. 0.75
   2 ?   -0.9   0.0       0.7   7.8e+02     260     282 ..     269     286 ..     258     303 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4e-12
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................ 57 
                                       +dv+viG+GpAG +aa++++++g+k++lve     +  +  g  + ska+    + + +a+                
  gi|518651527|ref|YP_008141047.1|   4 YDVLVIGAGPAGSSAARYASRYGLKTLLVEkrpdIGSPVRCGEGI-SKAWMPEVDIKPEAHwisdevkgariygpse 79 
                                       69***************************8765433333333333.5555444444445777999999999999999 PP

                                       ...................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEEC..........TCEEEEEESEEEE CS
                                       ...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...................evvkklnqgielllgeevvkidpgkkkvklekkke..........gdeekiaydklvl 105
                                                          e  +k+ ++i +l+++e+ +i  ++  + + k+ +          g+e ++ ++ ++ 
  gi|518651527|ref|YP_008141047.1|  80 kkpimltaesagnevgfvvE-RDKFDKHIATLAATEGADIWIKSPAMSVIKEGNrvvgakirhnGEEVEVRAKMVIA 155
                                       9999999999999999**74.488999999999977777777765555554444567777777899999999***** PP

                                       ---EEE-BCTCTTC CS
                                       xxxxxxxxxxxxxx RF
                       Pyr_redox_2 106 AtGssprdlgipGv 119
                                       A G+++      G+
  gi|518651527|ref|YP_008141047.1| 156 ADGFESEFSRWAGL 169
                                       ***98877766666 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.7
                                       --TTSBESSTTEEE-GGGCTECC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 260 vdeflrtnvpgiyaiGDvaggkg 282
                                       v++  + + pg+ aiGD a   +
  gi|518651527|ref|YP_008141047.1| 269 VKD--KMSLPGLLAIGDAA---R 286
                                       333..4489********99...3 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.1     4e-09   4.5e-06       1      36 [.       5      40 ..       5      87 .. 0.85
   2 !    9.2   0.0   0.00074      0.83     142     219 ..      97     175 ..      60     227 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 4e-09
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiagsga 36
                                      dv++iG+G +G+s+A++++r g  ++l+ek++++g  +
  gi|518651527|ref|YP_008141047.1|  5 DVLVIGAGPAGSSAARYASRYGlkTLLVEKRPDIG--S 40
                                      8******************************9887..3 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00074
                                       EEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEEEEEEE..EEE--GGGHH..HHHTTCTT CS
                               DAO 142 qvdpakltaalaraaealGveilegtevtgleeedgkvwgve.rttpgendaada..vVnaaGawsd..llgllkel 213
                                       +v+  k+ + +a  a++ G++i  ++++ ++ +e+++v+g + r++ ge+++++a  v+ a G  s    +     l
  gi|518651527|ref|YP_008141047.1|  97 VVERDKFDKHIATLAATEGADIWIKSPAMSVIKEGNRVVGAKiRHN-GEEVEVRAkmVIAADGFESEfsRW---AGL 169
                                       5678899999********************8788899999987544.666556777688888888773333...344 PP

                                       TSEEEE CS
                               DAO 214 dlpisp 219
                                       + pi  
  gi|518651527|ref|YP_008141047.1| 170 KSPILK 175
                                       445544 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00032      0.36       1      44 [.       5      47 ..       5      67 .. 0.84
   2 !   24.5   0.0     1e-08   1.1e-05     142     372 ..      89     336 ..      61     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-.SSS-.--SS-EE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves.eeig.tvgvGea 44
                                      +++++G+G+aG+ aA + ++++   l+ +lve+ ++ig +v+ Ge+
  gi|518651527|ref|YP_008141047.1|  5 DVLVIGAGPAGSSAARYASRYG---LKTLLVEKrPDIGsPVRCGEG 47
                                      699******************9...889999974678734667765 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 1e-08
                                       -B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-TTS-EEEEEETT...S-EEE-SEEEE-SGGG-IIII CS
                    Trp_halogenase 142 lsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqldedgrveslrled...greveadlfiDcsGfrgllie 215
                                       +++ + ++ +++ +++k++ + a  +G ++     +  +++e +rv + ++     + ev a ++i + Gf++    
  gi|518651527|ref|YP_008141047.1|  89 SAGNEVGFVVERDKFDKHIATLAATEGADIWIKSPAMSVIKEGNRVVGAKIRHngeEVEVRAKMVIAADGFESEFSR 165
                                       456678899**********************99999999999888876555444235567789************99 PP

                                       II.T---EEE-TTT----EEEEEEEE--H---SSEE....EEE-SSEEEEEEEETTEEEE.EEEE-TTTS.-HHHHH CS
                    Trp_halogenase 216 qa.LktgfedwsdvLltdrAlavqveseelvepytr....ataekaGWtWkiPLqhrlgn.Gyvyssaha.dddeAl 285
                                        a Lk+++ +  d++   +Al   +e+++  e +t+    ++a  aG  W  P      n G+ +   ++ d+ +  
  gi|518651527|ref|YP_008141047.1| 166 WAgLKSPILKKNDII---SALEYRMENVDSNEDFTDfylgSIA-PAGYLWVFPKGPHEANvGIGVTITMMkDRLDVK 238
                                       766************...***********99999988885666.79*******875555559999988884666777 PP

                                       HHHHHHCT--TTTS-.EEEE---EE......ES-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT-- CS
                    Trp_halogenase 286 aellaeldgkleaep.rkirfttGr......rkqawvknvvalGlasgfvePlestsihliqa....alrrLlallp 351
                                       + l ++++ ++++ + r i+  +G       + ++  ++++a+G+a+  ++P+ + +i+  +     a++   + + 
  gi|518651527|ref|YP_008141047.1| 239 NYLDSWIKSHPAYSKgRIIQQISGGvsvnkvKDKMSLPGLLAIGDAARLIDPITGGGIANGMIsgkfAAQVSKKAID 315
                                       7788889999999997888877777799998889999********************98655434556666666666 PP

                                       BTT--HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 352 dksdepaaiaefnrevarele 372
                                       ++ +++  +++++  v+ ++e
  gi|518651527|ref|YP_008141047.1| 316 ENDFSEEMMKNYDLMVKDKFE 336
                                       666777777777666666655 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.1   1.4e-08   1.6e-05       1     145 [.       5     162 ..       5     173 .. 0.74
   2 !    5.5   0.0    0.0067       7.6     257     302 ..     272     322 ..     255     373 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 1.4e-08
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsl...lfpnny...vWsdefedlgaleecvehsWsgtivyld. 70 
                                       Dv+viGaGpAg s A     +++glk +l+e  p++   ++ ++     W+ e  d++  ++ ++   +g+++y + 
  gi|518651527|ref|YP_008141047.1|   5 DVLVIGAGPAGSSAARYA--SRYGLKTLLVEKRPDIgspVRCGEGiskAWMPE-VDIKPEAHWISDEVKGARIYGPs 78 
                                       9**********9987777..************998722244454411245543.34444678899999999999983 PP

                     Lycopene_cycl  71 dgkkillg......raYgrvsskrlkeellerlv.engvklleakvesveeeea..geslvvleggr.kirarlvvd 137
                                       ++k+i+l+           v+++++ ++++   + e++ +  ++ + sv +e +      +  +g++ ++ra++v+ 
  gi|518651527|ref|YP_008141047.1|  79 EKKPIMLTaesagnEVGFVVERDKFDKHIATLAAtEGADIWIKSPAMSVIKEGNrvVGAKIRHNGEEvEVRAKMVIA 155
                                       56778888776664334479***********99955666889*******99887333445556666679******** PP

                     Lycopene_cycl 138 arglaslk 145
                                       a g ++++
  gi|518651527|ref|YP_008141047.1| 156 ADG-FESE 162
                                       ***.6655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0067
                     Lycopene_cycl 257 k.....vlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres.slsar 302
                                       k      laiG aa l+ P TG  +a+ +   + +a+ +++ +  + + s++
  gi|518651527|ref|YP_008141047.1| 272 KmslpgLLAIGDAARLIDPITGGGIANGMISGK-FAAQVSKKAIDEnDFSEE 322
                                       444444789********************9888.777777666544333333 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   2.8e-10   3.1e-07       1      52 [.       8      65 ..       8      72 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.8e-10
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EECE......TTCEECTS---E CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasyev......pgvrvdygahif 52
                                      ++GaG +G++aA++++++g++ ll+ekr+++G  +++ e       p+v ++  ah++
  gi|518651527|ref|YP_008141047.1|  8 VIGAGPAGSSAARYASRYGLKTLLVEKRPDIGSPVRCGEGiskawmPEVDIKPEAHWI 65
                                      8*******************************55555544334455556666666666 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2   3.7e-09   4.1e-06       1     147 [.       5     155 ..       5     172 .. 0.59

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.7e-09
                                       CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-T.........THHHHHHHHHHHT-SHHHHHH CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggi.........akgllvrEidalggliikaad 68 
                                       dv ViG+G AG+ AA  a+r G+k+lL+ ++ d    + C + i             +  +  E++  g  i    +
  gi|518651527|ref|YP_008141047.1|   5 DVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGSPVRCGEGISKAwmpevdikpEAHWISDEVK--GARIYGPSE 79 
                                       79**************************66655555566777666666655553332233333333..245566666 PP

                                       HHEEEEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHT.STTEEEEES-EEEEEECTTEEEEEE.ETTS-EEEEC. CS
                              GIDA  69 kagiqfrilNrskGpavralraqvdrelyskevteklen.epnleiieeeveeliveekkvkgvv.tedgetikak. 142
                                       k+ i +    +    a+++    v+r+++ k++     +   ++ i +  ++ +  e ++v g +  ++ge+++ + 
  gi|518651527|ref|YP_008141047.1|  80 KKPIMLT--AE---SAGNEVGFVVERDKFDKHIATLAATeGADIWIKSPAMSVI-KEGNRVVGAKiRHNGEEVEVRa 150
                                       6666222..23...4444444457777777777655444235566655555555.5566666643033444444333 PP

                                       EEEE- CS
                              GIDA 143 avvia 147
                                       ++via
  gi|518651527|ref|YP_008141047.1| 151 KMVIA 155
                                       44444 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.5e-08   3.9e-05      17      60 ..       3      45 ..       1     100 [. 0.83
   2 ?   -0.7   0.0      0.62     7e+02     156     180 ..     147     171 ..     105     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.5e-08
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTT CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlG 60
                                      + Dv+++GaG++G +aa+y ++  +lk++++e++  +G  +  G
  gi|518651527|ref|YP_008141047.1|  3 NYDVLVIGAGPAGSSAARYASRY-GLKTLLVEKRPDIGSPVRCG 45
                                      57*****************9999.*********99988765554 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.62
                                       EEEEEEEEE--GSSSTTTTHHHHHH CS
                              Thi4 156 virakvvvdatGhdgeivavvvkki 180
                                        +rak+v+ a G ++e+   +  k 
  gi|518651527|ref|YP_008141047.1| 147 EVRAKMVIAADGFESEFSRWAGLKS 171
                                       5799999999999999987766555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   4.5e-08     5e-05       1      40 [.       4      43 ..       4      48 .. 0.92
   2 ?   -2.3   0.0       1.2   1.3e+03     357     384 ..     261     284 ..     258     309 .. 0.70
   3 ?   -1.2   0.0      0.55   6.1e+02     302     344 ..     332     371 ..     302     380 .. 0.63

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.5e-08
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKil 40
                                      +dv+viG+G+AG  aA  a++ g ++ll+ek + +g+ ++
  gi|518651527|ref|YP_008141047.1|  4 YDVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGSPVR 43
                                      59********************************998665 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                                       EEEE-GGGB-TTT-BBTTSTTEEE-GGG CS
                       HI0933_like 357 aGGVdlkevssktmeskkvpgLffaGEv 384
                                        GGV++++v+ k m   ++pgL  +G  
  gi|518651527|ref|YP_008141047.1| 261 SGGVSVNKVKDK-M---SLPGLLAIGDA 284
                                       599999999887.4...58888888865 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.55
                                       -HHHHHHHHHC..TTT-TTBGGG--HHHHHHHHHHHHSEEE-- CS
                       HI0933_like 302 pkrlvevlleealieeedkklaqlskkelkklaealkaltvkv 344
                                       + ++ +  l +   + +++kl +ls+++l+kl++ + +++++ 
  gi|518651527|ref|YP_008141047.1| 332 KDKFERKHLRN---WFAKEKLGTLSDETLDKLVDVVADVKMTS 371
                                       44444444444...34567788889999999988888887765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.3e-05     0.014       2      46 ..       6      52 ..       5      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.3e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..TTSSHHHHHHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll..rllDeeaskil 46
                                      v+v+G+G  g  +A +++++g k+ +ve ++ +     ++e +sk++
  gi|518651527|ref|YP_008141047.1|  6 VLVIGAGPAGSSAARYASRYGLKTLLVEKRPDIGspVRCGEGISKAW 52
                                      89*****************************9997556666666665 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 !   13.0   0.0     4e-05     0.045       1      32 [.       7      38 ..       7      43 .. 0.86
   2 ?    1.6   0.0      0.12   1.3e+02     248     274 ..     138     166 ..     102     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4e-05
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg.ni 32
                                      ++iGaGPaG +aa  + + gl + l +Ek   i
  gi|518651527|ref|YP_008141047.1|  7 LVIGAGPAGSSAARYASRYGL-KTLLVEKRpDI 38
                                      69*******************.57899997455 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                       Pyr_redox_3 248 k.tedgkkvevkddvvla.tGykpdlsfl 274
                                       k  ++g++vev+ ++v+a  G+++++s  
  gi|518651527|ref|YP_008141047.1| 138 KiRHNGEEVEVRAKMVIAaDGFESEFSRW 166
                                       23567899999888777758**9999764 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   8.4e-06    0.0094      30      63 ..       5      38 ..       3      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.4e-06
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrpar 63
                                       vlviG+G aG +A++ a++ g k+ ++++rp+ 
  gi|518651527|ref|YP_008141047.1|  5 DVLVIGAGPAGSSAARYASRYGLKTLLVEKRPDI 38
                                      59**************************999975 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00026      0.29     127     173 ..     273     322 ..     253     344 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00026
                                SE 127 nekkGlillGDalnmRHPltggGmtvalnDivllskllkpl...edlsde 173
                                        +  Gl+ +GDa  +  P+tggG++ ++   +  +++ k+    +d+s+e
  gi|518651527|ref|YP_008141047.1| 273 MSLPGLLAIGDAARLIDPITGGGIANGMISGKFAAQVSKKAideNDFSEE 322
                                       4558*******************998887655555444443111344433 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0     0.002       2.3       2      33 ..       6      37 ..       5      52 .. 0.92
   2 ?    0.4   0.1      0.47   5.3e+02      13      51 ..     106     144 ..     104     161 .. 0.82
   3 ?   -0.2   0.1      0.72     8e+02     156     179 ..     353     376 ..     348     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.002
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdisee 33
                                      v viGaG  G++ a  + + gl++ lv+ +++
  gi|518651527|ref|YP_008141047.1|  6 VLVIGAGPAGSSAARYASRYGLKTLLVEKRPD 37
                                      78*************************99876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.47
                                       HHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N  13 giaavfasagleVvlvdiseealekalekieksleklve 51 
                                        ia+++a +g ++ +   + + ++++++ + +++++  e
  gi|518651527|ref|YP_008141047.1| 106 HIATLAATEGADIWIKSPAMSVIKEGNRVVGAKIRHNGE 144
                                       69*****************99999999988887766554 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.72
                                       -HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 156 seetvatvvelakkigktpvvvkd 179
                                       s+et++++v+++++++ t + v++
  gi|518651527|ref|YP_008141047.1| 353 SDETLDKLVDVVADVKMTSISVEE 376
                                       799***************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); 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 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2495.47
//
Query:       gi|518651528|ref|YP_008141048.1|  [L=549]
Description: hypothetical protein FACI_IFERC00001G0167 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-43  146.9   0.0    8.3e-43  146.0   0.0    1.5  1  TPP_enzyme_N   Thiamine pyrophosphate enzyme, N-terminal TPP 
    1.3e-37  129.0   0.1    1.8e-36  125.3   0.0    2.6  3  TPP_enzyme_C   Thiamine pyrophosphate enzyme, C-terminal TPP 
    9.4e-26   90.2   0.0    1.6e-25   89.5   0.0    1.4  1  TPP_enzyme_M   Thiamine pyrophosphate enzyme, central domain
    0.00018   21.0   0.0     0.0023   17.4   0.0    2.1  2  Peptidase_M55  D-aminopeptidase
     0.0046   16.7   0.0     0.0087   15.8   0.0    1.4  1  POR_N          Pyruvate flavodoxin/ferredoxin oxidoreductase,


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.0   0.0   2.3e-46   8.3e-43       2     171 ..       3     170 ..       2     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 2.3e-46
                                       EHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   2 tvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       tva++++++L + gv++++++pG++++p++da++++++i++v++rhE+g a  A+  ++ tg++++++ tsgpG ++
  gi|518651528|ref|YP_008141048.1|   3 TVADVIIKTLVNFGVKRIYAIPGDSLNPIIDAIRRNKDIKYVQVRHEEGGALSASYESKYTGNLAACMGTSGPGSIH 79 
                                       89*************************************************************************** PP

                                       CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPv 155
                                       +l++l++Ak+ ++P+++l+g+++t+l +++++q e++ ++lf +v  ++ r+ +p+++  ++ +A+r+a  +++g+ 
  gi|518651528|ref|YP_008141048.1|  80 LLNGLYDAKTQHVPVIALTGQVETELLHHDYFQ-EVNLVKLFDDVSVFNARIITPDNAHYLIWKACREA-ITKKGVG 154
                                       *********************************.***********************************.******* PP

                                       EEEEEHHHCC-EEEHH CS
                      TPP_enzyme_N 156 ylelpkdvlleevded 171
                                       +++ p d+l+e ++e+
  gi|518651528|ref|YP_008141048.1| 155 HIDMPVDILMESCKEE 170
                                       ***********99875 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.22   7.9e+02      61      80 ..      27      46 ..      18      67 .. 0.83
   2 ?   -1.6   0.0      0.59   2.1e+03      24      54 ..      64      99 ..      53     100 .. 0.63
   3 !  125.3   0.0   4.9e-40   1.8e-36       1     153 []     370     515 ..     370     515 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.22
                                      TGGGHHHHHHTT-SEEEEEE CS
                      TPP_enzyme_C 61 ilqelatavrrnlpitvvvl 80
                                      +l+ ++ a+rrn +i++v +
  gi|518651528|ref|YP_008141048.1| 27 SLNPIIDAIRRNKDIKYVQV 46
                                      578899**********9966 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
                                      ETTTS-TTTHHHHHHHHHH....HST.TSEEEEEEE CS
                      TPP_enzyme_C 24 sgglgtmGyglpaAiGakl....akp.drevvaivG 54
                                       ++ ++mG + p++i +      ak  + +v+a++G
  gi|518651528|ref|YP_008141048.1| 64 GNLAACMGTSGPGSIHLLNglydAKTqHVPVIALTG 99
                                      467899999999987443343433332557777666 PP

  == domain 3  score: 125.3 bits;  conditional E-value: 4.9e-40
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       d+G++tlw +r+l++ + ++++ s++lgtmG g+p+++G+++a  ++++  ++GDG+f+m+++el+t+ ++nlp+++
  gi|518651528|ref|YP_008141048.1| 370 DTGNVTLWSNRFLNAGNNNKFYFSSWLGTMGSGIPGSVGLAFA-SGKKICGLIGDGSFAMTVMELITIKKYNLPVKL 445
                                       89****************************************8.578****************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       +v++N+++gm++ ++e +g   ++g++   l+++dfaklae++G++g+rv++   e l++ +++ ++ +gpa+++v
  gi|518651528|ref|YP_008141048.1| 446 IVYDNSILGMIKLEEEVMGY-PEYGVD---LYNPDFAKLAESIGITGIRVDTV--EALDAGIDKFFKCDGPAVLDV 515
                                       **************999997.555666...99*****************8888..*******************97 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   0.0   4.4e-29   1.6e-25       1     136 [.     186     312 ..     186     313 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 4.4e-29
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       +++a++l+++  +pvi++Ggg +  + + e+ e+aek+g+P++ +l+gkgv+++++++ +g +gl+g+k+  +a+e+
  gi|518651528|ref|YP_008141048.1| 186 LDEAVNLINNRNKPVIMIGGGSR--NYRGEIDEFAEKIGAPIIYSLNGKGVFNDTDKKVMGGIGLLGTKPSIKAIEK 260
                                       589********************..**************************************************** PP

                                       -SEEEEES-SSSTCCCTTTTTTTTTT-EEEEEESSCCCCTTCC--SEEEECTHHHHHHH CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsepefapeakiihididpaeigknyqvdlaivgdvketlea 136
                                       +Dl+++lG+ f        +++f ++   i+++++  +++k  +++++ ++d+k +l++
  gi|518651528|ref|YP_008141048.1| 261 SDLIIFLGTIFP-------YTQFLKNVDNIQVNTNIDDLNKIMKANYSYLCDIKYFLDN 312
                                       ********9994.......5567777667*************************99975 PP

>> Peptidase_M55  D-aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   6.4e-07    0.0023     143     210 ..      87     153 ..      79     170 .. 0.88
   2 ?    1.1   0.0     0.059   2.1e+02      65      90 ..     180     205 ..     177     212 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 6.4e-07
                     Peptidase_M55 143 agelgVPvvlvsGDdalceeakellpevetvavkeglgrfaakslspeeaeeaireavkeavekakea 210
                                       a+   VPv+ ++G  +++   +++++ev+ v + + ++ f a+ ++p++a+ +i +a +ea++k++ +
  gi|518651528|ref|YP_008141048.1|  87 AKTQHVPVIALTGQVETELLHHDYFQEVNLVKLFDDVSVFNARIITPDNAHYLIWKACREAITKKG-V 153
                                       77899*********************************************************9987.4 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.059
                     Peptidase_M55  65 NllpeeLdervrlisGkpkplsmmeg 90 
                                       N  p  Lde v+li+ ++kp  m+ g
  gi|518651528|ref|YP_008141048.1| 180 NYNPGGLDEAVNLINNRNKPVIMIGG 205
                                       788999*****************988 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.4e-06    0.0087      36      92 ..      39      97 ..      28     100 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-06
                                      EE.EEEE-S.SHHHHHHHHHHHHCTT-EEEE.EEECCHHHHCCCCHHHHHHTT--EEEE CS
                             POR_N 36 gdvevvqme.sEigaisaviGAaaaGaraaT.aTSgqGllLmienlglaageelPvviv 92
                                      +d+++vq+  +E ga sa   + ++G +aa   TSg+G +     l+ a ++++Pv+  
  gi|518651528|ref|YP_008141048.1| 39 KDIKYVQVRhEEGGALSASYESKYTGNLAACmGTSGPGSIHLLNGLYDAKTQHVPVIAL 97
                                      47899998626899**************98637**********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (549 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3544.74
//
Query:       gi|518651529|ref|YP_008141049.1|  [L=457]
Description: hypothetical protein FACI_IFERC00001G0168 [Ferroplasma acidarmanus fer1]
Scores for complete 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-63  211.4   0.4    1.8e-62  210.4   0.4    1.5  1  SRP54        SRP54-type protein, GTPase domain
    3.7e-22   78.8   0.4    3.8e-21   75.6   0.0    2.7  3  SRP_SPB      Signal peptide binding domain
    1.5e-17   63.6   1.0    1.5e-17   63.6   1.0    4.5  6  SRP54_N      SRP54-type protein, helical bundle domain
    2.9e-05   24.1   0.0    0.00011   22.2   0.0    2.3  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00024   20.6   5.8     0.0024   17.4   0.0    3.3  3  SRPRB        Signal recognition particle receptor beta subuni
    0.00087   19.7   0.2    0.00087   19.7   0.2    2.5  3  AAA_17       AAA domain
     0.0044   17.5   4.0       0.75   10.2   0.3    4.1  3  AAA          ATPase family associated with various cellular a
     0.0081   15.8   3.1      0.029   13.9   3.1    1.9  1  cobW         CobW/HypB/UreG, nucleotide-binding domain
     0.0088   15.1   1.4        1.5    7.8   0.0    3.1  3  MeaB         Methylmalonyl Co-A mutase-associated GTPase MeaB
  ------ inclusion threshold ------
      0.015   15.4   1.9      0.048   13.7   0.7    2.5  2  MMR_HSR1     50S ribosome-binding GTPase
      0.016   15.1   0.0      0.036   13.9   0.0    1.6  1  APS_kinase   Adenylylsulphate kinase
      0.039   13.4   0.0      0.069   12.6   0.0    1.4  1  ParA         NUBPL iron-transfer P-loop NTPase
      0.056   12.7   0.0       0.12   11.6   0.0    1.6  1  6PF2K        6-phosphofructo-2-kinase
      0.072   13.4   1.1        9.3    6.6   0.1    2.6  2  Med15_fungi  Mediator complex subunit 15
      0.075   12.9   0.1       0.21   11.5   0.1    1.8  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.098   13.2   0.4        0.5   10.9   0.1    2.5  2  AAA_18       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 !  210.4   0.4   1.7e-65   1.8e-62       2     196 .]      98     290 ..      97     290 .. 0.98

  Alignments for each domain:
  == domain 1  score: 210.4 bits;  conditional E-value: 1.7e-65
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHH CS
                             SRP54   2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavek 78 
                                       + i+lvGl G GKTtt++KLa+l++k+g ++ l+aaD+ R++A+eQL+++   ++  ++++kee+++ +++++++++
  gi|518651529|ref|YP_008141049.1|  98 QTIMLVGLYGNGKTTTAGKLARLFMKKGLSTGLIAADVHRPGAFEQLQQISGDVNCGFYGEKEEKNALKIVRNGIKE 174
                                       789*************************************************************************9 PP

                                       HHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSS CS
                             SRP54  79 akeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdak 155
                                        ++  + + ++DT+Gr   d+el++e+++ik+ ++pd vl+v+dat+gq+a  qak+ ++av+i+gvi+tk+Dg+ k
  gi|518651529|ref|YP_008141049.1| 175 LED--FKIKIIDTSGRDSLDQELIDEVHEIKEKINPDTVLFVIDATLGQQAGPQAKTLHDAVNIDGVIITKMDGTGK 249
                                       988..77889******************************************************************* PP

                                       TTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
                             SRP54 156 gGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                                       +G+als++a +++P++fig+Ge+++d++ f+p++++srllg
  gi|518651529|ref|YP_008141049.1| 250 AGGALSAVADIQSPVYFIGTGEHMDDIQIFNPKKFLSRLLG 290
                                       ***************************************95 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       6.3     7e+03      19      44 ..       9      35 ..       7      40 .. 0.55
   2 ?   -0.4   0.0       1.6   1.8e+03      11      43 ..     285     314 ..     277     320 .. 0.64
   3 !   75.6   0.0   3.4e-24   3.8e-21       1      99 []     322     425 ..     322     425 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 6.3
                                      CCCHHHHCCC.......H...CCCCCHH CS
                           SRP_SPB 19 plskllsmiPgmsae..akaeeeaekkl 44
                                      +l++++ +i g s    +++ +e +k++
  gi|518651529|ref|YP_008141049.1|  9 SLKSIMRKISGSS-FidKDTIKEVTKEI 35
                                      6788899998833.33322224444554 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                                       HHHHHCCCCCCHHHHCCC.....H...CCCCCH CS
                           SRP_SPB  11 lqqikkmGplskllsmiPgmsaeakaeeeaekk 43 
                                       l+++  mG+++ l++ +  ++  +  eeeae +
  gi|518651529|ref|YP_008141049.1| 285 LSRLLGMGDIDALMEVVKETN-IT--EEEAEAS 314
                                       677889999999999987522.12..2333444 PP

  == domain 3  score: 75.6 bits;  conditional E-value: 3.4e-24
                                       SSCTHHHHHHHHHHHCCCCCCHHHHCCC...........H......CCCCCHHHHHHHHHTTSBHHHHHSGCG-..H CS
                           SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae......akae...eeaekklkrieaiidSMTkeErdspekllke 68 
                                       +f+l+d+++  ++  k G l+k+++ +P ++++         e   ++a++kl+ + +i+dSMT  E+++p+ +l++
  gi|518651529|ref|YP_008141049.1| 322 KFDLKDMYDVWEKFAKPGLLKKFFGALP-LGKMpggnklD--EsqlDQADEKLRLYRVILDSMTFYELENPD-VLNA 394
                                       6************************999.36666554441..15578899**********************.889* PP

                                       HHHHHHHHHTTS-HHHHHHHHHHHHHHHHHT CS
                           SRP_SPB  69 sRkrRiArGsGtsvqevnellkqfeqmkkmm 99 
                                       +R++RiA+GsG+  ++v++llk+++ mkk m
  gi|518651529|ref|YP_008141049.1| 395 KRIKRIAAGSGQGEKNVRQLLKEYNAMKKNM 425
                                       ****************************987 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.6   1.0   1.3e-20   1.5e-17       1      75 []       6      83 ..       6      83 .. 0.97
   2 ?   -2.3   0.0       4.8   5.4e+03      30      40 ..     126     136 ..     122     142 .. 0.82
   3 ?    0.5   0.1      0.64   7.2e+02      13      32 ..     186     204 ..     181     211 .. 0.77
   4 ?   -2.3   0.1       4.8   5.3e+03      12      29 ..     300     317 ..     294     319 .. 0.65
   5 ?   -1.8   0.0       3.4   3.8e+03      11      29 ..     352     370 ..     349     373 .. 0.76
   6 ?    0.2   0.5      0.79   8.8e+02      45      75 .]     412     442 ..     407     442 .. 0.62

  Alignments for each domain:
  == domain 1  score: 63.6 bits;  conditional E-value: 1.3e-20
                                      HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                                      L+++l+s+++k+sg+s id+++++e+ ke+++aLl+aDV+vk+v kl++ v+++a++ek    ++ ++ +++++++eL
  gi|518651529|ref|YP_008141049.1|  6 LSESLKSIMRKISGSSFIDKDTIKEVTKEIQRALLKADVNVKLVLKLTNTVQERALNEKPpagMTAQDYIIRVIYEEL 83
                                      799**************************************************99*9666*****************8 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 4.8
                                       HHHHHHHTT-- CS
                           SRP54_N  30 leeaLleaDVg 40 
                                       l + L+ aDV 
  gi|518651529|ref|YP_008141049.1| 126 LSTGLIAADVH 136
                                       7788*****96 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.64
                                       CCSSCGHHHHHHHHHHHHHH CS
                           SRP54_N  13 sgkskideedleealkelee 32 
                                       sg++++d+e+++e + e++e
  gi|518651529|ref|YP_008141049.1| 186 SGRDSLDQELIDE-VHEIKE 204
                                       5678899999999.666655 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4.8
                                       HCCSSCGHHHHHHHHHHH CS
                           SRP54_N  12 lsgkskideedleealke 29 
                                       + + ++i+ee  e+ l++
  gi|518651529|ref|YP_008141049.1| 300 VVKETNITEEEAEASLDK 317
                                       445678888888877765 PP

  == domain 5  score: -1.8 bits;  conditional E-value: 3.4
                                       HHCCSSCGHHHHHHHHHHH CS
                           SRP54_N  11 klsgkskideedleealke 29 
                                       k+ g+ k+de  l++a ++
  gi|518651529|ref|YP_008141049.1| 352 KMPGGNKLDESQLDQADEK 370
                                       5667889*****9996555 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.79
                                       HHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
                           SRP54_N  45 kklienvkkkavgekk...lkpkqqvkkivkdeL 75 
                                       ++l+++    +    +   +k+ + +kk++k +L
  gi|518651529|ref|YP_008141049.1| 412 RQLLKEYNAMKK---NmksIKKNRNFKKMLKTQL 442
                                       444444433233...2455999999999999876 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 !   22.2   0.0     1e-07   0.00011       9      88 ..     107     248 ..     106     433 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1e-07
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.............................. RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep.............................. 54 
                                       G GKTt+a +Lar++ ++gl + l+ aD+ ++ ++  l++ ++d+++                              
  gi|518651529|ref|YP_008141049.1| 107 GNGKTTTAGKLARLFMKKGLSTGLIAADVHRPGAFEqLQQISGDVNCgfygekeeknalkivrngikeledfkikii 183
                                       78******************************98866777777777799999999999******9999999999999 PP

                                       .........................................CCHCCCHHHHHHCHCHHHH.........EEEEEEEE CS
                                       .........................................xxxxxxxxxxxxxxxxxxx.......xxxxxxxxxx RF
                              CbiA  55 .........................................dlkrllellealgkkkall.......lkiagvvlnr 83 
                                                                                                  +       ++i gv++++
  gi|518651529|ref|YP_008141049.1| 184 dtsgrdsldqelidevheikekinpdtvlfvidatlgqqagP-----------------QaktlhdaVNIDGVIITK 243
                                       999999999999999999999996666666553332222220.................233344447777777777 PP

                                       ESS.. CS
                                       xxxxx RF
                              CbiA  84 vdgen 88 
                                        dg  
  gi|518651529|ref|YP_008141049.1| 244 MDGTG 248
                                       77764 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.077        86       4      24 ..      98     118 ..      96     133 .. 0.82
   2 !   17.4   0.0   2.1e-06    0.0024      43      90 ..     172     222 ..     146     234 .. 0.80
   3 ?    1.7   0.4      0.14   1.5e+02     131     180 ..     409     455 ..     359     456 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.077
                                       -EEEEE-STTSSHHHHHHHHH CS
                             SRPRB   4 pavllvGlsdsGKTslftrLt 24 
                                       ++++lvGl   GKT+   +L 
  gi|518651529|ref|YP_008141049.1|  98 QTIMLVGLYGNGKTTTAGKLA 118
                                       689***********9877775 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.1e-06
                                       G...GGTT-SEEEETT-GCCSHHHHHHH...HHHGGEEEEEEEEETTS-HH CS
                             SRPRB  43 vksekgskltliDfPGheklrqkllekl...kaksslkglvfvvDStidpk 90 
                                       +k+ +++k+++iD  G ++l q+l++++   k+k +  +++fv+D+t  ++
  gi|518651529|ref|YP_008141049.1| 172 IKELEDFKIKIIDTSGRDSLDQELIDEVheiKEKINPDTVLFVIDATLGQQ 222
                                       477899******************987511144444679*******98775 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.14
                                       HHHHHHHHHHHHHHHHCHHHHHH------T....T--------GGGSSS- CS
                             SRPRB 131 klikdaLEkElnkiierrskalkeldeeedksavlakkgkdFkfdqleak 180
                                       k ++ +L kE n + ++ +   k+ + ++  +++l  kg +F +d+le k
  gi|518651529|ref|YP_008141049.1| 409 KNVR-QLLKEYNAMKKNMKSIKKNRNFKKMLKTQL--KGGNFSLDDLESK 455
                                       3333.455676666555444444444444455555..9999****99976 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       3.5   3.9e+03      55      69 ..      25      39 ..       7      65 .. 0.53
   2 !   19.7   0.2   7.8e-07   0.00087       1     108 [.     103     214 ..     103     219 .. 0.84
   3 ?   -2.0   0.1         4   4.5e+03      39      55 ..     414     430 ..     383     451 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 3.5
                                      HHHHHHHHHHHHHHH CS
                            AAA_17 55 kelqkeaaekiaeea 69
                                      k++ ke+ ++i+++ 
  gi|518651529|ref|YP_008141049.1| 25 KDTIKEVTKEIQRAL 39
                                      233333333332222 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 7.8e-07
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC......TSHHHHHHHHHHHHHHHHHHHHHS CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr......klpleekkelqkeaaekiaeeakk 71 
                                       +G+ G GK+t + kl++ +  + ls+G l+ + + r g+ ++ ++++         ++e+k  +k++ + i+e ++ 
  gi|518651529|ref|YP_008141049.1| 103 VGLYGNGKTTTAGKLARLFMKKGLSTG-LIAADVHRPGAFEQLQQISgdvncgFYGEKEEKNALKIVRNGIKELEDF 178
                                       799***********************9.5667777888766777777655455346777778899********9999 PP

                                       SEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEE CS
                            AAA_17  72 kgvlvdghprikeqagfldglpkevleelkpdaiill 108
                                       k  ++d+  r   +++++d++  e++e+++pd+++++
  gi|518651529|ref|YP_008141049.1| 179 KIKIIDTSGRDSLDQELIDEVH-EIKEKINPDTVLFV 214
                                       99********999999999988.69********9985 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 4
                                       SHSSHHHHCTSHHHHHH CS
                            AAA_17  39 lakardemrklpleekk 55 
                                       l k+ ++m+k+ +++kk
  gi|518651529|ref|YP_008141049.1| 414 LLKEYNAMKKNMKSIKK 430
                                       33344444444333333 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.64   7.2e+02      18      54 ..       6      43 ..       1      54 [. 0.77
   2 !   10.2   0.3   0.00067      0.75       1     116 [.     100     277 ..     100     289 .. 0.56
   3 ?    3.0   0.0      0.11   1.3e+02      24      57 ..     381     422 ..     367     432 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.64
                                      HHHHHTHEEEEEETTTCS.SSSTTHHHHHHHHHHHHHH CS
                               AAA 18 vakelgvefleisgsell.skyvgesekkirelfkeak 54
                                      + ++l++ + +isgs+++ +++++e  k+i+  + +a 
  gi|518651529|ref|YP_008141049.1|  6 LSESLKSIMRKISGSSFIdKDTIKEVTKEIQRALLKAD 43
                                      566778888999******66699999999988877765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00067
                                       EEEESSTTSSHHHHHHHHHHHH.....THE............................................... CS
                               AAA   1 vllyGppGtGKTllakavakel.....gve............................................... 25 
                                       ++l+G  G GKT++a  +a+ +     + +                                               
  gi|518651529|ref|YP_008141049.1| 100 IMLVGLYGNGKTTTAGKLARLFmkkglS-Tgliaadvhrpgafeqlqqisgdvncgfygekeeknalkivrngikel 175
                                       5899999*********999995333221.033333333444444544444444444444444444333333333333 PP

                                       ......EEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHH CS
                               AAA  26 ......fleisgsellskyvgesekkirelfkeakekakp.silfiDEidalaksr...sgseseeeervvnqLlte 92 
                                             ++ +sg + l       ++ i e+ + +kek +p ++lf+  ida  +++   + ++  ++ ++  +++t+
  gi|518651529|ref|YP_008141049.1| 176 edfkikIIDTSGRDSL------DQELIDEVHE-IKEKINPdTVLFV--IDATLGQQagpQAKTLHDAVNIDGVIITK 243
                                       3333223333333333......3333333333.3333346677776..66666666444444445555555577778 PP

                                       HHHTTTS..........SSTEEEEEEESSGGGST CS
                               AAA  93 ldgvkkk..........eskvivigatnrpdkld 116
                                       +dg  k           +s+v +ig++ ++d+++
  gi|518651529|ref|YP_008141049.1| 244 MDGTGKAggalsavadiQSPVYFIGTGEHMDDIQ 277
                                       8877777999999999988899999999998885 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.11
                                       HEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTS CS
                               AAA  24 vefleisgsellsk........yvgesekkirelfkeakeka 57 
                                       ++f+e++ +++l+           g++ek++r+l+ke  +++
  gi|518651529|ref|YP_008141049.1| 381 MTFYELENPDVLNAkrikriaaGSGQGEKNVRQLLKEYNAMK 422
                                       567888888888556888888899999999999999865554 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 !   13.9   3.1   2.6e-05     0.029       3     156 ..     100     250 ..      98     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.6e-05
                                       EEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SSCHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHH CS
                              cobW   3 tvltGflGsGKTtLlnhll..enraglklavivNefgevsiDaellretgveivelenGciCctlredllkeleale 77 
                                       ++l+G  G GKTt   +l     ++gl++ +i  ++   +  ++l + +     +++ G    + ++++lk +++  
  gi|518651529|ref|YP_008141049.1| 100 IMLVGLYGNGKTTTAGKLArlFMKKGLSTGLIAADVHRPGAFEQLQQIS----GDVNCGFYGEKEEKNALKIVRNGI 172
                                       7899999999999999988777889999999999999555444443333....568888888887777777777766 PP

                                       HHHTT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHH CS
                              cobW  78 ereerldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDll 153
                                       ++ e++ + +i t+G  +  ++++ + +e+k++++ d+v++v+Da  l ++  +++++++d ++  d ++++K+D  
  gi|518651529|ref|YP_008141049.1| 173 KELEDFKIKIIDTSGrDSLDQELIDEVHEIKEKINPDTVLFVIDA-TLGQQAGPQAKTLHDAVNI-DGVIITKMDGT 247
                                       6668***********888888887779******************.5568888899999999876.99999****98 PP

                                       CHC CS
                              cobW 154 dee 156
                                        ++
  gi|518651529|ref|YP_008141049.1| 248 GKA 250
                                       877 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0013       1.5      30      66 ..      98     134 ..      82     143 .. 0.91
   2 ?    1.9   0.2     0.081        91     114     160 ..     228     278 ..     215     333 .. 0.75
   3 ?    2.5   0.0     0.053        59     175     245 ..     357     435 ..     341     448 .. 0.60

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0013
                                       EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB  30 qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                                       q + l G+ G Gk t+  +l+  ++++G   +++a D
  gi|518651529|ref|YP_008141049.1|  98 QTIMLVGLYGNGKTTTAGKLARLFMKKGLSTGLIAAD 134
                                       678899*****************************99 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.081
                                       HHHHHHTT-SEEEEEEE.SSTTHHHHHHTT-SEEEEEEESSTT...TTTTT CS
                              MeaB 114 vllleaaGfDvvlietv.GvGqsevdvaevvdtfvvlllpeaG...Delqg 160
                                        +l +a+  D v+i  + G G++  ++ +v+d+   +   ++G   D++q 
  gi|518651529|ref|YP_008141049.1| 228 KTLHDAVNIDGVIITKMdGTGKAGGALSAVADIQSPVYFIGTGehmDDIQI 278
                                       46889999998877654499****999999999999999999944456665 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.053
                                       E---HHHHHHHHHHHHHHHHHCST.......T.BTTB--EEEEEBCCCTBSHHHHHHHHHHHHHHHHHTTHHHHHHH CS
                              MeaB 175 nkaDkkeaekaarelraaleleee.......k.ekeWrpkvlktsavegeGidelvdaieehrevlkktGllekrrr 243
                                       nk D+++ ++a ++lr    ++++       + +     ++ +++a  g+G +++ + ++e+  + k+   ++k+r+
  gi|518651529|ref|YP_008141049.1| 357 NKLDESQLDQADEKLRLYRVILDSmtfyeleNpDVLNAKRIKRIAAGSGQGEKNVRQLLKEYNAMKKNMKSIKKNRN 433
                                       77775555555544444433333322233222123334467788999********9999999877666655555544 PP

                                       HH CS
                              MeaB 244 er 245
                                        +
  gi|518651529|ref|YP_008141049.1| 434 FK 435
                                       33 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.8   3.1e+03      28      42 ..      27      41 ..      12      69 .. 0.56
   2 ?   13.7   0.7   4.3e-05     0.048       2      99 ..     100     232 ..      99     244 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.8
                                      SSTTSSSSEEEEEEE CS
                          MMR_HSR1 28 dkpgtTrdinegrvk 42
                                       ++ +T++i+++ +k
  gi|518651529|ref|YP_008141049.1| 27 TIKEVTKEIQRALLK 41
                                      344455555554444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 4.3e-05
                                       EEEEESTTSSHHHHHHHHHT.........S.TEEESSSTTSSSSE..EEEEEE.....ETTEE.............. CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltg.........e.kaivsdkpgtTrdi..negrvk.....lkgke.............. 47 
                                       +++vG    GK+t   +l +            a   ++pg+  +   + g v+     +   +              
  gi|518651529|ref|YP_008141049.1| 100 IMLVGLYGNGKTTTAGKLARlfmkkglstGlIAADVHRPGAFEQLqqISGDVNcgfygE---Keeknalkivrngik 173
                                       67777777777777777775555444432122222233333333300333333333221...022334444555555 PP

                                       ......EEEEECGGCSSHHHHHHHHHHHHHHHHC...TSEEEEEEETT..TTCSHHHHHHHHH CS
                          MMR_HSR1  48 ......ielvDtpGliegaseekglgkaflalee...adlillvvdas..eeklkpldeelee 99 
                                             i+++Dt G   ++s +++l +++++++e    d +l+v+da+  + +  p+ ++l++
  gi|518651529|ref|YP_008141049.1| 174 eledfkIKIIDTSG---RDSLDQELIDEVHEIKEkinPDTVLFVIDATlgQ-QAGPQAKTLHD 232
                                       555555********...456666666666665554427********88652.24445555544 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.2e-05     0.036       2      50 ..      97     145 ..      96     155 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT-- CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdLg 50 
                                       + +++l Gl g GK+t a +l++  ++kg s+ l+  d+ R g  ++L 
  gi|518651529|ref|YP_008141049.1|  97 PQTIMLVGLYGNGKTTTAGKLARLFMKKGLSTGLIAADVHRPGAFEQLQ 145
                                       789******************************9999999988777776 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 ?   12.6   0.0   6.2e-05     0.069      14      46 ..     107     139 ..      96     173 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.2e-05
                              ParA  14 GVGKStvavnlAlaLakkglkvgllDaDiyGps 46 
                                       G GK+t+a +lA  + kkgl++gl+ aD++ p 
  gi|518651529|ref|YP_008141049.1| 107 GNGKTTTAGKLARLFMKKGLSTGLIAADVHRPG 139
                                       89***************************9775 PP

>> 6PF2K  6-phosphofructo-2-kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011      0.12       8      49 ..      92     133 ..      88     187 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                                       HT..S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEH CS
                             6PF2K   8 nlknsklvivlvGLpargKtyiskkltrylkwlgvrtkvFnv 49 
                                       n++ ++  i+lvGL   gKt+++ kl r     g++t    +
  gi|518651529|ref|YP_008141049.1|  92 NFDLKPQTIMLVGLYGNGKTTTAGKLARLFMKKGLSTGLIAA 133
                                       66677889********************99988888866555 PP

>> Med15_fungi  Mediator complex subunit 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0083       9.3      31      63 ..      24      56 ..       8      62 .. 0.90
   2 ?    4.9   0.1     0.028        31      47      83 ..     409     445 ..     395     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0083
                       Med15_fungi 31 qKaaikqqlqeiqqmlarvdaliplfykltkne 63
                                      +K++ik+ ++eiq  l + d  + l++klt+ +
  gi|518651529|ref|YP_008141049.1| 24 DKDTIKEVTKEIQRALLKADVNVKLVLKLTNTV 56
                                      8****************************9875 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.028
                       Med15_fungi  47 arvdaliplfykltkneeavkrLlqmrimlkeqlekl 83 
                                       ++v +l+  + +++kn +++k+   ++ mlk+ql+  
  gi|518651529|ref|YP_008141049.1| 409 KNVRQLLKEYNAMKKNMKSIKKNRNFKKMLKTQLKGG 445
                                       68999999999**********************9975 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 ?   11.5   0.1   0.00018      0.21       2      39 ..     100     137 ..      99     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00018
                              MobB   2 lgivgksgsGKTtLleklipelkarglrvgtiKhahhg 39 
                                       + +vg  g GKTt   kl + + ++gl+ g+i  ++h 
  gi|518651529|ref|YP_008141049.1| 100 IMLVGLYGNGKTTTAGKLARLFMKKGLSTGLIAADVHR 137
                                       7899****************************988885 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00045       0.5       1      25 [.     100     161 ..     100     242 .. 0.60
   2 ?   -2.8   0.0       7.8   8.8e+03      17      44 ..     284     313 ..     283     330 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00045
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf......................................g 25 
                                       I+l G  G GKtt a  L+++  +                                       
  gi|518651529|ref|YP_008141049.1| 100 IMLVGLYGNGKTTTAGKLARLF-MkkglstgliaadvhrpgafeqlqqisgdvncgfygekeE 161
                                       89****************9985.3557777445555555554444444444444444444443 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.8
                            AAA_18  17 eLskrlgf..gvnlrdvakenglllevdpe 44 
                                        Ls++lg+   + l++v+ke ++ +e+ ++
  gi|518651529|ref|YP_008141049.1| 284 FLSRLLGMgdIDALMEVVKETNITEEEAEA 313
                                       577777777777788888888877777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1272  (0.0709465); expected 358.6 (0.02)
Passed bias filter:                      790  (0.0440627); expected 358.6 (0.02)
Passed Vit filter:                       122  (0.00680462); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.49
# Mc/sec: 2779.99
//
Query:       gi|518651530|ref|YP_008141050.1|  [L=101]
Description: DNA-directed RNA polymerase subunit M [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   73.5   8.6    8.3e-20   70.4   1.4    3.0  3  TFIIS_C          Transcription factor S-II (TFIIS)
    8.5e-06   25.7   7.1    0.00027   20.9   0.9    2.3  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    2.3e-05   24.2   1.2    2.3e-05   24.2   1.2    2.6  2  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
    0.00011   21.6  11.3      0.016   14.7   1.6    3.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00031   20.7  10.5       0.13   12.3  10.6    2.6  1  DZR              Double zinc ribbon
    0.00039   20.0  15.4       0.97    9.2   0.7    4.0  4  zinc_ribbon_2    zinc-ribbon domain
    0.00044   20.1   8.2      0.049   13.5   0.7    2.4  2  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0016   18.4   1.6     0.0016   18.4   1.6    2.4  2  DUF4428          Domain of unknown function (DUF4428)
      0.005   16.5  12.4     0.0077   15.9   1.8    3.4  3  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
     0.0052   16.7  10.6        1.4    8.9   0.0    4.0  4  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0053   16.3   9.0        1.7    8.3   0.1    4.1  4  zf_UBZ           Ubiquitin-Binding Zinc Finger
       0.01   15.3  14.3      0.035   13.5   3.2    4.0  4  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
       0.01   15.8   8.8        0.3   11.1   3.5    2.9  2  zinc-ribbons_6   zinc-ribbons
      0.014   15.2   2.8      0.097   12.6   0.2    2.3  2  zf-C3HC4_5       Zinc finger, C3HC4 type (RING finger)
      0.016   14.8   4.5       0.37   10.4   0.0    3.0  3  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
      0.016   15.4   8.8       0.35   11.2   0.3    3.3  3  zinc_ribbon_9    zinc-ribbon
      0.017   14.9  13.2        9.5    6.1   0.0    4.3  3  A2L_zn_ribbon    A2L zinc ribbon domain
      0.022   14.5  15.1       0.78    9.5   0.1    4.1  4  Rubredoxin_2     Rubredoxin metal binding domain
      0.028   15.0   0.2      0.028   15.0   0.2    2.5  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.031   14.4   3.1       0.28   11.3   3.1    2.2  1  FYVE             FYVE zinc finger
      0.034   14.2   7.6       0.81    9.7   1.1    2.4  2  HypA             Hydrogenase/urease nickel incorporation, met
       0.11   12.2   2.9       0.23   11.1   0.3    2.1  2  zf-SNAP50_C      snRNA-activating protein of 50kDa MW C termi
       0.12   12.3   0.1       0.12   12.3   0.1    2.8  3  Gin              Inhibitor of sigma-G Gin
       0.16   12.0   6.1       0.53   10.3   0.4    3.0  3  Prok-RING_1      Prokaryotic RING finger family 1
       0.16   12.1  15.6        5.1    7.3   0.6    4.0  3  Zn-ribbon_8      Zinc ribbon domain
       0.17   11.5   5.9        2.1    8.0   0.4    2.4  2  TackOD1          Thaumarchaeal output domain 1
       0.21   11.8   4.9        2.8    8.2   0.3    2.2  2  FYVE_2           FYVE-type zinc finger
       0.25   11.0  10.7        3.1    7.5   0.0    3.4  2  GATA             GATA zinc finger
       0.25   11.2   5.1      0.042   13.7   1.1    1.6  2  FdhE             Protein involved in formate dehydrogenase fo
       0.26   12.2   4.0        0.4   11.6   4.0    1.5  1  Cytochrome_C554  Cytochrome c554 and c-prime
       0.27   11.4   5.3        1.7    8.8   0.4    2.2  2  TerY_C           TerY-C metal binding domain
       0.31   10.8  12.1        1.8    8.3   0.0    3.9  4  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.35   11.0   8.8       0.19   11.8   1.1    2.5  2  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
       0.62   10.6  11.0         53    4.4  11.1    2.6  1  zf-CHY           CHY zinc finger
       0.67   10.1  11.4        8.1    6.7   1.7    3.3  3  zf-piccolo       Piccolo Zn-finger
       0.68   10.3  11.4        1.2    9.5   1.4    3.1  2  C1_2             C1 domain
       0.69   10.2  10.3         80    3.6  10.3    3.3  1  Rpr2             RNAse P Rpr2/Rpp21/SNM1 subunit domain
        0.7   10.3   6.8          2    8.8   0.4    2.4  2  DnaJ_CXXCXGXG    DnaJ central domain
       0.75    9.8  17.4         12    5.9   4.5    4.1  4  Nudix_N_2        Nudix N-terminal
       0.88    9.4   0.1       0.88    9.4   0.1    3.4  4  ZZ               Zinc finger, ZZ type
        1.3    9.4  10.5         10    6.5   0.1    3.5  4  GFA              Glutathione-dependent formaldehyde-activatin
        1.4    8.9   0.1        1.4    8.9   0.1    3.5  3  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
        1.6    8.5  13.3       0.96    9.2   2.0    3.1  2  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
          2    8.4  12.4        3.2    7.7   0.2    4.0  4  zinc_ribbon_4    zinc-ribbon domain
        2.2    8.1   0.0        2.2    8.1   0.0    2.8  2  Baculo_LEF5_C    Baculoviridae late expression factor 5 C-ter
        2.7    8.0  14.9        4.9    7.1   3.3    3.4  3  zf-HIT           HIT zinc finger
        2.9    7.5   9.9        3.2    7.4   1.1    3.2  3  RecR             RecR protein
        2.9    8.7  11.3         18    6.2   2.3    3.1  2  zinc_ribbon_15   zinc-ribbon family
          3    7.3   9.6        2.3    7.7   0.3    2.9  3  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
        4.2    7.5  12.8         46    4.2   0.2    4.1  4  zf-ACC           Acetyl-coA carboxylase zinc finger domain
        6.6    6.7  10.6         31    4.6   0.0    3.7  3  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
        9.3    6.7  11.7         47    4.5   0.2    4.0  5  zf-IS66          zinc-finger binding domain of transposase IS
        9.3    6.4   8.9         16    5.7   1.9    3.1  2  DUF2318          Predicted membrane protein (DUF2318)
        9.9    5.8  12.5        8.6    6.0   0.1    3.5  4  zf_C2H2_13       Zinc finger 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 ?    1.2   0.1         1   3.4e+02       3       7 ..       3       7 ..       1      10 [. 0.68
   2 ?    5.5   0.1     0.045        15      27      36 ..      15      24 ..      11      26 .. 0.75
   3 !   70.4   1.4   2.5e-22   8.3e-20       2      39 .]      62      99 ..      61      99 .. 0.98

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 1
                           TFIIS_C 3 CpkCg 7
                                     C kCg
  gi|518651530|ref|YP_008141050.1| 3 CSKCG 7
                                     66666 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.045
                           TFIIS_C 27 vfykCtkCgh 36
                                        y C++Cg+
  gi|518651530|ref|YP_008141050.1| 15 DKYICNSCGN 24
                                      5699999998 PP

  == domain 3  score: 70.4 bits;  conditional E-value: 2.5e-22
                           TFIIS_C  2 kCpkCgsreayffqlQtRsaDEpmtvfykCtkCghrWr 39
                                       Cp C+++ ay+  +QtRsaDEp+t fy+C +CghrWr
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHHTGAYYLLKQTRSADEPETKFYTCESCGHRWR 99
                                      6************************************8 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.7    0.0068       2.3      21      45 ..       3      24 ..       1      25 [. 0.77
   2 !   20.9   0.9     8e-07   0.00027      19      45 ..      61      96 ..      55      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0068
                     Zn_Tnp_IS1595 21 CPhCgsrkayriktrglfqCkeCrk 45
                                      C +Cg   + + + r ++ C++C+ 
  gi|518651530|ref|YP_008141050.1|  3 CSKCG--ALMTPS-RDKYICNSCGN 24
                                      99999..555555.69*******85 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 8e-07
                     Zn_Tnp_IS1595 19 fvCPhCgsr.kayrikt........rglfqCkeCrk 45
                                       vCP C+++  +y +k+         + + C++C++
  gi|518651530|ref|YP_008141050.1| 61 AVCPVCHHTgAYYLLKQtrsadepeTKFYTCESCGH 96
                                      69*******88888888*****************98 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 !   24.2   1.2   6.9e-08   2.3e-05       3      33 ..       2      28 ..       1      31 [. 0.93
   2 ?    3.1   0.1      0.27        88      18      28 ..      85      95 ..      79      97 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.9e-08
                                      BESTTTSBEEEEECSCCCEEEESSSS-EEES CS
                    RNA_POL_M_15KD  3 FCpkCgNlLlpkedkegknfeCrqCgYeepa 33
                                      FC+kCg l+ p +dk      C +Cg e p+
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPSRDKYI----CNSCGNEIPK 28
                                      *****************....*****99886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.27
                                      CCCEEEESSSS CS
                    RNA_POL_M_15KD 18 egknfeCrqCg 28
                                      e+k + C +Cg
  gi|518651530|ref|YP_008141050.1| 85 ETKFYTCESCG 95
                                      45559999997 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   2.6    0.0016      0.54       1      29 [.       1      26 [.       1      30 [. 0.88
   2 !   14.7   1.6   4.9e-05     0.016       2      27 ..      62      96 ..      61     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                      EEETTTTCEECHEETSTTCEEESSSSBEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveDpergelvCtdCGlVl 29
                                      + C +Cg    +  p+r  ++C +CG+ +
  gi|518651530|ref|YP_008141050.1|  1 MFCSKCGA---LMTPSRDKYICNSCGNEI 26
                                      67999998...8899***********876 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.9e-05
                                      EETTTTCEE.C........HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon  2 kCPnCgstn.l........veDpergelvCtdCGl 27
                                      +CP+C++t  +          +pe+  ++C++CG 
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHHTGaYyllkqtrsADEPETKFYTCESCGH 96
                                      7******8765899**996666999999******6 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3  10.6    0.0004      0.13       1      37 [.       3      69 ..       3     101 .] 0.80

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0004
                               DZR  1 CpqCgeelppdar..fCseCgtklkavaa............................edrCpsCgek 37
                                      C++Cg+ ++p+     C+ Cg++++++ +                              +Cp C++ 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSRDkyICNSCGNEIPKAGTadqkiiskssdkeiimvakevnaepldsDAVCPVCHHT 69
                                      *******765443369********988879***************************7778888764 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.7    0.0029      0.97      15      21 ..       2       8 ..       1      10 [. 0.74
   2 !    9.2   0.8     0.003      0.98       2      11 ..      19      28 ..      18      30 .. 0.89
   3 ?    3.2   0.1      0.24        80      13      21 ..      60      68 ..      57      70 .. 0.65
   4 ?    6.6   0.2      0.02       6.5      12      21 ..      85      96 ..      83      98 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0029
                     zinc_ribbon_2 15 FCpyCGt 21
                                      FC++CG+
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGA 8 
                                      7777775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.003
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      C +CG+e+++
  gi|518651530|ref|YP_008141050.1| 19 CNSCGNEIPK 28
                                      ********85 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.24
                     zinc_ribbon_2 13 akFCpyCGt 21
                                      +  Cp C +
  gi|518651530|ref|YP_008141050.1| 60 DAVCPVCHH 68
                                      566777754 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.02
                     zinc_ribbon_2 12 nakF..CpyCGt 21
                                      + kF  C+ CG+
  gi|518651530|ref|YP_008141050.1| 85 ETKFytCESCGH 96
                                      567777999998 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 !   13.5   0.7   0.00015     0.049      31      56 ..       3      26 ..       2      39 .. 0.94
   2 !   10.6   1.7    0.0012       0.4      24      56 ..      56      98 ..      33     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00015
                    OrfB_Zn_ribbon 31 CseCgsknkealsgrtfkCpnCgfea 56
                                      Cs+Cg+ +++  s++++ C++Cg e+
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTP--SRDKYICNSCGNEI 26
                                      **********..***********875 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0012
                    OrfB_Zn_ribbon 24 payTSktCseCgsknke..........alsgrtfkCpnCgfea 56
                                      p  +   C++C +++ +          +++++ ++C++Cg+++
  gi|518651530|ref|YP_008141050.1| 56 PLDSDAVCPVCHHTGAYyllkqtrsadEPETKFYTCESCGHRW 98
                                      5556678*******9999999999999999999*******986 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   1.6   4.7e-06    0.0016       9      44 ..       6      41 ..       3      46 .. 0.78
   2 ?   -1.0   0.1       5.4   1.8e+03       2       5 ..      63      66 ..      58      69 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.7e-06
                           DUF4428  9 igl.lkrlkleDgyvCkdClkKl.seflsdvkikkilt 44
                                      +g  ++     D y+C++C +++ + +++d+ki +   
  gi|518651530|ref|YP_008141050.1|  6 CGAlMT--PSRDKYICNSCGNEIpKAGTADQKIISKSS 41
                                      554144..889*************999****9977655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 5.4
                           DUF4428  2 CaiC 5 
                                      C++C
  gi|518651530|ref|YP_008141050.1| 63 CPVC 66
                                      6676 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 !   15.9   1.8   2.3e-05    0.0077       5      30 ..       2      25 ..       1      26 [. 0.96
   2 ?    2.4   0.2      0.39   1.3e+02      23      29 ..      62      68 ..      59      72 .. 0.81
   3 ?    4.4   0.3     0.087        29      24      30 ..      91      97 ..      90      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-05
                     zf-NADH-PPase  5 FCgrCGaptepaeggwarvCpaCgle 30
                                      FC++CGa + p+++  +  C +Cg+e
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPSRD--KYICNSCGNE 25
                                      **************..99******98 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.39
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp C +
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHH 68
                                      8999966 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.087
                     zf-NADH-PPase 24 CpaCgle 30
                                      C++Cg++
  gi|518651530|ref|YP_008141050.1| 91 CESCGHR 97
                                      ******8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2       1.2   3.9e+02      20      26 ..       1       7 [.       1       8 [. 0.77
   2 !    8.9   0.0    0.0043       1.4      18      30 .]      15      27 ..      12      27 .. 0.85
   3 ?    3.6   1.2       0.2        66      21      27 ..      62      68 ..      61      69 .. 0.94
   4 ?    7.3   0.0     0.013       4.5      17      29 ..      86      98 ..      71      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 1.2
                    PhnA_Zn_Ribbon 20 lvCpeCa 26
                                      + C++C+
  gi|518651530|ref|YP_008141050.1|  1 MFCSKCG 7 
                                      6799997 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0043
                    PhnA_Zn_Ribbon 18 allvCpeCahEwe 30
                                      + ++C  C++E++
  gi|518651530|ref|YP_008141050.1| 15 DKYICNSCGNEIP 27
                                      669********95 PP

  == domain 3  score: 3.6 bits;  conditional E-value: 0.2
                    PhnA_Zn_Ribbon 21 vCpeCah 27
                                      vCp C+h
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHH 68
                                      8*****9 PP

  == domain 4  score: 7.3 bits;  conditional E-value: 0.013
                    PhnA_Zn_Ribbon 17 gallvCpeCahEw 29
                                      +  + C+ C+h w
  gi|518651530|ref|YP_008141050.1| 86 TKFYTCESCGHRW 98
                                      56688******99 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   0.1     0.041        14       4      13 ..       2      11 ..       1      14 [. 0.82
   2 !    8.3   0.1    0.0052       1.7       1      14 [.      15      28 ..      15      32 .. 0.90
   3 ?    0.4   0.1       1.5   5.1e+02       4      10 ..      62      68 ..      59      69 .. 0.82
   4 ?    5.3   0.3     0.044        15       3      11 ..      89      97 ..      87      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.041
                            zf_UBZ  4 lCerCgkeip 13
                                      +C++Cg+ + 
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMT 11
                                      7*****9875 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0052
                            zf_UBZ  1 dtylCerCgkeipe 14
                                      d y+C  Cg eip 
  gi|518651530|ref|YP_008141050.1| 15 DKYICNSCGNEIPK 28
                                      68**********97 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 1.5
                            zf_UBZ  4 lCerCgk 10
                                      +C+ C++
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHH 68
                                      8****97 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.044
                            zf_UBZ  3 ylCerCgke 11
                                      y+Ce Cg++
  gi|518651530|ref|YP_008141050.1| 89 YTCESCGHR 97
                                      9******85 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   3.2   0.00011     0.035       4      26 .]       2      26 ..       1      26 [. 0.87
   2 !    7.9   0.6    0.0061         2       3      14 ..      17      29 ..      15      31 .. 0.80
   3 ?    3.0   0.2      0.21        71      14      22 ..      58      66 ..      53      68 .. 0.72
   4 ?    3.8   0.2      0.12        39       4      24 ..      90      96 ..      87      98 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 0.00011
                       zf-ribbon_3  4 rCPnCGa.p.lssddnvCpyCGtkl 26
                                      +C++CGa   +s d  +C +CG ++
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGAlMtPSRDKYICNSCGNEI 26
                                      6******778888888******875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0061
                       zf-ribbon_3  3 vrCPnCGa.plss 14
                                      + C++CG+ ++++
  gi|518651530|ref|YP_008141050.1| 17 YICNSCGNeIPKA 29
                                      78*****988776 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.21
                       zf-ribbon_3 14 sddnvCpyC 22
                                      ++d vCp C
  gi|518651530|ref|YP_008141050.1| 58 DSDAVCPVC 66
                                      567778877 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.12
                       zf-ribbon_3  4 rCPnCGaplssddnvCpyCGt 24
                                      +              C +CG+
  gi|518651530|ref|YP_008141050.1| 90 T--------------CESCGH 96
                                      4..............555554 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.5   0.00091       0.3       3      28 ..       3      28 ..       1      72 [. 0.88
   2 ?    4.6   2.4     0.098        32       2      25 ..      62      97 ..      61     101 .] 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00091
                                      -SSS-S--EE-SSEEE-TTT--EEEE CS
                    zinc-ribbons_6  3 CpeCqqelekrgeqyhCeaCqedlkk 28
                                      C +C + ++ + ++y C++C +++ k
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSRDKYICNSCGNEIPK 28
                                      *********9999*******997755 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.098
                                      --SSS-S--EE-S............SEEE-TTT--E CS
                    zinc-ribbons_6  2 kCpeCqqelekrg............eqyhCeaCqed 25
                                       Cp C++                  + y+Ce+C ++
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHHTGAYYLlkqtrsadepetKFYTCESCGHR 97
                                      588888876544344557788888788999999875 PP

>> zf-C3HC4_5  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2      0.27        90      27      42 ..      16      31 ..       2      36 .. 0.79
   2 ?   12.6   0.2   0.00029     0.097       1      36 [.      60      97 ..      60     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.27
                        zf-C3HC4_5 27 hkmCesCvdRlFsdGP 42
                                        +C+sC + + + G 
  gi|518651530|ref|YP_008141050.1| 16 KYICNSCGNEIPKAGT 31
                                      568****999988885 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00029
                        zf-C3HC4_5  1 deiCPvCkss..rYlnpdleflinpeCYhkmCesCvdR 36
                                      d +CPvC+ +   Yl ++ +    pe     CesC  R
  gi|518651530|ref|YP_008141050.1| 60 DAVCPVCHHTgaYYLLKQTRSADEPETKFYTCESCGHR 97
                                      779****8653379*********************887 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.2         8   2.6e+03       9      13 ..       3       7 ..       3      10 .. 0.78
   2 ?   10.4   0.0    0.0011      0.37       4      16 ..      14      26 ..      11      31 .. 0.87
   3 ?    5.2   0.1     0.047        16       4      13 ..      86      95 ..      84      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 8
                                      -TTT- CS
                   Desulfoferrod_N  9 CevCG 13
                                      C  CG
  gi|518651530|ref|YP_008141050.1|  3 CSKCG 7 
                                      88898 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0011
                                      T-EEE-TTT--EE CS
                   Desulfoferrod_N  4 levYkCevCGniV 16
                                       ++Y C+ CGn++
  gi|518651530|ref|YP_008141050.1| 14 RDKYICNSCGNEI 26
                                      589********85 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.047
                                      T-EEE-TTT- CS
                   Desulfoferrod_N  4 levYkCevCG 13
                                      +  Y Ce CG
  gi|518651530|ref|YP_008141050.1| 86 TKFYTCESCG 95
                                      568******* PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.7     0.028       9.4       7      29 ..       5      24 ..       1      26 [. 0.59
   2 ?   11.2   0.3    0.0011      0.35      10      28 ..      50      67 ..      49      70 .. 0.80
   3 ?    1.7   0.1      0.93   3.1e+02      17      29 ..      84      96 ..      77      98 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.028
                     zinc_ribbon_9  7 qCdrfVsvspdedsdvlCPhCgg 29
                                       C    +  p+ d  + C++Cg+
  gi|518651530|ref|YP_008141050.1|  5 KCGALMT--PSRDKYI-CNSCGN 24
                                      5554444..3445556.****98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0011
                     zinc_ribbon_9 10 rfVsvspdedsdvlCPhCg 28
                                      ++V+++p ++++v CP C+
  gi|518651530|ref|YP_008141050.1| 50 KEVNAEPLDSDAV-CPVCH 67
                                      6899999877777.****8 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.93
                     zinc_ribbon_9 17 dedsdv..lCPhCgg 29
                                      +e+  +  +C +Cg 
  gi|518651530|ref|YP_008141050.1| 84 PET--KfyTCESCGH 96
                                      222..2448****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 ?    4.9   5.2     0.066        22       6      32 ..       3      27 ..       2      28 .. 0.72
   2 ?    6.1   0.0     0.029       9.5       2      16 ..      59      73 ..      58      81 .. 0.76
   3 ?    2.7   0.5      0.34   1.1e+02       4      11 ..      89      96 ..      87      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.066
                     A2L_zn_ribbon  6 CsvCggngilnseqgylvCieCgasfp 32
                                      Cs+Cg  +     ++ ++C+ Cg++ p
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMT--PSRDKYICNSCGNEIP 27
                                      666665333..47899*******9866 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.029
                     A2L_zn_ribbon  2 nlkvCsvCggngiln 16
                                      ++ vC vC++ g ++
  gi|518651530|ref|YP_008141050.1| 59 SDAVCPVCHHTGAYY 73
                                      5779*****988776 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.34
                     A2L_zn_ribbon  4 kvCsvCgg 11
                                      ++C+ Cg+
  gi|518651530|ref|YP_008141050.1| 89 YTCESCGH 96
                                      79999998 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.16        52       3       8 ..       3       8 ..       2      10 .. 0.85
   2 ?    9.5   0.1    0.0023      0.78       1      11 [.      17      27 ..      17      29 .. 0.86
   3 ?    3.5   0.3      0.18        59      17      22 ..      63      68 ..      62      71 .. 0.88
   4 ?    6.0   1.5     0.029       9.5       1       9 [.      89      97 ..      89     101 .] 0.86

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.16
                      Rubredoxin_2 3 CsqCGf 8
                                     Cs+CG+
  gi|518651530|ref|YP_008141050.1| 3 CSKCGA 8
                                     9***97 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                      Rubredoxin_2  1 YvCsqCGfesa 11
                                      Y+C++CG+e +
  gi|518651530|ref|YP_008141050.1| 17 YICNSCGNEIP 27
                                      9******9866 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.18
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp C++
  gi|518651530|ref|YP_008141050.1| 63 CPVCHH 68
                                      ****97 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.029
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y C++CG++
  gi|518651530|ref|YP_008141050.1| 89 YTCESCGHR 97
                                      99*****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 ?   15.0   0.2   8.3e-05     0.028       6      51 ..       1      44 [.       1      49 [. 0.75
   2 ?    0.1   3.1       3.6   1.2e+03      25      31 ..      87      93 ..      61     100 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.3e-05
                   Zn_ribbon_recom  6 lrCgeCGspmtrrkrkgkrhyYrCstyrrkgkkCsnhsireeklee 51
                                      ++C +CG+ mt ++   k+++  C++ + k  + +++ i++   +e
  gi|518651530|ref|YP_008141050.1|  1 MFCSKCGALMTPSRD--KYICNSCGNEIPKAGTADQKIISKSSDKE 44
                                      69***********87..78999999888665467777666665555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 3.6
                   Zn_ribbon_recom 25 hyYrCst 31
                                        Y C +
  gi|518651530|ref|YP_008141050.1| 87 KFYTCES 93
                                      5555544 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   3.1   0.00085      0.28      12      64 ..       3      68 ..       1     100 [. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00085
                                      -TTT--B--SSS--EE-TTT--EE-..........STTS-EEE.EEGGGTEEEEE...EE-HHHHH CS
                              FYVE 12 CeiCakkFsllrrrhhCrlCGkvvC..........ekCssklvallekeaeeksv...rvCkeCla 64
                                      C++C +  + +r ++ C  CG+ +           +k s+k + ++ ke++ +++    vC  C++
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSRDKYICNSCGNEIPkagtadqkiiSKSSDKEIIMVAKEVNAEPLdsdAVCPVCHH 68
                                      9**********************9944444444443333333333333333333355566666665 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 ?    9.7   1.1    0.0024      0.81      72      95 ..       2      25 ..       1      41 [. 0.81
   2 ?    8.4   0.8    0.0063       2.1      58      94 ..      48      96 ..      34     101 .] 0.74

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0024
                                      EETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 72 rCreCgkefeleekalrCpkCgsa 95
                                       C++Cg+ ++ +++++ C++Cg++
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPSRDKYICNSCGNE 25
                                      7******9998877899*****96 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0063
                                      TT-EEEEEEE--EEEETTTS-EEECHH.HHH............S-TTTSS CS
                              HypA 58 egaeLeieevpvkvrCreCgkefelee.kal............rCpkCgs 94
                                        +e++ e  +  + C +C++++     k              +C++Cg+
  gi|518651530|ref|YP_008141050.1| 48 VAKEVNAEPLDSDAVCPVCHHTGAYYLlK-QtrsadepetkfyTCESCGH 96
                                      456778888889999****9998844322.13456889999999999997 PP

>> zf-SNAP50_C  snRNA-activating protein of 50kDa MW C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.49   1.6e+02     167     181 ..      11      25 ..       2      49 .. 0.69
   2 ?   11.1   0.3   0.00069      0.23     145     178 ..      59      94 ..      50      99 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.49
                       zf-SNAP50_C 167 lpedpsyfCdkCfrs 181
                                       +p+   y+C++C ++
  gi|518651530|ref|YP_008141050.1|  11 TPSRDKYICNSCGNE 25 
                                       555666677776444 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00069
                       zf-SNAP50_C 145 rrkkCkvCekfsakwvvln..dkllpedpsyfCdkC 178
                                           C vC++  a +++ +  +   pe+++y C++C
  gi|518651530|ref|YP_008141050.1|  59 SDAVCPVCHHTGAYYLLKQtrSADEPETKFYTCESC 94 
                                       5678************999334455889******** PP

>> Gin  Inhibitor of sigma-G Gin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       9.1     3e+03      20      25 ..       3       8 ..       1      12 [. 0.71
   2 ?   12.3   0.1   0.00037      0.12      16      36 ..      15      35 ..      14      35 .. 0.89
   3 ?   -1.3   0.2       6.5   2.2e+03      19      23 ..      90      94 ..      87      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 9.1
                                      EHHHHH CS
                               Gin 20 CeeCek 25
                                      C++C +
  gi|518651530|ref|YP_008141050.1|  3 CSKCGA 8 
                                      888865 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00037
                                      S--EEHHHHHHHHHHS---S- CS
                               Gin 16 gkfICeeCekkivntevddpk 36
                                      +k+IC++C ++i +  + d+k
  gi|518651530|ref|YP_008141050.1| 15 DKYICNSCGNEIPKAGTADQK 35
                                      69***********99999875 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 6.5
                                      EEHHH CS
                               Gin 19 ICeeC 23
                                       Ce+C
  gi|518651530|ref|YP_008141050.1| 90 TCESC 94
                                      59999 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 ?   10.3   0.4    0.0016      0.53       7      27 ..       3      23 ..       1      29 [. 0.93
   2 ?    3.2   0.1      0.26        86      22      26 ..      62      66 ..      50      73 .. 0.71
   3 ?    0.3   0.1         2   6.7e+02       6      12 ..      90      96 ..      85     100 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0016
                       Prok-RING_1  7 CpvCgkelkeedDiVvCpeCg 27
                                      C+ Cg  +++  D  +C  Cg
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSRDKYICNSCG 23
                                      ********************9 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.26
                       Prok-RING_1 22 vCpeC 26
                                      vCp+C
  gi|518651530|ref|YP_008141050.1| 62 VCPVC 66
                                      46665 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 2
                       Prok-RING_1  6 kCpvCgk 12
                                       C+ Cg+
  gi|518651530|ref|YP_008141050.1| 90 TCESCGH 96
                                      4666654 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   2.2     0.038        13       8      36 ..       3      26 ..       1      29 [. 0.60
   2 ?    5.7   3.7     0.048        16       6      34 ..      17      68 ..      16      71 .. 0.63
   3 ?    7.3   0.6     0.015       5.1       6      14 ..      89      97 ..      88     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.038
                       Zn-ribbon_8  8 CeeCghefevlqsisdaplta.CPeCgsev 36
                                      C +Cg   ++ +      ++  C +Cg e 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSR------DKYiCNSCGNEI 26
                                      777774444433......445588888655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.048
                       Zn-ribbon_8  6 YrCeeCghefe........vlqsisdap...............ltaCPeCgs 34
                                      Y C++Cg+e          ++ ++sd++               + +CP C++
  gi|518651530|ref|YP_008141050.1| 17 YICNSCGNEIPkagtadqkIISKSSDKEiimvakevnaepldsDAVCPVCHH 68
                                      8888898887777776665444444555556666666666665566888875 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.015
                       Zn-ribbon_8  6 YrCeeCghe 14
                                      Y Ce+Cgh+
  gi|518651530|ref|YP_008141050.1| 89 YTCESCGHR 97
                                      99*****97 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0062       2.1     149     178 ..       3      32 ..       1      40 [. 0.81
   2 ?    6.5   0.9     0.018       6.1      66     111 ..      53      96 ..      32     101 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0062
                           TackOD1 149 CnsCkslfsepevkarClsCekesesddlk 178
                                       C +C+ l++ ++ k+ C sC++e  ++ + 
  gi|518651530|ref|YP_008141050.1|   3 CSKCGALMTPSRDKYICNSCGNEIPKAGTA 32 
                                       999999999999999999999998776555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.018
                           TackOD1  66 eeelvdrirlCpsCksghlnvrevCpkCkSidieeqelihhftCgn 111
                                       ++e +d+  +Cp C++    +    ++ +S+d  e+++  + +Cg+
  gi|518651530|ref|YP_008141050.1|  53 NAEPLDSDAVCPVCHHTGAYY--LLKQTRSADEPETKFYTCESCGH 96 
                                       566777778888887665444..45677888888888888888887 PP

>> FYVE_2  FYVE-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.6     0.041        14      81     102 ..       2      24 ..       1      33 [. 0.83
   2 ?    8.2   0.3    0.0083       2.8      54      88 ..      60      97 ..      33     101 .] 0.66

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.041
                            FYVE_2  81 vCkkCsve.nkkekvwlCkiCse 102
                                        C kC++  + ++  ++C+ C +
  gi|518651530|ref|YP_008141050.1|   2 FCSKCGALmTPSRDKYICNSCGN 24 
                                       5999998757889999**99965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0083
                            FYVE_2 54 ethCilClee..fkllvnsk.rqCldCklnvCkkCsve 88
                                      +  C  C+++  + ll++++ +   + k+++C++C++ 
  gi|518651530|ref|YP_008141050.1| 60 DAVCPVCHHTgaYYLLKQTRsADEPETKFYTCESCGHR 97
                                      45677777642244444333155567899999999986 PP

>> GATA  GATA zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.3      0.01       3.3       1      27 [.       3      23 ..       3      31 .. 0.71
   2 ?    7.5   0.0    0.0093       3.1      23      33 ..      91     101 .]      79     101 .] 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                              GATA  1 CsnCgttkTplWRrgpdgnksLCnaCG 27
                                      Cs+Cg+  Tp      +  k  Cn+CG
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTP------SRDKYICNSCG 23
                                      7777777766......33444999999 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0093
                              GATA  23 CnaCGlyykkk 33 
                                       C++CG +++ +
  gi|518651530|ref|YP_008141050.1|  91 CESCGHRWREY 101
                                       ********975 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 ?   -1.2   0.5       4.6   1.5e+03     197     216 ..       3      24 ..       1      28 [. 0.69
   2 ?   13.7   1.1   0.00013     0.042     157     205 ..      49      99 ..      22     101 .] 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.6
                                       ETTT--EEE--TTS..-TTT-- CS
                              FdhE 197 CslCeteWhvvRvk..CsnCee 216
                                       Cs C +    +R k  C +C++
  gi|518651530|ref|YP_008141050.1|   3 CSKCGALMTPSRDKyiCNSCGN 24 
                                       8888887777764333888876 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 0.00013
                                       -TTSSS-.-TT-SS-TTT---EEEEEEE----..---EEEEEETTT--EEE CS
                              FdhE 157 dakalaelaeekglCPvCgsaPvasvvrigge..aeglRylhCslCeteWh 205
                                        ++  ae  ++ ++CPvC  +    ++++  +  +  +++ +C  C ++W+
  gi|518651530|ref|YP_008141050.1|  49 AKEVNAEPLDSDAVCPVCHHTGAYYLLKQTRSadEPETKFYTCESCGHRWR 99 
                                       445556777899*******9999999987654115689************7 PP

>> Cytochrome_C554  Cytochrome c554 and c-prime
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   4.0    0.0012       0.4      27      82 ..      39      94 ..       3      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0012
                                      TTSSHHHHHHTT--TTS--TT-TTTGGGSBSTTTSTT---SSS--GGGBSS-HHHH CS
                   Cytochrome_C554 27 kekkaeakkkakldpakdaeeapeClkCHatgagkdkgfvlkektkllagVqCesC 82
                                      k++ +e+ + ak   a+  ++++ C  CH tga    + +++++++  +  +CesC
  gi|518651530|ref|YP_008141050.1| 39 KSSDKEIIMVAKEVNAEPLDSDAVCPVCHHTGAYYLLKQTRSADEPETKFYTCESC 94
                                      2233455555655566677899**********8766666777778888899***** PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.6     0.067        22      89     114 ..       4      28 ..       1      41 [. 0.77
   2 ?    8.8   0.4     0.005       1.7      62     110 ..      48      96 ..      33      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.067
                            TerY_C  89 CeCgkllCidgeeeatCpwCgkevkf 114
                                        +Cg l+    +++ +C  Cg+e+  
  gi|518651530|ref|YP_008141050.1|   4 SKCGALMT-PSRDKYICNSCGNEIPK 28 
                                       37999998.778899******99754 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.005
                            TerY_C  62 snlkvntseLeGapgCPhCgnalafavCeCgkllCidgeeeatCpwCgk 110
                                       + ++vn++ L   + CP C  + a  + +  +     +++  tC  Cg+
  gi|518651530|ref|YP_008141050.1|  48 VAKEVNAEPLDSDAVCPVCHHTGAYYLLKQTRSADEPETKFYTCESCGH 96 
                                       5688999999999999999998888877766666655666667777765 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.64   2.1e+02      23      28 ..       2       7 ..       1      15 [. 0.67
   2 ?    8.3   0.0    0.0055       1.8      21      31 ..      16      26 ..      16      27 .. 0.87
   3 ?    0.9   0.9       1.2   3.9e+02       6      10 ..      62      66 ..      61      68 .. 0.88
   4 ?    4.6   1.3      0.08        27      21      30 ..      88      97 ..      88      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.64
                           zf-RRN7 23 yCrrCh 28
                                      +C  C+
  gi|518651530|ref|YP_008141050.1|  2 FCSKCG 7 
                                      455555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0055
                           zf-RRN7 21 fyyCrrChtqe 31
                                      +y+C++C++ +
  gi|518651530|ref|YP_008141050.1| 16 KYICNSCGNEI 26
                                      6*******975 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 1.2
                           zf-RRN7  6 pCgvC 10
                                      +C+vC
  gi|518651530|ref|YP_008141050.1| 62 VCPVC 66
                                      79999 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.08
                           zf-RRN7 21 fyyCrrChtq 30
                                      fy C +C++ 
  gi|518651530|ref|YP_008141050.1| 88 FYTCESCGHR 97
                                      8*******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 ?    2.9   1.4      0.36   1.2e+02       2      23 ..       3      23 ..       2      29 .. 0.73
   2 ?   11.8   1.1   0.00058      0.19       2      23 ..      63      95 ..      62      98 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.36
                          zf-Mss51  2 CPvpkhkqtapkhvdfeCpdCG 23
                                      C  + + + +p++ ++ C  CG
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALM-TPSRDKYICNSCG 23
                                      55664333.6888999999999 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00058
                          zf-Mss51  2 CPvpkhkqt...........apkhvdfeCpdCG 23
                                      CPv++h+ +           +p+   ++C  CG
  gi|518651530|ref|YP_008141050.1| 63 CPVCHHTGAyyllkqtrsadEPETKFYTCESCG 95
                                      ****98888***********************9 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  11.1      0.16        53      16      74 ..      13      96 ..       1      97 [. 0.63

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.16
                            zf-CHY 16 CkklyaCreCH.....eeledhelerlevkevlcllCeteq....ekavlCkkCkk................efaeyfC 69
                                       ++ y C++C      + ++d+++  ++ ++ ++++ ++++    ++  +C  C++                e++ y+C
  gi|518651530|ref|YP_008141050.1| 13 SRDKYICNSCGneipkAGTADQKIISKSSDKEIIMVAKEVNaeplDSDAVCPVCHHtgayyllkqtrsadepETKFYTC 91
                                      567899****9666652255666655555555566666555222345567****9966677666666666665666689 PP

                            zf-CHY 70 piCkl 74
                                      + C +
  gi|518651530|ref|YP_008141050.1| 92 ESCGH 96
                                      99975 PP

>> zf-piccolo  Piccolo Zn-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.22        74      30      42 ..       2      14 ..       1      17 [. 0.83
   2 ?    6.1   0.3     0.037        12      28      42 ..      16      29 ..      13      36 .. 0.79
   3 ?    6.7   1.7     0.024       8.1       2      27 ..      62      95 ..      61      98 .. 0.56

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.22
                        zf-piccolo 30 vCnlCGFnptphl 42
                                       C++CG  +tp+ 
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPSR 14
                                      5*****9999986 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.037
                        zf-piccolo 28 kqvCnlCGFnptphl 42
                                      k +Cn CG n  p++
  gi|518651530|ref|YP_008141050.1| 16 KYICNSCG-NEIPKA 29
                                      679*****.777775 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.024
                        zf-piccolo  2 lCplCk.te....l.nvgskep..pnyntCteCk 27
                                      +Cp+C+ t     l ++ s+++  + + tC +C 
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHhTGayylLkQTRSADEpeTKFYTCESCG 95
                                      7*****7652222112233444345577888885 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.4    0.0037       1.2      20      38 ..       2      22 ..       1      27 [. 0.86
   2 ?    3.3   2.9      0.31     1e+02      15      38 ..      85      94 ..      45     100 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0037
                              C1_2 20 nCsaCgrkidgff..YsCseC 38
                                       Cs Cg  +++++  Y+C+ C
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPSRdkYICNSC 22
                                      69******8888889***999 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.31
                              C1_2 15 ssesfnCsaCgrkidgffYsCseC 38
                                      +               +fY+C+ C
  gi|518651530|ref|YP_008141050.1| 85 E--------------TKFYTCESC 94
                                      2..............223666666 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 ?    3.6  10.3      0.24        80      39      90 .]      10      95 ..       1      95 [. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.24
                                      -SSTCCCTB-TTT--B--CTTTEEEEEE-SSS-E............................................. CS
                              Rpr2 39 lppsvkrtvCkkCgsvlipgvtcsvrvenkskkkkkkkkka...................................... 79
                                      + ps  + +C++Cg+ + +  t++ ++ +ks+ k+                                            
  gi|518651530|ref|YP_008141050.1| 10 MTPSRDKYICNSCGNEIPKAGTADQKIISKSSDKE-----Iimvakevnaepldsdavcpvchhtgayyllkqtrsade 83
                                      67888888999999988888888888866554433.....123345677777777777777777777777777777777 PP

                                      ...EEEEETTTT CS
                              Rpr2 80 .dvlvvtClaCg 90
                                        +  +tC +Cg
  gi|518651530|ref|YP_008141050.1| 84 pETKFYTCESCG 95
                                      744459999997 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.5     0.075        25       1      24 [.       3      26 ..       3      78 .. 0.40
   2 ?    8.8   0.4    0.0061         2      14      48 ..      60      95 ..      50      99 .. 0.60

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.075
                     DnaJ_CXXCXGXG  1 CkkCkGsgakkgkkktCktCkGsG 24
                                      C+kC    + +++k  C++C+ + 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSRDKYICNSCGNEI 26
                                      666666665445555677775433 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0061
                     DnaJ_CXXCXGXG 14 kktCktCkGsG.vvreeqktlgpfvqqsqstCpeCe 48
                                         C+ C+ +G     +q++ +   +++  tC++C+
  gi|518651530|ref|YP_008141050.1| 60 DAVCPVCHHTGaYYLLKQTRSADEPETKFYTCESCG 95
                                      456999999994433444322222333456888886 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   4.5     0.036        12       2      29 ..       2      23 ..       1      26 [. 0.75
   2 ?    3.5   0.3      0.21        70      25      29 ..      19      23 ..      16      29 .. 0.64
   3 ?    3.9   1.4      0.16        52      23      31 ..      61      69 ..      61      70 .. 0.87
   4 ?    4.5   0.1     0.098        33       3       8 ..      91      96 ..      85     100 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.036
                                      B-TTT--B-EEE--TT-SS-EEEETTTT CS
                         Nudix_N_2  2 FCsqCGtpvelripdgDnreRlvCpaCg 29
                                      FCs+CG+ ++        r  ++C++Cg
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALMTPS------RDKYICNSCG 23
                                      9*****976544......3457888887 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.21
                                      ETTTT CS
                         Nudix_N_2 25 CpaCg 29
                                      C++Cg
  gi|518651530|ref|YP_008141050.1| 19 CNSCG 23
                                      55554 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.16
                                      EEETTTTEE CS
                         Nudix_N_2 23 lvCpaCgti 31
                                      +vCp C+++
  gi|518651530|ref|YP_008141050.1| 61 AVCPVCHHT 69
                                      69****985 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.098
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C++CG+
  gi|518651530|ref|YP_008141050.1| 91 CESCGH 96
                                      555555 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       4.4   1.5e+03       7      11 ..       3       7 ..       2      11 .. 0.66
   2 ?    9.4   0.1    0.0026      0.88       2      12 ..      14      24 ..      13      29 .. 0.85
   3 ?   -1.3   0.1       5.8   1.9e+03       7      12 ..      63      68 ..      59      73 .. 0.66
   4 ?    5.0   0.3     0.062        21       4      19 ..      88      97 ..      85     100 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 4.4
                                      -TTT- CS
                                ZZ  7 CdgCs 11
                                      C +C+
  gi|518651530|ref|YP_008141050.1|  3 CSKCG 7 
                                      66666 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0026
                                      SS-EE-TTT-S CS
                                ZZ  2 hkkytCdgCse 12
                                      ++ky+C+ C++
  gi|518651530|ref|YP_008141050.1| 14 RDKYICNSCGN 24
                                      689*******9 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 5.8
                                      -TTT-S CS
                                ZZ  7 CdgCse 12
                                      C +C +
  gi|518651530|ref|YP_008141050.1| 63 CPVCHH 68
                                      777766 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.062
                                      -EE-TTT-S..EESSE CS
                                ZZ  4 kytCdgCseapligvR 19
                                       ytC+ C++      R
  gi|518651530|ref|YP_008141050.1| 88 FYTCESCGH------R 97
                                      59******9......4 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.3      0.19        63      50      60 ..       1      11 [.       1      16 [. 0.80
   2 ?    6.5   0.1     0.031        10      48      68 ..      15      35 ..      10      41 .. 0.78
   3 ?   -0.1   0.1       3.6   1.2e+03      50      58 ..      61      69 ..      38      81 .. 0.69
   4 ?    4.6   0.9      0.12        41      39      58 ..      77      97 ..      64     100 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.19
                               GFA 50 sfCpeCgsply 60
                                      +fC++Cg+ ++
  gi|518651530|ref|YP_008141050.1|  1 MFCSKCGALMT 11
                                      59*****9887 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.031
                               GFA 48 trsfCpeCgsplyseesaape 68
                                      ++++C++Cg ++    +a+++
  gi|518651530|ref|YP_008141050.1| 15 DKYICNSCGNEIPKAGTADQK 35
                                      679*********976666655 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 3.6
                               GFA 50 sfCpeCgsp 58
                                       +Cp C  +
  gi|518651530|ref|YP_008141050.1| 61 AVCPVCHHT 69
                                      778888654 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.12
                               GFA 39 kt.adsgnkvtrsfCpeCgsp 58
                                      +t ++ + + + + C++Cg +
  gi|518651530|ref|YP_008141050.1| 77 QTrSADEPETKFYTCESCGHR 97
                                      443666777888******976 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 ?    0.9   0.1       1.3   4.4e+02       6      10 ..       3       7 ..       2       9 .. 0.87
   2 ?    8.9   0.1    0.0042       1.4       5      15 ..      18      28 ..      12      29 .. 0.85
   3 ?    2.6   0.2      0.41   1.4e+02       5      10 ..      90      95 ..      84      96 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1.3
                      zf-dskA_traR  6 CeeCG 10
                                      C++CG
  gi|518651530|ref|YP_008141050.1|  3 CSKCG 7 
                                      ****9 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0042
                      zf-dskA_traR  5 sCeeCGEpIpe 15
                                      +C  CG +Ip 
  gi|518651530|ref|YP_008141050.1| 18 ICNSCGNEIPK 28
                                      3********97 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.41
                      zf-dskA_traR  5 sCeeCG 10
                                      +Ce CG
  gi|518651530|ref|YP_008141050.1| 90 TCESCG 95
                                      3****9 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   3.8      0.31     1e+02      38      52 ..      10      24 ..       1      26 [. 0.69
   2 ?    9.2   2.0    0.0029      0.96      24      52 ..      62      96 ..      47      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                    zinc_ribbon_10 38 eeleevkyrCpkCga 52
                                       ++++ ky+C +Cg 
  gi|518651530|ref|YP_008141050.1| 10 MTPSRDKYICNSCGN 24
                                      466677899999985 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0029
                    zinc_ribbon_10 24 ICskChshnGlap......keeleevkyrCpkCga 52
                                      +C+ Ch++  ++        +e+e+  y C +Cg+
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHHTGAYYLlkqtrsADEPETKFYTCESCGH 96
                                      8****998888878887755666677899*****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 ?    4.1   0.1      0.14        45      28      35 ..       3      10 ..       1      11 [. 0.83
   2 ?    1.4   0.1      0.92   3.1e+02      28      33 ..      19      24 ..       8      27 .. 0.67
   3 ?    2.1   0.2      0.57   1.9e+02      28      33 ..      63      68 ..      58      69 .. 0.67
   4 ?    7.7   0.2    0.0097       3.2      27      36 .]      90      99 ..      83      99 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.14
                     zinc_ribbon_4 28 CskCghvF 35
                                      CskCg++ 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALM 10
                                      9***9875 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.92
                     zinc_ribbon_4 28 CskCgh 33
                                      C  Cg+
  gi|518651530|ref|YP_008141050.1| 19 CNSCGN 24
                                      777766 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.57
                     zinc_ribbon_4 28 CskCgh 33
                                      C+ C h
  gi|518651530|ref|YP_008141050.1| 63 CPVCHH 68
                                      677766 PP

  == domain 4  score: 7.7 bits;  conditional E-value: 0.0097
                     zinc_ribbon_4 27 rCskCghvFr 36
                                      +C  Cgh +r
  gi|518651530|ref|YP_008141050.1| 90 TCESCGHRWR 99
                                      7*******97 PP

>> Baculo_LEF5_C  Baculoviridae late expression factor 5 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4      0.35   1.2e+02      36      41 ..       2       7 ..       1       8 [. 0.85
   2 ?    8.1   0.0    0.0065       2.2      22      41 ..      76      95 ..      64      96 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.35
                     Baculo_LEF5_C 36 yCskCg 41
                                       CskCg
  gi|518651530|ref|YP_008141050.1|  2 FCSKCG 7 
                                      5****9 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0065
                     Baculo_LEF5_C 22 iQnRagDEivsfvryCskCg 41
                                      +Q+R+ DE      +C  Cg
  gi|518651530|ref|YP_008141050.1| 76 KQTRSADEPETKFYTCESCG 95
                                      6*******876666799998 PP

>> zf-HIT  HIT zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.3     0.015       4.9       4      21 ..       2      24 ..       1      26 [. 0.89
   2 ?    3.2   0.2      0.25        82       4      14 ..      62      72 ..      59      73 .. 0.85
   3 ?    5.1   0.4     0.063        21      14      22 ..      89      97 ..      84     101 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.015
                                      B-TTT-S.....B-SEE-TTT-- CS
                            zf-HIT  4 lCgvCgf.....pakYkCpkCnt 21
                                      +C+ Cg+       kY C  C+ 
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGAlmtpsRDKYICNSCGN 24
                                      8*****99998889*******85 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.25
                                      B-TTT-SB-SE CS
                            zf-HIT  4 lCgvCgfpakY 14
                                      +C vC+ ++ Y
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHHTGAY 72
                                      799***99888 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.063
                                      EE-TTT--E CS
                            zf-HIT 14 YkCpkCntr 22
                                      Y+C  C+ r
  gi|518651530|ref|YP_008141050.1| 89 YTCESCGHR 97
                                      999999876 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.1    0.0097       3.2      18      36 ..       2      24 ..       1      25 [. 0.77
   2 ?    3.3   0.1      0.18        61      30      35 ..      62      67 ..      57      70 .. 0.59
   3 ?    1.3   0.2       0.8   2.7e+02      18      24 ..      90      96 ..      85      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0097
                                      E-TTT--E....ESSSS-CCCCS CS
                              RecR 18 hCsrCgnl....teedlCaICsd 36
                                      +Cs+Cg l     ++ +C+ C +
  gi|518651530|ref|YP_008141050.1|  2 FCSKCGALmtpsRDKYICNSCGN 24
                                      8*******765445559999976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.18
                                      S-CCCC CS
                              RecR 30 lCaICs 35
                                      +C++C 
  gi|518651530|ref|YP_008141050.1| 62 VCPVCH 67
                                      566664 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.8
                                      E-TTT-- CS
                              RecR 18 hCsrCgn 24
                                       C+ Cg+
  gi|518651530|ref|YP_008141050.1| 90 TCESCGH 96
                                      7****97 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   2.3     0.054        18      40      76 ..       3      27 ..       1      32 [. 0.66
   2 ?    4.7   5.8      0.15        51      39      73 ..      18      68 ..      12     100 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.054
                    zinc_ribbon_15 40 cskCkslleaskelgkeiekkessekkeCknCgkeve 76
                                      cskC++l++ s+            +k++C++Cg+e+ 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSR------------DKYICNSCGNEIP 27
                                      666666666665............4677777777775 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.15
                    zinc_ribbon_15 39 acskCkslleaskelgkeiekkesse................kkeCknCgk 73
                                       c++C++ +++  +  ++i +k+s +                  +C+ C++
  gi|518651530|ref|YP_008141050.1| 18 ICNSCGNEIPKAGTADQKIISKSSDKeiimvakevnaepldsDAVCPVCHH 68
                                      577777777666666555555544445666666666666666344444433 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 ?   -1.2   0.1       4.2   1.4e+03      36      40 ..       3       7 ..       2      18 .. 0.83
   2 ?    5.2   0.5     0.041        14      33      60 ..      16      43 ..       8      45 .. 0.73
   3 ?    7.7   0.3    0.0069       2.3      10      40 ..      61      95 ..      52      97 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.2
                       Vps36-NZF-N 36 ClaCG 40
                                      C  CG
  gi|518651530|ref|YP_008141050.1|  3 CSKCG 7 
                                      99999 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.041
                       Vps36-NZF-N 33 lPpClaCGvkpdlelikksikasasskk 60
                                        +C++CG + + + + +  ++s+ss+k
  gi|518651530|ref|YP_008141050.1| 16 KYICNSCGNEIPKAGTADQKIISKSSDK 43
                                      558*****99888877777666666654 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0069
                       Vps36-NZF-N 10 WvCpICsfsNevpsnfdp....nastplPpClaCG 40
                                       vCp+C  +  +    +     + +t++  C++CG
  gi|518651530|ref|YP_008141050.1| 61 AVCPVCHHTGAYYLLKQTrsadEPETKFYTCESCG 95
                                      59****99998876333355678899999*****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 ?    2.6   0.1      0.44   1.5e+02       4      10 ..       3       9 ..       2      11 .. 0.85
   2 ?    4.2   0.2      0.14        46       4       9 ..      19      24 ..      14      28 .. 0.80
   3 ?    3.2   0.5      0.28        93      22      26 .]      62      66 ..      58      66 .. 0.93
   4 ?    4.2   0.1      0.14        47       3       8 ..      90      95 ..      88      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.44
                            zf-ACC  4 CpsCgem 10
                                      C +Cg++
  gi|518651530|ref|YP_008141050.1|  3 CSKCGAL 9 
                                      9999997 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.14
                            zf-ACC  4 CpsCge 9 
                                      C+sCg+
  gi|518651530|ref|YP_008141050.1| 19 CNSCGN 24
                                      888887 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.28
                            zf-ACC 22 VCPkC 26
                                      VCP C
  gi|518651530|ref|YP_008141050.1| 62 VCPVC 66
                                      9**** PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.14
                            zf-ACC  3 KCpsCg 8 
                                       C+sCg
  gi|518651530|ref|YP_008141050.1| 90 TCESCG 95
                                      69***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 ?    2.9   1.5      0.32   1.1e+02      14      25 ..       3      14 ..       2      25 .. 0.67
   2 ?    3.2   0.4      0.24        81      26      32 ..      61      67 ..      59      72 .. 0.79
   3 ?    4.6   0.0     0.092        31       4      19 ..      81      96 ..      79      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.32
                           DUF35_N 14 CpdCGtvqfPPr 25
                                      C++CG++  P r
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTPSR 14
                                      888988766655 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.24
                           DUF35_N 26 avCphCg 32
                                      avCp C+
  gi|518651530|ref|YP_008141050.1| 61 AVCPVCH 67
                                      79****5 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.092
                           DUF35_N  4 aaegrLvgqrCpdCGt 19
                                      a+e++  +  C +CG+
  gi|518651530|ref|YP_008141050.1| 81 ADEPETKFYTCESCGH 96
                                      5677778889*****8 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 ?    4.5   0.2      0.14        47       4      13 ..       3      12 ..       2      16 .. 0.84
   2 ?    3.1   0.3      0.37   1.2e+02      37      46 .]      14      23 ..      13      23 .. 0.89
   3 ?    1.9   0.3      0.88   2.9e+02       3      15 ..      18      30 ..      17      35 .. 0.74
   4 ?    2.6   0.0      0.57   1.9e+02       3       9 ..      62      68 ..      60      80 .. 0.82
   5 ?    2.0   0.2      0.87   2.9e+02       3       9 ..      90      96 ..      89     100 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.14
                           zf-IS66  4 CpcCGgllkp 13
                                      C++CG+l++p
  gi|518651530|ref|YP_008141050.1|  3 CSKCGALMTP 12
                                      ******9876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.37
                           zf-IS66 37 rpkyaCpcCe 46
                                      r ky C +C+
  gi|518651530|ref|YP_008141050.1| 14 RDKYICNSCG 23
                                      789******7 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.88
                           zf-IS66  3 tCpcCGgllkpig 15
                                      +C  CG +  ++g
  gi|518651530|ref|YP_008141050.1| 18 ICNSCGNEIPKAG 30
                                      5999998766666 PP

  == domain 4  score: 2.6 bits;  conditional E-value: 0.57
                           zf-IS66  3 tCpcCGg 9 
                                      +Cp C++
  gi|518651530|ref|YP_008141050.1| 62 VCPVCHH 68
                                      7****98 PP

  == domain 5  score: 2.0 bits;  conditional E-value: 0.87
                           zf-IS66  3 tCpcCGg 9 
                                      tC  CG+
  gi|518651530|ref|YP_008141050.1| 90 TCESCGH 96
                                      5777776 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   1.9     0.047        16      37      64 ..       3      29 ..       1      58 [. 0.53
   2 ?    3.8   1.2      0.19        62      31      61 ..      85      98 ..      34     101 .] 0.53

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.047
                           DUF2318 37 CevCekkgYvqegeelvCknCgvrfald 64
                                      C+ C+    + + ++ +C++Cg+++ ++
  gi|518651530|ref|YP_008141050.1|  3 CSKCGAL-MTPSRDKYICNSCGNEIPKA 29
                                      3344322.23345566677777665432 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.19
                           DUF2318 31 rvaldaCevCekkgYvqegeelvCknCgvrf 61
                                      ++                 +  +C++Cg r+
  gi|518651530|ref|YP_008141050.1| 85 ET-----------------KFYTCESCGHRW 98
                                      22.................334666666665 PP

>> zf_C2H2_13  Zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5       1.5   5.1e+02      20      25 ..       3       8 ..       2      11 .. 0.87
   2 ?    5.7   1.1     0.033        11      19      25 ..      18      24 ..       9      28 .. 0.87
   3 ?   -2.0   0.0       8.4   2.8e+03      10      21 ..      56      67 ..      54      71 .. 0.56
   4 ?    6.0   0.1     0.026       8.6      13      24 ..      84      95 ..      78      97 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.5
                        zf_C2H2_13 20 CnkCGk 25
                                      C kCG 
  gi|518651530|ref|YP_008141050.1|  3 CSKCGA 8 
                                      *****5 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.033
                        zf_C2H2_13 19 vCnkCGk 25
                                      +Cn+CG 
  gi|518651530|ref|YP_008141050.1| 18 ICNSCGN 24
                                      9*****6 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8.4
                        zf_C2H2_13 10 pLdtnlnYRvCn 21
                                      pLd+     vC 
  gi|518651530|ref|YP_008141050.1| 56 PLDSDAVCPVCH 67
                                      566555445555 PP

  == domain 4  score: 6.0 bits;  conditional E-value: 0.026
                        zf_C2H2_13 13 tnlnYRvCnkCG 24
                                       ++++  C++CG
  gi|518651530|ref|YP_008141050.1| 84 PETKFYTCESCG 95
                                      449999****** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                       112  (0.00624686); expected 17.9 (0.001)
Passed Fwd filter:                        67  (0.00373696); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              54  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 653.18
//
Query:       gi|518651531|ref|YP_008141051.1|  [L=129]
Description: succinyl-CoA synthetase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-35  121.3   0.1    3.3e-35  121.1   0.1    1.0  1  CoA_binding_2  CoA binding domain
    0.00084   20.0   0.0     0.0012   19.5   0.0    1.3  1  CoA_binding    CoA binding domain


Domain annotation for each model (and alignments):
>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.1   0.1   3.6e-39   3.3e-35       1     116 []      11     125 ..      11     125 .. 0.97

  Alignments for each domain:
  == domain 1  score: 121.1 bits;  conditional E-value: 3.6e-39
                                       --EEEET--S-TTSHHHHHHHHHHHHT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlryllehglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkeala 77 
                                       r iaVvG sd+p++++y+v +yl  +g++++pVnp  e  +g+kvy+++++ +++vd+vd+f++pe ++eivk+a+ 
  gi|518651531|ref|YP_008141051.1|  11 RDIAVVGISDKPDRASYQVSKYLMGNGYNIIPVNPVLEHWEGKKVYKDVKSIEGNVDVVDIFRKPEFVEEIVKDAKG 87 
                                       679***********************************************857**********************96 PP

                                       H--SEEEE-TT---HHHHHHHHHTT-EEE.ES-HHHHHH CS
                     CoA_binding_2  78 lgakavwlqpgsedeeaaelaeeagirvvgdrCilvege 116
                                       + a+++w+q+g+++e+a +la + g++v++d+C++ e++
  gi|518651531|ref|YP_008141051.1|  88 K-ARVIWMQEGIVNEDAKKLAIDMGMEVIMDKCMKKEHQ 125
                                       6.*********************************9985 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.3e-07    0.0012       4      82 ..      11      85 ..       8      94 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                                      EEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHH CS
                       CoA_binding  4 tkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdel 82
                                        ++v+G++ +     y++++ l  +   +++vnp    +  +g +vyk+v+ +e +  vdv  i+  +e+++e+v+++
  gi|518651531|ref|YP_008141051.1| 11 RDIAVVGISDKPDRASYQVSKYLMGNGYNIIPVNPV--LEHWEGKKVYKDVKSIEGN--VDVVDIFRKPEFVEEIVKDA 85
                                      579****************999999999*******9..99*****************..99999999999999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 858.84
//
Query:       gi|518651532|ref|YP_008141052.1|  [L=234]
Description: short-chain alcohol dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  108.5   0.0    5.4e-31  108.0   0.0    1.2  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    2.5e-28   98.9   0.2      3e-28   98.6   0.2    1.1  1  adh_short        short chain dehydrogenase
    4.8e-05   22.9   0.6    0.00019   21.0   0.5    1.8  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.015   14.7   0.0    1.1  1  DUF1776          Fungal family of unknown function (DUF1776)
       0.04   14.2   0.0      0.062   13.6   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.041   13.8   0.0      0.053   13.4   0.0    1.3  1  KR               KR domain
       0.16   11.6   0.0       0.26   10.9   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA


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 !  108.0   0.0   2.1e-34   5.4e-31       1     232 [.       9     225 ..       9     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.0 bits;  conditional E-value: 2.1e-34
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                       G+ +g+G  +A  l+   ++v l  ++ +    v+e+a +++ e++++D ++  q+ ++++++ +++g++D ++n a
  gi|518651532|ref|YP_008141052.1|   9 GVGKGMGSSLAYYLKGGDYNVFLISRGSN----VREVAGKTECEFYNADLNSYPQCVEAIKAADRSMGGIDAVINVA 81 
                                       8889******************9988877....69****************************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g   + +++++et+ e f +a+  n++ ++++a+aa+pl+k++  gsi+  s    +++ +++  y+a K+a+  ++
  gi|518651532|ref|YP_008141052.1|  82 GNYYS-NKSIEETEPEMFMEAILNNARTFYNIARAAIPLLKRQkhGSIIGFSAS-ENVYYNSNPGYAAGKGAVYYMV 156
                                       *9999.9*******************************9998888999999887.335555555************* PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       ++lA+el +++i+vN v+pg+i        k+ de+++++e    + r   p+++ +++ fL+   ++++tG+++ v
  gi|518651532|ref|YP_008141052.1| 157 KSLARELIKYNIKVNGVAPGFIG-------KDDDEMKSNIELG--ITRRYPPDDINRTIEFLIN--SEMVTGEIIPV 222
                                       **********************9.......6667777777544..455689************9..55********* PP

                                       STT CS
                      adh_short_C2 230 DgG 232
                                        gG
  gi|518651532|ref|YP_008141052.1| 223 AGG 225
                                       **9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.6   0.2   1.2e-31     3e-28       2     183 ..       4     179 ..       3     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.2e-31
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                        +++ G ++G+G  +a+ l   +++v++++r ++ ++eva + +       ++++D++++ ++ +++++a   +g++
  gi|518651532|ref|YP_008141052.1|   4 NIVIAGVGKGMGSSLAYYLKGGDYNVFLISRGSN-VREVAGKTE-----CEFYNADLNSYPQCVEAIKAADRSMGGI 74 
                                       589***************************9966.667777766.....78************************** PP

                                       SEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKa 154
                                       d+++n AG    +++++e++ e + + i  N    ++++ra++p +++q+ G+I+  s    +v +++ + Y+A K+
  gi|518651532|ref|YP_008141052.1|  75 DAVINVAGNyYSNKSIEETEPEMFMEAILNNARTFYNIARAAIPLLKRQKHGSIIGFSA-SENVYYNSNPGYAAGKG 150
                                       *********88899999999999********************************9865.556999*********** PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBS CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvd 183
                                       av  +++sla+el +++i+vn+vaPG++ 
  gi|518651532|ref|YP_008141052.1| 151 AVYYMVKSLARELIKYNIKVNGVAPGFIG 179
                                       **************************985 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.5   7.6e-08   0.00019       1     159 [.       5     162 ..       5     193 .. 0.75

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 7.6e-08
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.....T-SEEEE-- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkee.....qpdavihlA 72 
                                       i+++G+   +Gs l+ +l+  +y+v  ++r s+ ++ a + + e++++dl    ++ +++k       ++davi++A
  gi|518651532|ref|YP_008141052.1|   5 IVIAGVGKGMGSSLAYYLKGGDYNVFLISRGSNVREVAGKTECEFYNADLNSYPQCVEAIKAAdrsmgGIDAVINVA 81 
                                       7889998899*********************999999999999*********997777776432113469******9 PP

                                       S..---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH.TCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHH CS
                         Epimerase  73 a..vggvaassedpadfieknlqgtlnlleaarka.gvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaK 146
                                       +  +++ + + ++p+ f+e+ l+ +++  + ar+a  + +    +S  + G +a+    e++    +++n  Yaa K
  gi|518651532|ref|YP_008141052.1|  82 GnyYSNKSIEETEPEMFMEAILNNARTFYNIARAAiPLLKRQKHGS--IIGFSAS----ENV---YYNSNPGYAAGK 149
                                       9777888888899999999666666666666654422223333344..6664444....344...457777777777 PP

                                       HHHHHHHHHHHHH CS
                         Epimerase 147 lageklveayaaq 159
                                        a++ +v+++a++
  gi|518651532|ref|YP_008141052.1| 150 GAVYYMVKSLARE 162
                                       7777777777665 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 ?   14.7   0.0   5.9e-06     0.015      68     197 ..      54     175 ..      33     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-06
                           DUF1776  68 leefaqslesphvalpgakphvlrLkgvilvPslsyptgpietiplsswaselnerllspiltlqallplltsrakq 144
                                       l+ + q +e    a++ a++ +    +vi v   +y+   ie+  ++ + +++ ++  +++ +  a +pll+   ++
  gi|518651532|ref|YP_008141052.1|  54 LNSYPQCVE----AIKAADRSMGGIDAVINVAGNYYSNKSIEETEPEMFMEAILNNARTFYNIARAAIPLLKR--QK 124
                                       444444444....67888888889999****999**8888********************************8..57 PP

                           DUF1776 145 kakiivvnps..issslnlpfhapEalvssalsalfevLkrelrphnidvtqikL 197
                                       +  ii +++s  +  + n+ ++       +a+  ++++L+rel ++ni+v  +  
  gi|518651532|ref|YP_008141052.1| 125 HGSIIGFSASenVYYNSNPGYA----AGKGAVYYMVKSLARELIKYNIKVNGVAP 175
                                       8899999876113344444454....45678888888999999999999977655 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 ?   13.6   0.0   2.4e-05     0.062       2      86 ..       6      90 ..       5     129 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                      EEE--SH.HHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS.......SE CS
                   Sacchrp_dh_NADP  2 liiGaGs.vGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg.......dl 72
                                      +i G G+ +G+++a ++++ +d+  ++ +++r  +   +++a   ++++e++  d + y++  ++++k +       d+
  gi|518651532|ref|YP_008141052.1|  6 VIAGVGKgMGSSLA-YYLKGGDY--NVFLISRGSNV--REVA--GKTECEFYNADLNSYPQ-CVEAIKAAdrsmggiDA 76
                                      66677641455544.55566889..99999999998..5554..8999999999*****99.888888888899999** PP

                                      EEE-SSGGGHHHHH CS
                   Sacchrp_dh_NADP 73 vvnlsppissldvl 86
                                      v+n++++++s++ +
  gi|518651532|ref|YP_008141052.1| 77 VINVAGNYYSNKSI 90
                                      ********988766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.1e-05     0.053       4     109 ..       6     102 ..       3     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.1e-05
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       +i+G   g+G +la  l + g  ++ l+sR         ++++e++   +e+e+++aD+ +  +  +++++++++++
  gi|518651532|ref|YP_008141052.1|   6 VIAGVGKGMGSSLAYYL-KGGDYNVFLISRG--------SNVREVAG-KTECEFYNADLNSYPQCVEAIKAADRSMG 72 
                                       78888889999999887.6789999999999........34555554.6899************************* PP

                                       ---EEEE------.---TTT--HHHHHHHH CS
                                KR  81 pikGvihaAgvlr.dklleemtaedleqvl 109
                                        i  vi+ Ag    +k +ee++ e++ +++
  gi|518651532|ref|YP_008141052.1|  73 GIDAVINVAGNYYsNKSIEETEPEMFMEAI 102
                                       *********976427889999988887765 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0001      0.26       1      74 [.       5      79 ..       5     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0001
                                      EEEES-S.HHHHHHHHHHHHHTHCEEEE-SCHHHHH.HHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE CS
                              ApbA  1 iailGaG.aiGsllaakLakagadvtlilrsrrlea.lkknGlrltseggeeilrppealsaeekselepidlviv 74
                                      i+i+G G ++Gs la++L+   ++v li r+  + +   k+ ++++  + + + +  ea+ a+ +++++ id vi 
  gi|518651532|ref|YP_008141052.1|  5 IVIAGVGkGMGSSLAYYLKGGDYNVFLISRGSNVREvAGKTECEFYNADLNSYPQCVEAIKAA-DRSMGGIDAVIN 79
                                      799999988*********889999********8887566777888877744444444444444.678888888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1482.11
//
Query:       gi|518651533|ref|YP_008141053.1|  [L=607]
Description: hypothetical protein FACI_IFERC00001G0172 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-21   76.7  56.7    1.9e-21   76.2  56.7    1.2  1  AA_permease    Amino acid permease
    1.6e-17   63.5  61.8    2.4e-17   62.9  61.8    1.2  1  AA_permease_2  Amino acid permease
    5.4e-11   42.8   1.8    1.6e-05   25.3   0.2    2.8  2  CBS            CBS domain
  ------ inclusion threshold ------
        0.3   11.2   1.6        4.4    7.4   0.2    3.4  3  PspB           Phage shock protein B
        3.1    7.6   5.6         14    5.6   0.1    3.4  3  DDDD           Putative mitochondrial precursor protein


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2  56.7   5.4e-25   1.9e-21       2     452 ..      20     440 ..      19     476 .. 0.78

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 5.4e-25
                       AA_permease   2 vlvialggviG.tglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       v++ + gg+ + + +++  ++v+  +G   a ++++++++ ++  +l + +++  +++sgg+ytya + l+ + Gf 
  gi|518651533|ref|YP_008141053.1|  20 VFFLSFGGMSPlLSILTYAAFVITLVGY-DAPIVMVIGMLLVLVNGLVVTQLSKRFSSSGGYYTYAFQALSARIGFD 95 
                                       7888999999966667777777777777.************************************************ PP

                       AA_permease  78 iGlnylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                       +G++y f++i+++ + lt+a+ +i  +     ++ +++  +++++  +++ +vg+k++ +  + +  i i  ++a +
  gi|518651533|ref|YP_008141053.1|  96 TGWMYIFYSILYALAYLTGAIFIIVTV---LGIS-EYYAFLLIIIPSITFLIVGIKLSSRYALYAVAIEISLMLAIV 168
                                       ***********9999999998888777...7788.444444444445555699*******88888888888888888 PP

                       AA_permease 155 ivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeks 231
                                       ++++++  g++        ++ +++   ++ +++g          +f+ ++ +++   tG++++a ++gEv++P+k 
  gi|518651533|ref|YP_008141053.1| 169 VISFVVTKGAA--------YIPNPAV--YH-ISGG----------DFALGILFAMGIPTGYGSIAPVSGEVSNPKKV 224
                                       88855544444........2223333..33.3344..........6******************************* PP

                       AA_permease 232 iPkailqvviritifYvlslllig.llvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanss 307
                                       + +++++v+++ + + +l++++   l+++ n    ++d++ + +++   + + g+ +l   ++++++  a+ +++s+
  gi|518651533|ref|YP_008141053.1| 225 VGRSVISVILIGGTLATLMIYAFAnLILQNNIIIPTSDKLPVIGIILHNFGKYGI-YLYYAVAIATINDAILAILSF 300
                                       ***********99999998887651667777777788777665555555555554.5566777777888888999** PP

                       AA_permease 308 lysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwllii 384
                                         +asR+++ +  d+ +P++++k  k +  +++ ++s+i+++l ll++ + +  +++f  l +isal gl+++++++
  gi|518651533|ref|YP_008141053.1| 301 GSAASRTFFRMGYDKSFPSIFAKKVKDNPIVASFAVSAIMVALPLLIMHYITV-ETAFILLGTISALGGLFIHVSAN 376
                                       ******************99988877765555555666655555554444443.6********************** PP

                       AA_permease 385 lsyl..rfRkalkyqgrsie.elgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaa 452
                                       +s++  ++R+  ++ +r  +   +++  +   ++ lv a++++i+l+++ y  +        w +  f+ +
  gi|518651533|ref|YP_008141053.1| 377 FSLIriGLRRGRRLISRTQKgIYSYIKDFKEVILALVAAIISSIVLVYSAYSTVS-------WYTLLFLVW 440
                                       ****66455554443333221579************************9997777.......333333333 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9  61.8   6.6e-21   2.4e-17       1     414 [.      15     434 ..      15     453 .. 0.81

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 6.6e-21
                     AA_permease_2   1 lsllsafalvigsv...igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgk 74 
                                       l++ ++f+l++g +   +++  +++ +++ +g  + ++ +i++l++ l  +lv  +ls ++++sgG y+y+ +a + 
  gi|518651533|ref|YP_008141053.1|  15 LTFKDVFFLSFGGMsplLSILTYAAFVITLVGYDAPIVMVIGMLLV-LVNGLVVTQLSKRFSSSGGYYTYAFQALSA 90 
                                       67999*********88755555555468889998999899999998.89**************************** PP

                     AA_permease_2  75 kvaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                       +++f ++w++ f  ++ + ++l+ a+  ++++lg +     + ++l   +i+i  +++ i+gik s++++ + + + 
  gi|518651533|ref|YP_008141053.1|  91 RIGFDTGWMYIFYSILYALAYLTGAIFIIVTVLGIS----EYYAFL---LIIIPSITFLIVGIKLSSRYALYAVAIE 160
                                       ****************99999999999999999854....222333...344444445569**************** PP

                     AA_permease_2 152 illpliiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvsee..vkkkdvpkaifi 225
                                       i l+l+i++i  ++t ++ + +      +  + +++ g ++lg+l ++   +G+ s+a vs e  ++kk v +  ++
  gi|518651533|ref|YP_008141053.1| 161 ISLMLAIVVISFVVTKGAAYIP------NPAVYHISGGdFALGILFAMGIPTGYGSIAPVSGEvsNPKKVVGRSVIS 231
                                       *988888888888888888887......58999999998899*********************5555589******* PP

                     AA_permease_2 226 gllivlvlyllvniaflgvvpddei..anlsnlgsvaalffeavggk..vvaiivvilialsllgaintavigssrv 298
                                       ++li + l +l+  af+  + +++i   +++ l+ v+++ ++++g+    + ++v+i+++  +++ai+++  ++sr+
  gi|518651533|ref|YP_008141053.1| 232 VILIGGTLATLMIYAFANLILQNNIiiPTSDKLP-VIGIILHNFGKYgiYLYYAVAIATINDAILAILSFGSAASRT 307
                                       ***************9998888887565566655.9*********64568888888999999*************** PP

                     AA_permease_2 299 lealardgvlPrffakvnkfgspiraiiltaivslillllfllas.saaynfllsvsslgliisyllliigalilrk 374
                                       +++++ d+ +P+ fak  k + ++++  ++ai + + ll++ +++ ++a+ +l ++s+lg +++   + ++++ +  
  gi|518651533|ref|YP_008141053.1| 308 FFRMGYDKSFPSIFAKKVKDNPIVASFAVSAIMVALPLLIMHYITvETAFILLGTISALGGLFIHVSANFSLIRIGL 384
                                       ********************98999999999998666666666678**********************999998877 PP

                     AA_permease_2 375 krphl..kr...........pgkilvaiigalfllfllvalffppkgpatqss 414
                                       +r ++   r           ++ +++a+++a+++ ++lv  ++ +   + + +
  gi|518651533|ref|YP_008141053.1| 385 RRGRRliSRtqkgiysyikdFKEVILALVAAIISSIVLVYSAYST---VSWYT 434
                                       766555633454655444444447777777777776666666532...23333 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.2e-06     0.011      10      53 ..     490     533 ..     472     537 .. 0.80
   2 !   25.3   0.2   4.4e-09   1.6e-05       7      56 ..     550     599 ..     544     600 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.2e-06
                                       EEEETTSBHHHHHHHHHHHT..SSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  10 vtvppdttleealelmrekg..vsrlPVVdedgklvGivtlrDllr 53 
                                       v v  +++l+ ale++ +k+  + ++ V+d++ k+vG +   D+l 
  gi|518651533|ref|YP_008141053.1| 490 VIVGINDPLRAALEKLLSKNipY-AI-VLDGNMKPVGTLYVIDILL 533
                                       578889*********99***444.55.89*999***********96 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4.4e-09
                                       SSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS   7 rdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                       ++vv ++ ++ + +a+++++e++v+ l +Vd++gk+ G +t+r +l +l+
  gi|518651533|ref|YP_008141053.1| 550 EKVVNISVNDEVTDAVRILKENNVNILSIVDGSGKCTGTITEREILLKLA 599
                                       67899999999********9999*8778******************9886 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.52   1.9e+03       7      29 ..      51      73 ..      50      78 .. 0.77
   2 ?    7.4   0.2    0.0012       4.4       6      27 ..     331     352 ..     327     357 .. 0.85
   3 ?   -0.5   0.0      0.37   1.3e+03      38      64 ..     466     492 ..     429     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.52
                              PspB  7 vpliifvlfVapiWLiLHYrskk 29
                                      ++++i +l+V++ +L+    sk+
  gi|518651533|ref|YP_008141053.1| 51 IVMVIGMLLVLVNGLVVTQLSKR 73
                                      57899999999999987666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0012
                              PspB   6 avpliifvlfVapiWLiLHYrs 27 
                                       ++  ++  ++Va++ Li+HY++
  gi|518651533|ref|YP_008141053.1| 331 VASFAVSAIMVALPLLIMHYIT 352
                                       56678999************98 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.37
                              PspB  38 edekrLeellekAekleeRietLEriL 64 
                                       ++ k L+e l + + +++Ri  L  i+
  gi|518651533|ref|YP_008141053.1| 466 KEGKILAENLMNIKVMDARIPGLDVIV 492
                                       366777777778888888888887776 PP

>> DDDD  Putative mitochondrial precursor protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2      0.86   3.1e+03      37      58 ..      55      75 ..      50      76 .. 0.69
   2 ?    2.8   0.1     0.027        96      35      58 ..     130     153 ..     126     160 .. 0.87
   3 ?    5.6   0.1    0.0038        14      38      72 ..     228     262 ..     214     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.86
                              DDDD 37 lrvilvVipgllvGtliSknvA 58
                                      ++++lv + gl+v t++Sk++ 
  gi|518651533|ref|YP_008141053.1| 55 IGMLLVLVNGLVV-TQLSKRFS 75
                                      4556666777766.89999985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.027
                              DDDD  35 gLlrvilvVipgllvGtliSknvA 58 
                                       ++l +i+  i++l+vG  +S + A
  gi|518651533|ref|YP_008141053.1| 130 AFLLIIIPSITFLIVGIKLSSRYA 153
                                       678899999**********99877 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0038
                              DDDD  38 rvilvVipgllvGtliSknvAnlLeendlFvPeDD 72 
                                       +vi v++ g  + tl+   +Anl+ +n++ +P  D
  gi|518651533|ref|YP_008141053.1| 228 SVISVILIGGTLATLMIYAFANLILQNNIIIPTSD 262
                                       4677777888888888999*************877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.74u 0.31s 00:00:01.05 Elapsed: 00:00:00.47
# Mc/sec: 3913.34
//
Query:       gi|518651534|ref|YP_008141054.1|  [L=404]
Description: hypothetical protein FACI_IFERC00001G0173 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-48  162.9   0.2    1.2e-47  162.4   0.2    1.2  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 !  162.4   0.2     7e-52   1.2e-47       5     218 .]     161     381 ..     157     381 .. 0.96

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 7e-52
                           UPF0051   5 rtlivveegaevtiieey....agc....gvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvsl 73 
                                       +++i+v+++a+v+i + y     g+     ++ if ge++++ky  vq+++ed+vnl+ +r  + rd+++++++v+ 
  gi|518651534|ref|YP_008141054.1| 161 KNVIIVGKNASVEITDVYkkhnKGNgvhgRNIYIFCGEGSHVKYNYVQDEGEDTVNLTYVRPVLYRDSEIRIIDVNA 237
                                       799************888866622255669*********************************************** PP

                           UPF0051  74 ggkltrkepsvelkgegaeaelnglylakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqk 150
                                       g++ +  + ++e+  ++++++ +g+ +++g+q++d+       g+ ++++i++kgv+ d++ ++ rg+i+++++  k
  gi|518651534|ref|YP_008141054.1| 238 GANKVFYNHESEMY-DNTTMKSYGVNVSRGDQEMDIWDSSVQYGKYSNCDINIKGVVLDRSSTMHRGNIDIEPEGVK 313
                                       *****999999996.************************************************************** PP

                           UPF0051 151 tdahqenrnLllsdkaradtiPeleidaddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       ++++  +  Ll+s++++ +++P l i+++d k +H ++++++d eq+fYL+sRGlse+eA+++i++gf
  gi|518651534|ref|YP_008141054.1| 314 SSGFYGSAILLMSENGKGNSKPALLIKNNDTKSKHSSSISSLDPEQIFYLRSRGLSEAEATDMIINGF 381
                                       *******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2661.59
//
Query:       gi|518651535|ref|YP_008141055.1|  [L=835]
Description: hypothetical protein FACI_IFERC00001G0174 [Ferroplasma acidarmanus fer1]
Scores for complete 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-62  209.9   0.1    4.8e-59  199.7   0.1    2.2  2  UPF0051          Uncharacterized protein family (UPF0051)
    1.7e-10   40.9   0.0    1.8e-08   34.4   0.0    2.7  2  Intein_splicing  Intein splicing domain
    2.2e-07   31.1   3.3    1.4e-05   25.3   0.5    2.6  2  LAGLIDADG_3      LAGLIDADG-like domain


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 !    8.1   0.0   0.00032       1.9       2      26 ..     223     253 ..     222     335 .. 0.77
   2 !  199.7   0.1     8e-63   4.8e-59      23     218 .]     609     804 ..     567     804 .. 0.93

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00032
                           UPF0051   2 qfertlivveegaevtiieeyagc.........g 26 
                                       qfe+t++v++ega+v++i   +gc         g
  gi|518651535|ref|YP_008141055.1| 223 QFEHTIVVADEGAKVHYI---EGClpedelisqG 253
                                       89****************...7775555555440 PP

  == domain 2  score: 199.7 bits;  conditional E-value: 8e-63
                           UPF0051  23 agcgvveifvgenAklkyvkvqnwsedavnlstkraeegrdaklelttvslggkltrkepsvelkgegaeaelngly 99 
                                       ++ ++vei++ +n+ +ky++vqnws++++nl+ kra ++++a+++++t++lg+k+t+ +ps++l+g+ga+++   ++
  gi|518651535|ref|YP_008141055.1| 609 LHTAIVEIYARKNSDVKYTSVQNWSDSVYNLPVKRAWVDENAHMDWVTGELGSKVTMIYPSSYLRGRGASTSNLQIT 685
                                       4559********************************999************************************** PP

                           UPF0051 100 lakgkqhldtrtkvdhngpntssrilskgvlkdearavfrgkikvrkgaqktdahqenrnLllsdkaradtiPelei 176
                                       la+++ + d + k+ h +p+t+sri+sk+++ d++ + +rg +++++ga+++++h+++++Ll++++++++t P+ ei
  gi|518651535|ref|YP_008141055.1| 686 LATKDTFKDAGGKALHLAPDTTSRIVSKSISLDNGLTAYRGLVRMNEGAKRAKSHVQCDALLINSDSKNYTYPYDEI 762
                                       ***************************************************************************** PP

                           UPF0051 177 daddvkasHgAtvGkideeqlfYLmsRGlseeeArrlivrgf 218
                                       ++  ++ sH+AtvGki  ++l+YL+sRGlse+eA ++iv gf
  gi|518651535|ref|YP_008141055.1| 763 YEPTAEFSHEATVGKIGTDELTYLRSRGLSEDEASSMIVLGF 804
                                       ****************************************99 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   2.9e-12   1.8e-08      34     134 .]     274     598 ..     246     598 .. 0.91
   2 ?   -2.8   0.0      0.96   5.8e+03     101     120 ..     623     642 ..     607     663 .. 0.64

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.9e-12
                                       EEEEEEEEEEEEEE.EEEEEE.ETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEE............... CS
                                       xxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............... RF
                   Intein_splicing  34 evksvkkliklklk.elyeik.lesgrkikaTpeHkllvvrdegivEkradeLkegdliavp............... 93 
                                       ++ ++++   + ++  +y+i+ l+ g+  +aT+eH++l++++e++     + ++ g + +                 
  gi|518651535|ref|YP_008141055.1| 274 NQRKITRKYVHPYSgLMYKITpLSPGNAFRATSEHPVLSIKKEDV----TSRIRDGHYEISTkklmeaipeyrrmde 346
                                       33457777888888899***999*****************77666....666777776665567777789999999* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|518651535|ref|YP_008141055.1| 347 lsegdfivyvspveteddasidedmlkilglytaegsisfnkslnlyqmsfsfglsakeekiayelyniikekgera 423
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|518651535|ref|YP_008141055.1| 424 nifkadkkyytvstysktlidfclnnagkyadkkafsekimklppekqkllidyylkgdgnvyikkgkskmiragta 500
                                       ***************************************************************************** PP

                                       .........................................................HSCEEEEEEEEEEEEECEEE CS
                                       .........................................................xxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 .........................................................dadvvwdkvksievedeeey 113
                                                                                                +++ ++  +k++e e +++ 
  gi|518651535|ref|YP_008141055.1| 501 skilalqlqemlsrnntfasimirkasddvilgrnikrkeqyiveytenikfsrvrhKDNYYYVPIKKMEAEVYDDI 577
                                       ********************************************************8888***************** PP

                                       EEEEEETTT-EEEECTTEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing 114 VYdltvednhNFvangiivHN 134
                                       VY ++ve  + ++++g+ vHN
  gi|518651535|ref|YP_008141055.1| 578 VYNMEVETDDSYLVKGFAVHN 598
                                       ********************9 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.96
                                       EEEEEEEEECEEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing 101 kvksievedeeeyVYdltve 120
                                       +vk   v++  + VY l v+
  gi|518651535|ref|YP_008141055.1| 623 DVKYTSVQNWSDSVYNLPVK 642
                                       34444444555555555554 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.1    0.0031        18       7      56 ..     374     428 ..     368     449 .. 0.68
   2 !   25.3   0.5   2.3e-09   1.4e-05       3      74 ..     471     542 ..     469     551 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0031
                                       HHHHHHHCCECCECSTTTTSEEEEES-.........HHHHHHHHHHHHHCT.HSCEEEE CS
                       LAGLIDADG_3   7 LrGlfdaDGsvskskkkgvsisltsss.........kelledvqrlLlrlGIestiyek 56 
                                       + Gl++a+Gs+s +k     ++l++ s         +++++++ ++ ++ G  ++i + 
  gi|518651535|ref|YP_008141055.1| 374 ILGLYTAEGSISFNKS----LNLYQMSfsfglsakeEKIAYELYNIIKEKGERANIFKA 428
                                       78**********9996....455554444444444488888888888887777777777 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 2.3e-09
                                       HHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEEEEE-SCCCCECCCHCHCT CS
                       LAGLIDADG_3   3 kaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyekkkakgrgvyrlliisgen 74 
                                       ++ ++  +  +DG v  +k+k+++i+ +++sk l+ ++q++L+r + +++i  +k ++   + r +  +++ 
  gi|518651535|ref|YP_008141055.1| 471 QKLLIDYYLKGDGNVYIKKGKSKMIRAGTASKILALQLQEMLSRNNTFASIMIRKASDDVILGRNIKRKEQY 542
                                       667788899******************************************999444433333444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 5861.75
//
Query:       gi|518651536|ref|YP_008141056.1|  [L=247]
Description: hypothetical protein FACI_IFERC00001G0175 [Ferroplasma acidarmanus fer1]
Scores for complete 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   79.5   0.0    4.2e-22   79.1   0.0    1.2  1  ABC_tran     ABC transporter
    4.4e-08   33.3   0.6     0.0012   18.8   0.1    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    7.1e-08   32.2   1.6    6.2e-07   29.1   1.6    2.0  1  SMC_N        RecF/RecN/SMC N terminal domain
      0.003   17.5   0.1     0.0059   16.5   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0034   17.1   0.1     0.0071   16.1   0.1    1.5  1  AAA_29       P-loop containing region of AAA domain
     0.0055   17.1   1.4       0.15   12.5   1.4    2.2  1  AAA          ATPase family associated with various cellular a
  ------ inclusion threshold ------
       0.03   14.8   0.1      0.054   14.0   0.1    1.4  1  AAA_23       AAA domain
      0.069   13.4   0.1        3.4    7.9   0.0    2.2  2  AAA_22       AAA domain
      0.072   12.7   0.1       0.11   12.1   0.1    1.2  1  AAA_27       AAA domain
       0.14   11.7   0.1       0.31   10.6   0.0    1.7  2  AAA_25       AAA domain
       0.15   12.0   0.1        2.2    8.3   0.0    2.1  2  MutS_V       MutS domain V
       0.22   10.2   2.7        2.5    6.6   0.1    2.1  2  AAA_13       AAA domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   2.8e-25   4.2e-22       1     134 [.      21     172 ..      21     175 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.8e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp..teGeilldgkdlke.qeleslrkeigvlpqepqlfpel 74 
                                       lk ++l+++ ge++a++G+nGaGKStL ++l+g+ +   t G+il++g+dl++ +++e++r+ +   +q+p   +++
  gi|518651536|ref|YP_008141056.1|  21 LKGIDLTINSGEIHALMGPNGAGKSTLGEVLIGHPNYkiTGGKILINGRDLTNaTPEERARAGLFLAFQNPISISGV 97 
                                       789******************************866666*************9999**************9999999 PP

                                       BHHHH.................HHHTCHHHHHHHSTTGGTTCBGESTTS.GGS-HHHHHHHHHHHHHHHTSSEEEEE CS
                                       xxxxx.................xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  75 tvren.................esdeeiekalsklglkelkdtvvkssp.ssLSgGqkqrvalarallkkpkllllD 133
                                       ++ +                  e  + ++++++ ++++e   + +++s    +SgG+++r ++ ++++ kpk+++lD
  gi|518651536|ref|YP_008141056.1|  98 KISTFlrmaynnlypdekmplkEFFNMVKTVMKDVDMDE---SFISRSInDGFSGGERKRFEVLQMVILKPKIVILD 171
                                       988889999999977665544444444667776666666...555555559************************** PP

                                       S CS
                                       x RF
                          ABC_tran 134 E 134
                                       E
  gi|518651536|ref|YP_008141056.1| 172 E 172
                                       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 !   13.2   0.2   3.7e-05     0.056       2      19 ..      34      51 ..      33      74 .. 0.79
   2 !   18.8   0.1   7.8e-07    0.0012     164     300 ..      95     207 ..      55     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.7e-05
                            AAA_21  2 nvliGpNgsGKSnLLdal 19
                                       +l GpNg+GKS+L + l
  gi|518651536|ref|YP_008141056.1| 34 HALMGPNGAGKSTLGEVL 51
                                      6899**********9999 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 7.8e-07
                            AAA_21 164 e..rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelS 238
                                          +i+++   a +  +++ek  l+++ + +k+v   +++ + ++  +                         + +S
  gi|518651536|ref|YP_008141056.1|  95 SgvKISTFLRMAYNNLYPDEKMPLKEFFNMVKTVMKDVDMDESFISRSIN-----------------------DGFS 148
                                       35667777777777777777777777777777777777666655544443.......................2459 PP

                            AAA_21 239 dGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSpl 300
                                        G ++ + +l +++  +   +++++DE+++gL+  +l+ +   +k+ ++ ++ +++ TH   
  gi|518651536|ref|YP_008141056.1| 149 GGERKRFEVLQMVILKP---KIVILDEIDSGLDVDALKLVSAEIKKMHDQKVGFLIITHYQR 207
                                       99999999999999877...9***********************999999*********765 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 !   29.1   1.6   4.2e-10   6.2e-07      25     208 ..      32     216 ..      12     226 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.2e-10
                                       SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--....BTTCSSTTEEEEEEEEEETTEESSSSSSCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  25 sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk....skekasvkkaeveitfdnedkklkiekeev 97 
                                       ++ a++GpNG+GKs l + +   +G+ ++   + +  + li+     +++ ++  +a + + f+n+ +    +  ++
  gi|518651536|ref|YP_008141056.1|  32 EIHALMGPNGAGKSTLGEVL---IGHPNY---KITGGKILINGrdltNATPEERARAGLFLAFQNPISI---SGVKI 99 
                                       5889**************99...9*7666...5666667888876333344444455555555555544...55555 PP

                                       EEEEEEETTSEEEEEETTEEE-H..HHHHHHHHCTT-STT........CS-HHHHHHHHH.HHHHHHHCCS--SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx........xxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N  98 sisrrvkrkgeseykingkevtk..kevsellesagiske........lLSgGektLval.aLlfAiqkvkpaplyl 163
                                       s+  r+  ++   y  ++   ++  + v+ ++++++++++         +SgGe++   +  ++  i   kp+ +++
  gi|518651536|ref|YP_008141056.1| 100 STFLRMAYNNL--YPDEKMPLKEffNMVKTVMKDVDMDESfisrsindGFSGGERKRFEVlQMV--I--LKPK-IVI 169
                                       55444444443..2222222222223333333333333334444444479****9866540333..3..4444.89* PP

                                       ECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC-.SCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.xxx RF
                             SMC_N 164 lDeidaaLDeknvkkvaellkekskn.aQfivislreemleka.dkl 208
                                       lDeid+ LD    k v+  +k+ +++ + f++i++ +++l++   ++
  gi|518651536|ref|YP_008141056.1| 170 LDEIDSGLDVDALKLVSAEIKKMHDQkVGFLIITHYQRILKDIiPEF 216
                                       ********************97665549*********9998764555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   3.9e-06    0.0059      80     127 ..      11      59 ..       3      75 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                                       EE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT----- CS
                       RsgA_GTPase  80 llvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelkt 127
                                       l+ +++ ke l+ +   +++ ++ +l+G+ G+GKStL ++l+++ + k+
  gi|518651536|ref|YP_008141056.1|  11 LKAEVEGKEILKGIDLTINSgEIHALMGPNGAGKSTLGEVLIGHPNYKI 59 
                                       5666666777777887887779******************999866554 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   0.1   4.8e-06    0.0071      16      38 ..      25      47 ..      19      51 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.8e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTl 38
                                      +++i+  +++ l+Gp+G+GKSTl
  gi|518651536|ref|YP_008141056.1| 25 DLTINSGEIHALMGPNGAGKSTL 47
                                      567775559*************8 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   1.4    0.0001      0.15       3      74 ..      36     180 ..      34     219 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.0001
                                       EESSTTSSHHHHHHHHHHHHTHE....EEEEETTTCSSS...................................... CS
                               AAA   3 lyGppGtGKTllakavakelgve....fleisgsellsk...................................... 37 
                                       l+Gp G GK++l + ++ + + +     + i+g +l++                                       
  gi|518651536|ref|YP_008141056.1|  36 LMGPNGAGKSTLGEVLIGHPNYKitggKILINGRDLTNAtpeeraraglflafqnpisisgvkistflrmaynnlyp 112
                                       899*************9995544333335556666664456666666666666666666666666677777777777 PP

                                       .................................STTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHH CS
                               AAA  38 .................................yvgesekkirelfkeakeka..kpsilfiDEidalaksr 74 
                                                                         ++ +e+k  e+++        kp+i+++DEid+    +
  gi|518651536|ref|YP_008141056.1| 113 dekmplkeffnmvktvmkdvdmdesfisrsindGFSGGERKRFEVLQM----VilKPKIVILDEIDSGLDVD 180
                                       788888888888888888887777766666555444444444444444....04569*********976655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   3.6e-05     0.054      15      35 ..      24      47 ..       5      52 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.6e-05
                            AAA_23 15 idF...skgltlItGpNGaGKTTi 35
                                      id+   s  + ++ GpNGaGK+T+
  gi|518651536|ref|YP_008141056.1| 24 IDLtinSGEIHALMGPNGAGKSTL 47
                                      677776668999***********9 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0    0.0023       3.4       6      24 ..      32      50 ..      28      92 .. 0.87
   2 ?    3.4   0.0     0.056        83      92     125 ..     165     199 ..     148     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0023
                            AAA_22  6 gilvvtGesGtGKTtllrr 24
                                       i +++G+ G+GK+tl + 
  gi|518651536|ref|YP_008141056.1| 32 EIHALMGPNGAGKSTLGEV 50
                                      57789**********9775 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.056
                            AAA_22  92 ielliiDEaqh.lrseealeeL....rsllnlsrkgvql 125
                                       ++++i+DE++  l   +al+ +    +++++   ++v +
  gi|518651536|ref|YP_008141056.1| 165 PKIVILDEIDSgL-DVDALKLVsaeiKKMHD---QKVGF 199
                                       589********99.66665555311144444...44444 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   7.2e-05      0.11      17      42 ..      22      47 ..       6      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                            AAA_27 17 rsldfsaeeadlhliyGpNEAGKsta 42
                                      + +d+  ++ ++h ++GpN AGKst+
  gi|518651536|ref|YP_008141056.1| 22 KGIDLTINSGEIHALMGPNGAGKSTL 47
                                      55777778999**************7 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.31      29      49 ..      27      47 ..       5      91 .. 0.88
   2 ?   -2.3   0.0       1.9   2.8e+03     143     156 ..     165     178 ..     150     208 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
                            AAA_25 29 llpagelallaGapgtGKttl 49
                                       +  ge+++l+G+ g+GK+tl
  gi|518651536|ref|YP_008141056.1| 27 TINSGEIHALMGPNGAGKSTL 47
                                      68899***************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                            AAA_25 143 vrlvviDplsralg 156
                                       ++ v++D +++ l+
  gi|518651536|ref|YP_008141056.1| 165 PKIVILDEIDSGLD 178
                                       55566665554433 PP

>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.1      0.17   2.6e+02       3      14 ..      36      47 ..      34      50 .. 0.88
   2 ?    8.3   0.0    0.0015       2.2      79     125 ..     166     210 ..     153     229 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.17
                                      EE-STTSSHHHH CS
                            MutS_V  3 itGpnmaGksty 14
                                      + Gpn aGkst+
  gi|518651536|ref|YP_008141056.1| 36 LMGPNGAGKSTL 47
                                      67********95 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0015
                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGG CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltk 125
                                        +vilDE+  G   +d l +  a ++ +++ +k   l+ tHy+ + k
  gi|518651536|ref|YP_008141056.1| 166 KIVILDEIDSGLD-VDALKLVSAEIKKMHD-QKVGFLIITHYQRILK 210
                                       68********986.79************99.68889999***98765 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1    0.0017       2.5      21      39 ..      36      54 ..      27      91 .. 0.78
   2 ?    3.6   0.7     0.014        21     524     577 ..     162     212 ..     156     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0017
                            AAA_13 21 iYGwNGaGKTtLSrllrsl 39
                                      + G NGaGK+tL ++l   
  gi|518651536|ref|YP_008141056.1| 36 LMGPNGAGKSTLGEVLIGH 54
                                      569*********9998764 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkev 577
                                       i k kiv++D   S LD ++l +v+  ik+     ++   ++i TH    +k +
  gi|518651536|ref|YP_008141056.1| 162 ILKPKIVILDEIDSGLDVDALKLVSAEIKKMH---DQKVGFLIITHYQRILKDI 212
                                       5799******999*****************98...5555677889988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1719.70
//
Query:       gi|518651537|ref|YP_008141057.1|  [L=241]
Description: hypothetical protein FACI_IFERC00001G0176 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-05   24.3   0.1    4.2e-05   23.4   0.1    1.5  1  PadR         Transcriptional regulator PadR-like family
    0.00013   21.7   1.6    0.00027   20.6   1.5    1.6  1  ArsR         ArsR transcriptional regulator
    0.00063   19.8   0.1      0.025   14.7   0.0    2.4  2  HTH_9        RNA polymerase III subunit RPC82 helix-turn-heli
     0.0011   18.8   0.2      0.003   17.4   0.2    1.8  1  HTH_5        Bacterial regulatory protein, arsR family
     0.0014   18.5   1.3     0.0024   17.7   0.3    1.9  2  DUF3116      Protein of unknown function (DUF3116)
     0.0014   17.8   2.1     0.0019   17.4   2.1    1.1  1  Effector_1   Effector from type III secretion system
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.047   13.5   0.0    2.1  2  HTH_10       HTH DNA binding domain
      0.012   15.5   0.6      0.021   14.7   0.2    1.7  1  TFIIE_alpha  TFIIE alpha subunit
      0.018   15.0   0.2      0.039   13.9   0.2    1.7  1  MetOD1       Metanogen output domain 1
      0.022   15.0   0.1      0.057   13.6   0.1    1.7  1  HTH_34       Winged helix DNA-binding domain
      0.027   14.3   0.0      0.059   13.2   0.0    1.6  1  HxlR         HxlR-like helix-turn-helix
      0.038   14.3   0.4      0.089   13.1   0.1    1.7  2  DUF2513      Hypothetical protein (DUF2513)
      0.093   12.3   0.0       0.16   11.5   0.0    1.4  1  SMC_ScpB     Segregation and condensation complex subunit Scp
        0.1   12.5   0.1        0.3   11.0   0.1    1.8  1  TrmB         Sugar-specific transcriptional regulator TrmB


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 !   23.4   0.1   3.3e-08   4.2e-05      26      71 ..      55     100 ..      46     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.3e-08
                                       -CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCH CS
                              PadR  26 llelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrr 71 
                                       ++ +++  +      Le ++lv+s+ +++++g+p+kyY+lT++G +
  gi|518651537|ref|YP_008141057.1|  55 IMGINKNAVQEHIYYLETHNLVSSYFVRAKTGRPKKYYKLTKNGMQ 100
                                       555666666677788*****************************87 PP

>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.5   2.1e-07   0.00027      18     134 ..      34     158 ..      23     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 2.1e-07
                              ArsR  18 tkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhtsYskvq......anf 85 
                                       +k++++++l+ + +t ++l+e +g +   v+e + +L+  +l+ s    ++    p+k Y+ + + +q      +nf
  gi|518651537|ref|YP_008141057.1|  34 SKSTILSSLLYDDKTLDQLSEIMGINknaVQEHIYYLETHNLVSSYFVRAK-TGRPKKYYKLTKNGMQifpkqyINF 109
                                       67899999**************99766689******************999.789******8877666222222577 PP

                              ArsR  86 qcs.ledlsdiievafmsdeeleelvekiekeveegntsisdlsrklgls 134
                                       +   l+++   +  +   ++ l +++e+i+kev+++n+s+++l r+ +l+
  gi|518651537|ref|YP_008141057.1| 110 SSMlLKEVERELGTV-GLNKILMRMAEDIIKEVTSDNMSLTSLNREEKLE 158
                                       543156666665544.446779999******************9987766 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.9e-05     0.025       2      58 ..      22      77 ..      21      81 .. 0.93
   2 ?    2.8   0.0       0.1   1.3e+02      50      59 ..     184     193 ..     166     196 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
                                      HHHHHHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                             HTH_9  2 lcteiieehFGevvakVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                      + + i+ +++G   +++ + Ll +  +tl++l++  +++++ V    + L  h+lV+
  gi|518651537|ref|YP_008141057.1| 22 CMEVIVNDYLGNSKSTILSSLL-YDDKTLDQLSEIMGINKNAVQEHIYYLETHNLVS 77
                                      6689*****************9.5689****************************95 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.1
                                       HHHHTTSEEE CS
                             HTH_9  50 vLiqhrlVqy 59 
                                         i+h++++y
  gi|518651537|ref|YP_008141057.1| 184 KIIRHNCIFY 193
                                       579******9 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   2.4e-06     0.003       4      47 .]      35      78 ..      33      78 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.4e-06
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      ++ IL++L    ++  +l+e++g+++ +v +H   L+  +LV++
  gi|518651537|ref|YP_008141057.1| 35 KSTILSSLLYDDKTLDQLSEIMGINKNAVQEHIYYLETHNLVSS 78
                                      567**************************************986 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   1.8e-06    0.0024      35      79 ..      54     101 ..      27     106 .. 0.79
   2 ?   -1.8   0.0       2.3   2.9e+03      12      30 ..     137     155 ..     129     165 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.8e-06
                           DUF3116  35 svkkltkneLLytvYWLElkg....yilRkeekannkkrYelTekGell 79 
                                       + + ++kn +   +Y LE+++    y +R +     kk+Y+lT++G ++
  gi|518651537|ref|YP_008141057.1|  54 EIMGINKNAVQEHIYYLETHNlvssYFVRAKTG-RPKKYYKLTKNGMQI 101
                                       345679************9965555889*9997.99**********765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.3
                           DUF3116  12 vLelvkdpnftiknlqlee 30 
                                       +++ v + n+ +++l+ ee
  gi|518651537|ref|YP_008141057.1| 137 IIKEVTSDNMSLTSLNREE 155
                                       5566666677777776655 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 !   17.4   2.1   1.5e-06    0.0019     116     247 ..      24     170 ..      10     178 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                        Effector_1 116 sllldkylPkqeefLeklaselsfsnkaasllndileliksFvnaavyy....nl.asYlgq............skm 175
                                        ++++ yl + +    ++ s l + +k  + l++i+ + k+ v   +yy    nl +sY +             +k 
  gi|518651537|ref|YP_008141057.1|  24 EVIVNDYLGNSK---STILSSLLYDDKTLDQLSEIMGINKNAVQEHIYYlethNLvSSYFVRaktgrpkkyyklTKN 97 
                                       677777777766...478899***************************976665547888889***********99* PP

                        Effector_1 176 geneFagsieeakdklakEkeqvrkdlksaekAkekvkellkrveadk.kltteqkaklkdelngYadeleai 247
                                       g ++F++++ ++   l kE e+    +   +   ++ ++++k+v+ d+ +lt+  + +  +++ +Y++ l+ +
  gi|518651537|ref|YP_008141057.1|  98 GMQIFPKQYINFSSMLLKEVERELGTVGLNKILMRMAEDIIKEVTSDNmSLTSLNREEKLEKIGEYVNILNKL 170
                                       ***********************************************99*******************99975 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.4   6.9e+03      32      43 ..      30      41 ..      29      42 .. 0.73
   2 ?   13.5   0.0   3.7e-05     0.047      24      44 ..      47      67 ..      46      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.4
                            HTH_10 32 elGIskstlseh 43
                                       lG skst++  
  gi|518651537|ref|YP_008141057.1| 30 YLGNSKSTILSS 41
                                      578899998765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.7e-05
                            HTH_10 24 vtlkeLAkelGIskstlsehL 44
                                       tl++L++++GI k++++eh+
  gi|518651537|ref|YP_008141057.1| 47 KTLDQLSEIMGINKNAVQEHI 67
                                      689*****************8 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.2   1.7e-05     0.021       4      78 ..      24      96 ..      21     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                                      HHHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEEC CS
                       TFIIE_alpha  4 kevvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywriny 78
                                      + +v    g++   +l +Ll + ++  ++l++ ++i++n + + ++ L    lv+    r  +++  k y+++++
  gi|518651537|ref|YP_008141057.1| 24 EVIVNDYLGNSKSTILSSLLYDDKT-LDQLSEIMGINKNAVQEHIYYLETHNLVSSYFVRA-KTGRPKKYYKLTK 96
                                      5577888999**********77765.579*************************9766554.4566666666665 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.1e-05     0.039      34     114 ..     126     202 ..     110     240 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.1e-05
                            MetOD1  34 likqfadrveknlkpkfkeelkeaekeeedaekvlkayiewlnqlfanfgiktekkedeknvlleftnCpWgeeark 110
                                       l k ++++ e+++k+  ++++   + ++e++ + + +y+++ln+l+  +++k+e   d + v +  +nC   e a++
  gi|518651537|ref|YP_008141057.1| 126 LNKILMRMAEDIIKEVTSDNMSLTSLNREEKLEKIGEYVNILNKLG--YYAKME--VDHDTVKIIRHNCIFYELAKN 198
                                       567889999************9555555544455557********7..788888..55666778899******9998 PP

                            MetOD1 111 nPif 114
                                       n+ +
  gi|518651537|ref|YP_008141057.1| 199 NKDM 202
                                       8743 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   4.5e-05     0.057       5      72 ..      38     105 ..      36     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.5e-05
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYie.vdkefkgkkprtllriTpeGreafkky 72 
                                       +ls+L+ +d+ +  +l+e +++++ +   h+  Le+ + ++ +    k ++p+  +++T++G + f k 
  gi|518651537|ref|YP_008141057.1|  38 ILSSLLYDDK-TLDQLSEIMGINKNAVQEHIYYLETHNLVSsYFVRAKTGRPKKYYKLTKNGMQIFPKQ 105
                                       6667766665.6799*************************82456677888************999765 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.059       8      74 ..      36     103 ..      32     119 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                                       HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE..SSSS-EEEEEE-TCGGGGHH CS
                              HxlR   8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdglierevy..pevPpkveYsltekGrslep 74 
                                         il +ll   k   +l++++ +i ++   +++  Le+++l++   +  ++  pk  Y+lt++G ++ p
  gi|518651537|ref|YP_008141057.1|  36 STILSSLLYDDKTLDQLSEIM-GINKNAVQEHIYYLETHNLVSSYFVraKTGRPKKYYKLTKNGMQIFP 103
                                       6799999999********999.9********************97661145568999********9988 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     7e-05     0.089      27      80 ..      48     100 ..      33     103 .. 0.84
   2 ?   -2.0   0.0       3.5   4.5e+03      41      51 ..     159     169 ..     130     200 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7e-05
                           DUF2513  27 eeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrLtweGhd 80 
                                       + ++ls+i g +k+ + +h+++l+ ++L++++ ++ak++    ++++Lt +G++
  gi|518651537|ref|YP_008141057.1|  48 TLDQLSEIMGINKNAVQEHIYYLETHNLVSSYFVRAKTG-RPKKYYKLTKNGMQ 100
                                       234455*******************************99.77889999999976 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.5
                           DUF2513  41 eiiyhlkllae 51 
                                       +i + + +l +
  gi|518651537|ref|YP_008141057.1| 159 KIGEYVNILNK 169
                                       33333333333 PP

>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00013      0.16      73     144 ..      23      97 ..       5     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                          SMC_ScpB  73 vkekkktrLsqaaletLaiIaykqpvtr..aeieeiRGvnsdsvvrtLlerglieekgrkeepgrpil.YgtTek 144
                                       ++   +  L +++  +L+   y ++     +ei  i   ++++++  L   +l+++   + ++grp   Y++T++
  gi|518651537|ref|YP_008141057.1|  23 MEVIVNDYLGNSKSTILSSLLYDDKTLDqlSEIMGINKNAVQEHIYYLETHNLVSSYFVRAKTGRPKKyYKLTKN 97 
                                       444445578888889999999988765312456666666699************************985778876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   0.00024       0.3      17      63 ..      42      92 ..      35      96 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSE.....EEESSTTTEEE CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYevLrsLedkGlV.....erekgrpklYr 63
                                      Ll ++ +t d+++e+ g+ ++ v+e +  Le   lV     + + grpk+Y 
  gi|518651537|ref|YP_008141057.1| 42 LL-YDDKTLDQLSEIMGINKNAVQEHIYYLETHNLVssyfvRAKTGRPKKYY 92
                                      44.7889******************998777777661111155556688774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1684.81
//
Query:       gi|518651538|ref|YP_008141058.1|  [L=409]
Description: hypothetical protein FACI_IFERC00001G0177 [Ferroplasma acidarmanus fer1]
Scores for complete 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-94  315.3   0.0    5.8e-94  314.9   0.0    1.1  1  Nre_N     Archaeal Nre, N-terminal
    2.4e-33  114.3   0.0    4.4e-33  113.5   0.0    1.4  1  Nre_C     Archaeal Nre, C-terminal
  ------ inclusion threshold ------
       0.14   11.6   0.0       0.24   10.8   0.0    1.3  1  PRF       Plethodontid receptivity factor PRF


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 !  314.9   0.0   9.6e-98   5.8e-94       1     270 []      22     289 ..      22     289 .. 0.96

  Alignments for each domain:
  == domain 1  score: 314.9 bits;  conditional E-value: 9.6e-98
                             Nre_N   1 LcglkkcpileklravekakkkisskeleGsspPsvfVGrygYPkVsvgplvppvegdasvldspekwlglsledii 77 
                                       Lcgl++cp+   +++v+k+  + ++++++GsspPs+fVGrygYPk++++p++pp +gd++++++++kwl+++l++++
  gi|518651538|ref|YP_008141058.1|  22 LCGLSYCPVSI-VDRVKKVY-TFNGNSISGSSPPSLFVGRYGYPKINIYPSTPPFSGDTAYMEDESKWLSTDLNEFL 96 
                                       8*******753.33334433.345899************************************************** PP

                             Nre_N  78 klrlslvrgekkvkvkkak.edklleeiqelalsekpvdvevelekkpkaklkfdevlaPvGpsaeleklkvaenpk 153
                                       + rlsl+rg  k++ +ka+ +d  l+eiq ++ls++pvdve+++ek+ k ++ +de ++P+Gps++l+++k  +n +
  gi|518651538|ref|YP_008141058.1|  97 SSRLSLLRGGIKIEATKASdPDYRLQEIQISSLSSRPVDVEMTVEKSFKDNVVLDENITPMGPSSPLKSIKF-GNYH 172
                                       ***************9999889999***********************************************.**** PP

                             Nre_N 154 vprkveklveDtdlkAeeavveLyrsgvdvykiqrlLSvGlLGekkkrrlVPTrWsITAvddivgkelkkeikdlpe 230
                                       +++++ek+++D+dlkA +++++Ly++g+ ++ i+++LS G LG+ kkrr+VPTrWsITA+d+ ++++l++eikd+ e
  gi|518651538|ref|YP_008141058.1| 173 IDNRIEKIYYDKDLKAGSGILKLYERGMGINGISKALSSGSLGTGKKRRIVPTRWSITATDKSISDNLVEEIKDYRE 249
                                       ***************************************************************************** PP

                             Nre_N 231 idevevfsgeylgNrflviLaPgkwsfelvEawapgslwn 270
                                       ide+ev+ +e+ gN f++iLaPg+w+fe+ E w+pgs+wn
  gi|518651538|ref|YP_008141058.1| 250 IDEFEVYIRETSGNLFIAILAPGQWMFEWGESWFPGSTWN 289
                                       ***************************************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 !  113.5   0.0   7.4e-37   4.4e-33       1     107 [.     302     406 ..     302     409 .] 0.95

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 7.4e-37
                             Nre_C   1 egyegrkeyseiaGaYyaarlavleaLekikrqakvivlreitpeYwaPvGvWqvReavrkalekkpkefesleeal 77 
                                       egy grk+y+ i+G+Yy++rlav+e+ ++ikr+ +++++rei+p++++PvGvW vRe+vr+ l++kp++f+++++a+
  gi|518651538|ref|YP_008141058.1| 302 EGYYGRKTYPGIGGCYYSSRLAVAEKYREIKRTGSAMLWREIYPGFNIPVGVWYVRENVRELLKGKPEKFDNIQDAI 378
                                       7899************************************************************************* PP

                             Nre_C  78 eevseklklplkkllkkskllkelkkqktL 107
                                       ++v + +k+++k++++ks+ lk l   ++L
  gi|518651538|ref|YP_008141058.1| 379 KYVGKFTKVDIKAWKAKSNNLKYLV--SSL 406
                                       *******************999884..445 PP

>> PRF  Plethodontid receptivity factor PRF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.9e-05      0.24      48      95 ..      95     142 ..      71     156 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.9e-05
                               PRF  48 iqssadsllptylsfqgaplsdpdyqlphikvvnlptaamdydtfikq 95 
                                         ss  sll   + ++ +  sdpdy+l  i++  l +  +d +  +++
  gi|518651538|ref|YP_008141058.1|  95 FLSSRLSLLRGGIKIEATKASDPDYRLQEIQISSLSSRPVDVEMTVEK 142
                                       45889999****************************999998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2901.79
//
Query:       gi|518651539|ref|YP_008141059.1|  [L=275]
Description: radical SAM family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.9e-12   45.9   0.0    1.2e-11   45.3   0.0    1.3  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.057   13.1  10.2        1.8    8.3   0.1    2.8  3  DUF1848      Domain of unknown function (DUF1848)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   1.4e-15   1.2e-11       2     165 ..      29     201 ..      28     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 1.4e-15
                                       EEESEESS--TTTSCCTT........HHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet........vrregrgrslsveeileevkelk.aekgvkevilgggepllypdfveller 69 
                                       +++ gC ++C++C+   +         ++ + +r   +e +++e++ +k    g+ +++   +   + +++v ++  
  gi|518651539|ref|YP_008141059.1|  29 NPYLGCFHGCRYCYAIDMspaeaannWGKVVFVRKNIIELLEHEARTYKkGIVGISTITDPYQSIEMKYRIVPEAIG 105
                                       6788************99***97766555666666666677777777753333344444446666666777766666 PP

                                       HHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  70 laklavpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr 144
                                       +  +  +g+ +t+ t  +l+  + ++ l ++     v +++ +++ + v k+++   +++ ++l+al+kl+e gi+ 
  gi|518651539|ref|YP_008141059.1| 106 ILVK--NGFYVTIQTKSPLI-LKDIKILEKYKkNIDVGITVTTINRK-VSKILEpYAPDPFKRLNALKKLAETGIRT 178
                                       6666..9*************.**************************.9999999899999***************9 PP

                                       EEEEEEEBTTTSH..HHHHHHHH CS
                                       xxxxxxxxxxxxx..xxxxxxxx RF
                       Radical_SAM 145 vvdrivglpGend..eeleelle 165
                                         +  ++  G+nd  ++++ ++e
  gi|518651539|ref|YP_008141059.1| 179 WLYLGPIANGVNDniDDIDRIIE 201
                                       88888888888885556665555 PP

>> DUF1848  Domain of unknown function (DUF1848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   4.8   0.00072       6.5     253     265 .]      31      43 ..      28      43 .. 0.91
   2 ?    1.0   0.0     0.032   2.9e+02      50      95 ..      57     100 ..      50     110 .. 0.76
   3 ?    8.3   0.1    0.0002       1.8      28     108 ..      85     174 ..      76     182 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00072
                           DUF1848 253 yntClhgCvYCYA 265
                                       y  C hgC+YCYA
  gi|518651539|ref|YP_008141059.1|  31 YLGCFHGCRYCYA 43 
                                       778*********9 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.032
                           DUF1848  50 livFwtknpkpllkkleelkergiklyfqfTltdyekelepnvpsl 95 
                                        +vF+ kn  +ll++  +  +    ++   T+td  +++e +   +
  gi|518651539|ref|YP_008141059.1|  57 KVVFVRKNIIELLEHEARTYK--KGIVGISTITDPYQSIEMKYRIV 100
                                       589**********98887765..56677789999888888776555 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0002
                           DUF1848  28 lvrnPfnkkqvsrvslspedvdliv.......FwtknpkpllkkleelkergiklyfqfTlt...dyeke.lepnvp 93 
                                       ++++P+++ + +++++ pe + ++v         tk p  +lk ++ l++ + ++ + +T+t      ++ lep  p
  gi|518651539|ref|YP_008141059.1|  85 TITDPYQSIE-MKYRIVPEAIGILVkngfyvtIQTKSPL-ILKDIKILEKYKKNIDVGITVTtinRKVSKiLEPYAP 159
                                       5556665554.4455555555554433321113455554.67778888777666665555551114444469***** PP

                           DUF1848  94 sleerietfkelsek 108
                                       +  +r++++k+l+e+
  gi|518651539|ref|YP_008141059.1| 160 DPFKRLNALKKLAET 174
                                       ************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1973.49
//
Query:       gi|518651540|ref|YP_008141060.1|  [L=388]
Description: hypothetical protein FACI_IFERC00001G0179 [Ferroplasma acidarmanus fer1]
Scores for complete 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-118  395.0   0.0   3.1e-118  394.8   0.0    1.0  1  FMN_dh        FMN-dependent dehydrogenase
    7.9e-05   22.1   0.1      0.037   13.3   0.0    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    0.00015   20.9   0.3    0.00048   19.2   0.3    1.8  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    0.00046   19.7   0.2       0.84    9.1   0.0    2.7  3  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.076   12.4   0.0    2.3  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.03   13.5   0.0       0.11   11.6   0.0    1.9  2  IGPS          Indole-3-glycerol phosphate synthase
      0.038   12.8   0.3       0.49    9.2   0.0    2.6  3  Trp_syntA     Tryptophan synthase alpha chain
      0.066   12.4   0.0        4.7    6.3   0.0    2.3  2  DUF561        Protein of unknown function (DUF561)
      0.081   12.3   0.3       0.44    9.9   0.5    2.1  2  NMO           Nitronate monooxygenase
       0.13   11.4   0.1       0.46    9.6   0.1    1.7  2  Glu_synthase  Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.8   0.0  1.7e-121  3.1e-118       1     346 [.      33     382 ..      33     384 .. 0.92

  Alignments for each domain:
  == domain 1  score: 394.8 bits;  conditional E-value: 1.7e-121
                                       HHCCS-HHHHHHHH--STTSHHHHHHHHGGGGEEE---SSSS-SS-B--EEETTEEESSSEEE--BSTGGGTSTTHH CS
                            FMN_dh   1 ArkrlpkkafayvaggagdevtlrenraaferirlrprvlrdvskvdlsttllGqklslPvliaPvglaklahpdge 77 
                                       Ar  l+   + y++g+ag+e t+ en +af+r+r+rpr+l+dv++++ s+tl+G+k ++P++iaP+g+++++h+d+e
  gi|518651540|ref|YP_008141060.1|  33 ARMALQDGPWGYLEGAAGSEDTMIENIKAFSRYRIRPRYLHDVENRNQSITLFGRKQDSPFIIAPIGVQSIIHKDAE 109
                                       677788999******************************************************************** PP

                                       HHHHHHHHHHTS-EEEETT-SS-HHHHHHH.HTT-EEEEEE-CSSHHHHHHHHHHHHHCTESEEEEESSTSS---BH CS
                            FMN_dh  78 lalaraaakagipfvlstvastsleevaaa.aegplwfqlyvpkdrelteellkraeaagykalvltvDtpvlgkRe 153
                                        a a aaa++g+p++lstv+sts+e++aa+  e+++wfqly+ kd+++++++++rae+agyk++v+tvDt++lg+Re
  gi|518651540|ref|YP_008141060.1| 110 YASAGAAASLGMPYILSTVSSTSIEDIAAKfPESEKWFQLYPGKDENVMKSMVNRAEKAGYKVIVVTVDTTMLGWRE 186
                                       *****************************634569****************************************** PP

                                       HHHHCT-.-BSTT-T.G.TTGGGSTSGSCCTTH.....THHHH..HHCCCHB-TC--HHHHHHHHHHHSSEEEEEEE CS
                            FMN_dh 154 rdlrngf.slppklklrnllqelakpewaaeal...kkasaaa..efvgkqldpsltwddikwlreqtklplvvKGv 224
                                       +d++n +  + ++ +   +++  ++pe  +  +   +++++aa  ef+  +++ps+twd  +++r+ tklp+++KG+
  gi|518651540|ref|YP_008141060.1| 187 QDIKNAYlPFLQGEG---IANFITDPEFLKMLEtspENNMQAAieEFLMVYVNPSFTWDGFRKIRSWTKLPILIKGI 260
                                       *****5534445545...44455555444444433334444445799****************************** PP

                                       -SHHHHHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 225 ltaedakraveaGvdgivvSNHGGRqldgapatidvLpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGR 301
                                        ++ed++ av++G+dg+++SNHGGRq+dg+++++++L ei  + + ++++l+D+Gir+ +D++kAlalGA++vl+GR
  gi|518651540|ref|YP_008141060.1| 261 SSEEDVHTAVKYGADGVIISNHGGRQVDGSISSLEALDEITGENKPEFTILFDSGIRHAADAMKALALGASGVLIGR 337
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHHCGGE CS
                            FMN_dh 302 pflyglaagGeeGvervleilraelertmallGvksvaeldrsll 346
                                       p++y++a++G++G+er+l+ lrae++ +mal G +s+++l+r+ +
  gi|518651540|ref|YP_008141060.1| 338 PYCYAMAVAGQRGIERYLNQLRAEFDLQMALSGYSSISQLGRHTI 382
                                       *****************************************9987 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0028         5     169     204 ..     246     280 ..     240     287 .. 0.88
   2 !   13.3   0.0   2.1e-05     0.037     175     204 ..     307     336 ..     287     349 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0028
                                       HHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEES CS
                              ThiG 169 iiieeakvPvivDAGigspsdaaqamelGadavlln 204
                                        i++ +k+P+++  Gi s +d+ +a+++Gad+v++ 
  gi|518651540|ref|YP_008141060.1| 246 KIRSWTKLPILIK-GISSEEDVHTAVKYGADGVIIS 280
                                       5777789999995.*******************985 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.1e-05
                                       SS-BEEES---SHHHHHHHHHTT-SEEEES CS
                              ThiG 175 kvPvivDAGigspsdaaqamelGadavlln 204
                                       +  ++ D Gi+++ da++a+ lGa++vl+ 
  gi|518651540|ref|YP_008141060.1| 307 EFTILFDSGIRHAADAMKALALGASGVLIG 336
                                       67899***********************96 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   2.7e-07   0.00048     190     237 ..     291     337 ..     241     351 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.7e-07
                                       --HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 190 vpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGs 237
                                       ++ l A+ e++   +k + +++ D Gi++  d +kAla+Ga+ v++G+
  gi|518651540|ref|YP_008141060.1| 291 ISSLEALDEITG-ENKPEFTILFDSGIRHAADAMKALALGASGVLIGR 337
                                       455566555544.4556899***************************7 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.9   3.5e+03     116     130 ..     165     179 ..     155     190 .. 0.63
   2 !    7.7   0.0    0.0012       2.2     185     219 ..     246     279 ..     240     288 .. 0.56
   3 !    9.1   0.0   0.00047      0.84      63     103 ..     295     337 ..     286     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.9
                                       HHHHCGGGEEEEEEE CS
                      His_biosynth 116 aekfgsqkivvaiDa 130
                                       aek g + ivv +D+
  gi|518651540|ref|YP_008141060.1| 165 AEKAGYKVIVVTVDT 179
                                       455666677777775 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0012
                                       HHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEE CS
                      His_biosynth 185 elaeavkipviasGGvgsledlkelksegvdaviv 219
                                       ++++++k+p+++  G++s ed++++++ g+d+vi+
  gi|518651540|ref|YP_008141060.1| 246 KIRSWTKLPILIK-GISSEEDVHTAVKYGADGVII 279
                                       4444445554442.455555555555555555554 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00047
                                       HHHHHHHHH-S..SEEEEESSSSSHHHHHHHHHCT-SEEEESH CS
                      His_biosynth  63 dlveeiaeevf..ipvqvGGGIrsledveelleagadkviigt 103
                                       +++ ei+ e +   ++  ++GIr+  d+ ++l +ga+ v ig 
  gi|518651540|ref|YP_008141060.1| 295 EALDEITGENKpeFTILFDSGIRHAADAMKALALGASGVLIGR 337
                                       555555555443377889*********************9985 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.83   1.5e+03      32      48 ..     158     174 ..     132     194 .. 0.76
   2 ?   12.4   0.0   4.3e-05     0.076     116     170 ..     229     282 ..     204     283 .. 0.81
   3 ?   -2.6   0.0       1.8   3.2e+03     148     166 ..     316     334 ..     305     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.83
                                       HHHHHHHHHHTT-EEEE CS
                      G3P_antiterm  32 lkeiveklkkagkkvfv 48 
                                       +k++v++++kag kv+v
  gi|518651540|ref|YP_008141060.1| 158 MKSMVNRAEKAGYKVIV 174
                                       67788888888866665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.3e-05
                                       T-SEEEEESGGGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE--H CS
                      G3P_antiterm 116 kpdavevlPglvpkvikeikkelkipiiaGGLietkedveealkaGaiavstsnk 170
                                       +  +v v P++  +  ++i++ +k+pi+  G i+++edv++a+k Ga++v  sn+
  gi|518651540|ref|YP_008141060.1| 229 EFLMVYVNPSFTWDGFRKIRSWTKLPILIKG-ISSEEDVHTAVKYGADGVIISNH 282
                                       4456778999999999***************.899***************99985 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.8
                                       --SHHHHHHHCTT.SSEEE CS
                      G3P_antiterm 148 ietkedveealkaGaiavs 166
                                       i++  d ++al+ Ga++v 
  gi|518651540|ref|YP_008141060.1| 316 IRHAADAMKALALGASGVL 334
                                       6788999999999999986 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.032        57     101     136 ..     244     278 ..     240     281 .. 0.77
   2 ?   11.6   0.0   6.3e-05      0.11     165     239 ..     260     337 ..     249     345 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.032
                                       HHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEE CS
                              IGPS 101 LrevrqavslpvlrKdFiideyqieearalgadaiL 136
                                       +r++r+  +lp+l K  i +e  ++ a ++gad ++
  gi|518651540|ref|YP_008141060.1| 244 FRKIRSWTKLPILIKG-ISSEEDVHTAVKYGADGVI 278
                                       5778888888888887.5588888888888888776 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 6.3e-05
                                       ESSHHHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-...TTSEEEEESSS-SHHHHHHHCCTT-SEEEES CS
                              IGPS 165 vhdeeeleralklgakiiGvNnRnLktlevdlntteeLaklvp...kdvllvaeSGiktredveklkeegvnafLvG 238
                                       +++ee++++a+k ga+ + + n   ++ + ++   e L +       + ++   SGi++++d+ k  + g++++L+G
  gi|518651540|ref|YP_008141060.1| 260 ISSEEDVHTAVKYGADGVIISNHGGRQVDGSISSLEALDEITGenkPEFTILFDSGIRHAADAMKALALGASGVLIG 336
                                       789999**********9999998888887777666666665543326789999************************ PP

                                       H CS
                              IGPS 239 e 239
                                        
  gi|518651540|ref|YP_008141060.1| 337 R 337
                                       6 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.47   8.5e+02      70     102 ..     207     241 ..     200     245 .. 0.78
   2 ?    9.2   0.0   0.00027      0.49     191     226 ..     245     280 ..     240     301 .. 0.88
   3 ?    0.3   0.0      0.15   2.6e+02     205     227 ..     314     337 ..     283     359 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.47
                                       -HHHHHHHHHHHHHHCSSS-E..EEEE-CHHHCCC CS
                         Trp_syntA  70 tlekvlelveevrkkevevPi..vlltylnlvlsy 102
                                       t  ++l+++e+  ++++++ i  +l+ y+n+ +++
  gi|518651540|ref|YP_008141060.1| 207 TDPEFLKMLETSPENNMQAAIeeFLMVYVNPSFTW 241
                                       5567889999888888887776589*****98766 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00027
                                       HHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE- CS
                         Trp_syntA 191 erlkkltavPvavGFGistkeqvkqva.kvadGvivG 226
                                       +++++ t++P+++  Gis++e+v++++  +adGvi+ 
  gi|518651540|ref|YP_008141060.1| 245 RKIRSWTKLPILIK-GISSEEDVHTAVkYGADGVIIS 280
                                       789999*****995.*********99989******95 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.15
                                       SSS-SHHHHHHHH.TT-SEEEE-H CS
                         Trp_syntA 205 FGistkeqvkqva.kvadGvivGS 227
                                        Gi++++++ ++   +a+Gv++G 
  gi|518651540|ref|YP_008141060.1| 314 SGIRHAADAMKALaLGASGVLIGR 337
                                       488887776666559999999995 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0026       4.7      53      90 ..     244     282 ..     200     284 .. 0.78
   2 ?    3.4   0.0     0.021        37     185     215 ..     306     337 ..     284     359 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0026
                            DUF561  53 vkkvksvsniPiCvsaveakl.lleavkaGadlveiGnf 90 
                                        +k++s +++Pi + ++ +++ +  avk Gad v i n+
  gi|518651540|ref|YP_008141060.1| 244 FRKIRSWTKLPILIKGISSEEdVHTAVKYGADGVIISNH 282
                                       578999999999999998764377899999998888885 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                            DUF561 185 vslPvicasGlsdvtvpl.alslgasGiGigs 215
                                        +  ++  sG+ + +  + al+lgasG+ ig+
  gi|518651540|ref|YP_008141060.1| 306 PEFTILFDSGIRHAADAMkALALGASGVLIGR 337
                                       46778999***998877659********9986 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   2.7e+03      34      58 ..      39      63 ..      29      69 .. 0.84
   2 ?    9.9   0.5   0.00025      0.44     138     223 ..     255     337 ..     246     373 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                               NMO 34 aGgLGvlasgyltaDrlakeirkvk 58
                                      +G  G l ++ ++ D + ++i++  
  gi|518651540|ref|YP_008141060.1| 39 DGPWGYLEGAAGSEDTMIENIKAFS 63
                                      688899999************9865 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
                               NMO 138 vliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavd..iPviAaGGiidrrgvaaaL 212
                                       +li  iss +++  + + GaD +i+  ++ GG q + ++     ++ ++++    +    ++   Gi  + +   aL
  gi|518651540|ref|YP_008141060.1| 255 ILIKGISSEEDVHTAVKYGADGVII--SNHGGRQVDGSIS---SLEALDEITGENKpeFTILFDSGIRHAADAMKAL 326
                                       678899999999**********999..5889999966764...5555555554433459999999************ PP

                               NMO 213 alGAsgvqigt 223
                                       alGAsgv ig 
  gi|518651540|ref|YP_008141060.1| 327 ALGASGVLIGR 337
                                       *******9996 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 ?   -1.1   0.0      0.44   7.9e+02     282     303 ..     259     280 ..     246     284 .. 0.80
   2 ?    9.6   0.1   0.00026      0.46     274     310 ..     307     343 ..     294     350 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.44
                                       S--SHHHHHHHHHHT-SEEE-S CS
                      Glu_synthase 282 glktgadvvkalalGAdavgig 303
                                       g+ + +dv  a+  GAd v i+
  gi|518651540|ref|YP_008141060.1| 259 GISSEEDVHTAVKYGADGVIIS 280
                                       5788899999999999999886 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00026
                                       G-EEEEESS--SHHHHHHHHHHT-SEEE-SHHHHHHT CS
                      Glu_synthase 274 rvsliadGglktgadvvkalalGAdavgigtaalial 310
                                       + ++  d g++ +ad +kalalGA  v ig+    a+
  gi|518651540|ref|YP_008141060.1| 307 EFTILFDSGIRHAADAMKALALGASGVLIGRPYCYAM 343
                                       66788999**********************9776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2461.43
//
Query:       gi|518651541|ref|YP_008141061.1|  [L=403]
Description: hypothetical protein FACI_IFERC00001G0180 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-18   64.7   0.0      2e-17   63.5   0.0    1.6  2  Glycos_transf_2  Glycosyl transferase family 2
    8.5e-17   61.8   0.0      1e-16   61.5   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    6.8e-10   38.7   0.0      1e-08   34.9   0.0    2.1  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00033   20.6   0.2    0.00058   19.8   0.2    1.5  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    0.00074   18.2   2.3      0.002   16.9   1.5    2.0  2  Chitin_synth_2   Chitin synthase
      0.001   18.6   0.0     0.0017   17.9   0.0    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.021   13.5   0.5        2.4    6.7   0.0    2.1  2  Osmo_MPGsynth    Mannosyl-3-phosphoglycerate synthase (osmo_M
       0.15   12.3   0.0       0.29   11.3   0.0    1.5  1  Auxin_inducible  Auxin responsive protein


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 !   63.5   0.0   9.1e-21     2e-17       1     165 [.      39     192 ..      39     195 .. 0.87
   2 ?   -2.9   0.0       2.3   5.3e+03      52      85 ..     233     265 ..     219     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 9.1e-21
                                       EEEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       ++v+p+yNe  +  ++++ sl+ q      + ivv D+S +  + i e+      + r+i ++++ Gk +al +g++
  gi|518651541|ref|YP_008141061.1|  39 TIVMPVYNEdVEIFRQAIVSLALQ----GSKFIVVGDSSLEPYKTITEQN-----GGRFIYLSQRGGKKNALVQGIK 106
                                       69**********************....***********77777777777.....78888888899*********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTT CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsf 153
                                       +++++y++f+D+D++++ d+l+ ++ ++ + g ++v +++  ++++t+     ++   +       +  s+ gn+ +
  gi|518651541|ref|YP_008141061.1| 107 HVSTKYVMFVDSDTIIPADTLKSMLSYFSN-GIAGVGVNIHIKNDGTNISYASEF--IERLTEMISKSMSRHGNVYV 180
                                       ******************************.999****99999999999988876..46666666667777778888 PP

                                       CSTCCCEEEEHH CS
                   Glycos_transf_2 154 eigsaallrrea 165
                                         g +a++  ++
  gi|518651541|ref|YP_008141061.1| 181 LDGRCAMYITDV 192
                                       888888887665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.3
                                       C-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEE CS
                   Glycos_transf_2  52 edprvrvirreenvGkagalnaglraatgdyilf 85 
                                       +d +++v + +++ G  + ln+ +r+++  + +f
  gi|518651541|ref|YP_008141061.1| 233 KDYDITVETEPQK-GTRKFLNQQIRWSRRGWYFF 265
                                       4557777777877.88888888888777665554 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 !   61.5   0.0   4.6e-20     1e-16      72     228 ..      94     258 ..      35     260 .. 0.89

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 4.6e-20
                   Glyco_tranf_2_3  72 stgksralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrf 148
                                       ++gk +al++++++v++++v +vD+Dt++  dtlk++l +f + +++ vg++ + +n+ t +s  +a ef er +++
  gi|518651541|ref|YP_008141061.1|  94 RGGKKNALVQGIKHVSTKYVMFVDSDTIIPADTLKSMLSYF-SNGIAGVGVNIHIKNDGTNIS--YASEFIERLTEM 167
                                       4699*************************************.*********************..777777777765 PP

                   Glyco_tranf_2_3 149 ..laarralgvltlnGsgslirrevlkele.........gldplflltdDyelglrlrragfrtayvpgaavrevfp 214
                                          +++r ++v  l G++ ++ ++v+k ++          ++++ +l+dD  l+  l ++++++   ++ +v+++  
  gi|518651541|ref|YP_008141061.1| 168 isKSMSRHGNVYVLDGRCAMYITDVVKPFMvsdeflnkkIFGKKVVLGDDMQLTSFLIKNKYKMIKDYDITVETEPQ 244
                                       1156779999*99*****************9*999998657779999****************************** PP

                   Glyco_tranf_2_3 215 sslkayikqrnRwv 228
                                       + + ++ +q  Rw+
  gi|518651541|ref|YP_008141061.1| 245 KGTRKFLNQQIRWS 258
                                       *************8 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 !   34.9   0.0   4.5e-12     1e-08      17     173 .]      96     259 ..      91     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 4.5e-12
                   Glyco_transf_21  17 pKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakg..laaaleaaflntlagvl 91 
                                        K n+l+q+++ + ++++++ Dsd+++++d+L+++l +++   +g+ + +++  d  +   a+++   + ++ ++ +
  gi|518651541|ref|YP_008141061.1|  96 GKKNALVQGIKHVSTKYVMFVDSDTIIPADTLKSMLSYFSNGIAGVGVNIHIKNDGTNisYASEFIERLTEMISKSM 172
                                       5999************************************9666666666666666643377777777777777777 PP

                   Glyco_transf_21  92 qaklsglgfavGksmalrreaLeaiGGfeal........adeLAeDyalgkllraaGlkvvlspapiaqtsvprrss 160
                                       ++  + +    G + ++ +++++      ++        +  L +D++l+  l ++ +k++   +  ++t+ p ++ 
  gi|518651541|ref|YP_008141061.1| 173 SR-HGNVYVLDGRCAMYITDVVKPFMVSDEFlnkkifgkKVVLGDDMQLTSFLIKNKYKMIKDYDITVETE-P-QKG 246
                                       77.677777777777777777776666666511111211557*********************99989888.5.357 PP

                   Glyco_transf_21 161 lrallaRqlrWar 173
                                        r++l++q+rW+r
  gi|518651541|ref|YP_008141061.1| 247 TRKFLNQQIRWSR 259
                                       799********97 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 !   19.8   0.2   2.6e-07   0.00058       1     195 [.     112     309 ..     112     352 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.6e-07
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaelaspevaivqgpvlvmnvanwleelaalffaedhgkdilvrealgr.vvpsvGsg 76 
                                       +++++D+Dt +p+d l+  ++ ++ + +a v  ++ + n ++ +   +a++f e+ + +i+ +++ ++ v  + G++
  gi|518651541|ref|YP_008141061.1| 112 YVMFVDSDTIIPADTLKSMLSYFS-NGIAGVGVNIHIKNDGTNI--SYASEFIERLTEMISKSMSRHGnVYVLDGRC 185
                                       799****************99996.69**********9776555..6888887777776666664444154555777 PP

                   Glyco_trans_2_3  77 aflrrsalq..evg.......gwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc 144
                                       a+   ++++   v+        +  +   +++D+ +   l ++ y+ +   +  v ++     r +l+Q  Rw +  
  gi|518651541|ref|YP_008141061.1| 186 AMYITDVVKpfMVSdeflnkkIFG-KKVVLGDDMQLTSFLIKNKYKMIKDYDITVETEPQKGTRKFLNQQIRWSRRG 261
                                       777777777662225555554332.457********99999999998865555667777779***********9985 PP

                   Glyco_trans_2_3 145 eleklil...............lvrllgylgsllwsalplhlallllfsllalalvlllllllaal 195
                                          + ++               +                + +++ +l +++ ++l+l+  ++ +++
  gi|518651541|ref|YP_008141061.1| 262 ---WYFFfknlsdgttknggkfY---------------AFEMFYIYLIPIIGFILFLFRGMFILRF 309
                                       ...22212333333333333331...............2333333333333333333333333333 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.24   5.3e+02      28      50 ..      39      61 ..      22      65 .. 0.78
   2 !   16.9   1.5   8.7e-07     0.002     194     418 ..     102     308 ..      95     352 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.24
                    Chitin_synth_2 28 iclvtaysegeeglrttldslas 50
                                       +++++y e+ e +r+++ sla 
  gi|518651541|ref|YP_008141061.1| 39 TIVMPVYNEDVEIFRQAIVSLAL 61
                                      356799************99985 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.7e-07
                    Chitin_synth_2 194 viGvspdfyeivlmvdadtkvapdsltrlvaalvkdpeilglcGetkiankkeswvtaiqvfeyyishhlskafesv 270
                                       v G++    ++v+ vd+dt + +d+l+ +++ +++   i g+  + +i n       a    e  ++   sk++ s 
  gi|518651541|ref|YP_008141061.1| 102 VQGIKHVSTKYVMFVDSDTIIPADTLKSMLSYFSN--GIAGVGVNIHIKNDGTNISYASEFIE-RLTEMISKSM-SR 174
                                       7789999999*********************9986..57788888888887765555544444.4566777776.67 PP

                    Chitin_synth_2 271 fGsvtclPGcfslyrikaakgadgkwvPilvspeiveeysenvvdtlhkknllllGedrylttlllktfpkrktvfv 347
                                        G v  l G  ++y         + ++P +vs+e +++        + kk  + lG+d  lt++l+k  +k+k++  
  gi|518651541|ref|YP_008141061.1| 175 HGNVYVLDGRCAMYIT-------DVVKPFMVSDEFLNKK------IFGKK--VVLGDDMQLTSFLIK--NKYKMIKD 234
                                       9*************52.......46889**999988763......34444..468**********99..58999999 PP

                    Chitin_synth_2 348 pqakcktvaPdtfkvllsqrrrwinstvhnllelvl...vrdlcGtfcfsmrfvvfieligtvvlPvaiaftly 418
                                       ++ +++t      + +l q+ rw     + +++ +     ++   ++ f m ++  i +ig ++     +f+l 
  gi|518651541|ref|YP_008141061.1| 235 YDITVETEPQKGTRKFLNQQIRWSRRGWYFFFKNLSdgtTKNGGKFYAFEMFYIYLIPIIGFILFLFRGMFILR 308
                                       999999998899999********988766665544312144555577899999999998888877666666654 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   7.5e-07    0.0017       1     104 [.      39     132 ..      39     145 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7.5e-07
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv..ylkdeddkayslaaarNr 75 
                                       ++v+p+++++ +   ++ +   a +     ++ivv d S e+     ++i ++n+    yl++      ++  a  +
  gi|518651541|ref|YP_008141061.1|  39 TIVMPVYNEDVE-IFRQAIVSLALQ---GSKFIVVGDSSLEP----YKTITEQNGGRfiYLSQR----GGKKNALVQ 103
                                       577888877766.445556666666...7899***9999999....899999997543388777....578888999 PP

                   Glyco_tranf_2_2  76 GaskaesdlvlFlDaDcfissDkfekilk 104
                                       G+++  + +v+F+D+D  i  D ++ +l+
  gi|518651541|ref|YP_008141061.1| 104 GIKHVSTKYVMFVDSDTIIPADTLKSMLS 132
                                       ***************************98 PP

>> Osmo_MPGsynth  Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1    0.0034       7.6      45      90 ..      29      76 ..      21      85 .. 0.75
   2 ?    6.7   0.0    0.0011       2.4     143     178 ..      94     126 ..      76     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0034
                     Osmo_MPGsynth 45 eleeve.sklaivvpiknEelkvlegvlsgiP.hdclvilvSnssree 90
                                      ++++v   + +iv+p+ nE+++++++ + ++  + +  i+v +ss e+
  gi|518651541|ref|YP_008141061.1| 29 TISNVNpDEATIVMPVYNEDVEIFRQAIVSLAlQGSKFIVVGDSSLEP 76
                                      556665245689*************99988863567899999988744 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0011
                     Osmo_MPGsynth 143 rnGKgEgmllgillakllgkkyvgFiDaDnyvpgav 178
                                       r GK  +++ gi   k +  kyv F+D+D ++p+  
  gi|518651541|ref|YP_008141061.1|  94 RGGKKNALVQGI---KHVSTKYVMFVDSDTIIPADT 126
                                       567777877776...67889************9854 PP

>> Auxin_inducible  Auxin responsive protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.29      20      56 ..     173     209 ..     129     212 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                   Auxin_inducible  20 ssssssvpekGhvvVyvgderrRFvvpleyLnhpvfr 56 
                                       s++ +  +  G +++y +d  + F+v+ e+Ln+++f 
  gi|518651541|ref|YP_008141061.1| 173 SRHGNVYVLDGRCAMYITDVVKPFMVSDEFLNKKIFG 209
                                       3444444459*************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2541.79
//
Query:       gi|518651542|ref|YP_008141062.1|  [L=111]
Description: hypothetical protein FACI_IFERC00001G0181 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-05   23.4   1.9    8.6e-05   22.2   1.9    1.7  1  DUF3188         Protein of unknown function (DUF3188)
    0.00021   21.4   6.2    0.00026   21.1   6.2    1.0  1  DUF4870         Domain of unknown function (DUF4870)
  ------ inclusion threshold ------
      0.042   13.6   3.1       0.12   12.1   3.1    1.7  1  TIC20           Chloroplast import apparatus Tic20-like
      0.044   14.0   5.6      0.057   13.6   5.6    1.2  1  DUF2304         Uncharacterized conserved protein (DUF2304)
      0.065   12.8   7.1      0.081   12.5   7.1    1.0  1  Virul_fac_BrkB  Virulence factor BrkB
       0.31   11.2   0.1       0.31   11.2   0.1    3.0  3  AA_permease_C   C-terminus of AA_permease
        1.2    8.8   7.3        1.7    8.3   7.3    1.3  1  DUF2512         Protein of unknown function (DUF2512)
        2.2    8.0  11.1        1.6    8.5   0.1    2.0  2  DUF1282         Protein of unknown function (DUF1282)
        6.1    6.8   7.8          2    8.4   2.6    2.0  2  RseC_MucC       Positive regulator of sigma(E), RseC/MucC
        7.7    6.8  14.1         19    5.5   3.3    3.1  3  Chordopox_A13L  Chordopoxvirus A13L protein


Domain annotation for each model (and alignments):
>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   1.9   4.8e-08   8.6e-05      10      43 ..      23      56 ..      16      58 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.8e-08
                           DUF3188 10 llillysqrqgsdrlqslPallvGlgLivsgavg 43
                                      l+ +ly++r ++ r qs+ a+l G+ Liv+++++
  gi|518651542|ref|YP_008141062.1| 23 LVYILYGSRDSKLRFQSIQAILLGICLIVASIIF 56
                                      56788**************************995 PP

>> DUF4870  Domain of unknown function (DUF4870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   6.2   1.4e-07   0.00026      16     105 ..      11     103 ..       6     106 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.4e-07
                           DUF4870  16 lliplgniilPlviwllkkdksefvdeqgkealNFqislliysiilivls.llvligf.ll.lllllllllnlvlvi 89 
                                       +++ l+ +i  l++++l+  ++  ++ q+ +a+   i l+++sii++++  +++++g  ++  +l l+l+l + + i
  gi|518651542|ref|YP_008141062.1|  11 IVAYLIPLITGLLVYILYGSRDSKLRFQSIQAILLGICLIVASIIFGIFDiFITGVGGqVIsGILDLILVLVWLYGI 87 
                                       445556669999999999999999************************952555555564457777888899999** PP

                           DUF4870  90 iaaikanegeeyrypl 105
                                       +  ++a++g++ ++p 
  gi|518651542|ref|YP_008141062.1|  88 YTGYRASRGMNANIPY 103
                                       *********9999985 PP

>> TIC20  Chloroplast import apparatus Tic20-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.1   6.7e-05      0.12     108     181 .]      33     108 ..       6     108 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.7e-05
                             TIC20 108 rylRFhvmlailLdvalqv.vllesnfnPli.gfklklgmylwagvalalivtllecvrsaLlGkyprlPlvseaA 181
                                         lRF+ ++ailL + l+v  ++  +f+  i g +++++  +   + +++ +  +++   a  G+ +++P +s+ A
  gi|518651542|ref|YP_008141062.1|  33 SKLRFQSIQAILLGICLIVaSIIFGIFDIFItGVGGQVISGILDLILVLVWLYGIYTGYRASRGMNANIPYLSDYA 108
                                       458***************977788888776655666655544333333333333333344668*********9966 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.6   3.2e-05     0.057       6      93 ..      15     101 ..       8     108 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.2e-05
                           DUF2304   6 liivsvllllliirlvrkkklkleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfsl 82 
                                       li ++  ll++i++  r +kl+++ s+  +ll+++liv+s++ +i++++ + +G +  + +l l+++++ l+ +++ 
  gi|518651542|ref|YP_008141062.1|  15 LIPLITGLLVYILYGSRDSKLRFQ-SIQAILLGICLIVASIIFGIFDIFITGVGGQVISGILDLILVLVWLYGIYTG 90 
                                       67788899*************985.788899***********************999999999******99999999 PP

                           DUF2304  83 slklskleeki 93 
                                       + + + ++ +i
  gi|518651542|ref|YP_008141062.1|  91 YRASRGMNANI 101
                                       98888887776 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   7.1   4.5e-05     0.081     163     238 ..       9      85 ..       4      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                    Virul_fac_BrkB 163 rwlvallllvlafallYrvlpnvkvrlraalpGallaallwllvkilfslylsnfasy.naiYGslgaliilllWly 238
                                        ++va l+ +++ +l+Y +  ++  +lr+  + a+l ++++++++i+f+++     ++ +++   +  li++l+Wly
  gi|518651542|ref|YP_008141062.1|   9 MFIVAYLIPLITGLLVYILYGSRDSKLRFQSIQAILLGICLIVASIIFGIFDIFITGVgGQVISGILDLILVLVWLY 85 
                                       4567888889999**********************************996544444444888888889********9 PP

>> AA_permease_C  C-terminus of AA_permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00017      0.31      30      51 .]       8      33 ..       5      33 .. 0.78
   2 ?    2.9   0.6     0.065   1.2e+02      26      48 ..      39      61 ..      35      64 .. 0.80
   3 ?    0.8   0.5       0.3   5.4e+02      29      46 ..      77      91 ..      70      95 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                     AA_permease_C 30 irfgvwmli....glliYflYgirhs 51
                                      i+f+v  li    gll+Y+lYg r+s
  gi|518651542|ref|YP_008141062.1|  8 IMFIVAYLIplitGLLVYILYGSRDS 33
                                      5666666666667*********9986 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.065
                     AA_permease_C 26 sltwirfgvwmliglliYflYgi 48
                                      s + i+ g+++++  +i+ +++i
  gi|518651542|ref|YP_008141062.1| 39 SIQAILLGICLIVASIIFGIFDI 61
                                      56778999999999999988776 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.3
                     AA_permease_C 29 wirfgvwmliglliYflY 46
                                      +i+++vw+   + iY +Y
  gi|518651542|ref|YP_008141062.1| 77 LILVLVWL---YGIYTGY 91
                                      44555554...3455555 PP

>> DUF2512  Protein of unknown function (DUF2512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.3   0.00092       1.7      32      80 ..      43      89 ..       8     103 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00092
                           DUF2512 32 evllisllltlvsYlvgDlliLprtgnliAtiaDfglafvvvWlltavl 80
                                       +l i l+++ + + + D++i    g++i  i D++l++v ++  ++++
  gi|518651542|ref|YP_008141062.1| 43 ILLGICLIVASIIFGIFDIFITGVGGQVISGILDLILVLVWLY--GIYT 89
                                      33458899999999999******************99766555..4444 PP

>> DUF1282  Protein of unknown function (DUF1282)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1   0.00089       1.6      15      43 ..       2      30 ..       1      41 [. 0.89
   2 ?    2.9   6.2     0.046        82     109     143 ..      42      94 ..      32     102 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00089
                           DUF1282 15 reetgkvlyivlillllliglvvfiystf 43
                                      +++    ++iv++l++l+ gl v+i + +
  gi|518651542|ref|YP_008141062.1|  2 EHKENNIMFIVAYLIPLITGLLVYILYGS 30
                                      7888999*****************99876 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.046
                           DUF1282 109 lflgglalglsllllva..................lvslllllyvvvLlylGv 143
                                       ++l+g+ l++ ++++++                  l+ +l++ly ++ +y + 
  gi|518651542|ref|YP_008141062.1|  42 AILLGICLIVASIIFGIfdifitgvggqvisgildLILVLVWLYGIYTGYRAS 94 
                                       688888888888888888999999**********9999***********9986 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 ?    8.4   2.6    0.0011         2      67     110 ..      10      56 ..       1      61 [. 0.75
   2 ?    1.4   1.6      0.16   2.9e+02      78     112 ..      61      95 ..      49     110 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                         RseC_MucC  67 allvYllPllllilgallgsall...gssellaalgallglvlgfli 110
                                        +++Yl+Pl++ +l+++l  +       +++ a+l++++++v+++++
  gi|518651542|ref|YP_008141062.1|  10 FIVAYLIPLITGLLVYILYGSRDsklRFQSIQAILLGICLIVASIIF 56 
                                       4689*****98777777665555577778888888888888888765 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.16
                         RseC_MucC  78 lilgallgsallgssellaalgallglvlgflivr 112
                                       ++++ + g++++g  +l+ +l+ l g++ g+   r
  gi|518651542|ref|YP_008141062.1|  61 IFITGVGGQVISGILDLILVLVWLYGIYTGYRASR 95 
                                       33344444444444555555555555555554444 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.6      0.04        72      13      28 ..      18      33 ..       6      40 .. 0.72
   2 ?    5.5   3.3     0.011        19       5      23 ..      42      59 ..      39      61 .. 0.83
   3 ?    4.4   0.1     0.024        44      13      30 ..      78      95 ..      68     109 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                    Chordopox_A13L 13 aivglivYgiYnrkke 28
                                       i+gl+vY +Y  + +
  gi|518651542|ref|YP_008141062.1| 18 LITGLLVYILYGSRDS 33
                                      699*******976554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                    Chordopox_A13L  5 lllliiCvaivglivYgiY 23
                                      ++ll iC  iv+ i++gi+
  gi|518651542|ref|YP_008141062.1| 42 AILLGICL-IVASIIFGIF 59
                                      79*****7.6788999997 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.024
                    Chordopox_A13L 13 aivglivYgiYnrkketq 30
                                      ++v + +YgiY+  +++ 
  gi|518651542|ref|YP_008141062.1| 78 ILVLVWLYGIYTGYRASR 95
                                      4455669****9776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       875  (0.0488036); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 844.13
//
Query:       gi|518651543|ref|YP_008141063.1|  [L=769]
Description: hypothetical protein FACI_IFERC00001G0182 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 5016.84
//
Query:       gi|518651544|ref|YP_008141064.1|  [L=379]
Description: hypothetical protein FACI_IFERC00001G0183 [Ferroplasma acidarmanus fer1]
Scores for complete 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-70  237.4   0.0      3e-70  237.2   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    5.4e-06   25.6   0.0      0.017   14.1   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
  ------ inclusion threshold ------
      0.012   15.0   0.0      0.017   14.4   0.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
      0.013   14.1   0.0      0.019   13.5   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      0.025   13.9   0.0      0.043   13.1   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  237.2   0.0   8.3e-74     3e-70       5     363 .]      33     372 ..      29     372 .. 0.94

  Alignments for each domain:
  == domain 1  score: 237.2 bits;  conditional E-value: 8.3e-74
                                       ESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHH CS
                     Aminotran_1_2   5 nLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagali 81 
                                        +g++e+++     t++e++  + +  +a ++ + y+p+ g  el+e++a+ ++++++++ +++ +v+v++   +l+
  gi|518651544|ref|YP_008141064.1|  33 SFGIGEPDFT----TPEEIIDYAFK--EAREGKTHYTPSAGIMELREKIAEKMKKKNNIDATAS-NVLVTPTKFSLN 102
                                       6899*****9....******99988..8999999******************************.************ PP

                                       HHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS- CS
                     Aminotran_1_2  82 ealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesph 158
                                        al  +++  pg+e+l+p+p+y sy +i++l++g+++++p++  e+++ d++++++ ++       ktk + +++p 
  gi|518651544|ref|YP_008141064.1| 103 LALYSIID--PGEEVLLPAPYYVSYPDIIKLNQGKMITVPTD--ENYEFDFQEMKKYISP------KTKAFMFNNPV 169
                                       *****997..******************************77..***************9......*********** PP

                                       TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEE CS
                     Aminotran_1_2 159 NPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilg 235
                                       NPtG+v++++ l++l+d++ ++ l+l++De+Y+++ ++   + +   + ++ +++++++++sK+++++G+R+Gy ++
  gi|518651544|ref|YP_008141064.1| 170 NPTGKVYSEKSLRALADFILENDLYLISDEIYEDLIYKGRMFSPGSIEEMK-DKTVTLSGFSKSYAMTGWRIGYMVA 245
                                       **************************************8877774333333.3479********************* PP

                                       EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCSCSSEEE CS
                     Aminotran_1_2 236 naavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasqsgmfll 309
                                         +++++++k++++ l   +s+ q+ +++al+d++    ++ +mrq+++krr+  ++ L+e+ g++ ++++++++ +
  gi|518651544|ref|YP_008141064.1| 246 PLDIIKAANKVQQQTLTcaPSISQYGAMKALEDEE----SVAKMRQEFAKRRDLTVSLLKEIdGITLYEPEGAFYAF 318
                                       **************99999***************9....99************************************ PP

                                       EEETHH.CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 310 tdlsae.takelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                        ++s e ++++ls +Lle+++v+vtpg++f++pg++Ri++ +++++ ++e + ++
  gi|518651544|ref|YP_008141064.1| 319 PGYSTEkADDKLSMELLEKYNVIVTPGSPFGAPGHFRISY-ATSQDVIREGIGRI 372
                                       ******888999999*************************.99999998887776 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   4.7e-06     0.017      35     163 ..      62     183 ..      43     198 .. 0.79
   2 !    9.5   0.0   0.00011      0.41     255     358 ..     263     368 ..     242     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.7e-06
                                       SHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHH CS
                       Aminotran_5  35 hhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakr 111
                                       ++ ++ +++  e++ ek ++  n++ +   + +  t  ++nl+++s+   ++pg+e+++ +  + +      ++ k 
  gi|518651544|ref|YP_008141064.1|  62 YTPSAGIMELREKIAEKMKKKNNIDATASNVLVTPTKFSLNLALYSI---IDPGEEVLLPAPYYVSYP----DIIKL 131
                                       55666677777888888887777777777777777778*********...99********99999988....33333 PP

                                       HTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHH CS
                       Aminotran_5 112 tgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigk 163
                                          k   +p de+ e d +e++k++++ktk+ +++   n tG +   +++ +
  gi|518651544|ref|YP_008141064.1| 132 NQGKMITVPTDENYEFDFQEMKKYISPKTKAFMFNNPVNPTGKVYSEKSLRA 183
                                       34444477999*******************************9877766655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHH.HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHH CS
                       Aminotran_5 255 vagiiglgaaleyl.eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLde 330
                                       +a  i+   a++ l +e  +++++++ ++ ++ +++ lk+++g++ly+p  + +  +    ++++ + +  + lL++
  gi|518651544|ref|YP_008141064.1| 263 CAPSISQYGAMKALeDEESVAKMRQEFAKRRDLTVSLLKEIDGITLYEP--EGAFYAFPGYSTEKADDKLSMELLEK 337
                                       55555555667777688999**************************886..788888888899999999999***** PP

                                       TTEEEEEE-TTTHHHHHHTT.S...-EEEEE CS
                       Aminotran_5 331 egIavrsGhhcaqplmkrlale...gtvRaS 358
                                       +++ v+ G+    p + r++ +    ++R +
  gi|518651544|ref|YP_008141064.1| 338 YNVIVTPGSPFGAPGHFRISYAtsqDVIREG 368
                                       ********99998877766655444566655 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   4.7e-06     0.017      51     144 ..     101     198 ..      51     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.7e-06
                                       HHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEE...EB-GGGB- CS
                   DegT_DnrJ_EryC1  51 lhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIl...pVhlyGqv 124
                                       l laL    ++pg+eV+ p+  +v+    +  +  k + v  d + y  d +++++ i ++tka +   pV+  G+v
  gi|518651544|ref|YP_008141064.1| 101 LNLALYS-IIDPGEEVLLPAPYYVSYPDIIKLNQGKMITVPTD-ENYEFDFQEMKKYISPKTKAFMfnnPVNPTGKV 175
                                       4444443.478*************9999999999999999988.89*******************97778******* PP

                                       --HHHHHHHHH...HCT-EEEEE CS
                   DegT_DnrJ_EryC1 125 admdalkaiaa...khglkvieD 144
                                          ++l+a+a+   + +l++i+D
  gi|518651544|ref|YP_008141064.1| 176 YSEKSLRALADfilENDLYLISD 198
                                       98888888877555788998888 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.2e-06     0.019      72     154 ..      93     176 ..      68     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.2e-06
                                       EESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHH.TTCEEEEESTTSHHHHHHHCCTTEEEEEEESS- CS
                   Cys_Met_Meta_PP  72 avssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkk.lgievkfvdtsdleelekaikentklvylEtpt 147
                                       +v+    ++++a+ +++  G+e+++    Y +  +++k    k + + ++     d++e++k i+++tk++ +  p 
  gi|518651544|ref|YP_008141064.1|  93 LVTPTKFSLNLALYSIIDPGEEVLLPAPYYVSYPDIIKLNQGKmITVPTDENYEFDFQEMKKYISPKTKAFMFNNPV 169
                                       44444555678999****************999999997776635566666666899******************** PP

                                       TTTT--- CS
                   Cys_Met_Meta_PP 148 npllkvv 154
                                       np+ kv 
  gi|518651544|ref|YP_008141064.1| 170 NPTGKVY 176
                                       ***9985 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05     0.043      15     167 ..      48     198 ..      41     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       HHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEE.......ES-HHHHHHHHHHHH--TTEEEEEETT-HHH CS
                   Beta_elim_lyase  15 sdaq.aaamlGdesYgedktvnrLedavaelfgkeaalf.......vpqGtaAnsillkillqrgeevivtepahih 83 
                                       +d+   +a  G   Y  + ++++L +++ae + k+  +        v+    + +++l  ++ +geev++  p  + 
  gi|518651544|ref|YP_008141064.1|  48 IDYAfKEAREGKTHYTPSAGIMELREKIAEKMKKKNNIDatasnvlVTPTKFSLNLALYSIIDPGEEVLLPAPYYV- 123
                                       5555567777777777777777777777775555555533344444666666777777777778888877666333. PP

                                       HSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHC CS
                   Beta_elim_lyase  84 fdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakky 160
                                             i  l++ k+++++++e+ ++d++++++ i +      k+k+ +  + +n   G+v+s ++lr++a++  ++
  gi|518651544|ref|YP_008141064.1| 124 --SYPDIIKLNQGKMITVPTDENYEFDFQEMKKYISP------KTKAFMFNNPVNP-TGKVYSEKSLRALADFILEN 191
                                       ..344577889999*********************99......5889999**9995.9***************9999 PP

                                       T-EEEEE CS
                   Beta_elim_lyase 161 giplhlD 167
                                       ++ l+ D
  gi|518651544|ref|YP_008141064.1| 192 DLYLISD 198
                                       9998877 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:                      485  (0.0270511); 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: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2334.99
//
Query:       gi|518651545|ref|YP_008141065.1|  [L=242]
Description: hypothetical protein FACI_IFERC00001G0184 [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   33.1   0.3    9.4e-08   32.8   0.3    1.3  1  Metallophos    Calcineurin-like phosphoesterase
    4.5e-05   23.7   0.0    9.9e-05   22.6   0.0    1.5  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
  ------ inclusion threshold ------
       0.11   12.3   0.7       0.35   10.6   0.2    2.0  2  DUF1647        Protein of unknown function (DUF1647)


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 !   32.8   0.3   1.6e-11   9.4e-08       4     109 ..      26     151 ..      23     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 1.6e-11
                                       EEEESBTB...........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS......HHHHHHHHHHHHHHHH CS
                       Metallophos   4 lvigDlHl...........algggqlddllkllddllreekpdlvllaGDlvdrg......dlekellellaalvky 63 
                                       +vi+DlHl            l   q + ++k++d++ ++  p  ++++GD+ ++       +++  ++ ++++  k+
  gi|518651545|ref|YP_008141065.1|  26 VVISDLHLgfeeemnlhgiFLPKLQRSHVEKMVDQIMDRYSPSKIIINGDFKQEFsrnlpqEWDD-VNHFIDRYRKE 101
                                       89*******999996666655556666666999*****************999988877776776.66666666664 PP

                                       TSEEEEEC-TTS........CHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEE CS
                       Metallophos  64 pipvylllGNHe........gfeeellnkygylgifsepwrsdaevfnnlplas 109
                                          +++++GNH+            + l+ y+y+++++  +++ +  +++  l  
  gi|518651545|ref|YP_008141065.1| 102 -SELIFVRGNHDnylmtilkS---NGLEIYDYYETDNYYIYHGDRDMSYRKLTI 151
                                       .778********776653330...444444444444444433333333333333 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 !   22.6   0.0   1.7e-08   9.9e-05       4     100 ..      26     141 ..      23     172 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.7e-08
                     Metallophos_2   4 aiiSDlH................snldaleavlealke.vgvdaiihaGDl..eeeep........evleellela. 52 
                                       ++iSDlH                 +++ +e++++++ +  ++ +ii  GD+  e   +        + ++ +++++ 
  gi|518651545|ref|YP_008141065.1|  26 VVISDLHlgfeeemnlhgiflpkLQRSHVEKMVDQIMDrYSPSKIIINGDFkqE---FsrnlpqewDDVNHFIDRYr 99 
                                       79*****99999999999999996677777777766543899********8531...23445666668888888889 PP

                     Metallophos_2  53 ...pvlaVrGNnDeevveedvlreaaelgtdlpeeaelel....agekvlliHgd 100
                                          +++ VrGN+D ++           l+t l ++  le+    + ++ +++Hgd
  gi|518651545|ref|YP_008141065.1| 100 kesELIFVRGNHD-NY-----------LMTIL-KSNGLEIydyyETDNYYIYHGD 141
                                       999**********.22...........22222.3333443333344446666665 PP

>> DUF1647  Protein of unknown function (DUF1647)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.31   1.8e+03      70      96 ..      51      74 ..      17      94 .. 0.66
   2 ?   10.6   0.2   5.8e-05      0.35      51     107 ..      93     152 ..      82     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.31
                           DUF1647 70 ddhlkeakksiksirkyypkkklilys 96
                                      ++h+   +k+++ i   y  +k+i+ +
  gi|518651545|ref|YP_008141065.1| 51 RSHV---EKMVDQIMDRYSPSKIIING 74
                                      4444...45566666666666776654 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5.8e-05
                           DUF1647  51 dlselikneedvvFvsatsddhlkeakksik.sirkyypkkklilys..ldlseeeiekl 107
                                       ++ +  ++e++++Fv    d++l++  ks    i+ yy ++++ +y+   d+s ++++ l
  gi|518651545|ref|YP_008141065.1|  93 HFIDRYRKESELIFVRGNHDNYLMTILKSNGlEIYDYYETDNYYIYHgdRDMSYRKLTIL 152
                                       455667899***************999987636********9999961145555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1463.43
//
Query:       gi|518651546|ref|YP_008141066.1|  [L=372]
Description: citrate synthase [Ferroplasma acidarmanus fer1]
Scores for complete 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-107  357.1   0.0   1.1e-106  357.0   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.0   0.0  6.2e-111  1.1e-106       1     361 []       7     359 ..       7     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 357.0 bits;  conditional E-value: 6.2e-111
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl++v +  te++++dg+kg++rYRGydi+eLa ekssfe v yl+l+g+ P+ +elk+f+++++++ +l++ +++ 
  gi|518651546|ref|YP_008141066.1|   7 GLENVYIKYTELTFIDGQKGIMRYRGYDINELA-EKSSFEKVSYLMLFGKFPDDSELKNFQNKINSHLALDDYLKDI 82 
                                       7999*****************************.8****************************************** PP

                                       HHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHH CS
                      Citrate_synt  78 lealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaen 154
                                       l+a+p++++ + +l++ +sa ++++++++ ++   e+  ++  ++++++ +++a+iyr ++g++ ++p++++syae 
  gi|518651546|ref|YP_008141066.1|  83 LRAMPETSDSLGILQTLLSAKASKESNYKYTK---ENDGEKIPEILGSVLSMVANIYRLKSGNNIIDPEPGESYAET 156
                                       ********************888876533333...333344447******************85559**99****** PP

                                       HHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHH CS
                      Citrate_synt 155 flymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmleei 231
                                       fl+++ g  +d++ + ++d al+l++DHe+ aST aa v+aStl+d+ys++a++i+al Gplhgga e +++ + ei
  gi|518651546|ref|YP_008141066.1| 157 FLKACSG-SADKNKISAMDSALILYMDHEIPASTTAALVTASTLSDMYSSLASAIAALRGPLHGGAAEGAYRQFLEI 232
                                       *****99.99******************************************************************* PP

                                       SSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHGC CS
                      Citrate_synt 232 gsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekeek 308
                                       g++e +v ++ e+++ ++k+rl GfGHrvy+++DpR k +k++a+ l+ ++++++ l++a++lee+  +  ++ + k
  gi|518651546|ref|YP_008141066.1| 233 GEPE-NVNAWFENNILNGKRRLVGFGHRVYRTYDPRLKTFKKYADILSTTEEQKKILAIAKRLEEAGVK--AFGS-K 305
                                       ***9.*******9999999****************************999****************999..7778.* PP

                                       T-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH.HT------E CS
                      Citrate_synt 309 nlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql.adnkiiRPr 361
                                       ++y+N Dfy+g++++a+g+p ++ft+lf++sR+ G+lAhi e+  +++++iRPr
  gi|518651546|ref|YP_008141066.1| 306 GIYTNTDFYAGMVFNAIGFPVDMFTTLFGLSRISGILAHITEYVeTQERLIRPR 359
                                       ******************************************987889*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2571.73
//
Query:       gi|518651547|ref|YP_008141067.1|  [L=204]
Description: hypothetical protein FACI_IFERC00001G0186 [Ferroplasma acidarmanus fer1]
Scores for complete 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   83.2   0.0    2.8e-23   82.9   0.0    1.0  1  Lactamase_B    Metallo-beta-lactamase superfamily
    2.5e-07   30.4   0.0      3e-07   30.2   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.8e-06   27.5   0.0    2.8e-06   26.9   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    8.9e-05   22.4   0.0    0.00018   21.4   0.0    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   6.3e-27   2.8e-23       4     186 ..      13     187 ..      10     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 6.3e-27
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                        ++nsyli  dg +i++D+Gt+++ +++     +l+    ++da+++TH+H+DH+Ggl  + e++   +++ a e+ 
  gi|518651547|ref|YP_008141067.1|  13 AMANSYLIMIDGMNIIVDAGTPGSGKKIT---GYLEDHKIKLDAILITHYHVDHVGGLSRIYEKYHPEIFVPANELS 86 
                                       578*************************8...6******************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                          + e+ +  ++ +  + + +++    +++  ++ ++ + + + + +pgh+ ++ +++++++kv+f+GDa  + + 
  gi|518651547|ref|YP_008141067.1|  87 IISGSEPVPPKPFLP--KFASTIMRARKVKDLKPSSDMNISGIELVKTPGHTRDSTSYYLKEQKVVFSGDAAVNLKG 161
                                       *******99888877..699*****************************************************8888 PP

                                       CCCCC.TTCEEE-SHCHHHHHHHHHHHHH CS
                       Lactamase_B 158 gridltlrgaevrdpsdaekyldsllkla 186
                                       + +      +++  p  aek+l++++ + 
  gi|518651547|ref|YP_008141067.1| 162 VPGYN---KGFAANPENAEKSLKAIRTMD 187
                                       88888...566666666666666655553 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.7e-11     3e-07       2     144 ..      26     156 ..      25     194 .. 0.70

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.7e-11
                                       EEEES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHHHCCTTCGH CS
                     Lactamase_B_2   2 riLiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.lrpkklplyapkgvlavleanfvy 76 
                                       +i++Dag+   +   + +l      d+  ++da+l+th H+DH+ gl  + e  +p   ++++p+  l++++ + + 
  gi|518651547|ref|YP_008141067.1|  26 NIIVDAGTPGSGKkITGYL-----EDHKIKLDAILITHYHVDHVGGLSRIYEkYHP---EIFVPANELSIISGSEPV 94 
                                       5667776653333233333.....444469**********************4444...699999999999888776 PP

                                       HHCHTTTTEEEEEE-TTSEEEE.CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S CS
                     Lactamase_B_2  77 laleeepavnvheldwgesfel.gdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtg 144
                                         ++  p+ + + + + +  +l  +++++i  +++  + g      + d  ++ ++  +++v+++gD +
  gi|518651547|ref|YP_008141067.1|  95 PPKPFLPKFASTIMRARKVKDLkPSSDMNISGIELVKTPGH-----TRDSTSYYLK--EQKVVFSGDAA 156
                                       65555544455555444444443123444555544444443.....4568889888..78899999876 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 !   26.9   0.0   6.2e-10   2.8e-06       1      61 [.      19      76 ..      19      85 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.2e-10
                     Lactamase_B_6  1 lLeldnvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfks 61
                                      l+ +d+++i++D G+ +s    ++++ +le++  ++d+iL++h  ++h+G+++ +y k++ 
  gi|518651547|ref|YP_008141067.1| 19 LIMIDGMNIIVDAGTPGSG---KKITGYLEDHKIKLDAILITHYHVDHVGGLSRIYEKYHP 76
                                      6789************984...57899*************************999988765 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0     4e-08   0.00018       7      99 ..      15     151 ..       9     200 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4e-08
                     Lactamase_B_3   7 hnsflletagarilvDPf.....ka.nlgyeppaeeaDlvlisqaledHahletlkql................... 58 
                                        ns+l+ ++g +i+vD +     k+ +  +e  + + D++li++ + dH     l ++                   
  gi|518651547|ref|YP_008141067.1|  15 ANSYLIMIDGMNIIVDAGtpgsgKKiTGYLEDHKIKLDAILITHYHVDHV--GGLSRIyekyhpeifvpanelsiis 89 
                                       69**************8844444222333444559***********9996..4555556667888888888888888 PP

                     Lactamase_B_3  59 ....................aenvkvleegeslevggleiravatshdavggs.ergenngf 99 
                                                           a++vk l++ +++++ g+e+ ++++ ++++     +++ ++f
  gi|518651547|ref|YP_008141067.1|  90 gsepvppkpflpkfastimrARKVKDLKPSSDMNISGIELVKTPGHTRDSTSYyLKEQKVVF 151
                                       88888888888888888888777788888888888888888887777665544233444555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1475.95
//
Query:       gi|518651548|ref|YP_008141068.1|  [L=481]
Description: hypothetical protein FACI_IFERC00001G0187 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-57  195.7  53.7    1.3e-57  195.5  53.7    1.0  1  AA_permease    Amino acid permease
    1.3e-19   70.4  57.9    1.7e-19   70.0  57.9    1.1  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.5  53.7   1.4e-61   1.3e-57       3     478 ..      19     469 ..      17     470 .. 0.93

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 1.4e-61
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfvi 78 
                                       ++++lg+v +++ +  l v+  ++++++++ ++++++++++l m++ +e++ ++++sg++y+ya+  +++ +lG  +
  gi|518651548|ref|YP_008141068.1|  19 IFQSLGQVAPAADIAILLVASFSISGAQTVMSVIIGWIIYALWMITPYEFSKIKSNSGSYYAYAAGATEKgRLGPIT 95 
                                       799************************************************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwel.vtdlpkawvt.gavflvvlliinlvgvkvygeaefilalikiiaiiaf 153
                                       +l++++++it++a+++ ++s++i ++   vt++p++w+  + +f+++++i++++g++ +      ++ i ++  i f
  gi|518651548|ref|YP_008141068.1|  96 ALSFMYYDITGAAFGILGLSSFIFLMAPeVTSIPYLWILfAGIFTAFIIIVTYLGIRPSLN----YTAITGLLEIMF 168
                                       **************************999*********9877******************9....999999999999 PP

                       AA_permease 154 iivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkd 227
                                       +++g   ii+ +gg+++          + +    + +     + ++ f++++++ v+++++ftG + v++i++E++ 
  gi|518651548|ref|YP_008141068.1| 169 LLIGsiiIIIRVGGHNSVV--------PFE----ITG-----PYSVGFSSIMFASVFSILDFTGSGVVTTISEEISK 228
                                       9999753344444443333........222....334.....45999****************************** PP

                       AA_permease 228 PeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssa 304
                                       P+k+i k+i++++++++++ + ++++++++++ ++ g++++  +a  ++ +f +++g ++l  li+++i ++  + +
  gi|518651548|ref|YP_008141068.1| 229 PKKNIGKSIIFAMVLTAVALIPAAYALTVGWGVSSIGSFASHSDA--GLTVFSRYLGPIGLVLLIVFTINSYFSNGV 303
                                       *******************************************99..**********************99887777 PP

                       AA_permease 305 nsslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivw 380
                                       + +++++++++ +  +  ++P +++k  +k+++P++a ++++ +s+++ ++++l +++ ++  +l a ++++++iv+
  gi|518651548|ref|YP_008141068.1| 304 SKATAVSRWWYSAARDHVVFPeTIGKINEKHHSPANAAIIWAGLSFVLDVIMGLIFGPLSAAFVLEAGTGISIVIVH 380
                                       777777666666666667899******************************************************** PP

                       AA_permease 381 lliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivl 457
                                       +++++s++       +++r+++++    +++   + +++ +++i++++ ++++ +    +p+ ++ a+f+++ +++l
  gi|518651548|ref|YP_008141068.1| 381 MIANTSLT-------LYTRRVNRFNLLKHGILPSLATIIGLVVIYFTMSDIFKKFL--VTPSAVNDAYFVSFVVTIL 448
                                       ********.......9**********************************997655..89***************** PP

                       AA_permease 458 lfliilvgvklhvknkrpqll 478
                                       ++l+ +++v+l+++ k+p++l
  gi|518651548|ref|YP_008141068.1| 449 WILLGGIVVTLYYRIKKPEIL 469
                                       ******************987 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0  57.9   1.9e-23   1.7e-19       3     423 ..      15     450 ..      13     457 .. 0.74

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 1.9e-23
                     AA_permease_2   3 llsafalvigsv...igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaaf.gkk 75 
                                       ll+ ++ ++g v   + ++i+ + ++   g+ ++++v+i+ +i+    +++  E+s  +++sg  y y++ a+ + +
  gi|518651548|ref|YP_008141068.1|  15 LLQGIFQSLGQVapaADIAILLVASFSISGAQTVMSVIIGWIIYA-LWMITPYEFSKIKSNSGSYYAYAAGATeKGR 90 
                                       566666666766544224444444465588889999999999995.5777889****55555556666665557788 PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       +++++a ++++  + ++a+++ +++s+++++++p+++  ++l++l+a ++++++++++++gi+ s +++ i+g+l i
  gi|518651548|ref|YP_008141068.1|  91 LGPITALSFMYYDITGAAFGI-LGLSSFIFLMAPEVTSIPYLWILFAGIFTAFIIIVTYLGIRPSLNYTAITGLLEI 166
                                       99*********9999996665.56666666688***9**************************************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigl 227
                                        ++l+i  i+ +i v+g+ +  +  +t+    +++++++++ + +++ f+G  +++ +see   +kk++ k i++++
  gi|518651548|ref|YP_008141068.1| 167 -MFLLIGSIIIIIRVGGHNSVVPFEITGPYSVGFSSIMFASVF-SILDFTGSGVVTTISEEisKPKKNIGKSIIFAM 241
                                       .788887777777776666666666666666678888888888.7899*************644459********** PP

                     AA_permease_2 228 livlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                       ++++v  +  + a++ + + ++i + ++  +++  +f ++ g+++ ++++++++ s + ++ +  +++sr  +++ar
  gi|518651548|ref|YP_008141068.1| 242 VLTAVALIPAAYALTVGWGVSSIGSFASHSDAGLTVFSRYLGPIGLVLLIVFTINSYFSNGVSKATAVSRWWYSAAR 318
                                       *****9999988888777777776666655678888888888*********************************** PP

                     AA_permease_2 305 dgvlP.rffakvn.kfgspiraiiltaivslillllfl..lassaaynfllsvsslgliisyllliigalilrkkrp 377
                                       d v   + + k+n k++sp +a i+ a +s++l +++   +++ +a ++l + + ++++i+ +++ +++ ++ ++ +
  gi|518651548|ref|YP_008141068.1| 319 DHVVFpETIGKINeKHHSPANAAIIWAGLSFVLDVIMGliFGPLSAAFVLEAGTGISIVIVHMIANTSLTLYTRRVN 395
                                       *97655****************9987777766555544223343344444444555555555555555555444444 PP

                     AA_permease_2 378 hl..krpgk..ilvaiigalfllfll.....valffppkgpatqssliytiiltv 423
                                       ++   + g+   l +iig++++ f++      +l  p+++ ++++ +++  il++
  gi|518651548|ref|YP_008141068.1| 396 RFnlLKHGIlpSLATIIGLVVIYFTMsdifkKFLVTPSAVNDAYFVSFVVTILWI 450
                                       3322343333368999999999999855433333356666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); 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:                         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: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.66
# Mc/sec: 2207.87
//
Query:       gi|518651549|ref|YP_008141069.1|  [L=160]
Description: hypothetical protein FACI_IFERC00001G0188 [Ferroplasma acidarmanus fer1]
Scores for complete 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  222.0   0.4    3.3e-66  221.8   0.4    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 !  221.8   0.4   1.8e-70   3.3e-66       1     154 []       6     159 ..       6     159 .. 1.00

  Alignments for each domain:
  == domain 1  score: 221.8 bits;  conditional E-value: 1.8e-70
                                       EEE---TTEEEEEEEESSTTHHHHHHHHHHCCSTTSEEEEEEE--STT-EEEEEESSHHHHHHHHHHHHHH--TTEE CS
                     Adenosine_kin   1 vkiekpeevnvilgqshfiktvedlyealvtsvpgikfglafcEasgkrLvrvegndeelvelavknalaigaghvf 77 
                                       v+i+kpe+vn+ilg+shfiktved++e++ t++pg+++++ f+Easg++L+r+egn++el+++ ++n+++i+agh+f
  gi|518651549|ref|YP_008141069.1|   6 VEINKPEDVNIILGYSHFIKTVEDMNEIIKTTIPGCEYAIVFSEASGDKLIRYEGNNKELIDCGIENIKKISAGHTF 82 
                                       79*************************************************************************** PP

                                       EEEEEST-HHHHHHHHHHCTTCEEEEEEESSSEEEEEEEETTEEEEEEEEES---SEE--HHHHHHHHHHHHHTTS- CS
                     Adenosine_kin  78 villknafPinvlnaiksvpevvkifaAtanplevivaeteqgrgvlgvvDGfspkgveeeedkkerkellrkigYk 154
                                       +ill+nafPin+l ++k+++e+  ifaAtanp++vi+a+te+ ++v+gv DG+sp gve+++dk++r+++lr+igYk
  gi|518651549|ref|YP_008141069.1|  83 MILLRNAFPINILPQLKMTQELGAIFAATANPIKVILAKTENTNAVIGVADGYSPVGVETDKDKEKRRKFLRDIGYK 159
                                       ****************************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.32s 00:00:00.84 Elapsed: 00:00:00.52
# Mc/sec: 930.16
//
Query:       gi|518651550|ref|YP_008141070.1|  [L=140]
Description: hypothetical protein FACI_IFERC00001G0189 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-09   37.4   0.0    3.7e-09   37.1   0.0    1.1  1  SnoaL_2   SnoaL-like domain
      7e-08   32.3   0.0    8.5e-08   32.1   0.0    1.0  1  SnoaL     SnoaL-like polyketide cyclase
     0.0057   16.9   0.0     0.0081   16.4   0.0    1.2  1  SnoaL_3   SnoaL-like domain
     0.0073   16.7   0.0     0.0094   16.3   0.0    1.2  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   8.4e-13   3.7e-09       3      92 ..      10     109 ..       9     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 8.4e-13
                                       HHHHHHHTTCHHHHHHTEEEEEEEEETTSE...EESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           SnoaL_2   3 aflaalnagdldalaalfapdvvwedpgge...lrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt 76 
                                       +f++a+n++++ +l+ ++++d+ + +pg e   +r + ++  +++++f++fpd++f++ +v+ +++  + ew  ++t
  gi|518651550|ref|YP_008141070.1|  10 DFINAWNSHNIFELLKYYDDDMLYIHPGEEpkiIRKKGDFEVYLKKFFETFPDYTFTLINVAWNNNVGFGEWLGKAT 86 
                                       699************************888899***************************************99877 PP

                                       .......EETTSSEEEEEEEEEE CS
                           SnoaL_2  77 .......ipatgrgvtvrgvdvf 92 
                                               + + +++++ gvdv+
  gi|518651550|ref|YP_008141070.1|  87 fnglrynLKISNKPFEIYGVDVL 109
                                       66666665555556666666665 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   1.9e-11   8.5e-08       8     124 ..      12     132 ..       9     134 .. 0.90

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 1.9e-11
                                       HHHHHTT-HHHHHGTEEEEEEETCCTT..TCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEEES CS
                             SnoaL   8 eevwnsgdldaldelvaedvvdhnpee..eparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGtht 82 
                                        ++wns+++ +l +++++d+++  p+e  +  r + +f   ++++f++fPD +++   +   +     ++  ++t++
  gi|518651550|ref|YP_008141070.1|  12 INAWNSHNIFELLKYYDDDMLYIHPGEepKIIRKKGDFEVYLKKFFETFPDYTFTLINVAWNNNVGFGEWLGKATFN 88 
                                       579*******************9999954444566689999************************************ PP

                                       SEBTTBE-TT-EEEEEEEEEEEEET..TEEEEEEEEECHHHHHH CS
                             SnoaL  83 geflGipptGkkvkfeeitllrved..GkIveewdviDllgllr 124
                                       g   +++ ++k++++ ++++l +      I+ee  ++D l++l+
  gi|518651550|ref|YP_008141070.1|  89 GLRYNLKISNKPFEIYGVDVLVLNKshTCIKEEHVYFDVLSVLK 132
                                       ********************999884456999999999999987 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.8e-06    0.0081       7      66 ..      10      70 ..       8      83 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.8e-06
                           SnoaL_3  7 afyeaaaegdfdalfalwaddivfigtgadel.ltgreevrrslkqifakgegisfeltdv 66
                                      +f++a  ++++ +l++++ dd ++i++g+ ++ ++ + +++ +lk+ f+ ++  +f+l +v
  gi|518651550|ref|YP_008141070.1| 10 DFINAWNSHNIFELLKYYDDDMLYIHPGEEPKiIRKKGDFEVYLKKFFETFPDYTFTLINV 70
                                      58899999*******************99988456999***********999999988665 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0094       4      64 ..       7      70 ..       5      91 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                                      HHHHHHHHHHCT-HHHHHHCEEEEEEEE-TT..S-EEEHHHHHHHHHCCHCE.EEEEEEEEEEE CS
                           DUF4440  4 leealeeafvagdaealaallapdavlvgps..gtvldkeellealeagfaa.grslelteeev 64
                                      +e ++  a++++++ +l +++++d+++++p+   +++ k++ +e + ++f++ ++++++t + v
  gi|518651550|ref|YP_008141070.1|  7 FEIDFINAWNSHNIFELLKYYDDDMLYIHPGeePKIIRKKGDFEVYLKKFFEtFPDYTFTLINV 70
                                      5667889************************633335999999999888877458888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 990.48
//
Query:       gi|518651551|ref|YP_008141071.1|  [L=399]
Description: hypothetical protein FACI_IFERC00001G0190 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-37  128.5  38.1    6.6e-28   97.6  15.5    2.9  3  MFS_1     Major Facilitator Superfamily
      2e-10   40.2  23.7    4.8e-10   38.9  13.2    2.3  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
        6.4    4.9  30.5     0.0086   14.4   6.6    3.6  3  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  15.5   1.1e-31   6.6e-28       5     176 ..      12     178 ..       8     190 .. 0.92
   2 ?   -2.1   5.8      0.23   1.4e+03     135     164 ..     191     218 ..     188     227 .. 0.76
   3 !   44.6  14.6   1.4e-15   8.6e-12       3     171 ..     233     392 ..     231     397 .. 0.87

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 1.1e-31
                             MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllf 81 
                                       +f +al ++++++a+p  +++++ is se  ll+ ++ ++  ++++p++ ++d+ G ++v+++g ++++++  +l+f
  gi|518651551|ref|YP_008141071.1|  12 GFTAALEATMILLAIP-EISKEFSISYSESTLLIIIFVITETLLVIPFSLIADKKGIKKVMITGSFIMLIA-SILIF 86 
                                       5889999*********.9*****************************************************.55555 PP

                             MFS_1  82 asslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyil 157
                                       +s+ + ++l+lr++qG+g+++++ +++++++ ++++ +rg+ igl  + +slG+++g +lggl+a s+++ ++f++ 
  gi|518651551|ref|YP_008141071.1|  87 ISNNFiVMLLLRAIQGIGGSMVILTSLSYASLISSDINRGKSIGLNHTIISLGYVIGLPLGGLMA-SINYKYLFLFT 162
                                       588888***********************************************************.99********* PP

                             MFS_1 158 aivsllafvlfllllpeep 176
                                       a++sll+++   l +  ++
  gi|518651551|ref|YP_008141071.1| 163 AFLSLLSII---LIINIDE 178
                                       *******99...5555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.23
                             MFS_1 135 ilgpllggllasslgWravfyilaivslla 164
                                        ++ l++gl++s   +  +f+i+ai++l++
  gi|518651551|ref|YP_008141071.1| 191 YITLLFSGLILSI--YYIPFIIIAIIGLVL 218
                                       5778888888855..566799999999887 PP

  == domain 3  score: 44.6 bits;  conditional E-value: 1.4e-15
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       +++fl++++r++l++ +  +l  +l +sp  +gll+ +y l++ ++s++ G l d++G  ++  lg+l++++++lll
  gi|518651551|ref|YP_008141071.1| 233 FSGFLHSITRNMLAAYFV-FLLYSLKYSPLIVGLLVLIYPLFFTFTSFISGKLHDKYG-LKIASLGFLSMSVFSLLL 307
                                       899***************.9*************************************5.567777777777774666 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                       +   +   +l+  v+ G  +g+++++  a++    +k++r  + g+ s+   +  ++g ++++ l+  l+  +v +i
  gi|518651551|ref|YP_008141071.1| 308 F--FN---FLFPEVFLGSSTGVATTSNTAYTMNSLNKNDRITGSGIRSLQGIVTNAIGLGIASKLL--LNLNYVILI 377
                                       6..47...**************************************************99999999..455667777 PP

                             MFS_1 157 laivsllafvlflll 171
                                       + i+ l a+ + l+l
  gi|518651551|ref|YP_008141071.1| 378 IIIFNLTALSITLIL 392
                                       777777664443344 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9  13.2     8e-14   4.8e-10      45     193 ..      37     178 ..      10     184 .. 0.92
   2 !    6.8   2.7   0.00044       2.6      44      90 ..     259     305 ..     197     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 8e-14
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                        + s+l+  if++ +++  + ++l++d+ G kk++++++++++i+++l+++++   ++ v+++ R + Gig  ++  
  gi|518651551|ref|YP_008141071.1|  37 YSESTLLIIIFVITETLLVIPFSLIADKKGIKKVMITGSFIMLIASILIFISN---NFIVMLLLRAIQGIGGSMVIL 110
                                       45788999999999999999*********************************...********************* PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS-- CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPE 193
                                       ++  y+s i+ +  Rg+ ++l+ + i++G +++  +g  ++ +++    ++l+ ++++++ll +il++ ++E
  gi|518651551|ref|YP_008141071.1| 111 TSLSYASLISSDINRGKSIGLNHTIISLGYVIGLPLGGLMASINY----KYLFLFTAFLSLLSIILIINIDE 178
                                       ************************************999999999....99999999999999999877765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.00044
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfviga 90 
                                       s + +gl+v i+ +  +++s+++g+l d++G k + l +  ++v + 
  gi|518651551|ref|YP_008141071.1| 259 SPLIVGLLVLIYPLFFTFTSFISGKLHDKYGLKIASLGFLSMSVFSL 305
                                       567899*****************************999998888655 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 ?   14.4   6.6   1.4e-06    0.0086       3      89 ..       5      92 ..       4      94 .. 0.87
   2 ?    2.3   6.9    0.0069        41     132     196 ..      91     155 ..      86     212 .. 0.87
   3 ?    1.2   0.5     0.014        85     342     400 ..     272     332 ..     251     346 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.4e-06
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP  3 lvllsllglvqamvsgyfkstittiEkrFklpsstsgliassneignillilfvsYfggrghrPrwigigallmalgsl 81
                                      +v+ sl g++ a+  +++  +i +i k+F+++ s+s l+  ++ i+++ll++  s ++++    +++ +g+++m ++s+
  gi|518651551|ref|YP_008141071.1|  5 IVFTSLPGFTAALEATMILLAIPEISKEFSISYSESTLLIIIFVITETLLVIPFSLIADKKGIKKVMITGSFIMLIASI 83
                                      57889999999999**********************************************8888888888888888776 PP

                                      xx.xxxxxx RF
                              OATP 82 ll.alPhfi 89
                                      l+ ++ +fi
  gi|518651551|ref|YP_008141071.1| 84 LIfISNNFI 92
                                      650455555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.0069
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 132 vllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyv 196
                                       +++++l   ++GiG+++++   +sY    ++  n    +g+ +++  lG+++G  lG+l++++  
  gi|518651551|ref|YP_008141071.1|  91 FIVMLLLRAIQGIGGSMVILTSLSYASLISSDINRGKSIGLNHTIISLGYVIGLPLGGLMASINY 155
                                       348899999***************************************************99865 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.014
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 342 pgaalGillgGllvkklklsakklaklvl..vvsllsllllllllflgCetskvagvtvsy 400
                                       +++++  +++G l  k+ l++ +l +l++  ++ ll + +l++ +flg +t   ++ ++ y
  gi|518651551|ref|YP_008141071.1| 272 LFFTFTSFISGKLHDKYGLKIASLGFLSMsvFSLLLFFNFLFPEVFLGSSTGVATTSNTAY 332
                                       3456777888999988888777665544400444444444555566665555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2682.13
//
Query:       gi|518651552|ref|YP_008141072.1|  [L=73]
Description: N-methylhydantoinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 529.46
//
Query:       gi|518651553|ref|YP_008141073.1|  [L=219]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-17   64.1   2.9    1.8e-17   63.7   2.9    1.2  1  DDE_Tnp_1    Transposase DDE domain
     0.0063   16.0   0.5      0.016   14.7   0.1    1.8  2  PhoH         PhoH-like protein
  ------ inclusion threshold ------
      0.019   14.8   0.3          2    8.3   0.0    2.2  2  DUF4252      Domain of unknown function (DUF4252)
      0.037   14.1   1.3       0.08   13.0   0.0    2.3  3  La           La domain
      0.064   13.6   0.1       0.14   12.5   0.1    1.6  1  DDE_Tnp_1_5  Transposase DDE domain
        0.1   12.6   0.2        1.7    8.6   0.0    2.1  2  PGC7_Stella  PGC7/Stella/Dppa3 domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   2.9   5.9e-21   1.8e-17       7     212 ..      40     209 ..      34     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 5.9e-21
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaD 83 
                                        i+D+t  +++  + + r+++ +++   ++klh++++++  ++ls+ it+  +hdsk+++ ll  ++  +  ++++D
  gi|518651553|ref|YP_008141073.1|  40 CIIDSTGSKITIRGDYLRHKWHRKR-NGWLKLHVIISLKDVTVLSFTITDEHTHDSKAARKLLSKMKN-NILRIFGD 114
                                       79********999988888777666.69**************************************98.******** PP

                         DDE_Tnp_1  84 aGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnse 160
                                       +GY+  +++  +   g++ ii+++kn+ ++++       + +r ++ + i + s ++                    
  gi|518651553|ref|YP_008141073.1| 115 RGYD-SKYIYNMF--GYNAIIPPRKNASTKSR------GSSTRARIVRYIKKNSMEQLKE----------------- 165
                                       ***9.77777777..7***********99966......3333333333333333333333................. PP

                         DDE_Tnp_1 161 llsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                               + y +Rw +E  F+ lkr++  +  ++++ + + ++l l+   +
  gi|518651553|ref|YP_008141073.1| 166 -------NNSYGKRWLVEIYFSGLKRVMT-EIIKAKKIEYIIQELALKVVNY 209
                                       .......3668***************765.5666666666666665555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.46   1.4e+03     146     187 ..      46      85 ..      44     105 .. 0.60
   2 !   14.7   0.1   5.3e-06     0.016      76     117 ..     175     216 ..     150     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.46
                                       T-EEEEEE--------------THHHHHHTTT-TTEEEEE-- CS
                              PhoH 146 nskvvvtGdvtqidlpkgkksGlaealevlknvegieivelk 187
                                       +sk+ + Gd    + +++ ++G  ++  +++  +++++++++
  gi|518651553|ref|YP_008141073.1|  46 GSKITIRGDYLRHKWHRK-RNGWLKLHVIIS-LKDVTVLSFT 85 
                                       689999999888888776.566555443333.2344444443 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.3e-06
                                       --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                              PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                       v++y++ l   ++++++a+k+e+++++  ++v++ + mRG T
  gi|518651553|ref|YP_008141073.1| 175 VEIYFSGLKRVMTEIIKAKKIEYIIQELALKVVNYNIMRGMT 216
                                       789*************************************98 PP

>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0094        28      68     100 ..      73     105 ..      65     122 .. 0.86
   2 ?    8.3   0.0   0.00067         2      81     129 ..     140     190 ..     131     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0094
                           DUF4252  68 lkklksikvlttenkadaeklkkevkkilkknk 100
                                       + +lk ++vl+++ +++ +  +k+++k+l+k k
  gi|518651553|ref|YP_008141073.1|  73 IISLKDVTVLSFTITDEHTHDSKAARKLLSKMK 105
                                       4589*********99999999999999999876 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00067
                           DUF4252  81 nkadaeklkkevkkilkknkyeeLmrvkdkgek..vkiyvkekkdkvselv 129
                                       +k+  +  ++ + +++kkn++e+L + ++ g++  v+iy+ + k +++e++
  gi|518651553|ref|YP_008141073.1| 140 TKSRGSSTRARIVRYIKKNSMEQLKENNSYGKRwlVEIYFSGLKRVMTEII 190
                                       4566777889999*****************99999*****99999988875 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.4   7.2e+03      40      47 ..      20      27 ..       5      34 .. 0.62
   2 ?   13.0   0.0   2.7e-05      0.08      18      48 ..      54      84 ..      51     106 .. 0.88
   3 ?   -3.2   0.1         3     9e+03       5      10 ..     175     180 ..     175     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.4
                                      SSHHHHHH CS
                                La 40 fkrmkklt 47
                                      f+r+++++
  gi|518651553|ref|YP_008141073.1| 20 FRRIRRIK 27
                                      66666655 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHTTSTTS---HHHHHTSSHHHHHHS CS
                                La 18 kFLrkkmdkdpegwVplsliasfkrmkkltk 48
                                      ++Lr k  ++ +gw +l++i+s k +  l+ 
  gi|518651553|ref|YP_008141073.1| 54 DYLRHKWHRKRNGWLKLHVIISLKDVTVLSF 84
                                      79*******99**************998775 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 3
                                       HHHHHH CS
                                La   5 vEfYFS 10 
                                       vE YFS
  gi|518651553|ref|YP_008141073.1| 175 VEIYFS 180
                                       899**9 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.7e-05      0.14      66     110 ..       9      50 ..       1      52 [. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                       DDE_Tnp_1_5  66 aglellvpdystlsrraktlevkipvkrkskglhlvvdstGlkvl 110
                                       a+  ++   ys + rr ++++  +  ++ +  l  ++dstG k++
  gi|518651553|ref|YP_008141073.1|   9 AN--IKSISYSEIFRRIRRIKPDLN-SNINSKLDCIIDSTGSKIT 50 
                                       44..47789************9995.4445569*********986 PP

>> PGC7_Stella  PGC7/Stella/Dppa3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.056   1.7e+02      68     100 ..      88     119 ..      57     128 .. 0.82
   2 ?    8.6   0.0   0.00058       1.7      64     102 ..     154     199 ..     130     204 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.056
                       PGC7_Stella  68 eektlqerrweRtllsqrKkaflkhirrrrldh 100
                                       +e t +  +  R+lls+ K+++l+++  r  d 
  gi|518651553|ref|YP_008141073.1|  88 DEHT-HDSKAARKLLSKMKNNILRIFGDRGYDS 119
                                       6666.6677899************998876655 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00058
                       PGC7_Stella  64 q.......qyreektlqerrweRtllsqrKkaflkhirrrrldhma 102
                                               q++e+ +  +r+ +   +s +K++++++i+ ++ ++++
  gi|518651553|ref|YP_008141073.1| 154 YikknsmeQLKENNSYGKRWLVEIYFSGLKRVMTEIIKAKKIEYII 199
                                       2444567799*******************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1430.38
//
Query:       gi|518651554|ref|YP_008141074.1|  [L=334]
Description: transposase mutator type [Ferroplasma acidarmanus fer1]
Scores for complete 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-61  206.1   0.0    9.9e-61  205.7   0.0    1.1  1  Transposase_mut  Transposase, Mutator family
    2.8e-06   27.6   0.0    5.2e-06   26.8   0.0    1.5  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.7   0.0   1.1e-64   9.9e-61      21     302 ..      15     285 ..       3     296 .. 0.91

  Alignments for each domain:
  == domain 1  score: 205.7 bits;  conditional E-value: 1.1e-64
                   Transposase_mut  21 gkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspallery 96 
                                       + d +lke++k  +e+l+e el+++l        ee+ + +nG+++r+l+T++g++ +l++PrdR+ +F+++++e y
  gi|518651554|ref|YP_008141074.1|  15 DIDRILKEAIKEKIEKLMETELNAYL--------EENPGIKNGKYKRDLKTKYGEIkQLNVPRDRDSNFHTQVIEPY 83 
                                       45556666666666666666666665........6677889*************9957******************* PP

                   Transposase_mut  97 kRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylk 173
                                       +R+   +e+ ++++y +G+str+++ ++e++ g +++Sks++S+it+ + e+v +f +R+L++  y ++flD+l   
  gi|518651554|ref|YP_008141074.1|  84 NRSI-GMEDLIVSMYSNGISTRRIAGIMEDILG-NKYSKSTISRITDLTIEEVYKFINRPLDKR-YIAVFLDGLFFY 157
                                       **86.689*************************.66***************************9.************ PP

                   Transposase_mut 174 vReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpea 250
                                       +R  g v  ++v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L nrGlk+  l+v+D+ k L + + + +p +
  gi|518651554|ref|YP_008141074.1| 158 LR-RGNVDKEPVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGLKEPLLIVADGIKNLDEEVMEIYPRS 233
                                       **.788999******************************************************************** PP

                   Transposase_mut 251 avQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeeflekl 302
                                       + Q C++H++r l ++v  k+ d+++ +  +++k  + eea  ++++f   +
  gi|518651554|ref|YP_008141074.1| 234 EFQLCTIHYARGLKSNVREKDIDEITIDANKMFKCDNKEEAIIRFNDFKSFY 285
                                       ******************************************9999998755 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   5.8e-10   5.2e-06      15      94 ..     166     243 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 5.8e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ + y+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518651554|ref|YP_008141074.1| 166 EPVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGL--KEPLLIVADGIKNLDEEVMEIYPRSEFQLCTI 240
                                       5777899*******************************99644..6******************************* PP

                              MULE  92 Hia 94 
                                       H a
  gi|518651554|ref|YP_008141074.1| 241 HYA 243
                                       *76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       964  (0.0537676); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2414.59
//
Query:       gi|518651555|ref|YP_008141075.1|  [L=223]
Description: purine nucleoside phosphorylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.2e-19   67.8   0.0    1.9e-18   66.6   0.0    1.5  1  PNP_UDP_1  Phosphorylase superfamily
  ------ inclusion threshold ------
      0.023   13.8   0.1      0.031   13.3   0.1    1.1  1  Pes-10     Pes-10
      0.025   14.1   0.1      0.042   13.3   0.1    1.4  1  SPC22      Signal peptidase subunit


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 !   66.6   0.0   3.1e-22   1.9e-18       3     202 ..      14     204 ..      13     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 3.1e-22
                                       EEEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEE CS
                         PNP_UDP_1   3 aiivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGta 79 
                                       a++v++ ++++ ++++ l +++  +++ g+ ++tG +++k+ ++  +GiG ++ a + +++l k + +k iir+G+ 
  gi|518651555|ref|YP_008141075.1|  14 ALVVANVDRFNMVKNK-LSDIKLVNDFMGYYTYTGFYENKRLTLSWSGIGNTSLA-LDTLELYKLG-AKNIIRFGST 87 
                                       7899************.**************************************.********55.********** PP

                                       EESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEEEEEEEESESS- CS
                         PNP_UDP_1  80 GglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhrGvvatadgfya 156
                                        ++n+++k+G  v+p ++ +  g+      +ee+   +  +   ad +l+++     + +++++      t+d+   
  gi|518651555|ref|YP_008141075.1|  88 ASINKNIKPGSYVMPISYSHNNGGLF----NEEIKDNLSISLS-ADYDLLKKFDL--NLKDYEHYITDAFTTDSQKV 157
                                       *****************644333333....4443555555555.89999999777..44444455544555666666 PP

                                       CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEE.EETTT CS
                         PNP_UDP_1 157 eteaelrllrrlgadaveMEtaavaqlArelgipfaairvv.sdlaa 202
                                        t + +  l++lg+d+++ME++a++  +++++ +++++ +v s+l+ 
  gi|518651555|ref|YP_008141075.1| 158 RTNEFIDKLNKLGIDNLDMEGSALYLNSKLYNFKALSVLTVySNLIT 204
                                       6667777*****************************77777588554 PP

>> Pes-10  Pes-10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   5.2e-06     0.031     121     163 ..     128     170 ..     112     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-06
                            Pes-10 121 afrlLsdldlsledyleileraiefqeqieeAdeLvekvekll 163
                                        ++lL+++dl+l+dy + + +a     q +  +e ++k +kl 
  gi|518651555|ref|YP_008141075.1| 128 DYDLLKKFDLNLKDYEHYITDAFTTDSQKVRTNEFIDKLNKLG 170
                                       499************************************9995 PP

>> SPC22  Signal peptidase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.1e-06     0.042      49      99 ..     106     157 ..      73     166 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.1e-06
                             SPC22  49 svrdygs.nrkkkdraklkfdldaDlsslfnWNtKqlFvyltaeYetkknev 99 
                                       s ++ g  n++ kd+ +++++ d+Dl + f+ N+K    y+t  ++t++++v
  gi|518651555|ref|YP_008141075.1| 106 SHNNGGLfNEEIKDNLSISLSADYDLLKKFDLNLKDYEHYITDAFTTDSQKV 157
                                       333344457899**********************************999853 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1690.61
//
Query:       gi|518651556|ref|YP_008141076.1|  [L=41]
Description: hypothetical protein FACI_IFERC00001G0195 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 311.26
//
Query:       gi|518651557|ref|YP_008141077.1|  [L=362]
Description: hypothetical protein FACI_IFERC00001G0196 [Ferroplasma acidarmanus fer1]
Scores for complete 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-98  327.7   0.1    9.8e-98  327.5   0.1    1.0  1  Transposase_mut  Transposase, Mutator family
    4.6e-12   46.2   0.0    8.3e-12   45.4   0.0    1.4  1  MULE             MULE transposase domain
      0.001   18.6   0.0     0.0019   17.7   0.0    1.4  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.086   12.5   0.0    1.8  2  DDE_Tnp_ISL3     Transposase
      0.036   14.3   0.3        2.5    8.4   0.0    2.8  3  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.5   0.1  2.7e-101   9.8e-98      27     379 ..       2     348 ..       1     350 [. 0.96

  Alignments for each domain:
  == domain 1  score: 327.5 bits;  conditional E-value: 2.7e-101
                   Transposase_mut  27 kellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspallerykRrekal 103
                                       ++l k +l++l+++e++e+++a ryer  +r+ +RnG+++r+l T+ g++ l  P+ R+ sF++a++++y R ek +
  gi|518651557|ref|YP_008141077.1|   2 RDLKKWILNDLMNEEAEEQINASRYERNSNRKDYRNGYKQRSLLTTDGKVILDKPQFRETSFHTAVFDNYSRVEKSV 78 
                                       78999************************************************************************ PP

                   Transposase_mut 104 eavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrv 180
                                       e+ ++e y++Gvstr v+k++++l+   +vS+s vS+++ +ld++v++f eR ++ + y ++++D++ylk+R++gr 
  gi|518651557|ref|YP_008141077.1|  79 ESIILESYLSGVSTRSVNKVIKSLGI--EVSPSYVSSLSSRLDKTVNEFLERKIDGE-YKFIYIDGTYLKIRNNGRY 152
                                       ************************99..79**************************9.******************* PP

                   Transposase_mut 181 vskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrv 257
                                       ++ka++i +g+++dG+re+Lg ++ dsE e  W+ ++++Lk+rGl+gve+v+sD+ kG+++a++++fp++++Q C v
  gi|518651557|ref|YP_008141077.1| 153 RNKAIYICVGINSDGYREVLGARIYDSETEIEWELFFDDLKDRGLNGVEMVISDGNKGIREAVKQSFPGSSWQYCHV 229
                                       ***************************************************************************** PP

                   Transposase_mut 258 Hllrnllakvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlaflafpeqir.. 331
                                       H++rnl + + k++++ ++  +k+  +++d+    +      +kl +  + k  +++d+  + + ++ +f+++i+  
  gi|518651557|ref|YP_008141077.1| 230 HFMRNLRKSTGKQQWKFLSLLIKQALDNPDILPLLQ------DKLFDrGLDKCSTMFDKYYDSLYNYRSFNTNIQgl 300
                                       ******************************966554......44444378888899999999999999999988655 PP

                   Transposase_mut 332 rkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewk 379
                                       r+++  N +ErLN+ei+Rrt+++g FP ++s++rl g+++ + ++e+ 
  gi|518651557|ref|YP_008141077.1| 301 RRLRVSNTIERLNAEIKRRTKKIGAFPSDDSAMRLAGSIMIDINEEYV 348
                                       9********************************************997 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.3e-15   8.3e-12       2      96 .]     137     234 ..     136     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.3e-15
                              MULE   2 vvlDgTykt...n.kyklplltv.vgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekal 73 
                                       + +DgTy++   n +y+ + + + vg+++ g   +l+  + +se+e  +e ++++l+++    +  +++i+D +k++
  gi|518651557|ref|YP_008141077.1| 137 IYIDGTYLKirnNgRYRNKAIYIcVGINSDGYREVLGARIYDSETEIEWELFFDDLKDRGL--NGVEMVISDGNKGI 211
                                       789****863333477666544449*********************************644..69************ PP

                              MULE  74 lnaleevfpeakhrlClfHiakn 96 
                                       ++a+++ fp++  + C+ H+++n
  gi|518651557|ref|YP_008141077.1| 212 REAVKQSFPGSSWQYCHVHFMRN 234
                                       ********************987 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   5.3e-07    0.0019      11     165 ..      80     243 ..      72     271 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.3e-07
                      DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkg 87 
                                       +i+++ y  +++ + ++++++ lG+e+s++ ++++  r  ++++++ e+  +   + + i +D T l++ ++gr ++
  gi|518651557|ref|YP_008141077.1|  80 SIILESYLSGVSTRSVNKVIKSLGIEVSPSYVSSLSSRLDKTVNEFLERKID--GEYKFIYIDGTYLKIRNNGRYRN 154
                                       588999999************************9999999988887765333..47789*********999****** PP

                      DDE_Tnp_IS66  88 kksylWvyvtdkr....kpavlfeyspsRggevaealLag..fkG..vlvsDgyagYnklae...eqvthalCwaHl 153
                                       k  y+ v ++++       a +++ +++   e + + L++   +G  +++sDg +g ++  +   ++   ++C++H 
  gi|518651557|ref|YP_008141077.1| 155 KAIYICVGINSDGyrevLGARIYDSETEIEWELFFDDLKDrgLNGveMVISDGNKGIREAVKqsfPGSSWQYCHVHF 231
                                       **********9999777777777777777766665555666766655799********977779999999******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakk 165
                                        R++++ + +++
  gi|518651557|ref|YP_008141077.1| 232 MRNLRKSTGKQQ 243
                                       ****99987654 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.6   5.7e+03      20      47 ..      44      71 ..      16      83 .. 0.56
   2 ?   12.5   0.0   2.4e-05     0.086      39      90 ..     184     235 ..     144     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
                      DDE_Tnp_ISL3 20 dllvdggrlldilpgRkketlkaflesl 47
                                       l++dg+ +ld  + R+++  +a++++ 
  gi|518651557|ref|YP_008141077.1| 44 LLTTDGKVILDKPQFRETSFHTAVFDNY 71
                                      3334555555555555555555555544 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.4e-05
                      DDE_Tnp_ISL3  39 tlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvkla 90 
                                       + + f+++l+++  + ve+v+ D+++++++avk+ +P  +  + + H+++ +
  gi|518651557|ref|YP_008141077.1| 184 EWELFFDDLKDRGLNGVEMVISDGNKGIREAVKQSFPGSSWQYCHVHFMRNL 235
                                       55679**9*999*************************988877777777765 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       3.4   1.2e+04     105     128 ..      57      80 ..      54      83 .. 0.76
   2 ?    3.1   0.1     0.028     1e+02       6      79 ..     139     220 ..     135     252 .. 0.68
   3 ?    8.4   0.0   0.00068       2.5      85     124 ..     295     334 ..     265     342 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 3.4
                     DDE_Tnp_IS240 105 tlKkrlrptrgfkslksaaktlag 128
                                       ++++  ++t  f++ ++++k ++ 
  gi|518651557|ref|YP_008141077.1|  57 QFRETSFHTAVFDNYSRVEKSVES 80 
                                       577777888889998888888775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.028
                     DDE_Tnp_IS240   6 vDETyvkikGkwaY....lyrav..Dkegr..ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasal 74 
                                       +D Ty+ki+ + +Y    +y  v  +++g   +l++ + +   +    +f+  + ++  +  e ++ D+++   +a+
  gi|518651557|ref|YP_008141077.1| 139 IDGTYLKIRNNGRYrnkaIYICVgiNSDGYreVLGARIYDSETEIEWELFFDDLKDRGLNGVEMVISDGNKGIREAV 215
                                       899*****987777444444433225555334788888877777777778777777776666667778888777777 PP

                     DDE_Tnp_IS240  75 kelkr 79 
                                       k+ ++
  gi|518651557|ref|YP_008141077.1| 216 KQSFP 220
                                       77776 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00068
                     DDE_Tnp_IS240  85 devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                        +++ + +    n iE+ ++++K+r+++++ f s +sa +
  gi|518651557|ref|YP_008141077.1| 295 TNIQGLRRLRVSNTIERLNAEIKRRTKKIGAFPSDDSAMR 334
                                       566666677779********************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2687.33
//
Query:       gi|518651558|ref|YP_008141078.1|  [L=65]
Description: hypothetical protein FACI_IFERC00001G0197 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.2   0.0      0.034   14.0   0.0    1.1  1  DAO_C     C-terminal domain of alpha-glycerophosphate oxidase
      0.092   12.8   0.7       0.29   11.2   0.1    1.9  2  Annexin   Annexin


Domain annotation for each model (and alignments):
>> DAO_C  C-terminal domain of alpha-glycerophosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.8e-06     0.034      78     119 ..      17      58 ..      10      63 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.8e-06
                                       HHHS---SHHHHHHTTS-HHHH-HHHHHHHHHHHHHHHHHHT CS
                             DAO_C  78 vrhEmartlvDvlaRRtrlafldadaalealpevaelmaeel 119
                                       +++E  +   D++ RR+ l++  +d+++++ + + +lm+ ++
  gi|518651558|ref|YP_008141078.1|  17 IKNECPVYSGDIIRRRLALSIYSTDSGKSMENSINSLMESYY 58 
                                       7899999999****************************9875 PP

>> Annexin  Annexin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.054   4.8e+02      45      55 ..      11      21 ..       3      35 .. 0.75
   2 ?   11.2   0.1   3.3e-05      0.29      32      62 ..      31      61 ..      25      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.054
                                      S-HHHHHHHHS CS
                           Annexin 45 kdLekdIkset 55
                                       ++e+ Ik+e+
  gi|518651558|ref|YP_008141078.1| 11 DSIEDIIKNEC 21
                                      58999999987 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3.3e-05
                                      HHHHHHHHHHHHSS-HHHHHHHHS-HHHHHH CS
                           Annexin 32 lqaifeeYkkkygkdLekdIksetsGdfekl 62
                                      ++     Y + +gk++e++I+s +   +e++
  gi|518651558|ref|YP_008141078.1| 31 RRLALSIYSTDSGKSMENSINSLMESYYENT 61
                                      5666778*****************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 468.01
//
Query:       gi|518651559|ref|YP_008141079.1|  [L=297]
Description: hypothetical protein FACI_IFERC00001G0198 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-14   52.8   0.0    4.4e-14   52.2   0.0    1.3  1  DAGK_cat      Diacylglycerol kinase catalytic domain
  ------ inclusion threshold ------
       0.17   12.0   1.9       0.43   10.6   0.1    2.5  3  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain


Domain annotation for each model (and alignments):
>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   4.9e-18   4.4e-14       2     125 ..       3     119 ..       2     120 .. 0.87

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 4.9e-18
                                       EEEEE-TTCTTTTHHHHHHHCHHHHHHCTCEEEEEE--STTHHHHHHHHHHHCC-SEEEEEESHHHHHHHHHHHCTH CS
                          DAGK_cat   2 llvivNpksGkgkgekllrkvrelleeagvelelieteepgdakelakeakeegvdlivvaGGDGtvsevlngllee 78 
                                       ++++ N+++G+g++ k++++++++l+  ++ ++ ++ + p    +++ e  +  ++ ++++ GDGtv+ ++++l++ 
  gi|518651559|ref|YP_008141079.1|   3 IHILANEHAGSGNALKIMEEIKSILNRYEL-TSSFTEKDPANFIQFMDENPD--IKYLIAIDGDGTVNYAIQALAG- 75 
                                       789***********************8888.555555567777888888777..69********************. PP

                                       HCTTSEEEEEE-SS--HHHHHCT--S.SHHHHHHCHHCTBEEEEEEEE CS
                          DAGK_cat  79 latkpplgiiPlGtgNdlaralgigk.dieealesiikgetrkvdvgk 125
                                         +++ l  +P+Gtg dl r++  g+ +++e  e i  g+ rkvd+g 
  gi|518651559|ref|YP_008141079.1|  76 --KDTILIPVPAGTGSDLTRTI--GRvTVKEIPEIISGGRFRKVDLGL 119
                                       ..9999999************9..444899999999999999999986 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 ?   -1.4   0.0      0.27   2.4e+03      18      31 ..      21      34 ..      13      38 .. 0.82
   2 ?   10.6   0.1   4.8e-05      0.43       6      56 ..     145     196 ..     138     209 .. 0.78
   3 ?   -1.7   0.1      0.32   2.9e+03      55      65 ..     238     248 ..     234     271 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.27
                      MMR_HSR1_Xtn 18 etvkkilkeykihn 31
                                      e++k+il+ y +++
  gi|518651559|ref|YP_008141079.1| 21 EEIKSILNRYELTS 34
                                      78999**9998765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.8e-05
                      MMR_HSR1_Xtn   6 itstvkltkldeetvkkilk...eykihnaevliredvtvDdlidviegnrvYi 56 
                                       ++st   +++    vk+il      k   a+++i +++  +++id+i  n +Y 
  gi|518651559|ref|YP_008141079.1| 145 VNST--EHRTGSTFVKAILYyilTMKSIGADIKIGDEIIHEQIIDIIIANGQYF 196
                                       4444..33456677777775333678899*********************9996 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.32
                      MMR_HSR1_Xtn  55 YipclyvlNKi 65 
                                       Yi   yv+NK 
  gi|518651559|ref|YP_008141079.1| 238 YISDKYVINKK 248
                                       66666666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2150.35
//
Query:       gi|518651560|ref|YP_008141080.1|  [L=256]
Description: 3-ketoacyl-(acyl-carrier-protein) reductase [Ferroplasma acidarmanus fer1]
Scores for complete 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-50  169.9   0.0    8.1e-50  169.6   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    7.7e-48  162.5   0.8    8.3e-48  162.4   0.2    1.3  2  adh_short     short chain dehydrogenase
    2.8e-07   30.6   0.0    3.9e-07   30.2   0.0    1.1  1  KR            KR domain
     0.0006   19.2   0.2    0.00095   18.6   0.2    1.3  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
  ------ inclusion threshold ------
      0.023   14.2   0.0       0.85    9.0   0.0    2.3  2  Epimerase     NAD dependent epimerase/dehydratase family


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 !  169.6   0.0   2.3e-53   8.1e-50       3     232 ..      18     246 ..      16     248 .. 0.90

  Alignments for each domain:
  == domain 1  score: 169.6 bits;  conditional E-value: 2.3e-53
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnna 77 
                                        +gIG+aiA +la++G ++v+  +  e+   +++ee+ ++ +  +  +DV+ ee  ++l++++ ek+gk Dil+nna
  gi|518651560|ref|YP_008141080.1|  18 GRGIGKAIAIKLAQAGGKIVVNVRTHEDegMQTLEEVNKASSGILSMADVSTEEGRKKLFRDAIEKLGKPDILINNA 94 
                                       59******************999888775566666666654444699****************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeggsivnlssvgaervvpnynaygaaKaalealtry 154
                                       g+     +pf+++++++++ ++++nlys + l+++++    ++g i+n++s+++   +p+ ++yg++Kaal+++t+y
  gi|518651560|ref|YP_008141080.1|  95 GVGIL--EPFENIDEKHMQLMFNTNLYSPVWLSREFVSKY-DNGVIINMASLAGISPFPGLSVYGMTKAALISMTKY 168
                                       *****..*****************************9865.579********************************* PP

                                       HHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHH..HHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 155 lAvelgpkgiRvNavspgpikTlaasgikgfdellee..learaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       l  e + + iRvNav+pg++kT++ +++ +  +l e+  +++ +  g+l++p+eva+++l+L+ +e   +tGq++ +
  gi|518651560|ref|YP_008141080.1| 169 LSLEAAGHHIRVNAVAPGVVKTRMGDSLLKIMNLDEKnfSKKFTLTGKLIDPDEVADTVLYLIRNE--SMTGQVITI 243
                                       ***************************999666555421566677899***************998..69******* PP

                                       STT CS
                      adh_short_C2 230 DgG 232
                                       D+G
  gi|518651560|ref|YP_008141080.1| 244 DSG 246
                                       *99 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.4   0.2   2.3e-51   8.3e-48       1     189 [.      10     195 ..      10     200 .. 0.96
   2 ?   -4.1   0.0       2.6   9.3e+03     125     138 ..     234     247 ..     226     251 .. 0.70

  Alignments for each domain:
  == domain 1  score: 162.4 bits;  conditional E-value: 2.3e-51
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       kv +vtG ++GIG+aia +la++G k+vv v  +e++  ++++e++++ ++ +   +Dv+++e  ++l+++a++klg
  gi|518651560|ref|YP_008141080.1|  10 KVCIVTGSGRGIGKAIAIKLAQAGGKIVVnVRTHEDEGMQTLEEVNKA-SSGILSMADVSTEEGRKKLFRDAIEKLG 85 
                                       789**************************9***************996.56788889******************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       k d+L+nNAG+   +pf++++e+ ++ ++++Nl ++++l+r+++ +     +G I+n++S ag  p++g+++Y+ +K
  gi|518651560|ref|YP_008141080.1|  86 KPDILINNAGVGILEPFENIDEKHMQLMFNTNLYSPVWLSREFVSK---YDNGVIINMASLAGISPFPGLSVYGMTK 159
                                       ******************************************9999...56************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmake 189
                                       aa++++t+ l+ e a + irvnavaPG+v+T m  +
  gi|518651560|ref|YP_008141080.1| 160 AALISMTKYLSLEAAGHHIRVNAVAPGVVKTRMGDS 195
                                       *********************************876 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 2.6
                                       HCTTEEEEEEEEGG CS
                         adh_short 125 kqssGrIvnvsSva 138
                                       ++  G+++++ S  
  gi|518651560|ref|YP_008141080.1| 234 ESMTGQVITIDSGG 247
                                       45678889888865 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.1e-10   3.9e-07       4     162 ..      13     168 ..      11     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.1e-10
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tG   g+G+++a  la+ g + +v+  R+ ++de ++ +++e+++    +  +a Dvs ++  ++l++++ ++ +
  gi|518651560|ref|YP_008141080.1|  13 IVTGSGRGIGKAIAIKLAQAGGK-IVVNVRT-HEDEGMQ-TLEEVNKASSGILSMA-DVSTEEGRKKLFRDAIEKLG 85 
                                       89*****************9975.7777888.5566655.9999999999997765.**************999998 PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHH.HHTTTS--SEEEEEEEHHHHH--TT-HHHHHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLh.elledesldffvlfSSiagllgsagqanYaaaNafl 156
                                       +    i+ Agv   +++e+ ++++++ +++  +     L  e++++ +  +++ ++S+ag+   +g + Y  + a l
  gi|518651560|ref|YP_008141080.1|  86 KPDILINNAGVGILEPFENIDEKHMQLMFNTNLYSPVWLSrEFVSKYDNGVIINMASLAGISPFPGLSVYGMTKAAL 162
                                       9999****************************9987777615667789999*******************9999888 PP

                                       HHHHHH CS
                                KR 157 Dalaey 162
                                        ++ +y
  gi|518651560|ref|YP_008141080.1| 163 ISMTKY 168
                                       777666 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   0.2   2.6e-07   0.00095      31     127 ..       4      94 ..       1     102 [. 0.84

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.6e-07
                                       BS-GTTSEEEEES-SH.HHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-.SEEEE-S--STTT CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGr.IGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaes.Divslhlpltpet 105
                                        +++++k   + G Gr IG+a+a +l++ g k+++  r+++  +    +g  +++lee+ + s  i+s++   t+e 
  gi|518651560|ref|YP_008141080.1|   4 MYDIKDKVCIVTGSGRgIGKAIAIKLAQAGGKIVVNVRTHE--D----EG--MQTLEEVNKASsGILSMADVSTEEG 72 
                                       56899999999****88****************99988844..2....23..578999987651577777789**** PP

                                       TTSBSHHHHHCSTTTEEEEESS CS
                      2-Hacid_dh_C 106 rhlinaeelakmkkgailiNta 127
                                       r+ + +++++k+ k  iliN a
  gi|518651560|ref|YP_008141080.1|  73 RKKLFRDAIEKLGKPDILINNA 94 
                                       ********************87 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.0   0.00024      0.85       2      75 ..      13      97 ..      12     120 .. 0.72
   2 ?    3.4   0.0     0.012        45     134     160 ..     147     173 ..     126     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00024
                                      EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HH....HHHHHHHHH.T-SEEE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrs....alerlfkee.qpdavi 69
                                      +VtG    iG+a++ +l+++g ++++  r  +++  + le++       l  +d+  ++     +++++++  +pd+ i
  gi|518651560|ref|YP_008141080.1| 13 IVTGSGRGIGKAIAIKLAQAGGKIVVNVRTHEDEGMQTLEEVnkassgILSMADVSTEEgrkkLFRDAIEKLgKPDILI 91
                                      79*******************7744444444444444445555699996666666655533556777777778899999 PP

                                      E--S-- CS
                         Epimerase 70 hlAavg 75
                                      + A+vg
  gi|518651560|ref|YP_008141080.1| 92 NNAGVG 97
                                      988865 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.012
                                       S----SSHHHHHHHHHHHHHHHHHHHH CS
                         Epimerase 134 gplkpnspYaaaKlageklveayaaqy 160
                                       +p++  s Y+++K+a  ++++++  + 
  gi|518651560|ref|YP_008141080.1| 147 SPFPGLSVYGMTKAALISMTKYLSLEA 173
                                       688999*************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1797.57
//
Query:       gi|518651561|ref|YP_008141081.1|  [L=373]
Description: hypothetical protein FACI_IFERC00001G0200 [Ferroplasma acidarmanus fer1]
Scores for complete 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-95  318.7   0.0    4.6e-95  318.5   0.0    1.0  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    1.2e-20   74.3   0.1    1.5e-10   41.2   0.2    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase
     0.0082   15.3   0.0       0.37    9.9   0.1    2.5  2  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.21   11.9   0.0    1.8  1  FAM25         FAM25 family


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 !  318.5   0.0     1e-98   4.6e-95       3     364 .]       8     365 ..       6     365 .. 0.95

  Alignments for each domain:
  == domain 1  score: 318.5 bits;  conditional E-value: 1e-98
                                       EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-T CS
                            Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalare 79 
                                       +i+fg+ +l      l++l +kra+iv dk++ +k+g++d v++ l  +g e+ ++d+++++p+++ +++ ++ +++
  gi|518651561|ref|YP_008141081.1|   8 QIIFGDESLG----FLESLSIKRAVIVSDKNI-RKAGIVDLVIKNL--HGTELLIIDDIPEEPEYRAIAKHLDEINQ 77 
                                       6888887774....55666689*********6.5************..***************************** PP

                                       T.--EEEEEESHHHHHHHHHHHHHTT....................--EEEEESS-S-S-TT-SEEEEE.-TTSEEE CS
                            Fe-ADH  80 egadvviavGGGsviDtAKaialllanpe..vedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegekl 154
                                       +++d++i+vGGGsviD  K++ + +++p+  + d+    k + +++ +li iPTt+GtGse+t++avi+de e++k 
  gi|518651561|ref|YP_008141081.1|  78 FKPDYFISVGGGSVIDSSKILFFKYERPDleFYDVTPLVKLNLRQKSKLISIPTTSGTGSECTWAAVISDEMENRKD 154
                                       **************************987677777777788899999****************************** PP

                                       EE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 155 sifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedle 231
                                       ++++pe++Pd+ai+Dp+++ +lPk +t++t+ Da++ha+E y+s+ +np+sda+a++ai+li+ ++ ++v+d+e+le
  gi|518651561|ref|YP_008141081.1| 155 ELASPEIMPDYAILDPQMVKSLPKTQTINTATDAITHAIEGYTSRWNNPYSDAMAEKAIELIIPSIVKLVKDPENLE 231
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHSS---HHHHHHHHHHC.CGGGGGS-HHHHHHHHH..........HHHHHHT.......T- CS
                            Fe-ADH 232 areqmllastlaglafsnaglgavHalahalgalfgiphglanaillpavlrfnaeaaperlaqlaralggesdeea 308
                                        r ++++++ +agl+fsn+++g++Hal+h+lga+f+++hg +++i+lp v++fn++aa e++++l   +    +  +
  gi|518651561|ref|YP_008141081.1| 232 LRNNVHIGASMAGLSFSNSQIGLAHALGHSLGAMFHVAHGKSVGIFLPGVIKFNYAAAGEKYQRLNLLIP---EMYR 305
                                       *******************************************************9999*********94...679* PP

                                       -HHHHHHHHHHHHHTT---SHHHHT-TT-HH....HHHHHHHT-TSGGGGSSS---HHHH CS
                            Fe-ADH 309 aeeliealrellkelglptsLselgvdeedl....dklaeaalkdrslannpreltaedv 364
                                        + l e +  +lk+lg   ++se g+de+++    dkl++ a ++  + +np  ++++d+
  gi|518651561|ref|YP_008141081.1| 306 GKTLYESIVIILKALGQTIRISETGIDEKAFrnnlDKLVSLASESTGIVTNPADASRDDI 365
                                       ****************************8555555*******************999986 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 !   31.1   0.0     4e-11   1.8e-07      12     100 ..      17     104 ..      12     109 .. 0.90
   2 !   41.2   0.2   3.4e-14   1.5e-10      97     250 .]     121     275 ..     110     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4e-11
                          Fe-ADH_2  12 ellkelelkkvllvadentkka.agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGti 87 
                                        +l++l++k++++v+d+n+ ka + + v ++l+    ++ ++++  ee++  +++k ++++++ + d +++vGgG++
  gi|518651561|ref|YP_008141081.1|  17 GFLESLSIKRAVIVSDKNIRKAgIVDLVIKNLHGT--ELLIIDDIPEEPEYRAIAKHLDEINQFKPDYFISVGGGSV 91 
                                       589999**************998899999999777..6777999********************************* PP

                          Fe-ADH_2  88 iDiakyvsaklnv 100
                                       iD +k++ +k ++
  gi|518651561|ref|YP_008141081.1|  92 IDSSKILFFKYER 104
                                       ******9888766 PP

  == domain 2  score: 41.2 bits;  conditional E-value: 3.4e-14
                          Fe-ADH_2  97 klnvpyvsvpTaaSvDGfaspgaslvvd..gkkrtv.akaaaPlaviaDldvlaeAPrrllasGvGDllgkytalad 170
                                       +++ +++s+pT+    + +   a +  +  ++k  +  +  +P   i+D ++++  P+  +     D++   +  ++
  gi|518651561|ref|YP_008141081.1| 121 RQKSKLISIPTTSGTGSECTWAAVISDEmeNRKDELaSPEIMPDYAILDPQMVKSLPKTQTINTATDAITHAIEGYT 197
                                       677899*****9887777777777766566778888889999*999******************************* PP

                          Fe-ADH_2 171 wklanevseplaklsaamvqeaaeklvedkketealeellealalsgigisrpaSGsEHliSHaldmlalkqalHGe 247
                                       ++ +n +s+ +a+++++ +  ++ klv+d+++ e+ +++  +  ++g+++s++  G  H + H l +++  ++ HG+
  gi|518651561|ref|YP_008141081.1| 198 SRWNNPYSDAMAEKAIELIIPSIVKLVKDPENLELRNNVHIGASMAGLSFSNSQIGLAHALGHSLGAMF--HVAHGK 272
                                       *********************************************************************..****** PP

                          Fe-ADH_2 248 qVG 250
                                       +VG
  gi|518651561|ref|YP_008141081.1| 273 SVG 275
                                       **9 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.016        72      17      44 ..      66      93 ..      61     100 .. 0.87
   2 !    9.9   0.1   8.2e-05      0.37      94     208 ..     162     278 ..     159     342 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.016
                                      HHHHHHHHHTT--TT-EEEEEESHHHHH CS
                      DHQ_synthase 17 ekildalleakleRksllialGGGvvgD 44
                                      + i + l e +  + ++ i++GGG v D
  gi|518651561|ref|YP_008141081.1| 66 RAIAKHLDEINQFKPDYFISVGGGSVID 93
                                      678888899999999***********99 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 8.2e-05
                                       --SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHC.TTTHHHHHHHH..HHHHHHHHHHHH CS
                      DHQ_synthase  94 qPkavlidlevLktLperelraGlaEviKyalikdeelfelleenaeallk.eeeeealeeli..arsievkaevve 167
                                       +P++ ++d++++k+Lp+ ++++  +++i +a+   ++ ++   ++a a  + e    ++ +l+   + +e++ +v  
  gi|518651561|ref|YP_008141081.1| 162 MPDYAILDPQMVKSLPKTQTINTATDAITHAIEGYTSRWNNPYSDAMAEKAiELIIPSIVKLVkdPENLELRNNVHI 238
                                       69999************************998777766554433332222222222333333322122233322222 PP

                                       HCCTT..TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHH CS
                      DHQ_synthase 168 eDeke..kglralLnlGHtigHaiEallgyekllHGeaVaiGm 208
                                              +   + + l H +gH + a++++    HG++V i +
  gi|518651561|ref|YP_008141081.1| 239 GASMAglSFSNSQIGLAHALGHSLGAMFHV---AHGKSVGIFL 278
                                       211111133344588999999999999887...9**9998744 PP

>> FAM25  FAM25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.7e-05      0.21      39      61 ..     173     196 ..     169     199 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.7e-05
                             FAM25  39 vKevtekvt.ntvtnavtHAaEgL 61 
                                       vK   ++ t nt t+a+tHA+Eg 
  gi|518651561|ref|YP_008141081.1| 173 VKSLPKTQTiNTATDAITHAIEGY 196
                                       66665554449***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2769.83
//
Query:       gi|518651562|ref|YP_008141082.1|  [L=412]
Description: hypothetical protein FACI_IFERC00001G0201 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      4e-41  141.8   0.0    4.5e-41  141.6   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    6.7e-07   28.8   0.0    0.00032   20.0   0.0    2.2  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.6e-05   24.2   0.0    2.8e-05   23.5   0.0    1.4  1  Thi4            Thi4 family
      2e-05   23.9   0.0    0.00012   21.4   0.0    2.1  2  FAD_binding_2   FAD binding domain
    8.4e-05   22.7   0.0     0.0002   21.5   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00021   21.8   0.0       0.55   10.8   0.0    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.001   17.7   0.0     0.0014   17.3   0.0    1.1  1  Mqo             Malate:quinone oxidoreductase (Mqo)
     0.0012   18.8   0.0     0.0018   18.2   0.0    1.3  1  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.013   14.4   0.0      0.039   12.8   0.0    1.6  2  Trp_halogenase  Tryptophan halogenase
      0.015   14.3   0.0      0.022   13.9   0.0    1.2  1  Lycopene_cycl   Lycopene cyclase protein
      0.051   12.7   0.0      0.076   12.1   0.0    1.2  1  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.062   13.6   0.5      0.062   13.6   0.5    1.8  2  Rep_Org_C       Putative replisome organiser protein C-termin
      0.073   12.3   0.0       0.11   11.7   0.0    1.2  1  FAD_binding_3   FAD binding domain
      0.085   11.5   0.0       0.12   11.0   0.0    1.2  1  HI0933_like     HI0933-like protein
      0.088   11.9   0.0       0.16   11.1   0.0    1.4  1  GIDA            Glucose inhibited division protein A


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 !  141.6   0.0   3.8e-44   4.5e-41       1     352 []       4     379 ..       4     379 .. 0.80

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 3.8e-44
                                       EEEEECTSHHHHHHHHHHHHTT....EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHH CS
                               DAO   1 dvviiGGGiiGlstAyeLarrg....VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelrelee 73 
                                       dvv+iG+Gi+Gls Ay+L ++     +++++k + +++g + ++++ ++  +  l+e+ +   +++ a++++++l++
  gi|518651562|ref|YP_008141082.1|   4 DVVVIGAGITGLSSAYHLKKKDsslkILVVDKFKTFSQGNTAKSAAAFRDFFT-LREN-Q--VMAQTAINFYKHLQN 76 
                                       9*****************87756899************************776.7766.4..5777779******** PP

                                       HHSSTTSEEEEEEEEEESSHHHHHHHHHHHHHH..HHTTT.TE.EE.EEHHHHHHHSTTSTTTSEEEEETTEEEEEH CS
                               DAO  74 elgididyrrtGllslaadeeelealdkllall..leagl.da.el.ldaeevrelepalpgllgalfypdtgqvdp 145
                                       + ++d++ + tG+l+l++ e+ ++ + k  +++     +l +   l +d++ +re+   ++ ++ a+ + ++g+++p
  gi|518651562|ref|YP_008141082.1|  77 DMDVDLGMKFTGYLFLFDHEKARDFISKYPHSRfvD-EDLsEIfNLnIDKD-TREVMG-IDSIKSAVIDENAGIIEP 150
                                       ****************96555555554444444742.44423345667887.888886.679*************** PP

                                       HHHHHHHHHHHHHTT-EEEESECEEEEEE.EE............TCEEEEE.EECT.EEEEEEEEEEE--GGGHH.H CS
                               DAO 146 akltaalaraaealGveilegtevtglee.ed............gkvwgve.rttp.gendaadavVnaaGawsd.l 206
                                         l +++++++ + Gv++ ++t v++l   +d             k ++++  +t+ g+ ++ d  V+++ +w++ l
  gi|518651562|ref|YP_008141082.1| 151 DLLSKWYYDRLLEMGVNFMFNTFVKKLVLaPDtslnypgepfnwQK-SEIKyAETDkGILES-DFYVLCTDVWTTaL 225
                                       **************************83435456666655555422.333376777788766.99*********977 PP

                                       HHTTCTT..TSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE...EEETTTTEEEEEETTSEEEEEESSE....EETT CS
                               DAO 207 lgllkel..dlpispvrgqvlvlkplseklvspaailpvpe...tdddgrgvyvtprkdgrvlvGgtad....eesg 274
                                       l   +++  d  ++p + q++ +  +  + +  ++i+++      +   +gvy++p+++ +    + ad    + ++
  gi|518651562|ref|YP_008141082.1| 226 L---NPVgiDSHLRPKKRQIFQITSPGIQKLIGKNIFNDSGvfpFTIFPTGVYMRPYPQANSFWTSLADelnrD-FS 298
                                       7...555568899**********555555666667776666899888889999999987766666655568843.44 PP

                                       CSS.TSCSHHHHHH.HHHHHHHHSGG..GCGEEEEEEEEEE..ETTSSEEEEEEETEEEEEEEEECTTTHHHHHHHH CS
                               DAO 275 ddd.pevdeedide.llealrklfPq..lgdvlrkwaGlrp..lpdglpligetpgvkglylatGhsghGltlapat 345
                                       +++ pe++++ + + + + l ++fP+  +++++ +waG++   + d +p+i ++    +l++++G  g G++ +  +
  gi|518651562|ref|YP_008141082.1| 299 FTEnPEPEPDFYTYnIKPILDNYFPAseDSRITASWAGYYSynTIDFMPYIFNE---INLIVVSGSTGGGIMKGDSI 372
                                       444599999999998999999*****5447799********7447******994...6******************* PP

                                       HHHHHHH CS
                               DAO 346 Gkllael 352
                                       G+++a +
  gi|518651562|ref|YP_008141082.1| 373 GRIVAAR 379
                                       ****975 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 !   20.0   0.0   2.7e-07   0.00032       1      41 [.       3      45 ..       3     145 .. 0.83
   2 !    6.9   0.0    0.0026       3.1     184     234 ..     152     217 ..     137     224 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.7e-07
                                      CSEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHH CS
                                      xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcl 41
                                      +dvvviG+G+ Gl+ a +l++  +++k+++v++ +t+  g   
  gi|518651562|ref|YP_008141082.1|  3 YDVVVIGAGITGLSSAYHLKKkdSSLKILVVDKFKTFSQGNTA 45
                                      69*******************777*******877766655444 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHHHHTTEEEEESCEEEEEEETTE...............EEEEEETTSCEEEESEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 184 elsaaleealekeGvevklgtsvkeidgnge...............klevvledgeeidadlvvva 234
                                        ls+++ ++l ++Gv+++++t vk++   ++               ++++ ++d+  ++ d  v++
  gi|518651562|ref|YP_008141082.1| 152 LLSKWYYDRLLEMGVNFMFNTFVKKLVLAPDtslnypgepfnwqksEIKYAETDKGILESDFYVLC 217
                                       5799********************987776666777776776665555566666666766666666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.3e-08   2.8e-05      17      54 ..       2      40 ..       1      80 [. 0.86

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.3e-08
                                      EEEEEEE--SHHHHHHHHHHHHC.TTS-EEEEESSSS-- CS
                              Thi4 17 esDvvivGaGssGLtaayylakk.pdlkvailersvspG 54
                                      + Dvv++GaG +GL++ay l kk   lk++++++  ++ 
  gi|518651562|ref|YP_008141082.1|  2 KYDVVVIGAGITGLSSAYHLKKKdSSLKILVVDKFKTFS 40
                                      67*********************999*****99765554 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   9.7e-08   0.00012       1      43 [.       4      49 ..       4      73 .. 0.85
   2 ?   -0.7   0.0      0.47   5.6e+02     148     169 ..     158     179 ..     149     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.7e-08
                                      SEEEE--SHHHHHHHHHHHHTTT..-EEEEESSSGGGS.GGGG--S CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGl..kvavvekeqefgg.atawsqG 43
                                      Dv+ViG+G+ GL++A+ ++++    k++vv+k + f+  +ta s +
  gi|518651562|ref|YP_008141082.1|  4 DVVVIGAGITGLSSAYHLKKKDSslKILVVDKFKTFSQgNTAKSAA 49
                                      9*******************77656*******98876558887765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.47
                                       HHHHHTCTEEEEESEEEEEEEE CS
                     FAD_binding_2 148 vesarkagvdfqerteadeLiv 169
                                       +++++++gv f+++t++++L+ 
  gi|518651562|ref|YP_008141082.1| 158 YDRLLEMGVNFMFNTFVKKLVL 179
                                       78999***************87 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.7e-07    0.0002       1      29 [.       7      37 ..       7      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrd 29
                                      ++GaG++Gl+ Ay+L+k+   +++l+++k  
  gi|518651562|ref|YP_008141082.1|  7 VIGAGITGLSSAYHLKKKdsSLKILVVDKFK 37
                                      8***************9866889*****965 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00046      0.55       2      27 ..       5      30 ..       4      66 .. 0.80
   2 !    8.4   0.0    0.0026       3.1      38      70 ..     149     181 ..     136     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00046
                                      EEEECSSHHHHHHHHHHHHTTSEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtv 27
                                      vvv+G+G +gl  A  l++  ++ ++
  gi|518651562|ref|YP_008141082.1|  5 VVVIGAGITGLSSAYHLKKKDSSLKI 30
                                      8****************998764433 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0026
                                       SSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox  38 lDeeaskilqeklekngievllntkveeiegse 70 
                                       +++ +sk+  ++l ++g+++++nt v++++  +
  gi|518651562|ref|YP_008141082.1| 149 EPDLLSKWYYDRLLEMGVNFMFNTFVKKLVLAP 181
                                       566789*********************998655 PP

>> Mqo  Malate:quinone oxidoreductase (Mqo)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   1.2e-06    0.0014       2     116 ..       2     112 ..       1     120 [. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.2e-06
                               Mqo   2 kvdvvliGaGimsatlgvllkelepelsievlerldkvaeessnawnnaGtGHsalcElnYtpekedgsidiskAvk 78 
                                       k+dvv+iGaGi   + +  lk+ +++l+i v+++ ++ ++ ++++   a      +  l   +  ++  i+  k ++
  gi|518651562|ref|YP_008141082.1|   2 KYDVVVIGAGITGLSSAYHLKKKDSSLKILVVDKFKTFSQGNTAKSAAAFRD---FFTLRENQVMAQTAINFYKHLQ 75 
                                       68*************************************9999888777555...55555566667789******** PP

                               Mqo  79 ineqfevsrqfwaylvekgllkdpkefinkvpHlsfva 116
                                          + ++  +f  yl   ++  ++++fi+k pH  fv 
  gi|518651562|ref|YP_008141082.1|  76 NDMDVDLGMKFTGYLFLFDHE-KARDFISKYPHSRFVD 112
                                       **************9988875.789*********9996 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 !   18.2   0.0   1.5e-06    0.0018       1      48 [.       6      51 ..       6     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.5e-06
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdp.sepgagrvwrtdqse 48
                                      +++GaG++Gl+ + +L ++   +s+l+i ++d+ +++ +g  ++++ + 
  gi|518651562|ref|YP_008141082.1|  6 VVIGAGITGLSSAYHLKKK---DSSLKILVVDKfKTFSQGNTAKSAAAF 51
                                      69**************999...7**********6666878887776554 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05     0.039       1      70 [.       4      69 ..       4      73 .. 0.84
   2 ?    1.0   0.0      0.13   1.5e+02     123     184 ..      62     127 ..      44     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--THHHHTHHHHT--HHHHCHHCT-E CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatipsirkllrlLgideeeflreteat 70
                                      ++v++G+G+ G  +A +l+k    +l++++v++ +++    G  t  s   + +++ + e++ +++t   
  gi|518651562|ref|YP_008141082.1|  4 DVVVIGAGITGLSSAYHLKKKD-SSLKILVVDKFKTFS--QGN-TAKSAAAFRDFFTLRENQVMAQTAIN 69
                                      69******************99.558888887766555..554.7788899**************99876 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                       H-SCHHHHHTTB-SB-TT...S-B-S--EEEE-HHHHHHHHHHHHHHCT-EEEE--EEEEEE-T.T CS
                    Trp_halogenase 123 sleavaakakkfsprekd...glsalsyAyhldaalyakfLrrvaearGvtrvegkvvevqlde.d 184
                                        ++++a++  k  +  +d   g++ + y + +d+++  +f+ ++ ++r v+    ++ + ++d+ +
  gi|518651562|ref|YP_008141082.1|  62 VMAQTAINFYKHLQNDMDvdlGMKFTGYLFLFDHEKARDFISKYPHSRFVDEDLSEIFNLNIDKdT 127
                                       3444444444555555558888999999****************9999999998888888888744 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.8e-05     0.022       1      32 [.       4      35 ..       4      62 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      DvvviGaG  gls A +l ++   lk+++++ 
  gi|518651562|ref|YP_008141082.1|  4 DVVVIGAGITGLSSAYHLKKKDSSLKILVVDK 35
                                      9*****************99999*****9986 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.3e-05     0.076       3      39 ..       3      39 ..       1      41 [. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.3e-05
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalflerqpef 39
                                      +D++ iG+G   Ls a +l+++++ lk+l++++ ++f
  gi|518651562|ref|YP_008141082.1|  3 YDVVVIGAGITGLSSAYHLKKKDSSLKILVVDKFKTF 39
                                      9*******************************98888 PP

>> Rep_Org_C  Putative replisome organiser protein C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.5   5.2e-05     0.062       8      64 ..      33      87 ..      27     116 .. 0.84
   2 ?   -3.1   0.1       8.3     1e+04      59      71 ..     334     346 ..     318     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.2e-05
                         Rep_Org_C  8 ldsfinfsskniskravalaeflklpsfqkeqavigaknyiqsyknehpddkagkys 64
                                      +d f  fs+ n +k a a  +f+ l +   + + ++a n++++ +n+   d   k++
  gi|518651562|ref|YP_008141082.1| 33 VDKFKTFSQGNTAKSAAAFRDFFTLREN--QVMAQTAINFYKHLQNDMDVDLGMKFT 87
                                      699*********************9765..46778999*999999999888887775 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 8.3
                         Rep_Org_C  59 kagkysvnayefl 71 
                                        ag ys n+++f+
  gi|518651562|ref|YP_008141082.1| 334 WAGYYSYNTIDFM 346
                                       4678999999887 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.1e-05      0.11       2      39 ..       3      42 ..       2      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.1e-05
                                      EEEEEE--SHHHHHHHHHHHHTTHH..EEEEESSSSSCCS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvr..vvlvekrsttvvl 39
                                      +dV+++GaG +Gl++a  L+++  +   ++v+k +t ++ 
  gi|518651562|ref|YP_008141082.1|  3 YDVVVIGAGITGLSSAYHLKKKDSSlkILVVDKFKTFSQG 42
                                      79*****************998433558899998888775 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0001      0.12       1      35 [.       3      39 ..       3      42 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0001
                                      -SEEEE--SHHHHHHHHHHHHTT..--EEEE-SSSSS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrg..krVlllekakkl 35
                                      +dv+viG+G  Gl  A +++k++   ++l+++k k++
  gi|518651562|ref|YP_008141082.1|  3 YDVVVIGAGITGLSSAYHLKKKDssLKILVVDKFKTF 39
                                      59*****************666511678899987765 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00013      0.16       1      34 [.       4      38 ..       4      52 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE.ES-GGG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi.thkldt 34
                                      dv+ViG+G  G+  A++++++  + +++ + k++t
  gi|518651562|ref|YP_008141082.1|  4 DVVVIGAGITGLSSAYHLKKKDSSLKILvVDKFKT 38
                                      79******************998876553444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.57
# Mc/sec: 2191.36
//
Query:       gi|518651563|ref|YP_008141083.1|  [L=235]
Description: hypothetical protein FACI_IFERC00001G0202 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1528.11
//
Query:       gi|518651564|ref|YP_008141084.1|  [L=566]
Description: hypothetical protein FACI_IFERC00001G0203 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-39  134.4  61.9    4.3e-39  134.4  61.9    2.8  2  MFS_1     Major Facilitator Superfamily
    5.2e-06   25.1   7.4    5.2e-06   25.1   7.4    2.4  2  MFS_3     Transmembrane secretion effector
    0.00075   18.5  16.6    0.00075   18.5  16.6    2.8  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.63    8.3  15.3      0.023   13.0   3.0    3.2  3  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.4  61.9   9.5e-43   4.3e-39       2     351 ..      12     425 ..      11     427 .. 0.84
   2 ?   -1.1   0.3      0.16   7.1e+02     153     171 ..     525     541 ..     470     555 .. 0.63

  Alignments for each domain:
  == domain 1  score: 134.4 bits;  conditional E-value: 9.5e-43
                             MFS_1   2 llaaflsalarsilgpalpl.alaedlg....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfa 73 
                                        +++++++++ si+++alp+ +++ +l+    +s   + +l+  y+++ +v+ + +G lsd fGr +++ lg+l+f 
  gi|518651564|ref|YP_008141084.1|  12 TIGQLMATINTSIIIVALPSiFVGIHLNpmqaSSFPYLLWLIMSYMIVLSVLLVSIGKLSDIFGRVKIFNLGFLIFT 88 
                                       58999**************988888888877777777999************************************* PP

                             MFS_1  74 lglllllfa....sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla 145
                                       +g++ll +a     ++   l+++r++q++g+++++++  a+i+d f+++erg+ai++ s+++  G+ +g +lgg+l+
  gi|518651564|ref|YP_008141084.1|  89 IGSILLYIApgtgYTVAlELIIFRIVQAVGGAFIMANTFAIITDNFSPKERGFAISINSVAAVSGVSIGVVLGGILS 165
                                       **44444555655556666********************************************************** PP

                             MFS_1 146 sslgWravfyilaivsllafvlfllll.peepperkrkspkeee................................. 188
                                         + Wr +f+i  ++++++ +   + +   ++++++  ++  +                                  
  gi|518651564|ref|YP_008141084.1| 166 -TIYWRDIFLISIPIGVFGTL---WSFlKLKDVRERAARH-IDIpgnilfavgliilllgvtygitpyrnnpmgwtn 237
                                       .556***************99...4441333333333333.333366889***********************9999 PP

                             MFS_1 189 ....................kgtgpaplvpawkallkdpvlwillialllfffgfsglltllpl.....ylqevlgl 240
                                                           + +++ p+++  ++++++++  ++++a++++ + ++gl+++l+l     +    +g+
  gi|518651564|ref|YP_008141084.1| 238 plvisalaigaimlvlfpfvENRVKGPMFD-MRLFKSRNFSISIFTAFVSA-MTMMGLMYMLTLifqgiW-LPIRGY 311
                                       999********9999999999999999999.77777777333455555555.466665555555333432.333333 PP

                             MFS_1 241 s...glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfgl 314
                                           + l ag+++  l +++ il++l+++l+ r+ +r+ ++++l++  +a+l+l+ l    s+v+l++v+ ++G+g+
  gi|518651564|ref|YP_008141084.1| 312 RyavTPLWAGIYMLPLPIFMGILGVLSSKLAERFDARWLTTIGLFISGFALLALVTLTYNFSYVFLAIVISIFGIGY 388
                                       355647******************************999999999999999999999999999*9999********* PP

                             MFS_1 315 gfvfpsllalasdlappeeagtasglfntagslggal 351
                                       g+++++ l++a++++p++e+g+ sg+ nt+++ g a 
  gi|518651564|ref|YP_008141084.1| 389 GIFNVPNLTVAMSSVPADERGATSGILNTMRNTGYAA 425
                                       ********************************99875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.16
                             MFS_1 153 vfyilaivsllafvlflll 171
                                       vfy+  ++s++a++    l
  gi|518651564|ref|YP_008141084.1| 525 VFYVGFGASIIAGIA--SL 541
                                       444444444444442..22 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   7.4   1.2e-09   5.2e-06      58     164 ..      62     166 ..       3     200 .. 0.78
   2 !    4.4   1.2    0.0023        10      56     118 ..     327     389 ..     324     433 .. 0.68

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.2e-09
                             MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr 134
                                       +  l +  G l+D+f r k++  + l+  ++s+ll +   +g++    l+++ ++ ++G a+ +    A++ +  + 
  gi|518651564|ref|YP_008141084.1|  62 V--LLVSIGKLSDIFGRVKIFNLGFLIFTIGSILLYIAPGTGYTVALELIIFRIVQAVGGAFIMANTFAIITDNFSP 136
                                       2..223469******************************************************************** PP

                             MFS_3 135 rdvpaAvaLnsvginiaRsvGPAlgGvlva 164
                                       ++   A+ +nsv      s+G  lgG+l +
  gi|518651564|ref|YP_008141084.1| 137 KERGFAISINSVAAVSGVSIGVVLGGILST 166
                                       **************************9855 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0023
                             MFS_3  56 LPif..llsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaa 118
                                       LPif  +l +l+  la+ fd R++  ++  + +++ +ll++++++  +s + l +++ + giG  
  gi|518651564|ref|YP_008141084.1| 327 LPIFmgILGVLSSKLAERFDARWLTTIGL-F-ISGFALLALVTLTYNFSYVFLAIVISIFGIGYG 389
                                       888844599*************9766554.3.344444444444444444444444455555544 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5  16.6   1.7e-07   0.00075      41     188 ..      42     187 ..       6     193 .. 0.81
   2 !    3.7   4.9    0.0049        22      63     152 ..     335     424 ..     319     436 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.7e-07
                                       HHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT..SS-TGGGGGHHHHHHH CS
                          Sugar_tr  41 keessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk..nsvevlivgRvlvGig 115
                                       +++s  ++ ++  +++++  +  + +g+l+d+fGR k++  + ++f ig++l ++a+g+  +    li+ R++  +g
  gi|518651564|ref|YP_008141084.1|  42 QASSFPYLLWLIMSYMIVLSVLLVSIGKLSDIFGRVKIFNLGFLIFTIGSILLYIAPGTgyTVALELIIFRIVQAVG 118
                                       4445567789999999999999***********************************99766667899******999 PP

                                       HHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                          Sugar_tr 116 vGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                         ++ + +   i  +  +k Rg+ +s++ +a + G  ++ ++g +l+++     wr  + +++ + ++  ++ 
  gi|518651564|ref|YP_008141084.1| 119 GAFIMANTFAIITDNFSPKERGFAISINSVAAVSGVSIGVVLGGILSTIY----WRDIFLISIPIGVFGTLWS 187
                                       88777666666666666677***********************9998875....6777777777777766665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.0049
                                       HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHH CS
                          Sugar_tr  63 slfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgal 139
                                       ++++++l++rf+ ++   i+ +++  + +  ++ + ++s+  l++   + Gig G+++v   + +    p++ Rga 
  gi|518651564|ref|YP_008141084.1| 335 GVLSSKLAERFDARWLTTIGLFISGFALLALVTLTYNFSYVFLAIVISIFGIGYGIFNVPNLTVAMSSVPADERGAT 411
                                       45678899******9988887777555555555554466666666677777777777665555555555******** PP

                                       HHHHHHHHHHHHH CS
                          Sugar_tr 140 vslyqlaitfGil 152
                                        ++ +++  +G  
  gi|518651564|ref|YP_008141084.1| 412 SGILNTMRNTGYA 424
                                       ***9999999964 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 ?   13.0   3.0     5e-06     0.023     137     196 ..     110     169 ..      12     179 .. 0.94
   2 ?   -3.3   2.7      0.43   1.9e+03     295     348 ..     280     336 ..     264     377 .. 0.44
   3 ?    3.4   0.1    0.0041        18     461     504 ..     374     418 ..     369     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 137 laqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllklyv 196
                                       +  +++++G++ i++   + i Dn ++k+  + ++i +++++ G+ +G +lG++l  +y 
  gi|518651564|ref|YP_008141084.1| 110 IFRIVQAVGGAFIMANTFAIITDNFSPKERGFAISINSVAAVSGVSIGVVLGGILSTIYW 169
                                       5578999**************************************************995 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 0.43
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 295 ifllvilssvfeillvaGfitFlpkylE...tqFslsaseAnlltGvvvipgaalGi 348
                                       if+ ++ + +++ l+++   +F   +l     ++ +++  A +++ ++ i++++lG+
  gi|518651564|ref|YP_008141084.1| 280 IFTAFVSAMTMMGLMYMLTLIFQGIWLPirgYRYAVTPLWAGIYMLPLPIFMGILGV 336
                                       233333333333333333333333333211123444444444444444444444443 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.0041
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 461 llflill.flvsflgalgrvpallvilRcVkkedksfalGlqlll 504
                                       ++fl+++ +++ +   + +vp+l+v + +V+ +++  + G+  ++
  gi|518651564|ref|YP_008141084.1| 374 YVFLAIViSIFGIGYGIFNVPNLTVAMSSVPADERGATSGILNTM 418
                                       566655415666667899********************9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 3690.54
//
Query:       gi|518651565|ref|YP_008141085.1|  [L=229]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-09   37.0   0.0    4.7e-09   36.5   0.0    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00048   20.8   0.0    0.00065   20.4   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
     0.0009   19.2   0.0     0.0014   18.5   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0025   18.2   0.0     0.0044   17.4   0.0    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.053   13.7   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
       0.12   12.3   0.0        0.2   11.6   0.0    1.3  1  FR47             FR47-like protein


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.6e-12   4.7e-09      42     116 ..      46     117 ..       5     118 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.6e-12
                                       TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEETTEHHHHHHHHHTT CS
                    Acetyltransf_1  42 geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlaveedndaairlYeklG 116
                                       +e+ Gfi l +  d   +  +  +l V pe r++ +G++Ll+ ++++a ++g+k + + ve +n ++irl e +G
  gi|518651565|ref|YP_008141085.1|  46 QEIDGFIKLEPLAD---KSLWFSGLRVGPESRRNHVGTKLLKFALDHAINNGYKSLRCMVETNNIPSIRLMESFG 117
                                       55778888888888...889999************************************************9998 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   2.2e-07   0.00065      66     137 ..      49     118 ..       5     119 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.2e-07
                    Acetyltransf_3  66 iGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGf 137
                                        G++ l +l +++  +  g++++p+++++ ++t  ++ +l++a ++  ++ l++ ++++N  Sir++e+ G+
  gi|518651565|ref|YP_008141085.1|  49 DGFIKLEPLADKSL-WFSGLRVGPESRRNHVGTKLLKFALDHAINNG-YKSLRCMVETNNIPSIRLMESFGL 118
                                       57777777777765.8899************************8777.9********************996 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   4.8e-07    0.0014      40     117 ..      46     129 ..      19     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 4.8e-07
                   Acetyltransf_10  40 gkivGviel...rdgs.hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYeklGFkavg 110
                                       ++i G+i+l    d+s   s l V pe r++ +g++Ll++++++a ++g+k  +  v+ ++   +++ e++G  +v+
  gi|518651565|ref|YP_008141085.1|  46 QEIDGFIKLeplADKSlWFSGLRVGPESRRNHVGTKLLKFALDHAINNGYKSlRCMVETNNiPSIRLMESFGLSVVD 122
                                       5666777543112333678999**************************************99999999999999998 PP

                   Acetyltransf_10 111 eeqeenG 117
                                       + + ++G
  gi|518651565|ref|YP_008141085.1| 123 KYFFFSG 129
                                       8777766 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06    0.0044       5      73 ..      40     117 ..      34     117 .. 0.62

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                       EEEEEETTEEEEEEEEEEES...TCTEE..EEE-GGGTTSSHHHHHHHH....TT.SEEE.EE.EEEETHHHHHHHH CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld...aeitr..laVdpeyrgkGiGraLlea....ae.kgii.le.qlelnaekaikfY 69 
                                       v+V +  ++i Gfi l++l+    +  +  l V pe r++ +G++Ll++    a+ +g++ l   +e+n+ ++i++ 
  gi|518651565|ref|YP_008141085.1|  40 VYV-HISQEIDGFIKLEPLAdksLW--FsgLRVGPESRRNHVGTKLLKFaldhAInNGYKsLRcMVETNNIPSIRLM 113
                                       553.344555599999998864444..25599****************85544225554332222344443667666 PP

                                       HHTT CS
                    Acetyltransf_7  70 eklG 73 
                                       e++G
  gi|518651565|ref|YP_008141085.1| 114 ESFG 117
                                       6666 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.8e-05     0.053      11      59 ..      48      96 ..      39     100 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.8e-05
                   Acetyltransf_CG 11 evafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglk 59
                                        +f++ e   ++ l f    V +e r+  ++ kL k ald+a ++g+k
  gi|518651565|ref|YP_008141085.1| 48 IDGFIKLEPLADKSLWFSGLRVGPESRRNHVGTKLLKFALDHAINNGYK 96
                                      45788888788889999999**************************987 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.7e-05       0.2      25      83 ..      65     124 ..      57     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.7e-05
                                       EEEEE-GGG-SSSHHHHHHH.HHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEEEEE CS
                              FR47  25 galqvlpehrrrGlgsrlvk.alakeiaergktvllvvvasNtpsirlyeklGfekieet 83 
                                       ++l v pe rr   g++l k al ++i +  k +  +v ++N psirl e+ G  + +++
  gi|518651565|ref|YP_008141085.1|  65 SGLRVGPESRRNHVGTKLLKfALDHAINNGYKSLRCMVETNNIPSIRLMESFGLSVVDKY 124
                                       678999**********999846666666666667788889999**********9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1580.69
//
Query:       gi|518651566|ref|YP_008141086.1|  [L=247]
Description: cobalt-precorrin-3B C(17)-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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  112.5   0.0    3.1e-32  112.3   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.3   0.0   1.7e-36   3.1e-32       1     211 [.       3     209 ..       3     211 .. 0.87

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.7e-36
                      TP_methylase   1 klylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleeayeeiaeal..aea 75 
                                       klyl+G+GpG+   +T  A++ lk++d+++g+  ++ e++++++ +        +  + +++ + +ei +a   +++
  gi|518651566|ref|YP_008141086.1|   3 KLYLIGIGPGSNGEITGDAIESLKNSDIIMGYS-KYIELIEEFVSD--------K--EIESGPVTDEIGRANnaIKY 68 
                                       79*******************************.******998865........1..23456669999999999*** PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl..lpglakee 150
                                       + +gk+V +++sGD  +yg+++ ++e+++ ++  i+ ++iPG+++l++a + lg+p  +++++ s++  l++ + + 
  gi|518651566|ref|YP_008141086.1|  69 VMSGKTVSIVSSGDSAIYGMAGIVFEIIASHNYRIDLQIIPGITALSSAGSLLGVPFMNDFCSISLSnkLTPEDVIL 145
                                       ******************************89999999*****************************8866656666 PP

                      TP_methylase 151 ereleallangdtlvllkapr..k....laelaelLkea...lyddttpvavveragtedervvrgtlee 211
                                       +r  +a +  gd++ ++++p   k    +    +  +e    +++++tpv +v +a +++++v  +tl++
  gi|518651566|ref|YP_008141086.1| 146 KRIHAAGA--GDFVTAIYNPVslKrtelI----KKAREImlgYRNKDTPVGLVTNAYRKEQKVEISTLGD 209
                                       66665554..6*********966545544....44444444569999*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1762.60
//
Query:       gi|518651567|ref|YP_008141087.1|  [L=285]
Description: hypothetical protein FACI_IFERC00001G0206 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-51  175.5   0.0    1.3e-51  175.3   0.0    1.0  1  PEP_mutase  Phosphoenolpyruvate phosphomutase
      4e-15   55.3   0.9    5.6e-15   54.8   0.9    1.1  1  ICL         Isocitrate lyase family


Domain annotation for each model (and alignments):
>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.3   0.0   1.5e-55   1.3e-51       9     236 ..       8     238 ..       1     241 [. 0.91

  Alignments for each domain:
  == domain 1  score: 175.3 bits;  conditional E-value: 1.5e-55
                        PEP_mutase   9 eplvlpnawDalsakiveeagfkalatsSlavaaslGvpDgeelpleellaavraiaevvslPlivDledGygespe 85 
                                       + l +p ++++ sa+++e+ gfka+ +s+ +++as+G+pD   ++l+el ++vr i e +++P+ivD+++G+ge   
  gi|518651567|ref|YP_008141087.1|   8 KFLSVPGVYNPFSAMLAERKGFKAVYLSGGGLTASMGLPDLGVITLTELTNMVRGIHEITDIPIIVDADTGFGE-TL 83 
                                       68899*********************************************************************.67 PP

                        PEP_mutase  86 evaetvrrliaaGvvgvniEDk....kknd.aerqlldieefaekiaaaraaaeeagfvinARtdalllsagaglee 157
                                       +v +tv+ l++aG++++ iED+    +++  +++++++ ++++eki+aa+aa ++   +i+ARtda    a  g+e+
  gi|518651567|ref|YP_008141087.1|  84 SVYRTVKLLEEAGASAIQIEDQvspkRCGHlNGKEVISRDNMVEKIRAANAARKN--ALIIARTDAR---AVTGMED 155
                                       9*********************876433355788888************888766..8********3...6899*** PP

                        PEP_mutase 158 aieRaraYaeAGAdgvfvpglqkdaeiaelvaavdvplnvvp.l.kgt..lsvaelaelGvarislgnhllraalaa 230
                                       a++Ra+ Y + GAd +f   l++++e + +++++d pl + + + ++t  ++  e++e+G +++++   l+r a +a
  gi|518651567|ref|YP_008141087.1| 156 ALSRAKTYIKEGADIIFPEALTDRDEFKYFADNTDFPLLANMtEfGKTpfIKAGEFQEMGYRIVIFPVTLFRIAAKA 232
                                       *************************************99999445445889************************** PP

                        PEP_mutase 231 lreaae 236
                                       ++ a++
  gi|518651567|ref|YP_008141087.1| 233 MDLALD 238
                                       *98776 PP

>> ICL  Isocitrate lyase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.9   6.3e-19   5.6e-15     151     243 ..      70     157 ..      58     171 .. 0.87

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 6.3e-19
                                       -EEEE-TT-SSSHHHHHHHHHHHHHTT-SEEEE-SB-TT---------EEE--HHHHHHHHHHHHHHHHHTT---EE CS
                               ICL 151 piiadadtGhGGltavvkltklfierGaaGihiedqasgtkkcGhmaGkvlvpiqehinrlvairaqadilgsdllv 227
                                       pii dadtG+G + +v + +kl+ e Ga+ i iedq s  k+cGh+ Gk +++ ++ ++++ a+    +    + l+
  gi|518651567|ref|YP_008141087.1|  70 PIIVDADTGFGETLSVYRTVKLLEEAGASAIQIEDQVS-PKRCGHLNGKEVISRDNMVEKIRAA----NAARKNALI 141
                                       9***********************************87.699**********999988886554....4567899** PP

                                       EEE--GGGEEEES-TT CS
                               ICL 228 vartdseaatlitsti 243
                                       +artd+ a t ++ ++
  gi|518651567|ref|YP_008141087.1| 142 IARTDARAVTGMEDAL 157
                                       ********99877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1954.25
//
Query:       gi|518651568|ref|YP_008141088.1|  [L=429]
Description: hypothetical protein FACI_IFERC00001G0207 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.2e-101  340.4   0.0   1.5e-101  340.2   0.0    1.0  1  MmgE_PrpD  MmgE/PrpD family


Domain annotation for each model (and alignments):
>> MmgE_PrpD  MmgE/PrpD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  340.2   0.0  8.1e-106  1.5e-101       3     417 ..       6     409 ..       4     422 .. 0.96

  Alignments for each domain:
  == domain 1  score: 340.2 bits;  conditional E-value: 8.1e-106
                                       HHHHHHHH-----H..HHHHHHHHHHHHHHHHHHHHTT-HHHHTT-SSSTT-B-TT-EE-TTSS-EE-HHHHHHHHH CS
                         MmgE_PrpD   3 qlaefvaelryddlpeevverakrlilDtlGvalaglrepavkkaleavkgtggpggatvigtgerlspvkAAfvnG 79 
                                       +laef+++++y++l e+v +++kr+++D+lGva+ ++++p++ k+++++  +  pg+a++ig g + sp + Af+n+
  gi|518651568|ref|YP_008141088.1|   6 KLAEFITGVSYKSLGEDVKHEVKRRFIDALGVAYSSIDSPPALKIKKMIGLY--PGNAKIIGMG-TSSPDYSAFLNS 79 
                                       79*********************************************87766..5689999977.56********** PP

                                       HHHHCTS-S-BEESSSEE-GGGGHHHHHHHHHHHHHHBHHHHHHHHHHHHHHHHHCCC--SCCCT.B-THHHHHHHH CS
                         MmgE_PrpD  80 aaihalDfdDthlaaelhhpsdvlpaalAvAealgasgkdlLtAivvGyEvqgrlglalsfnhygfhdtvtlgtfga 156
                                        +i+++Df+Dt+l+ e  hpsd++++++ ++   +++gkdl+tA++vGyE+++rl+++ s+++ g  d+v ++ ++ 
  gi|518651568|ref|YP_008141088.1|  80 LFIRYMDFNDTYLSLEPLHPSDMFGPLVTLSSIFNKTGKDLITAAAVGYEIGTRLCDSTSLRAKG-YDHVNFTEIAM 155
                                       *****************************************************************.*********** PP

                                       HHHHHHHTT--HHHHHHHHHHHHCT-B-BSGGGSTTT--CHHCHHHHHHHHHHHHHHHHHTT---TTTTT-TTTSHH CS
                         MmgE_PrpD 157 aaaaakLlgLdaeqianAlgiaatqaaglrqyrhagtkskklwaaGdAarnGveaallAkrGftGpsdilegewGfl 233
                                       aaa ++Ll+ d+ q++nA++ia++ + +lrq r +  +++k+ aa++ arn v+  l    Gft+p++ l g++Gf 
  gi|518651568|ref|YP_008141088.1| 156 AAALSRLLEFDESQTINAISIALVPHVALRQPRVGDLTMWKAGAAANSARNSVFGTLATLYGFTSPTEPLSGKMGFK 232
                                       ***************************************************************************** PP

                                       HHHSTT-----S.S-SS...SHHHHC-B---SSS-CCCHHHHHHHHHHHHHHCCTCCCEEEEEEEE-HHHHHHC--- CS
                         MmgE_PrpD 234 avlsggkdlelevkplgegesweienvlfKpypaerhthaaidaalklraelklkpddIesieirtseaalriigkk 310
                                       ++++ + d+++    +g  +   i+++++K+yp+e+h+ aa++a lkl+++ +l  ++ +sie+ t+eaa+ i+ +k
  gi|518651568|ref|YP_008141088.1| 233 NIVAPDIDFSKL---EG-SKVNGIMRTYVKKYPVEYHAMAAVEASLKLVNDMDL--NHTDSIEVYTYEAAVSILADK 303
                                       ****99666666...44.56999******************************6..9*******************9 PP

                                       S..---SHHHHCT-CCHHHHHHHHCS---CCCCSCCCCTSCHHCCHHCCEEEEE-HHHHHHHTTT---EEEEETTS- CS
                         MmgE_PrpD 311 g..ppenradadhSlqyvvAvalldgrvtledfederladpevqaLrekvevvedpeltadypekrsivvvvlkdgg 385
                                       +  +pen+++adhSl++++A  l++++  ++ ++d r  ++++ +L+ k++v+e +e+t++yp+k + ++ + k +g
  gi|518651568|ref|YP_008141088.1| 304 EkwHPENKETADHSLPFIIASTLVNKDFWVNNYNDIR--NKQISELMGKIHVTELKEFTEQYPDKLP-IRLEAKCNG 377
                                       99********************************988..99**************************.888888899 PP

                                       B---EEESS-TTSGGHHHHHHHHHHHHHHHHH CS
                         MmgE_PrpD 386 rtleerveypkGhprnplsreeleeKfrrlae 417
                                       + +e ++e p+Gh +np+++ e+e Kf rl+ 
  gi|518651568|ref|YP_008141088.1| 378 KKVESEIEIPRGHYKNPMDDREIESKFVRLTG 409
                                       999*************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2994.82
//
Query:       gi|518651569|ref|YP_008141089.1|  [L=280]
Description: hypothetical protein FACI_IFERC00001G0208 [Ferroplasma acidarmanus fer1]
Scores for complete 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  166.7   6.0    7.1e-49  166.4   6.0    1.2  1  DUF929    Domain of unknown function (DUF929)
    4.1e-05   23.5   0.4    9.2e-05   22.3   0.4    1.6  1  OppC_N    N-terminal TM domain of oligopeptide transport perm
  ------ inclusion threshold ------
      0.077   13.3   0.4       0.13   12.6   0.4    1.3  1  Orf78     Orf78 (ac78)
        3.9    7.4   7.7        1.4    8.8   4.5    1.8  2  CoatB     Bacteriophage coat protein B


Domain annotation for each model (and alignments):
>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.4   6.0   1.6e-52   7.1e-49       2     244 ..      31     273 ..      30     278 .. 0.88

  Alignments for each domain:
  == domain 1  score: 166.4 bits;  conditional E-value: 1.6e-52
                            DUF929   2 kliviaiivliivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdlasngkvevyfvswegCPvgaaesW 78 
                                       + i ++i+ +iivviv+v++  +  +          as+    +++kvs+ dl sng+++v+f sw gCP+ga++sW
  gi|518651569|ref|YP_008141089.1|  31 NFIWTVIGTVIIVVIVLVAIFNPFFEPP--------ASIHPD-TYYKVSGGDLLSNGQSAVFFLSWIGCPIGATDSW 98 
                                       5677788888888777777777733333........466666.8********************************* PP

                            DUF929  79 aLyiaLsryGnl..nlephySdp....sdeypniPgLiFknftp....nskvefysiYiyneylnasrngtpi.nse 144
                                       a+y a++++ ++   +++h++dp    s+ ++++PgL+Fk++++      k +fy+ Y+yne+++ + +++ +  s+
  gi|518651569|ref|YP_008141089.1|  99 AIYSAINSTSDIysHVKLHTADPtdvySNGTTGQPGLLFKGNFTfttsGHKFTFYPLYMYNENMTGTVTNSKLnTSQ 175
                                       ************999********66666667789*******999998899*****************999999899* PP

                            DUF929 145 lvsvglqeLkeelpssvynlvkkYetesliqetsepsaylvsppHivttiiitGpkGtyilvgysinPsll...... 215
                                       l+ +gl+ ++e  p  v+ +++kY + +             +++H++tt++itGp+G+yil+ y+++P +       
  gi|518651569|ref|YP_008141089.1| 176 LIPYGLNLINETYPARVAAMFYKYSNYT------------EYDHHLTTTVLITGPHGSYILNSYMYTPVSGgllgsg 240
                                       *************************999............899*************************999999988 PP

                            DUF929 216 .......sgyspeyvlkqlengnsksaIlsaanlit 244
                                              +  +pe v+++l++++s   I  aa ++ 
  gi|518651569|ref|YP_008141089.1| 241 tpssgswQPNTPEHVMSHLSESKS---ITDAAGTFS 273
                                       8876655555**************...999887775 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 !   22.3   0.4   2.1e-08   9.2e-05      17      39 ..      36      58 ..      34      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.1e-08
                            OppC_N 17 vvglvilllllliaifaPliaPy 39
                                      v+g vi+++++l+aif+P++ P+
  gi|518651569|ref|YP_008141089.1| 36 VIGTVIIVVIVLVAIFNPFFEPP 58
                                      89******************543 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   2.8e-05      0.13      37      84 ..       4      51 ..       1      55 [. 0.77

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.8e-05
                             Orf78 37 kkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviy 84
                                      k++kk+++++++i++k++n +   ++ n +++++ +v++v+++l +i+
  gi|518651569|ref|YP_008141089.1|  4 KNNKKNNKSTKKINTKKENYTGFIKSRNFIWTVIGTVIIVVIVLVAIF 51
                                      556666777777777777767778888999999999999999999997 PP

>> CoatB  Bacteriophage coat protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.5   0.00031       1.4      23      40 ..      35      52 ..      34      53 .. 0.94
   2 ?   -3.3   0.1       1.9   8.7e+03       5      13 ..     118     126 ..     117     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00031
                             CoatB 23 aaiGaaVLvvlVgvavfk 40
                                      ++iG  ++vv+V+va+f+
  gi|518651569|ref|YP_008141089.1| 35 TVIGTVIIVVIVLVAIFN 52
                                      68***************7 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.9
                             CoatB   5 gvdvsaVtt 13 
                                        +d+++V +
  gi|518651569|ref|YP_008141089.1| 118 TADPTDVYS 126
                                       579999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2184.23
//
Query:       gi|518651570|ref|YP_008141090.1|  [L=318]
Description: glucose-inhibited division protein A [Ferroplasma acidarmanus fer1]
Scores for complete 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   1.8      4e-34  118.2   1.8    1.1  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    2.9e-16   59.6   4.6    1.8e-13   50.5   0.3    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    7.1e-07   28.9   0.1      2e-06   27.4   0.0    1.7  2  FAD_oxidored   FAD dependent oxidoreductase
    7.3e-06   26.4   2.3    0.00052   20.5   0.1    3.0  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
      1e-05   24.8   2.8    0.00032   19.9   0.2    2.4  2  GIDA           Glucose inhibited division protein A
    5.9e-05   22.3   3.6    0.00044   19.5   2.1    2.3  2  FAD_binding_2  FAD binding domain
    0.00015   21.1   1.5    0.00097   18.4   0.3    2.3  2  Thi4           Thi4 family
    0.00025   19.9   0.4      0.019   13.7   0.5    2.3  2  HI0933_like    HI0933-like protein
    0.00025   20.4   0.0    0.00038   19.8   0.0    1.3  1  FAD_binding_3  FAD binding domain
    0.00039   20.1   1.1      0.041   13.5   1.7    2.3  2  DAO            FAD dependent oxidoreductase
     0.0079   16.4   0.1      0.018   15.3   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.2   1.8   2.4e-37     4e-34       1     293 [.       4     288 ..       4     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: 118.2 bits;  conditional E-value: 2.4e-37
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHH..C CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxx..x RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqg..i 67 
                                       +d +++Gg  AGl+aa+++a++g+k++++   +   +g+ ll++ + +++++  i          e    + ++   
  gi|518651570|ref|YP_008141090.1|   4 YDTIIVGGASAGLSAAIYAARQGMKTLVI---TKDIGGQALLTTDIQNYPGFDMIGGfelankfkE----QAEHygT 73 
                                       5899*************************...3347899999999999999998888988855543....3333226 PP

                                       CCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  68 elllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkr 144
                                       e++++ ev+ki ++  k+ l+      ++++   +l+lA G +prdl+++G+    g+++++++ +++   k ++  
  gi|518651570|ref|YP_008141090.1|  74 EFVYD-EVLKISKEGDKFFLK----TAGKEYSSMSLILAFGKTPRDLDVEGESRLKGHGISYCAICDGPLFKGKE-- 143
                                       67777.8****99999****3....34669***************************************999999.. PP

                                       EEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE..EEE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx.. RF
                       Pyr_redox_2 145 ivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge..kle.. 217
                                       ++vvG+G  ++E   +l++++ +v+++  +++l+   d+el ++++   +k   e+++ +++  i+g ++  +++  
  gi|518651570|ref|YP_008141090.1| 144 VAVVGNGSHALEALVYLSSVAGKVYYITNAKKLV--GDDELLQTVNSIENK---EIYFDSVPASINGSESveSVTfq 215
                                       *********************************9..789999999887777...688889999***99996544442 PP

                                       .EEETTSCE.....EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HH CS
                                       .xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 .vvledgee.....idadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaq 288
                                               +     ++ + v+   G+ +++e++  +  + l+e++ +vvd++++t+ +g++a+GDv+  ++ +++a+
  gi|518651570|ref|YP_008141090.1| 216 nKS-----SgenktVKLSGVFAEKGYIAKSEFV--RNLVDLNENNEVVVDKYCKTSTDGVFACGDVT--DTPYKQAV 283
                                       333.....333466****************996..889*****************************..55556665 PP

                                       HHHHH CS
                                       xxxxx RF
                       Pyr_redox_2 289 aAvqq 293
                                        +  q
  gi|518651570|ref|YP_008141090.1| 284 ISAGQ 288
                                       55554 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.5   0.00011      0.18       1      34 [.       7      39 ..       7      51 .. 0.84
   2 !   50.5   0.3   1.1e-16   1.8e-13     101     305 .]      77     272 ..      53     272 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00011
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgnign 34
                                      iI+G+  aGl+aai + + g+ + l++ k+  g+
  gi|518651570|ref|YP_008141090.1|  7 IIVGGASAGLSAAIYAARQGM-KTLVITKDIGGQ 39
                                      8********************.578998875555 PP

  == domain 2  score: 50.5 bits;  conditional E-value: 1.1e-16
                       Pyr_redox_3 101 feeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgkn 174
                                       + eV +++ke+++f ++t  ++y++ ++i+A G+   P+ l+++Ge++   + + y  + +   ++g++v+V+G + 
  gi|518651570|ref|YP_008141090.1|  77 YDEVLKISKEGDKFFLKTAGKEYSSMSLILAFGK--TPRDLDVEGESRlkgHGISYCAICDGPLFKGKEVAVVGNGS 151
                                       578******************************9..**********9743456677777888899************ PP

                       Pyr_redox_3 175 SavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvkted 251
                                        a +a + l +   +V  +t+ +++  ++ +  ++++ + ++++    ++    +   ++v++++ +++      ++
  gi|518651570|ref|YP_008141090.1| 152 HALEALVYLSSVAGKVYYITNAKKLVGDD-ELLQTVNSIENKEIY--FDSVPASINGSESVESVTFQNK------SS 219
                                       ********************999776664.555555555555552..2332235555555666665433......34 PP

                       Pyr_redox_3 252 gkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       g++ +vk   v+a  Gy  + +f++ +l++l+e++++v+++  + t ++g+f +G
  gi|518651570|ref|YP_008141090.1| 220 GENKTVKLSGVFAeKGYIAKSEFVR-NLVDLNENNEVVVDK-YCKTSTDGVFACG 272
                                       555566777889989*********9.999999999988875.788999****998 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.2e-09     2e-06       1      58 [.       5      57 ..       5      99 .. 0.80
   2 ?   -1.4   0.0      0.68   1.1e+03     100     134 ..     190     225 ..     175     228 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.2e-09
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtg 58
                                      D ++vGG +aG+ AAi Aar+G k+l++ ++  +GG++   l++tdi+n+    +++g
  gi|518651570|ref|YP_008141090.1|  5 DTIIVGGASAGLSAAIYAARQGMKTLVITKD--IGGQA---LLTTDIQNYPGFDMIGG 57
                                      779*************************765..99984...78888888844466666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
                      FAD_oxidored 100 agvtvllntrlvevekegkriesvtveske.g.rkti 134
                                       ++ ++++++++ +++ ++  +esvt+++k+ g +kt+
  gi|518651570|ref|YP_008141090.1| 190 ENKEIYFDSVPASINGSE-SVESVTFQNKSsGeNKTV 225
                                       566778888888888885.8*******9997766655 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.041        67       3      29 ..       7      33 ..       5      48 .. 0.90
   2 ?   -1.0   0.0       1.6   2.6e+03      41      64 ..      59      82 ..      55      94 .. 0.71
   3 !   20.5   0.1   3.2e-07   0.00052       2      79 ..     144     215 ..     143     220 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                                      EEECSSHHHHHHHHHHHHTTSEEEEEE CS
                         Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvve 29
                                      ++vGg   gl +A ++a+ g k+ v+ 
  gi|518651570|ref|YP_008141090.1|  7 IIVGGASAGLSAAIYAARQGMKTLVIT 33
                                      89******************9998886 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHHTTEEEECSEEEE CS
                         Pyr_redox 41 easkilqeklekngievllntkve 64
                                      e+++ ++e+ e+ g e++++++++
  gi|518651570|ref|YP_008141090.1| 59 ELANKFKEQAEHYGTEFVYDEVLK 82
                                      466778888888899999887665 PP

  == domain 3  score: 20.5 bits;  conditional E-value: 3.2e-07
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvkl 78 
                                       v+vvG G  +lE+  +l+  + kV+ + +++kl    D+e+   lq+  + ++ e+++++++++i+gse+ vesv++
  gi|518651570|ref|YP_008141090.1| 144 VAVVGNGSHALEALVYLSSVAGKVYYITNAKKLV--GDDEL---LQTVNSIENKEIYFDSVPASINGSES-VESVTF 214
                                       89********************************..44443...33333334559**************9.*****9 PP

                                       E CS
                         Pyr_redox  79 k 79 
                                       +
  gi|518651570|ref|YP_008141090.1| 215 Q 215
                                       7 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2     2e-07   0.00032       1      33 [.       5      37 ..       5      62 .. 0.88
   2 !    4.9   0.1    0.0073        12     354     391 ..     264     303 ..     248     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GG CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLithkld 33
                                      d i++Gg  AG+ AA+ aar G+k+l it++++
  gi|518651570|ref|YP_008141090.1|  5 DTIIVGGASAGLSAAIYAARQGMKTLVITKDIG 37
                                      579*************************87654 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0073
                                       SSBTEEE-CGGGTB-SHHHH...HHHHHHHHHHHHHHHCTS CS
                              GIDA 354 kvkgLflAGqinGteGYeEa...aaqGllAGinaarkakgk 391
                                       + +g+f++G+++ t  Y  a   a+qG +A++ a +++++k
  gi|518651570|ref|YP_008141090.1| 264 STDGVFACGDVTDTP-YKQAvisAGQGAIAALSAYNYVQKK 303
                                       47899*******998.877622267**********999987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   2.1   2.7e-07   0.00044       1      31 [.       5      35 ..       5      41 .. 0.95
   2 ?    2.0   0.0     0.053        86     384     409 ..     255     282 ..     213     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.7e-07
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavveke 31
                                      D i++G+  AGL+AA+ aa++G k++v++k 
  gi|518651570|ref|YP_008141090.1|  5 DTIIVGGASAGLSAAIYAARQGMKTLVITKD 35
                                      89**************************995 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.053
                                       E..STTEEESSBTEEE-STCEESSSSTT CS
                     FAD_binding_2 384 v..ldadgqpipGLYAaGevaaggvhga 409
                                       v  ++  ++  +G +A+G v+ + ++ a
  gi|518651570|ref|YP_008141090.1| 255 VvvDKYCKTSTDGVFACGDVTDTPYKQA 282
                                       33355555699*********98777665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.3   5.9e-07   0.00097      18      51 ..       4      36 ..       1      45 [. 0.89
   2 ?    1.0   0.0      0.13   2.1e+02      18      39 ..     142     163 ..     137     177 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.9e-07
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersv 51
                                       D +ivG+ s+GL+aa y a++ ++k++++ + +
  gi|518651570|ref|YP_008141090.1|  4 YDTIIVGGASAGLSAAIYAARQ-GMKTLVITKDI 36
                                      599*******************.*******8875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                                       EEEEEE--SHHHHHHHHHHHHC CS
                              Thi4  18 sDvvivGaGssGLtaayylakk 39 
                                        +v++vG Gs  L a  yl+  
  gi|518651570|ref|YP_008141090.1| 142 KEVAVVGNGSHALEALVYLSSV 163
                                       6899***********9999875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.5   1.2e-05     0.019       2      31 ..       5      34 ..       4      43 .. 0.92
   2 ?    3.6   0.0     0.014        22     121     163 ..      70     109 ..      59     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      d+i++Gg  AGl aAi aa++g ++l++ k
  gi|518651570|ref|YP_008141090.1|  5 DTIIVGGASAGLSAAIYAARQGMKTLVITK 34
                                      89*************************976 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.014
                                       HHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 121 eagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       + g ++ +  ev +++ke d+ f +kt  ++e+++ +l+lA G
  gi|518651570|ref|YP_008141090.1|  70 HYGTEFVY-DEVLKISKEGDK-FFLKT-AGKEYSSMSLILAFG 109
                                       55555544.579999998888.88999.8************99 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   2.3e-07   0.00038       2      79 ..       4      79 ..       3     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.3e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealyne 79
                                      +d++IVG+  aGl++a   +++G ++++++k      l   d+ n   ++++    l++++++++  +++ +e++y e
  gi|518651570|ref|YP_008141090.1|  4 YDTIIVGGASAGLSAAIYAARQGMKTLVITKDIGGQALLTTDIQNYPGFDMIGGFELANKFKEQA--EHYGTEFVYDE 79
                                      6899************************************************************9..77788888887 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   1.7   2.5e-05     0.041       1      33 [.       5      38 ..       5      41 .. 0.90
   2 ?    3.7   0.0     0.023        38     146     232 ..      58     135 ..      48     196 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      d +i+GG  +Gls+A ++ar+g  ++++ k+ i g
  gi|518651570|ref|YP_008141090.1|  5 DTIIVGGASAGLSAAIYAARQGmkTLVITKD-IGG 38
                                      789********************99999999.655 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.023
                                       HHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTT.CTTTSEEEEE CS
                               DAO 146 akltaalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdllgll.keldlpispv 220
                                       ++l++ + ++ae  G e+++  ev ++++e++k   +  +t+g + ++   +++a G   + l  + +      s +
  gi|518651570|ref|YP_008141090.1|  58 FELANKFKEQAEHYGTEFVYD-EVLKISKEGDK-FFL--KTAGKEySS-MSLILAFGKTPRDL--DvEG---E-SRL 123
                                       6788999999**********9.*****776433.555..555766344.66999999332222..1122...2.667 PP

                                       EEEEEEEEECCT CS
                               DAO 221 rgqvlvlkplse 232
                                       +g+ + ++ + +
  gi|518651570|ref|YP_008141090.1| 124 KGHGISYCAICD 135
                                       777777755544 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 !   15.3   0.1   1.1e-05     0.018       1      36 [.       8      41 ..       8      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      IvG+  +Gl+aA ++a++g + l++ k  ++GG+a 
  gi|518651570|ref|YP_008141090.1|  8 IVGGASAGLSAAIYAARQGMKTLVITK--DIGGQAL 41
                                      9************************55..7999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1960.80
//
Query:       gi|518651571|ref|YP_008141091.1|  [L=81]
Description: thioredoxin [Ferroplasma acidarmanus fer1]
Scores for 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   0.0    2.2e-21   75.8   0.0    1.0  1  Thioredoxin    Thioredoxin
    1.2e-05   25.7   0.1    6.4e-05   23.4   0.1    1.8  1  Thioredoxin_2  Thioredoxin-like domain
    0.00015   21.2   0.0    0.00016   21.1   0.0    1.0  1  OST3_OST6      OST3 / OST6 family, transporter family
    0.00091   19.5   0.1      0.022   15.1   0.0    2.0  2  Thioredoxin_8  Thioredoxin-like
     0.0013   18.5   0.0     0.0015   18.3   0.0    1.1  1  Thioredoxin_9  Thioredoxin
     0.0033   17.3   0.0      0.004   17.1   0.0    1.1  1  HyaE           Hydrogenase-1 expression protein HyaE
     0.0085   15.9   0.0     0.0092   15.8   0.0    1.0  1  DIM1           Mitosis protein DIM1
  ------ inclusion threshold ------
      0.033   14.2   0.0      0.041   13.9   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain
        0.1   12.2   0.1       0.36   10.5   0.1    1.8  1  DUF953         Eukaryotic protein of unknown function (DUF953
        0.1   12.7   0.0       0.12   12.5   0.0    1.2  1  TrbC_Ftype     Type-F conjugative transfer system pilin assem
       0.13   12.1   0.0       0.15   11.8   0.0    1.1  1  TraF           F plasmid transfer operon protein


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.4e-24   2.2e-21      26     102 ..       2      78 ..       1      79 [. 0.98

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.4e-24
                                       E-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHH CS
                       Thioredoxin  26 yApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngkevkkyegarekeklaaflk 102
                                       +A wC++C+ l+P++++l++e+++   + kv+vden+ + ++y +e+iPt+++fkngk+v+   g  +ke la+++k
  gi|518651571|ref|YP_008141091.1|   2 WAAWCAPCRYLSPVVDELSKEYANVANFGKVNVDENPVTSRNYRIESIPTILFFKNGKAVDMSIGVVPKEVLAQKIK 78 
                                       9*************************************************************************998 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   3.9e-08   6.4e-05      14     108 ..       3      76 ..       1      77 [. 0.69

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.9e-08
                     Thioredoxin_2  14 dpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.fldg 89 
                                       + +C  C+ l  +++el                 ++++++     ++     ++en + +r y++++ Pti+ f +g
  gi|518651571|ref|YP_008141091.1|   3 AAWCAPCRYLSPVVDEL---S-------------KEYANVANFGKVN-----VDENPVTSRNYRIESIPTILfFKNG 58 
                                       56788888888888888...1.............2223333333333.....55666688**********6637777 PP

                     Thioredoxin_2  90 keivarlpGyvpaeeleal 108
                                       k  v++  G vp+e l++ 
  gi|518651571|ref|YP_008141091.1|  59 K-AVDMSIGVVPKEVLAQK 76 
                                       7.************99885 PP

>> OST3_OST6  OST3 / OST6 family, transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   9.8e-08   0.00016      46     106 ..       6      59 ..       3      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 9.8e-08
                         OST3_OST6  46 CelCrefepefelvakswrkdekskskklfFakvdfdegkdvFqklglnsaPhlllfppkk 106
                                       C++Cr + p ++ ++k + +          F+kv++de++ + + ++++s+P +l+f+  k
  gi|518651571|ref|YP_008141091.1|   6 CAPCRYLSPVVDELSKEYANV-------ANFGKVNVDENPVTSRNYRIESIPTILFFKNGK 59 
                                       *******************99.......36***************************9844 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.3e-05     0.022       8      53 ..       1      44 [.       1      48 [. 0.83
   2 ?    4.8   0.0     0.022        36      74      91 ..      40      57 ..      29      61 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                                      E--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS-HHHHHHH CS
                     Thioredoxin_8  8 fgaswcppckaftpklkelyeklkkkkkveivyvsldkkeeefeky 53
                                      ++a wc+pc+   p ++el++++   +  ++  v++d++    ++y
  gi|518651571|ref|YP_008141091.1|  1 MWAAWCAPCRYLSPVVDELSKEYA--NVANFGKVNVDENPVTSRNY 44
                                      59*********************9..77788788888776665555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.022
                                      HTT-S--TT-SEEEEE-T CS
                     Thioredoxin_8 74 lkkkynvkaiPtlvvldk 91
                                        ++y++++iPt++  ++
  gi|518651571|ref|YP_008141091.1| 40 TSRNYRIESIPTILFFKN 57
                                      5789********765544 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   8.9e-07    0.0015      50     121 ..       3      72 ..       1      79 [. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 8.9e-07
                                       -TT-HHHHHHHHHHHHHH.HH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEESS-HHH CS
                     Thioredoxin_9  50 edwCgDaavnvPvlakia.elnpnievkillrdenlelmdqyltngaraiPtliildeegeelgvwgerPaev 121
                                       + wC  ++   Pv+++++ e+++  ++  +  den+ + ++y+    ++iPt+++++++ ++ +  g  P+ev
  gi|518651571|ref|YP_008141091.1|   3 AAWCAPCRYLSPVVDELSkEYANVANFGKVNVDENPVTSRNYRI---ESIPTILFFKNGKAVDMSIGVVPKEV 72 
                                       68***************934455568999*************77...9*********9988888999999987 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.5e-06     0.004      49      97 ..      15      62 ..      11      72 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.5e-06
                                      HHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEE CS
                              HyaE 49 vlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylg 97
                                      v+ El k++ n+++   v+  +++ +  +++++   P++lf+++g+ + 
  gi|518651571|ref|YP_008141091.1| 15 VVDELSKEYANVANFGKVN-VDENPVTSRNYRIESIPTILFFKNGKAVD 62
                                      689*************999.7778888999***************9875 PP

>> DIM1  Mitosis protein DIM1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.6e-06    0.0092      37      99 ..      11      73 ..       4      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.6e-06
                                      HHHHHHHHHHHHTTTTEEEEEEETTT--TTSCCCTT-SSSEEEEEETTEEEEEE-SSS--SSB CS
                              DIM1 37 klDelLakiaeklknfaviylvdidevpdfnkmyeledpvtilffyrnkhmkvDfgtgdnnKl 99
                                       l  ++ + +++  n+a++  v++de p+ ++ y +e+  tilff ++k + + +g   ++ l
  gi|518651571|ref|YP_008141091.1| 11 YLSPVVDELSKEYANVANFGKVNVDENPVTSRNYRIESIPTILFFKNGKAVDMSIGVVPKEVL 73
                                      555667778888899999999************************999999988887666555 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.5e-05     0.041      10      67 ..       6      70 ..       3      79 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                                      STTCHHHHHHHHHHCHCC.T.CECEEECCTTHHHH.HHCT-SSSSEE..ECTTCEE..EESS--- CS
                     Thioredoxin_3 10 CakCpklekavkeaaaek.g.ikaevekvtdfeei.ekygVmsvPal..vidgkvv..vsGkvps 67
                                      Ca C+ l+ +v e+ +e  +  ++  ++v +++    +y+++s+P++  + +gk v  + G vp+
  gi|518651571|ref|YP_008141091.1|  6 CAPCRYLSPVVDELSKEYaNvANFGKVNVDENPVTsRNYRIESIPTIlfFKNGKAVdmSIGVVPK 70
                                      9****************9654444556667777778**********9766688875334565555 PP

>> DUF953  Eukaryotic protein of unknown function (DUF953)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00022      0.36      36     100 ..       4      59 ..       2      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00022
                                       BSSHHHHHHHHHHHHHHHH-SS-EEEEEEE---HHHHT-TTSHHHH..TS---SSSEEEEETSS- CS
                            DUF953  36 sWCPdCvkaepvieealkeapedvklvrvdvGdrevWkdpanpfRkdpklkltgvPtLlrwkgkk 100
                                       +WC  C    pv+ e  ke ++ +++ +v+v + +v            +++++ +Pt+l +k+ k
  gi|518651571|ref|YP_008141091.1|   4 AWCAPCRYLSPVVDELSKEYANVANFGKVNVDENPVTS---------RNYRIESIPTILFFKNGK 59 
                                       7*******************999999999999887632.........236667788888877755 PP

>> TrbC_Ftype  Type-F conjugative transfer system pilin assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.2e-05      0.12      51      87 ..      28      64 ..      10      79 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.2e-05
                        TrbC_Ftype 51 emekasvqidPllFrqfkitaVPalvlaeedkaseed 87
                                      +  k++v+ +P   r+++i+++P++ + ++ ka +++
  gi|518651571|ref|YP_008141091.1| 28 NFGKVNVDENPVTSRNYRIESIPTILFFKNGKAVDMS 64
                                      3467888889****************99998887664 PP

>> TraF  F plasmid transfer operon protein
   #    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     141     223 ..       6      77 ..       2      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                              TraF 141 cpyceaqapilqafadky..glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaGlls 215
                                       c  c+ ++p+++++ ++y        V+vd++p   ++          ++ ++++P++++++    k v  + G++ 
  gi|518651571|ref|YP_008141091.1|   6 CAPCRYLSPVVDELSKEYanVANFGKVNVDENPV--TSR---------NYRIESIPTILFFKNG--KAVDMSIGVVP 69 
                                       899***************43356778********..556.........89********999988..77788889998 PP

                              TraF 216 ldeleeri 223
                                        + l+++i
  gi|518651571|ref|YP_008141091.1|  70 KEVLAQKI 77 
                                       88888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 571.67
//
Query:       gi|518651572|ref|YP_008141092.1|  [L=122]
Description: transcriptional regulator, TrmB [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   32.1   0.1    1.1e-07   31.7   0.1    1.3  1  TrmB             Sugar-specific transcriptional regulator Trm
    1.1e-05   25.2   0.0    1.9e-05   24.5   0.0    1.3  1  MarR_2           MarR family
    0.00017   21.5   0.0    0.00028   20.8   0.0    1.3  1  MarR             MarR family
    0.00096   18.9   0.0     0.0016   18.2   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
     0.0016   18.3   0.1     0.0021   17.9   0.1    1.2  1  TFIIE_alpha      TFIIE alpha subunit
     0.0071   16.1   0.0      0.012   15.4   0.0    1.4  1  HTH_38           Helix-turn-helix domain
     0.0075   15.8   0.0      0.018   14.6   0.0    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.062   13.7   0.0      0.076   13.4   0.0    1.2  1  Penicillinase_R  Penicillinase repressor
       0.12   12.1   0.0       0.22   11.2   0.0    1.4  1  GntR             Bacterial regulatory proteins, gntR family


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   5.4e-11   1.1e-07       3      62 ..      21      86 ..      18      99 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 5.4e-11
                                      HCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST......TTEE CS
                              TrmB  3 klGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr......pklY 62
                                       ++Ls  ++ v   L ++  at d++a ++  +r++v ++L++L+  G+V+++k+       ++ Y
  gi|518651572|ref|YP_008141092.1| 21 FFDLSPADVAVLYSLDNETGATLDDVAVKVHKDRTTVFRSLQRLVGTGIVTKKKSIlekggyYYSY 86
                                      699**************************************************9877777554455 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   9.3e-09   1.9e-05       2      55 ..      23      74 ..      22      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 9.3e-09
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrp 55
                                      +l+pa+  vL+ L ++ g   t  ++a + + ++ +v r l+rLv  G v++++
  gi|518651572|ref|YP_008141092.1| 23 DLSPADVAVLYSLDNETG--ATLDDVAVKVHKDRTTVFRSLQRLVGTGIVTKKK 74
                                      79****************..9*****************************9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   1.4e-07   0.00028       1      52 [.      24      75 ..      24      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.4e-07
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRsks 52
                                      l+++ + +L++l+++ ++++ + a k++ +++tv r l rL+  G ++++ks
  gi|518651572|ref|YP_008141092.1| 24 LSPADVAVLYSLDNETGATLDDVAVKVHKDRTTVFRSLQRLVGTGIVTKKKS 75
                                      788999******************************************9986 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   8.2e-07    0.0016       7      50 ..      30      72 ..      29      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.2e-07
                                      HHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  7 aiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      a+L  l  ++++ tl ++A + +  ++tv+R Lq Lv  G+v++
  gi|518651572|ref|YP_008141092.1| 30 AVLYSLDNETGA-TLDDVAVKVHKDRTTVFRSLQRLVGTGIVTK 72
                                      677778888887.9***************************986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.1   1.1e-06    0.0021      16     101 ..      29     117 ..      19     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHH... CS
                       TFIIE_alpha  16 vlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkl... 89 
                                       v vl +L  +   t +d+a +++ d++ + + L rL + ++v  k++  e+ + y  y ri + k+v+ + ++    
  gi|518651572|ref|YP_008141092.1|  29 VAVLYSLDNETGATLDDVAVKVHKDRTTVFRSLQRLVGTGIVTKKKSILEKGGYYYSYSRISKAKIVELINNREgef 105
                                       679999999999999*********************************9*********************9986111 PP

                                       HHHHHHHHHHHC CS
                       TFIIE_alpha  90 eevvkkLeekle 101
                                       + v++ L +++e
  gi|518651572|ref|YP_008141092.1| 106 HSVLQCLLKDME 117
                                       455555555555 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.9e-06     0.012       5      43 ..      24      63 ..      23      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.9e-06
                            HTH_38  5 LsleeReeIerll.aeGlslreIArrLgrspsTIsRElkR 43
                                      Ls+++  +++ l  + G +l ++A +++++++T+ R l+R
  gi|518651572|ref|YP_008141092.1| 24 LSPADVAVLYSLDnETGATLDDVAVKVHKDRTTVFRSLQR 63
                                      89999999999973589*******************9998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.9e-06     0.018       4      48 .]      27      71 ..      24      71 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.9e-06
                            HTH_24  4 tdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       d ++L  L  + + +  ++A +++  ++tv r l+rL+  G+++
  gi|518651572|ref|YP_008141092.1| 27 ADVAVLYSLDNETGATLDDVAVKVHKDRTTVFRSLQRLVGTGIVT 71
                                      57789999999****************************999986 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   3.8e-05     0.076       2      64 ..      25      85 ..      24     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                      --S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE- CS
                   Penicillinase_R  2 gelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsreke..grafiYsp 64
                                      ++++ +v+  l ++  at ++v  +++++    ++TV   l+rLv  g+++++k+  ++   Y++
  gi|518651572|ref|YP_008141092.1| 25 SPADVAVLYSLDNETGATLDDVAVKVHKD----RTTVFRSLQRLVGTGIVTKKKSilEKGGYYYS 85
                                      77788888888888999999999999999....********************987644444443 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.22      29      57 ..      45      73 ..      36      76 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                      HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              GntR 29 eLaaefgVsrttvReALrrLeaeglverr 57
                                      ++a + + +rttv ++L+rL+  g+v+ +
  gi|518651572|ref|YP_008141092.1| 45 DVAVKVHKDRTTVFRSLQRLVGTGIVTKK 73
                                      567777889*****************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 830.59
//
Query:       gi|518651573|ref|YP_008141093.1|  [L=136]
Description: molybdopterin (MPT) converting factor, subunit 2 [Ferroplasma acidarmanus fer1]
Scores for complete 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-36  124.5   0.8    2.7e-36  124.3   0.8    1.0  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 !  124.3   0.8   1.5e-40   2.7e-36       1     111 [.       4     115 ..       4     116 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 1.5e-40
                                       EESS---HHHHHHHH--TT--EEEEEEEE------.TS-EEEEEECC-HHHHHHHHHHHHHHHHCCCTTSEEEEEEE CS
                              MoaE   1 lteepldvaeiealvaspkaGAvvlFvGtvRdsfd.gkkvteLeyeayepmaektleeiaeearerwelervavvHr 76 
                                       ++ee++d +++++ v+++kaGA+v+F GtvR   + ++++ +L yeaye+ma k++eei+++a++++++ +vav+ r
  gi|518651573|ref|YP_008141093.1|   4 IQEEKIDHETLVNEVKNDKAGAIVTFYGTVRSIDEtSDDIIALVYEAYEEMAIKKIEEIIKDAQKKYPVINVAVIQR 80 
                                       689****************************6555888*************************************** PP

                                       -EEEETTSEEEEEEEEESSHHHHHHHHHHHHHHHH CS
                              MoaE  77 lGelevgeasvvvavssahRkeafeaceylidelK 111
                                       +G+++vge s+ +avss+hR++af+ace++id++K
  gi|518651573|ref|YP_008141093.1|  81 IGRVNVGEDSIGIAVSSEHRDSAFHACEFIIDKIK 115
                                       **********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 968.37
//
Query:       gi|518651574|ref|YP_008141094.1|  [L=451]
Description: sugar transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-26   93.5  36.7    1.2e-26   93.5  36.7    1.8  2  MFS_1      Major Facilitator Superfamily
    5.6e-24   84.8  35.8      7e-24   84.5  35.8    1.1  1  Sugar_tr   Sugar (and other) transporter
  ------ inclusion threshold ------
        7.9    4.7  12.9      0.027   12.9   1.8    2.2  2  MFS_3      Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.5  36.7     2e-30   1.2e-26       4     347 ..      28     392 ..      25     398 .. 0.78
   2 !    5.7   3.1     0.001         6     107     164 ..     367     428 ..     363     439 .. 0.82

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 2e-30
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       ++fl  ++ + +g++l  + + dl+ +++ +g+ +++  +ga+++++++G+l+d+fGr+r+l+  +++f+++++l++
  gi|518651574|ref|YP_008141094.1|  28 SVFLDVWDLTSFGFVLD-FFKADLHPAGAMLGISVAAANIGAIAGAILGGYLTDKFGRKRLLMYNMAVFIIFAFLIA 103
                                       67888999999999999.******************************************************77777 PP

                             MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.....Wra 152
                                       ++++++ + ++r+++G+  g+ +++g ++i ++ ++++r+ +++l++ +fs+ a+++ +++ +l+ ++      Wr+
  gi|518651574|ref|YP_008141094.1| 104 ISTNIFEFTLFRLIMGFSIGSDVATGFSYIYEYISRKQRNHYYSLWAYSFSVVALIA-IASVFLLYHIThndsvWRY 179
                                       679999************************************************999.6666666666679****** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeee....................kgtgpaplvp...awkallkd 206
                                       +f+i +i++++ ++    l  +   ++ +  +  +                      ++ +  l++   +++  l++
  gi|518651574|ref|YP_008141094.1| 180 IFVIGGIFAAIILL----LRSRMTETPIWLYGNGKYketqdvikhvygedininqsGQKNHVTLKNiisLFRNGLNR 252
                                       ***********944....45444444444444444446788888889999999874333333333333344444444 PP

                             MFS_1 207 pvlwillialllfffgfsg...lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrllla 280
                                            l++a+ l++++ ++   + ++++ +l +   ++ +++++++ a+++ +g+++a+++  ++++lg  r+ ++ 
  gi|518651574|ref|YP_008141094.1| 253 E----LVFAFSLNGIVGFIgwgFAFYITYMLETLKLFT-FYQILGADAIIYSFGFAGAIISPVMAKHLGIYRASVIP 324
                                       4....777777776555556645555555444455555.8888888999999999999999999999**98888888 PP

                             MFS_1 281 llllllaalglallavtssavllllvlvliGfglgfv.fpsllalasdlappeeagtasglfntagsl 347
                                        +++++a ++l+++ +   +v l++++ +i +++      +++a+++ ++p++ +g  +g++ +++ +
  gi|518651574|ref|YP_008141094.1| 325 SIIAAIAIFALFITFAGILPVYLVIPFSIIIIFMNYSgPMAYNAVLNGFIPTSLRGVGNGWNYMFNKI 392
                                       88888888888888888677777775555444444441557777777788**************9976 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.001
                             MFS_1 107 aaliadwfpkeergraigllsagfslGailgpllggllasslg....Wravfyilaivslla 164
                                       +a++    p + rg ++g+ ++++ +  ++  l gg+++ ++g       +f+i+a+++++a
  gi|518651574|ref|YP_008141094.1| 367 NAVLNGFIPTSLRGVGNGWNYMFNKITEAVSGLTGGAILVLVGlkfnTIILFIIVAAFTVIA 428
                                       68888999999****************************99998844444466666666665 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.5  35.8   1.2e-27     7e-24      46     435 ..      55     431 ..       7     439 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.5 bits;  conditional E-value: 1.2e-27
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                         +g++v+++++Gai+G++++g+l+d+fGRk  l+   ++f+i a+l+a+++   ++  +++ R+++G+++G   ++
  gi|518651574|ref|YP_008141094.1|  55 AMLGISVAAANIGAIAGAILGGYLTDKFGRKRLLMYNMAVFIIFAFLIAIST---NIFEFTLFRLIMGFSIGSDVAT 128
                                       4579************************************************...9********************* PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllflPESPryl 198
                                          yi E+   k R    sl+  + ++  l+a+ + + l   t+n++ wr+ + +  ++a ++l+l+  + E+P +l
  gi|518651574|ref|YP_008141094.1| 129 GFSYIYEYISRKQRNHYYSLWAYSFSVVALIAIASVFLLyHITHNDSVWRYIFVIGGIFAAIILLLRSRMTETPIWL 205
                                       *********************************9999996777779******************************* PP

                                       HHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHH CS
                          Sugar_tr 199 vekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimy 275
                                       + +gk++e++ v++    + ++d ++++  ++++ +     + + +l+++ +  + l+ ++ l+ +  + G+ + + 
  gi|518651574|ref|YP_008141094.1| 206 YGNGKYKETQDVIKH---VYGEDININQSGQKNHVTL----KNIISLFRN-GLNRELVFAFSLNGIVGFIGWGFAF- 273
                                       ***************...6666667777777777663....348899999.8899****************76655. PP

                                       HTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...C CS
                          Sugar_tr 276 ysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaas 349
                                       y ++++e+l l +    l + +i++   f+  +++  + +++G  +  ++ ++++ai+ + l  +++++        
  gi|518651574|ref|YP_008141094.1| 274 YITYMLETLKLFTFyqiLGADAIIYSFGFAGAIISPVMAKHLGIYRASVIPSIIAAIAIFALF-ITFAGILP----- 344
                                       569999999999887877788999999********9*******99999999999999999997.66666666..... PP

                                       HHHHHHHHHHHHHHHTTTTHHHHH.HHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH.T-HHHHHHHH CS
                          Sugar_tr 350 ivaivfialfialfalgwgpvpwv.lvsElfpqsvRskalaiavavnwlanflisllfpiiteaig.ggyvflvfag 424
                                        v +v  +  i++f    gp+ +  ++  + p+s+R+++    ++ n +   + +l+   i+  +g ++ + ++f +
  gi|518651574|ref|YP_008141094.1| 345 -VYLVIPFSIIIIFMNYSGPMAYNaVLNGFIPTSLRGVGNGWNYMFNKITEAVSGLTGGAILVLVGlKFNTIILFII 420
                                       .334444444444555558888851457788**************************99999888866888888888 PP

                                       HHHHHHHHHHH CS
                          Sugar_tr 425 lavlfiifvff 435
                                       +a++++i v+ 
  gi|518651574|ref|YP_008141094.1| 421 VAAFTVIAVYT 431
                                       88888888875 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.8   4.5e-06     0.027     250     316 ..      51     117 ..      20     130 .. 0.74
   2 ?   -3.5   3.7      0.43   2.6e+03      82     169 ..     324     411 ..     302     438 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.5e-06
                             MFS_3 250 dgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvllslalasslwvavlvlll 316
                                       +   ++ Gi ++a  +GAi+ga+l   L ++++ +rl+++ ++++ + ++ +a++++++  +l  l+
  gi|518651574|ref|YP_008141094.1|  51 HPAGAMLGISVAAANIGAIAGAILGGYLTDKFGRKRLLMYNMAVFIIFAFLIAISTNIFEFTLFRLI 117
                                       4444566777778888888888888888888888888888888888888888887777655444333 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.43
                             MFS_3  82 qlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAl 158
                                        +++a+ ++++  +++ g+l ++l++ ++++i         a++A+++ +++ +        n +   i+ +v    
  gi|518651574|ref|YP_008141094.1| 324 PSIIAAIAIFALFITFAGILPVYLVIPFSIIIIFMNYSGPMAYNAVLNGFIPTSLRGVGNGWNYMFNKITEAVSGLT 400
                                       46778888999999999999999999998877554444444677777777666555555555666556666666666 PP

                             MFS_3 159 gGvlvaavGaa 169
                                       gG ++ +vG  
  gi|518651574|ref|YP_008141094.1| 401 GGAILVLVGLK 411
                                       66666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.67u 0.31s 00:00:00.98 Elapsed: 00:00:00.48
# Mc/sec: 2850.42
//
Query:       gi|518651575|ref|YP_008141095.1|  [L=470]
Description: hypothetical protein FACI_IFERC00001G0214 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-50  172.1   0.0    3.5e-50  171.0   0.0    1.6  1  FAD-oxidase_C  FAD linked oxidases, C-terminal domain
    1.6e-41  141.3   0.0    2.3e-41  140.8   0.0    1.3  1  FAD_binding_4  FAD binding domain
  ------ inclusion threshold ------
       0.14   10.0   0.0       0.17    9.7   0.0    1.1  1  Ycf1           Ycf1


Domain annotation for each model (and alignments):
>> FAD-oxidase_C  FAD linked oxidases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.0   0.0   5.8e-54   3.5e-50       2     250 .]     219     465 ..     218     465 .. 0.94

  Alignments for each domain:
  == domain 1  score: 171.0 bits;  conditional E-value: 5.8e-54
                                       -SEEEEEEEEESSHHHHHHHHHHHHHHT---SEEEEE-HHHHHHHHHTS-SSTTS-TTT-EEEEEEEEE-HHHHHHH CS
                     FAD-oxidase_C   2 pearavalvafpsfeaavkavreiaqagiipaalelmdkkaldlveatkgakkglpdeeealllvefegddeeeaee 78 
                                       pe +a ++ ++ ++ ++ k + +i+++gi p+  e+md  +++ +++ +g    +p  +++ll+v +++   e++e+
  gi|518651575|ref|YP_008141095.1| 219 PETTAKIMGFYRDILSVGKSMDTIKSQGITPIIAEFMDLPTINSIKKAMGI--EVPAYTQYLLMVDIDSAP-EALER 292
                                       7888888999*****************************************..******************.99999 PP

                                       HHHHHHHHTTT-EEEEE..........ETGGGGGGGGHHHHHHHHHCTTEEEEEEEEEEEHHHHHHHHHHHHHHHHH CS
                     FAD-oxidase_C  79 elealveaileatgaadvlvaqdeaeaealwkaRkaalpylrdallkagvavlseDtsvPvsrladlvrdikalldk 155
                                       +l+  + +i+++++   v v +d+++++++++aRk+a+  l +   +++  +++ D+ vP s+lad++ +i+  ++ 
  gi|518651575|ref|YP_008141095.1| 293 KLA-SAKDIMGKFSED-VIVIRDQKRMDEIYAARKGAYSALLEQRDNSNQLIVIGDVIVPSSQLADALGQIEGYART 367
                                       999.888888877766.6*********************9************************************* PP

                                       HHEEEEEEEEEETTEEEEEEEEEEE..--TT--THHHHHHHHHHHHTT-----------------------T....H CS
                     FAD-oxidase_C 156 yglevvlfgHagdgnlhlyilfdladeaeeeraeklvdevvdlavelgGsisgEHGvGldkkaylerekgee....g 228
                                        gl+++lfgH+gdgn+h +i +d   e+ +++++kl  +++++a++++Gs+s+EHG+G++k + l++e++e+    +
  gi|518651575|ref|YP_008141095.1| 368 DGLKTTLFGHIGDGNIHANIFMDN-TEEGRKKMAKLQMDIARVAIRHRGSVSAEHGIGTEKNELLYEEYKERnslyT 443
                                       ********************9987.6899999*******************************88877777633337 PP

                                       HHHHHHHHHHH-TT--BSTT-- CS
                     FAD-oxidase_C 229 lalmrriKaalDPkgiLNPgkv 250
                                       l++mr iK+a+DP++iLN gk+
  gi|518651575|ref|YP_008141095.1| 444 LEVMRLIKKAFDPNNILNRGKI 465
                                       9*******************96 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.8   0.0   3.9e-45   2.3e-41       1     139 []      43     182 ..      43     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.8 bits;  conditional E-value: 3.9e-45
                                       EEEEEEESSHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC.SCCEEEEEETTS--EEEEETTTTEEEEETTSBHHH CS
                     FAD_binding_4   1 paavvrpeseeevaaalrlaneaglpvlvrGgGssllgqav.atggvvldlsrlnrileideeegtatveaGvtlgd 76 
                                       p av  pe++++++++l+++n+ +++v++r+gG+sl+g++v  ++g+++++ +lnr+le+d ++++++ e+Gv+++ 
  gi|518651575|ref|YP_008141095.1|  43 PLAVCLPENADQISSILKICNKFKINVTARSGGTSLTGSSVeSFDGIIISTMNLNRLLELDLSSRYVVCEPGVRIDI 119
                                       789**********************************99999*********99************************ PP

                                       HHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--HHGTEEEEEEEETTSEEEEEE CS
                     FAD_binding_4  77 lvealaakglllglepgsgipgtvGGaiatnagGygsekyGlirdnvlglevvladGevvrls 139
                                       l+++l++++++++++p+s   +t+GG ++tnagG ++ +yG+++++vlg+evvl++Ge++r++
  gi|518651575|ref|YP_008141095.1| 120 LNAELKKHNFFYPPDPASSRASTIGGSLSTNAGGLRAVRYGATKEWVLGMEVVLPTGEIIRTG 182
                                       ************************************************************985 PP

>> Ycf1  Ycf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   2.9e-05      0.17     622     735 ..     269     393 ..     220     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 2.9e-05
                              Ycf1 622 kkvprws.yklideleeleGeneenlavekeirsrkakrvviftdkekkadtynatkdt.....dnsekkdevali. 691
                                        +vp ++ y l+ +++      e +la  k+i  + +  v+++ d+++  ++y+a k +     ++ ++++++ +i 
  gi|518651575|ref|YP_008141095.1| 269 IEVPAYTqYLLMVDIDSAPEALERKLASAKDIMGKFSEDVIVIRDQKRMDEIYAARKGAysallEQRDNSNQLIVIg 345
                                       3689885388999*****999********************************988865222223445555665441 PP

                              Ycf1 692 ....rysqqsdfrrdiikGsiraqrrkivil.elfqakvhsplfldrie 735
                                             sq +d   + i G  r++  k+ ++ ++ + ++h+ +f+d+ e
  gi|518651575|ref|YP_008141095.1| 346 dvivPSSQLADA-LGQIEGYARTDGLKTTLFgHIGDGNIHANIFMDNTE 393
                                       111134555665.56789*****999988872566889*******9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3230.72
//
Query:       gi|518651576|ref|YP_008141096.1|  [L=401]
Description: hypothetical protein FACI_IFERC00001G0215 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   44.5   1.2    1.6e-11   44.5   1.2    1.9  2  Fer4_8    4Fe-4S dicluster domain
    2.6e-08   33.4  14.5    1.6e-05   24.5   2.8    2.5  2  Fer4      4Fe-4S binding domain
    8.3e-08   32.7   1.7    8.3e-08   32.7   1.7    2.2  2  Fer4_17   4Fe-4S dicluster domain
    8.4e-08   31.9  12.4    0.00012   21.9   1.9    2.6  2  Fer4_2    4Fe-4S binding domain
    1.1e-07   31.9   2.4    2.8e-06   27.4   0.2    2.7  2  CCG       Cysteine-rich domain
    1.9e-07   31.5   8.6    1.3e-06   28.8   8.8    2.2  2  Fer4_7    4Fe-4S dicluster domain
    3.2e-07   30.4   5.0    1.8e-06   28.0   5.3    2.1  2  Fer4_9    4Fe-4S dicluster domain
    6.5e-07   29.2  20.1    0.00023   21.1   2.1    2.8  3  Fer4_6    4Fe-4S binding domain
    4.7e-06   26.7  15.3     0.0022   18.4   2.0    2.9  3  Fer4_4    4Fe-4S binding domain
    5.6e-06   26.5   2.8     0.0098   16.1   0.0    2.6  2  Fer4_18   4Fe-4S dicluster domain
    1.7e-05   24.8  19.5    0.00012   22.2  10.7    2.8  3  Fer4_10   4Fe-4S dicluster domain
     0.0018   18.3  13.0     0.0066   16.6   1.5    2.9  3  Fer4_21   4Fe-4S dicluster domain
     0.0033   18.3  10.6      0.012   16.6   8.9    2.6  3  Fer4_16   4Fe-4S double cluster binding domain
  ------ inclusion threshold ------
      0.039   14.9  17.3       0.28   12.2   5.4    2.7  2  Fer4_3    4Fe-4S binding domain
      0.052   14.4   9.7       0.79   10.6   1.5    3.1  3  Fer4_22   4Fe-4S dicluster domain
       0.18   12.4  12.6       0.52   10.9   2.3    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
        1.1   10.0   4.6        1.2    9.9   0.1    2.4  2  Fer4_15   4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   1.2   1.5e-14   1.6e-11       3      65 .]      12      79 ..      10      79 .. 0.87
   2 ?   -2.1   0.4       5.3   5.6e+03      15      15 ..     339     339 ..     303     379 .. 0.50

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 1.5e-14
                            Fer4_8  3 ekCieCgaCqsaCpvlrrtk.khlldargeaae....dvqeeqvleeeealwsCttcgaCtevCpvgi 65
                                      +kCi Cg+C+s Cp+l+  + +  + arg+++      ++++++le  ++++sC+ c aC++vCp g+
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCPTLEPDGyNSVFGARGRVILadfaLKESSEGLELGNSFYSCLDCYACVNVCPAGV 79
                                      79******************9***********9666544444454449*****************986 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.3
                            Fer4_8  15 C 15 
                                       C
  gi|518651576|ref|YP_008141096.1| 339 C 339
                                       1 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   2.8   1.5e-08   1.6e-05       4      20 ..      10      26 ..       7      27 .. 0.91
   2 !   14.1   4.0   2.9e-05      0.03       8      21 ..      65      78 ..      62      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.5e-08
                                      ETTTSSS-THHHHHSTT CS
                              Fer4  4 deekCigCGaCvevCPv 20
                                      +++kCi CG C++vCP+
  gi|518651576|ref|YP_008141096.1| 10 ITDKCISCGFCESVCPT 26
                                      68**************8 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 2.9e-05
                                      SSS-THHHHHSTTT CS
                              Fer4  8 CigCGaCvevCPvg 21
                                      C  C aCv+vCP g
  gi|518651576|ref|YP_008141096.1| 65 CLDCYACVNVCPAG 78
                                      99**********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 !   32.7   1.7   7.9e-11   8.3e-08       1      61 []      13      80 ..      13      80 .. 0.80
   2 ?   -2.0   0.0       5.1   5.4e+03      12      24 ..     374     386 ..     354     392 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 7.9e-11
                           Fer4_17  1 rCiqCgyClpeCpsyea......ydnepkkllraakl.glleeaekeekaslCieCgeCerkCPqgld 61
                                      +Ci+Cg+C+ +Cp++e        + + + +l++++l ++ e+ e  + + +C+ C  C+ +CP+g++
  gi|518651576|ref|YP_008141096.1| 13 KCISCGFCESVCPTLEPdgynsvFGARGRVILADFALkESSEGLELGNSFYSCLDCYACVNVCPAGVN 80
                                      6************9877552222334566799999995478888999*****************9985 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 5.1
                           Fer4_17  12 Cpsyeaydnepkk 24 
                                       Cp ++++  + ++
  gi|518651576|ref|YP_008141096.1| 374 CPLCYNNLAYDEN 386
                                       7777776655554 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   1.9   1.2e-07   0.00012       7      22 .]      11      26 ..       6      26 .. 0.91
   2 !   14.6   3.0   2.4e-05     0.026       9      22 .]      64      77 ..      62      77 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.2e-07
                            Fer4_2  7 tdrCigCgaCvsaCPa 22
                                      td+Ci+Cg C s+CP+
  gi|518651576|ref|YP_008141096.1| 11 TDKCISCGFCESVCPT 26
                                      89*************7 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
                            Fer4_2  9 rCigCgaCvsaCPa 22
                                      +C+ C aCv++CPa
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPA 77
                                      6************8 PP

>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.059        63      26      79 ..     208     262 ..     188     264 .. 0.72
   2 !   27.4   0.2   2.7e-09   2.8e-06       2      84 ..     301     381 ..     300     382 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.059
                               CCG  26 ealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79 
                                       ++ gv++ +l ++e   G      g+ ++++++a+  ++ ++e+g++ i++++p+
  gi|518651576|ref|YP_008141096.1| 208 QKSGVKFNYLgAEEPYPGMFLHELGYAKEFKEYAETVYNLLKEKGVKRIIAIDPH 262
                                       5555566655444444444444556778999*******************99986 PP

  == domain 2  score: 27.4 bits;  conditional E-value: 2.7e-09
                               CCG   2 ayfdgCh.llraaypevrkalkkllealgveleel..ekesCCGagggrsgkeelaealakrnvetaeetgadaivt 75 
                                       +++ +Ch +l++++ +   +l  +   + ++l+e   +  +CCG +      + +a+++  ++++ ++  + d ++t
  gi|518651576|ref|YP_008141096.1| 301 TVQEPCHiVLHNNNFKAMDILNSV---AEIKLPERsgKSTMCCGGPDELLFPD-TAKKVSMKRYKDLKA-KSDNVIT 372
                                       8899***66666677777777777...4455544446799******9966555.9**************.6999*** PP

                               CCG  76 acpgCllql 84 
                                       +cp C+++l
  gi|518651576|ref|YP_008141096.1| 373 ICPLCYNNL 381
                                       ******987 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.6     2e-05     0.021      36      50 ..      12      26 ..       5      28 .. 0.65
   2 !   28.8   8.8   1.3e-09   1.3e-06       1      52 []      13      79 ..      13      79 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-05
                            Fer4_7 36 ekClgCgaCvavCPt 50
                                      +kC++Cg C++vCPt
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCPT 26
                                      566666666666665 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 1.3e-09
                            Fer4_7  1 rCigCgaCvaaCpvkaield.eeenek..............gtekveidpekClgCgaCvavCPtga 52
                                      +Ci Cg+C+++Cp+   +    +  ++              +  ++  +  +Cl+C+aCv+vCP+g+
  gi|518651576|ref|YP_008141096.1| 13 KCISCGFCESVCPTLEPDGYnSVFGARgrviladfalkessEGLELGNSFYSCLDCYACVNVCPAGV 79
                                      7***********9544443212222221111111111111122444556789************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 !   12.6   1.8   0.00011      0.11      34      48 ..      12      26 ..       3      29 .. 0.74
   2 !   28.0   5.3   1.8e-09   1.8e-06       1      49 [.      13      78 ..      13      80 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                            Fer4_9 34 eaCigCgaCveaCpk 48
                                      ++Ci+Cg C+ +Cp+
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCPT 26
                                      478888888888886 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 1.8e-09
                            Fer4_9  1 kCtgCgaCveaCpagvvvedaaerkarlraase.................eaCigCgaCveaCpkg 49
                                      kC++Cg C+++Cp+    + ++   ar r   +                  +C++C aCv++Cp g
  gi|518651576|ref|YP_008141096.1| 13 KCISCGFCESVCPTLEPDGYNSVFGARGRVILAdfalkesseglelgnsfYSCLDCYACVNVCPAG 78
                                      7***********9999998888888888777668899*************99************87 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.1   2.2e-07   0.00023       6      21 ..      11      26 ..       7      31 .. 0.92
   2 !   17.7   5.0   2.5e-06    0.0027       8      23 ..      64      79 ..      64      81 .. 0.92
   3 ?   -2.3   0.2       5.2   5.5e+03       8      13 ..     373     378 ..     371     379 .. 0.58

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                            Fer4_6  6 pdkCigCgdCvrvCPe 21
                                       dkCi+Cg C++vCP+
  gi|518651576|ref|YP_008141096.1| 11 TDKCISCGFCESVCPT 26
                                      59*************7 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.5e-06
                            Fer4_6  8 kCigCgdCvrvCPega 23
                                      +C++C++Cv+vCP+g+
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPAGV 79
                                      6************986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 5.2
                            Fer4_6   8 kCigCg 13 
                                        C  C+
  gi|518651576|ref|YP_008141096.1| 373 ICPLCY 378
                                       366665 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.0     2e-06    0.0022       2      16 ..      12      26 ..      11      34 .. 0.92
   2 !   16.2   1.8     1e-05     0.011       3      17 .]      64      78 ..      62      83 .. 0.92
   3 ?   -1.6   0.1       5.3   5.6e+03       7      11 ..     374     378 ..     373     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 2e-06
                            Fer4_4  2 erCigCgsCvaaCPq 16
                                      ++Ci Cg C+++CP+
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCPT 26
                                      89************5 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1e-05
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                      +C++C +Cv++CP g
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPAG 78
                                      7************65 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.3
                            Fer4_4   7 CgsCv 11 
                                       C+ C+
  gi|518651576|ref|YP_008141096.1| 374 CPLCY 378
                                       88888 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.9    0.0011       1.1      56      73 ..       9      26 ..       2      29 .. 0.84
   2 !   16.1   0.0   9.3e-06    0.0098      55      76 ..      59      80 ..      32      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0011
                           Fer4_18 56 kgagdcidcescvkvcPt 73
                                      + + +ci+c++c +vcPt
  gi|518651576|ref|YP_008141096.1|  9 EITDKCISCGFCESVCPT 26
                                      55678************8 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.3e-06
                           Fer4_18 55 ekgagdcidcescvkvcPtgid 76
                                       ++   c+dc +cv+vcP g++
  gi|518651576|ref|YP_008141096.1| 59 GNSFYSCLDCYACVNVCPAGVN 80
                                      466778*************996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  10.7   1.1e-07   0.00012       5      56 .]      10      76 ..       6      76 .. 0.87
   2 !   15.8   1.5   1.1e-05     0.011       8      23 ..      64      79 ..      57     111 .. 0.76
   3 ?   -1.6   0.1         3   3.2e+03      26      49 ..     355     378 ..     338     382 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.1e-07
                           Fer4_10  5 dddtCirCgkCvkaCPadl................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                       +d+Ci Cg C ++CP+ l                 ++ a +e se+ +     ++C +c aCv +CP
  gi|518651576|ref|YP_008141096.1| 10 ITDKCISCGFCESVCPT-LepdgynsvfgargrviLADFALKESSEGLELGNSFYSCLDCYACVNVCP 76
                                      579**************.55*********9999986777777777777777799*************9 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.1e-05
                           Fer4_10  8 tCirCgkCvkaCPadl 23
                                      +C+ C +Cv++CPa +
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPAGV 79
                                      7999*********955 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3
                           Fer4_10  26 vgakgeaseeeavrkkvekCtgcg 49 
                                       v+ k +++ +++ + ++  C+ c 
  gi|518651576|ref|YP_008141096.1| 355 VSMKRYKDLKAKSDNVITICPLCY 378
                                       555666666666777777888886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   1.5   6.3e-06    0.0066      34      53 ..       7      26 ..       2      29 .. 0.85
   2 !    8.0   1.9     0.003       3.1      40      53 ..      64      77 ..      58      84 .. 0.82
   3 ?   -2.9   0.0       7.6     8e+03      42      47 ..     372     377 ..     353     379 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.3e-06
                           Fer4_21 34 lkvvedeCvGCnlCssvCPv 53
                                      ++ ++d+C+ C  C svCP+
  gi|518651576|ref|YP_008141096.1|  7 IEEITDKCISCGFCESVCPT 26
                                      56689**************7 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.003
                           Fer4_21 40 eCvGCnlCssvCPv 53
                                      +C  C  C++vCP 
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPA 77
                                      58888888888884 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.6
                           Fer4_21  42 vGCnlC 47 
                                       + C lC
  gi|518651576|ref|YP_008141096.1| 372 TICPLC 377
                                       346666 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   8.9   1.1e-05     0.012       1      66 [.      13      77 ..      13      78 .. 0.91
   2 !    8.9   2.6    0.0028         3       2      15 ..      65      78 ..      64      90 .. 0.85
   3 ?   -2.3   0.0       8.7   9.2e+03      48      60 ..     365     377 ..     346     379 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                           Fer4_16  1 rCgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66
                                      +C++Cg C +vCPt   ++  + ++ ar  +  ++   k+ +e  e  ++ + +  C +C++vCPa
  gi|518651576|ref|YP_008141096.1| 13 KCISCGFCESVCPTLEPDGY-NSVFGARGRVILADFALKESSEGLELGNSFYSCLDCYACVNVCPA 77
                                      5*************888888.688889999888999999999999999999**************8 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
                           Fer4_16  2 CgtCgkCaevCPtn 15
                                      C +C +C++vCP++
  gi|518651576|ref|YP_008141096.1| 65 CLDCYACVNVCPAG 78
                                      88999999999987 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 8.7
                           Fer4_16  48 ckkqeaitgCdiC 60 
                                        k+ + it C  C
  gi|518651576|ref|YP_008141096.1| 365 AKSDNVITICPLC 377
                                       2233556777777 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.1    0.0072       7.6       1      13 [.      14      26 ..      14      27 .. 0.95
   2 ?   12.2   5.4   0.00027      0.28       1      14 [.      65      78 ..      65      81 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0072
                            Fer4_3  1 CtgCgaCvevCPv 13
                                      C+ Cg C+ vCP+
  gi|518651576|ref|YP_008141096.1| 14 CISCGFCESVCPT 26
                                      ************6 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00027
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+ C+aCv+vCP g
  gi|518651576|ref|YP_008141096.1| 65 CLDCYACVNVCPAG 78
                                      999*********44 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   1.5   0.00075      0.79       1      14 [.      13      26 ..      13      34 .. 0.93
   2 ?    7.9   0.4    0.0054       5.7       1      20 [.      64      83 ..      64     109 .. 0.79
   3 ?   -2.2   0.0       7.3   7.7e+03       9      23 ..     371     385 ..     366     393 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00075
                           Fer4_22  1 rClsCgaCtlvCpt 14
                                      +C+sCg C  vCpt
  gi|518651576|ref|YP_008141096.1| 13 KCISCGFCESVCPT 26
                                      7************9 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0054
                           Fer4_22  1 rClsCgaCtlvCptCsCfdv 20
                                      +Cl+C aC  vCp+ +   v
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPAGVNAGV 83
                                      5************8766555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.3
                           Fer4_22   9 tlvCptCsCfdvede 23 
                                        ++Cp C+     de
  gi|518651576|ref|YP_008141096.1| 371 ITICPLCYNNLAYDE 385
                                       579999987666665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.3   0.00049      0.52       4      18 ..      12      26 ..      10      29 .. 0.92
   2 ?    6.1   2.9     0.015        16       5      18 ..      64      77 ..      63      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00049
                           Fer4_13  4 dtCiacgaCvelaPd 18
                                      d+Ci+cg C +++P 
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCPT 26
                                      89************6 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.015
                           Fer4_13  5 tCiacgaCvelaPd 18
                                      +C +c aCv+++P 
  gi|518651576|ref|YP_008141096.1| 64 SCLDCYACVNVCPA 77
                                      6************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1    0.0012       1.2       6      38 ..      12      41 ..      10      53 .. 0.83
   2 ?    0.6   1.1       0.9   9.5e+02       8      20 ..      65      77 ..      63      86 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0012
                           Fer4_15  6 daCigcglCvaeapevfeldedglasvllddge 38
                                      d+Ci+cg C  ++p   +l+ dg++sv +++g+
  gi|518651576|ref|YP_008141096.1| 12 DKCISCGFCESVCP---TLEPDGYNSVFGARGR 41
                                      89************...8888999988876654 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.9
                           Fer4_15  8 CigcglCvaeape 20
                                      C  c +Cv ++p 
  gi|518651576|ref|YP_008141096.1| 65 CLDCYACVNVCPA 77
                                      999********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2964.49
//
Query:       gi|518651577|ref|YP_008141097.1|  [L=348]
Description: aspartokinase (akH) [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-31  109.7   0.0    2.1e-31  109.4   0.0    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   1.1e-35   2.1e-31       3     238 ..       2     255 ..       1     258 [. 0.85

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1.1e-35
                                       EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHHTCCCCCHHHC............... CS
                         AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllalksglssgelaa.............. 64 
                                        VvK+GGs+l++ke+      ++ i++   + ++ ++V+++ +++t++l+++ ++ + ++++               
  gi|518651577|ref|YP_008141097.1|   2 QVVKIGGSILKNKED------LNLIKQKLIDCHNCIIVTSAlKNVTNMLIEA-YETKNTGIIDsiyhmhtdmiqldn 71 
                                       7**************......56666666666********************.666666666556655666666688 PP

                                       ..........E..HHHHHHHHH...........HHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE....HHHT CS
                         AA_kinase  65 .......glrstleeagevatr...........dalaslgerlvaallaaglpavglsaaaldateagr..degsdg 121
                                              g+r+ l+       +           d + s ger+++ +l + +++ g +++++         ++g ++
  gi|518651577|ref|YP_008141097.1|  72 siistlaGIREELK-------KlvvrenspslrDHIISYGERMSTLVLYNFFKDNGFNVSYIIEPLLVTdnNYGDSS 141
                                       77776643333333.......133334479999*****************************977766699999999 PP

                                       TTCEEECCHHHHHHHTT-EEEEESEEEEETTTE...EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCT CS
                         AA_kinase 122 nvesvdaeaieelleagvvpvltgfigldeege...lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpd 195
                                        +   +a++i++ +      +++gf+g++ eg+   +grg+sD++a  lA  l++  + i+tdV+G++++dpk  ++
  gi|518651577|ref|YP_008141097.1| 142 CLMDETARKIKNCVFG-DFTIVPGFYGATIEGKittVGRGGSDYTAMVLASILNC-DVRIITDVPGIMTSDPKLFKN 216
                                       999999*******966.79************************************.78888**************** PP

                                       TCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEE CS
                         AA_kinase 196 arllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvv 238
                                        r l e+s +e+++    ++++G k +  +++ ++ + +i++ 
  gi|518651577|ref|YP_008141097.1| 217 SRTLAEVSLSEVLK----MSYFGVKNFNYKTFMPVLGTDINIT 255
                                       **************....*******999999999988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2771.76
//
Query:       gi|518651578|ref|YP_008141098.1|  [L=339]
Description: hypothetical protein FACI_IFERC00001G0217 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-32  111.5   0.0    4.9e-32  110.9   0.0    1.3  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    5.1e-25   88.6   0.0    7.5e-25   88.1   0.0    1.2  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
     0.0014   18.3   0.0     0.0035   17.0   0.0    1.6  1  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
     0.0059   17.4   0.0       0.01   16.7   0.0    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 
  ------ inclusion threshold ------
       0.01   16.0   0.0       0.02   15.0   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
      0.044   13.9   0.0      0.083   13.0   0.0    1.5  1  Ldh_1_N          lactate/malate dehydrogenase, NAD binding do
      0.061   14.0   0.0       0.14   12.9   0.0    1.7  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   1.9e-35   4.9e-32       1     119 [.       5     129 ..       5     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.9e-35
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSG......GGTTTECEBEEEGGGGGCTT-SEEE CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavk......aleegkdlkvedvdeeelkevdivf 71 
                                       kv+++GatG+vGq++++lL++hp++elv l++s++  Gkk++e vk      ++e+ +d+k+ ++++e+ k+vd+v+
  gi|518651578|ref|YP_008141098.1|   5 KVSLLGATGMVGQKMIKLLADHPYIELVKLSASDSRIGKKYSETVKwiengsIPEKFRDMKLVSTSPEDNKDVDYVL 81 
                                       799************************************************************************** PP

                                       E-SCHHHHHHHHHHHHHTTSEEEESSSTTTTSTTSEBE-HHHHGGGGG CS
                    Semialdhyde_dh  72 lalpagvskelapklaeagvkviDlssdfRlkddavyvlpevnreaik 119
                                       +alp +++++++ kl+++g+ vi+++s +Rl++d++++ pe+n e+++
  gi|518651578|ref|YP_008141098.1|  82 SALPPEAAEPVELKLVKNGINVISNASPYRLSKDIPLINPEINFEHLR 129
                                       *********************************************986 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.0   2.9e-28   7.5e-25       4     183 ..     153     320 ..     151     321 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 2.9e-28
                                       HHHC.TT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHH CS
                   Semialdhyde_dhC   4 Llda.lgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelk 79 
                                       L++   ++ +r++ +++qa+SGaG                      g +++ i +N+ipyi +ee+k+  e+ +  +
  gi|518651578|ref|YP_008141098.1| 153 LVKLlGFDYDRISLVSMQAISGAGF--------------------SGLPYMSIDDNIIPYIHGEEEKIPAEISKMYG 209
                                       5554446789***************....................6******************************* PP

                                       HHHHHHHHCTESCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCS............TTEEEEESSHCH CS
                   Semialdhyde_dhC  80 avaetkkileftekvsatcvrVPvlrGhseavtiklklkdveveeveellaaa............pevkvvvneeed 144
                                        v++ k   ++   +s t vrVPv  Gh+  +++++k k v+vee  ++l +             p   +vv++e d
  gi|518651578|ref|YP_008141098.1| 210 TVQDGKINGKNIR-MSVTSVRVPVKVGHMGVLNMEIK-KGVDVEELIKNLNNFsplkgfnglynaPAHPIVVHNEAD 284
                                       ****999988886.9*********************7.999999999999999999*********999999999*** PP

                                       HSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTT CS
                   Semialdhyde_dhC 145 rPtpaavaggtnsvsVGRirkdemgdeglklvvvgDNll 183
                                       rP+ a ++ ++++v+VGRi       + l +v++g+Nl+
  gi|518651578|ref|YP_008141098.1| 285 RPQNAIDTYNGMEVHVGRISYTD---RNLRMVILGNNLV 320
                                       ********99*******998776...4499********8 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.4e-06    0.0035      70     126 ..     221     278 ..     216     306 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.4e-06
                                       TTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH.TTTTTTEEEEHSHHH CS
                           Gp_dh_C  70 gkldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaae.galkgilsyteeelv 126
                                       ++++ ++vrVP++ +++  l +e++k v vee ++ l++ +  + ++g+ +   +++v
  gi|518651578|ref|YP_008141098.1| 221 IRMSVTSVRVPVKVGHMGVLNMEIKKGVDVEELIKNLNNFSPlKGFNGLYNAPAHPIV 278
                                       678899********************************99955555555555555555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.9e-06      0.01       2      90 ..       5     104 ..       4     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.9e-06
                                       EEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.......EESSHHHHHTCT....TESEE CS
                      GFO_IDH_MocA   2 rvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeavaesfgve.......aysdleelladp....eidav 66 
                                       +v + Ga G++g+k ++ l ++ +  e+v l  +d+   ++ +e+ ++         + d++ ++++p    ++d+v
  gi|518651578|ref|YP_008141098.1|   5 KVSLLGAtGMVGQKMIKLLADH-PYIELVKLSASDSRIGKKYSETVKWIengsipeKFRDMKLVSTSPednkDVDYV 80 
                                       78889997888*****555555.999**********9999997666665556555788888777777766678**** PP

                                       EE-S-GGGHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA  67 ivatpngtheelakaaleagkhvl 90 
                                       + a p++  e ++++++++g++v+
  gi|518651578|ref|YP_008141098.1|  81 LSALPPEAAEPVELKLVKNGINVI 104
                                       ***********************9 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   7.6e-06      0.02       1      49 [.       4      50 ..       4     105 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.6e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSS CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdagellg 49
                                      ikv ++Ga+G +G++++k++ +++ +elv+   +++   +gk+ +e ++
  gi|518651578|ref|YP_008141098.1|  4 IKVSLLGATGMVGQKMIKLLADHPYIELVKLSASDS--RIGKKYSETVK 50
                                      79***************************9988876..56666666555 PP

>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.2e-05     0.083       1      73 [.       4      80 ..       4     105 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                                      EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHH...HHHHHHHHHHHCHCCSTS-.EEEEESSGGGGTTESEE CS
                           Ldh_1_N  1 vkvavvGaaGgiGqslalllankkladelaLlDiake...kleGvaldlshistflsvk.vkvsekeeealkdadvv 73
                                      +kv+++Ga+G++Gq++  lla +++ + ++L   +++   k +  +  ++++s++ +++ +k  ++  e+ kd+d+v
  gi|518651578|ref|YP_008141098.1|  4 IKVSLLGATGMVGQKMIKLLADHPYIELVKLSASDSRigkKYSETVKWIENGSIPEKFRdMKLVSTSPEDNKDVDYV 80
                                      59********************9999877766554434434444444456666665543134444666666666666 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.4e-05      0.14       1      38 [.       6      43 ..       6      84 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                                      EEEESTTSHHHHHHHHHHHHCTTTEEEEEEEE.SSTHHH CS
                   DXP_reductoisom  1 vviLGsTGSIGtqtLdvieenpdkfevvalaa.gsnvel 38
                                      v++LG+TG +G++ +++++++p  +e+v l+a +s++ +
  gi|518651578|ref|YP_008141098.1|  6 VSLLGATGMVGQKMIKLLADHP-YIELVKLSAsDSRIGK 43
                                      689*******************.999**99996666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2411.59
//
Query:       gi|518651579|ref|YP_008141099.1|  [L=471]
Description: ATPase [Ferroplasma acidarmanus fer1]
Scores for complete 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   80.0   4.8    2.4e-22   80.0   4.8    2.3  3  ATPase_2  ATPase domain predominantly from Archaea
    6.6e-22   77.8   1.0    2.1e-21   76.2   1.0    1.9  1  DUF234    Archaea bacterial proteins of unknown function
    4.6e-10   39.6   1.2    1.4e-09   38.1   1.2    1.9  1  AAA_14    AAA domain
    7.3e-07   29.7   0.0    2.9e-06   27.8   0.0    1.9  1  AAA_16    AAA ATPase domain
    0.00078   19.7   0.0     0.0015   18.8   0.0    1.5  1  AAA_22    AAA domain
     0.0017   18.3   0.6     0.0074   16.3   0.6    2.1  1  HTH_45    Winged helix-turn-helix
     0.0077   16.1   0.0      0.021   14.7   0.0    1.7  1  MarR      MarR family
     0.0083   16.3   0.1      0.031   14.5   0.1    1.9  2  UPF0102   Uncharacterised protein family UPF0102
     0.0083   16.0   0.2       0.03   14.2   0.0    2.0  2  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.017   14.7   1.3       0.18   11.4   0.3    2.7  2  HTH_24    Winged helix-turn-helix DNA-binding
      0.017   14.5   0.0      0.028   13.8   0.0    1.4  1  TniB      Bacterial TniB protein
      0.028   14.8   0.0       0.06   13.8   0.0    1.5  1  AAA       ATPase family associated with various cellular acti
      0.062   13.3   0.0       0.11   12.5   0.0    1.5  1  Mrr_cat   Restriction endonuclease
       0.17   12.2   0.0       0.39   11.0   0.0    1.5  1  E2R135    Coiled-coil receptor-binding R-domain of colicin E2


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.0   4.8   1.9e-25   2.4e-22       1     232 [.       2     206 ..       2     207 .. 0.84
   2 ?   -1.5   0.3       1.5   1.9e+03      91     112 ..     258     282 ..     212     353 .. 0.55
   3 ?   -3.5   0.0       6.3   8.1e+03     200     218 ..     435     454 ..     410     456 .. 0.73

  Alignments for each domain:
  == domain 1  score: 80.0 bits;  conditional E-value: 1.9e-25
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F+ R++e+++l + +++++++ ++iYG++++GKtaL+ e+i+ +     + iy+ a +++ +  +++f      + +
  gi|518651579|ref|YP_008141099.1|   2 FIGRKNEINYLTSQYRNNESSLILIYGRRRVGKTALIEEFIKSK-----KYIYLLATQQDINIIIRNF------SME 67 
                                       888**************************************998.....57*****************......444 PP

                          ATPase_2  78 lekalgiavp.kaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnlieslt 153
                                       +++ + +++  ++ l        ++ +  +++l++++++   kii  +De+ +l+     ++++ ++ L+++++   
  gi|518651579|ref|YP_008141099.1|  68 MAEFFHDDITyRNPL--------TNWDDLFKYLIKNLQNVDEKIIFALDEFTYLV----AKDKSILSILQKYYDLYF 132
                                       455554444303333........44445555555666666666************....678*************** PP

                          ATPase_2 154 kekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkeleelskedfeeiyryvGGkPk 228
                                       k+ +++++i +s  g++ +  +++es+l+gr+++ il++ +   + +++ ++        s +d+ +iy+++GG P+
  gi|518651579|ref|YP_008141099.1| 133 KDMKIFIIITGSLMGIINDkILSYESPLYGRRTGnILLNKM---NLWEIKDFF----PYYSVQDLIKIYSITGGLPY 202
                                       *****************996789******************...888888884....223889************** PP

                          ATPase_2 229 alve 232
                                       +l  
  gi|518651579|ref|YP_008141099.1| 203 YLSA 206
                                       *976 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.5
                          ATPase_2  91 leeilk...eksklvfkaielllek 112
                                       + ei +   ++s ++++++++l++ 
  gi|518651579|ref|YP_008141099.1| 258 IGEIASllnTNSGEITQYLDNLIKL 282
                                       4444443334444444554444433 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.3
                          ATPase_2 200 flkegfkel.eelskedfee 218
                                       f k gf e+  +ls+ d++ 
  gi|518651579|ref|YP_008141099.1| 435 FSKSGFDENlTKLSEIDKNI 454
                                       67777877777777777765 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   1.0   1.7e-24   2.1e-21       1      92 [.     312     410 ..     312     417 .. 0.92

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 1.7e-24
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwW.........kkee 68 
                                       +fr+++p++++ie+++++ +l+ ik++++ y++k FE+++r++l++   ++ +  ++t +G+wW         k+ee
  gi|518651579|ref|YP_008141099.1| 312 FFRYIFPYQNLIEIDNYNVLLNIIKNDFDFYTSKIFEDISRNILFKFG-KNLTGDNITGIGTWWgknklenngKNEE 387
                                       79*******************************************655.5677889**********99999888999 PP

                            DUF234  69 eiDivaldeeekkalfgEvKwkns 92 
                                       eiDi+al+e+++ +++gEvKw+n+
  gi|518651579|ref|YP_008141099.1| 388 EIDIIALTEDKN-IIVGEVKWRNK 410
                                       *********995.*********94 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   1.2   1.1e-12   1.4e-09       4     126 ..      23     174 ..      20     179 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.1e-12
                            AAA_14   4 ilvitGaRrvGKTtllkqlikell.......vkkesilyinldderd......kkladpe....kllelileklke. 62 
                                       +++i G RrvGKT l++++ik++         ++ +i+  n+  e         ++++p     +l +++ ++l++ 
  gi|518651579|ref|YP_008141099.1|  23 LILIYGRRRVGKTALIEEFIKSKKyiyllatQQDINIIIRNFSMEMAeffhddITYRNPLtnwdDLFKYLIKNLQNv 99 
                                       789*****************998888998776666777777777655555555333333244557888888886667 PP

                            AAA_14  63 ekktylflDEiqev....pewekalkslvd...egknldvivtGSnskllskeia...tslagrva.eielypls 126
                                       ++k ++ lDE  ++    +++ ++l++++d   ++ ++ +i+tGS+ +++  +i    + l gr + +i l+ ++
  gi|518651579|ref|YP_008141099.1| 100 DEKIIFALDEFTYLvakdKSILSILQKYYDlyfKDMKIFIIITGSLMGIINDKILsyeSPLYGRRTgNILLNKMN 174
                                       8999999****99988889999999999997665568899******99998877633344445443255555555 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   2.3e-09   2.9e-06       2      63 ..       2      58 ..       1     127 [. 0.84

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.3e-09
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      ++GR++e++ L+s ++    ++++l+l++G + vGK++l++e+ +  +k+++++l+++ d +
  gi|518651579|ref|YP_008141099.1|  2 FIGRKNEINYLTSQYR---NNESSLILIYGRRRVGKTALIEEFIK--SKKYIYLLATQQDIN 58
                                      89******99999998...44558********************8..666777777777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.2e-06    0.0015       5     131 ..      21     143 ..      17     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka..erlsse 76 
                                        ++++++G   +GKT l++++ +++           ++++  ++++      +++  e++++++++  +  +  + +
  gi|518651579|ref|YP_008141099.1|  21 SSLILIYGRRRVGKTALIEEFIKSK-----------KYIYLLATQQDiniIIRNFSMEMAEFFHDDITYrnPLTNWD 86 
                                       6799*******************86...........56666666666658889999999999998888888899999 PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlr..seealeeLrsllnlsrkgvqliLvGtp 131
                                       +l+++l ++l++ + + ++ +DE+ +l    + +l+ L + ++l  k++++++++t 
  gi|518651579|ref|YP_008141099.1|  87 DLFKYLIKNLQNVDEKIIFALDEFTYLVakDKSILSILQKYYDLYFKDMKIFIIITG 143
                                       *************99999********9775588999998888885555555555554 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   5.8e-06    0.0074       9      54 ..     245     290 ..     243     311 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-06
                            HTH_45   9 adILeaisegeakkTkimykanLsykllnkYLdmLvekglikkske 54 
                                       ++IL++is g+++  +i    n +   + +YLd L++ g+i+k+k 
  gi|518651579|ref|YP_008141099.1| 245 FSILNIISTGHNRIGEIASLLNTNSGEITQYLDNLIKLGIISKRKP 290
                                       78***************************************88764 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.6e-05     0.021      16      51 ..     254     289 ..     242     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                                       TTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  16 gplsvseLakklgvskstvtrvldrLekkGlieRsk 51 
                                       g  ++ e+a+ l+++++ +t  ld L+k G i+++k
  gi|518651579|ref|YP_008141099.1| 254 GHNRIGEIASLLNTNSGEITQYLDNLIKLGIISKRK 289
                                       556789***************************987 PP

>> UPF0102  Uncharacterised protein family UPF0102
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       4.9   6.3e+03      10      27 ..      53      70 ..      49      71 .. 0.79
   2 !   14.5   0.1   2.4e-05     0.031      18      46 ..     380     410 ..     375     425 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 4.9
                                      HHTT-EEEEEEEEETTEE CS
                           UPF0102 10 ekkgyeilernwrcragE 27
                                      +++ ++i+ rn+++++ E
  gi|518651579|ref|YP_008141099.1| 53 TQQDINIIIRNFSMEMAE 70
                                      578899999999887665 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.4e-05
                                       EEEEEETTEEEEEEE...TTEEEEEEEEE-.. CS
                           UPF0102  18 ernwrcragEiDiia...tevlvfvEVKtRss 46 
                                       e+n + +  EiDiia   ++ +++ EVK+R++
  gi|518651579|ref|YP_008141099.1| 380 ENNGK-NEEEIDIIAlteDKNIIVGEVKWRNK 410
                                       55554.358********9888*********54 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.4e-05      0.03       7      47 .]     247     287 ..     245     287 .. 0.97
   2 ?   -1.9   0.0       2.5   3.2e+03       2      14 ..     411     423 ..     410     425 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVek 47 
                                       IL++ + g   ++e+a  l+ + + + ++L  L ++G+++k
  gi|518651579|ref|YP_008141099.1| 247 ILNIISTGHNRIGEIASLLNTNSGEITQYLDNLIKLGIISK 287
                                       9999***********************************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.5
                                       HHHHHHHHHHTTS CS
                             HTH_5   2 ptRlkILklLaeg 14 
                                       p ++++L++L+++
  gi|518651579|ref|YP_008141099.1| 411 PLKIEVLYSLQNK 423
                                       7799******875 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 ?    1.0   0.0      0.25   3.2e+02       4      14 ..     116     126 ..     115     129 .. 0.90
   2 ?   11.4   0.3   0.00014      0.18       8      47 ..     247     285 ..     245     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.25
                            HTH_24   4 tdrkILelLqk 14 
                                       +d+ IL++Lqk
  gi|518651579|ref|YP_008141099.1| 116 KDKSILSILQK 126
                                       699*******8 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00014
                            HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       IL+++   ++  + e+A  l+  ++ ++++l++L++ G+I
  gi|518651579|ref|YP_008141099.1| 247 ILNIIST-GHNRIGEIASLLNTNSGEITQYLDNLIKLGII 285
                                       6666665.888899*************************9 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.2e-05     0.028      24      72 ..      10      59 ..       6     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                              TniB 24 eeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekd.edaekvpv 72
                                      + L +  ++++ + +l++G+  +GKt+++e+F ++++     ++++ +++
  gi|518651579|ref|YP_008141099.1| 10 NYLTSQYRNNESSLILIYGRRRVGKTALIEEFIKSKKYIYLlATQQDINI 59
                                      567777788888999******************99886653244444544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.7e-05      0.06       1     120 [.      24     154 ..      24     159 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.7e-05
                                       EEEESSTTSSHHHHHHHHHHH........HT......HEEEEEETTTCSSS..STTHHHHHHHHHHHH.HHHTS... CS
                               AAA   1 vllyGppGtGKTllakavake........lg......vefleisgsellsk..yvgesekkirelfke.akeka... 57 
                                       +l+yG   +GKT+l++  +k+        ++      ++ ++++++e++ +  +  +   +  +lfk  +k+ +   
  gi|518651579|ref|YP_008141099.1|  24 ILIYGRRRVGKTALIEEFIKSkkyiyllaTQqdiniiIRNFSMEMAEFFHDdiTYRNPLTNWDDLFKYlIKNLQnvd 100
                                       699******************66655543113333446678888888884467666677777788877334444775 PP

                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                       ++ i+ +DE+  l+ ++        +++++ L +  d + k+ + +++i+++  +  +++++l
  gi|518651579|ref|YP_008141099.1| 101 EKIIFALDEFTYLVAKD--------KSILSILQKYYDLYFKDMK-IFIIITGSLMGIINDKIL 154
                                       668888*******9999........8999999999999999755.888888888999988887 PP

>> Mrr_cat  Restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.8e-05      0.11      28     114 ..     381     465 ..     347     466 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.8e-05
                                       --B-TTSSB--EEEETTEEEEEEEEEEE--TS-B-HHHHHHHHHHCTTS..SEEEEEESS-B-HHHHHHHHTT--EE CS
                           Mrr_cat  28 tgrsgDggiDliakkdplgserilvqaKryknkvgvkeVqeligalkkrgadkgifvttsdftkaAreeaeelnkie 104
                                       +++++++ iD+ia +++  +  i+ ++K+++++ + +++ +l+      +  k i+ + s+f ++  +  e  ++i+
  gi|518651579|ref|YP_008141099.1| 381 NNGKNEEEIDIIALTED--KNIIVGEVKWRNKPLKIEVLYSLQNKSVFIKPYKYILFSKSGFDENLTKLSEIDKNII 455
                                       34588999****86654..358999***********************9********************99878*** PP

                                       EE-HHHHHHH CS
                           Mrr_cat 105 LldgdeLael 114
                                       L+d +++ el
  gi|518651579|ref|YP_008141099.1| 456 LVDLNKIGEL 465
                                       ****998776 PP

>> E2R135  Coiled-coil receptor-binding R-domain of colicin E2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00031      0.39      56     115 ..      70     122 ..      61     128 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00031
                            E2R135  56 eankddfvtynppheygsgwqdqvryldkdiqnqneklkaaqtslnemneslsrdkaals 115
                                       e  +dd +ty  p    + w+d  +yl k++qn +ek+  a   l+e+   +++dk+ ls
  gi|518651579|ref|YP_008141099.1|  70 EFFHDD-ITYRNPL---TNWDDLFKYLIKNLQNVDEKIIFA---LDEFTYLVAKDKSILS 122
                                       555555.5665554...57******************9765...7888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3147.45
//
Query:       gi|518651580|ref|YP_008141100.1|  [L=212]
Description: phosphoserine phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-13   50.4   0.0    4.2e-13   50.1   0.0    1.1  1  HAD              haloacid dehalogenase-like hydrolase
    9.2e-12   45.7   0.0    6.2e-10   39.7   0.0    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    8.2e-08   32.5   0.1    2.7e-07   30.9   0.1    1.7  1  HAD_2            Haloacid dehalogenase-like hydrolase
    4.5e-06   26.6   0.4    5.1e-05   23.2   0.3    2.3  3  Hydrolase_3      haloacid dehalogenase-like hydrolase
    9.1e-06   25.2   0.1    6.6e-05   22.4   0.1    1.9  1  Put_Phosphatase  Putative Phosphatase
  ------ inclusion threshold ------
      0.051   13.6   0.1       0.16   12.0   0.0    1.8  2  AAA_14           AAA domain


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 !   50.1   0.0   1.4e-16   4.2e-13       1     186 [.       5     174 ..       5     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 1.4e-16
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallagls.eelaaelerf 76 
                                       ++fD+Dg L+ + s ++++ ++l+         +re +l+++    ++ld+ ++ ++  a+++  + e   +e++ +
  gi|518651580|ref|YP_008141100.1|   5 IFFDMDGVLTVEKSSWFYVNNRLGI-------NNRENYLKYI---SGKLDYYDFFRMDIAAWREKYpEITMEEIKGI 71 
                                       79******************77765.......4556666666...44444445555555555555559999999999 PP

                               HAD  77 vaevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd..rltgelglegkpvrg 151
                                       ++e+    ++ pg+ + +a  +++ +  v+vSgg++ l  +l + +g+de +a+++ +d+  +l  e++++  p r+
  gi|518651580|ref|YP_008141100.1|  72 LDEIP---VI-PGIEKCMAYLKKNKIISVIVSGGISWLSDRLKNSFGIDEAYANRIFSDHegKLIPEGEVQVNPMRK 144
                                       96555...36.9*******999********************************99999999888888888888888 PP

                               HAD 152 egkvaalrewlaaegegidleevvayGDspsDlpl 186
                                           + + e   +++++ ++++++a GDs+sD+ +
  gi|518651580|ref|YP_008141100.1| 145 ----DIVME-KIMAEHNVSPKDCIALGDSESDYSM 174
                                       ....44444.4777999999*************99 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.1e-13   6.2e-10       1     209 [.       2     178 ..       2     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.1e-13
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpewl 77 
                                       ik+++fD+dG+Lt  ++s   v +++                           +++  ++       +y  gk ++ 
  gi|518651580|ref|YP_008141100.1|   2 IKLIFFDMDGVLTVEKSSWFYVNNRL---------------------------GINNRENYL-----KYISGKLDYY 46 
                                       89***********6665555555555...........................666777777.....8999999999 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +        +++i ++ ++  +  ++     ++  i d+++v p++++++a+Lk+++i  v+++g+ +   +r+ n 
  gi|518651580|ref|YP_008141100.1|  47 DFF------RMDIAAWREKYPEITME-----EIKGILDEIPVIPGIEKCMAYLKKNKIISVIVSGGISWLSDRLKNS 112
                                       999......88899999999999999.....5555668888***************************9999***** PP

                                       TT.GGGESEEEEHHCES......STTTSHHHHHHHHHHH....TSTGGGEEEEESSHHHHHHHHHT CS
                                       xx.xxxxxxxxxxxxxx......xxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lG.ddyfdaviasdiet......vakpspegkvaaireL....qgkpeevamVGDgvnDaaalaaA 209
                                       +G d+++++ i sd e+         ++p  k  +++++    +++p+++++ GD+  D ++ +a+
  gi|518651580|ref|YP_008141100.1| 113 FGiDEAYANRIFSDHEGklipegEVQVNPMRKDIVMEKImaehNVSPKDCIALGDSESDYSMYKAV 178
                                       ***5555666666666656553377778888888888884444699****************9987 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   8.9e-11   2.7e-07       1     171 [.       5     178 ..       5     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 8.9e-11
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrel.lrklgeseeeeekieellrkyneekkkk 76 
                                       i FD+Dg+l  ++  ++ + n+l         ++e++ k+i  +l+ + + ++ +  + e+  e  +++++  +  +
  gi|518651580|ref|YP_008141100.1|   5 IFFDMDGVLTVEKSSWFYVNNRLGI------NNRENYLKYISGKLDYYdFFRMDIAAWREKYPEITMEEIKGIL--D 73 
                                       67********999999999888874......4578888888777632223334444454445555555555555..5 PP

                             HAD_2  77 evkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpe..........viek 143
                                       e+ +++g+++ + +Lk++++   iv+ + +   ++  + +gi++ +   + s++ +k  P+ e          v+ek
  gi|518651580|ref|YP_008141100.1|  74 EIPVIPGIEKCMAYLKKNKIISVIVSGGISWLSDRLKNSFGIDEAYANRIFSDHEGKLIPEGEvqvnpmrkdiVMEK 150
                                       6****************************************************999987876611111111224667 PP

                             HAD_2 144 aleklklkkeeviyvGDsptDieaakka 171
                                       ++ + +++++++i  GDs +D    k++
  gi|518651580|ref|YP_008141100.1| 151 IMAEHNVSPKDCIALGDSESDYSMYKAV 178
                                       77777****************9876665 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0       0.2   6.1e+02       1      13 [.       5      17 ..       5      39 .. 0.84
   2 ?   -1.4   0.0      0.54   1.6e+03      85     105 ..      82     103 ..      79     134 .. 0.60
   3 !   23.2   0.3   1.7e-08   5.1e-05     186     241 ..     142     197 ..     135     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.2
                                      EEEEIIIIIS-TT CS
                       Hydrolase_3  1 ialDlDGTLlnsd 13
                                      i++D+DG L  ++
  gi|518651580|ref|YP_008141100.1|  5 IFFDMDGVLTVEK 17
                                      89*****886555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.54
                                       HHHHHHHHHTT.CEEEEEESSE CS
                       Hydrolase_3  85 keiikllkenn.veillytedk 105
                                       ++++++lk+n+ +++++++  +
  gi|518651580|ref|YP_008141100.1|  82 EKCMAYLKKNKiISVIVSGGIS 103
                                       5667777777744444443333 PP

  == domain 3  score: 23.2 bits;  conditional E-value: 1.7e-08
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSE CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdy 241
                                       + K   ++k++ e n+s++++ia GD+e D++M +a+++ +A ++ s+ +  +A+ 
  gi|518651580|ref|YP_008141100.1| 142 MRKDIVMEKIMAEHNVSPKDCIALGDSESDYSMYKAVNNFIAFNSDSDLLSRVARI 197
                                       56888899**********************************99888888777764 PP

>> Put_Phosphatase  Putative Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1   2.2e-08   6.6e-05       2     184 ..       4     174 ..       3     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.2e-08
                   Put_Phosphatase   2 lvvfDFDkti.idedsdnwvvdelpatelfeelretlrkglwnelmdrvlkelheqg..vseadikkvlrsiplspg 75 
                                       l+ fD D  + ++++s   v + l+ +++ + l+    k  + ++    ++  +e+    ++++ik +l +ip+ pg
  gi|518651580|ref|YP_008141100.1|   4 LIFFDMDGVLtVEKSSWFYVNNRLGINNRENYLKYISGKLDYYDFFRMDIAAWREKYpeITMEEIKGILDEIPVIPG 80 
                                       789****98758999999****************9999999999988888888888655899*************** PP

                   Put_Phosphatase  76 lvelikslakkkleldliiiSDaNsffieeileaagledlFseiftNPaavdasGeltvlpyhehsCklcpsNlCKg 152
                                       + + +  l+k+  ++  +i+S   s   + + +  g+ +     ++N    d++G+l  +       +   + + K 
  gi|518651580|ref|YP_008141100.1|  81 IEKCMAYLKKN--KIISVIVSGGISWLSDRLKNSFGIDEA----YANRIFSDHEGKLIPEG------EVQVNPMRKD 145
                                       ********554..455566777666666666666666555....55555557777775432......2233447889 PP

                   Put_Phosphatase 153 kvleelvaeqaregveyerliYvGDganDlCp 184
                                        v+e+++ae   ++v+ +  i +GD+  D+  
  gi|518651580|ref|YP_008141100.1| 146 IVMEKIMAE---HNVSPKDCIALGDSESDYSM 174
                                       999999988...46778899999999999865 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.4e-05      0.16      38     102 ..      43     103 ..      17     123 .. 0.71
   2 ?   -1.2   0.0      0.65     2e+03      94     117 ..     180     203 ..     145     207 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                            AAA_14  38 ldderdkkla...dpekllelileklkeekktylflDEiqevpewekalkslvdegknldvivtGSns 102
                                       ld  ++ +++     ek++e+ +e++k+      +lDEi  +p++ek++ +l +++  + viv+G  s
  gi|518651580|ref|YP_008141100.1|  43 LDYYDFFRMDiaaWREKYPEITMEEIKG------ILDEIPVIPGIEKCMAYLKKNK-IISVIVSGGIS 103
                                       3444443322111223466666666555......9*******************99.99*****9765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.65
                            AAA_14  94 dvivtGSnskllskeiatslagrv 117
                                       ++i+  S s lls+ ++ +l+g +
  gi|518651580|ref|YP_008141100.1| 180 NFIAFNSDSDLLSRVARINLSGNI 203
                                       566667777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1540.75
//
Query:       gi|518651581|ref|YP_008141101.1|  [L=470]
Description: hypothetical protein FACI_IFERC00001G0220 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-26   92.9   0.0    4.4e-26   91.9   0.0    1.5  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    6.1e-19   68.0   0.2    2.1e-18   66.3   0.1    1.9  2  HGTP_anticodon  Anticodon binding domain
    1.6e-06   28.2   0.1    3.6e-06   27.1   0.1    1.6  1  ProRS-C_1       Prolyl-tRNA synthetase, C-terminal
      0.006   16.6   0.4      0.013   15.6   0.4    1.5  1  Pam16           Pam16
  ------ inclusion threshold ------
      0.019   15.6   0.9        1.4    9.7   0.2    3.6  4  Plk4_PB2        Polo-like Kinase 4 Polo Box 2
      0.064   13.6   2.7       0.14   12.5   2.7    1.5  1  EbsA            EbsA-like protein


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   1.5e-29   4.4e-26       8     176 ..     105     272 ..      94     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.5e-29
                                       SEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEES.GGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                      tRNA-synt_2b   8 dreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfha.easlddslrd 82 
                                       d +++L+Pt+e++++ ++  + +rs  +LP+++yqi  +yR+E++ +r  +Rvre+h  +++  h   ++++ ++ +
  gi|518651581|ref|YP_008141101.1| 105 DIDLALRPTSEAAMYTMFPLW-IRShSDLPFRIYQIVNVYRYETKHTRSFIRVREIHFYEAHTAHVdFEDAEKQMDE 180
                                       6799***************88.***777*****************9********************6699******* PP

                                       HHHHHHHHHHHTT.SC.EEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEE CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  83 likaisriferlglef.raiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreks 158
                                       ++k ++r+  +l + f   i+ +++++ + + ++  f+  ++   + ++igti++ g+++++  g+++lden+  k 
  gi|518651581|ref|YP_008141101.1| 181 YLKIMERLSDDLCIYFsMDIRPDWDKF-PGAMYSVAFDTPMP-GYRSLQIGTIHEYGENFAKNYGIKYLDENGDMKY 255
                                       ***********9985538899999965.99************.677888**************************** PP

                                       EEEEEEEEEHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 159 vimicaaigveRllsail 176
                                       v  + ++++ eRl++a++
  gi|518651581|ref|YP_008141101.1| 256 VSQTTFGLS-ERLMAAVI 272
                                       *99999999.******97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0         2     6e+03      11      27 ..     174     190 ..     169     199 .. 0.81
   2 !   66.3   0.1   6.9e-22   2.1e-18       1      89 [.     291     380 ..     291     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHHHT CS
                    HGTP_anticodon  11 aeeleeyakklaeeLra 27 
                                       ae+ ++++ k+ e+L++
  gi|518651581|ref|YP_008141101.1| 174 AEKQMDEYLKIMERLSD 190
                                       56788999999999987 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 6.9e-22
                                       SEEEEESSSS.HHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTT CS
                    HGTP_anticodon   1 qvvviplnek.aeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdt 76 
                                       qv+++p+ ++  +e+ ey + ++++L + gir+ +d+s++++g+k++e+++ g+p+++++G++e++++t+t++ r+ 
  gi|518651581|ref|YP_008141101.1| 291 QVIIVPIPSDnYDEIIEYSNGIKSKLMEIGIRCQIDNSDYTPGYKFNEWEMRGVPVRIEIGKREVNDKTLTISLRTR 367
                                       899***99988667*************************************************************** PP

                                       CEEEEEETTHHHH CS
                    HGTP_anticodon  77 reqervsldelve 89 
                                       +++++++l+e+ +
  gi|518651581|ref|YP_008141101.1| 368 KKKIKIELEEISN 380
                                       **********976 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 !   27.1   0.1   1.2e-09   3.6e-06       6      69 .]     411     470 .]     407     470 .] 0.85

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.2e-09
                                       HHHHTT-EEEEEESSGHHHHHHHHHHHS-EEEEEESSB-SSCCCSB-TTT-SB-SEEEEEE-B- CS
                         ProRS-C_1   6 ealekkgfvlapWcgeeecEekIkeetgakslcipfdqepseegtkCivcgkpakkwvlfgrsY 69 
                                       e+++++++v a+Wcg+++c ++I+  +    l+   ++    ++  Civcg p k    f r+Y
  gi|518651581|ref|YP_008141101.1| 411 EKIKEDKMVTAYWCGSKACSDEIESLSEKAALGAVRND---GTSGPCIVCGSPGK-LSAFSRTY 470
                                       689999*********************88888886664...47889******976.66788877 PP

>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.4   4.2e-06     0.013      59     110 ..     362     416 ..     344     422 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.2e-06
                                       HHHHHHT--G--SHHHHHHHHHHHHHHT.-.CCCTS-HHHHHHHHH.HHHHHHHH CS
                             Pam16  59 eslkilnveedlnreevekryehlfevn.d.kskGGslylqskvfr.akerldee 110
                                        sl+    + +++ ee+ + y++l evn d ksk   +y+  kvf  + e+++e+
  gi|518651581|ref|YP_008141101.1| 362 ISLRTRKKKIKIELEEISNMYQYLKEVNlDiKSKASEFYMANKVFIdSLEKIKED 416
                                       44444444446778************996359************95256888775 PP

>> Plk4_PB2  Polo-like Kinase 4 Polo Box 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.31   9.4e+02      13      42 ..       5      32 ..       2      40 .. 0.74
   2 ?   -0.1   0.0       0.5   1.5e+03      83     108 ..      50      77 ..      44      78 .. 0.73
   3 ?   -2.5   0.0       2.9   8.5e+03      83     105 ..     104     126 ..      91     129 .. 0.80
   4 ?    9.7   0.2   0.00046       1.4       5      91 ..     305     398 ..     303     407 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.31
                          Plk4_PB2 13 KcmLmEnspeadfeasFydgakvtkssgek 42
                                      Kc+ mEn  + df+ ++ +     k s++ 
  gi|518651581|ref|YP_008141101.1|  5 KCQ-MENK-KIDFSEWYNEIIDTAKLSDKR 32
                                      776.9**9.69**99998877777766655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.5
                          Plk4_PB2  83 lklesalssleke..kseslFPviigrr 108
                                        +++s+l + +++   +e  FPv i+r+
  gi|518651581|ref|YP_008141101.1|  50 HSIDSLLREYSDDggIEEVSFPVLISRE 77 
                                       56777777777666556889*****996 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.9
                          Plk4_PB2  83 lklesalsslekekseslFPvii 105
                                       l+++ al  ++++   ++FP+ i
  gi|518651581|ref|YP_008141101.1| 104 LDIDLALRPTSEAAMYTMFPLWI 126
                                       67888888888888999***988 PP

  == domain 4  score: 9.7 bits;  conditional E-value: 0.00046
                          Plk4_PB2   5 vtlYtkkaKcmLmEnspeadfe.asFydgakvtkssgek..vki....ieksgksltleseeeleslsselkklleh 74 
                                       ++ Y++  K  LmE + + ++    +  g k+++++ ++  v+i     e ++k+lt++ +++ ++++ el+++ + 
  gi|518651581|ref|YP_008141101.1| 305 IIEYSNGIKSKLMEIGIRCQIDnSDYTPGYKFNEWEMRGvpVRIeigkREVNDKTLTISLRTRKKKIKIELEEISNM 381
                                       889*************7777773566679*****9999955333656555556899999999999999999999999 PP

                          Plk4_PB2  75 aeeclkqclklesalss 91 
                                       ++   +  l+++s  s+
  gi|518651581|ref|YP_008141101.1| 382 YQYLKEVNLDIKSKASE 398
                                       99888888888887765 PP

>> EbsA  EbsA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.7   4.5e-05      0.14      65     129 ..     356     416 ..     351     420 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.5e-05
                              EbsA  65 eedkliikslrffkkkkielseIkkvevekkkielklkekksrtflmrkkpkklfldalkenkak 129
                                       ++++l+i+     kk kiel+eI++++ + k+++l + ++k  +f+m  k   +f+d+l++ k +
  gi|518651581|ref|YP_008141101.1| 356 NDKTLTISLRTRKKKIKIELEEISNMYQYLKEVNLDI-KSKASEFYMANK---VFIDSLEKIKED 416
                                       6677999999999************************.999999***865...688888776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 3529.26
//
Query:       gi|518651582|ref|YP_008141102.1|  [L=345]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for 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   90.7  50.6    1.2e-25   90.5  50.6    1.0  1  SLAC1     Voltage-dependent anion channel


Domain annotation for each model (and alignments):
>> SLAC1  Voltage-dependent anion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5  50.6   6.5e-30   1.2e-25       4     323 ..       8     335 ..       5     336 .. 0.79

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 6.5e-30
                             SLAC1   4 pawFaivMGtgilalllk..alp..arglri.islilfllalvlfllllvlyllrfilypeavrkelrhpveslflg 75 
                                        +wF +v+Gt  ++l++   +    ++ l   i++i++++ l++f+++++ +++r+i +++ +++++++ ++  fl+
  gi|518651582|ref|YP_008141102.1|   8 STWFPVVLGTLSVSLAFFiiY-LvfHNVLIFnIGKIIYFIVLIFFAFVFASWIYRYIKNKKLIKEDYNDMTKLSFLA 83 
                                       58***************5331.13334444469************************************88888888 PP

                             SLAC1  76 tfpmgl.ltilnglllvlpgewlatlalvllWigvllslltavvvvfllftekeekleeitpawllpvvgllvvall 151
                                       ++ + + ++ + ++++v  +  +a+l ++ll++ ++l l++++++ + l+t+k +  + it a+l+p v +    +l
  gi|518651582|ref|YP_008141102.1|  84 FLGIFYyAFAFFYVAYVGVNAFVAYLFYYLLFLFYILVLVINIILNYNLYTNKYS-FDRITYAILVPNVVMSANIIL 159
                                       8877775666655555554456788889988889999999999999989898866.8**********9977666666 PP

                             SLAC1 152 gallaesqnpslqll.....gilvvslllwglGlllalvlfvlylyrlithklppaelrptlfiplGplgqgalall 223
                                        + +  +++ s          + ++ ++ +g++++ +l++ +  +   i++k+   + +p  +ip+G+ ++ ++ ++
  gi|518651582|ref|YP_008141102.1| 160 TSIM-LTPPMSGYYNttilrTVYFMVMVAFGISFFQFLFVGISAYISHISNKPNYLQTVPAAMIPVGASSMLIINIM 235
                                       6555.55444433335555545555566677777777777666777788888889999******************6 PP

                             SLAC1 224 llgkaapk..aaevlkv...lalllalflwglglfwllvavlsvlslpvrlkfslswWaftFPlgalalatielgka 295
                                        +    p+  +  +++v   la+ ++++lwg+ lf++lv+ ++ ++++ +++ s++ Wa++FP+g+ + a + +++ 
  gi|518651582|ref|YP_008141102.1| 236 FM----PQfnYIGIFNVppnLAIDISVILWGFDLFLFLVSGAIAITHI-KKRQSMTVWAYVFPVGVSTFADYMIYDY 307
                                       66....553333445445556666***************999999963.9************************999 PP

                             SLAC1 296 leseafkvlgtillvllvlvwllvlvgt 323
                                       +++e f +  ++++++l++++++  ++t
  gi|518651582|ref|YP_008141102.1| 308 TKLEIFVYSIIAFTAALIILYVYSWINT 335
                                       999999999999**********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); 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):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.32s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2164.29
//
Query:       gi|518651583|ref|YP_008141103.1|  [L=206]
Description: hypothetical protein FACI_IFERC00001G0222 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1507.05
//
Query:       gi|518651584|ref|YP_008141104.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G0223 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 684.62
//
Query:       gi|518651585|ref|YP_008141105.1|  [L=269]
Description: acid phosphatase SurE [Ferroplasma acidarmanus fer1]
Scores for 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-46  157.6   0.4    4.2e-46  157.2   0.4    1.2  1  SurE            Survival protein SurE
  ------ inclusion threshold ------
       0.02   14.8   0.0      0.038   13.9   0.0    1.4  1  Dev_Cell_Death  Development and cell death domain


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.4   4.6e-50   4.2e-46       1     193 [.       2     191 ..       2     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 4.6e-50
                                       EEEE-SS-TT-HHHHHHHHHHTTTTSEEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHH CS
                              SurE   1 iLltNDDGieapgiralvealaaaghevvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvkla 77 
                                       iL+tNDDG++a+gi++l+++ +    + v+vaPds rS++g+++t+++p+r++s e+  + + y+vsG Pad++ +a
  gi|518651585|ref|YP_008141105.1|   2 ILVTNDDGFNAAGIKQLYKNASMV-DDAVMVAPDSMRSASGMSITFTRPMRIQSLET-YGINGYCVSGYPADTITVA 76 
                                       8********************954.599************************97665.8****************** PP

                                       HHTTTTTS.SSEEEEEEEES---GGGG.GG-HHHHHHHHHHHTTSEEEEEEEESSSSS-SSS---HHHHHHHHHHHH CS
                              SurE  78 leellkekkpdlVvSGiNhGaNlgtdv.lySGTvgAaleaalegipaiAvSlaskkeeekkeedtfeaaakvaaklv 153
                                        + +lk kk dlV SGiN G+N++    + SGT++Aa++aal+gi++iA+S+ +++ +  +e  +f++a  + + ++
  gi|518651585|ref|YP_008141105.1|  77 QNIILKGKKIDLVASGINIGSNISLRSiYASGTISAAIAAALKGIKSIAFSMVTDQING-NEGPDFSKAGMYSRYII 152
                                       ******9999**************988799**********************9987555.45556************ PP

                                       TTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--CCSC CS
                              SurE 154 eklieklllekvellnvNvPeleeeeikgvkvtrlgrrry 193
                                       e++ ++ + e++++ln+N+P++ ++e + +kv  ++++ +
  gi|518651585|ref|YP_008141105.1| 153 EEFKKSGFPENADILNINFPAQITDETE-IKVVPMAENVF 191
                                       ***99999************76666655.88999988765 PP

>> Dev_Cell_Death  Development and cell death domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.3e-06     0.038      73     110 ..     168     205 ..     152     218 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.3e-06
                    Dev_Cell_Death  73 kskfpaQvrfkikkkckPLaesefkeaikenykekekk 110
                                       + +fpaQ+  +++ k+ P+ae+ f++ +++n   + k 
  gi|518651585|ref|YP_008141105.1| 168 NINFPAQITDETEIKVVPMAENVFHDYLEHNVDPNGKD 205
                                       568****************************9866554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1734.30
//
Query:       gi|518651586|ref|YP_008141106.1|  [L=279]
Description: hypothetical protein FACI_IFERC00001G0225 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-21   77.7   0.0    1.9e-21   77.0   0.0    1.3  1  ABC_tran     ABC transporter
      2e-12   47.6   0.1    5.2e-05   23.2   0.5    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    4.5e-06   26.6   0.1    0.00013   21.8   1.3    2.0  2  AAA_15       AAA ATPase domain
    2.7e-05   24.8   2.0    2.8e-05   24.7   0.5    1.7  1  AAA_23       AAA domain
    0.00049   20.1   0.1    0.00089   19.2   0.1    1.4  1  RsgA_GTPase  RsgA GTPase
     0.0025   17.3   0.1      0.012   15.1   0.1    1.9  1  SMC_N        RecF/RecN/SMC N terminal domain
     0.0033   16.2   1.1      0.026   13.2   0.3    2.0  2  AAA_13       AAA domain
     0.0036   17.7   0.0     0.0046   17.4   0.0    1.3  1  AAA_16       AAA ATPase domain
     0.0074   16.0   0.2      0.015   15.0   0.2    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0081   16.4   0.0      0.014   15.6   0.0    1.5  1  AAA_22       AAA domain
     0.0093   15.2   0.1      0.014   14.5   0.1    1.3  1  NB-ARC       NB-ARC domain
     0.0096   15.9   0.1      0.016   15.1   0.1    1.3  1  NACHT        NACHT domain
  ------ inclusion threshold ------
      0.018   14.8   0.0      0.064   13.0   0.0    1.8  2  AAA_30       AAA domain
      0.023   15.3   0.0       0.05   14.1   0.0    1.6  1  AAA_18       AAA domain
      0.025   12.1   0.1      0.035   11.6   0.1    1.1  1  DUF3584      Protein of unknown function (DUF3584)
      0.037   13.8   0.1        1.5    8.5   0.0    2.2  2  AAA_24       AAA domain
      0.079   12.9   0.2       0.14   12.0   0.2    1.4  1  MobB         Molybdopterin guanine dinucleotide synthesis pro
      0.082   12.9   0.0       0.17   11.9   0.0    1.5  1  TsaE         Threonylcarbamoyl adenosine biosynthesis protein
      0.092   12.8   0.3       0.27   11.3   0.2    1.8  2  MMR_HSR1     50S ribosome-binding GTPase
      0.099   12.1   0.1        2.8    7.3   0.0    2.3  2  SRPRB        Signal recognition particle receptor beta subuni
       0.12   12.0   0.1       0.65    9.6   0.1    2.0  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
       0.12   12.8   0.0       0.27   11.6   0.0    1.6  1  AAA          ATPase family associated with various cellular a


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.0   2.3e-24   1.9e-21      13     136 ..      29     160 ..      18     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.3e-24
                                       EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                          ABC_tran  13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.......... 79 
                                       +v i+G+nGaGK+tLl++l+ +lk  +G+  +dg ++++ ++++ r++i  +pqe++    lt++e+          
  gi|518651586|ref|YP_008141106.1|  29 IVSIIGKNGAGKTTLLRILSTQLKSSSGDAFIDGLSINK-DIKEIRNKIVSIPQEASPIGILTAYEQvflyltgkgf 104
                                       799************************************.************************************* PP

                                       ...HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ...esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                           +++e   al+ +gl ++ d +       LSgG+k+++ +a+al ++++ ++lDEpt
  gi|518651586|ref|YP_008141106.1| 105 sfhSARQESRMALKVVGLGDKMDVPT----DILSGGMKRKMFVAMALGCNAETVFLDEPT 160
                                       99766777888899999988666665....99***************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.5   6.4e-08   5.2e-05       3      55 ..      31      70 ..      29      92 .. 0.62
   2 !   22.0   0.0   1.5e-07   0.00012     237     297 ..     133     187 ..     103     191 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.4e-08
                            AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpe 55
                                       +iG+Ng+GK++LL++l+          ++        g + i++l+ ++d++
  gi|518651586|ref|YP_008141106.1| 31 SIIGKNGAGKTTLLRILSTQLKS-----SS--------GDAFIDGLSINKDIK 70
                                      69***************765442.....22........333333333333333 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 1.5e-07
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                       lS G+kr  +++ al   +    ++++DEp +gL+P    + ++ +kel+     v+ltTH
  gi|518651586|ref|YP_008141106.1| 133 LSGGMKRKMFVAMALGCNA---ETVFLDEPTTGLDPLSRMETWGAIKELTG---NVVLTTH 187
                                       6*******55555555555...99*************************99...******* PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.3   1.6e-07   0.00013      12      75 ..      16      75 ..      16      83 .. 0.72
   2 ?    2.4   0.0      0.12     1e+02     245     364 ..      65     187 ..      60     188 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
                            AAA_15 12 RslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifenisesk 75
                                      R+l++++ dl++ +  +iGkN++GK+++l++l   l+ +    +   +i+  ++++  ++ ++k
  gi|518651586|ref|YP_008141106.1| 16 RALDHITQDLDSGIVSIIGKNGAGKTTLLRILSTQLKSS----SGDAFIDGLSINKDIKEIRNK 75
                                      78999999************************8877766....333445544444444444443 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            AAA_15 245 iqeklkeidkklaeelk........kilkkkidkikkfnykgkkneeieik......................ddee 291
                                       i++++kei +k+ +  +          +++ +  +                                      d+++
  gi|518651586|ref|YP_008141106.1|  65 INKDIKEIRNKIVSIPQeaspigilTAYEQVFLYL-T-------------GkgfsfhsarqesrmalkvvglgDKMD 127
                                       55555555555544444444444432222222222.2.............022222333444446688999999*** PP

                            AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       +p +  + G++r +++++ +  + +          ++++EP + L p   ++ + ++kel  +     ++tTH
  gi|518651586|ref|YP_008141106.1| 128 VPTDILSGGMKRKMFVAMALGCNAET---------VFLDEPTTGLDPLSRMETWGAIKELTGNV----VLTTH 187
                                       *************9999988777777.........89999999999999999999999987665....78888 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   0.5   3.4e-08   2.8e-05      11      40 ..      19      48 ..       9      75 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 3.4e-08
                            AAA_23 11 rdqeidFskgltlItGpNGaGKTTildAik 40
                                      ++ + d+++g++ I+G+NGaGKTT+l+ + 
  gi|518651586|ref|YP_008141106.1| 19 DHITQDLDSGIVSIIGKNGAGKTTLLRILS 48
                                      5556699*******************9876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.1e-06   0.00089      85     126 ..      13      54 ..       4      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                                       TTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  85 ktkegleelkellkdktsvlvGqSGvGKStLinallpelelk 126
                                       k++++l+++++ l++ ++ ++G+ G+GK+tL+  l  +l+ +
  gi|518651586|ref|YP_008141106.1|  13 KHQRALDHITQDLDSGIVSIIGKNGAGKTTLLRILSTQLKSS 54 
                                       457899****************************99987654 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   1.5e-05     0.012      16      67 ..      19      62 ..      12     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                                      EEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 16 ktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk 67
                                      ++++ ++++++ +i+G+NG+GK+ ll  +    +    ++l+s++ ++ i  
  gi|518651586|ref|YP_008141106.1| 19 DHITQDLDSGIVSIIGKNGAGKTTLLRIL----S----TQLKSSSGDAFIDG 62
                                      5788999****************998765....3....35555555555555 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.12     1e+02     445     468 ..       3      26 ..       2      28 .. 0.92
   2 !   13.2   0.3   3.1e-05     0.026      21      51 ..      32      62 ..      29      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.12
                            AAA_13 445 eikeLekqlrdekpaaeeinkeLk 468
                                       +i+eLek+  ++++a + i++ L 
  gi|518651586|ref|YP_008141106.1|   3 QIRELEKEYGKHQRALDHITQDLD 26 
                                       79******************9986 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.1e-05
                            AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfang 51
                                      i G+NGaGKTtL r+l+ + + +  ++f  g
  gi|518651586|ref|YP_008141106.1| 32 IIGKNGAGKTTLLRILSTQLKSSSGDAFIDG 62
                                      67***************98777777777655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   5.6e-06    0.0046       6      51 ..       8      54 ..       3     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 5.6e-06
                            AAA_16  6 eeeleqLlsalervrsgrp.elvllsGesGvGKsslvrellralekd 51
                                      e+e  + ++al+ + ++   ++v ++G  G GK++l+r l ++l+ +
  gi|518651586|ref|YP_008141106.1|  8 EKEYGKHQRALDHITQDLDsGIVSIIGKNGAGKTTLLRILSTQLKSS 54
                                      677777888888555554469********************999987 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   1.8e-05     0.015      18      39 ..      24      44 ..      15      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.8e-05
                            AAA_29 18 eidlkgatlltGpsGsGKSTll 39
                                      ++d +g++ ++G++G+GK+Tll
  gi|518651586|ref|YP_008141106.1| 24 DLD-SGIVSIIGKNGAGKTTLL 44
                                      444.5699*************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.7e-05     0.014       5      31 ..      27      53 ..      23     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.7e-05
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqlde 31
                                       gi+ ++G  G+GKTtllr l  ql+ 
  gi|518651586|ref|YP_008141106.1| 27 SGIVSIIGKNGAGKTTLLRILSTQLKS 53
                                      58999*****************99964 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   1.8e-05     0.014       9      41 ..      15      48 ..       7      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                                      HHHHHC.TTTSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC  9 iekLle.kdelqslvvalvGmgGvGKttlakqil 41
                                      +  L++  ++l+s +v++ G+ G GKttl++   
  gi|518651586|ref|YP_008141106.1| 15 QRALDHiTQDLDSGIVSIIGKNGAGKTTLLRILS 48
                                      45555556788888***************97554 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     2e-05     0.016       3      28 ..      30      55 ..      28      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2e-05
                                      EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                      v + G++G GKTtLl+ l ++++++ 
  gi|518651586|ref|YP_008141106.1| 30 VSIIGKNGAGKTTLLRILSTQLKSSS 55
                                      6799****************999876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   7.9e-05     0.064       9      46 ..      17      56 ..      10      73 .. 0.73
   2 ?   -1.4   0.0         2   1.6e+03      43      89 ..     176     229 ..     169     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.9e-05
                            AAA_30  9 avealltsgd.rvavltGpAGtGKttalkalreaweaa.g 46
                                      a+++++++ d  ++ + G  G+GKtt+l+ l   ++++ g
  gi|518651586|ref|YP_008141106.1| 17 ALDHITQDLDsGIVSIIGKNGAGKTTLLRILSTQLKSSsG 56
                                      5556665533148899**************9777666635 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                            AAA_30  43 eaaggrviglAptgkaAkvLaeelgi.......eastiakllkrlkgrarlepg 89 
                                       ++  g+v++ ++  + A +L++++ +        + t ++ll+ l+g++r+e++
  gi|518651586|ref|YP_008141106.1| 176 KELTGNVVLTTHYMEEATELSRKIYMmdsgkfiGSGTADELLYDLRGKVRIESK 229
                                       444578888888888888888755533333333888888888888876777665 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   6.2e-05      0.05       3      36 ..      32      63 ..      30      95 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.2e-05
                            AAA_18  3 ltGtpGvGKttlakeLskrlgfgvnlrdvakeng 36
                                      + G+ G+GKttl + Ls  l     ++d + ++ 
  gi|518651586|ref|YP_008141106.1| 32 IIGKNGAGKTTLLRILSTQL--KSSSGDAFIDGL 63
                                      89***************999..444444333333 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.3e-05     0.035      18      37 ..      28      47 ..      22      48 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.3e-05
                           DUF3584 18 ghtnieGtNaaGKTtLlrLi 37
                                      g + i G N+aGKTtLlr++
  gi|518651586|ref|YP_008141106.1| 28 GIVSIIGKNGAGKTTLLRIL 47
                                      7799**************86 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0019       1.5       6      22 ..      31      47 ..      28      86 .. 0.86
   2 ?    3.2   0.0     0.077        63     117     150 ..     174     207 ..     168     239 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0019
                            AAA_24  6 liyGpsgiGKTtlakel 22
                                       i+G++g+GKTtl++ l
  gi|518651586|ref|YP_008141106.1| 31 SIIGKNGAGKTTLLRIL 47
                                      69***********9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.077
                            AAA_24 117 klqelrknvifiahektrkdedpegeakytrlep 150
                                       +++el +nv+++ h  ++  e  ++ ++ ++ + 
  gi|518651586|ref|YP_008141106.1| 174 AIKELTGNVVLTTHYMEEATELSRKIYMMDSGKF 207
                                       689999************9999888766655554 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 ?   12.0   0.2   0.00018      0.14       1      25 [.      29      53 ..      29      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
                              MobB  1 vlgivgksgsGKTtLleklipelka 25
                                      +++i+gk+g+GKTtLl  l ++lk+
  gi|518651586|ref|YP_008141106.1| 29 IVSIIGKNGAGKTTLLRILSTQLKS 53
                                      689**************99999986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00021      0.17       9      44 ..      20      52 ..       6      58 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00021
                                      HHHHHHHHCH.TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  9 algkklakal.gdvilLeGdLGaGKTtlvrglakalg 44
                                      ++ ++    l + ++ + G+ GaGKTtl r l  +l+
  gi|518651586|ref|YP_008141106.1| 20 HITQD----LdSGIVSIIGKNGAGKTTLLRILSTQLK 52
                                      33333....2335799**************9998886 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00033      0.27       2      26 ..      30      55 ..      29      80 .. 0.81
   2 ?   -1.9   0.0       4.2   3.4e+03      25      52 ..     184     203 ..     173     253 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                      EEEEESTTSSHHHHHHHHHTS.TEEE CS
                          MMR_HSR1  2 vaivGrpNvGKStLinaltge.kaiv 26
                                      v i+G+  +GK+tL++ l+ + k+  
  gi|518651586|ref|YP_008141106.1| 30 VSIIGKNGAGKTTLLRILSTQlKSSS 55
                                      78****************98755544 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.2
                                       EESSSTTSSSSEEEEEEEETTEEEEEEE CS
                          MMR_HSR1  25 ivsdkpgtTrdinegrvklkgkeielvD 52 
                                        ++++    ++  +        +i+++D
  gi|518651586|ref|YP_008141106.1| 184 LTTHYMEEATELSR--------KIYMMD 203
                                       44433333222222........222222 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0035       2.8       6      31 ..      30      55 ..      26      84 .. 0.73
   2 ?    2.4   0.0      0.11        91      16     101 ..     138     219 ..     130     232 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0035
                                      EEEE-STTSSHHHHHHHHHHSS---B CS
                             SRPRB  6 vllvGlsdsGKTslftrLttdsvkkt 31
                                      v ++G   +GKT+l+  L+t+ + ++
  gi|518651586|ref|YP_008141106.1| 30 VSIIGKNGAGKTTLLRILSTQLKSSS 55
                                      679****************9966554 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHSS---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHH CS
                             SRPRB  16 KTslftrLttdsvkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkev 92 
                                       K  +f  +  +   +tv   e+++ l+  s+ ++  ++ ++ G++ l ++ +e+    ++l + ++++DS  +    
  gi|518651586|ref|YP_008141106.1| 138 KRKMFVAMALGCNAETVFLDEPTTGLDPLSRMETWGAIKELTGNVVLTTHYMEE---ATELSRKIYMMDSGKFIGSG 211
                                       556777777777777777777777777777777777888889999999998888...67788889999998765432 PP

                                       HHHHHHHHH CS
                             SRPRB  93 kevAEllye 101
                                        +  Elly+
  gi|518651586|ref|YP_008141106.1| 212 -TADELLYD 219
                                       .33456665 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 ?    9.6   0.1   0.00079      0.65       3      24 ..      30      51 ..      28      82 .. 0.73
   2 ?    0.3   0.0      0.57   4.7e+02     100     125 ..     183     226 ..     124     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                                      EEEEESTTCCHHHHHHHHHCT- CS
                              cobW  3 tvltGflGsGKTtLlnhllenr 24
                                      + + G  G+GKTtLl+ l ++ 
  gi|518651586|ref|YP_008141106.1| 30 VSIIGKNGAGKTTLLRILSTQL 51
                                      5688999********9887443 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.57
                                       HTTSHHHHHCCCECEEEEEEETTTH................... CS
                              cobW 100 afteeelksdltldavvavvDaknl..................e 125
                                       ++t++ ++++++l+ +++++D+ ++                   
  gi|518651586|ref|YP_008141106.1| 183 VLTTHYMEEATELSRKIYMMDSGKFigsgtadellydlrgkvrI 226
                                       34456677788888888888887776665555555554444440 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00034      0.27       3      47 ..      32      77 ..      30      96 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00034
                                      EESSTTSSHHHHHHHHHHHHTHE.........EEEEETTTCSSSSTTHHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakelgve.........fleisgsellskyvgesekkir 47
                                      ++G  G GKT+l + + ++l+++          ++ +         +e  +ki 
  gi|518651586|ref|YP_008141106.1| 32 IIGKNGAGKTTLLRILSTQLKSSsgdafidglSINKDI--------KEIRNKIV 77
                                      78*****************9865333333332334444........44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.35s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 1685.84
//
Query:       gi|518651587|ref|YP_008141107.1|  [L=240]
Description: daunorubicin resistance ATP-binding protein DrrB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-10   41.1  25.0    1.3e-10   41.1  25.0    1.8  2  ABC2_membrane  ABC-2 type transporter


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1  25.0   7.1e-15   1.3e-10       7     203 ..      11     201 ..       7     207 .. 0.82
   2 ?    0.2   0.2     0.024   4.3e+02     105     126 ..     217     238 ..     213     240 .] 0.80

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 7.1e-15
                     ABC2_membrane   7 lkreflqrwrdpslgllwrliqplllalvfgtvfgnlgnsedgl.nr...pgllffsvlflafsaltsvapvferer 79 
                                       + + +++++r ps++ +++l++pl l++++ ++        ++l ++    gl++f        + ++ +++f  + 
  gi|518651587|ref|YP_008141107.1|  11 WYYGIKTIFRGPSYL-IASLATPLTLLFLVFVLSH------GALvKFaivGGLIAFVGSVGL--SGAGDSAFFRLQL 78 
                                       67789*******999.9999999766666555555......233122343666666666666..4555557777777 PP

                     ABC2_membrane  80 gvlerelvsplyslsayvlakvlvelpvsl..lqalifllivyflvgldlsrfflflllllltalaasslgllisal 154
                                       ++ +   +s++ s+++y++a +l++l++s+  ++  i+l ++y+l++l+ s   ++ll+++l+++ ++s++++is  
  gi|518651587|ref|YP_008141107.1|  79 RIQDLYVPSKV-SPFDYMAAFTLSYLVFSVpgIILYIYLGLSYHLFNLYDS--SMMLLVMVLLIISTTSISFIISGS 152
                                       78888888888.*************999995566677777**********7..************************ PP

                     ABC2_membrane 155 apsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyave 203
                                        ++++++  +++++++++ +l + f+p++ +pk + +i  l+P t a  
  gi|518651587|ref|YP_008141107.1| 153 IKHLRNIWGITGILTIITSILPPTFYPYSYVPKSFLYIIALSPTTPAAV 201
                                       *******************************98999999****998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.024
                     ABC2_membrane 105 lpvsllqalifllivyflvgld 126
                                       + +++++++i+++++ +lv ++
  gi|518651587|ref|YP_008141107.1| 217 FYIMIIETVIYTILARILVRWR 238
                                       6689999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       815  (0.0454571); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1535.87
//
Query:       gi|518651588|ref|YP_008141108.1|  [L=315]
Description: hypothetical protein FACI_IFERC00001G0227 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-28   99.0   1.0    4.9e-28   98.6   0.1    1.7  1  Radical_SAM  Radical SAM superfamily
    1.2e-25   89.9   0.2    2.7e-25   88.7   0.2    1.6  1  Mob_synth_C  Molybdenum Cofactor Synthesis C
    4.8e-09   36.6   0.0    9.5e-09   35.7   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain
    1.1e-08   35.2   0.0    3.1e-08   33.8   0.0    1.7  1  Fer4_14      4Fe-4S single cluster domain
  ------ inclusion threshold ------
       0.16   11.7   0.1         11    5.9   0.0    2.5  2  KRTDAP       Keratinocyte differentiation-associated


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 !   98.6   0.1   1.4e-31   4.9e-28       6     166 ..      28     182 ..      23     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.6 bits;  conditional E-value: 1.4e-31
                                       EESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   6 gCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritv 82 
                                        Cn+ C+fC+      +e+  +++++e+i++ v  + a++gv+ + ++ggepll+ d+ e+++r +k      +i++
  gi|518651588|ref|YP_008141108.1|  28 ICNFHCIFCHMEG---TERSMQYMTPEQIENVVAVA-ASHGVNKIKFTGGEPLLREDILEIVRRTRKH--ITGNISL 98 
                                       7***********8...7*******************.8*****************************9..7****** PP

                                       EECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  83 etngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvdrivglpGende 158
                                       +tng+ + ++ ++ l+e+g+drv+++ +a+d+  ++ ++  +++ +  v+++++++r+ag+ +++++ v++++ n++
  gi|518651588|ref|YP_008141108.1|  99 TTNGVEL-PKLAKGLKEAGLDRVNISMHAIDEYNFHFITDtKKNFLPIVKQGIQAARDAGLGPIKINFVLMKNINED 174
                                       *******.********************************999999******************************* PP

                                       HHHHHHHH CS
                                       xxxxxxxx RF
                       Radical_SAM 159 eleellel 166
                                       +++ ++++
  gi|518651588|ref|YP_008141108.1| 175 QVDGMIKF 182
                                       **999987 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 !   88.7   0.2   7.6e-29   2.7e-25       2     124 ..     189     312 ..     188     315 .] 0.87

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 7.6e-29
                                       EEEEEE---B-TTSSB--SSB--HHHHHHHHHHHS-EEEE--SS..T-SSEEEEETTT-..-EEEEE-TTTS-.-GG CS
                       Mob_synth_C   2 elrfIElmpvgegeewrekkvvsadeilerieerlalleakket..kgpakrykikdgk..geiglIapvsep.FCa 73 
                                       +l++IE+   +e e++  +++++++  le ie+r+++++ + e    ++++ry++k     ++i++++p++++ FC+
  gi|518651588|ref|YP_008141108.1| 189 TLQLIEFEANREKEHS--EEYLKYHVPLEPIERRIQKQAMDVEHnpLHNRERYTVKTDYgeVKIEFVKPMRNKdFCK 263
                                       699******9988765..******************9888844446*********66542378*********99*** PP

                                       G--EEEE-TTSEEESSSS-SS-.EEHHHHHHTT--HHHHHHHHHHHHHT--- CS
                       Mob_synth_C  74 sCnRlRltadGklktCLfaeee.idlrdllregaseeeLkelikealarkke 124
                                       +C+RlRltadG++ktCL +e++ +d++d+l +++   e+  ++++a++ + +
  gi|518651588|ref|YP_008141108.1| 264 HCTRLRLTADGQFKTCLLRENDyFDIKDMLGDES---EIDSMYRKAVEARVP 312
                                       ********************999*******9996...488888888888765 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   2.6e-12   9.5e-09      15     102 ..      29     111 ..      21     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.6e-12
                           Fer4_12  15 CnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdiwly 91 
                                       Cn++C +C+ + t +  s + +t e +e++++ ++ + ++++ ++GGEPll   +e++le+v++ +++   +  + +
  gi|518651588|ref|YP_008141108.1|  29 CNFHCIFCHMEGTER--SMQYMTPEQIENVVAVAASHGVNKIKFTGGEPLL---REDILEIVRRTRKHITGNISLTT 100
                                       *********777754..456679999*************************...9**************97788999 PP

                           Fer4_12  92 tgytleelskk 102
                                       +g+ l +l k 
  gi|518651588|ref|YP_008141108.1| 101 NGVELPKLAKG 111
                                       99999888765 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.0   8.7e-12   3.1e-08       6      90 ..      27     103 ..      24     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 8.7e-12
                           Fer4_14   6 sgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypekk 82 
                                       + Cn++C +C  +    +++ ++ t e++e++++ +  + +  +++ +tGGePL+    +++l++v+r ++++ + +
  gi|518651588|ref|YP_008141108.1|  27 AICNFHCIFCHMEG--TERSMQYMTPEQIENVVAVAASHGV--NKIKFTGGEPLLR---EDILEIVRRTRKHI-TGN 95 
                                       56*********877..5677778888888888854555555..779********55...9************9.99* PP

                           Fer4_14  83 iwletngt 90 
                                       i l tng+
  gi|518651588|ref|YP_008141108.1|  96 ISLTTNGV 103
                                       ******97 PP

>> KRTDAP  Keratinocyte differentiation-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.023        82      29      58 ..     117     146 ..     104     150 .. 0.85
   2 ?    5.9   0.0     0.003        11      20      54 ..     186     220 ..     170     227 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.023
                            KRTDAP  29 vdrlrsafkseeflnWhalfealkkklpfl 58 
                                       +dr+  ++++ +  n+h ++++ k+ lp +
  gi|518651588|ref|YP_008141108.1| 117 LDRVNISMHAIDEYNFHFITDTKKNFLPIV 146
                                       56777777777888***********99986 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.003
                            KRTDAP  20 ealkeqfLnvdrlrsafkseeflnWhalfealkkk 54 
                                       ++++ q++ ++  r+  +see+l +h+ +e + ++
  gi|518651588|ref|YP_008141108.1| 186 NDSTLQLIEFEANREKEHSEEYLKYHVPLEPIERR 220
                                       56678999*******************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2107.83
//
Query:       gi|518651589|ref|YP_008141109.1|  [L=78]
Description: molybdopterin synthase subunit MoaD / molybdopterin synthase subunit MoaE [Ferroplasma acidarmanus fer1]
Scores for complete 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    9.9e-13   48.5   0.0    1.0  1  ThiS      ThiS family


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   5.5e-17   9.9e-13       1      77 []       5      78 .]       5      78 .] 0.98

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 5.5e-17
                                      EEETTCCHHHHT.CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS  1 vllfaelrelag.eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      vl+fa++r+++g  +e+ + e  + + l+e++  +yp+l +++++ + vN+e+ +      +l+++D+va++ppV+GG
  gi|518651589|ref|YP_008141109.1|  5 VLYFAHVRDITGlPQEVFDLETGNMDLLREKIFSKYPQLRAINNLLISVNNEYYSG----LPLNENDRVAFFPPVSGG 78
                                      89**************************************99**************....9****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); 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 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 549.84
//
Query:       gi|518651590|ref|YP_008141110.1|  [L=483]
Description: hypothetical protein FACI_IFERC00001G0229 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-88  298.3   0.3    4.8e-87  292.9   0.3    2.1  1  G_glu_transpept  Gamma-glutamyltranspeptidase


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 !  292.9   0.3   2.7e-91   4.8e-87       2     469 ..      18     439 ..      17     472 .. 0.88

  Alignments for each domain:
  == domain 1  score: 292.9 bits;  conditional E-value: 2.7e-91
                                       HHHHTT--HHHHHHHHHHHHHHHSTTT-STTSEEEEEEEETTSCEEEEEEE--BB-TT--TTTTTSCBCCHHHHSSG CS
                   G_glu_transpept   2 evLrkGGnAvDAavAaalclgvvepqssGiGGGgfllvydaktkkvealdaretAPaaatkdmfdkegdsklsktga 78 
                                       e L++GGnA DA+ A++ +l vv+p+ +G+GG++f++++d++    + ++a++ A +aa+ d+++++g ++++k+g 
  gi|518651590|ref|YP_008141110.1|  18 EALERGGNAYDAMLASSSALVVVQPHFNGLGGDLFATIKDNGY---YCINASGYAASAASIDFYSRNGYQEIPKRGS 91 
                                       68************************************87653...379**************************** PP

                                       G.G-BB--HHHHHHHHHHHH-SS-HHHHHHHHHHHHHH-EE--HHHHHHHHHCHHHHHTSHHHHHHHEETTSE--TT CS
                   G_glu_transpept  79 l.avgVPGevagleeahkkyGklpwadllepaiklareGfpvsealaralaeaeerlkkdpelaklFlpegevlkag 154
                                       l +  +PG va+++ a +k  ++ + + ++ ai+ a++Gf+ s++l ra+++ e     d+++++++        + 
  gi|518651590|ref|YP_008141110.1|  92 LsSFSIPGLVASWKIAAEK-STMGIGENFKRAIQFAKDGFEPSRKLVRAINRFEG---GDEDFNNIYK------GTD 158
                                       999***********99988.89***************************998887...5666766664......466 PP

                                       SEE--HHHHHHHHHHHHHTTHHHHSSHHHHHHHHHHHHTT-S--HHHHHH---EEES-EEEEETTCEEEEE-TTCSH CS
                   G_glu_transpept 155 ellkqpalAktLerlaeeGaeaFYkGelAeklvaelqkagGiltaeDLanykvevreplsadyrggytvyepppssg 231
                                       ++l+q+ l +tLe+l +eG ++FY+G++A+k+ a+++++gG++t++DL +yk++++ep++++y +gy vy+ pp s+
  gi|518651590|ref|YP_008141110.1| 159 SWLVQKSLGNTLETLVTEGLDSFYNGNIADKIEADMKEKGGLITKKDLLDYKASITEPVKVNY-RGYNVYTNPPVSQ 234
                                       899************************************************************.99*********** PP

                                       HHHHHHHHHHHCTTTGGGCTTTCHHHHHHHHHHHHHHHHHHHHH-SSTTTSSSGHCHHHHHT-HHHHHHHHTT.BTT CS
                   G_glu_transpept 232 givllqiLnilegfdlkslssnsaetlhllvEamklayadRsrylgDpdfvknptelveellskeyakeraklIkdk 308
                                       g++++ +L+ l+ +dl  ++   +e++ +l+ +m+ ay+ R++y+ D    +                   ++I+d 
  gi|518651590|ref|YP_008141110.1| 235 GLTASVWLRDLNAYDLAGMEH--QEYYDTLIKTMHDAYNIRRKYVYDGVKLP-------------------ENIDDM 290
                                       ***************887766..7*********************9997776...................234443 PP

                                       B..SGGGCSCGGCSCG.TTEEEEEEEEETTS-EEEEEEEESSTTTTSEBETTTTEBE--GGGGSBSTS..TTSCSTT CS
                   G_glu_transpept 309 aatpsseyykaaeaaeesggTthlsvvDregnaVSltstinllFGsgvvvpgtGilLnnemddfstgvenafgldps 385
                                       + ++    +++ +++++ ++Tt +s+ D e   +S++++++++FGsg+ ++gtGi +nn+++ fs        ld++
  gi|518651590|ref|YP_008141110.1| 291 KPDN----DQPGNQKSNLSDTTAYSIFDGE-IEISAIQSNYMGFGSGHSIKGTGINMNNRGSYFS--------LDSE 354
                                       3333....244678889************9.789*******************************........**** PP

                                       STTB--TT----B----EEEEETTEEEEEEEEESGGGHHHHHHHHHHHHHTT-S-HHHHHHS--EEE..SSSST.EE CS
                   G_glu_transpept 386 panaiePgkRplssmaPtivlkdgkpvlvlGaaGGsriisavlqvlvnvldlgldlqeavdaprihh..qllpd.kv 459
                                       + n ++Pgk+++++++ +  l  gk  ++lG++GG+ ++++ +q+l +v+dlg ++ +a++ pr+    +++ d kv
  gi|518651590|ref|YP_008141110.1| 355 NKNSLKPGKKTFHTLMSI--LASGKKDVILGTMGGDVQPQVNVQILSRVIDLGSNMPDAIAYPRFAYpaSIYGDsKV 429
                                       ***************964..44689999*************************************998855555689 PP

                                       EESTTS.HHH CS
                   G_glu_transpept 460 evEegfseev 469
                                       ++E++++ + 
  gi|518651590|ref|YP_008141110.1| 430 YYESTLRLNH 439
                                       9998554333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (483 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 3479.52
//
Query:       gi|518651591|ref|YP_008141111.1|  [L=188]
Description: hypothetical protein FACI_IFERC00001G0230 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.5    3.1e-15   56.6   0.5    1.1  1  DUF4382   Domain of unknown function (DUF4382)
  ------ inclusion threshold ------
      0.048   13.5   0.2      0.096   12.5   0.2    1.6  1  DUF4307   Domain of unknown function (DUF4307)
       0.94    9.8   6.7        3.4    8.0   0.4    2.7  2  DUF2929   Protein of unknown function (DUF2929)


Domain annotation for each model (and alignments):
>> DUF4382  Domain of unknown function (DUF4382)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.5   5.2e-19   3.1e-15       1     128 [.      32     173 ..      32     181 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 5.2e-19
                           DUF4382   1 tGtvslslsDaPv..ddfeevvvtiskvelkpadgeesdggwveldeeevdepqtvdLlelqggkatllaelelpaG 75 
                                       tGt+++s  D  +   ++  v+vt+s+++l++++++++++gw++++      ++tv++l+l  ++a+ l++l++ aG
  gi|518651591|ref|YP_008141111.1|  32 TGTMKVSAADTSTglTGVMDVNVTFSSIALHSVNASSNSTGWTNYS----LHDKTVNILNLNASNAAFLSNLSVHAG 104
                                       69999999999767799******************88888888888....46779********************** PP

                           DUF4382  76 eYsqirlvlsd...................dlkvpsgqq.sglklpskftvtvaageskdlvlDfDlrkslvk 128
                                       +Y+++ +++++                    l+++   +  ++ l +++t  v+a +++++v D++l+++++ 
  gi|518651591|ref|YP_008141111.1| 105 SYNKMKIYIKSvtvyinsslqgiyslnstvSLHLAH--NfATIVLVHPVT--VSAHSTTSIVTDLALANNIHL 173
                                       **********99999999777777666655444422..224444434666..****************99986 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   1.6e-05     0.096       2      50 ..       4      55 ..       3      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                           DUF4307  2 rrllvillvvlvvvalalvawigysq...gsadvsaevvgfevvddstvevt 50
                                      ++l+++++++++++++a+  +++y++   g+ +vsa +++   +    v+vt
  gi|518651591|ref|YP_008141111.1|  4 KKLMAVIVAIIIIAVIAGGSYYAYHYettGTMKVSAADTSTGLTGVMDVNVT 55
                                      68999*********************75555555555555544444444444 PP

>> DUF2929  Protein of unknown function (DUF2929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   1.1    0.0087        52      36      50 ..       6      20 ..       1      23 [. 0.80
   2 ?    8.0   0.4   0.00057       3.4      15      55 ..     115     156 ..     110     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0087
                           DUF2929 36 ilavvfgvlviliia 50
                                       +av++++++i++ia
  gi|518651591|ref|YP_008141111.1|  6 LMAVIVAIIIIAVIA 20
                                      588999999998886 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00057
                           DUF2929  15 evvgYIgsaLtgv.tydfttalilavvfgvlviliialiskd 55 
                                       +v++YI s+L+g  + + t +l la  f+ +v++   + s++
  gi|518651591|ref|YP_008141111.1| 115 SVTVYINSSLQGIySLNSTVSLHLAHNFATIVLVHPVTVSAH 156
                                       5899***************************99988887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1010  (0.0563333); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1223.08
//
Query:       gi|518651592|ref|YP_008141112.1|  [L=547]
Description: hypothetical protein FACI_IFERC00001G0231 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-64  218.5   0.0    2.1e-64  218.0   0.0    1.2  1  Oxidored_FMN   NADH:flavin oxidoreductase / NADH oxidase fami
  ------ inclusion threshold ------
      0.015   14.8   0.2      0.054   12.9   0.0    1.9  2  PcrB           PcrB family
      0.019   15.2   0.0      0.065   13.5   0.0    1.9  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
      0.045   13.0   0.0      0.082   12.1   0.0    1.4  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
        0.1   11.8   0.0        0.2   10.9   0.0    1.4  1  Thi4           Thi4 family


Domain annotation for each model (and alignments):
>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.0   0.0   5.9e-68   2.1e-64       3     340 ..       4     321 ..       2     323 .. 0.86

  Alignments for each domain:
  == domain 1  score: 218.0 bits;  conditional E-value: 5.9e-68
                                       CS-EEETTEEESSSEEE----S-TTTTTCS.HHHHHHHHHHHHHHTT-SEEEEEEEESSC.CC-SCTTSEE-SSGGG CS
                      Oxidored_FMN   3 FkPikignmtLknRivmapmtrlraldkgnvledlaaeyysqraeipvtliiteaafvnp.ksggfdnapgiwdeeq 78 
                                       F+  +ig  ++knR+vmapm    ++++g+  e   + y ++ra+++ +liite+a v+  +++g +n+ gi++ +q
  gi|518651592|ref|YP_008141112.1|   4 FEKANIGGAEIKNRFVMAPMISNLCNPDGTTNE-NHIRYLEERARGGFGLIITEYAYVDDsNGKGSPNEMGIFSRSQ 79 
                                       5556899**********************6666.99*********************9862677************* PP

                                       HHHHHHHHHHHHHTT-EEEEEEE--GGGS..SCSTCEC..SS.ESSSSSTTT-.S...CS-EE--HHHHHHHHHHHH CS
                      Oxidored_FMN  79 ieewrklteavhengskvvvqlwhlGreakseyladqevdspsdpvaldaqeeesaeevykkeltkeeikqliqefv 155
                                       ++++  lte +h  gsk++vql h G++a+  y+  +   +ps + +++ +        ++ e+tk++ik++ ++fv
  gi|518651592|ref|YP_008141112.1|  80 LPKLSRLTERIHSAGSKIFVQLVHSGGKANPHYNTGKI-FAPSSVDYIG-S--------IPEEMTKDDIKKVEEKFV 146
                                       *****************************998887776.6666333333.2........467*************** PP

                                       HHHHHHHHTT-SEEEEEE-CTSHHHHHH-TTT----STTSSSHHHHHHHHHHHHHHHHHHH-SSS.EEEEEECE--S CS
                      Oxidored_FMN 156 eAAkraieAgfDgVeihganGYLlnqFlspksnkrtDeygGslenRarFllevvdaVkeavgeer.vgyRlSpedvv 231
                                       +AA++a  AgfDg+e hga+GYLl++F+sp  nkrtDeygGs+enR+r l e+  a+k +   ++ +g+RlS +++ 
  gi|518651592|ref|YP_008141112.1| 147 NAAELAYRAGFDGIELHGAHGYLLQEFISPALNKRTDEYGGSVENRIRILNEISSAIKSK--LNMpLGIRLSLYEDD 221
                                       ************************************************************..4455******98764 PP

                                       TTS--HHHHHHHHHHHCHCCEEEEEEETT-SSSSSTTS-TTTTHHHCCTTHHH...HHHCCCHSSEEEE-SS--SHH CS
                      Oxidored_FMN 232 ekgldfaetaqkivllkelekrlkdgkklalvhaaeprkrgagsvrteqeknt...efvkevwkkplitvgriadee 305
                                       e   ++ ++        +++ rl    ++++vh  + r   +gs+   +  n+    ++k+  +k+++ vg+i + e
  gi|518651592|ref|YP_008141112.1| 222 E---GGYDA----DYGIDVASRLE---NMDYVHFSSGRFAPPGSSASFYYDNVhigAKLKKKLDKNTMLVGSIRSME 288
                                       4...44444....11224445555...899999999999988887655443333459******************99 PP

                                       HHHHHHHTTS-SEEEESTHHHH-TTHHHHHHCCTC CS
                      Oxidored_FMN 306 kaaeivaegeadLvamgRefladpdlveklkkglp 340
                                         ++  a    d v +gR+ ladp  + k+k ++p
  gi|518651592|ref|YP_008141112.1| 289 --DIEKALTVSDFVVLGRQALADPYTPVKIKMKMP 321
                                       ..777777889*******************98775 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.054     164     209 ..     260     304 ..     256     317 .. 0.88
   2 ?   -1.9   0.1      0.53   1.9e+03     176     196 ..     358     378 ..     347     385 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                                       SSS-HHHHHHHHHHHSSSEEEEESS--SHHHHHHHHCCSSEEEE-C CS
                              PcrB 164 aledveevialkkklekarlivGGGirsaEkAkevveaADvivvGn 209
                                        +++v   ++lkkkl+k++++vG  irs E+ ++ ++  D +v G 
  gi|518651592|ref|YP_008141112.1| 260 YYDNVHIGAKLKKKLDKNTMLVG-SIRSMEDIEKALTVSDFVVLGR 304
                                       567888899************96.7******************996 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.53
                                       HHHSSSEEEEESS--SHHHHH CS
                              PcrB 176 kklekarlivGGGirsaEkAk 196
                                       +k ++++ ivG Gi+  E A 
  gi|518651592|ref|YP_008141112.1| 358 RKYHGEIAIVGSGIKGLEAAL 378
                                       66778889*******999986 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7   9.6e+03      32      50 ..     212     232 ..     211     238 .. 0.68
   2 ?   13.5   0.0   1.8e-05     0.065       1      37 [.     366     401 ..     366     419 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                       SGGG-EECE..TTCEECTS-- CS
                     NAD_binding_8  32 GGraasyev..pgvrvdygah 50 
                                       G r++ ye+  +g+ +dyg  
  gi|518651592|ref|YP_008141112.1| 212 GIRLSLYEDdeGGYDADYGID 232
                                       556666666445699999975 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.8e-05
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37 
                                       IvG+G+ Gl aA + a++gf+  ++e + ++GG+   
  gi|518651592|ref|YP_008141112.1| 366 IVGSGIKGLEAALYSANKGFKPIIYEES-SFGGQFNE 401
                                       9************************985.89998765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05     0.082       2      32 ..     363     392 ..     362     439 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvele 32 
                                       +++++G+G+ Gl+aal+ a++g+k +++e e
  gi|518651592|ref|YP_008141112.1| 363 EIAIVGSGIKGLEAALYSANKGFKPIIYE-E 392
                                       689**********************9995.3 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   5.5e-05       0.2      19      55 ..     363     397 ..     358     401 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.5e-05
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailersvspGG 55 
                                       +++ivG+G  GL aa y a+k ++k +i e+s s+GG
  gi|518651592|ref|YP_008141112.1| 363 EIAIVGSGIKGLEAALYSANK-GFKPIIYEES-SFGG 397
                                       799******************.****999987.7887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 3428.15
//
Query:       gi|518651593|ref|YP_008141113.1|  [L=155]
Description: phosphoribosylaminoimidazole carboxylase catalytic subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-66  220.6   1.1    6.7e-66  220.4   1.1    1.0  1  AIRC      AIR carboxylase
  ------ inclusion threshold ------
       0.06   12.9   0.2       0.14   11.8   0.1    1.9  1  PrpR_N    Propionate catabolism activator


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  220.4   1.1   7.5e-70   6.7e-66       1     147 [.       2     148 ..       2     149 .. 0.98

  Alignments for each domain:
  == domain 1  score: 220.4 bits;  conditional E-value: 7.5e-70
                                       EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSS CS
                              AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvasltt 77 
                                       kV++imGS+sD++vm++a++ lk++g+e+e+r+vSahrtpe +leya++a +++++viIagAGgaahLpg+vas+tt
  gi|518651593|ref|YP_008141113.1|   2 KVAVIMGSRSDFPVMQDAVNELKNFGIEVEYRIVSAHRTPEFMLEYARNAINNNIEVIIAGAGGAAHLPGMVASMTT 78 
                                       69*************************************************************************** PP

                                       S-EEEEEE--STTCCHHHHHHHHT--TTS--EE-SSTHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                              AIRC  78 lPVigvPvkskalkgldsllSivqmPsgvpvatvaigkaknAallAaqilalkdeelaekleeyreelke 147
                                       lPVigvPv+skal+g+dsllSivqmP+g+pvatv+i++a+nAallA++il++k+++++e l+++ +++++
  gi|518651593|ref|YP_008141113.1|  79 LPVIGVPVQSKALNGIDSLLSIVQMPPGIPVATVSINGARNAALLAVRILSIKYPKIKEMLQAFIDNQRD 148
                                       ***************************************************************9998875 PP

>> PrpR_N  Propionate catabolism activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.5e-05      0.14      15      56 ..      42      87 ..      28     155 .] 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.5e-05
                            PrpR_N 15 eeavelakeleaegvdviiSrGgtae....llrkhvsvPVveikvs 56
                                      e  +e+a+++++++++vii++ g a+    ++ + + +PV+ ++v+
  gi|518651593|ref|YP_008141113.1| 42 EFMLEYARNAINNNIEVIIAGAGGAAhlpgMVASMTTLPVIGVPVQ 87
                                      556899**************988887233345677799***99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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 0.29s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1026.06
//
Query:       gi|518651594|ref|YP_008141114.1|  [L=359]
Description: hypothetical protein FACI_IFERC00001G0233 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-39  133.4   0.0    8.3e-39  132.9   0.0    1.2  1  ATP-grasp       ATP-grasp domain
    1.7e-14   53.2   4.2    2.2e-14   52.9   0.4    2.3  2  PurK_C          Phosphoribosylaminoimidazole carboxylase C-te
     0.0023   17.3   0.0     0.0038   16.6   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
     0.0098   16.1   0.0      0.019   15.1   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.087   13.3   0.0         13    6.2   0.0    2.5  2  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.9   0.0   2.3e-42   8.3e-39       2     170 ..     101     259 ..     100     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 132.9 bits;  conditional E-value: 2.3e-42
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEE CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekEl 78 
                                       +++g+p++++ ++e+  ++ + a+++g ++v+K++++gydGk q+++ ++++ e   +       +vE+f+++e+E 
  gi|518651594|ref|YP_008141114.1| 101 KDHGFPIADYEYAETYRDAFNKAKNFG-KAVIKSCKGGYDGKNQYFIDNSSRFEGHPDIP----YVVEKFIDYEYEA 172
                                       789*************99888899*99.589******************99988776665....************* PP

                                       EEEEEEETTC-EEE--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEE CS
                         ATP-grasp  79 svlvvrsaeGetafypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnE 155
                                       s+++vr+a+G+++ +++  +++++gil +++ p      +  +  +iakk++++L+++Gv+++E +v+ dg++++nE
  gi|518651594|ref|YP_008141114.1| 173 SIIAVRDANGKFYHFEPSFNYNQNGILIYNISPIG----NTIEMIDIAKKLMDSLEYIGVMGIEYYVV-DGKVIINE 244
                                       ********************************996....678899***********************.******** PP

                                       EESS--GGGGGHHHH CS
                         ATP-grasp 156 lapRpHnsGhvtlda 170
                                        apR+Hn+Gh tl +
  gi|518651594|ref|YP_008141114.1| 245 YAPRVHNTGHHTLTG 259
                                       ************986 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3     0.066   2.4e+02      41      55 ..     253     267 ..     252     268 .. 0.90
   2 !   52.9   0.4     6e-18   2.2e-14       2      56 .]     287     341 ..     286     341 .. 0.96

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.066
                            PurK_C  41 GHitvvgdsaeelee 55 
                                       GH t++g+s  + ee
  gi|518651594|ref|YP_008141114.1| 253 GHHTLTGSSISQFEE 267
                                       9********999886 PP

  == domain 2  score: 52.9 bits;  conditional E-value: 6e-18
                            PurK_C   2 vMvNlLGedaeekleellaipgahlHlYgKeearpgRKmGHitvvgdsaeeleer 56 
                                        +vN++G+d  ek+ +ll++ ++++++Y+K+e+r +RKmGH++v g+s +++e++
  gi|518651594|ref|YP_008141114.1| 287 GIVNIIGTDIREKIGSLLNLGNTNIYWYHKNEVRGKRKMGHVNVYGESYNAVEQK 341
                                       579*******99999************************************9985 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0     1e-06    0.0038      38      99 ..       2      63 ..       1      70 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1e-06
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99
                                      +vGiiG G++G  ++++++   ++ +++d +k +++  +++ +++ + +e++ ++D+v+   
  gi|518651594|ref|YP_008141114.1|  2 KVGIIGSGQLGYMMINTMRRYPIEFYVIDDNKGPSAFIADKFFDVSQYKEFVDSCDYVTYEF 63
                                      89*******************************999777778899*************9765 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 !   15.1   0.0   5.4e-06     0.019       1      60 [.       2      60 ..       2      72 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEE CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvi 60
                                      k+g+iG G++G  m++ + +  ++ +v++ + +   +++a+++  +++ +e+v+s+d v 
  gi|518651594|ref|YP_008141114.1|  2 KVGIIGSGQLGYMMINTMRRYPIEFYVIDDN-KGPSAFIADKFFDVSQYKEFVDSCDYVT 60
                                      69***************************88.56678888999999**********9986 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 ?    4.4   0.0     0.013        48       1      21 [.       2      21 ..       2      33 .. 0.88
   2 ?    6.2   0.0    0.0038        13      90     112 ..     142     164 ..     126     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.013
                                      EEEEETTTSHHHHHHHHHHHC CS
                    Semialdhyde_dh  1 kvaivGatGyvGqellrlLee 21
                                      kv+i+G +G  G  +++ +++
  gi|518651594|ref|YP_008141114.1|  2 KVGIIG-SGQLGYMMINTMRR 21
                                      7*****.**********9987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0038
                                       TSEEEESSSTTTTSTTSEBE-HH CS
                    Semialdhyde_dh  90 gvkviDlssdfRlkddavyvlpe 112
                                       + + iD+ss f  ++d++yv+  
  gi|518651594|ref|YP_008141114.1| 142 NQYFIDNSSRFEGHPDIPYVVEK 164
                                       5588****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2954.43
//
Query:       gi|518651595|ref|YP_008141115.1|  [L=170]
Description: hypothetical protein FACI_IFERC00001G0234 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    0.00095   18.9   0.1     0.0017   18.1   0.1    1.5  1  ACT_7       ACT domain
  ------ inclusion threshold ------
      0.013   15.2   0.1       0.03   14.1   0.1    1.6  1  ACT         ACT domain
      0.074   12.8   0.0       0.13   12.0   0.0    1.4  1  SGTA_dimer  Homodimerisation domain of SGTA


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 !   18.1   0.1   2.9e-07    0.0017      17      42 ..     105     130 ..      89     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.9e-07
                                       --SS--HHHHHHHHHHTTT---EEEE CS
                             ACT_7  17 pfdvtGivaklaspLaeagIsifqiS 42 
                                       + +++Gi+a++ ++Lae gIs+ q+ 
  gi|518651595|ref|YP_008141115.1| 105 DASMPGIIAGVMNVLAESGISVRQFI 130
                                       5589******************8876 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1     5e-06      0.03      10      38 ..     108     136 ..     106     161 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5e-06
                                       STTHHHHHHHHHHHTTSEEEEEEEEEEST CS
                               ACT  10 rPGlLarvfgaladrgiNidsieqrssed 38 
                                       +PG++a v ++la+ gi+++       + 
  gi|518651595|ref|YP_008141115.1| 108 MPGIIAGVMNVLAESGISVRQFIADDPDL 136
                                       7******************9877666655 PP

>> SGTA_dimer  Homodimerisation domain of SGTA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   2.2e-05      0.13      28      66 ..      41      79 ..      39      80 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.2e-05
                        SGTA_dimer 28 ESleVAiqCIaeaFevdkedkaavkkakfggqsLleile 66
                                      ES+e+  + Ia aF+vd+    +++++ ++  +L + ++
  gi|518651595|ref|YP_008141115.1| 41 ESIEIKPNSIARAFHVDRRVIVNMIQKIINDPELFDFFS 79
                                      9*****************************999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 1117.06
//
Query:       gi|518651596|ref|YP_008141116.1|  [L=225]
Description: hypothetical protein FACI_IFERC00001G0235 [Ferroplasma acidarmanus fer1]
Scores for complete 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-68  228.7   1.2    4.5e-68  228.5   1.2    1.0  1  DUF3834    Protein of unknown function (DUF3834)
    0.00095   18.7   0.0     0.0014   18.1   0.0    1.2  1  SBP_bac_3  Bacterial extracellular solute-binding proteins, f


Domain annotation for each model (and alignments):
>> DUF3834  Protein of unknown function (DUF3834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.5   1.2     5e-72   4.5e-68       1     200 [.       1     204 [.       1     205 [. 0.97

  Alignments for each domain:
  == domain 1  score: 228.5 bits;  conditional E-value: 5e-72
                           DUF3834   1 mkivaaPGPVsyPliaatmkkkdielkfek.....eesadvvlDsivslvkrglridlvvikkllviipkigkekIa 72 
                                       mk++aaPGPV yPl+aa+m++kdi+++f+k     +++ dvvlDs+vslvk gl id+v+i++l+ + pk+g+ k++
  gi|518651596|ref|YP_008141116.1|   1 MKVIAAPGPVCYPLVAAMMERKDIDIEFKKsseigNDKPDVVLDSTVSLVKSGLPIDYVTINGLSRVAPKLGY-KVG 76 
                                       9***************************996434445679*********************************.*** PP

                           DUF3834  73 vwrkGsaaDvllrilldlkkikaevvyaddpeevlkllnegevdsavvaselkkgeafedllkklgvyvpGsCgaav 149
                                       ++rkG+aaD+l+r+++  +k   e+ y +++++++ +ln+++vd++vv++  ++g ++e+++kk +v +pGsCga+v
  gi|518651596|ref|YP_008141116.1|  77 MTRKGGAADILFRAYVGESKKDVEIEYFENMSDLMGALNSNKVDTVVVPAIDNSGVSIEEYMKKINVNIPGSCGATV 153
                                       ***************************************************************************** PP

                           DUF3834 150 keneeefidaYeeGIelikedpeeaaeyiaskLpikidkefiknilknael 200
                                        +ne+ef+daY+ GI+l+ke+peeaa++++++Lp++++ ef++n++kn++l
  gi|518651596|ref|YP_008141116.1| 154 YNNEKEFVDAYNLGIKLLKEKPEEAAKFVVEHLPMQFPVEFVANTMKNSNL 204
                                       ************************************************987 PP

>> SBP_bac_3  Bacterial extracellular solute-binding proteins, family 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.5e-07    0.0014     110     213 ..      72     175 ..      44     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-07
                                       TSEEEEETTSHHHHHHHHHHHC....TSEEEEESSHHHHHHHHHTTSSSEEEEEHHHHHHHHHHCCGCCEEEEECGG CS
                                       xxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 110 gkkvgvqagstaeellkeelkk....gaeivefdtleealqaLkngrvdavvadspvlaylvkknpdkkvvlveepl 182
                                       g kvg ++   a+++l +++      ++ei +f+++++++ aL++++vd vv+  +   ++  ++  kk+ +    +
  gi|518651596|ref|YP_008141116.1|  72 GYKVGMTRKGGAADILFRAYVGeskkDVEIEYFENMSDLMGALNSNKVDTVVVPAIDNSGVSIEEYMKKINV----N 144
                                       4468866666666665442222455699999*************************9999999999999988....9 PP

                                       CECEEEEEEETTTHHHHHHHHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         SBP_bac_3 183 sseeyaiavrkgdseLrkainkalaelkadg 213
                                        + ++++ v ++++e+++a n +++ lk+  
  gi|518651596|ref|YP_008141116.1| 145 IPGSCGATVYNNEKEFVDAYNLGIKLLKEKP 175
                                       99999******************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1482.44
//
Query:       gi|518651597|ref|YP_008141117.1|  [L=36]
Description: hypothetical protein FACI_IFERC00001G0236 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   12.6   0.0      0.096   12.5   0.0    1.0  1  T6PP_N    Trehalose-6-phosphate phosphatase N-terminal helica
       0.12   12.6   0.0       0.16   12.2   0.0    1.1  1  VPS11_C   Vacuolar protein sorting protein 11 C terminal


Domain annotation for each model (and alignments):
>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.1e-05     0.096      12      39 ..       1      28 [.       1      34 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                            T6PP_N 12 trevRrqIvervLkgieirehfvesLkn 39
                                      + + Rr+I+e+++k+ +i +   e+++n
  gi|518651597|ref|YP_008141117.1|  1 MAKGRRKIIEEIIKNSKILAGNYEIFNN 28
                                      6678**************9999888887 PP

>> VPS11_C  Vacuolar protein sorting protein 11 C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.8e-05      0.16       4      24 ..       9      29 ..       7      31 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.8e-05
                           VPS11_C  4 irelrraQeesadrhdlFkaa 24
                                      i+e++++ + +a+++++F++ 
  gi|518651597|ref|YP_008141117.1|  9 IEEIIKNSKILAGNYEIFNNL 29
                                      99****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (36 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 260.73
//
Query:       gi|518651598|ref|YP_008141118.1|  [L=88]
Description: DNA polymerase beta subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   25.5   0.0    1.5e-05   25.2   0.0    1.3  1  NTP_transf_2  Nucleotidyltransferase domain
    0.00024   21.1   0.0    0.00029   20.9   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
      0.064   13.1   0.0      0.066   13.0   0.0    1.1  1  DUF294        Putative nucleotidyltransferase DUF294


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 !   25.2   0.0   2.4e-09   1.5e-05      17      45 ..      39      67 ..      22      85 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-09
                                      EEEEHHHHCTTSCTTSSEEEEEEESTTCH CS
                      NTP_transf_2 17 vvlfGSyarGtalkgSDiDllvvlpeevs 45
                                       +l GS arG+ ++ SD D+++++++  s
  gi|518651598|ref|YP_008141118.1| 39 TILIGSLARGDCTPFSDADVIIITDSTRS 67
                                      5899*********************9944 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.9e-08   0.00029      11      45 ..      34      68 ..      22      83 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.9e-08
                                      HHHHSTTEEEEEE-S------EEEEEEEESS---H CS
                           Polbeta 11 keielaylFGSrakgkareeSDiDlavllkekldl 45
                                      k+  l +l GS a+g+ ++ SD D+ ++++++++ 
  gi|518651598|ref|YP_008141118.1| 34 KGSLLTILIGSLARGDCTPFSDADVIIITDSTRSE 68
                                      45678899*********************999443 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.1e-05     0.066      48      77 ..      35      64 ..       5      76 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                            DUF294 48 vpfallvmGSeGReEqtlktDqDnalvled 77
                                       +   + +GS +R++ t  +D D  ++ + 
  gi|518651598|ref|YP_008141118.1| 35 GSLLTILIGSLARGDCTPFSDADVIIITDS 64
                                      45556789****************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 612.51
//
Query:       gi|518651599|ref|YP_008141119.1|  [L=124]
Description: hypothetical protein FACI_IFERC00001G0238 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-30  105.4   1.2    2.1e-30  105.3   1.2    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.29   11.4   0.0    1.8  2  CdiA_C    Contact-dependent growth inhibition CdiA C-terminal


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   1.2   2.3e-34   2.1e-30       3     117 ..       2     120 ..       1     122 [. 0.97

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 2.3e-34
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHH CS
                              HEPN   3 ewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreelee 79 
                                       +wl++A++dle+Ae +l++++y++acf++qq+aeka+ Al+ + ++e  +  +++++l+ l +  +  ++++ ++ e
  gi|518651599|ref|YP_008141119.1|   2 DWLKQAKRDLEEAEGSLNNEKYEWACFASQQSAEKAVIALYHSINKE-IWSQSVSRMLSQLTEFNI-DNNIIATAME 76 
                                       8*********************************************9.9*************9999.********** PP

                                       HHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  80 LekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                       L++ yi srYpd+++e      y+ eda+++l++a+e++e++++
  gi|518651599|ref|YP_008141119.1|  77 LDRVYIGSRYPDYYSEgspfeyYSIEDAKRCLNYAKEIFEFCNK 120
                                       *****************************************865 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.44   3.9e+03      36      36 ..      60      60 ..      36      75 .. 0.56
   2 ?   11.4   0.0   3.3e-05      0.29       3      23 ..      87     105 ..      85     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.44
                            CdiA_C 36 Q 36
                                      Q
  gi|518651599|ref|YP_008141119.1| 60 Q 60
                                      3 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 3.3e-05
                            CdiA_C   3 PDylinGevfDvKsptsgngk 23 
                                       PDy+ +G +f+++s+++  +k
  gi|518651599|ref|YP_008141119.1|  87 PDYYSEGSPFEYYSIED--AK 105
                                       ****************3..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 912.44
//
Query:       gi|518651600|ref|YP_008141120.1|  [L=350]
Description: hypothetical protein FACI_IFERC00001G0239 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-41  141.5   0.1    1.8e-41  140.9   0.1    1.3  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    2.7e-38  131.6   0.0    4.1e-38  131.1   0.0    1.2  1  GATase           Glutamine amidotransferase class-I
      2e-09   37.5   0.2    9.1e-07   28.8   0.2    2.2  1  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.9   0.1   3.1e-45   1.8e-41       2     128 .]       3     130 ..       2     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 140.9 bits;  conditional E-value: 3.1e-45
                   CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglv 77 
                                       ++L+LedGt++eG+++g ++e+ GE+vf+T+m+GY e++tDpsYag+il++++p i ny +n e++es+k++vag++
  gi|518651600|ref|YP_008141120.1|   3 RYLLLEDGTTYEGTGYGyEGETNGEIVFTTSMSGYLETITDPSYAGEILIFAFPEIANYPLNLEHMESSKVQVAGII 79 
                                       79***************88********************************************************** PP

                   CPSase_sm_chain  78 vrelseepsnwraeesLsewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                                        +++++ +s  ++ + ++e+lk++ +p+i g+DTR+L++k+re+ga+kg i
  gi|518651600|ref|YP_008141120.1|  80 TKDAHSIYSGGESGTGFNEFLKQNMVPAIDGIDTRSLVEKIRESGAIKGYI 130
                                       ************************************************987 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   6.8e-42   4.1e-38       3     186 ..     171     341 ..     169     344 .. 0.91

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 6.8e-42
                                       EESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT...TTTHHHHHHHHCTSTS-EEE CS
                            GATase   3 iDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg...vegkieaikearenkiPiLG 76 
                                       iD++   +++l+++l e+  ++++vp+++++ +i   + ++d+i++++Gpg+pg    e   ++i+e   + +P++G
  gi|518651600|ref|YP_008141120.1| 171 IDVG--TKNSLIKRLSETA-SLHIVPYNYDFFNI---KFHYDAIFLPNGPGNPGhssLEPLRAFIREKS-SSMPVMG 240
                                       7777..8899999999876.**************...589**************666666666666655.5****** PP

                                       ETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                            GATase  77 ICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddee 153
                                       +CLG+Ql+a+++g+k++k+k ++h+g ++ +         g+ +++i++h+H+y+vn ++l  +g+e+ +++ +d++
  gi|518651600|ref|YP_008141120.1| 241 VCLGNQLIALSMGGKTEKMK-YGHRGINHAVLI-------GN-RVYITSHNHGYAVNGDSLKGTGMEICGTDINDGT 308
                                       ********************.********9988.......66.9**************99999*************9 PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnf 186
                                       ++ i +++ p+++vQFHPE+ ++p +++++fn 
  gi|518651600|ref|YP_008141120.1| 309 VEMIKHRELPVFSVQFHPEAYPGPYDSTWFFND 341
                                       999999999**********************98 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.2   1.5e-10   9.1e-07     103     216 .]     233     327 ..     225     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-10
                     Peptidase_C26 103 ergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaik 179
                                       ++++P++g+C+G ql++  +GG++ +  +       h        +hav + +   + ++           H  a++
  gi|518651600|ref|YP_008141120.1| 233 SSSMPVMGVCLGNQLIALSMGGKTEKMKYG------H-----RGINHAVLIGNRVYITSHN----------HGYAVN 288
                                       678*******************98765442......3.....3567999887665555544..........444444 PP

                     Peptidase_C26 180 e...laeelrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                            +++++++ ++  Dg++E i+++e   +v++vQ+HPE
  gi|518651600|ref|YP_008141120.1| 289 GdslKGTGMEICGTDInDGTVEMIKHRE--LPVFSVQFHPE 327
                                       33335789999999988*********99..56********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 2497.77
//
Query:       gi|518651601|ref|YP_008141121.1|  [L=1051]
Description: hypothetical protein FACI_IFERC00001G0240 [Ferroplasma acidarmanus fer1]
Scores for complete 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-80  267.1   0.0    1.7e-59  200.9   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    6.9e-30  103.9   0.0    1.9e-29  102.5   0.0    1.8  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    1.2e-16   60.6   0.6    1.2e-15   57.4   0.0    2.9  3  MGS              MGS-like domain
    5.1e-14   52.1   0.0    5.3e-07   29.4   0.0    2.8  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    5.4e-09   36.3   1.2     0.0026   17.8   0.2    3.0  2  ATP-grasp_3      ATP-grasp domain
    1.1e-08   34.8   0.0    0.00041   19.9   0.0    2.4  2  ATP-grasp        ATP-grasp domain
      8e-07   28.8   0.2    0.00091   18.8   0.0    2.6  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


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 !  200.9   0.0   6.5e-63   1.7e-59       1     210 [.     126     330 ..     126     331 .. 0.95
   2 !   64.1   0.0   4.8e-21   1.2e-17       3     205 ..     661     856 ..     659     861 .. 0.90

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 6.5e-63
                                       SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaa 77 
                                       D++++ +++kki++pv++s + + ++  + +   k  +yP i+++ f+lGG+G+ +++n +el++ +   ++     
  gi|518651601|ref|YP_008141121.1| 126 DRKKFFNLMKKIGEPVIESYTLTKNDYRDLMPGIK--KYPLILRTGFSLGGSGGVIIKNVKELSDYCDDYFSVH--- 197
                                       9*********************5555555555444..6*******************************99999... PP

                                       HSTS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHH CS
                       CPSase_L_D2  78 fgnkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrev 152
                                         +++v +++sl g keiE+e++rD++gn+i +c++en++++  +t+++i+  Ps tL+++++q+lr++a++vv+e+
  gi|518651601|ref|YP_008141121.1| 198 --DDMVELDESLLGLKEIEYEMMRDNNGNCISICNMENLDPMgvHTGESIVTTPSLTLSNDSYQKLRTSAIHVVNEI 272
                                       ..7************************************************************************** PP

                                       T-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT--GCG CS
                       CPSase_L_D2 153 gvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialgekLee 210
                                       gv+g ++++f+ld++++eyy++EvN+R s++sala+ka G++++ ++ kia+g++L+e
  gi|518651601|ref|YP_008141121.1| 273 GVIGSCNIQFALDQEKDEYYIVEVNPRTSRSSALASKASGYPIARVSTKIAVGYNLNE 330
                                       ********************************************************97 PP

  == domain 2  score: 64.1 bits;  conditional E-value: 4.8e-21
                                       HHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHS CS
                       CPSase_L_D2   3 esakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafg 79 
                                       + ++++l+ ++++  +  +a  ++++e  +  k i+ Pvii+++f +GG+ m ++++ + l+  v++ + e +    
  gi|518651601|ref|YP_008141121.1| 661 TIFSKTLRSLGIKQPDFIEA--SNINELEEKIKGISLPVIIRSSFIIGGRAMDIIYDYDILVSRVRELFIERP---- 731
                                       56777777777777766666..8999999999************************************99996.... PP

                                       TS-EEEEE--SSSEEEEEEEEEETTS-EEEEEEEEECCEC.TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-E CS
                       CPSase_L_D2  80 nkqvlvekslkgpkeiEvevlrDakgnvitvcerenslql.rtqkvievAPsqtLtdeerqalreaavkvvrevgvv 155
                                        + vlv  +lk+  ei+v+ ++ a+  +i   +     +  + ++   v    ++++++ ++l+e   k+ ++ +++
  gi|518651601|ref|YP_008141121.1| 732 GSPVLVSSYLKNATEIDVDFISSAEKSIIAGISVHIEEAGtHSGDATMVLGPGVVDSDTLEQLKEIVEKMRQNFNLS 808
                                       789**************************99988877776799*99888888899********************** PP

                                       EEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHHHHHHHHTT CS
                       CPSase_L_D2 156 gagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvkeaakialg 205
                                       g  +++ +++  ++e+yviE+N+R s++ +  +kaTG++ +   +k  lg
  gi|518651601|ref|YP_008141121.1| 809 GLSNLQLAIK--DSEIYVIELNARSSRSVPFVSKATGINWIDSGVKAMLG 856
                                       *********9..59************************999888887666 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   7.4e-33   1.9e-29       3     122 .]     417     532 ..     415     532 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 7.4e-33
                       CPSase_L_D3   3 lkeptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiael 79 
                                       +k p+d R+fai++ l +g+ v++i+el+ +d++F+ k++++v++ +++k+    + +e ++++k lG+sD++i+  
  gi|518651601|ref|YP_008141121.1| 417 MKVPNDLRLFAIFDGLFQGIGVDKISELSGYDKFFIVKIKNIVDAMETIKRG---VIPENMENLKMLGISDETISYY 490
                                       689*********************************************9988...689******************* PP

                       CPSase_L_D3  80 leeeeeeevrelrkklgilpvykrvDtcAaeFeaetpYlYstY 122
                                       ++   ++e+ ++r +++i pvyk++Dtc++eF+a+t YlYs+Y
  gi|518651601|ref|YP_008141121.1| 491 TG-IPQTEIIKYRIEKKIVPVYKNIDTCSGEFNADTTYLYSAY 532
                                       76.77888**********************************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.9     1e+04      57      75 ..      36      54 ..      32      84 .. 0.50
   2 ?   -0.6   0.0      0.59   1.5e+03      48      93 ..     276     326 ..     258     327 .. 0.77
   3 !   57.4   0.0   4.8e-19   1.2e-15       2      95 .]     937    1024 ..     936    1024 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.9
                                      HTTSCCEEEEE--THHHHH CS
                               MGS 57 kngeidlvintlypfkatv 75
                                      k+++i+ v  + +p + ++
  gi|518651601|ref|YP_008141121.1| 36 KEEGIKTVLLNSNPATIQT 54
                                      4444444444444443332 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.59
                                       HCHHHHHHHHTTSCCEEEEE--THHHHHH.....CHHHHHHHHHHHTTSHE CS
                               MGS  48 grveildaikngeidlvintlypfkatva.....kdgykirraaenidIpl 93 
                                       g ++i+ a+ +++ +++i+ ++p++++ +      +gy i+r+ ++i +++
  gi|518651601|ref|YP_008141121.1| 276 GSCNIQFALDQEKDEYYIVEVNPRTSRSSalaskASGYPIARVSTKIAVGY 326
                                       445677777888888889988888888888888888999999999999986 PP

  == domain 3  score: 57.4 bits;  conditional E-value: 4.8e-19
                                        HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHH CS
                               MGS    2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatva 76  
                                        ++++ +kl++++++++AT GT++++k+ag++  +vv ++++  ++g    i + ikn++i+++int+++    ++
  gi|518651601|ref|YP_008141121.1|  937 AIKIGRKLAAKNVKIYATPGTYNAMKDAGVK-SNVVYRVKDLRSPG----ISEIIKNEDISMIINTPSESYGSIR 1006
                                        678899*************************.**********9***....************************9 PP

                                        CHHHHHHHHHHHTTSHEES CS
                               MGS   77 kdgykirraaenidIplpt 95  
                                         dg++ir++ ++ dIpl+t
  gi|518651601|ref|YP_008141121.1| 1007 -DGFSIRNLGIKKDIPLIT 1024
                                        .****************98 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   2.6e-07   0.00066      48     124 ..     260     339 ..     252     345 .. 0.82
   2 !   29.4   0.0   2.1e-10   5.3e-07       5     113 ..     735     859 ..     732     873 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.6e-07
                      ATPgrasp_Ter  48 elielaerlaeefgldglvnvQvrededg..pkLLEiNpRas.GGlgysalaGvnlpylalklllgleteeveepee 121
                                       +l   a ++++e+g+ g  n+Q+  d+++  +++ E+NpR s +    s ++G  +++++ k + g + +e+++p +
  gi|518651601|ref|YP_008141121.1| 260 KLRTSAIHVVNEIGVIGSCNIQFALDQEKdeYYIVEVNPRTSrSSALASKASGYPIARVSTKIAVGYNLNEIKNPVT 336
                                       55667899***************998877779*********93445567788***********99998888877766 PP

                      ATPgrasp_Ter 122 glr 124
                                       + +
  gi|518651601|ref|YP_008141121.1| 337 KNT 339
                                       655 PP

  == domain 2  score: 29.4 bits;  conditional E-value: 2.1e-10
                      ATPgrasp_Ter   5 llvmeyLeg.pEySvDvlae.kgevlaavpRrKe.kgglq............elekdeelielaerlaeefgldglv 66 
                                       +lv  yL++ +E+ vD ++  + +++a +    e +g ++              ++ e+l e++e++ ++f+l+gl 
  gi|518651601|ref|YP_008141121.1| 735 VLVSSYLKNaTEIDVDFISSaEKSIIAGISVHIEeAGTHSgdatmvlgpgvvDSDTLEQLKEIVEKMRQNFNLSGLS 811
                                       667777765347777777774444444444443322222234446666653333445789999************** PP

                      ATPgrasp_Ter  67 nvQvrededgpkLLEiNpRasGGlg.ysalaGvnlpylalklllglet 113
                                       n+Q+  ++++ +++E N+R s  +  +s ++G+n ++  +k++lg e+
  gi|518651601|ref|YP_008141121.1| 812 NLQLAIKDSEIYVIELNARSSRSVPfVSKATGINWIDSGVKAMLGIEP 859
                                       *********************9998357788**************743 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     3e-06    0.0076     115     158 ..     256     300 ..     126     303 .. 0.71
   2 !   17.8   0.2     1e-06    0.0026       8     158 ..     664     831 ..     657     834 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
                                       -HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS- CS
                       ATP-grasp_3 115 elkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRl 158
                                       +  +++++ a +vv+++ g+ G+  + + l +  +e y++EvNPR 
  gi|518651601|ref|YP_008141121.1| 256 DSYQKLRTSAIHVVNEI-GVIGSCNIQFALDQekDEYYIVEVNPRT 300
                                       346789999999*****.***********98877899********6 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 1e-06
                                       HHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE...............EEEE- CS
                       ATP-grasp_3   8 ykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqef 69 
                                        k L+  g+k P        +  +e+++    ++++  +   gg ++ ++ + + + + + e+         lv+ +
  gi|518651601|ref|YP_008141121.1| 664 SKTLRSLGIKQPdfieasnINELEEKIKGISLPVIIRSSFIIGGRAMDIIYDYDILVSRVRELFierpgspvLVSSY 740
                                       56777777888855544221111233333377788888888888888888887777666666556677788888888 PP

                                       --.SEEEEEEEEE.SSSEEEEEEEEEEEET........TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEE CS
                       ATP-grasp_3  70 ie.GkplSvsllsdgekvlvlavnrqliekaeke....fvyaGnvtpietelkeevvelaeevvekleglaGyvGvD 141
                                       ++  +++ v+++s++ek  +  ++  + e ++++    +v   +v++++    e++ e++e++ +++ +l G+    
  gi|518651601|ref|YP_008141121.1| 741 LKnATEIDVDFISSAEKSIIAGISVHIEEAGTHSgdatMVLGPGVVDSD--TLEQLKEIVEKMRQNF-NLSGLSNLQ 814
                                       8636789999999998877777766655554444676444444666666..5677888888888888.********* PP

                                       EEESS.SEEEEEEESS- CS
                       ATP-grasp_3 142 lvlkdeepyviEvNPRl 158
                                       l +kd+e+yviE N+R 
  gi|518651601|ref|YP_008141121.1| 815 LAIKDSEIYVIELNARS 831
                                       ***************95 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   3.5e-05      0.09      20     161 ..     152     301 ..     114     309 .. 0.80
   2 !   19.9   0.0   1.6e-07   0.00041       2     160 ..     668     831 ..     667     834 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                                       HHHHHHHH.-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC...GTTCEEEEE----SEEEEEEEEEETTC-EEE CS
                         ATP-grasp  20 leeaaeel.glpvvvKarrlgydGkGqsvvrseedleqaleal...keekvivEefvpfekElsvlvvrsaeGetaf 92 
                                        ++++  + ++p++++    +  G G  ++++ ++l++  + +   ++  v + e     kE+   ++r+ +G+  +
  gi|518651601|ref|YP_008141121.1| 152 YRDLMPGIkKYPLILR-TGFSLGGSGGVIIKNVKELSDYCDDYfsvHDDMVELDESLLGLKEIEYEMMRDNNGNCIS 227
                                       4444455546788888.888999***************99999877666666667777779***************9 PP

                                       --EEEEEEETTEEE...EEEECE.E-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCT.EEEEEEESS-- CS
                         ATP-grasp  93 ypvvetvqedgilr...lsvapa.evsekaqkkaeeiakkiveeLggvGvfavElFvledge.llvnElapRpH 161
                                       +  +e++   g+     ++  p+ ++s++  +k ++ a ++v+e+g++G   + + + ++++  ++ E+ pR+ 
  gi|518651601|ref|YP_008141121.1| 228 ICNMENLDPMGVHTgesIVTTPSlTLSNDSYQKLRTSAIHVVNEIGVIGSCNIQFALDQEKDeYYIVEVNPRTS 301
                                       99*****99999753224455542566778899999999**************9988877768*********85 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 1.6e-07
                                       HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE---- CS
                         ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpf 74 
                                       ++lg++ p+f+ +++ +elee ++ + lpv+++ +     G+   ++ + + l + +++l     + +v+v ++ + 
  gi|518651601|ref|YP_008141121.1| 668 RSLGIKQPDFIEASNINELEEKIKGISLPVIIR-SSFIIGGRAMDIIYDYDILVSRVRELfierPGSPVLVSSYLKN 743
                                       6799*****************************.778899*********999998888888888899********** PP

                                       SEEEEEEEEEETTC-EE...E--EEEEEEETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETT CS
                         ATP-grasp  75 ekElsvlvvrsaeGeta...fypvvetvqedgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvled 148
                                        +E+ v  + sae ++    ++ + e   ++g+  +++ p  v+++ +++ +ei++k+ ++++  G+  + l ++ d
  gi|518651601|ref|YP_008141121.1| 744 ATEIDVDFISSAEKSIIagiSVHIEEAGTHSGDATMVLGPGVVDSDTLEQLKEIVEKMRQNFNLSGLSNLQLAIK-D 819
                                       ******99998887644111455666778899****************************************998.9 PP

                                       CTEEEEEEESS- CS
                         ATP-grasp 149 gellvnElapRp 160
                                       +e++v El  R 
  gi|518651601|ref|YP_008141121.1| 820 SEIYVIELNARS 831
                                       99*****99885 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   3.5e-07   0.00091      35     174 ..     160     298 ..     133     301 .. 0.79
   2 !    7.2   0.0    0.0013       3.4     117     174 ..     773     829 ..     668     831 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 3.5e-07
                                       C-SSEEEEES.SSSTTTTEEEESSGGGHHHHHHHHHT.T-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SS CS
                   Dala_Dala_lig_C  35 lgypvfVKpa.reGSSvGvskveseeelkeaieeafk.ydekvlvEeai.egreievavlgneklevsevgeivvkk 108
                                        +yp++ +    +G S Gv  +++++el+++ ++ f+ +d  v  +e +   +eie  ++ +++ ++ ++ ++    
  gi|518651601|ref|YP_008141121.1| 160 KKYPLILRTGfSLGGSGGV-IIKNVKELSDYCDDYFSvHDDMVELDESLlGLKEIEYEMMRDNNGNCISICNMEN-- 233
                                       4678777764256888777.689***********997467777666665599*********99988888776654.. PP

                                       SSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEES CS
                   Dala_Dala_lig_C 109 gfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNt 174
                                          d    ++++++  +   +l+++ ++k+++ a+++ + +++ G++ + f l +e++e ++ EvN+
  gi|518651601|ref|YP_008141121.1| 234 --LDPMGVHTGESIVTTPSLTLSNDSYQKLRTSAIHVVNEIGVIGSCNIQFALdQEKDEYYIVEVNP 298
                                       ..4444555677888888899********************************8899*********6 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
                                       HC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
                   Dala_Dala_lig_C 117 ysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                                       +s+d++++  p  +++++ e+++e++ k+ ++ +l+Gl+ + + ++ + ei++ E+N 
  gi|518651601|ref|YP_008141121.1| 773 HSGDATMVLGPGVVDSDTLEQLKEIVEKMRQNFNLSGLSNLQLAIK-DSEIYVIELNA 829
                                       466899999999*******************************998.899******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1051 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); 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: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 6709.67
//
Query:       gi|518651602|ref|YP_008141122.1|  [L=217]
Description: endonuclease III [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-18   66.8   0.0    2.7e-18   66.4   0.0    1.2  1  HhH-GPD        HhH-GPD superfamily base excision DNA repair p
    8.2e-06   25.4   0.0    1.9e-05   24.3   0.0    1.6  1  HHH            Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.064   13.9   0.1        1.8    9.3   0.1    2.2  2  HHH_5          Helix-hairpin-helix domain
       0.15   12.0   0.0       0.26   11.2   0.0    1.3  1  DUF2400        Protein of unknown function (DUF2400)
       0.23   11.8   9.8       0.37   11.2   9.8    1.3  1  EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   7.6e-22   2.7e-18       1     106 [.      31     164 ..      31     166 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 7.6e-22
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       + +ils +t+d ++ ++  +l++++   +   l +ad+++++++i+ +Gf++ K  +i+e+Ari+            
  gi|518651602|ref|YP_008141122.1|  31 ITTILSHRTKDIVTDQAARSLYNKYH--DSVGLENADPADVKAIIKYVGFSNVKSLRIIEIARIINheyggkvpdth 105
                                       579*********************86..************************************************* PP

                                       ....................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                                       ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 ....................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                                                           g++ ++i+vD+hv r+ +r++++++ k+++++e++l+ ++
  gi|518651602|ref|YP_008141122.1| 106 delvklpgtgsktanivltqGFNIPAIAVDTHVFRVSNRIGLVHT-KNPDETEEALKSIV 164
                                       **********************9**********************.6********97765 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.2e-09   1.9e-05       1      28 [.      96     123 ..      96     124 .. 0.93

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.2e-09
                                       SHHHHHTSSHHHHHTSTT-SHHHHHHHH CS
                               HHH   1 sleglipasreeLlalPGVGpktAeaIl 28 
                                       +++g +p++ +eL++lPG G ktA+ +l
  gi|518651602|ref|YP_008141122.1|  96 EYGGKVPDTHDELVKLPGTGSKTANIVL 123
                                       599*********************9876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.025        91      15      56 ..      48      91 ..      43      92 .. 0.68
   2 ?    9.3   0.1   0.00049       1.8      32      49 ..      95     120 ..      66     125 .. 0.57

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.025
                                      HHHHHTTT--SHHHHHHS...-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5 15 AlallsaGiesvedlaaa...dveeLakipGiGkktAeriilelk 56
                                      A++l+++ +     l +a   dv+++ k  G+++ +  rii+ ++
  gi|518651602|ref|YP_008141122.1| 48 ARSLYNK-YHDSVGLENAdpaDVKAIIKYVGFSNVKSLRIIEIAR 91
                                      6666666.5555556665222677788889999999999998765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00049
                                       S........-HHHHHTSTTS-HHHHH CS
                             HHH_5  32 a........dveeLakipGiGkktAe 49 
                                                + +eL k+pG G ktA 
  gi|518651602|ref|YP_008141122.1|  95 HeyggkvpdTHDELVKLPGTGSKTAN 120
                                       1344444424589***********96 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.3e-05      0.26     173     195 ..     132     154 ..     129     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.3e-05
                           DUF2400 173 iPlDvHvarvarklgllkrkqad 195
                                       i +D+Hv+rv++++gl+++k+ d
  gi|518651602|ref|YP_008141122.1| 132 IAVDTHVFRVSNRIGLVHTKNPD 154
                                       689**************999877 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 ?   11.2   9.8    0.0001      0.37       1      15 [.     184     198 ..     184     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
                     EndIII_4Fe-2S   1 CTARkPkCeaCPLaD 15 
                                       C++ +P+C +CP++D
  gi|518651602|ref|YP_008141122.1| 184 CKPVSPRCNICPVSD 198
                                       **************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1432.58
//
Query:       gi|518651603|ref|YP_008141123.1|  [L=530]
Description: Amidohydrolase 3 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-70  238.3   0.0    3.1e-70  238.0   0.0    1.0  1  Amidohydro_3  Amidohydrolase family
    7.7e-13   48.5   0.0    1.3e-09   37.9   0.0    2.3  2  Amidohydro_1  Amidohydrolase family


Domain annotation for each model (and alignments):
>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.0   0.0   3.4e-74   3.1e-70       1     453 [.      50     514 ..      50     520 .. 0.94

  Alignments for each domain:
  == domain 1  score: 238.0 bits;  conditional E-value: 3.4e-74
                      Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvltavrdqagttpkgrwivgeGwdeaqfaeerf 76 
                                       ev D++G++v+PG++DsH H   + ++l   ++ ++  v+s+e+  ++++++ ++     w+ g+G +e ++ e+r 
  gi|518651603|ref|YP_008141123.1|  50 EVLDLRGKFVTPGLIDSHDHFMLTSLKLkYQVDFSG--VRSFEDFRRVLEENRNK-IVHGWFQGYGINEYNMKEKRL 123
                                       799*********************************..****************9.45555555555********** PP

                      Amidohydro_3  77 pyalaeldevledapvllaaldtHaavrnsaaldlagiteatpdpaggeilrdangegatgllreg.afhlvldlap 152
                                       p   + +de++ ++pv++ +++ H  ++ns+ l+ agi+++t+dpa g++ r+++g+ + g+l e  a ++v+  +p
  gi|518651603|ref|YP_008141123.1| 124 P-DIKIIDEIMGNTPVFITQMTEHYGICNSRSLEIAGIDRNTADPANGKLGRNSDGN-PDGVLYEAnAMDMVKSRIP 198
                                       *.9******************************************************.********99999999997 PP

                      Amidohydro_3 153 l.areaeaaavaaalaalasyGitsv...eagggnvsslddleplfeltaeeklplrvi...ikelldaaerlglpl 222
                                       + + +++ +a+  + + +++ G+ +v    + g+ v+ +  + +l ++++e++  +r++   +   l++++r  +  
  gi|518651603|ref|YP_008141123.1| 199 EyTLDDYIEAIISGSEMYRKAGLSTVkdiGGTGNDVNEETRICALNRISKEGNHKIRIAvalPVYSLKDVSRKIELA 275
                                       77*************************9888899999999999*******************666677777777777 PP

                      Amidohydro_3 223 s..pgseeltigavklfadgvlgsrtalltepyf.....tgwpdfedealaelvaaadergldvaihaigdaavddv 292
                                       s    + ++ + ++k+f+dg+  srta++++ y      +g+p  + + ++e ++++ + g  + ih+igd a++ +
  gi|518651603|ref|YP_008141123.1| 276 SilEENQHIMFAGFKMFLDGSILSRTAWMKHSYVgskgnMGIPLWDIKNFREGLKQLSATGHHISIHTIGDRAIETA 352
                                       777799*********************************************************************** PP

                      Amidohydro_3 293 ldafeaaaekngnqdrrrlehaegvtesqiervaalqvaagvqpvfnf.edelldsrlgperargstpvkellnagv 368
                                       ld +e+  +  g    + l h+  + e++ie++++l v    q++f++   + l + +g    + ++p k++ ++g+
  gi|518651603|ref|YP_008141123.1| 353 LDSIEKL-KSSGIASTYALVHCYKLEEKTIEKIKKLDVGVETQLAFVYfIGDSLSDNIGLDQSKCLFPAKTMVEKGI 428
                                       ******9.4555555559******************************966788888888888888*********** PP

                      Amidohydro_3 369 kvalgsDapvgpfdpwprigaavmrktrrgg..evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlv 443
                                       +v+ gsD+pv+pfdp+++i++ v rkt +g+   v+  +e l++ee +++yT+++A+++g  +  G+Le G+  D++
  gi|518651603|ref|YP_008141123.1| 429 RVSNGSDSPVTPFDPLYGIYSSVFRKTLTGKnsSVYSNNESLTIEETVKTYTSESAAVIGWNEI-GSLETGKFSDFT 504
                                       ***************************************************************8.************ PP

                      Amidohydro_3 444 vldadpldvd 453
                                       v+d dp+++ 
  gi|518651603|ref|YP_008141123.1| 505 VWDPDPATAG 514
                                       ******9975 PP

>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00014       1.2       1      15 [.      58      72 ..      58     106 .. 0.77
   2 !   37.9   0.0   1.4e-13   1.3e-09     193     324 ..     334     513 ..     301     526 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00014
                                      EEEE-EEEEEEECET CS
                      Amidohydro_1  1 ivlPGlIDaHvHleq 15
                                      +v+PGlID+H H+  
  gi|518651603|ref|YP_008141123.1| 58 FVTPGLIDSHDHFML 72
                                      79***********53 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 1.4e-13
                                       HCTCEEE.....HH...HHHHHHHHHHHHCEE......HHHHHHHH............................... CS
                      Amidohydro_1 193 ahgvhlt.....pt...eaellkerlkeagva......hcpfsnsi............................... 224
                                       a+g h++     +    +a   +e+lk++g+a      hc + +++                               
  gi|518651603|ref|YP_008141123.1| 334 ATGHHISihtigDRaieTALDSIEKLKSSGIAstyalvHCYKLEEKtiekikkldvgvetqlafvyfigdslsdnig 410
                                       45555553333211344555556666666666666666666666666666666666666666666677777888888 PP

                                       ..SEHHHHHHHHHHHHTSCEEEEEECT......TSSCCGGHHHH...HHHHHHHHHHCCTTTTHCHCHHHHHHHHHT CS
                      Amidohydro_1 225 ..lrsgrealrkaldeGvkvglgtDga......asgnslnllee...lrlalklqrgllyedeegglslkealrmaT 290
                                          ++ +++++ ++++G++v+ g+D+         g   ++++    +++         y+  +  l+++e ++ +T
  gi|518651603|ref|YP_008141123.1| 411 ldQSKCLFPAKTMVEKGIRVSNGSDSPvtpfdpLYGIYSSVFRKtltGKNSS------VYS-NNESLTIEETVKTYT 480
                                       8899999******************999999996677767755544355555......333.3889*********** PP

                                       HHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGG CS
                      Amidohydro_1 291 ingAkalglddkvGsievGkdADlvvvdldilaa 324
                                          A ++g+ +++Gs+e Gk  D++v+d+d+ +a
  gi|518651603|ref|YP_008141123.1| 481 SESAAVIGW-NEIGSLETGKFSDFTVWDPDPATA 513
                                       *********.6****************9977444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.49
# Mc/sec: 3226.71
//
Query:       gi|518651604|ref|YP_008141124.1|  [L=262]
Description: metal dependent hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-13   50.0   0.0    4.6e-13   49.6   0.0    1.1  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.024   14.6   0.0    1.3  1  Lactamase_B_3  Beta-lactamase superfamily domain
      0.027   14.0   0.0      0.034   13.7   0.0    1.3  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   7.7e-17   4.6e-13       6     162 ..      43     206 ..      40     236 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 7.7e-17
                                       SEEEEEEETTCEEEES--SCHHHHHHHH............HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal............elaalglkpkdvdavilTHlHlDHiGglgglveatdv 70 
                                       +n+ +++ ++++i++D+G+++ +++ ++            +   +++ +k vd +il+H+H+DH G      + + +
  gi|518651604|ref|YP_008141124.1|  43 TNIPFLRVNDKNIMVDAGIGNNFSDRFRrifvpeknndiaDSLENDYHIKGVDNIILSHMHFDHNGHIFSGNKLFRN 119
                                       67779999********************************999*********************8866666666666 PP

                                       EETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEE CS
                       Lactamase_B  71 pvgavaeeapalfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlf 147
                                        +++ +e++ + f++  d+ ++      +++ +++  +++ e+     g  +   tgg++ gh+++ +e+ ++k+ +
  gi|518651604|ref|YP_008141124.1| 120 SQIIMQEKELKAFRHPNDFTRGS-----YIPGKIHGKIKTIEGSRKITGNITAINTGGHTEGHMVIFFEINSKKYMY 191
                                       66666666666666666666665.....689999******************************************* PP

                                       ECTTTSSHHCCCCCC CS
                       Lactamase_B 148 tGDallagetgridl 162
                                        GD++++  +++   
  gi|518651604|ref|YP_008141124.1| 192 GGDLFPSSFHLKPYY 206
                                       ****99887776655 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.9e-06     0.024      13     110 ..      49     177 ..      43     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.9e-06
                     Lactamase_B_3  13 etagarilvDPf...............kanlgyeppa..............eeaDlvlisqaledHa.hletlkqla 59 
                                       ++++++i+vD +               +        +              + +D +++s+ + dH+ h+   ++l+
  gi|518651604|ref|YP_008141124.1|  49 RVNDKNIMVDAGignnfsdrfrrifvpE--------KnndiadslendyhiKGVDNIILSHMHFDHNgHIFSGNKLF 117
                                       6677888888775555544444444440........0444444555566669**************64888999997 PP

                     Lactamase_B_3  60 envkvlee.........geslevggleiravatshdavggsergenngflleqdgltiyh 110
                                       +n +++ +         +++++ g+    +++++++  +gs++ ++n+  ++ +g+t +h
  gi|518651604|ref|YP_008141124.1| 118 RNSQIIMQekelkafrhPNDFTRGSYIPGKIHGKIKTIEGSRKITGNITAINTGGHTEGH 177
                                       787777775555555556778888888888888888888888888888888777776555 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 ?   13.7   0.0   5.7e-06     0.034       2      46 ..      54     109 ..      53     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.7e-06
                                       EEEES--TT.........HHHH.HTCGG.S--SSS--..SEEEEE-SS--HHHHGG CS
                     Lactamase_B_2   2 riLiDagpd.........lrqq.alral.qPvelrdelppidaVllthaHyDHlag 46 
                                       +i +Dag +         ++ +  +       e   +++ +d ++l+h H+DH   
  gi|518651604|ref|YP_008141124.1|  54 NIMVDAGIGnnfsdrfrrIFVPeKNNDIaDSLENDYHIKGVDNIILSHMHFDHNGH 109
                                       788888888888888777444433333324444666799**************754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1838.85
//
Query:       gi|518651605|ref|YP_008141125.1|  [L=95]
Description: ferredoxin like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   41.2   0.5    1.8e-10   40.9   0.5    1.1  1  ETF_QO       Electron transfer flavoprotein-ubiquinone oxidor
    4.7e-06   26.7   4.1    1.5e-05   25.0   4.5    1.6  2  Fer4_9       4Fe-4S dicluster domain
    1.2e-05   25.3   7.1    2.1e-05   24.5   7.1    1.4  1  Fer4_10      4Fe-4S dicluster domain
    0.00013   22.4   6.7     0.0045   17.5   8.3    2.3  3  Fer4_7       4Fe-4S dicluster domain
     0.0025   18.2   2.0       0.93   10.0   0.1    2.2  2  Fer4_8       4Fe-4S dicluster domain
     0.0069   16.4  11.4      0.029   14.5   1.7    2.5  2  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
      0.014   15.2   2.5      0.018   14.8   2.5    1.2  1  GF_recep_IV  Growth factor receptor domain IV
      0.055   14.0  12.4        1.4    9.6   3.3    2.7  2  Fer4_4       4Fe-4S binding domain
      0.077   13.9   5.7        5.2    8.1   0.1    2.9  3  Fer4_16      4Fe-4S double cluster binding domain
       0.27   11.4  10.7       0.96    9.6   3.4    3.4  3  Fer4_6       4Fe-4S binding domain
       0.85   10.2   7.3         18    5.9   3.4    2.6  2  Fer4_17      4Fe-4S dicluster domain
        1.8    9.7   8.7        4.6    8.4   3.0    2.7  2  Fer4_3       4Fe-4S binding domain
        4.4    7.5  11.2       0.81    9.9   0.6    2.7  2  Fer4_21      4Fe-4S dicluster domain
        7.9    6.5  17.9        3.8    7.5   1.1    3.6  3  Fer4         4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> 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 !   40.9   0.5   1.4e-13   1.8e-10      17     100 ..      11      89 ..       3      93 .. 0.86

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.4e-13
                                       B--SSS--SEEESSTTHHHHTHHHHHS-T..HHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EE CS
                            ETF_QO  17 nheedqpvhLklkdaevavkvnlekyagp..eqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqnie 91 
                                        +++d++ hL +kd +++ + ++e++ +p  +  +CPa+v+ + +      +++ i  +nCv C +  i  p++ni+
  gi|518651605|ref|YP_008141125.1|  11 RYKKDDKSHLGIKDVNTCLE-CTERFGEPqpCVSICPANVFTWEN------NRIIIGYENCVECGASRIACPYDNID 80 
                                       578999**********9986.67889875226799******9964......569*********************** PP

                                       E---STT-C CS
                            ETF_QO  92 wvvPeGggG 100
                                       w+ P  g+G
  gi|518651605|ref|YP_008141125.1|  81 WNYPRFGKG 89 
                                       ****99988 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   1.0   9.4e-05      0.12      33      49 ..      17      48 ..       4      50 .. 0.72
   2 !   25.0   4.5   1.2e-08   1.5e-05       2      49 ..      28      77 ..      27      79 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.4e-05
                            Fer4_9 33 e........eaCigCga.......CveaCpkg 49
                                      +        + C++C +       Cv +Cp +
  gi|518651605|ref|YP_008141125.1| 17 KshlgikdvNTCLECTErfgepqpCVSICPAN 48
                                      24444455578999999999999999999987 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 1.2e-08
                            Fer4_9  2 CtgC.......gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49
                                      C +C       + Cv+ Cpa+v++ ++++ ++ ++     +C++Cga   aCp +
  gi|518651605|ref|YP_008141125.1| 28 CLECterfgepQPCVSICPANVFTWENNRIIIGYE-----NCVECGASRIACPYD 77
                                      9999555555555******************9995.....6************97 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   7.1   1.6e-08   2.1e-05       3      56 .]      22      75 ..      20      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.6e-08
                           Fer4_10  3 vidddtCirCg.......kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      ++d +tC++C+        Cv+ CPa       + +++e++++ +++e+C +cga   aCP
  gi|518651605|ref|YP_008141125.1| 22 IKDVNTCLECTerfgepqPCVSICPA-------NVFTWENNRIIIGYENCVECGASRIACP 75
                                      57999*****999999999*******.......***************************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   2.1   0.00071      0.91      33      52 .]      23      49 ..       5      49 .. 0.68
   2 !   17.5   8.3   3.5e-06    0.0045       2      51 ..      28      77 ..      27      78 .. 0.83
   3 !   12.2   0.6   0.00016      0.21       2      21 ..      64      83 ..      63      90 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00071
                            Fer4_7 33 idpekClgCga.......CvavCPtga 52
                                       d ++Cl C++       Cv+ CP+++
  gi|518651605|ref|YP_008141125.1| 23 KDVNTCLECTErfgepqpCVSICPANV 49
                                      36889****644444556******986 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.5e-06
                            Fer4_7  2 CigCg.......aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51
                                      C +C         Cv+ Cp++++++++        ++ i +e+C+ Cga   +CP++
  gi|518651605|ref|YP_008141125.1| 28 CLECTerfgepqPCVSICPANVFTWENN-------RIIIGYENCVECGASRIACPYD 77
                                      8888444555559************654.......699*****************86 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 0.00016
                            Fer4_7  2 CigCgaCvaaCpvkaielde 21
                                      C++Cga   aCp++ i++++
  gi|518651605|ref|YP_008141125.1| 64 CVECGASRIACPYDNIDWNY 83
                                      ****************9986 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.3    0.0026       3.3      44      65 .]      17      49 ..       1      49 [. 0.70
   2 !   10.0   0.1   0.00073      0.93       3      17 ..      62      76 ..      60      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0026
                            Fer4_8 44 e....eealwsCttcga.......CtevCpvgi 65
                                      +     + +++C++c +       C++ Cp ++
  gi|518651605|ref|YP_008141125.1| 17 KshlgIKDVNTCLECTErfgepqpCVSICPANV 49
                                      03333788999****999999*********986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00073
                            Fer4_8  3 ekCieCgaCqsaCpv 17
                                      e+C+eCga + aCp 
  gi|518651605|ref|YP_008141125.1| 62 ENCVECGASRIACPY 76
                                      79***********94 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   1.7   2.3e-05     0.029       6      22 .]      24      47 ..      20      47 .. 0.83
   2 !    6.7   2.6    0.0067       8.5       3      15 ..      57      69 ..      55      76 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                            Fer4_2  6 dtdrCigC....g...aCvsaCPa 22
                                      d ++C++C    g   +Cvs CPa
  gi|518651605|ref|YP_008141125.1| 24 DVNTCLECterfGepqPCVSICPA 47
                                      789*****66552788*******8 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0067
                            Fer4_2  3 vvvdtdrCigCga 15
                                      + +  ++C++Cga
  gi|518651605|ref|YP_008141125.1| 57 IIIGYENCVECGA 69
                                      678899*****94 PP

>> GF_recep_IV  Growth factor receptor domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   2.5   1.4e-05     0.018      71     115 ..      24      70 ..      11      80 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                       GF_recep_IV  71 gadeClkCah.fkdgseCvseCPegvkgeke..lifkyadaeevCekC 115
                                       + ++Cl+C++ f + + Cvs CP++v + ++  +i+ y +   +C   
  gi|518651605|ref|YP_008141125.1|  24 DVNTCLECTErFGEPQPCVSICPANVFTWENnrIIIGYEN-CVECGAS 70 
                                       5678****853778999********985444335555554.4444444 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.3    0.0011       1.4       3      16 ..      27      47 ..      25      49 .. 0.75
   2 ?    8.7   1.7    0.0021       2.7       1      16 [.      61      76 ..      61      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0011
                            Fer4_4  3 rCigCgs.......CvaaCPq 16
                                      +C++C         Cv++CP 
  gi|518651605|ref|YP_008141125.1| 27 TCLECTErfgepqpCVSICPA 47
                                      6877775566666*******7 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0021
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +e+C++Cg+ ++aCP+
  gi|518651605|ref|YP_008141125.1| 61 YENCVECGASRIACPY 76
                                      599*****99999997 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 ?    2.6   3.5       0.2   2.6e+02      58      67 .]      39      48 ..       2      48 .. 0.64
   2 ?    5.6   2.0     0.024        31       7      20 ..      40      53 ..      27      59 .. 0.79
   3 ?    8.1   0.1    0.0041       5.2       1      18 [.      63      80 ..      63      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                           Fer4_16 58 diCqdvCPan 67
                                      + C+ +CPan
  gi|518651605|ref|YP_008141125.1| 39 QPCVSICPAN 48
                                      4688888876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.024
                           Fer4_16  7 kCaevCPtnaikek 20
                                       C+++CP+n+++ +
  gi|518651605|ref|YP_008141125.1| 40 PCVSICPANVFTWE 53
                                      49999999988755 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0041
                           Fer4_16  1 rCgtCgkCaevCPtnaik 18
                                      +C++Cg+   +CP + i+
  gi|518651605|ref|YP_008141125.1| 63 NCVECGASRIACPYDNID 80
                                      6*************9997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   3.4   0.00075      0.96       6      23 ..      25      49 ..      23      50 .. 0.80
   2 ?    3.3   0.1     0.078        99       7      14 ..      62      69 ..      58      69 .. 0.86
   3 ?    1.1   0.0      0.39   4.9e+02      18      23 ..      73      78 ..      71      79 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00075
                            Fer4_6  6 pdkCigCgd.......CvrvCPega 23
                                       + C+ C +       Cv++CP+++
  gi|518651605|ref|YP_008141125.1| 25 VNTCLECTErfgepqpCVSICPANV 49
                                      5778888666888888*******97 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.078
                            Fer4_6  7 dkCigCgd 14
                                      ++C+ Cg+
  gi|518651605|ref|YP_008141125.1| 62 ENCVECGA 69
                                      79****95 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.39
                            Fer4_6 18 vCPega 23
                                      +CP++ 
  gi|518651605|ref|YP_008141125.1| 73 ACPYDN 78
                                      8**975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   1.3     0.037        47      40      60 ..      21      49 ..       2      50 .. 0.62
   2 ?    5.9   3.4     0.014        18      42      59 ..      60      77 ..      39      79 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.037
                           Fer4_17 40 e.ekaslCieCge.......CerkCPqgl 60
                                        + +++C+eC e       C++ CP+++
  gi|518651605|ref|YP_008141125.1| 21 GiKDVNTCLECTErfgepqpCVSICPANV 49
                                      24678889999755555555888888775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.014
                           Fer4_17 42 kaslCieCgeCerkCPqg 59
                                        ++C+eCg  + +CP++
  gi|518651605|ref|YP_008141125.1| 60 GYENCVECGASRIACPYD 77
                                      5689************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 ?    8.4   3.0    0.0036       4.6       1      13 [.      28      47 ..      28      49 .. 0.83
   2 ?    3.9   0.3     0.097   1.2e+02       1      11 [.      64      74 ..      64      78 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0036
                            Fer4_3  1 CtgCg.......aCvevCPv 13
                                      C+ C        +Cv  CP 
  gi|518651605|ref|YP_008141125.1| 28 CLECTerfgepqPCVSICPA 47
                                      9999667888888******6 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.097
                            Fer4_3  1 CtgCgaCvevC 11
                                      C+ Cga   +C
  gi|518651605|ref|YP_008141125.1| 64 CVECGASRIAC 74
                                      89998433344 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   4.3      0.56   7.2e+02      46      53 ..      40      47 ..      13      52 .. 0.60
   2 ?    9.9   0.6   0.00063      0.81       3      20 ..      59      76 ..      57      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.56
                           Fer4_21 46 lCssvCPv 53
                                       C+s+CP 
  gi|518651605|ref|YP_008141125.1| 40 PCVSICPA 47
                                      47777774 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00063
                           Fer4_21  3 idedkCigCgkCliaCed 20
                                      i  ++C++Cg   iaC+ 
  gi|518651605|ref|YP_008141125.1| 59 IGYENCVECGASRIACPY 76
                                      566889999999999983 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2       1.3   1.7e+03       4      11 ..      24      31 ..      22      33 .. 0.62
   2 ?    7.5   1.1     0.003       3.8      14      23 ..      41      50 ..      40      51 .. 0.89
   3 ?    5.8   4.2      0.01        13       2      23 ..      58      79 ..      57      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 1.3
                                      ETTTSSS- CS
                              Fer4  4 deekCigC 11
                                      d + C  C
  gi|518651605|ref|YP_008141125.1| 24 DVNTCLEC 31
                                      55666666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                                      HHHHSTTTEE CS
                              Fer4 14 CvevCPvgAI 23
                                      Cv++CP ++ 
  gi|518651605|ref|YP_008141125.1| 41 CVSICPANVF 50
                                      *******986 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.01
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                      +i +e C+ CGa   +CP++ I
  gi|518651605|ref|YP_008141125.1| 58 IIGYENCVECGASRIACPYDNI 79
                                      6789*******97777777755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 615.59
//
Query:       gi|518651606|ref|YP_008141126.1|  [L=397]
Description: hypothetical protein FACI_IFERC00001G0245 [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   38.9   0.5    1.3e-06   28.2   0.4    2.2  2  DAO             FAD dependent oxidoreductase
    1.3e-09   37.9   0.1    1.8e-09   37.5   0.1    1.2  1  FAD_oxidored    FAD dependent oxidoreductase
    5.7e-08   31.9   2.8    1.4e-07   30.6   0.7    2.1  2  HI0933_like     HI0933-like protein
    9.8e-08   31.5   1.2    1.6e-07   30.8   1.2    1.3  1  FAD_binding_2   FAD binding domain
    1.5e-07   30.9   1.5    3.8e-07   29.6   0.4    2.0  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.3e-07   29.3   0.0    1.4e-06   28.5   0.0    1.5  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.5e-06   26.1   0.2    0.00016   21.0   0.2    2.6  1  FAD_binding_3   FAD binding domain
    6.2e-05   22.3   0.1     0.0001   21.7   0.1    1.3  1  Thi4            Thi4 family
    6.9e-05   22.1   1.3    0.00014   21.1   0.2    1.9  2  GIDA            Glucose inhibited division protein A
    0.00013   21.4   0.7    0.00036   19.9   0.5    1.8  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    0.00047   19.3   0.1     0.0023   17.0   0.1    1.8  2  Lycopene_cycl   Lycopene cyclase protein
    0.00054   20.5   0.2     0.0018   18.8   0.1    1.9  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
     0.0024   16.8   0.0       0.35    9.7   0.1    2.3  2  Trp_halogenase  Tryptophan halogenase
  ------ inclusion threshold ------
      0.082   13.5   0.3       0.25   12.0   0.1    1.9  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
       0.15   10.5   0.0       0.22    9.9   0.0    1.2  1  DUF515          Protein of unknown function (DUF515)


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 !   28.2   0.4   1.1e-09   1.3e-06       1      38 [.       5      45 ..       5      95 .. 0.87
   2 !    9.1   0.0   0.00075       0.9     147     210 ..      97     157 ..      85     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTS.SGGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiags.gaSg 38
                                      d+vi+G+G +G+++A+ +a +g  V+++e+g+++gs   Sg
  gi|518651606|ref|YP_008141126.1|  5 DIVIVGAGPAGSAAALKAASEGkkVLVIERGPEPGSkNVSG 45
                                      9******************9999********9999545554 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00075
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHHHHHTT CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsdllgll 210
                                       kl ++l +  e++G++i+ +t++ +l+ e+g ++ +  tt+ g + aa+  V+a G+ + l+ + 
  gi|518651606|ref|YP_008141126.1|  97 KLDKWLSSVSEQAGATIIPKTTALKLNWENGIAKSL--TTDrGDV-AAKSFVLAEGVNA-LVSMN 157
                                       56678888899***************8887777777..8888986.7799******997.33333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.1   1.5e-12   1.8e-09       1     139 [.       5     144 ..       5     164 .. 0.63

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.5e-12
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee.qvvtgiareflerlrqrggarlk 76 
                                       D+v+vG+gpaG aAA+ Aa +G+kvl++e+ +  G    sg+   + + ++ + +  +  +++ ++ ++    +   
  gi|518651606|ref|YP_008141126.1|   5 DIVIVGAGPAGSAAALKAASEGKKVLVIERGPEPGSKNVSGA--EVRKDYITSvFGEGMPYERTVDTMKL-SLY--- 75 
                                       9********************************998777766..33333333323444444444444433.111... PP

                      FAD_oxidored  77 krskw.n.tfepevakav....leeml....aeagvtvllntrlvevekegkriesvtveskegrktirAkvf 139
                                       ++ k+ n  f+pe + ++    l+++l    ++ag t++ +t++ + + e++  +s+t+     r  ++Ak f
  gi|518651606|ref|YP_008141126.1|  76 EKDKPvNiDFHPEGLVTTgrlkLDKWLssvsEQAGATIIPKTTALKLNWENGIAKSLTTD----RGDVAAKSF 144
                                       112221122444444333222255555666666777777777777777776455666663....555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.7   1.2e-10   1.4e-07       1      38 [.       4      41 ..       4      46 .. 0.94
   2 ?    0.9   0.1      0.12   1.4e+02     117     169 ..     104     155 ..      97     175 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 1.2e-10
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HH CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrK 38
                                      +d++++G+G+AG  aA++aa++gk+Vl++e+++++g+K
  gi|518651606|ref|YP_008141126.1|  4 YDIVIVGAGPAGSAAALKAASEGKKVLVIERGPEPGSK 41
                                      589*********************************99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.12
                                       HHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS-GG CS
                       HI0933_like 117 kelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlSiPk 169
                                       +  ++ag ++  +t+  +++ e++ + +++t +++ ++a++ vlA G +++ +
  gi|518651606|ref|YP_008141126.1| 104 SVSEQAGATIIPKTTALKLNWENGIAKSLTT-DRGDVAAKSFVLAEGVNALVS 155
                                       3445688899999999999888888888888.999**********99877655 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.2   1.4e-10   1.6e-07       1      36 [.       5      40 ..       5      46 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.4e-10
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      D++++G+G AG aAAl+aa +G+kv+v+e ++e g+
  gi|518651606|ref|YP_008141126.1|  5 DIVIVGAGPAGSAAALKAASEGKKVLVIERGPEPGS 40
                                      99*****************************99776 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 !   29.6   0.4   3.2e-10   3.8e-07       1     112 [.       4     153 ..       4     176 .. 0.63
   2 ?   -1.0   0.0      0.68   8.2e+02     268     278 ..     279     289 ..     266     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.2e-10
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE.......................TTHCHHHCSHHHHCHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve.......................legtclnggcllskallgvaedae 54 
                                       +d+v++G+GpAG aaal++a  g kv+++e                        ++ +++++ +             
  gi|518651606|ref|YP_008141126.1|   4 YDIVIVGAGPAGSAAALKAASEGKKVLVIErgpepgsknvsgaevrkdyitsvFGEGMPYERTVD------------ 68 
                                       69***************************655554444444444444444444444444444444............ PP

                                       HHH..................................HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEE CS
                                       xxx..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  55 ias..................................evvkklnqgielllgeevvkidpgkkkvklekkkegdeek 97 
                                         +                                   v  + ++g + + +++++k+  +++  k  ++++    +
  gi|518651606|ref|YP_008141126.1|  69 --TmklslyekdkpvnidfhpeglvttgrlkldkwlsSV--SEQAGATIIPKTTALKLNWENGIAKSLTTDR---GD 138
                                       ..1444444444444457888888888887777765422..2334455555555666666665555544443...45 PP

                                       EEESEEEE---EEE- CS
                                       xxxxxxxxxxxxxxx RF
                       Pyr_redox_2  98 iaydklvlAtGsspr 112
                                       +a+++ vlA G ++ 
  gi|518651606|ref|YP_008141126.1| 139 VAAKSFVLAEGVNAL 153
                                       899999999887665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.68
                                       STTEEE-GGGC CS
                                       xxxxxxxxxxx RF
                       Pyr_redox_2 268 vpgiyaiGDva 278
                                         ++y++GD +
  gi|518651606|ref|YP_008141126.1| 279 KGNVYLCGDAI 289
                                       579******87 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   1.1e-09   1.4e-06       1      33 [.       8      40 ..       8      71 .. 0.77

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33
                                      IvGaG +G++aA  +a +g++vl++e+++ +G 
  gi|518651606|ref|YP_008141126.1|  8 IVGAGPAGSAAALKAASEGKKVLVIERGPEPGS 40
                                      9******************************93 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2   1.4e-07   0.00016       1      35 [.       3      37 ..       3     309 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                                      EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrst 35
                                      e+d++IVGaGpaG  +al  ++ G +v+++e+  +
  gi|518651606|ref|YP_008141126.1|  3 EYDIVIVGAGPAGSAAALKAASEGKKVLVIERGPE 37
                                      5799***************************9765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   8.4e-08    0.0001      16      57 ..       2      42 ..       1      55 [. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 8.4e-08
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                       e D+vivGaG++G +aa   a + + kv+++er   pG   
  gi|518651606|ref|YP_008141126.1|  2 LEYDIVIVGAGPAGSAAALKAASE-GKKVLVIERGPEPGSKN 42
                                      589*****************9999.********988777655 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.2   1.2e-07   0.00014       1      28 [.       5      32 ..       5      54 .. 0.89
   2 ?   -1.1   0.1      0.64   7.6e+02     357     389 ..     281     319 ..     277     322 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.2e-07
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      d++++G+G AG++AAl+aa  G kvl i
  gi|518651606|ref|YP_008141126.1|  5 DIVIVGAGPAGSAAALKAASEGKKVLVI 32
                                      79***********************998 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.64
                                       TEEE-CGGGT.....B.-SHHHHHHHHHHHHHHHHHHHC CS
                              GIDA 357 gLflAGqinG.....t.eGYeEaaaqGllAGinaarkak 389
                                       +++l+G+  G     t  G + a+a+G+lAG  a+ +++
  gi|518651606|ref|YP_008141126.1| 281 NVYLCGDAIGlvdplTfDGITPAIASGTLAGEAAVMNYD 319
                                       566666666633333235888999*******99987765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.5     3e-07   0.00036       1      30 [.       7      35 ..       7      42 .. 0.92
   2 ?   -2.5   0.0         2   2.4e+03     114     133 ..     130     149 ..      94     152 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3e-07
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkg 30
                                      +I+GaGPaG aaa+++   g  ++l++E+g
  gi|518651606|ref|YP_008141126.1|  7 VIVGAGPAGSAAALKAASEGK-KVLVIERG 35
                                      7*******************9.7******9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2
                       Pyr_redox_3 114 fevetsketyeAkkviiAtG 133
                                        +++t+++++ Ak+ ++A G
  gi|518651606|ref|YP_008141126.1| 130 KSLTTDRGDVAAKSFVLAEG 149
                                       67899999999999999998 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   1.9e-06    0.0023       1      36 [.       5      38 ..       5      52 .. 0.92
   2 ?   -0.2   0.0      0.33   3.9e+02     234     281 ..     258     305 ..     229     348 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.9e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      D+v++GaGpAg + A +   a  g kv++ie +p++
  gi|518651606|ref|YP_008141126.1|  5 DIVIVGAGPAGSAAALKA--ASEGKKVLVIERGPEP 38
                                      9************99999..99***********987 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.33
                     Lycopene_cycl 234 evveeEqgviPvtlggslprleqk..vlaiGaaaglvhPaTGYsvarsla 281
                                       +  e    viP   gg+++   +k  v+  G a glv P T   +  ++a
  gi|518651606|ref|YP_008141126.1| 258 SLREYSAKVIPE--GGFPETNVAKgnVYLCGDAIGLVDPLTFDGITPAIA 305
                                       555556679999..999988888777999*********998555555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.5e-06    0.0018       2      41 ..       6      47 ..       5      62 .. 0.84
   2 ?   -2.7   0.0       7.8   9.3e+03      45      67 ..     101     123 ..      97     135 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.5e-06
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS..TTSSHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll..rllDee 41
                                      +v+vG+G  g  +A  +a  gkkV v+er++++   ++ ++e
  gi|518651606|ref|YP_008141126.1|  6 IVIVGAGPAGSAAALKAASEGKKVLVIERGPEPGskNVSGAE 47
                                      8*******************************9964444554 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.8
                                       HHHHHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox  45 ilqeklekngievllntkveeie 67 
                                       +l    e+ g +++ +t++ +++
  gi|518651606|ref|YP_008141126.1| 101 WLSSVSEQAGATIIPKTTALKLN 123
                                       55555566799999999988887 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00029      0.35       1      32 [.       5      33 ..       5      40 .. 0.79
   2 ?    4.4   0.0     0.011        13     155     336 ..      97     300 ..      92     309 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      +ivivG+G+aG+ aA   a  +    +v+++e
  gi|518651606|ref|YP_008141126.1|  5 DIVIVGAGPAGSAAALKAASEG---KKVLVIE 33
                                      69*********98877666666...5688877 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHCT-EEEE--EEEEEE-T.TS-EEEEEETTS-EEE-SEEEE-SGGG-IIIIIIT---EEE-TTT-- CS
                    Trp_halogenase 155 lyakfLrrvaearGvtrvegkvvevqlde.dgrveslrledgreveadlfiDcsGfrgllieqaLktgfedwsdvLl 230
                                       +++k+L  v+e++G t++  +    +l+  +g  +sl+++ g  v a  f+ + G ++l+  +   +   dw+ +  
  gi|518651606|ref|YP_008141126.1|  97 KLDKWLSSVSEQAGATIIPKTT-ALKLNWeNGIAKSLTTDRGD-VAAKSFVLAEGVNALVSMNS--GINVDWTPSNS 169
                                       6788899999999999888766.55555548888888887777.77777788899888886554..44445544432 PP

                                       --.EEEEEEEE--H---SSEEEEE-SSEEEEEEEETTEEEEEEEE-TTTS.................-HHHHHHHHH CS
                    Trp_halogenase 231 td.rAlavqveseelvepytrataekaGWtWkiPLqhrlgnGyvyssaha.................dddeAlaell 289
                                       +    ++ +++ ++ ++   +   ++ G  W++ +++ l +G+ y  +                     +  l+++l
  gi|518651606|ref|YP_008141126.1| 170 VQaVKMVYSIK-KGDLNNIFGFPDDDTGMSWRMIMSDPLVAGFMYTYKDSlavgigspikelvdrkiRPEALLDKFL 245
                                       22022333333.33566666777788899999999999999988877766456555555555544433333334444 PP

                                       HHCT--TTTS-EEEE---EE........ES-SEETTEEE-CCCTEE--CCCS-HH CS
                    Trp_halogenase 290 aeldgkleaeprkirfttGr........rkqawvknvvalGlasgfvePlestsi 336
                                       ++ + + + +   +r  + +        ++++ + nv + G+a g v+Pl   +i
  gi|518651606|ref|YP_008141126.1| 246 ETTGIAEKVKGYSLREYSAKvipeggfpETNVAKGNVYLCGDAIGLVDPLTFDGI 300
                                       4444444444444444444488888888888889999999999999999876655 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.25       2      38 ..       6      38 ..       5      51 .. 0.90
   2 ?   -2.9   0.0         9   1.1e+04       9      31 ..     357     380 ..     357     384 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCC CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpek 38
                                      i i+GaG  g+a a++++++g   ++++v+ +r pe 
  gi|518651606|ref|YP_008141126.1|  6 IVIVGAGPAGSAAALKAASEG---KKVLVI-ERGPEP 38
                                      8899*****************...****99.999985 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHTTS.-GGCEEEE CS
                     F420_oxidored   9 nmgealasgllaaga.qpheivva 31 
                                       nm ++l++g++a +    ++ +v+
  gi|518651606|ref|YP_008141126.1| 357 NMVSSLLEGWAAGDLiGIRNTMVG 380
                                       799999999998875545555555 PP

>> DUF515  Protein of unknown function (DUF515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00018      0.22     193     242 ..     313     363 ..     308     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
                            DUF515 193 kyllsldkkyYllkldkipt.sdvilekngekslitkdevkkiiksvgsls 242
                                         ++  dk++Y ++l k p  s++  e+  e+ ++t +++ ++i++v sl 
  gi|518651606|ref|YP_008141126.1| 313 AAVMNYDKEVYRYNLMKHPEiSKIAKERKLESDFMTSNKAGEYINMVSSLL 363
                                       567789*************74677788999*****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2874.56
//
Query:       gi|518651607|ref|YP_008141127.1|  [L=608]
Description: hypothetical protein FACI_IFERC00001G0246 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.1e-76  255.3   0.0    1.6e-40  138.9   0.0    2.2  2  ETF        Electron transfer flavoprotein domain
      2e-32  111.0   0.7    4.4e-32  110.0   0.7    1.6  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
  ------ inclusion threshold ------
       0.18   11.5   0.4         11    5.7   0.1    2.6  3  LDB19      Arrestin_N terminal like


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.9   0.0   2.7e-44   1.6e-40       3     171 ..      27     196 ..      25     213 .. 0.90
   2 !  114.3   0.0   9.8e-37   5.8e-33       1     174 [.     288     459 ..     288     475 .. 0.89

  Alignments for each domain:
  == domain 1  score: 138.9 bits;  conditional E-value: 2.7e-44
                                       EEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHH CS
                               ETF   3 vlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatak 79 
                                        l+++gv++++np dl+a+e+A+rlkek gg+v+ v++Gpp+ + +lre +a mGad+v+lv+d+a+ g+d++at++
  gi|518651607|ref|YP_008141127.1|  27 NLVREGVPAIINPPDLHAIEEALRLKEKYGGTVSIVSMGPPKGDITLRESVA-MGADNVYLVTDAAMVGSDTWATSY 102
                                       68999***********************99**********************.************************ PP

                                       HHHHHHHHC.--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESE.EEEETCC..EEEEEECCCCTEEEEEE-TS CS
                               ETF  80 alaalikke.dpdlvlagatai.g..kqvaprlAalLgvplitdvte.leveggk..ltvtRpieggnglaevvead 149
                                       +++  i+k+ +pd++l+g++a  g  +qv+p++A +Lg+p +++  + ++++ ++  ++++R +e    + e+ve++
  gi|518651607|ref|YP_008141127.1| 103 TISRSIEKIgKPDIILFGRRALdGetQQVGPQTAMWLGIPEVAYTDKiIDIDMETkiARLQRTTEF--DT-ETVEVK 176
                                       *********99***********99********************9996555655578999999998..77.****** PP

                                       SSEEEEE-TTSS----S-TT-- CS
                               ETF 150 lpavltvrpgafepaaimaakk 171
                                       +p v+t++++++ p++  a+ +
  gi|518651607|ref|YP_008141127.1| 177 MPFVATITENSNSPRE--ATLE 196
                                       **************33..3333 PP

  == domain 2  score: 114.3 bits;  conditional E-value: 9.8e-37
                                       EEEEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHH CS
                               ETF   1 vlvlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeat 77 
                                       ++v+++h  dg+ln+ +le l+aArr+++ + +++ a+++G+   e+ + ea + +Gad++++ +++  + yd + +
  gi|518651607|ref|YP_008141127.1| 288 IWVYIDHF-DGELNKTSLEILGAARRVADLMSTKLGAIIIGT-GDENLIDEAFK-YGADEAYYCETDNAKRYDNDIY 361
                                       599****7.********************777**********.66666777777.********************** PP

                                       HHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCC.EEEEEECCCCTEEEEEE-T.SSSE CS
                               ETF  78 akalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggk.ltvtRpieggnglaevvea.dlpa 152
                                       ++al  +i+k++p+  +++ t   +++a+ +A + +++li+d++ ++v++++ l++tRp +gg+ ++++ ++ ++p+
  gi|518651607|ref|YP_008141127.1| 362 TQALGMMINKYKPNSLFFPGTYNSRELAATTAIKVNTGLIADCIIFDVDEKGqLQATRPDFGGKETSTIICPnNKPV 438
                                       ************************************************75557************************ PP

                                       EEEE-TTSS----S-TT---EE CS
                               ETF 153 vltvrpgafepaaimaakkkev 174
                                       ++t+r+g+f +++++  k ++v
  gi|518651607|ref|YP_008141127.1| 439 MVTTRAGVFSALPERDFK-GKV 459
                                       ***********6544433.333 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.7   7.3e-36   4.4e-32       3      84 .]     485     566 ..     483     566 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 7.3e-36
                                       TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHG CS
                         ETF_alpha   3 LeeakvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhla 79 
                                       L+ a+vvv++GrG+ +k+n++l+e+la+++g+ vg+s++++d++w+p++rqvGqtG+t++P+lyia+GisGaiqhl+
  gi|518651607|ref|YP_008141127.1| 485 LAAAQVVVGVGRGIVNKDNIKLAEDLAKKIGGIVGVSKPLADSDWYPKDRQVGQTGTTIKPNLYIAMGISGAIQHLV 561
                                       899************************************************************************** PP

                                       GGTT- CS
                         ETF_alpha  80 Gmkes 84 
                                       G++ s
  gi|518651607|ref|YP_008141127.1| 562 GIQGS 566
                                       **987 PP

>> LDB19  Arrestin_N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0018        11     111     152 ..       4      45 ..       1      51 [. 0.86
   2 ?   -3.3   0.0         1     6e+03      75      97 ..     172     194 ..     163     217 .. 0.64
   3 ?    3.1   0.0     0.012        69      30      91 ..     350     409 ..     341     444 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0018
                             LDB19 111 ikvkravlrgPdknslrvfPPtelvatavlPsvvyPksafpl 152
                                       i++  +v + Pd   lr+ P t+   +  +P+++ P     +
  gi|518651607|ref|YP_008141127.1|   4 INIVVSVKQVPDADDLRIDPVTNNLVREGVPAIINPPDLHAI 45 
                                       788899*****************9999999***999765555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
                             LDB19  75 etkvkyeliavvvykdptprkga 97 
                                       +++vk  ++a+++   + pr+ +
  gi|518651607|ref|YP_008141127.1| 172 TVEVKMPFVATITENSNSPREAT 194
                                       45566666666666555555443 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.012
                             LDB19  30 tkteelksWdlqkntkdlkvGsysy.PfsylipGslpassslgsnaetkvkyeliavvvykdp 91 
                                       t   +    d+ +  + l + +++y P s ++pG+ ++  +l +++ +kv+  lia  +  d 
  gi|518651607|ref|YP_008141127.1| 350 TDNAKRYDNDIYT--QALGMMINKYkPNSLFFPGTYNSR-ELAATTAIKVNTGLIADCIIFDV 409
                                       4444333444444..4444445555499******99865.679************97666564 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 4250.86
//
Query:       gi|518651608|ref|YP_008141128.1|  [L=246]
Description: hypothetical protein FACI_IFERC00001G0247 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        5.5    6.6  15.0       0.47   10.1   0.8    2.2  2  Tetraspanin      Tetraspanin family
        6.2    6.4   8.3       0.82    9.2   1.7    2.2  2  Saf_2TM          SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   5.2e-05      0.47      10      98 ..       6      99 ..       4     112 .. 0.80
   2 ?    1.3   7.4     0.027   2.4e+02       9     106 ..     145     237 ..     138     246 .] 0.49

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 5.2e-05
                                      XXXXXXXXXXXXXX..XXXXX...XXX.....................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxx..xxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 10 llfwligivllavG..vwlrl...khaeaalacllsesaedpailaillivvGvllfllgflGcigalkenkcllltfs 83
                                      l+++++gi+++  G  ++ ++      e+ ++ +++++a   ++l  +++++G+l++ +++  +i ++     l  ++ 
  gi|518651608|ref|YP_008141128.1|  6 LILFMVGIIIILNGyeLYSKFgylFYPESYNYLASASTARLYTSLDDIIFILGALFIGISIYMFIKSRYSIPKLKHFYP 84
                                      678888999998886666666999555566666777888889999999******************9999999999999 PP

                                      XXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxx RF
                       Tetraspanin 84 llllvlfllelaagi 98
                                      +l +  ++l++  g+
  gi|518651608|ref|YP_008141128.1| 85 ILAIYTIILMVEGGM 99
                                      998888888876555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.027
                                       XXX.XXXXXXXXXXXXXXXXXXXX.....................XXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   9 nll.fwligivllavGvwlrlkhaeaalacllsesaedpailaillivvGv.llfllgflGcigalkenkcllltfs 83 
                                       +l+   ++g  ++a++++ + k ++a+  +l  +  ++      +  ++G  + +++g   ++ ++  n++   tf+
  gi|518651608|ref|YP_008141128.1| 145 SLIgASILGSSIFAFSIMGL-KLKKATPLSLVGAIGVC------PACATGTfFGLVIGASPFLSSFYLNQIYGSTFN 214
                                       33334455555555554441.22222222222222222......233344434444455558888888999999999 PP

                                       .XXXXXXXXXXXXXXXXXX--HHH CS
                                       .xxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  84 .llllvlfllelaagilgfvfsdk 106
                                        ++l v+ +++l +gi++++ ++ 
  gi|518651608|ref|YP_008141128.1| 215 eIILSVISIALL-LGIFLYMIRKN 237
                                       555555555544.56655555443 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7   9.2e-05      0.82      19      89 ..       2      72 ..       1     100 [. 0.91
   2 ?    0.9   0.6     0.034     3e+02      60      94 ..     205     237 ..     188     244 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 9.2e-05
                           Saf_2TM 19 rsaelllftigvalllailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGavllilr 89
                                      +++ l+lf +g+ ++l+++     + +++  ++++  +s s++     ++ ii+++g l+i +++++ i+ 
  gi|518651608|ref|YP_008141128.1|  2 KNKSLILFMVGIIIILNGYELYSKFGYLFYPESYNYLASASTARLYTSLDDIIFILGALFIGISIYMFIKS 72
                                      677789**************************************999*****************9998865 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.034
                           Saf_2TM  60 sse.ipeivlaiilvigvllivvGavllilryvnea 94 
                                        ++   + ++ iil + ++ +++G++l ++r    +
  gi|518651608|ref|YP_008141128.1| 205 LNQiYGSTFNEIILSVISIALLLGIFLYMIRK---N 237
                                       55545566777888888888889988888876...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1720.48
//
Query:       gi|518651609|ref|YP_008141129.1|  [L=141]
Description: CBS protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   63.6   0.3    1.3e-09   38.3   0.2    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 !   23.4   0.0   3.3e-09   5.9e-05       2      56 ..       6      59 ..       5      60 .. 0.92
   2 !   38.3   0.2   7.3e-14   1.3e-09       1      54 [.      68     122 ..      68     124 .. 0.92

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.3e-09
                                      HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56
                                      + im + + +++  +t+ + +++m+e++ ++l  + + +   Givt+rD+++a++
  gi|518651609|ref|YP_008141129.1|  6 SNIMQKHPAYIDGASTIYDGAKKMTEENKGSL-LLGSAESMKGIVTERDIIKAIA 59
                                      679*********************99998999.887788899***********97 PP

  == domain 2  score: 38.3 bits;  conditional E-value: 7.3e-14
                                       HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHHHHHHH CS
                               CBS   1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVV.dedgklvGivtlrDllra 54 
                                       Vgd+ t+ ++++v++d+++ +a+ lm ++++++l +V  e+g + G+++ rDl+r 
  gi|518651609|ref|YP_008141129.1|  68 VGDVATKeNLIFVHEDDSITKAAVLMSKHNIRHL-IVkSENGAVTGVLSTRDLMRE 122
                                       7899666699****************9999****.99888999**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1003.00
//
Query:       gi|518651610|ref|YP_008141130.1|  [L=374]
Description: hypothetical protein FACI_IFERC00001G0249 [Ferroplasma acidarmanus fer1]
Scores for 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-111  370.4   0.0     1e-110  370.2   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.2   0.0  5.8e-115    1e-110       1     361 []       6     356 ..       6     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 370.2 bits;  conditional E-value: 5.8e-115
                                       GGTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHH CS
                      Citrate_synt   1 glrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlea 77 
                                       gl++v +  t ++++dg++g lrYRGydi++L+ ++  feev+yl+ +gelP++++l+efk++++e+ klp++v+e 
  gi|518651610|ref|YP_008141130.1|   6 GLEDVFIKYTGLTFIDGNAGVLRYRGYDINDLV-QNTGFEEVCYLMTNGELPNSQQLAEFKKSVKEHYKLPDHVMEL 81 
                                       6788889999***********************.8****************************************** PP

                                       HHCSSTTS-HHHHHHHHHHHHHHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.--.---TTSSHHH CS
                      Citrate_synt  78 lealpkdahpmavlraavsalsaddeeseakeeseeaalrdalkliAklptiaaaiyrarlgrepl.epddklsyae 153
                                       +  lp++a+ ++++ +a+++ls+ d + +++++ ++++ +    ++++   i+ +iyr++ g   l +pd+k +yae
  gi|518651610|ref|YP_008141130.1|  82 ISDLPREADTLTMMETAFASLSSGDYQWNKEND-RKQVPK----ILGENLGIISNIYRHKMGM-GLqNPDPKYDYAE 152
                                       **********************99865554444.444555....*****************96.56589999***** PP

                                       HHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHHTTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
                      Citrate_synt 154 nflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvvaStladlysaiaagigalkGplhgganeavlkmlee 230
                                        fl+ ++g ++de+ + ++++alv+++DHe+ aST aa v++Stl+d+ys+i+a+ +alkGplhgga ea++k l +
  gi|518651610|ref|YP_008141130.1| 153 AFLRNCFG-NADEKKISAMNAALVIYVDHEVPASTTAALVASSTLSDMYSCITAATAALKGPLHGGAAEAAYKQLLD 228
                                       ********.99****************************************************************** PP

                                       HSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHHHHHHHHHHHHHCHHG CS
                      Citrate_synt 231 igsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklaeeleevapevlkekee 307
                                       ig+ + +ve++ ++++  +k+rl+GfGHrvy+++DpR ki+k+la++l ++ ++++l+++a +lee+  +  ++   
  gi|518651610|ref|YP_008141130.1| 229 IGNVD-NVENWFKTNILDGKRRLMGFGHRVYRTYDPRMKIFKKLATTLEQTDEQKKLFEIAVKLEELGVK--EFGG- 301
                                       ****9.*******9999999****************************9999***************999..6778. PP

                                       CT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH.HT------E CS
                      Citrate_synt 308 knlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql.adnkiiRPr 361
                                       k++ypN D+ysg++++ +g+p  +ft+lf++sRv+Gwl+hi e+  +++++iRPr
  gi|518651610|ref|YP_008141130.1| 302 KGIYPNTDYYSGIVFNEIGFPIYMFTTLFGFSRVLGWLSHITEYVeEEERLIRPR 356
                                       *******************************************98788******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2687.78
//
Query:       gi|518651611|ref|YP_008141131.1|  [L=557]
Description: hypothetical protein FACI_IFERC00001G0250 [Ferroplasma acidarmanus fer1]
Scores for complete 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-102  342.0   0.0   5.2e-102  341.6   0.0    1.2  1  AMP-binding      AMP-binding enzyme
    2.4e-22   79.7   0.7    4.7e-22   78.7   0.7    1.5  1  AMP-binding_C    AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.13   12.6   0.1       0.26   11.6   0.1    1.5  1  AMP-binding_C_2  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  341.6   0.0  8.7e-106  5.2e-102       3     421 ..      35     462 ..      33     464 .. 0.90

  Alignments for each domain:
  == domain 1  score: 341.6 bits;  conditional E-value: 8.7e-106
                                       HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEET CS
                       AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnp 79 
                                       ++a k+  +va+ +   g++++Y+ l+++++++A++L+ l++ kgd+  i+lpn p++v+ ++a +k+G+ vv +np
  gi|518651611|ref|YP_008141131.1|  35 RSASKYASHVAIDF--MGNRISYSRLKQEIESAASFLKGLNLHKGDKLTIMLPNIPQYVIFFFASMKLGISVVQMNP 109
                                       789999******88..99*********************************************************** PP

                                       TS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS........ CS
                       AMP-binding  80 tltaeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae........ 148
                                        +  +e++y l+ds+++ ++  v ++ l+k+l+ ++k  +  + + +++  ++ ++ l+++ ++ ++++        
  gi|518651611|ref|YP_008141131.1| 110 MYMLPEIEYELNDSGSRNIV--VMHDMLSKVLPLKEKMLDNIIDVRVEDYLPPVKALLYKAVKKGKSEKlaapagii 184
                                       ********************..8877888888888887777777777777777777777777666665356788999 PP

                                       .........-TSCCCS-BT.TSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH..HHHCSCCTTT-EEEESS-TTS CS
                       AMP-binding 149 .........kpeeeeelkp.ddlayiiYTSGTTGkPKGVmlshrnlvanvaslk..letrfklkeddvvlsilplah 213
                                                   ++e+++p +d a+++YT+GTTG PK++ l+hrnl+anv +l   ++  +++ke+  +ls  p++h
  gi|518651611|ref|YP_008141131.1| 185 pysgksrnpAA-DDESIDPyNDAALLQYTGGTTGVPKAATLTHRNLLANVNQLIewFP--EDFKESISYLSSIPFFH 258
                                       99***999633.44456667******************************99855444..3356899********** PP

                                       CHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 214 ifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvll 290
                                       ++g+++++l++l++G+t++ +p    +d k+ l+ i+k k+t ++g+P++++ +++ ++l+    ++d s ++l+++
  gi|518651611|ref|YP_008141131.1| 259 VYGMMTAMLTPLMQGSTIIPVPDP--RDLKMTLNIIKKKKPTAFPGIPTMYHSIINYPDLE----KYDISNIKLCIS 329
                                       ******************999944..4566889***********************98888....669********* PP

                                       ESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEE...CHCTTTCTSTTS-BEE-TTEEEEEE-TTTS.CBEETTS CS
                       AMP-binding 291 ggeplspellrffralfgeevlegYGlTEttgvvtv...lpleedkkklgsvGkplpgvevkivDeetg.epvpdge 363
                                       g+ pl+ el+++f+ ++g++++egYGl+E+++v+ +   lp+ ++++k+gs+G plp++  kivD ++g  +vp+g+
  gi|518651611|ref|YP_008141131.1| 330 GAMPLPLELQKKFEGKTGGTLVEGYGLSECSPVTNIsplLPEWKNRRKPGSIGLPLPETYEKIVDIDDGiTEVPQGV 406
                                       **********************************7778877778889*****************988663689**** PP

                                       EEEEEEEETTS-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEE CS
                       AMP-binding 364 eGellvrgpgvmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlik 421
                                       eGell++gp+vmkgY+++pe++++ ++  ++wl+TGD++++d +Gy++iv+Rkkd+i+
  gi|518651611|ref|YP_008141131.1| 407 EGELLIKGPQVMKGYWNRPEENKQILV--DGWLHTGDIAKMDSEGYFYIVDRKKDMII 462
                                       **************************9..57**************************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.7   7.9e-26   4.7e-22       1      76 []     472     546 ..     472     546 .. 0.95

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 7.9e-26
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrkelgpyavpkkvvfvdelpktrsGK 76 
                                       evE +l +hp+V+++aVvGvpd+ +Ge+++a++vl+d  + +e+e+k+++ ++l++y+vpk + f+d+lp+t  GK
  gi|518651611|ref|YP_008141131.1| 472 EVEKVLYEHPGVSQCAVVGVPDAHRGETVKAIIVLSDK-SVTEDEIKKYCQEKLAKYKVPKIIQFTDSLPLTPVGK 546
                                       8**********************************643.3479********************************9 PP

>> AMP-binding_C_2  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   4.4e-05      0.26       1      48 [.     465     512 ..     465     554 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.4e-05
                                       TEEE-HHHHHHHHHT-TTEEEEEEEEEEEETTEEEEEEEEEE-TT--- CS
                   AMP-binding_C_2   1 GvnvfPsqieevlkeieevepeYqivvtregelDelevkvEvkegfsd 48 
                                       G n++P ++e+vl e ++v++   + v + ++ ++++  + ++++ ++
  gi|518651611|ref|YP_008141131.1| 465 GYNIYPEEVEKVLYEHPGVSQCAVVGVPDAHRGETVKAIIVLSDKSVT 512
                                       89*****************99888888777777777766666664433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3725.55
//
Query:       gi|518651612|ref|YP_008141132.1|  [L=296]
Description: hypothetical protein FACI_IFERC00001G0251 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-42  146.3   0.1    1.7e-42  145.8   0.1    1.1  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.8   0.1   9.5e-47   1.7e-42       2     248 ..       6     255 ..       5     258 .. 0.89

  Alignments for each domain:
  == domain 1  score: 145.8 bits;  conditional E-value: 9.5e-47
                                       EEE-SSEEEEE-SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.......... CS
                       SAICAR_synt   2 lyeGKvrdvYeledddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksld...pe... 70 
                                       l +GKv+dvY+  d + l++ ++Dris+fd + +++ip+KG+ l+++s++w++ +++  i++ +i+ ++   ++   
  gi|518651612|ref|YP_008141132.1|   6 LRKGKVKDVYD--DGKDLVFKFSDRISVFDKIIPDSIPHKGESLCRTSTYWYNIVSSlgIDTDFIELVSdseMKvkk 80 
                                       679********..4668***************************************668******775554411444 PP

                                       ..-SSSEEEEE-EEEESEEEEEEEE--HHH........HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE- CS
                       SAICAR_synt  71 .qlegrsmlvkklkmlpvEvvvRgyltGslwkeykks.gkvcgirlpeglkegeklpepiftpstKaeegehDenis 145
                                        +  +r        m+p+E+++R yl+Gs++   k++   ++ + +++    geklp p f++stK e+   D  ++
  gi|518651612|ref|YP_008141132.1|  81 fRQIDRGYKFLSNYMVPLEFITRYYLAGSAYDRVKSGeIDYHSLGFKNPPVYGEKLPDPFFEVSTKFEKF--DRYLH 155
                                       533455555556678999************99999987889999999999*******************5..9**** PP

                                       HHHHH.HTT.-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEETTTTEEEEES--.STTTEEEEETTT.. CS
                       SAICAR_synt 146 eeevvealg.teeeaeeieelalavyekaaelaaergiilvDtKlEFGldeedgelvLaDevltpDssRfwdaetye 221
                                        +e++e+ g ++ e+ ei+e+ +++ +++++ +++rg+i +D K EF l   + + v++D + t D  Rfwd+++ye
  gi|518651612|ref|YP_008141132.1| 156 TDEALEISGlDAGELCEIQETIFKIDRRINSSVESRGLIHADGKKEFALGL-ERKPVIIDTFGTLDEDRFWDKKDYE 231
                                       *****9999*999************************************95.89*********************** PP

                                       ...GGGB-STHHHHTT-STHHHHHHHH CS
                       SAICAR_synt 222 egkeqeslDKqfvRdwleeveekwkek 248
                                       +g+  ++l K++vR++ ++  +++++k
  gi|518651612|ref|YP_008141132.1| 232 NGQV-NELSKEMVRQYYRK--TGYHQK 255
                                       8876.579********999..777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2079.07
//
Query:       gi|518651613|ref|YP_008141133.1|  [L=203]
Description: phosphoglycerate mutase [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.0      1e-34  119.9   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.9   0.0   5.7e-39     1e-34       1     192 [.       3     187 ..       3     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.9 bits;  conditional E-value: 5.7e-39
                                       EEEEE---BTTB--....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGG CS
                        His_Phos_1   1 lyLvRHGetewnaegrlqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegL 77 
                                       +y+vRHGet +na+  +    d++L+e+G eqA++++++l++  +da+ysSp  R +qT e ++     ++++d +L
  gi|518651613|ref|YP_008141133.1|   3 VYMVRHGETYNNAS-AVFPLDDTELNENGLEQARETGKYLEQLYFDAVYSSPVLRVKQTLENMGI---DRYITDNRL 75 
                                       69**********99.68899*****************************************9997...699****** PP

                                       S----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHH CS
                        His_Phos_1  78 rEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggviral 154
                                       r+i  G++ g++ +ei+++ p+++ +++++ ++    g E++ d+ +Rv++++  +  +  ++ vl+ +H  +ir +
  gi|518651613|ref|YP_008141133.1|  76 RDIGTGKLTGMKITEIESKDPAWYSTFQDGVEN--RYGVEKFSDLKKRVKEFIGSISGNGFKK-VLIATHLEPIRGM 149
                                       ****************************99984..678******************9999876.************* PP

                                       HHHHHT--GGGGGGB---TT-EEEEEE-SS-EEEEEEE CS
                        His_Phos_1 155 larllglpleelrrleldnaslsvlefdeggwrlvrln 192
                                       ++  +g++   l  le++n+s+s++++++   +l+ +n
  gi|518651613|ref|YP_008141133.1| 150 YSLSTGVEGLPLTSLEISNCSISIFSVEGFDIELKGFN 187
                                       ***************************99888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1439.02
//
Query:       gi|518651614|ref|YP_008141134.1|  [L=298]
Description: cysteine synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-50  172.1   0.0    2.5e-50  171.6   0.0    1.2  1  PALP        Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
      0.071   12.7   0.0        0.2   11.3   0.0    1.7  2  LDcluster4  SLOG cluster4 family


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 !  171.6   0.0   2.8e-54   2.5e-50       4     292 ..      15     280 ..      13     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 171.6 bits;  conditional E-value: 2.8e-54
                                       CSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH.HHTT..TTTSEEEEEBSSHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar.lkeg..tgaktvveassGNhgralAaaaall 77 
                                       gig+TPl ++          ++ KlE+ n + S+KdR+a +++ + lk g  ++ +t++eassGN+g+a+A +++ l
  gi|518651614|ref|YP_008141134.1|  15 GIGNTPLFKIGETG------IYSKLEYYNRFRSIKDRAAFFMIDYaLKSGelRSDQTIIEASSGNTGIAIAGISSIL 85 
                                       79*****9999866......*************************55555*************************** PP

                                       T-EEEEEEETTS-HHHHHHHHHTT-EEEEECCH.HHHHHHHHHHHHHH.STTCEE--TTTSHHHHHH.HHTHHHHHH CS
                              PALP  78 GlkvtivvpadaspekvallrllGaevvevggd.ydeavaaaaelaae.gegaylvsqfdnptvieg.ygtiglEil 151
                                       +lk +iv+p++a+ + ++ll ++G +vv ++g+ ++++ +++++++++  e++y +sq+ n  +  + y  +g+Ei 
  gi|518651614|ref|YP_008141134.1|  86 NLKNEIVIPESAPDATKKLLSSFGSRVVTTPGNsTENSINYVEDMIEKyPEKYYRLSQHANIMNSNAhYYGTGPEIN 162
                                       ******************************55549999*****99999999*************************9 PP

                                       HHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCS..CGT CS
                              PALP 152 eqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavg..sps 226
                                       e+l + +d +vv+vG+Gg+i+G+a+++ke+  +++v gv p++ + + + +                   ++  s+ 
  gi|518651614|ref|YP_008141134.1| 163 EKL-EHIDNLVVGVGTGGTITGLARYFKEKY-NINVTGVLPAEGSRIVGLR-------------------NPfkSNH 218
                                       999.6***********************965.59*****999555555555...................6777889 PP

                                       TCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE CS
                              PALP 227 elafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvvil 292
                                       +  ++ ++ l+d +vtvs+++a+e++r+l  +  ++v+pss+a++ a     a + ++g ++v+++
  gi|518651614|ref|YP_008141134.1| 219 RVLLDTYKSLIDNFVTVSEDDAYEGVRQLKAKYNLLVGPSSGANYMAS---LAISENKG-TTVTVF 280
                                       999************************************999999998...33333334.566665 PP

>> LDcluster4  SLOG cluster4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.37   3.3e+03     100     123 ..     171     194 ..     167     206 .. 0.60
   2 ?   11.3   0.0   2.2e-05       0.2      31      68 ..     248     285 ..     234     297 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.37
                        LDcluster4 100 viaiggrsGTlsEialaleegkpv 123
                                       +++  g+ GT++ +a  ++e+  +
  gi|518651614|ref|YP_008141134.1| 171 LVVGVGTGGTITGLARYFKEKYNI 194
                                       556666666666666555555444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.2e-05
                        LDcluster4  31 kegavlltGgrtGvmeaaskGakeagGltvGilpasse 68 
                                       k++++ll G  +G  ++as +++e++G+tv + p++  
  gi|518651614|ref|YP_008141134.1| 248 KAKYNLLVGPSSGANYMASLAISENKGTTVTVFPDDYY 285
                                       6789******************************9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.66u 0.38s 00:00:01.04 Elapsed: 00:00:00.59
# Mc/sec: 1511.58
//
Query:       gi|518651615|ref|YP_008141135.1|  [L=227]
Description: hypothetical protein FACI_IFERC00001G0254 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0015   18.8   0.3      0.003   17.8   0.3    1.4  1  DUF4181   Domain of unknown function (DUF4181)


Domain annotation for each model (and alignments):
>> DUF4181  Domain of unknown function (DUF4181)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.3   1.7e-07     0.003      34      89 ..     164     217 ..     148     217 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.7e-07
                           DUF4181  34 ielilrvlfiifiilsliiilsreyvdiiilifvflvvlelfRavmewkyereskr 89 
                                          +++++ i++i++s+   +  +y d ++++++++++++++R+   +ky++e k+
  gi|518651615|ref|YP_008141135.1| 164 LSNVIFLVAIVIIVFSTSLGIPGDY-D-FLILIIVIALSFVIRSAGRKKYQEEHKN 217
                                       4445555555555555555555555.3.3899999******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); 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):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1448.29
//
Query:       gi|518651616|ref|YP_008141136.1|  [L=515]
Description: hypothetical protein FACI_IFERC00001G0255 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   86.6   0.3    1.7e-24   85.6   0.3    1.5  1  Radical_SAM_C    Radical_SAM C-terminal domain
    5.7e-20   72.3   0.3    2.1e-19   70.5   0.0    2.1  3  Radical_SAM      Radical SAM superfamily
    6.5e-06   26.4   0.2      2e-05   24.8   0.1    1.9  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00023   21.1   0.0     0.0006   19.8   0.0    1.7  2  Acetyltransf_10  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Radical_SAM_C  Radical_SAM C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.3   3.8e-28   1.7e-24       1      81 [.     285     365 ..     285     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 3.8e-28
                     Radical_SAM_C   1 pdgvKlypllvikgTeLaelyksgeykplsleeyvdlvadilellppdirvhRltgdipkelliagpwhknlrelie 77 
                                       pd++K+yp+lv+k+T L++ +k+g+y p+++e++v++v+ +++ +pp++rv+R+++dip + + ag++++ l+ l++
  gi|518651616|ref|YP_008141136.1| 285 PDMLKIYPTLVVKNTALYKYWKEGKYIPYDTEKVVRMVTYFMKNMPPWVRVMRMQRDIPVNFIEAGVKRSDLHNLVD 361
                                       8**************************************************************************99 PP

                     Radical_SAM_C  78 krlk 81 
                                        +++
  gi|518651616|ref|YP_008141136.1| 362 LEME 365
                                       9997 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.86   3.9e+03      85     120 ..      13      53 ..       8      68 .. 0.69
   2 !   70.5   0.0   4.7e-23   2.1e-19       4     159 ..      77     269 ..      74     277 .. 0.89
   3 ?   -3.7   0.0         3   1.4e+04      34      55 ..     469     491 ..     468     491 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.86
                                       CSSCHG.....HHHHHHHHHTT-SEEEEEEBSSSHHHHHHH CS
                                       xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  85 ngtlpd.....eeklerllelgvdrvslgleaaddekvlkl 120
                                       ng   d     +ekl + ++ ++d+v  ++e++++ + ++ 
  gi|518651616|ref|YP_008141136.1|  13 NGKIKDkdqlqREKLLLSKKFNLDVVPSDVEILNYGDNRRF 53 
                                       55555566666899999999999999999999998844433 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 4.7e-23
                                       ESEESS-.-TTTSCCTT................HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTH CS
                                       xxxxxxx.xxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   4 trgCnlr.CsfCarpet................vrregrgrslsveeileevkelkaekgvkevilgggepllypdf 63 
                                        ++C+++ C+fC+ + +                +r++++  +    + l++++ + ++  +  +i++gg+ ++++++
  gi|518651616|ref|YP_008141136.1|  77 PEACPHGkCIFCPGGIDsnspqsytgyepsalrGRTNYYDSYNIAFSRLKQLETIGHDTSKVDLIVMGGTFTARSRE 153
                                       67899999********9****************666666666666666666666657877**************999 PP

                                       HHHHHHHHHTC..................CCTEEEEEEECSSCHG...HHHHHHHHHTT-SEEEEEEBSSSHHHHHH CS
                                       xxxxxxxxxxx..................xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  64 vellerlakla..................vpgiritvetngtlpd...eeklerllelgvdrvslgleaaddekvlk 119
                                       +++ +    ++                   + +r++  t +t+pd   e+ +++ l +g++ v+lg++ ++d+ +l+
  gi|518651616|ref|YP_008141136.1| 154 YQEEFVKGCIDgmnrkisptldqaileneFSQRRCVGMTIETKPDwfnEREIDEALSYGTTKVELGIQVLNDR-ILR 229
                                       9999999999999999999999999999*9999999999999999999*************************.*** PP

                                       HHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 120 lmnrghtfeevlealeklreagikrvvdrivglpGendee 159
                                       l++rgh++ee++++++++r+ag+k+ ++ ++g+ G + +e
  gi|518651616|ref|YP_008141136.1| 230 LNRRGHGVEEIVRSTQLARDAGLKVLYHLMPGMYGSSYKE 269
                                       ***********************************98865 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 3
                                       HHHHHHHHH.HHTTSEEEEEESS CS
                                       xxxxxxxxx.xxxxxxxxxxxxx RF
                       Radical_SAM  34 ileevkelk.aekgvkevilggg 55 
                                       +l+e+++++ +e g+k +i+ +g
  gi|518651616|ref|YP_008141136.1| 469 LLDEAERISlEEYGKKRIIVISG 491
                                       57889999989999666666554 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.8e+03      86     112 ..     205     231 ..     204     236 .. 0.82
   2 !   24.8   0.1   4.6e-09     2e-05      30     117 .]     401     503 ..     371     503 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                       HHHHHHTTESEEEEEEETTEHHHHHHH CS
                    Acetyltransf_1  86 eerareegikkivlaveedndaairlY 112
                                       +++a++ g +k++l +++ nd+  rl 
  gi|518651616|ref|YP_008141136.1| 205 IDEALSYGTTKVELGIQVLNDRILRLN 231
                                       578999999999**9999999888776 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 4.6e-09
                                       STTCEEEE.EEETTEEEEEEEEEEEETTSTTEEEEEEEEE................SGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  30 leaegllv.aeedgeliGfisllkipdekggvayieslaV................speyrgkGlGsaLlealeera 89 
                                         +e +l+  + +g +iG+++l++  +++ ++ ++ s ++                 ++++++G G++Ll+++e++ 
  gi|518651616|ref|YP_008141136.1| 401 GGDEIFLSfESSNGDIIGYLRLRIPSEMAHRKEVLSSSVIreikvmgnivpigeesGENWQHHGFGKKLLDEAERIS 477
                                       3444333357788**************55555555555557777799****************************** PP

                                       HHT.TESEE.EEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  90 ree.gikki.vlaveedndaairlYeklGF 117
                                       +ee g k+i v+    +  + +++++k G+
  gi|518651616|ref|YP_008141136.1| 478 LEEyGKKRIiVI----SGIGVRNYFRKYGY 503
                                       ***999998455....88888999977987 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       1.6   7.1e+03      31      49 ..     404     423 ..     384     430 .. 0.66
   2 !   19.8   0.0   1.3e-07    0.0006      62     111 ..     459     508 ..     457     513 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.6
                   Acetyltransf_10  31 alllvaeeg.gkivGvielr 49 
                                        ++l +e + g i+G+++lr
  gi|518651616|ref|YP_008141136.1| 404 EIFLSFESSnGDIIGYLRLR 423
                                       34444443348999999886 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.3e-07
                   Acetyltransf_10  62 eyrgqGigkaLleaveeeaekdgikleltvnaspyavpfYeklGFkavge 111
                                       ++++ G gk+Ll+++e+   ++ +k+++ v +    +++++k+G++++g+
  gi|518651616|ref|YP_008141136.1| 459 NWQHHGFGKKLLDEAERISLEEYGKKRIIVISGIGVRNYFRKYGYERLGP 508
                                       79****************64554444********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (515 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3418.67
//
Query:       gi|518651617|ref|YP_008141137.1|  [L=218]
Description: L-fuculose phosphate aldolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-43  149.0   0.1    1.7e-43  148.7   0.1    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 !  148.7   0.1   9.5e-48   1.7e-43       4     185 ..      11     183 ..       8     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 148.7 bits;  conditional E-value: 9.5e-48
                                       HHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-TTHHHHHHH CS
                       Aldolase_II   4 aeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkpssetplHlai 80 
                                        +a+r++   +l+ g +GniS+r + +++++itpsg ++ + +aed+v+ d+d g+v++g   ++kpsse+++H +i
  gi|518651617|ref|YP_008141137.1|  11 LNACREMVSSNLTVGSWGNISLRAK-DGNIVITPSGTNYNKSNAEDMVITDID-GKVIDG---KLKPSSERLMHYEI 82 
                                       689********************88.99************************9.****65...68************ PP

                                       HHH-TT-SEEEEE--HHHHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHHHHHHHHHHHHS-SEEEET CS
                       Aldolase_II  81 ykarpdaravvHtHspaavalsalagkeglppltqeaaklllgdevpvipyaapgteelgealaealkedakavllr 157
                                       yk+r d+ a+vHtHs +  +l+ +  ++g+pp+t++ a+ llg++v v +ya  gt el++ ++e l+  ++a +++
  gi|518651617|ref|YP_008141137.1|  83 YKNRADVMAIVHTHSIYSSVLAVT--GDGIPPVTEDTAM-LLGNRVNVSRYALTGTMELARYVVEGLE-LNNATIMK 155
                                       **********************66..8************.67899**********************9.557***** PP

                                       TTEEEEEESSHHHHHHHHHHHHHHHHHH CS
                       Aldolase_II 158 nHGlltvGetleeAvalaetleeaaeiq 185
                                       nHG++ vG+++e A   + +le++a+i 
  gi|518651617|ref|YP_008141137.1| 156 NHGAVSVGTDMERAIIASQVLEKSARIF 183
                                       *************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 1397.25
//
Query:       gi|518651618|ref|YP_008141138.1|  [L=294]
Description: universal stress protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-14   55.0   0.0    5.2e-08   33.5   0.0    3.8  3  Usp            Universal stress protein family
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.15   12.3   0.1    1.3  1  5_nucleotid_C  5'-nucleotidase, C-terminal domain
        2.9    7.9   4.8        2.5    8.2   0.0    2.9  4  NAC            NAC domain


Domain annotation for each model (and alignments):
>> Usp  Universal stress protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   8.7e-12   5.2e-08      11     139 ..      46     161 ..      36     163 .. 0.85
   2 !   10.3   0.0   0.00013      0.77       2      37 ..     171     206 ..     170     216 .. 0.91
   3 !    5.7   0.0    0.0032        19      93     141 .]     248     293 ..     230     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 8.7e-12
                                       SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCEEEEEEE CS
                               Usp  11 gseeskkAlewAlelakargaelillhvidprasgavsdadeeaeeeeleleeaeleadaakaaaeaggvkvevvve 87 
                                       + ++s k+l++  ++aka+++e++++++ +  ++   s     + ++  e ++             ag+++   +++
  gi|518651618|ref|YP_008141138.1|  46 KGTNSSKVLKMSYDMAKANNSEITAITIREKNDPIDISGRLGVVTTAYNEGKK-------------AGIKVIPKIQT 109
                                       55677788888888999999998888888887777777777777776666666.............5899******* PP

                                       ESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEE CS
                               Usp  88 egdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlv 139
                                       + +++e+++ +   + +dl+++ +r+rs ls  ++G+  +yvl+++++pV +
  gi|518651618|ref|YP_008141138.1| 110 FDNAREGLVMETSGHYYDLLILSTRKRSMLSSSIFGNIGDYVLKNSSIPVAI 161
                                       **************************************************98 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00013
                                       -SEEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEE CS
                               Usp   2 ykrIlVavDgseeskkAlewAlelakargaelillh 37 
                                       y +I++++ +s ++++A+ +Al+lak + + +++l 
  gi|518651618|ref|YP_008141138.1| 171 YSNIMLPLSESINTRAAVFFALQLAKLNRSNVTILD 206
                                       889***************************999985 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0032
                                       HHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  93 eeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       ee   + ++ ++d iVvG+++ s+  r  + S  + ++++ ++++++V+
  gi|518651618|ref|YP_008141138.1| 248 EEVGNYIKSDNPDCIVVGTSR-SHNIR--MTSDIKFIIKEPEIDTILVK 293
                                       5566788999***********.66666..88999999988888888886 PP

>> 5_nucleotid_C  5'-nucleotidase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.5e-05      0.15     102     155 ..      49     103 ..       7     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
                                       EEES.EEEEE-TTS-TT--EEEESSS-BEEE--TTSEEEEEEEHHHHTTGGG-HH CS
                     5_nucleotid_C 102 qvsG.lrytydlskpagervtslsvtvngkpldddktYkvatnsylasggdgfsm 155
                                         s  l++ yd++k++ + +t +++ ++++p+d +    v+t++y  +++ g+++
  gi|518651618|ref|YP_008141138.1|  49 NSSKvLKMSYDMAKANNSEITAITIREKNDPIDISGRLGVVTTAYNEGKKAGIKV 103
                                       55655999*****************99999***************9988888766 PP

>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00041       2.5      33      51 ..       2      20 ..       1      22 [. 0.92
   2 ?   -3.8   0.0       2.2   1.3e+04      44      50 ..      65      71 ..      59      77 .. 0.51
   3 ?   -2.8   0.1       1.1   6.3e+03       9      20 ..      97     108 ..      97     109 .. 0.87
   4 ?    0.5   0.1       0.1     6e+02      23      39 ..     271     287 ..     271     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00041
                               NAC 33 vfdnPkVqkspgsntyvvf 51
                                      +f++P+V + ++sn y+ f
  gi|518651618|ref|YP_008141138.1|  2 IFEEPQVVTLKNSNFYILF 20
                                      8***************987 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.2
                               NAC 44 gsntyvv 50
                                      +s++ ++
  gi|518651618|ref|YP_008141138.1| 65 NSEITAI 71
                                      4444333 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.1
                               NAC   9 kklglkeipgie 20 
                                       kk g+k ip i+
  gi|518651618|ref|YP_008141138.1|  97 KKAGIKVIPKIQ 108
                                       799999999987 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.1
                               NAC  23 tirksdgkvlvfdnPkV 39 
                                       +ir++ +  +++++P++
  gi|518651618|ref|YP_008141138.1| 271 NIRMTSDIKFIIKEPEI 287
                                       7888888********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       361  (0.020135); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2038.90
//
Query:       gi|518651619|ref|YP_008141139.1|  [L=285]
Description: hypothetical protein FACI_IFERC00001G0258 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.13   12.4   0.2       0.31   11.1   0.0    1.6  2  DNA_pol3_tau_5  DNA polymerase III tau subunit V interacting 


Domain annotation for each model (and alignments):
>> DNA_pol3_tau_5  DNA polymerase III tau subunit V interacting with alpha
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       0.2   3.5e+03      28      51 ..     122     145 ..     119     183 .. 0.63
   2 ?   11.1   0.0   1.7e-05      0.31      30      80 ..     228     279 ..     224     283 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.2
                                       HHHHT--SHHHHHHHTEEEEE-SS CS
                    DNA_pol3_tau_5  28 ieklklpklvkqlalnsvleqkee 51 
                                       i++++++++++++   s++++++ 
  gi|518651619|ref|YP_008141139.1| 122 IQNINVSGILQNMLNVSLKNTNTT 145
                                       667777777777654444444333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 1.7e-05
                                       HHT--SHHHHHHH.TEEEEE-SSE.EEEEE-GGGTTT--HHHHHHHHHHHHH CS
                    DNA_pol3_tau_5  30 klklpklvkqlal.nsvleqkeedkilLhlrssqkhLnsdsaqkeLaeaLse 80 
                                        l+++k++ q a+ ns ++++ +++ ++++ +sq hLn d+  ++L   L++
  gi|518651619|ref|YP_008141139.1| 228 DLQVDKFLIQTAIsNSNVSREIGNNYTITISNSQIHLNIDKGYTSLPAVLKT 279
                                       688888777766549***************************9999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1981.87
//
Query:       gi|518651620|ref|YP_008141140.1|  [L=273]
Description: multi drug ABC transporter permease protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   38.7  46.5    6.3e-10   38.7  46.5    2.0  2  ABC2_membrane_3  ABC-2 family transporter protein
    1.8e-09   37.3  31.3      4e-09   36.2  31.3    1.5  1  ABC2_membrane_2  ABC-2 family transporter protein
      8e-05   22.7  28.2      8e-05   22.7  28.2    2.1  2  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 ?   -1.4   4.5      0.16   9.5e+02       9     292 ..      22      45 ..      10      59 .. 0.53
   2 !   38.7  46.5   1.1e-13   6.3e-10     158     344 ..      62     264 ..      52     265 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.16
                   ABC2_membrane_3   9 llPiilvlllglifsnsveddentpiavvdednsslsqqlvealeaspsvelvyevdseeeakkalkngdidgilvi 85 
                                       +                                                                            
  gi|518651620|ref|YP_008141140.1|  22 F---------------------------------------------------------------------------- 22 
                                       2............................................................................ PP

                   ABC2_membrane_3  86 pkgfskdllkgesatvtvlinssnlnsskailnalnsllqqlnasalvlqseatstsaninvestqleeelsnvasf 162
                                                                                                                    
  gi|518651620|ref|YP_008141140.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                   ABC2_membrane_3 163 lvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipfgnlg 239
                                                                                                                    
  gi|518651620|ref|YP_008141140.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                   ABC2_membrane_3 240 lllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfp...led 292
                                                                        ++++++ll+g ++  f+   ++d
  gi|518651620|ref|YP_008141140.1|  23 ---------------------------------LMLFLILLIGSMMSYFSfkyVND 45 
                                       .................................22222223333333332333444 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 1.1e-13
                   ABC2_membrane_3 158 nvasflvg.liliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll.afgl. 231
                                       nv ++l + ++l+i++f +++f + +i +E e+++  +++  ++++++++++k+++ f+v ++++ ++l++ +f l 
  gi|518651620|ref|YP_008141140.1|  62 NVFYYLWTlVLLYIPVFASVFFGSPAISSEIENKTAYFIFPLPINRYKLFFGKYFAAFTVTMFIVGIYLIFeVFTLs 138
                                       666776667999**********************************************************9977777 PP

                   ABC2_membrane_3 232 ....gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlp.........s 295
                                           +ip + + + +++++lf+l++ ++++l+s++f++ + a+i +f vi   ++f +g+f++e l          +
  gi|518651620|ref|YP_008141140.1| 139 yllgAIPATYFSYSFIMLVLFILSIMSVTFLISAIFNKNTYAYITVF-VIY-YIFFEAGSFIIELLYkytpvyflnD 213
                                       8888***************************************8555.555.6888888888777774444544445 PP

                   ABC2_membrane_3 296 alkwifsiiPffapglgllrli..tgdplweillsliilalfavvylllal 344
                                       a+++i ++  +  pg+++++ i  + ++++ei+ls +i+++ av+ l++++
  gi|518651620|ref|YP_008141140.1| 214 AASIIERVYININPGNAFVSHIdiNPASFSEIMLSALIMVIYAVIALVIGM 264
                                       5555555556677777776666755568999*****************986 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 !   36.2  31.3   6.6e-13     4e-09      11     288 .]      15     272 ..       6     272 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.6e-13
                   ABC2_membrane_2  11 lvrsrrfllltvllplidvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtdqdlkvvstimavlipv 87 
                                         rsr+f l+ +l++li     +++ +++   ++ ++    t++ ++++   +           + + t++ ++ipv
  gi|518651620|ref|YP_008141140.1|  15 YYRSRSFFLMLFLILLI---GSMMSYFSFKYVNDLPSFLGGTVFPASMKVNVF-----------YYLWTLVLLYIPV 77 
                                       56788887777777777...666666777777777777777777666555222...........22578999***** PP

                   ABC2_membrane_2  88 iaal.fgadaiagEkergTlkllLskPvsRdeillgKfigglaiglaiavallatvllalaiilalgivlaledlll 163
                                       +a + fg+ ai+ E e++T  + + +P+ R ++ +gK  + +++   ++ ++++ ++++++   +l  ++++  +  
  gi|518651620|ref|YP_008141140.1|  78 FASVfFGSPAISSEIENKTAYFIFPLPINRYKLFFGKYFAAFTV---TMFIVGIYLIFEVFTLSYLLGAIPATYFSY 151
                                       *96537**************************************...888888888889999999999999999988 PP

                   ABC2_membrane_2 164 lvvasvlllllvvflalglllSsvarssreaaalalglfvvlailvpivlygvaellagpavp........qeindf 232
                                        +++ vl++l    +++++l+S+++    + + +++ +fv+ +i++   +  ++ell  ++ p          i+  
  gi|518651620|ref|YP_008141140.1| 152 SFIMLVLFIL--SIMSVTFLISAIFN---KNTYAYITVFVIYYIFFEAGS-FIIELLY-KYTPvyflndaaSIIERV 221
                                       8888887777..77***********9...556666777777777776555.2333333.232223334443334444 PP

                   ABC2_membrane_2 233 lsllsptsayntllneilagsdlnalgstatnllilllllavllvlgyvlFkrkDl 288
                                       +  ++p++a+   ++  +a+         + ++li+++++++ lv+g+ lF++k++
  gi|518651620|ref|YP_008141140.1| 222 YININPGNAFVSHIDINPASF-----SEIMLSALIMVIYAVIALVIGMLLFDKKEV 272
                                       444555555554444444444.....6899***********************985 PP

>> ABC2_membrane_4  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7  28.2   1.3e-08     8e-05      12     177 ..      19     190 ..      15     193 .. 0.72
   2 ?    2.3   0.2     0.024   1.4e+02     105     122 ..     247     264 ..     223     272 .. 0.55

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.3e-08
                   ABC2_membrane_4  12 skivwllvlaallvpllallyfnllgk......tgldpaefys..lsvfgftlllllplilgi.iasylifrEeqnd 79 
                                       ++++++l+l++l+  ++  + f+++ +       +++pa++    ++ +++ +ll +p+   + ++s  i+ E +n+
  gi|518651620|ref|YP_008141140.1|  19 RSFFLMLFLILLIGSMMSYFSFKYVNDlpsflgGTVFPASMKVnvFYYLWTLVLLYIPVFASVfFGSPAISSEIENK 95 
                                       446666666777667778888886655322222446777776644456666677778888888568*********** PP

                   ABC2_membrane_4  80 tlknLltiPvsrtklllaKlivllllsvllmlvtflitvlfallsgfvgfsvklvlellkkclelgllvffavlpii 156
                                       t   ++ +P++r kl+++K+++ + ++++++ +     ++f+++  +  + + + +++   +++l+l+++ ++++ +
  gi|518651620|ref|YP_008141140.1|  96 TAYFIFPLPINRYKLFFGKYFAAFTVTMFIVGI----YLIFEVFTLSYLLGAIPATYFSYSFIMLVLFILSIMSVTF 168
                                       **********************99986666554....4455555555556666777888888899999999999999 PP

                   ABC2_membrane_4 157 al.vllkksyvlpliltlvyti 177
                                       ++ ++++k+  + +++ ++y i
  gi|518651620|ref|YP_008141140.1| 169 LIsAIFNKNTYAYITVFVIYYI 190
                                       8845688888888888888877 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.024
                   ABC2_membrane_4 105 lsvllmlvtflitvlfal 122
                                       ls+l+m++ ++i++++++
  gi|518651620|ref|YP_008141140.1| 247 LSALIMVIYAVIALVIGM 264
                                       222222222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1217  (0.0678789); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 2023.25
//
Query:       gi|518651621|ref|YP_008141141.1|  [L=299]
Description: hypothetical protein FACI_IFERC00001G0260 [Ferroplasma acidarmanus fer1]
Scores for complete 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   80.6   0.0    2.5e-22   79.9   0.0    1.3  1  ABC_tran  ABC transporter
    3.6e-06   27.0   2.1      0.016   15.1   0.0    2.7  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
    3.8e-05   24.3   0.4    9.6e-05   23.0   0.4    1.6  1  AAA_23    AAA domain
     0.0013   18.4   0.1     0.0027   17.4   0.1    1.4  1  AAA_29    P-loop containing region of AAA domain
     0.0063   16.3   0.1     0.0063   16.3   0.1    2.5  3  AAA_15    AAA ATPase domain
     0.0079   15.9   0.0       0.04   13.6   0.0    1.8  2  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.067   12.6   0.2        1.8    7.9   0.1    2.2  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.067   13.1   0.0       0.18   11.7   0.0    1.7  2  Rad17     Rad17 P-loop domain
       0.11   12.8   0.0       0.18   12.2   0.0    1.5  1  AAA_16    AAA ATPase domain
       0.12   12.7   0.3       0.55   10.5   0.3    2.1  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 !   79.9   0.0   1.4e-25   2.5e-22       1     136 [.      18     161 ..      18     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 79.9 bits;  conditional E-value: 1.4e-25
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ ++lk++   +++++G+nGaGK+t+lkl ++  kp  G+++l++ ++   +++ l + +g l ++p++ + lt +
  gi|518651621|ref|YP_008141141.1|  18 LDSINLKIEGHGCTGLLGPNGAGKTTMLKLCTNIIKPSHGKVELNNVNVAIYPEKAL-EPVGALIEQPEFYSYLTGY 93 
                                       6899******************************************99999666655.5677777777888888777 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e              e ++e++++ +  g++      +++++ ++S G+kqr+al  a+l +p++++lDEpt
  gi|518651621|ref|YP_008141141.1|  94 EIleftskikgigkdEFKSEMKRLGELTGIDA----YADRKTGTYSRGMKQRLALSVAMLGNPEIIILDEPT 161
                                       77888999999555555555555555555555....555555*****************************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 !   10.7   0.5   0.00019      0.33       2      17 ..      31      46 ..      30      58 .. 0.91
   2 !   15.1   0.0   8.7e-06     0.016     237     297 ..     134     190 ..      60     194 .. 0.83
   3 ?   -1.3   0.0      0.85   1.5e+03      86     141 ..     203     258 ..     191     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00019
                            AAA_21  2 nvliGpNgsGKSnLLd 17
                                      ++l GpNg+GK++ L+
  gi|518651621|ref|YP_008141141.1| 31 TGLLGPNGAGKTTMLK 46
                                      89**********9887 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.7e-06
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTH 297
                                        S G+k+ lal +a+l  +    ++++DEp  gL+Pk +  +  ++k+ ++    v+l+TH
  gi|518651621|ref|YP_008141141.1| 134 YSRGMKQRLALSVAMLGNP---EIIILDEPTFGLDPKGMVDVRNIIKDIAK-EHLVLLSTH 190
                                       499*************999...9*************999777788866655.355688888 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.85
                            AAA_21  86 klssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfg 141
                                        +++ ++ + +  ++ +rsl ++ ++n+   + ++++++ ++ +  ++e n  +++
  gi|518651621|ref|YP_008141141.1| 203 IIINGGKIEYDSAMSAERSLLKITATNSIDITGDKIKDYSRDGNVFIIEKNPSFSN 258
                                       57778888888899999999999999999999999999999999888888877765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.4   5.4e-08   9.6e-05       5      38 ..      10      47 ..       9      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.4e-08
                            AAA_23  5 enfrsfrdqe.idF...skgltlItGpNGaGKTTildA 38
                                      +n+r+++  + i++   ++g t + GpNGaGKTT l  
  gi|518651621|ref|YP_008141141.1| 10 KNYRKIKALDsINLkieGHGCTGLLGPNGAGKTTMLKL 47
                                      79999999877***********************9975 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   1.5e-06    0.0027      17      55 ..      23      62 ..      11      65 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                            AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      ++i+ +g t l Gp+G+GK+T+l   + ++ p++ kv+ N
  gi|518651621|ref|YP_008141141.1| 23 LKIEGHGCTGLLGPNGAGKTTMLKLCTNIIKPSHgKVELN 62
                                      4556566999*************99999999999888888 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   3.5e-06    0.0063       9      42 ..      10      47 ..       8      75 .. 0.87
   2 ?    0.3   0.0      0.25   4.4e+02     323     364 ..     151     190 ..      90     191 .. 0.78
   3 ?   -1.6   0.3      0.92   1.7e+03     119     129 ..     249     259 ..     202     296 .. 0.46

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.5e-06
                            AAA_15  9 kNFRslkd.veidlsee...ltvliGkNnsGKSsilea 42
                                      kN+R++k   +i+l+ e    t l G+N++GK++ l++
  gi|518651621|ref|YP_008141141.1| 10 KNYRKIKAlDSINLKIEghgCTGLLGPNGAGKTTMLKL 47
                                      8*******889*****9*******************97 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.25
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                       ++ i++++EP   L p+    + + +k++a+++   v+++TH
  gi|518651621|ref|YP_008141141.1| 151 NPEIIILDEPTFGLDPKGMVDVRNIIKDIAKEH--LVLLSTH 190
                                       567899999999999999999999999999999..5999999 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.92
                            AAA_15 119 ikdkklklkkn 129
                                       i +k+  ++++
  gi|518651621|ref|YP_008141141.1| 249 IIEKNPSFSNY 259
                                       11111111111 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   2.2e-05      0.04      17      49 ..      27      59 ..      21      69 .. 0.85
   2 ?   -0.4   0.0      0.44   7.9e+02      60      98 ..     115     161 ..     110     187 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaweaaggrv 49
                                      g+ ++ l Gp G+GKtt+lk  +++++ + g+v
  gi|518651621|ref|YP_008141141.1| 27 GHGCTGLLGPNGAGKTTMLKLCTNIIKPSHGKV 59
                                      55678899****************999886666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.44
                            AAA_30  60 kvLaeelgieastiakllkrlk........grarlepgtllivDEag 98 
                                       k+L+e +gi+a+   k  +  +        + a l + +++i DE  
  gi|518651621|ref|YP_008141141.1| 115 KRLGELTGIDAYADRKTGTYSRgmkqrlalSVAMLGNPEIIILDEPT 161
                                       67888899988888888877778888888865677888999999965 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 ?    7.9   0.1     0.001       1.8      24      41 ..      28      45 ..       9      62 .. 0.81
   2 ?    2.2   0.0     0.058     1e+02     149     197 ..     142     190 ..     133     207 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.001
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                      ++ t ++GpNG+GK+ +l
  gi|518651621|ref|YP_008141141.1| 28 HGCTGLLGPNGAGKTTML 45
                                      56899**********987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.058
                                       HHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivisl 197
                                       L +++ +     + +lDe    LD k +  v +++k   k+  ++  ++
  gi|518651621|ref|YP_008141141.1| 142 LALSVAMLGNPEIIILDEPTFGLDPKGMVDVRNIIKDIAKEHLVLLSTH 190
                                       45566677777899**********************9998887777665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0    0.0001      0.18      38     114 ..      21      98 ..      10     158 .. 0.83
   2 ?   -1.8   0.0       1.4   2.5e+03      83     101 ..     252     270 ..     212     293 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                             Rad17  38 dvLesrkkriLLisGPsGCgkstvvkvLskelgikl.rewlnpvslkepdnqksdfkgltekesrflsqiesfkele 113
                                         L+ + +    + GP G gk+t++k  + +  ++  +  ln v++   + +  +  g ++ + +f s +  ++ le
  gi|518651621|ref|YP_008141141.1|  21 INLKIEGHGCTGLLGPNGAGKTTMLKLCTNIIKPSHgKVELNNVNVAIYPEKALEPVGALIEQPEFYSYLTGYEILE 97 
                                       55555555566688****************99998724579999999999999999999999999999999997665 PP

                             Rad17 114 L 114
                                        
  gi|518651621|ref|YP_008141141.1|  98 F 98 
                                       4 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
                             Rad17  83 kepdnqksdfkgltekesr 101
                                       k+p++ + d+ g+++k+  
  gi|518651621|ref|YP_008141141.1| 252 KNPSFSNYDIIGDLIKQGL 270
                                       4444444444444444443 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    0.0001      0.18      25      55 ..      29      59 ..      13     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.0001
                            AAA_16 25 elvllsGesGvGKsslvrellralekdggif 55
                                      +++ l G+ G GK+++++ + + ++ ++g +
  gi|518651621|ref|YP_008141141.1| 29 GCTGLLGPNGAGKTTMLKLCTNIIKPSHGKV 59
                                      68889****************9999886544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00031      0.55       4      29 ..      27      52 ..      24     193 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00031
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleql 29
                                      ++g++ + G+ G+GKTt l+  ++  
  gi|518651621|ref|YP_008141141.1| 27 GHGCTGLLGPNGAGKTTMLKLCTNII 52
                                      6899999************9888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2077.64
//
Query:       gi|518651622|ref|YP_008141142.1|  [L=163]
Description: hypothetical protein FACI_IFERC00001G0261 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0056   16.5   0.2     0.0098   15.7   0.2    1.6  1  RnlA_toxin  RNase LS, bacterial toxin


Domain annotation for each model (and alignments):
>> RnlA_toxin  RNase LS, bacterial toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   5.5e-07    0.0098     101     176 ..      36     110 ..      22     138 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-07
                                       GGGS-HHHHHHHHHHHHGGGGGGS-HHHHHHHHHHHHHHHC----S--GGGGHHHHHHHHHHHHHHHHCTT---BT CS
                        RnlA_toxin 101 ksklkeevireklkkrLpnayekldekikklLsssiclklskveledYsclvyPalrgLEgllkkllleksievkk 176
                                       ++++++ v+ +k+ k+++ + e  + k+kk+ +   ++   +++++dY  + ++++r++E ++++++ e s++v  
  gi|518651622|ref|YP_008141142.1|  36 IRNVSTFVAVRKMAKKIS-VEEYTNTKLKKVEQDDTMVIEQEIKMPDYKFVRLGVFRSMEDVISQAIDEPSMYVFI 110
                                       666777777777877775.667778888888888889999999**************************9999854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       997  (0.0556082); expected 358.6 (0.02)
Passed bias filter:                      633  (0.0353059); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1124.02
//
Query:       gi|518651623|ref|YP_008141143.1|  [L=148]
Description: hypothetical protein FACI_IFERC00001G0262 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-05   23.2   0.1     0.0021   18.2   0.1    2.5  1  RHH_8            Ribbon-Helix-Helix transcriptional regulator
  ------ inclusion threshold ------
      0.011   15.7   4.0      0.084   12.8   1.9    2.9  2  RHH_1            Ribbon-helix-helix protein, copG family
       0.08   13.1   0.6       0.15   12.1   0.2    1.6  2  HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antit


Domain annotation for each model (and alignments):
>> RHH_8  Ribbon-Helix-Helix transcriptional regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.5e-07    0.0021       2      41 ..      27      67 ..      26     130 .. 0.92

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.5e-07
                             RHH_8  2 etekvtinlgvvDLgqiD.lLveeGfYsnRtDlirtairaq 41
                                      ++ek+ti ++  +L +iD +L  +  Y++R+++ir a+ + 
  gi|518651623|ref|YP_008141143.1| 27 KSEKLTIRISNDELEEIDsFLSYNSNYASRSEFIRMAVLEY 67
                                      68****************5577899************9665 PP

>> RHH_1  Ribbon-helix-helix protein, copG family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.9   1.4e-05     0.084       2      37 ..      31      68 ..      30      69 .. 0.86
   2 ?   -1.0   0.0      0.33     2e+03       7      16 ..     105     114 ..     103     119 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                                      EEEEEEHHHHHHHHH.HHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  2 vsirldeellerLde.larrrg.rSrSelIReAlreyl 37
                                      ++ir++ ++le++d  l   ++  SrSe+IR A++ey+
  gi|518651623|ref|YP_008141143.1| 31 LTIRISNDELEEIDSfLSYNSNyASRSEFIRMAVLEYI 68
                                      688888888888887788888889************97 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.33
                                       EHHHHHHHHH CS
                             RHH_1   7 deellerLde 16 
                                       d+ + e + e
  gi|518651623|ref|YP_008141143.1| 105 DDAYEEIIKE 114
                                       5555555554 PP

>> HicB_lk_antitox  HicB_like antitoxin of bacterial toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   2.6e-05      0.15      84     120 ..      23      61 ..      10      64 .. 0.81
   2 ?   -1.8   0.0      0.54   3.2e+03      30      40 ..     104     115 ..      90     144 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.6e-05
                   HicB_lk_antitox  84 kldgkaeriNitlpervlkriDaavkaag..esRSgfla 120
                                        +++k+e++ i ++++ l++iD++ + +    sRS f+ 
  gi|518651623|ref|YP_008141143.1|  23 IMTEKSEKLTIRISNDELEEIDSFLSYNSnyASRSEFIR 61 
                                       35789*******************99888557*****96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.54
                   HicB_lk_antitox  30 leeaian.akea 40 
                                       +++a+++ +kea
  gi|518651623|ref|YP_008141143.1| 104 IDDAYEEiIKEA 115
                                       444444312333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1139.93
//
Query:       gi|518651624|ref|YP_008141144.1|  [L=203]
Description: translation initiation factor IF-2 subunit beta [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-34  117.4   0.1    5.4e-34  116.6   0.1    1.3  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
    3.8e-09   36.4   0.7    7.5e-09   35.5   0.7    1.5  1  TRAM             TRAM domain
  ------ inclusion threshold ------
      0.074   12.6   1.1       0.16   11.5   1.1    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.076   13.1   0.3       0.14   12.2   0.3    1.4  1  Elf1             Transcription elongation factor Elf1 like
       0.12   12.7   0.7       0.48   10.8   0.7    1.9  1  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.1   1.5e-37   5.4e-34       4     116 ..      19     129 ..      17     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 1.5e-37
                                       CCSSSS--SSTT--EEEETT.EEEETTHHHHHHHHTTSHHHHHHHHHHHHTSEEEESETTEEEESSSSSCCHHHHHH CS
                      eIF-5_eIF-2B   4 kedkkerykmpklqvkvegkkktvivNfeeiakaLnrdpehvlkyllkelgtqgsidengrlilngkfeakklekll 80 
                                       k+++++r+k+p++++ +egk  t+i+Nf +i+++Lnr+pe ++ky++ke+g+ +s+ +++rli+n k ++++++++l
  gi|518651624|ref|YP_008141144.1|  19 KNRTEDRLKVPEPEIIYEGK-STIIRNFIDITEMLNRNPEDLVKYFTKEFGIGASV-AGRRLIINRKLREEEIREKL 93 
                                       557789**************.***********************************.99****************** PP

                                       HHHHHHHTSTSSSTSTCEEECCSSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  81 dkyieeyVlCkeCkspetelekeerllvlkCkaCga 116
                                       ++y+ +yVlC+eC+sp+t++ek +r+++l CkaCga
  gi|518651624|ref|YP_008141144.1|  94 NAYMATYVLCYECSSPDTTIEKVGRTYLLVCKACGA 129
                                       ***********************************8 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.7   2.1e-12   7.5e-09       2      62 .]     146     202 ..     145     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 2.1e-12
                                       XXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEEE-SSEEEEEEE CS
                              TRAM   2 syvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItkvkrqyLrGell 62 
                                        ++G+t++V +++ + + geg++    +++++vpg+++  G++ +V I+k +++ + Ge++
  gi|518651624|ref|YP_008141144.1| 146 LTEGKTYTVQITEIG-KSGEGHAFYG-DFTIYVPGTKK--GERPKVLIKKIRKNIAIGEVV 202
                                       689************.**********.***********..*******************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 ?   11.5   1.1   4.5e-05      0.16       3      27 ..     103     129 ..     101     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
                                       ETTTTCEE.CHEETSTTCE.EESSSSB CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDpergel.vCtdCGl 27 
                                       C +C+s++ ++e   r+ l vC++CG+
  gi|518651624|ref|YP_008141144.1| 103 CYECSSPDtTIEKVGRTYLlVCKACGA 129
                                       99****99889999999999******6 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.3   3.9e-05      0.14       3      59 ..      82     135 ..      80     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.9e-05
                              Elf1   3 RkkkakkrkkkkkkklptkFdCpfCnheksvevkldkkekiaevsCkvCgesfetkv 59 
                                       Rk ++++ ++k + ++ t+  C  C++    + +++k  ++  + Ck Cg++  +k+
  gi|518651624|ref|YP_008141144.1|  82 RKLREEEIREKLNAYMATYVLCYECSSP---DTTIEKVGRTYLLVCKACGAEHPIKA 135
                                       666776667777777*************...88999**************9887765 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.7   0.00013      0.48       6      54 ..     103     146 ..      75     149 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                   Lar_restr_allev   6 CPfCggravlersqrvvaeigqcvyCadCgastpwfkiaedeaeaekea 54 
                                       C  C ++++ ++  ++++       C+ Cga ++ +k   + +e+e+++
  gi|518651624|ref|YP_008141144.1| 103 CYECSSPDTTIEKVGRTY----LLVCKACGA-EHPIKASREIKENEDQL 146
                                       556999999999999999....9********.67777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       810  (0.0451782); expected 358.6 (0.02)
Passed bias filter:                      658  (0.0367003); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1453.49
//
Query:       gi|518651625|ref|YP_008141145.1|  [L=118]
Description: hypothetical protein FACI_IFERC00001G0264 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-16   60.5   0.0    2.1e-16   60.3   0.0    1.0  1  PIN_9     PIN like domain
    1.8e-07   31.7   0.4    0.00077   20.0   0.1    2.1  2  PIN       PIN domain
     0.0011   19.3   0.0     0.0018   18.7   0.0    1.3  1  Fcf1      Fcf1
     0.0013   18.5   0.0      0.031   14.0   0.0    2.1  2  DUF5615   Domain of unknown function (DUF5615)
     0.0026   18.0   0.0     0.0045   17.3   0.0    1.4  1  PIN_4     PIN domain
  ------ inclusion threshold ------
      0.047   13.1   0.0       0.11   11.9   0.0    1.6  2  PIN_5     PINc domain ribonuclease
      0.094   12.9   0.0       0.13   12.5   0.0    1.3  1  PIN_10    PIN like domain
       0.11   12.7   0.0        5.5    7.2   0.0    2.0  2  PIN_2     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 !   60.3   0.0   9.3e-20   2.1e-16       1     113 [.       4     109 ..       4     112 .. 0.96

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 9.3e-20
                             PIN_9   1 vilDtnaLmipvqfgvdifeelerllgsvelvvpkavleELerlakagkgkertaakvalsLaerceiveaeeekaD 77 
                                       +ilDtn L+  +q ++d+ + +  +  + e ++p  vl+EL+ l      +++  ak al+ +er + +e++ +++D
  gi|518651625|ref|YP_008141145.1|   4 IILDTNILIYAIQNKIDLENGIMSITPRMEPLIPACVLAELRGL-----ATTKWYAKAALKYSERFKNIESH-GEGD 74 
                                       79******************************************.....6788999****************.**** PP

                             PIN_9  78 dailelakeldaavlvTnDreLkkrllekgipvilL 113
                                         i+ +ak+l+aavl TnDr  +k l++kgip +++
  gi|518651625|ref|YP_008141145.1|  75 FCIMVVAKSLNAAVL-TNDRRFRKILKNKGIPCVTM 109
                                       ***************.****************9986 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.6e-05      0.13       1      63 [.       4      62 ..       4      69 .. 0.68
   2 !   20.0   0.1   3.4e-07   0.00077      78     119 ..      54      98 ..      40     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.6e-05
                                      EEE-HHHHHHHHTTSHHHHHHHHHHHTS...SEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHH CS
                               PIN  1 ivlDTsvliallrgeekaeaarklleel...eelvtsalvlaEllyvlarrkskrekaaelvelll 63
                                      i+lDT++li+++ ++ + e     + ++    e +++a vlaEl+  ++     +++a++ ++  +
  gi|518651625|ref|YP_008141145.1|  4 IILDTNILIYAIQNKIDLE---NGIMSItprMEPLIPACVLAELRGLATT----KWYAKAALKYSE 62
                                      79**********6666653...3333334557889999999999988888....555555544444 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 3.4e-07
                                       HHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  78 aeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrv 119
                                       a+ a++++++ +     +  D  i ++Ak+ +++++ t+D++fr++
  gi|518651625|ref|YP_008141145.1|  54 AKAALKYSERFKniesHGEGDFCIMVVAKSLNAAVL-TNDRRFRKI 98 
                                       344445555555666899***************999.*******98 PP

>> Fcf1  Fcf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.9e-07    0.0018       7      92 ..      32     111 ..      27     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.9e-07
                                       EEEEEEHHHHHHHHHCT..-HHHHHHHTTSEEE----SS---HHHHHHHHH-BTB-TT-EEEE-S-HHHHHHHHTST CS
                              Fcf1   7 vkpliTqCviaeleklgkklkealkiaktferlkCnhkkptsaddClvsvvkkkknkkryivAtqDkdlrrrlrkip 83 
                                       ++pli  Cv+ael+ l  +   a +++k  er+k    ++ + d C++ v k    + +  v t+D+  r+ l k +
  gi|518651625|ref|YP_008141145.1|  32 MEPLIPACVLAELRGLATTKWYAKAALKYSERFKNIE-SHGEGDFCIMVVAK----SLNAAVLTNDRRFRKIL-KNK 102
                                       789**************88667777777678888766.6789999**98888....46789********9766.568 PP

                                       T--EEEEE- CS
                              Fcf1  84 gvPilyikr 92 
                                       g+P + + +
  gi|518651625|ref|YP_008141145.1| 103 GIPCVTMGN 111
                                       999988765 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0      0.05   1.1e+02      35      48 ..       5      18 ..       1      21 [. 0.85
   2 !   14.0   0.0   1.4e-05     0.031      28      68 ..      65     105 ..      50     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.05
                           DUF5615 35 asDeeileyAkeed 48
                                      + D++il yA++++
  gi|518651625|ref|YP_008141145.1|  5 ILDTNILIYAIQNK 18
                                      78*********997 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.4e-05
                           DUF5615  28 relglegasDeeileyAkeedriivTkDkDFgellllggpp 68 
                                       ++++ +g  D  i+ +Ak+ +++++T+D+ F+++l+++g p
  gi|518651625|ref|YP_008141145.1|  65 KNIESHGEGDFCIMVVAKSLNAAVLTNDRRFRKILKNKGIP 105
                                       567778888999*********************99988865 PP

>> PIN_4  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     2e-06    0.0045       1      89 [.       4      93 ..       4     102 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2e-06
                             PIN_4  1 fVlDTnvlLhdpealksf.......keehdvviPitVleELdklKkgsserelarlarqanrlldellekesgrlkvqt 72
                                      ++lDTn+l++ ++    +           +  iP  Vl EL++l +++     a++a + ++ ++++ ++ +g++ +  
  gi|518651625|ref|YP_008141145.1|  4 IILDTNILIYAIQNKIDLengimsiTPRMEPLIPACVLAELRGLATTKWY---AKAALKYSERFKNIESHGEGDFCIMV 79
                                      69********998755558888998899999***************9984...44443444444444455556666666 PP

                             PIN_4 73 saeelpeeeseseknDn 89
                                      +a++l++      +nD+
  gi|518651625|ref|YP_008141145.1| 80 VAKSLNAAV-L--TNDR 93
                                      666666642.2..4554 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.2   2.7e+03      47      62 ..      36      51 ..      27      65 .. 0.66
   2 ?   11.9   0.0   5.1e-05      0.11     158     193 ..      73     108 ..      58     116 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.2
                             PIN_5 47 ippsvykElkeflkre 62
                                      ip  v +El+ +++++
  gi|518651625|ref|YP_008141145.1| 36 IPACVLAELRGLATTK 51
                                      6666777776666554 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.1e-05
                             PIN_5 158 eDldvllLAkELdaavvssDeGikkwaeklGlrlve 193
                                        D+ +++ Ak L+aav+++D+  +k+ ++ G+ +v+
  gi|518651625|ref|YP_008141145.1|  73 GDFCIMVVAKSLNAAVLTNDRRFRKILKNKGIPCVT 108
                                       69999*********************9999998886 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.8e-05      0.13      13      64 ..      40      97 ..      33     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.8e-05
                            PIN_10 13 lakaLrelleeeg..hevvhlrdkf....aagtkDeeWiaalaeggwvvltkDrrirk 64
                                      + + Lr l+ +++   ++  ++++f     +g+ D   +  ++  + +vlt+Drr+rk
  gi|518651625|ref|YP_008141145.1| 40 VLAELRGLATTKWyaKAALKYSERFknieSHGEGDFCIMVVAKSLNAAVLTNDRRFRK 97
                                      5566676666555445566667777777799*************************98 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0024       5.5       1      41 [.       5      46 ..       5      64 .. 0.90
   2 ?    3.9   0.0     0.026        57      87     116 ..      67      96 ..      53     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                             PIN_2  1 VvdaNivvsallk.srikkrlilvekaleliapeeaveeiek 41
                                      ++d+Ni++ a+ +  + ++ ++ +++++e ++p+ +++e++ 
  gi|518651625|ref|YP_008141145.1|  5 ILDTNILIYAIQNkIDLENGIMSITPRMEPLIPACVLAELRG 46
                                      79********88788999999*****************9985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.026
                             PIN_2  87 iarvDpdDtpfvAlaLlleapiWTeDkdli 116
                                       i++  + D+ ++ +a  l+a++ T+D+ + 
  gi|518651625|ref|YP_008141145.1|  67 IESHGEGDFCIMVVAKSLNAAVLTNDRRFR 96 
                                       55556779999999999**********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.31s 00:00:00.72 Elapsed: 00:00:00.99
# Mc/sec: 361.86
//
Query:       gi|518651626|ref|YP_008141146.1|  [L=220]
Description: riboflavin kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-39  134.0   0.0    4.4e-39  133.3   0.0    1.4  1  CTP-dep_RFKase  Domain of unknown function DUF120
    2.7e-05   24.1   0.1    5.1e-05   23.2   0.1    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
    0.00043   20.1   0.0     0.0008   19.2   0.0    1.5  1  MarR_2          MarR family
    0.00071   19.5   0.1     0.0015   18.4   0.1    1.5  1  MarR            MarR family
     0.0031   17.0   0.1     0.0087   15.6   0.0    1.8  2  HTH_24          Winged helix-turn-helix DNA-binding
     0.0035   17.3   0.2      0.017   15.0   0.2    2.3  1  HTH_11          HTH domain
      0.006   16.5   0.1      0.013   15.5   0.1    1.6  1  HTH_36          Helix-turn-helix domain
     0.0062   16.7   0.0      0.017   15.3   0.0    1.7  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
     0.0092   16.0   1.7      0.017   15.1   0.1    2.2  3  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
  ------ inclusion threshold ------
      0.015   15.0   0.2      0.075   12.8   0.0    2.3  3  HTH_DeoR        DeoR-like helix-turn-helix domain
       0.11   12.4   0.0       0.29   11.0   0.0    1.7  1  HTH_10          HTH DNA binding domain


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 !  133.3   0.0   2.7e-42   4.4e-39       1     121 []      97     216 ..      97     216 .. 0.99

  Alignments for each domain:
  == domain 1  score: 133.3 bits;  conditional E-value: 2.7e-42
                                       EE--SSHHHHHHCSHHHHHHHHHHHSS---SS-EEEEESCCGHHHHCHHHHS--EEE--EEETTEEE--EEEEEEEE CS
                    CTP-dep_RFKase   1 VvsGlgeGkyyvslegykeqfeeklgfepypGTLNvkldeeslelrkaleklkgieiegfedeertfgavkvypaki 77 
                                       + sGlgeGkyy+s+egy+ qf +klg++pypGTLN+k+  e +++ +++++++gi+i gf+d+ertfg+vk++  +i
  gi|518651626|ref|YP_008141146.1|  97 IQSGLGEGKYYISQEGYMAQFLDKLGISPYPGTLNIKIFPEYENVLRRIRSADGIHIGGFKDKERTFGGVKCFSGRI 173
                                       579************************************************************************** PP

                                       CCEEEEEEEESS-SS.TTEEEEE-SS-HHHHTT--TT-EEEEEE CS
                    CTP-dep_RFKase  78 ekikaavvvperthyeedvlEiiapekLReklelkdgdevevev 121
                                       ++++a +++per++y +d++Eii+++ LR+ l+l+dgde++++v
  gi|518651626|ref|YP_008141146.1| 174 DGTRAWLIFPERSNY-TDIVEIISDKFLRKDLKLQDGDELNIRV 216
                                       ***************.9************************987 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   3.1e-08   5.1e-05      19      62 ..      21      69 ..       7      71 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 3.1e-08
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE.E..TEE..EEES-H CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis.r..grr..irildl 62
                                      ++ ++  elA+ lG++++t sr + eL ++++i+ +  +r+  i++l +
  gi|518651626|ref|YP_008141146.1| 21 TVYISSGELAEELGVSQQTSSRFIIELADKKYIErTlqNRKqkITLLEP 69
                                      4678999***************************725433237998876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.9e-07    0.0008      23      54 ..      25      56 ..      11      63 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.9e-07
                                      EHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 23 tvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + gela++lg+s+++ sr + +L ++ ++er+
  gi|518651626|ref|YP_008141146.1| 25 SSGELAEELGVSQQTSSRFIIELADKKYIERT 56
                                      679***************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   9.2e-07    0.0015       6      50 ..       9      56 ..       6      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 9.2e-07
                                      HHHHHHHHHSTT.EEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  6 fviLrilyeqgp.lsvs..eLakklgvskstvtrvldrLekkGlieRs 50
                                      ++iL +l+ +g+  ++s  eLa+ lgvs+ t +r++ +L +k +ieR+
  gi|518651626|ref|YP_008141146.1|  9 IKILKKLSGSGNtVYISsgELAEELGVSQQTSSRFIIELADKKYIERT 56
                                      6788888888887555567****************************7 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   5.4e-06    0.0087      17      48 .]      23      54 ..       2      54 .. 0.90
   2 ?   -3.4   0.0       4.7   7.7e+03      25      31 ..     119     125 ..     119     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.4e-06
                            HTH_24 17 risqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                       is  eLAe+lg+S++t +r + +L ++ +I+
  gi|518651626|ref|YP_008141146.1| 23 YISSGELAEELGVSQQTSSRFIIELADKKYIE 54
                                      5999******************9999999996 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.7
                            HTH_24  25 erlglSp 31 
                                       ++lg+Sp
  gi|518651626|ref|YP_008141146.1| 119 DKLGISP 125
                                       689**97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.2   1.1e-05     0.017       4      31 ..      10      39 ..       7      48 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                            HTH_11  4 qilelLleargp..isgeeLAeeLnvSrrt 31
                                      +il+ L  + ++  is+ eLAeeL+vS +t
  gi|518651626|ref|YP_008141146.1| 10 KILKKLSGSGNTvyISSGELAEELGVSQQT 39
                                      677777766666679************998 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   7.9e-06     0.013      13      55 .]      11      53 ..       7      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 7.9e-06
                            HTH_36 13 slasfanknggcfpsqetlakrlglsknTvsraikeLeqlGyi 55
                                      +l +++++++ ++ s   la+ lg+s +T sr i eL+++ yi
  gi|518651626|ref|YP_008141146.1| 11 ILKKLSGSGNTVYISSGELAEELGVSQQTSSRFIIELADKKYI 53
                                      78999*99999*****************************998 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     1e-05     0.017      19      53 ..      20      54 ..      11      58 .. 0.90
   2 ?   -3.5   0.0         8   1.3e+04       5      13 ..     137     145 ..     135     150 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      + ++++  +lae+L+vs  + s  + +L+++ y+e
  gi|518651626|ref|YP_008141146.1| 20 NTVYISSGELAEELGVSQQTSSRFIIELADKKYIE 54
                                      67899*************************99986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 8
                                       HHHHHHHHH CS
                    Fe_dep_repress   5 stEdYLetI 13 
                                       + E++L+ I
  gi|518651626|ref|YP_008141146.1| 137 EYENVLRRI 145
                                       679999988 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1     1e-05     0.017      15      41 ..      10      37 ..       8      39 .. 0.89
   2 ?   -3.3   0.0         6   9.7e+03      11      22 ..     136     147 ..     135     151 .. 0.69
   3 ?   -2.2   0.1       2.6   4.3e+03      44      48 ..     200     204 ..     195     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                                      HHHHHHHHTT.--EE-HHHHHHHCTS-H CS
                    Put_DNA-bind_N 15 ryLeelkeeg.veriSSteLaealgvta 41
                                      ++L++l+ +g + +iSS eLae+lgv+ 
  gi|518651626|ref|YP_008141146.1| 10 KILKKLSGSGnTVYISSGELAEELGVSQ 37
                                      6899999999789************985 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6
                                       HHHHHHHHHHHH CS
                    Put_DNA-bind_N  11 plYlryLeelke 22 
                                       p Y ++L+++++
  gi|518651626|ref|YP_008141146.1| 136 PEYENVLRRIRS 147
                                       667788877665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.6
                                       HHHHH CS
                    Put_DNA-bind_N  44 vRKDL 48 
                                       +RKDL
  gi|518651626|ref|YP_008141146.1| 200 LRKDL 204
                                       7***9 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.6e-05     0.075      14      47 ..      23      56 ..       9      58 .. 0.88
   2 ?   -2.7   0.0       3.2   5.3e+03      46      53 ..     161     168 ..     160     170 .. 0.81
   3 ?   -2.7   0.0       3.1   5.1e+03      27      36 ..     196     205 ..     195     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                          HTH_DeoR 14 klsveelvellgvSeaTiRRDLneLeeqglltRt 47
                                      ++s  el+e+lgvS++T  R + eL+ +  ++Rt
  gi|518651626|ref|YP_008141146.1| 23 YISSGELAEELGVSQQTSSRFIIELADKKYIERT 56
                                      68889************************99998 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.2
                          HTH_DeoR  46 RthGGavs 53 
                                       Rt GG++ 
  gi|518651626|ref|YP_008141146.1| 161 RTFGGVKC 168
                                       9****985 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.1
                          HTH_DeoR  27 SeaTiRRDLn 36 
                                       S++  R+DL+
  gi|518651626|ref|YP_008141146.1| 196 SDKFLRKDLK 205
                                       6666799996 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00018      0.29      24      42 ..      24      42 ..      23      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00018
                            HTH_10 24 vtlkeLAkelGIskstlse 42
                                      +++ eLA+elG+s++t s 
  gi|518651626|ref|YP_008141146.1| 24 ISSGELAEELGVSQQTSSR 42
                                      5789***********9775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 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:                        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: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1422.05
//
Query:       gi|518651627|ref|YP_008141147.1|  [L=209]
Description: hypothetical protein FACI_IFERC00001G0266 [Ferroplasma acidarmanus fer1]
Scores for complete 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-41  140.3   0.0      7e-41  140.1   0.0    1.0  1  Diphthami_syn_2  Diphthamide synthase
     0.0033   16.9   0.1     0.0083   15.6   0.0    1.7  2  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.062   12.9   0.1       0.12   12.0   0.1    1.6  2  ThiI             Thiamine biosynthesis protein (ThiI)


Domain annotation for each model (and alignments):
>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.1   0.0   1.2e-44     7e-41       1     188 [.       1     183 [.       1     208 [. 0.90

  Alignments for each domain:
  == domain 1  score: 140.1 bits;  conditional E-value: 1.2e-44
                   Diphthami_syn_2   1 mkvavlysGGkDsilaLykalke.sevesLvsvisenkesymfhvvnvhlvellaesvGiplikletaGeeekeved 76 
                                       mk+++l+sGGkDs l+   a+++ +e+++ v+v++e+  s mfh +n ++ e  a  +G  ++   +   +ek+ + 
  gi|518651627|ref|YP_008141147.1|   1 MKAVALFSGGKDSFLSAMMAVEQgYEIIYGVTVVPEEY-SMMFHYPNSRISEYAASLLGFSIKY--I---NEKDYRS 71 
                                       89*************888888877***********976.6*******************99864..4...4888899 PP

                   Diphthami_syn_2  77 LkgtlkkldveavviGaieseyqksriervCrelGlksvaPLWkkdpeelleeiveekfevivvavkaegldeslLG 153
                                         g++ + +++a+++Gai+s+yqk+rier C +       PLW+k+ e ++ + +    ++++v+v+aegl+e  LG
  gi|518651627|ref|YP_008141147.1|  72 YLGEICRNGIDAIITGAIASDYQKTRIERACYDTDTIIYSPLWRKNQECIIDQLILRDIRAMIVSVSAEGLGEGDLG 148
                                       999********************************************9999************************** PP

                   Diphthami_syn_2 154 rridkklidelkklsekygidkagegGeaetlvlD 188
                                         id+++ ++lk ++ kygi+ agegGe+et+v  
  gi|518651627|ref|YP_008141147.1| 149 ATIDRDYFQHLKYINGKYGINIAGEGGEYETFVYG 183
                                       ********************************974 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   1.4e-06    0.0083       1      27 [.       2      28 ..       2      55 .. 0.92
   2 ?   -2.2   0.0      0.41   2.4e+03     112     127 ..      79      94 ..      76      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-06
                                      EEEEE--SSHHHHHHHHHHHHH-SEEE CS
                              QueC  1 kavvllSGGlDSttvlalakkegkeve 27
                                      kav l+SGG DS   +++a ++g+e++
  gi|518651627|ref|YP_008141147.1|  2 KAVALFSGGKDSFLSAMMAVEQGYEII 28
                                      79**********************986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.41
                                       HT-SEEEE---S-STT CS
                              QueC 112 lgaeaiiiGvneedfs 127
                                        g++aii+G+ ++d++
  gi|518651627|ref|YP_008141147.1|  79 NGIDAIITGAIASDYQ 94 
                                       6899*******99986 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   1.9e-05      0.12       5      32 ..       2      29 ..       1      87 [. 0.79
   2 ?   -2.4   0.0      0.49   2.9e+03     109     116 ..      81      88 ..      75     124 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.9e-05
                              ThiI  5 kvlaLlSgGiDSpVaaylllkRGcrvvl 32
                                      k++aL SgG DS  +a ++++ G ++ +
  gi|518651627|ref|YP_008141147.1|  2 KAVALFSGGKDSFLSAMMAVEQGYEIIY 29
                                      789*********************9865 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.49
                              ThiI 109 akalvtGe 116
                                       ++a++tG 
  gi|518651627|ref|YP_008141147.1|  81 IDAIITGA 88 
                                       56666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1427.97
//
Query:       gi|518651628|ref|YP_008141148.1|  [L=151]
Description: aspartate carbamoyltransferase regulatory subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-29  102.1   9.0    2.4e-29  101.4   8.2    1.7  2  PyrI      Aspartate carbamoyltransferase regulatory chain, al
    1.3e-16   60.2   2.4    2.7e-16   59.2   2.4    1.6  1  PyrI_C    Aspartate carbamoyltransferase regulatory chain, me


Domain annotation for each model (and alignments):
>> PyrI  Aspartate carbamoyltransferase regulatory chain, allosteric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   8.2   2.7e-33   2.4e-29       1      93 [.       5      94 ..       5      95 .. 0.96
   2 ?   -1.8   0.0      0.42   3.8e+03      51      61 ..     100     110 ..      98     117 .. 0.78

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 2.7e-33
                                      X-----SCEEEEEEEETT-HHHHHHHCT--T...TS-EEEEEEEEETTTEEEEEEEEET----HHHHHHHCCC-TT-EE CS
                              PyrI  1 lkvkkienGiViDHIkagkalkvlklLkldklkseekvaiiknvkskklgkKdiikiegkelseeeldklaliapnati 79
                                      lk++ki++G+ViDHI+agkalkvl +L++d+ ++  +++i++ v+s+kl  Kd+ikie+k+l++ eldk+alia++ati
  gi|518651628|ref|YP_008141148.1|  5 LKISKIKDGTVIDHIAAGKALKVLAILGIDE-SN--SISIGIRVTSEKLAYKDVIKIENKFLEKLELDKIALIANEATI 80
                                      69****************************6.44..59***************************************** PP

                                      EEEETTEEEEEE-- CS
                              PyrI 80 niIkdgevveKkkv 93
                                      +iIk++e++eK+k+
  gi|518651628|ref|YP_008141148.1| 81 SIIKNYEIIEKFKL 94
                                      ***********997 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.42
                                       EEEEEEEET-- CS
                              PyrI  51 kKdiikiegke 61 
                                        K+i+k ++++
  gi|518651628|ref|YP_008141148.1| 100 FKGIVKCANQN 110
                                       69999998875 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 !   59.2   2.4   3.1e-20   2.7e-16       3      48 .]     101     147 ..      99     147 .. 0.97

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 3.1e-20
                                       ESSS--S-TTBGGGT.TS-.-EEEEEETTTTEEEETTT--EEEHHHH CS
                            PyrI_C   3 egvlkCpNpnCItnn.epveskFkvedkekvklkCkYCekeiseeei 48 
                                       +g++kC N+nCItn  epv+s+F +++ +++++kC YC ke+s eei
  gi|518651628|ref|YP_008141148.1| 101 KGIVKCANQNCITNAgEPVKSEFMTVNADPLTIKCVYCKKEMSGEEI 147
                                       79*************99***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1014.42
//
Query:       gi|518651629|ref|YP_008141149.1|  [L=308]
Description: hypothetical protein FACI_IFERC00001G0268 [Ferroplasma acidarmanus fer1]
Scores for 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-48  162.4   0.0    1.6e-47  161.2   0.0    1.6  2  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl
    1.6e-29  103.0   0.0    2.5e-29  102.4   0.0    1.3  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
  ------ inclusion threshold ------
      0.042   13.8   0.0        0.1   12.6   0.0    1.6  1  FliMN_C   Type III flagellar switch regulator (C-ring) FliN C


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 !  161.2   0.0   2.8e-51   1.6e-47       1     147 [.       8     149 ..       8     150 .. 0.94
   2 ?   -2.0   0.0      0.53   3.2e+03      39      74 ..     157     191 ..     153     253 .. 0.70

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 2.8e-51
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r+++s++dl+ e+i+e++++a+++ e++++ kk + +++k+la+lF+epStRTr+Sfe+A++rlGg+v+s+ ++   
  gi|518651629|ref|YP_008141149.1|   8 RSIISISDLDGEDINEVFSRADKMLENIESGKKINVMSSKILATLFYEPSTRTRLSFESAMERLGGSVISMADS--- 81 
                                       789********************************************************************966... PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEES..SHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhp..gaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                                       ++ss+skg  E+l+Dt+r++++y+d+iviRhp  ga  +    +++s p+iNagdg+geHPtQ+L+Dl+tir
  gi|518651629|ref|YP_008141149.1|  82 KTSSTSKG--ETLADTIRIVESYSDLIVIRHPleGA--AFLASRFSSKPIINAGDGSGEHPTQTLIDLYTIR 149
                                       67888999..**********************8655..44466788*************************8 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.53
                                       T-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEEST CS
                          OTCace_N  39 gktlallFeepStRTrvSfevAakrlGgkvlslsea 74 
                                       gkt++++   +  RT  S  +A +r   +v  +s +
  gi|518651629|ref|YP_008141149.1| 157 GKTITIIGDLKYGRTVHSLLSALSRYNVTVNLVS-P 191
                                       6666666666667777777777777766655555.3 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 !  102.4   0.0   4.1e-33   2.5e-29       1     156 [.     156     304 ..     156     305 .. 0.91

  Alignments for each domain:
  == domain 1  score: 102.4 bits;  conditional E-value: 4.1e-33
                                       CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEE CS
                            OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvy 76 
                                       +g++i+++Gd k++++++sl+ +l+r++++v+lv+P++l   k+v++ +k        +++i++d+++ + ++D++y
  gi|518651629|ref|YP_008141149.1| 156 DGKTITIIGDlKYGRTVHSLLSALSRYNVTVNLVSPENLAIPKHVYNDVKGR-----LNMNISTDITKYLGETDILY 227
                                       699***********************************99999999887765.....79****************** PP

                                       E--SSETTCCGGHH...HHHHHHCC.CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHH CS
                            OTCace  77 tdvwvsmgeekere...erlkklkd.yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlht 149
                                        ++++     ker+   ++++ l + y++t   +++ kk ai++H+LP  r +E+++eV++ p++ +f+qa +++ +
  gi|518651629|ref|YP_008141149.1| 228 VTRIQ-----KERFtdkNEYARLIGsYKITVSDVNKLKKGAIIMHPLP--RVDEISSEVDNTPAARYFKQAYYGVPV 297
                                       *****.....5555444555555555**********************..*************************** PP

                                       HHHHHHH CS
                            OTCace 150 ikAllvl 156
                                       ++A++ +
  gi|518651629|ref|YP_008141149.1| 298 RMAIISM 304
                                       ****976 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 ?   12.6   0.0   1.7e-05       0.1      14      54 ..     246     286 ..     244     286 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       EEEEEEEHHHHHHHHTTSEEE--TTGGGCEEEEETTEEEEE CS
                           FliMN_C  14 lgrtrltlrellnLkvGdvipLdkpadepvevyvngkpiar 54 
                                       +g+ ++t++++ +Lk+G++i+   p  ++++  v++ p ar
  gi|518651629|ref|YP_008141149.1| 246 IGSYKITVSDVNKLKKGAIIMHPLPRVDEISSEVDNTPAAR 286
                                       7999****************999999999999999988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2179.44
//
Query:       gi|518651630|ref|YP_008141150.1|  [L=117]
Description: hypothetical protein FACI_IFERC00001G0269 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-14   52.8   0.0    5.3e-14   52.7   0.0    1.0  1  SnoaL_2   SnoaL-like domain
      6e-08   32.5   0.0      1e-07   31.8   0.0    1.4  1  SnoaL     SnoaL-like polyketide cyclase
    1.3e-05   25.3   0.0    1.4e-05   25.2   0.0    1.2  1  SnoaL_4   SnoaL-like domain
    5.9e-05   23.6   0.1    8.6e-05   23.1   0.1    1.4  1  NTF2      Nuclear transport factor 2 (NTF2) domain
      0.003   17.8   0.0     0.0032   17.7   0.0    1.3  1  SnoaL_3   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.7   0.0   1.5e-17   5.3e-14       1      98 [.       8     104 ..       8     109 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.7 bits;  conditional E-value: 1.5e-17
                                       HHHHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                           SnoaL_2   1 vraflaalnagdldalaalfapdvvwedp.ggelrGreairaffralfaafpdlrfeihdvvadgdrvavewtvtgt 76 
                                       v++++ a+++ dld+l ++fa+++v+  p   +++G + +++f+++ +  + + ++++ +++a++ +v+ve+++ g 
  gi|518651630|ref|YP_008141150.1|   8 VKKYYIAVDKNDLDTLFSIFADNIVYKRPgYEPIEGMANFKEFYQKNRI-IKEGHHTLSNIIASDPYVIVEGEFNG- 82 
                                       7899*************************8888**************85.99***********************9. PP

                                       EETTSSEEEEEEEEEEEEETTE CS
                           SnoaL_2  77 ipatgrgvtvrgvdvfrvrdGk 98 
                                       i ++g++ + ++vdv+++  Gk
  gi|518651630|ref|YP_008141150.1|  83 ILKDGSKSHTTFVDVYTFSSGK 104
                                       ******************9997 PP

>> SnoaL  SnoaL-like polyketide cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.0   2.9e-11     1e-07       4     119 ..       8     114 ..       5     117 .] 0.88

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.9e-11
                                       HHHHHHHHHTT-HHHHHGTEEEEEEETCCTTTCECHHHHHHHHHHHHHHHCTTCEEEEEEEEEETTEEEEEEEEEEE CS
                             SnoaL   4 lrfyeevwnsgdldaldelvaedvvdhnpeeeparGlegfrafveelfkafPDlkvevedlvaegdkvaarltftGt 80 
                                       ++ y  ++++ dld+l  ++a+++v++ p+ ep  G ++f++f+++++  + + +++   ++a++++v ++ +    
  gi|518651630|ref|YP_008141150.1|   8 VKKYYIAVDKNDLDTLFSIFADNIVYKRPGYEPIEGMANFKEFYQKNR-IIKEGHHTLSNIIASDPYVIVEGE---- 79 
                                       44555555*************************************996.788*****************9865.... PP

                                       ESSEBTTBE-TT-EEEEEEEEEEEEETTEEEEEEEEECH CS
                             SnoaL  81 htgeflGipptGkkvkfeeitllrvedGkIveewdviDl 119
                                           f Gi   G k   + +++++++ Gk  ++  ++D 
  gi|518651630|ref|YP_008141150.1|  80 ----FNGILKDGSKSHTTFVDVYTFSSGKAIKRHTYFDG 114
                                       ....678889999***************98888888886 PP

>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.9e-09   1.4e-05       7      76 ..       2      67 ..       1     110 [. 0.82

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.9e-09
                                      HHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTS..--EESHHHHHHHHHSHHHHHH-EEEEE---E CS
                           SnoaL_4  7 eaIrdlvarygyylDtkdweeladlFtedavvdytgvgegvlegrdairaalrealdgfaltqHllsnpl 76
                                      e+ +d+v +y +++D++d + l ++F++++v++ +g     +eg++ ++++++++    +   H++ + +
  gi|518651630|ref|YP_008141150.1|  2 EDLKDTVKKYYIAVDKNDLDTLFSIFADNIVYKRPGY--EPIEGMANFKEFYQKNR--IIKEGHHTLSNI 67
                                      7899*******************************98..99************973..343333333333 PP

>> NTF2  Nuclear transport factor 2 (NTF2) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   2.4e-08   8.6e-05       4      55 ..       6      56 ..       4      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 2.4e-08
                                      HHHHHHHHHHHHHGGGGGGGGEEEEEEEEEETTEEEEESHHHHHHHHHHSSC CS
                              NTF2  4 afvqqYYaaldagdregllalyaadaslltpegsspvkgreaIteffrslpf 55
                                        v++YY a+d++d ++l   + ad+ ++ ++g +p+ g ++  ef++++  
  gi|518651630|ref|YP_008141150.1|  6 DTVKKYYIAVDKNDLDTLFSIF-ADNIVYKRPGYEPIEGMANFKEFYQKNRI 56
                                      5799******************.************************98754 PP

>> SnoaL_3  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   8.9e-07    0.0032       3      51 ..       6      53 ..       4      95 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 8.9e-07
                           SnoaL_3  3 alldafyeaaaegdfdalfalwaddivfigtgadelltgreevrrslkq 51
                                      +++ ++y a+ + d+d+lf+++ad+iv+  +g  e ++g++ +++++++
  gi|518651630|ref|YP_008141150.1|  6 DTVKKYYIAVDKNDLDTLFSIFADNIVYKRPGY-EPIEGMANFKEFYQK 53
                                      67899*************************999.8889*******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 816.14
//
Query:       gi|518651631|ref|YP_008141151.1|  [L=268]
Description: hypothetical protein FACI_IFERC00001G0270 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1679.59
//
Query:       gi|518651632|ref|YP_008141152.1|  [L=411]
Description: hypothetical protein FACI_IFERC00001G0271 [Ferroplasma acidarmanus fer1]
Scores for complete 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-101  337.7   3.9   9.8e-101  337.4   3.9    1.1  1  HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase


Domain annotation for each model (and alignments):
>> HMG-CoA_red  Hydroxymethylglutaryl-coenzyme A reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.4   3.9  5.4e-105  9.8e-101       2     367 .]      13     369 ..      12     369 .. 0.94

  Alignments for each domain:
  == domain 1  score: 337.4 bits;  conditional E-value: 5.4e-105
                                       HHHHHHHHHH...S-HHHHHHHTT----HHHHHHHSSS---------EEEEEEEETTEEEEEEE---STTHHHHHHH CS
                       HMG-CoA_red   2 veeRrkllee...lteeeleelkeesldeevadkmiEnviGyvqlPlGvagpllingkeylvPmAteEgslvAsasr 75 
                                       v+eRr++++e   l+ e++e+  ++ +d ++a++miEnv + +  P+G+a++++in+keyl+Pm  eE+s++A++s+
  gi|518651632|ref|YP_008141152.1|  13 VDERRQIIREfsgLSSEDMEA-MDYRMDISTAGNMIENVYTIMDYPVGIATNFKINDKEYLIPMSLEEPSVIAACSN 88 
                                       89********66566666666.478899************************************************* PP

                                       HHHHHHHTT-B.EEEE----EEEEEEEE.--S-HHHHHHHH.HTHHHHHHHHHHCSHH..CCT-EEEEEEEEE-SSE CS
                       HMG-CoA_red  76 gakainesgGvkttvlkdgmtraqvvllesvedaaelkkwi.ekkeeleelanaaest..srggglkdievvlagrl 149
                                       +a+ + + gG+ t+ ++++ +r+++ l+ +v d+  +   i ++ke++ ++an  ++t     +g+k+i+++++++ 
  gi|518651632|ref|YP_008141152.1|  89 AARYA-RPGGF-TAYSTNSYMRGEIELY-NVPDPDYAAINIlKNKENILKMANTRSKTlsGMNAGAKSIDLHFVNNE 162
                                       ***99.6789*.5556666*********.9999999999999****************988899************* PP

                                       EEEEEEEE-TTC--HHHHHHHHHHHHHHHHHHHTSEEEEEEE-S--GGGEEEEEEEEEHHHH..-SSTTHHHHHHHH CS
                       HMG-CoA_red 150 vvlrlkvdtgDAmGaNmvnkateaaaelieeefgeeellsilsNlctdkkasainaiegrgksvvaeatigeevvek 226
                                       +++++ +d+ DAmGaN++n+++e ++ +iee +g++++l+i sNl+t++++ a + ++g+ +        gee+v++
  gi|518651632|ref|YP_008141152.1| 163 LIINIIIDVADAMGANIINTMLEYVSGYIEELTGGQANLRIMSNLTTERITYAYAKFDGKML--------GEETVDR 231
                                       *****************************************************999998888........******* PP

                                       HHHHHHHHHH-HHHH..HHHHHHH.......HHHHHHHHHHTT--HHHHHHHHHHHTT......SEEE...TTTEEE CS
                       HMG-CoA_red 227 ilkasaealvdlnranigtankGiggfnahaaNgiaAvflAtGqDlaaveesshaiaa......leev...edgdly 294
                                       i++a+++a+ d++ra  +t+nkGi       +Ngi+Av+lAt +D++a e+ sha+a+      l+e+    dg+l 
  gi|518651632|ref|YP_008141152.1| 232 IIRANEFAKNDIYRA--TTHNKGI-------MNGIDAVLLATMNDFRAQEANSHAYASmggygpLTEYrkdIDGNLI 299
                                       ***************..*******.......***************************99999977777655667** PP

                                       EEEEEE.----SBSHHHHH-HHHHHH.HHTT---HH...HHHHHHHHHHHHHHHHHHHHHT-----HHHHHHHH CS
                       HMG-CoA_red 295 gsvtlPsleVGtvGGgtklppqaell.kllgvkgaknakeLaeiiaavgLAqelsalrALaaeglqkgHmklhr 367
                                       gs+++P ++VGtvGG+tk+  +a l+ k++g++g++   e+++i+ +vgLAq+++alrALaaeg+q+gHmklh+
  gi|518651632|ref|YP_008141152.1| 300 GSIKIP-IAVGTVGGATKTSRKAMLAmKIMGIHGSG---EFSNILGSVGLAQNFAALRALAAEGIQSGHMKLHA 369
                                       ******.*****************************...*********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 3115.60
//
Query:       gi|518651633|ref|YP_008141153.1|  [L=242]
Description: hypothetical protein FACI_IFERC00001G0272 [Ferroplasma acidarmanus fer1]
Scores for complete 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   30.0   3.9    0.00038   20.7   0.1    3.7  4  TPR_12    Tetratricopeptide repeat
    7.6e-06   25.7  16.5    0.00036   20.5   0.2    6.0  6  TPR_8     Tetratricopeptide repeat
    4.3e-05   23.3   7.8     0.0097   16.0   0.0    5.6  6  TPR_2     Tetratricopeptide repeat
     0.0073   16.9   0.0         12    6.7   0.0    3.2  4  TPR_16    Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.011   15.5   0.1    4.6  5  TPR_1     Tetratricopeptide repeat
      0.036   14.1   1.9        5.7    7.2   0.0    4.1  4  TPR_7     Tetratricopeptide repeat
      0.048   13.4   5.4      0.093   12.4   0.1    3.1  3  TPR_21    Tetratricopeptide repeat-like domain
      0.066   12.9   4.8        1.6    8.5   0.0    4.1  4  TPR_11    TPR repeat
       0.82   10.2   3.7       0.68   10.5   1.2    2.0  2  DUF2408   Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.024        47      11      60 ..      12      55 ..       7      60 .. 0.79
   2 !   20.7   0.1   1.9e-07   0.00038      23      75 ..      63     113 ..      63     115 .. 0.96
   3 ?    3.9   0.1     0.032        64      20      49 ..     141     168 ..     120     185 .. 0.85
   4 ?   -2.0   0.0       2.2   4.4e+03      13      28 ..     224     239 ..     215     242 .] 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.024
                            TPR_12 11 avlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgr 60
                                      ++  + +++ +A++ + ka++++      + +  a++ + L+++y+ l +
  gi|518651633|ref|YP_008141153.1| 12 DAFVKKEKFMDAIREYTKAYDAI-----SEDDIKAEICYKLSQCYSSL-D 55
                                      55667788999********9999.....44558899999999999877.3 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 1.9e-07
                            TPR_12  23 lellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleealaia 75 
                                       l++ e++le++ +l  +d++l++  l+n+g +y+ +g+ e+ ++++++a+++a
  gi|518651633|ref|YP_008141153.1|  63 LKYAEESLELHHKL--GDSELEVMDLINIGYIYLDSGKREDGISYFNKAIEAA 113
                                       689***********..9*********************************987 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.032
                            TPR_12  20 deAlellekaleiarrllGpdhpltattlr 49 
                                       +eA ++++ +le+ +++  +d++++ ++l+
  gi|518651633|ref|YP_008141153.1| 141 AEAMKIYDNVLELTEKS--EDWENYFEALY 168
                                       79999*********999..99999888876 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.2
                            TPR_12  13 lrrlgrydeAlellek 28 
                                        ++l++ deA ++  +
  gi|518651633|ref|YP_008141153.1| 224 AMELENIDEAMKIAAR 239
                                       5556666666555554 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       1.6   3.2e+03       9      29 ..      12      32 ..      11      36 .. 0.72
   2 ?    5.2   0.0     0.015        30       1      15 [.      41      55 ..      41      58 .. 0.89
   3 ?   -0.7   0.0       1.2   2.3e+03      10      18 ..      72      80 ..      64      83 .. 0.80
   4 !   20.5   0.2   1.8e-07   0.00036       5      31 ..      87     113 ..      86     115 .. 0.93
   5 ?    2.8   0.3     0.086   1.7e+02      15      33 ..     138     156 ..     124     157 .. 0.73
   6 ?    4.1   0.1     0.032        64       7      23 ..     220     236 ..     214     241 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.6
                                      HHHHHTT-HHHHHHHHHHHHH CS
                             TPR_8  9 siylklgdyeeAkeyyekale 29
                                      ++  k++++  A+  y ka +
  gi|518651633|ref|YP_008141153.1| 12 DAFVKKEKFMDAIREYTKAYD 32
                                      666777777778888888865 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                                      CCHHHHHHHHHHHTT CS
                             TPR_8  1 aeayynlgsiylklg 15
                                      ae++y+l+++y++l 
  gi|518651633|ref|YP_008141153.1| 41 AEICYKLSQCYSSLD 55
                                      799*********997 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                                      HHHHTT-HH CS
                             TPR_8 10 iylklgdye 18
                                      +++klgd e
  gi|518651633|ref|YP_008141153.1| 72 LHHKLGDSE 80
                                      788999987 PP

  == domain 4  score: 20.5 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleld 31 
                                        n+g+iyl+ g+ e  ++y++ka+e++
  gi|518651633|ref|YP_008141153.1|  87 INIGYIYLDSGKREDGISYFNKAIEAA 113
                                       69**********************986 PP

  == domain 5  score: 2.8 bits;  conditional E-value: 0.086
                                       T-HHHHHHHHHHHHHHHHH CS
                             TPR_8  15 gdyeeAkeyyekaleldpd 33 
                                        +  eA++ y  +lel ++
  gi|518651633|ref|YP_008141153.1| 138 SKQAEAMKIYDNVLELTEK 156
                                       46789*******9999765 PP

  == domain 6  score: 4.1 bits;  conditional E-value: 0.032
                                       HHHHHHHTT-HHHHHHH CS
                             TPR_8   7 lgsiylklgdyeeAkey 23 
                                        ++i ++l++++eA++ 
  gi|518651633|ref|YP_008141153.1| 220 VSDIAMELENIDEAMKI 236
                                       57999*********986 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.1      0.28   5.5e+02       8      28 ..      11      31 ..       5      34 .. 0.82
   2 ?    1.4   0.0      0.23   4.5e+02       1      15 [.      41      55 ..      41      58 .. 0.85
   3 ?   -1.7   0.0       2.2   4.4e+03      22      30 ..      64      72 ..      63      78 .. 0.76
   4 !   16.0   0.0   4.9e-06    0.0097       4      30 ..      86     112 ..      84     115 .. 0.93
   5 ?    2.3   0.1      0.12   2.3e+02       8      32 ..     130     155 ..     123     157 .. 0.73
   6 ?    1.5   0.0       0.2   4.1e+02       8      22 ..     221     235 ..     214     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.28
                             TPR_2  8 GlayyklgdyeeAleafekAl 28
                                      G+a  k+ ++ +A++ + kA 
  gi|518651633|ref|YP_008141153.1| 11 GDAFVKKEKFMDAIREYTKAY 31
                                      677778888889*******96 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                             TPR_2  1 aealynlGlayyklg 15
                                      ae++y l ++y  l+
  gi|518651633|ref|YP_008141153.1| 41 AEICYKLSQCYSSLD 55
                                      799********8876 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.2
                             TPR_2 22 eafekAlel 30
                                      ++ e++lel
  gi|518651633|ref|YP_008141153.1| 64 KYAEESLEL 72
                                      788888887 PP

  == domain 4  score: 16.0 bits;  conditional E-value: 4.9e-06
                             TPR_2   4 lynlGlayyklgdyeeAleafekAlel 30 
                                       l n+G++y+ +g+ e+ + +f+kA+e 
  gi|518651633|ref|YP_008141153.1|  86 LINIGYIYLDSGKREDGISYFNKAIEA 112
                                       689**********************96 PP

  == domain 5  score: 2.3 bits;  conditional E-value: 0.12
                             TPR_2   8 Glayyklgdy.eeAleafekAleldP 32 
                                       ++a+  l+   +eA + ++ +lel +
  gi|518651633|ref|YP_008141153.1| 130 AEALSSLKSKqAEAMKIYDNVLELTE 155
                                       555555555559***********976 PP

  == domain 6  score: 1.5 bits;  conditional E-value: 0.2
                             TPR_2   8 GlayyklgdyeeAle 22 
                                        +++++l + +eA +
  gi|518651633|ref|YP_008141153.1| 221 SDIAMELENIDEAMK 235
                                       67899********87 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0074        15       2      43 ..       9      50 ..       8      56 .. 0.78
   2 !    6.7   0.0    0.0058        12       2      27 ..      88     113 ..      87     152 .. 0.77
   3 ?   -1.7   0.0       2.5     5e+03      15      40 ..     142     170 ..     139     177 .. 0.73
   4 ?   -3.0   0.0       6.2   1.2e+04       6      18 ..     223     235 ..     221     239 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0074
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      + ++a+++  ++ dA++ ++ a ++ +++   ae  + l ++
  gi|518651633|ref|YP_008141153.1|  9 KNGDAFVKKEKFMDAIREYTKAYDAISEDDIKAEICYKLSQC 50
                                      5799****************9998866666566666666555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0058
                            TPR_16   2 alaraalragdyddAaaaleaalkrd 27 
                                       + ++++l++g+ +d + +++ a++++
  gi|518651633|ref|YP_008141153.1|  88 NIGYIYLDSGKREDGISYFNKAIEAA 113
                                       568999************99999987 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.5
                            TPR_16  15 dAaaaleaalkrdpssPd...aaeAllll 40 
                                       +A + ++ +l++  +s d     eAl+++
  gi|518651633|ref|YP_008141153.1| 142 EAMKIYDNVLELTEKSEDwenYFEALYGK 170
                                       67888888888887777777777777776 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 6.2
                            TPR_16   6 aalragdyddAaa 18 
                                       +a+++ + d+A +
  gi|518651633|ref|YP_008141153.1| 223 IAMELENIDEAMK 235
                                       5667777777765 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.05     1e+02       8      27 ..      11      30 ..      10      32 .. 0.91
   2 ?   -2.3   0.1       2.3   4.6e+03      21      32 ..      63      74 ..      63      76 .. 0.79
   3 ?   15.5   0.1   5.5e-06     0.011       5      29 ..      87     111 ..      86     113 .. 0.95
   4 ?   -0.2   0.1      0.52     1e+03      18      30 ..     141     153 ..     136     156 .. 0.85
   5 ?   -1.3   0.0       1.1   2.2e+03      12      22 ..     225     235 ..     223     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.05
                                      HHHHHHTT-HHHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyekA 27
                                      G a+ k++k+ +A+  y kA
  gi|518651633|ref|YP_008141153.1| 11 GDAFVKKEKFMDAIREYTKA 30
                                      678999**********9998 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.3
                                      HHHHHHHHHHST CS
                             TPR_1 21 leyyekALelnP 32
                                      l+y e+ Lel +
  gi|518651633|ref|YP_008141153.1| 63 LKYAEESLELHH 74
                                      688899999976 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 5.5e-06
                                       HHHHHHHHHTT-HHHHHHHHHHHHH CS
                             TPR_1   5 ynlGnayfklgkydeAleyyekALe 29 
                                        n+G++y+  gk ++ + y++kA+e
  gi|518651633|ref|YP_008141153.1|  87 INIGYIYLDSGKREDGISYFNKAIE 111
                                       7***********************8 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.52
                                       HHHHHHHHHHHHH CS
                             TPR_1  18 deAleyyekALel 30 
                                        eA + y+ +Lel
  gi|518651633|ref|YP_008141153.1| 141 AEAMKIYDNVLEL 153
                                       6999999999998 PP

  == domain 5  score: -1.3 bits;  conditional E-value: 1.1
                                       HHTT-HHHHHH CS
                             TPR_1  12 fklgkydeAle 22 
                                       ++l++ deA +
  gi|518651633|ref|YP_008141153.1| 225 MELENIDEAMK 235
                                       7899*****75 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.24   4.9e+02       6      31 ..      11      37 ..      11      42 .. 0.81
   2 ?   -1.1   0.0       1.2   2.5e+03      23      34 ..      67      78 ..      63      80 .. 0.58
   3 ?    7.2   0.0    0.0029       5.7       2      30 ..      86     114 ..      86     120 .. 0.81
   4 ?    1.4   0.1       0.2   4.1e+02      11      31 ..     135     156 ..     127     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.24
                             TPR_7  6 arlysrlGdyeeAielyeqsL.altkd 31
                                      ++++++  ++ +Ai+ y+++  a+ +d
  gi|518651633|ref|YP_008141153.1| 11 GDAFVKKEKFMDAIREYTKAYdAISED 37
                                      678888889999*******88777666 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
                             TPR_7 23 eqsLaltkdped 34
                                      e+sL+l+   +d
  gi|518651633|ref|YP_008141153.1| 67 EESLELHHKLGD 78
                                      666666655554 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0029
                             TPR_7   2 LlnLarlysrlGdyeeAielyeqsLaltk 30 
                                       L n++ +y + G++e+ i+++ ++++ ++
  gi|518651633|ref|YP_008141153.1|  86 LINIGYIYLDSGKREDGISYFNKAIEAAD 114
                                       679******************99665444 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.2
                             TPR_7  11 r.lGdyeeAielyeqsLaltkd 31 
                                       +   + +eA ++y  +L+lt+ 
  gi|518651633|ref|YP_008141153.1| 135 SlKSKQAEAMKIYDNVLELTEK 156
                                       55667789*******9999865 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   4.7e-05     0.093     152     188 ..      10      47 ..       3      52 .. 0.88
   2 ?   -0.6   0.0      0.45   8.9e+02     153     178 ..      90     115 ..      64     135 .. 0.83
   3 ?    1.4   0.4      0.11   2.2e+02      34      54 ..     138     158 ..     131     239 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.7e-05
                            TPR_21 152 rGDilvaqgkldeAraaYqaAlaaleeka.rellqlKl 188
                                        GD++v+++k+ +A  +Y++A++a++e++ ++ +  Kl
  gi|518651633|ref|YP_008141153.1|  10 NGDAFVKKEKFMDAIREYTKAYDAISEDDiKAEICYKL 47 
                                       6*************************999877777776 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                            TPR_21 153 GDilvaqgkldeAraaYqaAlaalee 178
                                       G i++  gk+++  + +++A++a ++
  gi|518651633|ref|YP_008141153.1|  90 GYIYLDSGKREDGISYFNKAIEAADA 115
                                       67899999999999999999988876 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.11
                            TPR_21  34 eqaeeAsalYqqlqeaveakd 54 
                                       ++++eA ++Y++++e +e+++
  gi|518651633|ref|YP_008141153.1| 138 SKQAEAMKIYDNVLELTEKSE 158
                                       566777777777776443322 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0008       1.6       1      20 [.      11      30 ..      11      39 .. 0.95
   2 ?   -1.6   0.0       1.2   2.3e+03      26      36 ..      68      78 ..      63      79 .. 0.72
   3 ?    1.3   0.2      0.14   2.7e+02       1      22 [.      90     111 ..      90     112 .. 0.90
   4 ?    1.8   0.1     0.095   1.9e+02       9      27 ..     139     157 ..     136     159 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0008
                            TPR_11  1 GdayyeqGkyeeAieaYkkA 20
                                      Gda++++ k+ +Ai +Y kA
  gi|518651633|ref|YP_008141153.1| 11 GDAFVKKEKFMDAIREYTKA 30
                                      9****************999 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                            TPR_11 26 dnaeayynLGl 36
                                      ++ e++++LG+
  gi|518651633|ref|YP_008141153.1| 68 ESLELHHKLGD 78
                                      56689999995 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.14
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlk 22 
                                       G++y + Gk e+ i  ++kA++
  gi|518651633|ref|YP_008141153.1|  90 GYIYLDSGKREDGISYFNKAIE 111
                                       899******9999999999986 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.095
                            TPR_11   9 kyeeAieaYkkAlkldPdn 27 
                                       k  eA++ Y + l+l++++
  gi|518651633|ref|YP_008141153.1| 139 KQAEAMKIYDNVLELTEKS 157
                                       7789***********9886 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.2   4.4e+03     102     115 ..      41      54 ..       6      85 .. 0.63
   2 ?   10.5   1.2   0.00034      0.68      39     125 ..     138     230 ..     119     231 .. 0.58

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                           DUF2408 102 kkvasslqpiYdrL 115
                                        ++  +l + Y++L
  gi|518651633|ref|YP_008141153.1|  41 AEICYKLSQCYSSL 54 
                                       33344444444443 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00034
                           DUF2408  39 evkeelkelkeeLkkieskrde.egkFkseegke......vvekgqavlngLlddcfdlvedlkaqdgeekkvassl 108
                                       + ++e  ++ +++ ++ +k ++ e+ F    gk         +++    +  ld+   +++ +k+++ ++k+ ++s+
  gi|518651633|ref|YP_008141153.1| 138 SKQAEAMKIYDNVLELTEKSEDwENYFEALYGKIsilrdaDINAAFDAGKAGLDKIDTVMNTIKTKK-DKKEFKDSV 213
                                       3444444444555555444444244443333322333222111122233444677778899999996.78******* PP

                           DUF2408 109 qpiYdrLleikttLenL 125
                                         +Yd+ ++i  +Len+
  gi|518651633|ref|YP_008141153.1| 214 SYLYDSVSDIAMELENI 230
                                       ***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1271  (0.0708907); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1548.37
//
Query:       gi|518651634|ref|YP_008141154.1|  [L=239]
Description: esterase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-17   62.7   0.0    1.5e-09   37.9   0.0    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    3.5e-16   60.5   0.0    3.7e-14   53.9   0.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.054   13.3   1.5        1.5    8.6   0.2    2.9  3  Abhydrolase_2  Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.6e-13   1.5e-09       2      92 ..      23     106 ..      22     112 .. 0.95
   2 !   23.1   0.0   8.1e-09   4.9e-05     171     255 ..     126     220 ..     121     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.6e-13
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       ++++lhG++g+++ w +    p+L+k   + +l+Dl+G+g+S+++      +y+    a+++  + + l++ k+ + 
  gi|518651634|ref|YP_008141154.1|  23 PVIFLHGFGGTGNTWLK--TTPYLEK-CIRPVLVDLLGHGHSDKPD----IEYTVQQQAESIVDLINTLDISKFSIA 92 
                                       9****************..*******.99999*************9....5799999******************** PP

                                       EETHHHHHHHHHHH CS
                     Abhydrolase_1  79 GhSmGGmialayaa 92 
                                       G S+GG i l +a+
  gi|518651634|ref|YP_008141154.1|  93 GNSYGGWITLKLAS 106
                                       ********999885 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 8.1e-09
                                       HHHHHHHCHHHHHHHHHHHHHHHHCCHHHHHHHHHC..........THHHHSEEEEEEETTCSSSCHHHHHHHHHCH CS
                     Abhydrolase_1 171 pssgsdnasslatgalksieqwpttdsaklllrlre..........lknvlaptlvisgtsDplvppkaledlaqll 237
                                        s+gs+ +++ +  +++ +  ++++    ++ + ++          l n++++t +i+g+ D+++p +++  +++++
  gi|518651634|ref|YP_008141154.1| 126 LSNGSRENMNRVLDSILKLRNYNNRNALERIMENNKkqeekisdtaLGNIKSKTTIIWGSVDNIIPVSYGHAMESKI 202
                                       567788888888888888888888888888888888999999999999***************************** PP

                                       TSEEEEEEETCSSSHHHH CS
                     Abhydrolase_1 238 pkkrlvvisdagHlafle 255
                                       ++++l+v +da H+ f++
  gi|518651634|ref|YP_008141154.1| 203 SGSELIVMPDASHTPFID 220
                                       ***************997 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.0   6.1e-18   3.7e-14       1     219 [.      24     227 ..      24     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 6.1e-18
                                       EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH.HHHHCCTT...TTSEEEEEETC CS
                     Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledladl.aalldelaa.gggpvvlvGHSl 74 
                                       v++lHG+g+++  Wl ++p +++  + v    +Dl GhG+sd p+ +++  +++ + ++d + + +  ++ + G+S+
  gi|518651634|ref|YP_008141154.1|  24 VIFLHGFGGTGNTWLkTTPYLEKCIRPV---LVDLLGHGHSDKPDIEYTV-QQQaESIVDLINTlDISKFSIAGNSY 96 
                                       79************87888888888887...6*************99988.444355555555557999******** PP

                                       HHHHHHHHHHCC..EEEEES-..----TTT...S----TTHHHHHHTT-CCCCHCCHS-HSCCCCHHHCCCCHCHCC CS
                     Abhydrolase_6  75 GGalalaaaplalvvgvlldppptalpagl...laaalelllallallrllawlsreplprlfladedadaawrarl 148
                                       GG++ l    la     +l+p   +  + +   +++al+   + + +++l+  l+   l+  + +     +   +r 
  gi|518651634|ref|YP_008141154.1|  97 GGWITLK---LAS---GMLEP--DMIFPVDsagISPALSNGSRENMNRVLDSILK---LR-NYNN-----RNALERI 156
                                       *******...884...67777..44444442334444444444444444444443...22.4444.....3333333 PP

                                       CGHHHHCCHHCHTTCCHHTT-TTGCEEEC.TT-CHHHHCHHCCCH..STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 149 arlaallaglgllpaaawadlpvpllvlg.geDplvprllerlla..qagarlpvvlpgaGHlphleepdevae 219
                                        +  + +   +  + +a+  + + + +++ + D ++p  + +++   + g +l +v+p+a+H p+++ p+e+ae
  gi|518651634|ref|YP_008141154.1| 157 MENNKKQE--EKISDTALGNIKSKTTIIWgSVDNIIPVSYGHAMEskISGSEL-IVMPDASHTPFIDMPKEFAE 227
                                       33333333..3445668889999997776499**9994455555588899999.************999***98 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.2   0.00025       1.5      17      33 ..      24      40 ..      20      53 .. 0.88
   2 ?    0.1   0.0       0.1   6.1e+02      86     123 ..      69     105 ..      51     111 .. 0.63
   3 ?    1.7   0.0     0.032   1.9e+02     159     182 ..     179     202 ..     151     230 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00025
                                      EEEE--TT--SHHHHHH CS
                     Abhydrolase_2 17 viflHGlGdsghawaea 33
                                      viflHG G +g+ w + 
  gi|518651634|ref|YP_008141154.1| 24 VIFLHGFGGTGNTWLKT 40
                                      9**********999876 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHHHTT--GGGEEEEEETHHHHHHHHHH CS
                     Abhydrolase_2  86 saekleelidaelkkgipssriiigGFSqGaalalyla 123
                                       ++++  e i  +l + ++ s+  i G S G+ ++l+la
  gi|518651634|ref|YP_008141154.1|  69 TVQQQAESIV-DLINTLDISKFSIAGNSYGGWITLKLA 105
                                       3333333332.223447888899999999999999875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.032
                                       EEEEEETT-SSS-HHHHHHHHHHH CS
                     Abhydrolase_2 159 ilqiHgeeDpvvplalgkaakevl 182
                                          i+g+ D+++p++ g a++  +
  gi|518651634|ref|YP_008141154.1| 179 TTIIWGSVDNIIPVSYGHAMESKI 202
                                       445789999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); 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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 1755.99
//
Query:       gi|518651635|ref|YP_008141155.1|  [L=169]
Description: hypothetical protein FACI_IFERC00001G0274 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1010.41
//
Query:       gi|518651636|ref|YP_008141156.1|  [L=72]
Description: hypothetical protein FACI_IFERC00001G0275 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.051   12.8   0.5      0.057   12.7   0.5    1.0  1  Enolase_C  Enolase, C-terminal TIM barrel domain


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 ?   12.7   0.5   3.2e-06     0.057     130     195 ..       4      69 ..       1      71 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-06
                                       GCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHH CS
                         Enolase_C 130 skkltseqladlykelvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkea 195
                                        k +++++++d+y e ++++ i si d  d+ d ++              + dd  vt  +++++a
  gi|518651636|ref|YP_008141156.1|   4 VKLIAEKNIKDMYGENISNFTINSIVDNSDRYDVSTEFDYAGFHYTVYLSIDDDGNVTKFNQIAKA 69 
                                       5678999*********************99999987655555555444557888899998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 528.78
//
Query:       gi|518651637|ref|YP_008141157.1|  [L=332]
Description: hypothetical protein FACI_IFERC00001G0276 [Ferroplasma acidarmanus fer1]
Scores for complete 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-05   22.7   0.0     0.0048   16.3   0.0    2.3  1  Amidohydro_1  Amidohydrolase family
  ------ inclusion threshold ------
       0.13   11.6   0.4       0.38   10.0   0.1    1.7  2  A_deaminase   Adenosine/AMP deaminase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.3e-07    0.0048       4     288 ..      41     286 ..      38     296 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.3e-07
                                       E-EEEEEEECETTECSSS...GHHHHH............STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHH CS
                      Amidohydro_1   4 PGlIDaHvHleqsllrga...tledwl............vppetaaealesgiktalksGtttvadmgattstgiea 65 
                                       P  ++aH+H+ +s++ ++   tl +++            ++++++  ++ +    + k+G+ +  d++++  +gi+ 
  gi|518651637|ref|YP_008141157.1|  41 PMPVNAHTHVGDSFINEEpkgTLPEIVgpdglkhrfldnADDNEVINYISKTNNFMEKNGIISYFDFRENGLKGINM 117
                                       55589*****99988777999999999999999999999999999999999999999************99999999 PP

                                       HHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHH CS
                      Amidohydro_1  66 lleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeak 142
                                       +++  ++        ++ v+++r  ++ +   + k++a                +++ ++     ++ +++++ + +
  gi|518651637|ref|YP_008141157.1| 118 IKRGNKKF-------IKPVIFARPYNNDD---IDKIIANS-------------NGIGISSISDMDYNDIYDISIKTH 171
                                       99999993.......34445553333334...55555554.............344444444444459999999999 PP

                                       HHTTEEEEEETSSCHH.HHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHH CS
                      Amidohydro_1 143 krdlpvaiHaletkge.vedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahc 218
                                       k+++ +a H++e+ +e +  + +            +              l hg+   ++++  + ++  +++++  
  gi|518651637|ref|YP_008141157.1| 172 KKNKIFALHFSENINEdIDKVMNLK---------PDL-------------LIHGIESNDNDLDKISKN--NVSIVIT 224
                                       9999999999665555033333333.........344.............778888888888888888..8888877 PP

                                       HHHHHHSEHHHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHH CS
                      Amidohydro_1 219 pfsnsilrsgrealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllyedeegglslkealrm 288
                                       p+sn     +r++ +k l+ +++ +lgtD +     ++++ e+ +++  qr l+y      +s++ +l+m
  gi|518651637|ref|YP_008141157.1| 225 PRSNI-FYGKRPDYNKFLKHNINLMLGTD-NVFVTEPDIFSEMDFLYRYQRFLNY------VSPENILKM 286
                                       77664.5667899999*************.6667889**********99999988......666666665 PP

>> A_deaminase  Adenosine/AMP deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   4.2e-05      0.38     210     293 ..     192     268 ..     177     276 .. 0.83
   2 ?   -1.1   0.0       0.1   9.3e+02     280     299 ..     307     326 ..     306     331 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 4.2e-05
                                       HHCS--SCECE-GGGGGSHHHHHHHHHCT-EEEE-HHHHCCCSST-TTTT-C.HHHHHHTT-EEEE--BSCCCCT-S CS
                       A_deaminase 210 llllkaerigHGvrlrkdpvLqyllalaqiplevcPlSNvalgafleyaenP.lkeflerglnvslntDDPlqfgtt 285
                                       ++ lk + + HG+++  d +L ++ +++++ + + P SN+  g      + P  ++fl++++n+ l+tD+  + + +
  gi|518651637|ref|YP_008141157.1| 192 VMNLKPDLLIHGIESN-DNDL-DKISKNNVSIVITPRSNIFYG------KRPdYNKFLKHNINLMLGTDNVFVTEPD 260
                                       5677888899***986.5666.568999************983......3332579**************9999999 PP

                                       HHHHHHHH CS
                       A_deaminase 286 LieeYaia 293
                                       +  e++ +
  gi|518651637|ref|YP_008141157.1| 261 IFSEMDFL 268
                                       99999876 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.1
                                       CCCT-SHHHHHHHHHHHHT- CS
                       A_deaminase 280 lqfgttLieeYaiaaqvfkl 299
                                       l f+ +L +eY+i+++++ +
  gi|518651637|ref|YP_008141157.1| 307 LFFKNELLNEYQIVTKKHYF 326
                                       578999********998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2506.14
//
Query:       gi|518651638|ref|YP_008141158.1|  [L=189]
Description: hypothetical protein FACI_IFERC00001G0277 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-28   98.8   0.0    4.5e-28   98.4   0.0    1.1  1  RibD_C    RibD C-terminal domain


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4   0.0   2.5e-32   4.5e-28       1     179 [.       3     165 ..       3     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.5e-32
                                       -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS- CS
                            RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqp 77 
                                       py+i+++a+Sl Gk++a +g  + i+ + + ++v ++r+++d++l+G++ v+ dnp    ++             + 
  gi|518651638|ref|YP_008141158.1|   3 PYIIINVAMSLNGKISAINGRYR-ISNDIDMTRVMDIRKNVDGVLLGANSVKVDNP--VLNY-------------AK 63 
                                       8*******************999.********************************..3333.............44 PP

                                       EEEEEETTS-S-TTSHHHHSSS-EEEEESSCSCHHHHHHCCE..SE-HHHHHHHHHHTT--EEEEEETHHHHHHHHH CS
                            RibD_C  78 vrvVvdstlrvpldakvltddaptlvatteeadkekveklkv..rvdlkelleeLkergirsllveGGatLagsllr 152
                                        r+++d + r+++++ v+++++++ ++++++ +k k  ++ +   + + ++l++L+++gi+s+lveGG+++++++++
  gi|518651638|ref|YP_008141158.1|  64 NRIILDEKFRLNDNYHVFDGKSKSYIFSKNN-KKIKNAEIIIldDLSITSILKKLYDMGIKSILVEGGSNVINQFID 139
                                       59*****************998888888885.3333333333799******************************** PP

                                       TTT-SEEEEEEESCE--TTSBCSSSSS CS
                            RibD_C 153 aglvDelrlyiaPkllGgagktlfdge 179
                                       ++++De+ ++i P l+ + g +lf++e
  gi|518651638|ref|YP_008141158.1| 140 EKIFDEFYIFINPGLILD-GISLFKEE 165
                                       *************99877.77777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1387.50
//
Query:       gi|518651639|ref|YP_008141159.1|  [L=236]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-51  173.9   0.0    3.2e-51  173.6   0.0    1.1  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
     0.0035   16.6   0.1     0.0051   16.0   0.1    1.2  1  PIF1           PIF1-like helicase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.6   0.0   3.5e-55   3.2e-51       1     191 [.       9     226 ..       9     227 .. 0.92

  Alignments for each domain:
  == domain 1  score: 173.6 bits;  conditional E-value: 3.5e-55
                                       HHHHHHHHTT--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-S..... CS
                     DHBP_synthase   1 eeaiealkaGkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveene..... 72 
                                       +eai+alk+ k+++++D +drene+d++ia+e+vtpe +++m+++++Glic++++e++a++++Lp++ +        
  gi|518651639|ref|YP_008141159.1|   9 DEAIRALKNKKIILIHDFNDRENETDMVIASEFVTPEIIRTMRKDGGGLICTTIKEKDAKKFNLPYLDD--Lfyksl 83 
                                       58*****************************************************************95..344556 PP

                                       .............STT---BB--EEESST-SSS-SHHHHHHHHHHHH-T............T--GGGEEEEEEEEEE CS
                     DHBP_synthase  73 .............dkhktaftvsvdaaegttTGIsaaDRalTirkladp............kakpedfrrPGhvfpl 124
                                                       k af+++v+ + +t TGI ++DR +T++++ +             k+  + fr PGh+++l
  gi|518651639|ref|YP_008141159.1|  84 nmdksvlnssdmgYDTKDAFSLTVNSR-DTYTGIPDNDRYKTVKHFSEFinalgnnvnvneKNFGKIFRVPGHIHLL 159
                                       777888999988845689*********.9****************99955689999988764455899********* PP

                                       EE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHHH CS
                     DHBP_synthase 125 rareggvleRrghTEaavdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedlie 191
                                       +ar++ ++eR+ghTE+++ +++ agl p a+i+e l+d+ +++++de e++a++h++ +i+++++i+
  gi|518651639|ref|YP_008141159.1| 160 IARNNYFKERKGHTELSTYIVEKAGLVPSATIVETLSDSFNSMTLDESEKYADEHNMVLINGKEIID 226
                                       ***************************************89***********************995 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   5.7e-07    0.0051     168     296 ..      88     211 ..      81     228 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.7e-07
                                       C...CSCHHHH--.EEEE-S-STTTT............HHHHHHHHHHHCT---CCCCHH................. CS
                              PIF1 168 asikeSklWkevk.vlkLtknmRllseslde.tekkelkeFskwllkigdGkineedeeealieiPedlllkksedk 242
                                       + +++S +    k  ++Lt n R + + + + + +k +k+Fs++++++g+    +e++  ++ ++P  + l  + + 
  gi|518651639|ref|YP_008141159.1|  88 SVLNSSDMGYDTKdAFSLTVNSRDTYTGIPDnDRYKTVKHFSEFINALGNNVNVNEKNFGKIFRVPGHIHLLIARN- 163
                                       556677666666669**********9998651567899***********97555555555799***9876443333. PP

                                       HHCHCCS---SS--...........EEEESSCCHHHHHHHHHHCCSSS--EEEE CS
                              PIF1 243 ieeivsevygdllqeltdkeyleerailcptnedvdeiNnyvlsklpgeekeyl 296
                                             + +++   +++ ++y+ e+a l+p+ + v+++ ++  s+   e ++y 
  gi|518651639|ref|YP_008141159.1| 164 ------NYFKERKGHTELSTYIVEKAGLVPSATIVETLSDSFNSMTLDESEKYA 211
                                       ......333444455566789999999999999999999998887777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1580.06
//
Query:       gi|518651640|ref|YP_008141160.1|  [L=162]
Description: riboflavin synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-12   46.0   0.0    5.9e-12   45.6   0.0    1.1  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   3.3e-16   5.9e-12       4     135 ..       4     127 ..       2     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 3.3e-16
                                       EEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-..SEEEEEEEEE--SSCHH CS
                     DMRL_synthase   4 iaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaessky.ldavialGvvirGetphf 79 
                                       i+iV ++f      ++ ++a+del + g    +i+++tVPG  + p+aa +l ++  y +d v+a+G  + G  p +
  gi|518651640|ref|YP_008141160.1|   4 IGIVDTTF---ARYDMASSAIDELYKTGTG-FEIKRYTVPGIKDTPVAALRLFSE--YnCDLVMAFG--MPGPMPVD 72 
                                       78999999...8899*************75.8*********************95..668*******..9******* PP

                                       HHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTC...CCHHHHHHHHHHH CS
                     DMRL_synthase  80 eyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggka...gnkGeeaaeaale 135
                                       ++ a+ +s glm+v+l+t      ++l v  +e++a++  +  a    n+ +e+a +a  
  gi|518651640|ref|YP_008141160.1|  73 KMSAQIASTGLMEVQLKTM----KHILEVFvHEDEAKDDREL-AwlcDNRSREHAVNAYY 127
                                       *****************95....7777777777777755533.24689999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.49
# Mc/sec: 997.20
//
Query:       gi|518651641|ref|YP_008141161.1|  [L=134]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  119.3   0.0    1.2e-34  119.2   0.0    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.063   13.1   0.0        0.1   12.4   0.0    1.3  1  ACT            ACT domain


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0   1.3e-38   1.2e-34       2     139 ..       1     130 [.       1     132 [. 0.96

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 1.3e-38
                                       EEEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCH CS
                     DMRL_synthase   2 lriaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetph 78 
                                       ++i++Vva+fn +it  ++e+a+d ++ +gv   ++++ +VPG+f++pl +kkl++  + +d++ia+G+vi+Get+h
  gi|518651641|ref|YP_008141161.1|   1 MKIGMVVAEFNYDITMMMVERAKDYADFLGV---EYKILKVPGTFDIPLGIKKLLKI-DDIDGIIAIGAVIKGETDH 73 
                                       69****************************9...6*********************5.347**************** PP

                                       HHHHHHHHHHHHHHHHHHCTS-EEEEEEEES.SHHCCHHCCTSTCCCHHHHHHHHHHHHHHH CS
                     DMRL_synthase  79 feyvaeavskglmrvsldtgvPvifgvltvd.teeqaleraggkagnkGeeaaeaalemanl 139
                                       + +++e+++++++++sl++++Pv+ g+  +  ++ qa++r+     + ++ea e++++m++ 
  gi|518651641|ref|YP_008141161.1|  74 HRIIMENAARKITDLSLEYEKPVALGISGPGeSRLQAEARI-----DMAKEALESCVKMVKS 130
                                       ******************************9899*******.....89***********985 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.1e-05       0.1      16      65 ..       2      54 ..       2      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHTTSEEEEEEEEEESTT...ECEEEEEEEEEEHHHHHHHHHHHHTT CS
                               ACT 16 rvfgaladrgiNidsieqrssedk...vagivfvvivvdeedleevlealkkl 65
                                      +++ ++a+ ++ i+++ + + +d    ++ ++ +  v+++ d++  +++l k+
  gi|518651641|ref|YP_008141161.1|  2 KIGMVVAEFNYDITMMMVERAKDYadfLGVEYKILKVPGTFDIPLGIKKLLKI 54
                                      68889*******************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 878.54
//
Query:       gi|518651642|ref|YP_008141162.1|  [L=92]
Description: hypothetical protein FACI_IFERC00001G0281 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0022   17.6   0.5     0.0027   17.2   0.5    1.0  1  YibE_F    YibE/F-like protein
  ------ inclusion threshold ------
      0.041   13.9   0.7      0.052   13.6   0.7    1.0  1  BCHF      2-vinyl bacteriochlorophyllide hydratase (BCHF)
      0.059   13.8   1.1       0.18   12.2   0.1    1.9  3  DUF3262   Protein of unknown function (DUF3262)
      0.071   13.5   2.2       0.17   12.3   2.2    1.5  1  DUF983    Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> YibE_F  YibE/F-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   6.1e-07    0.0027      18      71 ..      23      76 ..      21      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 6.1e-07
                            YibE_F 18 kkGlkallslvlnllvlilvllplllkgvspllvalilvilitvvtlllvngfn 71
                                      ++G+ka++  ++ ++++  +l    ++g++p + +++++ ++++vt+++++ + 
  gi|518651642|ref|YP_008141162.1| 23 ERGVKAFVITMVGIVIVTAALTSGTYNGYDPNAYSVAITGFFVIVTIVMTAAWY 76
                                      69*****9999************************************9998775 PP

>> BCHF  2-vinyl bacteriochlorophyllide hydratase (BCHF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.7   1.2e-05     0.052      26      82 ..      29      87 ..      26      89 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                              BCHF 26 flvflvslalvllylatg..egfalvtvsvllktlllvlilitGaifekevfgkylfak 82
                                      f++ +v++++v+  l++g  +g+   + sv +  +++++ ++  a + ++ +++y + +
  gi|518651642|ref|YP_008141162.1| 29 FVITMVGIVIVTAALTSGtyNGYDPNAYSVAITGFFVIVTIVMTAAWYRTKYDNYSYDP 87
                                      99*********99999887899**********998887777777888899999998865 PP

>> DUF3262  Protein of unknown function (DUF3262)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1      0.14   6.5e+02      19      30 ..      28      39 ..      10      44 .. 0.53
   2 ?    0.6   0.1      0.17   7.5e+02      20      34 ..      29      43 ..      23      52 .. 0.58
   3 ?   12.2   0.1     4e-05      0.18      14      50 ..      50      86 ..      40      92 .] 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.14
                           DUF3262 19 alklliagillv 30
                                      a+ ++++gi++v
  gi|518651642|ref|YP_008141162.1| 28 AFVITMVGIVIV 39
                                      233333333333 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.17
                           DUF3262 20 lklliagillvvllL 34
                                      + ++++gi++v++ L
  gi|518651642|ref|YP_008141162.1| 29 FVITMVGIVIVTAAL 43
                                      444555555554443 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 4e-05
                           DUF3262 14 GvspsalklliagillvvllLwaaWalvsvYkgWaee 50
                                      G +p+a +++i+g++++v ++++a  +++ Y  ++ +
  gi|518651642|ref|YP_008141162.1| 50 GYDPNAYSVAITGFFVIVTIVMTAAWYRTKYDNYSYD 86
                                      699***********99999888877789999888765 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   2.2   3.7e-05      0.17      26      72 ..      25      72 ..      14      80 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                            DUF983 26 gPayfvilivghlvvplallvevayep.plwvhlliwlpltlllslll 72
                                      g   fvi++vg+++v++al   ++    p   +++i+ ++++++++++
  gi|518651642|ref|YP_008141162.1| 25 GVKAFVITMVGIVIVTAALTSGTYNGYdPNAYSVAITGFFVIVTIVMT 72
                                      6678***************99998888666677777777777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1025  (0.0571699); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.41u 0.31s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 635.10
//
Query:       gi|518651643|ref|YP_008141163.1|  [L=389]
Description: hypothetical protein FACI_IFERC00001G0282 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-23   82.4  28.9    1.9e-22   80.2  28.9    1.8  1  Sulf_transp    Sulphur transport
  ------ inclusion threshold ------
        5.9    7.2   8.0        0.3   11.4   2.1    2.0  2  Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD


Domain annotation for each model (and alignments):
>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.2  28.9   2.1e-26   1.9e-22      24     305 ..      32     374 ..      24     380 .. 0.71

  Alignments for each domain:
  == domain 1  score: 80.2 bits;  conditional E-value: 2.1e-26
                       Sulf_transp  24 alllaiavaavgfqllaaaglidlpksafpv.vglivGGllFGvGMalaGgCasgtlyrvGeGslralitllffilg 99 
                                        +++ai++ a+++  laa+g++  ++ +  + +g+++G+ lFGvG+a++G  ++++++ +GeG+  a+++ll+  lg
  gi|518651643|ref|YP_008141163.1|  32 CIAIAIGAGALALYGLAAFGVAFHWGVKPDYvLGVAFGAALFGVGIAVSGYVPGTVWMGLGEGRRDAIYALLGGLLG 108
                                       56788899999***********99987776659******************************************** PP

                       Sulf_transp 100 ava....lltgilsswleq......llestvskeslyetlglsplllialllliallllvkelrkek.......... 156
                                       a+     + +  + +wl +      + +  +++++ly ++g++++++i+++ ++ +l  +k  +  +          
  gi|518651643|ref|YP_008141163.1| 109 AASwtliY-QTSFGQWLVSydnfgqIYFGGKVDTNLYVGFGIAVVWAIVMFSIAYFLPRYKGGKSCAytslhksrkm 184
                                       *7633322.33334444322222336677788999999****99999999988866655553333113444455566 PP

                       Sulf_transp 157 ......................lqeae..klektsla..kklfrkpwslvlgavllgllavlawllsaktgrs..fg 205
                                                             l +++  ++ ++ ++  +klf   + ++  ++++gl++vl ++l + +g s  ++
  gi|518651643|ref|YP_008141163.1| 185 stveqekyietagmlmegasmpLGKNNiaEKVNYHWTvsSKLF--GVVMMSVGIIIGLMVVLEMFLHQIFGESttYS 259
                                       6666666666666666666655333333322233333113444..4556788999*******999999899873245 PP

                       Sulf_transp 206 lgftv.pgakilqylvlgtskflnwgvvlvlGiilGaflaall.sgefk.le..apka..........rellaallG 267
                                       + +++ ++   ++ + +     + w+ ++++G ++Gafla+++ +++f+ ++  +p++          +++  a++G
  gi|518651643|ref|YP_008141163.1| 260 WIVAKlWLPAGAYSYSTLVVHTIGWEPFSDIGTLFGAFLASIFfTRRFQsFNsvIPPSwetrfgnsqiKRAGGAFTG 336
                                       556551444445556777788999*****************9724555423321444246666666666******** PP

                       Sulf_transp 268 GllMGfGarlAgGCniGaglsgiaslslsgwlalvfll 305
                                       G++M  Gar+A GC +G++lsg  ++++s+  +++ ++
  gi|518651643|ref|YP_008141163.1| 337 GFMMLLGARMADGCASGHILSGDLQMAVSSLEFFIVVI 374
                                       **********************9999999887777655 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   3.3e-05       0.3      27     103 .]     222     303 ..     158     303 .. 0.71
   2 ?   -4.0   0.2         2   1.8e+04      72      79 ..     370     377 ..     361     382 .. 0.47

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.3e-05
                                       SSSHHHHHHHHHHHHHG..GGCHH.HH---SSSSSTT-.HHHHHHHHH..HHHHHHHHHHHHTS-SSCCHHHHHHHH CS
                     Cytochrom_B_C  27 ipakllGvvamgaaivi..lfllp.wldrskvksiryrkplakvllal..lvvsfvvLgylGvqppeevavllsqia 98 
                                       + +kl+Gvv+m + i+i  +++l  +l++   +s++y   +ak++l +     s +v+  +G +p +++ +l++ ++
  gi|518651643|ref|YP_008141163.1| 222 VSSKLFGVVMMSVGIIIglMVVLEmFLHQIFGESTTYSWIVAKLWLPAgaYSYSTLVVHTIGWEPFSDIGTLFGAFL 298
                                       349********6655542144443258888889*****99999998763367788888999*************999 PP

                                       HHHHH CS
                     Cytochrom_B_C  99 tvlyF 103
                                       + ++F
  gi|518651643|ref|YP_008141163.1| 299 ASIFF 303
                                       99988 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2
                                       HHHHHHHH CS
                     Cytochrom_B_C  72 lvvsfvvL 79 
                                       ++v +++L
  gi|518651643|ref|YP_008141163.1| 370 FIVVIIFL 377
                                       33333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2463.33
//
Query:       gi|518651644|ref|YP_008141164.1|  [L=137]
Description: HIT-family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-23   83.6   2.1    1.6e-23   83.3   2.1    1.1  1  HIT       HIT domain
    3.5e-12   46.8   3.8    5.1e-12   46.3   3.8    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    3.7e-06   26.8   2.2    5.2e-06   26.3   2.2    1.2  1  CwfJ_C_1  Protein similar to CwfJ C-terminus 1


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   2.1   2.6e-27   1.6e-23       4      97 ..      12     105 ..       9     106 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 2.6e-27
                                       C-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGG CS
                               HIT   4 ipstvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngah 80 
                                        +s+++ye++++lafldi p + gh+Lvipk+h++++ +++ ++l + +++vk +   l++k++ ++++++  ng+ 
  gi|518651644|ref|YP_008141164.1|  12 VKSHKIYETNKTLAFLDIHPISNGHILVIPKEHYKDIYEMDSNILIETIKTVKAITGILKDKLNINAVNIMNSNGEI 88 
                                       5799************************************************************************* PP

                                       GT-SSSS-EEEEEEC-T CS
                               HIT  81 agqsvahlHiHviprre 97 
                                       a q+v+h+HiHviprre
  gi|518651644|ref|YP_008141164.1|  89 ANQTVFHYHIHVIPRRE 105
                                       ***************97 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 !   46.3   3.8   8.5e-16   5.1e-12       2     102 ..       2     103 ..       1     110 [. 0.84

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 8.5e-16
                                       -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T-E CS
                            DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekynevd 78 
                                       ++f++++++k ++  +ye++k++++ Di p ++ h+lvipk++ k++++++++ l    + ++ +  ++++k n   
  gi|518651644|ref|YP_008141164.1|   2 CIFCDIVNDKVKSHKIYETNKTLAFLDIHPISNGHILVIPKEHYKDIYEMDSNILIETIKTVKAITGILKDKLNINA 78 
                                       9*************************************************988666666667889999999986533 PP

                                       EEEE.--SCCCT--S-S--EEEEE. CS
                            DcpS_C  79 aeel.rvgvhyqPsvyhlHlHvisl 102
                                        + +   g  ++++v+h H+Hvi  
  gi|518651644|ref|YP_008141164.1|  79 VNIMnSNGEIANQTVFHYHIHVIPR 103
                                       3333146888899*********975 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 !   26.3   2.2   8.6e-10   5.2e-06      14     108 ..       2     102 ..       1     110 [. 0.85

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.6e-10
                                       -S--.--SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHHHHHHH.HHHTT-- CS
                          CwfJ_C_1  14 ClfC.lsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrkalvkm.ykkqdkd 88 
                                       C fC + n k+++h i    nk+ + l  +p+s+gH+l+ip eH +   ++d ++l e  k  ka++ +  +k + +
  gi|518651644|ref|YP_008141164.1|   2 CIFCdIVNDKVKSHKIYE-TNKTLAFLDIHPISNGHILVIPKEHYKDIYEMDSNILIETIKTVKAITGIlKDKLNIN 77 
                                       999988999999999987.5777788888***************************9999999****9945677777 PP

                                       EEEE.....EE-SSS-----EEEEE CS
                          CwfJ_C_1  89 avvf.....EissersvHlaiqvip 108
                                       av       Ei+++   H +i+vip
  gi|518651644|ref|YP_008141164.1|  78 AVNImnsngEIANQTVFHYHIHVIP 102
                                       7765334446669***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 988.10
//
Query:       gi|518651645|ref|YP_008141165.1|  [L=225]
Description: hypothetical protein FACI_IFERC00001G0284 [Ferroplasma acidarmanus fer1]
Scores for complete 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   91.2   4.9    1.4e-25   90.2   4.9    1.4  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   4.9     8e-30   1.4e-25       1     246 [.       3     210 ..       3     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 8e-30
                                       EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S CS
                           TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadg 77 
                                       ++lD+ d+++ik++ + + i+gvTt P  i++++++ +  +++i +i k+                      +  +g
  gi|518651645|ref|YP_008141165.1|   3 VFLDSSDINEIKEISDYGFIDGVTTDPVSIAREVTKGSTTEQVITSIIKA----------------------V--NG 55 
                                       69*************************88888788777**********99......................5..** PP

                                       -EEEE-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-S CS
                           TAL_FSA  78 rvslEVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagas 154
                                       +v+++V++   +d++ ++++A ++++l    nv++ iPat  GikA+ +L ++ +++ +  +++  qa++aa+  a+
  gi|518651645|ref|YP_008141165.1|  56 EVHIQVVS---QDYDSIMAQAFKIHSLGM--NVIVNIPATFTGIKAMLKLNEKKVKCSALSVYNTVQAIMAAQNYAE 127
                                       ********...******************..********************************************** PP

                                       EEEEBHHHHHTTT............S-HHHHHHHHHHHHHHHT-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHH CS
                           TAL_FSA 155 viSpFvgRiddllkkleekdklkgkddgvalvkeiynyykklgysTkvmaasfrnveeve..elagcdtvTippkll 229
                                       ++S+  g+i+++             +dg++l+ ++ + +k++g++ kv+   ++n+e ++    +g+ ++ ++  ll
  gi|518651645|ref|YP_008141165.1| 128 YVSIKTGKIKNTA------------EDGMELAYNVNQTFKNCGFDAKVLVGGISNPEDITraGIMGAGAISVTYPLL 192
                                       *************............7**********************************999999999999999** PP

                                       HHHT--HHH......... CS
                           TAL_FSA 230 ealakhgkts.ekleeee 246
                                       ++++ + +t  e +e+ e
  gi|518651645|ref|YP_008141165.1| 193 KQVEGDINTGtEIAEQME 210
                                       ****99999423222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 00:00:00.48
# Mc/sec: 1404.27
//
Query:       gi|518651646|ref|YP_008141166.1|  [L=159]
Description: hypothetical protein FACI_IFERC00001G0285 [Ferroplasma acidarmanus fer1]
Scores for complete 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  123.9   0.0    4.5e-36  123.5   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    4.3e-24   84.9   0.1    4.9e-24   84.7   0.1    1.0  1  Redoxin     Redoxin
      2e-05   24.7   0.0     0.0018   18.4   0.0    2.2  2  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
  ------ inclusion threshold ------
      0.011   15.6   0.1      0.018   15.0   0.1    1.4  1  SCO1-SenC   SCO1/SenC
       0.11   12.5   0.2       0.43   10.6   0.0    2.0  2  YyzF        YyzF-like protein


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 !  123.5   0.0   1.2e-39   4.5e-36       2     123 ..       8     135 ..       8     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.2e-39
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       g+ apdfe+ ++  ++++lsdykg+++vl f+p++++ vCt+e++ +++ + +f + +++v+g+svdsp+s+k+f+ 
  gi|518651646|ref|YP_008141166.1|   8 GELAPDFEALDTGLKSKKLSDYKGNVTVLAFFPGAFTSVCTKEMCTFRDSMANFNKFNAKVVGISVDSPFSLKEFAT 84 
                                       678************************************************************************** PP

                                       H-H.SSEEEE-TTSHHHHHTT-EETT......TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  79 keslnfpllsDeegkvakaygvlkee......kglalratfvidkegkiry 123
                                       k++l+f+llsD +++++ +yg+l +        ++  r++fv+dk gki+y
  gi|518651646|ref|YP_008141166.1|  85 KNKLQFDLLSDGNREISGKYGALYKSflningLTASKRSVFVLDKTGKIVY 135
                                       ***********************999****99999**************99 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.1   1.4e-27   4.9e-24       2     144 ..       7     149 ..       6     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.4e-27
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvke 78 
                                       +g+ aPdf+   ++t+ +s +ls++kg+++v+ f+pgaf+ +C++e++ +++  + +++ + +vv++++d+    ke
  gi|518651646|ref|YP_008141166.1|   7 EGELAPDFEA--LDTGLKSKKLSDYKGNVTVLAFFPGAFTSVCTKEMCTFRDSMANFNKFNAKVVGISVDSPFSLKE 81 
                                       7999*****6..67**********************************776666666999*******9999999*** PP

                                       HHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG...EEE-EEEEEEETTEEEEEEESSSCHTSTTSHH CS
                           Redoxin  79 fwgkeglkfpvlsDgsaaftkalGlrleedaseg...lrtpryavidedgkvvylevepepeteesnae 144
                                       f++k++l+f +lsDg+ +++ ++G+ ++     +      ++++v+d+ gk+vy+ v ++  + e++++
  gi|518651646|ref|YP_008141166.1|  82 FATKNKLQFDLLSDGNREISGKYGALYKSFLNINgltASKRSVFVLDKTGKIVYKWVSEDAGK-EPDYK 149
                                       ************************8876554444794555668999*********99998844.55554 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 !   18.4   0.0   4.9e-07    0.0018       6      52 ..      58     105 ..      53     123 .. 0.87
   2 ?    4.5   0.0      0.01        36      96     112 ..     124     140 ..     121     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.9e-07
                        AhpC-TSA_2   6 kpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalg 52 
                                        + +++ + k+v+i++++p s+k+F+  ++ +f+l+ D ++++  + g
  gi|518651646|ref|YP_008141166.1|  58 MANFNKFNAKVVGISVDSPfSLKEFATKNKLQFDLLSDGNREISGKYG 105
                                       577888999********************************9987766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.01
                        AhpC-TSA_2  96 tflfdkqgelvyehrdr 112
                                       +f++dk g++vy++  +
  gi|518651646|ref|YP_008141166.1| 124 VFVLDKTGKIVYKWVSE 140
                                       79************865 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1     5e-06     0.018       3     106 ..      13     111 ..      11     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5e-06
                         SCO1-SenC   3 pFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyl 79 
                                       +Fe +d+  ++ + +d++g+++++ f+    ++vC++++ + ++ ++++++   + +++ i+v    D+p  lke++
  gi|518651646|ref|YP_008141166.1|  13 DFEALDTGLKSKKLSDYKGNVTVLAFFPGAFTSVCTKEMCTFRDSMANFNKF--NAKVVGISV----DSPFSLKEFA 83 
                                       899999999999**************************************99..666777777....5899999999 PP

                         SCO1-SenC  80 eafdpriigltGskeeiakaake.frvy 106
                                        + + ++  l++ + ei+  + + ++ +
  gi|518651646|ref|YP_008141166.1|  84 TKNKLQFDLLSDGNREISGKYGAlYKSF 111
                                       9999999999998888876555555555 PP

>> YyzF  YyzF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012      0.43      10      30 ..       1      21 [.       1      29 [. 0.84
   2 ?   -1.1   0.1      0.56     2e+03      16      29 ..     141     154 ..     138     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                              YyzF 10 lDefVdeyeqaPdiekleeve 30
                                      + ++V+e e aPd+e+l++  
  gi|518651646|ref|YP_008141166.1|  1 MNDMVEEGELAPDFEALDTGL 21
                                      679*************99865 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.56
                              YyzF  16 eyeqaPdiekleev 29 
                                       + ++ Pd +k+eev
  gi|518651646|ref|YP_008141166.1| 141 DAGKEPDYKKIEEV 154
                                       66788999999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1020.28
//
Query:       gi|518651647|ref|YP_008141167.1|  [L=174]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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   55.9  11.6    4.4e-05   23.0   0.2    4.2  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    3.2e-05   23.6  12.4      0.015   15.0   0.5    4.2  4  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.2   4.9e-09   4.4e-05       4      36 .]      12      44 ..      10      44 .. 0.89
   2 !    7.1   0.1   0.00054       4.8      21      35 ..      50      64 ..      46      66 .. 0.57
   3 !   21.7   0.9   1.3e-08   0.00011       2      35 ..      71     103 ..      70     104 .. 0.95
   4 !   18.8   0.3     1e-07   0.00094       4      35 ..      90     121 ..      88     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 4.9e-09
                                      EETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
                           Hexapep  4 IGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                                      I  ++++  +a++ gnV+IGd+v Ig+g+v++g
  gi|518651647|ref|YP_008141167.1| 12 ISRKAYVFENATVIGNVHIGDYVWIGPGAVLRG 44
                                      667788888*********************986 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00054
                                      EE-TTEEEETTEEEE CS
                           Hexapep 21 kIGdnvkIgagvvig 35
                                       IG ++ I+ ++vi+
  gi|518651647|ref|YP_008141167.1| 50 SIGAYSAIEDNCVIH 64
                                      455555555555554 PP

  == domain 3  score: 21.7 bits;  conditional E-value: 1.3e-08
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       t+IG++v+Ig+ +vi+ ++ I d+++Ig ++++ 
  gi|518651647|ref|YP_008141167.1|  71 TTIGEHVTIGHLSVIHTGT-IDDYAVIGMNSTVS 103
                                       89*****************.************95 PP

  == domain 4  score: 18.8 bits;  conditional E-value: 1e-07
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       I + ++Ig+++++ + +++G+ + Ig+g+v++
  gi|518651647|ref|YP_008141167.1|  90 IDDYAVIGMNSTVSDFATVGKWAAIGEGAVVK 121
                                       67889999999999999999999999999996 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 !    7.9   0.9   0.00028       2.5       1      16 [.      27      42 ..      21      53 .. 0.58
   2 !   15.0   0.5   1.7e-06     0.015       4      27 ..      57      80 ..      56      88 .. 0.84
   3 !   10.3   0.3   4.9e-05      0.44       2      32 ..      71     102 ..      70     104 .. 0.89
   4 ?    2.7   0.3     0.012   1.1e+02       4      26 ..      96     120 ..      94     122 .. 0.51

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00028
                                      .EEE-TT-EE-TT-EE CS
                         Hexapep_2  1 pviIGdnCliGanagi 16
                                      +v+IGd + iG+ a+ 
  gi|518651647|ref|YP_008141167.1| 27 NVHIGDYVWIGPGAVL 42
                                      4566666666666664 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.7e-06
                                      E-TT-EE-TT-EESEEE-TT-EE- CS
                         Hexapep_2  4 IGdnCliGanagiGvslGdncvvg 27
                                      I+dnC+i+a+ g  +++G+ +++g
  gi|518651647|ref|YP_008141167.1| 57 IEDNCVIHARPGEKTTIGEHVTIG 80
                                      9*********99888888877775 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 4.9e-05
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvgaGvvi 32 
                                       ++IG+ + iG  ++i  G+ + d +v+g+++++
  gi|518651647|ref|YP_008141167.1|  71 TTIGEHVTIGHLSVIhtGT-IDDYAVIGMNSTV 102
                                       79************98675.89*******9988 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.012
                                       E-TT-EE-TT-EES..EEE-TT-EE CS
                         Hexapep_2   4 IGdnCliGanagiG..vslGdncvv 26 
                                       IG n+ +  +a++G    +G+++vv
  gi|518651647|ref|YP_008141167.1|  96 IGMNSTVSDFATVGkwAAIGEGAVV 120
                                       3333333333444666677777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1202.36
//
Query:       gi|518651648|ref|YP_008141168.1|  [L=86]
Description: hypothetical protein FACI_IFERC00001G0287 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 562.21
//
Query:       gi|518651649|ref|YP_008141169.1|  [L=150]
Description: CoxG protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-27   95.3   0.1    2.9e-27   95.1   0.1    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
    7.2e-09   36.1   0.0    8.6e-09   35.8   0.0    1.1  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
  ------ inclusion threshold ------
      0.038   14.0   0.0      0.093   12.8   0.0    1.7  2  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
      0.055   12.6   0.0      0.075   12.2   0.0    1.2  1  Glu_synthase     Conserved region in glutamate synthase


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1   0.1   6.4e-31   2.9e-27       2     138 ..       7     143 ..       6     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 6.4e-31
                                       EEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE..EEEEE CS
                              COXG   2 efrvaapkeavwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsfkarvelselekensttieikGkG 77 
                                       +f+v+ ++e++  ++ d e l ++iP + ++ek + +e+k ++k++v+++kg+f  ++ l   +k+ s +i  kGkG
  gi|518651649|ref|YP_008141169.1|   7 SFDVKTTPEKAYGYVVDQEALIKLIPDLLNYEKVDeNEMKLTAKAGVSFIKGKF--DLVLDITDKKASEHITLKGKG 81 
                                       79**************************************************55..677777788888889999999 PP

                                       E-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHH CS
                              COXG  78 rgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecissk 138
                                        g+g ++df++++   ++++ t+++w+a++n+ g +as+G+r+++saa+k i +l+ + +++
  gi|518651649|ref|YP_008141169.1|  82 NGSGASVDFTVNFDFLPDEDgTKVNWKADMNIVGTAASMGARMLKSAAQKYIVKLVGNYKKA 143
                                       999999999999999999999*******************************9999887766 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   1.9e-12   8.6e-09       1     143 []       1     145 [.       1     145 [. 0.73

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.9e-12
                                       EEEEEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSS..TTTEEEEECCCS.SEEEEEEEEEETTTTE CS
                   Polyketide_cyc2   1 mvkvtvsvviaappekVwalvsdfenwprWhpevarveleggggpa..rgvegtvrvggr.gtvreelvevdpegrl 74 
                                       m ++++s +++ +pek++ +v d e++ + +p ++ +e ++ ++ +  + ++g+   +g+ + ++  +++   +  +
  gi|518651649|ref|YP_008141169.1|   1 MLTFEDSFDVKTTPEKAYGYVVDQEALIKLIPDLLNYEKVD-ENEMklTAKAGVSFIKGKfD-LVLDITDKK-ASEH 74 
                                       67899********************************9887.33322444423333444332.444444444.5666 PP

                                       EEEEEE...SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  75 lsyriv..kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLerLkarle 143
                                       ++ ++   +     ++++++ + pd++gt+v w+++  + + ++ + + ++++a ++++ + + + k++le
  gi|518651649|ref|YP_008141169.1|  75 ITLKGKgnGSGASVDFTVNFDFLPDEDGTKVNWKADMNIVGTAASMGARMLKSAAQKYIVKLVGNYKKALE 145
                                       6666644356666699*******************888644445556778888888888888888888776 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.6   7.4e+03      31      48 ..      68      85 ..      61      86 .. 0.61
   2 ?   12.8   0.0   2.1e-05     0.093      42      62 ..     115     135 ..     106     147 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.6
                                      HHHHHHHHHHHTSBTTTB CS
                     ClpB_D2-small 31 tdealdalaekgydpeyG 48
                                      +++a +++  kg     G
  gi|518651649|ref|YP_008141169.1| 68 DKKASEHITLKGKGNGSG 85
                                      346777777777655555 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 2.1e-05
                                       TSBTTTBTCCHHHHHHHHTHH CS
                     ClpB_D2-small  42 gydpeyGARpLrriiqreied 62 
                                       g+   +GAR+L+++ q++i +
  gi|518651649|ref|YP_008141169.1| 115 GTAASMGARMLKSAAQKYIVK 135
                                       77889*************976 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.7e-05     0.075     184     250 ..      21      94 ..      10     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.7e-05
                                       -SSHHHHHHHHHHHHHH-TTSEEEEEEE-STTHHHHHHH.......HHHTT-SEEEEE-TT---SSEEHHHHHH CS
                      Glu_synthase 184 iysiedlaqliedLkevnkeakvsvKlvaeagvetiaag.......vakanadiilidGleGGTGAspkssikh 250
                                       ++++e l +li dL + +k  +  +Kl+a+agv  i+           k+  ++i++ G   G GAs +  ++ 
  gi|518651649|ref|YP_008141169.1|  21 VVDQEALIKLIPDLLNYEKVDENEMKLTAKAGVSFIKGKfdlvldiTDKKASEHITLKGKGNGSGASVDFTVNF 94 
                                       578999************99999***********9997678888866788889**************9877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 932.35
//
Query:       gi|518651650|ref|YP_008141170.1|  [L=270]
Description: prephenate dehydratase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-57  192.6   0.1    7.9e-57  192.0   0.1    1.2  1  PDT       Prephenate dehydratase
    2.8e-10   39.8   0.0    6.2e-10   38.7   0.0    1.6  1  ACT       ACT domain
     0.0018   18.8   0.0     0.0049   17.4   0.0    1.7  1  ACT_4     ACT domain


Domain annotation for each model (and alignments):
>> PDT  Prephenate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.0   0.1   1.3e-60   7.9e-57       1     181 [.       3     177 ..       3     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 192.0 bits;  conditional E-value: 1.3e-60
                                       EEEES-TTSHHHHHHCCCS.....EEEEES-HHHHHHHHCTTS-SEEEEEEEESSS-B-HHHHHHHHH.SSEEEEEE CS
                               PDT   1 vaylGpegtyshqAalkvfkaedvelipvasieevfeavekgeadyavvPiENsteGsVnetlDlLlkesdlkivgE 77 
                                       ++y+G++g+ysh Aa++++     e++p +s+++vf ++e+g++++avvP+ENs+eG+Vn+t+D L + ++++i++E
  gi|518651650|ref|YP_008141170.1|   3 IGYFGEPGAYSHIAAIQMA---TGEYVPLESVRAVFMSLEDGNINLAVVPVENSIEGAVNQTYDFLFR-MNFYIIKE 75 
                                       78**************999...89********************************************.99****** PP

                                       EEEE---EEEE-TT--TTT--EEEE-HHHHHHTHHHHHH-.TTSEEEE-S-HHHHHHHHHHCT-TTEEEEE-HHHHH CS
                               PDT  78 vvlpiehcLlakpktkleeikkvyShpqalgQcrkfLeehlpqvervavestaeAakkveassdkdaaaiasevaae 154
                                       ++l+i+hcL+++ + k ++i+ v+Shpqal+Qc++f+ +h  +++ v+ ++ta ++++++++   ++aaiase+aa+
  gi|518651650|ref|YP_008141170.1|  76 YYLRIKHCLIGHAGAKTDNITHVHSHPQALSQCSDFIYSH--GMKPVSEYDTAGSVQIIKENFGLSHAAIASEIAAN 150
                                       ****************************************..*********************************** PP

                                       HTT-EEEECS-SS-S--EEEEEEEEET CS
                               PDT 155 lyglkvleeniedkknntTRFlvlake 181
                                       l g+++le++ie++++ +TRF+++ak 
  gi|518651650|ref|YP_008141170.1| 151 LNGMQILEKDIENNRHSYTRFFLIAKA 177
                                       ************************986 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0     1e-13   6.2e-10       1      64 [.     187     250 ..     187     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1e-13
                                       EEEEEEEESSTTHHHHHHHHHHHTTSEEEEEEEEEESTTECEEEEEEEEEEHHHHHHHHHHHHT CS
                               ACT   1 tvlrvgvpDrPGlLarvfgaladrgiNidsieqrssedkvagivfvvivvdeedleevlealkk 64 
                                       t++ ++ +++PG+L +++ +l d+giN ++ie+r++ +    ++f++++++ +++++++  ++k
  gi|518651650|ref|YP_008141170.1| 187 TSIVFSTRNKPGALYKILKILNDYGINMTKIESRPVQYIPFQYIFFIDIENNKNTDAAITDIQK 250
                                       578999*********************************9999999999999999999999987 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   8.2e-07    0.0049       7      71 ..     187     250 ..     184     253 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.2e-07
                             ACT_4   7 vrleveaedrkglLaditqviseekanivsvnaktrkkdglaeikitveVkdvehLsrviakLra 71 
                                       +++   +++++g+L +i++++++ ++n+++++++  +    ++  + + +++ +  +  i+ +++
  gi|518651650|ref|YP_008141170.1| 187 TSIVFSTRNKPGALYKILKILNDYGINMTKIESRPVQ-YIPFQYIFFIDIENNKNTDAAITDIQK 250
                                       6788999****************************97.999999999999999998888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1786.36
//
Query:       gi|518651651|ref|YP_008141171.1|  [L=223]
Description: hypothetical protein FACI_IFERC00001G0290 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-09   36.9  17.0    3.3e-09   36.9  17.0    1.8  2  SpoIIM         Stage II sporulation protein M
  ------ inclusion threshold ------
       0.09   12.3   1.6       0.11   12.0   1.6    1.3  1  Stevor         Subtelomeric Variable Open Reading frame
       0.12   12.1   0.3       0.18   11.6   0.3    1.2  1  Abhydrolase_2  Phospholipase/Carboxylesterase
       0.29   11.1   6.2       0.13   12.2   2.4    2.3  2  DUF2678        Protein of unknown function (DUF2678)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9  17.0   7.5e-13   3.3e-09       6     152 ..      13     167 ..      11     168 .. 0.68
   2 ?   -4.2   0.7       3.5   1.5e+04      52      64 ..     185     196 ..     180     199 .. 0.44

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 7.5e-13
                            SpoIIM   6 lvgill...gallaa..........snfaeqis...seskensalslflaifanNlrvalllfllGllllgiptilv 66 
                                       l+++++   g+++ +          +    +++   s  +++s + ++l+if +Nl +a + f         ++++ 
  gi|518651651|ref|YP_008141171.1|  13 LLSFIIelvGFAVISslpihdpalyA----SFKsedSAIISQSFFPMWLSIFPHNLLIASIEF---------IPVVG 76 
                                       33333333355555546665544431....2224447889999999***********966666.........45555 PP

                            SpoIIM  67 llinGfvlGavaalvaef.......gglllflllilPhgilelpaiiiagaaglrlgkal.rsrrkalkeakrellk 135
                                       +l+ Gf++G++a+++a         g  ++  l+ilPh +lelpa+ +a++ ++++ ++l +        +k+  + 
  gi|518651651|ref|YP_008141171.1|  77 ILMFGFSIGSTASVIAVEgtatkvsGLAIFTSLMILPHSWLELPAYAVAVSTSIYILYYLfK----GELGKKYMKII 149
                                       6667999997766655555888889999****************************999941....22333334444 PP

                            SpoIIM 136 lllllvp.llliAaliEa 152
                                       +++++v+  l+ A+ iE+
  gi|518651651|ref|YP_008141171.1| 150 YMYIFVViELAFAGAIET 167
                                       444444479999999997 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.5
                            SpoIIM  52 fllGllllgipti 64 
                                       ++  + ++ i++i
  gi|518651651|ref|YP_008141171.1| 185 WIPAV-PIIIFLI 196
                                       44443.3333333 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.6   2.5e-05      0.11     235     271 ..     176     211 ..      78     215 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.5e-05
                            Stevor 235 pygiaalvllilavvliiLYiwlyrRRKnSwkhecKk 271
                                       ++ +  l + i av +ii+ iwlyrR   S  ++ Kk
  gi|518651651|ref|YP_008141171.1| 176 AHPLYSLYMWIPAVPIIIFLIWLYRRM-DSDEYKHKK 211
                                       345667888899************875.454555555 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.3   3.9e-05      0.18     102     159 ..      72     130 ..      39     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.9e-05
                                       --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS.-GGGGG-EE CS
                     Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessa.tavtkklpi 159
                                       ip   i+++GFS G   ++ ++  + +k++g  +f + ++l+ ++ + +  av++ ++i
  gi|518651651|ref|YP_008141171.1|  72 IPVVGILMFGFSIGSTASVIAVEGTATKVSGLAIFTSLMILPHSWLELPaYAVAVSTSI 130
                                       666779***********************************999977541455566665 PP

>> DUF2678  Protein of unknown function (DUF2678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.4   2.9e-05      0.13      69     108 ..     123     162 ..      79     170 .. 0.72
   2 ?   -0.7   0.1      0.29   1.3e+03      75      88 ..     192     205 ..     178     214 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                           DUF2678  69 llisssvivlifwyrqgdlepkfrnliyyilasivllclc 108
                                        ++ s++i ++++  +g+l  k+ ++iy  ++ ++ l + 
  gi|518651651|ref|YP_008141171.1| 123 AVAVSTSIYILYYLFKGELGKKYMKIIYMYIFVVIELAFA 162
                                       4455666777788889****************99988765 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.29
                           DUF2678  75 vivlifwyrqgdle 88 
                                       +i li+ yr+ d +
  gi|518651651|ref|YP_008141171.1| 192 IIFLIWLYRRMDSD 205
                                       45678889988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1481.76
//
Query:       gi|518651652|ref|YP_008141172.1|  [L=587]
Description: hypothetical protein FACI_IFERC00001G0291 [Ferroplasma acidarmanus fer1]
Scores for complete 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-88  295.9  33.2    4.4e-88  295.9  33.2    2.1  2  Voltage_CLC  Voltage gated chloride channel
      2e-07   31.3   0.0    0.00073   19.9   0.0    2.7  2  CBS          CBS domain


Domain annotation for each model (and alignments):
>> Voltage_CLC  Voltage gated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   1.0     0.015   1.3e+02     162     192 ..      13      43 ..       3      75 .. 0.78
   2 !  295.9  33.2   4.9e-92   4.4e-88       2     352 ..      81     430 ..      80     432 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.015
                                       GGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC 162 lelilfvllGilgGllgalfvrlllkverlf 192
                                        ++i+ +++G+++G+ + +f ++ + +e +f
  gi|518651652|ref|YP_008141172.1|  13 RWFIVGAIIGVVAGFGALAFYFTIRLFEFIF 43 
                                       578889999***9999999999888777544 PP

  == domain 2  score: 295.9 bits;  conditional E-value: 4.9e-92
                                       HHHHHHHCCCCC-GGGSC-SHHHHHHHCTTSS---HHHHHHHHHHHHHHHHCTT-S-BTHHHHHHHHHHHHHHHHHH CS
                       Voltage_CLC   2 ggllagllvklvapeaagsGipevkaalngvkgplslrvllvkflasvltvgsGlslGreGplvqiGAavgsglsrl 78 
                                       ggl+ g++++ + p ++g+G++  ++ ++ ++g+++ r+ +vk++as++t+gsG+s+GreGp+  i+A +gs l+++
  gi|518651652|ref|YP_008141172.1|  81 GGLITGFIIYTFDPSSEGHGTDAAIRSFHYNHGKIKRRTPVVKTIASAITIGSGGSAGREGPTALIAAGIGSFLADI 157
                                       89*************************************************************************** PP

                                       TT.--SHHHHHHHHHHHHHHHHHHHT-HHHHHHHHCTT.TSTSS--TTHHHHHHHHHHHHHHHHHHCTTS-S-.T.- CS
                       Voltage_CLC  79 lklsrndrdrrlvaaGaAAGiAAaFnaPlgGvlfalEe.vsrefslrallpvfvasvvaalvlrlllgeepafge.v 153
                                       l ls++d +r+ va+G++AGi+ +F+aP+gG++++ E+ ++r+f++++++p++vas +++ ++ +++g ep+fg  +
  gi|518651652|ref|YP_008141172.1| 158 LGLSPKD-RRIAVAVGIGAGIGTIFKAPIGGAVLGAEIlYRRDFESEVIFPSLVASSIGYSIFASVVGFEPIFGDyL 233
                                       ***9999.899***************************999*********************************744 PP

                                       --...--GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHHHHCCCSCC.CSSSSCC CS
                       Voltage_CLC 154 eslfalsllelilfvllGilgGllgalfvrlllkverlfrkleklkikkrlepalvgllvgllglllpasvlgggye 230
                                       +   ++++l l+++++lG+++Gl+++l++r+++ v++lf+k+   ki++ ++p+++g++vg+++ll+p+ +lg+gy+
  gi|518651652|ref|YP_008141172.1| 234 N---TFNVLRLPFYAVLGLVAGLFSILYIRTFYGVRNLFKKF---KIPNHFKPMIGGAIVGVIALLFPE-ILGTGYG 303
                                       4...6***********************************99...999*********************.******* PP

                                       HHHHHCTT-S-......HHHHHH...HHHHHHHHHHHHHCTT-CSBSHHHHHHHHHHHHHHHHHHHHHH-CTSSC.. CS
                       Voltage_CLC 231 liasllegstl......llsllllllllllkllataltlgsgvpgGifaPsLviGAalGrlvglvlalllpgaassd 301
                                       +++ l +g+ +      l  ll+l+ll ++k++at++t++sg +gG+faP ++iGA+lG+l+g++++++ pg ++  
  gi|518651652|ref|YP_008141172.1| 304 WVELLEYGKFNelvtfgLPILLILVLLPFIKIIATSFTVSSGGSGGVFAPGIFIGASLGALFGVLFHMISPGIVPV- 379
                                       **99999988899999999999999********************************************9988775. PP

                                       .HHHHHHCCTHHHHHCCS-HHHHHHHHHHCC--GCCHHHHHHHHHHHHHHH CS
                       Voltage_CLC 302 pgafalvGmaaflagvtrapltaiviviEltgdlelllplmlavliAkava 352
                                       ++ f+++Gm +f++++ +apl++i++v+E+tg+l+ll+  mlav iA++ +
  gi|518651652|ref|YP_008141172.1| 380 VAPFVIIGMLSFFGAAGKAPLAVILMVVEMTGSLQLLPGAMLAVSIAYIAS 430
                                       689*********************************************987 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0   0.00029       2.6      19      53 ..     482     515 ..     468     519 .. 0.80
   2 !   19.9   0.0   8.1e-08   0.00073      11      54 ..     531     573 ..     521     576 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00029
                                       HHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  19 eealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                         a ++m+e+++ +lPVV   +kl G v l D+++
  gi|518651652|ref|YP_008141172.1| 482 YRADNIMKENDLLSLPVV-YHEKLMGAVYLYDIVN 515
                                       5566799777766*****.7889**********87 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 8.1e-08
                                       EEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllra 54 
                                       +v+ + + e a elm +++     VV ++gk++Gi+tl  +l++
  gi|518651652|ref|YP_008141172.1| 531 YVKLENSAENAWELMMKNRTKWCAVV-DNGKFIGIITLDSILNK 573
                                       677778899999**7677788778**.6*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (587 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3835.09
//
Query:       gi|518651653|ref|YP_008141173.1|  [L=187]
Description: hypothetical protein FACI_IFERC00001G0292 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1296.90
//
Query:       gi|518651654|ref|YP_008141174.1|  [L=182]
Description: phosphoheptose isomerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   93.4   0.3    1.4e-26   93.1   0.3    1.1  1  SIS_2     SIS domain
    1.1e-07   31.8   0.0    2.3e-06   27.5   0.0    2.5  2  SIS       SIS domain


Domain annotation for each model (and alignments):
>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.3   1.6e-30   1.4e-26      11     138 .]      15     139 ..       5     139 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 1.6e-30
                                       HHHHHHSHHHHHHHHHHHHHHHHTT--EEEEESGGGHHHHHHTSSSTT-BTTEEEE--GGGSSSSST..THHHHHTT CS
                             SIS_2  11 erivetqaeaiekaaeliadslenggkvlvfGsGhSaalaeelaaragglaeferialpalalhtdaeatkssaler 87 
                                       ++i   ++++i+k a+ i +s +n+gk++vfG+G+Saa+a++++a++ g +  er alpa+al+t++  ++ +a+ +
  gi|518651654|ref|YP_008141174.1|  15 KNI---DTSQIKKIADGIINSFRNNGKLIVFGNGGSAADAQHFVAELTGHYMKERKALPAIALTTNT--SALTAIGN 86 
                                       444...889********************************************************98..9******* PP

                                       -TTHHHHHHHHTT-..-TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2  88 degyakqilrlvrl..kpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       d  y+++++r+v++  k++D  + iS+sGn+++vv+ +e+a+++g+ + ++t+
  gi|518651654|ref|YP_008141174.1|  87 DYSYNDIFSRQVQAlcKKEDYVVGISTSGNSKNVVAGIEEANSIGAFTLGFTG 139
                                       ***********99889******************************9999987 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.042   3.8e+02       2      24 ..      33      55 ..      32      61 .. 0.80
   2 !   27.5   0.0   2.5e-10   2.3e-06      39     104 ..      90     155 ..      79     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.042
                                      HCTSSEEEEEESHHHHHHHHHHH CS
                               SIS  2 LakakriyvlGaGtsyaiakela 24
                                      +++  +++v+G G s+a a+ + 
  gi|518651654|ref|YP_008141174.1| 33 FRNNGKLIVFGNGGSAADAQHFV 55
                                      5677899********99888765 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.5e-10
                                       EHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEEEEEESSTTSHHHHHSSEEEEE CS
                               SIS  39 daselkhgvlalideddlvilisfsgetkdlvaaaelakergakiiaITdskgsplareadlalyi 104
                                        ++ +  +v al++++d v+ is+sg++k++va +e+a++ ga ++++T+++g  la  ++ +++ 
  gi|518651654|ref|YP_008141174.1|  90 YNDIFSRQVQALCKKEDYVVGISTSGNSKNVVAGIEEANSIGAFTLGFTGKSGGKLAGICRDVFHS 155
                                       5677888899*********************************************99877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 1262.52
//
Query:       gi|518651655|ref|YP_008141175.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G0294 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.1e-11   42.1   0.0    3.6e-10   40.1   0.0    2.0  2  GHMP_kinases_C  GHMP kinases C terminal
    1.5e-10   41.2   0.0    3.2e-10   40.1   0.0    1.6  1  GHMP_kinases_N  GHMP kinases N terminal domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.39   3.5e+03      51      61 ..      93     103 ..      57     123 .. 0.64
   2 !   40.1   0.0     4e-14   3.6e-10       4      70 ..     228     294 ..     225     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.39
                    GHMP_kinases_C  51 aklsGaGgGpt 61 
                                          +G+G+G++
  gi|518651655|ref|YP_008141175.1|  93 IPSTGTGLGSS 103
                                       44567777765 PP

  == domain 2  score: 40.1 bits;  conditional E-value: 4e-14
                    GHMP_kinases_C   4 alergdlellgellnlsqrs..elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkd 70 
                                       al+  ++e lg+ll ++++s   l  + +i++p+++e  +++++lGa+g+ l GaGgG++++ +++ kd
  gi|518651655|ref|YP_008141175.1| 228 ALYDMNIEKLGKLLDQNWHSkrAL--YKEISTPVVDEYYSKALSLGAYGGNLIGAGGGGFLVFIVEAKD 294
                                       6777899*************7777..***************************************4433 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 !   40.1   0.0   3.6e-14   3.2e-10       2      66 .]      87     155 ..      86     155 .. 0.85

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.6e-14
                                       EEEEESSHT.TSSSCHHHHHHHHHHHHHHHHTTEHH..HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPv.gaGLGSSAAlavalvaAllallglsl..ee..aklaleaerlaqggngsggDvaasvyGg 66 
                                       i + s+iP  g+GLGSS+++ v+l+ Al a+   ++  +e  a+ a+e+er +    g+++D++ + +Gg
  gi|518651655|ref|YP_008141175.1|  87 ILSVSDIPStGTGLGSSSTFLVGLLNALHAYK-SEFasREqlAREAIEIERNVLQEPGGMQDQYMASFGG 155
                                       67889**98799***************87766.5544422579*******999779*************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 2246.62
//
Query:       gi|518651656|ref|YP_008141176.1|  [L=268]
Description: hypothetical protein FACI_IFERC00001G0295 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1591.04
//
Query:       gi|518651657|ref|YP_008141177.1|  [L=91]
Description: hypothetical protein FACI_IFERC00001G0296 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 591.53
//
Query:       gi|518651658|ref|YP_008141178.1|  [L=281]
Description: hypothetical protein FACI_IFERC00001G0297 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-50  170.5   0.2    2.6e-50  169.9   0.2    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    6.7e-27   94.1   0.2    4.4e-26   91.4   0.1    2.0  2  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
        0.2   11.6   0.0       0.38   10.8   0.0    1.3  1  Smg4_UPF3      Smg-4/UPF3 family


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.2   4.4e-54   2.6e-50       2     158 ..     121     274 ..     120     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 4.4e-54
                                       HHHHHHHHTT--SS--HHHHHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHC CS
                     THF_DHG_CYH_C   2 plnlgrlvkgeeallpctpkgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitr 78 
                                       ++n g+l++++e+++p+t+++vv++l+ ++i+    ++++++rs +vg+pla+lLl+++ tVt+chskt d+++i r
  gi|518651658|ref|YP_008141178.1| 121 SFNQGNLYTKNEMIAPATARAVVDILEYYKIQ--PGNACIINRSAVVGRPLAMLLLNRDYTVTLCHSKTVDIKRIAR 195
                                       689*************************9965..5799*************************************** PP

                                       CSSEEEE-SS-TT-B-GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHH CS
                     THF_DHG_CYH_C  79 eadivvvavGkpelikaemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntlea 155
                                       e +++vva+Gkp+ i++++v ++++viDvGin   ++k++GDv+f++v+++a+ itPvpgGVG +T++ +++n l+ 
  gi|518651658|ref|YP_008141178.1| 196 ENNVLVVAIGKPDYIDESYVTSESTVIDVGINYS-GNKISGDVNFDSVSNKAKNITPVPGGVGIVTATDIFENFLNG 271
                                       *********************************9.9**************************************998 PP

                                       HHC CS
                     THF_DHG_CYH_C 156 akr 158
                                        k 
  gi|518651658|ref|YP_008141178.1| 272 LKY 274
                                       876 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.1   7.3e-30   4.4e-26       1     116 []       2     117 ..       2     117 .. 0.97
   2 ?    0.5   0.0      0.12   7.2e+02      28      75 ..     197     243 ..     180     259 .. 0.66

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 7.3e-30
                                       E--HHHHHHHHHHHHHHHHHHHHHH.T---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHH CS
                       THF_DHG_CYH   1 lldGkalakeireelkeeveklkek.gvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellk 76 
                                       lldGk +a+e +e+lk+e++ + ek g++p+L  i+vg+dpas++Y+++k k+ +++Gi+++l k+ ++++  +l++
  gi|518651658|ref|YP_008141178.1|   2 LLDGKVVASEKMERLKSEIKGIIEKyGIEPELKLIQVGNDPASTIYANSKIKRGTKLGINVTLEKF-DNITMGKLVD 77 
                                       69*******************888779***************************************.68******** PP

                                       HHHHHHH-TT--EEEE-SS-STTS-HHHHHCCS-GGGBTT CS
                       THF_DHG_CYH  77 lieelneddsvdGilvqlPlpkhidekaileaispeKDVD 116
                                        i+++n++++++Gi+v  Plp +++ +++++ is  KD D
  gi|518651658|ref|YP_008141178.1|  78 YIKDANANSRINGIMVESPLPPSLNFQEVVDNISFYKDTD 117
                                       **************************************87 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.12
                                       --EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHH CS
                       THF_DHG_CYH  28 kpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeell 75 
                                       +  L+v   + d   e+Yv + + ++ +vGi+++  k++ dv+ + + 
  gi|518651658|ref|YP_008141178.1| 197 NNVLVVAIGKPDYIDESYVTS-ESTVIDVGINYSGNKISGDVNFDSVS 243
                                       334444444556678889876.55778899999988888777666555 PP

>> Smg4_UPF3  Smg-4/UPF3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   6.3e-05      0.38      11      63 ..      97     148 ..      95     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6.3e-05
                         Smg4_UPF3  11 LPPnLteeefleavsdkplpetvdykyFvpGklskd.slkeskysrayinfkdp 63 
                                       LPP+L  +e+++ +s   ++ t  +++F +G+l ++ +   ++++ra +++++ 
  gi|518651658|ref|YP_008141178.1|  97 LPPSLNFQEVVDNIS--FYKDTDGMTSFNQGNLYTKnEMIAPATARAVVDILEY 148
                                       9**************..9**9***********7665155678999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 1829.50
//
Query:       gi|518651659|ref|YP_008141179.1|  [L=358]
Description: hypothetical protein FACI_IFERC00001G0298 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.2e-18   65.1   0.0      8e-18   64.7   0.0    1.1  1  Glu_dehyd_C  Glucose dehydrogenase C-terminus
    4.6e-14   52.2   0.0    6.9e-14   51.7   0.0    1.3  1  ADH_N        Alcohol dehydrogenase GroES-like domain
      2e-05   24.6   0.0    3.3e-05   23.9   0.0    1.3  1  ADH_zinc_N   Zinc-binding dehydrogenase


Domain annotation for each model (and alignments):
>> Glu_dehyd_C  Glucose dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.3e-21     8e-18       4     211 ..     149     357 ..     146     358 .] 0.84

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.3e-21
                       Glu_dehyd_C   4 gvLvEPisiveKaielaea..srsafe.....wepesalvlGaGslGLLalalleaeerglervyvlgrrdrpdpti 73 
                                       + L+EP   v Ka+e   +  +rs fe     ++ +  l++G+Gs  +L + + +  e g++ vy ++r+   + ++
  gi|518651659|ref|YP_008141179.1| 149 STLTEPAKNVMKAFEIFNKlsARSIFEsedstYTSKNCLIIGTGSEAFLYAFMAR--EYGMT-VYLTNRHRLLEEKM 222
                                       679************98875466666532333667889***********944444..57775.************** PP

                       Glu_dehyd_C  74 dlveelGatYvdsretpvdeipeaseemdlvvEaTGsakhafeaiealapnGvaaLlGvpeds.evevdggelhrel 149
                                       +++e +   + +  e++         ++dl++++ G ++++++ + +l+ nG+a+L G      + ++ g++l+  +
  gi|518651659|ref|YP_008141179.1| 223 RIIEGIHCLFYNYLEENG------PDKIDLLIDTSGDPAAVMKFVGKLNYNGIAILFGTNGAApDSQLTGNDLN-YI 292
                                       *********998644433......4569********************************98857777777776.67 PP

                       Glu_dehyd_C 150 vleNkalvGsvNanrrhfeaavdtLaalpesl...ldelvtkvvdldeleeAfedddetiKtvve 211
                                       + +N a+ Gsv  + +h+  a+  L++ + s    +++l+t+ ++ ++ e   ++  e+iK++++
  gi|518651659|ref|YP_008141179.1| 293 IEHNIAVSGSVDGSKKHYMDAIGYLEKWKYSSsgiINKLITGIYKPEDTEIFRAKPPEEIKSIIK 357
                                       9*************************998775566*************99877888899999985 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   1.1e-17   6.9e-14       2     109 .]      25     140 ..      24     140 .. 0.84

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 1.1e-17
                                       TEEEEEEEEEEE-HHHHHHHTTS....TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHH CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkgg....kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCk 74 
                                       g++ i+  ++giCg+D   + g+     +++ +  +++GHE+v +v ++g++ ++++ Gd V+  ++   g+C +C+
  gi|518651659|ref|YP_008141179.1|  25 GKAKIRPVYTGICGTDRAEIAGHlpfaYNPTGQNYMVIGHEAVCQVIDIGENNSRIRPGDYVIP-IVRRRGTCINCR 100
                                       678999****************8666666666666**************************987.78889******* PP

                                       TT-GGG-....TTBEETTTS...S-SSSBSEEEECGGGEEEE CS
                             ADH_N  75 egeenlC....eeakllgvs...ldGgfaeyvvvpekklvkl 109
                                        g+++ C    ++ +    +    dG  +ey+  + ++l+k+
  gi|518651659|ref|YP_008141179.1| 101 IGRQDNCsdadNDITEA--GirgADGFNSEYFFDSPENLIKV 140
                                       *******5544333333..255899*******9999999986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.0   5.5e-09   3.3e-05      29     121 ..     201     311 ..     184     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 5.5e-09
                                       HHHHTTESEEEET.....TTC.HHHHHHHHHT.......TTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC.T CS
                        ADH_zinc_N  29 lakklGadeviny.....kea.dlverikelt.......ggegvdvvfecvGsgatleaalkllkpgGrlvvvGg.g 91 
                                       +a+++G+++++++     +e+ ++ e i+ l+       g++++d+ ++++G++a++   +  l+++G   ++G+ g
  gi|518651659|ref|YP_008141179.1| 201 MAREYGMTVYLTNrhrllEEKmRIIEGIHCLFynyleenGPDKIDLLIDTSGDPAAVMKFVGKLNYNGIAILFGTnG 277
                                       6899*******9977777444466666666669999998899*********************************86 PP

                                       SSEEE....EEHHHHHHTT-EEEEE-SSCHHHHH CS
                        ADH_zinc_N  92 kgeee....fdlrnlllkeksilGsllgslreef 121
                                         +++     dl++++ +++ + Gs+ gs+++ +
  gi|518651659|ref|YP_008141179.1| 278 AAPDSqltgNDLNYIIEHNIAVSGSVDGSKKHYM 311
                                       66666888999999************99955544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2352.75
//
Query:       gi|518651660|ref|YP_008141180.1|  [L=112]
Description: DNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-16   60.7   0.1    1.4e-16   60.3   0.1    1.3  1  CMD       Carboxymuconolactone decarboxylase family


Domain annotation for each model (and alignments):
>> CMD  Carboxymuconolactone decarboxylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.1   7.8e-21   1.4e-16       3      78 ..      24      98 ..      22     105 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 7.8e-21
                                      HHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHH CS
                               CMD  3 llraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaara 78
                                      ++  ++++++a++  +g+Ld k++e +ala  +a +ce+C+++H+++A++aG+t+ e++ev  + + + g+ a++ 
  gi|518651660|ref|YP_008141180.1| 24 FAGSFMNFMGATMG-KGALDTKTKEFLALALGIAARCEWCISYHVNEAIKAGATRKELMEVGYVTVLMYGSQALME 98
                                      66789********9.***************************************************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       559  (0.0311785); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 794.83
//
Query:       gi|518651661|ref|YP_008141181.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G0300 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   18.2   0.0     0.0026   17.3   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
  ------ inclusion threshold ------
      0.055   12.9   0.0        0.1   12.0   0.0    1.4  1  TehB             Tellurite resistance protein TehB


Domain annotation for each model (and alignments):
>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.9e-07    0.0026       3      60 ..      98     152 ..      96     200 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.9e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                        i+D+ sGaG + i f   f+ v ++ei+ ++ a+a+ N   Y   +++ ++  d+f+
  gi|518651661|ref|YP_008141181.1|  98 KIVDAGSGAGMQDIMFSG-FSDVTGVEIDSNRYAMANLNKIPY--ISNVNFINSDIFS 152
                                       699*************98.99**********************..8899999999998 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.2e-05       0.1       7      88 ..      74     154 ..      68     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.2e-05
                                       CHHHHHHT-----HHHHHHCCCS-S-EEEEES-TTSHHHHHHHHTT-.EEEE..EES-HHHHHHHHHHHHHTT-TTE CS
                              TehB   7 dyfskkynltathsevveavkivkpgkvldlgcgqgrnslylsllgy.dvta..wdknensiafleeikekenlkni 80 
                                       dy+s  y + ++ ++    +k +   k++d g g g + + +s   + dvt   +d n  ++a+l++i  + n++ i
  gi|518651661|ref|YP_008141181.1|  74 DYYSSMYSTPEIVGKY--RAKKLAGNKIVDAGSGAGMQDIMFSG--FsDVTGveIDSNRYAMANLNKIPYISNVNFI 146
                                       6777777777776654..46889999**********99988764..33777522699******************99 PP

                                       EEEE--GG CS
                              TehB  81 stalydin 88 
                                       ++ ++  n
  gi|518651661|ref|YP_008141181.1| 147 NSDIFSFN 154
                                       99988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2801.84
//
Query:       gi|518651662|ref|YP_008141182.1|  [L=192]
Description: GTP cyclohydrolase II [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-62  209.1   0.0    3.3e-62  208.9   0.0    1.0  1  GTP_cyclohydro2  GTP cyclohydrolase II


Domain annotation for each model (and alignments):
>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.9   0.0   1.8e-66   3.3e-62       4     163 .]       6     168 ..       3     168 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.9 bits;  conditional E-value: 1.8e-66
                                       EEEEEEETTEEEEEEEE--.....EEEEEE-.........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHHHHH-. CS
                   GTP_cyclohydro2   4 aeaklptrfgefrliayedkvdgkehlalvkgdi....pvlvRvHsecltgDvlgslrcdcgeqldealeliaeegr 76 
                                       a+aklptrfg f++++++++ d+k h +lv+gdi    +v+vR+HsecltgDv+gs+rcdc++ql  +l++i +++r
  gi|518651662|ref|YP_008141182.1|   6 AKAKLPTRFGVFNIYVFKNE-DKKDHAVLVHGDIeeeeNVPVRIHSECLTGDVFGSMRCDCRDQLITSLKYIGSRER 81 
                                       4799*************877.669*************999********************************77999 PP

                                       EEEEEE--TTTTTHHHHHHHHHHHHHCT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHCT CS
                   GTP_cyclohydro2  77 GvlvylrqegrgigllnklkayalqdeglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLeg 153
                                       G+l+ylrqegrgigllnk++ay+l+d+g DTvean ++glpad r+y+ a  ++k +++k+i+L+Tnnpek+++Le+
  gi|518651662|ref|YP_008141182.1|  82 GMLIYLRQEGRGIGLLNKIRAYNLEDNGKDTVEANIEQGLPADNRHYNFAIDVIKYFNIKSIELMTNNPEKIKNLEE 158
                                       ***************************************************************************** PP

                                       T....SEEEE CS
                   GTP_cyclohydro2 154 fgievvervp 163
                                        gi++ +r+p
  gi|518651662|ref|YP_008141182.1| 159 NGIKISKRIP 168
                                       *******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 00:00:00.40
# Mc/sec: 1443.37
//
Query:       gi|518651663|ref|YP_008141183.1|  [L=60]
Description: hypothetical protein FACI_IFERC00001G0302 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.07   13.0   0.0       0.17   11.8   0.0    1.7  2  UL11      Membrane-associated tegument protein


Domain annotation for each model (and alignments):
>> UL11  Membrane-associated tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.38   6.7e+03      20      25 ..      18      23 ..      17      24 .. 0.73
   2 ?   11.8   0.0   9.6e-06      0.17      21      35 ..      31      45 ..      25      47 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.38
                              UL11 20 TedGEv 25
                                       +dGE+
  gi|518651663|ref|YP_008141183.1| 18 SKDGEI 23
                                      579996 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.6e-06
                              UL11 21 edGEvveLdseffdt 35
                                       +GEvv++++e f+ 
  gi|518651663|ref|YP_008141183.1| 31 PSGEVVSMENENFEE 45
                                      59***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 464.12
//
Query:       gi|518651664|ref|YP_008141184.1|  [L=270]
Description: (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.2e-32  110.9  14.2    7.9e-32  110.5  14.2    1.2  1  UbiA        UbiA prenyltransferase family
     0.0023   17.7   2.9     0.0023   17.7   2.9    2.1  2  PGG         Domain of unknown function
  ------ inclusion threshold ------
        7.3    6.5   6.3        2.5    8.0   1.2    2.5  2  ECSCR       Endothelial cell-specific chemotaxis regulator
        7.7    6.6  10.1       0.25   11.4   2.0    2.5  3  Vma12       Endoplasmic reticulum-based factor for assembly o


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 !  110.5  14.2   1.8e-35   7.9e-32      19     236 ..      36     245 ..      17     267 .. 0.86

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 1.8e-35
                              UbiA  19 lllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltall 95 
                                       +  l l ++ ++l++a++n++Nd+ D+e+D+   ++p+RPl+sG i++k+a+ +ai ++i++++++  ++++++ l+
  gi|518651664|ref|YP_008141184.1|  36 IIPLTLGAISVFLVTAGGNIINDISDVETDKY--NHPDRPLPSGTITKKAAYYLAISFFIIAFIVS-TFISLFISLV 109
                                       356778888999********************..********************************.********** PP

                              UbiA  96 gllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDr 172
                                       +++a ll+v Y  + +K+++l g++++++  g+++l g ++++  +   +lll+l+ f+  ++  +++d++d++gD 
  gi|518651664|ref|YP_008141184.1| 110 VVIAELLLVSYE-FKTKKIGLPGNLTVSLLIGMIFLYGGFITGT-I-SKMLLLFLLAFFSNMSREIMKDIEDINGD- 182
                                       ************.9**************************9755.4.5677777777*******************. PP

                              UbiA 173 kagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraarlvrr 236
                                        + + t+p ++G  +a+i++a+++++++ + +l +++++l++y+l+a++l  l++++ ++ ++ 
  gi|518651664|ref|YP_008141184.1| 183 -VDRVTFPKKYGIGKAKIVSAIFVVITISVSVLPYYFHVLSIYYLYAVVLDDLLFAITIWYLKA 245
                                       .8889*************866555555555789999************9988888887777665 PP

>> PGG  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.9   5.1e-07    0.0023      51     114 ..      91     153 ..      73     155 .. 0.80
   2 ?   -2.5   1.4      0.98   4.4e+03     101     101 ..     228     228 ..     197     268 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 5.1e-07
                               PGG  51 aafkvFvisnaiAlvaSlvvvvlllis.slvedeakslpkklrvllvllvlsllsllvaFaagly 114
                                           +F++s  i+l++Slvvv+  l++ s   ++++++      l+v+l++ +++l++ F++g++
  gi|518651664|ref|YP_008141184.1|  91 FFIIAFIVSTFISLFISLVVVIAELLLvS--YEFKTKKIGLPGNLTVSLLIGMIFLYGGFITGTI 153
                                       45679*****************9774423..46667777778899999**************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.98
                               PGG 101 s 101
                                       +
  gi|518651664|ref|YP_008141184.1| 228 A 228
                                       2 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   1.2   0.00055       2.5      22      53 ..      93     126 ..      72     129 .. 0.78
   2 ?    0.0   0.3      0.16   7.3e+02      33      48 ..     202     217 ..     189     222 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00055
                             ECSCR  22 vaafgvisfiv..ilvvvviilvsvvslrfkcrk 53 
                                       + af v +fi   i +vvvi  + +vs  fk +k
  gi|518651664|ref|YP_008141184.1|  93 IIAFIVSTFISlfISLVVVIAELLLVSYEFKTKK 126
                                       66888888885114456777778899****9987 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.16
                             ECSCR  33 ilvvvviilvsvvslr 48 
                                        + vv+ i vsv+   
  gi|518651664|ref|YP_008141184.1| 202 AIFVVITISVSVLPYY 217
                                       3445555667776555 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.0   5.5e-05      0.25      90     130 ..      80     120 ..      76     127 .. 0.84
   2 ?   -3.8   0.1       2.8   1.3e+04      82      95 ..     132     145 ..     131     156 .. 0.76
   3 ?   -0.1   0.1      0.19   8.6e+02      73      91 ..     199     217 ..     162     266 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                             Vma12  90 vffavwialrsartpslpvrvllslvvallVgvAEvvvyak 130
                                       +  a ++++ s++   + v  ++sl+++l+V++AE+++++ 
  gi|518651664|ref|YP_008141184.1|  80 TKKAAYYLAISFFIIAFIVSTFISLFISLVVVIAELLLVSY 120
                                       556788888888899999******************99875 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.8
                             Vma12  82 NiliSvvavffavw 95 
                                       N+ +S ++ +++++
  gi|518651664|ref|YP_008141184.1| 132 NLTVSLLIGMIFLY 145
                                       67777777777777 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.19
                             Vma12  73 vnrqlilvlNiliSvvavf 91 
                                       + + + +v+ i +Sv+   
  gi|518651664|ref|YP_008141184.1| 199 IVSAIFVVITISVSVLPYY 217
                                       4445556666666665433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1940.87
//
Query:       gi|518651665|ref|YP_008141185.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G0304 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 726.54
//
Query:       gi|518651666|ref|YP_008141186.1|  [L=332]
Description: glycosylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-10   40.7   0.0    4.4e-10   39.6   0.0    1.5  1  Esterase       Putative esterase
    0.00068   19.0   0.0     0.0011   18.3   0.0    1.3  1  Hydrolase_4    Serine aminopeptidase, S33
    0.00079   19.1   0.0     0.0012   18.5   0.0    1.4  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   7.4e-14   4.4e-10      38     236 ..      79     314 ..      39     329 .. 0.80

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.4e-14
                                       CHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTEEETTCCCCCCHCHHHHTHHHHHHHHHCSEEC CS
                          Esterase  38 qnfrakelleslaregeiaeviivvvprggessfysdwdlgarfyenategpgaeayetfltqeLlplldanfrtap 114
                                       ++f  ++ll++l re++   v ++++ + g ++f ++                  +y++f++  L++++   +  ++
  gi|518651666|ref|YP_008141186.1|  79 TSFDFTDLLDRLDREYGYIIVLPDTMTKFGGNQFVDSTAI--------------GNYKSFIARDLVDYIHRLYGNRD 141
                                       5566666666666666666666666666555533333333..............49****************99999 PP

                                       CCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES--S-CC...................................... CS
                          Esterase 115 dgravaGqSmGGlgALilalkhpdrFgsvssfSpivnps...................................... 153
                                           ++G S GG+g++ + l++p++F+  +  S+    s                                      
  gi|518651666|ref|YP_008141186.1| 142 I--YLFGKSSGGFGSISITLDYPESFKGFIDISGD---Syfpycylpdfstaylamkgktlegfiesyrqqmvhsqd 213
                                       9..9**********************999999976...345589999****************************** PP

                                       .................................HCHHHCTTCCHHHCC-CCCCHCHHCHTTSEEEEEEEECTTBCCC CS
                          Esterase 154 .................................namWgqeekeawqendpvllakelsaslkalriyldvGtseddl 197
                                                                        +  W     ++w e dpv + ++++++lk+++i l+ G++++ +
  gi|518651666|ref|YP_008141186.1| 214 eleaynvvamaasyspdgkniqlpfsidtgeilPEVW-----NKWLEFDPVNRLSSEVEKLKGKKIILQTGNRDE-Y 284
                                       ******************9999999999999988889.....56******************************8.4 PP

                                       HTSCHHHHHHHHHHHCCHHHHCCCCCCTT-SCCCC--SS CS
                          Esterase 198 geqlsveilevlarnrelkeqlaargvegedheydGghs 236
                                       + +          ++  ++e l+ ++++++++ey+ gh 
  gi|518651666|ref|YP_008141186.1| 285 KINI---------GMNMIHEILKRNKIDHYYKEYPNGHF 314
                                       4343.........44555566666677777777774442 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.8e-07    0.0011      63     108 ..     127     172 ..     120     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-07
                       Hydrolase_4  63 aafvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsa 108
                                       + +v+ + + ++++ ++l+G S GG+ +++++l+yp++++g+i ++
  gi|518651666|ref|YP_008141186.1| 127 RDLVDYIHRLYGNRDIYLFGKSSGGFGSISITLDYPESFKGFIDIS 172
                                       56788999999******************************99554 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   2.1e-07    0.0012       2     106 ..      59     173 ..      58     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
                                       EEEEE-STTTCGGG..........GTTGHHHHHHHHT.TSEEEEEEET.TSTTSSSTTTGB.CHHSHHHHHHHHHHH CS
                     Abhydrolase_1   2 vlvilhGlpgssdv..........waerglapaLakd.gfdvillDlr.GvgySspapacinddygtasvaddldri 66 
                                       v++ l+G+ gs+++          +    l + L+++ g+ ++l+D +  +g  ++  ++   +y  +  +d +d+i
  gi|518651666|ref|YP_008141186.1|  59 VFIGLPGFFGSGNSflnksytsfdFTD--LLDRLDREyGYIIVLPDTMtKFGGNQFVDSTAIGNYKSFIARDLVDYI 133
                                       566677777777776666655533333..5555555588888888876323333333322226777774566666** PP

                                       HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE CS
                     Abhydrolase_1  67 ldalgddkltlvGhSmGGmialayaaeyperVkalvllga 106
                                          +g++ ++l G S GG+ +    ++ype+ k+++ +++
  gi|518651666|ref|YP_008141186.1| 134 HRLYGNRDIYLFGKSSGGFGSISITLDYPESFKGFIDISG 173
                                       **********************************998777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2212.20
//
Query:       gi|518651667|ref|YP_008141187.1|  [L=438]
Description: hypothetical protein FACI_IFERC00001G0306 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.1e-50  169.5   0.1    1.5e-49  168.9   0.1    1.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.3e-16   59.5   0.0    7.7e-16   58.3   0.0    1.6  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    1.7e-13   50.5   0.3    1.8e-09   37.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.1e-13   49.7   1.0    1.7e-07   31.7   0.0    3.3  4  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.2e-06   27.9   0.0    1.7e-05   24.1   0.0    2.2  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    2.8e-06   26.3   0.2     0.0008   18.2   0.7    2.9  3  HI0933_like     HI0933-like protein
    3.4e-06   26.9   0.3      0.016   14.8   0.4    3.3  4  DAO             FAD dependent oxidoreductase
    5.8e-06   26.5   0.2     0.0013   18.9   0.3    2.8  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      5e-05   22.6   0.4    0.00011   21.4   0.2    1.7  2  FAD_binding_2   FAD binding domain
    0.00029   20.2   1.4      0.011   15.1   0.7    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.003   17.0   1.2      0.005   16.2   1.2    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
     0.0052   15.7   0.2     0.0097   14.8   0.2    1.4  1  Trp_halogenase  Tryptophan halogenase
     0.0064   16.7   0.1        3.3    8.0   0.0    2.5  2  TrkA_N          TrkA-N domain
      0.007   16.8   0.0        1.6    9.2   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.013   14.6   0.7      0.013   14.6   0.7    3.1  4  GIDA            Glucose inhibited division protein A
      0.021   14.8   0.0        3.3    7.7   0.0    3.7  4  NAD_binding_9   FAD-NAD(P)-binding
      0.068   12.2   0.0       0.19   10.8   0.0    1.7  2  Lycopene_cycl   Lycopene cyclase protein
       0.23   11.3   1.0        0.5   10.2   0.0    2.0  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD 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 !  168.9   0.1   1.5e-52   1.5e-49       2     294 .]       2     295 ..       1     295 [. 0.90
   2 ?   -4.0   0.0       6.6   6.5e+03     153     181 ..     338     367 ..     328     382 .. 0.63

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.5e-52
                                       SEEEE--SHHHHHHHHHHHH..HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCC CS
                                       xxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq..agakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgie 68 
                                       ++vviGgG+AG++aa ++++  + a++t++e++g++ +  c +++ l g+ ed  +++        e+      ++e
  gi|518651667|ref|YP_008141187.1|   2 NIVVIGGGAAGMSAASKARRmdKTARITVIEQTGYVSYAECGMPYYLSGYFEDSGELLhyplseftEH-----RNLE 73 
                                       79******************999********************9999999999887778988644433.....4588 PP

                                       CCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-T.S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       Pyr_redox_2  69 lllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllp.k 143
                                        ++g++v  i pg+k v       g+ +k+ ydklv+AtG++pr++   +G    + + +r++d+a ++k+k +  +
  gi|518651667|ref|YP_008141187.1|  74 IITGVKVEFINPGEKYVFA-----GN-KKFPYDKLVIATGAEPRIPdEFKGY---A-YALRNMDDAIGIKEKIKGlD 140
                                       8888889999999966666.....33.48*****************888888...4.445***************** PP

                                       EEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 144 rivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvl 220
                                       +++++G+G+ G+El + l+  + +v l+   + +l+ +d ++++ l+  ++++G e+  ++++ +i g + +++v++
  gi|518651667|ref|YP_008141187.1| 141 NVTIIGAGVLGTELFSLLS-HKFKVKLISKHEYVLPHMDTDMGNVLTSIVNESGNEIEYNSVPSAISGTPGNYQVTT 216
                                       **************98864.3459***********************************************888777 PP

                                       TTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGC.......TECCSS--HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxx RF
                       Pyr_redox_2 221 edgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDva.......ggkggpelaqaA 290
                                       ++g+ ++++ v++a+G++pstel+ +k+glel+ +g i+v++fl+t+ p+iya+GD +       g  g + laq A
  gi|518651667|ref|YP_008141187.1| 217 GNGS-FNTQIVIFATGIKPSTELA-KKAGLELTADGLIKVNDFLQTSNPDIYAAGDNVatknivtGSYGYYPLAQIA 291
                                       7777.9******************.*******************************887999999999999999999 PP

                                       HHHH CS
                                       xxxx RF
                       Pyr_redox_2 291 vqqG 294
                                        ++G
  gi|518651667|ref|YP_008141187.1| 292 NKMG 295
                                       8887 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHT-EEEEEESSSSSS.TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                       Pyr_redox_2 153 iGvElAaalaklgkevtlveardrll.ral 181
                                       +G+++ +++ k++++  +++  d++l   +
  gi|518651667|ref|YP_008141187.1| 338 TGIDYGSVYIKAKSKSNYLHGSDIFLkIIY 367
                                       556666666666666666666666664444 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 !   58.3   0.0   7.8e-19   7.7e-16       6     103 ..     320     417 ..     316     422 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 7.8e-19
                                       ESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEEC.TTHHHHHHHHHH CS
                     Pyr_redox_dim   6 ftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivG.pgageliqelav 81 
                                       ++ ++v+++G++e+ Ak+ g  i++g++++ka +++ + + +++f+K+++++kt++++G +i+G ++a+ +++ +a+
  gi|518651667|ref|YP_008141187.1| 320 VFGYQVGYTGINEATAKKTG--IDYGSVYIKAKSKSNYLHGSDIFLKIIYNKKTEEIMGGQIIGkDNAAWRLNVIAT 394
                                       5789****************..9*****************************************556666******* PP

                                       HHHTTSBHH.HHHTSBSSSSSTG CS
                     Pyr_redox_dim  82 aikagltve.dladtihihPtls 103
                                       ai+  +    +l +++++ P + 
  gi|518651667|ref|YP_008141187.1| 395 AISGHMNLYdLLYNDLGYEPEYG 417
                                       ******99956********9875 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00015      0.15       1      30 [.       4      34 ..       4      41 .. 0.84
   2 !   37.3   0.0   1.8e-12   1.8e-09      84     305 .]      59     269 ..      44     269 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl.edylilEkg 30
                                      ++iG+G+aG++aa ++++++   +++++E+ 
  gi|518651667|ref|YP_008141187.1|  4 VVIGGGAAGMSAASKARRMDKtARITVIEQT 34
                                      79**************998763678899986 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.8e-12
                       Pyr_redox_3  84 leY.lrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnkl.nipGeeklvkhyskvk. 157
                                       l+Y l+e +++ +l+i +  +Ve +++ ++   v + ++++  +k++iAtG    P+ + +++G   ++ ++  +  
  gi|518651667|ref|YP_008141187.1|  59 LHYpLSEFTEHRNLEIITGVKVEFINPGEKY--VFAGNKKFPYDKLVIATGA--EPRIPdEFKGYA-YALRNMDDAi 130
                                       555478999*****************97654..45556667779*******9..888873599998.6665555432 PP

                       Pyr_redox_3 158 .efhkya.gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfn 232
                                          +k++  ++v++iG++  + +  + l ++  +V+++ +++        +  ++  d+ n l ++v+e+  ++++n
  gi|518651667|ref|YP_008141187.1| 131 gIKEKIKgLDNVTIIGAGVLGTEL-FSLLSHKFKVKLISKHEY-------VLPHMDTDMGNVLTSIVNESGNEIEYN 199
                                       24556664689***********97.7788888********985.......455689999999999999966899*** PP

                       Pyr_redox_3 233 aevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       +   +i+ +  +y+v+t +g+  + ++ v++atG kp++++ kk+++el++dg +++++  + t  p+++ aG
  gi|518651667|ref|YP_008141187.1| 200 SVPSAISGTPGNYQVTTGNGSF-N-TQIVIFATGIKPSTELAKKAGLELTADGLIKVNDFLQ-TSNPDIYAAG 269
                                       *******************854.4.5899****************************98765.5579999998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     3e-05     0.029       1      31 [.       2      34 ..       2      55 .. 0.88
   2 ?   -1.9   0.0       5.3   5.3e+03      51      69 ..      68      86 ..      63      90 .. 0.75
   3 !   31.7   0.0   1.7e-10   1.7e-07       1      77 [.     141     215 ..     141     219 .. 0.91
   4 ?   -2.2   0.0       6.2   6.2e+03      56      68 ..     364     376 ..     338     396 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-05
                                      EEEEECSSHHHHHHHHHHHHTT..SEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelg..kkVtvvers 31
                                      ++vv+GgG  g+ +A+ ++++   +++tv+e  
  gi|518651667|ref|YP_008141187.1|  2 NIVVIGGGAAGMSAASKARRMDktARITVIEQT 34
                                      59******************9844599**9976 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.3
                                      HHTTEEEECSEEEEEEEEE CS
                         Pyr_redox 51 ekngievllntkveeiegs 69
                                      e+++ e++++ kve i+  
  gi|518651667|ref|YP_008141187.1| 68 EHRNLEIITGVKVEFINPG 86
                                      6679999999999988755 PP

  == domain 3  score: 31.7 bits;  conditional E-value: 1.7e-10
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +v+++G+G++g El + l++   kV+++  ++ +l+ +D +++++l+  + + g e+ +n+++ +i g++ + ++v+
  gi|518651667|ref|YP_008141187.1| 141 NVTIIGAGVLGTELFSLLSHKF-KVKLISKHEYVLPHMDTDMGNVLTSIVNESGNEIEYNSVPSAISGTPGN-YQVT 215
                                       589************9998755.8*******************************************99985.5565 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 6.2
                                       EEECSEEEEEEEE CS
                         Pyr_redox  56 evllntkveeieg 68 
                                       ++++n+k+eei g
  gi|518651667|ref|YP_008141187.1| 364 KIIYNKKTEEIMG 376
                                       4566666666654 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.16   1.6e+02     193     222 ..       2      31 ..       1      41 [. 0.62
   2 !   24.1   0.0   1.7e-08   1.7e-05     150     241 ..     100     186 ..      88     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.16
                       K_oxygenase 193 riaVvGsGqSaaeifedllrrqkkvelklv 222
                                       +i+V+G+G  +   + ++ r  k++ ++++
  gi|518651667|ref|YP_008141187.1|   2 NIVVIGGGAAGMSAASKARRMDKTARITVI 31 
                                       467777776666666666666655555554 PP

  == domain 2  score: 24.1 bits;  conditional E-value: 1.7e-08
                       K_oxygenase 150 rnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrse 226
                                        +lv+++G ep iP+ ++ +     +   +++   ke+ +  ++++++G+G  + e+f  l +++k   +kl+++ e
  gi|518651667|ref|YP_008141187.1| 100 DKLVIATGAEPRIPDEFKGYA--YALRNMDDAIGIKEKIKGLDNVTIIGAGVLGTELFSLLSHKFK---VKLISKHE 171
                                       68****************998..5777778888888889999****************99987776...******** PP

                       K_oxygenase 227 aleplddspfvneif 241
                                        + p  d+++ n ++
  gi|518651667|ref|YP_008141187.1| 172 YVLPHMDTDMGNVLT 186
                                       ********9998765 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.7   8.1e-07    0.0008       2      32 ..       2      34 ..       1      38 [. 0.86
   2 ?   -0.2   0.0      0.31   3.1e+02     120     164 ..      68     108 ..      53     115 .. 0.71
   3 ?    3.4   0.0     0.025        25     112     165 ..     182     233 ..     155     257 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 8.1e-07
                                      SEEEE--SHHHHHHHHHH..HHTT--EEEE-SS CS
                       HI0933_like  2 dviviGgGaAGlmaAisa..akrgkrVllleka 32
                                      +++viGgGaAG+ aA +a   ++ +r++++e++
  gi|518651667|ref|YP_008141187.1|  2 NIVVIGGGAAGMSAASKArrMDKTARITVIEQT 34
                                      69****************666678899999986 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.31
                                       HHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 120 keagvklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                       ++++ ++ +  +v+ +  + ++   v + +++++  dklv+AtG 
  gi|518651667|ref|YP_008141187.1|  68 EHRNLEIITGVKVEFI--NPGE-KYVFA-GNKKFPYDKLVIATGA 108
                                       4566777777777777..3444.33444.68999*********97 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.025
                                       HHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
                       HI0933_like 112 vdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                                        ++l++ ++e+g ++++++  ++++  + g+++v+t ++++++++ +++AtG +
  gi|518651667|ref|YP_008141187.1| 182 GNVLTSIVNESGNEIEYNSVPSAIS-GTPGNYQVTT-GNGSFNTQIVIFATGIK 233
                                       5788899999999999998777775.56666*****.**************965 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.4   1.6e-05     0.016       2      29 ..       3      34 ..       2      41 .. 0.86
   2 !    6.9   0.0     0.004         4     139     232 ..      48     128 ..      38     138 .. 0.74
   3 ?    0.3   0.0      0.41   4.1e+02       2      12 ..     142     152 ..     141     173 .. 0.75
   4 ?   -2.1   0.0       2.3   2.3e+03     180     205 ..     212     235 ..     185     250 .. 0.60

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      EEEECTSHHHHHHHHHHHHT.T....EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarr.g....Vtllekg 29
                                      +v+iGGG +G+s+A  + rr      +t++e+ 
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKA-RRmDktarITVIEQT 34
                                      9****************.66435889*****86 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.004
                                       TEEEE.EHHHHHHHHHHHH.HHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGGHHHHHTTCT CS
                               DAO 139 dtgqv.dpakltaalaraa.ealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGawsdllgllke 212
                                        +g + d  +l+++ ++++ e +  ei++g +v+ + ++++k   v+    g++ + +d++V+a+Ga        ++
  gi|518651667|ref|YP_008141187.1|  48 LSGYFeDSGELLHYPLSEFtEHRNLEIITGVKVEFI-NPGEK--YVFA---GNKkFPYDKLVIATGAE-------PR 111
                                       4577778889999989996255569*****999988.66544..5543...5555789********99.......55 PP

                                       TTSEEEEEEEEEEEEEECCT CS
                               DAO 213 ldlpispvrgqvlvlkplse 232
                                       +  p   ++g+ ++l++ ++
  gi|518651667|ref|YP_008141187.1| 112 I--P-DEFKGYAYALRNMDD 128
                                       5..6.778888888866555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.41
                                       EEEECTSHHHH CS
                               DAO   2 vviiGGGiiGl 12 
                                       v iiG+G+ G 
  gi|518651667|ref|YP_008141187.1| 142 VTIIGAGVLGT 152
                                       89*******97 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.3
                                       EEEEEECT.EEEEEEEEEEE--GGGHH CS
                               DAO 180 wgverttp.gendaadavVnaaGawsd 205
                                       ++v  tt  g+    + v+ a+G+  +
  gi|518651667|ref|YP_008141187.1| 212 YQV--TTGnGSF-NTQIVIFATGIKPS 235
                                       555..6655653.3366*****98754 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 !   18.9   0.3   1.3e-06    0.0013       1      29 [.       5      35 ..       5      40 .. 0.85
   2 ?    4.4   0.0     0.045        45       1      30 [.     144     172 ..     144     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.3e-06
                                      EE--SHHHHHHHHHHHCC..TEEEEEE-SSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka..gfdvlllekrd 29
                                      ++G+G++G++aA+ +++    ++++++e+  
  gi|518651667|ref|YP_008141187.1|  5 VIGGGAAGMSAASKARRMdkTARITVIEQTG 35
                                      8****************633569*****865 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.045
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdr 30 
                                       I+GaG+ G  + +lL+  +f+v l+ k+++
  gi|518651667|ref|YP_008141187.1| 144 IIGAGVLGTELFSLLSH-KFKVKLISKHEY 172
                                       9**************97.6*****999986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.2   1.1e-07   0.00011       2      34 ..       3      37 ..       2      50 .. 0.87
   2 ?   -2.7   0.0       2.3   2.3e+03     113     413 ..     254     288 ..     228     302 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.1e-07
                                      EEEE--SHHHHHHHHHHHHTTT..-EEEEESSSGG CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGl..kvavvekeqef 34
                                      ++ViG+G+AG++AA +a++  +  +++v+e+++++
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKARRMDKtaRITVIEQTGYV 37
                                      79*****************666669******9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.3
                                       EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEE CS
                     FAD_binding_2 113 vrelGglsatartlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevr 189
                                       v+++ ++                                                                      
  gi|518651667|ref|YP_008141187.1| 254 VNDFLQT---------------------------------------------------------------------- 260
                                       3333333...................................................................... PP

                                       EEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB- CS
                     FAD_binding_2 190 irakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLi 266
                                                                                                                    
  gi|518651667|ref|YP_008141187.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       -THHHHTT-EEE-TTSSBTHGGGS-HHHHHHHHH.HHHHTTTSCCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT. CS
                     FAD_binding_2 267 tealrgeGgilvdkdGrrFmnelasrdvvsrailekeiaeggseanvyldashgldaegleatleaineeaangldk 343
                                                                                                                    
  gi|518651667|ref|YP_008141187.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                                       .....S-TTTSEEE.......EEEEEEEES-EEEBETTSBESTTEEESSBTEEE-STCE.....ESSSSTTS--T CS
                     FAD_binding_2 344 dfgrgidpadrpipgpfyavkvvpaqhytmgGvetdengrvldadgqpipGLYAaGeva.....aggvhganrlg 413
                                                                                        p+ YAaG         +g  g+++l+
  gi|518651667|ref|YP_008141187.1| 261 -----------------------------------------------SNPDIYAAGDNVatkniVTGSYGYYPLA 288
                                       ...............................................4455566663322444444444444443 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.7   1.1e-05     0.011      30      56 ..       2      28 ..       1      40 [. 0.83
   2 ?    3.5   0.0     0.037        37      30      42 ..     141     153 ..     126     197 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                                      +++viGgG aG++A++ a++++ + ++
  gi|518651667|ref|YP_008141187.1|  2 NIVVIGGGAAGMSAASKARRMDKTARI 28
                                      589******************865444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.037
                                       EEEEESTSHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlq 42 
                                       +v++iG+Gv G++
  gi|518651667|ref|YP_008141187.1| 141 NVTIIGAGVLGTE 153
                                       69*********97 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2     5e-06     0.005       2      32 ..       3      35 ..       2      37 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGa..kvlLveerg 32
                                      +vV+GGg+aG+ AA  A r+++  +  ++e++g
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKARRMDKtaRITVIEQTG 35
                                      8*******************9833455666665 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   9.8e-06    0.0097       1      33 [.       2      33 ..       2      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.8e-06
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                                      +iv++GGG aG  aA+  +++  +++++t++e+
  gi|518651667|ref|YP_008141187.1|  2 NIVVIGGGAAGMSAASKARRMD-KTARITVIEQ 33
                                      69*********88888877776.77******97 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.0    0.0033       3.3       1      30 [.       3      34 ..       3      55 .. 0.89
   2 ?    6.1   0.0     0.013        13       1      36 [.     142     176 ..     142     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                                      EEEES-SHHHHHHHHHHHH.TT.EEEEEEESS CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.gg.kdvvvidkd 30
                                      i++iG G  G+s a + ++ ++  +++vi++ 
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKARRmDKtARITVIEQT 34
                                      89*****************777866****985 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHH CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeervee 36 
                                       + iiG+G +G++l   Ls++  +v +i k e ++ +
  gi|518651667|ref|YP_008141187.1| 142 VTIIGAGVLGTELFSLLSHKF-KVKLISKHEYVLPH 176
                                       579****************99.5****998876655 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 !    9.2   0.0    0.0016       1.6       9      39 ..       2      34 ..       1      95 [. 0.83
   2 ?    5.4   0.0     0.024        24       9      40 ..     141     171 ..     135     245 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0016
                     NAD_binding_7  9 kvlvvGgGevAa...rkvrklleagakvtvvape 39
                                      +++v+GgG  ++   +k+r++ ++ a++tv+ ++
  gi|518651667|ref|YP_008141187.1|  2 NIVVIGGGAAGMsaaSKARRMDKT-ARITVIEQT 34
                                      689****99865222788887777.*****9876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.024
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev 40 
                                       +v ++G+G ++++ + +ll+ + kv+++++  
  gi|518651667|ref|YP_008141187.1| 141 NVTIIGAGVLGTE-LFSLLSHKFKVKLISKHE 171
                                       799********98.56677777*******983 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.7   1.3e-05     0.013       2      28 ..       3      29 ..       2      43 .. 0.78
   2 ?   -0.4   0.0      0.48   4.8e+02     106     150 ..      67     108 ..      62     125 .. 0.76
   3 ?    0.0   0.1      0.36   3.5e+02     320     335 ..     135     150 ..     123     172 .. 0.70
   4 ?   -3.2   0.0       3.4   3.4e+03     133     149 ..     215     231 ..     187     241 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi 28
                                      ++ViGgG AG+ AA +a r+     + 
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKARRMDKTARIT 29
                                      89*****************98665544 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                                       HTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
                              GIDA 106 enepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                                        ++ nleii++   e i      +  v + ++++  ++ viatG+
  gi|518651667|ref|YP_008141187.1|  67 TEHRNLEIITGVKVEFIN---PGEKYVFAGNKKFPYDKLVIATGA 108
                                       568899998886555533...35556778889999999*****98 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.36
                                       TSTT-TT--EEE--EE CS
                              GIDA 320 sipGLenaeivrpGya 335
                                       +i+GL+n++i+  G++
  gi|518651667|ref|YP_008141187.1| 135 KIKGLDNVTIIGAGVL 150
                                       5666666666655554 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 3.4
                                       ETTS-EEEECEEEE--T CS
                              GIDA 133 tedgetikakavviatG 149
                                       t+ +  +++++v+ atG
  gi|518651667|ref|YP_008141187.1| 215 TTGNGSFNTQIVIFATG 231
                                       45556678888888888 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0033       3.3       1      36 [.       4      36 ..       4      67 .. 0.87
   2 ?    0.9   0.0      0.41   4.1e+02     127     155 ..      80     108 ..      46     109 .. 0.77
   3 ?    0.1   0.0      0.71   7.1e+02       2      18 ..     144     160 ..     143     176 .. 0.74
   4 ?   -0.2   0.0      0.91   9.1e+02     126     154 ..     204     231 ..     182     233 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0033
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsep 36
                                      +++G+G++G++++ +  +    ++  +it+++++++
  gi|518651667|ref|YP_008141187.1|  4 VVIGGGAAGMSAASKARRM---DKTARITVIEQTGY 36
                                      69***********997776...799*******9765 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.41
                     NAD_binding_9 127 leeradgqavlladgaslaadaVvLAlGh 155
                                       +e  + g + + a+++++ +d++v+A+G 
  gi|518651667|ref|YP_008141187.1|  80 VEFINPGEKYVFAGNKKFPYDKLVIATGA 108
                                       4445555666789999***********95 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.71
                     NAD_binding_9   2 ivGaGprGlavlerLla 18 
                                       i+GaG+ G+ ++  L +
  gi|518651667|ref|YP_008141187.1| 144 IIGAGVLGTELFSLLSH 160
                                       9*******998765544 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.91
                     NAD_binding_9 126 dleeradgqavlladgaslaadaVvLAlG 154
                                       +++ ++++++v ++++ s+  + V+ A+G
  gi|518651667|ref|YP_008141187.1| 204 AISGTPGNYQV-TTGNGSFNTQIVIFATG 231
                                       46667777777.778889999******99 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.19       2      33 ..       3      34 ..       2      54 .. 0.89
   2 ?   -2.6   0.0       2.2   2.2e+03      23      42 ..      76      95 ..      69      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieas 33
                                      +vviG+G+Ag+s A +  +  +  ++++ie  
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKARRMDKTARITVIEQT 34
                                      8****************999999999999865 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                     Lycopene_cycl 23 pglkvvlieaspsllfpnny 42
                                      +g+kv  i+++++ +f++n+
  gi|518651667|ref|YP_008141187.1| 76 TGVKVEFINPGEKYVFAGNK 95
                                      7899*************996 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       2.7   2.7e+03       2      18 ..       3      19 ..       2      33 .. 0.77
   2 ?   10.2   0.0   0.00051       0.5       1      51 [.     141     190 ..     141     210 .. 0.81
   3 ?   -3.5   0.0       8.1   8.1e+03      11      38 ..     314     338 ..     311     357 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.7
                                      EEEE--SCCHHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavf 18
                                      + viG G  G + a+ +
  gi|518651667|ref|YP_008141187.1|  3 IVVIGGGAAGMSAASKA 19
                                      789****9999988765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00051
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                       +v++iGaG++G+++ ++ +s++++V+l+  +e  l +    + + l + v+
  gi|518651667|ref|YP_008141187.1| 141 NVTIIGAGVLGTELFSL-LSHKFKVKLISKHEYVLPHMDTDMGNVLTSIVN 190
                                       69***********9765.6789******99999888887777777666655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 8.1
                                       HHHHHHHHHHTT-EEEEE-S-HHHHHHH CS
                           3HCDH_N  11 GagiaavfasagleVvlvdiseealeka 38 
                                       G+ i +vf   g++V  + i+e++++k 
  gi|518651667|ref|YP_008141187.1| 314 GTTIINVF---GYQVGYTGINEATAKKT 338
                                       55555544...88888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3113.06
//
Query:       gi|518651668|ref|YP_008141188.1|  [L=251]
Description: dolichol-phosphate mannosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   93.9   0.2    1.3e-26   93.4   0.2    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    0.00015   21.8   0.0    0.00022   21.2   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00054   20.4   0.2     0.0021   18.5   0.2    1.9  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   0.2   2.1e-30   1.3e-26       1     167 [.       6     162 ..       6     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 2.1e-30
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svvip+ Ne+++l +++ +l++        i+++DD StD+t+++++++    p+v+++ r  + G+++a   g+r 
  gi|518651668|ref|YP_008141188.1|   6 SVVIPALNEKENLNRLIPALADD---NISSIYIIDDQSTDGTADLVKKY----PDVHFLFRGGRLGLISAEIDGMRL 75 
                                       8*****************99998...999********************....9*********************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       + ++y++++DaD+ + p++++ l++ + ++  d+v+g+r+  +g t+    +k     +r+ +   + s ++nl ++
  gi|518651668|ref|YP_008141188.1|  76 SGTEYVVVMDADLSHRPEDVPGLIDQAIRTSSDLVIGSRYTDKGITNDEFIRKI---ISRIANMLFRISFDINLNDC 149
                                       ********************************************9999999986...8******************* PP

                                       STCCCEEEEHHHH CS
                   Glycos_transf_2 155 igsaallrreale 167
                                       ++++++++r+a +
  gi|518651668|ref|YP_008141188.1| 150 TSGFRVYSRKACD 162
                                       **********986 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   3.8e-08   0.00022       5     102 ..       6      92 ..       3     119 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3.8e-08
                   Glyco_tranf_2_3   5 avlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksralne 81 
                                       +v++p++ne + l +++ +l+ +    + +++++d+s+++t++ ++    ++pdv  + +++  +lg    + a  +
  gi|518651668|ref|YP_008141188.1|   6 SVVIPALNEKENLNRLIPALADD--NISSIYIIDDQSTDGTADLVK----KYPDV--HFLFRGGRLG---LISAEID 71 
                                       8******************9995..34789*************776....6***6..8887755555...5555679 PP

                   Glyco_tranf_2_3  82 alravksdlvllvDdDtvveP 102
                                       ++r   +++v+++D+D    P
  gi|518651668|ref|YP_008141188.1|  72 GMRLSGTEYVVVMDADLSHRP 92 
                                       999999**********76666 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.2   3.6e-07    0.0021      13      45 ..      24      56 ..      13      87 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3.6e-07
                   Glyco_tranf_2_4 13 hhlalgfdrilvydndstDgtrailkelpevkl 45
                                      ++ +  ++ i+++d++stDgt++++k++p+v +
  gi|518651668|ref|YP_008141188.1| 24 ALADDNISSIYIIDDQSTDGTADLVKKYPDVHF 56
                                      555555789********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       921  (0.0513693); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1715.59
//
Query:       gi|518651669|ref|YP_008141189.1|  [L=342]
Description: hypothetical protein FACI_IFERC00001G0308 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-54  185.1   1.1    1.4e-54  184.8   1.1    1.1  1  Regulator_TrmB   Archaeal transcriptional regulator TrmB
    3.5e-22   78.1   0.1    8.7e-22   76.8   0.0    1.8  2  TrmB             Sugar-specific transcriptional regulator Trm
     0.0084   16.2   0.3      0.019   15.0   0.3    1.6  1  Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat
  ------ inclusion threshold ------
      0.038   13.8   0.0       0.18   11.7   0.0    2.0  2  HTH_5            Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   1.1     3e-58   1.4e-54       2     232 ..     112     336 ..     111     337 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 3e-58
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-GGGHHHHHHHHHHHHHTT-EEEEEESS----GGGSSSSEEEEEE-S- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslpselLeelreeliaaaergvtVllliypdedleeldleevatevrvrr 78 
                                       +w+ ++++ + e+++ ++ +Ae+e+i+sl   lL++l++++ +aa+rg++V+l+i+pd+d+ + + + + ++++ r 
  gi|518651669|ref|YP_008141189.1| 112 LWYLDNTNLIREQMKNMVINAETEIILSLRLPLLKYLDRYILDAADRGISVILTIFPDSDRYDISELVNRVVIKRRP 188
                                       89*************************************************************************** PP

                                       --S.EEEEETTTEEEEE-SSS-EEEE--HHHHHHHHHHHHHH........HHH-EEEEEEES-TT-EEES-HHHHHH CS
                    Regulator_TrmB  79 sgapllvivDrkrgvvaprevlrdkeeeyaiifkekelihvlshyFlttlWktseviktdepvekpitfssirlave 155
                                       +++p+++i Dr++++v +++   + + +ya+ f+e+e+ih++++y+++++Wk+s +i  +++ ++ ++f ++++++e
  gi|518651669|ref|YP_008141189.1| 189 GISPEIMIKDRDEAIVYVDN--VSARAKYALDFQEQEMIHIINYYYYNIVWKPSIYIS-KFQIRQKWEFKTSWISCE 262
                                       *******************9..8999********************************.****************** PP

                                       HHHHHT.TTS-EEEEEEEEETTT--EEEEEEEEEEEEEETTTT.EEEEEEEETTEEEEEE-TT--SSSEEEEEEEEE CS
                    Regulator_TrmB 156 dikkllraglkveaeveGrdtetgeevtieGrvveatlnstpg.vaslvvetedgevtVGGlgAvlEDieaeeitle 231
                                       +i+ ++++g+k++++v G +  +++e++i+G v +  ++ +pg ++s+++et+++++tVGG+ +++EDi+ e++ l+
  gi|518651669|ref|YP_008141189.1| 263 AINVFMNNGYKLTGRVIGET--QNGEIDISGNVKG--TDVIPGyKNSFLIETDERVFTVGGRLTRIEDIRLEKFQLT 335
                                       ********************..*************..*************************************997 PP

                                       E CS
                    Regulator_TrmB 232 r 232
                                       +
  gi|518651669|ref|YP_008141189.1| 336 A 336
                                       5 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   0.0   1.9e-25   8.7e-22       1      67 [.      10      76 ..      10      77 .. 0.98
   2 ?   -3.9   0.0         3   1.4e+04      27      37 ..      93     103 ..      89     110 .. 0.56

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1.9e-25
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE--H CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravdp 67
                                      L+k+GLs yE+kvY++Ll +gp t + i + +gvp+++vY+  ++L++kGl+e+++g++k+Yrav++
  gi|518651669|ref|YP_008141189.1| 10 LSKFGLSPYEIKVYKTLLLNGPQTSTSIVSTAGVPQPRVYDLFNNLLNKGLIEISPGKKKIYRAVPV 76
                                      89***************************************************************97 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                                       HHCCCTTSSCH CS
                              TrmB  27 eiaeelgvprs 37 
                                       e+ e ++v+++
  gi|518651669|ref|YP_008141189.1|  93 ELTEYVKVSEP 103
                                       55555555544 PP

>> Chlorovi_GP_rpt  Chlorovirus glycoprotein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   4.3e-06     0.019       5      30 ..     270     295 ..     266     296 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.3e-06
                   Chlorovi_GP_rpt   5 NGsfLtgvtatiPgtqniDIiGNVva 30 
                                       NG  Ltg +++ + ++ iDI GNV +
  gi|518651669|ref|YP_008141189.1| 270 NGYKLTGRVIGETQNGEIDISGNVKG 295
                                       9***********************76 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 ?   11.7   0.0     4e-05      0.18      10      46 ..      26      62 ..      25      62 .. 0.96
   2 ?   -1.5   0.0      0.51   2.3e+03      20      30 ..      93     103 ..      90     104 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4e-05
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      lL +g+++++ ++   g++q+ v   ++ L + GL+e
  gi|518651669|ref|YP_008141189.1| 26 LLLNGPQTSTSIVSTAGVPQPRVYDLFNNLLNKGLIE 62
                                      799********************************96 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.51
                                       HHHHHHTS-HH CS
                             HTH_5  20 elaeelglsqs 30 
                                       el+e++++s++
  gi|518651669|ref|YP_008141189.1|  93 ELTEYVKVSEP 103
                                       89*******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2283.12
//
Query:       gi|518651670|ref|YP_008141190.1|  [L=195]
Description: hypothetical protein FACI_IFERC00001G0309 [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  113.1   0.0    1.1e-32  112.6   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    7.7e-13   48.4   0.0    9.8e-13   48.1   0.0    1.1  1  Redoxin     Redoxin
  ------ inclusion threshold ------
       0.22   11.4   0.5       0.64    9.9   0.4    1.8  2  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin


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 !  112.6   0.0   1.8e-36   1.1e-32       1     123 [.       4     135 ..       4     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 1.8e-36
                                       TTSB----EEE.....STTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHH CS
                          AhpC-TSA   1 vgdkapdfelk.....nadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspes 72 
                                       +g++ap+f  +     +++ ++++lsdy+gk+v+l fyp+d+++vC t ++al   y++f ++g++v+g+s ds++s
  gi|518651670|ref|YP_008141190.1|   4 IGEAAPEFDTEtyfpeKKEIKKIKLSDYRGKWVILTFYPGDFTFVCATDIEALMGSYDKFLKEGAQVFGISEDSVFS 80 
                                       799********999988899********************************************************* PP

                                       HHHHHHH-H.....SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  73 hkkfiekes....lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       hk+++++       ++pl+ D ++++ak+yg l+++   a+r+ ++id+egki+y
  gi|518651670|ref|YP_008141190.1|  81 HKAWCDTSPrvskSKIPLIDDYTKEIAKNYGFLDSKGYQAQRGLVIIDPEGKIQY 135
                                       *******999999***********************999***************9 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   1.6e-16   9.8e-13       3     130 ..       5     136 ..       3     147 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.6e-16
                                       TSBB---E....CCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH CS
                           Redoxin   3 gdkaPdft....lplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf 75 
                                       g++aP+f     +p+ +++ ++++ls+++gk v+++f+pg f+ +C + + +l   ++++ ++g +v++++ d+  f
  gi|518651670|ref|YP_008141190.1|   5 GEAAPEFDtetyFPE-KKEIKKIKLSDYRGKWVILTFYPGDFTFVCATDIEALMGSYDKFLKEGAQVFGISEDS-VF 79 
                                       778888887888666.7999*******************************88888888899*****8876555.55 PP

                                       HHHHHHH.....TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEE CS
                           Redoxin  76 vkefwgk.....eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvyl 130
                                         ++w +      + k+p++ D +++++k++G  +   ++ + + + +++id +gk+ y 
  gi|518651670|ref|YP_008141190.1|  80 SHKAWCDtsprvSKSKIPLIDDYTKEIAKNYG--FLDSKGYQ-AQRGLVIIDPEGKIQYE 136
                                       55555555****777*****************..77666666.9999**********985 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 ?   -2.0   0.0      0.58   3.5e+03      21      36 ..     158     169 ..     156     172 .. 0.76
   2 ?    9.9   0.4   0.00011      0.64      11      20 ..     172     181 ..     165     183 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.58
                                       -EEE---SSHHHHHHH CS
                        1-cysPrx_C  21 kvivpPpateedavkr 36 
                                       kv+   + t+e ++ +
  gi|518651670|ref|YP_008141190.1| 158 KVL---HDTPE-GEGH 169
                                       899...99999.7665 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00011
                                       BB-TTT.TBT CS
                        1-cysPrx_C  11 atPAnWkpGd 20 
                                       a+PA+W+pG+
  gi|518651670|ref|YP_008141190.1| 172 AIPADWTPGE 181
                                       89*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1293.47
//
Query:       gi|518651671|ref|YP_008141191.1|  [L=207]
Description: iron-dependent repressor [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-17   63.3   0.0    3.4e-17   62.3   0.0    1.5  1  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    5.5e-10   39.3   0.0    1.6e-09   37.8   0.0    1.8  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    7.4e-05   22.6   0.1    0.00024   20.9   0.0    1.8  2  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00083   19.3   0.1     0.0018   18.2   0.1    1.5  1  HTH_45          Winged helix-turn-helix
     0.0033   17.2   0.2     0.0068   16.3   0.0    1.6  2  HTH_5           Bacterial regulatory protein, arsR family
     0.0043   16.9   0.1     0.0098   15.8   0.0    1.6  2  MarR            MarR family
     0.0093   15.9   0.0      0.022   14.8   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
  ------ inclusion threshold ------
      0.045   13.5   0.0      0.087   12.6   0.0    1.5  1  HTH_10          HTH DNA binding domain
       0.05   13.3   0.0       0.09   12.4   0.0    1.4  1  GntR            Bacterial regulatory proteins, gntR family
      0.062   13.6   0.0       0.11   12.8   0.0    1.4  1  FeoA            FeoA domain
      0.085   12.8   0.0       0.16   12.0   0.0    1.4  1  HTH_1           Bacterial regulatory helix-turn-helix protein
       0.12   12.0   0.0       0.22   11.2   0.0    1.4  1  DUF4423         Domain of unknown function (DUF4423)
       0.14   12.0   0.0       0.31   10.9   0.0    1.5  1  LacI            Bacterial regulatory proteins, lacI family


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 !   62.3   0.0   2.5e-20   3.4e-17       1      68 [.      63     130 ..      63     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 2.5e-20
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B- CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdpi 68 
                                       T++G  +A  ++r+hr+ e+f v++l+v+we  h  ++ +Eh + ++ ++ + + lg+p +cPhg+ i
  gi|518651671|ref|YP_008141191.1|  63 TKQGYSMAIPVIRKHRVSEVFAVKMLEVPWEYSHSAVMDIEHTIEDKYFDTFSKNLGNPLTCPHGNMI 130
                                       99***************************************************************988 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   1.2e-12   1.6e-09       4      52 ..       5      53 ..       2      59 .. 0.92
   2 ?   -2.8   0.0       5.4   7.4e+03      22      35 ..      73      86 ..      72      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.2e-12
                                      HHHHHHHHHHHHHHHHHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                    Fe_dep_repress  4 estEdYLetIYtlseekkvvktkdlaerLnvspssVsemlkkLekdGyv 52
                                      ++ EdY++tI++l e  + +   ++++ L+vs ++Vse l+kLe ++++
  gi|518651671|ref|YP_008141191.1|  5 NNEEDYIKTIFSLCEAFGSANENMVSKDLGVSMATVSEYLSKLEGKELI 53
                                      678*****************************************99987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.4
                                      SB-HHHHHHHHTS- CS
                    Fe_dep_repress 22 vvktkdlaerLnvs 35
                                      v+++ +++e+ +v+
  gi|518651671|ref|YP_008141191.1| 73 VIRKHRVSEVFAVK 86
                                      67889999999987 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.7e-07   0.00024      20      58 ..      21      59 ..       3      72 .. 0.87
   2 ?   -1.9   0.0       2.3   3.2e+03      41      51 ..     160     170 ..     159     171 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.7e-07
                                      HCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 20 lgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       g+a+ + ++++lgv+ ++v e+L++Le k l++r+ + 
  gi|518651671|ref|YP_008141191.1| 21 FGSANENMVSKDLGVSMATVSEYLSKLEGKELITRNNRD 59
                                      5889999***************************98665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.3
                                       HHHHHHHHCTS CS
                              TrmB  41 evLrsLedkGl 51 
                                       ++L++L d G+
  gi|518651671|ref|YP_008141191.1| 160 DILKKLADLGM 170
                                       689****9997 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   1.3e-06    0.0018      11      64 ..      14      68 ..       8      78 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 1.3e-06
                            HTH_45 11 ILeais.egeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGle 64
                                      I + ++  g+a+   + ++   s  ++++YL++L  k+li+ ++   +lT++G  
  gi|518651671|ref|YP_008141191.1| 14 IFSLCEaFGSANENMVSKDLGVSMATVSEYLSKLEGKELITRNNRDIYLTKQGYS 68
                                      555565447788888889999*******************************975 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.9e-06    0.0068      21      46 ..      29      54 ..      12      55 .. 0.83
   2 ?   -3.3   0.1       6.3   8.6e+03      36      43 ..     162     169 ..     161     170 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.9e-06
                                      HHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 21 laeelglsqstvShHLkkLreaGLVe 46
                                       +++lg+s +tvS++L+kL+   L++
  gi|518651671|ref|YP_008141191.1| 29 VSKDLGVSMATVSEYLSKLEGKELIT 54
                                      5899****************999986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.3
                                       HHHHHHTT CS
                             HTH_5  36 LkkLreaG 43 
                                       LkkL ++G
  gi|518651671|ref|YP_008141191.1| 162 LKKLADLG 169
                                       67777666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   7.1e-06    0.0098      23      50 ..      29      56 ..      14      59 .. 0.82
   2 ?   -2.7   0.0       4.2   5.8e+03      35      45 ..     159     169 ..     159     170 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.1e-06
                                      HHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 23 LakklgvskstvtrvldrLekkGlieRs 50
                                        k lgvs +tv++ l +Le k+li+R 
  gi|518651671|ref|YP_008141191.1| 29 VSKDLGVSMATVSEYLSKLEGKELITRN 56
                                      56789*********************95 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                                       HHHHHHHHHTT CS
                              MarR  35 trvldrLekkG 45 
                                       t +l++L + G
  gi|518651671|ref|YP_008141191.1| 159 TDILKKLADLG 169
                                       67889998766 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.6e-05     0.022      31      59 ..      33      62 ..      26      66 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.6e-05
                                      TTSSHHHHHHHHHHHHHTTSEEETEE.EEE CS
                         HTH_Crp_2 31 lGltretvsrilseLkreglisrgrr.iri 59
                                      lG++  tvs  ls+L+ + li+r++r i +
  gi|518651671|ref|YP_008141191.1| 33 LGVSMATVSEYLSKLEGKELITRNNRdIYL 62
                                      8*********************87555876 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   6.3e-05     0.087      28      50 ..      28      50 ..      23      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                            HTH_10 28 eLAkelGIskstlsehLrkaesk 50
                                       ++k+lG+s +t+se+L+k e k
  gi|518651671|ref|YP_008141191.1| 28 MVSKDLGVSMATVSEYLSKLEGK 50
                                      589****************9987 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   6.5e-05      0.09      27      59 ..      26      58 ..      25      59 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.5e-05
                                      HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 27 ereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      e+ +++ +gVs  tv e L++Le + l++r+++
  gi|518651671|ref|YP_008141191.1| 26 ENMVSKDLGVSMATVSEYLSKLEGKELITRNNR 58
                                      5667889***********************987 PP

>> FeoA  FeoA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-05      0.11      14      42 ..     151     179 ..     135     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                                       EEEE-TT.SSHHHHHHHHT--TT-EEEEE CS
                              FeoA  14 iarisdedpellrrLremGlvpGarievv 42 
                                         ri  e++++l++L+++G++pG+ +e+ 
  gi|518651671|ref|YP_008141191.1| 151 LNRIVYENTDILKKLADLGMYPGTPVEIF 179
                                       456666899*****************985 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.16      21      59 ..      31      66 ..      27      67 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                      HHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                             HTH_1 21 eeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                      + Lg+s ++vs  +++LE   g +L++R++r + LT +G
  gi|518651671|ref|YP_008141191.1| 31 KDLGVSMATVSEYLSKLE---GKELITRNNRDIYLTKQG 66
                                      78****************...99*****9999****998 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00016      0.22      19      77 ..       7      62 ..       2      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00016
                           DUF4423 19 ssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkdedgkyr 77
                                      ++ y+ +i++l ++    a+ + ++k l+  +s + v++ l+ L+  +l+++++ + y 
  gi|518651671|ref|YP_008141191.1|  7 EEDYIKTIFSLCEAFGS-ANENMVSKDLG--VSMATVSEYLSKLEGKELITRNNRDIYL 62
                                      7889999******9999.***********..**********************986554 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00022      0.31      10      22 ..      34      46 ..      29      54 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00022
                                      TS-HHHHHHHCTT CS
                              LacI 10 GVSkaTVSrvLnn 22
                                      GVS+aTVS +L++
  gi|518651671|ref|YP_008141191.1| 34 GVSMATVSEYLSK 46
                                      9*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1303.55
//
Query:       gi|518651672|ref|YP_008141192.1|  [L=260]
Description: hypothetical protein FACI_IFERC00001G0311 [Ferroplasma acidarmanus fer1]
Scores for 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  45.3     0.0026   18.0  12.7    3.5  3  ATG16            Autophagy protein 16 (ATG16)
    1.5e-05   24.5  50.1      0.019   14.3  23.5    3.1  3  GAS              Growth-arrest specific micro-tubule binding
    0.00029   20.5  40.0       0.35   10.4  17.7    3.2  3  Filament         Intermediate filament protein
    0.00039   20.4  49.2      0.075   13.1   8.3    3.3  3  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 
    0.00049   18.4  45.9     0.0089   14.2  22.5    2.1  2  HOOK             HOOK protein
    0.00054   19.7  30.0      0.013   15.2  16.4    3.2  2  DUF745           Protein of unknown function (DUF745)
     0.0011   18.4  37.8      0.044   13.1  16.4    3.0  3  DUF3450          Protein of unknown function (DUF3450)
     0.0015   17.3  31.6     0.0021   16.8  31.6    1.3  1  AAA_13           AAA domain
     0.0018   18.1  48.7      0.015   15.2  36.5    2.4  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
     0.0021   17.1  16.4     0.0021   17.1  16.4    2.4  2  IFT57            Intra-flagellar transport protein 57
     0.0022   18.1   3.3     0.0022   18.1   3.3    3.9  2  COG2             COG (conserved oligomeric Golgi) complex com
     0.0024   17.7  28.8      0.092   12.6   1.8    4.0  4  Spc29            Spindle Pole Component 29
     0.0029   17.2   0.2     0.0029   17.2   0.2    3.9  3  Nup54_57_C       NUP57/Nup54 C-terminal domain
     0.0031   16.4  46.7      0.094   11.6  24.1    2.8  2  Spc7             Spc7 kinetochore protein
      0.004   17.6  14.6     0.0043   17.5   5.7    2.2  2  HrpB7            Bacterial type III secretion protein (HrpB7)
      0.004   17.2   9.1      0.004   17.2   9.1    4.1  3  Med9             RNA polymerase II transcription mediator com
     0.0049   17.4   1.9     0.0049   17.4   1.9    5.3  5  SlyX             SlyX
  ------ inclusion threshold ------
      0.012   13.2  37.5      0.016   12.8  37.5    1.2  1  DUF3584          Protein of unknown function (DUF3584)
      0.013   15.3   4.6      0.013   15.3   4.6    3.1  3  MCPsignal        Methyl-accepting chemotaxis protein (MCP) si
      0.016   15.6  11.9      0.016   15.6  11.9    5.2  3  ZapB             Cell division protein ZapB
      0.016   15.4   1.5      0.016   15.4   1.5    6.1  5  HALZ             Homeobox associated leucine zipper
      0.017   15.7  40.4       0.32   11.6  10.8    4.0  3  YabA             Initiation control protein YabA
      0.018   15.1  27.9        0.5   10.4   7.3    3.4  4  DUF1664          Protein of unknown function (DUF1664)
      0.028   14.6  31.1       0.31   11.2   0.9    3.3  3  CREPT            Cell-cycle alteration and expression-elevate
      0.028   14.8  50.2      0.094   13.1  10.2    4.0  3  DUF4200          Domain of unknown function (DUF4200)
      0.029   14.0  39.1       0.15   11.6  14.5    2.2  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
       0.03   12.5  42.7     0.0057   14.9  38.2    1.8  1  EzrA             Septation ring formation regulator, EzrA
      0.041   13.8  23.4      0.069   13.0   0.1    4.2  2  CK2S             Casein Kinase 2 substrate
      0.045   14.1  37.6      0.094   13.1   3.7    6.0  5  FlaC_arch        Flagella accessory protein C (FlaC)
      0.052   13.6  34.6       0.35   10.9  10.9    3.7  4  Laminin_II       Laminin Domain II
      0.062   13.6  21.8        1.2    9.4   1.3    4.6  3  DUF948           Bacterial protein of unknown function (DUF94
      0.063   13.8  53.3       0.52   10.9  15.6    3.5  3  APG6_N           Apg6 coiled-coil region
      0.066   13.0  32.4       0.25   11.2  11.9    3.0  2  Bacillus_HBL     Bacillus haemolytic enterotoxin (HBL)
      0.073   12.3  32.8        0.2   10.9  15.2    2.3  2  TMPIT            TMPIT-like protein
      0.075   12.8  47.6        6.9    6.4  30.8    3.7  2  DUF4201          Domain of unknown function (DUF4201)
      0.081   13.0  48.5       0.25   11.4  20.6    3.0  3  UPF0242          Uncharacterised protein family (UPF0242) N-t
       0.09   12.8  47.0        0.5   10.4  11.4    3.3  4  DHR10            Designed helical repeat protein 10 domain
      0.097   11.3  34.7       0.17   10.5   9.9    2.2  1  GOLGA2L5         Putative golgin subfamily A member 2-like pr
       0.11   12.3  46.4      0.099   12.4  19.0    3.7  3  Phage_GP20       Phage minor structural protein GP20
       0.12   12.5  47.1       0.21   11.6  10.6    4.0  4  ADIP             Afadin- and alpha -actinin-Binding
       0.14   11.8  43.4       0.32   10.7  30.1    2.3  2  Laminin_I        Laminin Domain I
       0.16   11.7  44.7       0.32   10.7   8.6    3.3  2  SHE3             SWI5-dependent HO expression protein 3
       0.18   12.3  40.1        3.9    7.9  28.3    2.9  2  Fez1             Fez1
       0.18   11.6  39.3       0.11   12.2  12.6    2.9  3  DUF724           Protein of unknown function (DUF724)
        0.2   11.9  41.9       0.78   10.0   8.1    4.2  5  TMF_TATA_bd      TATA element modulatory factor 1 TATA bindin
       0.21   11.0  39.8      0.051   13.0  19.2    3.0  2  DUF4618          Domain of unknown function (DUF4618)
       0.21   11.8  43.8        8.5    6.6  29.9    3.2  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.22   11.6  47.8       0.48   10.5  24.4    3.6  4  TPR_MLP1_2       TPR/MLP1/MLP2-like protein
       0.22   12.1  35.8       0.17   12.5   2.5    4.6  4  DUF5344          Family of unknown function (DUF5344)
       0.26   11.4  34.9        1.1    9.4  14.1    3.0  2  Fib_alpha        Fibrinogen alpha/beta chain family
       0.29   10.4  28.6       0.17   11.2   9.8    2.2  2  DUF4407          Domain of unknown function (DUF4407)
       0.32   11.6  31.9        2.8    8.5   0.4    4.4  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.36   10.5  31.9       0.13   12.0  16.2    2.9  3  Syntaxin         Syntaxin
       0.45   10.9   8.6       0.18   12.2   1.1    3.6  3  kleA_kleC        Uncharacterized KorC regulated protein A
       0.56   10.1   2.2         11    6.0   0.1    3.1  2  gpW              gpW
       0.59   10.4  42.2        1.9    8.8  11.9    3.5  3  Seryl_tRNA_N     Seryl-tRNA synthetase N-terminal domain
       0.61   10.1  37.3       0.11   12.5  27.4    2.8  2  Rootletin        Ciliary rootlet component, centrosome cohesi
       0.62    9.7  36.7        1.8    8.2  16.6    2.2  2  LXG              LXG domain of WXG superfamily
       0.82    9.8  33.3        1.5    8.9   6.5    4.5  4  TolA_bind_tri    TolA binding protein trimerisation
       0.88    7.9  46.2        3.2    6.0  46.0    1.8  1  MAD              Mitotic checkpoint protein
       0.96    9.7  40.5      0.057   13.7  11.4    3.4  3  DUF5082          Domain of unknown function (DUF5082)
        1.1    9.1  44.7      0.087   12.6   3.8    5.7  6  DivIC            Septum formation initiator
        1.1    8.3  40.7        1.1    8.3  21.6    2.3  2  Atg14            Vacuolar sorting 38 and autophagy-related su
        1.1    8.7  42.2       0.68    9.4  21.0    2.5  2  MscS_porin       Mechanosensitive ion channel porin domain
        1.2    9.3  38.7       0.76    9.9   8.1    4.6  3  DivIVA           DivIVA protein
        1.4    9.4  24.6       0.95   10.0   3.6    4.3  4  NPV_P10          Nucleopolyhedrovirus P10 protein
        1.6    8.1  42.4        2.7    7.3  15.6    3.0  2  Tropomyosin      Tropomyosin
        1.6    8.6  40.5        0.3   10.9  25.2    2.1  2  CEP63            Centrosomal protein of 63 kDa
        1.7    9.4  40.7       0.49   11.1   8.2    4.1  4  DUF4472          Domain of unknown function (DUF4472)
        1.9    7.9  48.6        2.6    7.4  24.6    2.3  2  HMMR_N           Hyaluronan mediated motility receptor N-term
        2.1    8.0  47.6        4.7    6.8  28.5    3.3  3  Lebercilin       Ciliary protein causing Leber congenital ama
        2.3    8.7   4.6         30    5.1   0.1    3.2  3  MtrB             Tetrahydromethanopterin S-methyltransferase 
        2.3    8.3  11.1        3.1    7.9   1.9    2.9  3  DUF1515          Protein of unknown function (DUF1515)
        2.6    8.2  28.1        2.3    8.3   7.9    2.7  2  Nup54            Nucleoporin complex subunit 54
        2.6    8.2  39.6         10    6.2  12.2    4.2  3  RasGAP_C         RasGAP C-terminus
        2.6    6.8  44.9        3.9    6.3   6.4    2.6  2  DUF812           Protein of unknown function (DUF812)
          3    7.0  45.0        4.9    6.3  21.7    2.3  2  HAP1_N           HAP1 N-terminal conserved region
        3.2    7.0  31.0        3.1    7.0   7.5    2.6  2  DUF4763          Domain of unknown function (DUF4763)
        4.9    6.7  32.2          1    8.9   5.1    4.1  3  Fzo_mitofusin    fzo-like conserved region
        5.3    7.6  37.8        9.1    6.8  12.2    3.3  3  Spectrin         Spectrin repeat
        5.6    7.3  41.5         10    6.5  16.3    4.9  5  BLOC1_2          Biogenesis of lysosome-related organelles co
        5.8    7.3  36.2        1.3    9.3   7.1    3.9  3  KxDL             Uncharacterized conserved protein
        5.8    6.5  42.1        3.9    7.0   6.2    3.2  3  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
        6.3    6.3  40.8        9.8    5.7   5.0    3.7  4  DUF4795          Domain of unknown function (DUF4795)
        7.7    6.1  38.2        2.3    7.8   1.6    3.3  3  CENP-F_N         Cenp-F N-terminal domain
          8    5.8  35.0      0.036   13.5   8.6    3.5  2  Flagellar_rod    Paraflagellar rod protein
        8.4    6.8  33.2         25    5.3   0.3    4.5  1  GAT              GAT domain
        8.5    5.5  31.7       0.35   10.1   5.9    2.5  2  MPS2             Monopolar spindle protein 2
        8.7    6.3  31.4       0.58   10.1   2.9    4.3  4  DUF4446          Protein of unknown function (DUF4446)
        8.8    6.7  41.7        3.5    8.0  13.3    3.4  3  OmpH             Outer membrane protein (OmpH-like)
        9.7    5.7  32.3      0.076   12.5   3.7    3.9  1  DegS             Sensor protein DegS
        9.8    6.1  36.6       0.22   11.5   9.0    4.2  3  MIP-T3_C         Microtubule-binding protein MIP-T3 C-termina


Domain annotation for each model (and alignments):
>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7  23.3    0.0011      0.22      80     184 ..       5     109 ..       1     115 [. 0.92
   2 !   18.0  12.7   1.3e-05    0.0026      90     177 ..     124     211 ..     110     219 .. 0.87
   3 ?    0.2   0.0       3.7   7.3e+02      11      46 ..     220     254 ..     212     260 .] 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0011
                             ATG16  80 eqklaqlreelaelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       +++l   +e+l++++   +  +   +el++ + +l++k+ +  +r ++l++++++l+  l d +e+l+  +k ++d+
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDI 81 
                                       5678888999999999999999999999999999999**************************************** PP

                             ATG16 157 qDElsaLqlqlnqaEeklrklekENkeL 184
                                       q El+  + +l++  ek ++le+E ++L
  gi|518651672|ref|YP_008141192.1|  82 QHELEDKNTRLESTVEKIETLEEELEKL 109
                                       *******************999996655 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 1.3e-05
                             ATG16  90 laelyksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlq 166
                                        a ++k  +el+q++ +l++ +++le+k ++ +++++el+++ ++ + ++k++++e+++k+ l+++l      L+  
  gi|518651672|ref|YP_008141192.1| 124 TASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHD 200
                                       47799************************************************************987777777777 PP

                             ATG16 167 lnqaEeklrkl 177
                                       l+  E k + l
  gi|518651672|ref|YP_008141192.1| 201 LKTYEIKEKSL 211
                                       77777666655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 3.7
                             ATG16  11 arqekafaeliqaynrLldrtsaleaenaklekaaa 46 
                                       a  ++ f+ l + y+ Ll++  + ++++ + +k  +
  gi|518651672|ref|YP_008141192.1| 220 AA-NDNFKGLLEKYRFLLENNITVKKRSMSTKKPVK 254
                                       43.566888899999999998888888888755433 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 !    9.8  14.7    0.0024      0.47      31     116 ..       4      86 ..       2      87 .. 0.82
   2 !   14.3  23.5   9.7e-05     0.019      29     140 ..      72     184 ..      69     186 .. 0.91
   3 !   13.5   9.8   0.00017     0.034      33     119 ..     157     243 ..     154     251 .. 0.92

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0024
                               GAS  31 lKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwe 107
                                        K+++e+ +++ + +  +l+++++en++l+  +++++++++   + lk+ +  k++ ++lk+ l ++++ l++ k +
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIA---AGLKREDDLKNQNESLKSSLLDTNEALESFKKQ 77 
                                       59999999999999999999999999999999998877665...677777788888888888888888888888888 PP

                               GAS 108 hevleqrfe 116
                                       +e  ++++e
  gi|518651672|ref|YP_008141192.1|  78 NEDIQHELE 86 
                                       888887765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 9.7e-05
                               GAS  29 kslKeeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqsl.knlkarlkelekelkdl 104
                                       +s K++ e+++ + e ++ +l+ + ++ + l+e+L+k++ e+ + +++++n     q++  +lk+++ +l+k++++l
  gi|518651672|ref|YP_008141192.1|  72 ESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKIsSELKQKIDRLQKYISEL 148
                                       689***********************************************998877765268*************** PP

                               GAS 105 kwehevleqrfekvekerdelykkfeaaiqevqqkt 140
                                       + ++ + ++ ++++++   e +++ ++  +e++ k 
  gi|518651672|ref|YP_008141192.1| 149 ESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKN 184
                                       **************9999999999999999888875 PP

  == domain 3  score: 13.5 bits;  conditional E-value: 0.00017
                               GAS  33 eeieelkkkeernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlkwehe 109
                                       + i+el    ++++ +++ +++e k+ +  +++++  + eL+++lk+ye + +sl+++ + l+ +++++k l ++++
  gi|518651672|ref|YP_008141192.1| 157 KAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYR 233
                                       56899999999**************************************************************9999 PP

                               GAS 110 vleqrfekve 119
                                        l +   +v+
  gi|518651672|ref|YP_008141192.1| 234 FLLENNITVK 243
                                       9988776666 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   5.6    0.0019      0.37     213     268 ..       3      58 ..       1      63 [. 0.86
   2 !   10.4  17.7    0.0018      0.35     173     274 ..      52     155 ..      50     161 .. 0.89
   3 !    9.2   6.4    0.0041      0.79     194     266 ..     156     231 ..     150     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0019
                                       X-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 213 sakeeitelrrqiqsleieleslkkqkasleaqlaeleerleaeleklqeklsele 268
                                       +ak+++++ + q+q+++++le+++++++ l ++++el+++++a l++  +  +++e
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNE 58 
                                       7899************************************9999887766655555 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 173 eiraqyeelaek..nreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkasleaqla 247
                                       ++++q e+l ++   ++ea e +k++ e++q++ e ++  l+s+ e i+ l  ++++l+ie  ++++  +++ a+ +
  gi|518651672|ref|YP_008141192.1|  52 DLKNQNESLKSSllDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQ 128
                                       7888888887752256788899******************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 248 eleerleaeleklqeklseleeelaei 274
                                        +  +l++++++lq+ +sele++ ++ 
  gi|518651672|ref|YP_008141192.1| 129 KISSELKQKIDRLQKYISELESKDSQS 155
                                       *********************976665 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.0041
                                       XXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Filament 194 kskleelqeaaeknsealrsakeeitelrrqiqsl...eieleslkkqkasleaqlaeleerleaeleklqeklse 266
                                       ++ ++el+++ +++s++++s ++ei++ +  i++l   + el++  k+ +  e++l+e+ e l+a+ ++++  l++
  gi|518651672|ref|YP_008141192.1| 156 QKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELdlhNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEK 231
                                       556789999999*****************9999983334699************************9999998886 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 !   13.1   8.3   0.00038     0.075      49     111 ..       3      65 ..       1      70 [. 0.92
   2 !    8.9  28.1    0.0076       1.5      12     113 ..      53     162 ..      47     174 .. 0.49
   3 !    8.8  25.3    0.0081       1.6      24     123 ..      97     214 ..      96     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00038
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenlle 111
                                       ++k+++e ++e+++++ ++l+  +++ ++l+s  +eL++++    +r ++L++ n+sl++ l 
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLL 65 
                                       89********************************************************98664 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0076
                    CENP-F_leu_zip  12 LKe.serkadsLkdkvenLer...elemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsek.. 82 
                                       LK+ +e+ ++sL d  e+Le+   + e++++++e+  +  E+  +++etl+ee+e+l+ e  +++ d+++++     
  gi|518651672|ref|YP_008141192.1|  53 LKNqNESLKSSLLDTNEALESfkkQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSqk 129
                                       33213344455555544444322244555555555555555555555555555555555555555555555533300 PP

                    CENP-F_leu_zip  83 ..eeLekelqkkqervseLeslnsslenlleek 113
                                          eL++++   q+ +seLes  s+ ++ ++e+
  gi|518651672|ref|YP_008141192.1| 130 isSELKQKIDRLQKYISELESKDSQSQKAINEL 162
                                       112344444444666777777777777776665 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0081
                    CENP-F_leu_zip  24 dkvenLerelemseenqekvileaEtskaevet....lkeeieelaeelreleldLvalr..............sek 82 
                                       +k+e Le ele ++ ++ k+  ++E+  a  ++    lk++i++l++  +ele++ ++ +               + 
  gi|518651672|ref|YP_008141192.1|  97 EKIETLEEELEKLKIENGKIQEDMENTTASSQKisseLKQKIDRLQKYISELESKDSQSQkainelsstgreqsAQI 173
                                       69************999999999999877776655568888888888888888776666645555557777766667 PP

                    CENP-F_leu_zip  83 eeLekelqkkqervseLeslnsslenlleekEqekvqmkee 123
                                       ++L+ke+++k++ ++eL+  n +l++ l+  E +++ ++e 
  gi|518651672|ref|YP_008141192.1| 174 KSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRET 214
                                       77888888888888888888888888777777666665554 PP

>> HOOK  HOOK protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2  22.5   4.6e-05    0.0089     476     585 ..       4     110 ..       1     120 [. 0.85
   2 !    9.2  17.0    0.0015       0.3     499     603 ..     122     233 ..     109     251 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 4.6e-05
                              HOOK 476 eeekltelqelledanrrkneLetenrlanqrileLeaqveelqkalqeqgskaedssllkkkleehleklkevqee 552
                                        +++l++ qe+l+  + +++ ++ en+  + +i eL++++    k  +e++ k+++  +lk+ l    e l++ +++
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLK--REDDLKNQN-ESLKSSLLDTNEALESFKKQ 77 
                                       568899*********************************844444..344444443.67****************** PP

                              HOOK 553 lqkkkeqleelepklssnkqkieeleeaLkkkd 585
                                       ++  ++ le+ + +l+s+ +kie+lee L+k  
  gi|518651672|ref|YP_008141192.1|  78 NEDIQHELEDKNTRLESTVEKIETLEEELEKLK 110
                                       *****************************9854 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0015
                              HOOK 499 tenrlanqri.leLeaqveelqkalqeqgskaedssl....lkkkleehleklkevqeelqkkkeqleelepkl.ss 569
                                       +   ++ q+i +eL+++++ lqk  +e +sk  +s +    l ++  e+  ++k++q+e++ k+ ++eel+ +  + 
  gi|518651672|ref|YP_008141192.1| 122 N-TTASSQKIsSELKQKIDRLQKYISELESKDSQSQKaineLSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNyEL 197
                                       2.334456662478888888887766666665554440001444556788899999999999999999987654133 PP

                              HOOK 570 nk.qkieelee.aLkkkdedlkameerYkkyveKAk 603
                                       n   k+ e++e  L++  e l+a+++ +k  +eK +
  gi|518651672|ref|YP_008141192.1| 198 NHdLKTYEIKEkSLRETMELLNAANDNFKGLLEKYR 233
                                       445777777651577777777888888888888866 PP

>> DUF745  Protein of unknown function (DUF745)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2  16.4   6.6e-05     0.013      64     173 ..      15     124 ..       3     131 .. 0.76
   2 ?    5.5   7.3     0.065        13      59     154 ..     136     231 ..     121     248 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.6e-05
                            DUF745  64 veqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqelaektql 140
                                       ++ + ++l+  +a  qe ++ +++ +++++a  k  ++ ++q e+lk+ l  ++e+le+ ++ ++  q+el++k++ 
  gi|518651672|ref|YP_008141192.1|  15 LQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTR 91 
                                       233333333333344445555556666677777888999************************************** PP

                            DUF745 141 leaAkkRveeLkkqlkearkdlektkkaAykAa 173
                                       le+  +++e+L+++l++ + +  k+++  ++ +
  gi|518651672|ref|YP_008141192.1|  92 LESTVEKIETLEEELEKLKIENGKIQEDMENTT 124
                                       ******************999999888766655 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.065
                            DUF745  59 GKqqlveqleqelreaeavvqeekkslqsseanakaaakaakqaqqqlealkallkaakenlenaeqvaagaqqela 135
                                        K   ++++ +el+  +++ q+  ++l+s+ +  +a  k+ ++  +  ++l + l+  + +l++  ++ +  +++l+
  gi|518651672|ref|YP_008141192.1| 136 QKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLR 212
                                       23333444444444455555555555555555555555555555566666666666666666666777777777888 PP

                            DUF745 136 ektqlleaAkkRveeLkkq 154
                                       e  +ll+aA+  ++ L ++
  gi|518651672|ref|YP_008141192.1| 213 ETMELLNAANDNFKGLLEK 231
                                       8888888888888777665 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1  16.4   0.00023     0.044      14     112 ..       4     102 ..       1     113 [. 0.90
   2 ?    7.0   8.1     0.017       3.2      45     114 ..      77     146 ..      76     148 .. 0.92
   3 !    9.4  13.6    0.0031      0.61      19      94 ..     118     193 ..     112     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00023
                           DUF3450  14 laatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqiee 90 
                                       ++++l++ +++ +  +a+ +++q++ ++l+   +el +++ a  ++ ++l+ +ne l++++ + ++ ++s ++q e+
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNED 80 
                                       578999*********************************************************************** PP

                           DUF3450  91 ieeierelvpllekmidrLeqf 112
                                       i++  ++    le++++++e++
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRLESTVEKIETL 102
                                       *998888888888888888876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.017
                           DUF3450  45 ekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfve 114
                                       + ++++ e+++ +++les+  + e le+ +++++ e  +++e++e+ ++ +++++  l++ idrL++++ 
  gi|518651672|ref|YP_008141192.1|  77 QNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYIS 146
                                       778999999999999999999999999999**********************************999986 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0031
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieei 94 
                                       ++++++++++++++++  +kid+l++  +el+++  + ++ +++l+   ++++++++s+++ei++ +  iee++  
  gi|518651672|ref|YP_008141192.1| 118 EDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLH 193
                                       5678889999999999999999999999999999999999999999999999999999999999999888888755 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  31.6   1.1e-05    0.0021     281     464 ..       8     191 ..       2     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                            AAA_13 281 feekqerLekliekveskkselleklkavsdeasensafeed.keelkaeaealeeqLkglqralea.Krkepfksv 355
                                        e++qe+L+ + +++e  ++ + ++l++ ++e + ++a+  +  ++lk++ e l+++L   ++ale  K+++   + 
  gi|518651672|ref|YP_008141192.1|   8 LEDFQEQLQTMHANLEAVQA-ENQELTSHINELNNKIAAGLKrEDDLKNQNESLKSSLLDTNEALESfKKQNEDIQH 83 
                                       44555555555555555544.33444444443333333333324555555555555555555555441222222245 PP

                            AAA_13 356 elesvkakiesikklvaeineliakhNekvanleeekeeakkklelhlv....................eeleseld 412
                                       ele+ + ++es  +++++++e  +k                       +                    +el++++d
  gi|518651672|ref|YP_008141192.1|  84 ELEDKNTRLESTVEKIETLEEELEK---------------------LKIengkiqedmenttassqkisSELKQKID 139
                                       5555555555555555555555544.....................4444444444444444444444478999999 PP

                            AAA_13 413 eykkkykklekaieklekelkeeeaelkkleeeikeLekqlrdekpaaeein 464
                                       +++k +++le + ++ +k+++e ++  ++  ++ik L+k+++d++  +ee+ 
  gi|518651672|ref|YP_008141192.1| 140 RLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELD 191
                                       9999999999999999999999999999999999999999999999999873 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 !    8.4   8.1    0.0086       1.7      72     128 ..       4      60 ..       2      62 .. 0.78
   2 !   15.2  36.5   7.5e-05     0.015      11     181 ..      51     215 ..      47     221 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0086
                          KASH_CCD  72 lkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeL 128
                                       +k+ +++ +E+ + ++a+ + ++ enq L+++i++L++++   l  +d lk++ + L
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESL 60 
                                       677888888888888888888888888888888888888888888888888777665 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 7.5e-05
                          KASH_CCD  11 adLqlnNkkLaeenskLkkavetaeetnakLteeieeLkkklkstQqalqkaklleeEleelkalvkeleEkrarlk 87 
                                       +dL+  N +L+       +a+e+   +n+ +  e+e+  ++l st   ++k + leeEle lk    +++E  ++  
  gi|518651672|ref|YP_008141192.1|  51 DDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLEST---VEKIETLEEELEKLKIENGKIQEDMENTT 124
                                       589999999999999999999999999999999999988888885...899************************99 PP

                          KASH_CCD  88 aqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLk 164
                                       a ++++  e   L++ki+ Lq  +  l +  ++++k ++eL+++  e   q+++l++ + +k++l+ee   +  eL+
  gi|518651672|ref|YP_008141192.1| 125 ASSQKISSE---LKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELN 198
                                       999999776...99*************************************************************** PP

                          KASH_CCD 165 ltieEyssiieeLraek 181
                                         ++ y+   + Lr  +
  gi|518651672|ref|YP_008141192.1| 199 HDLKTYEIKEKSLRETM 215
                                       **999998888888665 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1  16.4   1.1e-05    0.0021     216     323 ..       5     108 ..       1     113 [. 0.87
   2 ?    0.7  17.7         1     2e+02     201     309 ..     110     220 ..     106     258 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.1e-05
                             IFT57 216 kadakdWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqleellqeyreaqeelsevkek 292
                                       k++ +d++++l++m+ + ++++++ +e++s++++l ++i+  l    +rE  l +q+e+l + + +++e l+++k++
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGL----KREDDLKNQNESLKSSLLDTNEALESFKKQ 77 
                                       5666788888888888888888888888888888888887777....79**************************** PP

                             IFT57 293 ykqlsegvseltrelaeiseelekvkqemee 323
                                        ++++ +++++++ l+++ e++e++++e+e+
  gi|518651672|ref|YP_008141192.1|  78 NEDIQHELEDKNTRLESTVEKIETLEEELEK 108
                                       ***************************9997 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 1
                             IFT57 201 klEleRvlpqLkvtikadak...dWrahleqmkkhkksieeslpetksqlkklhedisktlekiesrEkylnsqlee 274
                                       k+E  +++  +++t+++++k   + ++++++++k+ +++e++ +++++++++l++   ++  +i+s +k +  ++ +
  gi|518651672|ref|YP_008141192.1| 110 KIENGKIQEDMENTTASSQKissELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKN-S 185
                                       566666666666666666666667777777777777777777777777777777777777777777777774442.3 PP

                             IFT57 275 llqeyreaqeelsevkekykqlsegvseltrelae 309
                                       l++e+   + el++  + y+  ++++ e  + l+ 
  gi|518651672|ref|YP_008141192.1| 186 LIEELDLHNYELNHDLKTYEIKEKSLRETMELLNA 220
                                       44444444444444444444444444433333333 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 !   18.1   3.3   1.1e-05    0.0022      62     125 ..       6      70 ..       2      75 .. 0.88
   2 ?    4.6   7.9      0.17        32      63     117 ..      70     125 ..      62     151 .. 0.54

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-05
                              COG2  62 ghLvglqeeleevesplaaarkkvesvreklsereeeveskleeakeleekrellkl.llkldev 125
                                       ++L ++qe+l+++  +l+a++ + ++++++++e  +++ + l+   +l++++e+lk+ ll+++e 
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSsLLDTNEA 70 
                                       68**************************************************9988625555555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.17
                              COG2  63 hLvglqeeleevesplaaarkkvesvreklsereeeves.kleeakeleekrellk 117
                                       +L +++++ e ++++l+   +++es++ek++  eee+e+ k+e+ k  e++++   
  gi|518651672|ref|YP_008141192.1|  70 ALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKlKIENGKIQEDMENTTA 125
                                       45666666666666666666666666666666666666523333333333332222 PP

>> Spc29  Spindle Pole Component 29
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   1.8   0.00047     0.092     120     162 ..       2      48 ..       1      64 [. 0.82
   2 ?    5.3   3.1     0.078        15     122     165 ..      67     110 ..      54     117 .. 0.68
   3 ?    7.4   5.9     0.018       3.5     108     168 ..      88     152 ..      86     167 .. 0.69
   4 ?    8.0   3.8     0.012       2.3     117     173 ..     157     213 ..     153     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00047
                             Spc29 120 velekklddqkleIkeLkreleqqrtvnseLqekvaeleeev....k 162
                                       v+ +k+l+d ++++++++ +le  ++ n+eL+++++el++++    k
  gi|518651672|ref|YP_008141192.1|   2 VNAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIaaglK 48 
                                       5679************************************9965553 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.078
                             Spc29 122 lekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrla 165
                                       ++  l++ k + + ++ ele+++t  +   ek++ leee+++l+
  gi|518651672|ref|YP_008141192.1|  67 TNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLK 110
                                       55566666777777777777777777777777777777776664 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.018
                             Spc29 108 rldsiyssvkkivelek...klddqkleIk.eLkreleqqrtvnseLqekvaeleeevkrlaale 168
                                       ++ ++ s v+ki+ le    kl  ++ +I+  +++    ++ + seL++k+++l++ + +l++  
  gi|518651672|ref|YP_008141192.1|  88 KNTRLESTVEKIETLEEeleKLKIENGKIQeDMENTTASSQKISSELKQKIDRLQKYISELESKD 152
                                       456777788888888773333333344565258999999999****************9998753 PP

  == domain 4  score: 8.0 bits;  conditional E-value: 0.012
                             Spc29 117 kkivelekklddqkleIkeLkreleqqrtvnseLqekvaeleeevkrlaalehSnrk 173
                                       k i+el     +q  +Ik+L++e+++++ +++eL  +  el++ +k ++  e+S r+
  gi|518651672|ref|YP_008141192.1| 157 KAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRE 213
                                       55666666677899*******************************998888888655 PP

>> Nup54_57_C  NUP57/Nup54 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2   1.5e-05    0.0029       4      28 ..       4      28 ..       1      28 [. 0.93
   2 ?   -0.9   0.3       6.6   1.3e+03      18      28 ..      74      84 ..      71      85 .. 0.80
   3 ?    0.4   0.1       2.5   4.9e+02      13      22 ..     171     180 ..     170     182 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.5e-05
                        Nup54_57_C  4 aKKILeDYekQLqHLkKElEsikkD 28
                                      aKK LeD + QLq +   lE+++++
  gi|518651672|ref|YP_008141192.1|  4 AKKQLEDFQEQLQTMHANLEAVQAE 28
                                      9*********************986 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 6.6
                        Nup54_57_C 18 LkKElEsikkD 28
                                       kK+ E+i+ +
  gi|518651672|ref|YP_008141192.1| 74 FKKQNEDIQHE 84
                                      59999999987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 2.5
                        Nup54_57_C  13 kQLqHLkKEl 22 
                                        Q++ L+KE+
  gi|518651672|ref|YP_008141192.1| 171 AQIKSLQKEI 180
                                       69******96 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6  24.1   0.00048     0.094     157     254 ..       7     110 ..       1     122 [. 0.50
   2 ?    7.1  17.7     0.012       2.2     141     252 ..     117     224 ..     109     249 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00048
                              Spc7 157 lLekqeeeldel...lpeleeekaeleeeleklqe.aaeelesid..keeLeelreelaelkaeieekkkelaelqe 227
                                       +Le+ +e+l+++   l+++++e +el++ +++l++  a+ l+  d  k++ e+l+++l + ++ +e++kk+ ++ q 
  gi|518651672|ref|YP_008141192.1|   7 QLEDFQEQLQTMhanLEAVQAENQELTSHINELNNkIAAGLKREDdlKNQNESLKSSLLDTNEALESFKKQNEDIQH 83 
                                       33333333333211134444444455555555554222222222224555566666666666666666666666666 PP

                              Spc7 228 qleeleekieelkeqkseleeeiaeae 254
                                       +le++++++e++ e++++leee+++ +
  gi|518651672|ref|YP_008141192.1|  84 ELEDKNTRLESTVEKIETLEEELEKLK 110
                                       666666666666666666666666543 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.012
                              Spc7 141 kegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqeaaeelesidkeeLeelreelaelkaeiee 217
                                       +e +e++ ++ ++ +++L+++ + l+++  ele++ ++ ++ +++l +  +e    +++++++l++e+++ ++ iee
  gi|518651672|ref|YP_008141192.1| 117 QEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGRE----QSAQIKSLQKEIKDKNSLIEE 189
                                       3333333333333333333333333333333333333333333333332222....444555555555555555555 PP

                              Spc7 218 kkkelaelqeqleeleekieelkeqkseleeeiae 252
                                       +     el+ +l++ e k ++l+e ++ l+++  +
  gi|518651672|ref|YP_008141192.1| 190 LDLHNYELNHDLKTYEIKEKSLRETMELLNAANDN 224
                                       55555555555555555555555555444444444 PP

>> HrpB7  Bacterial type III secretion protein (HrpB7)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   1.5      0.12        24      84     118 ..      11      45 ..       2      64 .. 0.55
   2 !   17.5   5.7   2.2e-05    0.0043       9     126 ..      70     190 ..      65     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.12
                             HrpB7  84 legrvraaeaelaaarqaldaaedavaatarkiaR 118
                                        +++++ + a+l+a +++ ++ +  +++ + kia 
  gi|518651672|ref|YP_008141192.1|  11 FQEQLQTMHANLEAVQAENQELTSHINELNNKIAA 45 
                                       34455555555555555555555555555555543 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.2e-05
                             HrpB7   9 lverrarreerlraeleaaraalaaaeaalaaaqaqveaardavraheerlddlttgsspfsia...dylacrayrd 82 
                                       ++e  ++++e ++ ele++ ++l++  ++++  ++++e+ + +  +++e ++++t+ s  +s +   ++  ++ y++
  gi|518651672|ref|YP_008141192.1|  70 ALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSElkqKIDRLQKYIS 146
                                       56666899**************************************************99997611155667889** PP

                             HrpB7  83 vlegrvraaeaelaaarqaldaaedavaatarkiaRndaqidac 126
                                       +le +  ++++++  +  + +++ ++++  +++i   ++ i+  
  gi|518651672|ref|YP_008141192.1| 147 ELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       **********************************9888888765 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 ?    4.1   1.6      0.25        49      43      80 .]       6      43 ..       3      43 .. 0.87
   2 ?    3.6   6.7      0.37        71      43      77 ..      76     110 ..      45     113 .. 0.77
   3 !   17.2   9.1   2.1e-05     0.004      11      76 ..     118     190 ..     114     192 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.25
                              Med9 43 relpgidrsveeqeaeieeleeqlakKrelLkkyknrv 80
                                      ++l++ ++  +++ a +e+ + +++   + +++++n++
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKI 43
                                      68899999999999999999999999999999999875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.37
                              Med9  43 relpgidrsveeqeaeieeleeqlakKrelLkkyk 77 
                                       +++++i++  e+ + ++e+  e++++ +e L+k+k
  gi|518651672|ref|YP_008141192.1|  76 KQNEDIQHELEDKNTRLESTVEKIETLEEELEKLK 110
                                       46788999999999999999999999999999998 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.1e-05
                              Med9  11 ksiekdpnlsskdletktgelrhkLkkarelirelpg...........idrsveeqeaeieeleeqlakKrelLkky 76 
                                       +++e+ +  ss+++    +el++k+++  ++i+el+            ++ +  eq a+i++l+++++ K++l++++
  gi|518651672|ref|YP_008141192.1| 118 EDMENTT-ASSQKI---SSELKQKIDRLQKYISELESkdsqsqkaineLSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       4555555.555555...689****************99***********************************9986 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   1.8     0.062        12      27      56 ..       2      31 ..       1      35 [. 0.86
   2 ?    6.4   1.3     0.069        14      17      58 ..      34      75 ..      30      82 .. 0.84
   3 ?   -0.4   4.9       9.2   1.8e+03      33      44 ..      99     110 ..      69     146 .. 0.52
   4 !   17.4   1.9   2.5e-05    0.0049       2      50 ..     142     190 ..     141     200 .. 0.88
   5 ?   -0.0   0.1       7.3   1.4e+03      18      53 ..     186     221 ..     183     227 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.062
                                      HHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX 27 aeqqqqidrlqrqlrllaerlkeleessga 56
                                      ++  +q++  q+ql+ ++ +l+++++++++
  gi|518651672|ref|YP_008141192.1|  2 VNAKKQLEDFQEQLQTMHANLEAVQAENQE 31
                                      567899*****************9999874 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.069
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
                              SlyX 17 dtieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58
                                        i+eLn+ +a+  ++ d l+ q + l+  l + +e+ ++ +
  gi|518651672|ref|YP_008141192.1| 34 SHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFK 75
                                      579****************************88888877544 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 9.2
                                       HHHHHHHHHHHH CS
                              SlyX  33 idrlqrqlrlla 44 
                                       i+ l+++l++l+
  gi|518651672|ref|YP_008141192.1|  99 IETLEEELEKLK 110
                                       222222222222 PP

  == domain 4  score: 17.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXX CS
                              SlyX   2 eerleeLEiklafqedtieeLndvvaeqqqqidrlqrqlrllaerlkel 50 
                                       ++ + eLE+k +  +++i+eL+ +  eq  qi+ lq++++  +  ++el
  gi|518651672|ref|YP_008141192.1| 142 QKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       67799*********************************99877776666 PP

  == domain 5  score: -0.0 bits;  conditional E-value: 7.3
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXX CS
                              SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkelees 53 
                                       +ieeL+   +e +++++  + + + l+e ++ l+++
  gi|518651672|ref|YP_008141192.1| 186 LIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAA 221
                                       688888888888888888887777777777666655 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8  37.5   8.1e-05     0.016     252     471 ..       3     222 ..       1     250 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-05
                           DUF3584 252 eefeqleslelrLsllkgelkadeerlaekqeevqeakaelkqqlrtledelkeaidelnqelsaakaklaakesel 328
                                       ++ +qle   ++L++++++l+a + + +e   +++e ++++ + l+  ed+lk++ + l++ l +++++l+ ++++ 
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKR-EDDLKNQNESLKSSLLDTNEALESFKKQN 78 
                                       5679999*******************999999999999999998875.6789*******************999999 PP

                           DUF3584 329 eale...eqkkkyedadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeeleklker 402
                                       e ++   e+k+  +++ +ek +   ++l++++ e  +++e+++  t + q++ +++++++  +++   e  +k  ++
  gi|518651672|ref|YP_008141192.1|  79 EDIQhelEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQS 155
                                       9998333456677899999999999**********************************999999999988888888 PP

                           DUF3584 403 leaireekdrlkaaieealealesqlrkqleaqkeelneeekelesrlselklrldsatateEeleqie 471
                                       ++ai e   +   +++++ + l+++ +  ++  +eel  +++el++ l+  + + +s   t E+l + +
  gi|518651672|ref|YP_008141192.1| 156 QKAINELSSTG-REQSAQIKSLQKEIK-DKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAAN 222
                                       99999999885.567889999999998.8899*****************************99987655 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 ?    2.0   0.3      0.83   1.6e+02     126     166 ..       4      44 ..       1      51 [. 0.66
   2 ?   15.3   4.6   6.7e-05     0.013      90     160 ..      66     136 ..      51     144 .. 0.89
   3 ?    6.2   1.1     0.041         8     122     170 ..     137     185 ..     135     187 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.83
                                       HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 126 tgealkeiveavaevadlvqeiaaaseeqsasieevnqave 166
                                       ++++l++  e+ + + + ++ ++a  +e+++ i+e n+ ++
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIA 44 
                                       55666666666666667777777777777777777666654 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.7e-05
                                       HHHHHH..............HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal  90 eiealiieiqkeindsvesleetrqrveegselveetgealkeiveavaevadlvqeiaaaseeqsasiee 160
                                       +++++++  +k+ +d  + le+ ++r e+++e++e+ +e+l+++  + +++++ +++ +a+s+++s+ +++
  gi|518651672|ref|YP_008141192.1|  66 DTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQ 136
                                       5677888999*******************************************************998776 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.041
                                       HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         MCPsignal 122 lveetgealkeiveavaevadlvqeiaaaseeqsasieevnqaveevak 170
                                       ++++ ++ ++e+ ++ ++ ++ ++e++++  eqsa i++ ++ ++  ++
  gi|518651672|ref|YP_008141192.1| 137 KIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNS 185
                                       56777888899999999999*******************9999987765 PP

>> ZapB  Cell division protein ZapB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6  11.9   8.1e-05     0.016      11      70 ..      90     149 ..      83     150 .. 0.93
   2 ?    8.2   7.3     0.017       3.4      18      59 ..     136     181 ..     129     191 .. 0.55
   3 ?    1.2   4.8       2.6     5e+02      20      68 ..     173     231 ..     171     233 .. 0.52

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.1e-05
                              ZapB  11 skiqkaidtitlLqmeieeLkeeneelkeenreleeeneqlkeereawqerlkkLLgkle 70 
                                       ++ ++++++i++L +e+e+Lk en + +e +++ +++ ++   e ++  +rl+k + +le
  gi|518651672|ref|YP_008141192.1|  90 TRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELE 149
                                       67899*************************************************999997 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.017
                              ZapB  18 dtitlLqmeieeLkeeneelkeenrele....eeneqlkeereawq 59 
                                       ++i++Lq+ i+eL+ + ++ ++ ++el+    e+  q k  +++++
  gi|518651672|ref|YP_008141192.1| 136 QKIDRLQKYISELESKDSQSQKAINELSstgrEQSAQIKSLQKEIK 181
                                       4566666666666666666666666666555544444444444444 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.6
                              ZapB  20 itlLqmeieeLkeeneelkeenreleeeneqlk..........eereawqerlkkLLgk 68 
                                       i++Lq+ei++     eel   n el++ ++  +          e  +a ++  k+LL+k
  gi|518651672|ref|YP_008141192.1| 173 IKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEikekslretmELLNAANDNFKGLLEK 231
                                       66777776666666666666666666444333322222223335556666666666665 PP

>> HALZ  Homeobox associated leucine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   1.5   8.4e-05     0.016       8      41 ..      13      42 ..       6      44 .. 0.74
   2 ?   -0.6   6.8         8   1.6e+03      22      35 ..      51      64 ..      46      99 .. 0.78
   3 ?    0.6   1.0       3.4   6.7e+02      22      34 ..     100     112 ..      92     121 .. 0.65
   4 ?   -0.2   0.3       6.3   1.2e+03      24      41 ..     134     151 ..     132     152 .. 0.73
   5 ?   -0.6   0.3       8.5   1.7e+03      26      35 ..     181     190 ..     171     192 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.4e-05
                              HALZ  8 dvLKasYdaLksdydsLkkenekLkaelqeLkek 41
                                      + L+  +    ++ +++++en++L + ++eL++k
  gi|518651672|ref|YP_008141192.1| 13 EQLQTMH----ANLEAVQAENQELTSHINELNNK 42
                                      5555555....5555*****************99 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 8
                              HALZ 22 dsLkkenekLkael 35
                                      d Lk++ne+Lk+ l
  gi|518651672|ref|YP_008141192.1| 51 DDLKNQNESLKSSL 64
                                      56666666666654 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 3.4
                              HALZ  22 dsLkkenekLkae 34 
                                       + L++e ekLk+e
  gi|518651672|ref|YP_008141192.1| 100 ETLEEELEKLKIE 112
                                       4455555555544 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 6.3
                              HALZ  24 LkkenekLkaelqeLkek 41 
                                       Lk+  ++L++ + eL +k
  gi|518651672|ref|YP_008141192.1| 134 LKQKIDRLQKYISELESK 151
                                       666667888888888766 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 8.5
                              HALZ  26 kenekLkael 35 
                                       k++++L  el
  gi|518651672|ref|YP_008141192.1| 181 KDKNSLIEEL 190
                                       5677777776 PP

>> YabA  Initiation control protein YabA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   9.2     0.012       2.3      15      67 ..       6      58 ..       1      80 [. 0.52
   2 ?   11.6  10.8    0.0017      0.32       8      75 ..      76     143 ..      65     148 .. 0.85
   3 ?    4.5   7.2      0.29        56       8      76 ..     157     228 ..     148     258 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......XXXXXXXXXXXXXXX CS
                              YabA 15 eqleelleeleelkeelaelleenaeLeleneklrerl.......eeeekkekekkkels 67
                                      +qle+++e+l++++++l+++  en+eL+   ++l +++       +       + k++ +
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIaaglkreD-------DLKNQNE 58
                                      6666666666666666666666666666666666666644332221.......1111111 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerleeeekkekekkkelsegkenLar 75 
                                       ++ e+++++le+ +++le+  e++++l ee ++L++en k++e +e++++++++ ++el++  + L++
  gi|518651672|ref|YP_008141192.1|  76 KQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQK 143
                                       445678888999999999***************************99999999999999999998887 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...XXXXXXXXXXXXXXXXXXXXXXXX CS
                              YabA   8 dkleeleeqleelleeleelkeelaelleenaeLeleneklrerl...eeeekkekekkkelsegkenLarl 76 
                                       ++++el+++ +e ++++++l++e+++     +eL l n +l + l   e +ek+ +e+ + l+ +++n++ l
  gi|518651672|ref|YP_008141192.1| 157 KAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLktyEIKEKSLRETMELLNAANDNFKGL 228
                                       567777888888888888888888887777788888888888777554445555555555666666666655 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8    0.0047      0.92      80     118 ..       6      44 ..       1      49 [. 0.65
   2 ?    5.7   4.9     0.076        15      56     114 ..      52     110 ..      43     119 .. 0.52
   3 ?   10.4   7.3    0.0026       0.5      46     120 ..     116     190 ..     113     194 .. 0.92
   4 ?    5.7   2.3     0.076        15      51     114 ..     156     219 ..     149     228 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0047
                           DUF1664  80 eiskeikeevtevredlseigedvesvkeavegleskle 118
                                       +  ++ +e++++++ +l++++ + +++ + +++l++k++
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIA 44 
                                       444556667777777777777777777777777777764 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.076
                           DUF1664  56 slaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +l+++ + L+s +   ++ l++ k+  ++i++e+++ +  l+++ e++e+++e  e+l+
  gi|518651672|ref|YP_008141192.1|  52 DLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLK 110
                                       44445555555555555555555555555555555555555555555555555444443 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.0026
                           DUF1664  46 vskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       + +++e+  +s ++   +L+++idr++k + e +   ++ ++ ++e+++  +e + +++s+++ +++ +s +e++
  gi|518651672|ref|YP_008141192.1| 116 IQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       6788999999999*************************************************9999988888877 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.076
                           DUF1664  51 eqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       ++  ++l++t r+ s++i++++k++++ + +++e++ +  e+++dl++ + + +s++e++e l+
  gi|518651672|ref|YP_008141192.1| 156 QKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLN 219
                                       56678999999**************************999*****9999999999999988776 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 ?   11.2   0.9    0.0016      0.31      88     123 ..       4      39 ..       1      46 [. 0.92
   2 ?    9.7  11.2    0.0045      0.87      40     123 ..      65     148 ..      52     151 .. 0.74
   3 ?    4.1   4.8      0.25        49      45     116 ..     155     225 ..     149     235 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0016
                             CREPT  88 qkellakaeekleelkeklekvksvrkelkshiqsL 123
                                        k++l++ +e+l+ ++  le v+++++el shi+ L
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINEL 39 
                                       6899999**************************988 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0045
                             CREPT  40 ikdkeeaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkel 116
                                       +  +e+ e++ kq e+ ++ l++ n+rLe+ +e+ ++l++ le+++    +  ++ e++ ++ ++  +++k++ + l
  gi|518651672|ref|YP_008141192.1|  65 LDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRL 141
                                       345678899***********************************998776666666666665555555666666666 PP

                             CREPT 117 kshiqsL 123
                                       ++ i+ L
  gi|518651672|ref|YP_008141192.1| 142 QKYISEL 148
                                       6555544 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.25
                             CREPT  45 eaekllkqveealellaeYnkrLeaeleeRkklakmledfleaqkellakaeekleelkeklekvksvrkel 116
                                       ++++  +  +++ e+ +   k+L++e+++ ++l + l+     +++ l++ e k ++l+e +e +++++++ 
  gi|518651672|ref|YP_008141192.1| 155 SQKAINELSSTGREQ-SAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNF 225
                                       444444444444443.344689***************99999999999999999999999998888877665 PP

>> DUF4200  Domain of unknown function (DUF4200)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  25.8      0.24        47      24     105 ..      24     122 ..       1     131 [. 0.72
   2 ?   13.1  10.2   0.00048     0.094      25      99 ..     116     190 ..     114     192 .. 0.93
   3 ?    5.4   1.9      0.12        24       7      63 ..     189     245 ..     186     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.24
                           DUF4200  24 r.................leealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeik 83 
                                                         +  a  +re++l+++++ l+ +ll  ++ l++ +++ ++ + + e+++ + ++  ++i+
  gi|518651672|ref|YP_008141192.1|  24 AvqaenqeltshinelnnKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIE 100
                                       43344444444444444477777889999999999999999999999999999999999999999999999999999 PP

                           DUF4200  84 klkaeietlkseiekleeklee 105
                                        l++e+e+lk e+ k +e +e+
  gi|518651672|ref|YP_008141192.1| 101 TLEEELEKLKIENGKIQEDMEN 122
                                       9999999999888888887664 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00048
                           DUF4200  25 leealkqreeelekkeqeleedllkfdkflkendakraralkkaeeerklkkekeaeikklkaeietlkseiekl 99 
                                       ++e +++  +  +k  +el++++ +++k++ e ++k ++ +k ++e +   +e  a+ik l++ei++ +s ie+l
  gi|518651672|ref|YP_008141192.1| 116 IQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       6788888889999999**************************************************999988876 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.12
                           DUF4200   7 emfevqealeakkeeiqrleealkqreeelekkeqeleedllkfdkflkendakrar 63 
                                       e+++ +++l++  + ++ +e++l++  e l++++ +++  l+k+   l+ n   ++r
  gi|518651672|ref|YP_008141192.1| 189 ELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYRFLLENNITVKKR 245
                                       78999*********************************9999987777777655555 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  14.5   0.00076      0.15      62     149 ..      11      98 ..       3     101 .. 0.90
   2 ?    8.2  17.1    0.0086       1.7      48     145 ..     101     203 ..      98     236 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00076
                      HAUS-augmin3  62 kqedvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaqeelra 138
                                        qe+ + +++ le+ ++  ++L + ++eL +  a  lkr + L+ q  sl++ l + +e+ ++ kk+++++q el+ 
  gi|518651672|ref|YP_008141192.1|  11 FQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELED 87 
                                       34899999********************************************************************* PP

                      HAUS-augmin3 139 enaetnavLqq 149
                                       +n ++++  ++
  gi|518651672|ref|YP_008141192.1|  88 KNTRLESTVEK 98 
                                       ***99988776 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0086
                      HAUS-augmin3  48 aLeeaLktie....psdlkq....edvellevileeeeesleaLeqelqeLqkekalklkrlnkLqvqaaslqqelr 116
                                       +Lee L++++    +    q    +++ ++++i +e+++++  L++ ++eL++ +   +k  n+L  +  +++ + +
  gi|518651672|ref|YP_008141192.1| 101 TLEEELEKLKiengK---IQedmeNTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIK 174
                                       789999999974431...33223345555566777778888888888888888888888888888888888888888 PP

                      HAUS-augmin3 117 kleeeekeakkklkeaqeelraenaetna 145
                                       +l++e k ++  ++e++ ++ + n ++++
  gi|518651672|ref|YP_008141192.1| 175 SLQKEIKDKNSLIEELDLHNYELNHDLKT 203
                                       88888888888888888887777776654 PP

>> EzrA  Septation ring formation regulator, EzrA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9  38.2   2.9e-05    0.0057     256     435 ..       3     192 ..       1     194 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHHHTT-..-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSHHHHT--HHHHTTGGG-T CS
                              EzrA 256 elekkieeilerlkel..eledveeelktieeeidsLyddlekEveAkkeveknlkelkeklehlekqnkelkeeld 330
                                       +++k++e+  e+l+++  +le+v++e+++++++i++L + + +  + +++ +++ ++lk+ l  +++ ++  k++ +
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMhaNLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNE 79 
                                       46788888888888765588888888888888888888877666666666666666666655555555555555554 PP

                                       TTS.....-GGGSSTTTSTTHHHHHHHHHHHHHHHHHHHHHHS-SS--....-STTGGGTHHHHHHHHHHHHHHHHH CS
                              EzrA 331 rlk.....qsYeLseeeleklrelekelkelekdyeeleekleekkva....YSelqeeleeleekleeieekqeei 398
                                       +++     ++ +L e+ +ek++ le+el++l+ +  +++e++e+ +++     Sel++++++l++ ++e+e+k  + 
  gi|518651672|ref|YP_008141192.1|  80 DIQheledKNTRL-ESTVEKIETLEEELEKLKIENGKIQEDMENTTASsqkiSSELKQKIDRLQKYISELESKDSQS 155
                                       4441111133457.8999**************99999999998876651111688888888888999999999999* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-SS CS
                              EzrA 399 leslkslrkdEkrAreqldeikkelkeikrkieksnL 435
                                       ++++++l +  ++   q++ ++ke+k+ ++ ie+  L
  gi|518651672|ref|YP_008141192.1| 156 QKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDL 192
                                       *********9999999999999999999999998776 PP

>> CK2S  Casein Kinase 2 substrate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   1.5     0.048       9.4      62      95 ..       5      38 ..       4      50 .. 0.89
   2 ?   13.0   0.1   0.00036     0.069      74     120 ..     210     255 ..     205     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.048
                              CK2S 62 ekqlealeevlakLrekleelqkvrdsleklvrd 95
                                      +kqle ++e l++++  le +q  +++l ++ ++
  gi|518651672|ref|YP_008141192.1|  5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINE 38
                                      69**************************998766 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00036
                              CK2S  74 kLrekleelqkvrdsleklvrdalqlyeekadklslkeliersavtP 120
                                       +Lre++e l+ ++d ++ l+++   l+e++   ++++++ ++ +v+P
  gi|518651672|ref|YP_008141192.1| 210 SLRETMELLNAANDNFKGLLEKYRFLLENNIT-VKKRSMSTKKPVKP 255
                                       8***************************9999.9************9 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   3.7   0.00048     0.094       2      37 ..       8      43 ..       7      72 .. 0.93
   2 ?    4.9   1.9      0.18        35       7      32 ..      62      87 ..      51      98 .. 0.75
   3 ?    4.5   7.7      0.24        47       1      34 [.      98     131 ..      84     136 .. 0.70
   4 ?    0.7   6.9       3.8   7.4e+02       5      35 ..     134     164 ..     132     206 .. 0.72
   5 ?   -0.6   0.1         9   1.8e+03       8      34 ..     200     219 ..     187     232 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00048
                         FlaC_arch  2 idelEnklsklsteletvkkeneelsksveelkenV 37
                                      +++++++l+ +  +le v++en+el + ++el+ ++
  gi|518651672|ref|YP_008141192.1|  8 LEDFQEQLQTMHANLEAVQAENQELTSHINELNNKI 43
                                      5789999**************************998 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.18
                         FlaC_arch  7 nklsklsteletvkkeneelsksvee 32
                                      + l ++   le+ kk+ne+++ ++e+
  gi|518651672|ref|YP_008141192.1| 62 SSLLDTNEALESFKKQNEDIQHELED 87
                                      45555566899999999999999886 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.24
                         FlaC_arch   1 ridelEnklsklsteletvkkeneelsksveelk 34 
                                       +i++lE++l+kl++e + +++++e+   s +++ 
  gi|518651672|ref|YP_008141192.1|  98 KIETLEEELEKLKIENGKIQEDMENTTASSQKIS 131
                                       6777777777777777777777777777666665 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 3.8
                         FlaC_arch   5 lEnklsklsteletvkkeneelsksveelke 35 
                                       l +k+++l+  ++ ++++ ++ +k ++el  
  gi|518651672|ref|YP_008141192.1| 134 LKQKIDRLQKYISELESKDSQSQKAINELSS 164
                                       5566666666666666666666666666544 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 9
                         FlaC_arch   8 klsklsteletvkkeneelsksveelk 34 
                                       +       l+t + + ++l+++ e l+
  gi|518651672|ref|YP_008141192.1| 200 D-------LKTYEIKEKSLRETMELLN 219
                                       3.......3444444444444443332 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   4.9    0.0031      0.61       7      63 ..       3      59 ..       1      63 [. 0.82
   2 ?   10.9  10.9    0.0018      0.35      17      98 ..      55     144 ..      51     146 .. 0.82
   3 ?    6.1   8.3     0.053        10       6      82 ..     118     194 ..     114     209 .. 0.80
   4 ?    1.5   3.8       1.4   2.7e+02       3      68 ..     157     222 ..     155     253 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0031
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II  7 eanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkk 63
                                      +a+++++  +eql+ +++nle ++++ +e+ ++++e n+k+ +  k  +d +++   
  gi|518651672|ref|YP_008141192.1|  3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNES 59
                                      577888899999999999999999999999999999999999888888887776555 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH......... CS
                        Laminin_II  17 eqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeasss...... 87 
                                       +q + l+  l  t+e l++++++ e ++++++d+n+ +++  +++ +Le+++++L     ++++  e+  +      
  gi|518651672|ref|YP_008141192.1|  55 NQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTAssqkis 131
                                       56788999999********************************************8887888888888777445556 PP

                                       ..HHHHHHHHHHH CS
                        Laminin_II  88 ..lsdniseikel 98 
                                         l+++i+++++ 
  gi|518651672|ref|YP_008141192.1| 132 seLKQKIDRLQKY 144
                                       6666666666655 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.053
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II   6 aeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       ++ ++t+++ +++  +l+q+++++++ +se++++  + ++ +++++ + r+ + ++k L+k++ +  + ++el+ ++
  gi|518651672|ref|YP_008141192.1| 118 EDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHN 194
                                       56788999999***********************8899999999999999999999999998876555555555444 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 1.4
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TT CS
                        Laminin_II   3 elaaeanetakevleqlaplsqnlentkeklseinrsveetnekvkdankairdArrsvkkLekla 68 
                                       + ++e ++t  e  +q++ l+++++  ++ ++e++ +  e n+++k +    ++ r+ +  L+   
  gi|518651672|ref|YP_008141192.1| 157 KAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAAN 222
                                       456666667777777777777777777777777777777777777766666666666666555443 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0  10.5       1.3   2.6e+02      22      72 ..       2      52 ..       1     110 [. 0.81
   2 ?    9.4   1.3    0.0062       1.2      28      76 ..      99     147 ..      90     154 .. 0.87
   3 ?    2.9   0.4      0.65   1.3e+02      21      44 ..     159     182 ..     153     244 .. 0.62

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 1.3
                            DUF948 22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdp 72
                                      +++kk l+ ++++++++  +++++  e ++l++++nel + +   l++ d 
  gi|518651672|ref|YP_008141192.1|  2 VNAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDD 52
                                      567888999999999999999999999999999999988888777666554 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0062
                            DUF948  28 ldeaaatieelekqvdpilkevedllakvnelledvneklekvdpltea 76 
                                       ++ +++ +e+l+ + ++i +++e+++a ++++ +++++k++++++ +++
  gi|518651672|ref|YP_008141192.1|  99 IETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISE 147
                                       5677889999999******************************988765 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.65
                            DUF948  21 llklkktldeaaatieelekqvdp 44 
                                       +++l++t +e +a+i++l+k+++ 
  gi|518651672|ref|YP_008141192.1| 159 INELSSTGREQSAQIKSLQKEIKD 182
                                       455556666666666666655443 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9  15.6    0.0026      0.52      52     132 ..       4      84 ..       2      85 .. 0.94
   2 ?    6.2  21.8     0.073        14      31     121 ..      70     157 ..      68     163 .. 0.84
   3 ?    6.8  15.2     0.049       9.5      21      97 ..     134     214 ..     132     233 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0026
                            APG6_N  52 leeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreynelqlelleleeeldsleaqyeh 128
                                       ++++le+ +++ +++ ++L+++++e++el + +++l ++ +a  + e+   ++  +l+  ll+ +e l+s + q e+
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNED 80 
                                       6899********************************************************************99988 PP

                            APG6_N 129 aqnq 132
                                        q++
  gi|518651672|ref|YP_008141192.1|  81 IQHE 84 
                                       7776 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.073
                            APG6_N  31 flkklkkekkeeekqdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerfwreyne 107
                                        l+ +kk++++    ++ele+ + +le + ++ e+l+eeL++l+ e+ ++++++++ ++ ++++  e ++++ + ++
  gi|518651672|ref|YP_008141192.1|  70 ALESFKKQNEDI---QHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQK 143
                                       566677775554...469999999999999*************************************9999999999 PP

                            APG6_N 108 lqlelleleeelds 121
                                       +  el++++ + ++
  gi|518651672|ref|YP_008141192.1| 144 YISELESKDSQSQK 157
                                       99999888877765 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.049
                            APG6_N  21 aekerdaYeeflkklkkekkeeek....qdeeleeleeeleklekeeeelleeLkelekereeleaelaaleeelea 93 
                                       +++++d ++++ ++l++++++++k      +  +e   +++ l+ke +++ + ++el+ ++ el+ +l+++e +++ 
  gi|518651672|ref|YP_008141192.1| 134 LKQKIDRLQKYISELESKDSQSQKaineLSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKS 210
                                       56777777777777777766655555554444445555577777777777777777777777777777777777777 PP

                            APG6_N  94 leee 97 
                                       l e 
  gi|518651672|ref|YP_008141192.1| 211 LRET 214
                                       7665 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  11.4     0.017       3.3      97     175 ..       5      86 ..       1      88 [. 0.89
   2 ?   11.2  11.9    0.0013      0.25     102     175 ..     115     188 ..      89     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.017
                      Bacillus_HBL  97 kkdkaellellekLqeeiqqnqkevkqlikeLkklklkla...kdsknFktdvdeltsilagdsgvisqlqneiedl 170
                                       kk+ +++ e+l+ +++++   q+e ++l   +++l++k+a   k + ++k++ + l+s l  ++  ++  ++++ed+
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAaglKREDDLKNQNESLKSSLLDTNEALESFKKQNEDI 81 
                                       566799*********************************933345789***************************** PP

                      Bacillus_HBL 171 qgkik 175
                                       q +++
  gi|518651672|ref|YP_008141192.1|  82 QHELE 86 
                                       *9865 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0013
                      Bacillus_HBL 102 ellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdvdeltsilagdsgvisqlqneiedlqgkik 175
                                       ++ e++e+  ++ q+++ e kq+i  L+k+ ++l++++++ +++++el s+   +s++i+ lq+ei+d ++ i+
  gi|518651672|ref|YP_008141192.1| 115 KIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIE 188
                                       556667777777899999*************************************************9988775 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  10.0     0.013       2.6       2      89 ..       6      92 ..       5      99 .. 0.68
   2 ?   10.9  15.2     0.001       0.2       2     100 ..      97     191 ..      91     210 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.013
                             TMPIT  2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelkerkk 80
                                      +++e++++++++++++ + ++++ +el+++++++ ++i+   kr  +lk++ ++lk+s+  +++e++e+ k++ +++++
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSL-LDTNEALESFKKQNEDIQH 83
                                      56677777888888888888888888888888888888888888888888888888875.3555566666666666666 PP

                             TMPIT 81 vlkevesll 89
                                       l++ +  l
  gi|518651672|ref|YP_008141192.1| 84 ELEDKNTRL 92
                                      665544443 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.001
                             TMPIT   2 eeweelekefkeleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvkeeeeeeveelkeelker 78 
                                       e++e+le+e+++l+ ++ ++++++e+++++ +k+s+e+k++  rl++  s+l++ +++    ++++++el+++ +e+
  gi|518651672|ref|YP_008141192.1|  97 EKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQ----SQKAINELSSTGREQ 169
                                       6788999999999999999999999999999999988887777777777777665555....556666666666666 PP

                             TMPIT  79 kkvlkevesllpkknglylklv 100
                                       ++++k++++ +  kn+l  +l 
  gi|518651672|ref|YP_008141192.1| 170 SAQIKSLQKEIKDKNSLIEELD 191
                                       6666666666666666554444 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  30.8     0.035       6.9      28     176 ..       4     146 ..       1     161 [. 0.53
   2 ?    5.8   9.5     0.053        10      49     116 ..     171     238 ..     167     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.035
                           DUF4201  28 klekkeelgegLtli..dFeqlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelke 102
                                         +++e+  e+L++     e +q+enq+l+ +I+e n+++ +  k+  +   + + lk  l   ++ l+  kk+ ++
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMhaNLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNED 80 
                                       45777888888876423578888888888888888887776544444444444445555555555555555555555 PP

                           DUF4201 103 keerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrkvkilemrlk 176
                                       ++ +l++   +l+++ ++ + l+++ eklk ++g      + +D+++t +  +   k   +L++k+++l++ ++
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRLESTVEKIETLEEELEKLKIENGK-----IQEDMENTTASSQ---KISSELKQKIDRLQKYIS 146
                                       55555555555555555555555555555544444.....4445444444444...333344444444444332 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.053
                           DUF4201  49 ienqalnkkIeernkeLkrlkkkttktvhalthlkeklhmleselselkkelkekeerlaklrkelyk 116
                                       +++++l+k+I ++n  +++l +      h l+++  k++ l+++++ l+   ++ +  l+k+r  l++
  gi|518651672|ref|YP_008141192.1| 171 AQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYRFLLEN 238
                                       57889999999999999999999999999999999999999999999999999999999998877765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  20.6    0.0013      0.25      75     176 ..       6     103 ..       1     105 [. 0.91
   2 ?    9.6  28.8    0.0046      0.89      80     182 ..      68     183 ..      56     185 .. 0.74
   3 ?    2.7   7.9      0.62   1.2e+02     139     187 ..     161     207 ..     151     249 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0013
                           UPF0242  75 aklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqell 151
                                       ++l + +e+l+t + +le +q+e++eL  ++++ +++++   +++  L+ + e      + ++l+ +e+L+  +++ 
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNES----LKSSLLDTNEALESFKKQN 78 
                                       455666689999999**********************************88888....9999*************** PP

                           UPF0242 152 qeyqetieeqrsvlekrqdqieqLe 176
                                       ++ q+++e++   le+  ++ie Le
  gi|518651672|ref|YP_008141192.1|  79 EDIQHELEDKNTRLESTVEKIETLE 103
                                       ***********************99 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0046
                           UPF0242  80 ld..eglktkee....aleelqeeeeeLkeeldakeeelerlkeenqqLqekleaiaedfeelkleleeqLaekqel 150
                                       ++  e++k+++e    +le+ + + e   e+++  eeele+lk en ++qe +e++ +  ++ + el++++++ q+ 
  gi|518651672|ref|YP_008141192.1|  68 NEalESFKKQNEdiqhELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKY 144
                                       22446777666644446666666666666779999*********************999999999999999998888 PP

                           UPF0242 151 lqey.......qetieeqrsvlekrqdqieqLeskVrDl 182
                                       ++e+       q+ i+e+ s+  ++ +qi+ L+  ++D 
  gi|518651672|ref|YP_008141192.1| 145 ISELeskdsqsQKAINELSSTGREQSAQIKSLQKEIKDK 183
                                       876422222227889999999999999999999999996 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.62
                           UPF0242 139 eleeqLaekqellqeyqetieeqrsvlekrqdqieqLeskVrDl.nyEik 187
                                       el ++ +e+  +++ +q++i+++ s +e+ + ++++L+    Dl +yEik
  gi|518651672|ref|YP_008141192.1| 161 ELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNH---DLkTYEIK 207
                                       334444455555555555555555555555555555542...33134444 PP

>> DHR10  Designed helical repeat protein 10 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2  20.8     0.025       4.9       6     106 ..       3     104 ..       1     106 [. 0.92
   2 ?   10.4  11.4    0.0026       0.5      34      99 ..      91     157 ..      89     161 .. 0.82
   3 ?    8.2  15.6     0.012       2.4       7     103 ..     120     217 ..     116     226 .. 0.90
   4 ?    4.4   8.5      0.19        37       6      79 ..     154     231 ..     149     248 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.025
                             DHR10   6 eekeelaelErkarelqakidalqvvekdlrscikllee.ieaelakleeakkklkelrdaleekeielrelerkee 81 
                                       ++k++l++ +++ + ++a ++a+q   ++l s i+ l+  i+a l+++++ k + ++l+  l + ++ l+  +++ e
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNkIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNE 79 
                                       6899**************************9999888766************************************* PP

                             DHR10  82 rlqrqlenaeeklerlreqaeekre 106
                                        +q  le ++ +le   e+ e+ +e
  gi|518651672|ref|YP_008141192.1|  80 DIQHELEDKNTRLESTVEKIETLEE 104
                                       **************99988887655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0026
                             DHR10  34 dlrsciklleeieaelakleeakkklkelrdale.ekeielrelerkeerlqrqlenaeeklerlre 99 
                                        l+s+++ +e++e+el+kl+ ++ k++e +++ + + ++ ++el++k++rlq+ ++  e k ++ ++
  gi|518651672|ref|YP_008141192.1|  91 RLESTVEKIETLEEELEKLKIENGKIQEDMENTTaSSQKISSELKQKIDRLQKYISELESKDSQSQK 157
                                       58999********************99988876515566689************9999888666655 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.012
                             DHR10   7 ekeelaelErkarelqakidalqvvekdlrsciklleeieaelakl.eeakkklkelrdaleekeielrelerkeer 82 
                                       + ++ a+ ++ + el++kid lq++  +l+s   + +++ +el ++ +e+++++k+l++++++k+   +el+ +   
  gi|518651672|ref|YP_008141192.1| 120 MENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTgREQSAQIKSLQKEIKDKNSLIEELDLHNYE 196
                                       56788999999***************************99999987478899************************* PP

                             DHR10  83 lqrqlenaeeklerlreqaee 103
                                       l+  l+  e k   lre++e 
  gi|518651672|ref|YP_008141192.1| 197 LNHDLKTYEIKEKSLRETMEL 217
                                       ******999999999999886 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.19
                             DHR10   6 eekeelaelErkarelqakidalqvvekdlrsciklle....eieaelakleeakkklkelrdaleekeielreler 78 
                                       + +++++el    re +a+i++lq+  kd +s+i+ l+    e++ +l+ +e  +k l e+++ l+  + + + l  
  gi|518651672|ref|YP_008141192.1| 154 QSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDlhnyELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLE 230
                                       67889999999999999999999999999999999998666678888889999999999999999998888887766 PP

                             DHR10  79 k 79 
                                       k
  gi|518651672|ref|YP_008141192.1| 231 K 231
                                       5 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 ?   10.5   9.9   0.00089      0.17     278     348 ..       2      75 ..       1      82 [. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00089
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX..XXXXXXXXXXXXXXXXXXXXXX CS
                          GOLGA2L5 278 vqgkvalelarkeLqeaqerLealakenqqLkaqlsllaapse.Gdgves..eekeeeakkpklsipedlesre 348
                                       v++k +le  +++Lq  + +Lea++ enq+L +++++l ++ + G + e   ++++e  k++ l   e les +
  gi|518651672|ref|YP_008141192.1|   2 VNAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAaGLKREDdlKNQNESLKSSLLDTNEALESFK 75 
                                       67899*********************************888664433333003334557777788889888865 PP

>> Phage_GP20  Phage minor structural protein GP20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   4.3     0.028       5.5      23      66 ..       4      44 ..       1      50 [. 0.62
   2 ?   12.4  19.0   0.00051     0.099       4     100 ..      34     131 ..      31     139 .. 0.81
   3 ?    2.6  13.2      0.54   1.1e+02      17     122 ..     135     230 ..     127     250 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.028
                        Phage_GP20 23 veeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknk 66
                                      ++++ ++++eql++   +Le  ++   +n+eL+  i+el++k++
  gi|518651672|ref|YP_008141192.1|  4 AKKQLEDFQEQLQTMHANLEAVQA---ENQELTSHINELNNKIA 44
                                      444555555555555555555544...48888888888887765 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00051
                        Phage_GP20   4 kkvmkaengkdit.kakldeveeerdtlkeqlkdrdkqLedLkkkakdn.eeLqkqieelqaknkkakaeyeakiad 78 
                                         ++ ++n+k+ +  ++ d++++++++lk++l d ++ Le +kk+++d   eL+ + + l+ +++k  ++ e+++++
  gi|518651672|ref|YP_008141192.1|  34 SHIN-ELNNKIAAgLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIqHELEDKNTRLESTVEK-IETLEEELEK 108
                                       5676.77766666855559**************************877525788888888888887.77899***** PP

                        Phage_GP20  79 lkldn.aielaLkeakaknekav 100
                                       lk++n  i++ ++++ a+++k+ 
  gi|518651672|ref|YP_008141192.1| 109 LKIENgKIQEDMENTTASSQKIS 131
                                       **98857*********9999985 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.54
                        Phage_GP20  17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdneeLqkqieelqaknkkakaeyeakiadlkl.dnaielaLkea 92 
                                       k+k+d++++   +l+++  + +k +++L     +  e  +qi++lq+++k+     ++ i++l+l ++ ++  Lk++
  gi|518651672|ref|YP_008141192.1| 135 KQKIDRLQKYISELESKDSQSQKAINELSS---TGREQSAQIKSLQKEIKD----KNSLIEELDLhNYELNHDLKTY 204
                                       788888888888888888888888888844...588889999999999998....5666777766356788888888 PP

                        Phage_GP20  93 kaknekavkalldkdklklkedgelkgLde 122
                                       + k++++    ++   l++++d + kgL e
  gi|518651672|ref|YP_008141192.1| 205 EIKEKSLR-ETME--LLNAAND-NFKGLLE 230
                                       77765543.2232..3334333.5555555 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   6.3     0.063        12      80     119 ..       5      44 ..       2      56 .. 0.66
   2 ?    3.1  16.8      0.46        90      57     131 ..      52     126 ..      46     137 .. 0.62
   3 ?   11.6  10.6    0.0011      0.21      48     113 ..     116     182 ..     114     186 .. 0.88
   4 ?    9.5   4.7     0.005      0.97      59     124 ..     170     235 ..     163     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.063
                              ADIP  80 ktqleqlerelalvqakerqlekklktleqklknekeelq 119
                                       k+qle+++ +l++ +a++   ++++++l+++++++  +++
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIA 44 
                                       5677777777777777777777777777777776665554 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.46
                              ADIP  57 slnetirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlknalqqiktq 131
                                        l+ ++++l++++   + + e+ k+q+e+ + el+  + ++ ++  k++tle+ l ++k e+ + + +++++ ++
  gi|518651672|ref|YP_008141192.1|  52 DLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTAS 126
                                       456666677777777777777777777777777777777777777777777777777777777766666655432 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.0011
                              ADIP  48 rdrdleqreslnetir.kleaeierlqskierlktqleqlerelalvqakerqlekklktleqklkn 113
                                        ++d+e  ++++++i+ +l+  i+rlq+ i+ l+ + +q+++ +  + ++ r++ +++k+l++ +k 
  gi|518651672|ref|YP_008141192.1| 116 IQEDMENTTASSQKISsELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKD 182
                                       689999999999998626899999******************9999999999999999999998886 PP

  == domain 4  score: 9.5 bits;  conditional E-value: 0.005
                              ADIP  59 netirkleaeierlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                       +++i++l+ ei+ ++s ie l+  + +l   l++++ ke++l+ +++ l++++ n k  l++ +  
  gi|518651672|ref|YP_008141192.1| 170 SAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYRFL 235
                                       67999**********************************************999999888887655 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4  10.4      0.27        53     178     246 ..       4      72 ..       1      77 [. 0.66
   2 ?   10.7  30.1    0.0016      0.32      14     176 ..      71     237 ..      55     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.27
                         Laminin_I 178 lrdsLaeyeakLsDlrelleeAaaktrdanrlnlanqanlreiekkkeevseeknqleetlktardsLd 246
                                       ++++L++++++L+ + + le+ +a+ ++ +    + ++++ +  k+ + ++++++ l+ +l + ++ L 
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALE 72 
                                       477788888888888888888777777765444444444455667777777777777777777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.0016
                         Laminin_I  14 pykinanledltkeLqeklskesakkskieilekelesLaqeteeLqkkatqvlakaqkvnaesertlnnakeLaek 90 
                                       ++    + ed + eL+ k    +++ +kie le+ele+L+ e  + q+ ++ ++a+ qk+  e ++ + + ++   +
  gi|518651672|ref|YP_008141192.1|  71 LESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISE 147
                                       45556677888889999999999999999999999999999999999999999999999888888888888888888 PP

                         Laminin_I  91 ikkladnikeilekvatlneneealpssklseelaeaqrlLeelrsRdftkql.....eeaeaelkaAqkLLsrvqt 162
                                        +  + + + +++  + ++  e+ +  + l++e +  ++l+eel   + + ++     e  e+ l++  +LL+ ++ 
  gi|518651672|ref|YP_008141192.1| 148 LESKDSQSQKAINELSSTGR-EQSAQIKSLQKEIKDKNSLIEELDLHNYELNHdlktyEIKEKSLRETMELLNAAND 223
                                       88888888888888888888.55666788999999999999999888854443111114467788999999999999 PP

                         Laminin_I 163 llqklqeenkaLke 176
                                       +++ l e+ + L e
  gi|518651672|ref|YP_008141192.1| 224 NFKGLLEKYRFLLE 237
                                       99999999887765 PP

>> SHE3  SWI5-dependent HO expression protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   8.6    0.0016      0.32     134     197 ..      98     164 ..      96     171 .. 0.85
   2 ?    7.2   7.9     0.019       3.6      65     128 ..     170     233 ..     160     252 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0016
                                       HHHHHHHHHHHHHHHHHSSSXXXXXXXXXXX....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              SHE3 134 eieeLkesleklklenekqleelqerissndk...didtkldsynnkkknlesieeeknkkllkkle 197
                                       +ie+L+e+leklk en k  e++++++ s++k   ++++k+d +++   +les + + +k ++++ +
  gi|518651672|ref|YP_008141192.1|  98 KIETLEEELEKLKIENGKIQEDMENTTASSQKissELKQKIDRLQKYISELESKDSQSQKAINELSS 164
                                       79***************99999999999888644478899999999999999999999998887665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SHE3  65 errlkdlekelselkesveelklekkqlkkrlenssaseteleeelerlkvqYdalvdsqkeYk 128
                                         ++k l+ke+++ ++ +eel l++ +l+++l++ + +e++l+e +e l++  d      ++Y+
  gi|518651672|ref|YP_008141192.1| 170 SAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYR 233
                                       5689*********************************************998887666666666 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9  28.3      0.02       3.9      16     154 ..       5     155 ..       1     165 [. 0.63
   2 ?    5.0   7.6      0.15        29      32     107 ..     158     233 ..     149     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.02
                              Fez1  16 KqQLkdsqaevtqklseivalkaqlrelrakleekeeeik.eleesleektle....................levc 71 
                                       K+QL d q ++ +   ++ a++a+ +el+++++e +++i   l+ + + k+++                    +e +
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAaGLKREDDLKNQNeslksslldtnealesfkkqNEDI 81 
                                       78888888888888888888888888888888888877752355444444444557777777777777777777777 PP

                              Fez1  72 enelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqeaeeleelkreverlraeLkeer 148
                                       ++el+ k+++ e + ek+e+leeel++l+ e  + +++ e      ++a      ++ ++elk++++rl++ ++e +
  gi|518651672|ref|YP_008141192.1|  82 QHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDME-----NTTASS----QKISSELKQKIDRLQKYISELE 149
                                       7777777777777777777777777777775555333222.....222222....3345677777888877666555 PP

                              Fez1 149 qkkeeq 154
                                        k  + 
  gi|518651672|ref|YP_008141192.1| 150 SKDSQS 155
                                       443333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.15
                              Fez1  32 eivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelsels 107
                                        i +l ++ re +a++++ ++eik+ ++ +ee +l + +++++l+  + +++ lre++e l++   +++  l++  
  gi|518651672|ref|YP_008141192.1| 158 AINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYR 233
                                       4557888899999999999999999999999999999999999999999999999999999988888887666544 PP

>> DUF724  Protein of unknown function (DUF724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2  12.6   0.00059      0.11      98     184 ..       2      95 ..       1      98 [. 0.76
   2 ?    7.1  16.3     0.023       4.5      89     183 ..      91     182 ..      89     192 .. 0.75
   3 ?    2.5   4.0      0.57   1.1e+02     107     154 ..     169     216 ..     156     239 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00059
                            DUF724  98 lslkdeqtklleerkklekkieeeesekrkleeeidelekkil.......elerqlallkekkeaadkeiarlksea 167
                                       ++ k++ +  +e+++ ++ ++e  ++e+++l ++i+el++ki+       +l++q+++lk+   + ++ + + k+++
  gi|518651672|ref|YP_008141192.1|   2 VNAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAaglkredDLKNQNESLKSSLLDTNEALESFKKQN 78 
                                       567999999**********************************6666666666666666666666666666666666 PP

                            DUF724 168 ekleeeledveqeFeav 184
                                       e++++eled +++ e++
  gi|518651672|ref|YP_008141192.1|  79 EDIQHELEDKNTRLEST 95 
                                       66666666666666665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.023
                            DUF724  89 alqsrlnkLlslkdeqtklleerkklekkieeeesekrkleeeidelekkilelerqlallkekkeaadkeiarlks 165
                                        l+s ++k+  l +e +kl+ e  k+++++e+ +++++k+++e   l++ki +l++    l +k ++++k i +l+s
  gi|518651672|ref|YP_008141192.1|  91 RLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSE---LKQKIDRLQKYISELESKDSQSQKAINELSS 164
                                       5788999999999999999999999999999999999988766...6666666666666666666777777777777 PP

                            DUF724 166 eaekleeeledveqeFea 183
                                         ++ + ++++ ++e ++
  gi|518651672|ref|YP_008141192.1| 165 TGREQSAQIKSLQKEIKD 182
                                       777777777766666554 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.57
                            DUF724 107 lleerkklekkieeeesekrkleeeidelekkilelerqlallkekke 154
                                          ++k l+k+i++++s  ++l+ +  el++  ++ e ++++l+e +e
  gi|518651672|ref|YP_008141192.1| 169 QSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETME 216
                                       445678888899999999999999999999999999999999987766 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 ?    9.8   4.3    0.0047      0.91      13      67 ..       7      61 ..       1      64 [. 0.90
   2 ?   10.0   8.1     0.004      0.78      51      98 ..      63     110 ..      59     112 .. 0.94
   3 ?    4.7   9.9      0.17        33      12      75 ..      97     161 ..      94     164 .. 0.61
   4 ?    0.7  14.4         3   5.9e+02       7      80 ..     131     208 ..     117     219 .. 0.67
   5 ?    2.4   8.4      0.91   1.8e+02       5      81 ..     150     223 ..     146     239 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0047
                       TMF_TATA_bd 13 lverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkele 67
                                       +e ++ +++ + + l++++ e+++l++  +e+++ i++ +k+ ++lk+++++l+
  gi|518651672|ref|YP_008141192.1|  7 QLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLK 61
                                      58999*****************************************999998876 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.004
                       TMF_TATA_bd  51 klmkeneelkelkkeleelekeleelqeryetlLellGeksEeveELr 98 
                                       +l+ +ne+l++ kk++e+++ ele+ ++r+e++ e +   +Ee e L+
  gi|518651672|ref|YP_008141192.1|  63 SLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLK 110
                                       68899**************************************99998 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.17
                       TMF_TATA_bd  12 qlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneel.kelkkeleelekelee 75 
                                       + +e l+ e+ +l +E  +++e++e+ +a+ +++++e+ + + + ++  +el+++ ++ +k ++e
  gi|518651672|ref|YP_008141192.1|  97 EKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYiSELESKDSQSQKAINE 161
                                       55777777777777777777777777777777777777776655555413334444444444444 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 3
                       TMF_TATA_bd   7 agpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkele....elekeleelqer 79 
                                       ++   q ++rl++ i +lE+  +++++ +++l++  +e +++i +l ke  ++++l +el+    el+  l+  + +
  gi|518651672|ref|YP_008141192.1| 131 SSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDlhnyELNHDLKTYEIK 207
                                       34445678888888888888888888888888888888888888888888777777666651111344444444444 PP

                       TMF_TATA_bd  80 y 80 
                                       +
  gi|518651672|ref|YP_008141192.1| 208 E 208
                                       4 PP

  == domain 5  score: 2.4 bits;  conditional E-value: 0.91
                       TMF_TATA_bd   5 ssagpsvqlverlsseirrlEgElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqerye 81 
                                       s+ ++s++ +++lss+ r+  ++++sl++e++  ++  +e+       ++ n++lk+++ + ++l++ +e l+   +
  gi|518651672|ref|YP_008141192.1| 150 SKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHN---YELNHDLKTYEIKEKSLRETMELLNAAND 223
                                       667788888888888888888888888888876554444444333...33334444444444444444433333333 PP

>> DUF4618  Domain of unknown function (DUF4618)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  17.4     0.044       8.5     122     226 ..      15     116 ..      10     121 .. 0.55
   2 ?   13.0  19.2   0.00026     0.051       8     114 ..      99     208 ..      97     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.044
                           DUF4618 122 IanlvrqlqqlkdsqqdeldeleelikevleklskkiqkkkekllkslaektlkatqeaLlqktlenqvlkkeiekf 198
                                       ++++  +l+ +++++q+    ++el +++ + l+++ + k+++  +sl + +l  t+eaL+    +n+++++e+e  
  gi|518651672|ref|YP_008141192.1|  15 LQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQN--ESL-KSSLLDTNEALESFKKQNEDIQHELEDK 88 
                                       4455566666666666666666666666666665554444432..222.3334455666666666666666666666 PP

                           DUF4618 199 refieeleeeipeLkaeveqLqaqaeep 226
                                           e   e+i++L++e+e+L+ +  ++
  gi|518651672|ref|YP_008141192.1|  89 NTRLESTVEKIETLEEELEKLKIENGKI 116
                                       6666666666666666666666555444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 0.00026
                           DUF4618   8 leelkkheaeLtklnkeLvkeIqdtedstakkvrklLqqyeklktvisileksskkqleqakaeLqeweekeekkle 84 
                                       +e l++  ++L+ +n +++++  +t +s+ k  ++l q+ ++l++ is le++ + q ++a +eL ++  + + +++
  gi|518651672|ref|YP_008141192.1|  99 IETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDS-QSQKAINELSSTGREQSAQIK 174
                                       7899999*******************************************98765.579****************** PP

                           DUF4618  85 kLeqqleqlnakvqkl...qeelnv.LstYkDke 114
                                       +L+++++  n+ +++l   + eln  L+tY  ke
  gi|518651672|ref|YP_008141192.1| 175 SLQKEIKDKNSLIEELdlhNYELNHdLKTYEIKE 208
                                       *******999988875222678864488887666 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5  10.0     0.094        18      85     151 ..       9      78 ..       2      82 .. 0.73
   2 ?    6.6  29.9     0.044       8.5      36     145 ..      69     188 ..      66     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.094
                     Jnk-SapK_ap_N  85 dqweeerkelqekveqleeenrelelkaknaadqlsrleekeaelkkeysklhe...retellkklkelv 151
                                       + ++e+ +++++ +e ++ en+el   ++++++++++  ++e++lk+++++l++     +e l++ k++ 
  gi|518651672|ref|YP_008141192.1|   9 EDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSsllDTNEALESFKKQN 78 
                                       3466677778888888888888888888888888888888888888888888877776777777666654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.044
                     Jnk-SapK_ap_N  36 ElLeslasrne.......eeeaeleelreeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeen 105
                                       E Les+ ++ne        ++++le   e++e+Le+e+e+ k ++ + +e++e++  + ++  +el++k+ +l++ +
  gi|518651672|ref|YP_008141192.1|  69 EALESFKKQNEdiqheleDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYI 145
                                       66677776665111111145566777888999999999999999999999999999999999999999999999999 PP

                     Jnk-SapK_ap_N 106 relelkaknaadqlsrleekeaelkkeysklhe...retellk 145
                                        ele k +++++ +++l+++  e++ + ++l++    ++ l++
  gi|518651672|ref|YP_008141192.1| 146 SELESKDSQSQKAINELSSTGREQSAQIKSLQKeikDKNSLIE 188
                                       9999999999999999999999999999999986654555554 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 ?    8.3   9.2     0.011       2.2      62     124 ..       4      62 ..       1      66 [. 0.78
   2 ?    7.1  22.7     0.028       5.5       8     111 ..      48     151 ..      42     160 .. 0.92
   3 ?   10.5  24.4    0.0025      0.48       3     119 ..      78     194 ..      76     201 .. 0.77
   4 ?    5.2  10.5      0.11        21       3     106 ..     138     241 ..     137     248 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.011
                        TPR_MLP1_2  62 lreelnelkaeiaelkaeaesakaeleeseesweeqkeelekelselekriedlneqNklLhd 124
                                       ++++l++ +++++++ a++e+++ae++e +++++e    l ++++   kr +dl++qN+ L +
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINE----LNNKIAAGLKREDDLKNQNESLKS 62 
                                       67888888888888888888888888777777765....777778888999*******99865 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.028
                        TPR_MLP1_2   8 eeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelkaeaesak 84 
                                       +  ++lk+++e++++ l    e le+ +++ ++ q   e   +  +++v+++++l eel++lk e  +++++ e+++
  gi|518651672|ref|YP_008141192.1|  48 KREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTT 124
                                       56678999999****************************************************************** PP

                        TPR_MLP1_2  85 aeleeseesweeqkeelekelselekr 111
                                       a+ ++  ++++++ ++l+k +sele++
  gi|518651672|ref|YP_008141192.1| 125 ASSQKISSELKQKIDRLQKYISELESK 151
                                       ************************986 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.0025
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelqalreelnelkaeiaelk.. 77 
                                        +  + e+++++++ e+  +k+++l+e+lek + +  + q++ e+      + +    +l++++++l++ i+el+  
  gi|518651672|ref|YP_008141192.1|  78 NEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISS---ELKQKIDRLQKYISELEsk 151
                                       577899***********************************88887655555555...5566665555555555500 PP

                        TPR_MLP1_2  78 .aeaesakaeleeseesweeqkeelekelselekriedlneqN 119
                                        ++ ++a +el+    + + q ++l+ke+++ ++ ie+l+ +N
  gi|518651672|ref|YP_008141192.1| 152 dSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHN 194
                                       0566666666666677777778899**************9888 PP

  == domain 4  score: 5.2 bits;  conditional E-value: 0.11
                        TPR_MLP1_2   3 lksleeeikslkeekeeaeaklqklqedlekqaeiakeaqqkYerelvkhaedvkelq....alreelnelkaeiae 75 
                                       +++l++ i++l+++++++++++++l +  ++q+++ k  q+    e+  +++ ++el     +l+ +l++++ + ++
  gi|518651672|ref|YP_008141192.1| 138 IDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQK----EIKDKNSLIEELDlhnyELNHDLKTYEIKEKS 210
                                       67788888888888888888888888888888888888888....77777777777762222444444666666666 PP

                        TPR_MLP1_2  76 lkaeaesakaeleeseesweeqkeelekels 106
                                       l++  e ++a++++ +  +e+ +  le++++
  gi|518651672|ref|YP_008141192.1| 211 LRETMELLNAANDNFKGLLEKYRFLLENNIT 241
                                       7777777777766666666666666666665 PP

>> DUF5344  Family of unknown function (DUF5344)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   8.6         2   3.8e+02      10      77 ..      10      74 ..       2      84 .. 0.64
   2 ?    3.4   7.5      0.57   1.1e+02       7      55 ..      56     109 ..      50     127 .. 0.70
   3 ?    5.6   2.8      0.13        24       9      42 ..     132     165 ..     128     182 .. 0.82
   4 ?   12.5   2.5   0.00088      0.17      16      71 ..     188     244 ..     170     250 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 2
                           DUF5344 10 eVeqkLselktaaeelktsipetisgknsld.vvekineleeeleellkaYktlllknvedtesaVdsl 77
                                      + +++L+ +   +e+++++++e +s+ n+l+  +    ++e++l+++ +++k+ ll+  e+     +s+
  gi|518651672|ref|YP_008141192.1| 10 DFQEQLQTMHANLEAVQAENQELTSHINELNnKIAAGLKREDDLKNQNESLKSSLLDTNEAL----ESF 74
                                      44667777777777777777777777777752466667777777777777777666544444....444 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.57
                           DUF5344   7 nqaeVeqkLselktaaeelktsipe.....tisgknsldvvekineleeeleel 55 
                                       + +++++ L + ++a+e++k++++      + + +   ++veki+ leeele+l
  gi|518651672|ref|YP_008141192.1|  56 QNESLKSSLLDTNEALESFKKQNEDiqhelEDKNTRLESTVEKIETLEEELEKL 109
                                       5678888899999999999766543111112334445789************98 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.13
                           DUF5344   9 aeVeqkLselktaaeelktsipetisgknsldvv 42 
                                       +e++qk+++l++ ++el+++ ++  +  n+l+ +
  gi|518651672|ref|YP_008141192.1| 132 SELKQKIDRLQKYISELESKDSQSQKAINELSST 165
                                       7899**************9999999998888765 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00088
                           DUF5344  16 selktaaeelktsipet.isgknsldvvekineleeeleellkaYktlllknvedte 71 
                                       +el  +  el+ ++++  i++k+  +++e +n  +++++ ll++Y  ll++n++  +
  gi|518651672|ref|YP_008141192.1| 188 EELDLHNYELNHDLKTYeIKEKSLRETMELLNAANDNFKGLLEKYRFLLENNITVKK 244
                                       555555555665555541566666689*************************98655 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 ?    9.4  14.1    0.0057       1.1      28     127 ..       6     108 ..       3     112 .. 0.75
   2 ?    6.3  19.6     0.051       9.9      26     129 ..      74     184 ..      69     193 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0057
                                       CCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH...CCCHHHHHHHCCH CS
                         Fib_alpha  28 kyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskelee...eilrlketidaqe 101
                                       k+ +d++++l++++ +le ++ +++e  ++++e+++++++  k ++d +n  ++++++l +     + +k++  +  
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDtneALESFKKQNEDIQ 82 
                                       7889**************************************99999877777777777630003333444433333 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 snirvLqnvlesneqkiqkLeqdidq 127
                                       ++++   + les ++ki+ Le++ ++
  gi|518651672|ref|YP_008141192.1|  83 HELEDKNTRLESTVEKIETLEEELEK 108
                                       55555667788888888888887665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.051
                                       CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHH..... CS
                         Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketi..... 97 
                                       ++k+++d++++le+ + +le+  ++ ++ ee  +++k    + q+  ++++   +k+s+el+++i rl++ i     
  gi|518651672|ref|YP_008141192.1|  74 FKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYIseles 150
                                       56788888888888777777777777777777777777777777777766777777777777777777777722222 PP

                                       .HCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  98 .daqe.snirvLqnvlesneqkiqkLeqdidqke 129
                                        d+q  + i++L ++ ++++ +i+ L+++i+ k+
  gi|518651672|ref|YP_008141192.1| 151 kDSQSqKAINELSSTGREQSAQIKSLQKEIKDKN 184
                                       2234436799999999999999999999998775 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8  15.3     0.077        15     129     239 ..       9     126 ..       2     131 .. 0.46
   2 ?   11.2   9.8   0.00085      0.17     115     250 ..     111     235 ..     105     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.077
                           DUF4407 129 aaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk......gtgttgvaGkgpaakekkaqldaaqael 199
                                       ++++++l+++ a+++a qae +++ +++++l+++ ++ l+ +        +  +      +a ++ k+q++++q el
  gi|518651672|ref|YP_008141192.1|   9 EDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDdlknqnESLKSSLLDTNEALESFKKQNEDIQHEL 85 
                                       24556666666666666666666666666666666555555444433332222223333344444555555555555 PP

                           DUF4407 200 aelkakld.atarlaalraelaeleaerakeraasqaaaaa 239
                                       ++ +++l+   +++++l++el++l+ e  k++++ + ++a+
  gi|518651672|ref|YP_008141192.1|  86 EDKNTRLEsTVEKIETLEEELEKLKIENGKIQEDMENTTAS 126
                                       55555554544455555555555555555555444444333 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00085
                           DUF4407 115 eqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaq 191
                                       + + +++e  e+++a++++  +el+++i++lq+ i+++e++ ++ +++ + el+   +tg +    + +  k+ +++
  gi|518651672|ref|YP_008141192.1| 111 IENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAIN-ELS---STGRE----QSAQIKSLQKE 179
                                       55667777778888888888899999999999999999988777776666.777...45633....36778888999 PP

                           DUF4407 192 ldaaqaelaelkakldatarlaalraelaeleaerakeraasqaaaaaddGllarleal 250
                                       +++++  ++el+     + +l+++ ++++  e+ ++++ +  +aa+++++Gll++++ l
  gi|518651672|ref|YP_008141192.1| 180 IKDKNSLIEELDLH---NYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLEKYRFL 235
                                       99999999998888...88999********************************99875 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.4     0.014       2.8      52      85 ..       3      36 ..       1      45 [. 0.87

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.014
                      Syntaxin-6_N 52 siewdledLeetvriveknpskfkidekelsrrr 85
                                      +++++led++e  +++ +n + ++ +++el+++ 
  gi|518651672|ref|YP_008141192.1|  3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHI 36
                                      5789***************999*******99985 PP

>> Syntaxin  Syntaxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   8.2      0.21        41       1      79 [.       8      85 ..       5      95 .. 0.74
   2 ?   12.0  16.2   0.00064      0.13      10     102 ..      84     182 ..      71     185 .. 0.77
   3 ?   10.6   9.1    0.0016      0.32      10     113 ..     133     238 ..     128     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.21
                          Syntaxin  1 leeffkeveeikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks 79
                                      le+f ++ ++++ ++e+++ e ++l+++ +e+ ++  a  +   ++++++ ++ k +  + ++ Le+++k+n++ +++ 
  gi|518651672|ref|YP_008141192.1|  8 LEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLK-REDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHEL 85
                                      57788888888888888888888888888888777777666.7778888888888888888888888888888766544 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00064
                          Syntaxin  10 eikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks....... 79 
                                       e++++ + le+ v+k++  +ee+ +   ++ + ++++me+++++ +k + ++k+++++L+k + e e+k        
  gi|518651672|ref|YP_008141192.1|  84 ELEDKNTRLESTVEKIETLEEELEKLKIENGK-IQEDMENTTASSQKISSELKQKIDRLQKYISELESKDsqsqkai 159
                                       33445567889999999988888877777776.99999999999999999999999999998888777666666778 PP

                          Syntaxin  80 gegsavdRirksqtaaLrkklke 102
                                       +e s++ R +++q ++L+k++k+
  gi|518651672|ref|YP_008141192.1| 160 NELSSTGREQSAQIKSLQKEIKD 182
                                       999****************9997 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.0016
                          Syntaxin  10 eikkeiekleeevkklkkqneesktstraksvklkkrmesdikeikkraesvkarLeaLdksnkenekks...gegs 83 
                                       e+k++i+ l++ +++l+++ ++s ++ ++ s+ + ++ +++ik+ +k+ ++ ++ +e+Ld +n e ++     + ++
  gi|518651672|ref|YP_008141192.1| 133 ELKQKIDRLQKYISELESKDSQSQKAINELSS-TGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLktyEIKE 208
                                       789*****************************.777779*********************99998876655667888 PP

                          Syntaxin  84 avdRirksqtaaLrkklkevmteynelrek 113
                                        + R  + + +a + ++k ++++y+ l e+
  gi|518651672|ref|YP_008141192.1| 209 KSLRETMELLNAANDNFKGLLEKYRFLLEN 238
                                       89999999999999**********977665 PP

>> kleA_kleC  Uncharacterized KorC regulated protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.1       2.9   5.6e+02      12      43 ..       8      39 ..       6      41 .. 0.85
   2 ?   12.2   1.1   0.00092      0.18      19      61 ..      36      78 ..      27      93 .. 0.82
   3 ?    0.2   0.1       4.9   9.5e+02      24      46 ..     122     144 ..      99     161 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 2.9
                         kleA_kleC 12 LpevatdlvarRdkiAaklaeAeeLvrqaeeL 43
                                      L++ +++l+    ++ a +ae +eL+ +++eL
  gi|518651672|ref|YP_008141192.1|  8 LEDFQEQLQTMHANLEAVQAENQELTSHINEL 39
                                      777788888888999999*******9999988 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00092
                         kleA_kleC 19 lvarRdkiAaklaeAeeLvrqaeeLRakvyeesaaLedrakkr 61
                                      +    +kiAa l++ ++L+ q e L+   +  + aLe   k++
  gi|518651672|ref|YP_008141192.1| 36 INELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQN 78
                                      556679**************************99999877764 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 4.9
                         kleA_kleC  24 dkiAaklaeAeeLvrqaeeLRak 46 
                                       +  A  ++   eL++++++L + 
  gi|518651672|ref|YP_008141192.1| 122 NTTASSQKISSELKQKIDRLQKY 144
                                       55667777778888888887654 PP

>> gpW  gpW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.1     0.058        11      36      60 ..      25      49 ..      12      51 .. 0.86
   2 ?    2.5   0.1      0.71   1.4e+02      42      53 ..     140     151 ..     132     158 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.058
                                      EGGGHHHHHHHHHHHHHHTTST-SS CS
                               gpW 36 taasvtdLkkYiaeLekqlgitkrR 60
                                       +a  ++L++ i+eL++++++  +R
  gi|518651672|ref|YP_008141192.1| 25 VQAENQELTSHINELNNKIAAGLKR 49
                                      578999*************887666 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.71
                                       HHHHHHHHHHHH CS
                               gpW  42 dLkkYiaeLekq 53 
                                        L+kYi eLe +
  gi|518651672|ref|YP_008141192.1| 140 RLQKYISELESK 151
                                       6999*****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 ?    8.8  11.9    0.0095       1.9      29     104 ..      13      85 ..       1      89 [. 0.78
   2 ?    2.1  10.4       1.2   2.3e+02      41     102 ..      81     139 ..      76     144 .. 0.58
   3 ?    5.9  12.9     0.077        15      24      99 ..     138     217 ..     128     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0095
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                      Seryl_tRNA_N  29 delleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklllai 104
                                       ++l  + ++ +++q+e +el +  Nel+++I+   k++   ++l+++ ++lk  l +++++l+  +++ e++  ++
  gi|518651672|ref|YP_008141192.1|  13 EQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKRE---DDLKNQNESLKSSLLDTNEALESFKKQNEDIQHEL 85 
                                       55666777788888888888888888888888888764...78999999999999999999999999988887655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHC CS
                      Seryl_tRNA_N  41 lqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleaeleklll 102
                                       +q+ele+ +++  +  ++I+ +    e+ e+l+ e  +++e++++++a  +++++el++++ 
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRLESTVEKIETLE---EELEKLKIENGKIQEDMENTTASSQKISSELKQKID 139
                                       55555555555555555555554...456666667777777777777777777766666554 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.077
                                       CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCH....HHHHHHHHHHHHHHHHHHH CS
                      Seryl_tRNA_N  24 dkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevk....elkeelkaleaelkeleae 96 
                                        + + + + el++k  + q++++el +   e s++I+++ k+ +d+++li+e +    el+ +lk++e ++k l++ 
  gi|518651672|ref|YP_008141192.1| 138 IDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDlhnyELNHDLKTYEIKEKSLRET 214
                                       44555667889999999999999999999999999999999988888888887655558999999999999999988 PP

                                       HHH CS
                      Seryl_tRNA_N  97 lek 99 
                                       +e 
  gi|518651672|ref|YP_008141192.1| 215 MEL 217
                                       875 PP

>> Rootletin  Ciliary rootlet component, centrosome cohesion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5  27.4   0.00056      0.11       1     145 [.       5     154 ..       5     162 .. 0.81
   2 ?   -0.2   4.7       4.4   8.5e+02       7      54 ..     162     209 ..     145     240 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00056
                         Rootletin   1 rrrlqayqeaqqrqaqLvskLqaKvlqYkkrcseleqrlle.....ktselektkltlllssareleeeesadleea 72 
                                       +++l+ +qe+ q   + +++ qa  ++   +++el++++++     ++ + ++++l+ +l  ++e  e+ +++ e +
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAglkreDDLKNQNESLKSSLLDTNEALESFKKQNEDI 81 
                                       567888888877777777889999999999999999999987776655555555555555666777777777789** PP

                         Rootletin  73 lakLeeErqrseklaqvnslLreqleearqaneaLtedlqkltkdwerlreeleqkekewreeeeafneylss 145
                                        ++Le+   r e+ ++  ++L e+le+ + +n +++ed++++t+  +++  el+qk +++++   ++++  s+
  gi|518651672|ref|YP_008141192.1|  82 QHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQ 154
                                       **********************************************************999877666665555 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 4.4
                         Rootletin   7 yqeaqqrqaqLvskLqaKvlqYkkrcseleqrllektselektkltll 54 
                                        ++  ++q++ +++Lq+ +++    ++el+ +  e + +l++ +++++
  gi|518651672|ref|YP_008141192.1| 162 LSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEK 209
                                       344445566666666666666666666666555553333333332222 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  16.6    0.0093       1.8      70     170 ..       8     108 ..       3     124 .. 0.87
   2 ?    5.3  14.6     0.071        14      92     192 ..     122     221 ..     108     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0093
                               LXG  70 ieqyeefLkkikealesvepssngfidedf..Leqelenglkkakevteelkdeinkilasvsdivslpelddsevk 144
                                       +e+++e+L+++ ++le+v+ ++n ++ +++  L++ ++ gl k++ +++++ +++++ l ++++ ++  + + ++++
  gi|518651672|ref|YP_008141192.1|   8 LEDFQEQLQTMHANLEAVQ-AENQELTSHIneLNNKIAAGL-KREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQ 82 
                                       799**************87.889999887533666666665.567899***************************** PP

                               LXG 145 dslqkakkkvqetiekledfdqeqks 170
                                       ++l++ +  ++ t+ek+e++++e+  
  gi|518651672|ref|YP_008141192.1|  83 HELEDKNTRLESTVEKIETLEEELEK 108
                                       *********************99865 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.071
                               LXG  92 ngfidedfLeqelenglkkakevteelkdeinkilasvsdivslpelddsevkdslqkakkkvqetiekledfdqeq 168
                                       n+  +++++ +el+++++++++ ++el+++  +  + ++++ s+++ ++ + ++slqk +k  +  ie l+  ++e+
  gi|518651672|ref|YP_008141192.1| 122 NTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQ-IKSLQKEIKDKNSLIEELDLHNYEL 197
                                       555567777889999999999999999998888888888886666666666.889********************** PP

                               LXG 169 ksalanlesdlkalktyvseLeem 192
                                       +++l++ e + k+l  +++ L+++
  gi|518651672|ref|YP_008141192.1| 198 NHDLKTYEIKEKSLRETMELLNAA 221
                                       ***********9999999988876 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 ?    8.9   6.5    0.0079       1.5      13      66 ..       8      61 ..       2      71 .. 0.81
   2 ?    4.3   4.0      0.22        43      25      70 ..      62     107 ..      52     113 .. 0.69
   3 ?    8.0   6.0     0.015         3       8      72 ..     119     183 ..     116     186 .. 0.92
   4 ?    2.2   2.0      0.97   1.9e+02      22      47 ..     168     193 ..     156     222 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0079
                     TolA_bind_tri 13 learsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerl 66
                                      le  ++ l  ++ +lea q+e +eL  +i el++++   ++r  dl ++ +++ 
  gi|518651672|ref|YP_008141192.1|  8 LEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLK 61
                                      45556778899999*******************999999999988877666655 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.22
                     TolA_bind_tri  25 qqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkle 70 
                                       + l + ++ l + + q+E+ q++le+ ++r     ++++++ ++le
  gi|518651672|ref|YP_008141192.1|  62 SSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELE 107
                                       4455566666677778888888888888887777777777766666 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.015
                     TolA_bind_tri   8 rLErilearsqlllelqqqlealqqelreLRGqiEelqyqleqleerQrdlYldlDerlrkleag 72 
                                        +E+  +++++   el q++++lq+ ++eL  +  + q  +++l    r++  ++ ++ ++++ +
  gi|518651672|ref|YP_008141192.1| 119 DMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDK 183
                                       5899999********************************************99999999988765 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.97
                     TolA_bind_tri  22 elqqqlealqqelreLRGqiEelqyq 47 
                                       e+  q+++lq+e+++ +  iEel  +
  gi|518651672|ref|YP_008141192.1| 168 EQSAQIKSLQKEIKDKNSLIEELDLH 193
                                       55566666666666555555544322 PP

>> MAD  Mitotic checkpoint protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0  46.0     0.016       3.2       6     228 ..       3     230 ..       1     238 [. 0.73

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                               MAD   6 eskaaleqlknelkqkelehkrarielekkasalkrqleeesdrnqelqkrikllekreeekeealreqiElarlkk 82 
                                       + k +le+ +++l+ +  + +  ++e   +  +l   ++e  ++  + +kr   l+++ e  +++l ++ E   + k
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAEN--Q--ELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFK 75 
                                       556677777777766665554433333..3..344455555555555556666666666666666667777778888 PP

                               MAD  83 knlealnkkekekesklaearevisalknelaelkrqiekqelelsekesele....elqerldllkkklseleqli 155
                                       k++e +++++++k+++l++  e i++l++el++lk +  k + ++++++   +    el+++ d l+k +sele + 
  gi|518651672|ref|YP_008141192.1|  76 KQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQkissELKQKIDRLQKYISELESKD 152
                                       99999999999999999999999999999999999988888877777766655122257888888899999999999 PP

                               MAD 156 qqlekkqkela....eaeqrikeLefeiqsqeddslivknsksel.aripelekelerlreenkklnelkenkelLk 227
                                       +q +k+ +el+    e+ ++ik L+ ei+  ++  +++   + el   + + e + + lre  + ln  ++n + L 
  gi|518651672|ref|YP_008141192.1| 153 SQSQKAINELSstgrEQSAQIKSLQKEIKDKNSLIEELDLHNYELnHDLKTYEIKEKSLRETMELLNAANDNFKGLL 229
                                       77777766654222277889999999999999999999999999988999999999999999999999999965444 PP

                               MAD 228 E 228
                                       E
  gi|518651672|ref|YP_008141192.1| 230 E 230
                                       4 PP

>> DUF5082  Domain of unknown function (DUF5082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  13.1      0.14        27      16     108 ..       5     100 ..       1     102 [. 0.64
   2 ?    1.7   7.6       1.5     3e+02       9      50 ..      89     130 ..      75     134 .. 0.59
   3 ?   13.7  11.4   0.00029     0.057       1      63 [.     134     200 ..     134     251 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.14
                           DUF5082  16 rseiaaleekIerLkeaktklsdekeslkqkkkklekplnsse....sWkGkeennydgirsnlessyqtyvdklde 88 
                                       ++++++ +e+++   +  +++++e+++l +++++l+++++        +k+ ++++ ++ + ++ ++ + ++++ ++
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLkredDLKN-QNESLKSSLLDTNEALESFKKQNED 80 
                                       445555555555555555555555555555555555555544322213433.3445566666*************** PP

                           DUF5082  89 lidaieeEIerLenqiseaq 108
                                       ++ ++e++ +rLe+++++ +
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRLESTVEKIE 100
                                       **************998766 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 1.5
                           DUF5082   9 qaqiaelrseiaaleekIerLkeaktklsdekeslkqkkkkl 50 
                                       + + +++ ++i++lee +e+Lk    k+++  e++ ++ +k+
  gi|518651672|ref|YP_008141192.1|  89 NTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKI 130
                                       444555666666666666666666666666666665555554 PP

  == domain 3  score: 13.7 bits;  conditional E-value: 0.00029
                           DUF5082   1 lktkisklqaqiaelrseiaaleekIerLk....eaktklsdekeslkqkkkklekplnssesWkGk 63 
                                       lk+ki +lq+ i+el+s+ ++ ++ I +L     e + ++++ ++++k+k++ +e+ ++++ +++  
  gi|518651672|ref|YP_008141192.1| 134 LKQKIDRLQKYISELESKDSQSQKAINELSstgrEQSAQIKSLQKEIKDKNSLIEELDLHNYELNHD 200
                                       799**************************9888788999********************99988765 PP

>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.8   0.00044     0.087      17      53 ..       6      41 ..       1      48 [. 0.88
   2 ?    5.1   0.4     0.095        18      20      45 ..      37      62 ..      35      74 .. 0.70
   3 ?    1.4   3.7       1.4   2.7e+02      20      50 ..      58      88 ..      51      98 .. 0.74
   4 ?    5.6   2.8     0.067        13      20      50 ..      93     123 ..      88     130 .. 0.84
   5 ?    5.9   3.4     0.055        11      18      51 ..     130     163 ..     120     168 .. 0.79
   6 ?    6.7   2.1     0.032       6.3      11      50 ..     165     204 ..     162     214 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00044
                                      XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XXX CS
                             DivIC 17 laykqlkqeiaalqaelaklkaeneeLeaevkdLksd 53
                                       ++ + ++++++  a+l++++aen+eL++ +++L ++
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINEL-NN 41
                                      678899****************************.44 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.095
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLea 45
                                       +l+++iaa  +  + lk++ne+L++
  gi|518651672|ref|YP_008141192.1| 37 NELNNKIAAGLKREDDLKNQNESLKS 62
                                      56777777777777777777777776 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 1.4
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC 20 kqlkqeiaalqaelaklkaeneeLeaevkdL 50
                                       +lk+ + + ++ l++ k++ne+ ++e++d 
  gi|518651672|ref|YP_008141192.1| 58 ESLKSSLLDTNEALESFKKQNEDIQHELEDK 88
                                      5677777788888888888888888888764 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.067
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  20 kqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                        ++ ++i++l++el+klk en + ++  ++ 
  gi|518651672|ref|YP_008141192.1|  93 ESTVEKIETLEEELEKLKIENGKIQEDMENT 123
                                       566689***************9999988875 PP

  == domain 5  score: 5.9 bits;  conditional E-value: 0.055
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-X CS
                             DivIC  18 aykqlkqeiaalqaelaklkaeneeLeaevkdLk 51 
                                         ++lkq+i++lq+ + +l  +  + ++ +++L+
  gi|518651672|ref|YP_008141192.1| 130 ISSELKQKIDRLQKYISELESKDSQSQKAINELS 163
                                       5578899999999999999999999999999885 PP

  == domain 6  score: 6.7 bits;  conditional E-value: 0.032
                                       XXXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC- CS
                             DivIC  11 fgkkgllaykqlkqeiaalqaelaklkaeneeLeaevkdL 50 
                                       +g  +  ++k+l++ei++++  +++l   n eL++ +k +
  gi|518651672|ref|YP_008141192.1| 165 TGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTY 204
                                       6777888899999999999999999999999998877765 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1  16.4     0.025       4.9      18     127 ..       5     108 ..       2     113 .. 0.52
   2 ?    8.3  21.6    0.0055       1.1      22     126 ..      97     198 ..      92     251 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.025
                             Atg14  18 rngperlyelrerlaklksekeslkkkiekalegkeeaeqledkiknkkakleelksliadlrerlqelkdklsqlk 94 
                                       ++   +l++ +e+l+ + +  e+++ + +++ ++ +   +l++ki    ++ ++lk++ ++l++ l   ++ l++ k
  gi|518651672|ref|YP_008141192.1|   5 KK---QLEDFQEQLQTMHANLEAVQAENQELTSHIN---ELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFK 75 
                                       45...6666666666666666666666555555444...55555555555555555555555555555555555555 PP

                             Atg14  95 keieekkkklaklsdklkkRrsdleslqnelee 127
                                       k++e+ +++l+ ++  l    +++e l++ele+
  gi|518651672|ref|YP_008141192.1|  76 KQNEDIQHELEDKNTRLESTVEKIETLEEELEK 108
                                       555555555555555555555555555555444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0055
                             Atg14  22 erlyelrerlaklksekeslkkkiekalegke.eaeqledkiknkkakleelksliadlrerlqelkdklsqlkkei 97 
                                       e++++l e+l klk+e+  +++ +e   ++ +  +++l++ki++++++++el s+ +++++ ++el+ + +++ ++i
  gi|518651672|ref|YP_008141192.1|  97 EKIETLEEELEKLKIENGKIQEDMENTTASSQkISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQI 173
                                       68999************99999999877777768999999***************************9999999999 PP

                             Atg14  98 eekkkklaklsdklkkRrsdleslqnele 126
                                       +  +k+++ +++ +    ++l+++++el+
  gi|518651672|ref|YP_008141192.1| 174 KSLQKEIKDKNSLI----EELDLHNYELN 198
                                       99999999999999....46666666654 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 ?    9.4  21.0    0.0035      0.68      35     142 ..       4     112 ..       2     123 .. 0.70
   2 ?    5.0  12.6     0.079        15      43     111 ..     121     190 ..     112     199 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0035
                        MscS_porin  35 skkkaeelqkaiddaPkelrelqqelealqkkkeeaskeilakls.leeLeqrllqtssqlqelqeqlaqlnsqlve 110
                                        kk++e++q+++++  + l+++q+e ++l+   +e +++i a l+  ++L ++ ++ +s l++++e+l ++++q   
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKrEDDLKNQNESLKSSLLDTNEALESFKKQNED 80 
                                       56777777777777777777777777777777777777777777623468888888888888888888888888888 PP

                        MscS_porin 111 lqtrperaqqqltearqrlqeirnrLnstaaa 142
                                       +q+ +e   ++l +  +++++++ +L++++ +
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRLESTVEKIETLEEELEKLKIE 112
                                       88888888888888888888877777666444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.079
                        MscS_porin  43 qkaiddaPkelrelqqeleal.qkkkeeaskeilaklsleeLeqrllqtssqlqelqeqlaqlnsqlvel 111
                                       + + ++++k + el+q++++l +  +e +sk++ ++  ++eL +   ++s+q  +lq+++++ ns++ el
  gi|518651672|ref|YP_008141192.1| 121 ENTTASSQKISSELKQKIDRLqKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEEL 190
                                       5556667777888888888885555677888888888899999999999999999999999999988876 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   8.1    0.0039      0.76      24      82 ..      12      77 ..       5      82 .. 0.74
   2 ?   -0.2   5.7       5.1   9.9e+02      41      69 ..     187     215 ..     153     221 .. 0.67
   3 ?    3.4   3.2      0.39        76      41      80 ..     187     226 ..     171     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0039
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCTXX.......XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA 24 deFLdqvakdyeallkeneelkekvkeleeklk.......eykeleetLkktlvvaqetaeevkan 82
                                      +e L+ +  ++ea+  en+el++ ++el++k++       + k+++e+Lk +l+ + e+ e  k++
  gi|518651672|ref|YP_008141192.1| 12 QEQLQTMHANLEAVQAENQELTSHINELNNKIAaglkredDLKNQNESLKSSLLDTNEALESFKKQ 77
                                      566888888999999999999999999999986222222257777788888888888888888876 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 5.1
                                       HHHHHHHHHCCCCTXXXXXXXXXXXXXXX CS
                            DivIVA  41 neelkekvkeleeklkeykeleetLkktl 69 
                                        eel     el+++lk y+  e++L++t+
  gi|518651672|ref|YP_008141192.1| 187 IEELDLHNYELNHDLKTYEIKEKSLRETM 215
                                       34455555677778888888888888876 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.39
                                       HHHHHHHHHCCCCTXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            DivIVA  41 neelkekvkeleeklkeykeleetLkktlvvaqetaeevk 80 
                                        eel     el+++lk y+  e++L++t+ +   + ++ k
  gi|518651672|ref|YP_008141192.1| 187 IEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFK 226
                                       35666667799999**************977666666655 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   2.7      0.14        27      18      58 ..       6      43 ..       2      57 .. 0.66
   2 ?    1.3   6.3       2.5   4.9e+02      20      50 ..      71      98 ..      31     126 .. 0.54
   3 ?    1.2   6.8       2.7   5.3e+02      23      57 ..     116     151 ..      78     162 .. 0.68
   4 ?   10.0   3.6    0.0049      0.95      15      64 ..     133     186 ..     127     219 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.14
                           NPV_P10 18 dkVdalqqqvddvqenlpdvtelnekLdaqsaqLaeletkv 58
                                      ++++  q+q++ +++nl+ v+  n+   +++  ++el++k+
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQ---ELTSHINELNNKI 43
                                      5566667777777777777664443...4455555555554 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 2.5
                           NPV_P10 20 VdalqqqvddvqenlpdvtelnekLdaqsaq 50
                                      +++ ++q +d+q++l+d    n++L++  ++
  gi|518651672|ref|YP_008141192.1| 71 LESFKKQNEDIQHELED---KNTRLESTVEK 98
                                      23333333333333333...23333333333 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 2.7
                           NPV_P10  23 lqqqvddvqenlpdvt.elnekLdaqsaqLaeletk 57 
                                       +q+ +++ ++ +++++ el++k+d++++ + ele+k
  gi|518651672|ref|YP_008141192.1| 116 IQEDMENTTASSQKISsELKQKIDRLQKYISELESK 151
                                       566666666666665336777777777777777665 PP

  == domain 4  score: 10.0 bits;  conditional E-value: 0.0049
                           NPV_P10  15 avddkVdalqqqvddvqen....lpdvtelnekLdaqsaqLaeletkvenIqdi 64 
                                       ++++k+d lq+ + +++++     + ++el++   +qsaq+++l++++++ +++
  gi|518651672|ref|YP_008141192.1| 133 ELKQKIDRLQKYISELESKdsqsQKAINELSSTGREQSAQIKSLQKEIKDKNSL 186
                                       799**********99976422225678899999999**********99986665 PP

>> Tropomyosin  Tropomyosin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  15.6     0.014       2.7       4      97 ..       2      99 ..       1     100 [. 0.83
   2 ?    3.8  11.0      0.16        31       4     105 ..     128     226 ..     125     233 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.014
                       Tropomyosin  4 kqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriq...lleeelerteerleealekLeeaeka.adeser 78
                                       +++++l++++e+l++++++le+ +++ ++  +    ln++i    + e++l++ +e l+++l   +ea ++  +++e 
  gi|518651672|ref|YP_008141192.1|  2 VNAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAaglKREDDLKNQNESLKSSLLDTNEALESfKKQNED 80
                                      67899*************************************83335799********999988777776551455688 PP

                       Tropomyosin 79 arKvlEnrelkdeekleel 97
                                      +   lE+++ + e  +e+ 
  gi|518651672|ref|YP_008141192.1| 81 IQHELEDKNTRLESTVEKI 99
                                      8899999988877777665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.16
                       Tropomyosin   4 kqveeeldeaeerlekakkkleeaekkaekaeaEvaalnrriqlleeelerteerleealekLeeaekaadeserar 80 
                                       +++  el +  +rl+k  ++le+++ + +ka +E ++  r    + +++++ +++++++ + +ee+  ++ e +  +
  gi|518651672|ref|YP_008141192.1| 128 QKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGRE---QSAQIKSLQKEIKDKNSLIEELDLHNYELNHDL 201
                                       67888999999***********************9999986...55778888999999999999************* PP

                       Tropomyosin  81 KvlEnrelkdeekleeleaqlkeak 105
                                       K+ E +e +  e +e l+a+ ++ k
  gi|518651672|ref|YP_008141192.1| 202 KTYEIKEKSLRETMELLNAANDNFK 226
                                       **************99998877665 PP

>> CEP63  Centrosomal protein of 63 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3  11.8      0.67   1.3e+02      47     130 ..       4      92 ..       1      96 [. 0.42
   2 ?   10.9  25.2    0.0015       0.3      30     185 ..      85     237 ..      77     247 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.67
                             CEP63  47 arnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsk...lkrsyekLqrkqlkearek..eakskee 118
                                       a+++l+  ++  ++++ +le +++e+qel+++ ++  +k+ + l++   lk+  e L+   l  +++    +k++e+
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKReddLKNQNESLKSSLLDTNEALesFKKQNED 80 
                                       44555555555555555555555555555555555444444444322224555555544444333322112344444 PP

                             CEP63 119 drvelsrlnskl 130
                                        + el+  n++l
  gi|518651672|ref|YP_008141192.1|  81 IQHELEDKNTRL 92 
                                       444444444444 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0015
                             CEP63  30 traletrlkireeeLasarnaldekhkEvgllrqqleelekekqelvakyeqqlqklreelsklkrsyekLqrkqlk 106
                                        +  +trl+++ e ++++ + l++ + E g++++ +e++ ++ q + ++ +q++++l++ +s+l+    + q k + 
  gi|518651672|ref|YP_008141192.1|  85 LEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQ-KAIN 160
                                       445578899999999999999999999999999999999999999999999999999999999976544433.3344 PP

                             CEP63 107 earekeakskeedrvelsrlnskleefrqkslewekqrlqyqkqvasleaqrkaLaekleliqs..aaykvqlekrk 181
                                       e     +   +e+  +++ l++++++ ++   e + ++    ++++++e + k+L e +el+++    +k  lek +
  gi|518651672|ref|YP_008141192.1| 161 EL----SSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAanDNFKGLLEKYR 233
                                       44....467899999***********************************************996566777777766 PP

                             CEP63 182 qkLe 185
                                         Le
  gi|518651672|ref|YP_008141192.1| 234 FLLE 237
                                       6666 PP

>> DUF4472  Domain of unknown function (DUF4472)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.8     0.025       4.8      46     106 ..       3      63 ..       1      64 [. 0.90
   2 ?    9.9  11.6    0.0062       1.2      29     107 .]      56     134 ..      52     134 .. 0.95
   3 ?   11.1   8.2    0.0025      0.49      15      81 ..     109     182 ..     109     191 .. 0.83
   4 ?    2.7   1.3         1     2e+02      22      94 ..     186     247 ..     181     258 .. 0.44

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.025
                           DUF4472  46 elelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsle 106
                                       + + + e  +e+ q ++++l+++++e++el+     l++++ a  k  ++ k++++ l++ 
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSS 63 
                                       55667788999*********************************************99876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0062
                           DUF4472  29 ekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefekekkkqqelsl 105
                                       ++  lk+ +l  ++ + +++ ++e  ++e ++ ++rl+ + e+ + leee+  lk +  ++++++e+ ++ +q++s+
  gi|518651672|ref|YP_008141192.1|  56 QNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISS 132
                                       55679************************************************************************ PP

                           DUF4472 106 eL 107
                                       eL
  gi|518651672|ref|YP_008141192.1| 133 EL 134
                                       98 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.0025
                           DUF4472  15 lqietnklreqheae.......kfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvv 81 
                                       l+ie+ k++e +e++       + elk k+ +l++ + ele+++++ +++i++l++  +e  ++ k+l++e + 
  gi|518651672|ref|YP_008141192.1| 109 LKIENGKIQEDMENTtassqkiSSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKD 182
                                       789999999999875222222257***********************************999999999999765 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 1
                           DUF4472  22 lreqheaekfelknkvlalenrvlelelerekaaeeiqslrerlaeleeekkeleeeyvvlkknyqalekefe 94 
                                       l e+++  ++el+ ++ + e            ++++ ++++e l++++++ k l e+y  l +n ++++k  +
  gi|518651672|ref|YP_008141192.1| 186 LIEELDLHNYELNHDLKTYEI-----------KEKSLRETMELLNAANDNFKGLLEKYRFLLENNITVKKRSM 247
                                       445555555555554433222...........33333444444444444444444444444444444444433 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 ?    7.4  24.6     0.013       2.6     188     303 ..       5     113 ..       2     125 .. 0.71
   2 ?    5.4  17.4     0.056        11     209     314 ..     121     217 ..     114     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.013
                            HMMR_N 188 eaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndei 264
                                        ++l+  q++L++ +a++ +++  +++l  + +e   ++   l+  + l+n  e+l   k  +   +e l++ +++ 
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESL---KSSLLDTNEALESFKKQN 78 
                                       56777778888888888888888887777777777777777777788888888888...888888888888888888 PP

                            HMMR_N 265 esLkssLeekeqelskqvkdlnekckllekekeelvree 303
                                       e+++++Le+k++ l+ +     ek+++le+e+e+l  e+
  gi|518651672|ref|YP_008141192.1|  79 EDIQHELEDKNTRLEST----VEKIETLEEELEKLKIEN 113
                                       8888*******966555....567777777777553333 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.056
                            HMMR_N 209 keklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdl 285
                                       ++   s++k   e k+++++l +yi+el++   q    ++ i++l ++  e+  +i+sL++++++k+      +++l
  gi|518651672|ref|YP_008141192.1| 121 ENTTASSQKISSELKQKIDRLQKYISELESKDSQS---QKAINELSSTGREQSAQIKSLQKEIKDKNS----LIEEL 190
                                       44455666667888889999999999999999888...889999999999999999999999999988....66666 PP

                            HMMR_N 286 nekckllekekeelvreeeekeqtlsaEl 314
                                       + +  +l+++++    e +ek+ + + El
  gi|518651672|ref|YP_008141192.1| 191 DLHNYELNHDLK--TYEIKEKSLRETMEL 217
                                       666666666666..333333333333343 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 ?    5.5   1.8     0.063        12       9      37 ..       4      32 ..       1      35 [. 0.81
   2 ?    6.8  28.5     0.024       4.7      49     186 ..      23     159 ..      22     161 .. 0.92
   3 ?    6.8  13.0     0.025       4.8      56     143 ..     132     218 ..     130     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.063
                        Lebercilin  9 rllkikeLqnelaelqskleelrkEnklL 37
                                       +++++++q++l++++ +le+++ En+ L
  gi|518651672|ref|YP_008141192.1|  4 AKKQLEDFQEQLQTMHANLEAVQAENQEL 32
                                      56778899999999999999999999876 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.024
                        Lebercilin  49 skyedteaeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkk 125
                                       + ++ +++eL + +++ n+ + +  +r  ++++++++l+++l +++++l++ k+++++ ++  edkn    e   +k
  gi|518651672|ref|YP_008141192.1|  23 EAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNT-RLESTVEK 98 
                                       56778999*****************************************************999***8.7788899* PP

                        Lebercilin 126 LeeleakleekeekikeLerkleleeksfrrqlaaekkktkeaqeevkalqeeierlkqkl 186
                                       +e+le++le+ + ++ + +  +e+++ s ++     k+k+  +q+ +++l+++  + ++ +
  gi|518651672|ref|YP_008141192.1|  99 IETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAI 159
                                       *******************************9999999*9999999999998766666555 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.025
                        Lebercilin  56 aeLpqllarhneEvrvlrerlRksqekerelekklkekeaellrlkdklkklkkLsedknLaereeLqkkLeeleak 132
                                       +eL q ++r ++ +  l  +  +sq++ +el++  +e+ a++++l++++k+ ++L e+ +L    eL++ L++ e k
  gi|518651672|ref|YP_008141192.1| 132 SELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDL-HNYELNHDLKTYEIK 207
                                       7899999999999999999999999999999999999999999999999999999999999.677899999988877 PP

                        Lebercilin 133 leekeekikeL 143
                                        ++ +e+++ L
  gi|518651672|ref|YP_008141192.1| 208 EKSLRETMELL 218
                                       66666666555 PP

>> MtrB  Tetrahydromethanopterin S-methyltransferase subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.2       1.6   3.2e+02      39      65 ..      51      77 ..      11      82 .. 0.70
   2 ?    3.6   0.2      0.44        86      24      62 ..      57      95 ..      52     105 .. 0.82
   3 ?    5.1   0.1      0.15        30      32      74 ..     132     176 ..     108     182 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 1.6
                              MtrB 39 dkLekiaddlvnsLdpetallesypgR 65
                                      d+L++  + l +sL  +++ les+++ 
  gi|518651672|ref|YP_008141192.1| 51 DDLKNQNESLKSSLLDTNEALESFKKQ 77
                                      456677777777888888888888765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.44
                              MtrB 24 edvvllsldpvleeidkLekiaddlvnsLdpetallesy 62
                                      ++ +  sl + +e ++  +k  +d+ + L+ +++ les 
  gi|518651672|ref|YP_008141192.1| 57 NESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLEST 95
                                      556778888999999999999999999999999998885 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.15
                              MtrB  32 dpvleeidkLekiaddlvnsLdpetalle..sypgRektlviaGl 74 
                                       ++++++id+L+k+  +l+++ + +++ ++  s  gRe++  i +l
  gi|518651672|ref|YP_008141192.1| 132 SELKQKIDRLQKYISELESKDSQSQKAINelSSTGREQSAQIKSL 176
                                       57899************9887777766653477899999887765 PP

>> DUF1515  Protein of unknown function (DUF1515)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.6     0.083        16       5      74 ..      17      82 ..       8      86 .. 0.78
   2 ?    7.9   1.9     0.016       3.1       5      66 ..     101     162 ..      97     173 .. 0.89
   3 ?   -1.1   0.0       9.7   1.9e+03      19      19 ..     196     196 ..     162     253 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.083
                           DUF1515  5 gvlqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkaditsvkevtedvk 74
                                      +++ +l+ ++ae +el   +++ +++ +a+     ++ d+l ++ ++l++s+   ++ + s k+  ed++
  gi|518651672|ref|YP_008141192.1| 17 TMHANLEAVQAENQELTSHINELNNKIAAG----LKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQ 82
                                      556666666777777777776666666554....6899************************99999986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.016
                           DUF1515   5 gvlqqlgtllaevkelredlkrsedrsdasrakmyrkmdelvervtalegsvvklkaditsv 66 
                                       ++ ++l++l+ e  +++ed+ ++   s+ + +++++k+d l + ++ le+  ++ ++ i ++
  gi|518651672|ref|YP_008141192.1| 101 TLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINEL 162
                                       77888999999999************************************999988888776 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 9.7
                           DUF1515  19 e 19 
                                       e
  gi|518651672|ref|YP_008141192.1| 196 E 196
                                       2 PP

>> Nup54  Nucleoporin complex subunit 54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   7.9     0.012       2.3      55     125 ..       4      73 ..       1      90 [. 0.73
   2 ?    4.2  13.7      0.21        42      35     131 ..      89     188 ..      78     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SS---SSHHHHHHHHHHHHHHHS- CS
                             Nup54  55 isdrleeleqkhqletsvrlekakkrhvelshRllrllrkleilrsrgyaldaeEeelrarletleaqlnd 125
                                        +++le+ + ++ +++++ le ++ +++el++ + +l +k+    +r   l+++ e+l++ l + +++l++
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQ-EQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALES 73 
                                       567777887.7777788888888888888888888888888877788888888888888888877777773 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.21
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.TT-SS...---S CS
                             Nup54  35 akRvkaQqkevaqhrerlkeisdrleeleqkhqletsvrlekakkrhvelshRllrllrkleil.rsrgy...alda 107
                                       + R++   ++++ ++e l++++ +  +++ +   +t++  +k+ ++ ++ + Rl + ++ le   +++++    l+ 
  gi|518651672|ref|YP_008141192.1|  89 NTRLESTVEKIETLEEELEKLKIENGKIQ-EDMENTTASSQKISSELKQKIDRLQKYISELESKdSQSQKainELSS 164
                                       45677777777777777777777777777.77888888889999999999999999999999884333334446677 PP

                                       SHHHHHHHHHHHHHHHS-HHH.HH CS
                             Nup54 108 eEeelrarletleaqlndpaqlkg 131
                                         +e +a++++l+++++d+++l  
  gi|518651672|ref|YP_008141192.1| 165 TGREQSAQIKSLQKEIKDKNSLIE 188
                                       999999***********9988755 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   5.3     0.065        13      40      88 ..       3      51 ..       1      78 [. 0.77
   2 ?    6.2  12.2     0.054        10      31     118 ..      78     162 ..      70     168 .. 0.84
   3 ?    2.5  14.4      0.77   1.5e+02      13      94 ..     146     236 ..     135     259 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.065
                          RasGAP_C 40 nkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlk 88
                                      n +++ e  +e+l+++++ l++++  n+ l s+++++++ i   l+   
  gi|518651672|ref|YP_008141192.1|  3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKRED 51
                                      667888999******************************9998877653 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.054
                          RasGAP_C  31 lneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleqlkkkkgklpfskqyfkkrelk 107
                                        ++I++++  k+++ e++ e +e+lee l++L+  n ++++++e+  a  +++ ++lk+k   +   ++y ++ e+k
  gi|518651672|ref|YP_008141192.1|  78 NEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQK---IDRLQKYISELESK 151
                                       589********************************************************9...45556677777777 PP

                          RasGAP_C 108 ksgklpkfgsy 118
                                       +s++++  + +
  gi|518651672|ref|YP_008141192.1| 152 DSQSQKAINEL 162
                                       77766666555 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.77
                          RasGAP_C  13 keLeelgvisrennyqellneIakdirnkgrlrekrkeElesleetlktLseknnylesqlesYkayienvleql.. 87 
                                        eLe     s++ + q+ +ne+  + r+++ ++++ ++E++  ++ +++L+ +n  l+ +l++Y+   ++ +e++  
  gi|518651672|ref|YP_008141192.1| 146 SELE-----SKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMel 217
                                       4444.....4567789999*********************************************9888888877755 PP

                          RasGAP_C  88 .......kkkkgk.........l 94 
                                                   k         l
  gi|518651672|ref|YP_008141192.1| 218 lnaandnF----KgllekyrflL 236
                                       55543330....23333333331 PP

>> DUF812  Protein of unknown function (DUF812)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   6.4      0.02       3.9     328     382 ..       4      58 ..       1      67 [. 0.75
   2 ?    5.1  33.7     0.044       8.5     246     397 ..      49     198 ..      45     254 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.02
                            DUF812 328 reeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevk 382
                                        +++le+ qeq++++++++e++++e ++l+s+i+++++++ +  +    l+++++
  gi|518651672|ref|YP_008141192.1|   4 AKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNE 58 
                                       4678888899999999999999999999999999988888876666666666554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.044
                            DUF812 246 keklqkrlaeqlrkaalkseeaessasksksdlaellsefseksetdslktkgsrfthaeklqftkeelakkaetee 322
                                       +e  +k+ +e+l++++l+++ea +s +k+++d+++ l++ + + e+ ++++ ++  ++ ekl++++    k +e+ e
  gi|518651672|ref|YP_008141192.1|  49 REDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLES-TVEKIETLEEELEKLKIENG---KIQEDME 121
                                       5666788999999999999999999999999999988777444333.33333344445577777777...6788888 PP

                            DUF812 323 elkkkreeeleelqeqieeleskieeleeeikklessikqveeeleeekeeneelekevklkkktlell..pdaeen 397
                                       ++++  ++  +el+++i++l++ i+ele++ ++ ++ i++++++ +e+ ++ + l+ke+k k+ ++e l   + e n
  gi|518651672|ref|YP_008141192.1| 122 NTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELdlHNYELN 198
                                       888888888899******************************************************99932333333 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 ?    5.5  15.5     0.042       8.1     213     302 ..       3      92 ..       1      98 [. 0.91
   2 ?    6.3  21.7     0.025       4.9      96     236 ..     107     243 ..     100     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.042
                            HAP1_N 213 eanqqiaelseelarkleelerqqeeissLlaqivdlqqklkelgveneelkqhLaaskeaqrqLtaELqdlqekya 289
                                       +a++q+++++e+l+    +le  q e ++L+++i +l++k+    + +++lk++ ++ k    + ++ L+ ++++++
  gi|518651672|ref|YP_008141192.1|   3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQNE 79 
                                       6899****************************************9999******99999999999999********* PP

                            HAP1_N 290 evegmLheaqeev 302
                                       +++  L+++ + +
  gi|518651672|ref|YP_008141192.1|  80 DIQHELEDKNTRL 92 
                                       **99999987665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.025
                            HAP1_N  96 svLternekLeeqLesareeiaqlrhelslkddLLqlysdseeeseeeseeseelreeesleslqklvqldlLqekl 172
                                       ++L+ +n k++e++e+++ + ++++ el+ k d Lq y ++ e ++++s++     +e s++ +++  q+  Lq+ +
  gi|518651672|ref|YP_008141192.1| 107 EKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKA---INELSSTGREQSAQIKSLQKEI 180
                                       57888999****************************9999865555544444...4577888999999********* PP

                            HAP1_N 173 reLeeeNekLreeasqLktetdtlEekEqqLvldcveqlseanqqiaelseelarkleelerqq 236
                                       ++ +   e+L     +L+++ +t+E kE+ L  +  e l+ an + + l e+    le++ + +
  gi|518651672|ref|YP_008141192.1| 181 KDKNSLIEELDLHNYELNHDLKTYEIKEKSL-RETMELLNAANDNFKGLLEKYRFLLENNITVK 243
                                       *9999999999999**************998.67889999999999999998877777776655 PP

>> DUF4763  Domain of unknown function (DUF4763)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  16.2      0.04       7.8      45     152 ..      16     121 ..       2     124 .. 0.81
   2 ?    7.0   7.5     0.016       3.1      89     157 ..     117     186 ..     110     197 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.04
                           DUF4763  45 eeeeldLdeiydelekiKqrvlelrskLalnvpecPeidecvdedlelelltseqpeileLqrnnhkLrqqlaelqq 121
                                       +    +L+ +++e +++    +el++k+a  ++   e d   + +  ++ l +++ ++   +++n  ++++l++ + 
  gi|518651672|ref|YP_008141192.1|  16 QTMHANLEAVQAENQELTSHINELNNKIAAGLK--REDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNT 90 
                                       4456789**********************9985..333555554444444555************************ PP

                           DUF4763 122 hlkasrkslkelreslcqekkrlrklqkrln 152
                                       +l+++ ++++ l+e+l ++k    k q+ ++
  gi|518651672|ref|YP_008141192.1|  91 RLESTVEKIETLEEELEKLKIENGKIQEDME 121
                                       *****************99988888887765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.016
                           DUF4763  89 dlelelltseqpei.leLqrnnhkLrqqlaelqqhlkasrkslkelreslcqekkrlrklqkrlneldsf 157
                                       +++ e+ t  +++i  eL+++  +L+  ++el+++  +s+k+++el +  +++  ++++lqk+++  +s 
  gi|518651672|ref|YP_008141192.1| 117 QEDMENTTASSQKIsSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSL 186
                                       66777777778888358**********************************************9977665 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.9      0.05       9.7      95     158 ..      11      77 ..       2      78 .. 0.77
   2 ?    8.9   5.1    0.0053         1     103     155 ..      71     123 ..      66     126 .. 0.89
   3 ?    1.5   8.5      0.99   1.9e+02     110     142 ..     127     159 ..     119     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.05
                     Fzo_mitofusin  95 vqqelsstfarlcqqvdetekeleeeikelekei....ekleevqkkakllrnkaslleseLekfeeq 158
                                        q++l++++a+l+ +v+  ++el+++i+el+++i    ++ ++++++ + l+      ++ Le+f++q
  gi|518651672|ref|YP_008141192.1|  11 FQEQLQTMHANLE-AVQAENQELTSHINELNNKIaaglKREDDLKNQNESLKSSLLDTNEALESFKKQ 77 
                                       5778999999986.699999***********9983222355778888888888888888888888876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0053
                     Fzo_mitofusin 103 farlcqqvdetekeleeeikelekeiekleevqkkakllrnkaslleseLekf 155
                                       ++ +++q +  ++ele++ ++le+++ek+e++++++++l+ +  ++++++e+ 
  gi|518651672|ref|YP_008141192.1|  71 LESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENT 123
                                       56788999999*****************************9999999999875 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.99
                     Fzo_mitofusin 110 vdetekeleeeikelekeiekleevqkkakllr 142
                                       +++ ++el+++i++l+k i++le+  +++++  
  gi|518651672|ref|YP_008141192.1| 127 SQKISSELKQKIDRLQKYISELESKDSQSQKAI 159
                                       444455555555555555555555555544322 PP

>> Spectrin  Spectrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3  11.6      0.14        28      31     105 .]       6      87 ..       1      87 [. 0.65
   2 ?    6.8  12.2     0.047       9.1       2      88 ..      70     151 ..      69     161 .. 0.93
   3 ?    5.9   8.6     0.088        17       7     104 ..     135     237 ..     134     238 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.14
                                       SSHHHHHHHHH....HHHHHHHHHHHHHHHHHHHH.HHHHHH..HHTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  31 kdleevqallk....khkaleaelaaqqervkaln.elaekl..ldeghsaseeieerleelnerWeeLkelaaerk 100
                                       k+le+ q++l+     ++a++ae ++   ++++ln ++a  l  +d  + ++e ++++l + ne+ e+ k++ ++ +
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQtmhaNLEAVQAENQELTSHINELNnKIAAGLkrEDDLKNQNESLKSSLLDTNEALESFKKQNEDIQ 82 
                                       44555555555433355555555555555555555644444421444499999999999999999999999999999 PP

                                       HHHHH CS
                          Spectrin 101 qkLee 105
                                       ++Le+
  gi|518651672|ref|YP_008141192.1|  83 HELED 87 
                                       99985 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.047
                                       HHHHHHHHHHHHHHHHHHHHHHHCCSSCSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHTTHHHH CS
                          Spectrin   2 llqqfaqdadeleeWieekeellssedlgkdleevqallkkhkaleaelaaqqervkalnelaeklldeghsaseei 78 
                                        l+ f+++ ++++  +e+k + l     ++++e++++l+++++ l+ e    qe +++ ++ ++k+ +e +++ +++
  gi|518651672|ref|YP_008141192.1|  70 ALESFKKQNEDIQHELEDKNTRL-----ESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRL 141
                                       57889999999999999999999.....899**************************************9******* PP

                                       HHHHHHHHHH CS
                          Spectrin  79 eerleelner 88 
                                       ++ ++el+++
  gi|518651672|ref|YP_008141192.1| 142 QKYISELESK 151
                                       *****99986 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHHHH.CCSSCSSSHHHHHHHHH.HHHHHHHHHHHHHHHHHHHH....HHHHHHHHTTHTTHHH CS
                          Spectrin   7 aqdadeleeWieekeell.ssedlgkdleevqallk.khkaleaelaaqqervkaln....elaeklldeghsasee 77 
                                       +q++d l++ i+e e +  +s+   ++l+++ + +  + k l++e++++   +++l+    el  +l ++ + +++ 
  gi|518651672|ref|YP_008141192.1| 135 KQKIDRLQKYISELESKDsQSQKAINELSSTGREQSaQIKSLQKEIKDKNSLIEELDlhnyELNHDLKTY-EIKEKS 210
                                       6889999999999987773666669999999999988********************8888889999555.48899* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Spectrin  78 ieerleelnerWeeLkelaaerkqkLe 104
                                       ++e++e ln + ++ k l+++ +  Le
  gi|518651672|ref|YP_008141192.1| 211 LRETMELLNAANDNFKGLLEKYRFLLE 237
                                       ***********9999999998887776 PP

>> BLOC1_2  Biogenesis of lysosome-related organelles complex-1 subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   2.0     0.086        17      35      72 ..       7      41 ..       2      45 .. 0.47
   2 ?    6.5  16.3     0.053        10       9      93 ..      20     108 ..      11     110 .. 0.79
   3 ?    5.9   4.0      0.08        16      38      79 ..     119     150 ..     108     164 .. 0.52
   4 ?    3.7   2.4       0.4        79      50      93 ..     156     199 ..     152     202 .. 0.77
   5 ?    0.0   3.9       5.4   1.1e+03      11      65 ..     176     230 ..     173     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.086
                           BLOC1_2 35 kykklkdvaaslekkleklnekyeelqpylqqidqiek 72
                                      + ++ +++++ ++++le++++   e q++ ++i+++++
  gi|518651672|ref|YP_008141192.1|  7 QLEDFQEQLQTMHANLEAVQA---ENQELTSHINELNN 41
                                      444445555555555555555...44444444444444 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.053
                           BLOC1_2   9 kyleaeleatvedyklLeklNeaas...ekykklkdvaaslekkleklnekyeelqpylqqid.qiekqvteLeeav 81 
                                       + lea  +  +e  +++++lN++ +   ++ ++lk++ +sl+++l ++ne  e+++++ + i+ ++e++ t+Le++v
  gi|518651672|ref|YP_008141192.1|  20 ANLEAVQAENQELTSHINELNNKIAaglKREDDLKNQNESLKSSLLDTNEALESFKKQNEDIQhELEDKNTRLESTV 96 
                                       444444445556667777777776622267789*****************************757************ PP

                           BLOC1_2  82 seLDeyskeLEa 93 
                                       +++++   eLE+
  gi|518651672|ref|YP_008141192.1|  97 EKIETLEEELEK 108
                                       **********94 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.08
                           BLOC1_2  38 klkdvaaslekkleklnekyeelqpylqqidqiekqvteLee 79 
                                       ++++ +as +k +++l++          +id+++k ++eLe+
  gi|518651672|ref|YP_008141192.1| 119 DMENTTASSQKISSELKQ----------KIDRLQKYISELES 150
                                       333333333333333333..........34444444444443 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.4
                           BLOC1_2  50 leklnekyeelqpylqqidqiekqvteLeeavseLDeyskeLEa 93 
                                        +++ne++ + +++  qi+ ++k++++  ++++eLD    eL +
  gi|518651672|ref|YP_008141192.1| 156 QKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNH 199
                                       56677788888899999999999999999999999977666655 PP

  == domain 5  score: 0.0 bits;  conditional E-value: 5.4
                           BLOC1_2  11 leaeleatvedyklLeklNeaasekykklkdvaaslekkleklnekyeelqpylq 65 
                                       l++e++  ++ ++ L   N + ++  k ++ + +sl++++e ln+ +++++ +l+
  gi|518651672|ref|YP_008141192.1| 176 LQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDNFKGLLE 230
                                       5666666666777777778888888888888889999999999999998887776 PP

>> KxDL  Uncharacterized conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   1.2      0.11        22      40      75 ..       5      40 ..       1      47 [. 0.46
   2 ?    9.3   7.1    0.0067       1.3      22      80 ..      50     108 ..      37     109 .. 0.90
   3 ?    7.9   8.2     0.019       3.7       8      73 ..     117     182 ..     110     190 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.11
                              KxDL 40 qerlaklrarfkqgtkllkevkkdLesifkkirslk 75
                                      +++l++++++++     l  v+++ + ++++i+ l+
  gi|518651672|ref|YP_008141192.1|  5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELN 40
                                      344444444444444444444444444444444444 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0067
                              KxDL  22 sgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirslkaklak 80 
                                        + l+++n+ L+     ++e l++++++ ++ ++ l + +  Les+ +ki++l+++l+k
  gi|518651672|ref|YP_008141192.1|  50 EDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEK 108
                                       56799*************************************************99986 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.019
                              KxDL   8 sedldeilalQaqtsgrlnkknreLlelnalsqerlaklrarfkqgtkllkevkkdLesifkkirs 73 
                                       +ed++++ a  +++s +l++k  +L++++ +++++ ++ ++ +++   + +e  ++++s++k i+ 
  gi|518651672|ref|YP_008141192.1| 117 QEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKD 182
                                       79*************************************************************986 PP

>> PI3K_P85_iSH2  Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   6.2      0.02       3.9      80     133 ..      12      65 ..       2      69 .. 0.88
   2 ?    4.8  12.1     0.099        19      80     147 ..      75     142 ..      66     143 .. 0.89
   3 ?    5.9  15.9     0.044       8.5      14     115 ..     115     219 ..     112     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                     PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpell 133
                                       ++  ++++ nle +++  +el s  ++L++++ +  ++e  l  +  +lk+ ll
  gi|518651672|ref|YP_008141192.1|  12 QEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLL 65 
                                       556789********************************************9986 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.099
                     PI3K_P85_iSH2  80 ehEieklqenleqlksrlkelhsskekLeedlkqqkeeereleReinalkpellqLqkrkdkylewLk 147
                                       ++ +e++q+ le+ + rl++  ++ e Lee+l++ k e+ +++ ++ +     ++++ +  + + +L+
  gi|518651672|ref|YP_008141192.1|  75 KKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQ 142
                                       46678999****************************************99999999998888888887 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.044
                     PI3K_P85_iSH2  14 klseklrevskqlqekskeydqlkeeynkiseeiqlkr.qaleaFneaikmFeeqiklqekfskeaqehE..ieklq 87 
                                       k+ e+ +++    q+ s e+ q+ +  +k  +e++ k  q ++a ne  +  +eq + + +++ke ++++  ie+l+
  gi|518651672|ref|YP_008141192.1| 115 KIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDsQSQKAINELSSTGREQSAQIKSLQKEIKDKNslIEELD 191
                                       5778889999999************************8799*************************76663378999 PP

                     PI3K_P85_iSH2  88 enleqlksrlkelhsskekLeedlkqqk 115
                                        ++ +l++ lk+ + + ++L e ++   
  gi|518651672|ref|YP_008141192.1| 192 LHNYELNHDLKTYEIKEKSLRETMELLN 219
                                       999999*****99999999999998655 PP

>> DUF4795  Domain of unknown function (DUF4795)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   5.0      0.05       9.8      14      57 ..       6      49 ..       1      63 [. 0.47
   2 ?    5.0   9.3     0.083        16      11      58 ..      59     106 ..      51     121 .. 0.79
   3 ?    5.3  12.4     0.069        13       5      70 ..     127     192 ..     106     194 .. 0.90
   4 ?    2.3   3.3      0.56   1.1e+02       5      60 ..     169     224 ..     164     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.05
                           DUF4795 14 eaieklqeelekleekvkelekrledkekklealkkqieelekv 57
                                      +++e+ qe+l+ ++   + ++ + +++ ++++ l ++i +  k+
  gi|518651672|ref|YP_008141192.1|  6 KQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGLKR 49
                                      44455555555555555555555555555555555554443333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.083
                           DUF4795  11 klqeaieklqeelekleekvkelekrledkekklealkkqieelekvk 58 
                                        l++ +++  e le+ +++ ++++++ledk   le+  ++ie le++ 
  gi|518651672|ref|YP_008141192.1|  59 SLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEEL 106
                                       678888888899999999999999999999999999999998888764 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.069
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkadkeeveeelae 70 
                                       s++  ++l+++i  lq+++++le+k ++ +k ++++++       qi+ l+k+ +dk+ + eel++
  gi|518651672|ref|YP_008141192.1| 127 SQKISSELKQKIDRLQKYISELESKDSQSQKAINELSSTGREQSAQIKSLQKEIKDKNSLIEELDL 192
                                       566678999***********************************************9999999875 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.56
                           DUF4795   5 saellkklqeaieklqeelekleekvkelekrledkekklealkkqieelekvkad 60 
                                       ++  +k lq++i++    +e+l+    el+++l+++e k ++l++ +e l+ ++++
  gi|518651672|ref|YP_008141192.1| 169 QSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELLNAANDN 224
                                       55668899999999999999999999999999999999999999999999888765 PP

>> CENP-F_N  Cenp-F N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.6     0.012       2.3     270     303 ..      11      45 ..       2      50 .. 0.73
   2 ?    1.3   0.2       1.1   2.2e+02     279     306 ..      49      76 ..      44      77 .. 0.85
   3 ?    1.3  28.0       1.1   2.1e+02      25     171 ..      69     232 ..      57     258 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.012
                          CENP-F_N 270 lsedssssq.lldqlkaqnqeLkskvkelelrLqa 303
                                       ++e+ ++ +  l+ ++a nqeL s+++el++++ a
  gi|518651672|ref|YP_008141192.1|  11 FQEQLQTMHaNLEAVQAENQELTSHINELNNKIAA 45 
                                       555555544145899**************998765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 1.1
                          CENP-F_N 279 lldqlkaqnqeLkskvkelelrLqaqek 306
                                         d lk qn+ Lks + + ++ L++ +k
  gi|518651672|ref|YP_008141192.1|  49 REDDLKNQNESLKSSLLDTNEALESFKK 76 
                                       5799************999999988766 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 1.1
                          CENP-F_N  25 sqldklkkerqqrqfqLesLeaalqkqkqkveseksevaaLkRenqsLvesCdnlekakqkishelqvkesq....v 97 
                                         l+ +kk+ +  q +Le  +  l    +k+e+  +e  +Lk en ++ e  +n   + qkis el+ k       +
  gi|518651672|ref|YP_008141192.1|  69 EALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRlqkyI 145
                                       57999*************************************************************98854411225 PP

                          CENP-F_N  98 nflegqLssskkqiekLeqelkry..............kselersqqallssdvslsplstPqksfatpltpsqkks 160
                                       + le++ s s+k i++L    +                +s +e  + + +  +  l++++  +ks+  +++   +  
  gi|518651672|ref|YP_008141192.1| 146 SELESKDSQSQKAINELSSTGREQsaqikslqkeikdkNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELL-NAA 221
                                       5677777777777777754433331111111111111122222222223333333444455555555555443.233 PP

                          CENP-F_N 161 dskleelqeky 171
                                       + +++ l eky
  gi|518651672|ref|YP_008141192.1| 222 NDNFKGLLEKY 232
                                       33455555555 PP

>> Flagellar_rod  Paraflagellar rod protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   3.0     0.048       9.4      34      73 ..       3      42 ..       1      45 [. 0.91
   2 ?   13.5   8.6   0.00018     0.036      18      85 ..      50     117 ..      44     123 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.048
                     Flagellar_rod 34 adekqrkrykaqreesdkflqeneeqqeklvreieelere 73
                                      + +kq + +++q +++ ++l++++ + ++l  +i+el ++
  gi|518651672|ref|YP_008141192.1|  3 NAKKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNK 42
                                      5689********************************9876 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 0.00018
                     Flagellar_rod  18 eeDlekikekreeeaaadekqrkrykaqreesdkflqeneeqqeklvreieelereLqklaeerrelv 85 
                                       e+Dl++ +e+++    + +++ + +k+q+e  ++ l+  + + e+ v++ie+le+eL+kl+ e  ++ 
  gi|518651672|ref|YP_008141192.1|  50 EDDLKNQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQ 117
                                       79**********************************************************98876655 PP

>> GAT  GAT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3      0.13        25      50      76 ..     212     237 ..     206     238 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.13
                               GAT  50 eedllaelLqlNDeLnnvlerYerlkk 76 
                                       +e +++ l  +ND++  +le+Y  l++
  gi|518651672|ref|YP_008141192.1| 212 RE-TMELLNAANDNFKGLLEKYRFLLE 237
                                       56.8888999************98776 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3  19.5       2.6   5.1e+02     154     252 ..      45     150 ..       8     164 .. 0.59
   2 ?   10.1   5.9    0.0018      0.35     152     211 ..     159     218 ..     148     227 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 2.6
                              MPS2 154 rsnrklkaLevrveslkdELeakdevl.......rekeRelleLkkrlseykekYellqrefslykarrveksqnsl 223
                                         +++   L+ + eslk  L + +e l       ++ + el + + rl+   ek e l++e +  k  + + +++  
  gi|518651672|ref|YP_008141192.1|  45 AGLKREDDLKNQNESLKSSLLDTNEALesfkkqnEDIQHELEDKNTRLESTVEKIETLEEELEKLKIENGKIQEDME 121
                                       33344444555555555555555555422111002223456666677777778888888888855555555555556 PP

                              MPS2 224 ktaikheviisElkrklqeqteiisilke 252
                                       +t+   + i sElk+k+ + ++ is l  
  gi|518651672|ref|YP_008141192.1| 122 NTTASSQKISSELKQKIDRLQKYISELES 150
                                       67777777889999999999888888864 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                              MPS2 152 lrrsnrklkaLevrveslkdELeakdevlrekeRelleLkkrlseykekYellqrefsly 211
                                        +      +   ++++sl++E+++k+++++e + +  eL++ l++y+ k ++l +  +l 
  gi|518651672|ref|YP_008141192.1| 159 INELSSTGREQSAQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLRETMELL 218
                                       4445566788899***********************************999999988864 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   1.8     0.016         3      37      79 ..       5      47 ..       1      51 [. 0.88
   2 ?   10.1   2.9     0.003      0.58      38      83 ..      55     100 ..      47     103 .. 0.93
   3 ?    2.5   5.4      0.67   1.3e+02      34      78 ..     111     155 ..      98     172 .. 0.61
   4 ?    1.1   2.0       1.8   3.5e+02      38      79 ..     171     212 ..     156     235 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.016
                           DUF4446 37 gkdgksleellkekleeveelkeeseelekeieeleeklkksl 79
                                      +k+ ++ +e+l++  +++e++++e++el+++i+el++k+++ l
  gi|518651672|ref|YP_008141192.1|  5 KKQLEDFQEQLQTMHANLEAVQAENQELTSHINELNNKIAAGL 47
                                      56889999*****************************998766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.003
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                                       ++++sl++ l ++ e +e++k+++e++++e+e+ +++l+++++k++
  gi|518651672|ref|YP_008141192.1|  55 NQNESLKSSLLDTNEALESFKKQNEDIQHELEDKNTRLESTVEKIE 100
                                       5899***************************************997 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.67
                           DUF4446  34 lmkgkdgksleellkekleeveelkeeseelekeieeleeklkks 78 
                                       + +gk ++++e++ ++  +   elk++ ++l+k i+ele+k ++s
  gi|518651672|ref|YP_008141192.1| 111 IENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQS 155
                                       233555666666666666666666666666666666666665554 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 1.8
                           DUF4446  38 kdgksleellkekleeveelkeeseelekeieeleeklkksl 79 
                                       ++ ksl++ +k+k + +eel+ ++ el++++++ e k k+  
  gi|518651672|ref|YP_008141192.1| 171 AQIKSLQKEIKDKNSLIEELDLHNYELNHDLKTYEIKEKSLR 212
                                       355677777777777777777777777777776665555544 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  10.6      0.23        45      32     107 ..       5      76 ..       1      78 [. 0.50
   2 ?    8.0  13.3     0.018       3.5      16     104 ..      66     147 ..      59     153 .. 0.72
   3 ?    2.9  15.4      0.65   1.3e+02      23      87 ..     122     194 ..     115     244 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.23
                                       HHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  32 qaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqka...qelqkkqqellkpildkinkaikev 105
                                       +++le+ +++lq++ ++l++       +++ qel    +el++k ++      +l++++ e lk+ l   n+a++ +
  gi|518651672|ref|YP_008141192.1|   5 KKQLEDFQEQLQTMHANLEA------VQAENQELTSHINELNNKIAAGLkreDDLKNQN-ESLKSSLLDTNEALESF 74 
                                       56666667777777777752......334444444444444443333333325555555.44555566666666666 PP

                                       HH CS
                              OmpH 106 ak 107
                                        k
  gi|518651672|ref|YP_008141192.1|  75 KK 76 
                                       55 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  16 egkaaqeqlekkfkklqaeleakekelqklqeelqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellk 92 
                                       ++++a e ++k+ +++q ele+k++ l++ +e+++    +   ee+ ++l+ ++ ++q++++++    qk + el +
  gi|518651672|ref|YP_008141192.1|  66 DTNEALESFKKQNEDIQHELEDKNTRLESTVEKIE----T--LEEELEKLKIENGKIQEDMENTTASSQKISSELKQ 136
                                       56788899999999999999999999999999996....3..45666667777777777777777666666666555 PP

                                       HHHHHHHHHHHH CS
                              OmpH  93 pildkinkaike 104
                                       + +d+++k i+e
  gi|518651672|ref|YP_008141192.1| 137 K-IDRLQKYISE 147
                                       4.5666665555 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.65
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS..........-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              OmpH  23 qlekkfkklqaeleakekelqklqeelqkkakkl.e........keekeqelqkkeqelqqkqqqkaqelqkkq 87 
                                       +  + ++k+  el++k + lqk + el+ k +++ +         +e+  +++ +++e+++ ++   +el   +
  gi|518651672|ref|YP_008141192.1| 122 NTTASSQKISSELKQKIDRLQKYISELESKDSQSqKainelsstGREQSAQIKSLQKEIKD-KNSLIEELDLHN 194
                                       3333447777777777777777777777555554334444443333333336666666666.555556655554 PP

>> DegS  Sensor protein DegS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.7   0.00039     0.076      16      77 ..      16      77 ..       4      79 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00039
                              DegS 16 eeifeIaEsarkeverlkkeleelkeevsevikevdklekkerkarkrLaeVskdFkkysee 77
                                      + +    E++++e ++l+++++el+++++  +k+ d+l++++ + +  L++ +   ++++++
  gi|518651672|ref|YP_008141192.1| 16 QTMHANLEAVQAENQELTSHINELNNKIAAGLKREDDLKNQNESLKSSLLDTNEALESFKKQ 77
                                      455556799********************************************999999876 PP

>> MIP-T3_C  Microtubule-binding protein MIP-T3 C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   5.4      0.58   1.1e+02      97     135 ..       6      45 ..       2      58 .. 0.63
   2 ?   11.5   9.0    0.0011      0.22      73     140 ..      92     159 ..      90     163 .. 0.92
   3 ?    3.3   3.4      0.37        72      97     135 ..     154     189 ..     149     193 .. 0.69

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.58
                          MIP-T3_C  97 qaeelaeerrate.ealeplkaqlaeleeaIkdqkekisn 135
                                       ++ e+ +e+ +t+  +le ++a+ +el ++I++ ++ki +
  gi|518651672|ref|YP_008141192.1|   6 KQLEDFQEQLQTMhANLEAVQAENQELTSHINELNNKIAA 45 
                                       3444555555555145788999999999999999999876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.0011
                          MIP-T3_C  73 ldfiqdDidsMqrELemWrseyrqqaeelaeerrateealeplkaqlaeleeaIkdqkekisnvraki 140
                                       l+   + i+++++ELe+ + e+ + +e++++  +  ++ +++lk+++  l++ I++ ++k s++++ i
  gi|518651672|ref|YP_008141192.1|  92 LESTVEKIETLEEELEKLKIENGKIQEDMENTTASSQKISSELKQKIDRLQKYISELESKDSQSQKAI 159
                                       6777899*************************************************999988877665 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.37
                          MIP-T3_C  97 qaeelaeerrateealeplkaqlaeleeaIkdqkekisn 135
                                       q++++ +e + t     +  aq++ l+++Ikd+++ i++
  gi|518651672|ref|YP_008141192.1| 154 QSQKAINELSSTGR---EQSAQIKSLQKEIKDKNSLIEE 189
                                       44444444444443...44689************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3981  (0.222043); expected 358.6 (0.02)
Passed bias filter:                      885  (0.0493614); expected 358.6 (0.02)
Passed Vit filter:                       290  (0.0161749); expected 17.9 (0.001)
Passed Fwd filter:                       204  (0.0113782); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              92  [number of targets reported over threshold]
# CPU time: 2.41u 0.42s 00:00:02.83 Elapsed: 00:00:00.68
# Mc/sec: 1154.36
//
Query:       gi|518651673|ref|YP_008141193.1|  [L=325]
Description: hypothetical protein FACI_IFERC00001G0312 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.19   10.6   0.0        1.1    8.0   0.0    2.0  1  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0   6.2e-05       1.1     256     372 ..     167     274 ..     101     287 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 6.2e-05
                                       SEEEEEEEETTEEEEEEE.E-TTTS-HHHHHHHHHHHCT--TTTS-EEEE---EEES-SEETTEEE-CCCTEE--CC CS
                    Trp_halogenase 256 aGWtWkiPLqhrlgnGyv.yssahadddeAlaellaeldgkleaeprkirfttGrrkqawvknvvalGlasgfvePl 331
                                        G +W  PL ++++ G+   ss+          l++++ ++ +   r+ir+     +++ ++n++ +G+a g v P+
  gi|518651673|ref|YP_008141193.1| 167 RGYFWSFPLGKEFHIGVGsLSSEDF-------SLVRKYRKI-KIATRNIRMAP-LFNNMGKENIIGIGEAIGTVSPI 234
                                       5667777777776665431333333.......344444433.34446666654.46677899*************** PP

                                       CS-HHHHHHHHHHHHHHT--BTT--HHHHHHHHHHHHHHHH CS
                    Trp_halogenase 332 estsihliqaalrrLlallpdksdepaaiaefnrevarele 372
                                        + +i    ++++ L ++l ++ +    +ae+ + ++++++
  gi|518651673|ref|YP_008141193.1| 235 TGEGIVPSLESAEILFNCLKAGDVT-GILAEYRKLINQKFG 274
                                       ******9999999999999876444.445677777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2070.80
//
Query:       gi|518651674|ref|YP_008141194.1|  [L=194]
Description: carboxylesterase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-15   57.1   0.0    6.3e-14   52.2   0.0    2.0  2  Abhydrolase_1  alpha/beta hydrolase fold
    2.6e-14   53.1   0.0    9.2e-12   44.7   0.0    2.4  2  Hydrolase_4    Serine aminopeptidase, S33
    8.5e-09   36.3   0.0    9.6e-09   36.2   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
    1.1e-07   31.8   0.0    1.5e-07   31.3   0.0    1.1  1  Abhydrolase_5  Alpha/beta hydrolase family
    0.00013   20.7   0.0    0.00018   20.3   0.0    1.1  1  Ndr            Ndr family
  ------ inclusion threshold ------
      0.045   13.7   0.0      0.063   13.2   0.0    1.2  1  BAAT_C         BAAT / Acyl-CoA thioester hydrolase C terminal
      0.045   13.4   0.0      0.094   12.3   0.0    1.8  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   0.0   2.5e-17   6.3e-14       2     107 ..      24     123 ..      24     135 .. 0.88
   2 ?    3.3   0.0     0.021        54     212     251 ..     135     173 ..     126     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.5e-17
                                       EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEE CS
                     Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlv 78 
                                       +++++hG   ++  + e   ++a  ++gf+ i lD +G+g+S+  +         +++  ++  + dal++++++++
  gi|518651674|ref|YP_008141194.1|  24 PFIFCHGARFNARTYEETETIQAVVDSGFHAISLDFPGYGKSENLS---------IDMYTFISSFIDALKLEPVVIL 91 
                                       6899***877777777777***********************8888.........4588899999************ PP

                                       EETHHHHHHHHHHHHHGGGEEEEEEESE...C CS
                     Abhydrolase_1  79 GhSmGGmialayaaeyperVkalvllga...i 107
                                       G SmGG  ++ +a +yp++Vka++l+ga   +
  gi|518651674|ref|YP_008141194.1|  92 GASMGGEAVTGFATKYPDKVKAMILVGAvgiS 123
                                       ****************************6632 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.021
                                       SEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSS CS
                     Abhydrolase_1 212 aptlvisgtsDplvppkaledlaqllpkkrlvvisdagHl 251
                                       +p l+i+g +D +  p+++e l +  p+  ++   + +H 
  gi|518651674|ref|YP_008141194.1| 135 KPMLLIWGKNDAISVPGNYEMLMRYNPS-AEFSNIGRQHA 173
                                       39****************9999888777.66655555555 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   3.6e-15   9.2e-12       8     110 ..      26     120 ..      24     130 .. 0.91
   2 !    6.0   0.0    0.0024       6.1     188     220 ..     130     163 ..     121     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.6e-15
                       Hydrolase_4   8 vlvHGlaehsgryae..laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllG 82 
                                       +++HG    ++ y+e  +++a ++ Gf+ + lD  G+G+se+             D+ +f++ + +  + +p+++lG
  gi|518651674|ref|YP_008141194.1|  26 IFCHGARFNARTYEEteTIQAVVDSGFHAISLDFPGYGKSENLSI----------DMYTFISSFIDALKLEPVVILG 92 
                                       789**********99889**********************77777..........7777777777777789****** PP

                       Hydrolase_4  83 hSmGGliallyllrypdkvaglilsaPa 110
                                        SmGG  ++ ++++ypdkv+++il++++
  gi|518651674|ref|YP_008141194.1|  93 ASMGGEAVTGFATKYPDKVKAMILVGAV 120
                                       *************************975 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0024
                       Hydrolase_4 188 akit.lPllllhGeaDkvvdpeasrelyerlgsk 220
                                       +k++  P+ll+ G++D +  p++ + l++  +s+
  gi|518651674|ref|YP_008141194.1| 130 SKLEgKPMLLIWGKNDAISVPGNYEMLMRYNPSA 163
                                       555568**************99999988877765 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   3.8e-12   9.6e-09       1      97 [.      25     121 ..      25     184 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 3.8e-12
                                       EEEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHHHHHHCCTT..TTSEEEEEETCHH CS
                     Abhydrolase_6   1 vlllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldledladlaalldelaagggpvvlvGHSlGG 76 
                                       ++++HGa ++a+ +  +  ++a   +g+h +++D+pG+G s+   l+ + +  ++ ++d+l+    pvv++G S+GG
  gi|518651674|ref|YP_008141194.1|  25 FIFCHGARFNARTYEeTETIQAVVDSGFHAISLDFPGYGKSE--NLSIDMYTFISSFIDALK--LEPVVILGASMGG 97 
                                       58************6588999999***************663..333333444499999997..999********** PP

                                       H.HHHHHHHCC..EE..EEES-.. CS
                     Abhydrolase_6  77 a.lalaaaplalvvg..vlldppp 97 
                                         +  +a ++++ v+  +l+ + +
  gi|518651674|ref|YP_008141194.1|  98 EaVTGFATKYPDKVKamILVGAVG 121
                                       624444555775555567777722 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0   5.8e-11   1.5e-07       3     121 ..      26     155 ..      24     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 5.8e-11
                     Abhydrolase_5   3 ifYpGakveaesYae..laeklaksGyevvlvklP.....lnlavlgknkaeeiikeapklekfvvgGhslGGvvas 72 
                                       if  Ga+ +a++Y e    +++++sG++ + + +P      nl++     +++ i++  kle  v+ G s+GG +++
  gi|518651674|ref|YP_008141194.1|  26 IFCHGARFNARTYEEteTIQAVVDSGFHAISLDFPgygksENLSIDMYTFISSFIDAL-KLEPVVILGASMGGEAVT 101
                                       899**********7511679**************96666569999999999****965.5999************** PP

                     Abhydrolase_5  73 rfaaee.ekiegvvflasYPe...kdelse.lskkvlsivgteDgvlnvkslek 121
                                        fa++  +k+++++++++      + +ls+ ++k++l i+g++D++    ++e 
  gi|518651674|ref|YP_008141194.1| 102 GFATKYpDKVKAMILVGAVGIsdfEPDLSKlEGKPMLLIWGKNDAISVPGNYEM 155
                                       ****8868********9986522444676625678**********988777765 PP

>> Ndr  Ndr family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   7.1e-08   0.00018      87     133 ..      74     120 ..      53     126 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.1e-08
                                       TTHHHHHHHHT---EEEEEETHHHHHHHHHHHHSGGGEEEEEEES-- CS
                               Ndr  87 dqllavldhfklksviglGvgaGAyilarfalkhperveglvLinit 133
                                       + +++ +d +kl+ v+ lG+  G   ++ fa k+p++v++++L+ + 
  gi|518651674|ref|YP_008141194.1|  74 TFISSFIDALKLEPVVILGASMGGEAVTGFATKYPDKVKAMILVGAV 120
                                       5688999************************************9765 PP

>> BAAT_C  BAAT / Acyl-CoA thioester hydrolase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.063      23      94 ..      87     159 ..      76     180 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       SEEEEEETHHHHHHHHHHHHSS.SEEEEEEES--SB--SSEEEETTE..EE----B-GGG-EE-TTS-EE-TT CS
                            BAAT_C  23 kigllGiSkGgelalllasflk.kisavvlingsavvvegklvykdeskvlpelklsmeklkvnknglldivd 94 
                                        + +lG S Gge +   a++++ k++a++l+ +  +   ++++ k e+k++  ++ +++ ++v  n ++ +++
  gi|518651674|ref|YP_008141194.1|  87 PVVILGASMGGEAVTGFATKYPdKVKAMILVGAVGISDFEPDLSKLEGKPMLLIWGKNDAISVPGNYEMLMRY 159
                                       5789******************9*******9999999999999998888888888888888776666665554 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.7e-05     0.094     117     145 ..      88     115 ..      11     173 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.7e-05
                                       EEEEEETHHHHHHHHHHHCSTTTCCEEEE CS
                          Esterase 117 ravaGqSmGGlgALilalkhpdrFgsvss 145
                                        +++G+SmGG +    a+k+pd+ +    
  gi|518651674|ref|YP_008141194.1|  88 VVILGASMGGEAVTGFATKYPDKVKAM-I 115
                                       79*********************9644.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       332  (0.0185175); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1369.01
//
Query:       gi|518651675|ref|YP_008141195.1|  [L=787]
Description: hypothetical protein FACI_IFERC00001G0314 [Ferroplasma acidarmanus fer1]
Scores for complete 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-109  363.6   1.5   1.6e-108  362.9   1.5    1.3  1  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.4e-69  233.7   0.0    3.5e-69  233.1   0.0    1.2  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.9e-24   85.1   0.3    5.7e-24   83.6   0.3    1.9  1  PEP-utilizers    PEP-utilising enzyme, mobile domain


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 !  362.9   1.5  2.7e-112  1.6e-108       2     325 ..      21     339 ..      20     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 362.9 bits;  conditional E-value: 2.7e-112
                            PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelP 78 
                                       +lvGGK+anL+e+++ + +pvP+gf +t++a++ef+ en+l++ki +++k++d+++ ++l++as+eir+l+l+a++ 
  gi|518651675|ref|YP_008141195.1|  21 PLVGGKSANLGEMVKMKTVPVPNGFSTTSYAYKEFIIENDLDDKIINIIKHTDIENSRKLKEASEEIRQLFLNAHFN 97 
                                       69***********999************************************************************* PP

                            PPDK_N  79 eeleeaikeayeelgkkfgdeelpvaVRSSataEDlpkasfaGqqdtyLnvggeeevleaikavfaSlfnerAilYr 155
                                       ++l ++i+e+y++l +  +++++ vaVRSSat EDlp+asfaG qdtyLn++ge++v+++ika++aSlf++rAi+Yr
  gi|518651675|ref|YP_008141195.1|  98 ASLGKEIREYYRKLIE--KEKNVYVAVRSSATSEDLPDASFAGEQDTYLNIHGEDDVVQNIKACYASLFSPRAIYYR 172
                                       **************98..55679****************************************************** PP

                            PPDK_N 156 kekgldheevalavvvqkmvnsdlgasGVafsldpetGfkdevlinasyGlGeaVVaGrvtpdefvvekstrkilek 232
                                       ++k++ h+++ lav vqk  +s+  +sGV+f++d +tG++++++i++syGlGe +V+G vtpd+++v+kst ki++k
  gi|518651675|ref|YP_008141195.1| 173 EKKNFGHFNIYLAVAVQKQLFSE--VSGVMFTVDVSTGDNSKIIIESSYGLGEYIVGGVVTPDTYYVDKSTMKITNK 247
                                       ***********************..**************************************************** PP

                            PPDK_N 233 kigekeikivydekeegtkevevpeeereklaLsdeeveeLaeiakkiekhygtpmdiEfaideeegklyllQaRpe 309
                                        i +k++++++ e + gt+e  v++e ++k++Lsdeev  La+++ ++ekhyg+ md+E+a+d+ + k+y+lQaR e
  gi|518651675|ref|YP_008141195.1| 248 IITNKNKMLKCLETG-GTEELVVEKEMANKQSLSDEEVIHLANYGLQLEKHYGNSMDVEWAKDSFDHKIYILQARFE 323
                                       ************998.89*********************************************************** PP

                            PPDK_N 310 trtsekkekkaaetle 325
                                       t+++ + + + + ++e
  gi|518651675|ref|YP_008141195.1| 324 TVWNGNRVGEDKMQQE 339
                                       ***9876654444333 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 !  233.1   0.0   5.9e-73   3.5e-69      17     293 ..     477     766 ..     462     767 .. 0.94

  Alignments for each domain:
  == domain 1  score: 233.1 bits;  conditional E-value: 5.9e-73
                                       CXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCC.HHHHHH..........HHHHHHHHHHHTTTSEEEE CS
                   PEP-utilizers_C  17 gkkikvlaNidtpedaekalengaeGiGLlRtEflfmaree.lpteee..........qaeaykkvleamngrpvvv 82 
                                       ++ +kvl+N+++p+  ek+ + + +GiGL+R Ef++ +  e + ++++          + ++ +kv + + +rpvv+
  gi|518651675|ref|YP_008141195.1| 477 ITGTKVLVNMGEPQLSEKVSKLPSDGIGLMREEFIWAEIGEhPLSLIKngrgeyfvdrLSSELAKVCRDFAPRPVVL 553
                                       567899*********************************6648888889**************************** PP

                                       EXXXSSCC..GGSGGCHH.HH.XSXGGGSSXTHHHHCCS..HHHHHHHHHHHHHHCC...CCEEEEEESSXXSHHHH CS
                   PEP-utilizers_C  83 RtlDiggd..kelpelke.epeevNPmlGfRgirlglse..pelfetqlrAllrasa...agkleimlPmvasveel 151
                                       R+ D+++d  k l+ +ke epee NP+lG+Rg +++ +   +e f+ +l+ +++a+      +l++m+P+ ++veel
  gi|518651675|ref|YP_008141195.1| 554 RFSDFKSDeyKSLKGGKEfEPEEDNPLLGWRGASRYYDDryKEAFKLELQGIKKARDdylLKNLWVMIPFTRTVEEL 630
                                       *******9999****976358999*********999987679**************966566*************** PP

                                       HHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHCHHHHSXT CS
                   PEP-utilizers_C 152 eeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdneevaklydp 228
                                       ++ +ki+e         g++++k++k+  M E+ps +lladk+ ++vd+ SiG+NDLt ++l+ dR+n +++ ++d+
  gi|518651675|ref|YP_008141195.1| 631 KRVVKIMEDN-------GLERTKDFKLFLMAEIPSNILLADKFNQYVDGYSIGSNDLTMLLLGSDRNNGKMSSMFDE 700
                                       *******998.......89999******************************************************* PP

                                       TTCHHCCCHHHHHHHHHHCCXEEEEESCCCC.SCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
                   PEP-utilizers_C 229 lepavlrlikevikaaeekglkvgiCGelag.dpsavellvglGldelSmsaasvpaaraalaqve 293
                                        + a++r+i+++ik+a++ g+ v+iCG++++ ++++v +lv+ G+d +S+++++v  +r+++a+ve
  gi|518651675|ref|YP_008141195.1| 701 RDLAIKRAIRYLIKIAHRDGKIVSICGQAPSqYDEIVDFLVRSGIDDISVNPDAVTHVRKMVASVE 766
                                       *******************************889****************************9875 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 !   83.6   0.3   9.6e-28   5.7e-24       1      73 []     374     450 ..     374     450 .. 0.92

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 9.6e-28
                                       G--S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH.....HH--TEEEEEETTTT CS
                     PEP-utilizers   1 kleegvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati....elkegdlitvDgstG 73 
                                       k++eg+ILv+++t p++++ + ka++ivt++GG t+HaAi++relg+P++vg+++  +    +lk+g++it+D+++G
  gi|518651675|ref|YP_008141195.1| 374 KFKEGDILVTKMTAPDWVPIMGKAKAIVTDEGGLTCHAAIISRELGVPCIVGTSSYGKkateVLKDGETITIDAKNG 450
                                       589**************************************************86544455499**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.68u 0.30s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5224.07
//
Query:       gi|518651676|ref|YP_008141196.1|  [L=259]
Description: chorismate synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0024   18.0   0.0     0.0042   17.2   0.0    1.4  1  Acetyltransf_9  Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.3e-07    0.0042       3      99 ..       4      99 ..       2     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.3e-07
                                      EEE-.GGGHHHHHHHHHHHTT----H..HHHHHHH.HHHTTSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEE CS
                    Acetyltransf_9  3 relt.eedldevlellkyaFqdeespleeireyfr.klleesrvlgaedngelvgqlallplelnvpGktlkaagvtgV 79
                                      r+++ +++++ ++e+ k a++ +      ++   +   +  + vlga+d+++l+g+   +p   + ++ t+ +   tgV
  gi|518651676|ref|YP_008141196.1|  4 RRVEnSSEIENFMEIIKSAWHSDSALS-GFKDTIHsMAYHGGFVLGAWDEDKLIGMSFSYP--GYKNNYTYLYSHMTGV 79
                                      55553789*************999998.44444440455567*************986665..688899********** PP

                                      EE-CCGTTS-HHHHHHHHHH CS
                    Acetyltransf_9 80 avapehrgrgvlskLlaral 99
                                          ++ g g+l k+ ++ l
  gi|518651676|ref|YP_008141196.1| 80 IDQKKYSGAGYLMKMKQKEL 99
                                      ************99977765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1858.95
//
Query:       gi|518651677|ref|YP_008141197.1|  [L=306]
Description: hypothetical protein FACI_IFERC00001G0316 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-39  135.2   0.5    2.9e-39  135.0   0.5    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    2.6e-33  115.8   1.3      6e-33  114.6   1.3    1.5  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      7e-07   28.5   1.3    1.6e-06   27.4   1.3    1.5  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    3.3e-06   26.4   0.0    4.2e-06   26.1   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    2.4e-05   23.6   0.2     0.0026   16.9   0.2    2.5  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
     0.0002   21.0   0.1      0.092   12.3   0.1    2.3  2  NmrA             NmrA-like family
     0.0045   17.3   0.1      0.015   15.6   0.1    1.9  1  eRF1_2           eRF1 domain 2
  ------ inclusion threshold ------
      0.012   14.8   0.2        1.3    8.2   0.0    2.4  2  NAD_binding_4    Male sterility protein
      0.012   15.3   0.1       0.02   14.5   0.1    1.3  1  DUF4344          Putative metallopeptidase
      0.054   13.2   0.0         29    4.4   0.0    3.1  3  FAD_binding_4    FAD binding domain
       0.14   11.6   0.1        0.4   10.1   0.0    1.7  2  HVSL             Uncharacterised conserved protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.5   1.8e-42   2.9e-39       1     241 []       8     235 ..       8     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.8e-42
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHH.T-SEEEE--S--- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkee.qpdavihlAavgg 76 
                                       ilVtG++GfiGs+lv+ l + + +v +ld l+++s +++++  + +e      ++++++ + e +pd+++h++ +++
  gi|518651677|ref|YP_008141197.1|   8 ILVTGGAGFIGSNLVNTLSKDN-HVYALDDLQTGSMHNLKDSMDRIEFIK---DRVKNINDYEiNPDYIFHIGIYSS 80 
                                       8****************99866.8***********999999665444433...334444444449*******99777 PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHH CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklv 153
                                        + + ++p   i + +    ++le+a+k++  +++++s+s++Y   +eq ke+++     k +  Y  a +a+e+++
  gi|518651677|ref|YP_008141197.1|  81 SPMYKNNPHL-IANAIDDLITVLEYAKKNKS-KIVYASTSSIYNGIEEQ-KEDVI----PKVSDYYTEARIAMERIA 150
                                       7777777665.889*************9999.************99994.55555....588999************ PP

                                       HHHHHHHT-EEEEEEESEEESTT.S-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHH CS
                         Epimerase 154 eayaaqyglnaiilrlfnlyGpr.ngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehv 229
                                         y + yg+++  +r f++yG + + ++  ++++++++  ++++    +l+gdg+++Rdf++veD+++a++l++e+ 
  gi|518651677|ref|YP_008141197.1| 151 NLYCNLYGMDVSGMRFFSVYGYNeRSKKIYANLVSQFLWAMHDNI-APVLYGDGEQKRDFVFVEDLVKALMLAAEN- 225
                                       ***********************666666***************9.******************************. PP

                                       TT-STTEEEEES CS
                         Epimerase 230 dagdkgeiyniG 241
                                         ++k ++yn+G
  gi|518651677|ref|YP_008141197.1| 226 --NKKFNVYNVG 235
                                       ..77899****9 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.6   1.3   3.7e-36     6e-33       1     331 [.       9     299 ..       9     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 114.6 bits;  conditional E-value: 3.7e-36
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+l++ L +   +v+ ++     ++tg++++l+++      ++++++k  +++ +       e++pd
  gi|518651677|ref|YP_008141197.1|   9 LVTGGAGFIGSNLVNTLSKD-NHVYALD----DLQTGSMHNLKDS-----MDRIEFIKDRVKNIND-----YEINPD 70 
                                       9***************9876.6688775....4578899999863.....3689999977777543.....589*** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        +++ +  s  +   ++P+  a++ +   +++Le +++    +k +++ aSts +Y   +   q+E+   +    Y 
  gi|518651677|ref|YP_008141197.1|  71 YIFHIGIYSSSPMYKNNPHLIANA-IDDLITVLEYAKK----NKSKIVYASTSSIYNGIE--EQKEDVIPKVSDYYT 140
                                       *******************99988.9999*******98....4679**********8887..699************ PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTT.S-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhespr.rgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                        a+++ + i+  y + yg+ ++  ++f  ++   r++++  +++++++  ++ +  +vl +G++++kRd+ +v+D v
  gi|518651677|ref|YP_008141197.1| 141 EARIAMERIANLYCNLYGMDVSGMRFFSVYGYNeRSKKIYANLVSQFLWAMHDNIAPVL-YGDGEQKRDFVFVEDLV 216
                                       ******************************96516678999************999998.8**************** PP

                                       HHHHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB- CS
                     GDP_Man_Dehyd 231 eamwlmlqq.dkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdll 306
                                       +a+ l+ ++ +k + y+++tg++++++e+v++ +++lgk+i+                    e+ +++++++ v  +
  gi|518651677|ref|YP_008141197.1| 217 KALMLAAENnKKFNVYNVGTGKNYTLNELVKILNKHLGKDIKP-------------------EYIENPMKDTYVYYT 274
                                       **9999987255699***********************98764...................344567778888899 PP

                                       -B-THHHHHHH----SS-HHHHHHH CS
                     GDP_Man_Dehyd 307 lgdaskakeeLgWkpkvsfeelvre 331
                                       l+d++k ++++g+k+++s++e++++
  gi|518651677|ref|YP_008141197.1| 275 LADIKKTEQKIGFKASISLDEGIDK 299
                                       **********************986 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   1.3   9.5e-10   1.6e-06       1     231 [.       9     225 ..       9     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 9.5e-10
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +vtGgaGF+G++lv++L + +   +v +lD  +  ++++   +++++++i+  v++ ++ e    + d ++h+ ++ 
  gi|518651677|ref|YP_008141197.1|   9 LVTGGAGFIGSNLVNTLSKDN---HVYALDDLQTGSMHNLKDSMDRIEFIKDRVKNINDYE---INPDYIFHI-GIY 78 
                                       69**************99888...5999998888888899999999999998888777665...467899999.777 PP

                         3Beta_HSD  78 dvagkltedeimkvn.vkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKala 153
                                        +  +++++    +n +    +vle ++k+   ++vY S+ ++  +      i   + ++ + ++ +d y+e +   
  gi|518651677|ref|YP_008141197.1|  79 SSSPMYKNNPHLIANaIDDLITVLEYAKKNK-SKIVYASTSSIYNG------IE--EQKEDVIPKVSDYYTEARIAM 146
                                       777777777666665388999*****99987.679****9876544......33..223344566889999998888 PP

                         3Beta_HSD 154 EklvlkaNgrtlknggrlyTcaLRpagiyG..egdkllvpllkq....laklglalfkigdeevlsdrvYvgNvawa 224
                                       E++    N     n   +    +R   +yG  e++k++ + l+     +++ + a + +gd e++ d+v+v+ +++a
  gi|518651677|ref|YP_008141197.1| 147 ERIA---NL--YCNLYGMDVSGMRFFSVYGynERSKKIYANLVSqflwAMHDNIAPVLYGDGEQKRDFVFVEDLVKA 218
                                       8764...44..334445788899999999933334443333332122134556677889****************** PP

                         3Beta_HSD 225 hilAara 231
                                        +lAa +
  gi|518651677|ref|YP_008141197.1| 219 LMLAAEN 225
                                       ****987 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 !   26.1   0.0   2.6e-09   4.2e-06       2     154 ..       7     172 ..       6     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.6e-09
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT....T--TTSHHHHHHHH.........HHH--SEEEE------HH CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre....eldltdaeavaell.........keakpdvvvnaAAytavD 65 
                                       +ilvtG+ G +Gs+L++ l++++ +v+al+        +l+d+    e++          e++pd + + + y    
  gi|518651677|ref|YP_008141197.1|   7 EILVTGGAGFIGSNLVNTLSKDN-HVYALDDLqtgsMHNLKDSMDRIEFIkdrvknindYEINPDYIFHIGIYSSSP 82 
                                       69******************988.99**9554455533444443333333666677767799*************99 PP

                                       HHHHSHHH.HHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHH... CS
                     RmlD_sub_bind  66 kaEseeea.ayavnaeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavla... 138
                                          +++++ a+a++     ++ e+a++ ++++++ St  +++G +++  +ed  ++   +Y ++++a+E+  +    
  gi|518651677|ref|YP_008141197.1|  83 MYKNNPHLiANAIDD--LITVLEYAKKNKSKIVYASTSSIYNGIEEQ--KEDVIPKVSDYYTEARIAMERIANLycn 155
                                       999997761444444..45788*********************9888..899999999***********98766232 PP

                                       .H-SSEEEEEE-SEESS CS
                     RmlD_sub_bind 139 .agkkalivRtswvyge 154
                                        +g ++  +R+  vyg 
  gi|518651677|ref|YP_008141197.1| 156 lYGMDVSGMRFFSVYGY 172
                                       23344555666666665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   1.6e-06    0.0026       1     128 [.       8     117 ..       8     125 .. 0.73
   2 ?    3.9   0.0     0.015        25     192     252 ..     198     258 ..     182     269 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.6e-06
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +lvtG++G iGs+lv+++ k +     ++  d+l+  ++++ + ++++  ++          ++d+ +  +  e ++
  gi|518651677|ref|YP_008141197.1|   8 ILVTGGAGFIGSNLVNTLSKDNH----VYALDDLQTGSMHNLK-DSMD--RI--------EFIKDRVKNINDYE-IN 68 
                                       89**************9987653....4445555555555532.2222..34........33455444444444.78 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEE CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliSt 128
                                       +d++fh   +   P+  +np+  i + +    +v+e a++++ +k+v+ St
  gi|518651677|ref|YP_008141197.1|  69 PDYIFHIGIYSSSPMYKNNPH-LIANAIDDLITVLEYAKKNK-SKIVYAST 117
                                       ****************99996.79999999999999998877.67888888 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.015
                                       EEES-TT-EEEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH......... CS
                   Polysacc_synt_2 192 vtvTdpemtRyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleek 252
                                       v   d e  R f+ +e+ v+ ++ a+++ k+ +++ +  G+ +++ +l+k l +  g++ k
  gi|518651677|ref|YP_008141197.1| 198 VLYGDGEQKRDFVFVEDLVKALMLAAENNKKFNVYNVGTGKNYTLNELVKILNKHLGKDIK 258
                                       55566777899999************************************99988887654 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.0    0.0028       4.5       1      25 [.       8      31 ..       8      59 .. 0.88
   2 !   12.3   0.1   5.6e-05     0.092     161     230 ..     191     258 ..     166     303 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0028
                                      EEESSTTSHHHHHHHHHHHHHT-EE CS
                              NmrA  1 IlviGaTGrqGksvvrallkaghkv 25
                                      Ilv+G++G +G+ +v+ l k++h v
  gi|518651677|ref|YP_008141197.1|  8 ILVTGGAGFIGSNLVNTLSKDNH-V 31
                                      9***************9988776.4 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 5.6e-05
                                       -TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHHHTS-EE CS
                              NmrA 161 appedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgneivelfekkigktvk 230
                                       + ++   +l g+g+ k  ++  +eD  ++ + ++++ +k+++  +   g+ +++ne+v++++k +gk +k
  gi|518651677|ref|YP_008141197.1| 191 MHDNIAPVLYGDGEQKRDFV-FVEDLVKALMLAAENNKKFNVYNVGT-GKNYTLNELVKILNKHLGKDIK 258
                                       44455667899999999999.899***************99877765.6667***************975 PP

>> eRF1_2  eRF1 domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   9.5e-06     0.015      55     128 ..     173     250 ..     162     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHHHHHHHHHHHCHTTTESEEEEEESSTHHHHHH.....HHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHC CS
                            eRF1_2  55 eeflkkvaeaankafllvdkdklkgiilagpgfvkeefl.....dkdlldaelkkkviklvdvsyggesglnevlek 126
                                       +e  kk++ ++ ++fl +  d+++ + l g g+ k++f+      k l+ a +++k++ + +v++g+++ lne+++ 
  gi|518651677|ref|YP_008141197.1| 173 NERSKKIYANLVSQFLWAMHDNIAPV-LYGDGEQKRDFVfvedlVKALMLAAENNKKFNVYNVGTGKNYTLNELVKI 248
                                       566799**********8899999886.56899999988632111123333455669******************986 PP

                                       CH CS
                            eRF1_2 127 aa 128
                                        +
  gi|518651677|ref|YP_008141197.1| 249 LN 250
                                       55 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00077       1.3       1      27 [.      10      33 ..      10      62 .. 0.82
   2 ?    4.7   0.0    0.0087        14     114     158 ..      97     138 ..      68     219 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00077
                                      EE-TTSHHHHHHHHHHHHHS-.TEEEE CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttpevkiyl 27
                                      +TG+ GF+G+ L++ L +++    +y+
  gi|518651677|ref|YP_008141197.1| 10 VTGGAGFIGSNLVNTLSKDNH---VYA 33
                                      7*************9987764...555 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0087
                                       HHHHHHHHHTSSS--.-EEEEEE.GGGTTS-TTT--SSS-H..... CS
                     NAD_binding_4 114 GtrevlelakklkklkvllhvST.ayvngeregeveekvyeegeke 158
                                           vle akk k++  +++ ST ++ ng +e+  +e+v+++  + 
  gi|518651677|ref|YP_008141197.1|  97 DLITVLEYAKKNKSK--IVYASTsSIYNGIEEQ--KEDVIPKVSDY 138
                                       566799999977777..9999996666766664..46666654433 PP

>> DUF4344  Putative metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.2e-05      0.02     119     186 ..      93     162 ..      92     178 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                           DUF4344 119 DavDqlaailLlelgedgekvvlsaaelfaleaeeeeel..eelafadeHsldaqRyynllClvYGsdpe 186
                                       +a+D+l ++l    +++++ v +s++  ++  +e++e++  + +++  e  +++ R+ nl C +YG d +
  gi|518651677|ref|YP_008141197.1|  93 NAIDDLITVLEYAKKNKSKIVYASTSSIYNGIEEQKEDVipKVSDYYTEARIAMERIANLYCNLYGMDVS 162
                                       68999999888877788888889999999999999999889999**********************9976 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.16   2.6e+02      59      91 ..       3      35 ..       1      42 [. 0.82
   2 ?    4.4   0.0     0.018        29       9      41 ..      94     126 ..      90     136 .. 0.79
   3 ?    3.5   0.0     0.035        56      10      37 ..     212     241 ..     211     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.16
                                      EETTTTEEEEETTSBHHHHHHHHHHHTTECSSG CS
                     FAD_binding_4 59 ideeegtatveaGvtlgdlvealaakglllgle 91
                                      i+ +e  +t +aG ++++lv+ l++ + ++ l+
  gi|518651677|ref|YP_008141197.1|  3 IKNKEILVTGGAGFIGSNLVNTLSKDNHVYALD 35
                                      6677788999**************999999876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                                       SHHHHHHHHHHHHHCTSCEEEESSSTTEESTTC CS
                     FAD_binding_4   9 seeevaaalrlaneaglpvlvrGgGssllgqav 41 
                                        +++++++l++a++++ +++  ++ s ++g   
  gi|518651677|ref|YP_008141197.1|  94 AIDDLITVLEYAKKNKSKIVYASTSSIYNGIEE 126
                                       579*************99888887777777765 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.035
                                       HHHHHHHHHHHHHCTSCEEE..ESSSTTEE CS
                     FAD_binding_4  10 eeevaaalrlaneaglpvlv..rGgGssll 37 
                                       +e++++al la+e++ ++ v  +G+G +++
  gi|518651677|ref|YP_008141197.1| 212 VEDLVKALMLAAENNKKFNVynVGTGKNYT 241
                                       5899**********8886661156666665 PP

>> HVSL  Uncharacterised conserved protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.82   1.3e+03     154     189 ..      44      82 ..      29     129 .. 0.58
   2 ?   10.1   0.0   0.00025       0.4     134     178 ..     221     265 ..     186     293 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.82
                              HVSL 154 eLkklleavnkvleefglpply...kdeaFHiSiawslg 189
                                       +Lk+ +++++ + ++++  + y    d  FHi i  s  
  gi|518651677|ref|YP_008141197.1|  44 NLKDSMDRIEFIKDRVKNINDYeinPDYIFHIGIYSSSP 82 
                                       555555555555555555555555566788888876655 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00025
                              HVSL 134 sndektRsFlvlrvkspendeLkklleavnkvleefglpplykde 178
                                          e+++ F v++v + +n  L++l++++nk l +   p++ +++
  gi|518651677|ref|YP_008141197.1| 221 LAAENNKKFNVYNVGTGKNYTLNELVKILNKHLGKDIKPEYIENP 265
                                       56899****************************998888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       930  (0.0518713); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2308.77
//
Query:       gi|518651678|ref|YP_008141198.1|  [L=114]
Description: hypothetical protein FACI_IFERC00001G0317 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1181  (0.0658709); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 803.49
//
Query:       gi|518651679|ref|YP_008141199.1|  [L=220]
Description: uracil-DNA glycosylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-30  103.7   0.0      1e-29  103.5   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 !  103.5   0.0   5.8e-34     1e-29       2     151 ..      44     212 ..      43     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 103.5 bits;  conditional E-value: 5.8e-34
                                       HC-CTT-SEEEEESSTCHH.HHHHSSSS.-.STT--HHHHHHHCCCCCCCHHG........CTEEEEESSS....SE CS
                               UDG   2 gegppdakvvivGeaPgae.edatglpFsg.ragnllrkllneaglkrdlese........qgvyitnvvkcrppgn 68 
                                       g+g + ++++ivG aP  + +++tg+ F+g ++++ l + l++agl+++++se         + yit ++kc+pp n
  gi|518651679|ref|YP_008141199.1|  44 GYGSIGSRILIVGLAPAFDgGNRTGRIFTGdKSSDFLISSLYAAGLANMPTSErkddglkyIDTYITLALKCAPPDN 120
                                       899****************9**********9999****************999***********************9 PP

                                       CGCTTCCCCTCCHHHHHHHHHHHH.SSEEEEESHHHHHH...........HHHHSCESCCCSCT..SEEEEES-SST CS
                               UDG  69 rdtptsaeikacaplleeeiellk.prlivllGktaakall.........geklgklrgklleak.irvlplphPsp 134
                                       +  p ++e+++c+ ++e+eie+++  ++i++lGk+a+++ l          + +++++gk +++  +r++ ++hPsp
  gi|518651679|ref|YP_008141199.1| 121 K--PEKEELNNCSGFFEKEIEQMEnLKAILCLGKIAFDSTLkffrahqinTRGIKFIHGKYYNIGgVRLYCSYHPSP 195
                                       9..*********************9999***********8778898887555788999******99*********** PP

                                       TTTTTTTSHHHHHHHHH CS
                               UDG 135 lnrnffksnpelkaeaw 151
                                       +n+n++  ++e+    +
  gi|518651679|ref|YP_008141199.1| 196 RNVNTGLLRKEEFISLL 212
                                       ****8777777666555 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:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1720.14
//
Query:       gi|518651680|ref|YP_008141200.1|  [L=242]
Description: 3-oxoacyl-[acyl-carrier protein] reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-25   90.2   0.0      2e-25   89.8   0.0    1.1  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
      4e-21   75.4   0.2    5.1e-21   75.0   0.2    1.1  1  adh_short      short chain dehydrogenase
    0.00016   22.0   0.0      0.064   13.7   0.0    2.3  2  NAD_binding_7  Putative NAD(P)-binding
     0.0025   18.4   0.1     0.0068   17.0   0.1    1.8  1  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0032   17.5   0.3     0.0072   16.4   0.1    1.8  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
  ------ inclusion threshold ------
      0.011   14.7   0.3      0.015   14.3   0.3    1.2  1  3Beta_HSD      3-beta hydroxysteroid dehydrogenase/isomerase 
      0.013   15.2   0.0      0.021   14.5   0.0    1.4  1  ApbA           Ketopantoate reductase PanE/ApbA
       0.05   13.7   0.1      0.098   12.7   0.1    1.7  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      0.091   12.9   0.1       0.63   10.2   0.0    2.4  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


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 !   89.8   0.0   9.8e-29     2e-25      20     233 ..      35     239 ..      21     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 9.8e-29
                                       EEEEEESSGGH.HHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
                      adh_short_C2  20 evvltdlneea.kkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                                       +v++  ++  + k+ v e+   ++ +++++  +de ++++lv +++e+++++D l+  +g   +   +++++  +++
  gi|518651680|ref|YP_008141200.1|  35 RVIINSRDAGKlKEIVSEFSIYGKIDYIAMELKDEGSCKNLVVKAAESIKHIDSLIVMVGGFIE--DSIENL--DGL 107
                                       566666666665555555555555557********************************99999..776665..899 PP

                                       HHHHHHHTHHHHHHHHHHHHHCTSCCEEEEEEEGG.GTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE CS
                      adh_short_C2  96 draldvnlyslfllakaalplmkeggsivnlssvg.aervvpnynaygaaKaalealtrylAvelgpkgiRvNavsp 171
                                       + ++   l+  ++l+k+al++m  g+si+ +s  + + +  +n   y+++K ale++++ +A+el +kgiRvN+v+p
  gi|518651680|ref|YP_008141200.1| 108 ESMITNHLKIPLYLSKYALEHMVYGSSIIFVSNSSiSIKNKTNLLSYSISKYALEKSAKIMAAELLEKGIRVNVVAP 184
                                       99*****************************86640445555666******************************** PP

                                       --BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
                      adh_short_C2 172 gpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                                        +ik +   g +     ++++++   l   + pe++ +++ fL+  ++s+i+G+++ vDgG 
  gi|518651680|ref|YP_008141200.1| 185 EYIKQNFEIGRN-----YSKMRKYGDL--ETPPEDISDLIDFLVEGKSSWINGAIIPVDGGH 239
                                       ****55533332.....3333333333..4589****************************6 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.0   0.2   2.5e-24   5.1e-21       2     185 ..      12     190 ..      11     199 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.0 bits;  conditional E-value: 2.5e-24
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                        +l+ G +  +G+ +++ l+ ++ +v++ +r + kl+e+++e+     k+ +i++ ++d+ ++++lv ka++ ++++
  gi|518651680|ref|YP_008141200.1|  12 NILIAGTG-ELGKSLSYDLLLQNNRVIINSRDAGKLKEIVSEFSI-YGKIDYIAMELKDEGSCKNLVVKAAESIKHI 86 
                                       56666655.6********************************997.589**************************** PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEE.EGGGTSB-TTBHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvs.SvagkvpvagvaaYsAsKa 154
                                       d L+  +G     ++   + +  e++i   l+ ++ l++ +l++m+   + +I++vs S ++ +   ++ +Ys sK 
  gi|518651680|ref|YP_008141200.1|  87 DSLIVMVGGFIEDSI--ENLDGLESMITNHLKIPLYLSKYALEHMV--YGSSIIFVSnSSISIKNKTNLLSYSISKY 159
                                       ********9444333..34445999*********************..77789999878999999************ PP

                                       HHHHHHHHHHHHHGGGTEEEEEEEESSBSSH CS
                         adh_short 155 avagltrslakelaptgirvnavaPGlvdTd 185
                                       a+++ ++ +a el ++girvn+vaP +++ +
  gi|518651680|ref|YP_008141200.1| 160 ALEKSAKIMAAELLEKGIRVNVVAPEYIKQN 190
                                       **************************99855 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.2e-05     0.064       3      66 ..       6      77 ..       5     112 .. 0.74
   2 !    6.4   0.0    0.0062        12      23      51 ..     169     194 ..     162     232 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.2e-05
                     NAD_binding_7  3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.........elvklaeeelekdlegadlvi 66
                                      ++++gk++l++G Ge++ +  + ll ++ +v++ + +   +l+         ++++++  el+++ +   lv+
  gi|518651680|ref|YP_008141200.1|  6 IHMSGKNILIAGTGELGKSLSYDLLLQNNRVIINSRDA-GKLKeivsefsiyGKIDYIAMELKDEGSCKNLVV 77
                                      5799*****************************99995.3333244456566555555555555544444444 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0062
                     NAD_binding_7  23 vrklleagakvtvvapevkeeleelvkla 51 
                                       +  lle+g +v vvape    +++++++ 
  gi|518651680|ref|YP_008141200.1| 169 AAELLEKGIRVNVVAPE---YIKQNFEIG 194
                                       5789*************...455444443 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.1   3.4e-06    0.0068       4      48 ..      15      72 ..      12     104 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                      EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.................- CS
                     F420_oxidored  4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.................v 48
                                      i G+G++g++l   ll ++   + ++ +nsr+  k++e+ +e++                  
  gi|518651680|ref|YP_008141200.1| 15 IAGTGELGKSLSYDLLLQN---NRVI-INSRDAGKLKEIVSEFSiygkidyiamelkdegsC 72
                                      55****************9...9999.88*************99777755555554444442 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   3.6e-06    0.0072       9      59 ..       7      56 ..       2      90 .. 0.79
   2 ?   -2.9   0.0       3.3   6.6e+03      24      42 ..     165     182 ..     163     202 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.6e-06
                                      ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E CS
                      Shikimate_DH  9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkge 59
                                      ++++k++l+ G+Ge+++ +   Ll ++ + v++  R+  + ke+++e++ +
  gi|518651680|ref|YP_008141200.1|  7 HMSGKNILIAGTGELGKSLSYDLLLQNNR-VIINSRDAGKLKEIVSEFSIY 56
                                      5789********************98888.*****************9543 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.3
                                       HHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH  24 aelvakhLlakgvkkvvva 42 
                                       a+ +a  Ll+kg++ v v+
  gi|518651680|ref|YP_008141200.1| 165 AKIMAAELLEKGIR-VNVV 182
                                       56677788888887.4443 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 ?   14.3   0.3   7.5e-06     0.015       3     132 ..      15     148 ..      13     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.5e-06
                         3Beta_HSD   3 tGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdklee.alegvdvvihlaslvd 78 
                                       + g+G lG++l   L+  ++   + + D  + +e+ +e+s  + +++i   ++d+ + ++ +++ ++ + h+ sl+ 
  gi|518651680|ref|YP_008141200.1|  15 IAGTGELGKSLSYDLLLQNNRVIINSRDAGKLKEIVSEFSIYGKIDYIAMELKDEGSCKNlVVKAAESIKHIDSLIV 91 
                                       6799*************999999********************************999984678889999******* PP

                         3Beta_HSD  79 vagkltedeimkvnvkGTrnvleacv.......kagvrvlvYtSsaevvgpnslgeeilng 132
                                       + g + ed+i   n+ G ++++   +       k  ++ +vY Ss+  v +   +  i n 
  gi|518651680|ref|YP_008141200.1|  92 MVGGFIEDSIE--NLDGLESMITNHLkiplylsKYALEHMVYGSSIIFVSN--SSISIKNK 148
                                       9999*9**886..67887777766541111111446677888888766666..44445544 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.1e-05     0.021       1      76 [.      13      93 ..      13     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.1e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETT......CEEEEEECEEECCHSCCCCS-ESEE CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseg......geeilrppealsaeekselepidlv 72
                                      i+i+G+G +G  l + L  +++ v++  r++ +l++++++ +   + +      ++e   ++ ++   + +++++id +
  gi|518651680|ref|YP_008141200.1| 13 ILIAGTGELGKSLSYDLLLQNNRVIINSRDAgKLKEIVSEFSIYGKIDyiamelKDEGSCKNLVVK--AAESIKHIDSL 89
                                      89*****************************99999776655444444444444444444444444..44899999999 PP

                                      EE-S CS
                              ApbA 73 ivtv 76
                                      iv v
  gi|518651680|ref|YP_008141200.1| 90 IVMV 93
                                      9987 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.9e-05     0.098      18      55 ..       5      42 ..       1     145 [. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.9e-05
                                      -S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S- CS
                     AdoHcyase_NAD 18 dvllaGkvavvaGyGdvGkGcaaslkglGarvivtevd 55
                                       + ++Gk++++aG G++Gk  +  l  +  rvi+   d
  gi|518651680|ref|YP_008141200.1|  5 GIHMSGKNILIAGTGELGKSLSYDLLLQNNRVIINSRD 42
                                      5779*****************************98766 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00031      0.63       2      63 ..      13      93 ..      12     153 .. 0.71
   2 ?   -1.5   0.0       1.3   2.5e+03      14      29 ..     168     183 ..     166     192 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT...................EEE-SSHHHHHHHCSEEEE CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg...................akaaesieelvasldvvit 61
                                      i + G+G++G+++   ll ++ +v++  r++ k++e+v+e                     +++ +++e ++++d  i+
  gi|518651680|ref|YP_008141200.1| 13 ILIAGTGELGKSLSYDLLLQNNRVIINSRDAGKLKEIVSEFsiygkidyiamelkdegscKNLVVKAAESIKHIDSLIV 91
                                      5578**********************************98656666666666655555553333333333333344444 PP

                                      -S CS
                     NAD_binding_2 62 mv 63
                                      mv
  gi|518651680|ref|YP_008141200.1| 92 MV 93
                                      44 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                                       HHHHHHHTT-EEEEE- CS
                     NAD_binding_2  14 malnllkagykvavyn 29 
                                       ma +ll++g++v v+ 
  gi|518651680|ref|YP_008141200.1| 168 MAAELLEKGIRVNVVA 183
                                       9999******999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1690.97
//
Query:       gi|518651681|ref|YP_008141201.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G0320 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-11   42.6   0.0    6.9e-11   42.4   0.0    1.1  1  NfeD      NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
       0.12   12.6   0.0       0.13   12.4   0.0    1.1  1  UPF0731   UPF0731 family


Domain annotation for each model (and alignments):
>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   7.7e-15   6.9e-11       3      84 .]      14      99 ..      12      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 7.7e-15
                                      XXXXXXXXXXXXXXS---SSS--S.S---GGTTSEEEEEE-B.S.-EEEEETTEEEEEE-.SS...B-TT-EEEEEEE- CS
                              NfeD  3 avvsvlllvllrplllkklkkkekktnaealiGkegvvledi.g.tGrvkvdGeeWsarsege...iekgerVrVveve 76
                                      +v+ ++  ++ r +l++ +++k++ t++++l+Gk+g++ +++ +   ++ vd + W+a+ +++   ++kge   V +v+
  gi|518651681|ref|YP_008141201.1| 14 IVAFFIGAWFSRFWLRHPFRRKPA-TGKDSLVGKTGEIKSTLkNnFYEIAVDSQLWRAVPDDPgetFKKGEIAYVKSVR 91
                                      456668889999999999988666.*****************744699************977789************* PP

                                      SSSEEEEE CS
                              NfeD 77 GltliVep 84
                                       ltl++ +
  gi|518651681|ref|YP_008141201.1| 92 DLTLYISK 99
                                      ****9876 PP

>> UPF0731  UPF0731 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.5e-05      0.13       8      45 ..      33      70 ..      25      91 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                           UPF0731  8 rrfpveggdssvglesglsssaacnrkeisptrqlrrc 45
                                      rr p  g ds vg+   + s+   n  ei+ + ql r 
  gi|518651681|ref|YP_008141201.1| 33 RRKPATGKDSLVGKTGEIKSTLKNNFYEIAVDSQLWRA 70
                                      999*******************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 732.00
//
Query:       gi|518651682|ref|YP_008141202.1|  [L=163]
Description: hypothetical protein FACI_IFERC00001G0321 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-40  138.6   2.7    1.5e-40  138.4   2.7    1.0  1  LDcluster4       SLOG cluster4 family
    9.9e-05   21.7   0.3        0.1   11.8   0.0    2.0  2  DNA_processg_A   DNA recombination-mediator protein A
     0.0023   18.0   0.2     0.0035   17.4   0.2    1.3  1  Lysine_decarbox  Possible lysine decarboxylase
  ------ inclusion threshold ------
      0.043   13.8   0.1      0.052   13.6   0.1    1.2  1  DUF2112          Uncharacterized protein conserved in archaea


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 !  138.4   2.7   3.3e-44   1.5e-40       2     157 .]       4     148 ..       3     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 3.3e-44
                        LDcluster4   2 lkigVmGsaeteakeealelaeelGrliAkegavlltGgrtGvmeaaskGakeagGltvGilpassekehsnkyvdi 78 
                                       ++igV+G +   a+++  ++a+e+G+ +A++++ +++Gg++G+me++s+G+++ +G++vGilp++++ e  nky+ +
  gi|518651682|ref|YP_008141202.1|   4 YNIGVIGGSF--ADKKYCNIAYEVGKKLAENNCAVFCGGKEGIMECVSHGVHDSNGMVVGILPGENRME-GNKYLSL 77 
                                       79*****888..78889***********************************************66655.7778*** PP

                        LDcluster4  79 iiyTGlglagRnlilvlssdvviaiggrsGTlsEialaleegkpvivlkgtdellseiiekkekderkvivaespke 155
                                        i+TG+g++ Rn++++++sd++iai+g sGT+sE a+a++egk+v+ + +        i k+++ ++k++++++p++
  gi|518651682|ref|YP_008141202.1|  78 TIPTGIGYM-RNFLIIRASDAIIAIEGYSGTTSEAAFAITEGKTVVSIGNL------QI-KTKDTDGKLVHENDPEK 146
                                       *********.***************************************33......22.23333335777777776 PP

                        LDcluster4 156 lv 157
                                       +v
  gi|518651682|ref|YP_008141202.1| 147 AV 148
                                       64 PP

>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   2.3e-05       0.1      44     104 ..       5      65 ..       1      78 [. 0.93
   2 !    8.4   0.1   0.00026       1.2     145     202 ..      86     140 ..      81     149 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.3e-05
                    DNA_processg_A  44 avaiVGtRkaseygkevakklakelaeagitivSGlAlGiDaaahraaleaggktvavlgt 104
                                       +++++G   a ++  ++a ++ k+lae+++++  G+  Gi ++   +  +++g  v++l++
  gi|518651682|ref|YP_008141202.1|   5 NIGVIGGSFADKKYCNIAYEVGKKLAENNCAVFCGGKEGIMECVSHGVHDSNGMVVGILPG 65 
                                       789999999************************************************9986 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00026
                    DNA_processg_A 145 eRnriiaglseavlvveaaekSGalitaelAlelgrevfavpgditskesagtnklik 202
                                       +Rn +i   s+a++ +e    SG+   a +A+ +g+ v+ + g+++ k+ +   kl++
  gi|518651682|ref|YP_008141202.1|  86 MRNFLIIRASDAIIAIEG--YSGTTSEAAFAITEGKTVVSI-GNLQIKTKDTDGKLVH 140
                                       699999999***999986..79****************995.5555555555555554 PP

>> Lysine_decarbox  Possible lysine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.2   7.9e-07    0.0035       1      75 [.      45     117 ..      45     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHHHTTS-EEEEEECCHHHHHCCTTT-SEEEEESSHHHHHHHHHHHESEEEE-S-SHHHHHHHHHHHHH CS
                   Lysine_decarbox   1 meavakgaleaggrviGiipkillaeeapneevnelvivedmeeRkealveladafvilPGGiGTleElleiltl 75 
                                       me v++g+++++g v+Gi p     e   n++++ ++ +    +R+  +++ +da++++ G  GT+ E+  ++t 
  gi|518651682|ref|YP_008141202.1|  45 MECVSHGVHDSNGMVVGILPGENRMEG--NKYLSLTIPTGIGYMRNFLIIRASDAIIAIEGYSGTTSEAAFAITE 117
                                       999***************777655444..777776677777789************************8777775 PP

>> DUF2112  Uncharacterized protein conserved in archaea (DUF2112)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05     0.052      50     141 ..      66     160 ..      43     162 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                           DUF2112  50 edpkkGlkyaavevPsGvrGRlsligplieeaeaaiiveead.....ilfgcvGCartnelvkalirkkdiPilele 121
                                       e++++G+ky ++ +P+G+ G +  +  +i+ ++a+i +e  +      +f+ +  +    + +  i++kd     ++
  gi|518651682|ref|YP_008141202.1|  66 ENRMEGNKYLSLTIPTGI-GYMRNF-LIIRASDAIIAIEGYSgttseAAFAITEGKTVVSIGNLQIKTKDTDGKLVH 140
                                       7899*************9.888765.689999999999985545555677777667777777777777776654444 PP

                           DUF2112 122 yPkseeeaielvkkineFLk 141
                                         + e+ +   ++++++F++
  gi|518651682|ref|YP_008141202.1| 141 ENDPEKAVEIAIQEAKNFVE 160
                                       44444444445677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1156.24
//
Query:       gi|518651683|ref|YP_008141203.1|  [L=172]
Description: hypothetical protein FACI_IFERC00001G0322 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.089   12.9   0.0      0.089   12.9   0.0    2.4  2  CrgA           Cell division protein CrgA
       0.14   11.9   0.3       0.14   11.9   0.3    3.1  3  Synaptobrevin  Synaptobrevin
        0.7    9.7  12.2       0.27   11.1   1.4    2.9  3  DUF2976        Protein of unknown function (DUF2976)
          1    9.3  11.2        1.6    8.7   1.8    3.0  3  ODV-E18        Occlusion-derived virus envelope protein ODV-E


Domain annotation for each model (and alignments):
>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     2e-05     0.089      16      63 ..      29      76 ..       7      95 .. 0.78
   2 ?   -2.4   4.9       1.2   5.3e+03      39      57 ..     110     129 ..     102     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
                              CrgA 16 aaertpvkakaakpsprwyvpvmlglmllGllwlvvyYlageeipfma 63
                                      +++r++vk++ +k+++++   + +g++++G++ +++  ++ ++i  ++
  gi|518651683|ref|YP_008141203.1| 29 TQNREQVKTTPEKSDKHVKLYIEIGIVIVGIILIIIASVQIKSIAHVK 76
                                      7889999999999999999999**************999999888443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.2
                              CrgA  39 lglmllGllw.lvvyYlage 57 
                                       l+l+++ ++  +++yYl + 
  gi|518651683|ref|YP_008141203.1| 110 LTLVIIAVIGiILLYYLLAP 129
                                       44555555440455777655 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   3.2e-05      0.14      64      87 ..      44      67 ..      31      69 .. 0.90
   2 ?    3.3   0.3     0.015        69      69      84 ..     111     126 ..     101     131 .. 0.57
   3 ?   -1.7   0.9      0.56   2.5e+03      73      81 ..     149     157 ..     143     163 .. 0.45

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.2e-05
                                      HTXXXXXXXXXXXXXXXXXXXXXX CS
                     Synaptobrevin 64 knmkliiililvvlililiiiivi 87
                                      k++kl+i +++v++ +iliii+++
  gi|518651683|ref|YP_008141203.1| 44 KHVKLYIEIGIVIVGIILIIIASV 67
                                      789*****************9875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.015
                                       XXXXXXXXXXXXXXXX CS
                     Synaptobrevin  69 iiililvvlililiii 84 
                                       ++++i+v+ i++l+++
  gi|518651683|ref|YP_008141203.1| 111 TLVIIAVIGIILLYYL 126
                                       4444444444444443 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.56
                                       XXXXXXXXX CS
                     Synaptobrevin  73 ilvvlilil 81 
                                       i+++l++++
  gi|518651683|ref|YP_008141203.1| 149 IGIFLVIFM 157
                                       222222222 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4     6e-05      0.27      19      56 ..      45      82 ..      17      94 .. 0.89
   2 ?    3.6   0.4     0.013        58      40      77 ..      89     125 ..      83     132 .. 0.71
   3 ?    0.5   5.1      0.12   5.5e+02      33      82 ..     112     161 ..     109     165 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6e-05
                           DUF2976 19 likgylkdgvillgLvlaavaflaVakaalkkfneise 56
                                       +k y++ g++++g++l  +a +++ + a  k+ne se
  gi|518651683|ref|YP_008141203.1| 45 HVKLYIEIGIVIVGIILIIIASVQIKSIAHVKWNEFSE 82
                                      6899*******************************865 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.013
                           DUF2976  40 flaVakaalkkfneisegkaewgkfgltlvvGvvllvv 77 
                                       ++ ++   l  f+  ++ k  ++ + +++v+G++ll  
  gi|518651683|ref|YP_008141203.1|  89 IIFIVLPSLLYFKKLRSLKPALT-LVIIAVIGIILLYY 125
                                       55666666667777777777776.56678899999864 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.12
                           DUF2976  33 LvlaavaflaVakaalkkfneisegkaewgkfgltlvvGvvllvvviwLl 82 
                                       Lv+ av  +   + +l+ ++  s     +g++ +  ++G+ l++++i  l
  gi|518651683|ref|YP_008141203.1| 112 LVIIAVIGIILLYYLLAPYKMFSVRFGLLGDVLVEYLIGIFLVIFMISHL 161
                                       55555555566677888888888888889999999999999999988655 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0018         8      24      43 ..      46      65 ..      23      75 .. 0.72
   2 ?    8.7   1.8   0.00036       1.6      17      43 ..     101     127 ..      98     135 .. 0.87
   3 ?   -1.5   0.5      0.53   2.4e+03      30      44 ..     143     157 ..     133     162 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0018
                           ODV-E18 24 Psllltilvvlviiillvll 43
                                       +l++ i +v+v iil+++ 
  gi|518651683|ref|YP_008141203.1| 46 VKLYIEIGIVIVGIILIIIA 65
                                      57889999999999998874 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00036
                           ODV-E18  17 rrlarlePsllltilvvlviiillvll 43 
                                       ++l  l+P+l l i++v+ ii+l  ll
  gi|518651683|ref|YP_008141203.1| 101 KKLRSLKPALTLVIIAVIGIILLYYLL 127
                                       57899****************998776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.53
                           ODV-E18  30 ilvvlviiillvllv 44 
                                       +lv  +i i+lv+++
  gi|518651683|ref|YP_008141203.1| 143 VLVEYLIGIFLVIFM 157
                                       566666767777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1103  (0.0615204); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1126.83
//
Query:       gi|518651684|ref|YP_008141204.1|  [L=387]
Description: hypothetical protein FACI_IFERC00001G0323 [Ferroplasma acidarmanus fer1]
Scores for complete 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-77  260.3   0.9    2.1e-77  260.0   0.9    1.1  1  Thiolase_N     Thiolase, N-terminal domain
    9.2e-37  125.4   0.0    2.4e-36  124.1   0.0    1.8  1  Thiolase_C     Thiolase, C-terminal domain
     0.0013   18.3   0.3     0.0069   16.0   0.1    2.1  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
       0.12   12.6   1.3        1.2    9.3   0.2    2.4  2  Attacin_N      Attacin, N-terminal region


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 !  260.0   0.9   4.7e-81   2.1e-77       1     259 [.       4     256 ..       4     257 .. 0.98

  Alignments for each domain:
  == domain 1  score: 260.0 bits;  conditional E-value: 4.7e-81
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSE CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevp 77 
                                       v+ivsa+rtpigkfg sl++++a+eL+a+a+k+++++ g+d++ ++evi+Gnv+qa+ gqn+a qaa+ ag+  ev+
  gi|518651684|ref|YP_008141204.1|   4 VYIVSAKRTPIGKFGKSLAKIKATELGAAAIKGVIQDSGIDKDLIEEVIMGNVIQANVGQNPAGQAAFSAGLKPEVT 80 
                                       89*************************************************************************** PP

                                       EEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT...TGGSSSSEEEEEHHHHHHTEETTT CS
                        Thiolase_N  78 avtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr...sglklgdekakdllipdgladafn 151
                                         tvn vc+Sg+ a  +aa++i+  e d++v gG E+msn+p  +++++r   ++l +++ k++d ++ dgl+da+ 
  gi|518651684|ref|YP_008141204.1|  81 KNTVNVVCASGMLATENAAREIMLEEHDIIVSGGFENMSNSPLIMPSEFRwgpKQLLYKNLKIEDSMLVDGLVDAMY 157
                                       **************************************************87778999******************* PP

                                       TSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHT CS
                        Thiolase_N 152 eehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLak 228
                                       +ehmG++ae+ akky+i+R++ d f v+s+++a  a+++g+F++ei  vk+++      ++kde++r+ +++e Lak
  gi|518651684|ref|YP_008141204.1| 158 GEHMGVSAERSAKKYGITRDQTDGFSVESQNRAIRATESGEFAREI--VKLDN------LQKDEGMRK-TSMEDLAK 225
                                       **********************************************..55555......78******9.******** PP

                                       S-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 229 lkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                       l+paF+ +G  tAg +sq+sDGa+a++l+se
  gi|518651684|ref|YP_008141204.1| 226 LNPAFDRNGILTAGSSSQLSDGASALILASE 256
                                       *****************************98 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.0   5.4e-40   2.4e-36       1     122 [.     264     385 ..     264     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 5.4e-40
                                       ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHH CS
                        Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaia 77 
                                       lkp+aki+ +++++ d +++  +P++a++k+l+k+  +++  dl+E nEAF++  + v  +l++++e++NvnGGaia
  gi|518651684|ref|YP_008141204.1| 264 LKPIAKITGFSSASLDTRDFVEAPIPATRKLLEKQHKNIDYYDLVEHNEAFSVASIIVRDQLGVAQERFNVNGGAIA 340
                                       589************************************************************************** PP

                                       H-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEE CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalvie 122
                                       +GHPlG sG+Ri+vtl+++l+ ++ k+g+a++C ggg g++l +e
  gi|518651684|ref|YP_008141204.1| 341 IGHPLGNSGSRIIVTLINALQSRHMKTGLATICHGGGGGHTLTLE 385
                                       ****************************************99876 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 !   16.0   0.1   1.5e-06    0.0069     169     207 ..      82     120 ..      29     126 .. 0.83
   2 ?   -0.1   0.0      0.13   5.7e+02      54     116 ..     213     268 ..     183     335 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-06
                                       EEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 169 vtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                        tv   C+S+  a + a ++++  e d+++ GG e + +
  gi|518651684|ref|YP_008141204.1|  82 NTVNVVCASGMLATENAAREIMLEEHDIIVSGGFENMSN 120
                                       478889****99999999***************997754 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.13
                                       EE-BSS.EEE..S.TTEGGTTSTHHHHHHHCTS-HHHHHHHHHHHHHHHHHTS-HHTCTTGGEE CS
                     ketoacyl-synt  54 agkiktklggfld.vddfdpeffgispreaeamdpqqrllleaawealedagltpeeldgsrvg 116
                                       +g+ kt++  + + + +fd        +   +++  +  l+ a+++al+++gl+p       ++
  gi|518651684|ref|YP_008141204.1| 213 EGMRKTSMEDLAKlNPAFDRNGILTAGS-SSQLSDGASALILASEKALNEYGLKP-------IA 268
                                       4444444444444444444443333222.34677777778888899999999888.......33 PP

>> Attacin_N  Attacin, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00026       1.2       5      38 ..      61      98 ..      57     114 .. 0.83
   2 ?    1.5   0.0     0.073   3.3e+02      18      37 ..     324     343 ..     317     355 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00026
                         Attacin_N  5 ltsnPtGgAdarlklt..lgtpdhnvl..aqvFAagnt 38
                                      +  nP+G+A   ++l   ++++  nv+  +++ A+ n+
  gi|518651684|ref|YP_008141204.1| 61 VGQNPAGQAAFSAGLKpeVTKNTVNVVcaSGMLATENA 98
                                      567************99*********833567777666 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.073
                         Attacin_N  18 kltlgtpdhnvlaqvFAagn 37 
                                       +l ++++ +nv +++ A+g 
  gi|518651684|ref|YP_008141204.1| 324 QLGVAQERFNVNGGAIAIGH 343
                                       56689999*********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2458.51
//
Query:       gi|518651685|ref|YP_008141205.1|  [L=140]
Description: hypothetical protein FACI_IFERC00001G0324 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-20   72.7   2.0    2.7e-20   72.4   2.0    1.1  1  DUF86     Protein of unknown function DUF86
     0.0077   16.3   0.2      0.015   15.4   0.2    1.8  1  DUF4145   Domain of unknown function (DUF4145)


Domain annotation for each model (and alignments):
>> DUF86  Protein of unknown function DUF86
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   2.0     3e-24   2.7e-20       3     118 ..      15     131 ..       8     132 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 3e-24
                                       HHHHHHCCHH...TSTSCCGSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----SSC..HHHHHHHTTSS-HHHHH CS
                             DUF86   3 ealeklkefteeldeeeflsdeleydavernlqvigEaaidiakhlakklgikkpgdy..ifeilaekgviaeepee 77 
                                       ++l+++ e     ++++f +  + +d +++ ++ ++E++idi  ++ ++++++ p+d+   +++l+ k++i+e+ ++
  gi|518651685|ref|YP_008141205.1|  15 QSLDLVTENM-PDTFDKFNELGIIKDGIYKRIEYSIENLIDIFYMFNSDFKLGIPSDDsdLINNLKAKNIISEDIAI 90 
                                       5555555555.566999999********************************************************* PP

                                       HHHHHHCCHHHHHT-CCCTTHHHHHHHHHHTCHHHHHHHHH CS
                             DUF86  78 pwrkmiglRNrLvHgYlgidpeivwsiikenlpdleefles 118
                                       ++r ++g+RN++vH+Y +id++  ++ ik+nl+d+  ++++
  gi|518651685|ref|YP_008141205.1|  91 RMRDLKGFRNIVVHRYSKIDDRMAYDFIKTNLDDFYIIINA 131
                                       **********************************9988876 PP

>> DUF4145  Domain of unknown function (DUF4145)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   1.7e-06     0.015      38      80 ..      72     114 ..       3     122 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.7e-06
                           DUF4145  38 knkiealvekgvipeklkelldairviGNdgaHelkditkeda 80 
                                        + i++l +k++i+e+++  ++ ++ ++N+ +H++ +i    a
  gi|518651685|ref|YP_008141205.1|  72 SDLINNLKAKNIISEDIAIRMRDLKGFRNIVVHRYSKIDDRMA 114
                                       6789*****************************9888876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 926.91
//
Query:       gi|518651686|ref|YP_008141206.1|  [L=122]
Description: Nucleotidyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-13   50.3   0.4    2.5e-13   49.9   0.4    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
    4.3e-08   33.3   0.0      5e-08   33.1   0.0    1.3  1  NTP_transf_2  Nucleotidyltransferase domain


Domain annotation for each model (and alignments):
>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.4   2.8e-17   2.5e-13       8      92 ..      12      92 ..       5      93 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.8e-17
                                      HHHHHHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EE CS
                           Polbeta  8 ekekeielaylFGSrakgkareeSDiDlavllkekldleeelelaaelediklgkkvDlvdlneapplllyeilkegkl 86
                                        ++++ +++ +GS+ ++++++ SDiDl+++++ +  lee+ ++   + +  l++ +D++++++ p+++++ +l+ gkl
  gi|518651686|ref|YP_008141206.1| 12 YGNNKVVFIMNYGSYSNNTFHNGSDIDLCIYYNGT--LEERQKFRLSMLSS-LNDIFDVQIFQDLPLYIRKDVLN-GKL 86
                                      45679******************************..34433333333333.45669******************.*** PP

                                      EES-SH CS
                           Polbeta 87 lyskde 92
                                      ly kd+
  gi|518651686|ref|YP_008141206.1| 87 LYMKDK 92
                                      ***997 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   5.6e-12     5e-08      14      76 ..      17      70 ..       2     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.6e-12
                                      TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEEEECE CS
                      NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevdlvtr 76
                                      v+ +  +GSy ++t++ gSDiDl+++++   +     e+++ +  + + l+       d+ ++
  gi|518651686|ref|YP_008141206.1| 17 VVFIMNYGSYSNNTFHNGSDIDLCIYYNGTLE-----ERQKFRLSMLSSLND----IFDVQIF 70
                                      7778889***********************66.....444444444444444....3444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 786.75
//
Query:       gi|518651687|ref|YP_008141207.1|  [L=393]
Description: acetyl-CoA acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-59  201.6   0.0    2.2e-59  200.9   0.0    1.3  1  Thiolase_N     Thiolase, N-terminal domain
    4.1e-47  158.9   0.1    1.6e-46  156.9   0.1    1.9  2  Thiolase_C     Thiolase, C-terminal domain
    1.3e-07   31.5   0.3    1.3e-07   31.5   0.3    1.8  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.024   13.4   0.1      0.061   12.0   0.0    1.7  2  SpoVAD         Stage V sporulation protein AD (SpoVAD)


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 !  200.9   0.0     5e-63   2.2e-59       3     259 ..       6     262 ..       4     263 .. 0.90

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 5e-63
                                       EEEEEEE--EET......TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHTTS CS
                        Thiolase_N   3 ivsaartpigkf......ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalkagi 72 
                                       i+  +rtp+ +       + +++ +s++ Ll++++k+ l+ +g++pe++ +vi G+ +qage+++   r+ +l +++
  gi|518651687|ref|YP_008141207.1|   6 IAYYKRTPFSRAkpdnpsKDVYNGVSMDVLLSKLIKDSLS-TGINPEDIGDVITGCAIQAGENWTyGGRHQTLLSEL 81 
                                       55566666654211111167888999999*********96.89**********************999********* PP

                                       -TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEET CS
                        Thiolase_N  73 peevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdglada 149
                                       p +vp+++++++csS+l+a a +a +i++g++dvv+agG+E+m+++p +++      +k+++e +++   ++   d+
  gi|518651687|ref|YP_008141207.1|  82 PVSVPSMAIDRACSSSLNATAIGAMEIQTGNSDVVLAGGMEHMTHVPLYND----PYVKYNTELMEKPEYRK--YDM 152
                                       *************************************************98....45667777777766666..778 PP

                                       TTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHH CS
                        Thiolase_N 150 fneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekL 226
                                          +h+Gltae+la+  +isRee d+f  +s++  a a+++g +++ei+Pvkv++  + kt+++d+++r+e+t+e++
  gi|518651687|ref|YP_008141207.1| 153 DVTYHVGLTAEKLAAINNISREEMDKFSFESQKLTAHAIEEGFYNNEILPVKVTHDGSAKTINADQTPRPESTLEQM 229
                                       899***************************************************96666****************** PP

                                       HTS-BSSSTTSS-BTTSB--BEEEEEEEEEEEH CS
                        Thiolase_N 227 aklkpaFkkeGtvtAgnasqisDGaaavllmse 259
                                       ++lkpaF ++G vtAgn+ ++s Ga+ ++lms 
  gi|518651687|ref|YP_008141207.1| 230 SQLKPAFIENGRVTAGNSPPLSSGASLLMLMSG 262
                                       *******************************85 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.35   1.6e+03      12      57 ..      70     118 ..      64     126 .. 0.65
   2 !  156.9   0.1   3.7e-50   1.6e-46       1     123 []     270     392 ..     270     392 .. 0.99

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.35
                                       EEE--GGGGGGHHHHHHHHHHHHH...T--GGGESEEEE--SBHHHHHH CS
                        Thiolase_C  12 evgvdpeilglgPayaikkvlkka...gltvedidlfEinEAFaaqaLa 57 
                                       + g + + l   P+ + ++++++a    l+   i ++Ei+   + ++La
  gi|518651687|ref|YP_008141207.1|  70 YGGRHQTLLSELPVSVPSMAIDRAcssSLNATAIGAMEIQTGNSDVVLA 118
                                       5555566666666666666666652225777788888888777777665 PP

  == domain 2  score: 156.9 bits;  conditional E-value: 3.7e-50
                                       ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHH CS
                        Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaia 77 
                                       lkpla++ +ya +gvdp+i+g gP++a++k+lkk+ l+ ++id++EinEAFa++aL ++k+l+ld ++vN++GG+ia
  gi|518651687|ref|YP_008141207.1| 270 LKPLARVIDYAAAGVDPTIMGHGPVPATNKLLKKNKLSPDNIDYWEINEAFAVVALNAIKHLNLDRNRVNIHGGSIA 346
                                       589************************************************************************** PP

                                       H-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                       +GHPlGa+GaRi+ tl+++l++++g+lgva+lC gggqg +l+iek
  gi|518651687|ref|YP_008141207.1| 347 IGHPLGATGARIAGTLARTLQEKKGNLGVATLCVGGGQGYSLLIEK 392
                                       *******************************************986 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.3   2.8e-11   1.3e-07     167     207 ..      86     126 ..      79     130 .. 0.93
   2 ?   -2.3   0.1      0.57   2.6e+03     180     223 ..     323     365 ..     319     391 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 2.8e-11
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       ps+++d ACsSsl a +   +++++g++dv+laGG+e +++
  gi|518651687|ref|YP_008141207.1|  86 PSMAIDRACSSSLNATAIGAMEIQTGNSDVVLAGGMEHMTH 126
                                       9************************************9887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTTBB-TT CS
                     ketoacyl-synt 180 vavhaavqslrsgeadvalaGGvellltpeavagfsaagllspd 223
                                       va++a+ ++l   +  v + GG+ ++ +p +  g   ag l+++
  gi|518651687|ref|YP_008141207.1| 323 VALNAI-KHLNLDRNRVNIHGGSIAIGHPLGATGARIAGTLART 365
                                       455555.7777777777788888888888877777777766665 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.4e-05     0.061      95     137 ..      83     125 ..      49     130 .. 0.93
   2 ?   -2.6   0.0      0.38   1.7e+03      58      75 ..     296     313 ..     275     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.4e-05
                                       H---EEEB--GGGHHHHHHHHHHHHHHTTS-SEEEEEEEE-CC CS
                            SpoVAD  95 lkiPflglygaCstsaeslalaallvdggfakrvlaatsshfa 137
                                       +++P +++  aCs+s ++ a++a+ +++g ++ vla+   h +
  gi|518651687|ref|YP_008141207.1|  83 VSVPSMAIDRACSSSLNATAIGAMEIQTGNSDVVLAGGMEHMT 125
                                       68999*******************************9999976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.38
                                       HHHHHHHHTT--GGG-SE CS
                            SpoVAD  58 avkkalkkanlkkedidf 75 
                                       a++k lkk++l+ ++id+
  gi|518651687|ref|YP_008141207.1| 296 ATNKLLKKNKLSPDNIDY 313
                                       667888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2756.21
//
Query:       gi|518651688|ref|YP_008141208.1|  [L=116]
Description: hypothetical protein FACI_IFERC00001G0327 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 00:00:00.39
# Mc/sec: 887.18
//
Query:       gi|518651689|ref|YP_008141209.1|  [L=527]
Description: hypothetical protein FACI_IFERC00001G0328 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.4      6e-06   26.1   0.4    1.5  1  Peptidase_S24  Peptidase S24-like


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.4   3.4e-10     6e-06       2      61 ..     383     452 ..     382     462 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 3.4e-10
                                       XXSSTTCCTXXTTXEEEEECTS...---TTSEEEEEETTCE......-EEEEEEEEETTEEEEE.SST.T CS
                     Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs...epkrGdivvfrlpgee......eayiKrviglpgdrvllasnn.e 61 
                                       v+G SM+p+++ Gd +++++     e+k Gdi+  +  + +       ++ +r+ +  gd+++++ +n +
  gi|518651689|ref|YP_008141209.1| 383 VRGISMNPEFKAGDSVIIKRIKtwhELKVGDIITYKSSNINsplnasGYITHRIHEISGDIIRTKGDNnK 452
                                       8899***************999999**********99999899********************9988732 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); 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):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3635.48
//
Query:       gi|518651690|ref|YP_008141210.1|  [L=83]
Description: hypothetical protein FACI_IFERC00001G0329 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.011   16.2   0.8      0.012   16.1   0.8    1.1  1  DUF1690    Protein of Unknown function (DUF1690)
      0.016   15.8   4.1      0.018   15.6   3.7    1.3  1  TetR_C_19  Tetracyclin repressor-like, C-terminal domain
      0.036   14.1   0.5      0.041   14.0   0.5    1.1  1  DUF1539    Domain of Unknown Function (DUF1539)
      0.039   14.2   0.0      0.046   14.0   0.0    1.1  1  UBD        Ubiquitin-binding domain
       0.54   10.5   6.1       0.58   10.4   0.6    2.7  3  DUF5446    Family of unknown function (DUF5446)


Domain annotation for each model (and alignments):
>> DUF1690  Protein of Unknown function (DUF1690)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.1   0.8   3.3e-06     0.012      33      78 ..       8      51 ..       3      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.3e-06
                           DUF1690 33 kliqerVaeeLkkLraeeeetlkkfeeklekellkdeadakdelss 78
                                      k +++ ++e+L++ r+  e+  +++ +kl++++l++e  ++++ls 
  gi|518651690|ref|YP_008141210.1|  8 KKLEDNITEQLDNFRQTAEKNFNEIYDKLNNQKLSEE--NEENLSL 51
                                      567999******************************9..4444443 PP

>> TetR_C_19  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   3.7   5.1e-06     0.018      36      86 ..       9      61 ..       3      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.1e-06
                         TetR_C_19 36 kiekkftkefkkkkkker..lkelyelidkskLnieseeelklllkilmavtf 86
                                      k e+++t++ ++ ++  +  ++e+y+ ++++kL  e+ee l+l l+++ a+ +
  gi|518651690|ref|YP_008141210.1|  9 KLEDNITEQLDNFRQTAEknFNEIYDKLNNQKLSEENEENLSLALTMMEALGI 61
                                      67888899888888877778***************************998765 PP

>> DUF1539  Domain of Unknown Function (DUF1539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   1.1e-05     0.041      20      72 ..       4      59 ..       1      70 [. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
                           DUF1539 20 kelnrkLekeik....klaqnlrdeWkkilkylskkesseveseeaqalfrstlkkl 72
                                      +e ++kLe++i+    +  q+ ++++++i + l++ ++ ++e+ee+ +l+ +++  l
  gi|518651690|ref|YP_008141210.1|  4 TEDMKKLEDNITeqldNFRQTAEKNFNEIYDKLNN-QKLSEENEENLSLALTMMEAL 59
                                      556778888888333355566999***********.888888999999999999876 PP

>> UBD  Ubiquitin-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.3e-05     0.046      18      72 ..       9      64 ..       2      73 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.3e-05
                               UBD 18 ltraqlerereeFfdTrvtgrkeiWdalkaal.evleeddlataqaildaaeitlp 72
                                        + +++++ ++F +T+ ++ +ei+d l++   +  +e++l++a ++++a +i + 
  gi|518651690|ref|YP_008141210.1|  9 KLEDNITEQLDNFRQTAEKNFNEIYDKLNNQKlSEENEENLSLALTMMEALGIDIL 64
                                      56788999********************986503345666**********999775 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00016      0.58      16      51 ..       2      37 ..       1      43 [. 0.90
   2 ?    0.5   0.1      0.19     7e+02      23      37 ..      44      58 ..      39      60 .. 0.78
   3 ?    1.4   0.0       0.1   3.7e+02       9      22 ..      62      75 ..      60      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                           DUF5446 16 eiEeeltevEkelseavneteaekeekeeerldlle 51
                                      +  e++++ E +++e++ + ++ +e++ +e+ d+l+
  gi|518651690|ref|YP_008141210.1|  2 DSTEDMKKLEDNITEQLDNFRQTAEKNFNEIYDKLN 37
                                      55689**************************99997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.19
                           DUF5446 23 evEkelseavnetea 37
                                      e E++ls+a+ + ea
  gi|518651690|ref|YP_008141210.1| 44 ENEENLSLALTMMEA 58
                                      568999999988775 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.1
                           DUF5446  9 svLqlLeeiEeelt 22
                                      ++L+l+ + E+ ++
  gi|518651690|ref|YP_008141210.1| 62 DILHLIRDYEDLVD 75
                                      79*******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1925  (0.107368); expected 358.6 (0.02)
Passed bias filter:                      837  (0.0466841); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 565.50
//
Query:       gi|518651691|ref|YP_008141211.1|  [L=552]
Description: hypothetical protein FACI_IFERC00001G0330 [Ferroplasma acidarmanus fer1]
Scores for 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-204  679.0   4.0   4.6e-204  678.8   4.0    1.0  1  ILVD_EDD  Dehydratase family


Domain annotation for each model (and alignments):
>> ILVD_EDD  Dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  678.8   4.0  2.5e-208  4.6e-204       3     517 .]      34     549 ..      32     549 .. 0.98

  Alignments for each domain:
  == domain 1  score: 678.8 bits;  conditional E-value: 2.5e-208
                          ILVD_EDD   3 iigiansyselvpchvhlkelaeavkegveeaggvpaefntigvsDgiamgeegmrysLpsReliadsvetmleaql 79 
                                       ++g+a +++e  pc+ h+ +la++ keg+++ +g+p  f t  v Dgiamg+egm+ysL+sRel a++ve +++a+ 
  gi|518651691|ref|YP_008141211.1|  34 MVGVAAAWNEAGPCNIHVLSLANHTKEGIRSREGTPRVFATPVVIDGIAMGTEGMKYSLVSRELTANTVELTVNAHG 110
                                       69*************************************************************************** PP

                          ILVD_EDD  80 lDalvlisgCDKivPgllmaaarlniPaifvsgGpmeagkkk..kldlssvfeavgalaagkiseeeleeleeaacp 154
                                       +D++ ++sgCDK+ Pg++ma+ar+niP+i++++G+ ++g +k  ++ + + feavga+ +++++ ++++ +e++a+p
  gi|518651691|ref|YP_008141211.1| 111 YDGFAALSGCDKTSPGMMMAMARMNIPSIVMYSGTTLPGYYKgkRIAVGDLFEAVGAYMNNTMTLQDFKLMEDNAIP 187
                                       **************************************88665589999**************************** PP

                          ILVD_EDD 155 gaGsCsgmgTAntmaclaealGlslpgsasipatsaerkelaeeagkrivelvekdlkprdiltkeafeNAivvlla 231
                                       +aGsC+g++TAntma+++e+lGl+lpgsas pa++ +++++a+++g+++++l+e+ lkprdilt+e+f NAi+vl+a
  gi|518651691|ref|YP_008141211.1| 188 TAGSCGGLYTANTMAMMTEVLGLALPGSASPPAVDGAKQKFAYKTGETVMQLIETGLKPRDILTEESFYNAITVLMA 264
                                       ***************************************************************************** PP

                          ILVD_EDD 232 lGGStNavlHllAiAreagveltlddfdelsrkvpllaklkPsgkydmedlhraGGvpavlkeLlkagllhgdvltv 308
                                        GGStNavlHllAiA+ea+++l+lddfd++srkvp ++++kPsg+y m dl+++GGvp+++k L ++gl++gd ltv
  gi|518651691|ref|YP_008141211.1| 265 SGGSTNAVLHLLAIAHEAKIKLDLDDFDRISRKVPEIVNMKPSGEYVMADLNNIGGVPVLMKVLMDHGLIDGDQLTV 341
                                       ***************************************************************************** PP

                          ILVD_EDD 309 tgktlaenlee.aevkeqdvirplekplskegglavLkGnLapeGavvKtsaveeellkfegpArvfdseeeaveai 384
                                       tgkt++enl++ +  ++ dvi +++kp++++gg+++LkGnLa+eG v Ktsa +  ++ ++gpA+vf+seee ++ i
  gi|518651691|ref|YP_008141211.1| 342 TGKTVKENLKDiKIYTTGDVISDFDKPYKSDGGISILKGNLATEGGVFKTSASK--VKYHKGPAKVFNSEEETFKGI 416
                                       *********9988889*************************************9..88899**************** PP

                          ILVD_EDD 385 lkgkikagdvvviryeGPkGgpGmpEmlkptsallgkglgkkvalitDGRfSGaskglvighvsPEAaegGpialve 461
                                       +++kikagd vviryeGPkGgpGm+Eml++ts l+g+glg++valitDGRfSGa++g+++gh++PEA++gG ia+v+
  gi|518651691|ref|YP_008141211.1| 417 KDKKIKAGDTVVIRYEGPKGGPGMREMLSVTSELIGEGLGDSVALITDGRFSGATRGIMVGHIAPEAMDGGLIAIVK 493
                                       99*************************************************************************** PP

                          ILVD_EDD 462 dGDiieidiekrtlelevseeelaaRraawkpekkvkt.rgllakyaklvssaseGA 517
                                       dGD+ieid+++r+++l+v+e+e+++R ++wk+ ++ k+ +gll++yaklv s s+GA
  gi|518651691|ref|YP_008141211.1| 494 DGDMIEIDAPNRKINLLVDEAEITRRMKEWKK-PDIKYeTGLLNQYAKLVASSSKGA 549
                                       *******************************9.334334*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       313  (0.0174578); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 3495.62
//
Query:       gi|518651692|ref|YP_008141212.1|  [L=579]
Description: hypothetical protein FACI_IFERC00001G0331 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  186.2   0.0    9.6e-53  178.3   0.0    2.3  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    1.9e-41  141.4   1.6    2.8e-41  140.8   0.1    2.1  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.6e-34  117.9   0.0      5e-34  117.0   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
    0.00081   19.2   0.2      0.002   17.9   0.1    1.7  2  POR_N         Pyruvate flavodoxin/ferredoxin oxidoreductase, 
  ------ inclusion threshold ------
       0.04   13.7   0.1       0.18   11.6   0.1    2.0  1  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   2.7e-56   9.6e-53       3     170 ..       6     175 ..       4     177 .. 0.98
   2 !    5.6   0.0     0.003        11      79     160 ..     455     544 ..     430     550 .. 0.64

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 2.7e-56
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       ++++lv+ Lk++g +++fg+pG  ++p++d+l e     ++r++l+rhEq+aa+aAdgyaratg++gv+ +t+gpG+
  gi|518651692|ref|YP_008141212.1|   6 GSKLLVDSLKREGTKSIFGIPGLYNMPMYDSLIEDIesgELRHILMRHEQAAAHAADGYARATGNVGVCTATAGPGV 82 
                                       789*****************************9988889************************************** PP

                                       HHCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS-- CS
                      TPP_enzyme_N  77 tnaltalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirtalsgrpg 153
                                       tn++t+l++A++d++P+++++g +++   g+  +q e d l++  pvtkya++v++ ee+p+ +r A+ +a +grpg
  gi|518651692|ref|YP_008141212.1|  83 TNIVTGLITAYQDSSPVVAITGAVNRNAMGKLSFQ-ESDTLGVSFPVTKYAVEVKTIEEIPVWVRNAFYIASTGRPG 158
                                       ***********************************.*******99******************************** PP

                                       EEEEEEEHHHCC-EEEH CS
                      TPP_enzyme_N 154 Pvylelpkdvlleevde 170
                                       Pv++++p+d+++e++++
  gi|518651692|ref|YP_008141212.1| 159 PVVVDIPRDIQMENIEK 175
                                       *************9986 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.003
                                       CHHHHHHHHHHT--EEEEEEE--CCCHH...S..TC--T-CCHH..............HCCCSSEEEE-SSGGGHHH CS
                      TPP_enzyme_N  79 altalaeAkvdriPllvlsgdrptslrg...qgvlqqeldqlal..............frpvtkyaervtspeelpe 138
                                       + ++la+A  ++iP+++++ d+ t       q+++q+    + +              ++++  +a+  ++ +++ e
  gi|518651692|ref|YP_008141212.1| 455 TGNNLATAVDENIPVIAVVNDNRTLGLVrqvQDMFQS----KRIvgvdygnspnilkyAESFGADAFDANNYSDISE 527
                                       4478****************99998777455444443....333222333334444446666677777777777777 PP

                                       HHHHHHHHHHSSS--EEEEEEE CS
                      TPP_enzyme_N 139 alrrAirtalsgrpgPvylelp 160
                                        + +Air        P+++ +p
  gi|518651692|ref|YP_008141212.1| 528 FIGKAIRDN-----VPAVIRVP 544
                                       777777765.....55555555 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.1       2.2   7.8e+03      64      78 ..      88     102 ..      68     104 .. 0.59
   2 ?   -2.7   0.0       1.3   4.5e+03     126     153 .]     132     164 ..     123     164 .. 0.77
   3 !  140.8   0.1   7.9e-45   2.8e-41       1     153 []     395     543 ..     395     543 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.2
                                       GHHHHHHTT-SEEEE CS
                      TPP_enzyme_C  64 elatavrrnlpitvv 78 
                                        l+ta +   p++ +
  gi|518651692|ref|YP_008141212.1|  88 GLITAYQDSSPVVAI 102
                                       344444444444333 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       EESSH.HHHHHHHHHHHH.....CSSSEEEEEE CS
                      TPP_enzyme_C 126 rvekadveeleealkeal.....ekkgpaliev 153
                                        ve++++ee+   ++ a+      + gp+++++
  gi|518651692|ref|YP_008141212.1| 132 AVEVKTIEEIPVWVRNAFyiastGRPGPVVVDI 164
                                       677888888888888888788788999999986 PP

  == domain 3  score: 140.8 bits;  conditional E-value: 7.9e-45
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitv 77 
                                       ++G++++wa  +++  +prs+++s+g+gtmG+glp AiGak+ kp++ vv + GDG+f+m+++ latav +n+p++ 
  gi|518651692|ref|YP_008141212.1| 395 GVGQHQMWAETHWENLEPRSFFSSTGMGTMGFGLPCAIGAKVGKPEKVVVDYDGDGSFMMTGNNLATAVDENIPVIA 471
                                       69*************************************************************************** PP

                                       EEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEEE CS
                      TPP_enzyme_C  78 vvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpaliev 153
                                       vv +N+++g++++ q++f +kr +g+++  ++++++ k+ae++Ga+++  +++  +++ e + +a++ + pa+i v
  gi|518651692|ref|YP_008141212.1| 472 VVNDNRTLGLVRQVQDMFQSKRIVGVDY--GNSPNILKYAESFGADAFDANNY--SDISEFIGKAIRDNVPAVIRV 543
                                       *************************996..9999************9886777..******************976 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 !  117.0   0.0   1.4e-37     5e-34       2     137 .]     199     334 ..     198     338 .. 0.94

  Alignments for each domain:
  == domain 1  score: 117.0 bits;  conditional E-value: 1.4e-37
                                       HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH- CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmgkgvipedhplylgmlglhgskaanealeea 78 
                                       +++a  l +a++pvilvG+gv +++a+ee+ +l+e lg+Pvv+tl gk+++p d ply+g +g+ g ++a++++ e+
  gi|518651692|ref|YP_008141212.1| 199 REMATNLLKAEKPVILVGNGVTWANATEEVLKLSEFLGCPVVSTLPGKSAVPADYPLYVGAMGYYGRAEASMVALES 275
                                       6889999********************************************************************** PP

                                       SEEEEES-SSSTCCCTTTTTTTTTT-.EEEEEESSCCCCTTCC--SEEEECTHHHHHHHH CS
                      TPP_enzyme_M  79 DlvlalGarfddirttgsepefapea.kiihididpaeigknyqvdlaivgdvketleaL 137
                                       Dl+la+Garf+d rt+ s++e++  +  ++ i+ dp+++ k  ++d+++ g++k  +++L
  gi|518651692|ref|YP_008141212.1| 276 DLLLAVGARFSD-RTFTSYEEMNDTKkLFMAINLDPTDFTKGIKPDVSMAGNAKILVNEL 334
                                       ************.8888888888888567*************************777665 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 !   17.9   0.1   5.5e-07     0.002      22      95 ..      33     105 ..      30     212 .. 0.79
   2 ?   -2.5   0.0         1   3.6e+03     132     158 ..     452     478 ..     449     491 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.5e-07
                                       HHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHH.HHCTT-E.EEEEEECCHHHHCCCCHHHHHHTT--EEEEEEE CS
                             POR_N  22 iaeelaellakgevgdvevvqmesEigaisaviG.AaaaGar.aaTaTSgqGllLmienlglaageelPvvivvva 95 
                                       +++ l e +++ge+   + + m  E +a+ a+ G A a+G   + TaT+g+G+   +  l+ a  +  Pvv +  a
  gi|518651692|ref|YP_008141212.1|  33 MYDSLIEDIESGEL---RHILMRHEQAAAHAADGyARATGNVgVCTATAGPGVTNIVTGLITAYQDSSPVVAITGA 105
                                       56666666667775...99***************78899987267**************************98654 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1
                                       HHHHHHHHHHHHHCTSEEEEEEEHHHH CS
                             POR_N 132 fdlalvAfnlAekvrvPvivlfDgfll 158
                                       f ++ + +++A++ ++Pvi ++   ++
  gi|518651692|ref|YP_008141212.1| 452 FMMTGNNLATAVDENIPVIAVVNDNRT 478
                                       567777778888888888887766555 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     5e-05      0.18      25      69 ..     198     242 ..     187     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5e-05
                                       SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHHTSSSEEEEE CS
                             CO_dh  25 lkvvakmikkakrPllivGpqvlkaeneeakekkilekklkvvat 69 
                                       +++ a  + ka++P+++vG+ v +a   e+  k  +    +vv t
  gi|518651692|ref|YP_008141212.1| 198 VREMATNLLKAEKPVILVGNGVTWANATEEVLKLSEFLGCPVVST 242
                                       3556666899****************9999999887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (579 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3897.26
//
Query:       gi|518651693|ref|YP_008141213.1|  [L=104]
Description: hypothetical protein FACI_IFERC00001G0332 [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   26.0   0.0    8.7e-06   25.5   0.0    1.4  1  ACT_5     ACT domain


Domain annotation for each model (and alignments):
>> ACT_5  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.0   4.9e-10   8.7e-06       2      48 ..      15      60 ..      14      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 4.9e-10
                             ACT_5  2 apgvLeRvlrvvrrrgFevkslnmsttedggtvrieltVes.ersvel 48
                                      + g++eR+   +rr ++++k++nm+   d+g  +i +++++ +   +l
  gi|518651693|ref|YP_008141213.1| 15 DSGLVERIAASFRRFWVDIKWMNMEC--DSGVCTIYMSINDaHNLGNL 60
                                      679***********************..***********995554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 715.24
//
Query:       gi|518651694|ref|YP_008141214.1|  [L=336]
Description: hypothetical protein FACI_IFERC00001G0333 [Ferroplasma acidarmanus fer1]
Scores for complete 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-67  226.1   0.1    2.5e-67  225.5   0.1    1.2  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    3.7e-50  170.0   0.2    1.3e-49  168.2   0.7    1.6  2  IlvC            Acetohydroxy acid isomeroreductase, catalytic
    2.6e-07   31.1   0.0    5.8e-07   30.0   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
    4.6e-05   23.6   0.0    8.2e-05   22.8   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    6.7e-05   22.3   0.0    0.00013   21.4   0.0    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.019   14.9   0.9       0.77    9.7   0.2    2.9  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.051   13.2   0.1       0.14   11.8   0.1    1.7  1  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.5   0.1   9.9e-71   2.5e-67       2     165 .]      19     182 ..      18     182 .. 0.99

  Alignments for each domain:
  == domain 1  score: 225.5 bits;  conditional E-value: 9.9e-71
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHHHHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelqkevye 78 
                                       +k+k+iav+GyGsqG+a+ lnl dsgl+v +gl+++++s+kkA+e+g++ ++++ea k ad+v++l+PD++q+++y+
  gi|518651694|ref|YP_008141214.1|  19 VKEKNIAVLGYGSQGRAWVLNLLDSGLNVKLGLEREGNSWKKAQEDGVKPMKTEEALKGADIVIFLVPDMVQRKIYS 95 
                                       799************************************************************************** PP

                                       HHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHTT----EEEEEEE-SSS-HHHHHHHH CS
                              IlvN  79 eeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyeegkGvpaliaveqdasgkakelalay 155
                                       e+++p lk g  l+fahGfnih++li+pp++vdv++ APk+pG  vre + +g+Gvp+l++v+qd+sg+a ++ala+
  gi|518651694|ref|YP_008141214.1|  96 EKVKPVLKPGMDLVFAHGFNIHYKLIQPPENVDVYMAAPKAPGPSVREFFVKGGGVPVLVGVNQDYSGQALQKALAI 172
                                       ***************************************************************************** PP

                                       HHHTTHHHH- CS
                              IlvN 156 akgiGatraG 165
                                       akg+Gat+aG
  gi|518651694|ref|YP_008141214.1| 173 AKGLGATKAG 182
                                       *********9 PP

>> IlvC  Acetohydroxy acid isomeroreductase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.7   6.8e+03      44      83 ..      96     136 ..      90     144 .. 0.70
   2 !  168.2   0.7   5.1e-53   1.3e-49       1     141 [.     188     328 ..     188     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.7
                                       HHTHHH.HHHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHH CS
                              IlvC  44 eclhel.klivdliyegGiakmresiSdtaeygdltagprv 83 
                                       e ++ + k+ +dl+  +G++  ++ i    ++  + a+p++
  gi|518651694|ref|YP_008141214.1|  96 EKVKPVlKPGMDLVFAHGFNIHYKLIQPPENVDVYMAAPKA 136
                                       55555557778888888888888888877777777777765 PP

  == domain 2  score: 168.2 bits;  conditional E-value: 5.1e-53
                                       HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHTT--HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHS-HHHHHHHH CS
                              IlvC   1 FkeEtetDlfgEqavLcGgvselveagFetlveaGyspelAyfeclhelklivdliyegGiakmresiSdtaeygdl 77 
                                       FkeEtetDl+gEq  L+Gg++++++a F+t+v+ Gy pe+Ayfe ++e+kli+d+iye+G+++m++++Sdta+yg+l
  gi|518651694|ref|YP_008141214.1| 188 FKEETETDLMGEQLDLVGGLTAMLRATFHTIVDLGYRPEMAYFEAINEMKLITDQIYEKGLSGMLRAVSDTAKYGGL 264
                                       9**************************************************************************** PP

                                       HHHHHHS-HHHHHHHHHHHHHHHTTHHHHHHHHHHHTTSHHHHHHHHHHHTSHHHHHHHHHHHC CS
                              IlvC  78 tagprviteevkeemkeileeiqsGefakevieenkagrpelkklrkeeaeheiekvgkklral 141
                                       t+g+ vi+++vk++mke  e+i+sG+fa e+iee+++g ++l +l+++ +++  e+vg++lr++
  gi|518651694|ref|YP_008141214.1| 265 TVGTYVINDDVKKRMKEKAERIKSGKFADEWIEEYDEGSKNLASLMDDLDNSLEEQVGRELREI 328
                                       **************************************************************86 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   2.3e-10   5.8e-07       2      72 ..      24      88 ..      23     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 2.3e-10
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpe 72
                                      i+++G+G++g+a +++ll +g    ++ ++ +r+ ++ ++++e+   +v+++++eea++ ad+v++ v+  
  gi|518651694|ref|YP_008141214.1| 24 IAVLGYGSQGRAWVLNLLDSG---LNVKLGLEREGNSWKKAQED---GVKPMKTEEALKGADIVIFLVPDM 88
                                      9********************...******99999988877666...488888*************99855 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   3.2e-08   8.2e-05       1      84 [.      23     106 ..      23     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.2e-08
                                       EEEEE--SHHHHHHHHHHHHTT-EEE.EE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykva.vynrtkekveelvaegakaaesieelvasldvvitmvkagkavdeviegl 76 
                                       +i+++G G  G+  +lnll++g +v  + +r+ ++ +++ ++g+k++++ ee+++++d+vi++v++  + +   e++
  gi|518651694|ref|YP_008141214.1|  23 NIAVLGYGSQGRAWVLNLLDSGLNVKlGLEREGNSWKKAQEDGVKPMKT-EEALKGADIVIFLVPDMVQRKIYSEKV 98 
                                       69***********************73589999*************998.779*************99888888889 PP

                                       CCC--TT- CS
                     NAD_binding_2  77 lealkkgd 84 
                                       ++ lk+g 
  gi|518651694|ref|YP_008141214.1|  99 KPVLKPGM 106
                                       99999985 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 !   21.4   0.0   5.1e-08   0.00013      25     101 ..      10      87 ..       3     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.1e-08
                                       TTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EE.EEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  25 sekallgkelsgktvGiiGlGrIGqavakrlkafgmkv.iaydrskkkeeeeeelgvelvsleellaesDivslhlp 100
                                       +e++   k +++k ++++G+G+ G+a    l   g++v ++ +r  ++ ++++e gv+ ++ ee+l+ +Div+  +p
  gi|518651694|ref|YP_008141214.1|  10 TENDADLKYVKEKNIAVLGYGSQGRAWVLNLLDSGLNVkLGLEREGNSWKKAQEDGVKPMKTEEALKGADIVIFLVP 86 
                                       5667777889****************9999999999986789999998899***********************999 PP

                                       - CS
                      2-Hacid_dh_C 101 l 101
                                        
  gi|518651694|ref|YP_008141214.1|  87 D 87 
                                       5 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.2    0.0003      0.77      63     101 ..      71     110 ..      23     121 .. 0.88
   2 ?   -2.3   0.0       1.5   3.8e+03      97     125 ..     167     195 ..     156     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0003
                                       HHHHHTT--EEEE---HHHHHHHH.HHHCCC--TT-EEEE CS
                    NAD_Gly3P_dh_N  63 laealkgadiivlvvPsqalrevl.kklkgllkkkailvs 101
                                        +ealkgadi+++ vP  + r++  +k+k++lk+   lv 
  gi|518651694|ref|YP_008141214.1|  71 TEEALKGADIVIFLVPDMVQRKIYsEKVKPVLKPGMDLVF 110
                                       689*****************99862678888888877765 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.5
                                       -EEEE---SEET.TTEEHHHHHHHHH-S- CS
                    NAD_Gly3P_dh_N  97 ailvsliKGieegtlkllsevieeelkee 125
                                       ++++ ++KG+ + +  +l++  +ee++++
  gi|518651694|ref|YP_008141214.1| 167 QKALAIAKGLGATKAGVLETTFKEETETD 195
                                       56777889997777777777777777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.4e-05      0.14       1      39 [.      24      61 ..      24     113 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrlealkkn 39
                                      ia+lG G++G+ +  +L   g +v l l ++  +++kk+
  gi|518651694|ref|YP_008141214.1| 24 IAVLGYGSQGRAWVLNLLDSGLNVKLGLERE-GNSWKKA 61
                                      89***********************999888.4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2446.63
//
Query:       gi|518651695|ref|YP_008141215.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G0334 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-22   78.1   1.7    1.9e-20   73.1   0.1    2.0  2  DUF202       Domain of unknown function (DUF202)
     0.0011   18.5   0.0     0.0016   17.9   0.0    1.3  1  SfLAP        Sap, sulfolipid-1-addressing protein
     0.0031   17.6   3.2       0.02   15.0   0.1    2.1  2  SdpI         SdpI/YhfL protein family
     0.0054   15.6   0.3     0.0059   15.5   0.3    1.0  1  MscS_TM      Mechanosensitive ion channel inner membrane doma
  ------ inclusion threshold ------
      0.018   15.1   1.8      0.018   15.1   1.8    1.8  2  DHHC         DHHC palmitoyltransferase
      0.037   14.0   0.1      0.081   12.9   0.0    1.5  2  GRIM-19      GRIM-19 protein
      0.065   12.9   3.5        2.7    7.6   0.5    2.1  2  PRA1         PRA1 family protein
      0.068   13.3   0.4       0.19   11.9   0.4    1.8  1  CD225        Interferon-induced transmembrane protein
      0.082   12.4   0.1       0.11   12.0   0.1    1.1  1  DUF4960      Domain of unknown function (DUF4960)
       0.12   12.5   4.6      0.075   13.2   2.8    1.6  2  DUF4234      Domain of unknown function (DUF4234)
        4.5    6.9   6.7         12    5.6   6.7    1.7  1  Tetraspanin  Tetraspanin family


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 !   73.1   0.1   1.1e-23   1.9e-20       2      67 ..       6      79 ..       5      80 .. 0.86
   2 ?    4.7   0.2     0.025        40      41      57 ..      94     110 ..      83     112 .] 0.67

  Alignments for each domain:
  == domain 1  score: 73.1 bits;  conditional E-value: 1.1e-23
                            DUF202  2 dglAnERTfLaWlRtslalialglallrffl.........tgepsalgkilglilivlgiltllvglvrylrrqr 67
                                      d++An RTfLaW+Rt+++l+++g+++++f           t++ s ++ i+g ++i++gi+t+++g++ y+++++
  gi|518651695|ref|YP_008141215.1|  6 DHFANKRTFLAWMRTGISLMGFGFVIAKFVIflhalenkpTSSFS-TSLIAGEVMIIVGIITIGYGFYEYYSTEK 79
                                      8***************************86677888666433333.479**********************9986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.025
                            DUF202  41 kilglilivlgiltllv 57 
                                       +++ +i+i+++il+ll+
  gi|518651695|ref|YP_008141215.1|  94 FVFTAIIIGMAILLLLF 110
                                       45666777777777765 PP

>> SfLAP  Sap, sulfolipid-1-addressing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   9.8e-07    0.0016      38     123 ..      26     107 ..      15     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 9.8e-07
                             SfLAP  38 wlvvlvalglivlfvlrsllsgasaapssaikalqivlGvlllllaaveavrrpkassrselprllsrlesllegga 114
                                       ++ + +a ++i+l +l++ +  +s+++s +++++ i++G++ + ++++e+ ++   ++     +  sr+ +l    a
  gi|518651695|ref|YP_008141215.1|  26 GFGFVIAKFVIFLHALENKP-TSSFSTSLIAGEVMIIVGIITIGYGFYEYYST---EKDIDNNKYYSRTTELFVFTA 98 
                                       56667788888888888888.78899**************************9...888888888888888888888 PP

                             SfLAP 115 lwvAlvlgl 123
                                       ++ ++++ l
  gi|518651695|ref|YP_008141215.1|  99 IIIGMAILL 107
                                       888887766 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0     0.059        96      24      52 ..       8      36 ..       2      53 .. 0.70
   2 !   15.0   0.1   1.2e-05      0.02      28      64 ..      54     109 ..      43     112 .] 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.059
                              SdpI 24 kahrfagklwiiaGlilllla..lgavvlvl 52
                                      +a++     w+ +G+ l+ ++  +  + +v+
  gi|518651695|ref|YP_008141215.1|  8 FANKRTFLAWMRTGISLMGFGfvI--AKFVI 36
                                      555555557999999999999431..22333 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 1.2e-05
                              SdpI  28 fagklwiiaGlilllla...................lgavvlvllvlvlllvivpi 64 
                                       +ag ++ii+G+i++  +                   ++++++++ +++ +++++ +
  gi|518651695|ref|YP_008141215.1|  54 IAGEVMIIVGIITIGYGfyeyystekdidnnkyysrTTELFVFTAIIIGMAILLLL 109
                                       799******************************99844444444444444443333 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 !   15.5   0.3   3.6e-06    0.0059     111     210 ..       7     111 ..       5     112 .] 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.6e-06
                           MscS_TM 111 HFgwpkesvrrlrralkr..lilvllplllvlilaealsdalardvl..Grlaflllllllavflarllrpalglya 183
                                       HF  ++  ++ +r  +    +++v++ ++++l   e+ +++ ++ +l  G ++++++ +++ + ++ +   ++   +
  gi|518651695|ref|YP_008141215.1|   7 HFANKRTFLAWMRTGISLmgFGFVIAKFVIFLHALENKPTSSFSTSLiaGEVMIIVGIITIGYGFYEYYSTEKDIDN 83 
                                       7777777777677655541267899999**********999998876559*************************** PP

                           MscS_TM 184 nkkeeeknsl.rlrrllylllvlaPlal 210
                                       nk  + +++l ++  ++  +++l+ l++
  gi|518651695|ref|YP_008141215.1|  84 NKYYSRTTELfVFTAIIIGMAILLLLFI 111
                                       **87777666666666666666666655 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.4      0.36   5.9e+02      47      78 ..      10      42 ..       7      54 .. 0.49
   2 ?   15.1   1.8   1.1e-05     0.018      50     115 ..      48     111 ..      42     112 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.36
                              DHHC 47 NykyFllfllylllllilalv.lllialvklve 78
                                      N + Fl+ + + + l+ + +v + ++++++ +e
  gi|518651695|ref|YP_008141215.1| 10 NKRTFLAWMRTGISLMGFGFViAKFVIFLHALE 42
                                      667776555444444444333133444444444 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.1e-05
                              DHHC  50 yFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllll 115
                                        F + l++  +++i+ ++++ +++++++++ek  +++ +  ++ ++++++++  ++ +++l+ll++
  gi|518651695|ref|YP_008141215.1|  48 SFSTSLIAGEVMIIVGIITIGYGFYEYYSTEKDIDNNKY--YSRTTELFVFTAIIIGMAILLLLFI 111
                                       6999999*************************9888855..4556888888888888888888876 PP

>> GRIM-19  GRIM-19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.6   2.6e+03      19      44 ..      12      37 ..       7      48 .. 0.55
   2 ?   12.9   0.0     5e-05     0.081      23      69 ..      51      97 ..      44     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.6
                                      XXXXXXXSXSHHHHHHHHHHHHHHHH CS
                           GRIM-19 19 rklpktllsglsllalviavtavgly 44
                                      r+++  + +g sl+++++++  + ++
  gi|518651695|ref|YP_008141215.1| 12 RTFLAWMRTGISLMGFGFVIAKFVIF 37
                                      55555555556666655555544444 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5e-05
                                      XXXSXSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                           GRIM-19 23 ktllsglsllalviavtavglyavlksnkerrrekiekrsarlailP 69
                                       +l+ g+ +++++i+++ +g+y +++++k  +++k  +r+ +l ++ 
  gi|518651695|ref|YP_008141215.1| 51 TSLIAGEVMIIVGIITIGYGFYEYYSTEKDIDNNKYYSRTTELFVFT 97
                                      6788999***************************9999988887665 PP

>> PRA1  PRA1 family protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5    0.0016       2.7     104     139 ..      14      49 ..      11      52 .. 0.84
   2 ?    7.2   0.1    0.0022       3.5      50     108 ..      49     110 ..      45     112 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
                              PRA1 104 lllfltgavlvllwalliglllvllHAsfrkrndkf 139
                                       +l ++  +++++ ++++i+ ++++lHA   k+   f
  gi|518651695|ref|YP_008141215.1|  14 FLAWMRTGISLMGFGFVIAKFVIFLHALENKPTSSF 49 
                                       677888899******************987776665 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0022
                              PRA1  50 lllslltnplslivllllvlawlflyflrseplv...lfgrelsdrvvlivllvvsvlllfl 108
                                       +  sl+   + +iv+++++   ++ y+++++++     ++r+++  v+ ++++ +++lll++
  gi|518651695|ref|YP_008141215.1|  49 FSTSLIAGEVMIIVGIITIGYGFYEYYSTEKDIDnnkYYSRTTELFVFTAIIIGMAILLLLF 110
                                       66789999999999999999999999999777754334555555556666666666665554 PP

>> CD225  Interferon-induced transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   0.00012      0.19      37      67 ..      78     108 ..      45     109 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                             CD225  37 vGdvegAqsasstAkllniialvlgiiliil 67 
                                       + d++  + +s+t+ l+  +a+++g+++++l
  gi|518651695|ref|YP_008141215.1|  78 EKDIDNNKYYSRTTELFVFTAIIIGMAILLL 108
                                       57999999*******************9987 PP

>> DUF4960  Domain of unknown function (DUF4960)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   6.8e-05      0.11     217     246 ..      64      93 ..      58      99 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.8e-05
                           DUF4960 217 viCiGsgaYDWyseeedasanqYkenvekl 246
                                       +i iG g Y++ys+e+d  +n+Y++ +  l
  gi|518651695|ref|YP_008141215.1|  64 IITIGYGFYEYYSTEKDIDNNKYYSRTTEL 93 
                                       899********************9877655 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       3.5   5.8e+03      51      51 ..      25      25 ..       4      40 .. 0.57
   2 ?   13.2   2.8   4.6e-05     0.075       5      50 ..      58     103 ..      57     112 .] 0.73

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3.5
                           DUF4234 51 i 51
                                      +
  gi|518651695|ref|YP_008141215.1| 25 M 25
                                      1 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.6e-05
                           DUF4234   5 vvilLsivTlGIYslyWlykltrelnrlsgrkkttslllv.flllsl 50 
                                       v+i+  i+T G Y++y +y++ +++++ +  ++tt+l ++ ++++++
  gi|518651695|ref|YP_008141215.1|  58 VMIIVGIITIG-YGFYEYYSTEKDIDNNKYYSRTTELFVFtAIIIGM 103
                                       79*********.*************9998887777777776333222 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   6.7    0.0072        12      15      71 ..      20      77 ..      12     112 .] 0.50

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0072
                                      XXXXXXXXX.XXXXXXXX.....................XXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 15 igivllavG.vwlrlkhaeaalacllsesaedpailaillivvGvllfllgflGciga 71
                                      +gi l+++G v +++   + al+++ ++s + + i+  ++i+vG++++  gf   + +
  gi|518651695|ref|YP_008141215.1| 20 TGISLMGFGfVIAKFVIFLHALENKPTSSFSTSLIAGEVMIIVGIITIGYGFYEYYST 77
                                      5677777775555444444455555556666666666667777777777666654443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 738.33
//
Query:       gi|518651696|ref|YP_008141216.1|  [L=77]
Description: hypothetical protein FACI_IFERC00001G0335 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 538.23
//
Query:       gi|518651697|ref|YP_008141217.1|  [L=247]
Description: dihydroorotate dehydrogenase electron transfer subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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   37.2   0.6    3.8e-09   36.2   0.6    1.6  1  DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydr
     0.0041   17.7   1.0      0.029   15.0   1.0    2.1  1  NAD_binding_1    Oxidoreductase NAD-binding domain
  ------ inclusion threshold ------
      0.045   14.1   0.0        0.1   12.9   0.0    1.7  1  FAD_binding_6    Oxidoreductase FAD-binding domain


Domain annotation for each model (and alignments):
>> DHODB_Fe-S_bind  Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.6   6.4e-13   3.8e-09       1      41 [.     195     227 ..     195     228 .. 0.94

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.4e-13
                                       ----SSSSSSS-TTEEEETTCTT.CEEETTTT-CEEECCCB CS
                   DHODB_Fe-S_bind   1 eerMaCGvGaClgCvvktkggdggeykrvCkdGPvFdadev 41 
                                       e+ M+CG+G+C +C +            vC+dGPvF ++++
  gi|518651697|ref|YP_008141217.1| 195 ERSMKCGIGLCDSCSING--------FQVCRDGPVFSIEKL 227
                                       789*************99........78*********9987 PP

>> NAD_binding_1  Oxidoreductase NAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.0   4.8e-06     0.029      66     105 ..     141     177 ..      96     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                                       CTTTSSSEESSHHHHHHHHHHHHSSTTEEEEEECSHHHHH CS
                     NAD_binding_1  66 eeagweggkgrvqdalleellslkkeethvyvCGppgMik 105
                                       +++g+ g+kg+v +a+ +el+   ++ +++yvCGp+ M+ 
  gi|518651697|ref|YP_008141217.1| 141 TDDGSMGKKGFVATAM-DELDI--ESFDMIYVCGPEIMMF 177
                                       45677789********.66666..799***********95 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 ?   12.9   0.0   1.8e-05       0.1       4      96 ..       6      85 ..       3      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                                      EEEEEECCTTEEEEEEEESTTTS-----TT-EEEEEECETTCCEEEEEE.BSSTTECCEEEEEEE--TT-HHHHHHHCS CS
                     FAD_binding_6  4 ltekeevsedtrifrfklpsekqklglpvGqhvflrlkikgeaviRsYtpissenekGelellvkvypgGkmsqaLdel 82
                                      ++e+   s+d+ +++f+ +     +++ +Gq++++ ++  +     +Y p+s ++ +    + vk+y  G+ s +L  l
  gi|518651697|ref|YP_008141217.1|  6 IKENIMESRDVNTLTFEDD-----IKIKPGQFIMAWAP--R----INYIPLSFSSVSQIKSITVKIY--GEASAYLAGL 71
                                      5566666777777777655.....8899*******999..2....37999999999999999****9..9********* PP

                                      -TT-EEEEEEEE-S CS
                     FAD_binding_6 83 kigdtleikGPlGk 96
                                      k+g++l  +G +G+
  gi|518651697|ref|YP_008141217.1| 72 KPGEKLFYDGIYGN 85
                                      ******99998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1716.34
//
Query:       gi|518651698|ref|YP_008141218.1|  [L=298]
Description: hypothetical protein FACI_IFERC00001G0337 [Ferroplasma acidarmanus fer1]
Scores for complete 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-59  200.1   8.1    5.3e-59  199.8   8.1    1.0  1  DHO_dh        Dihydroorotate dehydrogenase
    2.2e-10   40.1   0.4    5.7e-08   32.2   0.0    2.3  2  Dus           Dihydrouridine synthase (Dus)
    0.00024   20.6   0.8     0.0065   15.9   0.2    2.4  2  His_biosynth  Histidine biosynthesis protein
     0.0025   16.9   2.5     0.0038   16.3   2.5    1.4  1  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 !  199.8   8.1   1.2e-62   5.3e-59      12     295 .]      12     281 ..       7     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: 199.8 bits;  conditional E-value: 1.2e-62
                                       SSSEEE-TTS.STTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHHHHHH CS
                            DHO_dh  12 knpiglAaGf.dkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlekllkr 87 
                                       +np++lA+G+ d +g  i+++l++g+ga+ ++s++ ++++G + P + ++    sv+N++Gl n+G++++ ++++  
  gi|518651698|ref|YP_008141218.1|  12 ANPFILASGIlDANGYTIKRILENGAGAAVTKSIGSEERKGFDPPVIYSDGR--SVINAIGLSNPGIENYGQEIKIA 86 
                                       7********7589********************************9988755..5******************9998 PP

                                       HHHHHCC.CEEEEEEE-TTSS.HHHHHHHHHHHHGGG.ESEEEEES-SCTCC.TSCCCGCHHHHHHHHHHHHHHHHS CS
                            DHO_dh  88 rkeqeekkelginlskakktenavddyvevvrkigpf.adilelNvSsPntp.glrdlqekeelkaillkvvkevsk 162
                                        +        +++ s+ ++t    ++++ +++k++ + a+++elN+S+P+++ ++ ++++++el ++++++vk + +
  gi|518651698|ref|YP_008141218.1|  87 TSS-----GKPVIGSIFGQT---PEEFAMLAEKMQAYgASAVELNLSCPHVKgYGTEIGSDPELVSAIVSAVKSRIN 155
                                       876.....348********9...9***********65499************889********************** PP

                                       SEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE...BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHH CS
                            DHO_dh 163 vpvlvKlaPdltdeekkdiadvllelkldgiivtNttvqrlaidlkseknvkanktGGlsGkalkdialkvirelyk 239
                                       +pv++Kl+P+ +d+  ++ia+   +++   i+    t++ ++id+++ k v  n  GGlsGk +k+++++ ++e++k
  gi|518651698|ref|YP_008141218.1| 156 IPVYAKLSPNTSDMLGQAIAAGK-ADGYVLIN----TIKAMKIDINTGKAVLSNIYGGLSGKSIKPVGIRYVYEVKK 227
                                       ***********999999998754.45555555....566666*********************************** PP

                                       HTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHHH CS
                            DHO_dh 240 rlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleelL 295
                                       ++ k   iIgvGGi+  eDale+i+aGAs+vq+++a+  +g  i+ ++ kele+ +
  gi|518651698|ref|YP_008141218.1| 228 ETGK--TIIGVGGINNFEDALEYIMAGASAVQIGSAISQAGIGIFANLTKELESYM 281
                                       ***5..68********************************************9876 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.0   1.3e-11   5.7e-08      54     131 ..      91     164 ..      76     179 .. 0.85
   2 !    5.9   0.1    0.0013       5.9     170     217 ..     217     263 ..     210     289 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.3e-11
                                       SCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEEGGGGGGSHHHHHHHHHHHHCCSSS-EEEEEE CS
                               Dus  54 tplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrggaGaaLlrkpdlvaqivkavvkaveiPvtvkir 130
                                       +p++  ++g+ p++ a  A++ +++ga++++lN+ CP  k  + ++G+    +p+lv  iv+av++ ++iPv +k +
  gi|518651698|ref|YP_008141218.1|  91 KPVIGSIFGQTPEEFAMLAEKMQAYGASAVELNLSCPHVKGYGTEIGS----DPELVSAIVSAVKSRINIPVYAKLS 163
                                       5788889******************************99877777776....9*******************99986 PP

                                       S CS
                               Dus 131 i 131
                                        
  gi|518651698|ref|YP_008141218.1| 164 P 164
                                       5 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0013
                                       --CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC CS
                               Dus 170 adweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal 217
                                       + ++ ++evk++   ++i+ G+I ++eda + +   Ga +v ig +  
  gi|518651698|ref|YP_008141218.1| 217 VGIRYVYEVKKETGKTIIGVGGINNFEDALEYIMA-GASAVQIGSAIS 263
                                       567789*************************9998.*****9998765 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.016        70     145     193 ..     101     153 ..      11     160 .. 0.61
   2 !   15.9   0.2   1.5e-06    0.0065      60     107 ..     217     264 ..     205     297 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.016
                                       EEEEHHHHHHHHHHTT-SEEEEE....ETTTTTTSS---HHHHHHHHHHHSSE CS
                      His_biosynth 145 tgldavelakkleelgageillt....didrdGtlsGpdleltkelaeavkip 193
                                       t  ++  la+k++ +ga+++ l+     ++  Gt+ G d el++++ +avk +
  gi|518651698|ref|YP_008141218.1| 101 TPEEFAMLAEKMQAYGASAVELNlscpHVKGYGTEIGSDPELVSAIVSAVKSR 153
                                       44556667777777777765433222278888999999999998888888654 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH CS
                      His_biosynth  60 anldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavk 107
                                       + + +v e+ +e+  ++   GGI+++ed+ e++ aga+ v ig+a  +
  gi|518651698|ref|YP_008141218.1| 217 VGIRYVYEVKKETGKTIIGVGGINNFEDALEYIMAGASAVQIGSAISQ 264
                                       5678999999**999999999**********************99754 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.5   8.5e-07    0.0038     151     240 ..     172     263 ..     142     288 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.5e-07
                                       EEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHH..HHHHHHHHHCTCT-EEEEES---SHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 151 GnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqlt..AvaevaeaakkagvpviaDGGikysgdivkA 225
                                         +a  ++   ++ + ++a+k+ i +G      +  g+    +    +  v+e+ k++g ++i  GGi++ +d    
  gi|518651698|ref|YP_008141218.1| 172 QAIAAGKADGYVLINTIKAMKIDINTGKAVLSNIYGGLSGKSIKpvGIRYVYEVKKETGKTIIGVGGINNFEDALEY 248
                                       5566666666666666778888888888888888888766666522578999************************* PP

                                       HHTT-SEEEESCCCT CS
                                       xxxxxxxxxxxxxxx RF
                             IMPDH 226 laaGadavmlGslla 240
                                       + aGa+av +Gs ++
  gi|518651698|ref|YP_008141218.1| 249 IMAGASAVQIGSAIS 263
                                       ************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1997.11
//
Query:       gi|518651699|ref|YP_008141219.1|  [L=156]
Description: hypothetical protein FACI_IFERC00001G0338 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.075   12.6   0.0      0.098   12.2   0.0    1.1  1  Poty_coat  Potyvirus coat protein


Domain annotation for each model (and alignments):
>> Poty_coat  Potyvirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.5e-06     0.098      58      94 ..      47      83 ..      28      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.5e-06
                         Poty_coat 58 eqlekWyeavrrelekteeefmstilpglivwCivng 94
                                      e+l k++e + +++  te  +m+ti++g  v  + n 
  gi|518651699|ref|YP_008141219.1| 47 EELAKFFELTVMNYPETESDLMDTIINGASVVVVNNN 83
                                      7999************************999888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1124.64
//
Query:       gi|518651700|ref|YP_008141220.1|  [L=224]
Description: hypothetical protein FACI_IFERC00001G0339 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.035   14.2   0.1         11    6.2   0.0    2.5  2  Hormone_3  Pancreatic hormone peptide


Domain annotation for each model (and alignments):
>> Hormone_3  Pancreatic hormone peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0   0.00098        18      13      26 ..     188     201 ..     184     203 .. 0.92
   2 ?    6.2   0.0   0.00061        11       7      20 ..     211     224 .]     209     224 .] 0.93

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.00098
                                       HHHHHHHHHHHHHH CS
                         Hormone_3  13 pEeLakYyaaLrhY 26 
                                       +E+La Y++ L++Y
  gi|518651700|ref|YP_008141220.1| 188 LEDLAIYMDTLNKY 201
                                       69***********9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00061
                                       XXTTS-HHHHHHHH CS
                         Hormone_3   7 PgedaspEeLakYy 20 
                                       Pg++++ E ++ Y+
  gi|518651700|ref|YP_008141220.1| 211 PGDNETMENIRDYF 224
                                       ************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.31s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 1355.74
//
Query:       gi|518651701|ref|YP_008141221.1|  [L=321]
Description: DNA polymerase [Ferroplasma acidarmanus fer1]
Scores for complete 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  128.7   0.0    2.5e-37  128.2   0.0    1.2  1  UDG       Uracil DNA glycosylase superfamily
    1.8e-14   53.9   0.0    3.3e-14   53.1   0.0    1.4  1  NUDIX     NUDIX domain


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 !  128.2   0.0   2.8e-41   2.5e-37       1     146 [.     168     302 ..     168     315 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.2 bits;  conditional E-value: 2.8e-41
                                       HHC-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHH.CCCCCCCHHGCTEEEEESSS....SECGCTTCCC CS
                               UDG   1 pgegppdakvvivGeaPgaeedatglpFsgragnllrkllne.aglkrdleseqgvyitnvvkcrppgnrdtptsae 76 
                                       pgeg+ +a + ivG+aPg++ed   +pF+gr+g+ll++l+ + ++ +r     + +yit+vv ++pp+nr  p+++e
  gi|518651701|ref|YP_008141221.1| 168 PGEGNLNAAIFIVGQAPGRNEDIMKKPFVGRSGKLLESLITDeLHMDR-----ESLYITSVVQFFPPENR-APSDDE 238
                                       799*********************************************.....*****************.****** PP

                                       CTCCHHHHHHHHHHHHSSEEEEESHHHHHH...HHHHSCESCCCSCT.SEEEEES-SSTTTTTTTTSHHHH CS
                               UDG  77 ikacaplleeeiellkprlivllGktaakall.geklgklrgklleakirvlplphPsplnrnffksnpel 146
                                       i+ c p+l+++ie+++p +ivllG+ aa++l+  ++++k +gkl+ +  ++++++hP++++rn     p++
  gi|518651701|ref|YP_008141221.1| 239 IALCLPYLMKQIEIVNPAIIVLLGAVAARTLVqVKSIMKEHGKLFMD--KYFVTLHPAAALRN-----PAN 302
                                       ******************************99555************..89************.....433 PP

>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   3.7e-18   3.3e-14      11     120 ..      15     123 ..       6     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 3.7e-18
                                       EETTSEEEEEEESSSSTTTE.ESSEEECBTTSHHHHHHHHHHHHHHS..EEE.EEE.EEEEEEEEEEEEEEEEEEEE CS
                             NUDIX  11 lnekgevLlvrrskkpfpgW.elPgGkvepgEtpeeAArREleEEtG..lea.ell.ellgrlhylapydgpygdeh 82 
                                       +n++ + Ll++r      gW ++P+G++e+gE+   AA+RE+ EE G  l++ +l+  ++  ++y+++y+g +  +h
  gi|518651701|ref|YP_008141221.1|  15 FNNECKYLLLKRE----EGWlDFPKGHIEKGEDGVKAALRETCEESGvcLQPgNLVhGFYYNIDYFFTYKGTKILKH 87 
                                       6666678999999....67956**********777************66699677777888*************888 PP

                                       EEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHHHHHHT CS
                             NUDIX  83 eilyvfleevegelepndenevsevrwvpleellkekl 120
                                         +y+ +  +e +++   + e++++ w++++e+++e  
  gi|518651701|ref|YP_008141221.1|  88 VGMYLSEVLPETTVK--VSYEHRGYVWLNYQEAMEELR 123
                                       888555555555544..469999**********43333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.52
# Mc/sec: 1865.33
//
Query:       gi|518651702|ref|YP_008141222.1|  [L=403]
Description: hypothetical protein FACI_IFERC00001G0341 [Ferroplasma acidarmanus fer1]
Scores for complete 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-16   58.2  43.5    6.6e-16   58.2  43.5    2.2  2  MFS_1     Major Facilitator Superfamily
    1.4e-06   27.2   6.0    1.4e-06   27.2   6.0    3.6  4  MFS_2     MFS/sugar transport protein


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 !   58.2  43.5   7.3e-20   6.6e-16       1     351 [.      25     359 ..      25     361 .. 0.81
   2 !   11.2  26.2   1.4e-05      0.12       6     170 ..     224     389 ..     222     399 .. 0.80

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 7.3e-20
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++++ +s+++++++++++p ++++ + +   ++  ++++  +g +++++ +G++sdr+Gr+ ++ll++ ++++g l
  gi|518651702|ref|YP_008141222.1|  25 IFFTVSISFFMWGVTLAIAP-LITTWYFVPQFSYYYIIGAAPAGLLAGNMSMGYISDRLGRKNIFLLTMGITVAG-L 99 
                                       69999***************.7888877788888889999999********************************.6 PP

                             MFS_1  78 lll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWra 152
                                       +++ ++ ++ +l+++ +++ +g g+  ++++a++ ++ p + rg+ai   s ++++G+ +++ l+  + +s +   +
  gi|518651702|ref|YP_008141222.1| 100 IGIgVSYNYVALIIFVFIAEFGLGGDETLSLAILIEYLPLKSRGFAIVESSNMANIGVtAIAGLFLVYPSSVITQKS 176
                                       6664657777***********************************************98888899888999999*** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..ll 227
                                       + +++ai++  a+++  + +  e++  ++ s+k      ++ +++p       ++     l  l+l+f+g+++   +
  gi|518651702|ref|YP_008141222.1| 177 LLLAIAIIAGGAAIF--ARYHMEESGLWNISKKLN----EKLEITP-------RN----TLKFLALTFMGMAIivGF 236
                                       ************996..666677777777766666....8888888.......44....455555555555552155 PP

                             MFS_1 228 tllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt...ssav 301
                                       +++ l +   ++++    +gl++ ++ l+    ++++g+++ + +r+ + + ++++ll+ + +++++ +     +  
  gi|518651702|ref|YP_008141222.1| 237 AFSDL-VIGPFHFP--EDTGLIIFFSVLAESLTGVIGGYYLGKSKRKSIAITGFSGLLI-SWAVIIVFLGaiiANLY 309
                                       55555.59******..99999999999999888********995554444444444444.44444444443444444 PP

                             MFS_1 302 llllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       llll+l++ ++++ + +++   l  +++  +++g+ +g++ +ag++  ++
  gi|518651702|ref|YP_008141222.1| 310 LLLLMLAISSIFGEIGWAARELLEPENFISKYRGRGIGVIRSAGYVLYII 359
                                       4455888888899999999999999**999***********999987776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 1.4e-05
                             MFS_1   6 flsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllll 80 
                                       +l++++++i+  ++ + ++   +++ ++  gl++ +  l+ +++ +++G+   +  r+++ ++g+ +++++ +++++
  gi|518651702|ref|YP_008141222.1| 224 ALTFMGMAIIVGFAFSdLVIGPFHFPED-TGLIIFFSVLAESLTGVIGGYYLGKSKRKSIAITGFSGLLISwAVIIV 299
                                       5677777776666666688899995555.6************************98888************888888 PP

                             MFS_1  81 f..a..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       f  a  ++l+lll++ +++++++ ++++a   l  + f  + rgr+ig++ ++  + +i+   + +l+ + ++  a 
  gi|518651702|ref|YP_008141222.1| 300 FlgAiiANLYLLLLMLAISSIFGEIGWAARELLEPENFISKYRGRGIGVIRSAGYVLYIIF--IFALINADISTYAY 374
                                       7553789999*****************************************9877777777..33455566666666 PP

                             MFS_1 154 fyilaivsllafvlfll 170
                                       f++   ++ +a+ l  l
  gi|518651702|ref|YP_008141222.1| 375 FILGVYIAGFAGSL--L 389
                                       66666666655554..2 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   6.0   1.5e-10   1.4e-06     209     339 ..       5     133 ..       2     139 .. 0.94
   2 ?   -1.2   0.7     0.061   5.5e+02     292     332 ..     179     237 ..     150     245 .. 0.56
   3 ?   -2.8   6.4      0.19   1.7e+03     299     339 ..     283     321 ..     253     334 .. 0.61
   4 ?   -1.0   1.8     0.054   4.8e+02     297     328 ..     355     386 ..     345     400 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 1.5e-10
                             MFS_2 209 eklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlgngsaasvfllvvtisallgiplwqplakr 285
                                       e ++l+e++ ++  nr+ +i+++++++ +++ gv+ +++ +  t +   ++ + ++ +++ ++ l+g + + ++  r
  gi|518651702|ref|YP_008141222.1|   5 ENINLSEKISRMPWNRKHWIIFFTVSISFFMWGVTLAIAPLITTWYFVPQFSYYYIIGAAPAGLLAGNMSMGYISDR 81 
                                       6788999999999**************************************************************** PP

                             MFS_2 286 lgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpwsml 339
                                       lg+kn++ll + +t+++l+++ +   +n+++++++++ia fg+g+  +l  ++l
  gi|518651702|ref|YP_008141222.1|  82 LGRKNIFLLTMGITVAGLIGIGVS--YNYVALIIFVFIAEFGLGGDETLSLAIL 133
                                       ********************9988..*****************99888877776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.061
                             MFS_2 292 yllgalltivllvlvlll.....................qpsnlllflvllviagfgvgvaa 332
                                        ++++++  +  +                          +p+n+l fl+l+++++ +++++a
  gi|518651702|ref|YP_008141222.1| 179 LAIAIIAGGAAIFA---RyhmeesglwniskklnekleiTPRNTLKFLALTFMGMAIIVGFA 237
                                       22222222222222...233466666666666666666666666666666666666655555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.19
                             MFS_2 299 tivllvlvlllqpsnlllflvllviagfgvgvaallpwsml 339
                                       +i ++ ++l+   + ++++++ ++ia++ + +++l++ s++
  gi|518651702|ref|YP_008141222.1| 283 AITGFSGLLIS--WAVIIVFLGAIIANLYLLLLMLAISSIF 321
                                       33333333333..5566666666666666555555555555 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 0.054
                             MFS_2 297 lltivllvlvlllqpsnlllflvllviagfgv 328
                                       +l+i++ + ++ ++ s ++ f++ + iagf+ 
  gi|518651702|ref|YP_008141222.1| 355 VLYIIFIFALINADISTYAYFILGVYIAGFAG 386
                                       44444444444445555555555555555542 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2578.22
//
Query:       gi|518651703|ref|YP_008141223.1|  [L=174]
Description: hypothetical protein FACI_IFERC00001G0342 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00093   19.1  16.0     0.0017   18.3   6.6    2.0  2  VIT1      VIT family
  ------ inclusion threshold ------
      0.056   13.7   1.5        8.8    6.6   0.0    2.5  2  DUF3007   Protein of unknown function (DUF3007)


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 !    7.8   1.8   0.00031       2.8       6      60 ..      11      66 ..       8      79 .. 0.79
   2 !   18.3   6.6   1.9e-07    0.0017     118     211 ..      81     168 ..      60     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00031
                              VIT1  6 lGanDGLvspfalvaG.lsaaslgssktvllaGlaellAGaiSMgiGeYlsvkser 60
                                      +G++DG+++ + l  G + + s  +    +   +   +AGa+S  i +Y   + e 
  gi|518651703|ref|YP_008141223.1| 11 IGLSDGIITALILASGgIIGKSSIDLFQAFRISFGSSFAGAFSYFIAQYAGLNEEL 66
                                      79*******9999998344444445666788899***************9887775 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 1.9e-07
                              VIT1 118 mlreelgpsaseelasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklv 194
                                       +l+ +lg++     +++l  Al+ a++ ++G+liPl + l+v ++++  ++   ++ l l+++G++ ++ t  +  +
  gi|518651703|ref|YP_008141223.1|  81 LLKGHLGIEIF---VESLLGALIAAFFGFLGALIPLSSSLIVRNNIEIPLF---LSYLSLAVLGLFISKTTAGRAKF 151
                                       44445554442...344557899999999************9954444333...479**************999999 PP

                              VIT1 195 salrmlliGalAaaaay 211
                                        ++ m+++G++ ++a y
  gi|518651703|ref|YP_008141223.1| 152 WIVVMVIVGIIVTIAGY 168
                                       9999********99988 PP

>> DUF3007  Protein of unknown function (DUF3007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0   0.00099       8.8       5      32 ..      38      65 ..      34      75 .. 0.87
   2 ?    5.5   0.5    0.0023        21      19      52 ..     129     164 ..     116     173 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00099
                           DUF3007  5 dvlaiglgvlllgglaylvlqalGldsl 32
                                      +++ i++g   +g+  y + q++Gl++ 
  gi|518651703|ref|YP_008141223.1| 38 QAFRISFGSSFAGAFSYFIAQYAGLNEE 65
                                      6788*********************975 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0023
                           DUF3007  19 laylvlqalGl..dslsagiwsqavlvlglvgWvlt 52 
                                       l yl l +lGl   +++ag +   ++v+++vg ++t
  gi|518651703|ref|YP_008141223.1| 129 LSYLSLAVLGLfiSKTTAGRAKFWIVVMVIVGIIVT 164
                                       678888888864456667655555555555544433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       766  (0.0427241); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1233.50
//
Query:       gi|518651704|ref|YP_008141224.1|  [L=88]
Description: hypothetical protein FACI_IFERC00001G0343 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-31  108.3   2.3    1.7e-31  108.2   2.3    1.0  1  DUF211    Uncharacterized ArCR, COG1888


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 !  108.2   2.3   9.7e-36   1.7e-31       1      85 [.       2      87 ..       2      88 .] 0.99

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 9.7e-36
                                      SEEEEEEEEEEE.SSS-HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHCTT-EEEEEEEE CS
                            DUF211  1 kirrlvLDvlkp.hepsivelakklaelegvdgvnitvkevDketenlkitieGenidyeeieeaieelggvihSiDev 78
                                      ++rr++LDv+k  ++p+++ela +++++ gvd+v+itv+e+D+et++++it+eG ni+y+ + ++ie++g++ihSiDev
  gi|518651704|ref|YP_008141224.1|  2 NLRRILLDVDKGlNRPTLTELAGSIEDVPGVDAVKITVTEMDMETMGTSITVEGININYNYLIKVIEDMGCAIHSIDEV 80
                                      69***************************************************************************** PP

                                      EEESS-- CS
                            DUF211 79 vaGkkiv 85
                                      ++Gk+iv
  gi|518651704|ref|YP_008141224.1| 81 ITGKHIV 87
                                      ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 567.96
//
Query:       gi|518651705|ref|YP_008141225.1|  [L=366]
Description: glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-18   65.9   0.0    6.3e-18   64.9   0.0    1.5  1  Glycos_transf_1  Glycosyl transferases group 1
    3.4e-16   59.9   0.0    9.9e-16   58.4   0.0    1.9  2  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 !   64.9   0.0     7e-22   6.3e-18      13     123 ..     190     290 ..     179     339 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.9 bits;  conditional E-value: 7e-22
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                        +   +l+vgrlek Kg+d ++ +f++       n+ l+++G+ge e  ++         +nv++l++ ++e+l e+
  gi|518651705|ref|YP_008141225.1| 190 RNSIRLLFVGRLEKSKGIDKIVNVFKKH----LLNIELTVVGSGELESLFST------PVKNVNYLKNPDNEKLAEI 256
                                       567789********************64....79********6665444444......457888999999******* PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEET CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasn 123
                                       ++n+d+f++psi E fG v+lEA+++gl vi s 
  gi|518651705|ref|YP_008141225.1| 257 YRNSDAFIFPSILENFGNVVLEALSSGLYVIGSE 290
                                       *******************************886 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.5   1.4e+04       8      29 ..     123     145 ..     121     150 .. 0.67
   2 !   58.4   0.0   1.1e-19   9.9e-16       3     102 ..     194     291 ..     192     322 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.5
                                       S---GG.GTHHHHHHHH.HHHH. CS
                   Glyco_trans_1_4   8 Grleenvkgvdllleav.pllrk 29 
                                       G++  n+ g++ l +a+ +l+++
  gi|518651705|ref|YP_008141225.1| 123 GNIPSNYTGIKALNNAIyALIKN 145
                                       55533778888888888666664 PP

  == domain 2  score: 58.4 bits;  conditional E-value: 1.1e-19
                                       EEEEES---GG.GTHHHHHHHH.HHHH.HHEEEEEES---..HHHHHHHT.T-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleav.pllrkkdvrlvivGdgprpeeleelaa.gleerveftGfv..edlaellaaadv 75 
                                       ++lfvGrl e+ kg+d +++ + ++l+  +++l++vG+g+    le+l +  + ++v ++     e+lae+++++d 
  gi|518651705|ref|YP_008141225.1| 194 RLLFVGRL-EKSKGIDKIVNVFkKHLL--NIELTVVGSGE----LESLFStPV-KNVNYLKNPdnEKLAEIYRNSDA 262
                                       79******.667**********88888..79******884....554454355.6899999887666********** PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TG CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdv 102
                                       f++Ps  e fg+++lEa+++gl v+ ++ 
  gi|518651705|ref|YP_008141225.1| 263 FIFPSilENFGNVVLEALSSGLYVIGSES 291
                                       *************************9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2564.75
//
Query:       gi|518651706|ref|YP_008141226.1|  [L=224]
Description: metal-dependent hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-26   93.6   0.0    1.4e-26   93.3   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    1.6e-26   93.2   0.1      2e-26   92.9   0.1    1.1  1  Lactamase_B_3  Beta-lactamase superfamily domain
      6e-10   39.5   0.8    1.8e-09   37.9   0.8    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.21   10.6   0.0       0.29   10.2   0.0    1.2  1  DUF2625        Protein of unknown function DUF2625


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 !   93.3   0.0   3.2e-30   1.4e-26       2     201 .]      20     189 ..      19     189 .. 0.89

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 3.2e-30
                                       EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHH CS
                     Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvyla 78 
                                       ++L+D++++    a+++    e ++   + d++l+th+H+DH  ++ t+++  +   p++++ +++++++++     
  gi|518651706|ref|YP_008141226.1|  20 NVLVDPFFS----ANPLS--SEDVNG-IKADLILVTHGHFDHAGDAVTIAKKNG--SPIVCSFELSEIIKKE----- 82 
                                       89*******....35665..112222.46799*******************544..69*************9..... PP

                                       CHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---.HHHHHHH CS
                     Lactamase_B_2  79 leeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip.eeigerl 154
                                            +v++ ++++g+++e +  g++ ta+pa h+s   ++  ag+++G++i++g+ ++y++gDt +++  e+  ++
  gi|518651706|ref|YP_008141226.1|  83 -----NVETIDINPGGTIEYN--GVKATAVPAIHSSSY-NGAYAGEAMGFIIDNGDLKIYHAGDTTFFKdMELIGEI 151
                                       .....567999*********9..799************.9*****************************53355588 PP

                                       CT-SEEEEE-S-SSTTHHHHHHT---STSHHHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 155 ggadllllditayeddemirhmgHltpeeaveaaadlgakrlvliHi 201
                                       + +d+++l+i+         +++++++++a+ea++ l++k ++++H+
  gi|518651706|ref|YP_008141226.1| 152 YHPDIAMLPIG---------GHYTMDVDGAIEALKLLKVKNAIPMHY 189
                                       88*********.........99************************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 !   92.9   0.1   4.4e-30     2e-26       1     163 []       4     188 ..       4     188 .. 0.86

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 4.4e-30
                     Lactamase_B_3   1 eltwlghnsflletagarilvDPfkanlgyeppa...eeaDlvlisqaledHahle.tlkql............... 58 
                                       e+ w+gh+ f ++ a +++lvDPf+    +  +     +aDl+l+++++ dHa  + t+++                
  gi|518651706|ref|YP_008141226.1|   4 EIIWHGHAGFSIKNA-VNVLVDPFFSANPLSSEDvngIKADLILVTHGHFDHAGDAvTIAKKngspivcsfelseii 79 
                                       588********9865.99******873333333345599*************9655155554888888888888888 PP

                     Lactamase_B_3  59 .aenvkvlee..geslevggleiravatshdav.ggsergenngflleqdgltiyhlGhlahelsseelkelgrvDv 131
                                        +env++++   g+++e +g++ +av++ h ++ +g+  ge +gf+++ ++l+iyh G++    ++e + e+ ++D+
  gi|518651706|ref|YP_008141226.1|  80 kKENVETIDInpGGTIEYNGVKATAVPAIHSSSyNGAYAGEAMGFIIDNGDLKIYHAGDTTFFKDMELIGEIYHPDI 156
                                       86666665434499****************8886899**************************************** PP

                     Lactamase_B_3 132 vltPvggpltlgqeealelakrLkpklvlPmh 163
                                        ++P+gg++t++ + a+e++k+Lk k  +Pmh
  gi|518651706|ref|YP_008141226.1| 157 AMLPIGGHYTMDVDGAIEALKLLKVKNAIPMH 188
                                       *******************************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 !   37.9   0.8     4e-13   1.8e-09      17     180 ..      20     177 ..      16     188 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4e-13
                                       EEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHH CS
                       Lactamase_B  17 viLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasr 93 
                                       ++L+D+ +s+           +++++ + d +++TH+H+DH+G++  ++++ + p+++  e  +  ++e +++    
  gi|518651706|ref|YP_008141226.1|  20 NVLVDPFFSANPLSS------EDVNGIKADLILVTHGHFDHAGDAVTIAKKNGSPIVCSFELSEIIKKENVETIDI- 89 
                                       578888888887776......799***********************************************88654. PP

                                       CCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC........ CS
                       Lactamase_B  94 kglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridl........ 162
                                               ++ + ++   + ++ ++ +++    g  +  ++++++++g+ k+  +GD+++  + ++i++        
  gi|518651706|ref|YP_008141226.1|  90 --------NPGGTIEYNGVKATAVPAIHSSSYNGAYAGEAMGFIIDNGDLKIYHAGDTTFFKDMELIGEiyhpdiam 158
                                       ........5667888899999************************************************99999988 PP

                                       ..TTCEEE-SHCHHHHHHH CS
                       Lactamase_B 163 .tlrgaevrdpsdaekyld 180
                                        +++g++++d ++a ++l+
  gi|518651706|ref|YP_008141226.1| 159 lPIGGHYTMDVDGAIEALK 177
                                       8888888888777777774 PP

>> DUF2625  Protein of unknown function DUF2625
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   6.4e-05      0.29      45      82 ..     108     145 ..      89     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.4e-05
                           DUF2625  45 vttrSvlGavvyetGGlliddGwlrvlGsgseklersl 82 
                                       + ++S+ Ga + e+ G +id+G l+++ +g++++ +++
  gi|518651706|ref|YP_008141226.1| 108 IHSSSYNGAYAGEAMGFIIDNGDLKIYHAGDTTFFKDM 145
                                       5678999***********************98876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1431.21
//
Query:       gi|518651707|ref|YP_008141227.1|  [L=680]
Description: hypothetical protein FACI_IFERC00001G0346 [Ferroplasma acidarmanus fer1]
Scores for complete 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   41.8   0.1    2.5e-05   23.4   0.0    2.2  2  AAA_10           AAA-like domain
    1.3e-07   31.9   0.1    4.9e-07   30.1   0.1    1.9  1  DUF87            Helicase HerA, central domain
    0.00012   22.3   0.1     0.0015   18.8   0.0    2.2  2  AAA_22           AAA domain
     0.0067   16.2   0.0      0.035   13.8   0.0    2.1  2  AAA_24           AAA domain
  ------ inclusion threshold ------
       0.01   15.3   0.4      0.054   12.9   0.0    2.1  2  Pox_A32          Poxvirus A32 protein
      0.036   13.8   0.0      0.068   12.9   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.044   13.3   0.1       0.13   11.8   0.0    1.8  2  CobU             Cobinamide kinase / cobinamide phosphate gua
      0.083   11.8   0.0       0.16   10.8   0.0    1.4  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.091   12.5   0.2        6.8    6.4   0.0    2.8  3  DEAD             DEAD/DEAH box helicase
       0.13   12.2   0.0       0.25   11.3   0.0    1.4  1  NACHT            NACHT domain
       0.13   12.4   0.0       0.27   11.4   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
       0.17   11.2   0.0       0.32   10.3   0.0    1.4  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.19   12.1   0.0       0.37   11.1   0.0    1.4  1  AAA_16           AAA ATPase domain


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 !   16.2   0.0   2.8e-06    0.0038      19      60 ..     399     438 ..     391     470 .. 0.81
   2 !   23.4   0.0   1.8e-08   2.5e-05     239     306 ..     565     636 ..     553     651 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.8e-06
                            AAA_10  19 tnasasliiGdlGnGKSvlakllvlyisllggkaliiDpkke 60 
                                        n+ + +i+G++G GKS++ak l  +    + k+ +iDp  e
  gi|518651707|ref|YP_008141227.1| 399 GNSYNIAITGETGSGKSYFAKKLLDQN--GNAKVYVIDPLGE 438
                                       588999***************999875..5789999999988 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 1.8e-08
                            AAA_10 239 kefkvvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknniglk....laFretdk 306
                                       + +k+v++DE+  f   +  +++++ l R  R + + ++ vtq+ +D+ +++ ++ i +     ++Fr++ k
  gi|518651707|ref|YP_008141227.1| 565 EGEKMVVMDESHLFLRNSREAEIIDMLARNSRHFRTSLITVTQNINDYYMNNYSESILMNsinyFIFRQHGK 636
                                       557899******************************************999966655332222288885444 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.1   3.5e-10   4.9e-07      26      67 ..     404     442 ..     401     476 .. 0.87

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 3.5e-10
                             DUF87  26 lAilgsTGsGKSntvavLleellekkgatililDpHGEYgka 67 
                                       +Ai g+TGsGKS++++ Ll++     +a++ ++Dp GEY+  
  gi|518651707|ref|YP_008141227.1| 404 IAITGETGSGKSYFAKKLLDQNG---NAKVYVIDPLGEYSYG 442
                                       79*******************99...9************975 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0015       6      41 ..     402     429 ..     398     446 .. 0.82
   2 ?    0.9   0.1      0.38   5.2e+02      92     126 ..     567     603 ..     544     612 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpe 41 
                                       + +++tGe+G+GK++ +++ll+q+         +++
  gi|518651707|ref|YP_008141227.1| 402 YNIAITGETGSGKSYFAKKLLDQNG--------NAK 429
                                       6799*******************96........444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.38
                            AAA_22  92 ielliiDEaqh.lr.s..eealeeLrsllnlsrkgvqli 126
                                        ++++ DE +  lr s  +e++  L + +   ++ ++li
  gi|518651707|ref|YP_008141227.1| 567 EKMVVMDESHLfLRnSreAEIIDMLARNSR--HFRTSLI 603
                                       5789*******7755233555555533333..5555444 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   2.6e-05     0.035       2      23 ..     401     427 ..     400     435 .. 0.80
   2 ?   -1.5   0.0       1.2   1.7e+03     114     163 ..     452     503 ..     445     511 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel.....g 23 
                                       +++i+i+G+ g+GK+++ak+l      
  gi|518651707|ref|YP_008141227.1| 401 SYNIAITGETGSGKSYFAKKLldqngN 427
                                       799*****************9665544 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                            AAA_24 114 llkklqelrk..nvifiahektrkdedpegeakytrlepklgkktanelkee 163
                                       +++ + e+++  n+i +a +k   +++++ ++  t+l +k g  t+nel +e
  gi|518651707|ref|YP_008141227.1| 452 YVDFFIETPEmaNIISTAIAKLTGIGENTITGILTGLMSKSGVATFNELISE 503
                                       556666777788*************999998888888888888888888765 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.9e-05     0.054       4      52 ..     392     438 ..     390     448 .. 0.77
   2 ?   -0.5   0.1      0.52   7.1e+02     112     139 ..     582     610 ..     556     630 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.9e-05
                           Pox_A32   4 FdresLlkkpFrlalvGgsGsGktvyLlsLlrtlvkkykhifLltpvkn 52 
                                       F  +  + + +++a++G++GsGk  + + Ll + +++   ++++ p+ +
  gi|518651707|ref|YP_008141227.1| 392 FYFQPFRGNSYNIAITGETGSGKSYFAKKLLDQNGNA--KVYVIDPLGE 438
                                       6667778899********************9875543..5666666555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.52
                           Pox_A32 112 tksktLlell.nvgRhlnvsiilLcqtyk 139
                                       +++ +++++l   +Rh ++s+i + q  +
  gi|518651707|ref|YP_008141227.1| 582 SREAEIIDMLaRNSRHFRTSLITVTQNIN 610
                                       45555555441678999999999988765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.9e-05     0.068      22      49 ..     401     428 ..     394     435 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.9e-05
                                       SS-EEEECSTTSSHHHHHHHHHHHSTTT CS
                   Sigma54_activat  22 dlsvlitGesGtGKellaraiheaskrk 49 
                                       + ++ itGe+G+GK+++a+++ +++ ++
  gi|518651707|ref|YP_008141227.1| 401 SYNIAITGETGSGKSYFAKKLLDQNGNA 428
                                       57899**************998876554 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.4e-05      0.13       2      29 ..     405     432 ..     404     434 .. 0.94
   2 ?   -2.6   0.0       2.5   3.5e+03     103     126 ..     586     609 ..     566     618 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.4e-05
                              CobU   2 lvtGgarSGKSefAeklaeeskekvvYi 29 
                                        +tG + SGKS fA+kl+ ++++  vY+
  gi|518651707|ref|YP_008141227.1| 405 AITGETGSGKSYFAKKLLDQNGNAKVYV 432
                                       69**********************9998 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                              CobU 103 eeveellealkelkatvvlVsnEv 126
                                       e ++ l++  ++ +++++ V++++
  gi|518651707|ref|YP_008141227.1| 586 EIIDMLARNSRHFRTSLITVTQNI 609
                                       445556666777788888888776 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.16      17      55 ..     403     439 ..     395     445 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                     TrwB_AAD_bind  17 hilivGttGsGKtqalekllrairargdraivlDltGaf 55 
                                        i+i+G tGsGK+  ++kll++  + + ++ v+D+ G++
  gi|518651707|ref|YP_008141227.1| 403 NIAITGETGSGKSYFAKKLLDQ--NGNAKVYVIDPLGEY 439
                                       799******************7..567788899999987 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       2.4   3.3e+03      86     112 ..     254     282 ..     233     293 .. 0.50
   2 ?    2.6   0.0     0.074     1e+02      16      30 ..     403     417 ..     393     436 .. 0.84
   3 ?    6.4   0.0    0.0049       6.8     123     149 ..     568     594 ..     549     609 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 2.4
                                       SHHHHHHHH..HTTCSEEEEEHHHHHHHH CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                              DEAD  86 aardqlskl..dngvdivvgtpgrlddll 112
                                       + + q+++l  +++++iv++ +g  + l+
  gi|518651707|ref|YP_008141227.1| 254 NPEMQVKRLlaSRKAEIVYTKTGHYAGLI 282
                                       22334444422244777777776666655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.074
                                       EEEEEESTTSSHHHH CS
                                       xxxxxxxxxxxxxxx RF
                              DEAD  16 dvlvaaeTGsGKTla 30 
                                       ++ + +eTGsGK+  
  gi|518651707|ref|YP_008141227.1| 403 NIAITGETGSGKSYF 417
                                       78899*******965 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0049
                                       EEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 123 rflVlDEadrlldqgfsdfinrilnql 149
                                       +++V+DE + +l ++++ +i  +l++ 
  gi|518651707|ref|YP_008141227.1| 568 KMVVMDESHLFLRNSREAEIIDMLARN 594
                                       89******************9999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00018      0.25       3      23 ..     404     424 ..     402     431 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00018
                                       EEEEC-TTTCHHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklala 23 
                                       ++++Ge GsGK+++++kl ++
  gi|518651707|ref|YP_008141227.1| 404 IAITGETGSGKSYFAKKLLDQ 424
                                       789**************9875 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00019      0.27      20      47 ..     400     427 ..     395     440 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00019
                                       -SS-EEEEEETT--HHHHHHCC--TTS- CS
                   Sigma54_activ_2  20 sklpvfltGekGsgkelvArlLhknsgp 47 
                                       ++ ++ +tGe Gsgk+++A+ L +++g+
  gi|518651707|ref|YP_008141227.1| 400 NSYNIAITGETGSGKSYFAKKLLDQNGN 427
                                       677899**************99998876 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00023      0.32      26      59 ..     387     421 ..     375     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                                       TTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  26 isgnplvldlkkma.shllvaGatgsGKStalntL 59 
                                       i+g+p++++       ++ + G tgsGKS + + L
  gi|518651707|ref|YP_008141227.1| 387 ITGKPFYFQPFRGNsYNIAITGETGSGKSYFAKKL 421
                                       4899999986555548*************998776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00027      0.37      21      56 ..     398     433 ..     392     492 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00027
                            AAA_16  21 sgrpelvllsGesGvGKsslvrellralekdggifl 56 
                                       +g + ++ ++Ge G+GKs  +++ll++   ++++++
  gi|518651707|ref|YP_008141227.1| 398 RGNSYNIAITGETGSGKSYFAKKLLDQNGNAKVYVI 433
                                       56667899*****************98888877775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 4200.98
//
Query:       gi|518651708|ref|YP_008141228.1|  [L=307]
Description: hypothetical protein FACI_IFERC00001G0347 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); 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):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2030.79
//
Query:       gi|518651709|ref|YP_008141229.1|  [L=85]
Description: hypothetical protein FACI_IFERC00001G0348 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
        4.8    7.5   7.8        2.5    8.4   0.2    2.1  2  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.2   0.00014       2.5      16      47 ..      20      51 ..      15      59 .. 0.85
   2 ?    4.3   2.5    0.0027        48       9      37 ..      51      80 ..      47      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00014
                       Sigma_reg_N 16 vlislivlllifvilvvtllylaekegnklre 47
                                      ++is++++l+ ++ + + l++++++e++k++ 
  gi|518651709|ref|YP_008141229.1| 20 IVISVSAVLITLLWIPIALNFFSTDENKKIMA 51
                                      89*************9999***9999999986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0027
                       Sigma_reg_N  9 rksilrivli.slivlllifvilvvtllyl 37
                                       + +l+++ i ++i++++i+ il+  ++y+
  gi|518651709|ref|YP_008141229.1| 51 ARERLKNAAIgTVIFIMAISGILFTVFNYV 80
                                      567888887768999999999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 582.49
//
Query:       gi|518651710|ref|YP_008141230.1|  [L=261]
Description: hypothetical protein FACI_IFERC00001G0349 [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  180.9   0.0    4.3e-53  180.6   0.0    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 !  180.6   0.0   2.4e-57   4.3e-53       6     213 ..      25     238 ..      20     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 180.6 bits;  conditional E-value: 2.4e-57
                                       .CCCHHHHHCCT-SEEEE-HHCCSSS-HHHHHHHHCTS-TT-EEEEE--CCCCCS..G-.SCHHHHHHHHHH.CHHH CS
                             DUF72   6 kkkerLeyYarhfntVEinstFYalpspetvakwaaqtpedFrFavKapraithe.rne.daeealerflesalepL 80 
                                       + +++L+ Yar f+tVEi+stFYa +s+etv+kwa+++pe+F F++K+pr+ithe r   ++e++l+ f+++ ++ L
  gi|518651710|ref|YP_008141230.1|  25 SPSNYLRDYARIFDTVEIDSTFYAAQSQETVEKWASSVPENFLFSPKMPRKITHEfR-LeRCEDDLAYFMKN-ISLL 99 
                                       56789*************************************************753.337**********8.**** PP

                                       CT-EEEEEEE--TT--S.HHHHHHHHHHTTTS-..S.EEEE--BGGGH..HHHHHHHHTT-EEEEE--SSC------ CS
                             DUF72  81 geklgpllfQlppsfkfdeenlerLeaflaalp..l.lavEvRhrswf..ellellrehgvavvldepkkpklpled 152
                                       +++lg +l+Qlpp f f+      Le+f++ lp    +a+E+Rh+swf  e++ +lr+ g+++ ++      +++ +
  gi|518651710|ref|YP_008141230.1| 100 NNRLGTVLIQLPPDFPFNT---GVLENFIELLPnnIkYAIEFRHPSWFidEVYGILRKSGITMAWS--VLDYIKTPE 171
                                       ***************6655...9*****999999956************55*********997775..445788899 PP

                                       --SSTEEEEEE--S....HHTTB----H......HHHHHHHHHHHHHHTCSSEEEEEE-SBCCCHHHHHHH CS
                             DUF72 153 vttadfvyvRlhgr....eeryayrYse......eelaewaerikawaaegrevyvffnndaegqaplnar 213
                                       ++t+++ yvR++g+    +    ++  e       e+++w+ +ik+  +++ +v+++ nn++eg +p++++
  gi|518651710|ref|YP_008141230.1| 172 IKTTENLYVRFLGNksleK----KDLGEirinrhGEIEQWVGKIKKQDSGQGTVFIYANNHYEGLSPDTIK 238
                                       9*************55541....44443444445*********************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1861.71
//
Query:       gi|518651711|ref|YP_008141231.1|  [L=257]
Description: DNA adenine methylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   4.1    1.3e-24   87.3   4.1    1.1  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0001   22.0   0.0       0.06   13.0   0.0    2.3  2  Cons_hypoth95    Conserved hypothetical protein 95


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 !   87.3   4.1   1.5e-28   1.3e-24       1     218 [.       7     203 ..       7     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 1.5e-28
                                       STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH.TC CS
                   MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakkqgkkvlinDinedlinlykaliknnveelikelekll 77 
                                       Y+G+K++++ eI+++++ +++++fv++F+G+g+V +++  q    + nD+n dl+ l++  +knn+ +l+ ++ +  
  gi|518651711|ref|YP_008141231.1|   7 YPGSKTAIVGEIQRVFDISQCTRFVDVFSGSGSVIINI--QAGIEVYNDLNRDLFILFN-SLKNNFSQLYRAADAVA 80 
                                       99***************99*******************..999999*************.66667*********755 PP

                                       TTGGC.TSHHHHHHHHHHHH...HHH-HHHHHHHHHHHHC.CBGGG---B-TTS-B---B-S-SS-....HHHHHHH CS
                   MethyltransfD12  78 ekeelenereyfyelreefnkkidaireaeeaidflylnr.llfsglervnkkgnfnvpygaykkpkkvaekelklr 153
                                       +      ++ +f + + +    +d+ + ++e++  +++n+ ++f g+  ++ k+   + +g y+k+      +l ++
  gi|518651711|ref|YP_008141231.1|  81 RD-----RKMFFDYYDGRIV--MDTGNPDIEKAFSIFFNFnTGFGGMGNSYGKK-DKSLFGTYRKN----VSNLLKA 145
                                       44.....5666666665555..78889999978888888747788888777777.47789999999....89999** PP

                                       HHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHH CS
                   MethyltransfD12 154 seklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlks 218
                                        +k+++ kie+ df +v+ k++++d ++YlDPPY +        +++  +f + d   l+++l s
  gi|518651711|ref|YP_008141231.1| 146 ESKIRKMKIENMDFREVIDKYNDPDTFFYLDPPYPG-------KDWYVHNFLESDFMELRNTLGS 203
                                       **********************************98.......4444444444444455555555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0   0.00042       3.7      42      57 ..      27      42 ..      11      84 .. 0.88
   2 !   13.0   0.0   6.7e-06      0.06      72     131 ..     127     187 ..     124     218 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00042
                                      C-EEEETT-TTSHHHH CS
                     Cons_hypoth95 42 garvLDlfaGsGalgl 57
                                        r++D+f+GsG++ +
  gi|518651711|ref|YP_008141231.1| 27 CTRFVDVFSGSGSVII 42
                                      4689*********966 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.7e-06
                                       S-HHHHHHHHHHHCCCT--T....TTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH.HH CS
                     Cons_hypoth95  72 kdkeavkilkenleelklee....etaelkedaleallklakkkeefdivflDPPyakelliee 131
                                       kdk+ + + ++n+++l   e    ++++ ++d  e ++k    + +  + +lDPPy  ++++ +
  gi|518651711|ref|YP_008141231.1| 127 KDKSLFGTYRKNVSNLLKAEskirKMKIENMDFREVIDKY---NDPDTFFYLDPPYPGKDWYVH 187
                                       7899999******987655555544455555555555555...5555899******99998543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1752.14
//
Query:       gi|518651712|ref|YP_008141232.1|  [L=548]
Description: hypothetical protein FACI_IFERC00001G0351 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-29  101.6   0.0      7e-29  101.0   0.0    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    3.9e-15   55.8   0.0    7.2e-15   55.0   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
      1e-06   29.1   0.0    1.7e-06   28.3   0.0    1.3  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
  ------ inclusion threshold ------
       0.15   12.3   0.4       0.43   10.8   0.4    1.8  1  DUF2508        Protein of unknown function (DUF2508)


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.0   0.0   1.6e-32     7e-29       4     149 ..     271     427 ..     268     428 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.6e-32
                                       HHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH---- CS
                     Acyl-CoA_dh_1   4 frvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealda 80 
                                       +++++e l+++Rl +aaaa g+ar+a+ ea+ y  +rk+fgk li+h+ + + l +m++ le++ +l+++ +e++++
  gi|518651712|ref|YP_008141232.1| 271 IYYITEDLMVSRLDNAAAACGIARKAYLEAYYYTGKRKTFGKLLIEHPGIVKDLLDMEVLLEGSIALTFKSIELFNN 347
                                       689************************************************************************99 PP

                                       ----...........HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHH CS
                     Acyl-CoA_dh_1  81 gkpd...........raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniia 146
                                         ++           r  ++++K+ +++   ++++ a +l+Gg G+l e pver++r+a++++i+eG+s+iq +++ 
  gi|518651712|ref|YP_008141232.1| 348 SINSkppyddeynytRLMTHIVKNITADSSARITQMATELHGGIGFLSEFPVERWHREALITPIWEGASNIQALDML 424
                                       9999999******************************************************************9999 PP

                                       HHH CS
                     Acyl-CoA_dh_1 147 rrl 149
                                       +++
  gi|518651712|ref|YP_008141232.1| 425 EAI 427
                                       887 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   1.6e-18   7.2e-15       1      95 [.     160     257 ..     160     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 1.6e-18
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GG....G CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdap....g 72 
                                       a+++TE q+Gsd+ ++kt+ ae  +g ++l+G K + +na+ a++al+ a  ++++ +a+glslfl+pr+++    +
  gi|518651712|ref|YP_008141232.1| 160 ATWFTEIQGGSDLGANKTR-AESGNGLWYLTGDKYFASNAGLADVALTSAF-HGDNhGAKGLSLFLIPRKNNdgelN 234
                                       5789**************5.5555559************************.555568**********666668889 PP

                                       EEE-----BSS-TTS-EEEEEEE CS
                     Acyl-CoA_dh_M  73 vsvrrieeklGlrglptgelvfe 95 
                                        ++rr++ek +++++p+ge++++
  gi|518651712|ref|YP_008141232.1| 235 YRLRRLKEKSATKSVPSGEVELD 257
                                       999*****************997 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   3.9e-10   1.7e-06       4     129 ..     286     412 ..     284     417 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.9e-10
                                       HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH.. CS
                     Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve.. 78 
                                       aa+a G+Ar a+ e+  ++++r++  +g+ l ++p +   l +++  l+   al+ + ++   + ++ + +++ e  
  gi|518651712|ref|YP_008141232.1| 286 AAAACGIARKAYLEAYYYTGKRKT--FGKLLIEHPGIVKDLLDMEVLLEGSIALTFKSIELFNNSINSKPPYDDEyn 360
                                       89**********************..**************************************9999999954423 PP

                                       .HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTS CS
                     Acyl-CoA_dh_2  79 .draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaH 129
                                        +r+   + +  +++ ++++++++ e++Gg + ++e p++R  R+a ++ ++
  gi|518651712|ref|YP_008141232.1| 361 yTRLMTHIVKNITADSSARITQMATELHGGIGFLSEFPVERWHREALITPIW 412
                                       35666666799**********************************9877665 PP

>> DUF2508  Protein of unknown function (DUF2508)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   9.5e-05      0.43      14      57 ..     439     482 ..     427     483 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                           DUF2508  14 edeeLleeIektkeelesakslfensvDlsdeliyqlklaeakY 57 
                                       + +++l+eI + k + es+++ + ns+D   ++ ++++  +akY
  gi|518651712|ref|YP_008141232.1| 439 DFKNILSEIREEKAAAESCYNSLKNSIDNLLSMGVEEAQFHAKY 482
                                       34789***********************9999999999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3710.45
//
Query:       gi|518651713|ref|YP_008141233.1|  [L=503]
Description: hypothetical protein FACI_IFERC00001G0352 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-69  234.6   0.0    1.9e-69  234.3   0.0    1.0  1  AMP-binding    AMP-binding enzyme
    3.3e-11   44.0   0.0    5.8e-11   43.2   0.0    1.4  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.3   0.0   2.1e-73   1.9e-69       7     422 ..      17     405 ..      11     406 .. 0.86

  Alignments for each domain:
  == domain 1  score: 234.3 bits;  conditional E-value: 2.1e-73
                                       HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding   7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                        +p+k ++ +  + +++TYr+l e+v +l+  + ++G+ kg+++a++  ns+e++ +l+a    G ++ p+n +l+ 
  gi|518651713|ref|YP_008141233.1|  17 LFPEKKVI-S--GSRSITYRDLFEKVLSLSTSMNKMGISKGTVIAVADYNSIEFMELLFASSLTGSIIYPVNIKLPW 90 
                                       56777755.7..79*************************************************************** PP

                                       HHHHHHHHHHTESEEEETCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTT CS
                       AMP-binding  84 eelayiledseakvliatvdsel.leklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpd 159
                                             +++s+a++++   ++e  ++ + +        ++++ l++++ +   +++++  s+      ++ee+++ +
  gi|518651713|ref|YP_008141233.1|  91 NMAMETVKESGAEYVF--ASKEFmNAGIYKGFR----DDHIVSLSENGDYI--KFHDMLTSD-----LHREEKTTGN 154
                                       ****************..777775555555444....34444444333222..233333222.....234557899* PP

                                       SEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHH.....HHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 160 dlayiiYTSGTTGkPKGVmlshrnlvanvaslk.....letr.fklkeddvvlsilplahifglilelllallsGat 230
                                       d + i++TSGTTGkPK V ++ +  v+ + s+      ++ +  kl+++d++ls  p++hi ++  + + a + Ga 
  gi|518651713|ref|YP_008141233.1| 155 DNYSILFTSGTTGKPKEVLYTNEKSVNGALSILyqlglFN-TpAKLTSSDTILSLIPFYHIWSW-GSAFHAAYLGAD 229
                                       **********************999999999865555333.3466777****************.************ PP

                                       EEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralf 307
                                        ++  k ++   + +l++i++ k+t i++vP+++  ll++++++      +l+++++ l+gg+p+s++l+++++a++
  gi|518651713|ref|YP_008141233.1| 230 YIITGKYNP---ENVLNAIKENKATWINAVPTMVYDLLSHDREN------RLNGIKM-LIGGSPISKNLAEKLNAKG 296
                                       ***887766...5578***********************98888......9*****9.68****************9 PP

                                       TCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SEBTT-HHH CS
                       AMP-binding 308 geevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkgYlkkpea 384
                                       ++ ++ +YG T +++  + l +++++++l sv  p+p v + + D + g+ +++g+ Gel++  p++ + Yl++pe 
  gi|518651713|ref|YP_008141233.1| 297 IK-FSTIYGGTDMLATSISLGRPDQHESLRSVTYPVPMVSATVRDNN-GNILENGTIGELWINAPWLPEKYLNRPEN 371
                                       98.************99667778888999****************99.**************************998 PP

                                       HHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 385 taeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                           +   ++w++TGD+g++++dG ++i++R kd++k+
  gi|518651713|ref|YP_008141233.1| 372 HD--YE--NGWFKTGDVGEMTPDGGIKILDRVKDVVKS 405
                                       65..54..47**************************97 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.2   0.0   6.4e-15   5.8e-11       2      76 .]     415     492 ..     414     492 .. 0.91

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.4e-15
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHHHH.....HT-TTTS-SEEEE-S---B-T CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahvrk.....elgpyavpkkvvfvdelpktr 73 
                                       +Es +++ p+++ aaV G+ de++Ge++va V  +++ e   +e+++++++     ++ +++ p ++++++e+p+t 
  gi|518651713|ref|YP_008141233.1| 415 IESLISEFPGIEIAAVTGIADEKWGERPVAWVKASEDIE--IKEIRQFMEThasngNINKWWIPVEFIIIEEMPMTS 489
                                       8********************************975634..699999996666666********************* PP

                                       TS- CS
                     AMP-binding_C  74 sGK 76 
                                        GK
  gi|518651713|ref|YP_008141233.1| 490 VGK 492
                                       **9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3123.33
//
Query:       gi|518651714|ref|YP_008141234.1|  [L=387]
Description: hypothetical protein FACI_IFERC00001G0353 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-34  117.7  73.1    1.6e-29  103.0  43.5    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 !  103.0  43.5   8.7e-34   1.6e-29       4     330 ..      23     326 ..      17     330 .. 0.83
   2 !   28.5  21.6     4e-11   7.1e-07      42     167 ..     252     380 ..     250     386 .. 0.86

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 8.7e-34
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.llll 79 
                                       ++ ++++ r+++ +++p +l ++l+is+   +ll+t+y lg+ v+++p+G +sdr+G  +v  ++++l++l+ +l+ 
  gi|518651714|ref|YP_008141234.1|  23 SFSMNSTLRFFIPVLIP-LLVSSLNISVYLGSLLITAYWLGYTVFQIPAGMISDRVGVSKVAKISFILMVLSfSLFY 98 
                                       55667777777888888.9*****************************************************54444 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfy 155
                                       +f  s++ +++  +l G ++++++ +  ++i +w p++ r+  +g++++gf +Ga lg +l+   l+  +g+r +f+
  gi|518651714|ref|YP_008141234.1|  99 FFMDSYTGIFIIQILLGSFSATVYLSDTSVIQKWLPQSSRATFVGIYQTGFFIGASLGeYLILRTLS--IGFRFAFI 173
                                       453666699999**********************************************888888887..9******* PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllpl 232
                                       ++  ++++a +l +++l+e+++++  k +k +                  ++ ++ + ++ ++++f + g+ tl+++
  gi|518651714|ref|YP_008141234.1| 174 VILSILIIATILNIVFLREPEHNKLAKHGKID------------------RKIIY-VAMIRFSAGFLYIGFITLFTT 231
                                       ************99***999999999999888..................23232.444444555578888888888 PP

                             MFS_1 233 ylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll.vlv 308
                                       ++++++  + + +a+l+  ++a++g+i ++l+g +s+r+++ + ++  l++++l a+ +++++ +  +v++++ +++
  gi|518651714|ref|YP_008141234.1| 232 FIVFDHIVP-YSSAYLYAWIPAAGGIITSPLGGMISRRMKHGKSIVSVLPVVAL-AVTIIYINYA--PVAVIFlISF 304
                                       878888888.889999999999999999**********9986666555555555.5555555666..4555554888 PP

                             MFS_1 309 liGfglgfvfpsllalasdlap 330
                                       l G+++g++ ++++ +asd+ +
  gi|518651714|ref|YP_008141234.1| 305 LTGMFYGLYAGPSMGMASDFSG 326
                                       89****************9875 PP

  == domain 2  score: 28.5 bits;  conditional E-value: 4e-11
                             MFS_1  42 algaavaslplGrlsdrf..Grrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfp 115
                                       a+g +++s+++G +s r+  G   v +l ++++a++ ++ + + +++ ++++  +l+G+++g+++  ++ +++d + 
  gi|518651714|ref|YP_008141234.1| 252 AAGGIITSPLGGMISRRMkhGKSIVSVLPVVALAVT-IIYInY-APVAVIFLISFLTGMFYGLYAGPSMGMASDFSG 326
                                       67899***********98335555666666666666.444456.8999999************************** PP

                             MFS_1 116 k.eergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvl 167
                                          + ++  ++l+ ++++G  + pll g++ s +g + ++f +++++s++ +++
  gi|518651714|ref|YP_008141234.1| 327 SdANLASSSSILNFSSQVGGTVSPLLMGFMFSIYGnFALAFTVVGAISIITLII 380
                                       *9999**************************88888**************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); 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:                         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: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 2667.06
//
Query:       gi|518651715|ref|YP_008141235.1|  [L=322]
Description: Zn-dependent hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-19   70.5   0.0    4.1e-19   69.4   0.0    1.6  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.5e-06   27.8   0.0    2.7e-06   27.1   0.0    1.4  1  Lactamase_B_2  Beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   4.6e-23   4.1e-19       6     197 .]      19     219 ..      15     219 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 4.6e-23
                                       SEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCC CS
                       Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapal 82 
                                       +n+y i +++ ++++DtG+s+   r+     a+ +++ ++d  i+THlH+DHiGg+ +l +  ++pv++ + ++   
  gi|518651715|ref|YP_008141235.1|  19 ANVYNI-NGDYNYIVDTGMSENGYRQI----ANTIDLSRIDMCIITHLHIDHIGGALYLEKNNKIPVYISKNDYDII 90 
                                       577777.89*****************9....5****************************************99999 PP

                                       HCHHHHHHHHHCCHH...................TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEE CS
                       Lactamase_B  83 fmeeaddaasrkgll...................lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvvey 140
                                       ++   ++++ + + +                    +   +++ ++ ++   ++ + ++++ ++  pgh++g++ +++
  gi|518651715|ref|YP_008141235.1|  91 KTMVDNRQEYFSEYRnlmmsngvpeelfrnitegNPVMKFMDYYASLNLNIIGNMAMKDTDIIDVPGHSPGSVAIYL 167
                                       999998888888888*******************999**************************************** PP

                                       TTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 141 gggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++    +tGD +l +  + i+      +    +  + y++sl+k+ + ++e+ +pgH
  gi|518651715|ref|YP_008141235.1| 168 KDIHAMVTGDHVLKNISPNISV-----YRNNVDYLGMYIESLKKIQNYDIEIAYPGH 219
                                       **********************.....88888999999******************* 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     3e-10   2.7e-06       2      70 ..      29      90 ..      28     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 3e-10
                                      EEEES--TT...HHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHC CS
                     Lactamase_B_2  2 riLiDagpd...lrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavl 70
                                      ++++D+g +    rq  +          +l++id+ ++th H+DH+ g+l l +  ++k+p+y +k  ++++
  gi|518651715|ref|YP_008141235.1| 29 NYIVDTGMSengYRQI-A-------NTIDLSRIDMCIITHLHIDHIGGALYLEK--NNKIPVYISKNDYDII 90
                                      6778888883333322.2.......345899***********************..4469***887655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); 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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2082.49
//
Query:       gi|518651716|ref|YP_008141236.1|  [L=121]
Description: dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1064  (0.0593452); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 885.53
//
Query:       gi|518651717|ref|YP_008141237.1|  [L=125]
Description: hypothetical protein FACI_IFERC00001G0356 [Ferroplasma acidarmanus fer1]
Scores for complete 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-12   46.3   0.0    4.1e-12   45.8   0.0    1.3  1  DUF302    Domain of unknown function DUF302


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   2.3e-16   4.1e-12       1      63 []      33      94 ..      33      94 .. 0.99

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.3e-16
                                      EEHHHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEEETTEEEEEEE-H CS
                            DUF302  1 iDvqatlkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVyekdgkttvsyvdP 63
                                      iD+++++  + g+++++ +++ +++P ++t +++++peig+ lP ++++y+ +  +++ y dP
  gi|518651717|ref|YP_008141237.1| 33 IDHRKNA-DNAGLEMQNETLILFGSPVVGTLLMKENPEIGIELPSKLLIYSTNSDVYILYKDP 94
                                      8******.*****************************************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 789.02
//
Query:       gi|518651718|ref|YP_008141238.1|  [L=111]
Description: hypothetical protein FACI_IFERC00001G0357 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-14   53.2   0.1    2.4e-14   53.0   0.1    1.1  1  Rieske    Rieske [2Fe-2S] domain
    3.3e-08   33.4   0.0      4e-08   33.1   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain
  ------ inclusion threshold ------
       0.19   12.3   0.0       0.29   11.8   0.0    1.3  1  VCBS      Repeat domain in Vibrio, Colwellia, Bradyrhizobium 


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.1     4e-18   2.4e-14       2      84 ..       3      86 ..       2      99 .. 0.83

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 4e-18
                                      EEEEEEGGGC-.TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEE.ETT.EEE-TTT--EEE.TTSBEE CS
                            Rieske  2 wvavakesdvp.egdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegki.dekgvleCpcHgwayd.adGkvi 77
                                      w ++   + ++ +g+ +++++g+ ++v++ +++g++y ++++C+H++++l +  + +++++++CpcH+++++  +Gk++
  gi|518651718|ref|YP_008141238.1|  3 WRKILGIKALEnSGNHVSINLGDGKVVFITKQNGKLYGINGICSHLKCILGN--VsEDGKHVICPCHNAKFElDTGKMV 79
                                      66677777788788999********9999999*****************944..3235559****************** PP

                                      E-TTHHH CS
                            Rieske 78 kgPaprp 84
                                      + P  +p
  gi|518651718|ref|YP_008141238.1| 80 EPPFIAP 86
                                      *998776 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   6.7e-12     4e-08       1     103 [.       2     109 ..       2     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 6.7e-12
                                       SEEEEEECCCS-TTB-.EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEET CS
                          Rieske_2   1 ewvpvckledlvketg.vaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdL 76 
                                       +w ++  +++l ++ + v   +++ +v+ +  +++++y i+ ++        + G v ++     v +P ++ kf+L
  gi|518651718|ref|YP_008141238.1|   2 TWRKILGIKALENSGNhVSINLGDGKVVFITKQNGKLYGINGICSHL---KCILGNVSED--GKHVICPCHNAKFEL 73 
                                       599999999999877636666799999999999***********994...4445666555..67899********** PP

                                       TT-BBSS.........-TTSB-BEE-EEESTSEEEE CS
                          Rieske_2  77 ktGecle.........deevslkvypvrvedgkvev 103
                                       +tG+++e          e+++l++y+ r e++ +e+
  gi|518651718|ref|YP_008141238.1|  74 DTGKMVEppfiapqtpMEKYTLETYNLREEGNFIEI 109
                                       **************99999***********999998 PP

>> VCBS  Repeat domain in Vibrio, Colwellia, Bradyrhizobium and Shewanella
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.8e-05      0.29      14      40 ..      13      39 ..       6      61 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.8e-05
                              VCBS 14 ndgglrvyrnngdGtftdvtktslggs 40
                                       ++g++v +n gdG+  ++tk+ +  +
  gi|518651718|ref|YP_008141238.1| 13 ENSGNHVSINLGDGKVVFITKQNGKLY 39
                                      5789*****************865553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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 0.23s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 863.68
//
Query:       gi|518651719|ref|YP_008141239.1|  [L=249]
Description: Enoyl-CoA hydratase/isomerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-42  145.7   0.0    1.7e-42  145.5   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    1.4e-31  110.3   0.0    2.5e-31  109.4   0.0    1.4  1  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.5   0.0   1.9e-46   1.7e-42       3     244 ..      11     247 ..       9     249 .] 0.95

  Alignments for each domain:
  == domain 1  score: 145.5 bits;  conditional E-value: 1.9e-46
                                       ETTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHH CS
                             ECH_1   3 eagvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevle 79 
                                       e+g   i ++r + +N+++ e+++E+  al ++e     r +v+  g k F+aGad+ +  e +++++ +++ +++e
  gi|518651719|ref|YP_008141239.1|  11 ENGTGFIYFDREDRLNTITVEMINEISSALSDMEST--CRSIVIG-GKKNFSAGADVLQFPELNPSEAYEFHRKLNE 84 
                                       67778899*************************998..*****95.5788*************************** PP

                                       HHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT CS
                             ECH_1  80 lwtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllg 156
                                       l    ++   pvi+ +nG+++gGGlel l +Di++++++a+ +++e+ lG+ +gagg  il+  vG+++A +++l+g
  gi|518651719|ref|YP_008141239.1|  85 LALYFREYTWPVISFLNGYVFGGGLELSLSTDIRVCSRDAQLSQPEIGLGINAGAGGNVILPHVVGRNRALYMILTG 161
                                       ***************************************************************************** PP

                                       -EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHH CS
                             ECH_1 157 kkisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddi 233
                                        +++aq a + Glvd  ++ +  leea  + + ++ k+++ ++ +k a+n++++++ ++ l+ ea lf  +fs +d 
  gi|518651719|ref|YP_008141239.1| 162 ARLNAQTAYEFGLVDI-LAGNA-LEEATRIGQVINTKPENTVKLAKRAVNNTSSSHIKTNLDYEAALFGILFSGQDT 236
                                       **************95.55555.5678889*********************************************** PP

                                       HHHHHHHHTCS CS
                             ECH_1 234 keGlqaflEkr 244
                                       k  ++ f+ k+
  gi|518651719|ref|YP_008141239.1| 237 KDRINNFIKKK 247
                                       **999999887 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.0   2.8e-35   2.5e-31       2     227 ..      15     232 ..      14     249 .] 0.80

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 2.8e-35
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       g+i ++r++ lN ++ em++++++al+++  +++++ +v+ g  +k f+AG Dv ++ e + +++ e   f r+  +
  gi|518651719|ref|YP_008141239.1|  15 GFIYFDREDRLNTITVEMINEISSALSDM--ESTCRSIVIGG--KKNFSAGADVLQFPELNPSEAYE---FHRKLNE 84 
                                       68999***********************8..57899999999..78***************998866...******* PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       l  +  +y+ pv+++++G+v GgG+ ls+++ +rv + +++++ PE+++G+    Gg  +L+++ g + +ly+ lTG
  gi|518651719|ref|YP_008141239.1|  85 LALYFREYTWPVISFLNGYVFGGGLELSLSTDIRVCSRDAQLSQPEIGLGINAGAGGNVILPHVVGrNRALYMILTG 161
                                       ***************************************************************977589******** PP

                                       --B-HHHHHHTTS--EE--GGGHHHHHHHHHTT........--------......----SHHHHHHHHHHHT. CS
                             ECH_2 155 arlkgadalaaglathyvpseklealeeaLaelessdeeaveevleelaeeaeeeeeeselaekreaidrlfs 227
                                       arl+++ a+++gl + +  ++  e+  +++ ++ +++ e++ +++++  +++++++ +++l  +++    lfs
  gi|518651719|ref|YP_008141239.1| 162 ARLNAQTAYEFGLVDILAGNAL-EEA-TRIGQVINTKPENTVKLAKRAVNNTSSSHIKTNLDYEAALFGILFS 232
                                       ***************9876653.332.2344443333344444444444444433334555544555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1801.86
//
Query:       gi|518651720|ref|YP_008141240.1|  [L=488]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete 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  144.6  52.7    3.6e-42  144.6  52.7    2.5  2  MFS_1     Major Facilitator Superfamily
    2.6e-08   33.2  17.7    2.6e-08   33.2  17.7    3.4  3  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6  52.7     4e-46   3.6e-42       2     353 .]      23     415 ..      22     415 .. 0.87
   2 ?    0.7   0.2     0.022   1.9e+02     237     265 ..     447     474 ..     428     486 .. 0.48

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 4e-46
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++a+ l+ +  +++ pa+p    + ++ +   ++++lt+y ++  va+ ++G l+d fG r+v+l+  l++a+++ +
  gi|518651720|ref|YP_008141240.1|  23 AFAGTLIVYVETMIVPAIP-VFITFFNTTYNNVSWILTAYLITGTVAAGIFGKLGDVFGKRKVFLILSLIYAISVSM 98 
                                       6889999999*********.66699*************************************************666 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + f +++   l+v r++qG+g  +++p+++a+i d++p+++ ++a gl+sa+f++Ga ++ ++g++++++++W++++
  gi|518651720|ref|YP_008141240.1|  99 GGF-ATSLdELIVIRIIQGIGF-GMYPLAYAIINDVVPRSRLALAQGLMSATFAVGAGMALVIGAYITEAYSWQWSY 173
                                       669.77787************7.****************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                        ++a+v++ +f+l +++l ++  + k k +                                               
  gi|518651720|ref|YP_008141240.1| 174 HAIAPVAFALFILSYFFLKDNTAPAKEKIDFAGVaimasglvmlifglsegntygwlsplilfsfvfsiaafyafik 250
                                       *************99***9999999999999999*****************99999999999999998888888888 PP

                             MFS_1 189 .kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls...glllaglllallalvgaila 261
                                        +   + ++++   +llk++ ++i+ ++ ll+++g+++l++++p++lq+    +   + +++gl++  + ++++++a
  gi|518651720|ref|YP_008141240.1| 251 yELASRYAFID--MHLLKSRNILIANFVGLLTMAGMYFLFFTVPTLLQDPAPSGfgkSIFTSGLIMLPATILAMVFA 325
                                       77777777777..5555555554455555555679999*******96655444455648999999999999999999 PP

                             MFS_1 262 llagrlsdrlgrrrrlllallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagta 337
                                       ++a+r+ d  g+++ +l++l++ ++a+++l+l   t   +l ++ +  ++G+g++fv + +++l+  ++p++++g a
  gi|518651720|ref|YP_008141240.1| 326 PVAARVTDARGPKISILIGLSVSFIAFILLILDRST---ILDIIeAATVLGTGFSFVLVGIINLLLISTPKSKSGEA 399
                                       *****9999776665555555555555555555555...6666658888**************************** PP

                             MFS_1 338 sglfntagslggalgp 353
                                       +g +++++ lg+ ++p
  gi|518651720|ref|YP_008141240.1| 400 TGMNTVFRELGMTIAP 415
                                       **************98 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.022
                             MFS_1 237 vlglsglllaglllallalvgailallag 265
                                       ++g++   +a+ +  +++++++ +a+l++
  gi|518651720|ref|YP_008141240.1| 447 TYGFP-SATAYNFTYITGIIFLLFAVLLT 474
                                       45555.12222222222222222222222 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2  17.7   2.9e-12   2.6e-08      47     190 ..      53     189 ..      18     195 .. 0.76
   2 ?   -1.2   0.7     0.079   7.1e+02      70     189 ..     224     249 ..     204     280 .. 0.48
   3 ?   -1.7   6.4      0.11     1e+03      46     153 ..     308     413 ..     273     435 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.9e-12
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                        +++i+ ++l+ +++ + ++g+lgd+fG++k++li ++++ i+  + ++a+   s+  liv R++ Gig G+ + l+
  gi|518651720|ref|YP_008141240.1|  53 NVSWILTAYLITGTVAAGIFGKLGDVFGKRKVFLILSLIYAISVSMGGFAT---SLDELIVIRIIQGIGFGM-YPLA 125
                                       4689***********************************************...****************96.7888 PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllf 190
                                          i+ + p +      +l     ++G  +a ++g+ + +  +   w++  +  +  a +l+il +f
  gi|518651720|ref|YP_008141240.1| 126 YAIINDVVPRSRLALAQGLMSATFAVGAGMALVIGAYITEAYS---WQWSYHAIAPVAFALFILSYF 189
                                       8999999996655555555555555555555555555555555...555555555555555555544 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.079
                                       HHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHH CS
                          Sugar_tr  70 gdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqla 146
                                       g+                                                                           
  gi|518651720|ref|YP_008141240.1| 224 GN--------------------------------------------------------------------------- 225
                                       12........................................................................... PP

                                       HHHHHHHHHHHHHHHHTSS-TTHHHHHHH.CCHHHHHHHHHHGG CS
                          Sugar_tr 147 itfGilvaaifglglnktsnadgwrillg.lqlvpallllilll 189
                                                           + gw  +l  +++v++++ +++++
  gi|518651720|ref|YP_008141240.1| 226 --------------------TYGWLSPLIlFSFVFSIAAFYAFI 249
                                       ....................223433332124444444444444 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 0.11
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                        +sgli+  + + a++ + +a  ++d  G k s+li+  +++i+ +l ++    +++  +i +  ++G g  ++ v 
  gi|518651720|ref|YP_008141240.1| 308 FTSGLIMLPATILAMVFAPVAARVTDARGPKISILIGLSVSFIAFILLILDR--STILDIIEAATVLGTGFSFVLVG 382
                                       5566666666677777777777777777777777777777777777777766..33444444445555544444444 PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilv 153
                                       +  ++   +pk++ g  ++++ ++  +G+ +
  gi|518651720|ref|YP_008141240.1| 383 IINLLLISTPKSKSGEATGMNTVFRELGMTI 413
                                       4444444555555555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       898  (0.0500865); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 3244.92
//
Query:       gi|518651721|ref|YP_008141241.1|  [L=452]
Description: hypothetical protein FACI_IFERC00001G0360 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-06   26.1   0.2      0.025   14.8   0.1    3.8  3  NPCBM_assoc      NPCBM-associated, NEW3 domain of alpha-galac
  ------ inclusion threshold ------
      0.013   15.5   0.5        1.7    8.7   0.0    2.6  2  DUF5316          Family of unknown function (DUF5316)
      0.053   13.1   0.4      0.053   13.1   0.4    3.2  4  4HB_MCP_1        Four helix bundle sensory module for signal 
       0.14   12.4   1.2       0.34   11.2   0.1    2.0  2  TrbC             TrbC/VIRB2 family
        1.1    9.6   9.7        3.8    7.8   0.4    3.5  3  Alpha_adaptinC2  Adaptin C-terminal domain


Domain annotation for each model (and alignments):
>> NPCBM_assoc  NPCBM-associated, NEW3 domain of alpha-galactosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.093   3.3e+02      42      68 ..     114     140 ..     109     145 .. 0.87
   2 !    4.7   0.0    0.0098        35       8      29 ..     188     209 ..     185     236 .. 0.93
   3 !   14.8   0.1   6.9e-06     0.025      21      78 ..     314     368 ..     286     369 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.093
                       NPCBM_assoc  42 asaaslapGetveatvkVtppagaaaG 68 
                                       ++++++++G + +    V ++++a  +
  gi|518651721|ref|YP_008141241.1| 114 NQIPEIQAGHSYTIMQLVNISKTASGS 140
                                       7899******************99865 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0098
                       NPCBM_assoc   8 tltltvtndgtaaatnvslsls 29 
                                       +lt++  n+gt+a++nv+++++
  gi|518651721|ref|YP_008141241.1| 188 KLTIYTENTGTSAMKNVNFNIT 209
                                       579999************9875 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 6.9e-06
                       NPCBM_assoc  21 atnvslslslPeGWtvvevspasaaslapGetveatvkVtppagaaaGdyevtakarl 78 
                                       + ++ +s s P G  + ++   ++a+l+pG++ ++t  +  +++aa G+y+v++ +++
  gi|518651721|ref|YP_008141241.1| 314 VLSIHVSSSNPLG--ALTANNVTFAQLQPGQSIKVTYIIDTSTSAA-GTYPVQLLVEY 368
                                       6677788888888..4488889999*******************99.9****998765 PP

>> DUF5316  Family of unknown function (DUF5316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.012        41       7      35 ..       7      35 ..       3      45 .. 0.87
   2 ?    8.7   0.0   0.00048       1.7       8      50 ..     404     446 ..     402     450 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.012
                           DUF5316  7 kisGfvglvfiliagllsGafvsgdrira 35
                                      +i+Gf+ l ++++a   sG + sgd    
  gi|518651721|ref|YP_008141241.1|  7 LITGFIVLSMVMLAIGASGLMPSGDANHS 35
                                      69******999999999*******98765 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00048
                           DUF5316   8 isGfvglvfiliagllsGafvsgdriranytseskedrrkrfk 50 
                                       ++G+++l+ i+++++   ++ + ++ r   ++ s+++ +k+++
  gi|518651721|ref|YP_008141241.1| 404 YAGMAALIIIILGAIGAAVLHTRKKNRKSRHAGSEKHEEKNNN 446
                                       68*************9999****99999998877777777665 PP

>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.5e-05     0.053       2      34 ..       1      33 [.       1      38 [. 0.90
   2 ?   -2.6   0.2      0.96   3.4e+03     100     140 ..     261     301 ..     260     305 .. 0.77
   3 ?   -1.4   0.0      0.41   1.5e+03     151     175 ..     369     393 ..     366     399 .. 0.75
   4 ?   -0.0   0.1      0.15   5.4e+02      14      36 ..     407     429 ..     403     433 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.5e-05
                         4HB_MCP_1  2 lkirkKLillflllallliivGvvGlyslkkin 34
                                      +k++kKLi +f++l+++++++G+ Gl+   ++n
  gi|518651721|ref|YP_008141241.1|  1 MKTYKKLITGFIVLSMVMLAIGASGLMPSGDAN 33
                                      899**********************99777666 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.96
                         4HB_MCP_1 100 ktilteeEkelleefkeqlnaYrevrkkvlelakegkkdeA 140
                                       +t++  +Ek+ l+   ++ ++ ++ +k++l++  ++  ++ 
  gi|518651721|ref|YP_008141241.1| 261 DTYIHGNEKNNLTVAIKNKDMISDTKKQLLTFYLNNTGNKV 301
                                       57888888888888888888888888888888888776655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.41
                         4HB_MCP_1 151 arekliealeelvdlnlkvAeeayk 175
                                       +++++ e+ +++ ++n+k   ++++
  gi|518651721|ref|YP_008141241.1| 369 HFNNTAETFNKVYTYNQKIVPTTTQ 393
                                       5788899999999999987666555 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.15
                         4HB_MCP_1  14 llallliivGvvGlyslkkinkn 36 
                                         al++ii+G++G   l++ +kn
  gi|518651721|ref|YP_008141241.1| 407 MAALIIIILGAIGAAVLHTRKKN 429
                                       67899999999998777776665 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.55     2e+03      47      68 ..       6      27 ..       1      34 [. 0.64
   2 ?   11.2   0.1   9.4e-05      0.34      40      67 ..     390     417 ..     361     425 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.55
                              TrbC 47 dfltgplakviatiaiivaGim 68
                                      + +tg ++  ++++ai ++G+m
  gi|518651721|ref|YP_008141241.1|  6 KLITGFIVLSMVMLAIGASGLM 27
                                      5566655555666666666655 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 9.4e-05
                              TrbC  40 tvlqnivdfltgplakviatiaiivaGi 67 
                                       t  q+i ++lt pl  ++a ++ii++G+
  gi|518651721|ref|YP_008141241.1| 390 TTTQQISNTLTEPLYAGMAALIIIILGA 417
                                       7789**********************97 PP

>> Alpha_adaptinC2  Adaptin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.47   1.7e+03      29      51 ..     145     167 ..     130     178 .. 0.83
   2 ?    7.8   0.4    0.0011       3.8      21      49 ..     182     210 ..     170     242 .. 0.86
   3 ?    5.3   1.0    0.0068        24       7      99 ..     268     373 ..     265     384 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.47
                                       EEEEEE-SSS-EEEEEEEEEEBT CS
                   Alpha_adaptinC2  29 tlsftNkssqpisnfsfqaavpk 51 
                                       ++s+ N++++  + f++ + +p+
  gi|518651721|ref|YP_008141241.1| 145 NISYDNTTMSGNTVFTIPVGKPD 167
                                       68999********9999988885 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                                       TSTTEEEEEEEEEE-SSS-EEEEEEEEEE CS
                   Alpha_adaptinC2  21 erpgqiritlsftNkssqpisnfsfqaav 49 
                                       ++ + i++t++++N+ ++ ++n++f +  
  gi|518651721|ref|YP_008141241.1| 182 QNEKFIKLTIYTENTGTSAMKNVNFNITS 210
                                       67788********************9865 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0068
                                       EETTEEEEEEEEE.TTSTTEEEEEEEEEE-SSS-EEEEEEEEEEBTTCEEE......EEEES-S-B-TT........ CS
                   Alpha_adaptinC2   7 ekddlqIgfkfek.perpgqiritlsftNkssqpisnfsfqaavpkslklq......lqppsstvlppn........ 68 
                                       ek++l + +k +   +  ++  +t ++ N+ ++   ++ +    p+ l ++      l + +      n        
  gi|518651721|ref|YP_008141241.1| 268 EKNNLTVAIKNKDmISDTKKQLLTFYLNNTGNKVYRDLEIHMLSPSVLSIHvsssnpLGALTA-----Nnvtfaqlq 339
                                       566666666666655556667788888888899999999999999999888444444444444.....244555599 PP

                                       CEEEEEEEEEEES..CTTS-EEEEEEEEEE.CTC CS
                   Alpha_adaptinC2  69 pggqitqvllien..pskkplrmrlrisyk.vgq 99 
                                       pg++i+ ++ i++   ++++ +++l + y+ +++
  gi|518651721|ref|YP_008141241.1| 340 PGQSIKVTYIIDTstSAAGTYPVQLLVEYHfNNT 373
                                       9**********99887788888888888884443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2903.83
//
Query:       gi|518651722|ref|YP_008141242.1|  [L=165]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-10   39.8   0.3    8.2e-10   38.5   0.1    1.8  2  PadR      Transcriptional regulator PadR-like family
    0.00082   19.2   0.0     0.0015   18.3   0.0    1.6  1  DUF4364   Domain of unknown function (DUF4364)
     0.0033   17.4   0.0     0.0078   16.2   0.0    1.6  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.076   13.4   0.5        7.4    6.9   0.0    2.2  2  Gp-FAR-1  Nematode fatty acid retinoid binding protein (Gp-FA


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 !   38.5   0.1   1.8e-13   8.2e-10       1      72 [.       8      73 ..       8      76 .. 0.95
   2 ?   -1.6   0.0      0.59   2.6e+03       7      22 ..     136     151 ..     132     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.8e-13
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      iL++l+ +++ Gy + ++l ++ +g  ++s+G l p+L+rL  +++++ + ++      +kyY+lT++G++ 
  gi|518651722|ref|YP_008141242.1|  8 ILYILNLEDMTGYGLSRKLYNSATG-KNISNGALIPVLNRLLSDNFIDFSVRN-----GKKYYHLTEKGKKF 73
                                      8************************.9*********************99776.....7**********986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
                                       CS-EEHHHHHHHHHCC CS
                              PadR   7 eqpsyGyeiikeleel 22 
                                       ++++ G e+ik + + 
  gi|518651722|ref|YP_008141242.1| 136 KKDEEGIELIKTMMDE 151
                                       5777899999887654 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.4e-07    0.0015      36      73 ..      40      77 ..       4     101 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.4e-07
                           DUF4364 36 lqqalseLvesglieeeekenktlykiTekGketlelf 73
                                      l  +l+ L+++++i+ + +++k++y++TekGk+ +  +
  gi|518651722|ref|YP_008141242.1| 40 LIPVLNRLLSDNFIDFSVRNGKKYYHLTEKGKKFVGNV 77
                                      55689************99*************988765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.7e-06    0.0078      30      74 ..      34      82 ..      30      85 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.7e-06
                            HTH_45 30 nLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkelee 74
                                      n+s   l   L+ L++ ++i    ++ k+ Y lTekG++++ ++ +l+e
  gi|518651722|ref|YP_008141242.1| 34 NISNGALIPVLNRLLSDNFIdfsvRNGKKYYHLTEKGKKFVGNVLDLNE 82
                                      55556666779999*****88887999*************988776665 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 ?    6.9   0.0    0.0017       7.4      67      95 ..      62      90 ..      53      96 .. 0.87
   2 ?    4.6   0.1    0.0088        40      14      60 ..     111     159 ..     107     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0017
                          Gp-FAR-1 67 kvdkLspeakeFvkkliakgrkleaqvla 95
                                      k   L++++k+Fv ++++ + ++++q + 
  gi|518651722|ref|YP_008141242.1| 62 KYYHLTEKGKKFVGNVLDLNEEVRDQAIF 90
                                      66689***************999999875 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0088
                          Gp-FAR-1  14 alknltdeekaqlkevvkn..ykgyknedellaalKkkspaLyekaekl 60 
                                       +lkn+ ++  + ++e++++  y g k  +e ++ +K   ++L e+a++ 
  gi|518651722|ref|YP_008141242.1| 111 LLKNIIKDIGHPIIEIIRQafYLGKKKDEEGIELIKTMMDELLERAKER 159
                                       6788888888889999998888889*******************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1176.37
//
Query:       gi|518651723|ref|YP_008141243.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G0362 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00011   22.0   0.1    0.00016   21.6   0.1    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0012   18.7   0.7     0.0017   18.3   0.7    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
     0.0066   16.5   3.3       0.37   11.0   0.0    2.4  2  Zn-ribbon_8      Zinc ribbon domain
  ------ inclusion threshold ------
      0.015   15.1   0.1      0.021   14.7   0.1    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.022   15.0   1.6        4.6    7.5   0.1    2.5  3  zf-RING_7        C4-type zinc ribbon domain
      0.059   13.1   0.1      0.059   13.1   0.1    2.2  2  zf-H2C2_5        C2H2-type zinc-finger domain
      0.077   12.4   1.8      0.091   12.2   0.1    1.9  2  zf-ribbon_3      zinc-ribbon domain
      0.082   13.0   0.1      0.091   12.9   0.1    1.3  1  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.16   11.7   1.4       0.98    9.1   0.2    2.1  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
       0.27   11.0   4.5        6.2    6.6   0.1    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.35   10.5   3.4        7.6    6.2   0.1    2.3  2  zf_UBZ           Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   9.6e-08   0.00016      20      55 ..       3      42 ..       1      44 [. 0.94

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 9.6e-08
                    OrfB_Zn_ribbon 20 eevnpayTSktCseCgsknke....alsgrtfkCpnCgfe 55
                                      ++++++ T k C++Cgs   +      +g ++kC++C+++
  gi|518651723|ref|YP_008141243.1|  3 IYMDEYRTTKICPQCGSLRINwiagGIAGPVYKCEECNYV 42
                                      7899********************99***********985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.7   1.1e-06    0.0017      18      45 ..      11      41 ..       7      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.1e-06
                     Zn_Tnp_IS1595 18 gfvCPhCgsrkayrikt...rglfqCkeCrk 45
                                      + +CP Cgs ++  i++     +++C+eC++
  gi|518651723|ref|YP_008141243.1| 11 TKICPQCGSLRINWIAGgiaGPVYKCEECNY 41
                                      567*******999999988778*******87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   0.00023      0.37      23      35 ..       7      21 ..       1      23 [. 0.73
   2 ?    5.1   1.9     0.015        25       6      13 ..      34      41 ..      33      60 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00023
                       Zn-ribbon_8 23 daplta.CPeCgs.e 35
                                      +   t+ CP+Cgs +
  gi|518651723|ref|YP_008141243.1|  7 EYRTTKiCPQCGSlR 21
                                      5556778*****955 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.015
                       Zn-ribbon_8  6 YrCeeCgh 13
                                      Y+CeeC+ 
  gi|518651723|ref|YP_008141243.1| 34 YKCEECNY 41
                                      9*****95 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.3e-05     0.021       7      37 ..       7      42 ..       3      43 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                      --SS--B-TTT-SB-....-S.SSS-EEEETTT--E CS
                              C1_1  7 nfkqptfCkhCgefl....wg.kekqglkCswCkll 37
                                       ++ ++ C +Cg++      g  + + +kC++C+++
  gi|518651723|ref|YP_008141243.1|  7 EYRTTKICPQCGSLRinwiAGgIAGPVYKCEECNYV 42
                                      578899*******9889886779999*******985 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 ?    6.5   0.1     0.006       9.8      26      31 ..      14      19 ..      10      20 .. 0.86
   2 ?    7.5   0.1    0.0028       4.6      20      30 ..      28      40 ..      21      40 .. 0.78
   3 ?   -3.2   0.0       6.2     1e+04      14      20 ..      58      64 ..      57      65 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.006
                                      -TTT-- CS
                         zf-RING_7 26 CpeCGR 31
                                      Cp+CG 
  gi|518651723|ref|YP_008141243.1| 14 CPQCGS 19
                                      *****6 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0028
                                      S..TB-EE-TTT- CS
                         zf-RING_7 20 g..devvtCpeCG 30
                                      g  + v +C+eC+
  gi|518651723|ref|YP_008141243.1| 28 GiaGPVYKCEECN 40
                                      455899******7 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 6.2
                                      HHHHCCS CS
                         zf-RING_7 14 lselrag 20
                                      ++e+r g
  gi|518651723|ref|YP_008141243.1| 58 QKEIREG 64
                                      6889876 PP

>> zf-H2C2_5  C2H2-type zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   2.7       1.5   2.4e+03       3       6 ..      14      17 ..      14      17 .. 0.98
   2 ?   13.1   0.1   3.6e-05     0.059       1      10 [.      34      43 ..      34      44 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                         zf-H2C2_5  3 CsqC 6 
                                      C+qC
  gi|518651723|ref|YP_008141243.1| 14 CPQC 17
                                      **** PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.6e-05
                         zf-H2C2_5  1 YKCsqCDYst 10
                                      YKC++C+Y+ 
  gi|518651723|ref|YP_008141243.1| 34 YKCEECNYVG 43
                                      9*******85 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   5.6e-05     0.091       2      11 ..      11      20 ..      10      26 .. 0.83
   2 ?   -0.8   0.3      0.67   1.1e+03       4       8 ..      35      39 ..      33      42 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.6e-05
                       zf-ribbon_3  2 tvrCPnCGap 11
                                      t+ CP+CG++
  gi|518651723|ref|YP_008141243.1| 11 TKICPQCGSL 20
                                      789*****96 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.67
                       zf-ribbon_3  4 rCPnC 8 
                                      +C +C
  gi|518651723|ref|YP_008141243.1| 35 KCEEC 39
                                      56566 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.6e-05     0.091      30      60 ..       8      42 ..       1      64 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.6e-05
                                      HHS-BEESSSSSSEEEEEETTE....EEETTTTEE CS
                   Ribosomal_L37ae 30 qhakytCpfcgktkvkRkavgi....wkCkkcgkt 60
                                       +++  Cp+cg+ ++++ a gi    +kC++c+++
  gi|518651723|ref|YP_008141243.1|  8 YRTTKICPQCGSLRINWIAGGIagpvYKCEECNYV 42
                                      455668**************985555799999875 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 ?    9.1   0.2    0.0006      0.98       1      11 [.       9      19 ..       9      19 .. 0.85
   2 ?    1.6   0.1      0.14   2.2e+02      23      29 ..      35      41 ..      29      43 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0006
                     zf-NADH-PPase  1 rthrFCgrCGa 11
                                      rt++ C++CG+
  gi|518651723|ref|YP_008141243.1|  9 RTTKICPQCGS 19
                                      78999999996 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.14
                     zf-NADH-PPase 23 vCpaCgl 29
                                       C+ C++
  gi|518651723|ref|YP_008141243.1| 35 KCEECNY 41
                                      7****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 ?    6.6   0.1    0.0038       6.2      17      22 ..      14      19 ..      13      25 .. 0.61
   2 ?    5.9   1.0    0.0065        11       1       9 [.      34      42 ..      34      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0038
                      Rubredoxin_2 17 CpsCgs 22
                                      Cp+Cgs
  gi|518651723|ref|YP_008141243.1| 14 CPQCGS 19
                                      666664 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0065
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      Y C++C+++
  gi|518651723|ref|YP_008141243.1| 34 YKCEECNYV 42
                                      99****996 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0047       7.6       2      10 ..      11      19 ..      10      20 .. 0.85
   2 ?    5.0   0.4     0.011        18       3       9 ..      34      40 ..      33      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0047
                            zf_UBZ  2 tylCerCgk 10
                                      t +C++Cg+
  gi|518651723|ref|YP_008141243.1| 11 TKICPQCGS 19
                                      789****96 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.011
                            zf_UBZ  3 ylCerCg 9 
                                      y Ce+C+
  gi|518651723|ref|YP_008141243.1| 34 YKCEECN 40
                                      89****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 480.87
//
Query:       gi|518651724|ref|YP_008141244.1|  [L=250]
Description: precorrin-6x reductase [Ferroplasma acidarmanus fer1]
Scores for complete 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-61  205.6   0.0    8.5e-61  205.4   0.0    1.0  1  CbiJ      Precorrin-6x reductase CbiJ/CobK


Domain annotation for each model (and alignments):
>> CbiJ  Precorrin-6x reductase CbiJ/CobK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.4   0.0   4.7e-65   8.5e-61       2     221 ..       2     232 ..       1     247 [. 0.94

  Alignments for each domain:
  == domain 1  score: 205.4 bits;  conditional E-value: 4.7e-65
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE---SSS----S..S-EEES--SHHHHHHHHHHHT--EEEE-S-TT-HHH CS
                              CbiJ   2 ililgGTsearelaeaLaeagievvvsvateygaellpekklevrvgrlgeeglaellreekidlvvDATHPfAaei 78 
                                       il+l GTs++r+l ++L + g++++++ +te g+e l++++++ + g+l+ e +++ +re +i++++D +HP+A  +
  gi|518651724|ref|YP_008141244.1|   2 ILLLDGTSDSRKLGSELISYGYSIIATATTEEGTEKLEKENIQAIKGKLDHETIISKCRELSINAIIDGSHPYADAM 78 
                                       9**************************************************************************** PP

                                       HHHHHHHHHHHT-EEEEE-------...EEEEESSHHHHH.........EEEESTSTTGGGGSTT...SEEEEEESS CS
                              CbiJ  79 sanaaeackelgipylrleRpswea...kiievdsleeaaella.....vllttGskelaafaealkkerllaRvlp 147
                                       ++na++a+ +lgip++r+eR++++    +i++ d++e+a+ l+      +++ttG++++++++  l+++++++Rvlp
  gi|518651724|ref|YP_008141244.1|  79 HENAINASIKLGIPLIRFEREMVKIksdRIVYTDNYEKAVALAGkigknIFVTTGVRNIENYKGLLEEHNVYFRVLP 155
                                       **********************9999**************6666********************************* PP

                                       --SS.--SSS....SEEEEE--SS--HHHHHHHHHHTT--EEEEES--SS.TTTHHHHHHHHTT-EEEEE---.... CS
                              CbiJ 148 tpeslekalplglkakeiiamrGpfskelerallreykidvlVtKeSGgaGgteeKleaArelgipvivikRp.... 220
                                        p+ +++ +++g++++ iiam+G f++ l+ra+++ y+id+++tK+SG +   e K+ aA +lgi++i+i+R+    
  gi|518651724|ref|YP_008141244.1| 156 DPDGIKALIDMGVRRASIIAMEGNFTESLDRAIMEYYGIDTVITKDSGFN--AEPKILAALSLGINIIIISRKnysw 230
                                       **************************************************..9*******************97744 PP

                                       .- CS
                              CbiJ 221 .e 221
                                        +
  gi|518651724|ref|YP_008141244.1| 231 eN 232
                                       31 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1719.35
//
Query:       gi|518651725|ref|YP_008141245.1|  [L=199]
Description: precorrin-8X methylmutase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-52  177.4   0.1    2.8e-52  177.3   0.1    1.0  1  CbiC      Precorrin-8X methylmutase
  ------ inclusion threshold ------
      0.023   14.6   0.1         11    6.0   0.0    2.4  2  DUF3173   Domain of unknown function (DUF3173)


Domain annotation for each model (and alignments):
>> CbiC  Precorrin-8X methylmutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.1   3.1e-56   2.8e-52       1     195 [.       9     194 ..       9     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 3.1e-56
                                       HHHHHHHHHHHCHC-TT.S-CHHHHHHHHHHHHHT-CCHHHHEEE-TTHHHHHHHHHHCT-EEEESSHHHHCCS-HH CS
                              CbiC   1 eIeaeSfaiideelgeeelseeeeevvrRvihatadfelaellrfspdaveaglealkagapivtDvemvkaGitkk 77 
                                       eI+++Sf +i+e++g +  ++ + +++ Rv+hatadfe+ + ++fs +  e  l+a+++g   ++D++mv +Gi++ 
  gi|518651725|ref|YP_008141245.1|   9 EIYRRSFTFIQEKMGLD--NSLKSSIITRVVHATADFEIGKSMVFSSS-FEDSLSAIEEGSIAIADINMVMSGISRY 82 
                                       69*************99..999***********************976.68999********************776 PP

                                       HHHTTC-EEEECTC-HHHHHHHHHHTS-HHHHHHHHHHHCTTTCEEEESS-HHHHHHHHHHHHHS..HTSEEEE--- CS
                              CbiC  78 rleklgnevlclladpevaelakekgitrsaaamekaaeelegaivviGnAPtALlellelieegkvkpalvigvPv 154
                                         +      +c++ d+++ ++ak++gi rs  +m++a ++ ++ai+viG APtAL +l++ i++g + p lvigvPv
  gi|518651725|ref|YP_008141245.1|  83 NNK------KCYIGDNDIIREAKRTGISRSYLSMSRACRDNPEAIYVIGDAPTALEALIDSIDAGICFPRLVIGVPV 153
                                       554......5******************************************************************* PP

                                       -SCCHHHHHHHHHCSSS-EEEESSS---HHHHHHHHHHHHH CS
                              CbiC 155 GFvgaaesKealaesevpyitveGrkGGsavAaaivnaLle 195
                                       GFv+a e K++l + +  +it+ ++kGGsavAa+i+na+++
  gi|518651725|ref|YP_008141245.1| 154 GFVSALEMKSRLLAFQGNFITNISNKGGSAVAASIFNAMVA 194
                                       **************************************985 PP

>> DUF3173  Domain of unknown function (DUF3173)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0012        11      25      41 ..      70      86 ..      66      89 .. 0.85
   2 ?    6.0   0.0    0.0012        11      19      34 ..      92     107 ..      91     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0012
                           DUF3173 25 aKkilVkkGysfYnnkr 41
                                      a  ++V  G+s Ynnk+
  gi|518651725|ref|YP_008141245.1| 70 ADINMVMSGISRYNNKK 86
                                      5578************8 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0012
                           DUF3173  19 rdiIrqaKkilVkkGy 34 
                                       +diIr+aK   ++++y
  gi|518651725|ref|YP_008141245.1|  92 NDIIREAKRTGISRSY 107
                                       69*******9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1238.83
//
Query:       gi|518651726|ref|YP_008141246.1|  [L=354]
Description: cobalamin biosynthetic protein CbiD [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-88  295.5   0.3      4e-88  295.0   0.3    1.2  1  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  295.0   0.3   2.2e-92     4e-88       1     250 [.      11     269 ..      11     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 295.0 bits;  conditional E-value: 2.2e-92
                              CbiD   1 lrsGyTtGscAaAAakaAllallkgekleeveielpkgekleipiekvalleee..aavikdaGddpDvTngaeiva 75 
                                       lr+GyTtG+cA+AA++aAl+++++g++++ vei+lp+++++++ ie+ ++ e+   a+v+kd+GddpDvT+g+ i++
  gi|518651726|ref|YP_008141246.1|  11 LRYGYTTGACATAATRAALIMMVTGKTVDYVEINLPAKKTARFLIENSKIYENYciASVKKDGGDDPDVTTGLYIYS 87 
                                       69************************************************8877999******************** PP

                              CbiD  76 eve....eeieiegGeGvGrvtkpgLevevgeaAInpvprkmieenveevleea..kegvevtisvpeGeelAkkTl 146
                                       +ve    + iei+gGeGvG+vtk+gL++++g++AInpvp km++++ +evl+++  ++g+++tisvp+G+e+A+kT+
  gi|518651726|ref|YP_008141246.1|  88 RVEysekSGIEITGGEGVGVVTKEGLPIKPGNPAINPVPLKMLRAAATEVLDSYevHRGLKITISVPGGAEVATKTC 164
                                       ******977*******************************************999999******************* PP

                              CbiD 147 NprlGivgGiSiLGTtGivepmSeeallesireelkvaaaeglkelvlvtGnkgeklakkkl.glpeealvkvsnfv 222
                                       Np+lGi+gGiSiLGT+Giv p+S++++++si   ++va + ++++lv++tG ++ ++++k + +++ee+++++++f+
  gi|518651726|ref|YP_008141246.1| 165 NPKLGIIGGISILGTRGIVIPFSDSSWKASIVLGIRVASRMDMDTLVFSTGGRSDTAVHKIFpDFKEEQFIEIGDFL 241
                                       ************************************************************989************** PP

                              CbiD 223 gealeeaaekgvkkvllvghiGKlvKla 250
                                       g++++ a++ g+++++++g+ GK+ Kla
  gi|518651726|ref|YP_008141246.1| 242 GFSVKRAVDTGIRNLVIAGMPGKISKLA 269
                                       ***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2326.87
//
Query:       gi|518651727|ref|YP_008141247.1|  [L=595]
Description: hypothetical protein FACI_IFERC00001G0366 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-39  135.5  63.5    2.3e-39  135.5  63.5    1.9  2  AA_permease_2  Amino acid permease
    1.6e-25   89.7  64.7    1.6e-25   89.7  64.7    2.2  2  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 !  135.5  63.5   2.5e-43   2.3e-39       4     416 ..      55     498 ..      52     507 .. 0.82
   2 ?   -4.9   9.6         1     9e+03      76     162 ..     483     566 ..     477     574 .. 0.72

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 2.5e-43
                     AA_permease_2   4 lsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                         a+++ +g ++gsgi+++   +++++gpa+i++++ia++ + + v l +aE+++++prsg    ++++ +g + +f
  gi|518651727|ref|YP_008141247.1|  55 HEAIMFGVGGAVGSGILFAAagGTGYAGPAIIVSWIIAAIFI-ILVTLPFAEYAAMFPRSGISARVAYYSYGSYGGF 130
                                       56899999********999989999**************988.89**********9999999999************ PP

                     AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgpdlqgn.....twltyliaiaililvalinirgikesakiqnilgil 150
                                       +s+w +++ +++++++i +va+s+++++ +p+l+++     t   +l+ai++l++++++n +gi   +k++++l+++
  gi|518651727|ref|YP_008141247.1| 131 MSGWGLLI-WAATIPAIEAVAVSTYASLYFPFLYDSttgvlTGYGILLAILLLLGFFALNMVGIARFGKFNKVLTWV 206
                                       ****9865.88999*****************998885665555667888**************************** PP

                     AA_permease_2 151 killpliiliilglitvdgggfssl....stetdt..ffpngwpgv...llglli..vlwsfdGfesaanvseevkk 216
                                       ki +++++++il+l++++ g f+s     s    +   f+++ p+v   + ++++  +l+sf+G+  +a ++ evk+
  gi|518651727|ref|YP_008141247.1| 207 KIGVVVAFIVILPLFIWHWGNFTSGlvgaS----SagGFAGFMPSVgglFIAIPAsgILFSFGGYRQVADMAGEVKN 279
                                       *****************8888887754332....223566677765333555544779******************9 PP

                     AA_permease_2 217 ..kdvpkaifigllivlvlyllvniaflgvvpddei...........anlsnlgsv............aalffeavg 268
                                         k++pk i  +l++ ++ly+ ++++++g v++ ++           a    lgs+            +++      
  gi|518651727|ref|YP_008141247.1| 280 pgKTMPKIIGTVLAVQSLLYIAMAVVIVGTVSWAGFgiqtgdwsfvaA----LGSPlssiihaniipgMTVA----E 348
                                       989********************************9877666644331....33336666776644444444....4 PP

                     AA_permease_2 269 gkvvaiivvi...lialsllgaintavigssrvlealardgvlPrffakvnkfgspiraiiltaivslillllflla 342
                                       ++ + ++v++   ++++s  g +  +++g+sr+++  +++++lP+ f+k+ k+g+p+ a+il +++++i+ll +   
  gi|518651727|ref|YP_008141247.1| 349 ADLLGGMVIVfflFAIFSPGGTLGVYLTGASRIIFGYSEEDALPKGFRKTTKHGAPYFALILALVLAIIFLLPL-P- 423
                                       4444444444000555566668888999***************************************6654333.3. PP

                     AA_permease_2 343 ssaaynfllsvsslgliisyllliigalilrkkrphlkrpgk....ilvaiigalfllfllvalffppkgpatqssl 415
                                          + ++l++  +++++  +++++i++ +lr+  p+ +rp k    + +a++++ +++fl++++ fp+   a +  l
  gi|518651727|ref|YP_008141247.1| 424 ---SWYALVDFVVVAAVANFAVASISLPVLRRLYPNVERPFKiphpMAWAFVSFEVATFLIYWATFPTTLYALGAVL 497
                                       ...589*******************************9976645445667777888889999999999877666555 PP

                     AA_permease_2 416 i 416
                                       +
  gi|518651727|ref|YP_008141247.1| 498 A 498
                                       5 PP

  == domain 2  score: -4.9 bits;  conditional E-value: 1
                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntw.ltyliaiaililvalinirgikesakiqnilgilk 151
                                       +a + + ++++++v++ ++++++ as   + +g +l ++ w ++y+ +++il +v      g +++a+   +++++ 
  gi|518651727|ref|YP_008141247.1| 483 WATFPTTLYALGAVLAGSVVFIYQASRKHF-MGLNLRNSVWiPVYIAGMIILSYVGGTPTGGLNIIAYPFDYVVLAI 558
                                       566667777777777777777777777666.5778888899889999999999999999999999888888877776 PP

                     AA_permease_2 152 illpliiliil 162
                                           +  ++++
  gi|518651727|ref|YP_008141247.1| 559 YA-AI--FFVI 566
                                       64.33..3333 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.7  64.7   1.8e-29   1.6e-25       2     401 ..      57     461 ..      56     505 .. 0.78
   2 ?   -4.4   9.4      0.58   5.2e+03      81     141 ..     481     547 ..     467     580 .. 0.46

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 1.8e-29
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       ++++ +gg++G g++++ +  ++ aGp ++++++++a ++i+lv+l ++e a ++p+sg  +  a  + g+  Gf+ 
  gi|518651727|ref|YP_008141247.1|  57 AIMFGVGGAVGSGILFAAAGGTGYAGP-AIIVSWIIAAIFIILVTLPFAEYAAMFPRSGISARVAYYSYGSYGGFMS 132
                                       68*************************.99*********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt..........gavflvvlliinlvgvkvygeaefilali 145
                                       G+ +l+  +t  a+e +a+s + ++   ++ l     t          ++++l+ ++++n+vg+  +g++  +l+++
  gi|518651727|ref|YP_008141247.1| 133 GWGLLIWAATIPAIEAVAVSTYASLY--FPFLY-DSTTgvltgygillAILLLLGFFALNMVGIARFGKFNKVLTWV 206
                                       ***55555555567777777777766..44444.444455689998877777778899******************* PP

                       AA_permease 146 kiiaiiafiivg..iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfv..ivvfaftGielv 218
                                       ki  ++afi+++  +i ++g  ++   g+++ g  ++     + p+        + + +++++   ++f+f G+  v
  gi|518651727|ref|YP_008141247.1| 207 KIGVVVAFIVILplFIWHWGNFTSGLVGASSAGGFAG-----FMPS--------VGGLFIAIPasGILFSFGGYRQV 270
                                       ************9888888877665545555555555.....6777........67777777611579********* PP

                       AA_permease 219 aiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa................aspfvif 279
                                       a +agEvk+P k++Pk i  v+    ++Y+ ++++i+ +v++   g+ ++  s                  +++ ++
  gi|518651727|ref|YP_008141247.1| 271 ADMAGEVKNPGKTMPKIIGTVLAVQSLLYIAMAVVIVGTVSWAGFGIQTGDWSFvaalgsplssiihaniIPGMTVA 347
                                       *******************************************9999887666688999998777766655555555 PP

                       AA_permease 280 ikesgvsvlaplinaviltaalssansslysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllas 356
                                          +   ++ +++ ++i++   +++  +l+ asR+++ +++++++Pk ++k +k+g P+ a++l ++++ ++ll   
  gi|518651727|ref|YP_008141247.1| 348 EADLLGGMVIVFFLFAIFSP-GGTLGVYLTGASRIIFGYSEEDALPKGFRKTTKHGAPYFALILALVLAIIFLLPLP 423
                                       55544444444444444432.334445799*******************************************7666 PP

                       AA_permease 357 lnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsi 401
                                       +  a       l+ ++ +++++++ ++++s++++R+ +   +r  
  gi|518651727|ref|YP_008141247.1| 424 SWYA-------LVDFVVVAAVANFAVASISLPVLRRLYPNVERPF 461
                                       6666.......999*********************9866555533 PP

  == domain 2  score: -4.4 bits;  conditional E-value: 0.58
                       AA_permease  81 nylfswitv.laleltaasiliqfwelvtd.....lpkawvtgavflvvlliinlvgvkvygeaefi 141
                                       +y+ ++ t+ +al+ + a++++ + +  ++     ++   v++ v ++ ++i+++vg    g   +i
  gi|518651727|ref|YP_008141247.1| 481 IYWATFPTTlYALGAVLAGSVVFIYQASRKhfmglNLRNSVWIPVYIAGMIILSYVGGTPTGGLNII 547
                                       3333332221344444444444443332110111122233446666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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):               2  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3776.06
//
Query:       gi|518651728|ref|YP_008141248.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G0367 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.27s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 597.52
//
Query:       gi|518651729|ref|YP_008141249.1|  [L=392]
Description: hypothetical protein FACI_IFERC00001G0368 [Ferroplasma acidarmanus fer1]
Scores for complete 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-98  329.1   0.3    3.7e-98  328.9   0.3    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
      0.046   13.8   0.2       0.57   10.3   0.1    2.2  2  SopE_GEF  SopE GEF domain


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.9   0.3  4.1e-102   3.7e-98       2     347 ..      19     384 ..      18     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 328.9 bits;  conditional E-value: 4.1e-102
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT..-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CSS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekag..lelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpke 76 
                                       i    gdgiGpe+++++ kv++aa++ka+  +++e++e+ vG +a++e+++ +pee+ eaik+++v l+ ++gtp +
  gi|518651729|ref|YP_008141249.1|  19 ILYTDGDGIGPEIMDVTRKVVDAAVKKAYknKKIEWKEILVGDKALKEKNDRFPEESQEAIKQYRVLLKSPLGTPIG 95 
                                       66779**********************99899********************************************* PP

                                       SSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET.......... CS
                            Iso_dh  77 kevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg.......... 143
                                       ++ ++ n  +++r +ldl++n+rpv ++   + +splk+  +e+v+l i+Re+t+++Y g+e+++++          
  gi|518651729|ref|YP_008141249.1|  96 TGFKSIN--VRIRVMLDLYSNIRPVSFM--KGLESPLKH--PENVNLTIFRENTDDLYTGIEYKYDSkeaaeirkff 166
                                       *******..*******************..7999****8..9************************9********** PP

                                       .....TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHHHHHHHHHCC........ CS
                            Iso_dh 144 .....sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwrkiveevaee........ 206
                                            ++ ++++++++k++s+  ++ri raa++ A++++kkk+t+++K+nv+k +e ++r++++e++++        
  gi|518651729|ref|YP_008141249.1| 167 kdklhVEISDDSGIGIKPMSKYKTQRITRAAAKFAIENNKKKITIMHKGNVMKYTEgAFREWAYETLKNefgnytst 243
                                       ***97447999**********************************************************9******* PP

                                       .TTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCC CS
                            Iso_dh 207 .eypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdi 282
                                        + ++i ++++++D++ +q++++p++++Vi+++N++GD++SD+a al+G +G l +a++g +  ++fEavHG+ap++
  gi|518651729|ref|YP_008141249.1| 244 dDSSKILVNDMIADNMFQQIITRPENYEVILAPNIDGDYISDAAGALIGNIGTLGGANVG-DDAGMFEAVHGTAPKY 319
                                       999*********************************************************.68************** PP

                                       TTSS-S-THHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS.TCCCHHHHHHHH CS
                            Iso_dh 283 agkdkaNpiavilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea.akevstsefgda 347
                                       ag+++a p++ i  a lm++y l+++ea d iekA+ +++e ++vTkDla+     ++ t+efgd 
  gi|518651729|ref|YP_008141249.1| 320 AGQNVADPLGLIRGAQLMIKY-LNWHEAFDVIEKAIGEAIETKKVTKDLAKFFdVPAMGTKEFGDS 384
                                       *********************.****************************987688999****996 PP

>> SopE_GEF  SopE GEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.051   4.6e+02      64     126 ..      24      86 ..      18      88 .. 0.61
   2 ?   10.3   0.1   6.4e-05      0.57      63     120 ..     178     234 ..     167     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.051
                                       T-SS-TCHHHHHHHHH.HHHCCHHCCCCHHCCHC.HHHHHHHHHHHHHCCTCCCHHHHHHHHHHH CS
                          SopE_GEF  64 GaGanPlinplkqsis.tkfkhelknenqkeklk.ayaekkviklvaellneeesktlsefrstl 126
                                       G+G  P i+++  ++     k+ +kn++   + k   +  k++k+ ++ ++ee+++  +++r +l
  gi|518651729|ref|YP_008141249.1|  24 GDGIGPEIMDVTRKVVdAAVKKAYKNKKI--EWKeILVGDKALKEKNDRFPEESQEAIKQYRVLL 86 
                                       66666766666555430333333333322..2223677888888888888888888888888765 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.4e-05
                                       TT-SS-TCHHHHHHHHHHHHCCHHCCCCHHCCHCHHHHHHHHHHHHHCCTCCCHHHHH CS
                          SopE_GEF  63 sGaGanPlinplkqsistkfkhelknenqkeklkayaekkviklvaellneeesktls 120
                                       sG G +P+ ++  q+i++  +++++ en+k+k+  + +  v+k ++ +++e + +tl+
  gi|518651729|ref|YP_008141249.1| 178 SGIGIKPMSKYKTQRITR-AAAKFAIENNKKKITIMHKGNVMKYTEGAFREWAYETLK 234
                                       8999****9999999965.6889*************************9999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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 0.23s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2810.03
//
Query:       gi|518651730|ref|YP_008141250.1|  [L=454]
Description: amino acid permease [Ferroplasma acidarmanus fer1]
Scores for complete 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-54  183.8  55.9    5.7e-54  183.6  55.9    1.0  1  AA_permease_2   Amino acid permease
    2.9e-52  177.9  54.8    3.5e-52  177.6  54.8    1.1  1  AA_permease     Amino acid permease
    5.7e-08   32.0  27.3    5.7e-08   32.0  27.3    2.6  3  Spore_permease  Spore germination protein
    0.00065   18.8  37.2     0.0011   18.1  37.0    1.5  1  Trp_Tyr_perm    Tryptophan/tyrosine permease family


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.6  55.9   1.3e-57   5.7e-54       1     397 [.      10     395 ..      10     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.6 bits;  conditional E-value: 1.3e-57
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+l+sa+++ +g++ig+gifv    +a+++gpa+i++++++++i  +  +l + E++ + +++gG+y y+k+ f + 
  gi|518651730|ref|YP_008141250.1|  10 LGLRSAIIINLGAIIGAGIFVIIgiAAGKAGPAIIISIFVSAIIA-IFTGLSFSEIAQHTSKEGGVYEYAKESFAPS 85 
                                       799****************9988778999***************9.79999******99****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                       ++f+ + + +f+ ++++++++ + +sy+ ++++ ++       ++++i i+i +a++n +gik sak  +il+ ++i
  gi|518651730|ref|YP_008141250.1|  86 AGFIGGTMWTFSNMIAISAVSLSTGSYINSLFHLHI-----DLIVFGIPIIIMFAILNMLGIKNSAKTLSILVGINI 157
                                       ******************************997544.....589999****************************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigl 227
                                         +lii+++ gl++++ + fs       +f p+g +g++ g + ++++f+Gf+ ++ + +evk+  k++pkai+i++
  gi|518651730|ref|YP_008141250.1| 158 -AILIIFVVSGLFYFKLTDFS-------NFDPHGFTGIMEGSALIFFAFTGFSRITTIGDEVKNpeKNIPKAIIISI 226
                                       .69999*********888887.......89*******************************999889********** PP

                     AA_permease_2 228 livlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                       +i++ ly  v+++++g +p +++a+ s    ++++  + ++++   iiv+i+++ + +g ++t ++g+srvl+a++r
  gi|518651730|ref|YP_008141250.1| 227 IISSALYSIVAVVAIGLIPSSNLASASA---PLSAAIAVLHNSYILIIVAIGGITATAGVVLTGILGTSRVLYAMGR 300
                                       ***********************97665...689999999999********************************** PP

                     AA_permease_2 305 dgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrphl.k 380
                                       d+++P  f +++kfg+p+++i l++ +sl+++  f +     + ++ ++s+++++i y ++ ++a++l++k +++ +
  gi|518651730|ref|YP_008141250.1| 301 DREIPGTFGRIDKFGTPFYSILLSMAISLLFV-YFVG-----FATIIEASNVSVLIAYSIIDFSAIMLWRKVKREnP 371
                                       ****************************6664.3433.....789****************7777777766665535 PP

                     AA_permease_2 381 r.....pgk..ilvaiigalfllf 397
                                       +     +++  i++  ++++f+++
  gi|518651730|ref|YP_008141250.1| 372 KhmreqKYFfiIPLIGMATIFITI 395
                                       567778555224444444444433 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.6  54.8   7.8e-56   3.5e-52       2     431 ..      15     397 ..      14     429 .. 0.90

  Alignments for each domain:
  == domain 1  score: 177.6 bits;  conditional E-value: 7.8e-56
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       +++i+lg +iG+g+fv +g+++++aGp ++++++ ++ ++ ++++ls++eia + +k gg y ya+++  p++Gf  
  gi|518651730|ref|YP_008141250.1|  15 AIIINLGAIIGAGIFVIIGIAAGKAGP-AIIISIFVSAIIAIFTGLSFSEIAQHTSKEGGVYEYAKESFAPSAGFIG 90 
                                       579************************.99*********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafii 155
                                       G +  fs  +++ +     +++i+ +  ++  + ++v+g+ +++++ i+n++g+k +++    l+++++i i+++ii
  gi|518651730|ref|YP_008141250.1|  91 GTMWTFSNMIAISAVSLSTGSYINSL--FHLHIDLIVFGIPIIIMFAILNMLGIKNSAK---TLSILVGINIAILII 162
                                       ***99999999999999999999999..66666699***********************...788888888888888 PP

                       AA_permease 156 vgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksi 232
                                       + +++l+  k++++             +n+ p+g        f++++ + + ++faftG++ +++i++Evk+Pek+i
  gi|518651730|ref|YP_008141250.1| 163 FVVSGLFYFKLTDF-------------SNFDPHG--------FTGIMEGSALIFFAFTGFSRITTIGDEVKNPEKNI 218
                                       889999999*9999.............3455888........*********************************** PP

                       AA_permease 233 PkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssanssly 309
                                       Pkai+  +i+   +Y +++++++ l+p ++l + +    a  p+  +i  + +s++  +++++ +ta+ ++++ ++ 
  gi|518651730|ref|YP_008141250.1| 219 PKAIIISIIISSALYSIVAVVAIGLIPSSNLASAS----A--PLSAAIAVLHNSYILIIVAIGGITATAGVVLTGIL 289
                                       ******************************66555....4..8888******************************* PP

                       AA_permease 310 sasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliils 386
                                        +sRvly++ +d+ +P  +++++k g P  +illsm+isll++   +++++        + +s ++ li + +i +s
  gi|518651730|ref|YP_008141250.1| 290 GTSRVLYAMGRDREIPGTFGRIDKFGTPFYSILLSMAISLLFVYFVGFATI--------IEASNVSVLIAYSIIDFS 358
                                       *******************************************88888888........99*************999 PP

                       AA_permease 387 yl.rfRkalkyqgrsieelgfkaallplgvilvlaaliiillilal 431
                                        +  +Rk ++++ +++       + + +++i+ l+ + +i+++ ++
  gi|518651730|ref|YP_008141250.1| 359 AImLWRKVKRENPKHM-------REQKYFFIIPLIGMATIFITISY 397
                                       9879****99999966.......55555666666666665555544 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0  27.3   1.3e-11   5.7e-08       8     293 ..      16     295 ..      10     304 .. 0.80
   2 ?    2.6   2.8     0.011        49     254     314 ..     303     362 ..     296     369 .. 0.70
   3 ?   -0.5   0.2     0.096   4.3e+02     197     241 ..     361     405 ..     359     417 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.3e-11
                    Spore_permease   8 fvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkf.pektliellkkilgkwLGsllsi 83 
                                       +++   +++G+gi ++ +++a +a+p   is+ + +ii+++  l ++++ ++  +e  ++e+ k+ +    G++ + 
  gi|518651730|ref|YP_008141250.1|  16 IIINLGAIIGAGIFVIIGIAAGKAGPAIIISIFVSAIIAIFTGLSFSEIAQHTsKEGGVYEYAKESFAPSAGFIGGT 92 
                                       55566789*****************************************998615678*********9887777777 PP

                    Spore_permease  84 lfilyFlllaafelRefseliqvflledtplwiiilllllvilYlvvkGieslar...eflfiivilliilllillf 157
                                       ++    ++ ++ +  + +  i+     ++ l+++ + ++++++ l + Gi++ a+    ++ i + +lii+++  lf
  gi|518651730|ref|YP_008141250.1|  93 MWTFSNMIAISAVSLSTGSYINSLFHLHIDLIVFGIPIIIMFAILNMLGIKNSAKtlsILVGINIAILIIFVVSGLF 169
                                       7666555555555555555555555567888888888888888888888888888654555566778888888889* PP

                    Spore_permease 158 slklaeiknlrPvlgngikpvlkslkttslsflgveillllvpflkdk.kkvkkaallgvlistllyllttlivilv 233
                                        +kl ++ n +P   +g+  +++++  + ++f+g+  ++ +   +k++ k++ ka++++++is  ly+++ +++i+ 
  gi|518651730|ref|YP_008141250.1| 170 YFKLTDFSNFDP---HGFTGIMEGSALIFFAFTGFSRITTIGDEVKNPeKNIPKAIIISIIISSALYSIVAVVAIGL 243
                                       ***********9...88888899************988888888887626789************************ PP

                    Spore_permease 234 lsveqlkkatwptlsllkvievpefierlevllivvwilvifakialylyaavlgisevf 293
                                           +l +a  p+   + v++ +       ++li+v i +i a+ a  ++  +lg+s+v+
  gi|518651730|ref|YP_008141250.1| 244 IPSSNLASASAPLSAAIAVLHNS-------YILIIVAIGGITAT-AGVVLTGILGTSRVL 295
                                       *9999999999999888888888.......66666655444444.444555567777776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.011
                    Spore_permease 254 evpefierlevllivvwilvifakialylyaavlgisevfkikkkkllvililiviliasi 314
                                       e+p  + r++ ++  ++ +++   i+l +    +g+++++++++ ++l++  +i +  +++
  gi|518651730|ref|YP_008141250.1| 303 EIPGTFGRIDKFGTPFYSILLSMAISLLF-VYFVGFATIIEASNVSVLIAYSIIDFSAIML 362
                                       56777778888888887777777666644.4456888888888888877777776666555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.096
                    Spore_permease 197 llvpflkdkkkvkkaallgvlistllyllttlivilvlsveqlkk 241
                                       +l+  +k ++ ++   ++ + i  l+ + t++i+i++l++ ++++
  gi|518651730|ref|YP_008141250.1| 361 MLWRKVKRENPKHMREQKYFFIIPLIGMATIFITISYLGLHAIEI 405
                                       666666666666666666666677777778888888888776654 PP

>> Trp_Tyr_perm  Tryptophan/tyrosine permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1  37.0   2.5e-07    0.0011       8     288 ..      15     282 ..      10     396 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.5e-07
                      Trp_Tyr_perm   8 gvlliagtviGaGmlalPvatagagfipsllllilswvlmlasgllllEvllaakeeasfttlakkllGkkgniiva 84 
                                       ++++  g++iGaG++ +  ++ag      ++ +++s+++++++gl + E+ +++++e ++ + ak+++  ++ +i +
  gi|518651730|ref|YP_008141250.1|  15 AIIINLGAIIGAGIFVIIGIAAGKAGPAIIISIFVSAIIAIFTGLSFSEIAQHTSKEGGVYEYAKESFAPSAGFIGG 91 
                                       344447*********9987777777777777788999**************************************** PP

                      Trp_Tyr_perm  85 lvllfllyiLlvAyisggGsilselleeasgialsarlavliftlvlgalvvlstkavdrinrvllflklvafvlll 161
                                           f   i + A   + Gs +++l++  +       +  + +++++++l +l+ k   ++ ++l+ + +  +++++
  gi|518651730|ref|YP_008141250.1|  92 TMWTFSNMIAISAVSLSTGSYINSLFHLHI----DLIVFGIPIIIMFAILNMLGIKNSAKTLSILVGINIAILIIFV 164
                                       ***999999999999999999999888877....4556666678889999999999999999*************** PP

                      Trp_Tyr_perm 162 alllskvksdvLlsaksdtskvslvlsalPvlllsf.GFhgivpslvkyldknvkkvkkailiGtliaLvlyllWel 237
                                       +++l+  k     ++  d+  +  +++   +++ +f GF + + ++   + + +k++ kai+i  +i+ +ly +  +
  gi|518651730|ref|YP_008141250.1| 165 VSGLFYFKLTDFSNF--DPHGFTGIMEGSALIFFAFtGF-SRITTIGDEVKNPEKNIPKAIIISIIISSALYSIVAV 238
                                       *****9999999884..59999******99999999566.667899999999************************* PP

                      Trp_Tyr_perm 238 ivlGnlpreelariiakggnldtlveallelleskslelavelFsflAlat 288
                                       + +G +p+++la + a+    +    a  ++l+++++ ++v + ++ A a 
  gi|518651730|ref|YP_008141250.1| 239 VAIGLIPSSNLASASAPL---S----AAIAVLHNSYILIIVAIGGITATAG 282
                                       ***********9887654...3....3334445555555555555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.32s 00:00:01.04 Elapsed: 00:00:00.49
# Mc/sec: 2770.37
//
Query:       gi|518651731|ref|YP_008141251.1|  [L=132]
Description: hypothetical protein FACI_IFERC00001G0370 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0056   16.4   0.0     0.0081   15.9   0.0    1.3  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
  ------ inclusion threshold ------
       0.03   14.5   0.0      0.034   14.4   0.0    1.4  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
        0.1   11.4   0.1       0.13   11.1   0.1    1.1  1  DUF5565          Family of unknown function (DUF5565)
       0.19   12.0   0.0       0.29   11.4   0.0    1.4  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.8e-06    0.0081       2      43 ..       6      47 ..       5      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                                      EEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEE CS
                              COXG  2 efrvaapkeavwefLndpeklarciPGvksvekegdeykvkv 43
                                      e++v+ ++e++we+++d++++ +   G  s+ekeg+ y v++
  gi|518651731|ref|YP_008141251.1|  6 EIEVNSDREDIWELIKDYKRIPEFWHGTRSIEKEGNYYMVQF 47
                                      6799********************************998876 PP

>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.5e-06     0.034       4      29 ..      12      37 ..       9     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.5e-06
                                      -HHHHHHHHTTTGGCCSCCCCEEEEE CS
                    Polyketide_cyc  4 padqvyalvadvesypeflphcssve 29
                                      + +++++l+ d+ + pef+ + +s e
  gi|518651731|ref|YP_008141251.1| 12 DREDIWELIKDYKRIPEFWHGTRSIE 37
                                      6799****************999744 PP

>> DUF5565  Family of unknown function (DUF5565)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.9e-05      0.13      97     127 ..       9      39 ..       1      47 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.9e-05
                           DUF5565  97 kkeskeftwnveedfkevPeswipakevkrk 127
                                        ++++e +w++ +d+k++Pe w  +++++++
  gi|518651731|ref|YP_008141251.1|   9 VNSDREDIWELIKDYKRIPEFWHGTRSIEKE 39 
                                       45677889*****************999875 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.5e-05      0.29       4      40 ..       3      39 ..       1      61 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.5e-05
                                      EEEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECS CS
                   Polyketide_cyc2  4 vtvsvviaappekVwalvsdfenwprWhpevarvele 40
                                      ++++++++ + e++w+l+ d++ +p+  ++ ++ e e
  gi|518651731|ref|YP_008141251.1|  3 FKKEIEVNSDREDIWELIKDYKRIPEFWHGTRSIEKE 39
                                      67899********************966666666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 981.29
//
Query:       gi|518651732|ref|YP_008141252.1|  [L=675]
Description: hypothetical protein FACI_IFERC00001G0371 [Ferroplasma acidarmanus fer1]
Scores for complete 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-73  246.0   0.0    7.2e-73  245.2   0.0    1.3  1  E1_dh            Dehydrogenase E1 component
    2.8e-41  141.2   0.0    5.3e-41  140.2   0.0    1.5  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.2e-37  128.5   0.0    2.1e-37  127.7   0.0    1.4  1  Transketolase_C  Transketolase, C-terminal domain
    2.1e-08   34.1   0.0      3e-07   30.4   0.0    2.5  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    3.4e-08   33.0   0.1    7.2e-08   32.0   0.1    1.4  1  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    0.00062   18.8   0.0     0.0011   18.1   0.0    1.3  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
     0.0023   18.2   0.0     0.0081   16.4   0.0    2.0  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  245.2   0.0   2.8e-76   7.2e-73      18     296 ..      42     318 ..      35     320 .. 0.96

  Alignments for each domain:
  == domain 1  score: 245.2 bits;  conditional E-value: 2.8e-76
                                       HTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T....TTSSGTT-.-E.. CS
                             E1_dh  18 krkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv....kgkggsrhelmya 90 
                                        + k+ g +hlsagqe  +  + + l ++D++ +++R + + +a+g++l+ + ae++gk     kgkgg +h +   
  gi|518651732|ref|YP_008141252.1|  42 AAGKIPGEMHLSAGQEPSAAWMSVLLRNDDFVYSTHRPHHTAIAKGVDLNRMTAEIMGKHgglsKGKGGHMH-IF-- 115
                                       56789999****************************************************999999999999.88.. PP

                                       BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEETTE CS
                             E1_dh  91 ekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkygisT 167
                                        k+++ +   givg+  p + G+ala+k +gk+++a+++ GDg+ nqG + e+lnla+lwklpvifv+eNN ++is+
  gi|518651732|ref|YP_008141252.1| 116 DKKVN-FACAGIVGSSFPSALGAALASKLDGKDSIAVAFGGDGSLNQGMFLESLNLASLWKLPVIFVIENNDWAISV 191
                                       45544.56789*****99999******************************************************** PP

                                       EHHHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHH CS
                             E1_dh 168 eaekasaskeladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtree 244
                                       e++ ++  k+ a ra g+g+pg+ ++ nDp+ +y+A+  A++rar+g+gp+li + tYRy+gH+e D p  yr++++
  gi|518651732|ref|YP_008141252.1| 192 ETKDSTPLKNDAIRADGFGMPGVYIENNDPVKMYKAAEKAVKRARSGEGPTLIAIDTYRYYGHFEGD-PEVYRPKDQ 267
                                       *******************************************************************.999**9999 PP

                                       HHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS-- CS
                             E1_dh 245 veevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskke 296
                                       v+e  +k dpi++++  L kkg++s++e+++i++++++e+ +a++ ae+++ 
  gi|518651732|ref|YP_008141252.1| 268 VKELLAK-DPIKIMESDLLKKGIISKDEDDRINNSAMEEISQAFAFAEDSPL 318
                                       *999998.****************************************9986 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.2   0.0   2.1e-44   5.3e-41       5     176 ..     347     519 ..     343     521 .. 0.97

  Alignments for each domain:
  == domain 1  score: 140.2 bits;  conditional E-value: 2.1e-44
                                       HHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEE CS
                      Transket_pyr   5 wrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvivea 79 
                                       + +a+ ea++++++ +++v+ +g+Dv+  gg f+++ gl +++g++r+ d++isE+a++g a+G+a+ag +++ive+
  gi|518651732|ref|YP_008141252.1| 347 VYMAISEAISQEMEGNKDVLYMGEDVGkyGGIFGATTGLFKKFGAERIRDTPISESAFIGSAAGLAAAG-KRPIVEL 422
                                       56899****************************************************************.6****** PP

                                       EEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHH CS
                      Transket_pyr  80 qFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhll 154
                                       +F+dF+ +    i+++ a+ +++++g ++++vv+ + +g g   ++++s+ l++++ ++pglkvv+Ps+ +++k+l+
  gi|518651732|ref|YP_008141252.1| 423 MFSDFVGVTldPIMNQIAKNHYMSGGTVNMPVVITTAVGGGYGDAAQHSQTLYSLFGHLPGLKVVVPSNSYDAKGLM 499
                                       **********99**************************9999999******************************** PP

                                       HHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 155 rrairredrkPvvlrlpksllr 176
                                         ai+  d++Pvv +++k+ll 
  gi|518651732|ref|YP_008141252.1| 500 VSAIK--DNNPVVYMFHKGLLG 519
                                       *****..99**********986 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.0   8.3e-41   2.1e-37       1     124 []     543     665 ..     543     665 .. 0.99

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 8.3e-41
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       gka+i regkd+t+++ G++v++a+eAa eLe++gi+aeV+dlr++kplD++t+  sv ktg l+v +e++  +G++
  gi|518651732|ref|YP_008141252.1| 543 GKARIAREGKDITIIGIGATVHMAMEAAMELEENGINAEVIDLRSIKPLDTDTVIRSVGKTGSLLVADEDYAAFGLA 619
                                       89*************************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       se+++a++  +f +ld++ ++++ pdv++p+s + +ek++++d++ki
  gi|518651732|ref|YP_008141252.1| 620 SEITSAVSHALFGKLDKAPESIVSPDVPVPYS-QPMEKYWLPDTQKI 665
                                       ********************************.88*********998 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.2e-10     3e-07      26     152 ..     123     245 ..     109     246 .. 0.74

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.2e-10
                                       TTS-TTTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SBCCCHHHH.HHHH CS
                      TPP_enzyme_C  26 glgtmGyglpaAiGakla....kpdrevvaivGDGgflmi..lqelatavrrnlpitvvvlnNegygmtggq.qepf 95 
                                         g  G ++p A+Ga+la     +d+  va+ GDG++     l+ l  a   +lp+++v+ nN +   ++ + ++p 
  gi|518651732|ref|YP_008141252.1| 123 CAGIVGSSFPSALGAALAskldGKDSIAVAFGGDGSLNQGmfLESLNLASLWKLPVIFVIENNDWAISVETKdSTPL 199
                                       57899************644433479**********643333888888888899**********9988777644444 PP

                                       TCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHH....HHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  96 ggkrksgpagkdlkpvdfaklaealGakgarvekadveel....eealkealekkgpalie 152
                                        +                a  a ++G++g+++e++d+ ++    e+a+k+a++ +gp+li 
  gi|518651732|ref|YP_008141252.1| 200 KN---------------DAIRADGFGMPGVYIENNDPVKMykaaEKAVKRARSGEGPTLIA 245
                                       33...............23458899999888888888777333355555555999999996 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 !   32.0   0.1   2.8e-11   7.2e-08      96     177 ..     110     191 ..      89     206 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 2.8e-11
                    DXP_synthase_N  96 gfpkrsEseyDafeagHsstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNe 172
                                       g++++ + +     ag  ++s   alG a a++l+g+++ +va  GDg+l  Gm +e+ln ++  k  ++ ++ +N+
  gi|518651732|ref|YP_008141252.1| 110 GHMHIFDKKVNFACAGIVGSSFPSALGAALASKLDGKDSIAVAFGGDGSLNQGMFLESLNLASLWKLPVIFVIENND 186
                                       6666777777777888899999******************************************************* PP

                    DXP_synthase_N 173 msisk 177
                                       ++is 
  gi|518651732|ref|YP_008141252.1| 187 WAISV 191
                                       *9985 PP

>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   4.1e-07    0.0011     143     248 ..     146     253 ..     108     263 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 4.1e-07
                                       ----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGGT..--S-HHHHHHHTT-EEEEE...T CS
                   Transketolase_N 143 vdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGeteis..ftedvakrfeaygWhviev...e 214
                                        d+   ++ gDg l+ G+  e+ +la+  kL  +  + ++n+ +i  et+ s  +++d   r + +g   +     +
  gi|518651732|ref|YP_008141252.1| 146 KDSIAVAFGGDGSLNQGMFLESLNLASLWKLPVIF-VIENNDWAISVETKDStpLKNDA-IRADGFGMPGVYIennD 220
                                       577788999**********************8655.55777666666665551045554.34444444333320003 PP

                                       TTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTT CS
                   Transketolase_N 215 dgedveaikaaieeakaekdkPsliklrtviGyg 248
                                         +  +a ++a+++a++  + P+li++ t   yg
  gi|518651732|ref|YP_008141252.1| 221 PVKMYKAAEKAVKRARSG-EGPTLIAIDTYRYYG 253
                                       333445566677777766.89******9976665 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 !   16.4   0.0   3.2e-06    0.0081       2      78 ..     553     630 ..     552     643 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--.TT-G-HHHHHHHHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnis.fgseGqlveevkaa 77 
                                       ++ i+++G+++  a +a++el e+gi++ ++ lr++ P  ++ + + + k+ +++v d +++ fg ++ + + v+ a
  gi|518651732|ref|YP_008141252.1| 553 DITIIGIGATVHMAMEAAMELEENGINAEVIDLRSIKPLDTDTVIRSVGKTGSLLVADEDYAaFGLASEITSAVSHA 629
                                       789********************************************************994255555555555555 PP

                                       T CS
                           PFOR_II  78 l 78 
                                       l
  gi|518651732|ref|YP_008141252.1| 630 L 630
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 4127.91
//
Query:       gi|518651733|ref|YP_008141253.1|  [L=78]
Description: acetoin/pyruvate dehydrogenase complex, E2 component, dihydrolipoamide succinyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-13   48.2   1.9      8e-13   48.0   1.9    1.1  1  Biotin_lipoyl    Biotin-requiring enzyme
  ------ inclusion threshold ------
       0.02   14.7   0.3       0.98    9.3   0.0    2.2  2  Biotin_lipoyl_2  Biotin-lipoyl like
      0.038   13.9   0.2      0.043   13.7   0.2    1.1  1  GCV_H            Glycine cleavage H-protein


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 !   48.0   1.9   1.3e-16     8e-13      14      71 ..      16      74 ..       3      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1.3e-16
                                      E..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEE CS
                     Biotin_lipoyl 14 eg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdlla 71
                                      ++ +++++vkvGd++k++ +++ + a K+++e+e +++G+v++i  + ++++  gd l+
  gi|518651733|ref|YP_008141253.1| 16 KAiITQWYVKVGDSIKEDTPVCQIMAGKVTVEVEGKAKGKVTKIFRDINAEIVPGDDLL 74
                                      34689*******************************************99998888776 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00016      0.98      11      26 ..      17      32 ..      11      39 .. 0.88
   2 ?    3.9   0.1    0.0079        47       3      34 ..      46      77 ..      38      78 .] 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                   Biotin_lipoyl_2 11 GrVaqlnVkdGqrVka 26
                                      + ++q++Vk G+ +k+
  gi|518651733|ref|YP_008141253.1| 17 AIITQWYVKVGDSIKE 32
                                      579**********997 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.0079
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelD 34
                                      v++  +  G+V++++   + ++  Gd L+e +
  gi|518651733|ref|YP_008141253.1| 46 VEVEGKAKGKVTKIFRDINAEIVPGDDLLEVE 77
                                      555566789******99999999999999875 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   7.2e-06     0.043      38      79 ..      23      64 ..      10      73 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.2e-06
                                      ---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GGGT CS
                             GCV_H 38 lpevgtkvkkgeslaavEsvKaasevyapvsGevvevNekle 79
                                        +vg+++k++ ++ ++ ++K + ev    +G+v+++ ++++
  gi|518651733|ref|YP_008141253.1| 23 YVKVGDSIKEDTPVCQIMAGKVTVEVEGKAKGKVTKIFRDIN 64
                                      4589******************************98876664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 541.54
//
Query:       gi|518651734|ref|YP_008141254.1|  [L=514]
Description: thermopsin precursor [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-73  247.2  24.2    1.9e-73  247.2  24.2    2.4  2  Thermopsin  Thermopsin
  ------ inclusion threshold ------
        1.4    9.3  10.9        0.3   11.4   1.1    2.9  3  FliC        Flagellin protein


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.2  24.2   2.1e-77   1.9e-73       3     260 .]      41     298 ..      39     298 .. 0.94
   2 ?   -0.2   0.1     0.063   5.6e+02     180     209 ..     330     360 ..     317     369 .. 0.81

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 2.1e-77
                        Thermopsin   3 vnvlslyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssn.spesaslQLNvvlevvtggkt 78 
                                       v +  +y++epaPmGiadyGi++ +    p s n ++++G vni++l++yn s +  p+++++QLN++ ++ +g++t
  gi|518651734|ref|YP_008141254.1|  41 VYPEGYYTKEPAPMGIADYGIGPGGT---PSSFNSTAFTGIVNITDLKTYNASISsCPNNMGIQLNLIYSFQNGNST 114
                                       678889*******************6...**********************998889******************** PP

                        Thermopsin  79 ysywvQnVvsfnttekqltfidNiWNftspsanlsnsaisGnGtvyasskgefYyayateylelslPltlkLvinvs 155
                                       y+ywvQnV+ +nt+++q+ fidN+WNfts++a+++ns+++GnGt+++ss+ + Yy  + + +  s++ +   + +vs
  gi|518651734|ref|YP_008141254.1| 115 YYYWVQNVAVLNTSNRQVVFIDNVWNFTSTNAEMHNSTMHGNGTLMNSSSAHLYYFASDNGTFRSFSYSNIKLRSVS 191
                                       ********************************************************999974444554444445789 PP

                        Thermopsin 156 ltsngvpevsFgYsid.ggvvtYDnvtinstgkasa..eilvngssltpsgllyDaeLvlgGpgngekttfnslnat 229
                                       +t++g+p+++  Y+ d +g+ tYD+  +++++++s+   ++vng++l p++++ Da L+lgGpgn+++t + ++n t
  gi|518651734|ref|YP_008141254.1| 192 YTASGYPHIYMEYN-DgNGWKTYDTLNFTFASSVSHnyGFIVNGQNLLPNNSYADAGLILGGPGNSTNTRVIQANLT 267
                                       9*************.66****************999999************************************** PP

                        Thermopsin 230 lsLyYlngtnyqpvknaydfGsdTaEtaenv 260
                                       + L+Y+ng+nyq v+nay+ GsdTaE++ nv
  gi|518651734|ref|YP_008141254.1| 268 MGLEYWNGHNYQVVSNAYNHGSDTAEGVCNV 298
                                       *****************************98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.063
                        Thermopsin 180 vtinstgkasa.eilvngssltpsgllyDae 209
                                       +++n+++++++ +i  ngs ++ +g +++  
  gi|518651734|ref|YP_008141254.1| 330 AVFNFKSTVKNtYIKLNGSRYNFTGQYLNLT 360
                                       4688888888889999999999999887765 PP

>> FliC  Flagellin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   3.4e-05       0.3      30     117 ..      81     169 ..      63     178 .. 0.80
   2 ?    0.5   0.1      0.08   7.1e+02      73      87 ..     333     347 ..     274     371 .. 0.59
   3 ?    3.0   0.9     0.013   1.2e+02       9      83 ..     337     425 ..     330     443 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.4e-05
                              FliC  30 agtvdvtgatvsa..dallsavksaaftattgtitynvgvltgkvtftagkaavYvdadgeLTttasytvtYfvqaD 104
                                        ++ ++++a++s+  +++  +++   ++ ++g+ ty   v++ +v  t +++ v++d+  ++T+t+ +  +  ++ +
  gi|518651734|ref|YP_008141254.1|  81 ITDLKTYNASISScpNNMGIQLNL-IYSFQNGNSTYYYWVQNVAVLNTSNRQVVFIDNVWNFTSTNAEMHNSTMHGN 156
                                       344788999999844455555543.39999*********99****999999****************999******* PP

                              FliC 105 GsVtngsGkavYv 117
                                       G+  n+s++ +Y 
  gi|518651734|ref|YP_008141254.1| 157 GTLMNSSSAHLYY 169
                                       **********995 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.08
                              FliC  73 tftagkaavYvdadg 87 
                                       +f+ +++++Y++ +g
  gi|518651734|ref|YP_008141254.1| 333 NFKSTVKNTYIKLNG 347
                                       333333445544444 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.013
                              FliC   9 aakkatittdsgttytlaga......tagt............vdvtgatvsadallsavksaaftattgtitynvgv 67 
                                       + k++ i+++ g  y+++g+      + gt            v + + t sa    s +++ ++++t + +  ++g 
  gi|518651734|ref|YP_008141254.1| 337 TVKNTYIKLN-GSRYNFTGQylnltlNPGTynftlfskygqpVYSRNYTLSAGGYYSYTSGPSYNVTFTEKGLAAG- 411
                                       6778889999.99999999988776633335555555556667777777777777777777777777777777777. PP

                              FliC  68 ltgkvtftagkaavYv 83 
                                       ++  v++++  +a Y 
  gi|518651734|ref|YP_008141254.1| 412 TEWGVQVNG--NALYS 425
                                       455577666..55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3393.02
//
Query:       gi|518651735|ref|YP_008141255.1|  [L=255]
Description: enoyl-CoA hydratase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-38  131.1   0.1    5.1e-38  130.8   0.1    1.0  1  ECH_1          Enoyl-CoA hydratase/isomerase
      2e-09   37.4   1.0    3.7e-09   36.5   1.0    1.3  1  ECH_2          Enoyl-CoA hydratase/isomerase
     0.0056   16.6   0.3       0.12   12.3   0.1    2.3  2  Peptidase_S49  Peptidase family S49
  ------ inclusion threshold ------
       0.18   11.6   0.0       0.38   10.5   0.0    1.5  1  TFA2_Winged_2  TFA2 Winged helix domain 2


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.8   0.1   1.1e-41   5.1e-38       4     241 ..      10     243 ..       7     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.8 bits;  conditional E-value: 1.1e-41
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlel 80 
                                         +  i +nr ++ Na+  ++++ l +a+ +++ d +   +++tG +++F+aGadl+++ +     q++l e+    
  gi|518651735|ref|YP_008141255.1|  10 GHITIISINRYNVRNAVGYKTSKMLGNAFLDFNMDAEQHIAIITGENGIFSAGADLNDAKA---MSQEVLGENGPMG 83 
                                       56899******************************************************99...589********** PP

                                       HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT- CS
                             ECH_1  81 wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgk 157
                                       +t++  + kpviaa++G++++GGle+ala+Di+ia+ ++ +g  e ++G+    ggtq+l+ ++G  +A  ++l+gk
  gi|518651735|ref|YP_008141255.1|  84 FTRMK-IVKPVIAAISGYCVAGGLEMALAADIRIADSDSMIGFLERRFGVPLIDGGTQRLPLIIGIGRALDMILTGK 159
                                       **975.678****************************************99989*********************** PP

                                       EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHH..HHHHHHHHHHHHHHHHHHHHHHHHCTSHH CS
                             ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlke..alnakledalaeqleaeaklfestfskdd 232
                                        +sa+ea+ +Glv+ v  + + l++a+e+a+ +   s  a+ +l +  al + l++ l e+l +ea+  ++t+++  
  gi|518651735|ref|YP_008141255.1| 160 LVSADEAKSIGLVNYVTEHGKSLDKAMEIAKLMD--SYPAVTMLNDrlALLEGLSRPLCEGLRIEAEYGKKTIDSGI 234
                                       ****************************876554..455566776622667999*********************99 PP

                                       HHHHHHHHH CS
                             ECH_1 233 ikeGlqafl 241
                                       ++ G q+f+
  gi|518651735|ref|YP_008141255.1| 235 VEDGAQKFI 243
                                       999999985 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   1.0   8.2e-13   3.7e-09       2     180 ..      13     184 ..      12     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 8.2e-13
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       ++i +nr +  Na+ ++  + l +a+ +++ d e ++ +++g++   f+AG D++      +e       +  e+  
  gi|518651735|ref|YP_008141255.1|  13 TIISINRYNVRNAVGYKTSKMLGNAFLDFNMDAEQHIAIITGEN-GIFSAGADLNDAKAMSQE-------VLGENGP 81 
                                       6899**************************************66.9*******9987766655.......6677888 PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       +  +  ++ kpv+a + G+++ gG+ +++ + +r++  ++++   E + G+    Gg+  L+ + g   +l + lTG
  gi|518651735|ref|YP_008141255.1|  82 MGFTRMKIVKPVIAAISGYCVAGGLEMALAADIRIADSDSMIGFLERRFGVPLIDGGTQRLPLIIGiGRALDMILTG 158
                                       8999999*******************************************977668888888876657788889*** PP

                                       --B-HHHHHHTTS--EE--GGGHHHH CS
                             ECH_2 155 arlkgadalaaglathyvpsekleal 180
                                       + +++ +a  +gl + + ++ k  + 
  gi|518651735|ref|YP_008141255.1| 159 KLVSADEAKSIGLVNYVTEHGKSLDK 184
                                       ***************99988765444 PP

>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   2.7e-05      0.12       4      40 ..      88     124 ..      85     126 .. 0.93
   2 ?    2.0   0.0     0.041   1.8e+02     115     152 ..     153     190 ..     149     192 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                       HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE CS
                     Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpstivg 40 
                                       k  kPv+a ++++   gg  +a aad  +a++ +++g
  gi|518651735|ref|YP_008141255.1|  88 KIVKPVIAAISGYCVAGGLEMALAADIRIADSDSMIG 124
                                       678********************************99 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.041
                                       HCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHCH CS
                     Peptidase_S49 115 dkiAegrvltgqqAlklgLvdelgtvddavaeleelak 152
                                       d i +g+  ++++A++ gLv  ++   + +++++e ak
  gi|518651735|ref|YP_008141255.1| 153 DMILTGKLVSADEAKSIGLVNYVTEHGKSLDKAMEIAK 190
                                       6667889999***********99999999988888766 PP

>> TFA2_Winged_2  TFA2 Winged helix domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.5e-05      0.38       6      31 ..     171     198 ..     169     201 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.5e-05
                     TFA2_Winged_2   6 LlalLkkrpk..aeGikvkdLkdswpdv 31 
                                       L++++ ++ k   + +++++L+ds+p v
  gi|518651735|ref|YP_008141255.1| 171 LVNYVTEHGKslDKAMEIAKLMDSYPAV 198
                                       788888888566899***********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1831.47
//
Query:       gi|518651736|ref|YP_008141256.1|  [L=485]
Description: hypothetical protein FACI_IFERC00001G0375 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-83  281.1   1.4    1.7e-83  280.5   1.4    1.3  1  HpaB_N         4-hydroxyphenylacetate 3-hydroxylase N termina
    1.9e-46  157.7   0.1    2.8e-46  157.2   0.1    1.2  1  HpaB           4-hydroxyphenylacetate 3-hydroxylase C termina
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.033   14.4   0.0    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain


Domain annotation for each model (and alignments):
>> HpaB_N  4-hydroxyphenylacetate 3-hydroxylase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.5   1.4   2.8e-87   1.7e-83       3     272 .]       6     272 ..       4     272 .. 0.94

  Alignments for each domain:
  == domain 1  score: 280.5 bits;  conditional E-value: 2.8e-87
                                       HHHHHHHHHS---EEETTEE-S-TTTSTTTHHHHHHHHHHHHHTTSTTTHHHHEEEE..TTEEEEGGG----SHHHH CS
                            HpaB_N   3 eeYlesLrdkgrevYvdGekVedvtthpafrpavrsvarlYdlahdpeykdlltatspetgekvnrffhiprskeDl 79 
                                       e Y +sL+d gr vY++G++Ve+v+ hpa+   v +++ +Y l++d++y++++ +t++e+ +k+++f++ip+++eDl
  gi|518651736|ref|YP_008141256.1|   6 ESYKNSLND-GRVVYYRGKRVENVAAHPALGVPVSHASGIYRLQQDSKYENMMCFTDKES-GKASIFYKIPQNTEDL 80 
                                       78*******.*********************************************99998.699************* PP

                                       HHHHHHHHHHHHHTTT--S..--THHHHHHHHHHHHTG.GGGG.G....GHHHHHHHHHHHHHHT--EEEEES--SS CS
                            HpaB_N  80 lkkrkairelarktggclg..Rcpdydalnalalvaaa.dvfekegtkeyaenfrkyleyvqendlvlthaitdpkg 153
                                       ++++k+i e++r   g ++  +++++dal+al++v+++ d  +k++t+ y++++ ++++yv e+dl l+ a+td kg
  gi|518651736|ref|YP_008141256.1|  81 VARHKLIYETTRLGRGQFNivKAIGSDALFALMYVSRRiD--SKYKTD-YYNRVMAFYRYVVEKDLSLSLAQTDMKG 154
                                       ******************999*****************99..878888.**************************** PP

                                       -TTS-GGGSSSTTSB-EEEEE-SSEEEEEEEEEEEE-.--SSEEEE---SS-..TTSGGG-EEEEEETT-TTEEEEE CS
                            HpaB_N 154 dRskrpseqedpdvyvrvveetddGivVrGakvlaTgaaladeilvlptramlkeedkdyavafavpvdapGlklic 230
                                       +Rs+rpseqedpd+yv++v+++++Gi+V+Gak+++T++++++ei+v+ptr+m +e dkdyavafa+p++++G+++i+
  gi|518651736|ref|YP_008141256.1| 155 NRSLRPSEQEDPDMYVHIVKRDKNGIYVSGAKAHTTQSIASNEIIVIPTRNM-TEADKDYAVAFAIPANTKGITMIA 230
                                       ****************************************************.************************ PP

                                       -------S...-TTT-TTTTT----EEEEEEEEEEEEGGGEEE CS
                            HpaB_N 231 resfedkle.esefdyplssrfdendalvvfDdVfVPwerVfl 272
                                       r+  e+++  +++    +  +  e++++++fD+Vf+P+erVfl
  gi|518651736|ref|YP_008141256.1| 231 RPLKETETTmNDSL-SVIGRENIEVETITIFDNVFIPMERVFL 272
                                       **999843313333.334445569******************6 PP

>> HpaB  4-hydroxyphenylacetate 3-hydroxylase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.2   0.1   4.7e-50   2.8e-46       2     198 ..     280     474 ..     279     477 .. 0.97

  Alignments for each domain:
  == domain 1  score: 157.2 bits;  conditional E-value: 4.7e-50
                                       HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGSHHHHHHHHHHHHHHHHHHHHHHHHHHT-EE-T. CS
                              HpaB   2 gklveefaalhrqsyqgvirkavkldfliGlaalaaeanGiekfshvqeklgelialrellyalliaaeaeaekdp. 77 
                                       g l++ f ++hr+++ +  ++a+++dfliG  +l+a +nG++++s+++  l+ li ++e+l+a +ia++++ + d+ 
  gi|518651736|ref|YP_008141256.1| 280 GLLAMMFPTFHRFTAIS--YRAAMADFLIGTGKLLASYNGVDDKSNIRRNLAVLISYKETLKATAIASSYSCTYDKq 354
                                       668899***********..******************************************************9984 PP

                                       TS-EE--HHHHHHHHHHHHHHHHHHHHHHHHHHGGGGT----HHHHHST.THHHHHHHT-BTT.B-HHHHHHHHHHH CS
                              HpaB  78 sGvylPdlllanaarvlvtrlypriveilqdiaGGglitlPseadfknpeigpllekylrgsegvsaeeRvkllkla 154
                                       + + +Pd +++n++++++++ y ++v+ + diaGG+++t+Ps +df+n   + +l kyl+g+++ ++ eRv+l++ +
  gi|518651736|ref|YP_008141256.1| 355 ASLAIPDIIFTNVGKLFANENYTDVVKNIVDIAGGLVATMPSYEDFENSNEKTYLMKYLAGRKKEETMERVRLFQTL 431
                                       666************************************************************************** PP

                                       HHHHTSHHHHHHHHHHHHTT--HHHHHHHHHHHS--HHHHHHHH CS
                              HpaB 155 wdltgsefggrhelyerhgaGspeaqriaiyrqydleekkelvk 198
                                       ++++ s  g+ ++  ++h++Gs ea  +++ r+yd++++++l+k
  gi|518651736|ref|YP_008141256.1| 432 REFISS-LGSLYLAGMIHAEGSIEASTMELCRSYDYSSSIDLAK 474
                                       ***766.**********************************998 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   5.5e-06     0.033      20      76 ..     172     231 ..     161     252 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 5.5e-06
                                       EEEETT.EEEEEEEEEEEETTTT.-SEEEEEEE..TS-------EEEEEEE..GGGEEE..- CS
                     Acyl-CoA_dh_M  20 aaerdggeyvlnGeKiwitnaai.atlalvlar..tekpdrarglslflvprdapgvsv..r 76 
                                        ++rd+++++++G+K   t++   ++++++ +r  te +d ++    f++p++++g+++  r
  gi|518651736|ref|YP_008141256.1| 172 IVKRDKNGIYVSGAKAHTTQSIAsNEIIVIPTRnmTE-AD-KDYAVAFAIPANTKGITMiaR 231
                                       5899999***********9987736666666776333.33.455559**********99433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.53
# Mc/sec: 2761.10
//
Query:       gi|518651737|ref|YP_008141257.1|  [L=545]
Description: hypothetical protein FACI_IFERC00001G0376 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-89  299.4   0.0    4.5e-89  299.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
      2e-19   70.3   0.1    3.8e-19   69.5   0.1    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.0   0.0     5e-93   4.5e-89       9     422 ..      37     447 ..      31     448 .. 0.84

  Alignments for each domain:
  == domain 1  score: 299.0 bits;  conditional E-value: 5e-93
                                       TTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHH CS
                       AMP-binding   9 pdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaee 85 
                                        +k alv+   g+++ Yrel+++v++l+ +++ +G +kgdr++i+++nsp+++++++ai + Ga++v ++p+l  e+
  gi|518651737|ref|YP_008141257.1|  37 GNKNALVY--YGNRIKYRELWQNVKNLSTYIKMMGFGKGDRIGIMMQNSPQFIISFFAISRSGATIVLMSPALDMET 111
                                       68999*99..89********************99******************************************* PP

                                       HHHHHHHHTESEEE..............E.TCTCCC.HHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCT CS
                       AMP-binding  86 layiledseakvli..............a.tvdsel.leklleaaakleavklvivldadellkeeelkeeeeseek 146
                                        +yi +d++ k++i              + ++  ++ l k   +++  + +  + vl + +++              
  gi|518651737|ref|YP_008141257.1| 112 AEYIARDTNLKMVIttaellkvpwdlheKfNIPVICgLLKDYIKEP--DIPVPEFVLADLDIKGV------------ 174
                                       **************77766666665543133333333333222222..22333333333343333............ PP

                                       TS..........-TSCCCS-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHCSCCTTT-EEEESS-TTS CS
                       AMP-binding 147 ae..........kpeeeeelkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletrfklkeddvvlsilplah 213
                                        +              + e  +d  a+i YTSGTTG PKG++++ r++++n+  +++   ++l+++   l  +p++h
  gi|518651737|ref|YP_008141257.1| 175 -PwseavenrpdA--GHIESGADAEALIAYTSGTTGIPKGCVHTNRSVISNAIGASIW--RRLTSSAIELGAAPFFH 246
                                       .033333333221..2335688999**************************9997633..345566777******** PP

                                       CHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEE CS
                       AMP-binding 214 ifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvll 290
                                       ++gl++++l +++sGat+ +l++++    ++ +e+iek++vt++++v  ++  ll++++l+    ++d+ss+r++  
  gi|518651737|ref|YP_008141257.1| 247 VTGLSFSMLSPVYSGATIAILTRWNS---EAAIEAIEKYRVTHFVSVAPMIVDLLNQKNLE----NRDFSSMRFIGG 316
                                       **********************9987...3458***********************87777....56********9* PP

                                       ESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEE CS
                       AMP-binding 291 ggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGel 367
                                       gg+++++ l++ +++lf  +++egYG+TEt g ++ ++++e+ +kl+ +G p  g ++ki+  etg pv++  +Ge+
  gi|518651737|ref|YP_008141257.1| 317 GGAAMPEILAENMEDLFHIPFVEGYGMTETMGQTH-INPPEH-RKLQCIGIPQFGYDAKIISTETGTPVEE-GTGEI 390
                                       *****************99***************9.554555.57899*********************65.58*** PP

                                       EEEETTS-SEBTT-HHHHHHHEEE..TCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 368 lvrgpgvmkgYlkkpeataeafds..egrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       +v gp+++ gYl+kp  t +af++  ++++lrTGD+g++d +G++++v+R+k +i++
  gi|518651737|ref|YP_008141257.1| 391 VVTGPSLFTGYLNKPLDTMQAFVDidGQKYLRTGDIGYMDNEGSFFVVDRLKRMINR 447
                                       ***********************864245**************************85 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.5   0.1   4.2e-23   3.8e-19       2      76 .]     457     534 ..     456     534 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 4.2e-23
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE-.--.---.HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TTS CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlk.dg.sea.leeeLkahvrkelgpyavpkkvvfvdelpktrsG 75 
                                       v s  ++h ++ ea+VvG pd+++Ge ++a+Vvl+ +g +++  e e++++++ke+g y+ p+ v+f+++lpkt++G
  gi|518651737|ref|YP_008141257.1| 457 VDSLMLKHSDILEACVVGTPDPRNGEEVKAYVVLRePGrNKKiSEMEIVEWAKKEIGGYKYPRIVEFIESLPKTATG 533
                                       789999****************************62564233699******************************** PP

                                       - CS
                     AMP-binding_C  76 K 76 
                                       K
  gi|518651737|ref|YP_008141257.1| 534 K 534
                                       9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.57
# Mc/sec: 2869.49
//
Query:       gi|518651738|ref|YP_008141258.1|  [L=482]
Description: hypothetical protein FACI_IFERC00001G0377 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-52  178.5  47.5    1.7e-52  178.5  47.5    1.8  2  MFS_1     Major Facilitator Superfamily
    9.7e-10   37.9  18.0    9.7e-10   37.9  18.0    3.0  2  Sugar_tr  Sugar (and other) transporter
      0.002   16.6   8.7      0.002   16.6   8.7    3.1  3  MFS_3     Transmembrane secretion effector
  ------ inclusion threshold ------
       0.64    9.7   0.0       0.64    9.7   0.0    3.5  5  CybS      CybS, succinate dehydrogenase cytochrome B small su
        1.3    7.2  24.7      0.032   12.5   1.9    3.8  4  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.5  47.5   4.8e-56   1.7e-52       1     351 [.      16     404 ..      16     406 .. 0.91
   2 ?   -0.5   0.1      0.13   4.6e+02     149     172 ..     443     464 ..     409     479 .. 0.60

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 4.8e-56
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +l++ ++sa++ +i+++alp +l+ dl++      +++ +y l+ a ++  +G l+d fGr r++ +g+++f++g++
  gi|518651738|ref|YP_008141258.1|  16 VLIGMLMSAIDTTIVILALP-TLTVDLHAPFINTIWVILVYLLVLATLTTQMGKLGDIFGRGRIFNVGFIIFIIGSV 91 
                                       58999***************.******************************************************66 PP

                             MFS_1  78 lllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWrav 153
                                       +    s+   +l+++r++qG+ga +l ++++a+iad+fp +ergra+g+ s+g+s+G +lg +lgg++++ +gWr++
  gi|518651738|ref|YP_008141258.1|  92 MSGA-SPTIdFLIFSRIIQGFGAVLLQANSNAIIADYFPARERGRAFGITSMGWSIGGVLGIVLGGIITTFIGWRYI 167
                                       6664.66666******************************************************************* PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeee.......................................... 188
                                       fyi+ +++l++f ++  ++ ++++++ +   +                                             
  gi|518651738|ref|YP_008141258.1| 168 FYINVPIGLIGFYIASKYIKDNKKSSTKIDYTGTAlivamlglisygaievasvganyfnlalviigliiiipfail 244
                                       ***********9988888877777777776666669******************************99999999998 PP

                             MFS_1 189 kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallag 265
                                       +++ ++p+++  + ++ ++ l + l+a+ l ++gf ++ + l +ylq v+gl+  ++a+l+l  ++l++ +l++  g
  gi|518651738|ref|YP_008141258.1| 245 EKRSKSPVID--TRVFQNRKLSMSLAAATLQAIGFLSVIFILIMYLQGVRGLT-PFYASLVLVPGYLLSSFLSPKMG 318
                                       8888888888..5555555454788888888899999****************.8********************** PP

                             MFS_1 266 rlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfn 342
                                       +lsdr+ +      ++ll++++ + +++l+v++   ++++++++ Gfg+++++ps ++ ++++ p++  g+ sgl  
  gi|518651738|ref|YP_008141258.1| 319 KLSDRIAPGMLAGTGILLMAAGIVVYLFLGVSTPVYVVIAGSIITGFGGSMFWPSNTSSVMSNSPKQLYGSSSGLLR 395
                                       *******9888888888888888899999999666666669999********************************* PP

                             MFS_1 343 tagslggal 351
                                       t+ ++g+++
  gi|518651738|ref|YP_008141258.1| 396 TLTNIGTLM 404
                                       *****9976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.13
                             MFS_1 149 gWravfyilaivsllafvlfllll 172
                                       g +++ ++  iv+++++++   ++
  gi|518651738|ref|YP_008141258.1| 443 GLHYALLVSMIVLVMGALM--SYM 464
                                       4444444444444444444..332 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9  18.0   2.7e-13   9.7e-10      49     186 ..      49     180 ..      11     186 .. 0.92
   2 !    8.8   8.7   0.00018      0.65      58     176 ..     306     429 ..     294     444 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.7e-13
                                       HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                        ++  ++l++ +     +g+lgd+fGR  ++ ++ ++f+ig+v+++a++   ++  li++R++ G+g+ l ++ +  
  gi|518651738|ref|YP_008141258.1|  49 IWVILVYLLVLATLTTQMGKLGDIFGRGRIFNVGFIIFIIGSVMSGASP---TIDFLIFSRIIQGFGAVLLQANSNA 122
                                       5666666666666666789******************************...9************************ PP

                                       HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHH CS
                          Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpalllli 186
                                        i+ + p++ Rg+  +++ +++++G ++++++g ++ ++ +   wr+ +++++ + l+ ++
  gi|518651738|ref|YP_008141258.1| 123 IIADYFPARERGRAFGITSMGWSIGGVLGIVLGGIITTFIG---WRYIFYINVPIGLIGFY 180
                                       ***********************************999999...********999988776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00018
                                       HHHHHHHHHHHHHHHTTHHH.HHHH..HHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS CS
                          Sugar_tr  58 GaiiGslfagllgdrfGRkk.slli..aavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiA 131
                                       G +++s+++ ++g+  +R   ++l+  +++l+ +g+v+  +    + v+v+i+g +++G+g  ++    +  +  ++
  gi|518651738|ref|YP_008141258.1| 306 GYLLSSFLSPKMGKLSDRIApGMLAgtGILLMAAGIVVYLFLGVSTPVYVVIAGSIITGFGGSMFWPSNTSSVMSNS 382
                                       6778888888888888887514554546788888888888888889***************999999999999999* PP

                                       -SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-.TTHHHHHHHC CS
                          Sugar_tr 132 pkklRgalvslyqlaitfGilvaaifglgl.nktsn.adgwrillgl 176
                                       pk+l g   +l  + + +G l+++++   + + t    +++ ++lg+
  gi|518651738|ref|YP_008141258.1| 383 PKQLYGSSSGLLRTLTNIGTLMSYVIAITVaASTVPrYVTFEVFLGV 429
                                       **************************999944444367777777776 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   8.7   5.6e-07     0.002      18     177 ..      19     173 ..       9     240 .. 0.82
   2 !    3.5   1.0    0.0051        18      52     130 ..     304     380 ..     294     401 .. 0.71
   3 ?   -0.8   0.1      0.11   3.9e+02     371     402 ..     443     474 ..     434     479 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-07
                             MFS_3  18 aslvsnlGtliqevaasWlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltv 94 
                                         l+s + t i   a   l  d++a  ++   v     L +  l+   G l D+f r +++ ++ ++ +++sv+   
  gi|518651738|ref|YP_008141258.1|  19 GMLMSAIDTTIVILALPTLTVDLHAPFINTIWVILVYLLVLATLTTQMGKLGDIFGRGRIFNVGFIIFIIGSVMSGA 95 
                                       556666666666666666666666666666666666667777788899*************************9998 PP

                             MFS_3  95 laalgllspwlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaala 171
                                       + ++++     l+ + ++ g Ga l +   +A++ +  ++r+   A  ++s+g+ i    G  lgG++ +++G  + 
  gi|518651738|ref|YP_008141258.1|  96 SPTIDF-----LIFSRIIQGFGAVLLQANSNAIIADYFPARERGRAFGITSMGWSIGGVLGIVLGGIITTFIGWRYI 167
                                       888776.....57777889********************************************************** PP

                             MFS_3 172 favnal 177
                                       f +n+ 
  gi|518651738|ref|YP_008141258.1| 168 FYINVP 173
                                       *99974 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0051
                             MFS_3  52 aaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspw.lllaltlligiGaalndPaWqAs 127
                                       + + L   +ls   G l+D +     +la+  +l++++ + +v  +lg+ +p+ +++a ++++g G ++  P+   s
  gi|518651738|ref|YP_008141258.1| 304 VPGYLLSSFLSPKMGKLSDRIAP--GMLAGTGILLMAAGI-VVYLFLGVSTPVyVVIAGSIITGFGGSMFWPSNTSS 377
                                       55555555666666777776653..588888777776655.4556777777661667789999*********99988 PP

                             MFS_3 128 vge 130
                                       v  
  gi|518651738|ref|YP_008141258.1| 378 VMS 380
                                       865 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.11
                             MFS_3 371 svtlaLlaaaaalllaaaillllklpeleasd 402
                                       +++ aLl++ + l+++a++++++  ++ +a+ 
  gi|518651738|ref|YP_008141258.1| 443 GLHYALLVSMIVLVMGALMSYMTVARKKKAAS 474
                                       78999********9999999998888887754 PP

>> CybS  CybS, succinate dehydrogenase cytochrome B small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.8         1   3.7e+03      53      81 ..      15      43 ..      11      67 .. 0.68
   2 ?    9.7   0.0   0.00018      0.64      40     109 ..      77     150 ..      72     159 .. 0.77
   3 ?   -1.0   0.1      0.37   1.3e+03      43      65 ..     232     255 ..     225     282 .. 0.73
   4 ?   -3.1   0.0       1.6   5.8e+03      87     111 ..     382     406 ..     375     408 .. 0.80
   5 ?   -3.5   0.4       2.1   7.7e+03      42      56 ..     448     462 ..     442     467 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1
                              CybS 53 plvagslspvlDavlavlllihshlgfes 81
                                      ++++g l +++D+++ +l+l    +++++
  gi|518651738|ref|YP_008141258.1| 15 SVLIGMLMSAIDTTIVILALPTLTVDLHA 43
                                      55556667778888777777666555554 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00018
                              CybS  40 RivavglvpltvvplvagslspvlDavlavlll.....ihshlgfesciiDYipkrvygklhklahylLalgtvl 109
                                       Ri++vg +  ++ ++++g+ sp++D+++ + ++     +  +++ +++i DY+p r  g++  ++ +   +g vl
  gi|518651738|ref|YP_008141258.1|  77 RIFNVGFIIFIIGSVMSGA-SPTIDFLIFSRIIqgfgaVLLQANSNAIIADYFPARERGRAFGITSMGWSIGGVL 150
                                       9999****99999999965.9*****99887764333356788999**********9998877776655555544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.37
                              CybS  43 avglvpltvvplva.gslspvlDa 65 
                                        +gl+ +++ +++   s spv+D+
  gi|518651738|ref|YP_008141258.1| 232 IIGLIIIIPFAILEkRSKSPVIDT 255
                                       456666677777766668999997 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 1.6
                              CybS  87 ipkrvygklhklahylLalgtvlsl 111
                                        pk+ yg+ + l   l+++gt++s 
  gi|518651738|ref|YP_008141258.1| 382 SPKQLYGSSSGLLRTLTNIGTLMSY 406
                                       5899999999999999999999875 PP

  == domain 5  score: -3.5 bits;  conditional E-value: 2.1
                              CybS  42 vavglvpltvvplva 56 
                                       + v+++ l++ +l++
  gi|518651738|ref|YP_008141258.1| 448 LLVSMIVLVMGALMS 462
                                       567888888888877 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.9   8.9e-06     0.032     131     194 ..      98     161 ..      16     172 .. 0.91
   2 ?    1.3   0.1     0.023        82     153     182 ..     182     211 ..     173     227 .. 0.90
   3 ?   -1.5   0.2      0.16   5.8e+02     289     349 ..     256     312 ..     237     353 .. 0.60
   4 ?    5.5   5.4    0.0012       4.2     131     193 ..     352     414 ..     346     479 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-06
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkl 194
                                        + +++++ +++G+Ga+++++   + i D+   ++    +gi+++ + +G +lG +lG++++ +
  gi|518651738|ref|YP_008141258.1|  98 TIDFLIFSRIIQGFGAVLLQANSNAIIADYFPARERGRAFGITSMGWSIGGVLGIVLGGIITTF 161
                                       56699******************************************************98764 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.023
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 153 GisYidDnvkkknsplylgilyalrilGpa 182
                                       +  Yi Dn k+++   y g++  +++lG +
  gi|518651738|ref|YP_008141258.1| 182 ASKYIKDNKKSSTKIDYTGTALIVAMLGLI 211
                                       568*************************75 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.16
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 289 rllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGil 349
                                       r+++n+ + + + +++++++++  +i  l  yl+   +l++ +A+l+    ++pg  l  +
  gi|518651738|ref|YP_008141258.1| 256 RVFQNRKLSMSLAAATLQAIGFLSVIFILIMYLQGVRGLTPFYASLV----LVPGYLLSSF 312
                                       56666666666666666666666666666666666666666666655....3333333333 PP

  == domain 4  score: 5.5 bits;  conditional E-value: 0.0012
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 131 lvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllk 193
                                        v++++++ ++ G+G++++++  +s +  n+ k+      g+l +l+ +G  + ++++  ++ 
  gi|518651738|ref|YP_008141258.1| 352 PVYVVIAGSIITGFGGSMFWPSNTSSVMSNSPKQLYGSSSGLLRTLTNIGTLMSYVIAITVAA 414
                                       6789***************************************************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.50
# Mc/sec: 2926.41
//
Query:       gi|518651739|ref|YP_008141259.1|  [L=197]
Description: hypothetical protein FACI_IFERC00001G0378 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-13   50.1   0.3    2.7e-13   49.4   0.3    1.4  1  DUF309    Domain of unknown function (DUF309)


Domain annotation for each model (and alignments):
>> DUF309  Domain of unknown function (DUF309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.4   0.3   1.5e-17   2.7e-13       4      55 ..      97     148 ..      94     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 49.4 bits;  conditional E-value: 1.5e-17
                            DUF309   4 aielfnegeffeaHEvlEelWkeageperkllqglIqlAvAlyhlrrgnvrg 55 
                                       a+ l+  ++++eaHEvlE  Wk++   e+  +q +I l++A +h +rg+ + 
  gi|518651739|ref|YP_008141259.1|  97 AVYLMEGERYWEAHEVLENNWKNSSGIEKLTYQYIILLCAAGVHMQRGHDSV 148
                                       789999***************888866*********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1273.84
//
Query:       gi|518651740|ref|YP_008141260.1|  [L=331]
Description: hypothetical protein FACI_IFERC00001G0379 [Ferroplasma acidarmanus fer1]
Scores for complete 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-34  116.5   0.1    1.6e-33  115.9   0.1    1.3  1  IMS           impB/mucB/samB family
    4.5e-07   29.8   0.0    1.3e-06   28.4   0.0    1.8  1  IMS_HHH       IMS family HHH motif
     0.0013   19.1   0.0     0.0032   17.9   0.0    1.6  1  BAF           Barrier to autointegration factor
  ------ inclusion threshold ------
       0.01   16.4   0.8      0.055   14.1   0.2    2.4  2  HHH_5         Helix-hairpin-helix domain
      0.031   14.5   0.0      0.082   13.2   0.0    1.6  1  Cdd1          Pathogenicity locus
       0.17   12.5   0.1        1.3    9.6   0.1    2.0  2  NPA           Nematode polyprotein allergen ABA-1
        0.2   11.9   0.4       0.61   10.4   0.1    2.0  3  PG_binding_3  Predicted Peptidoglycan domain


Domain annotation for each model (and alignments):
>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.9   0.1   6.1e-37   1.6e-33      15     148 ..       2     137 ..       1     139 [. 0.95

  Alignments for each domain:
  == domain 1  score: 115.9 bits;  conditional E-value: 6.1e-37
                                       T.T-TTS-EEEEET.......TEEEEE-HHHHTTT--TTSBHHHHHTTHTT.-EEEEEE-HHHHHHHHHHHHHHHHH CS
                               IMS  15 dpeLkgkPvvvaqgsek...rgiviavsyeArayGvkrgmrikeakklcpd.livvkvdlekyrraskkileilkrf 87 
                                       dp++k+kPvvv+ +s +   +g v++++y Ar+ G+k+gm++ +a  + +d +++++++ + y+++s++++++++++
  gi|518651740|ref|YP_008141260.1|   2 DPSIKDKPVVVCVYSGRtenSGAVATSNYIARSIGIKSGMPLPQAMNIGKDkAVFIPIRKDFYKEFSDRVMNTISTY 78 
                                       799********9998778889*****************************88************************* PP

                                       -S..EEEEETTEEEEE-HHHHHHHH-SHHHHHHHHHHHHHHHH---EEEEEESSHHHHHHH CS
                               IMS  88 ispkvekasiDEayldltgleelaesegaalakelrkaikeelgltvsiGiasnkllAKla 148
                                        s+k+e asiDEayld+tg  + +++   +l +e++++i++e g++vs+Gi+ nk +AK+ 
  gi|518651740|ref|YP_008141260.1|  79 -SDKMEIASIDEAYLDVTGECSTFQDA-VKLGEEIKEEIFKEYGMKVSAGISINKAIAKIL 137
                                       .77****************99999995.*******************************97 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0     5e-10   1.3e-06       3      32 .]     153     182 ..     151     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5e-10
                           IMS_HHH   3 dvkefLwplpitkipGiGgklgekLeklGi 32 
                                        v+efL+ l+++kipGiG+ l +kL++ Gi
  gi|518651740|ref|YP_008141260.1| 153 MVEEFLNTLEVKKIPGIGSILSKKLNDAGI 182
                                       689*************************98 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.3e-06    0.0032       9      47 ..     152     190 ..     148     193 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.3e-06
                               BAF   9 nFvsepmgdKevtalaGigevlgkkLeekGfdkAyvvlg 47 
                                       + v+e ++  ev++++Gig+ l+kkL+++G+++ + +lg
  gi|518651740|ref|YP_008141260.1| 152 SMVEEFLNTLEVKKIPGIGSILSKKLNDAGIKYLKDILG 190
                                       5688889999************************99998 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.2   2.2e-05     0.055       3      40 ..     162     199 ..     160     204 .. 0.90
   2 ?   -1.0   0.0       1.1   2.8e+03      32      55 ..     251     275 ..     247     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                       HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTS CS
                             HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLaki 40 
                                       e+ +++GiG  + ++l +aGi+ + d++ a++++  +i
  gi|518651740|ref|YP_008141260.1| 162 EVKKIPGIGSILSKKLNDAGIKYLKDILGANRQAMIEI 199
                                       6789**************************99988777 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                                       S-HHHHHTSTTS.-HHHHHHHHHHH CS
                             HHH_5  32 adveeLakipGi.GkktAeriilel 55 
                                       a   +++k+pG+ G+  A  i++ l
  gi|518651740|ref|YP_008141260.1| 251 AVDSAFSKAPGLpGEISAIGIMEDL 275
                                       3345899****98888887777665 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   3.2e-05     0.082       7      44 ..     162     199 ..     158     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                              Cdd1   7 elqdiPniGkalaedlvelGirsveelkgedpeelyek 44 
                                       e ++iP+iG  l+++l + Gi+ ++++ g + +++ e 
  gi|518651740|ref|YP_008141260.1| 162 EVKKIPGIGSILSKKLNDAGIKYLKDILGANRQAMIEI 199
                                       6789**************************99999875 PP

>> NPA  Nematode polyprotein allergen ABA-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00051       1.3      33     105 ..      68     142 ..      64     154 .. 0.88
   2 ?    0.4   0.0      0.37   9.4e+02      55      82 ..     173     200 ..     151     223 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00051
                               NPA  33 seeiekkvlefyealeadkkeeareklkgaCkeyikkl.lgeeeaeel.kklkesgasaeelkkkldeligeled 105
                                       s+++++ + ++ +++e  + +ea  ++ g+C ++ + + lgee  ee+ k++  + ++   ++k ++++ g++ +
  gi|518651740|ref|YP_008141260.1|  68 SDRVMNTISTYSDKMEIASIDEAYLDVTGECSTFQDAVkLGEEIKEEIfKEYGMKVSAGISINKAIAKILGDMAK 142
                                       5699999***************************99874788888887799999*****************9964 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.37
                               NPA  55 areklkgaCkeyikkllgeeeaeelkkl 82 
                                       +++kl++a  +y k++lg++  + ++ l
  gi|518651740|ref|YP_008141260.1| 173 LSKKLNDAGIKYLKDILGANRQAMIEIL 200
                                       5789999999999999999999988776 PP

>> PG_binding_3  Predicted Peptidoglycan domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.8   1.5e+04      50      61 ..      60      71 ..      59      74 .. 0.80
   2 ?   -1.6   0.0       1.3   3.3e+03      42      58 ..     173     189 ..     171     196 .. 0.79
   3 ?   10.4   0.1   0.00024      0.61      36      62 ..     190     216 ..     179     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.8
                                      HHHHHHHHHHHH CS
                      PG_binding_3 50 rrefyldlaerr 61
                                      r+ fy++ ++r 
  gi|518651740|ref|YP_008141260.1| 60 RKDFYKEFSDRV 71
                                      7899*9999875 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHHHHHHH CS
                      PG_binding_3  42 Llkainlarrefyldla 58 
                                       L k +n+a +++++d+ 
  gi|518651740|ref|YP_008141260.1| 173 LSKKLNDAGIKYLKDIL 189
                                       77889999999999985 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00024
                                       HS-HHHHHHHHHHHHHHHHHHHHHHHH CS
                      PG_binding_3  36 sadedaLlkainlarrefyldlaerri 62 
                                        a+ +a+++ +++ar ++++++ae r 
  gi|518651740|ref|YP_008141260.1| 190 GANRQAMIEILGNARYNYLVEIAENRY 216
                                       57899******************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2104.08
//
Query:       gi|518651741|ref|YP_008141261.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G0380 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-31  109.7   1.4    1.3e-31  109.4   0.4    1.6  2  Flavoprotein  Flavoprotein
      3e-27   95.6   0.0    5.8e-27   94.7   0.0    1.5  1  DFP           DNA / pantothenate metabolism 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 !  109.4   0.4   1.5e-35   1.3e-31       1     156 [.      15     179 ..      15     181 .. 0.93
   2 ?   -2.1   0.0      0.32   2.9e+03      97     134 ..     267     303 ..     253     321 .. 0.69

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 1.5e-35
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHGGS...........TCSSHHHHHHCTTESEEEE CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiskeklklaa.......redpilhielrrwadllvi 70 
                                       kki+++ + s++++ +++l++ Lk+eg++v   ++++A  +i +  +++a+       ++++i+hi++ ++  +l++
  gi|518651741|ref|YP_008141261.1|  15 KKIIIASSASISIYRIPDLIRDLKREGASVVSAMSQQAVSMIGQTIMEWATgnpavtqITGNIEHISMFDENTILLV 91 
                                       79*****************************************9966666688888889****************** PP

                                       EEEEHHHHHHHHTT--SSHHHHHHHT..HCCTTEEEEE.--HHCCTCSTCHHHHHHH.HT................G CS
                      Flavoprotein  71 aPasantlakianGiadnlltlilra..takkpiliaPamnpamyenpqtlknlekl.eegvtvikPsegdigkgkm 144
                                       aPas+nt++k+anGi+d+  +l++    ++  +i+++Pam+  m+enp++++n+ekl + gv v++P+  d+ k+k+
  gi|518651741|ref|YP_008141261.1|  92 APASYNTIGKMANGISDSIPSLFFSYalGHGNKIVVVPAMHRDMFENPVNKENIEKLkKHGVLVVDPE-FDETKAKI 167
                                       ********************9999434799999************************66*********.99999999 PP

                                       HHHHHHHHHHCH CS
                      Flavoprotein 145 aeieeivgkild 156
                                       a+ ++i++ + +
  gi|518651741|ref|YP_008141261.1| 168 ADNDRIIDYVCR 179
                                       999999998765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.32
                                       HCCTTEEEEE.--HHCCTCSTCHHHHHHHHT....... CS
                      Flavoprotein  97 takkpiliaPamnpamyenpqtlknlekleegvtvikP 134
                                       ++k   +i+P m  + ++ ++++ +l++  ++  v+ P
  gi|518651741|ref|YP_008141261.1| 267 VNKYDYIIMP-MALMDFDMKESKTKLDSGADQNLVLTP 303
                                       5667788888.888888888888777776444444444 PP

>> DFP  DNA / pantothenate metabolism flavoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.7   0.0   6.5e-31   5.8e-27       1     186 []     186     364 ..     186     364 .. 0.91

  Alignments for each domain:
  == domain 1  score: 94.7 bits;  conditional E-value: 6.5e-31
                                       TTT-EEEEEES-EEEECCTTEEEEE----HHHHHHHHHHHHTT-EEEEEE-S-SS---TT-EEEE--SHHHHHHHHH CS
                               DFP   1 legkkvlvtaGpTrEaiDpVRfisNrSSGkmGyalAeaaaarGaeVtlvsgpvsletpegvevvkvesaeemleave 77 
                                       l+gk+vl+ +G +  aiDpVR+i+NrSSG +Gy lA++a + Ga++    g+++ + p  +++++  + +++  +++
  gi|518651741|ref|YP_008141261.1| 186 LNGKNVLIISGRSELAIDPVRVITNRSSGYTGYWLARNAFRLGASIITYVGNSEYNIPGYATYMEKYNLRDIIVEIN 262
                                       689*************************************************99999988999999*******9999 PP

                                       HHH..TT-SEEEE---S--EEES-------------..----EEE---HHHHHHHC-S.S-EEEEEEE-SS-HHHHH CS
                               DFP  78 eal..keadivimaAAvaDyrpkeaaeeKikkeeeeeeltleleknpdilaelaekkkkkqllvGFaaeteellena 152
                                       + +  ++ d++im  A  D+ +ke +++K++    +++ +l l++ p++  ++ ++ ++  +lv F +e+e+  ++ 
  gi|518651741|ref|YP_008141261.1| 263 TYIsvNKYDYIIMPMALMDFDMKE-SKTKLDS---GADQNLVLTPRPKVRDRI-RQMAPGAVLVLFNLESEK--SYN 332
                                       88744777**************96.5667775...45679*************.5667889********985..788 PP

                                       HHHHHHTT-SEEEEEEGGGTTGGG-SS-EEEEE. CS
                               DFP 153 reklerkgldlivaNdvskeeagfgsdenevtll 186
                                       ++k+e+ + d++v+N+ +k+   fg+++n++t++
  gi|518651741|ref|YP_008141261.1| 333 SKKFEKSDPDMVVLNSFDKK--PFGDTKNDYTII 364
                                       9*****************87..9******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2733.86
//
Query:       gi|518651742|ref|YP_008141262.1|  [L=237]
Description: hypothetical protein FACI_IFERC00001G0381 [Ferroplasma acidarmanus fer1]
Scores for complete 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   72.8   0.0    3.8e-20   71.5   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00022   20.5   0.0    0.00029   20.1   0.0    1.2  1  Regulator_TrmB  Archaeal transcriptional regulator TrmB
      0.002   17.9   0.0     0.0044   16.8   0.0    1.6  1  HTH_IclR        IclR helix-turn-helix domain
  ------ inclusion threshold ------
        0.1   13.1   0.0       0.22   12.1   0.0    1.5  1  ATPgrasp_N      ATP-grasp N-terminal domain
       0.14   12.5   0.0       0.45   10.9   0.0    1.8  2  Rrf2            Transcriptional regulator
       0.16   11.9   0.0       0.25   11.2   0.0    1.3  1  PLDc_2          PLD-like 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 !   71.5   0.0   1.3e-23   3.8e-20       1      66 [.      15      80 ..      15      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.5 bits;  conditional E-value: 1.3e-23
                                      HHHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEEEE-- CS
                              TrmB  1 LqklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpklYravd 66
                                      L+ lGLs+yEa++++ L+ +g a+ad+ia  +g+pr+++Y+v++sL+++G+ +  +grp+++++ d
  gi|518651742|ref|YP_008141262.1| 15 LKILGLSSYEAQAFASLVYHGVANADTIADTAGIPRTSAYKVMESLVSRGFARETEGRPRMFKPED 80
                                      789***********************************************************9965 PP

>> Regulator_TrmB  Archaeal transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   9.6e-08   0.00029       2      60 ..     115     178 ..     114     219 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 9.6e-08
                                       EEEESSHHHHHHHHHHHHHH-SSEEEEEE-G..GGHHHHHHHHHHHHHTT-EEEEEESS...-- CS
                    Regulator_TrmB   2 vwvvksretvierieelIesAenelivslps..elLeelreeliaaaergvtVllliyp...de 60 
                                       v ++ +r++v ++++e+ + +e e+++++p   e+ +el++ + +a +rgv+V+++  p    +
  gi|518651742|ref|YP_008141262.1| 115 VFTIYGRSKVMNKMAEMFDLTEREILIATPRirEIRSELKKNIDNALKRGVKVVFITPPnkrVP 178
                                       67899************************9543777888889999999*****99988843322 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 !   16.8   0.0   1.5e-06    0.0044      24      50 ..      42      68 ..      29      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.5e-06
                                      HHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 24 lArrtglpkStvhRlLqtLvelGyveq 50
                                      +A+ +g+p+++++  + +Lv +G+ + 
  gi|518651742|ref|YP_008141262.1| 42 IADTAGIPRTSAYKVMESLVSRGFARE 68
                                      9***********************986 PP

>> ATPgrasp_N  ATP-grasp N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   7.3e-05      0.22       4      45 ..     160     202 ..     157     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.3e-05
                                       HHHTT-EEEEEEETTS----S-TT..EEEEEEE-TTT-HHHHH CS
                        ATPgrasp_N   4 AkaLGikvvlvdeedewapeelae.lvekfipldlaqdpdaal 45 
                                       A + G+kvv+++ +++  p +++    e +i++d+a d+ +a+
  gi|518651742|ref|YP_008141262.1| 160 ALKRGVKVVFITPPNKRVPHNTEVhRKEGLIATDVASDDSRAM 202
                                       5666***********99998887778999*********99887 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.8   8.3e+03      38      54 ..       4      20 ..       2      23 .. 0.81
   2 ?   10.9   0.0   0.00015      0.45      26      61 ..      37      72 ..      20      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.8
                                      -HHHHHHHHHHHHHTTS CS
                              Rrf2 38 spsylekilakLrkagl 54
                                      +p+++ k  ++L+  gl
  gi|518651742|ref|YP_008141262.1|  4 NPEHIMKTANMLKILGL 20
                                      78999999999987765 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                                      B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT CS
                              Rrf2 26 vsseeiaerqnispsylekilakLrkaglvksvrGk 61
                                      +++++ia+  +i+++ + k+++ L   g+ + ++G+
  gi|518651742|ref|YP_008141262.1| 37 ANADTIADTAGIPRTSAYKVMESLVSRGFARETEGR 72
                                      6799*************************9999886 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.4e-05      0.25       7      49 ..     134     180 ..     128     217 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.4e-05
                            PLDc_2   7 sAkksidiatyyf.vsdreildallkaakrgvkvrilldskkd...d 49 
                                        ++++i iat+ + +  +e+ +++ +a krgvkv  +++++k    +
  gi|518651742|ref|YP_008141262.1| 134 LTEREILIATPRIrEIRSELKKNIDNALKRGVKVVFITPPNKRvphN 180
                                       56899********7777778888888*************97654430 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1710.23
//
Query:       gi|518651743|ref|YP_008141263.1|  [L=282]
Description: endonuclease IV [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-27   96.3   0.0    2.1e-27   96.0   0.0    1.1  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
     0.0011   18.2   0.0     0.0014   17.9   0.0    1.1  1  UvdE          UV-endonuclease UvdE


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.0   0.0   2.3e-31   2.1e-27       2     210 .]      29     238 ..      28     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 96.0 bits;  conditional E-value: 2.3e-31
                                       HHHHHCT-SEEEEECCTCSHHHHC..HHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCS...HHHHHHHHH CS
                      AP_endonuc_2   2 aaaaeaGfdgvElfgrdlvpvsel..sdeelrelrkaldelglriaslslftrfgypdederear...reesvdalk 73 
                                       ++aa+ Gf+++++f ++  +++ +  ++ee++ +r  +++ ++  +++++++  +   e     +    e+s d++k
  gi|518651743|ref|YP_008141263.1|  29 ERAAAFGFNTFQIFVKSNLQWKYKpvTEEEVENFRDGVKKFHMAKPVVHATYLLNLGSE-----NrelVEKSMDDIK 100
                                       689*****************************************555555555555444.....446889******* PP

                                       HHHHHHHHHTBSEEEEEBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHHHHTSEEEEE--TTTTSSSTC..HHHHHHH CS
                      AP_endonuc_2  74 raielaaaLGapllvlhpGtagagpkgseeeawerlaeslneladyaekegvklalEtlagsgvelgd..eelarll 148
                                        +ie ++++G++ lvlhpG          ++++e + +s+ el+  +e+ +v+ ++E+  g+g+      ee+ ++l
  gi|518651743|ref|YP_008141263.1| 101 YEIEVCNRIGVDRLVLHPG---------SNSNREIALNSIMELLNSLETGNVTMLIENSSGKGNTVPAtsEEMGKML 168
                                       *******************.........8899999999999999999999*************98887999999999 PP

                                       HHHTTTTEEEEEEHHHHHHH....TTTHHHHHHHHHGG.....EEEEEE.EESSTTTTSSTTEESTTSSSS CS
                      AP_endonuc_2 149 davdspnvgvclDtgHllia....eedvddalraladr.....ikhvHikDakgdlgagrdrhvpigeGei 210
                                       d  +++ +g+clDt+H+++     ++ + + ++ l +      i+++Hi+D+  d g+++drh++ig G i
  gi|518651743|ref|YP_008141263.1| 169 DLSKNK-IGICLDTCHFFAGgydlKNGYKESIDSLRSNgitghIGALHINDSMFDIGSKKDRHENIGNGYI 238
                                       988865.*************888888888888888888******************************976 PP

>> UvdE  UV-endonuclease UvdE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.6e-07    0.0014      76     185 ..      46     149 ..      37     199 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.6e-07
                              UvdE  76 evgykletalaeeleevGelakelgl.RltfHPeqftllnSdrkevtesairdlayHdklldalklaeqqdavliiH 151
                                       + ++k+ ++ +ee+e+    +k+  + +  +H      l+S+ +e++e+++ d++y  ++ +++++++      ++H
  gi|518651743|ref|YP_008141263.1|  46 NLQWKYKPVTEEEVENFRDGVKKFHMaKPVVHATYLLNLGSENRELVEKSMDDIKYEIEVCNRIGVDRL-----VLH 117
                                       6789999999999999998888866526789***9******************************9876.....9** PP

                              UvdE 152 vGGkfgdkeaalerfkenikrlpdsvkerlvLEN 185
                                        G    ++e al+ + e++++l +   + + +EN
  gi|518651743|ref|YP_008141263.1| 118 PG-SNSNREIALNSIMELLNSLETGNVT-MLIEN 149
                                       99.88999********999999876544.44455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2222.19
//
Query:       gi|518651744|ref|YP_008141264.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G0383 [Ferroplasma acidarmanus fer1]
Scores for complete 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-64  216.1   0.0    8.4e-64  215.9   0.0    1.0  1  DUF1015   Protein of unknown function (DUF1015)
  ------ inclusion threshold ------
       0.19   12.0   0.4        4.7    7.6   0.4    2.6  1  ParBc     ParB-like nuclease domain


Domain annotation for each model (and alignments):
>> DUF1015  Protein of unknown function (DUF1015)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.9   0.0   9.3e-68   8.4e-64      17     393 ..      17     382 ..       5     383 .. 0.90

  Alignments for each domain:
  == domain 1  score: 215.9 bits;  conditional E-value: 9.3e-68
                           DUF1015  17 evasppYDviseeearelakknpysflrlilpeadledeedeedryekaaetleewleegvlvqdekpalyvyeqtf 93 
                                       + +spp+D i+ e++++l ++ +y+++ l+lpe                ++  ++w+ ++v+    k+ +++++q f
  gi|518651744|ref|YP_008141264.1|  17 DSVSPPFDTITIEQEKKL-RAAKYNITALSLPEYGN--------SSLTPEKLIKKWIGDNVIYPYGKDIIIILKQVF 84 
                                       568**********99999.789**********9644........34577899************************* PP

                           DUF1015  94 ed.g.grvrrGlvaavsledyeegvIlpHEkTlaekeedRlkllratkanlepifllyrdpeeieelieelkkkeee 168
                                          +   +r+G++ +++++     + ++HE T+++++ +R +++ +++ + epif++++d++ +++++++++ ++ e
  gi|518651744|ref|YP_008141264.1|  85 YInKeIITRYGIISLAEIDS----SLKAHESTFEKQVLERKNVMISLNGEPEPIFIVVPDNG-FDKMVRRFA-SNLE 155
                                       77745889**********87....89***********************************9.********5.5899 PP

                           DUF1015 169 plydfttdedgvrhrlwaitdpeaiekiaealadkklyIADGHHRyatalavreerkaeeeaatgeepanyflavlv 245
                                         ++f ++ +gv++ +++++d+e+iek+++ +++++ ++ADGHHR+++ + +++    e    tg++ +ny++a+++
  gi|518651744|ref|YP_008141264.1| 156 EKFKF-EEPSGVENYVYFLEDQEKIEKLKDSIKNDQGIVADGHHRTQAIKDLKK----E----TGDSFWNYAMAYIT 223
                                       99***.889*******************************************92....3....3699********** PP

                           DUF1015 246 nledpgLkilpihRvvkdlnglseeelleklaeafev..........apfglylkdgkwyklltlkdka.......v 305
                                       +++d+gL+i  + R+v ++   + ee + k+++ f+v          + + +y  +g +ykl+  k  a        
  gi|518651744|ref|YP_008141264.1| 224 SIYDNGLMIGGVDRLVYRT---NFEENIPKIENLFDVtvertivednN-IRVYS-RGLFYKLVPKKY-AidqvmdsK 294
                                       ****************996...47999********9988887776533.****8.888999999555.322333345 PP

                           DUF1015 306 rsLdvsvlqelllepilgiedprkderidyvhgleeavekvdsgeagvafllnptsveelfavadagevmPrKSTyf 382
                                        +  + +++++l+ ++lgi++ + +++i y+ ++ +a+++vd +e ++a++++p++++ + ++a  g + P+KSTyf
  gi|518651744|ref|YP_008141264.1| 295 YEVSTEIVNKILFGEVLGINKSNMQTKIGYIYNTTDAINAVDMHECDFAIIIPPWQKDVFLKMALDGVIFPQKSTYF 371
                                       567777*************9999****************************************************** PP

                           DUF1015 383 ePKlrsGlvle 393
                                       +PK+ sG+ ++
  gi|518651744|ref|YP_008141264.1| 372 YPKIPSGIAIY 382
                                       *******9986 PP

>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.4   0.00052       4.7      50      66 ..     192     208 ..     167     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00052
                             ParBc  50 eiiaGerRlrAakrlgl 66 
                                        + +G++R +A k l++
  gi|518651744|ref|YP_008141264.1| 192 IVADGHHRTQAIKDLKK 208
                                       57899999999998883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2838.51
//
Query:       gi|518651745|ref|YP_008141265.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G0384 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.42
# Mc/sec: 413.69
//
Query:       gi|518651746|ref|YP_008141266.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G0385 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); 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 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 376.43
//
Query:       gi|518651747|ref|YP_008141267.1|  [L=78]
Description: hypothetical protein FACI_IFERC00001G0386 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 642.25
//
Query:       gi|518651748|ref|YP_008141268.1|  [L=116]
Description: hypothetical protein FACI_IFERC00001G0387 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.62   10.5   7.0          3    8.3   0.6    2.6  2  YadA_head  Head domain of trimeric autotransporter adhesin


Domain annotation for each model (and alignments):
>> YadA_head  Head domain of trimeric autotransporter adhesin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6   0.00017         3       6      17 ..      40      51 ..      39      52 .. 0.87
   2 ?    5.0   1.0    0.0019        33       3      10 ..      78      85 ..      71      88 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00017
                         YadA_head  6 SiAiGynAtAsG 17
                                      SiA+G++At+ G
  gi|518651748|ref|YP_008141268.1| 40 SIALGSGATVAG 51
                                      899999999877 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0019
                         YadA_head  3 GknSiAiG 10
                                      G++S+AiG
  gi|518651748|ref|YP_008141268.1| 78 GVGSVAIG 85
                                      56666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 891.86
//
Query:       gi|518651749|ref|YP_008141269.1|  [L=70]
Description: hypothetical protein FACI_IFERC00001G0388 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 523.89
//
Query:       gi|518651750|ref|YP_008141270.1|  [L=82]
Description: hypothetical protein FACI_IFERC00001G0389 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.052   13.4   0.0      0.054   13.3   0.0    1.2  1  T6PP_N    Trehalose-6-phosphate phosphatase N-terminal helica


Domain annotation for each model (and alignments):
>> T6PP_N  Trehalose-6-phosphate phosphatase N-terminal helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-06     0.054       4      42 ..       2      40 ..       1      68 [. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-06
                            T6PP_N  4 eFyelmyrtrevRrqIvervLkgieirehfvesLknake 42
                                      eF+    r+ ++  +Ive++ k  +i ++ ve+L+  ++
  gi|518651750|ref|YP_008141270.1|  2 EFKLTIDRMEDLKSTIVEQITKMENIPAENVEILDVFYY 40
                                      899999***************************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 553.06
//
Query:       gi|518651751|ref|YP_008141271.1|  [L=102]
Description: MarR family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-15   56.0   0.0    2.8e-15   55.9   0.0    1.0  1  HxlR      HxlR-like helix-turn-helix
     0.0028   17.6   0.0     0.0039   17.1   0.0    1.2  1  PadR      Transcriptional regulator PadR-like family
     0.0062   16.5   0.1     0.0072   16.3   0.1    1.2  1  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
      0.083   13.1   0.0       0.12   12.6   0.0    1.2  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   6.3e-19   2.8e-15       3      84 ..      16      98 ..      14     102 .] 0.92

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 6.3e-19
                                      HSTTHHHHHHHH.TTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                              HxlR  3 ggkWkllilvel.lkgkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80
                                       gkW+ li+  l ++g+  +se+++ + +i+ k L++ L +L ++g+i ++++++ P++v Y lt+kG+++ + l++++
  gi|518651751|ref|YP_008141271.1| 16 RGKWEPLIIKYLsINGSSGYSEISNSMENITPKALTEALGKLSTEGIIGKNIISSKPVRVMYYLTDKGKAMIDPLDTIE 94
                                      68*******998356********************************************************99999988 PP

                                      HHHH CS
                              HxlR 81 kwge 84
                                       + +
  gi|518651751|ref|YP_008141271.1| 95 SLNK 98
                                      7665 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.7e-07    0.0039      28      72 ..      44      86 ..      31      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.7e-07
                                      CTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 28 elseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      ++ +  l  aL +L+ eg++ ++   s  +p r +Y lTd+G++ 
  gi|518651751|ref|YP_008141271.1| 44 NITPKALTEALGKLSTEGIIGKNIISS--KPVRVMYYLTDKGKAM 86
                                      45555666899************9975..9************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.6e-06    0.0072      17      76 ..      30      97 ..      16      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                            HTH_45 17 egeakkTkimyka.nLsykllnkYLdmLvekgli.......kkskekYvlTekGlelleklkeleela 76
                                      +g++  ++i  +  n++ k l + L +L  +g+i       k    +Y+lT+kG+ +++ l+++e+l 
  gi|518651751|ref|YP_008141271.1| 30 NGSSGYSEISNSMeNITPKALTEALGKLSTEGIIgkniissKPVRVMYYLTDKGKAMIDPLDTIESLN 97
                                      5556666666553378888888899999999998888888556899***************9999875 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   2.7e-05      0.12       5      68 ..      23      86 ..      22      96 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.7e-05
                            HTH_34  5 vlsyLasvdeadfvelkeal.eatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGrea 68
                                      ++ yL+ + +  ++e+++++ ++t  +L   l kL + g i  ++  ++k  r ++ +T++G++ 
  gi|518651751|ref|YP_008141271.1| 23 IIKYLSINGSSGYSEISNSMeNITPKALTEALGKLSTEGIIGKNII-SSKPVRVMYYLTDKGKAM 86
                                      789***************99559****************8865554.3343678999*****975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 780.54
//
Query:       gi|518651752|ref|YP_008141272.1|  [L=277]
Description: hypothetical protein FACI_IFERC00001G0391 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       952  (0.0530983); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); 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):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 1887.81
//
Query:       gi|518651753|ref|YP_008141273.1|  [L=481]
Description: hypothetical protein FACI_IFERC00001G0392 [Ferroplasma acidarmanus fer1]
Scores for complete 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-146  486.8   0.9   5.4e-146  486.6   0.9    1.0  1  UbiD      3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Domain annotation for each model (and alignments):
>> UbiD  3-octaprenyl-4-hydroxybenzoate carboxy-lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  486.6   0.9    3e-150  5.4e-146       2     406 .]      11     421 ..      10     421 .. 0.95

  Alignments for each domain:
  == domain 1  score: 486.6 bits;  conditional E-value: 3e-150
                                       HHCCCTTSEEEEESEB-TBTHHHHHHHHH.HHHT--EEEEEEBTTB.TT-EEEE-TTS-HCHHHHHHTS-GHHHHHH CS
                              UbiD   2 ealekagelvrikeevdpelEiaeiarrv.leeggpallFenvkgkgskfpvltnlfgtrervalalglssleeile 77 
                                       +  e++g+lvr++eevdpelE++ i+ +     +++ +lF+nvk  gsk+pv++n+f+++++++ +lg ++  +i+ 
  gi|518651753|ref|YP_008141273.1|  11 KYQESNGDLVRVNEEVDPELELTYILSEEeRIGKKRTMLFNNVK--GSKMPVIGNIFSSDKKIEAILG-DTPYNIGL 84 
                                       56799************************6445667*******6..468*******************.899***** PP

                                       HHHHHHHS..-...................---EE--GCG-GGGSEEECCCCC--HHHS---BSSTTSSS-EEECEE CS
                              UbiD  78 klaellepkpp...................ippkvvesekapcqeevvlegddvdLskLPvltlwpgDgGpyitlgl 135
                                       kl++l++   p                   i+pkv ++++  ++ +v     ++ Ls+ P+ + wpgDgG+yit+++
  gi|518651753|ref|YP_008141273.1|  85 KLKNLVRI--PddtesmisrglemlkemsgIKPKVYNRKNSEFE-VV-----EPHLSDYPITKNWPGDGGRYITMPV 153
                                       *****996..4567899*******************98876665.33.....59*********************** PP

                                       EEEE-TTTT-EEEEEEEEEEEETTEEEE--TTTHCHHHHHHHHHHCCT--EEEEEEES--HHHHHHCTS--TTT-TC CS
                              UbiD 136 vitrdpetgkrnlgiyRmqvldknklglhwqihkggaehlrkakkkggeplpvavaiGvdPaltlaAvaplPeglsE 212
                                       v+t+dp+tg+rn+g+yRmqv+d++++g+hw+ihkggaeh++k++++g + ++vavaiGvdP+++++++aplP g++E
  gi|518651753|ref|YP_008141273.1| 154 VMTKDPDTGTRNVGTYRMQVYDDETVGMHWHIHKGGAEHMDKYRNEG-KIMDVAVAIGVDPLTFFSSIAPLPNGIDE 229
                                       ***********************************************.8**************************** PP

                                       HHHHHHHHTS--EEEE-SSSSSEEETT-SEEEEEEEECCEEEECTTTC-TTSCEEC--CCEEEEEEEEEEE-TT-EE CS
                              UbiD 213 lefaGalrgepvelvkcetvdlevpadAEivleGeidpgetapEGPfgdhtGyysevrdefpvfkVtaithRkdpiy 289
                                       ++f G+l ++ +el+k etv++e p ++ ivleG+idp+et+ EGPfgdhtGyys + + fpvf+V+++  + +p+y
  gi|518651753|ref|YP_008141273.1| 230 FSFRGILAKKHLELIKGETVNMEYPRSSQIVLEGYIDPSETRIEGPFGDHTGYYSLE-EAFPVFHVKKVVQKLEPVY 305
                                       ******************************************************666.66***************** PP

                                       EE-SSSCCSHHHHCHHHHHHHHHHHHHHCCSTTEEEEEE-GGGTTTCEEEEECHHHTCCHHHHHHHHHHCCTTGGC- CS
                              UbiD 290 pttvvgkppeedallgkalealflpllkkqvpevkdvhlpeeggfhllavvsikkrypghakkvmealwalkqqlsl 366
                                        tt+vgk + ed+ +gka+e++flpl++ q+pe++d+++pee+++ +++vvsikkrypg+akkvm+a+w+++q +++
  gi|518651753|ref|YP_008141273.1| 306 STTIVGKLWHEDVRIGKAIEKMFLPLIQIQIPEIVDMNIPEETVVSNMIVVSIKKRYPGQAKKVMFAIWGTGQ-MMF 381
                                       ***********************************************************************88.*** PP

                                       SEEEEEEETTS-TTSHHHHHHHHHHC--CCCCEEEECCCE CS
                              UbiD 367 tKlvivvDedvdvrdlkevlwaiatrvdpdrDlviiegtr 406
                                       tK+v+vvD+dvdv+d+k+v+wa++tr+dp +D++++++t+
  gi|518651753|ref|YP_008141273.1| 382 TKIVVVVDDDVDVHDMKQVMWAMTTRIDPVNDVFMVPNTP 421
                                       *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (481 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3629.00
//
Query:       gi|518651754|ref|YP_008141274.1|  [L=196]
Description: SAM-dependent methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-15   55.4   0.0    1.1e-14   54.9   0.0    1.2  1  Methyltransf_25  Methyltransferase domain
    1.6e-12   47.9   0.0    2.4e-12   47.4   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.9e-12   47.3   0.0    2.4e-12   47.0   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    8.7e-12   45.1   0.0    1.1e-11   44.7   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.3e-10   41.1   0.0    3.4e-10   40.6   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    2.6e-09   36.8   0.0    3.7e-09   36.4   0.0    1.2  1  MTS              Methyltransferase small domain
    6.8e-06   25.6   0.0    8.5e-06   25.3   0.0    1.1  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    3.2e-05   23.3   0.0    3.8e-05   23.1   0.0    1.1  1  Methyltransf_2   O-methyltransferase domain
    0.00013   21.4   0.0    0.00019   20.9   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00089   18.4   0.0     0.0021   17.2   0.0    1.3  1  DREV             DREV methyltransferase
     0.0031   17.0   0.0      0.006   16.1   0.0    1.4  1  Methyltransf_4   Putative methyltransferase
     0.0061   16.0   0.0     0.0074   15.7   0.0    1.2  1  TehB             Tellurite resistance protein TehB
  ------ inclusion threshold ------
      0.012   14.9   0.0      0.016   14.5   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
      0.013   15.0   0.0      0.016   14.7   0.0    1.1  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
      0.053   12.8   0.0      0.066   12.5   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
      0.057   13.5   0.0      0.097   12.8   0.0    1.6  1  FtsJ             FtsJ-like methyltransferase
      0.068   13.2   0.0        0.1   12.6   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
       0.15   11.7   0.0       0.52    9.9   0.0    1.7  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
       0.16   11.9   0.0       0.26   11.2   0.0    1.3  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   1.2e-17   1.1e-14       1      94 [.      47     137 ..      47     140 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 1.2e-17
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld+G+G+G+l+l++++++++ak+ ++D+s +m++a ++++e++g+++++  g+ +d+pf++ +fDl++ + ++hh+
  gi|518651754|ref|YP_008141274.1|  47 ILDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSRDIPFDN-KFDLIYTTLSFHHW 122
                                       8******************99**************************************975.*******888***8 PP

                                       SHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLk 94 
                                       +d+d    +k i + L 
  gi|518651754|ref|YP_008141274.1| 123 QDRD--SNIKYILSKLA 137
                                       7554..55665555555 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.0   2.5e-15   2.4e-12       1      96 []      48     144 ..      48     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 2.5e-15
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       Ld+G+G G+l+  + +++  a+ +++D+s +m+k+ +++ +++g+k ++  ++ +++pf dn+fDl++ + ++hh++
  gi|518651754|ref|YP_008141274.1|  48 LDIGAGPGKLSLMVSQKFphAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSRDIPF-DNKFDLIYTTLSFHHWQ 123
                                       8**************9999*************************9999***********.77*************** PP

                                       CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGllvi 96 
                                       d+++ +k i   L  +G+++i
  gi|518651754|ref|YP_008141274.1| 124 DRDSNIKYILSKLADNGTFLI 144
                                       ***************999875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   2.5e-15   2.4e-12       7     147 ..      26     189 ..      20     194 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.5e-15
                   Methyltransf_23   7 eelsdklerllpk..lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaep 79 
                                       + l++++ ++l++  + +++++LdiG+G G l+   ++++   ++ ++D+s ++v+        ++++f      e+
  gi|518651754|ref|YP_008141274.1|  26 RLLKKLYGFALDEmkDMEPSSILDIGAGPGKLSLMVSQKFPhaKFFAIDPSLNMVKA-------EQKNF------EK 89 
                                       55666666666544478899***********9999988765589********99985.......34444......21 PP

                   Methyltransf_23  80 qg.................kfdlIvlrevlehvpdppellrqiatllkpgGylllseplasl............... 124
                                       +g                 kfdlI+ + +++h +d  ++++ i + l+++G +l+ e+ ++                
  gi|518651754|ref|YP_008141274.1|  90 AGikasckpgssrdipfdnKFDLIYTTLSFHHWQDRDSNIKYILSKLADNGTFLIIEFMQDYykspmslhgkhsisk 166
                                       1222222233555666666**************************************98877666666666655555 PP

                   Methyltransf_23 125 kedrllldwlylvpagrhisffs 147
                                       k +++l   +y+++ ++ + f+s
  gi|518651754|ref|YP_008141274.1| 167 KYAESLNFDGYEREINTSGEFIS 189
                                       45555555777777777666666 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   1.2e-14   1.1e-11       6     113 ..      46     148 ..      42     186 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 1.2e-14
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsne 82 
                                       ++lD+G+G G+l++    + +p+a+++ iD s ++++  ++n +k g++ ++ + g+  +++  +  +kfDli +  
  gi|518651754|ref|YP_008141274.1|  46 SILDIGAGPGKLSLMVS-QKFPHAKFFAIDPSLNMVKAEQKNFEKAGIK-ASCKPGSSRDIP--FD-NKFDLIYTTL 117
                                       79************999.779***************************8.************..76.9********9 PP

                   Methyltransf_31  83 vlnaladpdkileeiervlkpggilliedpr 113
                                        +++  d d+ ++ i + l ++g +li ++ 
  gi|518651754|ref|YP_008141274.1| 118 SFHHWQDRDSNIKYILSKLADNGTFLIIEFM 148
                                       99*************************9987 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   3.6e-13   3.4e-10       1      98 [.      48     141 ..      48     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 3.6e-13
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+iG+G G l+ ++ +k+p++++ ++D+s +++++ ++ + k +  ++++     +d+  +   ++fDl++    +h
  gi|518651754|ref|YP_008141274.1|  48 LDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGI-KASCKPGSSRDIPFD---NKFDLIYTTLSFH 120
                                       8********************************444444444443.444444444444322...5************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGr 98 
                                       h++d+++ ++ i + L+++G 
  gi|518651754|ref|YP_008141274.1| 121 HWQDRDSNIKYILSKLADNGT 141
                                       *******************97 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   3.9e-12   3.7e-09      24     138 ..      36     145 ..      33     168 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 3.9e-12
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                                       l+ +++ +  ++lD+G+G G l++++ ++ p+a+  ++d + + +++ ++n+e+ ++++++   +  +   ++kfdl
  gi|518651754|ref|YP_008141274.1|  36 LDEMKDMEPSSILDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSRDIPFDNKFDL 112
                                       55666666778*********************************************************999****** PP

                                       EEE---STTTCHCHHHHHHHHHHHHHHHEEEEEEEEEE CS
                               MTS 101 ivsNPPfhagkatelavaeeliaeAkeaLkegGeLliV 138
                                       i +   fh+ ++ + ++   l     + L+++G++li+
  gi|518651754|ref|YP_008141274.1| 113 IYTTLSFHHWQDRDSNIKYIL-----SKLADNGTFLII 145
                                       ********9999666654333.....345555555555 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0     9e-09   8.5e-06      38     156 ..      34     149 ..      18     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 9e-09
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS- CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfed 114
                                       f  + + + +++++lD+ +G g l++ +s++   + k   +D + nm+k  +k  ++ g i+     +++ ++pf d
  gi|518651754|ref|YP_008141274.1|  34 FALDEMKDMEPSSILDIGAGPGKLSLMVSQKF-PHAKFFAIDPSLNMVKAEQKNFEKAG-IKASCKPGSSRDIPF-D 107
                                       67788999******************999887.567999*********98877777666.5678889********.5 PP

                                       T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE-- CS
                   Ubie_methyltran 115 dsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefsk 156
                                       + fD++  +  +    D++  +k +   l   G+++++ef +
  gi|518651754|ref|YP_008141274.1| 108 NKFDLIYTTLSFHHWQDRDSNIKYILSKLADNGTFLIIEFMQ 149
                                       789*998889999**************************977 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     4e-08   3.8e-05      56     173 ..      37     153 ..      20     182 .. 0.80

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 4e-08
                                       HSS-GGG-SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HHHHHHHHHHS-----TTEEEEES-TTTS---...--S CS
                    Methyltransf_2  56 eafdleglkslvDvGGGtGalakaivsayPtikvivfDlpeVveaAkehlsageeervefvgGdffkdslP...eaD 129
                                        +++ ++ +s++D+G G G l  ++++++P+ k    D +  + +A+++   ++  + +   G+ +   +P   + D
  gi|518651754|ref|YP_008141274.1|  37 DEMKDMEPSSILDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSR--DIPfdnKFD 111
                                       55554555799***************************7777777777633444556677899999..56655789* PP

                                       EEEEESSGGGS-HHHHHHHHHHHHHH--TT-EEEEEE----TTS CS
                    Methyltransf_2 130 aillkrvlhDwsdekcvklLkrvkkalpagGkvivveavlgadp 173
                                       +i  +   h w+d + +  +k + + l ++G  +++e + +  +
  gi|518651754|ref|YP_008141274.1| 112 LIYTTLSFHHWQDRDSN--IKYILSKLADNGTFLIIEFMQDYYK 153
                                       ************99865..6777788899********9977554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0     2e-07   0.00019     155     230 ..      36     113 ..      31     117 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                              PrmA 155 lekl.vkegeevlDvGtGSGiLai.aaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadv 229
                                       l+++   e +++lD+G+G G L++ +++k+ ++k +a+D     vk+ ++N+e+ +++a+++   s++++ ++k+d+
  gi|518651754|ref|YP_008141274.1|  36 LDEMkDMEPSSILDIGAGPGKLSLmVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSRDIPFDNKFDL 112
                                       55551345579************736789******************************999888999998899999 PP

                              PrmA 230 i 230
                                       i
  gi|518651754|ref|YP_008141274.1| 113 I 113
                                       8 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.2e-06    0.0021      90     137 ..      39      87 ..      26      97 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.2e-06
                              DREV  90 asdqedkklldlGaGdGeitkrvaptfee..vyatelsetmrdrlkkkky 137
                                         d+e+  +ld+GaG G+++ +v++ f +   +a + s +m +   +k++
  gi|518651754|ref|YP_008141274.1|  39 MKDMEPSSILDIGAGPGKLSLMVSQKFPHakFFAIDPSLNMVKAE-QKNF 87 
                                       568899*********************98779********98654.4455 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.3e-06     0.006       4      49 ..      46      91 ..      43      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-06
                                      EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCT CS
                    Methyltransf_4  4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkieale 49
                                       +l+iG G G++ +  ++k+P+ +f++i+ + ++v++  k+ e+ +
  gi|518651754|ref|YP_008141274.1| 46 SILDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAG 91
                                      689****************************999998887777665 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.8e-06    0.0074      22     137 ..      35     149 ..      18     190 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.8e-06
                                       HHHHCCCS-S-EEEEES-TTSHHHHHHHHTT..-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-E CS
                              TehB  22 vveavkivkpgkvldlgcgqgrnslylsllg..ydvtawdknensiafleeikekenlknistalydineakldery 96 
                                        ++ +k ++p+ +ld+g g g+ sl +s +    +  a+d   n ++  ++  ek  +k  s++     ++ +d+++
  gi|518651754|ref|YP_008141274.1|  35 ALDEMKDMEPSSILDIGAGPGKLSLMVSQKFphAKFFAIDPSLNMVKAEQKNFEKAGIK-ASCKPGSSRDIPFDNKF 110
                                       56788999******************997641134557777777777777777777766.5566667888999**** PP

                                       EEEEEESSGGGS-GGGHHHHHHHHHHTEEEEEEEEEEEEB- CS
                              TehB  97 dfilstvvlmfleaeripsiienmqectkvggynlivaams 137
                                       d+i +t+ +   + +  ++ i+ +  +    g  li+  m+
  gi|518651754|ref|YP_008141274.1| 111 DLIYTTLSFHHWQDRD-SN-IKYILSKLADNGTFLIIEFMQ 149
                                       ******9988776542.33.333333333444456666664 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.016      61     164 ..      42     144 ..      29     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                       -TT-EEEEES-TTSHHHHHHHHHH.--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES- CS
                              CMAS  61 kpGmtlLdiGcGWGslvrravery.dvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvga 136
                                        + + +LdiG+G G+l     +++  +k +++  S +  k  +k++++++++ + +   +    +d+k+d + +   
  gi|518651754|ref|YP_008141274.1|  42 MEPSSILDIGAGPGKLSLMVSQKFpHAKFFAIDPSLNMVKAEQKNFEKAGIKASCKPGSSRDIPFDNKFDLIYTTLS 118
                                       455789*****************9679***********************99999988888888999*****99999 PP

                                       GGGTSGGGHHHHHHHHHHHS-TT-EEEE CS
                              CMAS 137 fehvgkenydtffkklkkllkedGllll 164
                                       f h   +  d  +k + ++l ++G++l+
  gi|518651754|ref|YP_008141274.1| 119 FHHWQDR--DSNIKYILSKLADNGTFLI 144
                                       9998655..4556667777777777766 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.7e-05     0.016      53     163 ..      41     148 ..      25     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
                   Methyltransf_PK  53 krevkvaldcGaGiGrvtknlLlkll.skvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWi 128
                                         e + +ld+GaG G+++  +  k+  +k   ++p  +++++ ++++ +    ++     g     P ++++dli++
  gi|518651754|ref|YP_008141274.1|  41 DMEPSSILDIGAGPGKLSLMVSQKFPhAKFFAIDPSLNMVKAEQKNFEK--AGIKASCKPGSSRDIPFDNKFDLIYT 115
                                       4566789**********9888777644788889*********9999866..88888999999999************ PP

                   Methyltransf_PK 129 qWcvghLtDedlvaflkrckkalkpnGlivvkenv 163
                                            h  D d  + +k   + l++nG++ + e +
  gi|518651754|ref|YP_008141274.1| 116 TLSFHHWQDRD--SNIKYILSKLADNGTFLIIEFM 148
                                       *********98..56677789999***99998765 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     7e-05     0.066      28      77 ..      37      85 ..      21     147 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7e-05
                             Rsm22 28 ervpdflPkslldvgegpgtalwaaselweeleevlvidaseelleiske 77
                                      + ++d  P s+ld+g+gpg   + +s+ +++  +   id s ++ +  ++
  gi|518651754|ref|YP_008141274.1| 37 DEMKDMEPSSILDIGAGPGKLSLMVSQKFPHA-KFFAIDPSLNMVKAEQK 85
                                      5678999**********************986.46788888877765554 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0    0.0001     0.097      24      57 ..      36      79 ..       6     152 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.0001
                                      E..........EEECT-TTSHHHHHHCCT.T.-SEEEEEES.SSS CS
                              FtsJ 24 t..........vvDlgaaPGgwsqvllqrlgakgkvvavDl.qpm 57
                                                 ++D+ga+PG  s +++q++ + +k +a+D   +m
  gi|518651754|ref|YP_008141274.1| 36 LdemkdmepssILDIGAGPGKLSLMVSQKFPH-AKFFAIDPsLNM 79
                                      02223344444******************986.9******85555 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00011       0.1      21      78 ..      39      92 ..      23     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                   Methyltransf_32 21 akesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklgkkf 78
                                      +k+ ++ +++D+GaG g Ls ++++   +  + k+++id + ++v++ +k  ek g  +
  gi|518651754|ref|YP_008141274.1| 39 MKDMEPSSILDIGAGPGKLSLMVSQ---KfPHAKFFAIDPSLNMVKAEQKNFEKAG--I 92
                                      45677899****************9...547899*****99999999999888887..4 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00055      0.52       8      69 ..      43     102 ..      37     114 .. 0.81
   2 ?   -0.5   0.0      0.89   8.4e+02     134     159 ..     112     138 ..     108     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00055
                                       TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CT CS
                   Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDar 69 
                                       e   ilD+ a+PG K +++     ++++ +A+d + + +k+ ++n ++ g++ + +  +  r
  gi|518651754|ref|YP_008141274.1|  43 EPSSILDIGAGPG-KLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIK-ASCKPGSSR 102
                                       4567********7.888888888999*********************99998.666655555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.89
                                       EEEEES--ST.TTTHHHHHHHHHH-TT CS
                   Methyltr_RsmB-F 134 lvYsTCsvlv.eEneevieeaLkkred 159
                                       l+Y+T s +  ++    i+++L+k +d
  gi|518651754|ref|YP_008141274.1| 112 LIYTTLSFHHwQDRDSNIKYILSKLAD 138
                                       899999987526667899999998766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00027      0.26      15      67 ..      44      96 ..      36     103 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00027
                   Methyltransf_18 15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledki 67
                                       s+++DiG+  g l++++ ++    k  a+D + + +++ ++n ekag++ ++
  gi|518651754|ref|YP_008141274.1| 44 PSSILDIGAGPGKLSLMVSQKFPHAKFFAIDPSLNMVKAEQKNFEKAGIKASC 96
                                      4789******************************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1351.55
//
Query:       gi|518651755|ref|YP_008141275.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G0394 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 457.99
//
Query:       gi|518651756|ref|YP_008141276.1|  [L=174]
Description: hypothetical protein FACI_IFERC00001G0395 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-10   41.1   0.0    5.6e-10   39.8   0.0    1.5  1  NTP_transf_3     MobA-like NTP transferase domain
    0.00023   20.8   0.7     0.0057   16.3   0.2    2.2  2  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.035   13.8   0.0      0.049   13.4   0.0    1.3  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.8   0.0   9.4e-14   5.6e-10       1     120 [.      10     122 ..      10     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.8 bits;  conditional E-value: 9.4e-14
                                       EEEEEESS-TTTTT.THHHHCCCCCCHHHHHHHHHCTT.-CEEEEE.CSHCHHHHHHTTCTS-EEE-TTSS-SHHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.dKallplggkpllervldalraagvdevvvv.ggdeevlaalarlgvrvvededpgkgplas 75 
                                       avi+AGG++sRmg+ +K ll+++g+ +++ +++ l+ ++++ + ++  ++   l      g++ ++    +   +  
  gi|518651756|ref|YP_008141276.1|  10 AVIMAGGKGSRMGTaEKMLLKINGEKVIDAIIKILQNLNFN-ISLCiSENTRFL-----DGYHSLRTIMGQGDYALD 80 
                                       79***********99***********************984.444403444444.....578888887777889999 PP

                                       HHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEE CS
                      NTP_transf_3  76 laaalraaadadavlvlacDmPlltpelverllaaaaasgadvvv 120
                                       l  a++ +  + +vl+++ D+  +tp++++ ++ +a + + +++ 
  gi|518651756|ref|YP_008141276.1|  81 LNYAIKTC--SLPVLIVPSDV-IITPDMIHDFVTSASSLDTAIAT 122
                                       99999998..699*******9.57*********999776666655 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   9.6e-07    0.0057       2      56 ..      10      59 ..       9      88 .. 0.86
   2 !    3.4   0.0    0.0083        49     105     134 ..      91     122 ..      77     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.6e-07
                                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETT CS
                   NTP_transferase  2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqe 56
                                      avI+aGG+G+R+      +a k++++ ++e++i+a ++ l n +++  ++++ + 
  gi|518651756|ref|YP_008141276.1| 10 AVIMAGGKGSRM-----GTAEKMLLKINGEKVIDAIIKILQNLNFNISLCISENT 59
                                      8**********7.....7999************************9988887654 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0083
                                       EEEEETTEEEEST.THHHHHHHHHTHSSTT.S CS
                   NTP_transferase 105 lvlvLggDhlikd.ayeeavkkaiekaakg.t 134
                                        vl++++D++i+   + ++v++a + + ++ t
  gi|518651756|ref|YP_008141276.1|  91 PVLIVPSDVIITPdMIHDFVTSASSLDTAIaT 122
                                       689*********97889999999999885433 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 ?   13.4   0.0   8.2e-06     0.049       2      40 ..       9      46 ..       8      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-06
                                      EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHC CS
                              IspD  2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdalla 40
                                       +vi A G+G+Rm++  +K++l+++g+ ++   ++ l++
  gi|518651756|ref|YP_008141276.1|  9 DAVIMAGGKGSRMGT-AEKMLLKINGEKVIDAIIKILQN 46
                                      68***********98.579***********998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1200.87
//
Query:       gi|518651757|ref|YP_008141277.1|  [L=397]
Description: hypothetical protein FACI_IFERC00001G0396 [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   43.0   0.0    8.5e-11   42.1   0.0    1.6  1  HD        HD domain
    0.00089   18.8   0.0     0.0016   17.9   0.0    1.3  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   0.0   9.5e-15   8.5e-11       1      67 [.      71     145 ..      71     192 .. 0.68

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 9.5e-15
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH........HHH..CTCCHHHHHHHHHHH CS
                                HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk........eee..fekflaHekvgaeil 67 
                                       r+eHs++ + +a +l e+lg   + e+  +aaLlHDiG++pf+++ e+         +e+  ++ +l+   +g + +
  gi|518651757|ref|YP_008141277.1|  71 RFEHSVGAMFMAHELSESLG--VKDEIPAIAALLHDIGHMPFSHGLENEfyglygkvHEDmtKDVILGKGPYGDSTI 145
                                       79******************..**********************888877665554422234444444444444444 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.8e-07    0.0016      96     152 ..      72     127 ..      66     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
                                       HHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHH CS
                              HDOD  96 wehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsllpeeleellekvae 152
                                        ehs+   ++a el e+lg +d e   +a+LLhdiG + + + l++e+  l  kv+e
  gi|518651757|ref|YP_008141277.1|  72 FEHSVGAMFMAHELSESLGVKD-EIPAIAALLHDIGHMPFSHGLENEFYGLYGKVHE 127
                                       58********************.********************99999877766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2819.66
//
Query:       gi|518651758|ref|YP_008141278.1|  [L=243]
Description: hypothetical protein FACI_IFERC00001G0397 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1649.75
//
Query:       gi|518651759|ref|YP_008141279.1|  [L=890]
Description: hypothetical protein FACI_IFERC00001G0398 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   95.9   8.0    3.1e-27   95.9   8.0    3.5  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    2.2e-20   73.5   0.0      5e-20   72.3   0.0    1.6  1  AAA_19           AAA domain
    9.5e-20   71.3   0.3    9.5e-20   71.3   0.3    4.1  3  UvrD_C           UvrD-like helicase C-terminal domain
    9.8e-08   32.2   0.1      3e-07   30.6   0.1    1.8  1  PDDEXK_1         PD-(D/E)XK nuclease superfamily
      3e-07   30.2   0.0     0.0066   16.2   0.0    2.5  2  UvrD_C_2         UvrD-like helicase C-terminal domain
    5.5e-06   26.1   8.6       0.21   11.2   0.2    4.8  4  AAA_12           AAA domain
    1.3e-05   25.1   0.4       0.87    9.3   0.0    3.9  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    4.7e-05   23.3   0.0      0.023   14.5   0.0    3.0  3  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.019   15.4   4.4       0.11   12.9   0.0    3.4  4  AAA              ATPase family associated with various cellul
      0.022   14.5   0.0       0.27   10.9   0.0    2.2  2  AAA_30           AAA domain
      0.025   14.7   2.2      0.029   14.5   0.2    2.2  2  Cas_Cas4         Domain of unknown function DUF83
      0.045   13.7   2.0        1.3    8.9   0.2    2.8  2  Phage_hub_GP28   Baseplate hub distal subunit
       0.19   11.0   0.5       0.34   10.1   0.5    1.3  1  DUF2800          Protein of unknown function (DUF2800)
       0.28   11.2  12.5       0.51   10.4   0.8    4.0  4  AAA_14           AAA domain


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.9   8.0   2.4e-30   3.1e-27      13     309 ..       3     261 ..       1     265 [. 0.75
   2 ?   -2.3   3.1       1.9   2.4e+03     186     186 ..     771     771 ..     543     889 .. 0.59

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 2.4e-30
                                       SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHHHHHC CS
                     UvrD-helicase  13 ggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnl 89 
                                       + ++lv++ +G+GKT+ + + +++like+ ++p++il++TFTn A  El++ i ++l  ++           +  ++
  gi|518651759|ref|YP_008141279.1|   3 NRDTLVISNPGTGKTTMISNEVINLIKEG-VKPEKILCITFTNNAVGELQKSIDKLLIDNK----------IKNVTA 68 
                                       6789*************************.*************************998875..........355788 PP

                                       TTSEEEEHHHHHHHHHHHHHGGTT....SHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHH CS
                     UvrD-helicase  90 seanisTlHsfcqkilkkeanrig....ldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikels 162
                                        ++ni+T+H+++ + l +   + +       ++ i+++        +e+++   e        + ++ + kl   + 
  gi|518651759|ref|YP_008141279.1|  69 YDVNIYTFHALAFQELFQSKAEKNivsyNIARYLIYKKLR-----DLEAFNYGRE-------YVIEDIVPKLENAIR 133
                                       9************999999998885555333333333333.....4444444443.......222222222222112 PP

                                       CCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHH CS
                     UvrD-helicase 163 ksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenalDfsdllhal 239
                                         + + +   + +k+  + ++ l +k+ ++ +++  l++       +++ +  f++ +  + +++++ Df+dll ++
  gi|518651759|ref|YP_008141279.1| 134 YIKSFGIMPVDIAKNRDIIMESLRKKYNSGIVRNIGLEE-------EEYLFDYFYQAFNYYEENKENPDFNDLLFQF 203
                                       222233444455555556666666666666666666665.......778888899999999999999********99 PP

                                       HHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEEEE-GGG--GGGGTB-THHHHH CS
                     UvrD-helicase 240 lelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfmvGDpkQsIYgFRgAdielflk 309
                                        + le+        ++ y+++++DE QD n i  ri     +g+   f+vGD kQsI+gF+g+ +++f++
  gi|518651759|ref|YP_008141279.1| 204 QK-LED--------KKTYEYVFVDELQDVNDIESRIAMS--TGN-VKFLVGDRKQSIFGFQGGALSVFNS 261
                                       99.565........589*****************99754..444.46******************99987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.9
                                       H CS
                     UvrD-helicase 186 v 186
                                       +
  gi|518651759|ref|YP_008141279.1| 771 F 771
                                       0 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.0   3.9e-23     5e-20      13     145 ..       6     251 ..       2     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 3.9e-23
                            AAA_19  13 llvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae............atTiHrlal 77 
                                        lv+  pGtGKT+++   v  l+++g vkpe+il+++ft+ A+ el++++++l+ +            ++T+H+la+
  gi|518651759|ref|YP_008141279.1|   6 TLVISNPGTGKTTMISNEVINLIKEG-VKPEKILCITFTNNAVGELQKSIDKLLIDnkiknvtaydvnIYTFHALAF 81 
                                       6899********************99.889********************99999999******************9 PP

                            AAA_19  78 ............................................................................. 77 
                                                                                                                    
  gi|518651759|ref|YP_008141279.1|  82 qelfqskaeknivsyniaryliykklrdleafnygreyviedivpklenairyiksfgimpvdiaknrdiimeslrk 158
                                       ***************************************************************************** PP

                            AAA_19  78 ...................................ldfddlltealelleeaeeekklqeeellivDEfqdvdelqy 119
                                                                           df+dll   +++  ++ e+kk    e+++vDE qdv++ + 
  gi|518651759|ref|YP_008141279.1| 159 kynsgivrnigleeeeylfdyfyqafnyyeenkenPDFNDLL---FQF--QKLEDKKT--YEYVFVDELQDVNDIES 228
                                       *************************99988776666666666...333..32233333..45*************** PP

                            AAA_19 120 rLlkallgekkklllvGDpdQliyvf 145
                                       r+      + k  +lvGD++Q+i+ f
  gi|518651759|ref|YP_008141279.1| 229 RIAMSTG-NVK--FLVGDRKQSIFGF 251
                                       *977666.556..9*********998 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   1.6      0.27   3.4e+02     177     267 ..      81     203 ..      17     234 .. 0.70
   2 !   71.3   0.3   7.4e-23   9.5e-20       3     347 ..     273     586 ..     272     588 .. 0.75
   3 ?   -4.1   3.8         6   7.7e+03     273     273 ..     750     750 ..     618     889 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.27
                                       xxxxxxxxxxxxx........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 177 Fieliraleeknl........................elllkkiektaeerqalvskyadlfkelaeklaelkekse 229
                                       F el+++  ekn+                        e++++ i ++ e++ +++++++     +a++   + e   
  gi|518651759|ref|YP_008141279.1|  81 FQELFQSKAEKNIvsyniaryliykklrdleafnygrEYVIEDIVPKLENAIRYIKSFGIMPVDIAKNRDIIMESLR 157
                                       55555555555557777777777777788888888877788888888887777666666666666666555544444 PP

                                       xxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 230 skr........kkeeklenlreLysllkelekkeeeeeveeklnei 267
                                       +k           ee+++  + +y++++++e+++e+++ ++ l ++
  gi|518651759|ref|YP_008141279.1| 158 KKYnsgivrniGLEEEEYLFDYFYQAFNYYEENKENPDFNDLLFQF 203
                                       4445666766633346777888999999999999998887766555 PP

  == domain 2  score: 71.3 bits;  conditional E-value: 7.4e-23
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C   3 LekNyRStksLlkaankflenilnr.ralekek..ktvekgekivvleaeteeeEaekiaatikalleknekledia 76 
                                       L++NyRSt+++l  ++++  ++ n+ ++le  +   t+++g+k+++ e ++ ee    i + i           +i 
  gi|518651759|ref|YP_008141279.1| 273 LKINYRSTETILAYSKQYYLKFENDvPELE--NfrGTNKNGNKVKIVEVDSPEESVMEIINSIPVSS------GNIG 341
                                       89*****************99988855555..4559**************99987766666666555......**** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C  77 vLvRsnkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatverise 153
                                       ++ R+n+++d+is  L +  i +   d++     +  kdi a+lk ++ ++ + +++ ++ +++ gi+ + + +i e
  gi|518651759|ref|YP_008141279.1| 342 IIARTNSQIDTISSLLDRYSIDYS-SDSNVHTINQAKKDITAFLKGILYDRPDDIINAMV-TPFSGISLKEAFKIAE 416
                                       ************************.666667778889********888777777777654.6888999888888833 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 154 elkklglsltDfikedtleygeeFieliraleeknlelllkkiektaeerqalvskyadlfkelaeklaelkekses 230
                                       +l+    +  D+++++     ++F     +l +k+              r++++  ++    ++a+ + +    +  
  gi|518651759|ref|YP_008141279.1| 417 SLR-SEENTIDLFDSS-----NPFF----SLRNKE------------LSRENIMDLFESRIFPIASSISREYFLTAA 471
                                       333.223333443333.....3555....333333............447777888888888888777654444433 PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 231 krkkeeklenlreLysllkelekkeeeeeveeklneileiatLseseleeskkkekipiiTiHqAKGlEFdvVflag 307
                                             k + + e++++ +++ +           +++     Ls se+ + + +++i ++T+H+AKG EFd+V+ + 
  gi|518651759|ref|YP_008141279.1| 472 TV----K-SSIGEFFDAERDYTR-----------KNFFDFLDLSYSENSSKSGNSRIILTTVHKAKGREFDNVIYLP 532
                                       33....3.678888888888888...........57888888889999888888********************999 PP

                                       xxxxxxx............xxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            UvrD_C 308 leegtfP............syrskk..........ekrleEEkRlfYVaiTRAkkrLfisys 347
                                           + P            s                +  +E  R+ +Va TRAk++L++ ++
  gi|518651759|ref|YP_008141279.1| 533 ----KKPrksdtyidiivsS----IieeikrinvdDELKNESVRIDFVAFTRAKEELWVCTN 586
                                       ....6775555556666650....0444556666466678999***************9865 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 6
                                       x RF
                            UvrD_C 273 L 273
                                       +
  gi|518651759|ref|YP_008141279.1| 750 M 750
                                       2 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 !   30.6   0.1   2.4e-10     3e-07      37     227 ..     690     857 ..     670     875 .. 0.60

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 2.4e-10
                          PDDEXK_1  37 GtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaekl.kevleklverlaeeleakr 112
                                       G   H+++e +y+                           +ei       + l + + k++l++  e +    + k 
  gi|518651759|ref|YP_008141279.1| 690 GLNAHEMAESLYK---------------------------NEI------KNELLGNVdKQILSNI-ESVVN--QIKS 730
                                       4444444444444...........................222......2222222212222222.33333..4555 PP

                          PDDEXK_1 113 gfrpvalelefg..............g.ekvrLkGriDrvddkegelriiDyKtgsappkskelaelkeglQlllYl 174
                                       gf ++++e+e++              +   + + G+iD v +++++++i+DyKt ++    ++     +++Qll+Y 
  gi|518651759|ref|YP_008141279.1| 731 GFNMEQIEAEVSaiarinqmfeefsgQpDNIMFFGKIDAVFSDGKKYVILDYKTDKTI---EK--ASHHRVQLLAYK 802
                                       5555555544444455555555666633668899******977778*******98844...33..446889****** PP

                          PDDEXK_1 175 lalaegeelkeegepagalylrleepkvkdeevvkkmalteeel..eallqelee 227
                                        ++  +++ ++e+ +  + y++++ +  ++e++   ++ +++++  ++l++++++
  gi|518651759|ref|YP_008141279.1| 803 ILYSIKNNINPENIDTAIGYISMRGKINTHENTSGLIYKQPDKRseDSLKKYISK 857
                                       ****994444444499999999976655555555555555555566666666665 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   5.2e-06    0.0066       4      19 ..     514     529 ..     512     537 .. 0.90
   2 !   11.2   0.0    0.0002      0.25      33      52 .]     565     584 ..     557     584 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5.2e-06
                          UvrD_C_2   4 altihkaQGsefpaVi 19 
                                        +t+hka+G ef++Vi
  gi|518651759|ref|YP_008141279.1| 514 LTTVHKAKGREFDNVI 529
                                       68*************9 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.0002
                          UvrD_C_2  33 lrrrlLYtavTRAreklilv 52 
                                       ++ r+ ++a+TRA+e+l+++
  gi|518651759|ref|YP_008141279.1| 565 ESVRIDFVAFTRAKEELWVC 584
                                       467888************96 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.27   3.4e+02      94     142 ..      19      65 ..      12      87 .. 0.79
   2 ?    4.6   0.0     0.018        23       4      38 ..     257     291 ..     255     303 .. 0.86
   3 !   10.5   0.2   0.00027      0.35      83     150 ..     310     375 ..     297     378 .. 0.82
   4 !   11.2   0.2   0.00017      0.21     129     198 ..     498     587 ..     480     588 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.27
                            AAA_12  94 lvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke 142
                                       ++ + v +l+k+g++   +ki  it+ ++ v  l+k +++   +++ k+
  gi|518651759|ref|YP_008141279.1|  19 MISNEVINLIKEGVKP--EKILCITFTNNAVGELQKSIDKLLIDNKIKN 65 
                                       5666777889999988..9******************998666665555 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.018
                            AAA_12   4 SlferllkkekekvvlLdtqYRmhpeIsrfpsklf 38 
                                       S+f+ l+ +   +++ L+++YR+ ++I+ ++++++
  gi|518651759|ref|YP_008141279.1| 257 SVFNSLIGNSGIEKKDLKINYRSTETILAYSKQYY 291
                                       7899999988889999*************987765 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00027
                            AAA_12  83 eksyiNeeEaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeeksekeievntvdg 150
                                       + +++   E++   + v +++++++ +   +ig+i+  ++q++++++ l++ + +  +++ +v+t+++
  gi|518651759|ref|YP_008141279.1| 310 NGNKVKIVEVDSPEESVMEIINSIPVS-SGNIGIIARTNSQIDTISSLLDRYSID-YSSDSNVHTINQ 375
                                       46777888999999999*********9.8*********************76555.556789999876 PP

  == domain 4  score: 11.2 bits;  conditional E-value: 0.00017
                            AAA_12 129 kklkekeeeksekeievntvdgfQGrekdviilslVRsnekk...................eigflkderrlN.Val 185
                                          +e+++++ +++i   tv +  Gre d +i+   + +++                    +  + +++ r+  Va+
  gi|518651759|ref|YP_008141279.1| 498 LSYSENSSKSGNSRIILTTVHKAKGREFDNVIYLPKKPRKSDtyidiivssiieeikrinvDDELKNESVRIDfVAF 574
                                       45556666666777999**************99877765444567777666666666665433356666666459** PP

                            AAA_12 186 TRAkskliivGnk 198
                                       TRAk++l++  n+
  gi|518651759|ref|YP_008141279.1| 575 TRAKEELWVCTNR 587
                                       *********9886 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.037        47       3      30 ..       8      34 ..       6      67 .. 0.69
   2 !    7.3   0.0    0.0027       3.4      47     102 ..     197     249 ..     174     324 .. 0.83
   3 !    9.3   0.0   0.00068      0.87     116     233 ..     437     584 ..     427     585 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.037
                   Viral_helicase1  3 vhGvpGcGKStlirkllrtsliltvnrp 30
                                      v   pG GK+t+i + + + li   ++p
  gi|518651759|ref|YP_008141279.1|  8 VISNPGTGKTTMISNEVIN-LIKEGVKP 34
                                      55669********987766.44444444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0027
                   Viral_helicase1  47 vrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvilfGDplQipf 102
                                       +  + +f++   k ++++++++DE + ++   i+  +a+s+  + +l+GD++Q+ f
  gi|518651759|ref|YP_008141279.1| 197 NDLLFQFQKLEDK-KTYEYVFVDELQDVND--IESRIAMSTGNVKFLVGDRKQSIF 249
                                       5555667776655.58*************6..9997788888999********855 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00068
                   Viral_helicase1 116 sslshrvgrrttyllpsdvaeilsak....vgteveversgel....kvetepkgq.e.kvlvyltftqalkealgv 182
                                        +  ++++ ++++l+ s  ++i s+     ++t  +v++s+      +++++ k   +  +l y++ + +  +   +
  gi|518651759|ref|YP_008141279.1| 437 LRNKELSRENIMDLFESRIFPIASSIsreyFLTAATVKSSIGEffdaERDYTRKNFfDfLDLSYSENSSKSGN---S 510
                                       5555666666677777777777776666666666666666666444433455554433445555555554444...3 PP

                   Viral_helicase1 183 r.evttvhevqGltfdkVtlvllketdlelis......................esrenllvAlTRhrkslvil 233
                                       r   ttvh + G +fd+V+ + +k+ + +++                       es    +vA+TR++++l ++
  gi|518651759|ref|YP_008141279.1| 511 RiILTTVHKAKGREFDNVIYLPKKPRKSDTYIdiivssiieeikrinvddelknESVRIDFVAFTRAKEELWVC 584
                                       34469**************9999888777666777788888888888888875433444478888888887766 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.8e-05     0.023      20      83 ..       6      63 ..       1     130 [. 0.79
   2 ?    5.1   0.0     0.013        17     211     253 ..     206     246 ..     200     246 .. 0.84
   3 ?   -2.2   0.0       2.3   2.9e+03     195     213 ..     509     527 ..     500     529 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.8e-05
                            AAA_11 20 tliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllrglldseg 83
                                      tl+   PGtgKT++i   + +l       +e+ ++++iL  + +N+Av el + + + l+d++ 
  gi|518651759|ref|YP_008141279.1|  6 TLVISNPGTGKTTMISNEVINL------IKEGVKPEKILCITFTNNAVGELQKSIDKLLIDNKI 63
                                      6777788********9766666......2589******************99887774444443 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.013
                            AAA_11 211 leklakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQ 253
                                       le+ +  +++v +DE      +++ i+++ g +   LvGD kQ
  gi|518651759|ref|YP_008141279.1| 206 LEDKK-TYEYVFVDELQDVNDIESRIAMSTG-NVKFLVGDRKQ 246
                                       34443.89***********************.5557******9 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 2.3
                            AAA_11 195 eaeivltTlsgagskllek 213
                                       +++i+ltT+++a+ +++++
  gi|518651759|ref|YP_008141279.1| 509 NSRIILTTVHKAKGREFDN 527
                                       679*********9988876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     9e-05      0.11       2      54 ..       7      62 ..       6      84 .. 0.84
   2 ?   -3.4   0.1       9.6   1.2e+04      50      71 ..     203     224 ..     198     232 .. 0.72
   3 ?   -1.8   0.0         3   3.9e+03      89     123 ..     326     359 ..     302     365 .. 0.69
   4 ?    2.3   0.1      0.17   2.2e+02      43      74 ..     744     774 ..     713     797 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9e-05
                                      EEESSTTSSHHHHHH.HHHHHH..THEEEEEETTTCSSSSTTHHHHHHHHHHHHHH CS
                               AAA  2 llyGppGtGKTllak.avakel..gvefleisgsellskyvgesekkirelfkeak 54
                                      l++ +pGtGKT++++  v++ +  gv+  +i + +++++ vge +k+i +l+ + k
  gi|518651759|ref|YP_008141279.1|  7 LVISNPGTGKTTMISnEVINLIkeGVKPEKILCITFTNNAVGELQKSIDKLLIDNK 62
                                      78899*****998862677777545999********************99987655 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 9.6
                                       HHHHHHTSTSEEEEEETGGGHH CS
                               AAA  50 fkeakekakpsilfiDEidala 71 
                                       f++++ k++   +f+DE+  ++
  gi|518651759|ref|YP_008141279.1| 203 FQKLEDKKTYEYVFVDELQDVN 224
                                       5666666544889999998765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3
                                       HHHHHHHTTTSSSTEEEEEEESS.GGGSTHHHHSTT CS
                               AAA  89 Llteldgvkkkeskvivigatnr.pdkldpallrgR 123
                                        ++ ++    +++++ +i+ tn+ +d++++ l   R
  gi|518651759|ref|YP_008141279.1| 326 VMEIINSIPVSSGNIGIIARTNSqIDTISSLLD--R 359
                                       455555555566789999999996666666554..4 PP

  == domain 4  score: 2.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHH CS
                               AAA  43 ekkirelfkeakekakp.silfiDEidalaksr 74 
                                        ++i+++f+e +  + p  i+f+  ida++++ 
  gi|518651759|ref|YP_008141279.1| 744 IARINQMFEEFS-GQ-PdNIMFFGKIDAVFSDG 774
                                       468999999864.44.66***********9876 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00021      0.27      22      67 ..       7      55 ..       3      93 .. 0.80
   2 ?    0.7   0.0      0.29   3.7e+02     111     159 ..     230     281 ..     196     311 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                            AAA_30 22 vltGpAGtGKttalkalreaweaag...grviglAptgkaAkvLaeelg 67
                                      ++   +GtGKtt+++  +  + ++g   ++++ ++ t++a  +L+++++
  gi|518651759|ref|YP_008141279.1|  7 LVISNPGTGKTTMISNEVINLIKEGvkpEKILCITFTNNAVGELQKSID 55
                                      67788*********8765444445555799**************98765 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                            AAA_30 111 aaekagakvilvGDerQlasVeaGg...vlrdlveaagigtaeLtevvRqke 159
                                       +a ++g    lvGD++Q     +Gg   v+++l+ ++gi+   L+ ++R +e
  gi|518651759|ref|YP_008141279.1| 230 IAMSTGNVKFLVGDRKQSIFGFQGGalsVFNSLIGNSGIEKKDLKINYRSTE 281
                                       34445666789*****987666676122455666668888888888888865 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 ?   -2.9   0.1       5.1   6.5e+03      47      62 ..     560     576 ..     546     589 .. 0.57
   2 ?   14.5   0.2   2.3e-05     0.029      21     100 ..     731     813 ..     724     866 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5.1
                          Cas_Cas4  47 kevelsesikiDvve..k 62 
                                        e++  es++iD+v   +
  gi|518651759|ref|YP_008141279.1| 560 DELKN-ESVRIDFVAftR 576
                                       33333.589999998532 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 2.3e-05
                          Cas_Cas4  21 eitleensetvelGkllhe..esyerekkevelsesikiDvvekekeklvvvEvKkskkkeeaa..klQllyYlllL 93 
                                       ++++e+ + +v++   +++  e+++ +  ++ +   +kiD v ++++k v+ ++K  k +e+a+  ++Qll+Y +l 
  gi|518651759|ref|YP_008141279.1| 731 GFNMEQIEAEVSAIARINQmfEEFSGQPDNIMF--FGKIDAVFSDGKKYVILDYKTDKTIEKAShhRVQLLAYKILY 805
                                       556666666666444444422222233366777..89******9************9999887667*******8877 PP

                          Cas_Cas4  94 e.kkgvei 100
                                         k++++ 
  gi|518651759|ref|YP_008141279.1| 806 SiKNNINP 813
                                       77777764 PP

>> Phage_hub_GP28  Baseplate hub distal subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2     0.001       1.3      23      74 ..      56     107 ..      45     125 .. 0.88
   2 ?    3.2   0.1     0.059        76      25      75 ..     803     852 ..     780     880 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                    Phage_hub_GP28  23 kllidsicpnlspaevdfvsihllefngkiksrkeidgytydindvyvcqrl 74 
                                       kllid+ + n++  +v++ + h l f+   +s+ e +  +y+i    + ++l
  gi|518651759|ref|YP_008141279.1|  56 KLLIDNKIKNVTAYDVNIYTFHALAFQELFQSKAEKNIVSYNIARYLIYKKL 107
                                       9********************************9999999999887776665 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.059
                    Phage_hub_GP28  25 lidsicpnlspaevdfvsihllefngkiksrkeidgytydindvyvcqrle 75 
                                       ++ si  n++p ++d  +i  + + gki+++++  g  y   d    + l+
  gi|518651759|ref|YP_008141279.1| 803 ILYSIKNNINPENIDT-AIGYISMRGKINTHENTSGLIYKQPDKRSEDSLK 852
                                       457999********95.7999****************99887765555554 PP

>> DUF2800  Protein of unknown function (DUF2800)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.5   0.00027      0.34      29     151 ..     683     801 ..     677     805 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00027
                           DUF2800  29 sSeyAeeGtlaHelaelklrkaldakekkgvkselkkkeeevteemeeavdey.vdfvlekieeakkdalvlvEqrv 104
                                       ++++   G  aHe+ae + +++++++   +v++       ++ +++e+ v++    f +e+ie+ +  a+  + q  
  gi|518651759|ref|YP_008141279.1| 683 KTDALYYGLNAHEMAESLYKNEIKNELLGNVDK-------QILSNIESVVNQIkSGFNMEQIEA-EVSAIARINQMF 751
                                       566666788999999999999999999999994.......556666666666513577888775.468999999987 PP

                           DUF2800 105 dfskyvpe...gfGtaDvviiaddvLeviDlKyGkgvkVsaekNpQlalY 151
                                       +  +  p+    fG  D+v   +++  + D+K  k ++   ++  Ql +Y
  gi|518651759|ref|YP_008141279.1| 752 EEFSGQPDnimFFGKIDAVFSDGKKYVILDYKTDKTIEKASHHRVQLLAY 801
                                       655555558999***********************************999 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.4    0.0044       5.7      13      57 ..      14      59 ..      12     152 .. 0.88
   2 ?   10.4   0.8    0.0004      0.51      32      83 ..     178     230 ..     162     241 .. 0.71
   3 ?   -2.5   0.1       3.9     5e+03      19      44 ..     645     671 ..     643     711 .. 0.63
   4 ?   -3.2   0.0       6.4   8.2e+03      62      71 ..     769     781 ..     729     781 .. 0.53

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0044
                            AAA_14 13 vGKTtllkqlikell...vkkesilyinldderdkkladpekllelil 57
                                      +GKTt++ + + +l+   vk+e+il i++ ++   +l+++  +++l+ 
  gi|518651759|ref|YP_008141279.1| 14 TGKTTMISNEVINLIkegVKPEKILCITFTNNAVGELQKS--IDKLLI 59
                                      7******9998899899**************998766654..344333 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.0004
                            AAA_14  32 silyinldderdkkla.dpekllelileklkeekktylflDEiqevpewekal 83 
                                       +++y +++  ++ k++ d+++ll  ++++  ++  +y+f DE q v+++e+ +
  gi|518651759|ref|YP_008141279.1| 178 DYFYQAFNYYEENKENpDFNDLLFQFQKLEDKKTYEYVFVDELQDVNDIESRI 230
                                       5667777776664443255566666666533356678**********999765 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.9
                            AAA_14  19 lkqlikellvkkesilyinldderd..k 44 
                                       lk++i+e + +++++l ++l + ++   
  gi|518651759|ref|YP_008141279.1| 645 LKNIIYEFF-QNKNVLSFSLISIENpfF 671
                                       567777776.777788877777666331 PP

  == domain 4  score: -3.2 bits;  conditional E-value: 6.4
                            AAA_14  62 e...ekktylflD 71 
                                       +   ++k+y++lD
  gi|518651759|ref|YP_008141279.1| 769 AvfsDGKKYVILD 781
                                       1333588888888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (890 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.79u 0.34s 00:00:01.13 Elapsed: 00:00:00.56
# Mc/sec: 4783.17
//
Query:       gi|518651760|ref|YP_008141280.1|  [L=332]
Description: hypothetical protein FACI_IFERC00001G0399 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-05   24.9  27.3    0.00011   22.1  13.1    3.2  2  Pectate_lyase_3  Pectate lyase superfamily protein


Domain annotation for each model (and alignments):
>> Pectate_lyase_3  Pectate lyase superfamily protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1  13.1   6.2e-09   0.00011      15     214 ..      37     216 ..      26     217 .. 0.73
   2 !    3.3   7.2    0.0034        61     117     202 ..     213     309 ..     212     320 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 6.2e-09
                                       EE-HHHHHHHH......HTSS-EEE-SEEEEESS-EEE-SSEEEEES-TTTEEEEE-TT-SS--SEEES-TTT-..- CS
                   Pectate_lyase_3  15 tDdtaaiqkaiscasatttgavVYfPaGtYlvsspiilksgvqLvGdgngrpvlkaaaafvgaglidgdpyvsggse 91 
                                       +  t  iq+ai    ++++ + +++++G Y +++ +i+ksg+ L+  +n++++l   ++ +    i  ++       
  gi|518651760|ref|YP_008141280.1|  37 NSLTSGIQEAI----DSSKSGYIFLSPGEYHIKTQLIIKSGTMLI--SNNKSILVNDMKNKYIPFIVVEQ------- 100
                                       55577799999....7788899***********************..55678777655323333332233....... PP

                                       EEEEEEEEEEEGGGG-SS---SSEEEES-EEEEEEEEEEES-SSEEE-SSS---TT--...-SS--EEEEES-EEES CS
                   Pectate_lyase_3  92 aliatnnfyrqirnlkiditavapgatgihwqtaqatslenvefemseasgtkhqgif...iengsggflndlvfsg 165
                                               y++i+ l++++++ +  + g + + +   +++ ++++++ +     ++i+     ng + ++n++ ++ 
  gi|518651760|ref|YP_008141280.1| 101 --------YSDIKYLILNSNNKSGISIG-KDNANNSINIDYIKIYNTGNGP--DNRIIkaiEINGFNIIINNIDIYL 166
                                       ........66799999999853222222.3456777778888888876663..33343221444555555******9 PP

                                       -SS-SEEE.S-EEEEEES-EEE-S--SEEE-TT-EEEEEEEEEESSSE.EE CS
                   Pectate_lyase_3 166 lgdigiav.gnqqftvrnitfnnattgievlwgwgwtlknvkinnceg.Gi 214
                                        g+ig+ +    ++ ++++++ n++tgi++   ++++++n +i++c+  G+
  gi|518651760|ref|YP_008141280.1| 167 -GNIGLSLeNASDIRIKELQVVNCSTGIRMFNANNISINNFSIDSCQYtGM 216
                                       .*******7799999****************9999***********97676 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0034
                                       EES-EEEEEEEEEEES-SSEEE-SSS.---TT---SS--E...EEE.ES-EEES-SS-SEEES.....-EEEEEES- CS
                   Pectate_lyase_3 117 atgihwqtaqatslenvefemseasg.tkhqgifiengsg...gfl.ndlvfsglgdigiavg.....nqqftvrni 183
                                       +tg++  + q+  ++  + ++++a   +++ gi+i + s+   ++l  d++++ +g++++ ++     n +++++n 
  gi|518651760|ref|YP_008141280.1| 213 YTGMQIDSTQNSYFQGTVWNNDKAYInNNEYGILIGKYSRdmnNILkIDVRIRDTGKTALHISnsmniNIDAIISNS 289
                                       5777888899999999999999999846666***9999995533336699999999999999667777777888888 PP

                                       EEE-S--SEEE-TT-E.EEE CS
                   Pectate_lyase_3 184 tfnnattgievlwgwg.wtl 202
                                        +++ + gi+ +++ + + +
  gi|518651760|ref|YP_008141280.1| 290 EYHKIEKGIYYGENIKnINI 309
                                       88888888888876553443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2327.56
//
Query:       gi|518651761|ref|YP_008141281.1|  [L=130]
Description: transferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 941.87
//
Query:       gi|518651762|ref|YP_008141282.1|  [L=91]
Description: hypothetical protein FACI_IFERC00001G0401 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 640.49
//
Query:       gi|518651763|ref|YP_008141283.1|  [L=748]
Description: hypothetical protein FACI_IFERC00001G0402 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.1e-117  393.6   0.2   1.4e-117  393.2   0.2    1.1  1  Topoisom_bac    DNA topoisomerase
    2.3e-13   49.7   0.7    2.3e-13   49.7   0.7    3.4  3  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
    1.1e-12   48.1   1.8      9e-12   45.1   0.1    2.9  3  Toprim          Toprim domain
  ------ inclusion threshold ------
      0.018   14.9   0.1      0.046   13.6   0.1    1.7  1  Cry1Ac_D5       Insecticidal delta-endotoxin CryIA(c) domain 
      0.099   12.9   0.1       0.46   10.7   0.1    2.2  2  DUF2283         Protein of unknown function (DUF2283)
       0.11   12.3   0.4       0.34   10.7   0.4    1.8  2  Synaptobrevin   Synaptobrevin
       0.13   12.4   6.4        3.4    7.9   0.8    2.5  2  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.2   0.2  5.5e-121  1.4e-117       3     412 ..     144     541 ..     142     542 .. 0.94

  Alignments for each domain:
  == domain 1  score: 393.2 bits;  conditional E-value: 5.5e-121
                      Topoisom_bac   3 nenlvdaaeaRrelDwliGinlsrlltkklkg..kkvlsaGRVqtptLaliveRereienFvpeeyweveatlkkek 77 
                                       n  l+d+a+aR+e+D+l+G+ l+r+++ + ++  k+++s+GRVqtptLaliveRe+ei++Fvpe+y+ +++t++k+ 
  gi|518651763|ref|YP_008141283.1| 144 NYGLADSAKAREEIDLLWGAVLTRFFSVTSNRlwKDFISVGRVQTPTLALIVEREEEIKSFVPEKYFVINVTFNKGI 220
                                       7789***********************96555789*************************************97776 PP

                      Topoisom_bac  78 kekekkkkkkkerikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkL 154
                                       +++       +++ikd++ea++i+++++ ++  v+s+++++k+ ++p pf+tt++++easr+ g++++++++ia+kL
  gi|518651763|ref|YP_008141283.1| 221 DFQ----GVYEKNIKDEDEANKIFNAINGNDGIVKSYKNEKKEVYKPPPFSTTDFLREASRI-GVTPSNAMKIAEKL 292
                                       654....789999**************7779*************7777*************8.************** PP

                      Topoisom_bac 155 YekaglitYpRTdstrlseeaelkailealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelpklke 231
                                       Y + gli+YpRTd+t+++++  lk+i ++++ +   e+   a+ +l ++k    +++ ++++H++I+P+ + pk k+
  gi|518651763|ref|YP_008141283.1| 293 YMS-GLISYPRTDNTVYQRSIPLKSIAQKFEGT---EFDTEAKMVLGQEKIYPSRGKVETTDHPPIYPV-SYPK-KA 363
                                       **7.****************88*********94...688888888876664336777777*********.6675.9* PP

                      Topoisom_bac 232 lsddekklYelIvrrflaslmkdakyeettvkleveeeefkasgktilekGfkkvykeekkeeeeeelpelkegeev 308
                                       l++ +k++YelIvrrfla+l+k+a++e+  +++++++++fk+sg++i+++G+  +yk++k +e++  lpel  ge+v
  gi|518651763|ref|YP_008141283.1| 364 LTGAYKNIYELIVRRFLATLYKNAVIEKSDADIDIKGYNFKVSGEKIIDNGWFDIYKYRKLRESK--LPELVIGETV 438
                                       *************************************************************9886..********** PP

                      Topoisom_bac 309 kvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkkkslvptelGkalvellekf.kd 384
                                       k k+ ++eek T+ppkry  asL+k+me+ ++Gt++Tr++ii+kl +r++++ +   l+pt+lG+  ++ ++++ +d
  gi|518651763|ref|YP_008141283.1| 439 KGKKWDMEEKYTEPPKRYDVASLLKLMESLNLGTKSTRHDIIQKLNDRNFATGNP--LRPTPLGIGFIKSITTIdSD 513
                                       *****************************************************66..**************99*9** PP

                      Topoisom_bac 385 lvspelTaeleekLdeIaegkadakevl 412
                                       +++p++Taele+++d+Iae++++ ++v+
  gi|518651763|ref|YP_008141283.1| 514 IAKPDMTAELEKEMDKIAENQKKLDDVV 541
                                       ***********************99998 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.8      0.68   1.7e+03      28      35 ..     647     654 ..     621     657 .. 0.81
   2 !   49.7   0.7     9e-17   2.3e-13       1      38 [.     658     696 ..     658     697 .. 0.96
   3 ?    4.1   2.6     0.016        40       2      37 ..     705     739 ..     704     741 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.68
                                       .T----EE CS
                    zf-C4_Topoisom  28 PeCkftkk 35 
                                       P+C++++k
  gi|518651763|ref|YP_008141283.1| 647 PNCEYNRK 654
                                       99999987 PP

  == domain 2  score: 49.7 bits;  conditional E-value: 9e-17
                                       -EE-SSS--EEEEEE-SSS.EEEEESST.T----EEB-G CS
                    zf-C4_Topoisom   1 vekCPkCggdLvlkrgkkG.kFvGCsnYPeCkftkklkk 38 
                                       v+kCP+  gdL+++++++G +F+GCsnYP+C++t++l++
  gi|518651763|ref|YP_008141283.1| 658 VGKCPSDDGDLIIRQSRYGkRFLGCSNYPKCTVTYPLPQ 696
                                       589*********************************997 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.016
                                       EE-SSS-.-EEEEEE-SSS.EEEEESST.T----EEB- CS
                    zf-C4_Topoisom   2 ekCPkCg.gdLvlkrgkkG.kFvGCsnYPeCkftkklk 37 
                                       e C  Cg   L+  +gk++ kF  C n  +C++++k+k
  gi|518651763|ref|YP_008141283.1| 705 EICRYCGaPLLIMVNGKRKwKF--CPNM-KCEYNRKDK 739
                                       7899***66778899***9999..9998.9**999987 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.1   3.5e-15     9e-12      11     102 ..      18     127 ..       8     128 .. 0.69
   2 ?   -3.3   0.1       4.2   1.1e+04      37      55 ..     224     239 ..     194     261 .. 0.46
   3 ?    0.8   0.0      0.23   5.8e+02      21      55 ..     335     367 ..     315     405 .. 0.76

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 3.5e-15
                                       HHHHHHT......HTSTEEEEEEESSSSEEEHS.......TTEEEEE..........ECTTTHHHHHH.HHHHHHHH CS
                            Toprim  11 aktiaka......lgsgfqavtaslGhildlet.......efkpvye..........eiedkkkvlka.lkelakra 63 
                                        k+ +++      ++++++++++++Ghil  ++             +          +i++ +++ +    ++ +  
  gi|518651763|ref|YP_008141283.1|  18 QKKTKNIsyiefeRNNEQNIMVSLSGHILGADFpeefkdwV-----KsdldklidsnIIYKVTNQRAYsALKSFSGI 89 
                                       44444442223334599****************76444440.....25555544475333333333333333337** PP

                                       SEEEEECSSSHHHHHHHHHHHHHHTHHHTTTEEEEEESS CS
                            Toprim  64 deiilatDpDreGeaiawellevlkellenkigrvefse 102
                                       d+ii+atD DreGe i+ e+l++++++  n i+r++fs 
  gi|518651763|ref|YP_008141283.1|  90 DNIIIATDYDREGELIGVEALKFIEPGYTN-IRRAKFSA 127
                                       *************************99999.******86 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.2
                                       STTEEEEE.ECTTTHHHHHH CS
                            Toprim  37 tefkpvye.eiedkkkvlka 55 
                                            vye +i+d+ ++ k+
  gi|518651763|ref|YP_008141283.1| 224 G----VYEkNIKDEDEANKI 239
                                       3....343322222222222 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.23
                                       TEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHH CS
                            Toprim  21 gfqavtaslGhildletefkpvyeeiedkkkvlka 55 
                                       g+ ++++s+G++ + ++  +p+y + ++kk   +a
  gi|518651763|ref|YP_008141283.1| 335 GQEKIYPSRGKVETTDH--PPIYPVSYPKKALTGA 367
                                       47899************..7777766666655554 PP

>> Cry1Ac_D5  Insecticidal delta-endotoxin CryIA(c) domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.8e-05     0.046      21      64 ..     386     430 ..     365     440 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
                         Cry1Ac_D5  21 nnitiqadnpi.fkghylhmsgakdidgtvfptyiyqkidesklk 64 
                                       n +  ++d  i +kg+ +++sg k id   f  y y+k+ eskl 
  gi|518651763|ref|YP_008141283.1| 386 NAVIEKSDADIdIKGYNFKVSGEKIIDNGWFDIYKYRKLRESKLP 430
                                       33444567666579*****************************95 PP

>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0         2   5.1e+03       9      18 ..      23      33 ..      20      47 .. 0.65
   2 ?   10.7   0.1   0.00018      0.46      31      46 ..      93     110 ..      63     112 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2
                           DUF2283  9 DalYIyl.seg 18
                                      ++ YI++  ++
  gi|518651763|ref|YP_008141283.1| 23 NISYIEFeRNN 33
                                      78899996333 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00018
                           DUF2283  31 i..lDfDedGrlvGIEiL 46 
                                       i   D+D++G+l+G+E L
  gi|518651763|ref|YP_008141283.1|  93 IiaTDYDREGELIGVEAL 110
                                       4257************77 PP

>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       2.7     7e+03      39      64 ..     310     335 ..     307     340 .. 0.73
   2 ?   10.7   0.4   0.00013      0.34      18      58 ..     522     563 ..     506     572 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.7
                                       CCHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Synaptobrevin  39 ktenLqssaqqFkkqarklkrkmwwk 64 
                                       ++  L+s aq+F+ +  + + km + 
  gi|518651763|ref|YP_008141283.1| 310 RSIPLKSIAQKFEGTEFDTEAKMVLG 335
                                       67779999999998877777777665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00013
                                       HHCCHHHHCHCCCCCHHHHCCCCHHHHHHH.HHHHHHHHHHH CS
                     Synaptobrevin  18 imkeNidkvlergekldeLvdktenLqssa.qqFkkqarklk 58 
                                        +++ +dk+ e+++kld+ v+ + n+  sa + F+ +  ++k
  gi|518651763|ref|YP_008141283.1| 522 ELEKEMDKIAENQKKLDDVVNDSRNMLHSAlKGFRGNKEEIK 563
                                       56889*********************9999456777766666 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.8    0.0013       3.4      12      27 ..     617     632 ..     616     649 .. 0.74
   2 ?    6.9   0.5    0.0026       6.8       9      37 ..     697     728 ..     694     730 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0013
                     Auto_anti-p27  12 tMLaetCpvCgvPLmr 27 
                                        M+++ C+vC+ P+ +
  gi|518651763|ref|YP_008141283.1| 617 QMTDKRCDVCSLPIIK 632
                                       5************987 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                     Auto_anti-p27   9 kGwtM.LaetCpvCgvPLmrdr..kggkvyCv 37 
                                       kG  M ++e C  Cg+PL+     k++ ++C+
  gi|518651763|ref|YP_008141283.1| 697 KGVIMpTGEICRYCGAPLLIMVngKRKWKFCP 728
                                       66666689*********976544455566776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (748 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 4707.04
//
Query:       gi|518651764|ref|YP_008141284.1|  [L=297]
Description: hypothetical protein FACI_IFERC00001G0403 [Ferroplasma acidarmanus fer1]
Scores for complete 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-58  195.9  36.4    1.1e-57  195.7  36.4    1.0  1  SPP              Signal-peptide peptidase, presenilin asparty


Domain annotation for each model (and alignments):
>> SPP  Signal-peptide peptidase, presenilin aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.7  36.4   6.1e-62   1.1e-57       3     281 ..      25     295 ..      23     297 .] 0.89

  Alignments for each domain:
  == domain 1  score: 195.7 bits;  conditional E-value: 6.1e-62
                               SPP   3 lfvvvqvlalllavpl.esaelqatedPtqvlnsvvyivlllvftlfvlivikkdkkliiskviyvivva.vifyvf 77 
                                       lf+v+   al la  l +++++ a  +    +  ++yiv++++ft+  l +ikk+ k  i+k i+++ v+ +if v 
  gi|518651764|ref|YP_008141284.1|  25 LFIVSTAFALYLAFNLdQISGIAAESNGISFIFVIYYIVFIVIFTAAALYIIKKHAK--IMKAIFIVLVLyMIFLVS 99 
                                       89999999****99994578899999999999999**********999988887766..567777666665888888 PP

                               SPP  78 lvllsivlvvaglvnlaslv.vaialvvllyaypeWyvidlaGvilavGvsalfGislgvlpavvllialavydais 153
                                        ++  iv v+   ++ a +  v+  + ++l++++eWy++d+aG+i+  G++a++Gi l  + a+ ll+++avyd+is
  gi|518651764|ref|YP_008141284.1| 100 SIVAGIVAVNLP-EYYAIIAiVTGFFAYMLIFRNEWYITDAAGLIMISGAAAILGILLRPYIAITLLVVFAVYDYIS 175
                                       889999977777.555555405555679************************************************* PP

                               SPP 154 vyktkhmialaegvvdlklPillvvPetlaysfveeafeeaeeaearnvlfiGlGdavlPsilvvsaavfleshila 230
                                       vyktkhm++la+ ++d ++P+++ +P + +  + + +f++++    ++v+++G+Gd+++P +l++s+a++   hi  
  gi|518651764|ref|YP_008141284.1| 176 VYKTKHMVTLAKAAIDNQFPLMFTLPSQGGIKIKDLTFDNRGT---HSVIMLGFGDMAIPELLIISSAIYNPLHIA- 248
                                       ******************************************9...679*********************988776. PP

                               SPP 231 glelavllalaGtlvGllvlsilvlrgrpaaGlPllnsGaiaGfligvlaa 281
                                          l+  l+laG+l  l +l++ ++ g+pa+GlP++n+G i+Gfli++ ++
  gi|518651764|ref|YP_008141284.1| 249 ---LFIALTLAGALSALGFLFF-FNHGKPAPGLPYINTGVIIGFLIAFAVV 295
                                       ...99999************99.9**********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1419  (0.0791455); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.29s 00:00:00.96 Elapsed: 00:00:00.42
# Mc/sec: 2126.00
//
Query:       gi|518651765|ref|YP_008141285.1|  [L=500]
Description: hypothetical protein FACI_IFERC00001G0404 [Ferroplasma acidarmanus fer1]
Scores for 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-96  322.4   0.9      4e-96  322.0   0.9    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    4.5e-14   52.4   0.0    1.1e-13   51.2   0.0    1.7  1  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.0   0.9  4.4e-100     4e-96       1     296 []     129     434 ..     129     434 .. 0.94

  Alignments for each domain:
  == domain 1  score: 322.0 bits;  conditional E-value: 4.4e-100
                                       HHHTTTT-EEE-SGGGHHHHHHHHHC.T.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH....CSE...EEEEEEE CS
                   AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkk.gevsletrkklaakaFahtaaYDaaiaeylskq....lpetlklslekkq 72 
                                       AAKN+k+V+v+++p+dY+ v + l+k g+++++tr+ l ++aF+++a+YD +i + l ++     pe+l +++ +++
  gi|518651765|ref|YP_008141285.1| 129 AAKNYKNVAVLSHPDDYSMVKDVLQKnGKIDMKTREILGLRAFSRSADYDIQIYNKLYRKlndrQPEELFIHGYDRT 205
                                       9*************************99*****************************8885554557899999889* PP

                                       EESSSSSTTS-EEEEE-TTSTTHHH-EEEESS---HHHHHHHHHHHHHHCTS..EEEEEEETTEEEEEEEESSHHHH CS
                   AICARFT_IMPCHas  73 kLrYGeNphQkaalyeeeeeeglakaeqlqGkelsynNllDadaalelvkef..aavaivKHanpcGvAvgetlaeA 147
                                       +LrYGeNp+Q+a +++ +e+ g+ +  ql+GkelsynN+lDa+aale+v++f   + +ivKH +p Gv+++ tl+eA
  gi|518651765|ref|YP_008141285.1| 206 DLRYGENPDQEAYMFKVNEKYGIPNSIQLNGKELSYNNILDANAALETVQDFqdITSVIVKHRTPSGVSSAGTLKEA 282
                                       ***************9999*********************************763566******************* PP

                                       HHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-ECEEEECEE-CCHHHCCTTSSS-EEEE-SS-.....EEEEET CS
                   AICARFT_IMPCHas 148 yekAlaaDpvSaFGgiialnrevdaetaeeikkefleviiApsfeeealeilkkkknlrvlelkee.....elrsvs 219
                                       + ++++aDp Sa+G ++alnr++d +ta+e++k+f+ev+iAp+++ +al++lkkkkn+r+l+++ +      + svs
  gi|518651765|ref|YP_008141285.1| 283 FINSYNADPESAYGFVVALNRKLDMDTAKEMQKKFIEVLIAPEYDTDALNLLKKKKNMRILKCSMDhdpekAIYSVS 359
                                       ***************************************************************984456669999** PP

                                       TEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEETTEEEEEE-SSSSHHHHHHHHHHH CS
                   AICARFT_IMPCHas 220 gglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlakdgqtvgiGaGqmsRvdsarlAvek 296
                                       gg+Lvq+r + +   ++l++ +++++ +e+l+dl+fawkvv h kSNa+vlak+++tvgiGaGq+sR++s+++A+e+
  gi|518651765|ref|YP_008141285.1| 360 GGVLVQSRLDYRY--DNLELKSTAEAGKEKLADLEFAWKVVAHAKSNAMVLAKNRTTVGIGAGQTSRIESLKIAIER 434
                                       *******997555..568888888889***********************************************986 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   0.0   1.2e-17   1.1e-13       2      94 ..      13     123 ..      12     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH.................HHHHHHHTTSC CS
                               MGS   2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv.................eildaikngei 61 
                                       lv++    k++  e++ T+GT k+lk+++i++ + +++tg+++ lggrv                 e   +++++++
  gi|518651765|ref|YP_008141285.1|  13 LVNFLSSIKDHIDEIYGTEGTVKYLKDNNIAANNSSNLTGFDDLLGGRVktlhpaifsgilskrdsESNMQLEKYHY 89 
                                       7788888888889***************************************************9955555555555 PP

                                       C...EEEEE--THHHHHHCHHHHHHHHHHHTTSHEE CS
                               MGS  62 d...lvintlypfkatvakdgykirraaenidIplp 94 
                                       +   +vi++lypf ++   +  ++++++enidI++ 
  gi|518651765|ref|YP_008141285.1|  90 KdfdMVICNLYPFVEAS--KTDDLEKMIENIDIGGL 123
                                       5666************8..67889**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3774.45
//
Query:       gi|518651766|ref|YP_008141286.1|  [L=572]
Description: hypothetical protein FACI_IFERC00001G0405 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-17   62.9   0.0    4.7e-17   61.9   0.0    1.6  1  DNA_pol_B_thumb  DNA polymerase beta thumb
    1.6e-14   54.0   0.5    2.7e-12   46.8   0.0    2.6  2  HHH_8            Helix-hairpin-helix domain
    7.1e-14   52.1   1.5    5.1e-10   39.8   0.5    3.2  3  HHH_5            Helix-hairpin-helix domain
    2.8e-09   37.5   1.3    8.3e-09   36.0   1.3    1.9  1  PHP              PHP domain
    1.2e-05   25.4   0.7    0.00035   20.7   0.0    2.5  2  DNA_pol_B_palm   DNA polymerase beta palm
     0.0046   17.0   0.1        2.1    8.5   0.0    3.0  3  HHH_2            Helix-hairpin-helix motif
     0.0066   16.3   0.1       0.52   10.3   0.1    3.0  2  HHH              Helix-hairpin-helix motif
  ------ inclusion threshold ------
      0.012   15.8   0.2        0.6   10.5   0.0    2.9  2  IMS_HHH          IMS family HHH motif
      0.041   13.7   0.2       0.67    9.7   0.4    2.8  3  RNA_pol_A_CTD    Bacterial RNA polymerase, alpha chain C term
      0.067   13.5   0.6          2    8.7   0.1    3.2  3  HHH_3            Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> DNA_pol_B_thumb  DNA polymerase beta thumb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   2.6e-20   4.7e-17       1      70 []     256     317 ..     256     317 .. 0.96

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.6e-20
                                       HHHHHHS-HHHHHHHHHHHHCTTEEEETTEEE.......ETCCCEEEC-SSHHHHHHHCTS----GGGTT CS
                   DNA_pol_B_thumb   1 allyfTGsktFnrdlRrlakkkglkLnssglrdekgkaeddddgelvevetErdvfelLglpyipPeeRe 70 
                                       al+yfTGsk++n+++R++a  +++kLn++gl+         +d + +++++E+ +++ L+++yipPe Re
  gi|518651766|ref|YP_008141286.1| 256 ALQYFTGSKDHNIKIRKIAIGNNYKLNEYGLF--------YNDSNIAAGKDEKFIYNRLNMDYIPPEMRE 317
                                       89******************************........678888899********************7 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   1.5e-15   2.7e-12       1      67 [.       3      74 ..       3      75 .. 0.96
   2 ?    4.8   0.2      0.02        37      34      63 ..     118     145 ..     113     149 .. 0.73

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.5e-15
                                      HHHHHHHHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH.TT....HCTTSTT--HHHHHHHHHHH CS
                             HHH_8  1 NkeiadaLeeladllelkgedpfrvraYrrAaraiealpeeitsl.ee....eltklpgiGkkiaakieeil 67
                                      N+eia ++e l  +l + +  +f ++aY+r+ar + ++p+++ +l ++    +l k+pg+Gk+i ++i e+l
  gi|518651766|ref|YP_008141286.1|  3 NSEIAGIFENLYNILSIDEKTKFEALAYQRVARELQSMPDDVSDLyDKygidGLMKIPGVGKGITQHIIEYL 74
                                      99*******************************************86678889******************9 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.02
                                       CCCC-SS-HHHHTTHCTTSTT--HHHHHHH CS
                             HHH_8  34 aiealpeeitsleeeltklpgiGkkiaaki 63 
                                       ++ +l+++ ++ + ++ ++pg+Gkk  + i
  gi|518651766|ref|YP_008141286.1| 118 NLNDLKKAAEE-H-KIADIPGFGKKSEELI 145
                                       55555555555.4.59********988776 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00076       1.4      23      56 ..      41      75 ..      31      76 .. 0.79
   2 !   39.8   0.5   2.9e-13   5.1e-10       1      52 [.      93     146 ..      93     149 .. 0.90
   3 ?   -2.5   0.0       4.6   8.3e+03       6      32 ..     397     421 ..     393     426 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00076
                                      --SHHHHHHS.-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5 23 iesvedlaaa.dveeLakipGiGkktAeriilelk 56
                                       + v dl ++  ++ L kipG+Gk   + ii+ lk
  gi|518651766|ref|YP_008141286.1| 41 PDDVSDLYDKyGIDGLMKIPGVGKGITQHIIEYLK 75
                                      567778887757899****************9988 PP

  == domain 2  score: 39.8 bits;  conditional E-value: 2.9e-13
                                       -HHHHTSTT--HHHHHHHHTT.T--SHHHHHHS-H.HHHHTSTTS-HHHHHHHH CS
                             HHH_5   1 feeLlsvsGiGpktAlallsa.Giesvedlaaadv.eeLakipGiGkktAerii 52 
                                       f +L +++G+Gpk A+ l+++ Gi+ + dl++a++ +++a+ipG+Gkk  e i+
  gi|518651766|ref|YP_008141286.1|  93 FGDLFRIEGLGPKKAILLYKKlGIKNLNDLKKAAEeHKIADIPGFGKKSEELIL 146
                                       678999***************99*******98865269***********99886 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 4.6
                                       TSTT--HHHHHHHHTTT--SHHHHHHS CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaa 32 
                                       +v++++ k+ +++l++    v+ l++ 
  gi|518651766|ref|YP_008141286.1| 397 TVDKLNQKYKIKILKG--AEVDILKDG 421
                                       6888999999999998..777777665 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   1.3   4.6e-12   8.3e-09       1      74 [.     342     448 ..     342     530 .. 0.75

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 4.6e-12
                                       EEEE--CCC.--.S-H..HHHHHHHHHCT-SEEEEEEEEBTT............HHHHHHHHHHHHTTTTSEEEEEE CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxx RF
                               PHP   1 dlHvHteys.lldgalsieelvkkakelglkaiaiTDhgnlf............gyvefykaakkkykagikpiiGl 64 
                                       dlH+Ht+ s +l  +   ee+v++a e+ ++ ia+T h                +y++ + ++++ky  +ik++ G+
  gi|518651766|ref|YP_008141286.1| 342 DLHLHTKESdGL-NTT--EEMVNAALEKRYEYIAMTNHTKNLkiahgmgdqdfiKYFDTVDKLNQKY--KIKILKGA 413
                                       89*****99777.677..********************98888********************9888..7******* PP

                                       E.................................. CS
                                       xxxxxxxxx.........................x RF
                               PHP  65 eayvaddse.........................k 74 
                                       e+++ +d+                          k
  gi|518651766|ref|YP_008141286.1| 414 EVDILKDGSldlkdetlgqmdcviasvhmntsmgK 448
                                       ****9998755555555555554444444444441 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0     2e-07   0.00035      26      56 ..     183     213 ..     166     240 .. 0.82
   2 ?    2.4   0.1     0.095   1.7e+02      25      73 ..     415     462 ..     397     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2e-07
                                       EEEE-HHHHTT-SEESSEEEEEEBTTBSTTS CS
                    DNA_pol_B_palm  26 evivcGSYRRgaessGDvDvlitkkdakses 56 
                                       ++ ++GS RR +e+ GD+D+l t kd+k++ 
  gi|518651766|ref|YP_008141286.1| 183 RCFIAGSTRRMKETLGDIDILATSKDSKKTM 213
                                       5789**********************99864 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.095
                                       -EEEE-HHHHTT-SEESSEEEEEEBTTBSTTSS--HHHHHHHHHHHHHT CS
                    DNA_pol_B_palm  25 vevivcGSYRRgaessGDvDvlitkkdakseskklkklleklvkklkkk 73 
                                       v+++  GS     e+ G +D++i   ++++ s  ++++++++++++k+ 
  gi|518651766|ref|YP_008141286.1| 415 VDILKDGSLDLKDETLGQMDCVIASVHMNT-SMGKEDMTQRVINAIKTG 462
                                       5566668888889999********999998.557999999999998875 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0011       2.1      34      60 ..      53      79 ..      31      82 .. 0.80
   2 ?    5.1   0.0     0.014        25       8      46 ..      99     140 ..      96     147 .. 0.83
   3 ?   -2.7   0.0       3.8   6.7e+03      20      31 ..     392     403 ..     389     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0011
                             HHH_2 34 leeLlevddiGeeiAqsivefFenekn 60
                                      ++ L +++++G+ i q i+e++++ k 
  gi|518651766|ref|YP_008141286.1| 53 IDGLMKIPGVGKGITQHIIEYLKTGKI 79
                                      67899*****************98765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.014
                             HHH_2   8 IrhVGektAklLakrFk..sldaLkkasle.eLlevddiGee 46 
                                       I   G k A lL k+ +  +l  Lkka +e +++ +++ G++
  gi|518651766|ref|YP_008141286.1|  99 IEGLGPKKAILLYKKLGikNLNDLKKAAEEhKIADIPGFGKK 140
                                       6678999*******99777*****998766379999999987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 3.8
                             HHH_2  20 akrFksldaLkk 31 
                                        k F+++d+L +
  gi|518651766|ref|YP_008141286.1| 392 IKYFDTVDKLNQ 403
                                       689999999987 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.1   0.00029      0.52      10      30 .]      53      73 ..      52      73 .. 0.87
   2 ?    2.6   0.0      0.08   1.4e+02      15      25 ..      98     108 ..      85     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00029
                                      HHHHHTSTT-SHHHHHHHHHH CS
                               HHH 10 reeLlalPGVGpktAeaIlsy 30
                                      ++ L+++PGVG+   ++I++y
  gi|518651766|ref|YP_008141286.1| 53 IDGLMKIPGVGKGITQHIIEY 73
                                      688*********988888877 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.08
                                       TSTT-SHHHHH CS
                               HHH  15 alPGVGpktAe 25 
                                        ++G Gpk+A 
  gi|518651766|ref|YP_008141286.1|  98 RIEGLGPKKAI 108
                                       589******96 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.21   3.8e+02      15      25 ..      58      68 ..      56      73 .. 0.81
   2 ?   10.5   0.0   0.00034       0.6      10      29 ..     128     148 ..     126     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.21
                           IMS_HHH 15 kipGiGgklge 25
                                      kipG+G+   +
  gi|518651766|ref|YP_008141286.1| 58 KIPGVGKGITQ 68
                                      8*****98766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00034
                           IMS_HHH  10 plpitkipGiGgklgek.Lek 29 
                                       + +i +ipG+G+k +e  L++
  gi|518651766|ref|YP_008141286.1| 128 EHKIADIPGFGKKSEELiLKN 148
                                       56899***********98875 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 ?   -0.9   0.0      0.78   1.4e+03      44      66 ..      53      75 ..      42      76 .. 0.75
   2 ?    9.7   0.4   0.00038      0.67      29      62 ..     112     146 ..     111     150 .. 0.82
   3 ?   -1.7   0.0       1.4   2.5e+03      19      37 ..     450     468 ..     448     469 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.78
                                      HHHHTTSSS-SSHHHHHHHHHHH CS
                     RNA_pol_A_CTD 44 eeeLlkikNlGkKSleEIkekLe 66
                                       + L+ki+ +Gk   + I+e L+
  gi|518651766|ref|YP_008141286.1| 53 IDGLMKIPGVGKGITQHIIEYLK 75
                                      4679********99999988876 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00038
                                       HHTT--BHHHHHHS-.HHHHTTSSS-SSHHHHHHH CS
                     RNA_pol_A_CTD  29 kragiktvgeLvkls.eeeLlkikNlGkKSleEIk 62 
                                       k+ gik +++L k   e+++  i+ +GkKS e I 
  gi|518651766|ref|YP_008141286.1| 112 KKLGIKNLNDLKKAAeEHKIADIPGFGKKSEELIL 146
                                       7899*******98751568***********87665 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.4
                                       T--HHHHHHHHHTT--BHH CS
                     RNA_pol_A_CTD  19 eLSvRslNcLkragiktvg 37 
                                       +++ R+ N+ k  +++ +g
  gi|518651766|ref|YP_008141286.1| 450 DMTQRVINAIKTGKVNILG 468
                                       6799*******98888765 PP

>> HHH_3  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0011         2      15      47 ..      55      86 ..      52     114 .. 0.87
   2 ?    1.5   0.0      0.21   3.8e+02      15      48 ..      95     124 ..      91     127 .. 0.64
   3 ?   -2.7   0.0       4.2   7.5e+03      42      57 ..     376     391 ..     356     407 .. 0.62

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                             HHH_3 15 eLqklpGlgpklAknIvayReknGpfksreeLl 47
                                       L+k+pG+g+ + + I++y  k G++++ e  +
  gi|518651766|ref|YP_008141286.1| 55 GLMKIPGVGKGITQHIIEYL-KTGKIEKYEKIK 86
                                      699****************9.778888777665 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.21
                             HHH_3  15 eLqklpGlgpklAknIvayReknGpfksreeLlk 48 
                                       +L +++Glgpk+A  I+ y+  + ++k++++L+k
  gi|518651766|ref|YP_008141286.1|  95 DLFRIEGLGPKKA--ILLYK--KLGIKNLNDLKK 124
                                       5667888888866..55555..335666666665 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 4.2
                             HHH_3  42 sreeLlkvkglgpktf 57 
                                       + + L+   g+g++ f
  gi|518651766|ref|YP_008141286.1| 376 HTKNLKIAHGMGDQDF 391
                                       4556666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (572 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 3704.66
//
Query:       gi|518651767|ref|YP_008141287.1|  [L=833]
Description: hypothetical protein FACI_IFERC00001G0406 [Ferroplasma acidarmanus fer1]
Scores for complete 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-151  505.2   0.0   5.2e-151  504.9   0.0    1.0  1  Penicil_amidase  Penicillin amidase


Domain annotation for each model (and alignments):
>> Penicil_amidase  Penicillin amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  504.9   0.0  2.9e-155  5.2e-151       8     665 ..      75     816 ..      68     819 .. 0.92

  Alignments for each domain:
  == domain 1  score: 504.9 bits;  conditional E-value: 2.9e-155
                                       GGGEEEEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHH-TBHHHHHHHHHHHT-HHHHHHHHHTS.... CS
                   Penicil_amidase   8 ewgvphIyAkneedlffaqGyvhAqdrlwqmellrrtarGrlaelfGpealesDrllrtlglrraaeaelaal.ldp 83 
                                       + g   +y +   +l++ qGy+ A+ rl qm +    a+G+l++l+G+++l+sD++ r l   + a+ e+++l +++
  gi|518651767|ref|YP_008141287.1|  75 SDGFIGVYSNHNWSLYYEQGYLEAKYRLAQMVFIKKEAQGTLSQLVGKSELSSDIFSRELMDCQIAKSEVNNLsKTS 151
                                       4788889999999*********************************************************8886666 PP

                                       ..HHHHHHHHHHHHHHHHH-..-ST-HH.HHHH---....S.........SS-.X.XXXXX.....XXX.XXXXXXX CS
                   Penicil_amidase  84 etralleaYaaGvNaylaelkakalPlefallgykpepWtpvdslavakvmaldl.agnleeelararalaaklgde 159
                                        t+ +   ++ G+N y+++l   + Pl f+ll+ykp+ ++ + ++a+++ + ++  ag++e  + +   + +k++++
  gi|518651767|ref|YP_008141287.1| 152 YTYMATSNFVSGINSYINNLSYGNTPLLFKLLNYKPNDFNITNIFAIQQTFLWENsAGGFEPLYFQ--YALQKMPEN 226
                                       77999***************96668******************************77777744444..467889*** PP

                                       X...................................................................X-EEEEE-T CS
                   Penicil_amidase 160 kvaelfpp............................................................gSNnwvvsg 176
                                        +++l+p+                                                             SN w+v+g
  gi|518651767|ref|YP_008141287.1| 227 IIKALYPAyqagiqnpivpyqcnpgiynetgdinnltlytpsvhipvnissipafssptslafpssesFSNDWAVNG 303
                                       *****9966677888899999999999999999999999999999998888888888888888877777******** PP

                                       TTBTTSS-EEEEE-EEESSGGG--EEEEEEETTEEEEEEE-TT-S.SSEEEESSEEEEEEE-SS-SEEEEEEEEETT CS
                   Penicil_amidase 177 erTasGkpllanDPHlglsapslwyqahlqapgldviGaslpGlPgvliGhnediAWglTnagadvqdlyaeklnpd 253
                                        +T++ ++llanDPHl  s+ps+w+  +l +pg++viG+ +pG+Pgv++Ghn +iAWg+Tn +++ + +yae+++ +
  gi|518651767|ref|YP_008141287.1| 304 VKTDNVSALLANDPHLTTSVPSIWIGFQLVSPGMNVIGVVFPGFPGVILGHNSYIAWGATNGQTQETYFYAEETSGA 380
                                       ***************************************************************************** PP

                                       EEEEEEETTEEEE-EEEEEEEEEE-TT.EEEEEEEEETTEEEE-.......TB--EEEEG-TTHHHHHHHHHT--SH CS
                   Penicil_amidase 254 dptrylydgkwepmetrtetikvkggddsvtltvreTrhGPvvsd..gkavalrwtalepgdrsldallalnrarnv 328
                                       +p++y  +g w ++++ +eti+vk++++ ++l++   ++G+vv++  g+++a++wt+l p+  +l+ +l+++ra++v
  gi|518651767|ref|YP_008141287.1| 381 HPYSYYSNGSWAKFTVINETINVKDSKP-YNLQLEVADNGVVVDNdsGTKIAMDWTGLSPS-YELTFFLHIDRAHTV 455
                                       *****99******************998.99*************966556*********98.*************** PP

                                       HHHHHHHHHH--.-SEEEEEEETT--EEEE--S--B---...TT--EEETT-GGGS--TB--GGGS-EEEE..SSEE CS
                   Penicil_amidase 329 aefraalkdlaa.paqnvvyADreGnigyqaagrvPvrpaaddgllpvpGsdsayeWtgyipfeelPqvvnPargyi 404
                                       ++fr+ l ++     qn+ +A ++Gnig++  g +Pv ++++ ++ +++G+ ++ +W g+ip +  P++++Parg++
  gi|518651767|ref|YP_008141287.1| 456 SQFRDNLTQYFKvAIQNWAVAGSKGNIGIFPYGDYPVIESGN-PRGVLNGT-GRSNWVGFIPLKYEPSLYDPARGFV 530
                                       *****99776555**************************767.9******9.889********************** PP

                                       EESSS----S.........--T-HHHHHHHHHH..SS...-B-HHHHHHHHHT-BBTHHHHHHHHH.......-..G CS
                   Penicil_amidase 405 vtaNnrvlpddypaalgsdwappyRarrirelLeekaagkkvtledmaalqtdtrsllaerllpll....aleaaea 477
                                       ++aN+ +++++yp++ g+ ++ + Ra++i++lL   +++  +++++m+++q+++++++   +l+ l    +   +  
  gi|518651767|ref|YP_008141287.1| 531 FSANQITVSPGYPYYTGWLYETGPRANEIYSLL---NSTSGFNTSKMEKVQLSVHDYSTNIFLKPLlksiE---KYY 601
                                       *****************99**************...66688*********************987877432...333 PP

                                       GGHHHHHHHHH-.SB-STT-THHHHHHHHHHHHTT.......................................... CS
                   Penicil_amidase 478 eaaaaldlLraWdgrmdadsaaaalfaawlaalvralfedelg......................rlaealeklle. 531
                                        +++ ++ L++W+g+md +s aa++f++w +++v+ +f + ++                       +   +e+l++ 
  gi|518651767|ref|YP_008141287.1| 602 GNTEIYNELASWNGDMDINSSAASVFHFWEHNIVNDTFLPYMEeygitsqdglynisfflgsdvtYHGPLMEDLVNw 678
                                       44669*********************************99999***************9999999555666666666 PP

                                       ......---TTSTTT-SE.SHH.HHHHHHHHHHHHHHHST-T-B.....HHHHEEEE.E............EE---B CS
                   Penicil_amidase 532 ...da.sfwwddptttpk.trdelllaalaealaeleaaglgadpakwrwgklhrlelrhplg...fnrg.lpvgGg 599
                                          ++ s ++++p + +  + ++l+l a++++++el++++ g+  +kw wg++h+  l + +g   +n++ +p++G+
  gi|518651767|ref|YP_008141287.1| 679 tinSPdSAYFNNPLNGNVeNFSSLALHAFNQTINELNKKY-GTISSKWDWGNIHTRYLSSFFGintLNTKeIPAAGN 754
                                       55433799********99*999*****************5.77779*********99999888************** PP

                                       -GGG.........EEEEEEE-EEEEEE--T.S.EEEEETT-S-S-TTSTTSSHHHHHHHTT--EEE CS
                   Penicil_amidase 600 eetvnatsysarafrvtrgpsyrmvvdladrdkaravlpgGqsgnpgsphyaDqlelwaegeylpl 665
                                        +t+na+         ++gps+r vv+l++++k+ +++pgG s+np s +y++ +  w++g y++l
  gi|518651767|ref|YP_008141287.1| 755 GNTINAAYG----LTSNFGPSWRLVVNLSNPAKSVGIYPGGVSENPLSSYYSNNFIPWNNGVYYTL 816
                                       *****7744....67899*******************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (833 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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: 0.75u 0.34s 00:00:01.09 Elapsed: 00:00:00.52
# Mc/sec: 4801.26
//
Query:       gi|518651768|ref|YP_008141288.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G0407 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); 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):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 781.15
//
Query:       gi|518651769|ref|YP_008141289.1|  [L=130]
Description: hypothetical protein FACI_IFERC00001G0408 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); 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 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 991.61
//
Query:       gi|518651770|ref|YP_008141290.1|  [L=151]
Description: hypothetical protein FACI_IFERC00001G0409 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1131.41
//
Query:       gi|518651771|ref|YP_008141291.1|  [L=404]
Description: hypothetical protein FACI_IFERC00001G0410 [Ferroplasma acidarmanus fer1]
Scores for complete 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-168  560.2   3.1   2.4e-168  560.0   3.1    1.0  1  AdoMet_Synthase  S-adenosylmethionine synthetase (AdoMet synt
  ------ inclusion threshold ------
      0.061   13.7   0.3       0.27   11.6   0.0    2.1  2  Trigger_N        Bacterial trigger factor protein (TF)


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 !  560.0   3.1  2.7e-172  2.4e-168       1     396 []       9     400 ..       9     400 .. 0.99

  Alignments for each domain:
  == domain 1  score: 560.0 bits;  conditional E-value: 2.7e-172
                                       --EEEEE-TTS-GTTSSEEEEEEE-TTSHHHHHHHHHHHHHHHHHHHHHHHHSS---EEEEEEEEE--EEEEETTEE CS
                   AdoMet_Synthase   1 rnivveelkkkpveeqevEivErKGiGHPDsiaDgiaeavsralskeylekfgailhhniDkvllvaGesepkfgGG 77 
                                       rni+ve++k++p+ ++evEivErKGiGHPDs+aDgiae+vsralsk+yl+++g+ilhhn+D+v++v+G+++pkf+GG
  gi|518651771|ref|YP_008141291.1|   9 RNIQVEAIKQSPTMSREVEIVERKGIGHPDSVADGIAESVSRALSKYYLKQYGRILHHNTDQVEVVGGQADPKFKGG 85 
                                       79*************************************************************************** PP

                                       EEEE-EEEEEEEEEEEEE.EEE--HHHHHHHHHHHHHHHH-SS--TTTSEEEEEEEEEEEEHHHHHHCH-SS..-BE CS
                   AdoMet_Synthase  78 eviepieillsgratkevegekipveeialeaakeylkenlraldlekdvivdvklgkgsadLkdvferkkkevpla 154
                                       +v++p++illsgrat +v++e+ipv+++a+++ak+yl+e+++ ld+++dv++d ++g+gs dL+++++++k    +a
  gi|518651771|ref|YP_008141291.1|  86 NVLDPTYILLSGRATASVGNERIPVKSLAIKSAKDYLREHFPDLDIDSDVMIDSRIGNGSVDLRGLYDTRKF---KA 159
                                       *********************************************************************655...8* PP

                                       SSSEEEEEEES--HHHHHHHHHHHHHTSHHHHHH-TTEEEEEEEEEEEETTEEEEEEEEEEEGGG--SHHHHHHHHH CS
                   AdoMet_Synthase 155 NDtSfgvgyaplseleklvleterllnskelkkklpevGeDiKvmglRekkkielTvavalvdrlvkdleeYlevke 231
                                       NDtSfgvg+ap++++e+lv  te+++n  +lkk+lp++G DiKvmg+R++++i+lTva+a+vd++vkd +eY+++k+
  gi|518651771|ref|YP_008141291.1| 160 NDTSFGVGFAPFTDTETLVKLTEKYING-DLKKSLPAIGYDIKVMGFRKGRTINLTVAAAYVDKYVKDPSEYYSIKD 235
                                       ***************************8.78********************************************** PP

                                       HHHHHHHHHHHHHSTTSEEEEEE-TT-BGGGTB--EESSSSGGGTT--EETTSS--TTSSB-TTS----S--TTS-T CS
                   AdoMet_Synthase 232 eikeeveelakkltkerevevevNtaDkkeeesvyltvtGtsaEegDdGsvGRGNRvnGlitpnrpmslEAaaGKNP 308
                                       e+ ++++++a k+t+ ++v+v+vNt D ++++++yltvtG s+E+gDdGsvGRGNRvnG+itp+rpms+EAaaGKNP
  gi|518651771|ref|YP_008141291.1| 236 ELVSKIKDNAVKYTD-EDVQVFVNTGDVQSDSVYYLTVTGLSMENGDDGSVGRGNRVNGIITPYRPMSMEAAAGKNP 311
                                       ***************.************************************************************* PP

                                       TT-HHHHHHHHHHHHHHHHHHH-TT.EEEEEEEEEE-TTSBTTS-SEEEEEEEESSS---HHSHHHHHHHHHHHHT- CS
                   AdoMet_Synthase 309 vsHvGKiYnvlaneiakeiveeveg.vkevyvrllsqiGkpidePlvasvqvilekgvsleevekeveeiideelek 384
                                       v+HvGK+Ynvl+n+ia+++v+e  g +kev vr++sqiG+p+deP+vas+q+i+e++v+ +++++++++i+d++l++
  gi|518651771|ref|YP_008141291.1| 312 VTHVGKLYNVLSNQIADKVVKEEGGdIKEVLVRIVSQIGRPVDEPHVASLQLIYEDNVDPSKHKNNIRAIADDKLAH 388
                                       *******************9988766*************************************************** PP

                                       HHHHHHHHTTT- CS
                   AdoMet_Synthase 385 ieeiteeliegk 396
                                       i+++t+++++gk
  gi|518651771|ref|YP_008141291.1| 389 IDQLTQMFVDGK 400
                                       *********986 PP

>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     3e-05      0.27      17      87 ..     178     249 ..     172     274 .. 0.68
   2 ?   -1.1   0.0      0.25   2.2e+03      47      92 ..     308     358 ..     296     379 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                                       EEE-HHHCHHHHHHHHHHHHTTS-BTTC-TT---CCCHHHHCTCC.CHHHHHHHHHHCCCCCCCCCS..-EE CS
                         Trigger_N  17 vevpaeevekavekalkklakkvkipGFRkGkvPrsiiekrygke.vleealeellnealeeaieeeklepv 87 
                                       v+++++ ++  ++k+l ++   +k+ GFRkG++    +   y ++ v++      ++++l   i+++ ++  
  gi|518651771|ref|YP_008141291.1| 178 VKLTEKYINGDLKKSLPAIGYDIKVMGFRKGRTINLTVAAAYVDKyVKDPSEYYSIKDELVSKIKDNAVKYT 249
                                       677888899999*******************96655555555544477777777777777777766665433 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.25
                                       T---CCCHHHHCT...CCCHHHHHHHH...HHCCCCCCCCCS..-EE.EE.E CS
                         Trigger_N  47 GkvPrsiiekryg...kevleealeel...lnealeeaieeeklepvgqpei 92 
                                       Gk P+ ++ k y+   +++ +++++e    ++e+l  ++ + + +pv++p++
  gi|518651771|ref|YP_008141291.1| 308 GKNPVTHVGKLYNvlsNQIADKVVKEEggdIKEVLVRIVSQIG-RPVDEPHV 358
                                       5666666666655443335555544432223333334443333.46666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2785.43
//
Query:       gi|518651772|ref|YP_008141292.1|  [L=155]
Description: ribosomal protein s18 alanine acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-11   44.4   0.1      2e-11   44.1   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.7e-10   40.5   0.2      4e-10   40.0   0.2    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.8e-10   38.5   0.0    1.2e-09   38.2   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    0.00046   20.1   0.1    0.00063   19.7   0.1    1.2  1  FR47             FR47-like protein
     0.0014   18.8   0.2     0.0023   18.1   0.1    1.3  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.068   13.9   0.0        0.1   13.3   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
       0.14   11.8   0.0        0.2   11.4   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   7.9e-15     2e-11      24     117 .]      46     132 ..      18     132 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 7.9e-15
                                       HHHHHHSTTCEEEEEEET.TEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEE CS
                    Acetyltransf_1  24 feesfsleaegllvaeed.geliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivl 99 
                                       ++ +    +  ++v +++ + ++Gfi + k+      ++ i  +aV+ e+r  G+G+aLl++ +  + + g+  + l
  gi|518651772|ref|YP_008141292.1|  46 YRAW----PQAFIV-YDNfDSVVGFIIGAKYSG---TEGRILLFAVRQEFRFAGIGKALLTQELNVMVRAGLSTVRL 114
                                       3333....444555.333589**********99...8999999*****************************999** PP

                                       EEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1 100 aveedndaairlYeklGF 117
                                       +v+ dn+  i++Y++ GF
  gi|518651772|ref|YP_008141292.1| 115 EVRTDNENGIKFYKRNGF 132
                                       *************88*99 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.2   1.6e-13     4e-10       6      75 ..      53     133 ..      46     134 .. 0.72

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1.6e-13
                                       EEEEET.TEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHHTT.....SEEE.EE.EEEETHHHHHHHHHH CS
                    Acetyltransf_7   6 fVaedd.gkivGfialslld...aeitrlaVdpeyrgkGiGraLleaae.....kgii.le.qlelnaekaikfYek 71 
                                       f+++d+ + +vGfi+ + ++   + i  +aV++e+r  GiG+aLl+ +       g+  +  ++++++e+ ikfY++
  gi|518651772|ref|YP_008141292.1|  53 FIVYDNfDSVVGFIIGAKYSgteGRILLFAVRQEFRFAGIGKALLTQELnvmvrAGLStVRlEVRTDNENGIKFYKR 129
                                       667788899*****999999755555559****************96223445455332112344444478****** PP

                                       TTEE CS
                    Acetyltransf_7  72 lGFe 75 
                                       +GF 
  gi|518651772|ref|YP_008141292.1| 130 NGFS 133
                                       ***6 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.2   0.0   4.8e-13   1.2e-09      32     109 ..      52     135 ..      27     141 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 4.8e-13
                   Acetyltransf_10  32 lllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnasp.yavpfYe 102
                                        ++v+++ +++vG+i   ++  ++++i l++V++e+r  GigkaLl + ++ + ++g+++ +l+v+ ++ + ++fY+
  gi|518651772|ref|YP_008141292.1|  52 AFIVYDNFDSVVGFIigaKYsGTEGRILLFAVRQEFRFAGIGKALLTQELNVMVRAGLSTvRLEVRTDNeNGIKFYK 128
                                       4677777799*****8655555555***************************99*********************** PP

                   Acetyltransf_10 103 klGFkav 109
                                       + GF  +
  gi|518651772|ref|YP_008141292.1| 129 RNGFSII 135
                                       ****866 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.1   2.4e-07   0.00063      22      80 ..      76     135 ..      61     143 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.4e-07
                                       SSEEEEEE-GGG-SSSHHHH.HHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsr.lvkalakeiaergktvllvvvasNtpsirlyeklGfeki 80 
                                       g +    v++e+r  G g+  l+++l   +++   tv l v+++N++ i++y++ Gf  i
  gi|518651772|ref|YP_008141292.1|  76 GRILLFAVRQEFRFAGIGKAlLTQELNVMVRAGLSTVRLEVRTDNENGIKFYKRNGFSII 135
                                       7888999***********86268889999999999**********************987 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0023      55     145 ..      56     143 ..      38     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                    Acetyltransf_4  55 ae.sdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhk 130
                                       ++  d +vG   +++      ++  +l + + ++  + +g+g++l++   +v+ + ++ +   e+  +nen i+f+k
  gi|518651772|ref|YP_008141292.1|  56 YDnFDSVVGFIIGAKYSG---TEGRILLFAV-RQEFRFAGIGKALLTQELNVMVRAGLSTVRLEVRTDNENGIKFYK 128
                                       554566666666664444...4444555666.5778899************************************** PP

                    Acetyltransf_4 131 alGFelvgifkkcik 145
                                       + GF++   +k+++ 
  gi|518651772|ref|YP_008141292.1| 129 RNGFSIISTLKNYYS 143
                                       **********99986 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     4e-05       0.1      55     137 ..      52     132 ..      14     133 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4e-05
                    Acetyltransf_3  55 gwaivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirv 131
                                        +++ ++ ++v+G++   ++++ ++   l + ++++f+  G+++  + + l+++  + gl++++ ++ ++Ne+ i+ 
  gi|518651772|ref|YP_008141292.1|  52 AFIVYDNFDSVVGFIIGAKYSGTEG-RILLFAVRQEFRFAGIGKALLTQELNVM-VRAGLSTVRLEVRTDNENGIKF 126
                                       3778776666899998888888876.6677889999*999*************9.6777****************** PP

                    Acetyltransf_3 132 leklGf 137
                                       +++ Gf
  gi|518651772|ref|YP_008141292.1| 127 YKRNGF 132
                                       *****9 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.7e-05       0.2      88     140 ..      84     135 ..      72     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.7e-05
                                       SHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EEE CS
                    Acetyltransf_8  88 eaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfeke 140
                                        +e+r  g+++all++ ++ +++  + + v +E + +Ne+ i+++++ Gf   
  gi|518651772|ref|YP_008141292.1|  84 RQEFRFAGIGKALLTQELNVMVRA-GLSTVRLEVRTDNENGIKFYKRNGFSII 135
                                       5789999************99998.9************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1105.32
//
Query:       gi|518651773|ref|YP_008141293.1|  [L=133]
Description: hypothetical protein FACI_IFERC00001G0412 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-26   92.0   7.2    2.4e-26   91.8   7.2    1.0  1  DUF1634          Protein of unknown function (DUF1634)


Domain annotation for each model (and alignments):
>> DUF1634  Protein of unknown function (DUF1634)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.8   7.2   1.3e-30   2.4e-26       1     102 []      10     126 ..      10     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.8 bits;  conditional E-value: 1.3e-30
                           DUF1634   1 igklLriGvllsaavvllGlilllvkhgs...............sesenseltslseilegllelkglaiiqlGllv 62 
                                       i+++L++Gv++s++++++G+i+l++k+g                 ++ +s+ +sls+i++gl++++gl +i++Gl+v
  gi|518651773|ref|YP_008141293.1|  10 ISYFLKAGVMISVSFIIVGVIILFAKNGGdgftlsqmsnynyalAHGIDSKSVSLSKIVSGLSAIDGLYFITVGLWV 86 
                                       89**************************87888877776655553399***************************** PP

                           DUF1634  63 LiatPvlrVvlsliaFlkekdilyviitliVLliLllsll 102
                                       Li+tP++ V++ +++F+ +k++lyv+++ iVL++L++++l
  gi|518651773|ref|YP_008141293.1|  87 LIFTPITVVFIGWLSFFDDKNYLYVGMASIVLFNLFFAML 126
                                       **************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 947.98
//
Query:       gi|518651774|ref|YP_008141294.1|  [L=331]
Description: hypothetical protein FACI_IFERC00001G0413 [Ferroplasma acidarmanus fer1]
Scores for complete 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-42  144.2  28.2    4.9e-42  144.2  28.2    1.8  2  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.15   12.1   0.4        1.9    8.6   0.0    2.1  2  OCRE      OCRE domain


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.2  28.2   5.5e-46   4.9e-42       3     236 .]      15     279 ..      13     279 .. 0.90
   2 ?    0.0   0.1      0.06   5.4e+02      91     112 ..     296     317 ..     283     331 .] 0.56

  Alignments for each domain:
  == domain 1  score: 144.2 bits;  conditional E-value: 5.5e-46
                              TauE   3 lagllaGfvagllGiGggliavPlLlll..lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       +  ++aGf+++l+G+Ggg+++vP+L+l+  +p   a+++sl++ +ats+++a a+ +++  ++++++ l +++  Ga
  gi|518651774|ref|YP_008141294.1|  15 FGSIIAGFIGSLTGLGGGTVLVPVLTLFygIPFIFAAGASLISTIATSAGSASAYTKKKIANIKIGIGLEIATTTGA 91 
                                       66799**********************75669999***********************989**************** PP

                              TauE  78 llGallllllpsel....lkllfgvlllllallmllrkkr...........................srakgrerrp 123
                                       ++G+l l  +++++    + ++fg++ll++ + ++ + ++                           ++   + +  
  gi|518651774|ref|YP_008141294.1|  92 IVGSLTLVFIDKHAliwsVYVIFGLVLLFSLIPTIKKIGKevppetkpdwstklfqltgsyyderlrKT--IKYHGI 166
                                       ***********9953445788999999999998888777699999999999999999998888765322..456677 PP

                              TauE 124 taillvligglvGllsGllGiGgGfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllp 200
                                       +++l  ++++++G++sGllGiG G+l v  + + ++lp+k+++ +s+++i +++++g  +y++ g++++ ++++ ++
  gi|518651774|ref|YP_008141294.1| 167 RWWLGEIVMFFAGFVSGLLGIGSGALKVLGMDWAMNLPMKVTTTSSNFMIGITAATGSSIYWYEGYINLFIAAATAI 243
                                       77766677677****************************************************************** PP

                              TauE 201 gallGallGarlarrlsertlrrlfallllvlgvkl 236
                                       g+l+Ga++Ga++  ++s++ +r++f+++l +lg  +
  gi|518651774|ref|YP_008141294.1| 244 GVLIGAFFGAKVLVKISNENIRWIFFAILSFLGFDM 279
                                       ******************************999765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.06
                              TauE  91 llkllfgvlllllallmll.rkk 112
                                       +++++++v++ ++ +++l+ + +
  gi|518651774|ref|YP_008141294.1| 296 MIQFFISVIISIVLISLLYyN-S 317
                                       456666666666666666532.2 PP

>> OCRE  OCRE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.038   3.4e+02      19      26 ..     149     156 ..     147     164 .. 0.72
   2 ?    8.6   0.0   0.00021       1.9      29      46 ..     313     330 ..     310     331 .] 0.91

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.038
                              OCRE  19 tGyYYDpn 26 
                                       tG YYD +
  gi|518651774|ref|YP_008141294.1| 149 TGSYYDER 156
                                       66666654 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00021
                              OCRE  29 lyydsrtgryysydettk 46 
                                       lyy+s+++ +++ +e++ 
  gi|518651774|ref|YP_008141294.1| 313 LYYNSKRKEWGKVNEKSR 330
                                       8**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1257  (0.0701099); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2227.80
//
Query:       gi|518651775|ref|YP_008141295.1|  [L=35]
Description: hypothetical protein FACI_IFERC00001G0414 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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 0.26s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 256.11
//
Query:       gi|518651776|ref|YP_008141296.1|  [L=519]
Description: amino acid permease-associated region [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-45  154.1  64.6      8e-45  153.4  62.7    1.9  1  AA_permease_2  Amino acid permease
    2.1e-42  145.4  55.1    3.5e-42  144.6  55.1    1.4  1  AA_permease    Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.4  62.7   8.9e-49     8e-45       1     418 [.      11     453 ..      11     464 .. 0.86

  Alignments for each domain:
  == domain 1  score: 153.4 bits;  conditional E-value: 8.9e-49
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                       ++l++++++ +g vigsgif+ +  ++++    +++ ++av+i++l+++l+yaEl+s+    gG y+  ++a g+  
  gi|518651776|ref|YP_008141296.1|  11 IGLVGLVGIGVGGVIGSGIFALPaIMGAVAGPGFVISVVAVGIIILILGLIYAELGSTYTMTGGPYSLPRKALGNDT 87 
                                       7999*******************97777555566666777777779*********777******************* PP

                     AA_permease_2  77 aflsawfnwfayvpvlasilsvaasyllnalgp....dlqgntwltyliaiaililvalinirgikesakiqnilgi 149
                                       +f+ +w +++ ++ ++a+i+ +++ yl + + p     l+  t l ++i  + l+++++in++g+k +a + +i++i
  gi|518651776|ref|YP_008141296.1|  88 GFVLGWGYFIYAFTGTAAIIDIFITYLGFYV-PglsvGLVL-TPLGIGISLVALAIFTIINVFGVKFGALFSVITTI 162
                                       ***************************8876.335444444.4599******************************* PP

                     AA_permease_2 150 lkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaif 224
                                        ki +pl+i+ ++g++++++  f+        f+p g  g  l+++  +++f+Gfes++  s evk+  k +p+a++
  gi|518651776|ref|YP_008141296.1| 163 GKI-IPLVIFAVIGFLVFKIANFT-------PFLPYGLGGLGLAMALDFFAFTGFESVVIPSGEVKNpsKVIPRAMI 231
                                       ***.8************9777776.......89*******************************9999889****** PP

                     AA_permease_2 225 igllivlvlyllvniaflgvvpddei.......anlsnlgsvaalffeavggkvvaiivvilialsllgaintavig 294
                                       + +liv+ +y  ++iaf+g  +++           ++nl s++a  ++  g +v+a+ivv+++++s lga+  +v+ 
  gi|518651776|ref|YP_008141296.1| 232 FTILIVIAVYAIMSIAFTGMFNWSAAgipvgdwGAIGNLSSPFATAADSIGLPVLAAIVVAGVIISTLGAGEDWVLL 308
                                       ***********************9988899999778888899*********************************** PP

                     AA_permease_2 295 ssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigal 370
                                       ++r+ +a+a  + +   + kvn k+++p +a+i++ +++ + ++l+   +  ++  ++ ++s+  +++y+++++++ 
  gi|518651776|ref|YP_008141296.1| 309 QARIPYAMADNDLFWAPMGKVNeKYKTPQNALIFSSVLTGVTMILL---P--SFPEVALLASITTLVPYAAAALSLP 380
                                       ***************************************8776555...3..68899999***************** PP

                     AA_permease_2 371 ilrkkrphlkr....pgk....................ilvaiigalfllfllvalffppkgpa..tqssliyt 418
                                       ilrk+ ++  r    +                      ++++iig +++l+  v+ +f+ k+ +   +++l++ 
  gi|518651776|ref|YP_008141296.1| 381 ILRKTDKDTTRpfklY-GgtifaffgfvlstfliyfasWPWTIIGGILILIGYVLYIFVKKEKTfeLKRNLWLI 453
                                       *********9965552.043333444455555555666777777777777777777777666553355555554 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6  55.1   3.9e-46   3.5e-42       3     447 ..      17     447 ..      15     477 .. 0.84

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 3.9e-46
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       + i +ggviG g+f   ++  + aGp g +++++ +g++i++ +l+ +e+ + +  +gg y + ++ lg   Gfv G
  gi|518651776|ref|YP_008141296.1|  17 VGIGVGGVIGSGIFALPAIMGAVAGP-GFVISVVAVGIIILILGLIYAELGSTYTMTGGPYSLPRKALGNDTGFVLG 92 
                                       66899*********************.99************************************************ PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilalikii 148
                                       + y+++ +t+ a+ + + + +++f   v+ l+    +        ++v l++++iin++gvk+ + +++i+++ kii
  gi|518651776|ref|YP_008141296.1|  93 WGYFIYAFTGTAAIIDIFITYLGFY--VPGLS-VGLVltplgigiSLVALAIFTIINVFGVKFGALFSVITTIGKII 166
                                       ******9999999988888888888..99999.555569************************************** PP

                       AA_permease 149 aiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEv 225
                                        +++f ++g+ +   ++ +++                lp g        + +   +++  +faftG+e+v+i +gEv
  gi|518651776|ref|YP_008141296.1| 167 PLVIFAVIGFLVFKIANFTPF----------------LPYG--------LGGLGLAMALDFFAFTGFESVVIPSGEV 219
                                       *********876666666666................8888........999************************* PP

                       AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa....aspfvifikesgvsvlaplinavilt 298
                                       k+P+k iP+a+++++++++ +Y +++++ + ++++++ g+  +   a    +spf ++  + g++vla +++a++++
  gi|518651776|ref|YP_008141296.1| 220 KNPSKVIPRAMIFTILIVIAVYAIMSIAFTGMFNWSAAGIPVGDWGAignlSSPFATAADSIGLPVLAAIVVAGVII 296
                                       *************************************88766444448899************************** PP

                       AA_permease 299 aalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisal 374
                                       ++l+++   +    R+ y++a+++l+   ++k+ +k++ P +a+++s+++  + ++l  + ++       +  ++ +
  gi|518651776|ref|YP_008141296.1| 297 STLGAGEDWVLLQARIPYAMADNDLFWaPMGKVNEKYKTPQNALIFSSVLTGVTMILLPSFPE-------VALLASI 366
                                       **************************956666778************9999888876666666.......2233445 PP

                       AA_permease 375 iglivwlliilsylrfRka.......lkyqgrsieel.g.fkaallplgvilvlaaliiillilalyayltvkkgpk 442
                                        +l+ + +++ls++ +Rk+       +k++g  i  + g + + +l++++ + ++++  il++ ++++y+ vkk   
  gi|518651776|ref|YP_008141296.1| 367 TTLVPYAAAALSLPILRKTdkdttrpFKLYGGTIFAFfGfVLSTFLIYFASWPWTIIGGILILIGYVLYIFVKKEK- 442
                                       5677788888888888876444444466666666554243567889999999999999999999888887655443. PP

                       AA_permease 443 dwgaa 447
                                       +++  
  gi|518651776|ref|YP_008141296.1| 443 TFELK 447
                                       33332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1148  (0.0640303); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.74u 0.32s 00:00:01.06 Elapsed: 00:00:00.49
# Mc/sec: 3203.06
//
Query:       gi|518651777|ref|YP_008141297.1|  [L=433]
Description: hypothetical protein FACI_IFERC00001G0416 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-47  161.7   0.2    5.8e-47  160.4   0.2    1.6  1  Amidinotransf   Amidinotransferase
  ------ inclusion threshold ------
       0.04   13.2   0.0        6.1    6.1   0.0    2.3  2  Glyco_hydro_43  Glycosyl hydrolases family 43


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.4   0.2   6.4e-51   5.8e-47       1     340 []      17     432 ..      17     432 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.4 bits;  conditional E-value: 6.4e-51
                                       E----HHHHT--TTTTTTTT-SS---HHHHHHHHHHHHHHHHTT.T-EEEEHHHHHHHHCTSHHHHHH.HHHHHSST CS
                     Amidinotransf   1 mvrPgrflenltetasdnllqddeiilekaqkEHdafvqvLrek.GveVlvledllaealeaeearke.kldeklle 75 
                                       +++Pg +++    +++  l+ +++++  ka++EHd+++++L+e+ Gv V  +++ l +  e+++ +k   +d++l+ 
  gi|518651777|ref|YP_008141297.1|  17 VHKPGIEMFMGLLDPEASLY-ERAFNRYKARSEHDTLQRTLKEEfGVTVQRMDKSLMDIAEKDNSVKSaLIDMALSV 92 
                                       79******************.********************9755**********9988888876665145666666 PP

                                       TTTITTT.......................GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEBSEE CS
                     Amidinotransf  76 selgikl.......................gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstigggv 129
                                        +++                          ++ l  ++ ++k+   ++a + +    +pl+nl+F+rd+++t+++g+
  gi|518651777|ref|YP_008141297.1|  93 LHFDGVEaevneakaqlkenidlydmnhfiDILLMRPEVHLKSARGASAMHMKITSNDPLSNLYFMRDQQATTDRGI 169
                                       6666555899******************99666666666666666666677777777******************** PP

                                       EE---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----GGGEEEEETTEEEEEESSSS-HHHHHHHHHH CS
                     Amidinotransf 130 vlnpmaapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEGGdfvvlskgvvaigvssRtdeegieelakk 206
                                       ++ +m +p+Rr+E ++++l +k+       ++l i g++++++t+EGGdf++++++ ++ g + Rt+ eg++++ ++
  gi|518651777|ref|YP_008141297.1| 170 FMSRMSKPQRRHEPEVTKLVWKA-------MNLPIAGEGKGNATIEGGDFIPMKDFALL-GNGDRTNDEGVKQMLES 238
                                       ***********************.......67************************999.*************9987 PP

                                       .HHHT..TS-SEEEEEE--GGSST....S-GGGTEEEEETTEEEE-HHHH.TT-E............SS-HHHHHHH CS
                     Amidinotransf 207 .lfyk..tvafkviaieipkgrai....mHldtvftvvdddavvclpsildaegv............kakereavaq 264
                                         +++   v+++ +   ip +++     mH dt f+v+++++v+  +  l++++v            k+   + +++
  gi|518651777|ref|YP_008141297.1| 239 gVGFDevAVVHQPLHPLIPGDQPDpmidMHVDTYFNVASSSTVIGSELLLNNAKVdvyykeemgnykKSGTHTNLHD 315
                                       3333357999999999999999834456***********************9988***********99999****** PP

                                       HTT-SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHHHHHHHHHT............................. CS
                     Amidinotransf 265 aLkekgleiIeigeeeqwnfggNvLelkpgvvvaydrntvtnekleea............................. 312
                                        +k kg++i+  +  eq+ + +N+L++k+g ++a d+    +  l++                              
  gi|518651777|ref|YP_008141297.1| 316 YIKSKGFNIVSLSTLEQMSYSSNFLCIKDGTILAIDSARIIKSVLNDLvykakenpsrygalldevkkeyaqftgag 392
                                       ********************************9999988888888888888899999999999999*********** PP

                                       ............T-EEEEE-HTTTGGGS--TTTT-EEEEE CS
                     Amidinotransf 313 ............gievievpiselerGgGgarCmsaplfr 340
                                                   gi+     +++++ G+Gga+Cm+a + r
  gi|518651777|ref|YP_008141297.1| 393 gvfpykkemyenGIDAYVLNLENITGGYGGAHCMTAAIER 432
                                       ************************************9987 PP

>> Glyco_hydro_43  Glycosyl hydrolases family 43
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0016        14     135     183 ..     155     209 ..     145     219 .. 0.77
   2 ?    6.1   0.0   0.00068       6.1       3      53 ..     253     311 ..     251     325 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0016
                                       EEEEEEHCCCSEEEEEEEEEETTTTEEEEEEEEEEECGC......CTCTTBBEEE CS
                    Glyco_hydro_43 135 lvwgqwdkreghseiylaeldddtlklkgektklikagt......elkglkvtEG 183
                                       l++++ ++ + +++i + +++++    + e+tkl++++       e kg  + EG
  gi|518651777|ref|YP_008141297.1| 155 LYFMRDQQATTDRGIFMSRMSKPQRRHEPEVTKLVWKAMnlpiagEGKGNATIEG 209
                                       55666556678*************************9996666666666666666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00068
                                       SESBCSSEESEEEEEETTCEEEEEEEBTEE........SEEEEEEESSSSSCEEEEECE CS
                    Glyco_hydro_43   3 nPvlsgfypDpsilrvgedyYlvtstfewf........pglrifhSkdLvnWkqvgrvl 53 
                                        P ++g+ pDp i +  ++y+ v+s+++ +         ++ ++  + + n+k+ g+ +
  gi|518651777|ref|YP_008141297.1| 253 HPLIPGDQPDPMIDMHVDTYFNVASSSTVIgselllnnAKVDVYYKEEMGNYKKSGTHT 311
                                       599**********************9876666666666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 3050.18
//
Query:       gi|518651778|ref|YP_008141298.1|  [L=312]
Description: ornithine carbamoyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-50  170.6   0.0    3.9e-50  170.0   0.0    1.2  1  OTCace    Aspartate/ornithine carbamoyltransferase, Asp/Orn b
    1.5e-43  148.4   0.0      2e-43  147.9   0.0    1.2  1  OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.0   0.0   4.3e-54   3.9e-50       1     148 [.     153     300 ..     153     307 .. 0.98

  Alignments for each domain:
  == domain 1  score: 170.0 bits;  conditional E-value: 4.3e-54
                                       CC.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE CS
                            OTCace   1 kglkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvyt 77 
                                       kglk++fvGd+ nn+ansl+ +++++g+d+++++P++++pd    + a+k  kk g+ it+t+++ + + gaD++yt
  gi|518651778|ref|YP_008141298.1| 153 KGLKMTFVGDGTNNMANSLMLACSMTGIDLTIATPDAYQPDASYKAFAEKLGKKAGSAITVTDNVHDSAIGADILYT 229
                                       79*************************************************************************** PP

                                       --SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHH CS
                            OTCace  78 dvwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlh 148
                                       dvwvsmgee+er++rl+++k++q+++ llkla++daiv+HcLPa+rg E+tdeV+++++sv ++q  N+++
  gi|518651778|ref|YP_008141298.1| 230 DVWVSMGEEAERQKRLEDFKGFQINSGLLKLARPDAIVMHCLPAERGLEITDEVIEGKQSVAWQQGVNKIY 300
                                       ********************************************************************988 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 !  147.9   0.0   2.3e-47     2e-43       1     148 []       6     147 ..       6     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.9 bits;  conditional E-value: 2.3e-47
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHT.TT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTT CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkk.ekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaed 76 
                                       r+ll+l+d+++ee++e++++a  +k+ + + +   + lkgk  +llFe+pStRTr+SfevA +r+Gg++l+ls +++
  gi|518651778|ref|YP_008141298.1|   6 RSLLTLKDIEPEEFTEMVNRAVYYKSMIGNkKMVVPVLKGKYAGLLFEKPSTRTRTSFEVASERMGGHALYLS-SDQ 81 
                                       79************************99886777899************************************.778 PP

                                       SCTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  77 iqlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       ++ls      +E+++D+ar+l+++ d++v+R++++++leel+ky+ +pviNa+ +d eHPtQ+  D+lti e
  gi|518651778|ref|YP_008141298.1|  82 LHLS---G--GEPVKDVARMLGGWLDIMVARVFAQSTLEELKKYSGIPVINAL-SDSEHPTQMVSDFLTIME 147
                                       8888...4..5**********************999*****************.****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2086.82
//
Query:       gi|518651779|ref|YP_008141299.1|  [L=285]
Description: carbamate kinase [Ferroplasma acidarmanus fer1]
Scores for complete 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  103.5   0.0    1.9e-29  103.0   0.0    1.2  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 !  103.0   0.0     1e-33   1.9e-29       2     241 .]       3     269 ..       2     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 1e-33
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC......E.. CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa..glrstl 70 
                                       r+V++lGG++l++++       ++  + +  ++++  ++n++v+  G+g+++ +++++  g++ + + +  + ++ +
  gi|518651779|ref|YP_008141299.1|   3 RIVIALGGNALDNGKSsideqiEKASETFLRLSEI-INNNEVVITYGNGPQVGEIYDK-TGYPLDISGSmsQGLLLH 77 
                                       9***********88888995554444444444444.6679******************.555555444333223333 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE.................HHHTTTCEEECCHHH CS
                         AA_kinase  71 eeagevatrdalaslgerlvaallaaglpavglsaaaldateagr...............degsdgnvesvdaeaie 132
                                         a+ + +    ++l + +v  l +  +++ +++ ++++++ + +                ++s+++ + ++++ i 
  gi|518651779|ref|YP_008141299.1|  78 ILAMAYGSLKISGKLKKNIVPILTNTVIDENKYTLKPIGPFFDHKiddtyamemnkgyrkMVKSPEPASILEIDSII 154
                                       333333334788888889999999999999999999999999998999999999999999999999999999***** PP

                                       HHHHTT-EEEEESEEEEETTTE.......EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEE CS
                         AA_kinase 133 elleagvvpvltgfigldeege.......lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpei 202
                                       +l+++g++p   g++g+++e          g++++D +++llA +l+A+k ii+tdV+ Vy +  +k     ++++i
  gi|518651779|ref|YP_008141299.1| 155 NLVSNGYLPLAVGGGGVPVEILnkkymgfQGVIDKDLSSSLLATLLNAKKFIIITDVNNVYLDFKNKS---DPINKI 228
                                       *******************99999*******************************************9...****** PP

                                       EHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEEEE CS
                         AA_kinase 203 svdeaee..saselatgGmkvkhpaalaaarrggipvvItn 241
                                       s+++++e  ++ ++  g +k+k++aal+++++gg +v+It+
  gi|518651779|ref|YP_008141299.1| 229 SYKQMLEyyNKIKFEEGTIKPKILAALRFIEHGGEKVYITS 269
                                       ***************************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1985.15
//
Query:       gi|518651780|ref|YP_008141300.1|  [L=381]
Description: hypothetical protein FACI_IFERC00001G0419 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-32  111.0   0.0    3.8e-18   65.5   0.0    3.1  3  p450      Cytochrome P450


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.5e-06     0.081      45     137 ..      28     122 ..       3     142 .. 0.80
   2 !   30.4   0.0   9.5e-12   1.7e-07     229     301 ..     178     246 ..     164     247 .. 0.83
   3 !   65.5   0.0   2.1e-22   3.8e-18     326     428 ..     253     344 ..     249     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.5e-06
                                       EEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTS...SSTTCGHHHHHHHHHHHHHHHTSHSTTTHHHHH CS
                              p450  45 pvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgk...gvlfangekwkklRrfltptltsfgklsleelv 118
                                       +++ + +++ + ++l +++ +fs+++++ l +  + + ++k   ++l+ +++ ++ lR ++  ++t   ++ +e+++
  gi|518651780|ref|YP_008141300.1|  28 NMIHIFKYNTISKILSDHQ-NFSSQFRDLLGEEMAAMLNEKttpSILLLDPPLHTTLRGLVGSAFTPRSIELFEPRI 103
                                       678899999*******996.88888888887776655444422289********************997779***** PP

                                       HHHHHHHHHHHHCCCCHCS CS
                              p450 119 eeeaedlveklrkkagess 137
                                        e+a++l +++ +k ++  
  gi|518651780|ref|YP_008141300.1| 104 REIARMLAHAIVEKENSDI 122
                                       ***********99988873 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 9.5e-12
                                       HCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHH CS
                              p450 229 etldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqeklre 301
                                       +++d++ ++ +++++ l     e +g+ klsd+e+a  ++ ll+aG +Tt++ ++ a++ L+++Pe+ +++r+
  gi|518651780|ref|YP_008141300.1| 178 KKIDRN-SKGNNLISRLSTV--EMDGR-KLSDKEIAGFAILLLVAGNETTTNLITNAILSLYDHPEIYNEMRK 246
                                       555555.5666777766666..46776.****************************************99986 PP

  == domain 3  score: 65.5 bits;  conditional E-value: 2.1e-22
                                       HHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TTTSSSTTS--GGGGB-TTSCTESSCTT- CS
                              p450 326 avikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpevfpnPeeFdpeRFldekgnskrksfaf 402
                                        v++EtLR++++v  ++ R+ + d++i+g  i k+++  ++l++ +rd+e f++ e+F+p R  +ek        ++
  gi|518651780|ref|YP_008141300.1| 253 GVVEETLRYRSPVQ-STRRYSKIDTEIEGEEILKNDILALYLGSANRDEEAFEDGESFNPYR--KEK--------RH 318
                                       69************.999******************************************87..443........49 PP

                                       -TTEEGGGS-TTHHHHHHHHHHHHHH CS
                              p450 403 lPFGaGpRnCiGerlArmelklflat 428
                                       ++FG G + C+G +lAr+e +++l  
  gi|518651780|ref|YP_008141300.1| 319 MAFGQGIHFCLGAPLARLEARIALEE 344
                                       **********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2473.58
//
Query:       gi|518651781|ref|YP_008141301.1|  [L=258]
Description: glycosyltransferase involved in cell wall biogenesis [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-19   68.1  10.4    1.3e-18   67.3  10.4    1.4  1  GtrA      GtrA-like protein
  ------ inclusion threshold ------
      0.059   12.8   0.0      0.089   12.2   0.0    1.3  1  eIF-6     eIF-6 family


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 !   67.3  10.4   1.5e-22   1.3e-18       1     117 []     147     258 .]     147     258 .] 0.95

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 1.5e-22
                              GtrA   1 rFlivGvlgtlvdlallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglll 77 
                                       r++ivG+ g++v+ ++llll    +l+  l+ + a++++i++nFiln+r+tFk r +     +++k+ l++l+g+++
  gi|518651781|ref|YP_008141301.1| 147 RYVIVGITGVIVNEGVLLLLH--GKLGSELSIIPAIEISIIYNFILNNRYTFKGRGHF--YMRLAKYNLFNLIGFAA 219
                                       8*******************8..57********************************8..8**************** PP

                              GtrA  78 nllilwllveklgleallaklvgiivalvlnyvlsklfvF 117
                                       nl++++  v++    + +a ++gi+va++++y++  ++v+
  gi|518651781|ref|YP_008141301.1| 220 NLGVYYTAVYYRTDIY-VADFLGILVAFIITYTTATMIVW 258
                                       ******9998866655.5****************999998 PP

>> eIF-6  eIF-6 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.9e-06     0.089      93     154 ..     100     164 ..      71     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.9e-06
                                       SS--HHHHEEE-SS...EEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  93 kltAlGNvilaNDk...vAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                       k   lGN++l  ++     ++++ l  ++    +d+L+  + rg++  + +vG ++v+ n+g+l+
  gi|518651781|ref|YP_008141301.1| 100 KNMILGNTLLLKNRsfeYKIINTGLRCRENIHFKDFLDLTIRRGNMFRYVIVGITGVIVNEGVLL 164
                                       556688887777752224689999999999999*****************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1715.68
//
Query:       gi|518651782|ref|YP_008141302.1|  [L=617]
Description: hypothetical protein FACI_IFERC00001G0421 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1216  (0.0678231); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 3826.56
//
Query:       gi|518651783|ref|YP_008141303.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G0422 [Ferroplasma acidarmanus fer1]
Scores for complete 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-130  433.7   2.3   4.3e-130  433.5   2.3    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  433.5   2.3  2.4e-134  4.3e-130       2     314 ..       5     315 ..       4     318 .. 0.98

  Alignments for each domain:
  == domain 1  score: 433.5 bits;  conditional E-value: 2.4e-134
                                       --GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE- CS
                              ALAD   2 krlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp 78 
                                       +r+rr r +++lr++++et+++ ++li+p+fv+e+e++k++iksmpg+yr++++e +k + +l + g+k++++Fg+p
  gi|518651783|ref|YP_008141303.1|   5 ERMRRYRLNSNLRDIFSETTINSDKLIMPVFVDETEKSKTAIKSMPGIYRYALNEYEKYIGHLEDIGVKNIIIFGIP 81 
                                       69*************************************************************************** PP

                                       SS-BSS-GGGGSTTSHHHHHHHHHHHH-TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT- CS
                              ALAD  79 eekdeegsealnedglvqrairaikeevpelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGa 155
                                       ++kd++g++++++dg+vq+air  k++ ++l vi+D+clceyt++Ghcg++++++vdnd+tl+++ k a+s+aeaG+
  gi|518651783|ref|YP_008141303.1|  82 KHKDSSGTASYDHDGIVQKAIRSAKSN-TKLNVIADLCLCEYTDTGHCGVISNGYVDNDKTLDIYGKEAISYAEAGV 157
                                       *************************99.89*********************************************** PP

                                       SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGGHHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHH CS
                              ALAD 156 divapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafYgPFrdaaesapsfgdrktYqmdpansrealrevel 232
                                       divapS+mmDg+v+air+a+d++g+ ++ i++Ys+K+aS++YgPFrdaa+s+p+fgdrk+Yqmd++n +ea+re++l
  gi|518651783|ref|YP_008141303.1| 158 DIVAPSGMMDGQVGAIRKAMDSNGYVNTLIMAYSSKFASNLYGPFRDAADSTPQFGDRKSYQMDYRNGDEAMREIDL 234
                                       ***************************************************************************** PP

                                       HHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHTT-SEEEET CS
                              ALAD 233 dleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsllsikRAGadliltY 309
                                       d++eGADi+mvKPal+ylD+i ++k+ +++p+a+y vSGEY+m+k+a+ +g+l   ++v E+l+s+ RAG+dl +tY
  gi|518651783|ref|YP_008141303.1| 235 DVKEGADIIMVKPALFYLDMIYRAKQLYKMPLATYMVSGEYSMVKNAVLSGALA-PDTVNEALISLFRAGSDLAITY 310
                                       ****************************************************96.56789***************** PP

                                       THHHH CS
                              ALAD 310 fakev 314
                                       fa+++
  gi|518651783|ref|YP_008141303.1| 311 FAEDY 315
                                       **987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2301.59
//
Query:       gi|518651784|ref|YP_008141304.1|  [L=239]
Description: hypothetical protein FACI_IFERC00001G0423 [Ferroplasma acidarmanus fer1]
Scores for complete 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-75  251.3   0.1      1e-74  250.6   0.0    1.3  2  QueC          Queuosine biosynthesis protein QueC
    9.6e-05   22.0   0.0     0.0031   17.1   0.0    2.1  2  ThiI          Thiamine biosynthesis protein (ThiI)
     0.0025   17.0   0.0        1.4    8.0   0.0    2.1  2  NAD_synthase  NAD synthase
  ------ inclusion threshold ------
      0.058   13.0   0.0      0.072   12.7   0.0    1.1  1  Asn_synthase  Asparagine synthase
       0.15   11.8   0.0        0.6    9.8   0.0    1.8  2  ATP_bind_3    PP-loop family


Domain annotation for each model (and alignments):
>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.6   0.0   2.8e-78     1e-74       1     209 [.       5     214 ..       5     215 .. 0.96
   2 ?   -3.5   0.2       1.7   6.2e+03     124     139 ..     220     235 ..     217     236 .. 0.83

  Alignments for each domain:
  == domain 1  score: 250.6 bits;  conditional E-value: 2.8e-78
                                       EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG----- CS
                              QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdeei 77 
                                       kav+l+SGGlDS tvla+a+++g++v+ ++fdYgqrh +el++ ++i++ +gv + k +++d ++++ggsaLtd+ i
  gi|518651784|ref|YP_008141304.1|   5 KAVILISGGLDSPTVLAYALDNGYKVYPVSFDYGQRHIRELQSSEDICNYYGV-KLKKIKID-MTQIGGSALTDK-I 78 
                                       79***************************************************.********.9*********98.7 PP

                                       ------.....--------TTHHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH....H CS
                              QueC  78 evpkeelee..eelpntfVpaRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg....e 148
                                       +vp++ le+  +e+p+t+VpaRN+if+slaa+y e+++a++i+iG+n+ d+sgYPDcr+ef+++++k+lnlg     
  gi|518651784|ref|YP_008141304.1|  79 DVPERGLENieKEIPVTYVPARNTIFISLAAAYGETIKANSIFIGANAIDYSGYPDCRPEFFNTMEKTLNLGtelgI 155
                                       9***55554449************************************************************98887 PP

                                       TS--EEE-TTTT--HHHHHHHHHHTTHHHHH-B-STTS.-BTTTTSSSHHHHHHHHHHHHH CS
                              QueC 149 dkkieieaPlidlsKaeivklgkelgvpleetlsCYegeeegkaCgeCdaCalRkkgfeea 209
                                       ++ ++i+ Pl+ l+K++ivklg +lgvp+++t+sCY+g  ++kaCg+Cd+C lR kgf ea
  gi|518651784|ref|YP_008141304.1| 156 TDGFRIMVPLQYLTKSDIVKLGRRLGVPYRLTWSCYNG--RDKACGKCDSCLLRLKGFMEA 214
                                       899***********************************..556***************986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.7
                                       -STT--GGGSHHHHHH CS
                              QueC 124 edfsgYPDcrdefvka 139
                                        ++++YP   +e++k+
  gi|518651784|ref|YP_008141304.1| 220 IEYEAYPEFYSEYLKS 235
                                       68999**999999985 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   8.7e-07    0.0031       3      60 ..       3      56 ..       1      85 [. 0.74
   2 ?    2.9   0.0      0.02        72     139     160 ..     160     181 ..     149     194 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 8.7e-07
                              ThiI  3 qgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyq 60
                                      ++k++ L+SgG+DSp     +l  G +v  v ++     +++ i  +++  ++ + y+
  gi|518651784|ref|YP_008141304.1|  3 NDKAVILISGGLDSPTVLAYALDNGYKVYPVSFD----YGQRHIRELQSSEDICNYYG 56
                                      6899***********998899************7....34444445555555555555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.02
                              ThiI 139 lilrPLigldKeeiiklAkeig 160
                                        i+ PL  l K +i+kl +++g
  gi|518651784|ref|YP_008141304.1| 160 RIMVPLQYLTKSDIVKLGRRLG 181
                                       6999****************99 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00069       2.5      19      83 ..       4      66 ..       1      89 [. 0.80
   2 !    8.0   0.0   0.00038       1.4     139     172 ..     151     186 ..     140     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00069
                                      SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HH CS
                      NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikp 83
                                      +++v+ +SGG+DS +v a a +  +  +v  + +   + + ++++ +  +++ +g++ k+i+i+ 
  gi|518651784|ref|YP_008141304.1|  4 DKAVILISGGLDSPTVLAYALD--NGYKVYPVSFDYGQRHIRELQSSEDICNYYGVKLKKIKIDM 66
                                      578888*******988554444..45789999998888888999999999999999999888875 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00038
                                       -TTT..TT--SBETTTTS-HHHHHHHHHHTT--HHH CS
                      NAD_synthase 139 TkyG..DgaadlapiaellKtevkeLakelnvPerv 172
                                       T  G  Dg   + p++ l+K+++ +L ++l+vP r+
  gi|518651784|ref|YP_008141304.1| 151 TELGitDGFRIMVPLQYLTKSDIVKLGRRLGVPYRL 186
                                       5555446666799********************886 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.072      20      79 ..       6      64 ..       1      83 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                      Asn_synthase 20 vGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvl 79
                                        +l+SGGlDS ++ a+a      ++  +s ++ +++  e++  + +++++g++  ++ +
  gi|518651784|ref|YP_008141304.1|  6 AVILISGGLDSPTVLAYALDNGY-KVYPVSFDYGQRHIRELQSSEDICNYYGVKLKKIKI 64
                                      5689**************99764.77777777788***************9999555544 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00017       0.6       2      70 ..       6      68 ..       5      80 .. 0.73
   2 ?   -0.9   0.0      0.32   1.1e+03     136     163 ..     157     184 ..     141     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00017
                                      EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--HHH CS
                        ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdvak 70
                                      +++ +SgGlDS + l  + ++    g k+  + +d+g r+   +e +  +++c+ +++kl+  k+d+ +
  gi|518651784|ref|YP_008141304.1|  6 AVILISGGLDSPTVLAYALDN----GYKVYPVSFDYGQRH--IRELQSSEDICNYYGVKLKKIKIDMTQ 68
                                      57789******8877776666....457888899998875..566677788888888888777777644 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.32
                                       TTCCEE-CCCT--HHHHHHHHHHTT--- CS
                        ATP_bind_3 136 asirlvRPlLkvskeeleeylkekkikw 163
                                       ++ r++ Pl  ++k+++ ++ ++ ++++
  gi|518651784|ref|YP_008141304.1| 157 DGFRIMVPLQYLTKSDIVKLGRRLGVPY 184
                                       5678999**********99988888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.32s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1435.15
//
Query:       gi|518651785|ref|YP_008141305.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G0424 [Ferroplasma acidarmanus fer1]
Scores for complete 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  199.5   0.0    3.8e-59  199.0   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    1.1e-31  109.2   0.1    1.3e-31  109.1   0.1    1.0  1  2-Hacid_dh       D-isomer specific 2-hydroxyacid dehydrogenas
    4.7e-05   23.6   0.1    0.00012   22.3   0.1    1.7  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0021   18.6   1.0     0.0078   16.8   0.2    2.4  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0026   18.1   0.8     0.0048   17.2   0.2    1.8  2  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
  ------ inclusion threshold ------
      0.045   14.0   0.3        2.6    8.3   0.1    2.7  2  TrkA_N           TrkA-N domain
      0.072   12.7   0.1       0.51    9.9   0.0    2.1  2  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.075   13.3   0.0       0.13   12.5   0.0    1.5  1  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 !  199.0   0.0   1.7e-62   3.8e-59       1     178 []     106     280 ..     106     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 199.0 bits;  conditional E-value: 1.7e-62
                                       HHHHHHHHTTHHHHHHHHHTTCC...HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHC CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregew...ksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeee 74 
                                       ++l++a++r++  +++ +++++w   ++++ +lg+e++gkt+GiiG+GrIG+a+a+r+++f+mk+i+y+r++++   
  gi|518651785|ref|YP_008141305.1| 106 FGLMIAAARNIVSGNDLIHKNDWkagWNPTFMLGSEIHGKTLGIIGMGRIGKAIARRASGFDMKIIYYSRHRHD--- 179
                                       589********************************************************************883... PP

                                       HHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEE CS
                      2-Hacid_dh_C  75 eeelgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaal 151
                                          + ++++s++ell++sD+v+++l l+++t h+++ ++++kmkk+a+liN  RG++v+e++L++aL+++ i+gaal
  gi|518651785|ref|YP_008141305.1| 180 ---VDADFASIDELLQQSDFVIIALDLNADTFHFMDYQKISKMKKTAFLINGTRGKIVNEKDLVRALNEKIIEGAAL 253
                                       ...345789******************************************************************** PP

                                       S--SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 152 DvfeeeplpedspllelpnviltPHia 178
                                       Dvfe ep+++ +p+l++ nv++tPH++
  gi|518651785|ref|YP_008141305.1| 254 DVFEDEPVDNTNPILSFSNVVVTPHLG 280
                                       *************************97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.1   0.1   5.7e-35   1.3e-31       2     130 ..       5     308 ..       4     311 .] 0.97

  Alignments for each domain:
  == domain 1  score: 109.1 bits;  conditional E-value: 5.7e-35
                                       EEEST.CHHHHHHHHHTTEEEEEES..CSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   2 lileplreeelellkeegvevevkd..ellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvD 76 
                                       l++++++ + +e +++  +e+ev +     ++ ll+ +  ad+++++ n k+++e++++ +kLkvi++++vG+D++D
  gi|518651785|ref|YP_008141305.1|   5 LVTRNIPGNYIEKIEN--MEIEVFSgnGNMRDWLLSNIGSADGILITLNEKIDKELIDHGKKLKVISTYSVGYDHID 79 
                                       6776766666677777..799999999999*********************************************** PP

                                       HHHHHHTT-EEEE-TTTTHHHHHHHH................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
                        2-Hacid_dh  77 ldaakerGilVtnvpgystesvAElt................................................... 102
                                       +++ak +Gi+Vtn+p++ t+++A+l                                                    
  gi|518651785|ref|YP_008141305.1|  80 VEYAKSKGIIVTNTPEVLTDATADLIfglmiaaarnivsgndlihkndwkagwnptfmlgseihgktlgiigmgrig 156
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|518651785|ref|YP_008141305.1| 157 kaiarrasgfdmkiiyysrhrhdvdadfasidellqqsdfviialdlnadtfhfmdyqkiskmkktaflingtrgki 233
                                       ***************************************************************************** PP

                                       ...............................................T-BHHHHHHHHHHHHHHHHHHHTTCCGT CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ...............................................aaTeeaqeniaeeaaenlvaflkgespa 130
                                                                                      +aT e++ ++ae+a++nlv++l+g++p 
  gi|518651785|ref|YP_008141305.1| 234 vnekdlvralnekiiegaaldvfedepvdntnpilsfsnvvvtphlgSATYETRDKMAETAVTNLVNVLNGKDPL 308
                                       ***********************************************************************9986 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.1   5.3e-08   0.00012       2     109 ..     147     248 ..     146     255 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 5.3e-08
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iG+G +G+ +a++    ++k++ y r++  v++        ++si el+++ d+vi+ +  ++++ ++++   +
  gi|518651785|ref|YP_008141305.1| 147 LGIIGMGRIGKAIARRASGFDMKIIYYSRHRHDVDAD-------FASIDELLQQSDFVIIALDLNADTFHFMDYqKI 216
                                       79****************************9988864.......489*************************98888 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekgl 109
                                       +++kk ++li+g+  ++ + ++l ++l+ek +
  gi|518651785|ref|YP_008141305.1| 217 SKMKKTAFLINGTRGKIVNEKDLVRALNEKII 248
                                       99**********************99999976 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 ?   -1.8   0.0       2.2   4.9e+03      22      22 ..      62      62 ..      25     106 .. 0.54
   2 !   16.8   0.2   3.5e-06    0.0078       2      68 ..     147     200 ..     146     207 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                                      T CS
                     F420_oxidored 22 g 22
                                      g
  gi|518651785|ref|YP_008141305.1| 62 G 62
                                      1 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.5e-06
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE- CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvla 68 
                                       +giiG+G++g+a+a++++  +    +i+   sr+ + +++  +++          e+++++d+v++a
  gi|518651785|ref|YP_008141305.1| 147 LGIIGMGRIGKAIARRASGFD---MKII-YYSRHRHDVDADFASID---------ELLQQSDFVIIA 200
                                       8**************999888...8888.56999998877666554.........455555555555 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 ?   -3.2   0.0         5   1.1e+04      61      77 ..      56      72 ..      48      92 .. 0.60
   2 !   17.2   0.2   2.2e-06    0.0048       3      78 ..     147     239 ..     145     247 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5
                                      TEEEETTEEEEEE--SS CS
                           Gp_dh_N 61 ealvvngkkikvlaekd 77
                                      ++l+ +gkk+kv+++ +
  gi|518651785|ref|YP_008141305.1| 56 KELIDHGKKLKVISTYS 72
                                      55666666666665543 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2.2e-06
                                       EEEESTSHHHHHHHHHHH.............HHTTCEEEEEE-.T..S-HHHHHHHHHEETTTEC-.SS-EEEETTE CS
                           Gp_dh_N   3 vainGfGRIGrlvlrall.............eekelevvaind.l..tdletlayllkyDsvhgrf.kgeveaeeea 62 
                                       ++i G+GRIG+ ++r +              ++ + ++  i + l   d   +a  l+ D+ h    ++  +++++a
  gi|518651785|ref|YP_008141305.1| 147 LGIIGMGRIGKAIARRASgfdmkiiyysrhrHDVDADFASIDElLqqSDFVIIALDLNADTFHFMDyQKISKMKKTA 223
                                       79**************999999999**9964444889999*994433455567778999999976515555566888 PP

                                       EEETTEEEEEE--SSG CS
                           Gp_dh_N  63 lvvngkkikvlaekdp 78 
                                       + +ng++ k+++ekd 
  gi|518651785|ref|YP_008141305.1| 224 FLINGTRGKIVNEKDL 239
                                       ***********99984 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.061   1.4e+02      34      73 ..      15      53 ..       4      71 .. 0.81
   2 ?    8.3   0.1    0.0012       2.6       3      19 ..     149     165 ..     147     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.061
                                      HHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
                            TrkA_N 34 veelreeglevvvgdatdeevLeeagiekadaviaatgdd 73
                                      +e++++ ++ev+ g++  ++ L   +i +ad+++++++++
  gi|518651785|ref|YP_008141305.1| 15 IEKIENMEIEVFSGNGNMRDWLL-SNIGSADGILITLNEK 53
                                      56667777889999999888776.59**********9987 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0012
                                       EES-SHHHHHHHHHHHH CS
                            TrkA_N   3 iiGlGrvGrslaeeLse 19 
                                       iiG+Gr+G+++a++ s 
  gi|518651785|ref|YP_008141305.1| 149 IIGMGRIGKAIARRASG 165
                                       9************9776 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 ?    0.3   0.0      0.21   4.7e+02      38      59 ..      77      98 ..      49     121 .. 0.61
   2 ?    9.9   0.0   0.00023      0.51       2      67 ..     142     200 ..     141     235 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.21
                                      -HHHHHHHHTT-EEEEHHHHHH CS
                              IlvN 38 sksvkkAkeegfevltvaeavk 59
                                      +  v+ Ak++g+ v+++ e+ +
  gi|518651785|ref|YP_008141305.1| 77 HIDVEYAKSKGIIVTNTPEVLT 98
                                      3346667777777777777654 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00023
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE- CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmil 67 
                                       ++gk++ +iG+G  G+a a+  r sg+d+ +  ++ ++          + ++++e+ +++d+v+i 
  gi|518651785|ref|YP_008141305.1| 142 IHGKTLGIIGMGRIGKAIAR--RASGFDMKIIYYSRHRHDVD-----ADFASIDELLQQSDFVIIA 200
                                       789*************9998..78888888877776643333.....3446778888888888775 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     6e-05      0.13       2      58 ..     148     205 ..     147     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH....TTTCEEEEE--TTT CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka....lgvrfeaialdaen 58 
                                        iiG G++G+a+a+  +  fd+  +i+  +r+++ ++a +a++    ++++f +iald + 
  gi|518651785|ref|YP_008141305.1| 148 GIIGMGRIGKAIARRASG-FDM--KIIYYSRHRHDVDADFASIdellQQSDFVIIALDLNA 205
                                       69************9876.678..9***************999999988888888888764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2022.84
//
Query:       gi|518651786|ref|YP_008141306.1|  [L=220]
Description: alkaline phosphatase like protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-24   84.3   6.5    8.5e-24   84.3   6.5    2.0  2  SNARE_assoc  SNARE associated Golgi protein
  ------ inclusion threshold ------
      0.012   16.0   0.6      0.018   15.5   0.6    1.2  1  DUF1180      Protein of unknown function (DUF1180)
        4.2    7.3   5.3        1.1    9.2   0.2    2.3  2  RseC_MucC    Positive regulator of sigma(E), RseC/MucC


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 !   84.3   6.5   1.4e-27   8.5e-24       1     119 [.      40     173 ..      40     174 .. 0.95
   2 ?   -0.3   0.0      0.25   1.5e+03     102     117 ..     189     204 ..     177     216 .. 0.67

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 1.4e-27
                       SNARE_assoc   1 lPsevllvaaGvlf............glllgtlvtslgallGaslayllgrylgr....kalrrkllsekrvkaler 61 
                                       +Pse+++++ G+l+            +++l ++v s+g l+Ga++ay++g+y g+    ++++  +l+++++++ ++
  gi|518651786|ref|YP_008141306.1|  40 IPSEIVMTFSGYLAfyrlldpyspyvSVVLLLIVGSVGDLIGAWIAYWIGKYGGDpfiiRYGKYLFLKPDTIDRTKA 116
                                       8************9999997776666666699********************************************* PP

                       SNARE_assoc  62 lverygflallllrllpivPrdlvnyvaGltrvsfkrFflatfiGsipwalvyaylGs 119
                                       +++ryg l +++ r++p++ r++++++aG++ ++f++F ++t+ G i+ ++v++ylG 
  gi|518651786|ref|YP_008141306.1| 117 WFNRYGDLSVFITRFIPVF-RTFISIPAGIATMNFRKFSIYTLSGDIIFNVVLIYLGI 173
                                       *****************98.************************************96 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                       SNARE_assoc 102 atfiGsipwalvyayl 117
                                       ++ +G+++ a++++yl
  gi|518651786|ref|YP_008141306.1| 189 YSYVGIAIFAVIIVYL 204
                                       5555666655555555 PP

>> DUF1180  Protein of unknown function (DUF1180)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.5   0.6     3e-06     0.018     104     129 ..     191     216 ..     184     220 .] 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3e-06
                           DUF1180 104 lvlvvvsaavivylvvRtvrlrrrnr 129
                                       +v +++ a++ivyl+vR++r r rn 
  gi|518651786|ref|YP_008141306.1| 191 YVGIAIFAVIIVYLIVRVIRNRNRNT 216
                                       78899****************77764 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.5      0.15   8.8e+02      80     116 ..      49      90 ..      33      96 .. 0.61
   2 ?    9.2   0.2   0.00019       1.1      76     122 ..     167     216 ..     161     220 .] 0.82

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.15
                         RseC_MucC  80 lgallgsall.....gssellaalgallglvlgflivrllsk 116
                                        g+l+++ ll       s +l ++++ +g ++g +i++++ k
  gi|518651786|ref|YP_008141306.1|  49 SGYLAFYRLLdpyspYVSVVLLLIVGSVGDLIGAWIAYWIGK 90 
                                       444444444466656555666666666677777777776655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00019
                         RseC_MucC  76 lllilgallgsall....gssellaalgallglvlgflivrllskrlkkks 122
                                       +l+ lg+l+gs +       +e   + +a++++++ +livr++++r +++ 
  gi|518651786|ref|YP_008141306.1| 167 VLIYLGILFGSHWEilskYFTEYSYVGIAIFAVIIVYLIVRVIRNR-NRNT 216
                                       66778888888888888888999999*******************9.4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       752  (0.0419432); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1559.17
//
Query:       gi|518651787|ref|YP_008141307.1|  [L=412]
Description: hypothetical protein FACI_IFERC00001G0426 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-17   63.1  60.2    1.5e-12   47.2  42.6    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 !   47.2  42.6   8.1e-17   1.5e-12      13     313 ..      26     325 ..      16     328 .. 0.73
   2 !   29.7   9.5   1.6e-11   2.9e-07       7     186 ..     229     404 ..     223     411 .. 0.81

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 8.1e-17
                             MFS_1  13 silgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwl. 87 
                                       ++++++l+l ++ + l++s  +i+l++    l+ +v++l+lGrl+d++G  ++l+lg ++ ++gllll++++++++ 
  gi|518651787|ref|YP_008141307.1|  26 ALIFVTLSLpLYLHFLHFSLVFISLIYIPIILFNVVLVLILGRLGDKIGYSKILILGEAFPVVGLLLLALSTNIYVi 102
                                       4455555555777999************************************************6666676776651 PP

                             MFS_1  88 ...llvlrvlqGlga..galfpagaaliadwfpk.eergraigllsagfslGailgpllgg...llasslgWravfy 155
                                           +++ +  G+g+  ga+ p++ a++a  +p+  +r   ++ll+a++s+ +i+g l+ +   +++s++g  + + 
  gi|518651787|ref|YP_008141307.1| 103 atgAIIAGITGGAGGmrGAFSPGMTAFVANNYPGeGNRVNRLSLLTATASFFSIFGGLFLSlygIISSAIGILLFYR 179
                                       33455555555555556899**************77999999*****999999999877765658888999555555 PP

                             MFS_1 156 ilaivsllafv..lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltll 230
                                       ++ ivs+l++   l++l  + e++++k+ + + +         ++ +k+ll+      +++   ++++++ +++ ll
  gi|518651787|ref|YP_008141307.1| 180 VFFIVSFLLVFgsLIALSRLHEYRRPKKTTRIMK--------KAS-FKYLLR------IILPNSINAAAIGIAMPLL 241
                                       5555555542211222233333333333322222........233.445554......88888888889999***** PP

                             MFS_1 231 plylqevlgls.glllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllll 305
                                       pl++   ++ + g  ++g ++ ++++++ai+++ +g+++  r+ + ++  +a +l  ++++++a++++   a+++++
  gi|518651787|ref|YP_008141307.1| 242 PLFFELKFHVDpG--TVGNIYTIAYAATAIGSFTSGKFInGRIDSLKMASIAHILQGALFIIIAFTPFLFIATAIYV 316
                                       ***********65..55555*******************99999888888888888888888888888866665555 PP

                             MFS_1 306 .vlvliGfg 313
                                         ++++G+g
  gi|518651787|ref|YP_008141307.1| 317 gRMAVAGIG 325
                                       444445555 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 1.6e-11
                             MFS_1   7 lsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsd.rfGrrrvlllglllfalglllllfa 82 
                                       ++a+a++i++p+lpl+    ++++p ++g ++t+ ++++a++s+  G +++ r+ + ++  ++ +l ++ +++++f 
  gi|518651787|ref|YP_008141307.1| 229 INAAAIGIAMPLLPLFFELKFHVDPGTVGNIYTIAYAATAIGSFTSGKFINgRIDSLKMASIAHILQGALFIIIAF- 304
                                       7899******************************************9998868*******9999999999777778. PP

                             MFS_1  83 sslwlllvlrvlqGlga.galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       +++ +++ +  +  ++  g++ p+ +a+ ++   ke+ g  +++ +++   +  l+ +++g+l+  l++  + +i +
  gi|518651787|ref|YP_008141307.1| 305 TPFLFIATAIYVGRMAVaGIGSPMRGAINVRGIDKEDYGTSTSIQGVSGRGSQ-LTTGASGYLM-DLNFAFPLLIGG 379
                                       7766444444444444459999********************99998666666.5559999999.7789999***** PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspke 186
                                       ++ + ++vl   +++  ++ ++ ks+++
  gi|518651787|ref|YP_008141307.1| 380 AMQAAGGVL---YYVLVKSWHPEKSSER 404
                                       ********5...5544444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2675.43
//
Query:       gi|518651788|ref|YP_008141308.1|  [L=212]
Description: phosphoglycerate mutase family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-36  124.2   0.0    6.4e-36  123.9   0.0    1.0  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   0.0   3.5e-40   6.4e-36       2     181 ..      18     190 ..      17     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 3.5e-40
                                       EEEE---BTTB--....TT----.B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GGG CS
                        His_Phos_1   2 yLvRHGetewnaegrlqgrtdvp.LteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldegL 77 
                                       +++RHGe+  n+e++l+   d   Lt++G++qAe+++e l g ++d i+sSp+kRa++Ta++i++  gl+v++d++L
  gi|518651788|ref|YP_008141308.1|  18 IFIRHGESNINVEKVLSDDVDHNtLTDTGEKQAERTGEQLTGLKFDGIISSPIKRAYDTANIISNYVGLDVKIDDRL 94 
                                       79*************999999888***************************************************** PP

                                       S----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHHH CS
                        His_Phos_1  78 rEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggviral 154
                                       rE+ +G+  g++ +e  ++    + + +   +  +  g E++e++++Rv+a+++e + ++     + VsH  +ira+
  gi|518651788|ref|YP_008141308.1|  95 REVYLGNANGHNINEFLDT---LYPNSHITGKVRDSLGMETWEHLQERVKACMDEYKGKY-----IFVSHSDPIRAI 163
                                       ***********88887777...4444444444445679***************9876665.....89********** PP

                                       HHHHHT--GGGGGGB---TT-EEEEEE CS
                        His_Phos_1 155 larllglpleelrrleldnaslsvlef 181
                                       +++++gl+  e   ++++nas++v+  
  gi|518651788|ref|YP_008141308.1| 164 ASYYMGLSEGESFGMAIKNASMTVIAR 190
                                       ***********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       579  (0.032294); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1323.05
//
Query:       gi|518651789|ref|YP_008141309.1|  [L=433]
Description: hypothetical protein FACI_IFERC00001G0428 [Ferroplasma acidarmanus fer1]
Scores for complete 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-57  192.5  40.8    1.1e-56  192.2  40.8    1.0  1  Ammonium_transp  Ammonium Transporter Family
  ------ inclusion threshold ------
        4.7    7.6   6.4         40    4.6   2.0    3.2  2  Wzz              Chain length determinant protein


Domain annotation for each model (and alignments):
>> Ammonium_transp  Ammonium Transporter Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.2  40.8   1.3e-60   1.1e-56       1     377 [.      18     420 ..      18     432 .. 0.88

  Alignments for each domain:
  == domain 1  score: 192.2 bits;  conditional E-value: 1.3e-60
                                       HHHHHHHHHHHHHHHHHHHHHHHHSSGGGHHHHHHHHHHHHHHHHHHHHHTHHHHHHSSCBSSSSSCE-........ CS
                   Ammonium_transp   1 aflllsaalvifmqagfalleaglvrsknvlnilvknlldlavvvllyvlfGyslafgkskgvsgfign........ 69 
                                       ++++++a++++ m++ +++le g   +k   n ++k ++ ++  +++  ++G+ +af     + g+ign        
  gi|518651789|ref|YP_008141309.1|  18 LWIVIAAIFIFAMTIAVGFLEVGELGKKFK-NSMLKTIVITGTAMFVMAIIGFNTAFAPT--LYGIIGNpfykdgfm 91 
                                       59***********************99985.5588888888878999999********98..***********9999 PP

                                       .............TTTTSCCGCCTTCCHHHHHHHHHHHHHHHHHHHHHHCTTTB-HHHHHHHHHHHHHHTHHHHHHH CS
                   Ammonium_transp  70 .............lglsaagvqdetlldglfflfqlafaataitivsgavaerikfsayllfsallgtlvyppvahw 133
                                                     +++++ + +  l+ g++f+f  a aa+++++v  +v +++kf a++ fs++ + ++    a w
  gi|518651789|ref|YP_008141309.1|  92 lggfspgvifntwWSMGTSYF-NTGLTTGSYFFFETACAAVTLALVGVIVLNKVKFGAFFAFSIVYFIFIWNLPAAW 167
                                       999987776665422222222.224445569********************************************** PP

                                       HHS.SSHHHHTT--.-SSSTTTTHHHHHHHHHHHHHHHS-STTTTG.TTTSS--GSB.HHHHHHHHHHHHHHHHHHH CS
                   Ammonium_transp 134 vwgeggwlaklgvliDfAgstvVHlvggvagLaaalvlgkregrfe.gkeeaikghn.lpfavlGtllLwfgWfgFN 208
                                       +w+  gwl+++g+  DfAg++vVH  +++agLa+++ + + e ++  +++ +++ +       +G l+Lw+gWfgFN
  gi|518651789|ref|YP_008141309.1| 168 IWNPSGWLYQMGMR-DFAGGIVVHGAAAIAGLAIVYEIWREERKKGlKTSLKVNIKPdYQWLAVGILILWIGWFGFN 243
                                       **************.*******************998877776665644444444430345668************* PP

                                       HGGGSSSSHHHHH.HHHHHHHHHHHHHHHHHHHHHHHCSS.-BHHHHHHHHHHHHHHHTTTTTTS-HHHHHHHHHHH CS
                   Ammonium_transp 209 aGsaltankrararaavtTllAaaagaltallisrlkegk.invlglanGilAGlVAiTaacavvepwgAliiGlvA 284
                                       +Gs l+ n+     ++++T +A+ ag++ ++l+sr+ +   + ++ ++nGil Gl+ +T+ +++v+p +Ali+Gl++
  gi|518651789|ref|YP_008141309.1| 244 PGSILAFNDDVLV-VVIATFVASGAGMVSTMLFSRMFDREtPIIIVAVNGILMGLIIVTPLAGFVSPASALILGLIG 319
                                       ***********99.*********************998554999999****************************** PP

                                       HHHHHHHHHHHHHHHTC-CTTHHHHHHHHHHHHHHHHHHHHTSHHHC.....SSHSSTTGGGT-C...HHHHHHHHH CS
                   Ammonium_transp 285 gvlsvlgvkklkeklkidDsldvvavHgvgGiwGllavgifaaekvv.....askisggllsgeg...kqlvvqlig 353
                                       g l v + k++++   + D+++ ++ HgvgGi G+l+ g+f +   +     a   +g l++g+    +ql+++++g
  gi|518651789|ref|YP_008141309.1| 320 GPLFVGAEKLFAKVKWFSDPVGLFPAHGVGGIFGVLMIGLFTQHAFAaasgnAILPNGLLFGGGFaalRQLGIEAFG 396
                                       ********9888888899*************************99888887666667778888779999******** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT CS
                   Ammonium_transp 354 ilvilayafvvtlilllllklllg 377
                                       + v+++++f+++++ +++++++  
  gi|518651789|ref|YP_008141309.1| 397 VFVVVITVFAISFLAIFIIGKISH 420
                                       *******************99865 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   2.0    0.0045        40       2      28 ..       4      30 ..       3      39 .. 0.81
   2 ?    3.3   0.1     0.011     1e+02       8      34 ..     274     300 ..     272     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0045
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Wzz  2 eiDLieLlsvLwkrkklIilvtllfal 28
                                       iD + + ++L+ + +++i+ +++fa+
  gi|518651789|ref|YP_008141309.1|  4 FIDYLSISNILINNLWIVIAAIFIFAM 30
                                      588899999********9999999875 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                               Wzz   8 LlsvLwkrkklIilvtllfallaviya 34 
                                       L+s+ ++r   Ii+v++ ++l+++i++
  gi|518651789|ref|YP_008141309.1| 274 LFSRMFDRETPIIIVAVNGILMGLIIV 300
                                       8999999****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2891.72
//
Query:       gi|518651790|ref|YP_008141310.1|  [L=82]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-11   43.2   0.2      4e-11   42.6   0.2    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
     0.0025   18.2   0.1     0.0059   17.0   0.0    1.6  2  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
  ------ inclusion threshold ------
      0.036   14.1   0.5      0.043   13.9   0.5    1.1  1  GutM            Glucitol operon activator protein (GutM)
      0.037   14.1   0.1      0.065   13.3   0.0    1.4  2  AbrB-like       AbrB-like transcriptional regulator


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.2   8.8e-15     4e-11       2      42 ..       7      47 ..       6      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 8.8e-15
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCH CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplk 42
                                      +vG++g+v+iP ++r+ l i +G++ ++ +dg+kiil++lk
  gi|518651790|ref|YP_008141310.1|  7 TVGSNGQVVIPVALRKTLKITPGSKMIFKIDGNKIILEKLK 47
                                      8*************************************987 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.3e-06    0.0059       1      43 [.       5      45 ..       5      53 .. 0.84
   2 ?   -0.3   0.0      0.34   1.5e+03      29      54 ..      53      78 ..      40      80 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.3e-06
                    PrlF_antitoxin  1 estltergqttiPasvRkaLklkkgrdkiaytilddgkvvisr 43
                                      e t+ + gq  iP ++Rk Lk+++g+ k+ ++i+ ++k+++++
  gi|518651790|ref|YP_008141310.1|  5 EMTVGSNGQVVIPVALRKTLKITPGS-KMIFKID-GNKIILEK 45
                                      6689999*****************87.999*996.55666666 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.34
                    PrlF_antitoxin 29 iaytilddgkvvisraeeeaeDpvle 54
                                      i  +  ++gk v + + +e eD +++
  gi|518651790|ref|YP_008141310.1| 53 IFRETSKKGKNVNEIKYSEYEDEIIK 78
                                      44445555555555566666666665 PP

>> GutM  Glucitol operon activator protein (GutM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   9.5e-06     0.043      34      95 ..      11      76 ..       2      82 .] 0.71

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.5e-06
                              GutM 34 kgkvai...GrkkgrfragvivllavdedgiivearvmkGvTvfarf.keleelegksleeieeek 95
                                      +g+v i    rk+ ++++g+ +++ +d ++ii+e  ++  v +f    k+ +++++ +++e e+e 
  gi|518651790|ref|YP_008141310.1| 11 NGQVVIpvaLRKTLKITPGSKMIFKIDGNKIILEKLKIDSVNIFRETsKKGKNVNEIKYSEYEDEI 76
                                      46666655557889*****************************97541444555555555555544 PP

>> AbrB-like  AbrB-like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.4e-05     0.065      33      69 ..       6      42 ..       3      43 .. 0.88
   2 ?   -3.2   0.0       2.1   9.2e+03      21      28 ..      56      63 ..      47      66 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.4e-05
                         AbrB-like 33 vsVqknGnLliGsaYTkklgLkpGdefeIklgrkhih 69
                                      ++V +nG+++i  a  k l ++pG ++  k+  ++i 
  gi|518651790|ref|YP_008141310.1|  6 MTVGSNGQVVIPVALRKTLKITPGSKMIFKIDGNKII 42
                                      5799*********************988888777765 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.1
                         AbrB-like 21 skkkrGrk 28
                                      +++k+G++
  gi|518651790|ref|YP_008141310.1| 56 ETSKKGKN 63
                                      45556654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 525.47
//
Query:       gi|518651791|ref|YP_008141311.1|  [L=87]
Description: hypothetical protein FACI_IFERC00001G0430 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 532.72
//
Query:       gi|518651792|ref|YP_008141312.1|  [L=166]
Description: hypothetical protein FACI_IFERC00001G0431 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-05   25.0   0.9      2e-05   24.4   0.1    1.6  2  Peptidase_M48  Peptidase family M48
    3.3e-05   23.3   0.8    4.5e-05   22.8   0.8    1.2  1  Peptidase_M56  BlaR1 peptidase M56
     0.0039   16.8   0.2     0.0051   16.4   0.2    1.2  1  DUF2268        Predicted Zn-dependent protease (DUF2268)


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 ?   -1.4   0.1      0.27   1.6e+03     111     131 ..      21      41 ..       9      56 .. 0.48
   2 !   24.4   0.1   3.4e-09     2e-05      23     103 ..      77     156 ..      59     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.27
                                       TT--S---HHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 111 gafldalavliglliillfla 131
                                        a+l + av+++++i+l+  +
  gi|518651792|ref|YP_008141312.1|  21 LASLISFAVILLIMIQLQSSK 41 
                                       223333333333333333333 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 3.4e-09
                                       -EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  23 pltkvyvvnspkrNAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivsllasillllgla 99 
                                       +  k+ +vn+  r   +++ gk+ +i++++  +   l+++e +a   HE+ H+ +++++++ i +l   ++  + l+
  gi|518651792|ref|YP_008141312.1|  77 EVFKFPEVNKTYRSPSFTPLGKQAKIFINENFF-HSLDDSEREALVFHEIHHFIRKDAAKTYILALTILLIAAVSLI 152
                                       556777777777777799***************.***************************9999998888888888 PP

                                       HHTT CS
                                       xxxx RF
                     Peptidase_M48 100 llis 103
                                       +li+
  gi|518651792|ref|YP_008141312.1| 153 VLIQ 156
                                       8775 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   0.8   7.4e-09   4.5e-05     103     221 ..      19     142 ..       2     157 .. 0.67

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.4e-09
                     Peptidase_M56 103 killliWivgalilllyliaallvlkkr.fvrklgklraeel...keaLkeakeemqlkrnikirlsssidsPavlg 175
                                       +il+ +  + +++l++  ++++ + +k  ++++ +++ +  l   + aL +   ++ l       ++++  sP ++ 
  gi|518651792|ref|YP_008141312.1|  19 NILASLISFAVILLIMIQLQSSKQGRKTdITQRFSAIIDYDLskkYTALTKHITHVDLEVFKFPEVNKTYRSPSFTP 95 
                                       444333333333334556677777777777777776655444000444444444444333333356778889*9999 PP

                     Peptidase_M56 176 llkp.rIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavl 221
                                       l k   I + ++f+++l+d e+e  + HE  H+ rkD+   +++a+ 
  gi|518651792|ref|YP_008141312.1|  96 LGKQaKIFINENFFHSLDDSEREALVFHEIHHFIRKDAAKTYILALT 142
                                       987527*******************************9988887764 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   8.5e-07    0.0051       5      84 ..      60     136 ..      56     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.5e-07
                           DUF2268   5 ieealekliealkkpdvdvfilpvneenrklieekgykgglaipdkiflfl.leneyskerlaallaHEyhHvvrlk 80 
                                       +++++++l ++++  d++vf +p  +++    +++   + l+ + kif+   + ++ ++++ +al+ HE+hH +r +
  gi|518651792|ref|YP_008141312.1|  60 LSKKYTALTKHITHVDLEVFKFPEVNKT-YRSPSF---TPLGKQAKIFINEnFFHSLDDSEREALVFHEIHHFIRKD 132
                                       6789999******99****988876666.344444...4777888999987778899999***************98 PP

                           DUF2268  81 qlek 84 
                                       + + 
  gi|518651792|ref|YP_008141312.1| 133 AAKT 136
                                       8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1210  (0.0674884); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); 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: 0.59u 0.36s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 893.51
//
Query:       gi|518651793|ref|YP_008141313.1|  [L=377]
Description: transposase mutator type [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-98  329.9   0.3    2.1e-98  329.7   0.3    1.0  1  Transposase_mut  Transposase, Mutator family
    4.3e-12   46.3   0.0    8.9e-12   45.3   0.0    1.6  1  MULE             MULE transposase domain
    0.00097   18.7   0.0     0.0021   17.6   0.0    1.5  1  DDE_Tnp_IS66     Transposase IS66 family
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.092   12.5   0.0    2.1  2  DDE_Tnp_ISL3     Transposase
      0.034   14.4   0.2        3.1    8.0   0.0    2.9  3  DDE_Tnp_IS240    DDE domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  329.7   0.3  5.8e-102   2.1e-98      18     379 ..      14     369 ..       1     371 [. 0.92

  Alignments for each domain:
  == domain 1  score: 329.7 bits;  conditional E-value: 5.8e-102
                   Transposase_mut  18 easgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdRsGsFspalle 94 
                                        +  +   +++l k +l+el+++e++e+l+a ryer ++ + +RnG+++r+l T+ g++ l  P+ R+ sF++a+++
  gi|518651793|ref|YP_008141313.1|  14 SYGLNRKNMRDLKKWFLNELMNEEAEEQLNASRYERNNNSKDYRNGYKQRSLLTTDGKVILDKPQFRETSFHTAVFD 90 
                                       344455689******************************************************************** PP

                   Transposase_mut  95 rykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDaly 171
                                       +y R ek +e+ ++e y++Gvstr v+k++++l+   +vS+s vS+++ +ld++v++f eR ++ + y ++++D++y
  gi|518651793|ref|YP_008141313.1|  91 NYSRVEKSVESIILESYLSGVSTRSVNKVIKSLGI--EVSPSYVSSLSSRLDKTVNEFLERKIDGE-YKFIYIDGTY 164
                                       *********************************99..79**************************9.********** PP

                   Transposase_mut 172 lkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfp 248
                                       lk+R++gr ++ka++i +g+++dG+re+Lg ++ dsE e  W+ ++++Lk+rGl+gve+v+sD+ kG+++a++++fp
  gi|518651793|ref|YP_008141313.1| 165 LKIRNNGRYRNKAIYICVGINSDGYREVLGARIYDSETEIEWELFFDDLKDRGLNGVEMVISDGNKGIREAVKQSFP 241
                                       ***************************************************************************** PP

                   Transposase_mut 249 eaavQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgk.kypkvaelldeaaedvlafl 324
                                       ++++Q C vH++rnl + + k++++ ++  +k+  +++d+    +      +kl +  + k  +++d+  + + ++ 
  gi|518651793|ref|YP_008141313.1| 242 GSSWQYCHVHFMRNLRKSTGKQQWKFLSLLIKQALDNPDILPLLQ------DKLFDrGLDKCSTMFDKYYDSLYNYR 312
                                       ***************************************966554......33333367777778888888888888 PP

                   Transposase_mut 325 afpeqir..rkikstNllErLNkeirRrtrvvgiFPneesilrlvgavlaeahdewk 379
                                       +f+++++  r+++  N +ErLN+ei+Rrt+++g FP ++s++rl g+++++ ++e+ 
  gi|518651793|ref|YP_008141313.1| 313 SFNTNMQglRRLRVSNTIERLNAEIKRRTKKIGAFPSDDSAMRLAGSIMMDINEEYV 369
                                       8877664449********************************************997 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.5e-15   8.9e-12       2      96 .]     158     255 ..     157     255 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.5e-15
                              MULE   2 vvlDgTykt...n.kyklplltv.vgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekal 73 
                                       + +DgTy++   n +y+ + + + vg+++ g   +l+  + +se+e  +e ++++l+++    +  +++i+D +k++
  gi|518651793|ref|YP_008141313.1| 158 IYIDGTYLKirnNgRYRNKAIYIcVGINSDGYREVLGARIYDSETEIEWELFFDDLKDRGL--NGVEMVISDGNKGI 232
                                       789****863333477666544449*********************************644..69************ PP

                              MULE  74 lnaleevfpeakhrlClfHiakn 96 
                                       ++a+++ fp++  + C+ H+++n
  gi|518651793|ref|YP_008141313.1| 233 REAVKQSFPGSSWQYCHVHFMRN 255
                                       ********************987 PP

>> DDE_Tnp_IS66  Transposase IS66 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   5.8e-07    0.0021      11     165 ..     101     264 ..      93     294 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 5.8e-07
                      DDE_Tnp_IS66  11 eilvlkyadhlPlyRqeeilarlGvelsrgtlanwvkraaelleplvealkaallasevihaDETtlrvlkpgrgkg 87 
                                       +i+++ y  +++ + ++++++ lG+e+s++ ++++  r  ++++++ e+  +   + + i +D T l++ ++gr ++
  gi|518651793|ref|YP_008141313.1| 101 SIILESYLSGVSTRSVNKVIKSLGIEVSPSYVSSLSSRLDKTVNEFLERKID--GEYKFIYIDGTYLKIRNNGRYRN 175
                                       588999999************************9999999988887765333..47789*********999****** PP

                      DDE_Tnp_IS66  88 kksylWvyvtdkr....kpavlfeyspsRggevaealLag..fkG..vlvsDgyagYnklae...eqvthalCwaHl 153
                                       k  y+ v ++++       a +++ +++   e + + L++   +G  +++sDg +g ++  +   ++   ++C++H 
  gi|518651793|ref|YP_008141313.1| 176 KAIYICVGINSDGyrevLGARIYDSETEIEWELFFDDLKDrgLNGveMVISDGNKGIREAVKqsfPGSSWQYCHVHF 252
                                       **********9999777777777777777766665555666766655799********977779999999******* PP

                      DDE_Tnp_IS66 154 rRkfvdaeeakk 165
                                        R++++ + +++
  gi|518651793|ref|YP_008141313.1| 253 MRNLRKSTGKQQ 264
                                       ****99987654 PP

>> DDE_Tnp_ISL3  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.68   2.5e+03     124     124 ..      53      53 ..       8     104 .. 0.57
   2 ?   12.5   0.0   2.6e-05     0.092      39      90 ..     205     256 ..     165     267 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.68
                      DDE_Tnp_ISL3 124 p 124
                                        
  gi|518651793|ref|YP_008141313.1|  53 S 53 
                                       1 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.6e-05
                      DDE_Tnp_ISL3  39 tlkafleslsekerekveavvmDmsaayksavkealPnAkivvDrFHvvkla 90 
                                       + + f+++l+++  + ve+v+ D+++++++avk+ +P  +  + + H+++ +
  gi|518651793|ref|YP_008141313.1| 205 EWELFFDDLKDRGLNGVEMVISDGNKGIREAVKQSFPGSSWQYCHVHFMRNL 256
                                       55679**9*999*************************988877777777765 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.6   1.3e+04     105     128 ..      78     101 ..      75     104 .. 0.76
   2 ?    3.1   0.0     0.029   1.1e+02       6      79 ..     160     241 ..     156     274 .. 0.68
   3 ?    8.0   0.0   0.00086       3.1      86     124 ..     317     355 ..     286     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.6
                     DDE_Tnp_IS240 105 tlKkrlrptrgfkslksaaktlag 128
                                       ++++  ++t  f++ ++++k ++ 
  gi|518651793|ref|YP_008141313.1|  78 QFRETSFHTAVFDNYSRVEKSVES 101
                                       577777888889998888888775 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.029
                     DDE_Tnp_IS240   6 vDETyvkikGkwaY....lyrav..Dkegr..ildflvskrRdtkaakaflrkalkkeklepeeivtDkasayasal 74 
                                       +D Ty+ki+ + +Y    +y  v  +++g   +l++ + +   +    +f+  + ++  +  e ++ D+++   +a+
  gi|518651793|ref|YP_008141313.1| 160 IDGTYLKIRNNGRYrnkaIYICVgiNSDGYreVLGARIYDSETEIEWELFFDDLKDRGLNGVEMVISDGNKGIREAV 236
                                       899*****987777444444433225555334788888777777777777777777776666667778888777777 PP

                     DDE_Tnp_IS240  75 kelkr 79 
                                       k+ ++
  gi|518651793|ref|YP_008141313.1| 237 KQSFP 241
                                       77776 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00086
                     DDE_Tnp_IS240  86 evshvqvkylnnriEsdhrtlKkrlrptrgfkslksaak 124
                                       +++ + +    n iE+ ++++K+r+++++ f s +sa +
  gi|518651793|ref|YP_008141313.1| 317 NMQGLRRLRVSNTIERLNAEIKRRTKKIGAFPSDDSAMR 355
                                       44455555668********************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2317.35
//
Query:       gi|518651794|ref|YP_008141314.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G0433 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0031   17.0   0.2     0.0034   16.9   0.2    1.0  1  DUF373    Domain of unknown function (DUF373)
     0.0097   16.2   0.5     0.0097   16.2   0.5    1.1  1  DUF4293   Domain of unknown function (DUF4293)


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.2   3.8e-07    0.0034     145     214 ..       6      76 ..       1      79 [. 0.84

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 3.8e-07
                            DUF373 145 kkalkdpelrktiLvplGlllliyalllllglpelalaiillllGl.ylllrGfgldelleelleklkesl 214
                                        + +k  ++++ +++p+ +l++i++ l+ +++ ++    +++ll + yl+l G  +d++l+++ +k+++s 
  gi|518651794|ref|YP_008141314.1|   6 SHKIKKRKISNKTFIPIFILFIIIGYLYYYNIFNYKNFYLTILLDVcYLILLGDAIDRYLDHIRKKWQNSS 76 
                                       56678899*********************99999888888888864399999******9999999988876 PP

>> DUF4293  Domain of unknown function (DUF4293)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.5   1.1e-06    0.0097      45      91 ..      10      56 ..       1      79 [. 0.79

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
                           DUF4293 45 eaetsvnvsvwvlvilllliailaliaIflyknRklQlrlclinlll 91
                                      +++++ n + ++++il ++i  l  ++If ykn  l + l ++ l+l
  gi|518651794|ref|YP_008141314.1| 10 KKRKISNKTFIPIFILFIIIGYLYYYNIFNYKNFYLTILLDVCYLIL 56
                                      455668999************************88877766555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1121  (0.0625244); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 533.88
//
Query:       gi|518651795|ref|YP_008141315.1|  [L=236]
Description: hypothetical protein FACI_IFERC00001G0434 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-12   45.1   4.0    1.5e-11   44.2   4.0    1.5  1  DnaJ      DnaJ domain
  ------ inclusion threshold ------
      0.087   13.1   2.8        4.4    7.6   0.6    2.3  2  DUF4375   Domain of unknown function (DUF4375)
       0.83   10.1   8.3       0.22   11.9   3.6    2.3  2  NBD94     Nucleotide-Binding Domain 94 of RH


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   4.0   2.6e-15   1.5e-11       2      55 ..     177     232 ..     176     236 .] 0.89

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.6e-15
                                       HHHHHTSSTTG-HHHHHHHHHHHHHHHSTT.TSCCHH.HHHHHHHHHHHHHHHHTS CS
                              DnaJ   2 yYeiLgvskdasedeIkkaYrklalkyHPD.knpkdp.eaeekFkeineAyevLsd 55 
                                       +++iL+++++ + + Ik+aYrk+a+ yHPD   p+++ e +ek k+in Aye L +
  gi|518651795|ref|YP_008141315.1| 177 LFKILEIDPTDNPEIIKNAYRKMAKIYHPDlTTPENEeEYSEKMKNINYAYEKLYK 232
                                       799***************************65566667**************9976 PP

>> DUF4375  Domain of unknown function (DUF4375)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1    0.0034        20      17      63 ..      93     142 ..      88     164 .. 0.81
   2 ?    7.6   0.6   0.00073       4.4      47      99 ..     182     235 ..     174     236 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0034
                                       HHHHHHHHHHHHHHHCT-HHHH...CCHHHHHHCTT--HHHHHHHHHHHH CS
                           DUF4375  17 lesevnnGGfvqlfqnssgefi...nealkalrliGaeelakllekakkl 63 
                                       l +++nnG ++ +++ns g+ +     + k+l++  a++  + l +a++ 
  gi|518651795|ref|YP_008141315.1|  93 LSEKINNGIILCYYHNSEGQKAfahIFINKSLKRKIAKKIIETLTEAAEK 142
                                       6799***************9987755667788877777777777777664 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00073
                                       CTT--HHHHHHHHHHH.HHHHHHHHHHHHHHTT-HHHHHHH.-GGGHHHHHHHH CS
                           DUF4375  47 liGaeelakllekakk.lykkgkeelereerdeelealyeeeeeefdelDdefy 99 
                                       +i+ +++ +++++a++ + k ++++l++ e++ee+++ +++ + + ++l +++y
  gi|518651795|ref|YP_008141315.1| 182 EIDPTDNPEIIKNAYRkMAKIYHPDLTTPENEEEYSEKMKNINYAYEKLYKKYY 235
                                       67889999********9****************999988887777888888887 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 ?   -0.7   0.1      0.33     2e+03      11      27 ..     122     138 ..     112     148 .. 0.55
   2 ?   11.9   3.6   3.7e-05      0.22      13      54 ..     191     233 ..     179     235 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.33
                             NBD94  11 idkkkkiyeniekllnE 27 
                                       +  k+ki ++i ++l E
  gi|518651795|ref|YP_008141315.1| 122 KSLKRKIAKKIIETLTE 138
                                       33344444444444444 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.7e-05
                             NBD94  13 kkkkiyenieklln.EleeiekektsleevknielsYgrsLik 54 
                                        +k+ y ++ k+++ +l+  e+e+  +e++kni+  Y+++ +k
  gi|518651795|ref|YP_008141315.1| 191 IIKNAYRKMAKIYHpDLTTPENEEEYSEKMKNINYAYEKLYKK 233
                                       389********97549**********************98766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       971  (0.0541581); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); 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: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1737.80
//
Query:       gi|518651796|ref|YP_008141316.1|  [L=409]
Description: hypothetical protein FACI_IFERC00001G0435 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-15   55.3   0.0    2.2e-14   53.7   0.0    1.8  2  Beta-Casp      Beta-Casp domain
    4.8e-13   49.0   0.0      1e-12   47.9   0.0    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
      1e-10   41.4   0.2    4.4e-10   39.3   0.0    2.1  3  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
    2.5e-09   37.4   0.1    1.4e-08   35.0   0.0    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
    7.9e-05   22.3   0.1    0.00024   20.7   0.1    1.8  2  Lactamase_B_2  Beta-lactamase superfamily domain
     0.0085   16.0   0.0      0.099   12.5   0.1    2.6  3  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.069   12.4   2.0       0.85    8.9   0.4    2.2  2  EcKinase       Ecdysteroid kinase


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 ?   -1.3   0.0         1   2.6e+03      23      43 ..      86     105 ..      66     216 .. 0.63
   2 !   53.7   0.0   8.7e-18   2.2e-14      18     110 .]     232     332 ..     220     332 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1
                                       EEEEE-HHHHHHHHHGGGGGG CS
                         Beta-Casp  23 piyldsplaskatevYkeyae 43 
                                       pi +ds l +  +e Y+++ +
  gi|518651796|ref|YP_008141316.1|  86 PILMDS-LKIMRLENYTKMFN 105
                                       666666.33222333332222 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 8.7e-18
                                       TS-S-EEEEE-HHHHHHHHHGGGGGG...............E-SHH....HHHH..HHHS-SSEEEEES-TTSSSSH CS
                         Beta-Casp  18 edlklpiyldsplaskatevYkeyae...............veakslewmeskkeelnsskgpkvilassgmlegGr 79 
                                       +d+++ iy+d+ +++++  +Y + +                ++ ++    +++++  +  ++  +i+++sgml+gG+
  gi|518651796|ref|YP_008141316.1| 232 RDMDYRIYVDG-MGNRISGIYMDTPGfikdpklfrrsmgrvIQVRN----NRMRQ--EAIREADIIITTSGMLDGGP 301
                                       356689*****.********999999**9***99988888755555....44453..3456899************* PP

                                       HHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  80 srellkklledprntvilvgyqaegTlgrkl 110
                                       +  ++ +++edp+++++l+gyq+ gT gr+l
  gi|518651796|ref|YP_008141316.1| 302 VLGYIDAFAEDPKSAIFLTGYQVDGTNGRSL 332
                                       ****************************986 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 !   47.9   0.0   3.9e-16     1e-12       6     152 ..      23     151 ..      17     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 3.9e-16
                     Lactamase_B_6   6 nvkiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayallyakfksklllnipvyatlpvvkLGrvs 82 
                                       + ki++D G + +k        e+    ++v+ i L+ha l+h Ga+++ y++f++      +  at  +++  +  
  gi|518651796|ref|YP_008141316.1|  23 QSKIMIDYGIEPEKPP------EYPLPPEKVNDIFLTHAHLDHTGALPVYYHNFQA------NFHATAMTANSIKPI 87 
                                       5789999999987542......344456799*****************99998865......557888888888888 PP

                     Lactamase_B_6  83 lldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGGtiWkiske 152
                                       l+d+ +  +l+    ++ ++ ed+d+ f+++ t kY+Q++++     +lt +a++aGh +G t+W  ++ 
  gi|518651796|ref|YP_008141316.1|  88 LMDSLKIMRLE--NYTKMFNEEDVDNLFKSMMTAKYEQPFQVD----NLTAVAHSAGHIPGSTMWWFQDA 151
                                       88988877665..44567999******************9776....6*****************98765 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 ?   -2.5   0.0       2.1   5.3e+03      32      47 ..      45      63 ..      42      69 .. 0.77
   2 ?   -2.7   0.0       2.4   6.1e+03      43      60 ..     196     215 ..     194     217 .. 0.57
   3 !   39.3   0.0   1.7e-13   4.4e-10       2      45 ..     345     388 ..     344     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.1
                             RMMBL 32 rn...vilvHGeeeatsal 47
                                      ++   ++l H + ++t al
  gi|518651796|ref|YP_008141316.1| 45 EKvndIFLTHAHLDHTGAL 63
                                      5555799999988888776 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.4
                             RMMBL  43 atsalarllk..eeegidvf 60 
                                        +++l++ ++   e+g +v+
  gi|518651796|ref|YP_008141316.1| 196 VIQRLKESIRetIENGGRVI 215
                                       56778888853334555665 PP

  == domain 3  score: 39.3 bits;  conditional E-value: 1.7e-13
                             RMMBL   2 ipvkarieeidfSgHadknellelirklkprnvilvHGeeeats 45 
                                       i+  ++i+++d+S+Ha++++l ++++++ p+ v+l HG++++++
  gi|518651796|ref|YP_008141316.1| 345 IKPAMKIDFFDLSAHAGHSDLVKFVKGVDPEIVVLCHGDQREKL 388
                                       6778************************************9876 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.0   5.3e-12   1.4e-08      11      79 ..      19      81 ..      11     217 .. 0.76
   2 ?   -2.7   0.0       1.9   4.8e+03     172     197 .]     356     381 ..     349     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 5.3e-12
                                      EEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHH CS
                       Lactamase_B 11 iegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeea 79
                                      ie++ + i+iD G+++e++ +        l+p++v +++lTH+HlDH+G+l+   + ++++ +a a +a
  gi|518651796|ref|YP_008141316.1| 19 IEDKQSKIMIDYGIEPEKPPEY------PLPPEKVNDIFLTHAHLDHTGALPVYYHNFQANFHATAMTA 81
                                      78999****************9......8***********************99998887766555555 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.9
                                       HCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 172 psdaekyldsllklaglkaevlvpgH 197
                                        s ++   d ++ ++g ++e++v++H
  gi|518651796|ref|YP_008141316.1| 356 LSAHAGHSDLVKFVKGVDPEIVVLCH 381
                                       56666677777888999999999998 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 !   20.7   0.1   9.5e-08   0.00024      28     172 ..      44     191 ..      26     216 .. 0.66
   2 ?   -2.2   0.0      0.96   2.5e+03     177     200 ..     358     381 ..     312     381 .. 0.62

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.5e-08
                                       ..SEEEEE-SS--HHHHGGGGCCCC.C--EEEEEEEEHHHHH.............HCCTTCGHHHCHTT.....TTE CS
                     Lactamase_B_2  28 lppidaVllthaHyDHlaglltlre.lrpkklplyapkgvla.............vleanfvylaleee.....pav 85 
                                       +++++ ++lthaH DH+  l+   + ++   ++++a+++++               le+ ++ ++   e      + 
  gi|518651796|ref|YP_008141316.1|  44 PEKVNDIFLTHAHLDHTGALPVYYHnFQ---ANFHATAMTANsikpilmdslkimRLENYTKMFN---EedvdnLFK 114
                                       568889***********77777766543...5788999998866666666665444444433222...134466667 PP

                                       EEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HH..HHHHHCT-SEE CS
                     Lactamase_B_2  86 nvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipee..igerlggadll 160
                                       ++ + + +++f+++  +  +ta++ + ++ +           ++++ + ++++ +gD+ + +     g++  + d+l
  gi|518651796|ref|YP_008141316.1| 115 SMMTAKYEQPFQVD--N--LTAVAHSAGHIP-------GSTMWWFQ-DARSFMITGDLYTRDTNllYGAKPVKTDVL 179
                                       77777788999997..4..666666666666.......44567777.678888888887666551234555558888 PP

                                       EEE-S-SSTTHH CS
                     Lactamase_B_2 161 llditayeddem 172
                                       +++ t+   d  
  gi|518651796|ref|YP_008141316.1| 180 IMESTYAGRDHE 191
                                       888888776664 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.96
                                       T---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 177 gHltpeeaveaaadlgakrlvliH 200
                                        H+  ++ v++++ ++++++vl H
  gi|518651796|ref|YP_008141316.1| 358 AHAGHSDLVKFVKGVDPEIVVLCH 381
                                       345555556666666666666666 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   3.9e-05     0.099       9      54 ..      16      64 ..      12     204 .. 0.78
   2 ?    0.2   0.0      0.24   6.2e+02      26      55 ..     163     196 ..     141     228 .. 0.66
   3 ?   -2.6   0.0       1.8   4.5e+03     143     163 .]     361     381 ..     352     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.9e-05
                     Lactamase_B_3  9 sflletagarilvDPf...kanlgyeppaeeaDlvlisqaledHahlet 54
                                      ++ +e++  +i++D++   ++  +y  p+e+++ + +++a+ dH  + +
  gi|518651796|ref|YP_008141316.1| 16 AIKIEDKQSKIMIDYGiepEKPPEYPLPPEKVNDIFLTHAHLDHTGALP 64
                                      57899999********665226789999****************86554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.24
                     Lactamase_B_3  26 a..nlgyeppaeeaDlvlisqale..dHahletl 55 
                                       +  nl y++++++ D++++ +  +  dH + +++
  gi|518651796|ref|YP_008141316.1| 163 RdtNLLYGAKPVKTDVLIMESTYAgrDHEDRDEV 196
                                       3368899999999999999875541155444433 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.8
                     Lactamase_B_3 143 gqeealelakrLkpklvlPmh 163
                                       g  + ++ +k ++p++v+  h
  gi|518651796|ref|YP_008141316.1| 361 GHSDLVKFVKGVDPEIVVLCH 381
                                       677889999999999999766 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.4   0.00033      0.85     125     176 ..      72     122 ..      68     137 .. 0.87
   2 ?    2.6   0.0     0.027        69     202     221 ..     364     383 ..     350     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00033
                          EcKinase 125 AkfHAaSlalkeekpevfkelkkglleedyvssalkeafeelleellkaale 176
                                       A+fHA++++ +  kp ++++lk  +  e+y++  ++e +++l+++++ a +e
  gi|518651796|ref|YP_008141316.1|  72 ANFHATAMTANSIKPILMDSLK-IMRLENYTKMFNEEDVDNLFKSMMTAKYE 122
                                       89********************.77777777777899999999999987655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.027
                          EcKinase 202 rllelveekeeefnvlnHGD 221
                                       +l+++v+  + e+ vl+HGD
  gi|518651796|ref|YP_008141316.1| 364 DLVKFVKGVDPEIVVLCHGD 383
                                       67788888899********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2836.87
//
Query:       gi|518651797|ref|YP_008141317.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G0436 [Ferroplasma acidarmanus fer1]
Scores for complete 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  151.8   0.0    1.9e-44  151.7   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 !  151.7   0.0   1.1e-48   1.9e-44       2     231 ..       4     235 ..       3     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.7 bits;  conditional E-value: 1.1e-48
                                       EEEEESSH.HHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEE.EEEE--....SSHHHHHHHHHHHHHHHC--SE CS
                         PNP_UDP_1   2 iaiivgsp.gevellaespleetpfgregrgfkfvtGtlkgkpv.vivstG....iGkpnaavvaeirllkefgvka 72 
                                       ++ii+gs+ + +   ++++  +tp+g++  +  + +G+++g++v ++ ++G    i ++++++ a+i +l+  gv +
  gi|518651797|ref|YP_008141317.1|   4 VGIIGGSGlYSIMETRKTMDIDTPYGKP--SAPLEIGEINGVEVaFLPRHGkkhtIPPHMVNYKANIFALQKAGVQR 78 
                                       89******98888888889*********..*********8888879******************************* PP

                                       EEEEEEEEESSTTT-TT-EEEEEEEEESSSCCGCCTHHCCTCCCCTTSSEE--HHHHHHHHHCHHTTTTTEEE.EEE CS
                         PNP_UDP_1  73 iiriGtaGglnpdlkvGDvvipddainfdgrsplygpkeegqyfpdsydapadpelrallkeaaealgikvhr.Gvv 148
                                       ii  +++G+l++++k+GD+vipd++i+f+ r++l++++ + +y++ ++d+ +++++ a++ ea ++l  +vh  G++
  gi|518651797|ref|YP_008141317.1|  79 IIGLNAVGSLKEEYKPGDIVIPDQFIDFTKRRDLTYYNGPDVYHISMADP-FCSDISAKAYEAGKKLSFPVHKnGAY 154
                                       **************************************************.***********999999888888*** PP

                                       EEESESS-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCCHHHHHHHHHH CS
                         PNP_UDP_1 149 atadgfyaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeveefaqeaakna 225
                                       ++ +g++++t+ae++++r++  d+++M+ +++  lA+el ++++ +++v+d ++ + d+  +  +v++ ++e+++++
  gi|518651797|ref|YP_008141317.1| 155 ICIEGPRFSTRAESKMFRNFA-DIIGMTLVPEINLAAELSMCYGMLATVTD-YDAWKDEAVEASDVMQIMKESEEKV 229
                                       ********************9.*****************************.888*****************99999 PP

                                       HHHHHH CS
                         PNP_UDP_1 226 aallla 231
                                       ++ l  
  gi|518651797|ref|YP_008141317.1| 230 SKMLYN 235
                                       998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); 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 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1826.94
//
Query:       gi|518651798|ref|YP_008141318.1|  [L=242]
Description: glutamine-hydrolyzing asparagine synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-18   67.3   0.0    1.2e-11   44.9   0.0    2.0  2  Asn_synthase  Asparagine synthase


Domain annotation for each model (and alignments):
>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.9   0.0   6.8e-16   1.2e-11       4     148 ..      10     145 ..       7     167 .. 0.82
   2 !   21.3   0.0   9.8e-09   0.00018     223     298 ..     155     231 ..     145     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 6.8e-16
                      Asn_synthase   4 elLedaVkrrlradvpvGalLSGGlDSSliaalaarqsksplktFsigfeekgsdeakyakevaehlgtehtelvlt 80 
                                         L++aV+    ad p+++  SGGlDSSl+ al       +   +++gf   +s +++    ++  l+++   + l+
  gi|518651798|ref|YP_008141318.1|  10 NELKAAVE--QTADKPCAIAYSGGLDSSLLLALSGY----RYIPYTLGF--SDSRDIENVDDASTILKINPKIILLD 78 
                                       67899999..569*******************9888....4578*****..************************** PP

                      Asn_synthase  81 eeelldalpdviyhleepfadrsai..plyllsrlakrkgvkvvLsGeGaDElfgGYpyfykaalsrsre 148
                                       e +++ ++ +++++  +++  ++ +   l++l+  +  +  k v +G+GaDElf GY+ f + +  ++++
  gi|518651798|ref|YP_008141318.1|  79 EIDIEGYISQLLKIDPKITKMEMGYelVLFILMDFI-PE--KYVVTGQGADELFYGYRRFIDNPRLKNDT 145
                                       *************66667777765511667777778.33..79***************988888665544 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 9.8e-09
                      Asn_synthase 223 llrkDrasmahglEaRvPflDhrlvevalrlppelklrggieKyiLRealegy.lPeeileRpKegfsapvgewklk 298
                                       l r+ +++     E+ +P+l    ++    +  e+++ g+++K iLRe++++  lPeei++R K ++++++g +k+ 
  gi|518651798|ref|YP_008141318.1| 155 LPREKKMAEYYDKELITPYLSPGMLKIRHYITREDNIEGNRNKLILREIAAKTsLPEEIYNRSKTAAQYGSGINKYL 231
                                       556667777777777888888888888888888999999**********99976***************99988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1738.59
//
Query:       gi|518651799|ref|YP_008141319.1|  [L=668]
Description: hypothetical protein FACI_IFERC00001G0438 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.14   11.8   1.7        2.1    8.1   0.1    3.5  5  ComJ      Competence protein J (ComJ)


Domain annotation for each model (and alignments):
>> ComJ  Competence protein J (ComJ)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.16   2.8e+03      88     102 ..     297     311 ..     254     320 .. 0.76
   2 ?    8.1   0.1   0.00012       2.1      81     106 ..     478     503 ..     469     518 .. 0.85
   3 ?   -2.8   0.0      0.26   4.7e+03      72      95 ..     515     538 ..     512     560 .. 0.73
   4 ?    0.3   0.1     0.029   5.3e+02      77     104 ..     558     585 ..     545     602 .. 0.78
   5 ?   -2.5   0.0      0.23   4.1e+03      74     113 ..     601     644 ..     598     650 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.16
                                       -EEE---SEEEEEEE CS
                              ComJ  88 klsvdipkGeYqltl 102
                                        + +++ +G+Y++tl
  gi|518651799|ref|YP_008141319.1| 297 YYITPLKNGSYKITL 311
                                       456678888888876 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00012
                                       EE-TTS--EEE---SEEEEEEEEEE- CS
                              ComJ  81 issilskklsvdipkGeYqltlqtve 106
                                          i +k++s+++p+G+Y  t++tv+
  gi|518651799|ref|YP_008141319.1| 478 LHMINEKNYSLNLPNGTYSYTVKTVN 503
                                       567889*****************997 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 0.26
                                       EEESSS-EEEE-TTS--EEE---S CS
                              ComJ  72 Ftvtedgvlissilskklsvdipk 95 
                                       Ftv++ +++ ++ l + +s + ++
  gi|518651799|ref|YP_008141319.1| 515 FTVQGSNITTTVKLLRGYSAQFNE 538
                                       999999999999999999887643 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.029
                                       S-EEEE-TTS--EEE---SEEEEEEEEE CS
                              ComJ  77 dgvlissilskklsvdipkGeYqltlqt 104
                                       + v + si+  ++ +++ +G+Y   + t
  gi|518651799|ref|YP_008141319.1| 558 QVVNSGSIAGSSYYLNLTNGTYFYKIST 585
                                       5678899***************766655 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 0.23
                                       ESSS-EEEE-TTS--EEE---.SEEEEEEEEEE-TT...T-TTS CS
                              ComJ  74 vtedgvlissilskklsvdip.kGeYqltlqtvele...eeels 113
                                       v + +v+ s+i  k++ v  + kG  +++ + vel+   ++ ++
  gi|518651799|ref|YP_008141319.1| 601 VNGKNVTESVIFYKTYRVTFEeKGLQKGIKWSVELNgtvKSSVT 644
                                       55677888888888888887525777777777777644444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 4539.29
//
Query:       gi|518651800|ref|YP_008141320.1|  [L=139]
Description: glycerol-3-phosphate cytidylyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-16   59.4   0.0    5.2e-16   59.1   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.036   14.0   1.0       0.17   11.7   1.0    2.1  1  FAD_syn          FAD synthetase


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   5.8e-20   5.2e-16       2     142 ..       6     133 ..       5     134 .. 0.89

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 5.8e-20
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST.-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkk.kkplasaeeRlemlelakevdevisvdpweltrevl 77 
                                       a G+FD++HlGH ++l++ k+ +++ l+v ++sd +++k  k+ +++++eR + + ++k vdev++   ++   +++
  gi|518651800|ref|YP_008141320.1|   6 ASGVFDILHLGHVHYLRESKSFGDY-LVVVIASDYTAQKHgKELVFNENERSALVSELKMVDEVMVGHSDDNIFKTV 81 
                                       78***********************.**************55*************************99999999** PP

                                       HHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTC..SHHHHHH CS
                   CTP_transf_like  78 kklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngi..Sstkire 142
                                        +lkpd  ++ +g d+  d   +  +e+  ++++l  ++r+          + ++ g   Ss+kir+
  gi|518651800|ref|YP_008141320.1|  82 AELKPD--IITLGYDQKFD---DSYIETECKKLGLNTKVRR----------TSPYDGTinSSSKIRQ 133
                                       ******..******99777...899***********99887..........3333333348888887 PP

>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.0   1.9e-05      0.17       9      37 ..       4      32 ..       2     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.9e-05
                           FAD_syn  9 vvtlGnFDGvHlGHqallkkaveaakekg 37
                                      v++ G FD +HlGH + l++ ++  +   
  gi|518651800|ref|YP_008141320.1|  4 VMASGVFDILHLGHVHYLRESKSFGDYLV 32
                                      8999************9999988774433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1143.63
//
Query:       gi|518651801|ref|YP_008141321.1|  [L=127]
Description: prefoldin subunit beta [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   76.8  19.4    1.3e-21   76.6  19.4    1.0  1  Prefoldin_2      Prefoldin subunit
    0.00081   19.5  18.8      0.002   18.3   9.0    2.0  2  ADIP             Afadin- and alpha -actinin-Binding
     0.0016   18.7  15.7      0.024   14.8   2.1    2.1  2  ATG16            Autophagy protein 16 (ATG16)
     0.0029   17.8   2.9     0.0029   17.8   2.9    2.0  2  COG5             Golgi transport complex subunit 5
     0.0073   16.1   1.1     0.0073   16.1   1.1    2.1  2  DUF4364          Domain of unknown function (DUF4364)
     0.0097   16.2   1.1     0.0097   16.2   1.1    2.1  2  Troponin         Troponin
  ------ inclusion threshold ------
      0.023   14.1   5.7      0.012   15.0   3.2    1.7  2  DUF4527          Protein of unknown function (DUF4527)
      0.026   14.4  16.7       0.63    9.8   0.5    2.0  2  KASH_CCD         Coiled-coil region of CCDC155 or KASH
      0.029   14.0  14.1       0.13   12.0   1.0    2.1  2  Med4             Vitamin-D-receptor interacting Mediator subu
      0.033   14.3  14.6        0.2   11.8   4.4    3.0  3  DUF3585          Bivalent Mical/EHBP Rab binding domain
      0.049   13.9  17.9        1.5    9.2   4.5    2.8  3  BLOC1_2          Biogenesis of lysosome-related organelles co
      0.074   13.1  12.6       0.61   10.1   2.4    2.1  2  Laminin_II       Laminin Domain II
       0.14   12.8   7.0       0.63   10.8   3.4    2.4  2  Vir_act_alpha_C  Virulence activator alpha C-term
       0.17   12.4  19.8        1.6    9.3  10.4    2.0  2  APG6_N           Apg6 coiled-coil region
       0.19   11.2  11.6        1.2    8.5   3.4    2.1  2  FliD_C           Flagellar hook-associated protein 2 C-termin
       0.26   11.5  19.1       0.44   10.7   1.4    2.0  2  Jnk-SapK_ap_N    JNK_SAPK-associated protein-1
       0.28   11.2   8.5       0.45   10.6   0.9    2.1  2  DUF1664          Protein of unknown function (DUF1664)
       0.32    8.5  16.9       0.55    7.7  16.9    1.3  1  DUF3584          Protein of unknown function (DUF3584)
       0.35   10.8  16.7        1.7    8.6   0.6    2.6  3  Prefoldin        Prefoldin subunit
       0.37   11.0  17.0       0.46   10.6   2.3    2.0  2  CREPT            Cell-cycle alteration and expression-elevate
       0.41   11.1  12.0        1.8    9.0   4.1    2.4  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.63    9.4  19.4       0.63    9.4   2.5    2.0  2  Cluap1           Clusterin-associated protein-1
       0.65    9.1  11.5        3.6    6.6  11.5    1.9  1  FH2              Formin Homology 2 Domain
       0.67   10.5   9.9         69    4.1   9.9    2.3  1  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.87    8.5  18.4        3.4    6.5  18.4    1.7  1  IFT57            Intra-flagellar transport protein 57
       0.92    9.6  15.5        0.4   10.7   6.2    2.0  2  UPF0242          Uncharacterised protein family (UPF0242) N-t
          1    9.2  18.7       0.44   10.3   2.6    2.4  2  Phage_GP20       Phage minor structural protein GP20
        1.3    9.3   9.9      0.097   12.9   3.6    2.2  2  Coat_F           Coat F domain
        1.3    8.9  15.8       0.75    9.6   6.7    2.2  2  Nsp1_C           Nsp1-like C-terminal region
        1.5    8.2  14.5        2.3    7.5  14.5    1.3  1  DUF4407          Domain of unknown function (DUF4407)
        1.6    9.2   7.0        6.6    7.2   1.1    2.4  2  DUF4140          N-terminal domain of unknown function (DUF41
        1.8    6.3   9.4        2.4    6.0   9.4    1.1  1  V_ATPase_I       V-type ATPase 116kDa subunit family
        1.9    8.0  16.9        2.3    7.7   7.3    2.0  2  HAUS-augmin3     HAUS augmin-like complex subunit 3
          2    8.6  16.2        2.2    8.4  14.6    1.7  1  Fib_alpha        Fibrinogen alpha/beta chain family
        2.1    8.6  13.2        9.1    6.5   7.0    2.3  2  JIP_LZII         JNK-interacting protein  leucine zipper II
        3.1    7.5  15.5        1.8    8.3   1.8    2.0  2  zf-CpG_bind_C    CpG binding protein zinc finger C terminal d
        3.3    6.9  18.1        0.7    9.2   2.0    2.0  2  DUF3450          Protein of unknown function (DUF3450)
        3.4    8.2  19.6        4.9    7.7   4.7    2.1  2  DUF16            Protein of unknown function DUF16
        3.8    7.6  10.9        1.3    9.1   0.6    2.1  2  DUF4337          Domain of unknown function (DUF4337)
          4    7.7  18.3         12    6.2   5.2    2.2  2  Spc24            Spc24 subunit of Ndc80
        4.6    8.3  14.6        1.1   10.3   7.0    2.4  2  Spt5_N           Spt5 transcription elongation factor, acidic
        6.4    6.6  12.0         26    4.6  12.0    1.8  1  PCRF             PCRF domain
        6.8    6.6  14.3        4.2    7.3   2.6    2.1  2  Cauli_AT         Aphid transmission protein
        7.1    7.3  19.2        4.7    7.9   3.6    2.4  2  BST2             Bone marrow stromal antigen 2
        8.5    6.8  12.1         16    5.9   1.0    2.4  2  E2F_CC-MB        E2F transcription factor CC-MB domain
          9    6.5  14.9          6    7.1   2.8    3.3  3  DUF2802          Protein of unknown function (DUF2802)


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 !   76.6  19.4   3.2e-24   1.3e-21       1     104 [.      11     115 ..      11     117 .. 0.98

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 3.2e-24
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE.-HHHHHHHHHHHHHHHHH CS
                       Prefoldin_2   1 qelinkfqqlqqqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkq.dkeevkeeLeerketlek 76 
                                       q++i++ q+ q+q++q+a+q+ q+++++kel+++l+el+++ +d+++yk+vG++ +k  d+e++ ++Lee+ke  ++
  gi|518651801|ref|YP_008141321.1|  11 QNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVGKDAPIYKNVGPIIYKIdDREKLVSDLEEQKELSQM 87 
                                       89*******************************************************989***************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCCTS CS
                       Prefoldin_2  77 eiktlekqleklekeleelkeelqkklq 104
                                       ++ktle+q+++le++++el++ +qk+++
  gi|518651801|ref|YP_008141321.1|  88 RLKTLENQQKTLEEKYKELEQAIQKRYE 115
                                       *************************976 PP

>> ADIP  Afadin- and alpha -actinin-Binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   2.2     0.015       5.7      63     101 ..      11      49 ..       3      55 .. 0.44
   2 !   18.3   9.0     5e-06     0.002      70     124 ..      69     123 ..      64     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                              ADIP  63 rkleaeierlqskierlktqleqlerelalvqakerqle 101
                                       ++     + +q++ie++ +q  q +++++ + +++++l+
  gi|518651801|ref|YP_008141321.1|  11 QNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       333333344444444444444444444444444444444 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 5e-06
                              ADIP  70 erlqskierlktqleqlerelalvqakerqlekklktleqklknekeelqrlkna 124
                                       +  ++ ++ l++q e ++++l+++++++++le k+k+leq++++  ee +r++n+
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQNN 123
                                       556777899*******************************************996 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   2.1   6.3e-05     0.024     106     152 ..       5      51 ..       4      56 .. 0.94
   2 !    9.9   6.0    0.0021      0.81      94     148 ..      58     112 ..      53     121 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-05
                             ATG16 106 elneelqkleeklkedeerlaeleaeraaletklkdreeelrekekl 152
                                       +ln+ lq + ++++ ++++++++ ++r ++  k+k+++++l+e++++
  gi|518651801|ref|YP_008141321.1|   5 NLNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTV 51 
                                       68999**************************************9876 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0021
                             ATG16  94 yksrgelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelre 148
                                       yk  g   +++ + ++ +++lee+ +  + rl+ le++ ++le+k+k++e++++ 
  gi|518651801|ref|YP_008141321.1|  58 YKNVGPIIYKIDDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQK 112
                                       666666678889999999********************************99976 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.6      0.13        49      13      52 ..       9      48 ..       5      59 .. 0.79
   2 !   17.8   2.9   7.4e-06    0.0029      57     107 ..      71     122 ..      67     125 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.13
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5 13 fanallkatnnnddteldlstplkrlnydiqeldkrlrql 52
                                      + ++ +k++++ + + + ++ ++ ++   ++eldk l++l
  gi|518651801|ref|YP_008141321.1|  9 YLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKEL 48
                                      5566677888888888888899999999999999998876 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 7.4e-06
                                       XXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX-TTHHHHHHHHHHHH CS
                              COG5  57 hleLlehlskskslss.vlselksslesLsasyerlkskvlepyeeaeklqs 107
                                        ++L + l+++k+ls+  l++l+ + + L++ y+ l++ + ++yee    q+
  gi|518651801|ref|YP_008141321.1|  71 REKLVSDLEEQKELSQmRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       689******************************************9776665 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   1.1   1.9e-05    0.0073      92     133 ..      10      51 ..       4      63 .. 0.90
   2 ?    1.1   1.4      0.78     3e+02      56      93 ..      85     122 ..      70     126 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-05
                           DUF4364  92 nkeelkkesevkadyykkengeytVklkikekdstllelkls 133
                                       +++++k+ ++++a++++  n++y++ +k+ke d+tl el+  
  gi|518651801|ref|YP_008141321.1|  10 LQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTV 51 
                                       5789********************************999875 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.78
                           DUF4364  56 nktlykiTekGketlelfenripksirekideylkenk 93 
                                       ++ ++k  e+ ++tle+ ++++ ++i+++ +e+ ++++
  gi|518651801|ref|YP_008141321.1|  85 SQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       44455555666677777777777777777776666554 PP

>> Troponin  Troponin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.1   2.5e-05    0.0097      47      85 ..      11      49 ..       3      52 .. 0.88
   2 ?    2.6   8.0      0.39   1.5e+02       6      36 ..      85     115 ..      67     125 .. 0.35

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.5e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          Troponin 47 eqlqelckklheridkleeekydieekvakkdkeieelk 85
                                      + + + +++++++i+++++++y+i+ kv++ dk  +el+
  gi|518651801|ref|YP_008141321.1| 11 QNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49
                                      6777889***************************99998 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.39
                                       HHHHHHHHHHHHHTXXXXXXXXXXXXXXXXX CS
                          Troponin   6 dllllkaaeelkfeqrkkeeerlrvLkerie 36 
                                       + ++lk++e+ ++  ++k +e ++++++r e
  gi|518651801|ref|YP_008141321.1|  85 SQMRLKTLENQQKTLEEKYKELEQAIQKRYE 115
                                       1222222222222222222222222222222 PP

>> DUF4527  Protein of unknown function (DUF4527)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   3.2   3.2e-05     0.012      27     103 ..       6      86 ..       4     106 .. 0.83
   2 ?    0.4   1.8      0.93   3.6e+02       8      50 ..      80     119 ..      76     124 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.2e-05
                           DUF4527  27 LqcqLRdqasahreLqasreeaerlreelqekleElqkkqhEanlAv..tPLkAklAsLvqkCreRnhlithLL..q 99 
                                       L+ +L +q    +++qa  e+ ++ r ++  k++El k  +E n     +P+   +  ++ k  +R++l++ L   +
  gi|518651801|ref|YP_008141321.1|   6 LNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVGkdAPIYKNVGPIIYKIDDREKLVSDLEeqK 82 
                                       7789999************************************9864449*********************974113 PP

                           DUF4527 100 elhr 103
                                       el +
  gi|518651801|ref|YP_008141321.1|  83 ELSQ 86 
                                       4444 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.93
                           DUF4527   8 aseedlrlrvkqLhHqvltLqcqLRdqasahreLqasreeaer 50 
                                         +e +++r k L+ q  tL  + ++   a   +q+  ee++r
  gi|518651801|ref|YP_008141321.1|  80 EQKELSQMRLKTLENQQKTLEEKYKELEQA---IQKRYEESTR 119
                                       556777788888888888888777665433...3555555544 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 ?    9.8   0.5    0.0016      0.63     132     173 ..       7      51 ..       4      59 .. 0.85
   2 ?    8.9  10.0    0.0031       1.2      70     123 ..      69     122 ..      65     125 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                          KASH_CCD 132 kaeLkkqlheleellaekealleek...tkqieeLkltieEyssi 173
                                       +a L++q+++++ + a+ e++++++    ++++eL  t++E++++
  gi|518651801|ref|YP_008141321.1|   7 NAYLQNQIKQAQDMQAQIEQVANQRyqiDMKVKELDKTLKELNTV 51 
                                       788999**9999999999999999833346999999999999887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0031
                          KASH_CCD  70 eelkalvkeleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkk 123
                                       ++  +lv++leE+++  + + k le  ++ L++k ++L++ ++k   e   +++
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       778899************************************999999888776 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 ?   12.0   1.0   0.00032      0.13      20      56 ..      13      49 ..       3      61 .. 0.83
   2 ?    7.4   6.0    0.0082       3.2      15      54 ..      72     112 ..      65     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00032
                              Med4 20 eleehqknearilqLraeveslDekikeivksLkeye 56
                                      ++++ q+ +a+i+q+ ++  + D k+ke+ k+Lke+ 
  gi|518651801|ref|YP_008141321.1| 13 QIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49
                                      556779999*************************986 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0082
                              Med4  15 skslkeleehqknea.rilqLraeveslDekikeivksLke 54 
                                       +k ++ lee+++ ++ r+++L+++++ l+ek ke+++++ +
  gi|518651801|ref|YP_008141321.1|  72 EKLVSDLEEQKELSQmRLKTLENQQKTLEEKYKELEQAIQK 112
                                       56788899999865449*****************9998865 PP

>> DUF3585  Bivalent Mical/EHBP Rab binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.034        13       1      30 [.      20      49 ..      20      60 .. 0.85
   2 ?    3.2   0.3      0.22        87     112     127 ..      68      83 ..      63      87 .. 0.84
   3 ?   11.8   4.4   0.00051       0.2       2      37 ..      86     121 ..      85     126 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.034
                           DUF3585  1 iqreleeieeeqreleergvelEkaLRgea 30
                                      +q+++e++ ++  +++ + +el k+L++ +
  gi|518651801|ref|YP_008141321.1| 20 MQAQIEQVANQRYQIDMKVKELDKTLKELN 49
                                      5899**********************9544 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.22
                           DUF3585 112 VeqRdelvdsleedrl 127
                                       +++R++lv++lee++ 
  gi|518651801|ref|YP_008141321.1|  68 IDDREKLVSDLEEQKE 83 
                                       6899********9875 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00051
                           DUF3585   2 qreleeieeeqreleergvelEkaLRgeaeesgeee 37 
                                       q +l+ +e++q++lee+ +elE+a+ +  ees++++
  gi|518651801|ref|YP_008141321.1|  86 QMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQ 121
                                       7799*********************97665443333 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 ?    9.2   4.5    0.0039       1.5      46      85 ..      10      49 ..       5      54 .. 0.57
   2 ?    2.9   0.0      0.35   1.3e+02      57      79 ..      58      80 ..      55      84 .. 0.89
   3 ?    8.5   5.9    0.0062       2.4      10      48 ..      77     115 ..      69     125 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0039
                           BLOC1_2 46 lekkleklnekyeelqpylqqidqiekqvteLeeavseLD 85
                                      l++++++ + +++++++  +q  qi+ +v+eL ++ +eL+
  gi|518651801|ref|YP_008141321.1| 10 LQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49
                                      4455555555555555555555566666666666655555 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.35
                           BLOC1_2 57 yeelqpylqqidqiekqvteLee 79
                                      y+++ p + +id+ ek v++Lee
  gi|518651801|ref|YP_008141321.1| 58 YKNVGPIIYKIDDREKLVSDLEE 80
                                      789999999***********997 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0062
                           BLOC1_2  10 yleaeleatvedyklLeklNeaasekykklkdvaaslek 48 
                                        le++ e +++ +k+Le+  ++ +ekyk+l++++++  +
  gi|518651801|ref|YP_008141321.1|  77 DLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYE 115
                                       57889999***********************99887555 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   2.4    0.0016      0.61      11      57 ..       9      55 ..       4      61 .. 0.89
   2 ?    8.9   2.7    0.0037       1.4      39      82 ..      67     110 ..      56     120 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0016
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                        Laminin_II 11 takevleqlaplsqnlentkeklseinrsveetnekvkdankairdA 57
                                       +++  +q +++++++e++ ++  +i+ +v+e ++ +k++n++ +dA
  gi|518651801|ref|YP_008141321.1|  9 YLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVGKDA 55
                                      567777999*******************************9998887 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0037
                                       XXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHH CS
                        Laminin_II  39 sveetnekvkdankairdArrsvkkLeklapqLldklkelkqle 82 
                                       +++  +++v+d+ ++ ++ +   k+Le++   L++k kel+q  
  gi|518651801|ref|YP_008141321.1|  67 KIDDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAI 110
                                       56666888999999999999999999999999999999998865 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 ?    3.3   0.1      0.34   1.3e+02      15      45 ..      18      48 ..       4      61 .. 0.72
   2 ?   10.8   3.4    0.0016      0.63      15      51 ..      69     104 ..      66     122 .. 0.73

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.34
                   Vir_act_alpha_C 15 ldpealieeLerrreeheekLaeyeeieerl 45
                                       d +a ie+++++r +   k +e+++  ++l
  gi|518651801|ref|YP_008141321.1| 18 QDMQAQIEQVANQRYQIDMKVKELDKTLKEL 48
                                      5666777888888888887777777666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0016
                   Vir_act_alpha_C  15 ldpealieeLerrreeheekLaeyeeieerleeargq 51 
                                        d+e+l+ +Le+++e+ + +L+++e  ++ l e+++ 
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQKELSQMRLKTLENQQKTL-EEKYK 104
                                       6899*********************666665.23333 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.9    0.0054       2.1      53      95 ..       7      49 ..       3      55 .. 0.82
   2 ?    9.3  10.4    0.0041       1.6      50     101 ..      69     120 ..      64     125 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0054
                            APG6_N 53 eeeleklekeeeelleeLkelekereeleaelaaleeeleale 95
                                      +  l++  k+ ++++++++++ ++r +++ ++++l ++l++l+
  gi|518651801|ref|YP_008141321.1|  7 NAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49
                                      5566777778889999999999999999999999999999987 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0041
                            APG6_N  50 eeleeeleklekeeeelleeLkelekereeleaelaaleeelealeeeeerf 101
                                       ++ e+ +++le+++e  +  Lk le++++ le++ ++le+  +++ ee +r 
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRN 120
                                       66788899***********************************999998775 PP

>> FliD_C  Flagellar hook-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   1.2    0.0042       1.6     177     221 ..       6      49 ..       2      53 .. 0.86
   2 ?    8.5   3.4     0.003       1.2     196     232 ..      82     116 ..      58     124 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                                       HHHHHHHHHSTT.SHHHHHHHHXXXXHHHHHHHHHHHHHCHHHHH CS
                            FliD_C 177 lenllksyvkssngtlqtasknltkqikdldkkiedldkrletle 221
                                       l+ +l++ +k   + +q +++++ +q +++d k+++ldk l++l+
  gi|518651801|ref|YP_008141321.1|   6 LNAYLQNQIKQA-QDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       567788888888.8999999******************9999876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.003
                                       HHHXXXXHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                            FliD_C 196 sknltkqikdldkkiedldkrletleerlkkqfaale 232
                                       ++  + ++k+l++++++l++++++le+ ++k+++  e
  gi|518651801|ref|YP_008141321.1|  82 KELSQMRLKTLENQQKTLEEKYKELEQAIQKRYE--E 116
                                       3444557777777777777777777777777777..4 PP

>> Jnk-SapK_ap_N  JNK_SAPK-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.4    0.0011      0.44      80     123 ..       6      49 ..       2      55 .. 0.85
   2 ?    6.2  10.4     0.029        11      57     107 ..      69     119 ..      66     125 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0011
                     Jnk-SapK_ap_N  80 leeiedqweeerkelqekveqleeenrelelkaknaadqlsrle 123
                                       l  + ++  ++++++q+++eq+ +++ ++++k+k++++ l++l+
  gi|518651801|ref|YP_008141321.1|   6 LNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       5666677778899***********************99998886 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.029
                     Jnk-SapK_ap_N  57 eeleqLeteyerekelrkraeeeleeiedqweeerkelqekveqleeenre 107
                                       +++e+L +++e++kel++   ++le+  +++ee+ kel++++++  ee  +
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTR 119
                                       567778888888888888888888888888888888888777776666554 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9    0.0011      0.45      71     114 ..       6      49 ..       4      54 .. 0.81
   2 ?    5.1   1.3     0.058        23      55      90 ..      76     111 ..      59     124 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0011
                           DUF1664  71 vdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                       +++ l++q++ ++++++++++v ++  +i+ +v++++++ ++l+
  gi|518651801|ref|YP_008141321.1|   6 LNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       66778888888888999999999999999999988888888876 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.058
                           DUF1664  55 eslaatkrhLssridrvdkkldeqkeiskeikeevt 90 
                                       ++l+++k+  + r+++++++++  +e  ke+++ ++
  gi|518651801|ref|YP_008141321.1|  76 SDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQ 111
                                       444444444444444444444444444444444443 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  16.9    0.0014      0.55     611     718 ..      10     121 ..       3     126 .. 0.54

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0014
                           DUF3584 611 leealqsaeakqkqaeeelkqlnaeleeakravaeaatalknardtlerlqne.....kesekdklekaiaerkqqa 682
                                       l++++++a++ q+q+e+ ++q + +++++ +++ +  ++l+   ++    +n+     k   ++kl   ++e+k+  
  gi|518651801|ref|YP_008141321.1|  10 LQNQIKQAQDMQAQIEQVANQ-RYQIDMKVKELDKTLKELNTVGKDAPIYKNVgpiiyKIDDREKLVSDLEEQKELS 85 
                                       445555555555555543333.3445555555555555555554444444443222224455666666667777777 PP

                           DUF3584 683 eeqlqkldaqlkqleeqqkaaleelkedlseerlek 718
                                       + +l++l++q+k lee+ k+++++++++++e + ++
  gi|518651801|ref|YP_008141321.1|  86 QMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQ 121
                                       777777777777777777777777777777666433 PP

>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.4      0.19        74      97     115 ..      11      29 ..       7      33 .. 0.39
   2 ?    8.6   0.6    0.0043       1.7       2      34 ..      21      53 ..      20      63 .. 0.90
   3 ?    8.3   7.1    0.0053       2.1      74     113 ..      77     116 ..      70     123 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.19
                                       HHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  97 eeeleklkdqittleanla 115
                                       ++++++++d   ++e+ ++
  gi|518651801|ref|YP_008141321.1|  11 QNQIKQAQDMQAQIEQVAN 29 
                                       3333333333333333333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                         Prefoldin  2 keeleslqaelaqlkeaieelektletlktlkk 34
                                      ++++e ++ ++ q++ + +el+ktl+ l+t+ k
  gi|518651801|ref|YP_008141321.1| 21 QAQIEQVANQRYQIDMKVKELDKTLKELNTVGK 53
                                      789**************************9977 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0053
                                       EHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  74 sleeAiellkkkleelekqlekleeeleklkdqittlean 113
                                       +lee +el + +l++le+q+++lee+ ++l ++i++  ++
  gi|518651801|ref|YP_008141321.1|  77 DLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEE 116
                                       5667777777777777777777777777777777765555 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 ?   10.6   2.3    0.0012      0.46      78     124 ..       3      49 ..       1      63 [. 0.91
   2 ?    6.3   7.0     0.026        10      65     104 ..      72     111 ..      65     123 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0012
                             CREPT  78 akmledfleaqkellakaeekleelkeklekvksvrkelkshiqsLP 124
                                       + +l+++l++q +++++ ++++e++ ++  +++ + kel+++++ L 
  gi|518651801|ref|YP_008141321.1|   3 EPNLNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       66899**************************************9985 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.026
                             CREPT  65 krLeaeleeRkklakmledfleaqkellakaeekleelke 104
                                       ++L ++lee k+l++m  + le+q+++l+++ ++le+  +
  gi|518651801|ref|YP_008141321.1|  72 EKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQ 111
                                       3455555555555555555555555555555555544333 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 ?    6.8   1.0     0.023       8.8      11      40 ..      19      48 ..       7      51 .. 0.82
   2 ?    9.0   4.1    0.0047       1.8       3      39 ..      76     112 ..      67     115 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.023
                         FlaC_arch 11 klsteletvkkeneelsksveelkenVkdl 40
                                      +++ ++e v ++  ++  +v+el+++ k+l
  gi|518651801|ref|YP_008141321.1| 19 DMQAQIEQVANQRYQIDMKVKELDKTLKEL 48
                                      556689999999999999999999999987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0047
                         FlaC_arch   3 delEnklsklsteletvkkeneelsksveelkenVkd 39 
                                        +lE++ +  +++l+t++++++ l+++ +el++ +++
  gi|518651801|ref|YP_008141321.1|  76 SDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQK 112
                                       567777777788*********************9986 PP

>> Cluap1  Clusterin-associated protein-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5    0.0016      0.63     166     224 ..       2      56 ..       1      61 [. 0.84
   2 ?    7.0   8.5    0.0086       3.4     164     214 ..      72     122 ..      52     124 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                            Cluap1 166 iekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqkrLqslqsvrP 224
                                       +e +l++ ++++ ++++++++++e+++++      +i+ k +el+++ k L+++ +  P
  gi|518651801|ref|YP_008141321.1|   2 VEPNLNAYLQNQIKQAQDMQAQIEQVANQRY----QIDMKVKELDKTLKELNTVGKDAP 56 
                                       7888999999999**************9999....666677899999999999876665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0086
                            Cluap1 164 eeiekalkeaikkvkeelektkkalenlesdeanLeakiekkkqeleraqk 214
                                       e++ + l+e+ +  + +l++++++ ++le+  ++Le+ i+k+ +e+ r+q+
  gi|518651801|ref|YP_008141321.1|  72 EKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       5566778899999999********************************996 PP

>> FH2  Formin Homology 2 Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  11.5    0.0092       3.6     256     306 ..      67     117 ..       5     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0092
                                       TSGGGGGHHHHTTTHHHCCTS-HHHHHHHHHHHHHHHHHHHHHHHHCCTTS CS
                               FH2 256 klpevldfsseLknvkkaakvnleslekevkklekglkklekelessekke 306
                                       k ++ +++ s+L++ k+++++ l++le++ k+le++ k+le+ +++  +++
  gi|518651801|ref|YP_008141321.1|  67 KIDDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEES 117
                                       8889999*************************************9998833 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   9.9      0.18        69      16      96 ..      16     107 ..       3     126 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.18
                      Syntaxin-6_N  16 kaeslyrrwerlledtss..stseeldetrteLr.........kalrsiewdledLeetvriveknpskfkidekel 81 
                                       +a+ + ++ e++ ++  +   + +eld+t +eL+         k+++ i ++++d e+ v+ +e++++  +++ k+l
  gi|518651801|ref|YP_008141321.1|  16 QAQDMQAQIEQVANQRYQidMKVKELDKTLKELNtvgkdapiyKNVGPIIYKIDDREKLVSDLEEQKELSQMRLKTL 92 
                                       44444444444333333332233444444444431111111113455556666666666666666555566666666 PP

                      Syntaxin-6_N  82 srrrafveevreevk 96 
                                       +++++ +ee  +e++
  gi|518651801|ref|YP_008141321.1|  93 ENQQKTLEEKYKELE 107
                                       666666555444443 PP

>> IFT57  Intra-flagellar transport protein 57
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  18.4    0.0088       3.4     207     308 ..       2     118 ..       1     125 [. 0.73

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0088
                             IFT57 207 vlpqLkv....tikadakdWrahleqmkkhkksieeslpetksqlkkl.........hedisktlekiesrEkyl.. 268
                                       v+p+L++    +ik +a+d +a++eq+ + + +i+ +++e+ + lk+l         ++++   + ki  rEk +  
  gi|518651801|ref|YP_008141321.1|   2 VEPNLNAylqnQIK-QAQDMQAQIEQVANQRYQIDMKVKELDKTLKELntvgkdapiYKNVGPIIYKIDDREKLVsd 77 
                                       56666663332554.45799999999999999999999999999988722222222246788889999999999854 PP

                             IFT57 269 .nsqleellqeyreaqeelsevkekykqlsegvseltrela 308
                                        ++q e +   +++++++ ++++ekyk+l++ ++++ +e +
  gi|518651801|ref|YP_008141321.1|  78 lEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEEST 118
                                       45666666666999999999999999999999999988765 PP

>> UPF0242  Uncharacterised protein family (UPF0242) N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   1.8     0.076        30     152     188 ..      11      47 ..       4      55 .. 0.53
   2 ?   10.7   6.2     0.001       0.4      69     120 ..      67     118 ..      57     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.076
                           UPF0242 152 qeyqetieeqrsvlekrqdqieqLeskVrDlnyEikt 188
                                       q+  ++ ++ ++ +e+  +q +q++ kV+ l   +k 
  gi|518651801|ref|YP_008141321.1|  11 QNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKE 47 
                                       3333444445555555555555555555555444443 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.001
                           UPF0242  69 kleekeaklteldeglktkeealeelqeeeeeLkeeldakeeelerlkeenq 120
                                       k++ +e+++++l+e+ +  +  l+ l+++++ L+e++++ e++++++ ee  
  gi|518651801|ref|YP_008141321.1|  67 KIDDREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEEST 118
                                       5778889999999888888889**********************99988864 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 ?   10.3   2.6    0.0011      0.44      17      51 ..      21      55 ..       5      61 .. 0.85
   2 ?    4.1   8.6     0.095        37      35      78 ..      69     112 ..      59     125 .. 0.42

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0011
                        Phage_GP20 17 kakldeveeerdtlkeqlkdrdkqLedLkkkakdn 51
                                      +a++++v ++r ++  ++k+ dk+L++L ++ kd+
  gi|518651801|ref|YP_008141321.1| 21 QAQIEQVANQRYQIDMKVKELDKTLKELNTVGKDA 55
                                      68999************************998885 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.095
                        Phage_GP20  35 kdrdkqLedLkkkakdneeLq.kqieelqaknkkakaeyeakiad 78 
                                       +dr+k ++dL+++ k+  ++  k++e+ q++++++ +e e+ i++
  gi|518651801|ref|YP_008141321.1|  69 DDREKLVSDLEEQ-KELSQMRlKTLENQQKTLEEKYKELEQAIQK 112
                                       4444444444444.2222221122233333333333333333322 PP

>> Coat_F  Coat F domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   3.6   0.00025     0.097      29      57 ..       3      31 ..       1      33 [. 0.94
   2 ?   -0.2   0.4         3   1.2e+03      36      49 ..      84      97 ..      75     118 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00025
                            Coat_F 29 npelRqtlkqilneeiemqeelfnlmnqk 57
                                       p+l + l+++ +++++mq ++ +++nq+
  gi|518651801|ref|YP_008141321.1|  3 EPNLNAYLQNQIKQAQDMQAQIEQVANQR 31
                                      69*************************97 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 3
                            Coat_F 36 lkqilneeiemqee 49
                                      l+q++ +++e q++
  gi|518651801|ref|YP_008141321.1| 84 LSQMRLKTLENQQK 97
                                      55555555555544 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   1.6     0.062        24      62      97 ..      10      48 ..       5      56 .. 0.62
   2 ?    9.6   6.7    0.0019      0.75      71     114 ..      79     123 ..      65     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.062
                            Nsp1_C 62 LysevleaeqeqnkidqeLe...yiesqqdeLeslLdny 97
                                      L++++ +a+ +q++i+q  +    i  + +eL++ L+++
  gi|518651801|ref|YP_008141321.1| 10 LQNQIKQAQDMQAQIEQVANqryQIDMKVKELDKTLKEL 48
                                      677778888888888874331114555555665555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0019
                            Nsp1_C  71 qeqnkidq.eLeyiesqqdeLeslLdnyEkeleellsklesqksd 114
                                       +eq+++ q +L+ +e+qq+ Le+  +++E+ +++  +++++++++
  gi|518651801|ref|YP_008141321.1|  79 EEQKELSQmRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQNN 123
                                       4566666537999******************99999998888876 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5  14.5    0.0058       2.3     123     235 ..      12     122 ..       2     127 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0058
                           DUF4407 123 lkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqk.eldgtkgtgttgvaGkgpaakekkaqldaaqae 198
                                       ++ + a++++a++++  +q+ +++ ++++++++l++l++  ++  +  + g  + ++  +++     ++q +  q +
  gi|518651801|ref|YP_008141321.1|  12 NQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVGKDaPIYKNVGPIIYKIDDREKLVSDLEEQKELSQMR 88 
                                       22233344666666666666666666666666666665544330333334666666666666666688888888888 PP

                           DUF4407 199 laelkakldatarlaalraelaeleaerakeraasqa 235
                                       l++l+++   +++l+++ +el+++ ++r +e +++q 
  gi|518651801|ref|YP_008141321.1|  89 LKTLENQ---QKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       8888888...889999999999988888888877775 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 ?    5.3   0.5     0.069        27      50      77 ..      20      48 ..       5      55 .. 0.55
   2 ?    7.2   1.1     0.017       6.6      65      89 ..      83     111 ..      60     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.069
                           DUF4140 50 ldvqvervpnreaeee.elkalraeleel 77
                                       + q+e+v+n++ + + ++k+l+++l+el
  gi|518651801|ref|YP_008141321.1| 20 MQAQIEQVANQRYQIDmKVKELDKTLKEL 48
                                      23344444444444443355555555555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.017
                           DUF4140  65 e....elkalraeleeledelaaledela 89 
                                       e    +lk+l+++ ++le++ ++le++++
  gi|518651801|ref|YP_008141321.1|  83 ElsqmRLKTLENQQKTLEEKYKELEQAIQ 111
                                       13444566666666666666666666554 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 ?    6.0   9.4    0.0061       2.4      26     106 ..      11     110 ..       3     126 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0061
                        V_ATPase_I  26 vkevrrcdemerklrfleeeieklekavikeeea...................eesleapeekeldeleeeleklee 83 
                                        +++++ ++m+ +++ + ++  + + +v + +++                      + +++ek +++lee+ e  + 
  gi|518651801|ref|YP_008141321.1|  11 QNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTlkelntvgkdapiyknvgpIIYKIDDREKLVSDLEEQKELSQM 87 
                                       57888888888888888888777555555555446777755555554444444333344444555555555555555 PP

                        V_ATPase_I  84 elkelnenleklkkelnelvelk 106
                                       +lk+l++++++l+++++el+++ 
  gi|518651801|ref|YP_008141321.1|  88 RLKTLENQQKTLEEKYKELEQAI 110
                                       55555555555555555554432 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 ?    5.9   2.0     0.021       8.1      90     133 ..       6      49 ..       4      55 .. 0.91
   2 ?    7.7   7.3    0.0059       2.3      82     133 ..      70     121 ..      64     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.021
                      HAUS-augmin3  90 LqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaq 133
                                       L  + + ++k+ + +q+q+ + ++++ + + + ke  k lke++
  gi|518651801|ref|YP_008141321.1|   6 LNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       7889999*********************************9987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0059
                      HAUS-augmin3  82 aLeqelqeLqkekalklkrlnkLqvqaaslqqelrkleeeekeakkklkeaq 133
                                       + e+++++L+++k+l + rl+ L+ q  +l+++ ++le++ ++  ++ ++ q
  gi|518651801|ref|YP_008141321.1|  70 DREKLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQ 121
                                       66999********************************999888777666655 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4  14.6    0.0057       2.2      25     128 ..       5     113 ..       1     119 [. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0057
                                       CCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH CS
                         Fib_alpha  25 lllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqe 101
                                        l+ y ++  k+ ++++ ++e+++n+  +++  vke++++l+e ++  kd   ++k++   +  +i + ++ +++ e
  gi|518651801|ref|YP_008141321.1|   5 NLNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVGKD-APIYKNVGPIIY-KIDDREKLVSDLE 79 
                                       6788889999999******************************9999996.566666655555.4444444444433 PP

                                       .......HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha 102 .......snirvLqnvlesneqkiqkLeqdidqk 128
                                               +++ L n  +++e+k ++Leq+i+++
  gi|518651801|ref|YP_008141321.1|  80 eqkelsqMRLKTLENQQKTLEEKYKELEQAIQKR 113
                                       1001211356677777777788888888887765 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 ?    5.8   0.4     0.039        15      44      71 .]      19      46 ..       8      54 .. 0.76
   2 ?    6.5   7.0     0.023       9.1      35      70 ..      75     110 ..      72     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.039
                          JIP_LZII 44 iLreEleslqkakerlesrikelEeelk 71
                                       ++  +e++ +++ ++ +++kel+++lk
  gi|518651801|ref|YP_008141321.1| 19 DMQAQIEQVANQRYQIDMKVKELDKTLK 46
                                      4566777777788888888888887776 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.023
                          JIP_LZII  35 vdeLtsereiLreEleslqkakerlesrikelEeel 70 
                                       v +L +++e  ++ l++l++++++le++ kelE+ +
  gi|518651801|ref|YP_008141321.1|  75 VSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAI 110
                                       67899****************************976 PP

>> zf-CpG_bind_C  CpG binding protein zinc finger C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.8    0.0046       1.8      16      58 ..       9      51 ..       2      62 .. 0.78
   2 ?    5.2   6.2     0.041        16      20      71 ..      73     122 ..      57     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0046
                     zf-CpG_bind_C 16 wqsspsvaeeenkkklekirkeqeeakkklkelekklkkLeel 58
                                      + +++ +  +  + ++e++ +++ ++  k+kel+k lk+L+++
  gi|518651801|ref|YP_008141321.1|  9 YLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTV 51
                                      5555666667778889999999999999999999999999876 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.041
                     zf-CpG_bind_C  20 psvaeeenkkklekirkeqeeakkklkelekklkkLeeliekakklslkeee 71 
                                       + v + e++k+l+++r ++  +++++k le+k k+Le+ i+k  + s ++++
  gi|518651801|ref|YP_008141321.1|  73 KLVSDLEEQKELSQMRLKT--LENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       4567788888888888765..5566788999999999999998887766655 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.0    0.0018       0.7      44      77 ..      15      48 ..       3      60 .. 0.52
   2 ?    3.7   8.5     0.084        33      37      86 ..      73     122 ..      65     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0018
                           DUF3450 44 dekqellaeyralkeeleslevyneqlerlvasq 77
                                      +++q+++a+++++ ++  +++++ ++l++ ++++
  gi|518651801|ref|YP_008141321.1| 15 KQAQDMQAQIEQVANQRYQIDMKVKELDKTLKEL 48
                                      3444444444444444444444444444444443 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.084
                           DUF3450  37 kkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                       k +++l+++k+  + ++++l+++++ le + ++le+ +++  +e ++ ++
  gi|518651801|ref|YP_008141321.1|  73 KLVSDLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRNQN 122
                                       66777788888888888888888888888888888777777776666555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   4.7     0.013       4.9      43      89 ..       6      52 ..       1      71 [. 0.67
   2 ?    7.0   7.0     0.021       8.2      24      67 ..      77     120 ..      60     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.013
                                      HH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHH CS
                             DUF16 43 vdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlelil 89
                                      +++  +++ k++q +++q e++ +++ +++ + +el+k  + l+ + 
  gi|518651801|ref|YP_008141321.1|  6 LNAYLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTVG 52
                                      55555555566666777777777777777777776776666666654 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.021
                                       HHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHH CS
                             DUF16  24 qlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikel 67 
                                       +l+e k+  + rLk +e++ ++l+e+ ++leq+++k  e+ ++ 
  gi|518651801|ref|YP_008141321.1|  77 DLEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKRYEESTRN 120
                                       56777888899999999999999999999999999987765444 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6    0.0033       1.3      73     113 ..      12      51 ..       2      61 .. 0.85
   2 ?    3.2   4.0      0.23        89      78     109 ..      81     112 ..      63     124 .. 0.43

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                           DUF4337  73 aavdkkiakykkkiarykkekkeikkkAkeleaerdeanea 113
                                       +++ k++++++++i++ ++++ +i  k kel+++ +e+n  
  gi|518651801|ref|YP_008141321.1|  12 NQI-KQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELNTV 51 
                                       334.68999**************************999875 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.23
                           DUF4337  78 kiakykkkiarykkekkeikkkAkeleaerde 109
                                       +++  + + +  ++++k +++k kele++ ++
  gi|518651801|ref|YP_008141321.1|  81 QKELSQMRLKTLENQQKTLEEKYKELEQAIQK 112
                                       23333333333333333333333333333322 PP

>> Spc24  Spc24 subunit of Ndc80
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.2      0.03        12       5      52 ..       9      50 ..       5      83 .. 0.73
   2 ?    4.6   8.7     0.099        38       9      47 ..      78     118 ..      65     126 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.03
                             Spc24  5 ekfriakelsdleselesleselaelkeeleeleeeseekeservede 52
                                       +++ +k+++d+++++e++ ++  +   +++el++  +e       ++
  gi|518651801|ref|YP_008141321.1|  9 YLQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKEL------NT 50
                                      5667789999999999999999999999999999988882......22 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.099
                             Spc24   9 iakelsdleselesleselaelkeeleeleeesee..kese 47 
                                       + ++ +  ++ l+ le++++ l+e+++ele+  ++  +es+
  gi|518651801|ref|YP_008141321.1|  78 LEEQKELSQMRLKTLENQQKTLEEKYKELEQAIQKryEEST 118
                                       45555556788888889999999999999988888553333 PP

>> Spt5_N  Spt5 transcription elongation factor, acidic N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.8      0.82   3.2e+02      42      84 ..      18      42 ..       5      56 .. 0.51
   2 ?   10.3   7.0    0.0027       1.1      41      83 ..      79     123 ..      51     126 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.82
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                            Spt5_N 42 erddrshreldrrrqaeededaeeiaealeeRYgrsskkayrg 84
                                      +                    + +i++  ++RY+   k ++ +
  gi|518651801|ref|YP_008141321.1| 18 Q------------------DMQAQIEQVANQRYQIDMKVKELD 42
                                      1..................223345555556665544433333 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXX CS
                            Spt5_N  41 serddrshreldrrrqaeed..edaeeiaealeeRYgrsskkayr 83 
                                       +e+++ s+ +l   +++++   e+  e+++a+++RY++s++++++
  gi|518651801|ref|YP_008141321.1|  79 EEQKELSQMRLKTLENQQKTleEKYKELEQAIQKRYEESTRNQNN 123
                                       222333333333333333333489999999999999998777664 PP

>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6  12.0     0.065        26      19      91 ..      36     111 ..       5     125 .. 0.57

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.065
                                       TTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.......-S-..-GGGTHHHHHHHHHH..HHHHHT- CS
                              PCRF  19 edqekakklskelaeleeivealeeleealedleeakelle...edeelaelaeeeleelekeleeleeelkklLl 91 
                                        + +++ k+ kel+ + + +  ++++     ++++ ++l++   e++el ++  + le+ +k+lee  +el++ + 
  gi|518651801|ref|YP_008141321.1|  36 MKVKELDKTLKELNTVGKDAPIYKNVGPIIYKIDDREKLVSdleEQKELSQMRLKTLENQQKTLEEKYKELEQAIQ 111
                                       2345566666666666666666777777777777777777324344555555544455555555555555555544 PP

>> Cauli_AT  Aphid transmission protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   2.6     0.011       4.2     116     155 ..      10      49 ..       3      55 .. 0.83
   2 ?    5.4   4.1     0.042        16     102     141 ..      70     111 ..      51     124 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.011
                          Cauli_AT 116 aqnrikkleeetkklaekivtekllkeevkdlderlseir 155
                                        qn+ik+ ++ + ++++  + + +++ +vk+ld++l+e++
  gi|518651801|ref|YP_008141321.1|  10 LQNQIKQAQDMQAQIEQVANQRYQIDMKVKELDKTLKELN 49 
                                       578888888888888888889999999*******999986 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.042
                          Cauli_AT 102 dkekktklletLkeaqn.rikkleeetkklaek.ivtekllk 141
                                       d+ek +  le  ke ++ r k le+++k l+ek  + e+ ++
  gi|518651801|ref|YP_008141321.1|  70 DREKLVSDLEEQKELSQmRLKTLENQQKTLEEKyKELEQAIQ 111
                                       344444444444444446888888888888888434444443 PP

>> BST2  Bone marrow stromal antigen 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   3.6     0.012       4.7      17      58 ..       5      49 ..       3      57 .. 0.61
   2 ?    4.8   7.8      0.11        41      50      86 ..      74     114 ..      70     119 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.012
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHH CS
                              BST2 17 nvtrlLerqLtqaqeslreaeaqaat...cnqtvvtLkasLekek 58
                                      n + +L++q++qaq+  ++ e+ a+     +  v++L + L++ +
  gi|518651801|ref|YP_008141321.1|  5 NLNAYLQNQIKQAQDMQAQIEQVANQryqIDMKVKELDKTLKELN 49
                                      667778888888887766666554440004444666666666655 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHH....HHHHHHHHHHHHHHHHHHHHHHHH CS
                              BST2  50 LkasLekekaqsq....kqqakvqelqgeikkLnqkLqdae 86 
                                       L ++Le++k  sq      +++ + l+++ k+L+q +q+  
  gi|518651801|ref|YP_008141321.1|  74 LVSDLEEQKELSQmrlkTLENQQKTLEEKYKELEQAIQKRY 114
                                       44455555444330000344455556666666666666655 PP

>> E2F_CC-MB  E2F transcription factor CC-MB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   1.0     0.041        16       1      31 [.      20      50 ..      20      87 .. 0.81
   2 ?    5.0   5.0     0.081        32       4      36 ..      88     121 ..      81     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.041
                         E2F_CC-MB  1 lkqelesleeeeqkLDelieklteqlknlte 31
                                      +++++e++ ++  ++D  +++l + lk+l+ 
  gi|518651801|ref|YP_008141321.1| 20 MQAQIEQVANQRYQIDMKVKELDKTLKELNT 50
                                      5899***********************9966 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.081
                         E2F_CC-MB   4 elesleeeeqkLDelieklteqlknl.tedeknq 36 
                                        l++le+++++L+e  ++l++ +++  +e+++nq
  gi|518651801|ref|YP_008141321.1|  88 RLKTLENQQKTLEEKYKELEQAIQKRyEESTRNQ 121
                                       68999******************98857766665 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   2.3      0.51     2e+02       9      28 ..      10      29 ..       7      34 .. 0.70
   2 ?    3.6   0.0      0.19        75       2      25 ..      34      50 ..      32      60 .. 0.59
   3 ?    7.1   2.8     0.015         6       3      32 ..      86     113 ..      84     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.51
                           DUF2802  9 lekrlkqleerleeleqqdp 28
                                      l++++kq ++ ++++eq  +
  gi|518651801|ref|YP_008141321.1| 10 LQNQIKQAQDMQAQIEQVAN 29
                                      67888888888888776553 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.19
                           DUF2802  2 mgqrlaelekrlkqleerleeleq 25
                                      ++ +++el+k+lk+l+       +
  gi|518651801|ref|YP_008141321.1| 34 IDMKVKELDKTLKELN-------T 50
                                      4556666666666654.......4 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.015
                           DUF2802   3 gqrlaelekrlkqleerleeleqqdpqskl 32 
                                       + rl++le++ k lee+ +eleq    +k+
  gi|518651801|ref|YP_008141321.1|  86 QMRLKTLENQQKTLEEKYKELEQAI--QKR 113
                                       679******************8865..444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      4019  (0.224162); expected 358.6 (0.02)
Passed bias filter:                     1023  (0.0570584); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        68  (0.00379274); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              46  [number of targets reported over threshold]
# CPU time: 0.70u 0.31s 00:00:01.01 Elapsed: 00:00:00.45
# Mc/sec: 854.69
//
Query:       gi|518651802|ref|YP_008141322.1|  [L=77]
Description: hypothetical protein FACI_IFERC00001G0441 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.7   0.1     0.0063   16.6   0.1    1.1  1  Pcc1      Transcription factor Pcc1


Domain annotation for each model (and alignments):
>> Pcc1  Transcription factor Pcc1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   3.5e-07    0.0063      19      74 .]      18      73 ..       3      73 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.5e-07
                                      HHHHHH.CHC-TTECEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHHHHHHHHH CS
                              Pcc1 19 rtLqvD.kelsplavkrslslegnvLqveykAttnrmLRvavngfleslglvletme 74
                                      ++++++  e     +++ ++ +++ + + ++A +  +LR++v+++ + l++  ++me
  gi|518651802|ref|YP_008141322.1| 18 EAIRPEvTETFG-RSSVAVKEDNSSIYIIITAPDTSSLRASVSSITRVLNVTKKIME 73
                                      555555322222.245555557789**************************999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       590  (0.0329076); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 576.01
//
Query:       gi|518651803|ref|YP_008141323.1|  [L=121]
Description: hypothetical protein FACI_IFERC00001G0442 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       381  (0.0212505); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 776.84
//
Query:       gi|518651804|ref|YP_008141324.1|  [L=191]
Description: hypothetical protein FACI_IFERC00001G0443 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-07   29.3  11.6      1e-06   28.8  11.6    1.3  1  DUF1453        Protein of unknown function (DUF1453)
  ------ inclusion threshold ------
      0.011   15.5  18.0        0.2   11.4  18.0    2.1  1  7TM-7TMR_HD    7TM receptor with intracellular HD hydrolase
      0.013   15.6   0.2        1.3    9.1   0.3    2.7  2  CcmD           Heme exporter protein D (CcmD)
        1.3    9.3  15.0      0.046   14.0   8.2    1.8  2  GtrA           GtrA-like protein
        6.8    6.4   6.2         52    3.5   6.3    2.1  3  FA_desaturase  Fatty acid desaturase
        7.7    6.3  17.2       0.34   10.7  10.2    2.0  2  DUF443         Protein of unknown function (DUF443)


Domain annotation for each model (and alignments):
>> DUF1453  Protein of unknown function (DUF1453)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8  11.6   3.5e-10     1e-06       3     143 ..      36     180 ..      31     182 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.5e-10
                           DUF1453   3 silvaivmallvifirikas...krpveakkiilPplfm.stGalmfvfpefrltllevleallvGalfsiplikts 75 
                                       +++v ++++  ++++r+k+    +r ++a+  i P +      ++m++f      ++ v+   +vG++ +++ +  +
  gi|518651804|ref|YP_008141324.1|  36 LVIVLLLIFSRILYRRLKQGingRRYKTARLFITPTIYFlLLVFFMVAFIGNVDYIIIVILLCVVGIIPGFIYGERV 112
                                       5677778888888888887522144455556667766442455566666655566777888899************* PP

                           DUF1453  76 kfevrdgkiylkrskafifillgLlvvRlvlksvlsssldieelsglFfllafgmivpwRiamylkyr 143
                                       +f  r+g+i+ krs ++++ +++  +vR++l+ +  s+l+i+ + +  +++++g iv   i+ y kyr
  gi|518651804|ref|YP_008141324.1| 113 TFFDRNGQIFYKRSPYILAFWVAGFMVRILLEFIFPSNLEIQFIVDAILAVTLGLIVGESIKTYRKYR 180
                                       *******************************************************************9 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4  18.0   6.7e-05       0.2       7     120 ..      33     170 ..      29     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                       7TM-7TMR_HD   7 llllvlllllilllflrrf.rkelrern.kkllllslllllvlllsklvvl.issiesiiylvplaavalLlsllld 80 
                                         +lv++llli+  +l+r  ++ ++ r+ k+  l+++ ++ +lll+ ++v+ i++ ++ii ++ l++v+++ +++++
  gi|518651804|ref|YP_008141324.1|  33 NTFLVIVLLLIFSRILYRRlKQGINGRRyKTARLFITPTIYFLLLVFFMVAfIGNVDYIIIVILLCVVGIIPGFIYG 109
                                       4566777777777777666699999998788899999999999999998888999********************** PP

                       7TM-7TMR_HD  81 srlal...................vvsvllsllisilf..gnnlellllalvsglvgallv 120
                                       +r+ +                   v+++++ +l+ ++f  ++++++++ a+++ ++g +++
  gi|518651804|ref|YP_008141324.1| 110 ERVTFfdrngqifykrspyilafwVAGFMVRILLEFIFpsNLEIQFIVDAILAVTLGLIVG 170
                                       ***9988888888888777777766666666666666644555555555666666665555 PP

>> CcmD  Heme exporter protein D (CcmD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.3   0.00044       1.3      14      36 ..      34      56 ..      33      60 .. 0.92
   2 ?    3.3   0.0     0.029        86      12      31 ..     162     181 ..     161     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                              CcmD 14 tllvlagLilwslrdrrrllrel 36
                                      t+lv+++L++ s++ +rrl++ +
  gi|518651804|ref|YP_008141324.1| 34 TFLVIVLLLIFSRILYRRLKQGI 56
                                      8******************9865 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.029
                              CcmD  12 gitllvlagLilwslrdrrr 31 
                                       ++tl +++g+ + + r++r 
  gi|518651804|ref|YP_008141324.1| 162 AVTLGLIVGESIKTYRKYRE 181
                                       79999*****9999999996 PP

>> GtrA  GtrA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.5      0.74   2.2e+03      94     104 ..      32      41 ..       4      52 .. 0.49
   2 ?   14.0   8.2   1.5e-05     0.046      14     107 ..      76     169 ..      67     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.74
                              GtrA  94 llaklvgiiva 104
                                         + +++i++ 
  gi|518651804|ref|YP_008141324.1|  32 S-NTFLVIVLL 41 
                                       1.222222222 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.5e-05
                              GtrA  14 lallllllellglsyllAnaiafivailfnFilnrrwtFkdrekakllkqflkFvlvsllglllnllilwllveklg 90 
                                       l++++++  + +++y++ +++  +v+i+  Fi  +r+tF dr+ +   k+    +++ ++g+++ +l+ +++ + l+
  gi|518651804|ref|YP_008141324.1|  76 LLVFFMVAFIGNVDYIIIVILLCVVGIIPGFIYGERVTFFDRNGQIFYKRSPYILAFWVAGFMVRILLEFIFPSNLE 152
                                       233333334599*******************************9976777777777899****************** PP

                              GtrA  91 leallaklvgiivalvl 107
                                       +++++ +++++ ++l++
  gi|518651804|ref|YP_008141324.1| 153 IQFIVDAILAVTLGLIV 169
                                       *****999999999876 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.3     0.017        52     108     177 ..      36     105 ..       7     137 .. 0.49
   2 ?   -0.7   0.1      0.34     1e+03     131     156 ..     124     147 ..      99     170 .. 0.51
   3 ?    0.4   0.0      0.16   4.8e+02      39      64 ..     153     179 ..     129     183 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.017
                     FA_desaturase 108 wllalvlglwlrrlarrrapsksrrrk..wrllawlllllawlglwlalllllglall...lwlvplllllflla 177
                                       +++ l+l++ +  ++r ++ +++rr+k  + +++  + +l   +l+++++++ g   +   ++++ l++++++  
  gi|518651804|ref|YP_008141324.1|  36 LVIVLLLIFSRILYRRLKQGINGRRYKtaRLFITPTIYFL---LLVFFMVAFIGN--VdyiIIVILLCVVGIIPG 105
                                       3333333334444444444444443333233333333333...222222222222..232444444444443333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.34
                     FA_desaturase 131 rrrkwrllawlllllawlglwlalll 156
                                       +r +++l  w++ +   + ++l +++
  gi|518651804|ref|YP_008141324.1| 124 KRSPYILAFWVAGFM--VRILLEFIF 147
                                       333344444444444..444444443 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.16
                     FA_desaturase  39 nrwl.ndllgallglplgisysawris 64 
                                        +++ +++l+ +lgl++g s++++r+ 
  gi|518651804|ref|YP_008141324.1| 153 IQFIvDAILAVTLGLIVGESIKTYRKY 179
                                       556646777777999999999999975 PP

>> DUF443  Protein of unknown function (DUF443)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7  10.2   0.00011      0.34      92     183 ..      27     104 ..       4     124 .. 0.65
   2 ?   -0.3   0.6      0.26   7.7e+02     153     184 ..     132     164 ..     126     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                            DUF443  92 klvnliillivlllvlvlriyiskklkkklynevelekkskekiilipkslknfllllfaylfflglvilalvalie 168
                                         +nl+ +++v++l+l++  ++ ++lk+ ++ +    +++  +++++p ++ ++ll+ f+  f++   ++ +v l+ 
  gi|518651804|ref|YP_008141324.1|  27 AGLNLSNTFLVIVLLLIFSRILYRRLKQGINGR----RYKTARLFITP-TIYFLLLVFFMVAFIGNVDYIIIVILL- 97 
                                       346778888888888888888888888888886....9**********.777777777777777666666666655. PP

                            DUF443 169 tqniiilivlllllf 183
                                                +++++ 
  gi|518651804|ref|YP_008141324.1|  98 --------CVVGIIP 104
                                       ........3333333 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.26
                            DUF443 153 lfflglvilalvalietqni.iilivlllllfl 184
                                       + ++g+++  l+ +i + n+ i +iv  +l++ 
  gi|518651804|ref|YP_008141324.1| 132 FWVAGFMVRILLEFIFPSNLeIQFIVDAILAVT 164
                                       567788888888999888874555554444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1034  (0.0576719); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.33s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1176.42
//
Query:       gi|518651805|ref|YP_008141325.1|  [L=210]
Description: endonuclease III [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-18   66.5   0.0    3.1e-18   66.2   0.0    1.1  1  HhH-GPD   HhH-GPD superfamily base excision DNA repair protei
  ------ inclusion threshold ------
      0.049   13.5   1.0       0.74    9.6   0.1    2.2  2  YhcG_C    YhcG PDDEXK nuclease domain
      0.055   14.1   0.2        2.7    8.7   0.0    2.7  3  HHH_5     Helix-hairpin-helix domain
      0.062   13.3   0.0       0.26   11.3   0.0    1.8  2  AAA_5     AAA domain (dynein-related subfamily)


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 !   66.2   0.0     7e-22   3.1e-18       1     106 [.      29     169 ..      29     171 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 7e-22
                                       HHHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                           HhH-GPD   1 vsailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv........... 66 
                                       +++il+q+ts+++++++ ++++e+    t++++a  d+e L+eli++ Gfy++K +y+  +++++            
  gi|518651805|ref|YP_008141325.1|  29 IGTILTQNTSWKNVEKALKKMKENH-VYTLDEIATTDQERLKELIKSSGFYNQKSRYLLTVSKEITekygnlpgmkn 104
                                       789*********************7.89************************************************* PP

                                       .............................S-SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHHHH CS
                                       .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           HhH-GPD  67 .............................gkpdvlivvDvhvrrilkrlrsikekktkkkvekkleell 106
                                                                    ++  +++vvD ++ r +kr+++ +    +k++++++ee +
  gi|518651805|ref|YP_008141325.1| 105 kdmkeiegfimgldgvgnetmesimlyalDY--PVFVVDAYTLRFFKRFYGKEFS--RKEIRNYAEEEF 169
                                       **************************86543..89***************98775..999999888765 PP

>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00017      0.74     102     150 ..      20      68 ..       7      73 .. 0.71
   2 ?    2.3   0.1     0.029   1.3e+02       8      44 ..     152     190 ..     142     192 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00017
                            YhcG_C 102 lkkeednptiGiilckekdktvveyalkeinkpigvseYelpkelpeel 150
                                         + +d++ iG il+++++ + ve alk+++++ + +  e+ ++  e+l
  gi|518651805|ref|YP_008141325.1|  20 PSETDDETVIGTILTQNTSWKNVEKALKKMKENHVYTLDEIATTDQERL 68 
                                       456778999********************99875544335555554555 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.029
                            YhcG_C   8 yvldflelke.eykErel.ekalieklkkfllelGkgFa 44 
                                       y  +f + +  +y+E+e  e   +++ + ++++lGk+F+
  gi|518651805|ref|YP_008141325.1| 152 YGKEFSRKEIrNYAEEEFsEIDQLKNFHGMIVNLGKDFC 190
                                       555665544346777776255678888999*******96 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0006       2.7      13      40 ..      44      71 ..      43      77 .. 0.87
   2 ?    2.4   0.0     0.054   2.4e+02      40      53 ..     117     130 ..      98     132 .. 0.80
   3 ?   -3.0   0.0       2.6   1.2e+04      25      40 ..     157     172 ..     155     175 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0006
                                      HHHHHHHTTT--SHHHHHHS-HHHHHTS CS
                             HHH_5 13 ktAlallsaGiesvedlaaadveeLaki 40
                                      k  +++ ++ + +++++a  d+e+L ++
  gi|518651805|ref|YP_008141325.1| 44 KALKKMKENHVYTLDEIATTDQERLKEL 71
                                      6678999999**************9874 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.054
                                       STTS-HHHHHHHHH CS
                             HHH_5  40 ipGiGkktAeriil 53 
                                       + G+G++t e+i+l
  gi|518651805|ref|YP_008141325.1| 117 LDGVGNETMESIML 130
                                       56888888888876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.6
                                       SHHHHHHS-HHHHHTS CS
                             HHH_5  25 svedlaaadveeLaki 40 
                                       s  ++ + ++ee+++i
  gi|518651805|ref|YP_008141325.1| 157 SRKEIRNYAEEEFSEI 172
                                       5678888889999887 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 ?   11.3   0.0   5.8e-05      0.26      35      86 ..      22      72 ..      18      91 .. 0.79
   2 ?   -0.8   0.0      0.31   1.4e+03       3      30 ..     113     140 ..     112     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.8e-05
                                      T--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHH CS
                             AAA_5 35 dtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLl 86
                                       t  e+++g + ++n   + v++ + ++++e +++ lDE+ + ++e l++L+
  gi|518651805|ref|YP_008141325.1| 22 ETDDETVIGTILTQNTSWKNVEK-ALKKMKENHVYTLDEIATTDQERLKELI 72
                                      56778888888864444444444.555**************99999998886 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.31
                                       EEE--SSSSHHHHHHHGGGGBS--EEEE CS
                             AAA_5   3 lLvGppGtgKselaerlaaalnreveyv 30 
                                       ++ G  G+g  ++   ++ al  +v++v
  gi|518651805|ref|YP_008141325.1| 113 FIMGLDGVGNETMESIMLYALDYPVFVV 140
                                       578999***************9999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1598  (0.0891293); expected 358.6 (0.02)
Passed bias filter:                      938  (0.0523175); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1508.92
//
Query:       gi|518651806|ref|YP_008141326.1|  [L=200]
Description: multiple antibiotic resistance protein marC [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  153.0  17.4    7.6e-45  152.8  17.4    1.0  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 !  152.8  17.4   4.3e-49   7.6e-45       4     200 ..       7     194 ..       4     197 .. 0.94

  Alignments for each domain:
  == domain 1  score: 152.8 bits;  conditional E-value: 4.3e-49
                              MarC   4 iikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgill 80 
                                       ++k+f+ L+++i+p+g++++f+s++ +++ + r+ i++ a+ +a +i+++f+l+G li+++fgisi+al iaGgi+l
  gi|518651806|ref|YP_008141326.1|   7 FLKVFMPLFVVIDPFGSLAIFVSMTGSFNRDTRRTISRDAVFYAGIIIILFALAGGLIIEFFGISIEALEIAGGIIL 83 
                                       7899************************************************************************* PP

                              MarC  81 fliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlaseassivekvavvlaillaalit 157
                                       +l++i+m++  +k      ++     ++ ++ +vP A+Pl+aGPgai+ v++l++      +k+++++++ll+++i+
  gi|518651806|ref|YP_008141326.1|  84 LLMGIEMVRQGAKP-----DTSV--DSSKNMGIVPFATPLLAGPGAISLVIILMKGDLF--TKILTIVSVLLVLVIV 151
                                       ********988873.....2222..23579************************87766..8*************** PP

                              MarC 158 llilllsslilrllgktginaleRlmGllLvalavqlivdGik 200
                                       + ++++ss il+llg + ++a++R++Gll +  a+q ++d++ 
  gi|518651806|ref|YP_008141326.1| 152 YFFFIYSSKILSLLGDKVMTAITRIFGLLVAGFAIQYFLDALV 194
                                       ***************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1342.29
//
Query:       gi|518651807|ref|YP_008141327.1|  [L=379]
Description: hypothetical protein FACI_IFERC00001G0446 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.0   0.0    9.5e-25   87.5   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    6.4e-21   75.1   0.0    3.4e-20   72.7   0.0    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0001   21.6   0.1     0.0013   17.9   0.2    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.5   0.0   1.6e-28   9.5e-25       1     239 [.       3     285 ..       3     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 87.5 bits;  conditional E-value: 1.6e-28
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...................EEEE--TT-HHHHHH CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...................elveldltdrsaler 58 
                                       +l++G+ G+iG  l+ +ll++gyev g d+  ++++ ++   +                   +++ +d+ +++ + +
  gi|518651807|ref|YP_008141327.1|   3 VLILGIDGYIGFPLALRLLDRGYEVYGADNFYTRRRVKNVGSKsavkinsfatrnkklnnaiKFYMGDVSNPKFVYD 79 
                                       79*****************************888887777766999******************************* PP

                                       HHHHHT-SEEEE--S.---H..HHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSS.SS.... CS
                         Epimerase  59 lfkeeqpdavihlAa.vggv..aassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdae.qp.... 126
                                       ++++ ++da++hlA   + +  + s ++++++++kn++ t+n++ a+++ + +  ++ l+S   YG ++  +p    
  gi|518651807|ref|YP_008141327.1|  80 IIRDSGADAIVHLAEqRSAPysMISLKTATETLDKNIESTMNIIYAVKDLNRDiHIVKLGSMGEYGTPNIdIPegfl 156
                                       **************9544332255678999*******************99988************77765466677 PP

                                       ...BSTCSTTS--..--SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTT.............S-TTSTTSH CS
                         Epimerase 127 ...keettltgpl..kpnspYaaaKlageklveayaaqyglnaiilrlfnlyGpr.............ngegevsrv 185
                                           +  +++ p+    +s Y ++K+     +  +++  gln+  ++   +yG r             + ++    v
  gi|518651807|ref|YP_008141327.1| 157 dvqFHGRSDKLPFprMGQSWYHLSKIFDTYNLMLANRIWGLNVSDVMQGVVYGTRtpeitkyklftrfDIDQIYGTV 233
                                       66655555555998788999******9999999999999****************9999999988866666668999 PP

                                       HHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT-STTEEEE CS
                         Epimerase 186 ipalirkilegkqevtllgdgtalRdflyveDvaeaillvlehvdagdkgeiyn 239
                                       + ++i+++  g  ++t++g+g+++R fl  eD +e++ l+l+h+++ ++ ++yn
  gi|518651807|ref|YP_008141327.1| 234 LNRFISQAVIGY-PLTVYGKGDQKRAFLSLEDSVECLNLILDHPAE-KEYKVYN 285
                                       999999999999.******************************999.5678887 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 !   72.7   0.0   5.7e-24   3.4e-20       1     301 [.       4     332 ..       4     351 .. 0.70

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 5.7e-24
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEE...EESS-TTH.....HHHHCTTT...TTGCCEEEEE--TT-HHHHHH CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivr...rsssfntg.....riehlakdpkeeleenlklhkgDltDsssler 69 
                                       Li Gi G+iG  la +Ll++gyev+g ++   r    n+g     +i++ a+ ++++l++ +k++ gD+++ + + +
  gi|518651807|ref|YP_008141327.1|   4 LILGIDGYIGFPLALRLLDRGYEVYGADNfytRRRVKNVGsksavKINSFAT-RNKKLNNAIKFYMGDVSNPKFVYD 79 
                                       89************************98844333334444111114444444.45678899**************** PP

                                       HHHHHT-SEEEE--S---HHHHT...TSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S...... CS
                     GDP_Man_Dehyd  70 llaevqpdevynLAAqshVdvsf...ekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq...... 137
                                       ++++   d++++LA q   ++s+   +++ +t++ n+  t++++ a+++l+  ++++++  ++   YG+++      
  gi|518651807|ref|YP_008141327.1|  80 IIRDSGADAIVHLAEQRSAPYSMislKTATETLDKNIESTMNIIYAVKDLN--RDIHIVKLGSMGEYGTPNidipeg 154
                                       ****************998887544499*********************87..68**************96522212 PP

                                       ..SSSB...-TT..S-----SHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-T........TS.....CC CS
                     GDP_Man_Dehyd 138 ..evpq...tEt..tpfyPrsPYaaaKlyadwivvnyreayglfavngilfnhesprrge........tf.....vt 194
                                         +v +   +++   p   +s Y  +K++  +  +  ++ +gl ++       ++ r  e        +f       
  gi|518651807|ref|YP_008141327.1| 155 flDVQFhgrSDKlpFPRMGQSWYHLSKIFDTYNLMLANRIWGLNVSDVMQGVVYGTRTPEitkyklftRFdidqiYG 231
                                       22222222123433444679************99999999*998776666666666655532233333233333245 PP

                                       CHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE.-TT-EEECHHCHHCCHHCCCHHH CS
                     GDP_Man_Dehyd 195 rkitravarialgkqevlylGnldakRdwghvkDyveamwlmlqqdkpedyvi.atgethsvrefvelaflelgkti 270
                                         + r+++++  g  + +++G++d+kR ++  +D ve++ l+l +   ++y + ++ +++   + +  ++++  ++i
  gi|518651807|ref|YP_008141327.1| 232 TVLNRFISQAVIGY-PLTVYGKGDQKRAFLSLEDSVECLNLILDHPAEKEYKVyNQFDEYYPLNYLAETVKNRYESI 307
                                       55678899999998.8999************************9976655543033333333333333344444444 PP

                                       HHH............TTGGCCCEECGG--SS CS
                     GDP_Man_Dehyd 271 ewegkgeeevgrakesgkvvvevdpkyfrpg 301
                                         ++ +      +++  + +ve++ +y+ p+
  gi|518651807|ref|YP_008141327.1| 308 YGKKVS------INHVPNPRVEMEDHYYNPA 332
                                       433222......2333445555555555555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   2.2e-07    0.0013      47     117 ..      55     128 ..      35     136 .. 0.81
   2 ?    1.1   0.0     0.028   1.7e+02     176     213 ..     231     269 ..     216     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.2e-07
                                       ..-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH...HSHHHHHHHHHHHHHHHHHHHHH CS
                   Polysacc_synt_2  47 lkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve...enpleaiktNvlgtenvieaaie 117
                                       +++kkl+  i   +gdv + + + +++++ + d+++h A  +  P      + ++e+++ N+ +t+n+i a ++
  gi|518651807|ref|YP_008141327.1|  55 TRNKKLNNAIKFYMGDVSNPKFVYDIIRDSGADAIVHLAEQRSAPYSMislKTATETLDKNIESTMNIIYAVKD 128
                                       4556777778888********************************75411257789999*********998765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.028
                                       TSSHHHHHHHHHTTSSEEES-T.T-EEEEE-HHHHHHHH CS
                   Polysacc_synt_2 176 GSviplFkkqikeggpvtvTdp.emtRyfmtieeavqLv 213
                                       G v+  F +q   g p+tv  + +  R f+++e++v+ +
  gi|518651807|ref|YP_008141327.1| 231 GTVLNRFISQAVIGYPLTVYGKgDQKRAFLSLEDSVECL 269
                                       999****************7543899*******999754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.31s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2486.54
//
Query:       gi|518651808|ref|YP_008141328.1|  [L=240]
Description: glucose-1-phosphate thymidylyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-17   61.9   0.0    8.4e-17   61.6   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
  ------ inclusion threshold ------
      0.029   14.7   0.0      0.033   14.5   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
      0.079   12.8   0.0       0.11   12.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   1.4e-20   8.4e-17       3     242 ..       4     227 ..       2     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.4e-20
                                       EEE--S--GGGTTCCTTSSGGGSEET...TET....ETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGT CS
                   NTP_transferase   3 vILaGGsGtRLwPLtrtlakklvpvl...gke....rliqatlsrlansgieeiivvltqehsflveeqlkegskfg 72 
                                       +I a G GtR   L   + k ++pv+   +++    ++++  +++l+ sg ++  +vl  +++++ +++l++ +   
  gi|518651808|ref|YP_008141328.1|   4 LITAAGLGTR-ANLPEGMRKEMLPVYavrNGKivlrPILECIIHNLSLSGADKFFIVLDAKDRHT-ADYLSTLN--- 75 
                                       6777777887.56777778888777622222234458999999**********666666666665.56777665... PP

                                       SEEEEEEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEEST..THHHHHHHHHTHSSTTSEEEEEEESS-CTT CS
                   NTP_transferase  73 vevlialepegkgtAdAvalaaelledeksdelvlvLggDhlikd..ayeeavkkaiekaakgtvtfgivpveeate 147
                                       v+ ++++++  +g  +Avala+e++  ++    +l  +gD li d  + +++v+  +++++    ++ ++ v ++++
  gi|518651808|ref|YP_008141328.1|  76 VKSEYIYQKRAEGYGKAVALAKEYIPGDF----IL-NAGDGLILDrnKTKNMVDLYRSTGK---TILSVMAVPNPQR 144
                                       88************************988....44.455655555589************9...56667788899** PP

                                       SEEEEECTTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECST CS
                   NTP_transferase 148 yGvieadeegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfk 224
                                       yGv+++++ g ve+ vEKP++++ s++a +  Yv +++v++ l           +e+t ++++ + +g+    f  +
  gi|518651808|ref|YP_008141328.1| 145 YGVANIKN-GIVESVVEKPEHPA-SKYALAAFYVIKKNVMDLL---------DGTELTPAINRHIINGNTVIPFKIR 210
                                       ******98.8***********99.******************9.........3456666777777777888887777 PP

                                       TEE-EEEXSSHHHHHHHH CS
                   NTP_transferase 225 daeyWsDvGtldsllean 242
                                        +  W  +G+ ++++++ 
  gi|518651808|ref|YP_008141328.1| 211 RS-DWLSIGNSNDYYKIL 227
                                       76.5********999975 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.5e-06     0.033       1     118 [.       3     133 ..       3     193 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-06
                                       EEEEEESS-TTTT...T.THHHHCC....CCC....CHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-.. CS
                      NTP_transf_3   1 aviLAGGrSsRmg...g.dKallpl....ggk....pllervldalraagvdevvvvggd..eevlaalarlgvr.. 61 
                                       a+i A+G ++R +   g  K +lp+    +gk    p+le ++ +l+ +g+d+ ++v ++  ++ +++l  l+v+  
  gi|518651808|ref|YP_008141328.1|   3 ALITAAGLGTRANlpeGmRKEMLPVyavrNGKivlrPILECIIHNLSLSGADKFFIVLDAkdRHTADYLSTLNVKse 79 
                                       6899********6544469******87777769999*********************76633677778888776533 PP

                                       EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSE CS
                      NTP_transf_3  62 vvededpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadv 118
                                       +++++   +g ++++a a + +     +++ a+D   l+++  + +++ ++++g+ +
  gi|518651808|ref|YP_008141328.1|  80 YIYQK-RAEGYGKAVALAKEYI--PGDFILNAGDGLILDRNKTKNMVDLYRSTGKTI 133
                                       67775.4788888888888887..467777788888888877777777777777665 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 ?   12.3   0.0   1.9e-05      0.11      29     112 ..      54     134 ..      31     179 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.9e-05
                                       EEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SSEEEEEESSEEE-TTHHHHHHHHHH CS
                   Glycos_transf_2  29 feiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgdyilflDaDdepdpdwleklveale 105
                                       ++ ++v D+   +t++ l  l   + +  +i +++ +G+++a+  + ++  gd+il   + ++ d+++ + +v+ + 
  gi|518651808|ref|YP_008141328.1|  54 DKFFIVLDAKDRHTADYLSTL---NVKSEYIYQKRAEGYGKAVALAKEYIPGDFILNAGDGLILDRNKTKNMVDLYR 127
                                       667899999999999999999...78*************************************************** PP

                                       H.TTCEE CS
                   Glycos_transf_2 106 kdgadvv 112
                                        +g+ + 
  gi|518651808|ref|YP_008141328.1| 128 STGKTIL 134
                                       9999543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1889.33
//
Query:       gi|518651809|ref|YP_008141329.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G0448 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-12   46.1   0.0    6.8e-12   45.5   0.0    1.3  1  ATP_bind_3     PP-loop family
    8.9e-08   31.3   0.0    1.3e-07   30.7   0.0    1.2  1  tRNA_Me_trans  tRNA methyl transferase
    0.00025   20.2   0.0    0.00039   19.6   0.0    1.3  1  NAD_synthase   NAD synthase
    0.00054   19.7   0.0    0.00074   19.3   0.0    1.2  1  Asn_synthase   Asparagine synthase
     0.0029   17.1   8.7     0.0038   16.8   1.9    3.3  3  RecR           RecR protein
     0.0069   16.4   0.0      0.019   15.0   0.0    1.8  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.008   15.7   0.1      0.021   14.3   0.1    1.9  1  QueC           Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.057   13.3   0.0       0.52   10.1   0.0    2.1  2  Peptidase_C97  PPPDE putative peptidase domain
       0.86    9.4   0.1       0.86    9.4   0.1    2.9  3  zf-HYPF        HypF finger
        5.3    7.3   7.5        3.8    7.7   0.0    3.1  4  C5HCH          NSD Cys-His rich domain


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 !   45.5   0.0   3.8e-15   6.8e-12       2     180 ..      51     241 ..      50     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 3.8e-15
                                       EEEE--SCHHHHHHHHHHHHHCTTTTT.EEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H......... CS
                        ATP_bind_3   2 vlvAvSgGlDSmaLllllaklkkklgi.klvaihvdhglreeskeeaelvkelckklnikleiekvdv......... 68 
                                       + vA+SgG DS a l+ll+k  ++    +l+a++vd g+        e  ++lc++l+i++ + + +          
  gi|518651809|ref|YP_008141329.1|  51 ISVAISGGKDSSATLYLLHKILSERRNlELTAFTVDEGIEGYRSTGLEKARKLCENLGIEHNVISYKEnygysldei 127
                                       679*************999986655444************999999****************999999999988877 PP

                                       .HHCTTSTCCCHHHHHHHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-.. CS
                        ATP_bind_3  69 .akkkgknleeaARelRYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvR.. 142
                                        + +k++        +R ++++++ +  + ++++l+ + dD+a  +l+++a+g     +a +++ s + ++ + R  
  gi|518651809|ref|YP_008141329.1| 128 mKIDKKTISCSHCGPMRRQLMNRISEYTESDYVALGINLDDYAQSILMNVAKGDVA-RYARMAPHSYTREGLVPRil 203
                                       533334445567889*************************************8875.88889999988877776666 PP

                                       CCCT--HHHHHHHHHHTT---B--CGGGCTTSHHHHHH CS
                        ATP_bind_3 143 PlLkvskeeleeylkekkikwveDesNadekyeRnriR 180
                                       Pl k+  +e+  y+  ++i++      + +  +Rn +R
  gi|518651809|ref|YP_008141329.1| 204 PLRKIPEKEVVLYAILNGIDFDSSWCPYYSMAQRNSFR 241
                                       99999999999999999999876666666666666666 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.0   7.5e-11   1.3e-07       2      75 ..      50     121 ..      49     131 .. 0.89

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 7.5e-11
                     tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekeyk 75 
                                       ++ va+SgG DSs +++ll++   e + + l   +  de   e   ++ l++a++ +e+lgi+++v++++++y 
  gi|518651809|ref|YP_008141329.1|  50 RISVAISGGKDSSATLYLLHKILSERRNLELTAFTV-DEGI-EGYRSTGLEKARKLCENLGIEHNVISYKENYG 121
                                       799*************************99999988.3333.5778899***********************95 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.2e-07   0.00039       6      99 ..      35     134 ..      29     164 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.2e-07
                                       HHHHHHHHHHCTT.SEEEEEE-SSHHHHHHHHHHHHHHTCGEEE...EEE--SSST..THHHHHHHHHHHHHHTSEE CS
                      NAD_synthase   6 vdflkeyvkkaga.kgvvlGlSGGvDSslvaalavkalgkenvl...alllPssvs..seedvedalalaenlgiev 76 
                                       +  ++e+v+  +  + + + +SGG DSs + +l  k+l + + l   a  + +  +      +e+a++l+enlgie 
  gi|518651809|ref|YP_008141329.1|  35 KREIREQVDFGNKkTRISVAISGGKDSSATLYLLHKILSERRNLeltAFTVDEGIEgyRSTGLEKARKLCENLGIEH 111
                                       55567777655552567799******************66665511144455333311567789************* PP

                                       EE---HHHHHHHHHHHHHHH-HH CS
                      NAD_synthase  77 ktidikpivrafeqelkeakedl 99 
                                       ++i+ k+ +  + +e+ +  +++
  gi|518651809|ref|YP_008141329.1| 112 NVISYKENYGYSLDEIMKIDKKT 134
                                       *****999988877666655554 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.1e-07   0.00074      18      86 ..      49     123 ..      32     151 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.1e-07
                      Asn_synthase  18 vpvGalLSGGlDSSliaalaarqsk....splktFsigf..eekgsdeakyakevaehlgtehtelvlteeelld 86 
                                        ++++ +SGG DSS+  +l+ + +      +l++F+++   e  +s  ++ a++++e lg+eh  + ++e+ +++
  gi|518651809|ref|YP_008141329.1|  49 TRISVAISGGKDSSATLYLLHKILSerrnLELTAFTVDEgiEGYRSTGLEKARKLCENLGIEHNVISYKENYGYS 123
                                       567899************9999998888899******9865669999****************988887765554 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.19   3.5e+02      19      23 ..       3       7 ..       1      14 [. 0.74
   2 ?    1.8   0.1       0.1   1.8e+02       8      23 ..     126     141 ..     124     146 .. 0.81
   3 !   16.8   1.9   2.1e-06    0.0038      16      36 ..     280     300 ..     275     302 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.19
                                      -TTT- CS
                              RecR 19 CsrCg 23
                                      Cs+Cg
  gi|518651809|ref|YP_008141329.1|  3 CSICG 7 
                                      77777 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.1
                                       HHHHHHHH-EE-TTT- CS
                              RecR   8 aLqeakekvrhCsrCg 23 
                                       ++ +  +k   Cs Cg
  gi|518651809|ref|YP_008141329.1| 126 EIMKIDKKTISCSHCG 141
                                       67777889999****8 PP

  == domain 3  score: 16.8 bits;  conditional E-value: 2.1e-06
                                       -EE-TTT--EESSSS-CCCCS CS
                              RecR  16 vrhCsrCgnlteedlCaICsd 36 
                                       +  C++Cg  t  ++C++Csd
  gi|518651809|ref|YP_008141329.1| 280 LNSCKICGAPTPGEICEVCSD 300
                                       668*****************9 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.1e-05     0.019       2     153 ..      51     222 ..      50     228 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.1e-05
                                       EEEE--SSCTCHHHHHHHHHHCTTH.....EEEEEE-STB..-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHH CS
                       PAPS_reduct   2 lvvsvsgGkdslVllhLalkafkpv.....pvvfvdtghe..fpetiefvdeleeryglrlkvyepeeevaekinae 71 
                                       + v++sgGkds+++l L+ k++ ++     + + vd g e   ++ +e   +l e++g++  v + +e+   ++ + 
  gi|518651809|ref|YP_008141329.1|  51 ISVAISGGKDSSATLYLLHKILSERrnlelTAFTVDEGIEgyRSTGLEKARKLCENLGIEHNVISYKENYGYSLDEI 127
                                       7899********************77888889999999873234446667777777777766666666655555444 PP

                                       H-S-THHHC.HHHHHHTHHHHHHHHHCT.TECEEE----CCCTTTTTTSSSEEECTTT-S............CEEE- CS
                       PAPS_reduct  72 khgsslyee.aaeriaKveplkkaLekl.dedalltGaRrdesksraklpiveidedfek............slrvf 134
                                        +  ++  +   +  ++ + +++ ++++ + d++  G+  d+ ++   +++ + d +  +            + r++
  gi|518651809|ref|YP_008141329.1| 128 MKIDKKTIScSHCGPMRRQLMNR-ISEYtESDYVALGINLDDYAQSILMNVAKGDVARYArmaphsytreglVPRIL 203
                                       43333322235556666665655.44442445555555555555555555555444433345555555555555666 PP

                                       CCCT--HHHHHHHHHHCT- CS
                       PAPS_reduct 135 PllnWteedvwqyilreni 153
                                       Pl +  e++v  y+  ++i
  gi|518651809|ref|YP_008141329.1| 204 PLRKIPEKEVVLYAILNGI 222
                                       6666666666666666665 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   1.2e-05     0.021       4      62 ..      53     117 ..      50     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
                                       EE--SSHHHHHHHHHHHH.....H-SEEEEEEEESS-T..TSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC   4 vllSGGlDSttvlalakk.....egkevealtfdYgqr..hkkeleaakkiakelgveehkildld 62 
                                       v +SGG DS++ l+l +k     +  e++a t+d g    +++ le+a+k++++lg+ eh++++ +
  gi|518651809|ref|YP_008141329.1|  53 VAISGGKDSSATLYLLHKilserRNLELTAFTVDEGIEgyRSTGLEKARKLCENLGI-EHNVISYK 117
                                       679********999887622211456899999999988778899*************.99998765 PP

>> Peptidase_C97  PPPDE putative peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00029      0.52      56     130 ..     108     186 ..      82     204 .. 0.80
   2 ?    0.7   0.0      0.24   4.2e+02      83     106 ..     236     259 ..     210     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00029
                                       -SE.EESTT-STT-.S-SEEEEEEEE---HHHHHHHHHHHHT...T--GGG-BTTTB-HHHHHHHHHHHHHS----H CS
                     Peptidase_C97  56 Gif.elkpgttsegakpresieigeTevteeevraileelss...eytgdkYnLiskNCnhFtdelvdfLtgkkiPe 128
                                       Gi  ++ +++ ++g+  +e+++i++ ++++ +   + ++l +   eyt+++Y  ++ N  ++++ ++  + ++ + +
  gi|518651809|ref|YP_008141329.1| 108 GIEhNVISYKENYGYSLDEIMKIDKKTISCSHCGPMRRQLMNrisEYTESDYVALGINLDDYAQSILMNVAKGDVAR 184
                                       444466677789*******************998888777774444******************9999988888777 PP

                                       HH CS
                     Peptidase_C97 129 wi 130
                                       + 
  gi|518651809|ref|YP_008141329.1| 185 YA 186
                                       65 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.24
                                       -HHHHHHHHHHHHTT--GGG-BTT CS
                     Peptidase_C97  83 teeevraileelsseytgdkYnLi 106
                                       +++ +r+i+e+l++e +g+k++++
  gi|518651809|ref|YP_008141329.1| 236 QRNSFRDIIEKLEKETPGTKFAIV 259
                                       67889**********999999987 PP

>> zf-HYPF  HypF finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.3       4.4   7.9e+03      24      28 ..       3       7 ..       2       9 .. 0.80
   2 ?    9.4   0.1   0.00048      0.86      21      29 ..     134     142 ..     131     145 .. 0.90
   3 ?    2.3   0.2     0.081   1.5e+02      22      29 ..     281     288 ..     277     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 4.4
                                      -TTTS CS
                           zf-HYPF 24 CtnCG 28
                                      C  CG
  gi|518651809|ref|YP_008141329.1|  3 CSICG 7 
                                      89999 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00048
                                       T---TTTS- CS
                           zf-HYPF  21 fisCtnCGP 29 
                                       +isC +CGP
  gi|518651809|ref|YP_008141329.1| 134 TISCSHCGP 142
                                       79******* PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.081
                                       ---TTTS- CS
                           zf-HYPF  22 isCtnCGP 29 
                                       +sC+ CG 
  gi|518651809|ref|YP_008141329.1| 281 NSCKICGA 288
                                       8******5 PP

>> C5HCH  NSD Cys-His rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0021       3.8       3      26 ..       2      25 ..       1      30 [. 0.96
   2 ?   -3.9   0.3       9.2   1.6e+04       4       8 ..     137     141 ..     135     142 .. 0.71
   3 ?   -2.0   0.0       2.3   4.1e+03      11      25 ..     182     196 ..     176     197 .. 0.77
   4 ?    1.1   2.0      0.26   4.6e+02       3      18 ..     282     298 ..     281     300 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0021
                             C5HCH  3 qCsvCgkaatsfCefCPssFCkeH 26
                                      +Cs+Cg++a+   ++  s+ Ck+H
  gi|518651809|ref|YP_008141329.1|  2 ECSICGATAVYEVKYNGSALCKNH 25
                                      7**********************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 9.2
                             C5HCH   4 CsvCg 8  
                                       Cs+Cg
  gi|518651809|ref|YP_008141329.1| 137 CSHCG 141
                                       77776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.3
                             C5HCH  11 atsfCefCPssFCke 25 
                                        +++  + P+s+ +e
  gi|518651809|ref|YP_008141329.1| 182 VARYARMAPHSYTRE 196
                                       56777899***9886 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.26
                             C5HCH   3 qCsvCgkaat.sfCefC 18 
                                        C++Cg+++    Ce C
  gi|518651809|ref|YP_008141329.1| 282 SCKICGAPTPgEICEVC 298
                                       6*****99852789999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1976.14
//
Query:       gi|518651810|ref|YP_008141330.1|  [L=338]
Description: hypothetical protein FACI_IFERC00001G0449 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2196.47
//
Query:       gi|518651811|ref|YP_008141331.1|  [L=62]
Description: hypothetical protein FACI_IFERC00001G0450 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 440.75
//
Query:       gi|518651812|ref|YP_008141332.1|  [L=144]
Description: hypothetical protein FACI_IFERC00001G0451 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1090.81
//
Query:       gi|518651813|ref|YP_008141333.1|  [L=880]
Description: hypothetical protein FACI_IFERC00001G0452 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  158.6   0.3    1.1e-46  158.6   0.3    3.8  4  E1-E2_ATPase     E1-E2 ATPase
    3.4e-28   98.6   8.2    3.4e-28   98.6   8.2    2.5  3  Cation_ATPase_C  Cation transporting ATPase, C-terminus
    2.2e-19   70.6   0.7    4.5e-19   69.6   0.7    1.6  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.8e-18   64.3   1.7    2.3e-17   62.4   0.0    2.6  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.5e-11   44.2   0.0    4.1e-11   42.8   0.0    1.8  1  Cation_ATPase    Cation transport ATPase (P-type)
    2.3e-06   27.6   3.3    6.3e-05   22.8   0.9    2.5  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   16.0   0.0      0.023   15.1   0.0    1.5  1  HAD              haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.0   0.8     0.006        15     108     154 ..      51      97 ..      39     100 .. 0.77
   2 !  158.6   0.3   4.4e-50   1.1e-46       2     181 .]     116     307 ..     115     307 .. 0.98
   3 ?    0.3   0.1      0.17   4.2e+02      90     139 ..     646     695 ..     643     711 .. 0.71
   4 ?   -3.8   0.6         3   7.6e+03     124     142 ..     751     769 ..     742     787 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.006
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHH CS
                      E1-E2_ATPase 108 ktplqkkldklgkvlvpvvlliallvflialllgkslaeallralal 154
                                          lq +ld+l + l++v ++i+++ fli    + +++ ++++a+ +
  gi|518651813|ref|YP_008141333.1|  51 HGILQIFLDQLKEPLILVLVVIGIIYFLIGTPFESFTVIIIVFAVIV 97 
                                       556999***********************976666665555555444 PP

  == domain 2  score: 158.6 bits;  conditional E-value: 4.4e-50
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-S.EEE-TTTS---S-EE-...........G- CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsa.evdesaLTGEslpvek...........ek 66 
                                       +  p+++v+r+g++ e  ++ lvpGDiv l++gd vpaDg++v++s   +des++TGEs pv k            +
  gi|518651813|ref|YP_008141333.1| 116 MVTPKTWVLRNGSLLEKSTSVLVPGDIVYLRTGDMVPADGIVVSSSGlYIDESLVTGESYPVNKvsfdepetkpgAN 192
                                       567999*****************************************************************999989 PP

                                       TTEE-TT-EEEE-EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSS CS
                      E1-E2_ATPase  67 gdmvfsGtvvvsgeakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgks 143
                                        ++v sGt vv+g+ k+ Vt tg +te+gki ++v++ k   tpl+k l+k ++ l+++++++++l+ li +++g++
  gi|518651813|ref|YP_008141333.1| 193 MHRVVSGTLVVQGNGKFAVTSTGLKTEIGKISESVKNHKDIPTPLEKSLNKTARLLIVIAVFFSALIPLIGYVHGDP 269
                                       ***************************************************************************** PP

                                       TTHHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 144 laeallralallvaaiPcaLplavplalalgarrlakk 181
                                       l +++l +l+++ a++P+ +p++++++la+ga +l+kk
  gi|518651813|ref|YP_008141333.1| 270 LDQMILMGLSMAFATVPEEIPILITITLAIGAYSLSKK 307
                                       **********************************9996 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.17
                                       TTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-ST CS
                      E1-E2_ATPase  90 edtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvfliall 139
                                       ed  +++ia++v e ++ +  l+k ++ +++v + ++l++++ ++li ++
  gi|518651813|ref|YP_008141333.1| 646 EDDNFHTIAEAVFEGRKMQYTLKKGIRYYIAVKISLILILLVPILLIIPF 695
                                       56678999999999999999999999999888555555555555555444 PP

  == domain 4  score: -3.8 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHS-STTTS CS
                      E1-E2_ATPase 124 pvvlliallvflialllgk 142
                                       ++++++a++++ + +++ +
  gi|518651813|ref|YP_008141333.1| 751 ALGVFLAVTFIYLYIYYSE 769
                                       3333333333333333333 PP

>> Cation_ATPase_C  Cation transporting ATPase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   1.2       1.7   4.3e+03      63      75 ..      86      98 ..      65     124 .. 0.53
   2 ?   -2.0   0.3      0.95   2.4e+03     126     146 ..     246     266 ..     236     302 .. 0.59
   3 !   98.6   8.2   1.3e-31   3.4e-28       1     182 []     694     866 ..     694     866 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                   Cation_ATPase_C 63 lvtllvffltlll 75
                                      + ++++ f+++ +
  gi|518651813|ref|YP_008141333.1| 86 FTVIIIVFAVIVI 98
                                      3333333333332 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.95
                   Cation_ATPase_C 126 kllllaillslllqvlivyvp 146
                                       +ll++++++  +l+ li yv 
  gi|518651813|ref|YP_008141333.1| 246 RLLIVIAVFFSALIPLIGYVH 266
                                       344444444446888888874 PP

  == domain 3  score: 98.6 bits;  conditional E-value: 1.3e-31
                   Cation_ATPase_C   1 plplsaiqiLwinLvtDllpalaLaleppekdimkrpPrkkkepliskkmlrriliqgllqalvtllvffltlllfg 77 
                                       p p+ +iqi+++++++D+ +   +  e  e++i+   P+k+ +  +++ m++ il+ +l ++l++ +++++ ++  +
  gi|518651813|ref|YP_008141333.1| 694 PFPFMPIQIIIMEMFMDVGALWGFLKERDEPGILHAAPQKRGADFMDRPMIISILTSALGVFLAVTFIYLYIYY--S 768
                                       67*********************************************************999999999966666..4 PP

                   Cation_ATPase_C  78 isekenklssnyaqtmaFitlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgt 154
                                         +        +aqt+aF t++lsq++ a+nlr++re++ + + +fsn+++l   l+ ++ +++i+ +p+l+a+++t
  gi|518651813|ref|YP_008141333.1| 769 EGDII------QAQTAAFATWILSQVILAQNLRTEREPVSQ-RPFFSNWVILSWGLIVVGALIVITVFPPLHAIIDT 838
                                       44444......4*****************************.******77777777777888888888********* PP

                   Cation_ATPase_C 155 aplsleewlialllalvvllvdelvKll 182
                                       + +   +w++++++++++  + el+K++
  gi|518651813|ref|YP_008141333.1| 839 STIEYRNWVLIIIVSVLSSSWIELRKII 866
                                       **************************86 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.7   1.7e-22   4.5e-19       2     209 ..     324     623 ..     323     624 .. 0.79

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1.7e-22
                                       SEEEEESBTTTBCHHHHHHHHHHHH...........CHHHHHHHHHH...........HHCHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxxxxxxxx...........xxxxxxxxxxxxxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa...........alalaaaletg...........sehpigkalvaaakarsga 56 
                                       ++++ Dk+GT+t+  + v  ++v                 +a+l+tg            + p   a+ ++a + + +
  gi|518651813|ref|YP_008141333.1| 324 TVIATDKTGTITENAMKVNHILVGEklyeaaqkgntSFLKSAVLATGnleieqkfsegYKDPMEVAILKYAINSGLD 400
                                       6899****************999998888888888866666666666777777777779999999999999999777 PP

                                       HHHHHH...ETTTE....................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH..... CS
                                       xxxxxx...xxxxx....................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx..... RF
                         Hydrolase  57 ltgfat...figrg....................ayaigkpewltal..dippdlgaaigsaqsqgrtvall..... 103
                                       +++ +    ++gr                     ay  g pe + +                               
  gi|518651813|ref|YP_008141333.1| 401 IHELESeylITGRFgfdsnikrasyvysghdgyvAYTSGAPEVVLSRctS---------------------Immdes 456
                                       76666644455555677777777777777778887777777755555331.....................022222 PP

                                       ...............................................TTHHHHHHHHHHTHHBHTTHHHHHHHHHHT CS
                                       ...............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 104 ...............................................qaralavftiadplkvkpeaaeavasLkaa 133
                                                                                      +    +++ + dp  + ++++ av+  + a
  gi|518651813|ref|YP_008141333.1| 457 snkvksesdlkiirdainevakvgertiafaykringqaeerdfvdsDMIFIGMISFIDP--PGKGVKNAVKLCQNA 531
                                       2222222222333344555667777777777999999999999999988***********..*************** PP

                                       TEEEEEEESSEHHHHHHHHHHTT............GGGE.SEEEEHHCES...STTTSHHHHHHHHHHHTSTGGGEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxx............xxxx.xxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 134 gievvlltgdnpetaeraanqlG............ddyf.daviasdiet...vakpspegkvaaireLqgkpeeva 194
                                       gi+v++ltgd p tae + + +G             +++ d ++++ ie+   +a    ++k+++++ Lq ++e va
  gi|518651813|ref|YP_008141333.1| 532 GIRVIMLTGDYPVTAETIGKMVGiknaestltgdqIRAMpDDELSKAIEKtsiFARITHDQKLRIVKALQKNGEIVA 608
                                       ************************999999999887777788888888889*******************99999** PP

                                       EEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx RF
                         Hydrolase 195 mVGDgvnDaaalaaA 209
                                       + GDg+nDa+al+aA
  gi|518651813|ref|YP_008141333.1| 609 VTGDGANDASALRAA 623
                                       *************99 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   0.0   9.1e-21   2.3e-17       5      68 ..      12      75 ..       8      76 .. 0.97
   2 ?    0.6   0.4      0.18   4.5e+02      47      68 ..      76      97 ..      75      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 9.1e-21
                   Cation_ATPase_N  5 sleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      ++e +l++L++d enGLt++ea +r++ yG N+++e kk  +++++l+q++ pl+++L+v +++
  gi|518651813|ref|YP_008141333.1| 12 DVESILKSLGVDVENGLTESEATRRIQSYGLNAIPEAKKHGILQIFLDQLKEPLILVLVVIGII 75
                                      799**********************************************************997 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.18
                   Cation_ATPase_N 47 wvkllkqftnplvilLlvaalv 68
                                      ++++   f +++vi+ ++a++v
  gi|518651813|ref|YP_008141333.1| 76 YFLIGTPFESFTVIIIVFAVIV 97
                                      56677789***********998 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   1.6e-14   4.1e-11      20      91 .]     382     451 ..     358     451 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.6e-14
                     Cation_ATPase  20 lGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilkrCthv 91 
                                         ++ E+A+l++a + gld++el++e+ +   + F+s+ Kr+s v++   + ++++y+ GApe++l+rCt++
  gi|518651813|ref|YP_008141333.1| 382 YKDPMEVAILKYAINSGLDIHELESEYLITGRFGFDSNIKRASYVYS--GHDGYVAYTSGAPEVVLSRCTSI 451
                                       5699*******************************************..67*******************86 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.011        29      20      70 ..     521     575 ..     517     593 .. 0.80
   2 !   22.8   0.9   2.5e-08   6.3e-05     195     254 ..     596     656 ..     592     657 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEE....ECTT CS
                       Hydrolase_3  20 tkeaikklkekgikvviATGRslravlpvleelgldlpvialNGali....ddek 70 
                                        k+a+k ++++gi v+  TG  +++++ + + +g++++  +l G  i    dde 
  gi|518651813|ref|YP_008141333.1| 521 VKNAVKLCQNAGIRVIMLTGDYPVTAETIGKMVGIKNAESTLTGDQIrampDDEL 575
                                       6899********************************9999999999963333333 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 2.5e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETT.S-HHHHHHSSEEE--GGGTHHHHH CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgn.aseevkkaAdyvtksnnedGVaka 254
                                       ++k l+ + e v++ GDg ND + L aa++g+ mg  ++e +k+a+d v ++ n + +a+a
  gi|518651813|ref|YP_008141333.1| 596 IVKALQKNGEIVAVTGDGANDASALRAAEIGISMGKrGTEVAKEASDIVLEDDNFHTIAEA 656
                                       789999999*************************963677777888888888888999987 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   9.1e-06     0.023      88     188 .]     516     621 ..     474     621 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.1e-06
                               HAD  88 p...galellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd.......rltge...lglegkpvrg 151
                                       p   g++ +++ ++ aG+rv++++g +   +e + + +g+++  +t l  d+        l++      ++  ++++
  gi|518651813|ref|YP_008141333.1| 516 PpgkGVKNAVKLCQNAGIRVIMLTGDYPVTAETIGKMVGIKNAEST-LTGDQirampddELSKAiekTSIFARITHD 591
                                       44668888899888*************************4444333.111112222233222220002222222222 PP

                               HAD 152 egkvaalrewlaaegegidleevvay.GDspsDlpllr 188
                                        +k++ +++ l+++g      e+va+ GD+ +D  +lr
  gi|518651813|ref|YP_008141333.1| 592 -QKLRIVKA-LQKNG------EIVAVtGDGANDASALR 621
                                       .44444444.22222......266667******99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (880 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.42
# Mc/sec: 6260.94
//
Query:       gi|518651814|ref|YP_008141334.1|  [L=202]
Description: hypothetical protein FACI_IFERC00001G0453 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); 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: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1607.37
//
Query:       gi|518651815|ref|YP_008141335.1|  [L=62]
Description: hypothetical protein FACI_IFERC00001G0454 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      0.006   16.7   0.3     0.0074   16.4   0.3    1.1  1  ParG            ParG
  ------ inclusion threshold ------
       0.03   14.7   0.2      0.039   14.4   0.2    1.2  1  CcdA            Post-segregation antitoxin CcdA
      0.035   14.6   0.1       0.05   14.1   0.1    1.2  1  BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin sys


Domain annotation for each model (and alignments):
>> ParG  ParG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.3   1.2e-06    0.0074      33      74 ..      10      51 ..       6      55 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                              ParG 33 kskrvnvnfdeekhtrfkaacakkGtsitdvinqlvdnwlke 74
                                      ++krv +  d   + +fk  c ++   ++  in l+  wl  
  gi|518651815|ref|YP_008141335.1| 10 RKKRVTLTIDISTYEKFKEVCKNEDIKMSTKINTLITKWLAV 51
                                      68*************************************964 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   6.6e-06     0.039       1      44 [.      11      58 ..      11      62 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.6e-06
                              CcdA  1 KkavnlsldsdllaqAral....giNlSatleeaLaeevkeekaerwk 44
                                      Kk+v+l++d   +++ +++    +i +S  ++++++++++ +++e +k
  gi|518651815|ref|YP_008141335.1| 11 KKRVTLTIDISTYEKFKEVckneDIKMSTKINTLITKWLAVQENENEK 58
                                      99***********9998875555788*************988887765 PP

>> BrnA_antitoxin  BrnA antitoxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   8.3e-06      0.05      35      69 ..      10      48 ..       6      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.3e-06
                    BrnA_antitoxin 35 tKkkvtlRLDadVleaFkatGkg....wQtriNeaLrky 69
                                      +Kk+vtl +D ++ e+Fk+  k       t+iN ++ k+
  gi|518651815|ref|YP_008141335.1| 10 RKKRVTLTIDISTYEKFKEVCKNedikMSTKINTLITKW 48
                                      699***************944444455999999998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1247  (0.0695521); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 490.47
//
Query:       gi|518651816|ref|YP_008141336.1|  [L=284]
Description: hypothetical protein FACI_IFERC00001G0455 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-27   97.0   5.0    6.7e-17   62.0   0.0    2.1  2  N6_N4_Mtase      DNA methylase
    3.4e-09   36.7   0.2    1.9e-07   30.9   0.2    2.7  1  UPF0020          Putative RNA methylase family UPF0020
    1.2e-05   25.8   0.0     0.0003   21.4   0.0    2.2  1  Methyltransf_11  Methyltransferase domain
    0.00013   21.3   0.1    0.00025   20.4   0.1    1.4  1  N6_Mtase         N-6 DNA Methylase
    0.00036   20.4   0.0    0.00055   19.7   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    0.00088   19.9   0.0      0.029   15.1   0.0    2.2  1  Methyltransf_25  Methyltransferase domain
      0.006   16.2   0.0      0.014   15.0   0.0    1.6  1  Cons_hypoth95    Conserved hypothetical protein 95
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.019   14.6   0.0    1.4  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
       0.18   11.3   0.3        0.5    9.9   0.0    1.9  2  MTS              Methyltransferase small domain
       0.24   11.7   7.9        1.8    8.9   0.1    2.6  3  DUF5625          Domain of unknown function (DUF5625)


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 !   62.0   0.0   3.7e-20   6.7e-17     133     224 ..      34     119 ..       7     126 .. 0.81
   2 !   36.0   2.2   3.3e-12   5.8e-09       1     108 [.     158     281 ..     158     283 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 3.7e-20
                                       HHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHHHHH CS
                       N6_N4_Mtase 133 lekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTavaa 209
                                       +e     + +k + +i+++W ++e+ + + +  +   +k+      +l++ +I+ ++k++d++lDpF GSGtT+++a
  gi|518651816|ref|YP_008141336.1|  34 IETL---EPEKFNLEIDNVWSFPERGKWCTHYLN---AKYRGNYAPQLPRNIILRYSKENDLILDPFSGSGTTLIEA 104
                                       3333...367778899****88888888887765...799************************************* PP

                                       HHTT-EEEEEESSHH CS
                       N6_N4_Mtase 210 kelgrkfiGieieee 224
                                       k l+r+ iG++i+  
  gi|518651816|ref|YP_008141336.1| 105 KLLKRHGIGMDINLG 119
                                       ************965 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3.3e-12
                                       EEEEEE--SSSSSCS.........GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT......HHHH CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy....endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk......elka 67 
                                       +dli+t pPY +  +y    + ++++   +s eey + ++kv+ke++r Lk+++   i i+d + k       + ++
  gi|518651816|ref|YP_008141336.1| 158 IDLIMTHPPYANIIKYskdnIIKDDLSSIESLEEYYKKFKKVIKEMHRTLKKGKYCAILIGDTRKKGyqipisFTIM 234
                                       89**************666666666666777*********************************999***9654444 PP

                                       HHHHHTT-EEEEEEEEEEES........SSTTTSTCC...S-B--EEEEEEE CS
                       N6_N4_Mtase  68 ladeifggffllnvivwkkp........nsmpesnkd...rltsthEyilvf 108
                                       ++  + g f+l+++i++ +          s++        ++  ++E+++vf
  gi|518651816|ref|YP_008141336.1| 235 QLFLKEG-FVLKEDIIKVQHntktrhywASLS----IknnFMLLAYEHLFVF 281
                                       4444445.*********999333332211111....1222455555555555 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.2   1.1e-10   1.9e-07      27     141 ..      85     177 ..      79     223 .. 0.79

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.1e-10
                                       -TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-..HHHHHHHHHHHHHTT- CS
                           UPF0020  27 kpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDld..rrvvqgareNaekagv 101
                                       k+++ +lDP++GsGt lIEa ll+++ +                          g+D++  +++++  r N ++ + 
  gi|518651816|ref|YP_008141336.1|  85 KENDLILDPFSGSGTTLIEAKLLKRHGI--------------------------GMDINlgSAMITMDRLNFNNSEN 135
                                       78899***********************..........................666654489*******9999988 PP

                                       GGGE.EEEE--GGG--.STTS---EEEE----------HHHH CS
                           UPF0020 102 gdli.efsqadaakLr.lkegevdvivtnpPYGerlgskkal 141
                                       + +  e+ + da++L+  +++++d+i t pPY + ++  k++
  gi|518651816|ref|YP_008141336.1| 136 NLIEpEIFNGDARNLNeIEDESIDLIMTHPPYANIIKYSKDN 177
                                       7654378899******755669**********9888766554 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.7e-07    0.0003       4      96 .]      96     215 ..      91     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.7e-07
                                       T-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-...EEEETTEECCCT.SS-TT-EEEEEEES....-CC CS
                   Methyltransf_11   4 GcGtGrlaealakrgarvvgvDlskemlklakekaseegl...kvefvvadaekl.pfednsfDlvvsse....vlh 72 
                                       G+Gt ++ ++l kr +  + ++l  +m+++ + + +++++   + e+  +da++l  +ed+s+Dl++ +      + 
  gi|518651816|ref|YP_008141336.1|  96 GSGTTLIEAKLLKRHGIGMDINLGSAMITMDRLNFNNSENnliEPEIFNGDARNLnEIEDESIDLIMTHPpyanII- 171
                                       5666655555665556667777788999999999999999999999*********88**********999555522. PP

                                       C-C......................CHHHHHHHHHHHEEEEEEEEE CS
                   Methyltransf_11  73 hve......................dpekalkeiaRvLkpgGllvi 96 
                                         +                      + +k++ke++R Lk+g +++i
  gi|518651816|ref|YP_008141336.1| 172 --KyskdniikddlssiesleeyykKFKKVIKEMHRTLKKGKYCAI 215
                                       ..23335666677777777777777****************99976 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.4e-07   0.00025      44     178 ..      84     211 ..      64     220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                          N6_Mtase  44 pksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvk..irlgdtlekp 118
                                       +k++  ++Dp +Gsg  l++a+  lk++          G+++n  ++ ++   l   ++e++ ++  i +gd+ + +
  gi|518651816|ref|YP_008141336.1|  84 SKENDLILDPFSGSGTTLIEAKL-LKRH--------GIGMDINLGSAMITMDRLNFNNSENNLIEpeIFNGDARNLN 151
                                       445557*************9976.5533........34888888877777767777888888877669999999999 PP

                          N6_Mtase 119 kfekdkkfdvvvaNppf.nqkewkektlekderfreavapksnadlafllhiieslkpkGr 178
                                       + e d+++d +++ pp+ n+ ++++++++kd+  +    ++  + +  +   ++ + +kG+
  gi|518651816|ref|YP_008141336.1| 152 EIE-DESIDLIMTHPPYaNIIKYSKDNIIKDDLSSIESLEEYYKKFKKVIKEMHRTLKKGK 211
                                       999.*************44567999999999855555555555555544444444444455 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-07   0.00055       3     112 ..      86     218 ..      84     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-07
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDis..eeaielAre..naqklgldnveFeqgdieeleklledekf 75 
                                       ++  +lD+ +G+G+ ++e+  +l  k + +G Di+    +i+  r   n ++++l + e   gd+ +l++ +ede++
  gi|518651816|ref|YP_008141336.1|  86 ENDLILDPFSGSGTTLIEAK-LL--KRHGIGMDINlgSAMITMDRLnfNNSENNLIEPEIFNGDARNLNE-IEDESI 158
                                       56679************999.54..5678888887447899999984455556667889999*****998.8***** PP

                   Methyltransf_31  76 Dlilsn......................evl.naladpdkileeiervlkpggilliedp 112
                                       Dli+++                      e l  + +  +k+++e++r lk+g +++i   
  gi|518651816|ref|YP_008141336.1| 159 DLIMTHppyaniikyskdniikddlssiESLeEYYKKFKKVIKEMHRTLKKGKYCAILIG 218
                                       ******9999999999988888777666555899999999**************998655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.029       1      70 [.      90     163 ..      90     210 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESS..HHHHHHHHHHHHH..TTT.TEEEEESBCCGBSS.STTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDis..eemleaareraee..egl.nvefvqgdaedlpf.edgsfDlvvs 70 
                                       +Ld   G+G++++++     k + +g+Di+  ++m+   r ++++  ++l + e+ +gda++l++ ed+s+Dl++ 
  gi|518651816|ref|YP_008141336.1|  90 ILDPFSGSGTTLIEAKLL--KRHGIGMDINlgSAMITMDRLNFNNseNNLiEPEIFNGDARNLNEiEDESIDLIMT 163
                                       789999999999998654..4999*****8445676555555544325558999********9854********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 !   15.0   0.0     8e-06     0.014      40     126 ..      85     170 ..      78     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8e-06
                                       HCC-EEEETT-TTSHHHHHH..HHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEA..lSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                        e+  +LD f+GsG+  +EA  l R     + ++  ++++++ + n ++ +++    e+ + ++++l++   ++e++
  gi|518651816|ref|YP_008141336.1|  85 KENDLILDPFSGSGTTLIEAklLKRH-GIGMDINLGSAMITMDRLNFNNSENNLIEPEIFNGDARNLNEI--EDESI 158
                                       456679**************644443.4444555556666666666666666664456666666666666..6889* PP

                                       EEEEE--SSSTT CS
                     Cons_hypoth95 115 divflDPPyake 126
                                       d++   PPya+ 
  gi|518651816|ref|YP_008141336.1| 159 DLIMTHPPYANI 170
                                       *********975 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 ?   14.6   0.0     1e-05     0.019       3      94 ..      89     183 ..      87     213 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1e-05
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdki...tlvlgdvfellaklklekikvdlvf 76 
                                       +ilD+fsG+G   i+ +l  ++ i+++inl    ++    ++ + ++++    +  gd    l++++ e+i  dl++
  gi|518651816|ref|YP_008141336.1|  89 LILDPFSGSGTTLIEAKLLKRHGIGMDINLGSAMITMDRLNFNNSENNLiepEIFNGDAR-NLNEIEDESI--DLIM 162
                                       79*****************999*********************99777622224566654.5778788888..**** PP

                   Methyltransf_15  77 lSpPwGG.psYkkqekf..dl 94 
                                       + pP    ++Y+k++    dl
  gi|518651816|ref|YP_008141336.1| 163 THPPYANiIKYSKDNIIkdDL 183
                                       ****97635888887532255 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.1   2.1e+03      77     104 ..      23      48 ..      16      48 .. 0.77
   2 ?    9.9   0.0   0.00028       0.5      73     111 ..     131     171 ..      80     184 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                                       HTTGCEEEEE-STTTTSTTS-EEEEEE- CS
                               MTS  77 anklevevvasdvleeveekkfdlivsN 104
                                       +nk  +++ +++++e++e++kf+l + N
  gi|518651816|ref|YP_008141336.1|  23 DNK--IKIGEKNIIETLEPEKFNLEIDN 48 
                                       343..78889999999999999986655 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00028
                                       HHHHHTTGCEEEEE-ST..TTTSTTS-EEEEEE---STTTC CS
                               MTS  73 enleanklevevvasdv..leeveekkfdlivsNPPfhagk 111
                                       +n e+n +e e+++ d+  l+e+e++++dli++ PP+ +  
  gi|518651816|ref|YP_008141336.1| 131 NNSENNLIEPEIFNGDArnLNEIEDESIDLIMTHPPYANII 171
                                       355566666999999974467999************97655 PP

>> DUF5625  Domain of unknown function (DUF5625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.5   6.2e+03     100     105 ..      36      41 ..       9      54 .. 0.50
   2 ?    7.3   1.3    0.0031       5.5      62     108 ..     169     214 ..     114     217 .. 0.80
   3 ?    8.9   0.1     0.001       1.8      46      87 ..     216     257 ..     213     270 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.5
                                       EE-SEE CS
                           DUF5625 100 sLkkGk 105
                                       +L++ k
  gi|518651816|ref|YP_008141336.1|  36 TLEPEK 41 
                                       344444 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0031
                                       EEEE-TTS-EEEEEEEEEEE-S--SSTTE...EEEEEE..EE-SEEEEE CS
                           DUF5625  62 kivknkkndkkvildkkinakglgsgaateyereIktl..sLkkGkYsi 108
                                       +i+k++k  +++i d++ + ++l+ + ++++++ Ik++  +LkkGkY +
  gi|518651816|ref|YP_008141336.1| 169 NIIKYSK--DNIIKDDLSSIESLEEY-YKKFKKVIKEMhrTLKKGKYCA 214
                                       6788444..46999999999999888.6669*9***98557******76 PP

  == domain 3  score: 8.9 bits;  conditional E-value: 0.001
                                       HH-TT--T---EEEEEEEEE-TTS-EEEEEEEEEEE-S--SS CS
                           DUF5625  46 llGstdkdgvivpvklkivknkkndkkvildkkinakglgsg 87 
                                       l+G+t k+g  +p++ +i++   +++ v+ +++i+ +++   
  gi|518651816|ref|YP_008141336.1| 216 LIGDTRKKGYQIPISFTIMQLFLKEGFVLKEDIIKVQHNTKT 257
                                       6799****************5555788888888888777544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       957  (0.0533772); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); 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: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1822.74
//
Query:       gi|518651817|ref|YP_008141337.1|  [L=282]
Description: site-specific DNA methylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  180.8  24.2    4.7e-53  180.5  24.2    1.0  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
  ------ inclusion threshold ------
      0.026   14.2   0.4      0.061   13.0   0.2    1.8  2  Cons_hypoth95    Conserved hypothetical protein 95


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 !  180.5  24.2   5.2e-57   4.7e-53       1     255 [.      16     259 ..      16     264 .. 0.91

  Alignments for each domain:
  == domain 1  score: 180.5 bits;  conditional E-value: 5.2e-57
                                       STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH. CS
                   MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelek 75 
                                       ++GgKr++++e+ + ip+ k + ++epFaGg+++ +++ +   +k   i+D+n +lin+y+ +ik n  e+++e +k
  gi|518651817|ref|YP_008141337.1|  16 WAGGKRQIINELYKRIPE-KFNYYYEPFAGGASFLIHLYNnnLIKYGAISDLNGELINFYN-VIKYNLNEFLEEEKK 90 
                                       9****************9.8899**************99887889999*************.99999******9995 PP

                                       TCTTGGC.TSHHHHHHHHHHHH...HHH-HHHH.HHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHH CS
                   MethyltransfD12  76 llekeelenereyfyelreefnkkidaireaee.aidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelk 151
                                        +++     +  ++y+lr+e n  i + +++++ a++fly+n+++++gl rvn++++fnvp+g+yk+ + ++ +++ 
  gi|518651817|ref|YP_008141337.1|  91 -DNL----PNNIEYYNLRDEYNDIIGDNNYKIRrAVLFLYFNKHAYNGLWRVNSNNKFNVPFGKYKNVNMFDYNNIY 162
                                       .444....689999********444444555556******************************************* PP

                                       HHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEE CS
                   MethyltransfD12 152 lrseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvl 228
                                       ++s +lkn  i ++df++v ++a +e+d+vY+DPPY+p+++t+ +t+y++++f++++++rl++v+k l  ++ v+v+
  gi|518651817|ref|YP_008141337.1| 163 NFSIMLKNINIFNSDFETVVKEA-KENDFVYFDPPYQPLNKTSYFTGYTKNGFDYDEQKRLFKVFKGL-ADKNVNVM 237
                                       **********************9.8888****************************************.6******* PP

                                       EEEESEESHHHHHHCTT...SEEEEEC CS
                   MethyltransfD12 229 lsnsfkdtklfrelyksYnnesileve 255
                                       lsns   ++++ ely++   ++i  v+
  gi|518651817|ref|YP_008141337.1| 238 LSNS--YNEKMLELYNE---FNINIVN 259
                                       ****..88878888888...6554443 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.26   2.3e+03     141     170 ..      76     105 ..      69     118 .. 0.68
   2 ?   13.0   0.2   6.8e-06     0.061      95     125 ..     172     199 ..     150     255 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.26
                                       -EEEEEEEEEEEECCSSS--.-TTEEEEEE CS
                     Cons_hypoth95 141 llkenalvvvetekekelpespenlelvke 170
                                       ++k n   ++e+ek+ +lp+++e+ +l +e
  gi|518651817|ref|YP_008141337.1|  76 VIKYNLNEFLEEEKKDNLPNNIEYYNLRDE 105
                                       556666667788888888888877766555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 6.8e-06
                                       EEEES-HHHHCTS--SS-EEEEEEE--SSST CS
                     Cons_hypoth95  95 elkedaleallklakkkeefdivflDPPyak 125
                                       ++     +++++ +k+++e d+v++DPPy+ 
  gi|518651817|ref|YP_008141337.1| 172 NIF---NSDFETVVKEAKENDFVYFDPPYQP 199
                                       233...34444555556778*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1744.68
//
Query:       gi|518651818|ref|YP_008141338.1|  [L=371]
Description: transposase, IS605 OrfB family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-21   75.6   0.1    3.5e-21   74.9   0.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.3e-08   34.3   0.3    6.9e-08   32.7   0.1    1.8  2  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.024   14.1   0.3      0.047   13.2   0.3    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.21   11.6   1.0        1.7    8.7   0.0    2.7  3  CpXC            CpXC protein
       0.51   10.5   1.5       0.97    9.6   1.5    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.66   10.0   2.9        1.4    9.0   2.9    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.1   1.2e-24   3.5e-21       1      69 []     277     346 ..     277     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 1.2e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++eykake+Gi+v++++p++TS +C++C  ++k+ ++++  fkC +Cg++  +D+ A++Ni +r
  gi|518651818|ref|YP_008141338.1| 277 FYQLRLFIEYKAKEAGIPVIVIDPHNTSRECPNCHTISKKnRPERSIFKCISCGLKGEADYIASLNIRNR 346
                                       7899************************************9999999********************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0         1   3.1e+03      47      75 ..      20      48 ..      17      60 .. 0.78
   2 !   32.7   0.1   2.3e-11   6.9e-08       5     111 ..     153     255 ..     149     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1
                        OrfB_IS605 47 ksdykylakeiaelqsklkksknykkasr 75
                                       +++k+++++   +++++ + k+y k s 
  gi|518651818|ref|YP_008141338.1| 20 LNTFKKFNEACNFVSRIAWDNKIYNKISL 48
                                      67889999999999999999999988775 PP

  == domain 2  score: 32.7 bits;  conditional E-value: 2.3e-11
                        OrfB_IS605   5 eveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                        v+v+ +p+ ++++++g+D+Gi n+ + +t++    +y+g+++k   +     + +lqs   +s     a r l++l
  gi|518651818|ref|YP_008141338.1| 153 SVDVPeQPVIEPKNVIGVDMGIANISVDSTGK----YYSGNEIKGVREHNLDLRSRLQSVNTRS-----AERHLKKL 220
                                       4444449999**********************....************************7777.....79****** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev....gvetL 111
                                       + k  r+ ++  h ++++++k+ k +    ++e+L
  gi|518651818|ref|YP_008141338.1| 221 SGKEHRFATNTNHIISKNIVKKAKGTssaiAIEDL 255
                                       ********************987655444466665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.3   1.6e-05     0.047       2      34 ..     306     338 ..     305     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34 
                                        CPnC++ +  + per  + C +CGl  e ++i
  gi|518651818|ref|YP_008141338.1| 306 ECPNCHTISKKNRPERSIFKCISCGLKGEADYI 338
                                       5******555899*************9998888 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       0.9   2.7e+03      81     110 ..     216     246 ..     197     252 .. 0.64
   2 ?   -0.5   0.1      0.41   1.2e+03      39      45 ..     306     312 ..     297     319 .. 0.70
   3 ?    8.7   0.0   0.00057       1.7       2      38 ..     325     361 ..     324     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.9
                              CpXC  81 aeek.egytlRlvidmaelaEkilileagld 110
                                       + +k +g + R++++ ++++ k ++ +a+ +
  gi|518651818|ref|YP_008141338.1| 216 HLKKlSGKEHRFATNTNHIISKNIVKKAKGT 246
                                       2222467777999999999999888777655 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.41
                              CpXC  39 tCpkCga 45 
                                       +Cp+C++
  gi|518651818|ref|YP_008141338.1| 306 ECPNCHT 312
                                       5666655 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00057
                              CpXC   2 tCpaCgkefeaeiwtsidadedpelkeklldgslfea 38 
                                       +C +Cg + ea+   s+++ ++  + + +++g++f +
  gi|518651818|ref|YP_008141338.1| 325 KCISCGLKGEADYIASLNIRNRAVANQPIVAGDFFVH 361
                                       7********************************9964 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 ?    9.6   1.5   0.00033      0.97      15      40 .]     304     330 ..     303     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00033
                     Auto_anti-p27  15 aetCpvCgvPLmrdr.kggkvyCvaCd 40 
                                       +  Cp+C ++  ++r ++    C++C+
  gi|518651818|ref|YP_008141338.1| 304 SRECPNCHTISKKNRpERSIFKCISCG 330
                                       678************9889999****6 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.9   0.00045       1.4      19      44 ..     305     330 ..     300     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00045
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                       + CP+C+   k  r + r  f+C +C+
  gi|518651818|ref|YP_008141338.1| 305 RECPNCHTIsKKNRPE-RSIFKCISCG 330
                                       78*****665555555.6********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      530  (0.029561); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2650.97
//
Query:       gi|518651819|ref|YP_008141339.1|  [L=53]
Description: hypothetical protein FACI_IFERC00001G0458 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.05   14.1   0.3      0.052   14.0   0.3    1.0  1  DUF2231   Predicted membrane protein (DUF2231)


Domain annotation for each model (and alignments):
>> DUF2231  Predicted membrane protein (DUF2231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.9e-06     0.052      40      86 ..       1      46 [.       1      52 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.9e-06
                           DUF2231 40 allHavggvlllalivaltvWrfvlrlreeeqvsplylalslvvvvl 86
                                      +++H  +g++ l  i++  vW+f++ ++++ + +p+ l+++ ++++l
  gi|518651819|ref|YP_008141339.1|  1 MNYHYFLGLITLTKIAY-RVWQFLVAVHDPVARKPMTLVIGGIATIL 46
                                      789*****999998888.9*********************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       274  (0.0152825); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 402.97
//
Query:       gi|518651820|ref|YP_008141340.1|  [L=80]
Description: transcriptional modulator of MazE/toxin, MazF [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-10   41.3   0.0    1.8e-10   41.2   0.0    1.0  1  PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antit


Domain annotation for each model (and alignments):
>> PemK_toxin  PemK-like, MazF-like toxin of type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   9.9e-15   1.8e-10       2      76 ..       9      78 ..       8      80 .] 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 9.9e-15
                                      TTEEEEEEE-S--TTS--SEEEEEE-S-HHHHCHSEEEEEEEESSSTSSGCSTTEEEE-HH.HCSSSSSSSSEEEE CS
                        PemK_toxin  2 rGeIvlvdldpsrgseqgkrRpvvVvsndafnekntvivvpltskdkdkkklpfhvelese.ildlngldkdswvk 76
                                       G+++ v+l++  g+eq+k+Rp+v +s+ +  e+++v v+p ts++  ++++p+ ++++++  ++l     ds+++
  gi|518651820|ref|YP_008141340.1|  9 SGSLYFVNLNDVTGHEQNKTRPAVAISKHV--ETGLVAVIPFTSQID-AARFPYTMKIKKStNNRL---TMDSIAL 78
                                      5899*****7666**************985..447***********5.6677******99844444...4567765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); 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 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 516.93
//
Query:       gi|518651821|ref|YP_008141341.1|  [L=170]
Description: hypothetical protein FACI_IFERC00001G0460 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.071   13.4   0.8       0.12   12.6   0.8    1.4  1  ABC_tran_CTD  ABC transporter C-terminal domain


Domain annotation for each model (and alignments):
>> ABC_tran_CTD  ABC transporter C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.8   6.8e-06      0.12      16      65 ..     118     167 ..     113     170 .] 0.94

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.8e-06
                      ABC_tran_CTD  16 eIeaLEeeiaeleaeladpelysdpeklaelsaeleeleaeLeelyerWe 65 
                                       + e  E++++e+   l+d ++ + ++k +el  + e l +eL+  +++W 
  gi|518651821|ref|YP_008141341.1| 118 DVELVEKKMKEIKPHLSDMDIINGQNKAKELLFKDEFLTDELKSEMMEWD 167
                                       56889********************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.20s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1222.16
//
Query:       gi|518651822|ref|YP_008141342.1|  [L=60]
Description: hypothetical protein FACI_IFERC00001G0461 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   11.1   0.0       0.16   11.1   0.0    1.1  1  TTL       Tubulin-tyrosine ligase family


Domain annotation for each model (and alignments):
>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   8.7e-06      0.16     249     263 ..      22      36 ..      12      58 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-06
                                       XXXXXXXXXXXXX.. CS
                               TTL 249 nlkpwLlEvNasPdl 263
                                       nlkp+LlE+N+ P  
  gi|518651822|ref|YP_008141342.1|  22 NLKPILLEINMVPGK 36 
                                       89***********54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); 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: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 452.06
//
Query:       gi|518651823|ref|YP_008141343.1|  [L=125]
Description: hypothetical protein FACI_IFERC00001G0462 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-09   37.6   0.1    2.9e-09   37.1   0.1    1.3  1  Nitro_FeMo-Co    Dinitrogenase iron-molybdenum cofactor
     0.0043   16.3   0.4     0.0048   16.2   0.4    1.1  1  Beta_lactamase3  Putative beta-lactamase-like family
  ------ inclusion threshold ------
      0.038   14.2   0.2      0.044   14.0   0.2    1.1  1  Imm15            Immunity protein 15


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 !   37.1   0.1   4.9e-13   2.9e-09      10      93 ..      18     100 ..      10     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 4.9e-13
                                       CC-SEEEEEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHHTT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBH CS
                     Nitro_FeMo-Co  10 GrapyFaiyeveegevkivenrveeaadaegggggklaqllaeegvdvvivgkiGpralakleaagievykgaggtv 86 
                                       G+  ++ i+eve+ ++k+ve  +++a +a + +g+ + +++ +++v+++iv++iG + ++ l+++ i++y + + + 
  gi|518651823|ref|YP_008141343.1|  18 GEGTEIHIFEVENTKYKLVESYENPAIKATSTRGIHMLKSVLSKNVNAIIVSEIGAPGVNFLKNK-IKIYYANNMNE 93 
                                       6778899***************999***************************************9.*****998888 PP

                                       HHHHHHH CS
                     Nitro_FeMo-Co  87 eealkev 93 
                                        ea++ +
  gi|518651823|ref|YP_008141343.1|  94 NEAMEFY 100
                                       8888876 PP

>> Beta_lactamase3  Putative beta-lactamase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.4     8e-07    0.0048      53     111 ..      55     113 ..      23     122 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8e-07
                   Beta_lactamase3  53 iikvkaenidkifvtssnslgifFlkkdvpiYiTkpvYeqlllrlkellslqvvyeeee 111
                                       +  v ++n++ i+v++  + g+ Flk++++iY  + + e   ++++   +l+ ++  ++
  gi|518651823|ref|YP_008141343.1|  55 LKSVLSKNVNAIIVSEIGAPGVNFLKNKIKIYYANNMNENEAMEFYINSKLEEITIATH 113
                                       4557789*************************999988888877777777766555554 PP

>> Imm15  Immunity protein 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   7.3e-06     0.044      31      80 ..      50     103 ..      28     119 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-06
                             Imm15  31 kqikflkrvlkkeekskllldk....alelvnkiklyaknkldekqiadffiav 80 
                                       + i++lk+vl+k+  + ++ ++    + +l nkik+y  n+++e +  +f+i  
  gi|518651823|ref|YP_008141343.1|  50 RGIHMLKSVLSKNVNAIIVSEIgapgVNFLKNKIKIYYANNMNENEAMEFYINS 103
                                       56899******99766666666333235788********************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 832.05
//
Query:       gi|518651824|ref|YP_008141344.1|  [L=210]
Description: hypothetical protein FACI_IFERC00001G0463 [Ferroplasma acidarmanus fer1]
Scores for complete 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   32.4   2.2    1.5e-07   30.9   2.2    1.9  1  zinc_ribbon_2   zinc-ribbon domain
    5.3e-08   32.0   3.4    6.8e-08   31.7   2.3    1.7  2  zf-ribbon_3     zinc-ribbon domain
    1.1e-07   31.8  10.2    0.00011   22.1   1.0    1.4  2  DZR             Double zinc ribbon
    8.8e-05   23.2   3.1    0.00016   22.3   3.1    1.6  1  zinc_ribbon_15  zinc-ribbon family
    0.00096   19.2   5.3     0.0074   16.3   5.8    2.0  2  UPF0547         Uncharacterised protein family UPF0547
      0.004   17.0   0.3      0.011   15.6   0.3    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.022   14.9   2.3        2.7    8.3   0.3    2.4  2  zf-RING_7       C4-type zinc ribbon domain
      0.025   14.2   3.9        1.3    8.8   0.1    3.0  3  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.028   13.9   1.4       0.08   12.5   1.4    1.8  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.05   13.5   0.9       0.11   12.5   0.9    1.4  1  Prok-RING_1     Prokaryotic RING finger family 1
      0.069   13.3   3.2       0.12   12.5   3.2    1.4  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
      0.074   13.0   2.6        6.8    6.7   0.2    2.4  2  Nudix_N_2       Nudix N-terminal
       0.26   11.8   2.0         22    5.7   0.2    2.5  2  zf-H2C2_2       Zinc-finger double domain
       0.26   11.3   6.5        6.6    6.8   2.4    2.3  2  DUF1610         Domain of unknown function (DUF1610)
       0.49   10.3   2.8        5.4    7.0   0.2    2.3  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
       0.63   10.6   4.6       0.46   11.1   2.4    2.1  1  Cript           Microtubule-associated protein CRIPT
        1.4    8.5   4.4         15    5.3   0.1    2.5  2  zf_C2H2_10      C2H2 type zinc-finger
        2.4    8.2   7.4        8.4    6.5   1.8    2.4  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        3.6    8.3   7.6        6.9    7.4   1.9    2.5  2  zf-ISL3         zinc-finger of transposase IS204/IS1001/IS109
          6    7.2   9.8          3    8.2   0.5    2.5  2  zf-LITAF-like   LITAF-like zinc ribbon domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   2.2   1.6e-10   1.5e-07       1      23 []     185     207 ..     177     208 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.6e-10
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtpl 23 
                                       +Cp+CG+++ ++  +Cp+CG++l
  gi|518651824|ref|YP_008141344.1| 185 RCPHCGYPVTEDMIYCPNCGYKL 207
                                       6********************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 ?   -2.0   0.0       3.1   2.8e+03      12      20 ..     112     120 ..     111     121 .. 0.74
   2 !   31.7   2.3   7.6e-11   6.8e-08       4      26 .]     185     207 ..     183     207 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
                       zf-ribbon_3  12 lssddnvCp 20 
                                       ++  +++C+
  gi|518651824|ref|YP_008141344.1| 112 ITRLATICK 120
                                       567799997 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 7.6e-11
                       zf-ribbon_3   4 rCPnCGaplssddnvCpyCGtkl 26 
                                       rCP+CG p+++d++ Cp+CG+kl
  gi|518651824|ref|YP_008141344.1| 185 RCPHCGYPVTEDMIYCPNCGYKL 207
                                       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 !   21.2   2.5   2.4e-07   0.00022      27      49 .]     176     204 ..     112     204 .. 0.81
   2 !   22.1   1.0   1.2e-07   0.00011       1      23 [.     186     208 ..     186     210 .] 0.92

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.4e-07
                               DZR  27 a......edrCpsCgekvdpearfCpeCG 49 
                                       +      ++rCp+Cg++v+++  +Cp+CG
  gi|518651824|ref|YP_008141344.1| 176 DenlpdtAHRCPHCGYPVTEDMIYCPNCG 204
                                       0555556899******************9 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.2e-07
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp+Cg ++++d ++C++Cg klk
  gi|518651824|ref|YP_008141344.1| 186 CPHCGYPVTEDMIYCPNCGYKLK 208
                                       9******************9998 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   3.1   1.8e-07   0.00016      52      86 .]     170     204 ..     102     204 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.8e-07
                    zinc_ribbon_15  52 elgkeiekkesse........kkeCknCgkeveeefkyCpkCg 86 
                                       ++ +        +        +++C++Cg  v+e++ yCp+Cg
  gi|518651824|ref|YP_008141344.1| 170 NMAE--------NndenlpdtAHRCPHCGYPVTEDMIYCPNCG 204
                                       1222........134445666*********************9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   1.5   0.00044      0.39       9      22 ..     178     191 ..     176     192 .. 0.81
   2 !   16.3   5.8   8.3e-06    0.0074       2      22 ..     185     205 ..     184     208 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00044
                           UPF0547   9 kvPvaaqfCphCGy 22 
                                        +P  a +CphCGy
  gi|518651824|ref|YP_008141344.1| 178 NLPDTAHRCPHCGY 191
                                       56667899*****9 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.3e-06
                           UPF0547   2 vCPeCeakvPvaaqfCphCGy 22 
                                       +CP C  +v +++  Cp CGy
  gi|518651824|ref|YP_008141344.1| 185 RCPHCGYPVTEDMIYCPNCGY 205
                                       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 !   15.6   0.3   1.3e-05     0.011      27      56 ..     182     207 ..     172     209 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.3e-05
                    OrfB_Zn_ribbon  27 TSktCseCgsknkealsgrtfkCpnCgfea 56 
                                       T  +C++Cg+ ++e    +  +CpnCg+++
  gi|518651824|ref|YP_008141344.1| 182 TAHRCPHCGYPVTE----DMIYCPNCGYKL 207
                                       8899********99....*********985 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 ?    6.3   0.1     0.013        11      24      30 ..     184     190 ..     167     190 .. 0.84
   2 ?    8.3   0.3     0.003       2.7      21      30 ..     195     204 ..     193     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.013
                                       EE-TTT- CS
                         zf-RING_7  24 vtCpeCG 30 
                                        +Cp+CG
  gi|518651824|ref|YP_008141344.1| 184 HRCPHCG 190
                                       69****9 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.003
                                       TB-EE-TTT- CS
                         zf-RING_7  21 devvtCpeCG 30 
                                       +++++Cp+CG
  gi|518651824|ref|YP_008141344.1| 195 EDMIYCPNCG 204
                                       5699*****9 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.9   1.7e+03      24      29 ..      45      50 ..      43      52 .. 0.87
   2 ?    5.0   0.5     0.021        19      19      25 ..     185     191 ..     179     194 .. 0.88
   3 ?    8.8   0.1    0.0014       1.3      15      26 ..     195     206 ..     193     207 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.9
                                      -----B CS
                    DNA_RNApol_7kD 24 GhRilY 29
                                      GhR+++
  gi|518651824|ref|YP_008141344.1| 45 GHRSMF 50
                                      9****8 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.021
                                       --SSS-- CS
                    DNA_RNApol_7kD  19 RCkeCGh 25 
                                       RC +CG+
  gi|518651824|ref|YP_008141344.1| 185 RCPHCGY 191
                                       9*****8 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0014
                                       SS----SSS--- CS
                    DNA_RNApol_7kD  15 gdpiRCkeCGhR 26 
                                       +d i C +CG++
  gi|518651824|ref|YP_008141344.1| 195 EDMIYCPNCGYK 206
                                       799*******98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.4   8.9e-05      0.08       2      31 ..     185     209 ..     184     210 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.9e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVled 31 
                                       +CP Cg + ++eD     ++C++CG+ l  
  gi|518651824|ref|YP_008141344.1| 185 RCPHCGYP-VTED----MIYCPNCGYKLKQ 209
                                       7*****54.6777....79*******9976 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   0.00012      0.11       4      27 ..     183     204 ..     181     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
                       Prok-RING_1   4 gkkCpvCgkelkeedDiVvCpeCg 27 
                                        ++Cp Cg +++e+  ++ Cp+Cg
  gi|518651824|ref|YP_008141344.1| 183 AHRCPHCGYPVTED--MIYCPNCG 204
                                       578*******9976..9******9 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   3.2   0.00014      0.12      15      40 .]     183     204 ..     182     204 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00014
                     Auto_anti-p27  15 aetCpvCgvPLmrdrkggkvyCvaCd 40 
                                       a  Cp Cg P  +d     +yC++C+
  gi|518651824|ref|YP_008141344.1| 183 AHRCPHCGYPVTED----MIYCPNCG 204
                                       678**********5....79*****6 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.012        11       3      10 ..     186     193 ..     184     197 .. 0.69
   2 ?    6.7   0.2    0.0076       6.8       2      11 ..     199     208 ..     199     210 .] 0.86

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                                       -TTT--B- CS
                         Nudix_N_2   3 CsqCGtpv 10 
                                       C++CG pv
  gi|518651824|ref|YP_008141344.1| 186 CPHCGYPV 193
                                       77777776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0076
                                       B-TTT--B-E CS
                         Nudix_N_2   2 FCsqCGtpve 11 
                                       +C++CG +++
  gi|518651824|ref|YP_008141344.1| 199 YCPNCGYKLK 208
                                       9*****9987 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.035        31      12      22 ..     181     191 ..     175     191 .. 0.84
   2 ?    5.7   0.2     0.025        22      15      25 ..     198     208 ..     194     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.035
                         zf-H2C2_2  12 ekpyeCplCdk 22 
                                       ++ + Cp C++
  gi|518651824|ref|YP_008141344.1| 181 DTAHRCPHCGY 191
                                       4669*****98 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.025
                         zf-H2C2_2  15 yeCplCdkaFk 25 
                                         Cp C+++ k
  gi|518651824|ref|YP_008141344.1| 198 IYCPNCGYKLK 208
                                       68******865 PP

>> DUF1610  Domain of unknown function (DUF1610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1     0.012        10      15      23 ..     182     190 ..     181     191 .. 0.92
   2 ?    6.8   2.4    0.0073       6.6      18      23 ..     199     204 ..     199     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.012
                           DUF1610  15 vvFpCPNCG 23 
                                       +++ CP CG
  gi|518651824|ref|YP_008141344.1| 182 TAHRCPHCG 190
                                       7899****9 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0073
                           DUF1610  18 pCPNCG 23 
                                       +CPNCG
  gi|518651824|ref|YP_008141344.1| 199 YCPNCG 204
                                       7****9 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2     0.006       5.4       5      14 ..     184     191 ..     177     194 .. 0.77
   2 ?    3.3   0.2     0.086        77       6      12 ..     199     205 ..     198     209 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.006
                    Zn_ribbon_SprT   5 YrCtgCgrey 14 
                                       +rC++Cg  y
  gi|518651824|ref|YP_008141344.1| 184 HRCPHCG--Y 191
                                       6888888..5 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.086
                    Zn_ribbon_SprT   6 rCtgCgr 12 
                                       +C++Cg 
  gi|518651824|ref|YP_008141344.1| 199 YCPNCGY 205
                                       7999993 PP

>> Cript  Microtubule-associated protein CRIPT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.4   0.00051      0.46      37      68 ..     161     206 ..      82     209 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00051
                             Cript  37 fnpyaayss...............kCkiCktkveqkgakYCqkCaYk 68 
                                        npy++                  +C  C   v++ +  YC +C Yk
  gi|518651824|ref|YP_008141344.1| 161 KNPYQNIREnmaenndenlpdtahRCPHCGYPVTE-DMIYCPNCGYK 206
                                       344444333344444444444445*********99.999*******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 ?    5.3   0.1     0.016        15       3      10 ..     184     191 ..     177     196 .. 0.90
   2 ?    4.0   0.8      0.04        35       5      12 ..     200     207 ..     198     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.016
                        zf_C2H2_10   3 fsCPKCqe 10 
                                       + CP C++
  gi|518651824|ref|YP_008141344.1| 184 HRCPHCGY 191
                                       89****99 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.04
                        zf_C2H2_10   5 CPKCqekl 12 
                                       CP C++kl
  gi|518651824|ref|YP_008141344.1| 200 CPNCGYKL 207
                                       ******97 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   1.8    0.0093       8.4      19      26 ..     184     191 ..     178     197 .. 0.79
   2 ?    4.8   0.3     0.031        28      20      27 ..     199     206 ..     194     210 .] 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0093
                     Zn_Tnp_IS1595  19 fvCPhCgs 26 
                                       ++CPhCg+
  gi|518651824|ref|YP_008141344.1| 184 HRCPHCGY 191
                                       67****96 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.031
                     Zn_Tnp_IS1595  20 vCPhCgsr 27 
                                        CP+Cg++
  gi|518651824|ref|YP_008141344.1| 199 YCPNCGYK 206
                                       4*****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 ?    7.4   1.9    0.0077       6.9       2      11 ..     183     192 ..     182     197 .. 0.81
   2 ?    3.9   0.3     0.095        85       5      11 ..     200     206 ..     196     210 .] 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0077
                           zf-ISL3   2 phrCPnCgsk 11 
                                        hrCP+Cg +
  gi|518651824|ref|YP_008141344.1| 183 AHRCPHCGYP 192
                                       69******87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.095
                           zf-ISL3   5 CPnCgsk 11 
                                       CPnCg k
  gi|518651824|ref|YP_008141344.1| 200 CPNCGYK 206
                                       *****87 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 ?    8.2   0.5    0.0033         3      52      64 ..     179     191 ..     177     195 .. 0.82
   2 ?    5.2   0.5     0.029        26      58      67 ..     199     208 ..     194     210 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0033
                     zf-LITAF-like  52 lkdvehyCpnCga 64 
                                       l d+ h+Cp+Cg 
  gi|518651824|ref|YP_008141344.1| 179 LPDTAHRCPHCGY 191
                                       6799*******96 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                     zf-LITAF-like  58 yCpnCgallg 67 
                                       yCpnCg +l+
  gi|518651824|ref|YP_008141344.1| 199 YCPNCGYKLK 208
                                       8999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1228  (0.0684924); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1574.60
//
Query:       gi|518651825|ref|YP_008141345.1|  [L=552]
Description: hypothetical protein FACI_IFERC00001G0464 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-89  299.1   0.4    1.9e-89  298.3   0.4    1.4  1  Urocanase_C  Urocanase C-terminal domain
    4.5e-82  274.8   0.2    6.1e-82  274.3   0.2    1.2  1  Urocanase    Urocanase Rossmann-like domain
    5.2e-57  191.0   0.0    1.2e-56  189.8   0.0    1.6  2  Urocanase_N  Urocanase N-terminal domain


Domain annotation for each model (and alignments):
>> Urocanase_C  Urocanase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.3   0.4   3.2e-93   1.9e-89       1     195 [.     347     540 ..     347     541 .. 0.98

  Alignments for each domain:
  == domain 1  score: 298.3 bits;  conditional E-value: 3.2e-93
                                       HHHTTT---EEEEETT--HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHH----SS-EEE----TTHHHHHHHHHHHH CS
                       Urocanase_C   1 plFsegkGPFRwvalsgdpeDlaktdeavlellkekedlirWikeAeekvkvqGlpaRilyldaeeRekialafnel 77 
                                       +lF+ g+GPFRw+alsg+p+D++k+dea+l+ + ++++l++Wik A e v++qGlpaRi+y+ ++eReki+l++n++
  gi|518651825|ref|YP_008141345.1| 347 DLFAVGSGPFRWLALSGNPDDIRKIDEAILKNI-DDKHLTDWIKLAGEYVHFQGLPARICYASYGEREKIGLMINDM 422
                                       69******************************9.56899************************************** PP

                                       HHHSSSSS-EEEEE-S-STTSEE-TTTTTTT-TTS-TTB-HHHHHHHHHHHHHT-SEEEEEESTTT-TTS-EEEEEE CS
                       Urocanase_C  78 vregeikapvvlgRDhlDvgsvasPfretenikDGsdaiaDwavlnallnaargatwvslhnGGgvgiGesinagfv 154
                                       vr+ge++ap+++gRDh+D+gsvasP+rete++kDGsdaiaDw++lnallna++ga+wvs+h+GGg+giG++i++gfv
  gi|518651825|ref|YP_008141345.1| 423 VRKGELEAPIAIGRDHHDTGSVASPYRETEAMKDGSDAIADWPILNALLNAVSGASWVSVHHGGGTGIGNAIHSGFV 499
                                       ***************************************************************************** PP

                                       EEE-SSHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHH CS
                       Urocanase_C 155 vvldGteeaeerlervltaDvalGvvRradagyeealevak 195
                                       +++dGt++a+er++rvl+aD+++Gv+R+adagye++++++k
  gi|518651825|ref|YP_008141345.1| 500 IIADGTDDAAERIKRVLNADPGIGVIRHADAGYESSRDIIK 540
                                       ************************************99887 PP

>> Urocanase  Urocanase Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.3   0.2     1e-85   6.1e-82       1     210 []     135     344 ..     135     344 .. 1.00

  Alignments for each domain:
  == domain 1  score: 274.3 bits;  conditional E-value: 1e-85
                                       TTHHHHHHHHHHHHHHHHHHST.T--TT-EEEEE--STTGGGHHHHHHHTT-EEEEEES-HHHHHHHHHTTS-SEEE CS
                         Urocanase   1 GpQGivqGTyetllnaarkklgkgdlkgklvvtaGlGgMsgaQplAatiagavalvvevdesriekrleqgyvdeva 77 
                                       G+QG++qGTyetl ++a+k +++++lkgk++++aGlG+M+gaQplAa+++g+++++vevd ++i++rl+ +y+d+++
  gi|518651825|ref|YP_008141345.1| 135 GTQGVLQGTYETLYALAKKVYHSDNLKGKWFLSAGLGEMGGAQPLAAKMNGCTSIIVEVDMEKINRRLRDKYLDKYT 211
                                       9**************************************************************************** PP

                                       S-HHHHHHHHHHHHHCT--EEEEEES-HHHHHHHHHCTT---SEE---S-TT-TTTS---TT--HHHHHHHHHH-HH CS
                         Urocanase  78 ddldealalikeakkekealsigllgnvvdvleelveegvlvdlvsdqtsahdplnGYlPegltleeakelrkedpe 154
                                       ++ldeal+l +ea k++e++si++lgn+++v++el ++g+++d+vsdqt+ahd   GY+Peg+t+e+ +++r+e+pe
  gi|518651825|ref|YP_008141345.1| 212 KTLDEALKLKDEAIKSGEPVSIAVLGNAATVYQELQDKGIVPDIVSDQTAAHDLNLGYVPEGYTIENFQKFREEHPE 288
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT-EE-B-SS-HHHHHHHTT-TTGGGS-BHHHHT CS
                         Urocanase 155 kfkeevkeslarhveailklqekGavvfdYGnnlrkeakeagvkeafkypsyvedi 210
                                       +fk++v+e+++++v+++l +q+kG+ vfdYGn +r++ake g+++af++++yv+++
  gi|518651825|ref|YP_008141345.1| 289 QFKKKVYETIVKQVKSMLYFQSKGSSVFDYGNDIRTRAKEGGLSNAFEIQGYVPAY 344
                                       ******************************************************98 PP

>> Urocanase_N  Urocanase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.0   2.1e-60   1.2e-56       1     127 []       6     132 ..       6     132 .. 0.99
   2 ?   -3.6   0.0       1.4   8.6e+03      71      80 ..     224     233 ..     207     235 .. 0.60

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2.1e-60
                                       -----SS--SSSSHHHHHHHHHHHHCT-TTT-SBGGGTEEETTTEESSSSHHHHHHHHHHHHH--TTEEEEEETTEE CS
                       Urocanase_N   1 ikakrgeelkaksweaeailrmleNnLdpevaekpeeLvvYggtgkaarnweqfelivktLkeleedetLlvqsGkp 77 
                                       i+a++g++l++k+w++e ++r+l+NnLdp va++p++L+vYgg+gkaarnwe++++i+++Lk+le+detLlvqsGkp
  gi|518651825|ref|YP_008141345.1|   6 IHAPHGNKLNTKGWSQEGAMRLLMNNLDPMVAKDPANLIVYGGKGKAARNWEAYDKIIESLKSLENDETLLVQSGKP 82 
                                       789************************************************************************** PP

                                       EEEEE--TTS-SEEEEES-B-GGG-SHHHHHHHHHTT---B-TTTTTTT- CS
                       Urocanase_N  78 vglfksheeaPrvliansnlvpkyateeefeeleakgltmyGqmtAgswi 127
                                       vg+f++++eaPrvli n+++vp++at++ f +lea+gltm+GqmtAgsw+
  gi|518651825|ref|YP_008141345.1|  83 VGIFRTTKEAPRVLIVNAQIVPHWATDDVFWDLEARGLTMFGQMTAGSWV 132
                                       *************************************************6 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.4
                                       EEETTEEEEE CS
                       Urocanase_N  71 lvqsGkpvgl 80 
                                        ++sG pv++
  gi|518651825|ref|YP_008141345.1| 224 AIKSGEPVSI 233
                                       5899999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (552 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 3542.35
//
Query:       gi|518651826|ref|YP_008141346.1|  [L=396]
Description: major facilitator transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-41  141.8  41.0    7.3e-31  107.5  12.9    2.0  2  Sugar_tr  Sugar (and other) transporter
    7.2e-37  127.1  49.1    1.5e-27   96.5  19.9    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.39    9.2  46.8       0.29    9.6  14.8    3.2  3  MFS_2     MFS/sugar transport protein


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.5  12.9   1.2e-34   7.3e-31       3     202 ..      12     198 ..      10     201 .. 0.92
   2 !   43.1  18.2   4.3e-15   2.6e-11     245     446 ..     205     396 .]     194     396 .] 0.76

  Alignments for each domain:
  == domain 1  score: 107.5 bits;  conditional E-value: 1.2e-34
                                       HHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHH CS
                          Sugar_tr   3 lvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksl 79 
                                       ++ a+g ll gY + vi++++ l+    ++   + +s      +++gl+ +++++GaiiG +++g+l+d +GR+ ++
  gi|518651826|ref|YP_008141346.1|  12 ILSAFGMLLDGYQLTVIAFAVLLIP---DYIHLSDYS------LDYGLLIASVIIGAIIGTILVGYLSDLVGRRRVY 79 
                                       6778999**************9999...333333333......3469****************************** PP

                                       HHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  80 liaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaai 156
                                       l + ++f+   ++++++    ++++l+++Rvl+G+ +G+++ ++  yi+E++p ++Rg+   +  ++ ++G + +ai
  gi|518651826|ref|YP_008141346.1|  80 LSTLMFFILFDMISVFSV---NFYMLFISRVLLGVVLGAEYPVANSYIAEVTPSDKRGFYLAFATVFFSVGSISSAI 153
                                       ******************...******************************************************** PP

                                       HHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT CS
                          Sugar_tr 157 fglglnktsnadgwrillglqlvpallllilllflPESPrylvekg 202
                                       + +++   +n  gwr++lg++++pa+++ ++++ lPES+ +  +k+
  gi|518651826|ref|YP_008141346.1| 154 VAVFMFPLGN-IGWRLMLGVAVIPAIIVEFMRFSLPESKLWEEKKE 198
                                       *****99999.9***************************9966665 PP

  == domain 2  score: 43.1 bits;  conditional E-value: 4.3e-15
                                       HHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHH CS
                          Sugar_tr 245 llssktvrqrlligvvlqifqqltGinaimyysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRt 318
                                       ++s+ ++ + ++++++++++   + +   + + pti++  ++ +    +l t  + v+ +v+ ++++  vd+fGR+ 
  gi|518651826|ref|YP_008141346.1| 205 MFSK-KYSKNIILAALIWFLYDIVAYGLSLTL-PTILKLGHFVTNvdnALLTTFFLVIGIVSGVFVMIKVDKFGRKG 279
                                       3333.367778888888887777776555555.5555555555555888999999999******************* PP

                                       HHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHH CS
                          Sugar_tr 319 llllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavn 395
                                       + ++G++ ma++f+il  + + + a+     i ++ f+ lf a+ ++++g +p    +E+  +++R++ + ++ ++ 
  gi|518651826|ref|YP_008141346.1| 280 IQITGFLLMAVLFLIL--PHFYYLAG----IITIVSFLELFNAFGGATVGIIP----AEVTITRFRGTSYGFSSMMG 346
                                       ****************..69999999....35555566788888888888888....******************** PP

                                       HHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CC CS
                          Sugar_tr 396 wlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtle 446
                                        +  ++  + +  +  + + ++  ++f ++ ++ +i   + +petk+ +le
  gi|518651826|ref|YP_008141346.1| 347 KIGAVIGVIAMSLLITSKN-YFNAYIFLAVIMIIAILLTLLLPETKNIKLE 396
                                       **98877776666666666.5555555555555556666789****99986 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5  19.9   2.4e-31   1.5e-27       3     235 ..      16     240 ..      14     245 .. 0.84
   2 !   36.1  21.3   5.5e-13   3.3e-09      35     172 ..     251     387 ..     245     395 .. 0.84

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 2.4e-31
                             MFS_1   3 laaflsalarsilgpalplalaedlgispse..igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++ +l +++ +++++a+  ++ +  ++s  +  +gll++ + +ga+++++++G+lsd +Grrrv+l +l +f+l+ +
  gi|518651826|ref|YP_008141346.1|  16 FGMLLDGYQLTVIAFAVL-LIPDYIHLSDYSldYGLLIASVIIGAIIGTILVGYLSDLVGRRRVYLSTLMFFILFDM 91 
                                       778888889999888888.78788887766666999***************************************44 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla..sslgWra 152
                                       + +f+ ++++l+++rvl G+  ga +p+++++ia+++p ++rg+++++++++fs+G+i  ++++ ++    ++gWr+
  gi|518651826|ref|YP_008141346.1|  92 ISVFSVNFYMLFISRVLLGVVLGAEYPVANSYIAEVTPSDKRGFYLAFATVFFSVGSISSAIVAVFMFplGNIGWRL 168
                                       444677888********************************************************999556777**9 PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltl 229
                                       +  ++ i ++++     + +  ++++ + +++++        ++++ +++  +++ ++ + ++++l  ++ +gl+ +
  gi|518651826|ref|YP_008141346.1| 169 MLGVAVIPAIIVEF---MRFSLPESKLWEEKKEKT-------GFLEMFSKKYSKNIIL-AALIWFLYDIVAYGLSLT 234
                                       99999999999955...666777777777766555.......7777777888888554.555555556677779999 PP

                             MFS_1 230 lplylq 235
                                       lp++l+
  gi|518651826|ref|YP_008141346.1| 235 LPTILK 240
                                       999754 PP

  == domain 2  score: 36.1 bits;  conditional E-value: 5.5e-13
                             MFS_1  35 gllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwl...llvlrvlqGlgagalfpagaa 108
                                        ll+t++ +  +v+ ++++  +d+fGr+ + ++g+ll+a+  +l+l  +++++   ++    +  l+ +++ +++++
  gi|518651826|ref|YP_008141346.1| 251 ALLTTFFLVIGIVSGVFVMIKVDKFGRKGIQITGFLLMAVL-FLIL--PHFYYlagIITIVSFLELFNAFGGATVGI 324
                                       57888899999******************************.6666..44443122455555888888999999999 PP

                             MFS_1 109 liadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       + a+++  + rg  +g+ s++  +Ga++g ++ +ll++s ++  ++++la+++++a++l  lll
  gi|518651826|ref|YP_008141346.1| 325 IPAEVTITRFRGTSYGFSSMMGKIGAVIGVIAMSLLITSKNYFNAYIFLAVIMIIAILL-TLLL 387
                                       999999999***********************************************995.2333 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0  15.3    0.0025        15     223     368 ..       8     146 ..       1     158 [. 0.73
   2 ?    9.6  14.8   4.9e-05      0.29     146     321 ..     147     306 ..     133     328 .. 0.66
   3 ?    3.7   6.1    0.0031        19     138     191 ..     334     386 ..     328     393 .. 0.55

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0025
                             MFS_2 223 nraflillllfllaalalgvlnglllYyltyvlg..ngsaasvfllvvtisallgiplwqplakrlgkkntyllgal 297
                                       n+  ++ +++ ll    l+v + ++l+  +y+       ++ ++ + v+i+a++g++l+ +l    g++++yl+ ++
  gi|518651826|ref|YP_008141346.1|   8 NKIVILSAFGMLLDGYQLTVIAFAVLLIPDYIHLsdYSLDYGLLIASVIIGAIIGTILVGYLSDLVGRRRVYLSTLM 84 
                                       555566666666666667777777777666665422344677788889**********************9998888 PP

                             MFS_2 298 ltivllvlvlllqpsnlllflvllviagfgvgvaallpwsmladvvDygelktGkrregvffavlsfiskl 368
                                       + i++ ++ ++    n +++++  v+ g+ +g+ + ++ s +a+v+          ++g++ a+ + +  +
  gi|518651826|ref|YP_008141346.1|  85 FFILFDMISVFS--VNFYMLFISRVLLGVVLGAEYPVANSYIAEVTP-------SDKRGFYLAFATVFFSV 146
                                       888887777776..999999999999999999999999999999853.......34455555555555554 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 4.9e-05
                             MFS_2 146 ggvlaailafllvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfr 222
                                       g++  ai+a+ ++         + g+++++ + ++ ++++ ++ ++        ++k  +e+kek+ +le++ +  +
  gi|518651826|ref|YP_008141346.1| 147 GSISSAIVAVFMFPL------GNIGWRLMLGVAVIPAIIVEFMRFSLP------ESKLWEEKKEKTGFLEMFSKKYS 211
                                       333333333333222......246888777765444444444443333......3445679**************** PP

                             MFS_2 223 nraflillllfllaalalgvlngl.llYyltyvlgngsaasvfllvvtisallgiplwqplakrlgkkntyllgall 298
                                       +   l+ l+ fl+ ++a+g+  +l +++ l +++ n ++a + +++++i+ + + +++   + ++g+k + + g+ll
  gi|518651826|ref|YP_008141346.1| 212 KNIILAALIWFLYDIVAYGLSLTLpTILKLGHFVTNVDNALLTTFFLVIGIV-SGVFVMIKVDKFGRKGIQITGFLL 287
                                       **********************996678888888888888777776666555.55555566789**********999 PP

                             MFS_2 299 tivllvlvlllqpsnlllflvll 321
                                       ++vl++++  +    ++l+ +++
  gi|518651826|ref|YP_008141346.1| 288 MAVLFLILPHF----YYLAGIIT 306
                                       99988776444....33333333 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.0031
                             MFS_2 138 vrsflsvlggvlaailafllvlilgglkserkgylifaliialLmllgviivvl 191
                                       +r ++  + ++++ i a++ v++ +    + k+y+ + ++ a++m+++++++ l
  gi|518651826|ref|YP_008141346.1| 334 FRGTSYGFSSMMGKIGAVIGVIAMSL-LITSKNYFNAYIFLAVIMIIAILLTLL 386
                                       55544444444444444444444443.455566777777777777776666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (396 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); 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):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2371.47
//
Query:       gi|518651827|ref|YP_008141347.1|  [L=418]
Description: hypothetical protein FACI_IFERC00001G0466 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-44  153.1   0.0    1.6e-44  153.0   0.0    1.0  1  DAO             FAD dependent oxidoreductase
    6.7e-06   26.2   0.3    3.5e-05   23.9   0.2    2.1  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      0.001   18.4   0.0      0.003   16.8   0.0    1.8  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0015   17.9   0.0     0.0053   16.0   0.0    1.7  1  FAD_binding_3   FAD binding domain
     0.0035   17.0   0.2       0.01   15.5   0.1    1.8  2  ApbA            Ketopantoate reductase PanE/ApbA
     0.0042   17.0   0.1      0.033   14.1   0.0    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.013   16.1   0.1        1.1    9.8   0.0    2.8  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.016   14.0   0.1      0.044   12.5   0.0    1.7  2  HI0933_like     HI0933-like protein
      0.026   13.6   0.0      0.046   12.8   0.0    1.4  1  FAD_binding_2   FAD binding domain
      0.026   13.6   1.1       0.25   10.4   0.0    2.8  4  GIDA            Glucose inhibited division protein A
      0.062   13.5   0.0       0.12   12.5   0.0    1.5  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
       0.16   11.6   0.1       0.38   10.3   0.1    1.6  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,


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 !  153.0   0.0   1.1e-47   1.6e-44       2     351 ..       4     348 ..       3     349 .. 0.82

  Alignments for each domain:
  == domain 1  score: 153.0 bits;  conditional E-value: 1.1e-47
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       + +iG+Gi+Gl+ A+ La  g  Vtl++++ i++ g+Sg+  g+lhsg ry  +    a+ ++e+++e + l+++  
  gi|518651827|ref|YP_008141347.1|   4 IGVIGAGITGLFSALNLALDGydVTLFDREYILS-GTSGKFHGMLHSGSRYSVND---AESAKECIHENALLSNTAS 76 
                                       77****************************8888.**************988875...4899999999999998743 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT.STTTSEEEEETTEEEEEHHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa.lpgllgalfypdtgqvdpakltaal 152
                                            ++tG ++la ++++ e+ dkll++ +e+g+++e l  +e+++lep+  +++l a+ +pd  ++ ++ ++aa+
  gi|518651827|ref|YP_008141347.1|  77 --SFIKNTGGYYLALNDADAEYGDKLLQKNKENGIPTEELGIDEMLDLEPNiNKNILRAFRVPD-KVISAHPFAAAV 150
                                       ..45899******99998999999*9**9999*****8888888******96669*********.999********* PP

                                       HHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE.EEEEEEEE--GGGHH.HHHTTCTTTSEEEEEEEEEEE CS
                               DAO 153 araaealGveilegtevtgleeedgkvwgve.rttpgen.daadavVnaaGawsd.llgllkeldlpispvrgqvlv 226
                                       a +a+  G+++++++ev + e +++ v  ++ r  + ++ +++d+++n++G+ws+ ll+ +++ d  ++p+ g++  
  gi|518651827|ref|YP_008141347.1| 151 AVEAQLMGAKLRFKSEVLKAEVDGKTVESIKyRSHSRIVnEKFDYIINTTGPWSGqLLKSFGIGDFEVMPTLGYMAS 227
                                       *******************988755555554844444444578************66666644477*********** PP

                                       EEECCTHSTGSGCSEEEEEEEETTTTEEEEEETTSEEEE.EESSEEETTCSSTSCSHHHHHHHHHHHHHHSGGGCGE CS
                               DAO 227 lkplseklvspaailpvpetdddgrgvyvtprkdgrvlv.GgtadeesgdddpevdeedidellealrklfPqlgdv 302
                                       ++ l       + il+    +++++g +++p+  g++ v G+ a   ++ d+ ++d+ed+d +l+++++++P+l++ 
  gi|518651827|ref|YP_008141347.1| 228 YDYLFS-----HGILNR--MREPSDGDILLPY--GSMSVaGTVAIISDNVDNNDIDPEDLDTMLSEVSEMVPSLSRH 295
                                       *88766.....333333..88999*******8..5566626666588888889********************9665 PP

                                       EE..EEEEEEEE.TTS......SEEEEEEETEEEEEEEEECTTTHHHHHHHHHHHHHH CS
                               DAO 303 lr..kwaGlrpl.pdg......lpligetpgvkglylatGhsghGltlapatGkllae 351
                                       ++   ++ +rpl + g      ++ i e +  ++l+   G     +t++ ++G+++++
  gi|518651827|ref|YP_008141347.1| 296 RYkkLYSSMRPLiREGysratrDFRIYE-N-MNNLFSIIGG---KFTTSRLMGQAVSQ 348
                                       53338889***54444444555999988.4.6688877666...99999999998875 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   0.2   2.4e-08   3.5e-05       1      35 [.       6      40 ..       6      56 .. 0.89
   2 ?   -1.0   0.0       1.4   2.1e+03      30      55 ..     331     356 ..     312     365 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 2.4e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      ++GaG++Gl  A  La +g+dv+l+++   l+G +
  gi|518651827|ref|YP_008141347.1|  6 VIGAGITGLFSALNLALDGYDVTLFDREYILSGTS 40
                                      8**************************99998865 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
                                       SSSGGG-EECETTCEECTS---EEET CS
                     NAD_binding_8  30 rlGGraasyevpgvrvdygahifhgs 55 
                                        +GG+ ++ ++ g++v    + ++g+
  gi|518651827|ref|YP_008141347.1| 331 IIGGKFTTSRLMGQAVSQKLSKITGT 356
                                       47899999988777776666666655 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0     2e-06     0.003       3      58 ..       4      69 ..       2     119 .. 0.65
   2 ?   -2.0   0.0       1.1   1.7e+03     186     232 ..     147     197 ..     134     207 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2e-06
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH...........H CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........x RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias...........e 58
                                      + viG+G+ Gl  al+la  g++vtl+ +++++l g+    + +l++++++++              
  gi|518651827|ref|YP_008141347.1|  4 IGVIGAGITGLFSALNLALDGYDVTLF-DREYILSGTSGKFHGMLHSGSRYSVNDaesakecihenA 69
                                      679************************.666665555555555555555554444433336655552 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHTTEEEEESCEEEEEEETTEEEE.EEETTSCE...EEESEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxx RF
                       Pyr_redox_2 186 saaleealekeGvevklgtsvkeidgngekle.vvledgee...idadlvv 232
                                       +aa++ + + +G +++++++v +++ +g+ +e  +  + ++   ++ d+++
  gi|518651827|ref|YP_008141347.1| 147 AAAVAVEAQLMGAKLRFKSEVLKAEVDGKTVEsIKYRSHSRivnEKFDYII 197
                                       444444455555666666666666666663332222222213345555555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.6e-06    0.0053       4     202 ..       4     243 ..       2     270 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.6e-06
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS.S--E.EEHHHHHHHHHTT-HHHHH.HHSEECCCCEEEEE CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp.radg.lnqrtmellrqlGledril.aegapnelmgealy 77 
                                       + ++GaG +Gl +al L+  G +v+l ++    + ++ + +g l++ +  + +++  +++++ +++  +++ + + +
  gi|518651827|ref|YP_008141347.1|   4 IGVIGAGITGLFSALNLALDGYDVTLFDREYILSGTSgKFHGmLHSGSRYSVNDAESAKECIhENALLSNTASSFIK 80 
                                       569**************************988888877655427889988999888887765055566666666666 PP

                                       EE.................................CCCC....CEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHH CS
                     FAD_binding_3  78 ne.................................lsdt....pkaradlelesspervtvypqteleriLvehaee 117
                                       n+                                 ++++    p+++ ++   ++ ++ +v++ + +  +++ +a+ 
  gi|518651827|ref|YP_008141347.1|  81 NTggyylalndadaeygdkllqknkengipteelgIDEMldlePNINKNILRAFRVPD-KVISAHPFAAAVAVEAQL 156
                                       6699999999999999999988888777776666633334434444444443344444.567777788888888899 PP

                                       HTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-.HHHHHHTGG.EEEEEEEEEEEEEEEEE CS
                     FAD_binding_3 118 rglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrS.tvrktlgie.fegeetvyeagvldvlf 192
                                        g+++rfk ev+  e d+++v++  ++++  ++ + + +Y++   G +S +  k+ gi  fe   t+  + + d lf
  gi|518651827|ref|YP_008141347.1| 157 MGAKLRFKSEVLKAEVDGKTVESI-KYRSHSRIVNEKFDYIINTTGPWSgQLLKSFGIGdFEVMPTLGYMASYDYLF 232
                                       **********99999999999864.4455566666778899999999884567777777777777777777777777 PP

                                       EC.-SCCCTTC CS
                     FAD_binding_3 193 da.dlsdivep 202
                                       +   l++++ep
  gi|518651827|ref|YP_008141347.1| 233 SHgILNRMREP 243
                                       76555555555 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   6.7e-06      0.01       1      30 [.       4      33 ..       4      63 .. 0.92
   2 ?   -2.0   0.0       1.6   2.4e+03      61      76 ..     179     200 ..     154     200 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.7e-06
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrs 30
                                      i ++GaG  G + a +La  g+dvtl +r+
  gi|518651827|ref|YP_008141347.1|  4 IGVIGAGITGLFSALNLALDGYDVTLFDRE 33
                                      78*************************997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                                       H......SCCCCS-ESEEEE-S CS
                              ApbA  61 e......ekselepidlvivtv 76 
                                       +      ++  +e++d++i t+
  gi|518651827|ref|YP_008141347.1| 179 SikyrshSRIVNEKFDYIINTT 200
                                       1223333466789999999886 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   2.2e-05     0.033       1      31 [.       3      33 ..       3      76 .. 0.89
   2 ?   -0.4   0.0       0.6     9e+02     121     140 ..     129     148 ..     126     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.2e-05
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdis 31
                                      k++viGaG+ G   a  +a  g++V+l+d++
  gi|518651827|ref|YP_008141347.1|  3 KIGVIGAGITGLFSALNLALDGYDVTLFDRE 33
                                      69**************************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.6
                                       HHCCCSSSGGGEEEEEE-SS CS
                           3HCDH_N 121 elaealkrperviglHFfnP 140
                                       ++ +a++ p++vi +H+f  
  gi|518651827|ref|YP_008141347.1| 129 NILRAFRVPDKVISAHPFAA 148
                                       6889999**********975 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00077       1.1       1      31 [.       3      33 ..       3      40 .. 0.93
   2 ?    3.0   0.0      0.11   1.6e+02      49      79 ..     153     183 ..     144     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00077
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvvers 31
                                      k+ v+G+G +gl  A +la  g +Vt+++r+
  gi|518651827|ref|YP_008141347.1|  3 KIGVIGAGITGLFSALNLALDGYDVTLFDRE 33
                                      688*************************996 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.11
                                       HHHHTTEEEECSEEEEEEEEETTSEEEEEEE CS
                         Pyr_redox  49 klekngievllntkveeiegsedgvesvklk 79 
                                       + + +g +++++++v + e ++++ves+k +
  gi|518651827|ref|YP_008141347.1| 153 EAQLMGAKLRFKSEVLKAEVDGKTVESIKYR 183
                                       55556999**************99***9986 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.9e-05     0.044       3      32 ..       4      33 ..       2      38 .. 0.91
   2 ?   -2.3   0.0      0.91   1.4e+03     113     154 ..     148     189 ..     139     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.9e-05
                                      EEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  3 viviGgGaAGlmaAisaakrgkrVllleka 32
                                      + viG+G  Gl+ A+++a  g +V+l++++
  gi|518651827|ref|YP_008141347.1|  4 IGVIGAGITGLFSALNLALDGYDVTLFDRE 33
                                      679*************************86 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.91
                                       HHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEE CS
                       HI0933_like 113 dallkelkeagvklrletevksvekeedgkfrvktkseeele 154
                                        a   e++  g klr ++ev ++e + + + ++k++s++++ 
  gi|518651827|ref|YP_008141347.1| 148 AAVAVEAQLMGAKLRFKSEVLKAEVDGKTVESIKYRSHSRIV 189
                                       566667777888899999999998888888888875555543 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.1e-05     0.046       4      39 ..       6      41 ..       4      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-05
                                      EE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGG CS
                     FAD_binding_2  4 ViGsGlAGLaAAleaaeaGlkvavvekeqefggata 39
                                      ViG+G+ GL +Al++a  G +v++ + e   +g++ 
  gi|518651827|ref|YP_008141347.1|  6 VIGAGITGLFSALNLALDGYDVTLFDREYILSGTSG 41
                                      9**************************999888875 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00017      0.25       2      35 ..       4      43 ..       3      82 .. 0.74
   2 ?   -0.5   0.0      0.33     5e+02     118     154 ..     167     206 ..     161     217 .. 0.73
   3 ?   -1.2   0.0      0.56   8.3e+02     331     351 ..     221     241 ..     197     246 .. 0.77
   4 ?   -1.9   0.1      0.89   1.3e+03     158     222 ..     332     398 ..     326     403 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00017
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE......ES-GGGT CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi......thkldti 35
                                      + ViG+G  G+  Al++a  G++v+L+          +++
  gi|518651827|ref|YP_008141347.1|  4 IGVIGAGITGLFSALNLALDGYDVTLFdreyilSGTSGKF 43
                                      67************************96666654444444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                                       EEEEEECTTEEEEEEETTS-EEEEC...EEEE--TT-BT- CS
                              GIDA 118 veeliveekkvkgvvtedgetikak...avviatGtflkg 154
                                       v + +v+ k+v+ ++ ++++ i ++    ++ +tG+++ +
  gi|518651827|ref|YP_008141347.1| 167 VLKAEVDGKTVESIKYRSHSRIVNEkfdYIINTTGPWSGQ 206
                                       44455556888899888887776665888999****6554 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.56
                                       E--EEEEEEEE-GGGB-TTSB CS
                              GIDA 331 rpGyaieydyvdprqllntLe 351
                                        +Gy+  ydy+ ++ +ln+++
  gi|518651827|ref|YP_008141347.1| 221 TLGYMASYDYLFSHGILNRMR 241
                                       57*********9999999886 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.89
                                       ETTEEEESSCTTC--B-THHHHHHH..TT--EEEEEEEE--EEEGGGS-TTTSEEE---SS-B-SSS CS
                              GIDA 158 igekelsaGrlgeltseglseslke..lgfellrlktgtppridkesidfskleeqsgdkegeefsy 222
                                       ig k + ++ +g+  s++ls+       +++ + l ++    i+k+  d+++++++  ++ g++++y
  gi|518651827|ref|YP_008141347.1| 332 IGGKFTTSRLMGQAVSQKLSKITGThsQDTSKIILNDAFDKFIEKHKQDLNTTFMNYISSYGTSMDY 398
                                       5555555555888888888887664246677788899999999999999988888777666666665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     8e-05      0.12       1      31 [.       3      33 ..       3      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8e-05
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SS CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrt 31
                                      kig+iG G+ G   alnl+  gy+v++++r+
  gi|518651827|ref|YP_008141347.1|  3 KIGVIGAGITGLFSALNLALDGYDVTLFDRE 33
                                      79***************************97 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00026      0.38       2      31 ..       3      32 ..       2      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00026
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDi 31
                                      ki viG+G  Gl +a+ la  g +v++ D 
  gi|518651827|ref|YP_008141347.1|  3 KIGVIGAGITGLFSALNLALDGYDVTLFDR 32
                                      89************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2839.37
//
Query:       gi|518651828|ref|YP_008141348.1|  [L=149]
Description: hypothetical protein FACI_IFERC00001G0467 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-28   99.8   0.2    1.2e-28   99.6   0.2    1.0  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox
  ------ inclusion threshold ------
      0.065   13.5   0.0       0.42   10.9   0.0    1.9  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra


Domain annotation for each model (and alignments):
>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.2   1.3e-32   1.2e-28       1     139 [.       5     146 ..       5     147 .. 0.95

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.3e-32
                                       EEEEESS-HHHHHHHHT-HHHHGGGSTTEEEEEEETTEEEEEEEEESSSSEEEE..EEEEEEEEEETTTEEE..EEE CS
                              COXG   1 GefrvaapkeavwefLndpeklarciPGvksvekegdeykvkvklkvGplkgsf..karvelselekensttieikG 75 
                                       G++ ++ +ke+v +fL d++++ +c+PGv +++ +g+e+++k+kl+++  k+s+  +++ ++s l k++   i i+G
  gi|518651828|ref|YP_008141348.1|   5 GKITIKNNKENVTAFLSDINNITPCLPGVYDFQNNGGEIQCKLKLDISAAKISAmsSVTGKMSFLYKAGLDSIDIDG 81 
                                       8999*********************************************99999887777888888999888***** PP

                                       EEE-SSEEEEEEEEEEEEEETT.EEEEEEEEEEEEEHHHHS-HHHHHHHHHHHHHHHHHHHHHHH CS
                              COXG  76 kGrgagvaidfalvvlveeggg.trlswsakvnvggllaslGsrlidsaarklinelfecisskl 139
                                       +Gr+ag++++f + ++ e  g+ t l+w++  + g +++++G+  ++++ r++i++++ ci skl
  gi|518651828|ref|YP_008141348.1|  82 SGRIAGSKVKFSISISYESKGEeTLLDWKSSFDFGLIVKMMGKDRVNEISRENIDRTMGCITSKL 146
                                       ****************9998888****************************************98 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.7e-05      0.42       5     137 ..       4     137 ..       1     142 [. 0.58

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                                       EEEEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSS......TTTEEEEECCCSSEEEEEEEEEETTTTEE CS
                   Polyketide_cyc2   5 tvsvviaappekVwalvsdfenwprWhpevarveleggggpa......rgvegtvrvggrgtvreelvevdpegrll 75 
                                       + +++i+   e V a++sd +n+    p+v + +  g  g          ++ ++++++  t ++ +  + +   ++
  gi|518651828|ref|YP_008141348.1|   4 SGKITIKNNKENVTAFLSDINNITPCLPGVYDFQNNG--GEIqcklklDISAAKISAMSSVTGKMSF-LYKAGLDSI 77 
                                       5567777777777777777777777777777665443..3322444442223333322212222221.122333444 PP

                                       EEEEE....SSS-TSEEEEEEEEECCETEEEEEEEEEEEE--TT--HHHHHHHHHHHHHHHHHHH CS
                   Polyketide_cyc2  76 syriv...kpvpvanyvatwtvtpdgggtrvtwtgefdagplggpfekpaaakavkgdleagLer 137
                                        +++    +  +v+ ++ +++ +  g+ t + w+  fd+    g+++k + +  v ++ +++++r
  gi|518651828|ref|YP_008141348.1|  78 DIDGSgriAGSKVK-FSISISYESKGEETLLDWKSSFDF----GLIVKMMGKDRVNEISRENIDR 137
                                       44442334444444.8999********9**********9....6666666666666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1018.96
//
Query:       gi|518651829|ref|YP_008141349.1|  [L=274]
Description: RimK-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-28  100.2   0.0    2.8e-28   98.8   0.0    1.6  2  RimK         RimK-like ATP-grasp domain
    1.1e-08   35.2   0.0    2.4e-08   34.2   0.0    1.5  1  ATP-grasp_3  ATP-grasp domain
    3.1e-07   30.0   0.0    4.5e-07   29.4   0.0    1.3  1  GSH-S_ATP    Prokaryotic glutathione synthetase, ATP-grasp do
    1.1e-06   28.3   0.0    2.7e-06   27.0   0.0    1.7  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin
    7.2e-06   25.5   0.0    0.00018   20.9   0.0    2.1  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
    0.00074   19.0   0.0     0.0018   17.8   0.0    1.6  1  ATP-grasp_5  ATP-grasp domain
     0.0073   15.9   0.0       0.06   12.9   0.0    2.1  1  ATP-grasp    ATP-grasp domain


Domain annotation for each model (and alignments):
>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.66   1.7e+03      21      51 ..      27      57 ..      20      69 .. 0.83
   2 !   98.8   0.0   1.1e-31   2.8e-28       2     188 .]      84     270 ..      83     270 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.66
                                      EEEESS-S-HHHHHHTT-.-SSEEEEE-TTT CS
                              RimK 21 talardeedaekliekiklrfPvvvKsvegs 51
                                       +l++ +++a +l  k++++ P +++ + ++
  gi|518651829|ref|YP_008141349.1| 27 LNLVNAKDNALNLTGKLDFGGPAIIRCMSSR 57
                                      5678888999999999999999999988776 PP

  == domain 2  score: 98.8 bits;  conditional E-value: 1.1e-31
                                       H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH....GGG CS
                              RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea....lke 74 
                                        +K+ +   L k++ik+p+t ++ ++++a ++ ++i  + Pvv K   gs G  + l ++e+ ++ v++      ++
  gi|518651829|ref|YP_008141349.1|  84 GNKVFTTSYLYKNGIKTPETSVSFSHDNALSTADNI--GYPVVFKPASGSWGRMISLLENENIAETVFSMndmvNEN 158
                                       688999999***************************..6****************************9877775556 PP

                                       --EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEEEE CS
                              RimK  75 ailvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGvDl 151
                                       +  +q+y++    +d+R +vv+d++ a++ r s e  +++nl +Gg++ek+ ls  + ++ ik+a++ +  ++G+D 
  gi|518651829|ref|YP_008141349.1| 159 SYYLQKYVNR-PPRDVRAIVVGDNISATIYRYSGE-GWKTNLALGGKVEKAVLSGSQLDMLIKVAHLFDPGIIGIDA 233
                                       67999**986.569******************999.59*************************************** PP

                                       EEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHHH CS
                              RimK 152 lrakrgllvlEvnsspglekiektlgidiakklieai 188
                                       +++++gl+v E+ns ++ ++ +k  g  i +++++++
  gi|518651829|ref|YP_008141349.1| 234 METDEGLIVHEINSRVEFKGASKVYGNKIINDIVQYL 270
                                       ***************************9999999875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   9.5e-12   2.4e-08       1     158 [.      83     249 ..      83     251 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 9.5e-12
                                       HTSHHHHHHHHTTT.S---...........-EESS--SSSEEEEESS-------B--SS--TTE............. CS
                       ATP-grasp_3   1 asdKlktykkLkeagvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...... 64 
                                       a +K++t+  L ++g+k+P       +    + +++  +++v Kp++G+ g  +++ e+++ ae+ + ++       
  gi|518651829|ref|YP_008141349.1|  83 AGNKVFTTSYLYKNGIKTPetsvsfsHDNALSTADNIGYPVVFKPASGSWGRMISLLENENIAETVFSMNDmvnens 159
                                       579****************877766555555666667***********************99998888777788999 PP

                                       .EEEE---SEEEEEEEEE.S..SSEEEEEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEE CS
                       ATP-grasp_3  65 .lvqefieGkplSvsllsdg..ekvlvlavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyv 138
                                         +q++++  p  v +++ g    + +   + + +++   +++  G+v ++   l+ +  ++  +v + +    G+ 
  gi|518651829|ref|YP_008141349.1| 160 yYLQKYVNRPPRDVRAIVVGdnISATIYRYSGEGWKT---NLALGGKVEKAV--LSGSQLDMLIKVAHLF--DPGII 229
                                       999****988877777764400344444444444433...455555555554..8888899999999999..57*** PP

                                       EEEEEESS.SEEEEEEESS- CS
                       ATP-grasp_3 139 GvDlvlkdeepyviEvNPRl 158
                                       G+D + +de+++v E+N+R+
  gi|518651829|ref|YP_008141349.1| 230 GIDAMETDEGLIVHEINSRV 249
                                       *******************7 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 !   29.4   0.0   1.8e-10   4.5e-07      11     151 ..      99     233 ..      85     247 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.8e-10
                                       CS--EEEES-HHHHHHHHHHHSS.EEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGGGG-EE CS
                         GSH-S_ATP  11 lipktlvskdkeeirafleeqgd.vilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpeikeGDk 86 
                                        +p+t vs ++++  + +++ g  v++KP +g+ G+ +  ++++ +  ++++++    +++   +q+y++   + D+
  gi|518651829|ref|YP_008141349.1|  99 KTPETSVSFSHDNALSTADNIGYpVVFKPASGSWGRMISLLENE-NIAETVFSMNDMVNENSYYLQKYVNRPPR-DV 173
                                       4699****9998888888888877************99888774.4456777777778888899******9888.** PP

                                       EEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEE CS
                         GSH-S_ATP  87 RillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDv 151
                                       R ++v G+ i++++ R + e   ++nla gg++e+  l+ ++  +  ++a  L + G+  +G+D 
  gi|518651829|ref|YP_008141349.1| 174 RAIVV-GDNISATIYRYSGE-GWKTNLALGGKVEKAVLSGSQLDMLIKVAH-LFDPGI--IGIDA 233
                                       *9887.88899899999765.589****************99999888874.556665..46665 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 !   27.0   0.0   1.1e-09   2.7e-06      13     109 ..      97     187 ..      85     222 .. 0.80
   2 ?   -2.0   0.0      0.81   2.1e+03     168     192 ..     237     259 ..     231     268 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 1.1e-09
                                       T-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE-- CS
                       CPSase_L_D2  13 nvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlveksl 89 
                                       ++++ + s     + ++al+ a++igyPv+ k+a g  G+   + +ne+ +ae+v +  ++      +++ +++k++
  gi|518651829|ref|YP_008141349.1|  97 GIKTPETSVS--FSHDNALSTADNIGYPVVFKPASGSWGRMISLLENEN-IAETVFSMNDMV----NENSYYLQKYV 166
                                       5555555555..7899************************999988765.555554444555....4899******* PP

                                       SS.SEEEEEEEEEETTS-EEE CS
                       CPSase_L_D2  90 kg.pkeiEvevlrDakgnvit 109
                                       ++ p+++ + v+ D+   +i+
  gi|518651829|ref|YP_008141349.1| 167 NRpPRDVRAIVVGDNISATIY 187
                                       98469*********9988886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.81
                                       TTEEEEEEEESS--CCHHHHHHHHS CS
                       CPSase_L_D2 168 skeyyviEvNtRlsvesalaekaTG 192
                                       ++  +v E+N+R++ +   a+k+ G
  gi|518651829|ref|YP_008141349.1| 237 DEGLIVHEINSRVEFKG--ASKVYG 259
                                       56678889999987654..455555 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 !   20.9   0.0   7.1e-08   0.00018       7      83 ..      71     143 ..      67     165 .. 0.84
   2 ?    2.5   0.0     0.028        72     229     271 ..     214     254 ..     212     269 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 7.1e-08
                       ATPgrasp_ST   7 irkyNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilvitere 83 
                                       i+ +N+ +   +  +K+ +++++ ++g+k+p++ +++++ + +s+++++  ++ + vv Kpa gs+G+ i+ + +++
  gi|518651829|ref|YP_008141349.1|  71 IKTINSFNTCNIAGNKVFTTSYLYKNGIKTPETSVSFSHDNALSTADNI--GY-P-VVFKPASGSWGRMISLLENEN 143
                                       67899999999*****************************999999987..56.5.7************99996643 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.028
                       ATPgrasp_ST 229 lelaakaaeklpglgylGwDivldeekgplllElNarpglaiv 271
                                       l++  k+a+ l   g++G+D   ++++g+++ E+N r+  +  
  gi|518651829|ref|YP_008141349.1| 214 LDMLIKVAH-LFDPGIIGIDAM-ETDEGLIVHEINSRVEFKGA 254
                                       567778887.8999******65.55555********9887665 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   6.9e-07    0.0018      20      56 ..      94     130 ..      87     168 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 6.9e-07
                       ATP-grasp_5  20 eaygipvvetrlassaeeaveaaeeigypvvlKivsp 56 
                                          gi+++et +  s ++a+++a++igypvv K +s 
  gi|518651829|ref|YP_008141349.1|  94 YKNGIKTPETSVSFSHDNALSTADNIGYPVVFKPASG 130
                                       5679*****************************8764 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   2.3e-05      0.06       3      84 ..      95     179 ..      93     255 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.3e-05
                                       TTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC...GTTCEEEEE----.S CS
                         ATP-grasp   3 klglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal...keekvivEefvpf.e 75 
                                       k+g+++p+  +  s++++ ++a+++g+pvv K +  g+ G+  s++++e+ +e+++++    +e++ ++ ++v+   
  gi|518651829|ref|YP_008141349.1|  95 KNGIKTPETSVSFSHDNALSTADNIGYPVVFK-PASGSWGRMISLLENENIAETVFSMNdmvNENSYYLQKYVNRpP 170
                                       7899999999999999999999**********.99**************9999999888777888899999887423 PP

                                       EEEEEEEEE CS
                         ATP-grasp  76 kElsvlvvr 84 
                                       + + ++vv 
  gi|518651829|ref|YP_008141349.1| 171 RDVRAIVVG 179
                                       566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1865.60
//
Query:       gi|518651830|ref|YP_008141350.1|  [L=316]
Description: hypothetical protein FACI_IFERC00001G0469 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  149.9   0.0    1.3e-43  149.6   0.0    1.0  1  Aminotran_1_2  Aminotransferase class I and II
    4.9e-07   28.9   0.0      6e-07   28.7   0.0    1.3  1  Alliinase_C    Allinase
  ------ inclusion threshold ------
       0.07   12.7   0.0       0.13   11.8   0.0    1.5  1  GTP_EFTU       Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.6   0.0   2.2e-47   1.3e-43       4     363 .]       4     308 ..       2     308 .. 0.92

  Alignments for each domain:
  == domain 1  score: 149.6 bits;  conditional E-value: 2.2e-47
                                       EESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHH CS
                     Aminotran_1_2   4 inLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagal 80 
                                       i L  ne+++     ++++v+k+ +   ++  ++n+y+    lp+l ++la + g      +  e +++  +G+++l
  gi|518651830|ref|YP_008141350.1|   4 IYLDKNENPFN----VPEKVKKEFIN-YAKDADFNRYPEKG-LPSLIKKLAGLTG------FSSE-NIIAANGSDEL 67 
                                       67999******....***********.99999999999876.*************......99**.*********** PP

                                       HHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS CS
                     Aminotran_1_2  81 iealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesp 157
                                       +++li+ ++   g +i+v++pt+++y+ ++r++g + + +pl+   df+ld+++++++ +         k+++++sp
  gi|518651830|ref|YP_008141350.1|  68 LDILIRRAE---G-DIVVSSPTFEMYSFYARNYGHKAIDVPLR--SDFSLDVNGILAQKDA--------KLVVICSP 130
                                       ******995...4.799************************99..************6654........8******* PP

                                       -TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEE CS
                     Aminotran_1_2 158 hNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyil 234
                                       +NPtG ++++e ++k+    ++ ++ +++D aY +f  ++  +     +++++ nl+i++++sKaf+laG R+Gy +
  gi|518651830|ref|YP_008141350.1| 131 NNPTGNLIDRESIKKI---LDS-GVTTILDNAYYEFSGED--Y---TDLIAKYSNLIILRTFSKAFSLAGMRIGYGI 198
                                       ****************...886.***************94..3...789**************************** PP

                                       EEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEE CS
                     Aminotran_1_2 235 gnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltd 311
                                       + ++++s ++kl++pf+   l ++++  ++++  l+     e  + + ++r+++++e+++   + ++s ++++ll  
  gi|518651830|ref|YP_008141350.1| 199 AESKFISEIKKLQAPFYMNILSAKMAEIMIDNYSLI----VEKIKYIVEERERVYNEIKD---IAYPSSANFLLL-K 267
                                       *************************99999999975....7899999***********44...455565777776.2 PP

                                       ETHHCHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 312 lsaetakelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                                              +l+  + e+ g+++++   + v+ r R+t+  +t++e+++++ea+
  gi|518651830|ref|YP_008141350.1| 268 K------DLYGYMEEN-GIHIRK--LPLVKDRSRLTI--GTKDENKRAIEAI 308
                                       3......455777777.******..9999********..***********98 PP

>> Alliinase_C  Allinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0     1e-10     6e-07     139     213 ..     123     204 ..      21     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1e-10
                                       EEEEEESS-TTT---..-----..-TT-EEEEEE-TT-S...TTTS---S-B--SEEEEEHHHHHS-GGG-EEEEEE CS
                       Alliinase_C 139 fielvtsPnnPdgll..reavv..kgseakviyDlayYW...PhytpitskadedimLftlskltGhaGsrlGWalv 208
                                        + ++ sPnnP g+l  re++    +s + +i D ayY     +yt + +k  + i+L t+sk    aG r+G+++ 
  gi|518651830|ref|YP_008141350.1| 123 KLVVICSPNNPTGNLidRESIKkiLDSGVTTILDNAYYEfsgEDYTDLIAKYSNLIILRTFSKAFSLAGMRIGYGIA 199
                                       455789*******997767764335777789*******633368******************************998 PP

                                       S-HHH CS
                       Alliinase_C 209 kdkev 213
                                         k +
  gi|518651830|ref|YP_008141350.1| 200 ESKFI 204
                                       76655 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 ?   11.8   0.0   2.2e-05      0.13      21     110 ..      45     136 ..      37     157 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.2e-05
                                       HHHHHHTTSSCHHHHHH.HHHSTHCHSHHHHHHTSCSSCEEEEEET.TCSSEEEEEEEESSSGGGHHHHHHHHHT-S CS
                          GTP_EFTU  21 drLlyktgaiskkgeka.eeervlDtlkeErergiTiksaaislek.etkkylinliDtPGHvdFskevirglrvlD 95 
                                        +L   tg  s++   a ++++ lD l    e  i ++s + ++++   ++y  + iD P   dFs +v   l++ D
  gi|518651830|ref|YP_008141350.1|  45 KKLAGLTGFSSENIIAAnGSDELLDILIRRAEGDIVVSSPTFEMYSfYARNYGHKAIDVPLRSDFSLDVNGILAQKD 121
                                       55555566666655555455788999999999999999999988866899*************************** PP

                                       EEEEEEETTTBSTHH CS
                          GTP_EFTU  96 gavlvvdaveGvepq 110
                                         ++v+++ + ++ +
  gi|518651830|ref|YP_008141350.1| 122 AKLVVICSPNNPTGN 136
                                       *******98876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2036.09
//
Query:       gi|518651831|ref|YP_008141351.1|  [L=298]
Description: hypothetical protein FACI_IFERC00001G0470 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-54  183.3   0.0    4.8e-54  182.8   0.0    1.2  1  FTCD_N    Formiminotransferase domain, N-terminal subdomain
    3.5e-20   72.5   0.0    7.5e-20   71.4   0.0    1.5  1  FTCD      Formiminotransferase domain
  ------ inclusion threshold ------
      0.013   15.5   0.0      0.036   14.1   0.0    1.7  1  DUF3674   RNA dependent RNA polymerase


Domain annotation for each model (and alignments):
>> FTCD_N  Formiminotransferase domain, N-terminal subdomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.0   8.1e-58   4.8e-54       1     176 []       3     179 ..       3     179 .. 0.96

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 8.1e-58
                            FTCD_N   1 lvecvpnfSegrdkevieaiekaarkaegvklldvfsdedynRtvvtlvgepealkeaalaaakkAlelIDlrkhkG 77 
                                       lve +pnfS+gr+k vi+ +ek +++++++klld ++d d+nR+v+t+v   +++ + a++++k+A e ID++ ++G
  gi|518651831|ref|YP_008141351.1|   3 LVELIPNFSDGRNKVVIDLLEKDVKSVPDAKLLDSEMDYDHNRSVITVVCPIDNVIDLAFNMIKTAGENIDMNVQTG 79 
                                       6899************************************************************************* PP

                            FTCD_N  78 eHPrlGavDvipfiPlkevtleecaelAkelaeelgeelgvpvylygaaaqkeerknLaaiRrg..efeglkeklke 152
                                        HPr+Ga+D +p++Pl+++++eec+el++el++++g+elg+pv++y+ +a+++erknL++iR++  + e+l++ + +
  gi|518651831|ref|YP_008141351.1|  80 FHPRFGATDIMPLVPLEDTSMEECIELSQELGKKVGKELGIPVFMYAYSAKTPERKNLENIRNKkfQIEELRSAIGT 156
                                       ****************************************************************5556778887888 PP

                            FTCD_N 153 eewkpdfGpaevspkaGvtvvGAr 176
                                        +  pd+Gp+ +  +aG+t++GAr
  gi|518651831|ref|YP_008141351.1| 157 GNYIPDYGPEVI-GRAGATIIGAR 179
                                       8999****7766.89********7 PP

>> FTCD  Formiminotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   1.3e-23   7.5e-20       1     107 [.     181     282 ..     181     292 .. 0.95

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.3e-23
                              FTCD   1 FLiAynvnlltt.keqakriAlniRekGrgkkepGrlkkvkaiGwyleeynlaqvslnltdievtplhvvfeevkke 76 
                                       FLiAyn+ l+t   +  ++iA  iR +       G + +vk++ + + e+n+ q+s+n+ ++++ p++ +fe+vk+e
  gi|518651831|ref|YP_008141351.1| 181 FLIAYNIYLNTDdIKIGRKIASAIRAR------DGGFACVKSLAFKMPEKNIVQISMNIVNYRKNPVYRIFEAVKTE 251
                                       9***********99**********975......688***************************************** PP

                              FTCD  77 aeelglevtgseivglvplealleaakyyle 107
                                       a+  g+  + se +g+vp+eal+++ ++yl 
  gi|518651831|ref|YP_008141351.1| 252 AKGFGVYPVRSEFIGMVPQEALVDSFNHYLM 282
                                       **************************99985 PP

>> DUF3674  RNA dependent RNA polymerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-06     0.036       3      40 ..     130     169 ..     129     170 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-06
                           DUF3674   3 ktEERAALEAmFnLkFnistHksq...PYYiPDYkGmEPiG 40 
                                       kt ER  LE + n kF i   +s      YiPDY G E iG
  gi|518651831|ref|YP_008141351.1| 130 KTPERKNLENIRNKKFQIEELRSAigtGNYIPDY-GPEVIG 169
                                       9******************9999633379*****.666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1994.35
//
Query:       gi|518651832|ref|YP_008141352.1|  [L=67]
Description: hypothetical protein FACI_IFERC00001G0471 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 491.09
//
Query:       gi|518651833|ref|YP_008141353.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G0472 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 417.56
//
Query:       gi|518651834|ref|YP_008141354.1|  [L=392]
Description: hypothetical protein FACI_IFERC00001G0473 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-14   51.7   0.8    1.3e-13   51.1   0.8    1.2  1  DDE_Tnp_1  Transposase DDE domain
    1.9e-12   47.1   0.0    1.3e-10   41.1   0.0    2.4  1  DDE_5      DDE superfamily endonuclease
      2e-11   43.7   0.8    3.5e-11   42.9   0.8    1.3  1  DDE_Tnp_2  Archaeal putative transposase ISC1217


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.8   2.2e-17   1.3e-13       5     194 ..      90     301 ..      86     314 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.2e-17
                         DDE_Tnp_1   5 evlivDattvrvpgtk.edarwgyk..ggkykygy.klhiavdtrsgl.ilsvvitpgnvhdskglkqlldelrpr. 75 
                                       +vl +D t ++  g++   a+w y+  +gk  yg+     +++++ g+ +ls+++   ++ dsk   q ++++++  
  gi|518651834|ref|YP_008141354.1|  90 PVLSLDDTILQRNGKHiDGAQWIYDhsQGKTVYGMqYTTSVISGNEGIfPLSMEL---KTDDSKIDLQ-INTIKKAm 162
                                       7899*********999999999777225556666654444555555548******...6666666666.66666666 PP

                         DDE_Tnp_1  76 ....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrk........................gaeskrrgr 124
                                           + ++v+ D++Y+s +l+++le++g dy++ +k+n ++ ++                        g++++ + +
  gi|518651834|ref|YP_008141354.1| 163 gaglRFSTVVFDSWYFSSKLVKFLESMGKDYVSEAKSNRTVCIDgkwirlrdyantldlksmksytvnGKTYFMKAI 239
                                       7799****************************************777777666666666666666555566666666 PP

                         DDE_Tnp_1 125 lrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlr 194
                                       +++  +  i++ + +rr          + +++tn+++ ++++++  y +Rw iE ++ +lk+  gl +l+
  gi|518651834|ref|YP_008141354.1| 240 TTRMKNAGIVKVIVSRRIN-------SLKFFVTNRTDWKVKTIIGKYLRRWDIEVFHEELKQ-DGLKHLY 301
                                       6666666666666666665.......8889************************99999998.4444444 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.2e-14   1.3e-10       2     217 ..      20     206 ..      19     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.2e-14
                             DDE_5   2 llealtradrrrglllylrgllldggr.ksvepmaarlehdgshqalqrflsrspwddaklrrrlarlvlpllapea 77 
                                       +++ ++r+++r+ ++ ++ g  ++++    + +++ +    ++  +l rfl + p d   + ++ + l+   +  ++
  gi|518651834|ref|YP_008141354.1|  20 FRPLFGRRQFRQFCRYIVSGIASSTRSsAHLNGIFVEH---TNQSNLNRFLRNIPAD--GIFNISCSLINRNC--SG 89 
                                       66677777777766666666555555544444444444...5677777777655544..44455555555556..45 PP

                             DDE_5  78 avlaiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrragvpdd 154
                                       +vl +DdT +++ Gk++ g ++ y+++ gk++ + +  +     ++  +pl+++l  +   ++d             
  gi|518651834|ref|YP_008141354.1|  90 PVLSLDDTILQRNGKHIDGAQWIYDHSQGKTVYGMQYTTSVISGNEGIFPLSMEL--K---TDD------------- 148
                                       55*********************************99999999**********96..3...333............. PP

                             DDE_5 155 vtaktkpeialelldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdralypp 217
                                           +k ++ ++ +++a+ ag++++ vv+D++Y + + l + l+++g +yv++ +s+r++ + 
  gi|518651834|ref|YP_008141354.1| 149 ----SKIDLQINTIKKAMGAGLRFSTVVFDSWYFS-SKLVKFLESMGKDYVSEAKSNRTVCID 206
                                       ....5888999**********************55.5566*******************9775 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.8   5.9e-15   3.5e-11     167     292 ..     149     299 ..     133     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 5.9e-15
                         DDE_Tnp_2 167 tkiellleile.ilkeefnvaavvfdsWyvnskllk......gnvvgelksnarvve..............gerhvp 222
                                       +ki+l +++++ ++  +++ ++vvfdsWy++skl+k       + v+e ksn+ v                  ++++
  gi|518651834|ref|YP_008141354.1| 149 SKIDLQINTIKkAMGAGLRFSTVVFDSWYFSSKLVKflesmgKDYVSEAKSNRTVCIdgkwirlrdyantlDLKSMK 225
                                       59****99997257789*****************98555443478********997768899998888874223333 PP

                         DDE_Tnp_2 223 vaelPeGeylveyldtvik...llvlddykkdgrrylfstdlnd.tdediittWenrWdievlirelkalGled 292
                                          +    y++  + t +k   +  ++  +  + +++f t+  d     ii  +  rWdiev + elk  Gl++
  gi|518651834|ref|YP_008141354.1| 226 SYTVNGKTYFMKAITTRMKnagIVKVIVSRRINSLKFFVTNRTDwKVKTIIGKYLRRWDIEVFHEELKQDGLKH 299
                                       33444446888877766663334444556778899999999877256889*******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2684.20
//
Query:       gi|518651835|ref|YP_008141355.1|  [L=268]
Description: hypothetical protein FACI_IFERC00001G0474 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.3e-12   45.0   0.1    3.9e-09   36.4   0.0    2.1  2  NmrA             NmrA-like family
      1e-11   44.8   0.1    1.6e-11   44.1   0.1    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.6e-11   44.4   0.0    2.3e-11   44.0   0.0    1.2  1  NAD_binding_10   NAD(P)H-binding
    2.8e-05   23.4   0.0      0.015   14.4   0.0    2.1  2  RmlD_sub_bind    RmlD substrate binding domain
    0.00041   19.5   0.2      0.046   12.7   0.0    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    0.00099   18.6   0.1     0.0085   15.5   0.1    1.9  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
  ------ inclusion threshold ------
       0.11   12.8   0.1       0.21   11.8   0.1    1.5  1  TrkA_N           TrkA-N domain
       0.13   11.3   0.2       0.19   10.7   0.2    1.2  1  DUF1512          Protein of unknown function (DUF1512)
       0.13   12.2   0.0       0.24   11.4   0.0    1.4  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
       0.13   11.3   0.0       0.28   10.3   0.0    1.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   2.2e-12   3.9e-09       2      74 ..      13      83 ..      13     102 .. 0.91
   2 !    6.6   0.0    0.0027       4.9     141     220 ..     166     242 ..     153     252 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.2e-12
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHSTTEEEES-TT-HHHHHHHHTT-SEEEE---G CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaGvelvkgdlddkeslvealkgvdvvfsvtgf 74
                                      +viGaTG+ G +v+++llk++ +vra+vR+++  +a +l  + v +vk d+ + + + + lkg+ v++++ +f
  gi|518651835|ref|YP_008141355.1| 13 VVIGATGAYGYAVTKILLKNKINVRAIVRNEE--KALKLFPKDVDIVKSDIFNMDKIIKDLKGASVIYIANNF 83
                                      69***************************975..677999999**************************9886 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0027
                                       E-EEGGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE-HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHH CS
                              NmrA 141 agffmenflsllaqlkvgdtappedkvtllgpgnpkavlldaeeDiGafvikilkdprklkgkriklagntlsgnei 217
                                       a f+  n++  l+   + + ++++ k++++ + +    +    +D +++++ +l + + + gk+++++g++++  e 
  gi|518651835|ref|YP_008141355.1| 166 ADFYGPNVTNDLYGGMFIKAMKNK-KAIWPVNPDIPHNFT-YIDDAAKATLLLLRNINSY-GKVYHVSGDIITAREF 239
                                       678999999999996666666665.888876666555555.99********999999887.788899******9998 PP

                                       HHH CS
                              NmrA 218 vel 220
                                       ++ 
  gi|518651835|ref|YP_008141355.1| 240 INK 242
                                       864 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.1   9.2e-15   1.6e-11       2     231 ..      13     222 ..      12     231 .. 0.80

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 9.2e-15
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       +V+GatG  G a++k ll+++++v ++ r++++  +   +d+++v+ d+ + +   +++k+ +   vi +A      
  gi|518651835|ref|YP_008141355.1|  13 VVIGATGAYGYAVTKILLKNKINVRAIVRNEEKALKLFPKDVDIVKSDIFNMD---KIIKDLKGASVIYIA------ 80 
                                       69****************************77777777777788888888766...555555444444442...... PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklvea 155
                                         ++ p + +++  + t n+l+ a +++   ++f + +  YGk +  p +e+    pl+ n   ++    +ekl+ +
  gi|518651835|ref|YP_008141355.1|  81 --NNFPYKNWQNYYISTENILKGAETSNS-TVVFPGNVYGYGKFDYLPVNEEH---PLNANGKKGILRNNIEKLLFE 151
                                       ..44455556667788*************.****************9*99999...********************* PP

                                       HHHHHT-EEEEEEESEEESTTS-TTSTTSHHHH.HHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
                         Epimerase 156 yaaqyglnaiilrlfnlyGprngegevsrvipa.lirkilegkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                                       y ++ ++  +i r    yGp+      + ++   +i+ ++++k  +  + + +    f y++D+a+a ll+l++ ++
  gi|518651835|ref|YP_008141355.1| 152 YYKKDKIGLVIPRFADFYGPN----VTNDLYGGmFIKAMKNKK-AIWPV-NPDIPHNFTYIDDAAKATLLLLRNINS 222
                                       *********************....333333330455555555.44444.5666689****************9766 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   1.3e-14   2.3e-11       1      89 [.      16     106 ..      16     122 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 1.3e-14
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TCCHHHH CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsalggggkdeeg 77 
                                       GAtG  G +++k ll+++ ++v+a+vRn+ek+ +l   + +++v+ d+ + +++ + lkga+++++a +   k+ + 
  gi|518651835|ref|YP_008141355.1|  16 GATGAYGYAVTKILLKNK-INVRAIVRNEEKALKLF-PKDVDIVKSDIFNMDKIIKDLKGASVIYIANNFPYKNWQN 90 
                                       9****************5.*************9998.79***************************99777773333 PP

                                       ....HHHHHHHHHHCT CS
                    NAD_binding_10  78 ....aknivdaakeag 89 
                                           ++ni++ a++++
  gi|518651835|ref|YP_008141355.1|  91 yyisTENILKGAETSN 106
                                       3466888888888765 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 !    7.1   0.0    0.0015       2.6       4      59 ..      13      80 ..      11      89 .. 0.82
   2 !   14.4   0.0   8.3e-06     0.015     103     235 ..     109     251 ..      92     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE-TT..........T--TTSHH..HHHHHHHHH--SEEEE-- CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlaltre..........eldltdae..avaellkeakpdvvvnaA 59
                                      +v+Ga+G+ G++++k l +++++v a+ r+          ++d+ +++  ++++++k+ k + v+  A
  gi|518651835|ref|YP_008141355.1| 13 VVIGATGAYGYAVTKILLKNKINVRAIVRNeekalklfpkDVDIVKSDifNMDKIIKDLKGASVIYIA 80
                                      689************************99988999999987777655522567788888877777665 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 8.3e-06
                                       GGS-S-....TTS-B-TTS----SSHHHHH...HHHHHHHHHH....H-SSEEEEEE-SEESS.SSS-HHHHHHHHH CS
                     RmlD_sub_bind 103 yVFdGe....kkrpYeeddetsPlnvYGrt...KlaGEqavla....agkkalivRtswvyge.kgknfvktmlrla 167
                                        VF+G+     k  Y + +e +Pln+ G+    + + E+   +    ++   +i R++  yg    +++   m+ +a
  gi|518651835|ref|YP_008141355.1| 109 VVFPGNvygyGKFDYLPVNEEHPLNANGKKgilRNNIEKLLFEyykkDKIGLVIPRFADFYGPnVTNDLYGGMFIKA 185
                                       6999998887677799999*****9999863335567888877443244467899******9845666777777777 PP

                                       .HH-SEE.EEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHTT CS
                     RmlD_sub_bind 168 .kereel.kvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkeagads 235
                                        k+++ +  v  D   + T+ +d A+++l ll+++ +   + +vyH++++  ++  ef ++i ++++ ++
  gi|518651835|ref|YP_008141355.1| 186 mKNKKAIwPVNPDIPHNFTYIDDAAKATLLLLRNINS---YGKVYHVSGDI-ITAREFINKIYNRLNLKT 251
                                       3555555367789999*****************9996...899*****998.777789999998887755 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 !   12.7   0.0   2.6e-05     0.046       1      77 [.      13      83 ..      13     115 .. 0.79
   2 !    5.0   0.0    0.0059        11     188     244 ..     177     232 ..     161     253 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.6e-05
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77
                                      vv+G++G  G a+ k L++ +   +vr++  +e++ l  +l+  +v+ +++ D+ + dk+ + l+g++v i++a   
  gi|518651835|ref|YP_008141355.1| 13 VVIGATGAYGYAVTKILLKNK--INVRAIVRNEEKAL--KLFPKDVD-IVKSDIFNMDKIIKDLKGASV-IYIANNF 83
                                      89*************999887..79999855555555..66666777.99*****************97.5666555 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0059
                         3Beta_HSD 188 llvpllkqlaklglalfkigdeevlsdrvYvgNvawahilAaralqdpkkkssvagq 244
                                       l   ++ +++k++ + +  +++++ ++++Y +  a+a +l  r++++  k  +v+g+
  gi|518651835|ref|YP_008141355.1| 177 LYGGMFIKAMKNK-KAIWPVNPDIPHNFTYIDDAAKATLLLLRNINSYGKVYHVSGD 232
                                       4445566777887.55567899999********************999666555554 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 !   15.5   0.1   4.7e-06    0.0085       2     268 ..      14     249 ..      13     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.7e-06
                                       EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SE CS
                     GDP_Man_Dehyd   2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpde 78 
                                       + G +G  G  +++ Ll+++ +v  ivr++++     + +l         +++ ++k D+ +   +++++++ +   
  gi|518651835|ref|YP_008141355.1|  14 VIGATGAYGYAVTKILLKNKINVRAIVRNEEKA----L-KLF-------PKDVDIVKSDIFN---MDKIIKDLKGAS 75 
                                       667777777777777777777777777766542....2.233.......2346677777776...667777666555 PP

                                       EEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHHH CS
                     GDP_Man_Dehyd  79 vynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYaa 155
                                       v+  A         + P + +++  + t ++L+ + + +      +++ +    YGk +  p++E++p++++   ++
  gi|518651835|ref|YP_008141355.1|  76 VIYIA--------NNFPYKNWQNYYISTENILKGAETSNS----TVVFPGNVYGYGKFDYLPVNEEHPLNANGKKGI 140
                                       55444........456888888899999999999988764....466788888899999****************** PP

                                       HHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHHH CS
                     GDP_Man_Dehyd 156 aKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyvea 232
                                        +   + +  +y+++ ++  v+ ++   ++p  +++     +++a+     ++++ +   n d    +++++D ++a
  gi|518651835|ref|YP_008141355.1| 141 LRNNIEKLLFEYYKKDKIGLVIPRFADFYGPNVTNDLYGGMFIKAM-----KNKKAIWPVNPDIPHNFTYIDDAAKA 212
                                       ********************************55554444444333.....3334455579999************* PP

                                       HHHHHHC.SS---EEE-TT-EEECHHCHHCCHHCCCH CS
                     GDP_Man_Dehyd 233 mwlmlqq.dkpedyviatgethsvrefvelaflelgk 268
                                         l+l++ ++  +++  +g+  + ref+++   +l  
  gi|518651835|ref|YP_008141355.1| 213 TLLLLRNiNSYGKVYHVSGDIITAREFINKIYNRLNL 249
                                       *****9955668888999*********9988777655 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00012      0.21       2      51 ..      13      63 ..      12      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00012
                                      EEES.-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTS CS
                            TrkA_N  2 iiiG.lGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatd 51
                                      ++iG  G  G+++++ L +++++v +i ++ee++ +l  + +++v+ d  +
  gi|518651835|ref|YP_008141355.1| 13 VVIGaTGAYGYAVTKILLKNKINVRAIVRNEEKALKLFPKDVDIVKSDIFN 63
                                      5666479************9989********************99999876 PP

>> DUF1512  Protein of unknown function (DUF1512)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.2    0.0001      0.19     270     336 ..       7      70 ..       3      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                           DUF1512 270 vaeGvGvaiGdpGvekikiErvatkygipldaviikmsleeAitaMtkeiaeavdkavervkeiike 336
                                       + +G+ v+iG +G   +++ ++  k++i+++a++   + e A++  +k++   v++ + ++++iik+
  gi|518651835|ref|YP_008141355.1|   7 IDNGLHVVIGATGAYGYAVTKILLKNKINVRAIV--RNEEKALKLFPKDVD-IVKSDIFNMDKIIKD 70 
                                       77899***************************87..677899999999984.455555556667755 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00013      0.24       4      36 ..      14      47 ..      12      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00013
                                      EE--.SHHHHHHHHHHHTTT--EEEE-S-HHHHH CS
                    NAD_Gly3P_dh_N  4 vlGa.GswGtalAkvlaenghevrlwvreeelie 36
                                      v+Ga G++G a+ k+l +n  +vr +vr+ee + 
  gi|518651835|ref|YP_008141355.1| 14 VIGAtGAYGYAVTKILLKNKINVRAIVRNEEKAL 47
                                      67755************************97654 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00016      0.28       3      66 ..      14      74 ..      13      85 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                                      EETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-H CS
                   Polysacc_synt_2  3 vtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdk 66
                                      v Ga+G++G ++++ +lk+k++   ++ ++E++l  + k+++  + k+++ +++ ++i d++ +
  gi|518651835|ref|YP_008141355.1| 14 VIGATGAYGYAVTKILLKNKINVRAIVRNEEKALKLFPKDVD--IVKSDI-FNMDKIIKDLKGA 74
                                      88*******************999999999999999998873..344455.6666888887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (268 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2009.41
//
Query:       gi|518651836|ref|YP_008141356.1|  [L=194]
Description: TetR family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   54.9   0.0    8.6e-15   54.3   0.0    1.3  1  TetR_N       Bacterial regulatory proteins, tetR family
     0.0044   17.2   0.1     0.0099   16.0   0.1    1.7  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
     0.0045   17.3   0.3      0.017   15.4   0.1    2.0  2  TetR_C_26    Tetracyclin repressor-like, C-terminal domain
     0.0052   16.9   0.1      0.012   15.7   0.1    1.6  1  TetR_C_17    Tetracyclin repressor-like, C-terminal domain
  ------ inclusion threshold ------
      0.035   13.7   0.0      0.072   12.7   0.0    1.5  1  CENP-B_N     CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> TetR_N  Bacterial regulatory proteins, tetR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.3   0.0   2.4e-18   8.6e-15       1      45 [.      16      60 ..      16      62 .. 0.97

  Alignments for each domain:
  == domain 1  score: 54.3 bits;  conditional E-value: 2.4e-18
                                      HHHHHHHHHHHHHTTT--HHHHHHHHTSSHHHHHHHTSSHHHHHH CS
                            TetR_N  1 IldaArelfaerGydattvreIAkrAGvskgalYryFpsKeeLle 45
                                      I++ A +lf + Gy++++++ IA+  G++kg+lY yF++KeeLl+
  gi|518651836|ref|YP_008141356.1| 16 IIESASKLFFQMGYNNAGMENIARDMGITKGTLYLYFKNKEELLN 60
                                      89*****************************************96 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 !   16.0   0.1   2.8e-06    0.0099      15     100 ..      20      97 ..       8     123 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.8e-06
                                       HHHHHHHHHH--S-HHHHHHHHTS-HHHHHHHH.H-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHSSS--HHHHH CS
                       HTH_Tnp_1_2  15 aaellvendyekltldeiaeevgvsrsTlykWk.kkkeFieyvnelaeefleeeraevykaLlrkilkgrssvkAie 90 
                                       a +l  +  y++  +++ia+++g+ + Tly +  +k+e  +   ++  ++le++       L++ ++++   +  ie
  gi|518651836|ref|YP_008141356.1|  20 ASKLFFQMGYNNAGMENIARDMGITKGTLYLYFkNKEELLNKTCKVNMDLLETN-------LKKSVSGN--MITGIE 87 
                                       56677888999*******************876366666666666666666654.......55555555..555555 PP

                                       HHHHHTT--E CS
                       HTH_Tnp_1_2  91 Lylkrrgelt 100
                                        ++  + +l 
  gi|518651836|ref|YP_008141356.1|  88 KFFADEMKLP 97 
                                       5555555555 PP

>> TetR_C_26  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.71   2.6e+03      83     102 ..      48      67 ..      44      90 .. 0.67
   2 !   15.4   0.1   4.8e-06     0.017      35      74 ..     121     160 ..      97     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.71
                                       HHT.S---SS-HHHHHHHHH CS
                         TetR_C_26  83 lylydeeeeeeveekkkell 102
                                       lyly +++ee ++++ k  +
  gi|518651836|ref|YP_008141356.1|  48 LYLYFKNKEELLNKTCKVNM 67 
                                       57777777766665544433 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.8e-06
                                       HHHHHHHHHHHHHHHHHHHHHTTSB-TT--HHHHHHHHHH CS
                         TetR_C_26  35 WeeiYePlYewleelleeakkkeeireeieveatakllig 74 
                                        e+ Y+ + +++++l+e+ k+ ++i+e+i+++  a++li+
  gi|518651836|ref|YP_008141356.1| 121 IENSYKRYVKYISDLIENLKQDGTISESINSTDLARILIA 160
                                       4788**********************************97 PP

>> TetR_C_17  Tetracyclin repressor-like, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.1   3.3e-06     0.012      33      90 ..     113     170 ..      98     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.3e-06
                                       G-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS---SS-HHHHHHHHHHHHHHHHHHHH CS
                         TetR_C_17  33 reeerrayleeRyerlvealkellqeGvergEfkPqlplesiakylisfldGliletl 90 
                                        +++ ++ +e+ y+r v+ +++l+++  + g  +  +  ++ a++li+f +G++++ +
  gi|518651836|ref|YP_008141356.1| 113 VNNNIKEIIENSYKRYVKYISDLIENLKQDGTISESINSTDLARILIAFHNGVLISIM 170
                                       47788999********************************************998765 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05     0.072      26      51 ..      35      60 ..      30      62 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                                      HHHHHHHT--CCHHHHHHHCHHHHCC CS
                          CENP-B_N 26 aelarrfnvpestlsdilknKkkllk 51
                                      + +ar+ ++ + tl+   knK++ll+
  gi|518651836|ref|YP_008141356.1| 35 ENIARDMGITKGTLYLYFKNKEELLN 60
                                      579*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1473.43
//
Query:       gi|518651837|ref|YP_008141357.1|  [L=154]
Description: hypothetical protein FACI_IFERC00001G0476 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.53    9.7   6.2       0.74    9.2   4.3    1.8  2  EBP           Emopamil binding protein
       0.72    9.4  11.6       0.47   10.0   1.9    2.1  2  E1-E2_ATPase  E1-E2 ATPase
          3    7.2  10.1       0.11   11.9   4.1    1.5  2  Caa3_CtaG     Cytochrome c oxidase caa3 assembly factor (Caa3
        3.7    7.4  12.6        3.6    7.5  10.8    1.8  2  DUF1980       Domain of unknown function (DUF1980)


Domain annotation for each model (and alignments):
>> EBP  Emopamil binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   4.3   0.00017      0.74      82     160 ..      19      99 ..      11     111 .. 0.70
   2 ?    0.2   0.0       0.1   4.5e+02      82     106 ..     121     146 ..     112     154 .] 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00017
                               EBP  82 vvslelltvllagplallvvy.aiakekplrhllqivlataelyGgvlyfatewlegslnldts.eplylwvYlvff 156
                                       +v+l +l +++ + la+l  +  i++ k   ++ ++ +a++ ++G  + f  e+l  +l++++  + l +wvYl+f+
  gi|518651837|ref|YP_008141357.1|  19 IVVLTFLFIIMFYRLAYLGSIgNIISAKYNFYTGIFPVAIIGFVGIDIIFYLEYLRDKLSHNSVrHNLAMWVYLLFI 95 
                                       4444455555555565554431455655666666777*******************99999887799*******997 PP

                               EBP 157 NalW 160
                                        ++ 
  gi|518651837|ref|YP_008141357.1|  96 FLFF 99 
                                       6554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.1
                               EBP  82 vvslelltvllagplallv.vyaiak 106
                                       ++++ l+t+ + g  +l + +y++++
  gi|518651837|ref|YP_008141357.1| 121 MLMINLITIGIPGVFSLSIpIYLLVT 146
                                       67788888888888887762333333 PP

>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   2.1    0.0025        11     113     166 ..       6      61 ..       2      76 .. 0.57
   2 ?   10.0   1.9    0.0001      0.47     121     178 ..      91     150 ..      71     153 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0025
                                       HHHHHHHHH..HHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
                      E1-E2_ATPase 113 kkldklgkv..lvpvvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                                       k+++k++++  +++vvl+++++++++ l + +s+ +++     + +++ P a++ +
  gi|518651837|ref|YP_008141357.1|   6 KNVKKISNYiiISIVVLTFLFIIMFYRLAYLGSIGNIISAKYNFYTGIFPVAIIGF 61 
                                       55566666522233333333333333444444444777667777777777777655 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                                       HHHHHHHHHHHHHHHS-STTTSSTT..HHHHHHHHHHHHHS-TTHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 121 vlvpvvlliallvflialllgksla..eallralallvaaiPcaLplavplalalgarrl 178
                                       +l ++ l+++l++ l+++++g+ ++     + ++ l+++ iP  + l +p+ l++   r 
  gi|518651837|ref|YP_008141357.1|  91 YLLFIFLFFSLILPLLLPSTGNRPQiiSHSMLMINLITIGIPGVFSLSIPIYLLVTSHRF 150
                                       57778888888888889999999988888888*********************9988776 PP

>> Caa3_CtaG  Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       0.6   2.7e+03     102     111 ..      21      30 ..      13      38 .. 0.44
   2 ?   11.9   4.1   2.5e-05      0.11     102     180 ..      56     135 ..      53     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.6
                         Caa3_CtaG 102 valllfvall 111
                                       v ++lf++++
  gi|518651837|ref|YP_008141357.1|  21 VLTFLFIIMF 30 
                                       2222222222 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 2.5e-05
                         Caa3_CtaG 102 valllfvallyllylpplfdaalrsealhalmhlhfllaGllfwwpvlgpd.peprrlspllrllylfaamvlhafl 177
                                       va++ fv++ +++yl  l d + ++ + h+l  +++ll  +lf+  +l    p+  ++++++   +l+++++  ++ 
  gi|518651837|ref|YP_008141357.1|  56 VAIIGFVGIDIIFYLEYLRDKLSHNSVRHNLAMWVYLLFIFLFFSLILPLLlPSTGNRPQIISHSMLMINLITIGIP 132
                                       89999***************************************9999654268899999***********999999 PP

                         Caa3_CtaG 178 gal 180
                                       g++
  gi|518651837|ref|YP_008141357.1| 133 GVF 135
                                       987 PP

>> DUF1980  Domain of unknown function (DUF1980)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.3     0.023     1e+02      67      87 ..       6      26 ..       2      27 .. 0.77
   2 ?    7.5  10.8   0.00079       3.6       4      90 ..      19     109 ..      16     119 .. 0.63

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.023
                           DUF1980 67 sfikkllsylilviPlllgll 87
                                      + +kk+ +y+i++i +l+ l+
  gi|518651837|ref|YP_008141357.1|  6 KNVKKISNYIIISIVVLTFLF 26
                                      558999999999998888776 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00079
                           DUF1980   4 fliLlg.FavllfkLhasgeiskYInpkyapllyfamvvllilalvq...liraqkkkecghdHe...eksfikkll 73 
                                       +++L + F ++++ L + g+i + I  ky+ ++ +  v  +i+++v    ++   + + ++ +H+   ++  +  +l
  gi|518651837|ref|YP_008141357.1|  19 IVVLTFlFIIMFYRLAYLGSIGNIISAKYNFYTGIFPV--AIIGFVGidiIFYLEYLR-DKLSHNsvrHNLAMWVYL 92 
                                       55665515566667****************98765544..444444433455555555.556666453333344444 PP

                           DUF1980  74 sylilviPlllglllpt 90 
                                        ++ l++ l+l lllp+
  gi|518651837|ref|YP_008141357.1|  93 LFIFLFFSLILPLLLPS 109
                                       44455678888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1188  (0.0662614); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1061.66
//
Query:       gi|518651838|ref|YP_008141358.1|  [L=332]
Description: hypothetical protein FACI_IFERC00001G0477 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       954  (0.0532099); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2610.14
//
Query:       gi|518651839|ref|YP_008141359.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G0478 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-27   96.5   0.3    2.5e-27   95.7   0.3    1.5  1  DEDD_Tnp_IS110  Transposase
    2.9e-24   85.2   0.0    5.5e-24   84.3   0.0    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.3   2.8e-31   2.5e-27       1     155 []      16     171 ..      16     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 2.8e-31
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       vGiD+ak+k+d c+i++e + +++  + n+  g++++l+   ++ +++++++e+t+ y+ +l+++l e+  + +++n
  gi|518651839|ref|YP_008141359.1|  16 VGIDIAKKKFDYCIINSEMNLIKRGILINNNYGFSEFLKI-IKNYRNIKIGMESTSIYHVNLYNYLIENSRSAIILN 91 
                                       8*******************999999999999******99.99********************************** PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllr.drgrlrpl.klddeayaeLrqltrqredlvkertrlknrlralLdq 152
                                        l +k l+++ +rk+KtD++DA+ IA++++ + +++ ++ k ++++y++L++ +  +  + +++t +kn+l+  +d 
  gi|518651839|ref|YP_008141359.1|  92 SLETKLLKSSRIRKNKTDKIDAEAIAKYIIiRKNNIITMdKNTENTYTNLKEYVYTYIRINRKITMAKNQLIVDMDL 168
                                       ****************************997777776664668999*************************987777 PP

                    DEDD_Tnp_IS110 153 vfp 155
                                       ++p
  gi|518651839|ref|YP_008141359.1| 169 LYP 171
                                       666 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   6.1e-28   5.5e-24       3      86 ..     260     343 ..     258     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 6.1e-28
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                        +++ipGiG++t + +l+ igd++rf+s  +l ay G++pv++qSG+++  ++iskrGn+ +R aLy  +++air+n
  gi|518651839|ref|YP_008141359.1| 260 KIKTIPGIGTITGSIILSSIGDINRFDSIIKLRAYSGMDPVVKQSGDYNITSKISKRGNPLIRYALYLSTVSAIRFN 336
                                       589*********************************************99*************************** PP

                    Transposase_20  80 pelrayy 86 
                                       p++++yy
  gi|518651839|ref|YP_008141359.1| 337 PVIKRYY 343
                                       ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1311  (0.0731218); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.37
# Mc/sec: 3108.53
//
Query:       gi|518651840|ref|YP_008141360.1|  [L=295]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-22   79.3   0.0    5.2e-22   78.3   0.0    1.5  2  rve       Integrase core domain
    3.1e-05   23.7   1.5     0.0013   18.5   1.5    2.6  1  rve_3     Integrase core domain
    4.2e-05   24.1   0.0    0.00011   22.8   0.0    1.7  1  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       2.5   1.5e+04      84     100 ..      84     100 ..      83     101 .. 0.77
   2 !   78.3   0.0   8.6e-26   5.2e-22       2     117 ..     127     245 ..     126     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 2.5
                               rve  84 refladlgirvsftrpg 100
                                       +++l+d gi++s++  +
  gi|518651840|ref|YP_008141360.1|  84 EKYLKDKGIQISHNIIY 100
                                       67899999999987766 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 8.6e-26
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ + +e++ ++++++le a++ +g+  pe++l+D+g+++
  gi|518651840|ref|YP_008141360.1| 127 EHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYSEETIDNTIETLEIAIDLYGK--PEEILTDHGTQF 196
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l +++i++ + r  +pq+nGk Er + t+k+
  gi|518651840|ref|YP_008141360.1| 197 FSNgkngipgdknKFQEYLDNNNIKHIVGRIDHPQTNGKLERLNYTIKR 245
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.5   2.2e-07    0.0013       2      62 ..     219     269 ..     218     272 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-07
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssL 62 
                                        i++ +++  +Pq+Ng+ E++n t+++   + + +          ++ + +YN++R+H sL
  gi|518651840|ref|YP_008141360.1| 219 NIKHIVGRIDHPQTNGKLERLNYTIKRLRPYFSTW----------DEVVYYYNYKRRHMSL 269
                                       689999999****************9865543333..........699***********99 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   1.8e-08   0.00011       9      73 .]      42     103 ..      34     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 1.8e-08
                            HTH_32   9 yneeGlegLkdrprrgrpr.klsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       y e G e L+     gr++  ++  +++ ii+++ + p  +p  + ++l +  g+++Sh  +yriL
  gi|518651840|ref|YP_008141360.1|  42 YLEYGKEELYKT---GRKKkNIDSNTEELIINIRDNYPLSGPLPIEKYL-KDKGIQISHNIIYRIL 103
                                       666666666655...778736*************8899888888*****.5556***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1991.11
//
Query:       gi|518651841|ref|YP_008141361.1|  [L=460]
Description: hypothetical protein FACI_IFERC00001G0480 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-39  134.0   2.0    6.1e-39  133.1   1.0    2.0  2  AAA_14        AAA domain
    3.3e-08   33.7   1.2    7.6e-08   32.5   1.2    1.8  1  DUF4143       Domain of unknown function (DUF4143)
    8.6e-08   32.4   2.4    0.00036   20.5   0.2    2.6  2  ATPase_2      ATPase domain predominantly from Archaea
    0.00021   21.1   0.3     0.0016   18.2   0.0    2.1  2  AAA_24        AAA domain
      0.006   16.9   0.0       0.13   12.5   0.0    2.4  1  AAA_22        AAA domain
     0.0068   15.5   0.0      0.016   14.3   0.0    1.5  2  T2SSE         Type II/IV secretion system protein
     0.0082   16.5   0.5      0.055   13.9   0.0    2.7  2  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.016   15.6   0.0      0.039   14.4   0.0    1.6  1  AAA           ATPase family associated with various cellular 
       0.14   11.1   0.0        0.2   10.5   0.0    1.2  1  DUF463        YcjX-like family, DUF463


Domain annotation for each model (and alignments):
>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   1.0   3.1e-42   6.1e-39       2     131 .]      54     188 ..      53     188 .. 0.92
   2 ?   -2.7   0.0       2.7   5.4e+03      89     103 ..     380     394 ..     339     403 .. 0.70

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 3.1e-42
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkla..dpekllelileklke..ekktylflDE 72 
                                       +ki++i G+Rr+GKT++l+ li+ell   +k++ilyin++der+ + +  d ++++ l+ e++++  +kk ylf+DE
  gi|518651841|ref|YP_008141361.1|  54 NKIITIIGPRRSGKTYFLYYLINELLktEPKNNILYINFEDERLMNVTisDMDNIIPLFIELANPskDKKIYLFFDE 130
                                       89*************************999**************8866224558999999985445689******** PP

                            AAA_14  73 iqevpewekalkslvdegknldvivtGSnskllskeiatslagrvaeielyplsfaEfl 131
                                       iq+++ wek++++++d++ +++++++GS+sklls+ei+tsl+gr  e++++plsf+E+l
  gi|518651841|ref|YP_008141361.1| 131 IQNIKFWEKYIRRVYDTS-KYKIFISGSSSKLLSREISTSLRGRNIEYTIMPLSFQEYL 188
                                       ****************99.99************************************97 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.7
                            AAA_14  89 egknldvivtGSnsk 103
                                       +gk++d++v+ S++ 
  gi|518651841|ref|YP_008141361.1| 380 NGKEVDFVVSDSLKI 394
                                       456778888877765 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   1.2   3.8e-11   7.6e-08      18     120 ..     273     401 ..     185     403 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 3.8e-11
                                       x..................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  18 k..................................glverlppwsespnskkrlrkspKlyfvDtGLlvallgldke 60 
                                                                          + ++ l+ +  ++ ++k+   + K+y vD+G+++al +  + 
  gi|518651841|ref|YP_008141361.1| 273 SkyfsiskiyntfksvgykisknklleflydsreiFFLFSLNIY--TRSENKKMSYNKKIYSVDPGIIYALKNEMS- 346
                                       05555555555555666666666677777777655555566666..8889999999**************765444. PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  61 elledsenkGallEnlVaqeLlkysekegaklyyyrdk...ngaEvDfvielkggkivpiEvK 120
                                                 +l+ n+V+ eL  +  +++ +++y+++    ng+EvDfv++++ + + +i+v 
  gi|518651841|ref|YP_008141361.1| 347 --------ITRLMKNIVFLELNHRCIENNLDVSYWKEYgkaNGKEVDFVVSDSLKIVELIQVT 401
                                       ........4589************8888********999978********9887777788875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.2   1.8e-07   0.00036      16      65 ..      50     100 ..      46     108 .. 0.87
   2 !   11.4   0.2   0.00011      0.23     106     207 ..     109     197 ..      97     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                          ATPase_2  16 erepneiyfiYGpegsGKtaLlkeiienl.edkdkyviyyialreesiskl 65 
                                       ++++n+i+ i Gp++sGKt +l  +i++l +   k+ i yi++++e++ ++
  gi|518651841|ref|YP_008141361.1|  50 SMDSNKIITIIGPRRSGKTYFLYYLINELlKTEPKNNILYINFEDERLMNV 100
                                       56789***********************966667899******99988776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00011
                          ATPase_2 106 ielllekikk.kgkkiiiiiDelqklidlglngaellvkeLlnliesltkekhlcvviclsSeglfiervynesele 181
                                       i l++e  +  k kki +++De+q+++   +   e+++   ++  ++      ++++  +sS+ l++e    +  l+
  gi|518651841|ref|YP_008141361.1| 109 IPLFIELANPsKDKKIYLFFDEIQNIK---FW--EKYIRRVYDTSKY------KIFISGSSSKLLSRE---ISTSLR 171
                                       555555555414566************...44..7899887766655......555555555556666...6778** PP

                          ATPase_2 182 grhkyilvddldketalnflkegfke 207
                                       gr   +++ +l +++ l+f +    +
  gi|518651841|ref|YP_008141361.1| 172 GRNIEYTIMPLSFQEYLEFNRMEYSN 197
                                       ******************98865554 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   7.9e-07    0.0016       2      89 ..      54     145 ..      53     159 .. 0.74
   2 ?    0.5   0.1      0.21   4.2e+02      48      93 ..     346     411 ..     320     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.9e-07
                            AAA_24   2 klkiliyGpsgiGKTtlakel.........gpkplfidtek.Glksldadkfpdieswedfldevvelaaeladyk. 67 
                                       ++ i i+Gp  +GKT++++ l         ++++l+i++e+  l ++   ++      ++++  + ela   +d k 
  gi|518651841|ref|YP_008141361.1|  54 NKIITIIGPRRSGKTYFLYYLinellktepKNNILYINFEDeRLMNVTISDM------DNIIPLFIELANPSKDKKi 124
                                       67799************************************55555555554......4556666666444444331 PP

                            AAA_24  68 tlviDtideleelclaevirqn 89 
                                        l++D i+ + +++ ++++r  
  gi|518651841|ref|YP_008141361.1| 125 YLFFDEIQNI-KFWEKYIRRVY 145
                                       5778888877.77777776655 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                            AAA_24  48 swedfldevvel....................aaeladyktlviDtideleelclaevirqnekae 93 
                                       s++ +++ +v+l                    +a+ ++ + +v D++  +e + + ++ +++e+ +
  gi|518651841|ref|YP_008141361.1| 346 SITRLMKNIVFLelnhrciennldvsywkeygKANGKEVDFVVSDSLKIVELIQVTYASDASEIDK 411
                                       77888888888888888888899999999999999************9998888888888877743 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   6.5e-05      0.13       4      50 ..      53     105 ..      50     164 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.5e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee......erpevvfvtlpss 50 
                                       + +i++++G+  +GKT+ l  l ++l + +  ++      e+ +++ vt++  
  gi|518651841|ref|YP_008141361.1|  53 SNKIITIIGPRRSGKTYFLYYLINELLKTEPKNNilyinfEDERLMNVTISDM 105
                                       679*********************99654333336666664444444443333 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 !   14.3   0.0   7.8e-06     0.016     115     163 ..      40      90 ..      19     107 .. 0.83
   2 ?   -3.9   0.0       2.8   5.6e+03      19      53 ..     386     420 ..     379     430 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.8e-06
                             T2SSE 115 kekiaevlrkavrerglilvsGgTgsGKttllyallkeinks..derivtv 163
                                        e+ ++ ++ ++ ++++i + G+  sGKt +ly l++e+ k+  +++i+ +
  gi|518651841|ref|YP_008141361.1|  40 PEAHKRNINVSMDSNKIITIIGPRRSGKTYFLYYLINELLKTepKNNILYI 90 
                                       5777889999999***********************999887677888776 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.8
                             T2SSE  19 vekpervkvrervdgielreveelekaalerlisr 53 
                                       +   +++k+ e ++ ++ ++++e++k+++++l+s 
  gi|518651841|ref|YP_008141361.1| 386 FVVSDSLKIVELIQVTYASDASEIDKREISALLSA 420
                                       55566666667777777777778887777777765 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.7e-05     0.055       1      42 [.      57      95 ..      57     155 .. 0.84
   2 ?   -1.3   0.2       1.4   2.8e+03      41      85 ..     247     293 ..     229     309 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.7e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpedd 42
                                      i + Gp++ GK+++ ++L+++ll   k++ k+++ + n ed+
  gi|518651841|ref|YP_008141361.1| 57 ITIIGPRRSGKTYFLYYLINELL---KTEPKNNILYINFEDE 95
                                      5789*******************...4556677766666555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                      RNA_helicase  41 ddfwdgYtgqevvvidDfgqvk.dee.npsdlaelirlvsstpypln 85 
                                        d+ + ++  ev+v d f++ + + + ++  ++ + ++++s+ y++ 
  gi|518651841|ref|YP_008141361.1| 247 MDMAEHFNISEVNVLDAFMKYSvSIYsKYFSISKIYNTFKSVGYKIS 293
                                       56666667778888888888773444444455556666655555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0     2e-05     0.039       3      70 ..      59     134 ..      57     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2e-05
                                       EESSTTSSHHHHHHHHHHHH.......THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGH CS
                               AAA   3 lyGppGtGKTllakavakel.......gvefleisgsellskyvgesekkirelfkeakeka.kpsilfiDEidal 70 
                                       ++Gp   GKT++   +++el       ++ +++++  +l++ +++++ + i  +++ a  ++ k+  lf+DEi ++
  gi|518651841|ref|YP_008141361.1|  59 IIGPRRSGKTYFLYYLINELlktepknNILYINFEDERLMNVTISDMDNIIPLFIELANPSKdKKIYLFFDEIQNI 134
                                       79*****************877776333556666777777777777777777777777666677899******876 PP

>> DUF463  YcjX-like family, DUF463
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0001       0.2       4      50 ..      58     103 ..      56     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                            DUF463   4 avTGLsraGKtvfitsLvnqLlaaekkarlplfeaaregrllgakle 50 
                                        + G  r+GKt f+  L+n+Ll++e k+++ l+   +++rl+++++ 
  gi|518651841|ref|YP_008141361.1|  58 TIIGPRRSGKTYFLYYLINELLKTEPKNNI-LYINFEDERLMNVTIS 103
                                       677889****************87777775.5555678899888754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.60u 0.31s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 2776.54
//
Query:       gi|518651842|ref|YP_008141362.1|  [L=503]
Description: hypothetical protein FACI_IFERC00001G0481 [Ferroplasma acidarmanus fer1]
Scores for complete 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-175  583.6   0.0     3e-175  583.4   0.0    1.0  1  Lyase_aromatic  Aromatic amino acid lyase


Domain annotation for each model (and alignments):
>> Lyase_aromatic  Aromatic amino acid lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.4   0.0  1.7e-179    3e-175       1     464 []       9     464 ..       9     464 .. 0.98

  Alignments for each domain:
  == domain 1  score: 583.4 bits;  conditional E-value: 1.7e-179
                                       --HHHHHHHHTCCCEEEE-HHHHHHHHHHHHHHHHHHHCTB--TTTSB-SGGGGGBB--HHHHHHHHHHHHHHC--- CS
                    Lyase_aromatic   1 LtledvvavargkakvelspearerveasravleeilaegepvYGvntGfGaladvripkedleelqrnllrshaaG 77 
                                       L++edv ava+g++kv ++++a+++++ s + l++il++g+pvYGvntGfG+l +v+++++++ +lq+nl+rsh++G
  gi|518651842|ref|YP_008141362.1|   9 LSIEDVNAVASGSEKVGIAESAIKQIQYSKKSLMKILDSGKPVYGVNTGFGSLLNVNVDRKNIVQLQTNLIRSHSSG 85 
                                       89*************************************************************************** PP

                                       EEEE--HHHHHHHHHHHHHHHTTS-S---HHHHHHHHHHHHCTEEE--EEES-------HHHHHHHHHHHTTSSTCC CS
                    Lyase_aromatic  78 vgeplpeevvRaamllrlnslakGysGvrpevverllellnagitPvvperGSvGaSGDLaplahlalvliGegevy 154
                                       +gepl+ e+vRa+ml+r+n+l+kGysGv+ ++++ ll +ln++i+P+vp+ GSvGaSGDLaplah++l+l+Geg+v+
  gi|518651842|ref|YP_008141362.1|  86 IGEPLDIETVRAIMLVRANTLVKGYSGVSENMIDFLLFMLNNNIIPAVPRYGSVGASGDLAPLAHIGLALMGEGDVF 162
                                       ***************************************************************************** PP

                                       ETTEEEEHHHHHHHTT------TTTHHHHCCSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BCGGG-HHH CS
                    Lyase_aromatic 155 ykgerlpaaealaeaglepleleakEgLAlinGtalmtalaalaledaerllrladvaaAlslealrGsteafdpri 231
                                       ykg++ +a  ++++ g ep++ ++kEg+AlinGt++++++ al +++ e+l+  a   +Al++e+l+G+++af++  
  gi|518651842|ref|YP_008141362.1| 163 YKGKIQNAGTVFKSLGKEPYSYGEKEGVALINGTSVICGILALEIKRSEKLVSEALGSFALAFEGLSGTDKAFTEWA 239
                                       ***************************************************************************** PP

                                       HCCS--HHHHHHHHHHHHHTTT-SSS..-SB-SS-SS--HHHHTHHHHHHHHHHHHHHHHHHHHHHHTS--SSSEE. CS
                    Lyase_aromatic 232 halrphpgqievAarlrallegSelvshekdeerlvQDayslRcaPqvhGavldalaaarevleiElnsatDNPlvd 308
                                        a rph+gq+ + +++r+l +gS ++++ +++++ vQDayslRc+Pqv+Gav+d+l++ar+vl++E+nsatDNPl+ 
  gi|518651842|ref|YP_008141362.1| 240 LASRPHEGQQMIGKAFRKLFNGSMIIEN-ANKSK-VQDAYSLRCTPQVYGAVWDTLQYARKVLTTEINSATDNPLL- 313
                                       **************************44.56555.*****************************************. PP

                                       EGCCTCCE---TT--HHHHHHHHHHHHHHHHHHHHHHHHHHHHC-TTTTTT--GGG-SSTCTTB-TTHHHHHHHHHH CS
                    Lyase_aromatic 309 deeegavlsgGnFhgepvalalDklaialaelaniserrierLvnpalsegLpafLaaeepglnsgfmiaqytaaal 385
                                          +++ +s+GnFhgepva+  D++aia+++ +n++err++r+v+++ls gLp+fL+ ++ glnsg+mi+qytaaal
  gi|518651842|ref|YP_008141362.1| 314 L--GNEYISTGNFHGEPVAMVSDFVAIAMTDFGNMVERRLARIVDTNLS-GLPPFLV-KDYGLNSGYMIPQYTAAAL 386
                                       4..789*******************************************.*******.99***************** PP

                                       HHHHHCHCS-SGGG--TCTTTTCSS---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTCC-HHHHHHHHHH CS
                    Lyase_aromatic 386 vsenktlahPasvdsiptsanqeDhvSmgliaarkllevvenlekvlAiellaaaqaldlrrklksspateavyeav 462
                                       ++ nktl hP s+d+iptsanqeDhvSmg++aa kl e+ +n++ ++Aie l  aq l++r+ +++spat  +y+++
  gi|518651842|ref|YP_008141362.1| 387 CNVNKTLVHPNSADTIPTSANQEDHVSMGTNAALKLIEINKNVKSIIAIEYLLGAQSLEFRK-HEPSPATLSIYKKI 462
                                       ************************************************************87.778**********9 PP

                                       HC CS
                    Lyase_aromatic 463 re 464
                                       re
  gi|518651842|ref|YP_008141362.1| 463 RE 464
                                       96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 3118.05
//
Query:       gi|518651843|ref|YP_008141363.1|  [L=376]
Description: hypothetical protein FACI_IFERC00001G0482 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-15   55.7   0.0    2.5e-12   46.8   0.0    2.1  2  Amidohydro_1  Amidohydrolase family
    1.6e-09   37.8   0.0    2.7e-06   27.1   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 !    7.0   0.0   0.00035       3.2       1      14 [.      45      58 ..      45     103 .. 0.79
   2 !   46.8   0.0   2.8e-16   2.5e-12     186     341 ..     231     370 ..     204     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00035
                                      EEEE-EEEEEEECE CS
                      Amidohydro_1  1 ivlPGlIDaHvHle 14
                                      +++P++ID H H+ 
  gi|518651843|ref|YP_008141363.1| 45 VITPAFIDPHSHIG 58
                                      69**********96 PP

  == domain 2  score: 46.8 bits;  conditional E-value: 2.8e-16
                                       THCCEEEHCTCEEE.HHHHHHHHHHHHHHCEE.....HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT.TSSCCG CS
                      Amidohydro_1 186 deiklilahgvhlt.pteaellkerlkeagva.....hcpfsnsilrsgrealrkaldeGvkvglgtDga.asgnsl 255
                                       ++ k i+ hg+ ++  + +e +k+r  + +++     + p   +  ++ +++++ + ++Gv+++l +D+     ++l
  gi|518651843|ref|YP_008141363.1| 231 GI-KPIINHGMDFHsEKIFEEIKKR--DLSLVygpldSHPYKVELKHETWRNAELVKKSGVRFALISDHPvILQRNL 304
                                       44.8899999999965588888888..777778999977888888999999*****999*********766555555 PP

                                       GHHHHHHHHHHHHHHCCTTTTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECCCTCGGGTTTCTSE CS
                      Amidohydro_1 256 nlleelrlalklqrgllyedeegglslkealrmaTingAkalglddkvGsievGkdADlvvvdldilaafvglkkdg 332
                                         + ++r+ +           + g s +++++ ++  +A++lgld ++G++e+Gk A + +++     + ++l    
  gi|518651843|ref|YP_008141363.1| 305 --FLTTRHFM-----------RFGASKEQCISYVSSRPAQILGLD-NLGTVEPGKLASFSIWNK----DPFELDA-- 361
                                       ..889*****...........99*********************6.****************44....4444422.. PP

                                       EEEEEEETT CS
                      Amidohydro_1 333 nvkkvivkG 341
                                        +++v+  G
  gi|518651843|ref|YP_008141363.1| 362 YPAMVFGEG 370
                                       344444444 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00014       1.3       8      21 ..      44      57 ..      42      80 .. 0.82
   2 !   27.1   0.0     3e-10   2.7e-06     363     454 ..     283     361 ..     256     374 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00014
                      Amidohydro_3  8 rlvlPGFvDsHtHl 21
                                      ++ +P+F+D+H+H+
  gi|518651843|ref|YP_008141363.1| 44 GVITPAFIDPHSHI 57
                                      6889*********3 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 3e-10
                      Amidohydro_3 363 llnagvkvalgsDapvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrkGtLevGad 439
                                        ++ gv++al sD pv    ++   ++++mr               s e+++  ++++pA++lgl+   Gt+e+G+ 
  gi|518651843|ref|YP_008141363.1| 283 VKKSGVRFALISDHPVILQRNLFLTTRHFMRFG------------ASKEQCISYVSSRPAQILGLDNL-GTVEPGKL 346
                                       566777777777766666666666666666555............4779******************8.******** PP

                      Amidohydro_3 440 ADlvvldadpldvdp 454
                                       A++ ++++dp+++d+
  gi|518651843|ref|YP_008141363.1| 347 ASFSIWNKDPFELDA 361
                                       ************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2642.65
//
Query:       gi|518651844|ref|YP_008141364.1|  [L=457]
Description: dihydropyrimidinase [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  114.5   0.0    8.3e-33  114.1   0.0    1.1  1  Amidohydro_1  Amidohydrolase family
    1.3e-14   54.5   0.0    2.4e-06   27.3   0.0    2.7  3  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 !  114.1   0.0   9.2e-37   8.3e-33       1     344 []      52     436 ..      52     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 9.2e-37
                                       EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH......HHHHHHHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst......giealleaae 71 
                                       +v+PG++D H+H+e               +  +a ++++g++ a  +Gtttv+d++ ++ +      +++ +++ ++
  gi|518651844|ref|YP_008141364.1|  52 LVIPGGVDPHTHIE---------------GYSSAGTIRNGTESAAIGGTTTVLDFSQANKNedtvaaAASKIKRFSD 113
                                       59**********96...............6799************************77656655533333333333 PP

                                       TSSSEEEEEEESSEGGS..GCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTT CS
                      Amidohydro_1  72 elplglrilggkvsldr..gsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdl 146
                                       +    l + ++ +++++  +s e  +    +l +       ++a +++ ++ +  +++a+ + ++ + ++ akk+++
  gi|518651844|ref|YP_008141364.1| 114 SS--SLDFTIKPMMVTEdfQSIEGLELIFSQLSKL-----GIMAVKIF-TTYKNLGRYANNY-QILQGMNTAKKYGI 181
                                       34..6777777666664666666666666666555.....57776666.6899999999975.55566779****** PP

                                       EEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC.......HHTTTHCCEE.....EHCTCEEEHHHHHHHHHHHH CS
                      Amidohydro_1 147 pvaiHaletkgevedaeaafgetiehgthlevaes.......lglldeikli.....lahgvhltpteaellkerlk 211
                                       +v+iHa +++    ++ea  + + ++  + + a s       ++++d++ ++      + +vhl+ +++  ++  ++
  gi|518651844|ref|YP_008141364.1| 182 MVQIHAENNDFLEGNMEALLAQGKTD--PKYHAISkppvsedVAVADSAVMAgdsgaKVYCVHLSTKTSPEIIDSAR 256
                                       ******66666666777777766666..6666666778999966666644445555599999999888999999999 PP

                                       HHCEE........................HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT.......TSSCCGGH CS
                      Amidohydro_1 212 eagva........................hcpfsnsilrsgrealrkaldeGvkvglgtDga.......asgnslnl 257
                                       ++gv+                         ++++ ++ +++++a+++a+++G+++++g+D++        +g  +n 
  gi|518651844|ref|YP_008141364.1| 257 KHGVNiygetcpqylilddsfldredgnlYLCSPPLRKKEDINAMWNAISSGKIQAVGSDHVpflayqkKKGIPFNK 333
                                       *********9999999988888777777666677777*******************************988888898 PP

                                       HHHHHHHHHHHHHCCTT..TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT......... CS
                      Amidohydro_1 258 leelrlalklqrgllye..deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di......... 321
                                       +  ++ +++++ +ll +  +++g ++l++++++ ++ + k+++l+ ++G+i  G dADl+v+d+             
  gi|518651844|ref|YP_008141364.1| 334 VPNGIPGIETRLPLLFSegVQKGRITLEKFVDVISTSPSKIFNLYPQKGTISIGSDADLTVIDTelEHglraedlhm 410
                                       899999999999999999999*******************************************7611567778899 PP

                                       ...CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 322 ...laafvglkkdgnvkkvivkGklv 344
                                          +a +  +k +g+++ +i +G++v
  gi|518651844|ref|YP_008141364.1| 411 gtdIAIYSHMKTKGWPVLTISGGEIV 436
                                       ***********************998 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.7e-10   2.4e-06       3      59 ..      46     100 ..      44     117 .. 0.79
   2 ?   -0.9   0.0     0.094   8.5e+02     190     287 ..     167     191 ..     135     262 .. 0.56
   3 !   23.9   0.0   2.9e-09   2.6e-05     406     473 .]     356     437 ..     336     437 .. 0.89

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.7e-10
                      Amidohydro_3   3 iDakGrlvlPGFvDsHtHlagggvnlrllrlpdarvtslegvltavrdqagttpkgr 59 
                                       i+++G+lv+PG+vD+HtH ++g + +  +r +  +  ++ g++t+++   +++++++
  gi|518651844|ref|YP_008141364.1|  46 INLSGKLVIPGGVDPHTH-IEGYSSAGTIRNGT-ESAAIGGTTTVLDFSQANKNEDT 100
                                       99****************.66655665555555.47789999999999888866555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.094
                      Amidohydro_3 190 leplfeltaeeklplrviikelldaaerlglplspgseeltigavklfadgvlgsrtalltepyftgwpdfedeala 266
                                       +++l+++  ++                                                                  
  gi|518651844|ref|YP_008141364.1| 167 YQILQGMNTAK------------------------------------------------------------------ 177
                                       44444444444.................................................................. PP

                      Amidohydro_3 267 elvaaadergldvaihaigda 287
                                              ++g+ v iha  ++
  gi|518651844|ref|YP_008141364.1| 178 -------KYGIMVQIHAENND 191
                                       .......44444444443333 PP

  == domain 3  score: 23.9 bits;  conditional E-value: 2.9e-09
                      Amidohydro_3 406 eelsleealalyTrgpAkalgledrkGtLevGadADlvvldadpldvdppelaear..............vrltvvd 468
                                        +++le+ ++ +++ p k+++l   kGt+ +G dADl+v+d+++ +   +e+ + +              ++lt+ +
  gi|518651844|ref|YP_008141364.1| 356 GRITLEKFVDVISTSPSKIFNLYPQKGTISIGSDADLTVIDTELEHGLRAEDLHMGtdiaiyshmktkgwPVLTISG 432
                                       689**************************************888775555555555589999999************ PP

                      Amidohydro_3 469 Grvvy 473
                                       G++v+
  gi|518651844|ref|YP_008141364.1| 433 GEIVA 437
                                       **995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2943.37
//
Query:       gi|518651845|ref|YP_008141365.1|  [L=419]
Description: allantoate amidohydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   95.6   0.2    4.9e-27   95.0   0.2    1.3  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.1e-11   44.8   0.0    1.7e-11   44.2   0.0    1.3  1  Peptidase_M28  Peptidase family M28
      7e-07   29.1   0.0    1.4e-06   28.1   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 !   95.0   0.2   8.2e-31   4.9e-27       1     207 []      87     415 ..      87     415 .. 0.92

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 8.2e-31
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.. 75 
                                       ++gsHlD+V     +g           G+++G        gv++a+e+l +lk++g++  ++iv ++++ EEg+   
  gi|518651845|ref|YP_008141365.1|  87 MMGSHLDSVV----QG-----------GMFDGA------MGVFSAFEVLLRLKESGYRNHRDIVAAAFTGEEGSAfh 142
                                       5789999999....45...........666666......*********************************87788 PP

                                       ...THHHHHHHHHHT.............................TTCESEEEEEEEESSSBTCHSTETEEEE..... CS
                                       ...xxxxxxxxxxxx.............................xxxxxxxxxxxxxxxxxxxxxxxxxxxx..... RF
                     Peptidase_M20  76 ...gGakalleglee.............................rekvdavfelhieepgileagklaigvv..... 115
                                           G++ +++++ +                               k+++++e hie++++le++++ igvv     
  gi|518651845|ref|YP_008141365.1| 143 qpmLGSNGFTGNISKanlwalknrdgvdfksamqrieylgdsefPGKPEYYLEYHIEQGPVLEEKGKEIGVVtsitg 219
                                       89999999999444235566667889999999999*9999999999*****************999*********** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|518651845|ref|YP_008141365.1| 220 qcvlsvevngiqghsgttpmemrsdalvraagiiamidkiareaskkynnhsvgtvgelsvepgrfnvipghvamki 296
                                       ***************************************************************************** PP

                                       ............................EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHH CS
                                       ............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ............................kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdar 164
                                                                   +++++ + + +p  ++ +++++a+++++++l g + ++++sg +g+d+ 
  gi|518651845|ref|YP_008141365.1| 297 dlrsehsdslaymkkkvleeletkrngvNIKYSIVAEVEPSIMS-DKVMDAIKASIKSL-GFSSMEMPSG-AGHDTI 370
                                       *************************9886777766999999999.*************9.***9999***.****** PP

                                       HHTTT.EEEEEEESS.GGCTTSTTTEEEHHHHHHHHHHHHHHHHH CS
                                       xxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 165 ffagi.ptvmifgpg.sglaHspnEyvdledlekgikvlarllee 207
                                        + +i  + mif+p+ +gl+H+p E++d +d+e+g++vl  ++++
  gi|518651845|ref|YP_008141365.1| 371 PMSKIaEAGMIFVPSiKGLSHTPLEWTDFKDVENGLEVLLGAVKN 415
                                       **9995677****9956**********************999875 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   2.8e-15   1.7e-11       1     101 [.      71     170 ..      71     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.8e-15
                                       EEEEEESTTCESE.EEEEEEE--B-TTTTCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEESSCSG... CS
                     Peptidase_M28   1 Nviatlegkatde.vlllgAHyDsvgvgrgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffdaEEa... 73 
                                       N+  tl+g+++d   +++g+H+Dsv +       G+ D A+gv +  e++  l++sg r++r+++ ++f++EE    
  gi|518651845|ref|YP_008141365.1|  71 NIFITLNGSNSDLgKIMMGSHLDSVVQ---G---GMFDGAMGVFSAFEVLLRLKESGYRNHRDIVAAAFTGEEGsaf 141
                                       8999******9666************6...7...9**************************************9999 PP

                                       ..SSHHHHHHHHHHCCCTTEEEEEEECS-S CS
                     Peptidase_M28  74 ..gllGSkafakakpelkkiaavlnlDmvg 101
                                          +lGS+ f   +  +++  a+ n D v 
  gi|518651845|ref|YP_008141365.1| 142 hqPMLGSNGFT-GNISKANLWALKNRDGVD 170
                                       999*****999.666777777777766665 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.4e-10   1.4e-06       9     103 ..     223     319 ..     215     323 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.4e-10
                                       EEEEEE-B-EEGG.-TTTTB-.HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C....CCCEESSEEEEE CS
                         M20_dimer   9 gkitvkgkagHsg.apgagaN.AieklarllaeledeegdiaeerslprttlnvtgiegGs....aknvipdeaeak 79 
                                         ++v+g +gHsg  p  +++ A+  +a ++a + +  ++       ++ + +v+++ + s      nvip+++ +k
  gi|518651845|ref|YP_008141365.1| 223 LSVEVNGIQGHSGtTPMEMRSdALVRAAGIIAMIDKIAREAS----KKYNNHSVGTVGELSvepgRFNVIPGHVAMK 295
                                       5688******************************99966544....4444444444444446669************ PP

                                       EEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  80 idiRllpgedpeevleeieeilek 103
                                       id+R +  ++++  ++++ e le+
  gi|518651845|ref|YP_008141365.1| 296 IDLRSEHSDSLAYMKKKVLEELET 319
                                       ****************99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3049.94
//
Query:       gi|518651846|ref|YP_008141366.1|  [L=195]
Description: hypothetical protein FACI_IFERC00001G0485 [Ferroplasma acidarmanus fer1]
Scores for complete 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   93.0  12.0      2e-26   92.7  12.0    1.0  1  DUF998           Protein of unknown function (DUF998)
  ------ inclusion threshold ------
       0.11   10.7  10.7       0.12   10.6  10.7    1.1  1  YfhO             Bacterial membrane protein YfhO
       0.34    9.8   2.6       0.82    8.6   2.7    1.5  1  DUF3488          Domain of unknown function (DUF3488)
        2.4    8.3   5.7        4.3    7.5   1.0    2.4  2  DUF872           Eukaryotic protein of unknown function (DUF8


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 !   92.7  12.0   4.5e-30     2e-26       3     181 ..      11     183 ..       9     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 4.5e-30
                            DUF998   3 aallalavilaaallrpgydplrhaiSeLgaeg.........gpggwlfnaglvllgllvlalavgllraargragr 70 
                                       a+++a+++i aa  ++p ++  ++a+S+Lg+++         +++++++n+gl+++gll++++a++ + ++r+ ++ 
  gi|518651846|ref|YP_008141366.1|  11 AIAAAWITIFAAISVNPWFRIQKNALSDLGGTNisnffqhqaPADPYIYNVGLMVTGLLIALFAIAAIANSRNSIEN 87 
                                       678999999999***9999************************************************999******* PP

                            DUF998  71 agrlllavaglglvlagvfptdpgggspslsglvHglasavaflalavavlllasaarrrawallrlvggvallllv 147
                                        g++++++agl+l+l+g+++++++         +H+++s+++f+   +a ++++      +  l +++  v++++l+
  gi|518651846|ref|YP_008141366.1|  88 TGSAFFIIAGLFLALIGIYHEGTY---------PHDFVSIWFFIIASIAYATIG------ISLLFTKFRKVGIAILI 149
                                       ************************.........9********************......***************** PP

                            DUF998 148 aalvwllaaaldgslllGlaerllvlaitawlla 181
                                       ++ v +++ +  ++++++  e+++v++i + +l+
  gi|518651846|ref|YP_008141366.1| 150 ILPVSWVLFIEIPWQSVAEDEIFGVIVIDIMVLL 183
                                       *****************************99987 PP

>> YfhO  Bacterial membrane protein YfhO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6  10.7   2.7e-05      0.12     266     417 ..      42     188 ..      14     195 .] 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 2.7e-05
                              YfhO 266 lligtfdfeqmgslpniy.vgllpllllilyFvlkkiklkeklafallllllilsfllpplnlvwhgfqaPvgfpyR 341
                                         i +f  +q ++ p iy vgl+++ lli++F+   i + +  +    ++++i+  l+ +l  ++h +++P  f+  
  gi|518651846|ref|YP_008141366.1|  42 TNISNFFQHQAPADPYIYnVGLMVTGLLIALFAIAAIANSRNSIENTGSAFFIIAGLFLALIGIYHEGTYPHDFVSI 118
                                       45556666666666776548999999999*************9999999***************************9 PP

                              YfhO 342 fsfilsflllllaaealkelkqlkklkllaailllvlllliilllknkksynfltssqlllgllllllalllllll 417
                                       + fi++ +  +++   l  + +++k++++++i+l v+ +l+i  +    + + +++++++  +++ +++ll ++++
  gi|518651846|ref|YP_008141366.1| 119 WFFIIASIAYATIGISLL-FTKFRKVGIAILIILPVSWVLFIE-IP---W-QSVAEDEIFGVIVIDIMVLLHIYTF 188
                                       999998877777777776.555667888888888888777665.22...2.2344444443333334444444444 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   2.7   0.00018      0.82     100     172 ..      68     162 ..      63     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00018
                           DUF3488 100 lllgffllatsflfsqsllfalylllalllllaalvalh......................asasapslaralrlal 154
                                       ll+++f++a+ +  ++s+ ++  +++++++l++al+ ++                      a+ + + l + +r ++
  gi|518651846|ref|YP_008141366.1|  68 LLIALFAIAAIANSRNSIENTGSAFFIIAGLFLALIGIYhegtyphdfvsiwffiiasiayATIGISLLFTKFRKVG 144
                                       56777788887778888888888888888888888887777777777777777777777776899999999999999 PP

                           DUF3488 155 kllllalPlalvLFllfP 172
                                       + +l+ lP+  vLF+ +P
  gi|518651846|ref|YP_008141366.1| 145 IAILIILPVSWVLFIEIP 162
                                       999999999999999888 PP

>> DUF872  Eukaryotic protein of unknown function (DUF872)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   1.0   0.00096       4.3      52      93 ..      63     107 ..      57     111 .. 0.73
   2 ?    2.8   0.2     0.029   1.3e+02      43      63 ..     119     139 ..     110     149 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00096
                            DUF872  52 LlllGlvLlllgvvilvep...seGvssavflvlGlllfiPGvYh 93 
                                       L+++Gl++ l +++  ++     e + sa f+++Gl l + G+Yh
  gi|518651846|ref|YP_008141366.1|  63 LMVTGLLIALFAIAAIANSrnsIENTGSAFFIIAGLFLALIGIYH 107
                                       77788776666666666553335667788899************9 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.029
                            DUF872  43 rkvvlaallLlllGlvLlllg 63 
                                       +  ++a+++  ++G++Ll++ 
  gi|518651846|ref|YP_008141366.1| 119 WFFIIASIAYATIGISLLFTK 139
                                       6679**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       966  (0.0538792); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1356.19
//
Query:       gi|518651847|ref|YP_008141367.1|  [L=461]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-09   38.0   0.1    3.6e-09   36.4   0.1    1.8  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.1e-08   33.9   4.5    9.5e-08   32.3   4.5    1.8  1  OrfB_IS605      Probable transposase
     0.0005   20.3   1.4      0.001   19.3   1.4    1.6  1  C1_2            C1 domain
     0.0053   16.8   2.3      0.017   15.1   0.7    2.3  2  DUF1451         Zinc-ribbon containing domain
     0.0072   16.0   6.9     0.0076   15.9   3.8    2.5  2  A2L_zn_ribbon   A2L zinc ribbon domain
  ------ inclusion threshold ------
       0.12   12.4   0.1       0.31   11.1   0.1    1.6  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.16   11.5   0.8         13    5.4   0.0    2.6  2  RecR            RecR protein
       0.25   10.9   1.3        1.2    8.7   1.6    2.0  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.56   10.6   2.4        1.7    9.1   2.4    1.8  1  DUF4379         Probable 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 !   36.4   0.1   1.8e-12   3.6e-09      18      65 ..     339     387 ..     328     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 1.8e-12
                    OrfB_Zn_ribbon  18 kveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiN 65 
                                       ++++ +++  T k+Cs+C  k + +l++r ++Cp+Cgf +drD+n+a+N
  gi|518651847|ref|YP_008141367.1| 339 TLILLDKFIpTTKECSNCHNKYDIKLDERIYNCPKCGFIIDRDYNSALN 387
                                       6677788888********999998***********************99 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   4.5   4.8e-11   9.5e-08      10     104 ..     201     301 ..     183     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 4.8e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylake.......iaelqsklkksknykkasrkla 78 
                                       +++++++k ++ DlGi+n +t+++++     ++k+r+  + +++l+++       + +l++  k+skny k ++kl 
  gi|518651847|ref|YP_008141367.1| 201 EKPVNNQKIISFDLGIKNQLTCSNGSILNyNIPKSRKEIRLQRSLSRKakyaegsKNKLSK--KQSKNYYKNKNKLN 275
                                       6788999*****************9844456666666655555555541100000444444..47788********* PP

                        OrfB_IS605  79 rlhrkrsrrrkhllhklathliktlk 104
                                       +   k +++rk+ ++k++++l+ +++
  gi|518651847|ref|YP_008141367.1| 276 KEQTKTANKRKDTINKIVHYLTSNYD 301
                                       *********************99886 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   1.4   5.2e-07     0.001       3      44 ..     335     380 ..     333     381 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 5.2e-07
                              C1_2   3 Hp.HpLtlskgedssesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                       H+  +L+l  ++    +++Cs C +k     d  +  Y+C++C f+++ 
  gi|518651847|ref|YP_008141367.1| 335 HKaSTLILL-DKFIPTTKECSNCHNKydikLD--EriYNCPKCGFIIDR 380
                                       787789999.999999**********885443..256*********995 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.36   7.1e+02      48      93 ..     246     291 ..     239     328 .. 0.58
   2 !   15.1   0.7   8.7e-06     0.017     112     139 ..     348     375 ..     344     377 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.36
                           DUF1451  48 eeaarsleeskeeleewlsldlelieesllealasiaDktqvelae 93 
                                       +  a++ e sk++l++++s ++   +++l ++ ++ a+k +  +++
  gi|518651847|ref|YP_008141367.1| 246 SRKAKYAEGSKNKLSKKQSKNYYKNKNKLNKEQTKTANKRKDTINK 291
                                       5555555555555555555555555555555555555444444433 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 8.7e-06
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C +C+++ ++k  e+i +CpkCg
  gi|518651847|ref|YP_008141367.1| 348 PTTKECSNCHNKYDIKLDERIYNCPKCG 375
                                       67889**********************8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.54   1.1e+03      14      23 ..     180     189 ..     177     189 .. 0.86
   2 !   15.9   3.8   3.8e-06    0.0076       4      30 ..     351     377 ..     350     378 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.54
                     A2L_zn_ribbon  14 ilnseqgylv 23 
                                       ++n++++y++
  gi|518651847|ref|YP_008141367.1| 180 LINKNSDYYI 189
                                       899*****96 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 3.8e-06
                     A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgas 30 
                                       k+Cs+C++  ++  +  +++C++Cg++
  gi|518651847|ref|YP_008141367.1| 351 KECSNCHNKYDIKLDERIYNCPKCGFI 377
                                       78***********************97 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 ?   11.1   0.1   0.00016      0.31      66      93 ..     346     375 ..     332     379 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00016
                                       EE--EEEETTTS-EEECHHH..HHS-TTTS CS
                              HypA  66 evpvkvrCreCgkefeleek..alrCpkCg 93 
                                        +p + +C++C+++++++ +   ++CpkCg
  gi|518651847|ref|YP_008141367.1| 346 FIPTTKECSNCHNKYDIKLDerIYNCPKCG 375
                                       5788899********9776435789****8 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1      0.02        41      16      24 ..     350     358 ..     343     361 .. 0.87
   2 ?    5.4   0.0    0.0065        13      12      29 ..     364     381 ..     362     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.02
                                       -EE-TTT-- CS
                              RecR  16 vrhCsrCgn 24 
                                        + Cs+C+n
  gi|518651847|ref|YP_008141367.1| 350 TKECSNCHN 358
                                       689*****9 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0065
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + e++  C++Cg + ++d
  gi|518651847|ref|YP_008141367.1| 364 LDERIYNCPKCGFIIDRD 381
                                       678999*******98887 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.1   2.2e+03      22      41 ..     222     240 ..     218     240 .. 0.78
   2 ?    8.7   1.6   0.00061       1.2       3      34 ..     353     383 ..     352     388 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                                       ESSSSBEEEECCCCCCCHHH CS
                      TF_Zn_Ribbon  22 CtdCGlVlednsidegpewr 41 
                                       C++ G++l +n+ ++++e r
  gi|518651847|ref|YP_008141367.1| 222 CSN-GSILNYNIPKSRKEIR 240
                                       554.9999999999999976 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00061
                                       ETTTTCEE.CHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDpergelvCtdCGlVlednsi 34 
                                       C nC++++ + +D+    + C++CG +++ +++
  gi|518651847|ref|YP_008141367.1| 353 CSNCHNKYdIKLDER--IYNCPKCGFIIDRDYN 383
                                       ******999999988..889*****99998776 PP

>> DUF4379  Probable Zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.4   0.00084       1.7      32      56 .]     353     374 ..     352     374 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00084
                           DUF4379  32 CakCgheWeasvsnrtkgsskCpkC 56 
                                       C++C++++  ++++r+   + CpkC
  gi|518651847|ref|YP_008141367.1| 353 CSNCHNKYDIKLDERI--YN-CPKC 374
                                       ****************..88.**** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2458  (0.137096); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.46
# Mc/sec: 3032.28
//
Query:       gi|518651848|ref|YP_008141368.1|  [L=155]
Description: hypothetical protein FACI_IFERC00001G0487 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   1.8      0.032   14.6   1.8    1.3  1  PhoR         Phosphate regulon sensor protein PhoR
        0.1   11.4   5.4       0.11   11.3   5.4    1.1  1  DUF2207      Predicted membrane protein (DUF2207)
          2    8.0   4.9          3    7.5   4.9    1.2  1  DUF4131      Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> PhoR  Phosphate regulon sensor protein PhoR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.8   5.4e-06     0.032       8      66 ..      77     135 ..      69     139 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.4e-06
                              PhoR   8 rlallllaallvgllvgalaallllalllllawhlyqllrLsrWLrkpkklepPdgsGl 66 
                                       +l+ll+la+  +gl +g + +++++a++ +l+ h+  +   s  L+++++    +g+G 
  gi|518651848|ref|YP_008141368.1|  77 LLMLLFLAFGYIGLSIGVFFFVVVIAIFTYLLSHTISVTSYSISLTNGSSIVLAEGTGT 135
                                       6788888888************************9998888888888777777777776 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   5.4   1.8e-05      0.11     380     433 ..      61     111 ..      14     123 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.8e-05
                           DUF2207 380 lkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                       + ++++l ++lii+g++l+ll+l++     ++l+i +++++++++i+++l+s++
  gi|518651848|ref|YP_008141368.1|  61 FRSINILRIILIIVGFLLMLLFLAFG---YIGLSIGVFFFVVVIAIFTYLLSHT 111
                                       66788999999999999888876654...5566666666666655555555554 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   4.9   0.00049         3       7      71 ..      71     130 ..      65     138 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00049
                           DUF4131   7 lvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles...gqeviv 71 
                                       l+++++ll+ll+l++          + l+++++++++++ ++ + ++++ +  s+ +++   +  v+ 
  gi|518651848|ref|YP_008141368.1|  71 LIIVGFLLMLLFLAF--------GYIGLSIGVFFFVVVIAIFTYLLSHTISVTSYSISLtngSSIVLA 130
                                       333344444444443........457999999999999999999999999999998887765555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1361  (0.0759105); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1085.77
//
Query:       gi|518651849|ref|YP_008141369.1|  [L=470]
Description: hypothetical protein FACI_IFERC00001G0488 [Ferroplasma acidarmanus fer1]
Scores for 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   81.2  50.8    8.1e-23   80.8  50.8    1.1  1  AA_permease    Amino acid permease
    6.7e-22   77.9  55.1    9.2e-22   77.5  55.1    1.2  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8  50.8     9e-27   8.1e-23      17     468 ..      34     453 ..      16     463 .. 0.79

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 9e-27
                       AA_permease  17 vglgvvlsqaGplga.llayllagvviflvmlslgeiatngpksggfytyasrflgp...elGfviGlnylfswitv 89 
                                       ++l +v  ++ +++   l+++la++++  ++l ++e +  + ++ + +++ ++  g+    l+f+ G++y ++++++
  gi|518651849|ref|YP_008141369.1|  34 TALFFVGIAGAVGSSmTLVIVLAFIIYCGMTLVTYEWSKEVASAYSWAAFHRKAFGDrgkFLSFYGGISYYYYYLLG 110
                                       44444444444444458999999999999*************9999999999888753438********88888776 PP

                       AA_permease  90 l.aleltaasiliqfwelvtdlpkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg.iill 161
                                       + ++++ ++  ++  +    ++ + w++    +++++  +++n++gvk++ +    + l+ ++a  +f+i++ i l+
  gi|518651849|ref|YP_008141369.1| 111 YtGFAMLGLTAFLYALDPSLAAAYPWIWiplTIIIIGETTVLNFFGVKLSLK----YVLYTGLAEFIFLIGTsIALI 183
                                       526899999999999999999999****888778888889************....****************98888 PP

                       AA_permease 162 aggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailq 238
                                       + ++p +     ++ + ++      ++        + +++++ ++  + +f G  +v+ +a+E+k+P+k+iP a   
  gi|518651849|ref|YP_008141369.1| 184 VIAGPHNS----YVPFTAA-----AVHF-------NYTDIAIEMILGIATFGGLNSVVPVAEETKNPKKNIPLALGI 244
                                       88888888....4444444.....4444.......6799************************************** PP

                       AA_permease 239 vviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvl 315
                                          +i+ + ++s+++ +++ + ++    +   ++  ++ +++k++g++v+a+++ ++i+ +  ss++++ +s+ R+ 
  gi|518651849|ref|YP_008141369.1| 245 LAGLIGAVIIISSYAQSVVYGVTNMFQYANLSDP--GIYVYTKYLGLAVAAVFV-LFIINSFNSSGVAFETSTVRTS 318
                                       ***************9999999997777777777..9**********9998776.5677799*************** PP

                       AA_permease 316 yslakdgl.aPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfR 391
                                       y++a+d++ +Pkv++ ++k++vP + ++++ ++s  + ++++l l++ +++ fl+ ++ +  ++++ ++ + + ++ 
  gi|518651849|ref|YP_008141369.1| 319 YAYARDKIlFPKVFTSINKHKVPGNLVIFTGLLSITIAIVSGLILGPLTASLFLIISNSIFSFSNHAIAGIGLGVYH 395
                                       ******97368*********************************************************999999444 PP

                       AA_permease 392 kalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvkl 468
                                       +           l+++ +l++ +++ + +++ i+++    +++++  ++p +       a+y++ + f+ i+v +++
  gi|518651849|ref|YP_008141369.1| 396 RR-------KGTLRIIQHLIIPWAVAIALVVAIVYV----VYPAP--APPLN------YASYISGIYFVFIIVLYFY 453
                                       44.......334455555544443333333333333....33333..33422......4445444444444444433 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.5  55.1     1e-25   9.2e-22       1     423 [.      15     449 ..      15     461 .. 0.78

  Alignments for each domain:
  == domain 1  score: 77.5 bits;  conditional E-value: 1e-25
                     AA_permease_2   1 lsllsafalvigsv...igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvyt...kaa 71 
                                       ls+++a+a  +g+    + ++ f+++ a+++g + +l++++a +i++  + lv  E s        +y+++   ++a
  gi|518651849|ref|YP_008141369.1|  15 LSMWQALAQGLGTNgpaAVTALFFVGIAGAVGSSMTLVIVLAFIIYCG-MTLVTYEWSK---EVASAYSWAafhRKA 87 
                                       678888887777755567788888889999***************985.7777777887...666788888444566 PP

                     AA_permease_2  72 f...gkkvaflsawfnwfayvpvlasilsvaasyllnalgpdlqg.ntwltyliaiaililvalinirgikesakiq 144
                                       f   gk++ f  ++++ + y+++ ++ + +++ ++l+al+p+l    +w+++ + i+i+  ++++n +g+k s k+ 
  gi|518651849|ref|YP_008141369.1|  88 FgdrGKFLSFYGGISYYYYYLLGYTGFAMLGLTAFLYALDPSLAAaYPWIWIPLTIIIIGETTVLNFFGVKLSLKYV 164
                                       677789999**************9999999***********99874699999999********************** PP

                     AA_permease_2 145 nilgilkillpliiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvseevkk..kd 218
                                        ++g++ ++ +li   i+ +++++++ +  +    +    +++ + ++  +   + +f+G +s++ v+ee k+  k+
  gi|518651849|ref|YP_008141369.1| 165 LYTGLAEFI-FLIGTSIALIVIAGPHNSYVP---FTAAAVHFNYTdIAIEMILGIATFGGLNSVVPVAEETKNpkKN 237
                                       ********5.555555566666666555533...4455666666633444556888**************6666489 PP

                     AA_permease_2 219 vpkaifigllivlvlyllvnia...flgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintav 292
                                       +p+a+ i +++++ + +  + a   ++gv ++ + anls+   ++  ++ ++ g +va+++v++i+ s   ++ ++ 
  gi|518651849|ref|YP_008141369.1| 238 IPLALGILAGLIGAVIIISSYAqsvVYGVTNMFQYANLSD---PGIYVYTKYLGLAVAAVFVLFIINSFNSSGVAFE 311
                                       *****99999999999987776333666666666666665...799999999989********************** PP

                     AA_permease_2 293 igssrvlealardgvlP.rffakvnkfgspiraiiltaivslillllfl...lassaaynfllsvsslgliisylll 365
                                       +++ r+ +a ard++l  ++f ++nk++ p + +i+t ++s+ ++++ +   l++ +a  fl    s+++++  +++
  gi|518651849|ref|YP_008141369.1| 312 TSTVRTSYAYARDKILFpKVFTSINKHKVPGNLVIFTGLLSITIAIV-SgliLGPLTASLFLIISNSIFSFSNHAIA 387
                                       ***************988**********************9544444.44555557788899999999999999999 PP

                     AA_permease_2 366 iigalilrkkrphlkr....pgkilvaiigalfllfllvalffppkgpatqssliytiiltv 423
                                        ig+ ++ +++  l+     +  + vai  ++ ++++++ +  pp + a + s iy ++++v
  gi|518651849|ref|YP_008141369.1| 388 GIGLGVYHRRKGTLRIiqhlIIPWAVAIALVVAIVYVVYPAPAPPLNYASYISGIYFVFIIV 449
                                       88776666665655332233444777887788888877777766666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3247.28
//
Query:       gi|518651850|ref|YP_008141370.1|  [L=221]
Description: NADH dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-25   88.5   0.2    5.1e-24   85.2   0.2    2.0  1  Nitroreductase  Nitroreductase family
    1.4e-05   24.7   0.1       0.22   11.1   0.0    3.0  3  TM1586_NiRdase  Putative TM nitroreductase


Domain annotation for each model (and alignments):
>> Nitroreductase  Nitroreductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.2   0.2   5.7e-28   5.1e-24       1     170 []       7     174 ..       7     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.2 bits;  conditional E-value: 5.7e-28
                                       HHH--B--.-B-S----HHHHHHHHHHHHTS--GGG---EEEEEE.-CCCHHHHHHHHHHHHHHHHTT-SS-GGGGG CS
                    Nitroreductase   1 irkRrSiR.kFddepvpkeelekileaarraPsagnlqpwrfvvvqdkelryklaeaalelllkaeaqaelaqryrk 76 
                                       i+kRr +R +F+d+ ++  +l +il+a+ +aPs g +qpw++++++d e+r+k++  + e+      ++ +  + + 
  gi|518651850|ref|YP_008141370.1|   7 IKKRRDVRsWFSDKHIDNNTLGRILKAGNYAPSVGLSQPWNYILIRDIETRKKIKAVVEEKRMDFYNSLPDEKKIK- 82 
                                       89*************************************************9999999999888888887777776. PP

                                       GHHHHHHHHHHHHSSEEEEE..---TTS---HHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEE-GGGGGHHHHH CS
                    Nitroreductase  77 eelklkaqkalagapvlivi..vatldkserkaaerayryalldagaaaqnllLaAtalGlgscpiggfdeaaeevr 151
                                          ++ + + + ++++ + +  + +    +    + + + +  ++ + ++n++LaA+a+G+g+ +i+++d +   v+
  gi|518651850|ref|YP_008141370.1|  83 --FQNIKIEGILESDLNMAVtcDVSRKGPDILGRATMPEMSEYSVVLSIENMWLAARAEGIGMGWISFIDPDM--VK 155
                                       ..7788888888888888882222222222223344455556789999*************************..** PP

                                       HHHT-S..SEEEEEEEEE- CS
                    Nitroreductase 152 kllglpdeeeivvliavGy 170
                                       k+lg+p+  ++v+ +avGy
  gi|518651850|ref|YP_008141370.1| 156 KILGIPESIKLVGYLAVGY 174
                                       ******99**********9 PP

>> TM1586_NiRdase  Putative TM nitroreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.1   0.00017       1.6       1      30 [.       2      32 ..       2      35 .. 0.87
   2 !    4.0   0.0    0.0035        31     161     200 ..      28      67 ..      24      75 .. 0.72
   3 !   11.1   0.0   2.4e-05      0.22      88     143 ..     129     187 ..     119     208 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00017
                                      -HHHHHHH--B---.B--S---HHHHHHHHH CS
                    TM1586_NiRdase  1 nlyeaiekRhsvRk.Ykdealeeelleelke 30
                                      ++yeai+kR+ vR+ ++d+ +++++l ++ +
  gi|518651850|ref|YP_008141370.1|  2 DVYEAIKKRRDVRSwFSDKHIDNNTLGRILK 32
                                      589**********9689*****999988765 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0035
                                       HHHHHHHHTS--GGG----EEE.E-SSEE.....EEE-S- CS
                    TM1586_NiRdase 161 keileaarlAPsAlNqqpwrfelkdddeikikasvlgkls 200
                                        +il+a  +APs   +qpw   l  d e + k + + + +
  gi|518651850|ref|YP_008141370.1|  28 GRILKAGNYAPSVGLSQPWNYILIRDIETRKKIKAVVEEK 67 
                                       579****************999777644443334444444 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHTT-EEEEES--SST............T-S-EEEEE-BS----...---- CS
                    TM1586_NiRdase  88 geqlvLkltalGlgtcWvggtykk.kkakvelkkgeklvivIalGyaktklv..eakrk 143
                                        e++ L + a+G+g  W+++  +  +k+ + ++++ klv  +a+Gy +++    e ++k
  gi|518651850|ref|YP_008141370.1| 129 IENMWLAARAEGIGMGWISFIDPDmVKKILGIPESIKLVGYLAVGYLSEDHDipELEEK 187
                                       5899***************98877788889****************9998733422222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1579.65
//
Query:       gi|518651851|ref|YP_008141371.1|  [L=136]
Description: NUDIX hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-17   64.4   0.0    1.4e-17   64.0   0.0    1.1  1  NUDIX     NUDIX domain
    2.2e-05   24.4   0.0    2.9e-05   24.0   0.0    1.1  1  NUDIX_4   NUDIX domain


Domain annotation for each model (and alignments):
>> NUDIX  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.0   0.0   1.5e-21   1.4e-17       5     120 ..       2     112 ..       1     121 [. 0.76

  Alignments for each domain:
  == domain 1  score: 64.0 bits;  conditional E-value: 1.5e-21
                                       EEEEEEEETTSEEEEEEES...SSSTTT.EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   5 avgvvllnekgevLlvrrs...kkpfpg.WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgp 77 
                                       a+ ++++n+++ +Ll++r+   ++p++g  +lPgG+ e +E+ e+AA+RE+ EE+Gl+    + lg       y++ 
  gi|518651851|ref|YP_008141371.1|   2 AAVALIFNRDK-FLLIKRAeqdGDPWSGqMALPGGHRERNESCEQAAIRETMEEVGLPITVKRSLG------IYHTL 71 
                                       67788999995.*******777777777668*************************9888899999......33333 PP

                                       EEEEEEEEEEEEEEECSGCSSTSTTTEEEEEEEEHHHH.HHHHT CS
                             NUDIX  78 ygdeheilyvfleevegelepndenevsevrwvpleel.lkekl 120
                                       +g  +  +  +++  +++  ++ +ne+s++ w + eel  k + 
  gi|518651851|ref|YP_008141371.1|  72 NG--NVSVEAYECFSTETAIHP-DNEISKYFWATREELmHKNET 112
                                       33..233335566666666666.***************433333 PP

>> NUDIX_4  NUDIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   3.2e-09   2.9e-05       1      95 [.       3     106 ..       3     112 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 3.2e-09
                                       EEEEEEECTEEEEEE--TTS..SSTT-EE-SEEE.-TTS-HHHHHH...HHHHS-EEEEEEEEEEEEEETTEEEEEE CS
                           NUDIX_4   1 avllirddgrvllekRpekg..llggLwefPgge.eegeeleeala...reelgieveelepgtvkHvftHfrltlt 71 
                                       av+li +++++ll kR e++   + g + +Pgg+ e +e+ e+a++    ee+g+ ++  + + + H++    + ++
  gi|518651851|ref|YP_008141371.1|   3 AVALIFNRDKFLLIKRAEQDgdPWSGQMALPGGHrERNESCEQAAIretMEEVGLPITVKRSLGIYHTLNG-NVSVE 78 
                                       6899************9975469********9996777775666554666788875443334556699987.88888 PP

                                       EEEE...EEE..S..---...EEEEEEGGGG CS
                           NUDIX_4  72 vylv...rve.egeeapa...elrwvtpeel 95 
                                        y++   +++ + +   +   ++ w+t+eel
  gi|518651851|ref|YP_008141371.1|  79 AYECfstETAiHPD---NeisKYFWATREEL 106
                                       88887553332333...1456*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 932.05
//
Query:       gi|518651852|ref|YP_008141372.1|  [L=433]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-26   92.6  31.1    2.2e-26   92.6  31.1    1.9  1  MFS_1     Major Facilitator Superfamily
    7.2e-23   81.2  33.6    7.1e-22   77.9   9.2    2.2  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6  31.1   2.5e-30   2.2e-26      12     352 ..      42     379 ..      30     380 .. 0.74

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 2.5e-30
                             MFS_1  12 rsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwl 87 
                                       ++  +p++++++ ++l +  + +gl++++   ga+++s+++G+++drfGrr+++++ l+lf+++ ++l+ ++++l++
  gi|518651852|ref|YP_008141372.1|  42 IFS-IPMISIFVEHSLRFGTTMLGLVTGATIGGASIGSVLGGYMVDRFGRRKLFFFNLILFLIS-AILSaLSINLTM 116
                                       333.444455999999999*********************************************.55553679*99* PP

                             MFS_1  88 llvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslg......Wravfyil 157
                                       l+++r+l+G+ aga +++++++i +  ++ +r    ++ ++++s+++  l   +  ll+s  g      W  + +i 
  gi|518651852|ref|YP_008141372.1| 117 LVIFRFLAGIPAGADIANVYSYIMETEKPGHREVTGAYNTLMASVAIlGLNGSVVILLIS--GlkataiWKIAILIQ 191
                                       ***************************998777766666666666653232333333333..3558899******** PP

                             MFS_1 158 aivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw...illialllfffgfsglltllp 231
                                        i  l++++    + + ++++ ++ s ke          ++ +++l++++v w   ++ +++ +++ +  g+++++ 
  gi|518651852|ref|YP_008141372.1| 192 IIPVLFLLL---SYKRIPESDIWKASNKEA-------TYIDFFRKLRHNRVQWrtsMYSWCCGIASGIEVGTFAFFI 258
                                       ******988...999999999999999888.......7777899********9966555555555545555666666 PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtssavllll.. 305
                                        y+   +g+sg++     + ++++ ++++   ag+l  + l++   + l++++++l+++gl++ +++    ++++  
  gi|518651852|ref|YP_008141372.1| 259 PYIILKFGISGAINDR--FIIIGIYSIGI--PAGYLGpKILPKIGLRKLSYSGFALSFAGLVISGLALLFNIYIVlp 331
                                       678*******545555..44444444333..7777774447778899********************6666666644 PP

                             MFS_1 306 vlvliGf.glgfv..fpsllalasdlappeeagtasglfntagslggalg 352
                                       v   + +  +g    + ++++  + +a  +++g+a+g+ n++++l ++l+
  gi|518651852|ref|YP_008141372.1| 332 V--SMMIfVWGNHwnNEPITTSQALVADSDMRGKAVGISNFIYQLPSFLS 379
                                       2..3222233333444444444444445589**************99986 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   9.2     8e-26   7.1e-22      45     206 ..      60     217 ..      30     231 .. 0.90
   2 !   12.0  14.6   7.9e-06     0.071     242     439 ..     220     416 ..     212     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 8e-26
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                       ++ +gl++++++ Ga iGs+++g+++drfGR+k + +  +lf+i+a+l+a++    ++ +l++ R+l+Gi++G+  +
  gi|518651852|ref|YP_008141372.1|  60 TTMLGLVTGATIGGASIGSVLGGYMVDRFGRRKLFFFNLILFLISAILSALSI---NLTMLVIFRFLAGIPAGADIA 133
                                       46789************************************************...9******************** PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHH..HHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilv..aaifglglnktsnadgwrillglqlvpallllilllflPESPr 196
                                        v  yi E  ++ +R   + ++ l+ ++ il   ++++ l ++  +++  w+i + +q++p l+ll+    +PES  
  gi|518651852|ref|YP_008141372.1| 134 NVYSYIMETEKPGHREVTGAYNTLMASVAILGlnGSVVILLISGLKATAIWKIAILIQIIPVLFLLLSYKRIPESDI 210
                                       *****************************98622566666667777799**************************88 PP

                                       HHHHTT-HHH CS
                          Sugar_tr 197 ylvekgkeee 206
                                       +  +++   e
  gi|518651852|ref|YP_008141372.1| 211 WKASNK---E 217
                                       877766...4 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 7.9e-06
                                       HTTHHHHSH....HHHHHHHHHHHHHHTTHHH..HHHHTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 242 wkellsskt.vrqrlligvvlqifqqltGina..imyysptifenlglsks...llvtiivgvvnfvatfvaiflvd 312
                                       +  ++++   +r +  + +  +++   +Gi +  + ++ p+i+ + g+s       + i+++ + + a   +  +  
  gi|518651852|ref|YP_008141372.1| 220 YIDFFRKLRhNRVQWRTSMYSWCCGIASGIEVgtFAFFIPYIILKFGISGAindRFIIIGIYSIGIPAGYLGPKILP 296
                                       44555554455666666667777777777765337789999999999999954444445555555555555568999 PP

                                       HS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHH.SHTTTHHHHH CS
                          Sugar_tr 313 rfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsEl.fpqsvRskal 388
                                       ++G R+l   G+a  ++ +vi g  al l +      iv+ v +++f  + +  w+  p  +++ l +++++R+ka 
  gi|518651852|ref|YP_008141372.1| 297 KIGLRKLSYSGFALSFAGLVISG-LAL-LFNI----YIVLPVSMMIF--VWGNHWNNEPITTSQALvADSDMRGKAV 365
                                       *************9999999998.333.3333....47777777776..5666688888778777626789****** PP

                                       HHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS-- CS
                          Sugar_tr 389 aiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpe 439
                                        i+ ++  l +fl   +fpi+++aig gy+ lv a+   ++ii+++  + e
  gi|518651852|ref|YP_008141372.1| 366 GISNFIYQLPSFLSISIFPIMFSAIGMGYSTLVVAIASFAGIIITLAVFNE 416
                                       *******************************************99877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3298.66
//
Query:       gi|518651853|ref|YP_008141373.1|  [L=379]
Description: sugar transporter related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-07   28.0  34.0    9.9e-07   28.0  34.0    2.1  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
          5    6.8   6.3        4.2    7.0   0.3    2.5  2  DUF4131   Domain of unknown function (DUF4131)


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 !   28.0  34.0   1.1e-10   9.9e-07       9     350 ..      16     338 ..       8     341 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.1e-10
                             MFS_1   9 alarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdr.fGrrrvlllglllfalglllllfass 84 
                                       ++  s+l+++ p +l++    ++  +g+++ +  +++ + ++++ +l  + +   +++ ++++l ++ ll ++f  +
  gi|518651853|ref|YP_008141373.1|  16 SFILSMLAVITPFYLSKF-V-NVFDVGIIVLFSIAFSTLIIYVFPALNIKnW--LKMYAISAALAIALLLNFIF-MN 87 
                                       566678888888555554.4.7999999777777777777777777766645..67777777777777566666.78 PP

                             MFS_1  85 lwlllvlrvlqGlgaga.....lfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfy 155
                                       +++++++ +l ++  ++       p+ ++++a++ ++ + + +a++l++ ++  ++i++  l  +++ ++ +r vf+
  gi|518651853|ref|YP_008141373.1|  88 FYVFIFSLMLGSISLSGrdispNQPIEQYAMAHYETDmKSKRMAFSLYNFFSYGASIIA-SLFLFFYVNIDYRIVFL 163
                                       77777777777777776111115566666666666664477777788887777777777.55588888********* PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg.lltllp 231
                                       +l++v+l  fv   l+l+ + p++kr ++k++        + +  k +++        + +++ +f+  + +++++ 
  gi|518651853|ref|YP_008141373.1| 164 LLTLVALCQFV---LYLFIRFPQHKRMKGKDL-------DVET-KKRVFSLS------YLFAMDSFAGGMvTVSMIS 223
                                       ***********...888888888888888888.......2333.33333333......2222223233334889999 PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlv 308
                                       ly++ v+++s l +agl++ ++ +++ i+ l++  +s ++g  r+++ + ++  ++++++ ++ v    +++ ++l+
  gi|518651853|ref|YP_008141373.1| 224 LYFKYVYHIS-LSTAGLIFVAVNIITTISILISPLISSKIGLIRTMVYTHSVSNIFLMLVPVIHVL---AISEIFLF 296
                                       999*******.******************************9999999999988888888888888...55555666 PP

                             MFS_1 309 liGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                       l  +++ + +p+  +l++ ++ ++++   +++f+ +++ + +
  gi|518651853|ref|YP_008141373.1| 297 LRQTTSQMDVPARDTLINTVIEENYRVNSNSIFSAVRNGALI 338
                                       666677777888888888888888888888888888876655 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.3     0.019   1.7e+02       5      39 ..      66      98 ..      38     117 .. 0.69
   2 ?    7.0   0.3   0.00046       4.2      10      56 ..     140     186 ..     133     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.019
                           DUF4131  5 lalvllalllllllllllllrrrprrrvlllllll 39
                                      l+  ++ ++l+++lll +++   + + ++++l+l 
  gi|518651853|ref|YP_008141373.1| 66 LKMYAISAALAIALLLNFIF--MNFYVFIFSLMLG 98
                                      44556666666666666666..5566666655554 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00046
                           DUF4131  10 lalllllllllllllrrrprrrvllllllllllallgfalrapqpna 56 
                                        ++ +++ l+l+++ +  +r  +lll l++l+ ++l++++r pq+ +
  gi|518651853|ref|YP_008141373.1| 140 YGASIIASLFLFFYVNIDYRIVFLLLTLVALCQFVLYLFIRFPQHKR 186
                                       56666777777777665666666666666666678888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 2653.67
//
Query:       gi|518651854|ref|YP_008141374.1|  [L=437]
Description: hypothetical protein FACI_IFERC00001G0493 [Ferroplasma acidarmanus fer1]
Scores for complete 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-111  372.4   0.0   3.1e-111  372.2   0.0    1.1  1  Aldedh         Aldehyde dehydrogenase family
    3.6e-05   23.0   0.8    0.00021   20.5   0.7    2.1  1  LuxC           Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.075   13.2   0.0        1.2    9.2   0.0    2.4  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
        1.7    8.9   3.4        1.3    9.2   0.6    2.2  2  WHEP-TRS       WHEP-TRS domain


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 !  372.2   0.0  6.8e-115  3.1e-111       9     462 .]       3     434 ..       1     434 [. 0.96

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 6.8e-115
                                       EEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH---HHH CS
                            Aldedh   9 ievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaeletletGkplae 85 
                                       i ++nP+t++++++++ a+ edv++ +++ ke + +w++ ++ +R ++L++  + +e++ e la+l++ e+Gkp+++
  gi|518651854|ref|YP_008141374.1|   3 ISTFNPFTEKELGRYKVASLEDVKETIRNLKENQLKWRE-NIDKRIDMLKESKKNFEKNVESLATLMSSEMGKPISQ 78 
                                       7899**********************************9.9************************************ PP

                                       HHHHHHHHHHHHHHHHHHHHH.HSEEEEEECTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT-EEEEEE CS
                            Aldedh  86 araeveeaidvlryyaelaek.legevlpssegklalvrrePlGvvgaItPWNfPlllaawklapalaaGNtvvlKP 161
                                       + aev+++++ ++yy+e  ek le e + + e k++++r +PlGv+ +I+PWNfPl  +a++++pal+aGN+v+lK 
  gi|518651854|ref|YP_008141374.1|  79 SIAEVQKTLRLFDYYIENGEKfLENEYIHT-EAKKSYIRFDPLGVIIIIMPWNFPLWQVARAAIPALLAGNAVLLKH 154
                                       *********************888899888.69******************************************** PP

                                       -TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSEEEEEE-- CS
                            Aldedh 162 aeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkrvtlElGG 238
                                       a+ ++ s+l++ elf+      + +    ++g+ + +a+  +   d vsftGst+ g  ia++a+kn+k++++ElGG
  gi|518651854|ref|YP_008141374.1| 155 ASIVSGSSLKIQELFNL-----DTFRSTITTGKIIDDAIKFS---DGVSFTGSTAAGSIIAAEAGKNIKKFVMELGG 223
                                       ****************9.....55555555699999999765...899***************************** PP

                                       -EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB---SSHH CS
                            Aldedh 239 knplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdvGPlisea 315
                                        +p ivl++ ++d+av++ v + + n+GQ Cia +r+l+++siydef  +++e+++++kvgd+ld+dt +GPl s +
  gi|518651854|ref|YP_008141374.1| 224 SDPYIVLDSSNIDEAVKNSVYARLQNNGQSCIASKRFLINDSIYDEFSRRMLEEYSRVKVGDQLDKDTYIGPLSSVS 300
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHHHHHHHHS CS
                            Aldedh 316 qlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeeeaieiaNd 392
                                       q + ++k+++e k+ g  + +G        + g++++P +++     ++ + eE+FGP++++ +fk+++eai++aNd
  gi|518651854|ref|YP_008141374.1| 301 QKDIITKQLKELKSMGTVISTGD-------NFGNVIRPALVKM----DKDYGEEVFGPIAMLSRFKTIDEAIKLAND 366
                                       ****************9999977.......68********993....55589************************* PP

                                       SSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 393 teyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       t+yGL+ ++++ d+++ae+++  +e G+v iN+  ++++   pfgG k+Sg+Gre +++g+ e+t++ktv
  gi|518651854|ref|YP_008141374.1| 367 TPYGLGCSIWG-DPDNAEKLVPYIESGTVSINKIVASDPRL-PFGGTKKSGIGRELSRYGILEFTNIKTV 434
                                       ***********.99*************************99.**************************98 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.7   4.7e-08   0.00021      74     263 ..     103     277 ..      21     292 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 4.7e-08
                              LuxC  74 deflktke.ksyekaqprglvlhvlsgNvpllpvm.silqglLvknvnllkvSssdpflaaallksladvdenhtla 148
                                       +e+++t++ ksy++  p g+++ +++ N pl  v  + + +lL++n+ llk  s  ++ + ++ ++l ++d      
  gi|518651854|ref|YP_008141374.1| 103 NEYIHTEAkKSYIRFDPLGVIIIIMPWNFPLWQVArAAIPALLAGNAVLLKHASIVSGSSLKI-QELFNLDT----- 173
                                       4566665569*********************999736779***********998777766665.56777776..... PP

                              LuxC 149 dslsvvyfksgdtkleeeivqnaDvvvawGgeeaikaiseklkpgkq..likfGakvSfavvdkealeeealdkaae 223
                                          s +       k+ + +++ +D+v+  G+ +a ++i++++  + +  +++ G      v+d++      +d+a++
  gi|518651854|ref|YP_008141374.1| 174 -FRSTI----TTGKIIDDAIKFSDGVSFTGSTAAGSIIAAEAGKNIKkfVMELGGSDPYIVLDSSN-----IDEAVK 240
                                       .33455....4557777777*****************99955544331156688888888888888.....666666 PP

                              LuxC 224 raAkDiivfdQqAClspqvvfvekddkieidefaeaLaaa 263
                                       +        + q+C++++  +++      +def++++ ++
  gi|518651854|ref|YP_008141374.1| 241 NSVYARLQNNGQSCIASKRFLIND---SIYDEFSRRMLEE 277
                                       666666677999999999999993...4799999988544 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 ?    9.2   0.0   0.00028       1.2       9      92 ..      71     157 ..      67     174 .. 0.76
   2 ?    1.1   0.0     0.091   4.1e+02      84     112 ..     227     255 ..     200     257 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHH..HHCSEEEE-SSSHHHHHHHHHSHCCC-.-T CS
                     NAD_binding_2   9 vMGsnmalnllkagykvavynrtkekveelvaegakaaesieelv..asldvvitmvkagkavdevieglleal.kk 82 
                                       +MG+++ + +++ + ++ +++   e+ e++++++   +e  ++ +  + l v+i++++ + +  +v +  ++al + 
  gi|518651854|ref|YP_008141374.1|  71 EMGKPISQSIAEVQKTLRLFDYYIENGEKFLENEYIHTEAKKSYIrfDPLGVIIIIMPWNFPLWQVARAAIPALlAG 147
                                       7********************************97666655554411456999999999999999999966655144 PP

                                       T-EEEE-S-- CS
                     NAD_binding_2  83 gdilidgsts 92 
                                       +++l+ ++++
  gi|518651854|ref|YP_008141374.1| 148 NAVLLKHASI 157
                                       4455555554 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.091
                                       -EEEE-S---HHHHHHHHHHHHHTT-EEE CS
                     NAD_binding_2  84 dilidgstsspedtrelakelkekglkfl 112
                                        i++d+s+++ +  + ++++l+++g + +
  gi|518651854|ref|YP_008141374.1| 227 YIVLDSSNIDEAVKNSVYARLQNNGQSCI 255
                                       5899*****************99987665 PP

>> WHEP-TRS  WHEP-TRS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.6    0.0003       1.3      10      41 ..      27      59 ..      23      63 .. 0.90
   2 ?   -2.0   0.1      0.95   4.2e+03      25      36 ..     305     313 ..     300     315 .. 0.51

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0003
                          WHEP-TRS 10 elVRkLKaek.apkdeidaaVkkLLaLKaqyka 41
                                      e +R LK+++ +  + id+ +  L++ K+++++
  gi|518651854|ref|YP_008141374.1| 27 ETIRNLKENQlKWRENIDKRIDMLKESKKNFEK 59
                                      689*****997777***************9975 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.95
                          WHEP-TRS  25 idaaVkkLLaLK 36 
                                       i ++ k+L   K
  gi|518651854|ref|YP_008141374.1| 305 ITKQLKEL---K 313
                                       55555544...4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      662  (0.0369234); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.35s 00:00:00.98 Elapsed: 00:00:00.49
# Mc/sec: 2665.95
//
Query:       gi|518651855|ref|YP_008141375.1|  [L=308]
Description: hypothetical protein FACI_IFERC00001G0494 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-27   94.3   0.0    1.3e-26   93.7   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    7.4e-07   29.7   0.0    9.4e-07   29.3   0.0    1.2  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 !   93.7   0.0   1.4e-30   1.3e-26       2     244 ..       3     228 ..       2     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.4e-30
                                       EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEE CS
                   NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlia 78 
                                       + ILaGG+G+RL P+t  ++k lv + +++++++ +l    n gi++ +++l+ + s+ +ee +k+ ++++  + ++
  gi|518651855|ref|YP_008141375.1|   3 GAILAGGYGKRLKPITDHIPKALVEIKDNYTIMDRQLFDFKNIGITD-VYILSGYLSEVIEERYKNYKDMN--IHYL 76 
                                       67*********************************************.*******************9877..**** PP

                                       EESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECT CS
                   NTP_transferase  79 lepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGvieade 155
                                        e+++ gt  ++    + +++++     +v +gD +++ +++ +v++ ++++      ++++ ++ ++ yG++e+++
  gi|518651855|ref|YP_008141375.1|  77 REDKPMGTLFSLSNLMKNINEDA-----IVRNGDTVTDINFRSFVEFSKSRDY----DVVMYVTKMQSPYGIVEFSG 144
                                       ***********999999999877.....9******************999999....355566777899******98 PP

                                       TSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-E.. CS
                   NTP_transferase 156 egrverfvEKPkeakaselassGiYvfnsevllflak.dleelkrgedeitdilpkaleegkvalaflfkdaeyW.. 229
                                        ++v +f EKP+ +    ++++G+Y+ ++++++   + ++     ++d  ++++p+++++ +  ++ ++++   W  
  gi|518651855|ref|YP_008141375.1| 145 -DKVDNFREKPELNH---YINAGLYYVKKSAFEAFFRkYM-----EKDIEKSVFPYLVNNNRMGVY-CEDA--LWlg 209
                                       .6***********77...***************9976333.....334444555555555444443.3333..3533 PP

                                       ....EEXSSHHHHHHHHHH CS
                   NTP_transferase 230 ....sDvGtldslleanek 244
                                           +D+Gt++ l++  e+
  gi|518651855|ref|YP_008141375.1| 210 idseKDLGTIKELYKGRED 228
                                       33337******99998766 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0     1e-10   9.4e-07       1     124 [.       3     132 ..       3     174 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1e-10
                                       EEEEEESS-TTTTT.....THHHHCC.CCCCHHHHHHHHHCTT.-CEEEEECSH.....CHHHHHHTTCTS-EEE-T CS
                      NTP_transf_3   1 aviLAGGrSsRmgg.....dKallpl.ggkpllervldalraagvdevvvvggd.....eevlaalarlgvrvvede 66 
                                       ++iLAGG ++R++      +Kal+++ ++ ++++r+l  ++  g+ +v++  g+     ee ++ +++ ++++++++
  gi|518651855|ref|YP_008141375.1|   3 GAILAGGYGKRLKPitdhiPKALVEIkDNYTIMDRQLFDFKNIGITDVYILSGYlseviEERYKNYKDMNIHYLRED 79 
                                       68**********8444579*******9999************************9755557777888999*****98 PP

                                       TSS-SHHHHHHHHHHHH.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                      NTP_transf_3  67 dpgkgplaslaaalraaadadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                       +   g+l sl   ++++  ++ ++v  +D+  +t    + +++  +++++dvv+ +++
  gi|518651855|ref|YP_008141375.1|  80 K-PMGTLFSLSNLMKNI--NEDAIVRNGDT--VTDINFRSFVEFSKSRDYDVVMYVTK 132
                                       6.58***********98..68899999999..56667888888888888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2182.29
//
Query:       gi|518651856|ref|YP_008141376.1|  [L=116]
Description: hypothetical protein FACI_IFERC00001G0495 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.1   0.0      0.085   13.0   0.0    1.1  1  DUF4732   Domain of unknown function (DUF4732)


Domain annotation for each model (and alignments):
>> DUF4732  Domain of unknown function (DUF4732)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.7e-06     0.085      55     117 ..      26      89 ..       9     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.7e-06
                           DUF4732  55 sqplc.lcmetlpeedfthlevlqaleaqlpgalesgrvssirfenlnvicgtagrrnrwliav 117
                                       s+ lc + +  +  ed+   +vl a e ++   le   + + + e++n++ g a r n+w +  
  gi|518651856|ref|YP_008141376.1|  26 SEDLCdFILSFFGYEDYIIDNVLSAAERDVFYNLEEYGIVTTHREEINIVHGKAWRINQWYLDK 89 
                                       566663345566789****************9999988889999****************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 839.08
//
Query:       gi|518651857|ref|YP_008141377.1|  [L=237]
Description: Bacterio-opsin activator HTH protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.1   0.6    8.1e-16   57.6   0.1    2.1  2  HTH_10    HTH DNA binding domain
     0.0025   17.7   0.0       0.28   11.1   0.0    3.2  3  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.091   12.8   0.6        9.3    6.4   0.0    3.1  3  HTH_Mga   M protein trans-acting positive regulator (MGA) HTH


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.087   5.2e+02      27      44 ..      74      91 ..      71      97 .. 0.81
   2 !   57.6   0.1   1.3e-19   8.1e-16       1      53 []     169     221 ..     169     221 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.087
                            HTH_10 27 keLAkelGIskstlsehL 44
                                      ++++++l +s s++ + L
  gi|518651857|ref|YP_008141377.1| 74 SAISEILRVSSSAYRKNL 91
                                      689999999999998877 PP

  == domain 2  score: 57.6 bits;  conditional E-value: 1.3e-19
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaesklie 53 
                                       LTd++  ++  Ay++GYF+ PR+  l+eLA + G+sks+l+e++rka+ k+++
  gi|518651857|ref|YP_008141377.1| 169 LTDQEAFTVYMAYQNGYFNIPREKYLSELATITGLSKSALEEYMRKATGKIMD 221
                                       9**************************************************95 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.048   2.9e+02      14      33 ..      20      39 ..      18      40 .. 0.85
   2 ?    0.4   0.0       0.1   6.1e+02      18      31 ..      73      86 ..      71      87 .. 0.84
   3 !   11.1   0.0   4.6e-05      0.28      14      37 ..     190     213 ..     186     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.048
                                      SSEEHHHHHHHHTS-HHHHH CS
                             HTH_5 14 gelcvcelaeelglsqstvS 33
                                       e+c +e+++ l+++  tvS
  gi|518651857|ref|YP_008141377.1| 20 HERCWTEITDGLNVNIHTVS 39
                                      599**********9977776 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.1
                                      HHHHHHHHTS-HHH CS
                             HTH_5 18 vcelaeelglsqst 31
                                      ++ ++e+l++s s+
  gi|518651857|ref|YP_008141377.1| 73 SSAISEILRVSSSA 86
                                      5789******9986 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 4.6e-05
                                       SSEEHHHHHHHHTS-HHHHHHHHH CS
                             HTH_5  14 gelcvcelaeelglsqstvShHLk 37 
                                       +e++ +ela ++gls+s++ ++ +
  gi|518651857|ref|YP_008141377.1| 190 REKYLSELATITGLSKSALEEYMR 213
                                       68999*************998876 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 ?    1.7   0.1     0.044   2.6e+02      25      56 ..      75     104 ..      64     107 .. 0.87
   2 ?    0.7   0.0     0.089   5.3e+02      33      45 ..     135     147 ..     135     157 .. 0.87
   3 ?    6.4   0.0    0.0015       9.3      22      43 ..     193     214 ..     190     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.044
                           HTH_Mga  25 elakeLglseltlqsdiseLnelFpeelsivi 56 
                                        +++ L+ s+++ ++ + e+   F+e++s +i
  gi|518651857|ref|YP_008141377.1|  75 AISEILRVSSSAYRKNLYEVS--FKEKYSNMI 104
                                       799****************99..***999777 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.089
                           HTH_Mga  33 seltlqsdiseLn 45 
                                       s +tl+s +seL 
  gi|518651857|ref|YP_008141377.1| 135 SVKTLKSSLSELG 147
                                       789*******996 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0015
                           HTH_Mga  22 tldelakeLglseltlqsdise 43 
                                       +l+ela+ +gls ++l ++ ++
  gi|518651857|ref|YP_008141377.1| 193 YLSELATITGLSKSALEEYMRK 214
                                       589*************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1714.48
//
Query:       gi|518651858|ref|YP_008141378.1|  [L=253]
Description: hypothetical protein FACI_IFERC00001G0497 [Ferroplasma acidarmanus fer1]
Scores for complete 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-58  196.4   0.0    6.3e-58  196.1   0.0    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    5.7e-47  159.7   1.3    6.8e-47  159.5   1.3    1.0  1  adh_short     short chain dehydrogenase
    3.9e-16   59.5   0.1    5.1e-16   59.1   0.1    1.1  1  KR            KR domain
      1e-05   25.1   0.1    1.7e-05   24.4   0.1    1.3  1  Epimerase     NAD dependent epimerase/dehydratase family
    0.00053   19.5   0.3    0.00073   19.0   0.3    1.1  1  DUF1776       Fungal family of unknown function (DUF1776)
  ------ inclusion threshold ------
      0.031   14.2   0.1      0.057   13.3   0.1    1.5  1  3HCDH_N       3-hydroxyacyl-CoA dehydrogenase, NAD binding do


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 !  196.1   0.0   2.1e-61   6.3e-58       3     233 ..      14     248 ..      11     249 .. 0.94

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 2.1e-61
                                       TTSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   3 asgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnn 76 
                                        +gIG +iAkala++Ga+v++t+ n+++ ++++ +  ++ g +   +++D +d  +++ l++ +++kf+++D+lvnn
  gi|518651858|ref|YP_008141378.1|  14 SRGIGNGIAKALADNGANVIITYGNNDNaADETVKYIRSKGVSGekYKIDQSDIGEIDGLMKFIKDKFKTVDVLVNN 90 
                                       59*********************99999755555555555544235******************************* PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC...CEEEEEEEGGGTSBSTTTTHHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalplmkeg...gsivnlssvgaervvpnynaygaaKaalea 150
                                       agi+p    +f +++++ f+++ +vn+ s f +++++ ++m e+   g+i+ +ss++a ++ + +++y+++K a+++
  gi|518651858|ref|YP_008141378.1|  91 AGICPF--MDFFNIDQNLFEKVWKVNVESHFFITQRVSQMMIENntkGKILFISSISAIVGGKFQAHYTTTKSAMNG 165
                                       ******..*******************************88776689****************************** PP

                                       HHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEE CS
                      adh_short_C2 151 ltrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtl 227
                                       l+++lA  lg++gi vN+  pg i T+++++  ++++ +e++e+r+pl+rlg+p+++a+ alfL+sde++yi+G++l
  gi|518651858|ref|YP_008141378.1| 166 LMHSLAIILGEHGIMVNSLEPGTILTDINTEDLSNKKKREYMENRIPLRRLGNPSDIASPALFLVSDENTYINGAEL 242
                                       ****************************8888889999*************************************** PP

                                       EESTTG CS
                      adh_short_C2 228 vvDgGl 233
                                        vDgG+
  gi|518651858|ref|YP_008141378.1| 243 LVDGGM 248
                                       *****8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5   1.3   2.3e-50   6.8e-47       1     192 [.       6     199 ..       6     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 2.3e-50
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       k ++vtG+s+GIG  iak+la +Ga+v++ ++++++++ e++k ++++g +   +++D +d  e++ l++ +++k++
  gi|518651858|ref|YP_008141378.1|   6 KNAIVTGGSRGIGNGIAKALADNGANVIItYGNNDNAADETVKYIRSKGVSGEKYKIDQSDIGEIDGLMKFIKDKFK 82 
                                       789**************************9*********************************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAs 152
                                       ++dvLvnNAGi  + +f +++++ +e+v +vN+ + f +t+ v ++m+ ++ +G+I ++sS+ + v+ + +a Y+++
  gi|518651858|ref|YP_008141378.1|  83 TVDVLVNNAGICPFMDFFNIDQNLFEKVWKVNVESHFFITQRVSQMMIeNNTKGKILFISSISAIVGGKFQAHYTTT 159
                                       ************************************************8999************************* PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                       K a++gl++sla  l ++gi vn++ PG + Td+++e  +
  gi|518651858|ref|YP_008141378.1| 160 KSAMNGLMHSLAIILGEHGIMVNSLEPGTILTDINTEDLS 199
                                       **********************************998765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.1   1.7e-19   5.1e-16       4     162 ..       9     169 ..       7     183 .. 0.92

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 1.7e-19
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tGG  g+G  +a+ la++ga+ ++  + +   d++++++++ ++++g++ e +++D sd  ++  l++ ik++++
  gi|518651858|ref|YP_008141378.1|   9 IVTGGSRGIGNGIAKALADNGANVIITYGNN---DNAADETVKYIRSKGVSGEKYKIDQSDIGEIDGLMKFIKDKFK 82 
                                       89***************************99...6677779************************************ PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT.....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled.....esldffvlfSSiagllgsagqanYaaa 152
                                       ++   ++ Ag+     + + +++ +e+v +  v+    + + +++     ++   ++++SSi++++g + qa+Y+++
  gi|518651858|ref|YP_008141378.1|  83 TVDVLVNNAGICPFMDFFNIDQNLFEKVWKVNVESHFFITQRVSQmmienNTKGKILFISSISAIVGGKFQAHYTTT 159
                                       ***********************************988888777755554555678999****************** PP

                                       HHHHHHHHHH CS
                                KR 153 NaflDalaey 162
                                        + +++l+++
  gi|518651858|ref|YP_008141378.1| 160 KSAMNGLMHS 169
                                       *******997 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.1   5.8e-09   1.7e-05       2     121 ..       9     150 ..       8     165 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 5.8e-09
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..........EEEE--TT-HHHHHHHHHHH..T-S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..........elveldltdrsalerlfkee..qpd 66 
                                       +VtG++  iG+ ++kal+++g +vi    ++++ + +  + +          ++ + d+ + + l +++k++   +d
  gi|518651858|ref|YP_008141378.1|   9 IVTGGSRGIGNGIAKALADNGANVIITYGNNDNAADETVKYIrskgvsgekyKIDQSDIGEIDGLMKFIKDKfkTVD 85 
                                       8**********************8877777454444444444999*************************99889** PP

                                       EEEE--S---HHHHHHSHHHH....HHHHTH....HHHHHHHHHHHHTCT.EEEEEEE.GGGGTS CS
                         Epimerase  67 avihlAavggvaassedpadf....ieknlq....gtlnlleaarkagvk.rllflsS.sevYGk 121
                                       + ++ A+++  ++ ++  + +    ++ n++    +t+++ +++ +++ k ++lf+sS s++ G 
  gi|518651858|ref|YP_008141378.1|  86 VLVNNAGICPFMDFFNIDQNLfekvWKVNVEshffITQRVSQMMIENNTKgKILFISSiSAIVGG 150
                                       *******888888776665541222444544333389**********9999*******8888874 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 !   19.0   0.3   2.4e-07   0.00073     110     214 ..     101     205 ..      93     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 2.4e-07
                           DUF1776 110 tiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelr 186
                                       +i  + ++++ + ++ s + ++q+  + + +++ +k ki++   sis+ +  +f+a  +++ sa++ l+++L+  l+
  gi|518651858|ref|YP_008141378.1| 101 NIDQNLFEKVWKVNVESHFFITQRVSQMMIENN-TKGKILF-ISSISAIVGGKFQAHYTTTKSAMNGLMHSLAIILG 175
                                       788888999999999999999999999999866.7888765.579******************************** PP

                           DUF1776 187 phnidvtqikLGnl..dlangsqsnskias 214
                                       +h+i v  +  G++  d+  +  sn+k+ +
  gi|518651858|ref|YP_008141378.1| 176 EHGIMVNSLEPGTIltDINTEDLSNKKKRE 205
                                       **********99984455445556655554 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.9e-05     0.057      10      78 ..      17      85 ..       8     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                                      CHHHHHHHHHHTT-EEEEE-S-HHHH.HHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC CS
                           3HCDH_N 10 mGagiaavfasagleVvlvdiseeal.ekalekieksleklvekgklkeeeveaalarisfttdleeavd 78
                                      +G+gia+++a +g +V ++  +++ + ++  + i++      ek k++++++ ++   ++f +d  + vd
  gi|518651858|ref|YP_008141378.1| 17 IGNGIAKALADNGANVIITYGNNDNAaDETVKYIRS-KGVSGEKYKIDQSDIGEIDGLMKFIKDKFKTVD 85
                                      8***************99887666550555555555.555568889999999888888888777665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); 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: 0.46u 0.33s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1683.75
//
Query:       gi|518651859|ref|YP_008141379.1|  [L=40]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                        86  (0.0047967); expected 358.6 (0.02)
Passed bias filter:                       83  (0.00462937); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 281.30
//
Query:       gi|518651860|ref|YP_008141380.1|  [L=453]
Description: hypothetical protein FACI_IFERC00001G0499 [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  113.7  63.4    8.8e-26   90.7  36.5    2.0  2  MFS_1     Major Facilitator Superfamily
    2.4e-30  105.8  22.5      3e-30  105.5  22.5    1.1  1  Sugar_tr  Sugar (and other) transporter
    4.4e-05   22.7  11.6     0.0043   16.1   0.2    2.7  3  PUCC      PUCC protein
  ------ inclusion threshold ------
        1.3    9.2   2.3          8    6.6   0.0    3.1  4  DUF2615   Protein of unknown function (DUF2615)


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 !   90.7  36.5     2e-29   8.8e-26       6     351 ..      28     396 ..      20     398 .. 0.72
   2 !   37.0  18.8   4.1e-13   1.9e-09      44     186 ..     299     445 ..     293     453 .] 0.82

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 2e-29
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.. 80 
                                       fl a + + +g++l  a+++ l+++  e gl + +  lgaa+++l +Grl+d+fGr+ ++ + +++++++++ll+  
  gi|518651860|ref|YP_008141380.1|  28 FLDAGMLAGTGITLL-AIGTLLNFTTLEDGLPALITLLGAAFGALGFGRLGDKFGRKFIYQVDMIIYGVSAILLAit 103
                                       344444444555555.99999*************************************************5555534 PP

                             MFS_1  81 ..fa...sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg... 149
                                         f+    ++ + +v+ +l G++ ga +p++ +li++ +pk+ rgr +++ ++++ +G+++  +++ +l+ + g   
  gi|518651860|ref|YP_008141380.1| 104 giFPsriFNIVWAMVFYALVGIAVGADVPTSWSLITEFSPKNYRGRLMSITTIMWYVGVLVELGIAIALY-NTGmvl 179
                                       433334444555888888****************************************************.777688 PP

                             MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeee.................kgtgpaplvpawkallkdpvl 209
                                       +r+++++l+++++++     +ll+++ +e++r    +                   +  +++ + + +k+l+k+   
  gi|518651860|ref|YP_008141380.1| 180 FRVIWIMLGLLAFVS-----WLLRRNLTESPRYDMMRGNktdlqksakllhidikdEENKKFTIDK-YKELFKKY-G 249
                                       998888888888888.....6665555555555554443444466677777777555555555555.77777666.3 PP

                             MFS_1 210 w.illialllfffgfsg..lltllplylqevlgls......g..lllaglllallalvgailallagrlsdrlgrrr 275
                                       w +ll+ +l+ ++g+ +  +  ++p +  + l+l       +  +++ g  +a++     ++ l++ +lsdr+gr +
  gi|518651860|ref|YP_008141380.1| 250 WfMLLAWFLYLMWGIPAstYGEFFPYI-FSSLHLVslrdtyAfeAIYFG--SAIV-----PGLLIFYYLSDRVGRVP 318
                                       555555555555555556644444443.333333323331110023333..2222.....3367999*******988 PP

                             MFS_1 276 rlllallllllaalglallavtssavllllvlvliGfglgfv.fpsllalasdlappeeagtasglfn.tagslgga 350
                                         l + + +++++++l++ ++ ++  +ll++++l+G+g+g+  +++   l  +++p++ + + +g++  t++  +g+
  gi|518651860|ref|YP_008141380.1| 319 LYLASAAMAAVSFFLLVYPPFLKNVYVLLASFLLFGIGQGLGiWTTTRLLSLEHFPTSLRNSGQGFVWfTMRFEAGI 395
                                       8888888888888888888888777777778888***999999**********************999666655555 PP

                             MFS_1 351 l 351
                                       +
  gi|518651860|ref|YP_008141380.1| 396 F 396
                                       5 PP

  == domain 2  score: 37.0 bits;  conditional E-value: 4.1e-13
                             MFS_1  44 gaavaslplGrlsdrfGrrrvlllglllfalglllllfa...sslwlllvlrvlqGlga.galfpagaaliadwfpk 116
                                       + + + l++ +lsdr+Gr +++l+++++ a++++ll+++    ++++ll++ +l G+g+  +++++   l  + fp 
  gi|518651860|ref|YP_008141380.1| 299 AIVPGLLIFYYLSDRVGRVPLYLASAAMAAVSFFLLVYPpflKNVYVLLASFLLFGIGQgLGIWTTTRLLSLEHFPT 375
                                       557889999***********************66666434559999*************5567999999999***** PP

                             MFS_1 117 eergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll.peepperkrkspke 186
                                       + r+++ g++  ++ + a +  l+ ++++ ++g +++ yi++++++laf+++ ll+ + ++  r   ++ e
  gi|518651860|ref|YP_008141380.1| 376 SLRNSGQGFVWFTMRFEAGIFGLFTPMIV-AFGIEYIGYIAGAFFVLAFIVVTLLYiFKPEYVRTERKSLE 445
                                       ******************9999*******.******************99665555244444444444444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5  22.5   6.8e-34     3e-30      45     439 ..      52     435 ..       5     450 .. 0.80

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 6.8e-34
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTT....SS-TGGGGGHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgk....nsvevlivgRvlvGigvG 117
                                       ++  gl + i+l+Ga++G+l +g lgd+fGRk ++ +  +++ ++a+l a++       +++   +v   lvGi+vG
  gi|518651860|ref|YP_008141380.1|  52 TLEDGLPALITLLGAAFGALGFGRLGDKFGRKFIYQVDMIIYGVSAILLAITGIFpsriFNIVWAMVFYALVGIAVG 128
                                       5556788899************************************999988866887867777777899******* PP

                                       HHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS--- CS
                          Sugar_tr 118 lasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPES 194
                                       +   ++  +i E++pk++Rg+l+s++  ++ +G lv  ++  +l +t+  + +r+   +  ++a +  +l+  l ES
  gi|518651860|ref|YP_008141380.1| 129 ADVPTSWSLITEFSPKNYRGRLMSITTIMWYVGVLVELGIAIALYNTGM-VLFRVIWIMLGLLAFVSWLLRRNLTES 204
                                       ********************************************77777.79999999999999999999999**** PP

                                       HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHH CS
                          Sugar_tr 195 PrylvekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGin 271
                                       Pry +++g++ + +++ +       + ++ +++k ++++        +kel+++ +  +    +++ +++  + Gi 
  gi|518651860|ref|YP_008141380.1| 205 PRYDMMRGNKTDLQKSAKL---LHIDIKDEENKKFTIDK--------YKELFKKYG--W---FMLLAWFLYLMWGIP 265
                                       ********76655554444...11122222222222222........467788866..2...222233344456888 PP

                                       HHHH..HTTTHHHHSS-THH...HHHHHHH.HHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHT CS
                          Sugar_tr 272 aimy..ysptifenlglsks...llvtiiv.gvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllv 342
                                       a +y  + p+if++l+l      +++ +i+ g   +   ++  +l+dr+GR +l+l +aa++a+ f++l  v  ++ 
  gi|518651860|ref|YP_008141380.1| 266 ASTYgeFFPYIFSSLHLVSLrdtYAFEAIYfGSAIVPGLLIFYYLSDRVGRVPLYLASAAMAAVSFFLL--VYPPFL 340
                                       8887778899****99998888855555550555555666668*****************999999999..477888 PP

                                       TSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHH CS
                          Sugar_tr 343 akskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvf 419
                                       ++     +v+++ ++lf +  +lg+ ++  +l+ E fp+s+R++++ ++ +++ +   + +l++p+i+      y++
  gi|518651860|ref|YP_008141380.1| 341 KN----VYVLLASFLLFGIGQGLGIWTTTRLLSLEHFPTSLRNSGQGFVWFTMRFEAGIFGLFTPMIVAFGI-EYIG 412
                                       88....8***********************************************************998777.7888 PP

                                       HHHHHHHHHHHHHH...HHHS-- CS
                          Sugar_tr 420 lvfaglavlfiifv...fffvpe 439
                                       ++ +++ vl++i+v   ++f pe
  gi|518651860|ref|YP_008141380.1| 413 YIAGAFFVLAFIVVtllYIFKPE 435
                                       88877777777666233555555 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       0.3   1.4e+03     132     170 ..      61     102 ..      54     106 .. 0.65
   2 !    9.2   5.5   0.00012      0.54      81     161 ..     106     187 ..      83     227 .. 0.78
   3 !   16.1   0.2   9.7e-07    0.0043     264     321 ..     307     363 ..     279     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.3
                              PUCC 132 mlligivvsaivvgallkdytearLir...vvqgvalitlvl 170
                                       + l+g +++a+ +g+l +++  + + +   ++ gv++i l++
  gi|518651860|ref|YP_008141380.1|  61 ITLLGAAFGALGFGRLGDKFGRKFIYQvdmIIYGVSAILLAI 102
                                       567888999999999988876554443111466666666555 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00012
                              PUCC  81 aaatwaglilaavafllvGlgvslsqTallALladlaeeeerpkvvgllyvmlligivvsaivvgallkd.ytearL 156
                                       +   ++  + a+v ++lvG++v++   +   L+++ + ++ r ++ +++ +m  +g+ v  ++  al ++ +   r 
  gi|518651860|ref|YP_008141380.1| 106 FPSRIFNIVWAMVFYALVGIAVGADVPTSWSLITEFSPKNYRGRLMSITTIMWYVGVLVELGIAIALYNTgMVLFRV 182
                                       55678888999*************999999***************************99877666666553344444 PP

                              PUCC 157 irvvq 161
                                       i+++ 
  gi|518651860|ref|YP_008141380.1| 183 IWIML 187
                                       44444 PP

  == domain 3  score: 16.1 bits;  conditional E-value: 9.7e-07
                              PUCC 264 glvlsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaa 321
                                          ls +++   l    ++++++sf+ll+   +l+nv +l+a+ ll+G+++Gl    +
  gi|518651860|ref|YP_008141380.1| 307 FYYLSDRVGRVPLYLASAAMAAVSFFLLVYPPFLKNVYVLLASFLLFGIGQGLGI-WT 363
                                       46788899999999999***********************************843.33 PP

>> DUF2615  Protein of unknown function (DUF2615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.4   0.1         4   1.8e+04      63      73 ..     112     122 ..     107     124 .. 0.58
   2 ?   -0.0   0.0      0.22   9.7e+02      56      76 ..     177     200 ..     167     222 .. 0.56
   3 ?   -1.1   0.0      0.46     2e+03      55      73 ..     243     261 ..     229     268 .. 0.76
   4 ?    6.6   0.0    0.0018         8      59      84 ..     418     443 ..     412     451 .. 0.73

  Alignments for each domain:
  == domain 1  score: -4.4 bits;  conditional E-value: 4
                           DUF2615  63 wlvvaavlfll 73 
                                        +v a+v+++l
  gi|518651860|ref|YP_008141380.1| 112 NIVWAMVFYAL 122
                                       34555666654 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.22
                           DUF2615  56 lfliallwlvvaavlf...llrPs 76 
                                       ++l+ ++w+++ ++ f   llr +
  gi|518651860|ref|YP_008141380.1| 177 MVLFRVIWIMLGLLAFvswLLRRN 200
                                       555666666655555400055544 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.46
                           DUF2615  55 slfliallwlvvaavlfll 73 
                                       +lf     ++++a +l+l+
  gi|518651860|ref|YP_008141380.1| 243 ELFKKYGWFMLLAWFLYLM 261
                                       55555667899999**998 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0018
                           DUF2615  59 iallwlvvaavlfllrPsslrnasak 84 
                                       +++l ++v+++l++++P+ +r  +++
  gi|518651860|ref|YP_008141380.1| 418 FFVLAFIVVTLLYIFKPEYVRTERKS 443
                                       4567788999********99986433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       915  (0.0510346); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 2961.79
//
Query:       gi|518651861|ref|YP_008141381.1|  [L=252]
Description: hypothetical protein FACI_IFERC00001G0500 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1602.48
//
Query:       gi|518651862|ref|YP_008141382.1|  [L=292]
Description: dihydrodipicoline synthase related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-24   86.2   0.0    1.6e-24   86.1   0.0    1.1  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.061   13.0   0.0       0.25   11.0   0.0    1.9  2  CENP-B_N  CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.1   0.0   1.8e-28   1.6e-24       2     187 ..       4     188 ..       3     273 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.1 bits;  conditional E-value: 1.8e-28
                                       -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE-- CS
                             DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvG 78 
                                       +sg+i+a+ t f+ + ++d+  +++ ief i++g+ ++  +  +GE+  l  +ek+++++ + + +  ri+++agv 
  gi|518651862|ref|YP_008141382.1|   4 ISGVIPAIPTIFKDNMEIDFDGIENCIEFAIKSGAGAIAPMLLGGEFYKLTFNEKIEIINNVSK-FRKRIKIFAGVS 79 
                                       589********************************************************98765.678********* PP

                                       -SSHHHHHHHHHCCCCCT-SEEEEE---SS...---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHH CS
                             DHDPS  79 snstseaiklakkaeeaGadgvlavtPYYn...kpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLa 152
                                        ++t  a kla+ka+++G+ g+++++PYY+   k +   + +hf  i ++ d pvi+ ++  r+++ l++   k++ 
  gi|518651862|ref|YP_008141382.1|  80 EPATFAAAKLAEKARDSGVSGIILMPPYYYpygKLENSIIAKHFIDISNSIDIPVIIQDFGYRSNMPLKLL--KTI- 153
                                       ****************************9833356777799********************9998777664..444. PP

                                       TSTTEEEEEE-SS-CTHHHHHHCCCSTTSEEEES- CS
                             DHDPS 153 elenivgvKeavgdleevikikkevgkdlviysGd 187
                                       + +ni+g+K    d  + i++ ++  +d++i+ G+
  gi|518651862|ref|YP_008141382.1| 154 AANNIAGIKTEGKDSARRIHLLHTNFPDISILGGY 188
                                       468******9999999999*****9******9995 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.7e-05      0.25       7      19 ..      53      65 ..      50      70 .. 0.89
   2 ?   -1.9   0.0      0.31   2.7e+03      29      38 ..     169     178 ..     166     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.7e-05
                                      --HHHHHHHHHHH CS
                          CENP-B_N  7 LTlreKievIqrl 19
                                      LT++eKie+I  +
  gi|518651862|ref|YP_008141382.1| 53 LTFNEKIEIINNV 65
                                      9*********865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.31
                                       HHHHT--CCH CS
                          CENP-B_N  29 arrfnvpest 38 
                                       arr++++ + 
  gi|518651862|ref|YP_008141382.1| 169 ARRIHLLHTN 178
                                       9****99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2149.28
//
Query:       gi|518651863|ref|YP_008141383.1|  [L=369]
Description: hypothetical protein FACI_IFERC00001G0502 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-49  166.2   0.0      1e-48  165.8   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
     0.0049   17.1   0.0     0.0084   16.3   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.8   0.0   1.1e-52     1e-48       2     217 ..     155     367 ..     154     369 .] 0.91

  Alignments for each domain:
  == domain 1  score: 165.8 bits;  conditional E-value: 1.1e-52
                                       HHHHHHHHHHHHT-SEEEEETSSS.....HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGT CS
                          MR_MLE_C   2 laeearelvaeqgfravKlkvggd.....dvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeld 73 
                                       l++ea+e +++qg++++K++++++      +++ +e v+ +r+avg   dv+l+ Da  +w+ + A++++++le +d
  gi|518651863|ref|YP_008141383.1| 155 LRKEAEE-YVSQGYKTMKMRFISGpsdinGLEKNIELVKTIRDAVGY--DVELAGDAWMSWNYNFALKMVKKLERYD 228
                                       7899988.5567********9999*********************66..66**********************99** PP

                                       ESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT CS
                          MR_MLE_C  74 llwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafg 149
                                       ++w+EEP+ p dd +++++l+  + +ipi  gE+ y ++df++ll+ag + i+qpd+ ++gGit+++k++alae++g
  gi|518651863|ref|YP_008141383.1| 229 MAWVEEPLMP-DDFDAMKMLSW-KtGIPISEGEHHYHVYDFKRLLDAG-IRILQPDAVWTGGITPMKKIIALAETYG 302
                                       **********.78********5.55*********************99.**************************** PP

                                       -EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGH..TSGCSBSSSSEEETTEEECTSSSBTSSEB- CS
                          MR_MLE_C 150 vpvapHsgsgglglaaslhlaaaipnllileyfldael..leeelleeplevedGrvtvpdgpGlGveld 217
                                         v+pH+     g +++lh++ + p++      +  ++  + e++ e++l +e+G++t++d+pG+G+e +
  gi|518651863|ref|YP_008141383.1| 303 AIVVPHT-----GNIYNLHVIGSEPESVTPVAEFLTKYreWMEQHMEGTLFPEKGYFTLSDKPGFGLEYK 367
                                       *******.....679*****99988766555444444457****************************87 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   9.4e-07    0.0084      73     117 .]      83     133 ..      57     133 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 9.4e-07
                                       THHHHHHHHHHHHCSS......CHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  73 anisdlaqllkravlg......nmsAkaaidmAlwDlkakalnlpladLlG 117
                                       ++i+ ++ +l+r  l+      +m A +a+++ ++D+  k+ln+p ++++G
  gi|518651863|ref|YP_008141383.1|  83 SEINMAWDMLYRLSLPlgrsgvMMHALSAVNIMMYDIYSKSLNVPAYKIMG 133
                                       78999**********999***99*************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2661.65
//
Query:       gi|518651864|ref|YP_008141384.1|  [L=250]
Description: competence damage-inducible protein A [Ferroplasma acidarmanus fer1]
Scores for 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-27   94.3   0.1      9e-27   93.5   0.1    1.3  1  MoCF_biosynth    Probable molybdopterin binding domain
  ------ inclusion threshold ------
       0.02   15.3   0.1       0.33   11.3   0.1    2.1  2  Radical_SAM      Radical SAM superfamily
      0.046   13.9   0.1         15    5.8   0.0    2.6  3  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2


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 !   93.5   0.1   1.5e-30     9e-27       2     138 ..       5     160 ..       4     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.5e-30
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                       +it+G+e+l+g++++tn + + + l+  g++v+k  +vpD+ e+i+ a+++a + ad+i+++GG+Gpt dD+t +  
  gi|518651864|ref|YP_008141384.1|   5 IITIGNEILKGRTVNTNFSDIGKILTYSGYDVIKGIIVPDNLEQIAGAFKEASSIADLIVSSGGLGPTYDDMTLKGF 81 
                                       8************************************************8887888********************* PP

                                       HHHHSEE-HHHHHHHHHHHHHHCC....................TTSHGGGGGGE.EE.TTEEEEE-SSHHHHHHHH CS
                     MoCF_biosynth  79 aklfekelegfeeafrrvslkpgk....................pvgvapgailsrav.gktiigLPGspkavkeal 134
                                       + +f+ ++e ++ a+++v +k ++                    + g+apg+  + ++ gk +i+LPG+p++v++++
  gi|518651864|ref|YP_008141384.1|  82 SLAFNLKMERNDNAMNMVLKKVHTltperekmgmipensipienKAGTAPGI-YE-NIsGKVFIILPGVPREVEAIM 156
                                       *********************988***************************4.44.34266688************* PP

                                       HHHH CS
                     MoCF_biosynth 135 eeil 138
                                       +e+ 
  gi|518651864|ref|YP_008141384.1| 157 KEVE 160
                                       9985 PP

>> 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     0.046   2.7e+02      29      73 ..      41      86 ..      32     115 .. 0.80
   2 ?   11.3   0.1   5.5e-05      0.33      29      99 ..     150     238 ..     145     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.046
                                      HHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 29 lsveeileevkelkaekg.vkevilgggepllypdfvellerlakl 73
                                      + ++++++++ ++k+    ++ ++++gg    y+d++ + + la +
  gi|518651864|ref|YP_008141384.1| 41 IVPDNLEQIAGAFKEASSiADLIVSSGGLGPTYDDMTLKGFSLAFN 86
                                      67889999999998555569999999**999999999998888876 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC...................CCTEEEEEEECS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxxxx RF
                       Radical_SAM  29 lsveeileevkelkaekgvkevilgggepllypdfvellerlakla...................vpgiritvetng 86 
                                       + ve i++ev++   +  +k ++ +    +l++ ++ ll+ l+++                    +p++++ v+++g
  gi|518651864|ref|YP_008141384.1| 150 REVEAIMKEVEQR-IR--IKDFHYVDRSIDLHDAKESLLAPLIAKLmkeygdrayikthpkldngKPWVEVEVSASG 223
                                       6788888888777.45..**************999999999999999999999************************ PP

                                       SCHG..HHHHHHHHH CS
                                       xxxx..xxxxxxxxx RF
                       Radical_SAM  87 tlpd..eeklerlle 99 
                                       t pd  e ++ r+le
  gi|518651864|ref|YP_008141384.1| 224 TDPDevENFVSRILE 238
                                       ***988666666665 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0025        15      26      53 ..       2      29 ..       1      33 [. 0.92
   2 ?   -2.9   0.0       1.3     8e+03      29      53 ..      82     107 ..      76     115 .. 0.57
   3 ?    5.2   0.0    0.0039        23      12      34 ..     220     242 ..     218     247 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0025
                   HU-CCDC81_euk_2 26 qetfqalgdllrngknvelefkgiGvLs 53
                                      ++++ ++g+ + +g++v+ +f +iG+++
  gi|518651864|ref|YP_008141384.1|  2 KAVIITIGNEILKGRTVNTNFSDIGKIL 29
                                      789999*******************986 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                   HU-CCDC81_euk_2  29 fqalgdllrngknv.elefkgiGvLs 53 
                                        +a++  ++++ n  ++++k + +L+
  gi|518651864|ref|YP_008141384.1|  82 SLAFNLKMERNDNAmNMVLKKVHTLT 107
                                       55555556655554477777776665 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0039
                   HU-CCDC81_euk_2  12 aaaglsrdvVescvqetfqalgd 34 
                                       +a+g+++d Ve++v++++  +++
  gi|518651864|ref|YP_008141384.1| 220 SASGTDPDEVENFVSRILEIIEK 242
                                       5899*************988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); 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: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1847.74
//
Query:       gi|518651865|ref|YP_008141385.1|  [L=154]
Description: hypothetical protein FACI_IFERC00001G0504 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-33  115.6   0.4    1.5e-33  115.5   0.4    1.0  1  DUF2240   Uncharacterized protein conserved in archaea (DUF22


Domain annotation for each model (and alignments):
>> DUF2240  Uncharacterized protein conserved in archaea (DUF2240)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.4   8.3e-38   1.5e-33       2     143 ..       5     149 ..       4     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 8.3e-38
                           DUF2240   2 lkiavaapfkkkrkdklsesdfvfalsldrkwlspdqakklldraeeegLlekkdgdlvpnfdvaeveiPlgFkpde 78 
                                       ++++++a+++ k++d +s+sdf + ls++r +l+p+ ++++l+   e+ Ll +k+g++vpnf++++v +Pl+F++d 
  gi|518651865|ref|YP_008141385.1|   5 MARKLIAIVASKKADGYSKSDFTNILSFKRTLLPPEDVDRFLQVSLESMLLVEKNGKYVPNFSTEGVIVPLDFSIDV 81 
                                       6899************************************************************************7 PP

                           DUF2240  79 ell....kekstferildaiaastgiekkevvaeinelqeelkglvdveaaalvvakkegvdvddliee 143
                                       + l     ek+ ++r+l+a++as++++kke++ ++++l + ++ ++d+e+a++ v+++ g+dv+ +++e
  gi|518651865|ref|YP_008141385.1|  82 DELfseaTEKPLIDRMLEAASASGKMTKKEAIIRAKDLLSGMQ-FIDFETAIITVLSDSGIDVTPFVQE 149
                                       7666**99***********************************.********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 1032.37
//
Query:       gi|518651866|ref|YP_008141386.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G0505 [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  179.8   0.0    2.3e-51  175.2   0.0    2.0  1  TRM            N2,N2-dimethylguanosine tRNA methyltransferase
  ------ inclusion threshold ------
      0.021   14.5   0.0      0.033   13.8   0.0    1.3  1  Cons_hypoth95  Conserved hypothetical protein 95


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 !  175.2   0.0   2.5e-55   2.3e-51      17     372 ..      31     347 ..      13     351 .] 0.85

  Alignments for each domain:
  == domain 1  score: 175.2 bits;  conditional E-value: 2.5e-55
                                       T--SS--GGGHHHHHHHHHH...HHHHHHHH-S-EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHH CS
                               TRM  17 keeVFYNPvqefnRDlsvlvirqlellkkklgekikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeN 93 
                                       ++  FYN  q+ nRD+++     l + k k+      lda+ ++G+R+iR   E +g k+v+  +i++k +e i+ N
  gi|518651866|ref|YP_008141386.1|  31 RTAGFYNMDQKLNRDITISF---LRTVKPKI-----ALDAFGGTGVRGIRINRE-AGIKAVI-SEINKKSYEYININ 97 
                                       4567*************999...88999995.....8*****************.8888887.89************ PP

                                       HHHTT--.GGEEEE-S-HHHHHC--SS-EEEEEE--SS--GGGHHHHHHHEEEEEEEEEEE--HHHHTTSSHHHHHH CS
                               TRM  94 vklneve.eivvineddAnvllaekkkrfdviDlDPfGspapfldsavqsvkekglLlvTaTDtavLaGaspekclr 169
                                        +ln+   e  v n+   +++l  ++  fd+iD+DP+Gs+ p++d a+  ++++g++ vTaTD+++L+G++p k lr
  gi|518651866|ref|YP_008141386.1|  98 RELNNSPvE--VYNK-TFQAIL--NDYLFDYIDIDPYGSVLPYMDDAMINIRNRGYIGVTATDLTSLTGSMPAKTLR 169
                                       ****99844..3333.457777..899************************************************** PP

                                       HHSSB---STTHHHHHHHHHHHHHHHHHHTTTEEEEEEEEEEETTEEEEEEEEEE-HHHHHHHHTTEEEEEEETTT- CS
                               TRM 170 kYgavalkselcHEvalRillkavareaakYekavepllslsadfYvrvfvkvktgaakvkkvleklglvlhCsgCl 246
                                       +Y a+ ++  + HE+++R+l++ ++++aa  +ka  p++sl + +Y+r+ +++ ++  k+++ l+++g+        
  gi|518651866|ref|YP_008141386.1| 170 RYRAFVINDIYRHESGIRLLIGEIVKRAAALDKAAIPMISLWHSHYYRIIFQIISSSSKADAQLDQVGIFDR----- 241
                                       ********************************************************************8876..... PP

                                       -EEEE--GGG--SB-TTT-SBEEEEEEEE-S-S--HHHHHHHHHHHCT..-TTS-HHHHHHHHHHHHHHS--SS-E. CS
                               TRM 247 seekvkglakfkaecehcgaklhlaGPlwlgplkdkefveevleeaekekeeelkkrvkklLklikeElldaplyy. 322
                                        ++  +g+           +  +  GPlwlg+l++ e+ +++   +e+       k+ +  ++ +k    d  ly+ 
  gi|518651866|ref|YP_008141386.1| 242 -HSGLSGV-----------YPSSREGPLWLGNLNS-EVAQKLDY-IEN-----PDKQFLSTMERLKTN--DLSLYFa 297
                                       .2334444...........456778*******975.45555443.444.....245556666666666..6677773 PP

                                       EHHHHHHHHT-SS---HHHHHHH....TT-EE-TTSTTEEE-SS-HHHHH CS
                               TRM 323 dlsqlasvlklsvpplkkvvsalkelgfevsrtHakpkaikTnapleavv 372
                                       d+ + a++   ++++ ++ + +l+++g e+ r+ +++++ik   ++ +  
  gi|518651866|ref|YP_008141386.1| 298 DIADFARISGKDTKSIESSMIKLRDAGIECGRSMFSNTGIKVSSTVPEAF 347
                                       5777888888888888888999*******************988776655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.6e-06     0.033      40     126 ..      54     138 ..      34     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.6e-06
                                       HCC-EEEETT-TTSHHHHHHHHTT-S.EEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgak.kavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                       ++ +  LD f+G+G+ g+  + R+a  kav+ e +k+ ++ ++ n e  +      e+ ++ ++a+l+       fd
  gi|518651866|ref|YP_008141386.1|  54 VKPKIALDAFGGTGVRGIR-INREAGiKAVISEINKKSYEYININRELNNSP---VEVYNKTFQAILND----YLFD 122
                                       677889************6.8999965899*************998766633...55666666666555....57** PP

                                       EEEE--.....SSSTT CS
                     Cons_hypoth95 116 ivflDP.....Pyake 126
                                       ++ +DP     Py+++
  gi|518651866|ref|YP_008141386.1| 123 YIDIDPygsvlPYMDD 138
                                       *****85555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2468.90
//
Query:       gi|518651867|ref|YP_008141387.1|  [L=181]
Description: hypothetical protein FACI_IFERC00001G0506 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-38  130.2   4.0    7.9e-38  130.0   4.0    1.0  1  NTPase_1  NTPase
    0.00065   19.3   0.1     0.0011   18.6   0.1    1.3  1  DUF2478   Protein of unknown function (DUF2478)
     0.0046   16.7   0.1     0.0083   15.9   0.1    1.4  1  AAA_30    AAA domain
  ------ inclusion threshold ------
      0.036   14.1   0.2       0.41   10.7   0.2    2.3  1  AAA_5     AAA domain (dynein-related subfamily)
      0.082   13.5   0.2       0.11   13.0   0.2    1.3  1  AAA_18    AAA domain


Domain annotation for each model (and alignments):
>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.0   4.0   2.2e-41   7.9e-38       1     168 []       4     171 ..       4     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 130.0 bits;  conditional E-value: 2.2e-41
                                       EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT---SSEETTEEE- CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarveakreprvgkyvvd 77 
                                       kv iTGp G+ Kt  ++k++e+l+++g  ++G +++e  e+gr +++ i+d+ ++++ ++ar +  ++++v+k  vd
  gi|518651867|ref|YP_008141387.1|   4 KVGITGPIGSIKTDALNKIMEMLQNNGKVIEGTLVSEKIEHGRVVAYYITDILTKRRVEFARIDLISRVKVDKLGVD 80 
                                       589************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHH-EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS--SHHHHHHHT-TT-EEEE CS
                          NTPase_1  78 vesfeelalealrkalseadviviDEiGkmElkskkfkeaveevLksekpvlavihrrkdlalveeirerkdvkvfe 154
                                       ++ +e l +++l+k+ +eadviv+DE Gk E ++k++k ++ee++ks+k +++++h+++++++++e+r  + v+vf+
  gi|518651867|ref|YP_008141387.1|  81 TKLLEGLLVPSLQKSREEADVIVLDELGKVENTTKQIKAEIEETMKSDKSIIVTLHKKSRNPVLQEFRGYESVRVFD 157
                                       ***************************************************************************** PP

                                       --TTTTTTHHHHHH CS
                          NTPase_1 155 vteenrdalleeil 168
                                       +t+ n++ l+ +il
  gi|518651867|ref|YP_008141387.1| 158 ITPINKNILPFKIL 171
                                       *********99996 PP

>> DUF2478  Protein of unknown function (DUF2478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   3.1e-07    0.0011      14     143 ..      17     149 ..       7     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.1e-07
                           DUF2478  14 alLaafaerlraeGlrvaGvvqenaeeaegkkcdmeledlatgeririsq.dlgsg..sqgCrLdpeaLaeaaaave 87 
                                       + L+++ e l+++G  + G + +++ e+ g+  +  ++d+ t +r++  + dl s+       +d++ L+       
  gi|518651867|ref|YP_008141387.1|  17 DALNKIMEMLQNNGKVIEGTLVSEKIEH-GRVVAYYITDILTKRRVEFARiDLISRvkVDKLGVDTKLLEGLLVPSL 92 
                                       6789999999999999999986666655.667799999999999987654355554004556679999999999999 PP

                           DUF2478  88 ralaegadlvivnkFGkqEaeGrGlreeiaaalaagiPvltaVseklle.aWraFag 143
                                       ++ +e+ad++++   Gk E + + + +ei++ ++++ ++++++++k  +   ++F g
  gi|518651867|ref|YP_008141387.1|  93 QKSREEADVIVLDELGKVENTTKQIKAEIEETMKSDKSIIVTLHKKSRNpVLQEFRG 149
                                       999***************************************998865415566655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   2.3e-06    0.0083      23     116 ..       7     128 ..       3     136 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                            AAA_30  23 ltGpAGtGKttalkalreaweaag..............grviglAptgkaAkv.La............eelgieast 72 
                                       +tGp G+ Kt al+++ e+++++g              grv+++  t    k+ ++            ++lg++++ 
  gi|518651867|ref|YP_008141387.1|   7 ITGPIGSIKTDALNKIMEMLQNNGkviegtlvsekiehGRVVAYYITDILTKRrVEfaridlisrvkvDKLGVDTKL 83 
                                       89*********************956555555555555444444444444433233666666666666688888888 PP

                            AAA_30  73 iakllkrlkgrarlepgtllivDEagmv..dtkqlaallkaaekag 116
                                       ++ ll    + ++ e++++++ DE g v   tkq++a +++  k++
  gi|518651867|ref|YP_008141387.1|  84 LEGLLVPSLQ-KSREEADVIVLDELGKVenTTKQIKAEIEETMKSD 128
                                       8888855444.566777***********666677766666655555 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 ?   10.7   0.2   0.00011      0.41       4      79 ..       7     112 ..       4     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                                       EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--............--------.......... CS
                             AAA_5   4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreik...ngttslvdsplvraar.......... 64 
                                       + Gp G+ K+    ++ ++l   ++ +e  + +++++   ++  + ++   +++ ++    l   ++          
  gi|518651867|ref|YP_008141387.1|   7 ITGPIGSIKTDALNKIMEMLqnnGKVIEGTLVSEKIEHGRVVAYYITDiltKRRVEFARIDLISRVKvdklgvdtkl 83 
                                       56888888888888888888554444555556666666666666655566777777777777777777888888888 PP

                                       ..............G-SEEEEESGGG--H CS
                             AAA_5  65 ..............egeilvlDEveraes 79 
                                                     e++++vlDE+ ++e 
  gi|518651867|ref|YP_008141387.1|  84 legllvpslqksreEADVIVLDELGKVEN 112
                                       8888888888*************999875 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   3.1e-05      0.11       1      95 [.       5     120 ..       5     146 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf...................gvnlrdvakenglllevdpealdeskrldedkl 57 
                                       +++tG++G+ Kt   + + ++l ++                    + ++d++++++ ++ + +  +++ k+ + +++
  gi|518651867|ref|YP_008141387.1|   5 VGITGPIGSIKTDALNKIMEMLqNNgkviegtlvsekiehgrvvAYYITDILTKRRVEFARIDL-ISRVKVDKLGVD 80 
                                       78********************777*****8888888888888777888888888888888888.666666666666 PP

                            AAA_18  58 dklldaleenss..aleegknlvidghlaeleseaakdik 95 
                                        kll++l   s   ++ee++++v+d +      ++++++ 
  gi|518651867|ref|YP_008141387.1|  81 TKLLEGLLVPSLqkSREEADVIVLDELGKVENTTKQIKAE 120
                                       6666666664449999*********999888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      612  (0.0341346); 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: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1198.49
//
Query:       gi|518651868|ref|YP_008141388.1|  [L=118]
Description: hypothetical protein FACI_IFERC00001G0507 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-42  142.7   0.1    6.2e-42  142.5   0.1    1.0  1  DHNA      Dihydroneopterin aldolase


Domain annotation for each model (and alignments):
>> DHNA  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.5   0.1   3.5e-46   6.2e-42       1     108 []      12     117 ..      12     117 .. 0.95

  Alignments for each domain:
  == domain 1  score: 142.5 bits;  conditional E-value: 3.5e-46
                                       -HHHHHHHHHHHHHHHHHHHHTT-EESTTTHHHHHHHHHHHHHTSTTEEEEEEEE-S-..GGCC-STS-EE--TTTE CS
                              DHNA   1 tdrerAvFEagiklgalyHqfvGtPvseesaeslekaieesielQPfvedvkvkidrekleekleefgYteLtgeml 77 
                                       tdrerA+FE+giklga++Hqf+G+Pv+ ++ + +e+aie+si+lQPfve+++vki+ e  ++  ++f+Y++L+g+ml
  gi|518651868|ref|YP_008141388.1|  12 TDRERAIFESGIKLGAIFHQFIGVPVNDSNRKDMENAIEKSIKLQPFVESISVKINIEGQRN--TSFQYVSLSGDML 86 
                                       89*****************************************************9985433..35*********** PP

                                       EEEEEEEETTEEEEEEEEEETTTTEEEEEEE CS
                              DHNA  78 dveitvkyeeaevkarleyieeldYplmkve 108
                                       dv++ ++y+++evkar++y+++l+Yplm++e
  gi|518651868|ref|YP_008141388.1|  87 DVRLAIRYNDQEVKARMQYMQDLNYPLMYLE 117
                                       *****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 840.59
//
Query:       gi|518651869|ref|YP_008141389.1|  [L=259]
Description: hypothetical protein FACI_IFERC00001G0508 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.4e-54  183.0   0.3    6.3e-54  182.8   0.3    1.0  1  PcrB            PcrB family
      2e-09   37.2   0.0    4.9e-09   36.0   0.0    1.6  2  His_biosynth    Histidine biosynthesis protein
      2e-05   24.1   0.4    0.00036   20.0   0.1    2.3  2  G3P_antiterm    Glycerol-3-phosphate responsive antiterminato
    0.00011   21.5   0.1    0.00083   18.7   0.1    2.1  2  TMP-TENI        Thiamine monophosphate synthase
    0.00062   19.1   0.2     0.0011   18.4   0.2    1.4  1  ThiG            Thiazole biosynthesis protein ThiG
    0.00098   18.3   0.0     0.0043   16.2   0.0    1.9  2  Dus             Dihydrouridine synthase (Dus)
     0.0025   16.9   0.4      0.013   14.5   0.1    1.9  2  IMPDH           IMP dehydrogenase / GMP reductase domain
      0.003   16.8   0.3     0.0047   16.2   0.3    1.3  1  DHO_dh          Dihydroorotate dehydrogenase
     0.0079   15.1   0.1      0.016   14.1   0.1    1.4  2  Trp_syntA       Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.018   14.5   0.5      0.052   12.9   0.2    1.8  3  NMO             Nitronate monooxygenase
      0.028   13.8   0.8       0.33   10.3   0.6    2.1  2  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.8   0.3   3.8e-57   6.3e-54       2     223 ..      25     256 ..      24     259 .] 0.90

  Alignments for each domain:
  == domain 1  score: 182.8 bits;  conditional E-value: 3.8e-57
                                       HGGGTS..EEEEE-TTSS-CHHHHHHH...HCTT-SEEEEECST...CHHHHHHHHHHHHHCTSSS-EEEEESSGGG CS
                              PcrB   2 dileer..hltklDPeeenpdEiveiv...iesgtDavmigGsq...svtldntvrllkkvsriklPivlepsnveg 70 
                                       +il+ +  h+t++DP  + pd  ve +    + gtD  +igGs+   s  +d+t+  +k+   ++  i+++p+  + 
  gi|518651869|ref|YP_008141389.1|  25 EILKYKrvHMTLIDPAAQSPDRSVELAekaDKAGTDFFLIGGSTdidSRLMDKTISGIKEK--TEKQIIIFPGSRSM 99 
                                       67787778*************888777554789**********965444578888888887..9999********** PP

                                       --TTSSEEEEEEETTBSSTTTTTHHHHHHHHHHHHHHHCTEEEEEEEEEBTTTSHHHHHTTB-.B-TTHHHHHHHHH CS
                              PcrB  71 vvryaDalFvmsllnsanadWivgahalglkkvkklieseeilaegYlvvePdskvaavteak.vdlnkediaayal 146
                                       ++ryaDa+++m l+ns+n d+ivg h+ g + + k++  +e +++gYl+ eP+ +v++v++a+ + ++ e+ a  ++
  gi|518651869|ref|YP_008141389.1| 100 ISRYADAIYYMMLMNSTNIDYIVG-HQIGSASILKMM-GIETIPMGYLIFEPGMTVGRVGNARlIGRDDENTALSYA 174
                                       ***********************9.566777888888.7************************************** PP

                                       HHHHHTT-SEEEEE-.TTSSS-H.HHHHHHHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH..HCH CS
                              PcrB 147 laakllglrliYlEa.sGaledv.eevialkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd..erk 218
                                       +aa+++g++l+YlEa sGa+e+v  +vi+  k   k+ +ivGGGir+  kA+ ++ a AD+iv+G+v+e+++   ++
  gi|518651869|ref|YP_008141389.1| 175 FAAEFFGFKLLYLEAgSGAPEPVgCNVIRRIKESVKIPVIVGGGIRDYGKARSIIDAgADIIVTGTVIEKHSnpYMA 251
                                       ***********************989999999999**********************************98745566 PP

                                       HHHHH CS
                              PcrB 219 idail 223
                                       ++ i+
  gi|518651869|ref|YP_008141389.1| 252 LKDII 256
                                       66665 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.2     2e+03      32     100 ..      48      63 ..      24     105 .. 0.60
   2 !   36.0   0.0     3e-12   4.9e-09      54     109 ..     191     246 ..     154     257 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEE CS
                      His_biosynth  32 velakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkvi 100
                                       vela++ +++g d +                                                      
  gi|518651869|ref|YP_008141389.1|  48 VELAEKADKAGTDFF-----------------------------------------------------L 63 
                                       333333333333322.....................................................2 PP

  == domain 2  score: 36.0 bits;  conditional E-value: 3e-12
                                       HCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-T CS
                      His_biosynth  54 akegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknp 109
                                       + + +++  +++++i e+v+ipv vGGGIr++ +++++++agad ++ gt+  k++
  gi|518651869|ref|YP_008141389.1| 191 SGAPEPVGCNVIRRIKESVKIPVIVGGGIRDYGKARSIIDAGADIIVTGTVIEKHS 246
                                       4467888899****************************************976665 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.079   1.3e+02     100     131 ..      70     101 ..      47     120 .. 0.79
   2 !   20.0   0.1   2.2e-07   0.00036     124     168 ..     194     239 ..     192     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.079
                                       -SHHHHHHHHHHHHHHT-SEEEEESGGGHHHH CS
                      G3P_antiterm 100 iDssalekalkqiekskpdavevlPglvpkvi 131
                                       iDs+ ++k+++ i++ + + + + Pg    + 
  gi|518651869|ref|YP_008141389.1|  70 IDSRLMDKTISGIKEKTEKQIIIFPGSRSMIS 101
                                       89*************9999999***9865444 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 2.2e-07
                                       SGGG.HHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE- CS
                      G3P_antiterm 124 Pglv.pkvikeikkelkipiiaGGLietkedveealkaGaiavsts 168
                                       P  v  +vi++ik+++kip+i GG i++  + +++++aGa+ + t+
  gi|518651869|ref|YP_008141389.1| 194 PEPVgCNVIRRIKESVKIPVIVGGGIRDYGKARSIIDAGADIIVTG 239
                                       6667789***********************************9986 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.2   3.3e+02     107     125 ..      49      67 ..      15      89 .. 0.79
   2 !   18.7   0.1   5.1e-07   0.00083     134     176 ..     194     237 ..     167     242 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                          TMP-TENI 107 eeaeeaealgadYigvGpi 125
                                       e ae+a+++g d++ +G  
  gi|518651869|ref|YP_008141389.1|  49 ELAEKADKAGTDFFLIGGS 67 
                                       4478888888888888865 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 5.1e-07
                          TMP-TENI 134 aeplgleglkelaealeiPvvaiGGitl.envaevleagadgva 176
                                       +ep+g++ +++++e+++iPv++ GGi+   ++ ++++agad + 
  gi|518651869|ref|YP_008141389.1| 194 PEPVGCNVIRRIKESVKIPVIVGGGIRDyGKARSIIDAGADIIV 237
                                       49************************8625899999***99875 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   6.6e-07    0.0011     165     215 ..     200     250 ..     188     259 .] 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 6.6e-07
                                       HHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 165 ealkiiieeakvPvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                       ++++ i e++k+Pviv  Gi+   +a   ++ Gad ++  t + + ++p +
  gi|518651869|ref|YP_008141389.1| 200 NVIRRIKESVKIPVIVGGGIRDYGKARSIIDAGADIIVTGTVIEKHSNPYM 250
                                       5789999*************************************9999965 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.29   4.7e+02     137     165 ..      44      72 ..      32      91 .. 0.78
   2 !   16.2   0.0   2.7e-06    0.0043     173     215 ..     200     241 ..     159     255 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.29
                                       TC.HHHHHHHHHHCT-SEEEEESSECCCT CS
                               Dus 137 eenalelakiveaaGaqaltvHgRtraqn 165
                                        + ++ela+++ +aG +++ + g t  + 
  gi|518651869|ref|YP_008141389.1|  44 PDRSVELAEKADKAGTDFFLIGGSTDIDS 72 
                                       567899************99988776555 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                               Dus 173 eaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                       + I+ +k++v+ipvi+ G+I+d  +a+ i++  Gad ++ g  
  gi|518651869|ref|YP_008141389.1| 200 NVIRRIKESVKIPVIVGGGIRDYGKARSIIDA-GADIIVTGTV 241
                                       679***************************99.9999998864 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.17   2.8e+02     102     146 ..      44      90 ..      11     107 .. 0.73
   2 !   14.5   0.1   8.2e-06     0.013     187     238 ..     190     241 ..     182     246 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.17
                                       STTHHHHHHHHHHTT-SEEEEE.-STSSSHHHHHHHHHHHHHTTT.S CS
                                       xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.x RF
                             IMPDH 102 kedalervkalveagvdvlvvd.sahghsekvleavkeikkkvee.v 146
                                        + + e +++  +ag d+ ++  s++  s+ + ++++ ik+k+e+ +
  gi|518651869|ref|YP_008141389.1|  44 PDRSVELAEKADKAGTDFFLIGgSTDIDSRLMDKTISGIKEKTEKqI 90 
                                       34567778888899999988862455677778889999999996533 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.2e-06
                                       SB---HHHHHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 187 gvGvpqltAvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsl 238
                                       g G p+      + ++ ++ ++pvi  GGi+  g+    + aGad+++ G +
  gi|518651869|ref|YP_008141389.1| 190 GSGAPEPVGCNVIRRIKESVKIPVIVGGGIRDYGKARSIIDAGADIIVTGTV 241
                                       5556665555555666666677777777777777777777777777776665 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.3   2.9e-06    0.0047     222     279 ..     191     245 ..     181     259 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                       EEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHH CS
                            DHO_dh 222 sGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfe 279
                                       sG++  +++ +vir++++ +k  ip+I  GGi     a   i aGA ++  +t + ++
  gi|518651869|ref|YP_008141389.1| 191 SGAP-EPVGCNVIRRIKESVK--IPVIVGGGIRDYGKARSIIDAGADIIVTGTVIEKH 245
                                       6655.7999************..*****************************988654 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.8   4.6e+03      22      41 ..      43      62 ..      33      65 .. 0.60
   2 !   14.1   0.1   9.8e-06     0.016     189     229 ..     201     242 ..     194     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.8
                                      -HHHHHHHHHHHHHCT-SSE CS
                         Trp_syntA 22 dleqsleilkalekagadvi 41
                                      + ++s+e+ ++ +kag+d  
  gi|518651869|ref|YP_008141389.1| 43 SPDRSVELAEKADKAGTDFF 62
                                      35667777777777777755 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 9.8e-06
                                       HHHHHHHCTSS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHH CS
                         Trp_syntA 189 lverlkkltavPvavGFGistkeqvkqva.kvadGvivGSal 229
                                       +++r+k+  + Pv vG Gi++  ++++++ ++ad ++ G  +
  gi|518651869|ref|YP_008141389.1| 201 VIRRIKESVKIPVIVGGGIRDYGKARSIIdAGADIIVTGTVI 242
                                       799**************************9999999999766 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       2.2   3.5e+03     145     164 ..      47      66 ..      12      68 .. 0.75
   2 ?   -2.9   0.0       2.2   3.5e+03       6      29 ..     138     163 ..     135     171 .. 0.78
   3 ?   12.9   0.2   3.2e-05     0.052     183     223 ..     200     240 ..     189     247 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.2
                               NMO 145 svkearkvearGaDalivqG 164
                                       sv+ a k+ ++G D + + G
  gi|518651869|ref|YP_008141389.1|  47 SVELAEKADKAGTDFFLIGG 66 
                                       67778888888888888777 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.2
                               NMO   6 ellkikppvvqpgmgg..iskarLaa 29 
                                       e +++ + ++ pgm +  + +arL++
  gi|518651869|ref|YP_008141389.1| 138 ETIPMGYLIFEPGMTVgrVGNARLIG 163
                                       55677899999999877799999986 PP

  == domain 3  score: 12.9 bits;  conditional E-value: 3.2e-05
                               NMO 183 aLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqigt 223
                                       +++ ++++ v+iPvi  GGi d      ++ +GA  +  gt
  gi|518651869|ref|YP_008141389.1| 200 NVIRRIKESVKIPVIVGGGIRDYGKARSIIDAGADIIVTGT 240
                                       68999*****************************9888887 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 ?    1.2   0.0      0.12     2e+02      90     135 ..      71     114 ..      31     119 .. 0.78
   2 ?   10.3   0.6    0.0002      0.33     160     196 ..     205     241 ..     197     242 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                                       T-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEES CS
                    Ribul_P_3_epim  90 alehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllms 135
                                       +++ +++ti+ ike+  k ++++  +   +++++ +++++ ++lm 
  gi|518651869|ref|YP_008141389.1|  71 DSRLMDKTISGIKEKTEKQIIIFPGS--RSMISRYADAIYYMMLMN 114
                                       45678899999999999999888544..467888888888888886 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0002
                                       HHHHT---EEEEESS--T.TTCHHHHHHT--EEEESHH CS
                    Ribul_P_3_epim 160 idekeldlkievDGGvkl.dnieqiaeagadvlVagsa 196
                                       i+e ++++ + v GG+++   ++ i++agad++V+g+ 
  gi|518651869|ref|YP_008141389.1| 205 IKE-SVKIPVIVGGGIRDyGKARSIIDAGADIIVTGTV 241
                                       333.5778999*****97357999************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1710.37
//
Query:       gi|518651870|ref|YP_008141390.1|  [L=317]
Description: hypothetical protein FACI_IFERC00001G0509 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-18   66.8   0.8    2.2e-18   65.9   0.8    1.5  1  YrhK      YrhK-like protein


Domain annotation for each model (and alignments):
>> YrhK  YrhK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.9   0.8   1.2e-22   2.2e-18       2      61 .]     251     308 ..     250     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.9 bits;  conditional E-value: 1.2e-22
                              YrhK   2 ryeaislandiigsllFlvGSilflpnsefwkwqiagvwlFliGSilflirpvirlvrei 61 
                                       +y+++s+andi+ +l F++GSi+flp+  + k  ++gv+lF+ GS+++lirp+i+++r+i
  gi|518651870|ref|YP_008141390.1| 251 FYDWLSIANDIMVGLEFVIGSIFFLPSE-L-KYSTLGVYLFITGSTQLLIRPMINIARRI 308
                                       7************************555.4.9************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 2123.47
//
Query:       gi|518651871|ref|YP_008141391.1|  [L=80]
Description: phosphoribosylformylglycinamidine synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-19   70.2   0.3    1.5e-19   69.9   0.3    1.0  1  PurS      Phosphoribosylformylglycinamidine (FGAM) synthase


Domain annotation for each model (and alignments):
>> PurS  Phosphoribosylformylglycinamidine (FGAM) synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.3   8.4e-24   1.5e-19       1      76 [.       2      76 ..       2      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 8.4e-24
                                      EEEEEEEE-TTS--HHHHHHHHHHHHTTHTTEEEEEEEEEEEEEEE-SSHHHHHHHHHHHHHHTTS-TTTEEEEEE CS
                              PurS  1 kakveVtlKkgvlDpqGkavkkalkslgyeevedvrvgkyieleleaedeeeaeeeveemceklLaNpviedyeie 76
                                      k+kv++++ ++v Dp++  +k++l+ +gye+++++   k++e+e +  d+e+  +e++e++eklL Npvi++y+ie
  gi|518651871|ref|YP_008141391.1|  2 KVKVQIKYLPNVEDPEALSIKRNLELIGYEGIKNIYSYKIYEFETS-LDREDSISEIREIAEKLLTNPVIQEYKIE 76
                                      79******************************************98.588999*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 605.41
//
Query:       gi|518651872|ref|YP_008141392.1|  [L=749]
Description: hypothetical protein FACI_IFERC00001G0511 [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  152.5   0.2    3.3e-30  105.3   0.1    2.2  2  AIRS_C          AIR synthase related protein, C-terminal doma
    1.1e-38  131.8   0.1    1.2e-23   83.6   0.4    2.5  2  AIRS            AIR synthase related protein, N-terminal doma
    1.4e-15   57.5   0.0    8.8e-15   55.0   0.0    2.4  3  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
      0.055   13.4   0.4       0.11   12.4   0.4    1.4  1  UPF0126         UPF0126 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 !  105.3   0.1   7.3e-34   3.3e-30       2     152 ..     214     365 ..     213     368 .. 0.95
   2 !   45.1   0.0   2.5e-15   1.1e-11       2     149 ..     587     719 ..     586     723 .. 0.80

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 7.3e-34
                                       TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHH CS
                            AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlg 74 
                                       +Gd+li+ g+    +G++g++ ++++ +++ ++++++avqlg+++ ++ li + +++ ++   + +++D++gGGL++
  gi|518651872|ref|YP_008141392.1| 214 EGDLLIVCGGrtgkDGIHGVN-FASKVLDKGSEENRNAVQLGNPIIKEPLIHAILEANEE-RIIDGMKDLGGGGLSS 288
                                       7********************.666669999999999**********************8.**************** PP

                                       HHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSE CS
                            AIRS_C  75 alaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeel 151
                                       a++em++a+g +  i+ldkv + d  ++p+e+++se+++r+++a++p + +++ +i+e++g+ e+++IGe+++ e+l
  gi|518651872|ref|YP_008141392.1| 289 AVSEMLFAGGMSGIINLDKVLLKDSHMEPWEIWVSESQERMFLAIKPSNLQKISRIFEKWGI-EYSIIGETVKNENL 364
                                       **************************************************************.8********98876 PP

                                       E CS
                            AIRS_C 152 s 152
                                        
  gi|518651872|ref|YP_008141392.1| 365 V 365
                                       5 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 2.5e-15
                                       TTEEEEEEET..SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHH CS
                            AIRS_C   2 pGdvliltgs..lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgal 76 
                                       pG+ ++l gs    l g+ +s++ + +++ +l+       d    + +   k++     + + ++hD++ GGLl a+
  gi|518651872|ref|YP_008141392.1| 587 PGNPIYLAGSiiNDLAGSQYSSIMGTVHT-KLP-------DMDIDELVNINKDLSDS-MDYIESMHDISTGGLLMAI 654
                                       89999999999888888887776644443.333.......44444333333333333.379**************** PP

                                       HHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESS CS
                            AIRS_C  77 aemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtake 149
                                        em +++  g+e d++++  +       e l+se   + l+ v++ +++ +l+++++ ++   + IG+v+++e
  gi|518651872|ref|YP_008141392.1| 655 LEMSFGGPYGIEADISDIHGRT-----NEKLFSELGTGILIEVRKSDEKDFLEAFSRSNI---RKIGTVIDGE 719
                                       ****************777776.....589**************************9865...8******986 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 !   83.6   0.4   2.6e-27   1.2e-23       1      94 []      83     201 ..      83     201 .. 0.93
   2 !   45.6   0.0   1.9e-15   8.4e-12       6      93 ..     471     572 ..     455     573 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.6 bits;  conditional E-value: 2.6e-27
                                       SSSEE.........EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.............HH CS
                              AIRS   1 dDaav.........vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.............wl 55 
                                       dDa+v         vv+++shn+p++vep+ + +a++v+++++D+++mGA+P+al++sl ++             +l
  gi|518651872|ref|YP_008141392.1|  83 DDAGVisfdkdyayVVKMESHNHPSAVEPYGG-AATGVGGIIRDVLCMGAQPVALVDSLYFGdpdnmdgnlterfIL 158
                                       67775555555555******************.******************************************** PP

                                       HHHHHHHHHHHHHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  56 eevvrglaeaaeelgvplvgGdtsfsne....ptisvtavGlv 94 
                                       ++vv+g++++++++g+p+v G t+f++     p+++++++G+v
  gi|518651872|ref|YP_008141392.1| 159 NRVVAGIRDYGNRVGIPTVAGSTHFNKVyngmPLVNAGCIGIV 201
                                       ************************9766788**********97 PP

  == domain 2  score: 45.6 bits;  conditional E-value: 1.9e-15
                                       EEEEEEEE.EECCTCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.........HHHHHHHHHHHHHHHTT-EE CS
                              AIRS   6 vvttdshnrpvlvepvhfiGakavavnlsDlaamGArPlalllslalp.........wleevvrglaeaaeelgvpl 73 
                                       ++t  s ++ v +ep+++ +  ++ + ++++++ G+rP  ++++l+++          + e ++ +++ +++ g pl
  gi|518651872|ref|YP_008141392.1| 471 CLTSGSIPEMVGIEPYNG-TMHVLSEGYRNILSSGGRPHSIVDALNFGnpenpetmyRFIESIHAISDFCKATGLPL 546
                                       6677778888999*****.***********************************9999999999999********** PP

                                       EEEEEEEESS......EEEEEEEEEE CS
                              AIRS  74 vgGdtsfsne......ptisvtavGl 93 
                                       v+G++sf+ne      pt+++  +G 
  gi|518651872|ref|YP_008141392.1| 547 VSGNVSFYNEtdieilPTPNMLLIGK 572
                                       *********99*****9999999997 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0     2e-18   8.8e-15       7      50 .]      16      59 ..      13      59 .. 0.96
   2 ?   -3.1   0.0       2.8   1.3e+04       4      28 ..     325     349 ..     323     351 .. 0.80
   3 ?   -3.4   0.0       3.3   1.5e+04      12      35 ..     617     640 ..     614     642 .. 0.72

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 2e-18
                    FGAR-AT_linker  7 elglaLsdeEidylqeafeklgrnPtdvElemfaqvwSEHCrHK 50
                                        +l+L+ +Ei +l+++f++lgrnPtd+E++ +aq wSEH ++K
  gi|518651872|ref|YP_008141392.1| 16 AGELGLTYDEIVMLRNYFTGLGRNPTDIEIQAIAQGWSEHSCYK 59
                                      568****************************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                    FGAR-AT_linker   4 ankelglaLsdeEidylqeafeklg 28 
                                        ++++ la++++  +++  +fek+g
  gi|518651872|ref|YP_008141392.1| 325 SQERMFLAIKPSNLQKISRIFEKWG 349
                                       5677789999999999999998765 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 3.3
                    FGAR-AT_linker  12 LsdeEidylqeafeklgrnPtdvE 35 
                                       L d +id l+++ ++l+    ++E
  gi|518651872|ref|YP_008141392.1| 617 LPDMDIDELVNINKDLSDSMDYIE 640
                                       566778888888777877777777 PP

>> UPF0126  UPF0126 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   2.5e-05      0.11      34      62 ..     115     141 ..     112     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHHHHTTSSSSGHHHSSTCH CS
                           UPF0126  34 vvTAvgGGvlRDvllgrevPvvllreely 62 
                                         T+v GG++RDvl+    Pv+l++ +ly
  gi|518651872|ref|YP_008141392.1| 115 AATGV-GGIIRDVLCMGAQPVALVD-SLY 141
                                       55665.78******98778998865.588 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (749 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 4575.19
//
Query:       gi|518651873|ref|YP_008141393.1|  [L=84]
Description: hypothetical protein FACI_IFERC00001G0512 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      0.006   16.5   0.2      0.011   15.7   0.2    1.4  1  Tnp_22_trimer  L1 transposable element trimerization domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.19   11.6   0.0    1.3  1  HTH_AsnC-type  AsnC-type helix-turn-helix domain


Domain annotation for each model (and alignments):
>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.2e-06     0.011       3      18 ..      62      77 ..      61      81 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-06
                                      HHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer  3 delEERvSaaEDeiee 18
                                      ++ EERv  +EDei+ 
  gi|518651873|ref|YP_008141393.1| 62 EQVEERVKKMEDEINS 77
                                      599***********95 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.1e-05      0.19      26      42 .]      56      72 ..      55      72 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                     HTH_AsnC-type 26 rvGlSestvlrRvrrLe 42
                                      ++Gl++++v +Rv+++e
  gi|518651873|ref|YP_008141393.1| 56 ECGLTPEQVEERVKKME 72
                                      58**************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 557.80
//
Query:       gi|518651874|ref|YP_008141394.1|  [L=170]
Description: hypothetical protein FACI_IFERC00001G0513 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.027   14.3   0.1       0.98    9.2   0.0    2.0  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
       0.13   11.9   0.1       0.13   11.9   0.1    2.1  2  DUF3098       Protein of unknown function (DUF3098)
        2.6    8.4   5.1        5.1    7.4   1.1    2.2  2  DUF3040       Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> 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 ?    9.2   0.0   0.00016      0.98      67     113 ..       5      51 ..       3      75 .. 0.81
   2 ?    3.4   0.1    0.0098        59     113     137 ..     134     157 ..     103     165 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00016
                      Trp_oprn_chp  67 rrvvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaav 113
                                       +++vg++l+++g+ +++ +++ +t++++ ++ ++ ++++ +s++ + 
  gi|518651874|ref|YP_008141394.1|   5 KVIVGIVLIVIGISLVIGGVATITGEPSDHTVKEYSSNVYTSTQFNF 51 
                                       589**********************9999998886656666665554 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0098
                      Trp_oprn_chp 113 veltawpvlalaggvllllagvlll 137
                                       +++t++ ++a+ag++l+   g++++
  gi|518651874|ref|YP_008141394.1| 134 ARVTDASYVAAAGALLT-GSGIIIA 157
                                       33777888877776665.4444443 PP

>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.1e-05      0.13      10      31 ..       6      40 ..       4      59 .. 0.66
   2 ?   -1.5   0.7      0.32   1.9e+03      55      64 ..     153     162 ..     141     166 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                           DUF3098 10 lliglaviilGfiLmsGggsd.............d 31
                                      +++g+++i++G+ L +Gg ++             +
  gi|518651874|ref|YP_008141394.1|  6 VIVGIVLIVIGISLVIGGVATitgepsdhtvkeyS 40
                                      57899999999999999988766666555333332 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                           DUF3098  55 GfvieiyaIl 64 
                                       G++i ++ Il
  gi|518651874|ref|YP_008141394.1| 153 GIIIAMVTIL 162
                                       4444444443 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.1   0.00086       5.1      44      65 ..       5      26 ..       1      31 [. 0.82
   2 ?    2.7   0.2     0.026   1.6e+02      45      73 ..     136     163 ..     120     168 .. 0.65

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00086
                           DUF3040 44 lavlavllfvaGllllvlGvaa 65
                                       ++++++l+v+G+ l+++Gva+
  gi|518651874|ref|YP_008141394.1|  5 KVIVGIVLIVIGISLVIGGVAT 26
                                      5789999999999999999875 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.026
                           DUF3040  45 avlavllfvaGllllvlGvaaaavvlgvv 73 
                                       ++ a  +++aG+ll   G++ a+ v +++
  gi|518651874|ref|YP_008141394.1| 136 VTDASYVAAAGALLTGSGIIIAM-VTILF 163
                                       45556666678888888877665.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1185.22
//
Query:       gi|518651875|ref|YP_008141395.1|  [L=51]
Description: hypothetical protein FACI_IFERC00001G0514 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 401.67
//
Query:       gi|518651876|ref|YP_008141396.1|  [L=455]
Description: hypothetical protein FACI_IFERC00001G0515 [Ferroplasma acidarmanus fer1]
Scores for 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-54  183.8   0.1    7.5e-54  183.2   0.1    1.2  1  Lyase_1       Lyase
    3.5e-15   56.3   0.2    1.4e-14   54.4   0.0    2.2  3  ADSL_C        Adenylosuccinate lyase C-terminus
    7.2e-05   22.9   0.3    0.00033   20.7   0.1    2.2  3  ASL_C         Adenylosuccinate lyase C-terminal
    0.00047   20.2   0.2     0.0013   18.8   0.2    1.7  1  Mur_ligase_M  Mur ligase middle domain
  ------ inclusion threshold ------
      0.013   15.9   0.1      0.033   14.6   0.1    1.7  1  FumaraseC_C   Fumarase C C-terminus
      0.055   13.8   0.1        3.5    8.0   0.0    2.8  2  ACDC          AP2-coincident C-terminal
      0.098   13.4   0.0        0.3   11.9   0.0    1.8  1  ASL_C2        Argininosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.2   0.1   2.9e-57   7.5e-54       7     307 ..      12     293 ..       7     295 .. 0.91

  Alignments for each domain:
  == domain 1  score: 183.2 bits;  conditional E-value: 2.9e-57
                                       TCHHHHHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHH CS
                           Lyase_1   7 adklmgiftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtav 83 
                                       +d++ +if+e+ r+n++l+     ++aa+++a    +++++e+ a+i k++d++  e+k+++  +++ i +++  ++
  gi|518651876|ref|YP_008141396.1|  12 RDNVKNIFSEETRLNIMLN-----VEAAIAQAESYYGIIPEEAYADIRKVVDNN--EVKIGRVKEIEAIINHDVMSI 81 
                                       789999*************.....99************************9986..479997677766666665555 PP

                                       HHHHHHHHHHHTTHSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETT CS
                           Lyase_1  84 nmnlnevigellgekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThl 160
                                          l+e            +++vh+g +snD+++ a ++++k+a+s  ++++le+L +al+ + ke+++++++GrTh+
  gi|518651876|ref|YP_008141396.1|  82 VEGLTEKCT-------TGKNYVHFGVTSNDINDSASAVQMKRAISI-IISDLEDLGKALVSRIKENEETIMVGRTHG 150
                                       555666666.......789*************************65.****************************** PP

                                       EEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCC.THHHHHHHHHHHHHCSTEESSSHH CS
                           Lyase_1 161 qdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnadp.efaelvakelakvtglpvkapnsf 236
                                       q+A P+tlg +++ y  ++ r++er++e++kr++++++ g +++g++l+ ++ + +e+ ++ l+ +t      +   
  gi|518651876|ref|YP_008141396.1| 151 QHASPITLGLKFAVYLSEIGRHLERIQEARKRIIAGKILGPVGTGAALGKNAlKIQEKTCEILG-ITH-----ETAS 221
                                       ************************************************9998788999999999.777.....6666 PP

                                       HHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHH CS
                           Lyase_1 237 eavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltgva 307
                                       +++  rD+++e+l++++++ +s+ kfa ++r l+  e   l e  +  ++ GSS MP K+NP+ +E++ + a
  gi|518651876|ref|YP_008141396.1| 222 TQIVGRDRYIEYLSIINNISVSMEKFATEIRNLQRPEiYELSEYFDSDKQVGSSSMPSKRNPIVSENIVSLA 293
                                       699****************************************************************98765 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.7   9.5e+03      16      28 ..      44      56 ..      34      73 .. 0.77
   2 ?   -3.2   0.0       5.2   1.3e+04      22      64 ..     260     273 ..     247     276 .. 0.56
   3 !   54.4   0.0   5.4e-18   1.4e-14       2      72 ..     362     437 ..     361     438 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                                      H-HHHHHHHHHHH CS
                            ADSL_C 16 lgReeAyelVqea 28
                                      +  eeAy+ +++ 
  gi|518651876|ref|YP_008141396.1| 44 IIPEEAYADIRKV 56
                                      5568888877764 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 5.2
                                       HHHHHHHHHHHHHCHHHHHHT-HHHHCHHCHHHHHT-GGGCCT CS
                            ADSL_C  22 yelVqeaamkaweellelLaadpevkkseeeldalfdpayylg 64 
                                       y                             el + fd ++ +g
  gi|518651876|ref|YP_008141396.1| 260 Y-----------------------------ELSEYFDSDKQVG 273
                                       3.............................5556666655555 PP

  == domain 3  score: 54.4 bits;  conditional E-value: 5.4e-18
                                       GGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC...HHHHHHT-HHHHC.HHCHHHHHT-GGGCCTTHHHHHHH CS
                            ADSL_C   2 lifservllaLv.kglgReeAyelVqeaamkawee...llelLaadpevkk.seeeldalfdpayylgsadeivdr 72 
                                       +i+se+v+  L+ +g+ R++A+e V+ea+m a ++   l+e+L     +++ se+ ld++++p+++lg + ei++ 
  gi|518651876|ref|YP_008141396.1| 362 FIMSESVTTTLTeNGMPRQDAHEFVREASMHAYKQkktLKETLVDMGILNHiSEKILDRAMEPENFLGVSKEICED 437
                                       8***********66******************************999999889999****************9875 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.8   9.7e+03      71     105 ..      49      69 ..      46      80 .. 0.51
   2 ?   -2.6   0.0       2.2   5.5e+03      50      85 ..     238     273 ..     233     280 .. 0.65
   3 !   20.7   0.1   1.3e-07   0.00033       4     114 ..     312     427 ..     310     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.8
                                       HHHHHHHHHTTS---HHHHHHHHHCS-S-HHHHHH CS
                             ASL_C  71 pYeklkeltrgkkitkeslkefieslevseeakee 105
                                       +Y  +++++ +++++                  +e
  gi|518651876|ref|YP_008141396.1|  49 AYADIRKVVDNNEVK--------------IGRVKE 69 
                                       555555555555444..............333333 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.2
                                       T-GGGGHHHHHHHHHHTT-TTHHHHHHHHHTTS--- CS
                             ASL_C  50 enwevlaEaiqtvlrregiekpYeklkeltrgkkit 85 
                                       +n +v  E   t +r+ + ++ Ye    +   k++ 
  gi|518651876|ref|YP_008141396.1| 238 NNISVSMEKFATEIRNLQRPEIYELSEYFDSDKQVG 273
                                       455666677777777777777777666666666655 PP

  == domain 3  score: 20.7 bits;  conditional E-value: 1.3e-07
                                       T--TCHHHHHTTCHHHHHHHHHH.HHHHHHHHCCEEE-HHHHHHHHHT-GGGGHHHHHHHHHHTT-..TTHHHHHHH CS
                             ASL_C   4 QRDLtdStvlRnlgvalahslia.lksllkglsklevneealaedLdenwevlaEaiqtvlrregi..ekpYeklke 77 
                                        RDLt+S+  R +   ++  +   +++++  +s+l +n+e++++       +++E++ t+l ++g+  ++++e ++e
  gi|518651876|ref|YP_008141396.1| 312 ERDLTNSALERFTIPYVSILADDiITKMTGVFSHLFINREEMKKRAYGDEFIMSESVTTTLTENGMprQDAHEFVRE 388
                                       6**********9866555444332467778899******************************99833589****** PP

                                       HHTTS---HHHHHHHHHCS-S-HHHHHHH..HC--CCC- CS
                             ASL_C  78 ltrgkkitkeslkefieslevseeakeeL..kaltpatY 114
                                           +  +k++lke + ++ + ++++e++  +a++p+++
  gi|518651876|ref|YP_008141396.1| 389 ASMHAYKQKKTLKETLVDMGILNHISEKIldRAMEPENF 427
                                       **************9999998888887773346777776 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   4.9e-07    0.0013      32     103 ..     365     436 ..     329     445 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.9e-07
                                       -THHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHHSSHHHHHHHHHHHHH CS
                      Mur_ligase_M  32 nneiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfhgtlenyaeaKaelfe 103
                                        +++++ +t + m +++a+ +v E+s+h++++ k l++ + +d+++++ is+  ld+  + en +   +e+ e
  gi|518651876|ref|YP_008141396.1| 365 SESVTTTLTENGMPRQDAHEFVREASMHAYKQkKTLKE-TLVDMGILNHISEKILDRAMEPENFLGVSKEICE 436
                                       577888888899********************888888.9*****************9999999888888876 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   1.3e-05     0.033      20      53 ..     392     428 ..     386     429 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                                       HHHHHT--HHHHHHHTT-....-HHHHHHHT-HHHHH CS
                       FumaraseC_C  20 eAlkegktlreavlelgl...lteeeldelldpekMt 53 
                                       +A+k++ktl+e  +++g+   ++e+ ld+++ pe+ +
  gi|518651876|ref|YP_008141396.1| 392 HAYKQKKTLKETLVDMGIlnhISEKILDRAMEPENFL 428
                                       8**************7775559************975 PP

>> ACDC  AP2-coincident C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0014       3.5       8      54 ..     115     180 ..     112     183 .. 0.85
   2 ?    2.5   0.0     0.073   1.9e+02      34      73 ..     285     338 ..     238     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0014
                              ACDC   8 KeaikliLeDLlnnclpqlasslanktss....................kelkrvieahikyvenak 54 
                                       K+ai++i++DL++   + ++   +n+ ++                      + + i +h++++++a 
  gi|518651876|ref|YP_008141396.1| 115 KRAISIIISDLEDLGKALVSRIKENE-ETimvgrthgqhaspitlglkfAVYLSEIGRHLERIQEAR 180
                                       99**********99988776666666.4469999999999999999999999999999999999986 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.073
                              ACDC  34 tss..............kelkrvieahikyvenakslkelqpylklFstcilkn 73 
                                       +s+               e++  ++ h +  +n++ +++ +py++++++ i  +
  gi|518651876|ref|YP_008141396.1| 285 VSEnivslarltrsfiiPEYEAGVQWHERDLTNSALERFTIPYVSILADDIITK 338
                                       33356666666667788899999999********************99887765 PP

>> ASL_C2  Argininosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012       0.3      10      67 ..     371     427 ..     364     429 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       HHHHCTS-HHHHHHHHHHHHHHHHHTT--GGG--HHHHHHH-TT--GGGGG.GSSHHHH CS
                            ASL_C2  10 yLvrkGlpFReAHeivgravrlaeekgkeleeltleelkeisplleedvee.aLdpeas 67 
                                        L+++G+p  +AHe+v +a  +a +++k+l+e  ++      ++++e++ + a++pe++
  gi|518651876|ref|YP_008141396.1| 371 TLTENGMPRQDAHEFVREASMHAYKQKKTLKETLVDMGI--LNHISEKILDrAMEPENF 427
                                       69999******************9999999876555433..446776665558888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       587  (0.0327403); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 3067.53
//
Query:       gi|518651877|ref|YP_008141397.1|  [L=194]
Description: hypothetical protein FACI_IFERC00001G0516 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1296.67
//
Query:       gi|518651878|ref|YP_008141398.1|  [L=218]
Description: hypothetical protein FACI_IFERC00001G0517 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-40  138.5   0.0    2.4e-40  138.2   0.0    1.1  1  Chlor_dismutase  Chlorite dismutase


Domain annotation for each model (and alignments):
>> Chlor_dismutase  Chlorite dismutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.2   0.0   1.3e-44   2.4e-40       5     192 ..      28     210 ..      24     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 138.2 bits;  conditional E-value: 1.3e-44
                                       HHHHHHHHHHTTSCEEEEEEEETSTTTT-SEEEEEEESSHHHHHHHHHHHHHSTGGGGEEEEEEEEEEEEEESSSSS CS
                   Chlor_dismutase   5 veelealleeaeegvlralysvlGlradaDlmlwllretleelqeaerelrrtalgkvlepaysyvsvtelseYkee 81 
                                        +++ +++++++++ l+++  + ++r+d D+++w +++ + +l+ +++ +++ a+g + +++ys++s++e+s Y   
  gi|518651878|ref|YP_008141398.1|  28 NSNIIHFINNYRKN-LISIKYYKSIRHDNDILIWSASDMPINLEGLKEGINS-AIGIYGKSEYSMFSLYEHSPY--- 99 
                                       56677788888888.89999999****************************9.*********************... PP

                                       -GGGHHHCHHHHS----SSSEEEEEEEEE-EEGGGS-HHHHHHHHHHHHHHHHGCTT...EEEEEEE-TTTSSSSEE CS
                   Chlor_dismutase  82 deenkshvearlapelpkkkyvcvYPmsksreWYllpeeeRrelmaeHgeigrkYgk...VrqiitgsfGldDyEwg 155
                                           +++ + + + ++++kky++vYPmsk+reWYl++ eeR++++a H+ ++r+ ++   + +++t+sfGl+D+E++
  gi|518651878|ref|YP_008141398.1| 100 ---VNATNSLEDTLKTDPKKYFVVYPMSKDREWYLINYEERKKILAGHIGTARSDKEspgIISYTTYSFGLGDQEFV 173
                                       ...4444444555556689*********************************98854577***************** PP

                                       EEEEESSTHHHHHHHHHHCTSHHHHHHEEE-S-EEEE CS
                   Chlor_dismutase 156 valeaddleefkdlvyelRfdeasakvaeegpfyvGr 192
                                       v +e ddl+++ ++ ++lR+  a++++ +e p++vG 
  gi|518651878|ref|YP_008141398.1| 174 VLYELDDLAAWSHVTEKLREVMARKWIINEAPIFVGI 210
                                       ***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.31s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1411.68
//
Query:       gi|518651879|ref|YP_008141399.1|  [L=118]
Description: rhodanese-related sulfurtransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-17   64.6   0.0    1.4e-17   64.2   0.0    1.2  1  Rhodanese  Rhodanese-like domain


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.0   7.7e-22   1.4e-17       2     106 ..      24     111 ..      16     112 .. 0.84

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 7.7e-22
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                       +++l +l ek    ++DvR+  eY +ghI+gA+             +    + +e+  ++    +++++++c++g+r
  gi|518651879|ref|YP_008141399.1|  24 PEKLTALKEKYP--VIDVRTGFEYRHGHIKGAIPY-----------KLGKEDEIEKKFPK----DDPIILICKTGHR 83 
                                       566666666665..9********************...........66666666666665....9************ PP

                         Rhodanese  79 aaaaaallkklGyknvsvldGGfkawke 106
                                       ++aaa+ l + Gyk++++l+GG+++w +
  gi|518651879|ref|YP_008141399.1|  84 SRAAANRLVRKGYKKLYHLEGGMDKWRK 111
                                       8888776666**999***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 843.80
//
Query:       gi|518651880|ref|YP_008141400.1|  [L=76]
Description: 30S ribosomal protein S17e [Ferroplasma acidarmanus fer1]
Scores for complete 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   41.0   0.7    1.7e-10   40.9   0.7    1.0  1  Ribosomal_S17e  Ribosomal S17
  ------ inclusion threshold ------
      0.015   15.1   1.3      0.016   14.9   1.3    1.3  1  DUF5507         Family of unknown function (DUF5507)


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 !   40.9   0.7   1.9e-14   1.7e-10       1      62 [.       1      63 [.       1      73 [. 0.89

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1.9e-14
                                      XX----HHHHHHHHHHHHS-TTT--S-HHHHHHHHHH.HS----SHHHHHHHHHHHHHHHHTT CS
                    Ribosomal_S17e  1 mgrvrtktvKkaarviiekyyskltndFhtnkkvcee.vaiipskklrnkiaGyvthlmkriq 62
                                      mg +r   +K+ +++++++ +  +++dF++nk++++  +    +kk  n iaGy+t+++ + +
  gi|518651880|ref|YP_008141400.1|  1 MGSIRPSNIKRISEELVDNNKDLFNEDFNHNKEILHSfIEKTVTKKTANAIAGYITRYILKKK 63
                                      8999******************************998789999*************9875533 PP

>> DUF5507  Family of unknown function (DUF5507)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3   1.8e-06     0.016      79     109 ..       8      38 ..       1      71 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
                           DUF5507  79 qlkrikyevgennlkvfnvhfnnnhelvssg 109
                                       ++kri  e+ +nn  +fn  fn n+e++ s 
  gi|518651880|ref|YP_008141400.1|   8 NIKRISEELVDNNKDLFNEDFNHNKEILHSF 38 
                                       69************************98774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 502.21
//
Query:       gi|518651881|ref|YP_008141401.1|  [L=145]
Description: universal stress protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.8e-23   81.5   0.0    1.4e-22   80.7   0.0    1.4  1  Usp        Universal stress protein family
  ------ inclusion threshold ------
      0.029   14.1   0.0      0.033   13.8   0.0    1.1  1  PRD_Mga    M protein trans-acting positive regulator (MGA) PR
       0.15   10.9   0.0       0.17   10.8   0.0    1.1  1  SBP_bac_5  Bacterial extracellular solute-binding proteins, f


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 !   80.7   0.0   2.4e-26   1.4e-22       4     141 .]       2     142 ..       1     142 [. 0.76

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 2.4e-26
                                       EEEEEE-SSHHHHHHHHHHHHHHHHCTSEEEEEEEEESSH..CCCCCCCHHHHHHHHHHHHHHHHHHHH..HHHHHH CS
                               Usp   4 rIlVavDgseeskkAlewAlelakargaelillhvidpra..sgavsdadeeaeeeeleleeaeleada..akaaae 76 
                                       ++lV +Dgse +++Al++Alel  +  +e ++++vi++    s++ + + +++ +e +++++++  ++a    +++e
  gi|518651881|ref|YP_008141401.1|   2 KVLVSYDGSEGAREALKYALELKCTV-DEYYIVYVIPTIVgiSASFDSYIPQSVYEGQDKTADQILEKAkkVLDKEE 77 
                                       89*******************87776.689******98542122222333333333333333322222235666777 PP

                                       CTTCEEEEEEEESSHHHHHHHHHHHTTSSEEEEESCCSSTTTTCSSBHHHHHHHHHTSSEEEEEE CS
                               Usp  77 aggvkvevvveegdpaeeilevaeeedadliVvGsrgrsglsrlllGSvseyvlrhapcpVlvVr 141
                                       a+ +  ++   + +    il++aee++++liV+G+r+++g+s+l+lGSvs+ +++h+++pV+vV+
  gi|518651881|ref|YP_008141401.1|  78 AKYELIKISSNGEEIPKIILKTAEEKGINLIVTGTRKLHGFSKLILGSVSSGIIAHSNIPVTVVP 142
                                       7777778888888888899*********************************************7 PP

>> PRD_Mga  M protein trans-acting positive regulator (MGA) PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.6e-06     0.033      75     150 ..      17      88 ..       1      93 [. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.6e-06
                           PRD_Mga  75 lklgleldedtldyLFliylqkdlsldslfwtsekkqsyvelsykllsykllldelsallkievenkdelikilHN 150
                                       lk+ lel+  t+d+ +++y++  +   s+ ++s + qs +e+  k  +  ++l++ ++ l +e e k+eliki  N
  gi|518651881|ref|YP_008141401.1|  17 LKYALELKC-TVDEYYIVYVIPTIVGISASFDSYIPQSVYEGQDKTAD--QILEKAKKVLDKE-EAKYELIKISSN 88 
                                       456666654.79***********9999*********************..*****99988887.789999998755 PP

>> 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 ?   10.8   0.0   2.9e-05      0.17     223     286 ..      13      80 ..       9     111 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTCCSCHCCCSHH..SH..HHHHHHHHHHTT-BC CS
                         SBP_bac_5 223 vRqAlsyAiDreeivkavlegyatpansllppsspgadeeykpayka..yd..pekAkklLkeaGykd 286
                                        R+Al yA+  +  v++++  y +p+   ++ s++++ +   ++ ++   d  +ekAkk L++   k 
  gi|518651881|ref|YP_008141401.1|  13 AREALKYALELKCTVDEYYIVYVIPTIVGISASFDSYIPQSVYEGQDktADqiLEKAKKVLDKEEAKY 80 
                                       69****************99999999999999999987777666554653356999999998654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      620  (0.0345808); 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: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.50
# Mc/sec: 867.14
//
Query:       gi|518651882|ref|YP_008141402.1|  [L=198]
Description: hypothetical protein FACI_IFERC00001G0521 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1402.12
//
Query:       gi|518651883|ref|YP_008141403.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G0522 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-68  231.9  28.1    1.6e-68  231.6  28.1    1.0  1  Sugar_tr  Sugar (and other) transporter
    6.5e-34  117.4  46.7    6.4e-33  114.1  38.3    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.6  28.1   1.8e-72   1.6e-68       2     449 ..      19     454 ..      18     456 .. 0.91

  Alignments for each domain:
  == domain 1  score: 231.6 bits;  conditional E-value: 1.8e-72
                                       HHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHH CS
                          Sugar_tr   2 alvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkks 78 
                                       +++ a+g +l gYd+ vi++f+ +l ++k f+++  ++         +++++++l+Ga++G++++g ++d +GR++ 
  gi|518651883|ref|YP_008141403.1|  19 TTLSAMGYFLDGYDLSVISVFTLVLVTFKPFHYDPFTE---------SFVTGAALLGAFVGAVIFGHFADNIGRRYL 86 
                                       56778999******************888887777775.........599*************************** PP

                                       HHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  79 lliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaa 155
                                       +++  ++f + a+l+a+++   +++ +i+ R++vG gvG+ ++l+P+y+ E+ p+k+Rga  ++  +++++G   a+
  gi|518651883|ref|YP_008141403.1|  87 YIFDLIFFAVFAILSALST---NIYEMIIFRFFVGWGVGADYALSPVYTTEMYPDKKRGAGYGWVWTFWSIGAGAAF 160
                                       *******************...9****************************************************** PP

                                       HHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHH.HHTT-HH.HHHHHHHHHHHCHHHHHHHHHHHHH CS
                          Sugar_tr 156 ifglglnktsnadgwrillglqlvpallllilllflPESPryl.vekgkee.eakevlaklrgeedadrelaeekds 230
                                        +g+++ +++  +gwr++l++ ++pa++ ++l++ +PES r+  +e gk +  ak   +  + +   ++++++++++
  gi|518651883|ref|YP_008141403.1| 161 AIGYVFYMINPLVGWRYTLAIGAIPAIVTVVLRTRMPESVRWDiLEPGKSKlSAKDLDSIAERVGITKEDIKAIIAE 237
                                       ******************************************83566677766777777688889999999999999 PP

                                       HHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHH.HHHHHHHH CS
                          Sugar_tr 231 leaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiiv.gvvnfvat 304
                                        e+e++    s   l++  ++ +r+ i+   +i+    G   i  ysp i+ +lg+s s  ll+++i+ + v f+  
  gi|518651883|ref|YP_008141403.1| 238 REKEENIAAGSFTALFKG-EYGKRTAIIWFQWILYDIAG-YGIGLYSPIILTTLGISHSssLLFSLIFnMPVGFLGA 312
                                       999977776666666666.57899999999999999999.78999****************8888776478****** PP

                                       HHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHH...HTTTTHHHHHHHHHH CS
                          Sugar_tr 305 fvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialf...algwgpvpwvlvsEl 378
                                       f a++l dr+GRR+l  lG+ gmai+++++    ++ +++   asi++i++ia f++ +   +lg+g ++ +++ El
  gi|518651883|ref|YP_008141403.1| 313 FGAVMLNDRLGRRPLQALGFGGMAIAMAMFF---IA-SSA--IASIGIIIGIAAFVIDYgigNLGPGDTMGLYAIEL 383
                                       ***************************9995...33.333..57999999999999877222568************ PP

                                       SHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCG CS
                          Sugar_tr 379 fpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeie 449
                                        p+++Rs+ +  a+ +  +a+fl +++fp i  ++g+  +f++  gl+vl+++f+ ff+petkg+tleei 
  gi|518651883|ref|YP_008141403.1| 384 LPTKLRSSSMGGATGITRIASFLAAFMFPLISASLGKSSFFFILLGLMVLAFVFTIFFTPETKGLTLEEIA 454
                                       *********************************************************************96 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.1  38.3   7.1e-37   6.4e-33       3     352 ..      24     407 ..      22     412 .. 0.82
   2 !   12.0   7.1   8.3e-06     0.074     108     176 ..     378     446 ..     366     469 .. 0.84

  Alignments for each domain:
  == domain 1  score: 114.1 bits;  conditional E-value: 7.1e-37
                             MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +++fl +++ s+++++       + ++++p + ++++++  lga+v+++++G+++d++Grr ++++ l++fa++ ++
  gi|518651883|ref|YP_008141403.1|  24 MGYFLDGYDLSVISVFTLVlVTFKPFHYDPFTESFVTGAALLGAFVGAVIFGHFADNIGRRYLYIFDLIFFAVF-AI 99 
                                       7899999999998888877677889*************************************************.55 PP

                             MFS_1  79 ll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg...llasslgWr 151
                                       l+ ++++++ ++++r++ G+g ga ++++ +++++++p+++rg ++g++ +++s+Ga  + ++g    ++  ++gWr
  gi|518651883|ref|YP_008141403.1| 100 LSaLSTNIYEMIIFRFFVGWGVGADYALSPVYTTEMYPDKKRGAGYGWVWTFWSIGAGAAFAIGYvfyMINPLVGWR 176
                                       553668899*******************************************************95533337777** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeee.............................kgtgpaplvp. 198
                                       ++  i ai +++ +    +l ++ p + +++  ++ +                             ++       + 
  gi|518651883|ref|YP_008141403.1| 177 YTLAIGAIPAIVTV----VLRTRMPESVRWDILEPGKsklsakdldsiaervgitkedikaiiaerEKE------En 243
                                       ************94....566666666666666666667788888999999888877777666644222......13 PP

                             MFS_1 199 ....awkallkdpvlw.....illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagr 266
                                            ++al+k    +     i+++ ++l  ++ +g+  ++p++  ++lg+s + +++l++ ++ + + +l+ +++ 
  gi|518651883|ref|YP_008141403.1| 244 iaagSFTALFKGE--YgkrtaIIWFQWILYDIAGYGIGLYSPII-LTTLGIS-HSSSLLFSLIFNMPVGFLGAFGAV 316
                                       3335466666666..223455799******99***********7.*******.888888888888888888888899 PP

                             MFS_1 267 ls.drlgrrrrlllallllllaalglallavtssavllll...vlvl.iGfglgfvfpsllalasdlappeeagtas 338
                                       ++ drlgrr+   l+++++++a +++++++ +  ++ +++   ++v+ +G+g      ++  +a +l+p++ + + +
  gi|518651883|ref|YP_008141403.1| 317 MLnDRLGRRPLQALGFGGMAIAMAMFFIASSAIASIGIIIgiaAFVIdYGIGNLGPGDTMGLYAIELLPTKLRSSSM 393
                                       889***************************99555555556656666999988888889999999999998887777 PP

                             MFS_1 339 glfntagslggalg 352
                                       g ++ +  ++++l+
  gi|518651883|ref|YP_008141403.1| 394 GGATGITRIASFLA 407
                                       77777777776665 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.3e-06
                             MFS_1 108 aliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeep 176
                                        ++ ++ p + r++ +g +++ + +++ l++   +l+++slg ++ f+il ++++lafv+ +++ pe++
  gi|518651883|ref|YP_008141403.1| 378 LYAIELLPTKLRSSSMGGATGITRIASFLAAFMFPLISASLGKSSFFFILLGLMVLAFVFTIFFTPETK 446
                                       4666788888*************************************************8555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 3163.78
//
Query:       gi|518651884|ref|YP_008141404.1|  [L=319]
Description: hypothetical protein FACI_IFERC00001G0523 [Ferroplasma acidarmanus fer1]
Scores for complete 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   48.9   2.0    4.2e-13   48.9   2.0    2.1  2  YrhK      YrhK-like protein


Domain annotation for each model (and alignments):
>> YrhK  YrhK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1     0.083   1.5e+03       2      17 ..     203     218 ..     202     239 .. 0.68
   2 !   48.9   2.0   2.4e-17   4.2e-13       2      60 ..     255     309 ..     254     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.083
                              YrhK   2 ryeaislandiigsll 17 
                                       r++ i ++n++ +++l
  gi|518651884|ref|YP_008141404.1| 203 RLNYIETINGMAAGGL 218
                                       5677888998887765 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 2.4e-17
                              YrhK   2 ryeaislandiigsllFlvGSilflpnsefwkwqiagvwlFliGSilflirpvirlvre 60 
                                       +y ++ + nd+ ++l Fl GSilfl     ++   +gv+lF++ Si++l++p i+++r+
  gi|518651884|ref|YP_008141404.1| 255 FYGWVAIGNDVAIGLEFLSGSILFL----SQADYFYGVYLFIAASIQLLVKPGIEIFRR 309
                                       799**********************....899************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 2054.03
//
Query:       gi|518651885|ref|YP_008141405.1|  [L=459]
Description: hypothetical protein FACI_IFERC00001G0524 [Ferroplasma acidarmanus fer1]
Scores for complete 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-76  254.9   0.0    1.1e-75  254.7   0.0    1.1  1  Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved do
    1.4e-07   30.9   0.0    9.6e-07   28.1   0.0    2.0  1  Aminotran_5    Aminotransferase class-V


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 !  254.7   0.0   1.3e-79   1.1e-75      11     375 .]      40     377 ..      31     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 254.7 bits;  conditional E-value: 1.3e-79
                                       SHHSSHH.HHHHHHHHHHCTGGGS--TTSTTBHCSSH....HHHHHHHHHHHHHT-BTSSTTTSHHHHHHHHHHHHH CS
                     Pyridoxal_deC  11 aapekaesleqilediekilapgvttwhspefhkllpagnslisllgdlLadainkngftweesPaltelevvvldw 87 
                                       a++ + e + ++++  e +la++vtt ++pe  +l++              + + kn+++  e+P++ + e+++++ 
  gi|518651885|ref|YP_008141405.1|  40 AYEMIHE-ELKLDGIPELNLATFVTTYMEPEAKNLYM--------------ENAHKNFIDSFEYPQIKKEETRIVNI 101
                                       4555555.8999*************************..............99************************ PP

                                       HHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHHH CS
                     Pyridoxal_deC  88 laellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqahssvekaalv 164
                                       l  l ++pe +      g+ ++gsses++lallA ++++  +m++ +k+        k++++ +++ h+ ++k+a++
  gi|518651885|ref|YP_008141405.1| 102 LSRLYNAPEGKDF---TGTSTIGSSESIMLALLAHKWNWKSKMEALKKD------ASKPNIVFGADTHVVWDKFAKY 169
                                       ********55554...69*****************************99......789******************* PP

                                       HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHH......CT-EEEEE- CS
                     Pyridoxal_deC 165 lgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicek......ydlwlHvDA 235
                                       ++v+ rv+pld   k r+ ++ k+ie+++e+  ++  v a lGtt +gaFdd+k ++ ++e+       d+++HvDA
  gi|518651885|ref|YP_008141405.1| 170 FDVEARVVPLDA--KTRVVDPDKLIENVDEN--TI-AVGAVLGTTFTGAFDDVKRINSLLEElkskkgLDIPIHVDA 241
                                       ***********8..67***************..77.8******************************9********* PP

                                       TTGGGGGGSGGGGG...GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCC CS
                     Pyridoxal_deC 236 AyaGsaficpeirh...llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgt 309
                                       A+aG  fi p+i +   +++++  ++Si+v++hK++lv+ + ++l++kdk +l++ l++ ++YL+        d++t
  gi|518651885|ref|YP_008141405.1| 242 ASAG--FITPFIEPeleWDFRLSHVKSINVSGHKFGLVYPGLGWLLFKDKADLPDDLVFYVNYLG-------DDMPT 309
                                       ****..***********************************************************.......89*** PP

                                       GSSSSSG..HHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECS.TTBSSEEEEEES CS
                     Pyridoxal_deC 310 kaiplsr..rvrilklwfvlralGveglqnqirksvelakyleklirkderfeiva.evelglVcFrlk 375
                                       +++++s+   + + +++ ++r lG  g++n  ++ +++akyl+++i +  + e+v+  ++++ V Fr k
  gi|518651885|ref|YP_008141405.1| 310 YTLNFSKsaANIAPQYYNIIR-LGKSGYRNIAENIMKNAKYLADKISEFPELEVVSrAEHIPVVTFRQK 377
                                       *******7556677*******.*********************************9999*******975 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   1.1e-10   9.6e-07      69     218 ..     121     291 ..      90     389 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.1e-10
                                       SHHHHHHHHHHHCCCC-TTTSEEEEETTSHGG......GTHHHHHHHHHHTEEEEEEEBETTS.CBEGGGHHHH--T CS
                       Aminotran_5  69 Gtteainlvalslarslkpgdeivvteaehha......nlvpwqelakrtgakvkvipldeeg.eldldelekllne 138
                                       G++e+i l++l+ + ++k + e++ ++a +        ++v w + ak   ++ +v+pld++   +d+d+l ++++e
  gi|518651885|ref|YP_008141405.1| 121 GSSESIMLALLAHKWNWKSKMEALKKDASKPNivfgadTHVVWDKFAKYFDVEARVVPLDAKTrVVDPDKLIENVDE 197
                                       566666666666655566666666666655431111114689*****************98751578********** PP

                                       TEEEEEEESBETTTTEB--HHHHHHHHHH...T...T-EEEEE-TTTTTTS---HHHHTESE.......EEEETTT. CS
                       Aminotran_5 139 ktklvaithvsnvtGtiqpveeigklakk...k...galvlvDaaqavghipidvkklgvDf.......lafsghK. 201
                                       +t +v      + tG +++v++i++l+ +   k   ++ ++vDaa+a    p+   +l+ Df       + +sghK 
  gi|518651885|ref|YP_008141405.1| 198 NTIAVGAVLGTTFTGAFDDVKRINSLLEElksKkglDIPIHVDAASAGFITPFIEPELEWDFrlshvksINVSGHKf 274
                                       ***********************9987432112235799********9999998888888885555555779****8 PP

                                       TTSSTT-EEEEEEHHHH CS
                       Aminotran_5 202 llgPtGiGvlyvrkell 218
                                        l  +G+G l +++++ 
  gi|518651885|ref|YP_008141405.1| 275 GLVYPGLGWLLFKDKAD 291
                                       79999********9653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2934.12
//
Query:       gi|518651886|ref|YP_008141406.1|  [L=203]
Description: bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP pyrophosphatase protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-30  102.4   0.3    1.3e-29  101.8   0.3    1.3  1  PRA-CH    Phosphoribosyl-AMP cyclohydrolase
    3.2e-12   46.7   0.1      5e-12   46.1   0.1    1.3  1  PRA-PH    Phosphoribosyl-ATP pyrophosphohydrolase
  ------ inclusion threshold ------
      0.055   13.6   0.2       0.12   12.6   0.2    1.6  1  MazG      MazG nucleotide pyrophosphohydrolase domain


Domain annotation for each model (and alignments):
>> PRA-CH  Phosphoribosyl-AMP cyclohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.8   0.3   2.2e-33   1.3e-29       2      73 ..      27      98 ..      26      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 101.8 bits;  conditional E-value: 2.2e-33
                                      EEEE-HHHHHHHHHHSB-EEEETTTTEEEETTTTTS--EEEEEEEE-TTSSEEEEEEEESS-SSTTSBSSS- CS
                            PRA-CH  2 laymnkealektletgkavyySrsrkklWkKGetSgnvqkvkeirlDcDqDalllkveqkgaaCHtgkesCF 73
                                      laym+ ea++k++etg ++yySrs++++ +KGe Sgn+q++k++++DcD+D+ll++v+qkgaaCH+g++sCF
  gi|518651886|ref|YP_008141406.1| 27 LAYMDGEAYRKSMETGLMHYYSRSKQRVRMKGEASGNIQEIKDVKIDCDNDSLLFMVKQKGAACHLGTKSCF 98
                                      79********************************************************************** PP

>> PRA-PH  Phosphoribosyl-ATP pyrophosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   8.3e-16     5e-12       3      82 ..     119     200 ..     117     201 .. 0.89

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 8.3e-16
                                       HHHHHCT----SS----.-HHHHHH....HHHHHHHHHHHHHHHT-SCHHHHHHHHHHHHHHHHHHHHHHCT--CHH CS
                            PRA-PH   3 efhrligerkpetPeas.taelasl....raaligEEavElleaasegdlaeladelaDllYvtygllvllGidlda 74 
                                       e++ li ++k++  ++s t el+      + +++gEEavE + a     +  +++e aDllY++++ l + +i+l +
  gi|518651886|ref|YP_008141406.1| 119 ELESLIAKTKNTPRKNSyTTELFESgeenIKKKVGEEAVESILAQ---GKDRIVYETADLLYHLLVFLSYENIKLSD 192
                                       67888866666655666899999999*******************...8**************************** PP

                                       HHHHHHHH CS
                            PRA-PH  75 vfeevhra 82 
                                       +++e+ ++
  gi|518651886|ref|YP_008141406.1| 193 IMDELSKR 200
                                       *****987 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     2e-05      0.12      15      63 ..     154     198 ..     143     203 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2e-05
                                       HHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHH CS
                              MazG  15 gEvaeaIkkedrdeleeELGDvLlqvlflaniaeeeggidledvaetil 63 
                                       +E +e I  + +d +  E +D+L+++l +        +i+l+d+++++ 
  gi|518651886|ref|YP_008141406.1| 154 EEAVESILAQGKDRIVYETADLLYHLLVFLSY----ENIKLSDIMDELS 198
                                       488999999******************99997....9999999998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (203 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.49
# Mc/sec: 1249.28
//
Query:       gi|518651887|ref|YP_008141407.1|  [L=250]
Description: hypothetical protein FACI_IFERC00001G0526 [Ferroplasma acidarmanus fer1]
Scores for complete 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-76  255.3   1.9      5e-76  255.2   1.9    1.0  1  His_biosynth  Histidine biosynthesis protein
    4.3e-07   29.6   0.6    2.5e-05   23.8   0.5    2.1  2  NMO           Nitronate monooxygenase
    1.2e-05   24.8   0.2       0.02   14.3   0.1    2.1  2  TMP-TENI      Thiamine monophosphate synthase
    1.9e-05   24.1   0.3      0.006   15.9   0.1    2.3  2  ThiG          Thiazole biosynthesis protein ThiG
    3.7e-05   23.0   0.2       0.21   10.6   0.1    2.1  2  Dus           Dihydrouridine synthase (Dus)
    0.00021   20.6   0.7    0.00036   19.8   0.1    1.6  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0054   16.2   0.1        2.3    7.6   0.0    2.4  2  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.2   1.9     2e-79     5e-76       1     229 []       5     233 ..       5     233 .. 0.98

  Alignments for each domain:
  == domain 1  score: 255.2 bits;  conditional E-value: 2e-79
                                       EEEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEE CS
                      His_biosynth   1 riipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvq 77 
                                       rii alD+   +vV   kG++f++ +++gdp++lakrye+eg+del+++D+ a++e+r+++  lve++a+e+ ip++
  gi|518651887|ref|YP_008141407.1|   5 RIIGALDIAGDRVV---KGVNFENVKDSGDPIQLAKRYESEGIDELVFLDIRATREKRNIMNMLVERVASEIYIPFT 78 
                                       8*************...************************************************************ PP

                                       EESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEE..C.EEEEETTTTEEEEEEHHH CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarr..g.ykvaikgwreetgldave 151
                                       vGGG  ++e++ +++++gad++ i+t av++pe+i ++++++gs + v+aiD+ r  g y v+++g++ + g+da++
  gi|518651887|ref|YP_008141407.1|  79 VGGGLTDIETMVKIIRNGADRIFINTYAVEHPEIIGKISDRIGSANTVIAIDSGRhnGnYYVYTHGGTLNAGIDAIS 155
                                       ****************************************************9886527****************** PP

                                       HHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHHSSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 152 lakkleelgageilltdidrdGtlsGpdleltkelaeavkipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       +a+k+e+lgage+l+t+i++dGt++G+d +l++++  +v+ipviasGG+gs+ed+  ++++g+d+++++s+++eg++
  gi|518651887|ref|YP_008141407.1| 156 WAQKAESLGAGELLVTSINTDGTKKGFDTDLIRKITGSVNIPVIASGGAGSPEDFLGVFQAGADGALAASIFHEGKY 232
                                       ***************************************************************************98 PP

                                       - CS
                      His_biosynth 229 t 229
                                       t
  gi|518651887|ref|YP_008141407.1| 233 T 233
                                       6 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.2   0.0     0.009        23     182     222 ..      63     103 ..      20     108 .. 0.79
   2 !   23.8   0.5   9.9e-09   2.5e-05     140     225 ..     148     227 ..     117     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.009
                               NMO 182 faLvpqvldavdiPviAaGGiidrrgvaaaLalGAsgvqig 222
                                         Lv++v++ + iP    GG+ d + +  +++ GA  + i 
  gi|518651887|ref|YP_008141407.1|  63 NMLVERVASEIYIPFTVGGGLTDIETMVKIIRNGADRIFIN 103
                                       45778888888899999999999988888888888776665 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 9.9e-09
                               NMO 140 iptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLalGA 216
                                          i ++  a+k+e++Ga  l v+  +  G +  ++      + L+ ++   v+iPviA GG    ++   ++ +GA
  gi|518651887|ref|YP_008141407.1| 148 NAGIDAISWAQKAESLGAGELLVTSINTDGTKKGFD------TDLIRKITGSVNIPVIASGGAGSPEDFLGVFQAGA 218
                                       5678889999999****9999999987766544255......57********************************* PP

                               NMO 217 sgvqigtrf 225
                                        g+  ++ f
  gi|518651887|ref|YP_008141407.1| 219 DGALAASIF 227
                                       **9888766 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0   0.00047       1.2     109     176 ..      36     101 ..      29     104 .. 0.82
   2 !   14.3   0.1   7.7e-06      0.02     114     175 ..     157     221 ..     146     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00047
                          TMP-TENI 109 aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPvvaiGGit.lenvaevleagadgva 176
                                       a++ e++g+d +++  i +T  K +       +++++a+++ iP+ + GG+t  e++ ++++ gad++ 
  gi|518651887|ref|YP_008141407.1|  36 AKRYESEGIDELVFLDIRATREKRNI---MNMLVERVASEIYIPFTVGGGLTdIETMVKIIRNGADRIF 101
                                       78888889999999999888888765...4456788999999********863699**********997 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 7.7e-06
                          TMP-TENI 114 algadYigvGpifpTdtKkda..eplgleglkelaealeiPvvaiGGi.tlenvaevleagadgv 175
                                       a++a  +g+G +  T+  +d   +  + ++++++  +++iPv+a GG  ++e+   v++agadg 
  gi|518651887|ref|YP_008141407.1| 157 AQKAESLGAGELLVTSINTDGtkKGFDTDLIRKITGSVNIPVIASGGAgSPEDFLGVFQAGADGA 221
                                       456777888888888888877446667899*****************845899999999999996 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.4   0.0    0.0019       4.9     164     207 ..      63     106 ..      25     135 .. 0.80
   2 !   15.9   0.1   2.4e-06     0.006     154     206 ..     175     226 ..     147     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                                       HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHH CS
                              ThiG 164 kealkiiieeakvPvivDAGigspsdaaqamelGadavllntav 207
                                       ++ ++ + +e+ +P  v  G+   +  ++ +  Gad +++nt  
  gi|518651887|ref|YP_008141407.1|  63 NMLVERVASEIYIPFTVGGGLTDIETMVKIIRNGADRIFINTYA 106
                                       456778889999*****************************943 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.4e-06
                                       STTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHH CS
                              ThiG 154 piGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGadavllnta 206
                                         G+ +G  +   ++ i+ ++++Pvi   G gsp+d   +++ Gad+ l ++ 
  gi|518651887|ref|YP_008141407.1| 175 TDGTKKGFDT-DLIRKITGSVNIPVIASGGAGSPEDFLGVFQAGADGALAASI 226
                                       4588888765.57999********************************98875 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.1   8.3e-05      0.21     140     225 ..      32     115 ..      20     128 .. 0.83
   2 !   10.5   0.0     9e-05      0.23     141     212 ..     154     223 ..     145     236 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.3e-05
                                       HHHHHHHHHHCT-SEEE.EESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCH CS
                               Dus 140 alelakiveaaGaqalt.vHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrg 215
                                        ++lak+ e +G+++l+ +  R  ++++++      ++ v  ++ ip+ + G+ +d+e + +i+++ Gad + i   
  gi|518651887|ref|YP_008141407.1|  32 PIQLAKRYESEGIDELVfLDIRATREKRNIMN--MLVERVASEIYIPFTVGGGLTDIETMVKIIRN-GADRIFINTY 105
                                       57899999999999876377887777776633..45888999**********************99.********** PP

                                       HCCSTTHHHH CS
                               Dus 216 algnPwlfae 225
                                       a + P ++++
  gi|518651887|ref|YP_008141407.1| 106 AVEHPEIIGK 115
                                       *****99985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEE CS
                               Dus 141 lelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaedaqaileetGadgvmi 212
                                       +  a+++e  Ga +l v    + ++ ++  d + I+++  +v+ipvia G+  ++ed   + +  Gadg ++
  gi|518651887|ref|YP_008141407.1| 154 ISWAQKAESLGAGELLVTS-INTDGTKKGFDTDLIRKITGSVNIPVIASGGAGSPEDFLGVFQA-GADGALA 223
                                       5566666666666666643.34455555788999***************************999.**99876 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.64   1.6e+03     246     290 ..      76     119 ..      58     123 .. 0.59
   2 !   19.8   0.1   1.4e-07   0.00036     231     292 ..     184     242 ..     177     244 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.64
                                       -EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHH CS
                            DHO_dh 246 piIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikke 290
                                       p    GG++  e  +  i+ GA  + + t    e p i+ ki + 
  gi|518651887|ref|YP_008141407.1|  76 PFTVGGGLTDIETMVKIIRNGADRIFINTYA-VEHPEIIGKISDR 119
                                       4444456666666666677777777666665.5666666666665 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.4e-07
                                       HHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHH CS
                            DHO_dh 231 lkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkele 292
                                       + +ir++   ++  ip+I++GG  s eD l  ++aGA      + +  eg + a++ikk l+
  gi|518651887|ref|YP_008141407.1| 184 TDLIRKITGSVN--IPVIASGGAGSPEDFLGVFQAGADGALAASIF-HEGKYTANEIKKYLK 242
                                       7899*******9..***********************976555554.899999999999875 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 !    6.0   0.0    0.0028       7.1     126     165 ..      61     100 ..      60     107 .. 0.86
   2 !    7.6   0.0    0.0009       2.3     129     164 ..     185     220 ..     181     225 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0028
                                       GGHHHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSEE CS
                      G3P_antiterm 126 lvpkvikeikkelkipiiaGGLietkedveealkaGaiav 165
                                       ++  +++++ +e+ ip+  GG +++ e++ +++++Ga+ +
  gi|518651887|ref|YP_008141407.1|  61 IMNMLVERVASEIYIPFTVGGGLTDIETMVKIIRNGADRI 100
                                       57778999999999**999999999999999***999987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0009
                                       HHHCTSTTS...EEEEESS--SHHHHHHHCTT.SSE CS
                      G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveealkaGaia 164
                                       ++i++i+ +++ip+ia+G   + ed   +++aGa++
  gi|518651887|ref|YP_008141407.1| 185 DLIRKITGSVNIPVIASGGAGSPEDFLGVFQAGADG 220
                                       689***************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1636.05
//
Query:       gi|518651888|ref|YP_008141408.1|  [L=229]
Description: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-43  148.8   0.1    2.1e-43  148.4   0.1    1.1  1  His_biosynth  Histidine biosynthesis protein
  ------ inclusion threshold ------
      0.079   13.1   0.0       0.14   12.2   0.0    1.4  1  Y1_Tnp        Transposase IS200 like
       0.12   11.5   0.0          2    7.5   0.0    2.0  2  IGPS          Indole-3-glycerol phosphate synthase
       0.18   12.1   0.0        1.3    9.3   0.0    2.1  2  DUF1611_N     Domain of unknown function (DUF1611_N) Rossmann


Domain annotation for each model (and alignments):
>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.4   0.1   4.6e-47   2.1e-43       2     228 ..       4     218 ..       3     219 .. 0.92

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 4.6e-47
                                       EEEEEEEETTEEEEECTTCSTCEEEETTSHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEE CS
                      His_biosynth   2 iipalDlkdGkvVrlvkGdrfqelryagdpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqv 78 
                                       i+pa+D+ +G++V l +G+  ++ +  gdpv++a+++++    +lh+vDl++a++g++an++l+++i+++v+  +q 
  gi|518651888|ref|YP_008141408.1|   4 IYPAIDIYNGEAVSLENGKI-EKIESFGDPVKFAQEFSS-ISGKLHIVDLNGAFTGNPANTNLIKNIRKNVKSFMQA 78 
                                       9******************9.788889**********55.5678********************************* PP

                                       ESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEEEEECEEEEETTTTEEEEEEHHHHHHH CS
                      His_biosynth  79 GGGIrsledveelleagadkviigtaavknpelikelaekfgsqkivvaiDarrgykvaikgwreetgldavelakk 155
                                       GGG r++e++e+  ++g+d +iigta ++++ +++e++ek+ +  i+++iDa +g  +  +gw   t++++ ++   
  gi|518651888|ref|YP_008141408.1|  79 GGGYRTMESIEAGYSLGIDSIIIGTASLDKK-ILEEVSEKHKN--ITISIDAYNG-YIKYNGWADGTEISYRDFY-S 150
                                       **************************99876.9******9666..**********.******************9.5 PP

                                       HHHTT-SEEEEEETTTTTTSS---HHHHHHHHHHH.SSEEEEESS--SHHHHHHHHHTTCSEEEESHHHHTTSS CS
                      His_biosynth 156 leelgageilltdidrdGtlsGpdleltkelaeav.kipviasGGvgsledlkelksegvdavivgsalyegel 228
                                       + +  a+++++t i++dGt +      ++++ +++ +  ++++GGv s++dlk+l+++g++++i+g+aly+g++
  gi|518651888|ref|YP_008141408.1| 151 MVKGRANRFIFTAINSDGTGH------ISRIEKFWdEGYFMYAGGVNSIDDLKKLENMGFNGAIIGKALYNGNI 218
                                       6677799***********975......44455555467899******************************997 PP

>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.2e-05      0.14      31     115 ..     111     197 ..     104     199 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.2e-05
                            Y1_Tnp  31 ikeiaekkevkilelelmpDHvHllvelp.pklsiskivkalkgassrlinkefpelkkkklkk.eslWqrgYfvst 105
                                       ++e++ek++   ++++ ++ ++ +   ++ +++s  ++   +kg+  r i++  ++    ++ + e++W +gYf+ +
  gi|518651888|ref|YP_008141408.1| 111 LEEVSEKHKNITISIDAYNGYIKYNGWADgTEISYRDFYSMVKGRANRFIFTAINSDGTGHISRiEKFWDEGYFMYA 187
                                       55555555555555555555555555554134578889999**********9999999999999*99********99 PP

                            Y1_Tnp 106 vgeasletvk 115
                                        g +s++ +k
  gi|518651888|ref|YP_008141408.1| 188 GGVNSIDDLK 197
                                       9998988876 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.024   1.1e+02     201     244 ..      63     108 ..      52     123 .. 0.71
   2 ?    7.5   0.0   0.00044         2     215     244 ..     187     216 ..     170     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.024
                                       HHCHCC-TT..SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                              IGPS 201 eLaklvpkd..vllvaeSGiktredveklkeegvnafLvGeslmrq 244
                                       +L+k ++k+  +++ a  G +t e +e+  + g++++++G++ +++
  gi|518651888|ref|YP_008141408.1|  63 NLIKNIRKNvkSFMQAGGGYRTMESIEAGYSLGIDSIIIGTASLDK 108
                                       5666666554356667777888888888888888888888875554 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00044
                                       ESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                              IGPS 215 eSGiktredveklkeegvnafLvGeslmrq 244
                                         G+++ +d++kl++ g+n+ ++G++l + 
  gi|518651888|ref|YP_008141408.1| 187 AGGVNSIDDLKKLENMGFNGAIIGKALYNG 216
                                       569***********************9765 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 ?    9.3   0.0   0.00028       1.3       8      50 ..      72     115 ..      67     129 .. 0.86
   2 ?   -0.0   0.0      0.23   1.1e+03      18      49 ..     191     222 ..     183     228 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                         DUF1611_N   8 agelldd.rgipvvssleealaagaevlviGiapeggklpeswr 50 
                                       ++ +++   g   ++s+e+ ++ g+++++iG+a  + k+ e++ 
  gi|518651888|ref|YP_008141408.1|  72 VKSFMQAgGGYRTMESIEAGYSLGIDSIIIGTASLDKKILEEVS 115
                                       5666676788999*****99******************988765 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.23
                         DUF1611_N  18 pvvssleealaagaevlviGiapeggklpesw 49 
                                       + + +l++ ++ g +  +iG+a   g ++ + 
  gi|518651888|ref|YP_008141408.1| 191 NSIDDLKKLENMGFNGAIIGKALYNGNIKIEE 222
                                       44445555567799999*****9999997654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1542.29
//
Query:       gi|518651889|ref|YP_008141409.1|  [L=189]
Description: Imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (hisH) [Ferroplasma acidarmanus fer1]
Scores for complete 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-18   65.0   0.0    9.2e-18   64.7   0.0    1.1  1  GATase         Glutamine amidotransferase class-I
    0.00031   20.6   0.0      0.067   13.0   0.0    2.0  2  SNO            SNO glutamine amidotransferase family
     0.0014   18.4   0.0        0.4   10.4   0.0    2.2  2  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.5e-21   9.2e-18      47     186 ..      36     185 ..       7     186 .. 0.82

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.5e-21
                                       EEEEESSCTT.TTTHHHHHHHHCT....STS-EEEETHHHHHHHHHTTT...........EEE..EEECEEEEEEEE CS
                            GATase  47 lvsgGpgspg.vegkieaikeare....nkiPiLGICLGmQllaiefgr...........kvv..kekekehhggtm 105
                                       ++ +G+gs + v + ie ik ++     ++iP+LGICLG+ +l++ + +           +v   +  + +h+g++ 
  gi|518651889|ref|YP_008141409.1|  36 IIFPGVGSFQyVSQIIEPIKDLLVekikSGIPYLGICLGLEILFENSEEgpgnglgvfngTVKkfNGVKTPHMGWNT 112
                                       899********888888887776545559********************999999888873335577779******* PP

                                       EEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHH CS
                            GATase 106 rlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpel 182
                                          + ++++++g +n+   ++ H+y + +     ++ +v +++e +++++  ie  n ++gvQFHPE++ + +  ++
  gi|518651889|ref|YP_008141409.1| 113 VNVKSPSKIMEGIGNDSFFYFMHSYYAPE-----NQYTV-METEYGNKFASGIEMGN-IYGVQFHPEKSGNDG-IRV 181
                                       99999*********************886.....45556.66668889**99**999.*********876654.666 PP

                                       HHHH CS
                            GATase 183 lfnf 186
                                       l+nf
  gi|518651889|ref|YP_008141409.1| 182 LKNF 185
                                       6665 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   1.1e-05     0.067      20     102 ..      19      99 ..       9     125 .. 0.87
   2 !    6.0   0.0    0.0017       9.9     148     182 ..     147     185 ..     129     186 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                                       SEEEEE-SGGGGCC-SEEEE-SS-H.HHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS-- CS
                               SNO  20 aenktvkrkedlaevdaliiPGGes.tamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlel 95 
                                       + +k+  ++ ++++   +i PG  s   +s++ie  +  + l e++k +  + lG C Gl +l ++ e+   + l++
  gi|518651889|ref|YP_008141409.1|  19 VRGKVTSDPYEIEKSVKIIFPGVGSfQYVSQIIEPIK--DLLVEKIKSG-IPYLGICLGLEILFENSEEGPGNGLGV 92 
                                       556777888899999999****66626799***9988..99******99.9*********99999998888888999 PP

                                       CCEEEET CS
                               SNO  96 lkvkvkr 102
                                       ++ +vk+
  gi|518651889|ref|YP_008141409.1|  93 FNGTVKK 99 
                                       9988886 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0017
                                       EECT.T.EEEE.EEETTEEEESS-GGGS.TTHCHHHHHH CS
                               SNO 148 yeld.g.eivv.akqkkilatsfhPela.eddirvhdyf 182
                                        e++ g +  + ++ ++i ++ fhPe + +d+irv + f
  gi|518651889|ref|YP_008141409.1| 147 METEyGnKFASgIEMGNIYGVQFHPEKSgNDGIRVLKNF 185
                                       4444453333303467**********9834568888766 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   6.7e-05       0.4      97     118 ..      57      78 ..      54      83 .. 0.90
   2 !    6.0   0.0    0.0015       9.2     207     216 .]     163     172 ..     146     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.7e-05
                     Peptidase_C26  97 LiraalergvPilgiCrGlqll 118
                                       L+ + +++g+P lgiC+Gl++l
  gi|518651889|ref|YP_008141409.1|  57 LLVEKIKSGIPYLGICLGLEIL 78 
                                       778999*************987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                     Peptidase_C26 207 fvlgvQwHPE 216
                                        ++gvQ+HPE
  gi|518651889|ref|YP_008141409.1| 163 NIYGVQFHPE 172
                                       689******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 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:                        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: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 1358.92
//
Query:       gi|518651890|ref|YP_008141410.1|  [L=176]
Description: imidazoleglycerol-phosphate dehydratase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-31  110.1   0.1    1.3e-31  109.8   0.1    1.1  1  IGPD      Imidazoleglycerol-phosphate dehydratase


Domain annotation for each model (and alignments):
>> IGPD  Imidazoleglycerol-phosphate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.8   0.1   7.3e-36   1.3e-31       1     144 []      23     159 ..      23     159 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.8 bits;  conditional E-value: 7.3e-36
                                       ....HHHHHHHHHHHHHT--EEEEEEESSH...HHHHHHHHHHHHHHHHHHS..-SSB--EEEEEEEETTEEEEEEE CS
                              IGPD   1 TgigfldhmLdqlakhggfdlkvkvkgdlevddHhtvedvgialGqalkealgdkrgikRfgsallpmDealaeval 77 
                                       Tg ++ldhm+++l  + g + k+k++ dl+   Hh+ ed+gi++   l+   g ++ +kRfgsa++pmDe+l+ v+l
  gi|518651890|ref|YP_008141410.1|  23 TGDKILDHMMRTLFFYMGRNAKIKCSYDLR---HHLWEDLGITIAMELTALKG-EKPVKRFGSATMPMDESLIMVSL 95 
                                       8999*************************8...*************9986655.5678******************* PP

                                       E--SS-EEE--..-SB--TT.--HHHHHHHHHHHHHHHT-EEEEEEEE--BHHHHHHHHHHHHHHHH CS
                              IGPD  78 dlsgrpylvleaelkrekigeldtelveeffeslaeaagitlhvkvlrgenahhivealfKafaraL 144
                                       d+s r+y+++++++++     ++ +l+ ef+ +la+++ +tlhv + +g n+hhi+e +fKa++ aL
  gi|518651890|ref|YP_008141410.1|  96 DIS-RAYINFQVDFRD--AEGFELNLLYEFLWALARTMPMTLHVIKFSGINSHHITENVFKALGAAL 159
                                       **9.99*****88885..568********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1320.73
//
Query:       gi|518651891|ref|YP_008141411.1|  [L=375]
Description: hypothetical protein FACI_IFERC00001G0530 [Ferroplasma acidarmanus fer1]
Scores for complete 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-121  404.7   0.0    1.8e-79  267.6   0.0    2.0  2  Histidinol_dh  Histidinol dehydrogenase


Domain annotation for each model (and alignments):
>> Histidinol_dh  Histidinol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.6   0.0     1e-83   1.8e-79      10     261 ..       2     248 ..       1     253 [. 0.95
   2 !  136.6   0.0   6.4e-44   1.1e-39     280     409 .]     246     375 .]     243     375 .] 0.96

  Alignments for each domain:
  == domain 1  score: 267.6 bits;  conditional E-value: 1e-83
                                       HHHHHHHHHHHHHHHHCHHHHHHHHHHCCSSSSGGCCEE-HHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHCC---- CS
                     Histidinol_dh  10 eveetvkeiledvreeGdealleytekFDkvkkleslrvseeeieealekldeelkealeeaaenirkfheaqkese 86 
                                       e+ee vk+il+d+++ G +a+ ey++kFD++     ++v+e+e++ea e ++e  k+ +++++++i + h+ q ++ 
  gi|518651891|ref|YP_008141411.1|   2 EIEEYVKNILNDIKSGGIDAVSEYSKKFDGYG--MPFKVPESEFAEANELIPEYQKDIINRTYKRIYENHAIQYNN- 75 
                                       68999************************774..579*************************************75. PP

                                       EEEEEECTTEEEEEEEEE-SEEEEE---STT--CHHHHHHHHHHHHHT-SEEEEEE-SS.GG.--HHHHHHHHHCT- CS
                     Histidinol_dh  87 eevketepgvvlgqkvrpiervGlYvPgGkaaypStvlmnavpAkvAgvkeivvvtPpq.dgkvnpavlaaaklagv 162
                                       ++v + ++g + g +++pier+G+Y+Pg k ++pStv+m ++pAk+Agv++iv+v+ p+ +g+vnp +l++a l+g+
  gi|518651891|ref|YP_008141411.1|  76 DKV-RFSRGSIYGIRYTPIERIGMYIPGKK-PLPSTVMMIGIPAKIAGVRDIVIVSAPEsNGRVNPYTLYIAGLLGI 150
                                       445.789********************766.********************************************** PP

                                       SEEEE--HHHHHHHHHH--SSS---SEEE---SHHHHHHHHHHCTTBEES----S-EEEEEE-TTS-HHHHHHHHHH CS
                     Histidinol_dh 163 deiykvGGaqAiaalAyGtesipkvdkivGPGniyVaaAKrlvsgevgiDmiaGPsEvlviaDetadpefvAaDLls 239
                                       +e+y++GG+qAi+ +AyG   ++kvdki+GPGn yV++AKr+v+g +giD + GPsEv+vi+D ta+ e++ aDL s
  gi|518651891|ref|YP_008141411.1| 151 HEVYRIGGVQAIGSMAYGIG-MKKVDKIFGPGNSYVNEAKRQVYGFTGIDGLYGPSEVMVISDGTAKDEYILADLNS 226
                                       ******************95.9******************************************************* PP

                                       HHTT-TT-EEEEEES-HHHHHH CS
                     Histidinol_dh 240 qaEHdedaqavlvttseelaea 261
                                       q EH+ +++a+l+tt +++ +a
  gi|518651891|ref|YP_008141411.1| 227 QLEHGITSKAWLLTTGKAISTA 248
                                       ***************9987665 PP

  == domain 2  score: 136.6 bits;  conditional E-value: 6.4e-44
                                       HHHHCCH-EEEE-SSHHHHHHHHHHH--SEEEEESTTHHHHGGG--S-SEEEESTT--HHHHHHTSSS------TTG CS
                     Histidinol_dh 280 ekslekqsaiilvedleeaielaneyApEHlelqvedpeellekiknaGaiflGeyspeslgDYaaGtnhvLPTsgt 356
                                       +++ +++  ++++e+++e i+ ane+ApEH+e+q++dp+e++++iknaGai++Gey+p+++gDY+ G nh LPT+gt
  gi|518651891|ref|YP_008141411.1| 246 STAGNERIGVMVFENMDELISKANEIAPEHMEIQAKDPMEIFTRIKNAGAIYIGEYAPVPAGDYFLGVNHLLPTGGT 322
                                       5566677889******************************************************************* PP

                                       GGT---S-GGGGEEEEEEEEE-HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                     Histidinol_dh 357 ArfssglsvedFlkkisvqelskealkelaeavetlAeaEgLeaHaeavkvRl 409
                                       +rfss+l+v+dF+kk+s+ ++s+e + +  e   +lA++Eg++ H +++++Rl
  gi|518651891|ref|YP_008141411.1| 323 SRFSSALTVDDFMKKTSFASVSREDFMADRELGLELAKIEGMPLHYKSMEARL 375
                                       **************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2542.66
//
Query:       gi|518651892|ref|YP_008141412.1|  [L=210]
Description: ATP phosphoribosyltransferase catalytic subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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-44  150.7   0.0    3.8e-44  150.5   0.0    1.1  1  HisG      ATP phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> HisG  ATP phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.5   0.0   2.1e-48   3.8e-44       1     157 [.      46     194 ..      46     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.5 bits;  conditional E-value: 2.1e-48
                                       -GGGHHHHHHTTSSSEEEEEHHHHHHCT...TEEEEEEESESEEEEEEEEETTSS--SGCGG.TT-.EEEEES-HHH CS
                              HisG   1 raadiptyVeegavdlGitGkDvveEskeeeeveelldLgfgkcklvvavpeesevkslkdlvedkgkriaTsypnl 77 
                                       ra+d+p+y e+ a d+Gi+G+D++ Es+  +++ + l L+fgkc+l++ +pe++++k+l++      + iaT+ pn+
  gi|518651892|ref|YP_008141412.1|  46 RARDVPVYTEY-AGDIGICGSDTLSESR--SRLFTPLTLNFGKCRLSLIAPEKYSIKDLEG------LDIATKHPNI 113
                                       799*****877.68************74..57********************887776664......59******** PP

                                       HHHHHHHTT-EEEEEE-SS-CTHHHHTTS-SEEEEEESSSHHHHHTTEEEEEEEEEEEEEEEEEHHHHH.SHHHHHH CS
                              HisG  78 akkyfeekglkveiiklsGsvEaapalglaDaIvDlvetGeTLrangLkaietilessavLiankkslk.kkekiee 153
                                       +++yf + g++++ii l+Gs E+ap++g+aDaIvD+v+tGeT+++n+L +i++i+++sa+L++n+ s+k k ++i++
  gi|518651892|ref|YP_008141412.1| 114 TRDYFFSMGIDANIIPLNGSLELAPETGIADAIVDVVQTGETMKKNNLVEIQKIMDISAILVVNRVSQKiKYKEINN 190
                                       *********************************************************************99999999 PP

                                       HHHH CS
                              HisG 154 ller 157
                                       ++e+
  gi|518651892|ref|YP_008141412.1| 191 FIEK 194
                                       8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1650.44
//
Query:       gi|518651893|ref|YP_008141413.1|  [L=254]
Description: ATP phosphoribosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-18   65.3   0.0    2.4e-08   33.6   0.0    3.0  3  tRNA-synt_His  Histidyl-tRNA synthetase


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 !    2.6   0.0    0.0036        65      12      36 ..       5      29 ..       1      37 [. 0.86
   2 !   25.8   0.0   3.3e-10     6e-06      95     190 ..      67     156 ..      50     176 .. 0.83
   3 !   33.6   0.0   1.3e-12   2.4e-08     237     310 .]     178     241 ..     161     241 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.0036
                                      HHHHHHHHHHHHHHHTT-EEEE--S CS
                     tRNA-synt_His 12 kieelrrrlldlfeswGYelVspPl 36
                                      k ++++ ++ + ++++GY+++ pP 
  gi|518651893|ref|YP_008141413.1|  5 KLSDIAYSIRKSCHDSGYSEIFPPA 29
                                      667888999999************7 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 3.3e-10
                                       EEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHHHHHHTT--HHHH CS
                     tRNA-synt_His  95 GsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvralleaaglsesle 171
                                        +v+  +++  +   e+l +G E+iG    ea++E+l++++++l+  +g+++ ++d++ +++++     +  ++++ 
  gi|518651893|ref|YP_008141413.1|  67 SRVYYISQQADEFLGESLKAGLEIIGPVPGEANIEILKMAIKILD-DLGIRDYNIDISITDVFDP----YR-KKKDG 137
                                       55666666666777899***************************7.*****************93....33.56677 PP

                                       HHHHHHHHCT-HHHHHHHH CS
                     tRNA-synt_His 172 eallaalarkdlaelkela 190
                                         +l+a++++++++l+++ 
  gi|518651893|ref|YP_008141413.1| 138 GIILNAVKNRNYPQLQNME 156
                                       8888888888888888775 PP

  == domain 3  score: 33.6 bits;  conditional E-value: 1.3e-12
                                       HHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS-SEEEEEECTTTGGGT---EEEEEEEEHHHH CS
                     tRNA-synt_His 237 elaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgqaiarGGrYdelgaafgrarpAtGfsldleal 310
                                       el ++le+++  + rv +Dl+ +r+ eYy Gl+F++y +  ++ +++GG Y  ++    ++ +++Gfsldl+al
  gi|518651893|ref|YP_008141413.1| 178 ELDSILEEIN--DPRVIIDLGTVRQPEYYRGLIFEIYGR--HEFLGGGGNY--VI----KKMNGCGFSLDLQAL 241
                                       6778899997..579**********************98..99********..44....5679********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 2015.73
//
Query:       gi|518651894|ref|YP_008141414.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G0533 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 409.35
//
Query:       gi|518651895|ref|YP_008141415.1|  [L=346]
Description: hypothetical protein FACI_IFERC00001G0534 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-17   63.7   0.8    1.1e-11   44.7   0.0    2.7  2  SIS         SIS domain
  ------ inclusion threshold ------
       0.15   12.1   0.1       0.45   10.6   0.0    1.9  2  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI


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 !   17.0   0.1   4.4e-07     0.004       4     110 ..      43     144 ..      40     163 .. 0.78
   2 !   44.7   0.0   1.3e-15   1.1e-11       3     127 ..     198     315 ..     196     319 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-07
                                       TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTT CS
                               SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakerg 80 
                                       ++k ++++G Gt y++a+ +a  l ++  + ++v++ +   +    ++     v+ is sg tk++++++ + k++ 
  gi|518651895|ref|YP_008141415.1|  43 SSKPLLFTGNGTAYHAAQIGAGFLYKTDLKYAFVQSYEL-LNY---YVPVHGTVVGISNSGKTKSTIDSLIYQKKFS 115
                                       678899****************99888777776666555.444...4666789******************999886 PP

                                       SEEEEEESSTTSHHHHHSSEEEEEEEECHC CS
                               SIS  81 akiiaITdskgsplareadlalyinaepet 110
                                         i++IT+  g+p+   +   + i a++++
  gi|518651895|ref|YP_008141415.1| 116 -YIVGITHYHGTPMELISNKSIVIDADDKS 144
                                       .58899998888887766666666666666 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.3e-15
                                       CTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHT CS
                               SIS   3 akakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelaker 79 
                                       +  +ri+vlGaG   ++a+e+a k++e + i++e+ + +e+ hg  +lid++ l+++i  +  ++++++ ++ +k  
  gi|518651895|ref|YP_008141415.1| 198 SYVNRIFVLGAGPEEPVAREAAQKIKEATHIHAEGIELEEFIHGCTSLIDDKSLLVIINSNTVNSRTDDIVRACKVV 274
                                       5679************************************************************************* PP

                                       TSEEEEEESSTTSHHHHHSSEEEEEEEECHCSSSHCHHHHHHHHHHHH CS
                               SIS  80 gakiiaITdskgsplareadlalyinaepetlvastksltaqlaalda 127
                                       g k+++I +  + ++   +        ++e+++a++++l+++++a+++
  gi|518651895|ref|YP_008141415.1| 275 GTKTVVINGDGDYSIDLPD-------LGDEYINALLNVLPLYYLAYYM 315
                                       *******877766665555.......4444455566666666666555 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 ?   -2.9   0.0      0.72   6.4e+03     127     149 ..     157     180 ..     155     182 .. 0.78
   2 ?   10.6   0.0     5e-05      0.45       5     139 ..     190     323 ..     186     327 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.72
                                       HHHHHHHHC.T---S-TTTTHHHH CS
                        bact-PGI_C 127 vSvylAllr.gvDPtpvpaIdelK 149
                                       +S+y+A  + g+D    ++I+ lK
  gi|518651895|ref|YP_008141415.1| 157 ASMYIASRYaGIDMNIDKTIETLK 180
                                       799999765489988888888888 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 5e-05
                                       HHHHHHHHTT.SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEESSHH CS
                        bact-PGI_C   5 akqlAlelag.klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllrdee 80 
                                        k++A +l+  +   ++g +++ e++Ar ++++++e   i+a   +l e+ h    +++      ++  lv+++++ 
  gi|518651895|ref|YP_008141415.1| 190 VKKIAHNLSYvNRIFVLG-AGPEEPVAREAAQKIKEATHIHAEGIELEEFIHGCTSLID------DKSLLVIINSNT 259
                                       689999999876677778.99*******************************9999994......556666666555 PP

                                       ..............HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT--- CS
                        bact-PGI_C  81 eh......prvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDP 139
                                        +       r  k++   + +++  g+  +++   g++ ++ l++   l  + ++y+A+ ++v+P
  gi|518651895|ref|YP_008141415.1| 260 VNsrtddiVRACKVVGTKTVVINGDGDYSIDLPDLGDEYINALLNVLPL-YYLAYYMAVEQNVNP 323
                                       3311211133334444444456667777777777788888888876555.588899999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 2325.86
//
Query:       gi|518651896|ref|YP_008141416.1|  [L=308]
Description: Carboxylesterase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-62  210.3   0.0    3.6e-62  210.0   0.0    1.1  1  Abhydrolase_3  alpha/beta hydrolase fold
    5.8e-06   25.4   0.0    7.9e-06   25.0   0.0    1.1  1  Say1_Mug180    Steryl acetyl hydrolase
    0.00069   18.6   0.1     0.0045   15.9   0.1    1.9  1  COesterase     Carboxylesterase family


Domain annotation for each model (and alignments):
>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  210.0   0.0     6e-66   3.6e-62       1     210 [.      79     284 ..      79     285 .. 0.95

  Alignments for each domain:
  == domain 1  score: 210.0 bits;  conditional E-value: 6e-66
                                       EEEE--STTTS--TTTTHHHHHHHHHHHTSEEEEEE---TTTS-TTHHHHHHHHHHHHHHHTHHHHTETTCEEEEEE CS
                     Abhydrolase_3   1 lvyfHGGGfvlgsldthdalcrelakelgavvvsvdYrlAPehpfPaavedalaalrwlaeqawelgadpsrivlaG 77 
                                       ++y+HGGGf++g+++t+d++cr lake+ + ++s++YrlAPeh+fP a++da+++++++a++++++g++  ri +aG
  gi|518651896|ref|YP_008141416.1|  79 ILYYHGGGFLFGNIETYDNYCRFLAKESWVKIISIEYRLAPEHKFPDAFNDAYDSFHYIAKKKKDFGIE-GRIGVAG 154
                                       69************************************************************8899986.59***** PP

                                       ETHHHHHHHHHHHHHHHTT---EEEEEEESE-SSTSSTTSHHHHHCHHTTTSSSSCHHHHHHHHHHHSS.GGGGGST CS
                     Abhydrolase_3  78 dSaGGnlaaavalrardegepkvagqvliyPvtdlertesesikkaeeladgplltraaldlfwrlylp.eadrddp 153
                                       dSaG+nlaaa++l++rd ++ ++a qvl+yP + + ++ s s+    e++d+++lt +++++f ++y +  +d+ +p
  gi|518651896|ref|YP_008141416.1| 155 DSAGANLAAALCLKCRDGKTEMPAVQVLFYPSLAP-DNFSRSF---IEYSDNYVLTGKMIRYFGNMYSKnMQDLINP 227
                                       *****************99999*********9977.5557777...799*******************77******* PP

                                       TTSGGGCS-SST---EEEEEETT-TTHHHHHHHHHHHHHTT--EEEEEETTEETTGG CS
                     Abhydrolase_3 154 laspllaedlsglpptlvvvaefDplrdegeayaerlraagvevelieyegmvHgfa 210
                                       ++spl+a+d+s+lpp+++v+ e+Dplrd +e y ++lr+agv++  i+  gm+Hg a
  gi|518651896|ref|YP_008141416.1| 228 YFSPLVADDFSNLPPAIMVTNEYDPLRDPEETYVKKLREAGVRAVGIRGIGMIHGSA 284
                                       *******99*********************************************976 PP

>> Say1_Mug180  Steryl acetyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.3e-09   7.9e-06     123     275 ..      77     223 ..      45     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.3e-09
                       Say1_Mug180 123 pvllylHGGgfalklipvtlvfLsnlrklfpdmailvsDYtvtaakdqskkYplqvleslavydylvksk...gfk. 195
                                         +ly+HGGgf ++ i +   +   l k  + + i+  +Y +       +k+p    ++   ++y+ k k   g+  
  gi|518651896|ref|YP_008141416.1|  77 SAILYYHGGGFLFGNIETYDNYCRFLAKE-SWVKIISIEYRLAP----EHKFPDAFNDAYDSFHYIAKKKkdfGIEg 148
                                       679*************9987777777665.6899******9988....889***************97653224444 PP

                       Say1_Mug180 196 nvvvlGdSaGGnlvLslllklsklnkvvlPkkaiaiSPWlnltildekekeylkasdklDvlclkglelfgklyvnn 272
                                        + v GdSaG nl   l lk+++ +k+ +P   ++  P l +  ++ + +ey     +  vl+ k    fg++y +n
  gi|518651896|ref|YP_008141416.1| 149 RIGVAGDSAGANLAAALCLKCRD-GKTEMPAVQVLFYPSLAPDNFSRSFIEYSD---N-YVLTGKMIRYFGNMYSKN 220
                                       799********************.999***********9999977776666655...3.488999*********999 PP

                       Say1_Mug180 273 rep 275
                                        + 
  gi|518651896|ref|YP_008141416.1| 221 MQD 223
                                       433 PP

>> COesterase  Carboxylesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.5e-07    0.0045     101     203 ..      72     166 ..      53     174 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.5e-07
                                       TTSSEEEEEEE--STTTS-BGCGS-T..HHHHHHHTSEEEEE----HHHHH-B-SSTTSBS-HHHHHHHHHHHHHHH CS
                        COesterase 101 akkklPVlVwihGggfqtgsaseydg..saLaaegnvivVtinYRlGvlGFlstgdeeapGNvGllDqvlALrWVke 175
                                       ++++ + + + hGggf +g  ++yd   ++La+e  v +++i+YRl +       + ++p   ++ D    ++++ +
  gi|518651896|ref|YP_008141416.1|  72 NNNAKSAILYYHGGGFLFGNIETYDNycRFLAKESWVKIISIEYRLAP-------EHKFPD--AFNDAYDSFHYIAK 139
                                       455668999**************986227999999999********87.......233333..56677777777777 PP

                                       HGGGGTEEEEEEEEEEETHHHHHHHHHH CS
                        COesterase 176 nIasFGGdpervtlfGesAGaasvslll 203
                                       + + FG    r+ ++G+sAGa ++++l 
  gi|518651896|ref|YP_008141416.1| 140 KKKDFGI-EGRIGVAGDSAGANLAAALC 166
                                       7777754.45677777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2284.82
//
Query:       gi|518651897|ref|YP_008141417.1|  [L=155]
Description: hypothetical protein FACI_IFERC00001G0536 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-25   89.4   0.0    3.7e-25   88.8   0.0    1.3  1  AAA_assoc_C  C-terminal AAA-associated domain
  ------ inclusion threshold ------
      0.024   14.2   0.5       0.13   11.9   0.1    2.2  3  HTH_47       winged helix-turn-helix
        0.2   11.8   0.1       0.88    9.7   0.0    1.9  2  Caudo_TAP    Caudovirales tail fibre assembly protein, lambda


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 !   88.8   0.0   6.1e-29   3.7e-25       1     117 [.      31     145 ..      31     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.8 bits;  conditional E-value: 6.1e-29
                       AAA_assoc_C   1 yeLaeelelevddLlpiveaaelLglveveegdielTelGrkfveadikerKeifreqllklvplaaairrvLdere 77 
                                       y++++e+e+++ddL+piv++a+ +glv++e+gdi + ++G++++++++++rK+i+r++l++++p+++ai+       
  gi|518651897|ref|YP_008141417.1|  31 YQMEKEMEVDLDDLMPIVYTASNIGLVNAESGDISISQKGIEYIKSGMNTRKQIIRDSLKNIEPFKTAISM------ 101
                                       799******************************************************************98...... PP

                       AAA_assoc_C  78 nkrlpeerfldeLeek.ls...eeeaertletai.eWgrYaelfe 117
                                        ++++ e+++d L+e+ ++   +++  ++le+++ eWg+Y+ l++
  gi|518651897|ref|YP_008141417.1| 102 -GEFTLEDIIDKLKENdVPtfnNPDGTHDLEVILiEWGIYSRLLK 145
                                       .9************998777779********9988******9987 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   0.1   2.1e-05      0.13      36      77 ..      16      58 ..       7      59 .. 0.87
   2 ?   -0.7   0.0      0.17     1e+03      56      75 ..      99     118 ..      96     121 .. 0.82
   3 ?   -2.5   0.0      0.66   3.9e+03      41      49 ..     122     130 ..     118     133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.1e-05
                                      HHHHH.HH-EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE CS
                            HTH_47 36 llwvL.nlaDGkrsLldiAeriglpfdrvaaiaraLaeaglla 77
                                      ll vL n+ DGk++L ++ ++++++ d++++i+    + gl++
  gi|518651897|ref|YP_008141417.1| 16 LLYVLnNIFDGKTDLYQMEKEMEVDLDDLMPIVYTASNIGLVN 58
                                      677883589************************9999999885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.17
                                       HT--HHHHHHHHHHHHHTT- CS
                            HTH_47  56 iglpfdrvaaiaraLaeagl 75 
                                       i ++  ++++i+++L+e+++
  gi|518651897|ref|YP_008141417.1|  99 ISMGEFTLEDIIDKLKENDV 118
                                       5677788999****999886 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.66
                                       HH-EEEEEH CS
                            HTH_47  41 nlaDGkrsL 49 
                                       n  DG+++L
  gi|518651897|ref|YP_008141417.1| 122 NNPDGTHDL 130
                                       5679**998 PP

>> Caudo_TAP  Caudovirales tail fibre assembly protein, lambda gpK
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00015      0.88      60      98 ..      70     108 ..      27     115 .. 0.79
   2 ?   -0.1   0.0      0.16   9.8e+02     102     116 ..     134     148 ..     127     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00015
                         Caudo_TAP  60 keeqiqqAeqekqqllaqAseqiaplqdavdlgiatdeE 98 
                                         e+i+   ++++q +++  + i+p ++a+++g+ t e+
  gi|518651897|ref|YP_008141417.1|  70 GIEYIKSGMNTRKQIIRDSLKNIEPFKTAISMGEFTLED 108
                                       77999999**************************99886 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.16
                         Caudo_TAP 102 LlawkkYrvlLnrvD 116
                                       L++w  Y  lL+ +D
  gi|518651897|ref|YP_008141417.1| 134 LIEWGIYSRLLKKTD 148
                                       89**********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1006.45
//
Query:       gi|518651898|ref|YP_008141418.1|  [L=540]
Description: hypothetical protein FACI_IFERC00001G0537 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-18   67.4  36.6    3.9e-14   52.8  11.7    3.2  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.03   14.4   0.0      0.059   13.5   0.0    1.5  1  Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
      0.035   14.1   0.0      0.035   14.1   0.0    3.5  5  DUF2116       Uncharacterized protein containing a Zn-ribbon 
      0.035   14.2   0.1      0.035   14.2   0.1    2.5  3  ETRAMP        Malarial early transcribed membrane protein (ET
      0.051   13.7   0.2      0.051   13.7   0.2    6.0  6  ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transpor
      0.079   13.5   0.2      0.079   13.5   0.2    4.6  6  DUF3899       Domain of unknown function (DUF3899)
       0.18   11.3   1.0        0.3   10.6   0.0    1.8  2  DUF334        Domain of unknown function (DUF334)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0  15.3   1.8e-07   0.00045       2     171 ..      26     204 ..      25     215 .. 0.76
   2 ?   -1.2   0.0      0.57   1.5e+03     152     171 ..     279     298 ..     265     302 .. 0.56
   3 !   52.8  11.7   1.5e-17   3.9e-14       1     175 [.     338     523 ..     334     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                      BPD_transp_1   2 illGilaa..lnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraa 75 
                                       il+G+++a    ++k++ ++  +li+v+ s+P++ ++++++++f  + ++     l++ +l+++  ++ + +  ++a
  gi|518651898|ref|YP_008141418.1|  26 ILTGWFLAyaSIKSKFFENIYIILIEVFESIPVITFFPVVLVIFiTHVGGTLGVELAADFLVFTAVVWNIWMGEYQA 102
                                       889*****999999***************************9997444444445555666666666666666779** PP

                      BPD_transp_1  76 lrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG........lgtlllea 144
                                       ++++p++ ve+ +    + + ++r+  +P ++p i + l+ ++ + +   ++ e +    G        +g++l ++
  gi|518651898|ref|YP_008141418.1| 103 FKTVPREMVEVVENSRFGLFSRLRYLYIPFSVPRITANLFPSVSNGFFYITVSEVFE--VGvhtyqtfgIGSVLDTF 177
                                       ***************************************999999999888888776..444455555566666666 PP

                      BPD_transp_1 145 ilgydyseisnggvlalviavlllnlv 171
                                         g ++ +i +++++ ++++v++++++
  gi|518651898|ref|YP_008141418.1| 178 VAGAQLFNIEMALLILGIVIVAIVIVL 204
                                       666666666644444444444444444 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.57
                      BPD_transp_1 152 eisnggvlalviavlllnlv 171
                                       ++s+g+++ +++++ +++l+
  gi|518651898|ref|YP_008141418.1| 279 YASIGIIILIALLYGVVSLI 298
                                       33344555555555555554 PP

  == domain 3  score: 52.8 bits;  conditional E-value: 1.5e-17
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..vilsilg.hlilp.viillllsaapyvrlirr 73 
                                       +i+lG+++a   nk+  k   p+i+ l++ P  + +++l+ +   ++ls +g +++   v+ l+++s++ yv++ + 
  gi|518651898|ref|YP_008141418.1| 338 AIFLGYYLA--VNKRAEKYWIPIIQSLSAYPAPIYFPFLFILTepFMLSLFGgFTNELyVLSLGFVSTFYYVFYSFW 412
                                       466677777..***************************99877**99999999666655****************** PP

                      BPD_transp_1  74 aalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydy 150
                                       ++++++p++++e  + l +++++ +rkv++P+++p++i+g+  ++ +++gg ++ e+  +  G  +l +++ l++ +
  gi|518651898|ref|YP_008141418.1| 413 MGVKAMPSEYWEITKNLKLGYFKKMRKVIIPSTFPYLISGISSTINSAWGGLMIGEYWPNIYGTHSLSVHTGLMKTI 489
                                       ***************************************************************55555555555555 PP

                      BPD_transp_1 151 seis.........nggvlalviavlllnlvadil 175
                                       + ++         +g++++++i+ +  +l+++ +
  gi|518651898|ref|YP_008141418.1| 490 DIATangdltlaaWGSLIFGIIVAIYSVLFTRKM 523
                                       5555555555553555555555555555555555 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.3e-05     0.059     107     169 ..     228     290 ..     215     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXXXXXXXXX CS
                      Spore_III_AB 107 keilkelgeslgysdregqlkalelaleeleeeieeareeakkkeklyrtlGvlaGlflvilL 169
                                       + +l+e ++ +  ++++   +  ++++ +  +++e+  e+++kk+k y+++ + +G++++i L
  gi|518651898|ref|YP_008141418.1| 228 RLNLRETARVFAALSKNPLTRLARYYKYREGDKHEQTYEKKEKKQKRYKYIYASIGIIILIAL 290
                                       56788888888888999999999999**********************************988 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 ?   -3.3   0.7       3.7   9.5e+03      45      53 ..       4      12 ..       2      15 .. 0.56
   2 ?   -0.6   2.4      0.52   1.3e+03      41      57 ..     191     205 ..     182     207 .. 0.60
   3 ?   14.1   0.0   1.4e-05     0.035      23      52 ..     260     289 ..     258     297 .. 0.79
   4 ?   -4.2   0.5       6.9   1.8e+04      46      56 ..     331     341 ..     329     344 .. 0.51
   5 ?   -4.0   0.6       6.1   1.6e+04      42      55 ..     507     517 ..     505     520 .. 0.50

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.7
                           DUF2116 45 ililllavv 53
                                      i++++lav+
  gi|518651898|ref|YP_008141418.1|  4 IILIILAVL 12
                                      445556665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.52
                           DUF2116  41 ilfgililllavvlvlk 57 
                                       +++gi+i+  a+v+vl+
  gi|518651898|ref|YP_008141418.1| 191 LILGIVIV--AIVIVLR 205
                                       44555555..7777765 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 1.4e-05
                           DUF2116  23 kCqeeyekkrkkvarsqqilfgililllav 52 
                                       k ++ yekk kk++r ++i++ i i++l+ 
  gi|518651898|ref|YP_008141418.1| 260 KHEQTYEKKEKKQKRYKYIYASIGIIILIA 289
                                       55789***************9997774433 PP

  == domain 4  score: -4.2 bits;  conditional E-value: 6.9
                           DUF2116  46 lilllavvlvl 56 
                                       l++ +++ ++l
  gi|518651898|ref|YP_008141418.1| 331 LLVSMVIAIFL 341
                                       44445554444 PP

  == domain 5  score: -4.0 bits;  conditional E-value: 6.1
                           DUF2116  42 lfgililllavvlv 55 
                                       +fgi   ++a++ v
  gi|518651898|ref|YP_008141418.1| 507 IFGI---IVAIYSV 517
                                       3444...4555544 PP

>> ETRAMP  Malarial early transcribed membrane protein (ETRAMP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1   3.1         7   1.8e+04      60      69 ..       6      15 ..       3      27 .. 0.48
   2 ?   14.2   0.1   1.4e-05     0.035      40      75 ..     259     294 ..     188     299 .. 0.91
   3 ?   -4.1   0.3       6.7   1.7e+04      67      74 ..     335     342 ..     329     349 .. 0.41

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 7
                            ETRAMP 60 tiatalallv 69
                                      +i+ a+++ +
  gi|518651898|ref|YP_008141418.1|  6 LIILAVLATA 15
                                      3333333333 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.4e-05
                            ETRAMP  40 kkiddkiekkkkkkKliiistiatalallvasalGl 75 
                                       +k +++ ekk+kk+K   +  +++++++l+a+++G+
  gi|518651898|ref|YP_008141418.1| 259 DKHEQTYEKKEKKQKRYKYIYASIGIIILIALLYGV 294
                                       788899999999999999999************996 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 6.7
                            ETRAMP  67 llvasalG 74 
                                       +++a+ lG
  gi|518651898|ref|YP_008141418.1| 335 MVIAIFLG 342
                                       22222333 PP

>> ATPase_gene1  Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.8      0.19   4.8e+02      12      25 ..      19      32 ..       6      50 .. 0.83
   2 ?    0.0   0.8      0.38   9.7e+02      18      44 ..     167     195 ..     150     203 .. 0.60
   3 ?   -2.6   1.6       2.5   6.3e+03       4      19 ..     279     294 ..     278     296 .. 0.74
   4 ?   13.7   0.2     2e-05     0.051       3      26 ..     323     346 ..     322     362 .. 0.84
   5 ?   -3.1   0.3       3.5     9e+03      42      52 ..     398     408 ..     396     409 .. 0.84
   6 ?    0.3   0.8      0.31   7.8e+02      40      52 ..     506     518 ..     502     520 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.19
                      ATPase_gene1 12 vapillggllGywL 25
                                      ++ ill++l G++L
  gi|518651898|ref|YP_008141418.1| 19 IGLILLSILTGWFL 32
                                      78899999999997 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.38
                      ATPase_gene1  18 ggllGywLDk......kfgtspwfliiglllGl 44 
                                        +++G  LD       +f+    +l    +lG+
  gi|518651898|ref|YP_008141418.1| 167 TFGIGSVLDTfvagaqLFNIEMALL----ILGI 195
                                       5788888888444443444443333....3443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                      ATPase_gene1   4 asqiGielvapillgg 19 
                                       + +iGi ++++ l g+
  gi|518651898|ref|YP_008141418.1| 279 YASIGIIILIALLYGV 294
                                       6788888888887776 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 2e-05
                      ATPase_gene1   3 lasqiGielvapillggllGywLD 26 
                                        + ++G+ l++++++ ++lGy+L 
  gi|518651898|ref|YP_008141418.1| 323 DYVRVGSILLVSMVIAIFLGYYLA 346
                                       589*******************85 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 3.5
                      ATPase_gene1  42 lGlaaGfynvy 52 
                                       lG+++ fy v+
  gi|518651898|ref|YP_008141418.1| 398 LGFVSTFYYVF 408
                                       89999999886 PP

  == domain 6  score: 0.3 bits;  conditional E-value: 0.31
                      ATPase_gene1  40 lllGlaaGfynvy 52 
                                       l++G+++++y+v 
  gi|518651898|ref|YP_008141418.1| 506 LIFGIIVAIYSVL 518
                                       799*******985 PP

>> DUF3899  Domain of unknown function (DUF3899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.7         3   7.7e+03      13      27 ..      18      32 ..       5      45 .. 0.56
   2 ?   -3.8   0.1         7   1.8e+04       1       7 [.     146     152 ..     141     156 .. 0.67
   3 ?   -3.2   1.6       4.8   1.2e+04      10      76 ..     189     198 ..     182     204 .. 0.48
   4 ?   13.5   0.2   3.1e-05     0.079      39      83 ..     253     300 ..     236     301 .. 0.80
   5 ?    8.0   1.4    0.0016         4      18      79 ..     393     459 ..     381     462 .. 0.74
   6 ?   -3.1   0.5       4.6   1.2e+04      69      82 ..     506     519 ..     502     521 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 3
                           DUF3899 13 iigillivlnsGfFd 27
                                      +ig++l+ + +G F 
  gi|518651898|ref|YP_008141418.1| 18 VIGLILLSILTGWFL 32
                                      444444444444444 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 7
                           DUF3899   1 iNilFll 7  
                                       +N++F++
  gi|518651898|ref|YP_008141418.1| 146 SNGFFYI 152
                                       4555554 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 4.8
                           DUF3899  10 llliigillivlnsGfFdgfsygfrklkklflkkskkddsyyeykekkkesskkstrplliiGllli 76 
                                       +lli+gi++                                                         +
  gi|518651898|ref|YP_008141418.1| 189 ALLILGIVI---------------------------------------------------------V 198
                                       344444333.........................................................2 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 3.1e-05
                           DUF3899  39 lflkkskkddsyyeykekkkes...skkstrplliiGlllivlsivll 83 
                                       +  ++ +k++  ye kekk+++   + +s+ ++++i+ll+ v+s++++
  gi|518651898|ref|YP_008141418.1| 253 YKYREGDKHEQTYEKKEKKQKRykyIYASIGIIILIALLYGVVSLIIS 300
                                       333458999999999999988889988888999999999999999986 PP

  == domain 5  score: 8.0 bits;  conditional E-value: 0.0016
                           DUF3899  18 livlnsGfFdgfsygfrklkklflkkskkddsyyeykek......kkes..skkstrplliiGlllivls 79 
                                       l+vl+ Gf ++f y f  +++ +   + + ++y e  ++      kk +  + +st p+li+G+ + + s
  gi|518651898|ref|YP_008141418.1| 393 LYVLSLGFVSTFYYVFYSFWMGV---KAMPSEYWEITKNlklgyfKKMRkvIIPSTFPYLISGISSTINS 459
                                       68999***************774...45555555555445556663333479************999987 PP

  == domain 6  score: -3.1 bits;  conditional E-value: 4.6
                           DUF3899  69 liiGlllivlsivl 82 
                                       li G++  ++s+++
  gi|518651898|ref|YP_008141418.1| 506 LIFGIIVAIYSVLF 519
                                       55566666666555 PP

>> DUF334  Domain of unknown function (DUF334)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00012       0.3     136     170 ..     264     298 ..     244     309 .. 0.78
   2 ?   -3.4   0.3       2.3   5.8e+03     152     167 ..     325     340 ..     322     343 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00012
                            DUF334 136 vkrshehyqkrqkqlftgigamllvfmlfalimti 170
                                         + +e+ qkr k++++ ig ++l+ +l+ ++  i
  gi|518651898|ref|YP_008141418.1| 264 TYEKKEKKQKRYKYIYASIGIIILIALLYGVVSLI 298
                                       33457899*******************99877544 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 2.3
                            DUF334 152 tgigamllvfmlfali 167
                                         +g++llv m++a+ 
  gi|518651898|ref|YP_008141418.1| 325 VRVGSILLVSMVIAIF 340
                                       5689*******99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1342  (0.0748508); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.45
# Mc/sec: 3595.48
//
Query:       gi|518651899|ref|YP_008141419.1|  [L=263]
Description: hypothetical protein FACI_IFERC00001G0538 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-27   96.7   0.0    2.2e-27   96.2   0.0    1.2  1  ABC_tran     ABC transporter
    1.9e-06   27.9   0.7     0.0041   17.0   0.7    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    0.00085   18.8   0.4       0.34   10.3   0.0    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00096   19.1   0.0     0.0022   17.9   0.0    1.6  2  RsgA_GTPase  RsgA GTPase
    0.00098   19.4   0.1      0.002   18.4   0.1    1.8  1  AAA_22       AAA domain
     0.0026   17.5   0.0     0.0062   16.3   0.0    1.6  1  AAA_29       P-loop containing region of AAA domain
     0.0031   17.9   0.0     0.0055   17.1   0.0    1.4  1  AAA_16       AAA ATPase domain
     0.0059   16.4   0.0      0.013   15.2   0.0    1.5  2  AAA_15       AAA ATPase domain
  ------ inclusion threshold ------
      0.022   14.5   0.3      0.062   13.0   0.1    1.7  1  AAA_24       AAA domain
      0.026   15.0   0.4      0.045   14.2   0.4    1.3  1  AAA_23       AAA domain
      0.052   13.5   0.0       0.15   11.9   0.0    1.7  2  Rad17        Rad17 P-loop domain
      0.081   13.0   0.2        0.3   11.2   0.1    1.9  2  MMR_HSR1     50S ribosome-binding GTPase
      0.085   13.1   0.1       0.21   11.9   0.1    1.6  2  AAA_28       AAA domain
      0.098   13.1   0.0        0.3   11.5   0.0    1.7  1  AAA          ATPase family associated with various cellular a
       0.15   11.9   0.1       0.38   10.6   0.1    1.5  1  ATPase_2     ATPase domain predominantly from Archaea


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   1.8e-30   2.2e-27       2     137 .]      32     171 ..      31     171 .. 0.96

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.8e-30
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n++++ ++g+ +ai+G++G GKStLl++l g lkp++G ++l gk+l e        e++ ++q    fp + ++e
  gi|518651899|ref|YP_008141419.1|  32 ENINIEAEPGKFIAIIGPSGIGKSTLLRILGGFLKPDKGIVRLMGKPLYE-----PTPEVALIHQSIVTFPWMDAKE 103
                                       79****************************************99999998.....9999****************** PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n             e++e+++  ls++gl++++d       +++SgG++qrva+ara++ +p ++l+DEp+a
  gi|518651899|ref|YP_008141419.1| 104 NvmlsmktknmtkdEMEEKATVSLSRVGLDGFEDLYP----KEMSGGMRQRVAIARAFAADPYVFLMDEPFA 171
                                       ***********99999999************999998....*****************************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 !   17.0   0.7   3.4e-06    0.0041       1      23 [.      43      65 ..      43      88 .. 0.82
   2 !    9.4   0.0   0.00068      0.81     197     299 ..      96     206 ..      73     211 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      + ++iGp g GKS+LL++l ++ 
  gi|518651899|ref|YP_008141419.1| 43 FIAIIGPSGIGKSTLLRILGGFL 65
                                      679****************7774 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00068
                            AAA_21 197 ielsdlgegeeliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEp 266
                                       ++++d +e + l++++++  +++        +  +  ++  +l + e+S G+++  a++ a+++++    ++l DEp
  gi|518651899|ref|YP_008141419.1|  96 FPWMDAKENVMLSMKTKNMTKDEmeekatvSLSRVGLDGFEDLYPKEMSGGMRQRVAIARAFAADP---YVFLMDEP 169
                                       55555555555555555555555666666666666666777888999********89999999888...79****** PP

                            AAA_21 267 EngLHP....kllrrllellkelsrngaQviltTHSp 299
                                        ++L+      l   ++ +l + ++ +  vi+++H+ 
  gi|518651899|ref|YP_008141419.1| 170 FAHLDEltaeGLRQDIYNILFSGETPLKSVIMVSHNL 206
                                       ****986666666777777745555577788888884 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0037       4.4      24      41 ..      41      58 ..      27      64 .. 0.79
   2 !   10.3   0.0   0.00028      0.34     130     178 ..     136     180 ..      85     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0037
                                      SSEEEEEESTTSSHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 24 ksftaivGpNGSGKsnll 41
                                       +f ai+Gp G GKs ll
  gi|518651899|ref|YP_008141419.1| 41 GKFIAIIGPSGIGKSTLL 58
                                      3699***********987 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00028
                                       TT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 130 agiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                       ++++++++SgG ++ va+a  fA   +    ++l+De  a+LDe   + 
  gi|518651899|ref|YP_008141419.1| 136 EDLYPKEMSGGMRQRVAIARAFAADPY----VFLMDEPFAHLDELTAEG 180
                                       567888*****************7655....456666666666554433 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.9e-06    0.0022      89     120 ..      30      62 ..       6      75 .. 0.78
   2 ?   -2.9   0.0       4.5   5.4e+03      31      63 ..      85     118 ..      79     134 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.9e-06
                                       THHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
                       RsgA_GTPase  89 gleelkellkd.ktsvlvGqSGvGKStLinall 120
                                        +e+++ + +  k+++++G+SG+GKStL+  l 
  gi|518651899|ref|YP_008141419.1|  30 VFENINIEAEPgKFIAIIGPSGIGKSTLLRILG 62 
                                       55666666666699***************9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.5
                                       -HHHHHHHHHHHHHTT-EEEEEEE.-GGG--HHH CS
                       RsgA_GTPase  31 slnlldrfLvlaeekgiepvivln.KiDlleeee 63 
                                       ++ l+++ +v++   +++  ++l+ K+  ++++e
  gi|518651899|ref|YP_008141419.1|  85 EVALIHQSIVTFPWMDAKENVMLSmKTKNMTKDE 118
                                       5555555555554444443333332444444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.7e-06     0.002       5      29 ..      41      65 ..      37     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.7e-06
                            AAA_22  5 agilvvtGesGtGKTtllrrlleql 29
                                       ++++++G+sG+GK+tllr l   l
  gi|518651899|ref|YP_008141419.1| 41 GKFIAIIGPSGIGKSTLLRILGGFL 65
                                      789***************9887666 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   5.2e-06    0.0062      12      39 ..      31      58 ..      27      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.2e-06
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                                      f++  ie ++  ++ ++GpsG GKSTll
  gi|518651899|ref|YP_008141419.1| 31 FENINIEAEPGKFIAIIGPSGIGKSTLL 58
                                      55556777777799*************8 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   4.6e-06    0.0055      24      59 ..      40      77 ..      29     101 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.6e-06
                            AAA_16 24 p.elvllsGesGvGKsslvrellralekdggif.lrgk 59
                                      p   + ++G+sG+GKs+l+r l   l+ d+gi+ l gk
  gi|518651899|ref|YP_008141419.1| 40 PgKFIAIIGPSGIGKSTLLRILGGFLKPDKGIVrLMGK 77
                                      357899**************998888888777766555 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.1e-05     0.013      14      55 ..      31      90 ..      27     128 .. 0.66
   2 ?   -1.6   0.0       1.5   1.7e+03     292     336 ..     138     173 ..     100     206 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.1e-05
                            AAA_15 14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn....................k 55
                                      ++++ i+ ++  +  +iG+ ++GKS++l++l  Fl+ +   +                    +
  gi|518651899|ref|YP_008141419.1| 31 FENINIEAEPGkFIAIIGPSGIGKSTLLRILGGFLKPD---KgivrlmgkplyeptpevaliH 90
                                      566666666558***********************977...2334555555555555555550 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.5
                            AAA_15 292 lplnknGsGvqrllllillileaekkdekeeknvilliEEPEahL 336
                                       l+ ++++ G+++ + ++  +++a +       + ++l++EP ahL
  gi|518651899|ref|YP_008141419.1| 138 LYPKEMSGGMRQRVAIA--RAFAAD-------PYVFLMDEPFAHL 173
                                       44455555555544432..333333.......3677777777776 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.2e-05     0.062       5      22 ..      44      61 ..      41      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.2e-05
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      i+i+GpsgiGK+tl++ l
  gi|518651899|ref|YP_008141419.1| 44 IAIIGPSGIGKSTLLRIL 61
                                      89************9877 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.4   3.8e-05     0.045      10      39 ..      31      61 ..      26      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.8e-05
                            AAA_23 10 frdqeidFsk.gltlItGpNGaGKTTildAi 39
                                      f++ +i+ ++ ++ +I+Gp G GK+T+l+ +
  gi|518651899|ref|YP_008141419.1| 31 FENINIEAEPgKFIAIIGPSGIGKSTLLRIL 61
                                      788888888856889************9865 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00013      0.15      40      66 ..      36      62 ..      29      70 .. 0.84
   2 ?   -2.8   0.0       4.3   5.2e+03     150     171 ..     179     202 ..     150     213 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
                             Rad17 40 LesrkkriLLisGPsGCgkstvvkvLs 66
                                      +e ++ + + i GPsG gkst +++L 
  gi|518651899|ref|YP_008141419.1| 36 IEAEPGKFIAIIGPSGIGKSTLLRILG 62
                                      6777888999***************96 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.3
                             Rad17 150 dalrevirkylrssea.l.plilv 171
                                       + lr+ i + l s+e+ l ++i+v
  gi|518651899|ref|YP_008141419.1| 179 EGLRQDIYNILFSGETpLkSVIMV 202
                                       567777777777776513444554 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00025       0.3       2      19 ..      44      61 ..      43      77 .. 0.87
   2 ?   -1.1   0.0       1.7     2e+03      67      94 ..     148     174 ..     102     205 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00025
                                      EEEEESTTSSHHHHHHHH CS
                          MMR_HSR1  2 vaivGrpNvGKStLinal 19
                                      +ai+G +  GKStL++ l
  gi|518651899|ref|YP_008141419.1| 44 IAIIGPSGIGKSTLLRIL 61
                                      89*************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                                       HHHHHHHHC..TSEEEEEEETTTTCSHHHH CS
                          MMR_HSR1  67 gkaflalee..adlillvvdaseeklkpld 94 
                                       +++++  +   ad  ++++d   e +++ld
  gi|518651899|ref|YP_008141419.1| 148 RQRVAIARAfaADPYVFLMD---EPFAHLD 174
                                       22222222233577777777...2333333 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00017      0.21       2      19 ..      44      61 ..      43      75 .. 0.90
   2 ?   -2.4   0.0       4.1   4.9e+03      99     120 ..     149     170 ..     134     187 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                            AAA_28  2 ivitGgestGKTtlleaL 19
                                      i+i+G+++ GK+tll+ L
  gi|518651899|ref|YP_008141419.1| 44 IAIIGPSGIGKSTLLRIL 61
                                      89*************988 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.1
                            AAA_28  99 eleaaarekrydlvfllppape 120
                                       + +a+ar+   d +++l  +p+
  gi|518651899|ref|YP_008141419.1| 149 QRVAIARAFAADPYVFLMDEPF 170
                                       4455666666777444444443 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00025       0.3       3      66 ..      46     168 ..      44     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00025
                                       EESSTTSSHHHHHHHHHHHHTHE.....................................EEEEETTTCSSS..... CS
                               AAA   3 lyGppGtGKTllakavakelgve.....................................fleisgsellsk..... 37 
                                       ++Gp G+GK++l + +   l+ +                                     +l+++ ++++ k     
  gi|518651899|ref|YP_008141419.1|  46 IIGPSGIGKSTLLRILGGFLKPDkgivrlmgkplyeptpevalihqsivtfpwmdakenvMLSMKTKNMT-Kdemee 121
                                       79*****************973334334445555555556666666666666555555555555555555.147888 PP

                                       .................STTHHHHHHHHHHHHHHHTS.TSEEEEEET CS
                               AAA  38 .................yvgesekkirelfkeakeka.kpsilfiDE 66 
                                                        y +e++  +r+ ++ a++ a +p ++++DE
  gi|518651899|ref|YP_008141419.1| 122 katvslsrvgldgfedlYPKEMSGGMRQRVAIARAFAaDPYVFLMDE 168
                                       89999999999999999999999999999999988888889999998 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00031      0.38      15      38 ..      36      59 ..      33      66 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                          ATPase_2 15 lerepneiyfiYGpegsGKtaLlk 38
                                      +e ep +++ i Gp g+GK++Ll+
  gi|518651899|ref|YP_008141419.1| 36 IEAEPGKFIAIIGPSGIGKSTLLR 59
                                      68899*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1874.04
//
Query:       gi|518651900|ref|YP_008141420.1|  [L=166]
Description: hypothetical protein FACI_IFERC00001G0539 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-17   63.2   0.5    2.6e-17   63.0   0.5    1.1  1  RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
  ------ inclusion threshold ------
      0.016   14.9   0.4      0.048   13.4   0.3    1.8  2  DUF5615        Domain of unknown function (DUF5615)


Domain annotation for each model (and alignments):
>> RNase_Zc3h12a  Zc3h12a-like Ribonuclease NYN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.0   0.5   2.9e-21   2.6e-17       4     143 ..      10     139 ..       7     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.0 bits;  conditional E-value: 2.9e-21
                     RNase_Zc3h12a   4 tivIDGsnVa.lshg....rqkifsvrglaiaveyFvkrgheeit.vfvpkfrkealkkekvsdkealeeLekenli 74 
                                       t++IDGsnVa +  g    ++k+    ++ ++++ +++   +ei+ + +++       +  +++k++++++  ++ +
  gi|518651900|ref|YP_008141420.1|  10 TVIIDGSNVAlY--GhkdsDKKTAVLGNILEVIRKLKELKASEIItICDANI------RYIIDEKDKFNRMLANKKL 78 
                                       8*********52..23477999999*************99988761556666......368**************** PP

                     RNase_Zc3h12a  75 vltpskyldgkksvsyddrlilelAeekdGvivsndnyrdllsenkelkdiveerllsftfvkdkfm.lp 143
                                       +l+ps+  +        d++il++A+ek++ ivsnd++r++ ++ + +++ + +  l f fv+ ++m  p
  gi|518651900|ref|YP_008141420.1|  79 ILSPSGIKA--------DTFILDYAREKNCLIVSNDKFREYRDN-DWVNKNIDNITLGFIFVGGDVMlEP 139
                                       *********........************************999.78888999999******99999433 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.13   1.1e+03      35      54 ..      46      65 ..      36      85 .. 0.68
   2 ?   13.4   0.3   5.3e-06     0.048      35      56 ..      86     109 ..      54     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.13
                           DUF5615 35 asDeeileyAkeedriivTk 54
                                       + +ei+ +++++ r i+ +
  gi|518651900|ref|YP_008141420.1| 46 LKASEIITICDANIRYIIDE 65
                                      55567777777777777644 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.3e-06
                           DUF5615  35 asDeeileyAkeedriivTkD..k 56 
                                         D+ il+yA+e++++iv++D  +
  gi|518651900|ref|YP_008141420.1|  86 KADTFILDYAREKNCLIVSNDkfR 109
                                       57999****************544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1048.77
//
Query:       gi|518651901|ref|YP_008141421.1|  [L=94]
Description: hypothetical protein FACI_IFERC00001G0540 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0025   18.2   0.9     0.0033   17.8   0.9    1.1  1  Rubrerythrin  Rubrerythrin
     0.0093   15.8   0.0      0.011   15.5   0.0    1.2  1  COQ7          Ubiquinone biosynthesis protein COQ7
  ------ inclusion threshold ------
      0.044   12.7   0.2      0.047   12.6   0.2    1.0  1  AAA_10        AAA-like domain
      0.054   13.5   0.1      0.083   12.9   0.0    1.4  2  RNase_H_2     RNase_H superfamily


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 !   17.8   0.9   7.3e-07    0.0033       6      66 ..      23      81 ..      20      92 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.3e-07
                                      HHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SS CS
                      Rubrerythrin  6 AiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevke 66
                                      +++ E +a+++Y e  +  k   p ++e+++   ++E+eH  +l + l+  +pel+ e ke
  gi|518651901|ref|YP_008141421.1| 23 SLIEEMQAIMFYDERLDASK--DPVLKEVIKHNRDDEKEHFSLLLEYLRRNDPELDRELKE 81
                                      7889*********9999999..9***************************99999944433 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.5e-06     0.011      13      59 ..      27      71 ..      15      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.5e-06
                              COQ7 13 ElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59
                                      E+ A + Y+  l++  +kdp lk+++k+  ++EkeH++++ e+l+++
  gi|518651901|ref|YP_008141421.1| 27 EMQAIMFYDERLDA--SKDPVLKEVIKHNRDDEKEHFSLLLEYLRRN 71
                                      88899999999999..899******************9988877765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     1e-05     0.047     100     173 ..      19      90 ..      10      93 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1e-05
                            AAA_10 100 keaeslaedilelllgvkkkesekkaalseaveavlegkqrgllavieelrkedekvareiarhlesvvkksla 173
                                       ++ +sl e++  ++  +++ +  k ++l+e++++  + +++++  ++e lr++d+++ re+ + l  + kk+l 
  gi|518651901|ref|YP_008141421.1|  19 RARQSLIEEMQAIMFYDERLDASKDPVLKEVIKHNRDDEKEHFSLLLEYLRRNDPELDRELKEIL--FSKKELK 90 
                                       4455566666667777778899999***********************************99888..6666655 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.8e-05     0.083     119     159 ..      21      61 ..       8      68 .. 0.84
   2 ?   -2.0   0.0      0.67     3e+03     133     143 ..      65      75 ..      57      83 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.8e-05
                         RNase_H_2 119 reedlsGsqavklyqeylrtgdeellekilaYNedDvrala 159
                                       r+  ++  qa+++y+e l   ++  l++++++N+dD  + +
  gi|518651901|ref|YP_008141421.1|  21 RQSLIEEMQAIMFYDERLDASKDPVLKEVIKHNRDDEKEHF 61 
                                       45668999****************************76655 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.67
                         RNase_H_2 133 qeylrtgdeel 143
                                        eylr++d+el
  gi|518651901|ref|YP_008141421.1|  65 LEYLRRNDPEL 75 
                                       46788877764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 596.00
//
Query:       gi|518651902|ref|YP_008141422.1|  [L=151]
Description: hypothetical protein FACI_IFERC00001G0541 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-14   52.3   0.0    6.8e-14   52.0   0.0    1.1  1  4HBT      Thioesterase superfamily
    1.1e-05   25.6   0.0    1.4e-05   25.2   0.0    1.1  1  DUF4442   Domain of unknown function (DUF4442)
     0.0012   19.2   0.0     0.0014   18.9   0.0    1.1  1  4HBT_3    Thioesterase-like superfamily


Domain annotation for each model (and alignments):
>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   1.1e-17   6.8e-14       2      78 ..      59     133 ..      58     134 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 1.1e-17
                                       SSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTSCEE CS
                              4HBT   2 GvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedgrlv 78 
                                       +v+hgG +++++D a+g+  ++ +++  + v+ e +++fl+p+  g ++++e++ +++grt + ve++++d++g+l+
  gi|518651902|ref|YP_008141422.1|  59 NVLHGGIMMTAVDYAGGITTMTVNDG-MDQVTQEVKVNFLAPMSEG-PFRIEGKAIKAGRTAVIVEIKLFDSEGKLG 133
                                       79***********************8.*******************.**************************9985 PP

>> DUF4442  Domain of unknown function (DUF4442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.4e-09   1.4e-05       7     132 .]      20     142 ..      16     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.4e-09
                                       HHHHHHSGGGGGG--EEEEEETTEEEEEE---GGGB-TTSSB-HHHHHHHHHHHHHHHHHHHS-TTEEEEEEEEEEE CS
                           DUF4442   7 aavslkaPYfgtvgprieelepgraevrlkkrrrvrNhigtvHAiAicnlaElamGllaeatlpdthrwipkgmevd 83 
                                       +++ +    f+ +g++i+++++g++e++l+   ++  +   +H++ ++++++ a G +++ t+ d++  + + ++v+
  gi|518651902|ref|YP_008141422.1|  20 KMFEQNENLFAYLGIKITKISKGYCELSLPYSEKITRAGNVLHGGIMMTAVDYAGG-ITTMTVNDGMDQVTQEVKVN 95 
                                       6666677779999****************************************988.57779*************** PP

                                       E-S-.--S-EEEEEE-TTS-TT-.-EEEEEEEEEEETTE.EEEEEEEEEEE CS
                           DUF4442  84 Ylak.atgdltavaelepedvge.keelvvevevrdekgeevvraeitlwv 132
                                       +la+ ++g  + + +     +++ ++ + ve+++ d++g+  + a  t++v
  gi|518651902|ref|YP_008141422.1|  96 FLAPmSEGPFRIEGK----AIKAgRTAVIVEIKLFDSEGKLGIVALGTWYV 142
                                       ****67787666554....4444257999**********988888778776 PP

>> 4HBT_3  Thioesterase-like superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.4e-07    0.0014       8      81 ..      58     138 ..      51     147 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.4e-07
                                       TTC.-HHHHHHHHHHHHHHT........-S.SS.EEEEEEE-S---SEEEEEEEEEEE--SS-EEEEEEEEE.TTEE CS
                            4HBT_3   8 ggagyGGyvlAlalraaqrtv.......pdprl.hslhvyFlrpgdagpviyhvervrdGrsfstrtvelsq.ggrp 75 
                                       g + +GG ++  +  a   t        +  ++   + v+Fl+p ++gp++++ + ++ Gr+   ++++l   +g+ 
  gi|518651902|ref|YP_008141422.1|  58 GNVLHGGIMMTAVDYAGGITTmtvndgmD--QVtQEVKVNFLAPMSEGPFRIEGKAIKAGRTAVIVEIKLFDsEGKL 132
                                       44459999998888888844336666532..3478**********************************96624776 PP

                                       EEEEEE CS
                            4HBT_3  76 iftata 81 
                                        ++a+ 
  gi|518651902|ref|YP_008141422.1| 133 GIVALG 138
                                       555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1037.51
//
Query:       gi|518651903|ref|YP_008141423.1|  [L=124]
Description: hypothetical protein FACI_IFERC00001G0542 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-13   48.9   2.9    2.5e-12   47.0   2.9    1.8  1  DUF2004   Protein of unknown function (DUF2004)
  ------ inclusion threshold ------
       0.23   11.2   2.9        1.1    9.0   2.6    1.9  2  G10       G10 protein


Domain annotation for each model (and alignments):
>> DUF2004  Protein of unknown function (DUF2004)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   2.9   2.8e-16   2.5e-12       5     106 .]      17     123 ..      13     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 2.8e-16
                                       HHHHHHHHHHHHH....TT---EEEEEEEE.................S--HHHHHHHHHH.HHHHHS-HHHHHHHH. CS
                           DUF2004   5 earkaladylkne....kdtvtkyidfHvd.................elgpeieeellek.ddlsklteeellkklk 59 
                                       ++++al + ++n+    +++++++++fHv+                 el+pe +++++ek d+ls++++++l+ ++ 
  gi|518651903|ref|YP_008141423.1|  17 DIVTALGNLTGNYfkneENMDITWRIFHVTldkekyyrvlykgekisELHPENRKKIKEKfDQLSRTDYNALMAQY- 92 
                                       678888888888887779**********************************************************. PP

                                       ................HGGGGT-------.-EEE-SSS-S.-SHHHH- CS
                           DUF2004  60 Lvrigllpdeearfavldfklepdftdellvveldeegdv.qdvtwes 106
                                                         ++ ++ f++ ++++el+ee+d+ qd++w++
  gi|518651903|ref|YP_008141423.1|  93 ----------------EKESRKQGFEK-IGIKELTEEYDLwQDPLWNY 123
                                       ................77888888876.66****************98 PP

>> G10  G10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   2.6   0.00013       1.1      39      73 ..      31      64 ..      16     104 .. 0.87
   2 ?    1.1   0.2     0.035   3.1e+02      10      39 ..      71      98 ..      64     117 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00013
                               G10 39 eskkkeeslWkiarinhersryvyelyykrkaisk 73
                                      +++++ + +W+i++++ ++ +y y ++yk ++is+
  gi|518651903|ref|YP_008141423.1| 31 KNEENMDITWRIFHVTLDKEKY-YRVLYKGEKISE 64
                                      566788899*************.9999******96 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.035
                               G10 10 kkppegfekiedtleeleaklreaekeske 39
                                      kk  e f++++ t  +++a + + ekes++
  gi|518651903|ref|YP_008141423.1| 71 KKIKEKFDQLSRT--DYNALMAQYEKESRK 98
                                      4444444444444..444444444444322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      621  (0.0346366); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 925.18
//
Query:       gi|518651904|ref|YP_008141424.1|  [L=444]
Description: hypothetical protein FACI_IFERC00001G0543 [Ferroplasma acidarmanus fer1]
Scores for 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-61  205.9   0.6    3.7e-60  203.7   0.6    1.8  1  DUF790    Protein of unknown function (DUF790)
  ------ inclusion threshold ------
      0.017   15.1   0.1        2.2    8.3   0.0    3.0  3  HTH_36    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DUF790  Protein of unknown function (DUF790)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.7   0.6   4.1e-64   3.7e-60       2     327 ..      11     321 ..      10     353 .. 0.94

  Alignments for each domain:
  == domain 1  score: 203.7 bits;  conditional E-value: 4.1e-64
                            DUF790   2 Lpsdllrvrr.rggkivpkflkeenlelaaelielfeehvGekrgeleeelkeleeeatdyklvrGLakllereaef 77 
                                       +psdl+ vr+ + g + p fl++en ++++++ ++f+e++G++r+ + ++lkele +++ +k +r+L+ l  r++ f
  gi|518651904|ref|YP_008141424.1|  11 FPSDLMIVRKlKTGLVFPVFLSDENSDYIDSVKTVFNENTGNNRETILKALKELELNSSSTKTIRALSLLFFRNSIF 87 
                                       79*******9899**************************************************************** PP

                            DUF790  78 etespldpeelReevFeaaaeavvseeereevleevaeelgvspeeveealyadleenkiLtefeeitpeeLlkrYN 154
                                       e + ++d  +lRe vF+ a+   v+++e++++l+ v+e++g+s +e+ ++lyad e++ +L ++ + +  e+ + YN
  gi|518651904|ref|YP_008141424.1|  88 EPPVDVDAPALREDVFKIARIPPVNQDEKRNILKPVEEKYGLSMDEIINGLYADKESELVLHQAYSASNIEIARAYN 164
                                       ********************99******************************************************* PP

                            DUF790 155 lslvqtlLfkatelrirvsdaeykelfravkllgLmyeieedaeegleitvdGPaslfkaterYGlalAkllpallk 231
                                       l++v+t++++++ l i++s+ ++   + ++k+lgL+++++ d ++  +i+++GP  +f++ erYG ++A+l+  + +
  gi|518651904|ref|YP_008141424.1| 165 LEQVETIMMRCSTLYITTSS-DWSYTITSIKRLGLLFTAQIDGSKLKSIKITGPLEMFESPERYGSRFAMLIHKISQ 240
                                       ********************.9**********************999****************************** PP

                            DUF790 232 vekWeleAeikdrd...kkkrelrfeldsedsglvshyeeekefdssveeefaerfeklktdwelerepellkiggs 305
                                        e+W +eA+ik +d   k+ ++++++l+++     s y +e++   s++ +f+e+              ++l ++g+
  gi|518651904|ref|YP_008141424.1| 241 LENWAIEADIKIKDkfeKTVKVYKLKLSDTV----SYYLPESNKTDSINYDFVEKA-------------QPLIVNGT 300
                                       **************88778888888888844....555555555667899998877.............6899**** PP

                            DUF790 306 vmiPDFaleekdgrrvyleIvG 327
                                       v++PD+ + + ++++vy++I G
  gi|518651904|ref|YP_008141424.1| 301 VYFPDYVM-KIGDKTVYINITG 321
                                       ********.9**********98 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0   0.00024       2.2      20      51 ..       6      66 ..       1      68 [. 0.83
   2 ?   -3.5   0.0       1.2   1.1e+04      26      42 ..     154     171 ..     154     172 .. 0.75
   3 ?    3.2   0.1    0.0096        86      36      52 ..     386     402 ..     372     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00024
                            HTH_36 20 knggcfps.............................qetlakrlglsknTvsraikeLeq 51
                                      +++ +fps                             +  + +++g +++T+ +a+keLe 
  gi|518651904|ref|YP_008141424.1|  6 GGEKVFPSdlmivrklktglvfpvflsdensdyidsvKTVFNENTGNNRETILKALKELEL 66
                                      4455888888888888888888888888888888898899999****************95 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                            HTH_36  26 psqetlakrlgls.knTv 42 
                                       +s+  +a++++l  ++T+
  gi|518651904|ref|YP_008141424.1| 154 ASNIEIARAYNLEqVETI 171
                                       578889999998766666 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.0096
                            HTH_36  36 glsknTvsraikeLeql 52 
                                       +l++n+v +++keLe+l
  gi|518651904|ref|YP_008141424.1| 386 ELDDNSVDSIKKELEKL 402
                                       5899***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3015.97
//
Query:       gi|518651905|ref|YP_008141425.1|  [L=443]
Description: hypothetical protein FACI_IFERC00001G0544 [Ferroplasma acidarmanus fer1]
Scores for 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   76.3   0.0    3.8e-21   75.4   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    1.5e-18   67.4   0.0      3e-18   66.4   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
    9.6e-16   58.1   0.0    1.9e-15   57.2   0.0    1.5  1  Helicase_C     Helicase conserved C-terminal domain
    2.1e-06   27.5   0.7      5e-06   26.3   0.2    2.0  2  XPB_DRD        Xeroderma pigmentosum group B helicase damage 
      3e-06   27.1   0.0    1.4e-05   25.0   0.0    2.1  2  DEAD           DEAD/DEAH box helicase


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 !   75.4   0.0   1.1e-24   3.8e-21      34     183 ..     293     433 ..     285     435 .. 0.90

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 1.1e-24
                     ERCC3_RAD25_C  34 kkkllyvmnpnkfracefLikyhekrgDkiivfsDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvnti 110
                                       k + ++    +k++ +++L++ h   g+kii+fs++  +   +++++  p ++  ts +er+k l+ fk+  ++ ++
  gi|518651905|ref|YP_008141425.1| 293 KSREIAFNAERKVEYLKYLLSKHA--GEKIIIFSEDTSTAYLISREFLVPALTYMTSGKERKKYLEMFKSG-EITVL 366
                                       5555666667899999***99885..99****************************************976.899** PP

                     ERCC3_RAD25_C 111 flskvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLrakkksneeefnaffYsLvskDtkemaystkrqq 183
                                         s++ D+ +D+P+a++ i i s  gs rq  qrlGriLr+ ++     + ++ Y Lvs+ t+e   s++r++
  gi|518651905|ref|YP_008141425.1| 367 ATSRILDEGVDVPDASIAI-IMSGSGSTRQFRQRLGRILRPSEG-----KASYLYELVSSGTTEYGTSRRRRK 433
                                       ****************999.556789***************877.....689**************9999985 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 !   66.4   0.0   8.3e-22     3e-18       1     171 []      60     200 ..      60     200 .. 0.94

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 8.3e-22
                                       --EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   1 klelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkf 77 
                                       +++lr+yQ++ +e +      +++  g i+++T +GKT++ + +i  l+       +++l+p+++l+ q++e+++++
  gi|518651905|ref|YP_008141425.1|  60 EINLRPYQKKSLEMWQ-----RNNYSGTIVLPTAAGKTILGIYAITMLKV-----PTIILAPTIELIIQWREKLRDL 126
                                       589************8.....7899*****************99999998.....89******************** PP

                                       TGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHH CS
                            ResIII  78 lseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreil 154
                                       l+ +   +g++  g+k+++        +i v+t++s++           e l +rf++ii DE+H++++ +s+ +i+
  gi|518651905|ref|YP_008141425.1| 127 LNVE---VGQIGGGEKEIR--------DISVSTYDSAYLMA--------ESLGNRFKFIIADEVHHMAS-ESYLQIA 183
                                       *998...688888888888........************99........99******************.******* PP

                                       HT---SEEEEEESS-S- CS
                            ResIII 155 ekfkeavllglTATper 171
                                       +++ + ++lglTAT er
  gi|518651905|ref|YP_008141425.1| 184 KYYASPYRLGLTATYER 200
                                       **************875 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   0.0   5.3e-19   1.9e-15       2     109 ..     304     405 ..     303     407 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 5.3e-19
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k+e+l++ll +++ g+ki+if++ ++++    l+  ++++ v +l+  ++ +er++ le f++ge++vL +++++ +
  gi|518651905|ref|YP_008141425.1| 304 KVEYLKYLL-SKHAGEKIIIFSEDTSTA---YLI--SREFLVPALTYMTSGKERKKYLEMFKSGEITVLATSRILDE 374
                                       8999****9.9***************99...466..5668888999999**************************** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       G+d+p+++  i+++   +++++ qr GR+ R
  gi|518651905|ref|YP_008141425.1| 375 GVDVPDASIAIIMSGSGSTRQFRQRLGRILR 405
                                       *****************************99 PP

>> XPB_DRD  Xeroderma pigmentosum group B helicase damage recognition domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   1.4e-09     5e-06       2      44 ..       4      41 ..       3      42 .. 0.91
   2 ?   -3.2   0.0       2.2   7.9e+03       5      13 ..      80      88 ..      79      92 .. 0.76

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.4e-09
                                      EEETTEEEECSSSTT...-CT.EEETTTTEEEEEGGGHHHHHH CS
                           XPB_DRD  2 rYdrGTllidgdprgkaslpfvewDeRvekyRapAlrYrdlve 44
                                       +++G +++d++ +g      + +DeR++kyRa+A+rY d+++
  gi|518651905|ref|YP_008141425.1|  4 YFKAGSIISDENYSG-----IFSYDERIKKYRALAYRYVDIIK 41
                                      5899*********98.....678*****************985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                                      TTEEEECSS CS
                           XPB_DRD  5 rGTllidgd 13
                                      +GT+++ + 
  gi|518651905|ref|YP_008141425.1| 80 SGTIVLPTA 88
                                      7***99765 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5   5.4e+03      87     120 ..      25      58 ..      15      59 .. 0.68
   2 !   25.0   0.0   3.8e-09   1.4e-05       2     146 ..      65     187 ..      64     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHTT.CSEEEEEHHHHHHHHHCTSSHCT CS
                                       xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  87 ardqlskldng.vdivvgtpgrlddllstgklnls 120
                                       + +++++l  + vd ++  pg +d++++++kl++s
  gi|518651905|ref|YP_008141425.1|  25 RIKKYRALAYRyVD-IIKKPGIIDNVFKDKKLEIS 58 
                                       55555666555344.46789999999999988765 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.8e-09
                                       HHHHHHHHHHHTTC.EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilggg.dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       ++Q+++++   +++ +  +  +T++GKT   + ++   +       +  ++i++Pt eL+ q  ++l+ +++   ++
  gi|518651905|ref|YP_008141425.1|  65 PYQKKSLEMWQRNNySGTIVLPTAAGKTILGIYAIT-ML-------KVPTIILAPTIELIIQWREKLRDLLN---VE 130
                                       78999999988554477899********98444444.33.......5678**********************...55 PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinril 146
                                       v  i gg+++      +    di v+t +    + +      ++++f++ DE++ + ++++ +  +  +
  gi|518651905|ref|YP_008141425.1| 131 VGQIGGGEKE------I---RDISVSTYDSAYLMAE-SL--GNRFKFIIADEVHHMASESYLQIAKYYA 187
                                       6555445433......4...4667777777776554.22..4689**************9988777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2962.52
//
Query:       gi|518651906|ref|YP_008141426.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G0545 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.0   0.0    1.3e-13   50.8   0.0    1.1  1  ABM       Antibiotic biosynthesis monooxygenase
     0.0013   17.7   0.4       0.58    9.0   0.1    2.0  2  SOR       Sulphur oxygenase reductase
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.013   15.8   0.0    1.1  1  DUF4188   Domain of unknown function (DUF4188)
       0.13   13.0   0.0       0.17   12.6   0.0    1.2  1  DUF4936   Domain of unknown function (DUF4936)


Domain annotation for each model (and alignments):
>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   2.9e-17   1.3e-13       1      75 [.       1      76 [.       1      79 [. 0.96

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.9e-17
                                      CEEEEEEEEESTTGHHHHHHHHHHHHH..HHHHTSTTEEEEEEEEEETSTTEEEEEEEESSHHHHHHHHTSHHHHHH CS
                               ABM  1 mviviaeirvkpgqaeafldafaeave..sllaeepGclgyellrstedpdevvvieeWeseaaleahlksphfkaa 75
                                      m++v  +++vk+g+ ++f++ f +++e  ++ ++e G+ +  l+++ + p+e+++++eW+s++a++++++  +fk++
  gi|518651906|ref|YP_008141426.1|  1 MIHVGLYYKVKEGHNDDFVKTFNNVLEllKS-KPETGFVDGKLYQEVDSPREYMIYTEWKSREAFKDFVEMKAFKDT 76
                                      99*************************8888.79****************************************985 PP

>> SOR  Sulphur oxygenase reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00018      0.82     164     194 ..       8      40 ..       2      46 .. 0.83
   2 !    9.0   0.1   0.00013      0.58     236     258 ..      42      64 ..      32      76 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00018
                               SOR 164 htvkeGkekeFeegavetlellke..apGllGy 194
                                       ++vkeG++++F ++  ++lellk+   +G++  
  gi|518651906|ref|YP_008141426.1|   8 YKVKEGHNDDFVKTFNNVLELLKSkpETGFVDG 40 
                                       58********************99566788865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
                               SOR 236 vleaaetPkeylvhveWesleaa 258
                                         +  ++P+ey++++eW+s ea 
  gi|518651906|ref|YP_008141426.1|  42 LYQEVDSPREYMIYTEWKSREAF 64 
                                       5677899***********99875 PP

>> DUF4188  Domain of unknown function (DUF4188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   0.0   2.9e-06     0.013      21      94 ..      17      93 ..       1      97 [. 0.79

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.9e-06
                           DUF4188 21 evleamprmlreleekkelGlLgaeslig...srevllvqYwrdvesLeafakseeHreawrkfnkkvkksgavgif 94
                                      + ++ + ++l+ l++k+e+G+++ + +     +re+++   w++ e+ ++f + +  +++ +  +   + +++  if
  gi|518651906|ref|YP_008141426.1| 17 DFVKTFNNVLELLKSKPETGFVDGKLYQEvdsPREYMIYTEWKSREAFKDFVEMKAFKDTTDYGKSILEGAPRNKIF 93
                                      667889999999***************955999******************99888887776666665656666666 PP

>> DUF4936  Domain of unknown function (DUF4936)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.7e-05      0.17       2      51 ..       6      58 ..       6      82 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.7e-05
                           DUF4936  2 vYYrvaeadaaaalaavralqaalaartg...vagrLlrrlddpesqdglaTw 51
                                      +YY+v+e+++++++++ +++++ l+ ++    v+g+L + +d p +    + w
  gi|518651906|ref|YP_008141426.1|  6 LYYKVKEGHNDDFVKTFNNVLELLKSKPEtgfVDGKLYQEVDSPREYMIYTEW 58
                                      5********************99965443224899999999999554444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 719.26
//
Query:       gi|518651907|ref|YP_008141427.1|  [L=542]
Description: hypothetical protein FACI_IFERC00001G0546 [Ferroplasma acidarmanus fer1]
Scores for complete 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-173  577.2  19.2   2.8e-173  577.0  19.2    1.0  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.035   14.0   0.1        5.5    7.0   0.0    3.3  3  M20_dimer   Peptidase dimerisation domain
        1.4    8.9   4.6        4.4    7.3   0.5    3.0  3  YwpF        YwpF-like protein


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  577.0  19.2  4.7e-177  2.8e-173       1     490 [.      33     523 ..      33     524 .. 0.98

  Alignments for each domain:
  == domain 1  score: 577.0 bits;  conditional E-value: 4.7e-177
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +a  +++tlGP+GmdKmlv++ g++v+TnDG+tilke+++ehPaak++ve++++qd+ vGDGTtt+vi+ag+Ll++a
  gi|518651907|ref|YP_008141427.1|  33 IATSIRSTLGPRGMDKMLVDSLGDIVITNDGVTILKEMDVEHPAAKMMVEVSKTQDSYVGDGTTTAVIIAGALLDQA 109
                                       6889************************************************************************* PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       ++l++++vhpt+i+egy++a+++a + L+ei  + +++ kd+e+L+k+a+tsl+sk  s e+e l+ +  +A+k+i 
  gi|518651907|ref|YP_008141427.1| 110 QSLVKQNVHPTVITEGYKTAAAQASRVLEEI--SRPVTLKDKEILIKMAKTSLNSKSASVEKELLGTISYNAIKTIA 184
                                       *******************************..8888888*********************************6666 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e++   + +d+++ +vvk++gg+++++el++G++ldk+ ++p+mpk ++nak++lld  Lei+k+e +t+++++d++
  gi|518651907|ref|YP_008141427.1| 185 EERdgkYLVDFDNLQVVKKNGGEINQTELIDGIILDKEKVHPNMPKLVKNAKIALLDLALEIKKPEFDTNLQINDPS 261
                                       66669999********************************************************************* PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                        ++k++ +ee+ l+e+++ki+++g+nvv++qkgidd+a+h+l k+gi a+rrvkk+d++++akatGat+vssle++ 
  gi|518651907|ref|YP_008141427.1| 262 MIQKFLGQEEDVLKEMVDKIKATGANVVITQKGIDDMAQHYLSKAGIYAVRRVKKSDVDKIAKATGATIVSSLEEIV 338
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                        ++lG a+ vee+kig++++t+++++k++k+ ++l+r+ t++v+deier+i d+l+vv++a+ed+ +  GGG++  e
  gi|518651907|ref|YP_008141427.1| 339 ASDLGAADAVEERKIGDDYMTFVTGSKNPKAISLLIRAGTEHVADEIERSITDSLHVVAAAVEDGAYTTGGGSAAEE 415
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       +a  l++ya++v g++qlaie+fa+ALe+ip++LaeNaGldpi++l k+r++h++g+k++g++v sg+++d+ +agv
  gi|518651907|ref|YP_008141427.1| 416 IAFNLRSYATKVGGRQQLAIEKFADALEEIPRALAENAGLDPIDILIKIRSEHANGHKTFGVNVFSGNVEDMEKAGV 492
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       ++p+++ +qa++++teaa +iLrid++i +k
  gi|518651907|ref|YP_008141427.1| 493 IEPIRIGKQAVEASTEAAVMILRIDDVIATK 523
                                       ****************************987 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.029   1.7e+02      48     104 ..     101     163 ..      25     168 .. 0.77
   2 ?    7.0   0.0   0.00092       5.5      15      48 ..     221     254 ..     214     298 .. 0.85
   3 ?    0.1   0.0      0.12   7.2e+02      29      65 ..     434     482 ..     426     494 .. 0.64

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.029
                                       ..........TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEHHHHHHHHHHHHHHHHHHTSC CS
                         M20_dimer  48 a......eerslprttlnvtgiegGsaknvipdeaeakidiRllpgedpeevleeieeileke 104
                                              + +sl + ++ +t+i +G+++ +  ++  ++ + R++   d e +++  ++ l+++
  gi|518651907|ref|YP_008141427.1| 101 IagalldQAQSLVKQNVHPTVITEGYKTAAAQASRVLEEISRPVTLKDKEILIKMAKTSLNSK 163
                                       044444455667788999********9999999999999999999999998888888877766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00092
                                       -B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.. CS
                         M20_dimer  15 gkagHsgapgagaNAieklarllaeledeegdia 48 
                                        +++H+++p+ + NA  +l +l  e+++ e+d++
  gi|518651907|ref|YP_008141427.1| 221 KEKVHPNMPKLVKNAKIALLDLALEIKKPEFDTN 254
                                       6789************************999965 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.12
                                       HHHHHHHHHHCSCTTEEC.................TCCTCCCCCEECCE CS
                         M20_dimer  29 Aieklarllaeledeegdia............eerslprttlnvtgieg 65 
                                       Aiek a++l+e++    ++a             e+  ++ t+ v++++g
  gi|518651907|ref|YP_008141427.1| 434 AIEKFADALEEIPRALAENAgldpidilikirSEHANGHKTFGVNVFSG 482
                                       6777777777777766666566666666666555555555555555555 PP

>> YwpF  YwpF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.045   2.7e+02      79     125 ..      78     129 ..      56     133 .. 0.68
   2 ?    7.3   0.5   0.00073       4.4       7      37 ..     197     225 ..     194     263 .. 0.85
   3 ?   -1.2   0.0       0.3   1.8e+03      50      73 ..     270     293 ..     258     297 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.045
                              YwpF  79 tlvvtvksitk..l..eekisvllegklvtkkkdlae.klLeeLvkeglege 125
                                       +++v+v+++++  +  +++  v++ g l+ + ++l++ ++  +++ eg+++ 
  gi|518651907|ref|YP_008141427.1|  78 KMMVEVSKTQDsyVgdGTTTAVIIAGALLDQAQSLVKqNVHPTVITEGYKTA 129
                                       5666666555422221356789999999999777665157778999999875 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.00073
                              YwpF   7 sleiledeeeeekqkeipllDGliinkedee 37 
                                       +l++++++ +  ++++ +l+DG+i++ke+ +
  gi|518651907|ref|YP_008141427.1| 197 NLQVVKKNGG--EINQTELIDGIILDKEKVH 225
                                       5889998864..588899*********9875 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.3
                              YwpF  50 yeeffeellekeeellvevvItkk 73 
                                       +e++++e+++k +   ++vvIt+k
  gi|518651907|ref|YP_008141427.1| 270 EEDVLKEMVDKIKATGANVVITQK 293
                                       567888888888888899999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3816.35
//
Query:       gi|518651908|ref|YP_008141428.1|  [L=95]
Description: hypothetical protein FACI_IFERC00001G0547 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0031   17.1   0.0     0.0043   16.7   0.0    1.2  1  GntR             Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.032   14.1   0.0    1.1  1  Phage_rep_org_N  N-terminal phage replisome organiser (Phage_


Domain annotation for each model (and alignments):
>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   4.8e-07    0.0043       3      55 ..      16      68 ..      15      74 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.8e-07
                                      HHHHHHHHHHHHTTSS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR  3 eqvyerLredIlsgelrpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      +q+y    ++I+sg+l   +k+Ps +++a  +g + + v +A+  L  + ++ 
  gi|518651908|ref|YP_008141428.1| 16 DQIYSGMIDEIRSGNLYYKTKIPSTEQVAGVLGLNLNAVDRAYGLLLKDRVIR 68
                                      58999999************************************999888875 PP

>> Phage_rep_org_N  N-terminal phage replisome organiser (Phage_rep_org_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.6e-06     0.032      42     105 ..      27      89 ..      15      95 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-06
                   Phage_rep_org_N  42 enGelylsenipytaemlalifnreletvrlaLkvlkdlelieisedkvikiknwekhqniesk 105
                                       ++G+ly++ +ip+t+ ++a ++  +l+ v  a  +l + ++i + ++k + ++  +  +n   k
  gi|518651908|ref|YP_008141428.1|  27 RSGNLYYKTKIPSTE-QVAGVLGLNLNAVDRAYGLLLKDRVIRQFKNKKYVMAPGDTDINPMIK 89 
                                       68**********996.689******************************999866655555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 680.28
//
Query:       gi|518651909|ref|YP_008141429.1|  [L=368]
Description: hypothetical protein FACI_IFERC00001G0548 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-10   39.2   0.0      4e-10   39.2   0.0    4.9  7  DUF1648        Protein of unknown function (DUF1648)
    0.00076   19.3   0.1    0.00076   19.3   0.1    2.7  3  Tetraspanin    Tetraspanin family
     0.0093   15.3   1.5     0.0093   15.3   1.5    2.4  3  NicO           High-affinity nickel-transport protein
  ------ inclusion threshold ------
        1.3    8.8   3.8          1    9.1   0.1    2.3  2  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> DUF1648  Protein of unknown function (DUF1648)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   2.3       1.5   6.9e+03       2      14 ..      59      71 ..      58      73 .. 0.76
   2 ?   -2.9   1.9       1.2   5.5e+03      41      49 .]      81      89 ..      78      90 .. 0.83
   3 ?   -0.3   0.1       0.2   8.9e+02      35      48 ..     128     141 ..     128     142 .. 0.86
   4 !   39.2   0.0   8.9e-14     4e-10       2      47 ..     142     188 ..     140     190 .. 0.84
   5 ?   -1.0   0.3      0.33   1.5e+03       3      14 ..     190     201 ..     188     207 .. 0.61
   6 ?   -5.4   3.4         4   1.8e+04       2      12 ..     260     270 ..     259     275 .. 0.57
   7 ?   -4.2   2.0       3.3   1.5e+04       2      10 ..     353     361 ..     350     365 .. 0.62

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.5
                           DUF1648  2 llllplvvgllly 14
                                       ++l++++++l y
  gi|518651909|ref|YP_008141429.1| 59 TFILTIILTVLTY 71
                                      5788888888877 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                           DUF1648 41 lfllPllml 49
                                       f++Pl+m+
  gi|518651909|ref|YP_008141429.1| 81 TFFMPLFMV 89
                                      699**9995 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.2
                           DUF1648  35 gsKlfalfllPllm 48 
                                       g K++ +f lP+++
  gi|518651909|ref|YP_008141429.1| 128 GKKFPWFFTLPGIL 141
                                       678999******97 PP

  == domain 4  score: 39.2 bits;  conditional E-value: 8.9e-14
                           DUF1648   2 llllplvvglllypkLPdqiPtHfnasGepDgygsK.lfalfllPll 47 
                                       +l+  +v g+l y ++P++ +tH+nasG +++y+ K  +++f+l ++
  gi|518651909|ref|YP_008141429.1| 142 VLVSLFVTGILDYKSIPERFATHYNASGIANAYSTKsIESVFILGFI 188
                                       55666667888*************************88888888776 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.33
                           DUF1648   3 lllplvvgllly 14 
                                       +++++++ l++y
  gi|518651909|ref|YP_008141429.1| 190 IIITIMMILIAY 201
                                       455555555555 PP

  == domain 6  score: -5.4 bits;  conditional E-value: 4
                           DUF1648   2 llllplvvgll 12 
                                       l+l+p++++++
  gi|518651909|ref|YP_008141429.1| 260 LILIPVFLLII 270
                                       55555555554 PP

  == domain 7  score: -4.2 bits;  conditional E-value: 3.3
                           DUF1648   2 llllplvvg 10 
                                       ++++p+++ 
  gi|518651909|ref|YP_008141429.1| 353 IIAIPVIIV 361
                                       556666554 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.6     0.038   1.7e+02      49      93 ..      49      93 ..       8     100 .. 0.63
   2 !   19.3   0.1   1.7e-07   0.00076       5      95 ..     182     277 ..     180     316 .. 0.79
   3 ?   -4.3   1.2       2.7   1.2e+04      53      61 ..     353     361 ..     343     367 .. 0.37

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.038
                                      ....XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin 49 laillivvGvllfllgflGcigalkenkcllltfsllllvlflle 93
                                       ++  i v+++++l+ +l ++  l  ++ l  tf++ l+++++ +
  gi|518651909|ref|YP_008141429.1| 49 RKMKKIYVSITFILTIILTVLTYLLSSYLLVITFFMPLFMVLVEF 93
                                      334455666666666666777788899999999999999998755 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 1.7e-07
                                       XXXXXXXXXXXXXXXXXXX.XXXXX..XXX.....................XXXXXX..XXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxx.xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   5 lfffnllfwligivllavG.vwlrl..khaeaalacllsesaedpailaillivvGv..llfllgflGcigalkenk 76 
                                       +f++ ++ ++i i+++ ++ v +r+  k++ a+ + ++     ++++++ +l+   +    +l+g +G  g++ken 
  gi|518651909|ref|YP_008141429.1| 182 VFILGFISIIITIMMILIAyVIARTplKTDNASPHGTERVVIYQERMVYLTLLTPVFinSSLLIGSFGEWGIIKENV 258
                                       8999999999999999999677777*98888888999999999999996666665556789***************9 PP

                                       XXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  77 cllltfsllllvlfllela 95 
                                       +l+l+ ++ll++++++  +
  gi|518651909|ref|YP_008141429.1| 259 FLILIPVFLLIIFVIAISV 277
                                       9998877777776666544 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 2.7
                                       XXXXXXXXX CS
                                       xxxxxxxxx RF
                       Tetraspanin  53 livvGvllf 61 
                                       +i++ v+++
  gi|518651909|ref|YP_008141429.1| 353 IIAIPVIIV 361
                                       111111111 PP

>> NicO  High-affinity nickel-transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.8      0.32   1.4e+03     227     233 ..      63      69 ..      41      97 .. 0.53
   2 !   15.3   1.5   2.1e-06    0.0093     219     282 ..     133     202 ..     119     204 .. 0.80
   3 ?   -3.7   0.5       1.3   5.8e+03      79      94 ..     260     275 ..     254     280 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.32
                              NicO 227 sitvall 233
                                        i++++l
  gi|518651909|ref|YP_008141429.1|  63 TIILTVL 69 
                                       2222222 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 2.1e-06
                              NicO 219 yamsitgtsitvalliglivtlklvakkfalsgs...lwaaiisle....leivGavlvllfallllgasl 282
                                         +++ g+ ++v+l++++i+  k + ++fa +++   +++a ++ +    + i+G++ ++++ ++ l+a++
  gi|518651909|ref|YP_008141429.1| 133 WFFTLPGILVLVSLFVTGILDYKSIPERFATHYNasgIANAYST-KsiesVFILGFISIIITIMMILIAYV 202
                                       558999**************************996643333333.245578899**999999999999986 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 1.3
                              NicO  79 gteiasFllvilllnl 94 
                                        ++i  Fll+i+++++
  gi|518651909|ref|YP_008141429.1| 260 LILIPVFLLIIFVIAI 275
                                       4455667777776654 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00023         1     117     189 ..      34     111 ..       9     139 .. 0.64
   2 ?   -0.2   0.9      0.16   7.3e+02     135     174 ..     226     270 ..     124     285 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00023
                     FA_desaturase 117 wlrrlarrrapsksrrrkwrllawlllllawlglwlalllllglalllwlvplllllfllalvlnyveHyg...... 187
                                       +  r+   +  s + r+++ ++    ++l++++++l +ll + l++  +++pl+++l+   ++  + eHy       
  gi|518651909|ref|YP_008141429.1|  34 FGVRVPTDKINSDTVRKMKKIYVSITFILTIILTVLTYLLSSYLLVITFFMPLFMVLV--EFMVYLPEHYSlerikr 108
                                       5556666666777777778888888888888888888888776664455555555544..44436788887544433 PP

                     FA_desaturase 188 .gd 189
                                        ++
  gi|518651909|ref|YP_008141429.1| 109 dEQ 111
                                       333 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.16
                     FA_desaturase 135 wrllawlllllawlglwlalllllglall.....lwlvplllllf 174
                                        r++++ ll ++++   l+++ ++ ++       l+l+p++ll++
  gi|518651909|ref|YP_008141429.1| 226 ERMVYLTLLTPVFINSSLLIGSFGEWGIIkenvfLILIPVFLLII 270
                                       333333333333444444444444444446664444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1215  (0.0677673); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.41
# Mc/sec: 2719.58
//
Query:       gi|518651910|ref|YP_008141430.1|  [L=650]
Description: hypothetical protein FACI_IFERC00001G0549 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-74  250.0   0.0    5.6e-74  249.6   0.0    1.1  1  Molybdopterin    Molybdopterin oxidoreductase
    2.3e-24   85.6   0.1    5.3e-24   84.4   0.0    1.6  2  Molydop_binding  Molydopterin dinucleotide binding domain
      4e-14   52.3   0.7    7.8e-14   51.4   0.7    1.5  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.6   0.0   9.4e-78   5.6e-74       1     432 []      55     470 ..      55     470 .. 0.90

  Alignments for each domain:
  == domain 1  score: 249.6 bits;  conditional E-value: 9.4e-78
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       Rl yP+++     +G+++r sW++  ++  +s+k+++kkyg+d+va f+ g  +s+e++++l+kl+++lg    +++
  gi|518651910|ref|YP_008141430.1|  55 RLYYPLKK---V-KGELERTSWEDSIKYTIESIKNIQKKYGKDSVA-FYGGCQNSLEEVYLLQKLARALGT---NNV 123
                                       9*******...6.9********************************.666667889**************9...566 PP

                                       ECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSSB-HC CS
                     Molybdopterin  78 dwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpryael 154
                                       d++a++++   ++++    + + + sn+ +++ +++++++ G  v   +p+l  +++ +a++k++k+i i+pr + +
  gi|518651910|ref|YP_008141430.1| 124 DSCARVCHDPSAKALKE-IVGVGAGSNSATEIPKAKVVVVAGESVTDSHPVLIQYFL-EAKEKGTKIILIDPRNTRF 198
                                       77777776665545544.4667777888889*********************44444.455557************* PP

                                       GGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHHHHHH CS
                     Molybdopterin 155 lkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarelarna 231
                                       ++fad++l+ikp +d  l++a +++++q+++   +f++ +t g+e++++ +++++ e + ++++   + ++e+a+ +
  gi|518651910|ref|YP_008141430.1| 199 ASFADLHLKIKPRSDIFLFNAVANYLIQNNMIKPDFIAARTEGYEKYKENVSKYTLELAVEQTGLAEKDIIEFAKYI 275
                                       *********************************************************88888888888999998766 PP

                                       HHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTHH CS
                     Molybdopterin 232 aktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkeek 308
                                        + +   ++++G gl++++ g+  ++  ++L ll+gn+g++g+g+  ++Gq +++g +       v ++ ++   ++
  gi|518651910|ref|YP_008141430.1| 276 SEDK--VIFSWGLGLTEST-GTKGIKSYLSLPLLTGNMGKEGAGVIVYRGQTNVQGSGDLIKPD-VFPNGEMNEANS 348
                                       6554..6*******99865.88888999****************************99999999.999999999988 PP

                                       HHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSHHHHTSSE CS
                     Molybdopterin 309 ikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrltstalyaDi 385
                                       +++   +  + + +++ +++   +  +s+++k+l+++g+np+ + +++++v++ l++l+l+vv d+++t+ta+yaDi
  gi|518651910|ref|YP_008141430.1| 349 EALSRIWGFKPPVNKGSSIID--TFYGSKNIKALFIMGYNPVRSLPNRKKVKEFLGSLELLVVQDIFMTDTARYADI 423
                                       777777777777778888885..5678889*********************************************** PP

                                       EEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHHH CS
                     Molybdopterin 386 iLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLakk 432
                                       +LPaa+w Eke+ + + ++ +  + +av+ppg a++d++Il++Lak+
  gi|518651910|ref|YP_008141430.1| 424 VLPAAAWAEKEGSVASLDRLVKWRFKAVDPPGMARPDYEILSDLAKA 470
                                       *********************************************95 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.5   9.1e+03      62      90 ..     411     437 ..     408     440 .. 0.75
   2 !   84.4   0.0   8.8e-28   5.3e-24       1     111 []     543     645 ..     543     645 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.5
                                       EEEEESSB-TTEEEEESSHCC.....S-G CS
                   Molydop_binding  62 rakvtervrpGvvfmpfgwweagekggna 90 
                                        ++ t++ r   +++p ++w+  ek+g++
  gi|518651910|ref|YP_008141430.1| 411 DIFMTDTARYADIVLPAAAWA--EKEGSV 437
                                       567788899999999999999..666665 PP

  == domain 2  score: 84.4 bits;  conditional E-value: 8.8e-28
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpepevveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfmp 77 
                                       l+L+tgr++ +++s    ++v+  ++ +p ++++np dA+ lGi++ d+V+++s+ G++   ak+t++v pGvvf +
  gi|518651910|ref|YP_008141430.1| 543 LILVTGRTVTRYNSDEVINRVPGMQEYNP-TLWVNPSDAKNLGIENEDMVKLASKSGELDIIAKITDDVIPGVVFTY 618
                                       79************************999.*********************************************** PP

                                       SSHCC.....S-GHCTS--SCSTTT--CSTT-EE CS
                   Molydop_binding  78 fgwweagekggnaNaltddatdplsgtpefksva 111
                                       ++ ++       +N+++++++d+ ++tp++k+++
  gi|518651910|ref|YP_008141430.1| 619 MHNPK-------INDIVSPEFDDETKTPKYKYTP 645
                                       *****.......*******************985 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.7   1.3e-17   7.8e-14       5      52 ..       2      49 ..       1      52 [. 0.95

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1.3e-17
                                      EEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHC CS
                    Molybdop_Fe4S4  5 ktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtller 52
                                      k++Cp+CgvgCgle+  +++ +v v++ p+h v++g+lC KG  ++e 
  gi|518651910|ref|YP_008141430.1|  2 KSICPFCGVGCGLELMAVNNIVVGVKPVPEHVVSRGHLCGKGSVAHEA 49
                                      8*****************************************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); 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: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.39
# Mc/sec: 4968.57
//
Query:       gi|518651911|ref|YP_008141431.1|  [L=43]
Description: hypothetical protein FACI_IFERC00001G0550 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.08   12.9   0.5       0.12   12.3   0.5    1.3  1  DUF3724   Protein of unknown function (DUF3724)


Domain annotation for each model (and alignments):
>> DUF3724  Protein of unknown function (DUF3724)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.5   6.7e-06      0.12       1      14 [.       6      19 ..       6      20 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.7e-06
                           DUF3724  1 RaeGdvVeDYsrYt 14
                                      R +G vV+ Ys Yt
  gi|518651911|ref|YP_008141431.1|  6 RVNGNVVQKYSGYT 19
                                      669**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       218  (0.0121591); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); 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: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 350.93
//
Query:       gi|518651912|ref|YP_008141432.1|  [L=210]
Description: hypothetical protein FACI_IFERC00001G0551 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  185.0   0.9    1.1e-54  184.8   0.9    1.0  1  Proteasome     Proteasome subunit
  ------ inclusion threshold ------
       0.13   12.0   0.1       0.24   11.1   0.1    1.4  1  Myb_CC_LHEQLE  MYB-CC type transfactor, LHEQLE motif


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 !  184.8   0.9   1.3e-58   1.1e-54       2     190 .]       5     185 ..       4     185 .. 0.97

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 1.3e-58
                                       HHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSG CS
                        Proteasome   2 kkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygrp 78 
                                       k+Gtt++Gi++ d+v++++d+rat+g+ + s+++++K++kid + g+++aGl++Da++lvr++rae++lyr++ + +
  gi|518651912|ref|YP_008141432.1|   5 KTGTTTLGITAGDYVIMGTDSRATMGNFI-SNKNAQKLYKIDTYAGMTIAGLVGDAQVLVRYMRAEMELYRVQRKIN 80 
                                       89***************************.66669****************************************** PP

                                       TCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHHS CS
                        Proteasome  79 ipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekeyk 155
                                       +p+e    ++a++l++++ +s+  p++v+ll++g+d  ++p++++id +G ++e++ ++++Gsgs +++++le+ey+
  gi|518651912|ref|YP_008141432.1|  81 MPIE----AAATLLSNMLNQSKYYPYMVQLLVGGFD--KKPHIFSIDAAGGSVEDE-YASTGSGSPFVYGVLEAEYQ 150
                                       ****....999999999999999*************..56***************6.******************** PP

                                       TTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
                        Proteasome 156 edltleeavelavkalkealerdklsgknievavi 190
                                       ++++l++a+ la+ka++ a +rd++sg+ ++++vi
  gi|518651912|ref|YP_008141432.1| 151 PNMKLDDAINLAIKAISVAKQRDSASGNMLQIGVI 185
                                       ********************************997 PP

>> Myb_CC_LHEQLE  MYB-CC type transfactor, LHEQLE motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.7e-05      0.24      23      45 ..      75      97 ..      70      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.7e-05
                     Myb_CC_LHEQLE 23 vQrhLqlRiEaqgkyLqkiLeka 45
                                      vQr++ + iEa ++ L ++L + 
  gi|518651912|ref|YP_008141432.1| 75 VQRKINMPIEAAATLLSNMLNQS 97
                                      9*******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1463.71
//
Query:       gi|518651913|ref|YP_008141433.1|  [L=637]
Description: hypothetical protein FACI_IFERC00001G0552 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-23   82.4   2.5    7.2e-22   77.1   0.1    3.1  3  KH_7           KH domain
    2.7e-22   79.1   0.0    5.4e-22   78.2   0.0    1.5  1  Beta-Casp      Beta-Casp domain
    1.5e-14   53.7   0.0    4.8e-14   52.0   0.0    1.9  1  RMMBL          Zn-dependent metallo-hydrolase RNA specificity
      7e-14   51.7   0.0    1.2e-13   51.0   0.0    1.3  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain
    2.8e-10   40.5   0.3    7.3e-10   39.2   0.3    1.7  1  Lactamase_B    Metallo-beta-lactamase superfamily
    1.1e-05   25.1   0.0    2.2e-05   24.1   0.0    1.5  1  Lactamase_B_2  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.024   14.5   0.0      0.054   13.4   0.0    1.5  1  Lactamase_B_3  Beta-lactamase superfamily domain
       0.17   11.2   0.1          1    8.7   0.0    2.1  2  DUF2092        Predicted periplasmic protein (DUF2092)


Domain annotation for each model (and alignments):
>> KH_7  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.1   3.2e-25   7.2e-22       2      68 .]       5      70 ..       4      70 .. 0.95
   2 ?    3.9   0.1     0.023        51       5      27 ..      74      96 ..      71     123 .. 0.75
   3 ?   -2.6   0.0       2.5   5.7e+03      51      64 ..     463     476 ..     452     479 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 3.2e-25
                              KH_7  2 evleelkekieeklPkevkitdveFEGPelViYtknpklfaengdlirklAkelrkRiviRpDpsvl 68
                                      ++l+e ++ +++ +P++ kit++++EG+++V+Ytk+++lf++++dl r++A+elr+Ri+iRpDps++
  gi|518651913|ref|YP_008141433.1|  5 DYLSEGRSIFDRLYPDN-KITEIDYEGSTIVVYTKDQNLFSQRDDLARQIAQELRRRIAIRPDPSIM 70
                                      67889999999****99.**********************************************985 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                              KH_7  5 eelkekieeklPkevkitdveFE 27
                                      +e  +ki   +P+++ ++d+ FE
  gi|518651913|ref|YP_008141433.1| 74 KEADAKIRGIIPSDAGLQDIYFE 96
                                      78899*****************9 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                              KH_7  51 lAkelrkRiviRpD 64 
                                       l ++lr +i+i+ +
  gi|518651913|ref|YP_008141433.1| 463 LNRDLRDQIMIKRE 476
                                       77899999999865 PP

>> Beta-Casp  Beta-Casp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.0   2.4e-25   5.4e-22       2     110 .]     422     547 ..     421     547 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.4e-25
                                       HHHHHHH..HCTT...TTS-S.-EEEEE-HHHHHHHHHGGGGGG.........................E-SHH... CS
                         Beta-Casp   2 qellylLeelwkekk.ledlk.lpiyldsplaskatevYkeyae.........................veakslew 51 
                                       qe++++Le++ ++k+ +   + +++yld+ ++ +at+++ +y+e                         ve+++   
  gi|518651913|ref|YP_008141433.1| 422 QEVMLVLEDAYRNKMiP---EnTKVYLDG-MIMEATAIHAAYPEflnrdlrdqimikrenpflspiftsVETRK--- 491
                                       9************8855...337******.************99888877777777777777766643333222... PP

                                       .HHHH...HHHS-SSEEEEES-TTSSSSHHHHHHHHHTTSTTSEEEESS---TTSHHHHH CS
                         Beta-Casp  52 meskke.elnsskgpkvilassgmlegGrsrellkklledprntvilvgyqaegTlgrkl 110
                                           ++ ++ +s++ kvila+ gm++gG++ e++k l  d+rnt+ +vgyqa gTlgr++
  gi|518651913|ref|YP_008141433.1| 492 ----QRiDVCDSPESKVILATAGMMNGGPVLEYFKTLSADSRNTLAFVGYQADGTLGRRI 547
                                       ....22345588899*******************************************97 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.0   2.1e-17   4.8e-14       3      59 ..     566     625 ..     564     628 .. 0.95

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 2.1e-17
                             RMMBL   3 pvkarieeid.fSgHadknellelirklkprn..vilvHGeeeatsalarllkeeegidv 59 
                                       ++++ +e+ + fSgH+ k+ell++i +++pr+  + ++HG+ +++ ++arl+++++g+++
  gi|518651913|ref|YP_008141433.1| 566 DINMAVENAEgFSGHSTKRELLNFIGGMQPRPnrILVNHGDGNKCYDFARLIHTKFGVEA 625
                                       799******************************99999*******************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 !   51.0   0.0   5.3e-17   1.2e-13       1     149 [.     194     338 ..     194     358 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.3e-17
                     Lactamase_B_6   1 lLeldnvkiLlDvGwdeskvslesalkelek..vi........ptvdliLLshatlehlGayallyakfksklllni 67 
                                       l++ +n k+L+D+G+ + ++  e   +++e+  ++         ++d+++L+ha l+h G ++ll++     ++ + 
  gi|518651913|ref|YP_008141433.1| 194 LISTNNSKVLVDCGMININDP-E---HPWEEapYLyapeiqpfTSLDAVVLTHAHLDHSGLLPLLFK-----YGYTG 261
                                       5778999*******9876543.2...22332112234444555799**************7776654.....67899 PP

                     Lactamase_B_6  68 pvyatlpvvkLGrvslldlyaskgllgpedseeleledideafdkiktlkYsQklelkskldgltitaynaGhtlGG 144
                                       pvy+t p+  L+ ++  d+ + + ++++++  + e + ++e  ++ ++lkY+ + +++    ++ +t ynaGh lG 
  gi|518651913|ref|YP_008141433.1| 262 PVYSTAPTRDLAALLQNDYLKVS-HSENHKL-SYESKHVREELKHTISLKYNETADITP---DIRLTFYNAGHILGS 333
                                       ************98777766655.4444444.47889******************9995...8*************9 PP

                     Lactamase_B_6 145 tiWki 149
                                       +  ++
  gi|518651913|ref|YP_008141433.1| 334 AAVHL 338
                                       97665 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.3   3.3e-13   7.3e-10       3     159 ..     187     361 ..     185     397 .. 0.83

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
                                       CCSSEEEEEEETTCEEEES--SCHHHHHHHH.....HHHHHTSGGG.GEEEEE-SBSSHHHHTTGGGCTTHHCCEET CS
                       Lactamase_B   3 pdpvnsyliegdggviLiDtGtsteaaraal.....elaalglkpk.dvdavilTHlHlDHiGglgglveatdvpvg 73 
                                       +++ +++li ++++ +L+D+G+ + ++ +        l+a +++p   +dav+lTH+HlDH G l+ l +     ++
  gi|518651913|ref|YP_008141433.1| 187 EVGRSATLISTNNSKVLVDCGMININDPEHPweeapYLYAPEIQPFtSLDAVVLTHAHLDHSGLLPLLFKYGYTGPV 263
                                       567899****************99999987799999555555555527***************************** PP

                                       CCEHHHHCCHCHHHHHHHHHCCHH............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEE CS
                       Lactamase_B  74 avaeeapalfmeeaddaasrkgll............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvv 138
                                       +  + ++ l     +d+     ++             +  + ++    e  + + +    ++ + ++ g+ ++h+++
  gi|518651913|ref|YP_008141433.1| 264 YSTAPTRDLAALLQNDYLKVSHSEnhklsyeskhvrEELKHTISLKYNETADITPDIRLTFYNAGHILGSAAVHLHI 340
                                       ****************99999999*******9997655555555555555555556666666677888999999999 PP

                                       EETTCCEEEECTTTSSHHCCC CS
                       Lactamase_B 139 eygggkvlftGDallagetgr 159
                                       + g  +v+++GD  ++  ++ 
  gi|518651913|ref|YP_008141433.1| 341 GEGLYNVVLSGDQKYEKTWLF 361
                                       99**********888665555 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 !   24.1   0.0   9.7e-09   2.2e-05      16     169 ..     221     383 ..     200     402 .. 0.57

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 9.7e-09
                                       TCGG.S--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHH.............HCCTTCGHHH CS
                     Lactamase_B_2  16 lral.qPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvla.............vleanfvyla 78 
                                       +++l  P    + + ++daV+lthaH DH  gll l   ++   p+y ++ +++             +         
  gi|518651913|ref|YP_008141433.1| 221 APYLyAPE--IQPFTSLDAVVLTHAHLDHS-GLLPLLFKYGYTGPVYSTAPTRDlaallqndylkvsH--------- 285
                                       44443443..455679**************.7777776455457999776666544433333332221......... PP

                                       CHTT..............TTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEES CS
                     Lactamase_B_2  79 leee..............pavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyig 141
                                                            ++  l+ +e+ +++ +++++t+  a h  g         ++ l i++g  +v+ +g
  gi|518651913|ref|YP_008141433.1| 286 ---SenhklsyeskhvreELKHTISLKYNETADIT-PDIRLTFYNAGHILGS-------AAVHLHIGEGLYNVVLSG 351
                                       ...12333333322222222233344455555555.4677777777776666.......677777777777777777 PP

                                       S-S---HHHH....HHHCT-SEEEEE-S-SST CS
                     Lactamase_B_2 142 Dtgyipeeig....erlggadllllditayed 169
                                       D +y + ++     +r+  ++ l+l+ t+   
  gi|518651913|ref|YP_008141433.1| 352 DQKYEKTWLFnpavNRFPRVETLMLESTYAGR 383
                                       77766633222222566667777777666555 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.4e-05     0.054       6      50 ..     189     248 ..     187     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.4e-05
                     Lactamase_B_3   6 ghnsflletagarilvDPf........kanlgyeppa...............eeaDlvlisqaledHa 50 
                                       g ++ l++t++ ++lvD +        +        +                + D+v++++a+ dH 
  gi|518651913|ref|YP_008141433.1| 189 GRSATLISTNNSKVLVDCGminindpeH--------PweeapylyapeiqpfTSLDAVVLTHAHLDHS 248
                                       78999************99444443330........2456667777778888***************7 PP

>> DUF2092  Predicted periplasmic protein (DUF2092)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0   0.00045         1      59     102 ..      20      61 ..      15      68 .. 0.82
   2 ?   -0.9   0.0      0.38   8.6e+02      73     103 ..     379     409 ..     377     437 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00045
                           DUF2092  59 dekdrefyyDGktftlydkaenvYaqapapgtidelldklqeky 102
                                       d+k +e+ y G t+++y+k++n+++q +  +  ++++++l+ + 
  gi|518651913|ref|YP_008141433.1|  20 DNKITEIDYEGSTIVVYTKDQNLFSQRDDLA--RQIAQELRRRI 61 
                                       68889999******************98766..66666666665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.38
                           DUF2092  73 tlydkaenvYaqapapgtidelldklqekyg 103
                                       t+ + ++  Y++ +a +t+ ++++++ ++ g
  gi|518651913|ref|YP_008141433.1| 379 TYAGRDDYSYTRNEATNTLIDVVNRTFDRGG 409
                                       778888889**************99988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); 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:                         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: 00:00:00.44
# Mc/sec: 4396.01
//
Query:       gi|518651914|ref|YP_008141434.1|  [L=459]
Description: hypothetical protein FACI_IFERC00001G0553 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      7e-25   87.6  71.5      9e-25   87.2  71.5    1.1  1  AA_permease    Amino acid permease
    8.7e-22   77.5  74.1    1.5e-21   76.7  74.1    1.4  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2  71.5     1e-28     9e-25       2     470 ..      15     454 ..      14     457 .. 0.80

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 1e-28
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       v+++ ++g  ++g  v++    ++  ++++ l+ ++a++++++ ++++  i+ ++  +gg+y+y+++ +g  +G ++
  gi|518651914|ref|YP_008141434.1|  15 VIFQGVAGSAPAGAAVATLTGSAAFALGSLPLSAVVAFIIVLINAVIINRISRHVAGAGGYYAYSREGIGNFAGIFT 91 
                                       78999************************************************************************ PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt....gavflvvll...iinlvgvkvygeaefilali..k 146
                                       G++y +++i+ la+    ++i++  +  +  ++ +++     ++++++++    ++++ gv+ + +  +++a i  +
  gi|518651914|ref|YP_008141434.1|  92 GWMYIMYQIMSLAFIGLSVAIFLPAL--LGTVFGIDIPfyswVLLLILIMGfgyFVSFSGVRNSVRYAMVMATIevV 166
                                       **********9998777666666655..5555555554444466666666511157777777777666664444113 PP

                       AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                       ++a+++ ii++      +kp+   +++ ++        + ++g        f++++ +  +++ af+G++  + +++
  gi|518651914|ref|YP_008141434.1| 167 VVAAVSIIIIT------AKPSIN-TVSVFTPV------YAVHG--------FTGVMLGVLFMYTAFSGFGTATPLGE 222
                                       34444444444......444444.22222222......34777........************************** PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaa 300
                                       E+k+    i +++l   i +++f++l++++ +++++ +     +  ++  ++++++ +++g++++ ++ ++++ + +
  gi|518651914|ref|YP_008141434.1| 223 EAKNANAVIGRGVLISAIVLGLFFTLVSYAFTVGWGPTRMLTYSTELV--PGIILAKNYLGLAGAIVITVLFVNS-L 296
                                       ***********************************9999777776665..5***********9998887777765.5 PP

                       AA_permease 301 lssansslysasRvlyslakdglaPkvl.kkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisalig 376
                                       +  ++ ++ s sRv++s+++d+++P +l +++s r+ P++a  ++ iis+++ +++ ++l+ +++f f+  +++l++
  gi|518651914|ref|YP_008141434.1| 297 FTDSVVFTNSLSRVVFSMSRDNVLPGILsSVHSHRQTPHVAAGVMVIISFIIGVISVITLGGFNAFLFAGIAATLSA 373
                                       555666999****************66615778999***************************************** PP

                       AA_permease 377 livwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaay 453
                                       l+v++++++s++++  ++k++        + + ++   v +v++a++++  + ++  +++       + ++sf+ + 
  gi|518651914|ref|YP_008141434.1| 374 LLVHMIANASLAGILHKMKLKMN------IAMDVVLPAVSIVILAFVFYGSFISIDNVVI-------IASVSFIVWA 437
                                       ************77666554443......4566666666666666666666666666666.......8888888888 PP

                       AA_permease 454 livllfliilvgvklhv 470
                                       +  l++ +i   + +hv
  gi|518651914|ref|YP_008141434.1| 438 IAGLIYSAISRKYLMHV 454
                                       88888888777776665 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.7  74.1   1.7e-25   1.5e-21      10     418 ..      21     436 ..      10     451 .. 0.75

  Alignments for each domain:
  == domain 1  score: 76.7 bits;  conditional E-value: 1.7e-25
                     AA_permease_2  10 vigsvigsgifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnw 85 
                                       + ++++g+++   + +aa +  +l l+ ++a +i+ l+ + ++  +s +    gG y y+++++g++++ +++w++ 
  gi|518651914|ref|YP_008141434.1|  21 AGSAPAGAAVATLTgSAAFALGSLPLSAVVAFIIV-LINAVIINRISRHVAGAGGYYAYSREGIGNFAGIFTGWMYI 96 
                                       33344444443332344446666999999999998.8999999999*99***************************7 PP

                     AA_permease_2  86 fayvpvlasilsv...aasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                       + ++ +la+i  +   ++ +ll+ +++ d+    + ++l+ i+i+ +  +++  g++ s +++++++++ ++++   
  gi|518651914|ref|YP_008141434.1|  97 MYQIMSLAFIGLSvaiFLPALLGTVFGiDIP--FYSWVLLLILIMGFGYFVSFSGVRNSVRYAMVMATIEVVVV--A 169
                                       7777777776544012555555554433443..34667777******************************644..4 PP

                     AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlvl 233
                                       ++ + +it+++++++ +   t     +g +gv+lg l +  +f+Gf +a+   ee+k+  + + ++  i++++ +++
  gi|518651914|ref|YP_008141434.1| 170 AVSIIIITAKPSINTVS-VFTPVYAVHGFTGVMLGVLFMYTAFSGFGTATPLGEEAKNanAVIGRGVLISAIVLGLF 245
                                       45567777777777743.233345556999*************************9997568*************** PP

                     AA_permease_2 234 yllvniaflgvvpddei.anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP 309
                                       ++lv+ af+ + ++  + + + +l+ ++ ++++++ g ++ai++ +l++ sl+     ++ + srv+++++rd+vlP
  gi|518651914|ref|YP_008141434.1| 246 FTLVSYAFTVGWGPTRMlTYSTELV-PGIILAKNYLGLAGAIVITVLFVNSLFTDSVVFTNSLSRVVFSMSRDNVLP 321
                                       ****999999999988745566665.8*********99*************************************** PP

                     AA_permease_2 310 rffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisylll..iigalilrkkrphlkr 381
                                         +++v+ ++++p +a  + +i+s+i+++++ ++    +a+ f   +++l+++++ +++  +++++++++k +    
  gi|518651914|ref|YP_008141434.1| 322 GILSSVHsHRQTPHVAAGVMVIISFIIGVISVITLggFNAFLFAGIAATLSALLVHMIAnaSLAGILHKMKLKMNIA 398
                                       ************************99998887532443444455555555555555555335666666666666555 PP

                     AA_permease_2 382 pgkilvaiigalfllfllvalffppkgpa..tqssliyt 418
                                       +  +++ ++++++l f+++  f+  ++ +  ++ s+i++
  gi|518651914|ref|YP_008141434.1| 399 MD-VVLPAVSIVILAFVFYGSFISIDNVViiASVSFIVW 436
                                       54.445555667777777666666555552244444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.50
# Mc/sec: 2750.68
//
Query:       gi|518651915|ref|YP_008141435.1|  [L=223]
Description: hypothetical protein FACI_IFERC00001G0554 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-61  207.1   1.5    7.6e-61  206.0   1.5    1.5  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase
  ------ inclusion threshold ------
      0.036   13.1   0.1      0.075   12.0   0.1    1.3  1  FMN_dh    FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.0   1.5   8.5e-65   7.6e-61       1     243 [.       3     206 ..       3     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 206.0 bits;  conditional E-value: 8.5e-65
                                       EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S CS
                           TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadg 77 
                                       +++Dta++e+ik++ e + i+gvTtNPsli ka k+ + +++   ei +e                      +  +g
  gi|518651915|ref|YP_008141435.1|   3 IFIDTANIEEIKEANEFGLIDGVTTNPSLIMKASKGGKSFKAIATEILRE----------------------V--NG 55 
                                       79*********************************998999999999988......................5..** PP

                                       -EEEE-S-...-SHHHHHHHHHHHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-S CS
                           TAL_FSA  78 rvslEVdarlsddteatieeArrlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagas 154
                                       +vslEV+a   +++e+++e+A +l+al    n +IKiP+t +G+kA+k Lk++ i+vn TliF++ qal+aa+ ga+
  gi|518651915|ref|YP_008141435.1|  56 PVSLEVVA---EKAEDMVEQALKLHALGS--NAVIKIPMTLQGLKAMKILKEKEIKVNTTLIFNAIQALLAAKNGAA 127
                                       ********...*****************9..********************************************** PP

                                       EEEEBHHHHHTTT............S-HHHHHHHHHHHHHHHT-S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHH CS
                           TAL_FSA 155 viSpFvgRiddllkkleekdklkgkddgvalvkeiynyykklgysTkvmaasfrnveeve..elagcdtvTippkll 229
                                       ++SpFvgR+dd++            +dg+a + +i + y ++gy+T+v+ as+rn+ +v+  +l+g+d+vTip +++
  gi|518651915|ref|YP_008141435.1| 128 FVSPFVGRLDDIG------------EDGMAIIDQIKTEYTNYGYKTEVLVASIRNPVHVLraALMGADAVTIPYDVI 192
                                       *************............7*************************************************** PP

                                       HHHT--HHH..... CS
                           TAL_FSA 230 ealakhgktsekle 243
                                       ++la h+kt+e l+
  gi|518651915|ref|YP_008141435.1| 193 KKLAMHPKTDEGLN 206
                                       *********54443 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   8.4e-06     0.075     230     309 ..     118     197 ..     111     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.4e-06
                                       HHHHHHTTESEEEE--GGGTSSTT---HHHCHHHHHHHH.....SS-EEEESS--SHHHHHHHHHTT-SEEEESHHH CS
                            FMN_dh 230 akraveaGvdgivvSNHGGRqldgapatidvLpeiveavgg...rievlvDgGirrGsDvlkAlalGAdavllGRpf 303
                                       a +a++ G+    vS   GR  d     + ++ +i  +  +   ++evlv + ir+ ++vl+A  +GAdav +   +
  gi|518651915|ref|YP_008141435.1| 118 ALLAAKNGAA--FVSPFVGRLDDIGEDGMAIIDQIKTEYTNygyKTEVLVAS-IRNPVHVLRAALMGADAVTIPYDV 191
                                       5666666654..578888888888888889999997777655669*****75.******************997666 PP

                                       HHHHHH CS
                            FMN_dh 304 lyglaa 309
                                       +  la+
  gi|518651915|ref|YP_008141435.1| 192 IKKLAM 197
                                       665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1471.46
//
Query:       gi|518651916|ref|YP_008141436.1|  [L=317]
Description: hypothetical protein FACI_IFERC00001G0555 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.8e-36  123.4   0.0    1.1e-35  122.9   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.8e-32  111.8   0.0    3.5e-32  110.9   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    6.4e-05   23.2   0.2      0.003   17.8   0.1    2.5  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.9   0.0   1.9e-39   1.1e-35       5     175 ..      10     171 ..       7     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 122.9 bits;  conditional E-value: 1.9e-39
                                       HHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEE CS
                      Transket_pyr   5 wrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqF 81 
                                        r+a+++ la+l+++++++v+++aD++ +t +  +g+++++   r++++gisEq ++ +a+G++lag  ++++  +F
  gi|518651916|ref|YP_008141436.1|  10 LRDAYGKELASLGEKNKDIVVLDADLSSSTKTGVFGKKFPE---RFFNMGISEQSMVSAAAGLSLAG--KTVFASTF 81 
                                       799**************************************...***********************..9******* PP

                                       HHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHH CS
                      Transket_pyr  82 gdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrra 157
                                       ++F++     +++ ir+     +++v+ vvt+ +i++gedGp+hq +e++ ++  +p++kv++P d  et  ++   
  gi|518651916|ref|YP_008141436.1|  82 AVFLS----NTYNVIRQSICYNEAPVNfVVTHSGISLGEDGPTHQILEDVGIMSGLPNMKVIVPVDSIETVSVIDYL 154
                                       *****....99999999999*******************************************************99 PP

                                       HHSSS.SEEEEEE-SSEE CS
                      Transket_pyr 158 irredrkPvvlrlpksll 175
                                       ++r+   P ++rl++++ 
  gi|518651916|ref|YP_008141436.1| 155 AARK-TSPYYVRLTREKF 171
                                       9987.59*******9876 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.0   5.8e-36   3.5e-32       1     124 []     184     304 ..     184     304 .. 0.97

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 5.8e-36
                                       TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHH CS
                   Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGig 77 
                                       gk ++ r+g+dvt+ +yG mv++al+Aae+L+++gi+a+V+++ ++kplD+  i +++++tg++v+ ee+++  G+g
  gi|518651916|ref|YP_008141436.1| 184 GKSVTFRDGSDVTIMGYGIMVSFALKAAEQLKNRGIDARVINMSSIKPLDRPAIIKAARETGKIVTAEEHSIYNGLG 260
                                       6777789********************************************************************** PP

                                       HHHHHHHHHCCCTTCSSEEEEEEE-SS.SSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  78 sevaaalaeeafdgldapvkrvggpdv.iepgsaeelekafgldaeki 124
                                       s va++ +e    + ++pv r+g+pd+ +++g+  el ++f + +++i
  gi|518651916|ref|YP_008141436.1| 261 SRVAEVTSE----EYPVPVMRIGMPDIfGKSGKGMELFDYFHIGVNDI 304
                                       *********....99******************99******9998876 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.023   1.4e+02      43      74 ..      16      48 ..       6      77 .. 0.76
   2 !   17.8   0.1     5e-07     0.003       2      77 ..     194     269 ..     193     282 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.023
                                      HHHHHHSTT-SEEEEEE-S--TT-G.-HHHHHH CS
                           PFOR_II 43 eelkellkkvkkvvvldrnisfgse.Gqlveev 74
                                      +el++l +k k +vvld + s +++ G+ ++  
  gi|518651916|ref|YP_008141436.1| 16 KELASLGEKNKDIVVLDADLSSSTKtGVFGKKF 48
                                      68889999************9888888877665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 5e-07
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       +v i+++G++++ a +a+++l+++gi++ ++ + ++ P  + ++ ++++++ k+v+ +    +   G  v ev + 
  gi|518651916|ref|YP_008141436.1| 194 DVTIMGYGIMVSFALKAAEQLKNRGIDARVINMSSIKPLDRPAIIKAARETGKIVTAEEHSIYNGLGSRVAEVTSE 269
                                       899******************************************************9998777778888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2104.94
//
Query:       gi|518651917|ref|YP_008141437.1|  [L=275]
Description: hypothetical protein FACI_IFERC00001G0556 [Ferroplasma acidarmanus fer1]
Scores for 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-52  176.9   0.0    7.4e-52  176.4   0.0    1.2  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    1.9e-10   40.5   0.2    0.00027   20.2   0.2    3.1  3  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    8.6e-06   25.6   0.1    0.00024   20.9   0.1    2.2  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
     0.0012   17.9   0.0     0.0017   17.3   0.0    1.3  1  E1_dh            Dehydrogenase E1 component
     0.0055   15.5   0.1      0.012   14.4   0.1    1.7  2  XFP_N            XFP N-terminal domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.4   0.0   2.1e-55   7.4e-52       6     274 ..      13     271 ..       9     275 .] 0.92

  Alignments for each domain:
  == domain 1  score: 176.4 bits;  conditional E-value: 2.1e-55
                                       HHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTSS--H CS
                   Transketolase_N   6 vnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGydlsl 82 
                                       +  iR   + +v +aksGhPG +l++ad+ ++l+ k ++ +P++p+  dRD  ++s Ghas   Y+ l L Gy +++
  gi|518651917|ref|YP_008141437.1|  13 AREIRKEIIKMVYSAKSGHPGGSLSIADVITALYFKEMNIDPEKPDKPDRDILIMSKGHASPAEYAALALRGY-FPV 88 
                                       66788888999**************************************************************.789 PP

                                       HHHTTTTSTT-SS-SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSH CS
                   Transketolase_N  83 edlksfrqlgsktpGhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeG 159
                                       e l+ fr+++sk  Gh   +  +gve  tG LGqG+  a+g+al  k              ++++y+ilgDg ++eG
  gi|518651917|ref|YP_008141437.1|  89 ELLEGFRKVNSKLEGHVH-RGIPGVESSTGSLGQGLGVAIGFALSSKLD----------SKTNKIYAILGDGEMEEG 154
                                       99**************99.889*********************988743..........34568************* PP

                                       HHHHHHHHHHHTT-TTEEEEEEESSEETTEEGGGT-.-S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS CS
                   Transketolase_N 160 vsseasslagtlkLgkLivlyDdnkisidGeteisf.tedvakrfeaygWhvievedgedveaikaaieeakaekdk 235
                                          e+   a++ +Lg+L ++ D n i +dG te  +   +va++ + +gW+vi+  +g+++ ++ +a+e+ak+ +d+
  gi|518651917|ref|YP_008141437.1| 155 NIWESLMAASKYHLGNLTAILDRNMIQLDGFTEDIMpLGNVAEKVAPFGWEVIT-INGNNMDEVVNALEYAKKPRDR 230
                                       ******************************9986652789*************9.8899****************** PP

                                       -EEEEEE--TTTTSTTTTTSGGGTSS---HHH..HHHHHHH CS
                   Transketolase_N 236 PsliklrtviGygspakagtedvhGapLgede..vaalkkk 274
                                       P +i  +t+ G g    +++ + hG+p  ++e  v+alk+ 
  gi|518651917|ref|YP_008141437.1| 231 PLFIVANTIKGKGVSYMENNPKYHGSPPANEEeyVQALKEI 271
                                       **************************976554347777765 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   1.1e-05     0.039      14      54 ..       5      46 ..       1      54 [. 0.90
   2 !   20.2   0.2   7.6e-08   0.00027     114     172 ..     120     179 ..     109     200 .. 0.84
   3 !    3.8   0.0     0.008        29     244     269 ..     208     234 ..     194     238 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                    DXP_synthase_N 14 skeeleelaeelrefliesv.sktggHlasnLgvveLtlalh 54
                                      + ++l++ a+e+r+++i++v s+++gH + +L++ ++  al+
  gi|518651917|ref|YP_008141437.1|  5 TINDLNATAREIRKEIIKMVySAKSGHPGGSLSIADVITALY 46
                                      568999************997899*************99997 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 7.6e-08
                    DXP_synthase_N 114 stsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelk.kkllvilNdNe 172
                                       +  + +a G+a +++l+++++k+ a++GDg +  G  +e+l  +++ +  +l  il  N 
  gi|518651917|ref|YP_008141437.1| 120 GQGLGVAIGFALSSKLDSKTNKIYAILGDGEMEEGNIWESLMAASKYHlGNLTAILDRNM 179
                                       4567889999999*****************************998876257888887775 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.008
                    DXP_synthase_N 244 pidGhdleelikvleevkkl.kgpvll 269
                                        i+G++++e++++le +kk  ++p ++
  gi|518651917|ref|YP_008141437.1| 208 TINGNNMDEVVNALEYAKKPrDRPLFI 234
                                       59***************9962455554 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   6.7e-08   0.00024      25      84 ..     114     180 ..     103     236 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.7e-08
                                       TTTS-TTTHHHHHHHHHH...H.STTSEEEEEEEHHHHHHT..GGGHHHHHHTT-.SEEEEEEE-SB CS
                      TPP_enzyme_C  25 gglgtmGyglpaAiGakl...a.kpdrevvaivGDGgflmi..lqelatavrrnl.pitvvvlnNeg 84 
                                       + +g++G gl++AiG +l   +  + ++++ai GDG +      + l+ a +++l ++t ++  N +
  gi|518651917|ref|YP_008141437.1| 114 SSTGSLGQGLGVAIGFALsskLdSKTNKIYAILGDGEMEEGniWESLMAASKYHLgNLTAILDRNMI 180
                                       56899*************765323457**********754333899999999999777777776655 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.8e-07    0.0017      94     212 ..     110     229 ..      80     265 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.8e-07
                                       ..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--E.EEEEEEESEETTEEH CS
                             E1_dh  94 srilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpv.ifvveNNkygisTea 169
                                         +    g +g    ++ G al +k + k++   ++ GDg   +G+++e+l  a+ ++l     +   N++ +   +
  gi|518651917|ref|YP_008141437.1| 110 PGVESSTGSLGQGLGVAIGFALSSKLDSKTNKIYAILGDGEMEEGNIWESLMAASKYHLGNlTAILDRNMIQLDGFT 186
                                       455556666666666677*********************************99999999874677789****99999 PP

                                       HHH-S---GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHH CS
                             E1_dh 170 ekasaskeladrargvgipglrVdgnDplavyeAvkfAaerar 212
                                       e      ++a++ + +g   ++++gn + +v +A   A++ ++
  gi|518651917|ref|YP_008141437.1| 187 EDIMPLGNVAEKVAPFGWEVITINGNNMDEVVNALEYAKKPRD 229
                                       99999999999999********************999998665 PP

>> XFP_N  XFP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.43   1.5e+03      64      87 ..      13      36 ..       9      51 .. 0.75
   2 !   14.4   0.1   3.3e-06     0.012     124     202 ..     101     180 ..      60     224 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.43
                             XFP_N 64 nriikkydqnmlyvvGPGhGgpal 87
                                       r i+k   +m+y +  Gh g +l
  gi|518651917|ref|YP_008141437.1| 13 AREIRKEIIKMVYSAKSGHPGGSL 36
                                      5889999999***99999966544 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 3.3e-06
                             XFP_N 124 ipshvaaetPGsiheGGelGyalshayGav....ldnPdlivacvvGdGeaetGPlatswhsnkflnPaedGavlPi 196
                                       +  hv   +PG     G lG  l +a+G +    ld     + +++GdGe e G +  s          + G +  i
  gi|518651917|ref|YP_008141437.1| 101 LEGHVHRGIPGVESSTGSLGQGLGVAIGFAlsskLDSKTNKIYAILGDGEMEEGNIWES---LMAASKYHLGNLTAI 174
                                       5679999999999999999999988888652222788889999***********88544...444444555555555 PP

                             XFP_N 197 lelnGy 202
                                       l+ n  
  gi|518651917|ref|YP_008141437.1| 175 LDRNMI 180
                                       555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1943.01
//
Query:       gi|518651918|ref|YP_008141438.1|  [L=170]
Description: ferripyochelin binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.3e-14   51.6  20.5    8.5e-05   22.1   1.8    4.3  4  Hexapep     Bacterial transferase hexapeptide (six repeats)
    2.6e-05   23.9  21.7    0.00041   20.0   4.1    4.6  5  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.038   14.3   8.9        1.1    9.6   2.7    2.8  3  Bactofilin  Polymer-forming cytoskeletal
       0.13   11.2   0.1       0.24   10.3   0.1    1.5  1  Fucokinase  L-fucokinase
        0.3    9.2   3.9       0.35    8.9   3.9    1.1  1  DUF4954     Domain of unknown function (DUF4954)


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   1.8   2.4e-08   8.5e-05       3      35 ..       3      35 ..       1      36 [. 0.92
   2 !   12.1   0.1   3.4e-05      0.12      18      34 ..      39      55 ..      38      56 .. 0.89
   3 !   18.7   5.6   2.9e-07     0.001       2      34 ..      63      94 ..      62      96 .. 0.94
   4 !   16.7   0.7   1.3e-06    0.0045       2      34 ..      80     112 ..      79     114 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.4e-08
                                      EEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep  3 vIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35
                                      ++G++ ++   avi gnV++Gdnv+I   +vi+
  gi|518651918|ref|YP_008141438.1|  3 KVGKGLYVADTAVIIGNVTVGDNVTIMDSAVIR 35
                                      7899999999******************99997 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3.4e-05
                                      TTEEE-TTEEEETTEEE CS
                           Hexapep 18 gnVkIGdnvkIgagvvi 34
                                      + +kIGdn+ I  +++i
  gi|518651918|ref|YP_008141438.1| 39 NSIKIGDNSNIQDNATI 55
                                      789************99 PP

  == domain 3  score: 18.7 bits;  conditional E-value: 2.9e-07
                                      EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep  2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                                      tvIG+nv +g++a++ +++++ d+v +g g+ +
  gi|518651918|ref|YP_008141438.1| 63 TVIGKNVSVGHNAIV-HGAIVDDDVLVGMGAIV 94
                                      89*************.**************988 PP

  == domain 4  score: 16.7 bits;  conditional E-value: 1.3e-06
                                       EEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                                       +++ ++vl+g++a++++ +++ ++++++ag+vi
  gi|518651918|ref|YP_008141438.1|  80 AIVDDDVLVGMGAIVLNKAHLRPGTVVAAGTVI 112
                                       67789***************************9 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   1.9    0.0039        14      14      26 ..      14      28 ..      11      36 .. 0.83
   2 !    5.9   0.1    0.0029        10       2      16 ..      41      55 ..      40      59 .. 0.65
   3 !   20.0   4.1   1.2e-07   0.00041       2      32 ..      63      94 ..      62      96 .. 0.94
   4 ?    1.6   0.0     0.067   2.4e+02      24      32 ..     104     112 ..      99     114 .. 0.84
   5 ?   -2.5   0.1       1.3   4.7e+03      13      18 ..     121     127 ..     120     128 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0039
                                      -E.ES.EEE-TT-EE CS
                         Hexapep_2 14 ag.iG.vslGdncvv 26
                                      a+ iG v++Gdn+++
  gi|518651918|ref|YP_008141438.1| 14 AViIGnVTVGDNVTI 28
                                      5536889*****997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0029
                                      EEE-TT-EE-TT-EE CS
                         Hexapep_2  2 viIGdnCliGanagi 16
                                      ++IGdn++i  na+i
  gi|518651918|ref|YP_008141438.1| 41 IKIGDNSNIQDNATI 55
                                      577888777666655 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 1.2e-07
                                      EEE-TT-EE-TT-EE.SEEE-TT-EE-TT-EE CS
                         Hexapep_2  2 viIGdnCliGanagi.GvslGdncvvgaGvvi 32
                                      + IG+n+ +G na++ G ++ d++ vg+G ++
  gi|518651918|ref|YP_008141438.1| 63 TVIGKNVSVGHNAIVhGAIVDDDVLVGMGAIV 94
                                      68***************************887 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.067
                                       -EE-TT-EE CS
                         Hexapep_2  24 cvvgaGvvi 32 
                                        vv+aG vi
  gi|518651918|ref|YP_008141438.1| 104 TVVAAGTVI 112
                                       59*****99 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.3
                                       T-EE.SE CS
                         Hexapep_2  13 nagi.Gv 18 
                                       n+ i Gv
  gi|518651918|ref|YP_008141438.1| 121 NCMIaGV 127
                                       5555555 PP

>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.3   0.00081       2.9      32      79 ..       5      58 ..       1      65 [. 0.55
   2 ?    9.6   2.7   0.00031       1.1      34      97 ..      56     122 ..      38     126 .. 0.69
   3 ?    3.5   0.0     0.024        87       1      32 [.     104     134 ..     104     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00081
                        Bactofilin 32 kgklvvgeggkvegnika.eevvvaGtvk.....GnveaeekvelkktakveGd 79
                                      ++ l v++++++ gn+++ ++v++  +        ++++ ++ +++++a+++ d
  gi|518651918|ref|YP_008141438.1|  5 GKGLYVADTAVIIGNVTVgDNVTIMDSAViradqNSIKIGDNSNIQDNATIHVD 58
                                      455667777777777777566666654222333345555555555555555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00031
                        Bactofilin  34 klvvgeggkvegnika.eevvvaGt.vkGnveaeekvelkktakve.GdikaksleieegavfeGkl 97 
                                       ++ +  ++++  n+++ ++++v+G  v+++v +    ++ ++a+++ G++ a+  +i e+ + +G++
  gi|518651918|ref|YP_008141438.1|  56 HVDLDCETVIGKNVSVgHNAIVHGAiVDDDVLVGMGAIVLNKAHLRpGTVVAAGTVIPENFESDGNC 122
                                       3333445556666888566888888666788888888888888888888888888888888888887 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.024
                        Bactofilin   1 tligegtkikGelevegdlridGkveGdieak 32 
                                       t++++gt+i  ++e++g++ i+G v G+++ +
  gi|518651918|ref|YP_008141438.1| 104 TVVAAGTVIPENFESDGNCMIAG-VPGKVKRT 134
                                       68999******************.99999665 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   6.7e-05      0.24     273     359 ..      25     136 ..       3     155 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.7e-05
                        Fucokinase 273 savvinSvl....essvsvgegsvie.........hsslk..gnvsigsnsivsglelessee.........slelp 325
                                       ++++++S +    ++s+++g++s i+         ++++   +nvs+g n iv+g  ++ +           + +l+
  gi|518651918|ref|YP_008141438.1|  25 NVTIMDSAViradQNSIKIGDNSNIQdnatihvdlDCETVigKNVSVGHNAIVHGAIVDDDVLvgmgaivlnKAHLR 101
                                       55555554433334567777777777777777888555444499999999999999998765466666666666666 PP

                        Fucokinase 326 ddtilqtlslklskeke.yvtvvfGieDdlkssve 359
                                         t++    +  ++ ++   +++ G+  ++k++ e
  gi|518651918|ref|YP_008141438.1| 102 PGTVVAAGTVIPENFESdGNCMIAGVPGKVKRTGE 136
                                       66665554444433333366666666666666655 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   3.9   9.8e-05      0.35     175     243 ..      21      88 ..       7     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 9.8e-05
                           DUF4954 175 eigekvkilnaglikN....vkigdyatiegasklengtinSskeapveiGegViledfiissGskikdgavi 243
                                       ++g++v+i+++ +i+     +kigd ++i+     +n+ti+   ++ + iG++V +    i +G+ + d +++
  gi|518651918|ref|YP_008141438.1|  21 TVGDNVTIMDSAVIRAdqnsIKIGDNSNIQ-----DNATIHVDLDCETVIGKNVSVGHNAIVHGAIVDDDVLV 88 
                                       689999****99998411124555555554.....69999999999999999999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1319.02
//
Query:       gi|518651919|ref|YP_008141439.1|  [L=248]
Description: cobalamin synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-35  120.9   9.3    9.3e-35  120.7   9.3    1.0  1  CobS      Cobalamin-5-phosphate synthase


Domain annotation for each model (and alignments):
>> CobS  Cobalamin-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.7   9.3   5.2e-39   9.3e-35       1     203 [.      11     232 ..      11     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 5.2e-39
                              CobS   1 alsflTrlPvp...el.aralaffPlvGlllGlll.llallllllllllaallavaalvlltgglHlDGlaDtaDgl 72 
                                       a+sf+T++P+    ++ +  ++ff ++Gl++Gl++ +++l+l    +l+a++++va+++ll g++HlD ++D++D +
  gi|518651919|ref|YP_008141439.1|  11 AISFFTIIPLGgnyKItGYTMYFFTFTGLIVGLIAgIPYLVLRPYNSLIASTVSVAIIILLYGFNHLDSIMDFGDSI 87 
                                       79********864423344****************999999999888999999999999****************** PP

                              CobS  73 gsgrdrerrleImkDsrvGafGvlalvlvlllkvaalaala.......lllapvlsRlaallaiallpyaeeglgal 142
                                       + +  +e++ +++kD  +G++G+ +l+++ +  +a+l+ +        +++ +++s++a l+++++ +   eglg++
  gi|518651919|ref|YP_008141439.1|  88 MVR-GKEEKQRVIKDRYTGSGGIGMLFIIYIPAIAFLTYFKpvtgffiIIAGEMASKYATLFSMYRAKAFGEGLGKM 163
                                       775.7****************************9998555466777767788****************6689***** PP

                              CobS 143 faeaqkk....lvllal.......avlllll.alllaallvalllrrlarrklggvtGDvlGavieltellvl 203
                                       f++++++    l            +++ l+  a+++a++++ +++r +++++ gg++GD++G + e+++ll++
  gi|518651919|ref|YP_008141439.1| 164 FIDKVSAnaivL----NviplllaFAFNLYNiAIIAALIFLSYFMRSAMEKHYGGLNGDLAGSIGEISRLLFY 232
                                       **9777644320....12333332222222223556666677899999999*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 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:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1775.46
//
Query:       gi|518651920|ref|YP_008141440.1|  [L=127]
Description: hypothetical protein FACI_IFERC00001G0559 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1623  (0.0905237); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 904.28
//
Query:       gi|518651921|ref|YP_008141441.1|  [L=177]
Description: hypothetical protein FACI_IFERC00001G0560 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-56  190.3   0.2    1.8e-56  190.1   0.2    1.0  1  ArsR            ArsR transcriptional regulator
  ------ inclusion threshold ------
      0.019   15.0   0.0       0.04   14.0   0.0    1.5  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.1   0.2     2e-60   1.8e-56       1     157 [.      19     173 ..      19     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.1 bits;  conditional E-value: 2e-60
                              ArsR   1 indpveLvpllqvfdsetkkkvyeelskeWlteeeleeklgeeveealklLkkikliEsqWrmpepgekpekeYhts 77 
                                       ind++eLv++++++d+++k+k++ +ls++W+t+ +++e++g e++++l++L+ki++iEsqW +++  ++pek+Yht+
  gi|518651921|ref|YP_008141441.1|  19 INDVGELVTIFHAADTDVKRKLLLDLSTGWVTMPQIDERYGVEGKKSLHYLDKIRMIESQWITGN--KGPEKAYHTY 93 
                                       8****************************************************************..********** PP

                              ArsR  78 YskvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrklglsplfiralakrsekldvkGqr 154
                                       Y++vq+n++ s+ dlsdii +++++de+l++++eki++++ +g ++++d++++l++s+++++++++rs+ l++kG+r
  gi|518651921|ref|YP_008141441.1|  94 YTNVQINLIGSMADLSDIIFATTLNDEQLQSYEEKIIAMMANGGVFVGDVADSLKISQTLLKGIVNRSSVLTIKGYR 170
                                       ***************************************************************************** PP

                              ArsR 155 lel 157
                                       +e+
  gi|518651921|ref|YP_008141441.1| 171 IEM 173
                                       *98 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   4.5e-06      0.04       8      42 ..      38      72 ..      33      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.5e-06
                    Sulfolobus_pRN  8 ekillilsrrcatleeleektGiekeellvyltrl 42
                                       k+ll ls + +t+ +++e+ G+e ++ l yl ++
  gi|518651921|ref|YP_008141441.1| 38 RKLLLDLSTGWVTMPQIDERYGVEGKKSLHYLDKI 72
                                      689****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1224.03
//
Query:       gi|518651922|ref|YP_008141442.1|  [L=349]
Description: hypothetical protein FACI_IFERC00001G0561 [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  145.9   0.2      9e-43  145.0   0.2    1.5  1  Trm56     tRNA ribose 2'-O-methyltransferase, aTrm56
    2.3e-16   60.1   0.4    4.5e-16   59.2   0.4    1.5  1  HD        HD domain


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 !  145.0   0.2     1e-46     9e-43       1     118 [.      53     168 ..      53     169 .. 0.96

  Alignments for each domain:
  == domain 1  score: 145.0 bits;  conditional E-value: 1e-46
                                       H-S--EEE.E--HHHHHHC-S...SEEEEE-TTSEEHHHHHHHHHC-SE...EEEEE------TCHHHHSSEEEESS CS
                             Trm56   1 wGgefkvevakslkklikefkkeggivvhltmyGenieevieeikkkek..dllvvvGaekvprevyeladynvsvg 75 
                                       +Gg+f++++  ++kk  k+f+   g++v+l+myG+n+++ i+ i+++ k  d++++vGaekvp ++y++adyn++++
  gi|518651922|ref|YP_008141442.1|  53 FGGNFSIKTGINWKKEFKDFN---GVKVNLSMYGINVDDRIDAIRESAKgkDVIILVGAEKVPIDAYNIADYNIAIA 126
                                       8*************9999998...********************9976555************************** PP

                                       SS---HHHHHHHHHHHHC.--TTT---TT-SSEEE--SSS-EE CS
                             Trm56  76 nqPhsevaalaifldrllegkelekefedaklkviPsergkkv 118
                                       nqPhsev+alaifldr++egkelek++e +k++viP+++gk v
  gi|518651922|ref|YP_008141442.1| 127 NQPHSEVSALAIFLDRFYEGKELEKKYE-GKMNVIPMDNGKMV 168
                                       ***************************9.9***********98 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.2   0.4     5e-20   4.5e-16       2     119 ..     191     294 ..     190     297 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 5e-20
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHHHHHCTCCHHHHHHHHHHHHHHHHHHHHHH CS
                                HD   2 leHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekkeeefekflaHekvgaeilrevekrlgldl 78 
                                       +eH   V+kla  ++++ g  ++ el++++aLlHDiG  +++              +H++ ga ilre  +++    
  gi|518651922|ref|YP_008141442.1| 191 IEHVTTVYKLAMAIGKYAG--ANMELIRAGALLHDIGRTKTNG------------IGHAVAGADILREKNIDE---- 249
                                       79*****************..*******************986............79****************.... PP

                                       HHHHHHHHTTCCHHHHHHHHH.....HHHCCTSCHHHHHHHHHHHH CS
                                HD  79 edvaklirehheswegkkrpr.....glaerqlslearivklaDrl 119
                                        ++++++++h++    + + +      +++ q +le++iv+ aD+l
  gi|518651922|ref|YP_008141442.1| 250 -AIVRIVEKHTGAGILPDEAKklglpDRNYIQETLEEKIVAQADNL 294
                                       .**************988884566779*****************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.19s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2913.64
//
Query:       gi|518651923|ref|YP_008141443.1|  [L=210]
Description: hypothetical protein FACI_IFERC00001G0562 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.7e-08   32.6   0.0    1.1e-07   31.7   0.0    1.4  1  MarR            MarR family
    1.7e-07   31.1   0.1    3.9e-07   29.9   0.1    1.7  1  HTH_11          HTH domain
    2.3e-07   30.2   0.0    5.4e-07   29.1   0.0    1.6  1  HTH_24          Winged helix-turn-helix DNA-binding
    0.00011   22.0   0.0    0.00021   21.1   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00044   20.3   0.0    0.00079   19.4   0.0    1.3  1  HTH_20          Helix-turn-helix domain
     0.0013   18.5   0.1     0.0068   16.2   0.1    2.0  2  HTH_10          HTH DNA binding domain
     0.0055   16.7   0.2      0.011   15.7   0.2    1.5  1  MetOD1          Metanogen output domain 1
     0.0064   16.1   0.0      0.016   14.8   0.0    1.6  1  Sigma70_r4_2    Sigma-70, region 4
  ------ inclusion threshold ------
      0.012   15.5   0.0      0.021   14.7   0.0    1.3  1  MarR_2          MarR family
      0.012   15.1   0.0      0.023   14.2   0.0    1.4  1  Sigma70_r4      Sigma-70, region 4
      0.016   15.0   0.0      0.031   14.0   0.0    1.5  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.023   14.6   0.0      0.051   13.5   0.0    1.6  1  TrmB            Sugar-specific transcriptional regulator TrmB
      0.033   14.2   0.1      0.068   13.2   0.1    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG
      0.048   13.7   0.0      0.088   12.9   0.0    1.4  1  Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
      0.069   13.0   0.0       0.13   12.1   0.0    1.4  1  HTH_23          Homeodomain-like domain
      0.089   12.7   0.0       0.31   10.9   0.0    1.9  3  Sigma70_ECF     ECF sigma factor
       0.12   12.7   0.4        2.3    8.6   0.0    2.5  2  HTH_WhiA        WhiA C-terminal HTH domain
       0.14   12.6   0.1       0.27   11.7   0.1    1.6  1  HTH_40          Helix-turn-helix domain
       0.21   11.4   0.0       0.35   10.7   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.0   1.1e-10   1.1e-07       6      50 ..       8      52 ..       4      55 .. 0.94

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1.1e-10
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++i+ +l+e ++l++ eLa+k+++sk++v + + +Le++G + R+
  gi|518651923|ref|YP_008141443.1|  8 VKIILLLKEFPGLTLDELAEKMSISKMAVLNHISALEQQGAVARK 52
                                      68999*************************************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.1   4.1e-10   3.9e-07       5      47 ..      10      54 ..       8      60 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 4.1e-10
                            HTH_11  5 ilelLleargp.isgeeLAeeLnvSrrtvrrdIkaLeelg...vpIe 47
                                      i+ lL  ++ p ++ +eLAe++++S+++v ++I aLe +g    +I+
  gi|518651923|ref|YP_008141443.1| 10 IILLL--KEFPgLTLDELAEKMSISKMAVLNHISALEQQGavaRKIV 54
                                      44444..44444****************************7664554 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   5.7e-10   5.4e-07       7      45 ..       9      47 ..       5      49 .. 0.95

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 5.7e-10
                            HTH_24  7 kILelLqknprisqreLAerlglSpstvnrrlkrLeeeG 45
                                      kI+ lL++ p+++  eLAe+  +S+ +v+ ++  Le++G
  gi|518651923|ref|YP_008141443.1|  9 KIILLLKEFPGLTLDELAEKMSISKMAVLNHISALEQQG 47
                                      9************************************99 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.2e-07   0.00021       2      45 ..       5      49 ..       5      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
                                      HHHHHHHHHHTTSS.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaege.lcvcelaeelglsqstvShHLkkLreaGLV 45
                                      pt +kI+ lL e + l+  elae++ +s+ +v  H ++L+++G V
  gi|518651923|ref|YP_008141443.1|  5 PTPVKIILLLKEFPgLTLDELAEKMSISKMAVLNHISALEQQGAV 49
                                      5669********888***************************965 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   8.3e-07   0.00079      11      55 ..       6      50 ..       2      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.3e-07
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +  +i  +L++  glt+ elae +++sk  + +H+ +Le+ g+v 
  gi|518651923|ref|YP_008141443.1|  6 TPVKIILLLKEFPGLTLDELAEKMSISKMAVLNHISALEQQGAVA 50
                                      55667777777789****************************997 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.2e-06    0.0068      25      49 ..      21      45 ..      19      46 .. 0.91
   2 ?   -1.0   0.0       1.7   1.6e+03      26      36 ..     159     169 ..     156     176 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.2e-06
                            HTH_10 25 tlkeLAkelGIskstlsehLrkaes 49
                                      tl+eLA+++ Isk+++++h+++ e+
  gi|518651923|ref|YP_008141443.1| 21 TLDELAEKMSISKMAVLNHISALEQ 45
                                      89******************98876 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                            HTH_10  26 lkeLAkelGIs 36 
                                       + +++k +GI+
  gi|518651923|ref|YP_008141443.1| 159 ILSISKNFGIA 169
                                       56799****98 PP

>> MetOD1  Metanogen output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.2e-05     0.011      13     153 ..      62     203 ..      51     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.2e-05
                            MetOD1  13 sfllsaiPtlaskippeekkilikqfadrveknlkpkfkeelk.......eaekeeedaekvlkayiewlnqlfanf 82 
                                       sf+  a+P+  +k+ +   ++++++f+d+++++ ++k+ ee+         +e   +   k l++ ++ l+ l +n 
  gi|518651923|ref|YP_008141443.1|  62 SFIFYALPVSNNKLGN-SSDSMLNDFMDFIKTTGNEKLLEEFLkdryskvRSEYTGAMRGKNLDEKVNELAILRRNA 137
                                       7999999999999665.67999***************9999876877655333333334445556666666666655 PP

                            MetOD1  83 giktekkedeknvlleftnCpWgeearknPifCllcraivsrsftwtglkgsveqkktlgngdekCvFeik 153
                                        +  e k  + n+ l   nCp  + +++  i C + ++++s++++      +v+ +++  ng   C+F i 
  gi|518651923|ref|YP_008141443.1| 138 DYYPEVKRAQGNFELIEYNCPILSISKNFGIACSMETKMFSQVLD-----ANVKSTHRQVNGYSACRFLIS 203
                                       5555544666677677789*********************99865.....669999999999999999886 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.7e-05     0.016      14      48 ..       7      41 ..       2      42 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHHTS---HHHHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 14 rqreifllryleglsykEIAellgisegtVksrls 48
                                        + i+ll+++ gl+ +E Ae++ is  +V +++s
  gi|518651923|ref|YP_008141443.1|  7 PVKIILLLKEFPGLTLDELAEKMSISKMAVLNHIS 41
                                      5688**************************99986 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.3e-05     0.021      10      54 ..      10      52 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                                      HHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 10 vLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++ L   pg  lt  ela+++ +sk av +++  L+++G v r+
  gi|518651923|ref|YP_008141443.1| 10 IILLLKEFPG--LTLDELAEKMSISKMAVLNHISALEQQGAVARK 52
                                      6677889999..****************************99885 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.4e-05     0.023      13      37 ..      11      36 ..       9      43 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.4e-05
                                      HHHHH.TTT--HHHHHHHHTS-HHHH CS
                        Sigma70_r4 13 lelrf.geglTleEIgerlgiSrerV 37
                                      + l   + glTl E++e++ iS+++V
  gi|518651923|ref|YP_008141443.1| 11 ILLLKeFPGLTLDELAEKMSISKMAV 36
                                      45555599****************98 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   3.3e-05     0.031       4      46 ..       9      51 ..       8      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.3e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +i+ llk+   l+++el+e   +S++ + + ++ Le+qg++ R
  gi|518651923|ref|YP_008141443.1|  9 KIILLLKEFPGLTLDELAEKMSISKMAVLNHISALEQQGAVAR 51
                                      68889999999****************************9887 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.4e-05     0.051      17      60 ..      13      57 ..       8      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.4e-05
                                      HH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB 17 Ll.klgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60
                                      Ll +   +t de+ae+  +++  v + ++ Le+ G V r+  ++k
  gi|518651923|ref|YP_008141443.1| 13 LLkEFPGLTLDELAEKMSISKMAVLNHISALEQQGAVARKIVKKK 57
                                      44577889*****************************99877744 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.2e-05     0.068      13      44 ..      12      43 ..       8      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.2e-05
                           HTH_Mga 13 lLteneksltldelakeLglseltlqsdiseL 44
                                      lL+++ + ltldela+++++s  ++ + is L
  gi|518651923|ref|YP_008141443.1| 12 LLLKEFPGLTLDELAEKMSISKMAVLNHISAL 43
                                      67777999*******************99998 PP

>> Sulfolobus_pRN  Sulfolobus plasmid regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.3e-05     0.088       9      54 ..      10      55 ..       1      69 [. 0.79

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                    Sulfolobus_pRN  9 killilsrrcatleeleektGiekeellvyltrlykrGlisrkWrk 54
                                       ill      +tl+el ek  i k  +l +++ l ++G + rk  k
  gi|518651923|ref|YP_008141443.1| 10 IILLLKEFPGLTLDELAEKMSISKMAVLNHISALEQQGAVARKIVK 55
                                      34444455689*******************************9744 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.13       9      46 ..       9      48 ..       8      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlkryreeGl 46
                                      +i+lll+e  Gl+  e A+++ +s++ v + +++ ++ G+
  gi|518651923|ref|YP_008141443.1|  9 KIILLLKEfpGLTLDELAEKMSISKMAVLNHISALEQQGA 48
                                      69**************************999999876774 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.31     146     169 ..      14      37 ..       4      50 .. 0.88
   2 ?   -1.9   0.0       2.8   2.6e+03      14      51 ..      94     131 ..      83     147 .. 0.62
   3 ?   -3.6   0.0       9.4   8.9e+03      80     100 ..     174     194 ..     171     205 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                       Sigma70_ECF 146 lrkleGlsveEiAeklgvskrtve 169
                                       l+ + Gl+ +E+Aek+ +sk +v 
  gi|518651923|ref|YP_008141443.1|  14 LKEFPGLTLDELAEKMSISKMAVL 37 
                                       6889****************9985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                       Sigma70_ECF  14 GdaeaaeqllelvydeLrrlagsklknerreetledta 51 
                                       G+++  e+ l+  y+++r+     ++ ++ +e+ ++ a
  gi|518651923|ref|YP_008141443.1|  94 GNEKLLEEFLKDRYSKVRSEYTGAMRGKNLDEKVNELA 131
                                       66666666666667766666666665555444444444 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.4
                       Sigma70_ECF  80 aeamrrilidhaRrrkrqkRG 100
                                        ++ +++l ++ ++++rq  G
  gi|518651923|ref|YP_008141443.1| 174 TKMFSQVLDANVKSTHRQVNG 194
                                       566677777777777777655 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0    0.0024       2.3      45      82 ..      10      45 ..       3      46 .. 0.85
   2 ?    1.5   0.0      0.41   3.9e+02      36      52 ..     121     137 ..     107     141 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0024
                                      HHHHHHH-TTS-HHHHHHTT..T--HHHHHHHHHHHHH CS
                          HTH_WhiA 45 vaelRlenpdaSLkeLgelleppisKSgvnhrlrklke 82
                                      ++ l +e p ++L eL+e +   isK +v + +  l++
  gi|518651923|ref|YP_008141443.1| 10 IILLLKEFPGLTLDELAEKM--SISKMAVLNHISALEQ 45
                                      56667899************..9***999888887775 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.41
                                       GGS-HHHHHHHHHHHH- CS
                          HTH_WhiA  36 eklpeklkevaelRlen 52 
                                       ++l+ek+ e+a lR + 
  gi|518651923|ref|YP_008141443.1| 121 KNLDEKVNELAILRRNA 137
                                       799**********9875 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   0.1   0.00028      0.27      12      41 ..      19      48 ..      13     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                            HTH_40 12 glsieeIAkerglkesTIegHLaelieege 41
                                      gl+++e A++ ++++  + +H+  l ++g 
  gi|518651923|ref|YP_008141443.1| 19 GLTLDELAEKMSISKMAVLNHISALEQQGA 48
                                      89**********************999984 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00037      0.35      11      50 ..      13      51 ..       8      52 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +l e p+ ltl elA++  ++k +v ++++ L+++G v +
  gi|518651923|ref|YP_008141443.1| 13 LLKEFPG-LTLDELAEKMSISKMAVLNHISALEQQGAVAR 51
                                      4555555.9***************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1493.95
//
Query:       gi|518651924|ref|YP_008141444.1|  [L=67]
Description: hypothetical protein FACI_IFERC00001G0563 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.069   12.9   0.4      0.077   12.8   0.4    1.1  1  AKAP28    28 kDa A-kinase anchor


Domain annotation for each model (and alignments):
>> AKAP28  28 kDa A-kinase anchor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4   4.3e-06     0.077      11      49 ..      15      54 ..       8      62 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.3e-06
                            AKAP28 11 kgleqIeefikt.welskswlyliefleekeaekskiyiy 49
                                      + +++I+ +i + w+ + swly  + +e+k ++ +++ i 
  gi|518651924|ref|YP_008141444.1| 15 RKKSEIDVYIDReWNGDRSWLYKKHNYEQKRHRTHRYCIR 54
                                      45789*****887************999999988875554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 442.02
//
Query:       gi|518651925|ref|YP_008141445.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G0564 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-42  144.0  62.0    6.5e-34  117.4  38.4    2.0  2  MFS_1     Major Facilitator Superfamily
    2.5e-07   29.5   2.2    2.5e-07   29.5   2.2    1.9  2  MFS_3     Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.4  38.4   7.2e-38   6.5e-34       8     351 ..      11     343 ..       4     344 .. 0.89
   2 !   40.4  15.7   1.9e-14   1.7e-10      37     172 ..     243     378 ..     240     398 .. 0.85

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 7.2e-38
                             MFS_1   8 salarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fa. 82 
                                        a +r   +++lpl+    ++is  e g++l++  l++++ ++  G l+dr+Grr +l+l  +  +l  ++ + f+ 
  gi|518651925|ref|YP_008141445.1|  11 RASGRVSSFIFLPLIFVFIYHISFIETGIVLGVAILLMSAIQYYSGILTDRIGRRVFLILIPVPAGLL-YISMyFTv 86 
                                       5555666777888888999*************************************999999999999.66665655 PP

                             MFS_1  83 .sslw.lllvlrvlqGlga.galfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                          l+ +ll++ + + ++  ++ +pa++a iad+++ ++r +++  + +++++Ga++gp+lg++l+  +g++++f++
  gi|518651925|ref|YP_008141445.1|  87 lYRLPvMLLIGLFYSTIAInALQYPAIQASIADVTSLKQRLSGYTEIRVMANAGAAIGPILGAILS-VYGFQYIFLM 162
                                       79****************99*********************************************9.99******** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                       ++i++++ +++ ++ + e++ ++k +  ++           + +k+  kd+++ +++i+ ++++f++ +  + l+ly
  gi|518651925|ref|YP_008141445.1| 163 AGIATFIEIIILYFNVKETYFPSKIEYLTKN----------D-IKLAYKDRFFILFIIIGIIMAFVLRQRGASLTLY 228
                                       **********978888888888888888888..........5.********88544444444445666699999999 PP

                             MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvli 310
                                       + +  gl+  l+++++++l +++++ l+  + +l++r    r+ l+  +++l+ +lg+++l ++++   +ll++ ++
  gi|518651925|ref|YP_008141445.1| 229 AFDFEGLP-ILYLAYIYSLNGILVVLLQYPIFKLMNR--ETRPVLFRSVGMLFYFLGFIVLMFSKNIDYFLLSMGIM 302
                                       88888999.8*************************99..7778999999999999999999999888999999999* PP

                             MFS_1 311 Gfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       ++g  fv p+ ++++++ ap+++ gt++g++n++ s+g++ 
  gi|518651925|ref|YP_008141445.1| 303 TVGEDFVAPTTQTIITSIAPNNMKGTYIGIYNLFISFGSFS 343
                                       **************************************985 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1.9e-14
                             MFS_1  37 lltlyalgaavaslplGrlsdr.fGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliad 112
                                       +++l +++ +++++p+  l++r   +  +  +g+l+++lg+++l+f+ ++ ++l++  ++ +g+ +++p+ +++i+ 
  gi|518651925|ref|YP_008141445.1| 243 IYSLNGILVVLLQYPIFKLMNReTRPVLFRSVGMLFYFLGFIVLMFSKNIDYFLLSMGIMTVGEDFVAPTTQTIITS 319
                                       678899999*************443333778*********77777955555************************** PP

                             MFS_1 113 wfpkeergraigllsagfslGailgpllggllasslg.Wravfyilaivsllafvlfllll 172
                                       ++p + +g +ig++++++s+G+  g ++g +++s++   +a+f++l ++s l++ +  l+l
  gi|518651925|ref|YP_008141445.1| 320 IAPNNMKGTYIGIYNLFISFGSFSGSIVGLYMLSYYEsATATFWLLIAMSSLVVSV--LYL 378
                                       *********************************88877888899999988887333..444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   2.2   2.8e-11   2.5e-07      61     187 ..      51     175 ..      31     201 .. 0.75
   2 ?    0.5   0.3     0.017   1.5e+02     313     388 ..     300     376 ..     269     396 .. 0.66

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.8e-11
                             MFS_3  61 lsilaGalaDnfdrRkvllavql..llalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrr 135
                                       +   +G+l+D + rR +l+ + +   l+  s+  tvl     l ++ll++l + +    al+ Pa qAs+ ++ + +
  gi|518651925|ref|YP_008141445.1|  51 IQYYSGILTDRIGRRVFLILIPVpaGLLYISMYFTVL---YRLPVMLLIGLFYSTIAINALQYPAIQASIADVTSLK 124
                                       33469**********9998765411344445444444...4455666777766666678***************998 PP

                             MFS_3 136 dvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivall 187
                                       +  +  +   v  n   ++GP l G ++++ G  + f ++ ++ ++ i++l 
  gi|518651925|ref|YP_008141445.1| 125 QRLSGYTEIRVMANAGAAIGPIL-GAILSVYGFQYIFLMAGIATFIEIIILY 175
                                       888999999999*********88.5789***********9998777776664 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.017
                             MFS_3 313 vlllgGaaWitalstlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGav...aealsvtlaLlaaaaallla 386
                                        ++  G  +++   t ++ +  + P+ ++g  + +Y   ++ g   Gs++   +    e++++t+ Ll+a  +l+++
  gi|518651925|ref|YP_008141445.1| 300 GIMTVGEDFVAP--TTQTIITSIAPNNMKGTYIGIYNLFISFGSFSGSIVGLYMlsyYESATATFWLLIAMSSLVVS 374
                                       444555555443..345667778999999999999988776666678876433311146667777788887777776 PP

                             MFS_3 387 aa 388
                                       ++
  gi|518651925|ref|YP_008141445.1| 375 VL 376
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1071  (0.0597356); 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:                         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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2604.32
//
Query:       gi|518651926|ref|YP_008141446.1|  [L=114]
Description: hypothetical protein FACI_IFERC00001G0565 [Ferroplasma acidarmanus fer1]
Scores for complete 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   26.0   0.0    1.1e-05   25.8   0.0    1.1  1  DrsE      DsrE/DsrF-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   5.9e-10   1.1e-05       2     117 .]       4     114 .]       3     114 .] 0.79

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.9e-10
                                       EEEEEE-S-TTTBSHHHHHHHHHHHHHTTT....-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EE CS
                              DrsE   2 kvfilvtggpygseaarealelalaaaalg....hevsvffygdGvllllkgqtanpadeknlaellkalkeygvkl 74 
                                       k++i++++g  ++ +   +l++a+  + +     ++v+v+f g+    l k  +     ++++  llk l++++v  
  gi|518651926|ref|YP_008141446.1|   4 KYLIIISSGLDQKGKMIVGLNFAK--NIYRkklaEDVKVVFFGPSEESLAK--H-----DPDVDTLLKILRDMNVIQ 71 
                                       678888876444444444444444..33335577*****************..2.....3569***********999 PP

                                       EEEHHHHHHTT--GGGE-.T--EEEE-HH.HHHHHHHH-SEEEE- CS
                              DrsE  75 yvCgqaakargldededl.gvgvevsglg.elaelqnegdrvitf 117
                                       ++C   a a +++e  d+ ++g+++ +++ ++ +++++g+r+itf
  gi|518651926|ref|YP_008141446.1|  72 IACSGYAVAKNVSE--DIsKIGMKLEDVSdTITNFADQGYRIITF 114
                                       99999999*****6..46678*******978899999*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 883.92
//
Query:       gi|518651927|ref|YP_008141447.1|  [L=43]
Description: hypothetical protein FACI_IFERC00001G0566 [Ferroplasma acidarmanus fer1]
Scores for complete 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   1.1      3e-05   24.2   1.1    1.1  1  DUF2283   Protein of unknown function (DUF2283)


Domain annotation for each model (and alignments):
>> DUF2283  Protein of unknown function (DUF2283)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.1   1.7e-09     3e-05       1      34 [.       3      38 ..       3      42 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.7e-09
                           DUF2283  1 kitYDpeaDalYIylsegpveeseev..dddiilDf 34
                                      ki YD  aD+lYIyl++ +++++     +++i+l +
  gi|518651927|ref|YP_008141447.1|  3 KIQYDIVADTLYIYLTNLKIVDTIPDnkNENIFLMY 38
                                      89*************888888887756688999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); 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: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 356.12
//
Query:       gi|518651928|ref|YP_008141448.1|  [L=44]
Description: hypothetical protein FACI_IFERC00001G0567 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-05   24.9   0.1      2e-05   24.9   0.1    1.1  1  DUF4258   Domain of unknown function (DUF4258)
  ------ inclusion threshold ------
      0.042   12.3   0.0      0.045   12.2   0.0    1.0  1  GerA      Bacillus/Clostridium GerA spore germination protein


Domain annotation for each model (and alignments):
>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   2.2e-09     2e-05       1      26 [.       4      29 ..       4      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 2.2e-09
                           DUF4258  1 fsaHArermaeRgIseedieevlenG 26
                                      +s+HA++r +eR I++++ie ++  +
  gi|518651928|ref|YP_008141448.1|  4 LSSHASDRIKERSIKTSEIETTIIAP 29
                                      699*******************9887 PP

>> GerA  Bacillus/Clostridium GerA spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     5e-06     0.045     112     145 ..      10      43 ..       2      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5e-06
                              GerA 112 kgyekRsveepetEkvvrGpregFvEslrtNtal 145
                                          ++Rs++++e E+++  p+++  E+++ Nt l
  gi|518651928|ref|YP_008141448.1|  10 DRIKERSIKTSEIETTIIAPNKSIKEDFELNTCL 43 
                                       56799**************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      167  (0.00931452); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 326.73
//
Query:       gi|518651929|ref|YP_008141449.1|  [L=127]
Description: hypothetical protein FACI_IFERC00001G0568 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.0    0.00027   21.4   0.0    1.4  1  PIN       PIN domain
  ------ inclusion threshold ------
      0.067   13.2   0.1      0.083   12.8   0.1    1.2  1  LRR_5     BspA type Leucine rich repeat region (6 copies)
       0.11   12.4   0.1       0.12   12.2   0.1    1.1  1  DUF2480   Protein of unknown function (DUF2480)


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   4.5e-08   0.00027       3     120 ..       4     115 ..       3     117 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.5e-08
                                       E-HHHHHHHHTTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEE...BCH CS
                               PIN   3 lDTsvliallrgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilp...ida 75 
                                       lDTs +++l+ + +      +++++    +t +l+++E+ +v+ + +s+++  ++ +e++++    +++++      
  gi|518651929|ref|YP_008141449.1|   4 LDTSSIFNLFQRGKY----TEIMDN----ATIPLAVYEVGNVIWK-NSNIKNTITQEEAKDIgSVLFELINsieQVI 71 
                                       788888888844443....467766....8999************.6666666666666666666666666211334 PP

                                       HHHHHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHHHH CS
                               PIN  76 eiaeeaaeialkygllpnDaliaAtAkehgikliatfDedfrrva 120
                                       + +  ++ +alk gl+ +D   ++ A+e g  li t D ++ rva
  gi|518651929|ref|YP_008141449.1|  72 PTWSSVLSLALKEGLTFYDSSFLVSAIEKGYGLI-TDDIKLFRVA 115
                                       56777788889999********************.****999987 PP

>> LRR_5  BspA type Leucine rich repeat region (6 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   1.4e-05     0.083      38      84 ..      24      69 ..      11      96 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.4e-05
                             LRR_5 38 sitlpsslteigsyaFsncssltsitipssltsigeyaFsncsslke 84
                                      + t+p  + e+g+ + +n+ ++++   +++ + ig+  F+ ++s+++
  gi|518651929|ref|YP_008141449.1| 24 NATIPLAVYEVGNVIWKNS-NIKNTITQEEAKDIGSVLFELINSIEQ 69
                                      3344444444444444444.444444444444444444444444443 PP

>> DUF2480  Protein of unknown function (DUF2480)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.1e-05      0.12      15      80 ..      13      78 ..       1     100 [. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                           DUF2480 15 ldledyypkeervelDlkdfLfeglilkEkdFrealkehdwsqykdkyvaltcstdaivPaWayml 80
                                      ++  +y++  + +++ l+ + + ++i k+ + ++++ + + +        l++s + ++P+W+ +l
  gi|518651929|ref|YP_008141449.1| 13 FQRGKYTEIMDNATIPLAVYEVGNVIWKNSNIKNTITQEEAKDIGSVLFELINSIEQVIPTWSSVL 78
                                      45567777788899999999999***************************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 909.67
//
Query:       gi|518651930|ref|YP_008141450.1|  [L=75]
Description: CopG family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.026   14.5   2.0       0.11   12.5   0.3    2.4  2  RHH_3            Ribbon-helix-helix domain
      0.061   13.8   0.1       0.31   11.5   0.0    1.8  2  CcdA             Post-segregation antitoxin CcdA
      0.087   13.0   1.1      0.091   12.9   1.1    1.0  1  DUF3347          Protein of unknown function (DUF3347)
       0.12   12.5   0.1       0.22   11.7   0.1    1.4  1  CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
       0.16   11.5   0.0       0.23   11.0   0.0    1.3  1  AA_permease_N    Amino acid permease N-terminal


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 ?   12.5   0.3     3e-05      0.11      22      44 .]      20      42 ..       7      42 .. 0.92
   2 ?    1.1   0.1      0.11   3.8e+02      10      20 ..      43      53 ..      43      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3e-05
                             RHH_3 22 ekTrIprSklldeAiellLekYe 44
                                      +k++I+ ++l+++Ai   ++kY+
  gi|518651930|ref|YP_008141450.1| 20 RKLGINPTELIRKAIHYEIKKYR 42
                                      799************99999995 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.11
                             RHH_3 10 dpelaekLkaL 20
                                      ++el ek+k +
  gi|518651930|ref|YP_008141450.1| 43 NNELMEKMKKI 53
                                      789*****986 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   8.8e-05      0.31       8      45 ..      11      48 ..       4      55 .. 0.81
   2 ?    3.3   0.0      0.03   1.1e+02       9      39 ..      43      73 ..      41      75 .] 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                              CcdA  8 ldsdllaqAralgiNlSatleeaLaeevkeekaerwke 45
                                      ++++  ++ r+lgiN  +++ +a+  e+k+ ++ +  e
  gi|518651930|ref|YP_008141450.1| 11 ITEEDREELRKLGINPTELIRKAIHYEIKKYRNNELME 48
                                      7889999*********************9877766444 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.03
                              CcdA  9 dsdllaqAralgiNlSatleeaLaeevkeek 39
                                      + +l+++ +++   lS++  + L + ++e +
  gi|518651930|ref|YP_008141450.1| 43 NNELMEKMKKIAPTLSKLKMDELVKDIREDR 73
                                      78999************99999999999877 PP

>> DUF3347  Protein of unknown function (DUF3347)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.1   2.5e-05     0.091      55     125 ..       2      72 ..       1      75 [] 0.93

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.5e-05
                           DUF3347  55 esYlklkdALvaddakeakkaakkleeklkavdtsklkekekkelkeiseelkekaekiaeskdieeqRea 125
                                       ++Y  l   ++++d +e +k + + +e +++    ++k+ +++el+e++++++ +++k++  + +++ Re+
  gi|518651930|ref|YP_008141450.1|   2 SKYTTLSAKITEEDREELRKLGINPTELIRKAIHYEIKKYRNNELMEKMKKIAPTLSKLKMDELVKDIRED 72 
                                       79*****************************9999*************************99988888874 PP

>> CSN4_RPN5_eIF3a  CSN4/RPN5/eIF3a helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   6.1e-05      0.22      15      38 ..      41      64 ..      40      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
                   CSN4_RPN5_eIF3a 15 yQVNeliEKIasaePeWmakalee 38
                                      y  Nel+EK+++++P   + +++e
  gi|518651930|ref|YP_008141450.1| 41 YRNNELMEKMKKIAPTLSKLKMDE 64
                                      778*************99999998 PP

>> AA_permease_N  Amino acid permease N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   6.5e-05      0.23      23      45 ..      38      60 ..      35      71 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.5e-05
                     AA_permease_N 23 idfYrntasvsgaklsRPsLaeL 45
                                      i  Yrn +++ + k++ P+L+ L
  gi|518651930|ref|YP_008141450.1| 38 IKKYRNNELMEKMKKIAPTLSKL 60
                                      556*****************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1367  (0.0762452); expected 358.6 (0.02)
Passed bias filter:                      635  (0.0354175); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 594.47
//
Query:       gi|518651931|ref|YP_008141451.1|  [L=130]
Description: hypothetical protein FACI_IFERC00001G0570 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0095   15.7   0.1      0.027   14.3   0.1    1.7  2  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.074   13.0   0.0       0.24   11.4   0.0    1.8  2  RMMBL            Zn-dependent metallo-hydrolase RNA specifici
       0.12   12.6   0.0       0.21   11.9   0.0    1.4  1  MLD              Membrane Localization Domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1   4.4e-06     0.027     151     171 ..      11      31 ..       2      32 .. 0.91
   2 ?   -1.9   0.0      0.42   2.5e+03     147     166 ..      63      82 ..      59      87 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.4e-06
                                       HHHHHT-SSCCHHHHHHCCCH CS
                   Phage_integrase 151 vqkllGHssisttqiYthvak 171
                                       vq l GH+ i+tt +Yth+++
  gi|518651931|ref|YP_008141451.1|  11 VQILVGHTRIETTTRYTHLTQ 31 
                                       899***************975 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.42
                                       SHHHHHHHHT-SSCCHH.HHH CS
                   Phage_integrase 147 dlrvvqkllGHssistt.qiY 166
                                       d++vv ++lG++  s++  iY
  gi|518651931|ref|YP_008141451.1|  63 DPNVV-EALGFERFSMIaPIY 82 
                                       55544.688999999987777 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.18   1.1e+03      18      33 ..      84      99 ..      83     100 .. 0.82
   2 ?   11.4   0.0     4e-05      0.24      22      40 ..     100     118 ..      95     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
                             RMMBL 18 dknellelirklkprn 33
                                      +k+  +++ir++k r+
  gi|518651931|ref|YP_008141451.1| 84 YKRNVMRFIRSVKRRY 99
                                      6788899****99987 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 4e-05
                             RMMBL  22 llelirklkprnvilvHGe 40 
                                       l+ li++++ +++ l+HG 
  gi|518651931|ref|YP_008141451.1| 100 LKSLINMFNAKPIRLIHGN 118
                                       899***************6 PP

>> MLD  Membrane Localization Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.5e-05      0.21      29      58 ..      26      55 ..      16      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.5e-05
                               MLD 29 eyhellgnmkllkleqvealfeLrkqiehY 58
                                        h ++++      e+vealf+L++q++++
  gi|518651931|ref|YP_008141451.1| 26 YTHLTQKEVGEAVKESVEALFRLNRQMTDF 55
                                      557777788888899************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 944.59
//
Query:       gi|518651932|ref|YP_008141452.1|  [L=135]
Description: hypothetical protein FACI_IFERC00001G0571 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 919.43
//
Query:       gi|518651933|ref|YP_008141453.1|  [L=236]
Description: hypothetical protein FACI_IFERC00001G0572 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1579.68
//
Query:       gi|518651934|ref|YP_008141454.1|  [L=712]
Description: hypothetical protein FACI_IFERC00001G0573 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0051   16.6   0.9     0.0083   16.0   0.9    1.3  1  zf-C3HC4_3    Zinc finger, C3HC4 type (RING finger)
  ------ inclusion threshold ------
       0.14   12.1   0.2       0.14   12.1   0.2    3.1  4  PEGA          PEGA domain
       0.17   11.7   1.1       0.31   10.8   1.1    1.4  1  Rubredoxin_2  Rubredoxin metal binding domain
        0.8    9.6   3.2        1.4    8.8   3.2    1.3  1  DUF35_N       Rubredoxin-like zinc ribbon domain (DUF35_N)


Domain annotation for each model (and alignments):
>> 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 !   16.0   0.9   1.9e-06    0.0083      24      48 ..     683     707 ..     675     709 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                                       EE-HHHHHHHHHTT-B-TTT--B-- CS
                        zf-C3HC4_3  24 vlCeeCaekllkrkkkCpiCrrpie 48 
                                       ++C++C ++  +  +kCp+C +pi+
  gi|518651934|ref|YP_008141454.1| 683 ITCKNCGTRHYATFDKCPVCLTPIK 707
                                       69********99***********98 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.89     4e+03      43      58 ..     240     255 ..     234     259 .. 0.78
   2 ?   -3.6   0.0       2.4   1.1e+04      44      53 ..     303     312 ..     302     322 .. 0.81
   3 ?   -3.0   0.1       1.5   6.8e+03      35      54 ..     531     550 ..     524     561 .. 0.66
   4 ?   12.1   0.2     3e-05      0.14       2      63 ..     583     646 ..     582     649 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.89
                              PEGA  43 eGYedlektvtvtage 58 
                                        GY ++++ +++ ++ 
  gi|518651934|ref|YP_008141454.1| 240 TGYYNYTANISLPQDI 255
                                       5889999999997765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.4
                              PEGA  44 GYedlektvt 53 
                                       GY ++++ ++
  gi|518651934|ref|YP_008141454.1| 303 GYNNYNMIIY 312
                                       899**99997 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.5
                              PEGA  35 nyslrvekeGYedlektvtv 54 
                                       n+++ +    Y++ ++ +t 
  gi|518651934|ref|YP_008141454.1| 531 NNTVSLPFKIYSNSTANITY 550
                                       55666666666666666654 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 3e-05
                              PEGA   2 gtltirSnpeGatVyidGkylG.kTPvtls.leaGnyslrvekeGYedlektvtvtagetvkln 63 
                                       +tl+i+S  +  +V+++ +++  +  v +  l++G y l+  k GY+  +  v+++++ t+ ++
  gi|518651934|ref|YP_008141454.1| 583 YTLIIKSPEPDWNVMLNDNNISeNGKVATFtLDKGHYILTMYKAGYTKETYNVNLSDNMTLYIS 646
                                       799******************9656666657***********************9999888776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.1     7e-05      0.31       3      20 ..     685     702 ..     684     704 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 7e-05
                      Rubredoxin_2   3 CsqCGfesakwfGrCpsC 20 
                                       C++CG ++ + f +Cp C
  gi|518651934|ref|YP_008141454.1| 685 CKNCGTRHYATFDKCPVC 702
                                       ****************** PP

>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.2   0.00032       1.4      14      32 ..     685     703 ..     683     705 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00032
                           DUF35_N  14 CpdCGtvqfPPr.avCphCg 32 
                                       C++CGt  ++++   Cp C+
  gi|518651934|ref|YP_008141454.1| 685 CKNCGTR-HYATfDKCPVCL 703
                                       *******.79*********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 4857.37
//
Query:       gi|518651935|ref|YP_008141455.1|  [L=586]
Description: hypothetical protein FACI_IFERC00001G0574 [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   26.1   0.0    7.1e-05   23.2   0.0    2.0  1  AAA_16        AAA ATPase domain
    1.1e-05   25.7   0.0      0.031   14.5   0.0    2.4  2  AAA_22        AAA domain
     0.0016   17.8   0.0      0.003   16.9   0.0    1.4  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
     0.0045   17.5   0.0       0.24   11.9   0.0    2.5  2  ABC_tran      ABC transporter
     0.0047   16.7   4.0     0.0047   16.7   4.0    2.0  2  DUF713        Protein of unknown function (DUF713)
  ------ inclusion threshold ------
      0.017   15.5   0.0       0.15   12.4   0.0    2.5  2  RNA_helicase  RNA helicase
       0.03   14.1   0.0        0.1   12.4   0.0    1.8  2  IstB_IS21     IstB-like ATP binding protein
      0.053   12.7   0.0       0.19   10.8   0.0    1.9  2  DUF815        Protein of unknown function (DUF815)
      0.073   12.8   0.0       0.18   11.6   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
       0.11   13.1   0.0       0.32   11.5   0.0    1.8  1  AAA_18        AAA domain
       0.16   12.0   7.4      0.087   12.8   1.3    3.0  2  ResIII        Type III restriction enzyme, res subunit
        0.7    9.9   9.2          1    9.4   0.0    3.6  4  DUF87         Helicase HerA, central domain
        7.1    6.8   5.7        3.4    7.8   0.2    3.0  4  z-alpha       Adenosine deaminase z-alpha 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 !   23.2   0.0   5.2e-08   7.1e-05      25     147 ..     109     298 ..     100     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.2e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekd.ggiflrgkcdql.esa.........................ipy.sala 73 
                                       ++vl+ G sG GKs+l+r ll +l+k+ ++if + ++d++ +++                         i+y ++  
  gi|518651935|ref|YP_008141455.1| 109 QNVLICGTSGQGKSRLMRYLL-YLSKEqKFIFSYKENDDYlKMGynilqvenempdpfmdteafvnaflITYpIQNM 184
                                       589******************.6666626***********8666778888888887777777777777766642244 PP

                            AAA_16  74 qalareellrqlldeaesaeleawrekleeala..........................................av 108
                                        ++   +++   l++  s+   +w ++l                                               + 
  gi|518651935|ref|YP_008141455.1| 185 GII-S-QYIPIFLRD-ISKISKDWNDFLYNLNIklksskdqiqrsaylfiiehskaligsnykknidladesivfDF 258
                                       444.3.444444444.3334444444444433355577777888888999999999999999999999888888877 PP

                            AAA_16 109 pelagaeasrllellkrll.allsrderplvlvlDdlqwa 147
                                       +++  ++++   el+ r+l ++l+++++++++++D+++++
  gi|518651935|ref|YP_008141455.1| 259 SQVNESSKTFYSELFLRILwKRLTKNSKKVLICIDEAHRL 298
                                       777777779***********999999999********986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.3e-05     0.031       6      34 ..     109     137 ..     104     162 .. 0.81
   2 !    8.7   0.0    0.0014       1.9      76     105 ..     270     303 ..     201     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.3e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeak 34 
                                       + ++++G sG GK++l+r ll+  +e+++
  gi|518651935|ref|YP_008141455.1| 109 QNVLICGTSGQGKSRLMRYLLYLSKEQKF 137
                                       5689*****************99876654 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0014
                            AAA_22  76 eell.ealeqalraravielliiDEaqhlr...s 105
                                       +el+ + l++ l + ++++l+ iDEa++l    +
  gi|518651935|ref|YP_008141455.1| 270 SELFlRILWKRLTKNSKKVLICIDEAHRLLynfE 303
                                       333336666666666668999*******844331 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.2e-06     0.003       8      60 ..      78     129 ..      74     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.2e-06
                                       SHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE   8 skkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLi 60 
                                       +++  ++++ +++++++   +   ++d+k++  ++l++G++g GKS  ++ L+
  gi|518651935|ref|YP_008141455.1|  78 KQYIGKDKEYNIIKIPVRSLNFLDYIDYKVNQ-NVLICGTSGQGKSRLMRYLL 129
                                       5566677777777777777788889*******.*************9998876 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00017      0.24      10      39 ..     107     136 ..     102     166 .. 0.86
   2 ?    2.8   0.1      0.12   1.6e+02      26      52 ..     429     460 ..     428     554 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00017
                                       TTSEEEEEESTTSSHHHHHHHHTTSS--SE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  10 egekvaivGenGaGKStLlkllagllkpte 39 
                                        ++ v i G +G GKS L++ l+ l+k ++
  gi|518651935|ref|YP_008141455.1| 107 VNQNVLICGTSGQGKSRLMRYLLYLSKEQK 136
                                       57899*****************99988765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.12
                                       HHHHHHTTSS--SEEEEEET.TCEGGG....B CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxx....x RF
                          ABC_tran  26 tLlkllagllkpteGeilld.gkdlke....q 52 
                                       t++++++++++ +e +++++ ++++++    +
  gi|518651935|ref|YP_008141455.1| 429 TIVEIISKNYSIDENTVKINvKNSISTliknK 460
                                       899**************999766666654331 PP

>> DUF713  Protein of unknown function (DUF713)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.0   3.4e-06    0.0047      42     153 ..     196     313 ..     187     319 .. 0.79
   2 ?   -2.9   0.0       3.4   4.7e+03     146     163 ..     557     574 ..     540     580 .. 0.62

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.4e-06
                            DUF713  42 epivklknrfsdfeeeikksdk.eekklekedleelqselsnL.....akkvlsaynkLeeafeklkelsekfedki 112
                                       + i+k+ + + df  +++ + k ++++++++   ++ +  + L     +k +  a +++  +f +++e s++f  ++
  gi|518651935|ref|YP_008141455.1| 196 RDISKISKDWNDFLYNLNIKLKsSKDQIQRSAYLFIIEHSKALigsnyKKNIDLADESIVFDFSQVNESSKTFYSEL 272
                                       5689999999999988876654045566665555555555444222216778888999999**************** PP

                            DUF713 113 FlkvLqksisdvatklleilevldeleldkekleelrelfs 153
                                       Fl++L k++ + ++k+l  +++   l ++ e ++++  ++s
  gi|518651935|ref|YP_008141455.1| 273 FLRILWKRLTKNSKKVLICIDEAHRLLYNFERYQSIYIEMS 313
                                       ***************************99999999988876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.4
                            DUF713 146 eelrelfskldpsdIptT 163
                                       ++l e+++kl+  ++ + 
  gi|518651935|ref|YP_008141455.1| 557 KNLMEKYNKLQNVSVIEI 574
                                       344445555555555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00011      0.15       1      47 [.     111     152 ..     111     184 .. 0.74
   2 ?   -1.0   0.0       1.7   2.3e+03      53      67 ..     253     266 ..     240     283 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfw.dgY 47 
                                       ++++G sg+GKS+l+++    ll  + +k+++ ++s + +dd++  gY
  gi|518651935|ref|YP_008141455.1| 111 VLICGTSGQGKSRLMRY----LL--YLSKEQKFIFSYKENDDYLkMGY 152
                                       689**************....33..22333344445666666664455 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                      RNA_helicase  53 vvidDfgqvkdeenp 67 
                                        +++Df+qv++++ +
  gi|518651935|ref|YP_008141455.1| 253 SIVFDFSQVNESS-K 266
                                       6899****99773.2 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 ?   12.4   0.0   7.2e-05       0.1      32      64 ..      91     125 ..      79     148 .. 0.81
   2 ?   -2.7   0.0       2.9     4e+03     115     146 ..     479     510 ..     477     513 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.2e-05
                         IstB_IS21  32 krkvkeLatlsfiek..kenivllGpsGvGKshla 64 
                                       k  v++L  l++i+   ++n++++G sG GKs l 
  gi|518651935|ref|YP_008141455.1|  91 KIPVRSLNFLDYIDYkvNQNVLICGTSGQGKSRLM 125
                                       5567889999999862269*************986 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.9
                         IstB_IS21 115 Ddlgllpldqaeaellfeviekryerrsiiit 146
                                       D   l  + +  +++++e++++r  r  +ii+
  gi|518651935|ref|YP_008141455.1| 479 DSANLSLFHKFMENKVLEILSERSIRGNVIIA 510
                                       55566666677788999999999999999986 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00014      0.19      43      79 ..      98     134 ..      68     155 .. 0.86
   2 ?   -3.0   0.0       2.4   3.3e+03     195     236 ..     223     265 ..     219     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00014
                            DUF815  43 nteqfleglpannvLLwGarGtGKSslvkallneyae 79 
                                       n   +++ +  +nvL+ G+ G GKS l++ ll   +e
  gi|518651935|ref|YP_008141455.1|  98 NFLDYIDYKVNQNVLICGTSGQGKSRLMRYLLYLSKE 134
                                       56678888999******************99865555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.4
                            DUF815 195 ldqeeYleiveklakklglelek.eeleeeAlewalergsrsg 236
                                       ++++ Yl i+e+  +  g +++k  +l +e++ +  ++ + s+
  gi|518651935|ref|YP_008141455.1| 223 IQRSAYLFIIEHSKALIGSNYKKnIDLADESIVFDFSQVNESS 265
                                       6788999999999988888888745777778777777766665 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00013      0.18      18      48 ..     104     131 ..      97     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                            AAA_29  18 eidlkgatlltGpsGsGKSTllDAiqalLvp 48 
                                       + ++++++l+ G+sG GKS l+    +lL+ 
  gi|518651935|ref|YP_008141455.1| 104 DYKVNQNVLICGTSGQGKSRLM---RYLLYL 131
                                       5666779************998...555555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00023      0.32       1      42 [.     111     157 ..     111     175 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00023
                            AAA_18   1 IlltGtpGvGKttlakeL...skrlgf..gvnlrdvakenglllevd 42 
                                       +l++Gt+G GK+ l ++L   sk+ +f  +++ +d   + g+ + + 
  gi|518651935|ref|YP_008141455.1| 111 VLICGTSGQGKSRLMRYLlylSKEQKFifSYKENDDYLKMGYNILQV 157
                                       79****************99988777777555555555555544444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   1.3   6.3e-05     0.087      14     157 ..      98     313 ..      90     321 .. 0.50
   2 ?   -0.9   0.4         1   1.4e+03      99     118 ..     517     536 ..     453     581 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.3e-05
                                       HHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHG................ CS
                            ResIII  14 nlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleef................ 74 
                                       n+l+ ++ k ++++li  + G GK++++  l +  ++    +kf+f   +++ + ++  ++                
  gi|518651935|ref|YP_008141455.1|  98 NFLDYIDYKVNQNVLICGTSGQGKSRLMRYLLYLSKE----QKFIFSYKENDDYLKMGYNIlqvenempdpfmdtea 170
                                       5556666677778888888888888877555444444....378888888887777776554554444555555555 PP

                                       ..................................................GGGTGG....GEEEESSS-B--..... CS
                            ResIII  75 ..................................................kkflseaykeigkkvsgdkkka..... 96 
                                                                                          ++                  +     
  gi|518651935|ref|YP_008141455.1| 171 fvnaflitypiqnmgiisqyipiflrdiskiskdwndflynlniklksskDQI------------------Qrsayl 229
                                       55555555555555555444444444443333222222222222111111111..................122222 PP

                                       .....................-SEEEEEHHHHHHTH......................................HHH CS
                            ResIII  97 ..............kekdstnkkilvttiqsldadseee..............................eeeseell 129
                                                     k                       +                                ++   +
  gi|518651935|ref|YP_008141455.1| 230 fiiehskaligsnyK-----------------------KnidladesivfdfsqvnessktfyselflrILWKRLTK 283
                                       222222222222221.......................034444444444444442222223666665333333444 PP

                                       TTT-SEEEEETGGGTTS..TTTHHH.HHT- CS
                            ResIII 130 rdrfdviiiDEaHrlgak.kswrei.lekf 157
                                       ++++ +i iDEaHrl ++ + +++i +e+ 
  gi|518651935|ref|YP_008141455.1| 284 NSKKVLICIDEAHRLLYNfERYQSIyIEMS 313
                                       444448889*******98779999865554 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1
                                       .....-SEEEEEHHHHHHTH CS
                            ResIII  99 kdstnkkilvttiqsldads 118
                                        d+++ k+ ++ +  l+ d+
  gi|518651935|ref|YP_008141455.1| 517 PDISTEKFNIEIETGLKHDI 536
                                       22333333333333333333 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       1.3   1.8e+03      86     104 ..      86     104 ..      71     107 .. 0.79
   2 ?    9.4   0.0   0.00072         1      22      44 ..     107     129 ..     100     137 .. 0.86
   3 ?    1.6   0.2      0.18   2.5e+02     163     226 ..     211     276 ..     165     277 .. 0.75
   4 ?    0.7   2.3      0.34   4.6e+02     132     211 ..     476     577 ..     410     585 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.3
                             DUF87  86 kdkelkinpwsldpeelld 104
                                       + + +ki+++sl++ +++d
  gi|518651935|ref|YP_008141455.1|  86 EYNIIKIPVRSLNFLDYID 104
                                       67889*********99987 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00072
                             DUF87  22 vtrHlAilgsTGsGKSntvavLl 44 
                                       v++ ++i g++G GKS ++++Ll
  gi|518651935|ref|YP_008141455.1| 107 VNQNVLICGTSGQGKSRLMRYLL 129
                                       68899****************98 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.18
                             DUF87 163 qaiarlldkledllrkggsf..snsstdliallleklekegkitiidlsgvdelaqqlvvsvilrr 226
                                       ++  +l++++++++r+ ++f   +s++ + +++ + ++   +  ++d+s+v+e+ +  +  ++lr 
  gi|518651935|ref|YP_008141455.1| 211 NLNIKLKSSKDQIQRSAYLFiiEHSKALIGSNYKKNIDLADESIVFDFSQVNESSKTFYSELFLRI 276
                                       4555666667777777777776555555666666666778888889*******9999999998886 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.34
                             DUF87 132 eekeklssdepveklleelk....................kekeelrklknqaiarlldkledllrkggsf..snss 186
                                       +   +++   + +++++++                       + + +k + +++ +l+++++dl++++++   sn  
  gi|518651935|ref|YP_008141455.1| 476 KTLDSANLSLFHKFMENKVLeilsersirgnviiakkgqnLPDISTEKFNIEIETGLKHDITDLKKRTNTGdkSNII 552
                                       45555555555555555555566666667777777766655566888888999999999999999999998777777 PP

                             DUF87 187 tdliallleklekegkitiidlsgv 211
                                         ++++l ek +k +++++i+++++
  gi|518651935|ref|YP_008141455.1| 553 IIPNKNLMEKYNKLQNVSVIEIKEL 577
                                       7788999999999999999998876 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 ?   -0.6   0.1         1   1.4e+03      30      46 ..     197     213 ..     195     226 .. 0.77
   2 ?   -1.3   0.0       1.7   2.4e+03      37      53 ..     294     310 ..     288     313 .. 0.86
   3 ?    7.8   0.2    0.0025       3.4      32      44 ..     456     468 ..     429     470 .. 0.66
   4 ?   -3.3   0.0       6.9   9.6e+03       6      17 ..     491     502 ..     490     514 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1
                                       HHCC-HHHHHHHHHHHH CS
                           z-alpha  30 gLstpkreiNrvLydle 46 
                                       ++s+  ++ N  Ly+l+
  gi|518651935|ref|YP_008141455.1| 197 DISKISKDWNDFLYNLN 213
                                       56777899999999986 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.7
                                       HHHHHHHHHHHTTSEEE CS
                           z-alpha  37 eiNrvLydlerkgkvyr 53 
                                       e+ r Ly+ er   +y 
  gi|518651935|ref|YP_008141455.1| 294 EAHRLLYNFERYQSIYI 310
                                       7789*******998886 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0025
                                       CC-HHHHHHHHHH CS
                           z-alpha  32 stpkreiNrvLyd 44 
                                         + +eiNrvLyd
  gi|518651935|ref|YP_008141455.1| 456 LIKNKEINRVLYD 468
                                       3358********8 PP

  == domain 4  score: -3.3 bits;  conditional E-value: 6.9
                                       HHHHHHHHHHC- CS
                           z-alpha   6 aekilelLeelg 17 
                                       ++k+le+L e +
  gi|518651935|ref|YP_008141455.1| 491 ENKVLEILSERS 502
                                       689999998866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1090  (0.0607954); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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):              13  [number of targets reported over threshold]
# CPU time: 0.70u 0.32s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 3579.04
//
Query:       gi|518651936|ref|YP_008141456.1|  [L=93]
Description: hypothetical protein FACI_IFERC00001G0575 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   15.1   0.5      0.015   14.8   0.5    1.0  1  BaxI_1    Bax inhibitor 1 like
       0.29    9.8   3.2       0.29    9.9   3.2    1.0  1  DUF2207   Predicted membrane protein (DUF2207)


Domain annotation for each model (and alignments):
>> BaxI_1  Bax inhibitor 1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.5   1.7e-06     0.015     128     198 ..      11      78 ..       7      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-06
                            BaxI_1 128 irvtpkftkivvaaligilllylvnlvlslfgvge.glrdgg..lgilfslvvivlAalsLllDFdqieqgvra 198
                                       i   +k++ki++  ++gill +l+ l l   +  + g       l ++  l+++++ a+sL+l++ +i + +r+
  gi|518651936|ref|YP_008141456.1|  11 ITNLEKLKKILFYLVTGILLSSLLLLYLYNNS--NyG----LfpLILFTVLIIVIVSAISLTLEYFHIVREIRY 78 
                                       556689**************999887776332..222....134778888899999*********999999886 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   3.2   3.2e-05      0.29     379     428 ..      16      66 ..       2      86 .. 0.45

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.2e-05
                           DUF2207 379 klkklsalglgliilglilillallllvll.lvfllilllillliaiivll 428
                                       klkk+ ++++ +i+l+ +l+l++    +++ + ++l+++li++++++i l 
  gi|518651936|ref|YP_008141456.1|  16 KLKKILFYLVTGILLSSLLLLYLYNNSNYGlFPLILFTVLIIVIVSAISLT 66 
                                       333333333333333333333333322222244444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 684.36
//
Query:       gi|518651937|ref|YP_008141457.1|  [L=104]
Description: hypothetical protein FACI_IFERC00001G0576 [Ferroplasma acidarmanus fer1]
Scores for complete 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   21.7   0.2    0.00027   21.0   0.2    1.4  1  MPTase-PolyVal  Metallopeptidase superfamily domain
  ------ inclusion threshold ------
      0.012   16.1   1.0      0.039   14.5   0.1    1.9  2  Aspzincin_M35   Lysine-specific metallo-endopeptidase
        0.1   12.5   0.8       0.17   11.7   0.2    1.6  2  SprT-like       SprT-like family
       0.11   12.7   1.4       0.27   11.4   0.4    1.9  2  DUF3920         Protein of unknown function (DUF3920)
       0.12   10.3   0.0       0.12   10.4   0.0    1.0  1  mit_SMPDase     Mitochondrial-associated sphingomyelin phosph
       0.33   11.0   3.1        4.8    7.2   1.0    2.1  2  WLM             WLM domain


Domain annotation for each model (and alignments):
>> MPTase-PolyVal  Metallopeptidase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.2     9e-08   0.00027      47     117 ..       9      74 ..       3      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9e-08
                    MPTase-PolyVal  47 tllHelvHwtghesRldrdlskrfgseayarEElvAelgaaflcaelgiepevrdhaaYiasWlkvLkedk 117
                                        +lH l+H   h  Rld     + ++  y   E  Ael++ ++ +++g + + + +aaY++ Wl+  k++ 
  gi|518651937|ref|YP_008141457.1|   9 DVLHTLIHEMSH-ARLDHL---NRKDIPYGIGEAEAELSTYLVGQHFGYHFKDE-SAAYMKGWLDNAKQEG 74 
                                       455666666555.477766...456899********************988877.*********9888765 PP

>> Aspzincin_M35  Lysine-specific metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.1   1.3e-05     0.039      95     122 ..      10      38 ..       3      46 .. 0.83
   2 ?   -0.1   0.1      0.41   1.2e+03     124     137 ..      76      89 ..      50      92 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.3e-05
                     Aspzincin_M35  95 qagtivHEltHftev.agtdDiaygqsaa 122
                                         +t++HE++H+     + +Di yg  +a
  gi|518651937|ref|YP_008141457.1|  10 VLHTLIHEMSHARLDhLNRKDIPYGIGEA 38 
                                       578*********977799****9997755 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.41
                     Aspzincin_M35 124 slaksnpsqAleNA 137
                                        l+++n ++A++NA
  gi|518651937|ref|YP_008141457.1|  76 TLSNENLDRAMNNA 89 
                                       34555666666666 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   5.7e-05      0.17      61      82 ..       7      28 ..       2      35 .. 0.81
   2 ?   -1.5   0.0      0.72   2.1e+03      84      94 ..      71      81 ..      47     101 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
                         SprT-like 61 edrllntLaHElcHlalfvisg 82
                                       +++l tL+HE+ H+ l ++++
  gi|518651937|ref|YP_008141457.1|  7 YEDVLHTLIHEMSHARLDHLNR 28
                                      68899**********8877765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.72
                         SprT-like 84 rnnpHGaeFka 94
                                      ++++H  + ++
  gi|518651937|ref|YP_008141457.1| 71 KQEGHTLSNEN 81
                                      34444433333 PP

>> DUF3920  Protein of unknown function (DUF3920)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.4   9.2e-05      0.27      71      88 ..       5      22 ..       2      41 .. 0.78
   2 ?    1.0   0.0      0.15   4.5e+02      41      68 ..      33      64 ..      21     103 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                           DUF3920 71 edyeqvlktllhelrhal 88
                                      e+ye+vl+tl+he+ ha 
  gi|518651937|ref|YP_008141457.1|  5 EEYEDVLHTLIHEMSHAR 22
                                      89**************84 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                           DUF3920 41 salgeeeeeflfplsg....vyhkekqlifvf 68
                                        +ge e+e   +l g    +++k++   ++ 
  gi|518651937|ref|YP_008141457.1| 33 YGIGEAEAELSTYLVGqhfgYHFKDESAAYMK 64
                                      56777777765555441111344555444444 PP

>> mit_SMPDase  Mitochondrial-associated sphingomyelin phosphodiesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   3.9e-05      0.12     581     632 ..      50     101 ..       9     103 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.9e-05
                       mit_SMPDase 581 wlkfgssdlngsysgndldelGqdsikktdeylekaleylcqifrlneaqls 632
                                        ++++ +d +++y+   ld++ q+    ++e l++a+++ ++i +  +aql+
  gi|518651937|ref|YP_008141457.1|  50 HFGYHFKDESAAYMKGWLDNAKQEGHTLSNENLDRAMNNARHIIQDINAQLE 101
                                       6899999*************************************99999986 PP

>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   1.0    0.0016       4.8      79      94 ..       6      21 ..       5      29 .. 0.87
   2 ?    4.1   0.0     0.015        44     114     144 ..      58      88 ..      54     104 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0016
                               WLM 79 pyesimgtllHELaHn 94
                                      +ye++++tl+HE+ H 
  gi|518651937|ref|YP_008141457.1|  6 EYEDVLHTLIHEMSHA 21
                                      69*************7 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                               WLM 114 veelkakGlkegflkeGkrlggkevrnksae 144
                                         ++++kG  ++ ++eG++l++++  +  ++
  gi|518651937|ref|YP_008141457.1|  58 ESAAYMKGWLDNAKQEGHTLSNENLDRAMNN 88 
                                       5678999**************9998876442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.29s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 741.16
//
Query:       gi|518651938|ref|YP_008141458.1|  [L=94]
Description: hypothetical protein FACI_IFERC00001G0577 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   11.3   5.6       0.33   10.7   5.6    1.3  1  DUF3188        Protein of unknown function (DUF3188)
        0.4    9.4   4.1       0.43    9.3   4.1    1.0  1  DUF2207        Predicted membrane protein (DUF2207)
          6    6.9  10.4        1.1    9.2   2.4    2.1  2  SafA           Two-component-system connector protein


Domain annotation for each model (and alignments):
>> DUF3188  Protein of unknown function (DUF3188)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.6   5.6e-05      0.33       6      43 ..      28      64 ..      25      66 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.6e-05
                           DUF3188  6 illgllillysqrqgsdrlqslPallvGlgLivsgavg 43
                                      ill+ll+lly  + +  +l+ l +l++Gl +++++a++
  gi|518651938|ref|YP_008141458.1| 28 ILLSLLLLLYLYNNSYYGLFPL-ILFTGLIIVIVSAIS 64
                                      9*********************.***********9985 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.1   7.3e-05      0.43     377     430 ..      16      68 ..       3      85 .. 0.61

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 7.3e-05
                           DUF2207 377 kkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllf 430
                                       k+k+ ++ ++ ++l+ l+l+l l+ +  ++l + ++l+++li++++++i l + 
  gi|518651938|ref|YP_008141458.1|  16 KTKQIIFYLVTVILLSLLLLLYLYNNSYYGL-FPLILFTGLIIVIVSAISLTFE 68 
                                       4445455555555555555555555444444.7777777777777777777664 PP

>> SafA  Two-component-system connector protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   2.4   0.00019       1.1       5      34 ..       6      35 ..       1      40 [. 0.87
   2 ?    3.0   1.2     0.017        99      27      63 ..      50      86 ..      38      89 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00019
                              SafA  5 tvknkitqrdnykeimsvivvvllltltli 34
                                       v  kit  +  k+i+  +v v+ll+l l+
  gi|518651938|ref|YP_008141458.1|  6 IVYTKITHLEKTKQIIFYLVTVILLSLLLL 35
                                      4789*********************99875 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.017
                              SafA 27 llltltliaifsaidqlsisemGriardlth..fiinsl 63
                                      +l+t  +i i sai  l+  e   i rd+ +  f++ sl
  gi|518651938|ref|YP_008141458.1| 50 ILFTGLIIVIVSAIS-LTF-ENFHIVRDIKYneFLLQSL 86
                                      577878899999995.444.5557777764322666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1206  (0.0672653); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 657.80
//
Query:       gi|518651939|ref|YP_008141459.1|  [L=345]
Description: hypothetical protein FACI_IFERC00001G0578 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-35  122.0   0.0    5.3e-35  121.2   0.0    1.4  1  N6_N4_Mtase      DNA methylase
    1.8e-05   24.5   0.0      0.017   14.8   0.0    2.6  3  UPF0020          Putative RNA methylase family UPF0020
  ------ inclusion threshold ------
      0.028   15.1   0.0        0.2   12.3   0.0    2.3  3  Methyltransf_11  Methyltransferase domain
      0.095   12.0   0.0       0.63    9.3   0.0    2.1  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family


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 !  121.2   0.0   1.2e-38   5.3e-35       1     231 []      23     271 ..      23     271 .. 0.84

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 1.2e-38
                                       EEEEEE--SSSSSCS.................GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHT.. CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy............endeqyeeedsyeeyleflekvlkevrrvLkddgsifiniddseikk.. 63 
                                       vdl +t+pPY + k +            e   ++++e+ +e + + l kv+kev+rvLk +g+++ini+d + +   
  gi|518651939|ref|YP_008141459.1|  23 VDLMITSPPYPMIKMWddmfsvqnpeiaEALREENGEKAFELMNKELDKVWKEVYRVLKIGGIACINIGDATRSLgg 99 
                                       79**************************9999****************************************988** PP

                                       ......HHHHHHHHHTT.-EEEEEEEEEEES........SSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSB CS
                       N6_N4_Mtase  64 ......elkaladeifg.gffllnvivwkkp........nsmpesnkdrltsthEyilvfsknkkyllkfnldaikv 125
                                             ++  +++ ++  gf  l  i w k+        +s   +++ ++t +hEyil+++k++k+       ++k 
  gi|518651939|ref|YP_008141459.1| 100 kfqiytNHARILNYCLSlGFHALPEILWLKEtnkpdkfmGSGMLPVGAYVTLEHEYILILRKGYKR-------EFKS 169
                                       ******6666666666666***********988888777555556666******************.......3333 PP

                                       SS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH.----SS---HHHHHHHHHHHS-TT-EEEETT-T CS
                       N6_N4_Mtase 126 pyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdt.kkkHpaqkPvallerlIklstkkgdivlDpFaG 201
                                         e+ +++++    + ++++++++d+W  ++++ + +  ++ + +++     P +l+ rlI++++ +gd++lDpF+G
  gi|518651939|ref|YP_008141459.1| 170 AEEKLNRQNSA--FFWEERNTWFSDKW--NDLNGVFQRLNHIKvRER-SGAYPIELAYRLINMFSVQGDTILDPFLG 241
                                       33333333332..4668889*******..333333333222224555.899************************** PP

                                       TTHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       N6_N4_Mtase 202 SGtTavaakelgrkfiGieieeeyvelaek 231
                                       +GtT   a++  r++iG+ei+ ++++++e+
  gi|518651939|ref|YP_008141459.1| 242 TGTTTLGAIASARNSIGYEIDGNFKDIVEE 271
                                       *********************999999875 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0   0.00095       4.3     110     131 ..      10      32 ..       2      73 .. 0.86
   2 ?   -3.1   0.0       1.1   5.1e+03      36      65 ..     137     166 ..     127     182 .. 0.60
   3 !   14.8   0.0   3.8e-06     0.017      15      91 ..     219     294 ..     206     310 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00095
                                       --GGG--.STTS---EEEE---- CS
                           UPF0020 110 adaakLr.lkegevdvivtnpPY 131
                                        da++++  k+++vd+++t pPY
  gi|518651939|ref|YP_008141459.1|  10 SDAREMKeVKSESVDLMITSPPY 32 
                                       577777765677*********** PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.1
                                       T-TTSHHHHHHHHHHTT--TTTT----SSH CS
                           UPF0020  36 mCGsGtilIEaallganiapgllrefvlel 65 
                                       + GsG +++ a +  ++ +   lr+     
  gi|518651939|ref|YP_008141459.1| 137 FMGSGMLPVGAYVTLEHEYILILRKGYKRE 166
                                       778998888887666666644555444433 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHH CS
                           UPF0020  15 tLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqg 91 
                                       +LA+ l+++  ++ g+++lDP+ G+Gt  + a   ++n +   +  ++  + +e  ++++++ ++y  +  +r+++ 
  gi|518651939|ref|YP_008141459.1| 219 ELAYRLINMFSVQ-GDTILDPFLGTGTTTLGAIASARNSIGYEIDGNFKDIVEERIKNIKDTSNIYIDERLSRHIEF 294
                                       6999999999886.789*************99999999995444444444555555555555556666666666655 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.96   4.3e+03      48      67 ..       8      28 ..       4      43 .. 0.82
   2 ?   12.3   0.0   4.5e-05       0.2      71      95 ..      62      87 ..      57      88 .. 0.85
   3 ?   -1.8   0.0       1.2   5.2e+03       6      40 ..     241     275 ..     236     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.96
                                      TTEECCCT.SS-TT-EEEEEE CS
                   Methyltransf_11 48 vvadaekl.pfednsfDlvvs 67
                                      + +da+++  ++++s+Dl + 
  gi|518651939|ref|YP_008141459.1|  8 IYSDAREMkEVKSESVDLMIT 28
                                      5678899877999****9875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.5e-05
                                      CCC-.CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11 71 lhhv.edpekalkeiaRvLkpgGllv 95
                                      ++ + ++++k++ke++RvLk gG+ +
  gi|518651939|ref|YP_008141459.1| 62 FELMnKELDKVWKEVYRVLKIGGIAC 87
                                      5556789****************986 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.2
                                       TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCH CS
                   Methyltransf_11   6 GtGrlaealakrgarvvgvDlskemlklakekase 40 
                                       GtG  +      +++ +g +++ ++ ++++e++++
  gi|518651939|ref|YP_008141459.1| 241 GTGTTTLGAIASARNSIGYEIDGNFKDIVEERIKN 275
                                       77777777776778888888888888888887776 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00014      0.63     131     157 ..      68      93 ..      60     133 .. 0.80
   2 ?    0.2   0.0     0.087   3.9e+02      45      90 ..     229     271 ..     167     298 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00014
                                       -HHHHHHHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran 131 DklkaLkeayrvlkpGGrlvvlefskv 157
                                       + +k+ ke+yrvlk GG+  ++++   
  gi|518651939|ref|YP_008141459.1|  68 ELDKVWKEVYRVLKIGGI-ACINIGDA 93 
                                       56899************6.57766554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.087
                                       S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHH CS
                   Ubie_methyltran  45 vkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgek 90 
                                       + +g ++lD   Gtg  ++    s++++    + +i+ n  ++ e+
  gi|518651939|ref|YP_008141459.1| 229 SVQGDTILDPFLGTGTTTLGAIASARNSI---GYEIDGNFKDIVEE 271
                                       45788899999999988888777777664...33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2400.58
//
Query:       gi|518651940|ref|YP_008141460.1|  [L=210]
Description: putative cytosolic protein [Ferroplasma acidarmanus fer1]
Scores for complete 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  169.7   4.3    5.6e-50  169.4   4.3    1.1  1  RE_MjaI   MjaI restriction endonuclease


Domain annotation for each model (and alignments):
>> RE_MjaI  MjaI restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   4.3   3.1e-54   5.6e-50       1     164 []       4     177 ..       4     177 .. 0.93

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 3.1e-54
                           RE_MjaI   1 eqilNlannraqltrkkvVgqvselikefegktleeWkkwYlekl..peaieeatkkiykkiee.lkeeieevdeed 74 
                                       e++lN+an r++lt+kk+Vg+v+e i+++++k+l++W+++Y++++  + ++ e+++k+y k++e +++e+++++eed
  gi|518651940|ref|YP_008141460.1|   4 EWVLNSANMRWGLTKKKQVGAVAEEIRKCSPKELKDWEDYYYNNVypKSHLIELGEKLYVKVTEvIRAEVDDITEED 80 
                                       79******************************************999999*************************** PP

                           RE_MjaI  75 vrkwvedLvinktfeGlkvq.eailkklakelnvkyrlatde.eeskgiDgyi....keigisiKpktykekekels 145
                                       ++++v +Lvin+tf+G++ + e+i+ +l++ l+vk+++a+d  ++ +++D++i    k+ig++iKp+ y+  ++ ++
  gi|518651940|ref|YP_008141460.1|  81 CIDFVVNLVINRTFDGYVSEkETIYGQLQDILGVKIEPAPDSwDRGYNVDFFIkikdKYIGLQIKPTGYEYITQIIN 157
                                       *********************************************************************77777555 PP

                           RE_MjaI 146 eekdvkiityk..kkksgikv 164
                                       e    + it+   ++k+g++v
  gi|518651940|ref|YP_008141460.1| 158 E-RTQQKITHGkfTQKYGGAV 177
                                       5.5556667765778887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1313.53
//
Query:       gi|518651941|ref|YP_008141461.1|  [L=205]
Description: integrase/recombinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-23   83.1   0.0    3.7e-23   82.2   0.0    1.5  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.08   12.4   0.0       0.12   11.8   0.0    1.2  1  iPGM_N           BPG-independent PGAM N-terminus (iPGM_N)


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.2   0.0   4.1e-27   3.7e-23      17     167 ..      46     188 ..      21     192 .. 0.86

  Alignments for each domain:
  == domain 1  score: 82.2 bits;  conditional E-value: 4.1e-27
                                       C....HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCH CS
                   Phage_integrase  17 e....slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskale 89 
                                       +     lk+rd l+l+ ++e G Ris++l+++++d+d++n++i + + +++g+    +p+s+++l  + + +     
  gi|518651941|ref|YP_008141461.1|  46 KkmipFLKARDMLMLKCMWELGGRISDILNIEINDIDFKNKIIVL-KVKKRGGFINRIPVSDNLLLDISNFMRAY-- 119
                                       255555788************************************.33445566799**************9999.. PP

                                       CCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHH CS
                   Phage_integrase  90 eaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiY 166
                                         ++ +  f +       r+t++k +k ++ + g++  l+pH++Rh +a  Ll +gv+++ +++ lGH++  tt +Y
  gi|518651941|ref|YP_008141461.1| 120 --PEVNGRFFKM-----DRETAWKKVKGYGDKIGLK--LHPHMFRHGLAIYLLMKGVPIQIIARRLGHKNAMTTLHY 187
                                       ..8899999887.....9****************99..************************************777 PP

                                       H CS
                   Phage_integrase 167 t 167
                                       +
  gi|518651941|ref|YP_008141461.1| 188 Y 188
                                       5 PP

>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.12     101     118 ..     122     139 ..     107     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                                       EEEHHHHT--SS-HHHHH CS
                            iPGM_N 101 vsGRyyaMDRdkrwerve 118
                                       v GR++ MDR++ w++v+
  gi|518651941|ref|YP_008141461.1| 122 VNGRFFKMDRETAWKKVK 139
                                       89**************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1534.91
//
Query:       gi|518651942|ref|YP_008141462.1|  [L=64]
Description: hypothetical protein FACI_IFERC00001G0581 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 444.12
//
Query:       gi|518651943|ref|YP_008141463.1|  [L=249]
Description: hypothetical protein FACI_IFERC00001G0582 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   87.7   0.6    3.2e-24   85.9   0.1    2.0  2  HEPN_AbiV  AbiV
     0.0074   16.2   0.0       0.18   11.8   0.0    2.9  3  DPPIV_rep  Dipeptidyl peptidase IV (DPP IV) low complexity re
  ------ inclusion threshold ------
      0.012   15.7   1.9       0.18   11.9   0.2    2.2  2  SDP_N      Sex determination protein N terminal
        1.7    9.7   4.3        1.4   10.0   0.3    2.8  4  RNase_J_C  Ribonuclease J C-terminal domain


Domain annotation for each model (and alignments):
>> HEPN_AbiV  AbiV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.1   7.2e-28   3.2e-24       4     155 ..      20     211 ..      17     217 .. 0.89
   2 ?   -0.6   0.0       0.3   1.3e+03      47      73 ..     213     242 ..     211     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 7.2e-28
                         HEPN_AbiV   4 egakalleNAeeLledAelLaengsyarAysLlilaiEElgKalllydalegfws.....edkdlkrlkkafrdHkk 75 
                                       + +k +++NAe+Ll+dA  L ++ s+++ ++L+ l++EE +K+++l+d+ +++++      +++ ++l k f++H++
  gi|518651943|ref|YP_008141463.1|  20 NDCKICMRNAERLLDDA--LNNDISIQTRTALMELSFEETAKSIFLFDYKRSDDHgqslvGGNVEETLIKIFQSHRI 94 
                                       56899************..**********************************99**999999************** PP

                         HEPN_AbiV  76 Khn.laylf...lkaftlllsaeesasfgaerldefeeliqleaeeela............................ 120
                                       K++ +++l+   +k++ +l  +e+s+++g +++d +++ ++  +  +++                            
  gi|518651943|ref|YP_008141463.1|  95 KIEiMKNLLddgSKKILTLDLNEYSSYIGGIIQDGMFGEKRDSRRIKISnerkiysseelsnsvkkmakdiidtmss 171
                                       ***888888***************9999999995554444444444444455666999999**************** PP

                         HEPN_AbiV 121 ...kklnllKnaglYVdldkng..issPseviskeaaeei 155
                                          k +n+lKn++lYV+ld ++  ++sP+   +k+++ +i
  gi|518651943|ref|YP_008141463.1| 172 qniKYYNDLKNESLYVGLDASTglLQSPPVPKNKKIVGYI 211
                                       ****************************999999887666 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.3
                         HEPN_AbiV  47 lllydalegfws...edkdlkrlkkafrdH 73 
                                       ++++ +l  +w+   e+k++k l +++++H
  gi|518651943|ref|YP_008141463.1| 213 FFIITQLIYQWDdfgEKKKVKNLLEKYKNH 242
                                       667777777777788999999999999999 PP

>> DPPIV_rep  Dipeptidyl peptidase IV (DPP IV) low complexity region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0     4e-05      0.18       8      20 ..      33      45 ..      33      45 .. 0.95
   2 ?    0.8   0.0      0.11   4.9e+02       1       9 [.     106     114 ..     106     114 .. 0.93
   3 ?   -2.9   0.0       1.7   7.5e+03       1       7 [.     144     150 ..     144     150 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4e-05
                         DPPIV_rep  8 LeDYlNntfrYKs 20
                                      L+D+lNn+++ ++
  gi|518651943|ref|YP_008141463.1| 33 LDDALNNDISIQT 45
                                      9*********997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.11
                         DPPIV_rep   1 dsrRtfTLe 9  
                                       +s++ +TL+
  gi|518651943|ref|YP_008141463.1| 106 GSKKILTLD 114
                                       79******8 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.7
                         DPPIV_rep   1 dsrRtfT 7  
                                       ++r+ ++
  gi|518651943|ref|YP_008141463.1| 144 NERKIYS 150
                                       6899998 PP

>> SDP_N  Sex determination protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2     4e-05      0.18      65     117 ..      53     106 ..       6     117 .. 0.86
   2 ?    3.2   0.1      0.02        88      99     128 ..     134     167 ..     126     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4e-05
                             SDP_N  65 stssaskseilsekLessdgtsplFkG.pegiqinateLrrikvdikrniptks 117
                                       s ++++ks  l++   s d+ + l  G +e++ i+  + +rik++i +n+  + 
  gi|518651943|ref|YP_008141463.1|  53 SFEETAKSIFLFDYKRSDDHGQSLVGGnVEETLIKIFQSHRIKIEIMKNLLDDG 106
                                       667899*******999999999999994577******************98765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                             SDP_N  99 ateLrrikvdikrniptksti....selkrdivn 128
                                       + + rrik++ +r+i  +++     + + +di++
  gi|518651943|ref|YP_008141463.1| 134 KRDSRRIKISNERKIYSSEELsnsvKKMAKDIID 167
                                       67889**********9988775444667788887 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   6.8e+03      12      23 ..      26      37 ..      23      60 .. 0.57
   2 ?   -2.0   0.0       1.7   7.8e+03      26      53 ..      81     108 ..      76     113 .. 0.69
   3 ?   10.0   0.3   0.00032       1.4      14      47 ..     150     183 ..     147     185 .. 0.94
   4 ?   -1.9   0.0       1.6   7.1e+03      14      25 ..     231     242 ..     218     248 .. 0.56

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                         RNase_J_C 12 vkeseeLieeak 23
                                      ++++e L+++a 
  gi|518651943|ref|YP_008141463.1| 26 MRNAERLLDDAL 37
                                      555555555543 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.7
                         RNase_J_C  26 vretieealeekesdwnelkrkirealk 53 
                                       v+et+ ++ ++++++ + +k+ + +  k
  gi|518651943|ref|YP_008141463.1|  81 VEETLIKIFQSHRIKIEIMKNLLDDGSK 108
                                       6677777777777777777777666555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00032
                         RNase_J_C  14 eseeLieeakkvvretieealeekesdwnelkrk 47 
                                        seeL +++kk+++++i++  +++++ +n+lk++
  gi|518651943|ref|YP_008141463.1| 150 SSEELSNSVKKMAKDIIDTMSSQNIKYYNDLKNE 183
                                       589****************************986 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 1.6
                         RNase_J_C  14 eseeLieeakkv 25 
                                       + ++L+e+ k++
  gi|518651943|ref|YP_008141463.1| 231 KVKNLLEKYKNH 242
                                       333444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1175  (0.0655363); expected 358.6 (0.02)
Passed bias filter:                      582  (0.0324614); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1724.81
//
Query:       gi|518651944|ref|YP_008141464.1|  [L=273]
Description: hypothetical protein FACI_IFERC00001G0583 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-23   83.9   0.0    2.3e-23   82.9   0.0    1.4  1  Aldose_epim  Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9   0.0   1.3e-27   2.3e-23       6     291 ..       5     261 ..       1     269 [. 0.74

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 1.3e-27
                                       EETTEEEEEECTCTTEEEEEEETT.STEESB-B-ST.HHHHHHSCCSSCEECSS-SEEETTEEEETTEEEECCCCBT CS
                       Aldose_epim   6 kngaglsakislyGAtllslkvpdkeqrevllgsdd.aeeylkdsyfgatlgrvanRianGeFeldGkpyqlpqnee 81 
                                          +++++ is+ GA + sl  ++    ++l + +d +e + +      +l+++a  +++++++++Gk+y lp+n  
  gi|518651944|ref|YP_008141464.1|   5 LE-NNSKVLISRKGAYVESLIING---INILKETNDnIEPHGG--L--SILIPYADIVSKATYKFNGKQYLLPKNAG 73 
                                       44.369******************...6888888882433443..3..799*************************9 PP

                                       ....TTCEETBSGGGSB-EEEEEEETTEEEEEEEEEEETCHCSTSEEEEEEEEEEETTEEEEEEEEEEESS.S-EEE CS
                       Aldose_epim  82 ....gknplHGgargreWeveevkeddgvtvslvlkpdgeegypgdlevrvtytLnednelkieyeatndg.kptpf 153
                                             n+ HG+  +++W+v +++ d+++ ++++l +  e+ yp +l + v y +++ + ++++y+++n g k++p+
  gi|518651944|ref|YP_008141464.1|  74 yegdLINSMHGLTLDQTWKVITKS-DKKIDFQVIL-N--ENFYPSKLLIDVIYMIDNAK-FSVDYSIKNIGdKSCPI 145
                                       998888****************99.6*********.3..445***************99.***************** PP

                                       EEEEEEEEETSSC.TCTGGEEEEEEEEEEEECTTSGEEEEEEECTTCCCCCCSSE.EHCSSETEEEEEEEESSCSEE CS
                       Aldose_epim 154 nltnHtYFnlsge.sidshelqieadeylevdeeliptgelkdvkgtpfdfrqpk.aigedlkglDhayllksklka 228
                                         ++H+YF  s   +++ h   ++     +++ ++i+t ++          ++    ++ +   +D+ay + +    
  gi|518651944|ref|YP_008141464.1| 146 MCGAHPYFIFSDYwKFEFHDAAVQ---LKRYNTKSITTQRI----------TDTIsNVPNK--LYDNAYFGGG---- 203
                                       ***********4453333333333...33344433443322..........3333033444..6888888888.... PP

                                       EEEETTTTEEEEEEEETTSSEEEEEECTTTTSEECCEEESSECTCETCCCECHHHT-EEEHTT CS
                       Aldose_epim 229 viidpdkksgiklevsttepalvvytgnflkkylsreglaletqmlpdepnhpefpsivlkpG 291
                                       ++  + k  ++++ ++ ++p + +y+g    +y+ + ++a+e+       ++++ ++ +lk++
  gi|518651944|ref|YP_008141464.1| 204 IVDFYTKYLKMEI-IRYNMPFFEIYNG----TYAGQNSVAFEPLTGAPNCFNNGMGLKTLKQN 261
                                       5555555555555.4555668888888....56666666666666666666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       350  (0.0195214); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1934.60
//
Query:       gi|518651945|ref|YP_008141465.1|  [L=392]
Description: hypothetical protein FACI_IFERC00001G0584 [Ferroplasma acidarmanus fer1]
Scores for complete 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   32.9   1.6    3.1e-07   29.7   1.6    2.6  1  SelA             L-seryl-tRNA selenium transferase
    1.5e-06   27.0   0.1    2.2e-06   26.4   0.1    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    0.00026   20.1   0.2    0.00034   19.7   0.2    1.2  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.6   5.2e-11   3.1e-07      56     308 ..      55     306 ..      11     362 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 5.2e-11
                                       HHHHHT-SEEEEES-HHHHHHHHHHH.HHBTSEEEEETTSGTEETT......TE..EHHH...HHHHHTBEEEEESB CS
                              SelA  56 lkeltgaedalvvnnnaaavllvLnt.laagkeviisrGeLveiGG......sf..riPd...vmkkaGvkLvevGt 120
                                       + + +g e+a + n  aaa++l +++ + + k  +    +L e+G       +f  +i +   ++k +G+k++e+Gt
  gi|518651945|ref|YP_008141465.1|  55 IAKSMGVESAYITNGAAAAIVLSVAScIVKSKPGLK--YKLPELGRdekfvlTFknQISEfkyLIKLTGAKIKEIGT 129
                                       455678999999999999988877662456666553..34444443111111231156654447999********** PP

                                       SSB--HHHHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEEEES-B-S-GGGGT-----BHH CS
                              SelA 121 tnkthlkDyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleDlGsGllvdlseyglskePtvq 197
                                       +  t    ++ka+++ +     v    ++ e   ++++++++v++++ +g+pv+ D+ +          ++   +++
  gi|518651945|ref|YP_008141465.1| 130 AKDTSELSFKKALKKFADKT--VAIVYFAFEPLRESLKIEDVVSITHSFGIPVIVDAAAE---------VPPIYNFK 195
                                       *************9877654..445679999*************************8653.........45556788 PP

                                       HHHHTT-SEEEEETTSTT-S.SS-EEEEE-HHHHHHHHHS.THHHHTB--HHHHHHHHHHHHHHH..TT-GGGSHHH CS
                              SelA 198 ealaeGvdlvsfsGDkllGg.pqaGiivGkkelieklkkn.plkraLrvDkltlaaleatlrlyldpeklaeklptl 272
                                         l++G+d+v  sG k +G+    G+++Gkke+ie  k+  p +  +   + +  ++  t+++   ++  a ++++ 
  gi|518651945|ref|YP_008141465.1| 196 RYLEAGADIVILSGGKAIGSfSDTGLMLGKKEIIEIAKEIgPHSEEISNSR-NTIFIGRTMKVSK-EDIVATTVAVD 270
                                       899****************94579**********97765313333333333.3335556666554.55666666666 PP

                                       HHHH--HHHHHHHHHHHHHHHTTSTT..EEEEEEEE CS
                              SelA 273 rlltqkleelrakaerlqkelkealgselevkvvks 308
                                       ++l+ +++e  +  +   ke+ + lg++ +++++k 
  gi|518651945|ref|YP_008141465.1| 271 KFLKLNESEFMNDMNTKCKEIIDILGNNTSIRIKKI 306
                                       666665555555555555566666666666665554 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 !   26.4   0.1   3.8e-10   2.2e-06     113     209 ..     125     220 ..     110     277 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 3.8e-10
                                       HHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHT...TTS-GGG CS
                   Cys_Met_Meta_PP 113 kklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvvDntfasp...llqrplk 186
                                       k++g   +  + s  ++l+k  ++ + +vy+     pl + + ie++++++++ g++v+vD++   p    + r l+
  gi|518651945|ref|YP_008141465.1| 125 KEIGTAKDTSELSFKKALKKFADKTVAIVYFA--FEPLRESLKIEDVVSITHSFGIPVIVDAAAEVPpiyNFKRYLE 199
                                       5666677777888899999999999999**95..68****************************99977335678** PP

                                       GT-SEEEEETTTTTTCSSS--EE CS
                   Cys_Met_Meta_PP 187 lgaDivvhSaTKylgGhsdvvaG 209
                                        gaDiv+ S+ K +g  sd+  G
  gi|518651945|ref|YP_008141465.1| 200 AGADIVILSGGKAIGSFSDT--G 220
                                       **************998885..4 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   5.7e-08   0.00034      85     225 ..      96     236 ..      29     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.7e-08
                                       -TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEE.EBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHH CS
                       Aminotran_5  85 lkpgdeivvteaehhanlvpwqelakrtgakvkvi.pldeegeldldelekllnektklvaithvsnvtGtiqpvee 160
                                       l +++++v+t  +  +++   + l k tgak+k i +++++ el  +++ k+ ++kt ++ + + +        +e+
  gi|518651945|ref|YP_008141465.1|  96 LGRDEKFVLTFKNQISEF---KYLIKLTGAKIKEIgTAKDTSELSFKKALKKFADKTVAIVYFAFEPLR-ESLKIED 168
                                       677778888888888888...888899********8889999********************9999887.6678999 PP

                                       HHHHHHHTT-EEEEE-TTTTTTS--..-HHHHTESEEEEETTTTTSS.TT-EEEEEEHHHHHTS..SS CS
                       Aminotran_5 161 igklakkkgalvlvDaaqavghipi..dvkklgvDflafsghKllgP.tGiGvlyvrkelleklepll 225
                                       ++++ +  g+ v+vDaa+ v+ i       + g+D++ +sg K +g  + +G++ ++ke++e ++ + 
  gi|518651945|ref|YP_008141465.1| 169 VVSITHSFGIPVIVDAAAEVPPIYNfkRYLEAGADIVILSGGKAIGSfSDTGLMLGKKEIIEIAKEIG 236
                                       99999***************987531134578***********7776367999999999988886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2604.53
//
Query:       gi|518651946|ref|YP_008141466.1|  [L=261]
Description: polyketide synthase chain 7 related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-49  168.7   0.0    2.1e-49  168.2   0.0    1.1  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    6.6e-39  133.4   0.0      8e-39  133.1   0.0    1.1  1  adh_short     short chain dehydrogenase
    6.9e-07   29.3   0.4    4.1e-06   26.8   0.4    1.9  1  KR            KR domain
  ------ inclusion threshold ------
      0.047   13.1   0.1      0.092   12.1   0.0    1.4  2  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 !  168.2   0.0   4.7e-53   2.1e-49       4     233 ..      21     258 ..      16     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 4.7e-53
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                       +gIG+ai  +l + G++v   d +  +  ++++  + ++++v  +    ++ +++e+l++ + +k  ++D+lvnnag
  gi|518651946|ref|YP_008141466.1|  21 QGIGKAIISQLISSGCKVYTIDPKFPN--TLDDKFT-VNKNVirYSGYTSNSDDMENLFQYIYSKESRVDFLVNNAG 94 
                                       8******************99998887..3443333.33444489999***************************** PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealtr 153
                                       i     +++++ s ++f+++++ n+ + f+++k++ +l+k++   sivn++sv+++r+ ++++ y+++K+a  a+t+
  gi|518651946|ref|YP_008141466.1|  95 IYFY--KDIENSSLQDFNNIVSANILGEFNMTKYCTKLLKNSthPSIVNIASVSGQRTEEGHTLYSTTKGATLAFTK 169
                                       ****..*******************************9998889********************************* PP

                                       HHHHHHGGGTEEEEEEEE--BHCTG.......GGGSTT..HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT CS
                      adh_short_C2 154 ylAvelgpkgiRvNavspgpikTla.......asgikg..fdelleelearaplgrlgtpeevaeaalfLasdeasy 221
                                       +lA+++g+++iRvN+vspg ikT++       +s+ikg  f e ++e  +++ l+r gt++eva+++lfL+s +++y
  gi|518651946|ref|YP_008141466.1| 170 ALAADFGKYKIRVNSVSPGNIKTPMndldieaQSKIKGrsFAETEKEYSSESILRRRGTADEVASVVLFLLSSASNY 246
                                       ***********************98433333235677688999********************************** PP

                                       --SEEEEESTTG CS
                      adh_short_C2 222 itGqtlvvDgGl 233
                                       i+G+++++DgGl
  gi|518651946|ref|YP_008141466.1| 247 INGEDIIIDGGL 258
                                       ***********7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.1   0.0   1.8e-42     8e-39       2     188 ..      13     196 ..      12     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1.8e-42
                                       EEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSE CS
                         adh_short   2 vvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkl 78 
                                       +++v G+ +GIG+ai  +l+++G+kv+ +d +  +   + +++   +++++ +++  ++++++e+l++ + +k  ++
  gi|518651946|ref|YP_008141466.1|  13 IAVVSGGFQGIGKAIISQLISSGCKVYTIDPKFPNT--LDDKFTV-NKNVIRYSGYTSNSDDMENLFQYIYSKESRV 86 
                                       799************************999886655..5555554.467999999999******************* PP

                                       SEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHH CS
                         adh_short  79 dvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaa 155
                                       d LvnNAGi   +++++ s ++++++++ N+ g f++t+ +++ ++++   +Ivn++Sv g+   +g + Ys++K+a
  gi|518651946|ref|YP_008141466.1|  87 DFLVNNAGIYFYKDIENSSLQDFNNIVSANILGEFNMTKYCTKLLKNSTHPSIVNIASVSGQRTEEGHTLYSTTKGA 163
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 156 vagltrslakelaptgirvnavaPGlvdTdmak 188
                                         ++t++la ++ +++irvn+v PG ++T+m+ 
  gi|518651946|ref|YP_008141466.1| 164 TLAFTKALAADFGKYKIRVNSVSPGNIKTPMND 196
                                       *******************************96 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.4   9.1e-10   4.1e-06       4     155 ..      15     163 ..      12     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 9.1e-10
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++ GG+ g+G++++ +l+++g +   +  +  +++ d+k         + +v  ++   s++d++e+l++ i ++e+
  gi|518651946|ref|YP_008141466.1|  15 VVSGGFQGIGKAIISQLISSGCKVYTIDPKF-PNTLDDK------FTVNKNVIRYSGYTSNSDDMENLFQYIYSKES 84 
                                       799******************9866555555.3222222......23345777778888****************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaN 153
                                       ++   ++ Ag+   k +e+ + +d+++++++ + G  n+ +++++    ++   +v ++S++g   + g++ Y+++ 
  gi|518651946|ref|YP_008141466.1|  85 RVDFLVNNAGIYFYKDIENSSLQDFNNIVSANILGEFNMTKYCTKllknSTHPSIVNIASVSGQRTEEGHTLYSTTK 161
                                       ***************************************999988776577788999*************9998765 PP

                                       HH CS
                                KR 154 af 155
                                         
  gi|518651946|ref|YP_008141466.1| 162 GA 163
                                       44 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 ?   -2.7   0.0      0.68     3e+03     214     236 ..      59      81 ..       3      86 .. 0.57
   2 ?   12.1   0.0     2e-05     0.092     105     204 ..      98     194 ..      92     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 0.68
                           DUF1776 214 svagsevlsWsesaralygpnyv 236
                                        +  s   s s+++++l++ +y+
  gi|518651946|ref|YP_008141466.1|  59 VIRYSGYTSNSDDMENLFQYIYS 81 
                                       33333334456666666666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 2e-05
                           DUF1776 105 tgpietiplsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevL 181
                                       +  ie+ +l+ +++ +  ++l  + +++   +ll++        iv  +s+s +     h + +++ +a  a++++L
  gi|518651946|ref|YP_008141466.1|  98 YKDIENSSLQDFNNIVSANILGEFNMTKYCTKLLKN---STHPSIVNIASVSGQRTEEGHTLYSTTKGATLAFTKAL 171
                                       556899999**************************8...5566677789**************************** PP

                           DUF1776 182 krelrphnidvtqikLGnldlan 204
                                       +++ ++++i v  +  Gn++   
  gi|518651946|ref|YP_008141466.1| 172 AADFGKYKIRVNSVSPGNIKTPM 194
                                       ******************98755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1796.96
//
Query:       gi|518651947|ref|YP_008141467.1|  [L=492]
Description: hypothetical protein FACI_IFERC00001G0586 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   57.0  63.1    1.4e-15   57.0  63.1    2.0  2  AA_permease_2  Amino acid permease
    2.5e-09   36.3  72.1      7e-09   34.8  72.1    1.7  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 !   57.0  63.1   1.6e-19   1.4e-15       1     371 [.      20     387 ..      20     391 .. 0.75
   2 !    3.5   5.8    0.0028        25     297     376 ..     391     470 ..     385     478 .. 0.89

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 1.6e-19
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgk 74 
                                       ++l++++al++gs++ + + v+n   ++ ++g a+ ++ +ia+ ++ l+v+   + +s   +  gG y+++++a   
  gi|518651947|ref|YP_008141467.1|  20 IGLWTLVALSMGSIYPLSFAVSNgasAVVYAGFAAPVVPLIAAAAI-LIVSVPAMLFSKYVSFAGGYYGFAEKAL-- 93 
                                       79************88777777767667789***999999999998.5666665668999************777.. PP

                     AA_permease_2  75 kvaflsawfn...wfayvpvlasilsvaasyllnalgpdlqgntw...ltyliaiaililvalinirgikesakiqn 145
                                        v  l+   n   w++++  +  +++va+sy+l+ + + +++ t    l+++ia + + + +++++++ik s+k   
  gi|518651947|ref|YP_008141467.1|  94 -VEVLVIHGNddlWYFIMMDV--VSVVAVSYILSTALSAIYNYTLpiyLYIIIALIATFVMFIFTVFNIKMSGKSVI 167
                                       .55666666654577777655..566666666665444444444400055555555555556666677766666555 PP

                     AA_permease_2 146 ilgilkillpliiliilglitvdgggfsslstetdtffpngwpg.vllgllivlwsfdGfesaanvsee..vkkkdv 219
                                        ++ + + +++ii  ++++i   +++f+     +    p g +g +l+++++ ++ f+G+ +  +++ee   +k+ v
  gi|518651947|ref|YP_008141467.1| 168 LVVAIQV-IIVIIYSLIVIIRTPFNTFQ---AFNIARAPAGISGvMLAAITGGFLFFTGYGAPFYFAEEshTPKRIV 240
                                       5555555.44444554444444555555...223335555888868***********************7666677* PP

                     AA_permease_2 220 pkaifigllivlvlyllvniaflgvvpddeianlsn.lgsvaalffeavggkvvaiivvilialsllgaintavigs 295
                                        k  ++++++ +++ +lv+ a + +v+ ++ ++l++ ++ ++ +f+   g +++  i+ i++  + ++a+    ++ 
  gi|518651947|ref|YP_008141467.1| 241 WKSVILSIILLTIVSVLVTYAEVVAVGLSNSSSLATdWNPAVVAFLPFIG-SIGVLIFLIIALTGQVWAGVVGGMSG 316
                                       *******************9999999998887777635544455555555.88888888888888888888888999 PP

                     AA_permease_2 296 srvlealardgvlP.rffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigal 370
                                       +r+++++ard ++  ++fa  n  +++p+ a  + + +++il++++ l       +l+s++ +++ i+y l+++gal
  gi|518651947|ref|YP_008141467.1| 317 ARLIYSMARDEFFFpKRFATLNkSRKTPVIAALFELAITSILSIISPL-------ILVSIYGYANGIFYSLFLFGAL 386
                                       9*********98877*******77***************999987766.......8*******************98 PP

                     AA_permease_2 371 i 371
                                        
  gi|518651947|ref|YP_008141467.1| 387 T 387
                                       5 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.0028
                     AA_permease_2 297 rvlealardgvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilr 373
                                        +++ l+ d +lP f++k+     +i  i lt++ ++i + lf +a+ + y  + + + +g++++++l++++ +++ 
  gi|518651947|ref|YP_008141467.1| 391 WIIQHLIADAALPFFLHKIGTSIFTIKNILLTMVTTIIAGGLFVYADIEGYIGIGEPYLFGFVLMVILIVFSIIYIA 467
                                       57899999************9999***********************999***************999999999988 PP

                     AA_permease_2 374 kkr 376
                                       +k 
  gi|518651947|ref|YP_008141467.1| 468 VKY 470
                                       775 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8  72.1   7.8e-13     7e-09       3     468 ..      26     470 ..      24     474 .. 0.75

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 7.8e-13
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       +  ++g++ ++ + v++g  +    + +a ++ l+a + i++v +    ++ +++ +gg+y +a++ l + l    +
  gi|518651947|ref|YP_008141467.1|  26 VALSMGSIYPLSFAVSNGASAVVYAGFAAPVVPLIAAAAILIVSVPAMLFSKYVSFAGGYYGFAEKALVEVLVIHGN 102
                                       5679*************977666666699*******************************************99999 PP

                       AA_permease  80 lnylfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilalikii 148
                                         +++ +i+   + ++a+s++++ +  ++++   +          +++ ++v++i++++++k++g+    ++l++ i
  gi|518651947|ref|YP_008141467.1| 103 DDLWY-FIMMDVVSVVAVSYILSTA--LSAIY-NYTLpiylyiiiALIATFVMFIFTVFNIKMSGK---SVILVVAI 172
                                       77443.3344444444445554444..33333.222234445668999******************...34444444 PP

                       AA_permease 149 aiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEv 225
                                        +i++ii + i++    ++++++f+ ++ +        p+g           +++++   ++ ftG+++  + a+E+
  gi|518651947|ref|YP_008141467.1| 173 QVIIVIIYSLIVI---IRTPFNTFQAFNIAR------APAG-------ISGVMLAAITGGFLFFTGYGAPFYFAEES 233
                                       4444444442222...223331222222222......2444.......233566777788999************** PP

                       AA_permease 226 kdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaals 302
                                         P++ + k+++  +i++ti+ vl++++ ++ v+ ++ ++l+   ++   +v f+ + g++++  ++++++ ++++ 
  gi|518651947|ref|YP_008141467.1| 234 HTPKRIVWKSVILSIILLTIVSVLVTYAEVVAVGLSNSSSLATDWNP--AVVAFLPFIGSIGVLIFLIIALTGQVWA 308
                                       ******************************************88877..***************************9 PP

                       AA_permease 303 sansslysasRvlyslakdgl.aPkvlkkvsk.rgvPlraillsmiisllal....llaslnlaapivfnfllaisa 373
                                        +++++ s+ R++ys+a+d+  +Pk ++ ++k r+ P+ a l+ ++i  ++     l+  +  +  ++  ++ ++  
  gi|518651947|ref|YP_008141467.1| 309 GVVGGM-SGARLIYSMARDEFfFPKRFATLNKsRKTPVIAALFELAITSILSiispLILVSIYG--YANGIFYSLFL 382
                                       999986.899*********97257777777772578*999887666655554355555555555..66666666666 PP

                       AA_permease 374 liglivwlliilsyl.rfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasf 449
                                       + +l +++ ii  ++      ++++++ ++ + +k  ll + + ++   l  ++ i +++ +           +   
  gi|518651947|ref|YP_008141467.1| 383 FGALTTFMWIIQHLIaDAALPFFLHKIGTSIFTIKNILLTMVTTIIAGGLFVYADIEGYIGIGE--------PYLFG 451
                                       6666666666655554455558888888888888888888888888888888888888887766........46667 PP

                       AA_permease 450 aaaylivllfliilvgvkl 468
                                       + + +i+++f ii+++vk+
  gi|518651947|ref|YP_008141467.1| 452 FVLMVILIVFSIIYIAVKY 470
                                       8888888999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1452  (0.0809861); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); 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):               2  [number of targets reported over threshold]
# CPU time: 0.87u 0.32s 00:00:01.19 Elapsed: 00:00:00.49
# Mc/sec: 3001.15
//
Query:       gi|518651948|ref|YP_008141468.1|  [L=230]
Description: hypothetical protein FACI_IFERC00001G0587 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-16   60.4   0.0    1.8e-16   59.6   0.0    1.4  1  HTH_10        HTH DNA binding domain
  ------ inclusion threshold ------
      0.051   13.3   0.1        0.1   12.3   0.1    1.5  1  Sigma70_r4_2  Sigma-70, region 4
      0.074   13.0   2.9        1.1    9.3   0.2    2.3  2  DUF1160       Protein of unknown function (DUF1160)
       0.13   12.3   0.1       0.45   10.5   0.0    2.0  2  HTH_11        HTH domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0     4e-20   1.8e-16       1      52 [.     167     218 ..     167     219 .. 0.99

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 4e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+++  ++++A+  G+Fd P+++++k++Akel+Is  ++ ++Lr ae+k++
  gi|518651948|ref|YP_008141468.1| 167 LTEQEKITIQIALSCGFFDNPKKCHIKDIAKELDISTVAADKYLRDAEKKIM 218
                                       9**************************************************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 ?   12.3   0.1   2.2e-05       0.1      29      54 .]     192     217 ..     189     217 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.2e-05
                                       HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  29 ykEIAellgisegtVksrlsRArkkL 54 
                                       +k+IA++l+is ++ +++l+ A kk+
  gi|518651948|ref|YP_008141468.1| 192 IKDIAKELDISTVAADKYLRDAEKKI 217
                                       69********************9996 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.2   0.00024       1.1      43     100 ..      33      91 ..       7      99 .. 0.84
   2 ?    4.2   0.3    0.0089        40      60     106 ..     109     158 ..      92     176 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00024
                           DUF1160  43 lkmFiereievediyeiveavdgi.kLtkkQidylvkqvyenekiisilqkfvdeqrLt 100
                                       +k+F++  i +++ + +    d     t+k++ ++++++ +n +i+s+ ++f +++ L+
  gi|518651948|ref|YP_008141468.1|  33 IKLFLTTSIAMKSNKYLFTIEDYYpINTNKKVSFIISNLKKNPSIVSMENSFLEGRMLR 91 
                                       6999999999999999998888885558899***********************99885 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0089
                           DUF1160  60 veavdgikLtkkQidylvkqvyen...ekiisilqkfvdeqrLtddeisd 106
                                       +  ++  +++++ idy+   + e+   ++ii+il++  + ++L++ +i++
  gi|518651948|ref|YP_008141468.1| 109 LGVINYREISQSGIDYISFLLPEEsniKQIIDILNSIGKITNLEKHKIDE 158
                                       55555556777777776555544411145566666666666666666655 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1         2     9e+03      36      43 ..     139     146 ..     135     151 .. 0.57
   2 ?   10.5   0.0    0.0001      0.45      17      41 ..     191     215 ..     183     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2
                            HTH_11  36 IkaLeelg 43 
                                       I++L+++g
  gi|518651948|ref|YP_008141468.1| 139 IDILNSIG 146
                                       55566555 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.0001
                            HTH_11  17 sgeeLAeeLnvSrrtvrrdIkaLee 41 
                                        ++++A+eL++S+ +  +++++ e+
  gi|518651948|ref|YP_008141468.1| 191 HIKDIAKELDISTVAADKYLRDAEK 215
                                       5799***************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1669.78
//
Query:       gi|518651949|ref|YP_008141469.1|  [L=399]
Description: allantoate amidohydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-26   90.7   0.0    1.3e-25   90.3   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.1e-05   25.3   0.0    1.9e-05   24.5   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.059   13.5   0.0       0.11   12.6   0.0    1.5  1  DUF2959        Protein of unknown function (DUF2959)


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 !   90.3   0.0   2.2e-29   1.3e-25       1     207 []      71     398 ..      71     398 .. 0.91

  Alignments for each domain:
  == domain 1  score: 90.3 bits;  conditional E-value: 2.2e-29
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.. 75 
                                       ++gsH+D+Vp    +g           G+++G       +gv++++++l+ l  +    +++i+ + +++EEg+r  
  gi|518651949|ref|YP_008141469.1|  71 AIGSHMDSVP----NG-----------GRFDGF------YGVMSGMQLLKDLGSTLK--NRKITAIDFTNEEGARfq 124
                                       589*******....88...........999999......************999973..89***********99999 PP

                                       ...THH....HHHHHHHHT...............................TTCESEEEEEEEESSSBTCHSTETEEE CS
                                       ...xxx....xxxxxxxxx...............................xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20  76 ...gGa....kalleglee...............................rekvdavfelhieepgileagklaigv 114
                                           G+    + +++   e                               ++++  ++elhie++++le ++ +ig+
  gi|518651949|ref|YP_008141469.1| 125 pslLGSgistGVFTK---EfaysrkdsdgitfedaleksgymgeeqnrvkNQDISRYIELHIEQGPVLELENYQIGI 198
                                       999555113244444...1334456777777778999999999999999999*****************99977777 PP

                                       E............................................................................ CS
                                       x............................................................................ RF
                     Peptidase_M20 115 v............................................................................ 115
                                                                                                                    
  gi|518651949|ref|YP_008141469.1| 199 Pkgivtmvvdnisftgesnqagptpmkvrkdalvaasrftvavrdiakssgkeltmtigkinnfpnaynvipgkvtm 275
                                       79999************************************************************************ PP

                                       ................................EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSB CS
                                       ................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ................................kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpgg 160
                                                                        v+++  +  + + ++ ++++k + +++++l ++k+++  s   g
  gi|518651949|ref|YP_008141469.1| 276 nldtrspdkktaeeyskmakeiseriaseegvPVDFKNQWTTETTLFD-EDMRKEIIKSCRAL-NLKYKELYSW-PG 349
                                       *****************************9877888888888888888.*************9.9998888899.9* PP

                                       HTHHHHTTT.EEEEEEESS.GGCTTSTTTEEEHHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 161 tdarffagi.ptvmifgpg.sglaHspnEyvdledlekgikvlarllee 207
                                       +da++++++ pt+mif p+ +g++H+ +Ey +++dl +g+ vl+r++e+
  gi|518651949|ref|YP_008141469.1| 350 HDAQYMNRVvPTAMIFIPShNGRSHTKEEYSSDRDLINGYSVLKRTVEN 398
                                       ******9999*******9956************************9986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   3.3e-09   1.9e-05       4     106 ..     200     303 ..     199     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.3e-09
                                       -EEEEEEEE...EE-B-EEGG.-TTTTB-.HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C.CCCEESS CS
                         M20_dimer   4 kGlaggkit...vkgkagHsg.apgagaN.AieklarllaeledeegdiaeerslprttlnvtgiegGs.aknvipd 74 
                                       kG++++ +    ++g++  +g  p +++  A+ +++r+  + +d  ++     s ++ t++++ i+    a nvip+
  gi|518651949|ref|YP_008141469.1| 200 KGIVTMVVDnisFTGESNQAGpTPMKVRKdALVAASRFTVAVRDIAKS-----SGKELTMTIGKINNFPnAYNVIPG 271
                                       78888888888899*******988887756***************776.....55************77******** PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilekeap 106
                                       ++++++d R +++ ++ee  +  +ei e+ a 
  gi|518651949|ref|YP_008141469.1| 272 KVTMNLDTRSPDKKTAEEYSKMAKEISERIAS 303
                                       ************************99998876 PP

>> DUF2959  Protein of unknown function (DUF2959)
   #    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      61     127 ..     285     350 ..     243     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.9e-05
                           DUF2959  61 keyeesekaaeevrerieaveevaealfkeWeeeldqyssaslrreSeqklketrkkykellkamkk 127
                                       k+ ee +k a+e++eri++ e v  ++ ++W++e + +++ ++r+e  +  ++ + kykel +   +
  gi|518651949|ref|YP_008141469.1| 285 KTAEEYSKMAKEISERIASEEGVPVDFKNQWTTETTLFDE-DMRKEIIKSCRALNLKYKELYSWPGH 350
                                       556777899*************************999865.68888888899999999999876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.54
# Mc/sec: 2217.25
//
Query:       gi|518651950|ref|YP_008141470.1|  [L=437]
Description: hypothetical protein FACI_IFERC00001G0589 [Ferroplasma acidarmanus fer1]
Scores for complete 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-86  288.2   0.0    9.9e-86  287.9   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
       0.13   12.1   0.0        0.3   10.9   0.0    1.6  1  NifZ         NifZ domain


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.9   0.0   1.1e-89   9.9e-86       8     406 .]      41     434 ..      37     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 287.9 bits;  conditional E-value: 1.1e-89
                                       -SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT CS
                       Aminotran_3   8 nlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklap 84 
                                        ++++i++ae++ ++d dg+ ++D vs+i+v+nlG++  ++ kavk+q+++++h     + +e  +++ e l + +p
  gi|518651950|ref|YP_008141470.1|  41 SFPIAIKRAENSLIEDLDGNIFIDWVSGISVLNLGFN-DNIRKAVKNQVDDIWHAL--EIPTEVRINFLEALRNSFP 114
                                       46699******************************96.68***************9..8888999************ PP

                                       -..S..EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEE CS
                       Aminotran_3  85 kgld..kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvr 159
                                        ++   k+++  sG++A etA+ +a +      +++ + +iaf+ga+HG   g +++t+   ky++ + +   +v+r
  gi|518651950|ref|YP_008141470.1| 115 PEMRnyKTIFGISGADACETAINIAHA-----IRKKNAPTIAFEGAYHGVSGGIIAATAG-RKYREAVYSDGFKVIR 185
                                       9998899******************99.....45567889********************.**************** PP

                                       E-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTT CS
                       Aminotran_3 160 lkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqt 236
                                       ++yp++   ++  +   ++++++ +  ++  d    vivEp+qgegG++v++++fl+++re+c+++d  +ivDEvq+
  gi|518651950|ref|YP_008141470.1| 186 VPYPYKLWYDYDVSDIISIMKKIMDDGEAGYDRPDSVIVEPVQGEGGYIVPPDGFLKAIREFCTEYDLTMIVDEVQS 262
                                       *****99999999888888888888789999********************************************** PP

                                       TTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTH CS
                       Aminotran_3 237 GfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekl 313
                                       G+GrTGk++A e+ +++pD+++++K+++gGlp+s v  +++  + l +  h +T+ +npla+a+ + v++ +   k+
  gi|518651950|ref|YP_008141470.1| 263 GVGRTGKMWAFEYENITPDIVCVSKSIGGGLPVSLVYYRDDYDKKLPKPFHLGTYRANPLAMAAGITVINEV--PKY 337
                                       **********************************************9999**************99999866..79* PP

                                       HHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETT..TEEEE CS
                       Aminotran_3 314 lenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGd..nvirl 384
                                        ++++  g+++ ++ ++++++   i+evRgkG mi+iel+++ +  +     e+ ++++++G+l+ ++G+  nv r+
  gi|518651950|ref|YP_008141470.1| 338 FDKVKSSGKEMLNKFNKIDSN--LIGEVRGKGYMIGIELVDNGKPVNskhmMELKHELLKNGLLMHTCGHygNVFRF 412
                                       ******************955..8*****************98844368898999********************** PP

                                       ---TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 385 lppliitdeeidelleilkkal 406
                                       + +l i++e ++ ++ei++ka+
  gi|518651950|ref|YP_008141470.1| 413 MGALNIEEELLNRGVEIFSKAV 434
                                       *******************986 PP

>> NifZ  NifZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   3.3e-05       0.3       3      46 ..     195     240 ..     194     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.3e-05
                              NifZ   3 kfevgdkVraakdirNDGtfpgkeigelLvk..kGdvGvvvsvGtf 46 
                                        ++v d + + k+i +DG+    ++++++v+  +G+ G++v    f
  gi|518651950|ref|YP_008141470.1| 195 DYDVSDIISIMKKIMDDGEAGYDRPDSVIVEpvQGEGGYIVPPDGF 240
                                       59999*************************8557******976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2890.04
//
Query:       gi|518651951|ref|YP_008141471.1|  [L=150]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-10   39.6   0.0    6.2e-10   38.8   0.0    1.5  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.1e-09   37.7   0.2    2.6e-09   36.5   0.2    1.7  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.4e-08   33.8   0.2    3.6e-08   33.3   0.2    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.047   13.6   0.1      0.093   12.7   0.1    1.5  1  HTH_11          HTH domain
      0.057   13.3   0.0       0.22   11.4   0.0    2.0  2  MarR_2          MarR family
      0.084   12.7   0.0       0.19   11.5   0.0    1.5  1  LexA_DNA_bind   LexA DNA binding domain


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 !   38.8   0.0   2.1e-13   6.2e-10       1      42 []       1      43 [.       1      43 [. 0.97

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 2.1e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGl.SestvlrRvrrLe 42
                                      +D +D+kIL++L +d+R + +e+++ +G+ S+s++ rR++ ++
  gi|518651951|ref|YP_008141471.1|  1 MDSFDLKILKELSKDSRKPLREIGKSIGIySPSAISRRIKEMQ 43
                                      9***************************98**********995 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.2   8.6e-13   2.6e-09       1      48 []       1      49 [.       1      49 [. 0.97

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 8.6e-13
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlgl.SpstvnrrlkrLeeeGlIk 48
                                      +d  d+kIL++L k++r + re+ + +g+ Sps+++rr+k+++++ lIk
  gi|518651951|ref|YP_008141471.1|  1 MDSFDLKILKELSKDSRKPLREIGKSIGIySPSAISRRIKEMQKDKLIK 49
                                      7999************************989***************997 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 !   33.3   0.2   1.2e-11   3.6e-08      11      74 ..      77     139 ..      69     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.2e-11
                                       THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  11 eqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       e+++ ++e++ +++ V+ +  + Gd d+ + +++r+ +++ ++l+e l ++ +++r++t+ vl+
  gi|518651951|ref|YP_008141471.1|  77 EYHDIVAEKIMKIKGVIDVLFLLGDIDFYILCATRNKDDYVNILDE-LEKIMEIERSDTHTVLN 139
                                       7899******************************************.***************97 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.1e-05     0.093       3      41 ..       6      44 ..       5      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.1e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnv.SrrtvrrdIkaLee 41
                                      l+il+ L ++++  +  e+ + +++ S +++ r+Ik++++
  gi|518651951|ref|YP_008141471.1|  6 LKILKEL-SKDSRKPLREIGKSIGIySPSAISRRIKEMQK 44
                                      589****.888889***********************976 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   7.5e-05      0.22      33      52 ..      30      49 ..       9      54 .. 0.91
   2 ?   -0.9   0.0      0.54   1.6e+03      11      36 ..     107     132 ..      93     140 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.5e-05
                                      SSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 33 lsksavsrilkrLvaaGLve 52
                                      +s+sa+sr++k++++  L+ 
  gi|518651951|ref|YP_008141471.1| 30 YSPSAISRRIKEMQKDKLIK 49
                                      599***************95 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.54
                                       HHHHHCTTTS.EEEHHHHHHHHTSSHH CS
                            MarR_2  11 LaaLgrrpgr.dltvgelarrlglsks 36 
                                       L a ++ +++ +    el++ + +++s
  gi|518651951|ref|YP_008141471.1| 107 LCATRNKDDYvN-ILDELEKIMEIERS 132
                                       444444443321.33455555555555 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.2e-05      0.19      28      52 ..      20      44 ..       8      51 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                      HHHHHHHHTS-.HHHHHHHHHHHHH CS
                     LexA_DNA_bind 28 ireiaralglkSpsaveehLkaLer 52
                                       rei++ +g+ Spsa+  + k +++
  gi|518651951|ref|YP_008141471.1| 20 LREIGKSIGIYSPSAISRRIKEMQK 44
                                      69*****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.32s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 952.75
//
Query:       gi|518651952|ref|YP_008141472.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G0591 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 508.48
//
Query:       gi|518651953|ref|YP_008141473.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G0592 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 530.66
//
Query:       gi|518651954|ref|YP_008141474.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G0593 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.039   13.8   0.0       0.04   13.7   0.0    1.1  1  VID27_N   VID27 N-terminal region


Domain annotation for each model (and alignments):
>> VID27_N  VID27 N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.3e-06      0.04      93     149 ..      14      70 ..       3      74 .] 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.3e-06
                           VID27_N  93 kvflldeeLkfrveekedgekvlaWrdlsgdegdlyeFvvdesvkeeevkqfelvay 149
                                         +l +++ +++v  ++++ +v++ ++l+   gdl++Fv+++s+++++ ++  ++++
  gi|518651954|ref|YP_008141474.1|  14 LEYLYQDSYQLNVPYESKKCQVFVNNQLRWKRGDLFRFVISRSIESTNNRAVRQIVT 70 
                                       45667777777777777899************************9999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 554.14
//
Query:       gi|518651955|ref|YP_008141475.1|  [L=474]
Description: major facilitator superfamily MFS_1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-42  146.2  29.2    1.6e-42  145.9  29.2    1.1  1  Sugar_tr  Sugar (and other) transporter
    3.8e-27   95.2  78.7      2e-23   82.9  43.2    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.9  29.2   1.8e-46   1.6e-42      36     447 ..      44     471 ..      23     474 .] 0.82

  Alignments for each domain:
  == domain 1  score: 145.9 bits;  conditional E-value: 1.8e-46
                                       -SHHHHHH.............HHHHHHHTHHHHHH.HHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS CS
                          Sugar_tr  36 ksksskee..........ssvlsglivsiflvGai.iGslfagllgdrfGRkkslliaavlfvigavlqaaakgkns 101
                                       +++++ ++          s++ ++  v +  +G + +G+++ag++gd +GR+  + +   ++ iga+++a++    +
  gi|518651955|ref|YP_008141475.1|  44 EQYNAGYAasgvssvfhiSASVISTQVEFITFGFMaVGAVIAGYMGDNLGRRFLYSFNLGIYAIGALISALSV---N 117
                                       4444444456666666666667777777777775438************************************...9 PP

                                       -TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-.....TTHHHH CS
                          Sugar_tr 102 vevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsn.....adgwri 172
                                       + ++++gR++vG+g+G++ ++  ++isEi p+++R++l++  +++  fGi+  ai+ l++   +++     +  wr+
  gi|518651955|ref|YP_008141475.1| 118 YSMFLFGRIVVGLGLGGEVAIGLTLISEIMPTRVRSQLTGAVNVGPGFGIFAVAILALIFiGPYEQifggsKLAWRW 194
                                       ************************************************************888888****999**** PP

                                       HHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHC.HHHHHHHHHHHHHHHHHHH............ CS
                          Sugar_tr 173 llglqlvpallllilllflPESPrylvekgkeeeakevlaklrge.edadrelaeekdsleaeqeee.........k 239
                                       +lg+ ++pall+l+ +  +PE+Pr+l++kg+++ea +v++ l ++   + ++l+++++  +  q+ +         k
  gi|518651955|ref|YP_008141475.1| 195 FLGILILPALLILLYRRYIPETPRFLISKGRQDEAFAVIKMLSENkLIPLKKLKNYYKVDDLRQQYNyiglkpineK 271
                                       *****************************************655535555555555555555544447788899999 PP

                                       ..HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHT...TTHHHHSS-THHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 240 aswkellssktvrqrlligvvlqifqqltGinaimyys...ptifenlglsksllvtiivgvvnfvatfvaiflvdr 313
                                        +++el+   ++ +r l+ + l ++++ t   + ++y+   +++   l+ls +++ t iv + + + tf a+fl  +
  gi|518651955|ref|YP_008141475.1| 272 PKTRELFAG-KYARRSLLLFILSFITFGTSASFTIIYPeifTSVATALHLSSTFTLTTIVNFGTLLGTFTAVFLATK 347
                                       999*****9.779999999********99966666665333344455677888999999999999999999999888 PP

                                       S-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHH CS
                          Sugar_tr 314 fGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalai 390
                                          R++l+  + + ai  + l      +v+ + ++++++++ +++f a+f+   ++++w++++E++p+++R++++ +
  gi|518651955|ref|YP_008141475.1| 348 N--RKILISTLGILAIIGAGL------TVTFH-SYAYIVVISLFIF-AIFSYASNTTIWLYSPEMYPTRIRNIGTGF 414
                                       4..555554444444444444......34443.2345555555554.789999************************ PP

                                       HHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCC CS
                          Sugar_tr 391 avavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtlee 447
                                         a++     ++ +l+ ++   ++ ++++lv  g  v+++i  ff    t  ++le 
  gi|518651955|ref|YP_008141475.1| 415 ILATSLGGVAIMEVLTSYVYALYNLTGIGLVAIGAFVVYVILAFFMADDTSKKDLEV 471
                                       **********************************************99999999985 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.9  43.2   2.2e-27     2e-23       2     320 ..      35     395 ..      34     398 .. 0.81
   2 !   26.2  27.5   3.8e-10   3.4e-06       1     180 [.     289     467 ..     289     472 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.9 bits;  conditional E-value: 2.2e-27
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       ++++f+ a+  +++g a++  +++ ++is+s+i++ +  + + ++av+++++G+++d++Grr ++ + l ++a+g+l
  gi|518651955|ref|YP_008141475.1|  35 VFGTFFDAIEQYNAGYAAS-GVSSVFHISASVISTqVEFITFGFMAVGAVIAGYMGDNLGRRFLYSFNLGIYAIGAL 110
                                       799****************.***************7666677789******************************77 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..... 149
                                       + +++ ++ ++l++r++ Glg g+ +++g++li+++ p + r++ +g +++g ++G+   ++l+ +++  +      
  gi|518651955|ref|YP_008141475.1| 111 ISALSVNYSMFLFGRIVVGLGLGGEVAIGLTLISEIMPTRVRSQLTGAVNVGPGFGIFAVAILALIFIGPYEqifgg 187
                                       777767888********************************************************999666699999 PP

                             MFS_1 150 ....Wravfyilaivsllafvlfllllpeepperkrkspkeee.................................. 188
                                           Wr+   il + +ll  +l   ++pe+p+    k  ++e                                   
  gi|518651955|ref|YP_008141475.1| 188 sklaWRWFLGILILPALLI-LLYRRYIPETPRFLISKGRQDEAfavikmlsenkliplkklknyykvddlrqqynyi 263
                                       9999**9988888888887.44455555555555555555555*******************************998 PP

                             MFS_1 189 ......kgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvg 257
                                             ++++ ++l+   k+ +++  l  +++++++f++  s+  ++  +++ + + l+ls+ +++++++ ++ l+g
  gi|518651955|ref|YP_008141475.1| 264 glkpinEKPKTRELFA-GKYARRSLLL--FILSFITFGTSASFtiIYPEIFTSVATALHLSSTFTLTTIVNFGTLLG 337
                                       8888777777777777.8888888855..666666665444443344444444688888885588888899999999 PP

                             MFS_1 258 ailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfvfps 320
                                        + a++++       +r++l+ +l++l+++ +gl ++ ++  a +++++l+++ +  ++  +++
  gi|518651955|ref|YP_008141475.1| 338 TFTAVFLATK-----NRKILISTLGILAIIGAGLTVTFHS-YAYIVVISLFIFAIfSYASNTTI 395
                                       7776666654.....556**********************.44444446666666466655554 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 3.8e-10
                             MFS_1   1 lllaaflsalarsilgpalpl.al..aedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfal 74 
                                       l+++ f+++ +++ +++++p+ +   a++l++s     +l+t++ +g++++++ + +l+++  r+ ++ +  +l ++
  gi|518651955|ref|YP_008141475.1| 289 LFILSFITFGTSASFTIIYPEiFTsvATALHLSS--TFTLTTIVNFGTLLGTFTAVFLATK-NRKILISTLGILAII 362
                                       5788888888888888888853332233344333..336999*******************.355555555555555 PP

                             MFS_1  75 glllll..fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                       g + l+  f +s+  +++++ ++ ++++ a+++++  +  +++p + r+ ++g++ a++  G+++  +l +++++++
  gi|518651955|ref|YP_008141475.1| 363 G-AGLTvtF-HSYAyIVVISLFIFAIFSYASNTTIWLYSPEMYPTRIRNIGTGFILATSLGGVAIMEVLTSYVYALY 437
                                       5.4444348.9***9************************************************************** PP

                             MFS_1 149 gWravfyilaivsllafvlfllllpeepperk 180
                                       + +++ +++ +++++ ++l  ++++++++++k
  gi|518651955|ref|YP_008141475.1| 438 NLTGIGLVAIGAFVVYVIL--AFFMADDTSKK 467
                                       *****99999999999887..77777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1020  (0.0568911); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 3659.63
//
Query:       gi|518651956|ref|YP_008141476.1|  [L=468]
Description: dihydropyrimidinase [Ferroplasma acidarmanus fer1]
Scores for 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   61.2   0.0    1.6e-16   60.6   0.0    1.3  1  Amidohydro_1  Amidohydrolase family
    1.8e-10   40.9   0.0    3.9e-05   23.3   0.0    2.8  2  Amidohydro_3  Amidohydrolase family
  ------ inclusion threshold ------
       0.12   12.7   0.5       0.29   11.5   0.2    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 !   60.6   0.0   2.7e-20   1.6e-16       2     327 ..      56     434 ..      55     450 .. 0.74

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 2.7e-20
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.......HHHHHHHHHH CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.......giealleaae 71 
                                        +PG+ID+H H+ ++              + ++  l+   ++a+ +G t+v+ + +  ++        i+ ++++ae
  gi|518651956|ref|YP_008141476.1|  56 AMPGFIDLHFHAGMGS------------INSVYNDLKLESRAAVAGGYTYVRSHLIIGEDgksgylkVIDHIIKNAE 120
                                       69**********9995............599***************************9977777777777777777 PP

                                       TSSSEEEEEEESSEGGS..........GCCCSHHHHHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHHHHHHH CS
                      Amidohydro_1  72 elplglrilggkvsldr..........gsaetskasreklkagaaetikgkadgvvk.valapheapafsdeelkea 137
                                       ++           s++           ++a+  ++++ k +     +i  +a ++ +   l+ + +  + d  +k +
  gi|518651956|ref|YP_008141476.1| 121 KV-----------SYSDfsfnpmigtmDQANELEELINKGINAY--KIYYNAYQGEEgRNLGIYVDEDIDDIVIKVL 184
                                       74...........3333344446656788888888888888888..6666677777777777777777766677666 PP

                                       HHHHHHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCC......HHTTTHCCEEEHCTCEEEHH....... CS
                      Amidohydro_1 138 lkeakkrdlpvaiHaletkgevedaeaafgetiehgthlevaes......lglldeiklilahgvhltpt....... 201
                                       + + k r++ + +Ha e++ +v+++ a   e+     + +++        +        i +   h+ ++       
  gi|518651956|ref|YP_008141476.1| 185 STASKYRKTRIIFHA-EDNSTVKYCTANEREKNGLDAFSRGRPPfaeaikI------DHIGHLALHFGAKihiahis 254
                                       6555555********.9999999*******777777777776666555552......33322222222222222333 PP

                                       ..HHHHHHHHHHHHCEE.......HHHHHHHH................SEHHHHHHHHHHHHTSCEEEEEECT.... CS
                      Amidohydro_1 202 ..eaellkerlkeagva.......hcpfsnsi................lrsgrealrkaldeGvkvglgtDga.... 249
                                         ea    er ++ gv        h+ f +++                 + ++e l k ++e ++ ++++D +    
  gi|518651956|ref|YP_008141476.1| 255 siEAYEAVERYRNLGVDitietepHYLFYDDSmwrllgvfgkvnpplrTSRDSEFLIKKISERKIDSISSD-Vnaln 330
                                       457777788889999999888888777777779999999999999999888888888889999********.437** PP

                                       ......TSSCCGGHHHH........HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB CS
                      Amidohydro_1 250 ......asgnslnllee........lrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkd 311
                                             ++++ +n+++         +   + l r l  + ++ g ls++ ++++++  + +++g   ++Gsi vGkd
  gi|518651956|ref|YP_008141476.1| 331 skqkikNANKYGNIWDAspgfdniqM---T-LPR-LITKfVSSGILSYETLVYIMSERPSQVIGA-VNKGSISVGKD 401
                                       **999999999999999997543221...1.222.3444799999*******************8.5********** PP

                                       --EEEECC...CT..............CGGGTT CS
                      Amidohydro_1 312 ADlvvvdl...di..............laafvg 327
                                       AD+v+vd    ++              ++++++
  gi|518651956|ref|YP_008141476.1| 402 ADIVLVDDknyHKatpellenvpgldwNPEINK 434
                                       ******997652255566666666666555555 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0   4.2e-06     0.025       3      25 ..      49      70 ..      47      94 .. 0.79
   2 !   23.3   0.0   6.6e-09   3.9e-05     311     456 ..     250     418 ..     239     424 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 4.2e-06
                      Amidohydro_3  3 iDakGrlvlPGFvDsHtHlaggg 25
                                      i+ +G+l +PGF+D H H ag g
  gi|518651956|ref|YP_008141476.1| 49 INGSGLLAMPGFIDLHFH-AGMG 70
                                      6778**************.5554 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 6.6e-09
                      Amidohydro_3 311 lehaegv.tesqiervaalqvaagvqpvfnf.....edelldsrlg..perargs....tpvkellnagvkvalgsD 375
                                       ++h + +  ++ +er + l+v++ +++ + +      ++ l +++g  +++ r+s    + +k + +  +  + +sD
  gi|518651956|ref|YP_008141476.1| 250 IAHISSIeAYEAVERYRNLGVDITIETEPHYlfyddSMWRLLGVFGkvNPPLRTSrdseFLIKKISERKID-SISSD 325
                                       67888888888888888888888888766667887666777777776555555568888888888888877.67888 PP

                      Amidohydro_3 376 apvgpfdpwprigaavmrktrrgg...............evlrpdeelsleealalyTrgpAkalgledrkGtLevG 437
                                         v+ +++   i  a+   +  ++               + +  +  ls+e+++  ++++p +++g+  + G++ vG
  gi|518651956|ref|YP_008141476.1| 326 --VNALNSKQKIKNANKYGNIWDAspgfdniqmtlprliTKFVSSGILSYETLVYIMSERPSQVIGAVNK-GSISVG 399
                                       ..6666666666666532222222566666667888777555567789*********************8.****** PP

                      Amidohydro_3 438 adADlvvldadpldvdppe 456
                                       +dAD+v+ d++  +  +pe
  gi|518651956|ref|YP_008141476.1| 400 KDADIVLVDDKNYHKATPE 418
                                       *********5544444444 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 ?   11.5   0.2   4.9e-05      0.29      67     100 ..       6      40 ..       1      49 [. 0.88
   2 ?   -2.8   0.0       1.3   7.7e+03      43      73 ..      87     119 ..      74     125 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.9e-05
                      Urease_alpha  67 DlvitnavilDatgivk.adigikdgrivaiGkag 100
                                        l itn+ i+  +gi   ad+ i++g+i++i ++g
  gi|518651956|ref|YP_008141476.1|   6 SLTITNVRIVSSSGISDpADVFINNGKIAGIHQTG 40 
                                       578************9659************9887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                      Urease_alpha  43 kfGggkviRdgm..gqssaakeeealDlvitna 73 
                                       + Gg   +R  +  g++ ++   +++D +i na
  gi|518651956|ref|YP_008141476.1|  87 VAGGYTYVRSHLiiGEDGKSGYLKVIDHIIKNA 119
                                       555555555543113333334444667777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 3053.31
//
Query:       gi|518651957|ref|YP_008141477.1|  [L=510]
Description: benzoylformate decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   95.3   0.0    6.7e-27   94.2   0.0    1.6  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.4e-22   77.8   0.0    2.4e-21   76.1   0.0    1.8  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.5e-14   53.9   0.0    3.1e-14   52.9   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
      0.027   14.3   0.0       0.75    9.5   0.0    2.6  2  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.2   0.0   1.5e-30   6.7e-27       4     167 ..       7     166 ..       4     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.2 bits;  conditional E-value: 1.5e-30
                                       HHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCH CS
                      TPP_enzyme_N   4 aealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnal 80 
                                        ++l ++Lk+ +   vfg+pG+++ p+l+ +s     +++l++h    +++Adg a++t+kp  v+++s  G+ n +
  gi|518651957|ref|YP_008141477.1|   7 YKILNKTLKNMKLFPVFGNPGTTEIPMLEGVSSD---EYILTLHDSISVGMADGRAQLTRKPSFVNLHSILGVGNSM 80 
                                       567888999999999******************9...7*************************************** PP

                                       HHHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EE CS
                      TPP_enzyme_N  81 talaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPv 155
                                         +++A+v r+P+++ +g+++++++      + l  ++ +++ p++ky+++v+s++++++ +rrA++ ++ ++    
  gi|518651957|ref|YP_008141477.1|  81 AFIYSAFVHRVPVIITAGEQDSRHIF---YDPLLsgNIGDMISPYVKYKFEVNSANDIEKSIRRAYTSSMAPPYSLS 154
                                       ********************999998...333335699*************************************** PP

                                       EEEEEHHHCC-E CS
                      TPP_enzyme_N 156 ylelpkdvllee 167
                                       +l +p+d++ ee
  gi|518651957|ref|YP_008141477.1| 155 FLGFPMDIMGEE 166
                                       *********987 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.92   4.1e+03      16      54 ..      62      98 ..      53     105 .. 0.65
   2 !   76.1   0.0   5.5e-25   2.4e-21      17     152 ..     374     497 ..     363     498 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.92
                                      SSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEE CS
                      TPP_enzyme_C 16 krprsyltsgglgtmGyglpaAiGaklakpdrevvaivG 54
                                      +r++s+++  +++ +G+g ++A   ++   + +v+ ++G
  gi|518651957|ref|YP_008141477.1| 62 TRKPSFVN--LHSILGVGNSMAFIYSAFVHRVPVIITAG 98
                                      55667777..78888888777765555333456666666 PP

  == domain 2  score: 76.1 bits;  conditional E-value: 5.5e-25
                                       SSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHH CS
                      TPP_enzyme_C  17 rprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqe 93 
                                       +p+sy+  g  g +G++lpaA G++  k   +v +++GDG+f+++ q l+t+ ++nlp+++++l+N+gyg  ++ ++
  gi|518651957|ref|YP_008141477.1| 374 KPDSYFI-GKSGQIGWALPAAAGMATVK--DKVLCVIGDGAFMYTSQTLWTIKNYNLPVKIIILDNHGYGILKKFSD 447
                                       5666666.6789*************973..59********************************************* PP

                                       HHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                        +++++k       + ++ + k+  ++ ++     +++ +e+ e +++ ++ kgpa + 
  gi|518651957|ref|YP_008141477.1| 448 VNYKESKKYL----SFSIELKKVLDSFNIE-----SRENDETMEDIEWLRNIKGPAALI 497
                                       ***9887664....56899********888.....333489999999999999999775 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 !   52.9   0.0   6.9e-18   3.1e-14       2     119 ..     188     304 ..     187     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 6.9e-18
                                       HHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHHH CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipedhplylgmlglhgskaanealee 77 
                                       + +ae+++++k+pv++ G + +  g    +r++a klgiPv ++ ++ +  +++ +++y+g l  + ++  n+ l e
  gi|518651957|ref|YP_008141477.1| 188 KYIAEMINSSKNPVMVTGYELDMYGGIGYARAFASKLGIPVfAEPFASRAPFDSGDKNYAGDLPPV-AALINDKLSE 263
                                       668**************************************7788888****************99.99******** PP

                                       -SEEEEES-SSSTCCCTTTTT.TTTTT-EEEEEESSC.CCCTTC CS
                      TPP_enzyme_M  78 aDlvlalGarfddirttgsep.efapeakiihididp.aeigkn 119
                                       +Dl++++G +    + + +++ +  + ++ii i  d   +ig +
  gi|518651957|ref|YP_008141477.1| 264 HDLIIIVGGDI---NLYPYSKaDLLEGKEIIKIGMDIsGKIGDS 304
                                       ********555...555555545555558999977743555555 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00017      0.75      18      46 ..     181     208 ..     173     234 .. 0.86
   2 ?    1.3   0.1     0.056   2.5e+02     117     143 ..     413     439 ..     400     462 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00017
                                       --EEE--SHHHHHHHHHSSSEEEEE-S-- CS
                             CO_dh  18 katleealkvvakmikkakrPllivGpqv 46 
                                        ++  +a+k +a+mi   k+P++++G ++
  gi|518651957|ref|YP_008141477.1| 181 VVD-INAVKYIAEMINSSKNPVMVTGYEL 208
                                       344.45669*****************876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHH-TT-EEEE-SSS-- CS
                             CO_dh 117 Yyasqalsslkkftdkittiaidkyyh 143
                                        y+sq+l  +k++   +++i+ d+ + 
  gi|518651957|ref|YP_008141477.1| 413 MYTSQTLWTIKNYNLPVKIIILDNHGY 439
                                       589***********9999999887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 3443.58
//
Query:       gi|518651958|ref|YP_008141478.1|  [L=136]
Description: hypothetical protein FACI_IFERC00001G0597 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      220  (0.0122706); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 1058.07
//
Query:       gi|518651959|ref|YP_008141479.1|  [L=196]
Description: hypothetical protein FACI_IFERC00001G0598 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.015   15.5   0.1       0.02   15.1   0.1    1.3  1  DUF4955      Domain of unknown function (DUF4955)
        0.3   10.9   6.0        4.7    7.0   0.2    2.2  2  DUF3449      Domain of unknown function (DUF3449)


Domain annotation for each model (and alignments):
>> DUF4955  Domain of unknown function (DUF4955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.1   2.2e-06      0.02      49     102 ..     111     162 ..      78     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                           DUF4955  49 ksraGGdeeqlPnhlkdLvlWnlkatgtkeeekkefkwwsaeek.ywkllpPiiv 102
                                       +s+  G  +++ +hl+d+  Wn+++t+++ +  ++f++w+a +k  w+l    i+
  gi|518651959|ref|YP_008141479.1| 111 RSQITGHGKTAIKHLEDVNKWNITETKSHIS--NAFALWKARSKmEWNLDI-SII 162
                                       566778889999***********99887776..58****988772454443.344 PP

>> DUF3449  Domain of unknown function (DUF3449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   1.5   0.00085       7.6      88      99 ..      62      73 ..      59      98 .. 0.70
   2 ?    7.0   0.2   0.00052       4.7      91     145 ..      99     149 ..      89     165 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00085
                                      XXXXXXXXXXXX CS
                           DUF3449 88 keykCeiCgnav 99
                                       eykCeiCg  +
  gi|518651959|ref|YP_008141479.1| 62 AEYKCEICGSEE 73
                                      69*******876 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00052
                                       XXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                           DUF3449  91 kCeiCgnavYkGrkaFekHFs.eerHaeglkcLgientklfkeitkiedaleLwek 145
                                        C  C +++++Gr +   H + + +H e++   +i++tk+     +i++a +Lw+ 
  gi|518651959|ref|YP_008141479.1|  99 ICPACHDTTHFGRSQITGHGKtAIKHLEDVNKWNITETKS-----HISNAFALWKA 149
                                       5999***************862579***********9985.....57777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.51
# Mc/sec: 1148.01
//
Query:       gi|518651960|ref|YP_008141480.1|  [L=87]
Description: hypothetical protein FACI_IFERC00001G0599 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       557  (0.031067); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 569.05
//
Query:       gi|518651961|ref|YP_008141481.1|  [L=192]
Description: hypothetical protein FACI_IFERC00001G0600 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0017   18.1   0.1     0.0029   17.4   0.1    1.4  1  HxlR         HxlR-like helix-turn-helix
  ------ inclusion threshold ------
      0.043   13.7   1.7       0.32   10.9   0.1    2.4  2  TFIIE_alpha  TFIIE alpha subunit


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.1   3.2e-07    0.0029       2      85 ..       7      89 ..       6      95 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.2e-07
                                      HHSTTHHHHHHHHTT.S-EEHHHHHHHST.TS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHH CS
                              HxlR  2 iggkWkllilvellk.gkkRfselkralp.kisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqe 78
                                      +++k  + +l  l + g+ + +el + +p +++ + L+++L+e    gli+ +      +   Ysl+e+G+ ++  l+e
  gi|518651961|ref|YP_008141481.1|  7 LSQKHAISVLLFLSErGSVKQNELLEVIPsNLTIEKLSNSLKE---AGLINITHQMMGRKIFIYSLSERGHVVALKLKE 82
                                      7788899999999988************955888999988876...67777666666666678**************** PP

                                      HHHHHHH CS
                              HxlR 79 lkkwgee 85
                                      + + +e 
  gi|518651961|ref|YP_008141481.1| 83 MLEAAEG 89
                                      *987765 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   3.5e-05      0.32      13      62 ..      10      58 ..       3      63 .. 0.89
   2 ?    1.3   0.1     0.033     3e+02      49      92 ..     143     186 ..     134     191 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.5e-05
                                      HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEE CS
                       TFIIE_alpha 13 eeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrr 62
                                      ++a+ vl  L e+g v+ ++l + +  +l+ + kl n L+ea+l+++  +
  gi|518651961|ref|YP_008141481.1| 10 KHAISVLLFLSERGSVKQNELLEVIPSNLT-IEKLSNSLKEAGLINITHQ 58
                                      56899******************9998886.89************99765 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.033
                                       HHHHHCTSEEEEEEEETTTEEEEEEEEEECCCHCCCHHHHHHHH CS
                       TFIIE_alpha  49 nrLyearlvkykrrrdeekswykyywrinyeklvdvvkrkleev 92 
                                        +L +  ++    ++d+  +  +  +    + ++ +v++++ +v
  gi|518651961|ref|YP_008141481.1| 143 VKLNGNNIIRLWCEVDNTYECVHTQYAWSLPDVQAMVQHQVLKV 186
                                       57888899999999999999999999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1331.21
//
Query:       gi|518651962|ref|YP_008141482.1|  [L=62]
Description: hypothetical protein FACI_IFERC00001G0601 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 422.05
//
Query:       gi|518651963|ref|YP_008141483.1|  [L=329]
Description: phage integrase family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-31  109.0   0.5    3.4e-31  108.3   0.5    1.3  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.3   0.5   1.9e-35   3.4e-31       6     171 ..     103     265 ..     101     266 .. 0.92

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.9e-35
                                       HHHHHHHHCCGC....HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHH CS
                   Phage_integrase   6 deverllaalee....slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseeale 78 
                                       ++++r+ +++ +     + +r+ +++ +l +tG+R++El+  +++d   +n+++++  r  Kg+k+r+vpl+ ++++
  gi|518651963|ref|YP_008141483.1| 103 EDIQRMREFCISrkdkYTWARNLCMMDMLIATGMRAGELIHANLEDY--KNSTLYI--RSEKGEKDRTVPLPGKLTS 175
                                       6677777777766554556789999*********************9..*******..******************* PP

                                       HHHHHHHHHCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHH CS
                   Phage_integrase  79 llkellskaleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkll 155
                                        + e+++k  + +++s +lf  + + + + +++r+ +k ++ ++g+  +++pH++Rh++at L++ gvd+r vq l 
  gi|518651963|ref|YP_008141483.1| 176 EVDEYIEKY-RYHSDSRALFTTR-TGRYNYNKLRQLIKYIGVHSGVP-DIHPHSFRHYYATTLVRLGVDIRRVQILV 249
                                       ********9.9999999999998.99********************9.***************************** PP

                                       T-SSCCHHHHHHCCCH CS
                   Phage_integrase 156 GHssisttqiYthvak 171
                                       GH+ i+tt +Yth+++
  gi|518651963|ref|YP_008141483.1| 250 GHARIETTTRYTHLTQ 265
                                       *************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2379.97
//
Query:       gi|518651964|ref|YP_008141484.1|  [L=33]
Description: hypothetical protein FACI_IFERC00001G0603 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 241.89
//
Query:       gi|518651965|ref|YP_008141485.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G0604 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00076   19.3   0.5       0.26   11.2   0.1    2.2  2  zinc_ribbon_4   zinc-ribbon domain
     0.0012   18.2   3.3        0.3   10.5   0.4    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0043   17.0   0.2      0.007   16.4   0.2    1.4  1  DZR             Double zinc ribbon
     0.0045   17.3   3.7       0.64   10.5   0.3    2.3  2  zf-H2C2_2       Zinc-finger double domain
     0.0052   17.1   1.7       0.85   10.0   0.2    2.1  2  zf-Di19         Drought induced 19 protein (Di19), zinc-bindi
     0.0067   16.5   0.5       0.46   10.5   0.1    2.0  2  CpXC            CpXC protein
  ------ inclusion threshold ------
      0.016   15.4   0.5        1.5    9.2   0.1    2.3  2  zinc_ribbon_9   zinc-ribbon
      0.017   15.0   4.1       0.59   10.1   0.1    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type
      0.022   14.2   0.7        3.1    7.4   0.1    2.3  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.025   14.5   0.1        6.8    6.7   0.0    2.1  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.031   15.0   0.2        1.1    9.9   0.0    2.0  2  FYDLN_acid      Protein of unknown function (FYDLN_acid)
      0.035   14.1   0.1      0.037   14.1   0.1    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.039   13.7   4.5        1.3    8.7   0.3    2.0  2  DUF2225         Uncharacterized protein conserved in bacteria
      0.041   13.8   1.1       0.58   10.2   0.1    2.2  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
       0.05   13.6   0.2        5.2    7.2   0.0    2.1  2  zf-BED          BED zinc finger
      0.056   13.6   0.2        2.5    8.3   0.0    2.0  2  DUF4451         Domain of unknown function (DUF4451)
      0.065   13.1   1.9        3.4    7.6   0.1    2.2  2  Cys_rich_CPXG   Cysteine-rich CPXCG
      0.078   13.1   1.5       0.15   12.2   1.5    1.5  1  zf-Mss51        Zinc-finger of mitochondrial splicing suppres
      0.079   12.6   1.5        0.2   11.3   0.1    2.0  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
        0.1   12.5   1.2          2    8.4   0.1    2.1  2  HNH_5           HNH endonuclease
        0.1   13.5   2.3         12    7.0   0.1    2.3  2  zf-C2H2_4       C2H2-type zinc finger
        0.1   12.1   6.9       0.27   10.8   0.2    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
        0.1   13.1   2.1        6.6    7.4   0.1    2.3  2  zf-C2H2         Zinc finger, C2H2 type
       0.12   12.4   6.6        2.2    8.3   1.1    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.16   12.1   4.3        6.5    6.9   0.9    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.21   11.7   1.3       0.57   10.3   0.1    1.9  2  SoxD            Sarcosine oxidase, delta subunit family
       0.25   11.1   2.6        6.8    6.5   0.2    2.4  2  zinc_ribbon_5   zinc-ribbon domain
       0.46   10.3   1.1        0.5   10.2   0.1    1.5  2  DUF4668         Domain of unknown function (DUF4668)


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1    0.0004      0.26       2      13 ..       4      15 ..       4      20 .. 0.86
   2 ?    6.4   0.0     0.013       8.4      19      32 ..      29      42 ..      27      44 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
                     zinc_ribbon_4  2 kitCpsCkakye 13
                                      ki+Cp+C+ ++ 
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNEEFD 15
                                      79******9986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                     zinc_ribbon_4 19 lpakgvkvrCskCg 32
                                      +p++ + ++C+ C+
  gi|518651965|ref|YP_008141485.1| 29 VPPGVGFIKCPYCK 42
                                      67777888888886 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   0.2    0.0018       1.2       2      10 ..       4      12 ..       3      18 .. 0.77
   2 !   10.5   0.4   0.00048       0.3      10      25 ..      28      44 ..      27      44 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                       zf-ribbon_3  2 tvrCPnCGa 10
                                      ++ CP+C++
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNE 12
                                      678999987 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00048
                       zf-ribbon_3 10 a.plssddnvCpyCGtk 25
                                      a p+  + ++CpyC +k
  gi|518651965|ref|YP_008141485.1| 28 AvPPGVGFIKCPYCKYK 44
                                      55566667899999876 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.1e-05     0.007      11      40 ..       3      47 ..       1      53 [. 0.86

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                               DZR 11 darfCseCgtklkavaa................edrCpsCgekvdp 40
                                      ++++C++C+++ +a+ +                 ++Cp C++k++ 
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEEFDAP-RwdkkrlgfgavppgvgFIKCPYCKYKAHR 47
                                      5679*******9854.4599**********************9875 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.2    0.0055       3.5      13      24 ..       3      14 ..       1      16 [. 0.82
   2 !   10.5   0.3     0.001      0.64      13      23 ..      34      44 ..      28      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0055
                         zf-H2C2_2 13 kpyeCplCdkaF 24
                                      ++  Cp+C+  F
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEEF 14
                                      5689*****998 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.001
                         zf-H2C2_2 13 kpyeCplCdka 23
                                       + +Cp+C+++
  gi|518651965|ref|YP_008141485.1| 34 GFIKCPYCKYK 44
                                      5689*****98 PP

>> zf-Di19  Drought induced 19 protein (Di19), zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.1     0.013       8.6       3      14 ..       5      16 ..       3      21 .. 0.78
   2 !   10.0   0.2    0.0013      0.85       4      16 ..      37      49 ..      35      55 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.013
                           zf-Di19  3 ftCPyCgkeltv 14
                                      + CP C++e+++
  gi|518651965|ref|YP_008141485.1|  5 IVCPKCNEEFDA 16
                                      579999999886 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0013
                           zf-Di19  4 tCPyCgkeltvke 16
                                      +CPyC+ + + +e
  gi|518651965|ref|YP_008141485.1| 37 KCPYCKYKAHRSE 49
                                      8****98655555 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1   0.00072      0.46       1      16 [.       5      20 ..       5      24 .. 0.91
   2 ?    4.9   0.0      0.04        26      38      48 ..      36      46 ..      33      58 .] 0.71

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00072
                              CpXC  1 ltCpaCgkefeaeiwt 16
                                      + Cp+C++ef+a+ w+
  gi|518651965|ref|YP_008141485.1|  5 IVCPKCNEEFDAPRWD 20
                                      68**********9997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.04
                              CpXC 38 atCpkCgatak 48
                                      ++Cp+C ++a+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYKAH 46
                                      57888887765 PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.1    0.0023       1.5      21      31 ..       4      14 ..       1      14 [. 0.77
   2 ?    4.8   0.1     0.053        34      22      28 ..      36      42 ..      26      44 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0023
                     zinc_ribbon_9 21 dvlCPhCgggF 31
                                       ++CP C+  F
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNEEF 14
                                      345*****998 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.053
                     zinc_ribbon_9 22 vlCPhCg 28
                                      + CP+C+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCK 42
                                      45****6 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 ?   10.1   0.1   0.00092      0.59       4      15 ..       6      17 ..       3      21 .. 0.77
   2 ?    6.4   0.9     0.013       8.3       3       9 ..      36      42 ..      34      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00092
                         zf-C2HC_2  4 pCpkCgRsFnpd 15
                                       CpkC+  F + 
  gi|518651965|ref|YP_008141485.1|  6 VCPKCNEEFDAP 17
                                      6********544 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.013
                         zf-C2HC_2  3 vpCpkCg 9 
                                      ++Cp+C+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCK 42
                                      89****7 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1    0.0048       3.1       2      10 ..       6      14 ..       5      24 .. 0.78
   2 ?    5.7   0.1     0.017        11       2       7 ..      37      42 ..      36      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0048
                                      EETTTTCEE CS
                      TF_Zn_Ribbon  2 kCPnCgstn 10
                                      +CP+C+ ++
  gi|518651965|ref|YP_008141485.1|  6 VCPKCNEEF 14
                                      8****9864 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.017
                                      EETTTT CS
                      TF_Zn_Ribbon  2 kCPnCg 7 
                                      kCP+C+
  gi|518651965|ref|YP_008141485.1| 37 KCPYCK 42
                                      9****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 ?    6.3   0.0     0.014       8.9      45      58 ..       3      16 ..       1      18 [. 0.86
   2 ?    6.7   0.0     0.011       6.8      47      58 ..      36      47 ..      27      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                    OrfB_Zn_ribbon 45 rtfkCpnCgfeadr 58
                                       + +Cp+C+ e+d+
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEEFDA 16
                                      5789*******997 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                    OrfB_Zn_ribbon 47 fkCpnCgfeadr 58
                                       kCp C+++a+r
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYKAHR 47
                                      589999999998 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 ?    9.9   0.0    0.0018       1.1      26      41 ..       4      19 ..       1      27 [. 0.79
   2 ?    3.7   0.1      0.16     1e+02      27      41 ..      36      50 ..      35      58 .] 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0018
                        FYDLN_acid 26 Pivcpkcgeefepeev 41
                                       ivcpkc+eef+  + 
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNEEFDAPRW 19
                                      59*********98766 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.16
                        FYDLN_acid 27 ivcpkcgeefepeev 41
                                      i cp+c+ + + +e+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYKAHRSEF 50
                                      68*****99998887 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   5.7e-05     0.037      69      96 ..       3      45 ..       1      55 [. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.7e-05
                                      -EEEETTTS-EEECHH.HHH..............S-TTTSSS- CS
                              HypA 69 vkvrCreCgkefelee.kal..............rCpkCgsad 96
                                       k+ C +C++ef+  + ++               +Cp C+ + 
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEEFDAPRwDKKrlgfgavppgvgfiKCPYCKYKA 45
                                      6899*********88743336799***************9765 PP

>> DUF2225  Uncharacterized protein conserved in bacteria (DUF2225)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3     0.002       1.3       3      22 ..       2      21 ..       1      28 [. 0.83
   2 ?    7.7   0.4     0.004       2.5      50      67 ..      37      54 ..      25      58 .] 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.002
                           DUF2225  3 kkkieCPvCeekfkkkkvks 22
                                      k ki+CP C+e+f++ +  +
  gi|518651965|ref|YP_008141485.1|  2 KSKIVCPKCNEEFDAPRWDK 21
                                      679**********9987655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.004
                           DUF2225 50 vCpkCgYaalkkdfekls 67
                                       Cp C Y a+ ++f+  +
  gi|518651965|ref|YP_008141485.1| 37 KCPYCKYKAHRSEFSVAE 54
                                      699999999999998655 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1    0.0009      0.58      20      29 ..       5      14 ..       1      15 [. 0.84
   2 ?    2.7   0.1       0.2   1.3e+02       4       9 ..      37      42 ..      31      43 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0009
                    PhnA_Zn_Ribbon 20 lvCpeCahEw 29
                                       vCp+C +E+
  gi|518651965|ref|YP_008141485.1|  5 IVCPKCNEEF 14
                                      69*****998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.2
                    PhnA_Zn_Ribbon  4 kCplCa 9 
                                      kCp C+
  gi|518651965|ref|YP_008141485.1| 37 KCPYCK 42
                                      677664 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.039        25      14      26 ..       2      14 ..       1      17 [. 0.85
   2 ?    7.2   0.0    0.0082       5.2       8      28 ..      27      47 ..      26      54 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.039
                                      SS--EETTTTEE- CS
                            zf-BED 14 eqkavCryCgkil 26
                                      + k+vC  C++++
  gi|518651965|ref|YP_008141485.1|  2 KSKIVCPKCNEEF 14
                                      579******9986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0082
                                      ----GGSS--EETTTTEE--- CS
                            zf-BED  8 tpvslkeqkavCryCgkilsr 28
                                      ++v+   ++++C yC+ +  r
  gi|518651965|ref|YP_008141485.1| 27 GAVPPGVGFIKCPYCKYKAHR 47
                                      556666789******977666 PP

>> DUF4451  Domain of unknown function (DUF4451)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0     0.004       2.5      83     103 ..       2      22 ..       1      29 [. 0.78
   2 ?    4.1   0.0     0.077        49      26      37 ..      38      48 ..      32      57 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.004
                           DUF4451  83 kegivCpkCneiievslsknk 103
                                       k++ivCpkCne ++   +++k
  gi|518651965|ref|YP_008141485.1|   2 KSKIVCPKCNEEFDAPRWDKK 22 
                                       6789******97777766665 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.077
                           DUF4451 26 CpiCeeevekke 37
                                      Cp+C+ +  +++
  gi|518651965|ref|YP_008141485.1| 38 CPYCKYKA-HRS 48
                                      99999543.333 PP

>> Cys_rich_CPXG  Cysteine-rich CPXCG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.025        16       1      11 [.       5      15 ..       5      17 .. 0.86
   2 ?    7.6   0.1    0.0053       3.4       1       9 [.      36      44 ..      36      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                     Cys_rich_CPXG  1 iqCPyCgeeie 11
                                      i CP C ee++
  gi|518651965|ref|YP_008141485.1|  5 IVCPKCNEEFD 15
                                      68******998 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0053
                     Cys_rich_CPXG  1 iqCPyCgee 9 
                                      i+CPyC  +
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYK 44
                                      79****865 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 ?   12.2   1.5   0.00024      0.15       2      38 ..       7      57 ..       2      58 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                          zf-Mss51  2 CPvpkhkqt..............apkhvdfeCpdCGiptycseehwedDye 38
                                      CP ++++ +              +p    ++Cp C +  + se   ++D+e
  gi|518651965|ref|YP_008141485.1|  7 CPKCNEEFDaprwdkkrlgfgavPPGVGFIKCPYCKYKAHRSEFSVAEDTE 57
                                      888876666888999999999988888889*******************99 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00031       0.2       2      15 ..       4      17 ..       3      20 .. 0.82
   2 ?    0.6   0.1      0.69   4.4e+02       3       9 ..      36      42 ..      34      51 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00031
                            zf_UBZ  2 tylCerCgkeipes 15
                                       ++C++C++e+  +
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNEEFDAP 17
                                      589*******9865 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.69
                            zf_UBZ  3 ylCerCg 9 
                                      + C+ C+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCK 42
                                      57**998 PP

>> HNH_5  HNH endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0031         2      30      44 ..       3      15 ..       1      22 [. 0.81
   2 ?    3.5   0.1       0.1        66       1      15 [.      38      52 ..      38      53 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0031
                             HNH_5 30 snlvtlCkkCNqkkg 44
                                      s++  +C kCN+++ 
  gi|518651965|ref|YP_008141485.1|  3 SKI--VCPKCNEEFD 15
                                      566..9******985 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.1
                             HNH_5  1 CiyCgkeiaekelse 15
                                      C yC+ + + +e+s 
  gi|518651965|ref|YP_008141485.1| 38 CPYCKYKAHRSEFSV 52
                                      9******99999885 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1      0.02        12       2      11 ..       6      15 ..       5      21 .. 0.84
   2 ?    6.5   0.4     0.027        18       2      10 ..      37      43 ..      36      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.02
                         zf-C2H2_4  2 kCpiCgksFs 11
                                       Cp C++ F 
  gi|518651965|ref|YP_008141485.1|  6 VCPKCNEEFD 15
                                      6******994 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.027
                         zf-C2H2_4  2 kCpiCgksF 10
                                      kCp+C   +
  gi|518651965|ref|YP_008141485.1| 37 KCPYC--KY 43
                                      8****..55 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 ?   10.8   0.2   0.00042      0.27       4      11 ..       6      13 ..       4      20 .. 0.83
   2 ?    4.3   1.9     0.047        30       5      12 ..      38      45 ..      36      46 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00042
                        zf_C2H2_10  4 sCPKCqek 11
                                       CPKC+e 
  gi|518651965|ref|YP_008141485.1|  6 VCPKCNEE 13
                                      5*****95 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.047
                        zf_C2H2_10  5 CPKCqekl 12
                                      CP C++k+
  gi|518651965|ref|YP_008141485.1| 38 CPYCKYKA 45
                                      ******97 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.1      0.01       6.6       2      12 ..       6      16 ..       5      19 .. 0.84
   2 ?    5.5   0.4     0.041        26       2       9 ..      37      44 ..      36      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.01
                                      EETTTTEEESS CS
                           zf-C2H2  2 kCpdCgksFkr 12
                                      +Cp+C++ F  
  gi|518651965|ref|YP_008141485.1|  6 VCPKCNEEFDA 16
                                      7******9976 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.041
                                      EETTTTEE CS
                           zf-C2H2  2 kCpdCgks 9 
                                      kCp+C+++
  gi|518651965|ref|YP_008141485.1| 37 KCPYCKYK 44
                                      8****965 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   0.8     0.006       3.9      17      27 ..       3      13 ..       2      26 .. 0.78
   2 ?    8.3   1.1    0.0034       2.2      19      28 ..      35      46 ..      15      52 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.006
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr 27
                                      ++ vCP+C  +
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEE 13
                                      5789****976 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0034
                     Zn_Tnp_IS1595 19 fv.CPhCgsr.k 28
                                      f+ CP+C+++ +
  gi|518651965|ref|YP_008141485.1| 35 FIkCPYCKYKaH 46
                                      555*****9854 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 ?    6.9   0.9      0.01       6.5      22      26 .]       6      10 ..       2      12 .. 0.79
   2 ?    6.7   0.1     0.012       7.5       1       8 [.      35      42 ..      35      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.01
                            zf-ACC 22 VCPkC 26
                                      VCPkC
  gi|518651965|ref|YP_008141485.1|  6 VCPKC 10
                                      88888 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.012
                            zf-ACC  1 WtKCpsCg 8 
                                      ++KCp C+
  gi|518651965|ref|YP_008141485.1| 35 FIKCPYCK 42
                                      79*****7 PP

>> SoxD  Sarcosine oxidase, delta subunit family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.97   6.2e+02       2       9 ..       5      12 ..       4      19 .. 0.81
   2 ?   10.3   0.1   0.00089      0.57       2      19 ..      36      54 ..      35      58 .] 0.82

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.97
                              SoxD  2 itCPlcge 9 
                                      i CP c+e
  gi|518651965|ref|YP_008141485.1|  5 IVCPKCNE 12
                                      78999986 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00089
                              SoxD  2 itCPlcge.rdesEFaygG 19
                                      i+CP+c+   ++sEF+++ 
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYkAHRSEFSVAE 54
                                      9******967889**9875 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.2     0.011       6.8      25      37 .]       4      16 ..       2      16 .. 0.66
   2 ?    4.6   0.2     0.042        27       3       9 ..      36      42 ..      35      57 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                     zinc_ribbon_5 25 kVrCakCaevFda 37
                                      k+ C kC e Fda
  gi|518651965|ref|YP_008141485.1|  4 KIVCPKCNEEFDA 16
                                      5667777777765 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.042
                     zinc_ribbon_5  3 irCpdCd 9 
                                      i+Cp C+
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCK 42
                                      89****5 PP

>> DUF4668  Domain of unknown function (DUF4668)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00078       0.5      74      92 ..       3      21 ..       1      27 [. 0.89
   2 ?   -1.8   0.1       3.9   2.5e+03      76      86 ..      36      46 ..      32      51 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00078
                           DUF4668 74 skikcsrcnarkkhPkwFk 92
                                      ski+c++cn +   P+w k
  gi|518651965|ref|YP_008141485.1|  3 SKIVCPKCNEEFDAPRWDK 21
                                      9****************77 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.9
                           DUF4668 76 ikcsrcnarkk 86
                                      ikc+ c+ +++
  gi|518651965|ref|YP_008141485.1| 36 IKCPYCKYKAH 46
                                      56777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              28  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 379.90
//
Query:       gi|518651966|ref|YP_008141486.1|  [L=137]
Description: hypothetical protein FACI_IFERC00001G0605 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-14   54.5   5.0    2.1e-14   54.0   5.0    1.1  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   5.0   1.2e-18   2.1e-14       2     118 ..       3     121 ..       3     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1.2e-18
                                       EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHH CS
                               PIN   2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidae 76 
                                       ++DT++li+l+ +++ k   a kl+ ++++ ++++l l E+  vl+r +  +e++++ ++++ll ++++ki++id +
  gi|518651966|ref|YP_008141486.1|   3 YIDTNILISLIdKKDSKYNLANKLMKNYDNKIITELNLLEIKSVLSR-SGVIEEEIDALDEYLLiKNDIKIVNIDFN 78 
                                       89*********66666666666777777*******************.88888999999999998********8876 PP

                                       HH.HHHHHHHHHHHSBHHHHHHHHHHHHHT-EEE.ESSTHHHH CS
                               PIN  77 ia.eeaaeialkygllpnDaliaAtAkehgikliatfDedfrr 118
                                           +  +i++  +l+++D+l++A A+   +++++tfD+df++
  gi|518651966|ref|YP_008141486.1|  79 RSiNTGIDIINSIKLKTLDCLHIANAIIIHADKFITFDKDFKN 121
                                       55156779999999************999999999******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 929.49
//
Query:       gi|518651967|ref|YP_008141487.1|  [L=82]
Description: hypothetical protein FACI_IFERC00001G0606 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00076   18.7   0.3    0.00084   18.6   0.3    1.0  1  DUF4518   Domain of unknown function (DUF4518)
  ------ inclusion threshold ------
       0.03   14.3   0.3      0.035   14.1   0.3    1.2  1  YolD      YolD-like protein
      0.038   13.9   0.6      0.063   13.2   0.1    1.7  2  RHH_1     Ribbon-helix-helix protein, copG family


Domain annotation for each model (and alignments):
>> DUF4518  Domain of unknown function (DUF4518)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.3   1.4e-07   0.00084      24      80 ..      17      72 ..       5      81 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.4e-07
                           DUF4518 24 LadtvtnklikvenveeAleailsy.skdaeelLkrkkvkrellFkYLaskgvsvppd 80
                                      + + +  k   v+++++A+++i+++ ++++++++k+k  ++ell kYL++    +p  
  gi|518651967|ref|YP_008141487.1| 17 INKLIAFKI--VNSRTDAINYIMEHgINNVNNVIKKKEKTQELLEKYLKEGLPELPAG 72
                                      333333332..689*********9957899******************9988777654 PP

>> YolD  YolD-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.3   5.9e-06     0.035      18      71 ..       3      56 ..       1      68 [. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.9e-06
                              YolD 18 kvekpeLDeqqleeineklqealeeeqpvtityyedgeleevtgyiekidelnk 71
                                      kv    L+e+ l+ in+++  ++ + ++  i+y  ++ + +v+ +i+k +++++
  gi|518651967|ref|YP_008141487.1|  3 KVVSIRLSEDMLNTINKLIAFKIVNSRTDAINYIMEHGINNVNNVIKKKEKTQE 56
                                      6666789***************************************99876654 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 ?   13.2   0.1   1.1e-05     0.063       2      29 ..       5      33 ..       4      33 .. 0.88
   2 ?   -2.8   0.1       1.2   7.2e+03      31      38 ..      56      63 ..      56      64 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                      EEEEEEHHHHHHHHHHHHHHT.SSHHHHH CS
                             RHH_1  2 vsirldeellerLdelarrrg.rSrSelI 29
                                      vsirl+e++l ++++l++     Sr ++I
  gi|518651967|ref|YP_008141487.1|  5 VSIRLSEDMLNTINKLIAFKIvNSRTDAI 33
                                      9****************988888887776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.2
                                      HHHHHHHH CS
                             RHH_1 31 eAlreyle 38
                                      e+l+ yl+
  gi|518651967|ref|YP_008141487.1| 56 ELLEKYLK 63
                                      45666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1590  (0.0886831); expected 358.6 (0.02)
Passed bias filter:                      825  (0.0460148); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 532.65
//
Query:       gi|518651968|ref|YP_008141488.1|  [L=64]
Description: hypothetical protein FACI_IFERC00001G0607 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       931  (0.051927); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 407.60
//
Query:       gi|518651969|ref|YP_008141489.1|  [L=534]
Description: hypothetical protein FACI_IFERC00001G0608 [Ferroplasma acidarmanus fer1]
Scores for complete 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-28   98.1  54.0    6.3e-28   97.6  54.0    1.1  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
      1e-05   25.8   0.0    0.00092   19.6   0.0    2.7  2  CBS             CBS domain


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  54.0     7e-32   6.3e-28       3     378 ..      13     378 ..      11     381 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 7e-32
                                       HHHHHHHHHHH...HHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHH.CTCGCCTGCCT CS
                    Na_H_Exchanger   3 llillallvgl...larrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaG.leldlrelrkn 75 
                                       ++++l+ll++l   l++++++ + v++ii+G+++Gp +lgli      ++++  lg+ +llF  G le++  e +k 
  gi|518651969|ref|YP_008141489.1|  13 FIGALLLLAKLgeeLFEKFRIVSYVAAIIIGIIIGPGVLGLITIL-PNISLFISLGINFLLFTGGaLEFKELETKKL 88 
                                       566668888889989******************************.****************988344444444444 PP

                                       HHH.HHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHH CS
                    Na_H_Exchanger  76 lks.illlallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvln 151
                                       l +  +l +++ +++++ li++++y+++    ++l al++g++  +++++ ++++l++ g+  ++ g+ ++   v  
  gi|518651969|ref|YP_008141489.1|  89 LNPsNILTGVIEFILPFGLISFVVYYIFH---SVLIALIVGLVTGMSSAGPLTRLLTDTGLNHTEEGNSIFQQVVTM 162
                                       444589999****************8655...9999***************************************** PP

                                       HHHCCCCCHHHHHHTXXXXXTSSSTSXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS...CTHHHHHHHHHHHHHHH CS
                    Na_H_Exchanger 152 Davavvllavllalakeeaggetslllllliflvvavgglllglvigwllrlitrft...dddrelevllvlllall 225
                                       ++++v+l+++l  l+    g +++++l+l+i++ ++v ++++ l+  ++l +++  +    + +e+ +++++ ++l+
  gi|518651969|ref|YP_008141489.1| 163 EISGVILFSFLADLY----GKVVTIYLVLKIAMELVVSLVFILLFSRYVLTRLLVKIdfsARANETVIAVIIGFVLV 235
                                       **************9....555666655555555555555555555666665555555668**************** PP

                                       HHHHHHTSXXXHHHHHHHHHHHHH.HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHHHHHXXHHHHHHHHHHHH CS
                    Na_H_Exchanger 226 aallaellgvsgilgaflaGlvls.eyefsnklseklesfreglfnplfFvlvGlsldlkvlnnhlsvlilvllilv 301
                                       + ++++l g+ +++ a++ G+ l    +++  ++ek++ f +g+f+plfF+ +Gl +  k+    l +++l lli++
  gi|518651969|ref|YP_008141489.1| 236 LGFVGQLYGFNSAIIALFIGISLReFINERPLVAEKVSTFTYGFFEPLFFIGLGLYFV-KIT---LPLITLGLLIFA 308
                                       ************************777777779999*********************9.444...999999999999 PP

                                       HHHTHHHHHHHHHTTTXS.SXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTT.SSTTTCSTSXHHHHHHHHHH CS
                    Na_H_Exchanger 302 aillgrilavflllrllg.lslrealiigfgglqrgavalalaalgpalgllarel.yallivvvlftvlvqGlslk 376
                                       + ++ +++a+ + +r+++  ++++a+  ++     g v +al++++  l+l+ r    a++i+++l+tv+     ++
  gi|518651969|ref|YP_008141489.1| 309 IAIILKPIAGTITSRFMHvDTWKNAFGTSVH----GGVDAALLVVALGLSLIGRYDySAVMIAITLLTVV-----IP 376
                                       9999***********9962345666666554....5599999999999999***9977777888888887.....55 PP

                                       HH CS
                    Na_H_Exchanger 377 pl 378
                                       +l
  gi|518651969|ref|YP_008141489.1| 377 AL 378
                                       54 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.014   1.3e+02      31      52 ..     438     459 ..     412     461 .. 0.79
   2 !   19.6   0.0     1e-07   0.00092      11      56 ..     481     526 ..     474     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                       SEEEEEETTTBEEEEEEHHHHH CS
                               CBS  31 srlPVVdedgklvGivtlrDll 52 
                                       +++ V+++  k++G +tl+D +
  gi|518651969|ref|YP_008141489.1| 438 RAVIVINSKLKVLGQLTLSDMV 459
                                       6776787555**********75 PP

  == domain 2  score: 19.6 bits;  conditional E-value: 1e-07
                                       EEETTSBHHHHHHHHHHHTSS..EEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvs..rlPVVdedgklvGivtlrDllrall 56 
                                        v+ d++  +++++++e  ++   + VVd++gk++G + +r +l+ ++
  gi|518651969|ref|YP_008141489.1| 481 KVRCDSPATDLIKIFKE--YDppIVAVVDKSGKFIGTILEREILKHVA 526
                                       7999***********66..544356799****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (534 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1164  (0.0649228); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.32s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3459.08
//
Query:       gi|518651970|ref|YP_008141490.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G0609 [Ferroplasma acidarmanus fer1]
Scores for complete 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-54  183.2   0.2    6.6e-31  107.5   0.1    2.1  2  FmdA_AmdA  Acetamidase/Formamidase family
  ------ inclusion threshold ------
      0.049   13.3   0.0      0.078   12.6   0.0    1.2  1  AMNp_N     Bacterial AMP nucleoside phosphorylase N-terminus


Domain annotation for each model (and alignments):
>> FmdA_AmdA  Acetamidase/Formamidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   1.2e-24     1e-20      12     156 ..       9     149 ..       5     154 .. 0.91
   2 !  107.5   0.1   7.4e-35   6.6e-31     204     366 ..     155     300 ..     149     305 .. 0.93

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.2e-24
                         FmdA_AmdA  12 eeklhNRwHpdipavaevkpgetvkvecldwtdgqiknndsaddvrtvdlkkvHeltgPvevegAepGDllvveild 88 
                                       +e+lh Rw p+  +v +v+pget+ +++ d   +qi+++ +++d++++d +kv    gPv+v+gAe GD l +ei++
  gi|518651970|ref|YP_008141490.1|   9 NENLHFRWSPANIPVEHVSPGETLTIKIPDSSTKQIQKDFNSEDLKKIDDSKVDAAVGPVYVDGAEKGDTLKIEIKS 85 
                                       5799************************************************************************* PP

                         FmdA_AmdA  89 ievleeaewGytgifdkenggGflkdafpeaakaiwdlegiyassrq...ipgvrfrglphpGllGtapsk 156
                                       iev +   wG++ i+   + +G l+  f++    iwd++++ a+ ++   + +v++++ p++G++Gtap +
  gi|518651970|ref|YP_008141490.1|  86 IEVGT---WGWSAIM---KDFGALSPEFDDR-LVIWDINKTEARCMNkgfLDNVKIPVNPFLGIIGTAPGN 149
                                       ***95...****665...6899999888875.568888888888777777*******************75 PP

  == domain 2  score: 107.5 bits;  conditional E-value: 7.4e-35
                         FmdA_AmdA 204 vpprengGnmDiknlsrGskvylPVkveGaklsvGDlHfsqGDGEisfcg.aiemsgvvtlkvevikggmeklgikn 279
                                       +ppr+ gGnmD k l +Gs +ylPV+v+Ga ls+ D H+sqGDGE+  cg aie s +  +kv++ikg+     ik 
  gi|518651970|ref|YP_008141490.1| 155 IPPRNFGGNMDNKFLGAGSVLYLPVNVNGALLSFADPHASQGDGEV--CGtAIETSCTAVVKVDLIKGK----AIKY 225
                                       9*********************************************..********************9....9999 PP

                         FmdA_AmdA 280 piflpeevepryseylsfeGisvdesgkqhyldltvAyrnallraieyLkkfGytkeqaylllsvapvegrisgivd 356
                                       p ++ +  +   ++ ++ +G  ++  +      l+ +++ a+ ++i  L+++G+++e+ay+l+sva  + +is++vd
  gi|518651970|ref|YP_008141490.1| 226 PRIESRGNAG--TDCIISMG--IE--D-----SLEKSAKAAIWEMIGILSEYGFSREEAYILCSVA-GNLKISEMVD 290
                                       9999988888..78999999..33..3.....4779999***************************.7999****** PP

                         FmdA_AmdA 357 iPnvvatlal 366
                                       +P+ v+++ l
  gi|518651970|ref|YP_008141490.1| 291 MPDYVVSMEL 300
                                       *****99876 PP

>> AMNp_N  Bacterial AMP nucleoside phosphorylase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.7e-06     0.078     101     148 ..      15      64 ..       8      69 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.7e-06
                                       EEEEEE--GGGCCTSS..T---SCCCHHHHHHCS--B-STXXXXXXXXXX CS
                            AMNp_N 101 geSdqeiPlhyvldes..elelegalsaeladvfdvpdLaaidDeiadGt 148
                                       + S  +iP+++v  ++  ++++ +++++++++ f++ dL++idD+ +d+ 
  gi|518651970|ref|YP_008141490.1|  15 RWSPANIPVEHVSPGEtlTIKIPDSSTKQIQKDFNSEDLKKIDDSKVDAA 64 
                                       568899******999955588999999******************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 2174.43
//
Query:       gi|518651971|ref|YP_008141491.1|  [L=595]
Description: hypothetical protein FACI_IFERC00001G0610 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-56  191.8   0.2    1.6e-56  191.2   0.2    1.3  1  DNA_ligase_A_M   ATP dependent DNA ligase domain
      4e-31  108.7   0.1    1.1e-30  107.2   0.1    1.7  2  DNA_ligase_A_N   DNA ligase N terminus
    1.5e-21   76.8   0.0    3.7e-21   75.6   0.0    1.7  1  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region
    4.1e-06   27.2   0.2      7e-06   26.4   0.2    1.4  1  RNA_ligase       RNA ligase
  ------ inclusion threshold ------
      0.011   15.6   0.2      0.029   14.2   0.1    1.8  2  mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
      0.089   12.8   0.1       0.91    9.6   0.0    2.6  2  DNA_ligase_OB_2  DNA ligase OB-like domain
       0.13   12.5   0.0        9.5    6.6   0.0    2.7  2  Nab2             Nuclear abundant poly(A) RNA-bind protein 2 


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 !  191.2   0.2   6.2e-60   1.6e-56       2     204 .]     239     439 ..     238     439 .. 0.98

  Alignments for each domain:
  == domain 1  score: 191.2 bits;  conditional E-value: 6.2e-60
                                       EEEEEESCHHHHHHHTTTSEEEEEEEESSEEEEEEEETTEEEEEETTS-B-GGGCHHHHHHHHHHBSTTESEEEEEE CS
                    DNA_ligase_A_M   2 mLAeslksiekalkkleekafivEiKyDGeRaqvhkegdkvklfSRrlkditaakpelvkalkeafkkdeksvilDG 78 
                                       mLAe+l+si ++ +k+ +  + +E+KyDG R ++hk+gdk+k+fSR l++ t+++p+++++ k+ +  +  s+i+DG
  gi|518651971|ref|YP_008141491.1| 239 MLAERLRSIDDIREKM-NHHVSFEYKYDGLRTELHKKGDKIKIFSRGLEETTENFPDIIENFKKSYSFE--SIIIDG 312
                                       9**************9.89999********************************************986..9***** PP

                                       EEEEEETTTTCBEHHHHHCHHHHCHCCTHHHHHHSEEEEEEEEEEEETTEEHTTSCHHHHHHHHHHHB--BTTTEEE CS
                    DNA_ligase_A_M  79 ElvavdketgeilpfqklasrkkkkkkveeklkeaelclfvFDiLyldgesltdeplkeRrklLeeilkesedrvel 155
                                       E v ++++tge +pfq +++r  +k+++ ek +e++l++f+FDiL l+g +l+++p++eRrk+Lee++  ++++++l
  gi|518651971|ref|YP_008141491.1| 313 ESVPFNPDTGELFPFQMVSKRRGRKYQITEKSTEIPLVMFIFDILELNGRTLVNLPYEERRKILEENF-VDNEHFRL 388
                                       **********************9999******************************************.999***** PP

                                       --EEEESSHHHHHHHHHHHHHTTECEEEEEE..TT-CC-TTCEEEEEEEEE CS
                    DNA_ligase_A_M 156 aeslevkdveeleelleeaiseglEGlvvKn..pdskYepgkrsknwlKvK 204
                                       a++l+ +d+ee+++++e++i++g+EG+v+K+   +s+Y++g r++ w+K+K
  gi|518651971|ref|YP_008141491.1| 389 ATRLSSDDSEEINKFFEQSIEDGCEGIVAKDtsDESVYRAGARGWLWIKFK 439
                                       *******************************7779***************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 !  107.2   0.1   4.3e-34   1.1e-30       2     172 ..      16     187 ..      15     188 .. 0.95
   2 ?   -2.4   0.0         2   5.1e+03      47      62 ..     327     343 ..     269     346 .. 0.65

  Alignments for each domain:
  == domain 1  score: 107.2 bits;  conditional E-value: 4.3e-34
                                       CHHHHHHHHHHCC.---HHHHHHHHHHHHHTS-..SHHHHHHHHHH....SS-CCCS------HHHHHHHHHHHHT- CS
                    DNA_ligase_A_N   2 FaelaelfekieestkkrlekrailanffrkvesagpedlypalrL....llPdydgreygigesllakalaealgl 74 
                                       F+e ++ f ++e+ t+krle ++il +++++   ag+ dl  +++L    l+Pdy+g+e+g+ ++l++k la ++g+
  gi|518651971|ref|YP_008141491.1|  16 FSEASKKFMEMES-TTKRLELTSILGSLLEN---AGD-DLKELVYLiqgkLAPDYEGIEFGVSGKLIVKSLAAISGM 87 
                                       8888899999999.899************54...467.9************************************** PP

                                       -HHHHHHHHHHHS-HHHHHHHHHCCHHHH.------BHHHHHHHHHHHHH-.STTHHHHHHHHHHHHHHHS-HHHHH CS
                    DNA_ligase_A_N  75 skkkikdalakvgDlgevaeevlskrstl.akkspltieevnelLdklaaa.gkgsedekkkilkkllkraspeEak 149
                                       +++++++   k gDlg +a+e+++k  +     ++lt+  v+  L +la++ g+gs + k +i ++l+ ++ pe++k
  gi|518651971|ref|YP_008141491.1|  88 DEEEVNKLFYKNGDLGITASEIREKMEQKpLFREDLTVHYVYTRLMELAKSaGHGSVKGKTDIYADLMVNSYPEDIK 164
                                       ***999995567***********999999999*****************888************************* PP

                                       HHHHHHCT---SS--HHHHHHHH CS
                    DNA_ligase_A_N 150 yliriilkdlriglsektvldal 172
                                       y++rii ++lr+g+++ t+ld l
  gi|518651971|ref|YP_008141491.1| 165 YITRIIMGKLRLGVADSTILDSL 187
                                       ********************987 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                                       H.SS-CCCS------HH CS
                    DNA_ligase_A_N  47 L.llPdydgreygiges 62 
                                       + ++ +++gr+y+i+e+
  gi|518651971|ref|YP_008141491.1| 327 FqMVSKRRGRKYQITEK 343
                                       33566777888888887 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 !   75.6   0.0   1.4e-24   3.7e-21       1      99 []     464     573 ..     464     573 .. 0.93

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.4e-24
                                       GGGSEEEEEEEEEE..TTEEEEEEEE-SS--HHHHHHHHHHHGGGEECTTCESS---HHHHTTEEE-TT-EEEEEES CS
                    DNA_ligase_A_C   1 rgglvgslllgvyd..dgkleyvgkvgtGfsdaeleelrkklkelerkkppfaekvpeeekrdvWvePelvveVkfa 75 
                                       r+g++g+ll++ y+  +  +e+v+k gtGfsd+ l  l k+l++l r+++p + + +    +d W+ P++v+e+++a
  gi|518651971|ref|YP_008141491.1| 464 RAGAYGALLMASYNeeTHAFESVTKLGTGFSDEVLFSLPKMLSDLVRDHKPAMVESK--MVPDIWIYPQIVMEIQGA 538
                                       6799**********77777********************************955554..55779************* PP

                                       EEECTSSSTT...........EECT-EEEEE-TTS CS
                    DNA_ligase_A_C  76 eitasgkyka...........slRfPrfkrlReDk 99 
                                       eit s+ +++           +lRfPr++++R+Dk
  gi|518651971|ref|YP_008141491.1| 539 EITVSPIHTCafgkiekdsglALRFPRLIKIRDDK 573
                                       **********************************8 PP

>> RNA_ligase  RNA ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2   2.7e-09     7e-06       5     155 ..     260     431 ..     256     439 .. 0.68

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
                                       EEEE-SSEEEEEEEE..TTEEEEETTCEBCTTTHHHHHHTHHHHHHHHHHHHH..ECCEEEEEEEES.......... CS
                        RNA_ligase   5 vtEKlDGtnfriylv..kevgvasRsqilpfgeekfkefkrwaaalrkklkeklaneelilyGElig.......... 69 
                                        + K DG ++ +++   k ++++sR+ +           +++  +  +++k+  + e++i+ GE +           
  gi|518651971|ref|YP_008141491.1| 260 FEYKYDGLRTELHKKgdK-IKIFSRGLEE---------TTENFPDIIENFKKSYSFESIIIDGESVPfnpdtgelfp 326
                                       567999999999998533.9999999777.........12222333445555555677********98765555554 PP

                                       ..SS.........TTSS.......EEEEEEEEEEECTTBECE--HHHH.HHHHHCCT...B..EEEEE.SSHHHHHC CS
                        RNA_ligase  70 .hsi.......kygglpk......efyvFdifdirdkeeqrylspdev.ealakglg...tvpvlyegkflaaeell 128
                                        + +       ky+  +k       ++ Fdi++++  ++   l+++e+ ++l++++    + +++++ + +++ee+ 
  gi|518651971|ref|YP_008141491.1| 327 fQ-MvskrrgrKYQITEKsteiplVMFIFDILELN-GRTLVNLPYEERrKILEENFVdneHFRLATRLSSDDSEEIN 401
                                       41.04444555555533378898899999999887.459999******77777755477899999888888888888 PP

                                       CC..HHHHTC--EEEEEESSSSBE.TTE.B CS
                        RNA_ligase 129 ell.lskgnkrEGlVikpeselyk.nkg.r 155
                                       +++ +s +  +EG+V k++s+    + g r
  gi|518651971|ref|YP_008141491.1| 402 KFFeQSIEDGCEGIVAKDTSDESVyRAGaR 431
                                       8865544569*******9987666555554 PP

>> mRNA_cap_enzyme  mRNA capping enzyme, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   6.6e+03      23      78 ..     263     313 ..     252     315 .. 0.54
   2 ?   14.2   0.1   1.1e-05     0.029      91     129 ..     349     387 ..     338     407 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                       EESSEEEEEEEEECTEEEEEEETTS-EEEESSST-BTTSSSSTCTSBGGSEEEEEE CS
                   mRNA_cap_enzyme  23 KaDGiRylmllteeeegvylidRenevyrvenlrfprekdkeklekvldetllDgE 78 
                                       K DG+R  +  + +  ++ ++ R  e    +   fp   ++ k++  +++ ++DgE
  gi|518651971|ref|YP_008141491.1| 263 KYDGLRTELHKKGD--KIKIFSRGLEETTEN---FPDIIENFKKSYSFESIIIDGE 313
                                       66777776665555..466666665544333...3333332233445666666666 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEEEEETTEEGTTSBHHHHHHHHHHHTHHHHHHH CS
                   mRNA_cap_enzyme  91 lryliyDivaingvtvaeeplskRleilkkelikprnee 129
                                       l + i+Di+++ng+t+++ p+++R +il+ ++++  +  
  gi|518651971|ref|YP_008141491.1| 349 LVMFIFDILELNGRTLVNLPYEERRKILEENFVDNEHFR 387
                                       5689***************************99877655 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 ?    9.6   0.0   0.00036      0.91       2      32 ..     460     496 ..     459     498 .. 0.79
   2 ?   -0.6   0.0      0.56   1.4e+03      54      66 .]     557     570 ..     547     570 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00036
                                       ...EEEEEEEEEEEEE.TTEE......EEE-SS--HH CS
                   DNA_ligase_OB_2   2 GkGkykgmlGallvetkkgkr......fkiGsGlsda 32 
                                       G+G+ +g  Gall+   + ++       k+G+G+sd+
  gi|518651971|ref|YP_008141491.1| 460 GRGRRAGAYGALLMASYNEEThafesvTKLGTGFSDE 496
                                       9*************997644223344599******97 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.56
                                       SSS.-EEEEEEEE- CS
                   DNA_ligase_OB_2  54 kgv.pRfPsflrvR 66 
                                       +g+ +RfP+  ++R
  gi|518651971|ref|YP_008141491.1| 557 SGLaLRFPRLIKIR 570
                                       45559****99988 PP

>> Nab2  Nuclear abundant poly(A) RNA-bind protein 2 (Nab2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0037       9.5      21      73 ..     156     205 ..     150     224 .. 0.83
   2 ?    2.6   0.0     0.063   1.6e+02      10      30 ..     236     256 ..     233     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0037
                              Nab2  21 lenfnedvnyvaeyivlllsnGgtvesvvqelstlfdsvskealadvvqtaff 73 
                                       ++ + ed++y++  i+  l  G    ++++ l+  f   s++  ad+v+ta+ 
  gi|518651971|ref|YP_008141491.1| 156 VNSYPEDIKYITRIIMGKLRLGVADSTILDSLVHAF---SSKDNADMVETAYN 205
                                       67899*****************99999988777666...66667788888875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                              Nab2  10 lkvivaeklktlenfnedvny 30 
                                       +kv++ae+l+++++  e +n+
  gi|518651971|ref|YP_008141491.1| 236 FKVMLAERLRSIDDIREKMNH 256
                                       69**************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (595 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3998.96
//
Query:       gi|518651972|ref|YP_008141492.1|  [L=158]
Description: single-stranded DNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0001   22.2   0.5    0.00016   21.6   0.5    1.5  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.002   17.9   0.0     0.0021   17.8   0.0    1.1  1  CDC24_OB3        Cell division control protein 24, OB domain 
     0.0069   16.3   0.2     0.0093   15.9   0.2    1.2  1  REPA_OB_2        Replication protein A OB domain
  ------ inclusion threshold ------
       0.11   12.2   0.1       0.17   11.5   0.1    1.3  1  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.5   3.5e-08   0.00016      11      67 ..      27      87 ..      17     124 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.5e-08
                                      E........EEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEE CS
                   tRNA_anti-codon 11 s........drsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggele 67
                                                ++ ++v+ +++ D+tg+i+++l++    ++ ++++ G v+++  G+++  +g  + 
  gi|518651972|ref|YP_008141492.1| 27 GepkeiktrFGEDKSVSEVIVADDTGKITLTLWD----DQTKDIRDGEVLKIDnGYISLLRGH-MR 87
                                      445555555588899*******************....9*************99999877665.44 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 !   17.8   0.0   4.7e-07    0.0021       1      58 [.       9      80 ..       9     118 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.7e-07
                         CDC24_OB3  1 DLrekmlnvtLlGrvvai.....freknsek.kkmdryslrieDttGaidatlweeagklhfk...........r 58
                                      DL ++   v ++G+vv +     +   ++   +   ++ + ++D+tG+i +tlw+   k+++            +
  gi|518651972|ref|YP_008141492.1|  9 DLTPSSRRVNVVGKVVVLgepkeI---KTRFgEDKSVSEVIVADDTGKITLTLWDDQTKDIRDgevlkidngyiS 80
                                      67777888999*******764332...333344555569********************9998776655555552 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 !   15.9   0.2   2.1e-06    0.0093       9      71 ..      13      71 ..       4      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                         REPA_OB_2  9 kdsivDvigvvksveevseitskstekelkkreltlvDesgasvevtlWgkeaekfesseepv 71
                                      +   v v+g v  ++e +ei ++ +e + +  e+ + D++g ++++tlW++++++++  + +v
  gi|518651972|ref|YP_008141492.1| 13 SSRRVNVVGKVVVLGEPKEIKTRFGE-DKSVSEVIVADDTG-KITLTLWDDQTKDIR--DGEV 71
                                      456799******************99.889999*******9.59*******998865..4444 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.17      57     129 ..       5      76 ..       2      86 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                           DUF4131  57 ndlsqllesgqeviveGvvaslpeltgsgtrfvlevervlsagktkpvsgrvlvtvpkspaeglrpGdrlrl.t 129
                                       +++ +l++s++ v v+G+v+ l e ++ +trf  + +  +s+   ++ +g++ +t+ +++ +++r G++l++ +
  gi|518651972|ref|YP_008141492.1|   5 TKIKDLTPSSRRVNVVGKVVVLGEPKEIKTRFGEDKS--VSEVIVADDTGKITLTLWDDQTKDIRDGEVLKIdN 76 
                                       56778888899*******************9996654..6777778889*********************9855 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:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1048.77
//
Query:       gi|518651973|ref|YP_008141493.1|  [L=130]
Description: hypothetical protein FACI_IFERC00001G0612 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (130 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 938.22
//
Query:       gi|518651974|ref|YP_008141494.1|  [L=621]
Description: hypothetical protein FACI_IFERC00001G0613 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-20   74.0   0.0    5.5e-20   72.2   0.0    1.9  2  Helicase_C_2  Helicase C-terminal domain
    1.7e-18   66.9   0.4    3.5e-18   65.8   0.4    1.5  1  DEAD_2        DEAD_2
    2.6e-07   30.8   0.3     0.0022   18.0   0.0    2.7  2  ResIII        Type III restriction enzyme, res subunit
    9.6e-05   22.2   0.0       0.11   12.3   0.0    2.8  3  DEAD          DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.027   14.7   0.4         52    4.1   0.0    3.4  3  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> Helicase_C_2  Helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   6.9e+03      18      40 ..     324     346 ..     322     381 .. 0.51
   2 !   72.2   0.0   1.5e-23   5.5e-20       4     164 ..     452     616 ..     449     620 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                      Helicase_C_2  18 Syklleevverlkeeleskkiei 40 
                                       S ++le+v+++l++    ++ ++
  gi|518651974|ref|YP_008141494.1| 324 SRNYLENVYNFLYDYQRMENGSV 346
                                       55666666666665332222222 PP

  == domain 2  score: 72.2 bits;  conditional E-value: 1.5e-23
                      Helicase_C_2   4 llevvpggvlvffpSyklleevverlkeel......eskkieifveekeesrekvleeykekkkkgaillavcrGkl 74 
                                       ++++  + vlv +pSy++l   +   k+ +      es +++ + e +++ + + +e+  +  +++ i+++v +Gkl
  gi|518651974|ref|YP_008141494.1| 452 VYSKSDKSVLVAVPSYRILFGDTY-TKTPGignylpESMRANCVFE-NKKISYSYIEKKAK--ERKIIIFSVHGGKL 524
                                       567778889999999998843222.222223344444444555555.56666666666666..9************* PP

                      Helicase_C_2  75 sEGidfs...ddllraviivglPfpnpkdpeveakreyldekgkknsgkewylpealravnQaiGRliRhkdDygai 148
                                        EGi +      l++ vii glP+ +++d + + k +yl++  kkn+++ +y + al +v+Qa+GR  R+ +D+++i
  gi|518651974|ref|YP_008141494.1| 525 LEGIQLVnrgKSLISDVIIAGLPLIPLDDYR-KDKIKYLEKVLKKNAYNLLYYEFALIKVKQAAGRSTRSPEDTSSI 600
                                       ****998443567889***********9888.8999*****9999******************************** PP

                      Helicase_C_2 149 vllDeRfakeeirekl 164
                                        l+D+Rf ++ ++++l
  gi|518651974|ref|YP_008141494.1| 601 WLCDDRFDEPFWQSNL 616
                                       ********99888776 PP

>> DEAD_2  DEAD_2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.4   9.8e-22   3.5e-18       1     166 [.      54     232 ..      54     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 9.8e-22
                                       EEESSHHHHHHHHHHHHHHHHHCHHHS---EEEE--CCCC-SCHHCCCHHCCCCHHHHHHHHHCCHHCCH....... CS
                            DEAD_2   1 ycsRThsqleqvvkelkklesykkkkekvkvviLgSRknlCineevkkekkekavneaCkelkkkkaeek....... 70 
                                       y +RTh++ +++ ++ +k        +++ ++ L ++++lC  +e   + + +  +++Ck    k ++ k       
  gi|518651974|ref|YP_008141494.1|  54 YLTRTHNEFTRLYEDNQKY-------FNIPALYLYGKSKLCPLKERWYDSEDDGQKNVCKGCPLKDKTIKldlknir 123
                                       6778888877777776665.......45899**********988888888888888999988777766667788875 PP

                                       .......TTTTTT-SCCCCHHHHHHHHHHC---CHHHHHHHHHCT--HHHHHHHHHCCTSEEEEEHHHHTSCCCHHH CS
                            DEAD_2  71 .......eekCsffenleelkklkkllleevvdiedlvelgeklklCPYylsrelledadiiilpYqyLldekires 140
                                              + + +  e  ++  ++k l  ++  ++ ++++  + ++ CPYy++r+++ da+ii + Y+yLl+++ir +
  gi|518651974|ref|YP_008141494.1| 124 spesfleDIEADSTELIRQDVESKALGRDTKGNLVTIKK-ENVKSYCPYYSVRSNMADAQIIAMTYNYLLNPSIRFN 199
                                       544443322222222222222223333333333333333.344689*****************************88 PP

                                       HH.......T..GCGCEEEECTCCCHHHHHHHC CS
                            DEAD_2 141 lk.......gislknsivilDEAhNiedvceea 166
                                       +        +i+l+++ +++DEAhN+++v+e+ 
  gi|518651974|ref|YP_008141494.1| 200 VFhgtegeeMIDLNECYIVFDEAHNLDSVIENF 232
                                       76577788889******************9986 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   6.2e-07    0.0022       1      44 [.       3      44 ..       3      77 .. 0.88
   2 !   10.2   0.1   0.00016      0.57      64     147 ..     147     228 ..     127     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 6.2e-07
                                      --EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHH CS
                            ResIII  1 klelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaakl 44
                                      k+++re+Q   i  + ++l  ++++++ i+++TG+GKT  ++ l
  gi|518651974|ref|YP_008141494.1|  3 KFTPREWQDALISTVSKNL--EEKNKIAIEAPTGSGKTSFILYL 44
                                      5789***************..5999*************776544 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHHGGGGTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH............HHHTTT-SEE CS
                            ResIII  64 kslleqtleefkkflseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseee....eeeseellrdrfdvi 136
                                       k+l   t+ ++  +++e++k+ +  +s ++++a      +++i+ +t++ l ++s +       e ee+ + ++ +i
  gi|518651974|ref|YP_008141494.1| 147 KALGRDTKGNLVTIKKENVKSYCPYYSVRSNMA------DAQIIAMTYNYLLNPSIRFnvfhGTEGEEMIDLNECYI 217
                                       555555566666666666666666666677777......999999999999999966666655556666666666** PP

                                       EEETGGGTTS. CS
                            ResIII 137 iiDEaHrlgak 147
                                       ++DEaH+l + 
  gi|518651974|ref|YP_008141494.1| 218 VFDEAHNLDSV 228
                                       *******9874 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   3.1e-05      0.11      11      36 ..      17      46 ..       7     108 .. 0.75
   2 !    6.9   0.0    0.0013       4.7      98     140 ..     181     234 ..     136     258 .. 0.65
   3 ?   -3.2   0.0       1.7   6.2e+03     160     170 ..     377     387 ..     350     392 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                                      HH....TTCEEEEEESTTSSHHHHHHHHHH CS
                                      xx....xxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 11 il....gggdvlvaaeTGsGKTlaflipvl 36
                                      +     +++++ ++a+TGsGKT   l  ++
  gi|518651974|ref|YP_008141494.1| 17 VSknleEKNKIAIEAPTGSGKTSFILYLAF 46
                                      443333678999**********98776665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0013
                                       CSEEEEEHHHHHH.HH.........HCTSSHCTTEEEEEEETHHHHHHT..TTHH CS
                                       xxxxxxxxxxxxx.xx.........xxxxxxxxxxxxxxxxxxxxxxxx..xxxx RF
                              DEAD  98 vdivvgtpgrldd.ll.........stgklnlsqvrflVlDEadrlldq..gfsd 140
                                       ++i+ +t   l++  +          ++ ++l+++ ++V+DEa++l +   +f++
  gi|518651974|ref|YP_008141494.1| 181 AQIIAMTYNYLLNpSIrfnvfhgteGEEMIDLNEC-YIVFDEAHNLDSVieNFGR 234
                                       55555555555553224555555432334667777.9*********998663333 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.7
                                       SEEEEEESSBS CS
                                       xxxxxxxxxxx RF
                              DEAD 160 rqvivlSATlp 170
                                       + vi++S T+p
  gi|518651974|ref|YP_008141494.1| 377 NSVIFMSGTMP 387
                                       459999*9998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.022        80       5      24 ..      24      43 ..      20      65 .. 0.85
   2 ?    4.1   0.0     0.015        52      17      65 ..      82     137 ..      81     168 .. 0.86
   3 ?    3.0   0.1     0.033   1.2e+02      94     112 ..     216     232 ..     202     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.022
                            AAA_22  5 agilvvtGesGtGKTtllrr 24
                                      ++ +++ +++G+GKT  +  
  gi|518651974|ref|YP_008141494.1| 24 KNKIAIEAPTGSGKTSFILY 43
                                      5568999********87765 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.015
                            AAA_22  17 GKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdllrellralg 65 
                                       GK+ l+    +++d e + ++        ++++++ +l++  s++++l+++  + +
  gi|518651974|ref|YP_008141494.1|  82 GKSKLCPLKERWYDSEDDGQKnvckgcpLKDKTIKLDLKNIRSPESFLEDIEADST 137
                                       9************988777779****************************988766 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.033
                            AAA_22  94 lliiDEaqhlrseealeeL 112
                                        ++ DEa++l+   ++e++
  gi|518651974|ref|YP_008141494.1| 216 YIVFDEAHNLD--SVIENF 232
                                       699*******5..333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.66u 0.30s 00:00:00.96 Elapsed: 00:00:00.47
# Mc/sec: 3980.32
//
Query:       gi|518651975|ref|YP_008141495.1|  [L=334]
Description: hypothetical protein FACI_IFERC00001G0614 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-24   86.5  52.5    5.4e-14   51.9  21.9    2.0  2  MFS_1           Major Facilitator Superfamily
    0.00033   20.1   6.1    0.00033   20.1   6.1    2.5  3  TssN            Type VI secretion system, TssN
  ------ inclusion threshold ------
       0.72    9.9   9.2        3.8    7.6   1.7    3.6  3  DUF454          Protein of unknown function (DUF454)
       0.96    9.5   4.8        3.2    7.8   0.7    2.3  2  Gly-zipper_Omp  Glycine zipper


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 !   48.1  22.6   1.6e-16   7.4e-13      92     323 ..       4     255 ..       1     265 [. 0.78
   2 !   51.9  21.9   1.2e-17   5.4e-14       3     178 ..     142     322 ..     141     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 1.6e-16
                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wravfyilaivsl 162
                                        +l  + a a++p++  li + + k+  + ++g +++ +++G++lg ++g l+++ ++       +++++++a ++l
  gi|518651975|ref|YP_008141495.1|   4 LILFQIVAMASVPVSTLLILENSDKSSWSNVMGKFNSYSAIGTVLGLGIGVLILTFFSgmgrklIPYLYIVAAWFYL 80 
                                       455556667999***************************************************************** PP

                             MFS_1 163 lafvlfllllpeepperkrkspkeee.........kgtgpaplvp...awkallkdpvlwillialllfffgfsgll 227
                                       +a+++    l+ ++p+ + +++k            ++ +p++lv       +++ + +l ++li+ l+ ++gf++++
  gi|518651975|ref|YP_008141495.1|  81 VAGII--SILVLKEPKTEISRGKIGYlfalhaierVRYFPTHLVHipgKENKIKIPDHLKLYLITTLILMMGFQLFF 155
                                       ****9..7777777777777777775667766666444444444454433444444455457777777778****** PP

                             MFS_1 228 tllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavt..ssavl 302
                                       +  p+++ ++++ s    +++++ l +l++a+ ++ agr+++ +g+ r+l ++ ++ ++++l + +++++  ++   
  gi|518651975|ref|YP_008141495.1| 156 IPYPVFVIDRMNAS-ENDIYIMYLLNSLFSAATFIPAGRYINYIGSNRMLSISTSIRVVLFLVMGVVSFFvfDTVGY 231
                                       **************.8999999************************************************7544444 PP

                             MFS_1 303 lllvlvl...iGfglgfvfpslla 323
                                       lll++v+   +G  ++f+ +s ++
  gi|518651975|ref|YP_008141495.1| 232 LLLFIVMygvFGAIWSFIGISEIT 255
                                       444555533344444444444444 PP

  == domain 2  score: 51.9 bits;  conditional E-value: 1.2e-17
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       +++++ ++++ ++++ +p ++ +  ++s+  i +++ l +l++a++ +p+Gr ++ +G+ r+l ++  + ++ +l++
  gi|518651975|ref|YP_008141495.1| 142 ITTLILMMGFQLFFIPYPVFVIDRMNASENDIYIMYLLNSLFSAATFIPAGRYINYIGSNRMLSISTSIRVVLFLVM 218
                                       7899***************999***************************************************5555 PP

                             MFS_1  80 l....fa...sslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllassl 148
                                            f+    ++  l++v+  + G+  +++  + ++ i+ +++   rg++ig++++ +++G i+g++l+g++a  +
  gi|518651975|ref|YP_008141495.1| 219 GvvsfFVfdtVGYLlLFIVMYGVFGAIWSFIGISEITSISNMATTLIRGKVIGYYNSLNGVGQIIGAGLSGFIAYDI 295
                                       5455333633444444555555555555666677788899999999******************************* PP

                             MFS_1 149 gWravfyilaivsllafvlfllllpeeppe 178
                                       g++  f++ ai+ l ++++  +++  + p+
  gi|518651975|ref|YP_008141495.1| 296 GYSFDFILSAIIVLSGLLI--IFYSKP-PD 322
                                       ****************774..555444.44 PP

>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   6.1   7.4e-08   0.00033      27     168 ..      37     174 ..       5     178 .. 0.87
   2 ?   -3.5   7.4       1.2   5.4e+03      30      78 ..     201     248 ..     175     266 .. 0.68
   3 ?   -3.4   0.1       1.1   4.8e+03      98     109 ..     302     313 ..     283     328 .. 0.54

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.4e-08
                              TssN  27 llkkkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhlylllkkffkelkekkilfeilltliv 103
                                       + ++ ++i ++L +g+ + ++ +++ ++ +++py yi++  +yl+ Gi+ +  +lk+ + e++  k  + +l++l +
  gi|518651975|ref|YP_008141495.1|  37 KFNSYSAIGTVLGLGIGVLILTFFSGMGRKLIPYLYIVAAWFYLVAGIISIL-VLKEPKTEISRGK--IGYLFALHA 110
                                       56778999*******************************************9.9999999999999..788888888 PP

                              TssN 104 illglvlfvlvfnllselqygvwaatsllvfiipllflktykallsIPveiYktwkypenkkeee 168
                                       i    ++ ++++++  + + ++ +  +l  ++i +l+l++  +l+ IP++++ + +++ ++++ +
  gi|518651975|ref|YP_008141495.1| 111 IERVRYFPTHLVHIPGKEN-KIKIPDHLKLYLITTLILMMGFQLFFIPYPVFVIDRMNASENDIY 174
                                       8877777777777665554.555699**************99999*********99999977655 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.2
                              TssN  30 kkkliiyiLlaglvlalpgllgflknefvpygyillqilylllGilhly 78 
                                       ++ l i   + ++++ ++g+++f+  ++v y ++l+ ++y ++G +  +
  gi|518651975|ref|YP_008141495.1| 201 NRMLSISTSIRVVLFLVMGVVSFFVFDTVGY-LLLFIVMYGVFGAIWSF 248
                                       4555555566677777888888877777744.34445566677766554 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.1
                              TssN  98 lltlivillglv 109
                                       +l+ i++l gl+
  gi|518651975|ref|YP_008141495.1| 302 ILSAIIVLSGLL 313
                                       222222222222 PP

>> DUF454  Protein of unknown function (DUF454)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1     0.069   3.1e+02       2      21 ..      70      89 ..      69      95 .. 0.87
   2 ?    3.5   0.1     0.016        70      64      96 ..     130     162 ..     122     188 .. 0.83
   3 ?    7.6   1.7   0.00084       3.8      55     110 ..     192     247 ..     180     253 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.069
                            DUF454  2 llllllGllslalGviGivl 21
                                      +l+++++++ l+ G+i i++
  gi|518651975|ref|YP_008141495.1| 70 YLYIVAAWFYLVAGIISILV 89
                                      68999999999999999875 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.016
                            DUF454  64 kraitlkaKvialllmllsllislllveslwvk 96 
                                       k +i+ + K+  +++++l++++ l++++ +++ 
  gi|518651975|ref|YP_008141495.1| 130 KIKIPDHLKLYLITTLILMMGFQLFFIPYPVFV 162
                                       55789999******************8876655 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.00084
                            DUF454  55 gpyirdwrekraitlkaKvialllmllsllislllveslwvkillalvllvvllyi 110
                                       g+yi+   ++r ++ ++ ++++l++++ ++ ++++ ++ ++ +++++  ++ +++ 
  gi|518651975|ref|YP_008141495.1| 192 GRYINYIGSNRMLSISTSIRVVLFLVMGVVSFFVFDTVGYLLLFIVMYGVFGAIWS 247
                                       789999999***************99999999999666666666666666666654 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.2     0.024   1.1e+02      23      38 ..      41      56 ..      33      57 .. 0.72
   2 ?    7.8   0.7   0.00072       3.2      10      41 ..     267     298 ..     266     300 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.024
                    Gly-zipper_Omp 23 GaliGAavGaavGgli 38
                                       ++iG+++G  +G li
  gi|518651975|ref|YP_008141495.1| 41 YSAIGTVLGLGIGVLI 56
                                      5677777777777665 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00072
                    Gly-zipper_Omp  10 GaliGgavggrgtGaliGAavGaavGgliGaa 41 
                                       G +iG++++  g+G +iGA++ +++ + iG+ 
  gi|518651975|ref|YP_008141495.1| 267 GKVIGYYNSLNGVGQIIGAGLSGFIAYDIGYS 298
                                       5689**888559***********999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); 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:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.51
# Mc/sec: 1956.51
//
Query:       gi|518651976|ref|YP_008141496.1|  [L=220]
Description: hypothetical protein FACI_IFERC00001G0615 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-22   79.8   0.1    2.6e-22   79.4   0.1    1.1  1  Glycos_transf_2  Glycosyl transferase family 2
    1.2e-11   44.9   0.0    1.4e-11   44.7   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00012   21.6   0.1    0.00032   20.2   0.0    1.6  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.034   14.6   0.0       0.09   13.3   0.0    1.7  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 !   79.4   0.1   5.7e-26   2.6e-22       2     167 ..       5     159 ..       4     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 79.4 bits;  conditional E-value: 5.7e-26
                                       EEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH- CS
                   Glycos_transf_2   2 vviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraa 78 
                                       ++ipt Nee+t+  +++ ll+    + +eiivvD +StD+t+ei+        + +vi  ++  G++ a+ +gl++a
  gi|518651976|ref|YP_008141496.1|   5 AIIPTINEEETIGSVIDGLLNS--VEGIEIIVVDTNSTDRTKEIATGR-----GATVINESRS-GYGMAYKTGLQHA 73 
                                       79*******************9..************************.....99***99966.************* PP

                                       -SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTCS CS
                   Glycos_transf_2  79 tgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfei 155
                                       +gd+i+++D D +++ d +++l++ +  d++  + + r+  +   +  + ++     + + +++ +   k+nl +  
  gi|518651976|ref|YP_008141496.1|  74 KGDIIVCMDGDNTYPTDIVRPLLDIIRMDEVNFISCDRMTLRTQHNYTSLHY---IGNSVLNFTMRLLFKINLNDSQ 147
                                       ****************************888666666655555555555444...5777777777888888888888 PP

                                       TCCCEEEEHHHH CS
                   Glycos_transf_2 156 gsaallrreale 167
                                       ++++++ r+ ++
  gi|518651976|ref|YP_008141496.1| 148 SGMWIFYRDFYD 159
                                       888888777665 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 !   44.7   0.0   3.2e-15   1.4e-11       4     138 ..       3     125 ..       2     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 3.2e-15
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++ ++pt+nee+++g+v++ ll++    +e++vv+++s++ t e a +      + + +v+  +r     g+  a++
  gi|518651976|ref|YP_008141496.1|   3 VTAIIPTINEEETIGSVIDGLLNS-VEGIEIIVVDTNSTDRTKEIATG------R-GATVINESR----SGYGMAYK 67 
                                       789*******************94.788****************9976......4.557763333....4788899* PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalga 138
                                        +l+++k+d+++ +D+D+    d+++ ll +++ ++v ++ +++++l+ ++  + l++
  gi|518651976|ref|YP_008141496.1|  68 TGLQHAKGDIIVCMDGDNTYPTDIVRPLLDIIRMDEVNFISCDRMTLRTQHNYTSLHY 125
                                       ********************************999*********99987776555554 PP

>> Glyco_tranf_2_2  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.0   7.2e-08   0.00032       2     111 ..       5     104 ..       4     118 .. 0.77
   2 ?   -1.1   0.0      0.23   1.1e+03     196     246 ..     134     185 ..     101     205 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 7.2e-08
                   Glyco_tranf_2_2   2 vviplraseerhyieerv...lqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNr 75 
                                        +ip  ++ee+  i   +   l+      e ie+ivvd  S++      + i   ++   + +e    y  + a   
  gi|518651976|ref|YP_008141496.1|   5 AIIPTINEEET--IGSVIdglLNS--V--EGIEIIVVDTNSTDR----TKEIATGRGATVI-NESRSGY--GMAYKT 68 
                                       58888888888..55555421333..3..57************9....5666777777763.4434555..566789 PP

                   Glyco_tranf_2_2  76 GaskaesdlvlFlDaDcfissDkfekilklitikkl 111
                                       G ++a++d+++ +D+D  + +D +  +l +i++ ++
  gi|518651976|ref|YP_008141496.1|  69 GLQHAKGDIIVCMDGDNTYPTDIVRPLLDIIRMDEV 104
                                       ************************999999987665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                   Glyco_tranf_2_2 196 llRlakaikslek.mpvellykarakslsnykGfrrflealakeaaalglvv 246
                                        +Rl+ +i+  +    + + y++   +++n +   +f e++  +a  lg+ +
  gi|518651976|ref|YP_008141496.1| 134 TMRLLFKINLNDSqSGMWIFYRDFYDKMKNLSNGMSFSEDIKIDAVRLGKLI 185
                                       4555555544433033457788888888888888888888888887777765 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     2e-05      0.09       2      87 ..      11      90 ..      10      99 .. 0.76
   2 ?   -2.2   0.0       1.4   6.3e+03      56      77 ..     132     154 ..     100     157 .. 0.53

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfd..rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvv 78
                                      ne+++++++++ +l+  ++  +i+v+d +stD+t +i     +  + ++++ y      +++ + l+  +a++d ++ +
  gi|518651976|ref|YP_008141496.1| 11 NEEETIGSVIDGLLNS-VEgiEIIVVDTNSTDRTKEIATGRGATVINESRSGYG-----MAYKTGLQ--HAKGDIIVCM 81
                                      8888999999987775.43237*****************987777777777664.....66666666..4578999999 PP

                   Glyco_tranf_2_4 79 DaDEflvvp 87
                                      D D+ + ++
  gi|518651976|ref|YP_008141496.1| 82 DGDNTYPTD 90
                                      999876555 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                   Glyco_tranf_2_4  56 rrqvellkalla.ryaeadwvlv 77 
                                       ++ ++ll +++  + + + w+++
  gi|518651976|ref|YP_008141496.1| 132 NFTMRLLFKINLnDSQSGMWIFY 154
                                       34445444443313344566666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1553.97
//
Query:       gi|518651977|ref|YP_008141497.1|  [L=205]
Description: ribonuclease HII [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-43  148.7   0.0    2.2e-43  148.4   0.0    1.1  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 !  148.4   0.0   1.2e-47   2.2e-43       1     197 [.       4     194 ..       4     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 148.4 bits;  conditional E-value: 1.2e-47
                                       EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHH.SEEEEEEE-HHHHH.HHTTTS- CS
                         RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklik.kkiekrklvaeeikyasenein 76 
                                       +GiDEaGrGp++Gp+v+a  ++ +++   l+ +gv+DSKkLs+ +re L+  ++  k +   ++ +ei+ + +++  
  gi|518651977|ref|YP_008141497.1|   4 CGIDEAGRGPLIGPMVMAI-LCGDRES--LEIIGVADSKKLSPGRRESLFARLQsYKYNFVIISPSEID-RYVEHQK 76 
                                       7**************9875.5655555..7899*********************333444455555555.3344445 PP

                                       HHHHHHHHHHHHHHHHHHTCEECCECCCE--SS.HHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHH CS
                         RNase_HII  77 lneikaaltlaviklleklgvkvdeilvdgvtt.peslkkkleqiikikvtvekkadekyllvaaASiiAkverdee 152
                                       ln +++   ++++      +   + ++vd ++  + +l+  l++ +k++++  +kade+y++v+aASiiAkv rd e
  gi|518651977|ref|YP_008141497.1|  77 LNVLEETYASKLAS----WAPASSTVYVDSFDVnELRLQSLLMENTKRQIVCRHKADEIYPCVSAASIIAKVIRDRE 149
                                       55555555555555....3444455666666654778999************************************* PP

                                       HHHHHHHCSH.--TTSSTTSHHHHHHHHHHHHH..S--TTB-TTSHH CS
                         RNase_HII 153 lellkrkpgtldkgsGyasdektrallkkgats..klpdivrlsfkt 197
                                       +++l++++g  d+gsGy+sd++t +++k+  ++  ++ +ivr+++kt
  gi|518651977|ref|YP_008141497.1| 150 IDKLHKDYG--DFGSGYPSDPRTINFVKNALKNgiNIDSIVRHQWKT 194
                                       *******98..**********************9999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1314.55
//
Query:       gi|518651978|ref|YP_008141498.1|  [L=177]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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   70.7   0.0    2.3e-19   70.5   0.0    1.1  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
    5.9e-10   39.5   0.4    7.3e-10   39.2   0.4    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    6.6e-09   36.0   0.1    8.6e-09   35.7   0.1    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    0.00074   19.9   0.1     0.0012   19.2   0.1    1.5  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.021   14.8   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
        0.2   11.3   0.0       0.27   10.9   0.0    1.2  1  Acetyltransf_8   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5   0.0   7.6e-23   2.3e-19      30     137 ..      44     151 ..      23     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 7.6e-23
                    Acetyltransf_3  30 e.pltleeaeewlerawaeeseeegygwaivl...kdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavr 102
                                       + p+t+e+a e++++   +  e eg  +ai      +++v G++gl d++ ++ + ++gy+++++++gkG+atea++
  gi|518651978|ref|YP_008141498.1|  44 HyPYTEEDAMEFIDKN--R--EVEGESFAIDFyiiYENNVAGVIGLSDIDYDNSRSHVGYWIGKDYRGKGIATEALK 116
                                       3489999999999953..3..2355555553244444449************************************* PP

                    Acetyltransf_3 103 alleyafeelglerlvavidkeNeaSirvleklGf 137
                                       a++ +a ++l+l+ l+  +  +N +Si vl++ Gf
  gi|518651978|ref|YP_008141498.1| 117 AVIYFAARTLRLHSLYTSALIDNIGSIIVLTRNGF 151
                                       **********************************9 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.4   2.5e-13   7.3e-10      37     152 ..      52     169 ..      40     172 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 2.5e-13
                    Acetyltransf_4  37 fekfleal.d.sek...eyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvl.k 107
                                       +  f+++  +   +    + f ++++ +++G   l+ +++   +  + + +++  +d + +g++ e ++a++ ++ +
  gi|518651978|ref|YP_008141498.1|  52 AMEFIDKNrEvE-GesfAIDFYIIYENNVAGVIGLSDIDY--DNSRSHVGYWIG-KDYRGKGIATEALKAVIYFAaR 124
                                       455555543322.22235669999999*************..***********7.9****************9999* PP

                    Acetyltransf_4 108 eqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiD 152
                                          +++l+++   +n+ si ++ + GF++ gi+k+c+ + +r + 
  gi|518651978|ref|YP_008141498.1| 125 TLRLHSLYTSALIDNIGSIIVLTRNGFSIDGISKDCFMYDNRFYS 169
                                       ******************************************996 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.1   2.9e-12   8.6e-09      15     117 .]      48     151 ..      33     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 2.9e-12
                                       HHHHHHHHHHHHHHHSTTCEEEE....EEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHH CS
                    Acetyltransf_1  15 pnedaseeefeesfsleaegllv....aeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealee 87 
                                       ++eda+e  f +  ++ +++ ++    + ++++++G i+l+ i+  ++ + ++ ++++ ++yrgkG++++ l+a++ 
  gi|518651978|ref|YP_008141498.1|  48 TEEDAME--FIDKNREVEGESFAidfyIIYENNVAGVIGLSDIDY-DNSRSHV-GYWIGKDYRGKGIATEALKAVIY 120
                                       2333333..444444445544544667778899************.8888888.9*********************9 PP

                                       HHHHT.TESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  88 raree.gikkivlaveedndaairlYeklGF 117
                                       +a +   ++ ++     dn ++i ++++ GF
  gi|518651978|ref|YP_008141498.1| 121 FAARTlRLHSLYTSALIDNIGSIIVLTRNGF 151
                                       9999999999999999**********99999 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.2e-07    0.0012       5      49 ..      71     122 ..      67     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.2e-07
                                       EEEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH....T CS
                    Acetyltransf_7   5 vfVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea....a 49 
                                       +++++++ ++ G i+ls +d     ++ + ++ ++yrgkGi+++ l+a    a
  gi|518651978|ref|YP_008141498.1|  71 FYIIYEN-NVAGVIGLSDIDydnsRSHVGYWIGKDYRGKGIATEALKAviyfA 122
                                       7877665.44488888888766555555599***************9833221 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     7e-06     0.021      30      81 ..      68     123 ..      43     136 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7e-06
                   Acetyltransf_10  30 ealllvaeeggkivGvielrdgs.....hisllfVdpeyrgqGigkaLleaveeeae 81 
                                       +  +++ +e+ +++Gvi+l+d +           + ++yrg+Gi+++ l+av+  a 
  gi|518651978|ref|YP_008141498.1|  68 AIDFYIIYEN-NVAGVIGLSDIDydnsrSHVGYWIGKDYRGKGIATEALKAVIYFAA 123
                                       4556666655.89999977655555555333469****************9998863 PP

>> Acetyltransf_8  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   9.2e-05      0.27      82     139 ..      97     153 ..      63     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 9.2e-05
                                       EEEEESSHHHCTTTCHHHHHHHHHHHHHCCTT--EEEE--BTT-HHHHHHHHHTT-EE CS
                    Acetyltransf_8  82 iHlligeaeargkglttallralvhylfadprtrrvvvEPdvrNerairllekaGfek 139
                                       + ++ig +++rgkg++t+ l+a++ ++ +  r  +  +   ++N  +i +l + Gf  
  gi|518651978|ref|YP_008141498.1|  97 VGYWIG-KDYRGKGIATEALKAVIYFAARTLRLHSLYTSALIDNIGSIIVLTRNGFSI 153
                                       556777.799**********************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1214.80
//
Query:       gi|518651979|ref|YP_008141499.1|  [L=558]
Description: hypothetical protein FACI_IFERC00001G0618 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-14   52.1   0.0    5.2e-13   49.7   0.0    2.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   2.9e-17   5.2e-13       1     165 [.     247     433 ..     247     435 .. 0.87
   2 ?   -1.5   0.0      0.16   2.9e+03      43      60 ..     505     522 ..     475     547 .. 0.72

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 2.9e-17
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       v+v+rgC  +C fC ++      ++ r+ s+++i++e++ + ++ g ++ +l+++e + y+++ +++ +  +  v+ 
  gi|518651979|ref|YP_008141499.1| 247 VEVMRGCGVGCDFCEVT-----LRPLRYYSLDRIKKEIEVN-VKGGNDHAWLHSDEIFEYKHEKMFTPNQDEM-VNL 316
                                       689**************.....69*****************.9999**************9888888888888.588 PP

                                       EEEEEEECSSCHG................HHHHHHHHHTT...-SEEEEEEBSSSHH..........HHHHHHTCTS CS
                                       xxxxxxxxxxxxx................xxxxxxxxxxx...xxxxxxxxxxxxxx..........xxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd................eeklerllelg...vdrvslgleaadde..........kvlklmnrgh 125
                                       +++++++ g++ +                  kl ++l++g   +  ++ g+e+++d           + l++  +g 
  gi|518651979|ref|YP_008141499.1| 317 MKTVMSIKGVTGSnpthgrisipaafpelIQKLSTILKAGpdnWIGIQTGVETGSDSlamkhmpnktMPLRIGADGS 393
                                       8888888888877888888888888888999**************************66666665543333333556 PP

                                       HHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 126 tfeevlealeklreagikrvvdrivglpGendeeleelle 165
                                        ++ v++++ + +++ +++ +++ vg   e+de+ ++ + 
  gi|518651979|ref|YP_008141499.1| 394 FRDIVWQGVYNETKYYWRSAFTIQVGQQEETDEDNWDSIA 433
                                       66********************************999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.16
                                       HHTTSEEEEEESSTGGGS CS
                                       xxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  43 aekgvkevilgggeplly 60 
                                       a+ g+++++++gge++l 
  gi|518651979|ref|YP_008141499.1| 505 ARAGTGTILSVGGEVMLK 522
                                       566777888888887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 4072.19
//
Query:       gi|518651980|ref|YP_008141500.1|  [L=226]
Description: hypothetical protein FACI_IFERC00001G0619 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   47.7   9.1    1.9e-12   47.0   9.1    1.3  1  PhoU_div   Protein of unknown function DUF47
  ------ inclusion threshold ------
      0.059   13.9   1.9        1.7    9.3   0.9    2.4  2  FeoB_Cyto  FeoB cytosolic helical domain
      0.059   13.5   3.5        6.6    6.9   0.6    2.7  3  MetOD2     Metanogen output domain 2
      0.076   13.4   1.7       0.28   11.5   0.3    2.3  2  Muted      Organelle biogenesis, Muted-like protein
      0.076   13.3   0.3          3    8.2   0.1    2.8  2  DUF948     Bacterial protein of unknown function (DUF948)
       0.11   12.8   2.8         10    6.4   2.0    2.6  2  Rx_N       Rx N-terminal domain
       0.13   12.7   0.3       0.13   12.7   0.3    2.4  3  NPV_P10    Nucleopolyhedrovirus P10 protein


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 !   47.0   9.1   7.2e-16   1.9e-12      40     212 ..      45     221 ..      15     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 7.2e-16
                          PhoU_div  40 ekveellkeiselEreADeikreirlklekglflPvdRedllelveslDeildvle.........diamlvtlrkve 107
                                       +++e+  + + ++E+++De+  + r ++++g++      +ll+l+e+ D+ild +          +i   +t  +v 
  gi|518651980|ref|YP_008141500.1|  45 SDIEKYNEIVRQIEKKGDEMDINFRHEVTSGAISSSLMGNLLDLIEKCDDILDKCYftsreinrfNINYSMTPDEVV 121
                                       57888888889******************************************995333333333566778888999 PP

                          PhoU_div 108 fpeelkdeflallkktveaiealaevieeleklletalskkdiveeieslEdeiDqlqrklikklfsredasnplev 184
                                       ++e+    f+++l+++ e+ e ++ +++e +    + +++    + ie +E+++D+++ ++i   +++   ++++ +
  gi|518651980|ref|YP_008141500.1| 122 IKEYAYGSFIKILEANKESLEFVHSILNEND---LSNMRG--DRKSIEAIEEQVDEIKDNIIDYTYKNSTKISYIVF 193
                                       999999********************99988...356665..5689******************************* PP

                          PhoU_div 185 lllveiieklenvsdraedvadrisiil 212
                                         l ++ +kl  + d  ed++d i  i+
  gi|518651980|ref|YP_008141500.1| 194 EHLNTLAHKLDDLLDDCEDISDLIFTIM 221
                                       **********************987665 PP

>> FeoB_Cyto  FeoB cytosolic helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.044   1.1e+02      36      66 ..      31      64 ..      14      92 .. 0.77
   2 ?    9.3   0.9   0.00065       1.7      32      86 ..     131     189 ..     129     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.044
                         FeoB_Cyto 36 egDeelleelkedpelraeveearkeleae...l 66
                                      e  ++l+ +lk++p + ++ +e+++++e++   +
  gi|518651980|ref|YP_008141500.1| 31 ESSSNLIFMLKNAPSDIEKYNEIVRQIEKKgdeM 64
                                      556677778999999************9983332 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00065
                         FeoB_Cyto  32 lklLegDeelleelk...edpelraeveearkeleae..lgedledvIvdarykfiegil 86 
                                       +k+Le ++e le ++   + +++ + ++  rk +ea     ++++d I+d  yk  ++i+
  gi|518651980|ref|YP_008141500.1| 131 IKILEANKESLEFVHsilN-ENDLSNMRGDRKSIEAIeeQVDEIKDNIIDYTYKNSTKIS 189
                                       8********9999998853.6777777777777776532347999999999999888876 PP

>> MetOD2  Metanogen output domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.004        10      36      83 ..      16      60 ..       4      62 .. 0.81
   2 ?    6.9   0.6    0.0026       6.6      20      72 ..     120     175 ..     117     182 .. 0.83
   3 ?   -1.6   0.0       1.2   3.1e+03      45      84 ..     181     217 ..     176     219 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.004
                            MetOD2 36 krllslLsqtydidddkaevseeieaalknlekkleaqeerlkqikke 83
                                      k+lls Ls   +    + e s+++  +lkn    +e+ +e ++qi+k+
  gi|518651980|ref|YP_008141500.1| 16 KNLLSRLS---QYPLMGIESSSNLIFMLKNAPSDIEKYNEIVRQIEKK 60
                                      45555554...4444489999************************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0026
                            MetOD2  20 eiidE..YarLaksvevnkrllslLsqtydidd.dkaevseeieaalknlekklea 72 
                                        +i+E  Y+   k  e nk  l+  +++ +++d ++++  +++ +a+++ ++++++
  gi|518651980|ref|YP_008141500.1| 120 VVIKEyaYGSFIKILEANKESLEFVHSILNENDlSNMRGDRKSIEAIEEQVDEIKD 175
                                       57889778899******************998735677888888999998888876 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.2
                            MetOD2  45 tydidddkaevseeieaalknlekkleaqeerlkqikkel 84 
                                       ty+ +    ++s    + l  l +kl +   +++ i++ +
  gi|518651980|ref|YP_008141500.1| 181 TYKNS---TKISYIVFEHLNTLAHKLDDLLDDCEDISDLI 217
                                       55544...45666666788888899988888888888876 PP

>> Muted  Organelle biogenesis, Muted-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1      0.26   6.8e+02      68      94 ..      41      67 ..      25      96 .. 0.72
   2 ?   11.5   0.3   0.00011      0.28      36      85 ..     158     214 ..     130     217 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.26
                             Muted 68 selnkkleaalekverllqkeleeekr 94
                                      ++  + +e+ +e v+++++k +e + +
  gi|518651980|ref|YP_008141500.1| 41 KNAPSDIEKYNEIVRQIEKKGDEMDIN 67
                                      445556666666666666665555444 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00011
                             Muted  36 revelLenikklvnelkeqllpkcles.......mkenLselnkkleaalekverll 85 
                                        + +++e+i++ v e+k+++++ + ++       + e+L++l +kl+++l+++e++ 
  gi|518651980|ref|YP_008141500.1| 158 GDRKSIEAIEEQVDEIKDNIIDYTYKNstkisyiVFEHLNTLAHKLDDLLDDCEDIS 214
                                       3457788999999999999888877777778887899*****************997 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 ?    1.6   0.0      0.13   3.3e+02      50      72 ..      44      66 ..      34      82 .. 0.66
   2 ?    8.2   0.1    0.0012         3      32      83 ..     160     216 ..     153     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.13
                            DUF948 50 edllakvnelledvneklekvdp 72
                                         ++k ne++ ++++k +++d 
  gi|518651980|ref|YP_008141500.1| 44 PSDIEKYNEIVRQIEKKGDEMDI 66
                                      44456667777777777666665 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0012
                            DUF948  32 aatieelekqvdpilkevedllakvne.....lledvneklekvdplteavadlges 83 
                                       +++ie +e+qvd+i +++ d + k  +     + e +n    k+d l +  +d+++ 
  gi|518651980|ref|YP_008141500.1| 160 RKSIEAIEEQVDEIKDNIIDYTYKNSTkisyiVFEHLNTLAHKLDDLLDDCEDISDL 216
                                       789999999999999999888777666688888888888888888888888888875 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.015        39      56      76 ..      80     100 ..      19     111 .. 0.77
   2 ?    6.4   2.0    0.0041        10      10      73 ..     145     215 ..     138     222 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.015
                              Rx_N  56 eWlkelrdlaydaeDvlDefe 76 
                                         + +l dl+ + +D+lD++ 
  gi|518651980|ref|YP_008141500.1|  80 SLMGNLLDLIEKCDDILDKCY 100
                                       57899*************986 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0041
                              Rx_N  10 adllaeea.kllkgvkeeleklkdeLesiqavLedaeerqikd......eavkeWlkelrdlaydaeDvlD 73 
                                        ++l e+  +  +g ++ +e ++++   i+  + d   ++ +       e++++  ++l dl  d eD+ D
  gi|518651980|ref|YP_008141500.1| 145 HSILNENDlSNMRGDRKSIEAIEEQVDEIKDNIIDYTYKNSTKisyivfEHLNTLAHKLDDLLDDCEDISD 215
                                       55666666678888899999999999999999999999888775666667777777777777777777766 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.77     2e+03      12      36 ..      46      70 ..      39     102 .. 0.53
   2 ?   -2.1   0.1       2.1   5.4e+03      55      67 ..     138     150 ..     131     156 .. 0.70
   3 ?   12.7   0.3   5.2e-05      0.13      10      64 ..     160     216 ..     158     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.77
                           NPV_P10 12 dikavddkVdalqqqvddvqenlpd 36
                                      di++ ++ V  ++++ d+++ n++ 
  gi|518651980|ref|YP_008141500.1| 46 DIEKYNEIVRQIEKKGDEMDINFRH 70
                                      5555555555555555555555544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.1
                           NPV_P10  55 etkvenIqdiLnp 67 
                                       ++++e +++iLn+
  gi|518651980|ref|YP_008141500.1| 138 KESLEFVHSILNE 150
                                       5567778888884 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.2e-05
                           NPV_P10  10 radikavddkVdalqqqv.ddvqenlpdvteln.ekLdaqsaqLaeletkvenIqdi 64 
                                       r+ i+a++++Vd +++++ d   +n+ +++ +  e+L+ ++ +L++l +  e+I+d+
  gi|518651980|ref|YP_008141500.1| 160 RKSIEAIEEQVDEIKDNIiDYTYKNSTKISYIVfEHLNTLAHKLDDLLDDCEDISDL 216
                                       7889**********9997466779999999885499******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1005  (0.0560544); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1520.12
//
Query:       gi|518651981|ref|YP_008141501.1|  [L=273]
Description: sodium-dependent phosphate transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-22   78.3  28.1    2.3e-20   72.9  28.1    2.1  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 !   72.9  28.1   1.3e-24   2.3e-20      10     335 ..       1     268 [.       1     270 [. 0.87

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1.3e-24
                              PHO4  10 fatsvgskaltlrqAvilaaifeflGavllGaeVaetirkgivdvelfdpselmlgmlaallgaavwlllatvlglP 86 
                                       ++t vgs+++     vi+ a   flG vl G     +  + ++      p+ + + ++ a l +++  l+a++ + P
  gi|518651981|ref|YP_008141501.1|   1 MGTLVGSRIVGRYGGVIIGAGGFFLGLVLEGRFLHGAALS-LI------PHSY-FYITYAFLVSFLIFLFANIGRAP 69 
                                       69****************************8755555555.55......4444.456667777899999******** PP

                              PHO4  87 vStthslvGaliGaalaaeggeavkwkklvkivlswvlsPllggiiaallfllvkrlilvkeklknalralpvlvlv 163
                                        S t++l G  +G+ + +  g+ ++ k ++  v++wv++P+++++++++    + r ++     k            
  gi|518651981|ref|YP_008141501.1|  70 LSLTMALAGTALGIDVRI--GRLIDYKFVILMVAFWVIAPVISIVVSYFAEKGIFRRNF-----K------------ 127
                                       ****************96..5799***9********************87766655522.....2............ PP

                              PHO4 164 tiailalsilfkgeskkddeeteklfkflqvvsaalvsfahGanDvanaiGpllaalisiykaskevplwvlllggl 240
                                                        +  ++ +++kfl v+s+ l +f+ Gan    + G + a +       +   +  + ++ +
  gi|518651981|ref|YP_008141501.1| 128 -----------------NVWNVARWLKFLIVISSFLTAFTLGAN----TLGFI-ANV-------EGFNFLTITVMTV 175
                                       .................223577889****************98....88888.655.......234688999**** PP

                              PHO4 241 aialGlllgGkrviktvGekitkkltpsrGfaaelaaaltvllasklglPvStThvlvgavvGvGlakkresavnwk 317
                                       ai  G +++   vik vGe++  ++++s++++  ++++l+v +a+ + +P+S T++l+++v+GvG+   + +a+ ++
  gi|518651981|ref|YP_008141501.1| 176 AIFSGAFFLSSGVIKRVGEEMY-SMRYSNALVSLVVSSLLVEIATFFAVPLSNTQTLTSSVFGVGISY-KYKAIYMR 250
                                       **********************.6********************************************.79****** PP

                              PHO4 318 lvrnivlaWvlTlpvsal 335
                                        +  i+l+W+l+  + ++
  gi|518651981|ref|YP_008141501.1| 251 PFLIIILTWILSPSIGFI 268
                                       ***********9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       785  (0.0437838); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1744.32
//
Query:       gi|518651982|ref|YP_008141502.1|  [L=255]
Description: hypothetical protein FACI_IFERC00001G0621 [Ferroplasma acidarmanus fer1]
Scores for complete 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-57  194.8   2.0      2e-57  194.5   2.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    8.5e-49  165.7   1.1      1e-48  165.4   1.1    1.1  1  adh_short        short chain dehydrogenase
    1.3e-10   41.5   0.6    1.9e-10   40.9   0.6    1.2  1  KR               KR domain
     0.0015   18.0   0.2     0.0057   16.1   0.2    1.9  1  Epimerase        NAD dependent epimerase/dehydratase family
  ------ inclusion threshold ------
      0.058   13.2   0.0       0.16   11.8   0.0    1.7  1  Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA 


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 !  194.5   2.0   5.5e-61     2e-57       1     232 [.      13     246 ..      13     247 .. 0.91

  Alignments for each domain:
  == domain 1  score: 194.5 bits;  conditional E-value: 5.5e-61
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHT.TSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE- CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeel.gaevlecDVtdeeqvealveevvekfgklDilvnn 76 
                                       G  +g+G+aiA ++a+eGa++++ + ++++  ++ el++ l g+e++++DV+d ++v+++v+e+ +k+g++Dilvnn
  gi|518651982|ref|YP_008141502.1|  13 GSSRGLGKAIAMKFASEGARIAINYNRDQK--SAMELKNMLaGSEIFQADVSDHAAVRNMVNEIHRKMGTIDILVNN 87 
                                       5679*********************99998..4555555541688******************************** PP

                                       ----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSCCEEEEEEEGGGTSB.STTTTHHHHHHHHHHHH CS
                      adh_short_C2  77 agiapklkgpfletsreefdraldvnlyslfllakaalp.lmkeggsivnlssvgaerv.vpnynaygaaKaaleal 151
                                       agi  +      e++++ +++++dvnl + +++++++++ l k++g i+nl+s ++  +  ++++ y+++Kaa+  l
  gi|518651982|ref|YP_008141502.1|  88 AGILSA--ITWDEFDDARVKKIFDVNLMGPVYTTRECIEdLKKQHGIIINLASNAGVGTaAKGTTFYSMTKAAITML 162
                                       ******..9999***************************677777*********88876256666************ PP

                                       HHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT...HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SE CS
                      adh_short_C2 152 trylAvelgpkgiRvNavspgpikTlaasgikg...fdelleelearaplgrlgtpeevaeaalfLasdeasyitGq 225
                                       t+ lA +l +  +RvNa++pg+i+ +++ g k+    ++l++ +++++ lg +g+pe++a+aa+fLas+e++y+ Gq
  gi|518651982|ref|YP_008141502.1| 163 TKRLAFDLMDWHVRVNAIAPGWIESDMTIGGKSeeeVNNLRQSFKSKTELGMTGKPENIADAAIFLASNESEYMDGQ 239
                                       ***************************777766223556999*********************************** PP

                                       EEEESTT CS
                      adh_short_C2 226 tlvvDgG 232
                                       +lvvDgG
  gi|518651982|ref|YP_008141502.1| 240 VLVVDGG 246
                                       ******9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.4   1.1   2.9e-52     1e-48       1     188 [.       7     191 ..       7     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.4 bits;  conditional E-value: 2.9e-52
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       k+vl+tG s+G+G+aia ++a+eGa++++ ++r ++ + e+++ l        ++q+Dv+d+++v+++v+++  k+g
  gi|518651982|ref|YP_008141502.1|   7 KIVLITGSSRGLGKAIAMKFASEGARIAInYNRDQKSAMELKNMLAG----SEIFQADVSDHAAVRNMVNEIHRKMG 79 
                                       79*************************99777776666666655555....799*********************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGG.TSB-TTBHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvag.kvpvagvaaYsAs 152
                                       ++d+LvnNAGi    +  e+++++++++++vNl+g++ +tr++++  lk++ G I+n +S+ag   + +g++ Ys +
  gi|518651982|ref|YP_008141502.1|  80 TIDILVNNAGILSAITWDEFDDARVKKIFDVNLMGPVYTTRECIED-LKKQHGIIINLASNAGvGTAAKGTTFYSMT 155
                                       **********************************************.56999***********667788999***** PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmak 188
                                       Kaa+++lt+ la +l ++ +rvna+aPG +++dm+ 
  gi|518651982|ref|YP_008141502.1| 156 KAAITMLTKRLAFDLMDWHVRVNAIAPGWIESDMTI 191
                                       **********************************86 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.6   5.4e-14   1.9e-10       3     142 ..       9     144 ..       8     167 .. 0.83

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 5.4e-14
                                       EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaee 79 
                                       +litG   gLG+++a   a++gar  +   R+       ++   el+++ a  e+++aDvsd++av+++++ei++++
  gi|518651982|ref|YP_008141502.1|   9 VLITGSSRGLGKAIAMKFASEGARIAINYNRD-------QKSAMELKNMLAGSEIFQADVSDHAAVRNMVNEIHRKM 78 
                                       79**********************99999999.......335578999999************************** PP

                                       S---EEEE---------TTT--HHHHHHHHTTTTHHHHHH.HHHTTT..S--SEEEEEEEHHHHH- CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqvlapKvkGawnL.helled..esldffvlfSSiagllg 142
                                       ++i   ++ Ag+l   + +e +++++++++   + G      e++ed  ++  +++ ++S ag+  
  gi|518651982|ref|YP_008141502.1|  79 GTIDILVNNAGILSAITWDEFDDARVKKIFDVNLMGPVYTtRECIEDlkKQHGIIINLASNAGVGT 144
                                       ******************************999999765514556657677778888888888643 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.6e-06    0.0057       1      81 [.       9      98 ..       9     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.6e-06
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC...EEEE--TT-HHHHHHHHHHHT.....-SEEEE- CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl...elveldltdrsalerlfkeeq.....pdavihl 71
                                      +l+tG +  +G+a++ +++++g ++    ++ ++s+ ++++ l   e+ ++d+ d++a++++++e +     +d+ ++ 
  gi|518651982|ref|YP_008141502.1|  9 VLITGSSRGLGKAIAMKFASEGARIAINYNRDQKSAMELKNMLagsEIFQADVSDHAAVRNMVNEIHrkmgtIDILVNN 87
                                      79**********************8887777777777777777999***********9998887642222237777777 PP

                                      -S.---HHHHH CS
                         Epimerase 72 Aa.vggvaass 81
                                      A+  + + +  
  gi|518651982|ref|YP_008141502.1| 88 AGiLSAITWDE 98
                                      77777777765 PP

>> Eno-Rase_NADH_b  NAD(P)H binding domain of trans-2-enoyl-CoA reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.4e-05      0.16      40      77 ..       6      41 ..       2      43 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.4e-05
                                      -SEEEEESTSSHHHHHHHHHHHHSS--EEEEEE----- CS
                   Eno-Rase_NADH_b 40 pkkvLviGaStGYGLAsriaaafgagadtigVsfekea 77
                                       k vL+ G+S G G    ia++f+++ + i + +++ +
  gi|518651982|ref|YP_008141502.1|  6 NKIVLITGSSRGLG--KAIAMKFASEGARIAINYNRDQ 41
                                      589*******9876..569*****99999****99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       701  (0.0390987); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1694.16
//
Query:       gi|518651983|ref|YP_008141503.1|  [L=325]
Description: hypothetical protein FACI_IFERC00001G0622 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-19   68.8   0.0    8.7e-19   67.6   0.0    1.7  1  Wyosine_form  Wyosine base formation
      2e-17   64.1   0.1    7.6e-17   62.2   0.1    1.9  1  Radical_SAM   Radical SAM superfamily
    0.00084   19.6   0.0     0.0016   18.7   0.0    1.4  1  Fer4_12       4Fe-4S single cluster domain


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 !   67.6   0.0   1.5e-22   8.7e-19       1      63 []     239     300 ..     239     300 .. 0.98

  Alignments for each domain:
  == domain 1  score: 67.6 bits;  conditional E-value: 1.5e-22
                                       HHT-SEEEEEE------------------HHHHHHHHHHHHTSSS.EEEEEEETTTTEEEEEE CS
                      Wyosine_form   1 kaepdFvEvKaytyvGssrsrLtmknvPwheevadfakrlegsaedYellaehrhSrvvllar 63 
                                       +a+pdF+E K+y +vG+s+ rLt +n+P+h+e+ +f+  l+++++ Y+  a++ +Srv+++a+
  gi|518651983|ref|YP_008141503.1| 239 RADPDFIESKGYVHVGQSEGRLTAENMPSHDEIMEFSSTLAKRLG-YTEYADRFESRVAMIAK 300
                                       699******************************************.***************96 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.1   1.3e-20   7.6e-17       4     157 ..      59     227 ..      56     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.3e-20
                                       ESEESS--TTTSCCTT.....HHHHHHHHHHHHHHHHHHHHHHH.H.........HTTSEEEEEE............ CS
                                       xxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxx.x.........xxxxxxxxxx............ RF
                       Radical_SAM   4 trgCnlrCsfCarpet.....vrregrgrslsveeileevkelk.a.........ekgvkevilg............ 53 
                                       ++ C+ +C fC+r +         e++++++  e+i++++k ++ +                  +            
  gi|518651983|ref|YP_008141503.1|  59 LNQCSENCDFCWRFQGfdsmhINEEDDPEFILEESIKAHLKLISgFkgnpkvkkeL--------Feeashprhmais 127
                                       678*****************999999999999999999999998664444444440........3556666666666 PP

                                       .SSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHH...HHHHHHT..CT CS
                                       .xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxx..xx RF
                       Radical_SAM  54 .ggepllypdfvellerlaklavpgiritvetngtlpdeeklerllelgvdrvslgleaadde...kvlklmn..rg 124
                                         gep+ly ++ el+e++ ++   gi+++v++ngt+  +++le+l +l+ +++++++  +++e   +    ++   g
  gi|518651983|ref|YP_008141503.1| 128 lTGEPTLYTRLGELIEAATRR---GITTFVVSNGTM--PKVLETLNPLP-TQLYITVAGPTKEifnD---VLHpaIG 195
                                       6*******************8...************..6**********.*************6664...4444478 PP

                                       SHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 125 htfeevlealeklreagikrvvdrivglpGend 157
                                       + +e + ++l++l +++ + +v+r+++++++n+
  gi|518651983|ref|YP_008141503.1| 196 NAWENFNKTLDLLPSLDTR-TVIRHTMVKNVNF 227
                                       *******************.**********997 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-07    0.0016      12     120 ..      59     183 ..      50     189 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-07
                           Fer4_12  12 vsgCnlsCkgCfnketwsfk.......................sgkeftkelleeiiedlkkesiegltllGGEPll 65 
                                       ++ C+ +C++C   +  +                         sg + + ++++e++e++++++   ++l+ GEP l
  gi|518651983|ref|YP_008141503.1|  59 LNQCSENCDFCWRFQGFDSMhineeddpefileesikahlkliSGFKGNPKVKKELFEEASHPRHMAISLT-GEPTL 134
                                       5689999999996666533366666777777777777777777999999**********************.5**** PP

                           Fer4_12  66 penaeallelvkevkeekpekdiwlytgytleelskkekeellkeidvlvdGkfe 120
                                          +  l el++   ++++  + ++++g++ + l+    ++l  ++ ++v G+ +
  gi|518651983|ref|YP_008141503.1| 135 ---YTRLGELIEAATRRGI-TTFVVSNGTMPKVLE--TLNPLPTQLYITVAGPTK 183
                                       ...999*************.59******9999887..579999999999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      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: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2506.37
//
Query:       gi|518651984|ref|YP_008141504.1|  [L=61]
Description: hypothetical protein FACI_IFERC00001G0623 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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 0.27s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 444.03
//
Query:       gi|518651985|ref|YP_008141505.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G0624 [Ferroplasma acidarmanus fer1]
Scores for complete 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-88  296.7   0.0    2.2e-88  296.4   0.0    1.1  1  ArsA_ATPase   Anion-transporting ATPase
    4.9e-17   61.2   0.0    8.8e-17   60.4   0.0    1.4  1  ArsA_HSP20    HSP20-like domain found in ArsA
    2.4e-13   50.4   0.0    4.3e-13   49.6   0.0    1.4  1  AAA_31        AAA domain
    4.7e-08   33.1   0.0    1.2e-07   31.9   0.0    1.8  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
    6.9e-07   29.0   0.1    1.2e-05   25.0   0.1    2.2  2  ParA          NUBPL iron-transfer P-loop NTPase
    5.9e-05   22.9   0.0     0.0001   22.1   0.0    1.4  1  AAA_24        AAA domain
    8.2e-05   22.2   0.0    0.00012   21.6   0.0    1.3  1  Fer4_NifH     4Fe-4S iron sulfur cluster binding proteins, Ni
    0.00027   20.6   1.5    0.00085   19.0   0.7    2.0  2  SRP54         SRP54-type protein, GTPase domain
  ------ inclusion threshold ------
       0.02   14.6   0.0      0.028   14.1   0.0    1.4  1  AAA_30        AAA domain
      0.057   13.3   0.1      0.089   12.7   0.1    1.3  1  APS_kinase    Adenylylsulphate kinase
      0.059   13.4   0.1       0.41   10.7   0.1    2.1  1  AAA_14        AAA domain
      0.064   12.7   0.1       0.19   11.1   0.0    1.9  3  CBP_BcsQ      Cellulose biosynthesis protein BcsQ
      0.075   13.3   0.0       0.14   12.4   0.0    1.5  1  AAA_22        AAA domain
      0.087   12.7   0.1       0.17   11.8   0.1    1.4  1  NTPase_1      NTPase
       0.11   12.0   0.2       0.18   11.3   0.2    1.3  1  AAA_7         P-loop containing dynein motor region
       0.12   11.8   0.0       0.19   11.1   0.0    1.3  1  PhoH          PhoH-like protein
       0.12   12.3   0.0       0.23   11.5   0.0    1.3  1  ResIII        Type III restriction enzyme, res subunit
       0.12   11.3   0.0       0.23   10.4   0.0    1.5  1  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
       0.13   12.3   0.1        0.4   10.7   0.1    1.7  2  AAA_5         AAA domain (dynein-related subfamily)
       0.13   12.2   0.1       0.46   10.4   0.1    1.9  2  Mur_ligase_M  Mur ligase middle domain
       0.15   11.8   0.0       0.22   11.2   0.0    1.2  1  PRK           Phosphoribulokinase / Uridine kinase family
       0.18   10.8   0.1       0.26   10.3   0.1    1.2  1  T2SSE         Type II/IV secretion system protein
       0.27   10.8   0.4       0.52    9.8   0.4    1.5  1  AAA_25        AAA domain


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 !  296.4   0.0   2.8e-91   2.2e-88       2     304 ..       3     302 ..       2     303 .. 0.98

  Alignments for each domain:
  == domain 1  score: 296.4 bits;  conditional E-value: 2.8e-91
                                       EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STTTHHHHHHTS--BSS-EEETSSEEEEE--HHHHHHHHHC CS
                       ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistDPAhslsDsfdqklgkeptkvkeNLsavEidpeveleeakq 78 
                                       +v+l +GKGGVGKttv+a+ta  l++++kk++++stDPAhsl Ds++ +++ +pt +++NL+a+E++++ +++  ++
  gi|518651985|ref|YP_008141505.1|   3 RVLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGDSLQAEIKSSPTEISKNLFAQEVNINDAIQSHWS 79 
                                       7999************************************************************************* PP

                                       CHHGGGSCCHHHHHHHHHHHHHHTSSTTHHHHHHHHHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHH CS
                       ArsA_ATPase  79 evqkeeeallgleeledvlaeelaslPGideilsfeellkyvkeeeydvvvlDtaPTGhtlrllslpevlekllekl 155
                                       +  ++ +al++ ++l+ + a+e a+lPG +e++ + ++++y+k++ ydv+v+D+aPTG++lr+ls+pev+ +++ek+
  gi|518651985|ref|YP_008141505.1|  80 DLREYLTALFQYQGLDPISADEIAILPGFEEATYLLYINDYIKNNSYDVIVVDSAPTGEALRMLSFPEVMRWYMEKV 156
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTTTEEEEEEEESSHHHHHHHHHHHHHHHH CS
                       ArsA_ATPase 156 vklkeklsplakqlvkllglggvsieealeeleetkeeikkveeiltdpertsfrlVvipEklslkEteRaikeLkk 232
                                       + + ++  ++a++l++ ++ + +  ++++++ e+ ++++ +++ il++p++ts+rlV++++++s++Et+Ra+++L +
  gi|518651985|ref|YP_008141505.1| 157 FPISRTAAKIARPLMRPFSGIPMPNDKVFKSAETLYDDLGDIHTILENPDITSIRLVTNADQMSFNETKRAFTYLLL 233
                                       **************998888888888*************************************************** PP

                                       TT-EEEEEEEEEE-TTCSSSTSHHHHHHHHHHHHHHHHHHHHTTTSEEEEEE--SS-S-SHHHHHHHHHHHC CS
                       ArsA_ATPase 233 ygikvdavivNkllpeeeqenCeflearkkiqkkylkeieelfedlevvklplleeEvvGlekleklselly 304
                                       yg  vdavi Nk+  e++ +   f+++++++q+  l +++  f ++++ k  l+++E+vG ek  k+ + ly
  gi|518651985|ref|YP_008141505.1| 234 YGYPVDAVIANKIYTEDTGD---FFQKWRETQSGILGDLDAAFPEIKILKSYLQNNELVGQEKALKFGQDLY 302
                                       ****************9995...***********************************************99 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 !   60.4   0.0   1.1e-19   8.8e-17       2      63 .]     324     385 ..     323     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.1e-19
                        ArsA_HSP20   2 deyvlkldLPfvdkeeidlsrsgdeLtIkignfrRqitLPsvlarkevtsAkfedgvLeIrF 63 
                                       ++ v+kl+LPf+dk++++l+++  eL+++++n++R   LP+++a++++++A+++dg+L I++
  gi|518651985|ref|YP_008141505.1| 324 GNSVVKLKLPFADKKNLNLYNKTGELIVEVNNWKRILYLPQTMANLQPSGAELKDGYLYITL 385
                                       6779********************************************************96 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.0   5.5e-16   4.3e-13       6     131 ..       6     139 ..       1     145 [. 0.78

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 5.5e-16
                            AAA_31   6 ianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevli.eeknikeaiiktkvenl 81 
                                       ++  KGGvGKTT +   a++lak++kk++++  Dp  ++  +l+ e ++  +++ + l+ +e+ni++ai+++ ++  
  gi|518651985|ref|YP_008141505.1|   6 LYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGDSLQAEIKSSPTEISKNLFaQEVNINDAIQSHWSDLR 82 
                                       6778*****************************************999999999999876**********6655555 PP

                            AAA_31  82 dlipssidLaeae......ielvelekkeeilkellekvkde.YDyiiiDcpPsLgl 131
                                       + + +  + ++++      i ++   ++ + l  + + +k++ YD+i++D  P+ + 
  gi|518651985|ref|YP_008141505.1|  83 EYLTALFQYQGLDpisadeIAILPGFEEATYLLYINDYIKNNsYDVIVVDSAPTGEA 139
                                       7787777766665211111333333344555777778888767**********8655 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 !   31.9   0.0   1.5e-10   1.2e-07       4      55 ..       7     194 ..       4     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.5e-10
                                       EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.......................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................... RF
                              CbiA   4 astkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.......................... 54 
                                         +kGGvGKTt+aa+ a  la++++++++  +Dp  ++     + e++  p                          
  gi|518651985|ref|YP_008141505.1|   7 YTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGD-SLQAEIKSSPteisknlfaqevnindaiqshwsdlr 82 
                                       679*******************************966655.233333333355566666666666667777777666 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|518651985|ref|YP_008141505.1|  83 eyltalfqyqgldpisadeiailpgfeeatyllyindyiknnsydvivvdsaptgealrmlsfpevmrwymekvfpi 159
                                       66666666666666666666666666666666666666666666666666666666666666666666666655555 PP

                                       ..................................C CS
                                       ..................................x RF
                              CbiA  55 ..................................d 55 
                                                                         d
  gi|518651985|ref|YP_008141505.1| 160 srtaakiarplmrpfsgipmpndkvfksaetlydD 194
                                       55555555555555555555555555555555550 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.1   1.5e-08   1.2e-05       6      41 ..       4      39 ..       2      68 .. 0.89
   2 ?    1.4   0.0      0.23   1.8e+02     124     176 ..     196     247 ..     194     257 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-08
                              ParA  6 iavlSgKGGVGKStvavnlAlaLakkglkvgllDaD 41
                                      ++   gKGGVGK+tva++ A +Lak+++k+ ++ +D
  gi|518651985|ref|YP_008141505.1|  4 VLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTD 39
                                      57789*************************999887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.23
                              ParA 124 gDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsg 176
                                       gD++ t++++ +++ + +Vt   +++++++k+a++ +     +v +v+ N  +
  gi|518651985|ref|YP_008141505.1| 196 GDIH-TILENPDITSIRLVTNADQMSFNETKRAFTYLLLYGYPVDAVIANKIY 247
                                       5666.788888999999*******************99999999999999655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   1.3e-07    0.0001       3      74 ..       3     134 ..       1     145 [. 0.91

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.3e-07
                            AAA_24   3 lkiliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie.......................sw 49 
                                       + +l +G+ g+GKTt+a++         +k++++ t+  ++sl +    +i+                        w
  gi|518651985|ref|YP_008141505.1|   3 RVLLYTGKGGVGKTTVAASTasmlakqNKKTIVMSTDP-AHSLGDSLQAEIKsspteisknlfaqevnindaiqsHW 78 
                                       566778************999*****99*********9.66777777777777889**999999999999999999* PP

                            AAA_24  50 edfldevvel...............................aaeladyktlviDti 74 
                                        d+++++++l                               + +++ y+++v+D++
  gi|518651985|ref|YP_008141505.1|  79 SDLREYLTALfqyqgldpisadeiailpgfeeatyllyindYIKNNSYDVIVVDSA 134
                                       ********99*******************************9999*********97 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.6e-07   0.00012       6      42 ..       7      44 ..       2      82 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.6e-07
                         Fer4_NifH  6 y.GkGGiGksttsqnlsaalaemgkkvlivGCDPkaDs 42
                                      y GkGG+Gk+t ++ ++++la+++kk +++  DP +  
  gi|518651985|ref|YP_008141505.1|  7 YtGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSL 44
                                      449*******************************8743 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.7   1.1e-06   0.00085       3      38 ..       4      39 ..       2      44 .. 0.94
   2 ?   -0.7   0.0       1.2   9.2e+02      79      92 ..     121     134 ..     111     138 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 1.1e-06
                                      EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEES CS
                             SRP54  3 villvGlqGaGKTttlaKLaallkkegkkvllvaaD 38
                                      v+l  G  G+GKTt +a  a +l k++kk++++++D
  gi|518651985|ref|YP_008141505.1|  4 VLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTD 39
                                      78999*****************************99 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                                       HHHTTSSEEEEEE- CS
                             SRP54  79 akeekidvvlvDTa 92 
                                        k++++dv++vD+a
  gi|518651985|ref|YP_008141505.1| 121 IKNNSYDVIVVDSA 134
                                       68899*******98 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   3.6e-05     0.028      19      71 ..       3      57 ..       1     144 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.6e-05
                            AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglA..ptgkaAkvLaeelgieas 71
                                      rv + tG  G GKtt+ ++ + ++++++++ i+++  p +   + L++e+     
  gi|518651985|ref|YP_008141505.1|  3 RVLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMStdPAHSLGDSLQAEIKSSPT 57
                                      68899*********************97666665512344444445555544444 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00011     0.089       3      39 ..       3      39 ..       1      62 [. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGd 39
                                       v++ tG  g GK+t+a   +++L +++++++++  d
  gi|518651985|ref|YP_008141505.1|  3 RVLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTD 39
                                      58899************************99998776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00052      0.41       4     100 ..       4     133 ..       2     140 .. 0.59

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00052
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd......................kkladpe.kllelil 57 
                                       +l+ tG   vGKTt++   ++ l  ++++++ ++ d  +                       +     e +++++i+
  gi|518651985|ref|YP_008141505.1|   4 VLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSlgdslqaeiksspteisknlfaQ-----EvNINDAIQ 75 
                                       677889999**********98888999999999999988866666555544444443322221.....122222222 PP

                            AAA_14  58 eklke.............ekktylflDEiqevpewekalkslvdeg....knldvivtGS 100
                                       ++                ++   +  DEi  +p++e+a   l+ ++    + +dviv  S
  gi|518651985|ref|YP_008141505.1|  76 SH--WsdlreyltalfqyQGLDPISADEIAILPGFEEATYLLYINDyiknNSYDVIVVDS 133
                                       22..02233334444433555667777777777777765555553323224577777776 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.19       4      54 ..       4      54 ..       1      81 [. 0.82
   2 ?   -3.7   0.0       8.7   6.8e+03      28      41 ..     123     136 ..     117     146 .. 0.69
   3 ?   -2.8   0.0       4.4   3.4e+03     179     193 ..     252     266 ..     245     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                          CBP_BcsQ  4 lalqGvRGGvGttsllaaLawalhelgesvlviDlspdnlLrlhFnvdieq 54
                                      + l   +GGvG+t+++a+ a  l +++++ +v+ + p+  L  + + +i++
  gi|518651985|ref|YP_008141505.1|  4 VLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGDSLQAEIKS 54
                                      5555558**************************999999887776666655 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.7
                          CBP_BcsQ  28 elgesvlviDlspd 41 
                                       +  + v+v+D +p 
  gi|518651985|ref|YP_008141505.1| 123 NNSYDVIVVDSAPT 136
                                       56678899998875 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 4.4
                          CBP_BcsQ 179 qDllqlWlqslrrll 193
                                        D++q W+++++ +l
  gi|518651985|ref|YP_008141505.1| 252 GDFFQKWRETQSGIL 266
                                       59999***9998765 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   0.00018      0.14       6     112 ..       3     114 ..       1     136 [. 0.64

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00018
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee....erpevv..fvtlpsstsskdllrellralglelkaerlsse 76 
                                       ++l+ tG  G+GKTt+++  ++ l +++k +      +++ +  + ++  ++s++++ ++l+ +  + ++a     +
  gi|518651985|ref|YP_008141505.1|   3 RVLLYTGKGGVGKTTVAASTASMLAKQNKKTIvmstDPAHSLgdSLQAEIKSSPTEISKNLFAQEVNINDAIQSHWS 79 
                                       678889******************77666555877644444456666666666666666665555555555566666 PP

                            AAA_22  77 ellealeqalraravielliiDEaqhlrs.eealeeL 112
                                       +l+e+l+  ++ ++    +  DE+  l +  e  ++L
  gi|518651985|ref|YP_008141505.1|  80 DLREYLTALFQYQGL-DPISADEIAIL-PgFEEATYL 114
                                       777777666666666.66666666666.444444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00022      0.17       4      30 ..       7      33 ..       4      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      EE--TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellkssgvkv 30
                                       TG+ GvGKtT+    +++l++++ k 
  gi|518651985|ref|YP_008141505.1|  7 YTGKGGVGKTTVAASTASMLAKQNKKT 33
                                      6*******************9998765 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   0.00023      0.18      36      92 ..       5      62 ..       1      69 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                             AAA_7 36 vllvGptGtGKtviikdllkkldkekylsltinfsaqts.anqlqdiiesklekrrkg 92
                                      +l++G+ G+GKt+++ ++ + l k++ ++++++     s   +lq  i+s+    +k+
  gi|518651985|ref|YP_008141505.1|  5 LLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSlGDSLQAEIKSSPTEISKN 62
                                      799********************99999998887654441456666666665555555 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00025      0.19      21      66 ..       4      49 ..       1      80 [. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00025
                                      EEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE-S--TT---- CS
                              PhoH 21 ivfaiGpaGtGKtylavalavealkkkkvkriiltrpaveageelG 66
                                      ++  +G+ G GKt +a ++a  + k++k + ++ t pa + g++l 
  gi|518651985|ref|YP_008141505.1|  4 VLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGDSLQ 49
                                      67889*************9988888888777777889988888775 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   0.00029      0.23      34     139 ..      12     132 ..       4     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                       TSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG.....GEEEESSS-B--........-SEEE CS
                            ResIII  34 GtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke.igkkvsgdkkka.kekdstnkkilv 108
                                       G+GKT vaa+++  l+k++k+  ++   p  sl + ++ e+k+   e  k+   ++v+ +  ++ + +d  +    +
  gi|518651985|ref|YP_008141505.1|  12 GVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLGDSLQAEIKSSPTEISKNlFAQEVNINDAIQsHWSDLREYLTAL 88 
                                       9****************987655555567889999999999876666555553444444444333466777777889 PP

                                       EEHHHHHHTH.....................HHHTTT-SEEEEE CS
                            ResIII 109 ttiqsldadseee.............eeeseellrdrfdviiiD 139
                                       +++q ld +s  e              + ++  +++++dvi++D
  gi|518651985|ref|YP_008141505.1|  89 FQYQGLDPISADEiailpgfeeatylLYINDYIKNNSYDVIVVD 132
                                       99999999997779999999877776666666777777799988 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.23      29      69 ..       2      42 ..       1      66 [. 0.90

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
                                      SEEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE---- CS
                              MeaB 29 aqvvGltGvPGaGkstlvealglelrrrGkrvavlavDPss 69
                                      a+v+  tG  G+Gk t+    +  l+++ k+  v++ DP+ 
  gi|518651985|ref|YP_008141505.1|  2 ARVLLYTGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAH 42
                                      567778*********************************85 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00051       0.4       4      34 ..       7      38 ..       4      43 .. 0.82
   2 ?   -2.7   0.0       6.8   5.3e+03      62      95 ..     257     289 ..     236     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                                      EE--SSSSHHHHHHHGGGGB.S--EEEEE--T CS
                             AAA_5  4 LvGppGtgKselaerlaaal.nreveyvqltr 34
                                        G+ G+gK+++a + a++l +++  ++ ++ 
  gi|518651985|ref|YP_008141505.1|  7 YTGKGGVGKTTVAASTASMLaKQNKKTIVMST 38
                                      4799*****************77777776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.8
                                       ---G-SEEEEESGGG--HHHHHHHHHHHHSSEEE CS
                             AAA_5  62 aaregeilvlDEveraesevlnsLlslleerrll 95 
                                       + re +  +l++++ a +e +++L s+l +++l 
  gi|518651985|ref|YP_008141505.1| 257 KWRETQSGILGDLDAAFPE-IKILKSYLQNNELV 289
                                       5556666777777766666.47888888887765 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00059      0.46       3      30 ..      11      49 ..      10      90 .. 0.63
   2 ?   -1.5   0.0       2.8   2.2e+03     110     159 ..     211     254 ..     184     268 .. 0.63

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00059
                                      SSS-HHHHHHHHHHHHHCTEEEEETTC...........S CS
                      Mur_ligase_M  3 GtnGKTTtteliaailekagkvigtvg...........t 30
                                      G  GKTT++  +a++l+k+ k++ ++             
  gi|518651985|ref|YP_008141505.1| 11 GGVGKTTVAASTASMLAKQNKKTIVMStdpahslgdslQ 49
                                      778****************88888887334443323220 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.8
                                       EEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEE CS
                      Mur_ligase_M 110 iavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegte 159
                                        +v+nad+     +++++k+a   ++ +g   +a  + a++i+ +++g+ 
  gi|518651985|ref|YP_008141505.1| 211 RLVTNADQM----SFNETKRAFTYLLLYGYPVDA--VIANKIYTEDTGDF 254
                                       456665555....777778877778888887777..66667777666554 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   0.00029      0.22       5      79 ..       8      86 ..       4      94 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00029
                               PRK  5 agsSGaGkttvarklekifgrekvkaaeiegdsflrl.draekdlel...eerkrakekevsflspeandfdllyevlk 79
                                      +g+ G Gkttva+   ++++++++k+ ++  d  ++l d+ + ++++   e  k+ +++ev+  ++    + +l e l 
  gi|518651985|ref|YP_008141505.1|  8 TGKGGVGKTTVAASTASMLAKQNKKTIVMSTDPAHSLgDSLQAEIKSsptEISKNLFAQEVNINDAIQSHWSDLREYLT 86
                                      899**********************999999988887333333333300023344556666666666666666666555 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 ?   10.3   0.1   0.00034      0.26     131     193 ..       4      75 ..       1      79 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00034
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks.derivtvEDpvEiqleganqvqlnak.........kakvtfadllr 193
                                       ++l +G  g GKtt++ +  ++++k+ ++ iv+  Dp+   l +  q +++++         +++v+++d+++
  gi|518651985|ref|YP_008141505.1|   4 VLLYTGKGGVGKTTVAASTASMLAKQnKKTIVMSTDPAH-SLGDSLQAEIKSSpteisknlfAQEVNINDAIQ 75 
                                       6899************88888888886889999999985.556666666666666666666666777777666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.4   0.00067      0.52      35      59 ..       4      28 ..       1      42 [. 0.83

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00067
                            AAA_25 35 lallaGapgtGKttlaldlalavat 59
                                      + l +G +g+GKtt+a + a  +a+
  gi|518651985|ref|YP_008141505.1|  4 VLLYTGKGGVGKTTVAASTASMLAK 28
                                      67889*************9998883 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2706.36
//
Query:       gi|518651986|ref|YP_008141506.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G0625 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-63  213.2   0.1    4.1e-63  212.8   0.1    1.0  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 !  212.8   0.1   2.3e-67   4.1e-63       2     244 ..      31     265 ..      30     276 .. 0.94

  Alignments for each domain:
  == domain 1  score: 212.8 bits;  conditional E-value: 2.3e-67
                                       HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCT CS
                   polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlv 78 
                                       ++l e+++y+++agGKr+Rpll++l++e+   + e +++ ++la   el+h+asL+hDDi+D+s+ RRG+++  +++
  gi|518651986|ref|YP_008141506.1|  31 PYLFEMSKYTIDAGGKRFRPLLTILSYEISC-N-EPYDSILDLASGYELIHTASLIHDDIIDKSKYRRGRETLASRY 105
                                       67889*************************9.3.369**************************************** PP

                                       CHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHC CS
                   polyprenyl_synt  79 GnklAindgdfllarafellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylf 155
                                       G ++Ai++gd+l+a+a+el +++  ++  + +++++ + +++eGq+++  +  + +l+   +e+y++i+ +KTay f
  gi|518651986|ref|YP_008141506.1| 106 GIDNAIVVGDYLFAKAYELGSRY--GK-VVSKVMADGSSHLAEGQIIEALNIGNLSLD---IETYNKIIMNKTAYFF 176
                                       ***********************..77.899*****************9898778888...**************** PP

                                       HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHH CS
                   polyprenyl_synt 156 alpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilkalelaspeqr 232
                                       +++++ a ++a a d++ ++l+++++++G+aFQi DD+lD++g+++++gKp+  D+++  +tlpi++al + + e++
  gi|518651986|ref|YP_008141506.1| 177 SACAEGATIAAMAPDNVRDKLSKFAYNMGMAFQITDDILDIVGNEKEMGKPTMVDLNHDVITLPIIHALSHVTGENK 253
                                       ************989999*********************************************************** PP

                                       HHHHHHTTSSHH CS
                   polyprenyl_synt 233 kvlkeilgkkae 244
                                       ++l +il  k +
  gi|518651986|ref|YP_008141506.1| 254 RTLVNILTGKYT 265
                                       999999984443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2083.46
//
Query:       gi|518651987|ref|YP_008141507.1|  [L=90]
Description: DNA/RNA-binding protein albA [Ferroplasma acidarmanus fer1]
Scores for complete 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   64.1   0.8    8.9e-18   63.9   0.8    1.1  1  Alba      Alba
     0.0074   16.2   0.1     0.0084   16.1   0.1    1.3  1  Rpp20     Rpp20 subunit of nuclear RNase MRP and P


Domain annotation for each model (and alignments):
>> Alba  Alba
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.8     1e-21   8.9e-18       1      64 [.       5      66 ..       5      69 .. 0.92

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1e-21
                                      CEEEE-STS-HHHHHHHHHHHHTHTTESEEEEEEETTHHHHHHHHHHHHHHHTCTT.EEEEEEE CS
                              Alba  1 neiyVsskspimsyvkralklLsnkkeeeVvlkatGraIskAvsvaeilkrrfgkglyqvnvlt 64
                                      n+i+V++ +p m+yv+++++++ n+  + +v+ka+G+aIskAv++aei k +f+ +  +++ ++
  gi|518651987|ref|YP_008141507.1|  5 NIIFVGK-KPTMNYVLAIVTQFNNSDMPRIVIKARGKAISKAVDIAEITKHKFI-QTAKYESIK 66
                                      89*****.**************9999***************************8.558888775 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 !   16.1   0.1   9.3e-07    0.0084      58      83 ..      27      52 ..       4      74 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 9.3e-07
                             Rpp20 58 elkkeeVfvkatGrAiekalsvgrwf 83
                                      + +   +++ka G+Ai ka+ +++  
  gi|518651987|ref|YP_008141507.1| 27 NSDMPRIVIKARGKAISKAVDIAEIT 52
                                      566789****************9754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 618.63
//
Query:       gi|518651988|ref|YP_008141508.1|  [L=129]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   50.5   0.5    1.9e-13   49.7   0.5    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.6e-12   46.4   0.0    4.1e-12   45.7   0.0    1.4  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.6e-05   24.8   1.6      4e-05   23.5   0.2    2.2  3  HTH_11          HTH domain
    0.00016   21.3   2.4    0.00017   21.2   0.2    2.1  2  HTH_DeoR        DeoR-like helix-turn-helix domain
    0.00017   21.4   0.0    0.00029   20.6   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00041   20.0   0.0    0.00084   19.1   0.0    1.5  1  HTH_23          Homeodomain-like domain
     0.0014   18.2   0.0     0.0039   16.8   0.0    1.7  2  Sigma70_r4_2    Sigma-70, region 4
     0.0021   18.0   0.2     0.0074   16.3   0.0    1.9  2  HTH_Mga         M protein trans-acting positive regulator (MG
     0.0035   16.9   1.2     0.0062   16.1   0.2    1.8  2  GerE            Bacterial regulatory proteins, luxR family
     0.0078   15.7   0.1      0.016   14.7   0.1    1.5  1  Sigma70_r4      Sigma-70, region 4
     0.0099   16.3   0.3      0.017   15.6   0.3    1.5  1  HTH_40          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.011   15.5   0.0       0.02   14.7   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
      0.013   15.5   0.1      0.022   14.7   0.1    1.5  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
      0.014   15.2   0.1      0.053   13.4   0.0    1.9  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.015   15.5   0.0      0.023   14.8   0.0    1.3  1  HTH_28          Helix-turn-helix domain
       0.02   14.5   0.8       0.18   11.5   0.1    2.1  2  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.025   14.4   0.1      0.048   13.4   0.1    1.5  1  HTH_38          Helix-turn-helix domain
      0.026   14.4   0.1      0.064   13.1   0.0    1.8  2  Phage_NinH      Phage NinH protein
      0.027   14.5   0.0      0.051   13.6   0.0    1.4  1  HTH_29          Winged helix-turn helix
      0.032   14.1   0.3      0.057   13.4   0.1    1.6  1  MarR            MarR family
      0.038   13.8   0.4      0.085   12.7   0.1    1.7  2  TFIIE_alpha     TFIIE alpha subunit
      0.039   14.5   0.2      0.091   13.4   0.1    1.7  2  Mga             Mga helix-turn-helix domain
      0.046   13.7   0.4       0.17   11.9   0.0    2.1  2  HTH_36          Helix-turn-helix domain
      0.086   13.0   0.0       0.19   11.8   0.0    1.6  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.088   12.7   0.0       0.14   12.0   0.0    1.4  1  MarR_2          MarR family
      0.092   13.0   0.1       0.83   10.0   0.0    2.4  2  NUMOD1          NUMOD1 domain
       0.12   12.7   0.0       0.22   11.9   0.0    1.4  1  FaeA            FaeA-like protein
       0.12   12.0   0.0       0.34   10.6   0.0    1.7  1  GntR            Bacterial regulatory proteins, gntR family
       0.13   12.0   0.1       0.26   11.1   0.1    1.5  1  HTH_39          Helix-turn-helix domain
       0.14   12.3   0.0       0.66   10.1   0.0    2.0  2  HTH_20          Helix-turn-helix domain
       0.14   11.6   0.0       0.32   10.4   0.0    1.6  2  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.5   3.3e-16   1.9e-13       1      48 []       1      48 [.       1      48 [. 0.99

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 3.3e-16
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +detd+kI+  L++++r ++ e+A++l++S +t+++r+ +L+++G+I+
  gi|518651988|ref|YP_008141508.1|  1 MDETDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIR 48
                                      8**********************************************7 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0     7e-15   4.1e-12       1      39 [.       1      39 [.       1      42 [. 0.96

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 7e-15
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvr 39
                                      +De+D kI++ L+ed+R ++ e+A+++++Se t+++R+ 
  gi|518651988|ref|YP_008141508.1|  1 MDETDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIM 39
                                      9************************************95 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.2   6.8e-08     4e-05       4      46 ..       7      52 ..       5      57 .. 0.81
   2 ?   -1.5   0.0       4.2   2.4e+03      33      43 ..      72      82 ..      64      90 .. 0.73
   3 ?   -1.5   0.0       4.5   2.6e+03      34      46 ..     101     113 ..      93     118 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 6.8e-08
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....vpI 46
                                      +i+ +L ++++  +  e+A++LnvS+ t+r++I  L  +g    + I
  gi|518651988|ref|YP_008141508.1|  7 KIIDFL-REDSRETNMEIARKLNVSEGTIRKRIMNLVNSGiirkFTI 52
                                      688888.555556999********************99986666555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.2
                            HTH_11 33 rrdIkaLeelg 43
                                       + +k+L++l 
  gi|518651988|ref|YP_008141508.1| 72 SNTLKTLKSLY 82
                                      57788888875 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 4.5
                            HTH_11  34 rdIkaLeelgvpI 46 
                                       + I++L++  ++I
  gi|518651988|ref|YP_008141508.1| 101 NTIEELNMEVDKI 113
                                       5566676665555 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 !   21.2   0.2     3e-07   0.00017       4      46 ..       7      49 ..       5      51 .. 0.92
   2 ?   -1.1   0.0       2.8   1.6e+03      33      47 ..     114     128 ..     114     129 .] 0.87

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 3e-07
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltR 46
                                      +i++ l+++   +  e++  l+vSe TiR+ + +L+++g++++
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIRK 49
                                      688899998888999*************************987 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 2.8
                          HTH_DeoR  33 RDLneLeeqglltRt 47 
                                       RDL+  ++ ++++R 
  gi|518651988|ref|YP_008141508.1| 114 RDLKGVVNTDTMVRL 128
                                       999999999999985 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     5e-07   0.00029       3      47 .]       4      49 ..       2      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 5e-07
                                      HHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  3 tRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                      t  kI+ +L+e +  +  e+a++l++s++t++     L ++G+++k
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREdSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIRK 49
                                      5569*******555*****************************986 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   1.5e-06   0.00084       9      40 ..       7      41 ..       6      49 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvy.rwlkr 40
                                      +i+  l+e  + +  eIAr+L+vs+ T++ r+ + 
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLREdsRETNMEIARKLNVSEGTIRkRIMNL 41
                                      7899999899*******************777665 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.8e-06    0.0039      31      48 ..      22      39 ..      12      40 .. 0.90
   2 ?   -2.7   0.0       8.3   4.8e+03       8      20 ..      75      87 ..      70      89 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.8e-06
                                      HHHHHHT--HHHHHHHHH CS
                      Sigma70_r4_2 31 EIAellgisegtVksrls 48
                                      EIA++l++segt+++r++
  gi|518651988|ref|YP_008141508.1| 22 EIARKLNVSEGTIRKRIM 39
                                      9**************996 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.3
                                      HTTS-HHHHHHHH CS
                      Sigma70_r4_2  8 laeLperqreifl 20
                                      l +L   ++ i++
  gi|518651988|ref|YP_008141508.1| 75 LKTLKSLYSDIYE 87
                                      5566666776665 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.3e-05    0.0074       6      45 ..       4      42 ..       2      55 .. 0.85
   2 ?   -2.0   0.0       6.6   3.8e+03      34      42 ..      75      83 ..      72      92 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.3e-05
                           HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      ++ k++++L e ++++++ e+a +L+ se t++++i +L 
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREDSRETNM-EIARKLNVSEGTIRKRIMNLV 42
                                      6789*******6666665.9****************9997 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.6
                           HTH_Mga 34 eltlqsdis 42
                                       +tl+s  s
  gi|518651988|ref|YP_008141508.1| 75 LKTLKSLYS 83
                                      455555433 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   1.1e-05    0.0062      19      41 ..      19      41 ..      18      43 .. 0.88
   2 ?   -1.8   0.1       4.1   2.4e+03      28      35 ..      97     104 ..      92     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                                      -HHHHHHHHTS-HHHHHHHHHHH CS
                              GerE 19 snkeIAeelniSekTVkvhksni 41
                                      +n eIA++ln+Se T++  + n+
  gi|518651988|ref|YP_008141508.1| 19 TNMEIARKLNVSEGTIRKRIMNL 41
                                      89**************9888776 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.1
                                       TS-HHHHH CS
                              GerE  28 niSekTVk 35 
                                        iS++T++
  gi|518651988|ref|YP_008141508.1|  97 RISKNTIE 104
                                       69999996 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   2.7e-05     0.016      24      41 ..      21      38 ..      11      42 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.7e-05
                                      HHHHHHHTS-HHHHHHHH CS
                        Sigma70_r4 24 eEIgerlgiSrerVrqie 41
                                       EI+++l++S++++r ++
  gi|518651988|ref|YP_008141508.1| 21 MEIARKLNVSEGTIRKRI 38
                                      69*************986 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.3   2.9e-05     0.017      16      81 ..      21      87 ..      15     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-05
                            HTH_40 16 eeIAkerglkesTIegHLaelieeg..eeidlerlvseeeekeIeeaiekvgseklkpikealpeevs 81
                                       eIA++ +++e+TI + +++l+++g  +++ +e  +s e +  Ie   ++  s+ lk +k    + ++
  gi|518651988|ref|YP_008141508.1| 21 MEIARKLNVSEGTIRKRIMNLVNSGiiRKFTIETSLSIEGIVLIELDSRQ-ASNTLKTLKSLYSDIYE 87
                                      79**********************97767888888888888888877776.45778888877766555 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   3.5e-05      0.02       8      49 ..       8      48 ..       6      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.5e-05
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      i+d+l+e  +e t+ e+Ar++ ++  t +  +  Lv+ G+++
  gi|518651988|ref|YP_008141508.1|  8 IIDFLREDSRE-TNMEIARKLNVSEGTIRKRIMNLVNSGIIR 48
                                      999*******9.**************************9998 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   3.8e-05     0.022      28      73 ..      84     128 ..      62     129 .] 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.8e-05
                                       EEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg  28 ecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivl 73 
                                        +y  +G+ d  +++    +e+l+  +++ +++l+gv +t+t++ l
  gi|518651988|ref|YP_008141508.1|  84 DIYEFSGSIDVAVRISKNTIEELNMEVDK-IRDLKGVVNTDTMVRL 128
                                       6899*********************9877.*************977 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   9.1e-05     0.053      21      54 ..      16      49 ..       3      56 .. 0.87
   2 ?   -1.2   0.0       3.4     2e+03      17      41 ..      63      87 ..      61      88 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.1e-05
                                      CCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB 21 gpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                       + t  eia++l+v++ ++ + + +L++ G++++
  gi|518651988|ref|YP_008141508.1| 16 SRETNMEIARKLNVSEGTIRKRIMNLVNSGIIRK 49
                                      567889*************************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.4
                                      HHHHCCCHHCHHCCCTTSSCHCHHH CS
                              TrmB 17 LlklgpatadeiaeelgvprskvYe 41
                                      L++l++ +a+   + l+  +s +Ye
  gi|518651988|ref|YP_008141508.1| 63 LIELDSRQASNTLKTLKSLYSDIYE 87
                                      6677777777777777777777776 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     4e-05     0.023       4      36 ..       7      41 ..       6      48 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4e-05
                            HTH_28  4 eiikllaaG.h.svreaArelgisrrtvyrWikry 36
                                      +ii  l +  + + +e+Ar+l++s+ t+++ i  +
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLREDsReTNMEIARKLNVSEGTIRKRIMNL 41
                                      677777743234999*************9988655 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00031      0.18      26      51 ..      20      45 ..       5      51 .. 0.76
   2 ?    1.6   0.1      0.37   2.2e+02       7      36 ..      72     101 ..      65     117 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00031
                      HrcA_DNA-bdg 26 geeiAevlkrneGtvRNqlqsLkalg 51
                                        eiA +l+  eGt+R  ++ L   g
  gi|518651988|ref|YP_008141508.1| 20 NMEIARKLNVSEGTIRKRIMNLVNSG 45
                                      469**************999886655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.37
                      HrcA_DNA-bdg   7 keilqaLielyrkkkravKgeeiAevlkrn 36 
                                        + l++L +ly    +   + ++A  +++n
  gi|518651988|ref|YP_008141508.1|  72 SNTLKTLKSLYSDIYEFSGSIDVAVRISKN 101
                                       577899999999888888888888888887 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   8.4e-05     0.048      21      39 ..      18      36 ..       8      40 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.4e-05
                            HTH_38 21 lslreIArrLgrspsTIsR 39
                                      +++ eIAr+L++s +TI +
  gi|518651988|ref|YP_008141508.1| 18 ETNMEIARKLNVSEGTIRK 36
                                      67779************87 PP

>> Phage_NinH  Phage NinH protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.064      17      37 ..      18      38 ..       3      52 .. 0.85
   2 ?   -1.8   0.0       5.3     3e+03      32      33 ..     102     103 ..      74     126 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
                        Phage_NinH 17 GnqtEvARrlkcsRatvRkYv 37
                                          E+AR+l+ s +t+Rk +
  gi|518651988|ref|YP_008141508.1| 18 ETNMEIARKLNVSEGTIRKRI 38
                                      5567**************976 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5.3
                        Phage_NinH  32 tv 33 
                                       t+
  gi|518651988|ref|YP_008141508.1| 102 TI 103
                                       33 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   8.8e-05     0.051      12      40 ..      18      45 ..       9      50 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.8e-05
                            HTH_29 12 vstvsqiAkllglsrrtvyrwlkrfeegG 40
                                      + t ++iA+ l++s+ t+++ ++  ++ G
  gi|518651988|ref|YP_008141508.1| 18 E-TNMEIARKLNVSEGTIRKRIMNLVNSG 45
                                      4.89***************9777776666 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   9.8e-05     0.057       4      50 ..       4      50 ..       1      55 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 9.8e-05
                                      HHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  4 tqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      t ++i+  l+e    ++ e+a+kl+vs +t+ + +  L+  G i++ 
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIRKF 50
                                      667777777777777888**************************986 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00015     0.085      14      57 ..       4      47 ..       1      51 [. 0.92
   2 ?   -2.3   0.0       7.1   4.1e+03      35      46 ..     104     115 ..      94     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00015
                                      HHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSE CS
                       TFIIE_alpha 14 eavlvldvLlekgevteedlakelkidlnelrklLnrLyearlv 57
                                         +++d L e++  t+ ++a++l++    +rk +++L + +++
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGII 47
                                      5679***********************************99988 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 7.1
                                       HHHTS-HHHHHH CS
                       TFIIE_alpha  35 kelkidlnelrk 46 
                                       +el+++  ++r 
  gi|518651988|ref|YP_008141508.1| 104 EELNMEVDKIRD 115
                                       566677666665 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00016     0.091      17      64 ..       4      53 ..       1      64 [. 0.79
   2 ?   -0.7   0.1       3.9   2.2e+03      19      29 ..      75      85 ..      46     113 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHH.HHHCH.CCT-E CS
                               Mga 17 lkyqllkflfeeeevsieelaqelyiSestlkrkikel.nklLk.efdle 64
                                      ++y++++fl e+ + +  e+a++l +Se t+ + i +l n  +  +f +e
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLvNSGIIrKFTIE 53
                                      78****************************97666555154433366665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 3.9
                                      HHHHHHHHHHS CS
                               Mga 19 yqllkflfeee 29
                                      ++ lk l+ + 
  gi|518651988|ref|YP_008141508.1| 75 LKTLKSLYSDI 85
                                      44444444332 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00029      0.17      28      55 .]      20      47 ..      15      47 .. 0.93
   2 ?   -0.7   0.1       2.4   1.4e+03      36      42 ..      97     103 ..      61     106 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00029
                            HTH_36 28 qetlakrlglsknTvsraikeLeqlGyi 55
                                      +  +a++l++s+ T+++ i +L+  G+i
  gi|518651988|ref|YP_008141508.1| 20 NMEIARKLNVSEGTIRKRIMNLVNSGII 47
                                      678**********************998 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.4
                            HTH_36  36 glsknTv 42 
                                        +sknT+
  gi|518651988|ref|YP_008141508.1|  97 RISKNTI 103
                                       3455555 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00033      0.19      17      57 ..       7      47 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00033
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSE CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlV 57
                                      k++++L + +r t  e+++k+++s   ++k  + L++ +++
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGII 47
                                      89*********************************998776 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.14      12      53 ..      10      49 ..       1      55 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                                      HHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 12 aaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLver 53
                                       +L+    r+ t  e+ar+l++s +++ +++  Lv  G +++
  gi|518651988|ref|YP_008141508.1| 10 DFLREDS-RE-TNMEIARKLNVSEGTIRKRIMNLVNSGIIRK 49
                                      5554444.44.888*************************986 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0014      0.83      21      35 ..      22      36 ..      18      38 .. 0.90
   2 ?   -0.2   0.0       2.3   1.3e+03      28      34 ..      98     104 ..      94     105 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0014
                            NUMOD1 21 eAakyLgishntInk 35
                                      e a++L++s+ tI+k
  gi|518651988|ref|YP_008141508.1| 22 EIARKLNVSEGTIRK 36
                                      78***********98 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 2.3
                            NUMOD1  28 ishntIn 34 
                                       is+ntI 
  gi|518651988|ref|YP_008141508.1|  98 ISKNTIE 104
                                       9****95 PP

>> FaeA  FaeA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00039      0.22       4      49 ..       7      51 ..       4      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00039
                                      HHHHHHHH.S----HHHHHHHHTS-HHHHHHHHHHHHHHSSEEEE- CS
                              FaeA  4 eIleylnsikapckTreiAdalglsaYQaRyYLeqLekegkikrsp 49
                                      +I+++l +  +  +  eiA  l +s   +R  +++L   g i++  
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLRE-DSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIRKFT 51
                                      69999999.7788889**************************9965 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0    0.0006      0.34      28      54 ..      21      47 ..      19      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0006
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 28 reLaaefgVsrttvReALrrLeaeglv 54
                                      +e+a +++Vs  t+R+ + +L+  g++
  gi|518651988|ref|YP_008141508.1| 21 MEIARKLNVSEGTIRKRIMNLVNSGII 47
                                      79********************99998 PP

>> HTH_39  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00045      0.26       5      42 ..       7      46 ..       5      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00045
                            HTH_39  5 rilaaLrqhgsittleamrelditr..laaRIkeLrekGy 42
                                      +i++ Lr++++ t +e  r+l++ +   ++RI +L ++G+
  gi|518651988|ref|YP_008141508.1|  7 KIIDFLREDSRETNMEIARKLNVSEgtIRKRIMNLVNSGI 46
                                      799**********************999***********6 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0011      0.66      11      55 ..       4      48 ..       1      51 [. 0.86
   2 ?   -0.6   0.0       2.4   1.4e+03      36      49 ..      66      79 ..      59      81 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0011
                                      HHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 11 vRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      + ++i + L+++   t  e+a+ l +s  t+++++  L+  g+++
  gi|518651988|ref|YP_008141508.1|  4 TDYKIIDFLREDSRETNMEIARKLNVSEGTIRKRIMNLVNSGIIR 48
                                      566788888777777778************************997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.4
                                      S-HHHHHHHHHHHH CS
                            HTH_20 36 lskntlsyHLrvLe 49
                                      l+  ++s+ L++L 
  gi|518651988|ref|YP_008141508.1| 66 LDSRQASNTLKTLK 79
                                      67789999999996 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 ?   10.4   0.0   0.00056      0.32      28      48 ..      18      38 ..       5      42 .. 0.83
   2 ?   -2.6   0.0       6.5   3.8e+03      37      44 ..      96     103 ..      95     104 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00056
                      HTH_Tnp_ISL3 28 rsvkavArqlgvSwtTVwril 48
                                       + +++Ar l+vS+ T++ ++
  gi|518651988|ref|YP_008141508.1| 18 ETNMEIARKLNVSEGTIRKRI 38
                                      57799************9776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.5
                      HTH_Tnp_ISL3  37 lgvSwtTV 44 
                                       +++S +T+
  gi|518651988|ref|YP_008141508.1|  96 VRISKNTI 103
                                       68999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 964.80
//
Query:       gi|518651989|ref|YP_008141509.1|  [L=83]
Description: hypothetical protein FACI_IFERC00001G0628 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   13.5   0.0      0.054   13.5   0.0    1.1  1  DUF3043   Protein of unknown function (DUF3043)


Domain annotation for each model (and alignments):
>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-06     0.054     117     169 ..      22      73 ..       7      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-06
                           DUF3043 117 lvvidgillgrkvkkkvrekFpetesekglglYavsRalqiRrlRlPkPqvkr 169
                                       +++ dg++l  k + +   k + ++ ++gl  Y ++ a +iR +R+Pk  v++
  gi|518651989|ref|YP_008141509.1|  22 VTLEDGTVLEIKTEIMSIMKVG-NDPNTGLPQYSINAAPMIRMMRVPKESVAK 73 
                                       5666888999999999999999.9999*********************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 564.30
//
Query:       gi|518651990|ref|YP_008141510.1|  [L=206]
Description: hypothetical protein FACI_IFERC00001G0629 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-24   86.5  34.6    2.4e-19   69.9  24.8    2.0  2  EamA      EamA-like transporter family
    3.3e-07   29.9  19.2    6.3e-06   25.8  10.0    2.0  2  TPT       Triose-phosphate Transporter family
  ------ inclusion threshold ------
        1.8    6.7  21.7        2.4    6.4  21.7    1.1  1  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   2.2   1.5e-08   8.9e-05      89     136 ..       2      48 ..       1      49 [. 0.95
   2 !   69.9  24.8     4e-23   2.4e-19       2     135 ..      57     187 ..      56     189 .. 0.95

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.5e-08
                              EamA  89 tsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       +++s+a ++ ++ Pv+++++s ll +ek+++  ll i ++++G+++++
  gi|518651990|ref|YP_008141510.1|   2 IPVSEAIIFYYTGPVIAILFSPLL-KEKIGKGGLLNISISFAGIIIMS 48 
                                       689*******************99.********************986 PP

  == domain 2  score: 69.9 bits;  conditional E-value: 4e-23
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +gillal + +++++  ++sk   ++vs++ l+f++++i+ i+ll++ ++ + ++   ++  ++++++ g + tvla
  gi|518651990|ref|YP_008141510.1|  57 IGILLALFSGITYGLLSITSKFSAKYVSSMNLVFLQSIISMIILLPFVFVIRFTI---NYDVIIIIVISGSVQTVLA 130
                                       79************************************************99999...88889999*********** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                        +l++ +lk+++ +++s++++l Pvf++i++ ++lg+ ++l++++g +l + + +l+
  gi|518651990|ref|YP_008141510.1| 131 LFLWYDSLKNLNIQIVSILSYLDPVFAIIFALVFLGQIPSLYTIIGGILLIGSGMLV 187
                                       **********************************************99988766555 PP

>> TPT  Triose-phosphate Transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8  10.0     1e-09   6.3e-06      90     199 ..       3     108 ..       1     118 [. 0.90
   2 !    9.1   3.3   0.00012      0.73      60     129 ..     111     181 ..     106     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1e-09
                               TPT  90 aVSfthtvKasePiFtvilsrlllgeklsllvylsLlpivgGvalasvtElsFnligfisAlisnltfslrnifsKk 166
                                       +VS + +   + P+ ++++s l l+ek+    +l + +  +G+++ s+  ls n+ig++ Al+s +t  l +i sK 
  gi|518651990|ref|YP_008141510.1|   3 PVSEAIIFYYTGPVIAILFSPL-LKEKIGKGGLLNISISFAGIIIMSAGSLSINIIGILLALFSGITYGLLSITSKF 78 
                                       5666666677889999999998.9***************************************************97 PP

                               TPT 167 llkklkdldalnlfaiitilslllllPvallve 199
                                         k    ++++nl ++ +i+s+++llP+++++ 
  gi|518651990|ref|YP_008141510.1|  79 SAKY---VSSMNLVFLQSIISMIILLPFVFVIR 108
                                       6655...9********************99876 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00012
                               TPT  60 isse.flkailplalvktlghvlavvslskvaVSfthtvKasePiFtvilsrlllgeklsllvylsLlpiv 129
                                       i+++  ++ ++  ++  +l+ +l   sl++ ++    ++  + P+F++i++ ++lg+ +sl  ++  + ++
  gi|518651990|ref|YP_008141510.1| 111 INYDvIIIIVISGSVQTVLALFLWYDSLKNLNIQIVSILSYLDPVFAIIFALVFLGQIPSLYTIIGGILLI 181
                                       66663344455567778889999999*******************************99887666544444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  21.7   0.00039       2.4      19     172 ..      40     188 ..      26     201 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00039
                           DUF2070  19 lliillalligllaflssklfgillfglpalvaflltlpvlrilggr.ltykrslflalltelivviisllaillsa 94 
                                        ++ ++++    + +ls++++gill +++ ++++ll     +i+++   +y  s+ l +l  +i++ii+l  +++  
  gi|518651990|ref|YP_008141510.1|  40 SFAGIIIM---SAGSLSINIIGILLALFSGITYGLL-----SITSKFsAKYVSSMNLVFLQSIISMIILLPFVFVIR 108
                                       22222222...2233333355666666665555554.....444444466777788888888888887776666666 PP

                           DUF2070  95 ll..qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavy 169
                                       ++  +++++  ++ + + ++   +l + ++ + ++  +++++ + p++ai+++++++++  +l +++  ++++   +
  gi|518651990|ref|YP_008141510.1| 109 FTinYDVIIIIVISGSVQTVLALFLWYDSLKNLNIQIVSILSYLDPVFAIIFALVFLGQIPSLYTIIGGILLIGSGM 185
                                       667666666666666666666677777799999999999*****************888888888888777776666 PP

                           DUF2070 170 lfi 172
                                       l+ 
  gi|518651990|ref|YP_008141510.1| 186 LVT 188
                                       655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); 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):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1311.64
//
Query:       gi|518651991|ref|YP_008141511.1|  [L=555]
Description: hypothetical protein FACI_IFERC00001G0630 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-09   37.5   0.0    5.9e-09   36.5   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    1.1e-05   25.5   0.0    2.4e-05   24.3   0.0    1.5  1  B12-binding  B12 binding domain
  ------ inclusion threshold ------
      0.034   14.0   0.1      0.082   12.7   0.1    1.6  1  DUF1450      Protein of unknown function (DUF1450)


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 !   36.5   0.0   9.9e-13   5.9e-09       5     164 ..     227     389 ..     223     391 .. 0.89

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 9.9e-13
                                       SEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   5 rgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpg 77 
                                       +gC+++C fC  +       ++ + + ++ +  i+ee+  +  e+ +  v+++g+  ++  +f+  l+++ k   ++
  gi|518651991|ref|YP_008141511.1| 227 HGCSFNCAFCGGSNFayknNYNSVAPLYRKPLVIAEEISLVG-EMLGSPVFITGDMNNAGEKFYSSLFKELKD--RK 300
                                       7************99****9999999************9996.55589999999999999************9..7* PP

                                       EEEEEEECSSCHG.HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHH...HHHHHHHHHHHHTTSETEEEEE CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.eeklerllelg.vdrvslgleaaddekvlklmnrghtf...eevlealeklreagikrvvdri 149
                                       +++ + t +++p  +e+l +l  +    +v+++ e+ ++  ++++++r++++   e++l++  ++ ++ i+  v+++
  gi|518651991|ref|YP_008141511.1| 301 VSLPLLTEYFTPPgKEYLNELSHRFpDFTVEISPESSSEV-IRNRNGRPYSNkglEDFLQNAVTAGAKKID--VYFT 374
                                       **********************988899***********8.999999777775558888888888888888..9*** PP

                                       EEBTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 150 vglpGendeeleell 164
                                       +g+ G++  ++++ +
  gi|518651991|ref|YP_008141511.1| 375 IGMSGQTVNDVNADI 389
                                       ********9998766 PP

>> B12-binding  B12 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   4.1e-09   2.4e-05       7     112 ..      33     143 ..      28     149 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 4.1e-09
                       B12-binding   7 tvggdlhplGlavlaaalrdagfeVqllganven.....edivaairaekpdvvglSalltsqleavkelvellkri 78 
                                       t  ++++p+G+ +  + l  +g++ ++ ++ + +      d v+ ++  k  + g+ +++  + +++ ++++ +k  
  gi|518651991|ref|YP_008141511.1|  33 TPVFEMYPVGFISMLNSLISSGYNARICNVAAMMvssasFDPVKYLKHVKSKIYGIDLHWLPHANGALKVAKIIKDL 109
                                       5667899***99999999999**999998888778889999************************************ PP

                       B12-binding  79 rprvkvvvGGahpsldpeetleaklgiddvvvge 112
                                       +p+ kv++GG  +s+ +++++ +  +id++  g+
  gi|518651991|ref|YP_008141511.1| 110 HPDSKVLLGGFSASYFADDIMTHYGYIDYILKGD 143
                                       *********************988999*987775 PP

>> DUF1450  Protein of unknown function (DUF1450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.4e-05     0.082      23      52 ..     216     245 ..     206     251 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.4e-05
                           DUF1450  23 lekdpdvdvieygClsnCglCakspfAlVn 52 
                                       l++   ++vie gC  nC  C  s fA+ n
  gi|518651991|ref|YP_008141511.1| 216 LDNTEAMTVIEHGCSFNCAFCGGSNFAYKN 245
                                       7788899********************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.50
# Mc/sec: 3354.88
//
Query:       gi|518651992|ref|YP_008141512.1|  [L=301]
Description: hypothetical protein FACI_IFERC00001G0631 [Ferroplasma acidarmanus fer1]
Scores for complete 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  180.3   0.0    4.5e-53  179.5   0.0    1.4  1  OTCace           Aspartate/ornithine carbamoyltransferase, As
    4.3e-41  140.4   0.1    6.5e-41  139.8   0.1    1.3  1  OTCace_N         Aspartate/ornithine carbamoyltransferase, ca
    0.00072   19.1   0.0     0.0013   18.2   0.0    1.4  1  Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase
  ------ inclusion threshold ------
      0.025   14.8   0.2       0.71   10.2   0.0    2.4  2  Spy1             Cell cycle regulatory protein
       0.19   11.6   0.0        0.3   11.0   0.0    1.3  1  YjeF_N           YjeF-related protein N-terminus


Domain annotation for each model (and alignments):
>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.0   1.3e-56   4.5e-53       2     156 ..     145     298 ..     144     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.3e-56
                                       C.EEEEESSTTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE- CS
                            OTCace   2 glkiafvGdkknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytd 78 
                                       +lk+a+vGd+ nnv nsl+ ++a +gmd+++++P++ epd ++l +ak+ a k+g++i+i  d   av+ aD++ytd
  gi|518651992|ref|YP_008141512.1| 145 NLKLAYVGDG-NNVSNSLLLGAALTGMDISVACPEHREPDRDILYRAKDLALKTGSRIEILRDARTAVDSADIIYTD 220
                                       79********.****************************************************************** PP

                                       -SSETTCCGGHHHHHHHHCCCSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHH CS
                            OTCace  79 vwvsmgeekereerlkklkdyqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllv 155
                                       vwvsmgeeke++++ k +k+yqv+eel + a+k+ i++HcLPa rg Evtde++++ +svvf++aeNrl+ +k +++
  gi|518651992|ref|YP_008141512.1| 221 VWVSMGEEKEKDQKEKLFKGYQVNEELADFADKNYIFMHCLPARRGLEVTDEIIEGIHSVVFDEAENRLYSEKGVIY 297
                                       ***************************************************************************98 PP

                                       H CS
                            OTCace 156 l 156
                                       +
  gi|518651992|ref|YP_008141512.1| 298 T 298
                                       6 PP

>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.8   0.1   1.8e-44   6.5e-41       1     148 []       3     138 ..       3     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 139.8 bits;  conditional E-value: 1.8e-44
                                       S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTS CS
                          OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaedi 77 
                                       r++ls++d++ +++++++d++ +lk+++    + k  ++k l+++Fe+pStRTr+S e+A+++l g++++ls ++++
  gi|518651992|ref|YP_008141512.1|   3 RDILSVADME-NDFDQIIDTSIKLKKDK----TIKFSDKKLLGMIFEKPSTRTRISLEAAMEQLNGHAIYLS-PHEM 73 
                                       799*****98.99************885....5788899*********************************.8899 PP

                                       CTTTGGSTTSSCHHHHHHHHHHHTSEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHHH CS
                          OTCace_N  78 qlssvskgrkEsleDtarvlsryvdaiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltire 148
                                       +l+      +E+++Dtarv+sr+ d+i +R+++ ++++elakya+vpv+Na+  ++eHP+Q+ aD++ti e
  gi|518651992|ref|YP_008141512.1|  74 HLG-----DGETIADTARVMSRFLDIISYRAYDYRNVRELAKYADVPVLNAL-DNMEHPLQIVADFMTIME 138
                                       999.....66**********************9999****************.899*************87 PP

>> Glyco_hydro_101  Endo-alpha-N-acetylgalactosaminidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   3.7e-07    0.0013     149     214 ..     195     259 ..     186     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.7e-07
                                       HHTT.HHHHHHHHHHHH-.T--EEEEESTSTTSHHHHHHHHHHHCTT-EEEES-TTS-TTT-SBBH CS
                   Glyco_hydro_101 149 lasgkllkRfkelreelgeeldfiYvDvyresgwaskklskelnkqGwrvasewaealeedstwsh 214
                                       l++g++ + +++ r +++ + d+iY Dv+ + g + +k +ke   +G++v +e+a+  +++  + h
  gi|518651992|ref|YP_008141512.1| 195 LKTGSRIEILRDARTAVD-SADIIYTDVWVSMGEEKEKDQKEKLFKGYQVNEELADFADKNYIFMH 259
                                       456777777777666666.99*********************99****************999999 PP

>> Spy1  Cell cycle regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0002      0.71      19      39 ..      25      45 ..      10      73 .. 0.75
   2 ?    2.3   0.1     0.055     2e+02      66     119 ..     227     279 ..     218     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0002
                              Spy1 19 LaaDkclkvsDkyllamvlay 39
                                      L++Dk++k+sDk ll m+++ 
  gi|518651992|ref|YP_008141512.1| 25 LKKDKTIKFSDKKLLGMIFEK 45
                                      89****************965 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.055
                              Spy1  66 Eedeeeskleifpfalgkewkskvpkflklrdkllarmeyr..aaVsreeceeiqa 119
                                       Ee e+++k ++f    g + ++++++f  + + +++++  r    V+ e++e i +
  gi|518651992|ref|YP_008141512.1| 227 EEKEKDQKEKLF---KGYQVNEELADFADKNYIFMHCLPARrgLEVTDEIIEGIHS 279
                                       677777777777...68888899***********9999887334677777777765 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 ?   11.0   0.0   8.3e-05       0.3      12      88 ..     130     204 ..     120     227 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-05
                            YjeF_N  12 vaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeeekldedaeralellkkaggkvvee 88 
                                       va++++ + +++  e+  l  vG+gnn +  l +++ L  +g+++ v + e +e+ ++   ra +l+ k+g ++   
  gi|518651992|ref|YP_008141512.1| 130 VADFMTIMEKKHRLENLKLAYVGDGNNVSNSLLLGAAL--TGMDISVACPEHREPDRDILYRAKDLALKTGSRIEIL 204
                                       555555555577778888999*****************..5555556557778888888888999999998887655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2134.13
//
Query:       gi|518651993|ref|YP_008141513.1|  [L=321]
Description: hypothetical protein FACI_IFERC00001G0632 [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  160.5   5.0    6.4e-47  160.2   5.0    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      9e-26   90.8   5.4    5.9e-21   75.0   0.5    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    3.6e-12   46.7   3.8    9.2e-09   35.8   0.2    3.0  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    3.6e-10   39.5  10.5    5.8e-08   32.2   0.6    4.1  5  FAD_binding_2   FAD binding domain
    1.1e-08   34.6   1.1    5.5e-07   29.1   0.1    2.6  3  Thi4            Thi4 family
    4.6e-08   32.2   7.3    0.00058   18.7   0.5    3.2  3  HI0933_like     HI0933-like protein
    4.7e-08   32.8   0.0    4.7e-08   32.8   0.0    2.3  3  FAD_oxidored    FAD dependent oxidoreductase
    5.1e-07   29.6  11.0    0.00021   21.0   2.3    3.1  3  DAO             FAD dependent oxidoreductase
    1.1e-06   28.1   9.7     0.0013   17.9   1.5    3.3  3  GIDA            Glucose inhibited division protein A
    2.4e-06   27.7   5.0    6.2e-06   26.4   0.2    2.3  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    4.1e-06   26.3   1.2    0.00044   19.6   0.2    2.2  2  FAD_binding_3   FAD binding domain
    2.4e-05   24.0   0.5      0.039   13.5   0.1    2.3  2  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin
    7.9e-05   22.0   0.1    0.00087   18.5   0.0    2.4  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00075   19.9   0.2      0.031   14.7   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
     0.0014   17.5   2.2       0.67    8.7   0.5    2.1  2  Trp_halogenase  Tryptophan halogenase
     0.0014   17.9   0.1       0.42    9.9   0.1    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.003   16.9   0.3        1.3    8.2   0.0    2.1  2  Amino_oxidase   Flavin containing amine oxidoreductase
  ------ inclusion threshold ------
      0.035   13.7   0.3        1.2    8.8   0.4    2.8  2  40S_S4_C        40S ribosomal protein S4 C-terminus
      0.042   12.6   0.1      0.076   11.8   0.1    1.5  1  MCRA            MCRA family
      0.047   13.1   0.6        5.4    6.3   0.1    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.084   11.9   4.8       0.33   10.0   0.3    2.6  3  Lycopene_cycl   Lycopene cyclase protein
       0.11   12.5   0.1        3.2    7.7   0.0    2.4  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
       0.14   11.8   3.9        5.7    6.6   0.2    2.7  3  ApbA            Ketopantoate reductase PanE/ApbA


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.2   5.0   8.2e-50   6.4e-47       1     293 [.      17     304 ..      17     305 .. 0.88

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 8.2e-50
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHHHCCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias........evvkklnqgiel 69 
                                       +dv++iG+G+AG++a  +++++g+ v+++ +++ +++g   +s+ ++++ + + i+         ++  +++   + 
  gi|518651993|ref|YP_008141513.1|  17 YDVIIIGAGAAGYSAGVYIKRSGMSVAIL-ERESVPGGNTAVSPLVENYLGYKAIEGadlaedfrKHYAQYG---KI 89 
                                       69***************************.9999******************99999977765544433222...22 PP

                                       CHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  70 llgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkriv 146
                                       +++  v +i ++  k+ + +++     +++++++++ tG + r+++++G+ e++gk+++++ +++++  k ++  ++
  gi|518651993|ref|YP_008141513.1|  90 ITEIDVRDIKKEGDKFRIITNR----SDFTAKAIIVTTGTTHRKMNVKGEDEYYGKGISYCSTCDGYLFKDKN--VA 160
                                       2333377777777788886554....58***************************************999998..** PP

                                       EES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.....EEE. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxx. RF
                       Pyr_redox_2 147 vvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.....kle. 217
                                       v+GgG+ G   A +l+ ++k+v ++ + +++     k++++a+ + + ++++ + l+++ +e++g+g+     k++ 
  gi|518651993|ref|YP_008141513.1| 161 VIGGGNSGAISALYLKGIAKNVSIIAH-SKI-----KKCEDAYIKSIDEKKIPFILNAETEEFIGDGKkltglKYKd 231
                                       ***********************9988.555.....47******************************888665669 PP

                                       EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 218 vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrtnvpgiyaiGDvaggkggpelaqaAvqq 293
                                       + ++++++++ d ++v +Gv p+t++l +++g++ld++g+i  de++rtn+pgiy +GDv    g+ e++ +Av  
  gi|518651993|ref|YP_008141513.1| 232 LATGEEKTENLDGIFVYIGVIPQTSFL-KNIGVKLDKHGFIIADEKGRTNIPGIYGAGDVL--AGSEEQIATAVGD 304
                                       99999**********************.*********************************..7777777777765 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 !   18.4   0.5   1.3e-06     0.001       1      32 [.      20      50 ..      20      56 .. 0.94
   2 !   75.0   0.5   7.6e-24   5.9e-21      79     305 .]      71     288 ..      52     288 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.3e-06
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                                      iIiGaG+aG +a++ +k++g+ ++ ilE++++
  gi|518651993|ref|YP_008141513.1| 20 IIIGAGAAGYSAGVYIKRSGM-SVAILERESV 50
                                      8********************.7******875 PP

  == domain 2  score: 75.0 bits;  conditional E-value: 7.6e-24
                       Pyr_redox_3  79 srkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeek...lvkh 152
                                       ++++++e +r+  +++  +i ++ +V+++kke+++f++ t++++++Ak +i+ tG     +k+n++Ge++   + + 
  gi|518651993|ref|YP_008141513.1|  71 EGADLAEDFRKHYAQYG-KIITEIDVRDIKKEGDKFRIITNRSDFTAKAIIVTTGT--THRKMNVKGEDEyygKGIS 144
                                       56666665555555544.589999*******************************9..8999*******87333445 PP

                       Pyr_redox_3 153 yskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikv 229
                                       y    +   +++++v+ViGg+nS++  Al l    ++V+++ +++ i+k e+ +  s+     + + ++ +ee   +
  gi|518651993|ref|YP_008141513.1| 145 YCSTCDGYLFKDKNVAVIGGGNSGAISALYLKGIAKNVSIIAHSK-IKKCEDAYIKSIDEKKIPFILNAETEE--FI 218
                                       55555666789*****************************99986.788776777777777777777766555..44 PP

                       Pyr_redox_3 230 lfnaevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        + ++++ +k k+    + t + +k+e + d +++ +G  p++sflk+ +++ld+ g++  +e +  tn+pg++ aG
  gi|518651993|ref|YP_008141513.1| 219 GDGKKLTGLKYKD----LATGE-EKTE-NLDGIFVyIGVIPQTSFLKNIGVKLDKHGFIIADE-KGRTNIPGIYGAG 288
                                       5566666666553....33433.3444.45555555*****************9999988766.568*******998 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   0.5   0.00068      0.53       2      41 ..      19      56 ..      18     113 .. 0.89
   2 !   35.8   0.2   1.2e-11   9.2e-09       1      79 [.     158     230 ..     158     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00068
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHH CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDee 41
                                      v+++G+G  g  ++ ++++ g +V ++er++ +    + +
  gi|518651993|ref|YP_008141513.1| 19 VIIIGAGAAGYSAGVYIKRSGMSVAILERESVPG--GNTA 56
                                      89***************************99887..4444 PP

  == domain 2  score: 35.8 bits;  conditional E-value: 1.2e-11
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       +v+v+GgG++g   A +l+ ++k+V+++  s+         ++++  +++ +++i ++ln+++ee+ g++++++++k
  gi|518651993|ref|YP_008141513.1| 158 NVAVIGGGNSGAISALYLKGIAKNVSIIAHSKIKK------CEDAYIKSIDEKKIPFILNAETEEFIGDGKKLTGLK 228
                                       599*************************9996666......9******************************99998 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                        k
  gi|518651993|ref|YP_008141513.1| 229 YK 230
                                       76 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.2   0.6   7.4e-11   5.8e-08       1      41 [.      18      58 ..      18      59 .. 0.98
   2 ?    0.7   0.0      0.27   2.1e+02     140     204 ..      72     128 ..      62     151 .. 0.66
   3 ?    2.0   1.8      0.12        90       2      30 ..     159     187 ..     158     197 .. 0.87
   4 ?   -1.6   0.0       1.4   1.1e+03     147     189 ..     197     239 ..     187     268 .. 0.82
   5 !    7.0   0.0    0.0033       2.6     374     404 ..     261     293 ..     211     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 7.4e-11
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG- CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggataws 41
                                      Dvi+iG+G+AG++A++ +++ G +va++e e++ gg+ta s
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERESVPGGNTAVS 58
                                      9*************************************987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.27
                                       HHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                       g  l++ + +++ ++  ++ ++++++++  e+++ + +     ++ +   ++aka++++tg  +r
  gi|518651993|ref|YP_008141513.1|  72 GADLAEDFRKHYAQY-GKIITEIDVRDIKKEGDKFRII-----TNRS--DFTAKAIIVTTGTTHR 128
                                       555566666666444.4666777777776644444443.....4444..5679999999999887 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                                       v ViG+G +G  +Al ++   ++v ++  
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYLKGIAKNVSIIAH 187
                                       89**************9999998888765 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.4
                                       HHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEE CS
                     FAD_binding_2 147 lvesarkagvdfqerteadeLivedgrvtGavvenpesgrevr 189
                                        ++s+++ ++ f  ++e +e+i ++++ tG   +++++g+e +
  gi|518651993|ref|YP_008141513.1| 197 YIKSIDEKKIPFILNAETEEFIGDGKKLTGLKYKDLATGEEKT 239
                                       57888899999**********99999****9999998888764 PP

  == domain 5  score: 7.0 bits;  conditional E-value: 0.0033
                                       -EEEBETTSBE..STTEEESSBTEEE-STCEES CS
                     FAD_binding_2 374 gGvetdengrv..ldadgqpipGLYAaGevaag 404
                                        Gv+ d +g    ++++ ++ipG Y aG v+ag
  gi|518651993|ref|YP_008141513.1| 261 IGVKLDKHGFIiaDEKGRTNIPGIYGAGDVLAG 293
                                       5778888877776777778***********965 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   7.1e-10   5.5e-07      16      57 ..      15      55 ..       4      94 .. 0.89
   2 ?    3.7   0.1     0.038        30      15      38 ..     154     177 ..     143     190 .. 0.73
   3 ?   -3.7   0.0       7.2   5.6e+03      73      88 ..     254     269 ..     251     273 .. 0.82

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 7.1e-10
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTT CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailersvspGGGa 57
                                       + Dv+i+GaG++G +a+ y+ ++ ++ vailer+  pGG +
  gi|518651993|ref|YP_008141513.1| 15 TDYDVIIIGAGAAGYSAGVYIKRS-GMSVAILERESVPGGNT 55
                                      467******************999.**************976 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.038
                                       HTEEEEEEE--SHHHHHHHHHHHH CS
                              Thi4  15 yaesDvvivGaGssGLtaayylak 38 
                                       + + +v+++G+G sG  +a yl  
  gi|518651993|ref|YP_008141513.1| 154 FKDKNVAVIGGGNSGAISALYLKG 177
                                       45678**********988888743 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 7.2
                                       THHHHHHTT---EEES CS
                              Thi4  73 akelLdelgikyedeg 88 
                                          +L+++g+k++++g
  gi|518651993|ref|YP_008141513.1| 254 QTSFLKNIGVKLDKHG 269
                                       5789******998875 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.5   7.5e-07   0.00058       1      36 [.      17      52 ..      17      58 .. 0.91
   2 !    8.6   0.0   0.00088      0.69     124     164 ..      87     125 ..      75     128 .. 0.88
   3 !    7.6   0.4    0.0017       1.3       2      33 ..     158     189 ..     157     192 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-07
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                                      +dvi+iG+GaAG  a + +++ g +V++le+++ +g
  gi|518651993|ref|YP_008141513.1| 17 YDVIIIGAGAAGYSAGVYIKRSGMSVAILERESVPG 52
                                      59****************************998776 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00088
                                       -EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
                       HI0933_like 124 vklrletevksvekeedgkfrvktkseeeleadklvlAtGG 164
                                        k+ +e +v++++ke d+ fr+ t +++ ++a++++++tG 
  gi|518651993|ref|YP_008141513.1|  87 GKIITEIDVRDIKKEGDK-FRIIT-NRSDFTAKAIIVTTGT 125
                                       5788999*****998888.*****.9*************96 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0017
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                                       +v+viGgG +G   A+ ++   k+V ++ + k
  gi|518651993|ref|YP_008141513.1| 158 NVAVIGGGNSGAISALYLKGIAKNVSIIAHSK 189
                                       79***********************9998865 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0     6e-11   4.7e-08       1      71 [.      18      87 ..      18     119 .. 0.81
   2 ?   -0.5   1.8      0.76   5.9e+02       2      19 ..     159     176 ..     158     190 .. 0.76
   3 ?   -2.3   0.0       2.7   2.1e+03      90     130 ..     194     235 ..     176     239 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 6e-11
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaeeqvvtg..iareflerlrqrg 71
                                      Dv+++G+g+aG+ A +  +r+G +v+++e++ v GG+++   v+++++n+   ++++g  +a++f+++ +q g
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERESVPGGNTA---VSPLVENYLGYKAIEGadLAEDFRKHYAQYG 87
                                      9***********************************986...5555555555556666568888888887744 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.76
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAa 19 
                                       v V+GGg +G + A+  +
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYLK 176
                                       89**********998655 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.7
                      FAD_oxidored  90 kavleemlaeagvtvllntrlvevekegkriesvtveske.g 130
                                       + ++ + ++e+++  +ln++ +e + +gk++++++ ++ + g
  gi|518651993|ref|YP_008141513.1| 194 EDAYIKSIDEKKIPFILNAETEEFIGDGKKLTGLKYKDLAtG 235
                                       344444559999999999999999999999999998876644 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.3   2.7e-07   0.00021       1      38 [.      18      56 ..      18      59 .. 0.91
   2 ?    4.5   0.0     0.028        22     161     202 ..      87     125 ..      64     138 .. 0.72
   3 !    8.8   0.4    0.0014       1.1       2      25 ..     159     184 ..     158     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.7e-07
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGG CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSg 38
                                      dv+iiG+G +G s+  +  r g  V++le+++ +g g + 
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGmsVAILERESVPG-GNTA 56
                                      9*****************7779*********9999.8765 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.028
                                       -EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GG CS
                               DAO 161 veilegtevtgleeedgkvwgverttpgendaadavVnaaGa 202
                                       ++i+++  v+++++e++k   +  t++ + ++a+a+++++G 
  gi|518651993|ref|YP_008141513.1|  87 GKIITEIDVRDIKKEGDKFRII--TNR-SDFTAKAIIVTTGT 125
                                       7999999*****8876664444..443.233579*******5 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0014
                                       EEEECTSHHHHHHHHHHHHTT....EEE CS
                               DAO   2 vviiGGGiiGlstAyeLarrg....Vtl 25 
                                       v++iGGG  G+  A++L  +g    V +
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYL--KGiaknVSI 184
                                       9****************..343334555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.5   1.7e-06    0.0013       1      29 [.      18      46 ..      18      64 .. 0.88
   2 !    6.5   0.2     0.005       3.9     117     163 ..      94     137 ..      76     149 .. 0.67
   3 !    7.8   0.1    0.0019       1.5       2      36 ..     159     193 ..     158     213 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                                      dvi+iG+G AG+ A + ++r+G++v+++ 
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILE 46
                                      8************************9984 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.005
                                       -EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEE CS
                              GIDA 117 eveeliveekkvkgvvtedgetikakavviatGtflkgkihigekel 163
                                        v +++ e +k + ++  + + ++aka++++tGt  + k+ ++ +  
  gi|518651993|ref|YP_008141513.1|  94 DVRDIKKEGDKFRIIT--NRSDFTAKAIIVTTGT-THRKMNVKGEDE 137
                                       5666655555555544..4567899*********.555555444443 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0019
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtia 36 
                                       v ViGgG +G   Al ++    +v +i+h+  + +
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYLKGIAKNVSIIAHSKIKKC 193
                                       89************************988765544 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.2     8e-09   6.2e-06       1      36 [.      21      56 ..      21      71 .. 0.95
   2 ?    3.0   0.7      0.16   1.2e+02       1      17 [.     161     177 ..     161     188 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 8e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      I+GaG++G +a  ++++ g +v +le+ + +GG+ a
  gi|518651993|ref|YP_008141513.1| 21 IIGAGAAGYSAGVYIKRSGMSVAILERESVPGGNTA 56
                                      9********************************976 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.16
                                       EE--SHHHHHHHHHHHC CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLak 17 
                                       ++G+G sG+  A +L+ 
  gi|518651993|ref|YP_008141513.1| 161 VIGGGNSGAISALYLKG 177
                                       8***********99974 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.2   5.6e-07   0.00044       2      34 ..      17      49 ..      16      55 .. 0.93
   2 ?    5.5   0.0     0.011       8.5       3      23 ..     158     178 ..     156     193 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 5.6e-07
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                                      +dV+I+GaG aG +++   ++ G +v ++e+ s
  gi|518651993|ref|YP_008141513.1| 17 YDVIIIGAGAAGYSAGVYIKRSGMSVAILERES 49
                                      79*****************************87 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.011
                                       EEEEE--SHHHHHHHHHHHHT CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLsea 23 
                                       +V+++G+G +G+++al L+  
  gi|518651993|ref|YP_008141513.1| 158 NVAVIGGGNSGAISALYLKGI 178
                                       79*************999755 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 !    8.6   0.0    0.0017       1.3       6      62 ..      18      74 ..      15      84 .. 0.80
   2 !   13.5   0.1     5e-05     0.039       2      47 ..     154     199 ..     153     210 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0017
                                      -EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-S CS
                              IlvN  6 kiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkad 62
                                       + +iG G+ G + +  ++ sg+ v++  re+    ++A +  +e +   +a++ ad
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERESVPGGNTAVSPLVENYLGYKAIEGAD 74
                                      699************************998887777777666666665555655555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHT CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkee 47 
                                       +k+k++aviG G+ G   al l+    +v +  +++ k+++ A  +
  gi|518651993|ref|YP_008141513.1| 154 FKDKNVAVIGGGNSGAISALYLKGIAKNVSIIAHSKIKKCEDAYIK 199
                                       699**************************99999988888887655 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 ?    0.3   0.0      0.39     3e+02       3      34 ..      17      46 ..      15      50 .. 0.72
   2 !   18.5   0.0   1.1e-06   0.00087     107     215 ..      77     180 ..      73     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.39
                       K_oxygenase  3 lDligiGiGpsnLsLailleevkkelkalfle 34
                                      +D+i+iG+G++  s  + ++     +++  le
  gi|518651993|ref|YP_008141513.1| 17 YDVIIIGAGAAGYSAGVYIKRSG--MSVAILE 46
                                      89*******99888777666655..5555555 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.1e-06
                       K_oxygenase 107 sqleeq.vrfgeeveevepdeeeee.elltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHssey 181
                                       + + ++  ++g+ ++e+++++ ++e + +++ +     +++ ++a+++++++Gt+    +v  +   +e      +y
  gi|518651993|ref|YP_008141513.1|  77 EDFRKHyAQYGKIITEIDVRDIKKEgDKFRIIT-----NRSDFTAKAIIVTTGTTHRKMNVKGE---DEYYGKGISY 145
                                       556643389************888889*****9.....7899***********88764333322...3444444466 PP

                       K_oxygenase 182 lerkee.llakkriaVvGsGqSaaeifedllrrqk 215
                                        ++ +  l + k++aV+G+G S+a  +  l   +k
  gi|518651993|ref|YP_008141513.1| 146 CSTCDGyLFKDKNVAVIGGGNSGAISALYLKGIAK 180
                                       66665557899************955554444444 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      0.16   1.3e+02       9      46 ..      18      68 ..      15     133 .. 0.61
   2 !   14.7   0.0     4e-05     0.031       5      71 ..     154     254 ..     152     276 .. 0.62

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.16
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev....keele.........e 46
                                       v+++G+G  +++    + ++g  v ++  e+    + +++         +
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERESvpggNTAVSplvenylgyK 68
                                      799*********999999999999999888854433222222333333331 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele............................elvklaee 53 
                                       +k+k+v v+GgG+ +a  +  l    ++v ++a    +++e                            +       
  gi|518651993|ref|YP_008141513.1| 154 FKDKNVAVIGGGNSGAISALYLKGIAKNVSIIAHSKIKKCEdayiksidekkipfilnaeteefigdgkK------- 223
                                       689********************************87777765555454444433333322222222221....... PP

                     NAD_binding_7  54 elekd.................legadlviaatdd 71 
                                                             l+g+++ i ++++
  gi|518651993|ref|YP_008141513.1| 224 ----LtglkykdlatgeektenLDGIFVYIGVIPQ 254
                                       ....0222222222222333336666666655555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.5   0.00086      0.67       1      37 [.      18      51 ..      18      61 .. 0.92
   2 !    8.5   0.0   0.00099      0.77       1      37 [.     158     191 ..     158     227 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00086
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37
                                      +++i+G+G aG+ a  ++++ +   ++v ++e e ++
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSG---MSVAILERESVP 51
                                      699******************9...899999999987 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00099
                                       EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS- CS
                    Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtlveseeig 37 
                                       ++ ++GGG +G ++A +l+   k   +v+++  ++i 
  gi|518651993|ref|YP_008141513.1| 158 NVAVIGGGNSGAISALYLKGIAK---NVSIIAHSKIK 191
                                       589****************9994...57777777775 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.1   0.00054      0.42      30      60 ..      18      48 ..      14      98 .. 0.87
   2 !    6.0   0.0    0.0082       6.4      29      61 ..     157     189 ..     138     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00054
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvr 60
                                       v++iG+G aG +A    k+ g +V +l+ +
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERE 48
                                      599************************9976 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0082
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrp 61 
                                        +v viGgG  G  ++   kg+  +V ++  ++
  gi|518651993|ref|YP_008141513.1| 157 KNVAVIGGGNSGAISALYLKGIAKNVSIIAHSK 189
                                       689***********************9986543 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.0   0.0    0.0041       3.2       2      31 ..      27      56 ..      26      74 .. 0.88
   2 !    8.2   0.0    0.0017       1.3     221     266 ..      85     129 ..      72     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0041
                                      HHHHHHHHHHHTTEEEEEEESSSSSBTTS- CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEardrvGGRir 31
                                      aG +a  + ++ G++V +lE ++ +GG  +
  gi|518651993|ref|YP_008141513.1| 27 AGYSAGVYIKRSGMSVAILERESVPGGNTA 56
                                      7889999********************865 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0017
                                       TTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHHHH CS
                     Amino_oxidase 221 rgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgvlk 266
                                         ++i ++  V++ik+egd+ ++ +++ ++++a+a++vT+   + k
  gi|518651993|ref|YP_008141513.1|  85 QYGKIITEIDVRDIKKEGDKFRI-ITNRSDFTAKAIIVTTGTTHRK 129
                                       45788888999*********999.7899***********9876655 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 ?    8.8   0.4    0.0016       1.2      12      37 ..     157     182 ..     155     192 .. 0.85
   2 ?    1.5   0.0      0.31   2.4e+02      17      29 ..     302     314 ..     300     316 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0016
                                       GGEEE--STTS-SS---SS-S----H CS
                          40S_S4_C  12 sNvFvIGkgnkpwvsLPkgkGiklsi 37 
                                       +Nv vIG gn+  +s    kGi +++
  gi|518651993|ref|YP_008141513.1| 157 KNVAVIGGGNSGAISALYLKGIAKNV 182
                                       6**************5555**98876 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.31
                                       --STTS-SS---S CS
                          40S_S4_C  17 IGkgnkpwvsLPk 29 
                                       +G+g+k+ ++L+ 
  gi|518651993|ref|YP_008141513.1| 302 VGDGSKAAITLYT 314
                                       8**********86 PP

>> MCRA  MCRA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   9.8e-05     0.076       3      69 ..      18      82 ..      16     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.8e-05
                                      EEEEE--SHHHHHHHHHHHHTT---GGGEEEE-SS----------..-------CCC----B-TT-HHH CS
                              MCRA  3 kaylvGsGiasLaaAvyLirdakvpgenihileelkvaggsldga..gdpekGyvlrggreleehyecl 69
                                      ++ ++G+G a+ +a vy+ r    +g  + ile+++v+gg +  +   ++  Gy +  g  l e +++ 
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKR----SGMSVAILERESVPGGNTAVSplVENYLGYKAIEGADLAEDFRKH 82
                                      578**************855....5678************98877334555699999988775544333 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.019        15      38      69 ..      18      49 ..       8      62 .. 0.88
   2 ?    6.3   0.1    0.0069       5.4      28      72 ..     148     192 ..     118     206 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.019
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrsk 69
                                       v iiG+G+ G ++  ++k  gm v + +r  
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYIKRSGMSVAILERES 49
                                      588**********************9998875 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0069
                                       CGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHH CS
                      2-Hacid_dh_C  28 allgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkke 72 
                                       +  g+  ++k v++iG G+ G   a +lk++  +v ++ +sk k+
  gi|518651993|ref|YP_008141513.1| 148 TCDGYLFKDKNVAVIGGGNSGAISALYLKGIAKNVSIIAHSKIKK 192
                                       566778899********************8877776666654422 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.3   0.00042      0.33       1      32 [.      18      47 ..      18      59 .. 0.85
   2 ?    3.3   0.0     0.045        35      79     144 ..      65     128 ..      54     144 .. 0.78
   3 ?   -1.5   0.2       1.3   9.8e+02       2      30 ..     159     185 ..     158     192 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00042
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dv++iGaG+Ag s    +  ++ g++v ++e 
  gi|518651993|ref|YP_008141513.1| 18 DVIIIGAGAAGYSAGVYI--KRSGMSVAILER 47
                                      9************99999..999999999975 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.045
                     Lycopene_cycl  79 raYgrvsskrlkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglasl 144
                                       + Y+ ++ ++l+e   ++ ++ g + +e  v  +++e + + ++ + +     a+++++ +g  ++
  gi|518651993|ref|YP_008141513.1|  65 LGYKAIEGADLAEDFRKHYAQYGKIITEIDVRDIKKEGD-KFRI-ITNRSDFTAKAIIVTTGTTHR 128
                                       67**********************************999.4443.334456778888888884443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.3
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvli 30 
                                       v+viG+G  g   A  l  +  + +v +i
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYL--KGIAKNVSII 185
                                       89********9988888..6666666666 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.17   1.4e+02       2      32 ..      19      49 ..      18      81 .. 0.87
   2 ?    7.7   0.0    0.0042       3.2       1      38 [.     158     196 ..     158     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.17
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvree 32
                                      + ++GaG+ G +    +++ g +v +  re+
  gi|518651993|ref|YP_008141513.1| 19 VIIIGAGAAGYSAGVYIKRSGMSVAILERES 49
                                      789*********************9999886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0042
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H.HHHHHH CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree.elieei 38 
                                       ++av+G+G+ G   A  l+  +++v+++++++ + +e+ 
  gi|518651993|ref|YP_008141513.1| 158 NVAVIGGGNSGAISALYLKGIAKNVSIIAHSKiKKCEDA 196
                                       59**************************99987444443 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0073       5.7       1      30 [.      19      48 ..      19      51 .. 0.91
   2 ?   -2.9   0.0       6.2   4.8e+03      62      80 ..     109     127 ..      76     133 .. 0.58
   3 ?    6.1   0.1    0.0099       7.7       1      58 [.     159     212 ..     159     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0073
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrs 30
                                      + i+GaGa G   ++++++ g  v ++ r+
  gi|518651993|ref|YP_008141513.1| 19 VIIIGAGAAGYSAGVYIKRSGMSVAILERE 48
                                      57**********************999886 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.2
                                       SCCCCS-ESEEEE-SSGGG CS
                              ApbA  62 ekselepidlvivtvKayq 80 
                                       +++++  +  +ivt+ +++
  gi|518651993|ref|YP_008141513.1| 109 TNRSDFTAKAIIVTTGTTH 127
                                       4555566667777775555 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0099
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEECEEE CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrppeal 58 
                                       +a++G G  G + a +L+  + +v +i++s+ +++ +++ +  +s + e+++++  ++
  gi|518651993|ref|YP_008141513.1| 159 VAVIGGGNSGAISALYLKGIAKNVSIIAHSK-IKKCEDAYI--KSID-EKKIPFILNA 212
                                       69***************778889*******9.775544444..3333.3344444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       644  (0.0359195); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              23  [number of targets reported over threshold]
# CPU time: 0.64u 0.32s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 1960.78
//
Query:       gi|518651994|ref|YP_008141514.1|  [L=545]
Description: hypothetical protein FACI_IFERC00001G0633 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.1e-178  594.9  22.8   1.2e-178  594.7  22.8    1.0  1  Cpn60_TCP1   TCP-1/cpn60 chaperonin family
  ------ inclusion threshold ------
      0.053   13.5   2.1        0.2   11.6   0.9    2.4  2  YwpF         YwpF-like protein
        0.6   10.1   0.0        0.6   10.1   0.0    2.6  3  Prefoldin_2  Prefoldin subunit


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 !  594.7  22.8  2.1e-182  1.2e-178       1     490 [.      34     522 ..      34     523 .. 0.98

  Alignments for each domain:
  == domain 1  score: 594.7 bits;  conditional E-value: 2.1e-182
                                       HHHHHHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHHHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHH CS
                        Cpn60_TCP1   1 ladivkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPaakllveaaesqdeevGDGTttvviLageLleea 77 
                                       +ad+v+ttlGPkGmdKm v+++g+++++nDGatilke++++hP+ak++vea++sqd+ vGDGTttvv++ageLl++a
  gi|518651994|ref|YP_008141514.1|  34 IADAVRTTLGPKGMDKMMVDSIGDIIISNDGATILKEMDVDHPTAKMIVEASKSQDTAVGDGTTTVVVFAGELLKQA 110
                                       79*************************************************************************** PP

                                       HHHHHCTXXHHHHHHHHHHHHHHHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHC CS
                        Cpn60_TCP1  78 ekliaagvhpttiiegyekalekaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklie 154
                                       e l+++gvh t i +gy+ a+e+a ++L ++  ++s +  d+ +L+k+a t+ls+k t    e+l++lvv+A+++++
  gi|518651994|ref|YP_008141514.1| 111 EALLDQGVHSTIIADGYHLAAEEARKQLLAM--SVSAK--DDAMLRKIAITALSGKNTGVAPEFLADLVVNAINSVT 183
                                       ****************************989..55543..679******************************6666 PP

                                       CCS...EECSCCCEECCCCEECECTTSEEESEEEESS--SSTTSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCC CS
                        Cpn60_TCP1 155 ene...keldlgrikvvkieggsledselveGlvldkgvlspdmpkklenakvllldvsLeiektetkttvvlsdae 228
                                       e++     +d  +ikv k+ ggs  d+++++Gl++dk+ ++++mp  ++nak++l++  Lei+kte++++v+++d++
  gi|518651994|ref|YP_008141514.1| 184 ETDgdkIIVDTANIKVDKKSGGSAADTKFINGLIIDKEKVHSKMPSVVKNAKIALINSALEIKKTEIDAKVQITDPS 260
                                       6666766678888**************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S--HHHHHHHHHHHT--EBSCGGGGG CS
                        Cpn60_TCP1 229 eleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrvkkkdlerlakatGatavssledlt 305
                                       ++++++++e + l+e+ eki+ksg+nvv+cqkgidd+++ +lak+gi ++rrvk++d+e+lakatGa+++++l+d+t
  gi|518651994|ref|YP_008141514.1| 261 KIQEFLDQESDTLKEMAEKIKKSGANVVLCQKGIDDTVQYYLAKYGIYGVRRVKQSDMEKLAKATGAKMITDLDDIT 337
                                       ***************************************************************************** PP

                                       CGC-EEEEEEEECCETTCCEEEEECESSSSXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHH CS
                        Cpn60_TCP1 306 peelGtakkveeekigsekttiieevksgkiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatele 382
                                       +e +G+a++vee+kig++++t+++++k++k++ il+rg t++v+dei r+++dA++vv+ + ed++++pGGGate e
  gi|518651994|ref|YP_008141514.1| 338 EETMGKAETVEERKIGDDRMTFVTGCKNPKAVNILIRGGTEHVVDEIDRSLNDAIRVVAITKEDGRYLPGGGATEAE 414
                                       ***************************************************************************** PP

                                       HHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHHHHHTTXTTEEEETTTTCEEECCCCTX CS
                        Cpn60_TCP1 383 lakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklraahnkgekelgidvesgeiidlveagv 459
                                       la kl++y++sv g+eql+ieafakALe+ip+tLaeNaG+dpi++l +l+++h+kg+k++g+d+e ++i+d+++agv
  gi|518651994|ref|YP_008141514.1| 415 LAMKLRSYSNSVGGREQLSIEAFAKALEIIPRTLAENAGMDPINTLISLKSEHEKGNKNFGVDMEANKITDMIKAGV 491
                                       ***************************************************************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHHCEEEEEXXX CS
                        Cpn60_TCP1 460 vDplkvkrqalksAteaastiLrideiikak 490
                                       +D ++vk+ a++sA+e+a++iLrid++i  k
  gi|518651994|ref|YP_008141514.1| 492 FDTFRVKTHAISSAVEVATMILRIDDVIASK 522
                                       ****************************987 PP

>> YwpF  YwpF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.19   1.1e+03      93     123 ..      97     128 ..      64     134 .. 0.74
   2 ?   11.6   0.9   3.4e-05       0.2      13      94 ..     200     280 ..     192     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.19
                              YwpF  93 kisvllegklvtkkkdlaek.lLeeLvkegle 123
                                       +  v++ g+l+++ + l ++ + ++++ +g++
  gi|518651994|ref|YP_008141514.1|  97 TTVVVFAGELLKQAEALLDQgVHSTIIADGYH 128
                                       45689999999999888887355678888886 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.4e-05
                              YwpF  13 deeeeekqkeipllDGliinkedeekeWlieavvekeyeeffeelle.keeellvevvItkksNdPatlvvtvksit 88 
                                       d+++  +  + +++ Glii+ke+ +++  +  vv++ +  +++++le k++e++++v It +s     l  +  + +
  gi|518651994|ref|YP_008141514.1| 200 DKKSGGSAADTKFINGLIIDKEKVHSK--MPSVVKNAKIALINSALEiKKTEIDAKVQITDPSKIQEFLDQESDTLK 274
                                       55555678899***********99887..6788888888888766543899*********99876666666666666 PP

                              YwpF  89 kleeki 94 
                                       ++ eki
  gi|518651994|ref|YP_008141514.1| 275 EMAEKI 280
                                       666655 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0    0.0001       0.6      12      84 ..      16      88 ..       8      95 .. 0.90
   2 ?   -0.3   0.5      0.17     1e+03      71      88 ..     263     280 ..     236     286 .. 0.55
   3 ?   -3.0   0.1       1.2     7e+03      58      76 ..     331     349 ..     321     350 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0001
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT--EEEEETTEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2 12 qqlqqlaqqikqletqlkelelvleelelldedtkvyklvGdvlvkqdkeevkeeLeerketlekeiktlekq 84
                                      +++q   +q++++e+ +  ++ v ++l     d+++  ++Gd+ +++d +++++e + ++ t+++ +++ ++q
  gi|518651994|ref|YP_008141514.1| 16 ERQQGKNAQKNNIEAAKAIADAVRTTLGPKGMDKMMVDSIGDIIISNDGATILKEMDVDHPTAKMIVEASKSQ 88
                                      56777789***********************************************999999999999888877 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.17
                                       HHHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  71 ketlekeiktlekqlekl 88 
                                       +e+l++e++tl++  ek+
  gi|518651994|ref|YP_008141514.1| 263 QEFLDQESDTLKEMAEKI 280
                                       344444444444444443 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.2
                                       E-HHHHHHHHHHHHHHHHH CS
                       Prefoldin_2  58 qdkeevkeeLeerketlek 76 
                                       +d+++++ee   ++et+e+
  gi|518651994|ref|YP_008141514.1| 331 TDLDDITEETMGKAETVEE 349
                                       5788888888888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3769.86
//
Query:       gi|518651995|ref|YP_008141515.1|  [L=531]
Description: hypothetical protein FACI_IFERC00001G0634 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-34  118.5   0.0    7.7e-19   68.2   0.0    2.2  2  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 !   48.3   0.0   5.5e-17   9.8e-13      30     188 .]      54     268 ..      31     268 .. 0.74
   2 !   68.2   0.0   4.3e-23   7.7e-19       4     188 .]     309     495 ..     306     495 .. 0.78

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 5.5e-17
                                       ......S.GCCHHHHHHHHH.HTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TT.SEEEE--TTTSGCCC.TC.... CS
                              Thy1  30 e.....e.eekkeklikkll.khghgsplehasftfeiegvSravlrqlvrHRi.asfsqqSqRYvessk.ea.... 93 
                                             +  +++ +++k+++ ++g +s+ e  ++++ i++vS  v++ +   Ri +s+ ++S RYv++ k  +    
  gi|518651995|ref|YP_008141515.1|  54 YgkefkNnPDRASNFYKRIFlDYGDESVAELTTAQMGIQNVSNIVTKVIEEPRIgLSYLEKSSRYVKYNKkVNgnyl 130
                                       23222222355569******9***********************************************884448864 PP

                                       BS--GGGCC.HHHHHHHHHHHHHHHHHH..........................................HHHHHT. CS
                              Thy1  94 fvippeieqkeeleelyeeamekaleay..........................................kellea. 127
                                       f +  e ++  ++e++y++++++ ++ y                                               + 
  gi|518651995|ref|YP_008141515.1| 131 F-LRGENAGVGAMESRYNSYCNDLFDFYsaaypemmkymedanpienftfeiggknykytnlesvdentlS----Ks 202
                                       2.333323235666778888888888886666766666666666666666666666665555555543330....14 PP

                                       ......TCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSHH CS
                              Thy1 128 ......gvarEdaryvLPlatktklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaPe 188
                                               + +  r +LP +t t++ +++N r+++  +e r++     E +++ e +++el+  +Pe
  gi|518651995|ref|YP_008141515.1| 203 yksslrSAVLDEIRALLPASTLTNIGISGNGRAFISLIE-RLKAYGTPEAEKYGELIYRELEPELPE 268
                                       4444445689**************************998.7799999**************999995 PP

  == domain 2  score: 68.2 bits;  conditional E-value: 4.3e-23
                                       EEE.CHHHHHHHHHHHHHTTCSSHHHH......SGCCHH......HHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHH CS
                              Thy1   4 dyt.dpeklvaaaarvcygsseeaeele.....eeekke......klikkllkhghgsplehasftfeiegvSravl 68 
                                       + + +++++  a+  + ygss ++++++     +           + ++   +h+ g+ +e ++++fe+  +  +++
  gi|518651995|ref|YP_008141515.1| 309 NFMdEKRAIDLATGMLLYGSSAGSSNVDippekQ----YsilkelESLRGNRRHKLGRAFEGITYSFEVN-MNYGAF 380
                                       5554445555666667777775555555433221....1123222455555677889*************.****** PP

                                       HHHTT-TTSEEEE-..-TTTSGCCCTCBS--GGGCC.HHHHHHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBE CS
                              Thy1  69 rqlvrHRiasfsqq..SqRYvesskeafvippeieqkeeleelyeeamekaleaykelleagvarEdaryvLPlatk 143
                                       r+++rHR +s+  +  S++Y       + ip+++ + +el+++y e m++a   y++++ +   r  a+yv+P a+k
  gi|518651995|ref|YP_008141515.1| 381 REFQRHRFFSIIRKplSTQYG------YDIPENLGKIPELRSRYVELMDEARILYNDIMGR-SGRKIAQYVVPYAYK 450
                                       ********7755441155554......678988887799999***************9843.35************* PP

                                       EEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHHHHHHHHHHHHSHH CS
                              Thy1 144 tklvvtmNlrsLlhflelracsrAqwEirelaeemleelkkvaPe 188
                                         +v++ Nl +L  f+elr+ ++ + + r++a  ++ e+kk++P+
  gi|518651995|ref|YP_008141515.1| 451 YPVVFSSNLNELTYFIELRSNQQVHPDLRKVALDIYSEIKKIHPH 495
                                       ********************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3430.97
//
Query:       gi|518651996|ref|YP_008141516.1|  [L=280]
Description: hypothetical protein FACI_IFERC00001G0635 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.1e-15   55.9   0.5    1.7e-12   47.0   0.4    2.3  2  3Beta_HSD       3-beta hydroxysteroid dehydrogenase/isomerase
    2.6e-11   43.8   0.0    3.5e-11   43.3   0.0    1.2  1  NAD_binding_10  NAD(P)H-binding
    3.5e-09   36.5   0.1    9.8e-08   31.7   0.1    2.1  2  Epimerase       NAD dependent epimerase/dehydratase family
    0.00014   21.0   0.0     0.0027   16.9   0.0    2.1  1  RmlD_sub_bind   RmlD substrate binding domain
  ------ inclusion threshold ------
      0.025   14.0   0.1       0.62    9.4   0.1    2.2  2  GDP_Man_Dehyd   GDP-mannose 4,6 dehydratase
      0.045   13.9   0.5        0.1   12.8   0.5    1.6  1  DUF211          Uncharacterized ArCR, COG1888


Domain annotation for each model (and alignments):
>> 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 !   47.0   0.4   5.6e-16   1.7e-12       1     119 [.       4     110 ..       4     116 .. 0.89
   2 !    6.9   0.0   0.00092       2.7     174     197 ..     135     158 ..     117     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 5.6e-16
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslv 77 
                                       +v+Gg+GF+G+++ k++  +e+          +s + ++el k+++k +i+gDv++ d+++ a+ + dv++h    +
  gi|518651996|ref|YP_008141516.1|   4 IVLGGSGFVGSNILKQMDAEEK--------AYFSRNNSDELDKLGIK-YIKGDVREYDDVKSAIADYDVIVHA---I 68 
                                       69*************9977775........56778888999******.************************8...8 PP

                         3Beta_HSD  78 dvagkltedeimkvnvkGTrnvleacvka.gvrvlvYtSsaev 119
                                       dv    te++  +  +kG +nv++a  +  g ++lvY S++++
  gi|518651996|ref|YP_008141516.1|  69 DVLA-ETEETHEDLSLKGVKNVVNAMQELrGNKKLVYFSAINA 110
                                       8888.56667899************99853899******9986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00092
                         3Beta_HSD 174 caLRpagiyGegdkllvpllkqla 197
                                         +Rp++++G+gdk+++ l++ ++
  gi|518651996|ref|YP_008141516.1| 135 LIIRPSTMFGPGDKFTKMLIEVAK 158
                                       569***********9988876554 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.2e-14   3.5e-11       1     107 [.       7     116 ..       7     138 .. 0.77

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.2e-14
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES-.......-- CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleaeeglevvegdvtdvedlaealkgadaVvsal.......gg 70 
                                       G++G vG+ ++k+  a+++     + Rn ++   l ++ g++ ++gdv + +d+++a++++d++v a+         
  gi|518651996|ref|YP_008141516.1|   7 GGSGFVGSNILKQMDAEEK---AYFSRNNSDE--L-DKLGIKYIKGDVREYDDVKSAIADYDVIVHAIdvlaeteE- 76 
                                       9*************99962...4678886653..3.3579****************************77753321. PP

                                       TCCHHHH........HHHHHHHHHH.CT--EEEEEEETTTTSGCGC CS
                    NAD_binding_10  71 ggkdeeg........aknivdaake.agvkRfvlvsaigvgdevpg 107
                                             +        +kn+v+a++e  g k++v+ sai++++ + +
  gi|518651996|ref|YP_008141516.1|  77 ------ThedlslkgVKNVVNAMQElRGNKKLVYFSAINADKGSTD 116
                                       ......122235566********99789************974333 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   3.3e-11   9.8e-08       2     115 ..       4     107 ..       3     115 .. 0.82
   2 ?    2.8   0.0     0.023        69     164     222 ..     134     182 ..     121     195 .. 0.67

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 3.3e-11
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC..EEEE--TT-HHHHHHHHHHHT-SEEEE--S--- CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledl..elveldltdrsalerlfkeeqpdavihlAavgg 76 
                                       +V+G++Gf+Gs+++k++ ++      +++        +l++l  + +++d+++ ++++ +++  + d+++h+  +  
  gi|518651996|ref|YP_008141516.1|   4 IVLGGSGFVGSNILKQMDAEEKAYFSRNNS------DELDKLgiKYIKGDVREYDDVKSAIA--DYDVIVHA--IDV 70 
                                       79*****************98777777777......4444445699****************..89******..666 PP

                                       HHHHHHSHHHHHHHHTHHHHHHHHHHHHH.TCTEEEEEEE CS
                         Epimerase  77 vaassedpadfieknlqgtlnlleaarka.gvkrllflsS 115
                                        a++ e+ +d     l+g+ n+++a+++  g k+l+++s 
  gi|518651996|ref|YP_008141516.1|  71 LAETEETHED---LSLKGVKNVVNAMQELrGNKKLVYFSA 107
                                       6666666666...568999999999998866669999985 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                                       EEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHH CS
                         Epimerase 164 aiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeai 222
                                        +i+r+++++Gp+        ++++++  +++gk    l ++g+     ++++Dv+++i
  gi|518651996|ref|YP_008141516.1| 134 SLIIRPSTMFGPG-------DKFTKMLIEVAKGK-VPMLPKSGNM--APVHINDVITVI 182
                                       5799*********.......44455555566666.3344343433..446666666665 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 !   16.9   0.0     9e-07    0.0027       1     100 [.       1     106 [.       1     224 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 9e-07
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...........T--TTSHHHHHHHHHHH--SEEEE------HHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltre...........eldltdaeavaellkeakpdvvvnaAAytavDk 66 
                                       mk++v+G++G +Gs++ kq+++e+ ++ + +++           + d+++ + v++++++   dv+v+a     +D 
  gi|518651996|ref|YP_008141516.1|   1 MKLIVLGGSGFVGSNILKQMDAEEKAYFSRNNSdeldklgikyiKGDVREYDDVKSAIAD--YDVIVHA-----IDV 70 
                                       89*********************9999998777899999999999999999999999999..8899985.....677 PP

                                       HHHSHHHHHHHHTHHHHHHHHHHHHC..T-EEEEEE CS
                     RmlD_sub_bind  67 aEseeeaayavnaeavealAeaaaav..galLihvS 100
                                         + ee  + +  ++v+++ +a ++   + +L++ S
  gi|518651996|ref|YP_008141516.1|  71 LAETEETHEDLSLKGVKNVVNAMQELrgNKKLVYFS 106
                                       666667778888999999988888653256788877 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.1   0.00021      0.62       2      81 ..       5      66 ..       4     109 .. 0.68
   2 ?    2.5   0.0     0.026        78     193     269 ..     145     216 ..     110     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00021
                                      EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEE CS
                     GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevy 80
                                      + G++Gf+Gs++++++ +++   +      s  n +++++l           +k +kgD+++ + +++++a++  d ++
  gi|518651996|ref|YP_008141516.1|  5 VLGGSGFVGSNILKQMDAEEKAYF------SRNNSDELDKLG----------IKYIKGDVREYDDVKSAIADY--DVIV 65
                                      78*************988755442......222334555553..........567888888888888888888..6666 PP

                                      E CS
                     GDP_Man_Dehyd 81 n 81
                                      +
  gi|518651996|ref|YP_008141516.1| 66 H 66
                                      6 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                                       CCCHHHHHHHHHHTTS-C-EEC.TTTT-EEEEEEHHHHHHHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCH CS
                     GDP_Man_Dehyd 193 vtrkitravarialgkqevlyl.GnldakRdwghvkDyveamwlmlqqdkpedyviatgethsvrefvelaflelgk 268
                                       +  k+t+++ ++a+gk ++l   Gn+ +     h++D+++++ + +++    ++ i++ e ++  +++++  ++lg+
  gi|518651996|ref|YP_008141516.1| 145 PGDKFTKMLIEVAKGKVPMLPKsGNMAP----VHINDVITVIKNSMERS--GTIDICSRERVTFADMFNIVRAKLGM 215
                                       5679999*********887764499986....59*********999865..57788899999999999988888876 PP

                                       H CS
                     GDP_Man_Dehyd 269 t 269
                                        
  gi|518651996|ref|YP_008141516.1| 216 P 216
                                       5 PP

>> DUF211  Uncharacterized ArCR, COG1888
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   3.4e-05       0.1      51      86 ..      44      79 ..      33      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.4e-05
                                      EEESSE-HHHHHHHHHCTT-EEEEEEEEEEESS--- CS
                            DUF211 51 ieGenidyeeieeaieelggvihSiDevvaGkkive 86
                                      i+G+  +y+++++ai +++ ++h iD ++  +++ e
  gi|518651996|ref|YP_008141516.1| 44 IKGDVREYDDVKSAIADYDVIVHAIDVLAETEETHE 79
                                      899999********************9998887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1902.71
//
Query:       gi|518651997|ref|YP_008141517.1|  [L=155]
Description: hypothetical protein FACI_IFERC00001G0636 [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  146.8   0.5    4.9e-43  146.7   0.5    1.0  1  DUF1940   Domain of unknown function (DUF1940)
  ------ inclusion threshold ------
      0.042   14.2   0.1      0.066   13.6   0.1    1.3  1  REV1_C    DNA repair protein REV1 C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1940  Domain of unknown function (DUF1940)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7   0.5   5.5e-47   4.9e-43       1     143 []       9     151 ..       9     151 .. 1.00

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 5.5e-47
                                       EETTTTEEEETT-HHHHHHHHHHHHHHHHHHHHHT-SSHHHHHHHHHHHHHHHHTTT-------HHHHHHHHH---- CS
                           DUF1940   1 yCdvlddeldaespyfkyrseiklaeaslGlaiseGikvqatrelldilDtlyqslsDpeskLkDeqrkkLnhadev 77 
                                       yC+++d  l+ ++++f y+s +k+ +++lGla+se   v++ r +ldilDtl q+l+D+e++L D++rk+L  + ++
  gi|518651997|ref|YP_008141517.1|   9 YCELIDRNLPPDHDFFLYESHVKIVKSFLGLAVSEARNVEKLRTMLDILDTLNQNLYDNETVLADNVRKQLRRETKE 85 
                                       9**************************************************************************** PP

                                       ---HHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTT--HHHHHHHHHHHHHHHHHHH- CS
                           DUF1940  78 WlDikekmsnGdrraayllaaaahlekavaylvrmkedeefkeivkdylikyllklsvfiyreaig 143
                                       W+Di +km+nGd+ +ayl+ aa+ l+ a++yl r+ + ++f++ +++y +++++kl  +i +ea+g
  gi|518651997|ref|YP_008141517.1|  86 WIDIDQKMDNGDKYTAYLVLAASNLRIALSYLWRLSKLPDFSDHITEYPLEFMQKLINMINNEAMG 151
                                       ****************************************************************97 PP

>> REV1_C  DNA repair protein REV1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   7.4e-06     0.066      19      69 ..      26      86 ..      21      96 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.4e-06
                            REV1_C 19 neeDvealakyLkkvveeerdlekavavlkwlrvlleee..........eeskeeeageaW 69
                                      +e  v++++++L   v+e r++ek++++l +l+ l ++            +++ ++++++W
  gi|518651997|ref|YP_008141517.1| 26 YESHVKIVKSFLGLAVSEARNVEKLRTMLDILDTLNQNLydnetvladnVRKQLRRETKEW 86
                                      6889*****************************9965557666666655555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1003.45
//
Query:       gi|518651998|ref|YP_008141518.1|  [L=356]
Description: hypothetical protein FACI_IFERC00001G0637 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   9.4e-115  382.8   0.0   1.1e-114  382.6   0.0    1.0  1  Chorismate_synt  Chorismate synthase
     0.0073   16.1   0.0      0.031   14.0   0.0    1.8  2  BCIP             p21-C-terminal region-binding protein


Domain annotation for each model (and alignments):
>> Chorismate_synt  Chorismate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  382.6   0.0  1.2e-118  1.1e-114       2     327 .]       9     351 ..       8     351 .. 0.96

  Alignments for each domain:
  == domain 1  score: 382.6 bits;  conditional E-value: 1.2e-118
                                       EEEEE-SCCSSEEEEEEE---BT-B--HHHHHHHHHHHTCTSSSSSSHHHCS-EEEEESSEETTEE-SS-EEEEEE- CS
                   Chorismate_synt   2 rvttfGeShgkalgavidgvpagleldeediqkeLdrRrpgqsklttqrkEkDeveilsGvfegktlGtpiallieN 78 
                                       ++t+fG Shg+ +g+++dg+pagl++d+e iqk LdrR+pgqs +tt+r+E+D++ei++G  +g t G+p+a++ +N
  gi|518651998|ref|YP_008141518.1|   9 KLTVFGSSHGPYIGGTVDGLPAGLAIDQEFIQKWLDRRKPGQSLITTPRNEDDKIEIIGGSRKGFTDGSPLAFIFKN 85 
                                       799**********************************************************99************** PP

                                       TTS-..SSSSSTSBE-TTSTCHHHHHHC.-S.STHCCCCCTHHCHHHHHHHHHHHHHHHHTTTEEEEEEEEEETTE. CS
                   Chorismate_synt  79 kdqrskdyeeikevpRpgHADltyalkY.girdlrgggrsSaReTaarvaaGavakklLkelgieivayvssigei. 153
                                       kd   k+y+++++ pRpgHADlt+  kY + r+++ggg +S+R T+  vaaGa a  +Lk+++i+iv+y++s g+i 
  gi|518651998|ref|YP_008141518.1|  86 KDYIDKHYDDLRDNPRPGHADLTMFYKYgEYRNYEGGGFFSGRMTMPLVAAGAFAMGVLKRYNIKIVTYIKSAGGIs 162
                                       ****************************999*******************************************888 PP

                                       ........CHHHHH.TT-BS-CCCHHHHHHHHHHHHHTT--B-EEEEEEEES--TT-SBTTTB-HHHHHHHHHHTST CS
                   Chorismate_synt 154 ........ekeaen.pvrcpdeeaaeemeeaieeakkegdslGgvvevvvkgvpaGlGepvfdkldakLakalmsip 221
                                               e+     ++r+pd+e+++ + ++i e  k+gds+G+v+++ + +vp+G+Gep+f+++++++++a++sip
  gi|518651998|ref|YP_008141518.1| 163 idnepqedEDYVYGfSTRMPDREKDSLLYNKILESIKNGDSMGSVISTHIYNVPPGIGEPFFNSVESEISRAMFSIP 239
                                       88887765333444589************************************************************ PP

                                       TEEEEEETTGGGGGGSBHHHHS--EE......EESS-TTTTEETTEEBSS-EEEEEEE--SS--SSEEEEEBTTS-E CS
                   Chorismate_synt 222 AvkgveiGsGfeaaelkGseanDeiv......lrktnnaGGieGGisnGepivvrvavKpipsiakeqktvdletke 292
                                       + k++e+GsGf+  ++ GseanDe++      l++tnn+GGi+GGi+nG+p+v+++a+Kp++si+ +qktv+l+++e
  gi|518651998|ref|YP_008141518.1| 240 GLKAIEFGSGFKLGNMYGSEANDEFYaengkiLSRTNNSGGILGGITNGMPVVFNIAMKPTSSIRISQKTVNLKSME 316
                                       **************************76665545******************************************* PP

                                       -EEEE--S-S-S-THHHHHHHHHHHHHHHHHHHHH CS
                   Chorismate_synt 293 evelevkgrhDpcvvpravvvveamvalvladall 327
                                       + e++vkgrhDp +  rav+v++am+a+v++d+++
  gi|518651998|ref|YP_008141518.1| 317 PSEVQVKGRHDPFISFRAVPVIQAMAAFVMLDLIM 351
                                       ********************************986 PP

>> BCIP  p21-C-terminal region-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0     0.076   6.8e+02      51      69 ..     153     180 ..     133     188 .. 0.67
   2 !   14.0   0.0   3.5e-06     0.031     101     145 ..     190     235 ..     171     246 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.076
                              BCIP  51 svvkv.........dgeesDpvygllsv 69 
                                       + +k           +e++D vyg+ + 
  gi|518651998|ref|YP_008141518.1| 153 TYIKSaggisidnePQEDEDYVYGFSTR 180
                                       555655555554343366777****985 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.5e-06
                              BCIP 101 klkklLss.skdkkvglliseRliNiPvevvpplykmLleeiewaq 145
                                         +k+L+s ++  ++g +is  + N+P+ +  p ++++ +ei++a 
  gi|518651998|ref|YP_008141518.1| 190 LYNKILESiKNGDSMGSVISTHIYNVPPGIGEPFFNSVESEISRAM 235
                                       44667776757789****************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); 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):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2359.53
//
Query:       gi|518651999|ref|YP_008141519.1|  [L=593]
Description: hypothetical protein FACI_IFERC00001G0638 [Ferroplasma acidarmanus fer1]
Scores for complete 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-120  403.0  16.4   1.9e-120  402.8  16.4    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 !  402.8  16.4  1.1e-124  1.9e-120       1     564 []      25     582 ..      25     582 .. 0.96

  Alignments for each domain:
  == domain 1  score: 402.8 bits;  conditional E-value: 1.1e-124
                           DUF2070   1 leklskyifrlPswkvsllliillalligllaflssklfgillfglpalvaflltlpvlrilggrltykrslflall 77 
                                       l++ls+yi+++P+w + +l+ i+ ++li+ +  ++     +++ +lp+++ +ll+  ++++++++++ +r ++l ++
  gi|518651999|ref|YP_008141519.1|  25 LAGLSRYIKKSPKW-YYFLIPIIAIFLIDGIILRNL-DALSFMSILPFIFFLLLDALTIKLTNKKFNNNRIMYLDFI 99 
                                       689***********.667777777777788888888.5999************************************ PP

                           DUF2070  78 telivviisllaillsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly.....f 149
                                       ++++v +++++++ll+ ++   +++ l+l++a+ ++lr+lvl+++  +++  a+ +++++++++i++++++     +
  gi|518651999|ref|YP_008141519.1| 100 SLTLVTLFFWIGVLLYPVIRMPLYYILALAIAFPAFLRFLVLYIYYPSNIYLAATLSMNYTFSYIIIALIFydiskI 176
                                       *******************999*********************************************99999****9 PP

                           DUF2070 150 spesfllllllslifalavylfivvvdrplkrnlgvsaldllsaFlahilegskel.Eeffeei.geeadvpvkvls 224
                                       + +++++l+++++i++l++y+f+v+ ++ + r+++ ++ +l+ +Fl    +++ ++ E+ff ++ ++++++pv +  
  gi|518651999|ref|YP_008141519.1| 177 AIKFIIPLIAATVIYVLFSYIFLVFTTIGFTRKYKSRPSELIDFFL--NRDNDGAIgEKFFTHVyNKKRQIPVITTN 251
                                       99********************************************..445566666******9999********** PP

                           DUF2070 225 frredgekallvvPniHPGPlgeiGGsnLpkilaerldel.vlvlHgtatHdfNlvserevekiveavkealeeley 300
                                       +r+e+ + ++lv+P++HPGP+g+++ snLp +++++++++ ++v+H+++t+++N++ ++++++i+e+vk++ ++++y
  gi|518651999|ref|YP_008141519.1| 252 IRKENRDLVTLVFPYVHPGPFGNLCTSNLPVKISSEMGRDnIMVFHTATTNSNNCSGKNDIKNIAESVKDSIKKMKY 328
                                       **9999********************************999************************************ PP

                           DUF2070 301 sskaskpvrvesgdvkllgqrfgdslllvitrapegiDDiplsvglsimaeakaegfedvllVDaHNsfseeagevl 377
                                       s+++s +v+++++ +++  q+fg+s + ++ + ++ +DDi    gl+++a  k++g+e+++l Da+Nsf+ +a+e  
  gi|518651999|ref|YP_008141519.1| 329 SDTVSDFVKFNVDGYDVSLQKFGNSGISAVIPFKKQFDDISIDAGLKVVAALKKNGAENFALLDAQNSFTRDAKE-- 403
                                       **************************************************************************9.. PP

                           DUF2070 378 pgsedaeeliraaekalekleaaeeselkvgvarsetpkltpeeglGdlgiqvlvlevdgqktayvliDgNNmepgl 454
                                          ++++ +i+ + + ++   + ++++  +g+ar+  +     +gl ++g+qvl++++++ + ++vl+D+NN+ +++
  gi|518651999|ref|YP_008141519.1| 404 --LDNCDMIINPLIEKFK--ATGSTYPAIIGYARNYEKI----DGLASMGVQVLAIKINDYYNVIVLTDSNNIGREV 472
                                       ..6888888888887778..8999*********888775....********************************** PP

                           DUF2070 455 reeirealke.vdlevevmTTDtHvvngvslgynpvGekvskdelielvlelvekAiadlepvevgyatervevkvf 530
                                        +  r+ +++ v+ ++ ++TTD+Hvvn  +l+ np+G +++++ +++l+ ++v +Ai+d +p+++g +te+++v++ 
  gi|518651999|ref|YP_008141519.1| 473 IKMARSGVDKrVK-NMDIYTTDNHVVNVSELDINPLGMHCEPQVVADLINRTVLQAIEDASPATAGTYTENITVTMG 548
                                       *********9999.*************************************************************** PP

                           DUF2070 531 gedrfeelvstvnsvvsvakilaaallllaills 564
                                       +e++f +l+++v +++++ak+++a++ll+ il+s
  gi|518651999|ref|YP_008141519.1| 549 EENAFHNLMEIVIASLRKAKYSIAFILLISILVS 582
                                       ******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (593 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3793.94
//
Query:       gi|518652000|ref|YP_008141520.1|  [L=354]
Description: hypothetical protein FACI_IFERC00001G0639 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.7e-38  131.8   0.0      3e-38  131.7   0.0    1.0  1  NAD_kinase  ATP-NAD kinase
     0.0084   15.7   0.0      0.043   13.4   0.0    2.1  2  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 !  131.7   0.0   3.4e-42     3e-38      24     291 ..      49     351 ..       7     352 .. 0.92

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 3.4e-42
                                       HHCT-..EEEEECCGGCCSSSTT--HHHHTTTT--.......EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHH CS
                        NAD_kinase  24 LldalsrvlevtveeklgeslaeaaefrsevisvlkkvkttddtrkaleafadagvdliivvGGDGTaldvarllqk 100
                                       ++ +  ++ ++++++ +g  +  +a+ +++ ++ + ++ t  dt++ +     ag+d+i ++GGDGTa+d+ r  + 
  gi|518652000|ref|YP_008141520.1|  49 IKCR--DIQFIVPDGPMGALEMDKANLKYTISYSPGNPTTAMDTINFIHSA--AGADIICFLGGDGTARDILRSGT- 120
                                       3333..88999**********************999999988****99888..9**********************. PP

                                       CT-EEEEEESSS--SS-SE..EGGGHHHHHHHHHHT-SEEEEEEEEE.........................EEEEE CS
                        NAD_kinase 101 aeiPvlgvnaGvkgfltef..epeaaaellekllegeirvekrevld.........................avimr 150
                                        + Pvlg++aGvk+++++f  + ++a+ + +++  +ei+++++ v d                          +i  
  gi|518652000|ref|YP_008141520.1| 121 -DLPVLGIPAGVKMYSSVFsmNVKHAIDVFDNFCGNEITLKDAGVADinedeyrsgkldvkqfgtlkipdssGIISS 196
                                       .8*****************9999***********************************************9988999 PP

                                       TTE............EEEEEEESSEEEEEESSSSS-EE..EEEEETTEEEEEEEESEE................... CS
                        NAD_kinase 151 skgee......diadiviensvlnevviirgpgstlie..lelyvdtelleadqldgl................... 200
                                       sk+e+      d+a+++i+n+ +n+ ++i+gpg+t++   + l+  t++l+ d+++g+                   
  gi|518652000|ref|YP_008141520.1| 197 SKAEYppsssyDMAEYIIDNM-VNDFYYIIGPGTTCKAitTSLGFHTNMLGFDIVKGKklivedageediyryaasg 272
                                       99988***************8.9**************999************************************* PP

                                       ...EEE-TGGGGTHHHHTT--EE-TT---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-T CS
                        NAD_kinase 201 ...ivstPtGstayslsaGgplisPgvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelsp 274
                                          i+++ +G+++++l++G++++s ++ +        ++  + + V+s+++kl        + l+++ +++++ ++ 
  gi|518652000|ref|YP_008141520.1| 273 svhIIISIIGGQGFLLGRGNQQLSGRIIK--------KAGFENISVISTPEKLI-----SLSGLAVDISDKDISVP- 335
                                       *****************************........****************9.....89999999999987665. PP

                                       T-EEEEEEESSEEEEEE CS
                        NAD_kinase 275 gdevrvtasdkkfklir 291
                                          +rv +++ +fk+ r
  gi|518652000|ref|YP_008141520.1| 336 -KFIRVLTGYGQFKIMR 351
                                       .699999*999999987 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.15   1.3e+03       3      27 ..       7      31 ..       6      58 .. 0.74
   2 !   13.4   0.0   4.8e-06     0.043      50      91 ..      94     130 ..      66     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
                                      EEEE-TTCTTTTHHHHHHHCHHHHH CS
                          DAGK_cat  3 lvivNpksGkgkgekllrkvrelle 27
                                       ++vNp +G g +++   + + +l+
  gi|518652000|ref|YP_008141520.1|  7 AFFVNPLAGYGGIRNNKGSDNMHLQ 31
                                      5899999998877776655555555 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 4.8e-06
                                       HHHHCC-SEEEEEESHHHHHHHHHHHCTHHCTTSEEEEEE-S CS
                          DAGK_cat  50 eakeegvdlivvaGGDGtvsevlnglleelatkpplgiiPlG 91 
                                        ++++g+d+i+ +GGDGt++ +l +  +     +p+  iP+G
  gi|518652000|ref|YP_008141520.1|  94 IHSAAGADIICFLGGDGTARDILRSGTD-----LPVLGIPAG 130
                                       2334467************999875444.....555556666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (354 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2556.49
//
Query:       gi|518652001|ref|YP_008141521.1|  [L=229]
Description: phosphoserine phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete 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   49.2   0.2    4.1e-09   36.6   0.0    3.0  3  Hydrolase_3  haloacid dehalogenase-like hydrolase
    1.9e-11   44.7   0.0      4e-07   30.5   0.0    2.1  2  Hydrolase    haloacid dehalogenase-like hydrolase
    1.3e-10   42.0   0.1    1.1e-09   38.9   0.1    2.1  1  HAD          haloacid dehalogenase-like hydrolase
    1.2e-06   28.7   0.2    7.6e-06   26.1   0.2    2.0  1  HAD_2        Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.097   12.8   0.1       0.48   10.6   0.1    2.2  1  Hydrolase_6  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 ?    2.2   0.0     0.036   1.3e+02       2      15 ..      27      40 ..      15      66 .. 0.80
   2 !    7.3   0.0     0.001       3.6      15      58 ..      91     134 ..      85     149 .. 0.89
   3 !   36.6   0.0   1.1e-12   4.1e-09     186     253 ..     152     219 ..     141     221 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.036
                                      EEEIIIIIS-TTS- CS
                       Hydrolase_3  2 alDlDGTLlnsdkk 15
                                      ++D+DG Ll++ ++
  gi|518652001|ref|YP_008141521.1| 27 VFDMDGVLLKNRNS 40
                                      78999999987765 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.001
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpv 58 
                                        ++ +++++i +lk+++ik +i ++ s++++ ++ e +g+d+++
  gi|518652001|ref|YP_008141521.1|  91 DVTSNIARTIGYLKDRNIKTAIVSAGSHVFAGYLSELFGIDNFI 134
                                       4788999*****************************99999665 PP

  == domain 3  score: 36.6 bits;  conditional E-value: 1.1e-12
                                       -SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GGGTHHHH CS
                       Hydrolase_3 186 vsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnnedGVak 253
                                       ++K t +k+++++++is++e++++GD+  D++M  ++++ vA + +++++  aAd+v++s+n  G+ +
  gi|518652001|ref|YP_008141521.1| 152 AKKDTNVKDIQSRYGISPAETVSVGDSYMDLSMRRRSKYFVAFNPGTRKLVDAADFVVNSTNLYGIIE 219
                                       57999*********************************************************988865 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   4.1e-05      0.15       1      26 [.      23      48 ..      23      82 .. 0.84
   2 !   30.5   0.0   1.1e-10     4e-07     117     207 ..      90     186 ..      70     188 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.1e-05
                                      SSEEEEESBTTTBCHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttgepsvedvivsa 26
                                      ik+ vfD+dG+L++ ++s   +i++ 
  gi|518652001|ref|YP_008141521.1| 23 IKLMVFDMDGVLLKNRNSWDVIINRS 48
                                      899*************9999999877 PP

  == domain 2  score: 30.5 bits;  conditional E-value: 1.1e-10
                                       HHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCES.STTTSHHHHHHHHHHHT.... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.... RF
                         Hydrolase 117 lkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdiet.vakpspegkvaaireLq.... 187
                                       + v   +a ++ +Lk+++i++++++ +++ +a  + + +G d+++ +++++ ++  ++ ++p  k   ++ +q    
  gi|518652001|ref|YP_008141521.1|  90 NDVTSNIARTIGYLKDRNIKTAIVSAGSHVFAGYLSELFGiDNFIGNEVNVKNHCfIKNVDPAKKDTNVKDIQsryg 166
                                       5588899*********************************5555577777777779****************99998 PP

                                       STGGGEEEEESSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 188 gkpeevamVGDgvnDaaala 207
                                       ++p+e++ VGD+  D+++ +
  gi|518652001|ref|YP_008141521.1| 167 ISPAETVSVGDSYMDLSMRR 186
                                       99**************9965 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   3.2e-13   1.1e-09      92     186 ..      98     184 ..      26     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 3.2e-13
                               HAD  92 ellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrewlaaegeg 168
                                       + +   +++++++++vS+g   ++  l +++g+d+++++e+ v+++++ +    ++  ++    + +++   +  +g
  gi|518652001|ref|YP_008141521.1|  98 RTIGYLKDRNIKTAIVSAGSHVFAGYLSELFGIDNFIGNEVNVKNHCFIK--NVDPAKKD----TNVKD--IQSRYG 166
                                       44555669************************************966666..33333333....66666..666*** PP

                               HAD 169 idleevvayGDspsDlpl 186
                                       i+++e+v +GDs+ Dl +
  gi|518652001|ref|YP_008141521.1| 167 ISPAETVSVGDSYMDLSM 184
                                       ****************98 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.2   2.1e-09   7.6e-06       2     170 ..      27     187 ..      26     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.1e-09
                             HAD_2   2 iFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkkev 78 
                                       +FD+Dg+ll  ++ +  ++n+ +++   ++  +  ++ ++     + l++   ++    ki ++      ++++   
  gi|518652001|ref|YP_008141521.1|  27 VFDMDGVLLKNRNSWDVIINRSMNKTTTGTGMQLTFDYIYQNGVPDRLYENLTET----KIMTY-----LNLND--- 91 
                                       8********************9988866555555555555444433333322221....33333.....34445... PP

                             HAD_2  79 kpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyF.dvivtsedvekk.....KPdpeviekaleklk 149
                                        + +++  ++ +Lk++++k +iv+ +s+  +    e +gi++++ + + ++++++ k     K + + ++ +  +++
  gi|518652001|ref|YP_008141521.1|  92 -VTSNIARTIGYLKDRNIKTAIVSAGSHVFAGYLSELFGIDNFIgNEVNVKNHCFIKnvdpaK-KDTNVKDIQSRYG 166
                                       .7899**************************************95567777776655442223.345688899999* PP

                             HAD_2 150 lkkeeviyvGDsptDieaakk 170
                                       ++++e++ vGDs  D+   ++
  gi|518652001|ref|YP_008141521.1| 167 ISPAETVSVGDSYMDLSMRRR 187
                                       ***************987665 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00013      0.48       2      42 ..      27     119 ..      26     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                                       EEESTTTSE....................................................ETTEE-TTHHHHHHHH CS
                       Hydrolase_6   2 lfDidGvLw....................................................rgdkaipgaaealnal 26 
                                       +fD+dGvL+                                                    + +++  + a+++ +l
  gi|518652001|ref|YP_008141521.1|  27 VFDMDGVLLknrnswdviinrsmnktttgtgmqltfdyiyqngvpdrlyenltetkimtylNLNDVTSNIARTIGYL 103
                                       8********99999999999999999999999999999999999999999999999999998999999999999999 PP

                                       HHTT-EEEEEE---SS CS
                       Hydrolase_6  27 raagkpvvllTNnssk 42 
                                       +++++++++++ +s  
  gi|518652001|ref|YP_008141521.1| 104 KDRNIKTAIVSAGSHV 119
                                       9999999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.53
# Mc/sec: 1289.10
//
Query:       gi|518652002|ref|YP_008141522.1|  [L=237]
Description: hypothetical protein FACI_IFERC00001G0641 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  159.1  13.2    1.5e-46  158.8  13.2    1.1  1  DUF92     Integral membrane protein DUF92
  ------ inclusion threshold ------
      0.097   12.6   0.1      0.097   12.6   0.1    2.7  3  TMEM154   TMEM154 protein family


Domain annotation for each model (and alignments):
>> DUF92  Integral membrane protein DUF92
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  158.8  13.2   1.6e-50   1.5e-46       2     201 ..      12     216 ..      11     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 158.8 bits;  conditional E-value: 1.6e-50
                             DUF92   2 ltlllalralrkksLtpsGalaavlvgvlialaplgllffllllvFfllgslltkvkkkvKa..kleeekegaRdav 76 
                                       l +ll+++al+ +  +++G +aa++vgv+i++  ++l +++l+l+F ++++++tk++ k+K+  kl+e ++g+R a 
  gi|518652002|ref|YP_008141522.1|  12 LLILLFVLALKFRIFDLKGTIAALIVGVIIVVL-GSLYWLILMLIFAITAQMATKYRIKEKTkmKLQEGENGERHAS 87 
                                       568999**********************99999.7779*****************887777755888888999**** PP

                             DUF92  77 qVlanslvalllally....lasdlllvgivasyAavaaDTlaSElGkilskskprlittlkkvppGtnGgVsllGl 149
                                       +V+  +++++++a ++      +  +++++  s+A v+aDT+aSE+G ++ + k ++it +kk+ pG+nGgVsllG 
  gi|518652002|ref|YP_008141522.1|  88 NVIYAAVIGIAIAAMHfakiG-GFPYFLIFGVSFASVNADTFASEIG-VFDS-KVYMITGFKKITPGVNGGVSLLGE 161
                                       ****************65531.4456788889***************.7755.8*********************** PP

                             DUF92 150 lasllGalliallavlllllel....lillltlaGllGsllDSlLGatlqasvvdk 201
                                        a+llGa++i+l +++l  ++      +l++t+ G++G+ +DS+LGa++++++  +
  gi|518652002|ref|YP_008141522.1| 162 GAALLGAFIIGLSYIIL-DFHGfaiiPLLAITILGFVGCQIDSILGAVFENKGKMS 216
                                       ***********997555.4655676666779999*****************95443 PP

>> TMEM154  TMEM154 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   1.6      0.19   1.7e+03      61      77 ..       4      20 ..       1      28 [. 0.74
   2 ?   12.6   0.1   1.1e-05     0.097      59     103 ..      39      83 ..      26     123 .. 0.85
   3 ?   -0.8   0.3      0.15   1.3e+03      63      77 ..     185     199 ..     182     205 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.19
                           TMEM154 61 miiiPlvllillllvvi 77
                                       +ii + +l++ll+v +
  gi|518652002|ref|YP_008141522.1|  4 YYIIESAVLLILLFVLA 20
                                      57888888888887765 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 1.1e-05
                           TMEM154  59 vlmiiiPlvllillllvviiliqkkkrkrsKddekseaesdelds 103
                                       v+++++ +   ++l+l+ +i  q+  + r+K+++k + ++ e ++
  gi|518652002|ref|YP_008141522.1|  39 VIIVVLGSLYWLILMLIFAITAQMATKYRIKEKTKMKLQEGENGE 83 
                                       899999999************************997766665544 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.15
                           TMEM154  63 iiPlvllillllvvi 77 
                                       iiPl ++ +l +v++
  gi|518652002|ref|YP_008141522.1| 185 IIPLLAITILGFVGC 199
                                       9*********99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1205  (0.0672095); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 1628.25
//
Query:       gi|518652003|ref|YP_008141523.1|  [L=115]
Description: hypothetical protein FACI_IFERC00001G0642 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-11   43.7   0.0    3.3e-11   43.6   0.0    1.0  1  DrsE      DsrE/DsrF-like family
    5.8e-05   23.0   0.1    9.3e-05   22.4   0.1    1.3  1  DrsE_2    DsrE/DsrF/DrsH-like family


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.0   3.7e-15   3.3e-11       2     117 .]       3     115 .]       2     115 .] 0.86

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.7e-15
                                       EEEEEE-S-TTTBSHHHHHHHHHH.HHHTTT-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEE CS
                              DrsE   2 kvfilvtggpygseaarealelal.aaaalghevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvC 77 
                                       k+f++ t+g  +  +   a ++ + a++++g+ v+  f g Gv +llk      ++ k++++l+ ++k +++++  C
  gi|518652003|ref|YP_008141523.1|   3 KIFVILTKGKDDLNMVNVAANFSYnAVKNAGATVNFMFLGRGVENLLK----DSNGIKPIIDLVDKMKSENIEVTYC 75 
                                       7899999888777777777777641557777*****************....778899******************* PP

                                       HHHHHHTT--GGGE-.T--EEEE-HHHHHHHHHH-SEEEE- CS
                              DrsE  78 gqaakargldededl.gvgvevsglgelaelqnegdrvitf 117
                                       + + k  gl+e++ l g++ +++g+ + a++++eg++vitf
  gi|518652003|ref|YP_008141523.1|  76 KVSTKGLGLSEEQMLgGIEPVMGGV-QTAKKIDEGFSVITF 115
                                       **********999886666666665.99************9 PP

>> DrsE_2  DsrE/DsrF/DrsH-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.1     1e-08   9.3e-05      74     145 ..      34     106 ..       4     110 .. 0.73

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1e-08
                                       SSS-GGGHHHHHHHHHHHHCT---HHHHHHHHHHTT-EEEEEHHHHHHHT--GGGB-TT-.EEE-HHHHHHHH CS
                            DrsE_2  74 skmnmagigtkmmkkvmkekgvasleeLleaakeagvklvaCqmtmdlmglkkeelidgv.eiagaatylkea 145
                                       + +n+  +g  + + + +++g++ + +L+++ k ++++++ C+++   +gl++e+++ g+ +++g  +  k++
  gi|518652003|ref|YP_008141523.1|  34 ATVNFMFLGRGVENLLKDSNGIKPIIDLVDKMKSENIEVTYCKVSTKGLGLSEEQMLGGIePVMGGVQTAKKI 106
                                       445555555555555558899***************************************7777766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 825.48
//
Query:       gi|518652004|ref|YP_008141524.1|  [L=105]
Description: hypothetical protein FACI_IFERC00001G0643 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   11.7   0.0       0.24   11.3   0.0    1.3  1  DUF2862   Protein of unknown function (DUF2862)


Domain annotation for each model (and alignments):
>> DUF2862  Protein of unknown function (DUF2862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.24      21      45 ..      36      60 ..      18      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
                                      HBT-..EEEEEEEE.E-SSSSEEEEE CS
                           DUF2862 21 klkkepvgtikdfK.mtDGsgiGvvv 45
                                       +++ p+g+i+d++  +DGs++G+ v
  gi|518652004|ref|YP_008141524.1| 36 SVGS-PRGQIRDYRgNVDGSNLGIHV 60
                                      4555.9********569******954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 806.81
//
Query:       gi|518652005|ref|YP_008141525.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G0644 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       417  (0.0232584); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 381.60
//
Query:       gi|518652006|ref|YP_008141526.1|  [L=207]
Description: hypothetical protein FACI_IFERC00001G0645 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.41   11.0  16.9       0.73   10.1  10.6    2.4  2  DUF4064        Protein of unknown function (DUF4064)
        1.6    9.3  19.4       0.71   10.4  14.2    2.2  2  FtsX           FtsX-like permease family
        4.6    6.7  11.8        6.6    6.2  10.8    1.6  2  Stevor         Subtelomeric Variable Open Reading frame
        6.5    6.9   9.3        2.3    8.3   2.1    2.1  2  DHHC           DHHC palmitoyltransferase


Domain annotation for each model (and alignments):
>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  10.6   0.00016      0.73       3      76 ..      82     150 ..      81     162 .. 0.84
   2 ?    4.3   0.4     0.011        48       6      26 ..     177     197 ..     171     205 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                           DUF4064   3 kaeiiLglIGgilgillglllllflfllssgefsqelteeqalsgedasavleflstllivlgvialiaivlgi 76 
                                       + ++++ +I++i ++++++++++f++ + s ++ +     + +s+  a+ +  ++ +l+ivl+v++li++++ i
  gi|518652006|ref|YP_008141526.1|  82 TIAFVIQIIAVISYAIAFVVYAGFAIATASVSTYT-----SVTSVPSANPAIFSIDVLIIVLIVVFLILLLIDI 150
                                       5789********************88886655333.....6788999999999999999999999999998866 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                           DUF4064   6 iiLglIGgilgillglllllf 26 
                                       i +g+++ i+g ll+++lll+
  gi|518652006|ref|YP_008141526.1| 177 IAFGILALIFGGLLTGILLLV 197
                                       556777777776666666665 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4  14.2   0.00016      0.71      23      93 ..      85     155 ..      76     160 .. 0.76
   2 ?    1.5   0.2     0.096   4.3e+02      26      43 ..     177     195 ..     171     205 .. 0.57

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00016
                              FtsX  23 teillitlvalviGlgl..gllaaqllsdvllssvfsselkisidlitvliiivlllllallagllsiskilk 93 
                                         i +i++++++i++++  g+++a ++ + + s+ + +++ + i  i+vlii++++++l+ll   + i+ +++
  gi|518652006|ref|YP_008141526.1|  85 FVIQIIAVISYAIAFVVyaGFAIATASVSTYTSVTSVPSANPAIFSIDVLIIVLIVVFLILLL--IDIYILRR 155
                                       455678888888887777799999999999999988888888888888888888888888877..55555544 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.096
                              FtsX  26 llitlvalviG.lglglla 43 
                                       ++++++al++G l+ g+l+
  gi|518652006|ref|YP_008141526.1| 177 IAFGILALIFGgLLTGILL 195
                                       4455555555533333333 PP

>> Stevor  Subtelomeric Variable Open Reading frame
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.8      0.14   6.3e+02     182     248 ..      25      93 ..       6     103 .. 0.53
   2 ?    6.2  10.8    0.0015       6.6     194     260 ..      87     155 ..      67     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.14
                            Stevor 182 lsaealkklasslsilnlfsesslesalkaavsaaaasdlagta..asaassafepygiaalvllilav 248
                                       +++++lk+ + ++++  ++++++   +++ +  +  + d++ t   ++ a sa +   ia ++ +i ++
  gi|518652006|ref|YP_008141526.1|  25 IKSSNLKNGIWHINTSFILNNEQKYYSVNVNNDSGFIEDMNETKlsTGDAGSAPTLVTIAFVIQIIAVI 93 
                                       445555555556666666666666666666666677777776663233344444444444444444443 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0015
                            Stevor 194 lsilnlfsesslesalk...aavsaaaasdlagtaasaassafepygiaalvllilavvliiLYiwlyrR 260
                                       ++i+ ++s  +++ ++    a ++a++ ++++ t + +a+ a+++  + ++vl+++ ++l+++ i++ rR
  gi|518652006|ref|YP_008141526.1|  87 IQIIAVISY-AIAFVVYagfAIATASVSTYTSVTSVPSANPAIFSIDVLIIVLIVVFLILLLIDIYILRR 155
                                       333333322.233333323233334444444555577888888888888888888777777777777777 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.6     0.017        75      93     126 ..      70     119 ..      33     127 .. 0.51
   2 ?    8.3   2.1   0.00051       2.3      55     115 ..     135     196 ..     119     205 .. 0.45

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.017
                              DHHC  93 k...............llsilllvls.llfllllgllllfhlylilrnlT 126
                                       +               +++i+ ++   + f++  g+ + +  +++++ +T
  gi|518652006|ref|YP_008141526.1|  70 StgdagsaptlvtiafVIQIIAVISYaIAFVVYAGFAIATASVSTYTSVT 119
                                       14444554544444433333333322133333333333334444445555 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00051
                              DHHC  55 llylllllilalvlllialvklveeekkseflavtllkk.llsilllvlsllfllllgllll 115
                                       +++l++++++ l++ +++l+++++ +k+ ++  ++  ++  +  + ++  ++ +ll+g+lll
  gi|518652006|ref|YP_008141526.1| 135 IIVLIVVFLILLLIDIYILRRIMKIRKFIRNGDYKSAYEkNTIAFGILALIFGGLLTGILLL 196
                                       22222333333333344444444444444333333222223445555555566666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1791  (0.099894); expected 358.6 (0.02)
Passed bias filter:                      706  (0.0393775); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 1418.63
//
Query:       gi|518652007|ref|YP_008141527.1|  [L=173]
Description: methylated-DNA-[protein]-cysteine S-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-30  104.0   0.0    6.2e-30  103.2   0.0    1.5  1  DNA_binding_1    6-O-methylguanine DNA methyltransferase, DNA
    4.4e-05   24.2   0.0    7.3e-05   23.5   0.0    1.4  1  Methyltransf_1N  6-O-methylguanine DNA methyltransferase, rib


Domain annotation for each model (and alignments):
>> DNA_binding_1  6-O-methylguanine DNA methyltransferase, DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   0.0   6.9e-34   6.2e-30       1      80 [.      89     168 ..      89     169 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 6.9e-34
                                       HHHHHHHHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHH CS
                     DNA_binding_1   1 afqqrVwellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLe 77 
                                       +fq++Vw++l +IpyG+++tY ++Ak++g+ ka+raV++a +an +a+++PcHRV++++g lggy gg+++k++lLe
  gi|518652007|ref|YP_008141527.1|  89 DFQKNVWNALLKIPYGTTITYLQLAKNIGNAKAVRAVANADGANAMAVIIPCHRVIESNGGLGGYGGGVAIKKQLLE 165
                                       59*************************************************************************** PP

                                       HTT CS
                     DNA_binding_1  78 aEg 80 
                                        E+
  gi|518652007|ref|YP_008141527.1| 166 LEK 168
                                       *96 PP

>> Methyltransf_1N  6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   8.2e-09   7.3e-05       5      75 ..       9      83 ..       5      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.2e-09
                                      EEEEETTEEEEEEEETTCEEEEEEEC-HHH......CCHHHCCCTTTSCCHCCHHHHHHHHHHHHHHHHS--B-SHC CS
                   Methyltransf_1N  5 tlidsplgrlllagdEkgllaidlldkdts......elkelpkllkqdeelpalaelkqaleeYfageekpaltlPl 75
                                       ++ +++g+l+l + E  l+ +d+  ++++          l++++  +e +  lae k+++ eY+ g++k ++ +Pl
  gi|518652007|ref|YP_008141527.1|  9 QYYKTKIGELILGSFEGNLCILDFRYSKKRttidnrIKTGLKANFLEEE-DEILAETKKQVAEYLDGNRK-EFDIPL 83
                                      6899********************99999999*9966667999999999.********************.*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1335.20
//
Query:       gi|518652008|ref|YP_008141528.1|  [L=371]
Description: transposase, IS605 OrfB family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   76.4   0.1    2.4e-21   75.4   0.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.3e-08   33.1   0.2    1.1e-07   32.1   0.2    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.015   14.8   0.3      0.036   13.6   0.3    1.6  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.12   12.4   1.8       0.67   10.0   0.0    2.8  3  CpXC            CpXC protein
       0.43   10.6   3.1       0.81    9.7   3.1    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.62   10.3   1.9        1.2    9.4   1.9    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.1     8e-25   2.4e-21       1      69 []     277     346 ..     277     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 8e-25
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++eyka+e+Gi+v++++p++TS +C++C  ++k+ ++++ +fkC +Cg++  +D+ A++Ni +r
  gi|518652008|ref|YP_008141528.1| 277 FYQLRLFIEYKAREAGIPVIVIDPHNTSRECPNCHTISKKnRPERSVFKCISCGLKGEADYIASLNIRNR 346
                                       7899************************************999************************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.2   3.7e-11   1.1e-07       5     111 ..     155     255 ..     149     263 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 3.7e-11
                        OrfB_IS605   5 evevelpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlh 81 
                                       ++++ +p+ ++++ +g+D+Gi n+ + +t++    +y+g ++k+  +     + +lqs   ks     a+r +++l+
  gi|518652008|ref|YP_008141528.1| 155 DIPE-QPVIEPKNIIGVDMGIANISVDSTGK----YYSGEKVKEVREHNLDLRSRLQSVNTKS-----AKRHIKKLS 221
                                       4443.8999**********************....************************7766.....8******** PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlkev....gvetL 111
                                        k  r+ ++  h ++++++k+   +    ++e+L
  gi|518652008|ref|YP_008141528.1| 222 GKEHRFATNTNHIISKNIVKKARGTssaiAIEDL 255
                                       *******************976544333366665 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3   1.2e-05     0.036       2      34 ..     306     338 ..     305     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34 
                                        CPnC++ +  + per  + C +CGl  e ++i
  gi|518652008|ref|YP_008141528.1| 306 ECPNCHTISKKNRPERSVFKCISCGLKGEADYI 338
                                       5******555899*************9998888 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1      0.54   1.6e+03      78     112 ..     213     248 ..     190     253 .. 0.64
   2 ?   -0.5   0.1      0.41   1.2e+03      39      45 ..     306     312 ..     297     319 .. 0.70
   3 ?   10.0   0.0   0.00023      0.67       2      38 ..     325     361 ..     324     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.54
                              CpXC  78 ieeaeek.egytlRlvidmaelaEkilileagldDr 112
                                       ++++ +k +g + R++++ ++++ k ++ +a+ +  
  gi|518652008|ref|YP_008141528.1| 213 AKRHIKKlSGKEHRFATNTNHIISKNIVKKARGTSS 248
                                       222222256777799999999999988888776555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.41
                              CpXC  39 tCpkCga 45 
                                       +Cp+C++
  gi|518652008|ref|YP_008141528.1| 306 ECPNCHT 312
                                       5666655 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00023
                              CpXC   2 tCpaCgkefeaeiwtsidadedpelkeklldgslfea 38 
                                       +C +Cg + ea+   s+++ ++  + + +++g++f +
  gi|518652008|ref|YP_008141528.1| 325 KCISCGLKGEADYIASLNIRNRAAANQPIVAGDFFVH 361
                                       7********************************9964 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   0.00027      0.81      19      44 ..     305     330 ..     300     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                       + CP+C+   k  r + r +f+C +C+
  gi|518652008|ref|YP_008141528.1| 305 RECPNCHTIsKKNRPE-RSVFKCISCG 330
                                       78*****665555555.6********7 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   1.9   0.00039       1.2      15      40 .]     304     330 ..     303     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00039
                     Auto_anti-p27  15 aetCpvCgvPLmrdr.kggkvyCvaCd 40 
                                       +  Cp+C ++  ++r ++    C++C+
  gi|518652008|ref|YP_008141528.1| 304 SRECPNCHTISKKNRpERSVFKCISCG 330
                                       678************9889999****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2662.38
//
Query:       gi|518652009|ref|YP_008141529.1|  [L=293]
Description: hypothetical protein FACI_IFERC00001G0648 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.8e-29  101.0   0.0    4.5e-29  100.3   0.0    1.3  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
    3.2e-11   43.5   0.0    4.5e-11   43.0   0.0    1.2  1  ETF        Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.3   0.0     5e-33   4.5e-29       2      84 .]     171     254 ..     170     254 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.3 bits;  conditional E-value: 5e-33
                                       -TTT-S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTT.TSS-CCCB-SSSS-----S-EEEES----HHH CS
                         ETF_alpha   2 dLeeakvvvsgGrGlkskenlelleelaealgaavgasRavvda.gwipeerqvGqtGktvaPklyiavGisGaiqh 77 
                                       d+++akv+vs+GrGl+s+en+e +  l + l+a+++ sR+v+ + +w++e++qvG +Gk+v+P+ yia+GisG+iqh
  gi|518652009|ref|YP_008141529.1| 171 DIRNAKVIVSIGRGLGSQENIEKIMPLVDVLHAEISGSRPVCLDyKWLSEDKQVGLSGKKVRPDFYIALGISGQIQH 247
                                       799*************************************98666******************************** PP

                                       HGGGTT- CS
                         ETF_alpha  78 laGmkes 84 
                                       +aG++ s
  gi|518652009|ref|YP_008141529.1| 248 IAGIRGS 254
                                       ****976 PP

>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0     5e-15   4.5e-11      51     180 ..      34     153 ..      14     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5e-15
                                       HHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEET CS
                               ETF  51 ealaamGadkvilvddpalagydaeatakalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveg 127
                                       ++l ++Ga +v++ ++   +     +  k la+ i k+++d +++ +t  g+++a+ l+ +L++ +  ++ ++e ++
  gi|518652009|ref|YP_008141529.1|  34 KELPEYGANTVYFYSNGFVD-----NLGKFLADYIGKNNYDFIFISSTNMGRELAGILSFKLKMKCMPEIFSFEHKE 105
                                       67778999999999888775.....789***********************************************96 PP

                                       CCEEEEEECCCCTEEEEEE-T.SSSEEEEE-TTSS----S-TT---EEEE--HH CS
                               ETF 128 gkltvtRpieggnglaevvea.dlpavltvrpgafepaaimaakkkeveeveva 180
                                       +   +tR  ++  g ++vve  ++ +++tv pg++e+  ++a kk ev++++++
  gi|518652009|ref|YP_008141529.1| 106 K--NITRRFYH--GGKTVVEEeSNFKMFTVSPGICEA--EKADKKSEVKNLTLE 153
                                       6..78888888..555777777***************..677889999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1991.39
//
Query:       gi|518652010|ref|YP_008141530.1|  [L=278]
Description: electron transfer flavoprotein subunit beta [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  109.0   0.3    3.2e-31  108.6   0.3    1.1  1  ETF       Electron transfer flavoprotein domain


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6   0.3   1.8e-35   3.2e-31      10     178 ..      65     235 ..      60     238 .. 0.90

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 1.8e-35
                                       CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHHHHHHHHH CS
                               ETF  10 dgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatakalaalik 86 
                                       + k++  +++a+eaA++lkek  g+vt++++G++++ ++ +ea+a mG+d+  +++  +   +d++ ta ++aa +k
  gi|518652010|ref|YP_008141530.1|  65 PLKMDILSKNAIEAAVQLKEKYSGKVTGFIFGTEKSTSTMKEAYA-MGVDEGTVIKGYQ--KSDPLVTAGVIAAELK 138
                                       56778889*************88**********999999******.*********7765..56************** PP

                                       HC--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCC...EEEEEECCCCTEEEEEE-TSSSEEEEE- CS
                               ETF  87 kedpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggk...ltvtRpieggnglaevveadlpavltvr 157
                                       k ++d++++g ++     + +a+ lA+ L++ +it+++++ev+ +k   +tv+ + e+      +ve+ lpav++v+
  gi|518652010|ref|YP_008141530.1| 139 KAKYDIIILGDQSSdSysGLLAGLLASELDLNVITNAINIEVK-DKianVTVESENED-----VTVETGLPAVVSVA 209
                                       **************55**************************9.55566666666666.....56999********* PP

                                       TTSS--.....--S-TT---EEEE-- CS
                               ETF 158 pgafep.....aaimaakkkeveeve 178
                                        +++ep      +im a+kk+++ v+
  gi|518652010|ref|YP_008141530.1| 210 QEINEPrlpkvMQIMMAGKKNINIVD 235
                                       ********99999********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1825.88
//
Query:       gi|518652011|ref|YP_008141531.1|  [L=91]
Description: hypothetical protein FACI_IFERC00001G0650 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 703.64
//
Query:       gi|518652012|ref|YP_008141532.1|  [L=1136]
Description: hypothetical protein FACI_IFERC00001G0651 [Ferroplasma acidarmanus fer1]
Scores for complete 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-157  522.7   0.0   2.4e-155  518.0   0.0    2.2  1  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    4.5e-28   97.1   0.0    1.1e-27   95.8   0.0    1.7  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
    7.2e-24   83.9   0.3      4e-21   75.1   0.2    3.0  2  LAGLIDADG_3      LAGLIDADG-like domain
    1.2e-19   70.7   1.2    3.7e-19   69.1   1.2    2.0  1  ATP-cone         ATP cone domain
    1.7e-15   57.1   0.2    4.3e-15   55.8   0.2    1.7  1  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  518.0   0.0  6.8e-159  2.4e-155       1     524 []     252    1083 ..     252    1083 .. 0.98

  Alignments for each domain:
  == domain 1  score: 518.0 bits;  conditional E-value: 6.8e-159
                                        EEE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC    1 ssCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGk 75  
                                        s+Cfvl v+ds++sI++t+k++a+++k+ggG+G+++s+lRa++++v++t+g asGpvsfm+++d ++dv+kqgGk
  gi|518652012|ref|YP_008141532.1|  252 SACFVLPVDDSIDSIFDTLKATAEIHKSGGGTGFSFSRLRASDDIVASTKGVASGPVSFMRIFDVTTDVIKQGGK 326 
                                        79************************************************************************* PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX........ CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC   76 RrGAamvylevwHpDiekfidaKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygee 150 
                                        RrGA+m++l+ +Hp+i++fi+ K      e++ lsn+nisvgv+d+F+e++ +d+++ L++Pr+     k+    
  gi|518652012|ref|YP_008141532.1|  327 RRGANMGILNYNHPNIMDFINSK-D---AENKILSNFNISVGVNDEFFEKLDNDENVDLINPRDG----KV---- 389 
                                        ***********************.4...5799*******************************31....22.... PP

                                        .................XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.......... CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                   Ribonuc_red_lgC  151 feeeyeeleekakikkkevkakeLfeeiaesawetgePgvlfkDtiNrrnvlekakggkIratNl.......... 215 
                                                       + +vka +L+++i+  aw t++Pg++f D+iN++n++  ++ g I++tN+          
  gi|518652012|ref|YP_008141532.1|  390 ---------------TGRVKATTLWNSIIDHAWLTADPGMIFLDEINKKNPV--KNIGYIESTNPcvtgdtkift 447 
                                        ...............239**********************************..999****************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Ribonuc_red_lgC  216 ........................................................................... 215 
                                                                                                                   
  gi|518652012|ref|YP_008141532.1|  448 segvkkarqlyeegnplnvkidgrfggefkpssnviytgfkdiykiqtkegfeikvtgdhkiysekngwtealnl 522 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Ribonuc_red_lgC  216 ........................................................................... 215 
                                                                                                                   
  gi|518652012|ref|YP_008141532.1|  523 kenekirilneggsfgssgtleegrvlgwlvgdghinngnnndravlnfysqdrvfadtfrkyvndivrpatnnr 597 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Ribonuc_red_lgC  216 ........................................................................... 215 
                                                                                                                   
  gi|518652012|ref|YP_008141532.1|  598 eynvgmvniesrncitiaserlkefaseydlieeklnvpdkvfagsmelqrgflqalfeadgtvysgqksrhsvr 672 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                   Ribonuc_red_lgC  216 ........................................................................... 215 
                                                                                                                   
  gi|518652012|ref|YP_008141532.1|  673 lgsislnllkqvqmlllnfgiysriyqnrkkagmrmlpdsnremrlyatqdfhelnisaenlikyadsigfiser 747 
                                        *************************************************************************** PP

                                        ........................................................XXXXXXXXXXX...XXXXX CS
                                        ........................................................xxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  216 ........................................................CgEiplleyesvavCnLas 234 
                                                                                                CgE+pll+yes   CnL+s
  gi|518652012|ref|YP_008141532.1|  748 knsklngavnsykkapvkpswlarvdkieyvgredvydlvepsthsfvangivvhnCGEQPLLPYES---CNLGS 819 
                                        *******************************************************************...***** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  235 inLakfvkkdeegkkefdwdelkkviqlvvraLdnvidvnkyplpeiekntkktRriGlGvmgladalaklgipy 309 
                                        inLakfv     ++ +f++++++++i++++r+L+nv+d+nk+p+++i++ t+ktR+iGlG+mg+adal++lgipy
  gi|518652012|ref|YP_008141532.1|  820 INLAKFV-----EDGKFNYERYRETIDVATRFLENVVDANKFPVESIKNMTRKTRKIGLGIMGFADALIMLGIPY 889 
                                        *******.....468************************************************************ PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  310 dseealkfarkitelltyyaykaSvelAkergpfplfekskyskgilpvdefeekekedweeLreeikkyGlrna 384 
                                        +s+eal+fa++++++l+ ++  +S +lA erg+fp++ +s+y+++      +                k  +rn+
  gi|518652012|ref|YP_008141532.1|  890 NSNEALEFAENVMKTLNDESHMESQKLAAERGVFPGWYGSEYEEKG-----I----------------K--MRNS 941 
                                        ******************************************9883.....3................3..7*** PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                   Ribonuc_red_lgC  385 mvtalaPTgsiSliagtssgiePifalvykksvtv.geflevnpvfeeeLkklglwseellkkiles.vqgleei 457 
                                        ++t++aPTg+iS+iag+ss+ieP+fal++++ v +  e+levnp +e++Lk+++lw++el +ki e+   g  ++
  gi|518652012|ref|YP_008141532.1|  942 TTTTIAPTGTISIIAGCSSSIEPLFALAFVRHVLNgQELLEVNPLLENALKSRNLWTQELMEKIAETgKLGNLDL 1016
                                        ***********************************456**************************5544667889* PP

                                        XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Ribonuc_red_lgC  458 peeikrvfktaldidqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvtyY 524 
                                        pe++k++f ta +id+ +h+ +qa+ qk+ d+++Sktinlp +at ed+++ y lA +l +Kg+t+Y
  gi|518652012|ref|YP_008141532.1| 1017 PEDVKNLFITAQEIDPDWHVLMQATFQKYCDSGVSKTINLPFDATREDIAKSYRLAKELHCKGITVY 1083
                                        ******************************************************************9 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   3.1e-31   1.1e-27       2      83 .]     114     249 ..     113     249 .. 0.98

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 3.1e-31
                   Ribonuc_red_lgN   2 kltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealyd............................... 47 
                                       kl++na+kvle+rYl+kd +g+i+E+p qmf+RvA++l i++ lyd                               
  gi|518652012|ref|YP_008141532.1| 114 KLSLNAVKVLEARYLFKDSEGKIIETPKQMFHRVAVHLGIIQGLYDyisyrktgklnekgtvysgitktqneelera 190
                                       799************************************************************************** PP

                   Ribonuc_red_lgN  48 .......................kleedkdlaeefydlmssqkflpasPtlmnaGtelg 83 
                                                              k++  + ++e+f+++m +++++p+sPtlmnaG +lg
  gi|518652012|ref|YP_008141532.1| 191 fnelkkekaidgtytefidfiktKKNMINYWIEKFENMMIKLEYVPNSPTLMNAGGPLG 249
                                       *******************************************************9986 PP

>> LAGLIDADG_3  LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.0    0.0053        19       7      44 ..     548     586 ..     543     625 .. 0.85
   2 !   75.1   0.2   1.1e-24     4e-21       1      83 []     645     742 ..     645     742 .. 0.98

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0053
                                       HHHHHHHCCECCECSTTTTS.EEEEES-HHHHHHHHHHH CS
                       LAGLIDADG_3   7 LrGlfdaDGsvskskkkgvs.isltssskelledvqrlL 44 
                                         G   +DG++++ +++ +  ++++s ++ +++ ++++ 
  gi|518652012|ref|YP_008141532.1| 548 VLGWLVGDGHINNGNNNDRAvLNFYSQDRVFADTFRKYV 586
                                       568899*********999999********9999988765 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 1.1e-24
                                       HHHHHHHHHHHHHCCECCECSTTTTSEEEEES-HHHHHHHHHHHHHCT.HSCEEEE.EEE-SCCCC........... CS
                       LAGLIDADG_3   1 evkaafLrGlfdaDGsvskskkkgvsisltssskelledvqrlLlrlGIestiyek.kkakgrgvy........... 65 
                                       e +++fL++lf+aDG+v   +k + s++l+s s++ll++vq lLl++GI s+iy++ kka+ r ++           
  gi|518652012|ref|YP_008141532.1| 645 ELQRGFLQALFEADGTVYSGQKSRHSVRLGSISLNLLKQVQMLLLNFGIYSRIYQNrKKAGMRMLPdsnremrlyat 721
                                       579*****************************************************9999999999*********** PP

                                       ...ECCCHCHCTTCGGGTTTX CS
                       LAGLIDADG_3  66 ...rlliisgenlkrFlekig 83 
                                          ++l is enl ++++ ig
  gi|518652012|ref|YP_008141532.1| 722 qdfHELNISAENLIKYADSIG 742
                                       ******************998 PP

>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   1.2     1e-22   3.7e-19       2      85 ..       7      98 ..       6      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 1e-22
                                      EEE-TTS-EEE--HHHHHHHHHHHHHH....-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHH.....HSS-H CS
                          ATP-cone  2 kViKRdGtvepfdvekIkraiekAceg....seeeideiaeeveaevrkrlrdgisteeIqdlvektli.....ehpdy 71
                                      +ViKRdG+ +pfd++kI+ ai kA+ +    s+ee++++a+ v++e++ +  + +++e Iqd vek+l+     +  + 
  gi|518652012|ref|YP_008141532.1|  7 TVIKRDGSSVPFDKKKIAMAIFKAMLSvkigSMEEANKLADYVAQELETS-SEVPTVELIQDTVEKVLMtrrinDVSYI 84
                                      59*********************************************777.568*******************999999 PP

                                      HHHHHHHHHHHHHH CS
                          ATP-cone 72 avaaayilyrnlrk 85
                                      a a+ayilyr++r+
  gi|518652012|ref|YP_008141532.1| 85 AAAKAYILYREKRN 98
                                      ***********996 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8   0.2   1.2e-18   4.3e-15       3     134 .]     446     803 ..     444     803 .. 0.95

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 1.2e-18
                                       ECTTCEEEEHHHHCCECTTEEEEEETTTTEEEEEEEEEEEEEEEEEEEEEEETTS-EEEEETT-EEEECCTTEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing   3 ledgeekvkieelvekegeevlslnledlklevksvkkliklklkelyeiklesgrkikaTpeHkllvvrdegivEk 79 
                                       +  +++k k ++l+e+ +  +++++    ++ ++s +++i +++k +y+i++++g +ik+T++Hk+ +  ++g+  +
  gi|518652012|ref|YP_008141532.1| 446 FTSEGVK-KARQLYEEGNPLNVKIDGRFGGEFKPS-SNVIYTGFKDIYKIQTKEGFEIKVTGDHKIYSE-KNGW--T 517
                                       5566777.899998866666777776666666666.9*****************************999.69**..9 PP

                                       ECCC--TT-EEEEE............................................................... CS
                                       xxxxxxxxxxxxxx............................................................... RF
                   Intein_splicing  80 radeLkegdliavp............................................................... 93 
                                       +a +Lke++ i +                                                                
  gi|518652012|ref|YP_008141532.1| 518 EALNLKENEKIRILneggsfgssgtleegrvlgwlvgdghinngnnndravlnfysqdrvfadtfrkyvndivrpat 594
                                       9**********9999************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|518652012|ref|YP_008141532.1| 595 nnreynvgmvniesrncitiaserlkefaseydlieeklnvpdkvfagsmelqrgflqalfeadgtvysgqksrhsv 671
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                   Intein_splicing  94 ............................................................................. 93 
                                                                                                                    
  gi|518652012|ref|YP_008141532.1| 672 rlgsislnllkqvqmlllnfgiysriyqnrkkagmrmlpdsnremrlyatqdfhelnisaenlikyadsigfiserk 748
                                       ***************************************************************************** PP

                                       ...............HSCEEEEEEEEEEEEECEEEEEEEEETTT-EEEECTTEEE- CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  94 ...............dadvvwdkvksievedeeeyVYdltvednhNFvangiivHN 134
                                                       +   + +v +ie+ + e+ VYdl  + +h Fvangi+vHN
  gi|518652012|ref|YP_008141532.1| 749 nsklngavnsykkapVKPSWLARVDKIEYVGRED-VYDLVEPSTHSFVANGIVVHN 803
                                       ************9986667889*********999.********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.82u 0.31s 00:00:01.12 Elapsed: 00:00:00.47
# Mc/sec: 7257.74
//
Query:       gi|518652013|ref|YP_008141533.1|  [L=200]
Description: formiminotransferase cyclodeaminase related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-40  136.9   0.7    7.3e-40  136.7   0.7    1.1  1  FTCD_C         Formiminotransferase-cyclodeaminase
  ------ inclusion threshold ------
      0.072   13.4   0.0       0.12   12.7   0.0    1.3  1  Phage_fiber_C  Putative prophage tail fibre C-terminus


Domain annotation for each model (and alignments):
>> FTCD_C  Formiminotransferase-cyclodeaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.7   0.7   8.1e-44   7.3e-40       2     175 ..       3     172 ..       2     178 .. 0.97

  Alignments for each domain:
  == domain 1  score: 136.7 bits;  conditional E-value: 8.1e-44
                                       HHHHHHHHHSSSSSS-HHHHHHHHHHHHHHHHHHHHHTTTT-TT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                            FTCD_C   2 ieefleelaskspaPGGGsvaAlvgalgaaLgsmvanltlgkkkyedveeemeellekleelrkellelideDaeaF 78 
                                       ++e++++l+s+s++PGGGs++A++  ++a+L sm+a l++gk k +++e++++++ e+ +++ ++l  l +eD++ F
  gi|518652013|ref|YP_008141533.1|   3 LDEYISRLKSSSATPGGGSASAISSIFAASLNSMAALLSTGKPKLSAYENDFKQISEESDNIIEKLKILSNEDEKSF 79 
                                       689************************************************************************** PP

                                       HHHHTTTT..........S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-GGGHHHHHHHHHHHHHHHHH CS
                            FTCD_C  79 nevmeayklpketeeekaareeaiqealkkavevPlelarkalellelleelaekgnknavSDagvaaklleaaveg 155
                                       + +m+a+++ k      ++r+ ai+ a+++ + v +++ar+++  +e +  l e+gn+n+++D   aa++++a+v++
  gi|518652013|ref|YP_008141533.1|  80 QGIMDALHMDKAD----KNRRTAIDMAIQNSIGVSWDIARISIHNMENALYLCEHGNRNLITDSITAAYMAYATVHT 152
                                       *********8855....68********************************************************** PP

                                       HHHHHHHHHTT---HHHHHH CS
                            FTCD_C 156 allnVkiNlksikDeefaee 175
                                       +l n+kiNlk  k  +f++e
  gi|518652013|ref|YP_008141533.1| 153 SLNNIKINLKFQKSVDFKAE 172
                                       ***********999999876 PP

>> Phage_fiber_C  Putative prophage tail fibre C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.3e-05      0.12      14      54 ..      53      92 ..      47      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.3e-05
                     Phage_fiber_C 14 denGiiPetDgalitqlviLadkDkkrvqgvvrhLqvlfaD 54
                                      d + i  e D  +i +l iL+++D+k  qg++  L + +aD
  gi|518652013|ref|YP_008141533.1| 53 DFKQISEESD-NIIEKLKILSNEDEKSFQGIMDALHMDKAD 92
                                      5555666778.9***********************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1117  (0.0623013); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1423.38
//
Query:       gi|518652014|ref|YP_008141534.1|  [L=537]
Description: hypothetical protein FACI_IFERC00001G0653 [Ferroplasma acidarmanus fer1]
Scores for complete 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-218  724.2   4.2   8.4e-218  724.1   4.2    1.0  1  FTHFS            Formate--tetrahydrofolate ligase
  ------ inclusion threshold ------
      0.023   14.8   0.5      0.023   14.8   0.5    2.6  4  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.056   13.5   0.5       0.23   11.5   0.0    2.1  2  Phageshock_PspD  Phage shock protein PspD (Phageshock_PspD)


Domain annotation for each model (and alignments):
>> FTHFS  Formate--tetrahydrofolate ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  724.1   4.2  1.4e-221  8.4e-218      12     553 ..       2     536 ..       1     537 [] 0.99

  Alignments for each domain:
  == domain 1  score: 724.1 bits;  conditional E-value: 1.4e-221
                                       ---HHHHHHCTT--CCCEEEBSTTEEEE-CHHCCTCTTTS-.-EEEEEEESS--TT--SHHHHHHHHHHHHHHTT-- CS
                             FTHFS  12 lkpieeiaeklglkeeelelyGkykakvslkvlerllkekkkgklilvtaitPtplGeGKttttigLaqalnklgkk 88 
                                       l++i+ei ++lg++  ++elyGky ak+ ++ ++     k++gklil+ta+tPtp+GeGKttt+igLaqal+klgk+
  gi|518652014|ref|YP_008141534.1|   2 LQDIQEILKSLGIN--DYELYGKYAAKIGISNCN---GGKRHGKLILMTAMTPTPAGEGKTTTAIGLAQALKKLGKN 73 
                                       579**********7..6789**********9996...57999*********************************** PP

                                       EEEEE----SHHHHCST--SCEETTEEEESHHHHHTTTTSHHHHHHHHHHHHHHHHHHHHHTTTTT-EECCCE---E CS
                             FTHFS  89 avaalRepslGPvfgiKGgAaGGGysqvvPmedinLhltGDihaitaannllaalidnrifheneldidpkkitwkr 165
                                       a +a+RepslGP+fg+KGgA+GGG s v P ++inL +tGD+ ai+aa+nll+a+i+n+i+ +nel idpkkit+ r
  gi|518652014|ref|YP_008141534.1|  74 AGIAIREPSLGPCFGVKGGATGGGKSTVEPSDKINLIFTGDFPAISAAHNLLSAMINNHIYFGNELGIDPKKITFPR 150
                                       ***************************************************************************** PP

                                       EESS--GGGSSEEES-SSTTS---EEE-EEEGGGSHHHHHHHH-SSHHHHHHHHHC-EEEEETTS-EEECCCCT-HH CS
                             FTHFS 166 vlDvndraLRkivvglggkekgvpretgfditvasEimailaLakdledlkerlgrivvaytkdgepvtaedlkvag 242
                                       ++D+ dr+LR+i+vg ggk++gv  +++f it+asEimai+aL+k+++dlk+rlg+i+++yt +++pv a+d+k++g
  gi|518652014|ref|YP_008141534.1| 151 TVDMDDRSLRSIIVGNGGKSNGVLANDSFVITAASEIMAIMALSKSFQDLKNRLGNIIIGYTPNNRPVFARDIKANG 227
                                       ***************************************************************************** PP

                                       HHHHHTTTTTS-EEEEETT--EEEE-----SSSS--B--HHHHHHHHHH-SEEEEEBSSSTTTHHHHHHHTHHHHHT CS
                             FTHFS 243 alavllkdaikPnlvqtlegtpalvHggPFAniahGcnsviatklalkladyvvtEaGFgadlgaekfldikcrasg 319
                                       a+a+ll da+kPn+ q++e+ pa++H+gPF niahG++s++ + +al++ +y+vtEaGFg+dlg+ekf+di +r+++
  gi|518652014|ref|YP_008141534.1| 228 AMAALLADALKPNIAQSVENVPAIIHTGPFGNIAHGTSSILGDYAALNMFEYTVTEAGFGSDLGFEKFMDIVTREAE 304
                                       ***************************************************************************** PP

                                       ---SEEEEEEEHHHHHHHTT--CCCTTS--HHHHHHHHHHHHHHHHHHCTTT--EEEEEE--TT--HHHHHHHHHHH CS
                             FTHFS 320 lkpdavvlvatvraLklhggvekeelkeenlealekGlanlekhienvkkfgvpvvvainkfktDteaelelvkela 396
                                       l  +avv+vat+ra+k+hg++  e++++enl a+ekG+ nl  h++nv++fg++ vva+n ++ Dte+e++ v  l+
  gi|518652014|ref|YP_008141534.1| 305 LPVNAVVIVATIRAIKHHGNA--ENIDSENLPAIEKGIGNLLAHVKNVRNFGIEPVVALNIHPLDTEQEIKKVCGLL 379
                                       *******************75..7899************************************************** PP

                                       HCTTSEEEEE-HHHHGGGGGHHHHHHHHHHCC--.---SS-TTS-HHHHHHHHHHHTT--SEEEE-HHHHHHHHHHH CS
                             FTHFS 397 eakavevalsevwakGgeGalelaeavvealeekefkflYdlelsieekietiakeiYgadgvelseeakkklkkle 473
                                       ++ ++++a s+v+++GgeG+++la++v+e + e++++++Y+++++i++kie+iak++Ygadgve+s+ea  ++k+ e
  gi|518652014|ref|YP_008141534.1| 380 DSAGIKYAESRVYSSGGEGGVDLARKVLESIGENKINYAYSMDDPIKAKIEKIAKTVYGADGVEYSKEALMDIKHAE 456
                                       ***************************************************************************** PP

                                       HTTCTTS-EEEE--SSSSSSSTT--SS--S-EEEEEEEEEETTTTEEEEESST--SS----SS-GGGC-EE-TTSEE CS
                             FTHFS 474 kqgldklpvciaKtqySlsddpklkgapegftltvrevrlsaGagfivalageimtmPGlpkkpaaekidvdeegki 550
                                       ++g++++ vc+aKtq Slsd+p+l ++p +f+++v++v+++aG++fi+++ g+imtmPGlp++paae+id+d++g i
  gi|518652014|ref|YP_008141534.1| 457 RNGFSSFYVCMAKTQSSLSDNPSLINVPVNFKVKVNSVSINAGSKFIIPILGSIMTMPGLPRHPAAENIDIDDKGVI 533
                                       ***************************************************************************** PP

                                       ES- CS
                             FTHFS 551 eGl 553
                                       +Gl
  gi|518652014|ref|YP_008141534.1| 534 TGL 536
                                       **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 ?   14.8   0.5   3.8e-06     0.023       8      28 ..      52      72 ..      46      74 .. 0.88
   2 ?   -7.4   4.1         3   1.8e+04       5      15 ..      91     101 ..      89     101 .. 0.83
   3 ?   -0.7   0.0      0.24   1.4e+03      82      82 ..     223     223 ..     128     416 .. 0.63
   4 ?   -2.9   0.0       1.1   6.7e+03      73      98 ..     501     528 ..     487     530 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.8e-06
                                      TTSSHHHHHHHHHHHHHHTT- CS
                                      xxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  8 GGvGKTtlaanLaralarrgl 28
                                       G+GKTt+a++La+al++ g+
  gi|518652014|ref|YP_008141534.1| 52 AGEGKTTTAIGLAQALKKLGK 72
                                      59***************9887 PP

  == domain 2  score: -7.4 bits;  conditional E-value: 3
                                       ESSTTSSHHHH CS
                                       xxxxxxxxxxx RF
                              CbiA   5 stkGGvGKTtl 15 
                                       ++  G GK+t+
  gi|518652014|ref|YP_008141534.1|  91 GGATGGGKSTV 101
                                       788999***97 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.24
                                       E CS
                                       x RF
                              CbiA  82 n 82 
                                        
  gi|518652014|ref|YP_008141534.1| 223 I 223
                                       0 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.1
                                       H....EEEEEEEEESS...-TTCHHHHH CS
                                       x..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  73 l..lkiagvvlnrvdgeneetllkeale 98 
                                       +  + i+g + ++++ +++ ++++ +++
  gi|518652014|ref|YP_008141534.1| 501 KfiIPILGSIMTMPGLPRHPAAENIDID 528
                                       2467788889999998888888777765 PP

>> Phageshock_PspD  Phage shock protein PspD (Phageshock_PspD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.9e-05      0.23       7      24 ..      36      53 ..      32      56 .. 0.91
   2 ?   -1.8   0.1      0.54   3.2e+03      40      57 ..     231     248 ..     224     250 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.9e-05
                   Phageshock_PspD  7 kiaGklvlltAlrYgPaG 24
                                      k+ Gkl+l+tA++ +PaG
  gi|518652014|ref|YP_008141534.1| 36 KRHGKLILMTAMTPTPAG 53
                                      899**************9 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.54
                   Phageshock_PspD  40 llLAvALEPlLrrvakrv 57 
                                        lLA AL P + + +++v
  gi|518652014|ref|YP_008141534.1| 231 ALLADALKPNIAQSVENV 248
                                       68999****988877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (537 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3579.42
//
Query:       gi|518652015|ref|YP_008141535.1|  [L=421]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-28   97.6  45.2    6.6e-28   97.6  45.2    1.8  2  MFS_1           Major Facilitator Superfamily
    8.3e-24   84.3  45.1    8.6e-19   67.7  18.8    2.2  2  Sugar_tr        Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.6  45.2   7.4e-32   6.6e-28       2     352 ..      20     366 ..      19     367 .. 0.82
   2 !    8.4   0.7    0.0001       0.9     114     178 ..     343     406 ..     332     416 .. 0.77

  Alignments for each domain:
  == domain 1  score: 97.6 bits;  conditional E-value: 7.4e-32
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++++f+++++++i+++al   + ++++     + ll +l ++ga++++++ G++sdrfGr ++l + +++f+ +++ 
  gi|518652015|ref|YP_008141535.1|  20 AISIFVASYNIAIISVALK-PIENAFQTGTGIVYLLGALIFVGAMIGAIISGVFSDRFGRVSILTIDIVTFIGAGIG 95 
                                       5899***************.8******99999999*****************************9999999999555 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wrav 153
                                        ++++++ +l+++r l G+g g+ + ++ ++i+++ + ++ +r ++l++ ++++G+++ +l+gg l+++++  Wr++
  gi|518652015|ref|YP_008141535.1|  96 SALSTNIAMLMFFRTLVGVGVGIDYVVIFTYISEILATKNSTRNLALIMFFANFGILFSYLIGGTLLTLGStgWRYA 172
                                       55668888********************************************************777555455**** PP

                             MFS_1 154 fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg....l 226
                                        +  ai++++ ++   +  + ++++ ++++ ++      ++ l++  ++  +++    +l+ + + +f +++    l
  gi|518652015|ref|YP_008141535.1| 173 LLSGAILAIVPLI---MRSRLKESTLWKFKRIKS----IKTILKD-VTSRENRK----YLYRFSIPWFLYQIgdqsL 237
                                       8888888888877...8999***********999....7777777.66666666....555555555555555555* PP

                             MFS_1 227 ltllplylqevlgls...glllaglllallalvgailallagrls.drlgrrrrlllallllllaalglallavtss 299
                                       +++lp++l + lg+s   g+++a+l+ a++  ++++++l++ rl  ++l++  +++ +++l++l++ +++ l +t  
  gi|518652015|ref|YP_008141535.1| 238 TMFLPFILISALGISvvsGAFSAVLVKAFTIPASIVAFLIIQRLGtRKLQATGFIIRSVFLGILGFGLYFALRFTGI 314
                                       ***************77744555555444444444446688888877788899999999999999999999999933 PP

                             MFS_1 300 avllllvlvliGfglgfv....fpsllalasdlappeeagtasglfntagslggalg 352
                                             +++l+Gf+++f       +   + ++ + ++ +g+ +g++ +ag +gg++g
  gi|518652015|ref|YP_008141535.1| 315 E-----IIILLGFAFFFGsmgpDKTTVIMPVEKYDESIRGSGQGFNEMAGRFGGLIG 366
                                       3.....444444422222224566777888888999*******************98 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0001
                             MFS_1 114 fpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                                       + ++ rg++ g+  ++  +G ++g l+ +l+   +g     ++l i ++l+f++ ++    + +e
  gi|518652015|ref|YP_008141535.1| 343 YDESIRGSGQGFNEMAGRFGGLIGILAFALFG-MAGIDIGLIFLSITCILGFIITVICRDKNIVE 406
                                       667789******************77777777.99999999999999999999755554444444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7  18.8   9.6e-23   8.6e-19       7     201 ..      21     200 ..      15     219 .. 0.85
   2 !   24.6  16.9   1.1e-09     1e-05     252     434 ..     216     397 ..     197     401 .. 0.74

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 9.6e-23
                                       HHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                          Sugar_tr   7 lggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                       ++ ++  Y++++i+++l+ ++    + +++ ++  +       l+ ++ +vGa+iG++++g ++drfGR ++l i +
  gi|518652015|ref|YP_008141535.1|  21 ISIFVASYNIAIISVALKPIE----NAFQTGTGIVY-------LLGALIFVGAMIGAIISGVFSDRFGRVSILTIDI 86 
                                       555777788888888888888....22333333333.......6778899*******************99888888 PP

                                       HHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  84 vlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                       v f+ +++ +a+++   ++ +l++ R lvG+gvG+ +v++ +yisEi  +k   +   l  ++  fGil+++ +g  
  gi|518652015|ref|YP_008141535.1|  87 VTFIGAGIGSALST---NIAMLMFFRTLVGVGVGIDYVVIFTYISEILATKNSTRNLALIMFFANFGILFSYLIGGT 160
                                       88888889999999...9*********************************************************** PP

                                       HHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHT CS
                          Sugar_tr 161 lnktsnadgwrillglqlvpallllilllflPESPrylvek 201
                                       l + ++ +gwr+ l + +++a++ li++  l ES  + +++
  gi|518652015|ref|YP_008141535.1| 161 LLTLGS-TGWRYALLSGAILAIVPLIMRSRLKESTLWKFKR 200
                                       *99999.9**************************7775544 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 1.1e-09
                                       ..HHHHHHHHHHHHHHTTHHHHHHHTTTH.HHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHH CS
                          Sugar_tr 252 rqrlligvvlqifqqltGinaimyyspti.fenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaa 325
                                        ++ l+ + + +f    G  +++ + p i ++ lg+s    +   ++v + ++ a++va++++ r+G R+l  +G++
  gi|518652015|ref|YP_008141535.1| 216 NRKYLYRFSIPWFLYQIGDQSLTMFLPFIlISALGISVVsgAFSAVLVKAFTIPASIVAFLIIQRLGTRKLQATGFI 292
                                       355566666666666667666666666552688899998888889999999999*********************** PP

                                       HHHHHHHHHH...HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 326 gmaicfvilg.ivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanfl 401
                                       + ++++ ilg +  ++l+ +  +++i+++ ++a+f  + ++g+  +  ++  E +++s+R++++ +  ++  +  ++
  gi|518652015|ref|YP_008141535.1| 293 IRSVFLGILGfGLYFALRFT--GIEIIILLGFAFF--FGSMGPDKTTVIMPVEKYDESIRGSGQGFNEMAGRFGGLI 365
                                       **********6555555555..6777777777777..899*****************************99877666 PP

                                       HHHHHHHHHCHHHT-HHHHHHHHHHHHH.HHHHH CS
                          Sugar_tr 402 isllfpiiteaigggyvflvfaglavlf.iifvf 434
                                        ++l   +++  g   ++l+f ++ ++  +i+++
  gi|518652015|ref|YP_008141535.1| 366 -GILAFALFGMAG-IDIGLIFLSITCILgFIITV 397
                                       .444444444444.66888877665544044444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1055  (0.0588432); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); 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):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.24s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3013.57
//
Query:       gi|518652016|ref|YP_008141536.1|  [L=106]
Description: DNA polymerase beta subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0014   18.9   0.0     0.0018   18.5   0.0    1.2  1  NTP_transf_2  Nucleotidyltransferase domain
     0.0063   16.6   0.0      0.007   16.4   0.0    1.2  1  Polbeta       Polymerase beta, Nucleotidyltransferase
  ------ inclusion threshold ------
       0.11   12.4   0.0       0.12   12.1   0.0    1.2  1  DUF294        Putative nucleotidyltransferase DUF294


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 !   18.5   0.0     3e-07    0.0018      17      48 ..      39      83 ..      28     104 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 3e-07
                                      EEEEHHHHCTTSCTTSSEEEEEEESTTCHHH...............H CS
                      NTP_transf_2 17 vvlfGSyarGtalkgSDiDllvvlpeevsre...............k 48
                                       +l GS ar ++++ SD D+++++++    +               +
  gi|518652016|ref|YP_008141536.1| 39 TILIGSLARRDYTPFSDDDVIIITDSTR--SeiefmdpympidiepR 83
                                      5799**********************94..33466666666554443 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.2e-06     0.007      14      46 ..      37      69 ..      22      97 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.2e-06
                                      HSTTEEEEEE-S------EEEEEEEESS---HH CS
                           Polbeta 14 elaylFGSrakgkareeSDiDlavllkekldle 46
                                       l +l GS a+ ++++ SD D+ ++++++++  
  gi|518652016|ref|YP_008141536.1| 37 LLTILIGSLARRDYTPFSDDDVIIITDSTRSEI 69
                                      67899*********************9994333 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.1e-05      0.12      50      77 ..      37      64 ..       6      76 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.1e-05
                            DUF294 50 fallvmGSeGReEqtlktDqDnalvled 77
                                         + +GS +R++ t  +D D  ++ + 
  gi|518652016|ref|YP_008141536.1| 37 LLTILIGSLARRDYTPFSDDDVIIITDS 64
                                      455789***************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 742.01
//
Query:       gi|518652017|ref|YP_008141537.1|  [L=124]
Description: hypothetical protein FACI_IFERC00001G0656 [Ferroplasma acidarmanus fer1]
Scores for complete 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  110.2   1.9    7.1e-32  110.0   1.9    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.053   13.7   0.1       0.17   12.1   0.0    1.9  2  CdiA_C    Contact-dependent growth inhibition CdiA C-terminal


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   1.9     8e-36   7.1e-32       3     117 ..       2     120 ..       1     122 [. 0.98

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 8e-36
                                       HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHHH CS
                              HEPN   3 ewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreelee 79 
                                       +wl++A++dle+Ae +l++++y++acf++qq+aeka+ Al+ + ++e  + h+++++l  l + ++  ++l++++ e
  gi|518652017|ref|YP_008141537.1|   2 DWLKQAKRDLEEAEGSLNNEKYEWACFASQQSAEKAVIALYHSINKE-IWSHSVSRMLLQLTEFDI-DKSLADKAME 76 
                                       8*********************************************9.9****************9.********** PP

                                       HHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  80 LekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                       L++ yi srYpd+++e      y+ eda+++l++a+e++e++++
  gi|518652017|ref|YP_008141537.1|  77 LDRVYIGSRYPDYYTEgspfeyYSIEDAKRCLNYAKEIFEFCNK 120
                                       *****************************************865 PP

>> CdiA_C  Contact-dependent growth inhibition CdiA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.32   2.9e+03      40      52 ..      57      69 ..      33      77 .. 0.66
   2 ?   12.1   0.0   1.9e-05      0.17       3      23 ..      87     105 ..      85     120 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                            CdiA_C 40 ivlnlrdsdlsie 52
                                       +l+l+++d++++
  gi|518652017|ref|YP_008141537.1| 57 MLLQLTEFDIDKS 69
                                      4555665555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.9e-05
                            CdiA_C   3 PDylinGevfDvKsptsgngk 23 
                                       PDy+ +G +f+++s+++  +k
  gi|518652017|ref|YP_008141537.1|  87 PDYYTEGSPFEYYSIED--AK 105
                                       ****************3..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); 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: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 814.71
//
Query:       gi|518652018|ref|YP_008141538.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G0657 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 546.26
//
Query:       gi|518652019|ref|YP_008141539.1|  [L=271]
Description: hypothetical protein FACI_IFERC00001G0658 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.11   12.4   0.1       0.17   11.9   0.1    1.2  1  ICAP-1_inte_bdg  Beta-1 integrin binding protein


Domain annotation for each model (and alignments):
>> ICAP-1_inte_bdg  Beta-1 integrin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   9.3e-06      0.17      21      75 ..     143     198 ..     132     219 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 9.3e-06
                   ICAP-1_inte_bdg  21 tksksvd.sslgglsrsstvasldtdstkssgqsnavsdasaefrvkyvgaieklk 75 
                                          + v+ +s+ g+s    +    t st  sg + a s++ +e  + y+gai  l 
  gi|518652019|ref|YP_008141539.1| 143 ILNHNVNkASVKGISSDVYIDLYATRSTGPSGWACAFSESNTEVLITYIGAIGALS 198
                                       55555542789999999999999*****************************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2141.72
//
Query:       gi|518652020|ref|YP_008141540.1|  [L=149]
Description: hypothetical protein FACI_IFERC00001G0659 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-10   39.8   0.0    5.9e-10   39.0   0.0    1.4  2  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    4.2e-05   23.1   4.9    6.8e-05   22.4   4.9    1.4  1  zinc_ribbon_2  zinc-ribbon domain
     0.0012   18.8  10.5      0.007   16.4   1.1    1.4  2  DZR            Double zinc ribbon
  ------ inclusion threshold ------
       0.02   14.8   2.1      0.072   13.0   2.1    1.8  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.092   12.8   0.0       0.12   12.4   0.0    1.2  1  HypA           Hydrogenase/urease nickel incorporation, metal
      0.095   12.5   0.9       0.14   12.0   0.2    1.7  1  zf-C2H2_3      zinc-finger of acetyl-transferase ESCO


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 ?   -3.2   0.0       2.9   8.7e+03      22      33 ..      25      36 ..      21      36 .. 0.78
   2 !   39.0   0.0     2e-13   5.9e-10       3      64 ..      71     133 ..      69     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.9
                                      S-EEEEEEEEEE CS
                     OB_aCoA_assoc 22 gfaeeaPyvvgv 33
                                      ++a++ P+ +++
  gi|518652020|ref|YP_008141540.1| 25 SYAQDSPFFIAL 36
                                      568899999986 PP

  == domain 2  score: 39.0 bits;  conditional E-value: 2e-13
                                       EE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT....-EE-EEEEEEES..TT-B-EEE- CS
                     OB_aCoA_assoc   3 elsgrGtvysftvvhrappgfaeeaPyvvgvVeLde.gvrimarlvgvdpdevriGmrVravf 64 
                                       el+ +G++ sft+ +++ ++f++++P+++++Ve+++     m+rl  +d + ++iGm   a f
  gi|518652020|ref|YP_008141540.1|  71 ELPLKGKIHSFTTCYYSGESFRNDVPFTLVLVEFPGiDSLFMSRLYADDTGKIKIGMDIIAKF 133
                                       8999********************************5555*****************876666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   4.9   2.3e-08   6.8e-05       1      22 [.      45      66 ..      45      67 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 2.3e-08
                     zinc_ribbon_2  1 fCpnCGaelqdnakFCpyCGtp 22
                                      +Cp+CG++     k+C yCG++
  gi|518652020|ref|YP_008141540.1| 45 RCPECGYKYGTYRKYCMYCGAE 66
                                      6*******************97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.1   2.3e-06     0.007      28      49 .]      43      64 ..      20      64 .. 0.86
   2 !   13.7   2.5   1.6e-05     0.049       1      23 [.      46      68 ..      46      95 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                        rCp+Cg+k     ++C +CG
  gi|518652020|ref|YP_008141540.1| 43 GSRCPECGYKYGTYRKYCMYCG 64
                                      579******************9 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.6e-05
                               DZR  1 CpqCgeelppdarfCseCgtklk 23
                                      Cp+Cg +     ++C +Cg++ +
  gi|518652020|ref|YP_008141540.1| 46 CPECGYKYGTYRKYCMYCGAETE 68
                                      88888888888888888887754 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 ?   13.0   2.1   2.4e-05     0.072       6      34 ..      38      66 ..      35      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.4e-05
                           DUF35_N  6 egrLvgqrCpdCGtvqfPPravCphCgsd 34
                                       ++L+g+rCp CG  +   r +C +Cg+ 
  gi|518652020|ref|YP_008141540.1| 38 KNKLLGSRCPECGYKYGTYRKYCMYCGAE 66
                                      579**********9999999999999875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.9e-05      0.12      38      99 ..       8      70 ..       3      82 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                                      T--HHHHHHHHHHHHCC.TTTT-EEEEE...EE--EEEETTTS-EEECHHHHHS-TTTSSS-EEE CS
                              HypA 38 gvepeaLefafellaegtvlegaeLeie...evpvkvrCreCgkefeleekalrCpkCgsadvei 99
                                      +++p ++e  +++  +++ ++++ + i    ++ +  rC eCg+++ + +k   C  Cg++  +i
  gi|518652020|ref|YP_008141540.1|  8 KIDPAVVEWNYNTEYRHSYAQDSPFFIAlgkNKLLGSRCPECGYKYGTYRK--YCMYCGAETEDI 70
                                      55666666666666666666666655441113344579********97754..6*****987666 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 ?   12.0   0.2   4.6e-05      0.14       3      23 ..      33      53 ..      32      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.6e-05
                         zf-C2H2_3  3 vLdlgqksfgasqCkeCgMvY 23
                                      ++ lg+++   s+C+eCg +Y
  gi|518652020|ref|YP_008141540.1| 33 FIALGKNKLLGSRCPECGYKY 53
                                      5889*9*9999*******988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1116.24
//
Query:       gi|518652021|ref|YP_008141541.1|  [L=410]
Description: hypothetical protein FACI_IFERC00001G0660 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   44.7   0.0    2.1e-11   43.7   0.0    1.5  1  Thiolase_N     Thiolase, N-terminal domain
    2.5e-06   27.1   0.0    6.7e-05   22.5   0.0    2.3  2  Thiolase_C     Thiolase, C-terminal domain
     0.0084   15.7   0.1      0.018   14.6   0.1    1.5  1  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
      0.057   13.3   0.1         11    5.9   0.0    2.4  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   4.8e-15   2.1e-11       7     260 .]       5     219 ..       1     219 [. 0.84

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 4.8e-15
                                       EEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHH.TTS-TTSEEEEEE CS
                        Thiolase_N   7 artpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalk.agipeevpavtvn 82 
                                        +t+++k    +++    +  ++    +l++ag++ +++d  + +      +gq ia +++ + +g+    p+ +++
  gi|518652021|ref|YP_008141541.1|   5 GMTKFVK--SNFREDFRLNV-KKSFDYALKDAGMSVKDIDGSVSAYFSDHLQGQLIAGAMSNDfIGL-AGKPSKRIE 77 
                                       5666665..33333333333.3445779***************9999999*****999988873688.999****** PP

                                       HGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTTTSEHHHHH CS
                        Thiolase_N  83 kvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafneehmGlta 159
                                          + g  a  +a ++ia+g++d ++a G E+ms++ t    d+   + lg++   d  +       f     +l a
  gi|518652021|ref|YP_008141541.1|  78 GGGATGGLAFQTAYEEIASGNMDTCLAYGFENMSHVGTWRGNDI---IALGSDANFDYPLGG-----FYTAYYALMA 146
                                       **************************************999776...667777777776655.....4444678999 PP

                                       HHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHTS-BSSSTT CS
                        Thiolase_N 160 enlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLaklkpaFkke 236
                                        +   +++ + e+ + + vk+h++a +++ a+       P++++          d+ ++s+v+  +L+ l       
  gi|518652021|ref|YP_008141541.1| 147 TRHMYEFGTTEEQMAMVSVKNHRNAINNPFAQ------APMNIT---------VDDVLKSPVVSTPLRML------- 201
                                       99999***********************9999......577665.........599**************....... PP

                                       SS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 237 GtvtAgnasqisDGaaavllmses 260
                                             + + +sDGaa+ +l+se+
  gi|518652021|ref|YP_008141541.1| 202 ------DICLMSDGAACAILASEE 219
                                       ......**************9986 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.039   1.8e+02      28      43 ..      26      41 ..      10      49 .. 0.85
   2 !   22.5   0.0   1.5e-08   6.7e-05      26      99 ..     278     371 ..     267     380 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.039
                                      HHHHHHHHT--GGGES CS
                        Thiolase_C 28 ikkvlkkagltvedid 43
                                         +lk+ag++v+did
  gi|518652021|ref|YP_008141541.1| 26 FDYALKDAGMSVKDID 41
                                      5679***********9 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 1.5e-08
                                       HHHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B-T CS
                        Thiolase_C  26 yaikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGHPl 82 
                                        a+k++ ++ g++   ++id+ E+ +A+++  +++ +++++ +                    vN++GG  a GH +
  gi|518652021|ref|YP_008141541.1| 278 LAAKMAYDRIGIKnpEKEIDFAELYDAYTSAEIQAYEDMGFCPygkggkfieegnpeldgsLPVNMEGGLQASGHAI 354
                                       578899999999855689***********************999**************99889************** PP

                                       TTHHHHHHHHHHHHHHH CS
                        Thiolase_C  83 GasGaRivvtllselkk 99 
                                       Ga+G  ++v +  +l+ 
  gi|518652021|ref|YP_008141541.1| 355 GATGIMQAVYAFWQLQG 371
                                       ****9999988877775 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 !   14.6   0.1     4e-06     0.018     140     214 ..      43     119 ..      22     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
                                       GSCTTHHHHHSTTHHHHHHHHH.HT--S.SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHH CS
                     ketoacyl-synt 140 kaspkavgavlanviagrisya.lglrG.psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagf 214
                                       ++s ++ +++  + iag  s+   gl G ps  ++   +++  a + a++++ sg+ d++la G e + + ++++g 
  gi|518652021|ref|YP_008141541.1|  43 SVSAYFSDHLQGQLIAGAMSNDfIGLAGkPSKRIEGGGATGGLAFQTAYEEIASGNMDTCLAYGFENMSHVGTWRGN 119
                                       44555677788999*****99878****88999***********************************999988875 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0    0.0025        11      12      54 ..      85     127 ..      77     130 .. 0.85
   2 ?    4.9   0.0    0.0054        24      50      65 ..     204     219 ..     195     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0025
                                       HHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-E CS
                       ACP_syn_III  12 yalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGD 54 
                                        a ++A + i+sg++ + L  g e++s++  w+ ++ + l +D
  gi|518652021|ref|YP_008141541.1|  85 LAFQTAYEEIASGNMDTCLAYGFENMSHVGTWRGNDIIALGSD 127
                                       5889************************998877666666655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0054
                                       TTB-EEEEEEEEEEES CS
                       ACP_syn_III  50 vlfGDGAgAvvlease 65 
                                        l++DGA++++l  +e
  gi|518652021|ref|YP_008141541.1| 204 CLMSDGAACAILASEE 219
                                       589*********9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (410 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3005.48
//
Query:       gi|518652022|ref|YP_008141542.1|  [L=380]
Description: hypothetical protein FACI_IFERC00001G0661 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-41  141.1   0.1    4.4e-41  140.6   0.1    1.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
      4e-33  114.5   0.0    7.6e-33  113.5   0.0    1.5  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    2.6e-23   82.0   0.0    5.4e-23   81.0   0.0    1.6  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    1.7e-15   57.5   0.0    2.3e-15   57.0   0.0    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.6   0.1   9.9e-45   4.4e-41       1     149 [.     220     368 ..     220     369 .. 0.99

  Alignments for each domain:
  == domain 1  score: 140.6 bits;  conditional E-value: 9.9e-45
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       + G +v +++ln eR+++a  ++g+arral+ a+ ya +rk+fg+p+ d++lv+ekla m+++ e++rl +++a ++
  gi|518652022|ref|YP_008141542.1| 220 NGGRNVLLSGLNLERAVLAFNSIGIARRALDLAIGYASERKQFGRPISDFELVQEKLAYMYTKFESSRLFAMEALKR 296
                                       67999************************************************************************ PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       ++++++d+ +a+ a l+ase  +++a++a+q++Gg+Gy ++ ++er +rd+ +l+ig+Gt+ei + +i+++l
  gi|518652022|ref|YP_008141542.1| 297 VQEDRMDSLDAASAILYASESSEYIAREALQIFGGYGYIKDFEIERVFRDSILLTIGAGTNEIRKKVISEAL 368
                                       ********************************************************************9986 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.5   0.0   1.7e-36   7.6e-33       2     113 .]       3     114 ..       2     114 .. 0.98

  Alignments for each domain:
  == domain 1  score: 113.5 bits;  conditional E-value: 1.7e-36
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       +e  +++++++efae+e+ p+aa++d+e+ fprel++k+++ G+lg+t+pe+ygG+g dy+++ai+ ee+++a+ +l
  gi|518652022|ref|YP_008141542.1|   3 DEYIMIQQSAKEFAEKEIIPVAAKMDRENFFPRELFRKMGKEGYLGVTIPEQYGGSGSDYVSQAIIEEEISYASGSL 79 
                                       67789************************************************************************ PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTTS CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasge 113
                                       +l++g+hs+l+   ++r G+e  +++yL kl+sge
  gi|518652022|ref|YP_008141542.1|  80 GLSYGAHSNLCLDNLYRNGSEYLREKYLEKLCSGE 114
                                       ************99********************8 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.0   1.2e-26   5.4e-23       1      96 [.     118     207 ..     118     208 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.2e-26
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       ++++TEp++Gsd+ s+kt+a + d+g+++lnG+K++itna++a+++lv+ar     + ++++ f+v++++ g+s ++
  gi|518652022|ref|YP_008141542.1| 118 SLGMTEPSSGSDALSMKTSA-TMDKGNFILNGSKTFITNAPYADIFLVYAR-----TGENITPFVVESSDRGFSRGQ 188
                                       589***************55.555557************************.....3568***************99 PP

                                       ---BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfed 96 
                                         +k+G+rg ptg ++f+d
  gi|518652022|ref|YP_008141542.1| 189 EFDKTGMRGSPTGTIFFND 207
                                       99***************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.0   0.0   5.2e-19   2.3e-15       2     127 ..     236     351 ..     235     358 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 5.2e-19
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                       ++a   +G+Ar+al+ ++ +a er++  +g++++d++ +q +la + ++ ++ r++  +a +r++    + ++    
  gi|518652022|ref|YP_008141542.1| 236 VLAFNSIGIARRALDLAIGYASERKQ--FGRPISDFELVQEKLAYMYTKFESSRLFAMEALKRVQ----E-DR---M 302
                                       578889********************..***********************************33....2.22...2 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHC CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaa 127
                                       d ++a+ a ++a+e +  +++++ +++Gg+++ k+ +++R++RD   ++
  gi|518652022|ref|YP_008141542.1| 303 DSLDAASAILYASESSEYIAREALQIFGGYGYIKDFEIERVFRDSILLT 351
                                       678999**************************************86665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2713.39
//
Query:       gi|518652023|ref|YP_008141543.1|  [L=401]
Description: hypothetical protein FACI_IFERC00001G0662 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2528.07
//
Query:       gi|518652024|ref|YP_008141544.1|  [L=129]
Description: hypothetical protein FACI_IFERC00001G0663 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------

   [No hits detected that satisfy 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:                      1285  (0.0716716); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 839.03
//
Query:       gi|518652025|ref|YP_008141545.1|  [L=32]
Description: hypothetical protein FACI_IFERC00001G0664 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (32 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.27s 00:00:00.58 Elapsed: 00:00:00.41
# Mc/sec: 234.54
//
Query:       gi|518652026|ref|YP_008141546.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-21   76.3   0.0    3.8e-21   75.5   0.0    1.4  1  rve          Integrase core domain
    4.1e-06   26.5   1.1    0.00019   21.1   1.1    2.6  1  rve_3        Integrase core domain
     0.0011   19.6   0.1     0.0032   18.1   0.1    1.9  1  HTH_32       Homeodomain-like domain
     0.0072   16.1   0.2      0.019   14.8   0.2    1.7  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.072   13.6   4.3        0.2   12.1   4.2    1.8  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.1e-24   3.8e-21       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ +  e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518652026|ref|YP_008141546.1| 125 KHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYGEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l + +i++ + r+ +p++nGk Er + t+k+
  gi|518652026|ref|YP_008141546.1| 195 FSNgkngipgdhnKFQEYLDNSNIKHILGRVKHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   5.3e-08   0.00019       2      63 ..     217     268 ..     216     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518652026|ref|YP_008141546.1| 217 NIKHILGRVKHPETNGKLERLNYTIKRLRPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       589999********************965554444..........799************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0032       3      73 .]      36     101 ..      33     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+    + +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518652026|ref|YP_008141546.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDIEIVKKIRYEYPMSGPERIRKYL-KRKGIIIAKNNIYRIL 101
                                       556778888876666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.3e-06     0.019      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518652026|ref|YP_008141546.1| 11 IIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.2   5.7e-05       0.2      40     111 ..       3      75 ..       1     127 [. 0.79
   2 ?   -1.6   0.0      0.93   3.3e+03      44     126 ..     217     243 ..     167     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vk+++ + ++
  gi|518652026|ref|YP_008141546.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNGEyTIGKRKHRELNSKDIEIVKKIRYEYPM 75 
                                       8999****************************88888888776663346678899999999999999874444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                       Terminase_2  44 kIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseevdkeilrevkegke....gvkvklkDk 116
                                       +Ik                                                                 +++++++ k
  gi|518652026|ref|YP_008141546.1| 217 NIK------------------------------------------------------------HilgrVKHPETNGK 233
                                       222............................................................13333455555555 PP

                       Terminase_2 117 lkAlellakh 126
                                       l+ l+ ++k+
  gi|518652026|ref|YP_008141546.1| 234 LERLNYTIKR 243
                                       5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2058.20
//
Query:       gi|518652027|ref|YP_008141547.1|  [L=252]
Description: metal dependent hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-16   59.7   0.0    3.8e-16   59.2   0.0    1.2  1  Lactamase_B_2  Beta-lactamase superfamily domain
    6.9e-15   55.6   0.2    3.9e-14   53.1   0.2    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    6.3e-07   29.4   0.1    1.4e-06   28.3   0.1    1.6  1  Lactamase_B_3  Beta-lactamase superfamily domain
  ------ inclusion threshold ------
      0.097   12.8   0.0       0.18   12.0   0.0    1.4  1  DUF3911        Protein of unknown function (DUF3911)


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 !   59.2   0.0   8.5e-20   3.8e-16       3     200 ..      28     226 ..      27     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 59.2 bits;  conditional E-value: 8.5e-20
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC....C--EE....EEEEEEHHHHHHCC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre....lrpkk....lplyapkgvlavle 71 
                                       i++D+gp + + +l          ++++id  l++h H DH+ gl  +      +   +    l++++pkg++++ e
  gi|518652027|ref|YP_008141547.1|  28 IVLDCGPHTIESMLEN------GIDPAKIDKMLISHMHLDHYGGLAEILWyrgaR---NvkdeLTIMGPKGIRKNTE 95 
                                       899*****98884444......46899*******************999866542...13357************** PP

                                       TTCGHHHCHTT....TTEEEEEE-.TTSEEEE.......CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEE CS
                     Lactamase_B_2  72 anfvylaleee....pavnvheld.wgesfel.......gdggleitatparhksgrrldrnagdtlGlriegggkr 136
                                       + ++  +++ +     + n +e++  ge  e+         ++  i+a+  +h  +            +r+e  g++
  gi|518652027|ref|YP_008141547.1|  96 KILQIYNTPDNymfsVKPNYVEINnNGEVYEIktefidkS-ENDYIEAFSGNHIIPD---------NMYRLEYRGNT 162
                                       **99999999999554444444443333334466666642.3335777777777777.........89********* PP

                                       EEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 137 vyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliH 200
                                       ++y+gDt+y +  i  + ++ad+ll+++t++++d  i+  + H+t + a++ + +  ak+lv++H
  gi|518652027|ref|YP_008141547.1| 163 IAYTGDTAYND-NIPLLGENADILLHEMTYTDKDAEIAkFWKHSTYSSAIKGFGESHAKKLVPVH 226
                                       ********766.77867788*************9999999************************* PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.2   8.6e-18   3.9e-14      15     197 .]      25     226 ..      16     226 .. 0.90

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 8.6e-18
                                       TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHH CS
                       Lactamase_B  15 ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaa 91 
                                       +g+i+ D+G +t ++++      +g++p ++d  +++H+HlDH+Ggl+++   +++  ++ +++   +++  ++++ 
  gi|518652027|ref|YP_008141547.1|  25 DGHIVLDCGPHTIESMLE-----NGIDPAKIDKMLISHMHLDHYGGLAEILWYRGARNVKDELTIMGPKGIRKNTEK 96 
                                       799**************8.....9*************************************************9988 PP

                                       HHCCHH..........TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTS...CCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  92 srkgll..........lagvsadkpdvdeeeldgnaggrralyvtggpghg...hghgvveygggkvlftGDallag 155
                                         +             + +v +++++++ e+ +++ +  +  y+    g +      +++ey+g ++++tGD+ ++ 
  gi|518652027|ref|YP_008141547.1|  97 ILQIYNtpdnymfsvkPNYVEINNNGEVYEIKTEFIDKSENDYIEAFSGNHiipDNMYRLEYRGNTIAYTGDTAYND 173
                                       776666**********99999999999999999999999999987766666111567******************** PP

                                       HCCCCCC............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 156 etgridl...........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       +++++++           t ++ae  + + ++ y ++++   ++ a++lvp H
  gi|518652027|ref|YP_008141547.1| 174 NIPLLGEnadillhemtyTDKDAEIAKFWKHSTYSSAIKGFGESHAKKLVPVH 226
                                       *******9999999999999999999999999999999988888888888877 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 !   28.3   0.1   3.2e-10   1.4e-06       2     133 ..       3     186 ..       2     199 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 3.2e-10
                     Lactamase_B_3   2 ltwlghnsflleta..garilvDPf..........kanlgyeppaeeaDlvlisqaledHahletlkql........ 58 
                                       +++lg  s  ++ +  +++i++D            +  l+ ++++ ++D  lis+ + dH+    l+++        
  gi|518652027|ref|YP_008141547.1|   3 IKFLGNWSSHIQAGkrNVSIIIDGHivldcgphtiESMLENGIDPAKIDKMLISHMHLDHYG--GLAEIlwyrgarn 77 
                                       778888787787733478888986677777776654466777888***************96..4555567888899 PP

                     Lactamase_B_3  59 ................................aenvkvlee...geslevggleirav.atshdavggsergenngf 99 
                                                                         +++++e    ge +e++   i +  + +++a  g++  ++n++
  gi|518652027|ref|YP_008141547.1|  78 vkdeltimgpkgirkntekilqiyntpdnymfSVKPNYVEInnnGEVYEIKTEFIDKSeNDYIEAFSGNHIIPDNMY 154
                                       988888888888888877777777776666663333333333335556666444444414555888999******** PP

                     Lactamase_B_3 100 lleqdgltiyhlGhlahelsseelkelgrvDvvl 133
                                       +le +g ti++ G++a++ + + l   +++D++l
  gi|518652027|ref|YP_008141547.1| 155 RLEYRGNTIAYTGDTAYNDNIPLL--GENADILL 186
                                       *****************6665555..55677776 PP

>> DUF3911  Protein of unknown function (DUF3911)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.9e-05      0.18       7      45 ..      88     126 ..      82     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.9e-05
                           DUF3911   7 kGtrkevvemlqlfdlmdtkGfckfknyveveanetkhn 45 
                                       kG rk+  ++lq+++  d   f+   nyve++ n +  +
  gi|518652027|ref|YP_008141547.1|  88 KGIRKNTEKILQIYNTPDNYMFSVKPNYVEINNNGEVYE 126
                                       89*****************************98876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.30s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1760.69
//
Query:       gi|518652028|ref|YP_008141548.1|  [L=460]
Description: general substrate transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.1e-72  242.9  23.6    7.2e-72  242.7  23.6    1.0  1  Sugar_tr      Sugar (and other) transporter
    1.2e-38  133.0  40.2    3.3e-32  111.8  31.4    2.1  2  MFS_1         Major Facilitator Superfamily
    2.2e-05   23.9   3.8    2.2e-05   23.9   3.8    1.7  2  MFS_4         Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
      0.067   12.9   1.4       0.11   12.3   1.4    1.3  1  Per1          Per1-like family
       0.38    9.1   8.7      0.021   13.2   2.9    1.7  2  MFS_3         Transmembrane secretion effector


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  242.7  23.6     2e-75   7.2e-72       5     450 ..      21     446 ..      17     447 .. 0.92

  Alignments for each domain:
  == domain 1  score: 242.7 bits;  conditional E-value: 2e-75
                                       HHHHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHH CS
                          Sugar_tr   5 aalgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksll 80 
                                        ++gg +l gYd+ +i+++l +++  + fgl++  +  +       +i++++ +G ++G++++g+++d +GR+  ++
  gi|518652028|ref|YP_008141548.1|  21 LSVGGtFLDGYDISIISVALIVMS-KTAFGLDTDFG--K------AMIAASTTIGMLVGAILFGYITDLYGRRTMYM 88 
                                       578899*****************9.88889988887..3......39****************************** PP

                                       HHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  81 iaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaif 157
                                          +lf++ ++  a++    s+  l+++R+++G+g+G+ +++ ++ i+E++p k+Rg+l + + l++ +G  vaa++
  gi|518652028|ref|YP_008141548.1|  89 YDMALFIVLTAAEAFSW---SFASLFIMRFILGLGLGADYAIGTTIIGEFSPVKYRGKLLVTNVLSWFLGAAVAAVT 162
                                       ********999999999...********************************************************* PP

                                       HHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 158 glglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdsleae 234
                                       g+ l   +n + wr+++ l ++pa ++l+l+  +PESPr+l  kg+ +ea+ + ++l    + +++l ++k+ ++  
  gi|518652028|ref|YP_008141548.1| 163 GYLLLPLGN-ESWRYMFLLGIIPAAIILVLRRDVPESPRWLSNKGNASEAEDIERRLT---GTSDNLTAIKRDNKNP 235
                                       ****99999.8*********************************************55...5556677777777777 PP

                                       HH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 235 qeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaif 309
                                              +kells+k +  + l+ v++ +f++      i ++spti+e lgl+    +l+++++ +  ++ +++ai+
  gi|518652028|ref|YP_008141548.1| 236 -------LKELLSRKYI--KSLLFVGIFWFTFDAAFYGISIFSPTILELLGLKARlaVLGSAVFDTFAIIGSLIAIL 303
                                       .......8889999664..56666777777777777799************************************** PP

                                       HHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS.....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTH CS
                          Sugar_tr 310 lvdrfGRRtllllGaagmaicfvilgivalllvaks..kaasivaivfialfialfalgwgpvpwvlvsElfpqsvR 384
                                       l+dr+GR+ + ++G++gm i ++ lgi+++ ++++s     +i++ +++++f +  a+g+g++ +v+  Elfp++ R
  gi|518652028|ref|YP_008141548.1| 304 LIDRIGRKGITIIGFSGMVISLLSLGIITFYVPDRSafITDGILIFALFLIFYITEAIGPGSTDFVYPVELFPTEDR 380
                                       **********************************99644445555555666667779******************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                          Sugar_tr 385 skalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                       ++a+ + + v+ +  +l  ++fp+i++ +g   + ++f+gl v++++ + f   etkg+tle+++e
  gi|518652028|ref|YP_008141548.1| 381 ASAQGFGTSVSRIGAILGITTFPFIVSIYGFSTSLFFFTGLSVIGLLATIFLATETKGKTLEQVNE 446
                                       ******************************889999***************************997 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.8  31.4   9.2e-36   3.3e-32       4     314 ..      25     353 ..      23     366 .. 0.82
   2 !   26.4   1.5   8.2e-10   2.9e-06     111     187 ..     372     446 ..     365     458 .. 0.83

  Alignments for each domain:
  == domain 1  score: 111.8 bits;  conditional E-value: 9.2e-36
                             MFS_1   4 aaflsalarsilgpalplalaedlgispse.igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       ++fl ++++si+++al  + ++++g++ ++   ++++  ++g++v+++++G+++d +Grr +++  ++lf++ +++ 
  gi|518652028|ref|YP_008141548.1|  25 GTFLDGYDISIISVALIVMSKTAFGLDTDFgKAMIAASTTIGMLVGAILFGYITDLYGRRTMYMYDMALFIVLTAAE 101
                                       799*************977778899999986777888899*********************************4444 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravf 154
                                       +f+ s+  l+++r++ Glg ga +++g ++i + +p + rg+ +    +++ lGa+++++ g ll+ +++  Wr++f
  gi|518652028|ref|YP_008141548.1| 102 AFSWSFASLFIMRFILGLGLGADYAIGTTIIGEFSPVKYRGKLLVTNVLSWFLGAAVAAVTGYLLLPLGNesWRYMF 178
                                       47666668**************************************************99999999777799***** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee...................kgtgpaplvpawkallkdpvlw.. 210
                                       ++  i +++ +v   l   +++++r+ +++   +                   k++ +     ++k+ll+++++   
  gi|518652028|ref|YP_008141548.1| 179 LLGIIPAAIILV---LRRDVPESPRWLSNKGNASeaedierrltgtsdnltaiKRDNKN----PLKELLSRKYIKsl 248
                                       *********977...77777788888877777779888888888877776444444444....46668888866322 PP

                             MFS_1 211 .illialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllll 286
                                        ++ i +++f ++f+g+++++p++  e lgl+ + la+l +a++  +++i++l+a  l+dr+gr+ +++++++++++
  gi|518652028|ref|YP_008141548.1| 249 lFVGIFWFTFDAAFYGISIFSPTI-LELLGLK-ARLAVLGSAVFDTFAIIGSLIAILLIDRIGRKGITIIGFSGMVI 323
                                       3466666666677777*******7.*******.555555599999999999************************** PP

                             MFS_1 287 aalglallavt..ssavllllvlvliGfgl 314
                                       ++l+l ++ ++  + ++++  +++++ ++l
  gi|518652028|ref|YP_008141548.1| 324 SLLSLGIITFYvpDRSAFITDGILIFALFL 353
                                       ***********8733333333444443333 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 8.2e-10
                             MFS_1 111 adwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                       +++fp e+r++a g+ ++ + +Gailg    ++++s +g++ + ++++++s+++++     +++++++ k+ +++ e
  gi|518652028|ref|YP_008141548.1| 372 VELFPTEDRASAQGFGTSVSRIGAILGITTFPFIVSIYGFSTSLFFFTGLSVIGLLA--TIFLATETKGKTLEQVNE 446
                                       689***************************************************775..555556555555555444 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.9   3.8   6.2e-09   2.2e-05      31     174 ..      57     200 ..      46     222 .. 0.82
   2 ?   -3.3   0.4       1.2   4.1e+03     320     347 ..     287     314 ..     275     332 .. 0.63

  Alignments for each domain:
  == domain 1  score: 23.9 bits;  conditional E-value: 6.2e-09
                             MFS_4  31 gllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvl 107
                                       +++aa   +G LvGa+l+ +       R++ +  + +  +l++a a+  sfa ++++Rf++G++ ++   +g++++ 
  gi|518652028|ref|YP_008141548.1|  57 AMIAASTTIGMLVGAILFGYITDLYGRRTMYMYDMALFIVLTAAEAFSWSFASLFIMRFILGLGLGADYAIGTTIIG 133
                                       5799999***********9999999999998889999999**************************99999999997 PP

                             MFS_4 108 ahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpraal 174
                                       + +  + r++++        lG av+++  +lll lg ++    ++l+++ a+++l++   +p++++
  gi|518652028|ref|YP_008141548.1| 134 EFSPVKYRGKLLVTNVLSWFLGAAVAAVTGYLLLPLGNESWRYMFLLGIIPAAIILVLRRDVPESPR 200
                                       7776677777666666667789999999999999999888888899999999999999998884443 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.2
                             MFS_4 320 TasfgigQilGpllasllaeatgslala 347
                                        a+f ++ i+G l+a ll ++ g     
  gi|518652028|ref|YP_008141548.1| 287 SAVFDTFAIIGSLIAILLIDRIGRKGIT 314
                                       5677777778888777777777754443 PP

>> Per1  Per1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.4     3e-05      0.11     125     197 ..      38     136 ..      31     187 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                              Per1 125 sglylavvrlfrlarekkrvk....llltalllalyllHvlyLllvrfdYtYnmaanvvvgllqnllwlllsl.... 193
                                       ++l+++    f l++   ++     +++ +l+ a+++ +++ L+  r  Y Y+ma+ +v++ ++++ w + sl    
  gi|518652028|ref|YP_008141548.1|  38 VALIVMSKTAFGLDTDFGKAMiaasTTIGMLVGAILFGYITDLYGRRTMYMYDMALFIVLTAAEAFSWSFASLfimr 114
                                       4455555555555443333324455788899999***********************************99995554 PP

                              Per1 194 ........ktl...........a 197
                                               +             +
  gi|518652028|ref|YP_008141548.1| 115 filglglgA-DyaigttiigefS 136
                                       444444430.0344444444430 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   2.9   5.9e-06     0.021      47     113 ..      56     123 ..      38     133 .. 0.81
   2 ?   -2.4   0.3      0.32   1.2e+03     263     304 ..     290     331 ..     265     341 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.9e-06
                             MFS_3  47 vAlvqaaatLPifllsilaGalaDnfdrRkv.llavqlllalvsvlltvlaalgllspwlllaltlli 113
                                        A++ a++t+ +++ +il G ++D + rR + +  + l+++l+++ + + ++  l+    +l+l l +
  gi|518652028|ref|YP_008141548.1|  56 KAMIAASTTIGMLVGAILFGYITDLYGRRTMyMYDMALFIVLTAAEAFSWSFASLFIMRFILGLGLGA 123
                                       59***************************862667788888888888888888888888887776654 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.32
                             MFS_3 263 lGvGAilgalllsrLRerlsserlvllaavalAlvllslala 304
                                       + + Ai+g+l+   L +r++ + ++ + + ++ + llsl++ 
  gi|518652028|ref|YP_008141548.1| 290 FDTFAIIGSLIAILLIDRIGRKGITIIGFSGMVISLLSLGII 331
                                       456688888888888888888888888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 2847.04
//
Query:       gi|518652029|ref|YP_008141549.1|  [L=401]
Description: hypothetical protein FACI_IFERC00001G0668 [Ferroplasma acidarmanus fer1]
Scores for 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-87  294.3   0.3    1.2e-87  294.0   0.3    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme
    1.5e-05   25.5   0.1    0.00048   20.7   0.0    2.4  2  ACT_4     ACT domain
     0.0024   17.6   0.0     0.0052   16.5   0.0    1.6  1  ACT       ACT domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.0   0.3   2.1e-91   1.2e-87       3     294 .]      16     302 ..      14     302 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.0 bits;  conditional E-value: 2.1e-91
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT- CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGl 79 
                                       + i +TPl ++  +s  + +++++K+E++++tgSfK Rga   +++l+ ++++ +v++as+GNh++++A+aa+ +G+
  gi|518652029|ref|YP_008141549.1|  16 GKIHRTPLFHSTTFSNMFSCDVYFKMENFQKTGSFKSRGAMVKFSTLTAEQKKNGVITASAGNHAQGVAFAASYYGV 92 
                                       6789******************************************888889************************* PP

                                       EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHHHTTT CS
                              PALP  80 kvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEileqlgg 156
                                       ++ iv+p++++p+kv + +++G +v++ g++ydea ++a ++  + e++ ++  +++++vi+g+gtiglEile+++ 
  gi|518652029|ref|YP_008141549.1|  93 DAKIVMPETTPPAKVNAVQSYGGTVILKGNSYDEAHEYAVQVSVD-EKREFIEAYNDEDVIAGQGTIGLEILEDVK- 167
                                       *********************************************.*****************************5. PP

                                       TEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CCSTCSCGTTCCHHHH CS
                              PALP 157 kpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdtiadglavgspselafell 233
                                        pd v+vp+GgGgli+Gi++++k+++ d+++igve+e ++a+  s+++g+ v++++ dtiadg+av+ p++ +fel+
  gi|518652029|ref|YP_008141549.1| 168 -PDIVIVPIGGGGLISGISFAIKSKNKDIKIIGVESEKANAMELSIKEGKIVPYTSNDTIADGIAVKYPGNITFELV 243
                                       .**************************************************************************** PP

                                       SEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 234 drlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       +++vd +vtvsde ++ a+ +l +re+++veps+aa+laal  +++ ++k++ +vv++l+g
  gi|518652029|ref|YP_008141549.1| 244 KKYVDGVVTVSDENIAYALFKLLEREKVLVEPSGAAGLAAL-FENKIDVKGK-KVVIVLSG 302
                                       *****************************************.**********.******98 PP

>> ACT_4  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.054   3.2e+02      11      52 ..     172     212 ..     167     213 .. 0.79
   2 !   20.7   0.0     8e-08   0.00048       8      71 ..     326     392 ..     321     395 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.054
                             ACT_4  11 veaedrkglLaditqviseekanivsvnaktrkkdglaeiki 52 
                                       ++ +   gl++ i+ +i++++ +i+ + ++++k  + +e++i
  gi|518652029|ref|YP_008141549.1| 172 IVPIGGGGLISGISFAIKSKNKDIKIIGVESEK-ANAMELSI 212
                                       5556668999**********9999999999987.55777665 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 8e-08
                             ACT_4   8 rleveaedrkglLaditqviseekanivsvnaktrkk...dglaeikitveVkdvehLsrviakLra 71 
                                       rle +  d +g++ +i+++is+++ani + ++++ +k    g+  + +t+++ d + +++++ +L +
  gi|518652029|ref|YP_008141549.1| 326 RLEFNLPDHPGIMEKIVNAISSSGANIYHAEVDNLNKdtpIGYQYLLFTINILDKSRIDELLGSLDK 392
                                       7888999***************************9885555788999******99999999999877 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.8e-07    0.0052       3      34 ..     327     358 ..     325     394 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.8e-07
                                       EEEEEESSTTHHHHHHHHHHHTTSEEEEEEEE CS
                               ACT   3 lrvgvpDrPGlLarvfgaladrgiNidsieqr 34 
                                       l++ +pD+PG++ ++ +a++  g Ni ++e+ 
  gi|518652029|ref|YP_008141549.1| 327 LEFNLPDHPGIMEKIVNAISSSGANIYHAEVD 358
                                       8999**********************998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2839.09
//
Query:       gi|518652030|ref|YP_008141550.1|  [L=89]
Description: acylphosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-19   69.6   0.0    2.6e-19   69.4   0.0    1.0  1  Acylphosphatase  Acylphosphatase


Domain annotation for each model (and alignments):
>> Acylphosphatase  Acylphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.4   0.0   1.5e-23   2.6e-19       2      85 .]       5      86 ..       4      86 .. 0.91

  Alignments for each domain:
  == domain 1  score: 69.4 bits;  conditional E-value: 1.5e-23
                   Acylphosphatase  2 rllvtGrVQgvgFRkfvrrlAkelglkGyvrNlsdgsVeivaegeeekvekfleelksgppkarvdeveveeleeeeef 80
                                      +++ +G VQg+gFR++v+++A elg+kG+v+N++dgsV +v++g+ee ++ +   +++ p  a+ ++ve  ++++++  
  gi|518652030|ref|YP_008141550.1|  5 KFVFHGTVQGIGFRAHVKKKAVELGIKGWVKNNQDGSVSAVFSGDEEMISIMDGYCRKIP-LAELSSVESMPADDANF- 81
                                      7899******************************************99988888877665.59999999999888887. PP

                   Acylphosphatase 81 kdFei 85
                                      ++Fei
  gi|518652030|ref|YP_008141550.1| 82 DSFEI 86
                                      99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 595.86
//
Query:       gi|518652031|ref|YP_008141551.1|  [L=208]
Description: DNA binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      1e-13   50.8   0.1    1.8e-13   50.0   0.1    1.4  1  HTH_10      HTH DNA binding domain
      1e-06   28.1   0.3    1.9e-06   27.3   0.3    1.4  1  Sigma70_r4  Sigma-70, region 4
     0.0013   19.0   0.5     0.0088   16.3   0.1    2.2  2  UPF0122     Putative helix-turn-helix protein, YlxM / p13 lik
     0.0093   15.8   0.0      0.018   14.9   0.0    1.5  1  MarR_2      MarR family
  ------ inclusion threshold ------
      0.022   15.3   0.2       0.14   12.7   0.1    2.2  2  HTH_27      Winged helix DNA-binding domain
      0.022   14.7   0.1      0.071   13.1   0.1    2.0  1  MarR        MarR family
      0.023   14.8   0.0      0.048   13.7   0.0    1.6  1  HTH_22      HTH domain
      0.033   14.0   0.0      0.073   12.9   0.0    1.6  1  HTH_23      Homeodomain-like domain
      0.038   13.8   0.1       0.59   10.0   0.0    2.2  2  HTH_IclR    IclR helix-turn-helix domain
      0.039   14.0   0.0      0.079   13.0   0.0    1.4  1  HTH_3       Helix-turn-helix
      0.039   13.5   0.1        0.1   12.1   0.1    1.7  1  HTH_24      Winged helix-turn-helix DNA-binding
      0.066   13.0   0.1        1.4    8.8   0.0    2.5  2  RRM_1       RNA recognition motif. (a.k.a. RRM, RBD, or RNP d
       0.11   12.4   0.0       0.23   11.4   0.0    1.4  1  HTH_37      Helix-turn-helix domain
        0.2   11.7   2.2        0.7   10.0   0.0    2.4  3  FeoC        FeoC like transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.0   0.1   1.4e-16   1.8e-13       1      52 [.     149     200 ..     149     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.0 bits;  conditional E-value: 1.4e-16
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       +T ++ e++   y+ GYFd  R+ +l e+A++l+Is ++lse+Lrk  +k++
  gi|518652031|ref|YP_008141551.1| 149 ITHREAEIIVRLYDEGYFDPERKLSLTEIAEQLDISTAALSEILRKTLRKIV 200
                                       699***********************************************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 !   27.3   0.3   1.5e-09   1.9e-06       6      48 ..     150     199 ..     148     199 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 1.5e-09
                                       -HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4   6 pererevlelrf.......geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       + re e+++  +       +++l+l EI+e+l+iS  + + i++++lrk+
  gi|518652031|ref|YP_008141551.1| 150 THREAEIIVRLYdegyfdpERKLSLTEIAEQLDISTAALSEILRKTLRKI 199
                                       78**********************************************96 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1       0.5   6.3e+02       8      27 ..     113     132 ..     107     147 .. 0.79
   2 !   16.3   0.1   6.9e-06    0.0088      32      67 ..     170     207 ..     148     208 .] 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.5
                           UPF0122   8 naLfdiYqsLLTekqanyle 27 
                                         Lf+ Y++LL  k +  ++
  gi|518652031|ref|YP_008141551.1| 113 RLLFQNYGKLLELKHMLEMN 132
                                       57999999999888776555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 6.9e-06
                           UPF0122  32 dDlSlsEiAeefnvsrqavydnikrt.eklleky.Eek 67 
                                         lSl+EiAe+ ++s  a+++ +++t +k++ +y E+k
  gi|518652031|ref|YP_008141551.1| 170 RKLSLTEIAEQLDISTAALSEILRKTlRKIVGEYiENK 207
                                       469********************998457777774666 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05     0.018      20      44 ..     165     194 ..     147     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                       S.....EEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  20 r.....dltvgelarrlglsksavsrilkr 44 
                                       +     +l+ +e+a+ l++s +a+s il++
  gi|518652031|ref|YP_008141551.1| 165 YfdperKLSLTEIAEQLDISTAALSEILRK 194
                                       3455559*********************98 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0         1   1.3e+03      56      65 ..      41      50 ..      36      69 .. 0.82
   2 ?   12.7   0.1   0.00011      0.14       5      48 ..     153     204 ..     149     207 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                            HTH_27 56 drrekrvrlT 65
                                      d++++++r+T
  gi|518652031|ref|YP_008141551.1| 41 DGKSTTHRIT 50
                                      8888888888 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                            HTH_27   5 qalvLhlir.....hrrrrkkladlcgrlnvedshisyslkkLtek...GLv 48 
                                       +a ++  ++      ++r+ +l+++++ l+++ ++ s++l+k  +k   +++
  gi|518652031|ref|YP_008141551.1| 153 EAEIIVRLYdegyfDPERKLSLTEIAEQLDISTAALSEILRKTLRKivgEYI 204
                                       555555555666667899***********************98887666665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.5e-05     0.071       2      40 ..     150     194 ..     149     198 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.5e-05
                                       -HHHHHHHHHHHHST......TEEHHHHHHHHTS-HHHHHHHHHH CS
                              MarR   2 tltqfviLrilyeqg......plsvseLakklgvskstvtrvldr 40 
                                       t+ + +i++ ly++g       ls++e+a++l +s+++++++l++
  gi|518652031|ref|YP_008141551.1| 150 THREAEIIVRLYDEGyfdperKLSLTEIAEQLDISTAALSEILRK 194
                                       56666666666666522222246777*****************97 PP

>> HTH_22  HTH 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     0.048      23      57 ..     151     187 ..     141     193 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                            HTH_22  23 eekieivraLdekGiFl..lkgavekvAekLgiSraT 57 
                                       ++  ei+ +L+++G F+   k +  ++Ae+L+iS a 
  gi|518652031|ref|YP_008141551.1| 151 HREAEIIVRLYDEGYFDpeRKLSLTEIAEQLDISTAA 187
                                       66789***********633799************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   5.7e-05     0.073      10      40 ..     157     194 ..     150     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                            HTH_23  10 illllae.......GlsvreIAreLgvsrrTvyrwlkr 40 
                                       i++l++e       +ls +eIA++L++s   ++ +l++
  gi|518652031|ref|YP_008141551.1| 157 IVRLYDEgyfdperKLSLTEIAEQLDISTAALSEILRK 194
                                       88999978888889***************999988776 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.25   3.2e+02      32      38 ..      43      49 ..      42      51 .. 0.88
   2 ?   10.0   0.0   0.00046      0.59      17      39 ..     170     192 ..     164     195 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.25
                                      HHHHHHH CS
                          HTH_IclR 32 kStvhRl 38
                                      kSt+hR+
  gi|518652031|ref|YP_008141551.1| 43 KSTTHRI 49
                                      9*****8 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00046
                                       SS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR  17 qeltlselArrtglpkStvhRlL 39 
                                       + l+l+e+A++++++ ++ + +L
  gi|518652031|ref|YP_008141551.1| 170 RKLSLTEIAEQLDISTAALSEIL 192
                                       459************99988877 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.1e-05     0.079       7      31 ..     169     193 ..     167     199 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.1e-05
                                       HTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3   7 qlglsqeeLAeklGvsrstisriEn 31 
                                       +++ls++e+Ae l++s +++s i +
  gi|518652031|ref|YP_008141551.1| 169 ERKLSLTEIAEQLDISTAALSEILR 193
                                       689*******************988 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.2e-05       0.1      17      40 ..     171     194 ..     169     198 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.2e-05
                            HTH_24  17 risqreLAerlglSpstvnrrlkr 40 
                                       ++s +e+Ae+l++S +++++ l++
  gi|518652031|ref|YP_008141551.1| 171 KLSLTEIAEQLDISTAALSEILRK 194
                                       5899****************9997 PP

>> RRM_1  RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0011       1.4      44      61 ..      49      63 ..      27      73 .. 0.83
   2 ?    1.6   0.0       0.2   2.5e+02      18      32 ..     115     129 ..     113     145 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0011
                                      EEESSHHHHHHHHHHHTT CS
                             RRM_1 44 VeFeskedAekAlealng 61
                                      ++Fes edAekAle   g
  gi|518652031|ref|YP_008141551.1| 49 ITFESAEDAEKALE---G 63
                                      89***********9...3 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.2
                                       HHHTTSCEEEEEEEE CS
                             RRM_1  18 lFskfGpiksiklvr 32 
                                       lF+++G+  ++k + 
  gi|518652031|ref|YP_008141551.1| 115 LFQNYGKLLELKHML 129
                                       9*******9999886 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00018      0.23      29      58 ..     169     198 ..     166     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                                       HCT--HHHHHHHHT--HHHHHHHHTT--TT CS
                            HTH_37  29 krelsqseaaqllgiaqPkvsrllrgklsr 58 
                                       +r+ls +e+a+ l i+ + +s++lr  l++
  gi|518652031|ref|YP_008141551.1| 169 ERKLSLTEIAEQLDISTAALSEILRKTLRK 198
                                       689*********************988876 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.52   6.6e+02      53      61 ..      81      90 ..      66      98 .. 0.72
   2 ?   -3.2   0.0       7.5   9.6e+03       4      12 ..     124     132 ..     122     137 .. 0.58
   3 ?   10.0   0.0   0.00054       0.7       8      41 ..     165     198 ..     163     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.52
                              FeoC 53 c.sgsCkkCg 61
                                      + s++C+ C 
  gi|518652031|ref|YP_008141551.1| 81 AkSSCCSACS 90
                                      2477888885 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
                              FeoC   4 elkeyleer 12 
                                       elk  le +
  gi|518652031|ref|YP_008141551.1| 124 ELKHMLEMN 132
                                       555555555 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00054
                              FeoC   8 yleergrvslkeLsrhfkaspealeamLeqwvrk 41 
                                       y + +++ sl e++ ++++s++al  +L    rk
  gi|518652031|ref|YP_008141551.1| 165 YFDPERKLSLTEIAEQLDISTAALSEILRKTLRK 198
                                       7778899******************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       978  (0.0545485); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); 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: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 1422.38
//
Query:       gi|518652032|ref|YP_008141552.1|  [L=488]
Description: hypothetical protein FACI_IFERC00001G0671 [Ferroplasma acidarmanus fer1]
Scores for complete 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  284.7  38.6    1.2e-84  284.4  38.6    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
  ------ inclusion threshold ------
      0.033   14.2   2.8       0.23   11.4   0.5    2.9  2  Borrelia_P13    Borrelia membrane protein P13


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.4  38.6   1.3e-88   1.2e-84       4     414 ..      11     455 ..       8     458 .. 0.90

  Alignments for each domain:
  == domain 1  score: 284.4 bits;  conditional E-value: 1.3e-88
                    Cyt_bd_oxida_I   4 lqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysr 80 
                                       ++fa+t++ H+++v++tl++al+++i e+++l++++++y++l++ ++  ++inFa+G+++G+ +++++++ W+ +++
  gi|518652032|ref|YP_008141552.1|  11 AMFAYTISAHIIIVAITLAMALMITITEYIALKHKNKYYEALTHKLSIALVINFAIGTASGVFMAVELMLFWPVFMK 87 
                                       68*************************************************************************** PP

                    Cyt_bd_oxida_I  81 fvGdifgapLaiEgllAFflEstflglmlfgwdrv.skklhllatwlvaigtllSalwIlaanswmqtPvG....ae 152
                                       +vG ++++ ++ E+ +AF++Es+ l ++++ wd + +++ h+l++w + igt +Sa++I+ +n+wm+tP+G    a+
  gi|518652032|ref|YP_008141552.1|  88 LVGAVAMLSFYAEV-FAFLVESVTLMVYVYFWDNFkNRWNHWLVSWGILIGTGASAWLITNVNAWMNTPTGsfniAK 163
                                       *************5.********************999*********************************755533 PP

                    Cyt_bd_oxida_I 153 lnpdtgraelt..dflavlfnpsalakflHtvlaalltaaffvagvsawyllr...reke..farkslkialvvalv 222
                                       + +++ +  +t  ++l+v+ +ps+ a+++H+++a+++++++ +++++a+++l+   ++ e  + + ++ki  ++++v
  gi|518652032|ref|YP_008141552.1| 164 YMSSG-ETIITgvNPLKVFYEPSTGAELFHMFMAMYFAGSMALLAYFAYKYLKsknEN-EkiIDKLAMKILSAIGIV 238
                                       32222.3333355****************************************97533.2479999*********** PP

                    Cyt_bd_oxida_I 223 aallqallGdlsgkevaetqpaKlAAmeglwetee..aplslfgipdeeeeknefa.ieiPgllsllatgsld...g 293
                                        ++l  ++G  + +++++++p+K+A++e + +     ap +lfg++++ +    ++ i + g++slla+  ++   g
  gi|518652032|ref|YP_008141552.1| 239 DIILIGISGSIELSTLLTVEPLKYAMLELNLHPVMagAPEHLFGFISNGK---AVDfIPLAGIQSLLAYPLTKgnaG 312
                                       *******************************877679********98844...345599999999999965543338 PP

                    Cyt_bd_oxida_I 294 evkGlndlpkeevPpvalvfwsfrimvglgvlllllallalll..........rwllrllllaiplpfiaveaGWiv 360
                                       +++Gl+++p+ ++ p  +++ + ++mvg+g+l+ l+++++l+l          + +l+ ++++++l+++++e GW++
  gi|518652032|ref|YP_008141552.1| 313 YIPGLSSYPTYTWAP-SVIHSTLDLMVGFGLLMGLFWFIVLVLrimkkdifkmKSILYGFIALGFLGIFTMEDGWYT 388
                                       8************99.9**********************9988999******978********************** PP

                    Cyt_bd_oxida_I 361 tevGRqPWivy...............gllrtadavspvsagevllslilflllylvLlvvevylllkli 414
                                       +evGR P+i+                g++++a+a+   +++ v++  i+++l+yl+++ +++y+ +k++
  gi|518652032|ref|YP_008141552.1| 389 AEVGRVPYIILmpynsagqpivaghyGVMTIAQAA--STSTIVWYLGIVIILFYLIIIPFTFYFNAKVL 455
                                       **********55556666666666669*******9..6888999999***************9988876 PP

>> Borrelia_P13  Borrelia membrane protein P13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   2.6e-05      0.23      69     113 ..      16      60 ..       7      73 .. 0.82
   2 ?    1.1   0.1     0.038   3.4e+02      63      98 ..     418     449 ..     396     474 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                      Borrelia_P13  69 visgkvlllaGvltlaasylteiilPfkfanrynkdlknrlnval 113
                                       +is++++++a +l++a    +  ++ +k +n+y++ l ++l++al
  gi|518652032|ref|YP_008141552.1|  16 TISAHIIIVAITLAMALMITITEYIALKHKNKYYEALTHKLSIAL 60 
                                       567777888777778777777779*******************98 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.038
                      Borrelia_P13  63 kkaeaavisgkvlllaGvltlaasylteiilPfkfa 98 
                                       + a+a   +++++   G++ +   yl  ii+Pf+f 
  gi|518652032|ref|YP_008141552.1| 418 TIAQA-ASTSTIVWYLGIVIIL-FYL--IIIPFTFY 449
                                       33333.3455666777776553.344..78888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (488 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1160  (0.0646996); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); 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):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.25s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3705.74
//
Query:       gi|518652033|ref|YP_008141553.1|  [L=364]
Description: hypothetical protein FACI_IFERC00001G0672 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00019   20.9  37.3    0.00026   20.5  37.3    1.2  1  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
  ------ inclusion threshold ------
      0.018   14.9   5.0      0.018   14.9   5.0    4.5  4  Promethin        Promethin


Domain annotation for each model (and alignments):
>> 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 !   20.5  37.3   2.9e-08   0.00026      29     301 ..      31     329 ..      10     331 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.9e-08
                   Cyt_bd_oxida_II  29 llpllakkdeerrlllnsigpvWdgnevWLvtaggalfaaFPlayatlfsglylpllliLlglilRgvafefrskae 105
                                       ++p++++ +++++++l+ i p+W+ + + +v++++ l   +  +   +   +  ++ l +++lilR va+ + + + 
  gi|518652033|ref|YP_008141553.1|  31 IYPIFSNYEKHKTVVLKHIVPIWEITGTMIVFFVVELELIYSGLVPISSYLFIPVIGLFVALLILRNVAIIYSEFIW 107
                                       5667677788***********************************9998888888889999**************97 PP

                   Cyt_bd_oxida_II 106 skrwrklwdlaffigSllaalllGvalgnllqGvpfdad........eyg....flsdllnpfallvglllvalf.. 168
                                       +k  +k   +++ ++ +l+ + + +a+++l+ G  +++         +      + ++ ++  all++ +  a++  
  gi|518652033|ref|YP_008141553.1| 108 KKVDSKPLMMFYSAATFLMVIGFVTAIAALMVGNSVSTAipslppllH-LdltnLSKSYVDYIALLTAPVYSAVYwe 183
                                       7789999***************************98644554554431.0233455556699999999887776633 PP

                   Cyt_bd_oxida_II 169 lllGalylalktegelqerarrlalvla.lvllvllvvvllwtll.............lvllllavlalllavlllr 231
                                        l G l++a  +++  ++ a+r++ + +  ++l l++ v +w ++             ++++++++++ ll +    
  gi|518652033|ref|YP_008141553.1| 184 FLFGTLFIAFGMSQVFYRIAKRTSYIPLfTIILGLFLNVNAWNVVatlagakfmgdymILPVIITIAIPLLYMYKPT 260
                                       69999999999999988888887776662555555555666666688999999887654444344443333332211 PP

                   Cyt_bd_oxida_II 232 k.kreglaflasaltvllvvlllavslfPyllpssltianaasseytlkvmlivalil.lplvlaytawlyr 301
                                       +   ++ +f++ ++t+++++l l ++   ++     +i + as++++l + ++ ++i+ ++++l++++++y 
  gi|518652033|ref|YP_008141553.1| 261 TnLASYKPFWFIVMTIAVLFLELPIT---RIAGGAYSINTFASPNSMLVANFWLSMIGgILFLLLMIMYAYV 329
                                       11224557888888887777666555...456666789999*********9999877527778888888885 PP

>> Promethin  Promethin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -5.1   8.2         2   1.8e+04      61     100 ..      39      90 ..       9     107 .. 0.47
   2 ?   -6.2  12.9         2   1.8e+04      43      81 ..     114     154 ..     110     203 .. 0.70
   3 ?   -3.1   5.1      0.84   7.6e+03      46      88 ..     189     238 ..     165     251 .. 0.60
   4 ?   14.9   5.0   2.1e-06     0.018      15      85 ..     256     326 ..     253     330 .. 0.94

  Alignments for each domain:
  == domain 1  score: -5.1 bits;  conditional E-value: 2
                         Promethin  61 g......................allfelfvvgvallvLvpvLfitsflallvwlwalasYl 100
                                                              ++++el ++  +l+ + + Lfi           +++ ++
  gi|518652033|ref|YP_008141553.1|  39 EkhktvvlkhivpiweitgtmivFFVVELELIYSGLVPISSYLFI----------PVIGLFV 90 
                                       155555555555533333333334444444444444444444443..........3333333 PP

  == domain 2  score: -6.2 bits;  conditional E-value: 2
                         Promethin  43 PlllFltfalstllfalvg..allfelfvvgvallvLvpvL 81 
                                       Pl++F + a + +++ +v+  a+l+ +  v++a   L p L
  gi|518652033|ref|YP_008141553.1| 114 PLMMFYSAATFLMVIGFVTaiAALMVGNSVSTAIPSLPPLL 154
                                       88888888888888888886655555555555555554444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.84
                         Promethin  46 lFltfalstllfalvg.......allfelfvvgvallvLvpvLfitsfla 88 
                                       lF+ f +s ++  +         ++++ ++ + v    +v++L+++ f++
  gi|518652033|ref|YP_008141553.1| 189 LFIAFGMSQVFYRIAKrtsyiplFTIILGLFLNVNAWNVVATLAGAKFMG 238
                                       34444443333333336666666666666666666666777777766665 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 2.1e-06
                         Promethin  15 klkalrafasenPllatflliqlllsllPlllFltfalstllfalvgallfelfvvgvallvLvpvLfits 85 
                                       ++k + + as +P+ +++++i +l++ lP+  +++ a s+  fa    +l++ f++++++ +L+  L+i+ 
  gi|518652033|ref|YP_008141553.1| 256 MYKPTTNLASYKPFWFIVMTIAVLFLELPITRIAGGAYSINTFASPNSMLVANFWLSMIGGILFLLLMIMY 326
                                       677788999*******************************************************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1031  (0.0575046); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2240.07
//
Query:       gi|518652034|ref|YP_008141554.1|  [L=360]
Description: hypothetical protein FACI_IFERC00001G0673 [Ferroplasma acidarmanus fer1]
Scores for 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   89.8   1.4    2.3e-25   88.6   1.4    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    2.8e-24   85.4   0.3    7.4e-24   84.0   0.3    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    4.3e-16   58.8   1.3      4e-15   55.7   0.2    2.2  2  FeoB_N        Ferrous iron transport protein B
    6.5e-15   54.9   0.0    1.7e-14   53.6   0.0    1.8  1  TGS           TGS domain
      7e-06   26.0   3.0      0.028   14.3   0.1    3.0  3  RsgA_GTPase   RsgA GTPase
      0.003   17.6   8.4       0.15   12.1   0.2    3.1  4  Dynamin_N     Dynamin family
     0.0034   17.0   0.2        2.1    7.9   0.0    2.4  2  Ras           Ras family
     0.0048   16.3   1.3     0.0062   15.9   0.1    1.7  2  AIG1          AIG1 family
  ------ inclusion threshold ------
      0.074   12.0   0.5        3.4    6.6   0.0    2.4  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea
      0.083   13.1   0.2       0.21   11.8   0.0    1.8  2  Roc           Ras of Complex, Roc, domain of DAPkinase
       0.12   12.7   2.2         12    6.3   0.4    2.8  2  DUF3991       Protein of unknown function (DUF3991)
       0.13   11.7   0.0       0.13   11.7   0.0    1.7  2  SRPRB         Signal recognition particle receptor beta subun
       0.31   11.5   2.6       0.51   10.9   0.1    2.5  3  ABC_tran      ABC transporter


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 !   88.6   1.4   1.7e-28   2.3e-25       2     106 .]     180     285 ..     179     285 .. 0.89

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 1.7e-28
                      MMR_HSR1_Xtn   2 gGikitstvkltkldeetvkkilkeykihnaevliredvtvDdlidviegnrvYipclyvlNKiDl.isleeldela 77 
                                       gG++i++  +  ++d+ ++++i ke+ki+n +++ire++++Ddlid+ +gn vYi++++v+NKiD+  ++e+l++  
  gi|518652034|ref|YP_008141554.1| 180 GGLRIHKPRN-VDIDNGDIRDIAKEFKIVNGDIYIRENIDMDDLIDFFKGNIVYIKSFMVVNKIDMpHDEEQLKRKL 255
                                       8999997655.44*****************************************************65666666544 PP

                      MMR_HSR1_Xtn  78 re.pnsvviSaekelnldeLkekiweeLnL 106
                                       ++  n++ +Sae++ nl+++k++i+++L++
  gi|518652034|ref|YP_008141554.1| 256 KDfGNYIEVSAETGHNLESMKNMIYKTLDM 285
                                       4437***********************986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.3   5.4e-27   7.4e-24       2     100 ..      62     161 ..      61     176 .. 0.86

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 5.4e-27
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TS CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.ad 77 
                                       +a+vG+pNvGKS+L+nalt++k+ v+++ +tT++++ g+++++g +i+++D+pG+i++a  + g g+++ + ++ +d
  gi|518652034|ref|YP_008141554.1|  62 MALVGYPNVGKSSLLNALTNKKSTVGNFEFTTLTVIPGTLNYNGAQIQILDLPGIIDNAALGAGRGREIISTIRnVD 138
                                       79****************************************************9999***********9988769* PP

                                       EEEEEEETTTTCSHHHHHHHHHH CS
                          MMR_HSR1  78 lillvvdaseeklkpldeeleel 100
                                       li+lv d++ ++l+++  el + 
  gi|518652034|ref|YP_008141554.1| 139 LIVLVTDIQLKGLDRIIAELYKA 161
                                       *******8866565555554443 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 !   55.7   0.2   2.9e-18     4e-15       2      59 ..      61     118 ..      60     154 .. 0.83
   2 ?    2.0   0.1     0.099   1.4e+02     101     155 ..     222     278 ..     206     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 2.9e-18
                                       EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS CS
                            FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs 59 
                                       t+alvG pnvGk++l+nalt++k++vgN+  +t     g+l+++g +++i+DlPGi +
  gi|518652034|ref|YP_008141554.1|  61 TMALVGYPNVGKSSLLNALTNKKSTVGNFEFTTLTVIPGTLNYNGAQIQILDLPGIID 118
                                       78*****************************************************954 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.099
                                       HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT..S-EEEEBTTTTBTHHHHHHH CS
                            FeoB_N 101 llelgvpvvlalnmideaekkgieidlkkLsekLg..vpvvktsakkkegieellka 155
                                       l+++ +  ++ +  + +++k  +  d+++L++kL+   + +++sa++++++e++++ 
  gi|518652034|ref|YP_008141554.1| 222 LIDFFKGNIVYIKSFMVVNKIDMPHDEEQLKRKLKdfGNYIEVSAETGHNLESMKNM 278
                                       66666777888888888999999999******998555899*******999999876 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.6   0.0   1.2e-17   1.7e-14       1      59 [.     286     357 ..     286     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 53.6 bits;  conditional E-value: 1.2e-17
                                       EEEEE.TTSSEEE......EETTB-HHHHHHHHSTTHHHHEEEEEECS......EEEETTSBB-SSEEEEEE CS
                               TGS   1 irvyt.PdGkvpd......lprgatveDfAykIhrslakkfiyAlVnG......qrvgldhvLedgdvveIv 59 
                                       +rvy+ ++  ++d      l +gat++D+ +kI+r+++ +f+yA++ G       rvgld++++d+dvv+++
  gi|518652034|ref|YP_008141554.1| 286 VRVYMrNKSGEVDyerpliLSEGATIRDVSRKISREMISTFRYAIITGptrkieARVGLDYKVNDEDVVTLI 357
                                       79****9**********************************************99***************97 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.1     2e-05     0.028      96     123 ..      56      83 ..      10      93 .. 0.76
   2 ?    0.0   0.0      0.51     7e+02      13      47 ..     134     163 ..     124     171 .. 0.76
   3 !   10.1   0.1   0.00041      0.57      47      99 ..     233     281 ..     226     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2e-05
                                       HCTTSEEEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  96 llkdktsvlvGqSGvGKStLinallpel 123
                                       +  d t++lvG   vGKS+L+nal++++
  gi|518652034|ref|YP_008141554.1|  56 KSGDATMALVGYPNVGKSSLLNALTNKK 83 
                                       4456899*****************9974 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.51
                                       EES--EEEEEEESTTTT--HHHHHHHHHHHHHTT- CS
                       RsgA_GTPase  13 vaNvdqllivvslkepelslnlldrfLvlaeekgi 47 
                                       + Nvd +++v+ ++     l+ ldr+++++ ++gi
  gi|518652034|ref|YP_008141554.1| 134 IRNVDLIVLVTDIQ-----LKGLDRIIAELYKAGI 163
                                       67899888887666.....7888888887777766 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00041
                                       -EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
                       RsgA_GTPase  47 iepvivlnKiDlleeeeeleelkeelealgyevllvsaktkegleelkellkd 99 
                                       i+  +v+nKiD+ ++ee   +lk +l+++g + + vsa+t+++le++k+++ +
  gi|518652034|ref|YP_008141554.1| 233 IKSFMVVNKIDMPHDEE---QLKRKLKDFG-NYIEVSAETGHNLESMKNMIYK 281
                                       77899***********9...7777888886.55889999*******9998866 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.3       2.3   3.1e+03      63      81 ..       5      23 ..       2      42 .. 0.61
   2 !   12.1   0.2   0.00011      0.15       2      32 ..      63      93 ..      62     107 .. 0.81
   3 !   10.1   0.0   0.00045      0.62     100     139 ..     105     147 ..      96     167 .. 0.88
   4 ?   -3.1   0.0         5   6.8e+03      59      80 ..     249     270 ..     238     292 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                                      --CHHHHHHHHHHHHHHHT CS
                         Dynamin_N 63 edfsevreeieketekiag 81
                                      e ++e+++ei+k ++++a+
  gi|518652034|ref|YP_008141554.1|  5 ERIKEIEDEIKKTQKNKAT 23
                                      4556666666665555552 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                                      EEEEBTTTTHHHHHHHHHTS--S---SSS-- CS
                         Dynamin_N  2 avvGsqSsGKSSvlnaLlgedilprgpnptT 32
                                      a+vG  + GKSS+lnaL+ ++  +   + tT
  gi|518652034|ref|YP_008141554.1| 63 ALVGYPNVGKSSLLNALTNKKSTVGNFEFTT 93
                                      789999************9986665555555 PP

  == domain 3  score: 10.1 bits;  conditional E-value: 0.00045
                                       S-SEEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETT CS
                         Dynamin_N 100 vkgltlvDlPGldsvnkrdq...elvkeyikkadiilavtsan 139
                                         ++ ++DlPG++++++      + + ++i++ d+i++vt+ +
  gi|518652034|ref|YP_008141554.1| 105 GAQIQILDLPGIIDNAALGAgrgREIISTIRNVDLIVLVTDIQ 147
                                       56899*********99888888899999************976 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 5
                                       T-EB--CHHHHHHHHHHHHHHH CS
                         Dynamin_N  59 ekkledfsevreeieketekia 80 
                                       e+  ++++++ ++ie + e+ +
  gi|518652034|ref|YP_008141554.1| 249 EQLKRKLKDFGNYIEVSAETGH 270
                                       4444444444444444444443 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0    0.0016       2.1       3      23 ..      63      83 ..      61     147 .. 0.79
   2 !    7.1   0.0    0.0026       3.6     105     159 ..     233     282 ..     204     285 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0016
                                      EEEESTTSSHHHHHHHHHHSS CS
                               Ras  3 vlvGdsavGKtslllrfvkdk 23
                                       lvG  +vGK+sll+  +++k
  gi|518652034|ref|YP_008141554.1| 63 ALVGYPNVGKSSLLNALTNKK 83
                                      79*************999875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                                       SEEEEEEETTTGGGG-SS-HHHHHHHHHHHT..SEEEEEBTTTTCTHHHHHHHHHHH CS
                               Ras 105 vpivLvGnKvDleekravsteegeelakelg..lkfletSAktnenveeafeellre 159
                                       ++  +v nK+D+ ++    +e+   l ++l+   +++e+SA+t +n+e + +++ ++
  gi|518652034|ref|YP_008141554.1| 233 IKSFMVVNKIDMPHD----EEQ---LKRKLKdfGNYIEVSAETGHNLESMKNMIYKT 282
                                       566788889998873....233...3333333358************9987777765 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       1.7   2.3e+03      67     101 ..       8      42 ..       3      46 .. 0.75
   2 !   15.9   0.1   4.5e-06    0.0062       2      94 ..      61     147 ..      60     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
                                       HCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHHHH CS
                              AIG1  67 dkiskeivrclllseegihalllvlslgrfteede 101
                                       ++i+ ei++  + +++  h+ ll  ++++++ e+e
  gi|518652034|ref|YP_008141554.1|   8 KEIEDEIKKTQKNKATEKHIGLLKARMSKLELEEE 42 
                                       67788888888888888888888888887776666 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.5e-06
                                       EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHH CS
                              AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrcll 78 
                                       t+ lvG   +GkS+  N++ +kk    ++  +  t ++   +   +g +i++ D Pg++d  +      +ei+    
  gi|518652034|ref|YP_008141554.1|  61 TMALVGYPNVGKSSLLNALTNKKSTVGNF--EFTTLTVIPGTLNYNGAQIQILDLPGIIDNAALGAGRGREIIS--- 132
                                       6779***************9999866665..44566677777799******************99999999996... PP

                                       HCTT-ESEEEEEEETT CS
                              AIG1  79 lseegihalllvlslg 94 
                                        +   ++ ++lv++++
  gi|518652034|ref|YP_008141554.1| 133 -TIRNVDLIVLVTDIQ 147
                                       .334478888887654 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0025       3.4      25      57 ..      56      87 ..      52     108 .. 0.77
   2 ?    3.3   0.1     0.025        34     156     190 ..     221     256 ..     206     294 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0025
                                      G-S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB 25 kaGraqvvGltGvPGaGkstlvealglelrrrG 57
                                      k+G a+ + l G P +Gks l++al+ +    G
  gi|518652034|ref|YP_008141554.1| 56 KSGDAT-MALVGYPNVGKSSLLNALTNKKSTVG 87
                                      667665.6799**************98876666 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.025
                                       TTTTT--CCCHHH-SEEEEE---.HHHHHHHHHHHH CS
                              MeaB 156 DelqgikkGileiaDiivvnkaD.kkeaekaarelr 190
                                       D +  +k  i+ i   +vvnk D +++ e+ +r+l+
  gi|518652034|ref|YP_008141554.1| 221 DLIDFFKGNIVYIKSFMVVNKIDmPHDEEQLKRKLK 256
                                       55677888899************7555666666665 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00015      0.21       2      26 ..      62      86 ..      61     115 .. 0.78
   2 ?   -3.6   0.1       8.9   1.2e+04     111     120 .]     235     244 ..     228     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                                      EEEESSTTSSHHHHHHCHCT-CCC- CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedkfse 26
                                      + lvG  +vGK+sll+ ++++k + 
  gi|518652034|ref|YP_008141554.1| 62 MALVGYPNVGKSSLLNALTNKKSTV 86
                                      579****************988654 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 8.9
                                       EEEEEE-TTT CS
                               Roc 111 vilvgnkiDl 120
                                        ++v+nkiD+
  gi|518652034|ref|YP_008141554.1| 235 SFMVVNKIDM 244
                                       5789999995 PP

>> DUF3991  Protein of unknown function (DUF3991)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.009        12      12      41 ..     153     181 ..     151     258 .. 0.86
   2 ?    5.1   0.1     0.021        29       6      20 ..     315     329 ..     314     337 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.009
                           DUF3991  12 eiiaefaekkllyedeygNavFvykDengk 41 
                                        iiae+++++++   +++N+ F  ++ +g 
  gi|518652034|ref|YP_008141554.1| 153 RIIAELYKAGIVLNRKKKNIAFKRTN-YGG 181
                                       69********************9999.333 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.021
                           DUF3991   6 qRkisreiiaefaek 20 
                                       +Rkisre+i++f ++
  gi|518652034|ref|YP_008141554.1| 315 SRKISREMISTFRYA 329
                                       6***********764 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 ?   -3.5   0.6       4.4   6.1e+03     138     150 ..      11      23 ..       5      48 .. 0.56
   2 ?   11.7   0.0   9.2e-05      0.13       5      58 ..      61     115 ..      57     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.4
                                       HHHHHHHHHCHHH CS
                             SRPRB 138 EkElnkiierrsk 150
                                       E E++k +++++ 
  gi|518652034|ref|YP_008141554.1|  11 EDEIKKTQKNKAT 23 
                                       5555555554443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 9.2e-05
                                       EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT CS
                             SRPRB   5 avllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG 58 
                                       ++ lvG  + GK sl++ Lt+++ +         ++   + + +g +++++D+PG
  gi|518652034|ref|YP_008141554.1|  61 TMALVGYPNVGKSSLLNALTNKKSTVGNFEFtTLTVIPGTLNYNGAQIQILDLPG 115
                                       6789****************9966555554422223333357799*********9 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       6.3   8.7e+03      49      66 ..      14      32 ..       3      46 .. 0.56
   2 ?   10.9   0.1   0.00037      0.51       9      36 ..      57      84 ..      50     117 .. 0.78
   3 ?   -0.1   0.0      0.91   1.3e+03      31      72 ..     200     241 ..     195     324 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.3
                                      GGG.B-HHHCCHCEEEE-S CS
                                      xxx.xxxxxxxxxxxxxxx RF
                          ABC_tran 49 lke.qeleslrkeigvlpq 66
                                      +k+ q+ + ++k+ig l+ 
  gi|518652034|ref|YP_008141554.1| 14 IKKtQKNKATEKHIGLLKA 32
                                      3333555666666666554 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00037
                                      ETTSEEEEEESTTSSHHHHHHHHTTSS- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  9 kegekvaivGenGaGKStLlkllagllk 36
                                      + + ++a+vG    GKS+Ll++l+++ +
  gi|518652034|ref|YP_008141554.1| 57 SGDATMALVGYPNVGKSSLLNALTNKKS 84
                                      556799*****************99876 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.91
                                       HTTSS--SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS--S-T CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  31 lagllkpteGeilld.gkdlkeqeleslrkeigvlpqepqlfp 72 
                                       +a++ k  +G+i ++ + d+++  + +++ +i +++    +++
  gi|518652034|ref|YP_008141554.1| 200 IAKEFKIVNGDIYIReNIDMDD-LIDFFKGNIVYIKSFMVVNK 241
                                       5666677777776664455555.55666666666665533332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       998  (0.055664); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.45
# Mc/sec: 2423.02
//
Query:       gi|518652035|ref|YP_008141555.1|  [L=180]
Description: methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.2e-20   71.4   0.0    1.3e-19   70.4   0.0    1.4  1  MTS              Methyltransferase small domain
    2.6e-11   43.7   0.0    6.5e-11   42.3   0.0    1.6  1  Methyltransf_23  Methyltransferase domain
    1.6e-09   38.3   0.0    7.5e-09   36.2   0.0    2.0  1  Methyltransf_25  Methyltransferase domain
    7.4e-09   35.6   0.0    1.1e-08   35.1   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    9.9e-09   35.0   0.1    1.4e-08   34.5   0.1    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    4.5e-07   29.8   0.0    5.2e-07   29.6   0.0    1.2  1  Met_10           Met-10+ like-protein
    6.2e-07   29.3   0.0    5.7e-06   26.2   0.0    1.9  2  Methyltransf_16  Lysine methyltransferase
    1.3e-06   29.0   0.0    1.1e-05   26.0   0.0    2.0  2  Methyltransf_11  Methyltransferase domain
      6e-06   26.9   0.0    3.4e-05   24.5   0.0    2.1  1  Methyltransf_12  Methyltransferase domain
    8.4e-06   25.6   0.0    1.2e-05   25.0   0.0    1.2  1  UPF0020          Putative RNA methylase family UPF0020
    3.5e-05   23.4   0.0    5.1e-05   22.9   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    7.4e-05   22.1   0.0     0.0001   21.6   0.0    1.1  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
    0.00016   21.4   0.0    0.00024   20.8   0.0    1.2  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0033   16.9   0.0     0.0056   16.1   0.0    1.3  1  TehB             Tellurite resistance protein TehB
     0.0034   16.7   0.0     0.0098   15.1   0.0    1.6  2  DUF43            Branched-chain polyamine synthase A C-termin
     0.0038   16.9   0.0     0.0063   16.2   0.0    1.4  1  TPMT             Thiopurine S-methyltransferase (TPMT)
  ------ inclusion threshold ------
      0.022   13.8   0.1      0.033   13.2   0.1    1.2  1  tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
      0.022   14.4   0.0      0.032   13.9   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.044   13.7   0.1      0.065   13.2   0.1    1.2  1  Methyltransf_18  Methyltransferase domain
      0.051   12.8   0.0      0.084   12.1   0.0    1.4  1  CMAS             Mycolic acid cyclopropane synthetase
      0.067   12.9   0.3       0.32   10.6   0.0    2.1  3  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
        0.1   12.5   0.1       0.26   11.2   0.0    1.7  2  UPF0146          Uncharacterised protein family (UPF0146)


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 !   70.4   0.0   1.6e-22   1.3e-19      31     151 ..      26     152 ..      16     163 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.6e-22
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE---S CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivsNPPf 107
                                         ++vl +G+G G+++++la++  +  vt+ d++ +A+++ k+n+  n++++e+v sd++e+++ +k+d+i+ NPP+
  gi|518652035|ref|YP_008141555.1|  26 CGKSVLEMGSGSGLIAITLARQGHS--VTAADISPEAINLIKHNAFINNVDMEIVRSDLFENIH-GKYDTIIFNPPY 99 
                                       5778****************97766..9************************************.**********98 PP

                                       .........TTTCHCHHHHHHHHHHHHHHHEEEEEEEEEEEETTSCHHHHHHH CS
                               MTS 108 .........hagkatelavaeeliaeAkeaLkegGeLliVanrklgyesllee 151
                                                 ag +   av+ +++a+A+e+L++gG+++++ +   ++es +e+
  gi|518652035|ref|YP_008141555.1| 100 lpvegespqWAGGKDGFAVTGKFLATAHEYLNPGGNIFLILSDLTDIESFIEK 152
                                       443333332367778899***********************999999998876 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0     8e-14   6.5e-11      12     121 ..      16     142 ..       6     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 8e-14
                   Methyltransf_23  12 klerllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae...kakkaqkdqfdeqeaaepqgkfdl 85 
                                        +  +l++ + g++vL++G G+G  +  l+++g+svt+ D+spea+++++    + +   + ++++  ++  gk+d+
  gi|518652035|ref|YP_008141555.1|  16 DTYLILDNAECGKSVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKhnaFINNVDMEIVRSDLFENIHGKYDT 92 
                                       5555677788899***********************************9866533333334444445566778**** PP

                   Methyltransf_23  86 Ivlrevlehvp..dpp............ellrqiatllkpgGylllsepl 121
                                       I+ +     v+  +p             + l++++++l+pgG+++l  ++
  gi|518652035|ref|YP_008141555.1|  93 IIFNPPYLPVEgeSPQwaggkdgfavtgKFLATAHEYLNPGGNIFLILSD 142
                                       ***986666665333366**************************997764 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   9.2e-12   7.5e-09       1      70 [.      30      95 ..      30     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 9.2e-12
                                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBC.CGBSSSTTTEEEEEE CS
                   Methyltransf_25  1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgda.edlpfedgsfDlvvs 70
                                      vL++G G+G +++ la+++  ++vt+ Dis+e+++ ++++a  +++++e+v+ d+ e++   +g++D ++ 
  gi|518652035|ref|YP_008141555.1| 30 VLEMGSGSGLIAITLARQG--HSVTAADISPEAINLIKHNAFINNVDMEIVRSDLfENI---HGKYDTIIF 95
                                      9*****************5..********************99999******9995555...477888877 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   1.3e-11   1.1e-08       4     122 ..      27     150 ..      25     172 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 1.3e-11
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlil 79 
                                       g++vl+ G+G+G +++ la +  ++  v+  Dis+eai+l + na  +++d +e  ++d +e +       k+D i+
  gi|518652035|ref|YP_008141555.1|  27 GKSVLEMGSGSGLIAITLA-R--QGHSVTAADISPEAINLIKHNAFINNVD-MEIVRSDLFEnIH-----GKYDTII 94 
                                       679****************.3..3456****************97766665.6666677777555.....99***** PP

                   Methyltransf_31  80 snevl..............naladpdkileeiervlkpggilliedprllaelpakv 122
                                        n +               + +a   k+l  ++++l+pgg + +   + l++    +
  gi|518652035|ref|YP_008141555.1|  95 FNPPYlpvegespqwaggkDGFAVTGKFLATAHEYLNPGGNIFLILSD-LTDIESFI 150
                                       **44445566666777888*********************99988877.44444444 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.1   1.7e-11   1.4e-08     161     233 ..      26      96 ..      18      97 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.7e-11
                              PrmA 161 egeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellk..eekadvivaN 233
                                        g++vl +G GSG++ai  a+ g+ +v+a Di + A++  k+Na +N+v+ ++ v   ++l++  ++k+d i+ N
  gi|518652035|ref|YP_008141555.1|  26 CGKSVLEMGSGSGLIAITLARQGH-SVTAADISPEAINLIKHNAFINNVDMEI-V--RSDLFEniHGKYDTIIFN 96 
                                       5789*****************997.699***********************99.4..455554445899*99977 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   6.3e-10   5.2e-07      94     177 ..      20      98 ..       2     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 6.3e-10
                                       HHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EE CS
                            Met_10  94 laklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqlad 170
                                       +   +e g+ V+++  G G  ai++a+  +++ v a d+ Pe+++++k+n   N+v+  +  + +D  e i + + d
  gi|518652035|ref|YP_008141555.1|  20 ILDNAECGKSVLEMGSGSGLIAITLAR--QGHSVTAADISPEAINLIKHNAFINNVDMEI--VRSDLFENI-HGKYD 91 
                                       66778999*******************..9999***********************9988..888888777.88888 PP

                                       EEEE--T CS
                            Met_10 171 rvvmnlp 177
                                        ++ n p
  gi|518652035|ref|YP_008141555.1|  92 TIIFNPP 98 
                                       8877765 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0     7e-09   5.7e-06      45     101 ..      25      78 ..      11      90 .. 0.84
   2 ?    1.1   0.0      0.36     3e+02      69      89 ..     134     154 ..     115     165 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7e-09
                   Methyltransf_16  45 lsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnknalkskvk 101
                                         ++svlE+GsG+Gl+ +++a++  + +v+ +D++  +++l+k+n  +n+  ++ +++
  gi|518652035|ref|YP_008141555.1|  25 ECGKSVLEMGSGSGLIAITLARQ--GHSVTAADISPeAINLIKHNAFINN--VDMEIV 78 
                                       55799****************99..9*******9755********99977..665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.36
                   Methyltransf_16  69 peakviltDleellellkkni 89 
                                       +++ +il+Dl +++ +++kn 
  gi|518652035|ref|YP_008141555.1| 134 GNIFLILSDLTDIESFIEKNR 154
                                       4567899***********995 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.0   1.3e-08   1.1e-05       1      53 [.      31      83 ..      31      97 .. 0.89
   2 ?    0.5   0.0       1.2   9.5e+02      79      95 ..     121     137 ..     114     138 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 1.3e-08
                                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECC CS
                   Methyltransf_11  1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadae 53
                                      L++G+G+G++a  la++g++v++ D+s+e+++l k++a  +++ +e+v++d+ 
  gi|518652035|ref|YP_008141555.1| 31 LEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNAFINNVDMEIVRSDLF 83
                                      899***********************************999988888888865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.2
                                       HHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  79 kalkeiaRvLkpgGllv 95 
                                       k+l+ ++  L pgG ++
  gi|518652035|ref|YP_008141555.1| 121 KFLATAHEYLNPGGNIF 137
                                       79999*********887 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.0   4.1e-08   3.4e-05       1      73 [.      31      96 ..      31     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 4.1e-08
                   Methyltransf_12  1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvas 73
                                      Le G+G+G ++  l+++  + ++t+ Disp+ai    + ++++   nn  +e+   dl++    +++D+++ +
  gi|518652035|ref|YP_008141555.1| 31 LEMGSGSGLIAITLARQ--GHSVTAADISPEAI----NLIKHNAFINNVDMEIVRSDLFENIH-GKYDTIIFN 96
                                      89***************..**************....55555555556677777777665555.5*****965 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   1.5e-08   1.2e-05      73     190 ..      45     165 ..      32     170 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1.5e-08
                                       HHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------H......HHHHH CS
                           UPF0020  73 araelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgsk......kalek 143
                                       ar+  ++ ++D+ +++++  + Na   +v+ +i  s+  + +++   g++d+i+ npPY    g+       k+  +
  gi|518652035|ref|YP_008141555.1|  45 ARQGHSVTAADISPEAINLIKHNAFINNVDMEIVRSD-LFENIH---GKYDTIIFNPPYLPVEGESpqwaggKDGFA 117
                                       55666799*********************99998888.899999...78**********665555411111134468 PP

                                       HHHHHHHHHHHH-TT..-EEEEEESSHHHHHCC---.ESEEEEEEETT CS
                           UPF0020 144 LYseflrelkrvlrgggrlvlltsenkalekaleer.alrkvkeknvk 190
                                        + +fl ++++ l+ gg + l++s+  ++e+++e++ + + +k+k + 
  gi|518652035|ref|YP_008141555.1| 118 VTGKFLATAHEYLNPGGNIFLILSDLTDIESFIEKNrKYEFIKLKSMS 165
                                       9*********************************99666666666655 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 !   22.9   0.0   6.2e-08   5.1e-05       3      64 ..      29      88 ..      27     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.2e-08
                   Methyltransf_15  3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellak 64
                                       +l + sG+G  +i++a+++++v a +i++e +++++hNa + +v+    +v  d+fe ++ 
  gi|518652035|ref|YP_008141555.1| 29 SVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNAFINNVDM--EIVRSDLFENIHG 88
                                      588999************************************97765..5578888886655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.2e-07    0.0001      52     105 ..      29      80 ..      14      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.2e-07
                                       EEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--.GGEEE CS
                               TRM  52 kvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneve.eivvi 105
                                       +vl+  s+sGl ai  a      ++v a Dis++A++lik+N+ +n+v+ eiv +
  gi|518652035|ref|YP_008141555.1|  29 SVLEMGSGSGLIAITLARQ---GHSVTAADISPEAINLIKHNAFINNVDmEIVRS 80 
                                       689999*********9988...7899**********************9555544 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   2.9e-07   0.00024      38     124 ..      23     100 ..      16     106 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 2.9e-07
                                       CCHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EE CS
                     Cons_hypoth95  38 aeiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeef 114
                                       ++  g++vL++ +GsG +++  l R+ +++++ + ++ea++++k+n    +++  +++++ d +e+++ +      +
  gi|518652035|ref|YP_008141555.1|  23 NAECGKSVLEMGSGSGLIAI-TLARQGHSVTAADISPEAINLIKHNAFINNVD--MEIVRSDLFENIHGK------Y 90 
                                       5555788***********99.79***********************8766644..899999999988666......8 PP

                                       EEEEE--SSS CS
                     Cons_hypoth95 115 divflDPPya 124
                                       d + ++PPy 
  gi|518652035|ref|YP_008141555.1|  91 DTIIFNPPYL 100
                                       *********5 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   6.9e-06    0.0056      33     100 ..      29      94 ..       6     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.9e-06
                                       EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEE CS
                              TehB  33 kvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfil 100
                                        vl++g g+g  ++ l+ +g+ vta d   ++i+ +++ + ++n++ ++    d+ e +++ +yd i+
  gi|518652035|ref|YP_008141555.1|  29 SVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNAFINNVD-MEIVRSDLFE-NIHGKYDTII 94 
                                       489************************************9999999.8888888876.7889999886 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 !   15.1   0.0   1.2e-05    0.0098      45     122 ..      27      99 ..      23     104 .. 0.85
   2 ?   -1.3   0.1       1.3     1e+03      80     105 ..     147     172 ..     139     179 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.2e-05
                                       T-EEEEES-TT-HHHHHHHHT--SEEEEE-S-HHHHHHHHHHHHHHT--EEEE---TTS---TTTSS-BSEEEE--- CS
                             DUF43  45 gkeilvlGdDDLtslalaLtglpkkvvvvDiDeRlikfiervakelglkieaivyDlrkplpeelkekFdvfitDPp 121
                                       gk +l +G      +a++L++  + v   Di +  i++i++ a   ++++e++  Dl     e+++ k+d++i +Pp
  gi|518652035|ref|YP_008141555.1|  27 GKSVLEMGSGS-GLIAITLARQGHSVTAADISPEAINLIKHNAFINNVDMEIVRSDL----FENIHGKYDTIIFNPP 98 
                                       56677777443.238999**********************************87775....688999*********9 PP

                                       S CS
                             DUF43 122 e 122
                                       +
  gi|518652035|ref|YP_008141555.1|  99 Y 99 
                                       8 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHHT--EEEE---TTS-- CS
                             DUF43  80 ikfiervakelglkieaivyDlrkpl 105
                                        +fie+  k + +k++ + +D    l
  gi|518652035|ref|YP_008141555.1| 147 ESFIEKNRKYEFIKLKSMSFDFEAIL 172
                                       47999999999999999999987655 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   7.7e-06    0.0063      35      80 ..      24      69 ..       5      92 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.7e-06
                                      -S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHT CS
                              TPMT 35 akaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeean 80
                                      a+ g++vl  + G++l ++ lA qg++v + ++s+ A++   ++a+
  gi|518652035|ref|YP_008141555.1| 24 AECGKSVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNAF 69
                                      55667788888999999*********************97655554 PP

>> tRNA_U5-meth_tr  tRNA (Uracil-5-)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     4e-05     0.033     203     255 ..      28      79 ..      18      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4e-05
                   tRNA_U5-meth_tr 203 gdllelycGnGnfslalarnfekvlateiakssveaaqyniaankidnvqiir 255
                                       + +le+  G G  +++lar+ + v a++i+  +++  ++n   n++d ++i+r
  gi|518652035|ref|YP_008141555.1|  28 KSVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNAFINNVD-MEIVR 79 
                                       5789*****************************************98.56666 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.9e-05     0.032      45     112 ..      28      95 ..      17      99 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                              NodS  45 adalevGcaaGalterlapyckrltvvdvveeaiararer.vkesshiswivsdvqqfstdekfdlivv 112
                                        ++le+G  +G ++  la   +++t  d+ +eai+  ++    +  ++  + sd+ + + + k+d+i+ 
  gi|518652035|ref|YP_008141555.1|  28 KSVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKHNaFINNVDMEIVRSDLFE-NIHGKYDTIIF 95 
                                       479*******************************97654323444888889999876.57789999985 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   7.9e-05     0.065       9      87 ..      21      94 ..      18      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7.9e-05
                   Methyltransf_18  9 aslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvv 87
                                       +  e g++v+  G+  g+++i l+++g+   v+a+Di++++++  k+n+  +++  ++e++ sd +e+++ +++dt++
  gi|518652035|ref|YP_008141555.1| 21 LDNAECGKSVLEMGSGSGLIAITLARQGHS--VTAADISPEAINLIKHNAFINNV--DMEIVRSDLFENIH-GKYDTII 94
                                      5666778999***************99865..*****************999988..689999****9996.6699987 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0001     0.084      61     132 ..      25      94 ..      15     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                                       -TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEE CS
                              CMAS  61 kpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvv 132
                                       + G+ +L++G G G ++++ +++ + +v +  +S e  +l k++   +++ + + v+   +e++++k+d ++
  gi|518652035|ref|YP_008141555.1|  25 ECGKSVLEMGSGSGLIAITLARQ-GHSVTAADISPEAINLIKHNA-FINNVDMEIVRSDLFENIHGKYDTII 94 
                                       679****************9999.**************9998763.3444556678888899******9997 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 ?   10.6   0.0   0.00039      0.32      22      64 ..      28      72 ..      19      93 .. 0.77
   2 ?    1.0   0.1      0.35   2.8e+02     150     190 ..      63     102 ..      62     108 .. 0.78
   3 ?   -0.7   0.0       1.2   9.4e+02      85     115 ..     145     176 ..     126     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00039
                                      SEEEETT-TTSCCHHCS...SSCEEEEES-HHHHHHHH..HHCCH CS
                   MethyltransfD12 22 ktfvepFaGggaVffeakkqgkkvlinDinedlinlyk..alikn 64
                                      k + e  +G+g +++ + +qg  v+++Di ++ inl k  a i+n
  gi|518652035|ref|YP_008141555.1| 28 KSVLEMGSGSGLIAITLARQGHSVTAADISPEAINLIKhnAFINN 72
                                      56677779****************************972245554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S CS
                   MethyltransfD12 150 lklrseklknakiecgdfdavllkakieddivYlDPPYnpr 190
                                       l + +  ++n+++e  + d +++++ + d  + + PPY p 
  gi|518652035|ref|YP_008141555.1|  63 LIKHNAFINNVDMEIVRSDLFENIHGKYD-TIIFNPPYLPV 102
                                       55667788889999999999999995555.66678***985 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.2
                                       SHHHHHHHHHHHH....HHH-HHHHHHHHHHH CS
                   MethyltransfD12  85 ereyfyelreefn.kkidaireaeeaidflyl 115
                                       + e f+e++++    k+++++++ eai++++l
  gi|518652035|ref|YP_008141555.1| 145 DIESFIEKNRKYEfIKLKSMSFDFEAILLYEL 176
                                       66888888888888888888888888877776 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       2.1   1.7e+03      56      68 ..       6      18 ..       4      24 .. 0.83
   2 ?   11.2   0.0   0.00032      0.26       9      51 ..      21      64 ..      14      93 .. 0.70

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.1
                                      E---SSS--HHHH CS
                           UPF0146 56 vrDDvtdPnleiY 68
                                      + DDv++P  + Y
  gi|518652035|ref|YP_008141555.1|  6 YSDDVYKPSDDTY 18
                                      78******98777 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00032
                                      HHHS-SS.EEEEET-TT--HHHHHHHHHS-EEEEE-SS-S..... CS
                           UPF0146  9 aeenarg.kvvEvGiGrkldvaealakrgvdlvatDikekkak.e 51
                                         +++g  v E+G G  l +a +la++g  ++a Di ++ ++  
  gi|518652035|ref|YP_008141555.1| 21 LDNAECGkSVLEMGSGSGL-IAITLARQGHSVTAADISPEAINlI 64
                                      45567775799*****976.899***************9954432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       408  (0.0227564); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 1310.30
//
Query:       gi|518652036|ref|YP_008141556.1|  [L=894]
Description: hypothetical protein FACI_IFERC00001G0675 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-21   76.8  27.9    3.2e-21   76.8  27.9    5.6  1  AAA_23          AAA domain
    1.6e-08   34.1   0.0    3.2e-08   33.2   0.0    1.5  1  AAA_29          P-loop containing region of AAA domain
    9.6e-07   28.6   0.1    9.6e-07   28.6   0.1    6.8  7  Rad50_zn_hook   Rad50 zinc hook motif
    6.4e-06   25.8  60.7    0.00013   21.5  60.7    2.4  1  SMC_N           RecF/RecN/SMC N terminal domain
    1.4e-05   25.1  32.5    1.5e-05   24.9  10.0    3.9  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    0.00045   19.9   5.0    0.00045   19.9   5.0    3.8  4  AAA_27          AAA domain
    0.00046   20.0  13.8    0.00046   20.0  13.8    6.2  6  DUF4201         Domain of unknown function (DUF4201)
     0.0012   18.9   1.6     0.0012   18.9   1.6    7.1  8  Med9            RNA polymerase II transcription mediator comp
     0.0022   17.5  12.4     0.0022   17.5  12.4    4.4  3  HMMR_N          Hyaluronan mediated motility receptor N-termi
     0.0026   17.5 105.3      0.014   15.1  61.8    4.1  1  AAA_15          AAA ATPase domain
     0.0034   17.6   0.0     0.0097   16.1   0.0    1.7  1  SbcCD_C         Putative exonuclease SbcCD, C subunit
  ------ inclusion threshold ------
       0.02   14.7   0.0      0.058   13.2   0.0    1.8  1  KDGP_aldolase   KDGP aldolase
       0.12   12.0   0.0       0.47   10.1   0.0    2.0  2  AAA_30          AAA domain
       0.92    9.6   5.5        6.2    6.9   0.0    4.2  4  SNARE           SNARE domain
        6.5    6.0  51.9       0.32   10.3   6.3    5.6  6  DUF3450         Protein of unknown function (DUF3450)
        8.2    6.5   9.9       0.38   10.8   0.3    3.7  3  DUF2089         Protein of unknown function (DUF2089)


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 !   76.8  27.9   2.8e-24   3.2e-21       1     198 [.       5     241 ..       5     289 .. 0.66

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 2.8e-24
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayvel 77 
                                       ++ki nf s++++ei F++g+++ItG+NGaGKT+ildAik+aL+ e++++++++       +      +k+k+y+e+
  gi|518652036|ref|YP_008141556.1|   5 SIKIINFLSHENTEITFEQGINIITGKNGAGKTSILDAIKFALFAESRNNEKNN-------EL----IKKGKNYFEI 70 
                                       69*******************************************865444433.......22....2244455444 PP

                            AAA_23  78 tfenkdgrytrsiererelsk.kkgkttkkaklellei....deleqfisellgskkiilnlilflgqer....... 142
                                       t++ + +++++++ r + l+k k++++    k++++ +    +  + +i+++l+++ + +++++f  q++       
  gi|518652036|ref|YP_008141556.1|  71 TLNFNVNGEHYEVYRHFGLKKaKNAERLASVKKNGVIVaetyEGVNVEITKILNVSREVFKNSVFVEQGQmdslisg 147
                                       43333333335555544444413333333334444444224444444555577777777777777777777777777 PP

                            AAA_23 143 .................................feefelkdkkerleelekeleeledekk.llekl....eqekek 181
                                                                        +e+++l++ +erl++++k++e+ ++ekk  +e      ++ +++
  gi|518652036|ref|YP_008141556.1| 148 tpkerktifsdiigltslsrsadrlreiigafrEEMILLQNSSERLDQAKKDIEKFKEEKKtAFESMsrakIESEKY 224
                                       77777777777777777777777777777777799999999999999999999998777764455556555333333 PP

                            AAA_23 182 ekeleeleeeleeilke 198
                                         eleel+ +++e + +
  gi|518652036|ref|YP_008141556.1| 225 YGELEELKAKQKERDRY 241
                                       33555555555544433 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   2.9e-11   3.2e-08       2      51 ..       4      52 ..       3      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 2.9e-11
                            AAA_29  2 krlqlvNWgtfdghtieidlkgatlltGpsGsGKSTllDAiqalLvpakk 51
                                      ++++++N  + ++++i+++ +g+ ++tG++G+GK+++lDAi++ L ++++
  gi|518652036|ref|YP_008141556.1|  4 ESIKIINFLSHENTEITFE-QGINIITGKNGAGKTSILDAIKFALFAESR 52
                                      68999***9999******9.889**********************99983 PP

>> Rad50_zn_hook  Rad50 zinc hook motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.86   9.6e+02       7      20 ..     251     264 ..     245     267 .. 0.82
   2 ?   -1.4   0.4         2   2.2e+03       2      16 ..     412     426 ..     408     428 .. 0.53
   3 !   28.6   0.1   8.5e-10   9.6e-07       4      45 ..     435     475 ..     433     478 .. 0.90
   4 ?   -1.6   0.4       2.3   2.5e+03       3      19 ..     509     525 ..     508     528 .. 0.79
   5 ?   -2.2   1.1       3.5   3.9e+03       3      19 ..     550     566 ..     548     568 .. 0.74
   6 ?   -1.8   0.3       2.6     3e+03      39      52 .]     639     652 ..     638     653 .. 0.86
   7 ?   -1.6   0.2       2.2   2.4e+03       8      18 ..     707     717 ..     700     726 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.86
                                       HHHHHHHHHTT-SE CS
                     Rad50_zn_hook   7 elnkkieelkeakg 20 
                                        + k+++e+ke++g
  gi|518652036|ref|YP_008141556.1| 251 NISKYLDEIKEREG 264
                                       5789*******987 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2
                                       HHHHHHHHHHHHHHT CS
                     Rad50_zn_hook   2 hqeteelnkkieelk 16 
                                       + e++e + +i+e+k
  gi|518652036|ref|YP_008141556.1| 412 NREISEKTSRISEIK 426
                                       445555555555555 PP

  == domain 3  score: 28.6 bits;  conditional E-value: 8.5e-10
                                       HHHHHHHHHHHHTT-SEE-TTT--EE-HHHHHHHHHHHHHHH CS
                     Rad50_zn_hook   4 eteelnkkieelkeakgcCPlCgReldeehrseLikelqskl 45 
                                       + +e ++++e lk +   CPlCg +l+++h+++++ke+ +k 
  gi|518652036|ref|YP_008141556.1| 435 TLTEVRENMETLKGKS-TCPLCGTNLTPDHMESISKEYDEKA 475
                                       6788899999999999.*********************9985 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 2.3
                                       HHHHHHHHHHHHHTT-S CS
                     Rad50_zn_hook   3 qeteelnkkieelkeak 19 
                                       qe+e    +i+e+k+ +
  gi|518652036|ref|YP_008141556.1| 509 QEIETAASYINEIKSLE 525
                                       78888889999999865 PP

  == domain 5  score: -2.2 bits;  conditional E-value: 3.5
                                       HHHHHHHHHHHHHTT-S CS
                     Rad50_zn_hook   3 qeteelnkkieelkeak 19 
                                       +e e l+k+i+el + +
  gi|518652036|ref|YP_008141556.1| 550 AENENLEKAIKELQQYE 566
                                       56677899999998876 PP

  == domain 6  score: -1.8 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHH... CS
                     Rad50_zn_hook  39 kelqsklerlpeel 52 
                                       +e++skle++++e+
  gi|518652036|ref|YP_008141556.1| 639 REMKSKLESIKDEI 652
                                       78999999999986 PP

  == domain 7  score: -1.6 bits;  conditional E-value: 2.2
                                       HHHHHHHHTT- CS
                     Rad50_zn_hook   8 lnkkieelkea 18 
                                       ++++iee++e+
  gi|518652036|ref|YP_008141556.1| 707 YTERIEETEEN 717
                                       44444444443 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  60.7   1.2e-07   0.00013       2     214 ..       3     885 ..       2     890 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                       EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N   2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkae 78 
                                       +++++i nF s   +++++ f++++++i+G+NG+GK+++ldAi+F L  +s     +ek ++li+k       +  e
  gi|518652036|ref|YP_008141556.1|   3 IESIKIINFLSH--ENTEITFEQGINIITGKNGAGKTSILDAIKFALFAESR---NNEKNNELIKK-----GKNYFE 69 
                                       899*********..7999*****************************96555...789999****8.....455667 PP

                                       EEEEEEETTEE......SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.............. CS
                                       xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                             SMC_N  79 veitfdnedkk......lkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.............. 135
                                       +++ f+ ++++      +   k+  + +r ++ k++  +  +  e  + e++++l+                     
  gi|518652036|ref|YP_008141556.1|  70 ITLNFNVNGEHyevyrhFGL-KKAKNAERLASVKKNGVIVAETYEGVNVEITKILN------Vsrevfknsvfveqg 139
                                       77777666555233322111.11122222222222222222223333333333333......122233345777789 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 140 qmdslisgtpkerktifsdiigltslsrsadrlreiigafreemillqnsserldqakkdiekfkeekktafesmsr 216
                                       9999999999999**************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 217 akiesekyygeleelkakqkerdryitvienikaniskyldeikeregqsvelsakiseitsiekrvtelqenpyyk 293
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 294 kmdfinryfleksgmdsaakdmekankrlseysdyagkleklseyhkkysdmhdkytlnsekikesrkmheeylsas 370
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 371 sniqsmvdrlnkmknyvdnylkssglslediqnfrpirekinreisektsriseiksnvasysktltevrenmetlk 447
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 448 gkstcplcgtnltpdhmesiskeydekagqiigdieklkleknsvesdqeklkdrykifgsqeietaasyineiksl 524
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 525 etekkelentienaskghelfnvlsaenenlekaikelqqyeneyiryssiisgmdpgaikkeieaagesfttfknr 601
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 602 inellsqigfvpeyneyqntgkisseinrlkteversremksklesikdeienrkksieglriemenkqsamhqydg 678
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                             SMC_N 136 ............................................................................. 135
                                                                                                                    
  gi|518652036|ref|YP_008141556.1| 679 ideqagniesryksayqenikmktlvdsyterieeteenaknleqdaekykktreaistlgkireafdyngiqsiir 755
                                       ***************************************************************************** PP

                                       .............................................CS-HHHHHHHHHHHHHHHHCC..S--SEEEEC CS
                                       .............................................xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                             SMC_N 136 .............................................lLSgGektLvalaLlfAiqkv..kpaplyllD 165
                                                                                    +LSgGekt +a+a+++++ ++  +  ++ ++D
  gi|518652036|ref|YP_008141556.1| 756 kdasasmtnltrkylqsfnldfddisidenfdikvtqnsmeqtleSLSGGEKTALAIAIRLSVTEYvlEIISIIIMD 832
                                       **************************************************************99983366799**** PP

                                       TTTTTS-HHHHHHHHHHHH..HHCTT..SEEEEE-SSHHHCCC-SCEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxx..xxxxx..xxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 166 eidaaLDeknvkkvaellk..ekskn..aQfivislreemlekadklvgvtkv 214
                                       e    LDe +++++ +++    k +n   Q+i+i++++e+++ ad+ + + k+
  gi|518652036|ref|YP_008141556.1| 833 EPTNFLDEDRRNNLKDIILysLKGENivPQMIMITHHSELISVADASYEIIKT 885
                                       **************999863223334447*******************99984 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  10.0   1.4e-08   1.5e-05       1     102 [.      25     159 ..      25     398 .. 0.85
   2 ?    3.5  13.5     0.047        53      55     302 ..     498     873 ..     471     874 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-08
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarl.......................drdvegltdelsggggirkipslldlydp 54 
                                       +n+++G+Ng+GK+++Lda++++ ++                       + +v+g+++e  +++g++k  +  +l + 
  gi|518652036|ref|YP_008141556.1|  25 INIITGKNGAGKTSILDAIKFALFAesrnneknnelikkgknyfeitlNFNVNGEHYEVYRHFGLKKAKNAERLASV 101
                                       79*************************************************************************** PP

                            AAA_21  55 eipfefeieeflsqgvryryglrlersqv..........eeklssvetllesgllldk 102
                                       ++ +++  e  +  +v+++ +l++ r+ +           ++l+s  +++++++++d 
  gi|518652036|ref|YP_008141556.1| 102 KKNGVIVAETYEGVNVEITKILNVSREVFknsvfveqgqMDSLISGTPKERKTIFSDI 159
                                       *********99***********999999965555555544444444444444444444 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.047
                            AAA_21  55 eipfefeieeflsqgvryryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkels 131
                                       + ++++ i   ++ ++  +y+ +++           ++ le ++   ++  e ++v ++e ++  + +++ +++e +
  gi|518652036|ref|YP_008141556.1| 498 KLKDRYKIFGSQEIETAASYINEIKSLET------EKKELENTIENASKGHELFNVLSAENENLEKAIKELQQYENE 568
                                       55555555544555555555555555555......777777777778888888888888888888888888888888 PP

                            AAA_21 132 vsepndlqfgkaltditsrawsllllldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeel 208
                                       ++ +++ ++g++   i+++++ + +++  + + ri+ l  ++ ++++++e + +++ ++++++   e++ ++e++ +
  gi|518652036|ref|YP_008141556.1| 569 YIRYSSIISGMDPGAIKKEIEAAGESFTTFKN-RINELLSQIGFVPEYNEYQNTGKISSEINRLKTEVERSREMKSK 644
                                       88888888888888888888888888888777.44444444445555555555666666666666666666666666 PP

                            AAA_21 209 iasvderlrer.................................................................. 219
                                        +s+++ +  r                                                                  
  gi|518652036|ref|YP_008141556.1| 645 LESIKDEIENRkksieglriemenkqsamhqydgideqagniesryksayqenikmktlvdsyterieeteenaknl 721
                                       66666666666666888888888888888888888888888888888888888888888888888888888888888 PP

                            AAA_21 220 ...............................................................gvvflengdgqelp 233
                                                                                                      ++ + +  +  e +
  gi|518652036|ref|YP_008141556.1| 722 eqdaekykktreaistlgkireafdyngiqsiirkdasasmtnltrkylqsfnldfddisideNFDIKVTQNSMEQT 798
                                       888888888888888888888888888888888888888888888888888889998999999************** PP

                            AAA_21 234 arelSdGtkrllalltallralkkg...sllliDEpEngLHPkllrrllell......kelsrngaQviltTHSpll 301
                                       + +lS G k +la++  l  +       s+++ DEp n+L+  +   l +++      ++      Q i+ TH  +l
  gi|518652036|ref|YP_008141556.1| 799 LESLSGGEKTALAIAIRLSVTEYVLeiiSIIIMDEPTNFLDEDRRNNLKDIIlyslkgENI---VPQMIMITHHSEL 872
                                       ***********99999999999888***************998887777666655444333...3488888888877 PP

                            AAA_21 302 l 302
                                       +
  gi|518652036|ref|YP_008141556.1| 873 I 873
                                       6 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   5.0     4e-07   0.00045       1     167 [.       1     174 [.       1     244 [. 0.62
   2 ?   -1.2   0.1       1.1   1.3e+03     133     200 ..     352     418 ..     302     428 .. 0.68
   3 ?   -2.6   0.4       3.2   3.5e+03     181     200 ..     515     534 ..     490     568 .. 0.51
   4 ?   -3.6   0.5       6.3     7e+03     158     202 ..     679     723 ..     671     732 .. 0.65

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4e-07
                            AAA_27   1 MrlerLdLeryGkftdrsldfsaeeadlhliyGpNEAGKstalrAisdllfGipertkdn.flhd..akkLrigavl 74 
                                       M +e++++  + + ++++++f+   +++ +i G N AGK+++l+Ai+  lf  +++ ++n  l +  ++  +i   +
  gi|518652036|ref|YP_008141556.1|   1 MIIESIKIINFLSHENTEITFE---QGINIITGKNGAGKTSILDAIKFALFAESRNNEKNnELIKkgKNYFEITLNF 74 
                                       899999***************8...8*************************97766554414444114556666666 PP

                            AAA_27  75 eeadgeelefaRr.....kgrkktlldaddq.........alpeevlaallggldretFealFgLdherLreGGeal 137
                                        + +ge+ e+ R+      ++ + l++ +++             +v  + + +++re F++   +++ ++    ++l
  gi|518652036|ref|YP_008141556.1|  75 -NVNGEHYEVYRHfglkkAKNAERLASVKKNgvivaetyeG--VNVEITKILNVSREVFKNSVFVEQGQM----DSL 144
                                       .8888888888862221112222333333334444322110..112222223455566655555555444....356 PP

                            AAA_27 138 leaegelgqlLfeasaGlaslrevleaLea 167
                                       ++++ +  +++f+   Gl+sl++  ++L++
  gi|518652036|ref|YP_008141556.1| 145 ISGTPKERKTIFSDIIGLTSLSRSADRLRE 174
                                       666666666666666666666666666654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                            AAA_27 133 GGealleaegelgqlLfeasaGlaslrevleaLeaeadelfkprkskkrainealeeleeakkelrea 200
                                         e++ e++ ++ +  ++as+ ++s+ + l+++++  d++ k+++ + + i++ +   e+ ++e+ e+
  gi|518652036|ref|YP_008141556.1| 352 NSEKIKESR-KMHEEYLSASSNIQSMVDRLNKMKNYVDNYLKSSGLSLEDIQNFRPIREKINREISEK 418
                                       444443333.4445556788888888888888888888888877777666666666666666666665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                            AAA_27 181 rainealeeleeakkelrea 200
                                       +++ ++ ++le+ kkel++ 
  gi|518652036|ref|YP_008141556.1| 515 ASYINEIKSLETEKKELENT 534
                                       44444444444444444332 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 6.3
                            AAA_27 158 lrevleaLeaeadelfkprkskkrainealeeleeakkelreaqv 202
                                       + e   ++e++ ++ ++++ + k+ +   +e++ee++++ ++ + 
  gi|518652036|ref|YP_008141556.1| 679 IDEQAGNIESRYKSAYQENIKMKTLVDSYTERIEETEENAKNLEQ 723
                                       556666777778888888877776666666666666666665554 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   9.0      0.15   1.7e+02      86     137 ..     186     237 ..     164     275 .. 0.82
   2 ?   -2.5   5.6       3.2   3.5e+03      46     132 ..     247     350 ..     242     360 .. 0.63
   3 !   20.0  13.8   4.1e-07   0.00046       5     173 ..     356     540 ..     352     543 .. 0.90
   4 ?   -1.0   0.1       1.1   1.3e+03      88     106 ..     547     565 ..     539     571 .. 0.58
   5 ?    4.9   3.7     0.017        19      71     119 ..     623     671 ..     619     677 .. 0.85
   6 ?    2.7  11.9     0.083        93      49     136 ..     643     733 ..     639     742 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.15
                           DUF4201  86 lhmleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggl 137
                                       l+  ++ l ++kk++++ +e+++   ++++++k e +k+  + e+lk++  +
  gi|518652036|ref|YP_008141556.1| 186 LQNSSERLDQAKKDIEKFKEEKKTAFESMSRAKIESEKYYGELEELKAKQKE 237
                                       55667889999************************************99876 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.2
                           DUF4201  46 qlqienqalnkkIeernkeLkrlkkkttktvhalthlkeklh..............mleselselkkelkekeerla 108
                                       ++++++ ++ ++I er+ + ++l+ k+     + + + e                   +s +  + k++++ ++rl 
  gi|518652036|ref|YP_008141556.1| 247 NIKANISKYLDEIKEREGQSVELSAKISEITSIEKRVTELQEnpyykkmdfinryfLEKSGMDSAAKDMEKANKRLS 323
                                       67777777888888888877777777777777777777766667777777777775444556666666666666666 PP

                           DUF4201 109 klrk...elykvklerdklrkqneklk 132
                                       ++ +   +l+k+ + ++k+ + ++k  
  gi|518652036|ref|YP_008141556.1| 324 EYSDyagKLEKLSEYHKKYSDMHDKYT 350
                                       655522245555555666655555544 PP

  == domain 3  score: 20.0 bits;  conditional E-value: 4.1e-07
                           DUF4201   5 rnelsklrlklislkhqlakiqeklekkeelge......gLtlidFeqlqienqalnkkIeernkeLkrlkkkttkt 75 
                                        +e  k++ + +s+ ++++ + ++l+k+++  +      gL+l+d ++ +   ++ n +I e++  ++++k+++++ 
  gi|518652036|ref|YP_008141556.1| 356 IKESRKMHEEYLSASSNIQSMVDRLNKMKNYVDnylkssGLSLEDIQNFRPIREKINREISEKTSRISEIKSNVASY 432
                                       5677899999999999999999999999998764444447************************************* PP

                           DUF4201  76 vhalthlkeklh...........mleselselkkelkekeerlaklrkelykvklerdklrkqneklkqqggllrvP 141
                                       +++lt+++e++              + +  +++++ ke +e+  ++   ++k+kle++ ++ ++eklk++  +++  
  gi|518652036|ref|YP_008141556.1| 433 SKTLTEVRENMEtlkgkstcplcGTNLTPDHMESISKEYDEKAGQIIGDIEKLKLEKNSVESDQEKLKDRYKIFGSQ 509
                                       ************7777777776655666678999******************************************* PP

                           DUF4201 142 aLlkDYdktkekveekrksvkkLrrkvkilem 173
                                       ++ +    + +++++++ + k+L+ +++++++
  gi|518652036|ref|YP_008141556.1| 510 EIET-AASYINEIKSLETEKKELENTIENASK 540
                                       ***9.9*********************99875 PP

  == domain 4  score: -1.0 bits;  conditional E-value: 1.1
                           DUF4201  88 mleselselkkelkekeer 106
                                        l++e+++l+k +ke++++
  gi|518652036|ref|YP_008141556.1| 547 VLSAENENLEKAIKELQQY 565
                                       4455555555555555554 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.017
                           DUF4201  71 kttktvhalthlkeklhmleselselkkelkekeerlaklrkelykvkl 119
                                       k+ +++ +l+++ e+  +++s+l+  k+e++++++ ++ lr e+++ + 
  gi|518652036|ref|YP_008141556.1| 623 KISSEINRLKTEVERSREMKSKLESIKDEIENRKKSIEGLRIEMENKQS 671
                                       67788889999999999**********************9999987665 PP

  == domain 6  score: 2.7 bits;  conditional E-value: 0.083
                           DUF4201  49 ienqalnkkIeernkeLkrlkkkttkt...vhalthlkeklhmleselselkkelkekeerlaklrkelykvklerd 122
                                        + ++ +++Ie+r+k ++ l+  + ++   +h+   + e +  +es ++ + +e  ++++  +++ +++++++++ +
  gi|518652036|ref|YP_008141556.1| 643 SKLESIKDEIENRKKSIEGLRIEMENKqsaMHQYDGIDEQAGNIESRYKSAYQENIKMKTLVDSYTERIEETEENAK 719
                                       566778899***********977655422288888899*************************************** PP

                           DUF4201 123 klrkqneklkqqgg 136
                                       +l+++ ek k+  +
  gi|518652036|ref|YP_008141556.1| 720 NLEQDAEKYKKTRE 733
                                       *******9998765 PP

>> Med9  RNA polymerase II transcription mediator complex subunit 9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1         2   2.2e+03      28      64 ..     169     205 ..     160     215 .. 0.61
   2 ?   -1.5   1.8       2.4   2.7e+03      34      71 ..     192     236 ..     191     252 .. 0.81
   3 ?    0.5   1.7      0.57   6.4e+02      11      66 ..     212     266 ..     206     278 .. 0.85
   4 ?   -0.1   0.2      0.92     1e+03      28      44 ..     373     389 ..     354     448 .. 0.56
   5 ?   -1.7   4.2       2.9   3.2e+03      35      63 ..     511     539 ..     474     568 .. 0.66
   6 !   18.9   1.6     1e-06    0.0012      19      76 ..     619     676 ..     598     678 .. 0.89
   7 ?   -0.4   0.3       1.1   1.3e+03      33      49 ..     726     742 ..     705     747 .. 0.68
   8 ?   -3.3   0.1       9.1     1e+04      42      62 ..     782     802 ..     781     803 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2
                              Med9  28 tgelrhkLkkarelirelpgidrsveeqeaeieelee 64 
                                       ++ lr  +  +re +  l++ ++  ++ ++ ie+ +e
  gi|518652036|ref|YP_008141556.1| 169 ADRLREIIGAFREEMILLQNSSERLDQAKKDIEKFKE 205
                                       5555555555555555555555556666666655554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.4
                              Med9  34 kLkkarelirelpg........idrsveeqeaeieeleeqlakKre 71 
                                       +L++a++ i++ ++        ++r + e e++  ele +l++K++
  gi|518652036|ref|YP_008141556.1| 192 RLDQAKKDIEKFKEekktafesMSRAKIESEKYYGELE-ELKAKQK 236
                                       89999999999998888888888888888888888888.5666654 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.57
                              Med9  11 ksiekdpnlsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeql 66 
                                       +s+++++ ++s++   ++ el+ k k+   +i  +++i  ++   ++ei+e e q 
  gi|518652036|ref|YP_008141556.1| 212 ESMSRAK-IESEKYYGELEELKAKQKERDRYITVIENIKANISKYLDEIKEREGQS 266
                                       6777788.88999999999999999999999******************9999875 PP

  == domain 4  score: -0.1 bits;  conditional E-value: 0.92
                              Med9  28 tgelrhkLkkarelire 44 
                                       +++  ++L+k+++++++
  gi|518652036|ref|YP_008141556.1| 373 IQSMVDRLNKMKNYVDN 389
                                       55555666666666554 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 2.9
                              Med9  35 Lkkarelirelpgidrsveeqeaeieele 63 
                                       +++a ++i+e++ ++  ++e e+ ie+ +
  gi|518652036|ref|YP_008141556.1| 511 IETAASYINEIKSLETEKKELENTIENAS 539
                                       34666777777777777777777777765 PP

  == domain 6  score: 18.9 bits;  conditional E-value: 1e-06
                              Med9  19 lsskdletktgelrhkLkkarelirelpgidrsveeqeaeieeleeqlakKrelLkky 76 
                                       +++ +++++++ l++  ++ re+ ++l+ i   +e++++ ie l+ ++++K++ +++y
  gi|518652036|ref|YP_008141556.1| 619 QNTGKISSEINRLKTEVERSREMKSKLESIKDEIENRKKSIEGLRIEMENKQSAMHQY 676
                                       5677899************************************************999 PP

  == domain 7  score: -0.4 bits;  conditional E-value: 1.1
                              Med9  33 hkLkkarelirelpgid 49 
                                        k+kk re+i++l  i 
  gi|518652036|ref|YP_008141556.1| 726 EKYKKTREAISTLGKIR 742
                                       47778888888777665 PP

  == domain 8  score: -3.3 bits;  conditional E-value: 9.1
                              Med9  42 irelpgidrsveeqeaeieel 62 
                                       i+e+ +i  ++ ++e+ +e+l
  gi|518652036|ref|YP_008141556.1| 782 IDENFDIKVTQNSMEQTLESL 802
                                       567778999999999999987 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 ?    2.2  14.9     0.091     1e+02     191     287 ..     186     288 ..     173     295 .. 0.73
   2 ?   -2.4  11.4       2.2   2.5e+03     197     330 ..     334     445 ..     304     452 .. 0.43
   3 !   17.5  12.4     2e-06    0.0022     195     333 ..     585     730 ..     577     732 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.091
                            HMMR_N 191 lqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldiaqleellkekndeies. 266
                                       lq   + L+++k+ + + ke +++  +     k e+ek   + eel++ +++ ++y   i++++ ++++  dei++ 
  gi|518652036|ref|YP_008141556.1| 186 LQNSSERLDQAKKDIEKFKEEKKTAFESMSRAKIESEKYYGELEELKAKQKERDRYITVIENIKANISKYLDEIKEr 262
                                       7888899************999999999999****************999999998777777777776666666531 PP

                            HMMR_N 267 ......LkssLeekeqelskqvkdlne 287
                                             L  +++e +  ++k+v +l+e
  gi|518652036|ref|YP_008141556.1| 263 egqsveLSAKISEITS-IEKRVTELQE 288
                                       1000004444444333.5555555544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                            HMMR_N 197 nLeeskakvaqLkeklvslekek.ieekseteklleyieelsnvseqlekykldiaqleellkekndeiesLkssLe 272
                                       +L e ++k + + +k  +l+ ek +e ++  e+ l   ++++++ ++l+k k   +++ ++lk+    +e++++   
  gi|518652036|ref|YP_008141556.1| 334 KLSEYHKKYSDMHDKY-TLNSEKiKESRKMHEEYLSASSNIQSMVDRLNKMK---NYVDNYLKSSGLSLEDIQNFRP 406
                                       3444444444555554.22222212223333344444444444444443333...3334444444444444443222 PP

                            HMMR_N 273 ekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleelkeklklkeqeaqk 330
                                        +e+ +++++++++++++++                   + + +  ++l+  +++++ 
  gi|518652036|ref|YP_008141556.1| 407 IREK-INREISEKTSRISEIK------------------SNVASYSKTLTEVRENMET 445
                                       2222.3344444444444444..................4444444444444444333 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 2e-06
                            HMMR_N 195 qknLeeskakvaqLkeklvslekek.....ieekseteklleyieelsnvseqlekykldiaqleellkekndeies 266
                                       +k++e++ + ++  k+++ +l  +       +e ++t k   +i++l+ + e+    k +++++++ ++++++ ie 
  gi|518652036|ref|YP_008141556.1| 585 KKEIEAAGESFTTFKNRINELLSQIgfvpeYNEYQNTGKISSEINRLKTEVERSREMKSKLESIKDEIENRKKSIEG 661
                                       5666666666666666666666665555546788899*****************99********************* PP

                            HMMR_N 267 LkssLeekeqelskqvkdlnekckllekekeelvree...eekeqtlsaEleelkeklklkeqeaqklqq 333
                                       L+ ++e+k+    +q +  +e+   +e+  +   +e+   ++  ++++  +ee++e+ k  eq+a+k+++
  gi|518652036|ref|YP_008141556.1| 662 LRIEMENKQS-AMHQYDGIDEQAGNIESRYKSAYQENikmKTLVDSYTERIEETEENAKNLEQDAEKYKK 730
                                       ******9999.788999**********77776655542226667889999*****************998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1  61.8   1.3e-05     0.014       1     255 [.       1     386 [.       1     513 [. 0.59

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdl.Flnnkekknkkvikiekedleifeniseskd 76 
                                       M+I++iki NF s++++ei ++  ++++ GkN++GK+sil+a+++ ++ ++           +++ +++  ++ ++ 
  gi|518652036|ref|YP_008141556.1|   1 MIIESIKIINFLSHENTEITFEQGINIITGKNGAGKTSILDAIKFaLFAES----------RNNEKNNELIKKGKNY 67 
                                       9******************************************76233323..........3456666667777888 PP

                            AAA_15  77 ikIdvef...................................................................... 83 
                                       ++I+++f                                                                      
  gi|518652036|ref|YP_008141556.1|  68 FEITLNFnvngehyevyrhfglkkaknaerlasvkkngvivaetyegvnveitkilnvsrevfknsvfveqgqmdsl 144
                                       8888888888899**************************************************************** PP

                            AAA_15  84 ............................................aekekakeyektlkskekkkadlllkkkesdlk 116
                                                                                                               +++l+
  gi|518652036|ref|YP_008141556.1| 145 isgtpkerktifsdiigltslsrsadrlreiigafreemillqnS---------------------------SERLD 194
                                       **********99999999988877777766666555555555441...........................33333 PP

                            AAA_15 117 ktikdkklklkknelsdekisvekkkskkelpkekeeklekekeelkid.kedlkklikkleeslkkee........ 184
                                       + +kd +   +++++  e+ s  k++s+k+  +++e k+++++ +  i+  e++k  i+k+   +k+ e        
  gi|518652036|ref|YP_008141556.1| 195 QAKKDIEKFKEEKKTAFESMSRAKIESEKYYGELEELKAKQKERDRYITvIENIKANISKYLDEIKEREgqsvelsa 271
                                       33333333333333333444444444444444444444444444444444444444444444444444422222222 PP

                            AAA_15 185 ......................elknvlksaiiklllisakRnvsd.edsekkssllgklkekileealqekl.... 234
                                                             +++ +   +++k+  +sa ++ ++ ++  ++ s +  ++ek++e+  +++     
  gi|518652036|ref|YP_008141556.1| 272 kiseitsiekrvtelqenpyykKMDFINRYFLEKSGMDSAAKDMEKaNKRLSEYSDYAGKLEKLSEY-HKKYSdmhd 347
                                       2222222222222222223333444444444455555555554444222222222222233333332.222223433 PP

                            AAA_15 235 ..................eeelteklkeiqeklkeidkk 255
                                                          ++  ++++++ + l++++++
  gi|518652036|ref|YP_008141556.1| 348 kytlnsekikesrkmheeYLSASSNIQSMVDRLNKMKNY 386
                                       333333333332233222222222222222222222222 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   8.6e-06    0.0097      20      84 ..     789     846 ..     771     850 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.6e-06
                           SbcCD_C  20 dgkekelsrssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatl 84 
                                       + ++ ++++  ++lSGGek +++++a+ +++  ++ +       ++++++DE  + lDe+++++l
  gi|518652036|ref|YP_008141556.1| 789 KVTQNSMEQTLESLSGGEK-TALAIAIRLSVTEYVLE------IISIIIMDEPTNFLDEDRRNNL 846
                                       3345568899*********.78888888887777766......69***************99876 PP

>> KDGP_aldolase  KDGP aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.2e-05     0.058      18      94 ..     533     611 ..     521     630 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.2e-05
                                       HHHHHHTTT-EEEEEEGGGSSSHHHHHHHHHHHHHCTTT..-EEEE-STT-GGGHHHHHHHCCCH--SEE--BGGGH CS
                     KDGP_aldolase  18 keiyeaaeghvviGvlsknyetveeavedvkkykkevdn..aisvGLGaGdpeqskmvaeiskklqpqhinqvftgv 92 
                                       + i +a++gh +  vls++ e+ e+a++++++y++e     +i  G+  G  ++  ++a  s ++  + in  ++++
  gi|518652036|ref|YP_008141556.1| 533 NTIENASKGHELFNVLSAENENLEKAIKELQQYENEYIRysSIISGMDPGAIKKEIEAAGESFTTFKNRINELLSQI 609
                                       457899****************************9865411555588888888888888888888888888888887 PP

                                       HH CS
                     KDGP_aldolase  93 gl 94 
                                       g+
  gi|518652036|ref|YP_008141556.1| 610 GF 611
                                       76 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00042      0.47      17      42 ..      22      47 ..      16      56 .. 0.81
   2 ?   -4.1   0.0       9.8   1.1e+04      48      67 ..     158     177 ..     153     198 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00042
                            AAA_30 17 gdrvavltGpAGtGKttalkalreaw 42
                                      ++ + ++tG  G+GKt +l a++ a+
  gi|518652036|ref|YP_008141556.1| 22 EQGINIITGKNGAGKTSILDAIKFAL 47
                                      45699****************98665 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 9.8
                            AAA_30  48 rviglAptgkaAkvLaeelg 67 
                                       ++igl++ ++ A++L+e +g
  gi|518652036|ref|YP_008141556.1| 158 DIIGLTSLSRSADRLREIIG 177
                                       58999999999999998776 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.49   5.5e+02      11      29 ..     187     205 ..     186     210 .. 0.84
   2 ?    6.9   0.0    0.0056       6.2      10      33 ..     308     331 ..     306     335 .. 0.91
   3 ?   -2.7   0.0       5.4   6.1e+03      13      31 ..     369     387 ..     368     390 .. 0.77
   4 ?    0.8   0.0      0.44   4.9e+02      15      29 ..     553     567 ..     547     568 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.49
                                       HHHHHHHHHHHHHHHHHHH CS
                             SNARE  11 enaqsnveraqkeLkkavk 29 
                                       +n+++++++a+k + k+ +
  gi|518652036|ref|YP_008141556.1| 187 QNSSERLDQAKKDIEKFKE 205
                                       699**********999875 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0056
                                       HHHHHHHHHHHHHHHHHHHHHHCT CS
                             SNARE  10 VenaqsnveraqkeLkkavkyqks 33 
                                       +++a  ++e+a+k+L  ++ y+ +
  gi|518652036|ref|YP_008141556.1| 308 MDSAAKDMEKANKRLSEYSDYAGK 331
                                       799*****************9987 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.4
                                       HHHHHHHHHHHHHHHHHHH CS
                             SNARE  13 aqsnveraqkeLkkavkyq 31 
                                       a+sn+++  ++L+k+ +y 
  gi|518652036|ref|YP_008141556.1| 369 ASSNIQSMVDRLNKMKNYV 387
                                       7888888889999988885 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.44
                                       HHHHHHHHHHHHHHH CS
                             SNARE  15 snveraqkeLkkavk 29 
                                       +n+e+a keL+++++
  gi|518652036|ref|YP_008141556.1| 553 ENLEKAIKELQQYEN 567
                                       79**********975 PP

>> DUF3450  Protein of unknown function (DUF3450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   4.2   0.00058      0.65      15     133 ..     169     288 ..     159     300 .. 0.85
   2 ?    6.7   4.3    0.0034       3.8      44     176 ..     316     450 ..     309     452 .. 0.86
   3 ?    1.9   2.1       0.1   1.2e+02      19      95 ..     462     535 ..     456     543 .. 0.67
   4 ?    2.8   2.4     0.054        61      27      79 ..     509     564 ..     506     571 .. 0.72
   5 ?    1.3   2.1      0.16   1.8e+02      47      86 ..     622     661 ..     613     673 .. 0.61
   6 ?   10.3   6.3   0.00028      0.32      31     100 ..     668     737 ..     663     738 .. 0.94

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                           DUF3450  15 aatldqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieei 91 
                                       a+ l++++ + ++ +   + s+++ d+ +++ ++ ++e +++ e  ++++++ e++   +++++++ ++ ++ i+ i
  gi|518652036|ref|YP_008141556.1| 169 ADRLREIIGAFREEMILLQNSSERLDQAKKDIEKFKEEKKTAFESMSRAKIESEKYYGELEELKAKQKERDRYITVI 245
                                       6777777777777777889999999**************************************************** PP

                           DUF3450  92 eeierelvpllekmidrLeqfveldlPf.lleeRqarlakLke 133
                                       e+i+++++ +l+++ +r  q vel   +   +  ++r+ +L+e
  gi|518652036|ref|YP_008141556.1| 246 ENIKANISKYLDEIKEREGQSVELSAKIsEITSIEKRVTELQE 288
                                       *************999999999998877445677777777776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0034
                           DUF3450  44 dekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvpllekmidrLeqfveldlPfl 120
                                       +++++ l+ey +   +le+l+ y ++++++ ++   + ++++e+ +  ee  ++ +  +++m+drL+++ +    +l
  gi|518652036|ref|YP_008141556.1| 316 EKANKRLSEYSDYAGKLEKLSEYHKKYSDMHDKYTLNSEKIKESRKMHEEYLSA-SSNIQSMVDRLNKMKNYVDNYL 391
                                       56778899*********************************9999988887665.5668999999999988888888 PP

                           DUF3450 121 le..eRqarlakLkelmdradvslaekyrrvleayqiEaeYgrtievyqgelel.dGee 176
                                       ++     + +++ +   ++ + + +ek  r+ e+ +  a+Y++t+   ++++e   G++
  gi|518652036|ref|YP_008141556.1| 392 KSsgLSLEDIQNFRPIREKINREISEKTSRISEIKSNVASYSKTLTEVRENMETlKGKS 450
                                       8733357889999999999999***********************99999998878876 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                           DUF3450  19 dqalkeaekavaaaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeie 95 
                                       d +++ +++  ++a q+   i+kl+ ek++++++ ++lk+   + +++ +q  +  as  +ei+sle++++e+e++ 
  gi|518652036|ref|YP_008141556.1| 462 DHMESISKEYDEKAGQIIGDIEKLKLEKNSVESDQEKLKD---RYKIFGSQEIETAASYINEIKSLETEKKELENTI 535
                                       5566666777777777777777888888877777777765...4556666666666777777777777777777664 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.054
                           DUF3450  27 kavaaaaqsqkkidklddekqellaeyralkeeles...levyneqlerlvasqeq 79 
                                       + +++aa+  ++i++l+ ek+el++ ++++++  e    l+++ne+le+ +++++q
  gi|518652036|ref|YP_008141556.1| 509 QEIETAASYINEIKSLETEKKELENTIENASKGHELfnvLSAENENLEKAIKELQQ 564
                                       56677788888888899999999999988887766422266677777777777765 PP

  == domain 5  score: 1.3 bits;  conditional E-value: 0.16
                           DUF3450  47 qellaeyralkeeleslevyneqlerlvasqeqeiaslee 86 
                                        ++++e+++lk+e+e+ +  +++le++ ++ e++ +s+e 
  gi|518652036|ref|YP_008141556.1| 622 GKISSEINRLKTEVERSREMKSKLESIKDEIENRKKSIEG 661
                                       4556666666666666666666666666666666665554 PP

  == domain 6  score: 10.3 bits;  conditional E-value: 0.00028
                           DUF3450  31 aaaqsqkkidklddekqellaeyralkeeleslevyneqlerlvasqeqeiasleeqieeieeierelvp 100
                                       +++++  ++d +d+++ +++++y+++ +e+ +++   + +++ +++ e++ ++le++ e+ ++++++++ 
  gi|518652036|ref|YP_008141556.1| 668 NKQSAMHQYDGIDEQAGNIESRYKSAYQENIKMKTLVDSYTERIEETEENAKNLEQDAEKYKKTREAIST 737
                                       67888899*********************************************************99975 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.9       6.2   6.9e+03      69     107 ..     192     222 ..     182     236 .. 0.53
   2 ?   -0.7   0.2       1.2   1.4e+03      70     113 ..     518     562 ..     509     564 .. 0.72
   3 ?   10.8   0.3   0.00034      0.38      50     106 ..     582     635 ..     559     659 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.2
                           DUF2089  69 rldeileaLgyeeeeeeeeeeeerkeileklekgeisve 107
                                       rld+  ++++  +        ee+k+ +e++++ +i+ e
  gi|518652036|ref|YP_008141556.1| 192 RLDQAKKDIEKFK--------EEKKTAFESMSRAKIESE 222
                                       4444444444433........445555555555555444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.2
                           DUF2089  70 ldeileaLgyeeeeeee..eeeeerkeileklekgeisveeAlerL 113
                                       ++ei ++L++e++e e+  e++++ +e+++ l++ + ++e+A+++L
  gi|518652036|ref|YP_008141556.1| 518 INEI-KSLETEKKELENtiENASKGHELFNVLSAENENLEKAIKEL 562
                                       5554.56777777654422247889999999999999999999988 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00034
                           DUF2089  50 GnlkevekelgisYpTvrnrldeileaLgyeeeeeeeeeeeerkeileklekgeisv 106
                                       G +k+  ++ g s++T +nr++e+l+++g+ +e +e    +++ +i +++++ + +v
  gi|518652036|ref|YP_008141556.1| 582 GAIKKEIEAAGESFTTFKNRINELLSQIGFVPEYNEY---QNTGKISSEINRLKTEV 635
                                       788888888999********************97732...33455555554444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (894 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2511  (0.140052); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                       118  (0.00658152); expected 17.9 (0.001)
Passed Fwd filter:                        70  (0.00390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 1.74u 0.31s 00:00:02.04 Elapsed: 00:00:00.58
# Mc/sec: 4636.77
//
Query:       gi|518652037|ref|YP_008141557.1|  [L=373]
Description: hypothetical protein FACI_IFERC00001G0676 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-15   56.5   0.1    9.3e-15   55.7   0.1    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    2.5e-07   31.0   0.0    7.1e-07   29.6   0.0    1.8  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 !   55.7   0.1     1e-18   9.3e-15       2     203 ..       3     196 ..       2     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 55.7 bits;  conditional E-value: 1e-18
                                       EEEEEESBTB........TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHH....TSE CS
                       Metallophos   2 rilvigDlHl........algggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvky....pip 66 
                                       r+l+++D+Hl         +++  ++++++++d  l+e ++d+++++GDl+d+ +++++ ++ +++        ++ 
  gi|518652037|ref|YP_008141557.1|   3 RFLHLSDTHLgyrqymmdLREEDFYESFNEAIDFGLEE-NVDFFVHTGDLFDTWSPSNRAMNEFKKAMIKlykkNKT 78 
                                       89****************9999**********999999.***************99999999965555556988888 PP

                                       EEEEC-TTSCHHHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEE.THHHHHHHHHHHSC CS
                       Metallophos  67 vylllGNHegfeeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspel.lvsldklgslnlel 141
                                        yl++G H+       +        +++ +  +  f++l +  lg+   + +++ +Gg +++ l  ++++++l ++ 
  gi|518652037|ref|YP_008141557.1|  79 MYLIMGDHD------RP--------KRTDEVASRIFDFLGVKLLGTEElQSIVINYGG-EDIlLSGISNMKGLRKNS 140
                                       9********......22........3333444788999999999999999********.444777777777777777 PP

                                       HHHHCCHHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHH.HH.HHHTTESEEEEESSSS CS
                       Metallophos 142 eapepgdewlkdlekrekadwvivlgHsplyrgsgylfgdeale.dl.lkkygvdlvisGHtHv 203
                                        +++ +    k + + +  +  i ++H +++    ++  +ea+e d      + ++  +GH+H 
  gi|518652037|ref|YP_008141557.1| 141 LVDQYR----KADIEAKSYKNSIMMSHQGVS----PYLIPEACEvDSkDLPVNYKYLAFGHVHD 196
                                       765443....224455556669*****9999....44444444435544455588999****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 !   29.6   0.0   7.9e-11   7.1e-07       2     155 ..       3     222 ..       2     239 .. 0.78
   2 ?   -3.8   0.0       1.4   1.2e+04      57     107 ..     288     296 ..     277     338 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 7.9e-11
                     Metallophos_2   2 klaiiSDlH.............snldaleavlealkevgvdaiihaGDl.eeeepe..vleellela........pv 54 
                                       +++++SD+H             + ++  +++++   e++vd  +h+GDl  + +p+  +++e+++           +
  gi|518652037|ref|YP_008141557.1|   3 RFLHLSDTHlgyrqymmdlreeDFYESFNEAIDFGLEENVDFFVHTGDLfDTWSPSnrAMNEFKKAMiklykknkTM 79 
                                       689*********9999999887667777777887788889********885555544488888877777889999** PP

                     Metallophos_2  55 laVrGNnD...................................eev....veedvlreaaelgtdlpeeaelelage 92 
                                       + + G++D                                   e++    + ++ + +++ l +++  +a++e++  
  gi|518652037|ref|YP_008141557.1|  80 YLIMGDHDrpkrtdevasrifdflgvkllgteelqsivinyggEDIllsgISNMKGLRKNSLVDQY-RKADIEAKSY 155
                                       ********9999999999999999999999999999999999833346778888888888888888.6666666555 PP

                     Metallophos_2  93 k..vlliHgdpl..gvkdalaellkeaeegsd..vvvcGHtHvpevekeggvlvvnPGsvgeprdgdpe 155
                                       k  + + H+  +    ++a + + k+   +++  ++++GH H  ++ +++  ++ ++Gs    ++ + +
  gi|518652037|ref|YP_008141557.1| 156 KnsIMMSHQGVSpyLIPEACEVDSKD--LPVNykYLAFGHVHDSYLITDKYPVFSYAGSTDLNSTNEIK 222
                                       55599999986655666666666666..444457*************9999999999999887766655 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.4
                     Metallophos_2  57 VrGNnDeevveedvlreaaelgtdlpeeaelelagekvlliHgdplgvkda 107
                                       ++G+ D                                          +d+
  gi|518652037|ref|YP_008141557.1| 288 IHGDAD------------------------------------------RDD 296
                                       444444..........................................222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (373 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.64u 0.35s 00:00:00.99 Elapsed: 00:00:00.56
# Mc/sec: 1994.33
//
Query:       gi|518652038|ref|YP_008141558.1|  [L=510]
Description: hypothetical protein FACI_IFERC00001G0677 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-34  119.9   0.3    3.3e-34  119.0   0.3    1.5  1  DUF87            Helicase HerA, central domain
    2.6e-12   46.7   0.2    1.1e-11   44.8   0.2    2.1  1  HAS-barrel       HAS barrel domain
    2.3e-06   26.5   0.1     0.0048   15.6   0.0    2.1  2  DUF853           Bacterial protein of unknown function (DUF85
    6.5e-06   25.3   0.0    0.00034   19.6   0.0    2.2  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      6e-05   22.0   0.0     0.0001   21.3   0.0    1.3  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
    0.00022   21.7   0.1     0.0049   17.3   0.0    2.6  2  AAA              ATPase family associated with various cellul
     0.0011   19.0   0.2      0.069   13.1   0.0    2.8  3  ResIII           Type III restriction enzyme, res subunit
     0.0077   15.6   0.1        2.4    7.4   0.0    2.3  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.011   14.7   0.0       0.19   10.6   0.0    2.2  2  AAA_10           AAA-like domain
      0.031   13.5   0.1       0.08   12.2   0.0    1.6  2  Zeta_toxin       Zeta toxin
      0.052   13.8   0.0        1.3    9.3   0.0    2.5  2  AAA_22           AAA domain
        0.1   12.2   0.0       0.44   10.1   0.0    1.9  2  Zot              Zonular occludens toxin (Zot)


Domain annotation for each model (and alignments):
>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.0   0.3   2.2e-37   3.3e-34       2     225 ..     130     340 ..     129     342 .. 0.89

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 2.2e-37
                             DUF87   2 eiGrllsgsevpvyldlnklvtrHlAilgsTGsGKSntvavLleellekkgatililDpHGEYgkal....ekllse 74 
                                       +iG+l  +++v v+l++n l +rHlAil++TG+GKS+t++v++eell kkga+i++lDpH +Y+ ++     k +se
  gi|518652038|ref|YP_008141558.1| 130 NIGSL-PDNNVNVSLNVNGL-RRHLAILAQTGAGKSHTASVIMEELL-KKGASIIVLDPHADYVFMKkgvdGKFYSE 203
                                       79***.8999*******999.**************************.***************************** PP

                             DUF87  75 kvkvitpspsa.........kdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqakakeekeklssdep 142
                                        ++v++++ s+         + ++++i++++l+p+++  ++++  k+ ++++ s+++++++++k     +k + +++
  gi|518652038|ref|YP_008141558.1| 204 GISVFRTPLSTgrytnndvgIINNFTIRFSDLTPDDVKGIMDI--KEGYTNLISIVDDIYKKMK-----GKKDLNDF 273
                                       *******8888********999*********************..****************777.....78888888 PP

                             DUF87 143 veklleelkkekeelrklknqaiarlldkledllrkggsfsnsstdliallleklekegkitiidlsgvdelaqqlv 219
                                       +e+  e+l      ++++k + + + l+k++d+++++ +       +++ l      +gk++++dlsg+d+  ++++
  gi|518652038|ref|YP_008141558.1| 274 LETA-ESLP----AEDYKKIKGRLTFLKKIKDIFQDYTTG------INDYL-----GPGKMSVMDLSGMDQFLANYF 334
                                       8843.3444....366666667777888888888888888......88888.....9*************9998887 PP

                             DUF87 220 vsvilr 225
                                          +l 
  gi|518652038|ref|YP_008141558.1| 335 SYRVLS 340
                                       776665 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.8   0.2     7e-15   1.1e-11       1      92 []       8      93 ..       8      93 .. 0.98

  Alignments for each domain:
  == domain 1  score: 44.8 bits;  conditional E-value: 7e-15
                        HAS-barrel  1 iGevigestssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddevalat 79
                                      iG++ige ts+ ++f++  + ++k +eyV+ +   +eiv+G+++ i+++ sel nd ++++s++++   + +d+v +  
  gi|518652038|ref|YP_008141558.1|  8 IGYIIGENTSGRFQFVISDDSNIKKWEYVYLKIK-NEIVIGRIEEIKSK-SELMNDGMDYQSIDKYAKTGMNDFVNICI 84
                                      8*********************************.*************5.***************************** PP

                        HAS-barrel 80 edtgvkvlGeved 92
                                           ++lG+++d
  gi|518652038|ref|YP_008141558.1| 85 S----TILGKLKD 93
                                      *....9***9986 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00033      0.49       9      60 ..     137     188 ..     130     199 .. 0.88
   2 !   15.6   0.0   3.2e-06    0.0048     257     362 ..     354     453 ..     314     499 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00033
                            DUF853   9 aeqelalalklanrhGliaGatGtGktvtLqvlaeslseaGvpvfladvkGd 60 
                                       ++ ++ l+++   rh  i   tG+Gk  t  v+ e+l + G ++++ d   d
  gi|518652038|ref|YP_008141558.1| 137 NNVNVSLNVNGLRRHLAILAQTGAGKSHTASVIMEELLKKGASIIVLDPHAD 188
                                       5677889999999*******************************99997776 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.2e-06
                            DUF853 257 PklvfffdeahLLfndapkallekveqvvrLirskG..vGvyfv..tqnPldlPdtvLaqLGnrvqhalraftpkdq 329
                                       P + +f +eah +    ++    ++ ++++ i   G   G+++v  tq P  +  +vL+q  +++   lr   p dq
  gi|518652038|ref|YP_008141558.1| 354 PVF-VFIEEAHNFVPPRSN---SNIAKMIKKIAGEGrkFGIFLVviTQRPGKIDADVLSQCNSQI--ILRVTNPSDQ 424
                                       444.477999976654444...455555666655443346665333**************98765..7********* PP

                            DUF853 330 kavkaaadtfranpefdveeaiteLgvGealvs 362
                                       +a+  +++ +       ++e + +L++Gea++ 
  gi|518652038|ref|YP_008141558.1| 425 NAILESSENIT----GYLMEDLPSLDTGEAIIV 453
                                       **998876554....456778899999999874 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 !   19.6   0.0   2.3e-07   0.00034       7      56 ..     141     190 ..     137     204 .. 0.92
   2 ?    3.3   0.0     0.021        31     260     312 ..     377     421 ..     370     437 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.3e-07
                     TrwB_AAD_bind   7 vplpkeretqhilivGttGsGKtqalekllrairargdraivlDltGafv 56 
                                       v+l+++  ++h++i+  tG+GK+ +++ +++++ ++g  +ivlD++ ++v
  gi|518652038|ref|YP_008141558.1| 141 VSLNVNGLRRHLAILAQTGAGKSHTASVIMEELLKKGASIIVLDPHADYV 190
                                       778888889************************************99986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.021
                     TrwB_AAD_bind 260 elksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsda 312
                                        +k+++ egRkfG+ +v+  q   ++ +         +ls +n+++ilrv++ 
  gi|518652038|ref|YP_008141558.1| 377 MIKKIAGEGRKFGIFLVVITQRPGKIDA--------DVLSQCNSQIILRVTNP 421
                                       57888999*********99999988864........45677888888887643 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 !   21.3   0.0   6.8e-08    0.0001      37      83 ..     142     190 ..     109     200 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 6.8e-08
                   T4SS-DNA_transf  37 llntdGdfehvlvvAptrsgK..gvgvviPnllkwkqsiVvlDpkgEla 83 
                                        ln +G   h  + A t++gK  +++v++  llk++ si+vlDp ++ +
  gi|518652038|ref|YP_008141558.1| 142 SLNVNGLRRHLAILAQTGAGKshTASVIMEELLKKGASIIVLDPHADYV 190
                                       456677679************6669*******************99865 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 ?    1.6   0.1      0.24   3.5e+02       6      26 ..     157     180 ..     152     278 .. 0.79
   2 !   17.3   0.0   3.3e-06    0.0049      58     129 ..     353     415 ..     316     418 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.24
                                       STTSSHHHHHHHHHHHH...THEE CS
                               AAA   6 ppGtGKTllakavakel...gvef 26 
                                         G GK+ +a+ +++el   g+++
  gi|518652038|ref|YP_008141558.1| 157 QTGAGKSHTASVIMEELlkkGASI 180
                                       569999999999999975443333 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.3e-06
                                       TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEEEE CS
                               AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrkie 129
                                        p+ +fi+E++++++ r       +++ ++++++++ g+ +k + ++++++t+rp k+d  +l + ++++i 
  gi|518652038|ref|YP_008141558.1| 353 YPVFVFIEEAHNFVPPR-------SNSNIAKMIKKIAGEGRKFG-IFLVVITQRPGKIDADVL-SQCNSQII 415
                                       5899*************.......78889**********99877.******************.99998875 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.5   2.3e+03      96     121 ..      31      59 ..      11      81 .. 0.59
   2 !   13.1   0.0   4.6e-05     0.069      23      60 ..     148     183 ..     111     200 .. 0.73
   3 ?    2.2   0.0       0.1   1.5e+02     121     159 ..     308     380 ..     224     385 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.5
                                       -..........-SEEEEEHHHHHHTH... CS
                            ResIII  96 a...kekdstnkkilvttiqsldadseee 121
                                       +   + + + +++i++  i++++++se  
  gi|518652038|ref|YP_008141558.1|  31 KkweYVYLKIKNEIVIGRIEEIKSKSELM 59 
                                       23333333447888888888888888554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.6e-05
                                       TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEE CS
                            ResIII  23 rdkrglikmaTGtGKTlvaaklierllkkgkeekflfl 60 
                                        ++++ i + TG+GK+ +a  ++e+llkkg    +++l
  gi|518652038|ref|YP_008141558.1| 148 LRRHLAILAQTGAGKSHTASVIMEELLKKGA--SIIVL 183
                                       3456669999******************987..56665 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.1
                                       .....................................HHHTTT-S...EEEEETGGGTTS.TTTHHHHHT--- CS
                            ResIII 121 e...............................eeeseellrdrfd...viiiDEaHrlgakkswreilekfke 159
                                       +                               ++  + +l+++f+   +++i EaH++    s  +i++++k+
  gi|518652038|ref|YP_008141558.1| 308 GindylgpgkmsvmdlsgmdqflanyfsyrvlSSIYDVKLSSEFKypvFVFIEEAHNFVPPRSNSNIAKMIKK 380
                                       1444444444444444444444443344433333444444444446778999999999998788888887775 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.1     0.006         9      10      63 ..     122     173 ..     117     179 .. 0.82
   2 !    7.4   0.0    0.0016       2.4     212     242 ..     370     400 ..     362     401 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.006
                                       HHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHH CS
                      FtsK_SpoIIIE  10 kfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSl 63 
                                       +f+te+s ++++l+ +  + ++ l+ ++   hl ++  tg GKS +  +++  l
  gi|518652038|ref|YP_008141558.1| 122 SFNTEESLNIGSLPDN--NVNVSLNVNGLRRHLAILAQTGAGKSHTASVIMEEL 173
                                       5777888888888888..888888888888**************9988888665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0016
                                       ....HHHHHHHHHHHCGGGTEEEEEEES--- CS
                      FtsK_SpoIIIE 212 ssvlvedaivRlarkgraaglHlllatqrls 242
                                       s+  + ++i+++a  gr+ g++l+++tqr++
  gi|518652038|ref|YP_008141558.1| 370 SNSNIAKMIKKIAGEGRKFGIFLVVITQRPG 400
                                       46778899*********************97 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00013      0.19      23      65 ..     151     192 ..     140     211 .. 0.88
   2 ?    1.5   0.0     0.076   1.1e+02     254     292 ..     370     408 ..     345     430 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                            AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfk 65 
                                       + +i+ ++G+GKS +a +++  ++  g  ++++Dp ++ + f+
  gi|518652038|ref|YP_008141558.1| 151 HLAILAQTGAGKSHTASVIMEELLKKGASIIVLDPHAD-YVFM 192
                                       7899*******************************998.4444 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.076
                            AAA_10 254 ssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelk 292
                                       s ++ +k++k++   GR++  +++ +tq +  ++ + l+
  gi|518652038|ref|YP_008141558.1| 370 SNSNIAKMIKKIAGEGRKFGIFLVVITQRPGKIDADVLS 408
                                       445557889999999*************99887766554 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   5.3e-05      0.08      23      51 ..     156     185 ..     144     187 .. 0.84
   2 ?   -3.6   0.0       3.6   5.4e+03     106     130 ..     370     394 ..     369     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 5.3e-05
                        Zeta_toxin  23 GqpGAGKselaellkdele.rqgnvvrldp 51 
                                       +q+GAGKs++a+ + +el  ++ ++++ldp
  gi|518652038|ref|YP_008141558.1| 156 AQTGAGKSHTASVIMEELLkKGASIIVLDP 185
                                       6****************9867778888886 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.6
                        Zeta_toxin 106 spdvvkklaealkkaGYevevvvva 130
                                       s ++++k++++++ +G++  +++v 
  gi|518652038|ref|YP_008141558.1| 370 SNSNIAKMIKKIAGEGRKFGIFLVV 394
                                       6678899999999999999999886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0009       1.3       5      32 ..     149     176 ..     145     202 .. 0.74
   2 ?    1.9   0.0      0.17   2.5e+02      90     117 ..     351     383 ..     270     422 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0009
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldee 32 
                                       +++l++ +++G+GK++++  ++e+l + 
  gi|518652038|ref|YP_008141558.1| 149 RRHLAILAQTGAGKSHTASVIMEELLKK 176
                                       689***************9999998654 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                            AAA_22  90 av.ielliiDEaqhlr...s.eealeeLrslln 117
                                       ++ ++++ i+Ea+++    s  ++ + +++++ 
  gi|518652038|ref|YP_008141558.1| 351 FKyPVFVFIEEAHNFVpprSnSNIAKMIKKIAG 383
                                       33678999******8765424444444444433 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.5   2.2e+03      34      59 ..     143     170 ..     137     183 .. 0.67
   2 ?   10.1   0.0    0.0003      0.44      83     138 ..     356     410 ..     344     418 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.5
                               Zot  34 tnidGlr..lerieqvlgekvstarlir 59 
                                        n++Glr  l  ++q    k +ta +i 
  gi|518652038|ref|YP_008141558.1| 143 LNVNGLRrhLAILAQTGAGKSHTASVIM 170
                                       5888888777777776666666777775 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                               Zot  83 llviDEcqeifpvrakegrkdpevi.naftehRhlgwDivlltqdiskihkevrala 138
                                       +++i E++++ p r++   +  ++i +   e R++g  +v +tq + ki+ +v   +
  gi|518652038|ref|YP_008141558.1| 356 FVFIEEAHNFVPPRSNS--NIAKMIkKIAGEGRKFGIFLVVITQRPGKIDADVLSQC 410
                                       99*************97..7889995667799******************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       736  (0.0410508); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3456.74
//
Query:       gi|518652039|ref|YP_008141559.1|  [L=347]
Description: hypothetical protein FACI_IFERC00001G0678 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-19   69.5   2.6    6.1e-19   68.7   2.6    1.3  1  NurA      NurA domain
  ------ inclusion threshold ------
      0.077   12.9   0.0       0.12   12.2   0.0    1.4  1  PSCyt2    Protein of unknown function (DUF1549)


Domain annotation for each model (and alignments):
>> NurA  NurA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.7   2.6   6.8e-23   6.1e-19       4     242 .]      56     313 ..      54     313 .. 0.93

  Alignments for each domain:
  == domain 1  score: 68.7 bits;  conditional E-value: 6.8e-23
                                       EEEEEEEEEE.EETTCEEEEEEEEEEECCEEECCCEEEECEBTCCHHEEEEEHHHHHHHHHHHHHHHHHHHCGGCCS CS
                              NurA   4 aAvDGSngvv.rlsggilyilsayavvgggkerleealslasvdsispsdelerrirllmetlElklgallleekge 79 
                                       aA+D+S + +  ++g  ++i++a    ++   + ++a  +a+ + +      ++ + llme+ E+k  ++ l+e+ +
  gi|518652039|ref|YP_008141559.1|  56 AATDSSEFLRmLYNGKNIVIVRAFTLYNNEVTSDFHADLVAVDPVDQ-----RNFTILLMEHSEHKSMLKFLDEHSP 127
                                       89********9999999********9999999999999999999999.....************************* PP

                                       CEEEEECSHHCCCHHHHHHHHHHHHHHHHHHHHHHTT-........TTCEEEEESS-SCTCCHCCC........... CS
                              NurA  80 dllllDGsligslvefdelheeleyeeylyslsrllea........glnlvgvaKsfrskellnll........... 137
                                       ++l++DGsl g l  + e  ++++ye   y+++++l++        g+ l+++aKs++++ ++++l           
  gi|518652039|ref|YP_008141559.1| 128 EYLFVDGSLKGRLSHRIETLPIEKYENFMYEYMKTLKElirksyekGTTLIFMAKSSYTECFKKYLletarndpetm 204
                                       **************8888888888888888888888888888*********************************** PP

                                       .......S--HHHHCCHHCCHCH---STTS-HHHHTT-HCCHHHHHH-EEEEEEESSTTTTEEEEEHHHHHHC.... CS
                              NurA 138 .letlligesisDiallgallrkpgytspllkilrekpllrealidkeiyfaYvrlegggsilrleipaevst.... 209
                                        + +++ g+  +D+ l+++ ++++gyt+p+       ++++ +  d +++++ +  ++ + +++++   ++s+    
  gi|518652039|ref|YP_008141559.1| 205 kIKEKESGIYRNDHYLIKSFAEESGYTTPVM------YRKNLEGTDINYVSFDILPDPVDLPMKVQ---VLSKsfik 272
                                       *******************************......9999999**********************...33434677 PP

                                       ........CHHHHHHHHHH..TTB-SSSBCC...HHHHHHHHCC CS
                              NurA 210 ........akdedvlsllasqrlsisGYprp...LalAhelaki 242
                                               ++de+++++l    + ++GY ++   L ++++++k+
  gi|518652039|ref|YP_008141559.1| 273 edldrkpyNLDEKIINTLF---YGYTGYKVYnlwLVDVDKKVKF 313
                                       78999999***********...********99889999999986 PP

>> PSCyt2  Protein of unknown function (DUF1549)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.12      63     125 ..     179     242 ..     148     288 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                            PSCyt2  63 lLaspaygerwarhwldlaryadskgyekdeerkeawryrdwviralnedkPYdq..fvreqlag 125
                                       ++a+++y+e + +++l+ ar++ ++ + k++e   ++r   ++i++++e+  Y    + r+ l g
  gi|518652039|ref|YP_008141559.1| 179 FMAKSSYTECFKKYLLETARNDPETMKIKEKES-GIYRNDHYLIKSFAEESGYTTpvMYRKNLEG 242
                                       578999****************98888766666.9*****************9862244555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2298.13
//
Query:       gi|518652040|ref|YP_008141560.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G0679 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-19   69.3   0.1      6e-19   68.4   0.1    1.5  1  rve            Integrase core domain
    6.1e-18   64.4   0.2    1.5e-17   63.1   0.2    1.7  1  rve_3          Integrase core domain
    3.2e-11   43.2   1.2    7.2e-11   42.1   1.2    1.5  1  HTH_21         HTH-like domain
    1.3e-05   25.3   1.2      5e-05   23.4   1.2    2.1  1  rve_2          Integrase core domain
     0.0054   16.9   0.8     0.0054   16.9   0.8    1.8  2  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.096   13.3   0.3      0.096   13.3   0.3    1.8  2  HTH_32         Homeodomain-like domain
        0.2   11.5   0.5       0.34   10.7   0.1    1.6  2  Calici_MSP     Calicivirus minor structural protein
       0.38   11.1   3.5         15    6.0   0.1    3.6  3  NUMOD1         NUMOD1 domain
       0.54   10.5   6.3        1.7    8.8   0.1    3.1  3  Alpha_Helical  Alpha helical domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.1     3e-22     6e-19       5     118 ..     113     227 ..     109     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 3e-22
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve...pervlsDngsey 78 
                                       ++lw++D+ +v+  + +g +yl +v d+fs++ + +  s+  +a+++++ +e+a+a +        +++++Dng++y
  gi|518652040|ref|YP_008141560.1| 113 NQLWETDIHYVS--THNGMYYLMAVKDCFSKRWISYNFSRTCTAKDCVKPIEEAYAIRYSNSnlsNLVLRTDNGTQY 187
                                       99**********..66667*************************************999988999************ PP

                               rve  79 tskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++k+f+++++ l+i++++ +++ p+dnG +E+fh  lk++
  gi|518652040|ref|YP_008141560.1| 188 IAKSFKDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTD 227
                                       *************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.2   7.7e-21   1.5e-17       2      67 .]     200     265 ..     199     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 7.7e-21
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLgykTP 67 
                                        i+++yi+  +P +Ng +Esf+++l++ ++ ++  +s ++a+e++e ++ dYN+ RPHss+gy+TP
  gi|518652040|ref|YP_008141560.1| 200 NIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYAFNDYNNYRPHSSIGYLTP 265
                                       699**************************************************************9 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.2   3.6e-14   7.2e-11      17      59 ..      56      97 ..      42      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.6e-14
                            HTH_21 17 skgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59
                                      ++ +YG+rriwa Lr+e gv++n k+VrR+ +  +L+ ++ + 
  gi|518652040|ref|YP_008141560.1| 56 KRVTYGHRRIWAVLRNE-GVKINIKTVRRIIKSRNLQLPYAKH 97
                                      346**************.789***************9998875 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   2.5e-08     5e-05       1      50 [.     218     271 ..     218     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkR....lkglsPvqYrnq 50 
                                       Esf  sLKt+ + +   ++ e ++ ++ +Y    YNn R    +++l+Pv++++q
  gi|518652040|ref|YP_008141560.1| 218 ESFHNSLKTDYIWQNDLESYEDAK-ELMEYAFNdYNNYRphssIGYLTPVEFEKQ 271
                                       9**************999999876.677886555*****888888********98 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   2.7e-06    0.0054       4     139 ..     116     257 ..     113     258 .. 0.81
   2 ?   -3.9   0.3       7.3   1.5e+04      92     108 ..     280     296 ..     266     302 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                     DDE_Tnp_IS240   4 wrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrka..lkkek..lepeeivtDkasay.asal 74 
                                       w+ D  yv  +   +Yl ++ D  ++  + + +s    +k + + ++ a  ++ ++  l++ ++ tD    y a+ +
  gi|518652040|ref|YP_008141560.1| 116 WETDIHYVSTHNGMYYLMAVKDCFSKrWISYNFSRTCTAKDCVKPIEEAyaIRYSNsnLSNLVLRTDNGTQYiAKSF 192
                                       7777788888888889988889888879999999999999888888875224544455999*****97766636788 PP

                     DDE_Tnp_IS240  75 kelkregelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                       k   r  +  +e  + q++  n  iEs h+ lK  +  ++ ++s + a++ ++     +n +++h
  gi|518652040|ref|YP_008141560.1| 193 KDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYAFNDYNNYRPH 257
                                       888887777777788899999*****************************999877777777776 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.3
                     DDE_Tnp_IS240  92 vkylnnriEsdhrtlKk 108
                                        k l +r+ ++ r+lK 
  gi|518652040|ref|YP_008141560.1| 280 NKFLEDRMKREERRLKS 296
                                       33555555555555554 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.8e-05     0.096      25      73 .]      37      85 ..      20      85 .. 0.85
   2 ?   -3.3   0.1       7.1   1.4e+04      21      22 ..     291     292 ..     274     305 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                            HTH_32 25 rpr.klsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      +++ ++++ +  r++++  ++ +++ r++ a l + egvk+   tv+ri+
  gi|518652040|ref|YP_008141560.1| 37 HKKsRIPENTINRVLEISGKRVTYGHRRIWAVL-RNEGVKINIKTVRRII 85
                                      34449*************55559**********.9999**********96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.1
                            HTH_32  21 pr 22 
                                       +r
  gi|518652040|ref|YP_008141560.1| 291 ER 292
                                       22 PP

>> Calici_MSP  Calicivirus minor structural protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.34      37     129 ..       8      98 ..       3     113 .. 0.75
   2 ?   -3.6   0.1       4.2   8.4e+03      37      54 ..     279     296 ..     273     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        Calici_MSP  37 qnelletllkkqealqksqleltrdlsinapaarvlsaldaGldevsarrlagsGerviwgnldrpimh..agtmds 111
                                       +n+l  + + k+  +q+s +   r ++++ +++r+  +  + ++e+s +r++  G+r iw  l    ++    t+  
  gi|518652040|ref|YP_008141560.1|   8 RNKLSVSRFSKITGIQRSYIYYNRKITVKHKKSRIPENTINRVLEISGKRVT-YGHRRIWAVLRNEGVKinIKTVRR 83 
                                       57777778899***************************************96.6999***99976544300334444 PP

                        Calici_MSP 112 irqtrhldslshslatfk 129
                                       i ++r    l    a  k
  gi|518652040|ref|YP_008141560.1|  84 IIKSRN---LQLPYAKHK 98 
                                       444444...344444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.2
                        Calici_MSP  37 qnelletllkkqealqks 54 
                                       +n+ le  +k+ e   ks
  gi|518652040|ref|YP_008141560.1| 279 RNKFLEDRMKREERRLKS 296
                                       689999999998876555 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.04        79      18      35 ..      12      29 ..      12      29 .. 0.93
   2 ?    6.0   0.1    0.0076        15      18      35 ..     191     208 ..     190     208 .. 0.87
   3 ?   -1.8   0.1       2.1   4.3e+03      23      31 ..     296     304 ..     296     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                            NUMOD1 18 SireAakyLgishntInk 35
                                      S+++++k+ gi +++I++
  gi|518652040|ref|YP_008141560.1| 12 SVSRFSKITGIQRSYIYY 29
                                      8999************86 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                            NUMOD1  18 SireAakyLgishntInk 35 
                                       S +++ + L+i+h +I+k
  gi|518652040|ref|YP_008141560.1| 191 SFKDTVRLLNIKHEYIKK 208
                                       66788899********97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                            NUMOD1  23 akyLgishn 31 
                                       +++++is++
  gi|518652040|ref|YP_008141560.1| 296 SRKINISRR 304
                                       6899***97 PP

>> Alpha_Helical  Alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.047        94      18      46 ..      79     107 ..      74     116 .. 0.83
   2 ?    8.8   0.1   0.00086       1.7      18      75 ..     190     247 ..     185     251 .. 0.94
   3 ?   -0.3   0.2      0.57   1.1e+03      84     104 ..     275     295 ..     271     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.047
                     Alpha_Helical  18 elferivegaklrgkwnkkkalelakeme 46 
                                       ++ +ri+++++l+ ++ k+k ++ +++++
  gi|518652040|ref|YP_008141560.1|  79 KTVRRIIKSRNLQLPYAKHKNRTNKRNLT 107
                                       56789***************999999886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00086
                     Alpha_Helical  18 elferivegaklrgkwnkkkalelakemeselqslkysylepedLakseevkklkeka 75 
                                       + f+ +v+  +++ ++ kk++ e   ++es  +slk  y+  +dL + e++k+l e+a
  gi|518652040|ref|YP_008141560.1| 190 KSFKDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYA 247
                                       57999*************************************************9875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.57
                     Alpha_Helical  84 geewsekfleeaekeekekte 104
                                       +ee+ +kfle+  k+e+++++
  gi|518652040|ref|YP_008141560.1| 275 SEEFRNKFLEDRMKREERRLK 295
                                       68999*****99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2529.02
//
Query:       gi|518652041|ref|YP_008141561.1|  [L=91]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-11   44.3   0.0    2.5e-11   43.7   0.0    1.3  1  HTH_Tnp_1     Transposase
    9.3e-07   28.8   0.0    1.5e-06   28.1   0.0    1.4  1  HTH_29        Winged helix-turn helix
    0.00016   21.7   0.0    0.00024   21.1   0.0    1.4  1  HTH_28        Helix-turn-helix domain
      0.004   16.9   0.0     0.0064   16.3   0.0    1.4  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.016   15.3   0.0       0.02   15.0   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa
      0.067   13.7   0.0      0.075   13.6   0.0    1.2  1  LZ_Tnp_IS481  leucine-zipper of insertion element IS481


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   8.5e-15   2.5e-11       6      74 ..       3      73 ..       1      74 [. 0.82

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.5e-15
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++++ +K++iV es  ++ +++e++rrhgvs +++ykWr ++    ++   +  ++   + ++en++lkr++
  gi|518652041|ref|YP_008141561.1|  3 KFTPDEKVAIVMES-FTSNNIAELCRRHGVSVASFYKWRDKFIesgKKGFYESGRSGENEYQKENEKLKRLV 73
                                      8*************.7899***********************866533333333357789999999999876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   5.2e-10   1.5e-06      14      51 ..      21      58 ..      10      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.2e-10
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                      +++++++++g+s  ++y+w++ f e G ++  ++ rsg
  gi|518652041|ref|YP_008141561.1| 21 NIAELCRRHGVSVASFYKWRDKFIESGKKGFYESGRSG 58
                                      89*****************************9977777 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.2e-08   0.00024       5      44 ..      12      51 ..       8      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.2e-08
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegGiagL 44
                                      i+++    ++++e++r++g+s  + y+W+ ++ e G  g 
  gi|518652041|ref|YP_008141561.1| 12 IVMESFTSNNIAELCRRHGVSVASFYKWRDKFIESGKKGF 51
                                      55555556799***********************997765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0064      20      45 ..      22      47 ..      10      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                      ++e +r++gvs    y+w+ ++ e+G
  gi|518652041|ref|YP_008141561.1| 22 IAELCRRHGVSVASFYKWRDKFIESG 47
                                      7899******************7676 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.8e-06      0.02      20      54 ..      13      45 ..       8      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                                      HHHHH--S-HHHHHHHHTS-HHHHHHHHH-HHHHH CS
                       HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWkkkkeFie 54
                                      v + +    ++e+++  gvs + +ykW++k  Fie
  gi|518652041|ref|YP_008141561.1| 13 VMESFTSNNIAELCRRHGVSVASFYKWRDK--FIE 45
                                      5567888899******************86..665 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05     0.075      25      59 ..      19      53 ..       5      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                      LZ_Tnp_IS481 25 rrtvaqvarelGvslrtaykwlarfraeGldGlld 59
                                         +a+ +r  Gvs  + ykw ++f   G +G+ +
  gi|518652041|ref|YP_008141561.1| 19 SNNIAELCRRHGVSVASFYKWRDKFIESGKKGFYE 53
                                      35689999*********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.29s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 591.76
//
Query:       gi|518652042|ref|YP_008141562.1|  [L=78]
Description: hypothetical protein FACI_IFERC00001G0681 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       204  (0.0113782); expected 358.6 (0.02)
Passed bias filter:                      186  (0.0103743); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 551.96
//
Query:       gi|518652043|ref|YP_008141563.1|  [L=59]
Description: hypothetical protein FACI_IFERC00001G0682 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      162  (0.00903564); 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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.42
# Mc/sec: 422.80
//
Query:       gi|518652044|ref|YP_008141564.1|  [L=283]
Description: hypothetical protein FACI_IFERC00001G0683 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   15.1   6.4       0.29   11.3   0.4    2.2  2  GxGYxYP_N  GxGYxY sequence motif in domain of unknown functio


Domain annotation for each model (and alignments):
>> GxGYxYP_N  GxGYxY sequence motif in domain of unknown function N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   1.0   0.00034       6.1     172     216 .]      43      90 ..      16      90 .. 0.89
   2 ?   11.3   0.4   1.6e-05      0.29      32     101 ..     146     218 ..     118     253 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00034
                                       HTS-TT-EEEE-TTS....HHHHHHHHHHTT-EEEE-TT---HHHHTT CS
                         GxGYxYP_N 172 skmpkgaivlGWgpds...EgagVslaseygvstvasdwasNlSvlSs 216
                                       s+m++  +  G++ ++   + +g+ +++  +  + ++++++N+Sv Ss
  gi|518652044|ref|YP_008141564.1|  43 SSMNYICSTSGYTYSQdysHSNGIGKTTISNTTVSPATYYYNVSVSSS 90 
                                       67888888999998888889999**********************986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 1.6e-05
                                       HHHHH..---EEEESSHHHHHHHHHH.---EEEEETTT..T--HHHHHHHHHHHHTEEEEEGG.GHHHHHHTT- CS
                         GxGYxYP_N  32 lkknygvtveskelkdlasllkkfkn.eidgyVlydpa..kdeslnvAltiAalenaivvtes.llelakelgl 101
                                       +  ny++tv++++  +++   + f   +++ yV+ + +  ++ +   A++++ +  ai ++++ ++ l  ++++
  gi|518652044|ref|YP_008141564.1| 146 Y-GNYNYTVNYSKAIQFSYYKTAFGTvKATEYVISEHEitSNSTPSTAASYCNVTGAIYISSAtNVILSLNANV 218
                                       3.68999******99**99999999889*******66666999*****************99943333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       787  (0.0438954); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1830.43
//
Query:       gi|518652045|ref|YP_008141565.1|  [L=462]
Description: hypothetical protein FACI_IFERC00001G0684 [Ferroplasma acidarmanus fer1]
Scores for complete 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   68.0  59.1      1e-18   67.4  59.1    1.2  1  AA_permease_2  Amino acid permease
    2.9e-07   29.5  53.4    4.3e-07   28.9  53.4    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 !   67.4  59.1   1.1e-22     1e-18       3     423 ..      19     445 ..      18     457 .. 0.78

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 1.1e-22
                     AA_permease_2   3 llsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                       ++++ al+++sv+ +++++++    a + g ++i+ ++i+  i+ l  ++++  +  + p+ g  y+++ ++ +k+ 
  gi|518652045|ref|YP_008141565.1|  19 FIDLSALSTSSVAPAFSIAASygvIAMYLGFYSIMAIIITFPIW-LGAAILFRKFNRLYPSAGASYHWGNKIVSKRY 94 
                                       67788999999999999988666555567777777666666666.4455566788888******************* PP

                     AA_permease_2  77 aflsawfnwfayvpvlasilsvaasyllnalgp......dlqgntwltyliaiaililvalinirgikesakiqnil 147
                                       ++l aw+ ++ay+++++ i++ a++y + +l+       +++ +t++++l+++a ++++ + +i+g + +a+++ i 
  gi|518652045|ref|YP_008141565.1|  95 GSLQAWIITLAYFFSIPPIVIPAGEYTAVLLYNtgiisySIYSSTVTIFLLGSAWILITLVASIMGARPTARLTEIF 171
                                       ***************************999987688888888889******************************** PP

                     AA_permease_2 148 gilkillpliiliilglitvdgggfsslstetdtffpngwpg......vllgllivlwsfdGfesaanvseevkk.k 217
                                        +l +  +++++ii++++++ g++ +   t    +f ++  +      ++l+++i++  +dG+e  ++ see  +  
  gi|518652045|ref|YP_008141565.1| 172 LVLEL-SIIAVFIIIAIYFLPGHTVN---TVSPGWFIGFGALlknpykFMLAFPIIATIMDGWEIDSYASEESFNrE 244
                                       *****.899****9***999888887...2233367775554243334599*********************66633 PP

                     AA_permease_2 218 dvpkai.figllivlvlyllvniaflgvvpddeianlsnlgsv.aalffeavggkvvaiivvilialsllgaintav 292
                                       + p ++ +igl+ v+ +yl++ ++++ + ++ ++  ls ++++ a++          + ++ i+++ s + ++   +
  gi|518652045|ref|YP_008141565.1| 245 KWPGTTgIIGLIAVFAIYLVT-MTLMDIETPMSL--LSASLDPlATWSHYIIP--QYSFVMDIAVIASTASSLWLTT 316
                                       555555055555566666555.555544444333..23333331455555544..4555666777778888888889 PP

                     AA_permease_2 293 igssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllas..saaynfllsvsslgliisyllli 366
                                       ++ sr  +a++r+  lP+ f  +n  ++sp++ +i+++i +  +  ++l+++  ++ +  lls+s ++l+  +++ +
  gi|518652045|ref|YP_008141565.1| 317 YILSRAWYAMSREHLLPKQFGYINkTRKSPYANLIIIMIAAESINAVMLFVPsiESFFAQLLSISGIFLMMEFGIDS 393
                                       99**********************77**************999999999999999********************** PP

                     AA_permease_2 367 igalilrkkrphlkrpgkilvaiigalfllfllvalffppkgpatqssliytiiltv 423
                                       +++++l+ +r++ + + ++ ++i ++ f+ f+++++f    g++t++ +i+++i+++
  gi|518652045|ref|YP_008141565.1| 394 LTGIYLYSHRKNVNMKHIY-LGISIFSFTGFFVMIMF----GIVTNTLFIILVIILI 445
                                       ************9776644.66666666666666666....3456666655544443 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9  53.4   4.8e-11   4.3e-07      31     436 ..      51     445 ..      23     456 .. 0.73

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 4.8e-11
                       AA_permease  31 allayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasiliqfwelv 107
                                        + a+++++ + + +++ +  +  ++p++g+ y++  + ++++ G   +++  + +++ ++  ++ a+ +   + ++
  gi|518652045|ref|YP_008141565.1|  51 SIMAIIITFPIWLGAAILFRKFNRLYPSAGASYHWGNKIVSKRYGSLQAWIITLAYFFSIPPIVIPAGEYTAVLLYN 127
                                       234444444455557777788888899************************55555555544444444333333355 PP

                       AA_permease 108 tdlpkawvt.........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkpnkgagfrfl 175
                                       t +++  ++         g+ ++++ l+ +++g++  ++   i++++ + +i+ fii+ i +l  g++ +   ++  
  gi|518652045|ref|YP_008141565.1| 128 TGIISYSIYsstvtifllGSAWILITLVASIMGARPTARLTEIFLVLELSIIAVFIIIAIYFL-PGHTVNT--VSPG 201
                                       555544444555556666*****************************************5444.4444444..1222 PP

                       AA_permease 176 gdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifYvlsll 252
                                                ++++   +    + + f+ +f+i++  ++G e+  ++++E+ + ek    ++  ++ +i++f + ++ 
  gi|518652045|ref|YP_008141565.1| 202 ---------WFIGF--GALLKNPYKFMLAFPIIATIMDGWEIDSYASEESFNREKWP--GTTGIIGLIAVFAIYLVT 265
                                       .........23333..233333689***************************99974..555555555555555555 PP

                       AA_permease 253 ligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdglaPkvlk 329
                                       +  + + +++ +ll++s+++        ++  ++  ++++ +++++++ ss+   +y+ sR+ y+++++ l+Pk ++
  gi|518652045|ref|YP_008141565.1| 266 MTLMDIETPM-SLLSASLDP----LATWSHYIIPQYSFVMDIAVIASTASSLWLTTYILSRAWYAMSREHLLPKQFG 337
                                       5555555555.567878888....6778888999******************************************* PP

                       AA_permease 330 kvsk.rgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl.rfRkalkyqgrsieel 404
                                       +++k r++P++ +++ mi++  +  ++ + ++ ++ f+ ll+is++  ++ +++ +l+ +  +   ++++ ++i  l
  gi|518652045|ref|YP_008141565.1| 338 YINKtRKSPYANLIIIMIAAESINAVMLFVPSIESFFAQLLSISGIFLMMEFGIDSLTGIyLYSHRKNVNMKHI-YL 413
                                       **996689***********999999999999999********************99998843333333444443.56 PP

                       AA_permease 405 gfkaallplgvilvlaaliiillilalyaylt 436
                                       g+ +  +  +++++++ +++ +l+  l+++l+
  gi|518652045|ref|YP_008141565.1| 414 GISIFSFTGFFVMIMFGIVTNTLFIILVIILI 445
                                       66666666555555555555555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (462 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3144.71
//
Query:       gi|518652046|ref|YP_008141566.1|  [L=137]
Description: hypothetical protein FACI_IFERC00001G0685 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.3   5.4      0.058   12.8   5.4    1.2  1  GPI2           Phosphatidylinositol N-acetylglucosaminyltrans
       0.61    8.3  17.9        0.7    8.1  17.9    1.0  1  DUF2070        Predicted membrane protein (DUF2070)
       0.72    9.4  15.5       0.22   11.1  13.0    1.4  1  Bac_rhodopsin  Bacteriorhodopsin-like protein
        1.3    8.4  10.1        1.7    8.1  10.1    1.1  1  MTABC_N        Mitochondrial ABC-transporter N-terminal five 


Domain annotation for each model (and alignments):
>> GPI2  Phosphatidylinositol N-acetylglucosaminyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   5.4   1.3e-05     0.058     194     275 ..      16     113 ..      13     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                              GPI2 194 VFslllfsievfglfPvfrrslrhrswrlhvvltvllvllagagvgiilk..............lllavvlllllal 256
                                       +F ++   + v++lf v+r++l + s++ +++++++++l  +++++  l               +++++++ l + +
  gi|518652046|ref|YP_008141566.1|  16 IFYIISWGMLVYILFLVYRKYLPESSTKKSILFSTVITLSILILLYYPLYdiyllttkdmfplgITGLIIVYLNISV 92 
                                       588999999**************999999888777777766666665555688899********6666655555555 PP

                              GPI2 257 imgv..cpwwliglqkyknei 275
                                       i+g+  +++++i l +yk  +
  gi|518652046|ref|YP_008141566.1|  93 IIGFasLSIIYITLDNYKAAL 113
                                       555501556666777999865 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  17.9   0.00016       0.7      97     198 ..      11     128 ..       1     131 [. 0.82

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00016
                           DUF2070  97 qalvllalvlslalvfalrllvlvavsde.sllkavlpaliqpllailllvly...............fspesflll 157
                                         +++ ++++s+ + + + +lv+  +  e s++k++l +++++l++++ll++                  +  ++++
  gi|518652046|ref|YP_008141566.1|  11 FIYLIIFYIISWGMLVYILFLVYRKYLPEsSTKKSILFSTVITLSILILLYYPlydiyllttkdmfplGITGLIIVY 87 
                                       336778899999999999999998877651566777888888888777777779***********999557789999 PP

                           DUF2070 158 lllslifalavylfivvvdrplkrnlgvsaldllsaFlahi 198
                                       l +s+i++ a++ +i++   ++k++l++++l  +  Fl+  
  gi|518652046|ref|YP_008141566.1|  88 LNISVIIGFASLSIIYITLDNYKAALKIGGLTSVVLFLYMN 128
                                       9*************************************865 PP

>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1  13.0   4.8e-05      0.22     114     215 ..       4     103 ..       1     112 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.8e-05
                                       HHHHHTSHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTSTHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTTTSS.C CS
                     Bac_rhodopsin 114 lvgaliestyrwvyftisvaallvvlylllgelaraakslsserrslfntLrnlvvvlwilYpvawllgeeGngi.q 189
                                       l g +++ +y  ++++is  +l+++l l++   ++ + ++s++   lf+t + l +++++ Yp+  +    +    +
  gi|518652046|ref|YP_008141566.1|   4 LYGLITGFIYLIIFYIISWGMLVYILFLVY---RKYLPESSTKKSILFSTVITLSILILLYYPLYDIYLLTTKDMfP 77 
                                       667788889999999999999999999999...7777777777778999999999999999999655555555788* PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCC CS
                     Bac_rhodopsin 190 pdveavvygilDlvtkvgfglillaa 215
                                        +++ +++++l + +++gf+ + + +
  gi|518652046|ref|YP_008141566.1|  78 LGITGLIIVYLNISVIIGFASLSIIY 103
                                       *******************9876554 PP

>> MTABC_N  Mitochondrial ABC-transporter N-terminal five TM region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1  10.1   0.00038       1.7      25     142 ..      14     128 ..       5     135 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00038
                           MTABC_N  25 tlvssvllgllllfgtlqlilyrkygtelepkaiprsrlyklqlvlallllllalarlilraallksgev..ygyli 99 
                                        ++  +++  +l++  +  ++yrky   l +++ ++s l++  ++l++l+ll + +  i+  ++ +   +   g +i
  gi|518652046|ref|YP_008141566.1|  14 LIIFYIISWGMLVY--ILFLVYRKY---LPESSTKKSILFSTVITLSILILLYYPLYDIYLLTTKDMFPLgiTGLII 85 
                                       33333443333333..233458888...777888999999999999999999999998888888666554338**** PP

                           MTABC_N 100 lalvlsllawlfsllllllerrkllpslptrgHglvlLlfwtl 142
                                       ++l +s+++   sl ++++   +  + l+  g   v+L++++ 
  gi|518652046|ref|YP_008141566.1|  86 VYLNISVIIGFASLSIIYITLDNYKAALKIGGLTSVVLFLYMN 128
                                       *************999999999999899889887777777763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       936  (0.0522059); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.67
# Mc/sec: 619.93
//
Query:       gi|518652047|ref|YP_008141567.1|  [L=56]
Description: hypothetical protein FACI_IFERC00001G0686 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 365.19
//
Query:       gi|518652048|ref|YP_008141568.1|  [L=426]
Description: hypothetical protein FACI_IFERC00001G0687 [Ferroplasma acidarmanus fer1]
Scores for complete 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-149  496.8   0.0   5.6e-149  496.6   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  496.6   0.0  3.1e-153  5.6e-149       2     419 .]       4     420 ..       3     420 .. 0.95

  Alignments for each domain:
  == domain 1  score: 496.6 bits;  conditional E-value: 3.1e-153
                                       EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHH CS
                   Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealle 78 
                                       v++G+q+GDEGKGki+D++++++d vvRf+GG+nAGHtvv++g+k+k+hl+pSG++++++v ++Gng+v+dpe+l++
  gi|518652048|ref|YP_008141568.1|   4 VILGLQFGDEGKGKITDFVSRDYDEVVRFNGGSNAGHTVVIKGEKFKFHLVPSGAMQSNKV-ILGNGMVIDPEELVS 79 
                                       89******************************************************97776.*************** PP

                                       HHTTSS-TT......TEEEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHH CS
                   Adenylsucc_synt  79 EieeleakgvelskerllisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeel 155
                                       E++ l++++ ++   +++is+ ah+v+++hk lDk ee+ ++k +iGtT +GiGp+y+dk+ar+gir+ dl ++e +
  gi|518652048|ref|YP_008141568.1|  80 ELDLLKKSKKDI---EIKISAGAHIVTKMHKCLDKKEEEIRSKLNIGTTSQGIGPTYEDKYARTGIRFIDLSNPEII 153
                                       ******987766...8************************9999********************************* PP

                                       HHHHHHHHHHTHHHHHHT....T-----HHHHHHHHHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSS CS
                   Adenylsucc_synt 156 eeklekllelknkllekldk.eeleveelleellkyaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGt 231
                                       ++k+e+++++k++ll+     ++ e ++++++l  + + + +y+  t++++n+ ++ gk++LfEGaqg +lDid+G 
  gi|518652048|ref|YP_008141568.1| 154 KDKIETIYNMKKQLLKGSIFeNPEERAKMVKDLCGFGNSIMQYMDYTENVINNDYRLGKNILFEGAQGGMLDIDFGI 230
                                       *************9987533355556789************************************************ PP

                                       TTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHHHHHHHHHTT-B-TTT--B-EEE-EE CS
                   Adenylsucc_synt 232 YPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdevgeklrekGkEfgtttgrpRrcGwlD 308
                                       YPfvTsSnt+ag   tg+g++ +k+d+v+gv+KAyt++vG+Gpfp+e+ ++   +lr+ G+E+gtttgrpRr+GwlD
  gi|518652048|ref|YP_008141568.1| 231 YPFVTSSNTLAGALSTGSGFSFRKVDRVIGVFKAYTSKVGSGPFPSEIIGDS--TLRDLGSEYGTTTGRPRRVGWLD 305
                                       ***********************************************84444..9********************** PP

                                       HHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEEETTEEESS--S.....-GEEEEEEEEE--.S--TT-.... CS
                   Adenylsucc_synt 309 lvllryavrvngvtelaltklDvldgldeikvcvaYkldgkeldefpasleelekvepvyeelpgWkedisgv.... 381
                                       l+ll+y++++n v++la+tk+D+l ++++i+++++Y++dgke+d+fp +l+++ek+++ y elpgW  di++     
  gi|518652048|ref|YP_008141568.1| 306 LPLLKYTIMMNDVDSLAITKVDILGKMKTIEIATKYTIDGKEIDYFPRRLDDFEKLHVDYVELPGW-GDIENPddii 381
                                       ******************************************************************.4555433336 PP

                                       .--GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-EE CS
                   Adenylsucc_synt 382 .rsfedlpenakkyvefieellgvpvkiisvGpereqti 419
                                        + +++lpen+kky+efiee +g  ++iis+G++r  ti
  gi|518652048|ref|YP_008141568.1| 382 aNGYQALPENMKKYIEFIEEKTGKTIDIISLGEDRRMTI 420
                                       799********************************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); 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: 0.58u 0.33s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2630.61
//
Query:       gi|518652049|ref|YP_008141569.1|  [L=234]
Description: hypothetical protein FACI_IFERC00001G0688 [Ferroplasma acidarmanus fer1]
Scores for complete 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-57  192.7   0.6    5.1e-57  192.4   0.6    1.1  1  Proteasome      Proteasome subunit
    2.3e-14   52.7   0.1    3.8e-14   52.0   0.1    1.4  1  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 !  192.4   0.6   5.7e-61   5.1e-57       1     189 [.      31     214 ..      31     215 .. 0.97

  Alignments for each domain:
  == domain 1  score: 192.4 bits;  conditional E-value: 5.7e-61
                                       HHHS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEEETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSS CS
                        Proteasome   1 vkkGttvvGikgkdgvvlaadkratagskllskstveKifkiddhigvafaGlaaDartlvrraraeaqlyrlrygr 77 
                                       vkkG+t++Gik+kdgv+l ++k+a   s l++k+++eKi  +dd+++ +++Gl+aDar+l+++ar+ aq+++++yg 
  gi|518652049|ref|YP_008141569.1|  31 VKKGSTALGIKFKDGVLLLSEKKAR--SRLVEKNSLEKIQLVDDNVATVTSGLVADARVLIDFARVGAQQEKVTYGS 105
                                       79***********************..************************************************** PP

                                       GTCHHHHHHHHHHHHHHHHHHCTTTTTSEEEEEEEEETTTEEEEEEEETTSEEEEESSEEEESTTHHHHHHHHHHHH CS
                        Proteasome  78 pipverlvarvaaklqaytqrsgrrpfgvslliagvdeeggpeLyqidpsGsyieekdavaiGsgseaaktalekey 154
                                         ++e+lv++va+++q+ytq +g+rp+gvs+++ag d  g p+L+ +dp+G++ e+k  vaiG g++a++ ++ekey
  gi|518652049|ref|YP_008141569.1| 106 LTNIENLVKKVADQMQQYTQFGGVRPYGVSIIFAGTDTIG-PRLFDCDPAGTINEYK-SVAIGAGKDAVTDYIEKEY 180
                                       *************************************777.***************8.******************* PP

                                       STTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEE CS
                        Proteasome 155 kedltleeavelavkalkealerdklsgknievav 189
                                       k+d++le++++l v alk+al  d++s k+ e+a 
  gi|518652049|ref|YP_008141569.1| 181 KDDMSLEDTIKLGVAALKSALA-DASSMKEPEIAS 214
                                       *********************9.889999888875 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.0   0.1   4.2e-18   3.8e-14       1      23 []       8      30 ..       8      30 .. 0.99

  Alignments for each domain:
  == domain 1  score: 52.0 bits;  conditional E-value: 4.2e-18
                    Proteasome_A_N  1 YDrslttFSPdGRLfQVEYAmkA 23
                                      YDr++t+FSPdGRLfQVEYA +A
  gi|518652049|ref|YP_008141569.1|  8 YDRAITVFSPDGRLFQVEYAREA 30
                                      *********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1534.50
//
Query:       gi|518652050|ref|YP_008141570.1|  [L=276]
Description: molybdenum cofactor biosynthesis protein A [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   41.9   0.0    1.4e-10   41.0   0.0    1.5  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
       0.13   12.8   0.1       0.62   10.6   0.0    2.1  2  GDPD_2      Glycerophosphoryl diester phosphodiesterase famil


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 !   41.0   0.0   1.6e-14   1.4e-10      40     249 ..      57     264 ..       8     270 .. 0.72

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.6e-14
                                       GHHHHHHHHTT.TTTEEEEE---GGGGGC.......C.CCHHHHHHHH.HHCCCTSEEEEEEEEEET-CCCCCGHHH CS
                        TatD_DNase  40 dskavlelakkypnkvyavlGiHPnevde.......asedlleelkel.anvkhskvvaiGeiGLDyysreestkea 108
                                       ++ +v + ++++  + ++++G +P +          + e++ + ++ + + +   ++ a GeiG ++++++e+  + 
  gi|518652050|ref|YP_008141570.1|  57 ETIDVAKTVRNAGVDTVITIGPYPLDYFYfqsagkdPVEEMKRGIDMAaSIITAGNADAMGEIGYPHFPVDEKVYSD 133
                                       45577888888999999*******65555666777667777788999988899************************ PP

                                       HHHHHHHHHHHHHHTTEEEEEEEES-HH.HHHHHHHHCG.GCCS.EEEETT--S-HHHHHHHHHTTEEEEE-GGGGT CS
                        TatD_DNase 109 qeevFeeqlrlAkelklplviHlrkaee.dlleilkeaa.eaka.kvvlHsfsgsaeeakkflklgyyislsglltf 182
                                         +++e+ l++ ++++ pl++H+++ +e  +l+i +  +   ++ +v+ H+ + +          ++  s+++    
  gi|518652050|ref|YP_008141570.1| 134 SGTILEYALDVCHDHDIPLILHTEDMDEgGYLRIESLIKmHYGVdRVIKHHANATDI--------NFNDSITKSFIA 202
                                       *************************55546666666665444447******555544........455555553222 PP

                                       TTTHHHHHHHHHS-GGGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHH CS
                        TatD_DNase 183 knakelrelvkavpldrlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeN 249
                                        + ++++ +v     + +L+ETD  y ++k + gk+     v++ +e++ +l +   e + +i +e 
  gi|518652050|ref|YP_008141570.1| 203 -SRNNIKTAV--SSGKDFLLETD--YTDQKDKPGKVIPVYSVPKRAEMIKNLYENYDEIFHRIFEEV 264
                                       .122344444..356789*****..787766777999999999999999998876666556655555 PP

>> GDPD_2  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   6.9e-05      0.62       3      26 ..      43      75 ..      43      75 .. 0.76
   2 ?   -1.3   0.0      0.38   3.4e+03      19      25 ..     175     181 ..     173     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 6.9e-05
                            GDPD_2  3 rfWtt.......dd..eavwrelvgaGVdgInT 26
                                      +f+t+       ++   +v ++ ++aGVd ++T
  gi|518652050|ref|YP_008141570.1| 43 YFYTPeshyeklYRetIDVAKTVRNAGVDTVIT 75
                                      799996665555224477*************99 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.38
                            GDPD_2  19 aGVdgIn 25 
                                       +GVd+++
  gi|518652050|ref|YP_008141570.1| 175 YGVDRVI 181
                                       79**997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 1912.23
//
Query:       gi|518652051|ref|YP_008141571.1|  [L=225]
Description: hypothetical protein FACI_IFERC00001G0690 [Ferroplasma acidarmanus fer1]
Scores for complete 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   19.3   0.9     0.0023   18.4   0.9    1.4  1  Sld5            GINS complex protein
  ------ inclusion threshold ------
      0.077   12.5   0.5       0.18   11.3   0.2    1.8  2  SieB            Super-infection exclusion protein B
       0.15   12.6   2.4        4.4    7.9   0.5    3.0  3  EF-G-binding_N  Elongation factor G-binding protein, N-termin


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 !   18.4   0.9   3.8e-07    0.0023      27     109 .]      19     114 ..       8     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.8e-07
                                       HHHHHHCCCHHTTSSSSTTTTTTHHHHHHH.HHHHHT...................HCHHHHHHHHHHHHHHHHHHH CS
                              Sld5  27 pesleailedetkssdlpslpphflelavk.llelard..................ldelkrllrdllevRlakirk 84 
                                        e+l+a+l +e+ks  l  ++p+f++       el ++                  lde+++  ++++ vR +ki k
  gi|518652051|ref|YP_008141571.1|  19 LEDLKAMLFSERKSRKLNRIEPNFYKNIHSlFVELTEEkdrvvssditeymeitklLDEVRKNFKAFFQVRFEKIGK 95 
                                       699**********************9995545666654556666667777778888********************* PP

                                       THCHHHHHHHTS-TCCHCCS-HHHH CS
                              Sld5  85 faenledaagggggellsglseeEk 109
                                       ++ + ++ +     e l ++s+eEk
  gi|518652051|ref|YP_008141571.1|  96 YSVY-DEIE-----EYLYNMSPEEK 114
                                       *955.5555.....5999***9996 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.48   2.9e+03      66      87 ..      41      62 ..      26      74 .. 0.72
   2 ?   11.3   0.2     3e-05      0.18      54      93 ..      85     124 ..      69     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.48
                              SieB 66 reqkkvekklknLteeekavLr 87
                                       ++k++ + +  Ltee+  v++
  gi|518652051|ref|YP_008141571.1| 41 NFYKNIHSLFVELTEEKDRVVS 62
                                      4677777778888888777765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3e-05
                              SieB  54 llaeikekikkkreqkkvekklknLteeekavLreflnqg 93 
                                       +++   eki k   ++++e++l n+++eek++++e+ +q 
  gi|518652051|ref|YP_008141571.1|  85 FFQVRFEKIGKYSVYDEIEEYLYNMSPEEKNIMKELNAQM 124
                                       344445555588899*******************987775 PP

>> EF-G-binding_N  Elongation factor G-binding protein, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.28   1.7e+03      64      78 ..      11      25 ..       5      28 .. 0.80
   2 ?    4.1   0.2     0.011        68      38      81 ..      43      84 ..      33      86 .. 0.81
   3 ?    7.9   0.5   0.00074       4.4       6      60 ..      67     121 ..      65     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.28
                    EF-G-binding_N 64 tkekaeklLeeLkey 78
                                      + +k +klLe+Lk +
  gi|518652051|ref|YP_008141571.1| 11 DISKYDKLLEDLKAM 25
                                      5578899*****976 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.011
                    EF-G-binding_N 38 aekIlelfpelseeqkelLeqiddiktkekaeklLeeLkeyVip 81
                                       ++I  lf+el+ee+ + +   +di++  +++klL e ++  ++
  gi|518652051|ref|YP_008141571.1| 43 YKNIHSLFVELTEEKDRVV--SSDITEYMEITKLLDEVRKNFKA 84
                                      57899**********9999..56888888888888887766655 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.00074
                    EF-G-binding_N   6 qYnfIkkqveqllnayrsvnDkkvveavkalaaekIlelfpelseeqkelLeqid 60 
                                       +Y  I k ++++ + +++    +  +  k ++ ++I+e + ++s+e+k+++++++
  gi|518652051|ref|YP_008141571.1|  67 EYMEITKLLDEVRKNFKAFFQVRFEKIGKYSVYDEIEEYLYNMSPEEKNIMKELN 121
                                       7888888888888888888888888999999*******************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1540.48
//
Query:       gi|518652052|ref|YP_008141572.1|  [L=61]
Description: hypothetical protein FACI_IFERC00001G0691 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.046   13.8   1.4      0.052   13.7   1.4    1.2  1  E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
      0.073   14.0   2.2       0.21   12.5   2.2    1.6  1  THAP             THAP domain


Domain annotation for each model (and alignments):
>> E3_UbLigase_RBR  E3 Ubiquitin Ligase RBR C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.4   5.9e-06     0.052      29      67 ..       9      47 ..       1      57 [. 0.69

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-06
                   E3_UbLigase_RBR 29 kCkVleqketkegvkdeaCgkdvaegqaglCelHYkEyL 67
                                       C+   ++ +++ ++ ++   + ++ +  lC++HYkEy 
  gi|518652052|ref|YP_008141572.1|  9 GCNEKSFQTVPADLAGKVFSLKEEKTKVHLCKVHYKEYK 47
                                      45555555556666666666677788899********95 PP

>> THAP  THAP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.2   2.3e-05      0.21       1      68 [.       5      53 ..       5      60 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.3e-05
                              THAP  1 CavpgCknrkkkkskkkvsfhrfPkdeelrkkWlkaikrkdkkkkkkskksrvCskHFeeekkkkkke 68
                                      C v+gC++       k  sf ++P d     k     + k     ++++k ++C+ H++e kk++kke
  gi|518652052|ref|YP_008141572.1|  5 CEVKGCNE-------K--SFQTVPADL--AGKVF---SLK-----EEKTKVHLCKVHYKEYKKNTKKE 53
                                      88999998.......2..699999666..22222...222.....1123358******6553222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1404  (0.0783089); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 444.90
//
Query:       gi|518652053|ref|YP_008141573.1|  [L=256]
Description: glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-23   81.9   0.0      7e-23   81.3   0.0    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    8.8e-18   64.7   0.6    1.3e-09   37.9   0.0    2.4  2  Glyco_tranf_2_2  Glycosyltransferase like family 2
    3.5e-15   56.5   0.0    2.3e-13   50.6   0.0    2.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    1.6e-07   31.4   0.0      2e-07   31.1   0.0    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    0.00098   18.7   0.3     0.0025   17.4   0.2    1.8  1  Glyco_transf_7C  N-terminal domain of galactosyltransferase
  ------ inclusion threshold ------
      0.018   15.6   0.0       0.04   14.4   0.0    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.3   0.0   2.4e-26     7e-23       1     133 [.       5     135 ..       5     166 .. 0.86

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 2.4e-26
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s++i++ Neek+++ +  sl++q   + fe+ivvD  StD+t++il+e+a++++ v+++r++     +g++n g+++
  gi|518652053|ref|YP_008141573.1|   5 SAIITVLNEEKNIRDLMVSLISQ--EQPFEVIVVDSMSTDKTPKILKEYAEKYDFVKYYRKKTT--RGGGRNYGASK 77 
                                       78*********************..*************************************66..8899******* PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS....E CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv....g 133
                                       ++ dy++f+D D +  + w++ l +  ++  + +v+g+   ++ +++ +er k +    +
  gi|518652053|ref|YP_008141573.1|  78 SNYDYLAFIDGDAIAGESWIKNLRALTQN--YNLVAGKSINTGNMRYSMERFKLYyggfE 135
                                       **********************9777766..55699999999999999999888755441 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 !   37.9   0.0   4.4e-13   1.3e-09       1     105 [.       5     103 ..       5     124 .. 0.86
   2 !   25.1   0.1   3.5e-09   1.1e-05     164     230 ..     139     203 ..     124     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 4.4e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrG 76 
                                       s +i + ++e++  i++ +    ++ ++ +e+ivvd  S++k+ + ++   ++   v y++++     + +  rN G
  gi|518652053|ref|YP_008141573.1|   5 SAIITVLNEEKN--IRDLMVSLISQ-EQPFEVIVVDSMSTDKTPKILKEYAEKYDFVkYYRKK----TTRGGGRNYG 74 
                                       5799********..****9999999.899***********************99999777766....468899**** PP

                   Glyco_tranf_2_2  77 askaesdlvlFlDaDcfissDkfekilkl 105
                                       ask++ d++ F+D+D       ++++  l
  gi|518652053|ref|YP_008141573.1|  75 ASKSNYDYLAFIDGDAIAGESWIKNLRAL 103
                                       ***************98766555555554 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 3.5e-09
                   Glyco_tranf_2_2 164 ssssilinrraflevGGyDErfrGhgaEDfdlllRlakaikslekmpvellykarakslsnykGfrr 230
                                        ss+++  +  f  +GG+DE+f   +aED d+ +R  k   + ++  + + y +  + ++++k    
  gi|518652053|ref|YP_008141573.1| 139 PSSNLMYSKSLFQSIGGFDENF--VTAEDIDMNIRAVKSGAKYAVCDTCIVYTKTRETFRDFKKQAY 203
                                       5899999***************..99**********************************9886544 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   7.6e-17   2.3e-13       4     223 ..       4     201 ..       2     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 7.6e-17
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksraln 80 
                                       ++ +++++nee+ ++++  sl++q + ++ev+vv+ +s+++t + ++e a++++   v+++++ +    t++  + n
  gi|518652053|ref|YP_008141573.1|   4 ISAIITVLNEEKNIRDLMVSLISQ-EQPFEVIVVDSMSTDKTPKILKEYAEKYDF--VKYYRK-K----TTRGGGRN 72 
                                       789*******************98.899*************************66..588854.3....34555669 PP

                   Glyco_tranf_2_3  81 ealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpv.fllnrstlvsalgalefaerhlrflaarralg 156
                                        + +  ++d+++++D+D++ +   +k  l+++ t+++  v ++  ++ n ++ +          r+       +++g
  gi|518652053|ref|YP_008141573.1|  73 YGASKSNYDYLAFIDGDAIAGESWIKN-LRAL-TQNYNLVAGKSiNTGNMRYSME---------RFK-----LYYGG 133
                                       ************************999.6665.8999999977635556655555.........222.....46677 PP

                   Glyco_tranf_2_3 157 v.ltlnG.sgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikq 223
                                       + +  ++ s +++  ++++ ++g+d++f++++D+++  r+ + g + a++   +v++ +++++ ++ kq
  gi|518652053|ref|YP_008141573.1| 134 FeV-TRPsSNLMYSKSLFQSIGGFDENFVTAEDIDMNIRAVKSGAKYAVCDTCIVYTKTRETFRDFKKQ 201
                                       744.455589999*************************************************9999887 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 !   31.1   0.0   6.8e-11     2e-07      73     144 ..     139     209 ..      80     252 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.8e-11
                   Glyco_trans_2_3  73 vGsgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc 144
                                       + s+ + + s++q++gg+d  ++ ++ED dm +r+ + G +   ++  +v++k++ t+r++ +Q++   yG 
  gi|518652053|ref|YP_008141573.1| 139 PSSNLMYSKSLFQSIGGFD-ENFVTAEDIDMNIRAVKSGAKYAVCDTCIVYTKTRETFRDFKKQAYWNGYGR 209
                                       56999**************.77999*********************99*****************9888882 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 !   17.4   0.2   8.4e-07    0.0025      21      62 ..     140     179 ..     120     225 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 8.4e-07
                   Glyco_transf_7C  21 gGvlalrkedfekiNGfsntfwgWGgEDdelyaRlakkglei 62 
                                       + +l+++k+ f++i+Gf+++f     ED ++  R +k+g + 
  gi|518652053|ref|YP_008141573.1| 140 SSNLMYSKSLFQSIGGFDENFVT--AEDIDMNIRAVKSGAKY 179
                                       6789******************8..9************9883 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   1.3e-05      0.04      21      94 ..      32     102 ..      16     104 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                   Glyco_tranf_2_4  21 rilvydndstDgtrailkelpevkllhvdksyederrqvellkallaryaeadwvlvvDaDEflvvpdsrslra 94 
                                       +++v+d +stD+t +ilke++e   ++++k y+++ +    ++  + + ++ d+++++D D +   ++ ++lra
  gi|518652053|ref|YP_008141573.1|  32 EVIVVDSMSTDKTPKILKEYAE--KYDFVKYYRKKTTRGGGRNYGA-SKSNYDYLAFIDGDAIAGESWIKNLRA 102
                                       479****************844..4555555554444444444333.33567*******997766665555655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 1839.47
//
Query:       gi|518652054|ref|YP_008141574.1|  [L=215]
Description: DNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-18   65.8   0.0    4.8e-18   64.7   0.0    1.6  1  HTH_10      HTH DNA binding domain
  ------ inclusion threshold ------
      0.021   14.3   0.0      0.044   13.3   0.0    1.5  1  Sigma70_r4  Sigma-70, region 4
      0.043   13.8   0.4       0.13   12.2   0.0    2.1  2  HTH_36      Helix-turn-helix domain
       0.05   13.2   0.1       0.23   11.1   0.0    2.3  2  HTH_24      Winged helix-turn-helix DNA-binding
       0.27   10.9   1.5        1.1    9.0   0.3    2.7  2  CENP-B_N    CENP-B N-terminal DNA-binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.0   1.4e-21   4.8e-18       1      52 [.     157     208 ..     157     209 .. 0.98

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 1.4e-21
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       LT+ + +++++Ay++GY d+PR+++l+++A ++ Isk+t++ h+r+ae+k++
  gi|518652054|ref|YP_008141574.1| 157 LTPTEKKIIQEAYNSGYLDWPRTTSLDDIARRFSISKPTALLHIRNAEKKIL 208
                                       9*************************************************98 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.2e-05     0.044       4      36 ..     156     195 ..     154     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.2e-05
                                       HS-HHHHHHHHHHH.......TTT--HHHHHHHHTS-HHH CS
                        Sigma70_r4   4 sLpererevlelrf.......geglTleEIgerlgiSrer 36 
                                       +L++ e+++++  +        +  +l +I++r+ iS+ +
  gi|518652054|ref|YP_008141574.1| 156 RLTPTEKKIIQEAYnsgyldwPRTTSLDDIARRFSISKPT 195
                                       8****************999888889***********865 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         2   7.2e+03      18      38 ..      17      34 ..      12      37 .. 0.57
   2 ?   12.2   0.0   3.7e-05      0.13      20      52 ..     170     206 ..     156     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2
                            HTH_36 18 anknggcfpsqetlakrlgls 38
                                      +++n++   s+  +++ +++s
  gi|518652054|ref|YP_008141574.1| 17 STENNE---SKIIISNIYNMS 34
                                      345555...666677766666 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 3.7e-05
                            HTH_36  20 kngg.cfp...sqetlakrlglsknTvsraikeLeql 52 
                                       + g+  +p   s +++a+r+ +sk T+  +i++ e++
  gi|518652054|ref|YP_008141574.1| 170 NSGYlDWPrttSLDDIARRFSISKPTALLHIRNAEKK 206
                                       467779999889*******************999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.81   2.9e+03       9      20 ..     118     129 ..     118     131 .. 0.82
   2 ?   11.1   0.0   6.4e-05      0.23      18      44 ..     180     206 ..     157     206 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.81
                            HTH_24   9 LelLqknprisq 20 
                                       Lel++kn +i +
  gi|518652054|ref|YP_008141574.1| 118 LELIEKNNKIKY 129
                                       899999999875 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 6.4e-05
                            HTH_24  18 isqreLAerlglSpstvnrrlkrLeee 44 
                                       +s  ++A+r  +S++t + ++++ e++
  gi|518652054|ref|YP_008141574.1| 180 TSLDDIARRFSISKPTALLHIRNAEKK 206
                                       7889*******************9986 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.88   3.1e+03      18      33 ..      17      32 ..      16      37 .. 0.67
   2 ?    9.0   0.3    0.0003       1.1      21      51 ..     178     209 ..     153     211 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.88
                                      HHHCTT-HHHHHHHHT CS
                          CENP-B_N 18 rleegeSkaelarrfn 33
                                      + e +eSk  +   +n
  gi|518652054|ref|YP_008141574.1| 17 STENNESKIIISNIYN 32
                                      6788889976655555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0003
                                       CTT-HHHHHHHHT--CCH.HHHHHHCHHHHCC CS
                          CENP-B_N  21 egeSkaelarrfnvpest.lsdilknKkkllk 51 
                                       ++ S  ++arrf + + t l  i +++kk+l 
  gi|518652054|ref|YP_008141574.1| 178 RTTSLDDIARRFSISKPTaLLHIRNAEKKILS 209
                                       466889********97553789*******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1458.32
//
Query:       gi|518652055|ref|YP_008141575.1|  [L=345]
Description: hypothetical protein FACI_IFERC00001G0694 [Ferroplasma acidarmanus fer1]
Scores for complete 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-44  150.7   0.4    2.9e-43  148.3   0.4    1.9  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.4   1.6e-47   2.9e-43       4     264 .]       2     243 ..       1     243 [. 0.95

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 1.6e-47
                                       EEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHHHH CS
                         HMGL-like   4 ivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdika 80 
                                       ++d tLR+G q+++ a+s +ek+++ak  + ag++   v  p a + +fev+ ai++    +++ +l r +++di++
  gi|518652055|ref|YP_008141575.1|   2 LTDDTLREGMQTPGFAMSYDEKIELAKLISSAGIKRALVAYPPAHKSEFEVTAAIVDGKYFQQVFGLGRTVKEDIDM 78 
                                       6899************************************************************************* PP

                                       HHH....TT-S.EEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHHH CS
                         HMGL-like  81 avealkgagak.rvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaae 156
                                         e    +ga+ ++h+     +              + ++ e +k+a +lgk ve+++ d  + ++e++++ ++++e
  gi|518652055|ref|YP_008141575.1|  79 INE----TGANiSLHLPFKLDN--------------MGQVYENIKYACTLGKIVEIGFVDIDMFSVEQITKFCHKME 137
                                       ***....665413455555555..............8899999********************************** PP

                                       HHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBBB CS
                         HMGL-like 157 eaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraGn 233
                                       e++++ ++++Dt G ++P +++++++a k+ ++  ++++ HcHnd+G+Avant+ A+ aG+d +d+t++G Ger+G 
  gi|518652055|ref|YP_008141575.1| 138 ELNVDVVQLPDTRGKMNPAAIKNVFEAAKKATN--IKIEAHCHNDYGMAVANTISAISAGVDYIDTTIFGTGERNGI 212
                                       *********************************..****************************************** PP

                                       -BHHHHHHHHHHTT-B----HHHHHHHHHHH CS
                         HMGL-like 234 aaleelvaalealgvdtgldlqklrsiaalv 264
                                       a+  +l+  l + ++++ ld++ + ++ ++v
  gi|518652055|ref|YP_008141575.1| 213 ADSITLADYLMKNNLEKSLDIKGIIKAYNYV 243
                                       ************************9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2335.26
//
Query:       gi|518652056|ref|YP_008141576.1|  [L=372]
Description: hypothetical protein FACI_IFERC00001G0695 [Ferroplasma acidarmanus fer1]
Scores for complete 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-77  261.2   0.0    1.9e-77  260.9   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 !  260.9   0.0   1.1e-81   1.9e-77       5     355 ..       3     341 ..       2     348 .. 0.94

  Alignments for each domain:
  == domain 1  score: 260.9 bits;  conditional E-value: 1.1e-81
                      CoA_transf_3   5 rVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkr 81 
                                       rV++l+q++aGp+a+ ++Ad+G eVIkvE+p +gD  R ++      +++ f+ +nr+K+s+ lD+k++ g+e+l +
  gi|518652056|ref|YP_008141576.1|   3 RVIELGQIVAGPTAGLIFADMGFEVIKVEKPCSGDISRELTG----TSAGTFMYYNRGKKSLELDIKTDFGKEVLTK 75 
                                       9**************************************965....6789*************************** PP

                      CoA_transf_3  82 LvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvk 158
                                       L+ +AD+++eN+ pg+++++g++ye++++in r+iy+s++gy  +Gp+++r ++D  ++ +sGl+++tg++d+p ++
  gi|518652056|ref|YP_008141576.1|  76 LLSTADIIVENMAPGTMKKIGFSYEDVKKINSRIIYVSIKGYM-EGPYENRKSLDYPVEIESGLAYMTGTKDRP-MR 150
                                       ******************************************9.7*************************9998.** PP

                      CoA_transf_3 159 vgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyr 235
                                       +g +++D+v+++l++      +    ++ kG  +++ l+e+a+ l ++++++y  +++  e+ ++ ++a+ +y+++ 
  gi|518652056|ref|YP_008141576.1| 151 MGASIVDMVAAILGVTKSFQLI----SENKGGLVEIGLFETAMFLAGQHIATYQIEKKGLEPINEMNFAWGIYDYFM 223
                                       ************9987755444....667999*********************9999999999************** PP

                      CoA_transf_3 236 tkdg.wvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaap 311
                                        +d+  ++ia+atd+qw+++c+ +g ++l +d++f++n++r+ +r+ l  +++++l + + +e+ ++l+ +++  + 
  gi|518652056|ref|YP_008141576.1| 224 SSDNkKLFIAVATDDQWKKFCEGFGLESLIADEKFSSNNARYMHRDFLIPLIQKRLLSMNYEEIKNILDLYNISYGT 300
                                       ***************************************************************************** PP

                      CoA_transf_3 312 vntleevlddpqlaarglvvevddpdygevpvvglpvrlsetpa 355
                                       +n++ e+l+dpq     + +++++     ++v++lp+++++ + 
  gi|518652056|ref|YP_008141576.1| 301 LNKPWELLHDPQALNYMVNMNYNNNS---YEVPRLPFSVAQNNN 341
                                       ***********987666666665555...9******99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2396.27
//
Query:       gi|518652057|ref|YP_008141577.1|  [L=454]
Description: hypothetical protein FACI_IFERC00001G0696 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.9e-35  122.6  26.9    2.5e-35  122.2  26.9    1.1  1  Sugar_tr     Sugar (and other) transporter
    3.8e-33  114.9  32.9    1.1e-30  106.7  23.4    2.0  2  MFS_1        Major Facilitator Superfamily
     0.0032   16.8  22.0       0.11   11.7   4.2    2.2  2  MFS_4        Uncharacterised MFS-type transporter YbfB
      0.005   15.5  11.8      0.005   15.5  11.8    3.3  4  MFS_2        MFS/sugar transport protein
  ------ inclusion threshold ------
      0.037   13.8   0.9      0.037   13.8   0.9    4.3  3  DUF2157      Predicted membrane protein (DUF2157)
        4.5    7.3   4.9        5.7    6.9   0.1    3.1  2  DUF3377      Domain of unknown function (DUF3377)
        7.2    6.5   6.8        3.4    7.5   0.9    3.0  3  SP_C-Propep  Surfactant protein C, N terminal propeptide


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.2  26.9   9.7e-39   2.5e-35      46     451 ..      61     454 .]      24     454 .] 0.84

  Alignments for each domain:
  == domain 1  score: 122.2 bits;  conditional E-value: 9.7e-39
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                       v + ++  +f+ G ++G + +g l+d++GRkk++ +  ++f iga++ ++     ++ ++ v  +++Gig G++  l
  gi|518652057|ref|YP_008141577.1|  61 VSTYIMPTAFYSGMVVGTFAFGRLADIYGRKKIYFVNLLVFAIGAIIAGLMS---NYILIGVFMFIAGIGTGAEIPL 134
                                       334467788999****************************************...99******************** PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylv 199
                                         +yisE  +k+ Rg+   l  +  ++   ++a+  l +++++ ad wri+l +  v al++ ++++ + ESPr+l 
  gi|518652057|ref|YP_008141577.1| 135 GDTYISETMTKRNRGRRLALVYTIGVISAPLGAFWLLEMSNINLADSWRIFLIVLGVAALVFQVIRFRMKESPRWLE 211
                                       ***************999999889999999999999999999999******************************** PP

                                       HTT-HHHHHHHHHHHHHC..HHHHHHHHHHH.HHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHH CS
                          Sugar_tr 200 ekgkeeeakevlaklrge..edadrelaeek.dsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinai 273
                                       ++g++++a   +  +++e  +  ++++      +++ e+ +ek +w  l+++ + r+ +++++  q +q  +  + +
  gi|518652057|ref|YP_008141577.1| 212 SVGRYKDANNLMNSIEEEvmK--EKDISSLPpVENHTEVLKEKPKWIDLFDK-KLRKNTIMVIIFQYAQSGVF-FGF 284
                                       **************9999552..4444433212333333455899*******.66999999999999998776.667 PP

                                       HHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS... CS
                          Sugar_tr 274 myysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaa 348
                                       + + pt++   g+s    +l++ii+++   v ++v ++ +d++ R+    +G++    ++ i+gi++ + +++    
  gi|518652057|ref|YP_008141577.1| 285 TALVPTLLIAKGYSLAstFLFSIIIYMGFLVGSLVNLLYIDKLERK----IGVCLFVGLAGIFGIIFSIANNS---- 353
                                       778888888888887778****************************....66666666666666344444444.... PP

                                       CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHH CS
                          Sugar_tr 349 sivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfagl 425
                                       + ++++++++ ++l ++     +  + +E+fp+++R++++ +   +n +a+  + +l+ +++ + g   vf v ++l
  gi|518652057|ref|YP_008141577.1| 354 AEIVLFGFIVAFMLWNM--SNFFHQYQAEIFPTKLRGSGTGMGQGINAIASASVPTLIVVFVLSHGSLAVFSVLGIL 428
                                       45555666655567775..57899999******************************9999999999********** PP

                                       HHHHHHHHHHHS--STT--CCCCGGG CS
                          Sugar_tr 426 avlfiifvfffvpetkgrtleeieel 451
                                       +v++i+ +++f p t  r+le i+++
  gi|518652057|ref|YP_008141577.1| 429 VVITIVDIMLFGPKTSQRELESISNM 454
                                       **********************9875 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7  23.4   4.5e-34   1.1e-30       6     324 ..      35     374 ..      30     379 .. 0.77
   2 !   20.9   9.9   5.6e-08   0.00014      56     180 ..     324     447 ..     322     453 .. 0.83

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 4.5e-34
                             MFS_1   6 flsalarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                       f++++   ++g++l  +++e +++s ++    + t+++ g++v+++ +Grl+d +Gr++++++ ll+fa+g++++  
  gi|518652057|ref|YP_008141577.1|  35 FIITFLVLLVGSLLA-IISEVFHLSTDVSTYiMPTAFYSGMVVGTFAFGRLADIYGRKKIYFVNLLVFAIGAIIAGl 110
                                       555555566666777.88999998888755559999***********************************555555 PP

                             MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg......Wr 151
                                       + s++ l+ v+ +++G+g+ga +p+g ++i++  +k++rgr ++l+++   +G+i +pl + +l++  +      Wr
  gi|518652057|ref|YP_008141577.1| 111 M-SNYILIGVFMFIAGIGTGAEIPLGDTYISETMTKRNRGRRLALVYT---IGVISAPLGAFWLLEMSNinladsWR 183
                                       6.88889****************************************9...55555555566677666666888999 PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeee..............................kgtgpaplvp 198
                                          ++l++++l++ v   + ++ ++++r+ +s  + +                              + +++ ++++
  gi|518652057|ref|YP_008141577.1| 184 IFLIVLGVAALVFQV---IRFRMKESPRWLESVGRYKdannlmnsieeevmkekdisslppvenhteVLKEKPKWID 257
                                       666666666666655...666677777777776666699****99*9999999999999999988885555555555 PP

                             MFS_1 199 aw.kallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrr 274
                                       ++ k+l+k+  +  ++i  +  + +f+g+++l+p+ l    g+s l ++ l++ ++++++++++l+   ++d+l r+
  gi|518652057|ref|YP_008141577.1| 258 LFdKKLRKNTIM--VIIFQYAQSGVFFGFTALVPT-LLIAKGYS-LASTFLFSIIIYMGFLVGSLVNLLYIDKLERK 330
                                       440666666644..7777777788***********.5*******.89999889999999988888888888**9987 PP

                             MFS_1 275 rrlllallllllaalglallavtssavllllvlvliGf.glgfvfpsllal 324
                                       +   l+++l+ ++ +++ +++++       + +vl+Gf  +++ + +++ +
  gi|518652057|ref|YP_008141577.1| 331 IGVCLFVGLAGIFGIIFSIANNS-------AEIVLFGFiVAFMLWNMSNFF 374
                                       77777777777777777777777.......666777774444446665554 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5.6e-08
                             MFS_1  56 sdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfsl 132
                                       +d++ r+  ++l + l +++++++++a+++  ++++ ++ +++   +    + + a++fp + rg+++g+ ++ +++
  gi|518652057|ref|YP_008141577.1| 324 IDKLERKIGVCLFVGLAGIFGIIFSIANNSAEIVLFGFIVAFMLWNMSNFFHQYQAEIFPTKLRGSGTGMGQGINAI 400
                                       79996666555555555566566666466559********************************************* PP

                             MFS_1 133 GailgpllggllasslgWravfyilaivsllafv.lfllllpeepperk 180
                                       +++  p l  +++ s g  avf +l+i+ ++ +v +  +l+  + ++r+
  gi|518652057|ref|YP_008141577.1| 401 ASASVPTLIVVFVLSHGSLAVFSVLGILVVITIVdI--MLFGPKTSQRE 447
                                       *************99999**************9965..77766666555 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   4.2   4.5e-05      0.11     238     342 ..      73     175 ..      42     201 .. 0.81
   2 !   10.9   9.9   8.1e-05      0.21      10     168 ..     282     439 ..     280     452 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.5e-05
                             MFS_4 238 aaivgvlvwlrvakrsglrralaaallieavgvllsllspsplglivssvllGltflaitalvlqlarelappat.r 313
                                       +++vg+++  r+a+  g ++++ ++ll+ a+g++++ l+  ++++ v   + G  + a ++l+ +++ e + + +  
  gi|518652057|ref|YP_008141577.1|  73 GMVVGTFAFGRLADIYGRKKIYFVNLLVFAIGAIIAGLMSNYILIGVFMFIAGIGTGAEIPLGDTYISETMTKRNrG 149
                                       678999*************************9988888777777777777889999999999999999998877733 PP

                             MFS_4 314 rllglmTasfgigQilGpllasllaeatg 342
                                       r    + +++ ig i +pl a +l e+++
  gi|518652057|ref|YP_008141577.1| 150 RR---LALVYTIGVISAPLGAFWLLEMSN 175
                                       44...556799***********9999876 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.1e-05
                             MFS_4  10 FsytpiLPallaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaafll 86 
                                       F +t ++P ll ++++sl+   l   + y+G+LvG+l+ +    + + ++++   + ++ +  +  +++++ a +  
  gi|518652057|ref|YP_008141577.1| 282 FGFTALVPTLLIAKGYSLASTFLFSIIIYMGFLVGSLVNLLYIDKLERKIGVCLFVGLAGIFGIIFSIANNSAEI-- 356
                                       89***********************************99777666666665444444444444444445555554.. PP

                             MFS_4  87 iRflaGvasAvvlvfgsslvlahaaaarrervgallfaGvGlGi.avsgllvllllqlglsassl...Wlalavlsa 159
                                         +l G   A++l  +s+   +  a+    ++ +    G G Gi a+++  v+ l ++++ ++ +     +l++l +
  gi|518652057|ref|YP_008141577.1| 357 --VLFGFIVAFMLWNMSNFFHQYQAEIFPTKLRGSG-TGMGQGInAIASASVPTLIVVFVLSHGSlavFSVLGILVV 430
                                       ..4567788*********999999999999999975.6788888555666666655555544433022445555555 PP

                             MFS_4 160 vllllvall 168
                                       + ++ ++l 
  gi|518652057|ref|YP_008141577.1| 431 ITIVDIMLF 439
                                       555544444 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5  11.8   1.9e-06     0.005     260     335 ..      62     135 ..      20     143 .. 0.77
   2 ?   -0.8   0.3      0.17   4.4e+02     285     328 ..     146     196 ..     137     205 .. 0.48
   3 !    5.1   3.1    0.0027       6.8     207     333 ..     249     373 ..     232     380 .. 0.70
   4 ?   -2.5   1.2      0.56   1.4e+03     300     327 ..     405     432 ..     392     445 .. 0.53

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.9e-06
                             MFS_2 260 aasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallp 335
                                          +++++++ ++++g++ + +la  +g+k++y++ +l+ +++ +++ l+  sn++l  v+++iag+g+g+   l 
  gi|518652057|ref|YP_008141577.1|  62 STYIMPTAFYSGMVVGTFAFGRLADIYGRKKIYFVNLLVFAIGAIIAGLM--SNYILIGVFMFIAGIGTGAEIPLG 135
                                       344678899*****************************************..****************99866655 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.17
                             MFS_2 285 rlgkkntyllgalltivllvlvlll.......qpsnlllflvllviagfgv 328
                                       r   ++++l+ ++ +i+  +++++l        + ++ +fl++l +a + +
  gi|518652057|ref|YP_008141577.1| 146 RNRGRRLALVYTIGVISAPLGAFWLlemsninLADSWRIFLIVLGVAALVF 196
                                       444444444444444444444444444555544445555555544444444 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0027
                             MFS_2 207 qkeklslleqlkevfrnraflillllfllaalalgvlnglllYyltyvlg.ngsaasvfllvvtisal..lgiplwq 280
                                        kek ++++ + + +r+      +++++++++  gv +g ++++ t  +   +s as+fl+ ++i +   +g+++  
  gi|518652057|ref|YP_008141577.1| 249 LKEKPKWIDLFDKKLRKNT----IMVIIFQYAQSGVFFGFTALVPTLLIAkGYSLASTFLFSIIIYMGflVGSLVNL 321
                                       5666666666666665544....445567778888888888888888888788888888887744432248888888 PP

                             MFS_2 281 plakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaal 333
                                           +l +k  + l+  l+ ++++++ ++  ++  ++l+ +++a++   ++++
  gi|518652057|ref|YP_008141577.1| 322 LYIDKLERKIGVCLFVGLAGIFGIIFSIA-NNSAEIVLFGFIVAFMLWNMSNF 373
                                       88889998888888888888888888888.66666666666666655555554 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 0.56
                             MFS_2 300 ivllvlvlllqpsnlllflvllviagfg 327
                                       ++ l++v++l+ ++l++f vl +++ ++
  gi|518652057|ref|YP_008141577.1| 405 VPTLIVVFVLSHGSLAVFSVLGILVVIT 432
                                       3444444444444444444444444333 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.9   1.4e-05     0.037      95     132 ..      33      70 ..      29      85 .. 0.85
   2 ?   -1.3   1.2      0.64   1.6e+03      43      56 ..     112     125 ..      78     126 .. 0.65
   3 ?   -2.4   9.3       1.4   3.6e+03      29      89 ..     146     260 ..     134     377 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.4e-05
                           DUF2157  95 geallllaalllgaaialvgqifqlsgdaysllllwal 132
                                       ge ++++ +ll+g ++a+++++f+ls+d +++++  a+
  gi|518652057|ref|YP_008141577.1|  33 GEFIITFLVLLVGSLLAIISEVFHLSTDVSTYIMPTAF 70 
                                       78999************************999876665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.64
                           DUF2157  43 alllglGlilfvAa 56 
                                       +  +++G+++f+A+
  gi|518652057|ref|YP_008141577.1| 112 SNYILIGVFMFIAG 125
                                       33577888888886 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                           DUF2157  29 arrrsfleallvlGalllglGlilfvA.anWqglsrlvkfllllvllllslllg.avlwrdr............... 88 
                                       ++r ++l +++++G++   lG +++   +n +    +  fl++l++++l++ ++ +++ + +               
  gi|518652057|ref|YP_008141577.1| 146 RNRGRRLALVYTIGVISAPLGAFWLLEmSNINLADSWRIFLIVLGVAALVFQVIrFRMKESPrwlesvgrykdannl 222
                                       34455588899999999999999888614555555555566677777777777767776655555555555555555 PP

                           DUF2157  89 .....................................r 89 
                                                                            +
  gi|518652057|ref|YP_008141577.1| 223 mnsieeevmkekdisslppvenhtevlkekpkwidlfD 260
                                       55555555555555555555555555555555555550 PP

>> DUF3377  Domain of unknown function (DUF3377)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0022       5.7      38      61 ..     187     210 ..     184     213 .. 0.83
   2 ?   -0.5   1.7      0.48   1.2e+03      37      61 ..     424     448 ..     394     449 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0022
                           DUF3377  38 LllciLvliyailqfrrkgtprrl 61 
                                        +l + +l++ +++fr+k++pr l
  gi|518652057|ref|YP_008141577.1| 187 IVLGVAALVFQVIRFRMKESPRWL 210
                                       46678889999999*******976 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
                           DUF3377  37 vLllciLvliyailqfrrkgtprrl 61 
                                       vL ++++++i+ i+ f  k ++r+l
  gi|518652057|ref|YP_008141577.1| 424 VLGILVVITIVDIMLFGPKTSQREL 448
                                       6777788888888888888888876 PP

>> SP_C-Propep  Surfactant protein C, N terminal propeptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.17   4.2e+02      28      59 ..      16      49 ..       2      86 .. 0.69
   2 ?   -2.8   0.3       2.2   5.6e+03      47      62 ..      96     111 ..      91     121 .. 0.72
   3 ?    7.5   0.9    0.0013       3.4      39      74 ..     419     454 .]     402     454 .] 0.87

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.17
                       SP_C-Propep 28 ripccplnlkrllivvv..vvvlvvvvvlgallm 59
                                      r+p+   + k ll v     ++  +v+++g+ll 
  gi|518652057|ref|YP_008141577.1| 16 RLPVSKFHTKFLLYVTGgeFIITFLVLLVGSLLA 49
                                      6788888888888876422455556677777764 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
                       SP_C-Propep  47 vlvvvvvlgallmglh 62 
                                       v ++v  +ga++ gl 
  gi|518652057|ref|YP_008141577.1|  96 VNLLVFAIGAIIAGLM 111
                                       4456677888888873 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0013
                       SP_C-Propep  39 llivvvvvvlvvvvvlgallmglhmsqkhtemvlem 74 
                                       l +  v+ +lvv+ ++  +l+g + sq+  e + +m
  gi|518652057|ref|YP_008141577.1| 419 LAVFSVLGILVVITIVDIMLFGPKTSQRELESISNM 454
                                       567778899*******************99998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.84u 0.35s 00:00:01.19 Elapsed: 00:00:00.56
# Mc/sec: 2444.89
//
Query:       gi|518652058|ref|YP_008141578.1|  [L=247]
Description: hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-08   32.3   0.0    1.8e-07   30.6   0.0    1.7  1  Hydrolase_4    Serine aminopeptidase, S33
    9.6e-08   32.9   0.0    1.1e-07   32.7   0.0    1.1  1  Abhydrolase_6  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.41   10.3   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
        0.1   12.7   0.0       0.13   12.4   0.0    1.2  1  Thioesterase   Thioesterase domain


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.6   0.0   4.1e-11   1.8e-07      65     238 ..      66     231 ..      57     232 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.1e-11
                       Hydrolase_4  65 fvekvkeehpelplfllGhSmGGliallyllrypdkvaglilsaPalkikaklkappllklllkllgkllpklqvsn 141
                                       +++ + ++++  p fl+GhSmG++i +++ll+ + k +g++++ + lk+  +   ++l+ l+++  g++    ++  
  gi|518652058|ref|YP_008141578.1|  66 IINDILTRNSFYPDFLFGHSMGATIMISLLLNFSVKPKGIVFIDSGLKPSVR--NSELMPLINRNSGNIGTYRTI-- 138
                                       346667788888***********************************99966..688888888888888777777.. PP

                       Hydrolase_4 142 nlkadslsrdpevva.ayeadplvhgkitvrlllelldamkr..leeraakitlPllllhGeaDkvvdpeasrelye 215
                                           +s  r+ ++ + +  +d++++ +i v  l   l+a++r   ++ a+ +tlP l++ Ge Dk  + e+ ++++ 
  gi|518652058|ref|YP_008141578.1| 139 ---LRSFFRNIDFNDlEKITDEFMQYNIDV--LKCQLKAISRydFTSTANFLTLPALIIFGEYDKNRNFEELQDVHI 210
                                       ...788899999988667788888777654..444444444311567788899**********************99 PP

                       Hydrolase_4 216 rlgskdktlklypglyHellnEp 238
                                       r++  + t+ ++++  H  ++E+
  gi|518652058|ref|YP_008141578.1| 211 RIK--NSTIVVFKNSAHCPMFEE 231
                                       999..79************9996 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.5e-11   1.1e-07      54     219 ..      64     237 ..      17     238 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.5e-11
                                       HHHHCCTT....TTSEEEEEETCHHHHHHHHHHCC.......EE.EEES-..----TTT.S----TTHHHHHHTT-C CS
                     Abhydrolase_6  54 aalldelaa..gggpvvlvGHSlGGalalaaapla.....lvvg.vlldppptalpagl.laaalelllallallrl 121
                                        ++++++ +  +  p +l+GHS+G++++     l+        g v++d+   +l ++   + +++l+ +  ++  +
  gi|518652058|ref|YP_008141578.1|  64 CNIINDILTrnSFYPDFLFGHSMGATIMIS---LLlnfsvKPKGiVFIDS---GLKPSVrNSELMPLINRNSGNIGT 134
                                       55566665444334448********96666...554555533448*****...666666477777777777777776 PP

                                       CCCHCCHS-HSCCCCHHH....C...CCCHCHCCCGHHHHCCHHC...HTTCCHHTT-TTGCEEECTT-C...HHHH CS
                     Abhydrolase_6 122 lawlsreplprlfladed....a...daawrarlarlaallaglg...llpaaawadlpvpllvlggeDp...lvpr 185
                                       ++        r+f+++ d    +   d+  +++ + l  +l++     + + a++ +lp+++ ++g+ D+       
  gi|518652058|ref|YP_008141578.1| 135 YRTIL-----RSFFRNIDfndlEkitDEFMQYNIDVLKCQLKAISrydFTSTANFLTLPALI-IFGEYDKnrnFEE- 204
                                       54443.....3666655544331333566666666666555533322255699999999999.7798888545333. PP

                                       CHHCCCH.STTEEETCE...SSS-HHHHSHHHHHH CS
                     Abhydrolase_6 186 llerlla.qagarlpvvlpgaGHlphleepdevae 219
                                        l++ +  +   ++ vv++++ H+p++eep ++a+
  gi|518652058|ref|YP_008141578.1| 205 -LQDVHIrIKNSTI-VVFKNSAHCPMFEEPLRFAD 237
                                       .4455555677777.***************99997 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0     9e-05      0.41      61     117 ..      65     122 ..      50     145 .. 0.79
   2 ?    3.0   0.0     0.015        65     190     257 .]     174     232 ..     154     232 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE.CSSCCHHHHHH CS
                     Abhydrolase_1  61 ddldrildalgddkltlvGhSmGGmialayaaeyperVkalvllga.idpaaslieaq 117
                                       ++++ il +    +  l GhSmG +i+  +++ +  + k++v++++ + p+   +e++
  gi|518652058|ref|YP_008141578.1|  65 NIINDILTRNSFYPDFLFGHSMGATIMISLLLNFSVKPKGIVFIDSgLKPSVRNSELM 122
                                       555555555555555689****************99999***9999866666555554 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.015
                                       HHHHHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 190 eqwpttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                       ++++ t +a++l           p+l+i g++D+    ++l d    +++++ vv+ ++ H+  +e+p
  gi|518652058|ref|YP_008141578.1| 174 SRYDFTSTANFLTL---------PALIIFGEYDKNRNFEELQDVHIRIKNSTIVVFKNSAHCPMFEEP 232
                                       44444444444444.........*******999877668888888779999***********999986 PP

>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05      0.13      56     162 ..      67     177 ..      51     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                                       HHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCCCCCHHCHHCCCHTTHHT..........H CS
                      Thioesterase  56 aealrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslflidssapseteaqeasrraedee..........f 122
                                       ++ +++++   P  lfGhS+G+++   + + L + + ++k++++ids  + + +++   +    ++          +
  gi|518652058|ref|YP_008141578.1|  67 INDILTRNSFYPDFLFGHSMGATI---MISLLLNFSVKPKGIVFIDSGLKPS-VRNSELMPLINRNsgnigtyrtiL 139
                                       33333344444667********99...6678888899999999998765444.333333322222235677777766 PP

                                       HHHHCCTTHHHCCTTTHCCHHHHHHHHHHHHHHHHHTCCS CS
                      Thioesterase 123 veeltdlggtepeelledeellsellpalradyraleqys 162
                                       +  ++ +  + + e  +de +++  +++l+   +a+ +y 
  gi|518652058|ref|YP_008141578.1| 140 RSFFRNIDFN-DLEKITDE-FMQYNIDVLKCQLKAISRYD 177
                                       6666666665.56666666.77777777777777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1454.99
//
Query:       gi|518652059|ref|YP_008141579.1|  [L=414]
Description: hypothetical protein FACI_IFERC00001G0698 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-40  139.3  27.2    2.1e-40  138.8  27.2    1.2  1  Nramp     Natural resistance-associated macrophage protein
  ------ inclusion threshold ------
        2.5    8.1   9.4        3.1    7.8   4.6    3.1  2  NdhL      NADH dehydrogenase transmembrane subunit


Domain annotation for each model (and alignments):
>> Nramp  Natural resistance-associated macrophage protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8  27.2   2.3e-44   2.1e-40       4     357 ..      40     390 ..      38     391 .. 0.88

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 2.3e-44
                             Nramp   4 dlqaGaqfGykLlwvlllstllaillqelsarLGlvTgkglaelirerlpkkvsillwilaelaiiatdlaeviGaA 80 
                                       ++q Ga+ Gy L+w++l+ ++ ++++qel+ r+G++T+ gl +++r++++k+++ ++++ + l  ++t   e +G++
  gi|518652059|ref|YP_008141579.1|  40 AAQTGATLGYGLIWLMLILIIPLYVIQELAGRIGIATKGGLGDIVRKNYGKRIASIVALPMALTDTVTYGIEYLGIG 116
                                       5799************************************************************************* PP

                             Nramp  81 ialnllfgipllvgvlitavlvllllflekggyrklEaliialvlvialsFiaelflvk..pdwgevlkglvvPslp 155
                                       i+l+++  ++++++++++ v+ +l+++  +++y+  E+ +i++ l++ ++ +++l+l    p  + +++ ++  +  
  gi|518652059|ref|YP_008141579.1| 117 IGLEIMG-LSIYYTIPVIYVIHILIVT--RKKYSEAEKPLIIISLLLIIALLLSLALRGiiPVSSPLANPIL-IKPT 189
                                       ****997.*********9999999999..********97777777766777777776541155555666555.4554 PP

                             Nramp 156 gkeslllavgilGatvmphnlflhsslvqerkitidr....seke.ealkyeriDtiialivaflinlailivaAav 227
                                        +++++l+++ +Ga++mp ++f+++s +  +  + d       ++ + l+ +r +t++++iv+ l +++  +++A +
  gi|518652059|ref|YP_008141579.1| 190 -AGYFFLLAANVGAVIMPFMIFFQASATGLKLGDLDGghirI-TRrRSLRIMRKETLAGAIVTELLMVIAEMAFAGI 264
                                       .59**************************9996655476642.33589***************************** PP

                             Nramp 228 ly.sggkdvesledaaeaLepllGskaasvlFaigLlaaGlsStitgtlagqyvmegflglrislwlrrlitralaf 303
                                        + s+   +++ +++ ++L p++G +++ ++ +igL+aaG++++it++l +++ +++ l+++ +      i  +l+ 
  gi|518652059|ref|YP_008141579.1| 265 PHaSHSSFFATPQQLGKVLIPVAG-DFSPIILGIGLIAAGFIALITISLGSAWGIAESLNMKKKS---YWIVYILES 337
                                       **8888899***************.7*********************************888777...555567889 PP

                             Nramp 304 vpalivilligaelelvkllvlsqvllslllPfaliplllltsskklMGefkns 357
                                        pa+i++l+i+ ++  + + ++  ++ +++l   l++++++ ++k++MG+++ s
  gi|518652059|ref|YP_008141579.1| 338 LPAVIAVLIINPSSM-IAIVLYLLIFFVFALIAPLAMMWIIGRNKNIMGDLVLS 390
                                       999999999988888.888888888888999889999************99876 PP

>> NdhL  NADH dehydrogenase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2     0.061   5.4e+02      14      34 ..      47      67 ..      39      75 .. 0.80
   2 ?    7.8   4.6   0.00034       3.1       8      63 ..     350     405 ..     344     411 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.061
                              NdhL 14 laylalsvlYllviPlilylw 34
                                      l y+++ ++ +l+iPl ++  
  gi|518652059|ref|YP_008141579.1| 47 LGYGLIWLMLILIIPLYVIQE 67
                                      56889999999****999765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00034
                              NdhL   8 dtllvllaylalsvlYllviPlilylwlrkRWyvaskiErlliymlvflfFPGlll 63 
                                       ++++ ++ yl++ +++ l+ Pl++++ + +  + ++ +       +v+lf  Gl++
  gi|518652059|ref|YP_008141579.1| 350 SSMIAIVLYLLIFFVFALIAPLAMMWIIGRNKNIMGDLVLSRKNEVVYLFMFGLII 405
                                       56788999*****************99999999********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1096  (0.06113); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); 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):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 2493.62
//
Query:       gi|518652060|ref|YP_008141580.1|  [L=73]
Description: DNA-directed RNA polymerase subunit N [Ferroplasma acidarmanus fer1]
Scores for complete 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-26   89.9   0.2    1.1e-25   89.6   0.2    1.1  1  RNA_pol_N  RNA polymerases N / 8 kDa subunit


Domain annotation for each model (and alignments):
>> RNA_pol_N  RNA polymerases N / 8 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6   0.2   6.4e-30   1.1e-25       1      58 [.       1      68 [.       1      69 [. 0.93

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 6.4e-30
                                      ----SS-TTT--B-STHHHHHHHHHHTT..........--HHHHHHHHT--SHHHHHHHHTB--THHH CS
                         RNA_pol_N  1 MiiPVrCFtCGkvigekweeylellekg..........eepkdaLdaLglkryCCrrmllthvdliek 58
                                      MiiPVrCF+CGkvig+++ +++e  +k           +e++++Ld+Lg++ryCCrrm+l++ dl ++
  gi|518652060|ref|YP_008141580.1|  1 MIIPVRCFSCGKVIGSDYVRFVEESKKIrkdtghdptgKEKSEILDNLGVDRYCCRRMILSNADLLDE 68
                                      9****************9999999866677789999999999***********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.29s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 503.80
//
Query:       gi|518652061|ref|YP_008141581.1|  [L=134]
Description: 30S ribosomal protein S9P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      3e-31  108.5   0.6    3.3e-31  108.3   0.6    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 !  108.3   0.6   1.9e-35   3.3e-31       1     121 []       9     134 .]       9     134 .] 0.92

  Alignments for each domain:
  == domain 1  score: 108.3 bits;  conditional E-value: 1.9e-35
                                       EECTTEEEEEEEEESSSEEEETTEECCHHSTTSCHHHHHCHHHHHTTTSSS.EEEEEEEESS-HHHHHHHHHHHHHH CS
                      Ribosomal_S9   1 GrrKesvArvwikegkgkilvngksleeYfkeeaarekvleplkltgllgk.fdvfvkvkgGGlsgqaeAirlgiar 76 
                                       G+rK++vAr+  ++g+gk+ +ngk++e Y + e  r+kv+eplk++g   + +d+++kv+gGG +gq++A+r+++a+
  gi|518652061|ref|YP_008141581.1|   9 GKRKTAVARAITRKGNGKVFINGKPVELY-PIELLRNKVMEPLKILGDRANeIDIEIKVTGGGNTGQTDAARTAMAK 84 
                                       8***************************5.669*************998766************************* PP

                                       HHHHHHHHHHHHHC......TCCCTS-B--------TTSSCTTB----S-- CS
                      Ribosomal_S9  77 aLvalekeekkeLk......kaglltrDpRvvErkKtgkkkARkkyqwskR 121
                                       ++v++ +   +eL+      ++++l++D R++ +kK+   +AR+k q+s+R
  gi|518652061|ref|YP_008141581.1|  85 GIVKYFS-DDHELEntirtyDRTMLVNDIRRKMPKKPMGSGARAKRQKSYR 134
                                       *****88.3444444444889****************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       396  (0.0220871); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        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: 00:00:00.43
# Mc/sec: 936.06
//
Query:       gi|518652062|ref|YP_008141582.1|  [L=137]
Description: 50S ribosomal protein L13P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-09   38.4   0.0    1.9e-08   34.6   0.0    2.1  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 !   34.6   0.0   1.1e-12   1.9e-08      35     114 ..      22      99 ..       1     105 [. 0.80

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 1.1e-12
                                       S--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHHCCSHHHHHHHHHHCCS-.SSHHHHHHGCTEE CS
                     Ribosomal_L13  35 vdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakellekkpeeilekaVkgmLp.knklgrrrlkrLk 110
                                          G+ vv++na+k+a+tg++      ++h + +g++++ +      + p++i+++ V+ mLp k++ g + lkr k
  gi|518652062|ref|YP_008141582.1|  22 LLSGEEVVIVNASKIAITGSRKFILDKFNHRRNIGSVRKGP---YYPRTPDQIMRRSVSEMLPiKKTKGLEALKRCK 95 
                                       45799**************8655555556666666666655...57799**************6666788999**** PP

                                       EESS CS
                     Ribosomal_L13 111 vyag 114
                                       vy+g
  gi|518652062|ref|YP_008141582.1|  96 VYSG 99 
                                       **98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1008.29
//
Query:       gi|518652063|ref|YP_008141583.1|  [L=122]
Description: 50S ribosomal protein L18e [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   38.7   0.1    7.1e-10   38.6   0.1    1.0  1  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e
     0.0022   18.7   0.9      0.018   15.7   0.9    2.1  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 !   38.6   0.1   7.9e-14   7.1e-10      33     138 ..      20     121 ..       2     122 .] 0.86

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 7.9e-14
                     Ribosomal_L18  33 fLar..RtdskFnkvvlkrLfmsrinrpplslsrlvkkvkkkeeekkiavvvgtvtdDvrllevPklsvaALrftet 107
                                       +L r   ++s F + +  rL +sr + + + l +l + v+    e+ ++v+ gt++    l++  k+++aA++ +++
  gi|518652063|ref|YP_008141583.1|  20 LLERsrESQSIFWRDIASRLNSSRNHYANVNLGKLDRVVS----EGDTVVIPGTLLSSGILHK--KVRIAAVKASDK 90 
                                       44443267888***************************99....469*********9988875..9*********** PP

                     Ribosomal_L18 108 ararilkaGGeiltlDqLalraPtGkntvLl 138
                                       a+ ++ ++G e + l +La ++P+G+n  ++
  gi|518652063|ref|YP_008141583.1|  91 AKLKLAESGSEFIELKDLANENPKGTNLKII 121
                                       **************************97665 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 !   15.7   0.9     2e-06     0.018      46     126 ..      43     102 ..       6     104 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2e-06
                                       .---EEEEHHHHHHTTTTGTTS------EEEGGGTTTTSSS........SEEEE--S---.--EEEESEE-HHHHHH CS
                    Ribosomal_L27A  46 kkeykvvnlkdLdelideerleladeaeeidleelaeaglikk....kdgvKvlgkgeltkklkvkaskfSkkAkek 118
                                       +++y+                        ++l +l   +++++         +l +g l kk+ + a k+S kAk k
  gi|518652063|ref|YP_008141583.1|  43 RNHYA-----------------------NVNLGKL--DRVVSEgdtvVIPGTLLSSGILHKKVRIAAVKASDKAKLK 94 
                                       23334.......................4555555..4444443332112256999********************* PP

                                       HHHTT-EE CS
                    Ribosomal_L27A 119 IeaaGGkv 126
                                         + G ++
  gi|518652063|ref|YP_008141583.1|  95 LAESGSEF 102
                                       99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 938.89
//
Query:       gi|518652064|ref|YP_008141584.1|  [L=447]
Description: hypothetical protein FACI_IFERC00001G0703 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.2e-48  163.6  30.5    8.9e-48  163.3  30.5    1.0  1  Sugar_tr  Sugar (and other) transporter
    2.2e-25   89.3  31.0    2.2e-25   89.3  31.0    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.3  30.5   9.9e-52   8.9e-48       4     445 ..      23     446 ..      20     447 .] 0.87

  Alignments for each domain:
  == domain 1  score: 163.3 bits;  conditional E-value: 9.9e-52
                                       HHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHH CS
                          Sugar_tr   4 vaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksll 80 
                                       + ++g ++ gY + +++ ++      ++++  +s ++ +    ++ ++ s++++G ++Gs+++g l+d++GRkk++ 
  gi|518652064|ref|YP_008141584.1|  23 LSSMGIFMDGYVLSIYSIAILY---MRDYFHLVSGTPFYV--YYIAFMGSSLFIGMFFGSIILGNLSDKYGRKKIYE 94 
                                       4556667777766666555544...456666666766663..6899999**************************** PP

                                       HHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  81 iaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaif 157
                                          +++++  +++++++   ++  +i+  +l+G+g+G+ + +++  ++E++pk++Rg++ +++ +++t+G +v   +
  gi|518652064|ref|YP_008141584.1|  95 YDLIITMVFLIMSGIST---NILEFIIFEILAGVGIGADYPISSSIQAEFSPKNKRGKFLVFNIFSWTIGGIVLLLV 168
                                       *****************...9******************************************************99 PP

                                       HHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                          Sugar_tr 158 glgl.nktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdslea 233
                                          +  ++ +a  wril    ++++ ++++ +  lPESP++l  kg+++ea ++   l ++++ + +    ++s + 
  gi|518652064|ref|YP_008141584.1| 169 AIPViLYIPAAINWRILYLTGAIIPFFVILSRRNLPESPFWLTGKGRDSEALKSSNYLGKSAGMEVDELPVVESGNS 245
                                       9999677777***********************************************99999988888888888888 PP

                                       HHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTH.HHHSS-THHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 234 eqeeekaswkellssktvrqrlligvvlqifqqltGinaimyyspti.fenlglsksllvtiivgvvnfvatfvaif 309
                                       +       ++ l+s+ ++++ ++ + v ++   ++ + +  y ++ + ++n  +   +l+t++     f+  ++ ++
  gi|518652064|ref|YP_008141584.1| 246 K-------IRDLFSK-KYLYYTIFVSVAWFSYDVSSYGVWEYTPSAFaYSNSNIVMVVLATLLEELPVFIGFLICMY 314
                                       8.......999**99.556666666667777777776777766666623455566669999999999999999999* PP

                                       HHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHH.HHHHHHHHHTTTTHHHHHHHHHHSHTTTHH CS
                          Sugar_tr 310 lvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivf.ialfialfalgwgpvpwvlvsElfpqsvRs 385
                                        v+++GR+ l l+G+ g+a+ ++i++ ++  +     a +i++++f +a +  ++++g++ + + +  E+fp+++R+
  gi|518652064|ref|YP_008141584.1| 315 YVEKTGRKSLELIGFGGAAVSLIIFA-AVSNFI----ALGILLTFFsFATMHLFHNMGPTNLTYDYPVEIFPTRIRG 386
                                       ***********************998.333333....446776665267788999********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--C CS
                          Sugar_tr 386 kalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtl 445
                                       +a+ +a+ v+ +  ++ ++ fpii+ ++  ++v ++ +++ v+++ ++f+  petkg++l
  gi|518652064|ref|YP_008141584.1| 387 TAMGFATSVSRIGAIVGTIAFPIILFTLPFTFVLIFLVVFEVIGFSITFLLAPETKGKSL 446
                                       *****************************88888999999******************98 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3  31.0   2.5e-29   2.2e-25       3     352 ..      26     403 ..      24     404 .. 0.80
   2 !   13.2   7.1   3.4e-06      0.03     111     178 ..     377     442 ..     371     447 .] 0.79

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 2.5e-29
                             MFS_1   3 laaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllfa 73 
                                       +++f+ ++  si+++a+  ++ + +++   +      i ++ +  ++g++++s++lG lsd++Gr++++   l+++ 
  gi|518652064|ref|YP_008141584.1|  26 MGIFMDGYVLSIYSIAIL-YMRDYFHLVSGTpfyvyyIAFMGSSLFIGMFFGSIILGNLSDKYGRKKIYEYDLIITM 101
                                       678999999999999999.*******55555577777999************************************* PP

                             MFS_1  74 lglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg....lla 145
                                       ++ l+++ +++++  ++++ +l+G+g ga +p++ ++ a+ +pk++rg+ + +   ++ +G i+  l++     ++ 
  gi|518652064|ref|YP_008141584.1| 102 VF-LIMSgISTNILEFIIFEILAGVGIGADYPISSSIQAEFSPKNKRGKFLVFNIFSWTIGGIVLLLVAIpvilYIP 177
                                       **.77775768888************************************************999998888865555 PP

                             MFS_1 146 sslgWravfyilaivsllafvlfllllpeepperkrkspkeee...................kgtgpaplvp....a 199
                                       ++++Wr +++  ai+ +++++        ++++ +   + +++                         p+v+     
  gi|518652064|ref|YP_008141584.1| 178 AAINWRILYLTGAIIPFFVIL---SRRNLPESPFWLTGKGRDSealkssnylgksagmevdeL-----PVVEsgnsK 246
                                       8889***************77...566555555555555555566778877777777444433.....333366666 PP

                             MFS_1 200 wkallkdpvlwillialllfffgfsg...lltllplylqevlgls..glllaglllallalvgailallagrlsdrl 271
                                       ++ l+++++l    +  +++++++++    ++ +  y+ + + +s  + ++++l+  l  l ++i++l++ +++ ++
  gi|518652064|ref|YP_008141584.1| 247 IRDLFSKKYL----YYTIFVSVAWFSydvSSYGVWEYTPSAFAYSnsNIVMVVLATLLEELPVFIGFLICMYYVEKT 319
                                       999*****55....4444444455554424455555889999999997788888999999999999*********** PP

                             MFS_1 272 grrrrlllallllllaalglallavtssavllllvlvliGf.glgfv..fpsllalasdlappeeagtasglfntag 345
                                       gr+   l+++++++++++++a ++++    +ll ++ ++++  +  +  + +   + ++ +p++ +gta+g++++++
  gi|518652064|ref|YP_008141584.1| 320 GRKSLELIGFGGAAVSLIIFAAVSNFIALGILLTFFSFATMhLFHNMgpTNLTYDYPVEIFPTRIRGTAMGFATSVS 396
                                       **************************33333333333344433333344555555778888**************** PP

                             MFS_1 346 slggalg 352
                                        +g+++g
  gi|518652064|ref|YP_008141584.1| 397 RIGAIVG 403
                                       *****99 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.4e-06
                             MFS_1 111 adwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeeppe 178
                                       +++fp + rg a+g++++ + +Gai+g ++ ++++  l ++ v ++l ++ +++f +   +l++++++
  gi|518652064|ref|YP_008141584.1| 377 VEIFPTRIRGTAMGFATSVSRIGAIVGTIAFPIILFTLPFTFVLIFLVVFEVIGFSI--TFLLAPETK 442
                                       589********************************7777777777777777777655..555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2907.14
//
Query:       gi|518652065|ref|YP_008141585.1|  [L=236]
Description: hypothetical protein FACI_IFERC00001G0704 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.0   0.0    1.2e-26   93.6   0.0    1.2  1  SpoU_methylase  SpoU rRNA Methylase family
  ------ inclusion threshold ------
      0.065   12.9   0.0       0.08   12.6   0.0    1.2  1  FANCI_S3        FANCI solenoid 3


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 !   93.6   0.0   1.3e-30   1.2e-26       2     142 .]       8     156 ..       7     156 .. 0.87

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 1.3e-30
                                       EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHH.EEEESSHHHHHHHHCCCTEE CS
                    SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevle.lkvvdsleealkelkeegfa 77 
                                       + vvlve++++gN+Ga+aR++++ g+s+l++vk    +++++ea+  +++ + +l+ +k+++sl+ea++ ++     
  gi|518652065|ref|YP_008141585.1|   8 ISVVLVEPKYQGNIGAVARSMANSGISDLRIVK----TPIETEAIYRSMHGRYILDnAKIFNSLKEAVSGFEII--- 77 
                                       579****************************99....58899999999********************998876... PP

                                       EEEEST...T-SEGCCS....HHH.........TTEEEEEEBTTTBS-HHHHCTSSEEEE----TTSSS--HHHHHH CS
                    SpoU_methylase  78 lvatsl...kgkslsei....dlk.........ekvalvfGnEdkGlsnelleladrlvkIpmsgeveSLNvavAva 138
                                         +ts    +g++++++    + +         +kvalvfG+Ed+Gl+ e+l  ++ ++kI  ++e++  N+++Ava
  gi|518652065|ref|YP_008141585.1|  78 -AGTSDiskSGEKFRRVptgpE-EfwstngltgQKVALVFGREDNGLNYEELGMCNFFLKIIGNPEYPVYNLSHAVA 152
                                       .444443336666664444440.1445778999******************************************** PP

                                       HHHH CS
                    SpoU_methylase 139 illy 142
                                       i+ly
  gi|518652065|ref|YP_008141585.1| 153 IILY 156
                                       ***9 PP

>> FANCI_S3  FANCI solenoid 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.9e-06      0.08     167     210 ..     182     225 ..     131     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.9e-06
                          FANCI_S3 167 LveilelLskklepssrqlvqvltwlvklckeneledasvakvl 210
                                       L   le L+ k+++++++++ +++ l++++   +++d+++ k++
  gi|518652065|ref|YP_008141585.1| 182 LAGRLEELLAKIDYNEQEIDTLMNMLNRIIARANITDSEFFKIM 225
                                       5567999*********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      632  (0.0352502); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1667.63
//
Query:       gi|518652066|ref|YP_008141586.1|  [L=257]
Description: peptidyl-prolyl cis-trans isomerase [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   25.8   2.2    8.2e-06   25.8   2.2    2.0  2  FKBP26_C   FKBP26_C-terminal
    0.00047   20.4   1.4    0.00097   19.4   1.1    2.1  1  FKBP_C     FKBP-type peptidyl-prolyl cis-trans isomerase
  ------ inclusion threshold ------
      0.022   14.9   1.7       0.03   14.5   0.7    1.7  2  Pox_A22    Poxvirus A22 protein
       0.14   12.1   6.2        2.3    8.2   0.6    3.2  3  RsgI_N     Anti-sigma factor N-terminus


Domain annotation for each model (and alignments):
>> FKBP26_C  FKBP26_C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.43   1.9e+03      28      46 ..      69      91 ..      57     116 .. 0.66
   2 !   25.8   2.2   1.8e-09   8.2e-06       3      64 ..     155     214 ..     153     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.43
                                      TEEEEE--TTGGG....STTHHH CS
                          FKBP26_C 28 ktvtIelpeeakF....ieniql 46
                                      k+ ++++p + ++     +ni +
  gi|518652066|ref|YP_008141586.1| 69 KEYEVTVPAKDAYgmrdTKNIKV 91
                                      56677788777777444444433 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHH-TT--..--EEEEETTEEEEE--TTGGGSTTHHHHHHHHHHHHHHH-TTEEE CS
                          FKBP26_C   3 ekikelIkryiPnidlekfkieiedktvtIelpeeakFieniqlaklrIAkdilkrieevek 64 
                                        k+ ++I + +    +++f +eie+ +++I++peeakF  n   +k +I++di+k+++e + 
  gi|518652066|ref|YP_008141586.1| 155 GKVNAIIDMGYSD--SDNFVVEIENDSISIQIPEEAKFDVNWIDSKYKIVNDIRKYMPEKDV 214
                                       6899999997765..55*********************999999*************99665 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.1   2.2e-07   0.00097       7      80 ..       3      90 ..       1     193 [. 0.83

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.2e-07
                                      TTCEEEEEEEEEE..............T.TSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGT CS
                            FKBP_C  7 egdtVtvhykgkl..............e.dgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippela 70
                                      +gd++++ ++ +               + ++++fd++ +++k++ +++G   + k + +  ++ ++G + ++t+p + a
  gi|518652066|ref|YP_008141586.1|  3 DGDFIELSFEMRAgqdkklistskedlAkQENIFDDK-KKYKNAVIVIGTDGLFKEINDSFKQAELGKEYEVTVPAKDA 80
                                      5677777777777433333333332222245566666.8**************************************** PP

                                      TTTTTBCTTT CS
                            FKBP_C 71 Ygekglaggv 80
                                      Yg ++ ++ +
  gi|518652066|ref|YP_008141586.1| 81 YGMRDTKNIK 90
                                      **98886644 PP

>> Pox_A22  Poxvirus A22 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       1.3   5.8e+03      28      59 ..      20      49 ..      11      53 .. 0.63
   2 ?   14.5   0.7   6.6e-06      0.03       4      61 ..     159     217 ..     156     228 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 1.3
                           Pox_A22 28 kvldiekldwssdwerrvardilsynvdvvll 59
                                      k+++ +k d++  +++++  d  +y+  v+++
  gi|518652066|ref|YP_008141586.1| 20 KLISTSKEDLA--KQENIFDDKKKYKNAVIVI 49
                                      56666677765..3556666666666666655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 6.6e-06
                           Pox_A22   4 aaiDiGvknpartllevkdnkarikvldiekldws.sdwerrvardilsynvdvvllEk 61 
                                       a iD+G       ++e+++++ +i++ +++k d    d ++++ +di +y +++ ++ k
  gi|518652066|ref|YP_008141586.1| 159 AIIDMGYSDSDNFVVEIENDSISIQIPEEAKFDVNwIDSKYKIVNDIRKYMPEKDVVVK 217
                                       569*******************************999************7655433333 PP

>> RsgI_N  Anti-sigma factor N-terminus
   #    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      13      20 ..       2       9 ..       2      10 .. 0.85
   2 ?    8.2   0.6   0.00052       2.3       4      41 ..      42      82 ..      40      92 .. 0.87
   3 ?    5.3   0.2     0.004        18      24      37 ..     101     115 ..      94     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.38
                            RsgI_N 13 pdGeFiki 20
                                      +dG+Fi++
  gi|518652066|ref|YP_008141586.1|  2 NDGDFIEL 9 
                                      69****85 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00052
                            RsgI_N  4 kkkkaivlTpdGeFikikrk.ggmkvGe..Eiefpekdiie 41
                                       k+ +iv   dG F++i+   ++ + G+  E+ +p+kd++ 
  gi|518652066|ref|YP_008141586.1| 42 YKNAVIVIGTDGLFKEINDSfKQAELGKeyEVTVPAKDAYG 82
                                      58999*************99788**************9875 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.004
                            RsgI_N  24 gg.mkvGeEiefpek 37 
                                       +  +++G+E+++++k
  gi|518652066|ref|YP_008141586.1| 101 KInPEIGKEVNINNK 115
                                       5559********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2738  (0.152713); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 1782.80
//
Query:       gi|518652067|ref|YP_008141587.1|  [L=493]
Description: hypothetical protein FACI_IFERC00001G0706 [Ferroplasma acidarmanus fer1]
Scores for complete 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-160  532.2   0.0   9.7e-160  532.0   0.0    1.0  1  Aldedh          Aldehyde dehydrogenase family
    0.00011   21.4   0.0    0.00015   20.9   0.0    1.4  1  LuxC            Acyl-CoA reductase (LuxC)
  ------ inclusion threshold ------
      0.072   13.0   0.0       0.17   11.8   0.0    1.6  1  Phage_integr_3  Archaeal phage integrase


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 !  532.0   0.0  1.6e-163  9.7e-160       1     462 []       9     471 ..       9     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 532.0 bits;  conditional E-value: 1.6e-163
                                       EET-SS.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHH CS
                            Aldedh   1 wveses.etievinPatgeviakvpaataedvdaavaaAkeafkawaklpaeeRaeiLrkaadlleerkeelaelet 76 
                                       w es++ +t++++nP+tgev+ ++paat++d+daa+++A++af++w+++  +eRa+iL+ka +l+ +++ el +l+t
  gi|518652067|ref|YP_008141587.1|   9 WKESSNgNTLNKYNPSTGEVLDTFPAATKDDIDAAMDSAESAFPSWSDMGTQERAKILYKAVELISQKRGELENLLT 85 
                                       777777688******************************************************************** PP

                                       HHH---HHHHHHHHHHHHHHHHHHHHHHHHHSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHH CS
                            Aldedh  77 letGkplaearaeveeaidvlryyaelaeklegevlps.segklalvrrePlGvvgaItPWNfPlllaawklapala 152
                                       le+Gk  +ea  ev+ +id ++yyae  +kl+g++++  s++++++ ++ P+G+v+aItPWNfP++++++klapal+
  gi|518652067|ref|YP_008141587.1|  86 LEVGKIKREAIDEVDGVIDQIQYYAEFERKLTGDIVEGsSSKRKIFQYKVPYGIVVAITPWNFPAAMVVRKLAPALL 162
                                       **************************************779999999999*************************** PP

                                       TT-EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTT CS
                            Aldedh 153 aGNtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknl 229
                                       +GNtv+lKP+++tpl+a  +++ f eag+Pkgvln+vtg+gse+g+++v+h++v +v++tGst++g+ki+++a++n+
  gi|518652067|ref|YP_008141587.1| 163 TGNTVILKPSSDTPLTANWIVNKFIEAGIPKGVLNFVTGRGSEIGDYIVNHKKVGLVTMTGSTSTGQKIMQNASSNM 239
                                       ***************************************************************************** PP

                                       SEEEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT- CS
                            Aldedh 230 krvtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedt 306
                                        +++lElGGk+p+iv++daD+ +a+++++++ ++n GQ Ciaa+rl+++e+iyd+f++k+v+ +kkl+ gdp  +++
  gi|518652067|ref|YP_008141587.1| 240 AKLILELGGKAPFIVWKDADMIRALKSLIWAKYLNVGQSCIAAERLYIHEDIYDKFMSKFVAITKKLTTGDP--DTS 314
                                       ************************************************************************..47* PP

                                       SB---SSHHHHHHHHHHHHHHHHTTSEEEE-TT..E.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEES CS
                            Aldedh 307 dvGPliseaqlekvekyveeakeegaklllGge..reeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfk 381
                                       dvGPli++++l+ + + v++ak+ g+k+l+Gg+    + ++++gyf++Pt+++nv++d+ ++q+EiFGP++   k++
  gi|518652067|ref|YP_008141587.1| 315 DVGPLINKNALAGMVQTVNNAKDSGYKILTGGNtpDLQGKYKNGYFFAPTIIENVPQDSGLFQDEIFGPIIGTEKIS 391
                                       *********************************9978999************************************* PP

                                       SHHHHHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEE CS
                            Aldedh 382 deeeaieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeyte 458
                                        ++e+ ++aNd+++GLa+++ft+d+e +++++e++++G++yiN +   a +   ++G++++g   eg+k+g++ey++
  gi|518652067|ref|YP_008141587.1| 392 GVDEMYRKANDSKFGLASYLFTEDPELMLEASEKIRFGELYINMPGPEASQG-YHTGFRMTGQAGEGSKYGINEYLK 467
                                       *********************************************9999988.************************ PP

                                       EEEE CS
                            Aldedh 459 vktv 462
                                       +k+v
  gi|518652067|ref|YP_008141587.1| 468 LKNV 471
                                       *987 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.6e-08   0.00015      80     188 ..     127     233 ..      61     304 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-08
                              LuxC  80 keksyekaqprglvlhvlsgNvpllp.vmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvy 155
                                       k k ++  +p g+v+ +++ N p    v  ++ +lL++n  +lk+Ss+ p +a+ ++ ++++  + +       v++
  gi|518652067|ref|YP_008141587.1| 127 KRKIFQYKVPYGIVVAITPWNFPAAMvVRKLAPALLTGNTVILKPSSDTPLTANWIVNKFIEAGIPK------GVLN 197
                                       44679999**************9866156899****************************9987642......3334 PP

                              LuxC 156 f.ksgdtkleeeiv..qnaDvvvawGgeeaikaise 188
                                       f  +   ++ + iv  +++  v + G+ ++ + i +
  gi|518652067|ref|YP_008141587.1| 198 FvTGRGSEIGDYIVnhKKVGLVTMTGSTSTGQKIMQ 233
                                       434555555555553333444555555555555555 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   2.8e-05      0.17     111     135 ..     180     204 ..     148     215 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHTT--HHHHHHHTTSS- CS
                    Phage_integr_3 111 kwvatklaelgvpeevidFiqGrkp 135
                                       +w+ +k++e g+p++v +F+ Gr +
  gi|518652067|ref|YP_008141587.1| 180 NWIVNKFIEAGIPKGVLNFVTGRGS 204
                                       8**********************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 3730.16
//
Query:       gi|518652068|ref|YP_008141588.1|  [L=559]
Description: hypothetical protein FACI_IFERC00001G0707 [Ferroplasma acidarmanus fer1]
Scores for complete 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-89  299.6   3.1    4.1e-89  298.9   3.1    1.3  1  PK        Pyruvate kinase, barrel domain
    1.4e-19   70.5   0.3    2.7e-19   69.5   0.3    1.5  1  PK_C      Pyruvate kinase, alpha/beta domain


Domain annotation for each model (and alignments):
>> PK  Pyruvate kinase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.9   3.1   4.5e-93   4.1e-89       2     341 ..       2     332 ..       1     337 [. 0.98

  Alignments for each domain:
  == domain 1  score: 298.9 bits;  conditional E-value: 4.5e-93
                                       --SEEEEEESCCCTSHHHHHHHHHHTEEEEEEETTSS-HHHHHHHHHHHHHHHHTTTTS-EEEEE---S-EBB--BT CS
                                PK   2 rrtkivctlGPasesvekleklieaGlnvvrlnfshGsheehqerienvreaekklgkkvaillDtkGpeirtgllk 78 
                                        +tkiv+tlGPas +   ++k++++Gl  +r+n +h s  + +++   v ++++k++kk++i++D+kGpe+rtg + 
  gi|518652068|ref|YP_008141588.1|   2 TKTKIVATLGPASFDESIITKMADKGLATIRINTAHISEGYITDVSRLVYKINEKYNKKLGIMVDLKGPELRTGEFP 78 
                                       69*************************************************************************** PP

                                       TCSSSEEE-TTSEEEEE-SCTCTTTBBTTEEEBS-TTHHHHS-TTEEEEETTTTEEEEEEEEETTEEEEEEESS-EE CS
                                PK  79 dgkkdielkegdklkvsldeklkeegdeelialdyknivkdvevGktilvdDGllslkvlevdeekeleveventgv 155
                                       +g   +++++g++  +s +  +k++     i+++yk i + v+  + i ++DG++ ++v+++++   +++++  tg+
  gi|518652068|ref|YP_008141588.1|  79 GGI--LNITAGNTYGISDNPGVKSD-----ISINYK-ISDYVDKDTLIAINDGRVRFNVESISNGV-ITTRAMDTGT 146
                                       *99..9************9999976.....9****7.9************************9998.********** PP

                                       E-SS-BEE-TTS---S-SS-HHHHHHHHHHHHCT-SEEEETTE-SHHHHHHHHHHHTCCCTTSEEEEEE-SCHHHHT CS
                                PK 156 lgskkgvnlpgtkvdlpalsekDkadlrfgvkqgvdliaasfvrkasDvkevrevleeegkeikiiakienqegven 232
                                       + ++  vn+pg  +dl  l+++Dk  l+ g+k+++++ a+sfv++ ++v e+++ + +++ +  ii+kie + g +n
  gi|518652068|ref|YP_008141588.1| 147 IHDRSRVNIPGKYIDLGVLTDRDKMFLEEGLKNNINFYALSFVQSRENVYELQDYIYDRKGQGDIISKIETKSGYDN 223
                                       ********************************************************999999*************** PP

                                       HHHHHHHSSEEEEEHHHHHHHSTCCCHHHHHHHHHHHHHHHT--EEEESSTTGGGGTSSS--HHHHHHHHHHHHHT- CS
                                PK 233 ldeileasDgimvarGDlGieipaekvllvqkklikkcnlagkpvitatqmlesmiknPrptraevsDvanavlDGt 309
                                       l+ i++asD imvarGDlG+e+p ++v ++qk++i  + +   p i+atqmlesm+++  ptraevsDv+na+lD t
  gi|518652068|ref|YP_008141588.1| 224 LESIVKASDFIMVARGDLGVELPLKEVAMAQKRIIDISHKYAVPTIVATQMLESMVNSDSPTRAEVSDVTNAILDDT 300
                                       ***************************************************************************** PP

                                       SEEEESHHHHTSS-HHHHHHHHHHHHHHHHHT CS
                                PK 310 DavmLsgetakGkyPveavkamaevaleaeka 341
                                       DavmLs eta GkyPveav+ + e+++  e++
  gi|518652068|ref|YP_008141588.1| 301 DAVMLSEETAIGKYPVEAVTYLYEISKYVESQ 332
                                       *************************9988765 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 !   69.5   0.3     3e-23   2.7e-19       3     117 .]     351     462 ..     350     462 .. 0.93

  Alignments for each domain:
  == domain 1  score: 69.5 bits;  conditional E-value: 3e-23
                                       HHHHHHHHHHHHT-SEEEEE-SSSHHHHHHHHT-TSSEEEEEESHHHHHHHHHHCTTEEHHH.HHHHH...TTSHHH CS
                              PK_C   3 iakaaveaaeelgakaIvvltesGetArliskyrpkvpiiavtpneltarqlalyrGvypvlvekaktaestdellr 79 
                                       +ak +  ++++++++ I+++t++G+tA+ +s +rp   i+a+ + e  ar+++l+rGv+pv +++a++    +e + 
  gi|518652068|ref|YP_008141588.1| 351 VAKGVKIMSNTIDVSSIIAMTRTGHTAKILSAIRPVNDIYAIVQTEWLARSINLMRGVIPVVLPEAQA---KEENIY 424
                                       788888899*****************************************************998655...555688 PP

                                       HHHHHHHHTTSS-STSEEEEEE-SSSS..SS--EEEEE CS
                              PK_C  80 eavkvakeaglvkkgdevvvtaGtpkgesgttNtlrVv 117
                                       ++++     gl+++g++ +v++G+p+   g tN +rV+
  gi|518652068|ref|YP_008141588.1| 425 DIINKIAPLGLLNPGEKAIVVSGSPSLYLGGTNNIRVI 462
                                       89999999******************99********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (559 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       410  (0.022868); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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 0.26s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 3943.34
//
Query:       gi|518652069|ref|YP_008141589.1|  [L=542]
Description: hypothetical protein FACI_IFERC00001G0708 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-25   89.0   4.9    2.8e-25   89.0   4.9    1.6  2  tRNA-synt_1d  tRNA synthetases class I (R)
    2.9e-19   69.4   0.7    5.9e-19   68.4   0.1    1.9  2  DALR_1        DALR anticodon binding domain
    0.00016   20.7   0.8       0.11   11.4   0.0    2.6  3  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
        0.1   12.7   1.0       0.39   10.8   0.0    2.5  3  ApoLp-III     Apolipophorin-III precursor (apoLp-III)
       0.11   12.6   0.2       0.29   11.2   0.2    1.8  1  DUF2433       Protein of unknown function (DUF2433)
       0.18   11.8   4.3        3.1    7.7   0.1    2.5  2  PBECR5        phage-Barnase-EndoU-ColicinE5/D-RelE like nucle


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 ?   -1.8   0.1      0.38   1.1e+03      94     165 ..      12      85 ..       5      90 .. 0.71
   2 !   89.0   4.9   9.2e-29   2.8e-25      11     349 .]      94     419 ..      84     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.38
                                       --SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHH..HHHHHHHHHHHHHHHCT---EC--CCC CS
                      tRNA-synt_1d  94 lqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkl..lvditrtelqklydrldvtlierGesl 165
                                       l++++++y   + d++    f +   ++++  ++++e + ++++   +  i r elq +y+++ + + ++ +++
  gi|518652069|ref|YP_008141589.1|  12 LDKIKTIYSVQDNDMELGTNFGDFTLKIFKFKDNREEVYSRIKSSmdMEFIDRVELQGNYINFYIKSSKMLDTV 85 
                                       56666777777777777777777777888888888888888887744566778888999999988887776555 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 9.2e-29
                                       TT.---SST-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTT CS
                      tRNA-synt_1d  11 klqkksrekkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdek 87 
                                       k+ +  ++  k +++++s n   ++hvG +r  iiGd++ r++e  G   +   +v D G+q   L  +  k+++++
  gi|518652069|ref|YP_008141589.1|  94 KYPNTFQDTSKALIEHTSSNPTGPIHVGRIRNSIIGDSIFRIIERYGTRSLTQYFVNDSGKQVISLYLGHIKYHKDE 170
                                       555566788899**************************************************866655554555544 PP

                                       TTS-----SCCCHHHHHHHHCCCSHCCCHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHCT---EC.--C CS
                      tRNA-synt_1d  88 llqeqelqdLeafykeakkdydeeeifaerarnyvvkLqsgdedirklwkllvditrtelqklydrldvtlie.rGe 163
                                          e+ +++L + y+++  + d +  ++++ ++   k ++gd+++ k  +    i+ +      ++l + +     e
  gi|518652069|ref|YP_008141589.1| 171 ---EMTVENLLDGYQKIYTNIDSDPDIKREVQELDEKYETGDNELIKEIQNTASIVLKSITDSLAKLGIHISTyVWE 244
                                       ...6789999999******************************9777777777888777888888888876544778 PP

                                       C..CCCCCHHHHHHHHHCTT-EEECTTCEEEEECCCTSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEE CS
                      tRNA-synt_1d 164 s..lykeslneivkelkkkglvkesdGalvvfldefgkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvi 238
                                       s  +   ++ ++++ l +  l   +  a+ + +    k+  + + ++DG+ ly ++D+    +  + +++d ++ v+
  gi|518652069|ref|YP_008141589.1| 245 SnfIMYGNVAQLIDSLSED-LK-SEGKAKYIEIG--DKK--IFLTRQDGTSLYFARDLV--YHMFKSENFDWIIDVL 313
                                       8655556666777766543.33.33334555554..333..456799**********96..55678889******** PP

                                       ECCCHHHHHHH.HHHHHCTTSSTTTSEEEEEEE--EE-TTSSBSBCSSSTC-BHHHHHHHHHHHHHHHHCCCCCCTS CS
                      tRNA-synt_1d 239 dsrqslhlqqi.flilkkigyvpeskdlehanfGmvlgkdkkkfktrkGetvkLadlLdealeralqlikeknkdkv 314
                                        +  + h +++ +++ + +++     ++++  +G v   d  k++trkG++v ++dl + ++e +   ik+k ++  
  gi|518652069|ref|YP_008141589.1| 314 GEDHKDHAKNLdYVLHNYLDF---PSRIDYLFYGFV-SLDTGKMSTRKGNIVTVNDLYEKTVEESAAIIKQKRPE-- 384
                                       **9999999983555555667...567888888888.889***********************************.. PP

                                       -CCCCHCHHHHHHHHHHHHCCCCTS-TTS-EE--H CS
                      tRNA-synt_1d 315 lqadelekvaeavgvgaikyaDlsknrindyifdw 349
                                        + +e +k+ +a++ ++i+y+ ++ n  +   f w
  gi|518652069|ref|YP_008141589.1| 385 YSKEEVDKISNAIAASSIRYNIIKINANKPLTFRW 419
                                       9*******************999988777777766 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.4   7.1e+03      31      51 ..     205     225 ..     186     235 .. 0.59
   2 !   68.4   0.1     2e-22   5.9e-19       1     119 []     433     542 .]     433     542 .] 0.92

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.4
                                       -SHHHHHHHHHHHTHHHHHHH CS
                            DALR_1  31 eeeeekeLlkalaqfpevlee 51 
                                        e  + eL+k++ +  +++ +
  gi|518652069|ref|YP_008141589.1| 205 YETGDNELIKEIQNTASIVLK 225
                                       333566677776666666555 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 2e-22
                                       HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH CS
                            DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn 77 
                                       ++ya+aR++s+  k ++ ++++ee       +e ek+L+ka+  +p  l+++++ l+ + +a y+  L ++f++fY 
  gi|518652069|ref|YP_008141589.1| 433 IMYAYARACSLISKTGNTESSTEEY------NEFEKALIKAMYVYPYYLQNSVDFLRADIIAGYILYLVKSFNEFYL 503
                                       69***********999777554443......4568****************************************** PP

                                       HCTSTTSCTHHH.HHHHHHHHHHHHHHHHHHHHTT----S-- CS
                            DALR_1  78 kervlkeeeeelaaaRLaLvkavrqvLangLdlLGieapekm 119
                                       ++++++++ee   ++R+++v+a ++++++  dlLGi+ +ek+
  gi|518652069|ref|YP_008141589.1| 504 NCPIIGNSEE---NKRMRIVRAFKKIMEDSADLLGIQLLEKI 542
                                       *******999...66************************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 !    7.1   0.0   0.00072       2.2      28      66 ..     109     147 ..      96     154 .. 0.79
   2 ?   -3.3   0.1       1.1   3.3e+03      71      88 ..     178     196 ..     168     204 .. 0.74
   3 !   11.4   0.0   3.6e-05      0.11     259     317 ..     330     387 ..     306     399 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00072
                      tRNA-synt_1f  28 esGispSGliHiGnlrevltadlvaralrkrgeevrlil 66 
                                        +   p G+iH+G++r+ + +d + r +++ g +  + +
  gi|518652069|ref|YP_008141589.1| 109 HTSSNPTGPIHVGRIRNSIIGDSIFRIIERYGTRSLTQY 147
                                       466779**********************99988755444 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                      tRNA-synt_1f  71 mDglRkvpenlpek.llek 88 
                                       +Dg++k++ n++++  +++
  gi|518652069|ref|YP_008141589.1| 178 LDGYQKIYTNIDSDpDIKR 196
                                       6899999999988755555 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 3.6e-05
                      tRNA-synt_1f 259 eilggeaPek.vvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkak 317
                                       + l+++  +  + Y +++l+ g kms  kGn++t++d++e   +e+ + +  + +P+ +k
  gi|518652069|ref|YP_008141589.1| 330 NYLDFPSRIDyLFYGFVSLDTG-KMSTRKGNIVTVNDLYEKTVEESAAIIKQK-RPEYSK 387
                                       5555555443157999***999.******************999998876665.887665 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013      0.39      57     112 ..     171     225 ..     145     239 .. 0.80
   2 ?   -2.3   0.0       1.4   4.3e+03      37      53 ..     252     268 ..     249     272 .. 0.82
   3 ?   -2.0   0.1       1.2   3.5e+03      65      83 ..     369     387 ..     356     399 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                         ApoLp-III  57 eealkevkkkieetadklseenPevkkkaqelqekvQsgvqslvkesqklaeslke 112
                                       e +++++ +  +++  ++ + +P++k+++qel ek  +g ++l+ke q++a+ + +
  gi|518652069|ref|YP_008141589.1| 171 EMTVENLLDGYQKIYTNIDS-DPDIKREVQELDEKYETGDNELIKEIQNTASIVLK 225
                                       56677777777888888888.*****************************987755 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.4
                         ApoLp-III  37 qlkqvikslqeelkkks 53 
                                       ++ q+i+sl+e+lk + 
  gi|518652069|ref|YP_008141589.1| 252 NVAQLIDSLSEDLKSEG 268
                                       78899999999999765 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.2
                         ApoLp-III  65 kkieetadklseenPevkk 83 
                                       k +ee a+ +++++Pe  k
  gi|518652069|ref|YP_008141589.1| 369 KTVEESAAIIKQKRPEYSK 387
                                       4566666667777777543 PP

>> DUF2433  Protein of unknown function (DUF2433)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   9.8e-05      0.29       1      45 [.      19      66 ..      19     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.8e-05
                           DUF2433  1 YgssyNefsvnpsleayrsklakskakfaevwetvkkeveaaid...e 45
                                      Y++  N++ +  ++  +  k+ k+k++ +ev+ ++k+++++++    e
  gi|518652069|ref|YP_008141589.1| 19 YSVQDNDMELGTNFGDFTLKIFKFKDNREEVYSRIKSSMDMEFIdrvE 66
                                      88899***********************************65432553 PP

>> PBECR5  phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   1.2      0.01        30     143     229 ..     137     230 ..     129     279 .. 0.76
   2 ?    7.7   0.1     0.001       3.1     195     236 ..     354     403 ..     276     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.01
                            PBECR5 143 ekllndeavkaaYLadkGeevevayvekektfteeqvevlekltdalgddeee..........geelaekiieekae 209
                                       e++ + ++  + +  d G++v   y+ +  ++ +++   +e+l d +++  ++          ++el+ek++ ++ e
  gi|518652069|ref|YP_008141589.1| 137 ERYGTRSL-TQYFVNDSGKQVISLYLGH-IKYHKDEEMTVENLLDGYQKIYTNidsdpdikreVQELDEKYETGDNE 211
                                       55544444.6778899999998888886.478887777888887777665555667777777799999999999999 PP

                            PBECR5 210 iakseakdrketekdkmedk 229
                                         k e+++  +  ++ + d 
  gi|518652069|ref|YP_008141589.1| 212 LIK-EIQNTASIVLKSITDS 230
                                       885.6666666666666655 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.001
                            PBECR5 195 e........geelaekiieekaeiakseakdrketekdkmedkidvnvlk 236
                                                ++ l ek++ee a+i k++ ++++++e dk+ ++i++  ++
  gi|518652069|ref|YP_008141589.1| 354 StrkgnivtVNDLYEKTVEESAAIIKQKRPEYSKEEVDKISNAIAASSIR 403
                                       144555666788999****************************9776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       748  (0.0417201); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3420.46
//
Query:       gi|518652070|ref|YP_008141590.1|  [L=357]
Description: 3-dehydroquinate synthase [Ferroplasma acidarmanus fer1]
Scores for complete 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-78  261.6   0.0    7.7e-78  261.3   0.0    1.1  1  DHQ_synthase  3-dehydroquinate synthase
    0.00023   21.0   0.3     0.0078   15.9   0.0    2.1  2  Fe-ADH_2      Iron-containing alcohol dehydrogenase


Domain annotation for each model (and alignments):
>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.3   0.0   8.6e-82   7.7e-78       4     261 ..      61     315 ..      58     316 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.3 bits;  conditional E-value: 8.6e-82
                                       E-SSGGGCCHHHHHHHHHHHHHTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-SHHHHHTTTSSSEEEE CS
                      DHQ_synthase   4 vpdgeksKsletlekildalleakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPttllaqvDssvGgKtai 80 
                                       ++dge+sKs + ++ ++++l+++++eR++ +  +GGG++gDl+G+ A++y+RGv+++ +PttllaqvDss+GgK+ai
  gi|518652070|ref|YP_008141590.1|  61 LKDGESSKSQKYVNIVIKKLINMEIERDNSVSYIGGGTIGDLIGYSASVYKRGVHLIGIPTTLLAQVDSSIGGKNAI 137
                                       79*************************************************************************** PP

                                       EETTEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHCTTTHHHHHHHHHH CS
                      DHQ_synthase  81 nlplgKNliGafaqPkavlidlevLktLperelraGlaEviKyalikdeelfelleenaeallkeeeeealeeliar 157
                                       n+++ KN +G+f++P+++++d+++L   ++  lr+G+aE++K+al+kd+++f++ ++++ +++   ++++le++i++
  gi|518652070|ref|YP_008141590.1| 138 NFENLKNAMGTFYNPDVIFADVDFLLGSDPALLRDGIAEAMKMALVKDRRFFNYFTSKNLNSIY--NRKSLEYVISK 212
                                       *******************************************************999977755..699******** PP

                                       HHHHHHHHHHHCCTT.TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHH CS
                      DHQ_synthase 158 sievkaevveeDeke.kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkll 233
                                       s ++k +vv+eD  + +++r lLn+GH+igHaiE+ ++  +++HG+aVa Gm+l+ +l+ k+g+  +  +e++++ +
  gi|518652070|ref|YP_008141590.1| 213 SAKIKLDVVSEDFFDsRKIRYLLNFGHSIGHAIESYTEN-RVSHGTAVANGMILESYLAYKAGFS-EPFYETVRDAV 287
                                       ***************7789******************99.*******************999887.6889******* PP

                                       HHTT---STTTT.-HHHHHHHHTTCTTX CS
                      DHQ_synthase 234 kklglpvslkelleveellealkkDkkv 261
                                       +++g+p+   +++e+++l++++k+Dkkv
  gi|518652070|ref|YP_008141590.1| 288 SAYGIPLLDFNTIETDKLVSFIKNDKKV 315
                                       ******8655556**************8 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 !   15.9   0.0   8.8e-07    0.0078      77     194 ..      89     214 ..      21     234 .. 0.76
   2 !    3.2   0.2    0.0067        60     229     250 .]     239     260 ..     237     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.8e-07
                          Fe-ADH_2  77 dlvvavGgGtiiDiakyvs..aklnvpyvsvpTa..aSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeA 149
                                       + v  +GgGti D+  y +  +k++v+++ +pT+  a vD+      ++  ++ k  + +   P  ++aD+d+l  +
  gi|518652070|ref|YP_008141590.1|  89 NSVSYIGGGTIGDLIGYSAsvYKRGVHLIGIPTTllAQVDSSIGGKNAINFENLKNAMGTFYNPDVIFADVDFLLGS 165
                                       345559*********998856799*********944467777777889999999*99988999************** PP

                          Fe-ADH_2 150 PrrllasGvGDllgkytaladwklan.....evseplaklsaamvqeaae 194
                                         +ll+ G+++++ k+  ++d +  n     +++  + ++s + v ++ +
  gi|518652070|ref|YP_008141590.1| 166 DPALLRDGIAEAM-KMALVKDRRFFNyftskNLNSIYNRKSLEYVISKSA 214
                                       **********987.555566665555444445566666666666655555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0067
                          Fe-ADH_2 229 HliSHaldmlalkqalHGeqVG 250
                                       H i Ha++   ++++ HG+ V+
  gi|518652070|ref|YP_008141590.1| 239 HSIGHAIESYTENRVSHGTAVA 260
                                       9**********9******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 2403.44
//
Query:       gi|518652071|ref|YP_008141591.1|  [L=102]
Description: hypothetical protein FACI_IFERC00001G0710 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); 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:                         0  (0); expected 0.2 (1e-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: 739.60
//
Query:       gi|518652072|ref|YP_008141592.1|  [L=262]
Description: shikimate 5-dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.2e-16   57.9   0.0    1.9e-15   56.9   0.0    1.5  1  Shikimate_dh_N   Shikimate dehydrogenase substrate binding do
      0.006   17.0   0.0      0.011   16.2   0.0    1.3  1  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.011   15.7   0.2      0.049   13.7   0.2    2.0  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.044   13.1   0.1       0.19   11.0   0.0    2.0  2  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
      0.066   13.9   0.4        0.2   12.3   0.4    1.8  1  PglD_N           PglD N-terminal domain
        0.1   12.0   0.0       0.15   11.4   0.0    1.2  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
       0.15   12.3   0.0        5.4    7.3   0.0    2.2  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Shikimate_dh_N  Shikimate dehydrogenase substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.9   0.0   7.3e-19   1.9e-15       1      83 []       6      87 ..       6      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.9 bits;  conditional E-value: 7.3e-19
                                      EEESS-TT-SHHHHHHHHHHHCTSSEEEEEEE-SCCTHHHHHHHHHHTTESEEEE-TTSCCHHHGGSSEE-HHHHHHT- CS
                    Shikimate_dh_N  1 viGnpikhSlSPaihnaafkalglngsyeafeveedelekaveelralglaGlnvTiPfKeaviplldelseeAkaigA 79
                                      +iGnp+ hS    i+n++f + g++  y+a++++ ++l+ +++  r  +++G+n+T P+Ke+ i+++d +++     g+
  gi|518652072|ref|YP_008141592.1|  6 LIGNPVGHSIGQDIYNSLFMDYGIDSMYIAIDLHRKNLPRFFDLSR-GNIEGFNITAPYKEESIQFIDYADKIVSDTGS 83
                                      79****************************************9777.8******************************* PP

                                      -SEE CS
                    Shikimate_dh_N 80 vNti 83
                                      vN +
  gi|518652072|ref|YP_008141592.1| 84 VNLV 87
                                      **86 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   4.2e-06     0.011       3      70 ..     113     178 ..     112     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.2e-06
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklle.agakvtvvapevkeeleelvklaeeelekdlegadlviaatd 70 
                                       +d++gk+v++ G G  A + ++++++ ++ ++ +v+ +  +  ++++ +a + + +d++++d++i +t+
  gi|518652072|ref|YP_008141592.1| 113 IDFSGKNVIIMGTGGAARTVAYSIMQnYNSNISIVSRN--PGEKKIYGIATTGY-NDIKEYDIIINCTP 178
                                       799*********************996779********..44456666666666.89********9995 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   1.9e-05     0.049       2      47 ..     107     152 ..     106     181 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       HHHHHHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHH CS
                      Shikimate_DH   2 lakkkleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtle 47 
                                       la+k+  ++++k+v+++G+G  a+ va  ++++   ++ ++ R+  
  gi|518652072|ref|YP_008141592.1| 107 LARKNNIDFSGKNVIIMGTGGAARTVAYSIMQNYNSNISIVSRNPG 152
                                       67777779***********************************964 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 ?   -1.5   0.0      0.54   1.4e+03      75      95 ..      69      89 ..      62      92 .. 0.84
   2 ?   11.0   0.0   7.6e-05      0.19      21      69 ..     102     150 ..      97     210 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.54
                                      HHHCCSSEEEE-SS-TT-B-G CS
                     THF_DHG_CYH_C 75 eitreadivvvavGkpelika 95
                                      +++  ad +v+ +G+ +l+k+
  gi|518652072|ref|YP_008141592.1| 69 QFIDYADKIVSDTGSVNLVKN 89
                                      56778999*******999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 7.6e-05
                                       HHHHHHHHHCT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TT CS
                     THF_DHG_CYH_C  21 kgvvellketgielegkkvvvvGrsnivgkplallLleknatVtvchsk 69 
                                       +g + l ++++i+ +gk+v+++G +         ++++ n+ ++++ ++
  gi|518652072|ref|YP_008141592.1| 102 AGFMMLARKNNIDFSGKNVIIMGTGGAARTVAYSIMQNYNSNISIVSRN 150
                                       68999*******************9998888888888888888887654 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   7.8e-05       0.2       1      44 [.     119     160 ..     119     176 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.8e-05
                            PglD_N   1 kivIiGaGGhgkvvadiieangeyeiigflDdnkktevegypvl 44 
                                       +++I+G GG ++ va  i +n   + i ++  n+ +e + y + 
  gi|518652072|ref|YP_008141592.1| 119 NVIIMGTGGAARTVAYSIMQNY-NSNISIVSRNP-GEKKIYGIA 160
                                       79*************9999988.56777777777.222223332 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 ?   11.4   0.0     6e-05      0.15      31     101 ..     112     179 ..      98     193 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6e-05
                                       BS-GTTSEEEEES-SHHHHHHH.HHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S-- CS
                      2-Hacid_dh_C  31 gkelsgktvGiiGlGrIGqava.krlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhlpl 101
                                         + sgk v i+G+G  +++va  +++  + ++ +++r++ +   ++ +g+  +  ++ ++e Di+++++pl
  gi|518652072|ref|YP_008141592.1| 112 NIDFSGKNVIIMGTGGAARTVAySIMQNYNSNISIVSRNPGE---KKIYGIATTGYND-IKEYDIIINCTPL 179
                                       55889****************945788************884...4577776666666.5788999998887 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0021       5.4       1      36 [.     120     153 ..     120     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                                       EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHH CS
                   Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskek 36 
                                       v+i G G+ ++ va  + ++ +   +i +++r+  +
  gi|518652072|ref|YP_008141592.1| 120 VIIMGTGGAARTVAYSIMQNYNS--NISIVSRNPGE 153
                                       68889999999999999998877..89999988655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       481  (0.026828); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1959.49
//
Query:       gi|518652073|ref|YP_008141593.1|  [L=272]
Description: shikimate kinase [Ferroplasma acidarmanus fer1]
Scores for 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-10   38.8   0.1    1.4e-09   38.0   0.1    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.027   14.8   0.0    1.6  1  GHMP_kinases_C  GHMP kinases C terminal
       0.07   12.3   0.1        0.1   11.8   0.1    1.3  1  Methyltransf_3  O-methyltransferase
       0.07   12.3   0.0       0.18   11.0   0.0    1.6  2  SdiA-regulated  SdiA-regulated
       0.17   11.6   0.0       0.26   11.0   0.0    1.3  1  DUF2989         Protein of unknown function (DUF2989)


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 !   38.0   0.1   3.9e-13   1.4e-09       2      66 .]      65     133 ..      64     133 .. 0.90

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.9e-13
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH..HH.HHHHHHHHHHHHHHHHHSHHH.HHHHHSS CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsl..ee.aklaleaerlaqggngsggDv.aasvyGg 66 
                                       i+i+s iP+g GL SS+A++++l++ + + + +++  +e +k+a ea  +  + +++ +D+ + ++yGg
  gi|518652073|ref|YP_008141593.1|  65 ININSQIPMGMGLKSSSAMTLSLIYGIFKINHMDIapQEvLKIASEASIHNKTSVTGAIDDlSIAYYGG 133
                                       89*****************************999666446*******988888888888888******8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.7e-06     0.027      39      84 ..     212     255 ..     210     256 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
                    GHMP_kinases_C  39 llealselGalgaklsGaGgGptvfalfkdkdeaeqvaralreefe 84 
                                       ++++++  Ga++a+ sG   Gp++f+++++++  e    +l++e++
  gi|518652073|ref|YP_008141593.1| 212 IVKKMLGTGAIYAGRSGK--GPAIFGIYETESSMESSFKQLTSEGY 255
                                       567777889*********..**********9998877777766655 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.9e-05       0.1     131     153 ..     172     194 ..     146     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.9e-05
                                       S-GGGHHHHHHHHHHTEEEEEEE CS
                    Methyltransf_3 131 aDkssyvnyyeklleLvkvGgli 153
                                        D s y+nyy +lleLvk G + 
  gi|518652073|ref|YP_008141593.1| 172 RDFSGYKNYYGRLLELVKDGHIF 194
                                       57899***************985 PP

>> SdiA-regulated  SdiA-regulated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.28     1e+03      44      87 ..     101     142 ..      62     163 .. 0.76
   2 ?   11.0   0.0   4.9e-05      0.18      23      65 ..     160     202 ..     145     213 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.28
                    SdiA-regulated  44 peelveLskeGevlrriplkgfkdpEaveylgdgrlaivdEreq 87 
                                       p+e++++  e ++ ++ +++g  d  +++y g+  +  +d  ++
  gi|518652073|ref|YP_008141593.1| 101 PQEVLKIASEASIHNKTSVTGAIDDLSIAYYGG--FCFTDNSSN 142
                                       678888888888888888888888888888765..455555554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.9e-05
                    SdiA-regulated  23 kdlSgltydpdtktLfavtnkpeelveLskeGevlrriplkgf 65 
                                       +d  +ltyd +++ +    n   +l+eL k+G++ +++ l+g+
  gi|518652073|ref|YP_008141593.1| 160 QDRMALTYDMRNRDFSGYKNYYGRLLELVKDGHIFESMMLNGY 202
                                       55779************************************94 PP

>> DUF2989  Protein of unknown function (DUF2989)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   7.2e-05      0.26      91     180 ..     108     199 ..      84     205 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 7.2e-05
                           DUF2989  91 kstkelerlqeetkeskdpellyyhWsrfgdqeAlkkflalekqgeleeaelqlalAtyylkrdaeka..kklllka 165
                                        s++ +++  + t   +d++++yy    f+d+++ + + +++ +++    elq ++A  y  r+++ +  k+++ ++
  gi|518652073|ref|YP_008141593.1| 108 ASEASIHNKTSVTGAIDDLSIAYYGGFCFTDNSSNRIISKQQIEEKYIILELQDRMALTYDMRNRDFSgyKNYYGRL 184
                                       5666666677777888999*****************************************88777655338999*** PP

                           DUF2989 166 Lelskkddkvdpeil 180
                                       Lel+k+++ +++ +l
  gi|518652073|ref|YP_008141593.1| 185 LELVKDGHIFESMML 199
                                       ****99976666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1717.56
//
Query:       gi|518652074|ref|YP_008141594.1|  [L=423]
Description: hypothetical protein FACI_IFERC00001G0713 [Ferroplasma acidarmanus fer1]
Scores for complete 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-71  240.4   0.0    3.5e-71  240.1   0.0    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.1   0.0   1.9e-75   3.5e-71       5     415 ..       8     402 ..       5     404 .. 0.94

  Alignments for each domain:
  == domain 1  score: 240.1 bits;  conditional E-value: 1.9e-75
                                       S--EEEEE--B-HHHHHHHHHHHGGGBSSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE- CS
                     EPSP_synthase   5 krlegevkvpGsksisnralllAaLaegestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeap 81 
                                       + ++g++ +p+sks+++r +l +a +++ ++i+n+  seD   +l++  +  a +i++  + + + +++    f+ p
  gi|518652074|ref|YP_008141594.1|   8 GTISGTIYAPSSKSYTQRYVLYSAFSNKPVKIKNVSFSEDEMVSLKIAESCNA-TINY--NRKDIEIKP---DFKCP 78 
                                       5799************************************************6.5566..445555556...69998 PP

                                       HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEETSS-BEEE CS
                     EPSP_synthase  82 eelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkglklkgve 158
                                         +++++g sgt+ rl ++ll  ++++++++G++++  RP+++l++aL  +G++ + +++ +   ++ +++  +gv+
  gi|518652074|ref|YP_008141594.1|  79 --DSIYVGESGTSYRLSIGLLVARKCKTTIKGEQQLAGRPVEPLIKALSDAGTNFKKHKD-GFYMVDGRNSASTGVS 152
                                       ..8*****************************************************6666.9999************ PP

                                       EETSSTTHHHHHHHHHHHTTSBSEEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B- CS
                     EPSP_synthase 159 ikaevsSqqvtsllllaallaegtteleelasepsiddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegD 235
                                       i++ +sSq+v+++l  +++l eg+ ++++++s+ ++++t++ l++fgi++ +  ++++  ++ +  + + e+ +egD
  gi|518652074|ref|YP_008141594.1| 153 IDGGTSSQFVSAMLYYYSILGEGNFTVSNMVSANYVNITINCLRNFGITVHN--NGNNYSIENGDYAVK-EIGIEGD 226
                                       ****************************************************..556688888888888.8****** PP

                                       HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEEEEEETTS--BEEEEEBGSTTSBH CS
                     EPSP_synthase 236 assAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasivvgpsglklkdvdietlpdeapt 312
                                       +ssA+yf+v ++ tg +++++n+gi+slq d+++++  l++++  i+ + ++ +v +++ +k++ vd +  pd ap+
  gi|518652074|ref|YP_008141594.1| 227 YSSASYFIVLGIFTG-NIKIKNLGIDSLQPDRQIIE-LLNNATECIKIGGNELTVDKANFIKGIIVDASATPDIAPV 301
                                       **************9.***************99988.**********999999999999****************** PP

                                       GGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHH CS
                     EPSP_synthase 313 lavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalal 389
                                       + v   f++    i + ++l+ ke+dr + ++++ r +Ga+v + e++++i+++   lk  e   ++DhR+ m+ ++
  gi|518652074|ref|YP_008141594.1| 302 ISVIGIFSTEGVKIYNYQRLKTKESDRWKGIIEMCRAFGATVSVCENFIEIKKGI--LKDPESIKFTDHRMIMSAII 376
                                       **************************************************99986..6666666677********** PP

                                       HHHHSBSEEEEETTHHHHHHSSSHHH CS
                     EPSP_synthase 390 aglvaegeveiddiectdksfpefee 415
                                       ag++a +++e +++e ++ks+pef  
  gi|518652074|ref|YP_008141594.1| 377 AGVIAGSHTEFKNAEKINKSYPEFLV 402
                                       ************************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2901.00
//
Query:       gi|518652075|ref|YP_008141595.1|  [L=72]
Description: protein translocase subunit Sss1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.1e-05   22.9   0.1    7.6e-05   22.6   0.1    1.1  1  SecE      SecE/Sec61-gamma subunits of protein translocation 


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.1   4.2e-09   7.6e-05      10      50 ..      31      71 ..      28      72 .] 0.93

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-09
                                      HHHCCCCCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 10 ElkKVtWPtrkEllkttvvVlvfvvimglflflvDlvfskl 50
                                       lk   +P+ +E++k  ++   ++v++gl++f++ ++++++
  gi|518652075|ref|YP_008141595.1| 31 ILKMAKKPNGNEYTKVVLIAGSGIVLLGLIGFIIYYIMQIV 71
                                      588999*******************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 518.00
//
Query:       gi|518652076|ref|YP_008141596.1|  [L=298]
Description: hypothetical protein FACI_IFERC00001G0715 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-14   53.0   0.2    5.3e-14   51.9   0.2    1.6  1  Spt5-NGN  Early transcription elongation factor of RNA pol II
    2.6e-05   24.0   0.0    5.4e-05   23.0   0.0    1.5  1  KOW       KOW motif
  ------ inclusion threshold ------
       0.21   11.7   0.6        1.5    9.0   0.0    2.3  2  GBR2_CC   Gamma-aminobutyric acid type B receptor subunit 2 c


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 !   51.9   0.2   8.9e-18   5.3e-14       5      84 .]     147     233 ..     144     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 8.9e-18
                          Spt5-NGN   5 vkctagqErevalslmkkilelakken.......leIkSvfapdelkGyiyvEAdrkaaveralegipnvrgvvqgl 74 
                                        kct+g+E ++a+ l++ +++ +++++       +e+++v+ p e+kGy ++E+++ ++v+ + ++i+ +rg+v+g 
  gi|518652076|ref|YP_008141596.1| 147 AKCTIGKELDIAIDLSNHAERDREERMamnknarNEVMAVMSPYEIKGYFFIETMHADRVDVLSKSIRGFRGFVSGD 223
                                       69***************988876665599999999****************************************** PP

                          Spt5-NGN  75 vpikEvedll 84 
                                       ++i+E+e++l
  gi|518652076|ref|YP_008141596.1| 224 IDISEIEKYL 233
                                       *******997 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   9.1e-09   5.4e-05       2      31 ..     245     274 ..     244     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 9.1e-09
                                       TSEEEESSSTTTTCEEEEEEEETTTTEEEE CS
                               KOW   2 GdhVkVvsGphkGktGkVvkvdqhkvrVfv 31 
                                       G  V++v Gp+kG+ +k++ +d  k+ V+v
  gi|518652076|ref|YP_008141596.1| 245 GSLVEIVEGPFKGERAKITAIDAAKEEVTV 274
                                       889**********************88887 PP

>> GBR2_CC  Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.16   9.8e+02      23      35 ..      76      88 ..      70      91 .. 0.83
   2 ?    9.0   0.0   0.00025       1.5      21      38 ..     259     276 ..     258     277 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.16
                           GBR2_CC 23 kitelDKdLEEVT 35
                                       +t+  K +EE+T
  gi|518652076|ref|YP_008141596.1| 76 EYTLSSKKIEEIT 88
                                      588899******9 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00025
                           GBR2_CC  21 RmkitelDKdLEEVTMQL 38 
                                       R kit +D   EEVT QL
  gi|518652076|ref|YP_008141596.1| 259 RAKITAIDAAKEEVTVQL 276
                                       789**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2023.81
//
Query:       gi|518652077|ref|YP_008141597.1|  [L=455]
Description: hypothetical protein FACI_IFERC00001G0716 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0029   16.8   0.4     0.0047   16.1   0.4    1.3  1  ChpXY     CO2 hydration protein (ChpXY)
  ------ inclusion threshold ------
       0.63   10.1   6.0        1.4    9.0   0.5    3.2  3  RNR_N     Ribonucleotide reductase N-terminal


Domain annotation for each model (and alignments):
>> ChpXY  CO2 hydration protein (ChpXY)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   5.3e-07    0.0047      58     140 ..     224     325 ..     182     356 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 5.3e-07
                             ChpXY  58 f..............ngevklkkllkhllhdrinyeyaeycmkamlwhgggkldayldseefkenaekaikaklksn 120
                                       +              +  +++k+ll+ l +d+iny   +     ++ + + ++d++ld  ef ++ +  i+ k+ s+
  gi|518652077|ref|YP_008141597.1| 224 MdfipdnpdiitefiHKRLSTKQLLSRLRKDKINYAIKN--NYYIINYENYGIDEFLDKLEFDDRLKPFIREKIASK 298
                                       0444444444544448999***************76554..45678888999*********************9988 PP

                             ChpXY 121 pl.......lllleklfpeflleqvrq 140
                                        +        ++le lfpe+  e vr 
  gi|518652077|ref|YP_008141597.1| 299 GFvldspsqRKVLEYLFPEYKNEIVRL 325
                                       772333333468999999999999986 PP

>> RNR_N  Ribonucleotide reductase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.1     1e+04      14      56 ..      52      93 ..      47      95 .. 0.64
   2 ?    2.2   0.2     0.021   1.8e+02      34      75 ..     119     161 ..     111     164 .. 0.80
   3 ?    9.0   0.5   0.00015       1.4      27      72 ..     235     276 ..     220     285 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                             RNR_N 14 dgkiqlekDkeAleaYlkehvnpntvkfesleekldyLvendY 56
                                      +++ ++ k ++ ++++l   v++ ++  es +  l   ++++Y
  gi|518652077|ref|YP_008141597.1| 52 KESSNFGKYHNSADQFLAG-VSETYRILESEKAPLMGVIKTNY 93
                                      5566677777777777665.77777777776666666666555 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.021
                             RNR_N  34 vnpntvkfesle.ekldyLvendYyeeevlekYskefieelyk 75 
                                       +     + ++++ +kl+     +Y+ ++  ek + +fi++l +
  gi|518652077|ref|YP_008141597.1| 119 IYRLLAFTNTVKlKKLRVYSTRNYFTATCREKIDIDFITDLLN 161
                                       55555566666678999999******************99976 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.00015
                             RNR_N  27 eaYlkehvnpntvkfesleekldyLvendYyeeevlekYskefiee 72 
                                       ++++++  + ++      ++k++y ++n+Yy  +  e+Y    i+e
  gi|518652077|ref|YP_008141597.1| 235 TEFIHKRLSTKQLLSRLRKDKINYAIKNNYYIINY-ENY---GIDE 276
                                       6788888888888888999************5443.444...3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2786.35
//
Query:       gi|518652078|ref|YP_008141598.1|  [L=149]
Description: PUA protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   70.9   0.0    9.7e-20   70.3   0.0    1.3  1  PUA       PUA domain
    1.9e-14   53.7   1.9    2.3e-14   53.4   0.1    2.1  3  DUF1947   Domain of unknown function (DUF1947)
     0.0004   20.6   0.0    0.00071   19.8   0.0    1.4  1  UPF0113   UPF0113 PUA domain


Domain annotation for each model (and alignments):
>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.0   1.6e-23   9.7e-20       2      74 .]      69     141 ..      68     141 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.6e-23
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveiervl 74 
                                        v+vd+gAv +l++g++L+apG+v+++ ++++gd+V i++ +g  +a+G+an s++ +++  +g +vei ++l
  gi|518652078|ref|YP_008141598.1|  69 NVTVDNGAVPHLMNGSNLFAPGIVDMDPNIKKGDMVFIKNMEGLYIAIGRANDSGDAIMSSRKGEAVEILHYL 141
                                       599*******************************************************************997 PP

>> DUF1947  Domain of unknown function (DUF1947)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   3.8e-18   2.3e-14       1      65 [.       2      62 ..       2      63 .. 0.91
   2 ?   -2.7   0.0       1.3   7.5e+03      13      25 ..     105     117 ..      99     121 .. 0.70
   3 ?   -1.9   0.0      0.74   4.4e+03       3      12 ..     139     148 ..     131     149 .] 0.74

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 3.8e-18
                                      --EE--HHHHHHHHHHHHTTT---TT--..-EEEE-SS-EEEEETTEEEEEESSSEEE-HHHHHH CS
                           DUF1947  1 kRHfLSkKeakeileklkekyisislesdkiEieeekkeklYlingvpilfeeekliPtLklLlk 65
                                      ++H+LSkK+ + ++ekl  ++i+ +   d iE+e +kk  +Y+++g+p+++   + +PtL+l+++
  gi|518652078|ref|YP_008141598.1|  2 SKHILSKKDYRAFMEKLSAFNIDGTSMAD-IEVETNKKNEVYYFSGKPVFY---NGMPTLYLINY 62
                                      69******************966555555.*********************...99*******96 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.3
                                       HHHHHHTTT---T CS
                           DUF1947  13 ileklkekyisis 25 
                                       +++ ++  yi i 
  gi|518652078|ref|YP_008141598.1| 105 FIKNMEGLYIAIG 117
                                       6778888887775 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.74
                                       EE--HHHHHH CS
                           DUF1947   3 HfLSkKeake 12 
                                       H+L +K +ke
  gi|518652078|ref|YP_008141598.1| 139 HYLNDKVMKE 148
                                       7777777776 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.0   1.2e-07   0.00071       7      59 ..      75     130 ..      69     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 1.2e-07
                           UPF0113   7 kaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt..k.asp 59 
                                        a   ++ G +++  +i+ +++++k++++v++ n++g  ++iG+++ ++    +s+
  gi|518652078|ref|YP_008141598.1|  75 GAVPHLMNGSNLFAPGIVDMDPNIKKGDMVFIKNMEGLYIAIGRANDSGdaImSSR 130
                                       55566777999**********************************87767633444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 976.64
//
Query:       gi|518652079|ref|YP_008141599.1|  [L=149]
Description: peroxiredoxin [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-40  137.5   0.5    2.6e-40  137.2   0.5    1.1  1  AhpC-TSA    AhpC/TSA family
    5.9e-29  100.7   0.3    6.7e-29  100.5   0.3    1.0  1  Redoxin     Redoxin
      4e-06   26.8   0.1    5.1e-06   26.4   0.1    1.2  1  SCO1-SenC   SCO1/SenC
     0.0013   18.8   0.1     0.0027   17.8   0.0    1.3  1  AhpC-TSA_2  AhpC/TSA antioxidant enzyme
     0.0063   16.1   0.0     0.0067   16.0   0.0    1.1  1  DUF899      Bacterial protein of unknown function (DUF899)


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2   0.5   7.1e-44   2.6e-40       1     123 [.       6     125 ..       6     126 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 7.1e-44
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +g++apdfe  ++dg++v+lsd+k+++vvl+fypkd++p+Ct e+++++++++ f+e+gv+v+gvsvds eshkkf+
  gi|518652079|ref|YP_008141599.1|   6 IGEQAPDFETIDQDGKNVKLSDFKDSVVVLYFYPKDNTPGCTMEAKNFRDNIDMFTEKGVKVFGVSVDSSESHKKFQ 82 
                                       89*************************************************************************** PP

                                       HH-H.SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekeslnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                       ek++lnf+llsD++++++k+ygvl     +a r t++i+ +gki+y
  gi|518652079|ref|YP_008141599.1|  83 EKYNLNFTLLSDKQKDIVKKYGVLGL--ATAKRVTYIIK-DGKIVY 125
                                       ************************55..599999*9998.588887 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.3   1.9e-32   6.7e-29       2     139 ..       6     136 ..       5     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.9e-32
                                       TTSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHH.HHHTHHHHHHCSTTTEEEEEESSSHHHH CS
                           Redoxin   2 agdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehp.yleklaellkekgvdvvavvadndafvk 77 
                                        g++aPdf++  +++dg++v+ls+fk+ +vv++f+p   +P C+ e+  + ++++ +  ekgv+v++v++d+++  k
  gi|518652079|ref|YP_008141599.1|   6 IGEQAPDFET--IDQDGKNVKLSDFKDSVVVLYFYPKDNTPGCTMEAKnFRDNIDMF-TEKGVKVFGVSVDSSESHK 79 
                                       5899*****7..56**********************************666666666.******************* PP

                                       HHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT.S CS
                           Redoxin  78 efwgkeglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet.e 139
                                       +f +k++l+f++lsD +++++k++G+           ++r++ i++dgk+vy++  ++p +  
  gi|518652079|ref|YP_008141599.1|  80 KFQEKYNLNFTLLSDKQKDIVKKYGVLGL------ATAKRVTYIIKDGKIVYVYPKVSPGEhA 136
                                       *************************7733......389*****************99995443 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.4e-09   5.1e-06       2      98 ..      11     101 ..      10     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.4e-09
                         SCO1-SenC   2 gpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkey 78 
                                        +Fe +dqdg++v+ +d+++++++++f     +  C+++ +n ++ +d++ e+   v+++ ++vD      e  k++
  gi|518652079|ref|YP_008141599.1|  11 PDFETIDQDGKNVKLSDFKDSVVVLYFYPKDNTPGCTMEAKNFRDNIDMFTEK--GVKVFGVSVDS----SESHKKF 81 
                                       58*************************9999999******************9..78889999975....5999999 PP

                         SCO1-SenC  79 leafdpriigltGskeeiak 98 
                                        e+++ +++ l++++++i k
  gi|518652079|ref|YP_008141599.1|  82 QEKYNLNFTLLSDKQKDIVK 101
                                       99999999999999988754 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 !   17.8   0.0   7.5e-07    0.0027       4      53 ..      55     105 ..      52     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 7.5e-07
                        AhpC-TSA_2   4 rdkpeldaagvklvaigigdp.sakkFvkltgfpfelyvDpsaklyqalgl 53 
                                       + ++ + ++gvk++++++++  s kkF++  + +f l+ D+++++ ++ g+
  gi|518652079|ref|YP_008141599.1|  55 DNIDMFTEKGVKVFGVSVDSSeSHKKFQEKYNLNFTLLSDKQKDIVKKYGV 105
                                       45678899*************77********************99888775 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.9e-06    0.0067      83     149 ..      41     107 ..      12     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.9e-06
                            DUF899  83 egCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsl 149
                                        + pgC++ a+++  ++  +++++v++  vs    e+ ++++++   ++ + s++++d  ++++v  
  gi|518652079|ref|YP_008141599.1|  41 DNTPGCTMEAKNFRDNIDMFTEKGVKVFGVSVDSSESHKKFQEKYNLNFTLLSDKQKDIVKKYGVLG 107
                                       4569*******************************************************99999843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 932.42
//
Query:       gi|518652080|ref|YP_008141600.1|  [L=101]
Description: 50S ribosomal protein L12P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-16   60.7  15.5    1.7e-16   60.5  15.5    1.1  1  Ribosomal_60s  60s Acidic ribosomal protein
    0.00021   21.5   1.3    0.00043   20.6   1.3    1.7  1  EF-hand_14     EF-hand domain
  ------ inclusion threshold ------
      0.063   11.8   1.8       0.07   11.7   1.8    1.0  1  RRN3           RNA polymerase I specific transcription initia
      0.084   13.5   4.4       0.12   13.0   4.4    1.2  1  DUF3824        Domain of unknwon function (DUF3824)
      0.087   12.6   1.5      0.099   12.4   1.5    1.1  1  TFB6           Subunit 11 of the general transcription factor
       0.12   12.2   4.8       0.12   12.1   4.8    1.2  1  Coilin_N       Coilin N-terminus
       0.17   12.0   3.8       0.23   11.6   3.8    1.2  1  DUF809         Protein of unknown function (DUF809)
        1.6    7.1   4.5        1.8    6.9   4.5    1.1  1  Cytomega_UL84  Cytomegalovirus UL84 protein


Domain annotation for each model (and alignments):
>> Ribosomal_60s  60s Acidic ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.5  15.5   7.8e-20   1.7e-16       1      88 []      16     100 ..      16     100 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.5 bits;  conditional E-value: 7.8e-20
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.X CS
                     Ribosomal_60s   1 eptaenikkvlkaagveveaarvkllvkalegkdieellangaaklaaaaaaaaaaaaaaaaaaaaeekkkeeeeeE 77 
                                       e+++en+kkvl +agv +++ar+k l++++++++iee+l+n+a    aa+ aaa+a +++++++++eekk+e++ e 
  gi|518652080|ref|YP_008141600.1|  16 EIDEENLKKVLTDAGVAADDARLKSLLESMKNVNIEEVLKNAA----AAPVAAAPAKEEKKEEKKKEEKKEEKKDES 88 
                                       699***************************************8....557788888888888888888888888766 PP

                                       X--SS--.STTT CS
                     Ribosomal_60s  78 eedddmG.fgLF 88 
                                       ++d ++G  +LF
  gi|518652080|ref|YP_008141600.1|  89 DSDAMAGlSSLF 100
                                       788899999999 PP

>> EF-hand_14  EF-hand domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   1.3   1.9e-07   0.00043      12      53 ..      12      53 ..       2      94 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.9e-07
                        EF-hand_14 12 eetdklsvakllkaLaetGirkdDpRLkellkklkkvekeks 53
                                      +  +++  ++l k+L ++G+  dD RLk+ll+ +k+v+ e+ 
  gi|518652080|ref|YP_008141600.1| 12 SAGKEIDEENLKKVLTDAGVAADDARLKSLLESMKNVNIEEV 53
                                      4557788899**************************998865 PP

>> RRN3  RNA polymerase I specific transcription initiation factor RRN3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   1.8   3.1e-05      0.07     178     256 ..       1      90 [.       1      98 [. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.1e-05
                              RRN3 178 vtYirnllklteycpelsedileliver..likiDVeiqveledlddeedeeleeelee..........deddeddd 242
                                       ++Yi   l l +  +e+ e+ l+ ++    ++  D+ ++  le +++ + ee  +++++          + ++e+++
  gi|518652080|ref|YP_008141600.1|   1 MEYIYGALLLHSAGKEIDEENLKKVLTDagVAADDARLKSLLESMKNVNIEEVLKNAAAapvaaapakeE-KKEEKK 76 
                                       579********************999762368999************99999988877789998877632.222222 PP

                              RRN3 243 eddeesdlddlssd 256
                                       +++++++ +d+s++
  gi|518652080|ref|YP_008141600.1|  77 KEEKKEEKKDESDS 90 
                                       22222222222222 PP

>> DUF3824  Domain of unknwon function (DUF3824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   4.4   5.4e-05      0.12      11      47 ..      55      90 ..      46      96 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                           DUF3824 11 eaalaaggaglAaheyakrrerkkaerererrreede 47
                                      + a+aa +a+  a+e +k+ e+kk+e+++e++ e d+
  gi|518652080|ref|YP_008141600.1| 55 KNAAAAPVAAAPAKE-EKKEEKKKEEKKEEKKDESDS 90
                                      445545544444443.455555555555555544433 PP

>> TFB6  Subunit 11 of the general transcription factor TFIIH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.5   4.4e-05     0.099      93     150 ..      33      89 ..      13      98 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.4e-05
                              TFB6  93 TdkVRlksivertR.vlvvevlereeeeeeee..edeeededeeeeeeeeeeeeeeedeed 150
                                        d  Rlks+ e+ + v++ evl+++  +      ++ee++e++++ee++    ee++de+d
  gi|518652080|ref|YP_008141600.1|  33 ADDARLKSLLESMKnVNIEEVLKNAAAAPVAAapAKEEKKEEKKKEEKK----EEKKDESD 89 
                                       5788*******98747788888888777763311222222222222222....22222211 PP

>> Coilin_N  Coilin N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.8   5.5e-05      0.12      89     128 ..      54      93 ..      18      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.5e-05
                          Coilin_N  89 sededsresasksasttkqkkkkKrekkqeeqdeqkasqa 128
                                        +++ +  +a++ a+++k+ +kkK+ekk+e++de+++++ 
  gi|518652080|ref|YP_008141600.1|  54 LKNAAAAPVAAAPAKEEKKEEKKKEEKKEEKKDESDSDAM 93 
                                       3456666778888899999999999999999998888765 PP

>> DUF809  Protein of unknown function (DUF809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   3.8    0.0001      0.23      78     119 ..      46      87 ..      36      94 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                            DUF809  78 snvpndevtkkvspiikgeiegkeekkegkgeiegkeekkeg 119
                                        nv  +ev k+ +         keekke k + e keekk+ 
  gi|518652080|ref|YP_008141600.1|  46 KNVNIEEVLKNAAAAPVAAAPAKEEKKEEKKKEEKKEEKKDE 87 
                                       588889999999888888899999999999998999999875 PP

>> Cytomega_UL84  Cytomegalovirus UL84 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.5   0.00082       1.8     159     183 ..      65      89 ..      38      98 .. 0.50

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00082
                     Cytomega_UL84 159 epekkkekeekkeeededdrnddre 183
                                        p k  +keekk+ee +++++d+ +
  gi|518652080|ref|YP_008141600.1|  65 APAKEEKKEEKKKEEKKEEKKDESD 89 
                                       2333333333333333333333222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2796  (0.155948); expected 358.6 (0.02)
Passed bias filter:                     1288  (0.0718389); expected 358.6 (0.02)
Passed Vit filter:                       164  (0.00914719); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 716.40
//
Query:       gi|518652081|ref|YP_008141601.1|  [L=318]
Description: acidic ribosomal protein P0 [Ferroplasma acidarmanus fer1]
Scores for complete 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-23   80.1   0.4    1.9e-22   79.1   0.4    1.6  1  RL10P_insert   Insertion domain in 60S ribosomal protein L10P
    6.2e-18   64.8   0.5    1.2e-17   63.9   0.5    1.5  1  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> RL10P_insert  Insertion domain in 60S ribosomal protein L10P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.4   2.1e-26   1.9e-22       1      71 []     107     177 ..     107     177 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.1e-26
                      RL10P_insert   1 AraGtiAtedviipagplelaPgsiepeLrklglptklkkGkivleedylvckkGetltseqaqlLklLgi 71 
                                       Ar G+iA+ed+ii++++++  Pg++++ ++k+g+p+ ++kGkiv++++++++kkGe++++e+aq+L++L+i
  gi|518652081|ref|YP_008141601.1| 107 ARGGEIAEEDIIIEPKETSFPPGPMISVFQKAGIPAGIEKGKIVIKSEVTLVKKGEVISKEKAQVLEKLEI 177
                                       9********************************************************************98 PP

>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.9   0.5   1.3e-21   1.2e-17       3      96 ..       5      99 ..       3     102 .. 0.95

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 1.3e-21
                                      CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.S..SCGCCSSSE CS
                     Ribosomal_L10  3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeek..lkellkgpv 79
                                       ++K + v+ l+e l+++ + +v++++gl+++++q++R ++r++ +++ v + +l+r+Al+++++++   ++e+ +g++
  gi|518652081|ref|YP_008141601.1|  5 AQWKVDKVNALTEELNESPVSAVISIKGLRNKEFQKIRSDIRGK-VKIEVLRARLLRLALQKSNKKNIagMTEHATGQI 82
                                      69******************************************.********************86369********* PP

                                      EEEEESS-TCHHHHCCC CS
                     Ribosomal_L10 80 alvftnedpvalakvle 96
                                      al+ t+e p+ ++++l 
  gi|518652081|ref|YP_008141601.1| 83 ALITTSETPKTVYDMLV 99
                                      ************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2261.50
//
Query:       gi|518652082|ref|YP_008141602.1|  [L=214]
Description: 50S ribosomal protein L1P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-40  138.2   1.6    3.6e-40  137.9   1.6    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 !  137.9   1.6     2e-44   3.6e-40       1     203 [.      12     203 ..      12     204 .. 0.96

  Alignments for each domain:
  == domain 1  score: 137.9 bits;  conditional E-value: 2e-44
                                       HHHHS-SSS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHH CS
                      Ribosomal_L1   1 LlkhakkkfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkkl 77 
                                       L++ +k++fdes+e+ +nl+++++  +++r++++i Lp + gk++k+++i+ ++ ++   +ak+a+     +++++l
  gi|518652082|ref|YP_008141602.1|  12 LKELKKRNFDESIEVGINLKDVDMVDPKNRINEEIILPAGRGKDLKVAVIASEEMRT---KAKNAD---YLYSVEDL 82 
                                       7888999**************************************************...999999...88889999 PP

                                       HHHHT-HHHHHHTCCH-SEEEEEGGGHHHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTT CS
                      Ribosomal_L1  78 kkkyksfeakrkllkefdlfladdrimpllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkg 154
                                       ++   ++++ +k+ k  d+f+a++ +m  ++k LG ++g+r+kmP p        +d ++ +e+++k +v  r++++
  gi|518652082|ref|YP_008141602.1|  83 NNFSDNKKSFKKIVKGIDFFVAESTLMGNVGKNLGIILGPRGKMPKPL-PP---GQDPSALIENLKK-SVRARSRDK 154
                                       9999898999**************************************.33...469**********.9******** PP

                                       SEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTTSGSEEEEEEEETTS CS
                      Ribosomal_L1 155 tclsvkvGklsftaeelaeNieavvkalvekvpkkwkniksiylkttms 203
                                        +++v++G+  +++e+l  N+++v+k ++++++k++ ni s y+k+tms
  gi|518652082|ref|YP_008141602.1| 155 ITFHVPIGTKAMSNEDLFTNLNTVLKRIISHLDKGKGNIASAYIKSTMS 203
                                       ************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1448.68
//
Query:       gi|518652083|ref|YP_008141603.1|  [L=158]
Description: 50S ribosomal protein L11P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-21   76.5   1.2      1e-21   76.5   1.2    1.6  2  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
      6e-20   71.5   0.8    9.9e-20   70.8   0.8    1.4  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
  ------ inclusion threshold ------
      0.038   13.9   0.2        3.3    7.7   0.0    2.4  2  p6               Histone-like Protein p6


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 !   76.5   1.2   1.7e-25     1e-21       8      61 ..       4      56 ..       1      62 [. 0.94
   2 ?   -3.1   0.0       1.2   7.1e+03      31      42 ..     138     149 ..     137     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.7e-25
                   Ribosomal_L11_N  8 vklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyq 61
                                      vk++v++GkAt +PplGpaLGplGln  +++k++n++Tkd++g+++pV++ v  
  gi|518652083|ref|YP_008141603.1|  4 VKTMVEGGKATSGPPLGPALGPLGLNLGQVIKDINEQTKDFAGMQVPVTVNV-V 56
                                      9*************************************************99.4 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.2
                   Ribosomal_L11_N  31 Glnikkfckefn 42 
                                       G+n+++  k+++
  gi|518652083|ref|YP_008141603.1| 138 GINAAELQKKIK 149
                                       899999888886 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 !   70.8   0.8   1.7e-23   9.9e-20       2      70 .]      69     136 ..      68     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 1.7e-23
                                       --SHHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
                     Ribosomal_L11   2 tPptsylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                                        Ppts+lLkk+agi kgsgk +++ +G+++++qv+++A+ Kks l ++ ++++av ++lgtA s+Gi+V
  gi|518652083|ref|YP_008141603.1|  69 IPPTSALLKKEAGIAKGSGKNKENYAGNLTMEQVKKVAESKKSGLLSY-TMKGAVLEVLGTALSLGITV 136
                                       5*****************************************999999.******************99 PP

>> p6  Histone-like Protein p6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1    0.0093        55      57      72 ..      50      65 ..      32      68 .. 0.88
   2 ?    7.7   0.0   0.00056       3.3      33      48 ..      90     105 ..      84     114 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.0093
                                p6 57 pvqvvsvepntevyel 72
                                      pv v  v+p t+ ye+
  gi|518652083|ref|YP_008141603.1| 50 PVTVNVVDPSTKKYEI 65
                                      99999*********98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00056
                                p6  33 setfvgnltmeqaqwr 48 
                                        e + gnltmeq +  
  gi|518652083|ref|YP_008141603.1|  90 KENYAGNLTMEQVKKV 105
                                       5899********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1108.44
//
Query:       gi|518652084|ref|YP_008141604.1|  [L=229]
Description: 2-phosphosulfolactate phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-44  151.8   0.0    1.5e-43  148.6   0.0    1.9  1  2-ph_phosp  2-phosphosulpholactate phosphatase


Domain annotation for each model (and alignments):
>> 2-ph_phosp  2-phosphosulpholactate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.6   0.0   8.2e-48   1.5e-43       8     224 ..      10     210 ..       4     212 .. 0.93

  Alignments for each domain:
  == domain 1  score: 148.6 bits;  conditional E-value: 8.2e-48
                                       EE-GTTT.EEEEE-TTTHHHHHHHHHHTT-SEEEEESSHHHHHHTCCH.HGCCEEEEE-BTTB--TTSSB-S-GGGH CS
                        2-ph_phosp   8 keeklkd.vvvviDvLRAtstivtaLanGakavipvssveealelakklpeekvllaGErgglkiegfdlgnSPley 83 
                                       +e+++ d + v iD++RAt+ti ++L ++ak++ipv+++ e +++++k p  ++l+ GEr g++i+ f++gnSP  +
  gi|518652084|ref|YP_008141604.1|  10 REKNFDDsTKVLIDIFRATTTIPLMLYRNAKSIIPVRTITETRKMKAKNP--DYLTSGERYGVRIPRFNYGNSPSVI 84 
                                       4567888899*************************************855..6************************ PP

                                       HHHHHTTSEEEEE-CCHHHHHHHCCT.SSEEEEE-STTHHHHHHHHHHHTSSEEEEE--BTTB--HHHHHHHHHHHH CS
                        2-ph_phosp  84 tkekvkgktvvltTtNGTralekaas.akrvligsllNakavaeklkelakevvivcaGtegefsleDtlcAgalve 159
                                       + e+++gkt+ +t+tNG ++l k+++   ++++ s++N +a+ +++k+++k v i+ + + + +s eD+++A +l +
  gi|518652084|ref|YP_008141604.1|  85 MGEDLSGKTLLFTSTNGIKVLFKIREfPGDIYLSSFINFTATYNAIKDREK-VSIIVSNRPDGISDEDYIYANMLKA 160
                                       **************************99*********************99.************************* PP

                                       HHHHHS.SEE-HHHHHHHHHHHC-STHHHHHHHSHHHHHHHHTT-HHHHHHHTSTSS----EEEE CS
                        2-ph_phosp 160 elekeeelelsDaalaalalyeskedllealkksshgkrLkelgleeDleycaqldlldvVpvlk 224
                                       +le e e++               +d+ ++++ s+ +krLk +g  +D+e  +++d+++  ++++
  gi|518652084|ref|YP_008141604.1| 161 KLEGE-EVN--------------VDDYCNQIRASHGAKRLKIMGAAADIESSLKVDIYHEPIIYS 210
                                       ***95.333..............46778899**************************98777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1723.41
//
Query:       gi|518652085|ref|YP_008141605.1|  [L=224]
Description: hypothetical protein FACI_IFERC00001G0724 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-22   80.5   0.5    1.5e-22   80.1   0.5    1.1  1  MAF_flag10  Protein of unknown function DUF115


Domain annotation for each model (and alignments):
>> MAF_flag10  Protein of unknown function DUF115
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.5   8.5e-27   1.5e-22      13     167 ..      36     178 ..      27     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 8.5e-27
                        MAF_flag10  13 pslkellnkfkgnkpaiivgaGPSLeknlellkelrdkaviiaadtalkaLlkegIkPDivvs.lDpqeasyevfke 88 
                                       ++ +++l+ ++g ++a+i+g+GP L++ ++ ++      ++i ad+a+++  +    PDi+v+ lD+   +++ + +
  gi|518652085|ref|YP_008141605.1|  36 HNSDNILDAYRG-RNAFIIGNGPNLKNAIKTIS----GGYVIVADSAIETYSSLYGNPDIIVTdLDG---NINSIID 104
                                       467899999999.*******************6....6788889***********************...8888777 PP

                        MAF_flag10  89 aekkgdiplvfasgvnpellkkykgpkiflvtgstqalelleeekneilfgGgsvantaldlAvklgfkeIiliGqD 165
                                         ++g+i+lv+a+g+n+++++ky +   +   ++tq++++     +  ++gG+s+++++ +lA +lg++ I+l+G+D
  gi|518652085|ref|YP_008141605.1| 105 SYNRGSIILVHAHGDNINAIEKYAKYFSN-GIATTQYIPMA----HLYNYGGFSDGDRSAFLADYLGARHITLLGFD 176
                                       77778******************998776.44445554444....2289**************************** PP

                        MAF_flag10 166 la 167
                                       + 
  gi|518652085|ref|YP_008141605.1| 177 FK 178
                                       97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1708.26
//
Query:       gi|518652086|ref|YP_008141606.1|  [L=375]
Description: hypothetical protein FACI_IFERC00001G0725 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-95  320.2  18.7    2.2e-95  319.9  18.7    1.1  1  DUF373    Domain of unknown function (DUF373)
  ------ inclusion threshold ------
       0.38   11.2   3.6        3.8    7.9   0.1    2.7  2  MFS_MOT1  Molybdate transporter of MFS superfamily
        0.6   10.5   8.4        3.9    7.8   0.6    2.6  2  DUF3995   Protein of unknown function (DUF3995)
        8.2    6.5  19.1        3.5    7.7   7.6    2.3  2  CD20      CD20-like family


Domain annotation for each model (and alignments):
>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.9  18.7     5e-99   2.2e-95       2     334 ..       3     351 ..       2     354 .. 0.96

  Alignments for each domain:
  == domain 1  score: 319.9 bits;  conditional E-value: 5e-99
                            DUF373   2 tLvlcvDrDdDlgrkagvktPvvGreavleaavklaladPeDSDvNalfgaikvydeLkaegedvevavvtGdekvg 78 
                                       tLvl+vDrD+D g kagv++Pv G+ ++++aa kl+ +dPeDSD+Nalfgaikvy++L++++e+ve+a++tGd++vg
  gi|518652086|ref|YP_008141606.1|   3 TLVLNVDRDNDYGIKAGVDGPVTGYGECYNAALKLISVDPEDSDANALFGAIKVYEDLQRKNEEVEIALITGDDDVG 79 
                                       8**************************************************************************** PP

                            DUF373  79 veadrkiaeqldevlskleadsaivVsDGaeDesvlpiiqsrvkvdsvkrVvVkqsrniEstyyllkkalkdpelrk 155
                                        ++d+ + +qld+vls  ++d+ i+VsDGaeD++++p+i+sr+++++vk++++++++niEs yy++ + +kd+++++
  gi|518652086|ref|YP_008141606.1|  80 AKSDEILGKQLDDVLSMEHYDDLILVSDGAEDDYIIPLISSRIRIRYVKHILIRHNENIESLYYYIIRGIKDKKIAR 156
                                       ***************************************************************************** PP

                            DUF373 156 tiLvplGlllliyallll..............lglpelalaiillllGlylllrGfgldelleelleklkesleegr 218
                                        + +p+Gllll y+++ll              l++++ a+++++++lG+y++ r++++++l+ +l++ +ke+ +e +
  gi|518652086|ref|YP_008141606.1| 157 KFTIPVGLLLLSYGVSLLaftiyamvitksyvLDPATGAVMFVTIVLGAYFVGRAVEINQLIIKLAADVKEYSQEAK 233
                                       ***************************************************************************** PP

                            DUF373 219 itfvtyvvallllligiisgyislesvssasvssglltlilafiygavewlalailtaslgkiideylkreekdiar 295
                                       i++++y+v++++++igi+++y+s+ ++        +++++l+fi+++v+w++++++   l  ++d y+ +e++ ++r
  gi|518652086|ref|YP_008141606.1| 234 ISMLSYLVSFFIIVIGIAYSYESIIKTVP------IMNKVLVFISAFVWWVLASFVSKELFDAFDVYM-EERHGMSR 303
                                       ***********************766665......99*******************************.66799*** PP

                            DUF373 296 llllpflvlaiglvlygasaylls.........lsilalslvvgivva 334
                                       +++ + + lai l++yg+++y+ +         +  +++ +++gi++a
  gi|518652086|ref|YP_008141606.1| 304 MWYGISFSLAIVLIVYGMMNYVRYiigfipyssMILYLTYIIAGIIIA 351
                                       **********************77999999988555555566666665 PP

>> MFS_MOT1  Molybdate transporter of MFS superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.021        93      60      97 ..     226     263 ..     174     276 .. 0.79
   2 ?    7.9   0.1   0.00086       3.8      26      61 ..     309     352 ..     277     364 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.021
                          MFS_MOT1  60 aqyrfgartgaagillGlvllllgltgllerllrliPk 97 
                                        +y ++a++ +   l++ +++++g+  + e + + +P 
  gi|518652086|ref|YP_008141606.1| 226 KEYSQEAKISMLSYLVSFFIIVIGIAYSYESIIKTVPI 263
                                       455668888888999*****************999995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00086
                          MFS_MOT1  26 slsltalllsvGlmnlltglfggvPmc........hgAgglaaq 61 
                                       s+sl+ +l+++G+mn +  ++g +P +         +Ag+++a 
  gi|518652086|ref|YP_008141606.1| 309 SFSLAIVLIVYGMMNYVRYIIGFIPYSsmilyltyIIAGIIIAL 352
                                       677899*********************99999999999999886 PP

>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.5    0.0024        11      35     105 ..     160     230 ..     145     252 .. 0.77
   2 ?    7.8   0.6   0.00088       3.9      56      94 ..     290     328 ..     247     337 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0024
                           DUF3995  35 vPsavatlavallllaaAllvlalarllgaplssrllrlaawvvaavlllRgilgdfkyvgvfkrvkdtaa 105
                                        P+ +++l  ++ lla+ + +++ ++ +   +++  +  +++v++a ++ R++     ++ + ++vk+ ++
  gi|518652086|ref|YP_008141606.1| 160 IPVGLLLLSYGVSLLAFTIYAMVITKSYVLDPATGAVMFVTIVLGAYFVGRAVEINQLIIKLAADVKEYSQ 230
                                       78888888889999999998888888888999999*****************9655556666666665555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00088
                           DUF3995  56 lalarllgaplssrllrlaawvvaavlllRgilgdfkyv 94 
                                       +  + + +++ +sr++  +++ +a+vl+++g++ +++y+
  gi|518652086|ref|YP_008141606.1| 290 AFDVYMEERHGMSRMWYGISFSLAIVLIVYGMMNYVRYI 328
                                       444455588999**********************99997 PP

>> CD20  CD20-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.6   0.00077       3.5       9      87 ..     169     259 ..     160     277 .. 0.84
   2 ?    4.5   3.6    0.0076        34      35      98 ..     304     367 ..     298     375 .] 0.57

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00077
                              CD20   9 lGllslvlGilllsvsss............tllasgypfWgGivfiisGvlgiaaekrstkllvklslllnlvslvl 73 
                                        G+  l++ i ++++++s            ++++ g+ f g +v i   ++ +aa  + +   +k+s+l+ lvs+++
  gi|518652086|ref|YP_008141606.1| 169 YGVSLLAFTIYAMVITKSyvldpatgavmfVTIVLGAYFVGRAVEINQLIIKLAADVKEYSQEAKISMLSYLVSFFI 245
                                       35555555555555555599999999999999999999999999999999*************************** PP

                              CD20  74 alaGiillilslal 87 
                                        ++Gi+++ +s+++
  gi|518652086|ref|YP_008141606.1| 246 IVIGIAYSYESIIK 259
                                       *********99987 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0076
                              CD20  35 fWgGivfiisGvlgiaaekrstkllvklslllnlvslvlalaGiillilslalltsaeelkese 98 
                                        W Gi+f ++ vl +   +++ ++ + +   ++++  ++ +++ i+++ls+ ++++++++ +s+
  gi|518652086|ref|YP_008141606.1| 304 MWYGISFSLAIVLIVYGMMNYVRYIIGFIPYSSMILYLTYIIAGIIIALSASAVHKYYSSSKSK 367
                                       6999999987555555555555666655545554444555555555555555555555553333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1119  (0.0624129); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2570.13
//
Query:       gi|518652087|ref|YP_008141607.1|  [L=53]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.5   1.0    1.6e-24   85.3   1.0    1.0  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   9.1e-29   1.6e-24       1      50 []       4      53 .]       4      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.1e-29
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++d+
  gi|518652087|ref|YP_008141607.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITRDE 53
                                      8**********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 375.31
//
Query:       gi|518652088|ref|YP_008141608.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518652088|ref|YP_008141608.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518652088|ref|YP_008141608.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518652088|ref|YP_008141608.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518652088|ref|YP_008141608.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518652088|ref|YP_008141608.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518652088|ref|YP_008141608.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518652088|ref|YP_008141608.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518652088|ref|YP_008141608.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2396.57
//
Query:       gi|518652089|ref|YP_008141609.1|  [L=71]
Description: transcription regulator (HTH) [Ferroplasma acidarmanus fer1]
Scores for complete 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   21.4   0.6    0.00047   19.8   0.2    1.8  2  HTH_41    Helix-turn-helix domain
     0.0019   18.1   0.4     0.0059   16.5   0.4    1.7  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.061   5.5e+02      29      37 ..      14      22 ..      12      25 .. 0.83
   2 !   19.8   0.2   5.2e-08   0.00047       4      38 ..      24      58 ..      22      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.061
                            HTH_41 29 lLeddkais 37
                                      +L++++a+s
  gi|518652089|ref|YP_008141609.1| 14 SLKAMGAVS 22
                                      699****97 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.2e-08
                            HTH_41  4 dRlktIeelakeleLSvGlvQkALklLeddkaisl 38
                                      +++kt +++ k++ L+  lv ++Lk L d k+++ 
  gi|518652089|ref|YP_008141609.1| 24 EKMKTADDIMKKVALGKALVNSGLKELMDGKMVKR 58
                                      79*******************************74 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.4   6.6e-07    0.0059       5      58 ..       3      62 ..       1      70 [. 0.78

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.6e-07
                                      HHHHHCCCHCHHHH......HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  5 GLseyEakvYlaLl......klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      GLs +  k+Y  L       +++ +tad+i +++ + ++ v++ L++L+d  +V+r+ ++
  gi|518652089|ref|YP_008141609.1|  3 GLSGNAEKIYSSLKamgavsEEKMKTADDIMKKVALGKALVNSGLKELMDGKMVKRVARQ 62
                                      6666666666666323333577889******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 530.24
//
Query:       gi|518652090|ref|YP_008141610.1|  [L=244]
Description: metallo-beta-lactamase superfamily hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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   47.7   0.0    3.4e-12   46.3   0.0    1.6  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.2e-08   32.3   0.2    2.5e-07   30.9   0.0    1.7  2  Lactamase_B    Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.14   12.2   0.8       0.65   10.1   0.8    2.1  1  KH_5           NusA-like KH 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 !   46.3   0.0   5.6e-16   3.4e-12       3     200 ..      20     201 ..      19     202 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 5.6e-16
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHC CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylal 79 
                                       i+iD+g ++ +  + + ++  + d l   + ++++h+H DH ag+  + +  +  ++ly   g+l++l  +      
  gi|518652090|ref|YP_008141610.1|  20 IIIDCGISMKKF-SEKTSQF-QIDGL--EKSIFISHEHSDHSAGAKAISRKLK--ADLYSRSGTLEKLHLEN----- 85 
                                       789999995433.2222222.33442..2579******************433..68*********999984..... PP

                                       HTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT CS
                     Lactamase_B_2  80 eeepavnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlgg 156
                                                   +++++++g  ++++t++ ++h++           + ++i++ g ++  + D+g + +e+ +++++
  gi|518652090|ref|YP_008141610.1|  86 ---------SYSINGEVAIG--NFTVTPVHVNHDAVD--------PVVYVIRNRGVKISVVSDLGIMNDELLDEMKN 143
                                       .........35788999**9..667777777777777........******************************** PP

                                       -SEEEEE-S-SSTTHHHH..............HHT---STSHHHHCTTSS..SSEEEEES CS
                     Lactamase_B_2 157 adllllditayeddemir..............hmgHltpeeaveaaadlg..akrlvliH 200
                                        +++ ++++  +d em +              ++gHl+ e+ +ea+       +  +l+H
  gi|518652090|ref|YP_008141610.1| 144 SNIMAIEAN--HDPEMLKngpytealkrrirsDHGHLSNEQSAEAIYSSAsdGTSIILTH 201
                                       *****8877..66667777************************99865443355666666 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   4.2e-11   2.5e-07       5     161 ..       7     140 ..       4     176 .. 0.83
   2 ?   -2.5   0.0      0.71   4.2e+03      38      53 ..     187     202 ..     174     202 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.2e-11
                                       SSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEE.EE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   5 pvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvda.vilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                        +ns++i+++ ++i+iD+G+s  +  ++       ++++ ++  ++++H H+DH +g++ + ++ ++  +  + +++
  gi|518652090|ref|YP_008141610.1|   7 RGNSTIIWDEYDAIIIDCGISMKKFSEKT----SQFQIDGLEKsIFISHEHSDHSAGAKAISRKLKADLYSRSGTLE 79 
                                       58**********************99974....5555555543499******************************9 PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHC CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallaget 157
                                       +l  e                        ++++  ++ + ++ +++ + +  ++++v++++g k+ ++ D++  +++
  gi|518652090|ref|YP_008141610.1|  80 KLHLENS--------------------YSINGEVAIGNFTVTPVHVNHDAVDPVVYVIRNRGVKISVVSDLGIMNDE 136
                                       9999999....................99999999999999999999999999999999999999999998887777 PP

                                       CCCC CS
                       Lactamase_B 158 grid 161
                                       ++++
  gi|518652090|ref|YP_008141610.1| 137 LLDE 140
                                       7665 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.71
                                       HTSGGGGEEEEE-SBS CS
                       Lactamase_B  38 lglkpkdvdavilTHl 53 
                                       ++    d + +ilTHl
  gi|518652090|ref|YP_008141610.1| 187 IYSSASDGTSIILTHL 202
                                       5556667778999996 PP

>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8   0.00011      0.65       2      52 ..      96     156 ..      95     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00011
                              KH_5   2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLk...........gekidvvewseDla 52 
                                       G+ t+  V+ +++ vdpv  ++ ++G +i+ vs+ L            + +i+ +e + D++
  gi|518652090|ref|YP_008141610.1|  96 GNFTVTPVHVNHDAVDPVVYVIRNRGVKISVVSD-LGimndelldemkNSNIMAIEANHDPE 156
                                       7778888999999****************87664.555667777777788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1666.74
//
Query:       gi|518652091|ref|YP_008141611.1|  [L=332]
Description: hypothetical protein FACI_IFERC00001G0730 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-38  131.9   4.8    3.2e-38  131.6   4.8    1.0  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    3.3e-27   95.5   7.9    4.5e-25   88.5   7.9    2.1  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    8.6e-15   55.1   2.7    6.3e-13   49.1   0.4    2.7  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    2.2e-10   39.8   1.6       0.03   13.0   0.0    4.0  4  HI0933_like    HI0933-like protein
    6.3e-10   38.7   0.1    2.9e-05   23.4   0.0    3.1  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
    1.8e-05   24.1   0.7      0.025   13.8   0.0    2.5  2  Thi4           Thi4 family
    0.00011   21.4   0.1       0.17   10.9   0.0    3.1  3  Lycopene_cycl  Lycopene cyclase protein
    0.00012   22.1   1.5        5.1    7.1   0.0    4.0  4  NAD_binding_9  FAD-NAD(P)-binding
    0.00013   20.5   0.6    0.00046   18.7   0.1    1.9  2  FMO-like       Flavin-binding monooxygenase-like
    0.00032   20.2   0.1       0.51    9.6   0.0    2.3  2  FAD_oxidored   FAD dependent oxidoreductase
    0.00044   19.9   1.7        6.4    6.3   0.0    3.2  3  DAO            FAD dependent oxidoreductase
    0.00047   20.3   0.0      0.012   15.9   0.0    2.4  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.055   12.7   0.0       0.55    9.5   0.0    2.0  2  Amino_oxidase  Flavin containing amine oxidoreductase
      0.056   12.5   1.8        2.7    7.0   0.0    3.2  3  FAD_binding_2  FAD binding domain
      0.083   12.1   0.2       0.86    8.8   0.0    2.1  2  FAD_binding_3  FAD binding domain
      0.085   13.3   1.3       0.17   12.3   0.6    2.0  1  NAD_binding_7  Putative 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 !  131.6   4.8   2.8e-41   3.2e-38       1     278 [.       4     286 ..       4     302 .. 0.84

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 2.8e-41
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH........HHHHCHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxx RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias........evvkklnq 65 
                                       +d+v+iG+Gp Gl a   ++   +k + +e     +g+++     + k +  v++ ++i +        e+ k +  
  gi|518652091|ref|YP_008141611.1|   4 YDLVIIGAGPTGLFATFLAGLRDIKSVTLEaldyTGGQIP--ELYPEKMVYDVQGIPKINAtelrdkmyEQAKLFDG 78 
                                       689**********887777778888888865544444333..33557788888888887778899999988888999 PP

                                       HCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E...EE-BCTCTTC.TTBEECCSECHHHHHHCCS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  66 gielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs...sprdlgipGvaenvgklvrtldsaealklk 139
                                       +i+l  +  v++i+p++ ++ +e  + +  ++++++++++AtG    +pr++g+pG+ e  gk+   ++ ++  k k
  gi|518652091|ref|YP_008141611.1|  79 EIKLSSK--VTDIIPDNDEYIIE--V-NGVKEYKCKAVLIATGIgdfTPRKIGCPGEDEFKGKG-VDYTVKDITKFK 149
                                       9999999..********999993..4.34469***********645577777*****9***999.788999999999 PP

                                       S-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                       Pyr_redox_2 140 llpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.. 214
                                        +   +++vGgG  ++++A +l+  +k+v+++++ +++     k+++++l ++++++G+ ++++tsv+ei+g+++  
  gi|518652091|ref|YP_008141611.1| 150 DMV--VAIVGGGDSALDYADELSGTAKKVYVLHHSEKF-----KAAEKTLDAVMNNKGISLMMNTSVTEIKGDSKir 219
                                       998..*********************************.....599*****************************88 PP

                                       EEE.EEETTSCE..EEESEEEE-S-EEES-HHCSHCCT-EEEETTE.EE--TTSBESSTTEEE-GGGC CS
                                       xxx.xxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 215 kle.vvledgee..idadlvvvavGvrpstelleeklgleldergg.ivvdeflrtnvpgiyaiGDva 278
                                       +++   ++d+++  i++d +v+a+G   + + + +++++e+ ++g+ i+v+   +tn +giya+GD a
  gi|518652091|ref|YP_008141611.1| 220 EIStINEKDKTTgsIKVDALVIAIGHVGKANVF-KSVNIETSKNGRtILVNNEFQTNLKGIYAVGDGA 286
                                       66655555666588******************9.*******8777626******************99 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 !   88.5   7.9   4.1e-28   4.5e-25      58     305 .]      58     283 ..       7     283 .. 0.74

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 4.1e-28
                       Pyr_redox_3  58 pdlnaiseetspafslkeeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsk.etyeAkkviiAtG 133
                                       p+                  +++ e+ + + e ak f+ +ikl ++V+++ ++++++++e +  ++y++k v+iAtG
  gi|518652091|ref|YP_008141611.1|  58 PK------------------INATELRDKMYEQAKLFDGEIKLSSKVTDIIPDNDEYIIEVNGvKEYKCKAVLIATG 116
                                       33..................3444455555667889999***********************956************ PP

                       Pyr_redox_3 134 efdk.PnklnipGeek..lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdps 207
                                         d+ P+k + pGe++   + + ++vk+++k+++  v+++Gg++Sa D+A el  + ++V v++++++ ++      
  gi|518652091|ref|YP_008141611.1| 117 IGDFtPRKIGCPGEDEfkGKGVDYTVKDITKFKDMVVAIVGGGDSALDYADELSGTAKKVYVLHHSEKFKAA----- 188
                                       98855**********752355999******************************************977776..... PP

                       Pyr_redox_3 208 yslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvev....kddvvlatGykpdlsflkkslfe 280
                                              e+ l+++++++ i ++ n++v+eik +++  +++t ++k  ++     d  v+a+G   +++++k+  +e
  gi|518652091|ref|YP_008141611.1| 189 -------EKTLDAVMNNKGISLMMNTSVTEIKGDSKIREISTINEKDKTTgsikVDALVIAIGHVGKANVFKSVNIE 258
                                       .......455666666655666666666666666655555543333222222336889999**************** PP

                       Pyr_redox_3 281 ldedgrpvlteeteetnvpglflaG 305
                                       ++++gr  l +++ +tn++g++ +G
  gi|518652091|ref|YP_008141611.1| 259 TSKNGRTILVNNEFQTNLKGIYAVG 283
                                       **********************998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.027        30       2      27 ..       6      32 ..       5      36 .. 0.85
   2 !   49.1   0.4   5.6e-16   6.3e-13       2      75 ..     153     220 ..     152     226 .. 0.92

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.027
                                      EEEECSSHHHHHHHHHHHHTT..SEEEE CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg..kkVtv 27
                                      +v++G+G +gl +A++la l+  k+Vt+
  gi|518652091|ref|YP_008141611.1|  6 LVIIGAGPTGL-FATFLAGLRdiKSVTL 32
                                      79********9.9999999986667775 PP

  == domain 2  score: 49.1 bits;  conditional E-value: 5.6e-16
                                       EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEE CS
                         Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgves 75 
                                       v++vGgG+++l++A +l+  +kkV+v++ s+k+      +a+k l   + ++gi +++nt+v+ei+g+++ +++
  gi|518652091|ref|YP_008141611.1| 153 VAIVGGGDSALDYADELSGTAKKVYVLHHSEKFK-----AAEKTLDAVMNNKGISLMMNTSVTEIKGDSK-IRE 220
                                       79********************************.....8888888888999***************998.555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0   6.6e-05     0.074       2      31 ..       5      34 ..       4      42 .. 0.81
   2 !   13.0   0.0   2.7e-05      0.03     107     163 ..      61     116 ..      56     130 .. 0.89
   3 ?    2.7   0.0     0.036        40       3      35 ..     153     185 ..     151     191 .. 0.92
   4 !    8.5   0.3   0.00064      0.72     114     163 ..     191     244 ..     187     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.6e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      d+++iG+G+ Gl+a+  a+ r+ + + le+
  gi|518652091|ref|YP_008141611.1|  5 DLVIIGAGPTGLFATFLAGLRDIKSVTLEA 34
                                      89**************99888877766665 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 2.7e-05
                                       -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       +a+++ d + +++k  + +++l+++v+++  ++d+ + +++++ +e++++++++AtG
  gi|518652091|ref|YP_008141611.1|  61 NATELRDKMYEQAKLFDGEIKLSSKVTDIIPDNDE-YIIEVNGVKEYKCKAVLIATG 116
                                       68888889999999999************999999.*****9**************9 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.036
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       v+++GgG + l  A +++ + k+V +l + +k+
  gi|518652091|ref|YP_008141611.1| 153 VAIVGGGDSALDYADELSGTAKKVYVLHHSEKF 185
                                       89**************************99886 PP

  == domain 4  score: 8.5 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE......TTEEEEESEEEE--- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvkt.k....seeeleadklvlAtG 163
                                       +l + ++++g++l+++t+v++++  ++++ +++t +    ++++++ d+lv+A+G
  gi|518652091|ref|YP_008141611.1| 191 TLDAVMNNKGISLMMNTSVTEIKG-DSKIREISTiNekdkTTGSIKVDALVIAIG 244
                                       5777899***************55.44444454433233367899********99 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.024        27       2      21 ..       3      21 ..       2      37 .. 0.69
   2 !   23.4   0.0   2.6e-08   2.9e-05     105     233 ..      72     190 ..      59     192 .. 0.79
   3 !    8.1   0.0    0.0012       1.3     289     339 ..     195     244 ..     189     246 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.024
                       K_oxygenase  2 ilDligiGiGpsnLsLaill 21
                                       +Dl++iG+Gp  L +a  l
  gi|518652091|ref|YP_008141611.1|  3 EYDLVIIGAGPTGL-FATFL 21
                                      59*********998.34444 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 2.6e-08
                       K_oxygenase 105 vasqleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHssey 181
                                        a+ ++ +++ +++v+++ pd++e  ++ +v+        +e++++++++++G     P  +      e+ +  + +
  gi|518652091|ref|YP_008141611.1|  72 QAKLFDGEIKLSSKVTDIIPDNDE--YIIEVNG------VKEYKCKAVLIATGIGDFTPRKIGCPG--EDEFKGKGV 138
                                       577899999************975..5555554......89********************99544..666666665 PP

                       K_oxygenase 182 lerkee..llakkriaVvGsGqSaaeifedllrrqkkvelklvtrsealepldd 233
                                        ++ ++  + +   +a+vG+G Sa + +++l  ++k  ++ ++  se+++++++
  gi|518652091|ref|YP_008141611.1| 139 DYTVKDitKFKDMVVAIVGGGDSALDYADELSGTAK--KVYVLHHSEKFKAAEK 190
                                       55555444889999****************999877..6777777777777776 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0012
                       K_oxygenase 289 vkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlATG 339
                                       v +++ ++l+ n++v++++ ++k   e+++ ne+++++ +++vda+v+A G
  gi|518652091|ref|YP_008141611.1| 195 VMNNKGISLMMNTSVTEIKGDSK-IREISTINEKDKTTGSIKVDALVIAIG 244
                                       5567889**************96.8999*********************98 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   2.2e-05     0.025      17      55 ..       3      40 ..       1      44 [. 0.84
   2 !    8.2   0.1    0.0011       1.3       8      49 ..     141     181 ..     137     189 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.2e-05
                                      EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
                              Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                                      e D+vi+GaG++GL a++  + + d+k + le+    GG
  gi|518652091|ref|YP_008141611.1|  3 EYDLVIIGAGPTGLFATFLAGLR-DIKSVTLEALDYTGG 40
                                      78*************99988888.*****9998555554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                                       HHHHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
                              Thi4   8 yfedllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                                       +++d+ k+ ++ v+ivG+G s L  a  l+     kv +l +
  gi|518652091|ref|YP_008141611.1| 141 TVKDITKFKDMVVAIVGGGDSALDYADELSGT-AKKVYVLHH 181
                                       6799***********************99988.678877765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.019        22       1      13 [.       5      17 ..       5      37 .. 0.79
   2 !   10.9   0.0   0.00015      0.17      83     144 ..      59     120 ..      47     143 .. 0.87
   3 ?    2.9   0.0     0.041        46       2      36 ..     153     185 ..     152     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.019
                     Lycopene_cycl  1 DvvviGaGpAgls 13
                                      D+v+iGaGp gl 
  gi|518652091|ref|YP_008141611.1|  5 DLVIIGAGPTGLF 17
                                      9**********94 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00015
                     Lycopene_cycl  83 rvsskrlkeellerlv.engvklleakvesveeeeageslvvleggrkirarlvvdarglasl 144
                                       +++ ++l+ ++ e+    +g + l++kv+ + ++++ e  + ++g ++ ++++v+ a+g++  
  gi|518652091|ref|YP_008141611.1|  59 KINATELRDKMYEQAKlFDGEIKLSSKVTDIIPDND-EYIIEVNGVKEYKCKAVLIATGIGDF 120
                                       68889999999887666799999*************.**********************7754 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.041
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       v+++G+G   l  A +l  + ++ kv ++  s++ 
  gi|518652091|ref|YP_008141611.1| 153 VAIVGGGDSALDYADEL--SGTAKKVYVLHHSEKF 185
                                       79***************..9999999999888876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.049        55       1      12 [.       7      18 ..       7      26 .. 0.88
   2 !    7.1   0.0    0.0046       5.1     121     154 ..      83     116 ..      71     118 .. 0.90
   3 ?    2.0   0.0      0.16   1.8e+02       1      24 [.     154     175 ..     154     212 .. 0.72
   4 !    6.2   0.0    0.0086       9.7     112     155 ..     196     245 ..     172     246 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.049
                     NAD_binding_9  1 aivGaGprGlav 12
                                      +i+GaGp+Gl +
  gi|518652091|ref|YP_008141611.1|  7 VIIGAGPTGLFA 18
                                      7********976 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0046
                     NAD_binding_9 121 raevvdleeradgqavlladgaslaadaVvLAlG 154
                                       +++v+d+ +++d++ +  ++ ++++++aV +A+G
  gi|518652091|ref|YP_008141611.1|  83 SSKVTDIIPDNDEYIIEVNGVKEYKCKAVLIATG 116
                                       689**********9998888899**********9 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.16
                     NAD_binding_9   1 aivGaGprGlavlerLlarakkks 24 
                                       aivG+G ++l  +++L   a  k+
  gi|518652091|ref|YP_008141611.1| 154 AIVGGGDSALDYADELSGTA--KK 175
                                       8**********999998886..44 PP

  == domain 4  score: 6.2 bits;  conditional E-value: 0.0086
                     NAD_binding_9 112 pegvtvevh.raevvdleeradgqavll...adg..aslaadaVvLAlGh 155
                                        ++  ++++ +++v++++ + + +++ +   +d+   s+++da+v+A+Gh
  gi|518652091|ref|YP_008141611.1| 196 MNNKGISLMmNTSVTEIKGDSKIREISTineKDKttGSIKVDALVIAIGH 245
                                       444455554388999999988776555443345522469**********9 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   4.1e-07   0.00046     141     211 ..     110     178 ..      85     186 .. 0.82
   2 ?    0.1   0.1      0.18     2e+02     305     337 ..     218     252 ..     174     278 .. 0.42

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 4.1e-07
                          FMO-like 141 avmvctGhhvnphlple.sfpGiekfkGqyfhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvll 211
                                       av++ tG     + p++   pG ++fkG+ +     k+   fk+  v ++G G+s+ d a els ta++v++
  gi|518652091|ref|YP_008141611.1| 110 AVLIATGI--GDFTPRKiGCPGEDEFKGKGVDY-TVKDITKFKDMVVAIVGGGDSALDYADELSGTAKKVYV 178
                                       66666663..3444544258*********9864.5788999*****************************87 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.18
                          FMO-like 305 ltetsaifed..gtveedidvvifatGytfafpfl 337
                                       ++e s+i e+  +t   ++d+++ a G+  +   +
  gi|518652091|ref|YP_008141611.1| 218 IREISTINEKdkTTGSIKVDALVIAIGHVGKANVF 252
                                       33333333321122222455555555554433333 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00045      0.51       1      38 [.       5      42 ..       5     119 .. 0.93
   2 !    8.7   0.1   0.00088      0.98      84     142 ..     183     238 ..     149     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00045
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll 38
                                      D+v++G+gp G+ A   A  ++ k + +e  ++ GG+ 
  gi|518652091|ref|YP_008141611.1|  5 DLVIIGAGPTGLFATFLAGLRDIKSVTLEALDYTGGQI 42
                                      99**********************************96 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00088
                      FAD_oxidored  84 fepevakavleemlaeagvtvllntrlvevekegkriesvtveskegrktirAkvfiDA 142
                                        + ++a+++l+++++++g+ +++nt ++e++ +  +i+++ + ++  + + ++++ +DA
  gi|518652091|ref|YP_008141611.1| 183 EKFKAAEKTLDAVMNNKGISLMMNTSVTEIKGDS-KIREISTINE--KDKTTGSIKVDA 238
                                       4568999************************985.8999888763..555566666665 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.3      0.01        11       1      24 [.       5      31 ..       5      41 .. 0.78
   2 !    6.3   0.0    0.0057       6.4     145     203 ..      62     118 ..      38     147 .. 0.75
   3 !    6.0   0.0    0.0066       7.4     155     203 ..     194     246 ..     177     308 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                                      EEEEECTSHHHHHHHHHHHHTT...EE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg...Vt 24
                                      d+viiG+G +Gl++ + +  r    Vt
  gi|518652091|ref|YP_008141611.1|  5 DLVIIGAGPTGLFATFLAGLRDiksVT 31
                                      89**********987766555445555 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE.EEEEEEEE--GGG CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgve.rttpgen.daadavVnaaGaw 203
                                       + +l   ++++a+   +ei + ++vt++  +d++ + +e +   g +  +++av +a+G++
  gi|518652091|ref|YP_008141611.1|  62 ATELRDKMYEQAKLFDGEIKLSSKVTDI-IPDNDEYIIEvN---GVKeYKCKAVLIATGIG 118
                                       555666788888888999*********9.444333444222...544446899******87 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0066
                                       H.HHHTT-EEEESECEEEEEEEETCEEEEE.....EECTEEEEEEEEEEE--GGG CS
                               DAO 155 a.aealGveilegtevtgleeedgkvwgve.....rttpgendaadavVnaaGaw 203
                                       a + ++G+ +  +t vt+++  d k+ ++      ++t g++ ++da+V+a G+ 
  gi|518652091|ref|YP_008141611.1| 194 AvMNNKGISLMMNTSVTEIKG-DSKIREIStinekDKTTGSI-KVDALVIAIGHV 246
                                       43778899***********54.44555554554643333554.68*******965 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 !   15.9   0.0     1e-05     0.012       1      36 [.       8      43 ..       8      57 .. 0.91
   2 ?    1.9   0.0      0.24   2.7e+02       1      25 [.     155     179 ..     155     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1e-05
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      I+GaG +Gl a  l+  ++++ + le+ d++GG++ 
  gi|518652091|ref|YP_008141611.1|  8 IIGAGPTGLFATFLAGLRDIKSVTLEALDYTGGQIP 43
                                      9********************************985 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.24
                                       EE--SHHHHHHHHHHHCCTEEEEEE CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlll 25 
                                       IvG+G s+l +A +L+   ++v +l
  gi|518652091|ref|YP_008141611.1| 155 IVGGGDSALDYADELSGTAKKVYVL 179
                                       9********9999999876666555 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00049      0.55     215     264 ..      68     119 ..      38     128 .. 0.86
   2 ?    1.0   0.0      0.18   2.1e+02     224     261 ..     202     244 ..     185     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00049
                                       HHHH..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S-HHH CS
                     Amino_oxidase 215 alae..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvplgv 264
                                        + e  +l +++i+l+++V++i  ++d++ +++   ++++++aV++++ +g 
  gi|518652091|ref|YP_008141611.1|  68 KMYEqaKLFDGEIKLSSKVTDIIPDNDEYIIEVNGVKEYKCKAVLIATGIGD 119
                                       55555556679*********************9999999********99885 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.18
                                       EEETSEEEEEEEEETTCEEEEETTSTEE.....EESEEEE-S- CS
                     Amino_oxidase 224 dirlntrVkeikregdgvtvtledgevv.....eaDaVvvTvp 261
                                       ++ +nt V+eik ++    + + + ++      ++Da v+++ 
  gi|518652091|ref|YP_008141611.1| 202 SLMMNTSVTEIKGDSKIREISTINEKDKttgsiKVDALVIAIG 244
                                       566799999999866666666655555455566*******985 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0024       2.7       1      37 [.       5      41 ..       5      43 .. 0.91
   2 ?    0.7   0.0       0.2   2.2e+02     143     204 ..     188     248 ..     158     262 .. 0.78
   3 ?    1.6   0.1       0.1   1.1e+02     377     402 ..     258     286 ..     256     302 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                                      D+++iG+G  GL A+  a  +  k + +e  +++gg+
  gi|518652091|ref|YP_008141611.1|  5 DLVIIGAGPTGLFATFLAGLRDIKSVTLEALDYTGGQ 41
                                      89**************998899999999999999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG CS
                     FAD_binding_2 143 llarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr 204
                                         ++l + +++ g+ ++ +t+++e+   d +++ +   n++++++  i+ +a+v+a g +g+
  gi|518652091|ref|YP_008141611.1| 188 AEKTLDAVMNNKGISLMMNTSVTEI-KGDSKIREISTINEKDKTTGSIKVDALVIAIGHVGK 248
                                       4455556666667***********9.5588999999999999999999999****9999997 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.1
                                       EBETTSBE...STTEEESSBTEEE-STCE CS
                     FAD_binding_2 377 etdengrv...ldadgqpipGLYAaGeva 402
                                       et  ngr+    ++ +++++G YA+G  a
  gi|518652091|ref|YP_008141611.1| 258 ETSKNGRTilvNNEFQTNLKGIYAVGDGA 286
                                       677777777666677789********866 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00077      0.86       2      27 ..       4      29 ..       3      39 .. 0.73
   2 ?    1.3   0.0      0.15   1.7e+02       3      35 ..     152     184 ..     150     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00077
                                      EEEEEE--SHHHHHHHHHHHHTTHHE CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrv 27
                                      +d +I+GaGp+Gl ++ l   + +++
  gi|518652091|ref|YP_008141611.1|  4 YDLVIIGAGPTGLFATFLAGLRDIKS 29
                                      6889*********9876655555555 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.15
                                       EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
                     FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                                        V+IVG+G + l  a +Ls    +v ++   ++
  gi|518652091|ref|YP_008141611.1| 152 VVAIVGGGDSALDYADELSGTAKKVYVLHHSEK 184
                                       589*****9999999999988777777655544 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   0.00015      0.17       3      51 ..     146     195 ..     145     280 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00015
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapev.keeleelvkla 51 
                                       +++k+  v +vGgG+ A+  +  l  + +kv v+     ++++e+++++ 
  gi|518652091|ref|YP_008141611.1| 146 TKFKDMVVAIVGGGDSALDYADELSGTAKKVYVLHHSEkFKAAEKTLDAV 195
                                       6899999**************************86653234444444332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       714  (0.0398237); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.49
# Mc/sec: 2033.25
//
Query:       gi|518652092|ref|YP_008141612.1|  [L=334]
Description: hypothetical protein FACI_IFERC00001G0731 [Ferroplasma acidarmanus fer1]
Scores for complete 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-68  231.4   0.0      2e-68  231.1   0.0    1.0  1  Diphthamide_syn  Putative diphthamide synthesis protein
  ------ inclusion threshold ------
      0.036   13.9   1.2      0.058   13.3   0.2    1.8  2  Vip3A_N          Vegetative insecticide protein 3A N terminal


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 !  231.1   0.0   2.2e-72     2e-68       2     295 ..      23     314 ..      22     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 231.1 bits;  conditional E-value: 2.2e-72
                   Diphthamide_syn   2 Pegllpdsaeiadil.eefgaevvilgDttYGaCcvdevaaehlgadllvHyGhsclspvd.rlpvlYv...fveie 73 
                                       P+gl+p s ++++++ +ef  +v+i++   YGaC++  +++ + ++d++v++Ghs++++++ + p+l++   + +ie
  gi|518652092|ref|YP_008141612.1|  23 PDGLKPESFNLFNKFsKEF--NVIISSQSFYGACDIGNMEVYR-DVDCIVQFGHSEIPNIKyTKPILFIeyfYKQIE 96 
                                       ***************6666..7*********************.***************99999****974233355 PP

                   Diphthamide_syn  74 ldvehlvetlkknfkekkkivlvstiqyahaleevkeeleeegyevv.kvpqsekplspgevlgctspklkeeeeev 149
                                       ld +++ + l++n+   k+++l+s++qy + +e v  +l+e gy+v+  + +  ++++pg+vlgc+++++++ +++v
  gi|518652092|ref|YP_008141612.1|  97 LD-DDIFSILAENL--VKNVGLLSSVQYYKEMEYVNGKLKELGYNVIvGNVDG-RMKYPGQVLGCNFSAAHSIAAKV 169
                                       54.67888888888..789*********************88**999444455.89********************* PP

                   Diphthamide_syn 150 dailyigdgrfhllslmlsnpklpvyrydpyskklteesydakkllrrRyaaiekakdakkvGiivgtlgvqgrlel 226
                                       da+l +++g fh +++ ls++k pvy +d  ++++++ + d++k+lr+Rya+ie a dakk++i++ t+ +q+r +l
  gi|518652092|ref|YP_008141612.1| 170 DAYLLVSTGLFHGIGAQLSTDK-PVYILDLNNRSIRNIQPDIDKFLRKRYARIEPAIDAKKFAIVIDTKIGQYRKKL 245
                                       ********************88.****************************************************** PP

                   Diphthamide_syn 227 verlkkllkeagkksylvlvgelnpakLanfaeidafVlvaCprlsiddgkeFekPvltpyElevalg.e 295
                                       + ++ +++k  g+++++v+ +++np   +n+  +da+V ++Cpr+sidd ++F+ Pvltp E+e ++g +
  gi|518652092|ref|YP_008141612.1| 246 AYSIYNRVKGMGRDAIIVTADNINPVDFQNL-MCDAVVFTGCPRVSIDDEDKFSMPVLTPIEFEQLFGfK 314
                                       *******************************.9********************************99932 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   6.5e-06     0.058     126     176 ..      86     136 ..      71     137 .. 0.91
   2 ?   -2.1   0.1      0.35   3.2e+03       9      30 ..     307     328 ..     305     331 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.5e-06
                           Vip3A_N 126 lqieylskqlqeisdkldiinvnvlinstlteitpayqrikyvnekfeelt 176
                                       l iey+ kq++   d + i+  n++ n  l      y+ + yvn k++el 
  gi|518652092|ref|YP_008141612.1|  86 LFIEYFYKQIELDDDIFSILAENLVKNVGLLSSVQYYKEMEYVNGKLKELG 136
                                       789*******9999999*******************************996 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.35
                           Vip3A_N   9 fngiygfatgikdimnmifktd 30 
                                       f+ ++gf +  k im+ i   d
  gi|518652092|ref|YP_008141612.1| 307 FEQLFGFKSNNKYIMDEIVGVD 328
                                       78899**********9998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2233.68
//
Query:       gi|518652093|ref|YP_008141613.1|  [L=400]
Description: hypothetical protein FACI_IFERC00001G0732 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.9e-15   56.6   0.0    9.5e-15   55.4   0.0    1.6  2  Radical_SAM  Radical SAM superfamily
    1.7e-14   53.7   0.1    3.1e-14   52.8   0.1    1.4  1  UPF0004      Uncharacterized protein family UPF0004
    9.6e-06   25.5   0.3      2e-05   24.5   0.1    1.7  2  TRAM         TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.2   7.1e+03      76     100 ..      42      64 ..      21      76 .. 0.65
   2 !   55.4   0.0   1.6e-18   9.5e-15       2     167 .]     120     291 ..     119     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                       CTEEEEEEECSSCHGHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpdeeklerllel 100
                                       + i ++v++ +t   +++++r+  l
  gi|518652093|ref|YP_008141613.1|  42 SLIGTCVVIKHTE--DRMVKRISSL 64 
                                       5666777777777..6666666554 PP

  == domain 2  score: 55.4 bits;  conditional E-value: 1.6e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS.....TTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly.....pdfvellerlakl 73 
                                       ++ +gC++ C+fC+ +     +g+  s+ +++i+++v     ++++ke+ +++ +  +y      d++el+ r++ +
  gi|518652093|ref|YP_008141613.1| 120 PINQGCTGSCNFCISHI---ARGKLLSRGIDKIVNQVNME-LDRNIKEIRISSLDTAAYgkdigTDLAELVNRISSI 192
                                       6678************8...8****************777.5667**************999999999999999999 PP

                                       CCCTEEEEEEECSSCHGHHHHHHHHHTT.....-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Radical_SAM  74 avpgiritvetngtlpdeeklerllelg.....vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr. 144
                                       + +++ ++v   +++ + ++l++l+++      +  ++l++++a +  vl  mnr +t+ee  ++ +k+++a +++ 
  gi|518652093|ref|YP_008141613.1| 193 D-RDFYLRVGMLEPRNTYDILDKLVDAYrhdrvFKFLHLPVQSAENN-VLSAMNREYTIEEAEAVWQKFHDA-FPDm 266
                                       6.99999999999999999***9999999999***************.************************.**** PP

                                       ..EEEEEEEBTTTSHHHHHHHHHHH CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 145 ..vvdrivglpGendeeleellell 167
                                          +d+i+g  + +++ +e+++++l
  gi|518652093|ref|YP_008141613.1| 267 siATDIILGYYNDSRAGFEKTMKFL 291
                                       **********************996 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.1   5.2e-18   3.1e-14       1      88 [.       2      87 ..       2      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 5.2e-18
                                      XEEEE--S-CCCCHHHHH.HHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHH CS
                           UPF0004  1 kvaietlGCqmNevdsee.laslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCm 78
                                      k+++e++GC+  +++s+  l +lLk+e+ ++v+++eeAd+ l+ TC v++++e+++++++++l++ +    +v vlGC+
  gi|518652093|ref|YP_008141613.1|  2 KIYFESYGCTLQKSESSLyLNKLLKDENNQIVNSPEEADLSLIGTCVVIKHTEDRMVKRISSLSKVS---GNVQVLGCL 77
                                      799***********99862556778889999**********************************99...68******* PP

                                      HHS-HHHHHH CS
                           UPF0004 79 aqrekeellk 88
                                      a  +++++ +
  gi|518652093|ref|YP_008141613.1| 78 ATVNGNTIES 87
                                      ****999876 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.2   7.3e+03      27      48 ..      28      51 ..      26      56 .. 0.65
   2 !   24.5   0.1   3.4e-09     2e-05       1      51 [.     343     389 ..     343     400 .] 0.81

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.2
                                      T.TEEEEETT-..-T..TEEEEEE CS
                              TRAM 27 dngkvvfvpgd..lpgIGdfVeVk 48
                                      +n+++v+ p    l+ IG  V +k
  gi|518652093|ref|YP_008141613.1| 28 ENNQIVNSPEEadLSLIGTCVVIK 51
                                      667777777766555588877777 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 3.4e-09
                                       XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT--T..TEEEEEEEEE CS
                              TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgdlpgIGdfVeVkItk 51 
                                       +sy G++  Vl+++++ ++g+++Gr  n+++v+++g +    ++ e+k t 
  gi|518652093|ref|YP_008141613.1| 343 DSYLGREEKVLITEKG-KNGTMVGRDINYRPVVLKG-NY--EKYSEIKCTI 389
                                       589*************.*******************.66..6666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2557.85
//
Query:       gi|518652094|ref|YP_008141614.1|  [L=179]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   48.4   0.1    9.3e-13   47.5   0.1    1.5  1  HTH_24           Winged helix-turn-helix DNA-binding
    7.3e-12   44.9   0.0    1.2e-11   44.2   0.0    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
    7.8e-10   38.6   0.0    1.3e-09   37.9   0.0    1.3  1  AsnC_trans_reg   Lrp/AsnC ligand binding domain
    4.2e-06   26.6   0.0    8.4e-06   25.7   0.0    1.5  1  HTH_Crp_2        Crp-like helix-turn-helix domain
    2.9e-05   23.7   0.0    5.4e-05   22.8   0.0    1.4  1  Sigma70_r4_2     Sigma-70, region 4
    0.00011   21.9   0.1     0.0007   19.3   0.1    2.0  2  HTH_38           Helix-turn-helix domain
    0.00013   21.4   0.1    0.00024   20.5   0.1    1.4  1  Sigma70_r4       Sigma-70, region 4
    0.00016   21.4   0.0    0.00034   20.4   0.0    1.5  1  HTH_IclR         IclR helix-turn-helix domain
    0.00017   21.2   0.1    0.00035   20.3   0.1    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
    0.00048   20.0   0.1    0.00094   19.1   0.1    1.4  1  HTH_11           HTH domain
    0.00067   19.4   0.1     0.0021   17.8   0.0    1.8  2  HTH_23           Homeodomain-like domain
     0.0018   18.2   0.0     0.0036   17.2   0.0    1.5  1  HTH_36           Helix-turn-helix domain
     0.0025   17.3   0.0     0.0084   15.6   0.1    1.8  2  GerE             Bacterial regulatory proteins, luxR family
      0.003   17.5   0.1     0.0065   16.4   0.1    1.5  1  MarR             MarR family
      0.003   16.9   0.1     0.0053   16.2   0.1    1.4  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
     0.0034   17.4   0.2      0.007   16.4   0.2    1.5  1  HTH_29           Winged helix-turn helix
     0.0036   17.3   0.0     0.0067   16.4   0.0    1.4  1  HTH_Mga          M protein trans-acting positive regulator (M
     0.0037   17.8   0.0     0.0069   16.9   0.0    1.4  1  Phage_rep_O      Bacteriophage replication protein O
     0.0038   17.1   0.0     0.0071   16.2   0.0    1.4  1  MarR_2           MarR family
  ------ inclusion threshold ------
      0.011   15.4   0.0       0.02   14.5   0.0    1.5  1  GntR             Bacterial regulatory proteins, gntR family
      0.013   15.9   0.1       0.06   13.7   0.0    1.9  2  Rrf2             Transcriptional regulator
      0.016   14.6   0.0      0.025   13.9   0.0    1.2  1  DUF1670          Protein of unknown function (DUF1670)
      0.025   14.5   0.0      0.032   14.1   0.0    1.2  1  Sigma70_ECF      ECF sigma factor
      0.032   14.3   0.0      0.065   13.3   0.0    1.5  1  HTH_20           Helix-turn-helix domain
      0.036   14.3   0.0       0.07   13.3   0.0    1.5  1  HTH_17           Helix-turn-helix domain
      0.084   12.8   0.0       0.15   12.0   0.0    1.4  1  Phage_antitermQ  Phage antitermination protein Q
      0.091   12.9   0.0       0.24   11.5   0.0    1.8  1  HTH_28           Helix-turn-helix domain
        0.1   12.6   0.0       0.27   11.3   0.0    1.7  2  DUF2089          Protein of unknown function (DUF2089)
       0.13   12.2   0.0       0.27   11.1   0.0    1.5  1  HTH_5            Bacterial regulatory protein, arsR family


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.1   1.5e-15   9.3e-13       2      48 .]      35      81 ..      34      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 1.5e-15
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d++d++I++ L+ n+r+s++e+A++l+ S +tv+rr+++L++  +I+
  gi|518652094|ref|YP_008141614.1| 35 DDLDKEIMCFLRYNARMSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      99****************************************99996 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   1.9e-14   1.2e-11       2      41 ..      35      74 ..      34      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.9e-14
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrL 41
                                      D++D+ I+  L+ +aR+s+ae+A++++ Se+tv+rR++ L
  gi|518652094|ref|YP_008141614.1| 35 DDLDKEIMCFLRYNARMSNAEIAKMLNTSEATVRRRINEL 74
                                      9************************************988 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   2.1e-12   1.3e-09       1      74 [.     100     169 ..     100     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 2.1e-12
                                       EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +++ +e+++   l+++++ la+ p+V+++yr  G  ++ll+  + +le +++f  + la+ +g+ +++t++v +
  gi|518652094|ref|YP_008141614.1| 100 IRIDTEGDR---LDAIADSLAANPNVLSLYRRRGQNQLLLQGLFLNLETIQEFE-DSLARKDGIVKYDTMVVSK 169
                                       689999888...*****************************************5.55**************965 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   1.4e-08   8.4e-06      19      52 ..      48      81 ..      34      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 1.4e-08
                                      EEEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 19 elpltqeelAsmlGltretvsrilseLkreglis 52
                                      + +++++e+A ml+++  tv r ++eL r+++i+
  gi|518652094|ref|YP_008141614.1| 48 NARMSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      568******************************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 !   22.8   0.0   8.7e-08   5.4e-05      21      47 ..      45      71 ..      43      76 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 8.7e-08
                                      HHHTS---HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 21 lryleglsykEIAellgisegtVksrl 47
                                      lry   +s +EIA++l++se+tV++r+
  gi|518652094|ref|YP_008141614.1| 45 LRYNARMSNAEIAKMLNTSEATVRRRI 71
                                      678888*******************98 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   1.1e-06    0.0007      14      39 ..      44      69 ..      38      72 .. 0.89
   2 ?   -0.4   0.0       1.6   9.9e+02      19      35 ..     105     121 ..     101     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.1e-06
                            HTH_38 14 erllaeGlslreIArrLgrspsTIsR 39
                                         +++ +s++eIA+ L+ s  T+ R
  gi|518652094|ref|YP_008141614.1| 44 FLRYNARMSNAEIAKMLNTSEATVRR 69
                                      56799*******************99 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.6
                            HTH_38  19 eGlslreIArrLgrsps 35 
                                       eG  l +IA  L  +p+
  gi|518652094|ref|YP_008141614.1| 105 EGDRLDAIADSLAANPN 121
                                       788999***99987776 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   3.9e-07   0.00024      15      46 ..      45      76 ..      37      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3.9e-07
                                      HHHTTT--HHHHHHHHTS-HHHHHHHHHHHHH CS
                        Sigma70_r4 15 lrfgeglTleEIgerlgiSrerVrqiekrAlr 46
                                      lr+   ++ +EI+++l+ S+ +Vr+++++ +r
  gi|518652094|ref|YP_008141614.1| 45 LRYNARMSNAEIAKMLNTSEATVRRRINELVR 76
                                      899***********************988665 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   5.5e-07   0.00034      11      48 ..      43      80 ..      41      81 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 5.5e-07
                                      T-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                          HTH_IclR 11 alaeapqeltlselArrtglpkStvhRlLqtLvelGyv 48
                                      ++ + + +++++e+A+ +  + +tv+R ++ Lv+++++
  gi|518652094|ref|YP_008141614.1| 43 CFLRYNARMSNAEIAKMLNTSEATVRRRINELVRRKII 80
                                      7889999***************************9976 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.6e-07   0.00035       3      45 ..      39      81 ..      38      82 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.6e-07
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      ++i+  l+    +s  e++  l++SeaT+RR +neL+   ++t
  gi|518652094|ref|YP_008141614.1| 39 KEIMCFLRYNARMSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      5677778888889999********************9988775 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.1   1.5e-06   0.00094      11      39 ..      46      74 ..      38      82 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.5e-06
                            HTH_11 11 eargpisgeeLAeeLnvSrrtvrrdIkaL 39
                                      + +  +s +e+A+ Ln S++tvrr+I +L
  gi|518652094|ref|YP_008141614.1| 46 RYNARMSNAEIAKMLNTSEATVRRRINEL 74
                                      55556999******************998 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   3.4e-06    0.0021      15      40 ..      48      73 ..      40      86 .. 0.81
   2 ?   -1.8   0.0         5   3.1e+03      17      28 ..     106     117 ..     101     134 .. 0.57

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.4e-06
                            HTH_23 15 aeGlsvreIAreLgvsrrTvyrwlkr 40
                                        ++s +eIA++L+ s+ Tv+r ++ 
  gi|518652094|ref|YP_008141614.1| 48 NARMSNAEIAKMLNTSEATVRRRINE 73
                                      3489*****************98775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 5
                            HTH_23  17 GlsvreIAreLg 28 
                                       G++  +IA+ L 
  gi|518652094|ref|YP_008141614.1| 106 GDRLDAIADSLA 117
                                       556666666554 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.8e-06    0.0036      24      55 .]      43      80 ..      36      80 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.8e-06
                            HTH_36 24 cfp......sqetlakrlglsknTvsraikeLeqlGyi 55
                                      cf       s++ +ak l+ s+ Tv+r i+eL++  +i
  gi|518652094|ref|YP_008141614.1| 43 CFLrynarmSNAEIAKMLNTSEATVRRRINELVRRKII 80
                                      6663333447***********************98766 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   1.4e-05    0.0084      18      43 ..      51      76 ..      38      85 .. 0.87
   2 ?   -1.5   0.0       3.2   1.9e+03      16      40 ..     105     129 ..      99     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.4e-05
                                      S-HHHHHHHHTS-HHHHHHHHHHHHH CS
                              GerE 18 ksnkeIAeelniSekTVkvhksnimk 43
                                      +sn eIA+ ln Se TV+  + ++ +
  gi|518652094|ref|YP_008141614.1| 51 MSNAEIAKMLNTSEATVRRRINELVR 76
                                      79***************998888766 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.2
                                       TTS-HHHHHHHHTS-HHHHHHHHHH CS
                              GerE  16 eGksnkeIAeelniSekTVkvhksn 40 
                                       eG     IA++l   ++  + ++++
  gi|518652094|ref|YP_008141614.1| 105 EGDRLDAIADSLAANPNVLSLYRRR 129
                                       6777778999998777776766665 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.1e-05    0.0065       8      47 ..      41      80 ..      39      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR  8 iLrilyeqgplsvseLakklgvskstvtrvldrLekkGli 47
                                      i++ l+++  +s++e+ak+l++s +tv r + +L+++  i
  gi|518652094|ref|YP_008141614.1| 41 IMCFLRYNARMSNAEIAKMLNTSEATVRRRINELVRRKII 80
                                      6778999999************************998665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   8.5e-06    0.0053      27      52 .]      51      75 ..      48      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.5e-06
                      HTH_Tnp_ISL3 27 srsvkavArqlgvSwtTVwrildryv 52
                                      + s +++A++l++S+ TV+r+++++v
  gi|518652094|ref|YP_008141614.1| 51 M-SNAEIAKMLNTSEATVRRRINELV 75
                                      5.999*****************9876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   1.1e-05     0.007       4      34 ..      43      72 ..      41      77 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                            HTH_29  4 allllaeGvstvsqiAkllglsrrtvyrwlk 34
                                      + l ++  +s  ++iAk+l+ s+ tv+r ++
  gi|518652094|ref|YP_008141614.1| 43 CFLRYNARMS-NAEIAKMLNTSEATVRRRIN 72
                                      5677888897.*****************776 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.1e-05    0.0067      13      45 ..      44      75 ..      36      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.1e-05
                           HTH_Mga 13 lLteneksltldelakeLglseltlqsdiseLn 45
                                      +L  ++ +++  e+ak L++se t++ +i+eL 
  gi|518652094|ref|YP_008141614.1| 44 FL-RYNARMSNAEIAKMLNTSEATVRRRINELV 75
                                      44.4599************************95 PP

>> Phage_rep_O  Bacteriophage replication protein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-05    0.0069      45      80 ..      46      81 ..      40      92 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-05
                       Phage_rep_O 45 kksdwisnsqlveltgisrtkvskalkeLirekvii 80
                                      + ++++sn +++++ ++s++ v++ ++eL+r+k+i+
  gi|518652094|ref|YP_008141614.1| 46 RYNARMSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      567899****************************96 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.2e-05    0.0071      11      52 ..      42      81 ..      38      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.2e-05
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      + +L+ + +  ++ +e+a+ l+ s ++v r++++Lv++  ++
  gi|518652094|ref|YP_008141614.1| 42 MCFLRYNAR--MSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      567788887..999***********************99886 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   3.2e-05      0.02      19      55 ..      46      81 ..      35      84 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                                      -TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              GntR 19 rpGdkLPsereLaaefgVsrttvReALrrLeaeglve 55
                                      r ++++ s  e+a+++++s  tvR+ +++L+++++++
  gi|518652094|ref|YP_008141614.1| 46 RYNARM-SNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      567788.999***********************9986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   9.7e-05      0.06      22      56 ..      48      81 ..      40      84 .. 0.84
   2 ?   -0.6   0.0       2.8   1.8e+03      27      43 ..     108     124 ..      91     129 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.7e-05
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + + +s +eia++ n+s+  +++ +++L + ++++
  gi|518652094|ref|YP_008141614.1| 48 NAR-MSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      333.999***********************99997 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 2.8
                                       -HHHHHHHHTS-HHHHH CS
                              Rrf2  27 sseeiaerqnispsyle 43 
                                       ++++ia++   +p++l+
  gi|518652094|ref|YP_008141614.1| 108 RLDAIADSLAANPNVLS 124
                                       46889999999998875 PP

>> DUF1670  Protein of unknown function (DUF1670)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   4.1e-05     0.025     104     135 ..      49      79 ..      46      88 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.1e-05
                           DUF1670 104 alltqsDlalllgvstrtvskqvkeyqeeegi 135
                                       a ++++++a +l++s++tv+++++e+ ++ +i
  gi|518652094|ref|YP_008141614.1|  49 ARMSNAEIAKMLNTSEATVRRRINELVRR-KI 79 
                                       67899*********************554.44 PP

>> Sigma70_ECF  ECF sigma factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.3e-05     0.032     146     179 ..      45      79 ..       7      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.3e-05
                       Sigma70_ECF 146 lrkleGlsveEiAeklgvskrtverrl.alaRawl 179
                                       lr+ + +s++EiA+ l+ s++tv+rr  +l+R ++
  gi|518652094|ref|YP_008141614.1|  45 LRYNARMSNAEIAKMLNTSEATVRRRInELVRRKI 79 
                                       56667789*****************9845888775 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011     0.065      19      55 ..      45      81 ..      36      82 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                                      HSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20 19 LaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      L+ ++ ++ +e+a+ l +s +t+++++++L++  +++
  gi|518652094|ref|YP_008141614.1| 45 LRYNARMSNAEIAKMLNTSEATVRRRINELVRRKIIT 81
                                      677888999***********************99987 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00011      0.07       2      23 ..      51      72 ..      50      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00011
                            HTH_17  2 ltveEaAelLgvsrstvyrlir 23
                                      ++ +E+A++L+ s++tv+r i+
  gi|518652094|ref|YP_008141614.1| 51 MSNAEIAKMLNTSEATVRRRIN 72
                                      7889**************9774 PP

>> Phage_antitermQ  Phage antitermination protein Q
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00025      0.15      72     101 ..      44      73 ..      35      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00025
                   Phage_antitermQ  72 vdyYvfgvskraiarklkisekevrkklqk 101
                                       + +Y +++s+ +ia+ l++se +vr++++ 
  gi|518652094|ref|YP_008141614.1|  44 FLRYNARMSNAEIAKMLNTSEATVRRRINE 73 
                                       679************************974 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00039      0.24       9      34 ..      47      72 ..      43      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00039
                            HTH_28  9 laaGhsvreaArelgisrrtvyrWik 34
                                      + a +s +e+A+ l++s+ tv+r i+
  gi|518652094|ref|YP_008141614.1| 47 YNARMSNAEIAKMLNTSEATVRRRIN 72
                                      66678999***************997 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00044      0.27      29      75 ..      32      76 ..       5      83 .. 0.79
   2 ?   -1.8   0.0       4.9   3.1e+03      68      82 ..     107     121 ..      89     140 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                           DUF2089 29 sefarLskeqlefvelfikarGnlkevekelgisYpTvrnrldeile 75
                                       +f+ L+ke + f++   ++  +  e++k l+ s  Tvr r++e+++
  gi|518652094|ref|YP_008141614.1| 32 LPFDDLDKEIMCFLRYNARM--SNAEIAKMLNTSEATVRRRINELVR 76
                                      57888888877777765544..446999****************987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 4.9
                           DUF2089  68 nrldeileaLgyeee 82 
                                        rld+i+ +L  +++
  gi|518652094|ref|YP_008141614.1| 107 DRLDAIADSLAANPN 121
                                       689999998888776 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 ?   11.1   0.0   0.00044      0.27       6      35 ..      40      70 ..      39      80 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00044
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHHHH CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvShH 35
                                      +I+++L+    ++  e+a++l+ s++tv++ 
  gi|518652094|ref|YP_008141614.1| 40 EIMCFLRYnARMSNAEIAKMLNTSEATVRRR 70
                                      89*****9666*****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1134.94
//
Query:       gi|518652095|ref|YP_008141615.1|  [L=455]
Description: hypothetical protein FACI_IFERC00001G0734 [Ferroplasma acidarmanus fer1]
Scores for complete 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-80  269.0   0.1    9.8e-80  268.2   0.0    1.4  2  Lyase_1      Lyase
      3e-11   43.6   0.1    9.2e-11   42.0   0.1    1.9  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.2   0.0   1.1e-83   9.8e-80       1     312 []       9     339 ..       9     339 .. 0.96
   2 ?   -3.0   0.0      0.41   3.7e+03     134     150 ..     369     385 ..     348     437 .. 0.51

  Alignments for each domain:
  == domain 1  score: 268.2 bits;  conditional E-value: 1.1e-83
                                       CEEEEETCHHHHHHHHHHHHHGGGHHHHHC......HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHC CS
                           Lyase_1   1 grftvkadklmgiftersrenfrlseedik......alaalkkaaakanvdl....keeaaaiikaldevleegkld 67 
                                       g+++   + ++gi t r++ nf +s+ + k      a+a++kk+aa an  +    ke  ++i ka+d +++ g+ d
  gi|518652095|ref|YP_008141615.1|   9 GEVQIDDSIYYGINTLRAKNNFNISGIKSKdrdhikAMAIVKKGAAYANYTAgklqKELYESISKACDRLIS-GDFD 84 
                                       5667777889***************98888999*****************9999999999************.**** PP

                                       GGHHHBSSSSSHHHHHHHHHHHHHH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHH CS
                           Lyase_1  68 dqfvlkviqegsgtavnmnlnevig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpa 134
                                       +qfv++v+q g+gt++nmn+ne+++    e l+      ++ +pnd ++++qS+nD++pT +r+ +  +   kL+++
  gi|518652095|ref|YP_008141615.1|  85 EQFVVDVFQAGAGTSFNMNTNEILAnlvlESLNhkkgeyKYAHPNDVINMSQSTNDIYPTMMRVSIMLKS-PKLIEN 160
                                       *************************7777555589999*9*****************************9.66**** PP

                                       HHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSC CS
                           Lyase_1 135 leqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtglnad 211
                                        e Li++lk+k kef++v k GrThlqdA+ vtlg e+ a+a a+ rd++ +k +l  +++el+ ggtavg+g+n+ 
  gi|518652095|ref|YP_008141615.1| 161 AEALIKSLKAKHKEFEKVYKTGRTHLQDAVRVTLGDEFNAWAFAIGRDLKEFKSAL-DYILELNIGGTAVGNGANTP 236
                                       ********************************************************.9******************* PP

                                       CTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSS CS
                           Lyase_1 212 pefaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesep 286
                                         ++e+ +k++++ tg++  + +n +  ++  ++   ++  l+++a++Lsk++ Dlrll sg+ agl+e+ l++ ++
  gi|518652095|ref|YP_008141615.1| 237 DGYKEYAVKKISEETGFNfRPGENLMGIMQFMTDFSRVINSLSNMALDLSKISDDLRLLYSGPgAGLHEIVLPAVQQ 313
                                       ***************************************************************************** PP

                                       C-TTSTTTEBTHHHHHHHHHHHHHHH CS
                           Lyase_1 287 GSSiMPgKvNPvqlElltgvagrvvG 312
                                       GSSiMPgK NP  +E++++++  + G
  gi|518652095|ref|YP_008141615.1| 314 GSSIMPGKINPSIAEAMNMICHSITG 339
                                       *********************99987 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.41
                                       HHHHHHHHHHHHHHHTT CS
                           Lyase_1 134 aleqLidalkekakefk 150
                                        +e+L++++k   +e  
  gi|518652095|ref|YP_008141615.1| 369 SIERLANGIKMLDEEAI 385
                                       33333333333322222 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.1     1e-14   9.2e-11       4      50 ..     408     454 ..     406     455 .] 0.95

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 1e-14
                                       GGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HH CS
                       FumaraseC_C   4 aLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpe 50 
                                        Lnp++GY++ akI+ e l++gk+++++vl+ g ++e++++e+++ +
  gi|518652095|ref|YP_008141615.1| 408 LLNPYLGYDTMAKIVEESLETGKSIKDLVLATGKIDEKKYKEIFNFL 454
                                       69*****************************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (455 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3106.82
//
Query:       gi|518652096|ref|YP_008141616.1|  [L=216]
Description: hypothetical protein FACI_IFERC00001G0735 [Ferroplasma acidarmanus fer1]
Scores for 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-47  159.6  20.8    9.2e-47  159.4  20.8    1.0  1  DUF981    Protein of unknown function (DUF981)
  ------ inclusion threshold ------
       0.18   10.7   0.2        0.3   10.0   0.2    1.3  1  TMEM171   Transmembrane protein family 171


Domain annotation for each model (and alignments):
>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4  20.8     1e-50   9.2e-47       1     186 [.      13     213 ..      13     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 1e-50
                            DUF981   1 MaFidyltlmlitlgagllllayyvlkal......eerekkeankalaapflivGllalitGlhmtltWPlpgsYni 71 
                                       M F+d+  ++l++++++ ++ +y+   ++      ++++ +e+ k+ a+p++i+G++++++Gl+++++WPlpg Yni
  gi|518652096|ref|YP_008141616.1|  13 MGFVDDTPMELFLISLVAIVSIYMSAWVYiefrknGAKNVNEILKPGALPLGILGAIIVLMGLWGEMVWPLPGAYNI 89 
                                       88999999999988888887777766666677999999999************************************ PP

                            DUF981  72 lfgdpallfGvllllaavalykkaklkalgilalflGlilivygvailklgLtaePlaalllyilvGLagllsplvl 148
                                       lf dp++++G+++l++a +++ k+kl+++gila+f+G+i i yg++ +  +Lt++P+a+++l++++GL+g+++++++
  gi|518652096|ref|YP_008141616.1|  90 LFDDPFMFLGIIVLMMAGTIALKQKLQYVGILAFFAGIISIWYGANAYVDKLTSSPIAMFGLFLAFGLTGVFTFPTT 166
                                       ***************************************************************************** PP

                            DUF981 149 lkldksrs.........vllvlaavlliiagllalliGieavyeHla 186
                                       l++d   +         v+lvl+++ l++++++a+liG+ea+++Hl 
  gi|518652096|ref|YP_008141616.1| 167 LIYDILPGktkvsnvwtVVLVLFWIGLVVSAVVAALIGLEAIPAHLV 213
                                       **998886678899999****************************95 PP

>> TMEM171  Transmembrane protein family 171
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   3.4e-05       0.3     124     174 ..      28      75 ..      21      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 3.4e-05
                           TMEM171 124 LisilgiwvPGCssdwaqellnetdsadae.pqiCgfLslqilGplivlvGL 174
                                       L++i+ i+     s w   ++ ++ +++++     g L+l ilG++ivl+GL
  gi|518652096|ref|YP_008141616.1|  28 LVAIVSIY----MSAWVYIEFRKNGAKNVNeILKPGALPLGILGAIIVLMGL 75 
                                       34444444....577888888888777765145689***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1417.17
//
Query:       gi|518652097|ref|YP_008141617.1|  [L=377]
Description: isocitrate dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  149.3   0.0    1.8e-43  149.0   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.36   11.1   0.0    1.9  2  TAF       TATA box binding protein associated factor (TAF)


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0     2e-47   1.8e-43       2     348 .]      26     370 ..      25     370 .. 0.91

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 2e-47
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT...-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekag...lelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk 75 
                                       i  + gdgiGpe++ a++ v+++a e a+   +++e++++ +G +a+++ g+ +pe++++ i++  ++++  ++   
  gi|518652097|ref|YP_008141617.1|  26 IGYIDGDGIGPEITGAMIGVVNSAIELAYqgsRSIEWHKILIGTEAYEKFGTYVPEDSIKEIQKMYIAMKSTLNFMP 102
                                       8899*********************99998999****************************************9876 PP

                                       SSSSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET......... CS
                            Iso_dh  76 ekevrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg......... 143
                                         ++r  n  + Lrk l+l++n+r  k++  ++   p+     + ++l i+R+ t    +  ++ +++         
  gi|518652097|ref|YP_008141617.1| 103 --DKRDLN--TILRKRLGLYSNIRILKYI--EGMDIPVNT--FNRLNLTIIRDSTPNSHIFYHSSESTddlirfisd 171
                                       ..899999..668****************..677778875..7889*********8864443333333346****** PP

                                       ....TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH..HHHHHHHHHHCCTTTTSEEE CS
                            Iso_dh 144 ....sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse..lwrkiveevaeeeypdiele 214
                                           +  t ++++ +++ s+  +++ia++a+ + +++gkkk+t+++      s++   + +++ e a+ + +d+ +e
  gi|518652097|ref|YP_008141617.1| 172 nyglN-ITPDSGIYMMPQSKFRTRKIAKQAVRYSRRNGKKKITILE------SQQnhEFANWCIEEAS-AQEDVGYE 240
                                       99865.58889**************************999887655......444459*********9.99****** PP

                                       EEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-TH CS
                            Iso_dh 215 hqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpi 291
                                            +++ +l+ sp+ f+Vi+++N+    l D +a   G + +  ++s+g ++ a+fEav  s p  ag d a p+
  gi|518652097|ref|YP_008141617.1| 241 VLKTREFMKRLISSPEDFEVILVDNVLSQTLVDYLA---GTINIEYGSSIG-DECAVFEAVQSSLPSEAGYDAADPL 313
                                       **************************9999999876...8999********.79*********************** PP

                                       HHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS.TCCCHHHHHHHHH CS
                            Iso_dh 292 avilSaalmLryslgleeaAdkiekAvekvleagivTkDlagea.akevstsefgdav 348
                                       + ilS   mL + +g+ eaA+ ie+A++++++++++ kD+ +      +++sef  ++
  gi|518652097|ref|YP_008141617.1| 314 SFILSGCEMLMH-IGWVEAAQIIENAISAAFRDNKIPKDINTRPdISPIKCSEFSSEI 370
                                       ************.***************************998768899999998765 PP

>> TAF  TATA box binding protein associated factor (TAF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.84   7.5e+03       3      15 ..      78      90 ..      77      91 .. 0.78
   2 ?   11.1   0.0     4e-05      0.36       4      57 ..     161     213 ..     158     216 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.84
                                      ---HHHHHHHHHH CS
                               TAF  3 ilpkesvkviAes 15
                                       +p++s+k i  +
  gi|518652097|ref|YP_008141617.1| 78 YVPEDSIKEIQKM 90
                                      6899999998665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4e-05
                                       --HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB- CS
                               TAF   4 lpkesvkviAeslGitnLsdeaaalLaedveyrlkeivqeaakfmrhskRqkLt 57 
                                       ++ + ++ i +  G+ n+  +    + +++++r ++i+++a+++ r    +k+t
  gi|518652097|ref|YP_008141617.1| 161 STDDLIRFISDNYGL-NITPDSGIYMMPQSKFRTRKIAKQAVRYSRRNGKKKIT 213
                                       5677799999*****.****************************9998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2525.45
//
Query:       gi|518652098|ref|YP_008141618.1|  [L=594]
Description: zinc metalloprotease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.07   12.4   1.0       0.14   11.4   0.3    1.7  1  Peptidase_M50  Peptidase family M50
      0.089   12.8   0.1       0.19   11.8   0.1    1.5  1  Sad1_UNC       Sad1 / UNC-like C-terminal
       0.36   10.9   9.0        5.1    7.2   3.9    3.5  3  YpmT           Uncharacterized YmpT-like


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 ?   11.4   0.3   2.3e-05      0.14     188     240 ..     236     279 ..     211     293 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.3e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghllfalleairrkplserkeevan 240
                                       +  +l+l+ +++++ + lN +P+ ++DGg +++ +l +           ++a+
  gi|518652098|ref|YP_008141618.1| 236 IPDPLELAGYVGIITTALNSMPVGFMDGGLVFSGILGKQF---------KYAS 279
                                       4478999************************999988665.........4444 PP

>> Sad1_UNC  Sad1 / UNC-like C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.1e-05      0.19      43     109 ..     373     442 ..     367     452 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                                       EEEEE---GGGSG.-TTSB-EEEEEEESSTT----EEEEEEE--TTS-SEEEEE--TT---..-EEEEEE CS
                          Sad1_UNC  43 avtlehveksvap.isSapKdfevsgskrypekkwvllgefsydedgknaqtFeleeskdi..lvkyvkl 109
                                       ++t+++   +++p +s +p +f+v g+++ ++++  +l  ++y+ + +   +F++  ++    + k+v +
  gi|518652098|ref|YP_008141618.1| 373 NITVQNHGVNISPlFSVTPGNFTVKGFTQNKTDTIYTLELITYNHNYSGRKNFTITVDTGMrsVQKTVSV 442
                                       68999999999999***************************************99988633335556655 PP

>> YpmT  Uncharacterized YmpT-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   3.9   0.00085       5.1      10      54 ..      85     128 ..      79     134 .. 0.79
   2 ?    2.7   0.3     0.022   1.3e+02      13      27 ..     179     193 ..     174     206 .. 0.84
   3 ?    0.6   0.0     0.095   5.7e+02      12      36 ..     384     408 ..     380     415 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00085
                              YpmT  10 llsllfslyFGglayqhlvaenmDkvYLnigYCaLFLsi.mvftld 54 
                                       +ls+   +y G + y ++     D +Y ni Y +LF +i ++f+l 
  gi|518652098|ref|YP_008141618.1|  85 FLSMAALIYTGSVYYSSYYSS--DLIYRNIIYGTLFYAIpVIFILL 128
                                       688888899999999999876..66*************94456665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.022
                              YpmT  13 llfslyFGglayqhl 27 
                                        +fsl+FG +a   l
  gi|518652098|ref|YP_008141618.1| 179 GTFSLLFGFFASVVL 193
                                       58*********8765 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.095
                              YpmT  12 sllfslyFGglayqhlvaenmDkvY 36 
                                       s lfs+  G +  + + ++  D +Y
  gi|518652098|ref|YP_008141618.1| 384 SPLFSVTPGNFTVKGFTQNKTDTIY 408
                                       679********************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (594 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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):               3  [number of targets reported over threshold]
# CPU time: 0.64u 0.29s 00:00:00.93 Elapsed: 00:00:00.47
# Mc/sec: 3823.70
//
Query:       gi|518652099|ref|YP_008141619.1|  [L=891]
Description: hypothetical protein FACI_IFERC00001G0738 [Ferroplasma acidarmanus fer1]
Scores for complete 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-89  300.9   0.0      4e-89  299.6   0.0    1.7  1  tRNA-synt_2c  tRNA synthetases class II (A)
    2.7e-11   43.4   0.5    5.9e-11   42.3   0.5    1.6  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.6   0.0   4.5e-93     4e-89       1     550 [.      62     585 ..      62     587 .. 0.88

  Alignments for each domain:
  == domain 1  score: 299.6 bits;  conditional E-value: 4.5e-93
                                       HHHHHHHHHHHCTT..-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGG CS
                      tRNA-synt_2c   1 eirekFldfFekkg..HtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlen 75 
                                       e+r++Fl+fF++    Ht++++++vvp++++++l+vnA++++f+p ++++   p+ ++++ sQ++iR+     Dl+ 
  gi|518652099|ref|YP_008141619.1|  62 EMRQEFLSFFKEDKlpHTIIEKYPVVPRWRDDVLLVNASIYDFQPQVTSGLVPPPGNPLAMSQPSIRML----DLDL 134
                                       89*********98888*****************************************************....**** PP

                                       TTTSSS--SEEEEEEEEESS.....SS-HHHHHHHHHHHHHTTTT--GGGEEEEEETTEH..HHHHHHHHTTTTEGG CS
                      tRNA-synt_2c  76 VGktarHhTfFeMlGnfsfg.....dYfkeeaiefawelltkelgldkerlyvtvfeedd..eaveiweklvgvpee 145
                                       VGkt+rH+T FeMl + +f+     +Y+k+e+ie+++ +lt++l++d  ++++++ ++ +  +a+++ e +v++ e 
  gi|518652099|ref|YP_008141619.1| 135 VGKTGRHLTSFEMLCHDAFNyenkyIYWKNETIEYSYRFLTEKLHVDGAEITYKEKPWFGggNAGNAVEVFVRGLEV 211
                                       **********************************************************9889*************** PP

                                       GEEEE-HHHHEEESSSS........EEEEEEEEEEEECETTSHHCHCCCCTTCTCCHEEEEEEEEEEEEEESTTSHE CS
                      tRNA-synt_2c 146 rilrfgekdnfwemgdt........gpcgpcseiyydrgeeigkrkaaseveadddrvleiwnlvfmqfnreedgtl 214
                                       ++l+f   ++ +e +d         +  +p +++++++g e+ ++ ++++++++++++ e ++ + ++     d++ 
  gi|518652099|ref|YP_008141619.1| 212 ATLVF---MDMKEDPDGeidiegtkYSMMPLKIVDTGYGLERLVWLSTGTPTVYESILGETIEYIRKNSSAG-DIDP 284
                                       ****9...56666666556666666***************************************99888777.9999 PP

                                       EEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT-- CS
                      tRNA-synt_2c 215 kpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvv 291
                                       ++++k s      +    + L    ++++  l  + i+  +e        + +   +l+ +aDH+++l  + ad v+
  gi|518652099|ref|YP_008141619.1| 285 EIMQKLSELSAEIDPYSESKL---LKQVAPWLKKKHISIDNEFLR-----RLKSFRSLYSLADHTKTLLLMFADYVI 353
                                       999988776654444443333...233333444444444444444.....4455799******************** PP

                                       SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHH CS
                      tRNA-synt_2c 292 psnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlkl 368
                                       psn++ gY++R l+Rr++++++++ ++++ + +l++ + e+++ +  +   +++++++ii+ E+e++a+  ++ +  
  gi|518652099|ref|YP_008141619.1| 354 PSNVKVGYLARTLVRRSLKFMDDISFSKD-FMDLMDFQHEIFSRIVSNY--DRDFIKNIIDIEKEKYAEINKSAEGK 427
                                       *****************************.779**********999875..6789********************** PP

                                       HHHHHHHCCCCSEEXHHHHHHHHHCHXXXHHHHHHHHHC.TTXEEXHHHHHHHHHHHHHHHCCHHSXSSXXXXXXXX CS
                      tRNA-synt_2c 369 leelikklkkkkelsgedafkLydtyGfPvdltkeiaee.kglkvdiegfekameeqrerskkekkekklikkdvea 444
                                       ++++i++     +l++++a++Lyd+ G+  dl++e  ++ +g + + ++++++ + +r+++++ kk+++       +
  gi|518652099|ref|YP_008141619.1| 428 VRKYIHS----GKLELKNAITLYDSEGMNEDLISESFKKiTGKDLELPDNFQEIVISRHETRHTKKKEA------PQ 494
                                       *****97....78********************998876589*******************87777765......22 PP

                                       TTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEE CS
                      tRNA-synt_2c 445 lkelkkteeflgyeeleaeakvlallkdkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvq 521
                                       +   + ++  l+y++    +k+      +ef+  v  + e+ ++ ++T+fY+e+GGq  D G+  ++g++++v+dvq
  gi|518652099|ref|YP_008141619.1| 495 F--PPVHTRPLYYDN----TKI------SEFTGIVLYSGEKCIIPNQTAFYPEGGGQPCDLGYFIANGKKVNVVDVQ 559
                                       2..233355589999....444......59999999999************************************** PP

                                       EETTEEEEEXSS.XSXXXTTSEEEEEEXH CS
                      tRNA-synt_2c 522 kakgvvlhkgkleegklkvgdkvkaevde 550
                                       k++  ++h+ +++   +  + +vk+ +d 
  gi|518652099|ref|YP_008141619.1| 560 KYNDSIVHFLDNN---IPANSRVKGYIDY 585
                                       ********99874...7777777777775 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 !   42.3   0.5   6.5e-15   5.9e-11       1      43 [.     686     728 ..     686     729 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 6.5e-15
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       +r+v+i  i+ e CgGtH+++T  Ig +ki++ e  ++g++RI
  gi|518652099|ref|YP_008141619.1| 686 IRIVTIDGIDSEGCGGTHLDSTAPIGFIKIMKVETLQEGIQRI 728
                                       7*****77*********************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (891 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); 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: 0.76u 0.30s 00:00:01.06 Elapsed: 00:00:00.51
# Mc/sec: 5209.62
//
Query:       gi|518652100|ref|YP_008141620.1|  [L=172]
Description: hypothetical protein FACI_IFERC00001G0739 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-29  101.3   0.4    2.9e-29  100.9   0.4    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.3e-21   76.8   0.0    1.6e-21   76.5   0.0    1.1  1  MafB19-deam      MafB19-like deaminase


Domain annotation for each model (and alignments):
>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.4   3.2e-33   2.9e-29       2     100 ..       9     128 ..       8     129 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 3.2e-33
                                       HHHHHHHHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTG.......................TTB-HH CS
                   dCMP_cyt_deam_1   2 ekdekllelalkaakeaqkcsnfkVGavivkngeiistgyngepaggs.......................ktiHAE 55 
                                       ++de+++++a++aa+++ +c++ kVGaviv+++++++tgyng p + +                       + +HAE
  gi|518652100|ref|YP_008141620.1|   9 SWDEYFMRMAYLAASRS-NCTRRKVGAVIVRDNNVLATGYNGPPSHTVncdivgcirdelnvpsgerhelcRGLHAE 84 
                                       79***************.*************99***********8888***************************** PP

                                       HHHHHHHHHHTSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
                   dCMP_cyt_deam_1  56 vnAilkaaknggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                                       +nAi++aa n gs+++g  +yvt+ PC  C+k+i +s i++++++
  gi|518652100|ref|YP_008141620.1|  85 QNAIIQAAVN-GSSIKGSKIYVTTHPCVVCSKMIMNSSIEEIIFA 128
                                       ********99.889****************************997 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.5   0.0   1.8e-25   1.6e-21       2     120 ..       9     148 ..       8     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 76.5 bits;  conditional E-value: 1.8e-25
                       MafB19-deam   2 dkekafrkalaevekatkikedkigavivkdkkviargsn........................ekelnakataHaE 54 
                                       +++++f+  + ++  +++++ +k+gaviv d++v+a+g+n                        e   +   + HaE
  gi|518652100|ref|YP_008141620.1|   9 SWDEYFMRMAYLAASRSNCTRRKVGAVIVRDNNVLATGYNgppshtvncdivgcirdelnvpsgE-RHELCRGLHAE 84 
                                       589****************************************************9999988742.33567789*** PP

                       MafB19-deam  55 iaalqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpkslnkLkvkekngrve 120
                                        +a+ qAa  ++s+  ++  +yvt  pC +C ++i+++ + +++++ g+p+ l +L + e+n+ ++
  gi|518652100|ref|YP_008141620.1|  85 QNAIIQAAVNGSSI--KGSKIYVTTHPCVVCSKMIMNSSIEEIIFAEGYPDDLAELMLLESNITIR 148
                                       *******7777777..9999*****************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 1358.20
//
Query:       gi|518652101|ref|YP_008141621.1|  [L=110]
Description: hypothetical protein FACI_IFERC00001G0740 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.019   14.9   9.1      0.024   14.6   9.1    1.2  1  Claudin_3        Tight junction protein, Claudin-like
      0.055   13.2   8.9      0.064   13.0   8.9    1.1  1  7TM-7TMR_HD      7TM receptor with intracellular HD hydrolase
      0.065   12.2   9.8       0.09   11.8   9.8    1.2  1  PalH             PalH/RIM21
       0.17   12.8   3.4        4.9    8.1   0.1    2.4  2  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
        0.2   11.4   8.1        0.3   10.8   8.1    1.2  1  Yip1             Yip1 domain
       0.28    9.9   3.2       0.15   10.7   0.4    1.7  2  ResB             ResB-like family
       0.46    8.7   6.5       0.55    8.4   6.5    1.0  1  DUF2070          Predicted membrane protein (DUF2070)
       0.53   10.6   0.1       0.53   10.6   0.1    3.0  3  Ost5             Oligosaccharyltransferase subunit 5
       0.65    9.8   9.3       0.21   11.4   4.7    2.0  2  Lig_chan         Ligand-gated ion channel
        1.3    9.0   3.6          1    9.4   2.5    1.4  1  DUF3043          Protein of unknown function (DUF3043)
        1.6    9.2   5.9         17    5.9   5.9    2.1  1  DUF202           Domain of unknown function (DUF202)
        1.6    8.4  11.2        1.7    8.3   8.6    1.6  1  Cation_ATPase_C  Cation transporting ATPase, C-terminus
          2    8.3   7.8         12    5.8   0.4    2.3  2  ECSCR            Endothelial cell-specific chemotaxis regulat
        2.1    8.7  12.2          3    8.3  12.2    1.2  1  Tmemb_170        Putative transmembrane protein 170
        2.1    8.4  10.0       0.17   12.0   4.1    2.1  2  CrgA             Cell division protein CrgA
        3.6    7.7   9.6         62    3.7   7.2    2.8  2  DUF3185          Protein of unknown function (DUF3185)
        4.5    7.1   8.1       0.87    9.4   2.9    2.1  2  DUF2976          Protein of unknown function (DUF2976)
        7.6    5.5  16.0         16    4.4  16.0    1.5  1  DUF973           Protein of unknown function (DUF973)


Domain annotation for each model (and alignments):
>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   9.1   2.4e-05     0.024      66     157 ..      11      98 ..       1     107 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.4e-05
                         Claudin_3  66 lflvviliyivivrkvkkngysksvrklffliallslliviltviaviliavnvskfndsfndsslqLGYsawlsvi 142
                                       l+++  ++ i++ + ++k+ y  s+  ++  ++l+++l+ ++++i++i+i+  +s+    + ++s q + s+w+ + 
  gi|518652101|ref|YP_008141621.1|  11 LMIIFSIVSIMFTFFLHKRRYDWSKSEQY--FTLFMMLANGIIAITLIVIGYPYSNRV--YAYNSIQTHESTWVVIY 83 
                                       23333355555555566666665665655..5789999**999999999999999555..56666789********* PP

                         Claudin_3 143 sailslinvaLsivl 157
                                         i+ +i  + si +
  gi|518652101|ref|YP_008141621.1|  84 GFIILIIGLIVSIIF 98 
                                       *****9999999987 PP

>> 7TM-7TMR_HD  7TM receptor with intracellular HD hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   8.9   6.5e-05     0.064       2      80 ..       6      99 ..       5     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                       7TM-7TMR_HD  2 lsllgllllvlllllilllflrrfrkelrernkkllllslllllvlllsklvvlis...............siesiiyl 65
                                      l ++ l+++  ++ +++ +fl++ r +  ++ ++++l++ l   +++++ +v+ ++               s++ +iy 
  gi|518652101|ref|YP_008141621.1|  6 LLWIELMIIFSIVSIMFTFFLHKRRYDWSKSEQYFTLFMMLANGIIAITLIVIGYPysnrvyaynsiqtheSTWVVIYG 84
                                      56999*****************************99999877777777766433334478888889*999999999999 PP

                       7TM-7TMR_HD 66 vplaavalLlsllld 80
                                      +++ +++l++s+++ 
  gi|518652101|ref|YP_008141621.1| 85 FIILIIGLIVSIIFK 99
                                      999999999999986 PP

>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   9.8   9.1e-05      0.09     189     275 ..      11     104 ..       2     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.1e-05
                              PalH 189 liildtilsalllf..sk......kfldalpalsylfelalvtlyaalviyYliskrkyilspkrmketilllilnl 257
                                       l+i+ +i+s++ +f  +k      k+ +    +++l + ++++   ++vi Y +s+r y++++ + +e   + i+ +
  gi|518652101|ref|YP_008141621.1|  11 LMIIFSIVSIMFTFflHKrrydwsKSEQYFTLFMMLANGIIAIT--LIVIGYPYSNRVYAYNSIQTHESTWVVIYGF 85 
                                       78888888888888773356656666666666666666666665..57889************99999999999999 PP

                              PalH 258 lvi.llpvvffildisnad 275
                                       ++  +  +v++i+++++ +
  gi|518652101|ref|YP_008141621.1|  86 IILiIGLIVSIIFKVKESK 104
                                       888799********99865 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.1    0.0049       4.9       4      36 ..       7      38 ..       4      79 .. 0.51
   2 ?    5.4   0.7     0.035        35       4      30 ..      80     106 ..      77     110 .] 0.67

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0049
                          EphA2_TM  4 aavaglvllvilvilvlvlvrrrsknrkqksdl 36
                                       ++  ++++  +v +++ ++ ++++++ +ks++
  gi|518652101|ref|YP_008141621.1|  7 LWIELMIIFS-IVSIMFTFFLHKRRYDWSKSEQ 38
                                      4444455555.5555666666666666666554 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.035
                          EphA2_TM   4 aavaglvllvilvilvlvlvrrrsknr 30 
                                       +++ g+++l+i +i+ +++  + sk+ 
  gi|518652101|ref|YP_008141621.1|  80 VVIYGFIILIIGLIVSIIFKVKESKKG 106
                                       577788888887777777765655554 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   8.1    0.0003       0.3      24     121 ..       7      98 ..       2     102 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                              Yip1  24 lallllalltlllgllaslnlgqtlasg......eevqgltlssllgaiiggylglllgllllalllhliakllg.g 93 
                                       l++ l+++ +++++ +++                +++ + + ++l+++++ g+++  ++l+++++ +    +++  +
  gi|518652101|ref|YP_008141621.1|   7 LWIELMIIFSIVSIMFTF---------FlhkrryDWSKSEQYFTLFMMLANGIIA--ITLIVIGYPYSN--RVYAyN 70 
                                       333333333333333333.........1223566677777899999999999996..788888887777..777788 PP

                              Yip1  94 kgsfkqtlsvvgyallPlilgaliaill 121
                                       ++   ++  vv y++++li+g++++i++
  gi|518652101|ref|YP_008141621.1|  71 SIQTHESTWVVIYGFIILIIGLIVSIIF 98 
                                       888999********************97 PP

>> ResB  ResB-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       0.3     3e+02     441     464 ..       8      31 ..       5      45 .. 0.83
   2 ?   10.7   0.4   0.00016      0.15     432     459 ..      71      98 ..      34     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.3
                              ResB 441 lvllgalllvlGlvlslyvrhrRv 464
                                       ++ l  ++ ++++++++++++rR 
  gi|518652101|ref|YP_008141621.1|   8 WIELMIIFSIVSIMFTFFLHKRRY 31 
                                       566677889999999999999995 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00016
                              ResB 432 qvsrdpgknlvllgalllvlGlvlslyv 459
                                        ++    +++v+ g+++l++Gl++s+ +
  gi|518652101|ref|YP_008141621.1|  71 SIQTHESTWVVIYGFIILIIGLIVSIIF 98 
                                       57778899*****************877 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   6.5   0.00056      0.55      19      96 ..       6      98 ..       3     107 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00056
                           DUF2070 19 lliillalligllaflssk..............lfgillfglpalvaflltlpvlrilggrltykrs.lflallteliv 82
                                      ll+i l+++++++++++ +              +f++++++   ++a+ l      ++++ + y+   ++ +    ++ 
  gi|518652101|ref|YP_008141621.1|  6 LLWIELMIIFSIVSIMFTFflhkrrydwskseqYFTLFMMLANGIIAITLIVIGYPYSNRVYAYNSIqTHESTWVVIYG 84
                                      5666666666666666666667788899999997777777777777777776666666666777777788888888888 PP

                           DUF2070 83 viisllaillsall 96
                                      +ii+++++++s+++
  gi|518652101|ref|YP_008141621.1| 85 FIILIIGLIVSIIF 98
                                      88888888888777 PP

>> Ost5  Oligosaccharyltransferase subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   4.7       1.4   1.3e+03      17      32 ..      13      28 ..       1      63 [. 0.50
   2 ?    1.5   0.2      0.36   3.6e+02      12      28 ..      43      59 ..      34      78 .. 0.60
   3 ?   10.6   0.1   0.00053      0.53      11      39 ..      79     107 ..      68     110 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.4
                              Ost5 17 fvllligllltalffl 32
                                      +++ ++++++t++   
  gi|518652101|ref|YP_008141621.1| 13 IIFSIVSIMFTFFLHK 28
                                      3444444444444433 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.36
                              Ost5 12 qptlafvllliglllta 28
                                      + +la   ++i+l++++
  gi|518652101|ref|YP_008141621.1| 43 FMMLANGIIAITLIVIG 59
                                      33333333444444444 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00053
                              Ost5  11 lqptlafvllligllltalfflyevtstk 39 
                                       +  +++f+ l+igl++  +f ++e+++ k
  gi|518652101|ref|YP_008141621.1|  79 WVVIYGFIILIIGLIVSIIFKVKESKKGK 107
                                       56789***************998887766 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   4.7   0.00021      0.21       4      53 ..       7      81 ..       5      85 .. 0.75
   2 ?    1.8   1.2      0.19   1.9e+02       3      26 ..      77     101 ..      75     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
                                      XXXXXXTXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..........................XXXHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxx RF
                          Lig_chan  4 vWlsvlvalilvsivlflverfspyewrepeeaaet..........................veneftlsnslwfs 53
                                      +W+ +++++ +vsi+++++ +  +y+w+++e+ + t                          + n+++ ++s w++
  gi|518652101|ref|YP_008141621.1|  7 LWIELMIIFSIVSIMFTFFLHKRRYDWSKSEQ-YFTlfmmlangiiaitlivigypysnrvyAYNSIQTHESTWVV 81
                                      7***************************8843.2225566666666666666666666666677777777777765 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                                       XXXXXX.XTXXXXXXXXXXXXXXXX CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxx RF
                          Lig_chan   3 evWlsv.lvalilvsivlflverfs 26 
                                       ++W+++  ++++++++++ ++ +++
  gi|518652101|ref|YP_008141621.1|  77 STWVVIyGFIILIIGLIVSIIFKVK 101
                                       6899996677778888888776655 PP

>> DUF3043  Protein of unknown function (DUF3043)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.5     0.001         1      80     151 ..      10      85 ..       6      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                           DUF3043  80 elflplalvvlvl.llv..slvkvpevqavvsllllvllllvvidgillgrkvkkkvrekFp.etesekglglYav 151
                                       el++++ +v +++ +++      +++ +++++l++++   +++i  i++g   +++v +    +t++ + +++Y +
  gi|518652101|ref|YP_008141621.1|  10 ELMIIFSIVSIMFtFFLhkRRYDWSKSEQYFTLFMMLANGIIAITLIVIGYPYSNRVYAYNSiQTHESTWVVIYGF 85 
                                       66677777666664444366778899999********999*****************9999988888888888876 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.9     0.017        17      13      56 ..       8      96 ..       5     100 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.017
                            DUF202 13 WlRtslalialglallrffl..............................................tgepsalgkilgl 45
                                      W+  ++ + ++++ ++ ffl                                              + ++s++ +i g+
  gi|518652101|ref|YP_008141621.1|  8 WIELMIIFSIVSIMFT-FFLhkrrydwskseqyftlfmmlangiiaitlivigypysnrvyaynsiQTHESTWVVIYGF 85
                                      7777777777777777.44447777777777777777777777777777889999999999999997777777899999 PP

                            DUF202 46 ilivlgiltll 56
                                      i++++g+++ +
  gi|518652101|ref|YP_008141621.1| 86 IILIIGLIVSI 96
                                      99999998865 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 ?    8.3   8.6    0.0018       1.7      97     180 ..      14      95 ..      10      97 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                   Cation_ATPase_C  97 tlvlsqifnalnlrsrreslfkfsglfsnkllllaillslllqvlivyvpglnavfgtaplsleewlialllalvvl 173
                                       ++ +++i+ ++ l +rr    k ++ f  +l+ + + ++++++++++ +p+ n+v   +++  +e +++++ ++++l
  gi|518652101|ref|YP_008141621.1|  14 IFSIVSIMFTFFLHKRRYDWSKSEQYF--TLFMMLANGIIAITLIVIGYPYSNRVYAYNSIQTHESTWVVIYGFIIL 88 
                                       333344444444444343343433333..223333334556777777778899999999999999999999999999 PP

                   Cation_ATPase_C 174 lvdelvK 180
                                       +++ +v 
  gi|518652101|ref|YP_008141621.1|  89 IIGLIVS 95 
                                       9888875 PP

>> ECSCR  Endothelial cell-specific chemotaxis regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.012        12      31      64 ..       4      37 ..       1      59 [. 0.71
   2 ?    4.8   2.9     0.025        25      29      56 ..      78     105 ..      56     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.012
                             ECSCR 31 ivilvvvviilvsvvslrfkcrknkesedpqkpe 64
                                      +++l + ++i+ s+vs+ f     k   d  k e
  gi|518652101|ref|YP_008141621.1|  4 VILLWIELMIIFSIVSIMFTFFLHKRRYDWSKSE 37
                                      3555667788899999999888777777777765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                             ECSCR  29 sfivilvvvviilvsvvslrfkcrknke 56 
                                       +++vi   +++i+  +vs+ fk++  k+
  gi|518652101|ref|YP_008141621.1|  78 TWVVIYGFIILIIGLIVSIIFKVKESKK 105
                                       6788888888888889999999887775 PP

>> Tmemb_170  Putative transmembrane protein 170
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3  12.2     0.003         3       8     100 ..       1      97 [.       1     101 [. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.003
                         Tmemb_170   8 mwlaiflWalvssllvhlvAalialvtlrkhkfgr...fvpilillvgvlepltagaitsaviaavyraaslem.st 80 
                                       m+  i+lW   +++++ +  ++  +++ r+  +++   +++++++l  +++++t  +i       vy   s++  ++
  gi|518652101|ref|YP_008141621.1|   1 MFGVILLWIELMIIFSIVSIMFTFFLHKRRYDWSKseqYFTLFMMLANGIIAITLIVIGYPYSNRVYAYNSIQThES 77 
                                       66679999887766665555555555556665554233777888777888888877777777777887777765246 PP

                         Tmemb_170  81 lyalvwGvgqtillviisft 100
                                       ++++++G++  i+ +i+s++
  gi|518652101|ref|YP_008141621.1|  78 TWVVIYGFIILIIGLIVSII 97 
                                       77899***********9975 PP

>> CrgA  Cell division protein CrgA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       1.2   1.2e+03      34      47 ..       8      21 ..       1      35 [. 0.62
   2 ?   12.0   4.1   0.00017      0.17      28      85 ..      35      96 ..      26      99 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.2
                              CrgA 34 yvpvmlglmllGll 47
                                      ++ +m+ + ++ ++
  gi|518652101|ref|YP_008141621.1|  8 WIELMIIFSIVSIM 21
                                      44455555555544 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00017
                              CrgA 28 kpsprwyvpvmlglmllGllwlvvyYlageeipfmaelg....awNlliGfgliivGllmtt 85
                                      k+++ +   +ml+  ++ +  +v+ Y  ++++   ++++    +w ++ Gf ++i+Gl+++ 
  gi|518652101|ref|YP_008141621.1| 35 KSEQYFTLFMMLANGIIAITLIVIGYPYSNRVYAYNSIQthesTWVVIYGFIILIIGLIVSI 96
                                      55666677899999**************9966655555544458***************986 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   1.8      0.24   2.4e+02      11      52 ..       3      53 ..       1      59 [. 0.57
   2 ?    3.7   7.2     0.062        62      37      57 ..      73      93 ..      43      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.24
                           DUF3185 11 GivLlvfGynasdSlgsqvseaft........Gstt.dktlllligGgvaa 52
                                      G++Ll+  +    S++s + ++f          s +  +  ++l+ G++a+
  gi|518652101|ref|YP_008141621.1|  3 GVILLWIELMIIFSIVSIMFTFFLhkrrydwsKSEQyFTLFMMLANGIIAI 53
                                      777777777777777777777776555555543333123334445555554 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.062
                           DUF3185 37 ttdktlllligGgvaaivGlv 57
                                      +t ++++ +i G + +i+Gl+
  gi|518652101|ref|YP_008141621.1| 73 QTHESTWVVIYGFIILIIGLI 93
                                      57899**************98 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   1.9      0.48   4.8e+02      55      63 ..      27      35 ..       1      61 [. 0.40
   2 ?    9.4   2.9   0.00087      0.87      29      86 ..      44     104 ..      34     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.48
                           DUF2976 55 segkaewgk 63
                                      ++ + +w+k
  gi|518652101|ref|YP_008141621.1| 27 HKRRYDWSK 35
                                      333333333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00087
                           DUF2976  29 illgLvlaavaflaVak...aalkkfneisegkaewgkfgltlvvGvvllvvviwLltkAa 86 
                                       ++l+  + a+ ++++ +   + +  +n i++  ++w  +  +++  + l+v +i+ ++++ 
  gi|518652101|ref|YP_008141621.1|  44 MMLANGIIAITLIVIGYpysNRVYAYNSIQTHESTWVVIYGFIILIIGLIVSIIFKVKESK 104
                                       5555556677777776522256778******************************999875 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  16.0     0.016        16     101     192 ..       4      97 ..       1     104 [. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                            DUF973 101 ltliligaiiiiigvilaivsll.......slilslillgviilligiilaliGqillglsfyklGevYnnglikig 170
                                       ++l+ i + +ii++++ +i++ +         + s+  + +++ +++  ++ i++i++g+ +++    Yn+  ++ +
  gi|518652101|ref|YP_008141621.1|   4 VILLWIEL-MIIFSIV-SIMFTFflhkrryDWSKSEQYFTLFM-MLANGIIAITLIVIGYPYSNRVYAYNSIQTHES 77 
                                       34433333.3355555.55444458999865555655555555.555555679999999999999999999999999 PP

                            DUF973 171 GiliiipvidilsfIGyilsyi 192
                                         ++i ++  i+ +IG+i+s+i
  gi|518652101|ref|YP_008141621.1|  78 TWVVIYGF--IILIIGLIVSII 97 
                                       99998884..789999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1305  (0.0727871); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        28  (0.00156172); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 685.78
//
Query:       gi|518652102|ref|YP_008141622.1|  [L=359]
Description: hypothetical protein FACI_IFERC00001G0741 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.052   13.4   0.0    1.4  1  DUF1478   Protein of unknown function (DUF1478)
       0.04   14.0   0.2       0.11   12.6   0.0    1.8  2  HTH_3     Helix-turn-helix
       0.07   13.8   5.9        1.6    9.5   0.8    3.0  3  DUF3139   Protein of unknown function (DUF3139)


Domain annotation for each model (and alignments):
>> DUF1478  Protein of unknown function (DUF1478)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.7e-06     0.052      79     132 ..     213     265 ..     200     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.7e-06
                           DUF1478  79 relfldlyrfiptltrtlltslgcgpggavvlrsgyrslvlacslgvslllsyh 132
                                       + +f  lyr     t ++lt++ +   g  v   g+  lv a sl vsl+ls  
  gi|518652102|ref|YP_008141622.1| 213 QTVFNGLYRHDG-STAAMLTTIFAAATGIAVETLGFSELVAAISLVVSLVLSNI 265
                                       567889999865.5788899999999999999*******************965 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11      22      53 ..      42      73 ..      36      75 .. 0.90
   2 ?   -3.5   0.0         2   1.2e+04      15      26 ..     234     245 ..     234     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                      SHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHH CS
                             HTH_3 22 srstisriEnGernPsletlkklakaLgvsld 53
                                      ++ +is++  ++++P+++t+  l++   vs++
  gi|518652102|ref|YP_008141622.1| 42 PQVAISKYVVNKSQPTITTISNLSNKIAVSFS 73
                                      6889*********************9999975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2
                                       HHHHHTSSHHHH CS
                             HTH_3  15 LAeklGvsrsti 26 
                                       +A+++G+ + t+
  gi|518652102|ref|YP_008141622.1| 234 FAAATGIAVETL 245
                                       699999998887 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.8   0.00026       1.6       1      65 [.       1      73 [.       1     101 [. 0.64
   2 ?   -2.4   0.0       1.3   7.8e+03      44      58 ..     121     135 ..      88     155 .. 0.57
   3 ?    6.0   0.1    0.0032        19       6      52 ..     256     300 ..     251     307 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00026
                           DUF3139  1 mkkiiiililliillvivkvfl.....glvgskpikkylan....kkldkyl...qekgykeddIksikpkydskkg 65
                                      m+k ++i+++l++ ++++ +f+        +  + ++ ++n     +++ky+   +    +   I++ + k  +  +
  gi|518652102|ref|YP_008141622.1|  1 MNKKKVIIGVLMAAIFVMLAFVpaadnM--HTAQSNTATGNispqVAISKYVvnkS--QPTITTISNLSNKIAVSFS 73
                                      899**************99999866431..22222223344666688888885330..2223344444444444444 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                           DUF3139  44 qekgykeddIksikp 58 
                                       + ++ ++ +++si++
  gi|518652102|ref|YP_008141622.1| 121 SFNKSNKMEVSSIES 135
                                       334444445555544 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0032
                           DUF3139   6 iililliillvivkvflglvgskpikkylankkldkylqekgykedd 52 
                                       ++++l+++ + +  v+l +  s   +k  +nk+l +yl+ + y++++
  gi|518652102|ref|YP_008141622.1| 256 LVVSLVLSNIKN--VYLEMYESTYANKPSGNKYLWSYLSIDQYDKNN 300
                                       444455555444..66655555555566788*************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       741  (0.0413297); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2433.25
//
Query:       gi|518652103|ref|YP_008141623.1|  [L=179]
Description: heat shock protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.4e-08   33.2   2.8    1.7e-06   28.1   2.8    2.2  1  HSP20       Hsp20/alpha crystallin family
    0.00034   20.1   0.1    0.00084   18.9   0.1    1.6  1  ArsA_HSP20  HSP20-like domain found in ArsA
    0.00092   20.2   2.0     0.0014   19.6   2.0    1.2  1  CS          CS domain
     0.0071   16.7   0.1       0.01   16.2   0.1    1.2  1  PIH1_CS     PIH1 CS-like domain


Domain annotation for each model (and alignments):
>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   2.8   3.7e-10   1.7e-06       1     101 [.      94     178 ..      94     179 .] 0.85

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.7e-10
                                       E--SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT-EEEEE CS
                             HSP20   1 dikeeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadkvkaslk 77 
                                       di e++e+  ++ ++pg++k+++++ v++n++  k  +                rk+ ++++   +vd ++v a++ 
  gi|518652103|ref|YP_008141623.1|  94 DINEDKENVYITYELPGVEKNDIDLVVNENNIELKVDKG--------S------RKYYKNIEFDRDVDINSVIAKFT 156
                                       6899***************************98877666........2......446666777667888******** PP

                                       TTEEEEEEEBSS--..-------- CS
                             HSP20  78 dGvLtvtvpkkepekkkkerkiqi 101
                                       +GvL +t++k +++  ++ r ++i
  gi|518652103|ref|YP_008141623.1| 157 NGVLDITIKKVNNK--STGRAVKI 178
                                       **********9998..57888877 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 !   18.9   0.1   1.9e-07   0.00084       6      62 ..     104     163 ..      99     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.9e-07
                        ArsA_HSP20   6 lkldLPfvdkeeidlsrsgdeLtIkig....nfrRqitLPsvlarkevtsAkfedgvLeIr 62 
                                       ++ +LP+v+k +idl  +++ + +k++    ++ ++i   + ++   v  Akf +gvL I+
  gi|518652103|ref|YP_008141623.1| 104 ITYELPGVEKNDIDLVVNENNIELKVDkgsrKYYKNIEFDRDVDINSV-IAKFTNGVLDIT 163
                                       5668***********************777777777********9999.9********997 PP

>> CS  CS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   2.0   3.1e-07    0.0014       7      76 .]      97     166 ..      93     166 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.1e-07
                                       EETTEEEEEEE-TTCTTTTTCEEEEEETTEEEEEE.TS.CEEEEECEBSS-BETTTEEEEEETTEEEEEEEB CS
                                CS   7 QtldeVvvtiyvkkvnikkkdvkvefkerslkvki.gk.eklliegeLfgpIdpeesswtieskkveitLkK 76 
                                       +++++V++t ++++v  +k+d+++  +e+ +++k+ ++ +k +++ e+   +d ++   ++++  ++it+kK
  gi|518652103|ref|YP_008141623.1|  97 EDKENVYITYELPGV--EKNDIDLVVNENNIELKVdKGsRKYYKNIEFDRDVDINSVIAKFTNGVLDITIKK 166
                                       7899**********9..9999999999********977799999999************************9 PP

>> PIH1_CS  PIH1 CS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.3e-06      0.01      33      87 ..     102     157 ..      88     165 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.3e-06
                           PIH1_CS  33 laieielPllksikevklrvgerrleleskk..akyfLslkLpYpvdedkveAkFvk 87 
                                         i+ elP++ + ++++l v+e+++el+ +k   ky  +++++  vd ++v AkF +
  gi|518652103|ref|YP_008141623.1| 102 VYITYELPGV-EKNDIDLVVNENNIELKVDKgsRKYYKNIEFDRDVDINSVIAKFTN 157
                                       67899*****.789*************99998899********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1317.50
//
Query:       gi|518652104|ref|YP_008141624.1|  [L=193]
Description: hypothetical protein FACI_IFERC00001G0743 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-05   24.3   0.1    3.8e-05   23.3   0.1    1.5  2  ArsR       ArsR transcriptional regulator
    4.1e-05   23.3   0.1    7.8e-05   22.5   0.1    1.5  1  HTH_5      Bacterial regulatory protein, arsR family
    0.00069   19.7   0.2      0.091   12.9   0.1    2.5  2  DUF2250    Uncharacterized protein conserved in archaea (DUF2
     0.0026   17.3   1.4     0.0032   17.0   0.2    1.7  2  HTH_24     Winged helix-turn-helix DNA-binding
     0.0029   17.5   0.9     0.0098   15.8   0.1    2.2  2  HTH_11     HTH domain
     0.0086   16.1   0.0       0.02   14.9   0.0    1.6  1  HTH_20     Helix-turn-helix domain
  ------ inclusion threshold ------
      0.012   15.4   0.0      0.023   14.6   0.0    1.5  1  MarR_2     MarR family
      0.015   15.3   0.0      0.026   14.5   0.0    1.4  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.017   14.9   0.0      0.025   14.3   0.0    1.5  1  DUF4423    Domain of unknown function (DUF4423)
      0.019   14.9   0.0      0.077   12.9   0.0    2.0  2  TrmB       Sugar-specific transcriptional regulator TrmB
      0.074   13.0   0.0       0.53   10.3   0.0    2.3  2  PadR       Transcriptional regulator PadR-like family
       0.12   12.3   0.0       0.25   11.3   0.0    1.5  1  MarR       MarR family


Domain annotation for each model (and alignments):
>> ArsR  ArsR transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   2.6e-08   3.8e-05       6     131 ..       4     131 ..       2     146 .. 0.84
   2 ?   -2.4   0.0       2.2   3.2e+03     122     142 ..     167     187 ..     140     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.6e-08
                              ArsR   6 eLvpllqvfdsetkkkvyeelskeWlteeeleeklgee...veealklLkkikliEsqWrmpepgekpekeYhts.Y 78 
                                       +L ++l +++++t ++++++l +      el+ ++g +    ++ l++L+k +li +  ++p+    p+k Y+++ +
  gi|518652104|ref|YP_008141624.1|   4 DLWSILIALENNTRREMLKTLANYNSYGLELSRMIGVSqqaINKQLEILEKLGLICTDGSIPSTMGPPRKVYRSMgF 80 
                                       7899*******************999999*****9966456899*****************************9669 PP

                              ArsR  79 skvqanfqcsledlsdiievafmsdeeleelvekiekeveegntsisdlsrkl 131
                                       s++ ++ + ++  + +i  +    de++e   +++ +++++ n  i ++ r+ 
  gi|518652104|ref|YP_008141624.1|  81 STIIIDYSKNFMKIKKI-DID-YVDENVEGDNSDLVNKLKDLNGEIDKIDRER 131
                                       99999999999999886.333.3467777777777777777777777776665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.2
                              ArsR 122 tsisdlsrklglsplfirala 142
                                       + is +++++g+ + ++++++
  gi|518652104|ref|YP_008141624.1| 167 MDISIVANNMGIPEELVKGIV 187
                                       456667788888888888877 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 !   22.5   0.1   5.2e-08   7.8e-05       2      45 ..      15      58 ..      14      60 .. 0.96

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 5.2e-08
                                      HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  2 ptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                       tR+++Lk La+ + +  el++++g+sq ++  +L +L+++GL+
  gi|518652104|ref|YP_008141624.1| 15 NTRREMLKTLANYNSYGLELSRMIGVSQQAINKQLEILEKLGLI 58
                                      59**********99999**************************8 PP

>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.1   6.1e-05     0.091      10      52 ..      17      58 ..      10      64 .. 0.84
   2 ?    4.5   0.0     0.026        39      21      43 ..      84     106 ..      78     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                           DUF2250 10 alkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLl 52
                                        ++lk l++ n  Y++ +++++ ++++ +++ l+ Le+lGL+
  gi|518652104|ref|YP_008141624.1| 17 RREMLKTLANYN-SYGLELSRMIGVSQQAINKQLEILEKLGLI 58
                                      556677777776.4****************************9 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.026
                           DUF2250  21 nvdYaksiakeleipleevrell 43 
                                         dY+k+ +k  +i++ +v+e +
  gi|518652104|ref|YP_008141624.1|  84 IIDYSKNFMKIKKIDIDYVDENV 106
                                       57***************999876 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       3.9   5.9e+03       2       6 ..      14      18 ..       7      25 .. 0.53
   2 !   17.0   0.2   2.1e-06    0.0032      22      47 ..      33      58 ..      32      58 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3.9
                            HTH_24  2 detdr 6 
                                      + t+r
  gi|518652104|ref|YP_008141624.1| 14 NNTRR 18
                                      34444 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 2.1e-06
                            HTH_24 22 eLAerlglSpstvnrrlkrLeeeGlI 47
                                      eL++++g+S++++n++l+ Le+ GlI
  gi|518652104|ref|YP_008141624.1| 33 ELSRMIGVSQQAINKQLEILEKLGLI 58
                                      9************************9 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.6e-06    0.0098      18      44 ..      31      57 ..      16      64 .. 0.81
   2 ?   -0.6   0.1      0.87   1.3e+03      33      51 ..     114     132 ..     113     133 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.6e-06
                            HTH_11 18 geeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      g eL++ ++vS +++ + +++Le+lg+
  gi|518652104|ref|YP_008141624.1| 31 GLELSRMIGVSQQAINKQLEILEKLGL 57
                                      679**********************94 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.87
                            HTH_11  33 rrdIkaLeelgvpIesepg 51 
                                       ++ +k+L+   ++I+ e++
  gi|518652104|ref|YP_008141624.1| 114 VNKLKDLNGEIDKIDRERN 132
                                       5889999999999998876 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.4e-05      0.02       4      54 ..       9      58 ..       6      64 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                                      HHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTE CS
                            HTH_20  4 aeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLv 54
                                      + AL + +Rr++l+ L  +      el + +++s++ ++++L++Le+ gL+
  gi|518652104|ref|YP_008141624.1|  9 LIALENNTRREMLKTL-ANYNSYGLELSRMIGVSQQAINKQLEILEKLGLI 58
                                      55999***********.88888888*************************9 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.5e-05     0.023      26      53 ..      33      60 ..       6      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.5e-05
                                      HHHHHHTSSHHHHHHHHHHHHHTTSEEE CS
                            MarR_2 26 elarrlglsksavsrilkrLvaaGLver 53
                                      el r  g+s++a+++ l+ L++ GL+ +
  gi|518652104|ref|YP_008141624.1| 33 ELSRMIGVSQQAINKQLEILEKLGLICT 60
                                      89***********************965 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.7e-05     0.026      26      53 ..      33      60 ..       7      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.7e-05
                                      HHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2 26 elAsmlGltretvsrilseLkreglisr 53
                                      el++m+G++++ +++ l  L++ gli +
  gi|518652104|ref|YP_008141624.1| 33 ELSRMIGVSQQAINKQLEILEKLGLICT 60
                                      89***********************974 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   1.7e-05     0.025      33      72 ..      25      62 ..      14     106 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                           DUF4423 33 kdfkadpeelakrlrpkisaeevekalefLlklgllkkde 72
                                       ++++   el+++++  +s++ ++k le+L+klgl+  d+
  gi|518652104|ref|YP_008141624.1| 25 ANYNSYGLELSRMIG--VSQQAINKQLEILEKLGLICTDG 62
                                      455666789******..*******************8776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.2e-05     0.077      22      58 ..      28      64 ..      19      79 .. 0.78
   2 ?   -1.3   0.0       1.4   2.1e+03      21      42 ..     165     186 ..     156     191 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
                                      CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 22 patadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      ++   e+++++gv+++ +++ L+ Le+ Gl+ +  + 
  gi|518652104|ref|YP_008141624.1| 28 NSYGLELSRMIGVSQQAINKQLEILEKLGLICTDGSI 64
                                      555679************************9877555 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                       CCCHHCHHCCCTTSSCHCHHHH CS
                              TrmB  21 gpatadeiaeelgvprskvYev 42 
                                       + ++++ +a++ g+p+  v  +
  gi|518652104|ref|YP_008141624.1| 165 ETMDISIVANNMGIPEELVKGI 186
                                       5667777889999998776655 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00035      0.53       2      64 ..      21      76 ..      20      77 .. 0.75
   2 ?   -2.1   0.0       2.6   3.9e+03      15      41 ..     141     167 ..     140     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
                                      HHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-S.TSSS-EEEEE CS
                              PadR  2 LalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglvesewees.gegpprkyYr 64
                                      L+ l++  syG+e+ + +          s+  + ++L+ Lek gl+ +  +   + gpprk+Yr
  gi|518652104|ref|YP_008141624.1| 21 LKTLANYNSYGLELSRMIGV--------SQQAINKQLEILEKLGLICTDGSIPsTMGPPRKVYR 76
                                      66666666777776655544........44567789**********988776669********7 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.6
                                       HHHHHHCCSTT-CCTTHHHHHHHHHHH CS
                              PadR  15 iikeleelsegllelseGslYpaLkrL 41 
                                       ii  l+e+ +g+ ++    +Y  L+++
  gi|518652104|ref|YP_008141624.1| 141 IIGMLKERASGFDNFYRKVIYGYLETM 167
                                       666788888888888888888877765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00017      0.25      22      47 ..      33      58 ..      18      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
                                      HHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              MarR 22 eLakklgvskstvtrvldrLekkGli 47
                                      eL +++gvs+ ++ ++l  Lek Gli
  gi|518652104|ref|YP_008141624.1| 33 ELSRMIGVSQQAINKQLEILEKLGLI 58
                                      89***********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); 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: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1491.73
//
Query:       gi|518652105|ref|YP_008141625.1|  [L=138]
Description: OsmC-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-13   51.1   0.0      2e-13   50.7   0.0    1.1  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.0   1.1e-17     2e-13       3      98 ..      32     127 ..      30     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.1e-17
                                       XSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT..CEEEEEEEEEEE-SS-H..HHHHHH CS
                              OsmC   3 gsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak..giteirlkvevkipgadseeklkkl 77 
                                       ++  sP+elll a+++C + ++  ++kk++ +++++++ev +e+ ++ +k  ++ ei++ +e +++    +e +kk+
  gi|518652105|ref|YP_008141625.1|  32 EEYHSPTELLLLAMGGCSSDDVLNILKKMKKEIKSYRCEVVGEKRDTDPKllKYGEIHYIFEGDMD----PESVKKA 104
                                       55679***********************************99666555555677777766666444....499**** PP

                                       HHHH.HHHSHHHHHH.CT-SSSE CS
                              OsmC  78 leka.ekrCpvsntl.kngvkve 98 
                                       ++++ ek+C+vs t+  +g++v+
  gi|518652105|ref|YP_008141625.1| 105 IDLSlEKYCSVSLTVkGAGIPVS 127
                                       ***************88888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 982.58
//
Query:       gi|518652106|ref|YP_008141626.1|  [L=337]
Description: hypothetical protein FACI_IFERC00001G0745 [Ferroplasma acidarmanus fer1]
Scores for complete 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-51  173.7   0.0    6.8e-51  173.4   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 !  173.4   0.0   3.8e-55   6.8e-51       2     294 .]      49     332 ..      48     332 .. 0.90

  Alignments for each domain:
  == domain 1  score: 173.4 bits;  conditional E-value: 3.8e-55
                                       GGCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHH...HHTT..TTTSEEEEEBSSHHHHHHHHH CS
                              PALP   2 tlgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllar...lkeg..tgaktvveassGNhgralAaa 73 
                                       tlg+ +TP+v++++       +l +Kl+++ pt S+KdRg  +l+++            + + e ssGN+g ++Aa+
  gi|518652106|ref|YP_008141626.1|  49 TLGEVRTPVVKINN-------DLSFKLDYFSPTYSYKDRGTRNLISYiasR--RkeLNIEMINEDSSGNAGSSIAAY 116
                                       788999******99.......59************************7653..14479******************* PP

                                       HHHHT-EEEEEEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHH CS
                              PALP  74 aallGlkvtivvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEi 150
                                       +  +G+k  i+vp++a+p+k+++++++Ga++++v+g+ d+ ++     a+   + +++s+  np   +g  t+++Ei
  gi|518652106|ref|YP_008141626.1| 117 GISAGFKTNIYVPSNANPAKLKQIESYGAHIIKVDGSRDHVQEE----AEH-AEGFYASHILNPEFRDGIRTLAYEI 188
                                       **********************************9988888888....666.6789999999*************** PP

                                       HHHTTTTEEEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B.SSS.CC CS
                              PALP 151 leqlggkpdavvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarslragrrvtvpvsdtiadg 219
                                          +g+ pd ++vp++ G l++G++ gl +    +  +    + ++gv+pe+ +++ +++   ++++    ++iad+
  gi|518652106|ref|YP_008141626.1| 189 -FLQGKMPDNIFVPISAGTLLSGLYSGLTHlynsG--EiskvPVIVGVQPENISPVCSFINGEKYDPDNNLSSIADA 262
                                       .56779************************77541..256767777**************99999999999****** PP

                                       STCS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 220 lavg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                       l ++  + +++ ++++++ +  +++vs++e++ a + la   g  +e ssa+++aa+   ++++++++   +++ltg
  gi|518652106|ref|YP_008141626.1| 263 LVAKrpVLMNKMIKIMKNGNR-CISVSENEIITARKDLA-LKGFYAEYSSATVFAAY---KKSHFEGS--SLLVLTG 332
                                       ****98889999999987776.*****************.*****************...99999999..7777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 2131.78
//
Query:       gi|518652107|ref|YP_008141627.1|  [L=736]
Description: hypothetical protein FACI_IFERC00001G0746 [Ferroplasma acidarmanus fer1]
Scores for complete 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-61  205.0   0.9    1.6e-60  204.0   0.9    1.5  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.3e-25   88.5   0.1    5.2e-25   87.3   0.1    1.7  1  EFG_C        Elongation factor G C-terminus
    1.2e-23   83.2   0.0    3.3e-23   81.7   0.0    1.8  1  EFG_IV       Elongation factor G, domain IV
    2.1e-23   82.2   0.1    4.2e-23   81.2   0.1    1.5  1  EFG_II       Elongation Factor G, domain II
    1.9e-12   47.4   1.4    5.1e-12   46.0   1.4    1.8  1  GTP_EFTU_D2  Elongation factor Tu domain 2
      0.004   17.2   0.1      0.011   15.8   0.1    1.7  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0086   15.9   0.0       0.02   14.7   0.0    1.5  1  RF3_C        Class II release factor RF3, C-terminal domain
  ------ inclusion threshold ------
      0.018   14.4   0.2      0.028   13.7   0.2    1.2  1  Septin       Septin
      0.032   13.7   0.0      0.074   12.5   0.0    1.6  1  SRPRB        Signal recognition particle receptor beta subuni
      0.046   13.3   0.0      0.096   12.3   0.0    1.5  1  Ras          Ras family
       0.14   11.9   0.1       0.55   10.0   0.0    1.9  2  T2SSM_b      Type II secretion system (T2SS), protein M subty
       0.17   12.1   0.3         11    6.2   0.1    3.2  3  DUF4115      Domain of unknown function (DUF4115)


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 !  204.0   0.9   1.1e-63   1.6e-60       3     193 ..      25     261 ..      23     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 204.0 bits;  conditional E-value: 1.1e-63
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEET..TCSSEEEEEEEE CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaislek..etkkylinliDt 77 
                                       irni i++h+DhGKtTL+d+L++ +g++s+    a+++  lD  ++E++rgiTi++a++s+ +  ++k++linliDt
  gi|518652107|ref|YP_008141627.1|  25 IRNIDIAAHIDHGKTTLSDNLIAGAGMMSE--DLAGKQLLLDYDEQEQARGITINAANASMVHevDGKEFLINLIDT 99 
                                       8****************************9..7778899***********************5479*********** PP

                                       SSSGGGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHH CS
                          GTP_EFTU  78 PGHvdFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrke 154
                                       PGHvdF  +v+r++r++Dg v+vvd+veGv+pqte+v+r+alke+v++++fiNK+Drl++elk   +e+++++ ++ 
  gi|518652107|ref|YP_008141627.1| 100 PGHVDFGGDVTRAMRAVDGTVIVVDSVEGVMPQTETVVRQALKERVKPVLFINKVDRLINELKLNGDEMQKRFIKVI 176
                                       *************************************************************************8885 PP

                                       HHHHHHHHTTT............TTEEEEEEBTTTTBTHH..................................HHH CS
                          GTP_EFTU 155 eklekygekge............kevpvvfgSalkgegvk..................................tll 185
                                       ++++k  +k              k+ +v+fgSa+++++++                                   +l
  gi|518652107|ref|YP_008141627.1| 177 TDVNKLITKYApkefadswlvnvKNGTVAFGSAYHNWALSvpamalfkvtfkdivdlvsagkqkelakkaplhkVVL 253
                                       5555554444456677788888899************8877777777777777777777777777777777776677 PP

                                       HHHHHHSH CS
                          GTP_EFTU 186 ealvellp 193
                                       ++++++lp
  gi|518652107|ref|YP_008141627.1| 254 DMVTKNLP 261
                                       77777766 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 !   87.3   0.1   3.5e-28   5.2e-25       1      86 [.     626     710 ..     626     713 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.3 bits;  conditional E-value: 3.5e-28
                                       EEEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEE CS
                             EFG_C   1 vllEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsg 77 
                                       vl+EP++kv i+vp+e++g v+s+l++rrG +edm+q+ ++ +++ a++P++++igfa+++rs+T G++++s+e sg
  gi|518652107|ref|YP_008141627.1| 626 VLMEPMQKVFISVPQELMGPVTSELQQRRGVVEDMQQN-GEEITVIANAPVSGMIGFASAIRSATGGKAIWSSENSG 701
                                       59************************************.************************************** PP

                                       EEE--HHHH CS
                             EFG_C  78 Yeevpgdkl 86 
                                       Y+ vp +++
  gi|518652107|ref|YP_008141627.1| 702 YQRVPYELQ 710
                                       ****98876 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 !   81.7   0.0   2.2e-26   3.3e-23      11     120 ..     518     623 ..     509     624 .. 0.91

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 2.2e-26
                                       S-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEE CS
                            EFG_IV  11 kpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvk 87 
                                       k++k++  +l + +g d ++a+  ++i        n + d+tkg+q+++e++e+  + f+e l++Gpla+e+v ++k
  gi|518652107|ref|YP_008141627.1| 518 KDKKAVMAILEE-AGLDHNEARGLVSIHG-----ANLLLDMTKGIQYLDETMELLIESFNESLDKGPLANEKVYGLK 588
                                       566646666655.9**************9.....79***************************************** PP

                                       EEEEEEE--T..TTC-HHHHHHHHCHHHHHHHHCC CS
                            EFG_IV  88 vtLldgslhe..vdsseaafkpaarralkeallkA 120
                                       v+L+d++lhe  +++++a+++pa+r+ ++ a+ +A
  gi|518652107|ref|YP_008141627.1| 589 VSLMDAKLHEdsIHRGPAQVIPAGRNSIYGAMCQA 623
                                       *********************************99 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 !   81.2   0.1   2.8e-26   4.2e-23       2      74 ..     391     463 ..     390     464 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.2 bits;  conditional E-value: 2.8e-26
                            EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                                       ++Pv++laie+k  ad  kl ++L+ +++ Dp+++v  ++eT+e ++sGmGelHlei++ r+k++y+v+v ++
  gi|518652107|ref|YP_008141627.1| 391 SDPVVTLAIEAKHTADLPKLIDVLRSVSKADPSIQVDINQETGEHLISGMGELHLEITMYRIKNDYHVDVVTS 463
                                       58********************************************************************875 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 !   46.0   1.4   3.4e-15   5.1e-12       1      73 [.     310     375 ..     310     376 .. 0.94

  Alignments for each domain:
  == domain 1  score: 46.0 bits;  conditional E-value: 3.4e-15
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       G++a grv+sG+++kG e+++   +  +k   ++++ l ++ ++ ++ +++ +aG+i+a++gl+ a i+G+t+
  gi|518652107|ref|YP_008141627.1| 310 GEIAVGRVFSGIIRKGSELYV--TGA-GK---SKVQLLSMMVGPDRISIDEIAAGNIAAVVGLKGA-IAGSTV 375
                                       89*******************..776.45...6********************************8.****98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   7.4e-06     0.011      11     112 ..      37     151 ..      30     153 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.4e-06
                                       SHHHHHHHHHT................STEEESSSTTSSSSEEEEEEE..ETTEE..EEEEECGGCSSHHHHHHHHH CS
                          MMR_HSR1  11 GKStLinaltg................ekaivsdkpgtTrdinegrvk..lkgke..ielvDtpGliegaseekglg 67 
                                       GK+tL   l+                 +  + ++  g T++   + +   ++gke  i+l+DtpG ++    + +++
  gi|518652107|ref|YP_008141627.1|  37 GKTTLSDNLIAgagmmsedlagkqlllDYDEQEQARGITINAANASMVheVDGKEflINLIDTPGHVD---FGGDVT 110
                                       7777777776433333333333322222334555556666664444332433333558*******665...222344 PP

                                       HHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHH.HHHTTSEEEEEE CS
                          MMR_HSR1  68 kaflaleeadlillvvdaseeklkpldeeleel.leeakkplilvl 112
                                       +a+   + +d  ++vvd+  e++ p+ e++ +  l+e+ kp +l +
  gi|518652107|ref|YP_008141627.1| 111 RAM---RAVDGTVIVVDSV-EGVMPQTETVVRQaLKERVKP-VLFI 151
                                       444...458********77.667777666554404545555.4444 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 !   14.7   0.0   1.3e-05      0.02      40      79 ..     425     463 ..     411     489 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                                       EEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEE CS
                             RF3_C  40 qvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrle 79 
                                       qv  ++ ++ e +++ +G+L +e+  +R+kn Y+v+v ++
  gi|518652107|ref|YP_008141627.1| 425 QVDINQ-ETGEHLISGMGELHLEITMYRIKNDYHVDVVTS 463
                                       555555.4567788889*******************9754 PP

>> Septin  Septin
   #    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      14     132 ..      35     163 ..      26     182 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.9e-05
                                       TSSCCCCCCTTSSSS----.........--------------S-E..EEEEEEEETTCEEEEEEEE---BSSSS.SH CS
                            Septin  14 glGkttlintlfetdliee.........ekleeasekkkktveik..kkkvvieedgvklnltviDtpgfGdav.dn 78 
                                         Gkttl + l++   + +            +  ++++++ ++i+  ++++v e dg ++ +++iDtpg+ d+  d 
  gi|518652107|ref|YP_008141627.1|  35 DHGKTTLSDNLIAGAGMMSedlagkqllL--DYDEQEQARGITINaaNASMVHEVDGKEFLINLIDTPGHVDFGgDV 109
                                       57999999888776554444566644332..2233355556666641444455668*************76653244 PP

                                       HCCCHHH..HHHHHHHHHHHHHHCTSS--SS-----EEEEEEEE-TTSSSS-HHHH CS
                            Septin  79 skswepi..veyideqfeeylreesklkRkkivDkRvHaclyfisPtghglkpldv 132
                                       +++ +++     + +  e ++ + +++ R+ ++ +Rv  +l fi+ + + +++l +
  gi|518652107|ref|YP_008141627.1| 110 TRAMRAVdgTVIVVDSVEGVMPQTETVVRQALK-ERVKPVL-FINKVDRLINELKL 163
                                       555555522234566789999999999998765.7999988.57777777777665 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 ?   12.5   0.0   4.9e-05     0.074      14      86 ..      57     126 ..      26     149 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.9e-05
                                       SSHHHHHHHHHHSS---.B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETT CS
                             SRPRB  14 sGKTslftrLttdsvkk.tvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDSt 86 
                                       +GK +l+    +++++  t  + ++s++++v + k++ ++liD PGh+ +  +++      + + g v vvDS 
  gi|518652107|ref|YP_008141627.1|  57 AGKQLLLDYDEQEQARGiTINAANASMVHEV-DGKEFLINLIDTPGHVDFGGDVTRA---MRAVDGTVIVVDSV 126
                                       4666666655555554414444477777777.7899999************999887...77899999999994 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.4e-05     0.096      26     115 ..      70     155 ..      55     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.4e-05
                                       SSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHST CS
                               Ras  26 eeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvae 102
                                       +    Ti +++ +   evdgke  +++ DT G  +f    +  +r ++g ++v d     s e v   +e + r+a 
  gi|518652107|ref|YP_008141627.1|  70 QARGITINAANASMVHEVDGKEFLINLIDTPGHVDFGGDVTRAMRAVDGTVIVVD-----SVEGVMPQTETVVRQAL 141
                                       5566799999****************************************99965.....66677755555544443 PP

                                       .TTSEEEEEEETTT CS
                               Ras 103 .envpivLvGnKvD 115
                                        e+v+ vL  nKvD
  gi|518652107|ref|YP_008141627.1| 142 kERVKPVLFINKVD 155
                                       37788888889988 PP

>> T2SSM_b  Type II secretion system (T2SS), protein M subtype b
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.3   3.4e+03      14      41 ..     136     163 ..     129     180 .. 0.51
   2 ?   10.0   0.0   0.00037      0.55      30      81 ..     371     427 ..     353     443 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.3
                           T2SSM_b  14 lagaalqqrvralvsaaggsltssqvlp 41 
                                       ++  al++rv+ ++  + ++ +  +++ 
  gi|518652107|ref|YP_008141627.1| 136 VVRQALKERVKPVLFINKVDRLINELKL 163
                                       5555555555555444444444444444 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00037
                           T2SSM_b  30 aggsltssqvlpageegk.....vrriavrvslegeleaLqklLasLeaqrPflfVD 81 
                                       ag +++s+q +++ e  +     v   a++++ +++l++L+ +L+s+ ++ P + VD
  gi|518652107|ref|YP_008141627.1| 371 AGSTVSSLQDMDDFEPMShysdpVVTLAIEAKHTADLPKLIDVLRSVSKADPSIQVD 427
                                       589999999999888887888888899999************************999 PP

>> DUF4115  Domain of unknown function (DUF4115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       3.8   5.7e+03      25      40 ..     233     248 ..     230     253 .. 0.79
   2 ?    1.8   0.0      0.19   2.8e+02      20      42 ..     316     338 ..     315     346 .. 0.83
   3 ?    6.2   0.1    0.0076        11      21      62 ..     656     697 ..     651     706 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.8
                           DUF4115  25 tlkaGetkevsgkppl 40 
                                       +++aG +ke+  k+pl
  gi|518652107|ref|YP_008141627.1| 233 LVSAGKQKELAKKAPL 248
                                       6789******888887 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.19
                           DUF4115  20 vlfegtlkaGetkevsgkppltl 42 
                                       ++f+g+ ++G+++ v+g+ + ++
  gi|518652107|ref|YP_008141627.1| 316 RVFSGIIRKGSELYVTGAGKSKV 338
                                       69*************98865455 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.0076
                           DUF4115  21 lfegtlkaGetkevsgkppltltiGnagavevsvnGkpvdll 62 
                                       ++e + + Ge+++v + +p++  iG a+a++ +  Gk++  +
  gi|518652107|ref|YP_008141627.1| 656 VVEDMQQNGEEITVIANAPVSGMIGFASAIRSATGGKAIWSS 697
                                       678899********9999***************999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (736 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 4553.46
//
Query:       gi|518652108|ref|YP_008141628.1|  [L=120]
Description: hypothetical protein FACI_IFERC00001G0747 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.088   13.7   0.7       0.17   12.8   0.1    1.9  2  WD40      WD domain, G-beta repeat


Domain annotation for each model (and alignments):
>> WD40  WD domain, G-beta repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.3e-06      0.17      15      38 .]      21      38 ..       6      38 .. 0.80
   2 ?   -2.9   0.1      0.89   1.6e+04       4      12 ..     109     116 ..     107     118 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.3e-06
                                      EEEEETTSSEEE.EEETTSEEEEEE CS
                              WD40 15 slafspdgawla.sGsdDgtvriWd 38
                                      ++      ++++ sG+ D+tv++Wd
  gi|518652108|ref|YP_008141628.1| 21 CF------HFISvSGG-DHTVYMWD 38
                                      55......66743899.*******9 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.89
                                       EEEEESSSS CS
                              WD40   4 lrtltGHss 12 
                                       ++  +GH +
  gi|518652108|ref|YP_008141628.1| 109 QKQPRGH-G 116
                                       5667899.4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       567  (0.0316247); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 788.20
//
Query:       gi|518652109|ref|YP_008141629.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G0748 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0007   19.7   4.2    0.00086   19.5   4.2    1.1  1  DUF3784          Domain of unknown function (DUF3784)
     0.0018   18.1   2.2     0.0019   18.0   2.2    1.0  1  PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-t
      0.007   15.2   2.5     0.0075   15.1   2.5    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
  ------ inclusion threshold ------
      0.038   13.3   0.6      0.044   13.1   0.6    1.0  1  DUF4191          Domain of unknown function (DUF4191)
      0.082   13.0   3.8       0.11   12.6   3.8    1.3  1  SPC12            Microsomal signal peptidase 12 kDa subunit (
       0.16   12.0   0.1       0.16   12.0   0.1    2.2  2  DUF2116          Uncharacterized protein containing a Zn-ribb
       0.18   11.9   0.1       0.18   11.9   0.1    1.8  2  RAMP4            Ribosome associated membrane protein RAMP4
       0.51    9.4   2.2       0.51    9.4   2.2    1.0  1  AC_N             Adenylyl cyclase N-terminal extracellular an
        1.6    8.5   3.8        4.5    7.1   3.8    1.6  1  ATG27            Autophagy-related protein 27
        4.5    6.4   5.2        4.9    6.2   5.2    1.0  1  Herpes_LMP1      Herpesvirus latent membrane protein 1 (LMP1)


Domain annotation for each model (and alignments):
>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   4.2   4.8e-07   0.00086      27      90 ..       3      63 ..       2      70 .. 0.60

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.8e-07
                           DUF3784 27 ntmskeekekydekklsrfmgivllligilflllgllsaiesealliialiviiiiviylivya 90
                                      nt +++e +k+ +kk  +  gi++ll+ ++  l+++   +  +++ i+ +i+ii++++y++v++
  gi|518652109|ref|YP_008141629.1|  3 NTHNNKEENKISKKKSIK-LGIIILLLFVIVELIAVA--YDISHINILLYIFIIGTIVYIVVVI 63
                                      899999999999999665.566666666666666666..3444444444455555555554443 PP

>> PhoLip_ATPase_C  Phospholipid-translocating P-type ATPase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   2.2   1.1e-06    0.0019     147     199 ..      15      67 ..       2      74 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.1e-06
                   PhoLip_ATPase_C 147 tndlqlfgtlvftalvlvvnlkvaletktwtliliililgsillyflflllys 199
                                       + +   +g+++    v+v ++ va ++++++++l+i+i+g+i+ ++++++l++
  gi|518652109|ref|YP_008141629.1|  15 KKKSIKLGIIILLLFVIVELIAVAYDISHINILLYIFIIGTIVYIVVVIYLVK 67 
                                       44556789********************************9965555555554 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.5   4.2e-06    0.0075     374     435 ..       9      67 ..       1      72 [. 0.46

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.2e-06
                           DUF2207 374 kkgkkklkklsalglgliilglilillallllvlllvfllilllillliaiivlllfsrllg 435
                                       +++k  +kk++ lg+++++l++i+ l+a++     ++ ++ill+i+++  i+++++  +l++
  gi|518652109|ref|YP_008141629.1|   9 EENKISKKKSIKLGIIILLLFVIVELIAVAY---DISHINILLYIFIIGTIVYIVVVIYLVK 67 
                                       2233333344444444444444444333322...2555555555555555555555555555 PP

>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.6   2.4e-05     0.044      16      72 ..      12      69 ..       2      72 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.4e-05
                           DUF4191 16 kltrkedkkllwlllaaflvvvvvfvvlglllgs.lilllilgillgllvalivltrr 72
                                      k+ +k+  kl  ++l++f++v +++v++ +   + l+++ i+g ++ ++v++++ ++r
  gi|518652109|ref|YP_008141629.1| 12 KISKKKSIKLGIIILLLFVIVELIAVAYDISHINiLLYIFIIGTIVYIVVVIYLVKNR 69
                                      78899999999999*******99999999997665899999**999999999888777 PP

>> SPC12  Microsomal signal peptidase 12 kDa subunit (SPC12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   3.8   6.3e-05      0.11      13      53 ..      22      63 ..      14      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 6.3e-05
                             SPC12 13 lqvilvlsaviafi.vGyitqdlkltlyillagvvltllvvv 53
                                        +il+l++++ +i v y ++ ++++lyi+++g+++ ++vv+
  gi|518652109|ref|YP_008141629.1| 22 GIIILLLFVIVELIaVAYDISHINILLYIFIIGTIVYIVVVI 63
                                      55778888888765389*********************9997 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 ?   12.0   0.1   8.8e-05      0.16      29      56 ..       7      34 ..       3      37 .. 0.88
   2 ?    0.8   3.1      0.27   4.9e+02      42      57 ..      47      62 ..      41      68 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.8e-05
                           DUF2116 29 ekkrkkvarsqqilfgililllavvlvl 56
                                      +k+ +k+ + + i +gi+illl v++ l
  gi|518652109|ref|YP_008141629.1|  7 NKEENKISKKKSIKLGIIILLLFVIVEL 34
                                      78999****************9999865 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                           DUF2116 42 lfgililllavvlvlk 57
                                      l+ i+i+  +v++v+ 
  gi|518652109|ref|YP_008141629.1| 47 LLYIFIIGTIVYIVVV 62
                                      4445544333333332 PP

>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1    0.0001      0.18      25      49 ..       8      32 ..       1      33 [. 0.71
   2 ?   -1.0   0.3       1.1     2e+03      35      48 ..      40      53 ..      38      62 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                             RAMP4 25 kslkkkekkspvgpwlLglfiFVVi 49
                                      k+ +k +kk+++   ++ l++FV++
  gi|518652109|ref|YP_008141629.1|  8 KEENKISKKKSIKLGIIILLLFVIV 32
                                      2233667899999999999999986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.1
                             RAMP4 35 pvgpwlLglfiFVV 48
                                       ++ + + l iF++
  gi|518652109|ref|YP_008141629.1| 40 DISHINILLYIFII 53
                                      56666666666654 PP

>> AC_N  Adenylyl cyclase N-terminal extracellular and transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   2.2   0.00029      0.51     200     249 ..      20      71 ..       6      75 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00029
                              AC_N 200 tmlmavlvlvcvvmlafhaar.gpl.evsyvvvlslaillilvlavlcnrna 249
                                        + + +l+l ++v l+  a   +++  + y+ ++   +++++v+ ++ nr +
  gi|518652109|ref|YP_008141629.1|  20 KLGIIILLLFVIVELIAVAYDiSHInILLYIFIIGTIVYIVVVIYLVKNRHN 71 
                                       4444555555555444433321344246799999999999999999999976 PP

>> ATG27  Autophagy-related protein 27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   3.8    0.0025       4.5     192     223 ..      16      69 ..       2      72 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                             ATG27 192 k......................sgwGfFtwlfiilflataaYlifgswlNynr 223
                                       k                        ++   +l+ i++++t++Y+++ ++l  nr
  gi|518652109|ref|YP_008141629.1|  16 KksiklgiiilllfviveliavaYDISHINILLYIFIIGTIVYIVVVIYLVKNR 69 
                                       1346678888888888888888866677779******************98887 PP

>> Herpes_LMP1  Herpesvirus latent membrane protein 1 (LMP1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   5.2    0.0027       4.9      79     128 ..      20      67 ..      11      74 .. 0.53

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                       Herpes_LMP1  79 plgalcllllmitlllialwnlhgqalylgivlfifgcllvlglwiylle 128
                                        lg + lll++i  l+   +++    + l   +fi+g ++ + + iyl++
  gi|518652109|ref|YP_008141629.1|  20 KLGIIILLLFVIVELIAVAYDISHINILL--YIFIIGTIVYIVVVIYLVK 67 
                                       35555444444444444444443333332..3456666666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1496  (0.0834402); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); 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: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 487.66
//
Query:       gi|518652110|ref|YP_008141630.1|  [L=279]
Description: hypothetical protein FACI_IFERC00001G0749 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1391  (0.0775838); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1860.36
//
Query:       gi|518652111|ref|YP_008141631.1|  [L=71]
Description: hypothetical protein FACI_IFERC00001G0750 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.049   13.5   0.1      0.053   13.4   0.1    1.1  1  Herpes_UL42  DNA polymerase processivity factor (UL42)


Domain annotation for each model (and alignments):
>> Herpes_UL42  DNA polymerase processivity factor (UL42)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   2.9e-06     0.053      38      77 ..      22      60 ..       6      67 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.9e-06
                                      EEECETTEEEEEEEECGGCCCEESS.EEEESECCCTEETT CS
                       Herpes_UL42 38 ihttlegeqvtlpveeeifssyrgPravvlsiteskrvli 77
                                      ++ tl +  v l ++ +++  y++P  +v+si +sk+  i
  gi|518652111|ref|YP_008141631.1| 22 VFATLISYIVLLILQSSMN-IYHTPAEIVRSIRNSKELDI 60
                                      7899888888887777766.679*************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       581  (0.0324056); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 497.71
//
Query:       gi|518652112|ref|YP_008141632.1|  [L=386]
Description: transposase (04) [Ferroplasma acidarmanus fer1]
Scores for complete 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-85  285.3   0.4    8.3e-85  284.9   0.4    1.1  1  Transposase_mut  Transposase, Mutator family
    3.5e-06   27.3   0.0    6.7e-06   26.4   0.0    1.5  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  284.9   0.4   9.3e-89   8.3e-85      22     368 ..      16     351 ..       3     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 284.9 bits;  conditional E-value: 9.3e-89
                   Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspalleryk 97 
                                        d +lke++k  +e+l+e el+++l        ee+ + +nG+++r+l+T++g++ +l++PrdR+ +F+++++e y+
  gi|518652112|ref|YP_008141632.1|  16 IDRILKEAIKEKIEKLMETELNAYL--------EENPGIKNGKYKRDLKTKYGEIkQLNVPRDRDSNFHTQVIEPYN 84 
                                       5556666666666666666666665........6677889*************9957******************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R+   +e+ ++++y +G+str+++ ++e++ g +++Sks++S+it+ + e+v +f +R+L++  y ++flD+l   +
  gi|518652112|ref|YP_008141632.1|  85 RSI-GMEDLIVSMYSNGISTRRIAGIMEDILG-NKYSKSTISRITDLTIEEVYKFINRPLDKR-YIAVFLDGLFFYL 158
                                       *86.689*************************.66***************************9.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R  g v  ++v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L nrGlk+  l+v+D+ k L + + + +p ++
  gi|518652112|ref|YP_008141632.1| 159 R-RGNVDKEPVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGLKEPLLIVADGIKNLDEEVMEIYPRSE 234
                                       *.788999********************************************************************* PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                        Q C++H++r l ++v  k+ d+++ +  +++k  + eea  ++++f  k+ +kypkv    +++  ++l f+++p 
  gi|518652112|ref|YP_008141632.1| 235 FQLCTIHYARGLKSNVREKDIDEITIDANKMFKCDNKEEAIIRFNDFKYKWKSKYPKVIYNTEKNLGKLLRFYNYPV 311
                                       ***************************************************************************** PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvg 368
                                       +ir+++kstN++Er N e+rRr++++  FP+e+s++++ +
  gi|518652112|ref|YP_008141632.1| 312 NIRKSLKSTNAIERFNGEVRRRVKTISSFPDEDSAMKVFY 351
                                       *************************************977 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   7.5e-10   6.7e-06      15      94 ..     166     243 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 7.5e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ + y+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518652112|ref|YP_008141632.1| 166 EPVIFALGIKETGEYEVLGFYLTVKESHNAYKEVLEDLYNRGL--KEPLLIVADGIKNLDEEVMEIYPRSEFQLCTI 240
                                       5677899*******************************99644..6******************************* PP

                              MULE  92 Hia 94 
                                       H a
  gi|518652112|ref|YP_008141632.1| 241 HYA 243
                                       *76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       911  (0.0508115); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2739.98
//
Query:       gi|518652113|ref|YP_008141633.1|  [L=282]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.3e-22   79.2   0.0    5.1e-22   78.6   0.0    1.3  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
       0.01   15.9   0.0      0.022   14.8   0.0    1.6  1  DDE_Tnp_1_3  Transposase DDE domain
      0.077   13.0   0.6       0.41   10.7   0.0    2.4  3  HTH_19       Helix-turn-helix domain
       0.18   11.9   0.9       0.56   10.3   0.3    2.1  2  LysM         LysM domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.1e-25   5.1e-22       3     179 ..     106     274 ..     104     278 .. 0.82

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.1e-25
                         DDE_Tnp_1   3 krevlivDattvrvpgtkedarwgykggkykygyklhiavdtr.sglilsvvitpgnvhdskglkqlldelrpr..k 76 
                                        ++vl++D+t++++  ++   +  y++g++++g+k+h+a  +    l+l++ itp+nvhdsk++++ll+ +++    
  gi|518652113|ref|YP_008141633.1| 106 LYSVLAIDSTFIETMVKG---SGIYQRGERRNGIKIHTAAIASpYPLPLKAIITPANVHDSKVFDDLLEYINEYisG 179
                                       589**********97777...55888***********8754441566**************************9*** PP

                         DDE_Tnp_1  77 gklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyy 153
                                       +++++ D GY + + + +l+ekg+++++r+kkn+ +    +e ++ ++ r ++  + +  s   +n+         +
  gi|518652113|ref|YP_008141633.1| 180 NTVLTFDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIKEETFNSKIVRFRNGLELRLVSLDINNR--------KR 248
                                       ***********************************99994444444444444444444444444444........45 PP

                         DDE_Tnp_1 154 vtntnsellsaeevaelyrlRwqiEr 179
                                        + t+  +l+   +  +y +Rw+iE 
  gi|518652113|ref|YP_008141633.1| 249 EYITDILDLPEIYIYYIYMRRWVIEK 274
                                       667889999999*************5 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0     5e-06     0.022      59     121 ..     151     219 ..     133     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5e-06
                       DDE_Tnp_1_3  59 lavkltpgnvdDrepveelakellgklfa......Dkgyiskklaeelleegielitklrknmkkklls 121
                                       l++ +tp+nv+D +  ++l + + + + +      D gy     + el+e+gi+++++++kn   ++++
  gi|518652113|ref|YP_008141633.1| 151 LKAIITPANVHDSKVFDDLLEYINEYISGntvltfDLGYYNLGRFMELKEKGINFVSRIKKNADYTVIK 219
                                       67789**********9888777665443322222399*************************8877765 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.2e-05      0.41      15      50 ..      53      88 ..      48      90 .. 0.76
   2 ?   -2.3   0.0       1.1   4.7e+03      28      41 ..     172     184 ..     163     187 .. 0.80
   3 ?   -2.1   0.1      0.88   3.9e+03      26      46 ..     203     224 ..     196     233 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.2e-05
                            HTH_19 15 qeelaerlgisrskisaiEngkkdvpsaelllkiae 50
                                      + ++a+++gis+s++s++ n + + +  +++++i++
  gi|518652113|ref|YP_008141633.1| 53 LTDIAYNNGISKSQLSKLNNKRPYSIFEKVFYSILR 88
                                      679***************977554554666677766 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                            HTH_19  28 kisaiEngkkdvps 41 
                                       +i+++++g++ v++
  gi|518652113|ref|YP_008141633.1| 172 YINEYISGNT-VLT 184
                                       7899999988.765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.88
                            HTH_19  26 rskisaiEng.kkdvpsaelll 46 
                                       +++ s i ++  + v++ e+++
  gi|518652113|ref|YP_008141633.1| 203 INFVSRIKKNaDYTVIKEETFN 224
                                       6778888888866678877775 PP

>> LysM  LysM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.3   0.00013      0.56       9      36 ..      53      79 ..      47      80 .. 0.87
   2 ?   -1.7   0.0      0.71   3.2e+03       1       9 [.     215     223 ..     215     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00013
                                      HHHHHHHCTCHHHHHHHHCTCSSCGG-- CS
                              LysM  9 LwsIAkrygitveklleaNnlsspdkif 36
                                      L +IA  +gi+ ++l ++Nn +++  if
  gi|518652113|ref|YP_008141633.1| 53 LTDIAYNNGISKSQLSKLNNKRPYS-IF 79
                                      99******************99988.76 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.71
                                       EEE-TT--H CS
                              LysM   1 YtVkkGDTL 9  
                                       YtV k +T 
  gi|518652113|ref|YP_008141633.1| 215 YTVIKEETF 223
                                       9******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2008.41
//
Query:       gi|518652114|ref|YP_008141634.1|  [L=70]
Description: hypothetical protein FACI_IFERC00001G0753 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1278  (0.0712812); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.44
# Mc/sec: 477.39
//
Query:       gi|518652115|ref|YP_008141635.1|  [L=103]
Description: hypothetical protein FACI_IFERC00001G0754 [Ferroplasma acidarmanus fer1]
Scores for complete 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-28   96.6   0.0    8.7e-28   96.4   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e
     0.0054   17.5   0.1      0.013   16.3   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 !   96.4   0.0   9.7e-32   8.7e-28       1      97 [.       6      99 ..       6     100 .. 0.99

  Alignments for each domain:
  == domain 1  score: 96.4 bits;  conditional E-value: 9.7e-32
                                      EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--.S--EEEEEEEEEEEEEEEE.E-HHHH CS
                     Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvd.kksreqfeirthkRlidisdatketi 78
                                      ri l++++ + ++ ++++i+ +ak++g+++ gp+plPtk+++v+++ksp ++ + +++++e+r+hkRl+d+ da+++t+
  gi|518652115|ref|YP_008141635.1|  6 RISLSGTENQIVDVVCNEIKAIAKRTGVEIHGPIPLPTKKLKVPLRKSPDGEgSPTWDRWEMRVHKRLMDV-DADERTL 83
                                      799********************************************************************.8****** PP

                                      HHHS-...S---SS-EEEE CS
                     Ribosomal_S10 79 dtllkllqlnlpegVsvev 97
                                      ++l++   +++p+gV +e+
  gi|518652115|ref|YP_008141635.1| 84 RQLMR---ISIPDGVRIEI 99
                                      *****...*********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 !   16.3   0.0   1.4e-06     0.013       6      52 ..       5      47 ..       2      52 .. 0.92
   2 ?   -1.9   0.0      0.67     6e+03      74      77 ..      84      87 ..      66     101 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                            PriA_C  6 alirvsgkdeekveeaaeelaellkealkleeveilgpapapiakik 52
                                      a+i +sg++ + v  +++e++++ k+    ++vei gp+p p +k+k
  gi|518652115|ref|YP_008141635.1|  5 ARISLSGTENQIVDVVCNEIKAIAKR----TGVEIHGPIPLPTKKLK 47
                                      89*******************99999....6799**********997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.67
                            PriA_C 74 kell 77
                                      ++l+
  gi|518652115|ref|YP_008141635.1| 84 RQLM 87
                                      2222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 722.90
//
Query:       gi|518652116|ref|YP_008141636.1|  [L=426]
Description: hypothetical protein FACI_IFERC00001G0755 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-54  184.1   0.1    2.4e-54  183.8   0.1    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    2.2e-36  124.6   1.0    5.4e-36  123.3   0.1    2.1  3  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    1.4e-15   57.4   1.0    7.7e-14   51.9   0.3    2.9  3  GTP_EFTU_D2  Elongation factor Tu domain 2
    2.5e-07   30.8   0.0    5.6e-06   26.4   0.0    2.4  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0011   18.8   0.4     0.0026   17.6   0.4    1.6  1  GTP_EFTU_D4  Elongation factor Tu domain 4
     0.0029   17.8   0.4       0.21   11.8   0.1    2.3  2  Roc          Ras of Complex, Roc, domain of DAPkinase
     0.0038   16.6   0.0       0.02   14.2   0.0    1.9  1  Gtr1_RagA    Gtr1/RagA G protein conserved region
     0.0049   16.6   0.1      0.036   13.8   0.0    2.2  2  PduV-EutP    Ethanolamine utilisation - propanediol utilisati
     0.0061   16.2   1.3      0.034   13.8   0.2    2.1  2  Ras          Ras family
     0.0071   16.4   0.0        4.2    7.4   0.0    2.4  2  Dynamin_N    Dynamin family
     0.0079   15.7   0.0      0.049   13.1   0.0    2.0  2  Arf          ADP-ribosylation factor family
  ------ inclusion threshold ------
      0.013   14.8   0.0      0.032   13.5   0.0    1.5  1  Septin       Septin
      0.042   13.4   0.1       0.41   10.2   0.1    2.5  2  FeoB_N       Ferrous iron transport protein B
       0.14   11.3   0.0        4.1    6.5   0.0    2.1  2  G-alpha      G-protein alpha subunit


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.8   0.1   1.9e-57   2.4e-54       2     186 ..       5     210 ..       4     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 183.8 bits;  conditional E-value: 1.9e-57
                                       CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH...HHHST.............HCHSHHHHHHTSCSSCEEEE CS
                          GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgeka...eeerv.............lDtlkeErergiTiksaais 62 
                                       +++n++iighvDhGK+T+++rLl+++g+i ++  ++   e                 +D+ keErerg+Ti+ ++ +
  gi|518652116|ref|YP_008141636.1|   5 PHMNLVIIGHVDHGKSTFVGRLLFEHGEIPQHIIDEykkE---SeekgkatfefawvMDRFKEERERGVTIDLTHRK 78 
                                       599**************************99877774331...235678889************************* PP

                                       EETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB..STHHHHHHHHHHHHTTTE.EEEEEESCGST. CS
                          GTP_EFTU  63 leketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG..vepqteevlrlalkegvp.iivfiNKmDrl. 135
                                       ++  t+ky +++iD+PGH+dF+k++i+g++++D avlvv+a+eG  v++qt+e++ la+++gv  +iv++NKmD + 
  gi|518652116|ref|YP_008141636.1|  79 FQ--TDKYYFTIIDAPGHRDFVKNMITGTSQADAAVLVVSAREGdgVMAQTREHAFLARTLGVSqLIVAVNKMDATq 153
                                       **..**************************************8777******************************9 PP

                                       ....HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH............HHHH CS
                          GTP_EFTU 136 ....kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk............tlle 186
                                           +++++e++e+v + l      l+ +g+k   +vp++++S++kg+++             t++e
  gi|518652116|ref|YP_008141636.1| 154 paysEKRYNEVKEQVTK-L------LTPIGFK---DVPIIPMSGYKGDNIMknsanlswwkgpTIME 210
                                       88888888888888884.4......5677777...49***********9875565555666654555 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       4.3   5.5e+03       8      60 ..     108     160 ..     102     169 .. 0.60
   2 ?   -2.5   0.0       4.9   6.2e+03      57      75 ..     275     293 ..     262     297 .. 0.70
   3 !  123.3   0.1   4.2e-39   5.4e-36       2     109 ..     313     418 ..     312     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4.3
                                       EEEEEEESSS...SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS- CS
                       GTP_EFTU_D3   8 feAqvyileke.rhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekk 60 
                                        +A v++++ +   + + +  +  + +rt  v+  +v++ +k+d  +   sek+
  gi|518652116|ref|YP_008141636.1| 108 ADAAVLVVSAReGDGVMAQTREHAFLARTLGVSQLIVAV-NKMDATQPAYSEKR 160
                                       566666666643455555666667777888777766666.66665555555554 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.9
                                       BSS-SSCCSTT-CEEEEEE CS
                       GTP_EFTU_D3  57 sekkpefvkpGdnviveve 75 
                                       +++  + + pGdn+ ++v+
  gi|518652116|ref|YP_008141636.1| 275 HHTAMQSAEPGDNIGFNVR 293
                                       3456678899999988876 PP

  == domain 3  score: 123.3 bits;  conditional E-value: 4.2e-39
                                       -EEECCEEEEEEESSS..SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECC CS
                       GTP_EFTU_D3   2 ikphtkfeAqvyilekerhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelik 78 
                                        + +++f+Aq+++l++  ++ i agY+pv++++ta+++++++e+++++++k + + ++kp+f+k Gd ++v+v + k
  gi|518652116|ref|YP_008141636.1| 313 PTVVKSFTAQIVVLQH--PSVIAAGYKPVFHVHTAQIACRFEEIIKTINPKDGTTLKEKPDFIKAGDIAVVKVIPDK 387
                                       57799***********..*********************************************************** PP

                                       EEEE--TTTHCCCCEEEEECTTCEEEEEEEE CS
                       GTP_EFTU_D3  79 pialekgseypqlGrFaiReggrTvaaGvvt 109
                                       p+++ek+se+pqlGrFaiR++g TvaaG+  
  gi|518652116|ref|YP_008141636.1| 388 PLVIEKVSEFPQLGRFAIRDMGMTVAAGQCI 418
                                       ****************************865 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 ?    2.8   0.0      0.12   1.6e+02      17      47 ..       7      35 ..       5      49 .. 0.86
   2 ?   -2.5   0.0       5.5   7.1e+03      31      46 ..     164     179 ..     156     192 .. 0.74
   3 !   51.9   0.3     6e-17   7.7e-14       1      73 [.     240     306 ..     240     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                                      EEEEEEC.TCTTSEEEEEEEEEEEEETEEESE CS
                       GTP_EFTU_D2 17 devrilg.ndtskkeivtrissletfhedede 47
                                      ++++i+g +d +k+   t +++l+ +h++  +
  gi|518652116|ref|YP_008141636.1|  7 MNLVIIGhVDHGKS---TFVGRLLFEHGEIPQ 35
                                      78899999**9999...**********98765 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.5
                                       EEEEEEEEEEETEEES CS
                       GTP_EFTU_D2  31 ivtrissletfheded 46 
                                        ++++++l+t+ + +d
  gi|518652116|ref|YP_008141636.1| 164 VKEQVTKLLTPIGFKD 179
                                       4589999999876665 PP

  == domain 3  score: 51.9 bits;  conditional E-value: 6e-17
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtv  grv++G++k +d+v +l+ n   k+   ++++s+e +h  ++ a++g+n+G++v+++  +d +++Gd+ 
  gi|518652116|ref|YP_008141636.1| 240 GTVPVGRVETGVIKINDKVIFLPaN---KS---GEVKSIEEHHTAMQSAEPGDNIGFNVRGIAKND-LKRGDVC 306
                                       99*******************7744...78...*********************************.9****95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   4.4e-09   5.6e-06       2     100 ..       9     133 ..       8     172 .. 0.73

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.4e-09
                                       EEEEESTTSSHHHHHHHHH....................T...........STEEESSSTTSSSSEEEEEEEETTEE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt....................g...........ekaivsdkpgtTrdinegrvklkgke 47 
                                        +i+G+   GKSt++ +l+                    +           ++ + +++ g+T+d +++++++++  
  gi|518652116|ref|YP_008141636.1|   9 LVIIGHVDHGKSTFVGRLLfehgeipqhiideykkeseeKgkatfefawvmDRFKEERERGVTIDLTHRKFQTDKYY 85 
                                       689***************988877777777766666555056666666655799******************999** PP

                                       EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT..TTCSHHHHHHHHHH CS
                          MMR_HSR1  48 ielvDtpGliegaseekglgkaflaleeadlillvvdas..eeklkpldeeleel 100
                                       ++++D pG  +    +  +++ +    +ad+++lvv+a+  + ++ ++ +e + l
  gi|518652116|ref|YP_008141636.1|  86 FTIIDAPG--H----RDFVKNMITGTSQADAAVLVVSARegD-GVMAQTREHAFL 133
                                       ********..3....234666666677799999999988431.343333333333 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.4     2e-06    0.0026      21      83 ..     244     304 ..     234     306 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS--TT- CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrqikegd 83 
                                       vG +v +Gvik + k+i    ++ Ge+++i++++ +++ a+ G++++  ++g     ++k gd
  gi|518652116|ref|YP_008141636.1| 244 VG-RVETGVIKINDKVIFLPANKSGEVKSIEEHHTAMQSAEPGDNIGFNVRGIA-KNDLKRGD 304
                                       88.9*********************************************99854.66666666 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.037        47       2      20 ..       9      27 ..       8      47 .. 0.82
   2 !   11.8   0.1   0.00016      0.21       9     119 ..      47     150 ..      44     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.037
                                      EEEESSTTSSHHHHHHCHC CS
                               Roc  2 vvlvGdsgvGKtsllkrfv 20
                                      +v++G    GK++++ r++
  gi|518652116|ref|YP_008141636.1|  9 LVIIGHVDHGKSTFVGRLL 27
                                      79**************997 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00016
                                       TSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEE CS
                               Roc   9 gvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalail 85 
                                       + GK ++   +v d+f+e+++  + +d+++++++   +       +k+ + i D  G+ +f + +    ++a++a+l
  gi|518652116|ref|YP_008141636.1|  47 EKGKATFEFAWVMDRFKEERERGVTIDLTHRKFQ---T-------DKYYFTIIDAPGHRDFVKNMITGTSQADAAVL 113
                                       579************************9888762...2.......3578*************999999999****** PP

                                       EEEGHHHHCH...HHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  86 vydsrssenl...keWlkelkkvagkspvilvgnkiD 119
                                       v+ +r+ + +    +    l +  g s++i+ +nk+D
  gi|518652116|ref|YP_008141636.1| 114 VVSAREGDGVmaqTREHAFLARTLGVSQLIVAVNKMD 150
                                       *998887644111445556677788899999999999 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 !   14.2   0.0   1.6e-05      0.02      30     154 ..      67     182 ..      61     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.6e-05
                         Gtr1_RagA  30 rlgatidveksevrflgnltlnlwDcgGqeafveeylssqkeeifrnvgvliyVfDvesreleedletlkeilealr 106
                                       + g+tid+++ ++  +++ ++ ++D +G ++fv+++++       ++ ++ + V+ ++  e +  +++ +e    +r
  gi|518652116|ref|YP_008141636.1|  67 ERGVTIDLTHRKF-QTDKYYFTIIDAPGHRDFVKNMITGT-----SQADAAVLVVSAR--EGDGVMAQTREHAFLAR 135
                                       5689*********.58999****************86554.....4456666677777..44455555554443333 PP

                         Gtr1_RagA 107 qyspeakvfvlihKmDliqedereeifeerkeeireeieklekeeiqf 154
                                        +    ++ v ++KmD  q    e+ ++e ke++++ +++++++++ +
  gi|518652116|ref|YP_008141636.1| 136 -TLGVSQLIVAVNKMDATQPAYSEKRYNEVKEQVTKLLTPIGFKDVPI 182
                                       .33345678999**********************99999888776655 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.77   9.9e+02       4      21 ..       9      26 ..       7      30 .. 0.84
   2 !   13.8   0.0   2.8e-05     0.036      25     102 ..      73     146 ..      68     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.77
                         PduV-EutP  4 illiGkvgsGKttLtqal 21
                                      +++iG+v+ GK t   +l
  gi|518652116|ref|YP_008141636.1|  9 LVIIGHVDHGKSTFVGRL 26
                                      689*********987665 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.8e-05
                         PduV-EutP  25 elkYkktqaiefsdeviDtPGeylenrklysalivtsaeadvialvqdateeesvfppgfasvfnkeviGiitkidl 101
                                       +l+ +k q+ +++ ++iD+PG    +r + + +i+ + +ad  +lv++a e + v++++  + f   ++G+   i  
  gi|518652116|ref|YP_008141636.1|  73 DLTHRKFQTDKYYFTIIDAPG----HRDFVKNMITGTSQADAAVLVVSAREGDGVMAQTREHAFLARTLGVSQLIVA 145
                                       5788999**************....79**********************************9999999998444333 PP

                         PduV-EutP 102 a 102
                                       +
  gi|518652116|ref|YP_008141636.1| 146 V 146
                                       3 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.21   2.7e+02       2      19 ..       9      26 ..       8      45 .. 0.84
   2 !   13.8   0.2   2.6e-05     0.034      11     119 ..      49     161 ..      45     180 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.21
                                      EEEEESTTSSHHHHHHHH CS
                               Ras  2 lvlvGdsavGKtslllrf 19
                                      lv++G    GK++++ r 
  gi|518652116|ref|YP_008141636.1|  9 LVIIGHVDHGKSTFVGRL 26
                                      89***********99775 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 2.6e-05
                                       SHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHH CS
                               Ras  11 GKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegillvyditsresf 87 
                                       GK+++ + +v d+Fkee e  + +d + +++++d  ++ ++i D  G  +f +   +  ++a++++lv +  + +  
  gi|518652116|ref|YP_008141636.1|  49 GKATFEFAWVMDRFKEERERGVTIDLTHRKFQTD--KYYFTIIDAPGHRDFVKNMITGTSQADAAVLVVSAREGDGV 123
                                       9*********************999988887765..68899***********9999999********9999998888 PP

                                       HTHHHHHHHHHHHSTTTSEEEEEEETTTGGG.......G CS
                               Ras  88 envkkwveeikrvaeenvpivLvGnKvDlee.......k 119
                                          ++ +  + r+     ++++  nK+D ++        
  gi|518652116|ref|YP_008141636.1| 124 MAQTREHAFLARTLG-VSQLIVAVNKMDATQpaysekrY 161
                                       777777777777777.36677777899988766555442 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0046       5.9       1      19 [.       9      27 ..       9      31 .. 0.88
   2 !    7.4   0.0    0.0033       4.2      49     152 ..      39     135 ..      28     149 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0046
                                      EEEEEBTTTTHHHHHHHHH CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLl 19
                                      ++++G++ +GKS+++  Ll
  gi|518652116|ref|YP_008141636.1|  9 LVIIGHVDHGKSTFVGRLL 27
                                      589***********99887 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0033
                                       S...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHH CS
                         Dynamin_N  49 ravkeelkekekkledfsevreeieketekiagankgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkey 125
                                       ++ k+e +ek k   +f  v + +++e+e+         ++ +++++++ ++   t++D PG  +  k   ++++ +
  gi|518652116|ref|YP_008141636.1|  39 DEYKKESEEKGKATFEFAWVMDRFKEERERGV-------TIDLTHRKFQTDKYYFTIIDAPGHRDFVK---NMITGT 105
                                       44566666667777888888888888887777.......346788899999999********988433...467777 PP

                                       HSTTEEEEEEEETTS..-CCC-.CHHHHHH CS
                         Dynamin_N 126 ikkadiilavtsanh..dlsns.ealflar 152
                                        +  +++l+v++ +    ++++ e  flar
  gi|518652116|ref|YP_008141636.1| 106 SQADAAVLVVSAREGdgVMAQTrEHAFLAR 135
                                       666666666654443333444435555555 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.53   6.8e+02      14      37 ..       6      29 ..       3      37 .. 0.86
   2 !   13.1   0.0   3.8e-05     0.049      39     167 ..      65     196 ..      46     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.53
                                      EEEEEEEESTTSSHHHHHHHHHHS CS
                               Arf 14 elrilllGLDnaGKtTilkklkle 37
                                      ++ ++++G    GK+T + +l  e
  gi|518652116|ref|YP_008141636.1|  6 HMNLVIIGHVDHGKSTFVGRLLFE 29
                                      68999***999*******999765 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.8e-05
                                       CEECSSSSSEEEEEEEETTEEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTSGCCTT CS
                               Arf  39 lvttvPTigfnveeleiknlkftvwDvGGqeklRplWknYfektdavifvvDsadreRleeakeeLkalleeeelke 115
                                         +   Ti  + ++ ++ ++ ft+ D  G++   +   + +++ da + vv + + + ++   +e + l   ++l  
  gi|518652116|ref|YP_008141636.1|  65 ERERGVTIDLTHRKFQTDKYYFTIIDAPGHRDFVKNMITGTSQADAAVLVVSAREGDGVMAQTREHAFLA--RTLGV 139
                                       233556999999*********************99999*******************9998888855554..46778 PP

                                       SEEEEEEE-TTSTTSS-HHHHHHHTTGGGSS.....SSSSEEEEEEBTTTTBTHHHH CS
                               Arf 116 vallvlaNKqDlpealseeelrellgleelk.....gkrkleiqkcsavkgeglkeg 167
                                        +l+v  NK+D+++ + +e+  ++++ +  k     g +++ i+  s  kg+++ + 
  gi|518652116|ref|YP_008141636.1| 140 SQLIVAVNKMDATQPAYSEKRYNEVKEQVTKlltpiGFKDVPIIPMSGYKGDNIMKN 196
                                       889999*****9986555554444444332222355678888888888888877665 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.032       5      78 ..       7     100 ..       5     107 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                                       EEEEEEEBTTSSCCCCCCT.TSSSS----.....................--------------S-EEEEEEEEETT CS
                            Septin   5 ftlmvvGesglGkttlint.lfetdliee.....................ekleeasekkkktveikkkkvvieedg 59 
                                       ++l+++G+   Gk+t++   lfe+  i++                       +++ +e+ ++ v+i+ ++ + + d 
  gi|518652116|ref|YP_008141636.1|   7 MNLVIIGHVDHGKSTFVGRlLFEHGEIPQhiideykkeseekgkatfefaWVMDRFKEERERGVTIDLTHRKFQTD- 82 
                                       89***************76257777777778888888888888888887644566667777888888888888777. PP

                                       CEEEEEEEE---BSSSSSH CS
                            Septin  60 vklnltviDtpgfGdavdn 78 
                                        k  +t+iD pg+ d+v n
  gi|518652116|ref|YP_008141636.1|  83 -KYYFTIIDAPGHRDFVKN 100
                                       .778899999999999988 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       1.4   1.7e+03       2      20 ..       8      26 ..       7      34 .. 0.82
   2 ?   10.2   0.1   0.00032      0.41      32      91 ..      69     120 ..      68     198 .. 0.54

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.4
                                      EEEEEESTTSSHHHHHHHH CS
                            FeoB_N  2 tvalvGnpnvGkttlfnal 20
                                      +++++G  + Gk+t++ +l
  gi|518652116|ref|YP_008141636.1|  8 NLVIIGHVDHGKSTFVGRL 26
                                      57899*********99877 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00032
                                       TSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEGGGH CS
                            FeoB_N  32 GvtvekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdvvvnvvdatnl 91 
                                       Gvt++ ++ k++++++ ++i+D PG  ++ +         ++++ ++++d+ v vv a + 
  gi|518652116|ref|YP_008141636.1|  69 GVTIDLTHRKFQTDKYYFTIIDAPGHRDFVK---------NMITgTSQADAAVLVVSAREG 120
                                       9************************865522.........111113333333333333333 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.044        57      23      44 ..       6      27 ..       3      56 .. 0.81
   2 ?    6.5   0.0    0.0032       4.1     188     247 ..      71     129 ..      57     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.044
                                      EEEEEEEESTTSSHHHHHHHHH CS
                           G-alpha 23 evkllllGqseSGKsTilkqlk 44
                                      +++l+++G+ + GKsT++  l 
  gi|518652116|ref|YP_008141636.1|  6 HMNLVIIGHVDHGKSTFVGRLL 27
                                      589**************87654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0032
                                       --SEEEEEEECT-TEEEEEEEE-SSHHHHHGTCCCTTTECEEEEEEEGGGTT-B-SS-TT CS
                           G-alpha 188 tvGisetkfevdsklefrivdvgGqrserkkWvpffddvdaiiFlvslsefdqvlyedek 247
                                       t+  ++ kf+ d k+ f+i+d  G+r+  k+ ++  +++da + +vs  e d v+++ ++
  gi|518652116|ref|YP_008141636.1|  71 TIDLTHRKFQTD-KYYFTIIDAPGHRDFVKNMITGTSQADAAVLVVSAREGDGVMAQTRE 129
                                       88999******9.********************999**********99888777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.46
# Mc/sec: 2772.99
//
Query:       gi|518652117|ref|YP_008141637.1|  [L=104]
Description: DNA-directed RNA polymerase subunit L [Ferroplasma acidarmanus fer1]
Scores for 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-12   46.2   0.1    3.8e-12   45.8   0.1    1.2  1  RNA_pol_L_2  RNA polymerase Rpb3/Rpb11 dimerisation domain
  ------ inclusion threshold ------
      0.019   14.2   0.2      0.032   13.5   0.1    1.3  1  GPI          Glucose-6-phosphate isomerase (GPI)


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 !   45.8   0.1   4.2e-16   3.8e-12       2      73 ..      15      85 ..      14      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 4.2e-16
                                      EEEEEES--HHHHHHHHHHHTTSTTEEEEEEECSSTTT..SEEEEEEEESTSS-HHHHHHHHHHHHHHHHHHHH CS
                       RNA_pol_L_2  2 ltfeingEDhTLgnlLrhlllknpsVefagYkipHPle..pkmnlriqtkssnnpleaLkkalkdlldicdele 73
                                      +++e+ + D T + +L +++lk+++V    Y i+HP +  p++++++ t    +p+ a+k+a+k++ +i+++l 
  gi|518652117|ref|YP_008141637.1| 15 IKVEMINYDNTVLRPLVEEILKDDKVVESHYYIKHPDIdnPEIYVKVST---GKPQAAIKRAIKRMNKIYESLD 85
                                      678999******************************8833555666665...59***************99885 PP

>> GPI  Glucose-6-phosphate isomerase (GPI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.5e-06     0.032      38      88 ..       8      59 ..       2      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.5e-06
                               GPI 38 taeegerlaadqliydvtvilP..gkiGeEriktrGHyHkevdrrstrPEvYe 88
                                        ++++ ++ + + yd tv+ P   +i ++ ++ + Hy  +     + PE+Y 
  gi|518652117|ref|YP_008141637.1|  8 ISKDKDSIKVEMINYDNTVLRPlvEEILKDDKVVESHYYIK-HPDIDNPEIYV 59
                                      5689999***************7779************988.7789******5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1769  (0.098667); expected 358.6 (0.02)
Passed bias filter:                      762  (0.042501); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 685.97
//
Query:       gi|518652118|ref|YP_008141638.1|  [L=323]
Description: hypothetical protein FACI_IFERC00001G0757 [Ferroplasma acidarmanus fer1]
Scores for 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-28   97.7   0.0    3.5e-27   95.4   0.0    1.9  1  UPF0020          Putative RNA methylase family UPF0020
    2.4e-08   34.0   0.1    2.1e-06   27.7   0.0    2.3  2  N6_N4_Mtase      DNA methylase
    7.5e-07   29.1   0.1    1.4e-05   24.9   0.1    2.1  2  Methyltransf_31  Methyltransferase domain
    4.5e-05   23.1   0.7     0.0001   22.0   0.3    1.8  2  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00029   21.5   0.0     0.0054   17.4   0.0    2.3  2  Methyltransf_25  Methyltransferase domain
     0.0037   16.6   0.0      0.013   14.8   0.0    2.0  1  N6_Mtase         N-6 DNA Methylase
     0.0084   15.6   0.1       0.94    8.9   0.0    2.2  2  AviRa            RRNA methyltransferase AviRa
  ------ inclusion threshold ------
      0.015   15.0   0.0      0.031   13.9   0.0    1.5  1  Cons_hypoth95    Conserved hypothetical protein 95
       0.03   14.0   1.5       0.18   11.5   0.0    2.4  3  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran


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 !   95.4   0.0   1.7e-30   3.5e-27       3     183 ..     149     302 ..     147     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 95.4 bits;  conditional E-value: 1.7e-30
                                       SS-SS---SS-HHHHHHHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--E CS
                           UPF0020   3 yRefngpapLketLAaalvrlagwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelkl 79 
                                       +R+f+ p +L ++ A+ lv+ +g  +g++llDP+CG+G+ilIEa +lg++i+                         
  gi|518652118|ref|YP_008141638.1| 149 MRPFFSPVSLHPKYARYLVNTSGTAEGDTLLDPFCGTGGILIEASMLGRKII------------------------- 200
                                       69**************************************************......................... PP

                                       EEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE----------HHHH.HHHHHHHHHHHHHH CS
                           UPF0020  80 ygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgskkal.ekLYseflrelkrv 155
                                        g D++ ++v g++ N ++ g+++  +++++d+a+L   +++vd ivt++PYG++ g ++    +LY+e   ++++ 
  gi|518652118|ref|YP_008141638.1| 201 -GNDSELNMVMGTKLNFKYFGIEN-YKMYNLDIASLS-LDKKVDGIVTDMPYGRSSGINNHDiVELYQESFIKFNEL 274
                                       .*********************87.678889******.6669**************97665549************9 PP

                                       -TT..-EEEEEESSHHHHHCC---.ESEE CS
                           UPF0020 156 lrgggrlvlltsenkalekaleer.alrk 183
                                       l++ g  ++++ +n ++ + + +  +++k
  gi|518652118|ref|YP_008141638.1| 275 LKS-GGKCSIIVNNIQFLDYAVKYfNIEK 302
                                       999.7788888888888776655446555 PP

>> N6_N4_Mtase  DNA methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0     1e-09   2.1e-06     179     223 ..     161     206 ..     114     227 .. 0.81
   2 ?    4.2   0.0     0.015        29       1      55 [.     240     284 ..     240     315 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1e-09
                                       HHHHHHH.HHHS-TT-EEEETT-TTTHHHHHHHHTT-EEEEEESSH CS
                       N6_N4_Mtase 179 allerlI.klstkkgdivlDpFaGSGtTavaakelgrkfiGieiee 223
                                       + +++l+  + t +gd+ lDpF+G+G ++++a  lgrk iG + e 
  gi|518652118|ref|YP_008141638.1| 161 KYARYLVnTSGTAEGDTLLDPFCGTGGILIEASMLGRKIIGNDSEL 206
                                       56677774567999************************99988765 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.015
                                       EEEEEE--SSSSSCS.....GCCGCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEE CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdyendeqyeeedsyeeyleflekvlkevrrvLkddgsifin 55 
                                       vd ivtd PY+ ++       ++ +d     +e+ ++ + +  ++Lk +g   i 
  gi|518652118|ref|YP_008141638.1| 240 VDGIVTDMPYGRSSG------INNHDI----VELYQESFIKFNELLKSGGKCSII 284
                                       6889*********99......555555....555556666666777777765554 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.081   1.6e+02      54      98 ..      12      55 ..       7     110 .. 0.82
   2 !   24.9   0.1   7.2e-09   1.4e-05       4     109 ..     175     283 ..     173     304 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.081
                   Methyltransf_31 54 dnveFeqgdieeleklledekfDlilsnevl.naladpdkileeie 98
                                      +n+e  + +i +++++++  +f +i+  + +     dp k++++++
  gi|518652118|ref|YP_008141638.1| 12 ENIEIAHTEIKSIQETYK--NFQIIFLSGKFaLIDGDPGKVMNSAF 55
                                      6999999*****997655..7******9999444468888887655 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 7.2e-09
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g ++lD+ CGtG +++e+   lg   +++G D + +++   + n +  g++n+++   di +l+  l d+k+D i++
  gi|518652118|ref|YP_008141638.1| 175 GDTLLDPFCGTGGILIEAS-MLG--RKIIGNDSELNMVMGTKLNFKYFGIENYKMYNLDIASLS--L-DKKVDGIVT 245
                                       6789***************.554..58************************************9..4.49******* PP

                   Methyltransf_31  81 nevl.........naladpdkileeiervlkpggilli 109
                                       + +          + +   ++ + +  ++lk+gg + i
  gi|518652118|ref|YP_008141638.1| 246 DMPYgrssginnhDIVELYQESFIKFNELLKSGGKCSI 283
                                       97777765544433333444455588888888888765 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   2.1e+03      30      64 ..      19      53 ..       8      64 .. 0.67
   2 !   22.0   0.3     5e-08    0.0001       3     109 ..     177     277 ..     175     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                   Methyltransf_15 30 inleklacaqhNaevYgvsdkitlvlgdvfellak 64
                                      ++++ ++ +++N ++   s k  l+ gd  +++++
  gi|518652118|ref|YP_008141638.1| 19 TEIKSIQETYKNFQIIFLSGKFALIDGDPGKVMNS 53
                                      45566667777777777788888888887776665 PP

  == domain 2  score: 22.0 bits;  conditional E-value: 5e-08
                   Methyltransf_15   3 vilDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvflSp 79 
                                       ++lD+f+G+GG  i+  + ++k+i+ +++l+ +  ++ N + +g+++  ++   d+ +l     l+k  vd +++  
  gi|518652118|ref|YP_008141638.1| 177 TLLDPFCGTGGILIEASMLGRKIIGNDSELNMVMGTKLNFKYFGIENY-KMYNLDIASLS----LDKK-VDGIVTDM 247
                                       68******************************************9874.44444554433....3332.46666667 PP

                   Methyltransf_15  80 PwGGpsYkkqek.fdlkkklkplkleqllke 109
                                       P G  s  ++++  +l +++  +k+++llk+
  gi|518652118|ref|YP_008141638.1| 248 PYGRSSGINNHDiVEL-YQESFIKFNELLKS 277
                                       7776655544331344.56666666666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.22   4.5e+02      45      86 ..      11      51 ..       3      59 .. 0.77
   2 !   17.4   0.0   2.7e-06    0.0054       2      71 ..     179     246 ..     178     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.22
                                      TTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHH CS
                   Methyltransf_25 45 glnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekal 86
                                      g n+e+ + +++++++  + f ++++sg + +++  d  k++
  gi|518652118|ref|YP_008141638.1| 11 GENIEIAHTEIKSIQETYKNFQIIFLSGKFALID-GDPGKVM 51
                                      4489999999999999999999999988888775.4555555 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.7e-06
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEE CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvss 71 
                                       Ld  cGtG ++++++   g  k++g D   +m+  ++ +++  g+ n ++++ d+ +l+++ +++D +v  
  gi|518652118|ref|YP_008141638.1| 179 LDPFCGTGGILIEASML-G-RKIIGNDSELNMVMGTKLNFKYFGIeNYKMYNLDIASLSLD-KKVDGIVTD 246
                                       7889**********988.5.********************99999*************976.599999983 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.3e-06     0.013      28     136 ..     152     250 ..     135     290 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.3e-06
                          N6_Mtase  28 ffTPrevsklivell....epksgesvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllh 100
                                       ff P ++    ++ l     + +g + +Dp cG+gg+l++a+             +i G +++ + +  +k+N+   
  gi|518652118|ref|YP_008141638.1| 152 FFSPVSLHPKYARYLvntsGTAEGDTLLDPFCGTGGILIEASML---------GRKIIGNDSELNMVMGTKLNFKYF 219
                                       67776665555554444447888889**************9874.........345556666655555566666666 PP

                          N6_Mtase 101 gieykkvkirlgdtlekpkfekdkkfdvvvaNppfn 136
                                       gie+ k+             + dkk+d +v+  p++
  gi|518652118|ref|YP_008141638.1| 220 GIENYKMYNLDI-----ASLSLDKKVDGIVTDMPYG 250
                                       665553222222.....2222344556666666665 PP

>> AviRa  RRNA methyltransferase AviRa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0098        19      45      92 ..     166     209 ..     155     222 .. 0.73
   2 !    8.9   0.0   0.00047      0.94     148     183 ..     223     256 ..     217     287 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0098
                             AviRa  45 llekkeegapltlyDpCCGgayLltvlgllhgkkikkvlasDvdeevl 92 
                                       l+++++++++ tl Dp CG++ +l   ++l +k    +++ D + +++
  gi|518652118|ref|YP_008141638.1| 166 LVNTSGTAEGDTLLDPFCGTGGILIEASMLGRK----IIGNDSELNMV 209
                                       56667788899**********999888888764....45555555555 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00047
                             AviRa 148 eievfkaditekeeeaekevdivitDlPYGelvswq 183
                                       + ++++ di+  + +  k+vd ++tD+PYG  +  +
  gi|518652118|ref|YP_008141638.1| 223 NYKMYNLDIA--SLSLDKKVDGIVTDMPYGRSSGIN 256
                                       5678888998..44556679**********987655 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.031      40     142 ..     173     269 ..     158     281 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                        eg ++LD f+G+G++ +EA   g +k++  +++ ++v   k n + +++e+  + ++ d ++  l +     ++d 
  gi|518652118|ref|YP_008141638.1| 173 AEGDTLLDPFCGTGGILIEASMLG-RKIIGNDSELNMVMGTKLNFKYFGIEN-YKMYNLDIASLSLDK-----KVDG 242
                                       567889**************7766.788899999999999999******886.666655555544444.....689* PP

                                       EEE--SSSTTCH.H.HHHHHHHHTT-E CS
                     Cons_hypoth95 117 vflDPPyakellie.evlelleekkll 142
                                       +  D Py ++  i+ + + +l +++ +
  gi|518652118|ref|YP_008141638.1| 243 IVTDMPYGRSSGINnHDIVELYQESFI 269
                                       *******99988541456666666555 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 ?   -3.7   0.0       3.8   7.6e+03     236     252 ..      19      34 ..      13      39 .. 0.70
   2 ?   11.5   0.0   8.8e-05      0.18      20      51 ..     174     205 ..     164     211 .. 0.88
   3 ?    0.7   0.2      0.17   3.3e+02     158     254 ..     222     306 ..     207     312 .. 0.57

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.8
                                       SHHHHHHCTT...SEEE CS
                   MethyltransfD12 236 tklfrelyksYnnesil 252
                                       t+ ++ + ++Y+n++i+
  gi|518652118|ref|YP_008141638.1|  19 TE-IKSIQETYKNFQII 34 
                                       44.77777777778876 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.8e-05
                                       --SEEEETT-TTSCCHHCS...SSCEEEEES- CS
                   MethyltransfD12  20 kgktfvepFaGggaVffeakkqgkkvlinDin 51 
                                        g+t+ +pF+G+g + +ea   g k++ nD +
  gi|518652118|ref|YP_008141638.1| 174 EGDTLLDPFCGTGGILIEASMLGRKIIGNDSE 205
                                       5789***************99*********76 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.17
                                       HHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEEEEESE CS
                   MethyltransfD12 158 knakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvllsnsfk 234
                                       +n+k+++ d     l++  + d +  D PY   +++ n ++  +l  ++e  +++ e+lks       k+ +  +  
  gi|518652118|ref|YP_008141638.1| 222 ENYKMYNLDIASLSLDK--KVDGIVTDMPYGR-SSGINNHDIVEL--YQESFIKFNELLKSG-----GKCSIIVN-- 286
                                       44444444444444444..4444567888875.555555555553..333333445555554.....46666666.. PP

                                       ESHHHHHHCTT...SEEEEE CS
                   MethyltransfD12 235 dtklfrelyksYnnesilev 254
                                       ++++ ++++k +n e+i+ v
  gi|518652118|ref|YP_008141638.1| 287 NIQFLDYAVKYFNIEKIVPV 306
                                       68888888888777777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         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: 00:00:00.42
# Mc/sec: 2299.77
//
Query:       gi|518652119|ref|YP_008141639.1|  [L=1024]
Description: hypothetical protein FACI_IFERC00001G0758 [Ferroplasma acidarmanus fer1]
Scores for 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-165  549.3   1.5   1.2e-164  548.9   1.5    1.1  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.2e-34  119.4   0.5    3.1e-34  118.1   0.5    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.1e-17   63.0   4.7    1.3e-08   34.1   0.1    3.8  4  tRNA-synt_1g   tRNA synthetases class I (M)
    8.7e-07   28.6   0.0    1.9e-06   27.6   0.0    1.5  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    1.1e-06   27.8   0.0      1e-05   24.7   0.0    2.4  2  tRNA-synt_1f   tRNA synthetases class I (K)
    2.1e-05   24.0   0.1     0.0012   18.3   0.0    2.4  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
     0.0066   16.4   0.4        9.7    6.3   0.0    3.1  3  DZR            Double zinc ribbon
  ------ inclusion threshold ------
      0.018   14.8   6.0        1.2    9.0   0.0    3.3  3  zinc_ribbon_2  zinc-ribbon domain
      0.052   12.9   0.4        3.2    7.2   0.0    2.6  2  zf-TFIIB       Transcription factor zinc-finger
       0.22   11.6   1.7         27    4.9   0.0    2.9  2  zf-ACC         Acetyl-coA carboxylase zinc finger domain
       0.34   11.1   1.7         17    5.7   0.1    2.7  3  Zn-ribbon_8    Zinc ribbon domain
        1.8    8.2   4.4        4.8    6.9   0.0    2.9  3  zf_UBZ         Ubiquitin-Binding Zinc Finger
        4.7    7.0   6.9        6.8    6.4   0.2    2.9  3  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  548.9   1.5    9e-168  1.2e-164       3     591 ..      23     618 ..      21     628 .. 0.93

  Alignments for each domain:
  == domain 1  score: 548.9 bits;  conditional E-value: 9e-168
                       tRNA-synt_1   3 yekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvp.GwDhaGlaiea 78 
                                        + W+e+++ +  l+k+++ k++++  gPP ++G++H+Gh +++t+kd+v+ryk+m+G++  +++ GwD++Gl++e 
  gi|518652119|ref|YP_008141639.1|  23 RKYWKENKIIEDILNKDRNLKRYTFLEGPPTANGRPHVGHLMTRTVKDTVMRYKYMSGYDIGRRTgGWDCHGLPVEL 99 
                                       578*********************************************************9776537********** PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                       + ek++g + kke +++g e+f+e +r+ + +y++e+++  +++G ++D ++ y+Tl ++++e+ + ++++l+d+ +
  gi|518652119|ref|YP_008141639.1| 100 EAEKHFGFNTKKEIEDFGIEKFNEYCRNSVFTYIDEWNEVDSEIGYWIDENKSYVTLRNDYMESEWYALKKLFDENM 176
                                       ***************************************************************************** PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEv..eykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyv... 227
                                       + +  k+v++++++ t+ls  Ev   yk+++d++++v+f ++++ + +l+++TTtP+Tl+++  ++vn+++dy+   
  gi|518652119|ref|YP_008141639.1| 177 LVKDYKIVPYCPRCGTSLSSHEVaqGYKNTDDTSVYVKFRIKGSMNRYLIAWTTTPWTLPSNELLVVNKDFDYSlvs 253
                                       ***********************988***********************************************9876 PP

                       tRNA-synt_1 228 .itkeklilaeallkslvkkesekkiledergkeLegkevelpl.....vnrkipiiaddyvdkeaGtGvVkiaPah 298
                                         + +++ ++++ ++sl+k   + kil++++gk+L+g ++e+++      +++++++ +d+v++e GtG+V+ aPa+
  gi|518652119|ref|YP_008141639.1| 254 dGN-NEYYVLSSTVQSLFK---DAKILKTIKGKDLVGTHYEQLMpflhvSKNALQVVPGDFVTAEDGTGIVHAAPAF 326
                                       444.455555666666665...78*****************988889998999************************ PP

                       tRNA-synt_1 299 dedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyr 375
                                       ++dD+ ++k+yn+++in++d++g++++++  ++   v d +  ++ +lke++ll+k++ki+h++pfc r ++ ++y+
  gi|518652119|ref|YP_008141639.1| 327 GADDFDIAKEYNVSLINPVDSEGKFDNSV-PWKDKFVMDVNPDIIGYLKENNLLFKSQKIKHTYPFCYRCGTKLLYY 402
                                       *************************9988.59********************************************* PP

                       tRNA-synt_1 376 ateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkel 451
                                         ++Wf++v+++++ + k+++kv+++p+  k+ r+ ++l++++dW++SR+r+WG+++p++  ++   + v  + +++
  gi|518652119|ref|YP_008141639.1| 403 PLDAWFIKVSTIRELLKKNNDKVNWYPEYlKDGRFGNFLNDAKDWALSRNRYWGTPLPIWKCSNGHYLAV-GSREDI 478
                                       ****************************9999*******************************9886665.444444 PP

                       tRNA-synt_1 452 vagreeeeaekkalekeakdkl....kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGl 524
                                       ++   +  +   +l++ ++d +     +  +++e+++ v+D+WF+Sgs  ++ ++yp++++ + +   p d+++e +
  gi|518652119|ref|YP_008141639.1| 479 EK---HGGNIPDDLHRPFIDAVklkcPECSETMEREPYVIDTWFDSGSASYAAMHYPFNKNFNTE-GIPVDFITEAI 551
                                       43...56666777888888877554456689****************************666655.9********** PP

                       tRNA-synt_1 525 DiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli 591
                                       D++rgW+++l ++s  l+g++ +k+v+  ++++de+G+KmSKs+gN +   d i+ ygad  Rl+  
  gi|518652119|ref|YP_008141639.1| 552 DQTRGWFYTLHVISSLLFGRNAYKNVMSMSFILDENGQKMSKSKGNFVTARDFISMYGADPARLFFY 618
                                       ***************************************************************9976 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 !  118.1   0.5   2.3e-37   3.1e-34       1     146 [.     673     815 ..     673     820 .. 0.93

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.3e-37
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       drw+ls+ln++++ ++++++e++++ a++++++ ++nd++++yl+l+++r++  + +d+++ a+e+l++ l ++l+l
  gi|518652119|ref|YP_008141639.1| 673 DRWLLSRLNSTIENTRKNMDEFDMHIALRNIMD-LINDFSNYYLRLSRKRFWEGKLDDEKKkAYETLYYTLINILKL 748
                                       9********************************.59*****************999998666*************** PP

                       Anticodon_1  77 laPfmPfitEelwqreeeel.gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpss 146
                                       laP +Pf t++++q    +l g +++i+ +++pe ++++ + +l e+e++++++i+++ r++r+e +ik ++
  gi|518652119|ref|YP_008141639.1| 749 LAPLAPFYTDYMYQ----KLsGPEKTIHSEKYPEpDNNYIDSDL-EKEFKYAISIMELSRRARQESNIKGRQ 815
                                       *************5....444999*********98887777777.89*********************9776 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 !   34.1   0.1   9.1e-12   1.3e-08       9     145 ..      53     193 ..      50     209 .. 0.86
   2 !    8.0   0.0   0.00076         1     167     239 ..     390     464 ..     379     472 .. 0.77
   3 !   20.4   0.0   1.3e-07   0.00017     310     361 ..     572     624 ..     530     649 .. 0.81
   4 ?   -3.6   0.1       2.6   3.5e+03      98     116 ..     881     899 ..     873     902 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 9.1e-12
                                       --SS---HHHHHHHHHHHHHHHHHHHTT-EE.EEEEEE---SHHHHHHHHHT.TS-HHHHHHHHHHHHHHHHHHTT- CS
                      tRNA-synt_1g   9 YangklHlGhllevisaDifaRykrlrgeev.lfvcgtDehGtpielkAeke.gvtpeelvekvheeikelfkklni 83 
                                        ang++H+Ghl++    D ++Ryk ++g+++    +g D hG p+el+Aek+ g + ++ +e++  e  + +++ ++
  gi|518652119|ref|YP_008141639.1|  53 TANGRPHVGHLMTRTVKDTVMRYKYMSGYDIgRRTGGWDCHGLPVELEAEKHfGFNTKKEIEDFGIEKFNEYCRNSV 129
                                       58**********9999**************72567789***********9987999999999999988888887665 PP

                                       ..--SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........ CS
                      tRNA-synt_1g  84 ..sfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckse 145
                                           d++++ +se  + + ++      ++++++++ ++     ++++   d  +   CP c+++
  gi|518652119|ref|YP_008141639.1| 130 ftYIDEWNEVDSEIGYWIDENKSYVTLRNDYMESEWYALKKLFDENMLVKDYKIVPYCPRCGTS 193
                                       32679999999999999999888888899999999888888888899999999********965 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00076
                                       ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET...T CS
                      tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP...g 239
                                       p +  +g+k  +   + +f k+s +++ lk+  ++ +   e        ++l++  kd+a+sr+  wG p+P    
  gi|518652119|ref|YP_008141639.1| 390 PFCYRCGTKLLYYPLDAWFIKVSTIRELLKKNNDKVNWYPEYLKDGRFGNFLND-AKDWALSRNRYWGTPLPiwkC 464
                                       78999999999999999*******999999988544433444444556677766.9***************96543 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 1.3e-07
                                       ---S-EEEE--EE.E--------------HHHHHHHH-HHHHHHHHHHHS-TT CS
                      tRNA-synt_1g 310 klpkkvvaheylt.vegkKlSkSrgvvvkakealerldadllRYylaaeapek 361
                                       ++ k+v++ +++   +g+K+SkS+g++v+a++++  + ad  R ++++ ap +
  gi|518652119|ref|YP_008141639.1| 572 NAYKNVMSMSFILdENGQKMSKSKGNFVTARDFISMYGADPARLFFYTGAPWN 624
                                       56789999999752679**************************9999877655 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 2.6
                                       HHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1g  98 elvqeifkklkekgliyek 116
                                         +++i+++lk++g+i+ k
  gi|518652119|ref|YP_008141639.1| 881 LNSENIYSELKKNGKITYK 899
                                       56789*********99765 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 !   27.6   0.0   1.3e-09   1.9e-06      10     145 ..     211     350 ..     207     369 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.3e-09
                     tRNA-synt_1_2  10 leiefkvees.eeklevfttrpdtlfGvtfvalape..hplveklaekkkelaafieevkkksesereletkekeGv 83 
                                       + ++f++++s ++ l  +tt p tl + + +++ ++    lv++ +++   l++ ++++ k+ ++ ++++ k+  G 
  gi|518652119|ref|YP_008141639.1| 211 VYVKFRIKGSmNRYLIAWTTTPWTLPSNELLVVNKDfdYSLVSDGNNEYYVLSSTVQSLFKDAKILKTIKGKDLVGT 287
                                       6799*****9888999*****************987225688888999999****************9999998888 PP

                     tRNA-synt_1_2  84 .ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                         ++l+ +  ++++ +++   ++v +e gtg v a Pa    Df+ ak+yn+ +++ + +e++
  gi|518652119|ref|YP_008141639.1| 288 hYEQLMPFLHVSKNALQVVPGDFVTAEDGTGIVHAAPAFGADDFDIAKEYNVSLINPVDSEGK 350
                                       556667777788999*************************************98887776654 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.35   4.8e+02       6      52 ..      30      73 ..      24      80 .. 0.66
   2 !   24.7   0.0   7.3e-09     1e-05     270     322 ..     579     631 ..     551     652 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.35
                      tRNA-synt_1f  6 klaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlva 52
                                      k+ e+++++ +   + k +  +e   ++ G++H+G l      d v+
  gi|518652119|ref|YP_008141639.1| 30 KIIEDILNKDR---NLKRYTFLEGPPTANGRPHVGHLMTRTVKDTVM 73
                                      34555663332...25667777777899*******987655555555 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 7.3e-09
                      tRNA-synt_1f 270 vYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldld 322
                                          +il+++g+kms+SkGn++t +d ++++  +  r++++   P ++k++d +
  gi|518652119|ref|YP_008141639.1| 579 SMSFILDENGQKMSKSKGNFVTARDFISMYGADPARLFFYTGAPWNSKSIDKK 631
                                       35799********************************************9987 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.037        51      17      48 ..      52      83 ..      37      85 .. 0.86
   2 !   18.3   0.0   8.6e-07    0.0012     247     283 ..     584     620 ..     563     632 .. 0.76

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.037
                                      EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EE CS
                      tRNA-synt_1e 17 ptvydashlGhaRslvafDilrrilqalgYdv 48
                                      pt+    h+Gh  +  + D + r+  ++gYd+
  gi|518652119|ref|YP_008141639.1| 52 PTANGRPHVGHLMTRTVKDTVMRYKYMSGYDI 83
                                      799999************************98 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 8.6e-07
                                       EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 247 lkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       l  +g+kmsks +nf+t +d++  + +   Rl++++ 
  gi|518652119|ref|YP_008141639.1| 584 LDENGQKMSKSKGNFVTARDFISMYGADPARLFFYTG 620
                                       45679***************************99874 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.014        19      14      24 ..     186     196 ..     178     208 .. 0.84
   2 !    6.3   0.0     0.007       9.7       6      22 ..     383     399 ..     382     421 .. 0.87
   3 ?    0.6   0.0      0.42   5.8e+02      29      38 ..     499     508 ..     461     513 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.014
                               DZR  14 fCseCgtklka 24 
                                       +C++Cgt+l++
  gi|518652119|ref|YP_008141639.1| 186 YCPRCGTSLSS 196
                                       89999999974 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.007
                               DZR   6 eelppdarfCseCgtkl 22 
                                       +++++   fC++Cgtkl
  gi|518652119|ref|YP_008141639.1| 383 QKIKHTYPFCYRCGTKL 399
                                       56778888*******98 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.42
                               DZR  29 drCpsCgekv 38 
                                        +Cp+C+e +
  gi|518652119|ref|YP_008141639.1| 499 LKCPECSETM 508
                                       5677777655 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   0.0   0.00085       1.2      15      23 .]     186     194 ..     183     199 .. 0.62
   2 ?    7.0   0.2    0.0036       4.9       9      23 .]     385     399 ..     383     399 .. 0.82
   3 ?   -0.6   0.3      0.87   1.2e+03       1       5 [.     500     504 ..     500     509 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00085
                     zinc_ribbon_2  15 FCpyCGtpl 23 
                                       +Cp+CGt l
  gi|518652119|ref|YP_008141639.1| 186 YCPRCGTSL 194
                                       555555543 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0036
                     zinc_ribbon_2   9 lqdnakFCpyCGtpl 23 
                                       ++ + +FC +CGt+l
  gi|518652119|ref|YP_008141639.1| 385 IKHTYPFCYRCGTKL 399
                                       666789*******97 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.87
                     zinc_ribbon_2   1 fCpnC 5  
                                       +Cp+C
  gi|518652119|ref|YP_008141639.1| 500 KCPEC 504
                                       79999 PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0023       3.2       1      14 [.     186     199 ..     186     205 .. 0.84
   2 ?    3.2   0.0     0.041        57       1      10 [.     500     509 ..     500     522 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0023
                          zf-TFIIB   1 kCPkCqdeleeser 14 
                                       +CP+C+++l  +e+
  gi|518652119|ref|YP_008141639.1| 186 YCPRCGTSLSSHEV 199
                                       7********99887 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.041
                          zf-TFIIB   1 kCPkCqdele 10 
                                       kCP C+ ++e
  gi|518652119|ref|YP_008141639.1| 500 KCPECSETME 509
                                       8******998 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 ?    4.9   0.0      0.02        27       4      18 ..     187     201 ..     186     204 .. 0.82
   2 ?    4.9   0.3      0.02        27       3      11 ..     500     508 ..     499     511 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                            zf-ACC   4 CpsCgemlykkeLer 18 
                                       Cp+Cg++l   e+++
  gi|518652119|ref|YP_008141639.1| 187 CPRCGTSLSSHEVAQ 201
                                       *******98888765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.02
                            zf-ACC   3 KCpsCgeml 11 
                                       KCp+C+e++
  gi|518652119|ref|YP_008141639.1| 500 KCPECSETM 508
                                       9*****987 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   0.0     0.046        63      22      35 ..     179     193 ..     169     196 .. 0.68
   2 ?   -3.4   0.1       7.9   1.1e+04      29      34 ..     392     397 ..     383     399 .. 0.65
   3 ?    5.7   0.1     0.012        17      20      38 ..     491     510 ..     482     511 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.046
                       Zn-ribbon_8  22 sdaplta.CPeCgse 35 
                                       +d + ++ CP+Cg  
  gi|518652119|ref|YP_008141639.1| 179 KDYKIVPyCPRCGTS 193
                                       55556666****975 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.9
                       Zn-ribbon_8  29 CPeCgs 34 
                                       C +Cg 
  gi|518652119|ref|YP_008141639.1| 392 CYRCGT 397
                                       666664 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.012
                       Zn-ribbon_8  20 sis.dapltaCPeCgsevrr 38 
                                       + + da + +CPeC ++++r
  gi|518652119|ref|YP_008141639.1| 491 RPFiDAVKLKCPECSETMER 510
                                       4443777778****889988 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0035       4.8       5      17 ..     187     199 ..     186     201 .. 0.89
   2 ?   -1.2   0.0       1.1   1.6e+03       4      12 ..     391     399 ..     389     400 .. 0.84
   3 ?    1.3   0.4      0.19   2.7e+02       4      13 ..     500     509 ..     498     511 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0035
                            zf_UBZ   5 CerCgkeipesel 17 
                                       C+rCg++++++e+
  gi|518652119|ref|YP_008141639.1| 187 CPRCGTSLSSHEV 199
                                       **********997 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.1
                            zf_UBZ   4 lCerCgkei 12 
                                       +C rCg+++
  gi|518652119|ref|YP_008141639.1| 391 FCYRCGTKL 399
                                       7*****875 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.19
                            zf_UBZ   4 lCerCgkeip 13 
                                        C++C ++++
  gi|518652119|ref|YP_008141639.1| 500 KCPECSETME 509
                                       7*****9986 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.005       6.8       5      12 ..     186     193 ..     185     198 .. 0.83
   2 ?    3.5   0.2      0.04        55       2      12 ..     388     398 ..     387     400 .. 0.88
   3 ?   -1.9   0.1       2.1   2.8e+03      22      28 ..     499     505 ..     498     507 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.005
                     zf-NADH-PPase   5 FCgrCGap 12 
                                       +C+rCG+ 
  gi|518652119|ref|YP_008141639.1| 186 YCPRCGTS 193
                                       9*****95 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.04
                     zf-NADH-PPase   2 thrFCgrCGap 12 
                                       t++FC rCG++
  gi|518652119|ref|YP_008141639.1| 388 TYPFCYRCGTK 398
                                       799******98 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.1
                     zf-NADH-PPase  22 rvCpaCg 28 
                                       + Cp C 
  gi|518652119|ref|YP_008141639.1| 499 LKCPECS 505
                                       68****7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1024 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.47
# Mc/sec: 6614.90
//
Query:       gi|518652120|ref|YP_008141640.1|  [L=105]
Description: hypothetical protein FACI_IFERC00001G0759 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 700.51
//
Query:       gi|518652121|ref|YP_008141641.1|  [L=93]
Description: 50S ribosomal protein L44e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-28   99.2   5.1    1.8e-28   98.8   5.1    1.2  1  Ribosomal_L44  Ribosomal protein L44
    5.5e-05   23.5   5.7     0.0019   18.6   1.8    2.4  2  Ribosomal_L33  Ribosomal protein L33
     0.0039   16.9   0.7     0.0039   16.9   0.7    1.6  2  zf-U1          U1 zinc finger
  ------ inclusion threshold ------
      0.028   14.7   0.8       0.53   10.6   0.1    2.1  2  zf-Di19        Drought induced 19 protein (Di19), zinc-bindin
      0.029   14.6   2.4       0.34   11.2   0.2    2.1  2  zf-LITAF-like  LITAF-like zinc ribbon domain
       0.05   13.6   0.4        5.9    7.0   0.1    2.1  2  zf-C2HC5       Putative zinc finger motif, C2HC5-type


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 !   98.8   5.1     6e-32   1.8e-28       1      76 []      16      91 ..      16      91 .. 0.99

  Alignments for each domain:
  == domain 1  score: 98.8 bits;  conditional E-value: 6e-32
                                      EEEEEEEEE-------SSSHHHHHHHH.H-SSSGGGGS----.--SSBB--EEEEETTT--EEE----BBS--EEE CS
                     Ribosomal_L44  1 kHtehkveqykkgkdselaqgkRrydrkqsgygGqtkpvfkkkaKttKKivlrleCteCkkkrlkalkRakkfelv 76
                                      kHt h ve+++k+k+sel++g+Rr++r +sgygG ++p++++++K+tK+i lrl+Ct Ckk+++ ++ Rakkfe+v
  gi|518652121|ref|YP_008141641.1| 16 KHTVHDVERVRKRKASELRAGQRRFRRVTSGYGGFPRPRYEGREKPTKRIALRLKCTVCKKSITPPTQRAKKFEIV 91
                                      8*************************************************************************96 PP

>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.8   6.3e-07    0.0019      30      43 ..       7      20 ..       4      23 .. 0.91
   2 !    6.5   0.1    0.0037        11       3      13 ..      67      77 ..      65      90 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 6.3e-07
                                      EEEEETTTTEEEEE CS
                     Ribosomal_L33 30 lkKYcprcrkhtlh 43
                                      +k Ycp+c+kht+h
  gi|518652121|ref|YP_008141641.1|  7 IKTYCPYCKKHTVH 20
                                      788*********** PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0037
                                      EEEEET..... CS
                     Ribosomal_L33  3 vtLeCtecksr 13
                                       +L+Ct ck++
  gi|518652121|ref|YP_008141641.1| 67 LRLKCTVCKKS 77
                                      58*******95 PP

>> zf-U1  U1 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.7   1.3e-06    0.0039       3      22 ..       8      27 ..       3      30 .. 0.92
   2 ?   -2.4   0.0       1.4   4.3e+03       6      21 ..      71      86 ..      71      88 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.3e-06
                                      SEEETTTTEEESS-SHHHHH CS
                             zf-U1  3 kYyCdYCdiyLthDspsvRk 22
                                      k yC YC++   hD  +vRk
  gi|518652121|ref|YP_008141641.1|  8 KTYCPYCKKHTVHDVERVRK 27
                                      67*****************9 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                      ETTTTEEESS-SHHHH CS
                             zf-U1  6 CdYCdiyLthDspsvR 21
                                      C  C++ +t  ++++ 
  gi|518652121|ref|YP_008141641.1| 71 CTVCKKSITPPTQRAK 86
                                      6668887776666665 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 ?   10.6   0.1   0.00018      0.53       4      15 ..      10      22 ..       8      33 .. 0.74
   2 ?    2.7   0.0     0.052   1.5e+02      32      42 ..      69      79 ..      64      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00018
                           zf-Di19  4 tCPyCgk.eltvk 15
                                       CPyC+k +++++
  gi|518652121|ref|YP_008141641.1| 10 YCPYCKKhTVHDV 22
                                      5*****9655444 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.052
                           zf-Di19 32 vvCPvCaekvt 42
                                        C vC++ +t
  gi|518652121|ref|YP_008141641.1| 69 LKCTVCKKSIT 79
                                      57999998765 PP

>> zf-LITAF-like  LITAF-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   0.00011      0.34       4      24 ..       7      27 ..       4      34 .. 0.81
   2 ?    3.5   0.1     0.029        88       6      21 ..      69      84 ..      66      89 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                     zf-LITAF-like  4 tqvdCpaCqqrvvTsveyksg 24
                                       +++Cp+C++++v  ve+  +
  gi|518652121|ref|YP_008141641.1|  7 IKTYCPYCKKHTVHDVERVRK 27
                                      578999999999999998766 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.029
                     zf-LITAF-like  6 vdCpaCqqrvvTsvey 21
                                      ++C  C++ ++  +++
  gi|518652121|ref|YP_008141641.1| 69 LKCTVCKKSITPPTQR 84
                                      6888888888776665 PP

>> zf-C2HC5  Putative zinc finger motif, C2HC5-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.008        24      34      50 ..       8      24 ..       3      27 .. 0.75
   2 ?    7.0   0.1     0.002       5.9      35      51 ..      69      85 ..      62      87 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.008
                          zf-C2HC5 34 skpCsfCgspllsseer 50
                                      +  C++C+++ + + er
  gi|518652121|ref|YP_008141641.1|  8 KTYCPYCKKHTVHDVER 24
                                      478*****998876665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.002
                          zf-C2HC5 35 kpCsfCgspllsseerq 51
                                       +C+ C++++ ++++r+
  gi|518652121|ref|YP_008141641.1| 69 LKCTVCKKSITPPTQRA 85
                                      69**********99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); 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: 0.45u 0.31s 00:00:00.76 Elapsed: 00:00:00.50
# Mc/sec: 564.84
//
Query:       gi|518652122|ref|YP_008141642.1|  [L=66]
Description: 30S ribosomal protein S27e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-16   58.7   1.2      4e-16   58.5   1.2    1.1  1  Ribosomal_S27e   Ribosomal protein S27
     0.0023   17.6   3.7     0.0034   17.1   3.7    1.3  1  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0059   16.6   0.1     0.0063   16.5   0.1    1.1  1  Zn_Tnp_IS91      Transposase zinc-binding domain
  ------ inclusion threshold ------
      0.011   15.6   0.4      0.012   15.5   0.4    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.014   15.5   0.4      0.026   14.6   0.4    1.5  1  Zn-ribbon_8      Zinc ribbon domain
      0.015   15.3   2.4      0.038   14.0   2.5    1.6  1  zinc_ribbon_6    Zinc-ribbon
      0.023   14.1   2.4        1.5    8.3   0.2    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.023   14.6   0.5        0.2   11.6   0.1    2.0  2  zf-trcl          Probable zinc-ribbon domain
      0.038   14.0   0.2      0.042   13.9   0.2    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.046   14.2   0.6        6.5    7.3   0.1    2.2  2  Zn_ribbon_recom  Recombinase zinc beta ribbon domain
      0.072   12.6   2.4       0.15   11.6   2.4    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.087   12.6   0.8        9.1    6.1   0.1    2.1  2  Rubredoxin_2     Rubredoxin metal binding domain
       0.12   12.4   0.5       0.12   12.4   0.5    2.1  2  zf-BED           BED zinc finger
       0.41   10.5   3.6        4.1    7.3   0.3    2.1  2  ZZ               Zinc finger, ZZ type
       0.63    9.8   4.6        1.6    8.5   0.6    2.2  2  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


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 !   58.5   1.2   3.4e-19     4e-16       4      48 ..      14      58 ..      12      65 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 3.4e-19
                                      -EEEEE-TTTS-EEEEESS-SS-EEESSSTCEEEEECSSSEEESS CS
                    Ribosomal_S27e  4 kFldvkCpdCenetvvFshaatvvkCisCgkvLvePtGGkaklka 48
                                      +Fl++kC+dC+ne++++s+ ++vv C +Cg+++++PtG  +  + 
  gi|518652122|ref|YP_008141642.1| 14 NFLKIKCKDCGNEQIIYSKVSSVVVCNICGSTIAKPTGSTLATSG 58
                                      8*************************************7665555 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   3.7   2.8e-06    0.0034       4      30 ..      18      45 ..      17      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.8e-06
                     A2L_zn_ribbon  4 kvCsvCggngiln.seqgylvCieCgas 30
                                      ++C+ Cg++ i++ + ++  vC+ Cg++
  gi|518652122|ref|YP_008141642.1| 18 IKCKDCGNEQIIYsKVSSVVVCNICGST 45
                                      69***********888999*******97 PP

>> Zn_Tnp_IS91  Transposase zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   5.3e-06    0.0063      36      66 ..      14      45 ..       2      56 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.3e-06
                       Zn_Tnp_IS91 36 GfaryeCeeCghekivyfsCksrh.CpsCqkk 66
                                       f +++C++Cg+e+i+y +  s   C+ C++ 
  gi|518652122|ref|YP_008141642.1| 14 NFLKIKCKDCGNEQIIYSKVSSVVvCNICGST 45
                                      577899****************999****976 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 ?   15.5   0.4     1e-05     0.012       6      43 ..      14      50 ..       5      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                    OrfB_Zn_ribbon  6 eqleykakeyGikveevnpayTSktCseCgsknkeals 43
                                      ++l+ k+k+ G + +  ++  +   C+ Cgs+  + ++
  gi|518652122|ref|YP_008141642.1| 14 NFLKIKCKDCGNEQIIYSKVSSVVVCNICGSTIAK-PT 50
                                      799****************************9888.44 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.4   2.2e-05     0.026       7      38 ..      19      48 ..      15      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                       Zn-ribbon_8  7 rCeeCghefevlqsisdaplta.CPeCgsevrr 38
                                      +C++Cg+e  +  ++s    ++ C  Cgs+  +
  gi|518652122|ref|YP_008141642.1| 19 KCKDCGNEQIIYSKVS---SVVvCNICGSTIAK 48
                                      8*****8888888888...5555*****98765 PP

>> zinc_ribbon_6  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.5   3.2e-05     0.038      22      55 ..      10      44 ..       4      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.2e-05
                     zinc_ribbon_6 22 eyknkkvkilCnDCekksevkfhvlg.lkCkeCgS 55
                                      e+ n+  ki C+DC++++ ++ +v   + C+ CgS
  gi|518652122|ref|YP_008141642.1| 10 EVGNNFLKIKCKDCGNEQIIYSKVSSvVVCNICGS 44
                                      6778899***********99998875267999998 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.2    0.0076       9.1      17      25 ..      18      26 ..      15      27 .. 0.83
   2 ?    8.3   0.2    0.0013       1.5       3      14 ..      37      49 ..      35      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0076
                       zf-ribbon_3 17 nvCpyCGtk 25
                                      ++C+ CG +
  gi|518652122|ref|YP_008141642.1| 18 IKCKDCGNE 26
                                      68****975 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0013
                       zf-ribbon_3  3 vrCPnCGa.plss 14
                                      v C+ CG+ ++++
  gi|518652122|ref|YP_008141642.1| 37 VVCNICGStIAKP 49
                                      78*****988776 PP

>> zf-trcl  Probable zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00017       0.2       4      15 ..      17      28 ..      16      32 .. 0.85
   2 ?    1.4   0.1      0.25     3e+02       5      13 ..      37      45 ..      34      47 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                           zf-trcl  4 tltCkdCgaefv 15
                                      +++CkdCg+e++
  gi|518652122|ref|YP_008141642.1| 17 KIKCKDCGNEQI 28
                                      589*******98 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                           zf-trcl  5 ltCkdCgae 13
                                      ++C+ Cg++
  gi|518652122|ref|YP_008141642.1| 37 VVCNICGST 45
                                      79****985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.5e-05     0.042      68      97 ..      15      47 ..       4      62 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-05
                                      --EEEETTTS-EEECHHH...HHS-TTTSSS-E CS
                              HypA 68 pvkvrCreCgkefeleek...alrCpkCgsadv 97
                                       +k++C++Cg+e  + +k    + C+ Cgs+  
  gi|518652122|ref|YP_008141642.1| 15 FLKIKCKDCGNEQIIYSKvssVVVCNICGSTIA 47
                                      5789******99885553235669*****9644 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 ?    5.7   0.1     0.017        21       5      13 ..      17      25 ..      16      32 .. 0.89
   2 ?    7.3   0.1    0.0055       6.5       3      14 ..      34      45 ..      33      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
                   Zn_ribbon_recom  5 llrCgeCGs 13
                                      +++C++CG+
  gi|518652122|ref|YP_008141642.1| 17 KIKCKDCGN 25
                                      699*****7 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0055
                   Zn_ribbon_recom  3 sGllrCgeCGsp 14
                                      s +++C  CGs+
  gi|518652122|ref|YP_008141642.1| 34 SSVVVCNICGST 45
                                      5689******98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   2.4   0.00013      0.15       2      28 ..      19      45 ..      18      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                      EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlV 28
                                      kC++Cg++++++   +  +vC  CG+ 
  gi|518652122|ref|YP_008141642.1| 19 KCKDCGNEQIIYSKVSSVVVCNICGST 45
                                      9************9999********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 ?    6.1   0.1    0.0076       9.1       3      10 ..      20      27 ..      19      30 .. 0.82
   2 ?    5.3   0.0     0.014        16       2      13 ..      38      49 ..      38      52 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0076
                      Rubredoxin_2  3 CsqCGfes 10
                                      C++CG+e+
  gi|518652122|ref|YP_008141642.1| 20 CKDCGNEQ 27
                                      99999986 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                      Rubredoxin_2  2 vCsqCGfesakw 13
                                      vC+ CG++ ak 
  gi|518652122|ref|YP_008141642.1| 38 VCNICGSTIAKP 49
                                      7*****997775 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.6      0.12   1.4e+02      16      25 ..      17      26 ..       9      32 .. 0.90
   2 ?   12.4   0.5    0.0001      0.12      14      32 ..      34      52 ..      28      57 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.12
                                      --EETTTTEE CS
                            zf-BED 16 kavCryCgki 25
                                      k++C+ Cg++
  gi|518652122|ref|YP_008141642.1| 17 KIKCKDCGNE 26
                                      79*****985 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.0001
                                      SS--EETTTTEE----SST CS
                            zf-BED 14 eqkavCryCgkilsrgggt 32
                                      + ++vC++Cg +++  +g+
  gi|518652122|ref|YP_008141642.1| 34 SSVVVCNICGSTIAKPTGS 52
                                      479*********9987444 PP

>> ZZ  Zinc finger, ZZ type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.2    0.0094        11       4      23 ..      17      36 ..      16      38 .. 0.83
   2 ?    7.3   0.3    0.0035       4.1       3      13 ..      35      45 ..      33      49 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0094
                                      -EE-TTT-S..EESSEEEES CS
                                ZZ  4 kytCdgCseapligvRyhcl 23
                                      k +C  C++  +i   ++++
  gi|518652122|ref|YP_008141642.1| 17 KIKCKDCGNEQIIYSKVSSV 36
                                      579******99998887775 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0035
                                      S-EE-TTT-S. CS
                                ZZ  3 kkytCdgCsea 13
                                       ++ C++C+++
  gi|518652122|ref|YP_008141642.1| 35 SVVVCNICGST 45
                                      6899*****93 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 ?    8.5   0.6    0.0013       1.6      18      25 ..      18      25 ..      16      32 .. 0.80
   2 ?    3.7   4.2     0.041        49       3      26 ..      20      45 ..      20      47 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0013
                                      ---SSS-- CS
                    DNA_RNApol_7kD 18 iRCkeCGh 25
                                      i+Ck+CG 
  gi|518652122|ref|YP_008141642.1| 18 IKCKDCGN 25
                                      9******5 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.041
                                      -SSS--B---..-SSS----SSS--- CS
                    DNA_RNApol_7kD  3 CgeCgaevsl..kkgdpiRCkeCGhR 26
                                      C +Cg+e  +  k + ++ C  CG+ 
  gi|518652122|ref|YP_008141642.1| 20 CKDCGNEQIIysKVSSVVVCNICGST 45
                                      88899888863356789999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.55
# Mc/sec: 363.15
//
Query:       gi|518652123|ref|YP_008141643.1|  [L=253]
Description: hypothetical protein FACI_IFERC00001G0762 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-18   66.5   0.2    6.2e-18   65.0   0.0    1.9  2  EIF_2_alpha  Eukaryotic translation initiation factor 2 alpha
    1.2e-11   44.7   0.2    2.3e-11   43.9   0.2    1.5  1  S1           S1 RNA binding domain
  ------ inclusion threshold ------
      0.027   14.2   0.9      0.027   14.2   0.9    1.8  2  DUF1955      Domain of unknown function (DUF1955)
       0.65    9.9   5.0       0.41   10.5   2.4    2.0  2  KilA-N       KilA-N 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 ?   -1.8   0.1      0.69   3.1e+03      72      84 ..      48      60 ..      34     113 .. 0.57
   2 !   65.0   0.0   1.4e-21   6.2e-18       3     116 .]     120     221 ..     118     221 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.69
                                      HHHHHHHHHHHST CS
                       EIF_2_alpha 72 veaIkeaLkagee 84
                                      +++Ik+  + +++
  gi|518652123|ref|YP_008141643.1| 48 IKHIKDFVRVNQR 60
                                      5666666652222 PP

  == domain 2  score: 65.0 bits;  conditional E-value: 1.4e-21
                                       HCTHHHHTTTTS-HHHHHHHHHSTTHHHHHTTS-TTTHHHHHHCTHHHHHHT-EEEEEEEEEEE-STTHHHHHHHHH CS
                       EIF_2_alpha   3 eevgwklyekyghaydaFklaitdeevldkleipeeveeaLveiikkklkpqkvkiradieltcftkdGveaIkeaL 79 
                                       +++   l  +yg+aydaF  a +++e++++   +e +++a+++ +k++++++ vki ++i++ + +++G+e I+eaL
  gi|518652123|ref|YP_008141643.1| 120 KNMEDYLVSEYGSAYDAFFEAASNKEFMSDK--NEPWKDAFIKVAKENISIPMVKIGGEIDMYSLASNGIELIREAL 194
                                       567778999*********8888888888874..799***************************************** PP

                                       HHHST.S..TTSSSEEEEEEEESSSSEEEEEEEES.. CS
                       EIF_2_alpha  80 kageeasneeeveeeeevkikliapPeYvltvetldk 116
                                                  v++ ++++i++ ++P+Y++++  +d+
  gi|518652123|ref|YP_008141643.1| 195 D----------VDSGNNIEITYAGSPKYRISIVDEDY 221
                                       *..........234589**************998886 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.9   0.2   5.1e-15   2.3e-11       2      75 .]       6      80 ..       5      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 43.9 bits;  conditional E-value: 5.1e-15
                                      STTTCEEEEEEEEEETTEEEEEET..TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
                                S1  2 pekgevveGeVtsvtkgGafVelg..ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75
                                      pe g+ v  ++++v ++Ga+V+l+   gv+gf++++e++    ++++++ ++v+++   kvl+vd +rr ++ls+k
  gi|518652123|ref|YP_008141643.1|  6 PEPGDLVVVTIKEVQNYGAIVQLDeyPGVSGFIHIAEVATG-WIKHIKDFVRVNQRTVCKVLNVDSNRRHVDLSLK 80
                                      7899************************************9.9*******************************86 PP

>> DUF1955  Domain of unknown function (DUF1955)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.9     6e-06     0.027      78     133 ..      63     119 ..      46     133 .. 0.80
   2 ?   -2.6   0.1      0.87   3.9e+03     116     130 ..     227     241 ..     214     244 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6e-06
                                       HH.HHTT---HHHHHHHHHHHHTT-HHHHHHHHHHH---S-HHHHHHHHHHHHHTT- CS
                           DUF1955  78 cy.vklnklseyvdlaldvlvkkgkkdqldkilkelkneikaelllkianalkklgd 133
                                       c  ++++ + ++vdl+l+ + +++k++++++ +++ k e   e++ k an  +k   
  gi|518652123|ref|YP_008141643.1|  63 CKvLNVDSNRRHVDLSLKRVNEHQKREKIEEWKNDQKSEKLLEIVAKEANISDKAIT 119
                                       44046788899***************************9999**9999998777544 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.87
                                       S-HHHHHHHHHHHHH CS
                           DUF1955 116 ikaelllkianalkk 130
                                          ++l ki++a kk
  gi|518652123|ref|YP_008141643.1| 227 KLKNVLEKISTACKK 241
                                       333445555555544 PP

>> KilA-N  KilA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   2.4   9.2e-05      0.41      28      65 ..      85     121 ..      78     152 .. 0.76
   2 ?   -2.3   0.0      0.87   3.9e+03      39      56 ..     227     244 ..     212     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 9.2e-05
                            KilA-N  28 aedtkriddWlrnkstkelleeleedynisekkksekt 65 
                                       ++++ +i++W++ +++++lle+++++ nis+k  ++k+
  gi|518652123|ref|YP_008141643.1|  85 HQKREKIEEWKNDQKSEKLLEIVAKEANISDKA-ITKN 121
                                       457789***********************9532.2223 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.87
                            KilA-N  39 rnkstkelleeleedyni 56 
                                       ++k+  e +++++++y+i
  gi|518652123|ref|YP_008141643.1| 227 KLKNVLEKISTACKKYSI 244
                                       445555666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1711  (0.095432); expected 358.6 (0.02)
Passed bias filter:                      647  (0.0360868); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1600.24
//
Query:       gi|518652124|ref|YP_008141644.1|  [L=59]
Description: H/ACA RNA-protein complex component Nop10p [Ferroplasma acidarmanus fer1]
Scores for complete 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   67.7   0.4    7.6e-19   67.5   0.4    1.1  1  Nop10p         Nucleolar RNA-binding protein, Nop10p family
    0.00026   20.6   0.1       0.09   12.5   0.0    2.2  2  zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
     0.0073   15.9   1.9     0.0091   15.6   1.9    1.2  1  RecR           RecR protein
      0.009   13.9   0.2      0.009   13.9   0.2    1.0  1  PolC_DP2       DNA polymerase II large subunit DP2
  ------ inclusion threshold ------
      0.011   15.7   1.0       0.18   11.8   0.1    2.3  2  Nudix_N_2      Nudix N-terminal
      0.022   14.2   1.7        1.9    8.0   0.1    2.2  2  zf-ribbon_3    zinc-ribbon domain
      0.037   14.2   0.5      0.053   13.7   0.5    1.4  1  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like


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 !   67.5   0.4     3e-22   7.6e-19       1      48 [.       1      48 [.       1      51 [. 0.98

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3e-22
                                      .----EE-TTT--EESSSB-TTT-SB-B-SS--S--TT-TTCHHHHHC CS
                            Nop10p  1 mksylrkcgkcrvYTLkkvcpecggptksahPaRFSPdDkyskyRral 48
                                      m+  +r c++c+ YT++++c +cg++t+ a P ++SP+Dk++kyR++l
  gi|518652124|ref|YP_008141644.1|  1 MRTLIRICPSCKLYTMNDICSNCGTATVMAIPMKYSPADKFQKYRIKL 48
                                      999*******************************************97 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0026       6.7      21      29 ..       5      13 ..       2      15 .. 0.81
   2 !   12.5   0.0   3.5e-05      0.09       6      16 ..      20      30 ..      17      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0026
                     zf-NADH-PPase 21 arvCpaCgl 29
                                       r Cp+C+l
  gi|518652124|ref|YP_008141644.1|  5 IRICPSCKL 13
                                      599****87 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.5e-05
                     zf-NADH-PPase  6 CgrCGaptepa 16
                                      C+ CG++t++a
  gi|518652124|ref|YP_008141644.1| 20 CSNCGTATVMA 30
                                      ********997 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.9   3.5e-06    0.0091      13      34 ..       2      23 ..       1      27 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.5e-06
                                      HHH-EE-TTT--EESSSS-CCC CS
                              RecR 13 kekvrhCsrCgnlteedlCaIC 34
                                      ++ +r C+ C  +t +d+C+ C
  gi|518652124|ref|YP_008141644.1|  2 RTLIRICPSCKLYTMNDICSNC 23
                                      5669****************99 PP

>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.2   3.5e-06     0.009     618     644 ..       5      31 ..       1      58 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.5e-06
                          PolC_DP2 618 rrkCkkCgketlearCeeCgekteekl 644
                                        r C++C+  t++  C++Cg+ t   +
  gi|518652124|ref|YP_008141644.1|   5 IRICPSCKLYTMNDICSNCGTATVMAI 31 
                                       589******************998754 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.2     0.057   1.5e+02      24      29 ..       7      12 ..       6      13 .. 0.79
   2 ?   11.8   0.1     7e-05      0.18       3      15 ..      20      32 ..      19      35 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.057
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      +Cp+C 
  gi|518652124|ref|YP_008141644.1|  7 ICPSCK 12
                                      799995 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 7e-05
                                      -TTT--B-EEE-- CS
                         Nudix_N_2  3 CsqCGtpvelrip 15
                                      Cs+CGt++ ++ip
  gi|518652124|ref|YP_008141644.1| 20 CSNCGTATVMAIP 32
                                      ***********99 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.2     0.004        10      18      22 ..       7      11 ..       5      13 .. 0.57
   2 ?    8.0   0.1   0.00074       1.9       4      10 ..      19      25 ..      16      28 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.004
                       zf-ribbon_3 18 vCpyC 22
                                      +Cp+C
  gi|518652124|ref|YP_008141644.1|  7 ICPSC 11
                                      45555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00074
                       zf-ribbon_3  4 rCPnCGa 10
                                       C+nCG+
  gi|518652124|ref|YP_008141644.1| 19 ICSNCGT 25
                                      5777774 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   2.1e-05     0.053       5      50 ..       2      44 ..       1      58 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-05
                      NOB1_Zn_bind  5 kswvlrChaCfkvtkdmtkkFCpkCGnktLkrvavsvdengelklh 50
                                      ++ +  C +C   t       C++CG +t+  +++ ++   +++ +
  gi|518652124|ref|YP_008141644.1|  2 RTLIRICPSCKLYT---MNDICSNCGTATVMAIPMKYSPADKFQKY 44
                                      67778888887765...4568************9999988776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 413.13
//
Query:       gi|518652125|ref|YP_008141645.1|  [L=250]
Description: hypothetical protein FACI_IFERC00001G0764 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-42  146.3   0.0    1.4e-42  146.1   0.0    1.0  1  PAC2      PAC2 family
  ------ inclusion threshold ------
      0.026   14.8   0.3      0.067   13.5   0.3    1.6  1  NES_C_h   Nicking enzyme C-terminal middle helical domain
        0.1   12.5   0.2       0.23   11.4   0.2    1.5  1  Sec20     Sec20


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 !  146.1   0.0   2.3e-46   1.4e-42       2     212 ..      20     233 ..      19     234 .. 0.94

  Alignments for each domain:
  == domain 1  score: 146.1 bits;  conditional E-value: 2.3e-46
                                       EEESSCGGGHHHHHHHHHHHHTTEEEEEEEEHCCHSBCCCC.SEEEEETT.EEE-SEEEEEE.TTT.SEEEEEEE.. CS
                              PAC2   2 ilGfpgiGnVgqlavdlLiesleaekvgeidsdyllpfvgprpvvlveeg.relepprlyak.dsgsrdllvlqg.. 74 
                                       + G+pgiGnVg+++vd+ +++l+++k++ ++s++ lp     p+v+++++ ++l   +ly+k  sg++d+++l+g  
  gi|518652125|ref|YP_008141645.1|  20 VGGLPGIGNVGKITVDYFVDKLKMKKLADVYSEF-LP-----PQVFINNNvVHLVRESLYYKkTSGEHDFIFLTGdf 90 
                                       679*******************************.9*.....*********999999999999999*********** PP

                                       ..E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-ES..TTS-.EEEEEESSHHHHHHHHCT........-CE CS
                              PAC2  75 ..repilqyeefakalldwaeelgvkevvvLggldageradvphtrpekvtgaatdeelleelees........eyg 141
                                          ++++qye ++  +l+++++++v+++++Lgg+  g+      ++p +v ga+td++l++ l ++        + g
  gi|518652125|ref|YP_008141645.1|  91 qgTTQEGQYE-LSYRMLEFLKKYEVSMIYTLGGYSVGKIV----EKP-RVLGAVTDKKLIKPLARKgvifsegePSG 161
                                       **********.************************98775....677.*************9952235556678*** PP

                                       EEEHHHHHHHHHH.HHTT-EEEEEEEEEECCC--HHHHHHHHHHHHHHHT---HCHHHHHHHHHHHHHHHHH CS
                              PAC2 142 givgitglLlsaa.kergipavgllaevphylpdPkaaaalleflskllglevdtedLeedaeeleeqleel 212
                                       givg +gl+l+++ +   ip++++++e+++y+ dPk+a++++ +l+k+l++ ++++d +e+ ++le   e++
  gi|518652125|ref|YP_008141645.1| 162 GIVGSAGLILGMGtELFSIPGACFMGETSGYFADPKSAREIIMVLAKVLKTRINLKDIDEKTRQLEDITEKM 233
                                       *************89999************************************************988876 PP

>> NES_C_h  Nicking enzyme C-terminal middle helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   1.1e-05     0.067       8      35 ..     201     228 ..     195     244 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.1e-05
                           NES_C_h   8 kqlselakelktfvnlesieekkrmLkn 35 
                                       +++  lak lkt +nl++i+ek r+L++
  gi|518652125|ref|YP_008141645.1| 201 EIIMVLAKVLKTRINLKDIDEKTRQLED 228
                                       578899********************86 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   3.8e-05      0.23      17      48 ..     205     236 ..     198     240 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                             Sec20  17 lsqevqqSeenleeldastkslekleeeykqv 48 
                                       + ++v++  +nl+++d++t++le++ e+ kq 
  gi|518652125|ref|YP_008141645.1| 205 VLAKVLKTRINLKDIDEKTRQLEDITEKMKQE 236
                                       45789***********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1068  (0.0595683); expected 358.6 (0.02)
Passed bias filter:                      812  (0.0452898); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.69u 0.39s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 1267.84
//
Query:       gi|518652126|ref|YP_008141646.1|  [L=205]
Description: hypothetical protein FACI_IFERC00001G0765 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); 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: 0.61u 0.34s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1100.19
//
Query:       gi|518652127|ref|YP_008141647.1|  [L=421]
Description: hypothetical protein FACI_IFERC00001G0766 [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   43.0   0.0    1.3e-06   28.3   0.1    2.3  2  DAO            FAD dependent oxidoreductase
      5e-11   42.6   0.0    1.1e-10   41.5   0.0    1.6  2  FAD_oxidored   FAD dependent oxidoreductase
    3.3e-10   39.6   0.8      5e-10   39.0   0.8    1.3  1  FAD_binding_2  FAD binding domain
    2.9e-08   32.8   0.1    3.8e-07   29.2   0.2    2.4  3  HI0933_like    HI0933-like protein
    3.3e-08   33.1   0.2    6.6e-06   25.6   0.6    2.4  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
      5e-08   32.6   1.3    0.00023   20.5   1.3    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
      4e-07   29.6   0.0      6e-07   29.0   0.0    1.2  1  FAD_binding_3  FAD binding domain
      7e-06   26.2   0.9    1.7e-05   24.9   0.9    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
    8.5e-06   25.1   0.8    1.6e-05   24.2   0.8    1.5  1  GIDA           Glucose inhibited division protein A
    4.1e-05   22.9   0.8    7.6e-05   22.1   0.8    1.3  1  Thi4           Thi4 family
    0.00012   22.5   1.4      0.028   15.0   1.2    3.2  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    0.00076   18.6   0.1     0.0021   17.2   0.1    1.6  2  Lycopene_cycl  Lycopene cyclase protein
  ------ inclusion threshold ------
      0.019   14.3   0.1      0.031   13.6   0.1    1.2  1  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.037   13.9   0.5      0.071   13.0   0.5    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d


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 !   28.3   0.1     1e-09   1.3e-06       1      42 [.       6      47 ..       6      87 .. 0.82
   2 !   12.5   0.0   6.5e-05     0.083     147     349 ..     104     322 ..      94     325 .. 0.62

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1e-09
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEE CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsg 42
                                      dv+++GGG +G+s+A  +a+ g  V++le+g+  + g+   ++g
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGlsVIVLERGEH-S-GSKNVSGG 47
                                      8******************************44.4.55555555 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 6.5e-05
                                       HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHH.HTT...CTT.TS CS
                               DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdll.gll...kel.dl 215
                                       ++ a++a++ae+lGv + + t v g+++edg+   v ++++ g    +++  v+ + Ga  +++ + l   k     
  gi|518652127|ref|YP_008141647.1| 104 RFDAWFASEAENLGVPVSYSTLVSGIDREDGG--LV-VKSDrGD---IRTplVIESDGAA-GFAsRYLgirK-EkAF 172
                                       78899*********************998754..33.3455576...4666588777755.33333332321.1222 PP

                                       EEEE...........EEEEEEEEEECCTHSTGSGCSEEEEE.....EEETTTTEEEEEETTSEEEEEESSEEETTCS CS
                               DAO 216 pisp...........vrgqvlvlkplseklvspaailpvpe.....tdddgrgvyvtprkdgrvlvGgtadeesgdd 276
                                       +++p            +  ++ +k++ +k   p+a + + +     ++  ++g +++  k +++ +G t     + d
  gi|518652127|ref|YP_008141647.1| 173 KMQPvknlqenpdfmPKQFMVGVKEIVDKK--PDADYGEAKtilglSNGVKGGGFAYTNK-DSTSIGLTL----KLD 242
                                       333333333334433377777777776632..3333333334557844445555666665.568888885....667 PP

                                       STSCSHHHHHHHHHHHHHHSGGGCGEEEEEEEEEE......E....TTSSEEEEEEETEEEEEEEEECTTTHHHHHH CS
                               DAO 277 dpevdeedidellealrklfPqlgdvlrkwaGlrp......l....pdglpligetpgvkglylatGhsghGltlap 343
                                       ++e  +e++  ++e  r+ +   g++l+  a l p      l     d+l + g      g++++ G+  +G+ +a+
  gi|518652127|ref|YP_008141647.1| 243 SLEGHSEKAFNIIEDFREKLGIEGKLLEYSAHLIPfyrfetLparyADNLMVTGD---AAGFLINDGFTIRGMDNAI 316
                                       7777777777777777777766666665555666654333212222466777777...4799999999999999999 PP

                                       HHHHHH CS
                               DAO 344 atGkll 349
                                        +G+l+
  gi|518652127|ref|YP_008141647.1| 317 ESGRLA 322
                                       999986 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   8.2e-14   1.1e-10       1     117 [.       6     133 ..       6     155 .. 0.59
   2 ?   -2.8   0.0       2.3     3e+03     395     410 ..     287     302 ..     283     328 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 8.2e-14
                      FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdignkaee...........qvvtgiarefler 66 
                                       Dv VvGGg+aG+ AAi+Aa++G +v+++e+ ++ G    sg+++ +   k+               +++   e++  
  gi|518652127|ref|YP_008141647.1|   6 DVAVVGGGLAGISAAISAAKNGLSVIVLERGEHSGSKNVSGGRMYIHSLKTLLgdryrdaplelP-IKKETFEIYTG 81 
                                       9******************************9999998888888877755111222222433321.22222222222 PP

                      FAD_oxidored  67 lrqrgga...rlkkrskwntfepevakavleeml....aeagvtvllntrlvevekeg 117
                                       +++  ++   ++k++        +++++ ++++     ++ gv v + t ++++++e+
  gi|518652127|ref|YP_008141647.1|  82 NNK--ASfsfENKDT----ENSYSILRSRFDAWFaseaENLGVPVSYSTLVSGIDRED 133
                                       222..1111111111....123344444444444443355666777777777776665 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.3
                      FAD_oxidored 395 RvepvcmalGqAaGva 410
                                       R     m++G AaG +
  gi|518652127|ref|YP_008141647.1| 287 RYADNLMVTGDAAGFL 302
                                       5555667777777764 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.8   3.9e-13     5e-10       1      45 [.       6      49 ..       6      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 3.9e-13
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                                      Dv V+G+GlAG +AA++aa++Gl+v+v+e ++  +g+   s+G +
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGLSVIVLERGEH-SGSKNVSGGRM 49
                                      9*******************************8.67777777766 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.2     3e-10   3.8e-07       2      43 ..       6      46 ..       5      69 .. 0.91
   2 ?    0.2   0.0      0.19   2.4e+02     115     159 ..     109     151 ..      93     161 .. 0.80
   3 ?   -2.0   0.0      0.87   1.1e+03      98     125 ..     381     409 ..     375     413 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3e-10
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      dv+v+GgG AG+ aAisaak+g +V++le++++ g+K   sG
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGLSVIVLERGEHSGSKNV-SG 46
                                      89***********************************54.44 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.19
                                       HHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEE CS
                       HI0933_like 115 llkelkeagvklrletevksvekeedgkfrvktkseeeleadklv 159
                                       + +e+++ gv + ++t v+++++e++g + vk  +++ +++  ++
  gi|518652127|ref|YP_008141647.1| 109 FASEAENLGVPVSYSTLVSGIDREDGG-LVVKS-DRGDIRTPLVI 151
                                       568999***************998877.88888.77777666555 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.87
                                       TTEEEETT.-C.HHHHHHHHHHHHHHT-E CS
                       HI0933_like  98 sgrlFpvsdka.edivdallkelkeagvk 125
                                         r+F+v+d+  e+i ++l+ e+k++++ 
  gi|518652127|ref|YP_008141647.1| 381 LERMFTVTDNPrENIKSVLMDEIKKNNIG 409
                                       57999999876256888999999999986 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.6   5.1e-09   6.6e-06       2      39 ..       6      48 ..       5      97 .. 0.69
   2 ?    4.8   0.0     0.011        14     181     236 ..     101     155 ..      92     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.1e-09
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclngg 39
                                      dv+v+GgG AG++aa+ +a++g+ v+++e       +++ +g+
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGLSVIVLErgehsGSKNVSGGR 48
                                      8***************************755554444444444 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.011
                                       S-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 181 ldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavG 236
                                       l +++ a+ + + e+ Gv v   t v  id+++  l vv +d   i + lv+ + G
  gi|518652127|ref|YP_008141647.1| 101 LRSRFDAWFASEAENLGVPVSYSTLVSGIDREDGGL-VVKSDRGDIRTPLVIESDG 155
                                       568899999*********************999833.7888888899999987766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.3   1.8e-07   0.00023       2      34 ..       9      40 ..       8      43 .. 0.92
   2 !   10.1   0.0   0.00026      0.33      88     148 ..     110     171 ..      73     197 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 1.8e-07
                       Pyr_redox_3  2 IiGaGPaGlaaaielkkagledylilEkgnign 34
                                      ++G+G aG++aai + k+gl ++++lE+g+++ 
  gi|518652127|ref|YP_008141647.1|  9 VVGGGLAGISAAISAAKNGL-SVIVLERGEHSG 40
                                      8*******************.7*******9875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00026
                       Pyr_redox_3  88 revaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkP.nklnipGeek 148
                                       ++ a++  +p+ + + V  +++ed+g +v++++++++++ vi + G  ++  ++l+i  e+ 
  gi|518652127|ref|YP_008141647.1| 110 ASEAENLGVPVSYSTLVSGIDREDGGLVVKSDRGDIRTPLVIESDGAAGFAsRYLGIRKEKA 171
                                       555778889*********************************98887666414566666654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.6e-10     6e-07       1     188 [.       4     180 ..       4     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.6e-10
                                       EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS.CCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEE CS
                     FAD_binding_3   1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrstt.vvlpradglnqrtmellrqlGledrilaegapnelmgeal 76 
                                       ++dV++VG+G+aG+++a   ++ G +v+++e+ +   +++  ++ +   ++ +l      d  l+   ++e++++ +
  gi|518652127|ref|YP_008141647.1|   4 DVDVAVVGGGLAGISAAISAAKNGLSVIVLERGEHSgSKNVSGGRMYIHSLKTLLGDRYRDAPLELPIKKETFEIYT 80 
                                       689*****************************87652666799999999*****99999999999999999999999 PP

                                       EEECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEE CS
                     FAD_binding_3  77 ynelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetv 153
                                       +n+     ka+   e +   e+ + +  ++++   +++ae+ g+ v  +t v ++ +++ g    +  k +++  ++
  gi|518652127|ref|YP_008141647.1|  81 GNN-----KASFSFE-NKDTENSYSILRSRFDAWFASEAENLGVPVSYSTLVSGIDREDGG----LVVK-SDRG-DI 145
                                       999.....9999999.89999999999**************************99998888....3333.2333.78 PP

                                       EEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEE CS
                     FAD_binding_3 154 rakYlvGaDGgrStvrktlgiefegeetvyeagvl 188
                                       r   ++  DG+ + + + lgi+ e   ++ +++ l
  gi|518652127|ref|YP_008141647.1| 146 RTPLVIESDGAAGFASRYLGIRKEKAFKMQPVKNL 180
                                       ********************996655555455444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.9   1.4e-08   1.7e-05       1      32 [.       9      40 ..       9      65 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.4e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlG 32
                                      +vG+Gl+G +aA  +ak+g++v +le++++ G
  gi|518652127|ref|YP_008141647.1|  9 VVGGGLAGISAAISAAKNGLSVIVLERGEHSG 40
                                      8*****************************98 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.8   1.3e-08   1.6e-05       1      28 [.       6      33 ..       6      58 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.3e-08
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                                      dv V+GgG+AG+ AA+ aa+ G++v+ +
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGLSVIVL 33
                                      79***********************988 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.8   5.9e-08   7.6e-05      18      64 ..       5      50 ..       2      58 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 5.9e-08
                                      EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTB CS
                              Thi4 18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlf 64
                                       Dv++vG+G +G++aa   ak+ +l v++ler    G     GG+++
  gi|518652127|ref|YP_008141647.1|  5 VDVAVVGGGLAGISAAISAAKN-GLSVIVLERGEHSGSKNVSGGRMY 50
                                      7*********************.**********99999999999987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   1.2   2.2e-05     0.028       2      33 ..       7      38 ..       6      46 .. 0.92
   2 ?    3.2   0.0      0.11   1.4e+02      42      73 ..     105     137 ..      94     142 .. 0.85
   3 ?   -0.2   0.0       1.2   1.5e+03      40      58 ..     393     411 ..     379     413 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.2e-05
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdk 33
                                      v+vvGgG+ g+ +A  +a+ g +V v+er+++
  gi|518652127|ref|YP_008141647.1|  7 VAVVGGGLAGISAAISAAKNGLSVIVLERGEH 38
                                      89***************************986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHTTEEEECSEEEEEEEEETTS.E CS
                         Pyr_redox  42 askilqeklekngievllntkveeiegsedg.v 73 
                                       + ++++ + e++g+ v ++t v  i+ ++ g v
  gi|518652127|ref|YP_008141647.1| 105 FDAWFASEAENLGVPVSYSTLVSGIDREDGGlV 137
                                       567899999*****************9999844 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHHTTEEEE CS
                         Pyr_redox  40 eeaskilqeklekngievl 58 
                                       e + ++l+++++kn+i  +
  gi|518652127|ref|YP_008141647.1| 393 ENIKSVLMDEIKKNNIGYY 411
                                       779999********99665 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.7e-06    0.0021       1      36 [.       6      39 ..       6      64 .. 0.93
   2 ?   -1.7   0.0       0.9   1.2e+03     120     144 ..     135     158 ..      89     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.7e-06
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                                      Dv+v+G+G+Ag+s A     ak gl+v+++e ++++
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISA--AKNGLSVIVLERGEHS 39
                                      9************99998..***********99875 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.9
                     Lycopene_cycl 120 slvvleggrkirarlvvdarglasl 144
                                        lvv ++   ir +lv+++ g a++
  gi|518652127|ref|YP_008141647.1| 135 GLVVKSDRGDIRTPLVIESDG-AAG 158
                                       4455555559********999.444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.4e-05     0.031      30      61 ..       6      37 ..       4      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.4e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                                       v v+GgG aG++A+  a++ g +V vl+  +
  gi|518652127|ref|YP_008141647.1|  6 DVAVVGGGLAGISAAISAAKNGLSVIVLERGE 37
                                      599***********************999765 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   0.5   5.6e-05     0.071       2      34 ..       7      39 ..       6      58 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHH CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdiseea 34
                                      vav+G G+ G + a  +a++gl+V ++++ e++
  gi|518652127|ref|YP_008141647.1|  7 VAVVGGGLAGISAAISAAKNGLSVIVLERGEHS 39
                                      9**************************997655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.50
# Mc/sec: 2556.59
//
Query:       gi|518652128|ref|YP_008141648.1|  [L=88]
Description: 4Fe-4S ferredoxin iron-sulfur binding protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-07   29.2   7.8      1e-06   28.8   7.8    1.2  1  Fer4_10          4Fe-4S dicluster domain
    1.1e-06   29.1   6.9     0.0016   19.0   0.1    2.1  2  Fer4_7           4Fe-4S dicluster domain
    9.9e-06   25.6   2.7    1.1e-05   25.4   2.7    1.1  1  Fer4_11          4Fe-4S dicluster domain
    1.5e-05   25.1   5.1      3e-05   24.1   5.1    1.5  1  Fer4_9           4Fe-4S dicluster domain
    0.00012   22.2   2.4       0.28   11.3   0.9    2.1  2  Fer4_21          4Fe-4S dicluster domain
    0.00054   20.8   5.6       0.79   10.7   0.1    2.9  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0027   17.7  11.9      0.018   15.1   2.7    2.6  2  Fer4_2           4Fe-4S binding domain
     0.0031   17.3  12.9       0.18   11.7   0.8    4.1  3  Fer4             4Fe-4S binding domain
     0.0037   17.3  10.3       0.27   11.4   3.5    2.9  2  Fer4_6           4Fe-4S binding domain
     0.0059   16.7   1.9     0.0082   16.3   1.9    1.2  1  ETF_QO           Electron transfer flavoprotein-ubiquinone ox
  ------ inclusion threshold ------
      0.014   16.2  11.1       0.15   13.1   1.3    2.5  2  Fer4_3           4Fe-4S binding domain
      0.019   15.4   3.1       0.67   10.4   0.1    2.1  2  Fer4_8           4Fe-4S dicluster domain
       0.11   12.3   7.4       0.38   10.5   2.0    2.1  2  Fer4_20          Dihydroprymidine dehydrogenase domain II, 4F
        3.4    8.4  10.8          2    9.1   1.1    3.2  2  Fer4_4           4Fe-4S binding domain
        7.2    6.5   8.7        1.1    9.1   3.2    2.4  2  Ephrin_rec_like  Putative ephrin-receptor like


Domain annotation for each model (and alignments):
>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   7.8   8.4e-10     1e-06       1      56 []      19      70 ..      19      70 .. 0.92

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.4e-10
                           Fer4_10  1 kvvidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                                      +++++++ C  C    C k+CPa      +++e+++e+ +++ +e+C +cga   aCP
  gi|518652128|ref|YP_008141648.1| 19 HIEVNTEMCKICVdkPCIKVCPA------GTYEEDKENGISVHYERCLECGAALYACP 70
                                      57889999*9997779*******......99999999999999**************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   2.6    0.0001      0.12      27      51 ..      16      42 ..       4      43 .. 0.78
   2 !   19.0   0.1   1.3e-06    0.0016      29      52 .]      50      73 ..      41      73 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
                            Fer4_7 27 gtekveidpekClgCga..CvavCPtg 51
                                       + ++e++ e+C  C    C++vCP+g
  gi|518652128|ref|YP_008141648.1| 16 NQSHIEVNTEMCKICVDkpCIKVCPAG 42
                                      34789**********7778******98 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 1.3e-06
                            Fer4_7 29 ekveidpekClgCgaCvavCPtga 52
                                        + +++e+Cl Cga   +CP+ga
  gi|518652128|ref|YP_008141648.1| 50 NGISVHYERCLECGAALYACPFGA 73
                                      44899*****************98 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   2.7   9.4e-09   1.1e-05       5      61 ..      22      76 ..      18      84 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 9.4e-09
                           Fer4_11  5 flpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrk 61
                                      +  e+C+ C+++pC++++p++   +d+e+G+ +  e+    e+ +   acP+ + + 
  gi|518652128|ref|YP_008141648.1| 22 VNTEMCKICVDKPCIKVCPAGTYEEDKENGISVHYERCL--ECGAALYACPFGALQF 76
                                      56799***********************99988777666..699999*****87655 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   5.1   2.5e-08     3e-05       2      50 ..      27      73 ..      26      74 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2.5e-08
                            Fer4_9  2 CtgC..gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkga 50
                                      C  C  + C+++Cpag+++ed+ +++  + +    +C++Cga + aCp ga
  gi|518652128|ref|YP_008141648.1| 27 CKICvdKPCIKVCPAGTYEEDKENGISVHYE----RCLECGAALYACPFGA 73
                                      77785567*****************999876....6************886 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.9   0.00024      0.28      29      53 ..      15      41 ..       4      46 .. 0.84
   2 !   10.7   0.0   0.00036      0.43       3      24 ..      54      75 ..      47      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
                           Fer4_21 29 daktvlkvvedeCvGC..nlCssvCPv 53
                                       ++++++v ++ C  C  + C++vCP 
  gi|518652128|ref|YP_008141648.1| 15 GNQSHIEVNTEMCKICvdKPCIKVCPA 41
                                      567899**********6668******5 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00036
                           Fer4_21  3 idedkCigCgkCliaCedtshq 24
                                      ++ ++C++Cg  l aC+ ++ q
  gi|518652128|ref|YP_008141648.1| 54 VHYERCLECGAALYACPFGALQ 75
                                      6788999999999999866655 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 ?    2.9   0.3      0.18   2.2e+02      50      62 ..      20      32 ..       4      33 .. 0.64
   2 !    9.2   2.5     0.002       2.4       2      23 ..      27      50 ..      25      57 .. 0.79
   3 !   10.7   0.1   0.00066      0.79       1      20 [.      58      77 ..      58      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.18
                           Fer4_16 50 kqeaitgCdiCqd 62
                                      ++ ++  C+iC+d
  gi|518652128|ref|YP_008141648.1| 20 IEVNTEMCKICVD 32
                                      3345589999986 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.002
                           Fer4_16  2 CgtCgk..CaevCPtnaikekkek 23
                                      C+ C    C++vCP++  +e+ke+
  gi|518652128|ref|YP_008141648.1| 27 CKICVDkpCIKVCPAGTYEEDKEN 50
                                      77775556********99999766 PP

  == domain 3  score: 10.7 bits;  conditional E-value: 0.00066
                           Fer4_16  1 rCgtCgkCaevCPtnaikek 20
                                      rC +Cg+ + +CP +a++ k
  gi|518652128|ref|YP_008141648.1| 58 RCLECGAALYACPFGALQFK 77
                                      6****************988 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   2.7   1.5e-05     0.018       2      22 .]      19      41 ..      18      41 .. 0.94
   2 !    7.3   1.9    0.0047       5.6       5      20 ..      54      69 ..      51      71 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                            Fer4_2  2 pvvvdtdrCigC..gaCvsaCPa 22
                                      +++v+t++C  C  ++C+++CPa
  gi|518652128|ref|YP_008141648.1| 19 HIEVNTEMCKICvdKPCIKVCPA 41
                                      799**********99*******8 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0047
                            Fer4_2  5 vdtdrCigCgaCvsaC 20
                                      v  +rC++Cga + aC
  gi|518652128|ref|YP_008141648.1| 54 VHYERCLECGAALYAC 69
                                      5679******644444 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3     0.067        80       6      15 ..      25      31 ..      20      33 .. 0.58
   2 !    7.2   0.7    0.0038       4.6      14      22 ..      35      43 ..      34      45 .. 0.88
   3 !   11.7   0.8   0.00015      0.18       2      23 ..      53      74 ..      52      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.067
                                      TTSSS-THHH CS
                              Fer4  6 ekCigCGaCv 15
                                      e+   C++Cv
  gi|518652128|ref|YP_008141648.1| 25 EM---CKICV 31
                                      55...55555 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0038
                                      HHHHSTTTE CS
                              Fer4 14 CvevCPvgA 22
                                      C++vCP g 
  gi|518652128|ref|YP_008141648.1| 35 CIKVCPAGT 43
                                      ******985 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00015
                                      EEETTTSSS-THHHHHSTTTEE CS
                              Fer4  2 videekCigCGaCvevCPvgAI 23
                                       +++e+C  CGa   +CP+gA+
  gi|518652128|ref|YP_008141648.1| 53 SVHYERCLECGAALYACPFGAL 74
                                      6899********99******98 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   3.5   0.00022      0.27       2      22 ..      20      42 ..      19      44 .. 0.83
   2 !    8.8   0.5    0.0015       1.7       3      24 .]      53      74 ..      52      74 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                            Fer4_6  2 veidpdkCigC.gd.CvrvCPeg 22
                                      +e++ + C  C ++ C++vCP+g
  gi|518652128|ref|YP_008141648.1| 20 IEVNTEMCKICvDKpCIKVCPAG 42
                                      899999**9776556******98 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0015
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                       + +++C+ Cg+   +CP+ga+
  gi|518652128|ref|YP_008141648.1| 53 SVHYERCLECGAALYACPFGAL 74
                                      5778999999999999999996 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 !   16.3   1.9   6.9e-06    0.0082      32      98 ..      21      82 ..       8      87 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 6.9e-06
                                      THHHHTHHHHHS-THHHH-TTS-EEEEETTTTSSEEEEE-CCC--S--HHHHH-TT--EEE---STT CS
                            ETF_QO 32 evavkvnlekyagpeqryCPagvyeivedeeakekklqinaqnCvhCktCdikdpsqniewvvPeGg 98
                                      ev+++++    ++p+ ++CPag ye  ++     + + +  + C+ C +     p   ++++ Pe g
  gi|518652128|ref|YP_008141648.1| 21 EVNTEMCKICVDKPCIKVCPAGTYEEDKE-----NGISVHYERCLECGAALYACPFGALQFKYPEKG 82
                                      4555566666789***********96544.....46889999******9999999999999999976 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   2.8    0.0063       7.5       3      14 ..      26      42 ..      24      43 .. 0.77
   2 ?   13.1   1.3   0.00013      0.15       1      15 []      59      73 ..      59      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0063
                            Fer4_3  3 gCg.....aCvevCPvg 14
                                      +C      +C +vCP g
  gi|518652128|ref|YP_008141648.1| 26 MCKicvdkPCIKVCPAG 42
                                      676666778******65 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00013
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cga + +CP gA
  gi|518652128|ref|YP_008141648.1| 59 CLECGAALYACPFGA 73
                                      9************99 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.5     0.016        19      46      64 ..      22      42 ..       3      43 .. 0.71
   2 ?   10.4   0.1   0.00056      0.67       3      19 ..      57      73 ..      55      84 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.016
                            Fer4_8 46 ealwsCttcga..CtevCpvg 64
                                       + + C +c    C +vCp g
  gi|518652128|ref|YP_008141648.1| 22 VNTEMCKICVDkpCIKVCPAG 42
                                      4567899997667******86 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00056
                            Fer4_8  3 ekCieCgaCqsaCpvlr 19
                                      e+C eCga   aCp+  
  gi|518652128|ref|YP_008141648.1| 57 ERCLECGAALYACPFGA 73
                                      79************765 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 ?   10.5   2.0   0.00032      0.38      16      39 ..      19      42 ..       8      47 .. 0.80
   2 ?    5.5   0.3     0.012        14      20      38 ..      55      71 ..      43      79 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00032
                                      HHHHHHTT----TT-HHHHCSTT- CS
                           Fer4_20 16 ealeeAsRClqCkkapcvkgCPve 39
                                      ++  + + C  C ++pc+k CP+ 
  gi|518652128|ref|YP_008141648.1| 19 HIEVNTEMCKICVDKPCIKVCPAG 42
                                      45567889**************87 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.012
                                      HHTT----TT-HHHHCSTT CS
                           Fer4_20 20 eAsRClqCkkapcvkgCPv 38
                                        +RCl+C  a    +CP 
  gi|518652128|ref|YP_008141648.1| 55 HYERCLECGAA--LYACPF 71
                                      568*****655..456886 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   2.7      0.35   4.2e+02      10      16 ..      35      41 ..      26      44 .. 0.70
   2 ?    9.1   1.1    0.0017         2       1      16 [.      56      71 ..      56      72 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.35
                            Fer4_4 10 CvaaCPq 16
                                      C+ +CP 
  gi|518652128|ref|YP_008141648.1| 35 CIKVCPA 41
                                      8888996 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0017
                            Fer4_4  1 qerCigCgsCvaaCPq 16
                                      +erC++Cg+  +aCP+
  gi|518652128|ref|YP_008141648.1| 56 YERCLECGAALYACPF 71
                                      69******86666886 PP

>> Ephrin_rec_like  Putative ephrin-receptor like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2         1   1.2e+03       7      14 ..      23      30 ..      15      33 .. 0.75
   2 ?    9.1   3.2    0.0009       1.1       9      35 ..      33      66 ..      31      77 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1
                   Ephrin_rec_like  7 gletCipC 14
                                      ++e C  C
  gi|518652128|ref|YP_008141648.1| 23 NTEMCKIC 30
                                      66788888 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0009
                   Ephrin_rec_like  9 etCip.CprgtYqn......eegqlsClaCPlgt 35
                                      ++Ci  Cp gtY +      ++    Cl+C++  
  gi|518652128|ref|YP_008141648.1| 33 KPCIKvCPAGTYEEdkengiSVHYERCLECGAAL 66
                                      578755********88777777788999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 591.25
//
Query:       gi|518652129|ref|YP_008141649.1|  [L=460]
Description: hypothetical protein FACI_IFERC00001G0768 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   6.3        1.6    9.2   0.5    3.3  3  DUF1132   Protein of unknown function (DUF1132)


Domain annotation for each model (and alignments):
>> DUF1132  Protein of unknown function (DUF1132)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1   0.00038       6.7      57      84 ..      11      38 ..       3      46 .. 0.85
   2 ?    9.2   0.5   8.8e-05       1.6      41      90 ..     146     201 ..     118     204 .. 0.72
   3 ?   -0.5   0.1     0.093   1.7e+03      45      76 ..     358     389 ..     340     415 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00038
                           DUF1132 57 sfsdesvavikeelkdgikikkfefcei 84
                                       +sd  +++i   l+d ikik+f++ e 
  gi|518652129|ref|YP_008141649.1| 11 ILSDTENTYISRVLEDRIKIKNFDIPEY 38
                                      579*********************9775 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 8.8e-05
                           DUF1132  41 fsfflnrrikndiwkisfsdesvavikeelkd.....gikikkfefc.eivdnpnv 90 
                                       f   +n+   +d ++++fsde   v k +++d        +++f ++   ++n ++
  gi|518652129|ref|YP_008141649.1| 146 FYAAMNKNFTEDNYLVFFSDEKFYVYKVSVHDraiieDEMVYRFSLItRAMENGDI 201
                                       44458999************************766655556777663134555555 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.093
                           DUF1132  45 lnrrikndiwkisfsdesvavikeelkdgiki 76 
                                        n +  n+i   ++s+ + +  + ++k+g  +
  gi|518652129|ref|YP_008141649.1| 358 NNSKYTNNIPDTYYSELAITCARRNIKEGLIV 389
                                       46778888888999988888888888887654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.32s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2818.63
//
Query:       gi|518652130|ref|YP_008141650.1|  [L=215]
Description: xanthine-guanine phosphoribosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-18   66.8   0.0    2.7e-18   66.0   0.0    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.1   13.0   0.1       0.15   12.5   0.1    1.4  1  DUF5582       Family of unknown function (DUF5582)
       0.11   11.9   0.0       0.16   11.4   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 !   66.0   0.0   4.5e-22   2.7e-18      16     157 ..      18     157 ..       5     158 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 4.5e-22
                                       EETTEEEEEE--GGGEEEEEEETTTHHHHHHHHHHS.TT-EE-EEEEEE-TTT--EE........EE----TTSEEE CS
                      Pribosyltran  16 arlaaeileeyngkpdvvvgiargGvpfakiladeL.evplayvrkvkyrpdgseeaargssdesrlledpagkkVl 91 
                                       + +++  +e+ n++pd+++giargG+++   +ad+L +  l  +  +      + + + ++++  +l  d+ gkkVl
  gi|518652130|ref|YP_008141650.1|  18 KGIMKMVIED-NYNPDIIIGIARGGLVPSRMVADYLfKKDLLSIKTEHWGLTATMDGKAVLKE--KLNYDITGKKVL 91 
                                       4555566666.*************************754455544444444444444444444..59********** PP

                                       EE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS.....EEEEEEE-SEE- CS
                      Pribosyltran  92 iVDDildtGgTllaalelLkekgpeevriavlvdkpateeevdknakrvfslspdnfvavvgfeld 157
                                       iVDDi dtG +++   + +k+ +p+ v++   ++ + +   +d++ k + + +  +f ++++++ d
  gi|518652130|ref|YP_008141650.1|  92 IVDDITDTGESMKLSYNYIKSLDPATVKTTSMLYVNGSNYTPDYYGKGLSKEQWAWFIFPWNVYED 157
                                       ******************************************999998876669999999998765 PP

>> DUF5582  Family of unknown function (DUF5582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05      0.15      89     116 ..     141     168 ..     102     198 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
                           DUF5582  89 eekqtyrkrfPpivyedPyqvsLrymek 116
                                       +++q     fP  vyed y++s ++me+
  gi|518652130|ref|YP_008141650.1| 141 SKEQWAWFIFPWNVYEDTYNLSKKFMED 168
                                       456777778*****************97 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.7e-05      0.16      71     147 ..      34     113 ..      14     128 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                           UPRTase  71 lVpilRaGegmeealrellpearvghlglqreeet...lepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlL 144
                                       ++ i R+G+   + + + l +  ++ ++ +    t     +    +kL  +i+ ++vl++D +  TG+s+    + +
  gi|518652130|ref|YP_008141650.1|  34 IIGIARGGLVPSRMVADYLFKKDLLSIKTEHWGLTatmDGKAVLKEKLNYDITGKKVLIVDDITDTGESMKLSYNYI 110
                                       5666677776666666665555555554444322211123457789***********************98777777 PP

                           UPRTase 145 ker 147
                                       k+ 
  gi|518652130|ref|YP_008141650.1| 111 KSL 113
                                       664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1521.29
//
Query:       gi|518652131|ref|YP_008141651.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G0770 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-09   36.4   0.2    4.6e-09   36.0   0.2    1.2  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an
  ------ inclusion threshold ------
       0.04   14.4   0.1      0.061   13.8   0.1    1.4  1  PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin


Domain annotation for each model (and alignments):
>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.2   5.1e-13   4.6e-09       2      42 ..       2      42 ..       1      46 [. 0.88

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 5.1e-13
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCCCCCH CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiilrplk 42
                                      k+G +g+v+iPke+r   g++e++ev+++ ++d i++++ k
  gi|518652131|ref|YP_008141651.1|  2 KIGPKGQVVIPKEIRNITGVKENTEVIVSLNDDCIVIKKSK 42
                                      89******************************977776655 PP

>> PrlF_antitoxin  prlF antitoxin for toxin YhaV_toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.1   6.8e-06     0.061       3      46 ..       2      43 ..       1      68 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.8e-06
                    PrlF_antitoxin  3 tltergqttiPasvRkaLklkkgrdkiaytilddgkvvisraee 46
                                      ++  +gq  iP+ +R++ ++k+++ ++   ++ d  +vi++ + 
  gi|518652131|ref|YP_008141651.1|  2 KIGPKGQVVIPKEIRNITGVKENT-EVIVSLN-DDCIVIKKSKP 43
                                      57789****************955.5555554.44566666544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 532.47
//
Query:       gi|518652132|ref|YP_008141652.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-21   76.3   0.0    3.8e-21   75.5   0.0    1.4  1  rve          Integrase core domain
    4.1e-06   26.5   1.1    0.00019   21.1   1.1    2.6  1  rve_3        Integrase core domain
     0.0011   19.6   0.1     0.0032   18.1   0.1    1.9  1  HTH_32       Homeodomain-like domain
     0.0072   16.1   0.2      0.019   14.8   0.2    1.7  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.072   13.6   4.3        0.2   12.1   4.2    1.8  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.1e-24   3.8e-21       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ +  e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518652132|ref|YP_008141652.1| 125 KHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYGEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l + +i++ + r+ +p++nGk Er + t+k+
  gi|518652132|ref|YP_008141652.1| 195 FSNgkngipgdhnKFQEYLDNSNIKHILGRVKHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   5.3e-08   0.00019       2      63 ..     217     268 ..     216     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518652132|ref|YP_008141652.1| 217 NIKHILGRVKHPETNGKLERLNYTIKRLRPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       589999********************965554444..........799************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0032       3      73 .]      36     101 ..      33     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+    + +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518652132|ref|YP_008141652.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDIEIVKKIRYEYPMSGPERIRKYL-KRKGIIIAKNNIYRIL 101
                                       556778888876666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.3e-06     0.019      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518652132|ref|YP_008141652.1| 11 IIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.2   5.7e-05       0.2      40     111 ..       3      75 ..       1     127 [. 0.79
   2 ?   -1.6   0.0      0.93   3.3e+03      44     126 ..     217     243 ..     167     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vk+++ + ++
  gi|518652132|ref|YP_008141652.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNGEyTIGKRKHRELNSKDIEIVKKIRYEYPM 75 
                                       8999****************************88888888776663346678899999999999999874444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                       Terminase_2  44 kIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseevdkeilrevkegke....gvkvklkDk 116
                                       +Ik                                                                 +++++++ k
  gi|518652132|ref|YP_008141652.1| 217 NIK------------------------------------------------------------HilgrVKHPETNGK 233
                                       222............................................................13333455555555 PP

                       Terminase_2 117 lkAlellakh 126
                                       l+ l+ ++k+
  gi|518652132|ref|YP_008141652.1| 234 LERLNYTIKR 243
                                       5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1926.92
//
Query:       gi|518652133|ref|YP_008141653.1|  [L=37]
Description: hypothetical protein FACI_IFERC00001G0772 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 268.23
//
Query:       gi|518652134|ref|YP_008141654.1|  [L=385]
Description: hypothetical protein FACI_IFERC00001G0773 [Ferroplasma acidarmanus fer1]
Scores for complete 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-35  120.4   0.1    1.3e-34  119.6   0.1    1.4  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.5e-24   86.8   0.0    3.5e-24   85.6   0.0    1.7  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    4.1e-19   68.6   0.6    7.7e-19   67.7   0.6    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    2.6e-08   34.2   0.0      4e-08   33.6   0.0    1.2  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.1   2.9e-38   1.3e-34       1     150 []     233     384 ..     233     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.9e-38
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       ++Gf++ m ++nh R++vaaa+ gl  + lee l+y+++rkafgk+l d+++++++ a++++++e+a ll+y+aa++
  gi|518652134|ref|YP_008141654.1| 233 NEGFYYSMDGFNHARIMVAAACNGLSYKMLEEGLNYIKERKAFGKHLSDFEAISFEAADLRTDVEMAALLNYKAAYL 309
                                       79*************************************************************************** PP

                                       -------.HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSS.S-HHHHHHHHHHHH. CS
                     Acyl-CoA_dh_1  78 ldagkpd.raeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrige.Gtseiqrniiarrll 150
                                       +d ++pd    +sm Kl+ +++a++ +++ m ++G++Gy+++ ++e ++r + ++ +g+ G+ +i++ ii++++l
  gi|518652134|ref|YP_008141654.1| 310 ADVEDPDfYIYSSMSKLKSPQIAMDTTKKVMMWFGAYGYTKDSGIEMAARGIFSYLVGAeGALNIMKVIISKAIL 384
                                       *********************************************************988***********9985 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.6   0.0   7.8e-28   3.5e-24       1     112 [.       6     118 ..       6     119 .. 0.95

  Alignments for each domain:
  == domain 1  score: 85.6 bits;  conditional E-value: 7.8e-28
                                       THHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   1 teeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       ++eq+ lr+  +ef+e++l+p ++e+d++ge+p e+++k++e+G++   ++ +ygG  l++++++i+ ee+ar d++
  gi|518652134|ref|YP_008141654.1|   6 SDEQKLLRKNTAEFLEKNLKPFVREIDNNGEIPMEFFRKAGENGIISPLIKLKYGGPSLSFMDSVIISEEIARIDTS 82 
                                       69**************************************************************************9 PP

                                       HHH.HHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  78 lal.llgvhsslvapailrfGteeqkrryLpklasg 112
                                       +a+ ++ + ++  a+++ ++G +e k++ Lp++a+g
  gi|518652134|ref|YP_008141654.1|  83 MATsVYYLLNTSWAYVLQKYGKQELKDKLLPEIANG 118
                                       999877777777779*******************98 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.6   1.7e-22   7.7e-19       1      97 []     123     221 ..     123     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 1.7e-22
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEE....EEEEETS---.----EEEEEEE..GGG CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatla....lvlartekpd.rarglslflvprdapg 72 
                                       ++a+TEp++Gsdva++ktt  + ++g++++nGeK++i++a +a+      l+l++ +k+  +++g+++++vp++a g
  gi|518652134|ref|YP_008141654.1| 123 GIASTEPSGGSDVANIKTTG-RIENGKVIINGEKMYISGAVEAKKNggghLTLVK-TKEGvGHKGITMVYVPANADG 197
                                       589***************55.555558***************8886666688888.344457*************** PP

                                       EEE-----BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  73 vsvrrieeklGlrglptgelvfedv 97 
                                       ++++++ +++G++g++t+ + +++v
  gi|518652134|ref|YP_008141654.1| 198 IEITKL-NNMGRMGISTSGIKYTNV 221
                                       *****9.69*********9988876 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.0     9e-12     4e-08       1     121 [.     248     359 ..     248     363 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 9e-12
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                     Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtv 77 
                                       +++aa++ G+   +l+e + +++er+   +g++l+d++a+ ++ a+++++++ A +l ++aa+     a+ +   ++
  gi|518652134|ref|YP_008141654.1| 248 IMVAAACNGLSYKMLEEGLNYIKERKA--FGKHLSDFEAISFEAADLRTDVEMAALLNYKAAYL----ADVE---DP 315
                                       589************************..***********************************....3333...34 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHH CS
                     Acyl-CoA_dh_2  78 edraearraaalavelaiaavdalfeaaGgsalrkesplqRlwR 121
                                       +    ++++++   ++a + +++++  +G+++++k+s ++ + R
  gi|518652134|ref|YP_008141654.1| 316 DFYIYSSMSKLKSPQIAMDTTKKVMMWFGAYGYTKDSGIEMAAR 359
                                       6679********************************99986666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2478.38
//
Query:       gi|518652135|ref|YP_008141655.1|  [L=190]
Description: hypothetical protein FACI_IFERC00001G0774 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       591  (0.0329634); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.32s 00:00:00.83 Elapsed: 00:00:00.51
# Mc/sec: 1129.91
//
Query:       gi|518652136|ref|YP_008141656.1|  [L=276]
Description: hypothetical protein FACI_IFERC00001G0775 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1833.76
//
Query:       gi|518652137|ref|YP_008141657.1|  [L=302]
Description: ABC transporter, ATP-binding protein related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   67.6   0.0    2.7e-18   66.8   0.0    1.4  1  ABC_tran       ABC transporter
    1.4e-10   41.0   0.6    7.7e-06   25.5   0.0    2.2  2  SMC_N          RecF/RecN/SMC N terminal domain
    2.1e-09   37.6   3.0    1.2e-05   25.3   0.1    2.3  2  AAA_21         AAA domain, putative AbiEii toxin, Type IV TA 
    1.7e-05   25.4   1.3    5.3e-05   23.8   0.3    2.0  2  AAA_23         AAA domain
      5e-05   22.9   0.1    0.00011   21.8   0.1    1.5  1  AAA_29         P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.011   15.5   0.4       0.02   14.7   0.4    1.4  1  Endonuc-PvuII  Restriction endonuclease PvuII


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 !   66.8   0.0   8.9e-22   2.7e-18       3     136 ..      40     176 ..      38     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 8.9e-22
                                       EEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   3 nvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren 79 
                                       n ++ + +g  + ++ +nG+GKSt++ l++g+++ ++Gei ++g +  + +++ +  + + +p++p  f   tvre+
  gi|518652137|ref|YP_008141657.1|  40 NSTFRVDKGV-TLLISPNGSGKSTIIYLIMGNYRINSGEIYVNGYNPVN-NHRLAFLNTSLMPENPVYFGSGTVREH 114
                                       6777787775.55777***************************666665.57777788999**************** PP

                                       .........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 .........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                 +++ei+ +ls ++++++ ++++    ssLS G+ q + + + l  + kl+++DEp 
  gi|518652137|ref|YP_008141657.1| 115 islfsrlkgVASSEIYGFLSYFKMEHIINSRI----SSLSMGEAQILYISCYLSGNYKLYIFDEPN 176
                                       ********99999*************999999....*****************************5 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 !   14.1   0.1     8e-06     0.024      17      44 ..      40      67 ..      33      76 .. 0.87
   2 !   25.5   0.0   2.6e-09   7.7e-06     136     213 ..     148     224 ..      70     229 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8e-06
                                      EEEEETTSSEEEEEESTTSSHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 17 tvilpfsksftaivGpNGSGKsnlldAi 44
                                      + + +++k++t ++ pNGSGKs ++  i
  gi|518652137|ref|YP_008141657.1| 40 NSTFRVDKGVTLLISPNGSGKSTIIYLI 67
                                      5678899****************99766 PP

  == domain 2  score: 25.5 bits;  conditional E-value: 2.6e-09
                                       CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEEE-SSHHHC.CC-SCEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxx.xxxxxxx RF
                             SMC_N 136 lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfivislreeml.ekadklv 209
                                       +LS Ge +++ ++  ++        ly++De +++LD+ n++++ae +k  + ++n+ f+++s+ ++ l ++a++++
  gi|518652137|ref|YP_008141657.1| 148 SLSMGEAQILYISCYLS----GNYKLYIFDEPNSNLDQPNRRRFAEAVKlkQLNSNSIFLITSHINDELnQQANQIL 220
                                       78888888877776665....45569********************987547778899*****97766515668888 PP

                                       EEEE CS
                                       xxxx RF
                             SMC_N 210 gvtk 213
                                        +t 
  gi|518652137|ref|YP_008141657.1| 221 TITG 224
                                       7765 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 !   12.2   0.6   3.8e-05      0.11       1      19 [.      49      67 ..      49      86 .. 0.87
   2 !   25.3   0.1     4e-09   1.2e-05     207     298 ..     112     208 ..      88     213 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.8e-05
                            AAA_21  1 lnvliGpNgsGKSnLLdal 19
                                      +++li pNgsGKS++++++
  gi|518652137|ref|YP_008141657.1| 49 VTLLISPNGSGKSTIIYLI 67
                                      6999************998 PP

  == domain 2  score: 25.3 bits;  conditional E-value: 4e-09
                            AAA_21 207 eliasvderlrer.......gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllr 276
                                       +++ s + rl+++       ++ ++++++  +  +++lS+G  ++  l+ +++      +l+++DEp ++L+    r
  gi|518652137|ref|YP_008141657.1| 112 REHISLFSRLKGVasseiygFLSYFKMEHIINSRISSLSMGEAQI--LYISCYLSGNY-KLYIFDEPNSNLDQPNRR 185
                                       444455555555577778889999*********************..44444444444.9***************** PP

                            AAA_21 277 rllellkelsr.ngaQviltTHS 298
                                       r++e +k+++   ++ +++t+H 
  gi|518652137|ref|YP_008141657.1| 186 RFAEAVKLKQLnSNSIFLITSHI 208
                                       ******66666346667*****6 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.3   1.8e-08   5.3e-05       8      39 ..      36      67 ..      31      69 .. 0.88
   2 ?    0.3   0.0      0.27   8.2e+02      93     126 ..     185     221 ..     107     263 .. 0.62

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.8e-08
                            AAA_23  8 rsfrdqeidFskgltlItGpNGaGKTTildAi 39
                                        f++ ++  +kg+tl++ pNG+GK+Ti+  i
  gi|518652137|ref|YP_008141657.1| 36 TIFENSTFRVDKGVTLLISPNGSGKSTIIYLI 67
                                      569999**********************9655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.27
                            AAA_23  93 erelskkkgkttkkaklellei...deleqfisellg 126
                                       +r+    k k+ + +  +l++    del+q+ +++l+
  gi|518652137|ref|YP_008141657.1| 185 RRFAEAVKLKQLNSNSIFLITShinDELNQQANQILT 221
                                       2222222222222222222222344555555555444 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 !   21.8   0.1   3.8e-08   0.00011      12      48 ..      38      69 ..      35      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.8e-08
                            AAA_29 12 fdghtieidlkgatlltGpsGsGKSTllDAiqalLvp 48
                                      f++ t+++d kg+tll+ p+GsGKST++    +l+++
  gi|518652137|ref|YP_008141657.1| 38 FENSTFRVD-KGVTLLISPNGSGKSTII----YLIMG 69
                                      788999999.889**************9....55555 PP

>> Endonuc-PvuII  Restriction endonuclease PvuII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   6.6e-06      0.02      35     119 ..     215     297 ..     185     301 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.6e-06
                     Endonuc-PvuII  35 kllqllillGlrispgreGndavdaeGkeyelktvnvelsrsvtthhhlneailekyrrvewyiavyknielkeiyr 111
                                       +  q+l ++G ++ +    +  +    k y++ktv+ +l+     h  +n++i+ k   ++ +i v  + ++kei r
  gi|518652137|ref|YP_008141657.1| 215 QANQILTITGNKVRAFYRDDINIAYALKFYDIKTVEGKLKG--LKHFMVNDSIVIKNASIRDIIDVIPESNIKEITR 289
                                       556999999999999999999999999*********99975..579999**************************** PP

                     Endonuc-PvuII 112 lkpesles 119
                                       + p ++e 
  gi|518652137|ref|YP_008141657.1| 290 IPPAMVEY 297
                                       ***99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 1944.36
//
Query:       gi|518652138|ref|YP_008141658.1|  [L=246]
Description: hypothetical protein FACI_IFERC00001G0777 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy 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:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.35s 00:00:00.93 Elapsed: 00:00:00.51
# Mc/sec: 1452.17
//
Query:       gi|518652139|ref|YP_008141659.1|  [L=187]
Description: hypothetical protein FACI_IFERC00001G0778 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.2       0.13   12.4   0.1    1.7  2  Ectoine_synth  Ectoine synthase


Domain annotation for each model (and alignments):
>> Ectoine_synth  Ectoine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   7.5e-06      0.13      45      85 ..      19      59 ..      11      62 .. 0.89
   2 ?   -2.1   0.0      0.24   4.3e+03      72      88 ..      80      97 ..      76     119 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.5e-06
                                      T--EEEE-TT-EEEEEEEE--EEEEETTT--EEEE-TTEEE CS
                     Ectoine_synth 45 gtetelkYknHleavycieGegeveeledgevyeikpgtlY 85
                                         t++ ++nH++  + ++ + +++e+ +g+++ i +g  Y
  gi|518652139|ref|YP_008141659.1| 19 VLITSIPFANHYDNSFTLNTKNNITEKYNGTTHYIIQGRYY 59
                                      5567899*******************************999 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.24
                                      TT--EEEE-TT.EEEEET CS
                     Ectoine_synth 72 edgevyeikpg.tlYlld 88
                                      e+g++y+i++  ++Y + 
  gi|518652139|ref|YP_008141659.1| 80 ENGQNYTINNCvSIYSVS 97
                                      567777776641355544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1362.00
//
Query:       gi|518652140|ref|YP_008141660.1|  [L=277]
Description: 2, 4-dienoyl-CoA reductase (NADPH) precursor related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  154.6   0.5    3.8e-45  154.3   0.5    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
      2e-37  128.6   0.4      3e-37  128.0   0.4    1.2  1  adh_short        short chain dehydrogenase
    1.1e-10   41.7   0.0    2.1e-10   40.8   0.0    1.3  1  KR               KR domain
    0.00024   20.3   0.1    0.00032   19.9   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00073   19.9   0.0     0.0013   19.2   0.0    1.3  1  NAD_binding_7    Putative NAD(P)-binding
     0.0012   18.0   0.0     0.0016   17.5   0.0    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
     0.0044   17.7   0.0     0.0082   16.8   0.0    1.5  1  Methyltransf_25  Methyltransferase domain
  ------ inclusion threshold ------
      0.015   14.8   0.0      0.022   14.2   0.0    1.3  1  Epimerase        NAD dependent epimerase/dehydratase family
      0.038   13.9   0.1      0.069   13.0   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.094   12.6   0.0       0.16   11.9   0.0    1.4  1  NAD_binding_10   NAD(P)H-binding
       0.14   11.6   0.0       0.18   11.2   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
       0.17   10.8   0.0       0.26   10.2   0.0    1.2  1  PARP_regulatory  Poly A polymerase regulatory subunit


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 !  154.3   0.5   2.5e-48   3.8e-45       4     232 ..      19     251 ..      16     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 2.5e-48
                                       TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE--- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnag 78 
                                        g+G+++ +++ + Ga+v +  ++ee   +++e  +++g ++  ++cD++++++++++v+ +++k+gk+++l+nna+
  gi|518652140|ref|YP_008141660.1|  19 TGLGKQMTETFLKLGATVSIISRKEEHLTAAKEYFNNMGYKIeaVKCDIRNPDEIKNAVDLIESKTGKINVLINNAA 95 
                                       699************************99**********88556********************************* PP

                                       --EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  79 iapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                             +++++++ + fd+++ + l+++++ + ++ +  + ++  g i+ +  + a  +       +++Ka++ alt
  gi|518652140|ref|YP_008141660.1|  96 GNFI--SRTEDLTPKAFDTVMGIVLHGTAYASLEMGKrWLSNSmkGTILSIVATYAWTGSGYVVPSAISKAGVLALT 170
                                       9999..9****************************9975555557999988888887777777799*********** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTG.GGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEE CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTla.asgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlv 228
                                       r+lA+e+g+kgiR  a++pg+ kT+  +s++   d+ ++++ +  p +rl+t ee+a++a+fL+sd+a+yi+G+++ 
  gi|518652140|ref|YP_008141660.1| 171 RSLAAEWGHKGIRTVAIAPGAFKTEGaWSRLLPGDDYEKQIISGNPERRLATKEEIANIAAFLISDMAAYINGEVVT 247
                                       ************************8758899999******************************************* PP

                                       ESTT CS
                      adh_short_C2 229 vDgG 232
                                       +DgG
  gi|518652140|ref|YP_008141660.1| 248 ADGG 251
                                       ***9 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.0   0.4     2e-40     3e-37       1     187 [.      10     197 ..      10     202 .. 0.97

  Alignments for each domain:
  == domain 1  score: 128.0 bits;  conditional E-value: 2e-40
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgk 77 
                                       k +l+tG++ G+G+++ ++++k Ga+v +++r+ee l ++++ +++ g k+ a+++D+++ +e++++v+ +++k+gk
  gi|518652140|ref|YP_008141660.1|  10 KNILITGGGTGLGKQMTETFLKLGATVSIISRKEEHLTAAKEYFNNMGYKIEAVKCDIRNPDEIKNAVDLIESKTGK 86 
                                       789**********************************9999999999****************************** PP

                                       ESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHH.HCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  78 ldvLvnNAGitgsgpfselseeewervievNltgvflltravlpaml.kqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       ++vL+nNA+ +  + +++l+ ++++ v+ + l+g+  ++ ++ + +l ++ +G+I  +  + +  ++  v++ + sK
  gi|518652140|ref|YP_008141660.1|  87 INVLINNAAGNFISRTEDLTPKAFDTVMGIVLHGTAYASLEMGKRWLsNSMKGTILSIVATYAWTGSGYVVPSAISK 163
                                       ******************************************999887999*********************99*** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHH CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdma 187
                                       a+v +ltrsla e+  +gir +a+aPG+++T+ a
  gi|518652140|ref|YP_008141660.1| 164 AGVLALTRSLAAEWGHKGIRTVAIAPGAFKTEGA 197
                                       *******************************976 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.0   1.4e-13   2.1e-10       4     115 ..      13     120 ..      11     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.4e-13
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       litGG  gLG++++++ ++ ga+ + ++sR+++      a  + ++++g ++e+v++D+ ++d+++++++ i+++++
  gi|518652140|ref|YP_008141660.1|  13 LITGGGTGLGKQMTETFLKLGAT-VSIISRKEEHLT---AAKEYFNNMGYKIEAVKCDIRNPDEIKNAVDLIESKTG 85 
                                       9********************85.88999*944333...445778899***************************** PP

                                       ---EEEE---------TTT--HHHHHHHHTTTTHH CS
                                KR  81 pikGvihaAgvlrdklleemtaedleqvlapKvkG 115
                                       +i+  i+ A     +  e++t +++++v+   ++G
  gi|518652140|ref|YP_008141660.1|  86 KINVLINNAAGNFISRTEDLTPKAFDTVMGIVLHG 120
                                       *******9999999999999999999999766665 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   2.2e-07   0.00032       1      76 [.      12      80 ..      12     121 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.2e-07
                                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT.. CS
                   Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleel 76
                                      +l+tG+g  +G+++++++lk  + ++ +++r+E +l + ++ +    +  ++ ++i +v +d+r+ +++++a++ +
  gi|518652140|ref|YP_008141660.1| 12 ILITGGGTGLGKQMTETFLKLGA-TVSIISRKEEHLTAAKEYF----N--NMGYKIEAVKCDIRNPDEIKNAVDLI 80
                                      89******************986.69999*******9988876....2..3445666889*********9998643 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.5e-07    0.0013       5     101 ..       7      99 ..       6     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.5e-07
                     NAD_binding_7   5 lkgkkvlvvGgGe.vAarkvrklleagakvtvvapevkeeleelvklaeeelekdlegadlviaatddrelneriae 80 
                                       lk+k++l+ GgG+ ++ +  +++l+ ga+v +++ +     ee +++a+e++++   +++ v + + ++++ ++ ++
  gi|518652140|ref|YP_008141660.1|   7 LKDKNILITGGGTgLGKQMTETFLKLGATVSIISRK-----EEHLTAAKEYFNNMGYKIEAVKCDIRNPDEIKNAVD 78 
                                       689*********76999*******************.....688999999999999999999999999999999999 PP

                     NAD_binding_7  81 aakarrilvnvadkpelcdfi 101
                                       +++++   +nv  + + ++fi
  gi|518652140|ref|YP_008141660.1|  79 LIESKTGKINVLINNAAGNFI 99 
                                       888877777777777777776 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06    0.0016       1      67 [.      13      80 ..      13     127 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                         3Beta_HSD  1 vvtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkk.viegDvtdkdkleealegv 67
                                      ++tGg+  lG+++ +++++l+    + +   ++ +  +e +++++ k   +++D+++ d++++a++ +
  gi|518652140|ref|YP_008141660.1| 13 LITGGGTGLGKQMTETFLKLGATVSIISRKEEHLTAAKEYFNNMGYKIeAVKCDIRNPDEIKNAVDLI 80
                                      699***9**************8777777778888999999****99877***************9843 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.5e-06    0.0082       3      77 ..      14      90 ..      12     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-06
                                      EET-TTS...HHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGS CS
                   Methyltransf_25  3 dlGcGtG...rltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhl 77
                                        G GtG   ++t+ ++k  g a+v  +   ee l aa+e +++ g+++e v++d+++ ++ ++ +Dl+ s  + +++l
  gi|518652140|ref|YP_008141660.1| 14 ITGGGTGlgkQMTETFLKL-G-ATVSIISRKEEHLTAAKEYFNNMGYKIEAVKCDIRNPDEIKNAVDLIESKTGkINVL 90
                                      5677777334466667776.5.********************99999**********************9977766664 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.022       1      61 [.      12      78 ..      12     116 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                                      EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.........EEEE--TT-HHHHHHHHH CS
                         Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.........elveldltdrsalerlfk 61
                                      il+tG+   +G+++++ +l+ g +v  ++r+++    a  +           e v++d++++++++++++
  gi|518652140|ref|YP_008141660.1| 12 ILITGGGTGLGKQMTETFLKLGATVSIISRKEEHLTAA--K-EyfnnmgykiEAVKCDIRNPDEIKNAVD 78
                                      89*****************************3333222..2.246899***************8887765 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   0.1   4.6e-05     0.069       3      67 ..      13      80 ..      11      95 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
                                      EEE--SC.CHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-...HHHHCCCHHCE CS
                           3HCDH_N  3 aviGaGt.mGagiaavfasagleVvlvdiseealekalekieksleklvekgklk...eeeveaalari 67
                                       + G Gt +G+++++ f++ g +V ++ ++ee l++a+e  ++   k +e+ k++    +e+++a++ i
  gi|518652140|ref|YP_008141660.1| 13 LITGGGTgLGKQMTETFLKLGATVSIISRKEEHLTAAKEYFNNMGYK-IEAVKCDirnPDEIKNAVDLI 80
                                      577888879******************************99983332.333333311245555555555 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0001      0.16       3      59 ..      18      78 ..      16     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                                      TSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH...CT..TTCEEEE--TT-CCHHHHHHT CS
                    NAD_binding_10  3 tGkvGrllvkellargghevtalvRnpeklaele...ae..eglevvegdvtdvedlaealk 59
                                        + G++ ++  l+ g  +v ++ R++e+l++ +   ++   ++e+v+ d+ +++++++a++
  gi|518652140|ref|YP_008141660.1| 18 GTGLGKQMTETFLKLG-ATVSIISRKEEHLTAAKeyfNNmgYKIEAVKCDIRNPDEIKNAVD 78
                                      4458***********5.9************854433333235999**************986 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00012      0.18       1      74 [.      13      80 ..      13     116 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHH CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaev 74
                                      LiTG+    G  ++e +l+ g +v +i r++++++ +   +  ++    +  +++ +k+D+++ ++++++++ +
  gi|518652140|ref|YP_008141660.1| 13 LITGGGTGLGKQMTETFLKLGATVSIISRKEEHLT-AAK-EYFNN----MGYKIEAVKCDIRNPDEIKNAVDLI 80
                                      899987779***************98877666544.333.44433....345799************9998766 PP

>> PARP_regulatory  Poly A polymerase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00017      0.26      60     101 ..      36      77 ..      23      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00017
                   PARP_regulatory  60 lYiGsakgtHirlLrelfkdlgvkikWvliDgrdhdeslegl 101
                                       + i s k  H++  +e+f+++g+ki  v  D+r++de+ + +
  gi|518652140|ref|YP_008141660.1|  36 VSIISRKEEHLTAAKEYFNNMGYKIEAVKCDIRNPDEIKNAV 77 
                                       678899******************************986655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.49
# Mc/sec: 1712.08
//
Query:       gi|518652141|ref|YP_008141661.1|  [L=121]
Description: hypothetical protein FACI_IFERC00001G0780 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        9.4    6.5   9.2        9.6    6.4   1.2    2.3  2  Pox_A14    Poxvirus virion envelope protein A14


Domain annotation for each model (and alignments):
>> Pox_A14  Poxvirus virion envelope protein A14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   1.2   0.00054       9.6      48      64 ..      16      32 ..       3      36 .. 0.84
   2 ?    4.6   1.5    0.0021        37      20      60 ..      60     101 ..      41     111 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00054
                           Pox_A14 48 sivsFilgivillglll 64
                                      si++Fi gi++ll l++
  gi|518652141|ref|YP_008141661.1| 16 SIITFISGIIVLLLLFI 32
                                      8**********998776 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0021
                           Pox_A14  20 iLLilacifafvdfskststtdkawrals..ivsFilgivill 60 
                                       i+ i+ +i+a++ + ++    ++  ++l   i+ F+  i++ll
  gi|518652141|ref|YP_008141661.1|  60 IIPIIWIILAYIIYTRADGG-RRKDKVLNgvIIIFLGFIILLL 101
                                       33456688999999998774.3344444410333444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 960.54
//
Query:       gi|518652142|ref|YP_008141662.1|  [L=418]
Description: sugar transport permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-35  122.3  51.6    2.1e-35  122.3  51.6    1.6  1  MFS_1     Major Facilitator Superfamily
    4.4e-09   35.7  42.2    1.2e-05   24.4  14.7    2.3  2  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.3  51.6   2.3e-39   2.1e-35      29     352 ..      61     365 ..      23     366 .. 0.85

  Alignments for each domain:
  == domain 1  score: 122.3 bits;  conditional E-value: 2.3e-39
                             MFS_1  29 ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfp 104
                                           +igl+lt+ya+g a++sl++G+l dr++ + +++l++l+f+++ ++++ f+++ + l+++r+  G+g g++ p
  gi|518652142|ref|YP_008141662.1|  61 PLYLSIGLILTGYAIGIAIFSLVGGYLFDRYSVKNTVILSVLVFSAF-TIMTgFVTTTPELFIARLGVGVGVGIFQP 136
                                       344569*****************************************.77777988888****************** PP

                             MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkr 181
                                       ag+al+ d+f +  rgra+++++++fs+G    p l   ++    +r++f i ++++++ + l  + ++ + + +k 
  gi|518652142|ref|YP_008141662.1| 137 AGVALLGDIFYE-TRGRAVSVWATFFSIGLFASPYLIEPFLP--AFRLPFEISGALAIIILAL--VIMVIPVTFKKE 208
                                       ***********9.********************888887774..58*************9664..666666666666 PP

                             MFS_1 182 kspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvga 258
                                       k+++++          + ++ +++++ +++ + +++++ + f+g+l ++  yl + l +s    a+++ ++++++g+
  gi|518652142|ref|YP_008141662.1| 209 KPTTKL----------N-IRNVFNRNIILLSISVFFFGIALFAGYLGYFSDYLIKGLLIS-KGNAAIIASMAGAGGF 273
                                       666666..........5.999*****66544444444444555588888889********.7899999********* PP

                             MFS_1 259 ilallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeag 335
                                       i+a+ +g+ +d++gr+ + +++ ll+++++lg+++l ++   + l+++ +++G g+g+++ +l al +d++  +  g
  gi|518652142|ref|YP_008141662.1| 274 IMAFPIGYTADKIGRKYMVIITSLLIAFGSLGMFFLFTS--FAGLIVSTFIFGAGWGVYVDLLVALGQDSVEDRIVG 348
                                       ***************999999999999999999999999..8888889999************************** PP

                             MFS_1 336 tasglfntagslggalg 352
                                       t+sg+  +++++g+++g
  gi|518652142|ref|YP_008141662.1| 349 TISGFLFFIFNVGTIIG 365
                                       ***************98 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4  14.7   1.4e-09   1.2e-05      46     189 ..      64     198 ..      26     212 .. 0.84
   2 !   16.6  19.7   3.1e-07    0.0028      48     190 ..     261     398 ..     224     402 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.4e-09
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                       + +gli+  + +G +i sl++g+l dr++ k++ + ++++f++ ++++++ +   ++  l+++R+ vG+gvG+++  
  gi|518652142|ref|YP_008141662.1|  64 LSIGLILTGYAIGIAIFSLVGGYLFDRYSVKNTVILSVLVFSAFTIMTGFVT---TTPELFIARLGVGVGVGIFQPA 137
                                       4789999*********************************************...99******************** PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGG CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilll 189
                                          +++ i   + Rg+ vs++ ++ ++G + +    + ++ +     +r+++ ++ ++a+++l+l++
  gi|518652142|ref|YP_008141662.1| 138 GVALLGDIF-YETRGRAVSVWATFFSIGLFAS---PYLIEPFLP--AFRLPFEISGALAIIILALVI 198
                                       *******95.788***************9865...455655555..577888888888877776664 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.1e-07
                                       HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHH CS
                          Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvP 124
                                         +i+s++ +G++i ++ +g+ +d++GRk+  +i+++l   g++ +++    +s+  liv+ ++ G g+G+   l  
  gi|518652142|ref|YP_008141662.1| 261 AAIIASMAGAGGFIMAFPIGYTADKIGRKYMVIITSLLIAFGSLGMFFLF--TSFAGLIVSTFIFGAGWGVYVDLLV 335
                                       4699**********************************************..79*********************** PP

                                       HHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHGGG CS
                          Sugar_tr 125 myisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllilllf 190
                                        + +    +++ g++ ++  +   +G +++  ++ +l ++  +    +  l + ++pa l +++++f
  gi|518652142|ref|YP_008141662.1| 336 ALGQDSVEDRIVGTISGFLFFIFNVGTIIGGPLYEALlSEGFK----KTSLLSVIIPAFLAVLFVVF 398
                                       **************************99998887777688888....78888888888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); 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:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 2797.59
//
Query:       gi|518652143|ref|YP_008141663.1|  [L=80]
Description: transcription regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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-07   28.7   0.0    1.2e-06   28.3   0.0    1.2  1  HTH_5     Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.016   15.1   0.0       0.02   14.7   0.0    1.2  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.0   1.3e-10   1.2e-06       4      45 ..       2      43 ..       1      44 [. 0.97

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.3e-10
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLV 45
                                      R+k++k+L+e+++ +  l++ lg++  t+ hH k+L   ++V
  gi|518652143|ref|YP_008141663.1|  2 RIKVMKSLMESPKNAYGLSCSLGVNYRTIEHHMKVLLSNNFV 43
                                      99**********************************999988 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   2.3e-06      0.02      18      66 ..       9      58 ..       3      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-06
                                      HHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST.TTEEEE-- CS
                              TrmB 18 lklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr.pklYravd 66
                                      l++ p++a+ ++  lgv + ++   ++ L++  +V ++ +   k+Y + +
  gi|518652143|ref|YP_008141663.1|  9 LMESPKNAYGLSCSLGVNYRTIEHHMKVLLSNNFVVVQGQGyGKVYFPSP 58
                                      45899*******************************99877456887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 596.00
//
Query:       gi|518652144|ref|YP_008141664.1|  [L=338]
Description: hypothetical protein FACI_IFERC00001G0783 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00019   21.6   0.1      0.019   15.1   0.0    2.3  2  SnoaL_4   SnoaL-like domain


Domain annotation for each model (and alignments):
>> SnoaL_4  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0023        42      25      62 ..      70     108 ..      52     170 .. 0.86
   2 !   15.1   0.0     1e-06     0.019      32     114 ..     218     306 ..     209     310 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0023
                                       HHHHHTTEEEEEEEEETTS...--EESHHHHHHHHHSHH CS
                           SnoaL_4  25 weeladlFtedavvdytgvg.egvlegrdairaalreal 62 
                                        + + + +t++a++ + g+  +gv++g+++i   +++ +
  gi|518652144|ref|YP_008141664.1|  70 LANVSAGYTDNATLHWIGGPlNGVYSGITSINSTWSKFF 108
                                       55677889*********855***********99998865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1e-06
                                       EEEEEEEEETTS...--EESHHHHHHHHHSHHHHHH.....-EEEEE---EEEEETTEEEEEEEEEEEEEETTEEEE CS
                           SnoaL_4  32 Ftedavvdytgvg.egvlegrdairaalrealdgfa.....ltqHllsnplieldgdtAtgrayllatlvrdgdggr 102
                                       ++++a++ + g+  +g+++g+++i   +++ +++ +      ++  + np i+++g+ At++a+++++ v +++++ 
  gi|518652144|ref|YP_008141664.1| 218 YANNATLHWIGGPlNGTYSGITSINSTWNKFFTAWKavwfyASTSTTNNPEISINGNMATVSANFTQFIVQNATTNA 294
                                       67889999997559****************999777788889999***********************988887765 PP

                                       EE..EEEEEEEE CS
                           SnoaL_4 103 qvlaggryedel 114
                                       +  +   y++++
  gi|518652144|ref|YP_008141664.1| 295 FQYINTTYAITY 306
                                       555667776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 2191.59
//
Query:       gi|518652145|ref|YP_008141665.1|  [L=94]
Description: membrane spanning protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      1159  (0.0646439); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.31s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 599.25
//
Query:       gi|518652146|ref|YP_008141666.1|  [L=381]
Description: hypothetical protein FACI_IFERC00001G0785 [Ferroplasma acidarmanus fer1]
Scores for complete 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-37  127.1   0.6    9.5e-37  126.7   0.6    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    5.5e-13   48.8   0.2    1.6e-12   47.3   0.2    1.8  1  M20_dimer      Peptidase dimerisation domain
  ------ inclusion threshold ------
      0.028   14.1   0.1       0.09   12.5   0.1    1.8  2  Peptidase_M28  Peptidase family M28


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.6   1.6e-40   9.5e-37       1     206 [.      63     375 ..      63     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 1.6e-40
                                       EEEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   1 llgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrg 76 
                                       ++++++D++p +ee++     + ++++ G+++++G+d +++++l+a++ l   k++    +g+i+l+fqp+EE   g
  gi|518652146|ref|YP_008141666.1|  63 AIRADIDALPvTEENKV---SYVSKNK-GVMHACGHDTHMAMLLGAAKMLIVEKEKL---NGNIRLIFQPAEELPPG 132
                                       589*******8777733...8999988.**********************8866665...*************988* PP

                                       HHHHHHH.HHHTTTCESEEEEEEEESSSBTCHSTETEEEE..................................... CS
                                       xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
                     Peptidase_M20  77 Gakalle.gleerekvdavfelhieepgileagklaigvv..................................... 115
                                       Ga  +++ g++  e+vd+v++ hi+ + i+  gk+ai  +                                     
  gi|518652146|ref|YP_008141666.1| 133 GAVGMIKnGAL--ENVDFVIGQHIM-GFIPA-GKIAIYYKemmanadefdikihgkgghgsapqdsidaiyitahli 205
                                       *******7666..69**********.*****.99777777************************************* PP

                                       .......................................................................EEEEEE CS
                                       .......................................................................xxxxxx RF
                     Peptidase_M20 116 .......................................................................kvevel 121
                                                                                                              ++e+e 
  gi|518652146|ref|YP_008141666.1| 206 emlntivsreidpqepavittgtvnsgyryniiaahaeltgtvrtfnievqekiikrikdileglksiygiEYEYE- 281
                                       *********************************************************************9889999. PP

                                       EEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEES.SSBHTHHHH.TTTE.EEEEEE.SSG.....GCTTSTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx.xxxx.xxxxxx.xxx.....xxxxxxxxxx RF
                     Peptidase_M20 122 leggapvtlndsplvkalaeaaeelfgekvelivsg.pggtdarff.agip.tvmifg.pgs.....glaHspnEyv 189
                                       +  g+pv +n+++++k ++eaa++++g++    +++ +gg+d+++f +++p +++++g  +s     ++ Hsp  +v
  gi|518652146|ref|YP_008141666.1| 282 YKKGYPVLVNNEKIAKYIEEAAKRIVGKDNIIHPKPnMGGEDFAYFlQKVPgAYYFIGgSNSergidSMNHSPTFDV 358
                                       99**********************99*8877778889*********9999967788997774577666677777777 PP

                                       EHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 190 dledlekgikvlarlle 206
                                       d+++l++g+kvl+++++
  gi|518652146|ref|YP_008141666.1| 359 DESALYTGAKVLKEAAM 375
                                       7***********99875 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.2   2.7e-16   1.6e-12       8     103 ..     176     269 ..     172     274 .. 0.92

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 2.7e-16
                                       EEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEH CS
                         M20_dimer   8 ggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRl 84 
                                       ++ i+++gk+gH++ap++ ++Ai++ a+l++ l+   +++    +  +  ++ +++++G+  n+i+++ae++ ++R+
  gi|518652146|ref|YP_008141666.1| 176 EFDIKIHGKGGHGSAPQDSIDAIYITAHLIEMLNTIVSREI--DPQEPAVITTGTVNSGYRYNIIAAHAELTGTVRT 250
                                       789*********************99999999999999977..666777889999********************** PP

                                       HHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  85 lpgedpeevleeieeilek 103
                                        + e  e+++++i++ile 
  gi|518652146|ref|YP_008141666.1| 251 FNIEVQEKIIKRIKDILEG 269
                                       ****************985 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.5e-05      0.09       2      96 ..      50     151 ..      49     185 .. 0.80
   2 ?   -1.6   0.0      0.31   1.9e+03     117     163 ..     293     336 ..     289     362 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.5e-05
                                       EEEEESTTCESEEEEEEEE--B-TTT.........TCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEEEES CS
                     Peptidase_M28   2 viatlegkatdevlllgAHyDsvgvg.........rgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrflffd 69 
                                       +ia+++g+  ++++++ A +D ++v+         + ++++ A    + +a+lL  a++l  ++++++ ++r++f  
  gi|518652146|ref|YP_008141666.1|  50 IIADIKGNG-KKTVAIRADIDALPVTeenkvsyvsKNKGVMHACGHDTHMAMLLGAAKMLIVEKEKLNGNIRLIFQP 125
                                       799999999.999***********998877666542223333333446689*********9999999********** PP

                                       SCSGSSHHHHHHHHHHCCCTTEEEEEE CS
                     Peptidase_M28  70 aEEagllGSkafakakpelkkiaavln 96 
                                       aEE    G+  ++ ++ +l+++++v+ 
  gi|518652146|ref|YP_008141666.1| 126 AEELPPGGAVGMI-KNGALENVDFVIG 151
                                       ****999999999.7778888877775 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.31
                                       HHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT--EEEE CS
                     Peptidase_M28 117 selekelkalakpvgraaaedpfdersgrgrsDhspflkagvpvldl 163
                                       +++ k+++++ak++  +   +++ ++   g  D++ fl+ +vp++ +
  gi|518652146|ref|YP_008141666.1| 293 EKIAKYIEEAAKRIVGK--DNIIHPKPNMGGEDFAYFLQ-KVPGAYY 336
                                       67888999888887664..37888888889999999986.4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2651.95
//
Query:       gi|518652147|ref|YP_008141667.1|  [L=330]
Description: Proline racemase [Ferroplasma acidarmanus fer1]
Scores for complete 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-84  283.0   0.0      3e-84  282.9   0.0    1.0  1  Pro_racemase   Proline racemase
    2.3e-06   27.3   0.0    7.5e-06   25.6   0.0    1.7  2  PhzC-PhzF      Phenazine biosynthesis-like protein
     0.0015   18.7   0.0        1.2    9.4   0.0    2.4  2  DAP_epimerase  Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> Pro_racemase  Proline racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.9   0.0     5e-88     3e-84       1     324 [.      11     327 ..      11     328 .. 0.94

  Alignments for each domain:
  == domain 1  score: 282.9 bits;  conditional E-value: 5e-88
                                       EEEEEETTEEEEEEEESS---SSSSHHHHHHHHHHH.HHHHHHHHSTTTS-TT-EEEEEE--SSTTSSEEEEEEESS CS
                      Pro_racemase   1 vvdsHteGevgrvvvgGvpelpgetlaekrrlleedldalRralllePRGhdvmsgallvppkepdadlgviflets 77 
                                       v+d+HteGe++r++     + + ++ +  r+++ +++d++R++lllePRGh++++ga+l+pp +pd+d+ vi+  t+
  gi|518652147|ref|YP_008141667.1|  11 VIDTHTEGEPTRIMFWNNIPKNLRDALSVRKYFIDHYDYIRKILLLEPRGHKDQFGAILLPPVNPDSDYTVIYPTTE 87 
                                       79************988888888999999************************************************ PP

                                       SB-SSTHHHHHHHHHHHHHTTSS-SEEEECEEEEEETTEEEEEEEECTSTSEEEEEEE-S-BEEEEEEEEEEETTTE CS
                      Pro_racemase  78 gylpmcGsntigvvtvlletGlvevqepetklsletpaGlvevtaecrdgkvervslenvpsfvyaldvevevpglG 154
                                        yl mcG++tigv+t+l+  G v+ + +e +l+ +t aG+v++ ++ ++g+  +vs+  v s+  +  ++v+v+g  
  gi|518652147|ref|YP_008141667.1|  88 SYLDMCGHATIGVSTALVALGYVPFEGNEKTLVYDTVAGTVKAMVKIENGEPVSVSIVDVKSYFVK-KIKVNVNGK- 162
                                       ***************************************************************986.588999886. PP

                                       EEEEEEEESSSEEEEEEGGGCTS-SSCCCHHHHHHHHHHHHHHHHHHH---TTCSTTC-SEEEEEEEEEETTTTSEE CS
                      Pro_racemase 155 kvkvDiayGGnfyaiveaeklgldlekaearelveageklrealneqlkvqhpenedirevslveltgkkeraeaea 231
                                       +v v i+yGGnfyaiv++++lg+d+e++  ++l+++g+ +re++ e+lk   pen++  +++   +  ++   ++++
  gi|518652147|ref|YP_008141667.1| 163 NVDVNISYGGNFYAIVNSKDLGVDVEPEYIDDLLAYGKIIREKAYETLKELYPENRK--NLEPLAMITDN---NHDY 234
                                       7***********************************************999999764..44443333333...3357 PP

                                       EEEEEETTSEB-SS--HHHHHHHHHHHHHTTSS-TT-EEEEEETTS-EEEEEEEEEEEECTCEEEEEEEEE-EEEEE CS
                      Pro_racemase 232 rnaviisdkkvDRSPcGtgtsArlAvlaakGklkvgeefvqesiiGseFegrveeeaevggrkaivpeisGrafitg 308
                                       r++v+++++ +DRSPcGtgt+Ar A l ++Gklk   ++v+esi+ ++Fe+r+ + ++v ++ ai+pei+Gra++t 
  gi|518652147|ref|YP_008141667.1| 235 RAIVTFAGNSFDRSPCGTGTAARAAFLVHEGKLKLDGSYVNESILRTKFECRIISWEKVNDTIAIIPEITGRAWVTQ 311
                                       9**************************************************************************** PP

                                       EEEEEE-TT-TTTT-B CS
                      Pro_racemase 309 laqllldpsDPfaeGf 324
                                       l ++++dpsDP+++Gf
  gi|518652147|ref|YP_008141667.1| 312 LCKIIVDPSDPLKHGF 327
                                       ***************9 PP

>> PhzC-PhzF  Phenazine biosynthesis-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   1.3e-09   7.5e-06      43     106 ..      69     134 ..      66     169 .. 0.84
   2 ?   -1.6   0.0      0.24   1.5e+03     219     236 ..     250     267 ..     246     282 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 1.3e-09
                                       EE--SSTTSSEEEEEE-SSSEES--HHHHHHHHHHHHHHCT-...S-SCEEEEEETTEEEEE.EEEE CS
                         PhzC-PhzF  43 llkpsdekarfrlRyFTPvaEvdlcGHatlasahalaekglv...asaetveletkaGilpvkslke 106
                                       ll+p++ ++++ + y T  + +d+cGHat++   al++ g v    +++t++ +t aG++++  +k 
  gi|518652147|ref|YP_008141667.1|  69 LLPPVNPDSDYTVIYPTTESYLDMCGHATIGVSTALVALGYVpfeGNEKTLVYDTVAGTVKAM-VKI 134
                                       7888899999******************************99998999************984.332 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.24
                                       -HHHHHHHHHHHHHCC-S CS
                         PhzC-PhzF 219 tGsAsgaLaaylseklnl 236
                                       +G++ +a aa+l ++++l
  gi|518652147|ref|YP_008141667.1| 250 CGTGTAARAAFLVHEGKL 267
                                       999999999999999887 PP

>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0002       1.2      57     114 ..      81     143 ..      55     149 .. 0.78
   2 !    6.9   0.1    0.0011       6.8      59      84 ..     239     265 ..     171     277 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0002
                                       EEEETTTEEESTTHCCHHHHHHHHHCTTS-....S-SEEEEEETTEEEEEEEECTTSS.EEEE CS
                     DAP_epimerase  57 ryfnrdgseaemCGnGvrvfaaylreggle....tkkevtvetlgGeleievkddgek.vkvd 114
                                        ++   +s+  mCG ++  ++++l + g +    ++k+++ +t +G++++ vk ++ + v+v 
  gi|518652147|ref|YP_008141667.1|  81 VIYPTTESYLDMCGHATIGVSTALVALGYVpfegNEKTLVYDTVAGTVKAMVKIENGEpVSVS 143
                                       46677789999****96666666666666668889*******************999887665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0011
                                       EETTTEEE.STTHCCHHHHHHHHHCTT CS
                     DAP_epimerase  59 fnrdgsea.emCGnGvrvfaaylregg 84 
                                         ++ s+  + CG+G+++ aa+l ++g
  gi|518652147|ref|YP_008141667.1| 239 TFAGNSFDrSPCGTGTAARAAFLVHEG 265
                                       44444444045****888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); 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: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 2146.93
//
Query:       gi|518652148|ref|YP_008141668.1|  [L=198]
Description: hypothetical protein FACI_IFERC00001G0787 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1466.59
//
Query:       gi|518652149|ref|YP_008141669.1|  [L=193]
Description: hypothetical protein FACI_IFERC00001G0788 [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   38.8   0.0    9.7e-10   38.4   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    2.3e-08   34.6   0.0    3.8e-08   33.9   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    4.5e-08   33.7   0.0    8.4e-08   32.9   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    1.4e-07   31.5   0.0    1.9e-07   31.1   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    1.5e-07   31.9   0.0    2.9e-07   31.0   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    1.7e-06   27.7   0.0    2.1e-06   27.4   0.0    1.2  1  MTS              Methyltransferase small domain
    2.7e-05   23.7   0.0    3.6e-05   23.3   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
     0.0024   17.9   0.0     0.0032   17.4   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
     0.0031   16.9   0.0     0.0038   16.6   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0079   15.7   0.0      0.018   14.5   0.0    1.6  1  Methyltransf_4   Putative methyltransferase
  ------ inclusion threshold ------
      0.022   13.9   0.0      0.029   13.5   0.0    1.1  1  Helveticin_J     Bacteriocin helveticin-J
      0.029   13.9   0.0       0.04   13.5   0.0    1.2  1  DOT1             Histone methylation protein DOT1


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 !   38.4   0.0   6.5e-13   9.7e-10       3     112 ..      40     154 ..      38     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.5e-13
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDi......seeaielArenaqklgld.nveFeqgdiee.leklle 71 
                                       +++++lD+GCG G+ +  +a + +p a ++GiDi      s  + e+A +n ++lg+d +v +   +  + +   +e
  gi|518652149|ref|YP_008141669.1|  40 QKINILDAGCGLGFMVSIAA-KHFPYASITGIDIfnhdslSGSSMEKALQNMKELGIDnRVVLINHNLLTpFT--IE 113
                                       789*****************.999*********8655555667899************555555566666555..77 PP

                   Methyltransf_31  72 dekfDlilsnevl.naladpdkileeiervlkpggilliedp 112
                                         kfDl +sn v+ n+ ++   ++ ++++ l+ g ++++ d 
  gi|518652149|ref|YP_008141669.1| 114 -TKFDLAMSNLVFhNLGKNRFRAYDNVIECLNGGAYFILIDL 154
                                       .8***********999999999*********99999998775 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.0   2.5e-11   3.8e-08       1      94 [.      44     144 ..      44     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 2.5e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEES......SHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDi......seemleaareraeeegl..nvefvqgdaedlpfedgsfDlvv 69 
                                       +Ld+GcG G ++  +ak+++ a++tg+Di      s + +e+a ++++e g+  +v ++++++ +    + +fDl +
  gi|518652149|ref|YP_008141669.1|  44 ILDAGCGLGFMVSIAAKHFPYASITGIDIfnhdslSGSSMEKALQNMKELGIdnRVVLINHNLLTPFTIETKFDLAM 120
                                       8******************99*******988777788889*******999997788888888866445677****** PP

                                       EESTGGGSSHHHHHHHHHHHHHHEE CS
                   Methyltransf_25  70 ssgalhhlsdedlekalkeiarvLk 94 
                                       s+ ++h l + ++ +a++++ ++L+
  gi|518652149|ref|YP_008141669.1| 121 SNLVFHNLGK-NRFRAYDNVIECLN 144
                                       *777999985.55678888887775 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   5.6e-11   8.4e-08       1      98 [.      45     148 ..      45     149 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 5.6e-11
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsai......edakeklakrennnnnnvelealdlldldgg.ssfDlv 70 
                                       L+ GcG G +++  ++++p +++tg+Di  +        e+a + +++ + +n  +v l + +ll  +    +fDl 
  gi|518652149|ref|YP_008141669.1|  45 LDAGCGLGFMVSIAAKHFPYASITGIDIFNHDSlsgssmEKALQNMKELGIDN--RVVLINHNLLTPFTIeTKFDLA 119
                                       89*************************96554445555599999999999877..44444455444433367***** PP

                   Methyltransf_12  71 vasnvlhhl.kdirevldnirklLkpgGr 98 
                                        ++ v+h+l k++ ++ dn+ ++L+ g++
  gi|518652149|ref|YP_008141669.1| 120 MSNLVFHNLgKNRFRAYDNVIECLNGGAY 148
                                       *********99999**********98875 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.0   1.2e-10   1.9e-07       6     133 ..      25     167 ..      19     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 1.2e-10
                   Methyltransf_23   6 eeelsdklerllpklraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiaekakkaqkdqfdeqeaaepq 80 
                                       +e++ + l+ l p   ++ ++Ld GcG G + +++++++   s+tg+D+  +++           +++  ++a +  
  gi|518652149|ref|YP_008141669.1|  25 KEKMNQVLDTLYP-ATQKINILDAGCGLGFMVSIAAKHFPyaSITGIDIFNHDSLSG--------SSM--EKALQ-- 88 
                                       4666677777776.89999**********8888776664448*******86533322........111..12222.. PP

                   Methyltransf_23  81 g.........................kfdlIvlrevlehvp.dppellrqiatllkpgGylllseplaslkedrlll 131
                                       +                         kfdl+ ++ v++++  +  ++ +++ ++l+ g+y++l + l +++ d+++l
  gi|518652149|ref|YP_008141669.1|  89 NmkelgidnrvvlinhnlltpftietKFDLAMSNLVFHNLGkNRFRAYDNVIECLNGGAYFILIDLLPEQSIDMDYL 165
                                       12245555667788888888888889**************97899******************99988876666555 PP

                   Methyltransf_23 132 dw 133
                                        +
  gi|518652149|ref|YP_008141669.1| 166 RN 167
                                       54 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0     2e-10   2.9e-07       1      95 [.      45     150 ..      45     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2e-10
                                       EEET-TTSHHHHHHHHTT..SEEEEEES-HHHH......HHHHHHCCHHT-..EEEETTEECCCTSS-T.T-EEEEE CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskeml......klakekaseegl..kvefvvadaeklpfed.nsfDlvv 66 
                                       Ld+GcG G ++   ak++  a+++g+D+ +         + a ++ +e g+  +v ++  ++ + pf    +fDl +
  gi|518652149|ref|YP_008141669.1|  45 LDAGCGLGFMVSIAAKHFpyASITGIDIFNHDSlsgssmEKALQNMKELGIdnRVVLINHNLLT-PFTIeTKFDLAM 120
                                       8**************9999*********998876665444444444444436555555555554.8876269***** PP

                                       EES-CCC-.CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  67 ssevlhhv.edpekalkeiaRvLkpgGllv 95 
                                       s+ v+h++ +++ +a +++  +L  g +++
  gi|518652149|ref|YP_008141669.1| 121 SNLVFHNLgKNRFRAYDNVIECLNGGAYFI 150
                                       ***********************9999987 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.4e-09   2.1e-06      28     122 ..      37     140 ..      26     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.4e-09
                                       HCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEES.BHHHH.....HHHHHHHHHTTGC..EEEEE-STTTTST.T CS
                               MTS  28 pkelsgkvlDlGcGaGvlgaalakespeaevtlvdv.darAl.....esakenleankle..vevvasdvleeve.e 95 
                                       p++++ ++lD GcG G++   +ak+ p a++t +d+ ++ +l     e a +n+++ +++  v ++++++l  ++ e
  gi|518652149|ref|YP_008141669.1|  37 PATQKINILDAGCGLGFMVSIAAKHFPYASITGIDIfNHDSLsgssmEKALQNMKELGIDnrVVLINHNLLTPFTiE 113
                                       3347778**************************99765555511100555666666666688888999999999889 PP

                                       S-EEEEEE---STTTCHCHHHHHHHHH CS
                               MTS  96 kkfdlivsNPPfhagkatelavaeeli 122
                                        kfdl +sN  fh+  + + ++ +++i
  gi|518652149|ref|YP_008141669.1| 114 TKFDLAMSNLVFHNLGKNRFRAYDNVI 140
                                       *************99888877777666 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   2.4e-08   3.6e-05     154     268 ..      31     161 ..       4     183 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.4e-08
                              PrmA 154 alekl..vkegeevlDvGtGSG.iLaiaaakLgakkvvavDi...Dev...AvkvakeNaelNkveaklevalseel 221
                                       +l++l    ++ ++lD G+G G + +iaa+ +  ++++++Di   D++   +++ a +N++  ++++++ v ++++l
  gi|518652149|ref|YP_008141669.1|  31 VLDTLypATQKINILDAGCGLGfMVSIAAKHFPYASITGIDIfnhDSLsgsSMEKALQNMKELGIDNRV-VLINHNL 106
                                       44444333344599********446****************8655444222688899999999999999.5455666 PP

                              PrmA 222 lk....eekadvivaNILaevl....ielaedikklvkeggllilSGilkekaee 268
                                       l+    e+k+d+ ++N + + l     + ++++ ++++ g+++il  +l e++ +
  gi|518652149|ref|YP_008141669.1| 107 LTpftiETKFDLAMSNLVFHNLgknrFRAYDNVIECLNGGAYFILIDLLPEQSID 161
                                       64455689*********98888443346789999999999999999888888655 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.2e-06    0.0032      14      75 ..      29      88 ..      20     117 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.2e-06
                   Methyltransf_32 14 akllkelakesgaltvvDvGaGkgYLsfvlalkeke.yklkvvgidakeelvekaekraeklg 75
                                      +++l++l  ++++++++D+G+G g++ ++ a    +    +++gid+ ++ + + + ++++l+
  gi|518652149|ref|YP_008141669.1| 29 NQVLDTLYPATQKINILDAGCGLGFMVSIAAK---HfPYASITGIDIFNHDSLSGSSMEKALQ 88
                                      556666677899****************9999...436789*****99998888888888887 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   2.5e-06    0.0038      49     153 ..      26     141 ..      11     162 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.5e-06
                                       HHHHHHHTTTT.--TT-EEEEES-TTSHHHHHHHHHH-.-EEEEE......ES-HHHHHHHHHHHHTS-SSS-EEE. CS
                              CMAS  49 aKldlilekle.lkpGmtlLdiGcGWGslvrraveryd.vkvvgl......TlSkeqaklakkrvdeldlerkvev. 116
                                       +K++ +l+ l    +  ++Ld GcG G +v  a++++  +++ g+       lS   +++a ++++el+++++v + 
  gi|518652149|ref|YP_008141669.1|  26 EKMNQVLDTLYpATQKINILDAGCGLGFMVSIAAKHFPyASITGIdifnhdSLSGSSMEKALQNMKELGIDNRVVLi 102
                                       6667777766524456689*****************96378889933444446777788888888888877766441 PP

                                       ..EES-GGG-----SEEEEES-GGGTSGGGHHHHHHHHH CS
                              CMAS 117 ..klldyedldekvdrvvsvgafehvgkenydtffkklk 153
                                         +ll    ++ k+d   s  +f  +gk+++ ++ ++++
  gi|518652149|ref|YP_008141669.1| 103 nhNLLTPFTIETKFDLAMSNLVFHNLGKNRFRAYDNVIE 141
                                       112222335667********************9977654 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   1.2e-05     0.018       3      61 ..      42     107 ..      40     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-H......HHHHHHHHHHHHCTTSS.EEEEES-CC CS
                    Methyltransf_4   3 pvvleiGcGkGeflvalAkknPdknflGiEirv......kvvakvlkkiealelkN.lrilrgdal 61 
                                         +l+ GcG G +++  Ak++P  ++ Gi+i +      ++++k+l+++++l++ N + +++++ l
  gi|518652149|ref|YP_008141669.1|  42 INILDAGCGLGFMVSIAAKHFPYASITGIDIFNhdslsgSSMEKALQNMKELGIDNrVVLINHNLL 107
                                       5689**************************987222222467889999999999984555566654 PP

>> Helveticin_J  Bacteriocin helveticin-J
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     2e-05     0.029     169     244 ..      27     104 ..      24     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                      Helveticin_J 169 evNkkLDeaetssvnvniaklkclkafkisnfnevqpikSvQGydldnkkniYiss..qnsltsgkegeareivkip 243
                                       ++N+ LD     + ++ni +  c   f +s   +  p  S+ G+d+ n+  +  ss  +  +++++ g ++++v i 
  gi|518652149|ref|YP_008141669.1|  27 KMNQVLDTLYPATQKINILDAGCGLGFMVSIAAKHFPYASITGIDIFNHDSLSGSSmeKALQNMKELGIDNRVVLIN 103
                                       79********999******************************************9887888999999999999887 PP

                      Helveticin_J 244 w 244
                                        
  gi|518652149|ref|YP_008141669.1| 104 H 104
                                       5 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05      0.04      28     100 ..      25      97 ..      21     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                                       HHHHHHHHHHTT--TT-E.EEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHHHHTTB-- CS
                              DOT1  28 peflsevldkvnlkkedv.FvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrlklfGkkl 100
                                        e +++vld +    +++  +D G G+G +v  aa ++  +  +G++i ++ s    ++++ l+  +k +G+++
  gi|518652149|ref|YP_008141669.1|  25 KEKMNQVLDTLYPATQKInILDAGCGLGFMVSIAAKHFPYASITGIDIFNHDSLSGSSMEKALQ-NMKELGIDN 97 
                                       567788888887666665268*****************************99977777776665.567777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1389.36
//
Query:       gi|518652150|ref|YP_008141670.1|  [L=408]
Description: hypothetical protein FACI_IFERC00001G0789 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-46  157.0  31.4    5.8e-46  157.0  31.4    1.7  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.51   10.6   6.8       0.64   10.2   4.7    2.3  2  DUF3270   Protein of unknown function (DUF3270)


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 !  157.0  31.4   6.5e-50   5.8e-46       5     353 .]       9     370 ..       6     370 .. 0.91
   2 !    4.5   2.1    0.0016        14     131     170 ..     363     403 ..     363     407 .. 0.84

  Alignments for each domain:
  == domain 1  score: 157.0 bits;  conditional E-value: 6.5e-50
                             MFS_1   5 aflsalarsilgpalplalaedlgispse....igllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++++l+r +l+ a++  +  d g+ +s+    +g++ +l+++++a+ ++++   ++++G r+++ ++++++++  +
  gi|518652150|ref|YP_008141670.1|   9 YVINFLDRVNLSYAISAGMFPDIGVPKSSadliAGIASALFFVAYAIPQVFTTLRINKVGVRKIFGIAFTAWGII-T 84 
                                       7899999********99999****9999966667778888***********************************.7 PP

                             MFS_1  78 lll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg...lla.sslg 149
                                       +++ f+++++ +++lr++ Gl+++ ++++++ ++  wf ++erg a+++++a++ ++ i+g ll+g    ++ ++ g
  gi|518652150|ref|YP_008141670.1|  85 IITgFVQNVPEIYALRFILGLAEAPFYAGVMFFMGVWFVESERGVANAFFNAAIPVAGIFGGLLSGeifTVYhDNPG 161
                                       777699************************************************************65533336666 PP

                             MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeee..........kgtgpaplvpawkallkdpvlw.illia 215
                                       Wr++f+i +i++l+++v+  l+++ ++ +++ k   ++e          +++ +a  +p wk+ l  p +  + l+ 
  gi|518652150|ref|YP_008141670.1| 162 WRYLFIIEGILALISVVI--LWIVLTDFPSQAKWMNKDEinalesdldiEQKNKALKIP-WKKALMEPDVIlLTLVY 235
                                       ***************776..9999999999999999999999******99999999999.********884133444 PP

                             MFS_1 216 lllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalgla 292
                                       ++++ ++++g++++lp+++ +  + + + ++++l+ ++++v+ai+ +++ r+sdr g   r  l+ +++++a++gla
  gi|518652150|ref|YP_008141670.1| 236 FFGV-TALYGYSIWLPSIIGSFAHVN-AASSSFLSDIPYIVAAIALIFILRYSDRKGD--RKKLTAIIFFIAFIGLA 308
                                       4444.47777********99999999.8***************************666..99999999999999999 PP

                             MFS_1 293 llavtssavllllvlvliGf.glgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       + a++ s+v + +++++i+  g +++ p ++++ ++++ +e +++ +gl+n +g+lgga+gp
  gi|518652150|ref|YP_008141670.1| 309 ISAFSISNVYVSFAFFTISAiGIFTFLPVFWNIPQESLTKESSAASIGLINGLGNLGGAVGP 370
                                       999999999999999999999****************************************8 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.0016
                             MFS_1 131 slGailgpllgglla.sslgWravfyilaivsllafvlfll 170
                                       +lG ++gp++ g l     ++ a  y +a+++l+a++l+l+
  gi|518652150|ref|YP_008141670.1| 363 NLGGAVGPIVVGGLEtVTHSFVAGVYGMALFALVAGILVLF 403
                                       6899***9999988867888*****************8444 PP

>> DUF3270  Protein of unknown function (DUF3270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0      0.85   7.6e+03      39      45 ..     233     239 ..     201     268 .. 0.61
   2 ?   10.2   4.7   7.1e-05      0.64      26      71 ..     285     335 ..     281     341 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 0.85
                           DUF3270  39 LlFFari 45 
                                       L++F  +
  gi|518652150|ref|YP_008141670.1| 233 LVYFFGV 239
                                       3333322 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 7.1e-05
                           DUF3270  26 fqelnensaklkeLlFFa.....riAvFsvitvlvsfillalklatllAfl 71 
                                       + + + +++kl  ++FF+      i+ Fs++ v vsf + +++   ++ fl
  gi|518652150|ref|YP_008141670.1| 285 YSDRKGDRKKLTAIIFFIafiglAISAFSISNVYVSFAFFTISAIGIFTFL 335
                                       556667899********733333699**************99877777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2876.73
//
Query:       gi|518652151|ref|YP_008141671.1|  [L=187]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-12   48.2   0.0    1.8e-12   47.6   0.0    1.3  1  DDE_Tnp_1_5  Transposase DDE domain
     0.0063   16.2   0.2      0.011   15.4   0.2    1.4  1  DDE_Tnp_1    Transposase DDE domain
     0.0065   16.5   0.1      0.025   14.6   0.0    2.0  2  La           La domain
  ------ inclusion threshold ------
      0.081   13.5   0.1       0.14   12.7   0.1    1.4  1  Mga          Mga helix-turn-helix domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.6   0.0     4e-16   1.8e-12      19     110 ..      51     138 ..      37     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.6 bits;  conditional E-value: 4e-16
                       DDE_Tnp_1_5  19 kekkkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsrraktlevkipvkrks 95 
                                        e++++gk g+p++ +da i  +  ++ +f++p+R l+G+++sl  +a++  +   ys + rr ++++ ++   ++ 
  gi|518652151|ref|YP_008141671.1|  51 LEENNSGKIGHPYKVPDALIMYLARLRSIFNIPFRTLEGMLRSLAIIANI--KSISYSEIFRRIRRIKPELNNINS- 124
                                       3567889****************************************999..8899***********999955444. PP

                       DDE_Tnp_1_5  96 kglhlvvdstGlkvl 110
                                         l  ++dstG k++
  gi|518652151|ref|YP_008141671.1| 125 -KLDCIIDSTGYKIT 138
                                       .49**********86 PP

>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.5e-06     0.011       7      60 ..     128     180 ..     122     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvh 60 
                                        i+D+t  +++  + + r+++ ++ +k ++klh++++++  ++ls+ it+  +h
  gi|518652151|ref|YP_008141671.1| 128 CIIDSTGYKITIRGDYLRHKWHRK-RKGWIKLHVIISLKDVTVLSFTITDEHTH 180
                                       699999999988887777766655.59**********************99887 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.7   3.1e+03      40      47 ..     109     116 ..      88     126 .. 0.59
   2 !   14.6   0.0   5.6e-06     0.025      18      48 ..     142     172 ..     139     179 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.7
                                       SSHHHHHH CS
                                La  40 fkrmkklt 47 
                                       f+r+++++
  gi|518652151|ref|YP_008141671.1| 109 FRRIRRIK 116
                                       55555554 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.6e-06
                                       HHHHHHHTTSTTS---HHHHHTSSHHHHHHS CS
                                La  18 kFLrkkmdkdpegwVplsliasfkrmkkltk 48 
                                       ++Lr k  ++ +gw++l++i+s k +  l+ 
  gi|518652151|ref|YP_008141671.1| 142 DYLRHKWHRKRKGWIKLHVIISLKDVTVLSF 172
                                       79******999**************998775 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.2e-05      0.14      35      75 ..      96     142 ..      67     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                                       HHHHHCT--HHHHHHHHHHHHHHCHCCT-EE......ETTCCEEES- CS
                               Mga  35 elaqelyiSestlkrkikelnklLkefdlel......tkknlklrGd 75 
                                        +a+   iS+s ++r i+++++ L++++ +l      t +++++rGd
  gi|518652151|ref|YP_008141671.1|  96 IIANIKSISYSEIFRRIRRIKPELNNINSKLdciidsTGYKITIRGD 142
                                       5677778********************99998888888888888886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1283.58
//
Query:       gi|518652152|ref|YP_008141672.1|  [L=89]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-10   40.5   0.0    3.7e-10   40.0   0.0    1.3  1  HTH_Tnp_1    Transposase
    6.6e-06   26.0   0.0    1.2e-05   25.2   0.0    1.5  2  HTH_29       Winged helix-turn helix
    0.00045   20.3   0.0    0.00074   19.6   0.0    1.4  1  HTH_28       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.027   14.6   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.039   13.7   0.0      0.057   13.2   0.0    1.4  1  HTH_23       Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     1e-13   3.7e-10       6      74 ..       3      71 ..       1      72 [. 0.83

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1e-13
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspaefeltaleeenrelkrel 74
                                      ++++ +K++iV es  +  +++e++rrhgvs + +ykWr ++  +g +    + +    e+e+ +lkr++
  gi|518652152|ref|YP_008141672.1|  3 KFTADEKVAIVMES-FTANNIAELCRRHGVSVSNFYKWRDKFIeSGKKGFYGSGVNNGYEKEIDKLKRLV 71
                                      8*************.66789*********************97666666666666677788888888875 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.3e-09   1.2e-05      11      55 ..      19      63 ..       9      69 .. 0.85
   2 ?   -2.4   0.0       1.4     5e+03      41      52 ..      78      89 .]      74      89 .] 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-09
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn 55
                                      +  +++++++++g+s + +y+w++ f e G ++    + ++g  ++
  gi|518652152|ref|YP_008141672.1| 19 AN-NIAELCRRHGVSVSNFYKWRDKFIESGKKGFYGsGVNNGYEKE 63
                                      45.8*****************************9998888887766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                            HTH_29 41 laalldrrrsgr 52
                                      ++ l++++r++r
  gi|518652152|ref|YP_008141672.1| 78 IDELKKNYRGRR 89
                                      667888888654 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00074      13      42 ..      20      49 ..       8      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegGia 42
                                      ++++e++r++g+s +  y+W+ ++ e G  
  gi|518652152|ref|YP_008141672.1| 20 NNIAELCRRHGVSVSNFYKWRDKFIESGKK 49
                                      589*********************999965 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 ?   14.6   0.0   7.6e-06     0.027      20      52 ..      13      43 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.6e-06
                                      HHHHH--S-HHHHHHHHTS-HHHHHHHHH-HHH CS
                       HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWkkkkeF 52
                                      v + +    ++e+++  gvs s +ykW++k  F
  gi|518652152|ref|YP_008141672.1| 13 VMESFTANNIAELCRRHGVSVSNFYKWRDK--F 43
                                      55678888999*****************86..5 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.057      20      45 ..      22      47 ..       6      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                      ++e +r++gvs +  y+w+ ++ e+G
  gi|518652152|ref|YP_008141672.1| 22 IAELCRRHGVSVSNFYKWRDKFIESG 47
                                      7899******************6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 659.77
//
Query:       gi|518652153|ref|YP_008141673.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G0792 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-18   65.9   0.0    6.2e-18   65.1   0.0    1.4  1  rve            Integrase core domain
    2.5e-17   62.4   0.2    8.3e-17   60.7   0.2    2.0  1  rve_3          Integrase core domain
    5.8e-12   45.6   0.6    1.6e-11   44.1   0.6    1.7  1  HTH_21         HTH-like domain
     0.0001   22.4   2.4    0.00018   21.6   0.9    2.3  3  rve_2          Integrase core domain
      0.006   16.8   0.1      0.016   15.4   0.1    1.8  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   15.1   0.6      0.062   13.9   0.6    1.6  1  HTH_32         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   2.1e-21   6.2e-18       5     118 ..     113     227 ..     109     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.1e-21
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve...pervlsDngsey 78 
                                       ++lw++D+ +vr  + +g +yl +v d+fs++ l +  s+  +a+++++ +e a+a + +      +++++Dng++y
  gi|518652153|ref|YP_008141673.1| 113 NQLWETDIHYVR--THNGMCYLMAVKDCFSKRWLSYNFSRACTAKDCVKPIEDAYAIRYKDSnlnNLVLRTDNGPQY 187
                                       99**********..66667***************************************99999************** PP

                               rve  79 tskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++++f++ ++ l+i +++  ++ p+dnG +E+fh  lk++
  gi|518652153|ref|YP_008141673.1| 188 IAREFKTPARLLNIPHEYIEKQTPEDNGDIESFHNSLKTD 227
                                       *************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.2   2.8e-20   8.3e-17       3      67 .]     201     265 ..     199     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 2.8e-20
                             rve_3   3 ielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLgykTP 67 
                                       i ++yi+  +P +Ng +Esf+++l++ ++  +  +s ++a+e++e ++ dYN+ RPHss+gy+TP
  gi|518652153|ref|YP_008141673.1| 201 IPHEYIEKQTPEDNGDIESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRPHSSIGYLTP 265
                                       7799************************************************************9 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.6   5.4e-15   1.6e-11      17      59 ..      56      97 ..      43      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.4e-15
                            HTH_21 17 skgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59
                                      ++ +YG+rriwa Lr+e gv++n k+VrR+ + ++L+ ++ + 
  gi|518652153|ref|YP_008141673.1| 56 KRVTYGHRRIWAVLRNE-GVKINIKTVRRIIKSNNLQLPYAKH 97
                                      3469*************.789***************9999875 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.4     1e+04      17      32 ..     192     207 ..     188     207 .. 0.74
   2 !   21.6   0.9   6.1e-08   0.00018       1      50 [.     218     271 ..     218     272 .. 0.90
   3 ?   -2.4   0.0       1.9   5.5e+03      43      52 .]     274     283 ..     273     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.4
                             rve_2  17 fktleeleaaiedYIe 32 
                                       fkt + l    ++YIe
  gi|518652153|ref|YP_008141673.1| 192 FKTPARLLNIPHEYIE 207
                                       7777777777789996 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6.1e-08
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIewYNnkR....lkglsPvqYrnq 50 
                                       Esf  sLKt+ +     ++ e +++ ie   + YNn R    +++l+Pv++++q
  gi|518652153|ref|YP_008141673.1| 218 ESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRphssIGYLTPVEFEKQ 271
                                       9**************9***99998887666778*****888888********98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                             rve_2  43 sPvqYrnqsL 52 
                                       s+ ++rn+ L
  gi|518652153|ref|YP_008141673.1| 274 SSEEFRNKFL 283
                                       7899***976 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.5e-06     0.016       3     139 ..     115     257 ..     113     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                     DDE_Tnp_IS240   3 swrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrka..lkkek..lepeeivtDkasayasal 74 
                                        w+ D  yv+ +   +Yl ++ D  ++  l + +s    +k + + ++ a  ++ ++  l++ ++ tD  + y   +
  gi|518652153|ref|YP_008141673.1| 115 LWETDIHYVRTHNGMCYLMAVKDCFSKrWLSYNFSRACTAKDCVKPIEDAyaIRYKDsnLNNLVLRTDNGPQYI--A 189
                                       588888899999999999999999888899999999999999999998762244444559999999*9999884..4 PP

                     DDE_Tnp_IS240  75 kelkregelf...devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                       +e+k   +l+   +e  + q++  n  iEs h+ lK  +   + ++s + a++ ++     +n +++h
  gi|518652153|ref|YP_008141673.1| 190 REFKTPARLLnipHEYIEKQTPEDNGDIESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRPH 257
                                       555554433323366667788999*******************************9888777777777 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.1e-05     0.062      23      73 .]      36      85 ..      15      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                            HTH_32 23 rgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      r r++++++    +++++  ++ +++ r++ a l + egvk+   tv+ri+
  gi|518652153|ref|YP_008141673.1| 36 RHRKSRIPENIINKVLEISGKRVTYGHRRIWAVL-RNEGVKINIKTVRRII 85
                                      236669*************55559**********.9999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2086.16
//
Query:       gi|518652154|ref|YP_008141674.1|  [L=116]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.2e-07   29.1   1.4    9.1e-07   28.7   1.4    1.2  1  DDE_Tnp_1  Transposase DDE domain
     0.0033   16.9   0.1      0.004   16.6   0.1    1.2  1  PhoH       PhoH-like protein


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   1.4     1e-10   9.1e-07      79     213 ..       7     107 ..       2     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1e-10
                         DDE_Tnp_1  79 lvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvt 155
                                       ++++D+GY+  +++  +   g++ +i+++kn+ ++++   s+ r ++ + ++++ ++++++ +              
  gi|518652154|ref|YP_008141674.1|   7 RIFGDRGYD-SKYIYNMF--GYNAVIPPRKNASTKSR--GSYARAKIVRFIKKNSMEQWKENNS------------- 65 
                                       79******9.77777777..7***********99976..4455677777777777777776555............. PP

                         DDE_Tnp_1 156 ntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                                      y++Rw +E  F+ lkr++  +  ++++ + + ++l l+   +n
  gi|518652154|ref|YP_008141674.1|  66 ---------------YSKRWIVEIYFSGLKRVMT-EIIKAKKIEYIIQELALKVVNYN 107
                                       ...............5***************765.66666666666666666666665 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   4.5e-07     0.004      76     117 ..      72     113 ..      44     115 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.5e-07
                                       --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                              PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                       v++y++ l   ++++++a+k+e+++++  ++v++ + mRG T
  gi|518652154|ref|YP_008141674.1|  72 VEIYFSGLKRVMTEIIKAKKIEYIIQELALKVVNYNIMRGMT 113
                                       789*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 814.10
//
Query:       gi|518652155|ref|YP_008141675.1|  [L=56]
Description: hypothetical protein FACI_IFERC00001G0794 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0089   16.5   0.0       0.01   16.3   0.0    1.1  1  Inhibitor_G39P  Loader and inhibitor of phage G40P


Domain annotation for each model (and alignments):
>> Inhibitor_G39P  Loader and inhibitor of phage G40P
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.8e-07      0.01       7      46 ..       4      42 ..       2      55 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.8e-07
                    Inhibitor_G39P  7 ikiLavlkaaYPrfyngrskkenkmvvevWadllkdydyk 46
                                      +++L ++   YP+f   rs  e+++v +  ad+l++ d+ 
  gi|518652155|ref|YP_008141675.1|  4 TELLDTVYSRYPKF-TKRSTFEKEVVDKYFADFLEENDIT 42
                                      7899999*******.99*****99999*********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 395.16
//
Query:       gi|518652156|ref|YP_008141676.1|  [L=65]
Description: hypothetical protein FACI_IFERC00001G0795 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-12   48.3   5.9    1.5e-12   48.1   5.9    1.1  1  VAPB_antitox  Putative antitoxin


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   5.9   8.1e-17   1.5e-12       1      57 [.       3      61 ..       3      65 .] 0.78

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 8.1e-17
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgil...seeea.dei 57
                                      KtI+I+ +vY+kL  +K+e+eSFs++++rL+++++  k + ll l+ ++    +e++ +e+
  gi|518652156|ref|YP_008141676.1|  3 KTITIKKSVYDKLIGFKKENESFSELLDRLIKSQS--KYELLLSLRQSVeleGKEDLlKEV 61
                                      9******************************8555..678899999998333222322333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 442.99
//
Query:       gi|518652157|ref|YP_008141677.1|  [L=103]
Description: virulence-associated protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-07   30.5   0.0    8.5e-07   29.5   0.0    1.5  1  PIN       PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   4.7e-11   8.5e-07      23     117 ..       3      91 ..       1      94 [. 0.74

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 4.7e-11
                                       HHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHHHHHHHHHHHHHHH..SBHHHHH CS
                               PIN  23 klleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidaeiaeeaaeialkyg..llpnDal 96 
                                       k++++ e+ +ts++ l E+ly++++      ++++ ++++++   + +  ++  ++ +e ++ ++  g  +   D +
  gi|518652157|ref|YP_008141677.1|   3 KIIDSGEDYCTSSINLHEVLYGIKK------YSKDSKLVMQIpVLGYSKSDTELSVDLELSAERS--GkaIPRMDVI 71 
                                       789999*******************......6666666666644444444444444444444444..355999**** PP

                                       HHHHHHHHT-EEE.ESSTHHH CS
                               PIN  97 iaAtAkehgikliatfDedfr 117
                                       iaA A+ +g++l  t D++f+
  gi|518652157|ref|YP_008141677.1|  72 IAAIAINNGCSLY-TLDNHFE 91 
                                       **********766.*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 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:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 674.29
//
Query:       gi|518652158|ref|YP_008141678.1|  [L=131]
Description: hypothetical protein FACI_IFERC00001G0797 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.43   10.1   6.8       0.33   10.5   5.5    1.4  1  PMT_4TMC   C-terminal four TMM region of protein-O-mannosyltr
        8.2    4.6  10.7        9.1    4.4  10.7    1.0  1  DUF2070    Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> PMT_4TMC  C-terminal four TMM region of protein-O-mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   5.5   3.7e-05      0.33      95     175 ..       6      92 ..       1     100 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 3.7e-05
                          PMT_4TMC  95 llnsglflllgwalhylPfflmgRvlflhhYlpAl......lfailllaalldfllkslkkslkkkklvklivvvvl 165
                                        + s+lf++ g al yl  fl +   +  h++ Al      +f++ ++++ +  ++++ + +l ++ +++l++ ++l
  gi|518652158|ref|YP_008141678.1|   6 TYKSLLFYVGGLALLYLSIFLSNNLKYNGHFISALpivlplVFSMAFIGVAVILIMEKDSPWLFRTGIMSLVIGITL 82 
                                       578899**************************9954444449**************999999988888888888888 PP

                          PMT_4TMC 166 lvlviavFif 175
                                       +++ i++F++
  gi|518652158|ref|YP_008141678.1|  83 FLFGILTFYM 92 
                                       7777777775 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4  10.7     0.001       9.1      14     117 ..       6     114 ..       1     128 [. 0.53

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.001
                           DUF2070  14 wkvsllliillalligllaflssk..lfgillfglpalvaflltlpvlrilggrltykrs..lflalltelivviis 86 
                                       ++ sll+ +   +l+ l  fls++  ++g ++  lp+++ +++   ++ ++ + +  k s  lf   ++ l++ i++
  gi|518652158|ref|YP_008141678.1|   6 TYKSLLFYVGGLALLYLSIFLSNNlkYNGHFISALPIVLPLVFSMAFIGVAVILIMEKDSpwLFRTGIMSLVIGITL 82 
                                       56677777777777666677777788888888888888888777777777655533333344444444444444443 PP

                           DUF2070  87 llaillsall.qalvllalvlslalvfalrll 117
                                       +l  +l++++  ++++ a  ++l + f+l  +
  gi|518652158|ref|YP_008141678.1|  83 FLFGILTFYMgVKSLVWAGSFALGILFILGAM 114
                                       33333333333333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); 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):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 926.52
//
Query:       gi|518652159|ref|YP_008141679.1|  [L=318]
Description: hypothetical protein FACI_IFERC00001G0798 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-17   63.0   0.2    5.7e-17   61.9   0.2    1.6  1  Rep_fac_C        Replication factor C C-terminal domain
    1.3e-13   51.5   0.0    2.7e-13   50.5   0.0    1.5  1  AAA              ATPase family associated with various cellul
    2.6e-12   46.8   0.0    1.1e-08   35.1   0.0    2.4  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.8e-06   28.2   0.1      1e-05   25.8   0.0    2.3  2  AAA_assoc_2      AAA C-terminal domain
      2e-05   24.7   0.0     0.0014   18.7   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
    0.00098   19.1   0.0     0.0022   17.9   0.0    1.6  1  Rad17            Rad17 P-loop domain
      0.001   18.9   0.2     0.0023   17.7   0.0    1.7  2  DNA_pol3_delta   DNA polymerase III, delta subunit
     0.0016   18.2   0.0     0.0061   16.3   0.0    2.0  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0018   18.3   0.0     0.0036   17.3   0.0    1.5  1  AAA_14           AAA domain
     0.0026   17.5   0.1      0.017   14.8   0.0    2.0  2  AAA_24           AAA domain
     0.0029   16.9   0.0       0.03   13.5   0.0    2.1  2  TIP49            TIP49 P-loop domain
     0.0047   17.5   0.3       0.25   11.9   0.0    2.6  2  AAA_18           AAA domain
     0.0057   16.4   0.0      0.012   15.4   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein
  ------ inclusion threshold ------
      0.011   16.1   0.3          3    8.1   0.0    2.3  2  AAA_22           AAA domain
      0.012   15.0   0.0       0.62    9.4   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.012   16.0   0.0       0.49   10.8   0.0    2.4  2  AAA_16           AAA ATPase domain
      0.014   14.8   0.0      0.051   13.0   0.0    1.9  2  PhoH             PhoH-like protein
      0.016   15.3   0.0      0.032   14.4   0.0    1.5  1  AAA_2            AAA domain (Cdc48 subfamily)
      0.022   14.3   0.0      0.045   13.3   0.0    1.5  1  AAA_25           AAA domain
      0.024   15.2   1.1      0.069   13.7   1.1    1.9  1  AAA_23           AAA domain
      0.031   13.8   0.0      0.053   13.0   0.0    1.3  1  AAA_7            P-loop containing dynein motor region
      0.083   12.9   0.1        0.9    9.5   0.1    2.3  1  AAA_5            AAA domain (dynein-related subfamily)


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 !   61.9   0.2     7e-20   5.7e-17       4      88 .]     226     309 ..     223     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 7e-20
                                       HHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS..S-HHHHHHHHHHHHHHHHHHHCTH-HHH CS
                         Rep_fac_C   4 teieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeqeelpeaqkleilellgeiekrlveGasehl 80 
                                       +e +++++ + +g+f++a++ l++ l+++G+s+ di++ +h  +  + ++  +qklei++ l+e+e+r+veG+++++
  gi|518652159|ref|YP_008141679.1| 226 DEYKNLINMAIEGNFNDARNYLDKMLIDYGLSGIDIIKGMHSSIRGE-QIAYKQKLEIIMALAEAEFRIVEGGTDNI 301
                                       678899999989*********************************95.7**************************** PP

                                       HHHHHHHH CS
                         Rep_fac_C  81 qlsallar 88 
                                       q+ alla+
  gi|518652159|ref|YP_008141679.1| 302 QMDALLAK 309
                                       ******96 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 !   50.5   0.0   3.4e-16   2.7e-13       2     126 ..      40     153 ..      39     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 3.4e-16
                                       EEESSTTSSHHHHHHHHHHHH.....THEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHH CS
                               AAA   2 llyGppGtGKTllakavakel.....gvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidala 71 
                                       ++ Gp GtGKT++a a+a +l     + +f+e+++s+ +   +    ++i+++ k  + ++  + +i+f+DE+d l+
  gi|518652159|ref|YP_008141679.1|  40 IFAGPQGTGKTSTAIALAISLfgdswKENFMELNASNDR--GIDIIRDNIKNFAKI-RPSNdlGFKIIFLDEADHLT 113
                                       899*****************87666689***********..777778888777755.55555777***********9 PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSE CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdr 126
                                       ++            +++L + ++ + +   ++ +i  +n+ +k+ p++  +R+ +
  gi|518652159|ref|YP_008141679.1| 114 GDA-----------QAALRRTMEMFYN---TTRFIFSCNYSSKIIPPIQ-SRCVV 153
                                       999...........***********99...589****************.99965 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 !    9.8   0.0    0.0008      0.65       6      49 ..      24      66 ..      19      77 .. 0.81
   2 !   35.1   0.0   1.3e-11   1.1e-08      84     162 ..      79     159 ..      66     160 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0008
                   DNA_pol3_delta2  6 lkilskalksgrlahayLfeGdegigkkelalnlakallceekn 49
                                      ++ l+  +k +++ h ++f+G++g+gk ++a +la +l+ ++ +
  gi|518652159|ref|YP_008141679.1| 24 INRLNAYVKDKNIPH-LIFAGPQGTGKTSTAIALAISLFGDSWK 66
                                      667777777777777.89*****************999987655 PP

  == domain 2  score: 35.1 bits;  conditional E-value: 1.3e-11
                   DNA_pol3_delta2  84 kldqir.elieelsrkpre.skkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelk 158
                                        +d ir +++++++ +p +    kii +++a+++t  A+ al +t+E   + + fi+  + ++k++++i+SRc +l+
  gi|518652159|ref|YP_008141679.1|  79 GIDIIRdNIKNFAKIRPSNdLGFKIIFLDEADHLTGDAQAALRRTMEMFYNTTRFIFSCNYSSKIIPPIQSRCVVLR 155
                                       67889977888888888875789****************************************************** PP

                   DNA_pol3_delta2 159 fspl 162
                                       f+p+
  gi|518652159|ref|YP_008141679.1| 156 FKPI 159
                                       **97 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 ?   -1.6   0.0       4.3   3.5e+03      20      36 ..     113     130 ..     103     134 .. 0.62
   2 !   25.8   0.0   1.2e-08     1e-05       2      49 ..     174     226 ..     173     258 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 4.3
                                       XXXXXXXXX.XXXXXXXX CS
                       AAA_assoc_2  20 dGDaRkaLn.lLElaaea 36 
                                        GDa +aL  ++E+  ++
  gi|518652159|ref|YP_008141679.1| 113 TGDAQAALRrTMEMFYNT 130
                                       467777764245555544 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 1.2e-08
                                       XX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX......XXXXXXXXX CS
                       AAA_assoc_2   2 ekklkleddalealaeladGDaRkaLnlLElaaeaaeak.....egkieitle 49 
                                       +++++++dd l+a+ e++dGD+Rka n+L+++  + + +     e + ei+++
  gi|518652159|ref|YP_008141679.1| 174 KENFEIDDDSLDAIYEISDGDMRKAVNVLQAVKLSGKVSataiyEISGEINRD 226
                                       5789**************************88777665555555333344444 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06    0.0014      12      63 ..      24      75 ..      18      99 .. 0.78
   2 ?    3.5   0.0     0.081        66     131     166 ..      99     136 ..      80     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
                                      HHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESS CS
                            ResIII 12 ienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvpr 63
                                      i++l + +k+k+  +++++ + GtGKT +a++l+ +l+   ++e+f+ l  +
  gi|518652159|ref|YP_008141679.1| 24 INRLNAYVKDKNIPHLIFAGPQGTGKTSTAIALAISLFGDSWKENFMELNAS 75
                                      67788888878888****************************9999866555 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.081
                                       TT-SEEEEETGGGTTS...TTTHHHHHT---SEEEEEE CS
                            ResIII 131 drfdviiiDEaHrlgak..kswreilekfkeavllglT 166
                                         f++i+ DEa +l+++  ++ r+ +e+f + +++ ++
  gi|518652159|ref|YP_008141679.1|  99 LGFKIIFLDEADHLTGDaqAALRRTMEMFYNTTRFIFS 136
                                       46889*********997444888888888877777665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   2.7e-06    0.0022       8      78 ..       4      70 ..       2     112 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                             Rad17  8 lWfekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLs.kelgiklrewln 78
                                       W eky+P k+ ++   k  i+ ++ ++k + +++     L+ +GP G gk+ +   L+   +g + +e+  
  gi|518652159|ref|YP_008141679.1|  4 IWTEKYRPSKLSDVIGEKGNINRLNAYVKDKNIPH-----LIFAGPQGTGKTSTAIALAiSLFGDSWKENFM 70
                                      7***********************99999998886.....599********866555551455777777654 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 !   17.7   0.0   2.9e-06    0.0023      62     173 ..     105     206 ..      66     207 .. 0.86
   2 ?   -2.5   0.1       4.8   3.9e+03     151     171 ..     228     249 ..     221     251 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 2.9e-06
                                       EEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHH CS
                    DNA_pol3_delta  62 vlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkr 138
                                       +l+ +      + l+ + +++L ++++    +t +i+ ++       k++  ++++ +v+++k+ + e +k+ ++++
  gi|518652159|ref|YP_008141679.1| 105 FLDEA------DHLTGDAQAALRRTMEMFYNTTRFIFSCN----YSSKIIPPIQSRCVVLRFKPIDRESMKNRLKDI 171
                                       44444......55677777888888888888888888888....44678888999999******************* PP

                                       HHHTT-EE-HHHHHHHHHHHTT-HHHHHHHHHHHH CS
                    DNA_pol3_delta 139 aqelglkiekealelLlelvennlsaikqelekLa 173
                                       a++++ +i++++l+ ++e + ++++ + + l+ ++
  gi|518652159|ref|YP_008141679.1| 172 AKKENFEIDDDSLDAIYEISDGDMRKAVNVLQAVK 206
                                       *************************9999998766 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.8
                                       HHHHHH.HHTT-HHHHHHHHHH CS
                    DNA_pol3_delta 151 lelLle.lvennlsaikqelek 171
                                        + L+  ++e+n++ + + l+k
  gi|518652159|ref|YP_008141679.1| 228 YKNLINmAIEGNFNDARNYLDK 249
                                       4444441578888888888887 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 !   16.3   0.0   7.5e-06    0.0061       2      57 ..      10      60 ..       9     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.5e-06
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakel 57
                                      rP++l++ ig +   ++l+ ++     +++++ h++++Gp G Gkt+ a  +a  l
  gi|518652159|ref|YP_008141679.1| 10 RPSKLSDVIGEKGNINRLNAYV-----KDKNIPHLIFAGPQGTGKTSTAIALAISL 60
                                      9999999999999999998776.....57899***************998888654 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.4e-06    0.0036       5      97 ..      39     135 ..      35     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.4e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek..lkeekktylflDEiqevp 77 
                                       l+  G+  +GKT  +  l+ +l+    ke+++++n  ++r  ++   +++++ + +    ++ + +++flDE+ +++
  gi|518652159|ref|YP_008141679.1|  39 LIFAGPQGTGKTSTAIALAISLFgdSWKENFMELNASNDRGIDII--RDNIKNFAKIrpSNDLGFKIIFLDEADHLT 113
                                       6789**********9999999998878899999999987776544..33455666643223368899******9886 PP

                            AAA_14  78 .ewekalkslvdeg.knldviv 97 
                                        +++ al++ ++   +  ++i+
  gi|518652159|ref|YP_008141679.1| 114 gDAQAALRRTMEMFyNTTRFIF 135
                                       2699999999997644556665 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   2.1e-05     0.017       7      88 ..      41     123 ..      37     136 .. 0.68
   2 ?   -0.1   0.1      0.77   6.3e+02      90     142 ..     173     228 ..     161     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                            AAA_24   7 iyGpsgiGKTtlakelgpkplfidtek.Glksldadkfpdieswedfldevvel....aaeladyktlviDtidele 78 
                                         Gp+g+GKT++a  l    lf d  k  + +l+a +   i   + ++d ++ +    + ++ ++k++++D +d+l 
  gi|518652159|ref|YP_008141679.1|  41 FAGPQGTGKTSTAIAL-AISLFGDSWKeNFMELNASNDRGI---DIIRDNIKNFakirPSNDLGFKIIFLDEADHLT 113
                                       67**************.555555533323444444444433...3333333333333699999*************9 PP

                            AAA_24  79 elclaevirq 88 
                                         + a ++r 
  gi|518652159|ref|YP_008141679.1| 114 GDAQAALRRT 123
                                       9988888765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.77
                            AAA_24  90 ekaeskedkgdgkG.ygelaeefrrllkklqelrk..nvifiahektrkdedpege 142
                                       +k++ + d+ ++ + y     ++r++++ lq+++    v ++a  ++    ++++ 
  gi|518652159|ref|YP_008141679.1| 173 KKENFEIDDDSLDAiYEISDGDMRKAVNVLQAVKLsgKVSATAIYEISGEINRDEY 228
                                       44333445667778888888899999999999888888888888877777766554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0   3.7e-05      0.03      43      87 ..      31      76 ..      23      90 .. 0.78
   2 ?    0.8   0.0      0.27   2.2e+02     194     226 ..     172     207 ..     159     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.7e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXX CS
                             TIP49 43 ikekklaGravLlaGpsgtGktalaiaiskelg...edvpfvalsgse 87
                                      +k+k++    +++aGp+gtGkt+ aia++ +l     +  f+ l++s+
  gi|518652159|ref|YP_008141679.1| 31 VKDKNIP--HLIFAGPQGTGKTSTAIALAISLFgdsWKENFMELNASN 76
                                      7888887..7999********988888887774222456788888875 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.27
                                       SS------...S--------S---S----XXXXXXX CS
                             TIP49 194 arakefDi...ekdefvelPkGevekkkevvqevtL 226
                                       a++++f+i   + d + e+ +G+++k  +v+q v L
  gi|518652159|ref|YP_008141679.1| 172 AKKENFEIdddSLDAIYEISDGDMRKAVNVLQAVKL 207
                                       567778883333456789999999999999999987 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00031      0.25       2      56 ..      40      87 ..      39     130 .. 0.78
   2 ?    2.9   0.4      0.18   1.5e+02      25      69 ..     165     207 ..     149     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                            AAA_18  2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedk 56
                                      + +G++G+GKt+ a +L+ +l      +d +ken ++l   ++  +  ++++++ 
  gi|518652159|ref|YP_008141679.1| 40 IFAGPQGTGKTSTAIALAISL-----FGDSWKENFMELNASND--RGIDIIRDNI 87
                                      679**************9987.....77777777777777777..5555555554 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.18
                            AAA_18  25 gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                         +l+d+ak+++ ++++d    d   ++ ++ + k+++ l++   
  gi|518652159|ref|YP_008141679.1| 165 KNRLKDIAKKENFEIDDDSL--DAIYEISDGDMRKAVNVLQAVKL 207
                                       67899**************9..88888888888888888777655 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 !   15.4   0.0   1.5e-05     0.012      49      85 ..      38      74 ..      22     142 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.5e-05
                         IstB_IS21 49 nivllGpsGvGKshlaialgveavraglsvlfvrved 85
                                       +++ Gp G+GK+  aial+ +   + ++  f+ +++
  gi|518652159|ref|YP_008141679.1| 38 HLIFAGPQGTGKTSTAIALAISLFGDSWKENFMELNA 74
                                      5899*******************99999999998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.021        17       7      22 ..      38      53 ..      32      61 .. 0.84
   2 ?    8.1   0.0    0.0037         3      88     118 ..      98     126 ..      70     142 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                            AAA_22  7 ilvvtGesGtGKTtll 22
                                      +l+  G+ GtGKT ++
  gi|518652159|ref|YP_008141679.1| 38 HLIFAGPQGTGKTSTA 53
                                      78899********987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0037
                            AAA_22  88 aravielliiDEaqhlrseealeeLrsllnl 118
                                       + +  +++ +DEa+hl + +a   Lr+ ++ 
  gi|518652159|ref|YP_008141679.1|  98 DLGF-KIIFLDEADHL-TGDAQAALRRTMEM 126
                                       4444.89*********.65555555544443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00076      0.62      23      58 ..      37      73 ..      13      91 .. 0.72
   2 ?    3.4   0.0     0.052        42     109     132 ..     103     126 ..     100     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00076
                      Mg_chelatase 23 HnlllvGppGsGKtmlakrlp.sllpplseeealeva 58
                                       +l+++Gp G+GKt  a +l+ sl+ +  +e+ +e +
  gi|518652159|ref|YP_008141679.1| 37 PHLIFAGPQGTGKTSTAIALAiSLFGDSWKENFMELN 73
                                      589***********99988862566777777777765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.052
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePled 132
                                       ++fLDE+ +++ ++  +LR+ +e 
  gi|518652159|ref|YP_008141679.1| 103 IIFLDEADHLTGDAQAALRRTMEM 126
                                       79******************9996 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0006      0.49       9      45 ..      24      57 ..      17      79 .. 0.78
   2 ?    2.7   0.0      0.18   1.5e+02     120     159 ..      84     124 ..      66     129 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0006
                            AAA_16  9 leqLlsalervrsgrpelvllsGesGvGKsslvrell 45
                                      +++L++++++      + +++ G++G+GK+s + +l+
  gi|518652159|ref|YP_008141679.1| 24 INRLNAYVKDK---NIPHLIFAGPQGTGKTSTAIALA 57
                                      67777777744...45799************986665 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.18
                            AAA_16 120 lellkrll.allsrderplvlvlDdlqwadeaslqllaaLl 159
                                       ++ +k+++  + s+d    +++lD+++ +  + +++l+ ++
  gi|518652159|ref|YP_008141679.1|  84 RDNIKNFAkIRPSNDLGFKIIFLDEADHLTGDAQAALRRTM 124
                                       56677777666666666689**********99999998776 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.2e-05     0.051      22      46 ..      39      63 ..      23      82 .. 0.82
   2 ?   -1.6   0.0       1.9   1.5e+03     121     133 ..     102     114 ..      85     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.2e-05
                                      EEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 22 vfaiGpaGtGKtylavalavealkk 46
                                      ++ +Gp GtGKt  a+ala++++ +
  gi|518652159|ref|YP_008141679.1| 39 LIFAGPQGTGKTSTAIALAISLFGD 63
                                      5778****************98765 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.9
                                       EEEEE-SGGG--H CS
                              PhoH 121 afvilDEAQnttk 133
                                       ++++lDEA  +t 
  gi|518652159|ref|YP_008141679.1| 102 KIIFLDEADHLTG 114
                                       5678888766654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   3.9e-05     0.032       5      81 ..      38     113 ..      34     124 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.9e-05
                                       -EEEE--TTSSHHHHHHHHHHHTT-.....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGG CS
                             AAA_2   5 silllgptgvGktelakalaellfv.kkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEid 78 
                                        ++++gp+g+Gkt +a ala  lf  + +++++ ++as+         ++   i +   +   ++ G  i++lDE d
  gi|518652159|ref|YP_008141679.1|  38 HLIFAGPQGTGKTSTAIALAISLFGdSWKENFMELNASNDRG----IDIIRDNIKNFAKIRPSNDLGfkIIFLDEAD 110
                                       679*******************99645578899999998888....88888888888888899999999******99 PP

                                       G-- CS
                             AAA_2  79 Kih 81 
                                         +
  gi|518652159|ref|YP_008141679.1| 111 HLT 113
                                       766 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   5.5e-05     0.045      14      64 ..      19      66 ..       8      79 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                            AAA_25 14 dlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwl 64
                                      + + ++ +++ +vk+  +     ++aG++gtGKt  a+ la+++  G++w 
  gi|518652159|ref|YP_008141679.1| 19 GEKGNINRLNAYVKDKNI--PHLIFAGPQGTGKTSTAIALAISLF-GDSWK 66
                                      555556666666664322..25799*****************998.66674 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.1   8.4e-05     0.069      23     167 ..      40     180 ..      34     291 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.4e-05
                            AAA_23  23 lItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkayveltfenkdgrytrsiererelskk 99 
                                       ++ Gp G+GKT+   A+   L+g++ +++  + + ++++ + i   ++ k++++++ +n+ g    +i   +    +
  gi|518652159|ref|YP_008141679.1|  40 IFAGPQGTGKTSTAIALAISLFGDSWKENFMELNASNDRGIDIIR-DNIKNFAKIRPSNDLG---FKI--IFLDEAD 110
                                       789********************8744333322233333333332.3555666666555444...112..1111111 PP

                            AAA_23 100 .kgkttkkaklellei.deleqfisellgskkiilnlilflgqerfeefelkdkkerleelekeleeled 167
                                         +   + a ++ +e+  ++++fi +   s+kii ++ + +   rf+++++++ k+rl+++ k+ + + d
  gi|518652159|ref|YP_008141679.1| 111 hLTGDAQAALRRTMEMfYNTTRFIFSCNYSSKIIPPIQSRCVVLRFKPIDRESMKNRLKDIAKKENFEID 180
                                       0111122222222222433333333332233344455555555555555555555555555555444443 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-05     0.053      35      73 ..      38      76 ..      25     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
                             AAA_7 35 pvllvGptGtGKtviikdllkkldkekylsltinfsaqt 73
                                      ++++ Gp+GtGKt+++  l  +l  ++++ ++++++a+ 
  gi|518652159|ref|YP_008141679.1| 38 HLIFAGPQGTGKTSTAIALAISLFGDSWKENFMELNASN 76
                                      7899**************88888889**99999999865 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 ?    9.5   0.1    0.0011       0.9       1      33 [.      38      71 ..      38     132 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                                      EEEEE--SSSSHHHHHHHGGGGB.S--EEEEE-- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal.nreveyvqlt 33
                                      +++  Gp+GtgK++ a  la  l ++++ +  + 
  gi|518652159|ref|YP_008141679.1| 38 HLIFAGPQGTGKTSTAIALAISLfGDSWKENFME 71
                                      68999**********9999877775544444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 1991.42
//
Query:       gi|518652160|ref|YP_008141680.1|  [L=59]
Description: hypothetical protein FACI_IFERC00001G0799 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 433.23
//
Query:       gi|518652161|ref|YP_008141681.1|  [L=78]
Description: hypothetical protein FACI_IFERC00001G0800 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.1      0.035   14.3   0.1    1.2  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 ?   14.3   0.1   1.9e-06     0.035       3      50 ..      18      66 ..      16      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.9e-06
                                      BX-STTTTHHHHHS-------.------THHHHHHHHHHHTTSSS--SS CS
                     Ribosomal_S30  3 hGsLarAGKVrnqTPKveKqe.kkKkptGRakkRlqYnrRfvnvvvggk 50
                                      + s+ + G  +n  + +++    kK+ tG++ kR+ +n R   ++ +  
  gi|518652161|ref|YP_008141681.1| 18 RESIEKYGSTKNMSKIINQRLgNKKSDTGKSGKRITFNVREDLASLDAD 66
                                      55777778888888888888559****************9877555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       755  (0.0421105); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.29s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 540.98
//
Query:       gi|518652162|ref|YP_008141682.1|  [L=135]
Description: hypothetical protein FACI_IFERC00001G0801 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-13   49.4   0.0    6.9e-13   49.2   0.0    1.1  1  PIN       PIN domain
  ------ inclusion threshold ------
       0.16   12.2   0.6       0.87    9.8   0.6    1.9  1  PIN_2     PIN domain


Domain annotation for each model (and alignments):
>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   7.7e-17   6.9e-13       2     119 ..       4     124 ..       3     127 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 7.7e-17
                                       EE-HHHHHHHH.TTSHHHHHHHHHHHTSSEEEEEHHHHHHHHHHHHSSCHCHHHHHHHHHHHHH.HHTSEEEEBCHH CS
                               PIN   2 vlDTsvliall.rgeekaeaarklleeleelvtsalvlaEllyvlarrkskrekaaelvellll.lsalkilpidae 76 
                                       v+DT+vl++   ++++++ +a ++++e e++++++l+++E+ +vl r +   + +   ++++ll  + + +  ++++
  gi|518652162|ref|YP_008141682.1|   4 VVDTNVLVYDAiENSPQHGRATEIINESENMIINSLSIIEIGFVLPR-YGINNNSVGMKLEELLhSDYFMVSWLSER 79 
                                       8*******9888***********************************.9999999999999999788888888**** PP

                                       HHHHHHHHHHHHH...SBHHHHHHHHHHHHHT-EEE.ESSTHHHHH CS
                               PIN  77 iaeeaaeialkyg...llpnDaliaAtAkehgikliatfDedfrrv 119
                                        +e  + ++ + +   ++ nD +ia  A++++++l+ tfD+++++ 
  gi|518652162|ref|YP_008141682.1|  80 MLEGTSTFIVENNfsfRDFNDWIIAYDALSRNAPLV-TFDKKLSKQ 124
                                       ************************************.*****9875 PP

>> PIN_2  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.6   9.6e-05      0.87       1     117 [.       4     123 ..       4     132 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9.6e-05
                             PIN_2   1 VvdaNivvsallk..srikkrlilvekaleliapeeaveeiekhkealvkksklseeeleellelletkikiveesl 75 
                                       Vvd+N++v  +++   +  + + +++++ ++i+    + ei    +    +++    +leell+     +    e +
  gi|518652162|ref|YP_008141682.1|   4 VVDTNVLVYDAIEnsPQHGRATEIINESENMIINSLSIIEIGFVLPRYGINNNSVGMKLEELLHSDYFMVSWLSERM 80 
                                       78899998888887544455555666666677777778888776664444444444555555555555666777777 PP

                             PIN_2  76 ye.skikeAkeriarvDpdDtpfvAlaLlleapiWTeDkdlig 117
                                       +e       ++    +D +D+ +   aL  +ap+ T Dk+l +
  gi|518652162|ref|YP_008141682.1|  81 LEgTSTFIVENNFSFRDFNDWIIAYDALSRNAPLVTFDKKLSK 123
                                       7765666667777789*****99999**************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1005.55
//
Query:       gi|518652163|ref|YP_008141683.1|  [L=156]
Description: hypothetical protein FACI_IFERC00001G0802 [Ferroplasma acidarmanus fer1]
Scores for complete 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   65.9   0.0    4.7e-18   65.5   0.0    1.1  1  TPR_5     Tetratrico peptide repeat
    4.1e-06   26.5   0.6      0.011   15.8   0.2    3.0  3  TPR_2     Tetratricopeptide repeat
    2.5e-05   24.4   0.4     0.0046   17.1   0.0    2.1  2  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
      3e-05   24.2   0.1      0.056   13.7   0.0    3.1  3  TPR_12    Tetratricopeptide repeat
    5.7e-05   23.6   0.1        3.5    8.7   0.0    3.5  3  TPR_14    Tetratricopeptide repeat
    0.00019   21.4   1.6      0.012   15.8   0.2    3.1  3  TPR_8     Tetratricopeptide repeat
    0.00026   21.4   0.5      0.018   15.5   0.1    2.4  2  TPR_19    Tetratricopeptide repeat
     0.0004   20.1   2.0        0.1   12.5   0.1    3.6  4  TPR_1     Tetratricopeptide repeat
    0.00049   20.7   0.1        0.7   10.6   0.0    3.1  3  TPR_16    Tetratricopeptide repeat
      0.007   15.6   0.0      0.016   14.4   0.0    1.6  1  TPR_15    Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.04   14.6   0.5         23    5.9   0.1    3.4  3  TPR_6     Tetratricopeptide repeat
       0.11   12.5   0.0       0.13   12.2   0.0    1.1  1  Suf       Suppressor of forked protein (Suf)


Domain annotation for each model (and alignments):
>> TPR_5  Tetratrico peptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   3.2e-21   4.7e-18       4     118 ..      39     154 ..      36     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 3.2e-21
                             TPR_5   4 aFeragarDstGhedkavplYrraLaeGLagarrrratiqLassLRnlGeaeealaLLraeleapsdelddalaafl 80 
                                       +Fe a + D+ G+e +a+plY++a++ GL g  + +a +qL ssL ++Ge e a+a+L++  ++  d    a   fl
  gi|518652163|ref|YP_008141683.1|  39 LFEYANVLDFLGKETEAIPLYQKAIKLGLPGKMKIQAEMQLGSSLSVIGEHESAIAILDGVYKDTAD---PASLEFL 112
                                       7***********************************************************9987665...6778899 PP

                             TPR_5  81 aLvLsdlgrereavsivll....alaehlprYqRsvtnYare 118
                                        ++L+  g+   a++ +l+    +    lp Y R++  Y +e
  gi|518652163|ref|YP_008141683.1| 113 CIALFRSGQADKALKYALNfilsSNQGMLPEYSRALSDYVNE 154
                                       99999999999988777651110445679**********876 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.5e-06     0.011       1      30 [.      36      65 ..      36      66 .. 0.96
   2 ?   -1.6   0.0       2.7   4.1e+03       6      22 ..      78      94 ..      75      97 .. 0.80
   3 !    7.7   0.0     0.003       4.4       4      24 ..     109     129 ..     106     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.5e-06
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAlel 30
                                      a +l++ ++++  lg+  eA+ +++kA++l
  gi|518652163|ref|YP_008141683.1| 36 AAYLFEYANVLDFLGKETEAIPLYQKAIKL 65
                                      679*************************98 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.7
                             TPR_2  6 nlGlayyklgdyeeAle 22
                                      +lG ++   g++e A++
  gi|518652163|ref|YP_008141683.1| 78 QLGSSLSVIGEHESAIA 94
                                      57888888899999986 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.003
                             TPR_2   4 lynlGlayyklgdyeeAleaf 24 
                                       l  l  a++++g+ ++Al++ 
  gi|518652163|ref|YP_008141683.1| 109 LEFLCIALFRSGQADKALKYA 129
                                       566889*************96 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0014       2.1      18      79 ..      29      96 ..      13      97 .. 0.80
   2 !   17.1   0.0   3.1e-06    0.0046       4      49 ..      88     132 ..      86     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0014
                                      HHH--HHHHHH..HHHHHHHTT-HHHHHHHHHCT.SHHHC-H...HHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3 18 aetespedayl..lAlclylngqykrAyellrka.klnsksl...gcrylfAqcllkLkkyeeAiaaL 79
                                      ++  s+++ayl  +A +l  +g+ ++A+ l++ka kl    +   ++ + ++ +l  ++++e Aia+L
  gi|518652163|ref|YP_008141683.1| 29 YDDFSENAAYLfeYANVLDFLGKETEAIPLYQKAiKLGLPGKmkiQAEMQLGSSLSVIGEHESAIAIL 96
                                      55667788777557********************9988777777788899999999999999999887 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.1e-06
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka 49 
                                        +++Ai +++ ++ ++t +p ++ +l+ +l+++gq ++A++++ ++
  gi|518652163|ref|YP_008141683.1|  88 EHESAIAILDGVY-KDTADPASLEFLCIALFRSGQADKALKYALNF 132
                                       689**********.***************************99988 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   3.7e-05     0.056      44      74 ..      35      65 ..      22      67 .. 0.80
   2 ?    2.0   0.0      0.17   2.6e+02       6      27 ..      76      97 ..      72     101 .. 0.75
   3 ?    4.8   0.0     0.023        34       8      26 ..     111     129 ..     105     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
                            TPR_12 44 tattlrnLgrlyralgryeeAlelleealai 74
                                       a++l+ ++ +++ lg+  eA+ l+++a+++
  gi|518652163|ref|YP_008141683.1| 35 NAAYLFEYANVLDFLGKETEAIPLYQKAIKL 65
                                      5889999999999999999999999999875 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                            TPR_12  6 lnnlaavlrrlgrydeAlelle 27
                                        +l++ l   g+++ A+++l+
  gi|518652163|ref|YP_008141683.1| 76 EMQLGSSLSVIGEHESAIAILD 97
                                      4458888888899999998886 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.023
                            TPR_12   8 nlaavlrrlgrydeAlell 26 
                                        l  +l+r g+ d+Al++ 
  gi|518652163|ref|YP_008141683.1| 111 FLCIALFRSGQADKALKYA 129
                                       5788999999999999985 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0024       3.5       4      30 ..      39      65 ..      36      69 .. 0.88
   2 ?    4.9   0.0     0.038        57       3      34 ..      75     106 ..      73     114 .. 0.77
   3 ?    6.3   0.1     0.014        20       8      24 ..     113     129 ..     106     133 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0024
                            TPR_14  4 llalaeallalGdpdeAiallrralal 30
                                      l ++a +l  lG+  eAi l+++a++l
  gi|518652163|ref|YP_008141683.1| 39 LFEYANVLDFLGKETEAIPLYQKAIKL 65
                                      5699********************997 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.038
                            TPR_14   3 allalaeallalGdpdeAiallrralalaPdd 34 
                                       a ++l++ l   G+++ Aia+l+ + ++  d+
  gi|518652163|ref|YP_008141683.1|  75 AEMQLGSSLSVIGEHESAIAILDGVYKDTADP 106
                                       667899999999**********9998854443 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.014
                            TPR_14   8 aeallalGdpdeAiall 24 
                                         al+++G+ d+A++++
  gi|518652163|ref|YP_008141683.1| 113 CIALFRSGQADKALKYA 129
                                       579***********986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   7.9e-06     0.012       2      30 ..      37      65 ..      36      65 .. 0.93
   2 ?    2.2   0.0      0.18   2.7e+02       6      24 ..      78      96 ..      75     101 .. 0.85
   3 ?    0.4   0.0      0.65   9.8e+02      11      23 ..     116     128 ..     113     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7.9e-06
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekalel 30
                                       +++  +++++ lg+  eA+  y+ka++l
  gi|518652163|ref|YP_008141683.1| 37 AYLFEYANVLDFLGKETEAIPLYQKAIKL 65
                                      578999*********************97 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.18
                                      HHHHHHHHTT-HHHHHHHH CS
                             TPR_8  6 nlgsiylklgdyeeAkeyy 24
                                      +lgs ++  g++e+A++ +
  gi|518652163|ref|YP_008141683.1| 78 QLGSSLSVIGEHESAIAIL 96
                                      688888889*******987 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.65
                                       HHHTT-HHHHHHH CS
                             TPR_8  11 ylklgdyeeAkey 23 
                                       ++  g+ ++A +y
  gi|518652163|ref|YP_008141683.1| 116 LFRSGQADKALKY 128
                                       5778899999888 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.044        65      11      50 ..      22      61 ..      11      66 .. 0.84
   2 !   15.5   0.1   1.2e-05     0.018       5      46 ..      87     127 ..      87     150 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.044
                            TPR_19 11 lalleqalqedpknaearllLAeallalgqldeAealLda 50
                                      l+++++ +++  +na+ +  +A++l  lg  +eA+ l ++
  gi|518652163|ref|YP_008141683.1| 22 LKIFQEPYDDFSENAAYLFEYANVLDFLGKETEAIPLYQK 61
                                      5778888899999999999999999999999999866655 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAea 46 
                                       g +++A+a+l  ++++ ++ a +   L++al+ +gq d+A +
  gi|518652163|ref|YP_008141683.1|  87 GEHESAIAILDGVYKDTADPASLEF-LCIALFRSGQADKALK 127
                                       7899*********999887777777.**************87 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   6.8e-05       0.1       8      30 ..      43      65 ..      40      65 .. 0.92
   2 ?    1.4   0.0      0.21   3.1e+02       3      22 ..      75      94 ..      73      95 .. 0.87
   3 ?    2.9   0.1     0.071   1.1e+02       8      23 ..     113     128 ..     109     129 .. 0.89
   4 ?   -2.4   0.0       3.4     5e+03      17      24 ..     144     151 ..     143     151 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.8e-05
                                      HHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  8 GnayfklgkydeAleyyekALel 30
                                      +n++  lgk  eA+  y+kA++l
  gi|518652163|ref|YP_008141683.1| 43 ANVLDFLGKETEAIPLYQKAIKL 65
                                      6788889**************98 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHHTT-HHHHHH CS
                             TPR_1  3 alynlGnayfklgkydeAle 22
                                      a  +lG  +   g+++ A++
  gi|518652163|ref|YP_008141683.1| 75 AEMQLGSSLSVIGEHESAIA 94
                                      6678999***********95 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.071
                                       HHHHHHTT-HHHHHHH CS
                             TPR_1   8 GnayfklgkydeAley 23 
                                         a+f+ g+ d+Al+y
  gi|518652163|ref|YP_008141683.1| 113 CIALFRSGQADKALKY 128
                                       67999*********98 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 3.4
                                       HHHHHHHH CS
                             TPR_1  17 ydeAleyy 24 
                                       y  Al +y
  gi|518652163|ref|YP_008141683.1| 144 YSRALSDY 151
                                       66676666 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00047       0.7      12      62 ..      17      64 ..      14      70 .. 0.85
   2 ?    3.3   0.0     0.091   1.4e+02      38      64 ..      77     105 ..      73     108 .. 0.78
   3 ?    2.3   0.1      0.18   2.7e+02       6      22 ..     115     131 ..     112     138 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                            TPR_16 12 dyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62
                                      +++  ++ +++  +++   +++a+ l+++++++  +g  +eA+ ly++a++
  gi|518652163|ref|YP_008141683.1| 17 KPEIMLKIFQEPYDDF---SENAAYLFEYANVLDFLGKETEAIPLYQKAIK 64
                                      5666677777778888...99**************************9986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.091
                            TPR_16  38 lllgdaalrqgrlaeAaalyraal..raa 64 
                                       + lg ++ + g+++ A+a ++  +  +a+
  gi|518652163|ref|YP_008141683.1|  77 MQLGSSLSVIGEHESAIAILDGVYkdTAD 105
                                       6689999999*******999988864444 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.18
                            TPR_16   6 aalragdyddAaaalea 22 
                                       a++r+g+ d+A++++  
  gi|518652163|ref|YP_008141683.1| 115 ALFRSGQADKALKYALN 131
                                       78999999999998755 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.1e-05     0.016     112     184 ..       3      75 ..       1     139 [. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.1e-05
                            TPR_15 112 lLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlala.pdsselra 184
                                        L + +e +++ +d ++i   + + e++++++++aa+l+ +a++    g++ +A+ +y++A++l  p++ +++a
  gi|518652163|ref|YP_008141683.1|   3 SLNNIIEEAWKYQDKPEIMLKIFQ-EPYDDFSENAAYLFEYANVLDFLGKETEAIPLYQKAIKLGlPGKMKIQA 75 
                                       678888999999999988665555.79***********************************985255555554 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.015        23       3      28 ..      39      64 ..      36      65 .. 0.86
   2 ?    1.3   0.0      0.43   6.5e+02       2      24 ..      75      97 ..      74     102 .. 0.82
   3 ?    3.3   0.0      0.11   1.6e+02      10      26 ..     116     132 ..     114     135 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.015
                                      HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  3 lyklalsyrklgdtdkAlealerlik 28
                                      l+  a  +  lg+ ++A+ ++++ ik
  gi|518652163|ref|YP_008141683.1| 39 LFEYANVLDFLGKETEAIPLYQKAIK 64
                                      677888888889***********997 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.43
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  2 AlyklalsyrklgdtdkAleale 24
                                      A ++l+ s+   g+++ A+++l+
  gi|518652163|ref|YP_008141683.1| 75 AEMQLGSSLSVIGEHESAIAILD 97
                                      6778899999878******9996 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.11
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6  10 yrklgdtdkAlealerl 26 
                                       +++ g++dkAl++  ++
  gi|518652163|ref|YP_008141683.1| 116 LFRSGQADKALKYALNF 132
                                       56656999999987665 PP

>> Suf  Suppressor of forked protein (Suf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.8e-05      0.13      46      98 ..      12      64 ..       8      90 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
                               Suf 46 yyiskdkkvAtkIFelGlKkFpedeefvlkYldyLislnddnnaRvlfekvvs 98
                                      +  ++++++  kIF      F+e+ +++ +Y + L  l ++++a  l++k+++
  gi|518652163|ref|YP_008141683.1| 12 WKYQDKPEIMLKIFQEPYDDFSENAAYLFEYANVLDFLGKETEAIPLYQKAIK 64
                                      56678999*********************************999999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1162.86
//
Query:       gi|518652164|ref|YP_008141684.1|  [L=77]
Description: hypothetical protein FACI_IFERC00001G0803 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-18   67.1   2.1    1.8e-18   67.1   2.1    1.5  2  VAPB_antitox    Putative antitoxin
  ------ inclusion threshold ------
       0.03   14.0   0.4      0.073   12.8   0.2    1.8  2  BRCA2           BRCA2 repeat
       0.18   11.1   0.0        0.2   11.0   0.0    1.1  1  Adenine_deam_C  Adenine deaminase C-terminal domain


Domain annotation for each model (and alignments):
>> VAPB_antitox  Putative antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1   2.1     3e-22   1.8e-18       1      67 [.       4      64 ..       4      66 .. 0.93
   2 ?    3.0   0.1      0.03   1.8e+02      31      49 ..      58      76 ..      58      77 .] 0.86

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 3e-22
                      VAPB_antitox  1 KtIsIsdevYekLkklKregeSFsdvIerLlekkkkgkkkellelfgilseeeadeiekaskelrke 67
                                      K+IsIsde+Y+kLkklK+++eSF+ vI+rL+  +       llel+g+ s+eea+ ++++++e r+ 
  gi|518652164|ref|YP_008141684.1|  4 KNISISDEAYNKLKKLKGKNESFTAVINRLFS-TI-----ILLELRGTISNEEANDMRNRIEESREA 64
                                      99****************************85.22.....4************************96 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.03
                      VAPB_antitox 31 lekkkkgkkkellelfgil 49
                                      +e++++ ++k++++lf+++
  gi|518652164|ref|YP_008141684.1| 58 IEESREARRKQIEKLFERW 76
                                      67889999999***99998 PP

>> BRCA2  BRCA2 repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   1.2e-05     0.073      13      28 ..       4      19 ..       3      19 .. 0.93
   2 ?   -2.8   0.0      0.92   5.5e+03       5       9 ..      32      36 ..      29      36 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.2e-05
                             BRCA2 13 KkIrVSkesLqKAkkl 28
                                      K+I++S+e+ +K kkl
  gi|518652164|ref|YP_008141684.1|  4 KNISISDEAYNKLKKL 19
                                      9***********9997 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.92
                             BRCA2  5 sgFkT 9 
                                       +F+T
  gi|518652164|ref|YP_008141684.1| 32 RLFST 36
                                      68998 PP

>> 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 ?   11.0   0.0   3.4e-05       0.2      80     132 ..      12      67 ..       6      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHTTS...EEEEEETTEEEEEEE-TBTTTBBSS-HHHHHHHHHHHHHHHHT CS
                    Adenine_deam_C  80 AvnrvielgG...GivvvedgkvlaelpLpiaGlmSdepaeevaekleeleaalke 132
                                       A+n++++l+G    +++v +    + + L++ G +S+e+a+++ +++ee ++a+++
  gi|518652164|ref|YP_008141684.1|  12 AYNKLKKLKGkneSFTAVINRLFSTIILLELRGTISNEEANDMRNRIEESREARRK 67 
                                       7888888888666688888888899999**********************988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1501  (0.0837191); expected 358.6 (0.02)
Passed bias filter:                      753  (0.041999); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 501.90
//
Query:       gi|518652165|ref|YP_008141685.1|  [L=64]
Description: hypothetical protein FACI_IFERC00001G0804 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 445.05
//
Query:       gi|518652166|ref|YP_008141686.1|  [L=171]
Description: hypothetical protein FACI_IFERC00001G0805 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         0  (0); expected 0.2 (1e-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: 1267.90
//
Query:       gi|518652167|ref|YP_008141687.1|  [L=59]
Description: hypothetical protein FACI_IFERC00001G0806 [Ferroplasma acidarmanus fer1]
Scores for complete 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   1.5       0.24   11.3   0.2    2.2  2  zinc_ribbon_4   zinc-ribbon domain
     0.0024   17.2   2.2       0.75    9.3   0.2    2.2  2  zf-ribbon_3     zinc-ribbon domain
     0.0052   16.9   0.3        1.9    8.7   0.1    2.1  2  Zn-ribbon_8     Zinc ribbon domain
  ------ inclusion threshold ------
      0.011   15.4   3.2        0.3   10.9   0.5    2.2  2  zinc_ribbon_5   zinc-ribbon domain
      0.012   15.2   2.9        2.2    8.0   0.8    2.3  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
      0.017   14.9   0.4       0.21   11.3   0.0    2.0  2  Ribosomal_S27e  Ribosomal protein S27
      0.025   14.7   1.0       0.61   10.3   0.1    2.3  2  CxC7            CxC7 like cysteine cluster associated with KD
      0.037   14.0   1.0          2    8.5   0.1    2.1  2  zf-BED          BED zinc finger
      0.038   13.7   1.4          1    9.2   0.1    2.1  2  A2L_zn_ribbon   A2L zinc ribbon domain
      0.039   13.9   1.1        4.2    7.4   0.0    2.1  2  ADK_lid         Adenylate kinase, active site lid
       0.04   14.0   2.1       0.96    9.6   0.2    2.1  2  UPF0547         Uncharacterised protein family UPF0547
      0.056   13.4   2.1        1.7    8.7   0.1    2.1  2  Prok-RING_1     Prokaryotic RING finger family 1
      0.058   13.4   0.0      0.069   13.2   0.0    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.069   12.9   0.8       0.87    9.4   0.1    2.1  2  PADR1           PADR1 (NUC008) domain
       0.08   12.9   1.0       0.26   11.3   0.0    1.9  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
      0.094   13.2   2.6          2    9.0   0.3    2.2  2  zf-C2H2         Zinc finger, C2H2 type
       0.11   12.3   6.0       0.95    9.3   0.5    2.2  2  zinc_ribbon_2   zinc-ribbon domain
       0.11   12.1   0.0        1.6    8.4   0.0    2.0  2  TackOD1         Thaumarchaeal output domain 1
       0.11   12.2   2.0        9.6    6.0   0.1    2.3  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.12   11.9   1.4        7.5    6.1   0.0    2.2  2  Mu-like_Com     Mu-like prophage protein Com
       0.12   12.4   5.6        1.3    9.1   0.2    2.2  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.13   12.4   1.1          1    9.4   1.1    1.9  1  CpXC            CpXC protein
       0.16   11.6   1.5        8.2    6.1   0.1    2.1  2  zf_UBZ          Ubiquitin-Binding Zinc Finger
       0.18   10.3   0.0        0.2   10.2   0.0    1.0  1  Terminase_GpA   Phage terminase large subunit (GpA)
        0.2   11.6   2.2        9.2    6.2   0.2    2.1  2  TFIIS_C         Transcription factor S-II (TFIIS)
       0.31   10.6   2.0        3.4    7.3   0.2    2.2  2  zf_C2H2_10      C2H2 type zinc-finger
        1.1    9.3   5.9        2.7    8.1   3.1    2.3  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        3.6    7.6   8.2        3.4    7.7   0.9    2.2  2  zf-C2HC_2       zinc-finger of a C2HC-type


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.2   0.00038      0.24      25      36 .]       3      14 ..       1      14 [. 0.88
   2 !    9.9   0.1    0.0011      0.68       2      15 ..      41      54 ..      41      56 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00038
                     zinc_ribbon_4 25 kvrCskCghvFr 36
                                       ++C kCg++F+
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGEIFK 14
                                      69********96 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.0011
                     zinc_ribbon_4  2 kitCpsCkakyeid 15
                                      +i+Cp+C+++ ++ 
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCGFEGSLK 54
                                      69******987765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0036       2.3      16      24 ..       3      11 ..       2      12 .. 0.87
   2 !    9.3   0.2    0.0012      0.75      17      24 ..      42      49 ..      41      50 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0036
                       zf-ribbon_3 16 dnvCpyCGt 24
                                      d++C +CG+
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGE 11
                                      899****95 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0012
                       zf-ribbon_3 17 nvCpyCGt 24
                                      +vCp+CG 
  gi|518652167|ref|YP_008141687.1| 42 IVCPKCGF 49
                                      57888885 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1     0.003       1.9       7      16 ..       5      14 ..       3      27 .. 0.85
   2 ?    6.8   0.0     0.012       7.4      27      33 ..      42      48 ..      34      53 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.003
                       Zn-ribbon_8  7 rCeeCghefe 16
                                      +C++Cg+ f 
  gi|518652167|ref|YP_008141687.1|  5 KCRKCGEIFK 14
                                      8*****9997 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
                       Zn-ribbon_8 27 taCPeCg 33
                                      ++CP+Cg
  gi|518652167|ref|YP_008141687.1| 42 IVCPKCG 48
                                      5699998 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.5   0.00047       0.3      26      36 ..       4      14 ..       2      15 .. 0.89
   2 ?    5.3   0.1     0.025        16       2       9 ..      41      48 ..      40      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                     zinc_ribbon_5 26 VrCakCaevFd 36
                                      ++C kC+e+F 
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIFK 14
                                      79********5 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.025
                     zinc_ribbon_5  2 iirCpdCd 9 
                                      ii Cp+C+
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCG 48
                                      899****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 ?    8.0   0.8    0.0034       2.2      18      24 ..       4      10 ..       2      17 .. 0.82
   2 ?    7.3   0.0    0.0057       3.6      15      25 ..      39      49 ..      36      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0034
                                      ---SSS- CS
                    DNA_RNApol_7kD 18 iRCkeCG 24
                                      i+C++CG
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCG 10
                                      9****** PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0057
                                      SS----SSS-- CS
                    DNA_RNApol_7kD 15 gdpiRCkeCGh 25
                                      g++i C +CG+
  gi|518652167|ref|YP_008141687.1| 39 GAIIVCPKCGF 49
                                      68899*****8 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00033      0.21      25      42 ..       2      19 ..       1      29 [. 0.86
   2 ?    2.0   0.1      0.26   1.7e+02       9      14 ..      43      48 ..      39      51 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00033
                                      S-EEESSSTCEEEEECSS CS
                    Ribosomal_S27e 25 tvvkCisCgkvLvePtGG 42
                                      t +kC +Cg++  +P+ G
  gi|518652167|ref|YP_008141687.1|  2 TDIKCRKCGEIFKKPRWG 19
                                      6799*******9999976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.26
                                      E-TTTS CS
                    Ribosomal_S27e  9 kCpdCe 14
                                       Cp+C+
  gi|518652167|ref|YP_008141687.1| 43 VCPKCG 48
                                      355554 PP

>> CxC7  CxC7 like cysteine cluster associated with KDZ transposases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00095      0.61      20      36 ..       4      20 ..       1      33 [. 0.87
   2 ?    4.4   0.0     0.066        42      18      26 ..      40      48 ..      17      56 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00095
                              CxC7 20 iecsecgdifkdspvGy 36
                                      i+c +cg+ifk    G+
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIFKKPRWGF 20
                                      79*********988887 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.066
                              CxC7 18 sliecsecg 26
                                      ++i c++cg
  gi|518652167|ref|YP_008141687.1| 40 AIIVCPKCG 48
                                      6789***98 PP

>> zf-BED  BED zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.1    0.0031         2      16      27 ..       3      14 ..       1      17 [. 0.86
   2 ?    4.4   0.1     0.059        37      17      27 ..      42      52 ..      39      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0031
                                      --EETTTTEE-- CS
                            zf-BED 16 kavCryCgkils 27
                                       ++Cr Cg+i++
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGEIFK 14
                                      589******987 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.059
                                      -EETTTTEE-- CS
                            zf-BED 17 avCryCgkils 27
                                      +vC  Cg++ s
  gi|518652167|ref|YP_008141687.1| 42 IVCPKCGFEGS 52
                                      89*****9877 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.066        42       3      10 ..       3      10 ..       1      15 [. 0.67
   2 ?    9.2   0.1    0.0016         1      21      29 ..      41      49 ..      35      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.066
                     A2L_zn_ribbon  3 lkvCsvCg 10
                                      +++C +Cg
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCG 10
                                      56677776 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0016
                     A2L_zn_ribbon 21 ylvCieCga 29
                                      + vC++Cg+
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCGF 49
                                      679*****8 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0065       4.2       4      12 ..       6      14 ..       4      30 .. 0.80
   2 ?    5.7   0.2     0.023        15       3       8 ..      43      48 ..      42      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0065
                                      -TTT--EEE CS
                           ADK_lid  4 CpkCGrsYh 12
                                      C+kCG+++ 
  gi|518652167|ref|YP_008141687.1|  6 CRKCGEIFK 14
                                      999999996 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.023
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vCpkCG
  gi|518652167|ref|YP_008141687.1| 43 VCPKCG 48
                                      9****9 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.065        42      16      25 ..       5      14 ..       4      15 .. 0.79
   2 ?    9.6   0.2    0.0015      0.96      14      23 ..      41      50 ..      39      50 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.065
                           UPF0547 16 fCphCGyvFq 25
                                      +C+ CG +F+
  gi|518652167|ref|YP_008141687.1|  5 KCRKCGEIFK 14
                                      7****97776 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                           UPF0547 14 aqfCphCGyv 23
                                        +Cp CG++
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCGFE 50
                                      679*****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 ?    4.8   0.2     0.042        27       4      16 ..       3      15 ..       1      17 [. 0.83
   2 ?    8.7   0.1    0.0026       1.7      20      27 ..      41      48 ..      31      50 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.042
                       Prok-RING_1  4 gkkCpvCgkelke 16
                                      + kC  Cg+ +k+
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGEIFKK 15
                                      679*****99986 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0026
                       Prok-RING_1 20 iVvCpeCg 27
                                      i+vCp+Cg
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCG 48
                                      99*****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 ?   13.2   0.0   0.00011     0.069      70      94 ..       3      49 ..       1      56 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00011
                                      EEEETTTS-EEECHHHHH......................S-TTTSS CS
                              HypA 70 kvrCreCgkefeleekal......................rCpkCgs 94
                                       ++Cr+Cg+ f++ +  +                       CpkCg 
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGEIFKKPRWGFkpleykagmkmpgglvalgaiiVCPKCGF 49
                                      589********9886423457889*********************96 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1       0.2   1.3e+02      15      21 ..       5      11 ..       4      27 .. 0.77
   2 ?    9.4   0.1    0.0014      0.87       8      20 ..      36      48 ..      34      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.2
                             PADR1 15 kCpeCke 21
                                      kC +C+e
  gi|518652167|ref|YP_008141687.1|  5 KCRKCGE 11
                                      8999996 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0014
                             PADR1  8 mlfGalekCpeCk 20
                                      +++Ga+  Cp+C+
  gi|518652167|ref|YP_008141687.1| 36 VALGAIIVCPKCG 48
                                      579*********8 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.4       1.2   7.8e+02       4       9 ..       5      10 ..       5      12 .. 0.77
   2 ?   11.3   0.0    0.0004      0.26      17      28 ..      39      50 ..      24      50 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.2
                    PhnA_Zn_Ribbon  4 kCplCa 9 
                                      kC +C+
  gi|518652167|ref|YP_008141687.1|  5 KCRKCG 10
                                      788885 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.0004
                    PhnA_Zn_Ribbon 17 gallvCpeCahE 28
                                      ga+ vCp+C+ E
  gi|518652167|ref|YP_008141687.1| 39 GAIIVCPKCGFE 50
                                      7899*****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 ?    9.0   0.3    0.0031         2       2      13 ..       5      16 ..       4      18 .. 0.89
   2 ?    4.7   0.1     0.075        48       2       8 ..      43      49 ..      42      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0031
                                      EETTTTEEESSH CS
                           zf-C2H2  2 kCpdCgksFkrk 13
                                      kC +Cg+ Fk +
  gi|518652167|ref|YP_008141687.1|  5 KCRKCGEIFKKP 16
                                      8********987 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.075
                                      EETTTTE CS
                           zf-C2H2  2 kCpdCgk 8 
                                      +Cp+Cg 
  gi|518652167|ref|YP_008141687.1| 43 VCPKCGF 49
                                      7****96 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.6     0.019        12       1       7 [.       5      11 ..       5      12 .. 0.78
   2 ?    9.3   0.5    0.0015      0.95      16      22 ..      44      50 ..      42      51 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +C +CG+
  gi|518652167|ref|YP_008141687.1|  5 KCRKCGE 11
                                      6888885 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                     zinc_ribbon_2 16 CpyCGtp 22
                                      Cp+CG++
  gi|518652167|ref|YP_008141687.1| 44 CPKCGFE 50
                                      6666654 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0025       1.6     145     164 ..       2      21 ..       1      31 [. 0.84
   2 ?    2.4   0.0      0.17   1.1e+02     104     110 ..      42      48 ..      35      58 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0025
                           TackOD1 145 evykCnsCkslfsepevkar 164
                                       ++ kC++C+++f++p++ ++
  gi|518652167|ref|YP_008141687.1|   2 TDIKCRKCGEIFKKPRWGFK 21 
                                       5679***********99886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.17
                           TackOD1 104 ihhftCg 110
                                       i + +Cg
  gi|518652167|ref|YP_008141687.1|  42 IVCPKCG 48 
                                       3333333 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2     0.015       9.8       3      15 ..       6      18 ..       5      19 .. 0.76
   2 ?    6.0   0.1     0.015       9.6       2       9 ..      43      50 ..      43      55 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.015
                      Rubredoxin_2  3 CsqCGfesakwfG 15
                                      C++CG  + k  +
  gi|518652167|ref|YP_008141687.1|  6 CRKCGEIFKKPRW 18
                                      9999988777655 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.015
                      Rubredoxin_2  2 vCsqCGfe 9 
                                      vC +CGfe
  gi|518652167|ref|YP_008141687.1| 43 VCPKCGFE 50
                                      56667665 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 ?    5.2   0.4     0.023        15      24      32 ..       3      11 ..       1      17 [. 0.86
   2 ?    6.1   0.0     0.012       7.5      24      31 ..      41      48 ..      35      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.023
                       Mu-like_Com 24 tiKCPRCGt 32
                                       iKC +CG 
  gi|518652167|ref|YP_008141687.1|  3 DIKCRKCGE 11
                                      59*****96 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                       Mu-like_Com 24 tiKCPRCG 31
                                       i CP+CG
  gi|518652167|ref|YP_008141687.1| 41 IIVCPKCG 48
                                      488****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 ?    9.1   0.2    0.0021       1.3       2      11 ..       4      13 ..       4      18 .. 0.83
   2 ?    5.9   1.0     0.021        14      22      26 .]      43      47 ..      42      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0021
                            zf-ACC  2 tKCpsCgeml 11
                                      +KC +Cge+ 
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIF 13
                                      8*******85 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.021
                            zf-ACC 22 VCPkC 26
                                      VCPkC
  gi|518652167|ref|YP_008141687.1| 43 VCPKC 47
                                      89998 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.1    0.0016         1       1      50 [.       4      54 ..       4      59 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0016
                              CpXC  1 ltCpaCgkefeaeiwtsidadedpelke...klldgslfeatCpkCgatakle 50
                                      ++C +Cg+ f+ + w    ++ +  +k     +  g    ++CpkCg +++l+
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIFKKPRWGFKPLEYKAGMKMpggLVALGA--IIVCPKCGFEGSLK 54
                                      6788888888888887777776666664111233333..37899999998875 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.029        19       3      13 ..       4      14 ..       2      18 .. 0.80
   2 ?    6.1   0.1     0.013       8.2       3      10 ..      42      49 ..      41      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.029
                            zf_UBZ  3 ylCerCgkeip 13
                                      + C +Cg+ + 
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIFK 14
                                      78*****9876 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.013
                            zf_UBZ  3 ylCerCgk 10
                                      ++C++Cg 
  gi|518652167|ref|YP_008141687.1| 42 IVCPKCGF 49
                                      58****96 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 ?   10.2   0.0   0.00031       0.2     199     236 ..       4      50 ..       3      58 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
                     Terminase_GpA 199 vpCphCgelqe...lsferlkwpege......aeekaryvCphcgsl 236
                                       ++C +Cge ++     f+ l++++g        +  a +vCp+cg +
  gi|518652167|ref|YP_008141687.1|   4 IKCRKCGEIFKkprWGFKPLEYKAGMkmpgglVALGAIIVCPKCGFE 50 
                                       68********986555788999554444466688999*******976 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 ?    6.2   0.2     0.014       9.2      29      38 ..       4      13 ..       1      14 [. 0.71
   2 ?    5.4   0.1     0.026        17       2       8 ..      43      49 ..      42      52 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.014
                           TFIIS_C 29 ykCtkCghrW 38
                                      +kC kCg+ +
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIF 13
                                      5788888766 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.026
                           TFIIS_C  2 kCpkCgs 8 
                                       CpkCg 
  gi|518652167|ref|YP_008141687.1| 43 VCPKCGF 49
                                      6999985 PP

>> zf_C2H2_10  C2H2 type zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1      0.12        77       5      11 ..       6      12 ..       3      13 .. 0.85
   2 ?    7.3   0.2    0.0054       3.4       5       9 ..      44      48 ..      41      51 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.12
                        zf_C2H2_10  5 CPKCqek 11
                                      C KC+e+
  gi|518652167|ref|YP_008141687.1|  6 CRKCGEI 12
                                      99**997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0054
                        zf_C2H2_10  5 CPKCq 9 
                                      CPKC+
  gi|518652167|ref|YP_008141687.1| 44 CPKCG 48
                                      ****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 ?    2.3   1.3      0.27   1.7e+02      21      26 ..       6      11 ..       2      20 .. 0.58
   2 ?    8.1   3.1    0.0042       2.7       6      27 ..       9      50 ..       7      58 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.27
                     Zn_Tnp_IS1595 21 CPhCgs 26
                                      C +Cg 
  gi|518652167|ref|YP_008141687.1|  6 CRKCGE 11
                                      555543 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0042
                     Zn_Tnp_IS1595  6 aralLealrWpng....................fvCPhCgsr 27
                                      + +++++ rW+ +                     vCP+Cg +
  gi|518652167|ref|YP_008141687.1|  9 CGEIFKKPRWGFKpleykagmkmpgglvalgaiIVCPKCGFE 50
                                      55566666666666666666666666666667689*****77 PP

>> zf-C2HC_2  zinc-finger of a C2HC-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.9    0.0054       3.4       3      13 ..       4      14 ..       4      18 .. 0.84
   2 ?    4.1   1.3      0.07        45       4       9 ..      43      48 ..      42      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
                         zf-C2HC_2  3 vpCpkCgRsFn 13
                                      ++C+kCg  F+
  gi|518652167|ref|YP_008141687.1|  4 IKCRKCGEIFK 14
                                      69*****9985 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.07
                         zf-C2HC_2  4 pCpkCg 9 
                                       CpkCg
  gi|518652167|ref|YP_008141687.1| 43 VCPKCG 48
                                      5****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 445.84
//
Query:       gi|518652168|ref|YP_008141688.1|  [L=174]
Description: hypothetical protein FACI_IFERC00001G0807 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.027   14.3   0.5      0.035   13.9   0.5    1.1  1  DUF445    Protein of unknown function (DUF445)


Domain annotation for each model (and alignments):
>> DUF445  Protein of unknown function (DUF445)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   1.9e-06     0.035      55     153 ..      36     155 ..      31     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.9e-06
                            DUF445  55 tkeslakkLkeaevasklaewlk........nptnkesl......aaiveellkeiledlddesikellkknlk... 114
                                       +++ +ak L e  + + +++w k        +pt k ++      ++++e  ++++led+++++i+  ++k++k   
  gi|518652168|ref|YP_008141688.1|  36 NPKLVAKELAEVFFEKDAKNWFKvdddkidfEPTYKVRVvlaeenNRKLEATVDDLLEDIKKDDISGTYSKQIKdds 112
                                       788999*****************888888884444444466666699999************************999 PP

                            DUF445 115 ...kkleevip.epllgkllellleeerhkkllddlldriknl 153
                                          ++l++ i  + + + +++   e+ ++ +++ddl + i + 
  gi|518652168|ref|YP_008141688.1| 113 vvdSHLQSTIAaSAIRSAIFRHSEEKVYAGSISDDLFTDILEK 155
                                       9995555544404444556666677777777777776555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); 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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 1285.39
//
Query:       gi|518652169|ref|YP_008141689.1|  [L=84]
Description: hypothetical protein FACI_IFERC00001G0808 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00014   22.0   1.7    0.00016   21.8   1.7    1.1  1  DUF2614          Zinc-ribbon containing domain
     0.0038   17.3   1.1     0.0045   17.0   1.1    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
  ------ inclusion threshold ------
      0.012   15.5   2.1      0.015   15.2   2.1    1.2  1  DUF2721          Protein of unknown function (DUF2721)
      0.015   14.6   1.5      0.017   14.5   1.5    1.1  1  SLATT_5          SMODS and SLOG-associating 2TM effector doma
      0.056   12.2   2.0      0.061   12.1   2.0    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
      0.072   12.7   0.9      0.085   12.4   0.9    1.1  1  PIRT             Phosphoinositide-interacting protein family
       0.19   11.4   1.1       0.26   11.0   1.1    1.3  1  DUF4579          Domain of unknown function (DUF4579)
       0.19   11.6   1.1       0.23   11.4   1.1    1.1  1  RseC_MucC        Positive regulator of sigma(E), RseC/MucC
       0.66   10.3   8.3       0.93    9.8   0.9    2.1  2  YiaAB            yiaA/B two helix domain
       0.72    9.9   3.2        6.1    6.9   0.1    2.1  2  DUF4337          Domain of unknown function (DUF4337)
        2.2    8.9   6.7        1.4    9.5   1.5    2.0  2  DUF1218          Protein of unknown function (DUF1218)


Domain annotation for each model (and alignments):
>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.7   9.6e-08   0.00016       5      64 ..       6      65 ..       3      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 9.6e-08
                           DUF2614  5 kinkirtfalllvfiglivmyigllfkeselllvlflllGlllvlastvvyfwiGl.lstk 64
                                       inki t   +l f++liv+ ig +f+++  +l+  +l G l++l+s+++   iGl + t+
  gi|518652169|ref|YP_008141689.1|  6 AINKIMTAGTFLFFVSLIVLAIGAIFHSNGTILADSFLYGGLAFLISIILLA-IGLvIGTR 65
                                      69**********************9999999999999999999999987654.34313333 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.1   2.8e-06    0.0045      41      92 ..      12      72 ..       6      82 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.8e-06
                   Phage_holin_3_6 41 gaagvlallalllllvala.....lala.a...lwlaalivaavllvlagvlalvglkklk 92
                                       a+ +l +++l++l ++++      +la       la+li  ++l++  ++  + g+ + +
  gi|518652169|ref|YP_008141689.1| 12 TAGTFLFFVSLIVLAIGAIfhsngTILAdSflyGGLAFLISIILLAIGLVIGTRSGKLQQR 72
                                      3455555666666666665556553332224567788888644444444444444444444 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   2.1   9.4e-06     0.015      70     125 ..      11      65 ..       4      75 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.4e-06
                           DUF2721  70 lvlsallvvlvvlllflsallsldlsllaailfvlalllllvslllflrEirlslr 125
                                       ++++++l+ ++ ++l+++a+++ + + ++a  f+ + l++l+s++l+++ + + +r
  gi|518652169|ref|YP_008141689.1|  11 MTAGTFLFFVSLIVLAIGAIFHSNGT-ILADSFLYGGLAFLISIILLAIGLVIGTR 65 
                                       57778899999999999999966555.55556778888888888888887777776 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.5     1e-05     0.017      26      85 ..       4      65 ..       2      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                           SLATT_5 26 lrrknklstfslsllSvylivlslls..nkssestinenlldflsiilSilvlvisllessk 85
                                      ++  nk++t   +l+ v+livl++     ++     ++ l+  l++++Si++l+i+l+++ +
  gi|518652169|ref|YP_008141689.1|  4 FHAINKIMTAGTFLFFVSLIVLAIGAifHSNGTILADSFLYGGLAFLISIILLAIGLVIGTR 65
                                      566677777777777778888888887678888999999999****************9875 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   2.0   3.7e-05     0.061     382     441 ..      10      76 ..       2      83 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                           DUF2207 382 klsalglgliilglilillallllvll........lvfllilllillliaiivlllfsrllgrrteeG 441
                                       ++ a  +++++ +++l+++a++  +++          +++++++ill i++++    s+ l++rt+e 
  gi|518652169|ref|YP_008141689.1|  10 IMTAGTFLFFVSLIVLAIGAIFHSNGTiladsflyGGLAFLISIILLAIGLVIGTR-SGKLQQRTDEI 76 
                                       44555555666666666666666655587776443222233333333332222222.34555566654 PP

>> PIRT  Phosphoinositide-interacting protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.9   5.2e-05     0.085      52     125 ..      10      82 ..       3      83 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 5.2e-05
                              PIRT  52 vlsvGgavfllGvvittlsrnstlknkdkevf..klsGpaflslGlmllvcGlvwvpiikkkrkqrqkslflqslk 125
                                       +++ G+ +f++ +++ ++    +++++ + +    l G  ++ + ++ll +Glv +     k++qr  ++f ++ k
  gi|518652169|ref|YP_008141689.1|  10 IMTAGTFLFFVSLIVLAI--GAIFHSNGTILAdsFLYGGLAFLISIILLAIGLV-IGTRSGKLQQRTDEIFSKKKK 82 
                                       666666666666665555..66666655544322799999999**********9.677888999999999988765 PP

>> DUF4579  Domain of unknown function (DUF4579)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.1   0.00016      0.26      29      71 ..       5      54 ..       1      82 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                           DUF4579 29 eylnerlwkgvllfivsvvvvslrlisevanqealtaflvfg........l 71
                                      +  n+ +  g++lf vs++v++++ i+++++       +++g        +
  gi|518652169|ref|YP_008141689.1|  5 HAINKIMTAGTFLFFVSLIVLAIGAIFHSNGTILAD-SFLYGglaflisiI 54
                                      566778889*******************99985555.55665444332221 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.1   0.00014      0.23      62     116 ..       9      68 ..       2      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
                         RseC_MucC  62 sllkaallvYllPllllilgallgsall.....gssellaalgallglvlgflivrllsk 116
                                       ++++a  +++ + l++l +ga++ s  +     +   +la+l+++++l++g++i ++  k
  gi|518652169|ref|YP_008141689.1|   9 KIMTAGTFLFFVSLIVLAIGAIFHSNGTiladsFLYGGLAFLISIILLAIGLVIGTRSGK 68 
                                       678888889999999999999998877777788888889999999999999998776555 PP

>> YiaAB  yiaA/B two helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.3     0.019        31       4      22 ..      13      31 ..      11      38 .. 0.82
   2 ?    9.8   0.9   0.00057      0.93       7      21 ..      47      61 ..      42      70 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.019
                             YiaAB  4 qswlsfllalvlllvGlwy 22
                                      +  ++f+++l++l++G ++
  gi|518652169|ref|YP_008141689.1| 13 AGTFLFFVSLIVLAIGAIF 31
                                      56789***********874 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00057
                             YiaAB  7 lsfllalvlllvGlw 21
                                      l+fl++++ll++Gl+
  gi|518652169|ref|YP_008141689.1| 47 LAFLISIILLAIGLV 61
                                      79************8 PP

>> DUF4337  Domain of unknown function (DUF4337)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.4     0.029        47     135     160 ..      10      35 ..       2      36 .. 0.83
   2 ?    6.9   0.1    0.0038       6.1     115     139 ..      40      64 ..      37      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.029
                           DUF4337 135 lltkkklllylslvlglvGlvlflag 160
                                       ++t  + l+++sl++ ++G ++  +g
  gi|518652169|ref|YP_008141689.1|  10 IMTAGTFLFFVSLIVLAIGAIFHSNG 35 
                                       56779999***********9998776 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0038
                           DUF4337 115 dkfdlasalLqiaIvlaaialltkk 139
                                       d f ++ +++ i+I+l ai l+++ 
  gi|518652169|ref|YP_008141689.1|  40 DSFLYGGLAFLISIILLAIGLVIGT 64 
                                       7799999************999875 PP

>> DUF1218  Protein of unknown function (DUF1218)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.5   0.00088       1.4      33      60 ..      12      39 ..       6      44 .. 0.88
   2 ?    2.6   0.3      0.12   1.9e+02      38      51 ..      48      61 ..      41      74 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00088
                           DUF1218 33 tlavvlfvlswivfaiAvalllvGaavn 60
                                      t++++lf++s+iv+ai++++   G+++ 
  gi|518652169|ref|YP_008141689.1| 12 TAGTFLFFVSLIVLAIGAIFHSNGTILA 39
                                      67899*******************9875 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.12
                           DUF1218 38 lfvlswivfaiAva 51
                                       f++s+i++ai+++
  gi|518652169|ref|YP_008141689.1| 48 AFLISIILLAIGLV 61
                                      44555555555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 578.25
//
Query:       gi|518652170|ref|YP_008141690.1|  [L=140]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-09   36.2   0.3    5.7e-09   35.4   0.3    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
    9.4e-07   28.6   0.1    2.9e-06   27.0   0.0    1.9  2  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    1.5e-06   27.9   0.1    2.8e-06   27.0   0.1    1.4  1  HTH_DeoR        DeoR-like helix-turn-helix domain
    3.4e-05   23.7   0.3    0.00038   20.3   0.1    2.4  2  HTH_11          HTH domain
    4.6e-05   23.1   0.0    0.00013   21.7   0.0    1.8  1  HTH_38          Helix-turn-helix domain
     0.0001   22.1   0.0    0.00022   21.0   0.0    1.5  1  HTH_5           Bacterial regulatory protein, arsR family
    0.00061   19.4   0.0     0.0019   17.9   0.0    1.9  1  Sigma70_r4_2    Sigma-70, region 4
    0.00094   19.1   0.0     0.0017   18.3   0.0    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0017   18.8   0.1     0.0029   18.0   0.1    1.6  1  HTH_40          Helix-turn-helix domain
     0.0041   17.1   0.1       0.17   11.9   0.0    2.2  2  HTH_Crp_2       Crp-like helix-turn-helix domain
     0.0042   17.2   0.0     0.0068   16.5   0.0    1.4  1  HTH_28          Helix-turn-helix domain
     0.0068   16.3   0.0      0.014   15.3   0.0    1.5  1  MarR_2          MarR family
     0.0089   15.8   0.0      0.023   14.5   0.0    1.7  1  HTH_23          Homeodomain-like domain
     0.0094   16.1   0.0      0.019   15.1   0.0    1.5  1  HTH_34          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.026   14.3   0.0    1.4  1  MerR            MerR family regulatory protein
      0.015   15.3   0.0      0.064   13.3   0.0    2.2  2  HTH_3           Helix-turn-helix
      0.016   15.6   0.0        1.8    8.9   0.0    2.3  2  Rrf2            Transcriptional regulator
      0.016   15.2   0.0      0.027   14.5   0.0    1.4  1  HTH_29          Winged helix-turn helix
      0.016   14.2   0.0      0.018   14.1   0.0    1.2  1  TnsD            Tn7-like transposition protein D
      0.017   14.8   0.0      0.033   13.8   0.0    1.5  1  GntR            Bacterial regulatory proteins, gntR family
      0.018   14.9   0.0      0.037   13.8   0.0    1.5  1  HTH_10          HTH DNA binding domain
      0.018   15.2   0.0      0.041   14.0   0.0    1.6  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
      0.018   15.2   0.0      0.035   14.3   0.0    1.5  1  HTH_17          Helix-turn-helix domain
       0.02   14.5   0.0      0.037   13.7   0.0    1.4  1  HTH_41          Helix-turn-helix domain
      0.035   13.7   0.0      0.085   12.5   0.0    1.7  1  HrcA_DNA-bdg    Winged helix-turn-helix transcription repress
      0.035   13.5   0.0       0.07   12.5   0.0    1.5  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
      0.038   13.9   0.1       0.15   12.0   0.0    2.1  1  HTH_36          Helix-turn-helix domain
      0.043   13.9   0.0      0.091   12.8   0.0    1.5  1  HTH_20          Helix-turn-helix domain
      0.053   14.1   0.1       0.19   12.4   0.0    1.9  2  Mga             Mga helix-turn-helix domain
      0.057   13.0   0.1       0.13   11.9   0.1    1.5  2  E3_UFM1_ligase  E3 UFM1-protein ligase 1
      0.073   12.9   0.0        6.6    6.7   0.0    2.3  2  DUF746          Domain of Unknown Function (DUF746)
      0.077   13.0   1.2       0.23   11.5   0.2    2.3  3  HTH_Mga         M protein trans-acting positive regulator (MG
       0.12   12.4   0.1       0.32   11.0   0.0    1.8  1  MarR            MarR family
       0.13   12.4   0.0        0.2   11.7   0.0    1.4  1  SpoIIID         Stage III sporulation protein D


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 !   35.4   0.3   1.1e-11   5.7e-09       2      47 ..       3      48 ..       2      49 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.1e-11
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      d++d +I ++L +n+++s+r+LA+ +++Sp+t++ +l+++e +  I
  gi|518652170|ref|YP_008141690.1|  3 DKLDTEIARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKMETDKQI 48
                                      8999999**********************************88766 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 !   27.0   0.0   5.5e-09   2.9e-06       2      42 .]       3      43 ..       1      43 [. 0.97
   2 ?   -0.9   0.0       2.9   1.5e+03       3      10 ..      43      50 ..      42      51 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.5e-09
                     HTH_AsnC-type  2 DeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      D++D  I + L  ++++s ++LA+ +++S+ t+++ ++++e
  gi|518652170|ref|YP_008141690.1|  3 DKLDTEIARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKME 43
                                      9**************************************98 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.9
                     HTH_AsnC-type  3 eiDrkILe 10
                                      e+D++I++
  gi|518652170|ref|YP_008141690.1| 43 ETDKQIIA 50
                                      79****96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.1   5.4e-09   2.8e-06       4      44 ..       8      48 ..       6      52 .. 0.92

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5.4e-09
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgll 44
                                      +i  +l +  kls+ +l+ l++vS+ TiR+ L+++e++  +
  gi|518652170|ref|YP_008141690.1|  8 EIARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKMETDKQI 48
                                      7999*******************************998765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   7.2e-07   0.00038       5      42 ..       9      45 ..       6      59 .. 0.85
   2 ?    0.6   0.0         1   5.5e+02      37      51 ..     112     126 ..     112     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.2e-07
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      i + L+++ + +s+ +LA+  nvS  t+r++++++e+ 
  gi|518652170|ref|YP_008141690.1|  9 IARYLIDNSK-LSIRDLAKLCNVSPGTIRNHLQKMETD 45
                                      6677877777.***********************9876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1
                            HTH_11  37 kaLeelgvpIesepg 51 
                                       k+L+e  ++Ie++ g
  gi|518652170|ref|YP_008141690.1| 112 KSLNECIAEIEATEG 126
                                       789*********987 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.4e-07   0.00013      12      42 ..       8      40 ..       7      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.4e-07
                            HTH_38 12 eIerll..aeGlslreIArrLgrspsTIsRElk 42
                                      eI+r l  + +ls+r+ A+++++sp+TI ++l+
  gi|518652170|ref|YP_008141690.1|  8 EIARYLidNSKLSIRDLAKLCNVSPGTIRNHLQ 40
                                      67776545688*******************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   4.1e-07   0.00022       7      40 ..       9      43 ..       7      45 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.1e-07
                                      HHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHH CS
                             HTH_5  7 ILklLae.gelcvcelaeelglsqstvShHLkkLr 40
                                      I ++L + ++l++ +la+  ++s++t++ HL k++
  gi|518652170|ref|YP_008141690.1|  9 IARYLIDnSKLSIRDLAKLCNVSPGTIRNHLQKME 43
                                      5678899677**********************997 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   3.5e-06    0.0019      25      49 ..      17      41 ..       8      42 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 3.5e-06
                                      S---HHHHHHHHT--HHHHHHHHHH CS
                      Sigma70_r4_2 25 eglsykEIAellgisegtVksrlsR 49
                                        ls+++ A+l+++s+gt++++l++
  gi|518652170|ref|YP_008141690.1| 17 SKLSIRDLAKLCNVSPGTIRNHLQK 41
                                      669********************96 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.2e-06    0.0017       8      73 ..      74     136 ..      67     138 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.2e-06
                                       GGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSH.HHHHHHHHHTTTTSTTEEEEEEEEEE CS
                    AsnC_trans_reg   8 ghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdl.ealerflreklaslpgvartetsivl 73 
                                       +h   +++  e+l++l  ++++++++Gd++ +++v ++   ++l++ + e + + +gv+++  siv 
  gi|518652170|ref|YP_008141690.1|  74 EH---YTRTLEELRKLTFIKSLFSTSGDHSAIAIVISKLYgKSLNECIAE-IEATEGVRNVYPSIVN 136
                                       44...9999*****************************75489*******.**************95 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   5.6e-06    0.0029       7      45 ..      12      51 ..       7     126 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.6e-06
                            HTH_40  7 ell.eeglsieeIAkerglkesTIegHLaelieegeeidl 45
                                       l+ +++lsi + Ak  +++++TI +HL ++  +++ i +
  gi|518652170|ref|YP_008141690.1| 12 YLIdNSKLSIRDLAKLCNVSPGTIRNHLQKMETDKQIIAY 51
                                      5666899**********************98888664444 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00031      0.17      21      51 ..      18      48 ..       5      60 .. 0.82
   2 ?    3.1   0.0      0.18        96      34      52 ..      72      90 ..      67     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00031
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkregli 51
                                      +l+ ++lA ++++++ t+   l++++ ++ i
  gi|518652170|ref|YP_008141690.1| 18 KLSIRDLAKLCNVSPGTIRNHLQKMETDKQI 48
                                      68999********************987654 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.18
                                      SHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 34 tretvsrilseLkreglis 52
                                       +e+ +r+l eL++   i+
  gi|518652170|ref|YP_008141690.1| 72 MPEHYTRTLEELRKLTFIK 90
                                      58999********987775 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   1.3e-05    0.0068       4      38 ..       8      44 ..       7      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.3e-05
                            HTH_28  4 eiikllaaGh..svreaArelgisrrtvyrWikryee 38
                                      ei ++l++    s+r++A++ ++s+ t++  +++ e+
  gi|518652170|ref|YP_008141690.1|  8 EIARYLIDNSklSIRDLAKLCNVSPGTIRNHLQKMET 44
                                      688999965338**********************998 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.6e-05     0.014      14      48 ..      13      45 ..       7      59 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.6e-05
                                      HHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHT CS
                            MarR_2 14 LgrrpgrdltvgelarrlglsksavsrilkrLvaa 48
                                      L ++    l++++la+ +++s++++ ++l++++  
  gi|518652170|ref|YP_008141690.1| 13 LIDNSK--LSIRDLAKLCNVSPGTIRNHLQKMETD 45
                                      555655..9***********************975 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   4.4e-05     0.023      15      40 ..      15      41 ..       7      49 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-05
                            HTH_23 15 ae.GlsvreIAreLgvsrrTvyrwlkr 40
                                      ++ +ls+r+ A++++vs+ T+++ l++
  gi|518652170|ref|YP_008141690.1| 15 DNsKLSIRDLAKLCNVSPGTIRNHLQK 41
                                      34799*****************98877 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.7e-05     0.019       4      46 ..       8      50 ..       5      62 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.7e-05
                            HTH_34  4 avlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYiev 46
                                      ++  yL+++++ + ++l +  +++ g +  hl+k+e+ ++i  
  gi|518652170|ref|YP_008141690.1|  8 EIARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKMETDKQIIA 50
                                      6778*********************************999865 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0     5e-05     0.026       1      17 [.      20      36 ..      20      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5e-05
                                      EHHHHHHHHTTTHHHHH CS
                              MerR  1 tIgevAeltGvsprtLR 17
                                      +I+++A+l++vsp t+R
  gi|518652170|ref|YP_008141690.1| 20 SIRDLAKLCNVSPGTIR 36
                                      79*************** PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   0.00012     0.064       7      27 ..      16      36 ..       9      49 .. 0.88
   2 ?   -1.8   0.0       6.2   3.3e+03      42      54 ..     104     116 ..     101     116 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                                      HTTHHHHHHHHHHTSSHHHHH CS
                             HTH_3  7 qlglsqeeLAeklGvsrstis 27
                                        +ls+++LA++++vs+ ti+
  gi|518652170|ref|YP_008141690.1| 16 NSKLSIRDLAKLCNVSPGTIR 36
                                      779****************97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 6.2
                                       HHHHHHHTSEHHH CS
                             HTH_3  42 kklakaLgvslde 54 
                                       + ++k +g sl e
  gi|518652170|ref|YP_008141690.1| 104 IVISKLYGKSLNE 116
                                       5689999999865 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0    0.0035       1.8      23      53 ..      16      46 ..       7      53 .. 0.86
   2 ?    4.8   0.0     0.068        36      33      57 ..      67      91 ..      46      98 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0035
                                      CC-B-HHHHHHHHTS-HHHHHHHHHHHHHTT CS
                              Rrf2 23 eepvsseeiaerqnispsylekilakLrkag 53
                                      ++++s++++a+  n+sp  ++  l+k++  +
  gi|518652170|ref|YP_008141690.1| 16 NSKLSIRDLAKLCNVSPGTIRNHLQKMETDK 46
                                      5569**********************98765 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.068
                                      HHHTS-HHHHHHHHHHHHHTTSEEE CS
                              Rrf2 33 erqnispsylekilakLrkaglvks 57
                                         +i p++  + l++Lrk  ++ks
  gi|518652170|ref|YP_008141690.1| 67 LGLDIMPEHYTRTLEELRKLTFIKS 91
                                      557899*****************98 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.1e-05     0.027      12      39 ..      19      45 ..      13      61 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.1e-05
                            HTH_29 12 vstvsqiAkllglsrrtvyrwlkrfeeg 39
                                      +s ++++Akl+++s+ t++++l  +e++
  gi|518652170|ref|YP_008141690.1| 19 LS-IRDLAKLCNVSPGTIRNHLQKMETD 45
                                      55.9*******************99987 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   3.3e-05     0.018     191     227 ..      10      46 ..       6     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.3e-05
                              TnsD 191 lkeLveeeglslkeiAkelgvdiktVlryakklgllk 227
                                       +++L+++++ls+++ Ak  +v+++t++ +++k +  k
  gi|518652170|ref|YP_008141690.1|  10 ARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKMETDK 46 
                                       6899999***********************9876444 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.3e-05     0.033      21      54 ..      16      48 ..       2      54 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-05
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglv 54
                                      ++kL s r+La+  +Vs  t+R  L++ e+++ +
  gi|518652170|ref|YP_008141690.1| 16 NSKL-SIRDLAKLCNVSPGTIRNHLQKMETDKQI 48
                                      789*.*********************99999866 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     7e-05     0.037      24      48 ..      19      43 ..      16      49 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7e-05
                            HTH_10 24 vtlkeLAkelGIskstlsehLrkae 48
                                       ++++LAk  ++s+ t+ +hL+k e
  gi|518652170|ref|YP_008141690.1| 19 LSIRDLAKLCNVSPGTIRNHLQKME 43
                                      5799******************987 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.7e-05     0.041      17      48 ..       8      39 ..       3      42 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.7e-05
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHH CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksL 48
                                       ++++L+++++l++r+l+k+ ++s+  +++ L
  gi|518652170|ref|YP_008141690.1|  8 EIARYLIDNSKLSIRDLAKLCNVSPGTIRNHL 39
                                      6899************************9977 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.7e-05     0.035       2      35 ..      19      59 ..      19      65 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.7e-05
                            HTH_17  2 ltveEaAelLgvsrstvyrlir....rgelpaa..k.iGrr 35
                                      l++ ++A+l +vs+ t+++ ++    +++++a+  +  G+r
  gi|518652170|ref|YP_008141690.1| 19 LSIRDLAKLCNVSPGTIRNHLQkmetDKQIIAYttRlQGKR 59
                                      799****************9965555777778866555554 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.1e-05     0.037       8      36 ..      20      48 ..      18      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                            HTH_41  8 tIeelakeleLSvGlvQkALklLeddkai 36
                                      +I +lak + +S G++   L+++e dk i
  gi|518652170|ref|YP_008141690.1| 20 SIRDLAKLCNVSPGTIRNHLQKMETDKQI 48
                                      699*********************99976 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 ?   12.5   0.0   0.00016     0.085      14      47 ..       9      42 ..       2      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00016
                      HrcA_DNA-bdg 14 ielyrkkkravKgeeiAevlkrneGtvRNqlqsL 47
                                      i  y  +++ +  +++A++ +  +Gt+RN lq +
  gi|518652170|ref|YP_008141690.1|  9 IARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKM 42
                                      56666677778889*****************986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   0.00013      0.07      18      46 ..       7      37 ..       4      40 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00013
                      HTH_Tnp_ISL3 18 ayilellles..rsvkavArqlgvSwtTVwr 46
                                        i++ l+++   s+++ A++++vS+ T+++
  gi|518652170|ref|YP_008141690.1|  7 TEIARYLIDNskLSIRDLAKLCNVSPGTIRN 37
                                      5677777777789****************86 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00029      0.15      27      50 ..      20      43 ..       9      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00029
                            HTH_36 27 sqetlakrlglsknTvsraikeLe 50
                                      s ++lak++++s  T+++++++ e
  gi|518652170|ref|YP_008141690.1| 20 SIRDLAKLCNVSPGTIRNHLQKME 43
                                      789*****************9976 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   0.0   0.00017     0.091      16      49 ..      10      43 ..       5      53 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00017
                                      HHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHH CS
                            HTH_20 16 lraLaraegltaselaerldlskntlsyHLrvLe 49
                                       r+L ++  l+  +la+++ +s+ t+++HL+++e
  gi|518652170|ref|YP_008141690.1| 10 ARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKME 43
                                      5677788889999*******************97 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00035      0.19      18      55 ..       6      43 ..       2      67 .. 0.79
   2 ?   -1.1   0.0       5.5   2.9e+03      20      79 ..      87     102 ..      73     110 .. 0.49

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00035
                                      HHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH CS
                               Mga 18 kyqllkflfeeeevsieelaqelyiSestlkrkikeln 55
                                      + ++ ++l+ + ++si +la+   +S  t+ +++++++
  gi|518652170|ref|YP_008141690.1|  6 DTEIARYLIDNSKLSIRDLAKLCNVSPGTIRNHLQKME 43
                                      667999****************************9986 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.5
                                       HHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHHCHCCT-EEETTCCEEES-HHHH CS
                               Mga  20 qllkflfeeeevsieelaqelyiSestlkrkikelnklLkefdleltkknlklrGdEeqi 79 
                                        ++k lf                                              +Gd + i
  gi|518652170|ref|YP_008141690.1|  87 TFIKSLF--------------------------------------------STSGDHSAI 102
                                       3333333............................................344444444 PP

>> E3_UFM1_ligase  E3 UFM1-protein ligase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00024      0.13      54     101 ..       3      48 ..       2      60 .. 0.84
   2 ?   -1.8   0.0       3.7   1.9e+03     211     245 ..      79     118 ..      62     126 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                    E3_UFM1_ligase  54 eqLekeikdelekagGRvnlvdLakilnvdlshiekkaeeivkedkel 101
                                       ++L++ei+  l  +  ++++ dLak+ nv    i ++++++  + k++
  gi|518652170|ref|YP_008141690.1|   3 DKLDTEIARYLIDN-SKLSIRDLAKLCNVSPGTIRNHLQKMETD-KQI 48 
                                       6899******9999.6************************9544.444 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3.7
                    E3_UFM1_ligase 211 lleeLikekeikGslkagre.....lyiPtiyskaqeewv 245
                                       +leeL k   ik+ ++++       + i ++y k+ +e++
  gi|518652170|ref|YP_008141690.1|  79 TLEELRKLTFIKSLFSTSGDhsaiaIVISKLYGKSLNECI 118
                                       4555555555555443333234455555555555555555 PP

>> DUF746  Domain of Unknown Function (DUF746)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.012       6.6      12      35 ..      18      41 ..      10      46 .. 0.91
   2 ?    4.1   0.0     0.078        41      10      39 ..      57      86 ..      52     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                            DUF746 12 plslaeaadllgtdegiiakwvre 35
                                      +ls+ ++a+l  +++g+i++ +++
  gi|518652170|ref|YP_008141690.1| 18 KLSIRDLAKLCNVSPGTIRNHLQK 41
                                      69******************9876 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.078
                            DUF746 10 sqplslaeaadllgtdegiiakwvreFrew 39
                                      +  l+l+ea+  l+ +++   ++++e r++
  gi|518652170|ref|YP_008141690.1| 57 GKRLGLEEAILGLDIMPEHYTRTLEELRKL 86
                                      66799********************99975 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 ?   11.5   0.2   0.00044      0.23       7      45 ..       6      43 ..       3      52 .. 0.89
   2 ?   -2.1   0.0       7.9   4.2e+03      43      53 ..      82      93 ..      79      96 .. 0.59
   3 ?   -1.3   0.0       4.5   2.4e+03      35      45 ..     112     122 ..     111     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00044
                           HTH_Mga  7 klkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      + ++  +L++ ++ l++ +lak  + s  t+++ ++++ 
  gi|518652170|ref|YP_008141690.1|  6 DTEIARYLID-NSKLSIRDLAKLCNVSPGTIRNHLQKME 43
                                      5677789***.**********************999985 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 7.9
                           HTH_Mga 43 eLnel.Fpeels 53
                                      eL+ l F+++l+
  gi|518652170|ref|YP_008141690.1| 82 ELRKLtFIKSLF 93
                                      555555777665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 4.5
                           HTH_Mga  35 ltlqsdiseLn 45 
                                       ++l+++i e+ 
  gi|518652170|ref|YP_008141690.1| 112 KSLNECIAEIE 122
                                       6899***9986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0    0.0006      0.32      17      43 ..      18      44 ..      11      49 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0006
                                      TEEHHHHHHHHTS-HHHHHHHHHHHHH CS
                              MarR 17 plsvseLakklgvskstvtrvldrLek 43
                                       ls+ +Lak  +vs++t+ + l ++e 
  gi|518652170|ref|YP_008141690.1| 18 KLSIRDLAKLCNVSPGTIRNHLQKMET 44
                                      57899********************96 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00039       0.2       9      41 ..       7      40 ..       1      54 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00039
                           SpoIIID  9 leiakyive.skatvRkaakvfgvskstvhkDvt 41
                                       eia+y+++ sk  +R+ ak  +vs  t+ + + 
  gi|518652170|ref|YP_008141690.1|  7 TEIARYLIDnSKLSIRDLAKLCNVSPGTIRNHLQ 40
                                      69****99725789***************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        91  (0.00507558); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1142.84
//
Query:       gi|518652171|ref|YP_008141691.1|  [L=231]
Description: hypothetical protein FACI_IFERC00001G0810 [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.4   0.0    6.6e-31  106.8   0.0    1.3  1  AhpC-TSA    AhpC/TSA family
      3e-16   59.5   0.0    3.7e-16   59.1   0.0    1.1  1  Redoxin     Redoxin
      5e-09   35.9   0.1    1.4e-08   34.5   0.1    1.7  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.8   0.0   1.1e-34   6.6e-31       1     123 [.       8     137 ..       8     138 .. 0.97

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 1.1e-34
                                       TTSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHH CS
                          AhpC-TSA   1 vgdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfi 77 
                                       +g+k+p++ + +++g ++  +dykgk+ vlf +p+d++pvCtte +++a++++ef++++ e+ig+svds+ sh ++i
  gi|518652171|ref|YP_008141691.1|   8 IGEKFPEMDVVTTQGSKKLPDDYKGKWFVLFSHPGDFTPVCTTEFFSFAQRNDEFTKLNTELIGLSVDSKISHMEWI 84 
                                       89***********9888888********************************************************* PP

                                       HH-H.......SSEEEE-TTSHHHHHTT-EETT.TTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  78 ekes......lnfpllsDeegkvakaygvlkee.kglalratfvidkegkiry 123
                                       + +       ++fp+++D+ g+vak++g+++ e ++ ++ra+f++d++ ++r+
  gi|518652171|ref|YP_008141691.1|  85 NWIHdnlkidVKFPIIADPMGNVAKSLGMIHAEsATSTVRAVFIVDDKAVVRA 137
                                       **9999************************9999999*************997 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.1   0.0   6.3e-20   3.7e-16       3     133 ..       9     141 ..       7     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 6.3e-20
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHH CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkef 79 
                                       g+k+P+     ++t+g++   +++kgk  v+++ pg f+P+C++e   +++ ++++ + + + +++++d+    +e+
  gi|518652171|ref|YP_008141691.1|   9 GEKFPEMDV--VTTQGSKKLPDDYKGKWFVLFSHPGDFTPVCTTEFFSFAQRNDEFTKLNTELIGLSVDSKISHMEW 83 
                                       889999886..447887777777**************************************************9999 PP

                                       HHH......TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEES CS
                           Redoxin  80 wgk......eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvyleve 133
                                       ++        ++kfp+++D+ ++++k+lG+  +e a++    ++++++d++ +v+++ + 
  gi|518652171|ref|YP_008141691.1|  84 INWihdnlkIDVKFPIIADPMGNVAKSLGMIHAESATS--TVRAVFIVDDKAVVRAILYY 141
                                       888888999889*****************766655555..79999999999999987655 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 !   34.5   0.1   2.3e-12   1.4e-08       1      39 [.     158     200 ..     158     202 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 2.3e-12
                                       HHHHHHHHT-BB-TTT.T.....BT-EEE---SSHHHHHHHHHH CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkp.....GdkvivpPpateedavkryle 39 
                                       ALQ++dk+++atPAnW p         i+pPpat +d+ +r+++
  gi|518652171|ref|YP_008141691.1| 158 ALQMVDKYKIATPANW-PdnelmKGRFIIPPPATMNDIPERLKK 200
                                       9***************.888888555678999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (231 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); 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: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1865.20
//
Query:       gi|518652172|ref|YP_008141692.1|  [L=94]
Description: hypothetical protein FACI_IFERC00001G0811 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0013   19.1   0.8     0.0018   18.7   0.8    1.2  1  Rubrerythrin  Rubrerythrin
     0.0079   16.0   0.0     0.0094   15.7   0.0    1.2  1  COQ7          Ubiquinone biosynthesis protein COQ7
  ------ inclusion threshold ------
       0.04   12.8   0.2      0.043   12.7   0.2    1.0  1  AAA_10        AAA-like domain
      0.046   13.7   0.1      0.073   13.1   0.1    1.4  1  RNase_H_2     RNase_H superfamily
       0.49   10.4   4.4        2.2    8.3   0.3    2.2  2  DUF4250       Domain of unknown function (DUF4250)


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 !   18.7   0.8   5.1e-07    0.0018       6      66 ..      23      81 ..      21      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.1e-07
                                      HHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SS CS
                      Rubrerythrin  6 AiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevke 66
                                      +++ E +a+++Y e  + +k   p ++e+++   ++E+eH  +l + l+  +pel+ e ke
  gi|518652172|ref|YP_008141692.1| 23 SLIEEMQAIMFYDERLDATK--DPVLKEVIKHNRDDEKEHFSLLLEYLRRNDPELDRELKE 81
                                      7889**********999999..9***************************99999944433 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   2.6e-06    0.0094      13      59 ..      27      71 ..      13      78 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 2.6e-06
                              COQ7 13 ElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59
                                      E+ A + Y+  l++  +kdp lk+++k+  ++EkeH++++ e+l+++
  gi|518652172|ref|YP_008141692.1| 27 EMQAIMFYDERLDA--TKDPVLKEVIKHNRDDEKEHFSLLLEYLRRN 71
                                      88999999999999..799******************9988877765 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.2e-05     0.043     100     173 ..      19      90 ..       8      93 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.2e-05
                            AAA_10 100 keaeslaedilelllgvkkkesekkaalseaveavlegkqrgllavieelrkedekvareiarhlesvvkksla 173
                                       ++ +sl e++  ++  +++ +  k ++l+e++++  + +++++  ++e lr++d+++ re+ + l  + kk+l 
  gi|518652172|ref|YP_008141692.1|  19 RARQSLIEEMQAIMFYDERLDATKDPVLKEVIKHNRDDEKEHFSLLLEYLRRNDPELDRELKEIL--FSKKELK 90 
                                       4445556666666777778899999***********************************99888..6666655 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     2e-05     0.073     119     159 ..      21      61 ..       5      68 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2e-05
                         RNase_H_2 119 reedlsGsqavklyqeylrtgdeellekilaYNedDvrala 159
                                       r+  ++  qa+++y+e l   ++  l++++++N+dD  + +
  gi|518652172|ref|YP_008141692.1|  21 RQSLIEEMQAIMFYDERLDATKDPVLKEVIKHNRDDEKEHF 61 
                                       4467999*****************************76655 PP

>> DUF4250  Domain of unknown function (DUF4250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00062       2.2      20      48 ..       7      34 ..       4      39 .. 0.88
   2 ?    3.6   0.5     0.018        63      19      46 ..      56      84 ..      54      91 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00062
                           DUF4250 20 yssldelcedldidkeeleekLasigYeY 48
                                      ++slde  +d+   ++ l+e++++i + Y
  gi|518652172|ref|YP_008141692.1|  7 ENSLDEKTKDMSRARQSLIEEMQAIMF-Y 34
                                      589********************9976.4 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.018
                           DUF4250 19 ey.ssldelcedldidkeeleekLasigY 46
                                      ++ + ++ l+e+l  +  el  +L++i +
  gi|518652172|ref|YP_008141692.1| 56 DEkEHFSLLLEYLRRNDPELDRELKEILF 84
                                      44367777788888888888888887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1106  (0.0616878); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 765.59
//
Query:       gi|518652173|ref|YP_008141693.1|  [L=202]
Description: phosphoribosylglycinamide formyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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  151.3   0.0    2.7e-44  151.1   0.0    1.1  1  Formyl_trans_N  Formyl transferase
  ------ inclusion threshold ------
      0.096   11.9   0.0       0.15   11.3   0.0    1.3  1  OSK             OSK domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.0     3e-48   2.7e-44       2     178 ..       3     181 ..       2     184 .. 0.96

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 3e-48
                                       EEEEEESESSHHHHHHHHHHHHTTSE.CEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHC CS
                    Formyl_trans_N   2 kivvlisgtgsnlqalldalkkgsle.advvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelke 77 
                                       +ivvl+sg+gsn+qa++da  +g ++ a++  +++n+++a+ l++a++ +i   +++ kk    + +++ + e l++
  gi|518652173|ref|YP_008141693.1|   3 NIVVLASGNGSNFQAVVDAIDNGVINdAKISKLICNNKRAYVLQRARDSGIMPVLVDSKK----EDYNNIISEILAA 75 
                                       89***********************99************************999998775....6778999999*** PP

                                       TT-SEEEEES--S---HHHHHSSTTSEEEEESSSTTTT.....BSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EE CS
                    Formyl_trans_N  78 lkadlivlagymkllpkelvqavrlkilniHpSLLPrf.....kGaaaiqraleaGdketGvtihfvdeelDtGail 149
                                       +++dli+l gymk++p+++++a++ k++n+HpSLLP+f     +G +++++++++G++ +G+tihf + ++D+G+i+
  gi|518652173|ref|YP_008141693.1|  76 ENPDLILLDGYMKIIPDNIIDAYPFKMINLHPSLLPAFggkgyYGGKVHEAVIKSGARFSGCTIHFATKDVDNGPII 152
                                       **************************************99999999******************************* PP

                                       EEEEEE--TT--HHHHHHHHHHHHHHHHH CS
                    Formyl_trans_N 150 aqkkveiiaedtkeeleqrvadaehkalv 178
                                        q  ve+   dt e+le++++++ehk lv
  gi|518652173|ref|YP_008141693.1| 153 DQRVVEVSDIDTPESLEEKIHEEEHKSLV 181
                                       **************************998 PP

>> OSK  OSK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.7e-05      0.15      42      75 ..     124     157 ..     118     185 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.7e-05
                                       T-SS-EETEEETT--HHHHHHHHHT----T-EEE CS
                               OSK  42 kesvlqsGlciSGlTiseaakrlekielissrvv 75 
                                       +e v++sG   SG Ti+ a+k +++ ++i++rvv
  gi|518652173|ref|YP_008141693.1| 124 HEAVIKSGARFSGCTIHFATKDVDNGPIIDQRVV 157
                                       57899************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 1544.91
//
Query:       gi|518652174|ref|YP_008141694.1|  [L=187]
Description: hypothetical protein FACI_IFERC00001G0813 [Ferroplasma acidarmanus fer1]
Scores for complete 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   44.9  14.3    2.1e-11   43.6  14.3    1.6  1  LysE             LysE type translocator
  ------ inclusion threshold ------
      0.045   13.4   0.8      0.045   13.4   0.8    2.2  2  TerC             Integral membrane protein TerC family
        9.8    6.3  10.1       0.28   11.3   0.3    2.5  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> LysE  LysE type translocator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6  14.3   3.5e-15   2.1e-11       2     192 ..      15     180 ..      14     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 3.5e-15
                              LysE   2 slllspGpqnllvlkqgikrgfkggilvalgvligdavlillgllGlalLlkaapivlsilrllGgayLlwlgvlal 78 
                                       sl+ +pG++n ++ ++++k+   +g lv+lg++++d+ ++ ++ l    +++  p +l+++ ++Gg++ l+lg++ l
  gi|518652174|ref|YP_008141694.1|  15 SLAGPPGSVNSIIANEALKSP-LHGTLVGLGAMTADLTFFAIVFLTNG-IIS--PEILKVIYVIGGIFMLYLGISIL 87 
                                       78889************9998.999*************9998888555.444..8********************** PP

                              LysE  79 rdakekkveaeksveaslvkpflkglllslsNPkailfwlsvisallakaeqygdagrlilaaglvvasliwfslla 155
                                       r+++ +k  +           +  g+   l+NP+ i++w+ v+  ll+   +      ++   gl +++++w ++  
  gi|518652174|ref|YP_008141694.1|  88 RSKMPSKTRKG---------NYVLGVTMGLTNPFQIIWWFTVGFFLLK---ELS----IFSITGLYSGIVVWTIVFP 148
                                       ****9996333.........356799999***************9999...333....4444566666666766655 PP

                              LysE 156 flaarlsrrlsskkvlriinvvvgvlligfavkllle 192
                                        ++ r  + + ++   ++i+++ ++++++fa+++l +
  gi|518652174|ref|YP_008141694.1| 149 YVVWR--FGTGYE---KYIKIISAAIIFAFAIYILFD 180
                                       44433..333444...5899999********999875 PP

>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.8   7.6e-06     0.045      37      83 ..      44      92 ..      23     106 .. 0.66
   2 ?   -0.1   3.2      0.11   6.3e+02      58      78 ..     147     185 ..      90     187 .] 0.61

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.6e-06
                              TerC 37 GilgAlvlRillillavallel..fdlilligglfLlytavkellekrl 83
                                      G + A ++ +++++l+  +++   +++i +igg+f+ly++++ l++k +
  gi|518652174|ref|YP_008141694.1| 44 GAMTADLTFFAIVFLTNGIISPeiLKVIYVIGGIFMLYLGISILRSKMP 92
                                      4555543333333333333332327*******************98662 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.11
                              TerC  58 l.................f.dlilligglfLlytavkel 78 
                                       +                 +   i++++++++l+ +++++
  gi|518652174|ref|YP_008141694.1| 147 FpyvvwrfgtgyekyikiIsAAIIFAFAIYILFDGLHLI 185
                                       044444444444444433236778888888888877776 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   4.6e-05      0.28      34     103 ..      38      97 ..      34      98 .. 0.80
   2 ?   -2.3   4.4      0.73   4.3e+03      30      48 ..     161     179 ..     112     186 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
                   Phage_holin_3_6  34 gsgagllgaagvlallalllllvala..lalaalwlaalivaavllvlagvlalvglkklkkakplpertie 103
                                       g+++gl ++++ l+++a+++l+ +++             i+ +++++ ++ ++++g++ l++  ++p +t++
  gi|518652174|ref|YP_008141694.1|  38 GTLVGLGAMTADLTFFAIVFLTNGIIspE----------ILKVIYVIGGIFMLYLGISILRS--KMPSKTRK 97 
                                       56778888888888888888888886333..........5689***************9888..67999875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.73
                   Phage_holin_3_6  30 akragsgagllgaagvlal 48 
                                         +++s+a++++ a ++++
  gi|518652174|ref|YP_008141694.1| 161 YIKIISAAIIFAFAIYILF 179
                                       3445555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      256  (0.0142785); 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: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 1531.34
//
Query:       gi|518652175|ref|YP_008141695.1|  [L=296]
Description: ornithine cyclodeaminase [Ferroplasma acidarmanus fer1]
Scores for complete 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  120.0   0.0    1.3e-34  119.6   0.0    1.1  1  OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin famil
    1.2e-07   31.9   0.0    2.2e-07   31.0   0.0    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
      0.005   17.4   0.0      0.013   16.0   0.0    1.7  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent


Domain annotation for each model (and alignments):
>> OCD_Mu_crystall  Ornithine cyclodeaminase/mu-crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.6   0.0   2.2e-38   1.3e-34       9     314 ..       8     293 ..       3     295 .. 0.93

  Alignments for each domain:
  == domain 1  score: 119.6 bits;  conditional E-value: 2.2e-38
                                       HHHHCCH-HCCCHHHHHHHHHHHHCC-CE----EEEEECCGTEEEEEEEEEETTTTEEEEEEEEEETTTCCCTSSSE CS
                   OCD_Mu_crystall   9 veveeelllddlakaveeafrrlasgkvkkpprvalevkdsrgelevmpaylagrellgvKlvnshpenkksglptv 85 
                                       ++v+++l+++++++ ++eaf ++ +g+ +  pr + + kd   ++  mpa  + r+ +g+K +  + +n        
  gi|518652175|ref|YP_008141695.1|   8 NDVKNNLPVKECVDELKEAFVSYGKGESDSSPRDRINGKD--FVFSTMPALYERRGIAGLKTYM-YGKNG------Y 75 
                                       6999************************************..*******************995.55554......4 PP

                                       EEEEEEE-TTT--EEEEEE-HHHHHHHHHHHHHHHHHHHS-TT--EEEEE--SHHHHHHHHHHCCCS--SEEEEE-S CS
                   OCD_Mu_crystall  86 talvvLndpetGvplalmdatlltalRTaAvsavaakyLarkdasvlaiiGaGvqaetqlealkavldikevriydr 162
                                         +v+L+++e+  +l  mda++l ++RT+A+sa+++  L +k     +iiG G q+e+ql+ +++  +++++ +y r
  gi|518652175|ref|YP_008141695.1|  76 RFFVILFSTENPGKLFAMDANVLGQIRTGAISAMVTTMLVKKKRINYTIIGSGFQSESQLNSISEYYELENAYVYSR 152
                                       579************************************************************************** PP

                                       SHHHHHHHHHHCCS.CTT-EEECSCHHHHTTSSEEEE----SS-SB-GGGS-TT-EEEE-S--STT--SB-HHHHHC CS
                   OCD_Mu_crystall 163 deeaaekfaenlqefefevsackseeeavegadivvtvTaakapilkaewvkpGahinavgadapgkteLdddilkr 239
                                       + e a+kfae+ +   ++v+ +k      ++ d++  +T +++pi+  +++ +  hin++g++  g +e d+d+  +
  gi|518652175|ref|YP_008141695.1| 153 NFEHAKKFAEKSR---INVEPVKGL-SCLKESDVIASATDTEEPIFNYSMLPENYHINLIGSNVLGSREADKDVFEN 225
                                       **********998...799998875.6899*********************************************** PP

                                       CEEEE..SHHHHHHHCCCCHCHHHTTSSTCGGEEEEHHHHHCTSS-..-STTSEEEEE----HHHHHHHHHHHHHHH CS
                   OCD_Mu_crystall 240 adifv..dseaqareeGeiqvaiekgvlaedakvaelgeviaGkkpGRtsdeeitlfdsvGlaveDvaaaklvyera 314
                                       + +++  +s + a e+ ei        +++  k+++lge +   ++ R+s++   +f+ +G++ eD+aa  +v  ++
  gi|518652175|ref|YP_008141695.1| 226 SGLVIeeNSRQSAMESSEISD------IKDRSKITTLGEFMLNPDKYRNSKS---VFKCLGIGLEDLAAGYVVLKNM 293
                                       ***99644566789999**99......9*************99999787775...9************999988775 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   3.6e-11   2.2e-07      11      96 ..     118     200 ..     108     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 3.6e-11
                                       TT-EEEEES-SHHHHHHHHHHHCC.T-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  11 kekkvlliGaGemaelvakhLlak.gvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatase 86 
                                       k+ + ++iG G  +e  ++ +++  ++++  v  R++e+ak++ae+    +i++ +++ l+ +l+e+dv+ sat +e
  gi|518652175|ref|YP_008141695.1| 118 KRINYTIIGSGFQSESQLNSISEYyELENAYVYSRNFEHAKKFAEKS---RINVEPVKGLS-CLKESDVIASATDTE 190
                                       455679***************99879********************9...56699**9998.*************** PP

                                       S-SB-HHHHH CS
                      Shikimate_DH  87 epilekeeve 96 
                                       epi++ +++ 
  gi|518652175|ref|YP_008141695.1| 191 EPIFNYSMLP 200
                                       ****999875 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06     0.013       3      67 ..     123     185 ..     121     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                                       EEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE CS
                     F420_oxidored   3 giiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvl 67 
                                        iiG+G + e+ ++ +++   + ++ +v  srn e a+++ae+  ++v++v+   +++e+dv+  
  gi|518652175|ref|YP_008141695.1| 123 TIIGSGFQSESQLNSISEYY-ELENAYVY-SRNFEHAKKFAEKSRINVEPVKGLSCLKESDVIAS 185
                                       79************999995.88899955.********************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); 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:                         3  (0.000167327); expected 0.2 (1e-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 0.20s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 2488.23
//
Query:       gi|518652176|ref|YP_008141696.1|  [L=41]
Description: hypothetical protein FACI_IFERC00001G0815 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      201  (0.0112109); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.19s 00:00:00.47 Elapsed: 00:00:00.35
# Mc/sec: 352.91
//
Query:       gi|518652177|ref|YP_008141697.1|  [L=218]
Description: hypothetical protein FACI_IFERC00001G0816 [Ferroplasma acidarmanus fer1]
Scores for complete 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   34.8   0.0    1.6e-08   34.5   0.0    1.1  1  Amdase    Arylmalonate decarboxylase


Domain annotation for each model (and alignments):
>> Amdase  Arylmalonate decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   8.9e-13   1.6e-08      87     208 ..      89     210 ..      63     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 8.9e-13
                            Amdase  87 savvealralgarRvAvataYidevnerLvayLeesglevaalesLdiedveavakvtaeelvelgkkavaaapead 163
                                       +av+e l+++  + + + t Yi+e  ++ ++y +++g++++  ++L+     ++a+++ ee+  +  k + + +++d
  gi|518652177|ref|YP_008141697.1|  89 EAVIEYLHESESKSMWLGTPYIKERTDEEKEYFSKKGFNITGSYGLNKIYALDIARTSLEEIRCMLDKNIGTVEKSD 165
                                       79********************************************9999999************************ PP

                            Amdase 164 allisCGGLrtldvvreledelglpvvssalAGlwdavrlaglda 208
                                        ++isC  + t ++  +l +  g+pv+s   A lw++ r  g   
  gi|518652177|ref|YP_008141697.1| 166 LIYISCTAMPTSKILDKLSSIYGKPVLSENSAILWKISRITGNPI 210
                                       *************************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); 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: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 1759.67
//
Query:       gi|518652178|ref|YP_008141698.1|  [L=368]
Description: hypothetical protein FACI_IFERC00001G0817 [Ferroplasma acidarmanus fer1]
Scores for complete 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   59.1   0.1    1.1e-15   58.4   0.1    1.3  1  Radical_SAM     Radical SAM superfamily
  ------ inclusion threshold ------
      0.055   13.6   0.0       0.11   12.6   0.0    1.5  1  Fer4_14         4Fe-4S single cluster domain
      0.064   12.4   0.0        0.1   11.7   0.0    1.2  1  N_Asn_amidohyd  Protein N-terminal asparagine amidohydrolase


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 !   58.4   0.1   1.9e-19   1.1e-15       2     163 ..      60     235 ..      59     239 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 1.9e-19
                                       EEESEESS--TTTSCCTT....HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpet....vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlakl 73 
                                       + +++C+  C+ Ca +      +++ ++g +lsve++ +e+ ++k e + ++  i+gg +p+l+ +++e++++++k+
  gi|518652178|ref|YP_008141698.1|  60 NYSNFCTASCPICAYYVPykikKYNPEKGFELSVEDVHKEAMKAK-ELNvTEIHIVGGFNPDLNLEYYEDIFKEVKK 135
                                       6789************99**************************5.77757777777889***************** PP

                                       C..........CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT..CTSHHHHHHHHHHHH CS
                                       x..........xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxx RF
                       Radical_SAM  74 a..........vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmn..rghtfeevlealekl 137
                                                   p+i +   t g  + +e+++r++++g   +   g+e++++e v+k +    + + e++le  +++
  gi|518652178|ref|YP_008141698.1| 136 VlpditlktftIPEIDFIARTTGNSI-PEVIDRFRKAGmDAHTGGGAEIFNEE-VRKQITtpEKISGEKWLEDAKLI 210
                                       99999999999999999999999999.***********88899999*******.9999987888888********** PP

                                       HHTTSETEEEEEEEBTTTSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 138 reagikrvvdrivglpGendeeleel 163
                                       +++g+k   ++++ +  en +++ ++
  gi|518652178|ref|YP_008141698.1| 211 HSLGVK-GNSTMTYGTVENYDDIINH 235
                                       ******.9999***999***999775 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05      0.11       6      96 ..      63     153 ..      59     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                           Fer4_14   6 sgCnlsCkgCd.....nketwkselgkpqteelleqilkdlkkseikiqglvltGG.ePLhyenkkellklvkrlke 76 
                                       + C+ sC+ C      + ++++ e g + + e+++++   +k++e +  ++ ++GG +P    n +   ++ k++k+
  gi|518652178|ref|YP_008141698.1|  63 NFCTASCPICAyyvpyKIKKYNPEKGFELSVEDVHKEA--MKAKELNVTEIHIVGGfNPD--LNLEYYEDIFKEVKK 135
                                       56********8777665555666665555555554444..6777778899*****96776..788999999999999 PP

                           Fer4_14  77 eypekkiwletngtleiele 96 
                                            +i+l+t    ei++ 
  gi|518652178|ref|YP_008141698.1| 136 VL--PDITLKTFTIPEIDFI 153
                                       99..7777777777666665 PP

>> N_Asn_amidohyd  Protein N-terminal asparagine amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.7e-05       0.1      73     140 ..      95     162 ..      84     178 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.7e-05
                    N_Asn_amidohyd  73 svqelseeske.grlelhlvGGFederglseklslkllealqkqkeeihletlcvlelnttve.kgialP 140
                                        v++ + ++ke +  e+h+vGGF+ + +   +   ++ ++++k   +i l+t+ + e++   + +g+++P
  gi|518652178|ref|YP_008141698.1|  95 DVHKEAMKAKElNVTEIHIVGGFNPDLN--LEYYEDIFKEVKKVLPDITLKTFTIPEIDFIARtTGNSIP 162
                                       4555444444425579*******98755..57799********************999888776677776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 2693.23
//
Query:       gi|518652179|ref|YP_008141699.1|  [L=240]
Description: solute-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.6e-21   74.8   0.1    9.8e-21   74.4   0.1    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
  ------ inclusion threshold ------
      0.086   12.5   2.4       0.19   11.5   0.2    2.1  2  DUF3236         Protein of unknown function (DUF3236)


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.1   1.1e-24   9.8e-21      32     252 ..      22     227 ..      11     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 1.1e-24
                                       EEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEESSSSEEEEESS-CCC-SSS.T.EEEESTTT CS
                    VitK2_biosynth  32 ivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGrvygvllvskvpleelegelgkrvalpges 108
                                       iv +  ++  r l+eg+ +++ +S + y++++d+++l++++ i    +  + +l+s++ + +     + ++ +++  
  gi|518652179|ref|YP_008141699.1|  22 IVRKSAADNYRDLEEGRTEIGMVSLVTYLKHMDKLNLVKSINIHTKANSISTILLSRSGYLKN----NIKINVTSLT 94 
                                       5556666667899*******************************************7733222....579******* PP

                                       SHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTSSEEEEECCHHHTGGGGTTEEEEEHHHHHHHHHSS-EEEEE CS
                    VitK2_biosynth 109 tTsvlLlrlllaeryglkprlvevpfdeieaavlegedagLlIgesaltyaeeglkkvlDLgelWeeltglPlvlgl 185
                                       +T    l+l+l+++ g++ +l e  +++ e+ +l+++d +L+Ig++a++  +   + +lD g ++ +l+gl  v+++
  gi|518652179|ref|YP_008141699.1|  95 KTTEFYLKLVLEKM-GISFELKESGYSDYEN-LLKDADYALVIGDDAIKAYSGSANILLDVGLEFSKLYGLEPVYAV 169
                                       **************.9**************9.77788***********888889*********************** PP

                                       EEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS.HHHHHHHHHHHCSHHHHS-CHH CS
                    VitK2_biosynth 186 wvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemddevlekhlelYvnelsydlgee 252
                                        + r+ ++++ +  l++ ++ S++y  ++ ++ + ++  ++ +m         e+Y++ ++y++++ 
  gi|518652179|ref|YP_008141699.1| 170 AASRNAIDNARIGDLDKHIEDSKKYIKESAEKNSLKFHVKKELM---------EEYYRVMDYSFNNS 227
                                       *************************9999888888777666666.........67777666666655 PP

>> DUF3236  Protein of unknown function (DUF3236)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.2     0.042   3.8e+02       3      60 ..      21      80 ..      19     109 .. 0.66
   2 ?   11.5   0.2   2.1e-05      0.19       8      59 ..     171     217 ..     167     235 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.042
                                      HHHHHHHHHHHTT---S--HHHHHHHHHHHHT-SEEEES-SS..HHHHHHHHHHHTTTT- CS
                           DUF3236  3 elikkayleslegaRkGDkeeeveaireyiknakkivvatkn..kkkvkvinkvlsklgl 60
                                      e+++k+  + + +  +G +e  + ++ +y+k+ +k+ ++++   ++k + i+++l +   
  gi|518652179|ref|YP_008141699.1| 21 EIVRKSAADNYRDLEEGRTEIGMVSLVTYLKHMDKLNLVKSIniHTKANSISTILLSRSG 80
                                      677777778888888888888888888888888887766543124566667777665543 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.1e-05
                                       HHHHHHTT---S--HHHHHHHHHHHHT-SEEEES-SSHHHHHHHHHHHTTTT CS
                           DUF3236   8 ayleslegaRkGDkeeeveaireyiknakkivvatknkkkvkvinkvlsklg 59 
                                       a  +++++aR GD  + +e  ++yik++     a+kn+ k++v +++++++ 
  gi|518652179|ref|YP_008141699.1| 171 ASRNAIDNARIGDLDKHIEDSKKYIKES-----AEKNSLKFHVKKELMEEYY 217
                                       6678899*********************.....99***********999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.44u 0.73s 00:00:01.17 Elapsed: 00:00:00.67
# Mc/sec: 1074.59
//
Query:       gi|518652180|ref|YP_008141700.1|  [L=365]
Description: hypothetical protein FACI_IFERC00001G0819 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-17   62.6   0.0    9.9e-17   61.8   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.026   14.6   0.0    1.5  1  Fer4_14      4Fe-4S single cluster domain
      0.095   13.0   0.0        0.2   11.9   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 !   61.8   0.0   1.7e-20   9.9e-17       3     154 ..      63     224 ..      61     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 1.7e-20
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgi 78 
                                        t+ Cn rC+fCa+++t ++ g++++ls++++++e+k +++  g    +i+gg + +l+ d++ +l+ ++k++ pg+
  gi|518652180|ref|YP_008141700.1|  63 YTNVCNVRCHFCAFYRT-QNDGDAYTLSIDDVVNEIKTYYEPYGiRQLLIQGGVNSFLDLDYYTELFGRIKKEFPGL 138
                                       6899************9.*********************9999989999999*********************8888 PP

                                       EEEEEECSSCHG.........HHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET CS
                                       xxxxxxxxxxxx.........xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  79 ritvetngtlpd.........eeklerllelg.vdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr 144
                                        i+  + + l+          ++ l +l+e g  +    g e++d   v+k+m+ +  +  ++le +e+++++gi+ 
  gi|518652180|ref|YP_008141700.1| 139 GIHGLSTAELHFislkahipmKDLLIKLRESGlETIPGAGGEILDGS-VRKRMGrPEASGRQWLEIMETAHKLGIHT 214
                                       888888888877888888889***********777788899999998.******999999****************6 PP

                                       EEEEEEEBTT CS
                                       xxxxxxxxxx RF
                       Radical_SAM 145 vvdrivglpG 154
                                       + ++++g+  
  gi|518652180|ref|YP_008141700.1| 215 SATMMFGHLE 224
                                       5555555544 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 ?   14.6   0.0   4.4e-06     0.026       5      92 ..      64     149 ..      60     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                           Fer4_14   5 lsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeypek 81 
                                       ++ Cn+ C +C    t+++      + +++++++ +++++ + i++l + GG    + + +   +l  r+k+e+p +
  gi|518652180|ref|YP_008141700.1|  64 TNVCNVRCHFCAFYRTQNDGDAYTLSIDDVVNEI-KTYYEPYGIRQLLIQGGVNS-FLDLDYYTELFGRIKKEFPGL 138
                                       789*********9888888666666666777777.67788888899*****9654.58999999**********999 PP

                           Fer4_14  82 kiwletngtle 92 
                                        i+  + + l+
  gi|518652180|ref|YP_008141700.1| 139 GIHGLSTAELH 149
                                       99976665554 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   3.3e-05       0.2      11      85 ..      63     137 ..      50     164 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.3e-05
                           Fer4_12  11 fvsgCnlsCkgCfnketwsfksgkeft.kelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpe 85 
                                       +++ Cn++C +C    t++       + +++ +ei +  + + i++l + GG  +     +  +el+ ++k+e+p 
  gi|518652180|ref|YP_008141700.1|  63 YTNVCNVRCHFCAFYRTQNDGDAYTLSiDDVVNEIKTYYEPYGIRQLLIQGGVNSF-LDLDYYTELFGRIKKEFPG 137
                                       7889********977777655554444799**********************5544.4899999999999999983 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 2541.58
//
Query:       gi|518652181|ref|YP_008141701.1|  [L=100]
Description: hypothetical protein FACI_IFERC00001G0820 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-20   72.4   0.0    3.1e-20   72.2   0.0    1.0  1  rhaM      L-rhamnose mutarotase


Domain annotation for each model (and alignments):
>> rhaM  L-rhamnose mutarotase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.7e-24   3.1e-20       1     108 []       2      99 ..       2      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.7e-24
                              rhaM   1 RyaqvlklkpeaieeYkklHaevwpevlealkeagirnysIyldeegntLfailevgddeeadaaaaaadpkvqeWw 77 
                                       Ry + l ++p+  e Y  +H+++wpe+le+lk+agirnys++   +gn + +++e+ dd e+ +++ +++ ++++W+
  gi|518652181|ref|YP_008141701.1|   2 RYFFKLSINPADKELYISRHQNIWPEMLEELKKAGIRNYSLF--LKGNDVYGYWEC-DDLESTMRILKDSRVNEKWQ 75 
                                       89999*************************************..57**********.7******************* PP

                              rhaM  78 almaklqeaapsaspakeeekwteleevFhl 108
                                       + m+ + +  ++  p        + eevFh+
  gi|518652181|ref|YP_008141701.1|  76 ESMKGIITGRDDIIP-------SPYEEVFHM 99 
                                       ******997777333.......478999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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 0.45s 00:00:00.84 Elapsed: 00:00:00.59
# Mc/sec: 510.20
//
Query:       gi|518652182|ref|YP_008141702.1|  [L=254]
Description: enoyl-CoA hydratase [Ferroplasma acidarmanus fer1]
Scores for complete 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  161.9   0.0    1.9e-47  161.7   0.0    1.0  1  ECH_1     Enoyl-CoA hydratase/isomerase
    2.3e-25   89.8   0.0    7.5e-22   78.3   0.0    2.0  2  ECH_2     Enoyl-CoA hydratase/isomerase


Domain annotation for each model (and alignments):
>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.7   0.0   2.1e-51   1.9e-47       6     250 ..      13     253 ..       8     254 .] 0.96

  Alignments for each domain:
  == domain 1  score: 161.7 bits;  conditional E-value: 2.1e-51
                                       EEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHHHH CS
                             ECH_1   6 vaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlelwt 82 
                                       v vi +nr +++Nal + ++ +l++a+++++ d++ r ++LtG +kaF+aGadl+    +e    ++l++++   ++
  gi|518652182|ref|YP_008141702.1|  13 VSVIEINRANKLNALGEDVRSDLLAAFKDFNSDPAKRIAILTGKGKAFSAGADLTSTSDKEVDIRDELSNSFHPILK 89 
                                       889**********************************************************9*************** PP

                                       HHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT-EE CS
                             ECH_1  83 klytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgkki 159
                                       ++ +++k+ i+a+nG a+g+G+ lalacDi  a+++ +f   +  + l p+ g++ il r  G  kA+  ll g ++
  gi|518652182|ref|YP_008141702.1|  90 EMVNSKKIFISAINGVAAGAGMSLALACDISFASRETNFIMGFHGIALAPDTGLVLILSRLAGA-KARPYLLYGGSF 165
                                       ************************************************************9995.79999******* PP

                                       EHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHHHH CS
                             ECH_1 160 saqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddikeG 236
                                       sa+ea+++Glv+ v  ++ ++  a+el ekl + +  a+   k+ +n+ l   l   l+ ea+l++++  ++d++eG
  gi|518652182|ref|YP_008141702.1| 166 SAKEAEEMGLVQVV--DDPFM-DAIELGEKLSNGPYRAYSVSKQLINQSLYYGLDDFLQDEARLQSDLGTSHDFREG 239
                                       ***********976..45565.69***************************************************** PP

                                       HHHHHTCSH----- CS
                             ECH_1 237 lqaflEkrkpefed 250
                                       + af Ekr p+f++
  gi|518652182|ref|YP_008141702.1| 240 VSAFREKRSPKFTG 253
                                       ************97 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.3   0.0   8.4e-26   7.5e-22       2     170 ..      14     178 ..      13     211 .. 0.90
   2 !   10.7   0.0     3e-05      0.27     258     316 ..     195     250 ..     179     254 .] 0.77

  Alignments for each domain:
  == domain 1  score: 78.3 bits;  conditional E-value: 8.4e-26
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                        vi++nr ++lNaL  ++ ++l +a+k++++d++ ++ +l+g+g kaf+AG D+ +  +++ + ++e   + ++ + 
  gi|518652182|ref|YP_008141702.1|  14 SVIEINRANKLNALGEDVRSDLLAAFKDFNSDPAKRIAILTGKG-KAFSAGADLTSTSDKEVDIRDE---LSNSFHP 86 
                                       699***************************************88.***********99999886644...8888899 PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSSTTHHHHHHHH-- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpgelGlylalTGa 155
                                       + + + + +k +++ ++G++ G G++l++ + +  ++ +t f m   +I l PD G   +Lsrl g+ ++   l G 
  gi|518652182|ref|YP_008141702.1|  87 ILKEMVNSKKIFISAINGVAAGAGMSLALACDISFASRETNFIMGFHGIALAPDTGLVLILSRLAGAKARPYLLYGG 163
                                       9999**************************************************************99998889999 PP

                                       -B-HHHHHHTTS--E CS
                             ECH_2 156 rlkgadalaaglath 170
                                       ++++++a ++gl + 
  gi|518652182|ref|YP_008141702.1| 164 SFSAKEAEEMGLVQV 178
                                       *******99999865 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 3e-05
                                       HS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------ CS
                             ECH_2 258 krsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPk 316
                                       +    +  v+ ++++++     l++ l+ E rl + l +++Df eGv a     +++Pk
  gi|518652182|ref|YP_008141702.1| 195 NGPYRAYSVSKQLINQSLYY-GLDDFLQDEARLQSDLGTSHDFREGVSAF--REKRSPK 250
                                       55555666777777777777.5*************************996..3335555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       390  (0.0217525); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1717.25
//
Query:       gi|518652183|ref|YP_008141703.1|  [L=55]
Description: hypothetical protein FACI_IFERC00001G0822 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                      2225  (0.124101); expected 358.6 (0.02)
Passed bias filter:                      778  (0.0433934); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.32s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 358.53
//
Query:       gi|518652184|ref|YP_008141704.1|  [L=433]
Description: hypothetical protein FACI_IFERC00001G0823 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-68  230.6   0.0      3e-68  230.3   0.0    1.0  1  SHMT           Serine hydroxymethyltransferase
    1.1e-06   28.0   0.0    1.7e-06   27.3   0.0    1.2  1  SelA           L-seryl-tRNA selenium transferase
    3.7e-06   26.3   0.0    2.7e-05   23.5   0.0    2.0  1  Aminotran_1_2  Aminotransferase class I and II


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 !  230.3   0.0   4.9e-72     3e-68      14     399 .]      21     389 ..      10     389 .. 0.92

  Alignments for each domain:
  == domain 1  score: 230.3 bits;  conditional E-value: 4.9e-72
                                       HHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE- CS
                              SHMT  14 kekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnv 90 
                                       k ++  +e+i liasen++s+ ++e+l + l  +yaeG+P kryy G+++vd++e+ + d  + lf+++    +v+ 
  gi|518652184|ref|YP_008141704.1|  21 KHNKFFEESIPLIASENIMSPMAMEMLLTDLGFRYAEGLPHKRYYQGNQIVDIIEDKVTDLGRALFNAK----YVDP 93 
                                       555667899************************************************************....**** PP

                                       --SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHH CS
                              SHMT  91 qplsGsqanlavytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkake 167
                                       +plsG++ n+av  a+ +pgd+i +  l+ GGh++         + +     ++++y  d ++  i+ d   k  k+
  gi|518652184|ref|YP_008141704.1|  94 RPLSGTNSNMAVLYAFTKPGDTITTPALSGGGHISSAPFGA---VGFR--GLKTLNYPFDVDEMNINVDGTIKLLKQ 165
                                       **********************************9654333...3444..468899999999*************** PP

                                       H--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTSS--GCCT.SSEEEEESSSTT-S-S-EEEE CS
                              SHMT 168 fkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagvipsPfey.advvtttthktlrGprgglil 243
                                        kPkl   G+s +      + lr+  +e+g++++ d ah+ Gl+ ++ + +P++  a+++t  thktl Gp+ g+i+
  gi|518652184|ref|YP_008141704.1| 166 AKPKLAWFGQSVFLFPTPLKELRDTLEEIGSTVVYDAAHVLGLIGGKQFQDPLREgAQIITGSTHKTLPGPQHGIII 242
                                       ****************************************************96439*******************9 PP

                                       EC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              SHMT 244 lrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakalaealkekg 320
                                        +            ++ee  kk++  vfPg+    +  ++aa+ v+l e l+    +y+kq++kna++l ++l + g
  gi|518652184|ref|YP_008141704.1| 243 GE------------TTEEKWKKVQRGVFPGTLSNHHLNAMAALGVTLAEHLDY-GEAYAKQIIKNAQTLGSELSKLG 306
                                       88............678899***************************998754.479******************** PP

                                       -EEGG...GS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS..STTTT-SEEEEESHHHHHTT--HHHH CS
                              SHMT 321 yklvs...gGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd..ksalvtsGlrlGtpaltsrgfkeedl 392
                                       ++++    g t +h + +d++++g  Gk++ + le++ni  nkn +P+d  k+++ +sG+r+Gt  +t+ gfke+d+
  gi|518652184|ref|YP_008141704.1| 307 FNVLGeknGFTKSHTLAIDVSKNG-GGKEVAEKLESCNIILNKNLLPYDdnKKSMNPSGIRIGTQEVTRIGFKEADI 382
                                       ***96231459********97655.8999999****************99999************************ PP

                                       HHHHHHH CS
                              SHMT 393 ekvakfi 399
                                       +++a++i
  gi|518652184|ref|YP_008141704.1| 383 KELAELI 389
                                       ***9986 PP

>> SelA  L-seryl-tRNA selenium transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.8e-10   1.7e-06     173     331 ..     190     348 ..     185     367 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.8e-10
                                       EEEEEES-B-S-GGG.GT-----BHHHHHHTT-SEEEEETTSTT-SSS-EEEEE-..HHHHHHHHHSTHHHHTB--H CS
                              SelA 173 vleDlGsGllvdlse.yglskePtvqealaeGvdlvsfsGDkllGgpqaGiivGk..kelieklkknplkraLrvDk 246
                                       +le++Gs ++ d ++  gl    ++q+ l+eG+++++ s  k l gpq Gii+G+   e  +k+++  +   L    
  gi|518652184|ref|YP_008141704.1| 190 TLEEIGSTVVYDAAHvLGLIGGKQFQDPLREGAQIITGSTHKTLPGPQHGIIIGEttEEKWKKVQRGVFPGTLSNHH 266
                                       68999*****998763699***********************************73357789999999999999999 PP

                                       HH.HHHHHHHHHHHH..TT-GGGSHHHHHHH--HHHHHHHHHHHH.HHHTTSTT..EEEEEEEEEE-TCSSS-SS-- CS
                              SelA 247 lt.laaleatlrlyldpeklaeklptlrlltqkleelrakaerlq.kelkealgselevkvvkslsqvGsGslPvee 321
                                       l+ +aal  tl  +ld  +++ k ++     +++++l ++ ++l  + l e+ g + + ++  ++s+ G+G    e+
  gi|518652184|ref|YP_008141704.1| 267 LNaMAALGVTLAEHLDYGEAYAKQII-----KNAQTLGSELSKLGfNVLGEKNGFTKSHTLAIDVSKNGGGKEVAEK 338
                                       85489999999999987776655322.....3333343344444312344444444444555556677999999999 PP

                                       EEEEEEEEEE CS
                              SelA 322 lpsaaltiae 331
                                       l+s  + +++
  gi|518652184|ref|YP_008141704.1| 339 LESCNIILNK 348
                                       9998887766 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 !   23.5   0.0   4.5e-09   2.7e-05      74     306 ..      96     316 ..      87     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 4.5e-09
                                       ESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHH.....HHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCT CS
                     Aminotran_1_2  74 gsGagaliealifllklnpgdeilvpdptyasykn.....ilrlsggevvryplyseedfhldlealeealkeapeg 145
                                       +sG++++ ++l +++k  pgd i  p+++ + ++      ++  +g++   yp  + +++++++++ +++lk+a   
  gi|518652184|ref|YP_008141704.1|  96 LSGTNSNMAVLYAFTK--PGDTITTPALSGGGHISsapfgAVGFRGLKTLNYP-FDVDEMNINVDGTIKLLKQA--- 166
                                       6899999999999999..99999999999999997222223456777777777.44799999999999999997... PP

                                       TETEEEEEEE.SS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSS CS
                     Aminotran_1_2 146 nkktkvilve.sphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsK 221
                                         k+k+ ++  s++      + +  l++l d+ ++ +  ++ D a+  +  g +++      + e+   +i+gs  K
  gi|518652184|ref|YP_008141704.1| 167 --KPKLAWFGqSVF------LFPTPLKELRDTLEEIGSTVVYDAAHVLGLIGGKQF---QDPLREGAQ-IITGSTHK 231
                                       ..555555541333......4444577777779999****************9987...678888888.99999999 PP

                                       TTSSGGG-EEEEEEEH...HHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS CS
                     Aminotran_1_2 222 afGlaGeRvGyilgna...avvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLael 295
                                        +  +G   G+i+g     ++++ +r +  + ls  +l a++a  +  a+   ++ e+ +++++k++++l +eL +l
  gi|518652184|ref|YP_008141704.1| 232 TL--PGPQHGIIIGETteeKWKKVQRGVFPGTLSNHHLNAMAALGVTLAEH-LDYGEAYAKQIIKNAQTLGSELSKL 305
                                       85..66668*****5557788888888888888888888877777777665.46*********************** PP

                                       TEEEECCSCSS CS
                     Aminotran_1_2 296 glkvlasqsgm 306
                                       g++vl++++g+
  gi|518652184|ref|YP_008141704.1| 306 GFNVLGEKNGF 316
                                       ******99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2882.22
//
Query:       gi|518652185|ref|YP_008141705.1|  [L=439]
Description: hypothetical protein FACI_IFERC00001G0824 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       880  (0.0490825); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2920.43
//
Query:       gi|518652186|ref|YP_008141706.1|  [L=91]
Description: hypothetical protein FACI_IFERC00001G0825 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.98s 00:00:01.45 Elapsed: 00:00:00.67
# Mc/sec: 407.33
//
Query:       gi|518652187|ref|YP_008141707.1|  [L=244]
Description: hypothetical protein FACI_IFERC00001G0826 [Ferroplasma acidarmanus fer1]
Scores for complete 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-58  195.8   0.3      7e-58  195.5   0.3    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 !  195.5   0.3   3.9e-62     7e-58       3     204 ..      45     241 ..      43     242 .. 0.98

  Alignments for each domain:
  == domain 1  score: 195.5 bits;  conditional E-value: 3.9e-62
                                       ---SEEEEEEEEE-TT---EEEEE--B-SS--TTSS-TT-B--B-HHHHHHHHHHHHGGGGGSTT-EEEE--S-SS- CS
                    tRNA_deacylase   3 edvdliiflSrHssesgkplLTvHvtGnlgeaelGGkpeelapaaPrllkallralkkiaekleefevtlEatHHGP 79 
                                       e v+ ++flS+Hss+++ ++LTvH++Gn+++aelGG ++ + p+ P  + a lr +k+   + ++fe+t+EatHHGP
  gi|518652187|ref|YP_008141707.1|  45 EGVEKVVFLSKHSSKADIKSLTVHPIGNFRKAELGGLDNVIVPSDPLGMGASLRYIKNNY-SGDHFEITFEATHHGP 120
                                       66899*****************************************************99.9*************** PP

                                       ----S-EEEEEEEESHHHHT-HHHHHHHHHHHHHHHH------EEEEEE-S-TT-HHHHHHHHHBSEEEEEEE-GGG CS
                    tRNA_deacylase  80 telkvPslFvEiGSteeeWkdedaaeavaeavlelleseeekekvlvgiGGgHYaprftklvletevavGhilskya 156
                                       + +++P++F+EiG+te+eWk+e  a+++a+a++e++e++     ++vg+GGgHYap+ + +++++++++Ghi++ky+
  gi|518652187|ref|YP_008141707.1| 121 Y-MEKPAYFIEIGTTENEWKQEGIAALMARAIMEGVEKD---YGNYVGVGGGHYAPKLSSYFFSNDINIGHIIPKYV 193
                                       *.*********************************9999...99********************************* PP

                                       GGG--HHHHHHHHHHH.T-SEEEE-TTT--HHHHHHHHHHHHHHT-EE CS
                    tRNA_deacylase 157 leelkeevikqaleksegadvalidkkslkseqkeaieelleelgiev 204
                                       +e ++e+ i++a+ k+ +++ +l+d  ++k++ k++i+++++++++ev
  gi|518652187|ref|YP_008141707.1| 194 HEIISEDEIENAVLKTMNCKGFLMDAHGTKGRVKDMITRIADKHSLEV 241
                                       ********************************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1836.46
//
Query:       gi|518652188|ref|YP_008141708.1|  [L=311]
Description: threonine synthase [Ferroplasma acidarmanus fer1]
Scores for complete 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-44  151.5   0.0    3.9e-44  151.2   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 !  151.2   0.0   2.2e-48   3.9e-44       8     294 .]      12     308 ..       7     308 .. 0.91

  Alignments for each domain:
  == domain 1  score: 151.2 bits;  conditional E-value: 2.2e-48
                                       --EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEE CS
                              PALP   8 TPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaallGlkvti 83 
                                       +Pl+r  ++   l    +f+K+E+ nptg  KdR     ++++ ++ g k + +a+ GN g+++A++a+ +G+k+++
  gi|518652188|ref|YP_008141708.1|  12 SPLIRDSAIGNYLERSnFFIKYEGVNPTGTQKDRISRKHVENAIKQ-GYKEISVATCGNFGASIAYYARGMGIKAIV 87 
                                       79********9999999*************************9999.9***************************** PP

                                       EEETTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTT..SHHHHHHHHTHHHHHHHHTTTTE CS
                              PALP  84 vvpadaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfd..nptviegygtiglEileqlggkp 158
                                        +pa  s+++ a + ++Ga+++e +  y+e v++++e a++ +++y +s+++   +  + gy+ i +Ei+ qlg +p
  gi|518652188|ref|YP_008141708.1|  88 GIPAEYSNSRHAEIAAYGADIIEKPLKYEEMVEYIREEAKN-NNWYDASPGSpnKSIDVSGYSEISFEIYNQLGFAP 163
                                       *****************************************.*********9866669999**************** PP

                                       EEEEEE-SSSHHHHHHHHHHHH....HSTT....-EEEEEEECTTCGGTTCCS..S.SS..B..SSS.CCSTCS... CS
                              PALP 159 davvvpvGgGgliaGiaaglke....rrpd....vrvigvepegsdalarslragrrvtvpvs.dtiadglavg... 223
                                       +++  pvG+G ++ Gi+ g+ +    r  +    +++i+  +eg +++  s+ +g r  v+   + i++  a+    
  gi|518652188|ref|YP_008141708.1| 164 EYISIPVGNGTTFYGIYYGFLKlyrnR--KidkmPKFIATSTEGGNPIVYSFINGFRNIVELNpENIVETYANEpli 238
                                       **********************87442..35689*********6666666666999988888875555555555555 PP

                                       ....CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 224 ....spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvviltg 294
                                            ++ +a+++l ++ +++  vsd  + e  r + + + + v p+sa a a++      +++++ ++v++ltg
  gi|518652188|ref|YP_008141708.1| 239 ayrsYDGQKALDALYKTHGKALYVSDMKMEEISRGFRKIDNLSVLPASASAAAGA-----LKFAGNNSCVIVLTG 308
                                       5789999************************************************.....899999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 2133.00
//
Query:       gi|518652189|ref|YP_008141709.1|  [L=342]
Description: hypothetical protein FACI_IFERC00001G0828 [Ferroplasma acidarmanus fer1]
Scores for complete 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  218.1   0.0    9.3e-65  217.7   0.0    1.2  1  DUF1611    Domain of unknown function (DUF1611_C) P-loop doma
      4e-27   94.3   0.0      7e-27   93.5   0.0    1.4  1  DUF1611_N  Domain of unknown function (DUF1611_N) Rossmann-li
     0.0023   17.7   0.3       0.46   10.3   0.1    3.2  4  DUF2064    Uncharacterized protein conserved in bacteria (DUF
  ------ inclusion threshold ------
      0.088   11.9   0.1       0.13   11.4   0.1    1.2  1  APG17      Autophagy protein Apg17


Domain annotation for each model (and alignments):
>> DUF1611  Domain of unknown function (DUF1611_C) P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7   0.0   2.1e-68   9.3e-65       3     197 ..     141     333 ..     139     336 .. 0.98

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 2.1e-68
                           DUF1611   3 adgkarevkakrvlvvGTdcavGKrttaleleealeerGlkaafvaTgqtgili.agegvvldavvvdfvaGavegl 78 
                                       ++gk++evk k+++v+GTd+a+GKrtta+ l++a++++  ++++++Tgqt++++   + vv+d++++dfvaG++e++
  gi|518652189|ref|YP_008141709.1| 141 FTGKIQEVKSKKIAVLGTDSAIGKRTTAVYLNDAMNRKKKQSELIGTGQTSWMQgFPYTVVMDSIINDFVAGSLEYI 217
                                       799************************************************************************** PP

                           DUF1611  79 vkkaaeeeepdlilveGQgsLthpaysgvtlglLlGsqPdalvLchrpgrkhirglpeialppleeeieliealaak 155
                                       + ka++e++p+++++eGQgs++hpay+g  ++++ + +Pda++L+h+p+rk+++g+pe++++ple++i+++e +++k
  gi|518652189|ref|YP_008141709.1| 218 TYKAWQEKQPEYMFLEGQGSILHPAYPG-GFEIIGAMRPDAIILQHAPKRKFYDGFPEYPIEPLEKYIKVLELVSNK 293
                                       ****************************.************************************************ PP

                           DUF1611 156 kkvvgislNtknlseeeakealeeleeelglpvvdpvregae 197
                                       k v++islNt+n+++ e++ +  +le+ +++pv+dp++e  e
  gi|518652189|ref|YP_008141709.1| 294 K-VIAISLNTENMEKSEIEVEKTKLEKIYNIPVFDPLEE-FE 333
                                       9.***********************************98.55 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 !   93.5   0.0   1.6e-30     7e-27       4      93 ..      41     132 ..      38     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.5 bits;  conditional E-value: 1.6e-30
                         DUF1611_N   4 aGkdagelldd..rgipvvssleealaagaevlviGiapeggklpeswreavkeAleaGldvvsGlHerLsddpela 78 
                                        G+dag +l +  +gi +vs+++ea a ga +l+iG+a+ gg+lp ++r++v +A+e+G+++v+GlH+++s+d+e++
  gi|518652189|ref|YP_008141709.1|  41 YGMDAGYVLMGrqNGIRIVSTIQEAKALGATTLIIGVATDGGYLPVEYRQYVSTAIEEGMNIVNGLHQYISNDNEFS 117
                                       6899999998779**************************************************************** PP

                         DUF1611_N  79 alakkkgvkiiDvRk 93 
                                       +lak ++v+i D+Rk
  gi|518652189|ref|YP_008141709.1| 118 KLAKIYDVEITDIRK 132
                                       **************8 PP

>> DUF2064  Uncharacterized protein conserved in bacteria (DUF2064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.37   1.7e+03      98     108 ..      44      54 ..      42      65 .. 0.81
   2 !   10.3   0.1    0.0001      0.46      83     107 ..      65      89 ..      59     100 .. 0.82
   3 ?   -2.3   0.0      0.83   3.7e+03      60      72 ..     149     161 ..     141     186 .. 0.66
   4 ?    3.4   0.0     0.014        64      86     110 ..     232     255 ..     230     267 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.37
                                       TSSEEEEEEEG CS
                           DUF2064  98 DGGYyllGlkk 108
                                       D GY+l+G ++
  gi|518652189|ref|YP_008141709.1|  44 DAGYVLMGRQN 54 
                                       89******875 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0001
                                       HHHTTT-SEEEEEBTTSSEEEEEEE CS
                           DUF2064  83 feaLeeadaVlgpaeDGGYyllGlk 107
                                       ++aL ++ +++g a+DGGY  + ++
  gi|518652189|ref|YP_008141709.1|  65 AKALGATTLIIGVATDGGYLPVEYR 89 
                                       689****************866555 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.83
                                       T-SEEEEE-SS-T CS
                           DUF2064  60 geepvlliGsDcp 72 
                                       +++++ ++G+D+ 
  gi|518652189|ref|YP_008141709.1| 149 KSKKIAVLGTDSA 161
                                       4558899999974 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.014
                                       TTT-SEEEEEBTTSSEEEEEEEG-G CS
                           DUF2064  86 LeeadaVlgpaeDGGYyllGlkkrl 110
                                       Le +  +l pa  GG+ ++G  + +
  gi|518652189|ref|YP_008141709.1| 232 LEGQGSILHPAYPGGFEIIGAMR-P 255
                                       556677999***********994.4 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   2.8e-05      0.13     284     345 ..      90     152 ..      84     170 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.8e-05
                                       .....HHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             APG17 284 ev.gkklpeylaifkaeeeflerweeekekieekleeleeLrefYegFlsaYdklllEveRRr 345
                                       +  +++++e ++i++  ++ +++ +e+ +  + +  e+++ r+ +++++ ++ ++++Ev+ ++
  gi|518652189|ref|YP_008141709.1|  90 QYvSTAIEEGMNIVNGLHQYISNDNEFSKLAKIYDVEITDIRKIFNNYEYSFTGKIQEVKSKK 152
                                       444999*****************************************************8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); 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:                         4  (0.000223102); expected 0.2 (1e-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 0.27s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2284.35
//
Query:       gi|518652190|ref|YP_008141710.1|  [L=471]
Description: hypothetical protein FACI_IFERC00001G0829 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


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:                      395  (0.0220313); 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: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2822.97
//
Query:       gi|518652191|ref|YP_008141711.1|  [L=164]
Description: hypothetical protein FACI_IFERC00001G0830 [Ferroplasma acidarmanus fer1]
Scores for complete 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-38  130.3   0.0    3.8e-38  130.1   0.0    1.1  1  Ribo_biogen_C  Ribosome biogenesis protein, C-terminal
    0.00017   21.3   0.0     0.0004   20.2   0.0    1.6  1  RLI            Possible Fer4-like domain in RNase L inhibitor
  ------ inclusion threshold ------
      0.055   13.2   0.0       0.12   12.1   0.0    1.6  1  DTW            DTW domain


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 !  130.1   0.0   6.4e-42   3.8e-38       3     126 ..      42     163 ..      40     164 .] 0.97

  Alignments for each domain:
  == domain 1  score: 130.1 bits;  conditional E-value: 6.4e-42
                                       E-TT-SSB--GGGHHHHHHT-EEEE---TTT--GGGTTT-E....EB--S-B--STTTTT-BS---HHHHHHHHHHH CS
                     Ribo_biogen_C   3 lspkakkvlspaDreiveksgiavvdcsWarleevkfkklkakeerlLPyLvAaNpvnYgkplkLscvEAlaaalyi 79 
                                       l+p+++++l ++++ + e++gi+v+d sW+r+++++  ++k+k+ ++LP+L+  NpvnYgkp kLs++EAlaaalyi
  gi|518652191|ref|YP_008141711.1|  42 LTPYSDNFLLNSNKMLFEDKGIVVIDGSWNRINTIE--NIKGKNGKKLPLLLPVNPVNYGKPGKLSSLEALAAALYI 116
                                       99******************************9998..88899********************************** PP

                                       TT-HHHHHHHHTSSTTHHHHHHHCHHHHHHH.TT--HHHHHHHHHHH CS
                     Ribo_biogen_C  80 lglkeeaeellskfkwgeeFlelnkelleeYakckdseevvevqkey 126
                                       +g++e a +++sk++w+++F++ n ++l++Y+kc+++ee ++vq++y
  gi|518652191|ref|YP_008141711.1| 117 MGYSELAGDVISKYSWAQNFIKTNINPLNDYMKCNSDEECIQVQDSY 163
                                       ********************************************998 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 !   20.2   0.0   6.6e-08    0.0004       3      29 ..       4      30 ..       3      36 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 6.6e-08
                                      EEEES---------TTHHHHHTTSEEE CS
                               RLI  3 lAivdadqCdPKKCtgkkcarfcpvrl 29
                                      ++ v+ +q+dPKK t kk++r++++ +
  gi|518652191|ref|YP_008141711.1|  4 IFYVYLGQDDPKKSTMKKLERYGLAIE 30
                                      66699*******************944 PP

>> DTW  DTW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     2e-05      0.12     106     177 ..      54     118 ..      15     149 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2e-05
                               DTW 106 kkeefeekrlillDGTWsqAkkilrrnprledlpqvkLk.kgesseyerlRkqpkkgclSTiEaiayaLkele 177
                                       +k  fe k ++++DG W+  + i  +n + ++ +++ L  + +  +y       k g lS +Ea a aL  ++
  gi|518652191|ref|YP_008141711.1|  54 NKMLFEDKGIVVIDGSWNRINTI--ENIKGKNGKKLPLLlPVNPVNY------GKPGKLSSLEALAAALYIMG 118
                                       455689999**********9999..4444444455555444455777......67888888888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.32s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1019.22
//
Query:       gi|518652192|ref|YP_008141712.1|  [L=453]
Description: hypothetical protein FACI_IFERC00001G0831 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-43  149.4  24.0    4.1e-42  144.6  24.0    2.1  1  Sugar_tr  Sugar (and other) transporter
    3.9e-42  144.5  43.9    1.3e-27   96.6  23.8    2.0  2  MFS_1     Major Facilitator Superfamily
     0.0029   17.0   4.2     0.0029   17.0   4.2    2.7  3  MFS_4     Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.6  24.0   6.8e-46   4.1e-42      49     448 ..      65     451 ..      30     452 .. 0.86

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 6.8e-46
                                       HHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  49 glivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPm 125
                                        + +s+ l+G +iGs+++g l+d+fGR  s++ + +l+ ig++  a++    +v  l++ R+++Gig+G+  +lv++
  gi|518652192|ref|YP_008141712.1|  65 FIALSVGLIGYAIGSYLIGSLADVFGRYRSMILTMALTAIGSLGDALSF---NVPELTIFRFITGIGLGADLNLVSI 138
                                       45678889*****************************************...************************* PP

                                       HHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT CS
                          Sugar_tr 126 yisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekg 202
                                       yi E+Ap+++Rg++++l+ l  +fG+ v+ ++g++l      +gwr+l+g+ +++a + ++l++ lPESPr+l +kg
  gi|518652192|ref|YP_008141712.1| 139 YITEFAPAAVRGKITVLTFLIGIFGQAVTPFIGYFLVPAFP-TGWRWLFGIGAIIAFIAVFLRTELPESPRWLATKG 214
                                       ************************************98888.8********************************** PP

                                       -HH.HHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.......HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHH CS
                          Sugar_tr 203 kee.eakevlaklrgeedadrelaeekdsleaeqeee..kaswkellssktvrqrlligvvlqifqqltGinaimyy 276
                                       +   +a++vl+    e+ a++++ e  + + +++  e  k  +  l+++  ++ r+++ ++++ f  + G+ a++  
  gi|518652192|ref|YP_008141712.1| 215 HNLeKAEKVLEM--MEATAKKKIGELPEPHPENVVVEepKFPTLYLFKK-PYTGRMVLLIAVW-FLWYIGNYAFLGD 287
                                       9877********..66777888888888888877766533444444443.5788888888775.56899******** PP

                                       TTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH...HHHHTTSS...C CS
                          Sugar_tr 277 sptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg.ivalllvakskaas 349
                                       + +++e++g+s+    l++ i+ ++   +  ++ ++++d+  R+ + +  +++ ++ ++ ++  ++           
  gi|518652192|ref|YP_008141712.1| 288 AASLLESIGFSEAaaiLYIAIGAIIGYPAGALIMLYTSDKYERKHVIFAATVVWFLGMISMAtRMT----------- 353
                                       *************999999999999999****************9999999999999999972222........... PP

                                       HHHHHHHHHHHHHHHTTTT...HHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHH CS
                          Sugar_tr 350 ivaivfialfialfalgwg...pvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfa 423
                                        +    +++  +l a+g+g    v +   +E +p++ Rs++  i+  +      l ++l pi++ +++ ++ f + +
  gi|518652192|ref|YP_008141712.1| 354 DL----LYFGSFLGAMGLGmylQVAYTFTAENYPTRARSSGFGITDGIGHGGGALGAILLPILVATYSWAFGFTFIG 426
                                       23....33333333444442226889999***************************************677777777 PP

                                       HHHHHHHHHHHHHS--STT--CCCC CS
                          Sugar_tr 424 glavlfiifvfffvpetkgrtleei 448
                                       +  +++ + ++++      r le+i
  gi|518652192|ref|YP_008141712.1| 427 ITGLVAGLLILIGGTKVSRRNLEDI 451
                                       7788888888888888777777766 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.6  23.8   2.2e-31   1.3e-27       2     260 ..      32     316 ..      31     322 .. 0.84
   2 !   55.6  19.9   6.6e-19   3.9e-15      23     182 ..     291     448 ..     288     453 .] 0.90

  Alignments for each domain:
  == domain 1  score: 96.6 bits;  conditional E-value: 2.2e-31
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                        l++f++++++s +g+a+p a+ +++++ +s i + +l++  +g+a++s+++G+l+d fGr r ++l+++l+a+g+l
  gi|518652192|ref|YP_008141712.1|  32 GLGYFFTFYDISDIGLAMP-AIDQQFNLHGSIILFiALSVGLIGYAIGSYLIGSLADVFGRYRSMILTMALTAIGSL 107
                                       689****************.*******9999988856777888********************************66 PP

                             MFS_1  78 lllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wra 152
                                         +++ +++ l ++r+++G+g ga + ++ ++i++ +p   rg+ + l  +   +G +++p +g +l+ ++   Wr+
  gi|518652192|ref|YP_008141712.1| 108 GDALSFNVPELTIFRFITGIGLGADLNLVSIYITEFAPAAVRGKITVLTFLIGIFGQAVTPFIGYFLVPAFPtgWRW 184
                                       5556689999**********************************************************888778*** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeee............................kgtgpaplvpawk 201
                                       +f i ai++++a  +  +l +e p ++++ ++k                               + +++ p +p   
  gi|518652192|ref|YP_008141712.1| 185 LFGIGAIIAFIA--V--FLRTELPESPRWLATKGHNlekaekvlemmeatakkkigelpephpeNVVVEEPKFP-TL 256
                                       ***********9..3..555444444444444444458899999999999988888887777776666666666.88 PP

                             MFS_1 202 allkdpvlw...illialllfffgfsglltllplylqevlglsglllaglllallalvgail 260
                                       +l+k+p+     +l+++++l+ +g++++l    + l e  g+s    a l++a++a++g ++
  gi|518652192|ref|YP_008141712.1| 257 YLFKKPYTGrmvLLIAVWFLWYIGNYAFLGDAAS-LLESIGFS-EAAAILYIAIGAIIGYPA 316
                                       8999996634467**************9999999.5*******.566666678888877444 PP

  == domain 2  score: 55.6 bits;  conditional E-value: 6.6e-19
                             MFS_1  23 laedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvlrvlqGl 97 
                                       l e+ g+s++++ l +++   +g+ +++l++ + sd++ r+ v++++ ++++lg  ++++a+ ++ ll+++ +l ++
  gi|518652192|ref|YP_008141712.1| 291 LLESIGFSEAAAILYIAIgAIIGYPAGALIMLYTSDKYERKHVIFAATVVWFLG--MISMATRMTdLLYFGSFLGAM 365
                                       5688899999999977773666****************9999************..4444599999*********** PP

                             MFS_1  98 gagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpe 174
                                       g g+++ ++++++a+ +p + r++++g+  +    G +lg++l ++l++ ++W   f +++i +l+a++l  +l+  
  gi|518652192|ref|YP_008141712.1| 366 GLGMYLQVAYTFTAENYPTRARSSGFGITDGIGHGGGALGAILLPILVATYSWAFGFTFIGITGLVAGLL--ILIGG 440
                                       *********************************************************************8..77777 PP

                             MFS_1 175 epperkrk 182
                                       ++++r++ 
  gi|518652192|ref|YP_008141712.1| 441 TKVSRRNL 448
                                       77766665 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   4.2   4.8e-07    0.0029      28     185 ..      61     219 ..      46     232 .. 0.74
   2 !    8.6   1.3   0.00017         1      19      77 ..     291     350 ..     279     363 .. 0.77
   3 ?   -1.4   0.2      0.18   1.1e+03     281     301 ..     412     432 ..     385     443 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.8e-07
                             MFS_4  28 sqaglla.aaNylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfg 102
                                       s + ++a ++ ++GY +G+ l   +l+    R r +   + +t++  l  al  ++  +++ Rf++G++ ++ l ++
  gi|518652192|ref|YP_008141712.1|  61 SIILFIAlSVGLIGYAIGSYLI-GSLADVFGRYRsMILTMALTAIGSLGDALSFNVPELTIFRFITGIGLGADLNLV 136
                                       5555666577889999999866.56666666666566677788899999**************************** PP

                             MFS_4 103 sslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpraalreasa 179
                                       s  + + a aa r+++  l f    +G av+  + ++l+ ++  +  + ++++++ a + + + + lp++++  a +
  gi|518652192|ref|YP_008141712.1| 137 SIYITEFAPAAVRGKITVLTFLIGIFGQAVTPFIGYFLVPAFPTGWRWLFGIGAIIAFIAVFLRTELPESPRWLATK 213
                                       *********************85557999999999988887766654445566666666666667777666666665 PP

                             MFS_4 180 aaeaak 185
                                         + +k
  gi|518652192|ref|YP_008141712.1| 214 GHNLEK 219
                                       555533 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00017
                             MFS_4  19 llaegqlsls.qagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamal 77 
                                       ll+  ++s + ++ ++a +  +GY +Gal+ +++  + + + ++ a++++ +l ++ ma 
  gi|518652192|ref|YP_008141712.1| 291 LLESIGFSEAaAILYIAIGAIIGYPAGALIMLYTSDKYERKHVIFAATVVWFLGMISMAT 350
                                       5666677655055799*************9977776666666688888888888888775 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.18
                             MFS_4 281 glivssvllGltflaitalvl 301
                                       +++  s  +G tf++it lv 
  gi|518652192|ref|YP_008141712.1| 412 LVATYSWAFGFTFIGITGLVA 432
                                       344456678999999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.34s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2777.43
//
Query:       gi|518652193|ref|YP_008141713.1|  [L=536]
Description: hypothetical protein FACI_IFERC00001G0832 [Ferroplasma acidarmanus fer1]
Scores for complete 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-116  387.5   2.0   3.8e-116  387.0   2.0    1.2  1  CTP_synth_N    CTP synthase N-terminus
    7.1e-50  169.4   0.0    1.2e-49  168.7   0.0    1.3  1  GATase         Glutamine amidotransferase class-I
    6.6e-06   26.0   0.0      0.002   17.9   0.0    2.5  2  Peptidase_C26  Peptidase C26
     0.0005   20.1   0.0    0.00081   19.4   0.0    1.6  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
     0.0014   18.6   0.0       0.13   12.1   0.0    2.4  2  SNO            SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.092   12.7   0.1    2.5  2  AAA_31         AAA domain
       0.06   12.3   0.6       0.11   11.5   0.0    1.6  2  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.099   11.7   0.0       0.59    9.2   0.0    2.0  1  GATase_5       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 !  387.0   2.0  1.7e-119  3.8e-116       2     262 ..       3     258 ..       2     261 .. 0.98

  Alignments for each domain:
  == domain 1  score: 387.0 bits;  conditional E-value: 1.7e-119
                                       EEEEEE--STTTTHHHHHHHHHHHHHCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT CS
                       CTP_synth_N   2 yilvtGGvvSglGkGiiaaslgallksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfld 78 
                                       yi++tGGv+SglGkG i++ l+ llk++g+kvt ikiDPYln+dagt++p++hGEvfvl+dG+e+DlDlGnYeRfld
  gi|518652193|ref|YP_008141713.1|   3 YIVITGGVISGLGKGTITSGLSYLLKNSGFKVTNIKIDPYLNYDAGTMNPYQHGEVFVLNDGGEVDLDLGNYERFLD 79 
                                       9**************************************************************************** PP

                                       ----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHHHHHH.HCT-SEEEEEE-S-TTSGGGHHHHHH CS
                       CTP_synth_N  79 ikltkennittGkiyksviekerrGdylGktvqviphvtdeikeriekvakkveadvviveigGtvgdieslpflea 155
                                       ++l++ nnittGkiyk+viekerrGdylG+tvq+iph+t+eik+ri+k+a+    d++++e+gGtvgdies+pflea
  gi|518652193|ref|YP_008141713.1|  80 TNLSSGNNITTGKIYKEVIEKERRGDYLGSTVQIIPHITNEIKNRIRKAAD--GYDITLIEVGGTVGDIESMPFLEA 154
                                       **************************************************8..8*********************** PP

                                       HHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS---HHHHHHHHHHCT--GG CS
                       CTP_synth_N 156 irqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsekeleeevkekialfcnveke 232
                                       +rq+k +  +++v++ hvtlvp     +e+ktkptqhsvkelr++Giqpdi++crs++ l+e+  +ki+lf++ve++
  gi|518652193|ref|YP_008141713.1| 155 LRQMKSDR-HDSVIFGHVTLVPES--GQEQKTKPTQHSVKELRAIGIQPDILFCRSQHILNEDSIKKISLFTDVEEK 228
                                       ****9996.789**********87..59************************************************* PP

                                       GEEEEE--S-GGGHHHHHHHCTHHHHHHHH CS
                       CTP_synth_N 233 avisvkdvesiyevpllleeqglaelilek 262
                                        +isv dv+++y vp++le+qg+ e+  e 
  gi|518652193|ref|YP_008141713.1| 229 GIISVYDVSNVYMVPMVLENQGILEYTREI 258
                                       ***********************9987765 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.7   0.0   5.2e-53   1.2e-49       2     189 ..     295     517 ..     294     518 .. 0.91

  Alignments for each domain:
  == domain 1  score: 168.7 bits;  conditional E-value: 5.2e-53
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHH.THHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeile.llknpdgilvsgGpgspgvegkieaikearenkiPiLGI 77 
                                       + D+y s +e+  h   ++g+kv++++id++++   + +l+++dgil++gG+g++gvegki a+++aren++P+LGI
  gi|518652193|ref|YP_008141713.1| 295 MQDAYISHKEAFSHVTGNTGIKVNIKWIDSDDLVRSKeQLEDIDGILIPGGFGYRGVEGKIIAARYARENHVPYLGI 371
                                       68****************************999997767************************************** PP

                                       THHHHHHHHHTTTEEE.......................EEECEEEEEEEEEEEETTT........CGGTTTTSEEE CS
                            GATase  78 CLGmQllaiefgrkvv.......................kekekehhggtmrlgddet........allyglknevi 123
                                       CLG+Q+++ie+ r+++                       ++k+ +++ggtmrlg+++           ly++ +++ 
  gi|518652193|ref|YP_008141713.1| 372 CLGFQAAVIELSRDLIgldnanstefepdtvnpvidilpEQKNIKDLGGTMRLGAKPViikkgtlaYDLYKS-EKIS 447
                                       *************5555666666666666666777999*9999************999*****998788887.99** PP

                                       EEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
                            GATase 124 erhrHryevnpk...elepaglevtakseddeelmeiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                                       erhrHr+evnp+   +le+ag ++++++e++  +mei e+++   ++++Q+H E++s+p +p+ +   +ik
  gi|518652193|ref|YP_008141713.1| 448 ERHRHRFEVNPAyikRLENAGAVFSGTDEEG-IRMEILELNDrDnYIATQYHAEFQSRPLNPSRVHLYFIK 517
                                       ****************************998.8*********757*****************999888776 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.5   0.0    0.0058        13      19      67 ..     294     345 ..     286     349 .. 0.72
   2 !   17.9   0.0     9e-07     0.002      98     216 .]     358     500 ..     349     500 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0058
                     Peptidase_C26  19 daeesyla.asyveavekagglpvllpieedee..dvkaildkldgllltGg 67 
                                       d++++y++ ++ ++ v++  g+ v +   ++++    k++l+ +dg+l++Gg
  gi|518652193|ref|YP_008141713.1| 294 DMQDAYIShKEAFSHVTGNTGIKVNIKWIDSDDlvRSKEQLEDIDGILIPGG 345
                                       5566666514567889999999999866544440145789***********9 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 9e-07
                     Peptidase_C26  98 iraalergvPilgiCrGlqllnvalGGtlyq..dieeqsgltdhrehe...........q.....saashavkvekg 156
                                        r a e++vP lgiC+G+q   + l  +l    ++++++ + d +++            +        ++ v ++kg
  gi|518652193|ref|YP_008141713.1| 358 ARYARENHVPYLGICLGFQAAVIELSRDLIGldNANSTEFEPDTVNPVidilpeqknikDlggtmRLGAKPVIIKKG 434
                                       56788999*************9*9999997511444444444444444888888776651555568889******** PP

                     Peptidase_C26 157 sllaellgseeievnslHhqaike.....laeelrv.eAvaeDgv.iEaieseeakafvlgvQwHPE 216
                                       +l ++l++se+i+    H++ ++      l++   v + ++e g+ +E +e+++++  +++ Q+H+E
  gi|518652193|ref|YP_008141713.1| 435 TLAYDLYKSEKISERHRHRFEVNPayikrLENAGAVfSGTDEEGIrMEILELNDRD-NYIATQYHAE 500
                                       *******************9876555555776666615566688669******977.999*****98 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   3.6e-07   0.00081       8      55 ..      12     154 ..       4     470 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.6e-07
                                       TTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH.............................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                              CbiA   8 GGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep.............................. 54 
                                       +G GK t++ +L  +l++ g++V  ++ Dp  n +a   g+ n  +                               
  gi|518652193|ref|YP_008141713.1|  12 SGLGKGTITSGLSYLLKNSGFKVTNIKIDPYLNYDA---GTMNPYQHgevfvlndggevdldlgnyerfldtnlssg 85 
                                       9******************************88877...66666666777888888888888888888888888887 PP

                                       ....................................................................C CS
                                       ....................................................................x RF
                              CbiA  55 ....................................................................d 55 
                                                                                                            
  gi|518652193|ref|YP_008141713.1|  86 nnittgkiykeviekerrgdylgstvqiiphitneiknrirkaadgyditlievggtvgdiesmpfleA 154
                                       777766666666666666666666555555555555555555555555555555555554444444440 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   5.6e-05      0.13       5      42 ..     296     345 ..     293     388 .. 0.79
   2 ?    4.0   0.0     0.017        39     139     185 ..     465     518 ..     449     521 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.6e-05
                                       SSSHHHHHHHHHHTTSEE............EEE-SGGGGCC-SEEEE-SS CS
                               SNO   5 qGaveehveaikkclaen............ktvkrkedlaevdaliiPGG 42 
                                       q a++ h ea  ++  ++              v++ke+l+++d+++iPGG
  gi|518652193|ref|YP_008141713.1| 296 QDAYISHKEAFSHVTGNTgikvnikwidsdDLVRSKEQLEDIDGILIPGG 345
                                       66666666666665555556666777777688*****************9 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.017
                                       -.TTTCEEEEECTT...EEEEEE.ETTEEEESS-GGGST...THCHHHHHHHHH CS
                               SNO 139 lddeavkvlyeldg...eivvak.qkkilatsfhPelae...ddirvhdyfvee 185
                                        +  av + ++ +g   ei+  + +++++at +h e+     +  rvh yf+++
  gi|518652193|ref|YP_008141713.1| 465 ENAGAVFSGTDEEGirmEILELNdRDNYIATQYHAEFQSrplNPSRVHLYFIKK 518
                                       55555555566666666788888466**********987444678*******97 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   4.1e-05     0.092      12      54 ..      13      55 ..       4     154 .. 0.58
   2 ?   -1.9   0.0       1.2   2.8e+03      51     104 ..     475     527 ..     465     533 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekne 54
                                      G GK T +  l++ l ++g kv  + +Dp  n   g+    ++
  gi|518652193|ref|YP_008141713.1| 13 GLGKGTITSGLSYLLKNSGFKVTNIKIDPYLNYDAGTMNPYQH 55
                                      88****************************9998855433333 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.2
                            AAA_31  51 ekneiektlyevlieeknikeaiiktkvenldlipssidLaeaeielvelekke 104
                                       +++ i  +++e+ +++ n+  + +++++++  l ps ++L  ++++l   ++k+
  gi|518652193|ref|YP_008141713.1| 475 DEEGIRMEILEL-NDRDNYIATQYHAEFQSRPLNPSRVHLYFIKKSLEYRKEKR 527
                                       555566667776.44455555555678888899999999999999998777665 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 ?   11.5   0.0   4.8e-05      0.11      32      75 ..       4      49 ..       1      51 [. 0.86
   2 ?   -2.9   0.1       1.2   2.6e+03     119     131 ..     129     141 ..     126     148 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.8e-05
                                      EEEEE..-TTSSHHHHHHHHHHHHHCTT--EEEEEE---------- CS
                              MeaB 32 vGltG..vPGaGkstlvealglelrrrGkrvavlavDPsspftGGs 75
                                      + +tG  + G Gk t+++ l   l++ G +v+ + +DP  ++  G+
  gi|518652193|ref|YP_008141713.1|  4 IVITGgvISGLGKGTITSGLSYLLKNSGFKVTNIKIDPYLNYDAGT 49
                                      556765568*****************************98887775 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.2
                                       HTT-SEEEEEEES CS
                              MeaB 119 aaGfDvvlietvG 131
                                       a G+D+ lie  G
  gi|518652193|ref|YP_008141713.1| 129 ADGYDITLIEVGG 141
                                       67********766 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00026      0.59      34      71 ..     324     359 ..     301     403 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00026
                          GATase_5  34 msdllegrvslddfqilalpGGfsygDelgsgkgwaks 71 
                                         dl++++++l+d+ ++ +pGGf y  +   gk++a++
  gi|518652193|ref|YP_008141713.1| 324 SDDLVRSKEQLEDIDGILIPGGFGYRGVE--GKIIAAR 359
                                       46899********************8776..4555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.46
# Mc/sec: 3500.96
//
Query:       gi|518652194|ref|YP_008141714.1|  [L=110]
Description: sterol binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-08   35.6   0.6    1.1e-08   35.5   0.6    1.1  1  SCP2            SCP-2 sterol transfer family
    1.9e-07   31.4   0.1      3e-07   30.7   0.1    1.3  1  Alkyl_sulf_C    Alkyl sulfatase C-terminal
  ------ inclusion threshold ------
      0.052   13.8   0.1        0.1   12.9   0.1    1.6  1  FCH             Fes/CIP4, and EFC/F-BAR homology domain
      0.075   11.8   0.2      0.084   11.7   0.2    1.0  1  RHSP            Retrotransposon hot spot protein
      0.079   12.6   2.3        2.7    7.6   0.1    2.1  2  Lipoprotein_16  Uncharacterized lipoprotein


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.6     3e-12   1.1e-08       3      92 ..      11     100 ..       5     109 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3e-12
                                       HHHHHH.HHHHHHHHHCCH-EEEEEEECTC.TEEEEEETTSTEEESSCTTBS-SEEEEEEHHHHHHHHCTSS-HHHH CS
                              SCP2   3 qllerl.kdpekkealkklagvlrfdltdlkgsltldlkegqldvaakdegkadvtlslsledllelaegklnpqka 78 
                                       +l +++ +d++++++l++++  + +   d+  s+++ + +g ++  ++++ +ad t+++s++ + +++++++n++ a
  gi|518652194|ref|YP_008141714.1|  11 KLNDKIaSDQTYAKKLQSITKSIDIVFDDK-DSYYFKVENGHITEPQEGKIDADITVTVSSDVFNKILSKEINAMDA 86 
                                       455555445588888888888888888888.88*******99999888899************************** PP

                                       HHTTSSEEEC-HHH CS
                              SCP2  79 fmqgkLkieGDiel 92 
                                       +m+ ++ki+  ++ 
  gi|518652194|ref|YP_008141714.1|  87 YMKQQIKIKSSLMD 100
                                       ********987765 PP

>> Alkyl_sulf_C  Alkyl sulfatase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1   8.5e-11     3e-07      28     102 ..      25      96 ..      19     108 .. 0.86

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 8.5e-11
                                       HHTT-EEEEEEEETTTTEEEEEEEETTEEEE.ECT---TTSSEEEEE-HHHHHHHHTTSS-HHHHHHTTTEEEEE CS
                      Alkyl_sulf_C  28 kaadkdltinlvvtDvdekyllrlsngvLthtrkaaqaddadltvtltreqLvalllgkatlgkevaagklkieG 102
                                       k+++   +i++v+ D+ + y  +++ng +t   ++ +  dad+tvt++ + ++++l+++ ++ ++  ++++ki+ 
  gi|518652194|ref|YP_008141714.1|  25 KLQSITKSIDIVFDDK-DSYYFKVENGHITE-PQEGK-IDADITVTVSSDVFNKILSKEINAMDAYMKQQIKIKS 96 
                                       55566679*****996.8*************.55455.8*********************************974 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 ?   12.9   0.1   2.9e-05       0.1      16      45 ..       5      34 ..       2      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.9e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHCT--- CS
                               FCH 16 ledlqeflkeRaeiEkeYakkLqkLakkyl 45
                                      l+ l + l  + + ++ YakkLq ++k+++
  gi|518652194|ref|YP_008141714.1|  5 LNNLVKKLNDKIASDQTYAKKLQSITKSID 34
                                      566677788999**************9876 PP

>> RHSP  Retrotransposon hot spot protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   2.4e-05     0.084     302     391 ..      11     101 ..       2     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                              RHSP 302 PllrqileeesykrrvakieeavdeissvdkesyakvlqtaaeW.etdkvserlarvvrvkkengeecrn.apvsay 376
                                        l  +i  ++ y ++++ i + +d + + ++ +y kv ++  +  ++ k+   ++  v     n  ++++ +++ ay
  gi|518652194|ref|YP_008141714.1|  11 KLNDKIASDQTYAKKLQSITKSIDIVFDDKDSYYFKVENGHITEpQEGKIDADITVTVSSDVFNKILSKEiNAMDAY 87 
                                       56678999******************************9987651555666666666666666877666669999** PP

                              RHSP 377 leqkildklrvlldt 391
                                       ++q+i      l+d+
  gi|518652194|ref|YP_008141714.1|  88 MKQQIK-IKSSLMDK 101
                                       999953.44555555 PP

>> Lipoprotein_16  Uncharacterized lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.3    0.0039        14     134     158 ..       2      26 ..       1      27 [. 0.88
   2 ?    7.6   0.1   0.00075       2.7      82     139 ..      43     100 ..      39     110 .] 0.86

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0039
                    Lipoprotein_16 134 ekalnkllsevlkeilnDpelqqfl 158
                                       +++ln+l++++  +i++D++ ++ l
  gi|518652194|ref|YP_008141714.1|   2 KEVLNNLVKKLNDKIASDQTYAKKL 26 
                                       689****************987776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00075
                    Lipoprotein_16  82 lladvkegtlrykikakvqlevtaenakgkltknynasaeregalsasnakiekalnk 139
                                       ++ +v+ g+++   + k++  +t++ ++  + k  +++ +  +a + ++ ki+ +l +
  gi|518652194|ref|YP_008141714.1|  43 YYFKVENGHITEPQEGKIDADITVTVSSDVFNKILSKEINAMDAYMKQQIKIKSSLMD 100
                                       7899************************999999999999999999998888887754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1254  (0.0699426); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 794.47
//
Query:       gi|518652195|ref|YP_008141715.1|  [L=1080]
Description: hypothetical protein FACI_IFERC00001G0834 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
          0 1106.0   2.2          0 1105.9   0.2    1.9  2  PolC_DP2        DNA polymerase II large subunit DP2
    0.00036   20.5   1.8       0.65   10.0   0.2    2.7  2  HypA            Hydrogenase/urease nickel incorporation, meta
     0.0011   18.9   6.7       0.12   12.4   1.1    2.4  2  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.045   13.7   3.6        3.7    7.6   0.5    2.5  2  zinc-ribbons_6  zinc-ribbons
      0.056   13.6   0.0      0.056   13.6   0.0    2.1  1  DUF3340         C-terminal domain of tail specific protease (
      0.067   13.3   0.4       0.24   11.5   0.4    2.1  1  DUF1931         Domain of unknown function (DUF1931)
      0.069   12.8   1.8        1.2    8.8   0.1    2.4  2  TackOD1         Thaumarchaeal output domain 1
       0.49   10.6  10.7       0.72   10.0   1.1    2.9  2  Zn-ribbon_8     Zinc ribbon domain
       0.58    9.9  10.3          6    6.7   0.9    3.3  3  Rubredoxin_2    Rubredoxin metal binding domain
        1.7    8.2  14.2         27    4.4   0.7    4.3  4  TF_Zn_Ribbon    TFIIB zinc-binding
        2.3    8.8   4.8         19    5.8   1.1    2.5  2  zf-CHY          CHY zinc finger
        2.6    8.1   6.4         43    4.2   0.1    3.5  3  ADK_lid         Adenylate kinase, active site lid


Domain annotation for each model (and alignments):
>> PolC_DP2  DNA polymerase II large subunit DP2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1105.9   0.2         0         0       1     864 []       8     826 ..       8     826 .. 0.97
   2 ?   -4.3   0.2       1.9   2.9e+03     618     638 ..     992    1016 ..     983    1040 .. 0.57

  Alignments for each domain:
  == domain 1  score: 1105.9 bits;  conditional E-value: 0
                          PolC_DP2   1 eYfeklekeleeayeiaekarskgldpkeevEiplAkdladRvekllgikgvaerirelekelsreevalkiakeia 77 
                                       +Y + le++++e+y+iae+ars g+d+++evEiplA+d+a+Rvekl++i+g+a+ irel+k++sreev+l+i++++a
  gi|518652195|ref|YP_008141715.1|   8 KYNKILENKVSECYQIAEEARSLGKDVSTEVEIPLANDMAERVEKLIQIDGIADDIRELSKTMSREEVSLAISRKVA 84 
                                       699*************************************************************************9 PP

                          PolC_DP2  78 egkvgeaeskeeavdkavrtalalltegvvaAPleGiakvkikknddgteylkvyyaGPiRsaGGtaqalsvLvaDy 154
                                       e+     ++++ a++k+vr++la+lteg+++APleGi++v+i +nddgtey++++y+GPiRsaGGtaqalsvL+aD+
  gi|518652195|ref|YP_008141715.1|  85 ERLK---DDRRLALEKSVRVGLAILTEGILVAPLEGIKTVDIVSNDDGTEYVDIVYSGPIRSAGGTAQALSVLMADI 158
                                       9876...67999***************************************************************** PP

                          PolC_DP2 155 vrkklgldrykpreeeieRyveEielYervaslqyspsdeeirlivknipveidGeatedeevsgyrdlervetnrv 231
                                       vr++l+++++k+++eeieRy+eEi+ Y+r ++lqy p++eeirl++ n pv+idGe +e+ee+sg+rd++r+ tnr+
  gi|518652195|ref|YP_008141715.1| 159 VRRELNIGSFKATDEEIERYIEEIQAYNRSKHLQYLPTPEEIRLVIGNSPVMIDGEGSEEEEISGHRDMRRIPTNRI 235
                                       ***************************************************************************** PP

                          PolC_DP2 232 RGGmllvlaeGialkakKikkkvkklklegWewleelikaekeekkeeeeekkevkpkekylrdliaGRpvlshpsr 308
                                       RGGm+lvl+eG+++k++K++k+++ +k+e+W+ le++ k+    kkee+ +     +++kylrd+iaGRpv+++p+r
  gi|518652195|ref|YP_008141715.1| 236 RGGMCLVLCEGLIQKSRKVLKYTSLMKMEEWNILENIGKN----KKEEKGD-----NSQKYLRDIIAGRPVFGYPNR 303
                                       ***********************************99998....3333332.....4789***************** PP

                          PolC_DP2 309 kGGfRLrYGRsrntglatagihPatmelldeflavGtqlkverPgKaaavvpvdsiegPtvklknGdvvriddveea 385
                                       +GGfRLrYGRsr +gla+a+i+P +m+++def+a+G+q+kve PgKaaa++p+d+i+gPtv lk+G++++i+++eea
  gi|518652195|ref|YP_008141715.1| 304 PGGFRLRYGRSRLSGLAAASINPVSMYIVDEFIAIGSQIKVELPGKAAAITPCDTIDGPTVLLKSGEHRKIKTIEEA 380
                                       ***************************************************************************** PP

                          PolC_DP2 386 leikkeveeildlGeiLvayGeflennhpLvpasyveewwiqelekaaakkeaeekpsaeealelseeldvpLhPky 462
                                       + +k+ev+ei dlGeiL+ayG+flenn++Lv+++++ eww   l+   +k+  e+kp++ ea+e+s+++++pL+P++
  gi|518652195|ref|YP_008141715.1| 381 ILVKDEVAEITDLGEILIAYGDFLENNKNLVTSPFTVEWWSYYLKGDLQKYM-EKKPDQFEAIEISKKYGIPLYPEF 456
                                       *******************************************997766665.67********************** PP

                          PolC_DP2 463 tylwhdisveelekLaeavaekkkleeeklvleleeevkeiLekllvehkvkeekivieealallkslgldleeekl 539
                                        y+whdi+++el++L +++++++ l++++l+++++  +++iL kl++e+k  ++++ i e+++ll + g+++e++  
  gi|518652195|ref|YP_008141715.1| 457 DYYWHDITEDELNSLISVLERSR-LHDGNLYIDTD--AQDILIKLGIEFKPISGSLEIAEYYPLLVCTGFSIENNIP 530
                                       ********************999.77799999885..56*******************************9997766 PP

                          PolC_DP2 540 eke...eekdalelvnelsglevrekaptrigaRmGRPeKskeRkmkpavhvLfpigeaggkrrsvkeaakkkgeie 613
                                        k+   +++++le+vnelsg++v++++p+r+gaR+GRPeK+ +Rkmkp+vh+Lfpi ++g++rrs+ +aak+k+e +
  gi|518652195|ref|YP_008141715.1| 531 VKTgsySSHNVLEAVNELSGINVKARSPIRVGARLGRPEKAGDRKMKPKVHSLFPILNYGDNRRSILNAAKNKSEYS 607
                                       555676777**************************************************************9***** PP

                          PolC_DP2 614 veiarrkCkkCgketlearCeeCgekteeklvCkkceeeveeekcekcekeakavkkkkidlkellekaleklgere 690
                                       +e+++r Ck+Cg+et  + Ce+Cg+ t +                      +k+ kk++idl+ +le+a ++l+++ 
  gi|518652195|ref|YP_008141715.1| 608 IELNERVCKNCGNETPLTVCENCGSVTYN----------------------QKRLKKMNIDLSMVLERAESRLNIKP 662
                                       ***************************99......................578899******************** PP

                          PolC_DP2 691 ekleelkgvkgltskekipEpleKgilRakhdvsvfkdgtvRyDmtdlplthfrpkeigvsveklrelGYteDieGk 767
                                       +++++lkgvk+l+s++ ++Ep+eKgilR+ hd+s++kdgt+RyDm+d+p+thf+ +e+++  e+l elGY       
  gi|518652195|ref|YP_008141715.1| 663 DQVKDLKGVKKLMSRNCAVEPMEKGILRSIHDISINKDGTCRYDMSDIPITHFKKSELNLASEQLIELGY------- 732
                                       **********************************************************************....... PP

                          PolC_DP2 768 plesedqivelkvqDivlsedaaeyllkvakfvDdlLeklyglerfYnvekkedLiGklviglaPHtsagvlgRiiG 844
                                           + ++ e+ +qDi+++ed+a+yll+va+fvDd+L+++y+l+++Y++++ +dLiG+lviglaPHts+g+++RiiG
  gi|518652195|ref|YP_008141715.1| 733 ---PDRELNEIYPQDIIIPEDSAKYLLNVANFVDDMLVRYYNLQPYYSCHSIDDLIGELVIGLAPHTSGGIVSRIIG 806
                                       ...67899********************************************************************* PP

                          PolC_DP2 845 ftkasvgyahPyfHaakRRn 864
                                       f+k+s++yahP++HaakRRn
  gi|518652195|ref|YP_008141715.1| 807 FSKVSGCYAHPFYHAAKRRN 826
                                       *******************9 PP

  == domain 2  score: -4.3 bits;  conditional E-value: 1.9
                          PolC_DP2  618 rrkCkkCgke....tlearCeeCge 638 
                                        + +C+kC+++     l+ +C +Cg+
  gi|518652195|ref|YP_008141715.1|  992 EFRCTKCNTKfrrvPLSGKCLKCGS 1016
                                        3344444433111123334444444 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 !    9.0   0.1    0.0009       1.3      69     107 ..     611     645 ..     583     649 .. 0.80
   2 !   10.0   0.2   0.00043      0.65      70     100 ..     992    1022 ..     986    1033 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0009
                                       -EEEETTTS-EEECHHHHHS-TTTSSS-EEEEESSSEEE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsadveivsGeellv 107
                                        +  C++Cg+e+ l+     C++Cgs   + ++ + +++
  gi|518652195|ref|YP_008141715.1| 611 NERVCKNCGNETPLT----VCENCGSVTYNQKRLKKMNI 645
                                       4568*******9988....7******9887776666666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00043
                                        EEEETTTS-EEECHHHHHS-TTTSSS-EEEE CS
                              HypA   70 kvrCreCgkefeleekalrCpkCgsadveiv 100 
                                        ++rC++C+++f+    + +C kCgs ++ ++
  gi|518652195|ref|YP_008141715.1|  992 EFRCTKCNTKFRRVPLSGKCLKCGSDNIILT 1022
                                        79*********97654679******987554 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   1.1   8.2e-05      0.12       8      40 ..     608     636 ..     603     640 .. 0.82
   2 !    9.2   0.4   0.00084       1.3      14      38 ..     994    1018 ..     989    1022 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
                               DZR   8 lppdarfCseCgtklkavaaedrCpsCgekvdp 40 
                                       ++ + r+C++Cg++ +     ++C +Cg+ + +
  gi|518652195|ref|YP_008141715.1| 608 IELNERVCKNCGNETP----LTVCENCGSVTYN 636
                                       5667899*******99....8*******98655 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00084
                               DZR   14 fCseCgtklkavaaedrCpsCgekv 38  
                                         C +C+tk ++v+ + +C +Cg+++
  gi|518652195|ref|YP_008141715.1|  994 RCTKCNTKFRRVPLSGKCLKCGSDN 1018
                                        5*********************975 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.5    0.0025       3.7      29      50 ..     612     635 ..     603     644 .. 0.81
   2 ?    6.3   0.1    0.0064       9.6      14      35 ..     990    1011 ..     979    1021 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0025
                                       EEE-SSS-S..---EEEETTEEEE CS
                    zinc-ribbons_6  29 ealCpeCeq..elevlkaCgavdy 50 
                                       e +C +C++  +l v++ Cg+v y
  gi|518652195|ref|YP_008141715.1| 612 ERVCKNCGNetPLTVCENCGSVTY 635
                                       678****753379********999 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0064
                                        SSEEE-TTT--EEEEEEE-SSS CS
                    zinc-ribbons_6   14 geqyhCeaCqedlkkealCpeC 35  
                                        +++++C +C++++++++l  +C
  gi|518652195|ref|YP_008141715.1|  990 TQEFRCTKCNTKFRRVPLSGKC 1011
                                        4789999999988888764444 PP

>> DUF3340  C-terminal domain of tail specific protease (DUF3340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.8e-05     0.056      38      97 ..      42     100 ..      32     127 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.8e-05
                           DUF3340  38 LkkksekRiakdpeFklleediawlkerkekktvsLnekkrkaereeqeakrlarenere 97 
                                       L +  ++R++k  + + + +di++l + +++++vsL ++   aer  ++++rla+e+  +
  gi|518652195|ref|YP_008141715.1|  42 LANDMAERVEKLIQIDGIADDIRELSKTMSREEVSLAISRKVAERL-KDDRRLALEKSVR 100
                                       5677899********************************9999999.8888899888655 PP

>> DUF1931  Domain of unknown function (DUF1931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.4   0.00016      0.24      16      83 ..       4      71 ..       1     123 [. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00016
                                      HHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHHHHHHHHHTT.TS--SHHHHHHHHT CS
                           DUF1931 16 edlkrisdfVekklydLllvaeenAkangrdviepaDLPiTkglqesireFrkl.eeeleleeileqla 83
                                      ++l++++ ++e+k+ +   +ae +A++ g+dv  + ++P+++++ e++++  ++   + +++e+ + + 
  gi|518652195|ref|YP_008141715.1|  4 HNLDKYNKILENKVSECYQIAE-EARSLGKDVSTEVEIPLANDMAERVEKLIQIdGIADDIRELSKTMS 71
                                      57899*************9997.5999**************************9434555655544433 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.054        81      72     101 ..     611     638 ..     584     643 .. 0.78
   2 ?    8.8   0.1    0.0008       1.2     145     178 ..     991    1024 ..     945    1032 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.054
                           TackOD1  72 rirlCpsCksghlnvrevCpkCkSidieeq 101
                                       + r+C++C     +   vC +C+S+  +++
  gi|518652195|ref|YP_008141715.1| 611 NERVCKNCGNE--TPLTVCENCGSVTYNQK 638
                                       56789999766..46678999999987776 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0008
                           TackOD1  145 evykCnsCkslfsepevkarClsCekesesddlk 178 
                                        + ++C +C++ f    ++ +Cl+C++ +    ++
  gi|518652195|ref|YP_008141715.1|  991 QEFRCTKCNTKFRRVPLSGKCLKCGSDNIILTIH 1024
                                        4567888888888888888888887766555555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   2.8      0.04        59       8      35 ..     615     634 ..     605     638 .. 0.77
   2 ?   10.0   1.1   0.00048      0.72       5      34 ..     992    1016 ..     991    1019 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.04
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgs.e 35 
                                       C++Cg         ++ plt+C +Cgs +
  gi|518652195|ref|YP_008141715.1| 615 CKNCG---------NETPLTVCENCGSvT 634
                                       77777.........3677999****9955 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00048
                       Zn-ribbon_8    5 eYrCeeCghefevlqsisdaplta.CPeCgs 34  
                                        e+rC++C+++f ++       l   C +Cgs
  gi|518652195|ref|YP_008141715.1|  992 EFRCTKCNTKFRRVP------LSGkCLKCGS 1016
                                        8*********99664......3344999999 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1     0.011        17       2      11 ..     614     623 ..     614     625 .. 0.90
   2 ?    2.8   0.5     0.066        99       2      10 ..     626     634 ..     626     636 .. 0.85
   3 ?    6.7   0.9     0.004         6       1      22 [.     993    1016 ..     993    1017 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.011
                      Rubredoxin_2   2 vCsqCGfesa 11 
                                       vC++CG+e++
  gi|518652195|ref|YP_008141715.1| 614 VCKNCGNETP 623
                                       7******986 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.066
                      Rubredoxin_2   2 vCsqCGfes 10 
                                       vC++CG+++
  gi|518652195|ref|YP_008141715.1| 626 VCENCGSVT 634
                                       7*****986 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.004
                      Rubredoxin_2    1 YvCsqCGfesak..wfGrCpsCgs 22  
                                        ++C +C+ ++++  + G+C  Cgs
  gi|518652195|ref|YP_008141715.1|  993 FRCTKCNTKFRRvpLSGKCLKCGS 1016
                                        8*********994459******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 ?    4.4   0.7     0.018        27      18      27 ..     611     620 ..     603     623 .. 0.77
   2 ?    4.0   7.3     0.024        36       2      28 ..     614     633 ..     613     637 .. 0.83
   3 ?    0.5   0.2      0.29   4.3e+02      18      25 ..     991     998 ..     988    1002 .. 0.81
   4 ?    3.6   0.0     0.031        46       2      14 ..    1010    1022 ..    1009    1029 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                       TCEEESSSSB CS
                      TF_Zn_Ribbon  18 gelvCtdCGl 27 
                                       +e vC++CG+
  gi|518652195|ref|YP_008141715.1| 611 NERVCKNCGN 620
                                       6888999986 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
                                       EETTTTCEECHEETSTTCEEESSSSBE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlV 28 
                                       +C+nCg++       +  +vC++CG+V
  gi|518652195|ref|YP_008141715.1| 614 VCKNCGNE-------TPLTVCENCGSV 633
                                       8*****85.......4458*******9 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.29
                                       TCEEESSS CS
                      TF_Zn_Ribbon  18 gelvCtdC 25 
                                        e++Ct+C
  gi|518652195|ref|YP_008141715.1| 991 QEFRCTKC 998
                                       68999999 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.031
                                        EETTTTCEECHEE CS
                      TF_Zn_Ribbon    2 kCPnCgstnlveD 14  
                                        kC +Cgs+n+++ 
  gi|518652195|ref|YP_008141715.1| 1010 KCLKCGSDNIILT 1022
                                        8********7765 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   1.1     0.013        19      38      62 ..     609     632 ..     596     643 .. 0.64
   2 ?    3.5   0.1     0.066        98      39      72 ..     990    1014 ..     981    1032 .. 0.61

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.013
                            zf-CHY  38 evkevlcllCeteqekavlCkkCkk 62 
                                       e +e +c++C +e +  ++C++C++
  gi|518652195|ref|YP_008141715.1| 609 ELNERVCKNCGNE-TPLTVCENCGS 632
                                       4455566666665.33445666654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.066
                            zf-CHY   39 vkevlcllCeteqekavlCkkCkkefaey....fCpiC 72  
                                        ++e+ c++C+t+              ++     +C +C
  gi|518652195|ref|YP_008141715.1|  990 TQEFRCTKCNTKF-------------RRVplsgKCLKC 1014
                                        4555666666554.............333333333333 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.088   1.3e+02       2       8 ..     613     619 ..     602     622 .. 0.84
   2 ?    4.2   0.1     0.029        43       3      13 ..     626     637 ..     625     648 .. 0.77
   3 ?    2.2   0.7      0.12   1.8e+02       4      29 ..     995    1016 ..     993    1020 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.088
                                       EE-TTT- CS
                           ADK_lid   2 rvCpkCG 8  
                                       rvC++CG
  gi|518652195|ref|YP_008141715.1| 613 RVCKNCG 619
                                       7788887 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.029
                                       E-TTT--.EEET CS
                           ADK_lid   3 vCpkCGr.sYhv 13 
                                       vC++CG  +Y+ 
  gi|518652195|ref|YP_008141715.1| 626 VCENCGSvTYNQ 637
                                       9*****999993 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
                                        -TTT--EEETTTB--SSTTB-TTT-- CS
                           ADK_lid    4 CpkCGrsYhvvfnpPkveglCDkCGe 29  
                                        C kC++ + +v       g+C kCG+
  gi|518652195|ref|YP_008141715.1|  995 CTKCNTKFRRVP----LSGKCLKCGS 1016
                                        899999998444....799*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1080 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       949  (0.052931); expected 358.6 (0.02)
Passed bias filter:                      751  (0.0418874); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.89u 0.31s 00:00:01.20 Elapsed: 00:00:00.48
# Mc/sec: 6807.70
//
Query:       gi|518652196|ref|YP_008141716.1|  [L=259]
Description: hypothetical protein FACI_IFERC00001G0835 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-56  191.8   0.0    1.7e-56  191.7   0.0    1.0  1  ATP_bind_1    Conserved hypothetical ATP binding protein
    3.5e-05   23.7   0.0    0.00025   20.9   0.0    2.1  1  CLP1_P        mRNA cleavage and polyadenylation factor CLP1 P
    0.00015   22.1   0.0    0.00033   21.0   0.0    1.6  2  AAA_22        AAA domain
      0.001   19.1   0.0     0.0098   15.9   0.0    2.2  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0012   18.6   0.0     0.0025   17.6   0.0    1.5  1  AAA_24        AAA domain
  ------ inclusion threshold ------
      0.012   14.8   0.0      0.025   13.7   0.0    1.5  1  ArsA_ATPase   Anion-transporting ATPase
      0.019   14.7   0.0      0.031   14.0   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.022   14.6   0.0        2.8    7.8   0.0    2.7  3  RsgA_GTPase   RsgA GTPase
      0.028   14.1   0.0      0.043   13.5   0.0    1.2  1  AAA_30        AAA domain
      0.049   13.5   0.0        0.1   12.5   0.0    1.5  1  NTPase_1      NTPase
       0.07   13.7   0.0       0.17   12.4   0.0    1.7  2  AAA_18        AAA domain
      0.071   13.5   0.0       0.12   12.7   0.0    1.4  1  AAA_16        AAA ATPase domain
        0.1   11.6   0.0       0.16   11.0   0.0    1.2  1  T2SSE         Type II/IV secretion system protein
       0.18   11.3   0.2        1.1    8.8   0.0    2.2  3  GTP_EFTU      Elongation factor Tu GTP binding domain


Domain annotation for each model (and alignments):
>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.7   0.0   1.3e-59   1.7e-56       1     236 [.       7     243 ..       7     248 .. 0.95

  Alignments for each domain:
  == domain 1  score: 191.7 bits;  conditional E-value: 1.3e-59
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflre 77 
                                       v+GpaG GK+tf+ga  ++l ++ ++  +vNLDP+ae lpYe+++dir +i+l++vm  + lgpnga vva+++l +
  gi|518652196|ref|YP_008141716.1|   7 VTGPAGTGKSTFCGAYKDWLVQNDYDAIIVNLDPGAEYLPYEPDIDIRGFISLNEVMSAYSLGPNGAQVVAADLLLD 83 
                                       89*************************************************************************** PP

                        ATP_bind_1  78 sldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsamlr 154
                                       ++d+++++le ++d y++fDtPGQielft+++    +v++L+   + ++ +++Ds ++++p+ fis+ ++  s+  r
  gi|518652196|ref|YP_008141716.1|  84 NVDKIKSKLELYDDYYVIFDTPGQIELFTFRPGSPLLVKSLA-GEKAMIAFIADSMVSQTPSGFISEKMLFGSVYSR 159
                                       *********999******************************.6888899*************************** PP

                        ATP_bind_1 155 lelPhvvvlnkfDllkek.lekeleffedvealslllekee.ekykklaeaiaelleefalvlrflplssekeesie 229
                                         +P+  vlnk+Dl+ e+  ++   + e+++ l     +e+ + +k+ + ++  +l++ +++ +++p+ss++  ++e
  gi|518652196|ref|YP_008141716.1| 160 FFVPMMFVLNKIDLIGEDkVKEITGWEENPDLLYDSFRDENtDSVKDYFLNVITALKDSDIINKIIPVSSKDSFGFE 236
                                       ****************9977777788888988888777777799999****************************** PP

                        ATP_bind_1 230 dllslid 236
                                       d+++ + 
  gi|518652196|ref|YP_008141716.1| 237 DIYTGMS 243
                                       9998665 PP

>> CLP1_P  mRNA cleavage and polyadenylation factor CLP1 P-loop
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.9e-07   0.00025       1      50 [.       9      64 ..       9     123 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.9e-07
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG......qseispPgtislalver 50
                                      Gp  +GKST++    ++++++ +  ++v+lD+G       ++i + g+isl  v +
  gi|518652196|ref|YP_008141716.1|  9 GPAGTGKSTFCGAYKDWLVQNDYDAIIVNLDPGaeylpyEPDIDIRGFISLNEVMS 64
                                      899****************************9833333346777777777776655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.5e-07   0.00033       6      43 ..       3      34 ..       2      56 .. 0.81
   2 ?   -3.6   0.0       9.4   1.2e+04      95     108 ..      80      94 ..      74     106 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.5e-07
                            AAA_22  6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                                      g+l+vtG++GtGK+t +  ++++l++       + + +
  gi|518652196|ref|YP_008141716.1|  3 GSLFVTGPAGTGKSTFCGAYKDWLVQN------DYDAI 34
                                      6899********************876......44444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.4
                            AAA_22  95 liiDEaqhlr.seea 108
                                       l++D+++++  + e+
  gi|518652196|ref|YP_008141716.1|  80 LLLDNVDKIKsKLEL 94 
                                       678888888433554 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.7e-06    0.0098      52      79 ..     158     185 ..     150     212 .. 0.73
   2 ?    0.7   0.0      0.39     5e+02      79      97 ..     218     239 ..     201     244 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.7e-06
                      MMR_HSR1_Xtn  52 nrvYipclyvlNKiDlisleeldelare 79 
                                       +r ++p+++vlNKiDli +++++e++  
  gi|518652196|ref|YP_008141716.1| 158 SRFFVPMMFVLNKIDLIGEDKVKEITGW 185
                                       6889*******************99873 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.39
                      MMR_HSR1_Xtn  79 e...pnsvviSaekelnldeLk 97 
                                           ++++++S+++ ++++++ 
  gi|518652196|ref|YP_008141716.1| 218 SdiiNKIIPVSSKDSFGFEDIY 239
                                       133378999*******999986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.9e-06    0.0025       5      73 ..       5      80 ..       3     109 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.9e-06
                            AAA_24  5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDt 73
                                      ++++Gp+g+GK+t++  +        +++++++++ G+  l      di++++ + + + + +  +++ +++  D 
  gi|518652196|ref|YP_008141716.1|  5 LFVTGPAGTGKSTFCGAYkdwlvqnDYDAIIVNLDPGAEYLPYEPDIDIRGFISLNEVMSAYSLGPNGAQVVAADL 80
                                      689***************99***999************************77777777666655555555544443 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0     2e-05     0.025       4      40 ..       5      41 ..       3      45 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2e-05
                                      EEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-STT CS
                       ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgkkvllistDPA 40
                                      ++v+G  G GK+t   a   +l +++++ +++ +DP 
  gi|518652196|ref|YP_008141716.1|  5 LFVTGPAGTGKSTFCGAYKDWLVQNDYDAIIVNLDPG 41
                                      79**********************************5 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.4e-05     0.031      24      48 ..       4      28 ..       1      37 [. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                            AAA_29 24 atlltGpsGsGKSTllDAiqalLvp 48
                                      + ++tGp G+GKST+  A++  Lv 
  gi|518652196|ref|YP_008141716.1|  4 SLFVTGPAGTGKSTFCGAYKDWLVQ 28
                                      5789***********9999877765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.042        54     103     118 ..       6      21 ..       3      36 .. 0.83
   2 ?   -1.8   0.0       1.9   2.5e+03     153     160 ..      99     106 ..      89     110 .. 0.70
   3 ?    7.8   0.0    0.0022       2.8      21      69 ..     134     183 ..     128     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.042
                                       EEECSTTSSHHHHHHH CS
                       RsgA_GTPase 103 vlvGqSGvGKStLina 118
                                       ++ G+ G GKSt+  a
  gi|518652196|ref|YP_008141716.1|   6 FVTGPAGTGKSTFCGA 21 
                                       578*********9765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.9
                                       EEEESS-S CS
                       RsgA_GTPase 153 glliDtPG 160
                                        ++ DtPG
  gi|518652196|ref|YP_008141716.1|  99 YVIFDTPG 106
                                       4688***9 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0022
                                       EEEESTTTT--HHHHHHHHHHHHHTT..-EEEEEEE-GGG--HHHHHHHHH CS
                       RsgA_GTPase  21 ivvslkepelslnlldrfLvlaeekg..iepvivlnKiDlleeeeeleelk 69 
                                       i  s+++++ s  + +++L+    ++  ++++ vlnKiDl+ e++ ++e+ 
  gi|518652196|ref|YP_008141716.1| 134 IADSMVSQTPSGFISEKMLFGSVYSRffVPMMFVLNKIDLIGEDK-VKEIT 183
                                       556666667777777778876655552258999**********99.66554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.3e-05     0.043      22      48 ..       6      32 ..       3      40 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.3e-05
                            AAA_30 22 vltGpAGtGKttalkalreaweaaggr 48
                                      ++tGpAGtGK+t  +a+++ + ++ ++
  gi|518652196|ref|YP_008141716.1|  6 FVTGPAGTGKSTFCGAYKDWLVQNDYD 32
                                      79*************999887777655 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   8.1e-05       0.1       2      28 ..       5      31 ..       4      34 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.1e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GG CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgv 28
                                      +f+TGp G+GK+T++    + l ++++
  gi|518652196|ref|YP_008141716.1|  5 LFVTGPAGTGKSTFCGAYKDWLVQNDY 31
                                      79*************988888777665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   0.00013      0.17       2      17 ..       6      21 ..       5      51 .. 0.88
   2 ?   -3.3   0.0       9.5   1.2e+04      43      61 ..     195     212 ..     180     223 .. 0.48

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                            AAA_18  2 lltGtpGvGKttlake 17
                                      ++tG++G+GK+t++ +
  gi|518652196|ref|YP_008141716.1|  6 FVTGPAGTGKSTFCGA 21
                                      79***********976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9.5
                            AAA_18  43 pealdeskrldedkldkll 61 
                                        +  de+   ++d+  +++
  gi|518652196|ref|YP_008141716.1| 195 SF-RDENTDSVKDYFLNVI 212
                                       22.2333333333334444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   9.6e-05      0.12      26      47 ..       4      25 ..       2      70 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 9.6e-05
                            AAA_16 26 lvllsGesGvGKsslvrellra 47
                                      +++++G++G+GKs+   + ++ 
  gi|518652196|ref|YP_008141716.1|  4 SLFVTGPAGTGKSTFCGAYKDW 25
                                      79************98877754 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00012      0.16     131     161 ..       4      36 ..       2      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00012
                             T2SSE 131 lilvsGgTgsGKttllyallkeinks..deriv 161
                                       ++ v+G+ g+GK+t+  a   ++ ++  d  iv
  gi|518652196|ref|YP_008141716.1|   4 SLFVTGPAGTGKSTFCGAYKDWLVQNdyDAIIV 36 
                                       689*************99988887763233344 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.1   1.4e+03       7      21 ..       6      20 ..       2      22 .. 0.83
   2 ?   -2.2   0.0       1.9   2.5e+03      70      82 ..      97     109 ..      85     112 .. 0.74
   3 ?    8.8   0.0   0.00083       1.1     123     186 ..     162     240 ..     153     247 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.1
                                      EEEESTTSSHHHHHH CS
                          GTP_EFTU  7 giighvDhGKtTLtd 21
                                       + g   +GK+T+++
  gi|518652196|ref|YP_008141716.1|  6 FVTGPAGTGKSTFCG 20
                                      68899999****987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                       EEEEEEEESSSGG CS
                          GTP_EFTU  70 ylinliDtPGHvd 82 
                                         + + DtPG ++
  gi|518652196|ref|YP_008141716.1|  97 DYYVIFDTPGQIE 109
                                       457789****865 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00083
                                       TEEEEEEESCGST.......HHHHHHHHHHHHHHHHHH.........HHHHHHHHHTTT........TTEEEEEEBT CS
                          GTP_EFTU 123 vpiivfiNKmDrl.......kaelkeiveevkqklsrk.........eeklekygekge........kevpvvfgSa 175
                                       vp+++++NK+D +       ++  +e ++ ++++++++             +                + +++++S+
  gi|518652196|ref|YP_008141716.1| 162 VPMMFVLNKIDLIgedkvkeITGWEENPDLLYDSFRDEntdsvkdyfL---N------VitalkdsdIINKIIPVSS 229
                                       899**********97777776666667777777775555555553331...2......1233333334567888888 PP

                                       TTTBTHHHHHH CS
                          GTP_EFTU 176 lkgegvktlle 186
                                       ++ +g++++  
  gi|518652196|ref|YP_008141716.1| 230 KDSFGFEDIYT 240
                                       88888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       511  (0.0285013); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1695.20
//
Query:       gi|518652197|ref|YP_008141717.1|  [L=281]
Description: prenyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-35  122.9  19.6    1.7e-35  122.6  19.6    1.1  1  UbiA          UbiA prenyltransferase family
  ------ inclusion threshold ------
        4.1    6.5   7.1        5.9    6.0   7.0    1.4  1  Bac_export_2  FlhB HrpN YscU SpaS Family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.6  19.6   1.9e-39   1.7e-35       3     250 ..      20     264 ..      19     270 .. 0.93

  Alignments for each domain:
  == domain 1  score: 122.6 bits;  conditional E-value: 1.9e-39
                              UbiA   3 ipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllil 79 
                                       +++++g+ +a+ggs d+   ++++++++ a++a++ +N++   + D+ ++r++n +lv+G++++  a+++ ++l+++
  gi|518652197|ref|YP_008141717.1|  20 PFIYAGAIIASGGSYDFVKYIIIFITATSARGAGMSINRIMGLKYDKTNPRKKNWALVTGKMKKIDAYALTLLLIAI 96 
                                       688999*********************************************************************** PP

                              UbiA  80 gllllalllnpltallgllalllyvvYtglrlKrrtllgtvvggiafglppllgwaavtgsl.sllalllalavfll 155
                                         +   ++ln ++++l+ +++l+ ++ +   +Kr+t +++++ g++ gl++l+g+ a+t    +l ++l+ l+  ++
  gi|518652197|ref|YP_008141717.1|  97 FEVST-YFLNRVVLALSPVVILFFIADP--LMKRVTSWRHLFMGLTIGLGVLGGFLAITPVApPLIIYLVVLISTFW 170
                                       ***99.**********************..***************************999986666667777779** PP

                              UbiA 156 twaialandlrdregDrkagiktlpvvlGrkaarillalllavlllallllllalllllylllalllaalallraar 232
                                       ++++++++ ++d++ Dr+ ++ktl v++G k+ +i++ l+ ++++++ +++ ++ +  +y+ ++l+ +++++++++ 
  gi|518652197|ref|YP_008141717.1| 171 IAGFDIIYTIPDIDYDRANNLKTLNVKYGLKNGMIISSLFHIFTIAL-FIFIAFIVKNIYYDILLVPIVALIIYQHI 246
                                       ***********************************855555555443.6779************************* PP

                              UbiA 233 lvrrrdakkaakfflfls 250
                                       +v   + k+++ +f++ +
  gi|518652197|ref|YP_008141717.1| 247 VVNPSNLKTIKVSFFNAN 264
                                       ***********9997655 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 ?    6.0   7.0   0.00066       5.9      27     147 ..     104     226 ..      63     279 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.00066
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2  27 lssalvllaglllllllgpslveelaellrevlsalelllelllallll..llplllvlllaallanllqvgflfst 101
                                       l+ +++ l  +++l+++++ l+++++++ + ++   ++ l +l  +l +  ++p l++ l ++l++++   gf +  
  gi|518652197|ref|YP_008141717.1| 104 LNRVVLALSPVVILFFIADPLMKRVTSWRHLFMGL-TIGLGVLGGFLAItpVAPPLIIYL-VVLISTFWIAGFDIIY 178
                                       56677777778888888888888888855555544.555555555443333666555555.5566666666777766 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXX CS
                      Bac_export_2 102 kalkpklsklnplkglkrifslrsl..vellksllkvvlvgavaylvl 147
                                           ++ ++ n lk l+  ++l++   +  l  ++ ++l++++a++v 
  gi|518652197|ref|YP_008141717.1| 179 TIPDIDYDRANNLKTLNVKYGLKNGmiISSLFHIFTIALFIFIAFIVK 226
                                       666777777777776666666655411344444444444444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2106.15
//
Query:       gi|518652198|ref|YP_008141718.1|  [L=657]
Description: hypothetical protein FACI_IFERC00001G0837 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-43  148.7   1.1    1.5e-42  145.6   1.1    2.1  1  ATP-grasp_5     ATP-grasp domain
    4.1e-43  146.5   0.2      9e-43  145.4   0.2    1.6  1  Succ_CoA_lig    Succinyl-CoA ligase like flavodoxin domain
    1.7e-23   83.3   0.3    4.7e-23   81.9   0.1    1.9  2  CoA_binding_2   CoA binding domain
    3.6e-07   30.8   1.1    3.6e-07   30.8   1.1    2.9  3  CoA_binding     CoA binding domain
    0.00011   21.8   1.0        0.3   10.6   0.0    3.3  3  ATP-grasp_2     ATP-grasp domain
     0.0063   16.5   0.1       0.02   14.9   0.1    1.8  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen


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 !  145.6   1.1     5e-46   1.5e-42       5     222 .]     457     657 .]     453     657 .] 0.92

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 5e-46
                       ATP-grasp_5   5 egrtlLteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaa 81 
                                       +g+++ + +ea++l+e ygi+++   +a++a+eave   ++gyp v+Ki  ++ +hKtdv+Gv +n+++ + v++++
  gi|518652198|ref|YP_008141718.1| 457 KGKNYIKDFEAMQLMEIYGIRTPAYAIAENAKEAVEKSTAVGYPLVMKISPDTPVHKTDVKGVIMNVEK-DTVESSF 532
                                       67889999*********************************************************9985.6788877 PP

                       ATP-grasp_5  82 eeilervkekspeariegvlVqemakrggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareli 158
                                        e+               ++ q      g E++vg  +DpvFGp i++G GG+++ev+k+ ++++ p+++ +a +++
  gi|518652198|ref|YP_008141718.1| 533 TELNY-----------PRTIMQAQIS--GAEIFVGGIKDPVFGPAIVVGIGGIYMEVIKSLSYGICPVSEDEAYQMM 596
                                       77643...........3466666666..************************************************* PP

                       ATP-grasp_5 159 ertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeIreldinPllveeegvvalDarirl 222
                                       +  k+  +l+  r++   d+++ ++ +++ls++++d   I+e+dinPl+v+e+g++a+D+ri+l
  gi|518652198|ref|YP_008141718.1| 597 KDSKVLGMLTS-RNR-DYDINSTVRAISKLSNMLID-LDIKEMDINPLIVNEKGAFAVDVRIVL 657
                                       *********97.666.79******************.57***********************86 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 !  145.4   0.2     3e-46     9e-43       1     137 [.     148     284 ..     148     285 .. 0.99

  Alignments for each domain:
  == domain 1  score: 145.4 bits;  conditional E-value: 3e-46
                      Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGneadvdvadlleylaedpetkvillylEsirdgrkflsaarr 77 
                                       +Gk al++qSG+l++ +l+wa+++++g+s+++slGn+advd++d +++l++d et++i+ y+E+++ g+kfls++  
  gi|518652198|ref|YP_008141718.1| 148 RGKAALVAQSGGLGVYMLNWAQESNVGISYFISLGNQADVDETDAFQFLSTDVETRAIFSYVEGVSSGQKFLSTLPD 224
                                       599************************************************************************** PP

                      Succ_CoA_lig  78 aarkkpvvvlksGrseagaraaashtgalagsdavvdaafrqaGvlrvdsleelfdaael 137
                                       + ++kp++ lk G  ++ga+a+++htg++ags ++++aa+r +G + vd++e+++++a++
  gi|518652198|ref|YP_008141718.1| 225 VIKRKPIIFLKGGMGKTGAAAVKTHTGSVAGSMDIFRAAVRTVGGIFVDNIEDMLNLAKI 284
                                       *********************************************************997 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.1   1.6e-26   4.7e-23       1     114 [.       9     133 ..       9     135 .. 0.96
   2 ?   -2.8   0.0       2.8   8.5e+03      32      78 ..     448     493 ..     445     498 .. 0.66

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 1.6e-26
                                       --EEEET--S-TTSHHHHHHHHHHH..HT--EEEESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHH CS
                     CoA_binding_2   1 rtiaVvGasdnpgkfgykvlrylle..hglpvvpVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkea 75 
                                       ++iaVvGas+++ k g+ +lr++ +  +g +v+pVn k  +i+g ++y+sl + +e vdlv++++p++a+p ++k+a
  gi|518652198|ref|YP_008141718.1|   9 KSIAVVGASSDSLKVGNIILRNITSsfSG-KVYPVNNKTASIDGLTAYKSLIDIKESVDLVVIVVPRDAVPGVMKDA 84 
                                       79***********************9999.**********************857********************** PP

                                       HHH--SEEEE-TT..........---HHHHHHHHHTT-EEE.ES-HHHH CS
                     CoA_binding_2  76 lalgakavwlqpg..........sedeeaaelaeeagirvvgdrCilve 114
                                       ++++a a+++  +          + +++++++a+e girv+g++ i+++
  gi|518652198|ref|YP_008141718.1|  85 ATIKAGAAVIITSgfketdqhgaELEDQIMAIAKESGIRVLGPNTIGLI 133
                                       ****9998888888********************************986 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.8
                                       EESSS-SEETTEES----T....T--EEEE-S-HHHHGGGHHHHHHH CS
                     CoA_binding_2  32 pVnpkeeeilgekvyaslaedpepvdlvdvftppeatpeivkealal 78 
                                       p+n  +e + g++ +++ + + + +++  + tp+ a++e +kea+++
  gi|518652198|ref|YP_008141718.1| 448 PINQARELVKGKNYIKDFE-AMQLMEIYGIRTPAYAIAENAKEAVEK 493
                                       6777777777766666666.345666666777777777777777665 PP

>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.1   1.2e-10   3.6e-07       2      96 .]       7      98 ..       6      98 .. 0.94
   2 ?   -2.3   0.0       2.5   7.5e+03      69      94 ..     372     400 ..     359     402 .. 0.68
   3 ?   -1.2   0.0       1.1   3.4e+03      71      86 ..     479     494 ..     466     507 .. 0.65

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.2e-10
                                      TTEEEEEETTTSHHHHHHHHHHHHHHECEE.EEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHH CS
                       CoA_binding  2 kdtkviviGagglgiaglyhfkeklkygik.avfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeav 79
                                      k+++++v+Ga+    +++  + +++  +++ +v++vn +     ++gl++yks+ +++e+  vd  vi+vP +++  ++
  gi|518652198|ref|YP_008141718.1|  7 KPKSIAVVGASSDSLKVGNIILRNITSSFSgKVYPVNNK--TASIDGLTAYKSLIDIKES--VDLVVIVVPRDAVPGVM 81
                                      7899**************8888888888888********..999****************..***************** PP

                                      HHHHHTT-SEEEEESST CS
                       CoA_binding 80 delveagikgiviiteg 96
                                      ++++  +   +viit+g
  gi|518652198|ref|YP_008141718.1| 82 KDAATIKAGAAVIITSG 98
                                      *****9999****9986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.5
                                       ES...-HHHHHHHHHHHHHTT-SEEEEES CS
                       CoA_binding  69 tv...Paesaqeavdelveagikgiviit 94 
                                        v   P+ s+ ++++  v+   kg++ +t
  gi|518652198|ref|YP_008141718.1| 372 IVqslPMVSCSDVAKSIVNYRGKGVIGVT 400
                                       44445888888888888887777776555 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.1
                                       -HHHHHHHHHHHHHTT CS
                       CoA_binding  71 Paesaqeavdelveag 86 
                                       Pa +++e ++e+ve++
  gi|518652198|ref|YP_008141718.1| 479 PAYAIAENAKEAVEKS 494
                                       6666666666666553 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0    0.0001       0.3       2      41 ..     462     501 ..     461     506 .. 0.88
   2 ?   -1.1   0.0      0.38   1.1e+03      23      49 ..     521     547 ..     511     557 .. 0.79
   3 !    7.9   0.0    0.0007       2.1     172     201 ..     613     642 ..     584     643 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0001
                                       E-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSS CS
                       ATP-grasp_2   2 lhEyqakeilakygvkvpegevaesaeeaeeaakklgeke 41 
                                       +++++a+++++ yg+++p  ++ae+a+ea e+ + +g   
  gi|518652198|ref|YP_008141718.1| 462 IKDFEAMQLMEIYGIRTPAYAIAENAKEAVEKSTAVGYPL 501
                                       6789***************************999887654 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.38
                                       EESSHHHHHHHHHHHTSSSEEEEE--S CS
                       ATP-grasp_2  23 vaesaeeaeeaakklgekelvvKaQvl 49 
                                       +  +++++e+ +++l+  ++++ aQ+ 
  gi|518652198|ref|YP_008141718.1| 521 MNVEKDTVESSFTELNYPRTIMQAQIS 547
                                       45577899999**************95 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0007
                                       HHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
                       ATP-grasp_2 172 lvkkaakiikklyklfveldatlvEiNPLv 201
                                        +++++++i+kl +++++ld + ++iNPL+
  gi|518652198|ref|YP_008141718.1| 613 DINSTVRAISKLSNMLIDLDIKEMDINPLI 642
                                       4788999**********************8 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 !   14.9   0.1   6.7e-06      0.02      56     134 ..      51     128 ..      42     132 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 6.7e-06
                                       TEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE---SE..ET.TTEEHHHHHHHHH-S--EEEE CS
                    NAD_Gly3P_dh_N  56 nlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliKGi..eegtlkllsevieeelkeekvavl 130
                                        l+a++ l +  + +d++v+vvP  a+  v+k++++ +k+ a +v+++ G+   ++    l++ i ++ ke+ + vl
  gi|518652198|ref|YP_008141718.1|  51 GLTAYKSLIDIKESVDLVVIVVPRDAVPGVMKDAAT-IKAGA-AVIITSGFkeTDQHGAELEDQIMAIAKESGIRVL 125
                                       6889999999999********************988.55554.5566789954334556677777777777656555 PP

                                       ESS- CS
                    NAD_Gly3P_dh_N 131 sGps 134
                                        Gp+
  gi|518652198|ref|YP_008141718.1| 126 -GPN 128
                                       .665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4790.47
//
Query:       gi|518652199|ref|YP_008141719.1|  [L=162]
Description: isochorismatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   54.7   0.0    1.7e-14   54.4   0.0    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.069   13.0   0.0       0.13   12.1   0.0    1.5  1  Cyclophil_like   Cyclophilin-like


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 !   54.4   0.0   1.9e-18   1.7e-14      29     175 .]       5     155 ..       3     155 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.9e-18
                   Isochorismatase  29 ninkllkaarkagipviftrdvhe.......leevkgdlderkaaphfkpgttgaelvpelaple.gdvvvdKtrfs 97 
                                        in ++++++   ipvift+ + +       l + ++  +e ++++  + +  ++ +++e++ +   + +v  ++ +
  gi|518652199|ref|YP_008141719.1|   5 YINNFIDKYK---IPVIFTERELNysvenpeLLKLRNRKEENRMKNMAPSSDYDKGFIEEFNKKIkVNNTVKTWKED 78 
                                       6778888886...***********9**9998777788888888888888999999999999999876777777799* PP

                   Isochorismatase  98 afagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspelhdaalkrlkqafatvitte 174
                                       +f+ ++l+e ++++g++ i l G+ td  +  +   a+ ++++++vvsD ++++s+ l+ ++l++++ +f++v++t 
  gi|518652199|ref|YP_008141719.1|  79 IFYRSSLEEEISKTGRRSIFLGGFFTDTDIFISSANANIREFNTIVVSDITSTYSERLYFQSLEMIS-QFVDVTDTR 154
                                       ******************************************************************9.9******97 PP

                   Isochorismatase 175 d 175
                                       d
  gi|518652199|ref|YP_008141719.1| 155 D 155
                                       6 PP

>> Cyclophil_like  Cyclophilin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.13      17      63 ..      54     100 ..      43     104 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                                       ETTHHHHHHHHC-SEEEEEEECTTEEEEE-S-----SSSEESSB-TT CS
                    Cyclophil_like  17 ddtetaraikealPiesrvntWgeEiYfstpvklekeenakevveag 63 
                                       +d+  ++++++++ ++ +v+tW+e+i++  +++ e +++ + ++ +g
  gi|518652199|ref|YP_008141719.1|  54 YDKGFIEEFNKKIKVNNTVKTWKEDIFYRSSLEEEISKTGRRSIFLG 100
                                       5778899*************************999999988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.31s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1058.24
//
Query:       gi|518652200|ref|YP_008141720.1|  [L=251]
Description: SAM-dependent methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-17   64.1   0.0    2.1e-17   63.5   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    2.7e-17   63.3   0.0    4.3e-17   62.6   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    5.1e-16   58.8   0.0    6.1e-16   58.6   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    8.1e-14   51.5   0.1    3.2e-13   49.6   0.1    1.7  2  Ubie_methyltran  ubiE/COQ5 methyltransferase family
      2e-09   37.5   0.0    3.8e-09   36.6   0.0    1.5  1  Methyltransf_23  Methyltransferase domain
    2.1e-09   38.0   0.0    3.4e-09   37.4   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0015   17.8   0.0      0.002   17.5   0.0    1.1  1  CMAS             Mycolic acid cyclopropane synthetase
     0.0044   16.6   0.1     0.0063   16.1   0.1    1.2  1  MTS              Methyltransferase small domain
  ------ inclusion threshold ------
      0.094   11.9   0.0       0.15   11.3   0.0    1.2  1  NanE             Putative N-acetylmannosamine-6-phosphate epi
       0.13   11.8   0.0       0.19   11.3   0.0    1.3  1  Methyltransf_15  RNA cap guanine-N2 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 !   63.5   0.0   1.2e-20   2.1e-17       1      94 [.      46     140 ..      46     142 .. 0.89

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.2e-20
                                       EEET-TTSHHHHHHHHTTSEEEEEES-HHHH.HHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-C CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskeml.klakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhve 75 
                                       Ld+++G+G  a  lak+ ++v+++D+ ++ml ++ak  a+e+gl +v  v++ + ++pfe+++fD+v+++ + hh++
  gi|518652200|ref|YP_008141720.1|  46 LDAATGSGFTAIRLAKKIEKVYALDMVDNMLlETAK-LAEENGLhNVFPVKGYVDSMPFENEKFDIVTCRRAAHHFD 121
                                       899****************************65554.444445546667**************************** PP

                                       CHHHHHHHHHHHEEEEEEE CS
                   Methyltransf_11  76 dpekalkeiaRvLkpgGll 94 
                                       d +++ +e+ RvLk +G++
  gi|518652200|ref|YP_008141720.1| 122 DKDEFASEAFRVLKANGMI 140
                                       *****************86 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.0   2.4e-20   4.3e-17       2      97 .]      46     138 ..      46     138 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 2.4e-20
                                       EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       Ld+++G+G ++++lak++  +kv+++D+ ++ml ++++ aee+gl nv  v+g ++++pfe+++fD+v+++ a hh+
  gi|518652200|ref|YP_008141720.1|  46 LDAATGSGFTAIRLAKKI--EKVYALDMVDNMLLETAKLAEENGLhNVFPVKGYVDSMPFENEKFDIVTCRRAAHHF 120
                                       8****************8..9************************99999********************999**** PP

                                       SHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  78 sdedlekalkeiarvLkpgG 97 
                                       +d+d  ++ +e++rvLk +G
  gi|518652200|ref|YP_008141720.1| 121 DDKD--EFASEAFRVLKANG 138
                                       9666..9**********998 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   3.4e-19   6.1e-16       4     129 ..      42     168 ..      39     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 3.4e-19
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g+  lD+++G+G+ +++la+++    +v+ +D+  +++    + a+++gl nv   +g + +++  +e ekfD++++
  gi|518652200|ref|YP_008141720.1|  42 GMIGLDAATGSGFTAIRLAKKI---EKVYALDMVDNMLLETAKLAEENGLHNVFPVKGYVDSMP--FENEKFDIVTC 113
                                       56669**************654...36*************************************..*********** PP

                   Methyltransf_31  81 nevlnaladpdkileeiervlkpggilliedprllaelp......akveeeskay 129
                                       + + +++ d+d++  e++rvlk +g + i+d+ + +  +      + ++++s++y
  gi|518652200|ref|YP_008141720.1| 114 RRAAHHFDDKDEFASEAFRVLKANGMIGIDDMTVPDSIIndlnevERIRDSSHMY 168
                                       ********************************94444443333666666666665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.6   0.1   1.8e-16   3.2e-13      32     149 ..      24     140 ..       7     152 .. 0.90
   2 ?   -0.4   0.0      0.34   6.1e+02     182     222 ..     152     193 ..     145     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.6 bits;  conditional E-value: 1.8e-16
                                       HHHHHH..HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE-- CS
                   Ubie_methyltran  32 hrlWkk..fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqan 106
                                       h + ++   ++++ +++ g   lD a+G+g  a++l+++++   kv  lD+ +nmL ++ k ++e+g  n+  +++ 
  gi|518652200|ref|YP_008141720.1|  24 HAKDRDldILMEMLSPQAGMIGLDAATGSGFTAIRLAKKIE---KVYALDMVDNMLLETAKLAEENGLHNVFPVKGY 97 
                                       555555546789999999*******************9998...578889999************************ PP

                                       TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEE CS
                   Ubie_methyltran 107 aeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrl 149
                                          +pfe++ fD+vt       + Dk++   ea+rvlk+ G +
  gi|518652200|ref|YP_008141720.1|  98 VDSMPFENEKFDIVTCRRAAHHFDDKDEFASEAFRVLKANGMI 140
                                       ***************************************9987 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.34
                                       HS-HHHHHHHHHHHHHS--.HHHHHHHHHHTTEEEEEEEEEG CS
                   Ubie_methyltran 182 akdldsyryLvesirafPd.qetlkeliedaGfksveyeslt 222
                                        +dl++ + + +s +++   ++    ++  aGf+  +y+ ++
  gi|518652200|ref|YP_008141720.1| 152 INDLNEVERIRDSSHMYAAsTDGWIRILSRAGFTGLKYKVYS 193
                                       57778888888888888651577889999******9998765 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   2.1e-12   3.8e-09      14     162 ..      35     186 ..      18     224 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 2.1e-12
                   Methyltransf_23  14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae......kakkaqkdqfdeqeaaepqgkfd 84 
                                       e l+   +ag+  Ld ++G+G ++  l+++  +v++ D+ +++  + +      + ++ ++++ + ++ +++++kfd
  gi|518652200|ref|YP_008141720.1|  35 EMLS--PQAGMIGLDAATGSGFTAIRLAKKIEKVYALDMVDNMLLETAklaeenGLHNVFPVKGYVDSMPFENEKFD 109
                                       3344..689999*********99999999888888888888877666678899988888888888899999****** PP

                   Methyltransf_23  85 lIvlrevlehvpdppellrqiatllkpgGylllseplaslkedrllldwlylvpagrhisffsarslkelleeaGle 161
                                       ++++r   +h++d  e  + +++ lk +G + + + +++++  ++l +++ +++   h++  s + + ++l +aG++
  gi|518652200|ref|YP_008141720.1| 110 IVTCRRAAHHFDDKDEFASEAFRVLKANGMIGIDDMTVPDSIINDLNEVERIRDS-SHMYAASTDGWIRILSRAGFT 185
                                       ***************************************9888888888777766.888888888888888888887 PP

                   Methyltransf_23 162 v 162
                                        
  gi|518652200|ref|YP_008141720.1| 186 G 186
                                       5 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   1.9e-12   3.4e-09       1      99 []      46     140 ..      46     140 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.9e-12
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L+  +G+G ++ +l++k    +++++D   +++  +++   +++ +n+  v+  +++     ++++fD+v++  + h
  gi|518652200|ref|YP_008141720.1|  46 LDAATGSGFTAIRLAKK--IEKVYALDMVDNMLLETAKLAEENGLHNVFPVKGYVDSMPF--ENEKFDIVTCRRAAH 118
                                       78999************..99999*********788888888888888888888888765..556************ PP

                   Methyltransf_12  78 hlkdirevldnirklLkpgGrl 99 
                                       h++d++e+ +++ ++Lk +G++
  gi|518652200|ref|YP_008141720.1| 119 HFDDKDEFASEAFRVLKANGMI 140
                                       ********************86 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.1e-06     0.002      44     171 ..      23     149 ..       4     170 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.1e-06
                                       HHHHHHHHHHHHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEE.ES CS
                              CMAS  44 eeAqlaKldlileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevk.ll 119
                                        +A+ + ld+++e l+ ++Gm  Ld  +G G +++r +++   kv +l + ++    + k  +e +l++   vk + 
  gi|518652200|ref|YP_008141720.1|  23 SHAKDRDLDILMEMLSPQAGMIGLDAATGSGFTAIRLAKK-IEKVYALDMVDNMLLETAKLAEENGLHNVFPVKgYV 98 
                                       467778899*******************************.569**********************99988886455 PP

                                       -GGG---.--SEEEEES-GGGTSGGGHHHHHHHHHHHS-TT-EEEEEEEEE-- CS
                              CMAS 120 dyedlde.kvdrvvsvgafehvgkenydtffkklkkllkedGllllhtitslh 171
                                       d   +++ k+d v    a  h+  +  d+f ++++++lk++G++ +  +t ++
  gi|518652200|ref|YP_008141720.1|  99 DSMPFENeKFDIVTCRRAAHHFDDK--DEFASEAFRVLKANGMIGIDDMTVPD 149
                                       666676669**99999999999765..89**************9988887765 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   3.5e-06    0.0063      21     134 ..      31     139 ..      22     161 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 3.5e-06
                                       HHHHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.E.EEEEESBH.HHHHHHHHHHHHTTGCEEEEE-STTTTSTT CS
                               MTS  21 klLletlpkelsgkvlDlGcGaGvlgaalakespeae.vtlvdvda.rAlesakenleanklevevvasdvleevee 95 
                                       ++L+e l+ ++    lD ++G G+ ++ lak+ +++  +++vd+   +  ++a+en  +n + v+ +  ++   +e+
  gi|518652200|ref|YP_008141720.1|  31 DILMEMLSPQAGMIGLDAATGSGFTAIRLAKKIEKVYaLDMVDNMLlETAKLAEENGLHNVFPVKGYVDSM--PFEN 105
                                       78999**99988889*****************999877899987642556667777777776666666655..3456 PP

                                       S-EEEEEE---STTTCHCHHHHHHHHHHHHHHHEEEEEE CS
                               MTS  96 kkfdlivsNPPfhagkatelavaeeliaeAkeaLkegGe 134
                                       +kfd++ +    h+      +  +e+  eA ++Lk +G 
  gi|518652200|ref|YP_008141720.1| 106 EKFDIVTCRRAAHH-----FDDKDEFASEAFRVLKANGM 139
                                       79**9998543333.....44477888888888888886 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.1e-05      0.15      64     137 ..      40     111 ..      22     121 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.1e-05
                                       T-SEEEEE--SS--T--HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-.SS--HHHH CS
                              NanE  64 gadiialDatdrerpvtieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeekaepDfalv 137
                                        a +i lDa++ +  + i +l+kki++ y l m D   le ++ a++ G+  v   + Gy+++   +++ f++v
  gi|518652200|ref|YP_008141720.1|  40 QAGMIGLDAATGSGFTAI-RLAKKIEKVYALDMVDNMLLETAKLAEENGLHNVF-PVKGYVDSMPFENEKFDIV 111
                                       567888888888777666.799****************************9996.5899999998888888877 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 ?   11.3   0.0   0.00011      0.19       5      60 ..      46     100 ..      42     138 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00011
                   Methyltransf_15   5 lDlfsGaGGnviqfalvfekviaieinleklacaqhNaevYgvsdkitlvlgdvfe 60 
                                       lD+ +G+G  +i +a++ ekv+a+++  + l  +++ ae  g  +++++v+g v +
  gi|518652200|ref|YP_008141720.1|  46 LDAATGSGFTAIRLAKKIEKVYALDMVDNMLLETAKLAEENG-LHNVFPVKGYVDS 100
                                       9****************************9999999999875.5778888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 1712.27
//
Query:       gi|518652201|ref|YP_008141721.1|  [L=216]
Description: hypothetical protein FACI_IFERC00001G0840 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.6e-10   39.9   0.0      5e-10   39.0   0.0    1.4  1  HTH_10        HTH DNA binding domain
     0.0053   16.8   0.7        5.8    7.5   0.0    3.5  3  MORN_2        MORN repeat variant
  ------ inclusion threshold ------
      0.093   12.7   0.3       0.14   12.1   0.3    1.4  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   8.4e-14     5e-10       8      48 ..     157     197 ..     151     201 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 8.4e-14
                            HTH_10   8 vlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkae 48 
                                       v+k+Ay++G+Fd+P+r++l eL+ +l+I ++tl  ++rk+ 
  gi|518652201|ref|YP_008141721.1| 157 VVKEAYDLGFFDVPKRINLLELSAILNIPPTTLDLIIRKSL 197
                                       89************************************986 PP

>> MORN_2  MORN repeat variant
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.5   0.0   0.00097       5.8       5      17 ..      41      53 ..      40      56 .. 0.83
   2 ?    0.1   0.0      0.23   1.4e+03       9      16 ..      70      77 ..      64      83 .. 0.66
   3 !    4.8   0.2    0.0075        45       3      17 ..      89     103 ..      88     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00097
                            MORN_2  5 ekeYyenGklkee 17
                                      ++ Yy+nG+l ++
  gi|518652201|ref|YP_008141721.1| 41 AEIYYHNGNLDKI 53
                                      678******9865 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.23
                            MORN_2  9 yenGklke 16
                                      ++nG+++ 
  gi|518652201|ref|YP_008141721.1| 70 FDNGNILI 77
                                      67888865 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.0075
                            MORN_2   3 GeekeYyenGklkee 17 
                                       G+ k Y e+Gk  ++
  gi|518652201|ref|YP_008141721.1|  89 GILKNYSESGKSVYK 103
                                       899********8776 PP

>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   2.3e-05      0.14      31     102 ..      52     121 ..      25     145 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                                       HHHHHHHHCTSEEEEEEECCCCCCEEEEE-BSSS-SBSSSEEEE-SBTTC--EE-CCC---CGGGTSEEEEE CS
                      Ribosomal_S8  31 eilkvLkeeGyikdfeveeekkkkikielkynkkkksvikklkrvskpgrrvYakvkelpkvlnglGiaivs 102
                                       +il  Lk+   ++++e+  ++ +++ i+l  n+  ++v+  lk++s++g+ vY++ ++++   n   + i s
  gi|518652201|ref|YP_008141721.1|  52 KILVSLKSSQGVTGVETLFDNGNILIIKLTTNE--CPVLGILKNYSESGKSVYKQEEKIEDGNNIWNMHIAS 121
                                       333334444334444444344555777777777..************************9988877777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       571  (0.0318478); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1587.78
//
Query:       gi|518652202|ref|YP_008141722.1|  [L=288]
Description: hypothetical protein FACI_IFERC00001G0841 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0016   17.8   0.2       0.46    9.7   0.1    2.7  2  Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   2.5e-05      0.46       1      39 [.       4      41 ..       4      97 .. 0.89
   2 !    5.1   0.0   0.00062        11     256     278 ..     178     199 ..     169     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 2.5e-05
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclngg 39
                                      ++v+++GgG +G++a   ++  +  v+++++++  +++g
  gi|518652202|ref|YP_008141722.1|  4 YSVLILGGGYGGINAYYGIRD-KRHVAIIDSKRDSVYHG 41
                                      689************999998.77899999887777765 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.00062
                                       TEEE--TTSBESSTTEEE-GGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 256 ggivvdeflrtnvpgiyaiGDva 278
                                       ++i vd++l +  ++ yaiGDv 
  gi|518652202|ref|YP_008141722.1| 178 NYINVDKNLMV-NENTYAIGDVL 199
                                       89*******88.8999******8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.47
# Mc/sec: 1842.25
//
Query:       gi|518652203|ref|YP_008141723.1|  [L=234]
Description: hypothetical protein FACI_IFERC00001G0842 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-26   93.2  15.9    2.1e-26   92.7  15.9    1.3  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.023   14.7   0.7      0.023   14.7   0.7    2.6  3  DUF2752   Protein of unknown function (DUF2752)


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 !   92.7  15.9   2.4e-30   2.1e-26      40     234 ..       4     201 ..       1     227 [. 0.80

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 2.4e-30
                              UbiA  40 NdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllalllyvvYtglrlKrrtl 116
                                       ++++Dr iDa+++rt  RPlv+G i++k+a++++++ l+  ++   +++n  ++ ++ l+ l+   Y+  ++Kr+t+
  gi|518652203|ref|YP_008141723.1|   4 DNLADRFIDAKNPRTMTRPLVTGVITVKNAYALIAIGLAGYFIST-YFINIIAFSISPLGALVIMTYP--YMKRHTA 77 
                                       349*****************************9999988888888.**********************..******* PP

                              UbiA 117 lgtvvggiafglppllgwaavtgsl.......sllalllalavflltwaialandlrdregDrkagiktlpvvlGrk 186
                                       +++  ++   gl +++g+ a+ g         ++ ++++ la+++++++++l+n+++d++ Dr+  +++++++lG++
  gi|518652203|ref|YP_008141723.1|  78 FANYQIASIQGLSVMAGAIAAVGLHspvyiiyHI-PWFFVLATLFWALGFDLYNHIPDIKYDRENKLHSFATLLGDR 153
                                       ********************54433588999743.4444445589******************************** PP

                              UbiA 187 aaril...lalllavllla..llllllalllllylllalllaalallraarlv 234
                                       a  +    +     +l+++  ++   ++ l+ l ++ ++l +a++l   +  +
  gi|518652203|ref|YP_008141723.1| 154 ALQFAglnQ-----ILSVSlaFTGDIVYRLGILSYATTTLHGAIMLSAFILAY 201
                                       ***955433.....444333334445555555555555555555544443333 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1      0.55   4.9e+03      31      43 ..      55      67 ..      53      71 .. 0.78
   2 ?   -2.5   1.3      0.61   5.5e+03      34      47 ..     109     122 ..     101     124 .. 0.67
   3 ?   14.7   0.7   2.6e-06     0.023      16      47 ..     193     224 ..     193     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.55
                           DUF2752 31 Afrynplgvlllp 43
                                      Af+  plg l+++
  gi|518652203|ref|YP_008141723.1| 55 AFSISPLGALVIM 67
                                      8899999988776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.61
                           DUF2752  34 ynplgvlllpllll 47 
                                       y++  +++l+ l++
  gi|518652203|ref|YP_008141723.1| 109 YHIPWFFVLATLFW 122
                                       56666666666655 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 2.6e-06
                           DUF2752  16 ltRavhallhgdfaaAfrynplgvlllpllll 47 
                                       ++ a++   +g+f +Af+yn+ + ++l+l ++
  gi|518652203|ref|YP_008141723.1| 193 MLSAFILAYRGNFGKAFYYNIYASVVLALGII 224
                                       56799999**************9998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (234 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       645  (0.0359752); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1605.95
//
Query:       gi|518652204|ref|YP_008141724.1|  [L=222]
Description: ribose-5-phosphate isomerase A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-53  178.8   0.1    8.2e-53  178.5   0.1    1.1  1  Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoribois
    9.2e-06   25.7   0.0       0.11   12.5   0.0    2.2  2  DeoRC           DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> Rib_5-P_isom_A  Ribose 5-phosphate isomerase A (phosphoriboisomerase A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.5   0.1   9.1e-57   8.2e-53       2     172 ..      52     212 ..      51     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 178.5 bits;  conditional E-value: 9.1e-57
                                       EEESSHHHHHHHHHTT--BE-GGCCSSEEEEEE--SEEETTS-EE--TTS-HHHHHHHHHTEEEEEEEEEGGGBESS CS
                    Rib_5-P_isom_A   2 gvptSeqteelaeelgipllsldeveeidlaiDGaDevdedlnliKGgGgallrEKivaaaakkfiviadesKlvek 78 
                                       gvptS +t+ la+++gi++ +   +e i++ +DGaDe+d + nliKGgGgal+rEKiva+++k+++++ad+sK++ek
  gi|518652204|ref|YP_008141724.1|  52 GVPTSLRTADLAKSYGIKIENN--LEGIEIDFDGADEFDGSGNLIKGGGGALVREKIVAYNSKEVYIMADHSKFSEK 126
                                       8*****************9855..6669************************************************* PP

                                       TTSS-EEEEE-GGGHHHHHHHHHHTTT-EEEE-TETTTTEE-B-TTS-EEEEEESSSBSSSHHHHHHHHHTSTTEEE CS
                    Rib_5-P_isom_A  79 lgkfpvPveVlpfaleavarelekllggkpelReakgkdgpvvTdngnlilDvkfeekiedpeelekelksipGVve 155
                                       l++fp+PveVlpf    +++++ek+ g+k+++R +    + + +dngn+ilD++f+   +d   le+e+k+ipGVve
  gi|518652204|ref|YP_008141724.1| 127 LHSFPLPVEVLPFMEDVTKKNIEKT-GCKATFRDG----KKFKSDNGNYILDCRFD--FTD-VVLETEIKMIPGVVE 195
                                       ***********************75.*******74....56**************4..324.58************* PP

                                       ESEE-S--SEEEEEETT CS
                    Rib_5-P_isom_A 156 tGlFlgladkvlvgked 172
                                       +G+F g+++kv++g+++
  gi|518652204|ref|YP_008141724.1| 196 VGIFSGITTKVFIGENE 212
                                       **************986 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   1.2e-05      0.11       4      43 ..       4      49 ..       2      71 .. 0.76
   2 !   11.3   0.0   2.8e-05      0.25     121     142 ..     105     126 ..      77     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.2e-05
                             DeoRC  4 eeKrrIAkaAaeliedgdtifldaGtTtlelaraLaekk......n 43
                                      +eKr  A +A++++++++ + l++G+Tt ++ + L e        +
  gi|518652204|ref|YP_008141724.1|  4 NEKRISAMEALKHVHSNMKLGLGTGSTTKYFLDGLGELVksgkitD 49
                                      689999************************9998877543443444 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.8e-05
                             DeoRC 121 ralieaarrvillaDssKfgkr 142
                                       + ++ ++++v+++aD+sKf ++
  gi|518652204|ref|YP_008141724.1| 105 KIVAYNSKEVYIMADHSKFSEK 126
                                       566779*************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1622.35
//
Query:       gi|518652205|ref|YP_008141725.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G0844 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-16   59.9   6.8    2.5e-15   56.7   0.8    2.9  3  PhoU            PhoU domain
    1.9e-05   24.4   0.0    4.6e-05   23.2   0.0    1.7  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> PhoU  PhoU domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       1.8   1.6e+04      43      66 ..      55      75 ..      51      83 .. 0.46
   2 !   56.7   0.8   2.7e-19   2.5e-15       1      88 [.     139     219 ..     139     220 .. 0.88
   3 !    5.9   0.2    0.0019        17      53      88 ..     280     308 ..     237     309 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHH.HGG-SHHHHHHH CS
                              PhoU 43 eiersllealak.rqplaedlrell 66
                                      eie++l+   +  +++    ++++l
  gi|518652205|ref|YP_008141725.1| 55 EIEKHLILNSKMdSKS----IERAL 75
                                      5555555444221222....33333 PP

  == domain 2  score: 56.7 bits;  conditional E-value: 2.7e-19
                                       HHHHHHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGG-SHHHHHHHHHHHHHHHHHH CS
                              PhoU   1 lrrmaeiveemlddalealeekdtelarevierddeidrlekeiersllealakrqplaedlrellsllriardlER 77 
                                       ++rm+  ve+m+ d+++ + + d +l++ vierddeidr++  i+r++  +  ++ +        +++l i+r lER
  gi|518652205|ref|YP_008141725.1| 139 IKRMSLNVESMIYDTIKGINDMDNDLLKNVIERDDEIDRFQWYIYREVKGKSCEDPN-------SIYYLIISRILER 208
                                       68******************************************9995444443222.......367********** PP

                                       HHHHHHHHHHH CS
                              PhoU  78 igDhavniaer 88 
                                       ++Dh vni+++
  gi|518652205|ref|YP_008141725.1| 209 MADHTVNICKI 219
                                       *********97 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0019
                                       HHHGG-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PhoU  53 akrqplaedlrellsllriardlERigDhavniaer 88 
                                       +       +  ++ ++   + ++ Ri+ ++++iae 
  gi|518652205|ref|YP_008141725.1| 280 G-------KSSDIATISFSSEEISRIALYSTDIAEL 308
                                       2.......244456688999**************96 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   5.1e-09   4.6e-05       2      38 ..      10      46 ..       9      47 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 5.1e-09
                                      EETTEEEEEE-CCCHHHCCEECTCEEEEEECTTCCCC CS
                    MazE_antitoxin  2 kvGnsgavriPkevrfelgireGdevelevdgdkiil 38
                                      ++G++++v++P  +++ +++++ +e+ +e+  +++il
  gi|518652205|ref|YP_008141725.1| 10 TGGSTYIVSLPSKWVKNNNLQRSSEIKIEESQNRLIL 46
                                      89****************************9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.21s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2421.69
//
Query:       gi|518652206|ref|YP_008141726.1|  [L=253]
Description: hypothetical protein FACI_IFERC00001G0845 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.49   10.8   5.8       0.47   10.9   3.5    2.1  2  Tmemb_18A  Transmembrane protein 188


Domain annotation for each model (and alignments):
>> Tmemb_18A  Transmembrane protein 188
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   3.5   2.6e-05      0.47      35      79 ..      15      60 ..       5      77 .. 0.81
   2 ?   -0.9   0.0      0.12   2.1e+03      28      48 ..      86     106 ..      74     125 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                         Tmemb_18A 35 avitavgalkwltdpetsevsllksLlshlvftisvivlilLf.ll 79
                                          ++ a k+ltd + + ++l+++L+s ++ftis++  +l++ ++
  gi|518652206|ref|YP_008141726.1| 15 HYKKIMQARKFLTDHNRIFIPLISILYSLMIFTISLFYAFLILlIF 60
                                      445678899**************************99765544255 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.12
                         Tmemb_18A  28 rivlvvvavitavgalkwltd 48 
                                        ++l+vv +i a + ++++ d
  gi|518652206|ref|YP_008141726.1|  86 IVILLVVLMISAGIYSTYVYD 106
                                       455555555555555566655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.48
# Mc/sec: 1580.02
//
Query:       gi|518652207|ref|YP_008141727.1|  [L=393]
Description: hypothetical protein FACI_IFERC00001G0846 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-16   60.3   0.0    2.8e-13   49.8   0.0    3.0  1  FAD_binding_3   FAD binding domain
    3.7e-05   23.9   0.0    9.3e-05   22.6   0.0    1.7  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.8e-05   22.5   0.0     0.0001   21.7   0.0    1.5  1  Thi4            Thi4 family
     0.0014   17.4   0.0     0.0051   15.6   0.0    1.8  2  HI0933_like     HI0933-like protein
     0.0039   16.3   0.0       0.28   10.2   0.0    2.1  2  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.014   13.9   0.0      0.029   12.9   0.0    1.4  1  GDI             GDP dissociation inhibitor
       0.04   12.8   0.0       0.13   11.1   0.0    1.8  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   1.1e-16   2.8e-13       2     335 ..      15     315 ..      14     321 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 1.1e-16
                                       EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EE.EHHHHHHHHHTT-HHHHHHHSEECCCCEEEEE CS
                     FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradgl.nqrtmellrqlGledrilaegapnelmgealy 77 
                                       +dV++ GaGp+G  l+ lLs+ G +v+ +e +++  +     gl ++r +   +         ++  +ne+ g ++ 
  gi|518652207|ref|YP_008141727.1|  15 YDVIVSGAGPSGSYLSYLLSRNGYKVLQLEEHREVGKPVECTGLvSERVFKYVN---------SRSMVNEVHGANVF 82 
                                       589*****************************9987766555541444444433.........33333444444444 PP

                                       EECCCCCEEEEEHHCHHCST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEE CS
                     FAD_binding_3  78 nelsdtpkaradlelesspervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvr 154
                                        +    +  ++++   s++e++ v+  +++++++++ a  +g+++r +++v+   +  +    ev+++e+ge++  r
  gi|518652207|ref|YP_008141727.1|  83 FP----NGKSIHI---SKGEKTIVMYRDDFDKDVSAMAIGAGADTRINARVL--DAKVNDSYGEVKYRENGEIKYAR 150
                                       44....1133333...6999999999************************99..5555555689************* PP

                                       EEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEEEEEC-SCCCTTC.CEEEEECCTTEE..EEEECCETEEEEEE CS
                     FAD_binding_3 155 akYlvGaDGgrStvrktlgiefegeetvyeagvldvlfdadlsdivep.lvlilsaesrgv..mviPlentlerfyv 228
                                       a+ +vGaDG++S++r +l  e   +++++    +d  f  d +   ++ +v+i+s++s+g+    +P  +     + 
  gi|518652207|ref|YP_008141727.1| 151 ANIIVGADGANSRIRLSLNYE--RPKKIISTYQVDSSFHLDDQ---DDvNVFIGSENSKGFfgWAVPSGE-----IT 217
                                       ************999888855..66667556666666665444...234778888888886332222222.....12 PP

                                       EEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEETTEEE-GGGTEEE-STTSHHHH CS
                     FAD_binding_3 229 qvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkgrvflaGDAaHihpPtgGqGlN 305
                                             +++   + +t  ++ +++    + k+ + +i  ++a ++  ++ +k   +r +l GDAa i+ P  G G+ 
  gi|518652207|ref|YP_008141727.1| 218 ------RIGVGVDHVTAIKYFRNI----NVKFNRSQILGINAGPIPINYLSKTYGNRSLLLGDAAGIVKPLSGGGIY 284
                                       ......222233444444444444....55667789999************************************** PP

                                       HHHHHHHHHHHHHHHHHT.TSS-GGGGHHHH CS
                     FAD_binding_3 306 taiqDavnLawkLaavlk.GeAkeelLdtYe 335
                                       t+i  a n ++++ +  +  + +e+ L++Y+
  gi|518652207|ref|YP_008141727.1| 285 TGIISAKNAYTAIDQSFNrNNFSEDALKAYQ 315
                                       ********99988765441445666666665 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 !   22.6   0.0   3.6e-08   9.3e-05       3      54 ..      21      84 ..      19      93 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.6e-08
                                      --SHHHHHHHHHHHCCTEEEEEE-SSSSSS......GGG-EECE...TT...CEECTS---EEE CS
                     NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllekrdrlG......Graasyev...pg...vrvdygahifhg 54
                                      GaG sG+++ ylL+++g++vl le ++ +G      G ++ + +   +    v   +ga++f++
  gi|518652207|ref|YP_008141727.1| 21 GAGPSGSYLSYLLSRNGYKVLQLEEHREVGkpvectGLVSERVFkyvNSrsmVNEVHGANVFFP 84
                                      9****************************96655555555554444422444444466666666 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0     4e-08    0.0001      12      77 ..       9      73 ..       1      99 [. 0.84

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 4e-08
                                      HHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEETTTHHHH CS
                              Thi4 12 llkyaesDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrkpakelL 77
                                      l+++++ Dv++ GaG+sG   +y l+++ + kv+ le++  +G  +   G + +++    +++ ++
  gi|518652207|ref|YP_008141727.1|  9 LISFIVYDVIVSGAGPSGSYLSYLLSRN-GYKVLQLEEHREVGKPVECTGLVSERVFKYVNSRSMV 73
                                      7899************************.*********9999987777777666655555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-06    0.0051       1      43 [.      15      57 ..      15      59 .. 0.96
   2 ?   -1.4   0.0      0.28   7.1e+02      54      90 ..     330     366 ..     324     370 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-HHHHHCG CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklgrKilisG 43
                                      +dviv G+G++G + +  ++++g +Vl le+ +++g+ +  +G
  gi|518652207|ref|YP_008141727.1| 15 YDVIVSGAGPSGSYLSYLLSRNGYKVLQLEEHREVGKPVECTG 57
                                      59***********************************999998 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.28
                                       -SGGGEEES...STTTTHHHHHHS-HHHHHHHHHHTT CS
                       HI0933_like  54 eepeellsrypenpkflksalsrftnedlialveelg 90 
                                       +++++++s++++n + l+++ ++ + ed+i+ +++lg
  gi|518652207|ref|YP_008141727.1| 330 AKIQQYFSKISTNDTLLNKIYDTINREDIIRRINSLG 366
                                       67899************************99888765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00011      0.28       1     144 [.      16     163 ..      16     182 .. 0.77
   2 !    4.2   0.0    0.0074        19     240     316 ..     249     324 ..     230     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                     Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvlieaspsllfpnnyvWsdefedlga.leecvehsWsgtivylddgkkil 76 
                                       Dv+v GaGp g  l   l  ++ g kv+ +e   ++  p + +    ++  +    + +    +g+ v +++gk+i 
  gi|518652207|ref|YP_008141727.1|  16 DVIVSGAGPSGSYLSYLL--SRNGYKVLQLEEHREVGKPVECTGLVSERVFKYvNSRSMVNEVHGANVFFPNGKSIH 90 
                                       9*****************..**************999999887666666555321334444558999********99 PP

                     Lycopene_cycl  77 lg..raYgrvsskrlkeellerlv.engvklleakvesveeeea.geslvvleggr.kirarlvvdarglasl 144
                                       ++   +   + ++++ + +    +  ++ ++ +a+v  ++ ++  ge+    +g+    ra ++v a g+ s+
  gi|518652207|ref|YP_008141727.1|  91 ISkgEKTIVMYRDDFDKDVSAMAIgAGADTRINARVLDAKVNDSyGEVKYRENGEIkYARANIIVGADGANSR 163
                                       99334445578**********99966667899****9888777746666555554457789999999996554 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0074
                     Lycopene_cycl 240 qgviPvtlggslprleqkvlaiGaaaglvhPaTGYsvarslaeapllasaiaaalres...slsarawatlwprerk 313
                                        g iP+      +   ++ l +G aag+v+P  G  +   +  a+    ai +  +++   + + +a ++lw+re+ 
  gi|518652207|ref|YP_008141727.1| 249 AGPIPI--NYLSKTYGNRSLLLGDAAGIVKPLSGGGIYTGIISAKNAYTAIDQSFNRNnfsEDALKAYQKLWKREIG 323
                                       566777..3333444556999*************9999999999988899999888875544444555666665543 PP

                     Lycopene_cycl 314 rqr 316
                                         r
  gi|518652207|ref|YP_008141727.1| 324 --R 324
                                       ..3 PP

>> GDI  GDP dissociation inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.1e-05     0.029       5      54 ..      15      66 ..      13      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.1e-05
                                      ECEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSSCG..GG-EE-HHHHHHH CS
                               GDI  5 ydvivlGtGlkecilsGllsvdgkkvlhldrndyyGg..esasltleqlyer 54
                                      ydviv G+G     ls lls +g kvl+l+ +   G   e++ l  e++++ 
  gi|518652207|ref|YP_008141727.1| 15 YDVIVSGAGPSGSYLSYLLSRNGYKVLQLEEHREVGKpvECTGLVSERVFKY 66
                                      9****************************99888775225555555566655 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.4     1e+03       1      32 [.      16      44 ..      16      50 .. 0.82
   2 ?   11.1   0.0   5.1e-05      0.13     311     373 ..     258     324 ..     210     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.4
                                      EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
                    Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlve 32
                                      ++++ G+G++G+    +l++ +   ++v+++e
  gi|518652207|ref|YP_008141727.1| 16 DVIVSGAGPSGSYLSYLLSRNG---YKVLQLE 44
                                      58999*******9999999988...5666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 5.1e-05
                                       S-SEETTEEE-CCCTEE--CCCS-HHHHHHH....HHHHHHHT--BTT--HHHHHHHHHHHHHHHHH CS
                    Trp_halogenase 311 kqawvknvvalGlasgfvePlestsihliqa....alrrLlallpdksdepaaiaefnrevareler 373
                                       ++++ +  ++lG+a+g v Pl + +i++       a + + + + ++ +++ a++ + +  +re++r
  gi|518652207|ref|YP_008141727.1| 258 SKTYGNRSLLLGDAAGIVKPLSGGGIYTGIIsaknAYTAIDQSFNRNNFSEDALKAYQKLWKREIGR 324
                                       5667777899*************9988744434559999********************99999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2399.81
//
Query:       gi|518652208|ref|YP_008141728.1|  [L=295]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete 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-34  117.4  45.9    2.7e-18   66.5  20.0    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
      0.018   15.0   4.5      0.018   15.0   4.5    3.9  3  Vps55     Vacuolar protein sorting 55


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 !   66.5  20.0     3e-22   2.7e-18       5     136 ..       9     136 ..       5     137 .. 0.93
   2 !   57.2  17.9   2.2e-19   1.9e-15       2     133 ..     146     277 ..     145     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.5 bits;  conditional E-value: 3e-22
                              EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafll 81 
                                       +l++ ++++w+++f+++k  l+++sp++l+ +rf+++++l+l+i + ++  +    +k+  +l ++g +  +la++ 
  gi|518652208|ref|YP_008141728.1|   9 MLLISVVVIWGATFPIMKLSLQYISPVMLLSFRFILSAALMLPIVFKNKMLI---ERKN-VILGIVGGILLFLAYYT 81 
                                       6889999***************************************999999...5555.566778888999999** PP

                              EamA  82 ffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       ++ +l++t++s+ +lit + +v+  i+s l+l+ kl++ +++++ ++++G++l++
  gi|518652208|ref|YP_008141728.1|  82 QTVGLEYTTSSQSGLITGMYVVLLPIISLLYLKIKLNKVDVIAVSIGFIGLILMS 136
                                       ****************************************************987 PP

  == domain 2  score: 57.2 bits;  conditional E-value: 2.2e-19
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvla 78 
                                       +g++l +  a+f+++ + +  +  ++++++ +tf+++l+ g+l +i+ ++++++   l++  ++ +++++l+++++a
  gi|518652208|ref|YP_008141728.1| 146 FGDILTFFCAIFYGLQTAYVFKYTKYLDSMVFTFYQLLMVGVLSSIFVPFSWEPSGLLKPIVIFTIVFTALFASFFA 222
                                       799*****************9999*******************************9999999*************** PP

                              EamA  79 fllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvl 133
                                        l+ +  l++++++ a++i   ePvf++i s+l+l+e +t   +lg ++i+++ l
  gi|518652208|ref|YP_008141728.1| 223 ILINTRVLQYIEPTAAGVIYVGEPVFAVISSILILKEIPTMDIILGGIIIVVAML 277
                                       ***************************************************9986 PP

>> Vps55  Vacuolar protein sorting 55
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   4.5     2e-06     0.018      67     110 ..      40      83 ..       4      89 .. 0.86
   2 ?   -2.4  10.9       0.5   4.4e+03       6      79 ..     123     195 ..     120     259 .. 0.60
   3 ?   -2.5   2.9      0.55   4.9e+03      84     102 ..     230     248 ..     206     283 .. 0.58

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-06
                             Vps55  67 tgvlvvsgiaLpivLahagiikwgalilslaggvviyltiivff 110
                                         +++  +++Lpiv++++++i+ + +il ++gg++++l++++ +
  gi|518652208|ref|YP_008141728.1|  40 FRFILSAALMLPIVFKNKMLIERKNVILGIVGGILLFLAYYTQT 83 
                                       56788899******************************998866 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.5
                             Vps55   6 fvlaiGfllvilsCalyk.nwwpLlvvlfyllaplPnliakrlsssed..................seessalkdla 63 
                                       ++++iGf+ +il + l+  +++++ ++l+++ a +  l +  + + ++                  s          
  gi|518652208|ref|YP_008141728.1| 123 IAVSIGFIGLILMSSLKFsSAYTFGDILTFFCAIFYGLQTAYVFKYTKyldsmvftfyqllmvgvlS---------- 189
                                       5789********999*764799999999999998877766665533322223333333344333330.......... PP

                             Vps55  64 kFltgvlvvsgiaLpi 79 
                                                 +i  p+
  gi|518652208|ref|YP_008141728.1| 190 ----------SIFVPF 195
                                       ..........333333 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.55
                             Vps55  84 agiikwgalilslaggvvi 102
                                        ++i+ +a++   +g+ v+
  gi|518652208|ref|YP_008141728.1| 230 LQYIEPTAAGVIYVGEPVF 248
                                       3556666666665555333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       995  (0.0554967); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.48
# Mc/sec: 1836.13
//
Query:       gi|518652209|ref|YP_008141729.1|  [L=471]
Description: phosphate transporter related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  160.6  29.2    7.4e-47  160.2  29.2    1.0  1  Sugar_tr  Sugar (and other) transporter
    1.8e-29  102.8  45.2      4e-25   88.5  35.8    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.2  29.2   8.2e-51   7.4e-47       7     450 ..      33     462 ..      27     463 .. 0.88

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 8.2e-51
                                       HHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                          Sugar_tr   7 lggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                       +g +   Yd+++ig++l++l    + g+  +k++       + li s+ l+ a++G+l +g l d++GRk ++    
  gi|518652209|ref|YP_008141729.1|  33 MGFFTDAYDLFIIGTVLAILP---MIGWHLTKTE-------IALIGSVSLIAAVLGALAFGRLLDYLGRKAIYGLEL 99 
                                       445777788888888887777...6666666653.......46999******************************* PP

                                       HHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  84 vlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                       vl+viga+ +a+   k + ++l++ R+l+G+g+G+ ++++++ ++E++  k Rg+ v++  ++ ++G +v++ + l 
  gi|518652209|ref|YP_008141729.1| 100 VLLVIGALGSAFLSFK-NPYALMAWRFLLGVGIGGDYATSSVIMAEYSNMKTRGKYVGMVFSMQSIGLVVSSLLALT 175
                                       *************977.9*********************************************************** PP

                                       HHTSS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHH CS
                          Sugar_tr 161 lnktsn....adgwrillglqlvpallllilllflPESPrylvekgkeeeakevlaklrgeedadrelaeekdslea 233
                                       +  +++    ad w+i+l + ++pa ++++ +  +PE Pry+v kg+  ea + l+   g + a  + +ee+++ ++
  gi|518652209|ref|YP_008141729.1| 176 FLLSTKiiplADAWKIMLSVGAIPAAIVIYYRRKMPEPPRYTVAKGRAAEASKNLKSYTGIDVAVSKNKEEVNAPWY 252
                                       *88888899************************************************99999999999999999999 PP

                                       HHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH....HHHHHHHHHHHHHHHHH CS
                          Sugar_tr 234 eqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks....llvtiivgvvnfvatfv 306
                                       +  +  +++ +l+++ +       +++++++   + i+a  ++++ i+ ++gls       +  i+++         
  gi|518652209|ref|YP_008141729.1| 253 TLFKDRKFLITLIGTAG------AWFLMDWAFYGNSIMASRIFATIIT-QTGLSGLirstEYSAIVFIGFALPGYWL 322
                                       96666777888888766......8999999999999999999997555.5677777555556666666677777777 PP

                                       HHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS....CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTT CS
                          Sugar_tr 307 aiflvdrfGRRtllllGaagmaicfvilgivalllvaks.kaasivaivfialfialfalgwgpvpwvlvsElfpqs 382
                                       a f+ d++GR+++ ++G+++ a+   il+   +++ ++   + +++a+ +i  f+++f+  ++ + +v  sE+fp  
  gi|518652209|ref|YP_008141729.1| 323 ATFTLDKLGRKPIQITGFIMLAVTYGILA--LFPILDTPsFVVEFIAVYGISYFFMMFG--PNVTTFVFPSEVFPVT 395
                                       88**************************9..8888888756788888888888888876..8889999********* PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGG CS
                          Sugar_tr 383 vRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeiee 450
                                       +R++++ i++a   +  f+ +++  +i  a        v a++ vl++i++ +++pe kgr +eei++
  gi|518652209|ref|YP_008141729.1| 396 TRGFGTGISAAGGKTGAFIGTFVDVFIIAAGL-SSLMTVLAIFSVLGVIVTILCLPEPKGRAMEEISR 462
                                       *******************9999777776666.78999***************************987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5  35.8   4.4e-29     4e-25       3     322 ..      33     382 ..      31     387 .. 0.78
   2 !   19.5   2.3   4.1e-08   0.00037     111     187 ..     389     464 ..     384     470 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 4.4e-29
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       +++f  a++ +i+g++l ++ +   +++++ei l+ ++  ++a++++l +Grl d +Gr+ ++ l l+l+++g+l  
  gi|518652209|ref|YP_008141729.1|  33 MGFFTDAYDLFIIGTVLAILPMIGWHLTKTEIALIGSVSLIAAVLGALAFGRLLDYLGRKAIYGLELVLLVIGALGS 109
                                       68899999999999999997778899***********************************************6666 PP

                             MFS_1  80 lfa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..... 149
                                       +f    + ++l++ r+l G+g g+ ++++ +++a++++ + rg+++g++ ++ s+G ++  ll+  ++ s       
  gi|518652209|ref|YP_008141729.1| 110 AFLsfKNPYALMAWRFLLGVGIGGDYATSSVIMAEYSNMKTRGKYVGMVFSMQSIGLVVSSLLALTFLLSTKiipla 186
                                       6634566559*******************************************************8885555899** PP

                             MFS_1 150 ..Wravfyilaivsllafvlfllllpeepperkrkspkeee.................kgtgpaplvpawkallkdp 207
                                         W  +  + ai ++++     ++++++ pe++r + ++ +                 +++ + ++  +w  l+kd+
  gi|518652209|ref|YP_008141729.1| 187 daWKIMLSVGAIPAAIV-----IYYRRKMPEPPRYTVAKGRaaeasknlksytgidvaVSKNKEEVNAPWYTLFKDR 258
                                       ****9999999999999.....45544444444444444444567888888887777644444444447999***** PP

                             MFS_1 208 vlw....illialllfffgfsg...lltllplylqevlglsglllaglllallalvgailallagrls.drlgrrrr 276
                                        ++        a++l+ ++f+g   + + ++  + ++ glsgl+ ++ ++a++++++a  + +++ +  d+lgr+++
  gi|518652209|ref|YP_008141729.1| 259 KFLitliGTAGAWFLMDWAFYGnsiMASRIFATIITQTGLSGLIRSTEYSAIVFIGFALPGYWLATFTlDKLGRKPI 335
                                       885333333333333333333354433333333588999997677776666666666666666666666******** PP

                             MFS_1 277 lllallllllaalglallavtssavllllvlvliGf.glgfvfpsll 322
                                        + +++ l++++ +lal++  +++++++ +++++G+  ++++f++  
  gi|518652209|ref|YP_008141729.1| 336 QITGFIMLAVTYGILALFPILDTPSFVVEFIAVYGIsYFFMMFGPNV 382
                                       ***************************99*******76666666544 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.1e-08
                             MFS_1 111 adwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                       +++fp + rg+++g+ +ag   Ga +g  +  +++ ++g ++++ +lai+s+l++++ +l lpe++ +   + ++e+
  gi|518652209|ref|YP_008141729.1| 389 SEVFPVTTRGFGTGISAAGGKTGAFIGTFVDVFII-AAGLSSLMTVLAIFSVLGVIVTILCLPEPKGRAMEEISREK 464
                                       689********************************.999***************99999999999999888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       728  (0.0406046); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3261.17
//
Query:       gi|518652210|ref|YP_008141730.1|  [L=399]
Description: hypothetical protein FACI_IFERC00001G0849 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.016   15.9   4.4       0.91   10.3   0.0    3.4  3  NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21


Domain annotation for each model (and alignments):
>> NADH-u_ox-rdase  NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.14   2.5e+03      28      60 ..     127     160 ..     113     180 .. 0.46
   2 ?    4.9   0.4    0.0024        43      28      68 ..     181     226 ..     164     236 .. 0.75
   3 ?   10.3   0.0   5.1e-05      0.91       7      70 ..     256     323 ..     255     330 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.14
                   NADH-u_ox-rdase  28 aaaitaafplallaleklsPsvagka..mtlagli 60 
                                        + + aa  l ll+++  +  ++ k+  +++a++i
  gi|518652210|ref|YP_008141730.1| 127 LLLVVAASLLFLLFMS-SNANHGDKRikLVFAAAI 160
                                       4444333333333332.222232222342222222 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0024
                   NADH-u_ox-rdase  28 aaaitaafplallalekls....Psvagka...mtlagligflg.gfll 68 
                                         +++  fp+++++ e+++    + +   +   m l ++i+ ++ g+ +
  gi|518652210|ref|YP_008141730.1| 181 LTFLALLFPILYILAERMElgfvRGM---GariMALQAYIAWFAvGMAF 226
                                       4566679************7554444...24569999999999877655 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 5.1e-05
                   NADH-u_ox-rdase   7 IdsdPsfsrvlrnfrpsDYvkaaa.itaafplallaleklsPsvagka....mtlagligflggfllay 70 
                                       I+ dP f+++ rn r++ ++ a + i++++ ++ l+l +l+    g++     t + +igf+g+f++a 
  gi|518652210|ref|YP_008141730.1| 256 IKFDPAFRKIKRNGRFQHFMRAGIqISFFWLALGLILFMLQAII-GHGyldpATHSIAIGFIGSFIVAH 323
                                       7789***************9886515555554445555566555.33358999************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       894  (0.0498633); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2814.14
//
Query:       gi|518652211|ref|YP_008141731.1|  [L=210]
Description: hypothetical protein FACI_IFERC00001G0850 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-13   48.4   0.0    9.8e-13   47.8   0.0    1.4  1  DUF2249       Uncharacterized conserved protein (DUF2249)
    0.00074   19.2   0.1     0.0015   18.2   0.1    1.5  1  Cupin_2       Cupin domain
  ------ inclusion threshold ------
      0.022   14.4   0.0       0.05   13.3   0.0    1.6  2  Auxin_BP      Auxin binding protein
      0.024   14.5   0.0       0.04   13.8   0.0    1.3  1  AraC_binding  AraC-like ligand binding domain


Domain annotation for each model (and alignments):
>> DUF2249  Uncharacterized conserved protein (DUF2249)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   0.0   2.2e-16   9.8e-13       1      61 [.      10      72 ..      10      81 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.2e-16
                           DUF2249  1 tlDvRelppperhaaIfeafeaLapGetlelvndhdPkpLlyqLearr..pgffsweylergp 61
                                      ++D+R ++p+er  +Ife+f aL +G++l +++dhdP++Ll  ++ +    +  ++++l +++
  gi|518652211|ref|YP_008141731.1| 10 EIDIRNIAPGERRGKIFERFLALGQGQELHVIADHDPVHLLGSMKSHKlpVDVAAYRTLTDKD 72
                                      69***************************************9998886553333555555555 PP

>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   3.4e-07    0.0015       5      66 ..     125     186 ..     121     190 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 3.4e-07
                                       EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEE.EE-SSS-EE CS
                           Cupin_2   5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrf.rNtgdepar 66 
                                       ++ G+ +p h+ p +d +f V +G g +  +++e+ +++G +v++ ag+  ++ +Nt  e+++
  gi|518652211|ref|YP_008141731.1| 125 IKAGQFIPVHS-PSTDLIFSVFKGNGSMVAGDREINIHPGSIVIVHAGEKRGVfANTDMEAFH 186
                                       56677778777.55569999********************************95555544554 PP

>> Auxin_BP  Auxin binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.77   3.5e+03      44      57 ..       9      22 ..       5      43 .. 0.80
   2 ?   13.3   0.0   1.1e-05      0.05      46      90 ..     120     165 ..     109     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.77
                                      EEEEEEEE-TT-B- CS
                          Auxin_BP 44 vevwlqtlapgsrt 57
                                      +e+ ++ +apg+r 
  gi|518652211|ref|YP_008141731.1|  9 IEIDIRNIAPGERR 22
                                      78888999999874 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
                                       EEEEEE-TT-B--EEEESS-EEEEEEE--EEEEE--SSSS.S--S- CS
                          Auxin_BP  46 vwlqtlapgsrtpihrhsceevfvvlkgkgtlylassssk.ypgkp 90 
                                       v +  +  g+  p+h  s + +f v+kg+g+++ ++ + + +pg  
  gi|518652211|ref|YP_008141731.1| 120 VIITYIKAGQFIPVHSPSTDLIFSVFKGNGSMVAGDREINiHPGSI 165
                                       66777899************************99977655257765 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.8e-06      0.04      13      57 ..     128     172 ..     119     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.8e-06
                                       T-SEEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS CS
                      AraC_binding  13 dhsfpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppge 57 
                                       ++  p h +++ +i  v +G+g+   ++r+ +++pG++++++ ge
  gi|518652211|ref|YP_008141731.1| 128 GQFIPVHSPSTDLIFSVFKGNGSMVAGDREINIHPGSIVIVHAGE 172
                                       5666779999999999**************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1493.43
//
Query:       gi|518652212|ref|YP_008141732.1|  [L=158]
Description: hypothetical protein FACI_IFERC00001G0851 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.62    9.4  10.8        0.8    9.0  10.8    1.2  1  TssN            Type VI secretion system, TssN
        6.4    6.9  12.7        1.9    8.5   0.0    3.2  3  DUF3185         Protein of unknown function (DUF3185)


Domain annotation for each model (and alignments):
>> TssN  Type VI secretion system, TssN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0  10.8     9e-05       0.8      34     159 ..      26     154 ..       5     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 9e-05
                              TssN  34 iiyiLlaglvlalpgllgf.lknefvpygyillqilylllGilhlylllkkffkelkekk..ilfeilltlivillg 107
                                       ++y L  ++++a+  ++++ ++ + + + +++  ++++++G+ +++     ++k+  + +  + +e++l+ i ++l 
  gi|518652212|ref|YP_008141732.1|  26 FVYFLAGLVIFAVNLIFSLnMHRDPIFVMWLFGGVVMIIFGLSYMF--SSGIAKNSAMANntVHIEYILLNIGVVLF 100
                                       6899999999999999999999999999999999999999998877..44444444433334777777777777777 PP

                              TssN 108 lvlfvlvfnllselqygv...waatsllvfiipllflktykallsIPveiYktwk 159
                                       ++ f+l   +    +yg+   +a+ + l+ ii+++++ + + ++ I  + Yk +k
  gi|518652212|ref|YP_008141732.1| 101 FLGFSLFLGFSGVGSYGIgkpLAI-TGLMAIIVSMLIHLINIFVMISRDPYKNKK 154
                                       777777666666666776554444.455667777777889999999999998765 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.32   2.9e+03      42      54 ..      26      38 ..      20      42 .. 0.61
   2 ?    8.5   0.0   0.00022       1.9       8      22 ..      56      70 ..      43      85 .. 0.72
   3 ?    4.7   2.3    0.0033        30       6      22 ..      91     107 ..      87     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.32
                           DUF3185 42 lllligGgvaaiv 54
                                       +++ +G v + v
  gi|518652212|ref|YP_008141732.1| 26 FVYFLAGLVIFAV 38
                                      4556666665555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00022
                           DUF3185  8 lvaGivLlvfGynas 22
                                      l++G+v+++fG++ +
  gi|518652212|ref|YP_008141732.1| 56 LFGGVVMIIFGLSYM 70
                                      566667777666554 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0033
                           DUF3185   6 iLlvaGivLlvfGynas 22 
                                       iLl +G+vL++ G++ +
  gi|518652212|ref|YP_008141732.1|  91 ILLNIGVVLFFLGFSLF 107
                                       89999999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 1146.07
//
Query:       gi|518652213|ref|YP_008141733.1|  [L=210]
Description: Bacterio-opsin activator HTH protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-16   60.2   0.1      2e-16   59.5   0.1    1.4  1  HTH_10    HTH DNA binding domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.5   0.1   1.1e-20     2e-16       1      52 [.     150     201 ..     150     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.5 bits;  conditional E-value: 1.1e-20
                            HTH_10   1 LTdkqlevlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       +T +q  v+++A+e+G+F+yP++++l+ L+ +l++s  tl e+Lr+ae+++i
  gi|518652213|ref|YP_008141733.1| 150 ITARQEYVVRTAFELGFFEYPKKINLEGLSTRLNVSYVTLAEILRRAEKNII 201
                                       69*************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1577.42
//
Query:       gi|518652214|ref|YP_008141734.1|  [L=299]
Description: hypothetical protein FACI_IFERC00001G0853 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.2   0.0        0.1   12.1   0.0    1.5  1  DUF1221        Protein of unknown function (DUF1221)
      0.093   12.5   0.7       0.22   11.3   0.7    1.6  1  Flagellar_put  Putative flagellar


Domain annotation for each model (and alignments):
>> DUF1221  Protein of unknown function (DUF1221)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.1e-05       0.1      96     209 ..      25     137 ..       7     144 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.1e-05
                           DUF1221  96 cvpvvieaietageisgldedelq..kkrlvlakkYdkelldpklfqwkfgkqylvtrelcarlesawkeDrwllle 170
                                        +   +   e+ g   ++d+d ++  +k  ++ + +++++l + l  +kf++ + ++ e ++   +    Dr++ ++
  gi|518652214|ref|YP_008141734.1|  25 LMNTFVS--EIYGSSVAVDPDSIEniEKLHAYIDVFQQKILGNTLLIRKFSHIFYISAEQVNGRANFTGPDRKTAIK 99 
                                       5555554..34455556666666511566788999***************************99999********** PP

                           DUF1221 171 llkekkksasltksekrladlLlkkleeseklngkllPs 209
                                       ll++ k+s + +  e +l + ++ +l +  +++  l+P 
  gi|518652214|ref|YP_008141734.1| 100 LLEDVKSSLT-AAGEAKLLESIASNLSRIGEVQMSLTPV 137
                                       ******9887.899*************999999999996 PP

>> Flagellar_put  Putative flagellar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.7   2.5e-05      0.22      13      20 ..     276     283 ..     273     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                     Flagellar_put  13 enVFTNID 20 
                                       +nVFTNID
  gi|518652214|ref|YP_008141734.1| 276 SNVFTNID 283
                                       7******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2019.15
//
Query:       gi|518652215|ref|YP_008141735.1|  [L=214]
Description: hypothetical protein FACI_IFERC00001G0854 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.063   13.7   0.1       0.13   12.7   0.1    1.5  1  DUF5598   Domain of unknown function (DUF5598)


Domain annotation for each model (and alignments):
>> DUF5598  Domain of unknown function (DUF5598)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.3e-06      0.13       3      59 ..      27      85 ..      25     102 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-06
                           DUF5598  3 llatDsYKlsHkkqypkgtekvysylesRkg..gkydevvffGLqyllkeylegqvvte 59
                                       ++t  YK++H + y   ++++ s l   +      d++++ G++++l++ l++  + e
  gi|518652215|ref|YP_008141735.1| 27 TMHTQIYKYTHANNYIMRINNINSILSFNEYfgFLADNTTLSGISAILNRNLRKMKIKE 85
                                      678999*********98888888777766654344599************999876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 1411.97
//
Query:       gi|518652216|ref|YP_008141736.1|  [L=168]
Description: hypothetical protein FACI_IFERC00001G0855 [Ferroplasma acidarmanus fer1]
Scores for 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-07   29.7   0.1    9.8e-07   28.8   0.1    1.6  1  Acid_PPase       Acid Phosphatase
    3.7e-05   24.2   0.0     0.0002   21.8   0.0    1.9  2  HAD              haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.014   15.7   0.0       0.84    9.9   0.0    2.1  2  Hydrolase        haloacid dehalogenase-like hydrolase
      0.086   12.2   0.2       0.12   11.7   0.2    1.2  1  Mannosyl_trans3  Mannosyltransferase putative
       0.14   12.1   0.0       0.24   11.4   0.0    1.3  1  NAD_binding_9    FAD-NAD(P)-binding


Domain annotation for each model (and alignments):
>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.1   2.7e-10   9.8e-07       3      87 ..       4      95 ..       2     147 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.7e-10
                                      -SEEEE-STTTSSSS-TTTSS-S-EEE-TTS.-EEETT--EE---TTHHHHHHHHHHTT--EEEEE--S-HHHHHHHHH CS
                        Acid_PPase  3 pklivFDLDyTLWpfevdtlvsaplkkeskksevvDrrgeelklypdveeileelkskevklavaSrtdepdlarelLk 81
                                      p +++ DLD T+W+      v++p ++ +++ ++v + + +++l+p++ + +++ ++++  + +  + ++ d a+e+L+
  gi|518652216|ref|YP_008141736.1|  4 PWILAMDLDGTVWDHLNISGVNPPYTRLDSN-SIVNQDNVTVTLFPEALDFIRWARENGA-ITTTLSWNRKDYAQEALE 80
                                      668899*******9999999***********.9999******************997665.4555556889******** PP

                                      HTT-G.......... CS
                        Acid_PPase 82 llein.........d 87
                                      ++ i          +
  gi|518652216|ref|YP_008141736.1| 81 TFGICnlfdynstdQ 95
                                      ****94443332221 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.23   8.3e+02       3      11 ..       9      17 ..       7      22 .. 0.86
   2 !   21.8   0.0   5.6e-08    0.0002      85     176 ..      46     124 ..      26     132 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                               HAD  3 fDfDgTLld 11
                                       D+DgT +d
  gi|518652216|ref|YP_008141736.1|  9 MDLDGTVWD 17
                                      6******98 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 5.6e-08
                               HAD  85 lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelglegkpvrgegkvaalrew 161
                                       l+ p+al++++++r++G  ++ +S + + ++++ l+ +g    +++       ++     +++p ++ +++ +l + 
  gi|518652216|ref|YP_008141736.1|  46 LF-PEALDFIRWARENGAITTTLSWNRKDYAQEALETFG----ICNL------FDYN-STDQTPDKD-QRLLKLISL 109
                                       45.************************************....***4......4444.344455555.333444445 PP

                               HAD 162 laaegegidleevva 176
                                       l++eg +i+  +vv+
  gi|518652216|ref|YP_008141736.1| 110 LKKEGVEIPVQRVVY 124
                                       778888888877554 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.018        63       4      15 ..       7      18 ..       6      25 .. 0.86
   2 ?    9.9   0.0   0.00024      0.84     118     199 ..      45     128 ..      34     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.018
                                      EEEESBTTTBCH CS
                                      xxxxxxxxxxxx RF
                         Hydrolase  4 vvfDkdGTLttg 15
                                      +++D+dGT+++ 
  gi|518652216|ref|YP_008141736.1|  7 LAMDLDGTVWDH 18
                                      79*******975 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00024
                                       HBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTT.SHHHHHHHHHHHT..... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxx..... RF
                         Hydrolase 118 kvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakp.spegkvaaireLq..... 187
                                       +++pea +++++ +++g  +  l+ + +  a++a++ +G  + f    ++ ++t   p + + ++++i  L+     
  gi|518652216|ref|YP_008141736.1|  45 TLFPEALDFIRWARENGAITTTLSWNRKDYAQEALETFGiCNLF----DY-NSTDQTPdKDQRLLKLISLLKkegve 116
                                       699*************999*****9**************32222....22.22223332667777778888766666 PP

                                       STGGGEEEEESS CS
                                       xxxxxxxxxxxx RF
                         Hydrolase 188 gkpeevamVGDg 199
                                       ++ ++v+ V+D+
  gi|518652216|ref|YP_008141736.1| 117 IPVQRVVYVDDR 128
                                       779999999997 PP

>> Mannosyl_trans3  Mannosyltransferase putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   3.3e-05      0.12      12      72 ..      99     154 ..      91     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                   Mannosyl_trans3  12 esllalrlIkvLralgnkLPIe.ivikk.eelekefcekilpaaeepkqevwfvnakcvlned 72 
                                       +++ +l+lI +L++ g ++P++ +v+ + ++l+ e ++k +        +++f+n+ ++ ++ 
  gi|518652216|ref|YP_008141736.1|  99 KDQRLLKLISLLKKEGVEIPVQrVVYVDdRDLHMEAIRKNIG-------DIVFINIWKTTKTY 154
                                       556679****************88888889998888888887.......89999987766554 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 ?   11.4   0.0   6.7e-05      0.24      37      92 ..      23      76 ..       9      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.7e-05
                     NAD_binding_9 37 gagrvwrtdqseelllNvpasemslftddpptfaeWlrergaleeaeeldpddfvp 92
                                      g   + +t+ +++ ++N    +++lf++   +f +W+re+ga++ + +++++d+++
  gi|518652216|ref|YP_008141736.1| 23 G-VNPPYTRLDSNSIVNQDNVTVTLFPE-ALDFIRWARENGAITTTLSWNRKDYAQ 76
                                      6.566777778899************96.8***********966567788888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       668  (0.0372581); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1024.56
//
Query:       gi|518652217|ref|YP_008141737.1|  [L=211]
Description: hypothetical protein FACI_IFERC00001G0856 [Ferroplasma acidarmanus fer1]
Scores for 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   39.4   0.1    8.3e-10   38.9   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.8e-07   30.9   0.0    5.4e-07   29.9   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    0.00032   20.6   0.0    0.00063   19.7   0.0    1.6  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.013   15.6   0.0       0.07   13.2   0.0    2.2  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
      0.038   14.1   0.0      0.069   13.3   0.0    1.4  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.1   2.3e-13   8.3e-10       3     116 ..      18     136 ..      16     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 2.3e-13
                                       HHHHHHHHHTHHHHHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHH CS
                    Acetyltransf_1   3 dlvellvesffppnedaseeefeesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGs 79 
                                       ++ e+++e f++ ++++ e++ +++ ++++e  ++a+++g ++ f +++++ d  ++  +++ +aV ++yrg+G+Gs
  gi|518652217|ref|YP_008141737.1|  18 EAIEIYEEAFPEGEKRPVEDIKRNI-EENNEKMFIARHNGDPVLFSMIWPVED--TDFLFLDYIAVGKNYRGQGVGS 91 
                                       5678999997776666666664444.556669999****************99..9********************* PP

                                       HHHHHHHHHHHHTTESEEEEEEETTEHHH........HHHHHHTT CS
                    Acetyltransf_1  80 aLlealeerareegikkivlaveedndaa........irlYeklG 116
                                         l+++ ++ ++ +++ + ++ve++ ++         i++Y++ G
  gi|518652217|ref|YP_008141737.1|  92 IFLQKIFDISENVNYNHMIFEVENPEEGDnkkqrserIKFYRRAG 136
                                       ********99999**998889998876655666777777775566 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   1.5e-10   5.4e-07       2      73 ..      46     136 ..      45     136 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 1.5e-10
                                       TEEEEEEEETTEEEEEEEEEEES....TCTEEEEE-GGGTTSSHHHHHHHH.......TTSEEE......EEEEEE. CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld....aeitrlaVdpeyrgkGiGraLlea.......aekgii......leqlel. 60 
                                       ++++f+a+++g +v f  +++++      + ++aV ++yrg+G+G+  l+        +    +         +e  
  gi|518652217|ref|YP_008141737.1|  46 NEKMFIARHNGDPVLFSMIWPVEdtdfLFLDYIAVGKNYRGQGVGSIFLQKifdisenV----NynhmifE--VENp 116
                                       789***********999999998865444444*****************9545544331....12232221..2222 PP

                                       ...THH.....HHHHHHHHTT CS
                    Acetyltransf_7  61 ...nae.....kaikfYeklG 73 
                                          + +     + ikfY++ G
  gi|518652217|ref|YP_008141737.1| 117 eegD-NkkqrsERIKFYRRAG 136
                                       2232.1345567899***987 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.8e-07   0.00063      19      92 ..      34     114 ..      12     162 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.8e-07
                   Acetyltransf_10  19 p.ealrerieegealllvaeeggkiv..Gvi.elrdgs..hisllfVdpeyrgqGigkaLleaveeeaekdgikl.e 88 
                                       p e +++ iee++ ++++a  +g +v   +i  ++d++   +  ++V ++yrgqG+g+  l+++ +  e+ ++++  
  gi|518652217|ref|YP_008141737.1|  34 PvEDIKRNIEENNEKMFIARHNGDPVlfSMIwPVEDTDflFLDYIAVGKNYRGQGVGSIFLQKIFDISENVNYNHmI 110
                                       248999*****************999899996557877889999*******************99999998888766 PP

                   Acetyltransf_10  89 ltvn 92 
                                       ++v+
  gi|518652217|ref|YP_008141737.1| 111 FEVE 114
                                       6664 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05      0.07       7     101 ..      13     100 ..       6     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                       GGGHHHHHHHHHHHTT----H..HHHHHHHHHHTTS.EEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEEEEEEE- CS
                    Acetyltransf_9   7 eedldevlellkyaFqdeespleeireyfrkllees.rvlgaedngelvgqlallplelnvpGktlkaagvtgVava 82 
                                       +++++e++e+ ++aF + e++   ++  +r++ e++ ++++a+ ng+ v    l+++ + v ++ +    +  +av 
  gi|518652217|ref|YP_008141737.1|  13 DTEFKEAIEIYEEAFPEGEKRP--VEDIKRNIEENNeKMFIARHNGDPV----LFSMIWPVEDTDF--LFLDYIAVG 81 
                                       789*************999996..6678899999754999*****9998....5666666666555..556777888 PP

                                       CCGTTS-HHHHHHHHHHHH CS
                    Acetyltransf_9  83 pehrgrgvlskLlaralee 101
                                        ++rg+gv s +l++ ++ 
  gi|518652217|ref|YP_008141737.1|  82 KNYRGQGVGSIFLQKIFDI 100
                                       8888888888888887765 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.9e-05     0.069      20      52 ..      68     100 ..      59     107 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.9e-05
                   Acetyltransf_CG  20 rkegvldfthTeVpeelrGkGiAkkLvkaaldd 52 
                                       ++++ l ++ + V + +rG+G+++ + ++++d 
  gi|518652217|ref|YP_008141737.1|  68 EDTDFLFLDYIAVGKNYRGQGVGSIFLQKIFDI 100
                                       6677888999*******************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); 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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1471.59
//
Query:       gi|518652218|ref|YP_008141738.1|  [L=623]
Description: hypothetical protein FACI_IFERC00001G0857 [Ferroplasma acidarmanus fer1]
Scores for complete 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-69  233.7   0.0    5.8e-69  232.9   0.0    1.4  1  TGT       Queuine tRNA-ribosyltransferase
    1.7e-13   50.4   0.0    4.8e-13   49.0   0.0    1.8  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos
    2.4e-08   33.8   0.1    1.6e-07   31.2   0.2    2.3  2  PUA       PUA domain
  ------ inclusion threshold ------
      0.035   14.7   0.0        0.2   12.2   0.0    2.3  3  SEP       SEP domain


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.9   0.0   1.3e-72   5.8e-69       3     349 ..       8     326 ..       5     327 .. 0.93

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 1.3e-72
                                       EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EE CS
                               TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpil 79 
                                       aR+Gk+++phg+ietP++mpv  +++++ lt++elk ++g+q++++n+y+++ +++ e  a   g+h+++++d+pi+
  gi|518652218|ref|YP_008141738.1|   8 ARIGKFSTPHGDIETPTVMPV-INPNLNFLTKEELK-SIGVQAVITNSYIIKRTASLEQDALKHGVHRLINFDGPIM 82 
                                       9********************.999**********5.99*************999999878888************* PP

                                       EE-SHHHHHHHEEEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHH CS
                               TGT  80 tdsggfqvfslkkiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwld 156
                                       tdsg+fq +               + G+ +++ ++e++++q+++gsDii++ld  +++++s+++++ +v +T r+l+
  gi|518652218|ref|YP_008141738.1|  83 TDSGTFQSYV--------------Y-GD-IEYGNKEIVQFQKDIGSDIITILDIFTKPQDSYEQAKAAVYETSRRLQ 143
                                       *******443..............4.**.************************************************ PP

                                       HHHHHHSEEEEEE--TT-HHHHHHHHHHHHHH--SEEEE-S.SSSSS..HHHHHHHHHHHHGGGS-TTS-EEETTB- CS
                               TGT 157 rcleahqalfgivqGglyedlreesaeelakrdfdgyaigG.lsvge..ekeellevveavtellpedkprylmGvg 230
                                       ++    +++ g++qG++y+dlr+esa+ +++   + ++igG +++ e  ++++l++++ +++ + + +kp++l+G g
  gi|518652218|ref|YP_008141738.1| 144 EVNTPDSIIAGPIQGSIYPDLRRESARLMSEA--SYLPIGGvVPLLEsyRYSDLVNIIINSKLNSDFSKPVHLFGGG 218
                                       **977678*********************998..5799***8889998899*******999999999********** PP

                                       SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTEEEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-H CS
                               TGT 231 tPedlleavalGvDmfdcvyptrtarngraltsegelnlknakyaedfspldegCsCytCknytraylhhllktkem 307
                                       +P+ ++ +v lGvD+fd++ ++++a+++r+l++eg+ nlk+ +   + spl +        +y++ +l +  ++   
  gi|518652218|ref|YP_008141738.1| 219 HPMFFAFSVLLGVDIFDSASYIKYAKDNRVLYTEGTRNLKEIRDFPEWSPLFN--------KYSPVELIKADEK--- 284
                                       ********************************************999999665........5998877666555... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHT CS
                               TGT 308 lgaiLltiHNlhyylelfkriReaIkegtfeefveefarkye 349
                                       +  +Ll++HNl+ +++++ +i+e I e+t+ ++vee  ++++
  gi|518652218|ref|YP_008141738.1| 285 TRLKLLSLHNLKAIFNEITEIKERIYENTLYQYVEEKSMAHP 326
                                       55**********************************999886 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.0   0.0   1.1e-16   4.8e-13       2      71 .]     478     545 ..     477     545 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.0 bits;  conditional E-value: 1.1e-16
                            TGT_C2   2 rlraiadYqFGagagdaLfpedvtitrs.atgrirqvlvdgerlatlraqdgrltLsleGarrlheslppP 71 
                                       +++ + + qF  +a ++Lf +  +i +s atg+ir++  +++ +at+r +dg+ltLs++G+++l+++l++P
  gi|518652218|ref|YP_008141738.1| 478 KINEVFHLQF--KARKNLFVNSDKIIKSkATGHIRNIKRGEKIIATMR-NDGFLTLSIYGGKLLNDMLDFP 545
                                       6889999***..9******9899************************5.*******************998 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.31   1.4e+03      49      74 .]      93     118 ..      81     118 .. 0.83
   2 !   31.2   0.2   3.6e-11   1.6e-07       2      73 ..     548     619 ..     547     620 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.31
                                       EEEESS-HHHHHHHCTSEEEEEEEEE CS
                               PUA  49 vGlanysseelakikggksveiervl 74 
                                        G  +y  +e+ +++++++ +i+ +l
  gi|518652218|ref|YP_008141738.1|  93 YGDIEYGNKEIVQFQKDIGSDIITIL 118
                                       6778999************9999876 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 3.6e-11
                                       EEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEEE CS
                               PUA   2 rvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveierv 73 
                                       rv+v d + ++ ++g +++ ++v +++ ++ +g  V + +  g l avG a +s++e+     g++v++++ 
  gi|518652218|ref|YP_008141738.1| 548 RVIVTDDSGEFNSQGYNVFFKFVEDCDREIIAGNDVMVTSASGDLYAVGHATVSGKEMGFYRNGIAVKVHEG 619
                                       89*******************************************************************986 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.6   1.6e+04      43      65 ..     191     213 ..     185     218 .. 0.71
   2 ?   12.2   0.0   4.5e-05       0.2       4      48 ..     390     434 ..     388     445 .. 0.86
   3 ?   -2.5   0.0       1.7   7.8e+03       3      11 ..     607     615 ..     606     619 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                               SEP  43 ekgeevevnledrrneeykppkk 65 
                                       ++ + v++ ++ + n ++ +p  
  gi|518652218|ref|YP_008141738.1| 191 RYSDLVNIIINSKLNSDFSKPVH 213
                                       46677888889999999998864 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 4.5e-05
                               SEP   4 wknGFsvdDGelrsyddpenaeflesikkGevPeelekve.kgeev 48 
                                       w+ GF v D+ lrsy+  +  +fl + ++  +P ele+++   + v
  gi|518652218|ref|YP_008141738.1| 390 WRHGFPVSDDILRSYE-TTDYNFLIEWNDIFIPMELENTYpVSQMV 434
                                       ****************.78899***************888555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.7
                               SEP   3 lwknGFsvd 11 
                                       +++nG+ v+
  gi|518652218|ref|YP_008141738.1| 607 FYRNGIAVK 615
                                       8****9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3784.24
//
Query:       gi|518652219|ref|YP_008141739.1|  [L=333]
Description: threonine dehydrogenase-related Zn-dependent dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for 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-38  128.5   4.0    1.4e-37  127.9   4.0    1.3  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    1.2e-10   41.5   0.0    2.3e-10   40.5   0.0    1.4  1  ADH_zinc_N     Zinc-binding dehydrogenase
    8.6e-07   28.7   0.0    1.3e-06   28.0   0.0    1.3  1  Glu_dehyd_C    Glucose dehydrogenase C-terminus
     0.0086   16.7   0.0      0.018   15.7   0.0    1.5  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
  ------ inclusion threshold ------
       0.04   13.3   0.0      0.063   12.6   0.0    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   4.0   3.8e-41   1.4e-37       2     109 .]      25     131 ..      24     131 .. 0.98

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 3.8e-41
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       gev ik++a+giCg+D+h ++g k+l vk+p+i+GHE++G++ ++g++vk++  GdrVvv+p+i+cg+C++Ck g+e
  gi|518652219|ref|YP_008141739.1|  25 GEVQIKTRACGICGTDFHAYNG-KHLAVKYPVIPGHEFSGVITSIGEGVKSFMPGDRVVVDPNITCGQCEYCKGGKE 100
                                       79********************.9***************************************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       n+Ce+ k++g++++Gg+ eyv+vpek ++k+
  gi|518652219|ref|YP_008141739.1| 101 NFCENIKTVGINYPGGYGEYVTVPEKVVYKI 131
                                       **************************99986 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   6.5e-14   2.3e-10       2     128 ..     172     294 ..     172     296 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 6.5e-14
                                       HHHHHHHHHHHTT-.EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   2 vGlaavqlAkalGa.eviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       +Gla +q++k +G   v+++d ++ +  lakk+G d +++  + dl e   ++  g +++vv+e++Gs++ l+  ++
  gi|518652219|ref|YP_008141739.1| 172 IGLAFLQILKGMGYyPVYTMDTNPTRNLLAKKYGSDKIYTGID-DLME--SDII-G-KANVVVEATGSNSILSKTID 243
                                       8*************99999*********************933.4333..3445.3.89****************** PP

                                       CEEEEEEEEECSC..TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGg..gkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                       ++ p G+++ + +  ++++ e+  +++  ke+si G ++     ++++a++++
  gi|518652219|ref|YP_008141739.1| 244 MASPSGKIFAFSVypPGEKIEIESNKIYSKEISIFGDFVNP--YTMRKAINMI 294
                                       *************96666666****************9998..8888888876 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 !   28.0   0.0   3.8e-10   1.3e-06      32     146 ..     162     271 ..     137     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 3.8e-10
                       Glu_dehyd_C  32 esalvlGaGslGLLalalleaeerglervyvlgrrdrpdptidlveelGatYvdsretpvdeipeaseemdlvvEaT 108
                                        sa++ G+G +GL  l +l+   +g+  vy+++++++  +++ l ++ G+  + +  +++ e  ++  + ++vvEaT
  gi|518652219|ref|YP_008141739.1| 162 GSAIISGTGFIGLAFLQILKG--MGYYPVYTMDTNPT--RNL-LAKKYGSDKIYTGIDDLMES-DIIGKANVVVEAT 232
                                       589************999985..79999*****7544..333.67899999888777777776.7999********* PP

                       Glu_dehyd_C 109 GsakhafeaiealapnGvaaLlGvpeds.evevdggelh 146
                                       Gs   + ++i+  +p G +    v+ +  ++e++ +++ 
  gi|518652219|ref|YP_008141739.1| 233 GSNSILSKTIDMASPSGKIFAFSVYPPGeKIEIESNKIY 271
                                       *****************8888888876548899887765 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 !   15.7   0.0     5e-06     0.018       1      74 [.     168     239 ..     168     251 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5e-06
                                       --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TTHHHHHT--CB---HHHHHHHH...S-EEEEE-S--HHHHT CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskdrkallasealtldlddliahl...dpdvvVEcasseavae 74 
                                       G G iG a+l++lk +  +     v  +d +  +++  +++ +s ++++ +ddl++     ++ vvVE+++s+++ +
  gi|518652219|ref|YP_008141739.1| 168 GTGFIGLAFLQILKGMGYY----PVYTMDTN-PTRNLLAKKYGSDKIYTGIDDLMESDiigKANVVVEATGSNSILS 239
                                       89************99975....33344444.5667788899**************769999*********998855 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.8e-05     0.063      40      95 ..     165     222 ..     155     250 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.8e-05
                                       EEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTC..EECSHHHHHHH-SEE CS
                      2-Hacid_dh_C  40 GiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgv..elvsleellaesDiv 95 
                                        i G+G IG a+ ++lk++g   v+ +d++++++  ++++g    ++ +++l+ esDi+
  gi|518652219|ref|YP_008141739.1| 165 IISGTGFIGLAFLQILKGMGYyPVYTMDTNPTRNLLAKKYGSdkIYTGIDDLM-ESDII 222
                                       589*****************989999999999888677766642345666665.47776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2274.00
//
Query:       gi|518652220|ref|YP_008141740.1|  [L=141]
Description: transcription regulator (SlyA-related) protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.6e-10   38.3   0.0    1.6e-09   37.5   0.0    1.4  1  MarR      MarR family
    1.7e-05   24.6   0.0    2.4e-05   24.1   0.0    1.2  1  MarR_2    MarR family
    0.00052   20.5   0.1    0.00075   20.0   0.1    1.3  1  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.018   15.2   0.1       0.03   14.5   0.1    1.3  1  HTH_34    Winged helix DNA-binding domain
       0.03   14.2   0.0      0.044   13.7   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.0   4.5e-13   1.6e-09       1      58 [.      31      87 ..      31      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 4.5e-13
                                      --HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR  1 ltltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      l+++ ++iL+++++ +p +++ La+ l++ k+ vt ++d Le+++l++R +s +DrR+
  gi|518652220|ref|YP_008141740.1| 31 LSMVDYKILHLVHS-EPKNMKYLADTLSLAKGWVTDITDGLEERNLVKRVHSSQDRRV 87
                                      789999***99986.678***************************************7 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   6.6e-09   2.4e-05       5      61 ..      33      86 ..      29      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 6.6e-09
                                      HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  5 paqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                        ++ +L+ ++ +p    +++ la++l l k+ v+ i + L+++ Lv r+ ++ D+R
  gi|518652220|ref|YP_008141740.1| 33 MVDYKILHLVHSEPK---NMKYLADTLSLAKGWVTDITDGLEERNLVKRVHSSQDRR 86
                                      566778888888887...**************************************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 !   20.0   0.1   2.1e-07   0.00075       5      68 .]      35      96 ..      31      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +  +Lhl+    ++k  + l+++l + +  +  + + L+e+ Lv+r ++ +drr   +++Td+G
  gi|518652220|ref|YP_008141740.1| 35 DYKILHLVH--SEPKNMKYLADTLSLAKGWVTDITDGLEERNLVKRVHSSQDRRVINIEITDEG 96
                                      566999999..99**************************************************9 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 ?   14.5   0.1   8.2e-06      0.03       9      80 .]      41     111 ..      36     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
                            HTH_34   9 LasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkkyvkaLksll 80 
                                       L+  +  ++++l ++l++ +g     ++ Le+ + +++  + +++ + + ++iT+eG++ ++k+ k +k ++
  gi|518652220|ref|YP_008141740.1|  41 LVHSEPKNMKYLADTLSLAKGWVTDITDGLEERNLVKRVHSSQDR-RVINIEITDEGLKIYNKVGKMIKTII 111
                                       55566667889999************************9999999.9*****************99999876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05     0.044      15      58 ..      39      82 ..      26     104 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                      l L+ ++p++++ +a  l + +  v ++   Le++ lV+r++++
  gi|518652220|ref|YP_008141740.1| 39 LHLVHSEPKNMKYLADTLSLAKGWVTDITDGLEERNLVKRVHSS 82
                                      5799************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1081.99
//
Query:       gi|518652221|ref|YP_008141741.1|  [L=576]
Description: hypothetical protein FACI_IFERC00001G0860 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-41  141.6  61.9    2.9e-41  141.6  61.9    3.4  2  MFS_1            Major Facilitator Superfamily
    0.00082   17.9   5.5    0.00082   17.9   5.5    2.5  3  MFS_3            Transmembrane secretion effector
  ------ inclusion threshold ------
        2.1    6.8  46.7     0.0071   14.9  12.9    4.0  4  MFS_2            MFS/sugar transport protein
        5.6    5.1  18.6        1.4    7.1   9.3    3.9  2  OATP             Organic Anion Transporter Polypeptide (OATP)


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 !  141.6  61.9   6.4e-45   2.9e-41       2     351 ..      13     426 ..      12     428 .. 0.84
   2 ?    1.1   2.8     0.032   1.4e+02     141     187 ..     517     558 ..     431     575 .. 0.73

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 6.4e-45
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispse......igllltlyalgaavaslplGrlsdrfGrrrvlllglllf 72 
                                        ++++++++++sil++alp a+ +  +++p        + ++l +y++++av+ + +Grlsd fGr +++ lg+l+f
  gi|518652221|ref|YP_008141741.1|  13 TIGVLMATINMSILIIALP-AIFSGIHLDPLKsnsfvyLLWILMGYMIVTAVLLVTIGRLSDIFGRVKLFNLGFLIF 88 
                                       58899**************.787777866665555555888************************************ PP

                             MFS_1  73 alglllllfa.....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggll 144
                                        +g++ll ++     ++   l+++r++q++g++++f++++a+i+d f+keerg+a+g+ ++++ +G+ +g ++gg+l
  gi|518652221|ref|YP_008141741.1|  89 TIGSILLYLTpgkgdTGALELIFFRIVQAVGGSFIFANSYAIITDNFKKEERGFALGINAIAATAGMSIGIVVGGIL 165
                                       ***44444545666666667********************************************************* PP

                             MFS_1 145 asslgWravfyilaivsllafvlfllllpeepperkrkspkeee................................. 188
                                       a  ++Wr++f++  +v++l+ v  +l l e+ p+ k k +                                     
  gi|518652221|ref|YP_008141741.1| 166 A-TINWRYIFLVSVPVGILGTVWSYLKLKETSPKIKQKLD---Ipgnitfaggliillvgvtygiapyksspmgwgn 238
                                       *.889***************99444444555555555544...3555****************************** PP

                             MFS_1 189 ....................kgtgpaplvpawkallkdpvlw...illialllfffgfsg.....lltllplylqev 237
                                                           ++++++p+++ +++++ + +     + +i++ +++ ++++       ++lp+     
  gi|518652221|ref|YP_008141741.1| 239 pwviaaliigavllvlfpfvERKVKQPMFN-LSLFKIRGFATgsfAGMISSMGMMGFMFMiiilfQGIWLPI---HG 311
                                       ********************9999999999.88888888663333222222222222222334346666666...46 PP

                             MFS_1 238 lgls..glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf 312
                                       ++++    + ag+++  + +++ i++++agr+sdr g r+   ++l++  +a+l+l+ll++   ++++ ++l+++G 
  gi|518652221|ref|YP_008141741.1| 312 YHYAsvP-FWAGIYMLPMTIAMGIFGPIAGRFSDRHGQRWLASFGLIVSGIALLLLVLLPADFIYIFMGILLFVFGA 387
                                       6666745.99998888899999999************9999999999999999999999999999999999****** PP

                             MFS_1 313 glgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       g+g+++++ +a+++++++p+ +g+asg  +t++++g+  
  gi|518652221|ref|YP_008141741.1| 388 GMGMFTAPNTAAVMSSVSPDVRGSASGMLTTLRNVGTTA 426
                                       ***********************************9876 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.032
                             MFS_1 141 ggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                       +++++ s   + vfy+ a++ + ++++    +++ep ++++k+++++
  gi|518652221|ref|YP_008141741.1| 517 APAFIKS--LHIVFYVGAAIVFAGAII---SILREPLSKSKKTKADK 558
                                       4444433..467999999999999884...44444444444444444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   5.5   1.8e-07   0.00082      60     185 ..      63     188 ..       6     203 .. 0.87
   2 ?   -1.1   2.4       0.1   4.7e+02      60     127 ..     334     400 ..     324     442 .. 0.62
   3 ?   -3.5   0.0      0.54   2.4e+03     263     284 ..     530     551 ..     526     556 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.8e-07
                             MFS_3  60 llsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrd 136
                                       +l +  G l+D+f r k++  + l+  ++s+ll ++   g +    l+ + ++ ++G ++      A++ +  k+++
  gi|518652221|ref|YP_008141741.1|  63 VLLVTIGRLSDIFGRVKLFNLGFLIFTIGSILLYLTPGKGDTGALELIFFRIVQAVGGSFIFANSYAIITDNFKKEE 139
                                       566788*********************************************************************** PP

                             MFS_3 137 vpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavna.lsylaliva 185
                                          A  +n++      s+G  +gG+l a++   + f v + +  l  ++ 
  gi|518652221|ref|YP_008141741.1| 140 RGFALGINAIAATAGMSIGIVVGGIL-ATINWRYIFLVSVpVGILGTVWS 188
                                       ************************86.55555566665542444455555 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.1
                             MFS_3  60 llsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAs 127
                                       ++  +aG  +D + +R++   + ++  ++ +ll++l a  +   + +l + + +g+G+ +++P   A+
  gi|518652221|ref|YP_008141741.1| 334 IFGPIAGRFSDRHGQRWLASFGLIVSGIALLLLVLLPADFIYIFMGILLFVFGAGMGM-FTAPNTAAV 400
                                       5556788888888888876666665555555555544444444444666666666664.445544443 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 0.54
                             MFS_3 263 lGvGAilgalllsrLRerlsse 284
                                       +G+  ++++++ s+LRe ls++
  gi|518652221|ref|YP_008141741.1| 530 VGAAIVFAGAIISILREPLSKS 551
                                       5777788888888888888776 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4  11.8   0.00061       2.7     259     382 ..      47     167 ..      11     173 .. 0.78
   2 ?   -1.2   2.7      0.13   5.6e+02      65     101 ..     235     271 ..     226     295 .. 0.62
   3 ?   14.9  12.9   1.6e-06    0.0071     260     383 ..     320     437 ..     309     478 .. 0.61
   4 ?   -1.5   0.0      0.16   7.2e+02     173     197 ..     526     550 ..     514     567 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.00061
                             MFS_2 259 saasvfllvv.tisallgiplwqplakrlgkkntyllgalltivllvlvlll......qpsnlllflvllviagfgv 328
                                       + + ++ l+  +i +++ ++ + +l   +g+ +++ lg+l+  ++++l++l       ++  l++f ++++++g + 
  gi|518652221|ref|YP_008141741.1|  47 FVYLLWILMGyMIVTAVLLVTIGRLSDIFGRVKLFNLGFLIFTIGSILLYLTpgkgdtGALELIFFRIVQAVGGSF- 122
                                       5555666666699999************************************765433333333333333333333. PP

                             MFS_2 329 gvaallpwsmladvvDygelktGkrregvffavlsfisklatgiglgvsgllLs 382
                                         ++   +++++d +          ++g++ ++++++  +++ ig++v g+l +
  gi|518652221|ref|YP_008141741.1| 123 --IFANSYAIITDNFKKE-------ERGFALGINAIAATAGMSIGIVVGGILAT 167
                                       ..5555666666666555.......59******************987766654 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.13
                             MFS_2  65 GrrrPwlllsaiilavsiillftppelsqsakfiwll 101
                                       G   Pw+ +++ii av ++l+ ++    + ++f + l
  gi|518652221|ref|YP_008141741.1| 235 GWGNPWVIAALIIGAVLLVLFPFVERKVKQPMFNLSL 271
                                       4455898888888888888875554433335554444 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1.6e-06
                             MFS_2 260 aasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallpw 336
                                       +a +++l +ti++ ++ p++ ++  r g + ++ +g+++  + l+l++ll p++ +  ++  +++ fg+g+ +++++
  gi|518652221|ref|YP_008141741.1| 320 WAGIYMLPMTIAMGIFGPIAGRFSDRHGQRWLASFGLIVSGIALLLLVLL-PADFIYIFMGILLFVFGAGMGMFTAP 395
                                       44444444455555666666666666667778888888888888888888.88877777777777777777666555 PP

                             MFS_2 337 smladvvDygelktGkrregvffavlsfisklatgiglgvsgllLsa 383
                                        + a +  ++        +g++ ++l+++ +++t+ ++g+++ +L +
  gi|518652221|ref|YP_008141741.1| 396 NTAAVMSSVSP-----DVRGSASGMLTTLRNVGTTASMGIFFTILIL 437
                                       55555444444.....4455555555555555555555555444422 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 0.16
                             MFS_2 173 ifaliialLmllgviivvlgtkerv 197
                                       i+  ++a+++++g+ii+ l    ++
  gi|518652221|ref|YP_008141741.1| 526 IVFYVGAAIVFAGAIISILREPLSK 550
                                       5666788888888888855444332 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 ?    7.1   9.3   0.00032       1.4     135     194 ..     109     168 ..      10     180 .. 0.69
   2 ?    0.2   1.8     0.038   1.7e+02     460     508 ..     374     423 ..     370     436 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.00032
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 135 fflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkl 194
                                       +++  +++++G++ i++  ++ i Dn kk++  + lgi   +++ G+ +G ++G++l+ +
  gi|518652221|ref|YP_008141741.1| 109 LIFFRIVQAVGGSFIFANSYAIITDNFKKEERGFALGINAIAATAGMSIGIVVGGILATI 168
                                       3444799************************************************99876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.038
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 460 lllfl.illflvsflgalgrvpallvilRcVkkedksfalGlqlllirll 508
                                       +++f+ illf++ + + +   p++ +++ +V+++ +  a G+ ++l ++ 
  gi|518652221|ref|YP_008141741.1| 374 IYIFMgILLFVFGAGMGMFTAPNTAAVMSSVSPDVRGSASGMLTTLRNVG 423
                                       566662455666677789999********************998877664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (576 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.47
# Mc/sec: 3689.40
//
Query:       gi|518652222|ref|YP_008141742.1|  [L=590]
Description: hypothetical protein FACI_IFERC00001G0861 [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  115.1   0.1    2.3e-15   57.3   0.0    2.7  2  ABC_tran     ABC transporter
    2.6e-16   59.7   2.3    2.4e-07   30.4   0.3    2.3  2  SMC_N        RecF/RecN/SMC N terminal domain
    5.3e-11   42.1   4.1    9.5e-11   41.3   4.1    1.4  1  RLI          Possible Fer4-like domain in RNase L inhibitor, 
      7e-09   35.9   6.4       0.29   10.9   0.0    4.2  4  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.4e-08   33.4   4.0    2.4e-08   33.4   4.0    1.9  1  Fer4         4Fe-4S binding domain
    1.5e-05   24.9   2.4    1.5e-05   24.9   2.4    2.1  2  Fer4_6       4Fe-4S binding domain
    1.9e-05   24.6   2.9        1.4    8.5   0.0    3.3  3  AAA_15       AAA ATPase domain
    4.8e-05   23.4   4.0      0.001   19.2   0.1    2.3  2  Fer4_10      4Fe-4S dicluster domain
    0.00051   20.1   5.2    0.00088   19.4   5.2    1.4  1  Fer4_21      4Fe-4S dicluster domain
    0.00057   20.4   0.9    0.00057   20.4   0.9    2.1  3  Fer4_7       4Fe-4S dicluster domain
    0.00075   19.6   6.5     0.0014   18.8   6.5    1.4  1  Fer4_9       4Fe-4S dicluster domain
     0.0013   19.3   3.0      0.015   15.8   0.0    2.7  3  AAA_23       AAA domain
     0.0085   16.1   2.1     0.0085   16.1   2.1    2.4  2  Fer4_2       4Fe-4S binding domain
  ------ inclusion threshold ------
       0.02   15.8   0.3       0.02   15.8   0.3    2.3  1  Fer4_16      4Fe-4S double cluster binding domain
      0.049   13.5   0.4        1.5    8.7   0.0    2.5  2  RsgA_GTPase  RsgA GTPase
      0.054   12.8   0.9        2.2    7.5   0.1    2.3  2  DHHW         DHHW protein
       0.06   13.6   0.4         17    5.7   0.1    3.4  2  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.075   13.5   0.1      0.075   13.5   0.1    2.1  2  Fer4_8       4Fe-4S dicluster domain
      0.094   13.3   0.1      0.094   13.3   0.1    2.3  1  Fer4_17      4Fe-4S dicluster domain
      0.095   12.4   0.2        9.5    5.9   0.1    2.4  2  AAA_24       AAA domain
        3.3    8.5  11.9       0.37   11.4   2.8    2.3  2  Fer4_4       4Fe-4S binding domain
        4.9    8.3  15.8       0.13   13.3   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 !   55.1   0.0   1.3e-17   1.1e-14       9     136 ..      97     239 ..      94     240 .. 0.84
   2 !   57.3   0.0   2.8e-18   2.3e-15       7     137 .]     360     482 ..     354     482 .. 0.83

  Alignments for each domain:
  == domain 1  score: 55.1 bits;  conditional E-value: 1.3e-17
                                       ETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                          ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...... 79 
                                         g++ ai+G+n  GK+t +++l+g l p+ G+i  +++d ++  ++++++ +g ++ +     ++ v +n      
  gi|518652222|ref|YP_008141742.1|  97 GTGRVNAILGQNALGKTTTMNILSGVLIPNFGNI-SKKNDKDYVIERFSKSIMGQYFRDLYNGTKKAVLKNqyvdli 172
                                       679999****************************.555666665566666667888888555555557777899999 PP

                                       ..............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       ..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ..............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     ++  +++ +++ l++k +  + v    ++LSgG+ q++a+  +l+k+++++l+DE++
  gi|518652222|ref|YP_008141742.1| 173 prvasgtvrdimkdNDHGNMDIIVDDLSMKTFLGRDV----KELSGGELQKLAIGITLMKDADIYLFDEAS 239
                                       9999999999875555555999999999999999999....****************************96 PP

  == domain 2  score: 57.3 bits;  conditional E-value: 2.8e-18
                                       EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH...H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...x RF
                          ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren...e 80 
                                        +++ e+++++G+n  GK+t++k+l+g  kp++G++             + + +i++ pq  + ++e tv+e    +
  gi|518652222|ref|YP_008141742.1| 360 YINREEIIGVLGQNALGKTTFVKILSGVIKPDSGSV-------------ENELKIAYKPQYISTDYEGTVYELlstA 423
                                       58999*******************************.............5678899999999999999999999984 PP

                                       HHTC......HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  81 sdee......iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        +e+       +++ls ++ +el d+ +      LSgG+ qr ++a +l+++++l+l+DEp+a
  gi|518652222|ref|YP_008141742.1| 424 LKEKmedvfiKNEILSPMNVSELYDNYI----GDLSGGELQRTSIALTLATDADLYLIDEPSA 482
                                       5555112344455566666666666666....*****************************75 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.3     3e-10   2.4e-07      20     210 ..      95     281 ..      79     289 .. 0.79
   2 !   29.0   0.1   8.2e-10   6.7e-07      79     216 ..     323     531 ..     292     534 .. 0.69

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 3e-10
                                       EETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  20 lpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekee 96 
                                          + +++ai+G+N  GK+  ++ ++ vL  +   ++ +++ +d + + + ++s++  +   +++ ++k ++ +++ 
  gi|518652222|ref|YP_008141742.1|  95 ELGTGRVNAILGQNALGKTTTMNILSGVLIPNFG-NISKKNDKDYVIE-RFSKSIMGQYFRDLYNGTKK-AVLKNQY 168
                                       4456689**********************96555.7776666666665.45666666666666655555.5889999 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-...STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagi...skelLSgGektLvalaLlfAiqkvkpaplyllDeidaa 170
                                       v +  rv ++   +++ ++ + +   + + l+++ +   + ++LSgGe + +a+     i  +k a +yl+De  + 
  gi|518652222|ref|YP_008141742.1| 169 VDLIPRVASGTVRDIMKDNDHGNMDIIVDDLSMKTFlgrDVKELSGGELQKLAIG----ITLMKDADIYLFDEASSY 241
                                       9999999999999999999999999999999999884445789*****7755554....667999************ PP

                                       S-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 171 LDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                                       LD +++ +v++++++ s++  ++v+ ++  +l k+   v 
  gi|518652222|ref|YP_008141742.1| 242 LDINERIRVSDIIRKLSQSKIVMVVEHDLAILDKMADQVN 281
                                       ***************************9999999855544 PP

  == domain 2  score: 29.0 bits;  conditional E-value: 8.2e-10
                                       EEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                             SMC_N  79 veitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiske.................... 135
                                       ++ t++ ++++ +++++ +s +   k+ g+ +  i +  ++++e+  +l +  + k+                    
  gi|518652222|ref|YP_008141742.1| 323 IDFTVKSSKRT-SVTTKVTSWTAMEKSYGSFNLNIGEGYINREEIIGVLGQNALGKTtfvkilsgvikpdsgsvene 398
                                       55554444444.44444444445555555666666666666666666666666666677777777777777777777 PP

                                       ......................................................CS-HHHHHHHHHHHHHHHHCCS- CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 136 ......................................................lLSgGektLvalaLlfAiqkvkp 158
                                                                                              LSgGe + +++aL +A+     
  gi|518652222|ref|YP_008141742.1| 399 lkiaykpqyistdyegtvyellstalkekmedvfikneilspmnvselydnyigDLSGGELQRTSIALTLATD---- 471
                                       7777777777777777777777777777777777777777777777777777779***************975.... PP

                                       -SEEEECTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SSHHHCCC-SCEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 159 aplyllDeidaaLDeknvkkvaellkekskn..aQfivislreemlekadklvgvtkven 216
                                       a lyl+De  a+LD +++ +va+++++  +n     iv+ ++  ++   +  + v+k e+
  gi|518652222|ref|YP_008141742.1| 472 ADLYLIDEPSAHLDSSYRMNVARIIRRVIENnkKSAIVVDHDIYLIDLISDALIVFKGEQ 531
                                       68************************6544422678888888777777766666666555 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 !   41.3   4.1   1.2e-13   9.5e-11       1      34 [.       1      31 [.       1      32 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 1.2e-13
                                      --EEEES---------TTHHHHHTTSEEEESS-- CS
                               RLI  1 mrlAivdadqCdPKKCtgkkcarfcpvrlvrtgk 34
                                      m++Ai d+++C+PKKC++ +c  +cp   vr+g 
  gi|518652222|ref|YP_008141742.1|  1 MHIAILDRERCHPKKCNH-ECRYYCPP--VRSGA 31
                                      9*****************.********..***96 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   1.0   0.00044      0.36       1      30 [.     101     128 ..     101     165 .. 0.71
   2 ?    4.8   0.0     0.025        20     220     294 ..     195     264 ..     149     274 .. 0.73
   3 !    9.9   0.0   0.00069      0.57       2      23 ..     367     388 ..     366     419 .. 0.72
   4 !   10.9   0.0   0.00036      0.29     235     287 ..     452     505 ..     443     518 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00044
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdve 30 
                                       +n++ G N+ GK++ + +l+++   ++++ 
  gi|518652222|ref|YP_008141742.1| 101 VNAILGQNALGKTTTMNILSGVL--IPNFG 128
                                       79*****************9986..22222 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.025
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                                        v  l ++    +++ elS G ++ la+   l  ++   +++l+DE  + L+     r+ +++++ls+  +++++
  gi|518652222|ref|YP_008141742.1| 195 IVDDLSMKTFLGRDVKELSGGELQKLAIGITLMKDA---DIYLFDEASSYLDINERIRVSDIIRKLSQ--SKIVM 264
                                       444555556666778899*******88888888888...9***********99999999999999999..88854 PP

  == domain 3  score: 9.9 bits;  conditional E-value: 0.00069
                            AAA_21   2 nvliGpNgsGKSnLLdaldlla 23 
                                        ++ G N+ GK+++ ++l+++ 
  gi|518652222|ref|YP_008141742.1| 367 IGVLGQNALGKTTFVKILSGVI 388
                                       5789**************9884 PP

  == domain 4  score: 10.9 bits;  conditional E-value: 0.00036
                            AAA_21 235 relSdGtkrllalltallralkkgsllliDEpEngLHPkll...rrll.ellkelsr 287
                                        +lS G ++   +++ l+ ++   +l+liDEp ++L+ +     +r++ ++++++++
  gi|518652222|ref|YP_008141742.1| 452 GDLSGGELQRTSIALTLATDA---DLYLIDEPSAHLDSSYRmnvARIIrRVIENNKK 505
                                       667777777745555555555...9*************7763333333244444443 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   4.0     3e-11   2.4e-08       1      24 []      44      67 ..      44      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 3e-11
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +vi e++CigCG+Cv+ CP+gAI+
  gi|518652222|ref|YP_008141742.1| 44 PVITESLCIGCGICVNRCPFGAIK 67
                                      6899*******************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   2.7       8.9   7.3e+03       5      15 ..       7      20 ..       7      29 .. 0.61
   2 !   24.9   2.4   1.8e-08   1.5e-05       1      24 []      43      66 ..      43      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.9
                            Fer4_6  5 dpdkCi..gCgd.C 15
                                      d+++C    C+  C
  gi|518652222|ref|YP_008141742.1|  7 DRERCHpkKCNHeC 20
                                      67777655565545 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1.8e-08
                            Fer4_6  1 vveidpdkCigCgdCvrvCPegai 24
                                      +++i +++CigCg Cv+ CP+gai
  gi|518652222|ref|YP_008141742.1| 43 FPVITESLCIGCGICVNRCPFGAI 66
                                      68999******************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0027       2.2      11      50 ..      88     126 ..      83     212 .. 0.79
   2 !    7.0   0.2    0.0051       4.2      25      50 ..     366     391 ..     347     449 .. 0.69
   3 !    8.5   0.0    0.0017       1.4     323     365 ..     471     513 ..     461     517 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0027
                            AAA_15  11 FRslkdveidlseeltvliGkNnsGKSsilealdlFlnnk 50 
                                       FR ++  e+     ++ + G N+ GK++ +++l   l  +
  gi|518652222|ref|YP_008141742.1|  88 FRLYSLPELGTGR-VNAILGQNALGKTTTMNILSGVLIPN 126
                                       6666666666566.99****************97666544 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0051
                            AAA_15  25 ltvliGkNnsGKSsilealdlFlnnk 50 
                                       +  + G N+ GK++++++l   ++ +
  gi|518652222|ref|YP_008141742.1| 366 IIGVLGQNALGKTTFVKILSGVIKPD 391
                                       77788**************8777765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0017
                            AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                                       + +++li+EP ahL  +  + +++ +++++++nk+  i+  H 
  gi|518652222|ref|YP_008141742.1| 471 DADLYLIDEPSAHLDSSYRMNVARIIRRVIENNKKSAIVVDHD 513
                                       679******************************9877776665 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.9     0.038        31       2      24 ..       4      27 ..       3      42 .. 0.73
   2 !   19.2   0.1   1.2e-06     0.001       3      25 ..      45      68 ..      43      90 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.038
                           Fer4_10  2 vvidddtC..irCg.kCvkaCPadlt 24
                                      +++d+++C   +C+ +C+  CP    
  gi|518652222|ref|YP_008141742.1|  4 AILDRERChpKKCNhECRYYCPP--V 27
                                      578999**6669*99*******9..2 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1.2e-06
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.ts 25
                                      vi ++ Ci+Cg Cv+ CP+ + + 
  gi|518652222|ref|YP_008141742.1| 45 VITESLCIGCGICVNRCPFGAiKI 68
                                      788999*************55433 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   5.2   1.1e-06   0.00088       1      58 [.       4      67 ..       4      68 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.1e-06
                           Fer4_21  1 AridedkCi..gCg.kCliaCe..dtshqaieidak.tvlkvv.edeCvGCnlCssvCPvedcie 58
                                      A++d+++C   +C+ +C   C+   ++ + ie+ ++   ++v+ e+ C+GC +C++ CP  ++i+
  gi|518652222|ref|YP_008141742.1|  4 AILDRERCHpkKCNhECRYYCPpvRSGAKTIEFPGQsDDFPVItESLCIGCGICVNRCPF-GAIK 67
                                      56777888433787359999984447888998875525678864789************7.8887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   3.2       8.9   7.3e+03      35      49 ..       8      25 ..       2      31 .. 0.67
   2 !   10.6  11.7    0.0008      0.65       4      52 .]      15      65 ..      10      65 .. 0.67
   3 !   20.4   0.9     7e-07   0.00057       2      23 ..      51      72 ..      50      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 8.9
                            Fer4_7 35 pekCl..gCga.CvavCP 49
                                       e+C    C++ C   CP
  gi|518652222|ref|YP_008141742.1|  8 RERCHpkKCNHeCRYYCP 25
                                      566643356666777777 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0008
                            Fer4_7  4 gCg.aCvaaCp.....vkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                                      +C+  C  +Cp     +k+ie++ +   +  + ++i ++ C+gCg Cv++CP+ga
  gi|518652222|ref|YP_008141742.1| 15 KCNhECRYYCPpvrsgAKTIEFPGQ--SD--DFPVITESLCIGCGICVNRCPFGA 65
                                      4644788888766633333333332..22..45688899**************97 PP

  == domain 3  score: 20.4 bits;  conditional E-value: 7e-07
                            Fer4_7  2 CigCgaCvaaCpvkaieldeee 23
                                      CigCg Cv+ Cp +ai++  + 
  gi|518652222|ref|YP_008141742.1| 51 CIGCGICVNRCPFGAIKIVSVP 72
                                      ****************987653 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   6.5   1.7e-06    0.0014       6      51 .]      14      66 ..       9      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.7e-06
                            Fer4_9  6 gaCveaCpagvvvedaaerkarlraase.......eaCigCgaCveaCpkgai 51
                                      ++C + C +     ++++++++   +s+       + CigCg Cv++Cp gai
  gi|518652222|ref|YP_008141742.1| 14 KKCNHECRYYCPPVRSGAKTIEFPGQSDdfpviteSLCIGCGICVNRCPFGAI 66
                                      469999999888888888888888777789999999*************9987 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   1.9e-05     0.015      20      64 ..     100     144 ..      84     274 .. 0.83
   2 ?   -1.9   0.1       4.7   3.9e+03      47     103 ..     293     347 ..     288     367 .. 0.56
   3 ?    2.7   0.5      0.19   1.5e+02      11      37 ..     350     382 ..     347     388 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.9e-05
                            AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve 64 
                                        +++I G+N  GKTT ++ +  +L   +++ s+k++++++ + ++
  gi|518652222|ref|YP_008141742.1| 100 RVNAILGQNALGKTTTMNILSGVLIPNFGNISKKNDKDYVIERFS 144
                                       58**********************999999999997777766554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.7
                            AAA_23  47 tprlsrks..grgfeksdveiesegkvkayveltfenkdgrytrsiererelskkkgkt 103
                                        +++++++   + f ++  + e+ +  ++++++t+++ +++       ++ +s++ +++
  gi|518652222|ref|YP_008141742.1| 293 ITKEKSTNkaINAFLSGYLREENVRVRPTSIDFTVKSSKRT----SVTTKVTSWTAMEK 347
                                       54444444224455566666666677777788887776663....33444444444444 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.19
                            AAA_23  11 rdqeidF......skgltlItGpNGaGKTTild 37 
                                       + ++++          +  + G+N  GKTT++ 
  gi|518652222|ref|YP_008141742.1| 350 GSFNLNIgegyinREEIIGVLGQNALGKTTFVK 382
                                       555555533333333578899*********986 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   2.0       0.4   3.2e+02       5      21 ..       6      25 ..       2      26 .. 0.71
   2 !   16.1   2.1     1e-05    0.0085       4      21 ..      45      62 ..      42      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.4
                            Fer4_2  5 vdtdrC.i.gCg.aCvsaCP 21
                                       d++rC    C+  C+  CP
  gi|518652222|ref|YP_008141742.1|  6 LDRERChPkKCNhECRYYCP 25
                                      57777753248568999999 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1e-05
                            Fer4_2  4 vvdtdrCigCgaCvsaCP 21
                                      v+ +  CigCg+Cv+ CP
  gi|518652222|ref|YP_008141742.1| 45 VITESLCIGCGICVNRCP 62
                                      566779************ 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 ?   15.8   0.3   2.4e-05      0.02       2      19 ..      51      68 ..      50      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.4e-05
                           Fer4_16  2 CgtCgkCaevCPtnaike 19
                                      C++Cg C++ CP +aik 
  gi|518652222|ref|YP_008141742.1| 51 CIGCGICVNRCPFGAIKI 68
                                      99************9985 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0018       1.5      94     135 ..      94     135 ..      74     137 .. 0.88
   2 ?    2.0   0.1      0.21   1.7e+02     100     132 ..     365     397 ..     354     401 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0018
                                       HHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S------- CS
                       RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinallpelelktgevseklg 135
                                        el ++++ +++Gq   GK+t +n l + l  + g++s+k++
  gi|518652222|ref|YP_008141742.1|  94 PELGTGRVNAILGQNALGKTTTMNILSGVLIPNFGNISKKND 135
                                       55567899**********************99*****99976 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.21
                                       SEEEEECSTTSSHHHHHHHHCTT-----S---- CS
                       RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevse 132
                                       +++ ++Gq   GK+t+++ l +  +   g+v +
  gi|518652222|ref|YP_008141742.1| 365 EIIGVLGQNALGKTTFVKILSGVIKPDSGSVEN 397
                                       677789*************99987777776665 PP

>> DHHW  DHHW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0027       2.2     246     314 ..     131     197 ..     126     208 .. 0.75
   2 ?    3.6   0.1     0.041        34      39     152 ..     241     362 ..     223     385 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0027
                              DHHW 246 aakgvkaldlskfekvdkpdfvGslyadtekiaLkdnPdtlvayaPqetnaltlinsdnsiveykivld 314
                                       ++k+ k + +++f k  ++++   ly  t+k +Lk++  +l   +     +++ i  dn+  +++i++d
  gi|518652222|ref|YP_008141742.1| 131 SKKNDKDYVIERFSKSIMGQYFRDLYNGTKKAVLKNQYVDLIPRVAS--GTVRDIMKDNDHGNMDIIVD 197
                                       566778899**************************987666554444..44555556666666666666 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.041
                              DHHW  39 fkslnarlkslyGirk...ddvkgevtkgvekddadeekeeldvienisseasteasdaakessa......esdsse 106
                                       +  +n+r++    irk    ++   v ++  + d+  ++ +l++ +++   + t+ ++++k+++a        +++ 
  gi|518652222|ref|YP_008141742.1| 241 YLDINERIRVSDIIRKlsqSKIVMVVEHDLAILDKMADQVNLVYGSPGAYGVITKEKSTNKAINAflsgylREENVR 317
                                       66677777777777765323344444444567889999999999999999999999999999998332222234555 PP

                              DHHW 107 aaskeavekeddskkdgeilnavlvlgdsaieyysfslevadeyaa 152
                                       + ++ + +   +s+k + +  +v         y sf+l++++ y+ 
  gi|518652222|ref|YP_008141742.1| 318 VRPTSI-DFTVKSSKRTSVTTKVTSWTAMEKSYGSFNLNIGEGYIN 362
                                       666666.555678888888888888888888899999999999875 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.021        17      26      43 ..     205     222 ..     189     256 .. 0.80
   2 ?    3.6   0.0     0.095        77      28      50 ..     449     470 ..     433     498 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.021
                           SbcCD_C  26 lsrssgtlSGGekqflay 43 
                                       l r++++lSGGe q+la 
  gi|518652222|ref|YP_008141742.1| 205 LGRDVKELSGGELQKLAI 222
                                       7899*********99875 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.095
                           SbcCD_C  28 rssgtlSGGekqflaylalaaal 50 
                                       + +g lSGGe q  +++al +a 
  gi|518652222|ref|YP_008141742.1| 449 NYIGDLSGGELQ-RTSIALTLAT 470
                                       567899999994.5555555553 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.0       4.4   3.6e+03       9      19 ..      18      28 ..      10      41 .. 0.64
   2 ?   13.5   0.1   9.2e-05     0.075       5      18 ..      51      64 ..      48      98 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.4
                            Fer4_8  9 gaCqsaCpvlr 19
                                        C+  Cp +r
  gi|518652222|ref|YP_008141742.1| 18 HECRYYCPPVR 28
                                      24555566555 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 9.2e-05
                            Fer4_8  5 CieCgaCqsaCpvl 18
                                      Ci+Cg C + Cp+ 
  gi|518652222|ref|YP_008141742.1| 51 CIGCGICVNRCPFG 64
                                      ***********953 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   0.00012     0.094      45      58 ..      50      63 ..      39      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 0.00012
                           Fer4_17 45 lCieCgeCerkCPq 58
                                      lCi+Cg C+ +CP 
  gi|518652222|ref|YP_008141742.1| 50 LCIGCGICVNRCPF 63
                                      56666666666664 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1     0.012       9.5       6      43 ..     103     139 ..      98     202 .. 0.64
   2 ?    4.3   0.0     0.037        30       5      22 ..     367     384 ..     363     411 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.012
                            AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkf 43 
                                       +i G++  GKTt+++ l   +l+ ++ + +k+ d d +
  gi|518652222|ref|YP_008141742.1| 103 AILGQNALGKTTTMNIL-SGVLIPNFGNISKKNDKDYV 139
                                       799**************.88888888775555555543 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.037
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       i + G++  GKTt++k l
  gi|518652222|ref|YP_008141742.1| 367 IGVLGQNALGKTTFVKIL 384
                                       7899***********977 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   1.9      0.52   4.2e+02       6      15 ..      15      25 ..       8      37 .. 0.75
   2 ?   11.4   2.8   0.00045      0.37       3      17 .]      50      64 ..      48      64 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.52
                            Fer4_4  6 gCg.sCvaaCP 15
                                       C   C+++CP
  gi|518652222|ref|YP_008141742.1| 15 KCNhECRYYCP 25
                                      55556*****9 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00045
                            Fer4_4  3 rCigCgsCvaaCPqg 17
                                       CigCg Cv+ CP+g
  gi|518652222|ref|YP_008141742.1| 50 LCIGCGICVNRCPFG 64
                                      5************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 ?    0.7   3.4       1.6   1.3e+03       4      13 ..      16      26 ..      11      31 .. 0.71
   2 ?   13.3   4.6   0.00016      0.13       1      15 []      51      65 ..      51      65 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 1.6
                            Fer4_3  4 Cg.aCvevCPv 13
                                      C+  C   CP+
  gi|518652222|ref|YP_008141742.1| 16 CNhECRYYCPP 26
                                      7658******4 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00016
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+gCg Cv+ CP gA
  gi|518652222|ref|YP_008141742.1| 51 CIGCGICVNRCPFGA 65
                                      *************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (590 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.52
# Mc/sec: 3433.35
//
Query:       gi|518652223|ref|YP_008141743.1|  [L=141]
Description: hypothetical protein FACI_IFERC00001G0862 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.11   11.9   0.0       0.12   11.7   0.0    1.1  1  Bestrophin  Bestrophin, RFP-TM, chloride channel


Domain annotation for each model (and alignments):
>> Bestrophin  Bestrophin, RFP-TM, chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.7e-06      0.12     125     191 ..      58     125 ..      14     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.7e-06
                        Bestrophin 125 ralssrvrkr....fptle..hlleagllteeeakilenkywvplqWavsllrrlaerlkelakegrikddqa 191
                                       r + + +  +    f t+e   +le++   +ee + ++ ++w+  +W++++lr l+  l+e++ ++++++d  
  gi|518652223|ref|YP_008141743.1|  58 RVIDNMLEPEdrdvFYTMEdlGILETE---REETTLFDGREWRIHYWLLNVLRVLE--LAEMNISNKVEHDSR 125
                                       333333333344448888877777777...88888999****************77..889999999988874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 971.51
//
Query:       gi|518652224|ref|YP_008141744.1|  [L=467]
Description: hypothetical protein FACI_IFERC00001G0863 [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  147.6  32.7    9.4e-43  146.7  32.7    1.3  1  Sugar_tr  Sugar (and other) transporter
    7.5e-32  110.6  53.7    1.3e-26   93.3  44.4    2.0  2  MFS_1     Major Facilitator Superfamily
    0.00057   19.3   4.2    0.00057   19.3   4.2    2.8  3  MFS_4     Uncharacterised MFS-type transporter YbfB


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.7  32.7   1.6e-46   9.4e-43       7     447 ..      27     456 ..      21     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: 146.7 bits;  conditional E-value: 1.6e-46
                                       HHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                          Sugar_tr   7 lggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaa 83 
                                       lg +   Yd+++ig+++ ll      g+ + +  ++      gl++s +l+ a+iGs+++g l d+ GRk ++ +  
  gi|518652224|ref|YP_008141744.1|  27 LGFFTDAYDLFIIGVVILLLP---YAGWHNISIFYK------GLVTSTALLAAVIGSVVFGRLLDYSGRKAIYGFEL 94 
                                       444778899999999999999...445554444333......9********************************** PP

                                       HHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  84 vlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglg 160
                                       v +++g++ +a+ +  n++ +l++ R+l+G+g+G+ ++++++ + E++ ++ Rg++v++  ++ +fG + +  +  +
  gi|518652224|ref|YP_008141744.1|  95 VALIAGSLGSAFLTPVNNIFMLLFWRFLLGVGIGGDYATSSTIMTEYSSTMNRGKFVGMIFSMQSFGLIAGPLISIA 171
                                       **************99**********************************************************999 PP

                                       H.HTSS-.TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHT.T-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 161 l.nktsn.adgwrillglqlvpallllilllflPESPrylvek.gkeeeakevlaklrgeedadrelaeekdsleae 234
                                       + +++ +   +wr+ll++ ++pa+++++++ ++PE Pry+  + g+++ a + l++  g +    + + + +  ++ 
  gi|518652224|ref|YP_008141744.1| 172 FlSNYVSpYITWRLLLAIGAIPAIIVIYFRRTMPEPPRYTADVrGDYKLAAKNLKTFAGLDSTGSKGKTINA-PWYV 247
                                       9866666699******************************87615566999999996666444444433333.3333 PP

                                       HH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTH..HHHSS-THHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 235 qeeekaswkellssktvrqrlligvvlqifqqltGinaimyyspti..fenlglsksllvtiivgvvnfvatfvaif 309
                                         +  +++ +l+++ +  + l+ ++ +      + i +++  s t+  ++++ ++++ +  ii+gv  f    +a+f
  gi|518652224|ref|YP_008141744.1| 248 LFRDRKFLLTLIGTAG-AWFLMDWAFYGNSIMSNSILSFLVPS-TVsgIHSIIMTNE-YSAIIFGVAAFPGYWIAAF 321
                                       3333578888888877.45555555555555555544444444.4424689999999.******************* PP

                                       HHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHH CS
                          Sugar_tr 310 lvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRsk 386
                                       ++dr+GR+++ ++G+a+mai f i++  a+ + ++     + ++   + + ++  +g++ + +v+ +E+fp s+R++
  gi|518652224|ref|YP_008141744.1| 322 TIDRIGRKPVQITGFAMMAISFGIIS--AFSFLTTYRFLDYFLLLYGISY-FFIMFGPNVTTFVYPPEVFPISTRGL 395
                                       *************************9..6666666668888888888887.677889******************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCC CS
                          Sugar_tr 387 alaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtlee 447
                                       ++ i++a   +  f+ +l  +ii++  g  +   + a++a++++i + + +petk r+l e
  gi|518652224|ref|YP_008141744.1| 396 GTGISAAGGKTGAFIGTLADTIILSITGLHFLMGMLAIIAAIGLILTIVLLPETKRRDLGE 456
                                       ***************9999999999999777778899********************9976 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.3  44.4   2.2e-30   1.3e-26       3     322 ..      27     378 ..      25     383 .. 0.78
   2 !   23.0   2.0   5.4e-09   3.2e-05     111     187 ..     385     461 ..     377     467 .] 0.91

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 2.2e-30
                             MFS_1   3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       l++f  a++ +i+g+++ l  +a  ++is    gl++++  l+a+++s+++Grl d  Gr+ ++ + l+++++g+l 
  gi|518652224|ref|YP_008141744.1|  27 LGFFTDAYDLFIIGVVILLlPYAGWHNISIFYKGLVTSTALLAAVIGSVVFGRLLDYSGRKAIYGFELVALIAGSLG 103
                                       7899999999999999999999999*************************************************666 PP

                             MFS_1  79 llf.a..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg... 149
                                        +f +  +++++ll+ r+l G+g g+ ++++ ++++++++ ++rg+ +g++ ++ s+G i gpl++ +++s++    
  gi|518652224|ref|YP_008141744.1| 104 SAFlTpvNNIFMLLFWRFLLGVGIGGDYATSSTIMTEYSSTMNRGKFVGMIFSMQSFGLIAGPLISIAFLSNYVspy 180
                                       667436799**********************************************************9996666699 PP

                             MFS_1 150 ..Wravfyilaivsllafvlfllllpeepperkrkspkeee................kgtgpaplvp..awkallkd 206
                                         Wr++  i ai ++++  +   + ++ p +++  ++++                   g +++      +w  l++d
  gi|518652224|ref|YP_008141744.1| 181 itWRLLLAIGAIPAIIV--I--YFRRTMPEPPRYTADVRGDyklaaknlktfagldsTGSKGKT--InaPWYVLFRD 251
                                       99***999999999999..3..445444444444444444456688888888877653333333..2457******* PP

                             MFS_1 207 pvl..........w.illialllfffgfsg........lltllplylqevlgls.....glllaglllallalvgai 259
                                       + +          w ++ +a++       g        l++l+p+   +v g+      +  +++++++++a+ g  
  gi|518652224|ref|YP_008141744.1| 252 RKFlltligtagaWfLMDWAFY-------GnsimsnsiLSFLVPS---TVSGIHsiimtN-EYSAIIFGVAAFPG-- 315
                                       *995554444444333333344.......2333333436666666...555555545543.55554444444444.. PP

                             MFS_1 260 lallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGf.glgfvfpsll 322
                                          +a++ +dr+gr++  + +++ +++++ ++  +++ +++ +l ++l+l+G+  ++++f++  
  gi|518652224|ref|YP_008141744.1| 316 -YWIAAFTIDRIGRKPVQITGFAMMAISFGIISAFSFLTTYRFLDYFLLLYGIsYFFIMFGPNV 378
                                       .88888888********************************************77777766544 PP

  == domain 2  score: 23.0 bits;  conditional E-value: 5.4e-09
                             MFS_1 111 adwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                        ++fp + rg+++g+ +ag   Ga +g l+  +++s  g + ++ +lai+++++++l ++llpe++++   +++ e 
  gi|518652224|ref|YP_008141744.1| 385 PEVFPISTRGLGTGISAAGGKTGAFIGTLADTIILSITGLHFLMGMLAIIAAIGLILTIVLLPETKRRDLGETSGEA 461
                                       6899*****************************************************99****99999888887776 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   4.2   9.5e-08   0.00057      30     177 ..      59     212 ..      50     231 .. 0.76
   2 ?    1.1   6.7     0.032   1.9e+02     213     312 ..     285     387 ..     264     447 .. 0.62
   3 ?   -0.6   0.7      0.11   6.4e+02     144     173 ..     426     450 ..     387     464 .. 0.57

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.5e-08
                             MFS_4  30 agllaaaNylGYLvGallaafalsagaeRlr....llagllatvllllamaltesfaaflliRflaGvasAvvlvfg 102
                                        gl+ +  +l   +G++++  +l     R       l++l+a  l  +    +++++++l +Rfl+Gv+ +      
  gi|518652224|ref|YP_008141744.1|  59 KGLVTSTALLAAVIGSVVF-GRLLDYSGRKAiygfELVALIAGSLGSAFLTPVNNIFMLLFWRFLLGVGIGGDYATS 134
                                       5778888888888999988.6666666677644444556666666666666678999999***************** PP

                             MFS_4 103 sslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslW...lalavlsavllllvalllpraalre 176
                                       s+++ + ++  +r++  +++f+   +G +++ l+ ++ l   +s   +W   la++++ a++++    ++p+ ++  
  gi|518652224|ref|YP_008141744.1| 135 STIMTEYSSTMNRGKFVGMIFSMQSFGLIAGPLISIAFLSNYVSPYITWrllLAIGAIPAIIVIYFRRTMPEPPRYT 211
                                       *****************************************999999993333455666666666666667555444 PP

                             MFS_4 177 a 177
                                       a
  gi|518652224|ref|YP_008141744.1| 212 A 212
                                       4 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.032
                             MFS_4 213 Flvaiardgaggalleall.WllvGlaaivgvlvwlrvakrsglrralaaallieavg..vlls.llspsplglivs 285
                                       Flv    +g ++ ++++ +  +++G+aa++g ++     +r g +++    +++ a++  ++ +   ++++  l   
  gi|518652224|ref|YP_008141744.1| 285 FLVPSTVSGIHSIIMTNEYsAIIFGVAAFPGYWIAAFTIDRIGRKPVQITGFAMMAISfgIISAfSFLTTYRFLDYF 361
                                       666656666666666555514689***********************999999998851133320233444445455 PP

                             MFS_4 286 svllGltflaitalvlqlarelappat 312
                                        +l G  ++ i+ ++ +++ +++pp++
  gi|518652224|ref|YP_008141744.1| 362 LLLYGISYFFIM-FGPNVTTFVYPPEV 387
                                       555555555443.45555555555555 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.11
                             MFS_4 144 glsasslWlalavlsavllllvalllpraa 173
                                       +l       +la+++a+ l+l ++llp+++
  gi|518652224|ref|YP_008141744.1| 426 FL-----MGMLAIIAAIGLILTIVLLPETK 450
                                       22.....22345555555666666666443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       715  (0.0398795); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 2968.28
//
Query:       gi|518652225|ref|YP_008141745.1|  [L=333]
Description: hypothetical protein FACI_IFERC00001G0864 [Ferroplasma acidarmanus fer1]
Scores for complete 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-59  201.8   0.0    1.6e-59  201.6   0.0    1.1  1  Pterin_bind  Pterin binding enzyme
     0.0032   17.6   1.0     0.0068   16.5   1.0    1.5  1  Mg296        Mg296 protein


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   0.0   1.7e-63   1.6e-59       1     244 []      77     311 ..      77     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 1.7e-63
                                       EEEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHHHCTSEEE CS
                       Pterin_bind   1 mgilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrdeadvpis 77 
                                       mgilN+tpdsf++g+++ +     + + +m+++  di+DiggestrPg+++vd+e+e +r+  vle +++ +++p+s
  gi|518652225|ref|YP_008141745.1|  77 MGILNATPDSFFEGSRI-S---NKEIVDSMLDAKPDIIDIGGESTRPGSKMVDPETEFNRIKDVLEYIKSCSNIPVS 149
                                       9**************99.3...34567899****************************************99***** PP

                                       EE-S-HHHHHHHHHTTSEEEEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHH CS
                       Pterin_bind  78 iDttkaevaeaAlkagadivNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearv 154
                                       +D+ +  ++++A++ g +++Nd+sg++ dp m+ ++a ++++++vmhmrg+p++m e++ +y+++  ++++++ +r+
  gi|518652225|ref|YP_008141745.1| 150 VDSRHLYTISRAMEYGIEYINDISGFS-DPGMIDIAAGSNVKCIVMHMRGNPENMGEYT-DYDNLYFQLNRYFYNRA 224
                                       ***************************.*******************************.***************** PP

                                       HHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHHTTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHH CS
                       Pterin_bind 155 eaaeeaGvaperillDpgigfgkteehnlellrrldelrealevpvllGvSrksflgrllelgkaeeRdagtaafla 231
                                       +++++ G++pe+i+lDpgigf+k+ + n+++l+    +    ++ +l G+Srk f+g+++   +++eR  gt+a + 
  gi|518652225|ref|YP_008141745.1| 225 DEMVKKGINPENIILDPGIGFAKDFNGNMDILSSPWSF--FIGFDTLFGTSRKGFIGKITG-STVKERLGGTIASSI 298
                                       **********************************9999..99****************983.3489*********** PP

                                       HHHHTT-SEEEES CS
                       Pterin_bind 232 laaaaGadivrVh 244
                                       +   +G+di+rVh
  gi|518652225|ref|YP_008141745.1| 299 YLNSNGVDILRVH 311
                                       ************9 PP

>> Mg296  Mg296 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   1.0   7.6e-07    0.0068      22      90 ..       8      76 ..       2      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 7.6e-07
                                      HHHHHHHHHHHHHHT-SSGGGSS---S-HH.HHHHHHHHHHHHHHHHH---.....-------------H CS
                             Mg296 22 kliqnynlileretstlliyedddyeeidf.feksieselfyvksklvkelndhiedllkvkvdddkgdl 90
                                       + +ny  i+e++++ +++ e   y   +  feksi+ e fy+k+++ +  +d i    + k+ ++k+ +
  gi|518652225|ref|YP_008141745.1|  8 SINKNYLNIYEESENGKIVIEGKKYTFSSVkFEKSILKE-FYIKNHIFEGYEDEISAKAENKITNKKSLI 76
                                      5679*********************987755******87.9**********9999999999999998433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2291.00
//
Query:       gi|518652226|ref|YP_008141746.1|  [L=283]
Description: hypothetical protein FACI_IFERC00001G0865 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-14   55.3   0.0    1.4e-14   54.9   0.0    1.2  1  Radical_SAM      Radical SAM superfamily
    5.6e-06   26.7   0.1    9.6e-06   26.0   0.1    1.4  1  LIAS_N           N-terminal domain of lipoyl synthase of Radi
      0.006   16.9   0.0      0.013   15.9   0.0    1.6  2  Toprim_3         Toprim domain
  ------ inclusion threshold ------
      0.031   13.8   0.0       0.23   10.9   0.0    2.0  2  EAL              EAL domain
      0.062   13.1   0.0        0.2   11.5   0.0    1.8  2  INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   3.8e-18   1.4e-14       2     164 ..      52     210 ..      51     213 .. 0.89

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 3.8e-18
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC..CC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla..vp 76 
                                       v +  C+++C+fCa+++     g    l+++e  +  +++ + ++ ++v++++ + ++ pd+   +++++ ++  + 
  gi|518652226|ref|YP_008141746.1|  52 VLGSNCSRGCRFCAVTH-----GNMLPLDPDEPQKVYDSI-KLMNLDYVVITSVDRDDLPDKGSSAFARVIEKvkEL 122
                                       56788***********8.....777778888888888888.5667***************************99999 PP

                                       TEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSET.EEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                       Radical_SAM  77 giritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikr.vvdrivg 151
                                       gi+i v ++ +  d   l+r+  +++d++++++e++        ++ ++ +++++l +l++++ ++  + +++ i++
  gi|518652226|ref|YP_008141746.1| 123 GIKIEVLIPDFGGDHADLDRIIAAEPDVIAHNIETVRRL--TPSVRdPRAGYDQTLSVLKYIKGSMKGViTKSSIMV 197
                                       99999999999999************************6..55555599****************87779******* PP

                                       BTTTSHHHHHHHH CS
                                       xxxxxxxxxxxxx RF
                       Radical_SAM 152 lpGendeeleell 164
                                       + Ge+dee+ee++
  gi|518652226|ref|YP_008141746.1| 198 GLGETDEEVEETM 210
                                       ***********97 PP

>> LIAS_N  N-terminal domain of lipoyl synthase of Radical_SAM family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   2.7e-09   9.6e-06      78     108 .]       6      36 ..       1      36 [. 0.94

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 2.7e-09
                            LIAS_N  78 ktkiPlGknynkikndlreLnLhtvCeeaRC 108
                                       k ++P+G+ y+ ikn++ + +L+tvCeea C
  gi|518652226|ref|YP_008141746.1|   6 KVNLPTGERYSFIKNTINSRQLNTVCEEAHC 36 
                                       889***************************9 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.6e-06     0.013      44      88 ..      95     140 ..      47     147 .. 0.86
   2 ?   -3.8   0.0       4.7   1.7e+04      60      77 ..     206     223 ..     202     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.6e-06
                          Toprim_3  44 vviaaDnDaand.GreaaeklaerleaagieavllepaegeDwndv 88 
                                       v++  D+D   d G  a+++++e++++ gi++ +l p+ g+D  d+
  gi|518652226|ref|YP_008141746.1|  95 VITSVDRDDLPDkGSSAFARVIEKVKELGIKIEVLIPDFGGDHADL 140
                                       6777896666666************************888877664 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 4.7
                          Toprim_3  60 aeklaerleaagieavll 77 
                                       +e++++ l  ag+e+ ++
  gi|518652226|ref|YP_008141746.1| 206 VEETMMDLRNAGVEILTV 223
                                       677788888888888776 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   6.5e-05      0.23     135     181 ..     109     158 ..      96     171 .. 0.81
   2 ?    0.4   0.0      0.11   3.9e+02     114     151 ..     189     220 ..     172     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.5e-05
                                       HHH..HHHHHHHCTT-EE..EEEEETSSTCCCHHHCCC--SEEEE-HHHH CS
                               EAL 135 alq.eevlarLralGiri..alddfgtgysslsylarlppdiiKldrsll 181
                                       + + ++v++++++lGi+i   + dfg ++++l+++   +pd+i  + + +
  gi|518652226|ref|YP_008141746.1| 109 SSAfARVIEKVKELGIKIevLIPDFGGDHADLDRIIAAEPDVIAHNIETV 158
                                       45556999*******9853389********************97666655 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.11
                                       T-GCC-EEEEEEHHHHHHTHHHHH.HHHHHHHCTT-EE CS
                               EAL 114 gpspsrLvleitesellarlealqeevlarLralGiri 151
                                        + +s++++ + e+     +e+++ e +++Lr +G+ i
  gi|518652226|ref|YP_008141746.1| 189 VITKSSIMVGLGET-----DEEVE-ETMMDLRNAGVEI 220
                                       56667799999999.....88998.9*********987 PP

>> INT_SG_DDX_CT_C  INTS6/SAGE1/DDX26B/CT45 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       1.7   6.1e+03      35      46 ..      11      22 ..       7      23 .. 0.80
   2 ?   11.5   0.0   5.6e-05       0.2       2      36 ..     153     187 ..     152     191 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.7
                   INT_SG_DDX_CT_C 35 levrkkfvedvi 46
                                      +  r++f++++i
  gi|518652226|ref|YP_008141746.1| 11 TGERYSFIKNTI 22
                                      567999999998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 5.6e-05
                   INT_SG_DDX_CT_C   2 iNaeikkqlvkevRrpgrnyekiFklLeevqGsle 36 
                                       +N e  ++l+  vR p   y++ +++L+ ++Gs++
  gi|518652226|ref|YP_008141746.1| 153 HNIETVRRLTPSVRDPRAGYDQTLSVLKYIKGSMK 187
                                       9********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1981.73
//
Query:       gi|518652227|ref|YP_008141747.1|  [L=344]
Description: hypothetical protein FACI_IFERC00001G0866 [Ferroplasma acidarmanus fer1]
Scores for complete 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-59  199.9   0.0      6e-59  199.4   0.0    1.1  1  E1_dh           Dehydrogenase E1 component
    9.1e-07   28.8   0.0    1.6e-06   28.0   0.0    1.4  1  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP
    8.8e-05   21.8   0.0    0.00019   20.8   0.0    1.5  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  199.4   0.0     1e-62     6e-59       2     297 ..      17     319 ..      16     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 199.4 bits;  conditional E-value: 1e-62
                                       HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-TT CS
                             E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkvk 78 
                                       k  ++ r++d+++ +++r++ ++fy++ +g ea+++g+ +a+ +eD+  ++YR+ gvl+  g++++ il+++   + 
  gi|518652227|ref|YP_008141747.1|  17 KNIVMERLFDKKMLNASRQGFLPFYIPLMGHEAIHIGMGMAIRDEDFFYPYYRDFGVLIQMGIPIDTILSQVFATAT 93 
                                       567899******************************************************************99998 PP

                                       TSSGTT-..-E..BTT..BEEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--E CS
                             E1_dh  79 gkggsrh.elmyaekesrilggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpv 154
                                       ++  +r  + +++ k+ +i     +v+     + Gia+a+k++++   +i+++GDgA++  d++ a+n+a ++klp+
  gi|518652227|ref|YP_008141747.1|  94 DNEIGRDmPDHFSLKKYNIGAVITPVAGHLTSATGIAYAKKYRKESGSVITTFGDGATSTPDFHVAMNFAGVYKLPM 170
                                       8888888788889999899999999999988888******************************************* PP

                                       EEEEEEESEETTEEH....HHH-S---......GGG..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEE CS
                             E1_dh 155 ifvveNNkygisTea....ekasaske......ladrargvgipglrVdgnDplavyeAvkfAaeraregkgpllie 221
                                       +f++eNN+++is+++    +ka + ++      ++++a  +g  g+r+dg+ +++vy A++ A e a+e   p+lie
  gi|518652227|ref|YP_008141747.1| 171 VFFCENNQFAISVPTyptdDKAFNQTYeetrgaIYKKAESYGFSGIRIDGTNFIEVYRATRKALENASE--DPILIE 245
                                       ************964232234444433333344899*******************************98..9***** PP

                                       EEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS--- CS
                             E1_dh 222 lvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaeskkel 297
                                       ++tYR+g+Hs+ Ddp +yr ++ v e  +k dp+   ++lL++  v+++   k+i++e+++     ++  e+++++
  gi|518652227|ref|YP_008141747.1| 246 AMTYRMGPHSTADDPNKYR-TDRVPEGSEK-DPLIVSQKLLKDMKVITDLDIKQINDEMEETTSKLIDTYEKAPKP 319
                                       *******************.8888887766.9**********************9999998877777777766666 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   2.6e-10   1.6e-06      31     152 ..     120     245 ..     101     246 .. 0.76

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 2.6e-10
                                       TTHHHHHHHHHHH....STTSEEEEEEEHHHHHHT.GG.GHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTCCTTT CS
                      TPP_enzyme_C  31 GyglpaAiGakla....kpdrevvaivGDGgflmi.lq.elatavrrnlpitvvvlnNegygmtggqqepfggkrks 101
                                          l  A+G++ a    k++  v+ + GDG++    ++ ++  a  ++lp+++++ nN+    +   ++   +  + 
  gi|518652227|ref|YP_008141747.1| 120 AGHLTSATGIAYAkkyrKESGSVITTFGDGATSTPdFHvAMNFAGVYKLPMVFFCENNQFAISVPTYPTDDKA--FN 194
                                       445566777777533325567**********99998651555566899************9777777555555..44 PP

                                       TSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHH..CSSSEEEEE CS
                      TPP_enzyme_C 102 gpagkdlkpvdfaklaealGakgarvekadveeleealkeal..ekkgpalie 152
                                       ++++  ++   + k ae++G +g+r++ ++  e+ +a ++al  +++ p lie
  gi|518652227|ref|YP_008141747.1| 195 QTYE--ETRGAIYKKAESYGFSGIRIDGTNFIEVYRATRKALenASEDPILIE 245
                                       4443..44557999****************************99899999998 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 !   20.8   0.0   3.1e-08   0.00019     117     237 ..     123     247 ..     117     258 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 3.1e-08
                    DXP_synthase_N 117 isaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvGalskylskllssk 193
                                       ++ a+G+a a+++++e+ +v++  GDga ++   + a+n +g  k  ++    +N+ +is +     +   + + ++
  gi|518652227|ref|YP_008141747.1| 123 LTSATGIAYAKKYRKESGSVITTFGDGATSTPDFHVAMNFAGVYKLPMVFFCENNQFAISVPTYPTDDKAFNQTYEE 199
                                       7789*******************************************************987655544433333333 PP

                    DXP_synthase_N 194 ayeklkkevkkll.k...kigkklaelakklkeslkellvpgtlfeel 237
                                       +  ++ k+++++  +     g+++ e+ + ++++l ++  +  l e++
  gi|518652227|ref|YP_008141747.1| 200 TRGAIYKKAESYGfSgirIDGTNFIEVYRATRKALENASEDPILIEAM 247
                                       333333333332212221336666666666666666665555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2279.36
//
Query:       gi|518652228|ref|YP_008141748.1|  [L=321]
Description: hypothetical protein FACI_IFERC00001G0867 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-46  157.6   0.0    3.6e-46  157.1   0.0    1.2  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.8e-30  105.4   0.0    2.9e-30  104.7   0.0    1.3  1  Transketolase_C  Transketolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.1   0.0     4e-50   3.6e-46       2     176 ..       3     178 ..       2     179 .. 0.98

  Alignments for each domain:
  == domain 1  score: 157.1 bits;  conditional E-value: 4e-50
                                       EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEE CS
                      Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllvi 76 
                                       ++++ ka++  l+  +++d++++l+g+Dv+  gg+f v+ gll + g++rv+d++++E +++gf +G+++ag l+ i
  gi|518652228|ref|YP_008141748.1|   3 QMTMVKALNSGLNNAMEKDDSIILLGEDVGtdGGVFRVTDGLLAKYGKERVMDTPLAELGIVGFGIGMSMAG-LKSI 78 
                                       68999*******************************************************************.9*** PP

                                       EEEEEHHHHGGG..HHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHH CS
                      Transket_pyr  77 veaqFgdFangA..qiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetk 151
                                        e+qF dF+ +A  qi+++ a+ ++++ g ++ ++v+r+p+g g  G   +s++ ea+++++ gl+vv+Ps+p+++k
  gi|518652228|ref|YP_008141748.1|  79 PEIQFQDFIYTAmdQIINQMAKLRYRTNGDYTLPMVLRTPYGGGVHGGPYHSQSGEAYFTHTQGLTVVTPSNPYDAK 155
                                       ***************************************************************************** PP

                                       HHHHHHHHSSS.SEEEEEE-SSEEC CS
                      Transket_pyr 152 hllrrairredrkPvvlrlpksllr 176
                                       +ll   i+   ++Pv++++pk+l+ 
  gi|518652228|ref|YP_008141748.1| 156 GLLLSSIE--LNDPVIFLEPKRLYY 178
                                       ********..567*********995 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   0.0   3.2e-34   2.9e-30       2     124 .]     195     311 ..     194     311 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 3.2e-34
                                       EEEEEETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHH CS
                   Transketolase_C   2 kaeilregkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigs 78 
                                       ka ++reg+d+t+++yG  v+++   +   ek++++a+++dlrt++p+D +til+ vkktg++++v+e  k++G+g+
  gi|518652228|ref|YP_008141748.1| 195 KASVIREGDDLTIITYGPAVPVVKSTV---EKNNVNAQIIDLRTLSPFDLDTILAGVKKTGKVLIVHESPKMFGVGA 268
                                       7999******************99877...6779******************************************* PP

                                       HHHHHHHHCCCTTCSSEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
                   Transketolase_C  79 evaaalaeeafdgldapvkrvggpdviepgsaeelekafgldaeki 124
                                       e++a+++e+a+d+l ap++rv+g d++ p++   le+++ ++ ++i
  gi|518652228|ref|YP_008141748.1| 269 ELSATISEKAVDYLAAPILRVTGLDIPIPFA---LEEYYVPNERRI 311
                                       **************************88887...9******99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2215.27
//
Query:       gi|518652229|ref|YP_008141749.1|  [L=384]
Description: hypothetical protein FACI_IFERC00001G0868 [Ferroplasma acidarmanus fer1]
Scores for complete 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-67  227.4   0.0    2.3e-67  226.9   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    6.6e-21   73.9   5.2    1.4e-20   72.9   5.2    1.6  1  Biotin_lipoyl    Biotin-requiring enzyme
    4.3e-11   43.0   0.4    9.8e-11   41.8   0.4    1.7  1  E3_binding       e3 binding domain
    7.1e-09   35.4   0.1    3.7e-05   23.5   0.0    3.0  3  Biotin_lipoyl_2  Biotin-lipoyl like
      0.005   17.5   0.4        4.5    8.0   0.0    2.7  2  HlyD_3           HlyD family secretion protein
  ------ inclusion threshold ------
      0.026   14.5   0.2      0.067   13.2   0.2    1.6  1  RnfC_N           RnfC Barrel sandwich hybrid domain
      0.034   13.3   0.4        1.3    8.2   0.1    2.7  3  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
      0.045   13.5   0.1       0.51   10.1   0.0    2.3  2  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.064   13.1   0.3       0.16   11.8   0.3    1.7  1  GCV_H            Glycine cleavage H-protein


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  226.9   0.0   1.1e-70   2.3e-67       5     229 ..     165     379 ..     161     382 .. 0.94

  Alignments for each domain:
  == domain 1  score: 226.9 bits;  conditional E-value: 1.1e-70
                                       XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG CS
                      2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPeln 81 
                                       e    +girk i++++t+skq iphft++d +d++++ +  +++ +k+       +++++f++kav+ A ++fP++n
  gi|518652229|ref|YP_008141749.1| 165 EVFTPTGIRKLIFDKMTKSKQIIPHFTITDFIDTENIEKAINQYSKKK------YVSFTAFFVKAVTVAFRDFPKFN 235
                                       5566789*******************************9999888866......69********************* PP

                                       -EE.EESEEEE--SS--EEEE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---- CS
                      2-oxoacid_dh  82 asvdeeekeivvkkhvniGvAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGm 158
                                       a ++e++ ++++kk++niGvAv++p GL v v+k++ +k++ +i++e+k++ae+ar+gkl  +d++g+tf+++N+G+
  gi|518652229|ref|YP_008141749.1| 236 AVYNENDRTYTIKKKYNIGVAVDSPAGLTVVVVKDVASKNIFQISEEIKDMAERARNGKLGLQDVQGSTFSVTNIGS 312
                                       ***************************************************************************** PP

                                       -----------TT-SEEEEE---.B--TTSTT-HT---EEEEEEEEETTT--HHHHHHHHHHHHHTT-HHX CS
                      2-oxoacid_dh 159 lGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvmtlslsaDHRvidGaeaarFlntlkkllenpe 229
                                       +G+ ++tPiin+p+vaIl +++   +  +++gel+ +  ++l+l++DHR+idGaeaar+l++lk++le p 
  gi|518652229|ref|YP_008141749.1| 313 IGGIMATPIINYPEVAILEINTR--TSGFVNGELKHG--LYLTLACDHRLIDGAEAARYLEKLKEVLEYPL 379
                                       ********************988..567789997766..59***************************885 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   5.2   6.9e-24   1.4e-20       2      73 .]       3      75 ..       2      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 6.9e-24
                                      EEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
                     Biotin_lipoyl  2 eiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                                      ++++P iGe ++eg +v+++vk+Gd++k+++ l+ev ++K +++i++p+aG+v++il+keG+t   gd +++i
  gi|518652229|ref|YP_008141749.1|  3 TVSLPPIGEGIQEGeIVKWTVKPGDSIKKDDELVEVMTDKITVKIPSPVAGKVSKILIKEGETAMIGDAMVEI 75
                                      5889*****************************************************************9987 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.4   4.9e-14   9.8e-11       1      35 [.     110     144 ..     110     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 4.9e-14
                                       SBE-HHHHHHHHHCT--TTTS---CTTTBE-HHHH CS
                        E3_binding   1 vlAsPaaRklAkelGidLsdvkGtGpgGRItkeDV 35 
                                       v+A+Pa+R +A+ +++d+ +vk+   +GRItkeDV
  gi|518652229|ref|YP_008141749.1| 110 VKATPAVRAYARSKNVDILKVKPAAQDGRITKEDV 144
                                       79********************************9 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0   0.00077       1.5      10      32 ..      15      37 ..      12      44 .. 0.89
   2 !   23.5   0.0   1.8e-08   3.7e-05       3      37 ..      45      79 ..      37      83 .. 0.93
   3 ?   -2.2   0.0       1.9   3.9e+03      33      44 ..     196     207 ..     195     223 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00077
                   Biotin_lipoyl_2 10 sGrVaqlnVkdGqrVkaGdvLae 32
                                       G ++++ Vk G+ +k+ d L+e
  gi|518652229|ref|YP_008141749.1| 15 EGEIVKWTVKPGDSIKKDDELVE 37
                                      799****************8876 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 1.8e-08
                   Biotin_lipoyl_2  3 vsIaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                                      v+I +pv+G+V+++++k+G     Gd  +e+Ds++
  gi|518652229|ref|YP_008141749.1| 45 VKIPSPVAGKVSKILIKEGETAMIGDAMVEIDSPD 79
                                      99*******************************97 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.9
                   Biotin_lipoyl_2  33 lDsralqlalaq 44 
                                       +D+++ ++a++q
  gi|518652229|ref|YP_008141749.1| 196 IDTENIEKAINQ 207
                                       899999999999 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0038       7.5       8      39 ..      16      46 ..      14      48 .. 0.86
   2 !    8.0   0.0    0.0022       4.5       2      34 ..      47      79 ..      46      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0038
                            HlyD_3  8 Gvvvelnveegevvqagdelleiippdtllve 39
                                      G++v++ v++g+ + + del+e++ +d++ v+
  gi|518652229|ref|YP_008141749.1| 16 GEIVKWTVKPGDSIKKDDELVEVM-TDKITVK 46
                                      99*********************9.6666554 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0022
                            HlyD_3  2 lrApvdGvvvelnveegevvqagdelleiippd 34
                                      + +pv+G+v+++ ++ege    gd+++ei  pd
  gi|518652229|ref|YP_008141749.1| 47 IPSPVAGKVSKILIKEGETAMIGDAMVEIDSPD 79
                                      669*************************98776 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.3e-05     0.067      39      81 ..      16      59 ..      13      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.3e-05
                            RnfC_N 39 GapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81
                                      G+  k  vk gd ++k + + e  +  +++++ ++v+G+V +i 
  gi|518652229|ref|YP_008141749.1| 16 GEIVKWTVKPGDSIKKDDELVEVMTdKITVKIPSPVAGKVSKIL 59
                                      6777889************999865588*************995 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 ?    2.8   0.0     0.029        58      27      54 ..      15      41 ..      13      44 .. 0.82
   2 ?    8.2   0.1   0.00066       1.3     108     140 ..      44      76 ..      39     153 .. 0.68
   3 ?   -2.4   0.0       1.2   2.3e+03       9      31 ..     319     341 ..     316     342 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.029
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 27 eGwveklyvnatgdkVkkGqpLaelysp 54
                                      eG + k +v+  gd++kk+++L+e+   
  gi|518652229|ref|YP_008141749.1| 15 EGEIVKWTVK-PGDSIKKDDELVEVMTD 41
                                      6888899999.99999999999998765 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00066
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23 108 tvtvkapisGvVteknvreGqyvqpgdtlftia 140
                                       tv++ +p++G V +  + eG++++ gd++++i 
  gi|518652229|ref|YP_008141749.1|  44 TVKIPSPVAGKVSKILIKEGETAMIGDAMVEID 76 
                                       445555555555555555555555555555553 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.2
                                       XXXXXXXXXXXXXXXXXXXXXXX CS
                          HlyD_D23   9 vGtvayderrlarvsarveGwve 31 
                                       +  ++y e  + ++++r++G+v+
  gi|518652229|ref|YP_008141749.1| 319 TPIINYPEVAILEINTRTSGFVN 341
                                       5568899999999*******995 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00025      0.51      80     111 ..      15      46 ..       1      52 [. 0.83
   2 ?    1.4   0.0      0.13   2.6e+02      80     104 ..      52      76 ..      44      83 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00025
                                       TTTTEEES----SEE-SEEEEEEE-HHHHGGG CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevdleaikka 111
                                       +ge  +  vk gd++k+ d+lvev  ++i+ +
  gi|518652229|ref|YP_008141749.1|  15 EGEIVKWTVKPGDSIKKDDELVEVMTDKITVK 46 
                                       799999*********************99866 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.13
                                       TTTTEEES----SEE-SEEEEEEE- CS
                        PTS_EIIA_1  80 kgegFellvkegdkVkagdklvevd 104
                                        g++ ++l+keg++   gd +ve+d
  gi|518652229|ref|YP_008141749.1|  52 AGKVSKILIKEGETAMIGDAMVEID 76 
                                       4566666667777777777766666 PP

>> GCV_H  Glycine cleavage H-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   8.1e-05      0.16      30      73 ..      15      57 ..       2      67 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.1e-05
                                      H-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEE CS
                             GCV_H 30 lgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevve 73
                                       g++v  ++++ g+++kk+++l  v + K + ++++pv G+v +
  gi|518652229|ref|YP_008141749.1| 15 EGEIVKWTVKP-GDSIKKDDELVEVMTDKITVKIPSPVAGKVSK 57
                                      58888888876.99***************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); 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: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2549.25
//
Query:       gi|518652230|ref|YP_008141750.1|  [L=429]
Description: hypothetical protein FACI_IFERC00001G0869 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.3e-65  219.5   1.7    6.8e-65  219.2   1.7    1.1  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.3e-24   84.6   6.3    1.2e-21   77.0   0.8    3.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      3e-19   69.4   1.4    3.8e-19   69.1   1.4    1.1  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
      1e-18   67.6   0.0    4.4e-18   65.5   0.0    2.1  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.4e-09   36.8   0.3    9.8e-06   24.9   0.1    3.5  4  FAD_binding_2   FAD binding domain
    4.9e-09   35.4   4.9    0.00079   18.2   0.0    3.6  4  HI0933_like     HI0933-like protein
    7.5e-08   32.5   0.2    3.8e-05   23.8   0.1    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.9e-06   27.8   5.9      0.011   15.4   0.1    3.9  4  DAO             FAD dependent oxidoreductase
    4.2e-05   22.8   7.2       0.03   13.4   1.7    4.0  3  GIDA            Glucose inhibited division protein A
     0.0002   20.7   0.3     0.0082   15.4   0.0    2.2  2  FAD_binding_3   FAD binding domain
    0.00034   20.0   0.2     0.0018   17.6   0.1    2.2  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00039   20.0   1.5     0.0027   17.3   0.3    2.4  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
    0.00055   19.4   0.2      0.013   14.9   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
     0.0013   18.6   0.5       0.03   14.2   0.1    2.3  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0038   17.6   0.3        2.5    8.6   0.0    2.4  2  NAD_binding_7   Putative NAD(P)-binding
     0.0041   17.4   0.6        1.3    9.3   0.1    2.5  2  TrkA_N          TrkA-N domain
     0.0092   15.1   1.0        2.6    7.0   0.0    3.0  3  Lycopene_cycl   Lycopene cyclase protein
  ------ inclusion threshold ------
      0.016   15.2   3.0        0.4   10.6   0.0    3.0  4  NAD_binding_9   FAD-NAD(P)-binding
      0.022   15.3   2.8        3.3    8.4   0.2    2.8  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
        0.1   12.2   2.8       0.32   10.6   0.3    2.6  3  ApbA            Ketopantoate reductase PanE/ApbA
       0.16   11.2   0.0          2    7.6   0.0    2.6  3  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.2   1.7     8e-68   6.8e-65       2     294 .]       4     307 ..       3     307 .. 0.96

  Alignments for each domain:
  == domain 1  score: 219.2 bits;  conditional E-value: 8e-68
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.................. 57 
                                       d ++iG+G++G+  al+l ++g kv+++e    +g+cln gc++skal + +e+   ++                  
  gi|518652230|ref|YP_008141750.1|   4 DAAIIGSGAGGYYSALRLLKHGKKVLIIEkekFGGECLNYGCIPSKALIELSENIGYLHdmpgvtmnykidmkewqe 80 
                                       779*************************99999***********************999****************99 PP

                                       ...HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECH CS
                                       ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ...evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtld 131
                                            vk+++ g e+l  + + k+ +g + vk++++++ ++++++++++++ tGs p ++  +G  +      + + 
  gi|518652230|ref|YP_008141750.1|  81 wkeSMVKRITGGAEKLCISLGAKVVYGVGSVKDRNTVTVNGTDYTAKNIIINTGSVPVKI--KGI-D------DVYY 148
                                       99988899999999999977************************************9886..666.2......3367 PP

                                       HHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 132 saealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvke 208
                                       + e l  +  p+++v++GgGyiGvE+  a++klg+ev++ve  dr+l++ +++l++++ ++l+k Gv++++g +v  
  gi|518652230|ref|YP_008141750.1| 149 NREMLAVETIPAKLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPEIEEDLAREVDKRLRKLGVNIMTGMKVLS 225
                                       799999*********************************************************************** PP

                                       EEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE-GGGCTECCSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 209 idgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiyaiGDvaggkggp 284
                                       ++++++ ++v  e  ++i+ad+v+++vG+ p+te+ + eklg+e+ ++++i++d++ rtn+p+iyaiGDv    g+p
  gi|518652230|ref|YP_008141750.1| 226 VKKDKN-YKVSIEGSDTIEADTVLMSVGRIPNTEGSGiEKLGIEM-DGRFIKTDSHKRTNIPNIYAIGDVS---GVP 297
                                       *****8.99************************************.99***********************...*** PP

                                       --HHHHHHHH CS
                                       xxxxxxxxxx RF
                       Pyr_redox_2 285 elaqaAvqqG 294
                                       +la++A   G
  gi|518652230|ref|YP_008141750.1| 298 MLAHKAFYDG 307
                                       ******8765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.1    0.0065       5.5       2      31 ..       5      34 ..       4      37 .. 0.93
   2 ?    0.5   0.0       1.1   9.4e+02      49      71 ..     123     145 ..     108     149 .. 0.80
   3 !   77.0   0.8   1.4e-24   1.2e-21       1      77 [.     161     235 ..     161     241 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0065
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      ++++G+G  g   A  l ++gkkV ++e +
  gi|518652230|ref|YP_008141750.1|  5 AAIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      58*************************975 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.1
                                       HHHHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  49 klekngievllntkveeiegsed 71 
                                         ++++i + +++++++i+g +d
  gi|518652230|ref|YP_008141750.1| 123 DYTAKNIIINTGSVPVKIKGIDD 145
                                       456778*************9887 PP

  == domain 3  score: 77.0 bits;  conditional E-value: 1.4e-24
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       k+v++GgGyig+E+++a+++lg++V++ve++d++l+ ++e++++++ ++l+k+g++++++ kv +++++++   +v 
  gi|518652230|ref|YP_008141750.1| 161 KLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPEIEEDLAREVDKRLRKLGVNIMTGMKVLSVKKDKNY--KVS 235
                                       68*****************************************************************99984..344 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 !   69.1   1.4   4.5e-22   3.8e-19       2     305 .]       7     291 ..       6     291 .. 0.81

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.5e-22
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkgnignsiyrypk..emtfispsftsekleipdlnaiseetspafslkee 76 
                                       IiG G+ G  +a+ l k+g  ++li+Ek++ g    +y    ++ +i     ++   ++d++ ++ + +  + +ke 
  gi|518652230|ref|YP_008141750.1|   7 IIGSGAGGYYSALRLLKHGK-KVLIIEKEKFGGECLNYGCipSKALIE--LSENIGYLHDMPGVTMNYK--IDMKEW 78 
                                       9******************9.7****************7622556666..45888899*******9998..567777 PP

                       Pyr_redox_3  77 klsrkealeYlrevaksfelpiklfee.VesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkh 152
                                       +  ++ +++  +  a++  l i l  + V  v + ++  +v+ +  +y+Ak++ii tG    P k  i+G +  v  
  gi|518652230|ref|YP_008141750.1|  79 QEWKESMVKRITGGAEK--LCISLGAKvVYGVGSVKDRNTVTVNGTDYTAKNIIINTGS--VPVK--IKGID-DVYY 148
                                       77788888888888777..555665551699***************************9..8876..****9.3444 PP

                       Pyr_redox_3 153 yskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikv 229
                                       ++++ ++ ++   k+v+iGg+  +v++ + + + g+eV +v  ++ i  e   ++  l   + +rl++l     +++
  gi|518652230|ref|YP_008141750.1| 149 NREMLAV-ETIPAKLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPE---IEEDLAREVDKRLRKL----GVNI 217
                                       4444455.666899****************************99865554...4555555666666554....4999 PP

                       Pyr_redox_3 230 lfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                       ++  +v ++k+ +++ykv+ e  +++e  d v++ +G  p+++    +++ ++ dgr   t++ + tn+p+++ +G
  gi|518652230|ref|YP_008141750.1| 218 MTGMKVLSVKK-DKNYKVSIEGSDTIE-ADTVLMSVGRIPNTEGSGIEKLGIEMDGRFIKTDSHKRTNIPNIYAIG 291
                                       9********97.588***999866554.4665666******9876556666667*******************999 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   5.2e-21   4.4e-18       1     109 [.     326     424 ..     326     425 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 5.2e-21
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p vv+tdpe+a++G+       ag   k  k+p+ an r+l++++++gf+Kl +d  +g + Ga + +p+ +e i 
  gi|518652230|ref|YP_008141750.1| 326 MPFVVYTDPEIAFTGK-------AG--TKSNKVPVLANPRSLTMNQKDGFFKLYYDD-DGTITGAGVAAPRSSESIT 392
                                       5889***********5.......56..67899*********************7776.******************* PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealkea 109
                                       e+++a++ gl+++dl  tih+hPt+se lk+a
  gi|518652230|ref|YP_008141750.1| 393 EISLAVESGLSIDDLFLTIHPHPTVSEGLKDA 424
                                       ***************************99987 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.1   1.1e-08   9.8e-06       1      33 [.       4      36 ..       4      42 .. 0.92
   2 ?    0.5   0.1       0.3   2.6e+02       2      31 ..     162     191 ..     161     194 .. 0.91
   3 !    6.7   0.0    0.0039       3.4     376     404 ..     274     296 ..     265     303 .. 0.82
   4 ?   -2.9   0.0       3.1   2.6e+03     140     187 ..     333     390 ..     327     400 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.1e-08
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33
                                      D+ +iGsG++G+ +Al++ ++G+kv+++eke+ 
  gi|518652230|ref|YP_008141750.1|  4 DAAIIGSGAGGYYSALRLLKHGKKVLIIEKEKF 36
                                      899***************************984 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                                       EEEE--SHHHHHHHHHHHHTTT-EEEEESS CS
                     FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavveke 31 
                                       +++iG+G  G   +++ ++ G +v +ve +
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGSEVYIVEMK 191
                                       69*************************965 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0039
                                       EEBETTSBESTTEEESSBTEEE-STCEES CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaag 404
                                       ++td + r+      +ip+ YA+G v ++
  gi|518652230|ref|YP_008141750.1| 274 IKTDSHKRT------NIPNIYAIGDVSGV 296
                                       567777777......**********9965 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 3.1
                                       HHHHHHHHHHHHHTCTEEEEESEEEEEEEECTT..........EEEEEEEEETTTTCE CS
                     FAD_binding_2 140 ghallarlvesarkagvdfqerteadeLivedg..........rvtGavvenpesgre 187
                                        ++++ ++ ++ ++++v ++++ + ++++++dg           +tGa v+ p+s++ 
  gi|518652230|ref|YP_008141750.1| 333 DPEIAFTGKAGTKSNKVPVLANPRSLTMNQKDGffklyydddgTITGAGVAAPRSSES 390
                                       5666666666666666777777766666666555555555556999999998866554 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   9.2e-07   0.00079       2      34 ..       4      36 ..       3      43 .. 0.90
   2 ?   -1.1   0.0      0.67   5.7e+02     139     163 ..     112     134 ..      63     149 .. 0.60
   3 ?    2.7   0.1     0.049        42       2      36 ..     161     195 ..     160     200 .. 0.90
   4 !   15.1   0.1   8.3e-06    0.0071     100     163 ..     193     252 ..     185     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.2e-07
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34
                                      d ++iG Ga G + A+++ k+gk+Vl++ek+k 
  gi|518652230|ref|YP_008141750.1|  4 DAAIIGSGAGGYYSALRLLKHGKKVLIIEKEKF 36
                                      789***************************975 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.67
                                       TTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 139 edgkfrvktkseeeleadklvlAtG 163
                                       +d+  +v++ +++ ++a+++++ tG
  gi|518652230|ref|YP_008141750.1| 112 KDR-NTVTV-NGTDYTAKNIIINTG 134
                                       222.45555.566666666666666 PP

  == domain 3  score: 2.7 bits;  conditional E-value: 0.049
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36 
                                       ++++iGgG  G+    + +k g++V ++e +++++
  gi|518652230|ref|YP_008141750.1| 161 KLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRIL 195
                                       689*********99999************998875 PP

  == domain 4  score: 15.1 bits;  conditional E-value: 8.3e-06
                                       EEEETT.-CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 100 rlFpvsdkaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       r+ p+    ed+ +   k+l++ gv++++ ++v sv+  +d++++v++++++++ead++++++G
  gi|518652230|ref|YP_008141750.1| 193 RILPEI--EEDLAREVDKRLRKLGVNIMTGMKVLSVK--KDKNYKVSIEGSDTIEADTVLMSVG 252
                                       555554..4677888899******************4..56668999999***********998 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   4.4e-08   3.8e-05       1      38 [.       7      43 ..       7      63 .. 0.93
   2 ?    6.4   0.0     0.012        11       1      31 [.     164     194 ..     164     222 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.4e-08
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                                      I+G+G++G + A +L k+g++vl++ek  ++GG +  y
  gi|518652230|ref|YP_008141750.1|  7 IIGSGAGGYYSALRLLKHGKKVLIIEKE-KFGGECLNY 43
                                      9**************************6.999998765 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.012
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G  G  +  + +k g +v ++e+ dr+
  gi|518652230|ref|YP_008141750.1| 164 IIGGGYIGVEMGTAFRKLGSEVYIVEMKDRI 194
                                       9**************************9997 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.2e-05     0.011       1      33 [.       4      37 ..       4      42 .. 0.91
   2 ?    0.5   0.1      0.41   3.5e+02     151     201 ..      92     134 ..      86     147 .. 0.68
   3 ?    5.7   0.3     0.011       9.1       2      30 ..     162     192 ..     161     195 .. 0.79
   4 !    5.9   0.0    0.0094       8.1     148     201 ..     202     252 ..     200     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                                      d +iiG+G  G   A+ L ++g  V+++ek+  +g
  gi|518652230|ref|YP_008141750.1|  4 DAAIIGSGAGGYYSALRLLKHGkkVLIIEKE-KFG 37
                                      789******************99********.666 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.41
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                       +  + + +lG+++++g  v +++++    ++v +   g+  +a+ +++ +G
  gi|518652230|ref|YP_008141750.1|  92 GAEKLCISLGAKVVYG--VGSVKDR--NTVTV-N---GTDYTAKNIIINTG 134
                                       56677999*******9..7777554..24555.4...66533466555555 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.011
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       +viiGGG+iG+    +  + g  V ++e++d
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGseVYIVEMKD 192
                                       79********988888855577888888775 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0094
                                       HHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECTEEE.EEEEEEEE--G CS
                               DAO 148 ltaalaraaealGveilegtevtgleeedgkvwgve.rttpgen.daadavVnaaG 201
                                       l++ + +++++lGv+i +g +v +++++  k ++v  +   g+   +ad+v ++ G
  gi|518652230|ref|YP_008141750.1| 202 LAREVDKRLRKLGVNIMTGMKVLSVKKD--KNYKVSiE---GSDtIEADTVLMSVG 252
                                       566677889****************664..45777332...444335688988887 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   1.7   3.5e-05      0.03       2      47 ..       5      52 ..       4     155 .. 0.91
   2 !    5.7   0.1    0.0077       6.5       2      30 ..     162     190 ..     161     196 .. 0.88
   3 ?    2.2   0.0     0.089        76     351     384 ..     280     314 ..     254     318 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-T CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggi 47
                                        +iG G  G+  Al + + G kvl+i   +  +++++ +C ps   i
  gi|518652230|ref|YP_008141750.1|  5 AAIIGSGAGGYYSALRLLKHGKKVLIIekEKFGGECLNYGCIPSKALI 52
                                      579************************86667899*********8766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0077
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLith 30 
                                       +++iGgG  G+e   a  +lG +v ++ +
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGSEVYIVEM 190
                                       79**********************99844 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.089
                                       BBSSSBTEEE-CGGGTB-SHHHHHH..HHHHHHHHH CS
                              GIDA 351 etkkvkgLflAGqinGteGYeEaaa..qGllAGina 384
                                       +  +++++++ G+++G+   +++ a   G +A+ n+
  gi|518652230|ref|YP_008141750.1| 280 KRTNIPNIYAIGDVSGVP-MLAHKAfyDGYVAAENI 314
                                       55679************7.55555556888888886 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.6e-06    0.0082       2      33 ..       3      34 ..       2      64 .. 0.93
   2 ?    3.2   0.1     0.051        43       4      34 ..     162     192 ..     160     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.6e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                                       d +I+G+G  G  +al L ++G +v+++ek 
  gi|518652230|ref|YP_008141750.1|  3 FDAAIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      5789**************************97 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.051
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                        +I+G+G  G+  ++  ++ G +v +ve  +
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGSEVYIVEMKD 192
                                       57*************************9765 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 ?   -1.6   0.0       1.6   1.3e+03      32      60 ..       6      34 ..       4      43 .. 0.87
   2 !   17.6   0.1   2.2e-06    0.0018      26      77 ..     157     208 ..     148     254 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.6
                                      EEESTSHHHHHHHHHHHHTT-EEEEEESS CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglgakVtvlDvr 60
                                       +iG G  G  ++    + g kV +++++
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      699******99999999999999999876 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2.2e-06
                                       B---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE CS
                       AlaDh_PNT_C  26 vepakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev 77 
                                       + pak ++iGgG  G++   + ++lg +V++++++ + l ++e+ l ++ v+ 
  gi|518652230|ref|YP_008141750.1| 157 TIPAKLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPEIEEdLARE-VDK 208
                                       447************************************9999955554.554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.36     3e+02       4      33 ..       6      35 ..       4      49 .. 0.86
   2 !   17.3   0.3   3.2e-06    0.0027       2      59 ..     161     218 ..     160     263 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.36
                                      EEE--STTHHHHHHHHHHCTSEEEEE-S-H CS
                    UDPG_MGDP_dh_N  4 sviGlGYvGlvtaavlaeighevigvDide 33
                                      ++iG+G  G  +a+ l ++g++v+++ +++
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHGKKVLIIEKEK 35
                                      79**********************998876 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 3.2e-06
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHC CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkkav 59 
                                       k+++iG GY+G+ +++++ ++g ev +v + ++   +++++    +++ L++l  + +
  gi|518652230|ref|YP_008141750.1| 161 KLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPEIEEDLAREVDKRLRKLGVNIM 218
                                       789******************************9999999999999999988865554 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.013       1      35 [.       4      38 ..       4      46 .. 0.91
   2 ?    2.3   0.0     0.098        83       2      32 ..     162     192 ..     161     194 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlG 35
                                      D  ++G+g++G+  A+   ++G+kvl++e++++ G
  gi|518652230|ref|YP_008141750.1|  4 DAAIIGSGAGGYYSALRLLKHGKKVLIIEKEKFGG 38
                                      5689**************************98744 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.098
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveerg 32 
                                       +v++GGg  Gv    a  + G +v +ve ++
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGSEVYIVEMKD 192
                                       69*************************9876 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 ?    2.4   0.0      0.14   1.2e+02       2      31 ..       5      34 ..       4      40 .. 0.92
   2 !   14.2   0.1   3.6e-05      0.03       2      56 ..     162     216 ..     161     245 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.14
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S- CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdis 31
                                       a+iG+G  G   a  ++++g +V +++ +
  gi|518652230|ref|YP_008141750.1|  5 AAIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      69***********************99875 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 3.6e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                                       + +iG G +G ++ ++f + g eV +v++++++l + +e ++++++k  +k  ++
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDRILPEIEEDLAREVDKRLRKLGVN 216
                                       679*************************************999999887776555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0029       2.5      10      49 ..       5      53 ..       2     130 .. 0.80
   2 !    7.0   0.1    0.0093         8       8      45 ..     160     196 ..     153     253 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0029
                     NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev.........keeleelvk 49
                                        ++G G  ++  + +ll+ g+kv ++ +e          +  ++ l++
  gi|518652230|ref|YP_008141750.1|  5 AAIIGSGAGGYYSALRLLKHGKKVLIIEKEKfggeclnygCIPSKALIE 53
                                      679*************************996555544444333444444 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0093
                     NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvapev..keele 45 
                                        k +++GgG ++ +    + + g +v +v  +       +
  gi|518652230|ref|YP_008141750.1| 160 AKLVIIGGGYIGVEMGTAFRKLGSEVYIVEMKDriL---P 196
                                       6899************************88774332...2 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.016        14       2      30 ..       6      34 ..       5      36 .. 0.89
   2 !    9.3   0.1    0.0015       1.3       2      41 ..     163     202 ..     162     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.016
                                      EEES-SHHHHHHHHHHHHTTEEEEEEESS CS
                            TrkA_N  2 iiiGlGrvGrslaeeLseggkdvvvidkd 30
                                      +iiG G  G+  a +L ++gk+v++i+k+
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      79****************7768*****96 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0015
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTT CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreeg 41 
                                       +iiG G +G ++   +++ g+ +v++++ +++ + e++e+ 
  gi|518652230|ref|YP_008141750.1| 163 VIIGGGYIGVEMGTAFRKlGS-EVYIVEMKDRILPEIEEDL 202
                                       8*****************777.6*******99999988765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.044        37       1      32 [.       4      33 ..       4      57 .. 0.93
   2 ?    2.3   0.0     0.082        70       2      36 ..     162     194 ..     161     198 .. 0.90
   3 !    7.0   0.0    0.0031       2.6      87     140 ..     200     252 ..     192     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.044
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      D ++iG+G+ g   A rl   k g kv++ie 
  gi|518652230|ref|YP_008141750.1|  4 DAAIIGSGAGGYYSALRL--LKHGKKVLIIEK 33
                                      789***************..99999***9975 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.082
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                                       +v+iG+G  g+ +       k g +v ++e  + +
  gi|518652230|ref|YP_008141750.1| 162 LVIIGGGYIGVEMGTAF--RKLGSEVYIVEMKDRI 194
                                       79*************99..9*********987766 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0031
                     Lycopene_cycl  87 krlkeellerlvengvkllea.kvesveeeeageslvvleggrkirarlvvdarg 140
                                       ++l++e+ +rl + gv+ + + kv sv+++++    v +eg  +i+a +v+ + g
  gi|518652230|ref|YP_008141750.1| 200 EDLAREVDKRLRKLGVNIMTGmKVLSVKKDKN--YKVSIEGSDTIEADTVLMSVG 252
                                       6899********99997766449******999..9999*************9998 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00047       0.4       1      43 [.       6      42 ..       6      96 .. 0.77
   2 ?   -2.6   0.0       5.6   4.8e+03     125     154 ..     106     134 ..      78     135 .. 0.71
   3 ?   -2.9   0.5       7.1   6.1e+03       1      12 [.     163     174 ..     163     185 .. 0.83
   4 ?    4.1   0.0     0.048        41     105     154 ..     204     252 ..     199     254 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00047
                     NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwr 43
                                      ai+G G+ G + + rLl++       ++ +++++++g g + +
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHG-----KKVLIIEKEKFG-GECLN 42
                                      8******************5.....789999999999.66554 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.6
                     NAD_binding_9 125 vdleeradgqavlladgaslaadaVvLAlG 154
                                         +   +d+   ++ +g+ ++a+++++ +G
  gi|518652230|ref|YP_008141750.1| 106 YGVGSVKDRN-TVTVNGTDYTAKNIIINTG 134
                                       4555555554.4588999999999999888 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7.1
                     NAD_binding_9   1 aivGaGprGlav 12 
                                       +i+G+G  G+ +
  gi|518652230|ref|YP_008141750.1| 163 VIIGGGYIGVEM 174
                                       79****999866 PP

  == domain 4  score: 4.1 bits;  conditional E-value: 0.048
                     NAD_binding_9 105 eellarlpegvtvevhra.evvdleeradgqavlladgaslaadaVvLAlG 154
                                       +e+ +rl +++ v+++++ +v++++++ ++++v  ++ ++++ad V + +G
  gi|518652230|ref|YP_008141750.1| 204 REVDKRL-RKLGVNIMTGmKVLSVKKD-KNYKVSIEGSDTIEADTVLMSVG 252
                                       5555555.4567777766578888766.568999***************99 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.2     0.016        13       3      32 ..       6      32 ..       4      39 .. 0.89
   2 ?    8.4   0.2    0.0038       3.3       1      78 [.     161     235 ..     161     253 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.016
                                      EEETTSHHHHHHHHHHHHTTS-GGCEEEEE CS
                     F420_oxidored  3 giiGaGnmgealasgllaagaqpheivvan 32
                                      +iiG+G  g   a++ll++g   ++++++ 
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHG---KKVLIIE 32
                                      8*******************...9999883 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0038
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedvee 76 
                                       k+ iiG+G +g  +   + + g   +e++++ + +   + e++e+l ++v ++  +  ++  + + vl+vk  +  +
  gi|518652230|ref|YP_008141750.1| 161 KLVIIGGGYIGVEMGTAFRKLG---SEVYIV-EMKDRILPEIEEDLAREVDKRLRKLGVNiMTGMKVLSVKKDKNYK 233
                                       678*******************...****88.666666677777777666554444444445555555555555555 PP

                                       HH CS
                     F420_oxidored  77 vl 78 
                                       v 
  gi|518652230|ref|YP_008141750.1| 234 VS 235
                                       55 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.3   0.00037      0.32       2      30 ..       6      34 ..       5      38 .. 0.91
   2 ?    0.2   0.1      0.62   5.3e+02       2      28 ..     163     189 ..     162     201 .. 0.85
   3 ?   -1.4   0.0       1.9   1.7e+03     113     145 ..     208     242 ..     197     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00037
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SC CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrs 30
                                      ai+G+Ga G + a +L k+g +v +i ++
  gi|518652230|ref|YP_008141750.1|  6 AIIGSGAGGYYSALRLLKHGKKVLIIEKE 34
                                      7**********************998765 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.62
                                       EEES-SHHHHHHHHHHHHHTHCEEEE- CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlil 28 
                                       +i+G G iG  ++    k g +v+++ 
  gi|518652230|ref|YP_008141750.1| 163 VIIGGGYIGVEMGTAFRKLGSEVYIVE 189
                                       69*************999999999885 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.9
                                       TTSTT..SEEEEEEEE-EEEEEETTEEEECS--EE CS
                              ApbA 113 ealpk..prvlggvtthgatregpgevhhagkgei 145
                                       ++l+k   +++ g+  ++++++++ +v   g+++i
  gi|518652230|ref|YP_008141750.1| 208 KRLRKlgVNIMTGMKVLSVKKDKNYKVSIEGSDTI 242
                                       44433214899999999999999999999998877 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.8   6.8e+02       7      24 ..      18      35 ..      14      39 .. 0.86
   2 ?    7.6   0.0    0.0024         2     218     260 ..     208     251 ..     190     253 .. 0.82
   3 ?   -1.1   0.0         1   8.7e+02     411     452 .]     277     315 ..     275     315 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.8
                                      HHHHHHTTEEEEEEESSS CS
                     Amino_oxidase  7 ArqLlsaGfdVtvlEard 24
                                      A +Ll +G +V+++E + 
  gi|518652230|ref|YP_008141750.1| 18 ALRLLKHGKKVLIIEKEK 35
                                      999************865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0024
                                       H..TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S CS
                     Amino_oxidase 218 e..elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTv 260
                                       +  +++g++i ++ +V ++k+ +  ++v +e ++++eaD V++ v
  gi|518652230|ref|YP_008141750.1| 208 KrlRKLGVNIMTGMKVLSVKK-DKNYKVSIEGSDTIEADTVLMSV 251
                                       245569***************.555999999**********9976 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 1
                                       HHHHCHHCSTTEEE.SGGGCTTTTTSHHHHHHHHHHHHHHHH CS
                     Amino_oxidase 411 dplakpegdprlffAGehtsreypgtvegAilSGlraAaril 452
                                       d + ++ ++p+++  G+     +p   ++A+  G  aA+ il
  gi|518652230|ref|YP_008141750.1| 277 DSHKRT-NIPNIYAIGDVSG--VPMLAHKAFYDGYVAAENIL 315
                                       556677.99********955..*99*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.51
# Mc/sec: 2548.50
//
Query:       gi|518652231|ref|YP_008141751.1|  [L=219]
Description: lipoate-protein ligase B [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00011   22.1   0.0    0.00017   21.5   0.0    1.2  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 !   21.5   0.0   9.6e-09   0.00017      16      94 ..      54     132 ..      43     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.6e-09
                                       GCGGG--TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHH..HHHHHHHHHHHH......HHTT- CS
                     BPL_LplA_LipB  16 lnsselesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlely..vsllvlavlealgyrdskpgieg 90 
                                       ++s+  + +++ v+++ +gG++++h+ +g l++ ++++++  + ++ v +l+  + ++ +a+l+++gy  +  g++g
  gi|518652231|ref|YP_008141751.1|  54 RKSDPENYRNVNVIKTDRGGDVTYHG-EGQLITYFIFDVRI-NGKKEVRKLLenIEESYIAMLKTYGYNAMLYGEPG 128
                                       55666667899***************.88888888888897.7888999999**************86557778888 PP

                                       TTEE CS
                     BPL_LplA_LipB  91 ipvf 94 
                                       i++ 
  gi|518652231|ref|YP_008141751.1| 129 IWID 132
                                       8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1509.55
//
Query:       gi|518652232|ref|YP_008141752.1|  [L=177]
Description: hypothetical protein FACI_IFERC00001G0871 [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  146.5   0.0    8.7e-43  146.3   0.0    1.0  1  Cob_adeno_trans  Cobalamin adenosyltransferase
     0.0009   17.9   0.1     0.0012   17.5   0.1    1.1  1  DUF5357          Family of unknown function (DUF5357)
     0.0037   17.5   0.2      0.006   16.8   0.2    1.2  1  DUF3340          C-terminal domain of tail specific protease 
  ------ inclusion threshold ------
      0.033   14.7   0.1      0.048   14.2   0.1    1.4  1  DUF16            Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   0.0   1.9e-46   8.7e-43       2     161 ..       2     157 ..       1     160 [. 0.94

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 1.9e-46
                                       XXXXXXXXXXXXXXX.XXXTTHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHHHHT.-BTC CS
                   Cob_adeno_trans   2 yTrtGDkGtTslvggervsKddprveayGtvDelnsaiglarallaeeeeelkeaLeeiqneLfdlgaelatpekkk 78 
                                       +Tr+GD+G+T+ +   r+ Kd+p+v++ Gt+Delns+ig a+  +++++++++++L +iqn++f lg++l    +++
  gi|518652232|ref|YP_008141752.1|   2 FTRRGDQGETDNGLRVRIGKDSPMVDFQGTLDELNSFIGNAL--INTKWDDIRNDLIKIQNDVFVLGEDLT---AES 73 
                                       7************99*************************99..566789********************6...457 PP

                                       CG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHHHHHHHHHHHHHHHHHHHHHHHHHS..HHHHHHHHHHHH CS
                   Cob_adeno_trans  79 ekkkiteeeveelekeideleaelpplksfilpggspaaaalhvaRtvcRraERavvelaeee.veeevlkylNRLS 154
                                       ++++i+ee+v++le+++ e+++e+ ++k f++p gs++a +lh+aRtv+RraER  v +++e   ++ +l ylNRLS
  gi|518652232|ref|YP_008141752.1|  74 QHRTIKEEDVKWLEQRVTEYRKEIGKIKLFVIPDGSQEAVSLHIARTVARRAERLSVFVSKEMpLNKYILIYLNRLS 150
                                       78899*999**************************************************9977889*********** PP

                                       HHHHHHH CS
                   Cob_adeno_trans 155 DlLfvla 161
                                       ++Lf+ a
  gi|518652232|ref|YP_008141752.1| 151 SVLFMQA 157
                                       ****987 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.7e-07    0.0012     202     276 ..      32     108 ..      22     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.7e-07
                           DUF5357 202 LnklqplveeqlakkpWsevErwLleadkevkslgkqv.ldknlekveEkklWrvearvvnlks.gYkldllsiWkG 276
                                       L++l++ + + l + +W ++   L++++++v  lg+++  +++ ++++E+++  +e+rv++ ++   k++l  i +G
  gi|518652232|ref|YP_008141752.1|  32 LDELNSFIGNALINTKWDDIRNDLIKIQNDVFVLGEDLtAESQHRTIKEEDVKWLEQRVTEYRKeIGKIKLFVIPDG 108
                                       99***********************************977888999999999889****998774557777666666 PP

>> DUF3340  C-terminal domain of tail specific protease (DUF3340)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.2   1.3e-06     0.006      16      66 ..      47      97 ..      40     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.3e-06
                           DUF3340 16 pWDkIspanykkygkiaallpkLkkksekRiakdpeFklleediawlkerk 66
                                      +WD I+   +k  +++  l + L+++s+ R+ k+++ k+le+++ +++++ 
  gi|518652232|ref|YP_008141752.1| 47 KWDDIRNDLIKIQNDVFVLGEDLTAESQHRTIKEEDVKWLEQRVTEYRKEI 97
                                      7************9**9******************************9975 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.1e-05     0.048      30      81 ..      49     100 ..      18     131 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                                       ..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..... CS
                             DUF16  30 dsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkv 81 
                                       d+  ++L+ki++ v +lge + +  q+ + ++e +k l++++   ++e+ k+
  gi|518652232|ref|YP_008141752.1|  49 DDIRNDLIKIQNDVFVLGEDLTAESQHRTIKEEDVKWLEQRVTEYRKEIGKI 100
                                       56789***************************************99999833 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1305.57
//
Query:       gi|518652233|ref|YP_008141753.1|  [L=59]
Description: DNA-directed RNA polymerase subunit K [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-14   51.9   0.0    5.9e-14   51.7   0.0    1.1  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.7   0.0   3.3e-18   5.9e-14       4      49 .]       3      54 ..       1      54 [. 0.80

  Alignments for each domain:
  == domain 1  score: 51.7 bits;  conditional E-value: 3.3e-18
                                      TSS--HHHHHHHHHHHHHHH....HT.........SS-..SSSSTTCHHHHTT-S-- CS
                      RNA_pol_Rpb6  4 skvltrYelvriaakRArQieegesl.........etq..kpvviAlrEiaegkipi 49
                                      s  lt++e++ri+++RA+Qi     +           +  +p++iA+ E ++g ipi
  gi|518652233|ref|YP_008141753.1|  3 SMMLTKFEKARIIGARALQI----AMgapvildvsP-DmiDPIDIAIFEFDNGVIPI 54
                                      6779****************....555555544432.145***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.30s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 408.99
//
Query:       gi|518652234|ref|YP_008141754.1|  [L=51]
Description: hypothetical protein FACI_IFERC00001G0873 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 387.82
//
Query:       gi|518652235|ref|YP_008141755.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G0874 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3579  (0.199621); expected 358.6 (0.02)
Passed bias filter:                      808  (0.0450667); expected 358.6 (0.02)
Passed Vit filter:                       146  (0.00814323); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 442.66
//
Query:       gi|518652236|ref|YP_008141756.1|  [L=721]
Description: hypothetical protein FACI_IFERC00001G0875 [Ferroplasma acidarmanus fer1]
Scores for complete 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-148  493.9   0.0   3.6e-148  493.5   0.0    1.2  1  tRNA-synt_1g  tRNA synthetases class I (M)
    1.4e-19   69.8   0.5    1.1e-09   37.2   0.0    4.9  4  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    7.6e-15   54.8   0.0    1.6e-14   53.8   0.0    1.5  1  tRNA_bind     Putative tRNA binding domain
    1.2e-09   37.9   0.0     0.0014   18.0   0.0    2.3  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    2.7e-05   23.2   0.0    6.9e-05   21.9   0.0    1.6  2  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0018   18.2   0.1     0.0042   17.1   0.1    1.6  1  Anticodon_1   Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
      0.066   11.7   0.0       0.12   10.8   0.0    1.3  1  Orbi_NS1      Orbivirus non-structural protein NS1, or hydrop
       0.14   12.1   0.0       0.27   11.1   0.0    1.4  1  DUF4202       Domain of unknown function (DUF4202)
        5.6    6.5   6.6         18    4.9   1.3    2.2  2  zf-ribbon_3   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.5   0.0  1.8e-151  3.6e-148       1     390 [.      26     417 ..      26     418 .. 0.99

  Alignments for each domain:
  == domain 1  score: 493.5 bits;  conditional E-value: 1.8e-151
                                       EEEEE--B--SS---HHHHH.HHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
                      tRNA-synt_1g   1 vlvttalpYangklHlGhll.evisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeike 76 
                                       +lv++alpYang+lHlGh++  ++ aDif+R++r++g+evlf++g+De+Gtpi+++Aek+ v p+e+++k+h e+ +
  gi|518652236|ref|YP_008141756.1|  26 ILVNCALPYANGPLHLGHIAgAYLGADIFVRFNRMSGNEVLFISGSDEYGTPITISAEKNHVPPQEIADKYHIEQIN 102
                                       69*************************************************************************** PP

                                       HHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-EE........-TTS-EE- CS
                      tRNA-synt_1g  77 lfkklnisfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpdryvegtCPkckseeargdqce 153
                                        f++l+i fdk++rt++ eh + v e+f +l ekg++ ++ +   +c++ ++f+pdry+eg+CP+c+++eargdqc+
  gi|518652236|ref|YP_008141756.1| 103 SFNSLDIIFDKFTRTSDPEHVKDVDEFFINLLEKGYLVKRYMISPFCVEINKFMPDRYIEGECPYCGYKEARGDQCD 179
                                       ***************************************************************************** PP

                                       TTSSB-E................EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS CS
                      tRNA-synt_1g 154 ecgkkleptelinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrd 230
                                       +cg++l+p elinp+++++g++p++k t+h+f+kl+++++kl+e+i  +++ ++ nv k++++++ egL+++ai+rd
  gi|518652236|ref|YP_008141756.1| 180 NCGQTLDPIELINPVCKMTGNSPIFKVTDHFFLKLDSLQEKLSEFI-DSKTYWRPNVLKFTQNFIGEGLHPRAITRD 255
                                       **********************************************.66769************************* PP

                                       -SSS-EET..TECCEEE-HHHHHHHHHHHTTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHH CS
                      tRNA-synt_1g 231 ldwGipvP..gaekkvlYVWldAligYisatkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaill 305
                                       ldwG+++P  g e+k +YVW++AligYi+    +++++g++e wke+W  dk+++ ++figkd+i+FHti+wPa+ll
  gi|518652236|ref|YP_008141756.1| 256 LDWGVKIPlkGYENKKIYVWFEALIGYITGARVYSEETGKPEYWKEFW-MDKNIKSYYFIGKDNIPFHTIIWPAMLL 331
                                       ************************************************.88************************** PP

                                       H.TT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCC CS
                      tRNA-synt_1g 306 g.aelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLad 381
                                       +  +++lp +v a+eyl +eg+K+SkSrg++ +++e+l+ +d++ lRYy+a+  pe+ D+dfs+++f+ +vNseL+d
  gi|518652236|ref|YP_008141756.1| 332 AhGGFNLPYNVPANEYLRFEGEKFSKSRGIGFTVDEMLKFVDKNSLRYYMASVLPETGDSDFSMNEFQLKVNSELID 408
                                       *999************************************************************************* PP

                                       HHHHHHHHH CS
                      tRNA-synt_1g 382 klgnlvnRv 390
                                       k+gn+++Rv
  gi|518652236|ref|YP_008141756.1| 409 KYGNYIYRV 417
                                       ********7 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   5.3e-13   1.1e-09       5     169 ..       5     152 ..       2     164 .. 0.72
   2 !   20.4   0.0   6.3e-08   0.00012     356     439 ..     186     270 ..     179     310 .. 0.86
   3 ?    2.0   0.0     0.023        46     560     598 ..     351     390 ..     343     394 .. 0.87
   4 ?    1.5   0.0     0.035        69     321     356 ..     669     704 ..     645     720 .. 0.72

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 5.3e-13
                       tRNA-synt_1   5 kWeeedvfkkele.kekekkefilvdgPPyvtGslHiGhalaktl.kdivirykrmkGkevlyvpGwDhaGlaieak 79 
                                       kW +++  + ++  ++ e+++  +    Py++G lH+Gh+    l  di +r++rm+G+evl+  G D  G +i   
  gi|518652236|ref|YP_008141756.1|   5 KWIDNKNLNFSVYyTTMEREKILVNCALPYANGPLHLGHIAGAYLgADIFVRFNRMSGNEVLFISGSDEYGTPITIS 81 
                                       6666555444433044457888888899*************999967***************************999 PP

                       tRNA-synt_1  80 vekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgli 156
                                        ek+    +                 e++++y+ e+ ++++ l ++  fd+   T d+e  + v e f +l +kg +
  gi|518652236|ref|YP_008141756.1|  82 AEKNHVPPQ-----------------EIADKYHIEQINSFNSLDII--FDKFTRTSDPEHVKDVDEFFINLLEKGYL 139
                                       999853333.................45566666666666666554..44556666666666666666666666666 PP

                       tRNA-synt_1 157 yrgkklvnwstkl 169
                                        ++  + ++++++
  gi|518652236|ref|YP_008141756.1| 140 VKRYMISPFCVEI 152
                                       6666666666665 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 6.3e-08
                       tRNA-synt_1 356 ekiehsvpfcerskkpiiyrateqWfvrvkeladaalkave.kvqfvpkskekryaswleniqdWciSRqrwWGhri 431
                                       ++ie+  p+c+ +++  i+++t+  f ++++l++++ + ++ k+++ p+  + + + + e  +  +i R++ WG++i
  gi|518652236|ref|YP_008141756.1| 186 DPIELINPVCKMTGNSPIFKVTDHFFLKLDSLQEKLSEFIDsKTYWRPNVLKFTQNFIGEGLHPRAITRDLDWGVKI 262
                                       6778889*********************************99*******9888777777889999************ PP

                       tRNA-synt_1 432 plfvsket 439
                                       pl   +++
  gi|518652236|ref|YP_008141756.1| 263 PLKGYENK 270
                                       *9655554 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.023
                       tRNA-synt_1 560 eGrKmSKslgNvidpldvikkygadalRltli.lsdvgrd 598
                                       eG K SKs g     ++++k +  ++lR++++   + + d
  gi|518652236|ref|YP_008141756.1| 351 EGEKFSKSRGIGFTVDEMLKFVDKNSLRYYMAsVLPETGD 390
                                       8******************************955555555 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.035
                       tRNA-synt_1 321 gtlteeaaefeglkvfdarkkvveelkekglllkae 356
                                       g+ t + +ef++++   +++ ++++l+ek l +  +
  gi|518652236|ref|YP_008141756.1| 669 GEETLTFKEFQKMEFTVSDHHIIAKLQEKSLPVMLN 704
                                       33344459********************98755444 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   8.1e-18   1.6e-14       2      85 ..     571     650 ..     570     657 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 8.1e-18
                                       EEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECCE CS
                         tRNA_bind   2 rvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeeld 78 
                                       + ++++++e+hp+ad+L+ +k+  G+++  q vs +k++y++++l++k+v ++ n++ +++rGveS+++ils  +  
  gi|518652236|ref|YP_008141756.1| 571 QLATIVSVEDHPGADSLYSIKLH-GDKI-YQTVSDLKKYYTKDDLQGKQVLILTNIEKARIRGVESQCLILSIWN-- 643
                                       6799**************99985.7777.9******************************************995.. PP

                                       SSCEEEE CS
                         tRNA_bind  79 ekevgil 85 
                                       +++++++
  gi|518652236|ref|YP_008141756.1| 644 GNSKEVI 650
                                       5555544 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   7.1e-07    0.0014      13     121 ..      29     139 ..      18     153 .. 0.86
   2 !   17.4   0.0   1.1e-06    0.0022     244     283 ..     345     384 ..     334     399 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 7.1e-07
                                       EEEEEBTTS--BHHH.HHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1e  13 YvCGptvydashlGh.aRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdle 88 
                                        +  p +    hlGh a +++  Di+ r+ +++g +v f++   +    i   a++++   +e+a+k+  e  + ++
  gi|518652236|ref|YP_008141756.1|  29 NCALPYANGPLHLGHiAGAYLGADIFVRFNRMSGNEVLFISGSDEYGTPITISAEKNHVPPQEIADKYHIEQINSFN 105
                                       55556666779****667899******************************************************** PP

                                       HTT----SB-.-BGGGGHHHHHHHHHHHHHTTSE CS
                      tRNA-synt_1e  89 aLnvlkptle.prvsekvdeiielvekliekgya 121
                                       +L++   +++ +   e+v+++ e+  +l+ekgy 
  gi|518652236|ref|YP_008141756.1| 106 SLDIIFDKFTrTSDPEHVKDVDEFFINLLEKGYL 139
                                       ***9985543144568****************95 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.1e-06
                                       E--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
                      tRNA-synt_1e 244 nghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                                       n++l++egek sks +  +t+ ++lk +d + lR++++s+
  gi|518652236|ref|YP_008141756.1| 345 NEYLRFEGEKFSKSRGIGFTVDEMLKFVDKNSLRYYMASV 384
                                       689**********************************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 ?   -3.1   0.0       1.4   2.7e+03      34      71 ..      36      74 ..      16      76 .. 0.72
   2 !   21.9   0.0   3.5e-08   6.9e-05     266     316 ..     339     389 ..     303     436 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                      tRNA-synt_1f 34 SGliHiGnlr.evltadlvaralrkrgeevrlilisDdm 71
                                       G++H+G +    l ad+ +r  r  g+ev +i  sD++
  gi|518652236|ref|YP_008141756.1| 36 NGPLHLGHIAgAYLGADIFVRFNRMSGNEVLFISGSDEY 74
                                      6999***98735566667777777778889999999987 PP

  == domain 2  score: 21.9 bits;  conditional E-value: 3.5e-08
                      tRNA-synt_1f 266 PekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkka 316
                                       P++v+ +  l  +gek s+S+G ++t++++l+++ +++lr+++++  P++ 
  gi|518652236|ref|YP_008141756.1| 339 PYNVPANEYLRFEGEKFSKSRGIGFTVDEMLKFVDKNSLRYYMASVLPETG 389
                                       555554444445677******************************999863 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 !   17.1   0.1   2.1e-06    0.0042      40     104 ..     475     536 ..     439     561 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                       Anticodon_1  40 cdwylelvkprlysesaedk.raaqevllevletllrllaPfmPfitEelwqreeeelgkkesiml 104
                                       +++y+  + p+   +++++k ++  +v l++ + l+ +l+P +P  +E +wq    ++g +e + +
  gi|518652236|ref|YP_008141756.1| 475 ANNYFTESAPWKLIKEDTEKlNEKLYVSLKIGQYLTAMLYPYVPSASESIWQ----TFGVSENLEN 536
                                       589999999***9*99999966699**************************5....5555544444 PP

>> Orbi_NS1  Orbivirus non-structural protein NS1, or hydrophobic tubular protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   5.9e-05      0.12     360     424 ..     566     631 ..     548     647 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.9e-05
                          Orbi_NS1 360 eltgcspfkmvkieehvgndsvfktklvrdeqigrigd..hyyttncytgaealittaihihhwirg 424
                                       ++  +    +v +e+h g ds++  kl  d+    + d  +yyt +   g + li t i     irg
  gi|518652236|ref|YP_008141756.1| 566 DILDIQLATIVSVEDHPGADSLYSIKLHGDKIYQTVSDlkKYYTKDDLQGKQVLILTNIEK-ARIRG 631
                                       55556666799*******************99999998657****************9974.34555 PP

>> DUF4202  Domain of unknown function (DUF4202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00014      0.27     105     146 ..     413     455 ..     395     470 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                           DUF4202 105 eiervaalvrkeelk.rdeetqlLEDvacLvFLedqfeeFakk 146
                                        i rv+++++k++l+ +++et    D+  + FLed+f+e++ +
  gi|518652236|ref|YP_008141756.1| 413 YIYRVESFIKKNGLSpHEPETMDTKDMEMMKFLEDKFSEYSME 455
                                       5789**********9669*********************9866 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   1.3    0.0089        18      19      25 ..     165     171 ..     164     172 .. 0.86
   2 ?    3.8   0.3      0.02        40       4      13 ..     177     186 ..     174     187 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0089
                       zf-ribbon_3  19 CpyCGtk 25 
                                       CpyCG+k
  gi|518652236|ref|YP_008141756.1| 165 CPYCGYK 171
                                       9999986 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.02
                       zf-ribbon_3   4 rCPnCGa.pls 13 
                                       +C nCG+ + +
  gi|518652236|ref|YP_008141756.1| 177 QCDNCGQtL-D 186
                                       799999844.6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (721 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.54
# Mc/sec: 4023.09
//
Query:       gi|518652237|ref|YP_008141757.1|  [L=98]
Description: hypothetical protein FACI_IFERC00001G0876 [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   26.1   4.2    9.5e-06   25.8   4.2    1.0  1  HPP       HPP family


Domain annotation for each model (and alignments):
>> HPP  HPP family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   4.2   5.3e-10   9.5e-06      28     116 ..       2      85 ..       1      87 [. 0.78

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 5.3e-10
                               HPP  28 gGhlisalvGvaiaklfglsllwlaaalavalaialmllt..rtlhPPagAtaliavlgkeikelgwafllvpvllg 102
                                       ++ +is ++G+a  ++++ +   +   la++ +i++mll+  r++hPPa+ +a++++l+k+    ++ f+l  +++g
  gi|518652237|ref|YP_008141757.1|   2 VSYIISGAIGIA-GAFIE-PYIGIYYTLAIVETIIAMLLVeaRAMHPPAMGIAVVFILEKA----NV-FALLFLFSG 71 
                                       567899999998.44444.4556789999999999999863379****************8....34.444448999 PP

                               HPP 103 slllvlvalllnnl 116
                                       ++l++++  +ln++
  gi|518652237|ref|YP_008141757.1|  72 MVLIIIFDKFLNKF 85 
                                       99999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 759.15
//
Query:       gi|518652238|ref|YP_008141758.1|  [L=287]
Description: hypothetical protein FACI_IFERC00001G0877 [Ferroplasma acidarmanus fer1]
Scores for complete 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   18.7  10.9     0.0014   18.7  10.9    2.7  2  SpoIIM    Stage II sporulation protein M
  ------ inclusion threshold ------
       0.99   10.0   4.7         12    6.5   1.3    2.5  2  DUF1279   Protein of unknown function (DUF1279)


Domain annotation for each model (and alignments):
>> SpoIIM  Stage II sporulation protein M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.7  13.8         2   1.8e+04      17      54 ..     114     170 ..      10     179 .. 0.70
   2 !   18.7  10.9   1.5e-07    0.0014       4     115 ..     167     279 ..     161     285 .. 0.75

  Alignments for each domain:
  == domain 1  score: -6.7 bits;  conditional E-value: 2
                            SpoIIM  17 a...................snfaeqis....seskensalslflaifanNlrvalllfll 54 
                                       +                   +   ++++    + +k++++ slfl++f   +++   +f+ 
  gi|518652238|ref|YP_008141758.1| 114 SniinslfilknkkflqneyD---NKFNlmsiK-NKNENKKSLFLQYFYSSMIMYYSIFFI 170
                                       123333333345555543332...222244443.344445588888888877665555542 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.5e-07
                            SpoIIM   4 lflvgillgallaasnfa.eqisseskensalslflaifanNlrvalllfllGllllgiptilvl.linGfvlG..a 76 
                                       +f++ i++  ++  + +  ++ + +s +++ +++f +i++nN+++ ++ ++ G   + ++t +++ l+ + +    +
  gi|518652238|ref|YP_008141758.1| 167 IFFILIIIYTFVQPAAPLaSSGTVKSGSYNYWHFFSTILKNNITLDVFEYMIGG--FSLFTGTFIeLFSSNIYEaiI 241
                                       444444444444442222323336777888999************999999995..888888888888888888533 PP

                            SpoIIM  77 vaalvaefgglllflllilPhgilelpaiiiagaaglrl 115
                                       +++l  ++g    f+ +ilP+ + e   ++++ +++l +
  gi|518652238|ref|YP_008141758.1| 242 MSSLDITHG-SSSFVKYILPQFFPETLGYVFGLSIALVM 279
                                       366666655.9**********************999987 PP

>> DUF1279  Protein of unknown function (DUF1279)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1    0.0059        53      16      52 ..      53      91 ..      49     136 .. 0.77
   2 ?    6.5   1.3    0.0014        12       3      34 ..     149     179 ..     147     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0059
                           DUF1279 16 gvylsislidlgicYllvks..gvdveelleklklsvkv 52
                                      g y ++ l+ +++cY+ ++s  g  ++e + kl++ +k+
  gi|518652238|ref|YP_008141758.1| 53 GLYNLLILFLISFCYYSIESltGHGIAEDIFKLEIINKY 91
                                      567788888899999999998887788777777766555 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0014
                           DUF1279   3 lKelfkkYGkvalgvylsislidlgicYllvk 34 
                                        K lf +Y + ++ +y si++i l+i+Y +v+
  gi|518652238|ref|YP_008141758.1| 149 KKSLFLQYFYSSMIMYYSIFFI-LIIIYTFVQ 179
                                       599****************999.667788886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); 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):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1976.13
//
Query:       gi|518652239|ref|YP_008141759.1|  [L=453]
Description: hypothetical protein FACI_IFERC00001G0878 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-12   46.8   0.0    7.9e-12   45.3   0.0    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0026   17.8   0.0      0.016   15.2   0.0    2.1  2  DDE_Tnp_1_3  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   8.8e-16   7.9e-12      34     212 ..     184     384 ..     164     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 8.8e-16
                         DDE_Tnp_1  34 ygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleekgvdyiirlkknt 110
                                       + +++++ ++     +  ++++pg+v+d+++l+ + +e++  +g+l+++D+G+   +++ +++ +g+++i +lk ++
  gi|518652239|ref|YP_008141759.1| 184 PMIRIIMGFSRLRNEPCYIRLVPGSVADIDTLRKTEQEVH--TGTLFVMDRGFIDDNNFGKMDTNGLYFITPLKRDS 258
                                       555666666666667888999*************999999..*********************************** PP

                         DDE_Tnp_1 111 klyrk...................................gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvy 152
                                       kl +                                    +a ++++     +  +k+l+  +k+            
  gi|518652239|ref|YP_008141759.1| 259 KLPDYsingdnffmfrkrairyssttiknydihvfedimlRAMEENEYYSLVDSGKKPLYSPEKAGKI--------- 326
                                       **999988777777776555555555544444433333333444444444444444444444444444......... PP

                         DDE_Tnp_1 153 yvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                          ++++   +++ + ely+ R  iE++F   k+ ++ d  ++rg +  + +++  +++l
  gi|518652239|ref|YP_008141759.1| 327 --ALITNVREKPQSIFELYKFRNDIEESFDVFKNLLQVDTPYLRGDDTLKGYVFVSFISL 384
                                       ..666667779******************************************9999987 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.016      61     133 ..     202     278 ..     196     290 .. 0.79
   2 ?   -0.8   0.0      0.16   1.4e+03     105     148 ..     326     363 ..     316     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                       DDE_Tnp_1_3  61 vkltpgnvdDrepveelakel.lgklf.aDkgyiskklaeelleegielitklrknmkkkllsll..dkllLrkrsl 133
                                       ++l pg v D +++++  +e+ +g+lf  D+g+i ++ + ++ ++g+ +it l+++ k    s+   +  ++rkr++
  gi|518652239|ref|YP_008141759.1| 202 IRLVPGSVADIDTLRKTEQEVhTGTLFvMDRGFIDDNNFGKMDTNGLYFITPLKRDSKLPDYSINgdNFFMFRKRAI 278
                                       68999*********777777636888846**************************9986555443215567888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                       DDE_Tnp_1_3 105 ielitklrknmkkkllslldkllLrkrslietvndelknisqie 148
                                       i+lit++r++      s+++  l + r  ie  +d +kn+ q++
  gi|518652239|ref|YP_008141759.1| 326 IALITNVREK----PQSIFE--LYKFRNDIEESFDVFKNLLQVD 363
                                       5555555543....333333..5566788888999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 2934.22
//
Query:       gi|518652240|ref|YP_008141760.1|  [L=263]
Description: transposase mutator type [Ferroplasma acidarmanus fer1]
Scores for complete 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-58  196.4   0.0    8.3e-58  196.1   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
    1.5e-06   28.5   0.0    2.5e-06   27.8   0.0    1.4  1  MULE             MULE transposase domain
  ------ inclusion threshold ------
       0.14   12.2   0.4        7.2    6.8   0.0    2.5  2  HTH_7            Helix-turn-helix domain of resolvase


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.1   0.0   1.4e-61   8.3e-58      31     276 ..      17     259 ..       3     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 196.1 bits;  conditional E-value: 1.4e-61
                   Transposase_mut  31 ktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspallerykRrekaleav 106
                                         +l++ +++++++ +++e  +  ee+ + +nG+++r+l+T++g++ +l++PrdR+ +F+++++e y+R+   +e+ 
  gi|518652240|ref|YP_008141760.1|  17 DKILKQTIKEKIEKLMEIELNAYLEENPGIKNGKYKRDLKTKYGEIkQLNVPRDRDSNFHTQVIEPYNRSI-GMEDL 92 
                                       3455555666666666666666677888999*************9957*********************86.689** PP

                   Transposase_mut 107 vielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvReegrvvsk 183
                                       ++++y +G+str+++ ++e++ g +++Sks++S+it+ + e+v +f +R+L++  y ++flD+l   +R  g v  +
  gi|518652240|ref|YP_008141760.1|  93 IVSMYSNGISTRRIAGIMEDILG-NKYSKSTISRITDLTIEEVYKFINRPLDKR-YIAVFLDGLFFYLR-RGNVDKE 166
                                       ***********************.66***************************9.**************.788999* PP

                   Transposase_mut 184 avliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaavQrCrvHll 260
                                       +v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L +rGlk+  l+v+D+ k L + + + +p ++ Q C++H++
  gi|518652240|ref|YP_008141760.1| 167 PVIFALGIKETGEYEVLGFYLTVKESHNTYKDVLEDLYSRGLKEPLLIVADGIKNLDEEVMEIYPRSEFQLCTIHYA 243
                                       ***************************************************************************** PP

                   Transposase_mut 261 rnllakvpkkkadkva 276
                                       r l ++v  k+ ++++
  gi|518652240|ref|YP_008141760.1| 244 RGLKSNVREKDIEEIT 259
                                       ********99998876 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   4.1e-10   2.5e-06      15      94 ..     166     243 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 4.1e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ ++y+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518652240|ref|YP_008141760.1| 166 EPVIFALGIKETGEYEVLGFYLTVKESHNTYKDVLEDLYSRGL--KEPLLIVADGIKNLDEEVMEIYPRSEFQLCTI 240
                                       5777899*******************************99644..6******************************* PP

                              MULE  92 Hia 94 
                                       H a
  gi|518652240|ref|YP_008141760.1| 241 HYA 243
                                       *76 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0012       7.2       5      29 ..      86     108 ..      84     111 .. 0.84
   2 ?    3.1   0.1     0.017     1e+02      19      41 ..     115     137 ..     112     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
                                       SS-HHHHGGGGSSTTTT--STTTSS CS
                             HTH_7   5 klskndinrvvkLleeGisiskIAk 29 
                                       ++ ++  + +v ++++Gis + IA 
  gi|518652240|ref|YP_008141760.1|  86 SIGME--DLIVSMYSNGISTRRIAG 108
                                       56677..99************9996 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.017
                                       TTT--STTTSSSS---SSSS--S CS
                             HTH_7  19 eeGisiskIAkevnisRsTvYRy 41 
                                        +++s+s+I ++++++ + vY+ 
  gi|518652240|ref|YP_008141760.1| 115 GNKYSKSTISRITDLTIEEVYKF 137
                                       6789************9999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       816  (0.0455129); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1843.62
//
Query:       gi|518652241|ref|YP_008141761.1|  [L=110]
Description: hypothetical protein FACI_IFERC00001G0880 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       487  (0.0271627); 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:                         0  (0); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 811.01
//
Query:       gi|518652242|ref|YP_008141762.1|  [L=318]
Description: hypothetical protein FACI_IFERC00001G0881 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-45  154.8   0.0    3.2e-45  154.5   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.6e-42  145.0   0.3    4.7e-42  144.6   0.3    1.2  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    1.1e-14   54.3   1.2    3.6e-13   49.3   1.2    2.5  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    3.2e-13   49.3   0.1    4.5e-13   48.8   0.1    1.2  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.9e-12   46.9   0.0    4.5e-12   45.7   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
    9.8e-11   41.3   0.1    1.2e-05   24.6   0.0    2.5  2  NAD_binding_4    Male sterility protein
     0.0011   18.5   0.0       0.06   12.8   0.0    2.5  2  adh_short        short chain dehydrogenase
     0.0024   17.8   0.0     0.0054   16.7   0.0    1.6  1  NAD_binding_10   NAD(P)H-binding


Domain annotation for each model (and alignments):
>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.5   0.0   1.4e-48   3.2e-45       1     241 []       6     238 ..       6     238 .. 0.92

  Alignments for each domain:
  == domain 1  score: 154.5 bits;  conditional E-value: 1.4e-48
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihl 71 
                                       il+tG++GfiGs++v++ll  + +++ ld+l++   +  + +       ++++ dl+  +    + + +++d+vih+
  gi|518652242|ref|YP_008141762.1|   6 ILITGGAGFIGSNMVEKLLPDN-NITILDNLNNHVGNRFITQFmenknfHFINTDLLSFD----YGSLKGIDTVIHF 77 
                                       8******************865.999*****77766666555599998899999999766....55555******** PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHH CS
                         Epimerase  72 AavggvaassedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKla 148
                                       Aa ++v+  sedp++ +++n++ t n+le++rk++vk +lf+sSs+vYG+   +p+ e+   gp+ p s Y+a+K+ 
  gi|518652242|ref|YP_008141762.1|  78 AANSDVRYGSEDPTKDFKNNVVATENILEYMRKYDVKDILFASSSTVYGEASIMPTPENY--GPYMPISSYGASKMS 152
                                       *************************************************99998977777..9************** PP

                                       HHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHH CS
                         Epimerase 149 geklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillv 225
                                        e  ++ay + yg++  i+r  n++G++    + ++vi  +i+k+l++  e+ +lgdgt++  +++v+D+++ ++++
  gi|518652242|ref|YP_008141762.1| 153 NEGFITAYSHYYGFKGSIFRFANIVGKN----STHGVIYDFINKLLKNPGELEILGDGTQKKSYMHVKDCVDSMIYF 225
                                       ****************************....99*************9999************************** PP

                                       HHHHTT-STTEEEEES CS
                         Epimerase 226 lehvdagdkgeiyniG 241
                                       +e+     k +i+n+G
  gi|518652242|ref|YP_008141762.1| 226 HEK---SMKTDIINLG 238
                                       ***...5667899998 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 !  144.6   0.3   2.1e-45   4.7e-42       1     269 [.       7     259 ..       7     286 .. 0.89

  Alignments for each domain:
  == domain 1  score: 144.6 bits;  conditional E-value: 2.1e-45
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTG+aGfiGs+++e+Ll    ++++++++++++  + i + ++      ++n+++++ Dl   +      +   +d
  gi|518652242|ref|YP_008141762.1|   7 LITGGAGFIGSNMVEKLLPD-NNITILDNLNNHVGNRFITQFME------NKNFHFINTDLLSFD----YGSLKGID 72 
                                       9*****************98.66778999999887777777664......5699*******8744....3334456* PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TT.S-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEt.tpfyPrsPY 153
                                       +v+++AA s V++  e+P + +++nv++t ++Le +r++ ++    +++aS+s+vYG+++  p  E+  p+ P s Y
  gi|518652242|ref|YP_008141762.1|  73 TVIHFAANSDVRYGSEDPTKDFKNNVVATENILEYMRKYDVK---DILFASSSTVYGEASIMPTPENyGPYMPISSY 146
                                       ***************************************986...6889**************988868******** PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       +a+K++ + ++++y + yg+  ++ ++ n  +           i +++ + +++  e  +lG++ +k+++ hvkD v
  gi|518652242|ref|YP_008141762.1| 147 GASKMSNEGFITAYSHYYGFKGSIFRFANIVGKNS----THGVIYDFINKLLKNPGELEILGDGTQKKSYMHVKDCV 219
                                       ******************************99994....456799********9999999***************** PP

                                       HHHHHHHHCSS---.EEE-TT-EEECHHCHHCCHHCCCHH CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkped.yviatgethsvrefvelaflelgkt 269
                                       + m  + ++  + d +++++ et+sv+++++  ++++g +
  gi|518652242|ref|YP_008141762.1| 220 DSMIYFHEKSMKTDiINLGNRETTSVKTIADYVVKRMGLK 259
                                       ****99998666552679999*********9999999875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   1.2   1.6e-16   3.6e-13       1     262 [.       6     266 ..       6     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.6e-16
                                       EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T CS
                   Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk 77 
                                       +l+tG++G iGs++v+++l  +  +i +l++  +++ +    +++ +++k++++      +d+   +     l+  +
  gi|518652242|ref|YP_008141762.1|   6 ILITGGAGFIGSNMVEKLLPDN--NITILDNLNNHVGNRF--ITQFMENKNFHFI----NTDLLSFD--YGSLK--G 70 
                                       89****************9875..6888887766654422..2223444445333....22222222..23455..9 PP

                                       -SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGG.....S..........S--SHHH CS
                   Polysacc_synt_2  78 vdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKA.....v..........nPtnvmG 139
                                       +d+v+h AA   V    e p++ +k+Nv++ten++e   +++vk++++ S+        +           P++ +G
  gi|518652242|ref|YP_008141762.1|  71 IDTVIHFAANSDVRYGSEDPTKDFKNNVVATENILEYMRKYDVKDILFASSSTVygeasImptpenygpyMPISSYG 147
                                       9**********************************************9998654222222232222222258899** PP

                                       HHHHHHHHHHHHGGG--SSS--EEEEEEE-EETT..GTTSSHHHH.HHHHHTTSSEEE.S-TT-EEEEE-HHHHHHH CS
                   Polysacc_synt_2 140 atKrlaekllqalakeseekktkfvvvRfGNVlg..SrGSviplF.kkqikeggpvtv.TdpemtRyfmtieeavqL 212
                                       a+K+  e +++a++++      k ++ Rf N++g  S   vi  F +k +k+ g++ +  d +  + +m +++ v+ 
  gi|518652242|ref|YP_008141762.1| 148 ASKMSNEGFITAYSHYY---GFKGSIFRFANIVGknSTHGVIYDFiNKLLKNPGELEIlGDGTQKKSYMHVKDCVDS 221
                                       **************999...7788899******94444445555516667777***98357888999********** PP

                                       HHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EEE- CS
                   Polysacc_synt_2 213 vlqalalakggeifvldmGepvkivdlakalielsgleekkeedieikit 262
                                       +++  +++ + +i  l   e+++++ +a  +++ +gl++      + ++t
  gi|518652242|ref|YP_008141762.1| 222 MIYFHEKSMKTDIINLGNRETTSVKTIADYVVKRMGLKNV-----KYRFT 266
                                       *999999999999999999*************99997543.....44444 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1     2e-16   4.5e-13       1     223 [.       7     220 ..       7     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 2e-16
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD...lrespelleelskvnvkkviegDvtdkdkleealegvdvvihla 74 
                                       ++tGgaGF+G+++v++L+  ++   + +lD    + +++   ++ + ++ ++i++D+++ d     l+g+d vih a
  gi|518652242|ref|YP_008141762.1|   7 LITGGAGFIGSNMVEKLLPDNN---ITILDnlnNHVGNRFITQFMENKNFHFINTDLLSFDY--GSLKGIDTVIHFA 78 
                                       69*****************997...55555322666677767777666666********996..78*********** PP

                         3Beta_HSD  75 slvdvag.kltedeimkvnvkGTrnvleacvkagvrvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesK 150
                                       + +dv+       +  k nv  T+n+le  +k +v+ +++ Ss  v g+   + ++    E  + + ++ + y  sK
  gi|518652242|ref|YP_008141762.1|  79 ANSDVRYgSEDPTKDFKNNVVATENILEYMRKYDVKDILFASSSTVYGE---ASIMP-TPE-NYGPYMPISSYGASK 150
                                       *****8646666777899*****************************99...44444.444.456778899999999 PP

                         3Beta_HSD 151 alaEklvlkaNgrtlknggrlyTcaLRpagiyGegdk..llvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                                          E ++ +        g  +     R a i G  ++  ++  ++++l+k+  +l  +gd  ++++++ v   ++
  gi|518652242|ref|YP_008141762.1| 151 MSNEGFITAYSH---YYG--FKGSIFRFANIVGKNSThgVIYDFINKLLKNPGELEILGDGTQKKSYMHVKDCVD 220
                                       999999887665...233..5666778888888776622466778888888878888888777777777766555 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 !   45.7   0.0     2e-15   4.5e-12       2     234 ..       5     259 ..       4     266 .. 0.81

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 2e-15
                                       EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT................T--TTSHHHHHHHH.........HHH--S CS
                     RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre................eldltdaeavaell.........keakpd 53 
                                       +il+tG+ G +Gs+++++l  ++ +++ l++                 ++ +                   + +  d
  gi|518652242|ref|YP_008141762.1|   5 NILITGGAGFIGSNMVEKLLPDN-NITILDNLnnhvgnrfitqfmenkNFHFI--------NtdllsfdygSLKGID 72 
                                       69**************9999876.55555433356777776665555533333........1333444444666789 PP

                                       EEEE------HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-E.EEEEEEGGGS-S-TTS-.B-TTS----SSHHHHH CS
                     RmlD_sub_bind  54 vvvnaAAytavDkaEseeeaayavnaeavealAeaaaavgal.LihvStDyVFdGekkrp.YeeddetsPlnvYGrt 128
                                        v++ AA  +v    +++ ++++ n+ a+e++ e+ ++++++ +++ S+  V+  +  +p  e+  +  P++ YG++
  gi|518652242|ref|YP_008141762.1|  73 TVIHFAANSDVRYGSEDPTKDFKNNVVATENILEYMRKYDVKdILFASSSTVYGEASIMPtPENYGPYMPISSYGAS 149
                                       ****************************************9758899******9999999445567889******** PP

                                       HHHHHHHHHH....H-SSEEEEEE-SEESS.SSS-HH.HHHHHHHHH-SEEEEESS..-EE--EEHHHHHHHHHHHH CS
                     RmlD_sub_bind 129 KlaGEqavla....agkkalivRtswvyge.kgknfv.ktmlrlakereelkvvaD..qlgsPTsardlAevllqll 197
                                       K+  E  + a    +g k  i+R++ + g+ + +  +   + +l+k+  el++  D  q  s  +++d  + +++  
  gi|518652242|ref|YP_008141762.1| 150 KMSNEGFITAyshyYGFKGSIFRFANIVGKnSTHGVIyDFINKLLKNPGELEILGDgtQKKSYMHVKDCVDSMIYFH 226
                                       *********96555556899********99433444415666777**********96666777789*********** PP

                                       HHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHHCHT CS
                     RmlD_sub_bind 198 ekaaeekelagvyHlanegetswlefArailkeagad 234
                                       ek+++      +  l+n+++ts   +A+ ++k++g +
  gi|518652242|ref|YP_008141762.1| 227 EKSMK----TDIINLGNRETTSVKTIADYVVKRMGLK 259
                                       ****9....99*********************99875 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   8.5e-06     0.019       1      21 [.       8      28 ..       8      57 .. 0.85
   2 !   24.6   0.0   5.3e-09   1.2e-05      86     216 ..      69     187 ..      59     222 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.5e-06
                                      EE-TTSHHHHHHHHHHHHHS- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                      +TG+ GF+G+ ++ekLL +++
  gi|518652242|ref|YP_008141762.1|  8 ITGGAGFIGSNMVEKLLPDNN 28
                                      8****************8874 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5.3e-09
                                       HH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H...... CS
                     NAD_binding_4  86 eevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekee 159
                                       + +d +ih aA+ ++ +  ++    ++ Nv +t+++le  +k   +  +l+ S+++v+ge +  +            
  gi|518652242|ref|YP_008141762.1|  69 KGIDTVIHFAANSDVRYGSEDptkDFKNNVVATENILEYMRKYDVK-DILFASSSTVYGEAS--I------------ 130
                                       679*********9998855552225678***************999.9************99..3............ PP

                                       HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE-.-SSST--- CS
                     NAD_binding_4 160 kldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg.esktGwin 216
                                        + + e          Y  sK+  E  + ++++  g++ +i+R  +i+g +s+ G+i 
  gi|518652242|ref|YP_008141762.1| 131 -MPTPENYGPYMPISSYGASKMSNEGFITAYSHYYGFKGSIFRFANIVGkNSTHGVIY 187
                                       .67888888888899*********************************9777778764 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   2.7e-05      0.06       1      59 [.       4      61 ..       4      70 .. 0.89
   2 ?    3.2   0.1     0.024        54     142     167 ..     139     164 ..      94     173 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTT CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvt 59
                                      k +l+tG+++ IG +++++l+ ++  +++ + ++   ++ ++++ e+ +++++i++D+ 
  gi|518652242|ref|YP_008141762.1|  4 KNILITGGAGFIGSNMVEKLLPDNNITILDNLNNHVGNRFITQFMEN-KNFHFINTDLL 61
                                      789********************999999888888899999999985.89*****9985 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.024
                                       B-TTBHHHHHHHHHHHHHHHHHHHHH CS
                         adh_short 142 pvagvaaYsAsKaavagltrslakel 167
                                       p+   ++Y+AsK   +g++ + ++ +
  gi|518652242|ref|YP_008141762.1| 139 PYMPISSYGASKMSNEGFITAYSHYY 164
                                       5566799***********99887755 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   2.4e-06    0.0054       1     106 [.      10     129 ..      10     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.4e-06
                                       TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHC.....HHHHCTTTCEEEE--TT-CCHHHHHHTT-SEEEES---TC CS
                    NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpekl.....aeleaeeglevvegdvtdvedlaealkgadaVvsalgggg 72 
                                       G+ G +G+  v++ll ++  ++t+l    +++     +++ ++++ + +  d+++ +     lkg+d+V+  +++++
  gi|518652242|ref|YP_008141762.1|  10 GGAGFIGSNMVEKLLPDN--NITILDNLNNHVgnrfiTQFMENKNFHFINTDLLSFDY--GSLKGIDTVIHFAANSD 82 
                                       89999**********997..555553333333211125777899*********98886..88*****9987775555 PP

                                       C.......HHHH........HHHHHHHHHHCT--EEEEEEETTTTSGCG CS
                    NAD_binding_10  73 k.......deeg........aknivdaakeagvkRfvlvsaigvgdevp 106
                                               +           ++ni++ +++ +vk +++ s+  v+ e+ 
  gi|518652242|ref|YP_008141762.1|  83 VrygsedpT--KdfknnvvaTENILEYMRKYDVKDILFASSSTVYGEAS 129
                                       546554332..144667789************************97543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2157.95
//
Query:       gi|518652243|ref|YP_008141763.1|  [L=65]
Description: metal-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-14   54.1   0.1    1.5e-14   53.9   0.1    1.0  1  DUF1059   Protein of unknown function (DUF1059)


Domain annotation for each model (and alignments):
>> DUF1059  Protein of unknown function (DUF1059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.9   0.1   8.3e-19   1.5e-14       2      54 ..       3      55 ..       2      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.9 bits;  conditional E-value: 8.3e-19
                           DUF1059  2 kefkCgDvgpdCgfeitaeteeEvlrkvaeHakaaHglteippelvekiksaI 54
                                      + fkC+D+g +C+fe +ae+ e++ +++++H ++aH  ++i +e+++ki s I
  gi|518652243|ref|YP_008141763.1|  3 YYFKCKDLGWNCSFENHAEKREDIFPRIRIHFHYAHATNDIDEETMKKIESVI 55
                                      78***********************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); 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: 0.35u 0.29s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 461.26
//
Query:       gi|518652244|ref|YP_008141764.1|  [L=429]
Description: hypothetical protein FACI_IFERC00001G0883 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-45  155.1   0.0    3.6e-45  154.6   0.0    1.1  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.8e-10   40.8   0.4    2.5e-09   37.1   0.0    2.2  2  HGTP_anticodon  Anticodon binding domain
    4.8e-07   29.9   0.0    8.7e-07   29.1   0.0    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0     6e-49   3.6e-45       1     305 [.       8     316 ..       8     318 .. 0.84

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 6e-49
                                       T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH.HS-EEE-TTSSEEEE-SSSHHHHH CS
                     tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld.qtfklvDqsgrllglRaDiTpqva 76 
                                       g+rd +pe++e ++   +++++++e+ GY+l+  P+lE ld +  ++g +   qtf ++D+ gr + + ++ Tp+ +
  gi|518652244|ref|YP_008141764.1|   8 GFRDHYPEDMEVRNYFFKKITNAAENFGYQLIDFPSLEPLDLYRLKSGTEIVnQTFSFTDKGGREVTMIPEATPSTV 84 
                                       89****************************************99999999644************************ PP

                                       HHHHHHHHTSS-EEEEEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSE.EEEEE CS
                     tRNA-synt_His  77 RiaahrlnrerplRlcYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkel.rldlg 152
                                       R+ + r   +rp R++++ +v+r ++ ++gr re +Q+ a ++G ++ ead+E++ l+ ++l+  +g++++ ++ ++
  gi|518652244|ref|YP_008141764.1|  85 RLLTARKDLPRPVRWYSFPKVWRYEEPQEGRFREHYQFNADVFGLDSEEADAEIVGLASSILD-YLGLSGVyEININ 160
                                       **************************************************************7.***876537**** PP

                                       ETCHHHHHHHHTT--HHHHHHHHHHHHC...T-HHHHHHHHHCCTTHHHCCHCC....HCCHCCCHHHHCHCCHCTH CS
                     tRNA-synt_His 153 hvglvralleaaglsesleeallaalar...kdlaelkelaaeaglkealrellkal.elygdaevleealealaaa 225
                                       +  l++ +l+++++++    + ++++++    d +++ e  +  g+ e++++ + +l   + d   +e++ ++++++
  gi|518652244|ref|YP_008141764.1| 161 DRFLMEYVLKDLNIED--IPDAFSIIDKykkVDKSSFIEAFKGIGAGEDEIKKILSLlGEKVDIGNMEKKIKRVVNN 235
                                       ***********99876..44555555540004445555555555555555555544434444555555555555444 PP

                                       HHHHHHHHHHHHHHHHHHHHHH.H-TTEEE-TT--TTTTT--SEEEEEEE.TT-SS-SEEEEEECTTTGGG.T---E CS
                     tRNA-synt_His 226 palqaaldeleelaallealak.pevrvtlDlaelrgyeYytGlvFaaya.egvgqaiarGGrYdelgaaf.grarp 299
                                          ++++ ++e++ ++++ ++   e ++++D++ +rg++YytG+vF+a+  +g+ +ai++GGrYd+l++ f  ++ p
  gi|518652244|ref|YP_008141764.1| 236 --YEEIKPRIERIKKTFDLIGLyTESKINFDFSIVRGLSYYTGIVFEAFDvKGELRAILGGGRYDGLSQLFtQEKIP 310
                                       ..55888888888888888887789************************6477889***************9999** PP

                                       EEEEEE CS
                     tRNA-synt_His 300 AtGfsl 305
                                       A+Gf++
  gi|518652244|ref|YP_008141764.1| 311 AAGFAI 316
                                       ****97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.062   3.7e+02      19      54 ..     207     242 ..     201     245 .. 0.88
   2 !   37.1   0.0   4.2e-13   2.5e-09       3      91 ..     341     424 ..     339     426 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.062
                                       HHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-S CS
                    HGTP_anticodon  19 kklaeeLraagirvelddsnesigkkireadllgip 54 
                                       +++++ L+  g +v++ + +++i++ ++++++++ +
  gi|518652244|ref|YP_008141764.1| 207 DEIKKILSLLGEKVDIGNMEKKIKRVVNNYEEIKPR 242
                                       5789999999999***99********9999999866 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 4.2e-13
                                       EEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEE CS
                    HGTP_anticodon   3 vviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreq 79 
                                       ++ +l++   e  +y  k+a+ +r  +  +++d  +++i  +++ a   g+ fav++Ge+e+e++t+tv+++++ eq
  gi|518652244|ref|YP_008141764.1| 341 YICNLSS---ENDDYIIKVASVIRSLNKIAVVDMTHRKISSQMKSA--SGFDFAVIIGEREIEENTLTVKNMHSSEQ 412
                                       6788899...899**************7788888**********98..5**************************** PP

                                       EEEETTHHHHHH CS
                    HGTP_anticodon  80 ervsldelvekl 91 
                                        ++ +de+  kl
  gi|518652244|ref|YP_008141764.1| 413 STIGYDEFFLKL 424
                                       *******97666 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 !   29.1   0.0   1.5e-10   8.7e-07       1     109 [.      63     164 ..      63     384 .. 0.79

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1.5e-10
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGS..SEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrL..PlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeas 75 
                                       + + d+ +re +++P++++  v+l   +    k+L  P++ y +  ++R+E++ + G  R re  q ++ vf++++ 
  gi|518652244|ref|YP_008141764.1|  63 FSFTDKGGREVTMIPEATPSTVRLLTAR----KDLprPVRWYSFPKVWRYEEP-QEG--RFREHYQFNADVFGLDS- 131
                                       678999*******************977....3331189**************.***..***************88. PP

                                       HHHHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  76 lddslrdlikaisriferlglefraiielmsaks 109
                                        ++ +++++ ++s i+  lgl+    i++++++ 
  gi|518652244|ref|YP_008141764.1| 132 -EEADAEIVGLASSILDYLGLSGVYEININDRFL 164
                                       .8999****************9755555555443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.23s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2855.49
//
Query:       gi|518652245|ref|YP_008141765.1|  [L=77]
Description: transcription regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-13   49.3   0.2      4e-13   49.1   0.2    1.0  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
     0.0051   16.8   0.1     0.0058   16.7   0.1    1.1  1  NapD            NapD protein


Domain annotation for each model (and alignments):
>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.2   4.4e-17     4e-13       1      70 [.       6      72 ..       6      76 .. 0.97

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 4.4e-17
                                      EEEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEE CS
                    AsnC_trans_reg  1 vlvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartets 70
                                      vl+++ pg+    +e+ +++ +l++V+e++ + G++d+l+++ ++d+ ++ +++ + ++s+ gv +t+t+
  gi|518652245|ref|YP_008141765.1|  6 VLIRVIPGK---EHEVYDRVSKLKYVTEIHPLLGEFDILVRIDTEDMSEIGKLIIQDIRSISGVVDTKTL 72
                                      7899999**...********************************************************97 PP

>> NapD  NapD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   6.5e-07    0.0058       2      68 ..       2      70 ..       1      74 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.5e-07
                              NapD  2 hIsSlvVqarperlaavkaalaalpgv.EvhasdeegklVvviEaesedeladt.ieaiealpgVlsas 68
                                      +++ +++++ p++  +v +++ +l+ v E+h   +e  + v i++e+  e+ +  i++i+++ gV++++
  gi|518652245|ref|YP_008141765.1|  2 SVAFVLIRVIPGKEHEVYDRVSKLKYVtEIHPLLGEFDILVRIDTEDMSEIGKLiIQDIRSISGVVDTK 70
                                      677799******************9865************************962577*******9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 550.50
//
Query:       gi|518652246|ref|YP_008141766.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G0885 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.028   13.3  14.2      0.034   13.0  14.2    1.1  1  LptF_LptG  Lipopolysaccharide export system permease LptF/Lpt
       0.43    9.1   4.6       0.45    9.0   4.6    1.1  1  DUF5357    Family of unknown function (DUF5357)
       0.77    9.9   0.0       0.77    9.9   0.0    3.1  3  TPPK_C     Thiamine pyrophosphokinase C terminal
        2.8    7.8   8.8        3.6    7.5   8.8    1.2  1  DUF5090    Domain of unknown function (DUF5090)
        3.5    7.4  12.5         12    5.7  12.5    1.8  1  DUF2157    Predicted membrane protein (DUF2157)
        9.9    6.7   6.6         98    3.5   6.5    2.2  1  DUF4231    Protein of unknown function (DUF4231)


Domain annotation for each model (and alignments):
>> LptF_LptG  Lipopolysaccharide export system permease LptF/LptG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0  14.2   1.1e-05     0.034     278     352 ..      19      94 ..      14      96 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.1e-05
                         LptF_LptG 278 lplaclvfaliaaplglvkrrggrglrlliaillfvl.yyvllslgkalaengvlppilaawlpnilflllglfll 352
                                       l+l+ +vf ++ a +g  k r  +g  l+++il++++  +    ++k       l+p + ++++ ++ +++gl ++
  gi|518652246|ref|YP_008141766.1|  19 LALSLIVFGVLTAYFGSNKSRMVGGGLLVVGILIGIFvILGSGDIFKVSFITRILEPTIFYIIAAVIGVVIGLLVF 94 
                                       899**********************************8888999999999999*******************9877 PP

>> DUF5357  Family of unknown function (DUF5357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   4.6   0.00015      0.45      68     124 ..      35      88 ..       1      93 [. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00015
                           DUF5357  68 tddplrvpgtflpvgalitgflvsvfafgeeed..eitprtivlwptisavitaipefl 124
                                       +++  +v       g l+ g+l+++f++  + d  +++ +t +l pti  +i+a++ ++
  gi|518652246|ref|YP_008141766.1|  35 SNKSRMVG-----GGLLVVGILIGIFVILGSGDifKVSFITRILEPTIFYIIAAVIGVV 88 
                                       44444444.....356788999****9887777224667899************98765 PP

>> TPPK_C  Thiamine pyrophosphokinase C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   2.6     0.012        37      14      31 ..       8      25 ..       3      31 .. 0.85
   2 ?    9.9   0.0   0.00026      0.77      17      33 ..      44      60 ..      35      72 .. 0.81
   3 ?   -0.4   3.4      0.41   1.2e+03      16      33 ..      80      93 ..      76      98 .. 0.56

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.012
                            TPPK_C 14 gallllvlAaLvAvaval 31
                                      + + llvl aL+A+  ++
  gi|518652246|ref|YP_008141766.1|  8 WDVFLLVLLALLALSLIV 25
                                      5899*********98776 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00026
                            TPPK_C 17 lllvlAaLvAvavallv 33
                                       llv+++L++++v+l  
  gi|518652246|ref|YP_008141766.1| 44 GLLVVGILIGIFVILGS 60
                                      69************976 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.41
                            TPPK_C 16 llllvlAaLvAvavallv 33
                                      +    +Aa+++v++ llv
  gi|518652246|ref|YP_008141766.1| 80 I----IAAVIGVVIGLLV 93
                                      4....4555555555544 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   8.8    0.0012       3.6      52     135 ..       9      95 ..       7     101 .] 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0012
                           DUF5090  52 diikitlllkavllipiyllviaengnkldflksksriifltlik...ivlsilvdlvvyfselsslfkvflllkii 125
                                       d+++++ll    l++ ++ + +a++g++++ + ++  +++++li    i++s  +  v +++++ ++  + +++ +i
  gi|518652246|ref|YP_008141766.1|   9 DVFLLVLLALLALSLIVFGVLTAYFGSNKSRMVGGGLLVVGILIGifvILGSGDIFKVSFITRILEPTIFYIIAAVI 85 
                                       78888999888899999988899999996666666555555555555455555566678999999999999999999 PP

                           DUF5090 126 kllitlivll 135
                                        ++i l+v+l
  gi|518652246|ref|YP_008141766.1|  86 GVVIGLLVFL 95 
                                       9988888876 PP

>> DUF2157  Predicted membrane protein (DUF2157)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7  12.5     0.004        12      54     120 ..       4      67 ..       1      99 [. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.004
                           DUF2157  54 vAanWqglsrlvkfllllvllllslllgavlwrdrrvpprlgeallllaalllgaaialvgqifqls 120
                                       +++nW+ +  lv ++ll++ l+++ +l+a+++   ++++ +g +ll+++ l+    i   g+if++s
  gi|518652246|ref|YP_008141766.1|   4 FSWNWDVFL-LVLLALLALSLIVFGVLTAYFGS--NKSRMVGGGLLVVGILIGIFVILGSGDIFKVS 67 
                                       788999998.55555555555555555556666..7889999999999999999999999****998 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   6.5     0.033        98      19      37 ..      18      69 ..      13     101 .] 0.61

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.033
                           DUF4231 19 llrlitivlgallpilvs.................................s 37
                                      ll+l +iv+g+l++ + s                                  
  gi|518652246|ref|YP_008141766.1| 18 LLALSLIVFGVLTAYFGSnksrmvgggllvvgiligifvilgsgdifkvsfI 69
                                      6889999999999999997666666655555555555555666644444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1369  (0.0763567); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        27  (0.00150594); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 627.74
//
Query:       gi|518652247|ref|YP_008141767.1|  [L=345]
Description: Kef-type K+ transporter NAD-binding component [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.2e-12   44.9  14.4    3.9e-11   42.7  14.0    2.1  2  Ion_trans_2  Ion channel
    2.3e-10   40.7   2.5      4e-10   40.0   0.8    2.1  2  TrkA_N       TrkA-N domain
    1.4e-06   28.2   0.2    1.7e-06   27.9   0.2    1.3  1  Lig_chan     Ligand-gated ion channel
    0.00068   18.9   4.5     0.0015   17.8   4.5    1.5  1  Ion_trans    Ion transport protein


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.5     0.067     3e+02      53      76 ..      19      42 ..      13      45 .. 0.84
   2 !   42.7  14.0   8.8e-15   3.9e-11      12      78 ..      35     105 ..      23     106 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.067
                                      HHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2 53 lftivyillGlalfalflavlgkv 76
                                      +f +v+il+ ++l++ +l++++++
  gi|518652247|ref|YP_008141767.1| 19 VFKTVLILIMIVLVGSYLEYISQI 42
                                      667899**********99999876 PP

  == domain 2  score: 42.7 bits;  conditional E-value: 8.8e-15
                                       HHHHT..........T---HHHHHHHHHHHHTTS----SSTT-----HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  12 viysl......eegwekwsfldalYfsfvtltTiGYGdivpetdagrlftivyillGlalfalflavlgkvlt 78 
                                        + ++      +  ++  s   a++f+f t+tT+GYGd+vp++ +gr+++i+++l G++++++++a ++ ++t
  gi|518652247|ref|YP_008141767.1|  35 YLEYIsqintlG--SQIKSPQLAIWFVFQTVTTVGYGDVVPVNLTGRIIAIIIMLAGIGTVTTLTASTAAYMT 105
                                       333335765332..44457777*******************************************99998886 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1     0.097   4.4e+02      58     103 ..      88     134 ..      84     151 .. 0.67
   2 !   40.0   0.8   8.9e-14     4e-10       2     115 ..     123     246 ..     122     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.097
                                       TTGGGESEEEE-SSSHHHHHHHHHHHHHHTSS.SEEEEEESSGGGHH CS
                            TrkA_N  58 agiekadaviaatgddeanilavllakelnpk.kkiiaraqdpehae 103
                                       agi ++ ++ a t  + +n+ + + +k+++ k  +ii   +d ++  
  gi|518652247|ref|YP_008141767.1|  88 AGIGTVTTLTASTAAYMTNVKLKHKIKSIRMKnHTIICNYNDYSKNI 134
                                       77888888888888888888888888777766566777777666633 PP

  == domain 2  score: 40.0 bits;  conditional E-value: 8.9e-14
                                       EEES-SHHHHHHHHHHHHTT...EEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS.... CS
                            TrkA_N   2 iiiGlGrvGrslaeeLsegg...kdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg.... 71 
                                       ii+ +++  ++++ +  +++   ++ v+i +   + + ++ + + +  gd+tde++Leea++++a+ +i++ +    
  gi|518652247|ref|YP_008141767.1| 123 IICNYNDYSKNIILNYLNRKlkiDSLVLIANL--KENPVKSDYVFFTPGDPTDEKTLEEANASEAKRFIVTGDfssn 197
                                       56666666666554444444455335555553..44555566777888***********************989999 PP

                                       .....SHHHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHHHTTSEEEE CS
                            TrkA_N  72 .....ddeanilavllakelnpkkkiiaraqdpehaellkklgadvvis 115
                                             d+++il +  +++ln+ ++iia++ +++++ ++k++gad+vi+
  gi|518652247|ref|YP_008141767.1| 198 vppnlIDAKTILNIFQIRKLNKSAEIIAQVASSDNVTNAKSAGADEVIT 246
                                       9999999999*************************************96 PP

>> Lig_chan  Ligand-gated ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.2   3.8e-10   1.7e-06      13     110 ..      23     117 ..      17     253 .. 0.81

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 3.8e-10
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXHHHHHHHHHHHHHHHHHHH.HXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  13 ilvsivlflverfspyewrepeeaaetveneftlsnslwfslgalvqqG.cdesprsvsgRivvavWwffvlillss 88 
                                       +l+ i+++lv  + +y  + +    +  ++  +   ++wf++ +++  G +d  p +++gRi++++ +++ +  +++
  gi|518652247|ref|YP_008141767.1|  23 VLILIMIVLVGSYLEYISQIN----TLGSQIKSPQLAIWFVFQTVTTVGyGDVVPVNLTGRIIAIIIMLAGIGTVTT 95 
                                       555566666666666665555....2233455666789***********9*************************** PP

                                       XXXXXXXXXXXXXXXXS-SSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                          Lig_chan  89 YtAnLaafltvermqtpiksle 110
                                        tA+ aa++t  +++++iks+ 
  gi|518652247|ref|YP_008141767.1|  96 LTASTAAYMTNVKLKHKIKSIR 117
                                       *******************986 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   4.5   3.3e-07    0.0015     176     231 ..      49      98 ..       3     109 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.3e-07
                                       SSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Ion_trans 176 FdnfftallwlfrlmttegwgdilyatldekskvaliyfvifiilgsflllNllia 231
                                        ++   a++++f++ tt+g+gd+++++l ++      + +i+i+l+++ ++  l a
  gi|518652247|ref|YP_008141767.1|  49 IKSPQLAIWFVFQTVTTVGYGDVVPVNLTGR------IIAIIIMLAGIGTVTTLTA 98 
                                       4466679************************......**********998877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (345 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2293.17
//
Query:       gi|518652248|ref|YP_008141768.1|  [L=306]
Description: hypothetical protein FACI_IFERC00001G0887 [Ferroplasma acidarmanus fer1]
Scores for complete 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  117.3   0.0    4.8e-34  116.3   0.0    1.6  1  GMP_synt_C    GMP synthase C terminal domain
    0.00019   20.6   0.0        0.3   10.2   0.0    2.2  2  NAD_synthase  NAD synthase
    0.00057   19.4   0.0     0.0051   16.3   0.0    2.0  1  QueC          Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.074   12.8   0.0       0.12   12.1   0.0    1.4  1  ATP_bind_3    PP-loop family
      0.085   12.9   0.0       0.12   12.4   0.0    1.3  1  PAPS_reduct   Phosphoadenosine phosphosulfate reductase famil


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 !  116.3   0.0   1.3e-37   4.8e-34       9      92 .]     222     305 ..     214     305 .. 0.96

  Alignments for each domain:
  == domain 1  score: 116.3 bits;  conditional E-value: 1.3e-37
                                       GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----HHHHHHHHHHHHHHSTT---EEEE---T CS
                        GMP_synt_C   9 ykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpyevLekissrivnevkgvnrvvyditsk 85 
                                        +k wQ+f+vllpvk++Gv+gd+Rty++++a+R++++ D+mt ++++ ++e++++is  i++ev+++nrvvydit+k
  gi|518652248|ref|YP_008141768.1| 222 GEKPWQYFCVLLPVKTTGVHGDQRTYGETIAIRMIDTLDGMTGTFSRPDWELISDISVNITDEVPEINRVVYDITDK 298
                                       5788************************************************************************* PP

                                       TTS-S-- CS
                        GMP_synt_C  86 PpatiEw 92 
                                       PpatiEw
  gi|518652248|ref|YP_008141768.1| 299 PPATIEW 305
                                       ******* PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   8.4e-05       0.3      20      85 ..      21      83 ..       4     100 .. 0.80
   2 !    8.3   0.0    0.0003       1.1     148     171 ..     158     181 ..     151     219 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.4e-05
                                      EEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHH CS
                      NAD_synthase 20 gvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpiv 85
                                      + +l  SGG+DS+l + +a  +    n+  + + +     ++v   + l e++g+++k id k+i 
  gi|518652248|ref|YP_008141768.1| 21 KGILACSGGQDSTLLSLIAAPIK---NIEIIFVDTGLLRLNEVDRVKSLFEKFGVKYKLIDAKKIF 83
                                      447899*********99998764...66667777889999999999************99999886 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0003
                                       BETTTTS-HHHHHHHHHHTT--HH CS
                      NAD_synthase 148 lapiaellKtevkeLakelnvPer 171
                                       ++p+ +l+K ev+e +++++ P+ 
  gi|518652248|ref|YP_008141768.1| 158 IEPLRDLYKDEVREVSRYFGLPDV 181
                                       68*******************975 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.4e-06    0.0051       3      62 ..      23      80 ..      21     182 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                                      EEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G CS
                              QueC  3 vvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildld 62
                                      ++  SGG+DSt + ++a + +k++e++ +d g  + +e++ +k++++++gv + k +d +
  gi|518652248|ref|YP_008141768.1| 23 ILACSGGQDSTLLSLIA-APIKNIEIIFVDTGLLRLNEVDRVKSLFEKFGV-KYKLIDAK 80
                                      6789******9877776.567******************************.99999987 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.3e-05      0.12       3     153 ..      23     170 ..      21     178 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.3e-05
                                       EEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EEEEEE--H...HHCTTSTC CS
                        ATP_bind_3   3 lvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikleiekvdv...akkkgknl 76 
                                       ++A SgG DS++L l++a  k+     + +i vd gl     +e + vk+l +k+++k++  +++    ++ kg   
  gi|518652248|ref|YP_008141768.1|  23 ILACSGGQDSTLLSLIAAPIKN-----IEIIFVDTGLLR--LNEVDRVKSLFEKFGVKYKLIDAKKiflDNLKGVVD 92 
                                       79***********999999865.....888889988753..234444555555555555544444444444444444 PP

                                       CCHHHHH....HHHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-S-SEEEETTCCEE-CCCT--H CS
                        ATP_bind_3  77 eeaARel....RYevlkealkkegievlllAhhadDqaEtfllrlargsglaglagikeaseiasirlvRPlLkvsk 149
                                        e+ R++      +v+k+ +++ g+++ll +  a D +E    +    ++ +++ g+++     + +l+ Pl +++k
  gi|518652248|ref|YP_008141768.1|  93 PETKRKIigktFIDVFKKEAETFGATYLLQGTIAPDWIESGGASRDTIKSHHNVGGLPADL---GFELIEPLRDLYK 166
                                       4444443111146777777777778888888777777777776666666666666666655...5566666666666 PP

                                       HHHH CS
                        ATP_bind_3 150 eele 153
                                       +e++
  gi|518652248|ref|YP_008141768.1| 167 DEVR 170
                                       6655 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   3.4e-05      0.12       3      59 ..      23      78 ..      21     111 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.4e-05
                                      EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE CS
                       PAPS_reduct  3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvye 59
                                      ++++sgG ds+ ll L+    k+++++fvdtg    + ++ v+ l e++g++ k+ +
  gi|518652248|ref|YP_008141768.1| 23 ILACSGGQDST-LLSLIAAPIKNIEIIFVDTGLLRLNEVDRVKSLFEKFGVKYKLID 78
                                      6899*999997.788888899999********9999999999999999888755554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 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:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2210.57
//
Query:       gi|518652249|ref|YP_008141769.1|  [L=200]
Description: hypothetical protein FACI_IFERC00001G0888 [Ferroplasma acidarmanus fer1]
Scores for complete 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   91.9   1.0    1.3e-12   47.4   0.3    2.0  2  Ribosomal_S2  Ribosomal protein S2


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 !   43.5   0.0   1.1e-15   2.1e-11       3      95 ..      15     104 ..      14     114 .. 0.92
   2 !   47.4   0.3   7.4e-17   1.3e-12     150     213 ..     114     177 ..     108     179 .. 0.95

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 1.1e-15
                      Ribosomal_S2   3 eagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakr 78 
                                       ++g+h+G q +   ++m +yI++ rn g +i+d++kt +al +a k++ +   + ++il v+ ++ a + v++ ++ 
  gi|518652249|ref|YP_008141769.1|  15 KSGIHIGTQVK--SKDMDRYIFKIRNdGLYILDIKKTNHALIEAGKMLARY--QPEQILVVAQRQYAFKPVAKFSEI 87 
                                       589****8877..899********9868*******************9875..6789******************** PP

                      Ribosomal_S2  79 angyyvnerWlgGtLTN 95 
                                       +++  +  r+++GtLTN
  gi|518652249|ref|YP_008141769.1|  88 VGSSSIIGRFIPGTLTN 104
                                       ***************** PP

  == domain 2  score: 47.4 bits;  conditional E-value: 7.4e-17
                      Ribosomal_S2 150 dlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpaNddsirsiklilgvladaie 213
                                       ++++++dp  ++ a+kEa + gipvi+++D n  +d vd +Ip N++   s+ +i+ +l++ i 
  gi|518652249|ref|YP_008141769.1| 114 KVILITDPLADTQAMKEAIRIGIPVISLCDANNKTDFVDLIIPTNNKGRMSLAVIYWLLSREIL 177
                                       689********************************************************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1458.61
//
Query:       gi|518652250|ref|YP_008141770.1|  [L=288]
Description: tRNA splicing endonuclease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-16   60.7   2.9    7.3e-15   54.8   0.3    2.9  2  tRNA_int_endo    tRNA intron endonuclease, catalytic C-termin
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.034   13.8   0.0    1.7  1  tRNA_int_endo_N  tRNA intron endonuclease, N-terminal domain
      0.031   14.5   0.1       0.12   12.5   0.0    2.0  2  Atg8             Autophagy protein Atg8 ubiquitin like


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 !    4.8   0.2    0.0048        29       5      58 ..      73     120 ..      70     139 .. 0.69
   2 !   54.8   0.3   1.2e-18   7.3e-15       6      77 ..     205     272 ..     203     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0048
                                       HHHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHH CS
                     tRNA_int_endo   5 yavyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdl 58 
                                       y vy  L+ kG++v+ +   G +F     +p+ e   + V +++e++ +d+++l
  gi|518652250|ref|YP_008141770.1|  73 YFVYSILKGKGLIVKRD---GNKFFYK--KPGGE-YGIPVILIKEGDLIDFSSL 120
                                       789999999***99999...8898755..44444.4444445577777766655 PP

  == domain 2  score: 54.8 bits;  conditional E-value: 1.2e-18
                                       HHHHHHHHTT-EEEECGGGTSSEEEETSCTTTSSCSEEEEEEETTSEEEHHHHHHHHHHHHHTTSEEEEEEE CS
                     tRNA_int_endo   6 avyrdLrekGyvvrsGlkFGadFrvYqrrpslehseylVvvvsedeeldwpdlsaavrlahsvkKklilaiv 77 
                                       + yrdL ++ ++v+sG+k+G++Fr+Y +++ + h+e+lV +    +  +w+++s+a+rl++sv+Kk ++a  
  gi|518652250|ref|YP_008141770.1| 205 KLYRDLIKRHFIVKSGFKYGQNFRIY-SDSMENHAEFLVSL---MTSEKWYKISRAIRLSTSVRKKTLIAGF 272
                                       57************************.999**********9...555689*****************99975 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 ?   13.8   0.0   5.7e-06     0.034      22      53 ..      21      51 ..      10      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-06
                                      HHTTT-SEECCTSSEEEEHHHHHHHHHTTSEE CS
                   tRNA_int_endo_N 22 yekgfYGkplidepLqLslvEAlYLlekGkle 53
                                       +k + Gk +  + L+L++ E +YL  kGk+ 
  gi|518652250|ref|YP_008141770.1| 21 INKYHVGK-MRANVLELDPCECIYLYMKGKIM 51
                                      55556699.99*******************95 PP

>> Atg8  Autophagy protein Atg8 ubiquitin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05      0.12      54      98 ..      32      77 ..       4      83 .. 0.83
   2 ?   -1.5   0.0      0.48   2.9e+03      28      61 ..     205     239 ..     198     259 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                                      HHTT--TTS-EEEEETT.E-SSTTSBHHHHHHHH--TTSSEEEEEE CS
                              Atg8 54 krlqlepekalfllvne.tlpstsatmsalyeeekdedgflyvvys 98
                                        l+l+p + ++l+++   +p+  + + ++ ++   ed ++y vys
  gi|518652250|ref|YP_008141770.1| 32 NVLELDPCECIYLYMKGkIMPEPEMGLPQVISSVFSEDLYIYFVYS 77
                                      4589***********99789999**********************9 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.48
                                       S.S---S-SEEEEETTSBHHHHHHHHHHHTT--TT CS
                              Atg8  28 k.lpeldkkkylvPedltvgqlvliirkrlqlepe 61 
                                       k + +l k+ ++v + +  gq + i +  ++ ++e
  gi|518652250|ref|YP_008141770.1| 205 KlYRDLIKRHFIVKSGFKYGQNFRIYSDSMENHAE 239
                                       44567778888888888877777776666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2313.23
//
Query:       gi|518652251|ref|YP_008141771.1|  [L=165]
Description: GTP-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   32.1   0.6    1.5e-07   31.2   0.6    1.4  1  Ras       Ras family
    0.00015   21.9   0.3    0.00028   21.0   0.3    1.4  1  MMR_HSR1  50S ribosome-binding GTPase
    0.00047   20.4   0.4     0.0038   17.4   0.4    2.1  1  Roc       Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.017   15.1   0.2      0.025   14.6   0.2    1.3  1  AAA_14    AAA domain
      0.044   13.7   0.2      0.087   12.7   0.2    1.5  1  NTPase_1  NTPase
      0.047   13.1   0.1       0.16   11.4   0.1    1.8  1  Arf       ADP-ribosylation factor family


Domain annotation for each model (and alignments):
>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.6   4.9e-11   1.5e-07       1     144 [.       8     142 ..       8     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 4.9e-11
                                       EEEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHHHHHTTESEEEE CS
                               Ras   1 KlvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslrelyyrdaegill 77 
                                       K+ + G+++ GK+s++ r v ++ ++ +       + +++++ ++ ++ l  +       +++l+++++++++ +l 
  gi|518652251|ref|YP_008141771.1|   8 KVTVTGKKNSGKSSIVSRAVYNTATQISSRGFIRKKVNTNFMSEDYDIDLLFLE----MPYETLNDKFLSKSTFVLF 80 
                                       78999***************9987776666553444555555556666666664....58***************** PP

                                       EEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG-SS-HHHHHHHHHHHTSEEEEEBTT CS
                               Ras  78 vyditsresfenvkkwveeikrvaeenvpivLvGnKvDleekravsteegeelakelglkfletSAk 144
                                       v dit+ es++++ k+++e+      ++++ ++++K+D++   +  + e ++la+++g  ++  S +
  gi|518652251|ref|YP_008141771.1|  81 VVDITDMESLQDAGKFLSEFP-----DMEVFIIATKSDMRYASEFWEPEISKLADKYGSIYFIYSSH 142
                                       ****************99975.....47789***************************666666654 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   0.3   9.3e-08   0.00028       1     111 [.       8     108 ..       8     112 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 9.3e-08
                                       EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHC CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflalee 75 
                                       +v + G+ N+GKS+++++ + + + ++s++ +  +++n+  ++++   ++ ++ +p   e       l+++fl+  +
  gi|518652251|ref|YP_008141771.1|   8 KVTVTGKKNSGKSSIVSRAVYNtATQISSRGFIRKKVNTNFMSEDYdIDLLFLEMPY--E------TLNDKFLS--K 74 
                                       5899*************9998846699******999999988855556777788875..6......89999997..7 PP

                                       TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEE CS
                          MMR_HSR1  76 adlillvvdaseeklkpldeeleellee.akkplilv 111
                                       +  +l+vvd++ + ++ l ++  ++l+e  + +++++
  gi|518652251|ref|YP_008141771.1|  75 STFVLFVVDIT-D-MESL-QDAGKFLSEfPDMEVFII 108
                                       78*******88.3.4333.555555544333444544 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 !   17.4   0.4   1.3e-06    0.0038       1     119 [.       8     113 ..       8     114 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.3e-06
                                       EEEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH CS
                               Roc   1 KvvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplyl 77 
                                       Kv + G++++GK+s+++r v ++ ++      +  f++k+v +++ +++d    ++ l +     +  +++l++ +l
  gi|518652251|ref|YP_008141771.1|   8 KVTVTGKKNSGKSSIVSRAVYNTATQI----SSRGFIRKKV-NTNFMSEDY---DIDLLFL----EMPYETLNDKFL 72 
                                       8999****************9998644....3445777877.445444433...3444333....44688999**** PP

                                       CTSCEEEEEEEGHHHHCHHHHHHHHHHHCSSS-EEEEEE-TT CS
                               Roc  78 reaalailvydsrssenlkeWlkelkkvagkspvilvgnkiD 119
                                       +++  +++v+d ++ e+l++  k l ++ ++  v+++++k D
  gi|518652251|ref|YP_008141771.1|  73 SKSTFVLFVVDITDMESLQDAGKFL-SEFPDMEVFIIATKSD 113
                                       **********998888886644444.4456677888888888 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   8.5e-06     0.025       5     104 ..       9     116 ..       8     146 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.5e-06
                            AAA_14   5 lvitGaRrvGKTtllkqlikell..vkkesilyinldderdkkladpekllelilek.lke.......ekktylflD 71 
                                       +++tG + +GK+ ++ + +++    +  +s  +i  + +++ +++d+ +++ l+le+ +++       + + +lf  
  gi|518652251|ref|YP_008141771.1|   9 VTVTGKKNSGKSSIVSRAVYNTAtqI--SSRGFIRKKVNTNFMSEDY-DIDLLFLEMpYETlndkflsKSTFVLFVV 82 
                                       689***************99998443..3333333333333444444.34455555432224455664567779999 PP

                            AAA_14  72 Eiqevpewekalkslvdeg.knldvivtGSnskl 104
                                        i  ++++++a k l +    ++ +i+t S    
  gi|518652251|ref|YP_008141771.1|  83 DITDMESLQDAGKFLSEFPdMEVFIIATKSDMRY 116
                                       9999999999999999955245666666665554 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   2.9e-05     0.087       1      42 [.       8      48 ..       8     108 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.9e-05
                                      EEEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE---- CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevregg 42
                                      kv +TG+  +GK+ +v++++ +    +++ +Gf+ ++v  + 
  gi|518652251|ref|YP_008141771.1|  8 KVTVTGKKNSGKSSIVSRAVYNT-ATQISSRGFIRKKVNTNF 48
                                      589****************9999.567*******99998765 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   5.5e-05      0.16      16     131 ..       8     118 ..       2     130 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                                       EEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEETTEEEEEEEE-S...SGGGGGGGGGGCTTESEEEEEE CS
                               Arf  16 rilllGLDnaGKtTilkklkleelvttvPTigfnveeleiknlkftvwDvGG...qeklRplWknYfektdavifvv 89 
                                       ++ + G  n+GK+ i+ +   +  + ++   gf  ++++++ +  + +D+     +     l +++++k + v+fvv
  gi|518652251|ref|YP_008141771.1|   8 KVTVTGKKNSGKSSIVSRAVYNTAT-QISSRGFIRKKVNTN-FMSEDYDIDLlflEMPYETLNDKFLSKSTFVLFVV 82 
                                       6677788889999999887776654.455788888888764.3345555543111455667889999********** PP

                                       ETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS CS
                               Arf  90 DsadreRleeakeeLkalleeeelkevallvlaNKqDlpeal 131
                                       D +d e l++a + L++        ++ + ++a K D++ a 
  gi|518652251|ref|YP_008141771.1|  83 DITDMESLQDAGKFLSE------FPDMEVFIIATKSDMRYAS 118
                                       ***********998875......4566678888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.31s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 1096.30
//
Query:       gi|518652252|ref|YP_008141772.1|  [L=400]
Description: hypothetical protein FACI_IFERC00001G0891 [Ferroplasma acidarmanus fer1]
Scores for complete 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  142.0   0.0    3.3e-41  141.7   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    1.3e-09   37.4   0.0    3.1e-09   36.1   0.0    1.5  1  Aminotran_MocR   Alanine-glyoxylate amino-transferase
    9.7e-05   21.8   0.0     0.0002   20.8   0.0    1.5  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
      0.014   14.1   0.0       0.15   10.8   0.0    2.1  2  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
      0.036   13.3   0.0      0.054   12.8   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
      0.077   12.7   0.0       0.31   10.7   0.0    1.9  2  SKIP_SNW         SKIP/SNW domain


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7   0.0   1.1e-44   3.3e-41      35     363 .]      60     389 ..      42     389 .. 0.92

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 1.1e-44
                                       TSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHH CS
                     Aminotran_1_2  35 gtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilr 111
                                       +++ +yg + glpel+e+la +l+++e++++++e ++++++G+++++ al+ ++ +n gd ++  +pty  +   l 
  gi|518652252|ref|YP_008141772.1|  60 SSALQYGQTNGLPELKEQLAAYLKSDENINVDPE-NILLTTGSQQALYALPLIF-ANEGDYVITEAPTYVGMLSSLT 134
                                       57889*****************************.*******************.9********************* PP

                                       HTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEE.ESS-TTT--B--HHHHHHHHHHHHHTTEEEEEE CS
                     Aminotran_1_2 112 lsggevvryplyseedfhldlealeealkeapegnkktkvilv.esphNPtGtvatleeleklldlakkynlllfvD 187
                                       +sg+  +++++   +d ++  ++lee++k+ +++ + +k+i++  + +NP G  ++l+  + ll+la++yn+ ++ D
  gi|518652252|ref|YP_008141772.1| 135 ASGIRSQSVSM---DDNGMITDELEEKIKSMKSKGVMPKFIYTiPTFQNPAGYTMPLDRRKHLLELAQQYNIPVIED 208
                                       **********5...5889******************99999853899****************************** PP

                                       ETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS..SHHHHHHHHH CS
                     Aminotran_1_2 188 eaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpfls..ssllqaavaa 262
                                         Y+++ +  ++  +t+  +++ + +  +g++sK + ++G+R G+++++++v+   +kl++++    +sl q+++ +
  gi|518652252|ref|YP_008141772.1| 209 NPYGDLRYSGKKL-PTLKSLDTNDMVTYLGTFSKIM-APGLRTGFTVSQPEVLGEFNKLKQSLDLasDSLSQYIAYE 283
                                       ********98764.558888888889********99.5***********************9877868888888888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS..TEEEECCSCSSEEEEEETHH.CHHHHHHHHHHTCTEEEEEGG CS
                     Aminotran_1_2 263 alsdallkqseleemrqrlqkrrkelrdeLael..glkvlasqsgmflltdlsae.takelskkLleevgvyvtpgt 336
                                        +++   + +++ ++ + + ++r+ + ++L++   + ++  +++gmfl++ l++  +a ++ k  +++ +++ + g+
  gi|518652252|ref|YP_008141772.1| 284 YIRKGIIY-KQIPKTIELYRRKRDIMLEALDDEmsDATWSRPEGGMFLWVKLNKDmDALKMLKRAINN-KIAYVTGS 358
                                       88888866.6********************999********************9977777777799*9.77777779 PP

                                       GGTS....TTEEEEECTTS-HHHHHHHHHHH CS
                     Aminotran_1_2 337 sftv....pgrlRitvAglteeeleelveal 363
                                        f+      +  R+++   ++e+l+e v++l
  gi|518652252|ref|YP_008141772.1| 359 AFYHnnpeMNTMRLNFTYSSDEDLKEGVKRL 389
                                       99999*987789999999********99986 PP

>> Aminotran_MocR  Alanine-glyoxylate amino-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0     1e-12   3.1e-09      63     410 ..      63     394 ..      50     398 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 1e-12
                                       TSSS-TT--HHHHHHHHHHTTS-GGGEEE-SS-HHHHHHHHHHHHHHC--TT-SS-GGGG.--EEEEEES--HHHHH CS
                    Aminotran_MocR  63 rnyGGlaGlpelralfaelldvkaenvlvqnnsslelqglvltlallhGvrdsegpwvkeekvkllvtvpGydrhfl 139
                                         yG  +Glpel+  +a +l+   en+ v  +  l   g   +l  l  +   eg +v       +  +p y   + 
  gi|518652252|ref|YP_008141772.1|  63 LQYGQTNGLPELKEQLAAYLKS-DENINVDPENILLTTGSQQALYALPLIFANEGDYV-------ITEAPTYVGMLS 131
                                       5799999999999999999984.57777776666666666555555566666666665.......558999*99*** PP

                                       HHHHHT-EEEEEEEETTEE-HHHHHH....HHHC-TTEEEEEE-SSS-TTT-----HHHHHHHHT---SSTT-EEEE CS
                    Aminotran_MocR 140 lleelGielltvdlqddGpdvdavek....lvaedasvkGilavpkysnptGetiseevarrlaalkaaapdfrifa 212
                                        l   Gi+  +v ++d+G   d +e+    + ++    k i+++p++ np+G t+  ++ ++l  l     +  +  
  gi|518652252|ref|YP_008141772.1| 132 SLTASGIRSQSVSMDDNGMITDELEEkiksMKSKGVMPKFIYTIPTFQNPAGYTMPLDRRKHLLELAQ-QYNIPVIE 207
                                       ******************98887766111144555566999******************999999854.56788999 PP

                                       E-TTSS-BS.SSSS----HHHHHHHHT-TTSEEEEEESTTTS-TTSS-EEEEE-HHHHHHHHHHHHHC-S---HHHH CS
                    Aminotran_MocR 213 ddayavhdlvaeedkdanivalardaGhpdrafvlastskitfaGaGvafvassedniawlkkylGlqsiGpdkveq 289
                                       d+ y   dl   ++k + +    ++    d    l + ski   G   +f  s ++ ++ ++k      +  d + q
  gi|518652252|ref|YP_008141772.1| 208 DNPYG--DLRYSGKKLPTL----KSLDTNDMVTYLGTFSKIMAPGLRTGFTVSQPEVLGEFNKLKQSLDLASDSLSQ 278
                                       99996..665567776655....55566788899999****************************9999*******9 PP

                                       HHHHHHHHHSTH.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTSSEEE---SBSS-EEEEES.SS-HHHHHHHHHHC CS
                    Aminotran_MocR 290 lrhvkflkdyeG.lealmrdhaeliapkfeavlevleaelggaevatwteprGGyfisldtl.dgvakrvvklaeea 364
                                            +++  +G +  ++ +  el + k + +le+l++e++    atw+ p+GG f+ +    d  a +++k a + 
  gi|518652252|ref|YP_008141772.1| 279 YIAYEYIR--KGiIYKQIPKTIELYRRKRDIMLEALDDEMSD---ATWSRPEGGMFLWVKLNkDMDALKMLKRAINN 350
                                       88777765..451567889999****************9975...8**********988865166789999999999 PP

                                       TEE---TTTTSSTT--SSS-EEEE--SSS-HHHHHHHHHHHHHHHH CS
                    Aminotran_MocR 365 GvsltaaGatypaGedpkdrnirlaptlppleevetamdvvatcvk 410
                                        ++  +  a y   ++p+ + +rl  t  + e++++ ++ +a  +k
  gi|518652252|ref|YP_008141772.1| 351 KIAYVTGSAFYH--NNPEMNTMRLNFTYSSDEDLKEGVKRLAKTIK 394
                                       999988777764..789999***************99999988776 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   6.9e-08    0.0002      27     146 ..      73     210 ..      50     229 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.9e-08
                                       HHHHHHHHHHT-SEEEEE.......SSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTT CS
                   DegT_DnrJ_EryC1  27 eFEkafaaylgvkhaiav.......ssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdt 96 
                                       e+ +++aayl+++  i v       ++G++  + aL  + +++gd+VI+ + t+v+  ++ + +g + + v +d d 
  gi|518652252|ref|YP_008141772.1|  73 ELKEQLAAYLKSDENINVdpenillTTGSQQALYALPLIFANEGDYVITEAPTYVGMLSSLTASGIRSQSVSMD-DN 148
                                       56667777777666555433332338899999999999999*********************************.45 PP

                                       SSB-GGGCGGG--TTE......EEEEEB-GGGB--..-H..H...HHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1  97 ynidpaaieaaitert......kaIlpVhlyGqva..dm..d...alkaiaakhglkvieDaA 146
                                        +i+ +++e++i +        k I ++ ++ ++a   m  d   +l ++a++++++vieD  
  gi|518652252|ref|YP_008141772.1| 149 GMIT-DELEEKIKSMKskgvmpKFIYTIPTFQNPAgyTMplDrrkHLLELAQQYNIPVIEDNP 210
                                       5554.56788887765555566666666655555533342244447999************65 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 ?   10.8   0.0   4.9e-05      0.15     165     203 ..     136     173 ..     123     208 .. 0.89
   2 ?    0.9   0.0     0.051   1.5e+02      20      83 ..     233     303 ..     216     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.9e-05
                                       HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEE CS
                     Pyridoxal_deC 165 lgvklrvipldengklrgaalekaieedkekGlipffvv 203
                                        g++ +++ +d+ng +++++le++i++ k kG +p f+ 
  gi|518652252|ref|YP_008141772.1| 136 SGIRSQSVSMDDNG-MITDELEEKIKSMKSKGVMPKFIY 173
                                       5778899*****99.*******************97764 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.051
                                       HHHHHHHHHCTGGGS--T...TSTTBHCSSH....HHHHHHHHHHHHHT-BTSS....TTTSHHHHHHHHH CS
                     Pyridoxal_deC  20 eqilediekilapgvttw...hspefhkllpagnslisllgdlLadainkngft....weesPaltelevv 83 
                                        + l+   ki+apg++t+   ++pe+   ++ +++   l++d L++ i+  ++     +++ P ++el  +
  gi|518652252|ref|YP_008141772.1| 233 VTYLGTFSKIMAPGLRTGftvSQPEVLGEFNKLKQSLDLASDSLSQYIAYEYIRkgiiYKQIPKTIELYRR 303
                                       45567778888888887544367999999999999999********9997765422227788888888655 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.8e-05     0.054      94     167 ..     136     208 ..      65     209 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.8e-05
                                       C--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEE CS
                   Beta_elim_lyase  94 agvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlD 167
                                       +g++ + +  ++ + m  ++le++ik  ++    +k+i++  T +  +G  ++l+  + + ++a++y+ip++ D
  gi|518652252|ref|YP_008141772.1| 136 SGIRSQSVSMDD-NGMITDELEEKIKSMKSKGVMPKFIYTIPTFQNPAGYTMPLDRRKHLLELAQQYNIPVIED 208
                                       566666666666.77899********98888899************************************9877 PP

>> SKIP_SNW  SKIP/SNW domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0    0.0001      0.31      76      93 ..     175     192 ..     168     209 .. 0.84
   2 ?   -2.0   0.0      0.81   2.4e+03     104     125 ..     257     278 ..     249     287 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0001
                          SKIP_SNW  76 iSnwkNpkGytipLdkRl 93 
                                       i  ++Np Gyt+pLd+R 
  gi|518652252|ref|YP_008141772.1| 175 IPTFQNPAGYTMPLDRRK 192
                                       7889************95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.81
                          SKIP_SNW 104 eindkFaklseaLeeAerkare 125
                                       e+  +F+kl ++L+ A  +  +
  gi|518652252|ref|YP_008141772.1| 257 EVLGEFNKLKQSLDLASDSLSQ 278
                                       667789********99887666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2720.96
//
Query:       gi|518652253|ref|YP_008141773.1|  [L=324]
Description: phosphopantetheine adenylyltransferase/unknown protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.5   0.0    9.2e-31  106.8   0.0    1.3  1  NTPase_I-T       Protein of unknown function DUF84
    4.8e-13   49.5   0.0    7.3e-13   48.9   0.0    1.3  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
       0.18   12.0   1.4         63    3.8   0.0    3.5  4  TPM_phosphatase  TPM domain
       0.27   11.3   1.3       0.49   10.5   1.3    1.4  1  OCRE             OCRE domain


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 !  106.8   0.0   2.1e-34   9.2e-31       2     162 ..     155     313 ..     154     314 .. 0.96

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 2.1e-34
                                       ---HHHHHHHHHHHHHHCTTEEEEEEE---SS-SS-BSHHHHHHHHHHHHHHHHHHSTTSSEEEEEEEEEET..... CS
                        NTPase_I-T   2 SkNpvKveAvkeafeklfkdvevegvsvpsgvsdqPmgdeetlkGAinRaknaleaaeeadygvGlEgGveeleek. 77 
                                       + N+ K+eA+++ +++++k++++++     + s+qP+g ++t++ A+ Ra + l++    dy +G+E+G++    + 
  gi|518652253|ref|YP_008141773.1| 155 TGNELKLEATEKFIKTIMKNYRITRNTEYATGSEQPFG-SDTIRFATDRAMYGLKD---NDYSIGIESGIFYNPVNn 227
                                       78**********************99999999******.****************9...79*********8877667 PP

                                       .TEEEEEE.EEEESS-EEEEE---EE--HHHHHHHCTT--HHHHHHHHHTHCCHHHTTHHHHHHTTTSS-HHHHHHH CS
                        NTPase_I-T  78 .lldvawaavvdkegrvsvgrsasfelPeevveevkegeelgevmdelfgtenikqkeGaigllTkglvtRedlyeq 153
                                        ++d+++++v+d+ + +++g++++f++P++v++++k+g   +e ++  +g ++i++  G+ gl++++ vtR++l+ +
  gi|518652253|ref|YP_008141773.1| 228 mYYDLHYCVVIDRYSVITTGFGSGFQMPDQVIDAIKNGTSTNEFVETEYGIKKIGHGIGISGLISEDSVTRATLVYE 304
                                       7**************************************************************************** PP

                                       HHHHHTHHH CS
                        NTPase_I-T 154 avilAlipf 162
                                       +v  A+ip+
  gi|518652253|ref|YP_008141773.1| 305 SVRNAFIPR 313
                                       *******97 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.0   1.6e-16   7.3e-13       1     142 [.       4     136 ..       4     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 1.6e-16
                                       EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEEEESEHHHH CS
                   CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvdpweltrev 76 
                                       l+gGtF+ +H+GH +ll  a + ++  +++gv+sde ++k k  ++s++ R + +e++ ++  + +++ p ++   +
  gi|518652253|ref|YP_008141773.1|   4 LVGGTFNRFHKGHEQLLLAAYNTGNR-VMIGVTSDEYARKHKNIVISYKRRKARVEKFmQKFTDNYEIHPLDSM--F 77 
                                       689***********************.**************9****************7444444666666666..7 PP

                                       HHHTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  77 lkklkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                        + l++++ +lv++ ++++ + + +e +  +g+++l +v++p       +   ++  +iSst+i++
  gi|518652253|ref|YP_008141773.1|  78 GNTLDVKDAILVVSPETHAGAIRINEQRLSMGKNPLHIVKIP-------FTLGEDLFPISSTRIIK 136
                                       888888889******************************999.......***************97 PP

>> TPM_phosphatase  TPM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.72   3.2e+03      69      80 ..      47      58 ..      19     101 .. 0.63
   2 ?    3.8   0.0     0.014        63      77     114 ..     151     186 ..     139     191 .. 0.78
   3 ?    1.3   0.0     0.082   3.7e+02      98     119 ..     199     220 ..     192     221 .. 0.81
   4 ?    3.0   0.0     0.024   1.1e+02      69     111 ..     237     276 ..     231     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.72
                                      EEETTTTEEEEE CS
                   TPM_phosphatase 69 liavddrkvrie 80
                                      +i+ + rk r+e
  gi|518652253|ref|YP_008141773.1| 47 VISYKRRKARVE 58
                                      333344444444 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.014
                                       EEEEE-STTTTT--HHHHHHHHHHTHHHHHHHT-HHHH CS
                   TPM_phosphatase  77 vrietgyglegaltdaraesildetilpalkdgdyagg 114
                                       ++i+tg++l+   t+++++ i+++  +   ++ +ya+g
  gi|518652253|ref|YP_008141773.1| 151 IAISTGNELKLEATEKFIKTIMKN--YRITRNTEYATG 186
                                       899*******************99..444555577776 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.082
                                       HHHTHHHHHHHT-HHHHHHHHH CS
                   TPM_phosphatase  98 ldetilpalkdgdyaggilaav 119
                                        ++   + lkd+dy+ gi++++
  gi|518652253|ref|YP_008141773.1| 199 ATDRAMYGLKDNDYSIGIESGI 220
                                       55668899**********9886 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.024
                                       EEETTTTEEEEEE-STTTTT--HHHHHHHHHHTHHHHHHHT-H CS
                   TPM_phosphatase  69 liavddrkvrietgyglegaltdaraesildetilpalkdgdy 111
                                       +i   dr   i+tg g    ++d+ ++ i + t ++++ + +y
  gi|518652253|ref|YP_008141773.1| 237 VI---DRYSVITTGFGSGFQMPDQVIDAIKNGTSTNEFVETEY 276
                                       44...888999999999999***********999999988877 PP

>> OCRE  OCRE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   1.3   0.00011      0.49      10      25 ..     217     232 ..     210     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00011
                              OCRE  10 esGyYyDpetGyYYDp 25 
                                       esG +y+p  ++YYD 
  gi|518652253|ref|YP_008141773.1| 217 ESGIFYNPVNNMYYDL 232
                                       79************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.53
# Mc/sec: 1848.99
//
Query:       gi|518652254|ref|YP_008141774.1|  [L=296]
Description: PAGO protein related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-38  132.1  43.1      4e-22   78.9  19.8    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 !   78.9  19.8   2.2e-26     4e-22       4     136 ..       7     137 ..       4     138 .. 0.96
   2 !   59.6  15.3     2e-20   3.5e-16       2     135 ..     147     282 ..     146     284 .. 0.92

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 2.2e-26
                              EamA   4 illallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafl 80 
                                       ill+ + +++w+i+++++ki+l+++ p+tl+f+r+l+++i+  ii  +k + +  +++ ++  l++l+ll++++ + 
  gi|518652254|ref|YP_008141774.1|   7 ILLFAIMVISWSINYPVIKIALNYTGPFTLLFYRILFSFIFIYIIFRPKLHLR--ITKDEIVPLFILSLLNVLIWME 81 
                                       6788999999******************************9998888888888..********************** PP

                              EamA  81 lffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvllil 136
                                       l+f a +++s+s  s+i+++ P++++++++++l+e+ +++ +lgi+++++G+l+i+
  gi|518652254|ref|YP_008141774.1|  82 LWFLAETTISSSLTSIIIYTYPIISTLMAIIFLKEQYNKYVFLGIGIGFAGLLVIF 137
                                       *****************************************************996 PP

  == domain 2  score: 59.6 bits;  conditional E-value: 2e-20
                              EamA   2 lgillallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegkl..aklslkdwllllllgllgtv 76 
                                        gi++all+a++w++++++  +   k +  t++f++f +a +  l+ia +   ++   ++sl  +ll+l++++ gt+
  gi|518652254|ref|YP_008141774.1| 147 PGIIIALLGAIVWSVGTIYFMKYHVKKDRETTNFFQFGFALLPSLLIAGIATPSIsiFEPSLLLILLVLIISIPGTA 223
                                       69******************999999*********************99999999444555555777799999**** PP

                              EamA  77 lafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlillGvlli 135
                                       +a+++f+ + +k ++s++s +++l+P+++++++v++l e +++++++g++l+ +G+++ 
  gi|518652254|ref|YP_008141774.1| 224 VAYFAFLHLNRKYGVSTISSFLFLVPALSVVFGVIILDEIPSSYEIIGLALVGIGIYFS 282
                                       ********************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       927  (0.0517039); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 1946.66
//
Query:       gi|518652255|ref|YP_008141775.1|  [L=100]
Description: hypothetical protein FACI_IFERC00001G0894 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-21   74.2   0.3    8.9e-21   73.8   0.3    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 !   73.8   0.3     5e-25   8.9e-21       1      72 [.       4      76 ..       4      78 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 5e-25
                                      HHHHHHHHTT-B-TTTSSBCCCCT---EEEE-T.-EEEEEE--SSTT-TTHHHHHHHHHHHHC.STT--EEEE CS
                    FeS_assembly_P  1 keavlaaLrtVtDPelgvdlvslglvreidieg.gkVsvditltypacslaeairadaeaalralpgvevveV 72
                                      ke+vl+aL++V DPe+g d+v+lglv++++i++ ++V++++t+t p c++ + i ++a++ ++ l+ ve + +
  gi|518652255|ref|YP_008141775.1|  4 KEEVLEALKEVSDPEIGMDVVNLGLVYDVEITDgNRVYIKMTMTAPTCPVTPWILSEAQKSVENLADVEAADI 76
                                      79*****************************************************************766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); 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 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 672.07
//
Query:       gi|518652256|ref|YP_008141776.1|  [L=184]
Description: hypothetical protein FACI_IFERC00001G0895 [Ferroplasma acidarmanus fer1]
Scores for complete 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  196.3   0.1    2.2e-28   98.0   0.0    2.0  2  TBP       Transcription factor TFIID (or TATA-binding protein
    3.2e-07   30.4   0.0      0.024   14.7   0.0    2.7  2  DUF3378   Domain of unknown function (DUF3378)
  ------ inclusion threshold ------
      0.041   14.0   1.0       0.14   12.3   1.0    1.9  1  DUF2120   Uncharacterized protein conserved in archaea (DUF21
      0.086   12.5   0.0         15    5.3   0.0    2.5  2  NdhS      NAD(P)H dehydrogenase subunit S


Domain annotation for each model (and alignments):
>> TBP  Transcription factor TFIID (or TATA-binding protein, TBP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.7   0.0   1.3e-31   5.8e-28       2      84 ..       7      87 ..       6      88 .. 0.97
   2 !   98.0   0.0   4.9e-32   2.2e-28       2      84 ..      98     180 ..      97     181 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 1.3e-31
                                      EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHHHH CS
                               TBP  2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakkiap 80
                                      ++i+N+vas++l  +ldL+++al +  +++eYepe+fpgl+yrl++pk+++liF+sGkv +tGak+ e++++ ++ i++
  gi|518652256|ref|YP_008141776.1|  7 ITIENIVASTSLAEHLDLSRIALAL--EGSEYEPEQFPGLIYRLKDPKTAVLIFRSGKVNCTGAKNLENVKKTIDIIID 83
                                      89********************998..**************************************************** PP

                                      HHHH CS
                               TBP 81 ilkk 84
                                      +lkk
  gi|518652256|ref|YP_008141776.1| 84 KLKK 87
                                      **98 PP

  == domain 2  score: 98.0 bits;  conditional E-value: 4.9e-32
                                       EEEEEEEEEEE-SSCE-HHHHHHHCCTTTEEE-TTTSSSEEEEETTTTEEEEE-TTSEEEEECESSHHHHHHHHHHH CS
                               TBP   2 fkiqNvvasanlgleldLeklalkaekrnaeYeperfpglvyrlrepkvtaliFssGkvvitGakseeelreaakki 78 
                                       + +qN+va ++l+++l+L+ +a+++  +n+eYepe+fpglvyr++epkv++l+F sGkvv+tGak+e+e+++a+ k+
  gi|518652256|ref|YP_008141776.1|  98 IIVQNIVAVYDLESDLNLTDIAMSLGLENVEYEPEQFPGLVYRVEEPKVVLLLFGSGKVVCTGAKEESEIEQAVIKV 174
                                       679*********************88*************************************************** PP

                                       HHHHHH CS
                               TBP  79 apilkk 84 
                                        + l+k
  gi|518652256|ref|YP_008141776.1| 175 KKELQK 180
                                       999998 PP

>> DUF3378  Domain of unknown function (DUF3378)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   2.8e-05      0.12      23      49 ..      37      63 ..      33      76 .. 0.86
   2 !   14.7   0.0   5.4e-06     0.024      24      60 ..     131     167 ..     124     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.8e-05
                           DUF3378 23 rskkppyavfaakkndttItaYtSgKV 49
                                      + ++ p+ +++ k+++t + +++SgKV
  gi|518652256|ref|YP_008141776.1| 37 EPEQFPGLIYRLKDPKTAVLIFRSGKV 63
                                      56789*********************9 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 5.4e-06
                           DUF3378  24 skkppyavfaakkndttItaYtSgKVlFQGknaeaeA 60 
                                        ++ p+ v++ ++++++  ++ SgKV+  G++ e+e 
  gi|518652256|ref|YP_008141776.1| 131 PEQFPGLVYRVEEPKVVLLLFGSGKVVCTGAKEESEI 167
                                       5789***************************999885 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   1.0   3.1e-05      0.14      24      71 ..      54     107 ..      50     184 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.1e-05
                           DUF2120  24 eiLivrg...vsrkkeeleeleskleellekldaeevdlese...eakkliekl 71 
                                        +Li r+    + + ++le+++++++ +++kl++ ++++ ++    ++++++  
  gi|518652256|ref|YP_008141776.1|  54 AVLIFRSgkvNCTGAKNLENVKKTIDIIIDKLKKAKIEVYDNpdiIVQNIVAVY 107
                                       67777764446999999*********************9987422234555444 PP

>> NdhS  NAD(P)H dehydrogenase subunit S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0    0.0033        15      18      34 ..      40      56 ..      32      62 .. 0.88
   2 ?    4.7   0.0    0.0054        24      17      37 ..     132     152 ..     120     156 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0033
                              NdhS 18 gfeGlvQrvsdgkaaVl 34
                                      +f Gl+ r+ d k aVl
  gi|518652256|ref|YP_008141776.1| 40 QFPGLIYRLKDPKTAVL 56
                                      799*************8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0054
                              NdhS  17 ygfeGlvQrvsdgkaaVlFeG 37 
                                        +f Glv rv + k+  l+ G
  gi|518652256|ref|YP_008141776.1| 132 EQFPGLVYRVEEPKVVLLLFG 152
                                       5799**********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1269.26
//
Query:       gi|518652257|ref|YP_008141777.1|  [L=414]
Description: hypothetical protein FACI_IFERC00001G0896 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-128  429.6   0.0   1.2e-128  429.5   0.0    1.0  1  TruD      tRNA pseudouridine synthase D (TruD)


Domain annotation for each model (and alignments):
>> TruD  tRNA pseudouridine synthase D (TruD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  429.5   0.0  6.9e-133  1.2e-128       2     416 .]       6     408 ..       5     408 .. 0.96

  Alignments for each domain:
  == domain 1  score: 429.5 bits;  conditional E-value: 6.9e-133
                              TruD   2 lgielyvtdtegigGrlrespeDFiVeEieefsgeeeadegeylvlrvekrnwdtldlvrelaralgisrkrvgfaG 78 
                                       +gi+ y tdt+gi+G+++ +pe FiV+Ei+ +  e  +++g+y++l+v++rnwdt++++  la++l+is+kr+++aG
  gi|518652257|ref|YP_008141777.1|   6 IGINGYSTDTPGIDGNIKYDPESFIVNEIPVTIPE--NNNGKYTILKVRLRNWDTNKFLMYLADQLHISNKRITYAG 80 
                                       79***************************887665..899************************************* PP

                              TruD  79 tKDkrAvTtQlisirkvepeelealeikdvelevvgrarrklrlGdLaGNkFeirvrdvaeeeeaakraeeileele 155
                                       tKDk ++TtQ+++i+  e++++++++ikd+e+ + +r+++ ++lGdL GN+F i ++ +   +++++++ e++e++ 
  gi|518652257|ref|YP_008141777.1|  81 TKDKIGITTQYFCINMPENQQINNISIKDAEIISSFRTDKLVKLGDLLGNEFIISIQST---DDNTQKIGETVESIV 154
                                       **********************************************************5...45579********** PP

                              TruD 156 ekggvPNyfGvQRFGsrrpvthlvGkaivkgdleeAvelyvgkpfeeesedtreareavaetgdleealeelpkslr 232
                                       ++gg+PN++G+QRFGs+r +th++Gk +v++++e+Av++y+ +p  ++++     r+ + etgd+++a++e+p+ l+
  gi|518652257|ref|YP_008141777.1| 155 KNGGFPNFYGYQRFGSIRANTHKIGKLLVQNKYEDAVKTYIYDPEFDREDY----RRTFGETGDAKRAIKEFPEYLT 227
                                       ********************************************8766555....88899***************** PP

                              TruD 233 yErallkrLaekpkdykkAlealpknLqrlFvhAyqSylFNrvlseRlerglpldepveGDvvifaeer.lpdtdrl 308
                                       +Er+ll ++++ +++yk+A++++p+nL++lF+hAyqSylFNr+ls+R++   ++++++eGD+++  ++  +pd+++l
  gi|518652257|ref|YP_008141777.1| 228 FERSLLGYIIR-ENTYKNAFSVFPRNLSMLFIHAYQSYLFNRILSDRMKYAGSMHKVLEGDLLYPVDRYfNPDRSQL 303
                                       ***********.******************************************************77799****** PP

                              TruD 309 qlvteknveevkrliergrafvtaplvGtetelaegevgeierevleeegleledFklpklpelsskGtrRaillrv 385
                                        ++++ n+e++++l +++r+ +++pl+G++tel++g +geie+++++eeg+e++dF+l++  +l+s+G++R +++ +
  gi|518652257|ref|YP_008141777.1| 304 IRASSYNIEKLNKLSSENRIRTVIPLIGYSTELSSGIEGEIESRIMAEEGIEKKDFNLSSDRRLGSSGDYRIMSVLP 380
                                       *********************************************************99999*************** PP

                              TruD 386 edlelsaeedeltleFsLpkGsYATvvlrEi 416
                                        d+++ +   +  ++FsL kG YAT++lrE+
  gi|518652257|ref|YP_008141777.1| 381 VDFKIIE---KNRINFSLGKGIYATSLLREL 408
                                       **99555...5689***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2989.42
//
Query:       gi|518652258|ref|YP_008141778.1|  [L=85]
Description: hypothetical protein FACI_IFERC00001G0897 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.3   0.0      0.077   13.1   0.0    1.2  1  Mrr_N     Mrr N-terminal domain


Domain annotation for each model (and alignments):
>> Mrr_N  Mrr N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.3e-06     0.077       7      63 ..       5      60 ..       3      75 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-06
                             Mrr_N  7 plLealadgsehrlkeirervaerfglseeeraellpsgkqtrfknrvgWartyLkk 63
                                       +Le+l + + ++ ++i ++++ +++ s++ +a +l+ g q +++n + + +++++ 
  gi|518652258|ref|YP_008141778.1|  5 NVLEILGNTEMTQ-DQIADKMIGKYSTSDNSKAGYLKIGAQILVENELEFLLNEMVD 60
                                      69**********9.***********************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 660.40
//
Query:       gi|518652259|ref|YP_008141779.1|  [L=485]
Description: hypothetical protein FACI_IFERC00001G0898 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.2e-149  498.0   7.6   1.4e-149  497.8   7.6    1.0  1  IMPDH         IMP dehydrogenase / GMP reductase domain
    4.1e-23   81.6   3.9      6e-12   45.8   0.3    3.4  3  CBS           CBS domain
    4.3e-10   39.1   8.3      1e-09   37.9   8.0    2.0  2  FMN_dh        FMN-dependent dehydrogenase
    1.1e-09   38.2  12.5    5.3e-07   29.3   6.1    3.1  3  NMO           Nitronate monooxygenase
    5.1e-06   26.1   5.7    0.00081   18.9   0.1    2.7  3  His_biosynth  Histidine biosynthesis protein
    7.7e-05   22.0   4.4    0.00015   21.1   4.4    1.4  1  Glu_synthase  Conserved region in glutamate synthase
    0.00023   20.5   1.2    0.00091   18.5   1.0    2.0  2  DHO_dh        Dihydroorotate dehydrogenase
     0.0019   17.4   1.6       0.11   11.5   0.0    2.8  3  Dus           Dihydrouridine synthase (Dus)
     0.0029   16.8   4.7       0.41    9.8   0.7    2.4  2  DUF561        Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.018   14.6   0.1       0.18   11.3   0.0    2.2  2  EAL           EAL domain
      0.023   14.0   1.2      0.023   14.0   1.2    2.2  2  ThiG          Thiazole biosynthesis protein ThiG
       0.12   11.8   3.9        0.5    9.8   0.1    3.0  3  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
       0.43    9.7   6.3          3    7.0   0.5    3.4  3  NanE          Putative N-acetylmannosamine-6-phosphate epimer


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  497.8   7.6    1e-152  1.4e-149       1     345 []      12     468 ..      12     468 .. 0.99

  Alignments for each domain:
  == domain 1  score: 497.8 bits;  conditional E-value: 1e-152
                                       E--GGGEEEE---B-S-GGGSB--EESSTTEEESSSEEE-SSTTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH   1 gltfddvllvpaksevlpkevdlktkltkkiklniPlvsaamdtvtesemAialareGgigvihknlsieeqaeevk 77 
                                       g+tfddvll p +s+++pk++++++k++++i++ iP+vs++mdtvte++mAia+ar G+igvih+n+s++eq+e+vk
  gi|518652259|ref|YP_008141779.1|  12 GYTFDDVLLKPLHSSIEPKNANVSSKFSRHISIGIPIVSSPMDTVTEESMAIAMARYGAIGVIHRNMSANEQVEMVK 88 
                                       79*************************************************************************** PP

                                       HHHTS........................................................................ CS
                                       xxxxx........................................................................ RF
                             IMPDH  78 kvkrs........................................................................ 82 
                                       kvk++                                                                        
  gi|518652259|ref|YP_008141779.1|  89 KVKKEesiiirdvfsiasdtpvnvartlmktkniaglpvvasgkligiltkrdlefsesegtvkdimtkdvitaden 165
                                       ****9************************************************************************ PP

                                       ..........................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT- CS
                                       ..........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH  83 ..........................................pnaakdekgrllvgaavgvkedalervkalveagv 117
                                                                                 pna++de+g+l+vgaa+g+ +  ++r+ +l +ag 
  gi|518652259|ref|YP_008141779.1| 166 vsiedakfilyknrveklplvdskgrlvglitakdiktrekfPNASRDEQGQLMVGAAIGAYD--IDRAINLENAGS 240
                                       *************************************************************95..9*********** PP

                                       SEEEEE-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 118 dvlvvdsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqlt 194
                                       d+lv+d+ah+h+++vl+ +k+i++++ ++++iaGn+atae+a++Li+ g+d+++vGiGpGsiCttr+vagvG+pqlt
  gi|518652259|ref|YP_008141779.1| 241 DFLVIDTAHAHNKNVLSSLKKIRNAI-HIDIIAGNIATAEAAEDLISLGVDGLRVGIGPGSICTTRIVAGVGIPQLT 316
                                       **************************.8************************************************* PP

                                       HHHHHHHHHCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 195 AvaevaeaakkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkk 271
                                       A+++va++a+++g+pviaDGGi+ysgd++kAlaaGa++vmlGsllagteEspg  ++i+grkyK+yrGmgs+ga k+
  gi|518652259|ref|YP_008141779.1| 317 AISDVADVASEHGIPVIADGGIRYSGDMIKALAAGASTVMLGSLLAGTEESPGTEMIINGRKYKAYRGMGSIGAIKA 393
                                       ***************************************************************************** PP

                                       -SS-TTS-...--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                                       xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 272 gskdryfq.kkeklvpeGvegrvpykgsvkevveqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                                       g++dry +  ++++++eGveg+vpy+g+v+e + q+vgg+++gmgylGa+++eelk+ka f++it++gl+esh+H
  gi|518652259|ref|YP_008141779.1| 394 GKSDRYEKlGTNEFIAEGVEGSVPYRGKVSENLFQFVGGIKTGMGYLGAENLEELKKKAVFIKITNSGLRESHPH 468
                                       ******875477**************************************************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.8   0.2   2.6e-11   3.5e-08       4      51 ..      96     142 ..      90     142 .. 0.93
   2 !   45.8   0.3   4.4e-15     6e-12       1      51 [.     151     201 ..     151     205 .. 0.97
   3 ?    0.8   0.0      0.51     7e+02      14      40 ..     314     337 ..     299     342 .. 0.68

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 2.6e-11
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       i  rdv+++  dt++  a  lm+ k++ +lPVV  +gkl+Gi+t+rDl
  gi|518652259|ref|YP_008141779.1|  96 IIIRDVFSIASDTPVNVARTLMKTKNIAGLPVV-ASGKLIGILTKRDL 142
                                       677999****************8888*******.7************8 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 4.4e-15
                                       HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       V+dimt+dv+t++++ ++e+a  ++ +++v  lP Vd+ g+lvG++t +D+
  gi|518652259|ref|YP_008141779.1| 151 VKDIMTKDVITADENVSIEDAKFILYKNRVEKLPLVDSKGRLVGLITAKDI 201
                                       89**********************98999*********************9 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.51
                                       TTSBHHHHHHHHHHHTSSEEEEEETTT CS
                               CBS  14 pdttleealelmrekgvsrlPVVdedg 40 
                                         t ++++++   e   +++PV+ + g
  gi|518652259|ref|YP_008141779.1| 314 QLTAISDVADVASE---HGIPVIADGG 337
                                       44558888888866...8****95454 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   8.0   7.5e-13     1e-09     200     302 ..     251     360 ..      43     393 .. 0.84
   2 ?   -1.6   0.0      0.79   1.1e+03     325     346 ..     432     453 ..     421     454 .. 0.83

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.5e-13
                                       -TC--HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH.. CS
                            FMN_dh 200 dpsltwddikwlreqtklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg 270
                                       +++   +++k++r++ ++ ++   + tae a+ ++ +Gvdg+ v    G     R + g+ ++ + ++ ++++ + +
  gi|518652259|ref|YP_008141779.1| 251 HNKNVLSSLKKIRNAIHIDIIAGNIATAEAAEDLISLGVDGLRVGIGPGsicttRIVAGVgIPQLTAISDVADVASE 327
                                       34445568************************************988886666666655425556666666776666 PP

                                       S.S-EEEESS--SHHHHHHHHHTT-SEEEESHH CS
                            FMN_dh 271 r.ievlvDgGirrGsDvlkAlalGAdavllGRp 302
                                       + i+v++DgGir   D++kAla GA+ v+lG  
  gi|518652259|ref|YP_008141779.1| 328 HgIPVIADGGIRYSGDMIKALAAGASTVMLGSL 360
                                       45****************************965 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.79
                                       HHHHHHHHHT-SBHHHHHCGGE CS
                            FMN_dh 325 elertmallGvksvaeldrsll 346
                                        +++ m  lG+++++el+++++
  gi|518652259|ref|YP_008141779.1| 432 GIKTGMGYLGAENLEELKKKAV 453
                                       58999************99865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   0.00014      0.19       6      58 ..      40      91 ..      35      99 .. 0.82
   2 ?   -0.7   0.0      0.53   7.3e+02     192     217 ..     123     151 ..      93     229 .. 0.67
   3 !   29.3   6.1   3.8e-10   5.3e-07     116     235 ..     244     371 ..     197     383 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                               NMO  6 ellkikppvvqpgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvk 58
                                        + i  p+v ++m  ++++ +a a +  G++Gv+    ++a +  + ++kvk
  gi|518652259|ref|YP_008141779.1| 40 RHISIGIPIVSSPMDTVTEESMAIAMARYGAIGVIH-RNMSANEQVEMVKKVK 91
                                      5577999****************************9.6666666666666665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.53
                               NMO 192 vdiPviAaG...GiidrrgvaaaLalGAs 217
                                         +Pv+A G   Gi ++r+++   + G  
  gi|518652259|ref|YP_008141779.1| 123 AGLPVVASGkliGILTKRDLEFSESEGTV 151
                                       34788888877788888887655555554 PP

  == domain 3  score: 29.3 bits;  conditional E-value: 3.8e-10
                               NMO 116 vvsfgfglpteevvarlke.agvvli....ptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaL..v 185
                                       v+ ++ + + ++v+ +lk+  ++++i    + i+++++a  ++++G D l v G   G    t+ v+++g  +L  +
  gi|518652259|ref|YP_008141779.1| 244 VIDTAHAHN-KNVLSSLKKiRNAIHIdiiaGNIATAEAAEDLISLGVDGLRV-GIGPGSICTTRIVAGVGIPQLtaI 318
                                       444444444.3344443331445554111145789*************9977.777777777788888665555226 PP

                               NMO 186 pqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakd 235
                                         v+d+ +   iPviA GGi    ++  aLa+GAs v +g+ + +t+es+  +
  gi|518652259|ref|YP_008141779.1| 319 SDVADVASehgIPVIADGGIRYSGDMIKALAAGASTVMLGSLLAGTEESPGTE 371
                                       67888877899**************************************8766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.2   1.7e+03     149     212 ..      83     148 ..      58     157 .. 0.60
   2 !    9.0   0.4   0.00063      0.87      48     100 ..     242     295 ..     229     308 .. 0.83
   3 !   18.9   0.1   5.9e-07   0.00081      61     105 ..     317     361 ..     307     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHTT-SEEEEEETTTTTTSS---HHH.HHHHHHHHSSEEEEES...S--SHHHHHHHHHT CS
                      His_biosynth 149 avelakkleelgageilltdidrdGtlsGpdlel.tkelaeavkipviasG...Gvgsledlkelkse 212
                                        ve++kk+++   ++i++ d+ +  + + +++   + + ++   +pv+asG   G+ +  dl+  +se
  gi|518652259|ref|YP_008141779.1|  83 QVEMVKKVKKE--ESIIIRDVFSIASDTPVNVARtLMKTKNIAGLPVVASGkliGILTKRDLEFSESE 148
                                       33444444433..3466666666666666666432556666667777777766666666666655555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00063
                                       EEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-S..EEE CS
                      His_biosynth  48 vvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagad..kvi 100
                                       ++ +d a++++++ l+ +++i+++++i++   G I + e++e+l+++g+d  +v 
  gi|518652259|ref|YP_008141779.1| 242 FLVIDTAHAHNKNVLSSLKKIRNAIHIDII-AGNIATAEAAEDLISLGVDglRVG 295
                                       44578899999*************999884.566***************955554 PP

  == domain 3  score: 18.9 bits;  conditional E-value: 5.9e-07
                                       HHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  61 nldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                        ++ v+ +a+e  ipv  +GGIr   d+ ++l aga+ v++g+  
  gi|518652259|ref|YP_008141779.1| 317 AISDVADVASEHGIPVIADGGIRYSGDMIKALAAGASTVMLGSLL 361
                                       5677889999999***************************99975 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 !   21.1   4.4   1.1e-07   0.00015     215     304 ..     267     359 ..     245     362 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 1.1e-07
                                       THHHHHHH..HHHTT-SEEE..EE-TT---SSE...EHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS-- CS
                      Glu_synthase 215 gvetiaag..vakanadiil..idGleGGTGAs...pkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglk 284
                                        +++ia     a+a  d+i+  +dGl+ G G      + ++  +G+P ++a++ v  +  e+g    + +iadGg++
  gi|518652259|ref|YP_008141779.1| 267 HIDIIAGNiaTAEAAEDLISlgVDGLRVGIGPGsicTTRIVAGVGIPQLTAISDVADVASEHG----IPVIADGGIR 339
                                       444444331146677799875579*9999997511146788899**********998877765....78******** PP

                                       SHHHHHHHHHHT-SEEE-SH CS
                      Glu_synthase 285 tgadvvkalalGAdavgigt 304
                                        + d++kala GA +v +g+
  gi|518652259|ref|YP_008141779.1| 340 YSGDMIKALAAGASTVMLGS 359
                                       ****************9997 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.0   6.6e-07   0.00091     229     276 ..     316     361 ..     306     371 .. 0.86
   2 ?   -3.1   0.0       2.6   3.6e+03     155     170 ..     443     458 ..     434     473 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 6.6e-07
                                       HHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
                            DHO_dh 229 ialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                                       +a+  + +++++    ip+I+ GGi  + D +  + aGAs v +++ l
  gi|518652259|ref|YP_008141779.1| 316 TAISDVADVASEHG--IPVIADGGIRYSGDMIKALAAGASTVMLGSLL 361
                                       46666777777766..****************************9976 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.6
                                       HHHHHHHSSEEEEEE- CS
                            DHO_dh 155 kvvkevskvpvlvKla 170
                                       + ++e +k++v++K++
  gi|518652259|ref|YP_008141779.1| 443 ENLEELKKKAVFIKIT 458
                                       5678889999999997 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       0.5   6.8e+02       3      44 ..      51      91 ..      48     104 .. 0.80
   2 ?    3.6   0.1     0.021        29     172     213 ..     256     295 ..     232     300 .. 0.86
   3 !   11.5   0.0   8.3e-05      0.11     172     213 ..     318     358 ..     311     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.5
                                      ---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHH CS
                               Dus  3 aPmagvtdlpfRelvrefgataLvvtemvtakaivreekvri 44
                                      +Pm  vt+  +   ++++ga   v+   ++a+++v+  k++ 
  gi|518652259|ref|YP_008141779.1| 51 SPMDTVTEESMAIAMARYGAI-GVIHRNMSANEQVEMVKKVK 91
                                      499999999999999999999.66677778888888776655 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.021
                                       CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                       +++ k++++a+ i +ia G+I +ae+a++ ++  G+dg+ +g
  gi|518652259|ref|YP_008141779.1| 256 LSSLKKIRNAIHIDIIA-GNIATAEAAEDLISL-GVDGLRVG 295
                                       567899********998.***********9998.***98777 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 8.3e-05
                                       CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
                               Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                                       ++++++v  +  ipvia G+I++  d+ ++l+  Ga  vm g
  gi|518652259|ref|YP_008141779.1| 318 ISDVADVASEHGIPVIADGGIRYSGDMIKALAA-GASTVMLG 358
                                       455666666667********************9.******99 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.2   0.00083       1.1     165     237 ..      24      97 ..       8     102 .. 0.71
   2 !    9.8   0.7   0.00029      0.41     136     219 ..     279     363 ..     242     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00083
                            DUF561 165 ndliekslstlastyeiskkvslPvicasGlsdvt.vplalslgasG.iGigsavsklndeeemvallseikkai 237
                                       +  ie     ++s ++   ++ +P+++ s + +vt  ++a+++   G iG+ +   + n+++emv+ +++ +++i
  gi|518652259|ref|YP_008141779.1|  24 HSSIEPKNANVSSKFSRHISIGIPIVS-SPMDTVTeESMAIAMARYGaIGVIHRNMSANEQVEMVKKVKKEESII 97 
                                       555666666778887777777888876.556666624688877665558888888899********999866655 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00029
                            DUF561 136 kLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvicasGlsdvtvpl.alslgasGi 211
                                       + a++L slgvd ++   +  si  ++ v ++    l++++ +  ++++  +Pvi+  G+  +   + al++gas +
  gi|518652259|ref|YP_008141779.1| 279 EAAEDLISLGVDGLRVGIGPGSICTTRIVAGVGIPQLTAISDVADVASEHGIPVIADGGIRYSGDMIkALAAGASTV 355
                                       56899999999999999889999999999999999999**********************988766659******** PP

                            DUF561 212 Gigsavsk 219
                                        +gs +  
  gi|518652259|ref|YP_008141779.1| 356 MLGSLLAG 363
                                       99997765 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.18     187     229 ..     249     291 ..     240     293 .. 0.90
   2 ?    0.3   0.0      0.31   4.2e+02     193     212 ..     317     336 ..     309     336 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                                       SCHHHHHHHHCHHHHCCCT-EEEE-S--SHHHHHHHHHHT-SE CS
                               EAL 187 deeaqalvkalialakelgikvvaegVeteeqlealrelgcdl 229
                                       ++ +++++++l ++ ++++i+++a  + t e +e+l++lg+d 
  gi|518652259|ref|YP_008141779.1| 249 HAHNKNVLSSLKKIRNAIHIDIIAGNIATAEAAEDLISLGVDG 291
                                       5789999**********************************96 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.31
                                       HHHHCHHHHCCCT-EEEE-S CS
                               EAL 193 lvkalialakelgikvvaeg 212
                                        ++ ++++a+e gi+v+a+g
  gi|518652259|ref|YP_008141779.1| 317 AISDVADVASEHGIPVIADG 336
                                       578899************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.36   4.9e+02     180     230 ..     220     276 ..     197     292 .. 0.61
   2 ?   14.0   1.2   1.6e-05     0.023     155     212 ..     306     366 ..     299     373 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.36
                                       EES---SHH.HHHHHH.HTT-SEEEESHHHHTSSSHHHHHH....HHHHHHHHHHHH CS
                              ThiG 180 vDAGigsps.daaqam.elGadavllntavaeakdpvamAr....afklaveaGrla 230
                                       v A ig    d a  + + G d ++++ta a+ k+  +  +    a++  + aG +a
  gi|518652259|ref|YP_008141779.1| 220 VGAAIGAYDiDRAINLeNAGSDFLVIDTAHAHNKNVLSSLKkirnAIHIDIIAGNIA 276
                                       566666432133333314688888888888888887654440000444444555555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 1.6e-05
                                       TTS----S-HHHHHHHH...HH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSS CS
                              ThiG 155 iGsglGllnkealkiii...eeakvPvivDAGigspsdaaqamelGadavllntavaeakd 212
                                       i +g G+ + +a++ +    +e  +Pvi D Gi+ + d ++a+  Ga++v+l + +a +++
  gi|518652259|ref|YP_008141779.1| 306 IVAGVGIPQLTAISDVAdvaSEHGIPVIADGGIRYSGDMIKALAAGASTVMLGSLLAGTEE 366
                                       556667766666665540005668****************************999998765 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.41   5.7e+02      80     115 ..      84     119 ..      57     141 .. 0.72
   2 ?    1.2   0.1      0.16   2.2e+02     131     163 ..     259     290 ..     244     295 .. 0.64
   3 ?    9.8   0.1   0.00036       0.5     131     167 ..     321     357 ..     312     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.41
                                       HHHHHHHHHTT--EEEEEE--SHHHHHHHHHHHHHH CS
                      G3P_antiterm  80 sslikkakklglltiqrlfliDssalekalkqieks 115
                                        +++kk kk++ + i  +f i s++  ++ +++ k+
  gi|518652259|ref|YP_008141779.1|  84 VEMVKKVKKEESIIIRDVFSIASDTPVNVARTLMKT 119
                                       467888888888888888888777766666666543 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.16
                                       HCTSTTS...EEEEESS--SHHHHHHHCTT.SS CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaGai 163
                                       +k+i+++++i iiaG  i t e  e++++ G++
  gi|518652259|ref|YP_008141779.1| 259 LKKIRNAIHIDIIAG-NIATAEAAEDLISLGVD 290
                                       456666666666664.35555555555555554 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00036
                                       HCTSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
                      G3P_antiterm 131 ikeikkelkipiiaGGLietkedveealkaGaiavst 167
                                       ++++ +e  ip+ia G i+ + d+ +al+aGa+ v+ 
  gi|518652259|ref|YP_008141779.1| 321 VADVASEHGIPVIADGGIRYSGDMIKALAAGASTVML 357
                                       55677888*************************9975 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.6      0.33   4.5e+02      21      33 ..      84      96 ..      58     183 .. 0.56
   2 ?    7.0   0.5    0.0022         3     129     173 ..     251     295 ..     105     308 .. 0.87
   3 ?    3.8   0.0     0.021        29     141     177 ..     326     362 ..     313     368 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                      HHHHHHHHTT--S CS
                              NanE 21 vedikaikavvdl 33
                                      ve +k++k++ ++
  gi|518652259|ref|YP_008141779.1| 84 VEMVKKVKKEESI 96
                                      3333333333332 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0022
                                       .SS--HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE- CS
                              NanE 129 kaepDfalvkalseaglkviaeGrintPekakkaieiGvdavvvG 173
                                       ++++ ++ +k++ +a    i+ G i t e a++ i +Gvd + vG
  gi|518652259|ref|YP_008141779.1| 251 HNKNVLSSLKKIRNAIHIDIIAGNIATAEAAEDLISLGVDGLRVG 295
                                       3556667788888887778889*******************9998 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.021
                                       HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH CS
                              NanE 141 seaglkviaeGrintPekakkaieiGvdavvvGsait 177
                                       se g+ via+G i       ka+  G+ +v++Gs ++
  gi|518652259|ref|YP_008141779.1| 326 SEHGIPVIADGGIRYSGDMIKALAAGASTVMLGSLLA 362
                                       6789*****************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 3383.77
//
Query:       gi|518652260|ref|YP_008141780.1|  [L=467]
Description: hypothetical protein FACI_IFERC00001G0899 [Ferroplasma acidarmanus fer1]
Scores for 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-12   44.8   0.1    4.8e-11   42.4   0.0    2.0  2  DNA_pol_E_B      DNA polymerase alpha/epsilon subunit B
    9.7e-12   45.8   0.2    1.8e-11   45.0   0.2    1.4  1  Metallophos      Calcineurin-like phosphoesterase
    1.5e-05   25.3   0.0    4.6e-05   23.7   0.0    1.7  1  Metallophos_2    Calcineurin-like phosphoesterase superfamily
    0.00093   19.1   0.2       0.01   15.8   0.1    2.4  2  tRNA_anti-codon  OB-fold nucleic acid binding domain


Domain annotation for each model (and alignments):
>> DNA_pol_E_B  DNA polymerase alpha/epsilon subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.1e-14   4.8e-11      16     209 ..     231     414 ..     213     416 .. 0.76
   2 ?   -0.2   0.0      0.11   5.1e+02     116     131 ..     438     453 ..     425     466 .. 0.57

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.1e-14
                                       -HHHHHHHHHHH.HTT--SEEEEES-SSBTTSHHHHHT---S--SSHHHHHHHHTHHHHTTS-.TTSEEEEE--TTB CS
                       DNA_pol_E_B  16 leaLrkiLqgyapeesppdvlilaGnfvdaahkaiasskvstdekkenfdalalllsilesll.ekttvvlvPgpnD 91 
                                       + ++  +++  ++e+s+ + lil G  vd      ++ k  + e  +  +  ++l + ++  +   ++v+++Pg  D
  gi|518652260|ref|YP_008141780.1| 231 FMKMISWIKASEEEASKLKYLILSGDVVDGIGVYPGQDK--DLEILNPYEQYEKLAEYVNM-VpDDVNVFIMPGNHD 304
                                       555666777777999*************94333333222..12333333333333334444.35899********** PP

                                       TT-S-SBSB----TTTTT--TTT...EEE--BSEEEEETTEEEEE--S-HHHH---EEESHHHHHS-HHHHHHHHHH CS
                       DNA_pol_E_B  92 panstvlPqqPlprlllsrikrvfkelklvtNPsrielnsvevvltsddivkdlkreslkesntdverlrklvktil 168
                                        +   + Pq+ + +++ +  +    +++l++NP+ + l++  v+++ +  ++d+ + +   s      +   ++ +l
  gi|518652260|ref|YP_008141780.1| 305 IVRL-AEPQPVFSQKIKNFFND---NVTLLPNPYNLVLENKNVLVYHGMSLNDMIELVPGASY---ASVGSSIEELL 374
                                       9999.99*99986665555555...5*****************************99998888...7999******* PP

                                       HHTBS---SS--B-GGGGGGGB-GGG---SEEE---SS--E CS
                       DNA_pol_E_B 169 dqrhlaPlaptlrpvswdkddalvleplPdvlvlpdelpeF 209
                                       + rhlaP++    p+   k+d  v++++Pd+++ +    +F
  gi|518652260|ref|YP_008141780.1| 375 KRRHLAPVYGGKTPIIPSKRDYHVIDQVPDIFITGH-IHSF 414
                                       *********************************998.6665 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.11
                                       ..EEE--BSEEEEETT CS
                       DNA_pol_E_B 116 kelklvtNPsrielns 131
                                       k +++++NPs ++l++
  gi|518652260|ref|YP_008141780.1| 438 KMMNFSPNPSIMTLFD 453
                                       2355555555555554 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.2     4e-15   1.8e-11       5     203 ..     215     413 ..     212     414 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4e-15
                                       EEESBTBTTCCTHHHHHHHHHHHHHHH....TTESEEEEESTSSSSS..............HHHHHHHHHHHHHHHH CS
                       Metallophos   5 vigDlHlalgggqlddllkllddllre....ekpdlvllaGDlvdrg..............dlekellellaalvky 63 
                                        ++D+H+ +   + +d++k++++++++    +k  +++l GD+vd+               ++e+ +++l a+ v++
  gi|518652260|ref|YP_008141780.1| 215 SLSDIHVGSKTFRQNDFMKMISWIKASeeeaSKLKYLILSGDVVDGIgvypgqdkdleilnPYEQ-YEKL-AEYVNM 289
                                       589****9999999**********5552333455888889******88***9*999998875555.6666.444444 PP

                                       ...TSEEEEEC-TTSCHHH.HHHHHHHHHHHH.HHHHEHHHCEEETSEEEEEETTEEEEEEEESECEEETHHHHHHH CS
                       Metallophos  64 ...pipvylllGNHegfee.ellnkygylgif.sepwrsdaevfnnlplaslgsgslkvlllhGgspellvsldklg 135
                                          +++v++++GNH+   +  l ++++ +    ++ ++++++ + n++  +l ++  +vl++hG       sl+++ 
  gi|518652260|ref|YP_008141780.1| 290 vpdDVNVFIMPGNHD---IvRLAEPQPVFSQKiKNFFNDNVTLLPNPYNLVLENK--NVLVYHGM------SLNDMI 355
                                       5779999********...2244444444444425555555666677777777777..99999999......778888 PP

                                       HHHHSCHHHHCC...HHHHHHHHHHTTCSEEEEEESSESSCSSSCSCCHHHHHHH.HHHTTESEEEEESSSS CS
                       Metallophos 136 slnleleapepg...dewlkdlekrekadwvivlgHsplyrgsgylfgdealedl.lkkygvdlvisGHtHv 203
                                        l+    ++  g   +e+lk+              H  +  ++g++   ++ +d+   +  +d+ i GH+H 
  gi|518652260|ref|YP_008141780.1| 356 ELVPGASYASVGssiEELLKR-------------RHLAPV-YGGKTPIIPSKRDYhVIDQVPDIFITGHIHS 413
                                       888887888888899999999.............555555.3444444444445535555699999999996 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 !   23.7   0.0     1e-08   4.6e-05       3     147 ..     213     431 ..     212     443 .. 0.70

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1e-08
                     Metallophos_2   3 laiiSDlH............snldaleavlealkevgvdaiihaGD................leeeep...evleel 48 
                                       +a +SD+H            + ++ ++a  e++   ++ ++i++GD                +    +   e  e+l
  gi|518652260|ref|YP_008141780.1| 213 VASLSDIHvgsktfrqndfmKMISWIKASEEEA--SKLKYLILSGDvvdgigvypgqdkdleI----LnpyEQYEKL 283
                                       5779****9976666644444444444444444..4559*******66666655555544441....0333222222 PP

                     Metallophos_2  49 lela.......pvlaVrGNnD.......eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl......... 102
                                        e          v + +GN+D       + v+ +++ + +++  t lp+  +l l++++vl++Hg  l         
  gi|518652260|ref|YP_008141780.1| 284 AEYVnmvpddvNVFIMPGNHDivrlaepQPVFSQKIKNFFNDNVTLLPNPYNLVLENKNVLVYHGMSLndmielvpg 360
                                       222255578889*********99998744448888888899999999******************987********* PP

                     Metallophos_2 103 ..........................gvkdalaellke..........aeegsdvvvcGHtHvpevekeggvlvvnP 143
                                                                                        +++ d+++ GH+H  +    +gv+++n+
  gi|518652260|ref|YP_008141780.1| 361 asyasvgssieellkrrhlapvyggkT----------PiipskrdyhvIDQVPDIFITGHIHSFSQGSYRGVRYINA 427
                                       ****77777777766666666664431..........04444444454557888***********99999***9998 PP

                     Metallophos_2 144 Gsvg 147
                                          +
  gi|518652260|ref|YP_008141780.1| 428 STWQ 431
                                       6655 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 ?    0.2   0.0      0.17   7.5e+02      46      74 ..      52      79 ..      44      80 .. 0.89
   2 !   15.8   0.1   2.3e-06      0.01       1      73 [.     124     193 ..     124     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.17
                                      S-TTSEEEEEEEEEECTTSSEEEEEEEEE CS
                   tRNA_anti-codon 46 lkeGdvvrvtGrvkrrpggelelkveeie 74
                                      l+e+dv++    ++r +   +e+++++i+
  gi|518652260|ref|YP_008141780.1| 52 LTENDVIKLIRSPQRKKMD-FEVYIPDIK 79
                                      7899999999999999999.******997 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 2.3e-06
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfreeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       V+++G+v+ +s + ++++  + l+D  ++i+v+l + ++   +e + e+ v++v G v+ + +  + l ++ei
  gi|518652260|ref|YP_008141780.1| 124 VKIVGMVSEVS-TTKNGHKRLLLEDLDDNINVFLLK-GKGLNNELILEDEVLGVIGSVSNTGKD-PVLFADEI 193
                                       89********9.************************.***********************9777.88888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (467 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.58
# Mc/sec: 2431.98
//
Query:       gi|518652261|ref|YP_008141781.1|  [L=113]
Description: hypothetical protein FACI_IFERC00001G0900 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0015   18.0   3.1     0.0015   17.9   3.1    1.0  1  DUF1574          Protein of unknown function (DUF1574)
     0.0048   17.9   5.3      0.011   16.8   1.4    2.6  3  RNase_J_C        Ribonuclease J C-terminal domain
     0.0051   17.1   6.5      0.054   13.9   1.0    2.9  3  RICH             RICH domain
  ------ inclusion threshold ------
      0.011   15.1   3.8      0.011   15.1   3.8    1.5  2  DUF3387          Domain of unknown function (DUF3387)
      0.019   15.5   3.1       0.49   11.0   3.1    2.4  1  YtxH             YtxH-like protein
       0.03   15.1   0.4        1.6    9.6   0.2    2.3  2  CTD_bind         RNA polymerase II-binding domain.
      0.031   14.1   1.0      0.035   13.9   1.0    1.1  1  Baculo_p24       Baculovirus P24 capsid protein
      0.032   13.9   1.7      0.039   13.6   1.7    1.3  1  MIF4G            MIF4G domain
      0.046   12.9   3.8       0.28   10.4   0.7    2.1  2  Dynamin_M        Dynamin central region
      0.071   13.0   1.9       0.22   11.4   0.8    2.3  2  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
       0.11   12.3   1.9        0.1   12.4   0.4    1.8  2  VHS              VHS domain
       0.13   12.3   4.3       0.52   10.3   1.9    2.5  3  DUF1160          Protein of unknown function (DUF1160)
       0.15   12.6   1.4        1.2    9.7   1.4    2.1  1  IZUMO            Izumo sperm-egg fusion, Ig domain-associated
       0.19   12.4   5.2       0.85   10.4   5.2    2.2  1  COMPASS-Shg1     COMPASS (Complex proteins associated with Se
        0.2   12.1   2.7       0.32   11.4   2.7    1.3  1  DHHA1            DHHA1 domain
       0.22   12.1   4.7       0.62   10.6   0.2    2.6  2  PNPase           Polyribonucleotide nucleotidyltransferase, R
       0.55   10.7   5.8       0.86   10.0   0.4    2.5  2  YgaB             YgaB-like protein
       0.75   10.0   8.0        6.3    7.0   0.2    2.6  2  T4_Rnl2_C        T4 RNA ligase 2 C-terminal
        2.2    9.3   9.2        7.7    7.5   6.1    2.7  3  Ribosomal_L18_c  Ribosomal L18 C-terminal region
        2.6    7.9   6.8        9.4    6.1   0.1    3.4  3  ScsC_N           Copper resistance protein ScsC N-terminal do


Domain annotation for each model (and alignments):
>> DUF1574  Protein of unknown function (DUF1574)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   3.1   1.7e-06    0.0015     131     228 ..       3      98 ..       1     113 [] 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                           DUF1574 131 ksssefldeiLsysydkdyilrllekfskkdvseylakklFavyklkprleliiarakekklkeykklssetieklk 207
                                       k  +e+l++i++   +++ +++ + ++ k+ v+ey++kk+ +   lk +++++i ++ e k+key++l   +++k+ 
  gi|518652261|ref|YP_008141781.1|   3 KDVNEYLNNIINSAPSEEMYFEAIRDIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIKEYDSL--AKMAKVT 77 
                                       566889999999999999999***********************************************..5666666 PP

                           DUF1574 208 lkkgeglspneaqvekpqekl 228
                                       +k g    pn ++ e  ++++
  gi|518652261|ref|YP_008141781.1|  78 AKIGLVSAPNGIKQEALNDFM 98 
                                       666666667777766555443 PP

>> RNase_J_C  Ribonuclease J C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.1   2.8e+03      49      64 ..       2      17 ..       1      19 [. 0.70
   2 !   16.8   1.4   1.2e-05     0.011      16      61 ..      20      65 ..      12      67 .. 0.91
   3 ?    1.7   0.1       0.6   5.4e+02      16      32 ..      95     111 ..      87     113 .] 0.62

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                         RNase_J_C 49 realkkflykktkrrP 64
                                      +++++++l++ ++  P
  gi|518652261|ref|YP_008141781.1|  2 KKDVNEYLNNIINSAP 17
                                      6777888877777666 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.2e-05
                         RNase_J_C 16 eeLieeakkvvretieealeekesdwnelkrkirealkkflykktk 61
                                      e  +e++++++++ ++e++++k+++ ++lk++i e +++f++ k+k
  gi|518652261|ref|YP_008141781.1| 20 EMYFEAIRDIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIK 65
                                      455899***********************************99987 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.6
                         RNase_J_C  16 eeLieeakkvvretiee 32 
                                       +++++  kk ++e+i++
  gi|518652261|ref|YP_008141781.1|  95 NDFMNTFKKEIEEIIKS 111
                                       56666677777776665 PP

>> RICH  RICH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.28   2.6e+02       8      20 ..       2      14 ..       1      20 [. 0.79
   2 ?    4.1   0.5     0.065        58       4      28 ..      27      50 ..      24      52 .. 0.76
   3 !   13.9   1.0     6e-05     0.054       4      68 ..      49     110 ..      45     113 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.28
                              RICH  8 kdeVkeylekiLs 20
                                      k++V+eyl+ i++
  gi|518652261|ref|YP_008141781.1|  2 KKDVNEYLNNIIN 14
                                      7789999999886 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.065
                              RICH  4 skkakdeVkeylekiLseikkqldK 28
                                      ++  kd Vkey+ k ++e  + l+K
  gi|518652261|ref|YP_008141781.1| 27 RDIFKDLVKEYIRKKINED-EDLKK 50
                                      5667899*******99885.55555 PP

  == domain 3  score: 13.9 bits;  conditional E-value: 6e-05
                              RICH   4 skkakdeVkeylekiLseikkqldKrkhtqnvaLikkLseIkteyLyelkvlkekskaeleelvs 68 
                                       +k+  + ++e++e  ++e  +  +  k t  + L+   + Ik+e+L++  +  +k   e+ee ++
  gi|518652261|ref|YP_008141781.1|  49 KKQISEVIEEFMEAKIKEYDSLAKMAKVTAKIGLVSAPNGIKQEALNDFMNTFKK---EIEEIIK 110
                                       67778899**********97777789***********************987655...7777655 PP

>> DUF3387  Domain of unknown function (DUF3387)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   3.8   1.3e-05     0.011     158     228 ..       8      79 ..       4      87 .. 0.88
   2 ?   -1.8   0.0       1.8   1.6e+03     144     165 ..      87     108 ..      82     112 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.3e-05
                           DUF3387 158 flee.vkkmkeknlavelLkklLadeikarsrkNlvkskkFserLeelikkYnnraltsaevieeLielake 228
                                       +l++ +++ + +++ +e+++ + +d +k++ rk + + ++++++++e+i+++++ ++++ + ++++ ++  +
  gi|518652261|ref|YP_008141781.1|   8 YLNNiINSAPSEEMYFEAIRDIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIKEYDSLAKMAKVTAK 79 
                                       5554145778999************************************************99999887765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                           DUF3387 144 aglekpdisiLseefleevkkm 165
                                        g++++ ++++ ++f +e++++
  gi|518652261|ref|YP_008141781.1|  87 NGIKQEALNDFMNTFKKEIEEI 108
                                       5666666666666666666654 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.1   0.00055      0.49      29      72 ..      47     110 ..       1     112 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00055
                              YtxH  29 dlkekaddlkekakelleeakeka...........................kekaedlkekvkekadelke 72 
                                       dlk++ +++ e + e+                                   +e  +d+++++k++++e+ +
  gi|518652261|ref|YP_008141781.1|  47 DLKKQISEVIEEFMEA-------KikeydslakmakvtakiglvsapngikQEALNDFMNTFKKEIEEIIK 110
                                       3444444444444333.......2333334466678889***********9999*************9876 PP

>> CTD_bind  RNA polymerase II-binding domain.
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2    0.0018       1.6      22      61 ..      21      63 ..       3      64 .. 0.64
   2 ?    3.7   0.0      0.13   1.1e+02      20      38 ..      94     112 ..      83     113 .] 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0018
                          CTD_bind 22 efapaFapvlpeafadayk...kapekikkklkrllniWeern 61
                                       + +a   +++++++  ++   +++e++kk+++++++ + e +
  gi|518652261|ref|YP_008141781.1| 21 MYFEAIRDIFKDLVKEYIRkkiNEDEDLKKQISEVIEEFMEAK 63
                                      4444444444444444444666899***********9988876 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.13
                          CTD_bind  20 kdefapaFapvlpeafada 38 
                                        ++f ++F++ ++e+++++
  gi|518652261|ref|YP_008141781.1|  94 LNDFMNTFKKEIEEIIKST 112
                                       5799**********99875 PP

>> Baculo_p24  Baculovirus P24 capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   1.0   3.9e-05     0.035      72     166 ..       7      99 ..       4     113 .] 0.63

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.9e-05
                        Baculo_p24  72 kyLssynlsdsahppeyyvlkqLvrDLlvGaqseavdplkdiktqlctlqecleesnvlvn.......sttesssne 141
                                        yL ++  s+ +++  + +++ +++DL+    ++++++ +d+k+q+ ++ e + e++ +         +        
  gi|518652261|ref|YP_008141781.1|   7 EYLNNIINSAPSEEMYFEAIRDIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIKEYdslakmaK-------- 75 
                                       79999999999999999*****************************99888777766443333332220........ PP

                        Baculo_p24 142 nieslreilrseeasllsnlnslle 166
                                        ++    ++ + +      ln+ ++
  gi|518652261|ref|YP_008141781.1|  76 -VTAKIGLVSAPNGIKQEALNDFMN 99 
                                       .222222222222222222222222 PP

>> MIF4G  MIF4G domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.7   4.4e-05     0.039      16      94 ..      30     106 ..       6     112 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.4e-05
                                       HHHHHHHHHHHHHCS...CHHHHHHHHHHHHHHHHHCGGGHHHHHHHHHHHHHHSH.HHHHHHHHHHHHHHHHHHC- CS
                             MIF4G  16 fevlikqllklamdd...dknelkevielifekaveepsfsplyarlcgklnsrfq.qnFrikllnklqeefekrye 88 
                                       f++l+k+ +++++++    k +++evie ++e  ++e++++   a++++k+      + +++  ln ++  f+k   
  gi|518652261|ref|YP_008141781.1|  30 FKDLVKEYIRKKINEdedLKKQISEVIEEFMEAKIKEYDSLAKMAKVTAKIGLVSApNGIKQEALNDFMNTFKK--- 103
                                       89999999988888834444555555666699999999999999999998876655667888888888888887... PP

                                       S-HHHH CS
                             MIF4G  89 lenele 94 
                                          e+e
  gi|518652261|ref|YP_008141781.1| 104 ---EIE 106
                                       ...222 PP

>> Dynamin_M  Dynamin central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00031      0.28     213     263 ..       4      57 ..       1      64 [. 0.66
   2 ?    4.7   0.8     0.017        15      84     130 ..      65     111 ..      46     113 .] 0.56

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00031
                         Dynamin_M 213 lVyeelekiveklekelkrFpnLreeikevvedllreqeep...tkemienlie 263
                                        V e+l++i++++ +e   F ++r+ +k+ v++++r++ ++    k++i+++ie
  gi|518652261|ref|YP_008141781.1|   4 DVNEYLNNIINSAPSEEMYFEAIRDIFKDLVKEYIRKKINEdedLKKQISEVIE 57 
                                       577888888888666666788888888888888888764431114555555554 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.017
                         Dynamin_M  84 kineklqklekeleelg.eskpsdeektklllqlitkfkedfkklieG 130
                                       k  ++l+k+ k  +++g  s p+   k+++l + ++ fk++++++i+ 
  gi|518652261|ref|YP_008141781.1|  65 KEYDSLAKMAKVTAKIGlVSAPNG-IKQEALNDFMNTFKKEIEEIIKS 111
                                       223455555555555554333333.88889999999999999988875 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 ?    1.9   0.0      0.22     2e+02      14      33 ..      18      37 ..       7      37 .. 0.83
   2 ?   11.4   0.8   0.00025      0.22       1      33 [.      35      67 ..      35      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.22
                                      -HHHHHHHHHHHHTTSS-HH CS
                   Glycos_trans_3N 14 taeeirfaihgilkgevtda 33
                                      ++e   +ai++i+k+ v+++
  gi|518652261|ref|YP_008141781.1| 18 SEEMYFEAIRDIFKDLVKEY 37
                                      66777899999999999876 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                                      HHHHHHHHTT.---HHHHHHHHHHHHTTSS-HH CS
                   Glycos_trans_3N  1 kdiikklrdgeeLtaeeirfaihgilkgevtda 33
                                      k++i+k+++  e  + +i ++i+++++ +++++
  gi|518652261|ref|YP_008141781.1| 35 KEYIRKKINEDEDLKKQISEVIEEFMEAKIKEY 67
                                      68********6666789************9996 PP

>> VHS  VHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   0.00011       0.1      85     136 ..      27      79 ..       7      82 .. 0.86
   2 ?   -1.4   0.0       2.2   1.9e+03      84      96 ..      94     106 ..      89     111 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHCTTTCHCS.HHHHHHHHHHHHHHH.TTT-TTGHHHHHHHHH CS
                               VHS  85 keflnelvklilekknsklakvkkkvlelleeWada.fknkpelkkisdvykl 136
                                       ++   +lvk   +kk ++++++kk++ e++ee+ +a +k+ ++l k+++v  +
  gi|518652261|ref|YP_008141781.1|  27 RDIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAkIKEYDSLAKMAKVTAK 79 
                                       5667789999999*****9*************987626999999999888765 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
                                       SHHHHHHHHHHHH CS
                               VHS  84 skeflnelvklil 96 
                                        ++f+n+++k i+
  gi|518652261|ref|YP_008141781.1|  94 LNDFMNTFKKEIE 106
                                       4567777766554 PP

>> DUF1160  Protein of unknown function (DUF1160)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.041        36      18      53 ..       5      40 ..       3      46 .. 0.69
   2 ?   10.3   1.9   0.00058      0.52      23      58 ..      35      72 ..      29      86 .. 0.74
   3 ?    0.6   0.0      0.61   5.5e+02       8      40 ..      73     102 ..      67     112 .. 0.35

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.041
                           DUF1160 18 vntelkkylkelerdetfrkklvkvlkmFiereiev 53
                                      vn++l+++++    +e + + ++ ++k  +++ i +
  gi|518652261|ref|YP_008141781.1|  5 VNEYLNNIINSAPSEEMYFEAIRDIFKDLVKEYIRK 40
                                      788888888888888887777777766666655543 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00058
                           DUF1160 23 kkyl.kelerdetfrkklvkvlkmFiereiev.ediye 58
                                      k+y+ k++++de+++k++ +v++ F+e +i+  +++++
  gi|518652261|ref|YP_008141781.1| 35 KEYIrKKINEDEDLKKQISEVIEEFMEAKIKEyDSLAK 72
                                      666525677*********************86144444 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.61
                           DUF1160   8 stpvvaKVavvntelkkylkele..rdetfrkklv 40 
                                       + +v+aK+ +v++      + ++    ++f+++++
  gi|518652261|ref|YP_008141781.1|  73 MAKVTAKIGLVSAP-----NGIKqeALNDFMNTFK 102
                                       44444444444332.....1111001223333333 PP

>> IZUMO  Izumo sperm-egg fusion, Ig domain-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.4    0.0013       1.2      12      61 ..      29      78 ..      23     113 .] 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0013
                                      HHHHHHHTHHHHHSGGHHHHHHHHHHHHHTTT---SGGGGGGSEEEHHHH CS
                             IZUMO 12 alksLeedllpselehreklleraealledlsekelaenkflgvvdeetl 61
                                       +k+L ++++ ++++++e+l++++ +++e++ e +++e   l+++++ t 
  gi|518652261|ref|YP_008141781.1| 29 IFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIKEYDSLAKMAKVTA 78
                                      578999********999999999999999999666665555444444333 PP

>> COMPASS-Shg1  COMPASS (Complex proteins associated with Set1p) component shg1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   5.2   0.00094      0.85      30      95 ..      28     107 ..       1     113 [] 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00094
                      COMPASS-Shg1  30 qnlrkkveeivesevkkdpsllfknrgkaaaliegeidrsdvykkle............egvdrivdqdlq..eepk 92 
                                       + +++ v+e++++++++d++l  +  + +++ +e++i + d++ k++            +g+++   +d     +++
  gi|518652261|ref|YP_008141781.1|  28 DIFKDLVKEYIRKKINEDEDLKKQISEVIEEFMEAKIKEYDSLAKMAkvtakiglvsapNGIKQEALNDFMntFKKE 104
                                       56788899999999999999999999999999999999999988777777777776666444443333333233334 PP

                      COMPASS-Shg1  93 lre 95 
                                       ++e
  gi|518652261|ref|YP_008141781.1| 105 IEE 107
                                       444 PP

>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.7   0.00036      0.32       2      69 ..      39     107 ..      38     112 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00036
                                       HHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEEC.TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT CS
                             DHHA1   2 eslneerkelekeleelkealaklkaeellekaeevk.gvkvlvaevgeewdagalgiaadklksklkk 69 
                                       ++  +e ++l+k++ e  e+  ++k++e+ + a+ +k + k+ ++   +++++ al    + +k+++++
  gi|518652261|ref|YP_008141781.1|  39 RKKINEDEDLKKQISEVIEEFMEAKIKEYDSLAKMAKvTAKIGLVSAPNGIKQEALNDFMNTFKKEIEE 107
                                       6778999*****************************9*8888888888****************98765 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.2    0.0007      0.62      48      75 ..      18      45 ..       2      47 .. 0.75
   2 ?    2.5   0.8      0.24   2.1e+02      12      42 ..      68      98 ..      46     112 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0007
                                      STTS-HHHHHHHHHHHHHHHHHHHHHHT CS
                            PNPase 48 edeedekeikeifkalekkvvRsrilde 75
                                       +e   + i +ifk+l k+ +R++i ++
  gi|518652261|ref|YP_008141781.1| 18 SEEMYFEAIRDIFKDLVKEYIRKKINED 45
                                      45677789****************9765 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                                      HHHHHHTTSSSHHHHHHHHHHHHHHHHHHHH CS
                            PNPase 12 erisealtiteKqeRyaaldeikekvveafa 42
                                      +++++  ++t K +  +a + ik+++++ f+
  gi|518652261|ref|YP_008141781.1| 68 DSLAKMAKVTAKIGLVSAPNGIKQEALNDFM 98
                                      3344445555555555666666666666666 PP

>> YgaB  YgaB-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   1.5      0.17   1.6e+02      44      74 ..      37      67 ..      24      70 .. 0.65
   2 ?   10.0   0.4   0.00096      0.86      50      73 ..      88     111 ..      60     112 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.17
                              YgaB 44 siqeeikrkkkeLkeiqkvFekQteevirsY 74
                                       i+++i++  +  k+i +v e+ +e  i+ Y
  gi|518652261|ref|YP_008141781.1| 37 YIRKKINEDEDLKKQISEVIEEFMEAKIKEY 67
                                      4666666666555667777777777777666 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00096
                              YgaB  50 krkkkeLkeiqkvFekQteevirs 73 
                                         k++ L++  ++F+k +ee+i+s
  gi|518652261|ref|YP_008141781.1|  88 GIKQEALNDFMNTFKKEIEEIIKS 111
                                       347899****************98 PP

>> T4_Rnl2_C  T4 RNA ligase 2 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.7     0.019        17      45      80 ..      25      64 ..       9      66 .. 0.61
   2 ?    7.0   0.2     0.007       6.3      41      63 ..      89     111 ..      70     113 .] 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.019
                                      HHHHHHHHHHHT.......T--SSSSSSHHHHHHHHHHHH CS
                         T4_Rnl2_C 45 fvqDaledfnkee....eaelsslskeeqkvikkklnkei 80
                                       ++D+ +d  ke+     +e ++l+k+  +vi++ ++ +i
  gi|518652261|ref|YP_008141781.1| 25 AIRDIFKDLVKEYirkkINEDEDLKKQISEVIEEFMEAKI 64
                                      4566666666666543355556666666666666655555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.007
                                       HHHHHHHHHHHHHHHT...T--S CS
                         T4_Rnl2_C  41 vlkafvqDaledfnkeeeaelss 63 
                                       + ++ ++D +++f+ke e++++s
  gi|518652261|ref|YP_008141781.1|  89 IKQEALNDFMNTFKKEIEEIIKS 111
                                       668889**********9998876 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 ?    7.5   6.1    0.0086       7.7      29      74 ..       2      51 ..       1      79 [. 0.67
   2 ?    5.2   4.9     0.045        40       7      53 ..      28      77 ..      26     104 .. 0.64
   3 ?    1.0   0.1      0.94   8.5e+02       9      26 ..      90     107 ..      84     112 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0086
                   Ribosomal_L18_c 29 kkqFskyikkgieaddleelykkahaaIredpvkk...ek.kekkevkke 74
                                      kk  ++y+++ i++   ee+y +a + I +d vk+   +k +e ++ kk+
  gi|518652261|ref|YP_008141781.1|  2 KKDVNEYLNNIINSAPSEEMYFEAIRDIFKDLVKEyirKKiNEDEDLKKQ 51
                                      67778999999999999999999999999999976665444555555552 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.045
                   Ribosomal_L18_c  7 rIfgkhvaeYmeeLkeedeekykkqFs....kyikkgiea.ddleelykkah 53
                                       If   v+eY+++  +ede+  kkq s    ++++++i+  d+l ++ +k+ 
  gi|518652261|ref|YP_008141781.1| 28 DIFKDLVKEYIRKKINEDED-LKKQISevieEFMEAKIKEyDSLAKM-AKVT 77
                                      58888899999988888876.44454401114555666541344443.4444 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.94
                   Ribosomal_L18_c   9 fgkhvaeYmeeLkeedee 26 
                                         +  +++m+++k+e ee
  gi|518652261|ref|YP_008141781.1|  90 KQEALNDFMNTFKKEIEE 107
                                       445566777777777666 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.053        47       5      15 ..      30      40 ..      27      41 .. 0.87
   2 ?   -0.3   0.3       1.1   9.5e+02       2      11 ..      49      58 ..      49      67 .. 0.66
   3 ?    6.1   0.1     0.011       9.4       2      13 ..     102     113 .]     102     113 .] 0.94

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.053
                            ScsC_N  5 iekivrdYLle 15
                                      ++++v++Y+++
  gi|518652261|ref|YP_008141781.1| 30 FKDLVKEYIRK 40
                                      799******87 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.1
                            ScsC_N  2 kaaiekivrd 11
                                      k++i +++++
  gi|518652261|ref|YP_008141781.1| 49 KKQISEVIEE 58
                                      5666666665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.011
                            ScsC_N   2 kaaiekivrdYL 13 
                                       k++ie+i++ +L
  gi|518652261|ref|YP_008141781.1| 102 KKEIEEIIKSTL 113
                                       89*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2195  (0.122427); expected 358.6 (0.02)
Passed bias filter:                      925  (0.0515924); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.62u 0.37s 00:00:00.99 Elapsed: 00:00:00.53
# Mc/sec: 641.30
//
Query:       gi|518652262|ref|YP_008141782.1|  [L=183]
Description: hypothetical protein FACI_IFERC00001G0901 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00025   20.6   5.1       0.02   14.5   0.6    2.6  3  DUF3098        Protein of unknown function (DUF3098)
  ------ inclusion threshold ------
      0.016   15.2   0.2      0.016   15.2   0.2    2.8  2  DUF3185        Protein of unknown function (DUF3185)
      0.053   13.8   3.7        2.5    8.4   1.4    2.5  2  DUF3040        Protein of unknown function (DUF3040)
      0.055   13.7   0.5       0.28   11.4   0.1    2.0  2  DUF2371        Uncharacterised conserved protein (DUF2371)
       0.28   11.0   1.4       0.33   10.8   0.9    1.4  1  Peptidase_M73  Camelysin metallo-endopeptidase
        3.2    7.9  11.5       0.63   10.2   2.1    3.0  3  DUF1206        Domain of Unknown Function (DUF1206)


Domain annotation for each model (and alignments):
>> DUF3098  Protein of unknown function (DUF3098)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.6   6.7e-06      0.02       6      36 ..       2      32 ..       1      39 [. 0.90
   2 ?   -3.2   0.0       2.2   6.5e+03      52      60 ..      55      63 ..      48      68 .. 0.53
   3 !    7.8   0.1   0.00079       2.4      15      65 ..     147     162 ..     137     181 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.7e-06
                           DUF3098  6 nyillliglaviilGfiLmsGggsddpnvFn 36
                                      n ++l+ig+++iilG+ + +Gg    +++Fn
  gi|518652262|ref|YP_008141782.1|  2 NKKILAIGIVMIILGIAMAAGGTEYFESSFN 32
                                      7789*****************9998888888 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.2
                           DUF3098 52 vliGfviei 60
                                      + +G+++ i
  gi|518652262|ref|YP_008141782.1| 55 IKTGYLVLI 63
                                      334444333 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00079
                           DUF3098  15 aviilGfiLmsGggsddpnvFnediFsfrRirlAPivvliGfvieiyaIlk 65 
                                       ++ i+Gfi+m+                                   y+ +k
  gi|518652262|ref|YP_008141782.1| 147 LIGIIGFIVMI-----------------------------------YGAIK 162
                                       33355555555...................................54444 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   5.5e-06     0.016       3      30 ..       8      35 ..       7      47 .. 0.90
   2 ?   -1.2   5.5      0.71   2.1e+03      38      56 ..     135     153 ..     118     156 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.5e-06
                           DUF3185  3 iGiiLlvaGivLlvfGynasdSlgsqvs 30
                                      iGi+++++Gi+++  G + ++S  ++vs
  gi|518652262|ref|YP_008141782.1|  8 IGIVMIILGIAMAAGGTEYFESSFNSVS 35
                                      9****************99999888887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.71
                           DUF3185  38 tdktlllligGgvaaivGl 56 
                                        d+   l +gG+   i+G 
  gi|518652262|ref|YP_008141782.1| 135 FDTMAGLAVGGVLIGIIGF 153
                                       4444444455555567775 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0091        27      52      66 ..       6      20 ..       3      37 .. 0.75
   2 ?    8.4   1.4   0.00083       2.5      59      82 ..     137     160 ..     117     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0091
                           DUF3040 52 fvaGllllvlGvaaa 66
                                      +++G+++++lG+a a
  gi|518652262|ref|YP_008141782.1|  6 LAIGIVMIILGIAMA 20
                                      455888888886554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00083
                           DUF3040  59 lvlGvaaaavvlgvvGfvvmlagv 82 
                                        ++G+a+  v++g++Gf+vm+ g+
  gi|518652262|ref|YP_008141782.1| 137 TMAGLAVGGVLIGIIGFIVMIYGA 160
                                       6789888889**********9886 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   9.4e-05      0.28      43      79 ..       5      41 ..       2      67 .. 0.75
   2 ?    0.1   0.0      0.28   8.3e+02      45      62 ..     143     160 ..     135     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.4e-05
                           DUF2371 43 vlllGllvllvGiamavlgywpkkaklaseeksssss 79
                                      +l++G++++++Giama  g ++ +++ +s ++s+ + 
  gi|518652262|ref|YP_008141782.1|  5 ILAIGIVMIILGIAMAAGGTEYFESSFNSVSNSHYTY 41
                                      6899*************99888875555544444433 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.28
                           DUF2371  45 llGllvllvGiamavlgy 62 
                                       + G+l+ ++G  + + g 
  gi|518652262|ref|YP_008141782.1| 143 VGGVLIGIIGFIVMIYGA 160
                                       456666666655555554 PP

>> Peptidase_M73  Camelysin metallo-endopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.9   0.00011      0.33       3      89 ..       3      86 ..       1     106 [. 0.59

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                     Peptidase_M73  3 kkklgmgvitaalglsligGGtyayfsDset.annsfaa.GtldlsvdptviidvknlkPGDtvtrefklenkGtLdik 79
                                      kk l++g++   lg+++ +GGt  + s  +  +n++++   t  l+v + +      +k G  v+ e ++ ++G ++ +
  gi|518652262|ref|YP_008141782.1|  3 KKILAIGIVMIILGIAMAAGGTEYFESSFNSvSNSHYTYnATTALNVSNPI-----HIKTGYLVLIEGSVGDSGLVTNS 76
                                      6779******************64433333303333322123334443222.....35666666666666666666666 PP

                     Peptidase_M73 80 kvlleteyev 89
                                      ++++ t+ + 
  gi|518652262|ref|YP_008141782.1| 77 NLSMVTNLTA 86
                                      6666666555 PP

>> DUF1206  Domain of Unknown Function (DUF1206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   3.0       1.3   3.8e+03      51      64 ..       7      20 ..       5      24 .. 0.65
   2 ?    2.1   0.0     0.071   2.1e+02      20      46 ..      85     111 ..      78     115 .. 0.86
   3 ?   10.2   2.1   0.00021      0.63      34      61 ..     133     160 ..     124     162 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.3
                           DUF1206 51 lvglgllgyglwql 64
                                      ++g++++++g+ ++
  gi|518652262|ref|YP_008141782.1|  7 AIGIVMIILGIAMA 20
                                      67777777777655 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.071
                           DUF1206  20 aalggggssasgsdgalatlleqpfGr 46 
                                       +al++ +++ ++s++ ++ +l++p+G+
  gi|518652262|ref|YP_008141782.1|  85 TALKSHEEKVTDSSDGIELFLGLPAGT 111
                                       67888888888***************8 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.00021
                           DUF1206  34 galatlleqpfGrvllglvglgllgygl 61 
                                       g + t++++ +G+vl+g++g+++++yg+
  gi|518652262|ref|YP_008141782.1| 133 GQFDTMAGLAVGGVLIGIIGFIVMIYGA 160
                                       6678999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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 0.29s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1214.53
//
Query:       gi|518652263|ref|YP_008141783.1|  [L=369]
Description: hypothetical protein FACI_IFERC00001G0902 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.067   12.1  55.9         87    1.9  56.1    3.0  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 ?    1.9  56.1    0.0048        87       9     273 ..      30     333 ..      20     350 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.0048
                             MFS_1   9 alarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfass 84 
                                       ++ ++   +a+ +  + ++l+++  e  +ll++ ++g +v+ +++++++  +G  r+ ll+++++a+ ++++ +  +
  gi|518652263|ref|YP_008141783.1|  30 FFLMD---FAFFInDIVNTLHFTYIESFILLGIPFIGRMVTPFVYSYVGK-IGVPRLALLAITSMAIISFIMGY-ET 101
                                       33333...3333337899********99********************76.7****999999999999788888.77 PP

                             MFS_1  85 lw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg.......... 149
                                        +  l+++r++ G++ g++++a++ + +    ++  g+ +g +++g+ +Gai+ ++lg++ + s +g          
  gi|518652263|ref|YP_008141783.1| 102 TFiELFASRFIIGIFFGLATSAAIEVSSITGDRKIIGLTMGGWAIGWLMGAIFFMILGSWELvSIAGivfapallfs 178
                                       8879***********96666666666665555588899999999999999999999988766355556666666666 PP

                             MFS_1 150 ............Wravfyilaivsllafvlfllllpeepperkrkspkeee..............kgtgpaplvp.. 198
                                                   ++  f i  ++ +l++   + +l + p+  +++s +e                +           
  gi|518652263|ref|YP_008141783.1| 179 rkhnvispmlkkFHFDFSIKVFLVFLLGFTPAYVLEVVPSYLGPSSFTESIiaysiavfaylllpALII-----Rfs 250
                                       666666666666444455555555555443334444444444444444443444433333222221111.....111 PP

                             MFS_1 199 awkallkdpvlwillialllfffgfsg...............lltllplylqevlglsglllaglllallalvgail 260
                                       + k l++     +l+i+++++ ++f++               + +llp++    ++++ +  +g  + ++a++g+i+
  gi|518652263|ref|YP_008141783.1| 251 LKKTLFS-----SLIIVAISGIIFFATtnivfavlftafglgVNSLLPII-SRNMDID-ANKIGPSMNFSAVAGFIF 320
                                       1112222.....22222222211111111111111112222244444443.4445555.566666666666666555 PP

                             MFS_1 261 allagrlsdrlgr 273
                                        ++++     l++
  gi|518652263|ref|YP_008141783.1| 321 PVVLTIGNEALNS 333
                                       4444443343444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      234  (0.0130515); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2401.61
//
Query:       gi|518652264|ref|YP_008141784.1|  [L=416]
Description: hypothetical protein FACI_IFERC00001G0903 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-67  228.3   0.6    1.1e-36  126.9   0.0    2.1  2  Aconitase  Aconitase family (aconitate hydratase)
    6.6e-06   25.1   0.0    9.2e-06   24.6   0.0    1.1  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.9   0.0   1.2e-40   1.1e-36      84     297 ..      74     274 ..      59     284 .. 0.92
   2 !   99.4   1.0   2.6e-32   2.3e-28     331     461 .]     281     408 ..     274     408 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 1.2e-40
                         Aconitase  84 keryefLksaakafgi.rvvppg.qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqp 158
                                       ++r+++L++  ++ gi +++++g  GI H+ + E+g+  pg ++  tDSHT   g++ +l+ G G+ e+ +++++ +
  gi|518652264|ref|YP_008141784.1|  74 ANRVNRLRKLVNRWGItDFYDVGrGGISHVLGGEKGWFRPGSLIANTDSHTIATGAFNTLGRGLGTPEIMNIIATGK 150
                                       568999********99679****778*************************************************** PP

                         Aconitase 159 lelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfp 235
                                       +++ + ++++v+l+ +++ g++akD+  ++++ ++  +v +k +Ef G+g+ sL++++r +i+ M+aEv A  ++fp
  gi|518652264|ref|YP_008141784.1| 151 TWFLLGETLKVNLENSMRLGTSAKDVFFYMASVIG--DVPNKNIEFLGNGIYSLNIDQRSSISTMCAEVSAEFAVFP 225
                                       ********************************997..589************************************* PP

                         Aconitase 236 vdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrP 297
                                        d+ + +Y+   +r + +     y  a+       d+daey +++++d+ ++ep+va p r 
  gi|518652264|ref|YP_008141784.1| 226 EDKVLRQYMV--ERGYGN-----YRPAA------PDRDAEYVNEVNIDMGKIEPMVALPDRI 274
                                       **********..775555.....55544......5999********************9875 PP

  == domain 2  score: 99.4 bits;  conditional E-value: 2.6e-32
                         Aconitase 331 gtklkdgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfev 407
                                         ++ ++++d+a++gSC+N++++d+r +a+ ++     ++k++++v+++v+P+S+++ +++ + G+ +++ k  + v
  gi|518652264|ref|YP_008141784.1| 281 VSEIGKVEIDVAVVGSCANGRLSDLRDVAEAVK-----NKKINDNVRFIVTPASKEIYEEALKLGYIDTIIKSNAMV 352
                                       56788999*************************.....99************************************* PP

                         Aconitase 408 vgagCstCig.nsdrleegeaivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                       +++ C+ C+g   + + +g++++ss++RNF+gR+g+++   yLaS   v+ +A++G
  gi|518652264|ref|YP_008141784.1| 353 TNPTCGACLGgHMGVVGNGDTVLSSTTRNFKGRMGAGGARiYLASARSVAISAING 408
                                       **********999999******************9776666*************98 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     1e-09   9.2e-06     288     358 ..     286     358 ..     253     383 .. 0.88

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-09
                            DUF521 288 eekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtCm 358
                                       + ++d+ ++G c    l++lr++ae++k+kk +++v+++vt +s+e++eea +lg+++++ k+++ v + tC 
  gi|518652264|ref|YP_008141784.1| 286 KVEIDVAVVGsCANGRLSDLRDVAEAVKNKKINDNVRFIVTpASKEIYEEALKLGYIDTIIKSNAMVTNPTCG 358
                                       55778777775788899***********************956888**************************5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2968.15
//
Query:       gi|518652265|ref|YP_008141785.1|  [L=167]
Description: 3-isopropylmalate dehydratase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-11   44.0   0.0    4.9e-11   43.1   0.0    1.4  2  Aconitase_C    Aconitase C-terminal domain
    0.00095   18.9   0.7      0.062   12.9   0.7    2.3  1  Aconitase_2_N  Aconitate hydratase 2 N-terminus


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.0   5.4e-15   4.9e-11      73     128 ..      51     104 ..      12     106 .. 0.74
   2 ?   -3.2   0.0       1.1   9.8e+03      32      54 ..     115     137 ..     113     150 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5.4e-15
                                       T--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEE CS
                       Aconitase_C  73 gaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLplef 128
                                       ++++ +iagknfG+GSSR  AA   + lGi  v+aeS +  f +n+++ gl  le+
  gi|518652265|ref|YP_008141785.1|  51 NSDI-IIAGKNFGTGSSRP-AADNIKNLGISCVLAESLNGLFLRNSVNSGLPSLEV 104
                                       4455.5566*********6.999***************************988775 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.1
                                       CCGGTTTCCCCTTTSBBSEEEET CS
                       Aconitase_C  32 tianiglgnelveekrankttdl 54 
                                        i+ i++ ++ v +k+ +k+ ++
  gi|518652265|ref|YP_008141785.1| 115 NIVAIDFSSNTVMDKETGKVMKF 137
                                       56667777777777777776655 PP

>> Aconitase_2_N  Aconitate hydratase 2 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.7   6.9e-06     0.062      96     175 ..      81     162 ..       9     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.9e-06
                                       EEEEEE-HHHHHHHHHTT-EEEE--..-TT--TT-EEEEETTTTEEEETT--EEEE---S-TCHHHHHHHTSHHHHH CS
                     Aconitase_2_N  96 vlGgkiaPiFfntvedsGalpiead..vskletGdvieikpkegkikkeegevvsefklkpetlldevraggripli 170
                                       vl  ++  +F+    +sG   +e++     +++G+++ i+  +++++++e   v++fk  p  l++ +  gg i+++
  gi|518652265|ref|YP_008141785.1|  81 VLAESLNGLFLRNSVNSGLPSLEVHgiSGIVKEGNIVAIDFSSNTVMDKETGKVMKFKPLPAFLMEIIDNGGIINIL 157
                                       44555666676666667644444331145689***************9888899999999****************9 PP

                                       HHHHH CS
                     Aconitase_2_N 171 igrgl 175
                                         +gl
  gi|518652265|ref|YP_008141785.1| 158 KNKGL 162
                                       88887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1274.52
//
Query:       gi|518652266|ref|YP_008141786.1|  [L=389]
Description: resistance protein NorA [Ferroplasma acidarmanus fer1]
Scores for 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-39  133.6  77.8    5.7e-36  124.2  43.4    2.0  2  MFS_1          Major Facilitator Superfamily
    2.2e-09   36.7  15.3    2.2e-09   36.7  15.3    2.4  2  Sugar_tr       Sugar (and other) transporter
  ------ inclusion threshold ------
      0.036   12.6  45.6     0.0037   15.9  29.2    3.0  3  MFS_2          MFS/sugar transport protein
       0.16   12.1   0.3       0.16   12.1   0.3    3.7  5  Col_cuticle_N  Nematode cuticle collagen N-terminal domain
       0.43    9.4  40.6      0.085   11.7   8.8    3.4  4  MFS_1_like     MFS_1 like family
        9.6    5.8   6.7        2.1    7.9   1.7    2.2  2  DUF1155        Protein of unknown function (DUF1155)


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 !  124.2  43.4   1.9e-39   5.7e-36       6     323 ..      15     320 ..      10     326 .. 0.81
   2 !   23.1  26.4     1e-08     3e-05      17     171 ..     225     377 ..     221     382 .. 0.90

  Alignments for each domain:
  == domain 1  score: 124.2 bits;  conditional E-value: 1.9e-39
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.f 81 
                                       +l+al+++  +pal  ++++d ++++ e+g+l+t++++g av+++++G+ls  +G + + l+gll+ +++ ++ + +
  gi|518652266|ref|YP_008141786.1|  15 ALYALNWMDMAPALE-YIKTDMNLTVVELGTLVTAFYVGIAVFQVLGGYLSSYIGDKTTSLIGLLFVSIF-AITSgL 89 
                                       567777777899999.******************************************************.555556 PP

                             MFS_1  82 asslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyila 158
                                       + +++ l+v+r+++Gl a+++f+ +++l+a ++p+++ ++ ig+++++f++G  +g +  ++l ++ g+r +f+i++
  gi|518652266|ref|YP_008141786.1|  90 SVNFTELIVSRFFAGLSAALFFSPALSLLASIVPENKYAFHIGIYNGAFNVGGGVGIIGWAILDQYMGYRIPFIIAG 166
                                       67777***************************************************99999999************* PP

                             MFS_1 159 ivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg...lltllpl 232
                                       +++l +f + ++l++  +  + +ks++            + +k++++++ +  +l+a+++++ ++ +   l +++  
  gi|518652266|ref|YP_008141786.1| 167 VLTLALFFVLVFLFRNIENIKTNKSDIFA----------S-FKKVFSNRII--ILVAFIGIA-AMVAetiLGQFFVY 229
                                       ******88555555555555555544444..........6.********66..555555553.44445646666655 PP

                             MFS_1 233 ylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl 309
                                       y  e  ++s   lag +++l+ l+g+ +++l+g+   r++    +  +l++ ++++l+l+l+++ + +++++++ + 
  gi|518652266|ref|YP_008141786.1| 230 Y-LESIKYS-IDLAGSISSLYLLIGFLGGVLGGYHFSRTKY--KIGTFLAINIVLSLLLILIGFVHYYIFIIIIAIA 302
                                       6.*******.789999999999999999******9999666..9999999999999999999999555555542222 PP

                             MFS_1 310 ...iGf.glgfvfpslla 323
                                          i++ g++++++++ +
  gi|518652266|ref|YP_008141786.1| 303 mgmITVyGMSITYTLVRY 320
                                       233444444444544444 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 1e-08
                             MFS_1  17 palplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalglllll.fasslw.lllv 90 
                                        ++  ++ e+  +s + +g + +ly l  +++ +++G+   r   +  ++l+  ++++l  l+l+ f  +++ ++++
  gi|518652266|ref|YP_008141786.1| 225 QFFV-YYLESIKYSIDLAGSISSLYLLIGFLGGVLGGYHFSRTKYKIgTFLAINIVLSLL-LILIgF-VHYYiFIII 298
                                       5566.6779999*******************************9****************.555558.6667699** PP

                             MFS_1  91 lrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvl 167
                                         + +G+ +  ++++ ++l++ ++ ++  ++ ++++++   l a+  p++  +++s+++++++++ ++i++l+++ l
  gi|518652266|ref|YP_008141786.1| 299 IAIAMGMITVYGMSITYTLVRYLARRDLVSLTLSFVNTLQLLVAVAVPIIFTIIVSQYNYELAWVSMGILGLIFVPL 375
                                       *************************************************************************9554 PP

                             MFS_1 168 flll 171
                                         ++
  gi|518652266|ref|YP_008141786.1| 376 --IF 377
                                       ..33 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7  15.3   7.4e-13   2.2e-09      44     191 ..      38     179 ..      12     181 .. 0.92
   2 ?   -0.0  23.2       0.1     3e+02     233     433 ..     188     373 ..     179     380 .. 0.72

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 7.4e-13
                                       ...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHH CS
                          Sugar_tr  44 ssvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlas 120
                                       + v +g +v +f+vG ++ ++++g+l+ ++G k + li+ ++++i a+ ++++    ++  liv+R+++G+++ l+ 
  gi|518652266|ref|YP_008141786.1|  38 TVVELGTLVTAFYVGIAVFQVLGGYLSSYIGDKTTSLIGLLFVSIFAITSGLSV---NFTELIVSRFFAGLSAALFF 111
                                       67889*************************************************...******************99 PP

                                       HHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS CS
                          Sugar_tr 121 vlvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllfl 191
                                         +  +++ i p+++  + +++y+ a  +G  v++i  ++l+++ +   +ri++ ++ v++l+l+++l+fl
  gi|518652266|ref|YP_008141786.1| 112 SPALSLLASIVPENKYAFHIGIYNGAFNVGGGVGIIGWAILDQYMG---YRIPFIIAGVLTLALFFVLVFL 179
                                       999999999**************************999999***99...*******************997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.1
                                       HHHH........HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 233 aeqeee...kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksllvtiivgvvnfvatfv 306
                                        +   +    as k+++s++ +   ++ig++ +++    G  ++ yy  +i  +++l  s  ++ ++  + f+  + 
  gi|518652266|ref|YP_008141786.1| 188 TN---KsdiFASFKKVFSNRIIILVAFIGIAAMVAETILG-QFFVYYLESIKYSIDLAGS--ISSLYLLIGFLGGVL 258
                                       23...12348899******99999****************.88999**************..555555555555555 PP

                                       HHHHHHHS-SHH....HHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHS CS
                          Sugar_tr 307 aiflvdrfGRRt....llllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElf 379
                                       +     +f+R +    ++l   ++ +++++++      +v+    + i++i+  + +i +++++++ +   lv  l+
  gi|518652266|ref|YP_008141786.1| 259 GG---YHFSRTKykigTFLAINIVLSLLLILI-----GFVHY--YIFIIIIAIAMGMITVYGMSITYT---LVRYLA 322
                                       53...455544300003344444444444444.....45555..4789999999********998755...577799 PP

                                       HTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHH CS
                          Sugar_tr 380 pqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifv 433
                                         ++ s++l+++ +++ l+ +++ ++f+ii+++++   + l ++++ +l++ifv
  gi|518652266|ref|YP_008141786.1| 323 RRDLVSLTLSFVNTLQLLVAVAVPIIFTIIVSQYN---YELAWVSMGILGLIFV 373
                                       ***********************************...5556666666666665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   5.5     0.024        73     259     345 ..      40     124 ..      25     128 .. 0.82
   2 ?   15.9  29.2   1.2e-06    0.0037      79     323 ..      76     308 ..      71     312 .. 0.75
   3 ?   -0.5  16.2      0.12   3.5e+02      75     187 ..     275     377 ..     260     386 .. 0.63

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                             MFS_2 259 saasvfllvvtisallgiplwqplakrlgkkntyllgalltivllvlvlllqpsnlllflvllviagfgvgvaallp 335
                                        +  ++ ++++++ +++ +l  +l + +g k+t l+g+l++ ++ +   l    n + ++v  + ag++++++++ +
  gi|518652266|ref|YP_008141786.1|  40 VELGTLVTAFYVGIAVFQVLGGYLSSYIGDKTTSLIGLLFVSIFAITSGLS--VNFTELIVSRFFAGLSAALFFSPA 114
                                       566778899999999******************999999887776666555..899999999999999999999999 PP

                             MFS_2 336 wsmladvvDy 345
                                        s+la +v +
  gi|518652266|ref|YP_008141786.1| 115 LSLLASIVPE 124
                                       9999988755 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 1.2e-06
                             MFS_2  79 avsiillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaailaf 155
                                       ++ ++ +f+  + + s  f  l+v+ +   +  +lf  p  sl++ + ++++    +  +   ++v+ggv++  +  
  gi|518652266|ref|YP_008141786.1|  76 GLLFVSIFAITS-GLSVNFTELIVSRFFAGLSAALFFSPALSLLASIVPENKYAFHIGIYNGAFNVGGGVGI--IGW 149
                                       455555666555.566999999999999999*********************999******99999999864..444 PP

                             MFS_2 156 llvlilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklslleqlkevfrnraflillll 232
                                       +++  +        gy+i  +i  +L+l++++++v+ +++ ++        +++k  ++  +k+vf+nr  ++++++
  gi|518652266|ref|YP_008141786.1| 150 AILDQY-------MGYRIPFIIAGVLTLALFFVLVFLFRNIENI-------KTNKSDIFASFKKVFSNRIIILVAFI 212
                                       443444.......47************************99877.......9************************* PP

                             MFS_2 233 fllaalalgvlnglllYyl...tyvlg.ngsaasvfllvvtisallgiplwqplakrlgkk.nt.yllgalltivll 303
                                       +++a++a ++l   ++Yyl   +y ++ +gs  s++ll+ +++++lg   +++ + ++g   ++ ++l++ll ++++
  gi|518652266|ref|YP_008141786.1| 213 GIAAMVAETILGQFFVYYLesiKYSIDlAGSISSLYLLIGFLGGVLGGYHFSRTKYKIGTFlAInIVLSLLLILIGF 289
                                       ******************72225778877777777777778888888888888888888553221233333333444 PP

                             MFS_2 304 vlvlllqpsnlllflvllvi 323
                                       v  +++    +++++ + ++
  gi|518652266|ref|YP_008141786.1| 290 VHYYIF-IIIIAIAMGMITV 308
                                       444444.3333333333333 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.12
                             MFS_2  75 aiilavsiillftppelsqsakfiwllvtyillrilytlfeipyvslvpvltkdydeRtsltsvrsflsvlggvlaa 151
                                       ai +++s++l+ +         f+ ++++ i+ +i++ ++++  +s++++l  +y  R +l s +  + +   +l+a
  gi|518652266|ref|YP_008141786.1| 275 AINIVLSLLLILIG--------FVHYYIFIIIIAIAMGMITVYGMSITYTL-VRYLARRDLVSLTLSFVNTLQLLVA 342
                                       44444444444443........78899999999999999999999999999.6666666666666666666666666 PP

                             MFS_2 152 ilafllvlilgglkserkgylifaliialLmllgvi 187
                                       + +++++ i  +  + + ++  ++++  l+++ +++
  gi|518652266|ref|YP_008141786.1| 343 VAVPIIFTIIVSQYNYELAWVSMGIL-GLIFVPLIF 377
                                       66666666655525555555544444.444444444 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.6       4.8   1.4e+04       5      12 ..      79      86 ..      75      87 .. 0.60
   2 ?   12.1   0.3   5.4e-05      0.16       5      42 ..     163     200 ..     162     203 .. 0.92
   3 ?   -2.8   0.1       2.3     7e+03      12      25 ..     281     294 ..     278     296 .. 0.61
   4 ?   -2.2   0.9       1.5   4.5e+03      10      22 ..     295     307 ..     293     314 .. 0.73
   5 ?   -2.1   0.5       1.5   4.3e+03      13      22 ..     340     349 ..     329     356 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 4.8
                     Col_cuticle_N  5 alStvail 12
                                       +S++ai+
  gi|518652266|ref|YP_008141786.1| 79 FVSIFAIT 86
                                      45666665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.4e-05
                     Col_cuticle_N   5 alStvailsslitlpsiyndiqsfqsevldemdefktr 42 
                                       ++++v +l+++++l +++  i +++++ +d +++fk++
  gi|518652266|ref|YP_008141786.1| 163 IIAGVLTLALFFVLVFLFRNIENIKTNKSDIFASFKKV 200
                                       5899**************************99999975 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                     Col_cuticle_N  12 lsslitlpsiyndi 25 
                                         +li +++++ +i
  gi|518652266|ref|YP_008141786.1| 281 SLLLILIGFVHYYI 294
                                       34566666666666 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 1.5
                     Col_cuticle_N  10 ailsslitlpsiy 22 
                                        i+++ i++++i 
  gi|518652266|ref|YP_008141786.1| 295 FIIIIAIAMGMIT 307
                                       4777788888875 PP

  == domain 5  score: -2.1 bits;  conditional E-value: 1.5
                     Col_cuticle_N  13 sslitlpsiy 22 
                                        + +++p+i+
  gi|518652266|ref|YP_008141786.1| 340 LVAVAVPIIF 349
                                       4566777776 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 ?   11.7   8.8   2.8e-05     0.085     255     370 ..      35     148 ..      27     164 .. 0.85
   2 ?    6.0  17.5    0.0015       4.4     164     268 ..     146     247 ..     144     316 .. 0.68
   3 ?   -6.6  10.9         6   1.8e+04     257     336 ..     275     354 ..     244     364 .. 0.59
   4 ?    2.1   1.6     0.023        69      25      80 ..     320     375 ..     315     382 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.8e-05
                        MFS_1_like 255 lgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllw 331
                                       ++ +   lG+lv+   v+  ++ +++ +l  ++G  +  +i+ll++ +  +  ++  n+  +++  ++ g+s +l++
  gi|518652266|ref|YP_008141786.1|  35 MNLTVVELGTLVTAFYVGIAVFQVLGGYLSSYIGDKTTSLIGLLFVSIFAITSGLSVNFTELIVSRFFAGLSAALFF 111
                                       5566667899999999998899999999**************998888777777779******************** PP

                        MFS_1_like 332 aaaveyvskiapksleatgqgllsglyfglGralGsliG 370
                                       + a +  + i+p++  a+ +g+++g+ f +G+++G +iG
  gi|518652266|ref|YP_008141786.1| 112 SPALSLLASIVPENKYAFHIGIYNGA-FNVGGGVG-IIG 148
                                       *************************9.999*9999.445 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0015
                        MFS_1_like 164 itGili.dhysvnllp.ysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvalilg 238
                                       i+G++i d+y    +p + a +++la+++v+++l+  i      + k++   +  +++++++n+ +i++ ++ +   
  gi|518652266|ref|YP_008141786.1| 146 IIGWAIlDQYMGYRIPfIIAGVLTLALFFVLVFLFRNI-----ENIKTNKSDIFASFKKVFSNRIIILVAFIGIAAM 217
                                       45665414444433445445556666666666666222.....222333344447899****998888888888888 PP

                        MFS_1_like 239 mswgiienFlflYLkelgasntllGslval 268
                                       ++  i+++F+  YL++ ++s  l+Gs+  l
  gi|518652266|ref|YP_008141786.1| 218 VAETILGQFFVYYLESIKYSIDLAGSISSL 247
                                       8999********************997655 PP

  == domain 3  score: -6.6 bits;  conditional E-value: 6
                        MFS_1_like 257 asntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaii..enawlvlpievLhgisfgllw 331
                                       a n++l+ l++l     +  ++f   +   +G++++  ++++ + +r+l    +    +++v  +++L ++++ +++
  gi|518652266|ref|YP_008141786.1| 275 AINIVLSLLLILIG--FVHYYIFIIIIAIAMGMITVYGMSITYTLVRYLARRDLvsLTLSFVNTLQLLVAVAVPIIF 349
                                       33334443333322..2333444445556788888888888888888887766645556677778888888888888 PP

                        MFS_1_like 332 aaave 336
                                        ++v+
  gi|518652266|ref|YP_008141786.1| 350 TIIVS 354
                                       87775 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.023
                        MFS_1_like  25 ylkskglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl 80 
                                       yl  ++l      ++ ++  l++++ p i++ ++ +++ + + v++++l  + + l
  gi|518652266|ref|YP_008141786.1| 320 YLARRDLVSLTLSFVNTLQLLVAVAVPIIFTIIVSQYNYELAWVSMGILGLIFVPL 375
                                       9999999999999*************************999999998876655444 PP

>> DUF1155  Protein of unknown function (DUF1155)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.7   0.00072       2.1       3      19 ..     103     119 ..     101     121 .. 0.93
   2 ?   -0.4   0.2      0.27     8e+02       6      18 ..     328     340 ..     326     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00072
                           DUF1155   3 ATLSTTLSFEPPLSLLA 19 
                                       A LS  L F P LSLLA
  gi|518652266|ref|YP_008141786.1| 103 AGLSAALFFSPALSLLA 119
                                       78**************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                           DUF1155   6 STTLSFEPPLSLL 18 
                                       S TLSF   L LL
  gi|518652266|ref|YP_008141786.1| 328 SLTLSFVNTLQLL 340
                                       88****9999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1336  (0.0745161); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 2698.59
//
Query:       gi|518652267|ref|YP_008141787.1|  [L=202]
Description: hypothetical protein FACI_IFERC00001G0906 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1347.06
//
Query:       gi|518652268|ref|YP_008141788.1|  [L=502]
Description: hypothetical protein FACI_IFERC00001G0907 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.3   0.0      0.098   12.8   0.0    1.8  1  Sod_Cu    Copper/zinc superoxide dismutase (SODC)


Domain annotation for each model (and alignments):
>> Sod_Cu  Copper/zinc superoxide dismutase (SODC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.5e-06     0.098      33      94 ..     427     490 ..     389     501 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.5e-06
                                       SS-STEEEEEEEESSTTT.TTTTGGG.-SB-STT-.CSSTTTTTCS-TTEEEEEEESTTSE.EEE CS
                            Sod_Cu  33 glppggkhgfHiHengdc.sagfksa.gghfnptgkkhgapndeerhaGDLgnievdadgt.akl 94 
                                       g  p+  h + +He+gdc + +f++  g h np+  +    ++ +    D+  +e +++++ a++
  gi|518652268|ref|YP_008141788.1| 427 GFIPE-YHTYDVHEFGDClEFHFQQPyGTHTNPYTDPMTYTSTFTITNSDMKPVEFENQQYkAQI 490
                                       55564.6***********55567766699999988777765666778888888888555442444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); 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: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.49
# Mc/sec: 3109.99
//
Query:       gi|518652269|ref|YP_008141789.1|  [L=236]
Description: serine/threonine protein phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-24   86.6   0.0    2.5e-24   86.3   0.0    1.1  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
    2.7e-13   50.9   2.7    4.7e-13   50.1   2.7    1.4  1  Metallophos    Calcineurin-like phosphoesterase
    5.8e-05   21.6   0.4     0.0012   17.2   0.1    2.1  2  FBPase_2       Firmicute fructose-1,6-bisphosphatase


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 !   86.3   0.0   4.3e-28   2.5e-24       1     164 [.       8     199 ..       8     200 .. 0.89

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 4.3e-28
                     Metallophos_2   1 MklaiiSDlHsnldaleavlealkevgvdaiihaGDl..eeeepevleellelapvlaVrGNnD............. 62 
                                       Mkl+++SD+H+n+dal+ v+++ ++   d++i++GD+  ++ ep+ + ++l+ +  + + GN+D             
  gi|518652269|ref|YP_008141789.1|   8 MKLLVLSDIHGNFDALQSVYNK-EQY--DKMIFLGDAvdYGPEPDRVLDFLKANSDINILGNHDnavltgsscncsf 81 
                                       ********************99.555..********99*************************************** PP

                     Metallophos_2  63 ..........eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl......gvkdalaellke..aeegsdv 121
                                                 +++  + + ++   l + ++   + e++g+k+++ H +p+        +++ ++++++    +++d+
  gi|518652269|ref|YP_008141789.1|  82 dmlelsdytrDNISMKLLDKNDMALLKTFKLNTDTEIDGKKFYMAHASPYnnldgyLFANEAEKVFRDkpFFDNHDY 158
                                       ***9998876666778888888888899999999999***********99*9998755566666666666689999* PP

                     Metallophos_2 122 vvcGHtHvpevekeggvlvvnPGsvgeprdgdpe.tyaildtde 164
                                       ++ GHtH   v +     ++nPGsvg+prd   + +ya++dt++
  gi|518652269|ref|YP_008141789.1| 159 ILIGHTHFMMVYRN---KIINPGSVGQPRDFTGKpSYAVIDTET 199
                                       *********99999...8**********9766666*******97 PP

>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   2.7   7.9e-17   4.7e-13       1     202 [.       8     165 ..       8     167 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 7.9e-17
                                       EEEEEEESBTBTTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSSHHHHHHHHHHHHHHHHTSEEEEEC-TTSCH CS
                       Metallophos   1 lrilvigDlHlalgggqlddllkllddllreekpdlvllaGDlvdrgdlekellellaalvkypipvylllGNHegf 77 
                                       +++lv++D+H     g++d+l+ ++++   e + d ++++GD vd g+ + ++l++l+a  +     + +lGNH+  
  gi|518652269|ref|YP_008141789.1|   8 MKLLVLSDIH-----GNFDALQSVYNK---E-QYDKMIFLGDAVDYGPEPDRVLDFLKANSD-----INILGNHD-- 68 
                                       799*******.....**********44...4.99999999*******99999****999999.....********.. PP

                                       HHHHHHHHHHHHHHHHHHEHHHCEEETSEEEEEETTE.EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH CS
                       Metallophos  78 eeellnkygylgifsepwrsdaevfnnlplaslgsgs.lkvlllhGgspellvsldklgslnleleapepgdewlkd 153
                                                       +  s++  f+ l l+++  ++    ll++++       l k  +ln ++e++         
  gi|518652269|ref|YP_008141789.1|  69 ---NA---------VLTGSSCNCSFDMLELSDYTRDNiSMKLLDKND-----MALLKTFKLNTDTEIDG-------- 120
                                       ...11.........44556789999*******999998666666776.....56777777777777665........ PP

                                       HHHHTTCSEEEEEESSESS.CSSSCSCCHHHHH.....HHHHHTT...ESEEEEESSS CS
                       Metallophos 154 lekrekadwvivlgHsply.rgsgylfgdeale.....dllkkyg...vdlvisGHtH 202
                                                ++ ++H  +y +  gylf++ea +     +          d+++ GHtH
  gi|518652269|ref|YP_008141789.1| 121 --------KKFYMAHASPYnNLDGYLFANEAEKvfrdkP-----FfdnHDYILIGHTH 165
                                       ........578999*****98889999998888444433.....3444679999**** PP

>> FBPase_2  Firmicute fructose-1,6-bisphosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.0    0.0043        26      36      52 ..      12      28 ..       5      31 .. 0.87
   2 !   17.2   0.1     2e-07    0.0012     183     224 ..      31      71 ..      22      84 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0043
                          FBPase_2 36 flsDiHGeyeafshvlk 52
                                       lsDiHG+++a++ v +
  gi|518652269|ref|YP_008141789.1| 12 VLSDIHGNFDALQSVYN 28
                                      69**********99876 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 2e-07
                          FBPase_2 183 avdklhivGDiyDRGpeadkildeLmkyhsvdiqWGNHDilW 224
                                         dk+  +GD  D Gpe+d++ld L + ++++i  GNHD   
  gi|518652269|ref|YP_008141789.1|  31 QYDKMIFLGDAVDYGPEPDRVLDFLKANSDINI-LGNHDNAV 71 
                                       569999***********************9999.6****654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1536.54
//
Query:       gi|518652270|ref|YP_008141790.1|  [L=118]
Description: ArsR family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   47.8   0.3    1.6e-12   47.1   0.3    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
    7.7e-06   25.9   0.0    1.1e-05   25.4   0.0    1.2  1  HTH_20          Helix-turn-helix domain
    0.00015   21.6   0.1    0.00029   20.7   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00098   19.0   0.1     0.0016   18.3   0.1    1.3  1  MarR            MarR family
      0.004   16.7   0.1     0.0074   15.8   0.1    1.5  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0045   16.9   0.0      0.006   16.4   0.0    1.2  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.019   14.9   0.0       0.03   14.2   0.0    1.4  1  TBPIP           TBPIP/Hop2 winged helix domain
      0.021   14.8   0.1      0.033   14.2   0.1    1.4  1  HTH_45          Winged helix-turn-helix
      0.029   14.6   0.0      0.057   13.6   0.0    1.5  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.034   13.9   0.0      0.048   13.5   0.0    1.3  1  HTH_23          Homeodomain-like domain
      0.051   13.9   0.0      0.075   13.4   0.0    1.3  1  Rrf2            Transcriptional regulator


Domain annotation for each model (and alignments):
>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.3   9.8e-16   1.6e-12       1      46 [.      28      73 ..      28      74 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 9.8e-16
                                      SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      d+ Rl I+klL+e+ + v++++++l++ q+ vSh Lk Lre GL  
  gi|518652270|ref|YP_008141790.1| 28 DEIRLHIMKLLSEKDMPVSDIVNALNIEQPLVSHKLKELRENGLAI 73
                                      799*****************************************75 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   0.0   6.9e-09   1.1e-05       5      60 ..      24      78 ..      20      79 .. 0.92

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 6.9e-09
                                      HHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20  5 eALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLvevvreg 60
                                      + L+++ R+ i+++L +++ + +s++  +l + +  +s+ L++L+e gL  ++++g
  gi|518652270|ref|YP_008141790.1| 24 KMLSDEIRLHIMKLL-SEKDMPVSDIVNALNIEQPLVSHKLKELRENGLAISRKSG 78
                                      6799***********.*********************************7777776 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.8e-07   0.00029      16      64 ..      36      85 ..      26      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                      HHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT.EEEE CS
                              TrmB 16 aLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk.lYra 64
                                      +Ll+++ + +++i ++l+++++ v   L++L + Gl   +k+ ++ +Y+ 
  gi|518652270|ref|YP_008141790.1| 36 KLLSEKDMPVSDIVNALNIEQPLVSHKLKELRENGLAISRKSGKNiIYSI 85
                                      79**********************************99999765437765 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   9.8e-07    0.0016      10      50 ..      35      75 ..      31      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 9.8e-07
                                      HHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR 10 rilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++l ++ ++ vs++ ++l+++++ v+  l++L ++Gl  ++
  gi|518652270|ref|YP_008141790.1| 35 MKLLSEKDMPVSDIVNALNIEQPLVSHKLKELRENGLAISR 75
                                      34555678****************************94444 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   4.6e-06    0.0074       2      46 ..      28      71 ..      27      72 .. 0.97

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.6e-06
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGl 46
                                      de+++ I++lL +  +++ +++  +l++ ++ v+  lk+L e+Gl
  gi|518652270|ref|YP_008141790.1| 28 DEIRLHIMKLLSE-KDMPVSDIVNALNIEQPLVSHKLKELRENGL 71
                                      899**********.99***************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.7e-06     0.006      20      56 ..      41      77 ..      26      80 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.7e-06
                                      SEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEES CS
                            MarR_2 20 rdltvgelarrlglsksavsrilkrLvaaGLverrpg 56
                                      +d+ v++++ +l+++++ vs  lk+L + GL   r++
  gi|518652270|ref|YP_008141790.1| 41 KDMPVSDIVNALNIEQPLVSHKLKELRENGLAISRKS 77
                                      259****************************987765 PP

>> TBPIP  TBPIP/Hop2 winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.8e-05      0.03       6      61 ..      34      85 ..      29      86 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.8e-05
                             TBPIP  6 vleylqeqnrPfsvqdvvanlqkklgKtavqkaLdeLvdegkiieKeyGKqkiYla 61
                                      + ++l e+  P  v+d+v++l  ++    v   L eL+++g+ i++  GK  iY +
  gi|518652270|ref|YP_008141790.1| 34 IMKLLSEKDMP--VSDIVNAL--NIEQPLVSHKLKELRENGLAISRKSGKNIIYSI 85
                                      66677777766..56999999..6999***************************86 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1     2e-05     0.033       6      55 ..      29      79 ..      26     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-05
                            HTH_45  6 eIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgl.ikkskek 55
                                      eI + I++ +se++   + i+ + n++  l++  L+ L e+gl i+ +++k
  gi|518652270|ref|YP_008141790.1| 29 EIRLHIMKLLSEKDMPVSDIVNALNIEQPLVSHKLKELRENGLaISRKSGK 79
                                      89999**************************************77665554 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 ?   13.6   0.0   3.5e-05     0.057      24      55 ..      44      75 ..      33      78 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.5e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                    Fe_dep_repress 24 ktkdlaerLnvspssVsemlkkLekdGyveye 55
                                       ++d+  +Ln++ + Vs  lk+L+++G+ +  
  gi|518652270|ref|YP_008141790.1| 44 PVSDIVNALNIEQPLVSHKLKELRENGLAISR 75
                                      478999*********************98765 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   2.9e-05     0.048       2      47 ..      26      72 ..      25      75 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                            HTH_23  2 asereRlrillllae.GlsvreIAreLgvsrrTvyrwlkryreeGle 47
                                      +s ++Rl+i++ll e  ++v++I  +L++ +  v++ lk  re+Gl+
  gi|518652270|ref|YP_008141790.1| 26 LSDEIRLHIMKLLSEkDMPVSDIVNALNIEQPLVSHKLKELRENGLA 72
                                      7899**************************99999888888999986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   4.6e-05     0.075      17      59 ..      35      76 ..      28      95 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.6e-05
                                      HHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 17 LakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      +++ +e+  + +++i +  ni+++ +++ l++Lr++gl  s++
  gi|518652270|ref|YP_008141790.1| 35 MKLLSEKD-MPVSDIVNALNIEQPLVSHKLKELRENGLAISRK 76
                                      44444544.99***************************77764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 846.54
//
Query:       gi|518652271|ref|YP_008141791.1|  [L=429]
Description: hypothetical protein FACI_IFERC00001G0910 [Ferroplasma acidarmanus fer1]
Scores for complete 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-118  395.6  40.3   4.2e-118  395.3  40.3    1.0  1  ArsB           Arsenical pump membrane protein
    6.3e-17   61.7  38.5    6.3e-17   61.7  38.5    2.1  2  CitMHS         Citrate transporter
     0.0058   15.7  12.0     0.0058   15.7  12.0    2.9  2  Na_sulph_symp  Sodium:sulfate symporter transmembrane region


Domain annotation for each model (and alignments):
>> ArsB  Arsenical pump membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.3  40.3    7e-122  4.2e-118       1     422 [.       7     425 ..       7     426 .. 0.97

  Alignments for each domain:
  == domain 1  score: 395.3 bits;  conditional E-value: 7e-122
                              ArsB   1 lavfiflltlvlviwqpknlsigwsacggavlaliagvvnfhdvltvtgivwnatlafvaiilislildnigffewa 77 
                                       la++if +tlvlv+ +pkn+ ig+sa  gav+++i g+  +hd++tv  ivwnat++f+++i+islild+ gffe+ 
  gi|518652271|ref|YP_008141791.1|   7 LALLIFAITLVLVLKKPKNIGIGYSALAGAVVTIILGISTLHDIITVWDIVWNATFTFISVIIISLILDEAGFFEFI 83 
                                       799************************************************************************** PP

                              ArsB  78 alhmakaakgygvrmfvyvsllgaivaalfandgaaliltpivlamvralhfneklvfpfiiasgfiadttslpfvv 154
                                       a +ma  +kg g ++f+ + llg+ ++a+fandg+aliltpiv a++    f ++ ++pfi+a+gfiadt+s+pf+v
  gi|518652271|ref|YP_008141791.1|  84 AYKMALYSKGNGKKLFMLIILLGSGISAIFANDGTALILTPIVYAILYRSNFSKNRILPFIMATGFIADTASIPFIV 160
                                       ***************************************************************************** PP

                              ArsB 155 snlvnivsadyfhitfidyasrmvvpylfsllasiivlylffrksipkrydltevkkpveaikdqnmfrlswyilgl 231
                                       snlvn+v+a yfhitf  y+  m++p ++s+++s+ vly+++rk+i   +      kp   ikd+ +f +++    l
  gi|518652271|ref|YP_008141791.1| 161 SNLVNLVTAGYFHITFSRYTEIMIIPDIVSVVSSLFVLYIYYRKNIRDDFHTDPAVKPSSFIKDRRIFLMAFPATVL 237
                                       ***************************************************************************** PP

                              ArsB 232 lligyfaseffsipvsvvagsiaiifliaaqkspavhtkkvvkeapwaivffsigmyvvvygvrnagltdvlsdviq 308
                                       l++ yf s f+ +p+s +a   a+if i a+    + +++v+k apw +v+fs+gmy++v+gv   gl  +   +++
  gi|518652271|ref|YP_008141791.1| 238 LMVLYFLSGFIGVPISFIAMPFALIFYIVARLGGRIDANHVIKIAPWQVVLFSLGMYIIVFGVSSNGLDSIYIVILN 314
                                       ********************************************************************999998888 PP

                              ArsB 309 aaadqglfagtigmgfiaailssimnnlptvmidalaiagtdthgmmrealiyanvigsdlgpkitpigslatllwl 385
                                         +        i  gf  a+ ++ mnn+p+vmi  +ai+g    g+    l+yan+ig+d+gpk tpigslatllwl
  gi|518652271|ref|YP_008141791.1| 315 YFSSLPGPFPIITTGFFFAMNAAFMNNMPSVMIGDIAISGIAHPGL----LMYANIIGNDIGPKFTPIGSLATLLWL 387
                                       776655555789*****************************99987....79************************* PP

                              ArsB 386 hvlshk.gmkiswgtyfktgiiltiptllitlvglyiw 422
                                       + l +k  +kis+  y+ktg il++p l+ tl+ lyi 
  gi|518652271|ref|YP_008141791.1| 388 YTLERKnSIKISFSYYMKTGFILAVPVLFFTLLSLYIM 425
                                       ***987369***************************95 PP

>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7  38.5   1.1e-20   6.3e-17       4     279 ..      18     352 ..       7     368 .. 0.70
   2 ?    0.9   1.6     0.036   2.1e+02     116     164 ..     361     422 ..     349     429 .] 0.52

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.1e-20
                                       xxxxx...xxxxxxxxxxxxxx.xxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS   4 lilek...lrldvvallvlvll.vltiee.....alsgiaspiillllgamiigaaleetGlfdrlaakllrlaggk 71 
                                       l+l+k   +++   al ++v++ +l+i +      +  i ++++++++ ++ii+ +l+e+G+f+++a k++  ++g+
  gi|518652271|ref|YP_008141791.1|  18 LVLKKpknIGIGYSALAGAVVTiILGISTlhdiiTVWDIVWNATFTFISVIIISLILDEAGFFEFIAYKMALYSKGN 94 
                                       44444667777777887777777555555444544555999999********************************* PP

                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS  72 rd.llvllvlltallsafvsndgvvlimipivlslakrlkklppl....lliplalaaniggaltpiGtpttraaar 143
                                        + l++l++ll   +sa++ ndg++li++piv ++  r ++++      ++++ +++a + ++  ++ +        
  gi|518652271|ref|YP_008141791.1|  95 GKkLFMLIILLGSGISAIFANDGTALILTPIVYAILYR-SNFSKNrilpFIMATGFIADTASIPFIVSNL------- 163
                                       *************************************9.899888899*************999999999....... PP

                                       xxxxxxxxxx...................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                            CitMHS 144 pglslpnlll...................lalllvgllplvllfmfgvalalpvnapkvkkqkaiieaiarsllpv. 200
                                            +nl+                    ++ ++  l++l++++  ++    +                        
  gi|518652271|ref|YP_008141791.1| 164 -----VNLVTagyfhitfsryteimiipdIVSVVSSLFVLYIYY-RKNIRDDFHT--------------------Dp 214
                                       .....888887777777777777766666555555566666666.2222222222....................02 PP

                                       ...................xxxxxxx......................................xxxxxxxxxxxxx RF
                            CitMHS 201 ...................atillla......................................ykkveWsvlllfa 220
                                                          at+ll++                                      +k  +W+v+l+  
  gi|518652271|ref|YP_008141791.1| 215 avkpssfikdrriflmafpATVLLMVlyflsgfigvpisfiampfalifyivarlggridanhvIKIAPWQVVLFSL 291
                                       22222333333333334443333333445566666666666666666666778888888888888999********* PP

                                       xxxxxxxxxxxxx.......xxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            CitMHS 221 GvfllvgaleqtG.......ilealadllga.ggplvalalvlgliallsafisnvavaalmapial 279
                                       G+ + v +++  G       i     +++++ +gp+  ++ + +++a+  af++n++ + ++  ia+
  gi|518652271|ref|YP_008141791.1| 292 GMYIIVFGVSSNGldsiyivI----LNYFSSlPGPFP-IITTGFFFAMNAAFMNNMPSV-MIGDIAI 352
                                       *****9999999988854444....444433434433.23457777889********97.3333333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.036
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxx RF
                            CitMHS 116 lliplalaaniggaltpiGtpttraaarpglslpnlll.........................lalllvgllpl 164
                                       l+ + ++++ ig  +tpiG             ++ l+l                         ++l+++ ll l
  gi|518652271|ref|YP_008141791.1| 361 LMYANIIGNDIGPKFTPIGSL-----------ATLLWLytlerknsikisfsyymktgfilavPVLFFT-LLSL 422
                                       555667777788888888888...........4444444444555555555555554443331222222.3222 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 !   15.7  12.0   9.7e-07    0.0058     274     396 ..      10     130 ..       1     150 [. 0.73
   2 ?   -5.7  16.3         3   1.8e+04     162     456 ..     133     416 ..     123     428 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 9.7e-07
                     Na_sulph_symp 274 ilfvlllllWifgeslnidattvaivvlvillllrvldWkDivkq.ktaWntllllgglialakllersgliewlgn 349
                                       ++f + l+l + ++  ni  +  a+ + v+ ++l + + +Di+      Wn  + + ++i ++ +l+++g++e+++ 
  gi|518652271|ref|YP_008141791.1|  10 LIFAITLVL-VLKKPKNIGIGYSALAGAVVTIILGISTLHDIITVwDIVWNATFTFISVIIISLILDEAGFFEFIAY 85 
                                       334444443.444555699999999999999999999999877642789**************************** PP

                     Na_sulph_symp 350 klttslsglspavaiiiilslfvlvhylfaSatAttaallpillava 396
                                       k++  ++g   ++ ++iil+ + ++ ++   +tA+  +l pi+ a++
  gi|518652271|ref|YP_008141791.1|  86 KMALYSKGNGKKLFMLIILLGSGISAIFANDGTAL--ILTPIVYAIL 130
                                       ***99997666666666666666666665566665..5677776665 PP

  == domain 2  score: -5.7 bits;  conditional E-value: 3
                     Na_sulph_symp 162 sepekqserkigaylmltvvqsasitsiaflTamApNllllglinsilgveitwasWflaaiptgvillllvpllly 238
                                       s++ k+   +i  ++m t ++++ + si f+ +   Nl+++g  +      it+ ++  ++i++ +++++   ++ly
  gi|518652271|ref|YP_008141791.1| 133 SNFSKN---RILPFIMATGFIAD-TASIPFIVSNLVNLVTAGYFH------ITFSRYTEIMIIPDIVSVVSSLFVLY 199
                                       555553...57777787777765.567777777777777777766......************************** PP

                     Na_sulph_symp 239 vlyppeikkkeeakavaktelkelGpltarekallil..fvlllllWifgeslnidattvaivvlvi.llllr...v 309
                                       + y  +i    +   ++k        ++ r   l++    vll++l++ ++++++  + +a+    i  ++ r    
  gi|518652271|ref|YP_008141791.1| 200 IYYRKNIRDDFHTDPAVKPSS----FIKDRRIFLMAFpaTVLLMVLYFLSGFIGVPISFIAMPFALIfYIVARlggR 272
                                       ***999987755555555432....2333333333322258889999999999998888888544440444445555 PP

                     Na_sulph_symp 310 ldWkDivkqktaWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAtta 386
                                       +d +  v + ++W+++l+  g++ +  + +  gl +        +l+ +s  +  + i+    ++ ++fa ++A + 
  gi|518652271|ref|YP_008141791.1| 273 IDAN-HVIKIAPWQVVLFSLGMYIIVFGVSSNGLDSIYIV----ILNYFSSLPGPFPII----TTGFFFAMNAAFMN 340
                                       6777.55667999999988888888889999995554443....444444444444443....46678899999999 PP

                     Na_sulph_symp 387 allpillavaqaipg.appllvalllalatslagfllpyatgpnpiv.fgag.....ylkvkdywrlGfilsiigll 456
                                        + ++++       g a p l++ +  + + ++   +p+++ +  +  +  +     +++   y ++Gfil++  l 
  gi|518652271|ref|YP_008141791.1| 341 NMPSVMIGDIAIS-GiAHPGLLMYANIIGNDIGPKFTPIGSLATLLWlYTLErknsiKISFSYYMKTGFILAVPVLF 416
                                       9999988754444.425566667777778888888999998887775144441111123445677788888765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2875.94
//
Query:       gi|518652272|ref|YP_008141792.1|  [L=377]
Description: hypothetical protein FACI_IFERC00001G0911 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.7e-60  202.5   0.2    1.1e-59  202.1   0.2    1.1  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  202.1   0.2   6.2e-64   1.1e-59       2     260 ..       5     261 ..       4     265 .. 0.93

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 6.2e-64
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B......--EE-SS CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkar....ilalvrar 74 
                                       v i+d+tLR+Geq++++ ++ ++ ++ia+ L++a v+ iE+g p  s+d   ++++i++   +      i+a+ ra+
  gi|518652272|ref|YP_008141792.1|   5 VGILDSTLREGEQTPGVLFNKNQRIEIAQLLSDAHVAMIEAGHPLVSPDIYSAIKEIMDMKASGMinseIIAHSRAV 81 
                                       789******************************************************987654423346******** PP

                                       HHHHHHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHH CS
                         HMGL-like  75 ekdikaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaev 151
                                        +di+ a++     g++r+ +f  +s++hl  k +++r e+++++ + + +a+s g+ v++ +edasrtd++fl +v
  gi|518652272|ref|YP_008141792.1|  82 NSDIDSAAS----LGVDRIAIFYGVSDIHLDNKTHRSRTEALDIIYDSISYASSTGIPVRFTAEDASRTDINFLRNV 154
                                       *********....**************************************************************** PP

                                       HHHHHHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS-- CS
                         HMGL-like 152 veaaeeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlG 228
                                       v +a++aGa+r++iaDt+G+ltP++ a +++ l++     v+  +H+Hnd+G+A+an laA+e Ga+ + +tvnGlG
  gi|518652272|ref|YP_008141792.1| 155 VRTAVDAGADRVSIADTLGILTPEKTAYIFNNLSDIKG--VEYDFHGHNDMGMALANGLAAAESGATIIHSTVNGLG 229
                                       *********************************99877..************************************* PP

                                       SSBBB-BHHHHHHHHHHTT-B----HHHHHHH CS
                         HMGL-like 229 eraGnaaleelvaalealgvdtgldlqklrsi 260
                                       er G +++ +l + l+       ++l +l  +
  gi|518652272|ref|YP_008141792.1| 230 ERVGIIPTQALGVLLNYHLGVDAINLLSLKPL 261
                                       **********9998876554455666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2342.65
//
Query:       gi|518652273|ref|YP_008141793.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G0912 [Ferroplasma acidarmanus fer1]
Scores for complete 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  105.5   6.3      4e-30  105.2   6.3    1.1  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
      0.017   15.5   2.9      0.034   14.6   2.8    1.8  1  FtsA         Cell division protein FtsA
      0.073   12.5   3.4       0.37   10.2   1.0    2.6  3  ROK          ROK family


Domain annotation for each model (and alignments):
>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   6.3   6.7e-34     4e-30       3     264 ..      12     293 ..      10     295 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 6.7e-34
                                       EEE-SSEEEEEEEETTTE.EEEEEEE--TTS-HHH.........HHHHHHHHHHT--GGGECEE..EEESTTCCCTC CS
                       BcrAD_BadFG   3 iDgGsTttkavlmdekge.vlgrgitnsanlesvrfeaaekvleealtealerageeeadieetylvgtgyGratlp 78 
                                       +DgG+T+t a+++dek   ++g g+++++n++sv   + +k++ +a+++a + ag    +i   + + +gyG++ + 
  gi|518652273|ref|YP_008141793.1|  12 VDGGGTKTAAIIVDEKNYrLAGFGVAGPSNVRSVTASTSRKNILKAIKNAEKMAGSV--SITGSIYGIAGYGDSIAY 86 
                                       9**************9999***********************************987..999999************ PP

                                       TTBSEEE-.........HHHHHHHHHHHH-TT--...EEEEEETTEEEEEEEETTEEEEEEEESS--TTSHHHHHHH CS
                       BcrAD_BadFG  79 ekfekeiirs.......eilvhgdGavalypgtr...tvldigGqdskgiqidkgkvenfqmndrcaageGrylgii 145
                                       ++  k i++s       +  + +dG  a+y  t+   +++   G++s+g  i++gkv+++++++    + +++++i+
  gi|518652273|ref|YP_008141793.1|  87 TEEIKSIVKSieaisdgKAVITNDGEAAVYLVTMgddGIVTALGTGSVGAYIKDGKVNRIGGWSYLTDDVASGYWIA 163
                                       9999*****9*******99999999999999999999**************************************** PP

                                       HHHHT--TTTHHHHHTT--....................S-------SHHHHHHHHHHHHHTT--HHHHHHHHHHHH CS
                       BcrAD_BadFG 146 adelnmglreldglaekat....................kkarinstcavfaeaelrdalsggekaedIlaglhrai 202
                                       ++ ++m+ + +dg+  k++                    + +  ++ +a +a  +  +a++g++++e++l  + ++i
  gi|518652273|ref|YP_008141793.1| 164 RNGIEMAEKSYDGIIGKTSlieklqehfklplrdlvadlEAHFNKRVMASLAMDVDTEAEKGDKISENVLYMAFNEI 240
                                       **************************************87777778899**************************** PP

                                       HHHHHHHHHTT---SS.EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHH CS
                       BcrAD_BadFG 203 alrvialisrsggvtdevtltGGvakneaavkelrklvkenygevkininpdsiytgalGAa 264
                                       +l +  + + ++     v   GGv+++    +++r+l+  +y++    i++ + y  a+G a
  gi|518652273|ref|YP_008141793.1| 241 KLMIDGMKKNFEKPVA-VGSIGGVMQS----RTIRELLHREYNG----IKIFYGYHVAIGNA 293
                                       *******999988854.999*******....999999*******....77888888888876 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   2.8   5.7e-06     0.034       3      71 ..      12     130 ..      10     297 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.7e-06
                                       EEE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHHHH.HHHT--HHHHHHHHHHH--S--............ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx............ RF
                              FtsA   3 vDiGagktdvavaedgalvhlrvigv......ggngitkdia.kalrtaveeAerikikyGsala............ 60 
                                       vD G++kt +++++++   ++r  g+      + + +t +++ k + +a+++Ae+++   Gs++             
  gi|518652273|ref|YP_008141793.1|  12 VDGGGTKTAAIIVDEK---NYRLAGFgvagpsNVRSVTASTSrKNILKAIKNAEKMA---GSVSItgsiygiagygd 82 
                                       999************5...56666665575455566666654156889999999999...55554444444444454 PP

                                       .......EEEEEHHHHH......................................G CS
                                       .......xxxxxxxxxx......................................x RF
                              FtsA  61 .......ekeigrkels......................................g 71 
                                                       +                                      g
  gi|518652273|ref|YP_008141793.1|  83 siayteeI--------KsivksieaisdgkavitndgeaavylvtmgddgivtalG 130
                                       44443221........1222334444454444555555555555555555555550 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   1.0   6.3e-05      0.37       2     109 ..      10     114 ..       9     147 .. 0.66
   2 ?    1.1   0.0     0.038   2.3e+02      81     116 ..     191     226 ..     173     240 .. 0.65
   3 ?    0.0   0.0     0.078   4.7e+02      28      75 ..     228     269 ..     211     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6.3e-05
                                       EEEEE-SSEEEEEEEETTS-EEEEEEE...EEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEE...ETTC CS
                               ROK   2 igidiGgtkialalvdeegeilarekv...etptetteetlvdaiaelvdeaerkadeliavgigspGli...sdks 72 
                                       +++d Ggtk+a+++vde+   la   v   ++ ++ t+ t ++ i +++++ae+ a+     ++ ++G i       
  gi|518652273|ref|YP_008141793.1|  10 LSVDGGGTKTAAIIVDEKNYRLAGFGVagpSNVRSVTASTSRKNILKAIKNAEKMAG-----SVSITGSIygiAGYG 81 
                                       68********************99999777777888889999999999999987775.....444455552111222 PP

                                       CEBSSGGCGCCCCTTHHHHHHHHHTS-EEEEEHHHHH CS
                               ROK  73 gkivstpnitwenfdlvekleerlnvpvevenDvnaa 109
                                        +i++t +i    + +v+++e+  +   +++nD  aa
  gi|518652273|ref|YP_008141793.1|  82 DSIAYTEEI----KSIVKSIEAISDGKAVITNDGEAA 114
                                       333333333....356666666666666666665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.038
                                       GCCCCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHH CS
                               ROK  81 itwenfdlvekleerlnvpvevenDvnaaalaEavf 116
                                        +    dlv++le+++n  v+++      + aE+ +
  gi|518652273|ref|YP_008141793.1| 191 FKLPLRDLVADLEAHFNKRVMASLAMDVDTEAEKGD 226
                                       444778999999999999998775555555555554 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 0.078
                                       EEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEEEEEEESSEEETTCCEB CS
                               ROK  28 vetptetteetlvdaiaelvdeaerkadeliavgigspGlisdksgki 75 
                                       +  +++ ++ +  + i+ ++d ++++++    v++gs G +  +s++i
  gi|518652273|ref|YP_008141793.1| 228 I--SENVLYMAF-NEIKLMIDGMKKNFE--KPVAVGSIGGV-MQSRTI 269
                                       4..455555555.889999999999998..68889999999.666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2276.46
//
Query:       gi|518652274|ref|YP_008141794.1|  [L=138]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.0    5.6e-06   26.2   0.0    1.7  1  PadR        Transcriptional regulator PadR-like family
     0.0012   18.8   2.2     0.0024   17.8   0.6    2.3  2  HTH_45      Winged helix-turn-helix
      0.008   16.0   1.1      0.026   14.4   0.0    2.2  2  RuvB_C      RuvB C-terminal winged helix domain
     0.0086   16.2   0.2      0.024   14.8   0.1    1.7  2  Stork_head  Winged helix Storkhead-box1 domain
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.076   13.2   0.0    1.5  1  MotA_activ  Transcription factor MotA, activation domain
      0.064   13.3   0.5      0.094   12.8   0.5    1.2  1  DUF4840     Domain of unknown function (DUF4840)
      0.082   12.9   0.2        0.1   12.6   0.2    1.2  1  Focal_AT    Focal adhesion targeting region


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 !   26.2   0.0   2.2e-09   5.6e-06       1      72 [.      10      72 ..      10      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 2.2e-09
                                      HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR  1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      iL+ ++e+p   y iik +   ++ ++++s G +Ypa +rL k g+++++++          Y +T++G+++
  gi|518652274|ref|YP_008141794.1| 10 ILEQVSESPKKPYRIIKGIVGKFDIEYKPSTGMIYPAIDRLLKAGYIKKTMDG---------YIITEEGKKY 72
                                      799999*******************************************9885.........7777777765 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.6   9.5e-07    0.0024      11      71 ..      10      78 ..       7      85 .. 0.70
   2 ?   -0.4   0.1      0.45   1.2e+03      49      56 ..     108     115 ..      76     135 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.5e-07
                            HTH_45 11 ILeaisegeakkTkimy....kanLsyk....llnkYLdmLvekglikkskekYvlTekGlelleklke 71
                                      ILe++se+ +k+ +i++    k +++yk    ++   +d L++ g+ikk+ + Y +Te+G+++ ++ +e
  gi|518652274|ref|YP_008141794.1| 10 ILEQVSESPKKPYRIIKgivgKFDIEYKpstgMIYPAIDRLLKAGYIKKTMDGYIITEEGKKYRSNNRE 78
                                      677777777777666552222456777622223444589***********************9887655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.45
                            HTH_45  49 ikkskekY 56 
                                       ik+s+++Y
  gi|518652274|ref|YP_008141794.1| 108 IKESDKSY 115
                                       35555544 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     1e-05     0.026      48      70 ..      50      72 ..      38      74 .. 0.94
   2 ?    0.1   0.2       0.3   7.6e+02      36      47 ..     112     123 ..      78     136 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1e-05
                                      HHHTTSEEEETTEEEE-HHHHHH CS
                            RuvB_C 48 LlkeglIertsrGRilTkkglky 70
                                      Llk g+I++t  G i+T++g+ky
  gi|518652274|ref|YP_008141794.1| 50 LLKAGYIKKTMDGYIITEEGKKY 72
                                      99******************998 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.3
                                       -HHHHHHTTHHH CS
                            RuvB_C  36 eketiedviEPy 47 
                                       +k+ i ++ E +
  gi|518652274|ref|YP_008141794.1| 112 DKSYIRENQETI 123
                                       444444444433 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 !   14.8   0.1   9.3e-06     0.024      44      76 ..      33      65 ..      11      67 .. 0.85
   2 ?   -1.7   0.0       1.3   3.3e+03      28      39 ..     116     127 ..      94     135 .. 0.49

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.3e-06
                        Stork_head 44 peiqiPseeviydaLgsLikerkiYhtgeGYfi 76
                                      +    Ps+ +iy a+  L+k++ i +t +GY i
  gi|518652274|ref|YP_008141794.1| 33 DIEYKPSTGMIYPAIDRLLKAGYIKKTMDGYII 65
                                      43349**************************87 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.3
                        Stork_head  28 qsatletlveaL 39 
                                          ++et++e++
  gi|518652274|ref|YP_008141794.1| 116 IRENQETIIEEI 127
                                       233455555554 PP

>> MotA_activ  Transcription factor MotA, activation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     3e-05     0.076      49      85 ..      44      80 ..      33      86 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3e-05
                                      HHHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHH CS
                        MotA_activ 49 nsnigvlikkglveksgdgliitgeaqdiisnaatly 85
                                         i  l+k g ++k+ dg iit e +   sn    y
  gi|518652274|ref|YP_008141794.1| 44 YPAIDRLLKAGYIKKTMDGYIITEEGKKYRSNNRENY 80
                                      567889********************99999976655 PP

>> DUF4840  Domain of unknown function (DUF4840)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.5   3.7e-05     0.094       8      77 ..      62     135 ..      59     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                           DUF4840   8 gkmiflspaknegneedktDvldisvaevkdstltienf..PvkdLaksi.......vdeeeelkeaieavgdvtlk 75 
                                       g +i+ + +k  +n+ + ++ l   +++  d++l+++n+   v+dL++ i       +   e+++++ie++g+++ k
  gi|518652274|ref|YP_008141794.1|  62 GYIITEEGKKYRSNNRENYEKL---ISNFMDNKLFFRNLrkAVRDLISTIkesdksyIR--ENQETIIEEIGEISRK 133
                                       7778877788888888888888...89999*********889********888876555..89**********9998 PP

                           DUF4840  76 vk 77 
                                       +k
  gi|518652274|ref|YP_008141794.1| 134 IK 135
                                       87 PP

>> Focal_AT  Focal adhesion targeting region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     4e-05       0.1      29      90 ..      72     136 ..      63     138 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                          Focal_AT  29 vetakaeeyvslvksvgle...lrkLltsvdellsslpasarreielaekvlskdlaelisamkl 90 
                                        ++ + e+y +l+ + +++    r+L ++v +l+s++++s++  i   ++++ +++ e++ ++k+
  gi|518652274|ref|YP_008141794.1|  72 YRSNNRENYEKLISNFMDNklfFRNLRKAVRDLISTIKESDKSYIRENQETIIEEIGEISRKIKN 136
                                       55667778888888877643337***************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1073  (0.0598472); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); 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 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 958.85
//
Query:       gi|518652275|ref|YP_008141795.1|  [L=327]
Description: hypothetical protein FACI_IFERC00001G0914 [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  113.9   0.0    1.6e-32  112.9   0.0    1.5  1  ABC_tran        ABC transporter
    3.9e-13   49.9   0.5    8.3e-13   48.9   0.5    1.6  1  DUF4162         Domain of unknown function (DUF4162)
    9.7e-09   35.4   4.4    3.9e-05   23.6   0.1    2.5  3  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
      6e-05   23.1   0.4    0.00013   22.0   0.3    1.8  1  MMR_HSR1        50S ribosome-binding GTPase
    0.00077   19.0   2.5        4.2    6.7   0.0    3.1  3  SMC_N           RecF/RecN/SMC N terminal domain
     0.0012   19.3   2.8     0.0024   18.4   2.5    1.8  1  AAA_23          AAA domain
     0.0015   18.9   0.1     0.0035   17.6   0.1    1.7  1  AAA_22          AAA domain
     0.0017   18.3   0.4     0.0043   17.0   0.4    1.7  1  RsgA_GTPase     RsgA GTPase
      0.002   17.9   0.8     0.0045   16.7   0.8    1.6  1  AAA_29          P-loop containing region of AAA domain
     0.0077   16.7   0.2       0.11   12.9   0.2    2.5  1  AAA             ATPase family associated with various cellula
  ------ inclusion threshold ------
      0.015   14.6   0.4      0.032   13.5   0.4    1.5  1  Zeta_toxin      Zeta toxin
      0.033   13.2   0.5      0.057   12.4   0.5    1.3  1  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
        0.1   12.5   0.1       0.33   10.9   0.1    1.8  2  Ploopntkinase3  P-loop Nucleotide Kinase3
       0.14   12.6   0.0       0.23   11.8   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 !  112.9   0.0   1.3e-35   1.6e-32       1     136 [.      21     164 ..      21     165 .. 0.97

  Alignments for each domain:
  == domain 1  score: 112.9 bits;  conditional E-value: 1.3e-35
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       ++nvslk+  g++++++G+nGaGKStL+k+l+g l+pt+G+ ++ g dl++ +  + rk  gv+pq+ + + +l+ r
  gi|518652275|ref|YP_008141795.1|  21 VDNVSLKIGSGQIYGLLGQNGAGKSTLIKMLTGSLTPTSGTAKIAGLDLTK-DSMKIRKITGVVPQDLTTDGDLSGR 96 
                                       58*************************************************.88999******************** PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       en             e+ e+i+ +l+ ++l +++d+++    +++SgG+++r++la+ l++ p++l+lDEpt
  gi|518652275|ref|YP_008141795.1|  97 ENlkliadlygipkkEALERIDVLLHMVDLYDVRDRHA----ENYSGGMRKRLELACGLMNTPEVLFLDEPT 164
                                       ************99888899*****************9....*****************************9 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.9   0.5   6.5e-16   8.3e-13       1      81 []     219     306 ..     219     306 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.9 bits;  conditional E-value: 6.5e-16
                                       E-HHHHHTTS-SSEEEEE....-------..---EEEE-TT.S-EEEEE--.-----------.----EEEEEEEE- CS
                           DUF4162   1 GtleeiKrsygknrieve....adaeelleepgveeveeeg.gelelkled.eeaanellkal.tsgveirsFeeee 70 
                                       Gt +e+K+s+++++i+++    ++ ++l++ p+  e+++ + g++++k+++ +e+ ++l+k l ++ ++ + ++ ++
  gi|518652275|ref|YP_008141795.1| 219 GTSDELKKSLKGDIITLKvkndDEYSKLEKFPESLEIKRMEtGDVRMKVNNsDEVLPKLMKFLgENEISPEAISIRK 295
                                       999*************9998755599999999988888888799******99***********99************ PP

                                       --HHHHHHHHH CS
                           DUF4162  71 PsLndIFiekv 81 
                                       PsL+++Fie++
  gi|518652275|ref|YP_008141795.1| 296 PSLDEVFIEYT 306
                                       *********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 !   13.2   0.7   4.7e-05      0.06       2      21 ..      34      53 ..      33      78 .. 0.77
   2 !   23.6   0.1     3e-08   3.9e-05     220     298 ..     120     196 ..      64     201 .. 0.72
   3 ?   -2.8   0.0       3.4   4.4e+03     183     202 ..     272     291 ..     225     314 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                            AAA_21  2 nvliGpNgsGKSnLLdaldl 21
                                       +l G Ng+GKS+L++ l +
  gi|518652275|ref|YP_008141795.1| 34 YGLLGQNGAGKSTLIKMLTG 53
                                      689*************9943 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 3e-08
                            AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr.ngaQvilt 295
                                        ++ ++  d +++ a + S G+++ l l+  l  ++    +l++DEp +gL+    + l++ +++ ++   + +ilt
  gi|518652275|ref|YP_008141795.1| 120 LLHMVDLYDVRDRHAENYSGGMRKRLELACGLMNTP---EVLFLDEPTLGLDVTTRENLWKYIRSVQKeFHITIILT 193
                                       344444444444556677******999999999999...9***********************888877899***** PP

                            AAA_21 296 THS 298
                                       +H 
  gi|518652275|ref|YP_008141795.1| 194 SHY 196
                                       **6 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.4
                            AAA_21 183 rllqrlvrslklveielsdl 202
                                       + l +l++ l ++ei ++++
  gi|518652275|ref|YP_008141795.1| 272 EVLPKLMKFLGENEISPEAI 291
                                       33334444444444444444 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   0.3     1e-07   0.00013       3      98 ..      35     135 ..      33     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1e-07
                                       EEEESTTSSHHHHHHHHHTS...TEEESSSTTSSSSEEEEEEE.......ETTEE............EEEEECGGCS CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltge...kaivsdkpgtTrdinegrvk.......lkgke............ielvDtpGli 57 
                                       +++G+  +GKStLi+ ltg+   ++ +++++g  ++    +++          +               ++D+ G  
  gi|518652275|ref|YP_008141795.1|  35 GLLGQNGAGKSTLIKMLTGSltpTSGTAKIAGLDLTKDSMKIRkitgvvpQ--DLttdgdlsgrenlKLIADLYG-- 107
                                       789****************97555666666654333333333332243220..1211222222222123344444.. PP

                                       SHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHH CS
                          MMR_HSR1  58 egaseekglgkaflaleeadlillvvdaseeklkpldeele 98 
                                               + k+ + le+ d++l++vd+     +  d++ e
  gi|518652275|ref|YP_008141795.1| 108 --------IPKKEA-LERIDVLLHMVDLY----DVRDRHAE 135
                                       ........334433.6789*******954....22333333 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.4    0.0038       4.9      25      43 ..      32      50 ..      12      61 .. 0.82
   2 !    6.7   0.0    0.0033       4.2     160     202 ..     156     197 ..     125     214 .. 0.75
   3 ?    4.2   0.1     0.019        25      74     138 ..     228     292 ..     204     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0038
                                      SEEEEEESTTSSHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlldA 43
                                      ++  ++G+NG+GKs l+  
  gi|518652275|ref|YP_008141795.1| 32 QIYGLLGQNGAGKSTLIKM 50
                                      456789********99875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0033
                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkeksknaQfivislreeml 202
                                        + +lDe    LD + ++++ +++++ +k++ + +i l+++ l
  gi|518652275|ref|YP_008141795.1| 156 EVLFLDEPTLGLDVTTRENLWKYIRSVQKEFHITII-LTSHYL 197
                                       34569*********************9998765444.444444 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.019
                                       TTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  74 vkkaeveitfdnedkklkiekeevsisrrvkrkgeseykingkevtkkevsellesagiskelLS 138
                                       +k   +++ ++n+d+ +k ek   s++ + +++g+ ++k+n+++    +++++l + +is+e++S
  gi|518652275|ref|YP_008141795.1| 228 LKGDIITLKVKNDDEYSKLEKFPESLEIKRMETGDVRMKVNNSDEVLPKLMKFLGENEISPEAIS 292
                                       33334678889999998888888899999999****************************99877 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   2.5   1.9e-06    0.0024      19      68 ..      31      79 ..      16     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.9e-06
                            AAA_23 19 kgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese 68
                                        ++ + G+NGaGK+T++  ++  L+   +++ +  g ++ k++ +i + 
  gi|518652275|ref|YP_008141795.1| 31 GQIYGLLGQNGAGKSTLIKMLTGSLTPT-SGTAKIAGLDLTKDSMKIRKI 79
                                      4688999*******************85.555566677777777776555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   2.7e-06    0.0035       6     128 ..      32     193 ..      27     203 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..............erpevvfvtlpsst..sskdllrellralgl 66 
                                       +i  + G+ G+GK+tl+++l+ +l+  +  ++              +  +vv  +l+ ++  s ++ l+ ++  +g 
  gi|518652275|ref|YP_008141795.1|  32 QIYGLLGQNGAGKSTLIKMLTGSLTPTSGTAKiagldltkdsmkirKITGVVPQDLTTDGdlSGRENLKLIADLYGI 108
                                       566689******************88777777999***999966654445556666666688888889999999999 PP

                            AAA_22  67 elka.....................erlsseellealeqalraravielliiDEaqh.lr...seealeeLrsllnl 118
                                       ++k+                     +++ s  ++++le a+    ++e+l +DE    l+   +e++++++rs ++ 
  gi|518652275|ref|YP_008141795.1| 109 PKKEaleridvllhmvdlydvrdrhAENYSGGMRKRLELACGLMNTPEVLFLDEPTLgLDvttRENLWKYIRSVQK- 184
                                       9999888888888777777776666666666666666666666666***********9998755999******999. PP

                            AAA_22 119 srkgvqliLv 128
                                        ++++++iL 
  gi|518652275|ref|YP_008141795.1| 185 -EFHITIILT 193
                                       .999999996 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.4   3.4e-06    0.0043      95     124 ..      26      56 ..       8      80 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.4e-06
                                       HHCTT.SEEEEECSTTSSHHHHHHHHCTT-- CS
                       RsgA_GTPase  95 ellkd.ktsvlvGqSGvGKStLinallpele 124
                                        ++ + ++  l+Gq G+GKStLi++l+++l+
  gi|518652275|ref|YP_008141795.1|  26 LKIGSgQIYGLLGQNGAGKSTLIKMLTGSLT 56 
                                       5554449999****************99854 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   0.8   3.5e-06    0.0045      14      50 ..      23      59 ..      14      64 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.5e-06
                            AAA_29 14 ghtieidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      + +++i   +++ l G++G+GKSTl+  ++  L+p++
  gi|518652275|ref|YP_008141795.1| 23 NVSLKIGSGQIYGLLGQNGAGKSTLIKMLTGSLTPTS 59
                                      56667764448899************88877777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   8.6e-05      0.11       3     118 ..      36     203 ..      34     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.6e-05
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       l G  G GK++l+k +  +l   +   +i g +l+++                                        
  gi|518652275|ref|YP_008141795.1|  36 LLGQNGAGKSTLIKMLTGSLTptSGTAKIAGLDLTKDsmkirkitgvvpqdlttdgdlsgrenlkliadlygipkke 112
                                       789****************9644667888888888446788888888888888888888888888888888888888 PP

                                       ....................STTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHH CS
                               AAA  38 ....................yvgesekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLltel 93 
                                                           + ++ +  +r+ ++ a     +p +lf+DE                 ++ + L + +
  gi|518652275|ref|YP_008141795.1| 113 aleridvllhmvdlydvrdrHAENYSGGMRKRLELACGLMnTPEVLFLDEPTLGLDV----------TTRENLWKYI 179
                                       888888888888888877775555555555555554443357899999996444333..........3668899999 PP

                                       HHTTTSSSTEEEEEEESSGGGSTHH CS
                               AAA  94 dgvkkkeskvivigatnrpdkldpa 118
                                         v+k+ + +++i+++++ d++d  
  gi|518652275|ref|YP_008141795.1| 180 RSVQKEFH-ITIILTSHYLDEVDAL 203
                                       99999766.9999999998888865 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   2.5e-05     0.032      21      49 ..      36      64 ..      28      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                        Zeta_toxin 21 lgGqpGAGKselaellkdelerqgnvvrl 49
                                      l Gq GAGKs+l+++l+ +l+++++  ++
  gi|518652275|ref|YP_008141795.1| 36 LLGQNGAGKSTLIKMLTGSLTPTSGTAKI 64
                                      66******************988777666 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 ?   12.4   0.5   4.5e-05     0.057      20      54 ..      22      56 ..      15      71 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.5e-05
                                      HHHGGG-S-SEEEEEEE-TTSSHHHHHHHHHHHHH CS
                              MeaB 20 erllakaGraqvvGltGvPGaGkstlvealglelr 54
                                      ++++ k G  q  Gl G  GaGkstl++ l+ +l+
  gi|518652275|ref|YP_008141795.1| 22 DNVSLKIGSGQIYGLLGQNGAGKSTLIKMLTGSLT 56
                                      667788999********************998886 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00026      0.33       8      31 ..      36      59 ..      30      98 .. 0.76
   2 ?   -2.0   0.0       2.3   2.9e+03     160     181 ..     209     229 ..     171     233 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                    Ploopntkinase3  8 lvGqPGaGkstlmaeltkgfdrsk 31
                                      l+Gq GaGkstl+  lt ++  ++
  gi|518652275|ref|YP_008141795.1| 36 LLGQNGAGKSTLIKMLTGSLTPTS 59
                                      89***************9987544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.3
                    Ploopntkinase3 160 aaekgkvkvlaGhPdelrsile 181
                                         ++gk+ +++G  del++ l+
  gi|518652275|ref|YP_008141795.1| 209 IIDHGKI-IISGTSDELKKSLK 229
                                       4556654.56788888888876 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00018      0.23      21      53 ..      28      59 ..      19     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00018
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekdgg 53
                                       g++++  l G+ G GKs+l+++l  +l+ +  
  gi|518652275|ref|YP_008141795.1| 28 IGSGQIYGLLGQNGAGKSTLIKMLTGSLTPT-S 59
                                      567788889***************9999988.2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 2077.95
//
Query:       gi|518652276|ref|YP_008141796.1|  [L=267]
Description: hypothetical protein FACI_IFERC00001G0915 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-31  109.0  23.5      2e-31  109.0  23.5    1.9  2  ABC2_membrane    ABC-2 type transporter
    1.8e-17   63.5  29.9    1.8e-17   63.5  29.9    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein
    2.4e-05   23.8  22.4    3.2e-05   23.4  22.4    1.1  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.012   13.9   1.9      0.016   13.5   1.9    1.2  1  SpecificRecomb   Site-specific recombinase
        9.6    6.1  23.1        1.1    9.2  15.8    2.3  2  ABC2_membrane_4  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane  ABC-2 type transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.0  23.5   5.7e-35     2e-31       6     208 ..       7     225 ..       4     227 .. 0.90
   2 ?   -1.8   3.7      0.46   1.7e+03     131     150 ..     240     259 ..     222     264 .. 0.48

  Alignments for each domain:
  == domain 1  score: 109.0 bits;  conditional E-value: 5.7e-35
                     ABC2_membrane   6 llkreflqrwrdpslgllwrliqplllalvfgtvfgnlg....nsedglnr...........pgllffsvlflafsa 67 
                                       l+ r++++++r+p +  ++ +iqp++++++fg++f  ++     s+ +  +            g+l ++ lf++  +
  gi|518652276|ref|YP_008141796.1|   7 LTIRDLKRWYRNPISA-VVGVIQPIFWIVLFGSAFDIAKfggpASSAF--FegapnyitylmGGILTIIGLFTG--M 78 
                                       688**********888.99*****************877764333333..246899999987777777777777..* PP

                     ABC2_membrane  68 ltsvapvferergvlerelvsplyslsayvlakvlvelpvsllqalifllivyflv.gldls.rf.....flfllll 137
                                       ++++ ++++r+ g+l+r l +p+  ++++v++++l++++++l+q++i++++++++  gl+++  f     + ++ ++
  gi|518652276|ref|YP_008141796.1|  79 FSGINIIWDRRLGILQRFLIAPI-NRASIVFSRILSSVARILVQIVILFVVAFLIPdGLKIEhGFtamdaVVLVSAV 154
                                       ***********************.******************************99999999744666878899999 PP

                     ABC2_membrane 138 lltalaasslgllisalapsfedasqlaslvllpllllsGffipidsmpkwlqwiaylnPltyavealrsn 208
                                       l++++++ssl+ +i++ ++++e +  +++l+ lpl++ s +++p+d m +wl  +a++nP+++  +++r +
  gi|518652276|ref|YP_008141796.1| 155 LMISFIFSSLFSIIAVRTTKMESVFGIVNLINLPLMFASFAMFPPDLMAGWLENVARYNPVSWSAQSIRMV 225
                                       9***********************************************88*****************9987 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.46
                     ABC2_membrane 131 flflllllltalaasslgll 150
                                       +l+++ ll+++++++ l  +
  gi|518652276|ref|YP_008141796.1| 240 LLYMMGLLALTVFMLVLTYV 259
                                       33333333333333333333 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.5      0.13   4.5e+02     213     234 ..      21      43 ..      20      55 .. 0.71
   2 !   63.5  29.9   5.1e-21   1.8e-17     152     344 ..      53     258 ..      47     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.13
                   ABC2_membrane_3 213 dflvyllqlllilll...afglgip 234
                                       +++v+++q +++++l   af+  i 
  gi|518652276|ref|YP_008141796.1|  21 SAVVGVIQPIFWIVLfgsAFD--IA 43 
                                       578999999999997566676..43 PP

  == domain 2  score: 63.5 bits;  conditional E-value: 5.1e-21
                   ABC2_membrane_3 152 leeelsnvasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllillla 228
                                        +e ++n+  +l+g il i+ ++t++f   +i+ +++ +i+++ l+++++++++++s+il++++  l+q+++++++a
  gi|518652276|ref|YP_008141796.1|  53 FFEGAPNYITYLMGGILTIIGLFTGMFSGINIIWDRRLGILQRFLIAPINRASIVFSRILSSVARILVQIVILFVVA 129
                                       589999********66666666667777779*******************************************988 PP

                   ABC2_membrane_3 229 fgl........gipfgnlglllllfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsal 297
                                       f +        g++ ++ ++l+  +l+ ++++++l+  + + ++++e++++++ +++l+l+++++++fp + ++++l
  gi|518652276|ref|YP_008141796.1| 130 FLIpdglkiehGFTAMDAVVLVSAVLMISFIFSSLFSIIAVRTTKMESVFGIVNLINLPLMFASFAMFPPDLMAGWL 206
                                       877777877888888888888888888899999999999************************************** PP

                   ABC2_membrane_3 298 kwifsiiPffapglgllrli.tgd.plwe...illsliilalfavvylllal 344
                                        ++++++P ++ ++++  +i +g+ + +e   +ll ++ l++++v++l+l++
  gi|518652276|ref|YP_008141796.1| 207 ENVARYNPVSWSAQSIRMVIiNGTlSASEahtVLLYMMGLLALTVFMLVLTY 258
                                       ****************999756665555588888888889999999998875 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 !   23.4  22.4     9e-09   3.2e-05      54     282 ..      30     260 ..      20     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 9e-09
                   ABC2_membrane_2  54 aleyveaasasdeaedtdqdlkv...........vstimavlipviaalfgadaiagEkergTlkllLskPvsRdei 119
                                        ++ v ++sa+d+a+ + +++ +           +++ + ++i+++  +f+   i  ++  g l + L  P+ R++i
  gi|518652276|ref|YP_008141796.1|  30 IFWIVLFGSAFDIAKFGGPASSAffegapnyityLMGGILTIIGLFTGMFSGINIIWDRRLGILQRFLIAPINRASI 106
                                       5667777888888888888877788888888888888888999999999999999999******************* PP

                   ABC2_membrane_2 120 llgKfigglaiglaiavallatvllalaiilalgiv..laledllllvvasvlllllvvflalglllSsvarssrea 194
                                       +++ +++++a +l+    +++ +++a++i  +l+i+  ++++d ++lv a++ ++     + ++ l+S++a  +++ 
  gi|518652276|ref|YP_008141796.1| 107 VFSRILSSVARILV---QIVILFVVAFLIPDGLKIEhgFTAMDAVVLVSAVL-MIS----FIFSSLFSIIAV-RTTK 174
                                       ***********555...55555555555565555551155566555554444.444....457889999999.9999 PP

                   ABC2_membrane_2 195 aalalglfvvlailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlna..lgstatnllill 269
                                       ++ ++g++ + ++  + +++++  + ++    + +  ++  ++p s+  + ++ ++ ++ l+a        +++ ll
  gi|518652276|ref|YP_008141796.1| 175 MESVFGIVNLINLPLMFASFAMFPPDLM----AGWLENVARYNPVSWSAQSIRMVIINGTLSAseAHTVLLYMMGLL 247
                                       ***********99999999885555553....467************999999999999666553333333444455 PP

                   ABC2_membrane_2 270 lllavllvlgyvl 282
                                       +l++ +lvl+yv+
  gi|518652276|ref|YP_008141796.1| 248 ALTVFMLVLTYVI 260
                                       5555566677665 PP

>> SpecificRecomb  Site-specific recombinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.9   4.5e-06     0.016     427     498 ..     149     216 ..     146     248 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.5e-06
                    SpecificRecomb 427 vvipvalliallilallgapliseekaeallesldplgslallyAaitGvlLFlssLiaGyadNlavynrid 498
                                       v + ++l+i++++ +l+   ++ ++k+e+++  +++++   l++A+++   +F   L+aG+ +N+a yn + 
  gi|518652276|ref|YP_008141796.1| 149 VLVSAVLMISFIFSSLFSIIAVRTTKMESVFGIVNLINL-PLMFASFA---MFPPDLMAGWLENVARYNPVS 216
                                       45677899*****************************88.******98...9****************9886 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 ?    9.2  15.8   0.00031       1.1      15     170 ..      31     182 ..      17     198 .. 0.72
   2 ?    1.0   0.7       0.1   3.7e+02     101     121 ..     238     258 ..     216     265 .. 0.48

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00031
                   ABC2_membrane_4  15 vwllvlaallvpllallyfnllgktgldpaefyslsvfgftlllllplilgiiasylifrEeqndtlknLltiPvsr 91 
                                       +w+++++++    + ++ f   +++++++      + ++ ++l+++ l +g+++++ i   +  + l   l+ P++r
  gi|518652276|ref|YP_008141796.1|  31 FWIVLFGSA----FDIAKFGGPASSAFFEGAPNYITYLMGGILTIIGLFTGMFSGINIIWDRRLGILQRFLIAPINR 103
                                       444444433....233444444444444433333455666889999999**************************** PP

                   ABC2_membrane_4  92 tklllaKlivllllsvllmlvtflitvlf.allsgfvgfsvklvlellkkclelgllvffavlpiialvllkksyvl 167
                                       ++++++ ++  +  +++ ++++f++++l+   l    gf+++  +  l+  ++++ ++f  +  iia+ + k ++v+
  gi|518652276|ref|YP_008141796.1| 104 ASIVFSRILSSVARILVQIVILFVVAFLIpDGLKIEHGFTAMDAVV-LVSAVLMISFIFSSLFSIIAVRTTKMESVF 179
                                       *********9999999999999999999844444444565555444.455566667788888889999999999999 PP

                   ABC2_membrane_4 168 pli 170
                                       +++
  gi|518652276|ref|YP_008141796.1| 180 GIV 182
                                       987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.1
                   ABC2_membrane_4 101 vllllsvllmlvtflitvlfa 121
                                       ++ll+++ l+ +t+++ vl+ 
  gi|518652276|ref|YP_008141796.1| 238 TVLLYMMGLLALTVFMLVLTY 258
                                       333333322222222222222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 1724.43
//
Query:       gi|518652277|ref|YP_008141797.1|  [L=225]
Description: hypothetical protein FACI_IFERC00001G0916 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-26   93.9   0.8    7.8e-26   91.1   0.8    1.9  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.8   4.3e-30   7.8e-26       3     241 .]       4     203 ..       2     203 .. 0.89

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 4.3e-30
                                       EEEEE-TTCCCCTCC..HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHH CS
                         AA_kinase   3 vVvKlGGssltdkee..aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeageva 77 
                                       vV+ lGGs+++++    + ++++ e  + + +   k  +V+Ggg+ ++ +++  ++++ + +++             
  gi|518652277|ref|YP_008141797.1|   4 VVISLGGSIISKERLnlKLMEEFSETMKSI-STYDKFGIVVGGGKLARTYISDLKKYNVNDNIL------------- 66 
                                       8**********55558*9999999999999.777888****************55555555553............. PP

                                       HHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE CS
                         AA_kinase  78 trdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeege 154
                                         d++++ ++r++a  ++  +++v+ +                      +++  +e+l++   +v++g    +e+g+
  gi|518652277|ref|YP_008141797.1|  67 --DEIGINATRINALAMTTFFDDVNSKIP-------------------TNINDAAEMLHNYRYVVMGG----TEPGH 118
                                       ..9*******************9999855...................3579999*****55555555....58998 PP

                                       EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHH CS
                         AA_kinase 155 lgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaa 229
                                           ++Dt+++llAe +g + li++t+VdGVy++dpk++ da++++++s++ea +  +++  + g    ++   l +
  gi|518652277|ref|YP_008141797.1| 119 ----TTDTVSTLLAERIGSKVLINATSVDGVYSSDPKIDNDAKKFSKLSYNEAISlsIKNSTGAGTNVFMDITSLTI 191
                                       ....9***************************************************8888888888888******** PP

                                       HHCTT-EEEEEE CS
                         AA_kinase 230 arrggipvvItn 241
                                       a+r+gi+++++n
  gi|518652277|ref|YP_008141797.1| 192 AKRAGIKIFVIN 203
                                       **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1644.59
//
Query:       gi|518652278|ref|YP_008141798.1|  [L=412]
Description: hypothetical protein FACI_IFERC00001G0917 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-40  138.0   0.0    5.2e-40  136.8   0.0    1.6  1  eRF1_2          eRF1 domain 2
    6.6e-27   94.2   0.0    2.1e-26   92.6   0.0    1.9  1  eRF1_3          eRF1 domain 3
    4.2e-15   55.9   0.0    6.6e-15   55.2   0.0    1.3  1  eRF1_1          eRF1 domain 1
    1.1e-11   45.1   0.0    2.2e-11   44.2   0.0    1.4  1  acVLRF1         Actinobacteria/chloroflexi VLRF1 release fact
    6.1e-09   36.3   0.0    9.7e-09   35.6   0.0    1.3  1  baeRF_family10  Bacterial archaeo-eukaryotic release factor f
  ------ inclusion threshold ------
      0.017   14.7   2.9      0.042   13.4   2.9    1.8  1  TF_Zn_Ribbon    TFIIB zinc-binding


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 !  136.8   0.0   1.7e-43   5.2e-40       2     133 .]     140     270 ..     139     270 .. 0.98

  Alignments for each domain:
  == domain 1  score: 136.8 bits;  conditional E-value: 1.7e-43
                                       EEEEEEETTEEEEEEEESSCEEEEEEEE------BSTTBSCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCHTTTES CS
                            eRF1_2   2 vglivldegeAtigllkgsrtevlkkievsvPkKhkrGgqsarrfeRlreekleeflkkvaeaankafllvdkdklk 78 
                                       +gliv+d++eAtig+l+g++++v++   + vP Kh++Ggqs+rrfeRl+e +++ef+kk+++ an++f+   ++++ 
  gi|518652278|ref|YP_008141798.1| 140 YGLIVIDRKEATIGFLRGTKIDVVDYEYSLVPSKHRQGGQSSRRFERLIEIAANEFFKKIGDIANSTFMP-VIKDVI 215
                                       8********************************************************************5.588999 PP

                                       EEEEEESSTHHHHHHHHHHHHHHHHTCCEEEEE-S-TSCHHHHHHHHCCHHHHCC CS
                            eRF1_2  79 giilagpgfvkeefldkdlldaelkkkviklvdvsyggesglnevlekaaevlkd 133
                                       +i+++gpg +ke f++kd+l++e k+k+ +l+d++y++esgl+e++eka+e++kd
  gi|518652278|ref|YP_008141798.1| 216 TIFVGGPGATKEYFIEKDYLRNEIKDKIKDLFDIGYTDESGLRELVEKASESIKD 270
                                       ***************************************************9987 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0   7.2e-30   2.1e-26       2     111 ..     274     404 ..     273     406 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 7.2e-30
                                       HHHHHHHHHHHHHHHC.TCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS.................-H CS
                            eRF1_3   2 iqekklleefleelak.dtgkavYGveevlkalemgAvetLLvseelersrdtlkekv.................ke 60 
                                        +ek+++++fl+e++k d+g+ vYG+  + +al+m+ +e L+vs+++++ ++ +k++v                 ++
  gi|518652278|ref|YP_008141798.1| 274 TREKDIINRFLREIKKsDGGLGVYGEASIINALKMKNIELLIVSDSIRKIKYFYKCPVcgaektftdepteepvcDN 350
                                       79**************9**************************************9999*************98855 PP

                                       HH-HHHHHH...HHHHHHHHHHHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS CS
                            eRF1_3  61 tgeelelve...lieelvenveesgakveiisseseeGeqlvkafgGiaaiLRy 111
                                       +++ ++  +   +ie+l++++eesg+kve++s++s+eG  l++afgG+a+iLRy
  gi|518652278|ref|YP_008141798.1| 351 DNTPMNFEKeddFIEDLYKMAEESGTKVEMVSEDSDEGRLLKTAFGGLAGILRY 404
                                       555555444679****************************************** PP

>> eRF1_1  eRF1 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.0   2.2e-18   6.6e-15       2     127 ..      13     132 ..      12     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 2.2e-18
                                       EEEEE..CTBTTSCCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH.......--CEEEEEEEEEEEEEEECT CS
                            eRF1_1   2 kllkr..dlekdgsgsvtLipeddedlwhlynliapgdsvrastvrkvqresstgsreservklkLtikvekvdfdk 76 
                                       k +++  +l+++g+++++L++++d++++++ ++++++ s+++++++k +r         ++v+ ++++ + +++++k
  gi|518652278|ref|YP_008141798.1|  13 KAMEElsKLHGRGTELISLYIPPDKQISDVVQYLREEFSTSSNIKSKTTR---------KNVLGAIESIMSRLKYYK 80 
                                       6666666899**************************************99.........9***************** PP

                                       T...SSEEEEEEEEEEGGGG--TTSEEEEEE-TTSEEEEEECE.ESHHHHHHHHH CS
                            eRF1_1  77 d...agvlrisGkvieenehvklgafhtldlelkrpftiikee.wdsfalerLke 127
                                       +   +g++ + G v++  +   ++++ t  +e+++ ++++ ++ ++sf+le+L +
  gi|518652278|ref|YP_008141798.1|  81 QppeHGLVFFVGHVATRGD---QTEMYTKIIEPPQAIQTFLYKcDSSFHLEQLTD 132
                                       *9999**************...8999***************888********986 PP

>> acVLRF1  Actinobacteria/chloroflexi VLRF1 release factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   7.4e-15   2.2e-11       4     125 ..     142     265 ..     139     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 7.4e-15
                           acVLRF1   4 gvllvrrggfavgvveggelvaskvgtrdvqgrtaaGGwSqqRfaRrrenqadalleavaeaaarllaeesae...v 77 
                                       +++++r+ + ++g ++g+++  +  + + v +++++GG+S +Rf+R +e  a++ ++++ + a+  + +  ++   +
  gi|518652278|ref|YP_008141798.1| 142 LIVIDRKEA-TIGFLRGTKIDVVDYEYSLVPSKHRQGGQSSRRFERLIEIAANEFFKKIGDIANSTFMPVIKDvitI 217
                                       456677777.***************************************************************999* PP

                           acVLRF1  78 vlgGdrslvaevledarlap.latlareelldvpdprravLedavrrar 125
                                       ++gG+ ++ + + e+  l++ +++  ++ l+d++  +++ L++ v++a 
  gi|518652278|ref|YP_008141798.1| 218 FVGGPGATKEYFIEKDYLRNeIKDKIKD-LFDIGYTDESGLRELVEKAS 265
                                       *************997755415555555.99999999999999999875 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 !   35.6   0.0   3.2e-12   9.7e-09       2     104 ..     126     229 ..     126     268 .. 0.82

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 3.2e-12
                    baeRF_family10   2 ylapLlealdeyerygvvlvdreraRlfevylgeleeveevegevpgrtktggwksqdrfqrreeeqaerhlkevAe 78 
                                       +l++L++ l+e e yg++++dr++a + + ++ +++ v+   + vp ++++gg+ s +rf+r  e  a +++k++++
  gi|518652278|ref|YP_008141798.1| 126 HLEQLTDQLKEKELYGLIVIDRKEATIGFLRGTKIDVVDYEYSLVPSKHRQGGQ-SSRRFERLIEIAANEFFKKIGD 201
                                       6899**************************************************.********************** PP

                    baeRF_family10  79 llaklleerg..verlvlgGdeeetaal 104
                                       ++++ + +    v  +++gG+ + ++ +
  gi|518652278|ref|YP_008141798.1| 202 IANSTFMPVIkdVITIFVGGPGATKEYF 229
                                       ***9998854347788888887776666 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   2.9   1.4e-05     0.042       1      23 [.     327     349 ..     327     350 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.4e-05
                                       EEETTTTCEECHEETSTTCEEES CS
                      TF_Zn_Ribbon   1 ykCPnCgstnlveDpergelvCt 23 
                                       ykCP+Cg +++ +D+ + e vC 
  gi|518652278|ref|YP_008141798.1| 327 YKCPVCGAEKTFTDEPTEEPVCD 349
                                       8*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1027  (0.0572815); expected 358.6 (0.02)
Passed bias filter:                      793  (0.04423); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3015.63
//
Query:       gi|518652279|ref|YP_008141799.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G0918 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   37.7   7.3    2.5e-09   36.9   7.3    1.4  1  Ion_trans_2   Ion channel
    5.3e-09   36.4   0.3    5.3e-09   36.4   0.3    2.2  2  TrkA_N        TrkA-N domain
     0.0015   17.8   2.6     0.0023   17.2   2.6    1.2  1  Ion_trans     Ion transport protein
     0.0054   16.9   0.1       0.36   11.0   0.0    2.6  2  BK_channel_a  Calcium-activated BK potassium channel alpha su


Domain annotation for each model (and alignments):
>> Ion_trans_2  Ion channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9   7.3   5.7e-13   2.5e-09       9      77 ..       9      86 ..       2      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 5.7e-13
                                      HHHHHHHT...............T---HHHHHHHHHHHHTTS----SSTT.-----HHHHHHHHHHHHHHHHHHHHHHH CS
                       Ion_trans_2  9 fgaviysl...........eegwekwsfldalYfsfvtltTiGYGdivpe.tdagrlftivyillGlalfalflavlgk 75
                                      +++++ys+           ++    +s++++l++++ t+tT+GYGd +p+ + agr+  ++++++G++ +++++a l++
  gi|518652279|ref|YP_008141799.1|  9 IAVIVYSVfseffiedsivSS--GIHSLFSSLWWTMQTITTVGYGD-TPVyGLAGRANGMLIMVIGIGSLGYLMAGLTS 84
                                      444444444555565464433..368********************.8888**********************999888 PP

                                      HH CS
                       Ion_trans_2 76 vl 77
                                      +l
  gi|518652279|ref|YP_008141799.1| 85 ML 86
                                      77 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.32   1.4e+03       1      14 [.      67      80 ..      67      84 .. 0.88
   2 !   36.4   0.3   1.2e-12   5.3e-09       1     107 [.     106     216 ..     106     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.32
                                      EEEES-SHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrsla 14
                                      i++iG G +G+ +a
  gi|518652279|ref|YP_008141799.1| 67 IMVIGIGSLGYLMA 80
                                      79********9887 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 1.2e-12
                                       EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SS...... CS
                            TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatg...... 71 
                                       i+++ +++ +++++++++ +g+d+v+   +e  v+   ++++++++g+  +e+ L +agi+ka++vi+         
  gi|518652279|ref|YP_008141799.1| 106 IVLCNYNESTKKVLDKIKYDGIDIVILNENE--VKG--DNEYTYIKGSFLRENDLIRAGIKKASSVIIFSRsedkeq 178
                                       79999************99998899888876..444..6689***************************88888888 PP

                                       ..SHHHHHHHHHHHHHHTSSSEEEEEESSGGGHHHHHH CS
                            TrkA_N  72 ..ddeanilavllakelnpkkkiiaraqdpehaellkk 107
                                          d+++il ++++++lnp+++ii ++ +p+  e +++
  gi|518652279|ref|YP_008141799.1| 179 maMDAESILSAMIIRKLNPEIRIIGEILNPDSREHASS 216
                                       8789**************************99887765 PP

>> Ion_trans  Ion transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   2.6   5.1e-07    0.0023     143     227 ..      12      76 ..       4      90 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.1e-07
                                       HHHHHHHHHHTTSCCCCCCSCCSTSSSTTTSSSSSSHHHHHHHHHHHHTTSSHHHHHHHHHHHSHHHHHHHHHHHHH CS
                         Ion_trans 143 ifaligvqlfkgklreknecaktwenpnngntnFdnfftallwlfrlmttegwgdilyatldekskvaliyfvifii 219
                                       i ++++ ++f               ++    +  +++f++l+w+++++tt+g+gd   + l ++        +++i+
  gi|518652279|ref|YP_008141799.1|  12 IVYSVFSEFF--------------IEDSIVSSGIHSLFSSLWWTMQTITTVGYGDTPVYGLAGR------ANGMLIM 68 
                                       3333333444..............233333444789**************************99......5555555 PP

                                       HHHHHHHH CS
                         Ion_trans 220 lgsflllN 227
                                       ++++  l 
  gi|518652279|ref|YP_008141799.1|  69 VIGIGSLG 76 
                                       55544444 PP

>> BK_channel_a  Calcium-activated BK potassium channel alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.023     1e+02      11      44 ..      11      44 ..       7     123 .. 0.86
   2 !   11.0   0.0     8e-05      0.36       5      60 ..     215     270 ..     211     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.023
                      BK_channel_a 11 vicleelKlglLAqsclcpGistllanLissasi 44
                                      vi+ + +   ++  s+++ Gi +l+++L  ++++
  gi|518652279|ref|YP_008141799.1| 11 VIVYSVFSEFFIEDSIVSSGIHSLFSSLWWTMQT 44
                                      888999999999999*********9999866664 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 8e-05
                      BK_channel_a   5 vksaddvicleelKlglLAqsclcpGistllanLissasikeestkseewlkeYlr 60 
                                        ++ dd+i+  ++   l+  s+++pGi  ++  L+ s si ee+ +++   + Y +
  gi|518652279|ref|YP_008141799.1| 215 SSFMDDIIIKGDVSSMLIYSSIMIPGIPEFINDLLMSNSISEEDIDKKYASNTYRE 270
                                       67889**********************************99885555544444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       860  (0.047967); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.33s 00:00:00.92 Elapsed: 00:00:00.55
# Mc/sec: 1710.31
//
Query:       gi|518652280|ref|YP_008141800.1|  [L=744]
Description: hypothetical protein FACI_IFERC00001G0919 [Ferroplasma acidarmanus fer1]
Scores for 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-100  332.4   0.0    8.2e-49  165.4   0.0    2.4  2  AAA              ATPase family associated with various cellul
    6.7e-29   99.4   0.1    1.4e-16   60.0   0.1    2.7  2  AAA_lid_3        AAA+ lid domain
    5.4e-23   81.0   1.4    9.7e-22   77.0   2.6    2.6  1  CDC48_N          Cell division protein 48 (CDC48), N-terminal
    2.2e-16   60.5   0.0      5e-07   30.0   0.0    2.6  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.7e-15   57.1   0.0    5.7e-07   29.4   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.4e-13   51.0   0.2    2.7e-05   24.2   0.1    3.8  2  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-12   47.9   0.1      5e-05   23.7   0.0    3.1  3  AAA_16           AAA ATPase domain
    6.9e-12   45.2   0.8    0.00015   21.1   0.0    3.6  3  TIP49            TIP49 P-loop domain
    1.7e-11   44.3   0.0      1e-05   25.6   0.0    2.7  2  AAA_14           AAA domain
    7.9e-10   39.1   1.4     0.0054   17.0   0.0    4.2  3  AAA_22           AAA domain
    2.4e-09   37.8   0.0     0.0035   17.9   0.0    3.7  3  AAA_18           AAA domain
      8e-09   35.8   0.0     0.0014   18.8   0.0    2.8  2  AAA_33           AAA domain
    1.1e-07   31.7   0.1      0.055   13.2   0.0    4.1  2  Sigma54_activat  Sigma-54 interaction domain
    4.8e-07   29.7   0.0      0.015   15.1   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
    1.3e-06   28.1   0.1    3.5e-06   26.7   0.1    1.8  1  CDC48_2          Cell division protein 48 (CDC48), domain 2
    1.3e-06   28.3   0.0      0.022   14.6   0.0    2.7  2  AAA_3            ATPase family associated with various cellul
    1.8e-06   28.3   0.0      0.093   13.1   0.0    2.7  2  RNA_helicase     RNA helicase
    2.3e-06   27.1   0.2      0.059   12.7   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.3e-06   27.1   0.0       0.11   12.8   0.0    2.3  2  AAA_28           AAA domain
    4.5e-06   26.3   0.0        0.1   12.1   0.0    2.5  2  AAA_7            P-loop containing dynein motor region
    4.6e-06   26.1   0.0      0.023   13.9   0.0    2.2  2  DUF2075          Uncharacterized conserved protein (DUF2075)
    1.1e-05   25.2   0.1       0.03   14.1   0.0    2.6  2  AAA_24           AAA domain
    1.7e-05   24.8   0.0       0.14   12.1   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    2.1e-05   24.0   2.9        0.5    9.7   0.0    4.0  4  ATPase           KaiC
    3.4e-05   23.8   0.0      0.086   12.6   0.0    2.4  2  AAA_11           AAA domain
    4.5e-05   22.8   0.1        0.3   10.4   0.0    2.5  2  Zeta_toxin       Zeta toxin
    0.00014   22.0   0.0       0.16   12.1   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
    0.00016   21.2   0.2        0.8    9.1   0.0    3.1  2  PhoH             PhoH-like protein
    0.00019   22.0   0.0       0.53   10.8   0.0    2.5  2  ABC_tran         ABC transporter
    0.00028   20.6   0.6       0.85    9.3   0.0    3.3  3  AAA_30           AAA domain
    0.00033   19.8   0.6          3    6.8   0.0    3.8  4  T2SSE            Type II/IV secretion system protein
    0.00033   21.1   0.1          1    9.7   0.0    3.3  2  AAA_17           AAA domain
    0.00036   20.2   5.4        2.3    7.8   0.0    4.1  4  AAA_25           AAA domain
    0.00046   19.4   0.0       0.31   10.1   0.0    2.5  2  DUF815           Protein of unknown function (DUF815)
     0.0015   18.9   1.1        3.3    8.0   0.8    3.2  2  AAA_19           AAA domain
     0.0018   17.4   0.2        1.1    8.2   0.0    2.3  2  Parvo_NS1        Parvovirus non-structural protein NS1
     0.0018   18.2   0.5        4.4    7.2   0.0    3.4  3  ATPase_2         ATPase domain predominantly from Archaea
      0.003   16.8   0.1        1.8    7.7   0.0    2.6  2  NB-ARC           NB-ARC domain
     0.0031   17.3   0.3          2    8.1   0.0    2.8  2  Cytidylate_kin   Cytidylate kinase
     0.0031   17.4   3.1        6.1    6.7   0.0    4.0  3  NTPase_1         NTPase
     0.0032   17.4   0.1        4.3    7.2   0.0    2.8  2  NACHT            NACHT domain
     0.0073   16.4   0.1        3.4    7.8   0.0    2.6  2  SKI              Shikimate kinase
     0.0098   16.0   0.0        1.3    9.1   0.0    2.4  2  Cytidylate_kin2  Cytidylate kinase-like family
  ------ inclusion threshold ------
      0.018   15.0   0.0        3.2    7.7   0.0    2.8  2  Rad17            Rad17 P-loop domain
      0.031   14.3   0.0         11    6.0   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
      0.039   13.7   0.0        1.5    8.5   0.0    2.2  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.044   13.6   0.0        1.3    8.8   0.0    2.7  2  Bac_DnaA         Bacterial dnaA  protein
      0.048   13.7   1.2         11    6.1   0.1    3.3  2  Vps4_C           Vps4 C terminal oligomerisation domain
       0.05   13.3   0.0        3.9    7.1   0.0    2.5  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
      0.087   12.7   0.0        1.9    8.3   0.0    2.5  2  CPT              Chloramphenicol phosphotransferase-like prot
       0.11   11.9   0.0        5.9    6.2   0.0    2.3  2  IPT              Isopentenyl transferase
       0.12   12.1   0.1         20    5.0   0.0    2.5  2  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 fami


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.8   0.0   3.8e-51   1.3e-48       1     131 [.     227     356 ..     227     357 .. 0.97
   2 !  165.4   0.0   2.4e-51   8.2e-49       2     131 ..     505     634 ..     504     635 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.8 bits;  conditional E-value: 3.8e-51
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       vll GppGtGKTl+akava+e+g++f+ i+g+e++sky g+se+k+re+f++a e++ psi+fiDEid++a++r++ 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANFFAINGPEIMSKYYGQSEQKLREIFQKADESE-PSIIFIDEIDSIAPKREDV 302
                                       79****************************************************998.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       + e+e+rvv+qLlt +dg+k++ + vivigatnr d +dpal+r gRfdr+i i+
  gi|518652280|ref|YP_008141800.1| 303 QGEVERRVVAQLLTLMDGLKDRGH-VIVIGATNRLDAVDPALRRpGRFDREIVIG 356
                                       *********************866.**************************9886 PP

  == domain 2  score: 165.4 bits;  conditional E-value: 2.4e-51
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH.TTC CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr.sgs 77 
                                       llyGppGtGKTllakava+e++++f++++g+e+lsk+vg+sek +re+fk+ak+ + p i+f+DEid++a++r ++ 
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFISVKGPEVLSKWVGDSEKAVREIFKKAKQVS-PAIIFMDEIDSIAPRRgTSM 580
                                       9******************************************************9.****************8888 PP

                                       CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallr.gRfdrkieie 131
                                       +s+++er+vnqLlt +dg +  ++ v+vi+atnrpd +dpallr gRfd++i+i+
  gi|518652280|ref|YP_008141800.1| 581 DSGVTERIVNQLLTSMDGIEVLKG-VVVIAATNRPDIIDPALLRaGRFDKIIYIP 634
                                       *********************877.****************************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0     8e-12   2.8e-09       4      40 ..     387     423 ..     385     444 .. 0.76
   2 !   60.0   0.1   4.2e-19   1.4e-16       1      44 [.     657     702 ..     657     703 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8e-12
                         AAA_lid_3   4 lkeLAerTeGySGADlaalcreAallAlrrgikeitm 40 
                                       ++++A  T G++GADlaal re+a++Alrr ++ei+ 
  gi|518652280|ref|YP_008141800.1| 387 FSRIADITYGFVGADLAALTRESAMNALRRYLPEIDL 423
                                       578***************************6555543 PP

  == domain 2  score: 60.0 bits;  conditional E-value: 4.2e-19
                         AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgik..eitmedfe 44 
                                       dvdlk++A++T+Gy+GADl++lcreA+++A+r + +  e++++ f+
  gi|518652280|ref|YP_008141800.1| 657 DVDLKDIARKTDGYVGADLENLCREAGMMAYRNNPEatEVNQDAFI 702
                                       9********************************9775459999886 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 !   77.0   2.6   2.8e-24   9.7e-22       2      85 .]       9      92 ..       8      92 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 2.8e-24
                                      EEEECCSS-CSSTTEEEE-HHHHHHHTS-TTSEEEEECCCCEEEEEEEBSTTSTTTTEEEE-HHHHHHHT--TTEEEEE CS
                           CDC48_N  2 LrVaeapqedvgrgivridpedmeelglepgdvveiegkrkTvaivwpaepedegkgiIrmdgvtRknagvsiGdkVtV 80
                                      Lr+aea+ +d g  +vr+d+    +l++e gdvv ie+ r+Tv  v++++pede+kgi+r+d+v+R+n+g+siGdkV+V
  gi|518652280|ref|YP_008141800.1|  9 LRIAEANATDPGMARVRLDEISRLDLDVEIGDVVAIEKVRSTVGRVFRSRPEDENKGIVRIDSVMRNNCGASIGDKVKV 87
                                      89*****99*****************************999************************************** PP

                                      EEE-- CS
                           CDC48_N 81 rkaev 85
                                      +k+ev
  gi|518652280|ref|YP_008141800.1| 88 KKVEV 92
                                      **985 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   1.4e-09     5e-07       6     105 ..     227     320 ..     223     324 .. 0.85
   2 !   27.6   0.0     8e-09   2.8e-06       6     107 ..     504     600 ..     500     610 .. 0.84

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 1.4e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt++aka+a+   +    ++  ++  e++     + + ++++  ++  ++a+e+   i+++DEid i
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGA----NFFAINGPEIMS----KYYGQSEQKLREIFQKADESEpsIIFIDEIDSI 295
                                       6899******************96....************....88888888888888888887788********** PP

                                       ---.---------HHHHHHHHHHHH- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileg 105
                                       +pk e  + +v r  V+  LL +++g
  gi|518652280|ref|YP_008141800.1| 296 APKrEDVQGEVER-RVVAQLLTLMDG 320
                                       **85555566655.577788999987 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 8e-09
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidKi 80 
                                       +ll gp g+Gkt+laka+a+  ++    ++i +   e+l     + + ++++  ++  ++a++    i+++DEid i
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNA----NFISVKGPEVLS----KWVGDSEKAVREIFKKAKQVSpaIIFMDEIDSI 572
                                       8999******************96....************....88888888888888888888888********** PP

                                       ---.---------HHHHHHHHHHHH--E CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileggt 107
                                       +p+ ++s      e +++ LL  ++g +
  gi|518652280|ref|YP_008141800.1| 573 APRrGTSMDSGVTERIVNQLLTSMDGIE 600
                                       **96333333446788888888888755 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   1.7e-09   5.7e-07      35     103 ..     226     302 ..     220     349 .. 0.85
   2 !   24.6   0.0     5e-08   1.7e-05      36      98 ..     504     574 ..     495     627 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.7e-09
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl......ekagdlaalltnleekd..vlfideihrlsraveev 103
                                        vll GpPG Gkt +ak +a+e g+++ +  gP +      + ++ l  ++++ +e++  ++fidei  ++++ e+v
  gi|518652280|ref|YP_008141800.1| 226 GVLLNGPPGTGKTLIAKAVANESGANFFAINGPEImskyygQSEQKLREIFQKADESEpsIIFIDEIDSIAPKREDV 302
                                       59*******************************993333333457899999988766444*********99998876 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 5e-08
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsgPvl.ek.agd....laalltnleek..dvlfideihrlsr 98 
                                        llyGpPG Gkt lak +a+e ++++ +  gP + +k  gd    +  ++++ ++    ++f+dei  +++
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNANFISVKGPEVlSKwVGDsekaVREIFKKAKQVspAIIFMDEIDSIAP 574
                                       69******************************762332344111144555555543225899999988766 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 !   24.2   0.1   7.9e-08   2.7e-05       1     136 [.     226     345 ..     226     346 .. 0.70
   2 !   21.8   0.0   4.3e-07   0.00015       2     135 ..     504     622 ..     503     624 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 7.9e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEve 75 
                                       +vlL GppGtgK+ +a+ +a   +++++ +++++ +++    g+ e        +  ++ ++a   e++i+++DE++
  gi|518652280|ref|YP_008141800.1| 226 GVLLNGPPGTGKTLIAKAVANESGANFFAINGPEIMSKYY--GQSE-------QKLREIFQKADesEPSIIFIDEID 293
                                       59********************************887643..3333.......1223333333358*********** PP

                                       G--...HHHHHHHHHHHHSSEEE..-SSSEEE---........-EEEEEESS--.-TT-TTHHHHT CS
                             AAA_5  76 rae...sevlnsLlslleerrllleeggelvkaknddller..frviatanpldrslnelspalrs 136
                                        +     +v++++ +          ++ +l++  +d    r  + vi+++n+ld     ++palr+
  gi|518652280|ref|YP_008141800.1| 294 SIApkrEDVQGEVERRVVA------QLLTLMDGLKD----RghVIVIGATNRLD----AVDPALRR 345
                                       9982223566666444444......55555544443....12299999999999....77888876 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 4.3e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------.G-SEEEEESGGG- CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar.egeilvlDEvera 77 
                                       +lL GppGtgK+ la+ +a   n+++  v +++      ++ ++   ++ ++ v  ++++a + +++i+++DE++ +
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNANFISVKGPE------VLSKWV--GDSEKAVREIFKKAKQvSPAIIFMDEIDSI 572
                                       89****************************998......778888..67777888888877779***********99 PP

                                       -HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHH CS
                             AAA_5  78 esevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalr 135
                                        +    s+ s   er +   ++ + ++  +   l+ + via++n++d     ++pal+
  gi|518652280|ref|YP_008141800.1| 573 APRRGTSMDSGVTERIVN--QLLTSMDGIE--VLKGVVVIAATNRPD----IIDPALL 622
                                       988888888877777776..4444444444..455699999999988....6666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   1.5e-07     5e-05      16     145 ..     216     334 ..     213     344 .. 0.69
   2 !   19.7   0.0   2.6e-06   0.00091      15      62 ..     492     536 ..     487     558 .. 0.81
   3 ?   -0.9   0.0       5.3   1.8e+03     122     147 ..     548     572 ..     539     593 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 1.5e-07
                            AAA_16  16 lervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqlldeaesa 92 
                                       +er+    p  vll G++G+GK+ ++++++++  ++   f++ +  +  ++  y +  q l r e++++ ++     
  gi|518652280|ref|YP_008141800.1| 216 FERLGITPPKGVLLNGPPGTGKTLIAKAVANESGAN---FFAINGPEI-MSKYYGQSEQKL-R-EIFQKADES---E 283
                                       56666666799*******************877766...766666666.334444466666.5.666665555...3 PP

                            AAA_16  93 eleawrekleealaavpelagaeasrllellkrllallsrderplvlvlDdlq 145
                                           + +++++ +    ++ g+ ++r+ ++l  l++ l+ +++  v+v+    
  gi|518652280|ref|YP_008141800.1| 284 PSIIFIDEIDSIAPKREDVQGEVERRVVAQLLTLMDGLKDRGH--VIVIGATN 334
                                       334444445555555555666666***************9999..77665555 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 2.6e-06
                            AAA_16  15 alervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdq 62 
                                       +++r+    p   ll+G++G+GK+ l+++++++ +++   f++ k  +
  gi|518652280|ref|YP_008141800.1| 492 VFSRLGIRAPKGFLLYGPPGTGKTLLAKAVANESNAN---FISVKGPE 536
                                       567777788999*******************988777...66655544 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 5.3
                            AAA_16 122 llkrllallsrderplvlvlDdlqwa 147
                                       +++++++++++  +p ++++D+++ +
  gi|518652280|ref|YP_008141800.1| 548 AVREIFKKAKQ-VSPAIIFMDEIDSI 572
                                       56778889999.888*******9965 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.3      0.36   1.2e+02     170     197 ..      35      62 ..      23      96 .. 0.85
   2 !   21.1   0.0   4.3e-07   0.00015      51     105 ..     225     278 ..     218     318 .. 0.87
   3 !   18.2   0.0   3.4e-06    0.0012      50     107 ..     501     557 ..     495     570 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.36
                                       T--TT-EEEEETTT--EEE-SSS-SS-- CS
                             TIP49 170 kvkegDviviekesGkvkklGrsearak 197
                                        v+ gDv+ iek + +v ++ rs+ + +
  gi|518652280|ref|YP_008141800.1|  35 DVEIGDVVAIEKVRSTVGRVFRSRPEDE 62 
                                       6899****************99986655 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 4.3e-07
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXX CS
                             TIP49  51 ravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktev.ltqalrk 105
                                       ++vLl Gp+gtGkt +a a+++e g    f a++g e+ s    ++e  l + ++k
  gi|518652280|ref|YP_008141800.1| 225 KGVLLNGPPGTGKTLIAKAVANESG--ANFFAINGPEIMSKYYGQSEQkLREIFQK 278
                                       89*********************98..78***********9988887525555655 PP

  == domain 3  score: 18.2 bits;  conditional E-value: 3.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXX CS
                             TIP49  50 GravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkte.vltqalrksi 107
                                        ++ Ll Gp+gtGkt la a+++e +    f++++g ev s  v  +e ++ + ++k+ 
  gi|518652280|ref|YP_008141800.1| 501 PKGFLLYGPPGTGKTLLAKAVANESN--ANFISVKGPEVLSKWVGDSEkAVREIFKKAK 557
                                       5899*******************966..89************99998835667777775 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0   2.9e-08     1e-05       5     104 ..     227     336 ..     224     354 .. 0.79
   2 !   15.6   0.0   3.7e-05     0.013       6      76 ..     505     572 ..     501     602 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2.9e-08
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..... 76 
                                       +++ G+  +GKT ++k +++e+     +++ in  +   k + ++e+ l++i++k+ e++ +++f+DEi  +     
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESG---ANFFAINGPEIMSKYYGQSEQKLREIFQKADESEPSIIFIDEIDSIapkre 300
                                       7899***************9999...**********9998888777556666666555699***********99999 PP

                            AAA_14  77 .......pewekalkslvd.egknldvivtGSnskl 104
                                              +++   l  l+d  +++++viv G  + l
  gi|518652280|ref|YP_008141800.1| 301 dvqgeveRRVVAQLLTLMDgLKDRGHVIVIGATNRL 336
                                       999888877777777777752246788888877765 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.7e-05
                            AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                                       ++ G+  +GKT l+k +++e+     +++ ++  +   k   d+ek  ++i++k+k+    ++f+DEi  +
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESN---ANFISVKGPEVLSKWVGDSEKAVREIFKKAKQVSPAIIFMDEIDSI 572
                                       7899**************8888...8888888888888888888888888888866668899******876 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   0.00011     0.038       9      59 ..     228     278 ..     223     282 .. 0.80
   2 ?    6.6   0.1     0.026       9.1      73     132 ..     267     334 ..     259     339 .. 0.71
   3 !   17.0   0.0   1.6e-05    0.0054       9      49 ..     505     536 ..     499     608 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 0.00011
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllre 59 
                                       ++ G++GtGKT+ ++ ++++  +  +a  ++pe++ +++ +s+ ++++++++
  gi|518652280|ref|YP_008141800.1| 228 LLNGPPGTGKTLIAKAVANESGANFFAI-NGPEIMsKYYGQSEQKLREIFQK 278
                                       678*****************86554444.57777778999998899999887 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.026
                            AAA_22  73 lsseellealeqalraravielliiDEaqhlr...s.......eealeeLrsllnlsrkgvqliLvGtpe 132
                                       +s++ l+e +++a ++    +++ iDE++ +    +        +++ +L +l++  ++  ++i++G ++
  gi|518652280|ref|YP_008141800.1| 267 QSEQKLREIFQKADESEP--SIIFIDEIDSIApkrEdvqgeveRRVVAQLLTLMDGLKDRGHVIVIGATN 334
                                       555556665555555555..5**********887515667788889999999999877888888888874 PP

  == domain 3  score: 17.0 bits;  conditional E-value: 1.6e-05
                            AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlps 49 
                                       +++G++GtGKT+l++ ++++          ++ +++v+ p+
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANES---------NANFISVKGPE 536
                                       79*****************98.........66666666554 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     1e-05    0.0035       1      78 [.     227     329 ..     227     359 .. 0.70
   2 !   12.7   0.0   0.00042      0.14       2      25 ..     505     546 ..     505     615 .. 0.69
   3 ?    2.5   0.0      0.57     2e+02      16      69 ..     661     713 ..     654     732 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf.................gvnlrdvakenglllevdpe..........aldes 49 
                                       +ll+G+pG+GKt +ak+++++  ++                  ++lr+++++ + +++   +            d +
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESgANffaingpeimskyygqsEQKLREIFQKADESEPSIIFideidsiapkREDVQ 303
                                       79****************88863335888888888888888866666666665555555555553555555444455 PP

                            AAA_18  50 krldedkldklldaleenssaleegknlv 78 
                                        ++++ ++++ll+++++  +    g+++v
  gi|518652280|ref|YP_008141800.1| 304 GEVERRVVAQLLTLMDGLKD---RGHVIV 329
                                       55555555555555555543...555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00042
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf..................g 25 
                                       ll G+pG+GKt lak+++++ +                    
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNAnfisvkgpevlskwvgdsE 546
                                       589**************8775223466665544444444443 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.57
                            AAA_18  16 keLskrl.gf.gvnlrdvakenglllevdpealdeskrldedkldklldaleenss 69 
                                       k +++++ g+ g  l  +++e g+  +++++   e  ++++d   k++++++ +++
  gi|518652280|ref|YP_008141800.1| 661 KDIARKTdGYvGADLENLCREAGMMAYRNNP---EATEVNQDAFIKAMKTIRPSID 713
                                       5567888888999*****************9...9999999998888888877655 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0     4e-06    0.0014       2      47 ..     227     296 ..     227     353 .. 0.71
   2 !   14.0   0.0   0.00012     0.042       3      39 ..     505     543 ..     504     639 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4e-06
                            AAA_33   2 vllvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqskt......................d 47 
                                       vll G+pG+GK+  a+ ++++ g  ++ ++ ++++++++g+ +q+++                       
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGanFFAINGPEIMSKYYGQSEQKLReifqkadesepsiifideidsiA 296
                                       7899*******************99999***********9766665544555555555555555555550 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 0.00012
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfg 39 
                                       ll G+pG+GK+ la+ ++++    ++ +  ++++++ +g
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNanFISVKGPEVLSKWVG 543
                                       678***************999966666666665555555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   0.00016     0.055      23      61 ..     225     260 ..     214     335 .. 0.80
   2 !   11.2   0.0   0.00063      0.22      24      57 ..     503     533 ..     494     633 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                                       S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                         vl++G  GtGK+l+a+a+ ++s    ++f a+n  +i
  gi|518652280|ref|YP_008141800.1| 225 KGVLLNGPPGTGKTLIAKAVANESG---ANFFAINGPEI 260
                                       569****************998776...67777776554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00063
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEE CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavn 57 
                                         l+ G  GtGK+lla+a+ ++s+   ++f++v 
  gi|518652280|ref|YP_008141800.1| 503 GFLLYGPPGTGKTLLAKAVANESN---ANFISVK 533
                                       579***************998876...6677765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00037      0.13      48      71 ..     225     248 ..     214     293 .. 0.88
   2 !   15.1   0.0   4.3e-05     0.015      45      75 ..     499     529 ..     493     551 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00037
                         IstB_IS21  48 enivllGpsGvGKshlaialgvea 71 
                                       ++++l Gp+G+GK+ +a a++ e 
  gi|518652280|ref|YP_008141800.1| 225 KGVLLNGPPGTGKTLIAKAVANES 248
                                       6799***************99875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4.3e-05
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavrag 75 
                                       ++ ++++l Gp+G+GK+ la a++ e  ++ 
  gi|518652280|ref|YP_008141800.1| 499 RAPKGFLLYGPPGTGKTLLAKAVANESNANF 529
                                       666789*****************99876655 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 !   26.7   0.1     1e-08   3.5e-06       4      63 ..     114     178 ..     111     179 .. 0.90

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 1e-08
                                       CCCCH.HHHCCCTTEEE-TTEEEEECCT....CCCEEEEEEEECCCC.SCEEECTSCCEEESTTCC CS
                           CDC48_2   4 gdema.ylkrqFlgrpvtkGdlvvfefk....gqeiklvVvstePkg.pvgitetTeielgtkpve 63 
                                       ++ ++  +++++  rp+ + d + ++ +     + + ++V +t P+  pv ++e+T +e++++p++
  gi|518652280|ref|YP_008141800.1| 114 EG-IDdFVQKALIRRPLIEQDSISVPGLtlagHTGLLFKVIKTIPSKiPVEVSEETRVEIREDPAS 178
                                       44.55599*******************99998778*****************************97 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00094      0.33       2      31 ..     227     256 ..     226     312 .. 0.80
   2 !   14.6   0.0   6.3e-05     0.022       3     111 ..     505     612 ..     503     621 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00094
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriq 31 
                                       vll+g PG++ktl++ka+a+  +++f  i 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANFFAIN 256
                                       89******************9999997775 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 6.3e-05
                             AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappktq 79 
                                       ll g PG++ktll+ka+a+  +++f  ++  p++l    +G +  e++ +e+  k+  v   +++ dei+  +p+  
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFISVK-GPEVLSK-WVGDS--EKAVREIFKKAKQVSPAIIFMDEIDSIAPRRG 577
                                       8999*********************9997.6888755.55654..45556777777889999********9999988 PP

                             AAA_3  80 salleameerqvtv...egethklpepflvlatqn 111
                                       +++   + er v     + +  ++ +  +v+a+ n
  gi|518652280|ref|YP_008141800.1| 578 TSMDSGVTERIVNQlltSMDGIEVLKGVVVIAATN 612
                                       88877777776543110223334444444444443 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.0   0.00043      0.15       1      69 [.     227     286 ..     227     299 .. 0.74
   2 !   13.1   0.0   0.00027     0.093       2      27 ..     505     535 ..     504     613 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00043
                      RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYtgqevvvidDfgqvkdeenpsd 69 
                                       ++l Gp+g+GK+++ak +a++           +++   +  +++++Y gq      ++ q+ de++ps+
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESG--------ANFF-AINGPEIMSKYYGQSEQKLREIFQKADESEPSI 286
                                       5789*************443333........3343.356788999999999999999999988866663 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 0.00027
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl.....k 27 
                                       +lyGp+g+GK++lak +a++   ++      
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFisvkgP 535
                                       69**************999887666444431 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00036      0.12      25      42 ..     227     244 ..     221     247 .. 0.90
   2 !   12.7   0.0   0.00017     0.059      25      42 ..     504     521 ..     498     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll GppG+GKt++ak++
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAV 244
                                       89*************987 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00017
                      Mg_chelatase  25 lllvGppGsGKtmlakrl 42 
                                       +ll+GppG+GKt+lak++
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAV 521
                                       79*************987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00031      0.11       2      49 ..     227     275 ..     226     319 .. 0.72
   2 !   11.9   0.0   0.00058       0.2       3      35 ..     505     542 ..     504     566 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00031
                            AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv 49 
                                       + + G+++tGKT +++a a++ g + ++  + ei+++ + + e++l++ 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANEsGANFFAINGPEIMSKYYGQSEQKLREI 275
                                       5788***************877777665555555555555555555544 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00058
                            AAA_28   3 vitGgestGKTtlleaLaar...gypvv..pEaareil 35 
                                        + G+++tGKT l++a a++   ++  v  pE+  + +
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANEsnaNFISVkgPEVLSKWV 542
                                       689***************76545333333777666555 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   0.00047      0.16      33      59 ..     224     250 ..     214     303 .. 0.83
   2 !   12.1   0.0   0.00029       0.1      27      62 ..     495     529 ..     489     535 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00047
                             AAA_7  33 kkpvllvGptGtGKtviikdllkkldk 59 
                                        k vll Gp GtGKt+i+k + ++   
  gi|518652280|ref|YP_008141800.1| 224 PKGVLLNGPPGTGKTLIAKAVANESGA 250
                                       5789***************99887764 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00029
                             AAA_7  27 elllknkkpvllvGptGtGKtviikdllkkldkeky 62 
                                       +l +++ k +ll+Gp GtGKt+++k + ++ +  ++
  gi|518652280|ref|YP_008141800.1| 495 RLGIRAPKGFLLYGPPGTGKTLLAKAVANESN-ANF 529
                                       5567788999***************9999887.444 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   6.7e-05     0.023       4      75 ..     227     293 ..     224     312 .. 0.69
   2 !   10.1   0.0   0.00098      0.34       4      44 ..     504     537 ..     501     578 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.7e-05
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl.vlrealakkeekkkkkeafekls.sfinnls 75 
                                       vl +G +GtGKt+++ ++++e         a+++  N+p+++ +++ + ++k ++   k++ +++s  fi +++
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANES-------GANFFAINGPEIMsKYYGQSEQKLREIFQKADESEPSiIFIDEID 293
                                       6789**************9998.......677777777775537777777777444444445554424555555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplv 44 
                                       +l  G +GtGKt+++ ++++e        +a+++sv +p+v
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANES-------NANFISVKGPEV 537
                                       7889************999998.......666666666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0043       1.5       5      76 ..     227     294 ..     224     334 .. 0.71
   2 !   14.1   0.0   8.6e-05      0.03       5      59 ..     504     572 ..     500     607 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0043
                            AAA_24   5 iliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdieswedfldevvelaaeladyktlviDtide 76 
                                       +l+ Gp+g+GKT +ak      g +++ i+  + + s +  +     s +++++ +++ ++ ++  ++++iD id 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVanesGANFFAINGPEIM-SKYYGQ-----SEQKLREIFQKADESEP--SIIFIDEIDS 294
                                       7899************9966555555555544422.222222.....44556665555544444..6667776665 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 8.6e-05
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfi.............dtekGlksldadkfpdieswedfldevvel 59 
                                       +l+yGp+g+GKT lak    + ++ fi             d ek + +  ++k ++++  + f+de++++
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVanESNANFIsvkgpevlskwvgDSEKAV-REIFKKAKQVSPAIIFMDEIDSI 572
                                       79**************998877777775555555555666666644.33344445555666666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00041      0.14      19      60 ..     224     265 ..     198     277 .. 0.79
   2 !   10.1   0.0    0.0018      0.62      20      51 ..     502     535 ..     473     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00041
                                       TEEEEEEESTTSSHHHHHHHHHHHTT--..----TTTTSEEEEE CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve..evkSPTFtlveeYe 60 
                                        + +lL+G+ G+GKT +++++a++ g +  +++ P   ++++Y 
  gi|518652280|ref|YP_008141800.1| 224 PKGVLLNGPPGTGKTLIAKAVANESGANffAINGP--EIMSKYY 265
                                       4559*********************9998889888..4666664 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0018
                                       EEEEEEESTTSSHHHHHHHHHHHTT--..----T CS
                              TsaE  20 dvilLeGdLGaGKTtlvrglakalgve..evkSP 51 
                                       + +lL+G+ G+GKT l++++a++ + +  +vk P
  gi|518652280|ref|YP_008141800.1| 502 KGFLLYGPPGTGKTLLAKAVANESNANfiSVKGP 535
                                       3489*****************9998876667666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.1    0.0029         1      15      38 ..     220     243 ..     213     253 .. 0.83
   2 ?    2.5   0.0      0.22        76     114     154 ..     278     321 ..     256     333 .. 0.68
   3 !    9.7   0.0    0.0015       0.5      14      38 ..     496     520 ..     488     534 .. 0.83
   4 ?   -1.7   0.0       4.4   1.5e+03     125     155 ..     569     600 ..     544     607 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0029
                            ATPase  15 GipegrvvlitGepGtGKtifalq 38 
                                       Gi   + vl+ G pGtGKt++a+ 
  gi|518652280|ref|YP_008141800.1| 220 GITPPKGVLLNGPPGTGKTLIAKA 243
                                       77778889************9975 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.22
                            ATPase 114 aikeikakrvviDsitgl...ayeekeavaReilrqlvrvlkkl 154
                                         +e + + + iD i+++    ++ + +v R+ + ql++ + +l
  gi|518652280|ref|YP_008141800.1| 278 KADESEPSIIFIDEIDSIapkREDVQGEVERRVVAQLLTLMDGL 321
                                       33445557777777777742144455677899999999999765 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0015
                            ATPase  14 gGipegrvvlitGepGtGKtifalq 38 
                                        Gi   +  l++G pGtGKt++a+ 
  gi|518652280|ref|YP_008141800.1| 496 LGIRAPKGFLLYGPPGTGKTLLAKA 520
                                       588888999*************986 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 4.4
                            ATPase 125 iDsitgl.ayeekeavaReilrqlvrvlkklg 155
                                       iDsi++   +++++ v+ +i+ ql++ + +++
  gi|518652280|ref|YP_008141800.1| 569 IDSIAPRrGTSMDSGVTERIVNQLLTSMDGIE 600
                                       78888877778888889999999999987765 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0043       1.5      20      39 ..     227     246 ..     206     283 .. 0.82
   2 !   12.6   0.0   0.00025     0.086      18      76 ..     502     558 ..     477     576 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0043
                            AAA_11  20 tliqGPPGtgKTktivells 39 
                                       +l+ GPPGtgKT    ++ +
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVAN 246
                                       799*********76655555 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00025
                            AAA_11  18 eitliqGPPGtgKTktivellsqllsrrkseeeksakpriL..vCapSNaAvDellerllr 76 
                                       + +l+ GPPGtgKT    ++ ++ +     +    ++p++L    + S++Av e+ ++  +
  gi|518652280|ref|YP_008141800.1| 502 KGFLLYGPPGTGKTLLAKAVANESN----ANFISVKGPEVLskWVGDSEKAVREIFKKAKQ 558
                                       45799*********99999999993....34466777777733589999999999887665 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   0.00086       0.3      16      50 ..     224     256 ..     216     269 .. 0.88
   2 !    9.6   0.0    0.0015       0.5      15      50 ..     500     533 ..     493     537 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00086
                        Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                       Pk +ll G pG GK+ +a+++++e   + n+  ++
  gi|518652280|ref|YP_008141800.1| 224 PKGVLLNGPPGTGKTLIAKAVANES--GANFFAIN 256
                                       999********************98..67776666 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0015
                        Zeta_toxin  15 rPklillgGqpGAGKselaellkdelerqgnvvrld 50 
                                        Pk  ll G pG GK+ la+++++e   + n++ ++
  gi|518652280|ref|YP_008141800.1| 500 APKGFLLYGPPGTGKTLLAKAVANES--NANFISVK 533
                                       79999********************8..89988876 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   0.00046      0.16      24      83 ..     227     297 ..     221     306 .. 0.70
   2 ?    7.1   0.0     0.016       5.5      25      81 ..     505     572 ..     499     584 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00046
                                       EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..........HHHHHHT...TTSEEEEEE-TT--H CS
                   Sigma54_activ_2  24 vfltGekGsgkelvArlLhknsgpwleifvverlaklp..........ldlleqa...kggtLylkdiadlsk 83 
                                       v+l G++G+gk+l+A++ +++sg +   f ++ +  +            +++++a   ++ ++++ +i+++ +
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANF--FAINGPEIMSkyygqseqklREIFQKAdesEPSIIFIDEIDSIAP 297
                                       9********************99853..333222221122233333447888886555888999999988765 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.016
                                       EEEEETT--HHHHHHCC--TTS-EE.--SSTTHHHH-H.........HHHHHHT...TTSEEEEEE-TT- CS
                   Sigma54_activ_2  25 fltGekGsgkelvArlLhknsgpwl.eifvverlaklp.........ldlleqa...kggtLylkdiadl 81 
                                       +l G++G+gk+l A++ +++s  +  +++  e l+             +++++a   +++++++ +i+++
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFiSVKGPEVLS--KwvgdsekavREIFKKAkqvSPAIIFMDEIDSI 572
                                       799**************998876421222112222..112222233366666533337777777777765 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.1    0.0037       1.3      22      41 ..     227     246 ..     221     253 .. 0.86
   2 !    9.1   0.0    0.0023       0.8      24      42 ..     506     524 ..     498     531 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0037
                                       EEEE--TTSSTTHHHHHHHH CS
                              PhoH  22 vfaiGpaGtGKtylavalav 41 
                                       v   Gp GtGKt++a a+a 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVAN 246
                                       5678***********99985 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0023
                                       EE--TTSSTTHHHHHHHHH CS
                              PhoH  24 aiGpaGtGKtylavalave 42 
                                         Gp GtGKt+la a+a e
  gi|518652280|ref|YP_008141800.1| 506 LYGPPGTGKTLLAKAVANE 524
                                       68***********999865 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.0    0.0075       2.6       8      74 ..     221     286 ..     218     336 .. 0.73
   2 !   10.8   0.0    0.0015      0.53      12      75 ..     502     564 ..     494     612 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0075
                                       EETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                          ABC_tran   8 lkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpel 74 
                                       + + + v + G+ G+GK+ ++k++a+++  +     ++g ++ ++   +++++++ ++q+ ++  p +
  gi|518652280|ref|YP_008141800.1| 221 ITPPKGVLLNGPPGTGKTLIAKAVANESGANF--FAINGPEIMSKYYGQSEQKLREIFQKaDESEPSI 286
                                       5566678899***************9987544..4458888888888888888888888855555555 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.0015
                                       SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                          ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpelt 75 
                                       +   + G+ G+GK+ L+k++a++++  +  i ++g ++ ++    ++k ++ ++++ +q+ p + 
  gi|518652280|ref|YP_008141800.1| 502 KGFLLYGPPGTGKTLLAKAVANESN--ANFISVKGPEVLSKWVGDSEKAVREIFKKaKQVSPAII 564
                                       556799*****************97..57888899999998888888888888888677777664 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0    0.0025      0.85      21      40 ..     227     246 ..     214     255 .. 0.85
   2 ?   -1.4   0.0       4.7   1.6e+03     104     133 ..     310     341 ..     279     342 .. 0.76
   3 !    7.6   0.0    0.0081       2.8      22      41 ..     505     524 ..     499     535 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0025
                            AAA_30  21 avltGpAGtGKttalkalre 40 
                                       ++l+Gp+GtGKt + ka+++
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVAN 246
                                       689***********999975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 4.7
                            AAA_30 104 qlaallkaaek..agakvilvGDerQlasVea 133
                                        +a+ll+ ++   +  +vi++G ++ l++V++
  gi|518652280|ref|YP_008141800.1| 310 VVAQLLTLMDGlkDRGHVIVIGATNRLDAVDP 341
                                       55555555554213789999999999999975 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0081
                            AAA_30  22 vltGpAGtGKttalkalrea 41 
                                       +l Gp+GtGKt + ka+++ 
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANE 524
                                       678***********999865 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0087         3     117     167 ..     120     177 ..      84     199 .. 0.74
   2 ?    2.8   0.1      0.15        51     131     152 ..     226     247 ..     215     255 .. 0.85
   3 ?    5.4   0.0     0.024       8.2     126     155 ..     498     527 ..     458     535 .. 0.87
   4 ?   -2.1   0.0       4.7   1.6e+03      36      70 ..     705     739 ..     689     742 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0087
                             T2SSE 117 kiaevlrkavrerglilvsGgTgsGKttllyallkeinks.......derivtvEDpv 167
                                        +++++r+++ e+ +i v G T  G t ll  ++k+i+++       + r+ + EDp+
  gi|518652280|ref|YP_008141800.1| 120 VQKALIRRPLIEQDSISVPGLTLAGHTGLLFKVIKTIPSKipvevseETRVEIREDPA 177
                                       457789*******************************998333333233333333433 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.15
                             T2SSE 131 lilvsGgTgsGKttllyallke 152
                                        +l+ G+ g+GKt ++ a+ +e
  gi|518652280|ref|YP_008141800.1| 226 GVLLNGPPGTGKTLIAKAVANE 247
                                       5899**********99998765 PP

  == domain 3  score: 5.4 bits;  conditional E-value: 0.024
                             T2SSE 126 vrerglilvsGgTgsGKttllyallkeink 155
                                       +r+ + +l+ G+ g+GKt l+ a+ +e n+
  gi|518652280|ref|YP_008141800.1| 498 IRAPKGFLLYGPPGTGKTLLAKAVANESNA 527
                                       55667899**************99988776 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 4.7
                             T2SSE  36 lreveelekaalerlisriaalakldiseerplqd 70 
                                       +++++ + ++ ++ + s +aa++++dise+++  d
  gi|518652280|ref|YP_008141800.1| 705 MKTIRPSIDKNVTKFYSDLAATMGRDISEKKKTED 739
                                       455666667888999999***********998765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0     0.016       5.6       2      55 ..     231     285 ..     230     308 .. 0.65
   2 !    9.7   0.0     0.003         1       1      37 [.     507     545 ..     507     661 .. 0.63

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.016
                                       E-TTSSHHHHHHHHHHHHTEEE..EEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfth..lsaGdllreeakrgglakardemrklpleekk 55 
                                       G+PG GK+ +++ ++ + g  +  ++  +++ +    ++ +k r+ ++k++++e  
  gi|518652280|ref|YP_008141800.1| 231 GPPGTGKTLIAKAVANESGANFfaINGPEIMSKYY-GQSEQKLREIFQKADESEPS 285
                                       9**************99865551155444444433.33334556666666666655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.003
                                       EE-TTSSHHHHHHHHHHHHTEEEEEH..HHHHHHHHHTT CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsa..Gdllreeakrg 37 
                                       +G+PG GK+ +++ ++ + +  ++s    ++l + + ++
  gi|518652280|ref|YP_008141800.1| 507 YGPPGTGKTLLAKAVANESNANFISVkgPEVLSKWVGDS 545
                                       7***************99877766654144444444333 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.032        11      36      52 ..     227     243 ..     220     258 .. 0.87
   2 ?    6.0   0.0     0.023       8.1     127     177 ..     269     319 ..     258     335 .. 0.83
   3 !    7.8   0.0    0.0066       2.3      37      52 ..     505     520 ..     498     525 .. 0.86
   4 ?   -0.3   0.0         2   6.8e+02     128     172 ..     547     592 ..     536     610 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.032
                            AAA_25  36 allaGapgtGKttlald 52 
                                       +ll G+pgtGKt +a  
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKA 243
                                       689*********99855 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.023
                            AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdv.galvealeriar 177
                                       +++++++ ++++e  ++  + iD ++++ +  e+ + +v +++v++l  + +
  gi|518652280|ref|YP_008141800.1| 269 EQKLREIFQKADE-SEPSIIFIDEIDSIAPKREDVQGEVeRRVVAQLLTLMD 319
                                       5678899999999.67**********************99999999987765 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0066
                            AAA_25  37 llaGapgtGKttlald 52 
                                       ll+G+pgtGKt la  
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKA 520
                                       89**********9965 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 2
                            AAA_25 128 advdaleaaieevegvrlvviDplsralgg.densnsdv.galveal 172
                                        +v+++ +++++v  ++ +  D ++++ +  +   +s v +++v++l
  gi|518652280|ref|YP_008141800.1| 547 KAVREIFKKAKQVS-PAIIFMDEIDSIAPRrGTSMDSGVtERIVNQL 592
                                       6789999999**75.***********999976667777667777776 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0      0.01       3.5      52      84 ..     223     255 ..     175     330 .. 0.78
   2 !   10.1   0.0   0.00091      0.31      54     115 ..     502     568 ..     449     573 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                            DUF815  52 pannvLLwGarGtGKSslvkallneyaeegLrl 84 
                                       p + vLL G  GtGK  + ka+ ne  ++  ++
  gi|518652280|ref|YP_008141800.1| 223 PPKGVLLNGPPGTGKTLIAKAVANESGANFFAI 255
                                       56789*******************998877544 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00091
                            DUF815  54 nnvLLwGarGtGKSslvkallneyaeeg..Lrlievekedlkelpklvellrerper...filfvDD 115
                                       +  LL+G  GtGK  l ka+ ne +++   ++  ev  + + + +k v+++ +++++    i+f+D 
  gi|518652280|ref|YP_008141800.1| 502 KGFLLYGPPGTGKTLLAKAVANESNANFisVKGPEVLSKWVGDSEKAVREIFKKAKQvspAIIFMDE 568
                                       568********************99998344446787777777777777665444431125788776 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   0.8    0.0097       3.3      11      33 ..     225     247 ..     220     386 .. 0.88
   2 ?    7.4   0.0     0.015       5.2      12      32 ..     503     523 ..     498     573 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0097
                            AAA_19  11 kvllvtaGpGtGKTrvlkhival 33 
                                       k +l+ ++pGtGKT + k++ ++
  gi|518652280|ref|YP_008141800.1| 225 KGVLLNGPPGTGKTLIAKAVANE 247
                                       66899*********998887665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.015
                            AAA_19  12 vllvtaGpGtGKTrvlkhiva 32 
                                        +l+ ++pGtGKT + k++ +
  gi|518652280|ref|YP_008141800.1| 503 GFLLYGPPGTGKTLLAKAVAN 523
                                       57899********98777655 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 !    6.8   0.1    0.0088         3     117     137 ..     227     247 ..     219     251 .. 0.88
   2 !    8.2   0.0    0.0033       1.1     118     137 ..     505     524 ..     502     528 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0088
                         Parvo_NS1 117 vwfyGpantGktnlaeaIaka 137
                                       v++ Gp+ tGkt +a+a a+ 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANE 247
                                       7888*************9985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0033
                         Parvo_NS1 118 wfyGpantGktnlaeaIaka 137
                                       ++yGp+ tGkt la+a a+ 
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANE 524
                                       68**************9985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.023       7.8      23     119 ..     227     327 ..     214     332 .. 0.57
   2 ?    7.2   0.0     0.013       4.4      24      45 ..     505     526 ..     500     533 .. 0.86
   3 ?    0.1   0.1       1.8   6.3e+02     107     131 ..     546     573 ..     527     613 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.023
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal...........giavpk 88 
                                       +++ Gp g GKt + k +++++       ++ i+  e+ ++++ ++   e++ +++ +++            i+   
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANES-G---ANFFAINGPEIMSKYYGQS---EQKLREIFQKAdesepsiifidEIDSIA 296
                                       5677999999997777777766.2...4678888888888888888...4444444444445554444444222222 PP

                          ATPase_2  89 aeleeilkeksklvfkaielllekikkkgkk 119
                                        + e +  e  + v +++  l++ +k++g  
  gi|518652280|ref|YP_008141800.1| 297 PKREDVQGEVERRVVAQLLTLMDGLKDRGHV 327
                                       2222333355555555555555555555554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.013
                          ATPase_2  24 fiYGpegsGKtaLlkeiienle 45 
                                       ++YGp g GKt L k ++++++
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESN 526
                                       68************99999874 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 1.8
                          ATPase_2 107 elllekikkkgkk...iiiiiDelqkli 131
                                       e++ ++i kk+k+    ii++De+  + 
  gi|518652280|ref|YP_008141800.1| 546 EKAVREIFKKAKQvspAIIFMDEIDSIA 573
                                       4556666777777775677889998775 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.016       5.4      23      43 ..     227     247 ..     215     263 .. 0.90
   2 !    7.7   0.0    0.0052       1.8      25      44 ..     506     525 ..     500     534 .. 0.89

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.016
                                       EEEEESTTSSHHHHHHHHCCS CS
                            NB-ARC  23 valvGmgGvGKttlakqilnk 43 
                                       v l G +G GKt +ak + n+
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANE 247
                                       6799**************998 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0052
                                       EEESTTSSHHHHHHHHCCSH CS
                            NB-ARC  25 lvGmgGvGKttlakqilnks 44 
                                       l+G +G GKt lak + n+s
  gi|518652280|ref|YP_008141800.1| 506 LYGPPGTGKTLLAKAVANES 525
                                       89**************9995 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0058         2       3      27 ..     229     253 ..     227     257 .. 0.91
   2 ?    6.3   0.0     0.021       7.3       5      28 ..     508     531 ..     505     533 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0058
                                       EE-STTSSHHHHHHHHHHHHT-EEE CS
                    Cytidylate_kin   3 iDGPagsGKssvaralaeklglkyl 27 
                                       + GP g+GK  +a+a+a++ g++++
  gi|518652280|ref|YP_008141800.1| 229 LNGPPGTGKTLIAKAVANESGANFF 253
                                       78*****************999987 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.021
                                       -STTSSHHHHHHHHHHHHT-EEEE CS
                    Cytidylate_kin   5 GPagsGKssvaralaeklglkyld 28 
                                       GP g+GK  +a+a+a++ ++++++
  gi|518652280|ref|YP_008141800.1| 508 GPPGTGKTLLAKAVANESNANFIS 531
                                       9******************99986 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0     0.038        13       2      22 ..     227     247 ..     226     262 .. 0.83
   2 ?    2.8   0.2      0.29        99      81     118 ..     268     306 ..     257     318 .. 0.75
   3 ?    6.7   0.0     0.018       6.1       3      32 ..     505     534 ..     503     554 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.038
                                       EEEE--TTSSHHHHHHHHHHH CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlel 22 
                                       v++ GppG+GKt + k v+++
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANE 247
                                       7899*******9999998876 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.29
                                       HHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHHH CS
                          NTPase_1  81 feelalealrkal.seadviviDEiGkmElkskkfkeav 118
                                        e+   e+++ka+ se+ +i iDEi ++  k + ++ +v
  gi|518652280|ref|YP_008141800.1| 268 SEQKLREIFQKADeSEPSIIFIDEIDSIAPKREDVQGEV 306
                                       566777888888878888*******77766666665555 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.018
                                       EEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellkssgvkvgG 32 
                                       ++ GppG+GKt l k v+++ + + ++v+G
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFISVKG 534
                                       678***************999888888877 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1     0.014       4.8       3      22 ..     227     246 ..     225     251 .. 0.89
   2 ?    7.2   0.0     0.012       4.3       4      23 ..     505     524 ..     503     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.014
                                       EEEEC-TTTCHHHHHHHHHH CS
                             NACHT   3 vilqGeaGsGKTtLlqklal 22 
                                       v+l+G++G GKT  ++ +a 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVAN 246
                                       79*************99986 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                                       EEEC-TTTCHHHHHHHHHHH CS
                             NACHT   4 ilqGeaGsGKTtLlqklala 23 
                                       +l G++G GKT L++ +a +
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANE 524
                                       689************99875 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0098       3.4       1      44 [.     233     281 ..     233     283 .. 0.71
   2 ?    6.1   0.0     0.033        11       1      23 [.     510     532 ..     510     559 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0098
                                       TTSSHHHHHHHHHHHHTSEEEEHH..HHHHHHHT...S-HHHHHHHHHH CS
                               SKI   1 mGaGKstvGkllAkklglefiDlD..eliekrtg...ksiaeifeeege 44 
                                       +G+GK+ ++k++A++ g +f+ +   e+++k  g   ++ +eif++ +e
  gi|518652280|ref|YP_008141800.1| 233 PGTGKTLIAKAVANESGANFFAINgpEIMSKYYGqseQKLREIFQKADE 281
                                       69******************87752145566555333556777777666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.033
                                       TTSSHHHHHHHHHHHHTSEEEEH CS
                               SKI   1 mGaGKstvGkllAkklglefiDl 23 
                                       +G+GK+ ++k++A++ + +fi +
  gi|518652280|ref|YP_008141800.1| 510 PGTGKTLLAKAVANESNANFISV 532
                                       69******************976 PP

>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0038       1.3       8      65 ..     233     294 ..     227     332 .. 0.70
   2 ?    4.3   0.0      0.11        39       9      60 ..     511     563 ..     507     614 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0038
                   Cytidylate_kin2   8 yGsgGetigeaLAekLglpfydreiieevakelglseeev....eevdersrlssflsklla 65 
                                        G+g++ i++a+A++ g +f+  + +e ++k  g se+++    +++de++++  f++++ +
  gi|518652280|ref|YP_008141800.1| 233 PGTGKTLIAKAVANESGANFFAINGPEIMSKYYGQSEQKLreifQKADESEPSIIFIDEIDS 294
                                       79*******************99999999999999998886334555555555555555544 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.11
                   Cytidylate_kin2   9 GsgGetigeaLAekLglpfydreiieevakelglseeev.eevdersrlssfl 60 
                                       G+g++ +++a+A++ + +f++ + +e ++k  g se+ v e +++++ +s ++
  gi|518652280|ref|YP_008141800.1| 511 GTGKTLLAKAVANESNANFISVKGPEVLSKWVGDSEKAVrEIFKKAKQVSPAI 563
                                       9********************************99999955555544444443 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0091       3.2      48     105 ..     227     285 ..     216     321 .. 0.74
   2 ?    4.0   0.0      0.12        41      48      80 ..     504     536 ..     492     577 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0091
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn..qksdfkgltekesrflsq 105
                                       +L+ GP+G gk+ + k ++ e g ++   +n+ ++ +  +   ++ ++ +++k ++  + 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANFFA-INGPEIMSKYYgqSEQKLREIFQKADESEPS 285
                                       689********************99875.5555555555432455566666666655555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.12
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpv 80 
                                        L+ GP+G gk+   k ++ e   +++    p 
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNANFISVKGPE 536
                                       5889********999999999888777666654 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 ?    6.0   0.0     0.031        11      22      45 ..     222     245 ..     195     254 .. 0.78
   2 ?    4.8   0.0     0.071        25      22      50 ..     499     527 ..     463     573 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.031
                                       .TTSEEEEEESTTSTHHHHHHHHH CS
                            ResIII  22 krdkrglikmaTGtGKTlvaakli 45 
                                       +  k +l++ + GtGKTl+a +++
  gi|518652280|ref|YP_008141800.1| 222 TPPKGVLLNGPPGTGKTLIAKAVA 245
                                       5678899************96665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.071
                                       .TTSEEEEEESTTSTHHHHHHHHHHHH-S CS
                            ResIII  22 krdkrglikmaTGtGKTlvaaklierllk 50 
                                       +  k +l+  + GtGKTl+a +++ +   
  gi|518652280|ref|YP_008141800.1| 499 RAPKGFLLYGPPGTGKTLLAKAVANESNA 527
                                       5678889999********99777766554 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 ?    2.8   0.0      0.24        84       3      71 ..     229     292 ..     227     297 .. 0.68
   2 ?    8.5   0.0    0.0043       1.5       5      71 ..     508     569 ..     505     574 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.24
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                         G pG GK+ + + ++++s  ++ +++   e+ ++   +++++  + ++++ ++        i+++DE+
  gi|518652280|ref|YP_008141800.1| 229 LNGPPGTGKTLIAKAVANESgANFFAING-PEIMSKYYGQSEQKLREIFQKADESE-----PSIIFIDEI 292
                                       5789*******999999998855555555.46666666566666566666555543.....358888886 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0043
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ l + ++++s  ++ +++   e+l++++ ++++   + +++  ++ ++     i+++DE+
  gi|518652280|ref|YP_008141800.1| 508 GPPGTGKTLLAKAVANESnANFISVKG-PEVLSKWVGDSEKAVREIFKK-AKQVSP----AIIFMDEI 569
                                       77****************977767776.8*******8888885555554.444443....59999997 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.58     2e+02      37     112 ..     227     298 ..     224     373 .. 0.59
   2 ?    8.8   0.0    0.0038       1.3      37      76 ..     504     538 ..     498     668 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.58
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++ g+ G Gkt + ka++ne  +n+       +++ e +++     ++k  e f++    +  ++ iD+i  +a k
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANFF-----AINGPEIMSKYYGQSEQKLREIFQKADEsEPSIIFIDEIDSIAPK 298
                                       678889999999999999887665543.....344444444444444444444444433214556666666666654 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0038
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHH CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFl 76 
                                       +++yg+ G Gkt L ka++ne  +n+ +      ++ e l
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNANFISV-----KGPEVL 538
                                       799***************99877766544.....344444 PP

>> Vps4_C  Vps4 C terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.032        11      19      44 ..     427     452 ..     419     456 .. 0.80
   2 ?    4.3   0.0      0.12        40      28      47 ..     695     714 ..     690     721 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.032
                            Vps4_C  19 ipsdkllePpvtlkDflkalkkarpt 44 
                                       ip++ l +  vt +Df++alk+  p+
  gi|518652280|ref|YP_008141800.1| 427 IPTEVLEKMIVTEDDFMEALKTIEPS 452
                                       5555555569*************998 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.12
                            Vps4_C  28 pvtlkDflkalkkarptVsk 47 
                                       +v+ + f+ka+k+ rp++ k
  gi|518652280|ref|YP_008141800.1| 695 EVNQDAFIKAMKTIRPSIDK 714
                                       577788***********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 ?    3.3   0.0      0.16        54      18      66 ..     228     282 ..     222     322 .. 0.79
   2 ?    7.1   0.0     0.011       3.9      18      78 ..     505     611 ..     500     619 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                                       EEEESTTSSHHHHHHHHHHHSSTS.....S.EEEEEEESEEHHHHHHHHHHCHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsd.....d.aiiyvgiGergnevaevleefpeg 66 
                                       l+ g  g+Gkt i+++++++s ++        i     G+ +++++e++++  e+
  gi|518652280|ref|YP_008141800.1| 228 LLNGPPGTGKTLIAKAVANESGANffainGpEIMSKYYGQSEQKLREIFQKADES 282
                                       567899**************97776666523666666888888888888877775 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                                       EEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................................. RF
                       ATP-synt_ab  18 lipgafgvGktvisqslskqsnsddaiiyvg.............................................. 48 
                                       l+ g  g+Gkt ++++++++sn++   i v                                               
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNAN--FISVKgpevlskwvgdsekavreifkkakqvspaiifmdeidsiaprrgts 579
                                       578999**************9888..555545788888877777777777777777777777777777777777777 PP

                                       ..ESEEHHHHHHHHHHCHHSSGGGGEEEEEEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 ..iGergnevaevleefpegtimkrtvlvant 78 
                                          G  ++ v+++l+++   +++k +v++a+t
  gi|518652280|ref|YP_008141800.1| 580 mdSGVTERIVNQLLTSMDGIEVLKGVVVIAAT 611
                                       77777777777777777777777777777666 PP

>> CPT  Chloramphenicol phosphotransferase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.0    0.0055       1.9       4      39 ..     227     262 ..     225     330 .. 0.83
   2 ?    1.2   0.0      0.82   2.8e+02       5      32 ..     505     532 ..     503     555 .. 0.91

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0055
                                       EEEEE-TTSSHHHHHHHHHHHSSS-EEEEEHHHHHH CS
                               CPT   4 ilLnGgsssGKsslaralqevldepwlhlgvDafve 39 
                                       +lLnG + +GK+ +a+a+ + + + +++++  + + 
  gi|518652280|ref|YP_008141800.1| 227 VLLNGPPGTGKTLIAKAVANESGANFFAINGPEIMS 262
                                       89*******************999999987665555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.82
                                       EEEE-TTSSHHHHHHHHHHHSSS-EEEE CS
                               CPT   5 lLnGgsssGKsslaralqevldepwlhl 32 
                                       lL G + +GK+ la+a+ + +++ ++ +
  gi|518652280|ref|YP_008141800.1| 505 LLYGPPGTGKTLLAKAVANESNANFISV 532
                                       799**************99999998876 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.14        49       5      29 ..     228     252 ..     225     257 .. 0.88
   2 ?    6.2   0.0     0.017       5.9       4      31 ..     504     531 ..     501     554 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.14
                               IPT   5 lifGatttGKtaeaiklaketgapv 29 
                                       l+ G+ +tGKt  a ++a+e ga  
  gi|518652280|ref|YP_008141800.1| 228 LLNGPPGTGKTLIAKAVANESGANF 252
                                       788*****************99875 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.017
                               IPT   4 ylifGatttGKtaeaiklaketgapviv 31 
                                       +l++G+ +tGKt  a ++a+e  a  i+
  gi|518652280|ref|YP_008141800.1| 504 FLLYGPPGTGKTLLAKAVANESNANFIS 531
                                       69*******************9998887 PP

>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.097        33      19      49 ..      82     112 ..      71     121 .. 0.84
   2 ?    5.0   0.0     0.059        20      48      86 ..     516     554 ..     510     561 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.097
                                       SHHHHHHHHHTTTESEEEEETTSSSGGHHHH CS
                    Ribosomal_L7Ae  19 GlkevtkalergeaklvilAedvepeekkkl 49 
                                       G k  +k +e  eak v+lA+ +++++k  +
  gi|518652280|ref|YP_008141800.1|  82 GDKVKVKKVEVEEAKKVVLAPIIRKDQKLRF 112
                                       5566689**************9999998765 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.059
                                       HHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEEEE CS
                    Ribosomal_L7Ae  48 kllealckekevpyvkvkskkeLGelvgkkrpvsalaik 86 
                                        l +a+++e + ++++vk+ + L ++vg +  ++  ++k
  gi|518652280|ref|YP_008141800.1| 516 LLAKAVANESNANFISVKGPEVLSKWVGDSEKAVREIFK 554
                                       477999**********************98766555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                        52  (0.00290033); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              52  [number of targets reported over threshold]
# CPU time: 0.89u 0.30s 00:00:01.19 Elapsed: 00:00:00.49
# Mc/sec: 4545.60
//
Query:       gi|518652281|ref|YP_008141801.1|  [L=144]
Description: hypothetical protein FACI_IFERC00001G0920 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1219  (0.0679904); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1010.87
//
Query:       gi|518652282|ref|YP_008141802.1|  [L=291]
Description: hypothetical protein FACI_IFERC00001G0921 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   2.4       0.34   10.8   2.4    1.6  1  SurA_N_2  SurA N-terminal domain


Domain annotation for each model (and alignments):
>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.4   1.9e-05      0.34       7      85 ..       3      90 ..       1      93 [. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 1.9e-05
                          SurA_N_2  7 ksqgllvii...iglallaFi.lgdlfgvgsy....lfss..ssnevaeVnGekIslqefqqaveearqqlqqqlgenf 75
                                      k++ l++++    ++++++F+ +++++++++     ++s+   +  +   nG++I++ +++  v+++++++ +++  ++
  gi|518652282|ref|YP_008141802.1|  3 KKK-LIIGVliaAIFVMVSFApVTNATNNTDQrvnvVTSDisAQPHASNLNGKQINVVKYNDSVNMLSNRIYMNMAFSV 80
                                      444.555552133344455558666666443222325555668889999*********************999988888 PP

                          SurA_N_2 76 deseedeaql 85
                                      +++  +++++
  gi|518652282|ref|YP_008141802.1| 81 TNNTGNNQHI 90
                                      8777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       667  (0.0372023); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2059.07
//
Query:       gi|518652283|ref|YP_008141803.1|  [L=309]
Description: hypothetical protein FACI_IFERC00001G0922 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-10   40.6   1.8    3.8e-10   39.9   1.8    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
    5.7e-06   26.6   0.0    1.4e-05   25.4   0.0    1.6  2  GHMP_kinases_C  GHMP kinases C terminal


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   1.8   4.2e-14   3.8e-10       1      66 []      82     149 ..      82     149 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 4.2e-14
                                       EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHH.HH..HHHHHHHHHHHHHHHHHSHHHHHHHHSS CS
                    GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsl.ee..aklaleaerlaqggngsggDvaasvyGg 66 
                                       di+ik+ +P+g GLGSS+A + a+v+ +++ll+l + ++  +  +  +e +a  g+ ++++v+  +yGg
  gi|518652283|ref|YP_008141803.1|  82 DITIKKGVPIGLGLGSSGASSSAAVRSVNELLDLGMgKDemVYYSMYGEIAAC-GSAHPDNVSSGIYGG 149
                                       79******************************988763346999*****9999.**************8 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       1.4   1.3e+04      49      57 ..      93     101 ..      83     113 .. 0.63
   2 !   25.4   0.0   1.5e-09   1.4e-05       2      76 ..     212     281 ..     211     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.4
                    GHMP_kinases_C  49 lgaklsGaG 57 
                                       lg + sGa+
  gi|518652283|ref|YP_008141803.1|  93 LGLGSSGAS 101
                                       455555553 PP

  == domain 2  score: 25.4 bits;  conditional E-value: 1.5e-09
                    GHMP_kinases_C   2 lealergdlellgellnlsqrselkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqva 76 
                                       l  + +gd ++++e++n+    e    ++ ++p  ++++e+  +  a +a++sGa  Gpt  ++++dk + ++++
  gi|518652283|ref|YP_008141803.1| 212 LYGFMKGDRDAIREGMNDDIV-ER--SREAMFPFYRDIKEKVINRNAVSACISGA--GPTMLIFADDKTRKDEML 281
                                       5667899**********5555.55..****************88889********..********9999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.48
# Mc/sec: 1937.47
//
Query:       gi|518652284|ref|YP_008141804.1|  [L=362]
Description: hypothetical protein FACI_IFERC00001G0923 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.4e-106  356.3   0.0   1.6e-106  356.1   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    2.2e-08   33.5   0.1    5.8e-08   32.1   0.1    1.9  1  Aminotran_5      Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  356.1   0.0  1.8e-110  1.6e-106      19     381 ..      12     360 ..       2     361 .. 0.97

  Alignments for each domain:
  == domain 1  score: 356.1 bits;  conditional E-value: 1.8e-110
                                       S--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEE CS
                   Cys_Met_Meta_PP  19 avpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeiv 95 
                                       + piy+ts+y +         e ++y YsR  npt+++l  +i ++eg+e   ++ssGm+Ai++++l+l k Gd+i+
  gi|518652284|ref|YP_008141804.1|  12 TYPIYQTSSYIVP--------EGQKYRYSREYNPTVENLGIKIKEMEGAEDYNVFSSGMGAITTTLLSLSKPGDRIL 80 
                                       67***********........7889**************************************************** PP

                                       EESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEE CS
                   Cys_Met_Meta_PP  96 vsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDiekiaklakkagvlvvv 172
                                       ++ d +  ++++++ ++ k+gi+ ++ ++  +e++ + ik+ t +v++E++tnp l+v Di +i++ ++++g+++vv
  gi|518652284|ref|YP_008141804.1|  81 THLDTFARSYHFIRDFMGKWGIKPDIANP-GTENIINGIKKGTGIVFIESVTNPILRVNDISTISEKCHDVGAILVV 156
                                       ****************************9.56888999*************************************** PP

                                       EGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B--HHHHHHHHHHHTTH CS
                   Cys_Met_Meta_PP 173 DntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGavlspfdawlllrGlkTL 249
                                       D t+ +p++++ lklgaDivvhS +K+++Gh++v+ G+++  g+++l++++  + ++lG  l+p++a+l+  G+kTL
  gi|518652284|ref|YP_008141804.1| 157 DSTVPTPYNVKSLKLGADIVVHSSSKFIAGHNNVISGLAA--GRNDLMEKIDAMRRTLGTSLDPNSAFLTENGMKTL 231
                                       ***************************************9..667******************************** PP

                                       HHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHHHHHHHHHC-SSSEECS CS
                   Cys_Met_Meta_PP 250 slRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseeekakkfvdnlklfslae 326
                                       ++R+e+ ++nA+++A  L+k+p++++v Ypglp+hp+he+akk++kg++g++ F++k++    +kf+ +l+ +  a+
  gi|518652284|ref|YP_008141804.1| 232 EIRMEKINSNAMEIAAELQKNPEISRVIYPGLPEHPDHEIAKKYMKGYSGIVCFKVKTDP---EKFIGKLEKIVPAN 305
                                       *********************************************************996...5************* PP

                                       S-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 327 slGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqal 381
                                        +Gg+e++i++pasm+h+s+++ee +  gv  +++RlsvGiEd d+++ D+++al
  gi|518652284|ref|YP_008141804.1| 306 TMGGTETVISTPASMSHRSLTSEELNVLGVDSTFMRLSVGIEDPDEIVRDINRAL 360
                                       ******************************************************9 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.1   6.5e-12   5.8e-08      35     222 ..      29     206 ..      14     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 6.5e-12
                                       SHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHH CS
                       Aminotran_5  35 hhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakr 111
                                       ++++ e +  ve+   k++e+ +ae+ +  +f sG + ai++ +lsl    kpgd+i+ t+++  a     + ++++
  gi|518652284|ref|YP_008141804.1|  29 YRYSREYNPTVENLGIKIKEMEGAED-Y-NVFSSGMG-AITTTLLSL---SKPGDRIL-THLDTFARS--YHFIRDF 96 
                                       55667777778888889999999996.4.47888888.999999999...89999987.578888887..7777766 PP

                                       HTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HH CS
                       Aminotran_5 112 tgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvk 188
                                        g       + +  +  ++++ + +++ t +v+i  v n +  ++++  i + ++++ga+++vD++   + ++++  
  gi|518652284|ref|YP_008141804.1|  97 MGKWG---IKPDIANPGTENIINGIKKGTGIVFIESVTNPILRVNDISTISEKCHDVGAILVVDSTVPTP-YNVKSL 169
                                       66332...222335566789999*****************************************876654.788888 PP

                                       HHTESEEEEETTT.TTSSTT-..EEEEEEHHHHHTS. CS
                       Aminotran_5 189 klgvDflafsghK.llgPtGi..Gvlyvrkellekle 222
                                       klg+D+++ s+ K + g + +  G+  +r++l ek+ 
  gi|518652284|ref|YP_008141804.1| 170 KLGADIVVHSSSKfIAGHNNVisGLAAGRNDLMEKID 206
                                       9************666766666677777777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2590.26
//
Query:       gi|518652285|ref|YP_008141805.1|  [L=198]
Description: 2-phosphoglycerate kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-06   28.7   0.0    2.2e-06   28.2   0.0    1.2  1  AAA_18        AAA domain
    3.8e-06   27.4   0.0    2.6e-05   24.6   0.0    2.2  1  AAA_17        AAA domain
    0.00062   20.5   0.1     0.0023   18.6   0.1    1.8  2  CsgA          Minor curli fiber component A
     0.0011   19.1   0.0     0.0029   17.8   0.0    1.7  1  AAA_33        AAA domain
     0.0022   17.3   0.0     0.0034   16.7   0.0    1.5  1  Zeta_toxin    Zeta toxin
     0.0091   16.1   0.0      0.015   15.4   0.0    1.6  1  ADK           Adenylate kinase
  ------ inclusion threshold ------
      0.011   15.5   0.1      0.026   14.2   0.0    1.6  2  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
      0.068   13.6   0.0       0.13   12.7   0.0    1.5  1  RNA_helicase  RNA helicase
       0.12   12.8   0.0       0.19   12.2   0.0    1.4  1  AAA           ATPase family associated with various cellular 


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 !   28.2   0.0   1.1e-09   2.2e-06       1     113 [.       5     138 ..       5     154 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.2 bits;  conditional E-value: 1.1e-09
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.gvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss... 69 
                                       Il+ G+pGvGKt+l+  +s++ ++  + ++d+++e    + ++p+     ++ +++  e++ ++++++  ++s+   
  gi|518652285|ref|YP_008141805.1|   5 ILIGGIPGVGKTSLSGFISREFNInIILSGDYLREFLRPYADNPAmgesVYNAYRIYGEKNEENIIKGYLNQSEfmy 81 
                                       99*******************98895555555555444444444455554444666666666677777777777888 PP

                            AAA_18  70 .........aleegknlvidghlaeleseaakdikk...vvLtasp.eelleRlekR 113
                                                + ++g++l+++ +  ++e  a  +++k   ++++ ++ + +  Rl++R
  gi|518652285|ref|YP_008141805.1|  82 kginavlrrSIDNGEPLILETLYFNPEMIASDIRNKiimIYIHIPDkSLHGNRLKER 138
                                       8999999998889999***99998888666666666688999999966777888887 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0   1.3e-08   2.6e-05       2     123 ..       9     138 ..       8     147 .. 0.73

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.3e-08
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTT................SHSSHHHHCTSHHHHHHHHHHHHH CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgg................lakardemrklpleekkelqkeaa 62 
                                       G+PG+GK+ ++  + +++++ ++  Gd+lre  ++                   +k+++++ k++l++ + + k + 
  gi|518652285|ref|YP_008141805.1|   9 GIPGVGKTSLSGFISREFNINIILSGDYLREFLRPYAdnpamgesvynayriyGEKNEENIIKGYLNQSEFMYKGIN 85 
                                       9******************************9877644556667788888775578888888888777665555554 PP

                                       HHHHHHH.HSSE.EEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  63 ekiaeea.kkkg.vlvdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdr 123
                                        ++ +++ ++++ +++++ + +  ++ +     +++ +++   ++i+++++++ ++  rlk+r
  gi|518652285|ref|YP_008141805.1|  86 -AVLRRSiDNGEpLILETLYFN--PEMIA----SDIRNKI---IMIYIHIPDKSLHGNRLKER 138
                                       .555555333334788887764..33333....3444566...78999999999998888875 PP

>> CsgA  Minor curli fiber component A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.1   1.1e-06    0.0023       6      61 ..      35      93 ..      32      96 .. 0.89
   2 ?   -1.6   0.0       2.4   4.7e+03      22      42 ..     132     153 ..     124     160 .. 0.56

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.1e-06
                              CsgA  6 aYLrEvlsnyteesevgkeiykkleekeykseeefvkd.LseeEief..LnkiLeeeik 61
                                      +YLrE l  y+++  +g+++y+  +    k+ee+ +k  L+++E  +  +n++L++ i+
  gi|518652285|ref|YP_008141805.1| 35 DYLREFLRPYADNPAMGESVYNAYRIYGEKNEENIIKGyLNQSEFMYkgINAVLRRSID 93
                                      6**********************9999999****9995499***877668999999886 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 2.4
                              CsgA  22 gkeiykkleekeykse.eefvk 42 
                                       g+++ ++++ ++++s  e++v+
  gi|518652285|ref|YP_008141805.1| 132 GNRLKERIDYTHFNSPgERLVE 153
                                       5556666666666553133444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.4e-06    0.0029       1     136 [.       4     154 ..       4     161 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.4e-06
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqskt.....................dytrvldrl 55 
                                       ++l+ G pG+GK+ l+  + ++    ++ls d+lr+ l++  +++                        y + ++ +
  gi|518652285|ref|YP_008141805.1|   4 VILIGGIPGVGKTSLSGFISREFNiNIILSGDYLREFLRPYADNPAMgesvynayriygekneeniikGYLNQSEFM 80 
                                       78999*****************999999*****88877773333222344555555555555556666778888889 PP

                            AAA_33  56 yqilnelarkalsagrnvildatnlsrrerarflklarrlgvpvrivvvetde.etlkeRlakRaangddrsevpee 131
                                       y+ +n+++r+    g ++il   +++++       +a+++  ++ +++++ ++ +++  Rl++R +   + ++ p e
  gi|518652285|ref|YP_008141805.1|  81 YKGINAVLRRSIDNGEPLILETLYFNPEM------IASDIRNKIIMIYIHIPDkSLHGNRLKERIDY--THFNSPGE 149
                                       99999999999999999999876666653......34444444555555544303444555555554..44666666 PP

                            AAA_33 132 aldrq 136
                                        l +q
  gi|518652285|ref|YP_008141805.1| 150 RLVEQ 154
                                       66555 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.7e-06    0.0034      18      63 ..       4      46 ..       3     116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.7e-06
                        Zeta_toxin 18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelhPeyee 63
                                      +il+gG pG GK++l+  + +e+  + n + l++D lRe+ + y++
  gi|518652285|ref|YP_008141805.1|  4 VILIGGIPGVGKTSLSGFISREF--NIN-IILSGDYLREFLRPYAD 46
                                      69********************9..555.669*********99987 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.7e-06     0.015       3      67 ..       9      73 ..       6     169 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.7e-06
                                      ESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  3 GaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkee 67
                                      G Pg GK   +  + ++++++ + +Gd lR+ ++  +++  + ++v ++ ++  ++   +++k  
  gi|518652285|ref|YP_008141805.1|  9 GIPGVGKTSLSGFISREFNINIILSGDYLREFLRPYADNPAMGESVYNAYRIYGEKNEENIIKGY 73
                                      89****************************98876666555555555555555555555555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.3e-05     0.026      36      62 ..       5      31 ..       2      39 .. 0.88
   2 ?   -2.7   0.0       2.2   4.4e+03     104     128 ..     157     181 ..     149     190 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.3e-05
                            RuvB_N 36 vllyGpPGlGkttlakiiakelgvklk 62
                                      +l+ G PG+Gkt+l+  i++e+++++ 
  gi|518652285|ref|YP_008141805.1|  5 ILIGGIPGVGKTSLSGFISREFNINII 31
                                      78899******************9985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.2
                            RuvB_N 104 lysamedfrldivigkGpsarsikl 128
                                       +ys +e +++d   ++     ++ +
  gi|518652285|ref|YP_008141805.1| 157 VYSVIEKYSMDHCGDDVFIVDNTDF 181
                                       6888888888865555555555555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.3e-05      0.13       1      61 [.       5      87 ..       5     119 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.3e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl......................klkkkdsvysrnpeddfwdgYtgqevvvidD 57
                                      i++ G +g+GK++l+  +++++  ++                         ++ ++y  ++e+++ +gY +q   ++  
  gi|518652285|ref|YP_008141805.1|  5 ILIGGIPGVGKTSLSGFISREFNINIilsgdylreflrpyadnpamgeSVYNAYRIYGEKNEENIIKGYLNQSEFMYKG 83
                                      5678999****************888999999**************99888899******************9999987 PP

                      RNA_helicase 58 fgqv 61
                                      +++v
  gi|518652285|ref|YP_008141805.1| 84 INAV 87
                                      7776 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.5e-05      0.19       1      27 [.       5      31 ..       5      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.5e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEE CS
                               AAA  1 vllyGppGtGKTllakavakelgvefl 27
                                      +l+ G pG+GKT+l   + +e++++++
  gi|518652285|ref|YP_008141805.1|  5 ILIGGIPGVGKTSLSGFISREFNINII 31
                                      5788*****************988764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1393.54
//
Query:       gi|518652286|ref|YP_008141806.1|  [L=207]
Description: hypothetical protein FACI_IFERC00001G0925 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-25   88.9   0.1    3.4e-25   88.2   0.1    1.3  1  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    6.1e-09   36.2   0.6    1.6e-08   34.9   0.1    1.8  2  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin
    0.00068   20.0   0.0     0.0018   18.6   0.0    1.7  2  DUF4281   Domain of unknown function (DUF4281)


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   0.1   5.7e-29   3.4e-25       4     102 .]      96     193 ..      94     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 5.7e-29
                                       HHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTCEEEEEE-SGGGTHHHH CS
                          Sod_Fe_C   4 elaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeakplLalDvwehAYyldy 79 
                                       +++++ie+dfgs+ekf + fka+++a   +Gwa Lv+d + +kL+++ ++ ++   +++a  +L lDv+ehAYy+dy
  gi|518652286|ref|YP_008141806.1|  96 SVKAQIEKDFGSYEKFVALFKATGTA--FRGWAHLVFDLNcGKLRVLGADIHNASAIWNALMILPLDVYEHAYYTDY 170
                                       6899********************99..89********8879********99999999999**************** PP

                                       TT-HHHHHHHHGGGBBHHHHHHH CS
                          Sod_Fe_C  80 qnkradYieafwnvvnWkeveer 102
                                         kra Y++af+n vnWk ve+r
  gi|518652286|ref|YP_008141806.1| 171 GAKRAPYLDAFMNNVNWKVVEKR 193
                                       ********************987 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   0.1   2.7e-12   1.6e-08      18      82 .]      20      87 ..      17      87 .. 0.88
   2 ?   -1.6   0.0      0.64   3.8e+03      33      50 ..     180     197 ..     177     206 .. 0.60

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 2.7e-12
                                      S-HHHHHHHHHTHHHHHHHHHHHHHHCH...HHHCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTB- CS
                          Sod_Fe_N 18 isketlelHhdkHhktYvnnlNkalekl...eeakkkleelvlkklekalrnnagghvnHslfwknls 82
                                      is +++++H+d H+k+Yv +lN++ +kl   ++ k++++  +l++++ + ++n  g ++H+ ++++ls
  gi|518652286|ref|YP_008141806.1| 20 ISDKQIDYHFDVHYKGYVSKLNEIWSKLpdvDLTKANQNYSDLREMKLEETFNYDGSMLHEYYFESLS 87
                                      8999*******************988876335666777778888999999***************986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.64
                                       HHHHHHHHHHHCHHHHCH CS
                          Sod_Fe_N  33 tYvnnlNkalekleeakk 50 
                                       +++nn+N  + +  ++++
  gi|518652286|ref|YP_008141806.1| 180 AFMNNVNWKVVEKRLDRA 197
                                       788999976655444443 PP

>> DUF4281  Domain of unknown function (DUF4281)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.82   4.9e+03      80     104 ..      43      67 ..      39      72 .. 0.80
   2 !   18.6   0.0   3.1e-07    0.0018      49     110 ..      93     153 ..      75     160 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.82
                           DUF4281  80 aWvhlLafDLfvgrwiyldglrrgv 104
                                        W  l  +DL  + + y d ++ ++
  gi|518652286|ref|YP_008141806.1|  43 IWSKLPDVDLTKANQNYSDLREMKL 67 
                                       6888888999999999999988776 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 3.1e-07
                           DUF4281  49 aaklsevaaaasfsslegiaelfaneevlaaaWvhlLafDLfvgrwiyldglrrgvpallta 110
                                        +++++++   +f s+e++ +lf+ + ++  +W+h L+fDL +g+  +l +  ++ +a++ a
  gi|518652286|ref|YP_008141806.1|  93 MPESVKAQIEKDFGSYEKFVALFKATGTAFRGWAH-LVFDLNCGKLRVLGADIHNASAIWNA 153
                                       566677788899***********************.68******999998888777666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.47
# Mc/sec: 1335.30
//
Query:       gi|518652287|ref|YP_008141807.1|  [L=209]
Description: N-glycosylase/DNA lyase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00024   21.3   0.2    0.00051   20.3   0.1    1.5  1  DUF1477         Protein of unknown function (DUF1477)
  ------ inclusion threshold ------
      0.036   14.4   0.6      0.081   13.2   0.4    1.6  1  T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain


Domain annotation for each model (and alignments):
>> DUF1477  Protein of unknown function (DUF1477)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.6e-08   0.00051      25      73 ..      21      71 ..       2      78 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.6e-08
                           DUF1477 25 v...tlsnlvdtskrngrklfyelcisfvkklltknslaletlknlfdtiie 73
                                          ++ +++++ k+++++lf elc++++++  t+ ++ + t + ++d  ie
  gi|518652287|ref|YP_008141807.1| 21 KineRVIDFINMGKSRNDSLFMELCFCILTAN-TSAEMGIRTQRMIMDGFIE 71
                                      2346899***********************77.9999************997 PP

>> T3RM_EcoP15I_C  Type III R-M EcoP15I C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.4   9.1e-06     0.081      16      81 ..      72     138 ..      63     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-06
                    T3RM_EcoP15I_C  16 ygltekveevdlegYtayliekkLYliekglesealkaLiekld..edkefniekivlfgysfeskel 81 
                                       y++++  ee++ ++Y+ y  ++  Y+i++++ ++++k+Li+ ++  + +e  ++++  +gy+ +s+ l
  gi|518652287|ref|YP_008141807.1|  72 YSMEQLSEELKKAKYRFYN-KRAGYIINARFIRKNIKKLISSMEhfTLREYLVNNVKGLGYKEASHFL 138
                                       5666667777777777654.4457*******************9666677777777777776665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 1490.67
//
Query:       gi|518652288|ref|YP_008141808.1|  [L=473]
Description: hypothetical protein FACI_IFERC00001G0927 [Ferroplasma acidarmanus fer1]
Scores for 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-42  144.0   0.0    6.9e-42  143.3   0.0    1.4  1  ThiI       Thiamine biosynthesis protein (ThiI)
    9.4e-14   51.7   0.5      3e-13   50.1   0.0    1.9  2  THUMP      THUMP domain
    1.4e-08   35.2   0.1    6.6e-07   29.8   0.0    2.8  2  Rhodanese  Rhodanese-like domain
     0.0011   18.5   0.0       0.11   12.0   0.0    2.8  2  QueC       Queuosine biosynthesis protein QueC


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 !  143.3   0.0   1.5e-45   6.9e-42       2     195 ..     167     357 ..     166     359 .. 0.95

  Alignments for each domain:
  == domain 1  score: 143.3 bits;  conditional E-value: 1.5e-45
                              ThiI   2 tqgkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlke 78 
                                       ++gk+++L SgGiDSpVa+++++kRG+  +l++   ++ ++ ++   ++ + +ll +y+ + + +++++d +++++ 
  gi|518652288|ref|YP_008141808.1| 167 SEGKAISLFSGGIDSPVATFMVMKRGMATDLLFC--SLAHPSDTLYMLKAARNLLFRYSYGYNSNIYILDGTSLITG 241
                                       579****************************999..69*************************************** PP

                              ThiI  79 ilekvkekltivllkrkmlriAekvaeeegakalvtGesLgqVaSqtleNlrvisavvnllilrPLigldKeeiikl 155
                                       il++ ++k+  +++k+ ++  Ae++ +e++++a+vtGes+gqV+Sq  +Nl+ +s  +n++++rPLig+dKee i+ 
  gi|518652288|ref|YP_008141808.1| 242 ILRNPEQKYANLIFKKLLYSYAEELCQENDYDAIVTGESIGQVSSQIPKNLKSLSYDINTPVFRPLIGFDKEETINY 318
                                       ***************************************************************************** PP

                              ThiI 156 AkeigtyeisiekedkCsvlakhPttkakleevekaeekl 195
                                        k+ g y       + Cs+++k+P +++   +++ + ek+
  gi|518652288|ref|YP_008141808.1| 319 SKRKGLYM-DESIGEFCSLFSKNPGINTAYRDLKPEVEKF 357
                                       *****994.3444589*********999998888777765 PP

>> THUMP  THUMP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.0   6.6e-17     3e-13      22     141 ..      45     153 ..      27     156 .. 0.84
   2 ?   -1.0   0.1      0.39   1.7e+03      34      81 ..     330     376 ..     311     388 .. 0.57

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 6.6e-17
                                       TEEEEECTEEEEEETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHHCT-EEEEEEEESSSTSS CS
                             THUMP  22 grivvelkgekpeedeellkealekargiqrvipvcevceadledileaakeivkkkfeeeketFaVrvkrrgkhfe 98 
                                       gri++++       d  +l ++l  ++g+++++ + e +++++edi    +e  + + +++  tFaVrv+r+g h  
  gi|518652288|ref|YP_008141808.1|  45 GRIYLYS-------DSPELMNILPDIFGVKSFSRANEYTFNTIEDIVTRCVENYYSYVKNK--TFAVRVTRKGTH-N 111
                                       5555555.......45578888889999999999988888888888877777777777776..************.* PP

                                       SHHHHHHHHHHHHHHCCTT-EE-SSS-SEEEEEEEETTEEEEE CS
                             THUMP  99 ftsreinrevGkaivektglkVdlenPdivvrveiikdkayis 141
                                       fts++++ ++G  + ++ +  V+le+P+  + +e++++++y +
  gi|518652288|ref|YP_008141808.1| 112 FTSKDLEIAIGNKLYDNSS-GVNLESPEAPIYIEVRDKNFYTF 153
                                       ****************999.*******************9965 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.39
                                       EETHHHHHHHHHTSTTECEEEEEEEEEESSHHHHHHHHHHHHHHHHHH CS
                             THUMP  34 eedeellkealekargiqrvipvcevceadledileaakeivkkkfee 81 
                                       +++ + l +++  + ++ r + + ev    l++il  + +i+k+++ +
  gi|518652288|ref|YP_008141808.1| 330 IGEFCSLFSKNPGINTAYRDLKP-EVEKFPLKEILHEIIKIKKEEIDD 376
                                       44455554444444455555555.566666667777666666666554 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0     0.054   2.4e+02      82      99 ..     216     235 ..     197     236 .. 0.72
   2 !   29.8   0.0   1.5e-10   6.6e-07      14      98 ..     393     462 ..     375     470 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.054
                         Rhodanese  82 aaallkk.lGykn.vsvldG 99 
                                          l+++ +Gy+  +++ldG
  gi|518652288|ref|YP_008141808.1| 216 RNLLFRYsYGYNSnIYILDG 235
                                       234666679*9888*****9 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.5e-10
                         Rhodanese  14 vallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggraaaaaallkklG 90 
                                        +++D R+  +++ +h+pgA n+           + ++ + ++e      +++k   +yc++g  +a aa +++++G
  gi|518652288|ref|YP_008141808.1| 393 SIIIDLRDNKDFDLWHVPGAMNM-----------PVSSIDSLAESG----NPDKNYFFYCKKGLNSAYAASIMRSHG 454
                                       34*********************...........444444444444....579************9999******** PP

                         Rhodanese  91 yknvsvld 98 
                                       y+  +  +
  gi|518652288|ref|YP_008141808.1| 455 YNSFYSTE 462
                                       76677655 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    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       1      26 [.     170     195 ..     170     207 .. 0.89
   2 ?    3.3   0.0     0.011        50     149     180 ..     298     329 ..     251     335 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
                                       EEEEE--SSHHHHHHHHHHHHH-SEE CS
                              QueC   1 kavvllSGGlDSttvlalakkegkev 26 
                                       ka+ l+SGG+DS +++++++k+g + 
  gi|518652288|ref|YP_008141808.1| 170 KAISLFSGGIDSPVATFMVMKRGMAT 195
                                       79******************998765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.011
                                       TS--EEE-TTTT--HHHHHHHHHHTTHHHHH- CS
                              QueC 149 dkkieieaPlidlsKaeivklgkelgvpleet 180
                                       d +  +  Pli ++K+e+++ +k+ g+ ++e+
  gi|518652288|ref|YP_008141808.1| 298 DINTPVFRPLIGFDKEETINYSKRKGLYMDES 329
                                       44556778999999999999999999888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3431.49
//
Query:       gi|518652289|ref|YP_008141809.1|  [L=184]
Description: FMN-reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.3e-38  130.5   0.0    5.2e-38  130.2   0.0    1.1  1  FMN_red       NADPH-dependent FMN reductase
    8.7e-07   28.8   0.0    1.1e-06   28.6   0.0    1.2  1  Flavodoxin_2  Flavodoxin-like fold


Domain annotation for each model (and alignments):
>> FMN_red  NADPH-dependent FMN reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.0   5.8e-42   5.2e-38       2     153 ..       5     149 ..       4     151 .. 0.96

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 5.8e-42
                                       EEEEEES--STT-HHHHHHHHHHCCT-T.T-CEEEEETTTS.--..---HCHGHTCGGSHHHHHHHHHHHH-SCEEE CS
                           FMN_red   2 kilvisGSlrkgsntrklaewaaealkeagaevelidladlilpcalcdkdlesegqtsddvaellekiaaadalii 78 
                                       ki+++ GSlrk+s++r l+e a   ++e+  ++el+d+++   p  l ++d+e+  + +++v++++++i+++d++++
  gi|518652289|ref|YP_008141809.1|   5 KIAGFGGSLRKESYSRYLLENAVGLMPEN-SKLELLDIKN--FP--LMNQDEEN--NYPENVKKFKRQIKESDGVLM 74 
                                       9*************************995.9*********..59..99999965..79******************* PP

                                       EEEECTTCE-HHHHHHHHCHT-.SSCHCCTT-EEEEEEE-SSTTTTHHHHHHHHHHHHHTT-EEEECSEEEETSH CS
                           FMN_red  79 vtPeYngsysgllKnalDrlsrtrgkkelrgKpvalvavgggrrgglraeeqlrqvlaelgaivvpraavavgka 153
                                       vtPeYn+s++g lKn+lD++sr++g+++++gKpva+++ + g+ gg+ra+++lrqv+ +l++i+v++++v + +a
  gi|518652289|ref|YP_008141809.1|  75 VTPEYNYSIPGYLKNVLDVASRPYGDNPFNGKPVAIMSSSIGMLGGSRAQYHLRQVCVFLDMIPVNTPEVFLTFA 149
                                       ********************************************************************9998776 PP

>> Flavodoxin_2  Flavodoxin-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   1.2e-10   1.1e-06      31     170 ..      33     139 ..      11     171 .. 0.65

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.2e-10
                                       CTTTEEEEEEHHCCT-----CCCCHCCHHHHTTCHHHHHHHHHHHHCSSEEEEEEE-BTTB--HHHHHHHHHHS-TT CS
                      Flavodoxin_2  31 agphevtvrdLyadflpvlttrdlaaklayeekpadveseqiekllaadaivlqfPlwwfgvPailKgwiDrvltag 107
                                       ++  + + +d+ +   p ++++  +   +y   p +v++ +  +++++d +++++P +++++P  lK+ +D   ++ 
  gi|518652289|ref|YP_008141809.1|  33 NS--KLELLDIKN--FPLMNQDEEN---NY---PENVKKFK-RQIKESDGVLMVTPEYNYSIPGYLKNVLDVASRP- 97 
                                       33..255555555..4555553333...33...45788888.9****************************96444. PP

                                       TSCEETTCSSCCCCTTTTSEEEEEEEESS-GGGSSTTSSS-S-HHHHHHHHHHHHHHTT-EEE CS
                      Flavodoxin_2 108 fafyteeggegrgggLkgkkalvivttGgpeesyqerglegaamdellpplrgilgfiGikdv 170
                                         +        +++ + gk++ +++++ g         l g +  +++  lr+++ f+ + +v
  gi|518652289|ref|YP_008141809.1|  98 --Y--------GDNPFNGKPVAIMSSSIGM--------LGG-SRAQYH--LRQVCVFLDMIPV 139
                                       ..4........2567999999999999888........222.112222..5555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1379.01
//
Query:       gi|518652290|ref|YP_008141810.1|  [L=96]
Description: hypothetical protein FACI_IFERC00001G0929 [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   73.8   0.1    8.5e-21   73.7   0.1    1.0  1  Thiamine_BP      Thiamine-binding protein
  ------ inclusion threshold ------
      0.054   13.7   0.1       0.14   12.4   0.1    1.7  1  Antimicrobial_8  Uperin family


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 !   73.7   0.1   9.5e-25   8.5e-21       1      91 [.       4      95 ..       4      96 .] 0.95

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 9.5e-25
                                      EEEEEEECSSSSSGHHHHHHHHHHHHHTTS.SEEEEETTEEEEEEE.HHHHHHHHHHHHHHHHCTTSSEEEEEEEEEEE CS
                       Thiamine_BP  1 veisviPlgtegesvskyVakvvevlkesg.lkyeltpmgTtiege.ldevmevvkkahealfeaGakRvstvikiddr 77
                                      ++++ +P+g+ g sv + ++kvv  lk+++ +k++ ++m T+ie + +d +m++vk+a++ + ++G +Rv t+++id+r
  gi|518652290|ref|YP_008141810.1|  4 ADVTFYPIGK-GVSVGDTIEKVVSRLKNNNsIKCYPNSMATVIECNnIDILMDAVKDAEKFIENMGFPRVETILRIDSR 81
                                      6899*****8.***************76655************************************************ PP

                                      SSS---HHHHHHHH CS
                       Thiamine_BP 78 rdkeqtleeKvksv 91
                                      +d+e+++e+K+k v
  gi|518652290|ref|YP_008141810.1| 82 TDVENSVERKMKYV 95
                                      **********9976 PP

>> Antimicrobial_8  Uperin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.5e-05      0.14       2      15 ..      17      30 ..      16      30 .. 0.97

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.5e-05
                   Antimicrobial_8  2 VGDliRKiVsaIKN 15
                                      VGD i K+Vs  KN
  gi|518652290|ref|YP_008141810.1| 17 VGDTIEKVVSRLKN 30
                                      9************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); 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 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 730.57
//
Query:       gi|518652291|ref|YP_008141811.1|  [L=391]
Description: hypothetical protein FACI_IFERC00001G0930 [Ferroplasma acidarmanus fer1]
Scores for complete 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-51  173.6   0.0    5.4e-51  173.3   0.0    1.1  1  MR_MLE_C  Enolase C-terminal domain-like
    5.9e-10   39.4   0.0    1.1e-09   38.5   0.0    1.4  1  MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.3   0.0     6e-55   5.4e-51       4     219 ..     145     364 ..     142     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 173.3 bits;  conditional E-value: 6e-55
                                       HHHHHHHHHHT-SEEEEETSSS........HHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGG CS
                          MR_MLE_C   4 eearelvaeqgfravKlkvggd........dvaedvervravreavgpgddvdlmvDanqawdlatAirvareleel 72 
                                        +a++ ++++g+ a+K++++g+         v++  e v+++r  +g+g+  dl+++++++++++ Ai  +++lee+
  gi|518652291|ref|YP_008141811.1| 145 SKAKS-LVSRGYSAFKFDPFGSnydkitvdGVKKAQEIVAQMRSSLGEGV--DLLIECHGRFSPKYAIMAGKALEEY 218
                                       56655.6778************************************8877..************************* PP

                                       TESEEESSSSTTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHT CS
                          MR_MLE_C  73 dllwlEEPvppeddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeaf 148
                                       ++l++EEP++p +  + l e r ++ +ip+a+gE+l + +df++++++g vd++qpd++++ Gi ea+k+ a+ae f
  gi|518652291|ref|YP_008141811.1| 219 NPLFIEEPIHP-ELERFLPEFR-ARvDIPVALGERLLNKEDFARYISDGMVDVIQPDLTNSKGILEAKKIGAIAESF 293
                                       ***********.56999*****.6669************************************************** PP

                                       T-EEEEBSCSSHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                          MR_MLE_C 149 gvpvapHsgsgglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveldee 219
                                       g+ va H+  g++++aa+l +  ++pn+li+e+f+ +++  ++ l   + ve+ +++++ +pGlG+e++e+
  gi|518652291|ref|YP_008141811.1| 294 GISVAYHNAFGPVQTAATLNVDYTLPNFLIQESFEESWPSWKKNLFTGYSVENCTMALSGKPGLGIEVNEK 364
                                       ********658****************************7777777788999999*************986 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   1.2e-13   1.1e-09      27     117 .]      25     119 ..      19     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.2e-13
                                       EEEEEEEEECTTEEEEEEEE-STTGHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHHHCSS......CHHHHHHHH CS
                          MR_MLE_N  27 slvlvkietseGvvGigeatsvggraetikaelddhlapllvgkdaanisdlaqllkravlg......nmsAkaaid 97 
                                       ++ ++k+++s+G vG gea +   + + +k  +++ +a    gk+   i++  +  +r +++       ++A +a +
  gi|518652291|ref|YP_008141811.1|  25 TILILKLTSSDGRVGFGEAPTTM-MTLPVKESMNE-VARVFQGKNYFDIEKNLRDYYRNAFYvaksveETAALSAFE 99 
                                       6789***************9888.88999888877.*************************99****999******* PP

                                       HHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  98 mAlwDlkakalnlpladLlG 117
                                       +A wDl +k l+ p+++LlG
  gi|518652291|ref|YP_008141811.1| 100 IASWDLIGKNLGSPIYNLLG 119
                                       *******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2511.32
//
Query:       gi|518652292|ref|YP_008141812.1|  [L=642]
Description: hypothetical protein FACI_IFERC00001G0931 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-26   93.1   4.9    6.3e-21   74.0   1.0    2.5  2  V_ATPase_I  V-type ATPase 116kDa subunit family


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 !   74.0   1.0   3.5e-25   6.3e-21     226     460 ..     187     425 ..     139     430 .. 0.78
   2 !   20.1   0.1   7.3e-09   0.00013     716     811 ..     540     628 ..     537     630 .. 0.68

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 3.5e-25
                        V_ATPase_I 226 icesfgaklyelpeseeereeklkeveeriedlekvleqteealkevleei...akeleewklkvkkekaiyhtLnl 299
                                       i +s   ++ ++pe + + +e+++ ++++i++ ++++e  +++l+++ +++     +++e   +  ke +i +++ +
  gi|518652292|ref|YP_008141812.1| 187 ILSSKTYDMMKIPELNGTVKENIELIHNTINEASNAIEGIKSSLNALSDKYyepVAQITEQLEIYVKEEEILSNIAF 263
                                       66777778888999999999999999999999999999999988888888744433343334444456666555544 PP

                        V_ATPase_I 300 fnldvtkkvliaegWvpkeeleeiqkalkeateessssvpsilneietketpPTyfrtnkfteafQeivdaYGiarY 376
                                            +++ +  egW+p++e e+++++l+e +     +++ ++++ietke+pPT     k  + f  ++  Y+ ++ 
  gi|518652292|ref|YP_008141812.1| 264 -----SENAFALEGWIPESEYEKVSSVLNEDS-----NNTMFIQKIETKEDPPTKLSNPKHFKIFEFFIRFYSLPEE 330
                                       .....46899*******************955.....67899*********************************** PP

                        V_ATPase_I 377 rEvNpalftiitFPFlFavMFGDiGHGlllllfalllvlkekklkkk.....kkdeilemlfsgRYiillm...... 442
                                        E  p+++    FP  F++M GD+G Gl++ll++l+++ + ++  +k     k + ++ m+++   + +l       
  gi|518652292|ref|YP_008141812.1| 331 YEFDPTMIFALVFPVFFGLMVGDAGYGLVILLISLFIIHRVDHPPAKshipkKLSGFILMIMGKNSLKTLAkalips 407
                                       **************************************998777666456645555555665555544432222233 PP

                        V_ATPase_I 443 GlfsiYtGliYNdifsks 460
                                       ++ +i  G+++N++f+ +
  gi|518652292|ref|YP_008141812.1| 408 SIIAIIFGIVFNEFFGFT 425
                                       678888888888888765 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 7.3e-09
                        V_ATPase_I 716 ciSnTASYLRLWALSLAHaqLseVlwemvlkkallksksvlgvillvilfavfavltvavLllmeglsafLHaLRLh 792
                                       +iS+  SY R+  + LA   L+ V+ + v++ +l++       ++++i+++v +v  ++  l++ +++  +   RL 
  gi|518652292|ref|YP_008141812.1| 540 IISHILSYTRIVGILLASVVLALVI-DTVFRATLSD--P---FYFIIIGVVVLVVGQLFN-LIIAVFEPGIQGARLL 609
                                       6899999999999988888888776.5556653422..2...222233333333333332.3345677778899*** PP

                        V_ATPase_I 793 WVEfqsKFykgdGykFepf 811
                                        VEf sKFy g+G +F+pf
  gi|518652292|ref|YP_008141812.1| 610 YVEFFSKFYFGNGKPFSPF 628
                                       ******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1379  (0.0769145); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.32s 00:00:01.07 Elapsed: 00:00:00.51
# Mc/sec: 3767.64
//
Query:       gi|518652293|ref|YP_008141813.1|  [L=107]
Description: V-type ATP synthase subunit H [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.074   13.5   1.7       0.11   13.0   1.6    1.4  1  DUF4497        Protein of unknown function (DUF4497)
       0.15   12.0   5.9       0.17   11.8   5.9    1.1  1  PDDEXK_6       PDDEXK-like family of unknown function
       0.33   10.5   6.4       0.38   10.3   6.4    1.0  1  Exonuc_VII_L   Exonuclease VII, large subunit
       0.46   10.3   9.6       0.54   10.1   9.6    1.1  1  PIN_8          PIN like domain
       0.53   10.8   7.7       0.63   10.5   7.7    1.1  1  DUF2115        Uncharacterized protein conserved in archaea (
       0.54    9.0  14.4        0.6    8.9  14.4    1.1  1  Mitofilin      Mitochondrial inner membrane protein
       0.63   10.4   4.8       0.82   10.0   4.0    1.6  1  Aconitase_C    Aconitase C-terminal domain
       0.69   10.5  16.5       0.91   10.1  13.5    2.0  2  V-ATPase_G     Vacuolar (H+)-ATPase G subunit
        1.5    8.0   8.5        1.8    7.7   8.5    1.1  1  TMPIT          TMPIT-like protein
        1.5    9.1  16.3        1.4    9.2  14.5    1.5  1  OmpH           Outer membrane protein (OmpH-like)
        4.6    6.5   9.5        5.4    6.3   9.5    1.1  1  DUF4407        Domain of unknown function (DUF4407)
        6.3    6.9  11.1       0.71    9.9   2.4    2.2  2  Adhesin_P1_N   Adhesin P1 N-terminal domain


Domain annotation for each model (and alignments):
>> DUF4497  Protein of unknown function (DUF4497)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.6   7.1e-05      0.11      30      66 ..       7      46 ..       5      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 7.1e-05
                           DUF4497 30 isvlkkgeepkkkliGsaeislselfnklikevkek...k 66
                                      + v+k++ee kk+ i++ + ++++++n+ i+e++ek    
  gi|518652293|ref|YP_008141813.1|  7 LKVIKNKEEAKKRSIAELKEEMEKQLNQQIAECNEKaknL 46
                                      78999999***************************95552 PP

>> PDDEXK_6  PDDEXK-like family of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   5.9   0.00011      0.17      27      95 ..      13      88 ..       2     101 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                          PDDEXK_6 27 efeeeseedsdeekdsseeaaellkellesassaerklladvseavekakkevk.......kkeeekrsclrrava 95
                                      ++e+++++  + +++  ++ ++++ e+ e+a+++e+++++d ++a+e+ kk+         +++++++++++  ++
  gi|518652293|ref|YP_008141813.1| 13 KEEAKKRSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIEEIKKSESrkmadalDTQRARSNVMKVDIS 88
                                      22333444444455577888999*************************8777665666666444455555555554 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 ?   10.3   6.4   0.00025      0.38     142     217 ..      14      83 ..       3     105 .. 0.44

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00025
                      Exonuc_VII_L 142 kaeleeqleelerrlekaikrlleekkqrleklasrl.kspeellerk.rqrldeleerleralkkqlkkkrerlee 216
                                       ++  +++++el++++ek++++++ e +++ ++l++++ ++ ++ +e+  +++ +++++ l+++        r+r + 
  gi|518652293|ref|YP_008141813.1|  14 EEAKKRSIAELKEEMEKQLNQQIAECNEKAKNLENQIiNDYNKAIEEIkKSESRKMADALDTQ--------RARSNV 82 
                                       233355566666666666666666666666666554422222222221133333333333332........222222 PP

                      Exonuc_VII_L 217 l 217
                                       +
  gi|518652293|ref|YP_008141813.1|  83 M 83 
                                       2 PP

>> PIN_8  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   9.6   0.00036      0.54      49     135 ..       7      97 ..       4     107 .] 0.59

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00036
                             PIN_8  49 esviskekkayedlekel.eklkkaaekkleealkkwakkkaldteelrkelkkqleelkeel..........kael 114
                                       ++vi+++++a++   +el e+++k++++   +++++++k k+l+ +++ ++++k++ee+k++           +   
  gi|518652293|ref|YP_008141813.1|   7 LKVIKNKEEAKKRSIAELkEEMEKQLNQ---QIAECNEKAKNLE-NQIINDYNKAIEEIKKSEsrkmadaldtQ--- 76 
                                       5788888888888888887888888884...6667777777777.88888899999998887744433321111... PP

                             PIN_8 115 eelkksskadkeedpilkkle 135
                                       ++ ++  k d+++ ++++k++
  gi|518652293|ref|YP_008141813.1|  77 RARSNVMKVDISNRKLEEKVY 97 
                                       111111222223333444444 PP

>> DUF2115  Uncharacterized protein conserved in archaea (DUF2115)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   7.7   0.00042      0.63      10      95 ..      13      94 ..       5     106 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                           DUF2115 10 kkeaskisieDlm.kisarlekeikklpekyrkelseslteylfeaykelknkrsgdkseykeevideeelkeflemle 87
                                      k+ea+k si +l+ +++++l+++i++ +ek  k+l++++++ + +a++e+k+   ++++++    +d+++ ++ + +++
  gi|518652293|ref|YP_008141813.1| 13 KEEAKKRSIAELKeEMEKQLNQQIAECNEKA-KNLENQIINDYNKAIEEIKK---SESRKMA-DALDTQRARSNVMKVD 86
                                      68999******973699***********987.7899999999*********9...4445554.5678887777777766 PP

                           DUF2115 88 eqceeeke 95
                                         ++ +e
  gi|518652293|ref|YP_008141813.1| 87 ISNRKLEE 94
                                      55444433 PP

>> Mitofilin  Mitochondrial inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9  14.4    0.0004       0.6     310     380 ..       9      78 ..       2      93 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0004
                         Mitofilin 310 elkkeeekkieralekqkeelekqeealsarleeerakeerqlrlelereleeireeyeekLrteLerqae 380
                                        +k + e+  +r++++ kee ekq ++++a+  e++++ e+q+   + +++eei+++  +k+  +L++q++
  gi|518652293|ref|YP_008141813.1|   9 VIK-NKEEAKKRSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIEEIKKSESRKMADALDTQRA 78 
                                       334.445556899*****99***********************************************9987 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   4.0   0.00055      0.82       6      56 ..       9      59 ..       4      83 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00055
                                      CCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTT CS
                       Aconitase_C  6 klkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdldd 56
                                        k++++ +++s ++ +++++kq++++ia ++ +++++e++  n+++++ +
  gi|518652293|ref|YP_008141813.1|  9 VIKNKEEAKKRSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIE 59
                                      56899999*******************************998888776544 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  13.5   0.00061      0.91      33      94 ..      11      73 ..       4      86 .. 0.88
   2 ?    2.5   0.2      0.14   2.1e+02      73     103 ..      76     106 ..      66     107 .] 0.81

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00061
                                      HHHHHHHH.HHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHH CS
                        V-ATPase_G 33 qAkeeAek.Eieeyrakkekefkekeaeklgseeelekkieketeekikelkesvkknkeavv 94
                                      + keeA+k  i+e ++++ek+++++ ae+  + ++le++i ++ ++ i+e+k+s ++++++ +
  gi|518652293|ref|YP_008141813.1| 11 KNKEEAKKrSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIEEIKKSESRKMADAL 73
                                      4578886538********************************************999988766 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.14
                                       HHSSHHHHHHHHHHHHHHHHHHHHHHHHHTS CS
                        V-ATPase_G  73 keteekikelkesvkknkeavvkellklvld 103
                                       +++++++ +++ s +k +e+v + +l+++++
  gi|518652293|ref|YP_008141813.1|  76 QRARSNVMKVDISNRKLEEKVYNLILEYITK 106
                                       567778888889999999*********9997 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   8.5    0.0012       1.8      13      79 ..       9      77 ..       2     104 .. 0.44

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
                             TMPIT 13 eleetakeykqkleelsk.lqskcskeikkqkkrlkelkssl.kklkksvkeeeeeeveelkeelkerk 79
                                       ++++++  k++++el++ +++++ ++i+++++++k+l++++ ++++k+++e +++e +++++ l++++
  gi|518652293|ref|YP_008141813.1|  9 VIKNKEEAKKRSIAELKEeMEKQLNQQIAECNEKAKNLENQIiNDYNKAIEEIKKSESRKMADALDTQR 77
                                      333333333333333332123333444444444444444332133444444444444444444433333 PP

>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2  14.5   0.00095       1.4      48     110 ..       6      66 ..       1      90 [. 0.73

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00095
                                       HHHHHTTTS.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                              OmpH  48 elqkkakklekeekeqelqkkeqelqqkqqqkaqelqkkqqellkpildkinkaikevakekg 110
                                       el+   k++ +e+k++ ++++++e++++++q+  e ++k + l ++i++  nkai+e+ k + 
  gi|518652293|ref|YP_008141813.1|   6 ELKVI-KNK-EEAKKRSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIEEIKKSES 66 
                                       44322.221.566666699999999999999999999999999999*********99999764 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   9.5    0.0036       5.4     113     190 ..      10      80 ..       2      98 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0036
                           DUF4407 113 aeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekk 189
                                       +++++e++k   +++a+  ++  ++l++qia+ +++ +++e+++ + +++a +e++   +    +++ +   +++++
  gi|518652293|ref|YP_008141813.1|  10 IKNKEEAKK---RSIAELKEEMEKQLNQQIAECNEKAKNLENQIINDYNKAIEEIKKSES----RKMADALDTQRAR 79 
                                       333333333...355555577788899999999999999999999999999999986332....2333333333333 PP

                           DUF4407 190 a 190
                                       +
  gi|518652293|ref|YP_008141813.1|  80 S 80 
                                       3 PP

>> Adhesin_P1_N  Adhesin P1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   3.1     0.077   1.1e+02      32      64 ..      12      42 ..       6      46 .. 0.46
   2 ?    9.9   2.4   0.00048      0.71      30      57 ..      37      64 ..      36      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.077
                      Adhesin_P1_N 32 taeeadaKkaeIkaDYnkQakeikaatdeYkek 64
                                      ++eea  Kk  I++  ++ +k++++ ++e +ek
  gi|518652293|ref|YP_008141813.1| 12 NKEEA--KKRSIAELKEEMEKQLNQQIAECNEK 42
                                      55554..33334444444444444443333333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00048
                      Adhesin_P1_N 30 aktaeeadaKkaeIkaDYnkQakeikaa 57
                                      a+ +e a++ ++ I +DYnk ++eik+ 
  gi|518652293|ref|YP_008141813.1| 37 AECNEKAKNLENQIINDYNKAIEEIKKS 64
                                      56788999999***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3817  (0.212895); expected 358.6 (0.02)
Passed bias filter:                      927  (0.0517039); expected 358.6 (0.02)
Passed Vit filter:                       142  (0.00792013); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 743.42
//
Query:       gi|518652294|ref|YP_008141814.1|  [L=35]
Description: hypothetical protein FACI_IFERC00001G0933 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.14   11.0   2.9       0.14   11.0   2.9    1.0  1  DUF677       Protein of unknown function (DUF677)
        3.2    7.9   6.1        3.3    7.8   6.1    1.0  1  Podoplanin   Podoplanin
        3.7    7.9   8.5        3.8    7.9   8.5    1.1  1  Sigma_reg_N  Sigma factor regulator N-terminal


Domain annotation for each model (and alignments):
>> DUF677  Protein of unknown function (DUF677)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   2.9   2.3e-05      0.14     171     199 ..       5      33 ..       3      35 .] 0.92

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.3e-05
                            DUF677 171 kklrniktkraisnvvfvaafvaVlvlSv 199
                                       +k ++i++  +i n++++ af+a+l++ +
  gi|518652294|ref|YP_008141814.1|   5 EKFKRIRKIIRIINILLAIAFIAILIMVI 33 
                                       699**********************9866 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   6.1   0.00055       3.3     135     154 ..      16      35 .]       9      35 .] 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00055
                                       XXXXXXXXXXXXXXXXXXXX CS
                        Podoplanin 135 ivGvllaigfiggiiivvvr 154
                                       i+ +llai+fi+ +i+v+++
  gi|518652294|ref|YP_008141814.1|  16 IINILLAIAFIAILIMVIIK 35 
                                       789*************9986 PP

>> Sigma_reg_N  Sigma factor regulator N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.5   0.00064       3.8       8      33 ..       9      34 ..       4      35 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00064
                       Sigma_reg_N  8 krksilrivlislivlllifvilvvt 33
                                      + + i+ri+ i l+++++ ++i+v++
  gi|518652294|ref|YP_008141814.1|  9 RIRKIIRIINILLAIAFIAILIMVII 34
                                      34668888888888888888888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1179  (0.0657594); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 254.72
//
Query:       gi|518652295|ref|YP_008141815.1|  [L=212]
Description: V-type ATP synthase subunit D [Ferroplasma acidarmanus fer1]
Scores for complete 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-46  156.6   5.8    7.6e-46  156.4   5.8    1.0  1  ATP-synt_D    ATP synthase subunit D
     0.0032   16.8   3.5       0.25   10.7   0.2    2.2  2  GAS           Growth-arrest specific micro-tubule binding
  ------ inclusion threshold ------
       0.12   12.6   0.7        4.5    7.5   0.0    3.1  3  UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, c


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 !  156.4   5.8   1.3e-49   7.6e-46       1     195 [.      11     201 ..      11     202 .. 0.95

  Alignments for each domain:
  == domain 1  score: 156.4 bits;  conditional E-value: 1.3e-49
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTSTTSTSHHHHHHHSSS.SS-. CS
                        ATP-synt_D   1 eLirlkkrlklaqrghslLkkKrdaLilefreilkelkelreeleeelkeayfslaeafaaggeediesavlesvkl 77 
                                       eLi+ kkr+k+a rg++lLk+Kr+ L++ef++i +e++ lre++++ +++  ++++ a + +g  +ie+++ +    
  gi|518652295|ref|YP_008141815.1|  11 ELINTKKRIKVASRGLELLKMKRQSLVMEFFKISNEVRGLRENIKNDIEKGLNAIKVAEIIDGTLEIERISYMF--- 84 
                                       79********************************************************99999*****999844... PP

                                       .TSS-SEEEEEEBTTSEEEEEEE-..S.SSTSSSSSSSSTCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D  78 akvvkvelktenvaGVkvpvfeleeeksdstelygllrtgaqldeavealrellellvelasletslelLdeeikkt 154
                                        ++ ++++  +n++GV++p+++ +  k+   ++y   + + ++ +a++ +++++++l+e+ ++e s+++L +ei kt
  gi|518652295|ref|YP_008141815.1|  85 -SSPEIKIGGKNIMGVTIPEMSAQAGKKIIDDSYLANSVPVSIYDAITLFNKIFKELLEVSQKESSMRKLLNEIDKT 160
                                       .459*****************99776666677888889999************************************ PP

                                       HHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_D 155 nrRvNaLekvvIPrleetikyIkseLdEqereeffrlkkvk 195
                                       nrR Na+e+++IPr++++ k I++ LdE er +f+ lk vk
  gi|518652295|ref|YP_008141815.1| 161 NRRSNAIENIMIPRFNNNYKIIREHLDELERDSFATLKFVK 201
                                       ***************************************99 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 !   10.7   0.2   4.2e-05      0.25      84     134 ..       9      59 ..       3      71 .. 0.89
   2 !    7.2   0.4    0.0005         3      26      60 ..     131     165 ..     126     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.2e-05
                               GAS  84 kqslknlkarlkelekelkdlkwehevleqrfekvekerdelykkfeaaiq 134
                                       + +l n+k+r+k++ + l+ lk++ ++l ++f k+++e   l+++ ++ i+
  gi|518652295|ref|YP_008141815.1|   9 RIELINTKKRIKVASRGLELLKMKRQSLVMEFFKISNEVRGLRENIKNDIE 59 
                                       56789*************************************999988876 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0005
                               GAS  26 elIkslKeeieelkkkeernekelseisqenkrlk 60 
                                       +l ++  +e+ e  +ke +++k+l+ei + n+r +
  gi|518652295|ref|YP_008141815.1| 131 TLFNKIFKELLEVSQKESSMRKLLNEIDKTNRRSN 165
                                       6667777899*********************9975 PP

>> UDPG_MGDP_dh  UDP-glucose/GDP-mannose dehydrogenase family, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.044   2.6e+02       9      27 ..       1      19 [.       1      34 [. 0.85
   2 ?    7.5   0.0   0.00075       4.5      32      64 ..      64      96 ..      27     122 .. 0.84
   3 ?   -0.7   0.0      0.29   1.7e+03      65      93 ..     134     162 ..     131     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.044
                      UDPG_MGDP_dh  9 aaNaflatkIsfiNelanl 27
                                      +aN+++ t+I +iN  +++
  gi|518652295|ref|YP_008141815.1|  1 MANTVRLTRIELINTKKRI 19
                                      68************87665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00075
                      UDPG_MGDP_dh 32 gidveeVieavgldprigpkflkpglGvGGscl 64
                                       i v+e+i++    +ri+++f +p++ +GG+ +
  gi|518652295|ref|YP_008141815.1| 64 AIKVAEIIDGTLEIERISYMFSSPEIKIGGKNI 96
                                      37899999999999****************876 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.29
                      UDPG_MGDP_dh  65 pkDvkaLvalaeelgleaelleavrevNe 93 
                                       +k  k L++ +++++   +ll++++++N+
  gi|518652295|ref|YP_008141815.1| 134 NKIFKELLEVSQKESSMRKLLNEIDKTNR 162
                                       56667899999999999999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      595  (0.0331865); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 1667.75
//
Query:       gi|518652296|ref|YP_008141816.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G0935 [Ferroplasma acidarmanus fer1]
Scores for complete 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-63  213.8   0.0    2.8e-63  213.4   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      3e-11   43.7   0.3    5.9e-11   42.7   0.3    1.5  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
      0.019   15.1   0.1      0.051   13.7   0.1    1.8  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 !  213.4   0.0   4.6e-67   2.8e-63       1     213 []     132     350 ..     132     350 .. 0.98

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 4.6e-67
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS....S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd....d.aiiyvgiGergnevaevleefpegtimkrt 72 
                                       Gi+++D + ++v Gq++ i++++g+ ++ ++ +++kq+++     +  +++ +iG  ++e++ ++++f+++++++++
  gi|518652296|ref|YP_008141816.1| 132 GISTIDGMNTLVMGQKLPIFSGAGLSHNRLATQIAKQAKTLkggeKfGVVFGAIGITSEEANYFMKQFESSGALSES 208
                                       899**********************************86658997679***************************** PP

                                       EEEEEETTS-HHHHHHHHHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  73 vlvantsnepvaareasiytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklasl 148
                                       v+++n +++p + r++ +++++t+AEy+++ +++n+l+i++++++++eAlreis + +e+p+++gyp+y++++l+++
  gi|518652296|ref|YP_008141816.1| 209 VIFLNLASDPSMDRIILPRVALTTAEYLAYeKDMNMLVILTDMTNYCEALREISSSREEIPGRRGYPGYMYTDLSTI 285
                                       *****************************9999******************************************** PP

                                       HTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 149 yERagkapdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       yERagk++ r+Gs+t++++++++g+D+++pv++ t +it+g+i L+++l ++ ++P ++vl S+S
  gi|518652296|ref|YP_008141816.1| 286 YERAGKIKGRNGSITQIPILTMPGDDITNPVPDLTGYITEGQITLSRDLSRKDIYPEVDVLLSLS 350
                                       ***************************************************************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 !   42.7   0.3   9.8e-15   5.9e-11       1      69 []       9      75 ..       9      75 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.7 bits;  conditional E-value: 9.8e-15
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBT.TSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsr.GteVkrTG 69
                                      i+q++Gp++ v++++     +++++++ l + g+ ++g++l+ ++++++v+v+gst+  s+  t V +TG
  gi|518652296|ref|YP_008141816.1|  9 ISQINGPLLFVDDVKN--ASYNEIVSIILDN-GERVKGQVLETRNGVAVVQVFGSTTSMSPkSTGVSFTG 75
                                      89**************..5555555555437.*****************************999999998 PP

>> HAS-barrel  HAS barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   8.5e-06     0.051       7      75 ..       9      54 ..       4      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.5e-06
                        HAS-barrel  7 estssslifrvegskdvkvGeyVeielpdgeivlGmvtdirrgnselsndlalvlsleeleeangddev 75
                                       s++++++ +v+ +k+ ++ e V+i+l+ ge+v G+v+  r+                       + +v
  gi|518652296|ref|YP_008141816.1|  9 ISQINGPLLFVDDVKNASYNEIVSIILDNGERVKGQVLETRN-----------------------GVAV 54
                                      4566*************************************9.......................4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 3770.99
//
Query:       gi|518652297|ref|YP_008141817.1|  [L=589]
Description: hypothetical protein FACI_IFERC00001G0936 [Ferroplasma acidarmanus fer1]
Scores for complete 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-93  310.2   0.0    9.7e-93  309.7   0.0    1.2  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    1.9e-41  140.7   0.1    4.3e-41  139.6   0.1    1.6  1  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens
    1.6e-11   44.5   1.7    3.2e-11   43.6   0.9    2.0  2  ATP-synt_ab_N    ATP synthase alpha/beta family, beta-barrel 
  ------ inclusion threshold ------
       0.28   11.1   2.8         11    6.0   0.2    3.5  3  Myosin_N         Myosin N-terminal SH3-like domain
        2.9    8.3   5.2        5.4    7.4   0.3    2.4  2  TSNAXIP1_N       Translin-associated factor X-interacting N-t


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 !  309.7   0.0   2.7e-96   9.7e-93       1     213 []     211     434 ..     211     434 .. 0.98

  Alignments for each domain:
  == domain 1  score: 309.7 bits;  conditional E-value: 2.7e-96
                                       SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHH......SS.GGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xx.xxx RF
                       ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpe......gt.imk 70 
                                       G+rv+D++fp+++G+++++pg fg Gktvi+++lsk+s++d +++yvg+Gergne++e+l++fpe      g+ +m+
  gi|518652297|ref|YP_008141817.1| 211 GQRVIDSFFPVAKGGTVAVPGPFGSGKTVIQHQLSKWSDAD-ITVYVGCGERGNEMTEILSTFPElqdpksGKpLME 286
                                       9************************************9888.***********************999876337*** PP

                                       GEEEEEEETTS-HHHHHHHHHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  71 rtvlvantsnepvaareasiytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklas 147
                                       +t+l+antsn+pvaareasiytg+t+AEy+rd+g++v l+ads+srwaeAlreis+rl+emp+++gypaylg ++++
  gi|518652297|ref|YP_008141817.1| 287 KTILIANTSNMPVAAREASIYTGVTIAEYYRDMGYDVALMADSTSRWAEALREISGRLEEMPGEEGYPAYLGRRISE 363
                                       ***************************************************************************** PP

                                       HHTTSEEE.....TSSEEEEEEEEEEE-GGCSTTSHHHHHHHHHSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab 148 lyERagka.....pdrtGsvtivaavspaggDfsdpvttatlgitdgfivLdkklaqrkhfPainvlvSvS 213
                                       +yER+g+a     ++rtGs+t + avsp+ggD+sdpv ++tl++t +f+ Ld +la+r+hfP+in+l+S+S
  gi|518652297|ref|YP_008141817.1| 364 FYERSGNAqiiaqDERTGSITLIGAVSPPGGDLSDPVVQNTLRVTRAFWALDASLASRRHFPSINWLNSYS 434
                                       ***********99889******************************************************9 PP

>> ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.6   0.1   1.2e-44   4.3e-41       1     120 [.      84     201 ..      84     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.6 bits;  conditional E-value: 1.2e-44
                                       EETTS-BHHHHHHHHTSBE-TT----SS-SSS-EEEEESS-TT-EEETT-EEEEEECTTCEEEEEE--TT-EEEEEE CS
                   ATP-synt_ab_Xtn   1 yDGiqrpLekiaeksgsfierGvkvpaldrekkwefkpkvkvgdkvsggdilGtvqeteliehkimvppkvegkvke 77 
                                       yDGiqrpL+ i++++g+fi rG+++p+ld++k+w+f+p +k+gd+v++g ilGtvqet++i+hkimvp++++g +k+
  gi|518652297|ref|YP_008141817.1|  84 YDGIQRPLDIIQSETGDFIVRGATAPPLDEKKEWDFVPLLKEGDEVEQGYILGTVQETNIITHKIMVPYGIRGIIKS 160
                                       9**************************************************************************** PP

                                       E--EEEE-TTSECEEECETT.ECEEEESSEEEETTS---ESEE CS
                   ATP-synt_ab_Xtn  78 iaeegeytvedtiaeveteegkekeltllqkwPvrkprpvkek 120
                                       i+ +g+++v+dt++ ++t++ ++++++l q wPvr++r+v  k
  gi|518652297|ref|YP_008141817.1| 161 IS-KGKFKVSDTVCMIDTGT-SKYDIKLKQIWPVRQARKVFLK 201
                                       *9.**************998.6****************99765 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 !   43.6   0.9   8.9e-15   3.2e-11       1      69 []       7      68 ..       7      68 .. 0.98
   2 ?   -3.1   0.0       3.3   1.2e+04      27      46 ..     461     479 ..     451     480 .. 0.70

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 8.9e-15
                                      EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
                     ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                                      i++++Gpvv++ +  g   ++ ++++v+  e   +l+g+++ + +dk  ++v+++t+Gl++G++V++TG
  gi|518652297|ref|YP_008141817.1|  7 IYSISGPVVIATDLDG---KMFDVVRVG--E--MGLVGEVIKIVGDKFTIQVYEDTSGLKPGEPVYSTG 68
                                      789********99999...*********..9..***********************************9 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.3
                                       ECCETCSTEEEEEEEEEETT CS
                     ATP-synt_ab_N  27 velvefgtlllgvalnlged 46 
                                       + l+ +++ l++ ++ +g d
  gi|518652297|ref|YP_008141817.1| 461 GILQ-KESELQEIVQLVGYD 479
                                       4444.489999999999876 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.2    0.0029        11      16      32 ..      37      54 ..      35      57 .. 0.90
   2 ?    2.4   0.0     0.038   1.4e+02      10      21 ..     130     141 ..     128     142 .. 0.89
   3 ?   -0.1   0.1      0.24   8.6e+02      14      28 ..     154     168 ..     154     169 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0029
                                      EEEEEEESSEEEEEE.TT CS
                          Myosin_N 16 GeIkeeeGdkvtVet.ed 32
                                      Ge++++ Gdk+t++  ed
  gi|518652297|ref|YP_008141817.1| 37 GEVIKIVGDKFTIQVyED 54
                                      9*************9876 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.038
                                       TTS-EEEEEEEE CS
                          Myosin_N  10 kegyvkGeIkee 21 
                                       ++gy+ G+++e+
  gi|518652297|ref|YP_008141817.1| 130 EQGYILGTVQET 141
                                       79********97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.24
                                       EEEEEEEEESSEEEE CS
                          Myosin_N  14 vkGeIkeeeGdkvtV 28 
                                       ++G Ik+++ +k+ V
  gi|518652297|ref|YP_008141817.1| 154 IRGIIKSISKGKFKV 168
                                       6799********998 PP

>> TSNAXIP1_N  Translin-associated factor X-interacting N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.0     0.049   1.7e+02      46      87 ..     513     557 ..     466     566 .. 0.72
   2 ?    7.4   0.3    0.0015       5.4      38      56 ..     566     584 ..     561     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.049
                        TSNAXIP1_N  46 eIKkEYel..yiahllesqreaqylkakl.ktlsessdkralele 87 
                                       +IKk+Ye+  +i++l e q++  ++  kl +t++ +  +++  ++
  gi|518652297|ref|YP_008141817.1| 513 SIKKQYEMltIIKTLNEMQEKSIASGLKLtQTATLPVRMKISRMK 557
                                       7******63368888888888777766664555544445555555 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0015
                        TSNAXIP1_N  38 kaYkdlLseIKkEYelyia 56 
                                       k Y d+ +eI +EY+++++
  gi|518652297|ref|YP_008141817.1| 566 KFYNDVIKEINNEYDNIME 584
                                       459*************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (589 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4294.76
//
Query:       gi|518652298|ref|YP_008141818.1|  [L=102]
Description: V-type ATP synthase subunit F [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-12   47.6   0.0    1.7e-12   47.5   0.0    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.5   0.0   9.5e-17   1.7e-12       3      83 ..       6      87 ..       4      95 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 9.5e-17
                                      EEESHHHHHHHHHTTCEEEECSSHHHHHHHHHHHHHHTTEEEEEEEHHHHCCCH.HHHHHCTCSSSSEEEEESCSCCGG CS
                        ATP-synt_F  3 vIGdedtvtgfrlaGvgevevtdeeeieealkelleredigiilitekiaeeir.elideykeealPaileIPskegpy 80
                                       IG+++ v gf+l+G++++  +d+e+ ++++kel +++++++i++++ + + +  ++i+ y  +  P+++ IP  + + 
  gi|518652298|ref|YP_008141818.1|  6 LIGERELVAGFKLVGINDTFTADPENGKSIVKELFNSKKYNVIMVSQSFEKYMTpDEINLYAGSISPLVIFIPLPGIKE 84
                                      6**************************************************9877*****************9877655 PP

                                      SHH CS
                        ATP-synt_F 81 dee 83
                                      +e+
  gi|518652298|ref|YP_008141818.1| 85 EES 87
                                      555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 861.62
//
Query:       gi|518652299|ref|YP_008141819.1|  [L=353]
Description: hypothetical protein FACI_IFERC00001G0938 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  123.7  12.8    1.4e-35  123.5  12.8    1.0  1  vATP-synt_AC39  ATP synthase (C/AC39) subunit
  ------ inclusion threshold ------
       0.17   11.8   0.0       0.33   10.8   0.0    1.4  1  MRP-L27         Mitochondrial ribosomal protein L27


Domain annotation for each model (and alignments):
>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.5  12.8   1.5e-39   1.4e-35       9     335 ..      20     350 ..      13     351 .. 0.85

  Alignments for each domain:
  == domain 1  score: 123.5 bits;  conditional E-value: 1.5e-39
                                       GGGS--HHHHHHHTTS.-HHHHHHHHHTSGGGGG--......SSSHHHHHHHHHHHHHHHTTTGGGGS-H..HHHHH CS
                    vATP-synt_AC39   9 rsglLteedyenLlqcesledvkryLketdYgnfladel.seplsrsdiekalreklarefnklreqapgp.srefl 83 
                                        +  L+++  ++Ll+  +++d+++ L et+Y++++ +++  ++ +++ +  a++++ ++  +k+  +a+ p  + f+
  gi|518652299|ref|YP_008141819.1|  20 FNDYLSDSFVKSLLEL-DIKDIRLKLYETSYRDDIDKATtISNDDVDILITAINRHVIN-NAKIALFAVPPqIKSFM 94 
                                       56679999********.****************97666655555555555566666665.55666677777699*** PP

                                       HHHHHHHHHHHHHHHHHHHHH..T-.....-GGGS-..--.S..SSS-HHHHHHHHHSSSHHHHHHHHHT-HHHHHH CS
                    vATP-synt_AC39  84 dyllyrydidNvklllrgklsg.dl.....dleeleeklhpl..gelsaldldklieaksveelyeallgtpyakyl 152
                                       + ++ ++di+ +k+++++k+ + d+         +++  + +  g+l+ +d+++++e+++v++++++ll+  +   l
  gi|518652299|ref|YP_008141819.1|  95 KSYVSKWDIESIKAIITSKVIHhDIkyndsFIMSFRDIPMGIyaGNLKRDDFRAIMEKNDVDSVINYLLNYGFNYLL 171
                                       *********************999997766555555555555988************************99998777 PP

                                       HHHHCC...--SHHHHHHHHHHHHHHHHHHHHHTSS-HH...HHHHHHHHHHHHHHHHHHHTTTSS......T...- CS
                    vATP-synt_AC39 153 eealdeleetgdleiienaLdkayledllkfckklggetaeilreilgfeiDlrniniilrskkygelskedrkkll 229
                                       +e l+e+++tgd + + +a+d  y++dl+k +   +g++   + +++++ +Dl+ni ++ +++  +   ++ +++ +
  gi|518652299|ref|YP_008141819.1| 172 KE-LEEYKKTGDTSSLLSAMDYRYYNDLIKTALFYNGDE-GQIIKYVKTLVDLKNILTLAKAIELNVPFEK-IENSI 245
                                       77.****************************88666555.45999*******************9943344.88889 PP

                                       -SS-S--HHHHHHHHTT-G.....GG.GGSSTSSTTGGGTT--S.HHHHHHHHHHHHHHHHHTTTSSSTSTHHHHHH CS
                    vATP-synt_AC39 230 ipggslypeglealaeaedveellaalkyteygelleealeeagslksledaldealvkllkkafrqqfsvgvfyaY 306
                                       i+ g++++  l++  ++ +v ell+ +k  ++ e l+ + e+ ++l+++e  +++ l + +            ++aY
  gi|518652299|ref|YP_008141819.1| 246 IDNGNFSRTALSDTFRSGSVIELLSLFKHFNIDEALDYYKEN-KNLSQFEIGMRKSLFHEFVPVMIRDTASLFIFAY 321
                                       *************************************77665.66******************555555666789** PP

                                       HHHHHHHHHHHHHHHHHHHHT--SHHHHG CS
                    vATP-synt_AC39 307 lklkeqEirnlrwIaegiaqglpkekIre 335
                                       ++  e+E +nlr+I+ g++++l++++I++
  gi|518652299|ref|YP_008141819.1| 322 ILYAERERDNLRTIIIGKSYKLDNNTIER 350
                                       ***************************86 PP

>> MRP-L27  Mitochondrial ribosomal protein L27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.7e-05      0.33      33      81 ..      71     119 ..      62     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.7e-05
                                       TTEEEE-TTTS-EE-----TT----SEE-TTS---------HHHHHHHH CS
                           MRP-L27  33 sgkyveirekvrelvvPdlegfkLKpyVsykapevkqseltsqdLfnev 81 
                                         ++v++++k+  + vP +    +K yVs+   e ++  +ts+ +  ++
  gi|518652299|ref|YP_008141819.1|  71 INRHVINNAKIALFAVPPQIKSFMKSYVSKWDIESIKAIITSKVIHHDI 119
                                       57899*************99999******99888888889998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 2421.12
//
Query:       gi|518652300|ref|YP_008141820.1|  [L=189]
Description: V-type ATP synthase subunit E [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0017   18.2   2.9     0.0023   17.7   2.9    1.2  1  FAM184          Family with sequence similarity 184, A and B
  ------ inclusion threshold ------
      0.043   13.7   0.0      0.082   12.8   0.0    1.4  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.057   13.3   1.6      0.071   13.0   1.6    1.1  1  SNAD1           Secreted Novel AID/APOBEC-like Deaminase 1
      0.061   13.7   4.7       0.11   12.8   2.7    2.3  2  CPL             CPL (NUC119) domain
        0.1   13.1   1.4        0.3   11.6   0.7    2.3  2  HSCB_C          HSCB C-terminal oligomerisation domain
       0.36   10.9   3.4        0.5   10.4   0.7    2.4  2  DUF1870         Domain of unknown function (DUF1870)
       0.84   10.0   7.6        1.5    9.1   1.3    2.4  2  DUF2175         Uncharacterized protein conserved in archaea 
       0.89   10.1   6.5        1.6    9.3   0.5    2.6  2  V-ATPase_G      Vacuolar (H+)-ATPase G subunit
        0.9    9.6   4.2        2.3    8.2   4.2    1.8  1  Baculo_PEP_C    Baculovirus polyhedron envelope protein, PEP,


Domain annotation for each model (and alignments):
>> FAM184  Family with sequence similarity 184, A and B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   2.9   1.2e-06    0.0023      12     106 ..      14     114 ..       6     135 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                            FAM184  12 heaeiqalkeaHeeeiqqilaetrekilqyks..kveeeldlkqkiaeleesleqhek....ekrqalaefeqykrr 82 
                                        +ae++a+++   + i++i++  ++ki  +k+  +v+++ d k+ i++ e++++ + k    +k++ +  + ++k r
  gi|518652300|ref|YP_008141820.1|  14 TQAELKAIRDEYSAKIEAIIKSCNDKISRIKNyyAVKSDNDVKNIIKQYEDNIRLQSKkiidDKKKEILVNTMQKLR 90 
                                       58999**************************85579999*************999876333346666666669**** PP

                            FAM184  83 veerelkleaehsqkvvelsreve 106
                                       +  + l++ +++ + + ++ +e +
  gi|518652300|ref|YP_008141820.1|  91 SYVTSLNKSSNYPELLKAMVNESK 114
                                       ************999999977653 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05     0.082      53     172 ..       3     130 ..       2     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                                       CCCCHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHH.HHHHHHHHHHHHHHHHCHHHHHHH. CS
                    Apolipoprotein  53 lepyrdevqeqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaee.lrerlerhvealkarlapyveelr. 127
                                       le+ ++e+ ++ +++l+++r + ++ +e++ ++ + ++  +++  av++++ +++ +++  ++++ + + ++++ + 
  gi|518652300|ref|YP_008141820.1|   3 LENILNEIDNTTQAELKAIRDEYSAKIEAIIKSCNDKISRIKNYYAVKSDNdVKNIIKQYEDNIRLQSKKIIDDKKk 79 
                                       6677889999999**********************************998779999999999999999999999996 PP

                                       .......HHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHHHHH CS
                    Apolipoprotein 128 .......qklaerleelkeslaphaeeveerlssrveelrekleeqaeelre 172
                                              qkl++ +  l++s  ++ e +++++++  +el  k++ + +e+++
  gi|518652300|ref|YP_008141820.1|  80 eilvntmQKLRSYVTSLNKS-SNYPELLKAMVNESKKELGNKFTVYCDEMEN 130
                                       66666666666666666666.4456677799999999999999999888875 PP

>> SNAD1  Secreted Novel AID/APOBEC-like Deaminase 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.6   3.6e-05     0.071       4     112 ..       3     116 ..       1     125 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.6e-05
                             SNAD1   4 Lakivqyvrrntlgd.....kQYAlavllpqaqCtqanadiedvlseeqlqdvkdklardeavylgksenliaarpk 75 
                                       L++i++++ ++t+ +       Y   +    + C+++++ i+++ + +  +dvk+ + + e     +s+++i  ++k
  gi|518652300|ref|YP_008141820.1|   3 LENILNEIDNTTQAElkairDEYSAKIEAIIKSCNDKISRIKNYYAVKSDNDVKNIIKQYEDNIRLQSKKIIDDKKK 79 
                                       5666666644443331111157999999999**************************9999999999********** PP

                             SNAD1  76 eevkaskkkeHaEylLlggeenspnplkalLaaakpn 112
                                       e+  ++ +k  +    l +++n+p+ lka+++++k++
  gi|518652300|ref|YP_008141820.1|  80 EILVNTMQKLRSYVTSLNKSSNYPELLKAMVNESKKE 116
                                       **9999999999999****************999876 PP

>> CPL  CPL (NUC119) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.7   5.8e-05      0.11      24      71 ..      54     106 ..      41     115 .. 0.87
   2 ?   -0.1   0.0      0.52     1e+03      36      66 ..     157     187 ..     139     189 .] 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.8e-05
                               CPL  24 eviklLkegdelakktSKKdaevRrkELleaispallsaia.....knaeell 71 
                                       +v++++k+++ + + +SKK  + ++kE+l +  ++l s+++     +n+ ell
  gi|518652300|ref|YP_008141820.1|  54 DVKNIIKQYEDNIRLQSKKIIDDKKKEILVNTMQKLRSYVTslnksSNYPELL 106
                                       6899*********99************************99666666666665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.52
                               CPL  36 akktSKKdaevRrkELleaispallsaiakn 66 
                                        ++  KK+ ++R + + ++is    +++ +n
  gi|518652300|ref|YP_008141820.1| 157 VSADGKKEVDMRLSSIFDEISYDVETYLYEN 187
                                       4567899999999999999998777777666 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 ?   11.6   0.7   0.00015       0.3      15      51 ..       6      46 ..       1      97 [. 0.80
   2 ?   -1.5   0.0       1.9   3.8e+03      36      50 ..     107     121 ..      88     135 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00015
                                      HHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHH.....H CS
                            HSCB_C 15 eleeaeeaadkeeleelkaeveerieeleaeleeaf.....e 51
                                       l e+ +++ ++el+++++e +++ie++++++++ +      
  gi|518652300|ref|YP_008141820.1|  6 ILNEI-DNTTQAELKAIRDEYSAKIEAIIKSCNDKIsriknY 46
                                      46677.44477********************99998544440 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHHHHHH CS
                            HSCB_C  36 eerieeleaeleeaf 50 
                                       +++++e+ +el + f
  gi|518652300|ref|YP_008141820.1| 107 KAMVNESKKELGNKF 121
                                       455555555655555 PP

>> DUF1870  Domain of unknown function (DUF1870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.7   0.00025       0.5      42      85 ..       9      51 ..       2      73 .. 0.79
   2 ?    0.5   0.2       0.3     6e+02      49      49 ..     104     104 ..      54     155 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00025
                                      ---HHHHHHHHHHHHHHHHHHHHHHHHHCCS-S--EEE--SSHH CS
                           DUF1870 42 pipdeivaelkelkklrkkkieeiveklndrignstlryystlt 85
                                       i ++ +aelk++++    kie+i+++ nd+i +    yy+ ++
  gi|518652300|ref|YP_008141820.1|  9 EIDNTTQAELKAIRDEYSAKIEAIIKSCNDKI-SRIKNYYAVKS 51
                                      57788899************************.44556776544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                                       H CS
                           DUF1870  49 a 49 
                                       +
  gi|518652300|ref|YP_008141820.1| 104 E 104
                                       1 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 ?    9.1   1.3   0.00077       1.5      41      85 ..      22      66 ..       8      73 .. 0.83
   2 ?    4.3   1.3     0.025        50      36      87 ..      70     119 ..      66     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00077
                           DUF2175 41 esedaaaLleleevlneeivklkelervaedeevkkvleqkrkel 85
                                       +e  a +  + +  n++i ++k+   v++d++vk++++q + ++
  gi|518652300|ref|YP_008141820.1| 22 RDEYSAKIEAIIKSCNDKISRIKNYYAVKSDNDVKNIIKQYEDNI 66
                                      457778899999999************************998776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.025
                           DUF2175  36 rkklkesedaaaLleleevlneeivklkelervaedeevkkvleqkrkelEk 87 
                                       +kk+  ++++++L +  + l++ ++ l+++++ +e   +k ++++ +kel +
  gi|518652300|ref|YP_008141820.1|  70 SKKIIDDKKKEILVNTMQKLRSYVTSLNKSSNYPE--LLKAMVNESKKELGN 119
                                       677777899******************99999987..899999999998865 PP

>> V-ATPase_G  Vacuolar (H+)-ATPase G subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.5   0.00081       1.6      65     102 ..       4      41 ..       2      44 .. 0.86
   2 ?    2.1   1.7      0.14   2.7e+02      70      96 ..      50      76 ..      39     115 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00081
                                       HHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                        V-ATPase_G  65 eelekkieketeekikelkesvkknkeavvkellklvl 102
                                       e++ ++i+++t+ ++k ++++++++ ea++k   +++ 
  gi|518652300|ref|YP_008141820.1|   4 ENILNEIDNTTQAELKAIRDEYSAKIEAIIKSCNDKIS 41 
                                       567799************************98766665 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                                      HHHHHSSHHHHHHHHHHHHHHHHHHHH CS
                        V-ATPase_G 70 kieketeekikelkesvkknkeavvke 96
                                      k ++++++ ik+++++++ ++++++++
  gi|518652300|ref|YP_008141820.1| 50 KSDNDVKNIIKQYEDNIRLQSKKIIDD 76
                                      556666666666666666666666653 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   4.2    0.0012       2.3      18      99 ..       3      98 ..       1     130 [. 0.69

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0012
                      Baculo_PEP_C 18 LtnvLnairlqnvqilaqlatlldaietqLnalsedlksllaeldt........rldtlltnLtdalnalq........ 80
                                      L n+Ln i     ++ a+l+++ d+   +++a+ ++ ++ ++ +++        ++++ +++ +d +  lq        
  gi|518652300|ref|YP_008141820.1|  3 LENILNEI---DNTTQAELKAIRDEYSAKIEAIIKSCNDKISRIKNyyavksdnDVKNIIKQYEDNIR-LQskkiiddk 77
                                      889*****...445559**************************9998777666645554444444443.2234444555 PP

                      Baculo_PEP_C 81 ..dtlrneLtnlnsiltnLls 99
                                        + l n ++ l s +t+L+ 
  gi|518652300|ref|YP_008141820.1| 78 kkEILVNTMQKLRSYVTSLNK 98
                                      555666666666666666653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2086  (0.116348); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1306.31
//
Query:       gi|518652301|ref|YP_008141821.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G0940 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.2e-10   39.3  11.0    7.7e-10   39.0  11.0    1.1  1  ATP-synt_C  ATP synthase subunit C
  ------ inclusion threshold ------
        1.3    8.0   5.4        1.4    7.9   5.4    1.0  1  PHO4        Phosphate transporter family


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 !   39.0  11.0   8.6e-14   7.7e-10       1      60 []      11      70 ..      11      70 .. 0.98

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 8.6e-14
                                      HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnpklftksliilafaeaialygLivalil 60
                                      l+a +a++ + +g+G+++  +g+ag++++a++p+ f+++l +++++e++ ++g++ ++il
  gi|518652301|ref|YP_008141821.1| 11 LAASIAIAGGLIGTGMAQQGIGAAGMGIIAEKPEKFGQVLFFFVIPETLWIIGFVLGIIL 70
                                      79********************************************************97 PP

>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   5.4   0.00016       1.4      88     138 ..      12      72 ..       7      75 .] 0.65

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00016
                              PHO4  88 StthslvGaliGaalaaeggeavkw.......kklvkivlswvls...Pllggiiaallfl 138
                                         + ++ G+liG ++a +g  a  +       +k+++++++ v+     ++g++++++l+l
  gi|518652301|ref|YP_008141821.1|  12 AASIAIAGGLIGTGMAQQGIGAAGMgiiaekpEKFGQVLFFFVIPetlWIIGFVLGIILLL 72 
                                       5789************855333333345556557888877766532225677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 560.93
//
Query:       gi|518652302|ref|YP_008141822.1|  [L=494]
Description: hypothetical protein FACI_IFERC00001G0941 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-11   42.9  17.2    1.6e-10   40.8  17.2    2.0  1  ABC2_membrane_2  ABC-2 family transporter protein
    8.8e-06   25.1  39.9    2.8e-05   23.4  39.9    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
  ------ inclusion threshold ------
        3.3    7.7  13.1       0.37   10.8   7.0    2.5  3  DUF441           Protein of unknown function (DUF441)


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 !   40.8  17.2   2.7e-14   1.6e-10       9     287 ..       9     494 .]       4     494 .] 0.68

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.7e-14
                   ABC2_membrane_2   9 rdlvrsrrfllltvllpli..............dvalaylkdlgsslqseakaikeatlaleyveaasasdeaedtd 71 
                                       +++++ + +++l vll+l+                              ++ ai++   ++      + +d++++++
  gi|518652302|ref|YP_008141822.1|   9 KRTITGKFTIILIVLLVLVtaasaygagvssdyA-------------HPGNTAIVMPYINQTG-NSVNITDYVINGY 71 
                                       5666666667777777766222222222222220.............2222333333333222.2223334444444 PP

                   ABC2_membrane_2  72 qdlkv........................................................................ 76 
                                        d                                                                           
  gi|518652302|ref|YP_008141822.1|  72 GDPVSglhitsslyynlnnslikhfsgttngtgyvhfsiknlstnltyryneyyrdgialvgsnntmnyyngqnili 148
                                       43333555555555555555555555555555555555566666666666666777777777777777777777777 PP

                   ABC2_membrane_2  77 ............................................................................. 76 
                                                                                                                    
  gi|518652302|ref|YP_008141822.1| 149 ndaftfaapyysinfndskyplyavnlkdksdpalvstmiynpdykstdspdvyyntsstllntdhfnktntvyigk 225
                                       77777777777777777777777777777777777777777777777777777777777777777777777777777 PP

                   ABC2_membrane_2  77 ......................................................vstimavlipviaalfgadaiag 99 
                                                                                                +  +lip++++  ++ + ++
  gi|518652302|ref|YP_008141822.1| 226 vnsnrfivtpplktadagksvniyivnstgavivpflnyeytyikpgsilqdelAIFFGVLLIPIMGIFSAYFYYSK 302
                                       78888888888888888888888888888888888888888888888888777666778899*************** PP

                   ABC2_membrane_2 100 EkergTlkllLskPvsRdeillgKfigglaigla.iavallatvllalaiilalgivlaledllllvvasvlllllv 175
                                       +k++g l+    +P++++++ ++ f g+++++la +++al+ +    +++ ++ g+ ++ + +l++++  ++ ++  
  gi|518652302|ref|YP_008141822.1| 303 DKTSGVLESIIVRPITKGKLMMSRFAGNSVSFLAgLLIALGLA---DFILYHYTGVFISSGTFLTILLGYLVEII-- 374
                                       ****************************************999...999************99999999887777.. PP

                   ABC2_membrane_2 176 vflalglllSsvarssreaaalalglfvvlailvpivlyg.vaellagpavp...qeindflsllsptsayntllne 248
                                        f+++ +l+S + +++ + +   lg++++  ++++ ++++ +++ll +++      +  ++++ +sp    +++ + 
  gi|518652302|ref|YP_008141822.1| 375 GFAGIIYLVSQFEKTQGQVLGTGLGMLFIMGFMWSTIVSPaILYLLRVKSTGiayFKDLLIVNSFSPSYFPDLISDY 451
                                       58*********************************999985556665555544442222233333332222222222 PP

                   ABC2_membrane_2 249 ilagsdlna.......lgstatnllilllllavllvlgyvlFkrkD 287
                                        l +    +        +   + +++ l++++v+  l++++ ++kD
  gi|518652302|ref|YP_008141822.1| 452 HLGSY---StykasavGINIYSIIAVGLIWILVPSLLALYFARKKD 494
                                       22222...12446663344555567789***********9988887 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4  39.9   4.6e-09   2.8e-05       3     341 ..      17     480 ..      15     487 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.6e-09
                   ABC2_membrane_3   3 fliitlllPiilvlllglifsnsve.d...dentpi..avvdednsslsqqlv........................ 49 
                                       ++i+++ll+++ ++ ++ +   +v+ d   + nt i   ++++++  +s +++                        
  gi|518652302|ref|YP_008141822.1|  17 TIILIVLLVLVTAASAYGA---GVSsDyahPGNTAIvmPYINQTG--NSVNITdyvingygdpvsglhitsslyynl 88 
                                       3434444444444444433...33321222333333335666654..333333222344444444444444444444 PP

                   ABC2_membrane_3  50 ...................................................ealeaspsvelvyevdseeeakkalk 75 
                                                                                                                    
  gi|518652302|ref|YP_008141822.1|  89 nnslikhfsgttngtgyvhfsiknlstnltyryneyyrdgialvgsnntmnY------------------------- 140
                                       4444444444444444444444444444444444444444433333333330......................... PP

                   ABC2_membrane_3  76 ngdidgilvipkgfskdll...................................................kgesatv 101
                                                         +                                                   ++++++ 
  gi|518652302|ref|YP_008141822.1| 141 ------------------YngqnilindaftfaapyysinfndskyplyavnlkdksdpalvstmiynpdYKSTDSP 199
                                       ..................14444444444444444444444444444445555555555557777777776778888 PP

                   ABC2_membrane_3 102 tvlinssnlnsskailnalns.llqqlnasalv..lqseatstsaninvestql........eeelsnvasf..... 162
                                        v++n+s ++ ++   n  n+ ++ + n ++    ++ +++++ +++n+ + +              n++++     
  gi|518652302|ref|YP_008141822.1| 200 DVYYNTSSTLLNTDHFNKTNTvYIGKVNSNRFIvtPPLKTADAGKSVNIYIVNStgavivpfL----NYEYTyikpg 272
                                       888888886555444444466566666666666898888889999999998888666744440....4444455666 PP

                   ABC2_membrane_3 163 ......lvgliliilifitasf.iavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilll....a 228
                                             l++++ ++li i+++f + +++ ++k+s+++e ++v ++++ ++++s++ g  + +l  ll++l+l    +
  gi|518652302|ref|YP_008141822.1| 273 silqdeLAIFFGVLLIPIMGIFsAYFYYSKDKTSGVLESIIVRPITKGKLMMSRFAGNSVSFLAGLLIALGLadfiL 349
                                       66666666655555544444440444679****************************************98544455 PP

                   ABC2_membrane_3 229 fgl...gipfgnlglllllfllfglayialgyllsslfkns......etaqilifivilllsgffgglfpledlp.. 294
                                       +++   +i+ g ++ +ll +l+ ++ ++ ++yl+s + k++      + ++++i+ +++++++  ++l++l      
  gi|518652302|ref|YP_008141822.1| 350 YHYtgvFISSGTFLTILLGYLVEIIGFAGIIYLVSQFEKTQgqvlgtGLGMLFIMGFMWSTIVSPAILYLL---Rvk 423
                                       55576688888999999************************554433333444444444444444444543...143 PP

                   ABC2_membrane_3 295 .salkwi..fsiiPffapglgllrli.......tgdplwe.....illsliilalfavvyll 341
                                        ++++++  + i+ +f+p+++   ++       +     +     +++++   ++ +++++l
  gi|518652302|ref|YP_008141822.1| 424 sTGIAYFkdLLIVNSFSPSYFPDLISdyhlgsyS-----TykasaVGINIYSIIAVGLIWIL 480
                                       4555554445555555555555333344445432.....13344477777777777777765 PP

>> DUF441  Protein of unknown function (DUF441)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.2         1   6.2e+03      49      59 ..      18      28 ..       8      38 .. 0.59
   2 ?   -0.6   0.0       0.2   1.2e+03      55      87 ..     312     344 ..     307     352 .. 0.73
   3 ?   10.8   7.0   6.1e-05      0.37      56     137 ..     338     419 ..     331     420 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1
                            DUF441 49 viiltiavLvP 59
                                      +i++++ vLv 
  gi|518652302|ref|YP_008141822.1| 18 IILIVLLVLVT 28
                                      44444444443 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.2
                            DUF441  55 avLvPiatgkislkellealkslkgliallvgi 87 
                                        ++ Pi +gk+ +++++ +  s+ + + +++g+
  gi|518652302|ref|YP_008141822.1| 312 IIVRPITKGKLMMSRFAGNSVSFLAGLLIALGL 344
                                       577899999999988888777777766666665 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 6.1e-05
                            DUF441  56 vLvPiatgkislkellealkslkgliallvgilvavlsgkGvellkeqpevvvalvlGtilgvvflkGvpvGPliaa 132
                                       +L+ +   +  l + + ++ s  +++++l+g lv +++  G+ +l +q e + + vlGt lg++f+ G     +++ 
  gi|518652302|ref|YP_008141822.1| 338 LLIALGLADFILYHYTGVFISSGTFLTILLGYLVEIIGFAGIIYLVSQFEKTQGQVLGTGLGMLFIMGFMWSTIVSP 414
                                       566666666667778889999999********************************************999888888 PP

                            DUF441 133 Gital 137
                                       +i++l
  gi|518652302|ref|YP_008141822.1| 415 AILYL 419
                                       88877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (494 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); 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):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 3232.15
//
Query:       gi|518652303|ref|YP_008141823.1|  [L=297]
Description: ABC transporter ATP-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-23   81.6   0.0    3.1e-22   79.6   0.0    1.9  2  ABC_tran        ABC transporter
    1.6e-07   31.4   0.1     0.0012   18.8   0.0    2.4  2  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    0.00061   20.3   3.4    0.00069   20.2   2.5    1.7  1  AAA_23          AAA domain
     0.0044   16.5   0.6        1.9    7.9   0.1    2.4  2  SMC_N           RecF/RecN/SMC N terminal domain
     0.0071   15.5   0.2     0.0071   15.5   0.2    1.5  2  Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like
  ------ inclusion threshold ------
       0.07   12.9   1.2      0.091   12.5   0.2    1.6  2  AAA_29          P-loop containing region of AAA domain
      0.074   12.9   0.1       0.13   12.0   0.1    1.4  1  MukB            MukB N-terminal


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.6   0.0   1.2e-25   3.1e-22       2     136 ..      18     160 ..      17     161 .. 0.93
   2 ?   -0.4   0.0      0.61   1.6e+03      23      46 ..     182     205 ..     181     272 .. 0.70

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 1.2e-25
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       ++++l++++g+++++ G nGaGK+t +++ +g   pt+G+i++++ d+ + e+ +++++ig++p+ p++ p+ +   
  gi|518652303|ref|YP_008141823.1|  18 SDLNLEINNGQIMGLAGLNGAGKTTTIRAACGIIFPTSGTITVNNFDIVK-EKIKASRNIGWVPELPNFEPDARPVP 93 
                                       689***********************************************.56667789**************7433 PP

                                       H.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       x.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                                     e+++++ ++++++++ + +++++    + +S+G+k+r al +a++ +p+ +l+DE  
  gi|518652303|ref|YP_008141823.1|  94 LlkyyagfygikpdEAEKNAIEMMKQFDIYNYRNRKL----KYYSQGMKKRFALIAAMIGNPDNYLFDETL 160
                                       379*********9999999******************....99**************************86 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.61
                                       SHHHHHHHHTTSS--SEEEEEETT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  23 GKStLlkllagllkpteGeilldg 46 
                                       GKS Ll+  + +l++ +++i + +
  gi|518652303|ref|YP_008141823.1| 182 GKSILLSSHILELQNVADKIAIVK 205
                                       788888877777777777775442 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 !    9.9   0.4   0.00022      0.57       1      23 [.      29      51 ..      29      97 .. 0.68
   2 !   18.8   0.0   4.5e-07    0.0012     237     299 ..     133     192 ..      94     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00022
                            AAA_21  1 lnvliGpNgsGKSnLLdaldlla 23
                                      +++l G Ng+GK++ ++a  ++ 
  gi|518652303|ref|YP_008141823.1| 29 IMGLAGLNGAGKTTTIRAACGII 51
                                      6789**************84443 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 4.5e-07
                            AAA_21 237 lSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                        S+G+k+ +al++a++  ++    +l+DE  ngL+P  ++++ +l+ +l++ g  ++l++H  
  gi|518652303|ref|YP_008141823.1| 133 YSQGMKKRFALIAAMIGNPDN---YLFDETLNGLDPNGVKEVRDLIINLKKQGKSILLSSHIL 192
                                       5******************77...9*********************888888*********65 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   2.5   2.7e-07   0.00069       4      64 ..      11      71 ..      10     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.7e-07
                            AAA_23  4 ienfrsfrdqeidFsk.gltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve 64
                                       +nf+  +d +++ ++  +  + G NGaGKTT ++A + + +  +++   ++  +++k++++
  gi|518652303|ref|YP_008141823.1| 11 FKNFKAVSDLNLEINNgQIMGLAGLNGAGKTTTIRAACGIIFPTSGTITVNNF-DIVKEKIK 71
                                      69************6647********************999987776666542.45555554 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 !    7.9   0.1   0.00073       1.9       9      43 ..      10      46 ..       1      56 [. 0.67
   2 !    6.6   0.0    0.0018       4.6     162     211 ..     154     204 ..     116     211 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00073
                                      SETTEEC.EEEEEETTS.SEEEEEESTTSSHHHHHHH CS
                                      xxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  9 nFksyag.ktvilpfsk.sftaivGpNGSGKsnlldA 43
                                       Fk+++  +   l++++ ++  + G NG+GK+  + A
  gi|518652303|ref|YP_008141823.1| 10 SFKNFKAvSDLNLEINNgQIMGLAGLNGAGKTTTIRA 46
                                      4666642123333333314778999*******98877 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0018
                                       EEECTTTTTS-HHHHHHHHHHHHHHCTTSEEE.EE-SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx RF
                             SMC_N 162 yllDeidaaLDeknvkkvaellkeksknaQfi.vislreemlekadklvgv 211
                                       yl+De    LD + vk+v +l+ + +k+   i   s+  e+ + adk+  v
  gi|518652303|ref|YP_008141823.1| 154 YLFDETLNGLDPNGVKEVRDLIINLKKQGKSIlLSSHILELQNVADKIAIV 204
                                       9**********************9999965550556666666666666554 PP

>> Phage_prot_Gp6  Phage portal protein, SPP1 Gp6-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.8e-06    0.0071     315     358 ..     117     160 ..     108     202 .. 0.87
   2 ?   -3.4   0.0       1.6     4e+03     107     122 ..     253     268 ..     237     280 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.8e-06
                    Phage_prot_Gp6 315 ykyslleqkaelkerefekalkeliklilellnaldekdgddve 358
                                       +k ++ ++ +++k +++++++k+++ li++++++ d++ +d+++
  gi|518652303|ref|YP_008141823.1| 117 MKQFDIYNYRNRKLKYYSQGMKKRFALIAAMIGNPDNYLFDETL 160
                                       68899*********************************999865 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.6
                    Phage_prot_Gp6 107 lvyvdeegeikvkvvd 122
                                       ++y++++ge++v+ ++
  gi|518652303|ref|YP_008141823.1| 253 YYYIKNNGEVDVSELN 268
                                       5666666666665544 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.6e-05     0.091      13      54 ..      18      60 ..      10      62 .. 0.77
   2 ?   -3.9   0.0       4.6   1.2e+04      33      39 ..     181     187 ..     174     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                            AAA_29 13 dghtieidlkg.atlltGpsGsGKSTllDAiqalLvpak.kvrf 54
                                      ++  +ei+  g ++ l+G +G+GK+T + A   ++ p++ +++ 
  gi|518652303|ref|YP_008141823.1| 18 SDLNLEINN-GqIMGLAGLNGAGKTTTIRAACGIIFPTSgTITV 60
                                      555677774.45999*************9999999998755555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 4.6
                            AAA_29  33 sGKSTll 39 
                                        GKS ll
  gi|518652303|ref|YP_008141823.1| 181 QGKSILL 187
                                       5888877 PP

>> MukB  MukB N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.1e-05      0.13      27      61 ..      28      62 ..       9      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.1e-05
                                      HHHHHHS--SHHHHHHHHHHHHHHS--TTT----- CS
                              MukB 27 lvttlsGgnGaGksttmaafvtaliPdlsllhfrn 61
                                       +  l G nGaGk+tt+ a+  ++ P    +   n
  gi|518652303|ref|YP_008141823.1| 28 QIMGLAGLNGAGKTTTIRAACGIIFPTSGTITVNN 62
                                      56789******************999887776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2039.63
//
Query:       gi|518652304|ref|YP_008141824.1|  [L=166]
Description: C4-type Zn-finger-containing protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-32  112.5   0.3    1.9e-32  112.3   0.3    1.0  1  zf-ZPR1         ZPR1 zinc-finger domain
     0.0066   15.9   2.9        1.3    8.6   0.3    2.5  2  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
      0.014   15.4   2.6       0.42   10.7   0.1    2.6  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
      0.032   14.1   2.8       0.47   10.4   2.8    2.2  1  RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
      0.047   13.6   1.2        2.1    8.3   0.2    2.4  2  Zn_ribbon_SprT  SprT-like zinc ribbon domain
      0.055   13.7   0.7        1.7    9.0   0.1    2.2  2  zf-LITAF-like   LITAF-like zinc ribbon domain
      0.075   12.8   4.2        1.5    8.6   0.2    2.2  2  Rubredoxin_2    Rubredoxin metal binding domain
       0.14   12.0   2.0       0.23   11.3   2.0    1.3  1  PADR1           PADR1 (NUC008) domain
       0.15   11.8   4.1        3.3    7.5   0.4    2.8  3  zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal
       0.18   12.0   1.2         15    5.8   0.1    2.3  2  Zn-ribbon_8     Zinc ribbon domain
        0.3   10.8   3.7       0.83    9.4   0.2    2.2  2  zf-RRN7         Zinc-finger of RNA-polymerase I-specific TFII
        8.3    6.5   7.2         65    3.6   7.2    2.1  1  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !  112.3   0.3   1.3e-35   1.9e-32       2     158 ..       9     155 ..       8     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.3 bits;  conditional E-value: 1.3e-35
                           zf-ZPR1   2 lCpsCgkengetrlllt.kiPyfkeviimsfeCehCgyknnevksageieekGkritlkveseedlnrqvlkSetat 77 
                                        Cp+C+ +    ++    +iPy +++ i +++C++C+ykn  ++  ++ e+  k i++k+++++dl++ v++S  a+
  gi|518652304|ref|YP_008141824.1|   9 RCPNCN-S-FLYYIEADnEIPYEGKITIHTYVCKNCNYKNITIDRHEKGEP--KIIKFKIKNKNDLKTIVYRSPDAS 81 
                                       7****5.6.455555445*********************************..************************ PP

                           zf-ZPR1  78 veipeleleippg.tlegrlttvEGlLeqikeelekeegdqaeredeekekieeflekleeliegee.pftlildDp 152
                                       v+ipele ei+pg +++g++tt+EG+L++ike+l+          d   e+i+ + +++e +i+g e ++t+ildD 
  gi|518652304|ref|YP_008141824.1|  82 VHIPELEAEISPGiASKGYITTIEGILTSIKEKLS-------IMGD--DENINVLRQRIEGIISGAEeSVTIILDDD 149
                                       **********************************3.......2233..689999********9988669******** PP

                           zf-ZPR1 153 agnSfi 158
                                       +g+S i
  gi|518652304|ref|YP_008141824.1| 150 SGQSRI 155
                                       ****99 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.1    0.0024       3.5       2       8 ..       9      15 ..       2      26 .. 0.66
   2 !    8.6   0.3   0.00086       1.3       1      19 [.      37      56 ..      37      56 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                                      EETTTTC CS
                      TF_Zn_Ribbon  2 kCPnCgs 8 
                                      +CPnC+s
  gi|518652304|ref|YP_008141824.1|  9 RCPNCNS 15
                                      5888888 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00086
                                      EEETTTTCEECHEE.TSTTC CS
                      TF_Zn_Ribbon  1 ykCPnCgstnlveD.perge 19
                                      y+C+nC+ +n++ D +e ge
  gi|518652304|ref|YP_008141824.1| 37 YVCKNCNYKNITIDrHEKGE 56
                                      89********6666488876 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00028      0.42       3      15 ..       9      21 ..       8      25 .. 0.88
   2 ?    4.2   0.3      0.03        45      19      26 .]      35      42 ..      31      42 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00028
                            zf-ACC  3 KCpsCgemlykke 15
                                      +Cp C++ ly+ e
  gi|518652304|ref|YP_008141824.1|  9 RCPNCNSFLYYIE 21
                                      8*********987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.03
                            zf-ACC 19 nlyVCPkC 26
                                      + yVC +C
  gi|518652304|ref|YP_008141824.1| 35 HTYVCKNC 42
                                      669***** PP

>> RNA_POL_M_15KD  RNA polymerases M/15 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.8   0.00032      0.47       4      30 ..      10      45 ..      10      46 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                                      ESTTTSBEEEEECS.....CCCE....EEESSSS-E CS
                    RNA_POL_M_15KD  4 CpkCgNlLlpkedk.....egkn....feCrqCgYe 30
                                      Cp C++ L++ e++     egk+    + C +C Y+
  gi|518652304|ref|YP_008141824.1| 10 CPNCNSFLYYIEADneipyEGKItihtYVCKNCNYK 45
                                      *********999874444445556678889999997 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.033        49      26      36 ..       9      19 ..       4      21 .. 0.73
   2 ?    8.3   0.2    0.0014       2.1      13      31 ..      25      43 ..      23      52 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.033
                    Zn_ribbon_SprT 26 rCrrCkgtLrg 36
                                      rC+ C ++L +
  gi|518652304|ref|YP_008141824.1|  9 RCPNCNSFLYY 19
                                      89999888865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
                    Zn_ribbon_SprT 13 eythhlsirrhnYrCrrCk 31
                                      e++++ +i  h+Y C+ C 
  gi|518652304|ref|YP_008141824.1| 25 EIPYEGKITIHTYVCKNCN 43
                                      5667777888999999997 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 ?    9.0   0.1    0.0011       1.7      53      68 ..       4      19 ..       2      21 .. 0.86
   2 ?    3.1   0.1      0.08   1.2e+02       6      24 ..      37      55 ..      34      62 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0011
                     zf-LITAF-like 53 kdvehyCpnCgallgt 68
                                      k++e +CpnC+++l +
  gi|518652304|ref|YP_008141824.1|  4 KKTESRCPNCNSFLYY 19
                                      78999*******9976 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.08
                     zf-LITAF-like  6 vdCpaCqqrvvTsveyksg 24
                                        C++C+ + +T  ++++g
  gi|518652304|ref|YP_008141824.1| 37 YVCKNCNYKNITIDRHEKG 55
                                      5799999999988777776 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.5    0.0085        13      16      23 ..       9      16 ..       9      16 .. 0.88
   2 ?    8.6   0.2     0.001       1.5       1      10 [.      37      46 ..      37      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0085
                      Rubredoxin_2 16 rCpsCgsW 23
                                      rCp+C+s+
  gi|518652304|ref|YP_008141824.1|  9 RCPNCNSF 16
                                      8****985 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.001
                      Rubredoxin_2  1 YvCsqCGfes 10
                                      YvC++C+++ 
  gi|518652304|ref|YP_008141824.1| 37 YVCKNCNYKN 46
                                      9******975 PP

>> PADR1  PADR1 (NUC008) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   2.0   0.00016      0.23      15      52 ..       9      51 ..       7      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                             PADR1 15 kCpeCkegqlvfdss..gYkCtGnms....ewtkCtfktkdpkR 52
                                      +Cp+C+ + l++ +   ++  +G+++      + C++k+ +++R
  gi|518652304|ref|YP_008141824.1|  9 RCPNCN-SFLYYIEAdnEIPYEGKITihtyVCKNCNYKNITIDR 51
                                      7*****.8888877779*********99777889*****99999 PP

>> zinc_ribbon_10  Predicted integral membrane zinc-ribbon metal-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.018        27      42      53 ..       5      16 ..       2      17 .. 0.77
   2 ?    7.5   0.4    0.0022       3.3      44      54 .]      36      46 ..      26      46 .. 0.82
   3 ?   -2.0   0.0       2.1   3.1e+03       9      15 ..     117     123 ..     116     142 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.018
                    zinc_ribbon_10 42 evkyrCpkCgal 53
                                      +++ rCp+C+++
  gi|518652304|ref|YP_008141824.1|  5 KTESRCPNCNSF 16
                                      66779****985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0022
                    zinc_ribbon_10 44 kyrCpkCgaln 54
                                      +y+C +C+ +n
  gi|518652304|ref|YP_008141824.1| 36 TYVCKNCNYKN 46
                                      89*****9987 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.1
                    zinc_ribbon_10   9 LvGddet 15 
                                       ++Gdde+
  gi|518652304|ref|YP_008141824.1| 117 IMGDDEN 123
                                       5777772 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      0.01        15      24      34 ..       4      15 ..       1      18 [. 0.65
   2 ?    5.0   0.2     0.018        27       4      13 ..      35      44 ..      33      56 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.01
                       Zn-ribbon_8 24 aplta.CPeCgs 34
                                      ++ +  CP+C+s
  gi|518652304|ref|YP_008141824.1|  4 KKTESrCPNCNS 15
                                      444444****87 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.018
                       Zn-ribbon_8  4 YeYrCeeCgh 13
                                        Y C++C+ 
  gi|518652304|ref|YP_008141824.1| 35 HTYVCKNCNY 44
                                      67******85 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00055      0.83       6      18 ..       9      22 ..       6      23 .. 0.87
   2 ?    2.4   0.4     0.087   1.3e+02      21      27 ..      36      42 ..      36      43 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00055
                           zf-RRN7  6 pCgvCgcrsftl.d 18
                                      +C+ C++ ++++ +
  gi|518652304|ref|YP_008141824.1|  9 RCPNCNSFLYYIeA 22
                                      8**********955 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.087
                           zf-RRN7 21 fyyCrrC 27
                                      +y+C++C
  gi|518652304|ref|YP_008141824.1| 36 TYVCKNC 42
                                      6999999 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   7.2     0.043        65       1      17 [.       6      24 ..       6      44 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.043
                    PhnA_Zn_Ribbon  1 tlpkCplCaSeytY..edg 17
                                      t++ Cp+C+S   Y  +d+
  gi|518652304|ref|YP_008141824.1|  6 TESRCPNCNSFLYYieADN 24
                                      5799******777777444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1015  (0.0566122); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); 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: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1334.64
//
Query:       gi|518652305|ref|YP_008141825.1|  [L=349]
Description: hypothetical protein FACI_IFERC00001G0944 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-22   78.7   0.0    9.9e-12   44.5   0.0    2.4  2  FMN_dh         FMN-dependent dehydrogenase
    2.4e-05   23.5   4.7      0.014   14.4   0.5    3.7  4  IMPDH          IMP dehydrogenase / GMP reductase domain
    0.00027   20.3   0.6     0.0036   16.6   0.1    2.3  2  DHO_dh         Dihydroorotate dehydrogenase
     0.0044   16.2   0.8      0.026   13.7   0.1    2.3  2  Glu_synthase   Conserved region in glutamate synthase
  ------ inclusion threshold ------
      0.064   13.7   0.1       0.16   12.4   0.1    1.6  1  Phage_TAC_12   Phage tail assembly chaperone protein, TAC
      0.068   12.6   0.2       0.16   11.3   0.0    1.6  2  NMO            Nitronate monooxygenase
       0.15   11.7   0.0       0.21   11.2   0.0    1.3  1  Peptidase_M28  Peptidase family M28


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 !   31.8   0.0   2.9e-11   7.3e-08      20     102 ..      15      98 ..       2     119 .. 0.81
   2 !   44.5   0.0   3.9e-15   9.9e-12     213     344 ..     179     333 ..     153     337 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 2.9e-11
                                       SHHHHHHHHGGGGEEE---SSSS-S..S-B--EEETTEEESSSEEE--BSTGGGTSTTHHHHHHHHHHHHTS-EEEE CS
                            FMN_dh  20 evtlrenraaferirlrprvlrdvs..kvdlsttllGqklslPvliaPvglaklahpdgelalaraaakagipfvls 94 
                                       ++ +++ ++ +++irl +r++ +v   ++++++++lG+++ lP+li+++   +  +++ + +laraa++++i ++++
  gi|518652305|ref|YP_008141825.1|  15 NMNVTSEHNFWDDIRLIHRAIPEVDydSINTKINFLGTEFGLPFLISSMTGGTEKARKINENLARAAEEFKIGMGVG 91 
                                       4445566678***********8875226799999***************777777778999***************9 PP

                                       TT-SS-HH CS
                            FMN_dh  95 tvastsle 102
                                       ++ ++++e
  gi|518652305|ref|YP_008141825.1|  92 SM-RAAIE 98 
                                       99.44444 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 3.9e-15
                                       HHHS.SEEEEEEE...-SHHHHHHHHHTTESEEEE--GGG.............TSSTT---HHHCH.......HHHH CS
                            FMN_dh 213 eqtk.lplvvKGv...ltaedakraveaGvdgivvSNHGG.............RqldgapatidvL.......peiv 265
                                       e  k  p++ K+     + +da ++ +aGv++i v   GG              q    + t ++        p+  
  gi|518652305|ref|YP_008141825.1| 179 EIAKsYPVIAKETgsgFSRDDALELKDAGVKAIDVGGLGGtsfaaieyyraekIQNKEKMHTGQTFwnwgvpsPASI 255
                                       4444368888888777899*********************6665555555555333333333333334444444445 PP

                                       HHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-SBHHHHH CS
                            FMN_dh 266 eavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyglaagGeeGvervleilraelertmallGvksvaeld 342
                                       + +   ++++ +gGir+G+Dv+k + +GAd+ +++R fl  + +  e+ v ++ +i+ ++++ +m l+  k+v+el+
  gi|518652305|ref|YP_008141825.1| 256 KFCSVGLPIIGSGGIRNGQDVVKSIIMGADMGAMARNFLKDADTSYEDLVFHIKNII-KDIKISMFLTASKDVSELK 331
                                       555778***********************************9999999998876665.69****************8 PP

                                       CG CS
                            FMN_dh 343 rs 344
                                       ++
  gi|518652305|ref|YP_008141825.1| 332 NK 333
                                       76 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.034        86     160     179 ..      75      93 ..      57     110 .. 0.73
   2 !    5.1   0.0    0.0038       9.8     129     176 ..     170     218 ..     163     226 .. 0.86
   3 !   14.4   0.5   5.6e-06     0.014     206     234 ..     260     288 ..     245     307 .. 0.84
   4 ?    0.6   0.0     0.088   2.3e+02     302     330 ..     307     335 ..     295     339 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.034
                                       HHHHHTT-SEEEE-SS-STT CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 160 kaLieagadavkvGiGpGsi 179
                                       ++L +  a+  k+G+G Gs+
  gi|518652305|ref|YP_008141825.1|  75 ENL-ARAAEEFKIGMGVGSM 93 
                                       334.4458889999999997 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0038
                                       SHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-.SS- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                             IMPDH 129 sekvleavkeikkkveeveviaGnvataegakaLieagadavkvG.iGp 176
                                        ++v++ +kei k+++ +   +G+  +++ a +L +ag++a+ vG +G 
  gi|518652305|ref|YP_008141825.1| 170 ARGVMSRLKEIAKSYPVIAKETGSGFSRDDALELKDAGVKAIDVGgLGG 218
                                       57899999*******8888899**********************72454 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 5.6e-06
                                       CT-EEEEES---SHHHHHHHHHTT-SEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 206 agvpviaDGGikysgdivkAlaaGadavm 234
                                        g p+i  GGi++ +d+vk++ +Gad+  
  gi|518652305|ref|YP_008141825.1| 260 VGLPIIGSGGIRNGQDVVKSIIMGADMGA 288
                                       689**********************9844 PP

  == domain 4  score: 0.6 bits;  conditional E-value: 0.088
                                       HHHHHHHHHHHHHHHHT-SSHHHHHHH-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 302 vveqlvgglrsgmgylGaktieelkekak 330
                                        +++++++++ +m  + +k+++elk+k  
  gi|518652305|ref|YP_008141825.1| 307 HIKNIIKDIKISMFLTASKDVSELKNKRY 335
                                       578999******************98865 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.057   1.5e+02     243     273 ..     182     214 ..     168     235 .. 0.75
   2 !   16.6   0.1   1.4e-06    0.0036     244     274 ..     261     291 ..     255     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.057
                                       T.S-EEE..ESS--SHHHHHHHHHHTECEEEES CS
                            DHO_dh 243 keipiIg..vGGiesgeDalekieaGAslvqvy 273
                                       k+ p+I+  +G  +s +Dale   aG  ++ v+
  gi|518652305|ref|YP_008141825.1| 182 KSYPVIAkeTGSGFSRDDALELKDAGVKAIDVG 214
                                       466777644677899999999999999999887 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.4e-06
                                       .S-EEEESS--SHHHHHHHHHHTECEEEESH CS
                            DHO_dh 244 eipiIgvGGiesgeDalekieaGAslvqvyt 274
                                        +piIg+GGi  g+D++  i  GA + ++  
  gi|518652305|ref|YP_008141825.1| 261 GLPIIGSGGIRNGQDVVKSIIMGADMGAMAR 291
                                       48**********************9976655 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.18   4.6e+02     194     242 ..     174     222 ..     167     231 .. 0.81
   2 !   13.7   0.1     1e-05     0.026     277     305 ..     264     292 ..     258     296 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.18
                                       HHHHHHH-TTSEEEEEEE-STTHHHHHHHHHHTT-SEEEEE-TT---SS CS
                      Glu_synthase 194 iedLkevnkeakvsvKlvaeagvetiaagvakanadiilidGleGGTGA 242
                                       ++ Lke+ k+ +v  K +      + a+ + +a++ +i + Gl G   A
  gi|518652305|ref|YP_008141825.1| 174 MSRLKEIAKSYPVIAKETGSGFSRDDALELKDAGVKAIDVGGLGGTSFA 222
                                       6789***********9887777777788899*********998665444 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1e-05
                                       EEEESS--SHHHHHHHHHHT-SEEE-SHH CS
                      Glu_synthase 277 liadGglktgadvvkalalGAdavgigta 305
                                       +i +Gg++ g+dvvk++++GAd   +++ 
  gi|518652305|ref|YP_008141825.1| 264 IIGSGGIRNGQDVVKSIIMGADMGAMARN 292
                                       7789******************9887765 PP

>> Phage_TAC_12  Phage tail assembly chaperone protein, TAC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.3e-05      0.16      13      55 ..      65     107 ..      61     113 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                      Phage_TAC_12  13 fglkfvreidkelglkveginfgeGlsllvpgLesgdpevLve 55 
                                        g++ +r+i+++l   +e++++g+G+ +  + +e+++++    
  gi|518652305|ref|YP_008141825.1|  65 GGTEKARKINENLARAAEEFKIGMGVGSMRAAIENKNIADTFS 107
                                       68999********************************976555 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.3   3.3e+03     259     276 ..      69      86 ..      58     113 .. 0.52
   2 ?   11.3   0.0   6.2e-05      0.16     192     232 ..     260     300 ..     252     323 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                               NMO 259 paRalatelleeleeaki 276
                                       +aR ++ +l +  ee+ki
  gi|518652305|ref|YP_008141825.1|  69 KARKINENLARAAEEFKI 86 
                                       344444444444444332 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 6.2e-05
                               NMO 192 vdiPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesd 232
                                       v +P+i  GGi ++++v   + +GA   +++  fL   +  
  gi|518652305|ref|YP_008141825.1| 260 VGLPIIGSGGIRNGQDVVKSIIMGADMGAMARNFLKDADTS 300
                                       569*******************************9766655 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   8.3e-05      0.21      87     173 ..     135     239 ..      77     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 8.3e-05
                                       CCTTEEEEEEECS-SSSS--EEE......HHHHHHCHHHHHHHHHHHHHTT-TTSCCEEEEESSTT-STTHHHHTTT CS
                     Peptidase_M28  87 elkkiaavlnlDmvgsggkellf......esgdkssselekelkalakpvgraaaedpfdersgrgrsDhspflkag 157
                                         k+i++ +nl  +      + f       +gdk+++++   lk+ ak + ++    + + +sg++r+D++ +++ag
  gi|518652305|ref|YP_008141825.1| 135 SDKDIEYIFNLIGAKYLIVHFNFlqemvqPEGDKNARGVMSRLKEIAKSYPVI----AKETGSGFSRDDALELKDAG 207
                                       55556666666555555555555777666778888888888888888888775....556677************** PP

                                       --EEEE................CTSSS-TTTT CS
                     Peptidase_M28 158 vpvldl................aetgfpevyH 173
                                       v+++d+                ++ +++e+ H
  gi|518652305|ref|YP_008141825.1| 208 VKAIDVgglggtsfaaieyyraEKIQNKEKMH 239
                                       *****988877777666666655555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2419.27
//
Query:       gi|518652306|ref|YP_008141826.1|  [L=275]
Description: kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-31  109.0   0.0    3.3e-31  108.7   0.0    1.1  1  AA_kinase  Amino acid kinase family
     0.0032   17.3   0.0       0.39   10.5   0.0    2.9  3  Staygreen  Staygreen protein


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 !  108.7   0.0   3.7e-35   3.3e-31       2     241 .]      34     255 ..      33     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 108.7 bits;  conditional E-value: 3.7e-35
                                       EEEEEE-TTCCCCTCC......HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HH CS
                         AA_kinase   2 rvVvKlGGssltdkee......aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstlee 72 
                                       ++V+K+GGs++tdk+       + ++++++ ++++   ++++v++hGggsf++  +++ +gl+ + +++    t e 
  gi|518652306|ref|YP_008141826.1|  34 MIVIKIGGSIITDKSMykkfngQIVENIVKTLKRI---DKQMVIIHGGGSFGHIKSKE-YGLPGQVSER----TMEG 102
                                       79************99**9**99************...999*****************.***9999983....3333 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEE CS
                         AA_kinase  73 agevatrdalaslgerlvaallaaglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigl 149
                                       ++  + +  +a l  +++  ++++ + +++l++++l   +++            + + + ++le g+ p+  g+  +
  gi|518652306|ref|YP_008141826.1| 103 MN--IVHNDMAELDLKISKIFQENKIYNISLPVSSLVYNNKK------------NYNIFSKYLELGITPISYGDTYI 165
                                       22..33399***********************9999966555............5******************9844 PP

                                       ETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHH CS
                         AA_kinase 150 deegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselatgGmkvkhpaa 226
                                        + +e+g+ s+D ia  + + l+++ +i+++dVdG++d++pk +pda+ll++is d   ++ + ++tgG+  k  ++
  gi|518652306|ref|YP_008141826.1| 166 -HSNEIGIYSGDNIAYDISKILHPEFVIFFSDVDGIFDKNPKNNPDAKLLKTISTDFQYDTINPDVTGGIMNKYNKM 241
                                       .555679**********************************************99988888999************* PP

                                       HHHHHCTT-EEEEEE CS
                         AA_kinase 227 laaarrggipvvItn 241
                                         +   g ipv+++n
  gi|518652306|ref|YP_008141826.1| 242 KLISDIG-IPVYLIN 255
                                       *******.****997 PP

>> Staygreen  Staygreen protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.045     4e+02      30      51 ..     107     127 ..     103     133 .. 0.84
   2 !   10.5   0.0   4.4e-05      0.39      72     115 ..     128     167 ..     121     174 .. 0.75
   3 ?    2.3   0.0     0.015   1.3e+02      35      66 ..     211     242 ..     206     260 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.045
                         Staygreen  30 hsDltaeLtLtigekfaldklq 51 
                                       h+D +aeL L+i++ f+ +k+ 
  gi|518652306|ref|YP_008141826.1| 107 HND-MAELDLKISKIFQENKIY 127
                                       766.689*********999985 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 4.4e-05
                         Staygreen  72 hvhvyvsggelllelaaelRyeiFrkeLplvLkaivygdrelfa 115
                                       ++ + vs  +l +  ++++ y+iF+k L+l ++ i ygd+ + +
  gi|518652306|ref|YP_008141826.1| 128 NISLPVS--SLVY--NNKKNYNIFSKYLELGITPISYGDTYIHS 167
                                       5555554..3333..47889*******************98765 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.015
                         Staygreen  35 aeLtLtigekfaldklqkklrDeVlaeWkkdk 66 
                                       a+L  ti+++f++d ++ ++   ++ +++k+k
  gi|518652306|ref|YP_008141826.1| 211 AKLLKTISTDFQYDTINPDVTGGIMNKYNKMK 242
                                       678889***********776666666665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 1748.44
//
Query:       gi|518652307|ref|YP_008141827.1|  [L=368]
Description: hypothetical protein FACI_IFERC00001G0946 [Ferroplasma acidarmanus fer1]
Scores for complete 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-79  266.5   0.0    2.5e-79  266.3   0.0    1.1  1  GCV_T     Aminomethyltransferase folate-binding domain
    4.6e-15   55.3   0.0    7.8e-15   54.6   0.0    1.4  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 !  266.3   0.0   2.8e-83   2.5e-79       1     256 [.      13     267 ..      13     268 .. 0.96

  Alignments for each domain:
  == domain 1  score: 266.3 bits;  conditional E-value: 2.8e-83
                             GCV_T   1 lydrhkalgakfvefagwemPvqYasesikaehlavreaaglfDvShmgkievsGpdaaalLqrlltndisklkpgk 77 
                                       lyd hk+l+a++++f+gw+mP+qY  +si++eh  vr+++g+fD+Shmg+i +sGp++  +++++++++is lk ++
  gi|518652307|ref|YP_008141827.1|  13 LYDEHKKLNATMIDFHGWDMPLQY--TSIIKEHMSVRNDVGMFDISHMGDIVISGPGSDNYVDYIFPSRISLLKNNE 87 
                                       79**********************..*************************************************** PP

                             GCV_T  78 atytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldvevedvteelallalqGPkarevl 154
                                       + yt++ln++G +idD+i++rl+ ++f+l+ na+n +k+++w+ +    kd+dv++e+ ++ ++ +a+qGPk+ +vl
  gi|518652307|ref|YP_008141827.1|  88 CMYTAFLNPSGNMIDDTIIYRLSGEKFFLIPNASNIDKIYKWMIDNK--KDYDVTIENYSNIISHIAVQGPKSVDVL 162
                                       *********************************************55..5*************************** PP

                             GCV_T 155 skllgadlselkffsfaevela...ggkkvlvsRtgytGedGfeiyipaeeaeelweaLleagkeegvkpaGlgArd 228
                                       + l     +++kf  +   +++   g++++++s tgytGe+G+e+++p+e a+++w+ +l+++k+ +  p+GlgArd
  gi|518652307|ref|YP_008141827.1| 163 KNLGMEFPEQFKFLYSDAKKYNaitGKNEIIISGTGYTGEKGVELIVPNELAADMWNSVLNEVKKLNGLPCGLGARD 239
                                       ****5557777777777777669988888************************************************ PP

                             GCV_T 229 tlRlEaglrlyghdldeettPleaglgw 256
                                       tlR+E+g+ l g+d++e+ +P+ea++ +
  gi|518652307|ref|YP_008141827.1| 240 TLRMEKGMLLSGQDFNENKNPYEASISF 267
                                       ************************9876 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 !   54.6   0.0   8.7e-19   7.8e-15       5      77 ..     294     365 ..     292     368 .] 0.93

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 8.7e-19
                           GCV_T_C   5 glelddgapllrggepilrdgevvGhvTSgaysptlgksialAyvkaelaklgtevevevrgkrvpaevvkkp 77 
                                       g++l+++  ++r g  i+ +g++ G++TSg+ sp l+  i+l+y++++++k gte  +++r+++v+ae+vk+ 
  gi|518652307|ref|YP_008141827.1| 294 GFKLENR-NIPRNGFNIYINGNIEGTITSGTVSPILNTGIGLGYINRKYSKSGTEAFIKIRDNMVKAEIVKPK 365
                                       8999644.688***********************************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (368 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2615.00
//
Query:       gi|518652308|ref|YP_008141828.1|  [L=77]
Description: hypothetical protein FACI_IFERC00001G0947 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 571.42
//
Query:       gi|518652309|ref|YP_008141829.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G0948 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.68   10.0   2.6       0.81    9.8   2.6    1.1  1  DHHC      DHHC palmitoyltransferase
          1    9.4   7.7          3    7.9   8.1    1.6  2  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.6     9e-05      0.81      49     109 ..       6      60 ..       2      64 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 9e-05
                              DHHC  49 kyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllflll 109
                                       +yF +f +y l+ +il+l  ++++l + +e++  ++   ++       ++ l+l  l++++
  gi|518652309|ref|YP_008141829.1|   6 EYFTVFFFYRLTGIILFLSGFVFYLFWGIEYSGWKDSGLISF------VVPLILLGLLTIW 60 
                                       79*******************999999999999988886653......3344444444444 PP

>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   8.1   0.00033         3      21      45 ..       9      34 ..       2      62 .. 0.75
   2 ?   -0.3   0.2      0.12   1.1e+03      30      45 ..      43      56 ..      40      69 .. 0.50

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00033
                           Sdh_cyt 21 wlsilhritGvallv.glllllvwll 45
                                      +++ + r+tG++l++ g+++ l+w++
  gi|518652309|ref|YP_008141829.1|  9 TVFFFYRLTGIILFLsGFVFYLFWGI 34
                                      67899**********99999999965 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.12
                           Sdh_cyt 30 Gvallvglllllvwll 45
                                      G++ +v+ l+ll   l
  gi|518652309|ref|YP_008141829.1| 43 GLISFVVPLILLG--L 56
                                      5555552222221..2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       687  (0.0383178); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 497.24
//
Query:       gi|518652310|ref|YP_008141830.1|  [L=388]
Description: hypothetical protein FACI_IFERC00001G0949 [Ferroplasma acidarmanus fer1]
Scores for 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-80  268.9   0.0    7.1e-80  268.4   0.0    1.2  1  HMGL-like  HMGL-like


Domain annotation for each model (and alignments):
>> HMGL-like  HMGL-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.4   0.0   3.9e-84   7.1e-80       2     264 .]      30     282 ..      29     282 .. 0.97

  Alignments for each domain:
  == domain 1  score: 268.4 bits;  conditional E-value: 3.9e-84
                                       -EEEE-TTTHHHHTSSS---HHHHHHHHHHHHHHT-SEE--TSGGGT.THHHHHHHS---TT-B..--EE-SSHHHH CS
                         HMGL-like   2 vkivdttLRDGeqalkaalsveeklaiakaLdeagvdeiEvgfpaaseddfevvraiakavkkarilalvrarekdi 78 
                                       + i+dttLRDGeq++++++++++k +iak+L +agv+ iE+gfpa s+d+++++++i + +  ++i++l+r++ +di
  gi|518652310|ref|YP_008141830.1|  30 ISIFDTTLRDGEQTPGVSFNTDQKYKIAKMLYDAGVNIIEAGFPAVSNDEMKSIKKINHDM--ENICSLARCNRNDI 104
                                       89*********************************************************99..569*********** PP

                                       HHHHH....TT-SEEEEEEES-HHHHHHHHSSTHHHHHHHHHHHHHHHHHTT-ETTT-BTTTBS--HHHHHHHHHHH CS
                         HMGL-like  79 kaavealkgagakrvhvfiatselhlkaklkkdreevakkaeeavkaarslgkdvelsledasrtdleflaevveaa 155
                                       ++ +e       +++h+fiats++h+k+klkk+re+v++++ e + +ars+g+++ +s+eda+rt+++fl ++v   
  gi|518652310|ref|YP_008141830.1| 105 DKVIE----SDSRIIHLFIATSDIHMKYKLKKTREQVFDSIMESIDYARSYGMRIIFSPEDATRTSMDFLKQIVSS- 176
                                       *****....***************************************************************9875. PP

                                       HHHT-SEEEEEETTS---HHHHHHHHHHHHHHS-.GGGEEEEEB-TTS-HHHHHHHHHHTT--EEEEBTTS--SSBB CS
                         HMGL-like 156 eeaGatriniaDtvGvltPneaaelisalkervkdkvilsvHcHndlGlAvantlaAveaGadrvdgtvnGlGeraG 232
                                         + + +in++Dt+G+++P +++  i+++k+ ++  + +s+HcHnd+G+A+antla+++aGa++  +tvnG+GeraG
  gi|518652310|ref|YP_008141830.1| 177 --IKVETINFPDTIGIMNPISMYYFINKIKSFTS--TGISIHCHNDFGMATANTLAGLMAGANEAQVTVNGIGERAG 249
                                       ..569*****************************..***************************************** PP

                                       B-BHHHHHHHHHHTT.-B----HHHHHHHHHHH CS
                         HMGL-like 233 naaleelvaalealg.vdtgldlqklrsiaalv 264
                                       na+lee+v  +++     t+++++kl+si+++v
  gi|518652310|ref|YP_008141830.1| 250 NASLEEVVSSIYGFLnSYTDIKMEKLYSISKYV 282
                                       ************976699************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       824  (0.0459591); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2449.67
//
Query:       gi|518652311|ref|YP_008141831.1|  [L=413]
Description: hypothetical protein FACI_IFERC00001G0950 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-96  324.5   3.5    2.5e-59  201.5   0.1    2.3  2  Aconitase  Aconitase family (aconitate hydratase)
    4.7e-06   25.6   0.0      7e-06   25.0   0.0    1.2  1  DUF521     Protein of unknown function (DUF521)


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.5   0.1   2.8e-63   2.5e-59       1     300 [.       7     276 ..       7     283 .. 0.89
   2 !  123.8   0.5     1e-39   9.2e-36     336     461 .]     283     405 ..     277     405 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.5 bits;  conditional E-value: 2.8e-63
                         Aconitase   1 ekiwdahlvee..egiayv...pdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsvgaeeal 72 
                                       eki++++  ++  +  +y+   +d v+ +d+t++ a+  +++ + +  + ++ +   dh vp +     ++      
  gi|518652311|ref|YP_008141831.1|   7 EKIFSEKSGTDskS-GDYIvanVDYVMANDITAPIAIDAFNELGMKP-KSDKIIIIPDHFVPPK-----DI------ 70 
                                       57776554433223.45555668**********************99.99999999******99.....33...... PP

                         Aconitase  73 eknledefernkeryefLksaakafgirvvppg.qGIvHqvnlEyglalpgktvvgtDSHTtmigglGvlaiGvGgi 148
                                               ++ +++y+  k++a + g  ++++g  G++Hqv++E+g+a pg ++ g DSHT+++g+l ++ +G+G++
  gi|518652311|ref|YP_008141831.1|  71 --------NS-AKQYKKSKDFALENGTWFYDIGhGGVCHQVMMEKGFAAPGRLIAGADSHTNTYGALSAISTGIGST 138
                                       ........12.3578888888889999999999778***************************************** PP

                         Aconitase 149 eaeavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaa 225
                                       ea  ++++ ++++kip++++++ltGk ++gv+ kD++l+v +k+++ g+  k++Ef G  ++ + +++r+T+aNM++
  gi|518652311|ref|YP_008141831.1| 139 EAGVIFATGKMWFKIPETIKINLTGKPGKGVEGKDIILHVLSKIKNGGAAYKCMEFSG-NIKYIDINERMTMANMTT 214
                                       **********************************************************.59**************** PP

                         Aconitase 226 EvGAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqda 300
                                       E+GA++++f +dekt+eYL+  +r+        y+       +++de+a++++++++d++++eps+a p++P+++
  gi|518652311|ref|YP_008141831.1| 215 EAGAKCSFFDTDEKTIEYLN--QRNTGS-----YK------IVKSDENADFSQTFNIDMNNIEPSIAIPNSPDNV 276
                                       ********************..774444.....22......25689**************************975 PP

  == domain 2  score: 123.8 bits;  conditional E-value: 1e-39
                         Aconitase 336 dgkvdiaaigSCTNssnedvraaagllakavekglkvkpgvktsvaPGSevvkayleaeGlleiLekaGfevvgagC 412
                                       + k+d+a+igSCTN+++ed+r+aa++l+     g+kv+++v+++v+P+S++v +++ +eGl +++ +aG  + g  C
  gi|518652311|ref|YP_008141831.1| 283 HEKIDQAYIGSCTNGRIEDIRKAAAILK-----GRKVNRNVRLMVVPASQEVYNQALREGLINTIVEAGGYFSGTTC 354
                                       689*************************.....******************************************** PP

                         Aconitase 413 stCig.nsdrleegeaivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                                       + C+g   + l ++e+++ss+NRNF gR+g +t + yLa P +v+ +A+ G
  gi|518652311|ref|YP_008141831.1| 355 GACLGgYMGVLGPDEVCISSTNRNFIGRMGDKTSKvYLANPSIVASSAILG 405
                                       *****999*********************9777666*************87 PP

>> DUF521  Protein of unknown function (DUF521)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   7.8e-10     7e-06     286     357 ..     281     354 ..     242     368 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7.8e-10
                            DUF521 286 akeekvdlvalG.cPhlsleElrelaellkgkkkkvkvelwvt.tsrevkeeaerlglveklekaGvkvlsdtC 357
                                       a +ek+d  ++G c    +e++r+ a++lkg+k++ +v+l+v+ +s+ev+++a r+gl++++ +aG+ +   tC
  gi|518652311|ref|YP_008141831.1| 281 AIHEKIDQAYIGsCTNGRIEDIRKAAAILKGRKVNRNVRLMVVpASQEVYNQALREGLINTIVEAGGYFSGTTC 354
                                       557888888888677889*********************987647889************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.35s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2379.07
//
Query:       gi|518652312|ref|YP_008141832.1|  [L=160]
Description: 3-isopropylmalate dehydratase small subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.4e-19   69.5   0.5    3.5e-18   66.2   0.5    2.2  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.2   0.5   1.9e-22   3.5e-18      61     126 ..      43     105 ..       9     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 66.2 bits;  conditional E-value: 1.9e-22
                                       EHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEE CS
                       Aconitase_C  61 dvvdaaerykkegaklvviagknfGeGSSRehAAkalrllGikaviaeSFerIfennliknglLpl 126
                                       + +d a +    + +++v++ knfG+GSSRehA    + lGi  +iaeSF+rIf +n+i+ g+  +
  gi|518652312|ref|YP_008141832.1|  43 EYPDLAANIM--KGDIIVAG-KNFGSGSSREHAVITIKGLGISCIIAESFARIFFRNAINTGIPVI 105
                                       4555555555..67788777.*****************************************8655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); 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 0.27s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1068.35
//
Query:       gi|518652313|ref|YP_008141833.1|  [L=356]
Description: hypothetical protein FACI_IFERC00001G0952 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-71  240.8   0.0    2.5e-71  240.6   0.0    1.0  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.6   0.0   1.4e-75   2.5e-71       2     348 .]       4     345 ..       3     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 240.6 bits;  conditional E-value: 1.4e-75
                                       EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHSSSS-HHHHHHHHHSSEEEEEE---CS.SS CS
                            Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetgeplpeetleaikeadvvllgavgtpk.ek 77 
                                       ia+++gdgiG+e+++++ +++++++  +  +++f  ++++ + + ++g ++ +  ++ +k+++ + +ga+g    + 
  gi|518652313|ref|YP_008141833.1|   4 IAVIPGDGIGKEIIPQVCDLVTSID--P--SVNFTFYNISSERYINKGITIKDSEIDELKSYNSIFFGAIGDFRvKP 76 
                                       99********************999..3..46677778887777777*************************99666 PP

                                       SSSHHHHHHHHHHHTTEEEEEEEEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEET........... CS
                            Iso_dh  78 evrpengLlaLrkeldlfanlrpvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkg........... 143
                                       ++  +  +l+Lrkeldl+ n+rp+ +f      s +     +++ + i+Re+ ++ Y+ +    ++           
  gi|518652313|ref|YP_008141833.1|  77 GIMEQGVILRLRKELDLYMNIRPAISF------SRITG---NNIHMTILRENKEDFYSDISGSLNEhklfrqkgnfy 144
                                       66666689*******************......44443...5799***************99999999********* PP

                                       .......TG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHHHHHHHHHHHHCCTTTTSEE CS
                            Iso_dh 144 .......sifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksselwrkiveevaeeeypdiel 213
                                              s+ +++  +++  +s+++ +r+ ++a ++A ++   +vt++dKan  +++ lwr+i+ e  e + ++i++
  gi|518652313|ref|YP_008141833.1| 145 nynidinSESDDTIYYTMGFLSRKNLKRFFNMAYKIADTE---TVTITDKANAVDMYSLWREIAIEESEPAGKKINF 218
                                       ****9964478889999999*****************999...**********************999977777666 PP

                                       EEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-T CS
                            Iso_dh 214 ehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNp 290
                                         +++Ds a++++++p ++  i+++Nl+GDilSD+ +a+vG+lG +pS ++g +   +fE+vHGsapdiagk++aNp
  gi|518652313|ref|YP_008141833.1| 219 --EYADSLAYNMINNPLKYRYIIAPNLYGDILSDMSSAMVGGLGYAPSGNIG-DYSSMFEPVHGSAPDIAGKNIANP 292
                                       ..69************************************************.789********************* PP

                                       HHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTSTCCCHHHHHHHHH CS
                            Iso_dh 291 iavilSaalmLryslgleeaAdkiekAvekvleagivTkDlageaakevstsefgdav 348
                                       +a+ilS  +mL++ l+++e+A  +ek+ve+v+++g++    +g+a     t+ef+++v
  gi|518652313|ref|YP_008141833.1| 293 VASILSCIMMLKH-LNQTETAGIMEKSVENVIRNGTIPIESGGNA----GTHEFINKV 345
                                       *************.*********************9998888888....999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2452.58
//
Query:       gi|518652314|ref|YP_008141834.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G0953 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       878  (0.0489709); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); 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: 422.31
//
Query:       gi|518652315|ref|YP_008141835.1|  [L=411]
Description: hypothetical protein FACI_IFERC00001G0954 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   83.6   0.0    1.2e-22   80.5   0.0    1.9  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
     0.0019   18.7   0.2        4.7    7.8   0.1    3.5  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.085   12.4   0.1        3.3    7.2   0.0    2.2  2  DAO            FAD dependent oxidoreductase
       0.17   12.1   0.0       0.44   10.8   0.0    1.7  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.5   0.0   2.7e-26   1.2e-22       2     280 ..       3     312 ..       2     325 .. 0.86

  Alignments for each domain:
  == domain 1  score: 80.5 bits;  conditional E-value: 2.7e-26
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHH.CCCCHCCT CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlvelegtclnggcllskallgvaedaeiasevvkklnqg.ielllgee 74 
                                       +++v+Gg +AGl+aa t+++    +++vtl+  ++    +++ ++++  gv ++++ + +  + l ++ i+++lg +
  gi|518652315|ref|YP_008141835.1|   3 KLLVLGGRFAGLTAAYTAKRllgDKVDVTLI-NNTPYAAFRPGMPHVSIGVFKAEDLEVDLATALPAKgIKFVLG-T 77 
                                       789*****************9888*******.99999999***********999998885555555555******.* PP

                                       CEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T...SEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxx RF
                       Pyr_redox_2  75 vvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp...krivvv 148
                                       v +id +k kv++++ + g++e+i+yd+lv+A G++    ++ G  +++g +v + d a al++kl +    +i  +
  gi|518652315|ref|YP_008141835.1|  78 VNAIDAKKNKVEYSAPD-GKKENITYDYLVVAFGAKLGVEHLNGW-DDYGSSVCEPDFATALHEKLEKfegGNI-AI 151
                                       *************8877.999**************99999*****.8888888999999999999988543333.34 PP

                                       S-SHHHHHHHHHHHHHT-.....................................EEEEEESSSSSSTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxx.....................................xxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 149 GgGyiGvElAaalaklgk.....................................evtlveardrllraldkelsaa 188
                                       G+G   v + ++l+  gk                                     ++t+   ++++l    ke +  
  gi|518652315|ref|YP_008141835.1| 152 GSG---VFYQGTLKPRGKypenwasvadsacegpifemslmipaylkkrgimdktHITIFSPGEEILTDIAKESRGV 225
                                       533...334444555555777777777788899999999999999999******99********************* PP

                                       HHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 189 leealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflr 265
                                       ++  + + G +++++ + ke+++ +     v edg++i+ad  +v   ++++++ + ++     d++g++v+de++r
  gi|518652315|ref|YP_008141835.1| 226 VKSLFAQAGFDTVWNFKLKELKKGE----IVSEDGKTIKADIAIVLPPYEANDAVK-NSTPDLFDDGGFVVTDEHMR 297
                                       **********************777....69**********************998.555556799**********9 PP

                                       ES.STTEEE-GGGCTE CS
                                       xx.xxxxxxxxxxxxx RF
                       Pyr_redox_2 266 tn.vpgiyaiGDvagg 280
                                       +   p++y +GD   +
  gi|518652315|ref|YP_008141835.1| 298 SVkYPNVYSCGDSN-Q 312
                                       755*********76.4 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1     0.001       4.7       1      32 [.       3      37 ..       3      92 .. 0.80
   2 ?   -3.0   0.0       2.6   1.2e+04      38      52 ..     129     143 ..     125     148 .. 0.81
   3 !    6.0   0.0    0.0039        17      22      69 ..     198     249 ..     187     261 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.001
                                      EEEEECSSHHHHHHHHHHHH.TT..SEEEEEESSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalae.lg..kkVtvversd 32
                                      k++v+Gg + gl +A ++++ lg   +Vt++ + +
  gi|518652315|ref|YP_008141835.1|  3 KLLVLGGRFAGLTAAYTAKRlLGdkVDVTLINNTP 37
                                      689****************9888434557777665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.6
                                       SSHHHHHHHHHHHHH CS
                         Pyr_redox  38 lDeeaskilqeklek 52 
                                       ++++++++l+eklek
  gi|518652315|ref|YP_008141835.1| 129 CEPDFATALHEKLEK 143
                                       578889999999987 PP

  == domain 3  score: 6.0 bits;  conditional E-value: 0.0039
                                       T....SEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox  22 g....kkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       g     ++t++  ++++l  + +e + +++  + + g + ++n k++e+++ 
  gi|518652315|ref|YP_008141835.1| 198 GimdkTHITIFSPGEEILTDIAKESRGVVKSLFAQAGFDTVWNFKLKELKKG 249
                                       55444689**********999999999999999999*************954 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.015        67       2      29 ..       4      36 ..       3      42 .. 0.81
   2 ?    7.2   0.0   0.00073       3.3     151     204 ..      61     113 ..      49     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.015
                                      EEEECTSHHHHHHHHHHHHT..T....EEEEESS CS
                               DAO  2 vviiGGGiiGlstAyeLarr..g....Vtllekg 29
                                      +++ GG  +Gl++Ay + +r  g    Vtl+   
  gi|518652315|ref|YP_008141835.1|  4 LLVLGGRFAGLTAAYTA-KRllGdkvdVTLINNT 36
                                      6899999**********.554877899*999765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.00073
                                       HHHHHHHHTT-EEEESECEEEEEEEETCEEEEE....EECTEEE..EEEEEEEE--GGGH CS
                               DAO 151 alaraaealGveilegtevtgleeedgkvwgve....rttpgen..daadavVnaaGaws 204
                                        la a+ a+G+++++g +v +++++     +ve    +   g +   ++d++V+a Ga  
  gi|518652315|ref|YP_008141835.1|  61 DLATALPAKGIKFVLG-TVNAIDAKK---NKVEysapD---GKKenITYDYLVVAFGAKL 113
                                       58889999********.*****7764...555543342...4442236799******985 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.8e-05      0.44       1      28 [.       6      36 ..       6      42 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.8e-05
                                      EE--SHHHHHHHHHHHCC...TEEEEEE-SS CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLaka...gfdvlllekr 28
                                      ++G+ ++Gl+aAy++++    ++dv+l+ + 
  gi|518652315|ref|YP_008141835.1|  6 VLGGRFAGLTAAYTAKRLlgdKVDVTLINNT 36
                                      789999**********9555599***99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 3192.74
//
Query:       gi|518652316|ref|YP_008141836.1|  [L=215]
Description: hypothetical protein FACI_IFERC00001G0955 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-13   48.2   2.4    6.9e-13   48.2   0.3    2.2  2  DUF1641   Protein of unknown function (DUF1641)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1      0.49   8.8e+03      14      18 ..     119     123 ..     115     125 .. 0.45
   2 !   48.2   0.3   3.9e-17   6.9e-13       4      39 .]     167     203 ..     164     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.49
                           DUF1641  14 LlraL 18 
                                       ++++L
  gi|518652316|ref|YP_008141836.1| 119 IMGLL 123
                                       33333 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 3.9e-17
                           DUF1641   4 eepkpv.GlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       + + pv G++g lra++D+D q+GLG+++++L++lGk
  gi|518652316|ref|YP_008141836.1| 167 DTVTPVgGMMGTLRAMKDEDAQKGLGIVFSILRSLGK 203
                                       6678********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1625.71
//
Query:       gi|518652317|ref|YP_008141837.1|  [L=64]
Description: hypothetical protein FACI_IFERC00001G0956 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00014   21.9   0.2    0.00017   21.5   0.2    1.1  1  ThiS-like  ThiS-like ubiquitin
    0.00016   22.2   0.0    0.00018   22.1   0.0    1.0  1  ThiS       ThiS family


Domain annotation for each model (and alignments):
>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.2   1.9e-08   0.00017       9      54 ..      11      58 ..       8      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.9e-08
                         ThiS-like  9 eveveegttlealkekikpdaD..vvIlNGFpikeDteLkegDevflI 54
                                      ++ +ee + l+++   ++ d+D  v IlNG p+++D  ++ +D++++ 
  gi|518652317|ref|YP_008141837.1| 11 KIHIEESKKLSDIYSAFNIDEDgfVAILNGNPATSDAIVNPEDNLVFL 58
                                      78899999**************************************97 PP

>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0     2e-08   0.00018       9      77 .]       3      64 .]       1      64 [] 0.94

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2e-08
                                      HHHT..CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGCCTTTSB--TTCEEEEEESTTC- CS
                              ThiS  9 elag..eeelelaegstvaelleaLgerypelalerrvavavNgeivprlwldtelkdgDevailppVaGG 77
                                      e+ g  ++++ ++e ++++++  a + +       +++++ +Ng+ +++   d+++++ D +++l +++GG
  gi|518652317|ref|YP_008141837.1|  3 EIIGkeKRKIHIEESKKLSDIYSAFNIDE------DGFVAILNGNPATS---DAIVNPEDNLVFLEIFSGG 64
                                      67777788999****************99......**************...******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.30s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 423.74
//
Query:       gi|518652318|ref|YP_008141838.1|  [L=427]
Description: hypothetical protein FACI_IFERC00001G0957 [Ferroplasma acidarmanus fer1]
Scores for complete 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-33  113.6   0.0    1.1e-32  112.6   0.0    1.5  1  tRNA_NucTransf2  tRNA nucleotidyltransferase, second domain
      5e-12   46.0   0.1    1.7e-11   44.3   0.1    1.9  1  NTP_transf_2     Nucleotidyltransferase domain
     0.0011   19.0   0.3     0.0046   17.0   0.0    2.2  2  Polbeta          Polymerase beta, Nucleotidyltransferase
     0.0043   17.2   0.1      0.012   15.8   0.1    1.8  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 !  112.6   0.0   2.5e-36   1.1e-32       2     112 ..     150     256 ..     149     257 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.6 bits;  conditional E-value: 2.5e-36
                                       HHHHHHHHHHHTT-BSSSTTT-SB-HHHHHHHHHHHSSHHHHHHHHTT--TTEEEE......EEE..-SS-EEEETT CS
                   tRNA_NucTransf2   2 evrllKkflkgigvYGselkvkGfsGYlaEllvleygsfeevleaaakwkpkvvidleekeallkkfdeplvviDPv 78 
                                       ++rllK flk+i+vYGse+  +GfsGY++E+ ++++g+fe++++ +a+ k k+++  e+     k+f+ep+++iDPv
  gi|518652318|ref|YP_008141838.1| 150 DIRLLKVFLKEINVYGSEVAKSGFSGYICEIAIIAFGTFEKFIQYMANLKGKLIVP-EN---CDKEFNEPVIIIDPV 222
                                       89****************************************************95.33...4579*********** PP

                                       EEEEETTTTS-HHHHHHHHHHHHHHHHS--GGGG CS
                   tRNA_NucTransf2  79 DpkRNvaaalsleklaefilaareflkkpseeff 112
                                       Dp+RN++aa+s+e+l++++laa+ ++++ +  +f
  gi|518652318|ref|YP_008141838.1| 223 DPTRNAGAAVSVENLSKLKLAAKLYVTRREDILF 256
                                       *************************998876665 PP

>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.1   3.7e-15   1.7e-11      18      94 ..      46     134 ..      30     135 .. 0.88

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 3.7e-15
                                       EEEHHHHCTTSCTTSSEEEEEEESTTCHHH............HHHEHHHHHHHHCCCEEECTTEEEEEECEEECCCC CS
                      NTP_transf_2  18 vlfGSyarGtalkgSDiDllvvlpeevsre............kkeegleklaeiikfleellglevdlvtrekledp 82 
                                         +GS+ +Gt+lk SDiDl+++++++ + e            + e+  ek+ae++++  ++ g+++d+v+   + + 
  gi|518652318|ref|YP_008141838.1|  46 LEVGSVSKGTNLKSSDIDLFITFSRSYPVEyiekkgleighaVLENAIEKYAEHPYVSGSVSGIKIDIVPAFRINEG 122
                                       559***********************8888************899999*********************99999998 PP

                                       TEEEEEECEEEH CS
                      NTP_transf_2  83 llvksileerpl 94 
                                       +++ s ++++pl
  gi|518652318|ref|YP_008141838.1| 123 ERIVSSVDRTPL 134
                                       888888888876 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0     1e-06    0.0046       3      51 ..      32      80 ..      30     100 .. 0.77
   2 ?   -2.1   0.1      0.97   4.4e+03      43      59 ..     378     397 ..     369     420 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                                      TTTTHHHHHHHHSTTE.EEEEE-S------EEEEEEEESS---HHHHHHH CS
                           Polbeta  3 ikeilekekeielayl.FGSrakgkareeSDiDlavllkekldleeelel 51
                                      i++i+++e +i++  l  GS+ kg+  ++SDiDl++ ++++  +e+  + 
  gi|518652318|ref|YP_008141838.1| 32 INAICKTE-GIDATPLeVGSVSKGTNLKSSDIDLFITFSRSYPVEYIEKK 80
                                      67777777.777777756*********************99666655544 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.97
                                       --HHHHHHHHHHHHHH.... CS
                           Polbeta  43 ldleeelelaaeledi...k 59 
                                        +lee ++++ e +di    
  gi|518652318|ref|YP_008141838.1| 378 TELEEIIKIELEKSDIgknL 397
                                       44555666666655554331 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 !   15.8   0.1   2.6e-06     0.012       6     136 ..       3     122 ..       1     131 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-06
                             SMODS   6 qFkeflsnielsqttkdsissrvkaitkrLnkdfrelkskiaesllvGSyardTaikpvsdkdmlfeldvdllvvvn 82 
                                       ++++ l++ ++  ++++++++ v+ai + +n+   +++   a  l vGS  ++T +k          +d+dl+++++
  gi|518652318|ref|YP_008141838.1|   3 YLENKLQEQTPTLQEQEKLKNIVSAIASDINAIC-KTEGIDATPLEVGSVSKGTNLK---------SSDIDLFITFS 69 
                                       5666677777778999999************999.88888888899*********99.........45666666666 PP

                             SMODS  83 evegdepsdlleklkkal.kktyks.seirqdrqvvvvelneikidvvPavenkdg 136
                                        +    p +++ek    + ++  ++  e+  +++ v  ++++ikid+vPa++ ++g
  gi|518652318|ref|YP_008141838.1|  70 RS---YPVEYIEKKGLEIgHAVLENaIEKYAEHPYVSGSVSGIKIDIVPAFRINEG 122
                                       53...566666665555553333320344778999****************97664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2813.20
//
Query:       gi|518652319|ref|YP_008141839.1|  [L=110]
Description: nascent polypeptide-associated complex protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-15   56.9   2.6    2.1e-15   56.4   2.0    1.6  2  NAC       NAC domain
  ------ inclusion threshold ------
        1.5    8.9   6.0       0.21   11.6   0.8    2.3  4  UPF0154   Uncharacterised protein family (UPF0154)


Domain annotation for each model (and alignments):
>> NAC  NAC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   2.0   2.4e-19   2.1e-15       1      57 []       3      62 ..       3      62 .. 0.97
   2 ?   -2.1   0.0      0.45     4e+03      30      40 ..      76      86 ..      71      98 .. 0.64

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.4e-19
                               NAC  1 ekKlrkalkklgl..keipgieeVtirksdgkvlvfdnPkVq..kspgsntyvvfGeaeek 57
                                      ++++r++++++g+  +e+p+++eV+++ +d k ++++n++V+  +++g++t++v G+ +ek
  gi|518652319|ref|YP_008141839.1|  3 PRDVRRMMNQMGIksTEMPDVKEVILKGKD-KDYIIENASVTmiEAQGQKTFQVLGTMKEK 62
                                      6899**************************.****************************97 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.45
                               NAC 30 kvlvfdnPkVq 40
                                        lv ++  V 
  gi|518652319|ref|YP_008141839.1| 76 IKLVMSQCNVS 86
                                      66677776665 PP

>> UPF0154  Uncharacterised protein family (UPF0154)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.8   2.4e-05      0.21      31      48 ..       2      19 ..       1      28 [. 0.85
   2 ?   -1.5   0.1       0.3   2.7e+03      37      45 ..      43      51 ..      31      61 .. 0.71
   3 ?   -3.3   0.0       1.1     1e+04      50      57 ..      75      82 ..      73      85 .. 0.61
   4 ?   -2.2   0.0       0.5   4.5e+03      30      41 ..      86      97 ..      76     102 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.4e-05
                           UPF0154 31 nekmirammkqmGrkPSe 48
                                      n   +r mm qmG k +e
  gi|518652319|ref|YP_008141839.1|  2 NPRDVRRMMNQMGIKSTE 19
                                      7889*********99988 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.3
                           UPF0154 37 ammkqmGrk 45
                                      +m ++ G+k
  gi|518652319|ref|YP_008141839.1| 43 TMIEAQGQK 51
                                      677777776 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.1
                           UPF0154 50 qikqvmrs 57
                                      +ik vm +
  gi|518652319|ref|YP_008141839.1| 75 DIKLVMSQ 82
                                      46666665 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 0.5
                           UPF0154 30 inekmirammkq 41
                                        ek+i a+ k+
  gi|518652319|ref|YP_008141839.1| 86 SREKAIEALRKA 97
                                      456777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 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:                        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: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 861.02
//
Query:       gi|518652320|ref|YP_008141840.1|  [L=397]
Description: hypothetical protein FACI_IFERC00001G0959 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        3.9    7.7   5.2        4.6    7.5   0.2    3.3  3  MWFE      NADH-ubiquinone oxidoreductase MWFE subunit


Domain annotation for each model (and alignments):
>> MWFE  NADH-ubiquinone oxidoreductase MWFE subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00026       4.6       7      32 ..     106     131 ..     103     141 .. 0.86
   2 ?    0.6   0.0     0.038   6.7e+02      10      29 ..     310     329 ..     307     335 .. 0.82
   3 ?   -4.1   0.8         1   1.8e+04      10      21 ..     354     365 ..     352     368 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00026
                              MWFE   7 pygImiamfgitgaglskirklqngg 32 
                                       +y I ++m++i  +g s+i ++ n  
  gi|518652320|ref|YP_008141840.1| 106 SYLILVVMIAILAFGGSIIDNWNNTY 131
                                       79*********************943 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.038
                              MWFE  10 Imiamfgitgaglskirklq 29 
                                       I +++f ++g+ ++++rk+ 
  gi|518652320|ref|YP_008141840.1| 310 IPAVAFLVPGYRTYITRKFP 329
                                       55799************985 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 1
                              MWFE  10 Imiamfgitgag 21 
                                       I+++++g++ ++
  gi|518652320|ref|YP_008141840.1| 354 IILTFIGFPMYA 365
                                       777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1314  (0.0732891); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 2742.96
//
Query:       gi|518652321|ref|YP_008141841.1|  [L=441]
Description: glutamine synthetase [Ferroplasma acidarmanus fer1]
Scores for complete 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-121  405.1   0.0   2.8e-121  404.8   0.0    1.1  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    5.7e-23   80.4   0.1    1.5e-22   79.1   0.1    1.8  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 !  404.8   0.0  3.1e-125  2.8e-121       2     345 .]     104     437 ..     103     437 .. 0.98

  Alignments for each domain:
  == domain 1  score: 404.8 bits;  conditional E-value: 3.1e-125
                                       T-HHHHHHHHHHHHHHTTCEEEEEEEEEEEEESEECCCESSEEEEEEE.TB...B.TSS-TTBHCCCCCTCCHHHHH CS
                        Gln-synt_C   2 rdPRsvlkralarlaeeGltvvvgpElEFflfdkeedkeasksllevdseekgrpaekggyfsvapvdeaedlrrei 78 
                                       +dPR++l++++++l++e+ t+++gpElE+flf+++e++e            + +p++ ggyf+ +p+d+a  + +ei
  gi|518652321|ref|YP_008141841.1| 104 GDPRYILEKQVEKLTKENKTYYLGPELEYFLFKQDENGE-----------PTIEPSDYGGYFDKEPLDRAFTVKQEI 169
                                       79*********************************9987...........56779999******************* PP

                                       HHHHHHTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEE CS
                        Gln-synt_C  79 vealealgieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlS 155
                                       ++ le l +  eashhEva +Q+Ei++k++da+++aD+++++K vvke+A+++g++atFmpKp++g nG+gmHvh+S
  gi|518652321|ref|YP_008141841.1| 170 IRKLEGLHYYPEASHHEVAYSQHEIDVKYSDAVTMADRIIMIKSVVKETANEYGYYATFMPKPVKGVNGNGMHVHQS 246
                                       ***************************************************************************** PP

                                       EEECTTEESSB-TTSGGGB-HHHHHHHHHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-T CS
                        Gln-synt_C 156 lwdkdgknlfadeddeyalselarhfigGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipas 232
                                       ++ + ++nlf++e+ +y+ls+ a h++gG+l+ +++ ++++a+tvnSYkRlvpgyeaPv++aw++rNRsal+Ripa+
  gi|518652321|ref|YP_008141841.1| 247 IF-SGDENLFYNESSKYGLSDYAMHYLGGILHNVADASLVLASTVNSYKRLVPGYEAPVYIAWANRNRSALVRIPAA 322
                                       **.888*********************************************************************** PP

                                       SGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-SSSS-TTTH..TSS-B--SSHHHHHHHHHCS CS
                        Gln-synt_C 233 kekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdlyelspeer..kgieelPasleeAlealeed 307
                                        +k+kr+ElR+pda+ N YL +Aa+l  gldGienk++p+e++ek+++e++ +er  +gi+++P sl +A+e+++++
  gi|518652321|ref|YP_008141841.1| 323 PPKGKRMELRFPDAAGNQYLQFAAILGMGLDGIENKINPPEAIEKNIFEMDLAERqkNGIKSMPGSLGQAIESFRNS 399
                                       ***************************************************9999999******************* PP

                                       HHHCCSS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
                        Gln-synt_C 308 ellkevlgeevieaylalkraEleeleeevsdwelery 345
                                       el+k+++ge+v+++ l++k++E++e+++ev+dwe+++y
  gi|518652321|ref|YP_008141841.1| 400 ELMKKIFGESVFNNLLRIKENEWNEFRSEVTDWEINKY 437
                                       ***********************************988 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 !   79.1   0.1   1.7e-26   1.5e-22       1      82 [.      15      96 ..      15      97 .. 0.97

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.7e-26
                                      T--EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGGGEEE-SS-SS-..EEEEEE CS
                        Gln-synt_N  1 evkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdlstavidPfreek.ktarvic 78
                                      ev+f++lqFtDi g++k++tip +++ ed++ +gv+FDGSsi g+++ie+SDm  +P+ls+++i+  ++   kt+r++c
  gi|518652321|ref|YP_008141841.1| 15 EVEFLQLQFTDISGSVKSLTIPHNRF-EDVIYNGVMFDGSSIVGYKQIEDSDMKAVPELSSYTILTNENYAgKTVRFVC 92
                                      599***********************.***************************************9998889****** PP

                                      EEE- CS
                        Gln-synt_N 79 dvyd 82
                                      ++++
  gi|518652321|ref|YP_008141841.1| 93 KIFN 96
                                      **97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3349.04
//
Query:       gi|518652322|ref|YP_008141842.1|  [L=772]
Description: hypothetical protein FACI_IFERC00001G0961 [Ferroplasma acidarmanus fer1]
Scores for 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-102  341.4   3.9   1.3e-100  337.5   3.9    2.0  1  tRNA-synt_1     tRNA synthetases class I (I, L, M and V)
    1.8e-34  118.9   0.7    3.8e-34  117.8   0.7    1.5  1  Anticodon_1     Anticodon-binding domain of tRNA
      3e-21   75.6   6.8    5.8e-12   45.1   0.0    3.6  4  tRNA-synt_1g    tRNA synthetases class I (M)
    1.6e-07   30.9   0.0     0.0097   15.3   0.0    2.5  2  tRNA-synt_1e    tRNA synthetases class I (C) catalytic domain
    3.4e-05   23.4   0.0    8.3e-05   22.2   0.0    1.7  1  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2
  ------ inclusion threshold ------
      0.019   13.9   0.0       0.15   11.0   0.0    2.2  2  tRNA-synt_1f    tRNA synthetases class I (K)
      0.032   14.1   0.5      0.032   14.1   0.5    2.6  2  DUF4041         Domain of unknown function (DUF4041)
      0.036   14.1   0.7        2.6    8.1   0.2    2.7  2  DZR             Double zinc ribbon
      0.087   13.6   0.1        8.1    7.3   0.0    2.8  2  zinc_ribbon_15  zinc-ribbon family
       0.23   11.6   1.5         10    6.3   0.2    2.8  2  Zn-ribbon_8     Zinc ribbon domain
       0.43   10.6   3.3        4.8    7.2   0.1    3.1  3  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !  337.5   3.9  7.9e-104  1.3e-100       2     601 ..      11     549 ..       6     550 .. 0.91

  Alignments for each domain:
  == domain 1  score: 337.5 bits;  conditional E-value: 7.9e-104
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       + + W ++++f      +k  k++++  +PP v G++H+Gha+    +d++ rykrmkG++v y  G+D  Gl++e+
  gi|518652322|ref|YP_008141842.1|  11 WKDYWFNNNIFA----FKKGDKNYTIDTPPPTVSGKMHVGHAFSYPQQDFIARYKRMKGYNVFYPWGFDDNGLPTEK 83 
                                       334455555554....45889******************************************************** PP

                       tRNA-synt_1  79 kvekklgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgl 155
                                        vek+    +k +  +   ++++e +re   e+ +   +++ + G+s+Df++   T ++   +  +e+f  l+ k  
  gi|518652322|ref|YP_008141842.1|  84 FVEKE----RKVTIDNTPLKDYIEICREVSRESEKGLYQAWYDTGISADFKNYIDTSSDFSIKISQEMFLDLVAKKR 156
                                       ***99....4556779999*******************************99888887777788899********** PP

                       tRNA-synt_1 156 iyrgkklvnwstklktalselEveykdkkdalihvafpladkeevklviaTTtPeTllgdtavavnpeldyvitkek 232
                                        yr + +   +++++ta+s++E++    +  l++++f+        ++iaTT+Pe l + +a+ vnp+         
  gi|518652322|ref|YP_008141842.1| 157 AYRDEAPYITCPTCRTAISQIEMKDAIISTELVYINFN-------GIEIATTRPEMLGACVAIFVNPD--------- 217
                                       ***********************999999999999996.......488********************......... PP

                       tRNA-synt_1 233 lilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPahdedDyevgkky 309
                                                             der k+++g +v+ p+ +  +++++d  +d+e+GtG+  +    d+ D e+ kky
  gi|518652322|ref|YP_008141842.1| 218 ----------------------DERFKKFVGTTVNVPVYGYPVKVMSDPSIDMEFGTGAEMLCTFGDQHDLELWKKY 272
                                       ......................9*************************************999999*********** PP

                       tRNA-synt_1 310 nlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke 386
                                       +++   il+++ ++++  +    + ++darkk+++el+ k+ ++k+eki+hsv + er ++pi+  +++qW+++  +
  gi|518652322|ref|YP_008141842.1| 273 GIKARIILKNN-RIND-GSVIINMPIKDARKKIIDELQSKNYIIKIEKIKHSVNTHERCGTPIEIGISKQWYIKDLD 347
                                       ***98888766.5554.456789****************************************************** PP

                       tRNA-synt_1 387 ladaalkavekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaek 462
                                       +++++++  +k+++vp   ++ry +w+   + dWciSRqr+ G++ p+++ ++ +e++   + +  v  r  ++++k
  gi|518652322|ref|YP_008141842.1| 348 IKNELIEFGNKIEWVPGHMKTRYDNWVTGLKwDWCISRQRYFGVPFPVWYCDNCGEIILAGNEELPVDPRLDNKKRK 424
                                       ****************************9866***************************554444444333333333 PP

                       tRNA-synt_1 463 kalekeakdklkkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillsl 539
                                        +         k++ +++  ++dv+D+W  S+++p+  l++ +    +++  +p+d   +G Dii  W  + il s 
  gi|518652322|ref|YP_008141842.1| 425 CE---------KCGSDNIVPETDVMDTWATSSLSPTLYLKHIN----QMD-LYPMDSRFQGHDIITSWAFTTILRSY 487
                                       22.........5689999******************9999444....465.89************************ PP

                       tRNA-synt_1 540 altgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgrdinl 601
                                          g+ P+++++++g v d  G+KmSKs+gN+++p  +i++ygadalR++  ++ +g++i+l
  gi|518652322|ref|YP_008141842.1| 488 LHYGEIPWRKIVISGNVYDPFGQKMSKSKGNIVEPRAIIENYGADALRYWASTTMQGENIKL 549
                                       ****************************************************9999999886 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.7   2.4e-37   3.8e-34       1     150 [.     590     734 ..     590     736 .. 0.88

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 2.4e-37
                       Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrl 76 
                                       +rwi +++++++kevte++e+ ++ ka  +l +ffwn++cd+yle++k++ +++   d+r  + ++ + v+e++l++
  gi|518652322|ref|YP_008141842.1| 590 NRWITTKMERTIKEVTEYMENNEIMKARISLDKFFWNEYCDNYLEMIKNESSKD---DRRDeTLSTAFSVFENILKM 663
                                       59**********************************************997554...4444599************* PP

                       Anticodon_1  77 laPfmPfitEelwqr..eeeelgkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselkv 150
                                        +P+mPfitEel+++         + si l+++pe + +  ++e+  +ev++++ ++  ir+l+s++k++ +++l++
  gi|518652322|ref|YP_008141842.1| 664 YSPIMPFITEELFHQanP----SFSGSIGLEPYPEfDGQMIYNEE--NEVDYIIGVIDKIRNLKSQMKLSMAAPLDI 734
                                       *************55542....23489*******98777776655..8**********************9999876 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.4       3.1     5e+03     269     279 ..       8      18 ..       4      21 .. 0.75
   2 !   45.1   0.0   3.5e-15   5.8e-12       2     130 ..      31     174 ..      30     183 .. 0.78
   3 !    7.8   0.1   0.00076       1.2     172     238 ..     329     394 ..     285     405 .. 0.83
   4 !   25.0   0.0   4.4e-09   7.2e-06     288     372 ..     470     555 ..     455     568 .. 0.77

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.1
                                       SGGGG.G--S. CS
                      tRNA-synt_1g 269 eekwkeyWakd 279
                                       e+kwk yW ++
  gi|518652322|ref|YP_008141842.1|   8 EKKWKDYWFNN 18 
                                       789*****443 PP

  == domain 2  score: 45.1 bits;  conditional E-value: 3.5e-15
                                       EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS....-HH....HHHHH CS
                      tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gv....tpe....elvek 69 
                                        + t+ p ++gk+H+Gh+ ++ + D +aRykr++g++v++  g D  G p+e   eke +v    tp     e++++
  gi|518652322|ref|YP_008141842.1|  31 TIDTPPPTVSGKMHVGHAFSYPQQDFIARYKRMKGYNVFYPWGFDDNGLPTEKFVEKErKVtidnTPLkdyiEICRE 107
                                       57888899*******************************************98877762331222332333345666 PP

                                       HHHHHHH....HHHHTT--..-SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE CS
                      tRNA-synt_1g  70 vheeike....lfkklnis..fdkygrttseehkelvqeifkklkekgliyekeieqlycpkderfl 130
                                       v++e ++     + + +is  f +y+ t+s+   +++qe+f  l +k+  y+ e   + cp++ + +
  gi|518652322|ref|YP_008141842.1| 108 VSRESEKglyqAWYDTGISadFKNYIDTSSDFSIKISQEMFLDLVAKKRAYRDEAPYITCPTCRTAI 174
                                       665544321115555667633779*********************************99*9998766 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.00076
                                       .....EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT---.-EE-ESS-SSS-EET CS
                      tRNA-synt_1g 172 sgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLk.dlaisrdldwGipvP 238
                                       +g+  e+  +++++ k  +++++l e+  ++ +  + ++k+   +w+   Lk d++isr+  +G+p+P
  gi|518652322|ref|YP_008141842.1| 329 CGTPIEIGISKQWYIKDLDIKNELIEFG-NKIEWVPGHMKTRYDNWVTG-LKwDWCISRQRYFGVPFP 394
                                       77777888899999999999******99.444457889999999**987.555*************99 PP

  == domain 4  score: 25.0 bits;  conditional E-value: 4.4e-09
                                       EEGGGHHH..HHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
                      tRNA-synt_1g 288 igkdiikF..HtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                                        g dii+    t ++ + l+  e+   k v++ +     g+K+SkS+g++v ++ ++e++ ad+lRY+ ++ + + +
  gi|518652322|ref|YP_008141842.1| 470 QGHDIITSwaFTTILRSYLHYGEIPWRKIVISGNVYDPFGQKMSKSKGNIVEPRAIIENYGADALRYWAST-TMQGE 545
                                       566666531124455566666788888888888889999****************************8655.44556 PP

                                       -EEE-HHHHH CS
                      tRNA-synt_1g 363 Dldfswedfv 372
                                       +++++++d++
  gi|518652322|ref|YP_008141842.1| 546 NIKLREQDLM 555
                                       6777766665 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 !   13.1   0.0   2.8e-05     0.046      12      50 ..      32      70 ..      22     103 .. 0.87
   2 !   15.3   0.0     6e-06    0.0097     251     297 ..     509     555 ..     485     559 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.8e-05
                                      EEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 12 lYvCGptvydashlGhaRslvafDilrrilqalgYdvqf 50
                                      + +  ptv  ++h+Gha s+   D ++r+ +++gY+v +
  gi|518652322|ref|YP_008141842.1| 32 IDTPPPTVSGKMHVGHAFSYPQQDFIARYKRMKGYNVFY 70
                                      555669*******************************98 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6e-06
                                       TBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHH CS
                      tRNA-synt_1e 251 gekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelle 297
                                       g+kmsks +n++  +++++++ + +lR+   ++   ++++++e++l 
  gi|518652322|ref|YP_008141842.1| 509 GQKMSKSKGNIVEPRAIIENYGADALRYWASTTMQGENIKLREQDLM 555
                                       79***************************999998999998888876 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 !   22.2   0.0   5.1e-08   8.3e-05      84     145 ..     224     285 ..     195     321 .. 0.87

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.1e-08
                     tRNA-synt_1_2  84 ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                                       f g+++  P+ g  + +     + me+gtga m +   dq+D+e +kky+++ + ++k++  
  gi|518652322|ref|YP_008141842.1| 224 FVGTTVNVPVYGYPVKVMSDPSIDMEFGTGAEMLCTFGDQHDLELWKKYGIKARIILKNNRI 285
                                       568899999********************************************999987654 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.23   3.8e+02      31      61 ..      37      67 ..      10      77 .. 0.73
   2 ?   11.0   0.0     9e-05      0.15     278     320 ..     508     550 ..     500     577 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.23
                      tRNA-synt_1f 31 ispSGliHiGnlrevltadlvaralrkrgee 61
                                       ++SG++H+G +    + d++ar  r +g +
  gi|518652322|ref|YP_008141842.1| 37 PTVSGKMHVGHAFSYPQQDFIARYKRMKGYN 67
                                      589*******999888888888877666655 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9e-05
                      tRNA-synt_1f 278 ggekmssSkGnvltledwlevaepevlrflilrrkPkkakkld 320
                                        g+kms+SkGn++ ++ ++e +  + lr+    +   +++kl 
  gi|518652322|ref|YP_008141842.1| 508 FGQKMSKSKGNIVEPRAIIENYGADALRYWASTTMQGENIKLR 550
                                       578**************************98887766666665 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5     2e-05     0.032      13      52 ..     302     341 ..     301     343 .. 0.93
   2 ?   -2.7   0.3       3.6   5.8e+03      31      49 ..     601     619 ..     593     621 .. 0.52

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2e-05
                           DUF4041  13 aaiskVkynnietlekRIeksfeainklgktmnirItpeY 52 
                                        +i ++  +n+    ++I+ s+++++++g++++i I+++ 
  gi|518652322|ref|YP_008141842.1| 302 KIIDELQSKNYIIKIEKIKHSVNTHERCGTPIEIGISKQW 341
                                       58999999*****************************985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                           DUF4041  31 eksfeainklgktmnirIt 49 
                                       +k ++ +  ++++m++rI+
  gi|518652322|ref|YP_008141842.1| 601 IKEVTEYMENNEIMKARIS 619
                                       3333444445677777775 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.054        87      13      24 ..     165     176 ..     155     209 .. 0.83
   2 ?    8.1   0.2    0.0016       2.6      14      37 ..     397     431 ..     395     439 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.054
                               DZR  13 rfCseCgtklka 24 
                                       ++C++C+t++++
  gi|518652322|ref|YP_008141842.1| 165 ITCPTCRTAISQ 176
                                       578888887764 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0016
                               DZR  14 fCseCgtklkavaa...........edrCpsCgek 37 
                                       +C++Cg+ + a ++           +++C +Cg++
  gi|518652322|ref|YP_008141842.1| 397 YCDNCGEIILAGNEelpvdprldnkKRKCEKCGSD 431
                                       67777777543333577777777777777777776 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.12     2e+02      33      51 ..     160     178 ..     142     191 .. 0.77
   2 ?    7.3   0.0     0.005       8.1      36      73 ..     394     430 ..     389     436 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.12
                    zinc_ribbon_15  33 kkkpylacskCkslleask 51 
                                        + py++c +C++ +++ +
  gi|518652322|ref|YP_008141842.1| 160 DEAPYITCPTCRTAISQIE 178
                                       5578899999988887766 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.005
                    zinc_ribbon_15  36 pylacskCkslleaskelgkeiekkessekkeCknCgk 73 
                                       p+ +c++C++++ a + ++  ++ + +++k++C++Cg+
  gi|518652322|ref|YP_008141842.1| 394 PVWYCDNCGEIILAGN-EELPVDPRLDNKKRKCEKCGS 430
                                       5789******999997.677788899999*******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 ?    3.3   0.1     0.055        89      23      35 ..     161     173 ..     154     177 .. 0.74
   2 ?    6.3   0.2    0.0062        10       8      35 ..     398     432 ..     395     434 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.055
                       Zn-ribbon_8  23 dapltaCPeCgse 35 
                                       +ap ++CP+C  +
  gi|518652322|ref|YP_008141842.1| 161 EAPYITCPTCRTA 173
                                       777888****765 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0062
                       Zn-ribbon_8   8 CeeCghefe......vlqsisdapltaCPeCgs.e 35 
                                       C++Cg+         ++ +  d+++ +C +Cgs +
  gi|518652322|ref|YP_008141842.1| 398 CDNCGEIILagneelPVDPRLDNKKRKCEKCGSdN 432
                                       999996666777766666555777888*****955 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.62     1e+03      22      26 ..     167     171 ..     157     175 .. 0.75
   2 ?    1.6   0.1      0.16   2.7e+02      19      26 ..     395     402 ..     392     404 .. 0.88
   3 ?    7.2   0.1     0.003       4.8       4      18 ..     424     438 ..     422     440 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.62
                    PhnA_Zn_Ribbon  22 CpeCa 26 
                                       Cp+C 
  gi|518652322|ref|YP_008141842.1| 167 CPTCR 171
                                       89985 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                    PhnA_Zn_Ribbon  19 llvCpeCa 26 
                                       ++ C++C+
  gi|518652322|ref|YP_008141842.1| 395 VWYCDNCG 402
                                       899****8 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.003
                    PhnA_Zn_Ribbon   4 kCplCaSeytYedga 18 
                                       kC++C+S++   +++
  gi|518652322|ref|YP_008141842.1| 424 KCEKCGSDNIVPETD 438
                                       9******98655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (772 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); 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):              11  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.53
# Mc/sec: 4397.94
//
Query:       gi|518652323|ref|YP_008141843.1|  [L=87]
Description: hypothetical protein FACI_IFERC00001G0962 [Ferroplasma acidarmanus fer1]
Scores for complete 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   17.4   4.8     0.0015   17.3   4.8    1.0  1  CitMHS_2       Putative citrate transport
  ------ inclusion threshold ------
      0.041   14.2   0.4      0.044   14.1   0.4    1.1  1  MscL           Large-conductance mechanosensitive channel, Ms
        1.2    9.1  12.9       0.57   10.1   0.2    2.1  2  TB2_DP1_HVA22  TB2/DP1, HVA22 family


Domain annotation for each model (and alignments):
>> CitMHS_2  Putative citrate transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   4.8   2.5e-07    0.0015      28      99 ..       3      76 ..       1      84 [. 0.74

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.5e-07
                          CitMHS_2 28 kfWekhygkvavawallll..vplavllgveaaleellhallaeylpFivlllaLfvvaggilikgnlkgtplv 99
                                      ++W+k+   +++ +++ +l  v+++++ +  +    ++h ++  +l+Fi++ +aLf+ +  i+ik  ++ ++ +
  gi|518652323|ref|YP_008141843.1|  3 HYWKKYLIYAILGYTAYMLyaVIFFYYAKSVHLQMGTFHYFVYSHLNFIIMGIALFYLSKAIAIKRAQAPRTNI 76
                                      89***99998887776555115555555555666678999999*********************9876654444 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.4   7.4e-06     0.044      59     100 ..      26      72 ..       5      87 .] 0.61

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 7.4e-06
                              MscL  59 l..kaeaavlkyga...fiqavinFliiafviFlivkainkkkkeee 100
                                       +   a+++ l++g+   f+ + +nF+i+++++F + kai  k++++ 
  gi|518652323|ref|YP_008141843.1|  26 FfyYAKSVHLQMGTfhyFVYSHLNFIIMGIALFYLSKAIAIKRAQAP 72 
                                       1344455566655411178899***************9997544322 PP

>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   7.6     0.021   1.2e+02      21      53 ..       2      33 ..       1      37 [. 0.81
   2 ?   10.1   0.2   9.6e-05      0.57      32      73 ..      42      84 ..      34      87 .] 0.80

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.021
                     TB2_DP1_HVA22 21 ltYWvvfafltvvesladvllswiPfYylfKll 53
                                      + YW  + ++ ++ ++a +l ++i f+y++K++
  gi|518652323|ref|YP_008141843.1|  2 IHYWKKYLIYAILGYTAYMLYAVI-FFYYAKSV 33
                                      79**************97777666.77777776 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 9.6e-05
                     TB2_DP1_HVA22 32 vvesla.dvllswiPfYylfKllfllwlvlpqtqgatyvYekf 73
                                       + +   ++++  i ++yl K +++   ++p+t+  t+vY ++
  gi|518652323|ref|YP_008141843.1| 42 YFVYSHlNFIIMGIALFYLSKAIAIKRAQAPRTNIKTTVYVRV 84
                                      333333377887899*************************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       779  (0.0434492); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); 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: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 664.90
//
Query:       gi|518652324|ref|YP_008141844.1|  [L=110]
Description: hypothetical protein FACI_IFERC00001G0963 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0013   18.9   1.8     0.0016   18.6   1.8    1.2  1  DUF3792         Protein of unknown function (DUF3792)
  ------ inclusion threshold ------
      0.017   14.6   2.7       0.02   14.5   2.7    1.1  1  Peptidase_A22B  Signal peptide peptidase
      0.024   14.0   5.4       0.03   13.6   5.4    1.1  1  AgrB            Accessory gene regulator B
       0.46    9.8   2.4       0.52    9.6   2.4    1.1  1  DUF3810         Protein of unknown function (DUF3810)
        3.2    8.0   6.8         16    5.7   2.2    2.2  2  DUF4519         Domain of unknown function (DUF4519)


Domain annotation for each model (and alignments):
>> DUF3792  Protein of unknown function (DUF3792)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   1.8   4.5e-07    0.0016      37      91 ..      12      66 ..       3      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.5e-07
                           DUF3792 37 lsililiililsvfigGflagkkakkkgllnGllvGllyflillllsllikksgs 91
                                      + i++++++i+ v + G++++ ++ kk +l  l ++l+ ++i++ l +l++ ++ 
  gi|518652324|ref|YP_008141844.1| 12 VAIAVVMSVIAYVYLPGLYLSMRITKKQFLRTLPTALISIVIVITLFFLFNPQKL 66
                                      4556666666666777**************************8888888844433 PP

>> Peptidase_A22B  Signal peptide peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.7   5.5e-06      0.02       9      62 ..      10      63 ..       5      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.5e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    Peptidase_A22B  9 itkkeaillpitaslvlllLylffkslakeflvvlltvlivllgvvalasllsp 62
                                      +t   a+++ ++a + l +Lyl +++++k+fl +l t+li ++ v++l +l++p
  gi|518652324|ref|YP_008141844.1| 10 LTVAIAVVMSVIAYVYLPGLYLSMRITKKQFLRTLPTALISIVIVITLFFLFNP 63
                                      67889*****************************************99999987 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   5.4   8.4e-06      0.03     106     173 ..       9      77 ..       2      88 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 8.4e-06
                              AgrB 106 llliilliisliiilllaPvdtpnkpisskekkkklkilsiivllilliialll..knekisnaillgll 173
                                       +l +++++++ +i +++ P    +++i++k+  ++l   ++i+++i++ +++l+  ++ ++s  ++++  
  gi|518652324|ref|YP_008141844.1|   9 VLTVAIAVVMSVIAYVYLPGLYLSMRITKKQFLRTLPT-ALISIVIVITLFFLFnpQKLNLSDPLSYAWE 77 
                                       566778889999******************98888887.5555555555555554755555554443333 PP

>> DUF3810  Protein of unknown function (DUF3810)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   2.4   0.00015      0.52      22      76 ..       3      60 ..       1      78 [. 0.62

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00015
                           DUF3810 22 FSvgellivllillvilylvlai....klkkrkkkkkrllkvllrvllvllvvyflftl 76
                                      F + e +++++i++v+ +++++     +l  r  k k++l++l ++l+ +++v++lf l
  gi|518652324|ref|YP_008141844.1|  3 FPFFETVLTVAIAVVMSVIAYVYlpglYLSMRITK-KQFLRTLPTALISIVIVITLFFL 60
                                      77788888888888777777777788644433333.45555555555555555555443 PP

>> DUF4519  Domain of unknown function (DUF4519)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   2.2    0.0045        16      32      51 ..       7      26 ..       2      28 .. 0.87
   2 ?    4.7   0.2    0.0094        34      35      51 ..      44      60 ..      32      65 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0045
                           DUF4519 32 tvVlPvlavlillivvfvYl 51
                                        Vl v +++++ ++++vYl
  gi|518652324|ref|YP_008141844.1|  7 ETVLTVAIAVVMSVIAYVYL 26
                                      56889999***********8 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0094
                           DUF4519 35 lPvlavlillivvfvYl 51
                                      lP+ ++ i++++ +++l
  gi|518652324|ref|YP_008141844.1| 44 LPTALISIVIVITLFFL 60
                                      78876666655555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       933  (0.0520386); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 845.87
//
Query:       gi|518652325|ref|YP_008141845.1|  [L=438]
Description: hypothetical protein FACI_IFERC00001G0964 [Ferroplasma acidarmanus fer1]
Scores for complete 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-26   90.9   0.0    1.4e-25   90.4   0.0    1.2  1  Lyase_1   Lyase


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   7.8e-30   1.4e-25      97     308 ..      92     292 ..      22     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 7.8e-30
                                       HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHH CS
                           Lyase_1  97 ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqels 173
                                       e+  +++   +  S+n+qv T+++ +l + l    l++ + + ++++   k  ++ +++G+Th ++ +Pvt+   + 
  gi|518652325|ref|YP_008141845.1|  92 ETNGAANNMRMFMSRNEQVHTDVNFFLIDIL----LEYEKIIYNTITGLEKLTQNGIMPGYTHYRQGMPVTFQTYVD 164
                                       5556677788889*************97655....77888889999999999999********************** PP

                                       HHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHH CS
                           Lyase_1 174 ayaealerdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrDavvell 249
                                          + +  + +++  +l++l+ ++lg g++ g   +a+ +    va+ ++    ++ +++++ f  +   D+++++l
  gi|518652325|ref|YP_008141845.1| 165 FIKNIMVYNFNNIDSILNELKELPLGYGSGFGSMSDANFK---EVAEYMG----MKkQIKNPLFSFMLYSDNYIKVL 234
                                       *****************88888888877766666665555...5677777....4559******************* PP

                                       HHHHHHHHHHHHHHHHHHHHTSTTTSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHH CS
                           Lyase_1 250 galkllatsLskfaeDlrllssgeaglvelslaesepGSSiMPgKvNPvqlElltgvag 308
                                       +a++ + +++s++ +D++++s  e+ ++el   + + GSS+MP KvNP+ lE  +g a+
  gi|518652325|ref|YP_008141845.1| 235 SAINSFLIDISRIFQDMIIFSGDEMKIIELPAGYVT-GSSLMPNKVNPDFLEIFQGYAA 292
                                       ************************************.****************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3171.81
//
Query:       gi|518652326|ref|YP_008141846.1|  [L=413]
Description: hypothetical protein FACI_IFERC00001G0965 [Ferroplasma acidarmanus fer1]
Scores for complete 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-132  441.7   2.4   3.4e-132  441.4   2.4    1.0  1  Arginosuc_synth  Arginosuccinate synthase
    8.7e-05   22.1   0.1    0.00019   21.0   0.1    1.7  1  QueC             Queuosine biosynthesis protein QueC
  ------ inclusion threshold ------
      0.037   13.6   0.0      0.068   12.7   0.0    1.4  1  ThiI             Thiamine biosynthesis protein (ThiI)
      0.071   13.0   1.7        5.2    7.0   0.1    3.0  2  Curto_V2         Curtovirus V2 protein


Domain annotation for each model (and alignments):
>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  441.4   2.4  7.7e-136  3.4e-132       2     380 ..      23     394 ..      22     401 .. 0.98

  Alignments for each domain:
  == domain 1  score: 441.4 bits;  conditional E-value: 7.7e-136
                   Arginosuc_synth   2 LaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDakeefvedyifpaikanalY 78 
                                       L ysGGlDtsv+ k++++++++ev+++++++G+   +l+++kekal lg  +++v D+k+ef e+yi + i a+++Y
  gi|518652326|ref|YP_008141846.1|  23 LLYSGGLDTSVMAKWIQKEMKKEVVTLTLNIGNS--NLQKIKEKALGLGVSDAIVLDVKNEFSEKYIAKEIYADGMY 97 
                                       78******************************99..***************************************** PP

                   Arginosuc_synth  79 edrYllgtalaRPliakklvevakkegaeavahGctGkGnDqvRfevsirslaPdlkviaPvReleltReeeieyak 155
                                       e+ Y+l+ta+aRPl+a+k v  a+++g++++ahG+tGkGnDqvRfev++++l+ d++viaPvR++++ R +ei+yak
  gi|518652326|ref|YP_008141846.1|  98 EG-YPLSTAIARPLMAEKAVLYAEEYGCNTIAHGSTGKGNDQVRFEVTMKALNEDINVIAPVRDWNMNRPDEIKYAK 173
                                       **.************************************************************************** PP

                   Arginosuc_synth 156 ekgipvevtkkkpysiDenllgrsieagiLedpknappediyeltkdpakapdepeeveiefekGvPvaldgeelsv 232
                                       ++gi++++     ys+Den++grs+e++ +e ++n    d+ye++k+++++  + ++++ief++GvPv+l+g+++  
  gi|518652326|ref|YP_008141846.1| 174 ANGIDIPMG--GKYSVDENIWGRSVEGSSIETVSNPLEYDVYEWVKPLEETG-NGDIIDIEFKNGVPVSLNGKQYAL 247
                                       *******98..56*********************************999988.89********************** PP

                   Arginosuc_synth 233 lelieklneiagkhGvGRiDivedRlvglksReiYeapaalvLikahkdlekltlerevakfkkiveekyaelvYkG 309
                                        el+ekln iag++G+G i+++edR+ g+ks e+Ye p+a+++i+ahk +e+ltl+++++ +k+ +++++++ vY+G
  gi|518652326|ref|YP_008141846.1| 248 KELVEKLNVIAGNNGIGLINHMEDRVTGIKSHEVYEVPGAMAIIQAHKMMESLTLNKSELDIKNYMDNQWSNFVYNG 324
                                       ***************************************************************************** PP

                   Arginosuc_synth 310 lwfsPlkealdafiektqervtGtvrvklfkGsvvvlgReseeslYdeelasydeedefdqkeaeGfikih 380
                                       lw++P +e++++f ++ ++ v+G++++kl+kG++v+++ ese+s+Y+ +  syd +++f+q +a+Gfi+i+
  gi|518652326|ref|YP_008141846.1| 325 LWYDPVMEHINQFESSINKYVNGNIKLKLYKGNIVMQSIESENSIYNYDKISYD-NSNFNQDSAKGFIDIY 394
                                       ******************************************************.99***********997 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.1   4.2e-08   0.00019       1     121 [.      20     131 ..      20     180 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 4.2e-08
                                       EEEEE--SSHHHHHHHHHHHHH-.SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG---- CS
                              QueC   1 kavvllSGGlDSttvlalakkeg.kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtdee 76 
                                       k+++l SGGlD ++++ + +ke+ kev +lt++ g+   ++l++ k+ a  lgv++  +ld++  +e++++ + +e 
  gi|518652326|ref|YP_008141846.1|  20 KVLLLYSGGLDTSVMAKWIQKEMkKEVVTLTLNIGN---SNLQKIKEKALGLGVSDAIVLDVK--NEFSEKYIAKE- 90 
                                       578999**********9998887579********96...578888999999***999999999..99999887766. PP

                                       -------...--------TTHHHHHHHHHHHHHHHHT-SEEEE-- CS
                              QueC  77 ievpkeeleeeelpntfVpaRNliflslaasyaealgaeaiiiGv 121
                                         +   +   e+ p +   aR  ++   a+ yae++g+++i+ G 
  gi|518652326|ref|YP_008141846.1|  91 --IYA-DGMYEGYPLSTAIARP-LMAEKAVLYAEEYGCNTIAHGS 131
                                       ..344.4567888888888886.5788999999999999999886 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.5e-05     0.068       4     117 ..      19     132 ..      17     177 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.5e-05
                              ThiI   4 gkvlaLlSgGiDSpVaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeil 80 
                                       +kvl+L SgG+D  V a   +++ ++ ++v+l+  +  ++ + +k+++ a  l   ++ +      ++ k + kei 
  gi|518652326|ref|YP_008141846.1|  19 DKVLLLYSGGLDTSVMAK-WIQKEMKKEVVTLT--LNIGNSNLQKIKEKALGLGVSDAIVLDVKNEFSEKYIAKEIY 92 
                                       69*************986.57889999999996..455556667777777777766664333334566777888887 PP

                              ThiI  81 ekv.kekl..tivllkrkmlriAekvaeeegakalvtGes 117
                                            e++   + + +  m   A  +aee+g++++  G++
  gi|518652326|ref|YP_008141846.1|  93 ADGmYEGYplSTAIARPLMAEKAVLYAEEYGCNTIAHGST 132
                                       654355542278999*******************998864 PP

>> Curto_V2  Curtovirus V2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0012       5.2      28      77 ..      35      86 ..      28     122 .. 0.67
   2 ?    3.8   0.3     0.011        48      33     114 ..     291     380 ..     286     392 .. 0.58

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                          Curto_V2 28 nkwcilgirqevealtleegevflqfqkevkkll..klkvtfsrkcelyeki 77
                                       kw    +++ev +ltl+ g+  lq  ke    l     + ++ k e+ ek 
  gi|518652326|ref|YP_008141846.1| 35 AKWIQKEMKKEVVTLTLNIGNSNLQKIKEKALGLgvSDAIVLDVKNEFSEKY 86
                                      69999*****************998887743222112223333333333333 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.011
                          Curto_V2  33 lgirqevealtleegevflq..fqkevkkllklkvtfs...rkcelyekiykkylsdvpe...kkgelskvvveeee 101
                                       +  ++ +e+ltl++ e  ++  ++++  +++   + ++    + + +e   +ky+    +    kg++    +e e+
  gi|518652326|ref|YP_008141846.1| 291 IQAHKMMESLTLNKSELDIKnyMDNQWSNFVYNGLWYDpvmEHINQFESSINKYVNGNIKlklYKGNIVMQSIESEN 367
                                       55666667777766665443112222233333333332111455667888888887554411147888888899999 PP

                          Curto_V2 102 dyyefekipmeea 114
                                         y+++ki  +++
  gi|518652326|ref|YP_008141846.1| 368 SIYNYDKISYDNS 380
                                       99***99998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 2868.42
//
Query:       gi|518652327|ref|YP_008141847.1|  [L=196]
Description: hypothetical protein FACI_IFERC00001G0966 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00019   21.2   0.0     0.0004   20.1   0.0    1.6  1  ScsC_N    Copper resistance protein ScsC N-terminal domain
    0.00024   20.9   1.4     0.0014   18.4   0.1    2.4  2  ACT_7     ACT domain


Domain annotation for each model (and alignments):
>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.5e-08    0.0004       5      22 ..       9      26 ..       6      27 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.5e-08
                            ScsC_N  5 iekivrdYLleNPEiLvE 22
                                      +e++vrdY+ +NPE+++ 
  gi|518652327|ref|YP_008141847.1|  9 VETMVRDYIKKNPELIIS 26
                                      89*************985 PP

>> ACT_7  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.049   4.4e+02      37      49 ..      98     111 ..      98     117 .. 0.88
   2 !   18.4   0.1   1.5e-07    0.0014       2      63 ..     131     193 ..     130     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.049
                                       --EEEE.-SS-EEE CS
                             ACT_7  37 sifqiS.tyrtdyi 49 
                                       +++++S ty td+i
  gi|518652327|ref|YP_008141847.1|  98 NLNFLSaTYLTDSI 111
                                       5789999*****98 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.5e-07
                                       EEEEEEEEEE-S-.---SS--HHHHHHHHHHTTT---EEEE.-SS-EEEEEEGGGHHHHHHHH CS
                             ACT_7   2 sedgwiklsvvgsglpfdvtGivaklaspLaeagIsifqiS.tyrtdyiLVpeedlekAveaL 63 
                                       +e++++ l + +s   + ++G+v k+ + L    I+++q+  + +  +i+V+ +d+ +A+eaL
  gi|518652327|ref|YP_008141847.1| 131 IERNVSSLHIFSSMEIVKTPGFVMKINERLFSYEINVLQLIsCSNETIIIVNRKDAIRAYEAL 193
                                       6778888888888444679********************998********************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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 0.32s 00:00:00.80 Elapsed: 00:00:00.49
# Mc/sec: 1200.55
//
Query:       gi|518652328|ref|YP_008141848.1|  [L=144]
Description: ferredoxin [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-12   45.1  11.0    5.7e-06   25.9   2.7    2.3  2  Fer4      4Fe-4S binding domain
    2.6e-09   37.1  16.9    1.3e-07   31.7   6.2    2.1  2  Fer4_10   4Fe-4S dicluster domain
    5.6e-09   36.4  13.8    3.5e-07   30.7   8.3    2.1  2  Fer4_7    4Fe-4S dicluster domain
    4.5e-07   29.9   5.3    1.8e-06   28.0   5.5    1.8  1  Fer4_9    4Fe-4S dicluster domain
    1.1e-06   29.5   4.1    1.8e-06   28.8   4.1    1.4  1  Fer4_16   4Fe-4S double cluster binding domain
    2.3e-06   27.6   4.4     0.0052   16.9   0.7    2.2  2  Fer4_21   4Fe-4S dicluster domain
    2.3e-05   24.9   7.3      0.013   16.0   0.1    2.4  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    2.5e-05   24.4   1.1       0.01   16.0   0.3    2.2  2  Fer4_18   4Fe-4S dicluster domain
    6.5e-05   23.3   6.0    0.00067   20.1   6.7    2.0  2  Fer4_8    4Fe-4S dicluster domain
    8.8e-05   23.2  11.9      0.024   15.5   4.8    2.3  2  Fer4_3    4Fe-4S binding domain
    0.00017   21.5   9.3      0.014   15.5   2.4    2.3  2  Fer4_6    4Fe-4S binding domain
    0.00017   21.8   4.8       0.13   12.8   1.5    2.3  2  Fer4_4    4Fe-4S binding domain
    0.00039   20.9   5.4      0.026   15.1   7.1    2.2  2  Fer4_17   4Fe-4S dicluster domain
    0.00098   19.8   7.1      0.055   14.2   0.1    2.7  3  Fer4_15   4Fe-4S single cluster domain
     0.0061   16.6  10.6       0.26   11.4   3.4    2.4  2  Fer4_2    4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.3   1.6e-08   1.9e-05       2      21 ..      63      82 ..      62      85 .. 0.92
   2 !   25.9   2.7   4.7e-09   5.7e-06       3      24 .]     119     140 ..     118     140 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.6e-08
                                      EEETTTSSS-THHHHHSTTT CS
                              Fer4  2 videekCigCGaCvevCPvg 21
                                       +d++ Ci+ G C++vCPv+
  gi|518652328|ref|YP_008141848.1| 63 AVDWDGCIADGSCMDVCPVD 82
                                      69****************98 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 4.7e-09
                                       EETTTSSS-THHHHHSTTTEEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAIt 24 
                                       + e+ Ci+C+aCv +CP  +I+
  gi|518652328|ref|YP_008141848.1| 119 VRESECIFCMACVTACPWSVIK 140
                                       6799*************99885 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   6.2     1e-10   1.3e-07       4      56 .]      64     135 ..      61     135 .. 0.83
   2 !   17.5   2.9   2.7e-06    0.0033       6      24 ..     121     139 ..     116     144 .] 0.78

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 1e-10
                           Fer4_10   4 idddtCirCgkCvkaCPadl.....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +d d Ci  g C+++CP+dl                     t    k+ ++++++vr+  ++C++c aCv aCP
  gi|518652328|ref|YP_008141848.1|  64 VDWDGCIADGSCMDVCPVDLfewklnpgnsgtgndkkvekgTPEWEKYRTDKSNPVRE--SECIFCMACVTACP 135
                                       67899******************************99975555555555555555555..9************9 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 2.7e-06
                           Fer4_10   6 ddtCirCgkCvkaCPadlt 24 
                                       ++ Ci C +Cv+aCP+++ 
  gi|518652328|ref|YP_008141848.1| 121 ESECIFCMACVTACPWSVI 139
                                       568999********99554 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.9e-05     0.023      29      51 ..      60      82 ..      18      83 .. 0.78
   2 !   30.7   8.3   2.9e-10   3.5e-07       2      51 ..      69     137 ..      67     138 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.9e-05
                            Fer4_7 29 ekveidpekClgCgaCvavCPtg 51
                                       +v++d + C+  g+C++vCP++
  gi|518652328|ref|YP_008141848.1| 60 TTVAVDWDGCIADGSCMDVCPVD 82
                                      56789999*************97 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 2.9e-10
                            Fer4_7   2 CigCgaCvaaCpvkaield..........eeenekgtekv.........eidpekClgCgaCvavCPtg 51 
                                       Ci  g C+++Cpv+ +e++          ++++ekgt+++          +++++C++C aCv++CP+ 
  gi|518652328|ref|YP_008141848.1|  69 CIADGSCMDVCPVDLFEWKlnpgnsgtgnDKKVEKGTPEWekyrtdksnPVRESECIFCMACVTACPWS 137
                                       77779************99666666665556667777666655665554556677************97 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   5.5   1.5e-09   1.8e-06       2      49 ..      69     137 ..      67     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1.5e-09
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.....................eaCigCgaCveaCpkg 49 
                                       C+  g+C+++Cp ++++ + +++     ++++                     ++Ci+C+aCv aCp  
  gi|518652328|ref|YP_008141848.1|  69 CIADGSCMDVCPVDLFEWKLNPGNSGTGNDKKvekgtpewekyrtdksnpvreSECIFCMACVTACPWS 137
                                       555589***********999999988877777999******************99************66 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   4.1   1.5e-09   1.8e-06       2      66 ..      69     136 ..      68     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.5e-09
                           Fer4_16   2 CgtCgkCaevCPtnaikek...kekeiearecisyntaekkdlaedeekckkqeaitgCdiCqdvCPa 66 
                                       C+  g C++vCP++ ++ k    +    +++++++ t+e +++++d+ +  ++ ++++C +C+++CP+
  gi|518652328|ref|YP_008141848.1|  69 CIADGSCMDVCPVDLFEWKlnpGNSGTGNDKKVEKGTPEWEKYRTDKSNPVRESECIFCMACVTACPW 136
                                       788899*********9966332223334455566689999***************************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 !   12.2   0.2   0.00012      0.15      32      54 ..      60      82 ..      53      85 .. 0.83
   2 !   16.9   0.7   4.3e-06    0.0052      30      56 ..     113     138 ..     105     141 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                           Fer4_21 32 tvlkvvedeCvGCnlCssvCPve 54
                                      t+++v  d C++   C++vCPv+
  gi|518652328|ref|YP_008141848.1| 60 TTVAVDWDGCIADGSCMDVCPVD 82
                                      456778899************94 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 4.3e-06
                           Fer4_21  30 aktvlkvvedeCvGCnlCssvCPvedc 56 
                                       +++  +v+e+eC+ C  C++ CP   +
  gi|518652328|ref|YP_008141848.1| 113 TDKSNPVRESECIFCMACVTACPW-SV 138
                                       566778999999999999999995.55 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 !   16.0   0.1   1.1e-05     0.013       1      21 [.      64      85 ..      64     103 .. 0.88
   2 !   10.8   3.0   0.00046      0.55       3      17 ..     121     135 ..     119     137 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.1e-05
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFe 21
                                      VD d Cia+g+C +++P d+Fe
  gi|518652328|ref|YP_008141848.1| 64 VDWDGCIADGSCMDVCPvDLFE 85
                                      899**************55665 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                           Fer4_13   3 rdtCiacgaCvelaP 17 
                                       +++Ci c+aCv ++P
  gi|518652328|ref|YP_008141848.1| 121 ESECIFCMACVTACP 135
                                       589***********9 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0042         5      58      74 ..      66      82 ..      34      86 .. 0.82
   2 !   16.0   0.3   8.6e-06      0.01      41      75 ..     104     138 ..      91     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0042
                           Fer4_18 58 agdcidcescvkvcPtg 74
                                         ci+ +sc++vcP++
  gi|518652328|ref|YP_008141848.1| 66 WDGCIADGSCMDVCPVD 82
                                      5679***********86 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.6e-06
                           Fer4_18  41 kkekkalkekeerkekgagdcidcescvkvcPtgi 75 
                                        + + ++ ++++ +   +++ci c +cv+ cP  +
  gi|518652328|ref|YP_008141848.1| 104 GTPEWEKYRTDKSNPVRESECIFCMACVTACPWSV 138
                                       444455556677788899**************765 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00019      0.23      45      64 ..      63      82 ..      18      83 .. 0.70
   2 !   20.1   6.7   5.6e-07   0.00067       3      64 ..      67     137 ..      65     138 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                            Fer4_8 45 eealwsCttcgaCtevCpvg 64
                                      +  ++ C + g+C +vCpv+
  gi|518652328|ref|YP_008141848.1| 63 AVDWDGCIADGSCMDVCPVD 82
                                      55678899999999999986 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.6e-07
                            Fer4_8   3 ekCieCgaCqsaCp..vlrrtk.khlldargeaae.............dvqeeqvlee..eealwsCttcgaCtevC 61 
                                       + Ci  g C++ Cp  +  ++k +  ++  g+ ++             d        +       +C  c+aC+++C
  gi|518652328|ref|YP_008141848.1|  67 DGCIADGSCMDVCPvdL-FEWKlNPGNSGTGNDKKvekgtpewekyrtD--------KsnPVRESECIFCMACVTAC 134
                                       569999*******9542.3333255555555555555555444322221........133455799*********** PP

                            Fer4_8  62 pvg 64 
                                       p +
  gi|518652328|ref|YP_008141848.1| 135 PWS 137
                                       *65 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   0.6   0.00028      0.34       3      14 ..      68      82 ..      67      82 .. 0.77
   2 !   15.5   4.8     2e-05     0.024       1      13 [.     124     136 ..     124     138 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00028
                            Fer4_3  3 gC...gaCvevCPvg 14
                                      gC   g C++vCPv+
  gi|518652328|ref|YP_008141848.1| 68 GCiadGSCMDVCPVD 82
                                      6765578******85 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2e-05
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ C+aCv +CP+
  gi|518652328|ref|YP_008141848.1| 124 CIFCMACVTACPW 136
                                       ************6 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.6    0.0005       0.6       9      22 ..      69      82 ..      61      84 .. 0.81
   2 !   15.5   2.4   1.2e-05     0.014       9      24 .]     124     139 ..     119     139 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0005
                            Fer4_6  9 CigCgdCvrvCPeg 22
                                      Ci  g C++vCP +
  gi|518652328|ref|YP_008141848.1| 69 CIADGSCMDVCPVD 82
                                      999999******86 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.2e-05
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       Ci C++Cv++CP  +i
  gi|518652328|ref|YP_008141848.1| 124 CIFCMACVTACPWSVI 139
                                       888*********8776 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.1   0.00084         1       3      16 ..      68      81 ..      65      89 .. 0.86
   2 !   12.8   1.5   0.00011      0.13       3      15 ..     123     135 ..     115     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00084
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                       Ci  gsC+++CP+
  gi|518652328|ref|YP_008141848.1| 68 GCIADGSCMDVCPV 81
                                      588889*******7 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                            Fer4_4   3 rCigCgsCvaaCP 15 
                                        Ci C++Cv aCP
  gi|518652328|ref|YP_008141848.1| 123 ECIFCMACVTACP 135
                                       5999********9 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.1   0.00036      0.43      42      60 ..      65      83 ..      34      84 .. 0.83
   2 !   15.1   7.1   2.2e-05     0.026       2      58 ..      69     136 ..      68     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00036
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                       ++ Ci  g C  +CP +l
  gi|518652328|ref|YP_008141848.1| 65 DWDGCIADGSCMDVCPVDL 83
                                      6899************887 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.2e-05
                           Fer4_17   2 CiqCgyClpeCps..yea........ydnepkkllraaklglleeaekee.kaslCieCgeCerkCPq 58 
                                       Ci  g C+++Cp   +e+        ++n++k      ++++ ++ + ++ + s+Ci C  C+++CP 
  gi|518652328|ref|YP_008141848.1|  69 CIADGSCMDVCPVdlFEWklnpgnsgTGNDKKVEKGTPEWEKYRTDKSNPvRESECIFCMACVTACPW 136
                                       888899******754444444443333333333333334456666555555789*************5 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.6   6.7e+03      24      30 ..      29      35 ..      13      49 .. 0.60
   2 !   14.2   0.1   4.6e-05     0.055       1      19 [.      62      80 ..      62     110 .. 0.86
   3 !    8.4   1.5    0.0031       3.7       6      19 ..     122     135 ..     119     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.6
                           Fer4_15 24 ldedgla 30
                                       +edgl+
  gi|518652328|ref|YP_008141848.1| 29 GEEDGLK 35
                                      3445555 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.6e-05
                           Fer4_15  1 VvvDrdaCigcglCvaeap 19
                                      V vD+d Ci +g C++++p
  gi|518652328|ref|YP_008141848.1| 62 VAVDWDGCIADGSCMDVCP 80
                                      89****************7 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0031
                           Fer4_15   6 daCigcglCvaeap 19 
                                       ++Ci c +Cv+++p
  gi|518652328|ref|YP_008141848.1| 122 SECIFCMACVTACP 135
                                       68***********8 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.7     0.001       1.2       6      21 ..      65      80 ..      62      81 .. 0.73
   2 !   11.4   3.4   0.00022      0.26       8      21 ..     123     135 ..     117     136 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.001
                            Fer4_2  6 dtdrCigCgaCvsaCP 21
                                      d d Ci+ g+C ++CP
  gi|518652328|ref|YP_008141848.1| 65 DWDGCIADGSCMDVCP 80
                                      556666559******* PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00022
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       + Ci C aCv+aCP
  gi|518652328|ref|YP_008141848.1| 123 E-CIFCMACVTACP 135
                                       4.888********* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1032.49
//
Query:       gi|518652329|ref|YP_008141849.1|  [L=335]
Description: hypothetical protein FACI_IFERC00001G0968 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-20   73.6   0.0    2.9e-20   73.0   0.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    5.3e-13   49.4   1.0    9.5e-13   48.6   1.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.0   3.2e-24   2.9e-20       2     152 ..     164     323 ..     163     325 .. 0.84

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 3.2e-24
                                       TTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT......TSEHHHHHHHHHHHHHHHHHHHH.HTTECEEEE--TTH CS
                            AIRS_C   2 pGdvliltgslGlggagtslkrkileeegldds......avqlgdvlleptliyvkralaal.kglvkaahDvTgGG 71 
                                       +Gd+++ ++s+Gl+++g+  +rki+++++ d++      ++ ++dvllept+iyv + l a+   ++k+++ +TgGG
  gi|518652329|ref|YP_008141849.1| 164 DGDLIFALKSSGLHSNGFTTVRKIIKDNEIDYEdqfpgdSKRVADVLLEPTRIYVREVLDAMsIVPIKGMANITGGG 240
                                       6*****************************999*****6666*********************************88 PP

                                       HHHHHHHHHHTTTEEEEEECG....THHHHHHHH...HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEE CS
                            AIRS_C  72 Llgalaemapasgvgaeidld....kvpifdele...splemllsensGrllvavppeea.davlaileeeglpeaa 140
                                       +  ++a+m +    + +id +    +v ++   +   s +em+ ++n+G ++++v  +e+   +l+i++ + +p ++
  gi|518652329|ref|YP_008141849.1| 241 I-KNIARMKD---MKYVIDNPfdvdNVFLRLMDMgnlSFSEMFEIFNMGMGYIVVIDPESkTDFLNIVRNR-VP-VK 311
                                       5.78999955...45777777766633333333367999**********876666555555********76.76.** PP

                                       EEEEEEESSSEE CS
                            AIRS_C 141 vIGevtakeels 152
                                       ++G+v+++ + +
  gi|518652329|ref|YP_008141849.1| 312 EVGHVENGSGIT 323
                                       ******998765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   1.0   1.1e-16   9.5e-13       4      94 .]      48     151 ..      43     151 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.1e-16
                                       EEEEEEEEEE.EECC....TCCCCHHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT- CS
                              AIRS   4 avvvttdshnrpvlv....epvhfiGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgv 71 
                                       av +  d++++++++    +++++iG  +va+n++D +++GA+P+a+l++l+l+     +++++  g++ +a+ ++ 
  gi|518652329|ref|YP_008141849.1|  48 AVSFNNDGVGTKTIIaaetNKYNTIGIDCVAMNVNDAITVGAEPIAMLDYLSLKemdneIARQLGIGFNVGAQIANL 124
                                       566777888888888665566777**********************************99999************** PP

                                       EEEEEEEEEESS....EEEEEEEEEEE CS
                              AIRS  72 plvgGdtsfsne....ptisvtavGlv 94 
                                       ++vgG+t+  ++    + is+ta+Gl+
  gi|518652329|ref|YP_008141849.1| 125 NIVGGETAIVPDlvknIDISATALGLI 151
                                       ********99888999*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2651.70
//
Query:       gi|518652330|ref|YP_008141850.1|  [L=117]
Description: hypothetical protein FACI_IFERC00001G0969 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.15   12.4   0.0       0.21   11.9   0.0    1.2  1  Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor


Domain annotation for each model (and alignments):
>> Nitro_FeMo-Co  Dinitrogenase iron-molybdenum cofactor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   1.2e-05      0.21      17      94 ..      22      99 ..      21     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.2e-05
                                      EEEESSSCEEEEEEEE.GCCCTSSCSSTHHHHHHHH.TT-SEEEESSSCHHHHHHHCTTTSEEEES-SSBHHHHHHHHH CS
                     Nitro_FeMo-Co 17 iyeveegevkivenrveeaadaegggggklaqllae.egvdvvivgkiGpralakleaagievykgaggtveealkevl 94
                                      i+ ++++++ki e +++ + +++gg++ ++a +l+   ++ vv  ++  p++++    + ++ ++++++++++++k ++
  gi|518652330|ref|YP_008141850.1| 22 IFLIDDETKKIEEYENPGFGRTHGGREVAMAGILSLkPDMFVVTENSLCPGSYNMSLGK-VKYVVTEEKPISDVIKNLK 99
                                      6778888888888888899999**************99*****99******99988888.999999*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 855.93
//
Query:       gi|518652331|ref|YP_008141851.1|  [L=112]
Description: DNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-18   66.0   0.1    2.9e-18   65.7   0.1    1.2  1  CMD           Carboxymuconolactone decarboxylase family
  ------ inclusion threshold ------
      0.041   14.0   0.0       0.05   13.7   0.0    1.2  1  Carmo_coat_C  Carmovirus coat protein


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 !   65.7   0.1   3.3e-22   2.9e-18       2      78 ..      23      98 ..      22     105 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 3.3e-22
                                      HHHHHHHHHHHHHCCGSSTS-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSHHHHHH CS
                               CMD  2 ellraltalreallareggLdpkereLialavsaangceyCvdaHtraAleaGvteeeiaevlaqaaayagwpaara 78
                                      e++ a++ l+++++   g L+ k++eLiala s+a +ce+C+++H++ A+eaG+t+ e++e+  + + + g+ a++ 
  gi|518652331|ref|YP_008141851.1| 23 EYMGAFMGLMQNTMR-AGTLSVKQKELIALALSIAARCEWCISYHVKSAIEAGATKKELMETGYVVVLMYGSQAMME 98
                                      7899**********7.9***************************************************999999875 PP

>> Carmo_coat_C  Carmovirus coat protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.5e-06      0.05      22      66 ..      50      96 ..      34     110 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.5e-06
                                      EEEEEE-SSEEEEEE..EE-SSSSSB---EEESTTEEEEEEEETTTT CS
                      Carmo_coat_C 22 elqlrvvaagkwcii..vrgtveggftkptligpgisgdvdyesarp 66
                                       l l + a  +wci   v+ ++e g tk  l+  g    + y s   
  gi|518652331|ref|YP_008141851.1| 50 ALALSIAARCEWCISyhVKSAIEAGATKKELMETGYVVVLMYGSQAM 96
                                      467899999****954499*************999888887777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       655  (0.036533); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.28s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 804.94
//
Query:       gi|518652332|ref|YP_008141852.1|  [L=204]
Description: hypothetical protein FACI_IFERC00001G0971 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.1e-36  125.4   0.0    1.5e-36  125.0   0.0    1.2  1  AhpC-TSA    AhpC/TSA family
    2.2e-14   53.4   0.0    2.8e-14   53.0   0.0    1.1  1  Redoxin     Redoxin
    6.3e-09   35.5   0.1    1.1e-08   34.8   0.1    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
  ------ inclusion threshold ------
      0.083   12.8   0.0       0.13   12.1   0.0    1.4  1  SCO1-SenC   SCO1/SenC
        0.1   12.9   0.1        0.2   12.0   0.1    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 !  125.0   0.0   4.2e-40   1.5e-36       2     123 ..       6     132 ..       5     133 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.0 bits;  conditional E-value: 4.2e-40
                                       TSB----EEESTTCEEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHH CS
                          AhpC-TSA   2 gdkapdfelknadgetvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfie 78 
                                       g+kap f +++++ ++ sl+dykg++v+lf +p+d++pvCtte  a+a++y+efk+ + e+ig+svds +sh ++++
  gi|518652332|ref|YP_008141852.1|   6 GQKAPGFLVNTTK-GPLSLEDYKGNWVILFSHPADFTPVCTTEFMAFARRYDEFKKINTELIGLSVDSIYSHIEWMK 81 
                                       9********9887.9************************************************************** PP

                                       H-H.......SSEEEE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
                          AhpC-TSA  79 kes......lnfpllsDeegkvakaygvlkeekglalratfvidkegkiry 123
                                        ++      ++fp+++D +++va++y++++e++g ++r++f+id+++++r 
  gi|518652332|ref|YP_008141852.1|  82 NIKekfgieIPFPVIADINKDVAREYNMMDEKTGSTVRGVFIIDPNMIVRL 132
                                       *************************************************95 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   7.9e-18   2.8e-14       3     138 ..       6     141 ..       5     151 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 7.9e-18
                                       TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH.... CS
                           Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf.... 75 
                                       g+kaP f    ++t   ++sl+++kg+ v++++ p+ f+P+C++e  +++  ++++k+ + + +++++d+       
  gi|518652332|ref|YP_008141852.1|   6 GQKAPGFL---VNTTKGPLSLEDYKGNWVILFSHPADFTPVCTTEFMAFARRYDEFKKINTELIGLSVDSIYShiew 79 
                                       78888877...779999******************************777777777**********99999885554 PP

                                       HHHHHHH..TT-TSEEEE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
                           Redoxin  76 vkefwgk..eglkfpvlsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                                       +k+  +k   +++fpv++D +++++++++  ++ d ++g   + +++id +  v+ +++ p +++
  gi|518652332|ref|YP_008141852.1|  80 MKNIKEKfgIEIPFPVIADINKDVAREYN--MM-DEKTGSTVRGVFIIDPNMIVRLMIYYPAETG 141
                                       5555555885569999*************..55.444455899******9999999998888743 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 !   34.8   0.1   2.9e-12   1.1e-08       1      40 []     153     192 ..     153     192 .. 0.97

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 2.9e-12
                                       HHHHHHHHT-BB-TTT.TBT-EEE---SSHHHHHHHHHHT CS
                        1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateedavkryleg 40 
                                       ALQ+ +  + a P+nW+pG + iv++p t ++a+ r ++g
  gi|518652332|ref|YP_008141852.1| 153 ALQMNWDRKLAAPVNWQPGNDGIVSAPGTLDEAINREKNG 192
                                       9***********************************9886 PP

>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.7e-05      0.13       6      86 ..      13      91 ..      10     130 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.7e-05
                         SCO1-SenC  6 lvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdp 84
                                      lv+++  + + ed++g+++++f   +  + vC+t+    a+ +d++++   + +++  +vD  +   e +k+  e+f+ 
  gi|518652332|ref|YP_008141852.1| 13 LVNTTKGPLSLEDYKGNWVILFSHPADFTPVCTTEFMAFARRYDEFKKI--NTELIGLSVDSIYSHIEWMKNIKEKFGI 89
                                      7899999*************99999999999999999999999999887..8999999***999999999999999987 PP

                         SCO1-SenC 85 ri 86
                                      +i
  gi|518652332|ref|YP_008141852.1| 90 EI 91
                                      65 PP

>> DUF4368  Domain of unknown function (DUF4368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   5.4e-05       0.2      13      63 ..      46      96 ..      43     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.4e-05
                           DUF4368 13 ekFlalvrkytdieeLtpeilnelIekIeVheaekkdgkrtqeieIyYnfv 63
                                      ++F+a +r+y +++++  e++   ++ I+ h +  k+ k++  ieI +  +
  gi|518652332|ref|YP_008141852.1| 46 TEFMAFARRYDEFKKINTELIGLSVDSIYSHIEWMKNIKEKFGIEIPFPVI 96
                                      78**************************99987777777778888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:01.10
# Mc/sec: 560.59
//
Query:       gi|518652333|ref|YP_008141853.1|  [L=79]
Description: hypothetical protein FACI_IFERC00001G0972 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       611  (0.0340789); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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 0.29s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 524.33
//
Query:       gi|518652334|ref|YP_008141854.1|  [L=276]
Description: hypothetical protein FACI_IFERC00001G0973 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-94  314.4   0.5    5.5e-94  314.2   0.5    1.0  1  ParA           NUBPL iron-transfer P-loop NTPase
    7.8e-16   58.3   0.0    1.1e-15   57.8   0.0    1.2  1  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    4.7e-11   42.9   1.2    2.2e-10   40.7   1.2    1.8  1  AAA_31         AAA domain
    3.9e-07   29.5   2.1    3.9e-06   26.3   0.5    2.5  3  ArsA_ATPase    Anion-transporting ATPase
    1.3e-06   28.0   0.2    2.5e-06   27.0   0.2    1.5  1  MipZ           ATPase MipZ
      1e-05   25.5   2.6    0.00023   21.1   2.6    2.2  1  AAA_26         AAA domain
    0.00072   19.2   0.0     0.0012   18.5   0.0    1.3  1  AAA_25         AAA domain
    0.00081   18.9   2.2     0.0054   16.2   2.2    2.2  1  Fer4_NifH      4Fe-4S iron sulfur cluster binding proteins, N
     0.0031   17.3   0.1     0.0059   16.4   0.1    1.4  1  CLP1_P         mRNA cleavage and polyadenylation factor CLP1 
     0.0033   16.8   0.1     0.0062   15.9   0.1    1.4  1  VirC1          VirC1 protein
     0.0038   17.1   0.0     0.0063   16.4   0.0    1.4  1  APS_kinase     Adenylylsulphate kinase
     0.0043   16.7   0.2      0.013   15.1   0.4    1.6  2  SRP54          SRP54-type protein, GTPase domain
     0.0083   16.0   0.3      0.015   15.2   0.3    1.3  1  RsgA_GTPase    RsgA GTPase
  ------ inclusion threshold ------
       0.02   14.1   0.3      0.032   13.4   0.3    1.2  1  NB-ARC         NB-ARC domain
      0.047   12.7   0.1      0.083   11.9   0.1    1.3  1  MeaB           Methylmalonyl Co-A mutase-associated GTPase Me
      0.064   13.2   0.1       0.16   12.0   0.1    1.6  1  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
      0.071   12.8   0.1       0.29   10.9   0.1    1.8  2  IstB_IS21      IstB-like ATP binding protein
      0.092   13.1   0.0       0.17   12.3   0.0    1.4  1  RNA_helicase   RNA helicase
       0.15   12.0   0.6       0.24   11.3   0.6    1.2  1  NACHT          NACHT domain
       0.15   12.2   0.0       0.21   11.8   0.0    1.3  1  AAA_33         AAA domain
       0.17   12.2   0.1        0.3   11.3   0.1    1.5  1  AAA_22         AAA domain
       0.21   11.0   0.0        0.3   10.5   0.0    1.2  1  KTI12          Chromatin associated protein KTI12
       0.28   10.6   0.8       0.58    9.6   0.8    1.4  1  PhoH           PhoH-like protein


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 !  314.2   0.5     7e-97   5.5e-94       1     244 [.      25     269 ..      25     271 .. 0.95

  Alignments for each domain:
  == domain 1  score: 314.2 bits;  conditional E-value: 7e-97
                              ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqs.ekkliPvea.kgikv 75 
                                       +vk++i+v+SgKGGVGKStva+nlA++La+k +kvgllDaDi Gp+ p++lgvee+k+  + e k+ P ++ +++ v
  gi|518652334|ref|YP_008141854.1|  25 NVKHTIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGPDDPKMLGVEEAKAFGNeEGKIEPAKTkYNVDV 101
                                       69*****************************************************988777466799**9989**** PP

                              ParA  76 mSigfllesedeavvwrGpmkskaikqllkdvewgelDyLiiDlPPGtgDeqltvaqkl.plagaviVttpqevala 151
                                       +S+++ l+++d++vvwrG++ +ka++q+l+d++w + D+L+iDlPPGtgDe l+++q + + +g+viV tpqeval 
  gi|518652334|ref|YP_008141854.1| 102 ISMEMALPTHDTPVVWRGAIRHKAVQQFLEDTSWTDKDLLVIDLPPGTGDEPLSICQLIpDADGIVIVITPQEVALL 178
                                       ***********************************************************8789************** PP

                              ParA 152 dvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggeklaeelgvpllgeipldpeireasdegkplvlk 228
                                       d+kkai++++kv++++lG++eNmsgfvcp+cg++t+if+kgg+e++a+e+++p+lg+ip+ pei++ sd+g p+v++
  gi|518652334|ref|YP_008141854.1| 179 DAKKAINFARKVNMPILGIIENMSGFVCPHCGQETDIFKKGGTEQIAKEYNIPYLGNIPIMPEIVQDSDSGIPAVAN 255
                                       *************************************************************************9977 PP

                              ParA 229 epeseaakaleeiaek 244
                                       +  + ++k ++ +a++
  gi|518652334|ref|YP_008141854.1| 256 N--DYIKKFFDVVADN 269
                                       5..5677777776666 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 !   57.8   0.0   1.4e-18   1.1e-15       1     126 [.      30     250 ..      30     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.4e-18
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH....................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep....................... 54 
                                       i+++s+kGGvGK+t+a+nLa+ la++ ++V l+DaD  ++ +    g+e+ ++                        
  gi|518652334|ref|YP_008141854.1|  30 IMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGPDDPKMLGVEEAKAFgneegkiepaktkynvdvismem 106
                                       89*****************************************75555555555888888889************** PP

                                       ........................................................................CCHCC CS
                                       ........................................................................xxxxx RF
                              CbiA  55 ........................................................................dlkrl 59 
                                                                                                               d+k+ 
  gi|518652334|ref|YP_008141854.1| 107 alpthdtpvvwrgairhkavqqfledtswtdkdllvidlppgtgdeplsicqlipdadgivivitpqevallDAKKA 183
                                       ***************************************************************************** PP

                                       CHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE--CCHCCCCHHTS CS
                                       xxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  60 lellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprdeavaeaparge 126
                                       +++++++  +   l    ++ g+v    + e ++   k + e++ ++y++p lg ip   ++++   +g 
  gi|518652334|ref|YP_008141854.1| 184 INFARKVNMP--ILgiiENMSGFVCPHCGQE-TDIFKKGGTEQIAKEYNIPYLGNIPIMPEIVQDSDSGI 250
                                       ****999977..4567889999999998877.6777777888888899******9998888877776665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   1.2   2.8e-13   2.2e-10       3     168 ..      29     191 ..      27     199 .. 0.79

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.8e-13
                            AAA_31   3 vIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyevlieeknikeaiiktkv 78 
                                       +I ++  KGGvGK+T ++nla++la++  kv l D+D  +      lg+e+ +         +ee +i+ a +    
  gi|518652334|ref|YP_008141854.1|  29 TIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGPDDPkMLGVEEAK------AFGNEEGKIEPAKT---K 96 
                                       7999*********************************9886554144543322......22246677777666...5 PP

                            AAA_31  79 enldlipssidLaeaeielvelekk.eeilkellekvk.deYDyiiiDcpPsLg...lltenaLvasdsviipvqae 150
                                        n+d+i  ++ L   ++ +v      +++++++le+ +  + D+ +iD pP  g   l   + +  +d ++i++ ++
  gi|518652334|ref|YP_008141854.1|  97 YNVDVISMEMALPTHDTPVVWRGAIrHKAVQQFLEDTSwTDKDLLVIDLPPGTGdepLSICQLIPDADGIVIVITPQ 173
                                       789*************99886665426667999988763679*********998443344455568*********** PP

                            AAA_31 151 ayaleGleqllktieevk 168
                                       + al  +++ +++ ++v+
  gi|518652334|ref|YP_008141854.1| 174 EVALLDAKKAINFARKVN 191
                                       ****99999999988876 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.5   5.1e-09   3.9e-06       2      38 ..      29      65 ..      28      69 .. 0.89
   2 ?    1.5   0.1      0.17   1.3e+02     206     243 ..     163     200 ..      71     202 .. 0.83
   3 ?    2.0   0.0      0.12        94     206     244 ..     163     201 ..     152     243 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 5.1e-09
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
                       ArsA_ATPase  2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38
                                      ++++++GKGGVGK+tv++ +av l++k  kv l+  D
  gi|518652334|ref|YP_008141854.1| 29 TIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDAD 65
                                      6889***********************9998777655 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.17
                                       TEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEE CS
                       ArsA_ATPase 206 rtsfrlVvipEklslkEteRaikeLkkygikvdavivN 243
                                          +++V++p +++l + ++ai+   k+++ +  +i N
  gi|518652334|ref|YP_008141854.1| 163 ADGIVIVITPQEVALLDAKKAINFARKVNMPILGIIEN 200
                                       34578888888888888888888888888887777765 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.12
                                       TEEEEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE CS
                       ArsA_ATPase 206 rtsfrlVvipEklslkEteRaikeLkkygikvdavivNk 244
                                          +++V++p +++l + ++ai+   k+++ +  +i N 
  gi|518652334|ref|YP_008141854.1| 163 ADGIVIVITPQEVALLDAKKAINFARKVNMPILGIIENM 201
                                       45699*************************999999885 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2   3.2e-09   2.5e-06       1     108 [.      28     146 ..      28     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.2e-09
                                       EEEEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HH........HHHHHHHHHHHH..HHT----.--E CS
                              MipZ   1 hvivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtl........arylenraatae..rkglsLp.lpe 66 
                                       h i++   kGG Gkst+a  +av+L++k ++v+ +d d+             a+ ++n     e  +++ +++ +++
  gi|518652334|ref|YP_008141854.1|  28 HTIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGPDDpkmlgveeAKAFGNEEGKIEpaKTKYNVDvISM 104
                                       78999999*****************************9875443000111113444444433331122223321233 PP

                                       EE-SSS-HHHHTTS-HHHHHHHHHHHHHHHH.HH-SEEEEE-- CS
                              MipZ  67 alalseaeeaeveeeeeaevaeleelvadle.aeldfividtP 108
                                        +al++ ++  v +++  + +++++ ++d++ ++ d++vid P
  gi|518652334|ref|YP_008141854.1| 105 EMALPTHDTPVVWRGAIRH-KAVQQFLEDTSwTDKDLLVIDLP 146
                                       4556666665555555444.55666655554256788888865 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   2.6   2.9e-07   0.00023       1     195 [.      28     243 ..      28     246 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.9e-07
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie...............ededselikellgldq.ty 61 
                                       +ti+v +   gvGK++v++ L+  l +k +kvg +   ++g                 e++++e +k+ +++d  ++
  gi|518652334|ref|YP_008141854.1|  28 HTIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGPDdpkmlgveeakafgnEEGKIEPAKTKYNVDViSM 104
                                       69********************************9998888875666666666666555556666666555554234 PP

                            AAA_26  62 elpeplalsaplspelaarqegedidlekivkelekdadivvVEGagglgvpiteellnadiaknlgapvilVargg 138
                                       e + p+  ++p+  + a r++ +++ le   ++ + d+d++v++   g+g+  +   ++ +++   +  +++V++++
  gi|518652334|ref|YP_008141854.1| 105 EMALPT-HDTPVVWRGAIRHKAVQQFLE---DTSWTDKDLLVIDLPPGTGDEPL---SICQLIPDAD-GIVIVITPQ 173
                                       433333.344544445555555444455...559**********9999996554...4566666666.7999***** PP

                            AAA_26 139 lgtinqllltiealrqknvrvlGvilNk....vrnp....e.......nvetlekksgipvlGvvPylpdle 195
                                       + ++ ++  +i+++r+ n ++lG+i N     +  p    e         e++ k  +ip lG +P  p++ 
  gi|518652334|ref|YP_008141854.1| 174 EVALLDAKKAINFARKVNMPILGIIENMsgfvC--PhcgqEtdifkkgGTEQIAKEYNIPYLGNIPIMPEIV 243
                                       *************************99855432..23444145555667788888888********998875 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.5e-06    0.0012      19      60 ..      10      55 ..       4      68 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.5e-06
                            AAA_25 19 ppprrwlvkg....llpagelallaGapgtGKttlaldlalavatG 60
                                      pppr  l +g    + +++++ +  G +g+GK+t+a++la+++a+ 
  gi|518652334|ref|YP_008141854.1| 10 PPPRPSLTPGksvkYNVKHTIMVMSGKGGVGKSTVATNLAVTLAQK 55
                                      5666666666555555689999********************9974 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.2   6.9e-06    0.0054       4      37 ..      32      65 ..      29     276 .] 0.62

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.9e-06
                         Fer4_NifH  4 aiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37
                                       + GkGG+Gkst ++nl+ +la++  kv ++  D
  gi|518652334|ref|YP_008141854.1| 32 VMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDAD 65
                                      678********************99998776665 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   0.1   7.6e-06    0.0059       1      33 [.      35      67 ..      35      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 7.6e-06
                            CLP1_P  1 GpkdsGKSTlarlLlNyalrkgrkpvyvDlDvG 33
                                      G+  +GKST+a++L+ ++++k  k+ ++D+D++
  gi|518652334|ref|YP_008141854.1| 35 GKGGVGKSTVATNLAVTLAQKAFKVGLLDADIN 67
                                      66789**************************97 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1     8e-06    0.0062       4      43 ..      30      69 ..      27      83 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8e-06
                             VirC1  4 itfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                                      i + s kGG Gk+t    l  +la++  +v+l++ad n P
  gi|518652334|ref|YP_008141854.1| 30 IMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADINGP 69
                                      667899******************************9988 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   8.1e-06    0.0063       3      40 ..      29      66 ..      27      94 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.1e-06
                                      EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLvekgisvylLdGdn 40
                                      +++ ++G  g GKst+a++l+ +L +k  +v lLd d 
  gi|518652334|ref|YP_008141854.1| 29 TIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADI 66
                                      57789******************************995 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.4   1.7e-05     0.013       2      39 ..      29      66 ..      28      70 .. 0.93
   2 ?   -3.3   0.0       7.5   5.8e+03      38      49 ..     214     225 ..     213     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-05
                                      EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEEST CS
                             SRP54  2 nvillvGlqGaGKTttlaKLaallkkegkkvllvaaDt 39
                                      +++++ G  G+GK t ++ La  l +++ kv l  aD+
  gi|518652334|ref|YP_008141854.1| 29 TIMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDADI 66
                                      578999***************************99996 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.5
                                       STSSTTHHHHHH CS
                             SRP54  38 DtfRaaAveQLk 49 
                                       D+f+ + +eQ++
  gi|518652334|ref|YP_008141854.1| 214 DIFKKGGTEQIA 225
                                       888888888874 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.3   1.9e-05     0.015      92     126 ..      21      55 ..      16      63 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.9e-05
                                       HHHHHCTTSEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  92 elkellkdktsvlvGqSGvGKStLinallpelelk 126
                                       ++k ++k+ ++v+ G+ GvGKSt+  +l+ +l +k
  gi|518652334|ref|YP_008141854.1|  21 SVKYNVKHTIMVMSGKGGVGKSTVATNLAVTLAQK 55 
                                       67788999****************99998877665 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   4.1e-05     0.032      17      41 ..      25      49 ..      20      59 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-05
                                      TSCSEEEEEEESTTSSHHHHHHHHC CS
                            NB-ARC 17 elqslvvalvGmgGvGKttlakqil 41
                                      +++  ++ ++G+gGvGK+t+a++  
  gi|518652334|ref|YP_008141854.1| 25 NVKHTIMVMSGKGGVGKSTVATNLA 49
                                      67889****************9865 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   0.00011     0.083      31      66 ..      30      65 ..      21      72 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                      EEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
                              MeaB 31 vvGltGvPGaGkstlvealglelrrrGkrvavlavD 66
                                       + + G  G+Gkst+  +l+++l+++  +v++l  D
  gi|518652334|ref|YP_008141854.1| 30 IMVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDAD 65
                                      5567899************************99877 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   0.00021      0.16      17      28 ..     202     213 ..     201     223 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
                     Zn_Tnp_IS1595  17 ngfvCPhCgsrk 28 
                                       +gfvCPhCg ++
  gi|518652334|ref|YP_008141854.1| 202 SGFVCPHCGQET 213
                                       58*******874 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 ?   10.9   0.1   0.00037      0.29      43      78 ..      24      59 ..      18      65 .. 0.85
   2 ?   -1.2   0.0       1.8   1.4e+03      32      60 ..     123     151 ..     106     157 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
                         IstB_IS21 43 fiekkenivllGpsGvGKshlaialgveavraglsv 78
                                      +  k+  +v+ G  GvGKs +a+ l+v  +++ ++v
  gi|518652334|ref|YP_008141854.1| 24 YNVKHTIMVMSGKGGVGKSTVATNLAVTLAQKAFKV 59
                                      556788899**************9999999988887 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.8
                         IstB_IS21  32 krkvk.eLatlsfiekkenivllGpsGvGK 60 
                                       +++v+  L  +s+++ k+ +v+  p+G+G 
  gi|518652334|ref|YP_008141854.1| 123 HKAVQqFLEDTSWTD-KDLLVIDLPPGTGD 151
                                       455662456677766.56778888999996 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00022      0.17       2      26 ..      32      56 ..      31      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00022
                      RNA_helicase  2 wlyGpsgeGKStlakeLakallkkl 26
                                      +++G+ g+GKSt+a++La +l++k 
  gi|518652334|ref|YP_008141854.1| 32 VMSGKGGVGKSTVATNLAVTLAQKA 56
                                      789****************999765 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6    0.0003      0.24       3      28 ..      31      56 ..      29      61 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0003
                                      EEEEC-TTTCHHHHHHHHHHHHCTS- CS
                             NACHT  3 vilqGeaGsGKTtLlqklalawaegk 28
                                      +++ G+ G+GK+t +  la+++a++ 
  gi|518652334|ref|YP_008141854.1| 31 MVMSGKGGVGKSTVATNLAVTLAQKA 56
                                      8999*******************975 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00026      0.21       2      31 ..      31      65 ..      30     138 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                            AAA_33  2 vllvGlpGsGKstlaerllkklg.....avllssd 31
                                      +++ G  G+GKst+a++l+  l+     + ll+ d
  gi|518652334|ref|YP_008141854.1| 31 MVMSGKGGVGKSTVATNLAVTLAqkafkVGLLDAD 65
                                      6899**************75554444444455555 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   0.00039       0.3       5      54 ..      28      73 ..      24     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00039
                            AAA_22  5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstssk 54
                                      ++i+v  G  G+GK+t++ +l+ +l + a+    +++++  +++++ ++k
  gi|518652334|ref|YP_008141854.1| 28 HTIMVMSGKGGVGKSTVATNLAVTLAQKAF----KVGLLDADINGPDDPK 73
                                      6799999***************99976554....4444444444444444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00038       0.3       4      38 ..      31      65 ..      29      92 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00038
                                      EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-TH CS
                             KTI12  4 vvltGlPssGKstrakeLakaleeekrsvvvidde 38
                                      +v++G   +GKst+a +La +l+++  +v ++d +
  gi|518652334|ref|YP_008141854.1| 31 MVMSGKGGVGKSTVATNLAVTLAQKAFKVGLLDAD 65
                                      6999*********************9999988866 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.8   0.00074      0.58      18      46 ..      27      55 ..      19      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00074
                                      H-SEEEEE--TTSSTTHHHHHHHHHHHHT CS
                              PhoH 18 kndivfaiGpaGtGKtylavalavealkk 46
                                      k++i+++ G+ G GK+ +a+ lav++ +k
  gi|518652334|ref|YP_008141854.1| 27 KHTIMVMSGKGGVGKSTVATNLAVTLAQK 55
                                      899*********************98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                       127  (0.0070835); 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 0.28s 00:00:00.80 Elapsed: 00:00:00.43
# Mc/sec: 1929.63
//
Query:       gi|518652335|ref|YP_008141855.1|  [L=298]
Description: ribokinase [Ferroplasma acidarmanus fer1]
Scores for 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-52  178.4   0.0    2.2e-52  178.3   0.0    1.0  1  PfkB          pfkB family carbohydrate kinase
    4.7e-08   32.7   0.0    8.5e-08   31.9   0.0    1.4  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
     0.0019   17.7   0.0     0.0027   17.2   0.0    1.1  1  Carb_kinase   Carbohydrate kinase


Domain annotation for each model (and alignments):
>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.3   0.0   3.7e-56   2.2e-52       2     299 ..       2     285 ..       1     288 [. 0.92

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 3.7e-56
                                       EEEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHTT CS
                              PfkB   2 tkvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkkeg 76 
                                       + + v+G++++d+i  s +l   ge++++ ++ +++GG+gaN+Av +ar g++ ++ig++G+D f+e++ ++l+ke+
  gi|518652335|ref|YP_008141855.1|   2 QGIKVVGSINMDIIMSSARLpeTGETIKADKYYMYPGGKGANQAVSVARTGVKPQLIGKIGNDYFAEMITNYLRKEN 78 
                                       56789****************99999*************************************************** PP

                                       EEETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHHH CS
                              PfkB  77 vdtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleelae 153
                                       +d   +   +d +tg+a+i v++ g++ i++++g + +++ +       ++++ +l      +++e+p ++ +  ++
  gi|518652335|ref|YP_008141855.1|  79 LDL--CLTYGD-KTGIAMINVESSGKNMITVYPGSNGNMSYD-------DFHNIELKNSIVMFQQEIPLKTIRDFIS 145
                                       *99..664455.**********99*****************6.......6677666666667889************ PP

                                       HHHHTTEEEEEECESSSHHHHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGG CS
                              PfkB 154 aaknggtfdpnlldplgaqfkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGke 230
                                         +++g   + + dp++    ++   +l+ + +l+pne+E++ ++g ++++ie+a +a   +  k++++v+++lG++
  gi|518652335|ref|YP_008141855.1| 146 SNRENG--NLFITDPSP---FSEDNYILENSGILTPNETEAQLIAGCAINSIEDAEKASTLISGKYKNNVIIKLGSR 217
                                       ******..9999*****...45677888******************************998889999********** PP

                                       EEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTSSSSSTCS CS
                              PfkB 231 GalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqkkgaiasl 299
                                       G++   +++  ++++ + vk vDttGAGD+f+g+f++ +l+  ++ ++ +fan +Aal+++ +ga  s 
  gi|518652335|ref|YP_008141855.1| 218 GSISNFEGEIKYHKP-YNVKTVDTTGAGDCFNGAFASEFLRTGDVDKSMEFANIAAALSTTGYGAFPSF 285
                                       **9995555555555.99*********************************************997665 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   1.4e-11   8.5e-08     113     224 ..     164     268 ..     136     276 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 1.4e-11
                                       HHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE CS
                      Phos_pyr_kin 113 keeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveeleae 189
                                        + +l+ + ++tPN  Ea+ ++g  i++ ed+++a + ++   +++V+ik g   g+ ++       ++e++  +  
  gi|518652335|ref|YP_008141855.1| 164 DNYILENSGILTPNETEAQLIAGCAINSIEDAEKASTLISGKYKNNVIIKLGSR-GSISN------FEGEIKYHKPY 233
                                       567889999*****************************************9983.32222......46677777778 PP

                                       ----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHH CS
                      Phos_pyr_kin 190 rietknthGtGCtlssaiaaelakgesleeAvkkA 224
                                        ++t +t G+G+ +  a a+e  +  ++ ++++ A
  gi|518652335|ref|YP_008141855.1| 234 NVKTVDTTGAGDCFNGAFASEFLRTGDVDKSMEFA 268
                                       8999********************99999999877 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.5e-07    0.0027     117     199 ..     169     253 ..     156     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.5e-07
                                       TSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHT.TEEEEESTTSEEEECTTEEEEE----GG.G-STTHHH CS
                       Carb_kinase 117 kaeviLTPhkkEfkrLlkaivkkeddrlelarelaqkln.avvllkgekdvivspegevlinstgssa.lakGGsGD 191
                                       ++  iLTP+  E + ++++++++ +d  ++   ++ k++  v++  g+   i + ege++  +  ++    + G GD
  gi|518652335|ref|YP_008141855.1| 169 ENSGILTPNETEAQLIAGCAINSIEDAEKASTLISGKYKnNVIIKLGSRGSISNFEGEIKYHKPYNVKtVDTTGAGD 245
                                       5667*****************9999999999999999962577777999999999****98887776516799**** PP

                                       HHHHHHHH CS
                       Carb_kinase 192 vLaGliga 199
                                          G+ ++
  gi|518652335|ref|YP_008141855.1| 246 CFNGAFAS 253
                                       ***99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.38
# Mc/sec: 2343.69
//
Query:       gi|518652336|ref|YP_008141856.1|  [L=141]
Description: asymmetrical bis(5''''-nucleosyl)-tetraphosphatase [Ferroplasma acidarmanus fer1]
Scores for complete 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   76.4   0.1    2.9e-21   76.0   0.1    1.2  1  HIT       HIT domain
    3.9e-09   37.0   0.2    5.2e-09   36.6   0.2    1.2  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
    3.5e-06   26.9   0.3    7.8e-06   25.8   0.3    1.6  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 !   76.0   0.1   4.9e-25   2.9e-21       7      96 ..      19     108 ..      14     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 76.0 bits;  conditional E-value: 4.9e-25
                                       CEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCCHHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT- CS
                               HIT   7 tvvyeddlvlafldidpkapghlLvipkkhlselhdlteeelakllsavkkvakalqkkfknkglrvvinngahagq 83 
                                        +vy+  ++laf d+ p  +gh+Lvip++h++++ d+++++  +l  avk++  a+++++k++gl++  nng+ a q
  gi|518652336|ref|YP_008141856.1|  19 AFVYRGLNILAFMDNAPIEEGHVLVIPRNHYENIYDIDKDIYLELQLAVKRISIAVKNVLKTDGLNIGQNNGRVANQ 95 
                                       678888899******************************************************************** PP

                                       SSSS-EEEEEEC- CS
                               HIT  84 svahlHiHviprr 96 
                                       +v+h+H+H+ipr+
  gi|518652336|ref|YP_008141856.1|  96 VVMHYHVHIIPRY 108
                                       ***********97 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 !   36.6   0.2   8.7e-13   5.2e-09       2     102 ..       6     107 ..       5     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 8.7e-13
                                       -HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTTHHHHHHHHHHHHHHHTT-T.- CS
                            DcpS_C   2 wvfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlpllkemrekakkvieekyne.v 77 
                                       ++f++ + +k ++++vy+  +++++ D  p ++ h+lvip+++ ++++d++k+ +  l+  ++ +  ++++  ++ +
  gi|518652336|ref|YP_008141856.1|   6 CIFCREIANKGNAAFVYRGLNILAFMDNAPIEEGHVLVIPRNHYENIYDIDKDIYLELQLAVKRISIAVKNVLKTdG 82 
                                       99***999999***************************************999888888888888888877664443 PP

                                       EEEEE--SCCCT--S-S--EEEEE. CS
                            DcpS_C  78 daeelrvgvhyqPsvyhlHlHvisl 102
                                            + g  +++ v h H+H+i  
  gi|518652336|ref|YP_008141856.1|  83 LNIGQNNGRVANQVVMHYHVHIIPR 107
                                       3334567777888999999999864 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 !   25.8   0.3   1.3e-09   7.8e-06      12     108 ..       4     106 ..       1     118 [. 0.75

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.3e-09
                                       HH-S----SS---SS--S-B-SSEEEE---S-SSTT-EEEEESS--SSTTSS-HHHHHHHHHHHH....HHHHHHHH CS
                          CwfJ_C_1  12 dsClfClsnpklekhlivsignkvYlalpkgpLssgHvliipieHisallsldeevldeirkfrk....alvkmykk 84 
                                       ++C fC + ++  ++  v  g ++ + + + p+++gHvl+ip +H ++   +d+++  e++   k    a+ ++ k 
  gi|518652336|ref|YP_008141856.1|   4 ETCIFCREIANKGNAAFVYRGLNILAFMDNAPIEEGHVLVIPRNHYENIYDIDKDIYLELQLAVKrisiAVKNVLKT 80 
                                       79****************************************************88888765444010044444433 PP

                                       TT--EEEEEE-.....SSS-----EEEEE CS
                          CwfJ_C_1  85 qdkdavvfEis.....sersvHlaiqvip 108
                                        + ++     +     ++  +H ++++ip
  gi|518652336|ref|YP_008141856.1|  81 DGLNIGQ---NngrvaNQVVMHYHVHIIP 106
                                       3333322...2224456667777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1098.15
//
Query:       gi|518652337|ref|YP_008141857.1|  [L=193]
Description: orotate phosphoribosyltransferase-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-17   61.5   0.3    1.1e-16   60.7   0.3    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
      7e-05   22.4   0.0    0.00012   21.7   0.0    1.3  1  PRTase_2      Phosphoribosyl transferase
      0.001   18.7   0.0     0.0021   17.7   0.0    1.5  1  Sigma70_r4_2  Sigma-70, region 4
     0.0075   16.0   0.0      0.019   14.7   0.0    1.6  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.013   15.0   0.1      0.038   13.5   0.1    1.7  1  GerE          Bacterial regulatory proteins, luxR family
      0.013   15.0   0.0      0.029   13.9   0.0    1.6  1  HTH_24        Winged helix-turn-helix DNA-binding
      0.019   14.4   0.1      0.025   14.0   0.1    1.3  1  UPRTase       Uracil phosphoribosyltransferase
       0.12   12.9   0.0       0.26   11.8   0.0    1.6  1  HTH_40        Helix-turn-helix domain
       0.19   11.9   0.0       0.39   10.9   0.0    1.5  1  DUF2802       Protein of unknown function (DUF2802)


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 !   60.7   0.3   5.6e-20   1.1e-16      12     129 ..      65     175 ..      58     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 5.6e-20
                                       EEEEEETTEEEEEE..--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----T CS
                      Pribosyltran  12 ldavarlaaeilee..yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpa 86 
                                       ++++a+ +a+i+ e     + + ++gi   G+pfa+ l+d L+ +l + r     ++g+ +          + + ++
  gi|518652337|ref|YP_008141857.1|  65 IEKIAEVMADIVTEeiSMDNVTSIIGITINGIPFATMLSDLLDRELIVYRPHPSGKEGMFSS---------NFAGVK 132
                                       45788888888888766678889********************9999887766655555555.........99**** PP

                                       TSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEEE-HHH CS
                      Pribosyltran  87 gkkVliVDDildtGgTllaalelLkekgpeevriavlvdkpat 129
                                       gkk++i+DD+++tG T+++++e ++++g e+v ++vlv k  +
  gi|518652337|ref|YP_008141857.1| 133 GKKIVIIDDVISTGETMKRTIEDVHNQGGEVVLCVVLVSKLNS 175
                                       **************************************88654 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   5.8e-08   0.00012     121     159 ..     133     171 ..     120     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 5.8e-08
                          PRTase_2 121 akelvLvDDEistGktalnliralqeklprkryvvvslv 159
                                        k++v++DD istG+t+ ++i++++++  +  + vv + 
  gi|518652337|ref|YP_008141857.1| 133 GKKIVIIDDVISTGETMKRTIEDVHNQGGEVVLCVVLVS 171
                                       589**********************99776554444444 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   1.1e-06    0.0021       9      43 ..       2      35 ..       1      41 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.1e-06
                                      TTS-HHHHHHHHHHHTS---HHHHHHHHT--HHHH CS
                      Sigma70_r4_2  9 aeLperqreifllryleglsykEIAellgisegtV 43
                                       +L e + ++++l   +g+s kEI+ +l++s++t+
  gi|518652337|ref|YP_008141857.1|  2 KSLEELYNRALEL-KNKGMSDKEISTELHLSVNTI 35
                                      689**********.58******************8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   9.7e-06     0.019      10      35 ..      11      36 ..      10      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.7e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvy 35
                                      +l l  +G+s +eI++eL+ s +T+ 
  gi|518652337|ref|YP_008141857.1| 11 ALELKNKGMSDKEISTELHLSVNTIT 36
                                      4555556*****************94 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.9e-05     0.038      11      35 ..      12      36 ..      10      41 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.9e-05
                                      HHHHCTTS-HHHHHHHHTS-HHHHH CS
                              GerE 11 LrllaeGksnkeIAeelniSekTVk 35
                                      L+l  +G+s keI+ el++S +T++
  gi|518652337|ref|YP_008141857.1| 12 LELKNKGMSDKEISTELHLSVNTIT 36
                                      667779*****************97 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.5e-05     0.029      14      39 ..      15      40 ..      10      41 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.5e-05
                            HTH_24 14 knprisqreLAerlglSpstvnrrlk 39
                                      kn ++s +e++ +l+lS++t+++ l 
  gi|518652337|ref|YP_008141857.1| 15 KNKGMSDKEISTELHLSVNTITWLLS 40
                                      799*******************9876 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.2e-05     0.025     120     162 ..     132     171 ..      66     181 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.2e-05
                           UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlas 162
                                       + ++++++D vi+TG+++   i+ + ++g    +++++ vl+s
  gi|518652337|ref|YP_008141857.1| 132 KGKKIVIIDDVISTGETMKRTIEDVHNQGG---EVVLCVVLVS 171
                                       66889**********************776...4555555554 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.26       5      64 ..      11      75 ..       8      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
                            HTH_40  5 tlelleeglsieeIAkerglkesTIegHLaelieeg....eeidlerlvse.eeekeIeeaiekv 64
                                      +lel ++g+s +eI++e +l+++TI   L + ++ +     +i ++ +    +++++I+e+++++
  gi|518652337|ref|YP_008141857.1| 11 ALELKNKGMSDKEISTELHLSVNTITWLLSKDLKGNrvsdTKIGWRSVGVYgNRIEKIAEVMADI 75
                                      688999*******************9888887777433335677777754448888888877765 PP

>> DUF2802  Protein of unknown function (DUF2802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0    0.0002      0.39      31      57 ..       6      32 ..       2      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.0002
                           DUF2802 31 klYsqAiklvrqGasveelaeecgLsr 57
                                       lY++A++l ++G+s  e+  e +Ls 
  gi|518652337|ref|YP_008141857.1|  6 ELYNRALELKNKGMSDKEISTELHLSV 32
                                      68***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       677  (0.0377601); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1516.52
//
Query:       gi|518652338|ref|YP_008141858.1|  [L=507]
Description: hypothetical protein FACI_IFERC00001G0977 [Ferroplasma acidarmanus fer1]
Scores for complete 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-118  395.3   0.0   2.7e-118  395.0   0.0    1.1  1  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0099   15.8   1.2       0.02   14.8   1.2    1.4  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
  ------ inclusion threshold ------
      0.013   14.2   0.0        2.9    6.6   0.0    2.6  3  tRNA-synt_1g     tRNA synthetases class I (M)
      0.028   14.3   0.1      0.055   13.3   0.1    1.4  1  DUF3116          Protein of unknown function (DUF3116)
      0.096   12.7   3.4       0.17   11.9   3.4    1.4  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.38   10.7   1.7       0.87    9.5   1.7    1.6  1  eIF-5_eIF-2B     Domain found in IF2B/IF5
        1.2    8.5   4.0        1.4    8.3   0.7    2.1  2  zf-RanBP         Zn-finger in Ran binding protein and others
        4.5    7.0   5.2        1.9    8.2   0.7    2.2  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
        5.9    6.7   6.0        4.5    7.1   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain


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 !  395.0   0.0  1.3e-121  2.7e-118      22     359 ..      12     346 ..       1     347 [. 0.97

  Alignments for each domain:
  == domain 1  score: 395.0 bits;  conditional E-value: 1.3e-121
                      tRNA-synt_1f  22 kdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmDglRkvpenlpekllekylgkpltsiP 98 
                                       ++++++++GispSG+iH+Gn+re+lt+d++++a  +++ e r+i+++Dd+D+lRkv+++l+ + +++y+g+pl+ iP
  gi|518652338|ref|YP_008141858.1|  12 NGTQLISTGISPSGPIHVGNMREILTGDILYKASLDKKLESRFIYLCDDLDPLRKVYPFLDGS-YSQYVGMPLSYIP 87 
                                       46899**********************************************************.************* PP

                      tRNA-synt_1f  99 dpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyrgeereetyspylp 175
                                       +p+g+  +y+++f ++++e+L++++++ve+is+t lY++g ++eai++a+++re+i++i++ + g ++  +++py+p
  gi|518652338|ref|YP_008141858.1|  88 APEGD-GKYSDYFLKPFLETLKKINVNVEVISTTGLYREGKLAEAIDIAMNHREEIAKIMHDVAGYDIGPEWYPYEP 163
                                       ***99.99********************************************************************* PP

                      tRNA-synt_1f 176 vcekcgrvdttevvevdaeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvd 252
                                        c+kcg++++ +v++++  + +  Ykc++cG+e ++dir+ +gK++W+v+w+++W+algV++Ep+GkDhaa+GgS+d
  gi|518652338|ref|YP_008141858.1| 164 RCSKCGKINSSTVTKYE--NPYAYYKCKACGNEDKADIRKDDGKMPWRVEWPAKWYALGVTIEPFGKDHAASGGSYD 238
                                       ****************9..9********************************************************* PP

                      tRNA-synt_1f 253 vsskia.eilggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrl 328
                                       ++++ia +i+++++P++++Ye illkg + m+sS+G+ +t ++++++a+pe+lrfli+r+ P +++++d+++++l+l
  gi|518652338|ref|YP_008141858.1| 239 TGKEIAaKIFKISPPVPLMYERILLKGVGVMHSSTGVAITASEVTTFAPPEILRFLIARNDPGRHIDFDPGMGLLNL 315
                                       ***************************************************************************** PP

                      tRNA-synt_1f 329 vdeYdklerkyfaeqeeeeekekrvyelsav 359
                                       +d+Y+k+er+yf  +e+++e+ kr+ye+s++
  gi|518652338|ref|YP_008141858.1| 316 IDDYEKMERAYFGLDESNNENFKRIYEMSRI 346
                                       ************99999999********986 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.2     1e-05      0.02      30      60 ..     164     199 ..     162     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1e-05
                    OrfB_Zn_ribbon  30 tCseCgsknke.....alsgrtfkCpnCgfeadrDv 60 
                                       +Cs+Cg++n+      ++    +kC++Cg e  +D+
  gi|518652338|ref|YP_008141858.1| 164 RCSKCGKINSStvtkyENPYAYYKCKACGNEDKADI 199
                                       6**********999999999***************8 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0014       2.9      10      42 ..      23      55 ..      15      61 .. 0.77
   2 ?    4.8   0.0    0.0049       9.8     328     360 ..     269     301 ..     256     308 .. 0.87
   3 ?   -3.2   0.0       1.3   2.6e+03      88     124 ..     419     453 ..     394     464 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0014
                                      -SS---HHHHHHHHHHHHHHHHHHHTT-EEEEE CS
                      tRNA-synt_1g 10 angklHlGhllevisaDifaRykrlrgeevlfv 42
                                      ++g++H+G+++e++ +Di+++ +  ++ e  f+
  gi|518652338|ref|YP_008141858.1| 23 PSGPIHVGNMREILTGDILYKASLDKKLESRFI 55
                                      689****************99876666655554 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0049
                                       ----------HHHHHHHH-HHHHHHHHHHHS-T CS
                      tRNA-synt_1g 328 lSkSrgvvvkakealerldadllRYylaaeape 360
                                       + +S gv+++a+e+++  ++++lR+ +a++ p 
  gi|518652338|ref|YP_008141858.1| 269 MHSSTGVAITASEVTTFAPPEILRFLIARNDPG 301
                                       7889***********************999875 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.3
                                       EEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEET CS
                      tRNA-synt_1g  88 ygrttseehkelvqeifkklkekgliyekeieqlycp 124
                                       +  t+  +++++ qe++ kl + +  + +  +++y+ 
  gi|518652338|ref|YP_008141858.1| 419 FLLTD--DQRSILQEFLDKLASAEWTSDSIHTVIYDI 453
                                       33333..344566666666666666666666666665 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   2.8e-05     0.055       9      80 ..     360     429 ..     352     434 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                           DUF3116   9 ilevLelvkdpnftiknlqleeldeksvkkltkneLLytvYWLElkgyilRkeekannkkrYelTekGelly 80 
                                       i+  +++ +d n  + +l+    d+++ +++ kne+  + YWL   +y   + +   + k++ lT++   ++
  gi|518652338|ref|YP_008141858.1| 360 IVTLIQIYRDDNSFFSALKRSGYDKDQIDDYLKNEIVIAKYWLS--KYAPENIKFSLTDKQFLLTDDQRSIL 429
                                       445555559999999***************************95..56666666666666666666655555 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 ?   11.9   3.4   8.7e-05      0.17      16      45 ..     160     193 ..     157     194 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.7e-05
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayrikt....rglfqCkeCrk 45 
                                       p  ++C +Cg+  + ++++      +++Ck+C+ 
  gi|518652338|ref|YP_008141858.1| 160 PYEPRCSKCGKINSSTVTKyenpYAYYKCKACGN 193
                                       55699*****997777777777999*******85 PP

>> eIF-5_eIF-2B  Domain found in IF2B/IF5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   1.7   0.00044      0.87      90     116 ..     165     193 ..     164     194 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00044
                                       TSSSTSTCEEECC..SSSCEEEEESSSTC CS
                      eIF-5_eIF-2B  90 CkeCkspetelek..eerllvlkCkaCga 116
                                       C++C++ + + ++  e+   + kCkaCg+
  gi|518652338|ref|YP_008141858.1| 165 CSKCGKINSSTVTkyENPYAYYKCKACGN 193
                                       *****9887666656899999*******7 PP

>> zf-RanBP  Zn-finger in Ran binding protein and others
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.7   0.00071       1.4       7      20 ..     165     178 ..     164     178 .. 0.93
   2 ?    1.0   0.1      0.14   2.7e+02      20      27 ..     187     194 ..     180     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00071
                                       -SSS--EEESSSSB CS
                          zf-RanBP   7 CskClvqNfawstk 20 
                                       CskC+  N+++ tk
  gi|518652338|ref|YP_008141858.1| 165 CSKCGKINSSTVTK 178
                                       **********9987 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.14
                                       B-TTT--B CS
                          zf-RanBP  20 kCvaCqap 27 
                                       kC aC+++
  gi|518652338|ref|YP_008141858.1| 187 KCKACGNE 194
                                       78888876 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.37   7.4e+02       8      15 ..     164     171 ..     163     173 .. 0.91
   2 ?    8.2   0.7   0.00093       1.9       6      15 ..     185     194 ..     181     196 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.37
                                       E-TTT--E CS
                   Desulfoferrod_N   8 kCevCGni 15 
                                       +C  CG i
  gi|518652338|ref|YP_008141858.1| 164 RCSKCGKI 171
                                       8*****98 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00093
                                       EEE-TTT--E CS
                   Desulfoferrod_N   6 vYkCevCGni 15 
                                        YkC+ CGn+
  gi|518652338|ref|YP_008141858.1| 185 YYKCKACGNE 194
                                       5********6 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.2    0.0023       4.5       1      13 [.     164     176 ..     164     178 .. 0.83
   2 ?    1.6   1.2      0.12   2.5e+02       1       8 [.     187     194 ..     187     196 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0023
                     zinc_ribbon_2   1 fCpnCGaelqdna 13 
                                       +C++CG+ ++ ++
  gi|518652338|ref|YP_008141858.1| 164 RCSKCGKINSSTV 176
                                       6******998776 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                     zinc_ribbon_2   1 fCpnCGae 8  
                                       +C+ CG+e
  gi|518652338|ref|YP_008141858.1| 187 KCKACGNE 194
                                       7*****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3691.92
//
Query:       gi|518652339|ref|YP_008141859.1|  [L=362]
Description: AAA family ATPase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-10   41.1   0.0    4.1e-10   40.1   0.0    1.4  1  AAA_22         AAA domain
    1.1e-07   32.3   0.0    7.6e-07   29.7   0.0    2.0  2  AAA_16         AAA ATPase domain
    0.00043   20.7   0.0     0.0009   19.7   0.0    1.6  1  AAA            ATPase family associated with various cellular
     0.0015   18.5   0.0     0.0034   17.3   0.0    1.7  1  Cdc6_C         CDC6, C terminal winged helix domain
     0.0021   18.1   0.0     0.0048   17.0   0.0    1.5  1  TIP49_C        TIP49 AAA-lid domain
     0.0036   16.5   0.0     0.0072   15.5   0.0    1.6  1  DUF815         Protein of unknown function (DUF815)
  ------ inclusion threshold ------
      0.021   14.2   0.0       0.13   11.6   0.0    2.0  1  TniB           Bacterial TniB protein
      0.023   15.2   0.0      0.046   14.3   0.0    1.5  1  AAA_18         AAA domain
       0.04   13.4   0.0       0.11   12.0   0.0    1.7  2  AAA_7          P-loop containing dynein motor region
      0.043   13.7   0.0      0.078   12.9   0.0    1.5  1  Rad17          Rad17 P-loop domain
       0.05   14.1   0.1       0.32   11.5   0.0    2.3  2  ABC_tran       ABC transporter
       0.07   12.5   0.0       0.14   11.5   0.0    1.4  1  FtsK_SpoIIIE   FtsK/SpoIIIE family
       0.11   12.2   0.4       0.28   10.9   0.1    1.9  2  AAA_24         AAA domain
       0.18   12.1   0.1       0.43   10.9   0.1    1.6  1  CBFD_NFYB_HMF  Histone-like transcription factor (CBF/NF-Y) a
       0.19   11.9   0.0       0.58   10.4   0.0    1.9  2  AAA_lid_6      AAA lid domain
       0.19   11.9   0.0       0.38   10.9   0.0    1.5  1  AAA_33         AAA domain


Domain annotation for each model (and alignments):
>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.0   3.6e-13   4.1e-10       7     105 ..      43     132 ..      41     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 3.6e-13
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseelleale 83 
                                        ++++G sGtGKT +++ l+++          ++++++ ++ s ++ k+ll+++ + lg + ++ +ls +e++++l+
  gi|518652339|ref|YP_008141859.1|  43 NIIIHGDSGTGKTSTVKFLMRE----------NKSIIYENALSFKNVKNLLEHVISRLGKPVSYHGLSYSEIFSMLN 109
                                       589******************9..........79999**************************************** PP

                            AAA_22  84 qalraravielliiDEaqh.lr.s 105
                                         ++ r++  +l+iDEa   l   
  gi|518652339|ref|YP_008141859.1| 110 SIISFRGD-IVLVIDEATGfLKgD 132
                                       ********.********8844342 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0   6.8e-10   7.6e-07       1      49 [.      17      66 ..      17     109 .. 0.75
   2 ?   -0.2   0.0       1.1   1.2e+03     134     164 ..     116     145 ..      94     155 .. 0.76

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 6.8e-10
                            AAA_16  1 rlvGReeeleqLlsale.rvrsgrpelvllsGesGvGKsslvrellrale 49
                                      +l+ R++ +++++sa+  ++  g +++++++G+sG+GK+s v+ l+r+ +
  gi|518652339|ref|YP_008141859.1| 17 KLFFRDDKIAAIRSAVLaPAGNGISNNIIIHGDSGTGKTSTVKFLMRENK 66
                                      6899********8888725555555*****************99997332 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.1
                            AAA_16 134 erplvlvlDdlqwadeaslqllaaLlrlles 164
                                       ++ +vlv+D++  +  ++ + l++L+r++e 
  gi|518652339|ref|YP_008141859.1| 116 GD-IVLVIDEATGFLKGDTAGLYNLFRASEI 145
                                       33.99****9999999998889999998775 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   8.1e-07    0.0009       1      70 [.      44     128 ..      44     154 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 8.1e-07
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTSTSEE CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk................yvgesekkirelfkeakekakpsi 61 
                                       ++++G  GtGKT+++k +++e + +++  ++ ++ +                 y g s ++i  +++++ + ++  +
  gi|518652339|ref|YP_008141859.1|  44 IIIHGDSGTGKTSTVKFLMRENK-SIIYENALSFKNVknllehvisrlgkpvsYHGLSYSEIFSMLNSIISFRGDIV 119
                                       589******************54.2333333333322234444666677788899999999999999976665569* PP

                                       EEEETGGGH CS
                               AAA  62 lfiDEidal 70 
                                       l+iDE+  +
  gi|518652339|ref|YP_008141859.1| 120 LVIDEATGF 128
                                       *****8665 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 !   17.3   0.0     3e-06    0.0034      32      76 ..     302     345 ..     273     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 3e-06
                                       TT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C  32 egvdpltqrevsdllseLemlgileleksskGrregrtrkisLnv 76 
                                       +g+ + + +e+++++++Le+l i+++  +s G r+  ++++s+n 
  gi|518652339|ref|YP_008141859.1| 302 YGI-QYKKTEIYRVIRKLESLDIISSSLKSSGNRSSVSKLVSIND 345
                                       555.6789**********************************975 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   4.3e-06    0.0048      18      63 ..     206     252 ..     194     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.3e-06
                           TIP49_C  18 ldlLakigte.tSLRYaiqLltpasilakkrkkkevevedveeveeL 63 
                                       l ++++i+ +  S R+ai+Ll+ a  +a+ r +k++e +dv+++ +L
  gi|518652339|ref|YP_008141859.1| 206 LGYISEISGKfGSARFAIELLQKAAYMAEYRLSKTIENDDVRSAVSL 252
                                       66666765552589****************************99876 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   6.4e-06    0.0072      50      78 ..      38      66 ..      13     110 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 6.4e-06
                            DUF815 50 glpannvLLwGarGtGKSslvkallneya 78
                                      +  +nn+++ G+ GtGK s+vk+l++e +
  gi|518652339|ref|YP_008141859.1| 38 NGISNNIIIHGDSGTGKTSTVKFLMRENK 66
                                      5568********************98765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00012      0.13      36     135 ..      42     132 ..      25     140 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                              TniB  36 pnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkara.rvskleqqv 111
                                       +n++++Gds +GKt+ v+  +r++            +++ +a +  + k+l ++++ +lg+p++ +  + s++ ++ 
  gi|518652339|ref|YP_008141859.1|  42 NNIIIHGDSGTGKTSTVKFLMREN----------KSIIYENALSFKNVKNLLEHVISRLGKPVSYHGlSYSEIFSML 108
                                       6999***********997555543..........4578888888889999999999999999988764666777777 PP

                              TniB 112 lrllrelkvrvLiiDEihnllags 135
                                        ++++  +  vL+iDE   +l+g 
  gi|518652339|ref|YP_008141859.1| 109 NSIISFRGDIVLVIDEATGFLKGD 132
                                       788888888899999999999886 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   4.1e-05     0.046       1      43 [.      44      80 ..      44      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.1e-05
                            AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdp 43
                                      I++ G +G+GKt+  k L +++      +++++en l++ + +
  gi|518652339|ref|YP_008141859.1| 44 IIIHGDSGTGKTSTVKFLMREN------KSIIYENALSFKNVK 80
                                      99****************9997......555555555554444 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001      0.11      33      65 ..      41      72 ..      26      90 .. 0.80
   2 ?   -3.2   0.0       4.5   5.1e+03     131     166 ..     301     338 ..     298     339 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                             AAA_7 33 kkpvllvGptGtGKtviikdllkkldkekylsl 65
                                      ++++++ G++GtGKt+++k l+++ + + +  +
  gi|518652339|ref|YP_008141859.1| 41 SNNIIIHGDSGTGKTSTVKFLMRENK-SIIYEN 72
                                      57899**************9999877.444444 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.5
                             AAA_7 131 dyggwYdrkkl..efkeikdvqlvaamgppgggrneit 166
                                       +yg  Y+++++   +++++ + ++++  + +g+r++++
  gi|518652339|ref|YP_008141859.1| 301 EYGIQYKKTEIyrVIRKLESLDIISSSLKSSGNRSSVS 338
                                       57777887775446678888888888888888888876 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     7e-05     0.078      25     110 ..      22     106 ..      12     159 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                             Rad17  25 kkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdnqksdfkgltekesr 101
                                         ki +++ ++ a   +   ++ ++i G sG gk+ +vk L +e     + + n++s+k+ +n  + + + + k  +
  gi|518652339|ref|YP_008141859.1|  22 DDKIAAIRSAVLAPAGNGISNN-IIIHGDSGTGKTSTVKFLMRENKS--IIYENALSFKNVKNLLEHVISRLGKPVS 95 
                                       5688888888888877766444.579****************99755..5566889999999977777777766666 PP

                             Rad17 102 f..lsqiesfk 110
                                       +  ls  e f+
  gi|518652339|ref|YP_008141859.1|  96 YhgLSYSEIFS 106
                                       64444444444 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   0.00029      0.32      13      37 ..      43      67 ..      40     109 .. 0.80
   2 ?   -0.8   0.0       1.7     2e+03      79     106 ..     296     332 ..     230     339 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                       + i G++G+GK++ +k l+++ k 
  gi|518652339|ref|YP_008141859.1| 43 NIIIHGDSGTGKTSTVKFLMRENKS 67
                                      6789****************99875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.7
                                       H.........HHHTCHHHHHHHSTTGGTTCBGESTTS CS
                                       x.........xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.........esdeeiekalsklglkelkdtvvkssp 106
                                       +         +++ ei+++++kl+  ++  + +kss+
  gi|518652339|ref|YP_008141859.1| 296 QlqgeeygiqYKKTEIYRVIRKLESLDIISSSLKSSG 332
                                       0223334444677777777777777777776666665 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.14      39      60 ..      35      62 ..       4      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                                      -.......SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE 39 a......shllvaGatgsGKStalntLi 60
                                      +      ++++++G +g+GK+ +++ L+
  gi|518652339|ref|YP_008141859.1| 35 PagngisNNIIIHGDSGTGKTSTVKFLM 62
                                      15556669****************9987 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00025      0.28       3      23 ..      42      63 ..      40     134 .. 0.79
   2 ?   -2.9   0.0       4.3   4.8e+03     103     121 ..     303     321 ..     290     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                            AAA_24  3 lkiliyGpsgiGKTtlakel.g 23
                                      ++i+i G+sg+GKT+++k l  
  gi|518652339|ref|YP_008141859.1| 42 NNIIIHGDSGTGKTSTVKFLmR 63
                                      689*************997753 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.3
                            AAA_24 103 Gygelaeefrrllkklqel 121
                                       G ++ ++e+ r+++kl++l
  gi|518652339|ref|YP_008141859.1| 303 GIQYKKTEIYRVIRKLESL 321
                                       7788999999999999987 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 ?   10.9   0.1   0.00038      0.43      36      65 .]     221     250 ..     219     250 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                                       HHHHHHHHHHHHHCCTTSSCE-HHHHHHHH CS
                     CBFD_NFYB_HMF  36 fieelaseAaeickkekrKtikaehiklAv 65 
                                       f+ el+++Aa  ++ + +Kti  +++++Av
  gi|518652339|ref|YP_008141859.1| 221 FAIELLQKAAYMAEYRLSKTIENDDVRSAV 250
                                       999*************************98 PP

>> AAA_lid_6  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.1   5.7e+03      26      36 ..      79      89 ..      78      91 .. 0.86
   2 ?   10.4   0.0   0.00052      0.58      19      45 ..     215     244 ..     179     273 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.1
                         AAA_lid_6 26 VRnllekairr 36
                                      V+nlle  i r
  gi|518652339|ref|YP_008141859.1| 79 VKNLLEHVISR 89
                                      89****99976 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00052
                         AAA_lid_6  19 nfGNARfVRnllekairrqadRlatt...d 45 
                                        fG ARf+  ll+ka    ++Rl++t   d
  gi|518652339|ref|YP_008141859.1| 215 KFGSARFAIELLQKAAYMAEYRLSKTienD 244
                                       59***********************85431 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00033      0.38       2      26 ..      44      68 ..      44     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00033
                            AAA_33  2 vllvGlpGsGKstlaerllkklgav 26
                                      ++++G +G+GK+  ++ l+++++ +
  gi|518652339|ref|YP_008141859.1| 44 IIIHGDSGTGKTSTVKFLMRENKSI 68
                                      689****************999844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2554.11
//
Query:       gi|518652340|ref|YP_008141860.1|  [L=637]
Description: hypothetical protein FACI_IFERC00001G0979 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   1.7    2.6e-06   26.4   0.1    3.3  3  DNA_pol_B        DNA polymerase family B
  ------ inclusion threshold ------
      0.079   12.8   0.0       0.35   10.7   0.0    2.1  1  DUF3368          Domain of unknown function (DUF3368)
       0.13   12.1   0.0       0.61   10.0   0.0    2.1  2  ATP-synt_ab_Xtn  ATPsynthase alpha/beta subunit N-term extens


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 !   26.4   0.1   4.4e-10   2.6e-06      42      88 ..     291     342 ..     250     348 .. 0.76
   2 !   20.4   0.0   2.9e-08   0.00017     121     204 ..     345     422 ..     341     453 .. 0.80
   3 !   18.1   0.0   1.5e-07    0.0009     283     428 ..     480     611 ..     475     625 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.4e-10
                                       .......-S----BE----EEESS-EEEEEETTHHHHHHHHTT-STTTCE-HC CS
                         DNA_pol_B  42 e......gYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNlcyttlvase 88 
                                       +      + +G+ V++P+ g+y++ v  +DF+S+YP ii+++ ++++ +   +
  gi|518652340|ref|YP_008141860.1| 291 NpfelfsADAGGIVFNPEPGIYSD-VYEIDFSSMYPGIIVEYGISPESISGGN 342
                                       1555554468************86.899******************9987655 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 2.9e-08
                                       HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHHHHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHH CS
                         DNA_pol_B 121 llpklLkdllakRkaikkelkeekdefekalldkqQlalKvtaNsvYGftGvansrlpclalAasvTtiGRemLekt 197
                                        l++ L+ ll++R  +k        + ++ ++ ++ +alK++    +G+tG++n ++  +++ + +T iGR+++   
  gi|518652340|ref|YP_008141860.1| 345 YLSQFLRGLLDRRLLYKYV------NSRSDIYASRNKALKILLLNSFGYTGYKNAKFGRIDVHEKITGIGRKIIADS 415
                                       5788888888888877753......225679**********987778****************************99 PP

                                       HHHHHHT CS
                         DNA_pol_B 198 kelvekk 204
                                        ++ ek+
  gi|518652340|ref|YP_008141860.1| 416 MRISEKN 422
                                       9988877 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 1.5e-07
                                       EEEEEEEEESSTTSEEEEESSGGGSTTS-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S- CS
                         DNA_pol_B 283 kYaglkvektskanklliKGvdlvRrdncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvp 359
                                       +Y+gl  +     + + ++G++l Rrd+ +lv++  ++ l+ l  d     +l+ + e+l ++     + ++ +++p
  gi|518652340|ref|YP_008141860.1| 480 RYIGLRKD-----GTFKVRGIELRRRDSPPLVRKFQEQALDVLNCD---FDELPLKKEKLDDLK---NRYMKLENFP 545
                                       78888777.....7889************************99999...566666666665555...477889999* PP

                                       GGGG-EEEEESS.CCCSSGCCSHHHHHHHHHHHHCSS---TTCEEEEEEBETSS.....SS-GGGTEEE CS
                         DNA_pol_B 360 lekfvlskelskepenyksknlphlevakrlkkrneeapevgdrisYvivekkkevkkknllaseraed 428
                                       +e+f +   ++++ ++yk++n +  ++ k l ++  +++ +g +is ++v kk++v+k++++  +r++ 
  gi|518652340|ref|YP_008141860.1| 546 IEDFRIEFGINRHIDDYKTRN-STYYLLKSLGRE--KKIYPGMVISGIVVDKKHNVIKSHSEFFDRKYY 611
                                       ******************998.777777777666..688999999999999998887777766666654 PP

>> DUF3368  Domain of unknown function (DUF3368)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   5.8e-05      0.35      23      41 ..     184     202 ..     181     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.8e-05
                           DUF3368  23 lldaLiqaGfrispklyae 41 
                                       lld+++++G++i+++ y+e
  gi|518652340|ref|YP_008141860.1| 184 LLDQMKKHGYYINARFYRE 202
                                       79***************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 ?   -2.1   0.0      0.55   3.3e+03      65      85 ..     134     155 ..     125     186 .. 0.61
   2 ?   10.0   0.0    0.0001      0.61      42      71 ..     254     283 ..     228     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.55
                                       EE--TT-EEEEEEE--EEE.E- CS
                   ATP-synt_ab_Xtn  65 imvppkvegkvkeiaeege.yt 85 
                                       ++ p++  g++k++a +g+ y+
  gi|518652340|ref|YP_008141860.1| 134 VIEPVSRYGRIKYVAINGNrYS 155
                                       5556666677777776665343 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0001
                                       TT-EEETT-EEEEEECTTCEEEEEE--TT- CS
                   ATP-synt_ab_Xtn  42 vgdkvsggdilGtvqeteliehkimvppkv 71 
                                         +++++g+++ +++e+e+++ ki+vp++ 
  gi|518652340|ref|YP_008141860.1| 254 IVSSITPGTVVSSIEEKEALKRKILVPFRK 283
                                       55789**********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 4193.02
//
Query:       gi|518652341|ref|YP_008141861.1|  [L=86]
Description: hypothetical protein FACI_IFERC00001G0980 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.067   13.5   0.1      0.073   13.4   0.1    1.1  1  ATP-synt_F  ATP synthase (F/14-kDa) subunit


Domain annotation for each model (and alignments):
>> ATP-synt_F  ATP synthase (F/14-kDa) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   4.1e-06     0.073      27      78 ..      24      75 ..       9      84 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.1e-06
                                      HHHHHHHHHHHHHTTEEEEEEEHHHHCCCHHHHHHCTCSSSSEEEEESCSCC CS
                        ATP-synt_F 27 eeieealkelleredigiilitekiaeeirelideykeealPaileIPskeg 78
                                      ee    +++++++edi i+ +   +ae+ +++i+++++    +ile+ +k  
  gi|518652341|ref|YP_008141861.1| 24 EEEILSMRTYMKKEDIEILKVIMSMAEKHSNEISNFNQFFAAIILELYKKLD 75
                                      333445788889**************************66667777755555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1173  (0.0654247); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 613.26
//
Query:       gi|518652342|ref|YP_008141862.1|  [L=116]
Description: hypothetical protein FACI_IFERC00001G0981 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 775.51
//
Query:       gi|518652343|ref|YP_008141863.1|  [L=151]
Description: peptidyl-prolyl cis-trans isomerase [Ferroplasma acidarmanus fer1]
Scores for 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-52  177.7   0.7    2.2e-52  177.5   0.7    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.5   0.7   1.2e-56   2.2e-52       3     156 ..       5     148 ..       3     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 177.5 bits;  conditional E-value: 1.2e-56
                     Pro_isomerase   3 dietsskGrivieLfadkaPktvenFlklvkegfYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdE 79 
                                        +ets +G+i+ieLf++++P+t++nF+klv++gfY++t+FhRvi++fm+qgGdptg++        gg   ++i+dE
  gi|518652343|ref|YP_008141863.1|   5 VLETS-MGDIEIELFEKDMPVTAGNFRKLVEQGFYNNTIFHRVIPDFMIQGGDPTGTGM-------GG-PGYKIKDE 72 
                                       68996.**************************************************955.......33.2469**** PP

                     Pro_isomerase  80 itsklkhkrGalamartgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetde.erpkknvkivs 155
                                       +t++ +++rG++ama++g  pn++gsqFfI++ ++++ld+ + vFGkVv+G+dv +ki+k+++d+ ++p ++++i++
  gi|518652343|ref|YP_008141863.1|  73 FTKNNRNDRGTIAMANAG--PNTGGSQFFINVVNNNYLDKMHPVFGKVVKGLDVADKISKAKRDRnDKPLEKIVIKK 147
                                       **999***********98..8******************************************************98 PP

                     Pro_isomerase 156 a 156
                                       a
  gi|518652343|ref|YP_008141863.1| 148 A 148
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       356  (0.0198561); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1136.04
//
Query:       gi|518652344|ref|YP_008141864.1|  [L=470]
Description: hypothetical protein FACI_IFERC00001G0983 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-47  162.7  21.7    1.7e-47  162.3  21.7    1.0  1  Sugar_tr  Sugar (and other) transporter
    5.7e-26   91.3  33.3    2.9e-25   89.0  29.2    2.0  2  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  162.3  21.7   1.9e-51   1.7e-47      45     447 ..      55     443 ..      15     447 .. 0.87

  Alignments for each domain:
  == domain 1  score: 162.3 bits;  conditional E-value: 1.9e-51
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHH CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasv 121
                                        vl+ + ++++ vG ++G++++g+++d +GRk+++l  ++ + + av++a+a+    +  ++++R+ +G+++G+ ++
  gi|518652344|ref|YP_008141864.1|  55 PVLVAMATAAYWVGVAAGAILGGIASDAIGRKQIFLYDTIGMAVFAVISAIAT---GYISYFLARLALGLFIGMDYA 128
                                       5788999**********************************************...99******************* PP

                                       HHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-.TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                          Sugar_tr 122 lvPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsn.adgwrillglqlvpallllilllflPESPry 197
                                        +  ++sE++p k+Rg l s  +l+  fG + + ++g+++ ++ +    wr+ + +++vpa++l+ l++ +P S r+
  gi|518652344|ref|YP_008141864.1| 129 AAVPLLSEYSPSKKRGGLLSTEKLFFMFGTIATVVIGMVFTYYVGvLLAWRYDFLIAAVPAIILFGLRFDMPASLRW 205
                                       ****************************************999998889**************************** PP

                                       HHHTT-HHHHHHHHHHHHHC.HHHHHHHHH..HHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHH CS
                          Sugar_tr 198 lvekgkeeeakevlaklrge.edadrelae..ekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGin 271
                                           g+++   ++l+kl +e  d d+e ++  + +s++         + e++ sk+ ++ + +++ + ++  lt  n
  gi|518652344|ref|YP_008141864.1| 206 AKASGRKDLIPKILKKLHKEgIDIDPETVKvdKPQSIK-------ENIHEFFNSKN-KKTVAYIFWIGAAYALTV-N 273
                                       ****************7777523333322200223333.......3499*****88.777777777777777775.* PP

                                       HHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS. CS
                          Sugar_tr 272 aimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvaksk 346
                                        +  y+++++e+lg s     ++t+i+ +v ++ ++  + +vdr+GRR + l+G++ +ai +++l iva+++ a + 
  gi|518652344|ref|YP_008141864.1| 274 LVSVYASVVLEDLGASSFfaEEGTLIIDIVGTLGVVLTLIVVDRIGRRLMGLFGFVLGAIPLTVL-IVADIYHAMT- 348
                                       *****************9777899999999999999999**************************.6999999883. PP

                                       ..CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHH CS
                          Sugar_tr 347 aasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfa 423
                                          +++++++++fi +    +g++ ++ ++E+++++ R++    av    l+ f  sl   ++   ig +y+f++ a
  gi|518652344|ref|YP_008141864.1| 349 IPLVISMFGLFFFINVGL--VGTLQYLPAAEVSTTKSRGL----AVGWEKLFEFGLSLPALTLYALIGLFYSFIYDA 419
                                       445555555555555555..899***************85....688999*************************** PP

                                       HHHHHHHHHHHHHS--STT--CCC CS
                          Sugar_tr 424 glavlfiifvfffvpetkgrtlee 447
                                       ++++++ i+ +f  +etk+r+le 
  gi|518652344|ref|YP_008141864.1| 420 IMVIIGGIVLYFLSFETKNRSLER 443
                                       **********************85 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0  29.2   3.2e-29   2.9e-25       6     324 ..      31     373 ..      26     395 .. 0.78
   2 !    4.7   0.2    0.0014        12     144     187 ..     405     448 ..     375     468 .. 0.64

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 3.2e-29
                             MFS_1   6 flsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa 82 
                                       f  a++ + ++++l  a++  +++ p  + +++++y +g a++++++G  sd +Gr+ ++l   +++a+++++ ++a
  gi|518652344|ref|YP_008141864.1|  31 FTDAFNEFGASISLI-AVGILFHLPPVLVAMATAAYWVGVAAGAILGGIASDAIGRKQIFLYDTIGMAVFAVISAIA 106
                                       666777777777777.77778*************************************************6666666 PP

                             MFS_1  83 sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg....Wravfy 155
                                       +++   +++r+  Gl+ g+ ++a++ l+++++p ++rg  ++   ++f +G+i + ++g +++ ++g    Wr+ f+
  gi|518652344|ref|YP_008141864.1| 107 TGYISYFLARLALGLFIGMDYAAAVPLLSEYSPSKKRGGLLSTEKLFFMFGTIATVVIGMVFTYYVGvllaWRYDFL 183
                                       787789******************************************************99999999999****** PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee......................kgtgpaplvpawkallkdp... 207
                                       i+a+ ++++f     l ++ p + ++ +   ++                      k ++p+++++ + ++++++   
  gi|518652344|ref|YP_008141864.1| 184 IAAVPAIILFG----LRFDMPASLRWAKASGRKdlipkilkklhkegididpetvKVDKPQSIKENIHEFFNSKnkk 256
                                       ********944....34444444444444444446666666*******99999998888888888666666666222 PP

                             MFS_1 208 .vlwillialllfffgfsglltllplylqevlgls...glllaglllallalvgailallagrlsdrlgrrrrllla 280
                                        v +i++i+++++   +++++++  +   e+lg s   +  +++l++ +++ +g    +l+  ++dr+g   r+l++
  gi|518652344|ref|YP_008141864.1| 257 tVAYIFWIGAAYAL-TVNLVSVYASVV-LEDLGASsffA-EEGTLIIDIVGTLG---VVLTLIVVDRIG---RRLMG 324
                                       24446777777775.777788888885.99999999855.77777777777777...66777777**88...5999* PP

                             MFS_1 281 llllllaalglallavtssavllllvlvliGfglgfv.....fpsllal 324
                                       l++++l+a+ l +l v++ ++++ ++lv+  fgl+f+     +++l++l
  gi|518652344|ref|YP_008141864.1| 325 LFGFVLGAIPLTVLIVADIYHAMTIPLVISMFGLFFFinvglVGTLQYL 373
                                       *****************999****9999966644444223334444444 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0014
                             MFS_1 144 lasslgWravfyilaivsllafvlfllllpeepperkrkspkee 187
                                       l++++g  ++f+  ai+ ++++++ ++l +e++ ++   +  e 
  gi|518652344|ref|YP_008141864.1| 405 LYALIGLFYSFIYDAIMVIIGGIVLYFLSFETKNRSLERNAMEA 448
                                       44666777789999999999988655555555544444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.42
# Mc/sec: 3342.59
//
Query:       gi|518652345|ref|YP_008141865.1|  [L=336]
Description: hypothetical protein FACI_IFERC00001G0984 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-28   98.2   0.1    6.4e-28   96.8   0.1    1.8  1  ADH_N          Alcohol dehydrogenase GroES-like domain
    1.5e-26   92.9   0.0    2.2e-26   92.3   0.0    1.2  1  ADH_zinc_N     Zinc-binding dehydrogenase
    1.3e-07   32.8   0.0    2.1e-07   32.1   0.0    1.4  1  ADH_zinc_N_2   Zinc-binding dehydrogenase
     0.0016   18.6   0.0     0.0033   17.6   0.0    1.4  1  ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.8   0.1   1.4e-31   6.4e-28       2     109 .]      26     132 ..      25     132 .. 0.98

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 1.4e-31
                                       TEEEEEEEEEEE-HHHHHHHTTSTTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-G CS
                             ADH_N   2 gevlikvkaagiCgsDlhilkggkelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegee 78 
                                       +ev+i+ k++g+C  D+ + +g   ++v+lp+i+GHEi G++ + g++vk++++GdrV   + ++cg+C+ C +g+e
  gi|518652345|ref|YP_008141865.1|  26 NEVTIEQKYTGVCFRDILTQQG-FFPRVSLPVIPGHEIGGTIIKKGKNVKDFNIGDRVSSLIYVPCGKCEFCLSGNE 101
                                       89*******************9.8***************************************************** PP

                                       GG-TTBEETTTSS-SSSBSEEEECGGGEEEE CS
                             ADH_N  79 nlCeeakllgvsldGgfaeyvvvpekklvkl 109
                                       nlC+++  +g +++Gg+++yv ++e++lvk+
  gi|518652345|ref|YP_008141865.1| 102 NLCPNKVAYGEGRNGGYSRYVNADERSLVKV 132
                                       ****************************996 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.3   0.0     5e-30   2.2e-26       1     128 [.     175     299 ..     175     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 92.3 bits;  conditional E-value: 5e-30
                                       HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHH CS
                        ADH_zinc_N   1 gvGlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalk 77 
                                       gvG++avq+ kalG ++ia  +s+ k e + klGa++v+ +++ ++++++ke+t g+g+d+v+e vG  at++ +l+
  gi|518652345|ref|YP_008141865.1| 175 GVGVHAVQMVKALGGHPIAETGSKWKEEELYKLGAEYVVSPER-EYNKDVKEIT-GQGADIVLEDVG-IATFSKSLR 248
                                       9****************************************88.**********.89**********.********* PP

                                       CEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHH CS
                        ADH_zinc_N  78 llkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdll 128
                                       +lk gGrlvv+G    ++ e++l+ ++lk  si+Gs+ ++ r+++k+al+l 
  gi|518652345|ref|YP_008141865.1| 249 SLKTGGRLVVIGNlKPEPVELPLGLIILKGNSIKGSISST-RDDLKKALELS 299
                                       ************98788888********************.*******9985 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 !   32.1   0.0   4.7e-11   2.1e-07       1     132 [.     207     333 ..     207     334 .. 0.74

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.7e-11
                                       TT-SEEE..ETT.STTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE--.--.S-EEE-CHHHCTTT-EE CS
                      ADH_zinc_N_2   1 lGAdevi..dyr.tedfeaatggegvDvvldtvggealleaslkvlpggGrlvsig.gpplsaallkpakkrkgrsv 73 
                                       lGA+ v+    + ++d+++ t g+g D+vl+ vg +++ ++sl+ l+ gGrlv+ig  +p + +l+          +
  gi|518652345|ref|YP_008141865.1| 207 LGAEYVVspEREyNKDVKEIT-GQGADIVLEDVGIATF-SKSLRSLKTGGRLVVIGnLKPEPVELPLG-----LIIL 276
                                       899999987444478886555.999***********9*.*******999*******443333332222.....2333 PP

                                       EE--GGG...-.-HHHHHHHHHHHHHHH----EEEEEEGGGHHHHHHHHHSS--SSEEE CS
                      ADH_zinc_N_2  74 kyeflfsmkasaqadileelaalieeGklrpvvdrvfpleeaaeAhrylesgrarGKiV 132
                                       k + +    +s + d l++ ++l ++  + pv++   +l+++++ ++ +  +++ G++ 
  gi|518652345|ref|YP_008141865.1| 277 KGNSIKGSISSTRDD-LKKALELSKSQ-ISPVIGNKIELQDINDGYANMLDRKVLGRLL 333
                                       333333222233666.******98876.9******************999999998875 PP

>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.3e-07    0.0033      50      86 ..     144     181 ..     130     184 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.3e-07
                                       GGHHHHHHHHHH.HTTSS-TT-EEEEEEEETTTEEEEE CS
                     ACP_syn_III_C  50 aasiplaLdeav.eegklkpgdlvllvgfGaGltwgaa 86 
                                       aa ++ +L +a+ + gk+k+gd vl++g+G+G+ + a+
  gi|518652345|ref|YP_008141865.1| 144 AACVIAMLYHAIgRVGKIKKGDYVLITGAGGGVGVHAV 181
                                       6777777777772568****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2194.04
//
Query:       gi|518652346|ref|YP_008141866.1|  [L=287]
Description: hypothetical protein FACI_IFERC00001G0985 [Ferroplasma acidarmanus fer1]
Scores for complete 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   77.7   0.3    8.3e-21   74.1   0.0    2.6  3  Pribosyltran_N   N-terminal domain of ribose phosphate pyroph
    1.6e-17   63.5   0.2    4.2e-16   58.9   0.1    2.5  3  Pribosyltran     Phosphoribosyl transferase domain
    5.1e-10   39.7   1.5      6e-10   39.5   0.1    1.8  2  Pribosyl_synth   Phosphoribosyl synthetase-associated domain
    2.6e-05   23.8   0.0    4.7e-05   22.9   0.0    1.4  1  UPRTase          Uracil phosphoribosyltransferase
  ------ inclusion threshold ------
      0.035   13.6   0.1       0.06   12.8   0.1    1.3  1  PRTase_2         Phosphoribosyl transferase
      0.042   13.1   0.7       0.06   12.6   0.1    1.6  2  PRTase_3         PRTase ComF-like
      0.055   13.4   0.3       0.19   11.7   0.1    1.9  2  Intein_splicing  Intein splicing domain
       0.45   10.5   4.8       0.35   10.8   0.3    2.7  3  DUF2393          Protein of unknown function (DUF2393)


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 !   74.1   0.0   3.7e-24   8.3e-21       1     113 [.       1     112 [.       1     114 [. 0.95
   2 ?   -1.6   0.0       1.1   2.4e+03      18      56 ..     173     212 ..     169     223 .. 0.78
   3 ?    0.1   0.1      0.32   7.2e+02       3      46 ..     242     282 ..     240     286 .. 0.58

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 3.7e-24
                    Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvrgkdvfiiqslskpvndnlmelllmidalrra 77 
                                       + i++ s++ + ++k+a+   +++  +  +rf+d+E++++i ++v+g+dv ++ ++ ++  ++++e ll++da+++ 
  gi|518652346|ref|YP_008141866.1|   1 MYIVPSSTAYNVSRKLASIFSCNVSGVVRKRFPDNEMYLKIIDDVKGEDVLLVGNTRSD--QDIIEYLLLLDAIKEE 75 
                                       678999999999*******************************************9987..99************** PP

                    Pribosyltran_N  78 sakritaViPylgysrqdrk.ksrepisaklvaklLe 113
                                         k+itaV+P++gy+rq+ + ++ ep+s+k+  + ++
  gi|518652346|ref|YP_008141866.1|  76 EPKSITAVVPFFGYARQHMRyNNGEPVSSKVFTQAIN 112
                                       ********************99*********998876 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                    Pribosyltran_N  18 krlgvelgkakvsrfadgEikveiee.svrgkdvfiiqsl 56 
                                       ++lg++   ++ +r  +  +k+++ e + ++k++ i+ ++
  gi|518652346|ref|YP_008141866.1| 173 SKLGIPAYYIDKKRIDSTTVKMTLPEeDYKDKNILILDDI 212
                                       5678888888888888888888887646788888888776 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.32
                    Pribosyltran_N   3 ifagssskeLaekiakrlgvelgkakvsrfadgEikveieesvr 46 
                                       +fa +s++++ + +++ + +  +++   ++++  i+ ei es++
  gi|518652346|ref|YP_008141866.1| 242 VFANNSNEKIERYVNELTVTDTIET---KYSNITISGEIAESLK 282
                                       5677777777777776655555554...5555555555555554 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.5   3.4e+03      81      93 ..      41      53 ..       8      53 .. 0.53
   2 ?    1.9   0.0     0.065   1.5e+02     107     131 ..      69      93 ..      65     116 .. 0.74
   3 !   58.9   0.1   1.9e-19   4.2e-16      20     138 ..     146     256 ..     133     276 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.5
                                      E----TTSEEEEE CS
                      Pribosyltran 81 lledpagkkVliV 93
                                         d++g+ Vl+V
  gi|518652346|ref|YP_008141866.1| 41 IIDDVKGEDVLLV 53
                                      3456777777766 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.065
                                       HHHHHCC-BSEEEEEEEEE-HHHHH CS
                      Pribosyltran 107 lelLkekgpeevriavlvdkpatee 131
                                       l+++ke++p+++ ++v++   a++ 
  gi|518652346|ref|YP_008141866.1|  69 LDAIKEEEPKSITAVVPFFGYARQH 93 
                                       899*************994444443 PP

  == domain 3  score: 58.9 bits;  conditional E-value: 1.9e-19
                                       EEEEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SE CS
                      Pribosyltran  20 aeileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDi 96 
                                       ++++++   ++d v+ ++ gG+ ++k + ++L++p  y++k++ ++ +   +         ++ed+++k +li DDi
  gi|518652346|ref|YP_008141866.1| 146 YKYFMD--KNIDFVISPDDGGYERVKLMGSKLGIPAYYIDKKRIDSTTVKMTL--------PEEDYKDKNILILDDI 212
                                       445555..89******************************9999888888887........9*************** PP

                                       ESSSHHHHHHHHHHHCC-BSEEEEEEEE...E-HHHHHHHHHH-T CS
                      Pribosyltran  97 ldtGgTllaalelLkekgpeevriavlv...dkpateeevdknak 138
                                       ++tGgT+++a   Lk+kg+  + +++++   ++++ e+ +++ + 
  gi|518652346|ref|YP_008141866.1| 213 ISTGGTIIKASGMLKDKGARNIYACAIHgvfANNSNEKIERY-VN 256
                                       ********************9999999999844444443333.22 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       1.1   2.4e+03      76      95 ..      40      59 ..      22     142 .. 0.55
   2 !   39.5   0.1   2.7e-13     6e-10      80     150 ..     200     269 ..     174     281 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 1.1
                                      -EES--TTSEEEEEEEEE-S CS
                    Pribosyl_synth 76 tvvGdvgGriaiivddlidd 95
                                      +++ dv+G   ++v +   d
  gi|518652346|ref|YP_008141866.1| 40 KIIDDVKGEDVLLVGNTRSD 59
                                      55556665555555443322 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 2.7e-13
                                       --TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHH CS
                    Pribosyl_synth  80 dvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiq 150
                                       d + +  +i+dd+i    ++++a+ +lk++Ga  iy+ a hG++++++ +++e   ++e+ vt+ti  +  
  gi|518652346|ref|YP_008141866.1| 200 DYKDKNILILDDIISTGGTIIKASGMLKDKGARNIYACAIHGVFANNSNEKIER-YVNELTVTDTIETKYS 269
                                       556677899*******************************************97.69*********87765 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.1e-08   4.7e-05     103     173 ..     184     255 ..     173     273 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.1e-08
                           UPRTase 103 eetlepveyynkLPkki.aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkrlaeef 173
                                       ++  ++  +   LP++  +++++l+lD +i+TGg++++a  +Lk++g++      +  + +++  +++ + +
  gi|518652346|ref|YP_008141866.1| 184 KKRIDSTTVKMTLPEEDyKDKNILILDDIISTGGTIIKASGMLKDKGARNIYACAIHGVFANNSNEKIERYV 255
                                       5555566667789987779**************************998755555555566665555555544 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   2.7e-05      0.06     120     179 ..     202     260 ..     189     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.7e-05
                          PRTase_2 120 aakelvLvDDEistGktalnliralqeklprkryvvvslvdwrseedeaafaaleeelgi 179
                                       ++k++++ DD istG t+++    l++k  r+ y  +++  +  +++++++++  +el++
  gi|518652346|ref|YP_008141866.1| 202 KDKNILILDDIISTGGTIIKASGMLKDKGARNIY-ACAIHGVFANNSNEKIERYVNELTV 260
                                       57889999*************9999999887655.5678888888888888888877776 PP

>> PRTase_3  PRTase ComF-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       1.3   2.9e+03      98     131 ..     120     151 ..     105     162 .. 0.55
   2 ?   12.6   0.1   2.7e-05      0.06     127     198 ..     193     263 ..     163     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
                          PRTase_3  98 kvklhraatksedygslsaedreklilndkyhid 131
                                       +v+lh  +t   +y++++++d + ++   ky +d
  gi|518652346|ref|YP_008141866.1| 120 TVELHDEQT--LNYSKVPFTDIKIINPIYKYFMD 151
                                       444444322..24555555554444444444444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.7e-05
                          PRTase_3 127 kyhidkerlkgktlifldDiritgshedkirkslkeeklendivflYlaeldnkaidpaienrlnsvvvesi 198
                                       k ++++e  k+k +++ldDi  tg +  k + +lk ++++n i++  +  +  ++ + +ie ++n+ +v + 
  gi|518652346|ref|YP_008141866.1| 193 KMTLPEEDYKDKNILILDDIISTGGTIIKASGMLKDKGARN-IYACAIHGVFANNSNEKIERYVNELTVTDT 263
                                       345666667******************************77.555555555666678899999999998876 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.54   1.2e+03      81     109 ..      42     125 ..      32     153 .. 0.53
   2 ?   11.7   0.1   8.6e-05      0.19      51      96 ..     225     270 ..     177     279 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.54
                                       CCC--TT-EEEEE.......................................................HSCEEEEEE CS
                                       xxxxxxxxxxxxx.......................................................xxxxxxxxx RF
                   Intein_splicing  81 adeLkegdliavp.......................................................dadvvwdkv 102
                                        d++k +d++ v                                                          + + d++
  gi|518652346|ref|YP_008141866.1|  42 IDDVKGEDVLLVGntrsdqdiieylllldaikeeepksitavvpffgyarqhmrynngepvsskvftqAINQYADRI 118
                                       56666666666555555555555555555555555555555555555555555555555554444444222333333 PP

                                       EEEEEEE CS
                                       xxxxxxx RF
                   Intein_splicing 103 ksieved 109
                                         +e +d
  gi|518652346|ref|YP_008141866.1| 119 ITVELHD 125
                                       3333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 8.6e-05
                                       EEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEEHSC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  51 eiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavpdad 96 
                                        +k +  r+i+a + H +++ + ++ +E+ ++eL++ d+i +  ++
  gi|518652346|ref|YP_008141866.1| 225 MLKDKGARNIYACAIHGVFANNSNEKIERYVNELTVTDTIETKYSN 270
                                       56778899*************887777************9876555 PP

>> DUF2393  Protein of unknown function (DUF2393)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.33   7.5e+02     114     137 ..      70      93 ..      63      98 .. 0.85
   2 ?   -0.9   0.2      0.65   1.5e+03      38      71 ..     109     143 ..     102     150 .. 0.71
   3 ?   10.8   0.3   0.00016      0.35      62     109 ..     219     265 ..     189     280 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.33
                           DUF2393 114 edlkpgeskeFrviidyfpyfkny 137
                                       + +k++e k+++++++ f y +++
  gi|518652346|ref|YP_008141866.1|  70 DAIKEEEPKSITAVVPFFGYARQH 93 
                                       67999*************997765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.65
                           DUF2393  38 liidkyl.kkaeltilsqkrllyteafvvdgtitN 71 
                                        +i++y  +++++++ + + l+y++  + d++i N
  gi|518652346|ref|YP_008141866.1| 109 QAINQYAdRIITVELHDEQTLNYSKVPFTDIKIIN 143
                                       56666652566777777888888888888888866 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00016
                           DUF2393  62 afvvdgtitNeGkftikeCkleiklvnkshnkkskellkklkplvsks 109
                                        + ++g  + +G ++i  C ++  + n+s++k ++++ ++l++  + +
  gi|518652346|ref|YP_008141866.1| 219 IIKASGMLKDKGARNIYACAIHGVFANNSNEK-IERYVNELTVTDTIE 265
                                       55678999************************.999999888554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1983.08
//
Query:       gi|518652347|ref|YP_008141867.1|  [L=190]
Description: hypothetical protein FACI_IFERC00001G0986 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.1e-58  196.2   0.0    3.5e-58  196.0   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 !  196.0   0.0     2e-62   3.5e-58       2     182 ..       4     181 ..       3     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 196.0 bits;  conditional E-value: 2e-62
                                       GSEEEEEEEEE.....-SS-EEEEEEEEETT.EEEEEEEEEE-TT-S-HHHHHHHHHCC-TTTTEEEEEESSSEETT CS
                             DUF99   2 eirvlGiddsfferkkkdgksvlvGvvmradrvvdgvafgrvtvdGtDateaiielvkrleredirvvlldGitiag 78 
                                       ++rvlG dd++f+ +++d+k+v+vGv+mr +++v+g+  g++tvdG+D+te+i+++++  + +di+ ++ +Git++g
  gi|518652347|ref|YP_008141867.1|   4 GLRVLGLDDGPFN-RNSDTKTVMVGVLMRLNSYVEGISTGTITVDGMDSTETIMSMLNGRFSKDIDFIMSNGITFGG 79 
                                       78***********.567************************************************************ PP

                                       TEE--HHHHHHHH---EEEEESS---HHHHHHCCT.TSTTHHHHHHHHHHC.---EEETT....EEEEEESS-HHHH CS
                             DUF99  79 FNvvDlerlheetglPviavtreepdlgklekaLrkhfpdeeeRlelieklgerieevektgeelyvravGieleea 155
                                       FN++D++ + +  g+P+i++tr++pd++++ +aL+ hf+d  +R el+++   +i+++e +g+++y +++Gi++++a
  gi|518652347|ref|YP_008141867.1|  80 FNIMDIPMINRLSGIPIISITRKKPDMDSMFSALKLHFSDYMQRTELLKNT--SINKIEFSGKTVYANCCGISVNDA 154
                                       *************************************************99..99999999**************** PP

                                       HHHHHHC-SSSSS-HHHHHHHHHHHHH CS
                             DUF99 156 aklvrkltlegriPEPlRvAhliAsal 182
                                         l++k+t+ g+iPEP+R+AhliA+a+
  gi|518652347|ref|YP_008141867.1| 155 LYLIKKTTIMGNIPEPVRMAHLIATAI 181
                                       *************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1301.52
//
Query:       gi|518652348|ref|YP_008141868.1|  [L=453]
Description: hypothetical protein FACI_IFERC00001G0987 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-12   46.8   0.0    7.9e-12   45.3   0.0    1.8  1  DDE_Tnp_1    Transposase DDE domain
     0.0026   17.8   0.0      0.016   15.2   0.0    2.1  2  DDE_Tnp_1_3  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   8.8e-16   7.9e-12      34     212 ..     184     384 ..     164     386 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 8.8e-16
                         DDE_Tnp_1  34 ygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleekgvdyiirlkknt 110
                                       + +++++ ++     +  ++++pg+v+d+++l+ + +e++  +g+l+++D+G+   +++ +++ +g+++i +lk ++
  gi|518652348|ref|YP_008141868.1| 184 PMIRIIMGFSRLRNEPCYIRLVPGSVADIDTLRKTEQEVH--TGTLFVMDRGFIDDNNFGKMDTNGLYFITPLKRDS 258
                                       555666666666667888999*************999999..*********************************** PP

                         DDE_Tnp_1 111 klyrk...................................gaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvy 152
                                       kl +                                    +a ++++     +  +k+l+  +k+            
  gi|518652348|ref|YP_008141868.1| 259 KLPDYsingdnffmfrkrairyssttiknydihvfedimlRAMEENEYYSLVDSGKKPLYSPEKAGKI--------- 326
                                       **999988777777776555555555544444433333333444444444444444444444444444......... PP

                         DDE_Tnp_1 153 yvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                          ++++   +++ + ely+ R  iE++F   k+ ++ d  ++rg +  + +++  +++l
  gi|518652348|ref|YP_008141868.1| 327 --ALITNVREKPQSIFELYKFRNDIEESFDVFKNLLQVDTPYLRGDDTLKGYVFVSFISL 384
                                       ..666667779******************************************9999987 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.8e-06     0.016      61     133 ..     202     278 ..     196     290 .. 0.79
   2 ?   -0.8   0.0      0.16   1.4e+03     105     148 ..     326     363 ..     316     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.8e-06
                       DDE_Tnp_1_3  61 vkltpgnvdDrepveelakel.lgklf.aDkgyiskklaeelleegielitklrknmkkkllsll..dkllLrkrsl 133
                                       ++l pg v D +++++  +e+ +g+lf  D+g+i ++ + ++ ++g+ +it l+++ k    s+   +  ++rkr++
  gi|518652348|ref|YP_008141868.1| 202 IRLVPGSVADIDTLRKTEQEVhTGTLFvMDRGFIDDNNFGKMDTNGLYFITPLKRDSKLPDYSINgdNFFMFRKRAI 278
                                       68999*********777777636888846**************************9986555443215567888876 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.16
                       DDE_Tnp_1_3 105 ielitklrknmkkkllslldkllLrkrslietvndelknisqie 148
                                       i+lit++r++      s+++  l + r  ie  +d +kn+ q++
  gi|518652348|ref|YP_008141868.1| 326 IALITNVREK----PQSIFE--LYKFRNDIEESFDVFKNLLQVD 363
                                       5555555543....333333..5566788888999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3148.92
//
Query:       gi|518652349|ref|YP_008141869.1|  [L=275]
Description: SMP-30/gluconolaconase/LRE protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-61  207.5   0.2    2.8e-61  207.2   0.2    1.1  1  SGL              SMP-30/Gluconolactonase/LRE-like region
  ------ inclusion threshold ------
      0.045   13.9   0.0        0.2   11.8   0.0    2.1  2  Str_synth        Strictosidine synthase
      0.084   12.8   1.3       0.23   11.4   0.1    2.5  3  HCBP_related     Haemolysin-type calcium binding protein rela
       0.23   10.3   3.0        0.1   11.5   0.8    1.4  2  PARP_regulatory  Poly A polymerase regulatory subunit


Domain annotation for each model (and alignments):
>> SGL  SMP-30/Gluconolactonase/LRE-like region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.2   0.2   6.2e-65   2.8e-61       1     245 [.      15     247 ..      15     248 .. 0.97

  Alignments for each domain:
  == domain 1  score: 207.2 bits;  conditional E-value: 6.2e-65
                               SGL   1 lgEGpvwdeeegaLlwvDilgqrihrldpatgketvldtpesvGaiaprkdgrlvvasksglalldlasgeletlad 77 
                                       lgE+p+w   +g L++vDil+++i+ +   +++ t+l+t++ + +i+p +d++l++a k+++  l l+sg++et+++
  gi|518652349|ref|YP_008141869.1|  15 LGESPIWR--DGLLYYVDILNGKIYSY---GENITQLHTDSIIPFIVP-CDDGLIFATKDSIKHLILKSGKVETIFK 85 
                                       79******..9***************9...7788889***********.****************99********** PP

                               SGL  78 eeedekpllrfNDgvvdpdGrlwfGtmgdeeakgeevgalyrldpdgklervlddltipNGlawspdgktlYlaDsl 154
                                          + ++ +rfNDg++d +G l++Gtm+++e+++   g+ly +d +   ++vld++ti+NG  w+ d+k +Y++Ds+
  gi|518652349|ref|YP_008141869.1|  86 M--KFDEIVRFNDGKCDMNGVLFAGTMDMNEKDPL--GSLYGFDNK--ESKVLDRITISNGTIWNYDKKIMYYIDSP 156
                                       9..4447****************************..*****9988..899************************** PP

                               SGL 155 trkiwaydvdaeggklsnrrvfadlkkgegepDGlavDaeGnvwvAvwgggkvvrfdpdGklieeiklpakrvtsca 231
                                       trki ++++d  ++ + +    +d++ ++g+pDG+++D+ Gn++vA  gg+ v++fd +Gk+i++i + ak+v sc+
  gi|518652349|ref|YP_008141869.1| 157 TRKIRVFNYDNRNSAILDEMESIDVSVFPGVPDGMTIDSMGNLYVAFHGGSSVIVFDSNGKVIKKIYVSAKNVDSCV 233
                                       ***************************************************************************** PP

                               SGL 232 FgGpdlrtLyitsa 245
                                       FgG dl+tLyit+a
  gi|518652349|ref|YP_008141869.1| 234 FGGDDLKTLYITTA 247
                                       *************8 PP

>> Str_synth  Strictosidine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   4.5e-05       0.2      28      81 ..     110     160 ..      90     167 .. 0.89
   2 ?   -1.5   0.0      0.61   2.7e+03      68      86 ..     206     224 ..     189     227 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.5e-05
                         Str_synth  28 lallegdktGrllkydkstkvvkvlldkLyfanGialsedgsfvlvcetamkri 81 
                                       +++ e+d+ G l+ +d++  +v   ld++  +nG     d++ + + + ++++i
  gi|518652349|ref|YP_008141869.1| 110 MDMNEKDPLGSLYGFDNKESKV---LDRITISNGTIWNYDKKIMYYIDSPTRKI 160
                                       799*************988877...8****************999998888875 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.61
                         Str_synth  68 gsfvlvcetamkrisrywi 86 
                                       gs+v+v +   k i++ ++
  gi|518652349|ref|YP_008141869.1| 206 GSSVIVFDSNGKVIKKIYV 224
                                       4566666666666666665 PP

>> HCBP_related  Haemolysin-type calcium binding protein related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       2.5   1.1e+04      30      35 ..      92      97 ..      90      97 .. 0.80
   2 ?   11.4   0.1   5.1e-05      0.23      18      41 ..     123     146 ..     121     147 .. 0.86
   3 ?   -2.5   0.0       1.1     5e+03      12      24 ..     159     169 ..     154     175 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                      HCBP_related 30 ieFaDG 35
                                      ++F+DG
  gi|518652349|ref|YP_008141869.1| 92 VRFNDG 97
                                      789999 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 5.1e-05
                      HCBP_related  18 wfsssgsyrieqieFaDGtvWdaa 41 
                                       +f++ +s  +++i+ ++Gt+W+++
  gi|518652349|ref|YP_008141869.1| 123 GFDNKESKVLDRITISNGTIWNYD 146
                                       688778888************986 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                      HCBP_related  12 sitiknwfsssgs 24 
                                       +i++ n+ +   +
  gi|518652349|ref|YP_008141869.1| 159 KIRVFNYDNR--N 169
                                       7899999874..4 PP

>> PARP_regulatory  Poly A polymerase regulatory subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.1       1.3     6e+03       6      23 ..      25      42 ..      24      45 .. 0.78
   2 ?   11.5   0.8   2.2e-05       0.1     216     252 ..     132     171 ..     122     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.3
                   PARP_regulatory  6 ylyfsdlaneleYdeenn 23
                                      +ly+ d+ n ++Y++ +n
  gi|518652349|ref|YP_008141869.1| 25 LLYYVDILNGKIYSYGEN 42
                                      589999999999988754 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 2.2e-05
                   PARP_regulatory 216 lrtvtld..eaeeyekk.lfylnkvvrkkiilnfdyenqe 252
                                       l ++t++     +y+kk ++y+++ +rk  ++n+d+ n++
  gi|518652349|ref|YP_008141869.1| 132 LDRITISngTIWNYDKKiMYYIDSPTRKIRVFNYDNRNSA 171
                                       5566666335679***94556678899999********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1814.62
//
Query:       gi|518652350|ref|YP_008141870.1|  [L=105]
Description: biphenyl dioxygenase, Rieske iron-sulfur component related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-15   54.3   0.0    1.1e-14   54.2   0.0    1.1  1  Rieske    Rieske [2Fe-2S] domain
    1.8e-06   27.8   0.0    2.1e-06   27.6   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain
  ------ inclusion threshold ------
      0.055   13.4   0.0       0.07   13.1   0.0    1.3  1  CreA      CreA protein


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.8e-18   1.1e-14       2      83 ..       2      82 ..       1      93 [. 0.89

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.8e-18
                                      EEEEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE- CS
                            Rieske  2 wvavakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvikg 79
                                      w  + k ++++++  + ++v g pl+v r  dg++y+++ +CtH++++lseg i e+  ++C+ H ++++ +dGkvi g
  gi|518652350|ref|YP_008141870.1|  2 WETLFKMDKIEDNALKDITVKGVPLLVSR-IDGKIYVTDLYCTHEQTSLSEGFI-EGCSVVCSAHFASFNlKDGKVISG 78
                                      55667788899999***************.6***********************.888********************* PP

                                      TTHH CS
                            Rieske 80 Papr 83
                                      P  +
  gi|518652350|ref|YP_008141870.1| 79 PEGE 82
                                      9755 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.5e-10   2.1e-06       2     102 ..       2     102 ..       1     104 [. 0.90

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.5e-10
                                       EEEEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT CS
                          Rieske_2   2 wvpvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLkt 78 
                                       w ++ k++++  +  +   v+g   ++ r+ ++++y +d +++  e+  ls+G+++       v++  +   f+Lk+
  gi|518652350|ref|YP_008141870.1|   2 WETLFKMDKIEDNALKDITVKGVPLLVSRI-DGKIYVTDLYCTH-EQTSLSEGFIEGC----SVVCSAHFASFNLKD 72 
                                       999*********************999999.************9.799*******876....788889999****** PP

                                       -BBSS......-TTSB-BEE-EEESTSEEE CS
                          Rieske_2  79 Gecle......deevslkvypvrvedgkve 102
                                       G++++       + + lk y++++e+g ++
  gi|518652350|ref|YP_008141870.1|  73 GKVISgpegetGTIKDLKSYNTKIENGMIM 102
                                       *****77776545589***********997 PP

>> CreA  CreA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.2e-05      0.07       8      44 ..       2      38 ..       1      76 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                              CreA  8 fkllgandkivvealdDpkvegvtcyvsrakkglikg 44
                                      +++l++ dki+ +al+D +v+gv + vsr++ ++  +
  gi|518652350|ref|YP_008141870.1|  2 WETLFKMDKIEDNALKDITVKGVPLLVSRIDGKIYVT 38
                                      8999**************************9887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 736.46
//
Query:       gi|518652351|ref|YP_008141871.1|  [L=557]
Description: hypothetical protein FACI_IFERC00001G0990 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-54  184.0   0.0    5.5e-35  120.9   0.0    2.2  2  ETF        Electron transfer flavoprotein domain
    1.2e-21   76.5   0.1      3e-21   75.2   0.1    1.7  1  ETF_alpha  Electron transfer flavoprotein FAD-binding domain
  ------ inclusion threshold ------
      0.033   14.6   0.2       0.54   10.8   0.0    2.4  2  EF-hand_7  EF-hand domain pair
      0.035   13.7   0.1       0.89    9.3   0.0    2.5  2  EF-hand_1  EF hand


Domain annotation for each model (and alignments):
>> ETF  Electron transfer flavoprotein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.9   0.0   1.2e-38   5.5e-35       3     177 ..      24     195 ..      22     200 .. 0.95
   2 !   61.2   0.0   2.6e-20   1.2e-16      69     180 ..     310     419 ..     278     421 .. 0.90

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 1.2e-38
                                       EEE-EC.CCCE-HHHHHHHHHHHHHHHHHT--EEEEEEES....S-CHHHHHHCT-SEEEEEE-GGGSS--CCHHHH CS
                               ETF   3 vlaehgvdgklnpvdlealeaArrlkekaggevtavvvGppeaeealrealaamGadkvilvddpalagydaeatak 79 
                                        ++++gv+ ++n +d+ a+eaA+rl ek ++e  +v++Gp  a ++l + ++ mG+ ++il++dp +ag+d++ t++
  gi|518652351|ref|YP_008141871.1|  24 RIIRAGVKLSFNSYDKKAVEAAVRLSEKYKCETYVVSMGPGDARDVLNDSMK-MGINHAILLNDPNFAGSDTYVTSR 99 
                                       58999***********************88**********************.************************ PP

                                       HHHHHHHHC--SEEEEESSCC.H..HHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEEE-TSSSEE CS
                               ETF  80 alaalikkedpdlvlagatai.g..kqvaprlAalLgvplitdvteleveggkltvtRpieggnglaevveadlpav 153
                                       +l+ li  ++pd+vl g+++  g   qv+p +A++ g+ ++++v+++e+++++++v R+ ++  g+ + +e++ p++
  gi|518652351|ref|YP_008141871.1| 100 ILSSLIMHISPDIVLSGKSSLdGetSQVPPETAEMAGYNFVSNVSSIEIAENRVIVARDEDN--GI-RKLEVSFPVF 173
                                       *********************99**************************9898*****9999..**.99999***** PP

                                       EEE-TTSS----S-TT---EEEE- CS
                               ETF 154 ltvrpgafepaaimaakkkeveev 177
                                       l+v ++++++++i++++  +ve++
  gi|518652351|ref|YP_008141871.1| 174 LSVSEKINRARQIDPSA--KVENI 195
                                       *************9965..55555 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 2.6e-20
                                       GSS--CCHHHHHHHHHHHHC--SEEEEESSCCHHHHHHHHHHHCT-EEEEEESEEEEETCCEEEEEECCCCTEEEEE CS
                               ETF  69 lagydaeatakalaalikkedpdlvlagataigkqvaprlAalLgvplitdvteleveggkltvtRpieggnglaev 145
                                       l+++d    ++ +a++i+k+++ +vla+++  g+++   +Aa  g++l++d+++++ e gk+++ +p +gg ++a +
  gi|518652351|ref|YP_008141871.1| 310 LDNSDYVSFSEYVAEFIRKNKVRHVLAPSNLNGRDISSHIAASIGLGLTADCVDIKFESGKMVQYKPSFGGGIIAVI 386
                                       45566678899***********************************************9****************** PP

                                       E-TSSSEEEEE-TTSS----S-TT---EEEE--HH CS
                               ETF 146 veadlpavltvrpgafepaaimaakkkeveeveva 180
                                       ++ + p ++tvr+g f+   + ++k+ +v++v+++
  gi|518652351|ref|YP_008141871.1| 387 KSKTEPDMATVRKGMFPI--KFRSKSYDVQTVNLE 419
                                       *****************9..567788888888765 PP

>> ETF_alpha  Electron transfer flavoprotein FAD-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   0.1   6.8e-25     3e-21       7      82 ..     442     516 ..     439     518 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 6.8e-25
                                       S-EEEE-GGGSSGGGHHHHHHHHHHHT-EEEE-HHHHTTTSS-CCCB-SSSS-----S-EEEES----HHHHGGGT CS
                         ETF_alpha   7 kvvvsgGrGlkskenlelleelaealgaavgasRavvdagwipeerqvGqtGktvaPklyiavGisGaiqhlaGmk 82 
                                        v+ ++G G++ +e++  + e+ae+++a+vga+R vvd+g ip++ q+G tG +++P+ly+a+GisG+ +h++G++
  gi|518652351|ref|YP_008141871.1| 442 PVIFGIGTGVH-AEDIPHILEIAEKINASVGATRRVVDMGRIPRQFQIGLTGMSISPSLYVALGISGSDNHIVGIR 516
                                       68999*****7.69************************************************************97 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.54      36      68 ..     205     236 ..     173     239 .. 0.78
   2 ?    1.0   0.0      0.13   5.9e+02      55      68 ..     310     323 ..     304     326 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
                         EF-hand_7  36 gegsklsdeelellfkefDtdkdGvisfdEFlk 68 
                                         gs+ s++++ + f + +t+++  i+f+EFl 
  gi|518652351|ref|YP_008141871.1| 205 WKGSD-SPTSVVDTFSMANTRNNKFITFQEFLG 236
                                       56666.7889*********************86 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
                         EF-hand_7  55 tdkdGvisfdEFlk 68 
                                       +d+++++sf+E+++
  gi|518652351|ref|YP_008141871.1| 310 LDNSDYVSFSEYVA 323
                                       6999*******986 PP

>> EF-hand_1  EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0002      0.89       4      27 ..     216     239 ..     214     241 .. 0.87
   2 ?    1.5   0.0     0.058   2.6e+02      12      23 ..     311     322 ..     310     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0002
                                       HHHHHHTTTSSSEEEHHHHHHHHH CS
                         EF-hand_1   4 eiFrefDkDgdGkIdfeEfkellk 27 
                                       + F+++ + ++ +I+f+Ef+ +l+
  gi|518652351|ref|YP_008141871.1| 216 DTFSMANTRNNKFITFQEFLGILN 239
                                       579999999**********99987 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.058
                                       TSSSEEEHHHHH CS
                         EF-hand_1  12 DgdGkIdfeEfk 23 
                                       D++ +++f+E++
  gi|518652351|ref|YP_008141871.1| 311 DNSDYVSFSEYV 322
                                       9*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       300  (0.0167327); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.58u 0.24s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 3823.56
//
Query:       gi|518652352|ref|YP_008141872.1|  [L=193]
Description: hypothetical protein FACI_IFERC00001G0991 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 1287.68
//
Query:       gi|518652353|ref|YP_008141873.1|  [L=157]
Description: hypothetical protein FACI_IFERC00001G0992 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-17   64.3   0.1    1.5e-17   63.9   0.1    1.2  1  PIN_6           PIN domain of ribonuclease
    1.5e-06   27.8   0.3    4.3e-06   26.3   0.3    1.8  1  PIN_5           PINc domain ribonuclease
     0.0026   17.8   2.0     0.0055   16.8   2.0    1.5  1  Zn-ribbon_8     Zinc ribbon domain
     0.0089   16.0   0.4      0.021   14.9   0.4    1.5  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.015   15.0   3.0       0.15   11.8   2.0    2.2  2  zinc_ribbon_2   zinc-ribbon domain
      0.018   15.2   1.6      0.037   14.2   1.6    1.5  1  NOB1_Zn_bind    Nin one binding (NOB1) Zn-ribbon like
      0.022   15.3   1.2      0.049   14.1   0.4    1.8  2  PIN             PIN domain
       0.05   13.7   0.2      0.081   13.0   0.2    1.3  1  DUF1272         Protein of unknown function (DUF1272)
       0.05   13.4   0.0       0.09   12.5   0.0    1.4  1  DUF5615         Domain of unknown function (DUF5615)
       0.12   12.3   0.2       0.28   11.1   0.1    1.7  2  DUF4411         Domain of unknown function (DUF4411)
       0.13   12.2   1.8        0.2   11.5   1.8    1.3  1  zf-C3HC4_3      Zinc finger, C3HC4 type (RING finger)
       0.13   12.3   2.2       0.68   10.0   0.1    2.3  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai


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 !   63.9   0.1   9.9e-21   1.5e-17       2      89 .]       8      90 ..       7      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 63.9 bits;  conditional E-value: 9.9e-21
                             PIN_6  2 VlDagaliknslsslqnlaeklyttpeVvaEirdkkarerlellplelevrePspesvkkvtefakktGDlsvLSktDi 80
                                      ++D++a+++    +l+ + + ++  ++V++Ei++ + ++ le+   ++++r+P +e+++k++e+a  tGD++ LS+tDi
  gi|518652353|ref|YP_008141873.1|  8 IIDTSAMLSG---NLNISEDGYVYPESVINEIKKGSLEKILEV--ANITTRSPGKEYIAKAREAALSTGDYNALSATDI 81
                                      89******98...99999999**********************..69******************************** PP

                             PIN_6 81 evlALtyeL 89
                                      +vlAL++eL
  gi|518652353|ref|YP_008141873.1| 82 DVLALAIEL 90
                                      ******998 PP

>> PIN_5  PINc domain ribonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.3   2.9e-09   4.3e-06     156     191 ..      77     112 ..       6     115 .. 0.75

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.9e-09
                             PIN_5 156 saeDldvllLAkELdaavvssDeGikkwaeklGlrl 191
                                       sa D+dvl LA EL++ ++++D  i+++a+  G+ +
  gi|518652353|ref|YP_008141873.1|  77 SATDIDVLALAIELNGIIITDDYAIQNVAKYCGIAY 112
                                       899****************************99975 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   2.0   3.7e-06    0.0055       4      38 ..     126     153 ..     125     154 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                       Zn-ribbon_8   4 YeYrCeeCghefevlqsisdapltaCPeCgsevrr 38 
                                         YrC+ C++ +++         ++CP Cg++v+r
  gi|518652353|ref|YP_008141873.1| 126 WKYRCTGCHKIYDEYI-------KTCPICGHDVKR 153
                                       57*******9999885.......57********98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.4   1.4e-05     0.021      27      49 .]     117     148 ..      98     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.4e-05
                               DZR  27 a.........edrCpsCgekvdpearfCpeCG 49 
                                                 ++rC  C++  d+  ++Cp CG
  gi|518652353|ref|YP_008141873.1| 117 IsgikkgiiwKYRCTGCHKIYDEYIKTCPICG 148
                                       133444778899*******************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 ?    1.8   0.0      0.14   2.1e+02       9      16 ..     101     108 ..      99     109 .. 0.84
   2 ?   11.8   2.0    0.0001      0.15       1      22 [.     129     150 ..     129     151 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.14
                     zinc_ribbon_2   9 lqdnakFC 16 
                                       +q+ ak+C
  gi|518652353|ref|YP_008141873.1| 101 IQNVAKYC 108
                                       89999**9 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0001
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCGtp 22 
                                       +C+ C++  ++  k Cp CG+ 
  gi|518652353|ref|YP_008141873.1| 129 RCTGCHKIYDEYIKTCPICGHD 150
                                       699*****************97 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.6   2.5e-05     0.037       6      32 ..     125     150 ..     120     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.5e-05
                      NOB1_Zn_bind   6 swvlrChaCfkvtkdmtkkFCpkCGnk 32 
                                        w +rC++C+k++ +  k  Cp CG++
  gi|518652353|ref|YP_008141873.1| 125 IWKYRCTGCHKIYDEYIKT-CPICGHD 150
                                       699**********998887.*****86 PP

>> PIN  PIN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.1   1.6e+03       1      10 [.       7      16 ..       7      30 .. 0.84
   2 ?   14.1   0.4   3.3e-05     0.049      65     121 ..      47     106 ..      25     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.1
                                      EEE-HHHHHH CS
                               PIN  1 ivlDTsvlia 10
                                      +++DTs++++
  gi|518652353|ref|YP_008141873.1|  7 YIIDTSAMLS 16
                                      689****987 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.3e-05
                                       HHTSEEEEBCHHHHHHHHHHHHHHH....SBHHHHHHHHHHHHHT-EEE.ESSTHHHHHHH CS
                               PIN  65 lsalkilpidaeiaeeaaeialkyg....llpnDaliaAtAkehgikliatfDedfrrvak 121
                                        +++   + ++e  ++a+e al  g    l++ D  ++A+A+e + ++i t D  + +vak
  gi|518652353|ref|YP_008141873.1|  47 VANITTRSPGKEYIAKAREAALSTGdynaLSATDIDVLALAIELNGIII-TDDYAIQNVAK 106
                                       3444444468999999999999999*********************999.******99997 PP

>> DUF1272  Protein of unknown function (DUF1272)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.2   5.4e-05     0.081      21      50 ..     122     150 ..     118     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.4e-05
                           DUF1272  21 earicsyEctFCaeCaeevlenvCPncgGe 50 
                                       + +i  y ct C++  +e   ++CP cg +
  gi|518652353|ref|YP_008141873.1| 122 KGIIWKYRCTGCHKIYDEY-IKTCPICGHD 150
                                       567999************9.789****976 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0     6e-05      0.09      20      55 ..      63      98 ..      53     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6e-05
                           DUF5615 20 aghdvlhvrelglegasDeeileyAkeedriivTkD 55
                                      a   +l++ + +  +a+D ++l++A+e + ii+T D
  gi|518652353|ref|YP_008141873.1| 63 AREAALSTGDYNALSATDIDVLALAIELNGIIITDD 98
                                      555677788888889*******************99 PP

>> DUF4411  Domain of unknown function (DUF4411)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0       3.7   5.5e+03       1      10 [.       7      16 ..       7      22 .. 0.83
   2 ?   11.1   0.1   0.00019      0.28      76     134 ..      41     107 ..      16     122 .. 0.65

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                           DUF4411  1 YllDtnvfie 10
                                      Y++Dt+++ +
  gi|518652353|ref|YP_008141873.1|  7 YIIDTSAMLS 16
                                      99***98865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00019
                           DUF4411  76 veevgkvakwv.ivesekyskaa........kkeflsvaDpfliAaAlaknatvVTkEvkkpnkkknk 134
                                       +e++ +va+++     ++y  +a        + + ls  D  ++A+A++ n +++T + + +n  k +
  gi|518652353|ref|YP_008141873.1|  41 LEKILEVANITtRSPGKEYIAKAreaalstgDYNALSATDIDVLALAIELNGIIITDDYAIQNVAK-Y 107
                                       44555555554222222222222233333223333499*******************999777666.4 PP

>> zf-C3HC4_3  Zinc finger, C3HC4 type (RING finger)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.8   0.00013       0.2      26      49 ..     130     153 ..     127     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00013
                                       -HHHHHHHHHTT-B-TTT--B--E CS
                        zf-C3HC4_3  26 CeeCaekllkrkkkCpiCrrpiek 49 
                                       C  C + + +  k+CpiC  ++++
  gi|518652353|ref|YP_008141873.1| 130 CTGCHKIYDEYIKTCPICGHDVKR 153
                                       9*******99********999876 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2      0.18   2.6e+02      18      22 ..     128     132 ..     125     135 .. 0.85
   2 ?   10.0   0.1   0.00045      0.68       1      11 [.     143     153 ..     143     156 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.18
                    DNA_ligase_ZBD  18 yRCtn 22 
                                       yRCt+
  gi|518652353|ref|YP_008141873.1| 128 YRCTG 132
                                       9***8 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00045
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CP+CG+ v R
  gi|518652353|ref|YP_008141873.1| 143 TCPICGHDVKR 153
                                       7******9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       739  (0.0412181); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1104.52
//
Query:       gi|518652354|ref|YP_008141874.1|  [L=256]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-33  115.8  40.0    2.8e-33  115.5  40.0    1.0  1  TauE       Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.23   11.6   0.3       0.92    9.6   0.2    1.8  2  TLE_N      Groucho/TLE N-terminal Q-rich domain


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5  40.0   3.1e-37   2.8e-33       2     234 ..       9     247 ..       7     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 3.1e-37
                              TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGa 77 
                                       l++g+++G++ g++G  g l++vP+L ++ ++ +++v+tsll+ v+t+++ ++ ++r+++++  ++++l++g++iGa
  gi|518652354|ref|YP_008141874.1|   9 LIIGIAVGALTGITGSSGVLVVVPVLSYMgINFKTSVGTSLLVDVVTTTIVIYVYLRKKTLNPGIGIVLGIGAIIGA 85 
                                       789*************************769********************************************** PP

                              TauE  78 llGallllllpsellkllfgvlllllallmllrkkr.....srakgrerrptaillvliggl.vGllsGllGiGgGf 148
                                       +lG+l++  lp   l+++f ++ ++++++++ ++        r+ + +r   +i+ +++  + vG+l+G++G +gG+
  gi|518652354|ref|YP_008141874.1|  86 QLGSLIAGILPVLPLEIIFTAMAAYMSYYVIKKSYNidshgVRKMELSRNLALIIGFAL-SIpVGILTGVIGTSGGI 161
                                       ******************************98776667654223344555555544454.677************** PP

                              TauE 149 llvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrrlf 225
                                       + v + ++++ +  +++v+t++l++++++++g +gy+  g++d+ +++l+++ al+ ++  + +a++++++++ r++
  gi|518652354|ref|YP_008141874.1| 162 MFVLIIMVFFSMKAQNMVGTATLAMFLSAASGSIGYYDIGHIDFLAAILIGVVALVSGYYFSIFAHKIKQKYIYRFI 238
                                       ***************************************************************************** PP

                              TauE 226 allllvlgv 234
                                       +++ +++ +
  gi|518652354|ref|YP_008141874.1| 239 GVVFIIVVI 247
                                       ***999876 PP

>> TLE_N  Groucho/TLE N-terminal Q-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.14   1.3e+03      79      98 ..      83     102 ..      69     109 .. 0.85
   2 ?    9.6   0.2    0.0001      0.92      58      91 ..     109     144 ..     104     149 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.14
                             TLE_N  79 iakrlnaiiaqvlpflsqeh 98 
                                       i+ +l+++ia +lp+l+ e 
  gi|518652354|ref|YP_008141874.1|  83 IGAQLGSLIAGILPVLPLEI 102
                                       6778999*********9885 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0001
                             TLE_N  58 hyvmYyemsygLniemh..kqteiakrlnaiiaqvl 91 
                                        y+ Yy + ++ ni++h  +++e+++ l+ ii   l
  gi|518652354|ref|YP_008141874.1| 109 AYMSYYVIKKSYNIDSHgvRKMELSRNLALIIGFAL 144
                                       69***************999*********9987555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1325  (0.0739026); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1766.36
//
Query:       gi|518652355|ref|YP_008141875.1|  [L=257]
Description: molybdopterin biosynthesis MoeB protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-58  197.6   0.1    2.5e-58  197.3   0.1    1.0  1  ThiF             ThiF family
    7.5e-05   22.2   0.1    0.00013   21.4   0.1    1.3  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
    9.1e-05   22.5   0.8    0.00042   20.4   0.3    2.1  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0033   17.7   0.1     0.0098   16.2   0.1    1.9  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
       0.01   15.1   0.0      0.015   14.6   0.0    1.2  1  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
      0.011   15.3   0.0      0.016   14.8   0.0    1.2  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
       0.04   14.2   0.1      0.085   13.1   0.1    1.5  1  TrkA_N           TrkA-N domain
       0.04   13.2   0.0      0.056   12.7   0.0    1.2  1  FAD_binding_3    FAD binding domain
      0.049   13.3   0.0      0.074   12.7   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
      0.053   14.2   0.3       0.15   12.8   0.1    1.9  2  PglD_N           PglD N-terminal domain
       0.11   13.1   0.2       0.29   11.7   0.2    1.8  1  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
       0.11   12.9   0.0       0.18   12.2   0.0    1.3  1  NAD_binding_7    Putative NAD(P)-binding
       0.14   11.8   0.0       0.22   11.2   0.0    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
       0.17   11.7   0.0       0.26   11.1   0.0    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.3   0.1   1.9e-61   2.5e-58       1     243 [.       6     236 ..       6     237 .. 0.95

  Alignments for each domain:
  == domain 1  score: 197.3 bits;  conditional E-value: 1.9e-61
                                       THHHHHH..HHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHH CS
                                       xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF   1 ysrqlal..lgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKae 75 
                                       ysrq++l  +ge++q+kL ++++l++G+Gg Gs +++++ ++Gv+kl lvD D+ie++Nl+Rq+l+  +d +++Kae
  gi|518652355|ref|YP_008141875.1|   6 YSRQIVLkqIGEANQKKLLEKTILIIGLGGTGSAAAEMFSRLGVKKLILVDRDRIEITNLHRQILYDMDDLKEYKAE 82 
                                       89**98899******************************************************************** PP

                                       HHHHHHHHT-TTSEEEEEES-CCGCCS-HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF  76 vaaealqeinpdveveavteritdetvleellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvvi 152
                                       +aa++lq+inpdveve ++  ++++     +++s+DlV+d++Dn+++r+++n+ac k+gip++ +++ +++g + +i
  gi|518652355|ref|YP_008141875.1|  83 TAAKKLQKINPDVEVEFHNSAFDSSL--AYMVNSADLVFDGTDNMTTRFIINDACDKYGIPWVFTSAIEMYGEFKAI 157
                                       **********************8874..589********************************************** PP

                                       EECCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHHHHHHHHHHHHTTBCGGGCCEEEECCTTTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 153 ipgktgcyeCldpsstedptekkvplctsiagnipaiatttavvaglaalellkllsgkeklenslltqvdllesrf 229
                                       ipgkt+cy C +      +++++ p+c ++ g   ++ t++a++a+  ++ ++k+l       +   +++d+++   
  gi|518652355|ref|YP_008141875.1| 158 IPGKTSCYACFN------SEPAELPSC-EVTG---VLNTVPALIASYGVNLAVKILLDY--GIDGSIYFIDAFNFEI 222
                                       ***********6......688999***.****...*********************544..45555559******** PP

                                       EEECCEEEEEEC-T CS
                                       xxxxxxxxxxxxxx RF
                              ThiF 230 envelerakkskcl 243
                                       +++++er++k++c+
  gi|518652355|ref|YP_008141875.1| 223 NKINVERNSKCRCC 236
                                       *********99996 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 !   21.4   0.1     1e-07   0.00013      27      85 ..      16      76 ..       2      85 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1e-07
                                      CCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHHCHHHHTC.EECSH CS
                      2-Hacid_dh_C 27 kallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkeeeeeelgv.elvsl 85
                                       +  +k+l +kt+ iiGlG  G+a+a++++ +g+ k+i +dr + + ++ +++ + ++++l
  gi|518652355|ref|YP_008141875.1| 16 GEANQKKLLEKTILIIGLGGTGSAAAEMFSRLGVkKLILVDRDRIEITNLHRQILyDMDDL 76
                                      567788999*************************889999999886664433322244455 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.3   3.3e-07   0.00042       6      71 ..      19      78 ..      14      85 .. 0.81
   2 ?   -0.7   0.0         1   1.3e+03      67      86 ..     106     125 ..      81     134 .. 0.64

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.3e-07
                                      HHS..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHH CS
                      Shikimate_DH  6 kleslkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelke 71
                                      + ++l ek++l+iG G +++ +a+++++ gvkk++ + R++    +l +++        ++++lke
  gi|518652355|ref|YP_008141875.1| 19 NQKKLLEKTILIIGLGGTGSAAAEMFSRLGVKKLILVDRDRIEITNLHRQI------LYDMDDLKE 78
                                      4557889**********************************9999999998......333444443 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1
                                       CGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  67 eelkellaeadvvisatase 86 
                                       ++l  ++++ad+v+  t   
  gi|518652355|ref|YP_008141875.1| 106 SSLAYMVNSADLVFDGTDNM 125
                                       45777899999999988654 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   7.6e-06    0.0098       1      45 [.      28      84 ..      28     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 7.6e-06
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..............T CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..............l 45
                                      +liiG G++G+a+ae+ +r +    +++++dr++ +  +l  ++              +
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRLGVK--KLILVDRDRIEITNLHRQIlydmddlkeykaetA 84
                                      89******************987..9**********99999888777776666444441 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.1e-05     0.015     136     180 ..      19      64 ..       7     105 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       HCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSS.TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
                       Pyr_redox_2 136 lklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrll.ra 180
                                        ++kll+k i+++G G +G+  A ++++lg++  ++ +rdr+   +
  gi|518652355|ref|YP_008141875.1|  19 NQKKLLEKTILIIGLGGTGSAAAEMFSRLGVKKLILVDRDRIEiTN 64 
                                       4567778************************766666666665333 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.2e-05     0.016       2      63 ..      27      88 ..      26     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                                      EEEEE--STTHHHHHHHHHHCT.SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTT CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeig.hevigvDideekvdklnsgkipiyepgLeelvkkavesgr 63
                                      +i +iGlG  G   a +++++g +++i+vD d+  + +l+++ ++ +  +L+e+ ++ ++++ 
  gi|518652355|ref|YP_008141875.1| 27 TILIIGLGGTGSAAAEMFSRLGvKKLILVDRDRIEITNLHRQILYDM-DDLKEYKAETAAKKL 88
                                      799*******************889***********99998765433.466666665554443 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   6.6e-05     0.085       1      38 [.      28      66 ..      28      73 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.6e-05
                                      EEEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelr 38
                                      i+iiGlG +G++ ae +s+ g k+ +++d+d+  + +l 
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRlGVKKLILVDRDRIEITNLH 66
                                      79*****************88899******986666654 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.4e-05     0.056       3      34 ..      27      59 ..      25      72 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.4e-05
                                      EEEEE--SHHHHHHHHHHHHTTHH.EEEEESSS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvr.vvlvekrs 34
                                      ++lI+G G +G  +a + s+ Gv+  +lv++ +
  gi|518652355|ref|YP_008141875.1| 27 TILIIGLGGTGSAAAEMFSRLGVKkLILVDRDR 59
                                      689********************9456678876 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   0.0   5.7e-05     0.074       1      40 [.      28      67 ..      28     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.7e-05
                                      EEEES-SHHHHHHHHHHHH.HTHCEEEE-SCH.HHHHHHHHC CS
                              ApbA  1 iailGaGaiGsllaakLak.agadvtlilrsr.rlealkknG 40
                                      i+i+G+G+ Gs  a + ++    + +l++r+r ++ +l+   
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRlGVKKLILVDRDRiEITNLH--R 67
                                      89*****************66666*******95555543..3 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   0.00011      0.15       2      57 ..      28      82 ..      27      86 .. 0.74
   2 ?   -1.9   0.0       4.4   5.6e+03      28      45 ..     235     252 ..     206     256 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00011
                            PglD_N  2 ivIiGaGGhgkvvadiieangeyeiigflD.dnkktevegypvlgkaiellkslsee 57
                                      i+IiG GG g   a++  + g  + ++++D d+ + +    ++l  ++++lk++++e
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRLG-VKKLILVDrDRIEITNLHRQILY-DMDDLKEYKAE 82
                                      99*******************.66666666155554455567777.57778888554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.4
                            PglD_N  28 gflDdnkktevegypvlg 45 
                                       ++ D+++k   ++y ++g
  gi|518652355|ref|YP_008141875.1| 235 CCHDKDYKYLGKEYSGIG 252
                                       344445544445555555 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00023      0.29       2      35 ..      28      61 ..      27      78 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                                      ++++G G +g  +A+++++lg k  +++ +d++ 
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRLGVKKLILVDRDRIE 61
                                      89*******************9888888888875 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.18       6      88 ..      24     141 ..      21     151 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                     NAD_binding_7   6 kgkkvlvvGgGevAarkvrklleag.akvtvvapevkeele........................elvklaeeelek 57 
                                        +k++l++G G  +   ++ + + g +k+++v+ +     e                        +           
  gi|518652355|ref|YP_008141875.1|  24 LEKTILIIGLGGTGSAAAEMFSRLGvKKLILVDRDRI---EitnlhrqilydmddlkeykaetaaK----------- 86 
                                       589********************99788999999953...33347777777666444433333330........... PP

                     NAD_binding_7  58 d........................legadlviaatddrelneriaeaakarril 88 
                                       +                        ++ adlv+  td+   +  i +a+ +++i+
  gi|518652355|ref|YP_008141875.1|  87 KlqkinpdvevefhnsafdsslaymVNSADLVFDGTDNMTTRFIINDACDKYGIP 141
                                       12333333444444445555567768889*******9999999999999999987 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00017      0.22      17      92 ..      10      91 ..       3     119 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00017
                                      HHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEE..ETTEE..-HHHHHHHHHCSSS..S CS
                     ELFV_dehydrog 17 yveemlkklkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviy..dpeGl..dieellelkeerks..v 89
                                      +v + + ++++++l +k++ i G G  gs+aa+++++lg k + ++D + + +      +  d+++l+e+k+e+++  +
  gi|518652355|ref|YP_008141875.1| 10 IVLKQIGEANQKKLLEKTILIIGLGGTGSAAAEMFSRLGVKKLILVDRDRIEItnLHRQIlyDMDDLKEYKAETAAkkL 88
                                      4444445558889999*************************99999987553311112224577777777666655445 PP

                                      TTH CS
                     ELFV_dehydrog 90 key 92
                                      +++
  gi|518652355|ref|YP_008141875.1| 89 QKI 91
                                      555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0002      0.26       2      73 ..      28      97 ..      27     127 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
                                      EEEE--SCCHHHHHHHHHHTT-E.EEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagle.Vvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdl 73
                                      + +iG G  G+  a++f + g++   lvd+++  +++ +++i   ++ l+e    k+e++++ l++i+++ ++
  gi|518652355|ref|YP_008141875.1| 28 ILIIGLGGTGSAAAEMFSRLGVKkLILVDRDRIEITNLHRQILYDMDDLKEY---KAETAAKKLQKINPDVEV 97
                                      679******************9638899**9999999999998866666443...334444444444443332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       858  (0.0478554); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1848.39
//
Query:       gi|518652356|ref|YP_008141876.1|  [L=176]
Description: hypothetical protein FACI_IFERC00001G0995 [Ferroplasma acidarmanus fer1]
Scores for complete 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   19.4   1.6     0.0011   19.4   1.6    2.1  2  DUF4199         Protein of unknown function (DUF4199)
  ------ inclusion threshold ------
       0.13   12.6   2.7       0.15   12.4   0.3    2.2  3  DUF1440         Protein of unknown function (DUF1440)
       0.15   11.2   0.2       0.15   11.2   0.2    2.9  3  FTR1            Iron permease FTR1 family
        1.6    8.4   6.5         13    5.4   4.8    2.4  1  CbtA            Probable cobalt transporter subunit (CbtA)
        2.4    7.7  10.9          3    7.4  10.9    1.2  1  Virul_fac_BrkB  Virulence factor BrkB
        3.2    8.2  14.7        0.5   10.8   1.2    3.3  3  Romo1           Reactive mitochondrial oxygen species modulat


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 !   19.4   1.6   3.7e-07    0.0011      71     164 ..       9      89 ..       4      93 .. 0.69
   2 ?    2.0   2.1     0.083   2.5e+02       8      47 ..     109     149 ..     102     164 .. 0.46

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.7e-07
                           DUF4199  71 gfgflislvagllsavfqyiyfnfidpdfienyiaeilekleeakeesaeeenaemseeeikealeslspiiv.alq 146
                                       ++g++  lv g+l ++f y+ +  +  d ++ + + + +++           +++ + +++ ++      + +  + 
  gi|518652356|ref|YP_008141876.1|   9 KAGVVAGLVYGILDGIFAYVVLVIFKTDVMKVMSTLAAKET---------SLGIKVTGAQLYST-----DLTLaPVE 71 
                                       67888888888888888888885557777777776665553.........34566666777331.....12233578 PP

                           DUF4199 147 sflgnliiGlilsliiAl 164
                                       +++g liiG+il++i+A 
  gi|518652356|ref|YP_008141876.1|  72 GIVGGLIIGIILGIIFAY 89 
                                       9**************995 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.083
                           DUF4199   8 lvwilifllilyllglhqi.lstgpllglla.llllllv.pfl 47 
                                       ++wi++ +l + +++   +   t+ + ++ + ++ l++  ++l
  gi|518652356|ref|YP_008141876.1| 109 ILWIIFDVL-IGAVDI-STyGLTYYIASIAFdIIPLVVFgFIL 149
                                       345555553.222233.23234445666666433222222333 PP

>> DUF1440  Protein of unknown function (DUF1440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.44   1.3e+03      83      97 ..      16      30 ..       7      51 .. 0.56
   2 ?   12.4   0.3   4.9e-05      0.15      33     100 ..      50     117 ..      34     122 .. 0.78
   3 ?   -1.9   0.0       1.3     4e+03      61      70 ..     143     152 ..     117     159 .. 0.51

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.44
                           DUF1440 83 lwqGalfGllvtiav 97
                                      l++G+l G+++++++
  gi|518652356|ref|YP_008141876.1| 16 LVYGILDGIFAYVVL 30
                                      344444444444443 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.9e-05
                           DUF1440  33 qlGipedltsatytysgqkvnwvs.vlvhilfsivfavlYvvvaevfpkikl.wqGalfGllvtiavHli 100
                                       +lGi  ++t a+ +  + ++  v+ ++  ++++i+++++++++ +++p  ++  +G +fGl+++i++ ++
  gi|518652356|ref|YP_008141876.1|  50 SLGI--KVTGAQLYSTDLTLAPVEgIVGGLIIGIILGIIFAYTHNKIPGKNMiIKGEIFGLILWIIFDVL 117
                                       4788..78888777777776555505557899**************996665279**********99765 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.3
                           DUF1440  61 ilfsivfavl 70 
                                       ++f++++++l
  gi|518652356|ref|YP_008141876.1| 143 VVFGFILGTL 152
                                       3333444433 PP

>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   1.2       0.1   3.1e+02     170     191 ..      10      31 ..       6      44 .. 0.79
   2 ?   11.2   0.2   4.9e-05      0.15     154     200 ..      55     101 ..      53     106 .. 0.83
   3 ?    5.7   2.5    0.0024       7.1     256     303 ..     101     151 ..      97     154 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.1
                              FTR1 170 lgvvlGaliavvlglliyrglv 191
                                       +gvv+G+  +++ g+++y++lv
  gi|518652356|ref|YP_008141876.1|  10 AGVVAGLVYGILDGIFAYVVLV 31 
                                       6899999999999999998875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4.9e-05
                              FTR1 154 vaaivaytvkrvsalilgvvlGaliavvlglliyrglvklslqsffi 200
                                       v++++ y ++ ++a++ g+v+G++i+++lg+++ +  +k+ ++ ++i
  gi|518652356|ref|YP_008141876.1|  55 VTGAQLYSTDLTLAPVEGIVGGLIIGIILGIIFAYTHNKIPGKNMII 101
                                       55666666666799********************9999999988776 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.0024
                              FTR1 256 lavereg...leivlaliGwantgplglivyaavwlvvlillgllliklgv 303
                                       +++e+ g   ++i+ +liG ++  ++gl  y+a +++ +i l+++ ++lg 
  gi|518652356|ref|YP_008141876.1| 101 IKGEIFGlilWIIFDVLIGAVDISTYGLTYYIASIAFDIIPLVVFGFILGT 151
                                       56777788889**********************************999886 PP

>> CbtA  Probable cobalt transporter subunit (CbtA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   4.8    0.0044        13       8     120 ..      11     114 ..       5     120 .. 0.62

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0044
                              CbtA   8 gllaGllAGllaflvqrlvvePlilaAeayEeaaaaaeaaeaaaeHehaeaeepelvsrgvqrtlgtvlanvltgva 84 
                                       g++aGl+ G+l ++++++v      +  ++ +  aa+e++   +        +++l s +++   +  + +++ g+ 
  gi|518652356|ref|YP_008141876.1|  11 GVVAGLVYGILDGIFAYVVLVIFKTDVMKVMSTLAAKETSLGIK------VTGAQLYSTDLT---LAPVEGIVGGLI 78 
                                       55555555555555555554444444444444333333333332......223333333333...346677899999 PP

                              CbtA  85 lglllaavfallegrlgklsaralalllalagflav 120
                                       +g +l+++fa++++++++ +   ++ +++l+ ++ +
  gi|518652356|ref|YP_008141876.1|  79 IGIILGIIFAYTHNKIPGKNMIIKGEIFGLILWIIF 114
                                       999999999999999999999999999999999876 PP

>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4  10.9     0.001         3     111     224 ..      19     130 ..       7     153 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.001
                    Virul_fac_BrkB 111 krllsllllllllvllllslvlsvflqslllasa...pllglglelsellllqllrwlvallllvlafallYrvlpn 184
                                       ++l+ ++++++l+++   ++ +++ l +  +  +   ++ g++l +++l +l  ++ +v  l++ +++ +++ ++ n
  gi|518652356|ref|YP_008141876.1|  19 GILDGIFAYVVLVIFKTDVMKVMSTLAAKET--SlgiKVTGAQLYSTDL-TLAPVEGIVGGLIIGIILGIIFAYTHN 92 
                                       4555555556555555555555555544333..1357777777777777.68888888999999************* PP

                    Virul_fac_BrkB 185 vkvrlraalpGallaallwllvkilfslylsnfasynaiY 224
                                       + +    ++ G +++ +lw+++ +l++  +   ++y+ +Y
  gi|518652356|ref|YP_008141876.1|  93 KIPGKNMIIKGEIFGLILWIIFDVLIG-AVD-ISTYGLTY 130
                                       *************************99.444.46777777 PP

>> Romo1  Reactive mitochondrial oxygen species modulator 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   1.7     0.011        32       7      30 ..       5      28 ..       1      51 [. 0.63
   2 ?   10.8   1.2   0.00017       0.5      15      58 ..      74     110 ..      70     114 .. 0.88
   3 ?   -1.0   0.1      0.78   2.3e+03      19      26 ..     144     151 ..     143     154 .. 0.58

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.011
                             Romo1  7 kmGalmGaaVGlaiGllfGtfsal 30
                                        Ga+ G++ Gl+ G+l G f+ +
  gi|518652356|ref|YP_008141876.1|  5 GLGAKAGVVAGLVYGILDGIFAYV 28
                                      456666777777777776666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00017
                             Romo1  15 aVGlaiGllfGtfsalryglrgrgllrtlgksmlgsaatFGfFm 58 
                                       + Gl+iG+++G + a+++        +  gk+m+  + +FG+++
  gi|518652356|ref|YP_008141876.1|  74 VGGLIIGIILGIIFAYTHN-------KIPGKNMIIKGEIFGLIL 110
                                       44899*************9.......9999***********998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.78
                             Romo1  19 aiGllfGt 26 
                                       ++G+++Gt
  gi|518652356|ref|YP_008141876.1| 144 VFGFILGT 151
                                       45555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1217.01
//
Query:       gi|518652357|ref|YP_008141877.1|  [L=291]
Description: hypothetical protein FACI_IFERC00001G0996 [Ferroplasma acidarmanus fer1]
Scores for complete 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  120.9   0.0    6.4e-35  120.7   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 !  120.7   0.0   3.6e-39   6.4e-35       5     197 ..      11     270 ..       7     282 .. 0.77

  Alignments for each domain:
  == domain 1  score: 120.7 bits;  conditional E-value: 3.6e-39
                                       HHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBC...SSSB--TTEEEE CS
                     Peptidase_M24   5 kaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytp...ndrvlkegdlvl 78 
                                        a++i + ale++ + i+pg   +++a+++e++  +r  +  ++fp  v +++n++++hytp   +++++k gdlv+
  gi|518652357|ref|YP_008141877.1|  11 LAGKIGRDALEYAQTLIEPGALFYDVAEKAEQF--IRDKGAVPSFP--VNLSINNEAAHYTPyegDKKKFKTGDLVK 83 
                                       599****************************99..555566799**..9999999999****9988999******** PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                       +d+ga +dgy+sD + T+ vG  t  + +l++a+++a++ aik ++p +++  i++ + +v++s+g+  +++++ GH
  gi|518652357|ref|YP_008141877.1|  84 VDLGAMVDGYMSDNAATIEVG-NTGNYSDLIDATRDALNSAIKILRPLINIYRIGEEIGNVITSRGF-NPIKNLGGH 158
                                       ******************888.456799***************************************.999****** PP

                                       EESS.SSSEEEEEESS.STTCSSB--TTBEEEEEE...............EEEEETTT................... CS
                     Peptidase_M24 156 gvGl.evhdegpsvsr.esndgrkleeGmvftiEp...............giyfapge................... 196
                                       g+ + ++h e  ++++ + +++++++   v++iEp                iy                        
  gi|518652357|ref|YP_008141877.1| 159 GINRyDLHSE-IFIPNyDDGNDETIKTDKVIAIEPfastgigmihsgqmgNIY----Iidkpgvrdrdeilyknfnt 230
                                       ***99***99.6665433558**************988855444444444333....03322334444444444444 PP

                                       .......................................E CS
                     Peptidase_M24 197 .......................................g 197
                                                                              +
  gi|518652357|ref|YP_008141877.1| 231 apfaerwvsrlmkndqeyirkkmstkyvsgfpvlkehskS 270
                                       4444444555555555555555555555555555555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1973.45
//
Query:       gi|518652358|ref|YP_008141878.1|  [L=206]
Description: thymidylate kinase [Ferroplasma acidarmanus fer1]
Scores for complete 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   75.3   0.1    8.6e-21   74.4   0.1    1.5  1  Thymidylate_kin  Thymidylate kinase
    1.5e-15   57.6   1.2    2.7e-15   56.8   1.2    1.4  1  dNK              Deoxynucleoside kinase
    3.2e-05   24.5   0.4    0.00017   22.1   0.3    2.1  1  AAA_18           AAA domain
     0.0011   18.8   0.1       0.86    9.3   0.0    2.2  2  PRK              Phosphoribulokinase / Uridine kinase family
  ------ inclusion threshold ------
      0.012   14.7   0.5      0.018   14.2   0.5    1.2  1  G-alpha          G-protein alpha subunit
      0.016   15.6   0.0      0.023   15.1   0.0    1.3  1  AAA_16           AAA ATPase domain
      0.017   15.0   0.1       0.31   10.9   0.1    2.1  1  NACHT            NACHT domain
      0.017   15.4   0.0      0.027   14.7   0.0    1.4  1  AAA_28           AAA domain
      0.017   14.5   0.0      0.038   13.4   0.0    1.6  1  Arf              ADP-ribosylation factor family
      0.034   14.4   0.0       0.06   13.6   0.0    1.5  1  AAA_22           AAA domain
      0.045   14.2   0.0        8.2    6.9   0.0    2.4  2  AAA_17           AAA domain
      0.056   13.6   0.0       0.27   11.4   0.0    2.0  1  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.1   5.8e-24   8.6e-21       1     181 [.       5     192 ..       5     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 5.8e-24
                                       EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHH CS
                   Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpal 77 
                                       iEG+DG+GKtt ++ l++ +++ +    +trep++      ++ l   ++ +++    +lf+ dr  +++++i    
  gi|518652358|ref|YP_008141878.1|   5 IEGIDGSGKTTLVNSLRKIFDNIH----FTREPTDKFQLANLKTL---STPFNSFYNFFLFTYDR-LEHQDEIN--- 70 
                                       8*******************9877....89*99976544445554...5788888899*******.44454555... PP

                                       HTT-EEEEES-HHHHHHHHHT.TTTT....TCHHHHHHGGGTTS.E-SEEEEEESSHHHHHTSCCTTSS........ CS
                   Thymidylate_kin  78 kqgktvivdRylfSslaYqga.kegv....dldlvlslnedvll.kPdltflldvdpevalkRlakrde........ 140
                                          k vi+dRyl+Ss+aY+g+  e++       +++ l+ + +l  Pd++++ld   +val+R++  ++        
  gi|518652358|ref|YP_008141878.1|  71 -GFKNVICDRYLASSIAYEGPmIEELfgdkKETVLWMLEVSKMLkLPDMIIYLDAHLDVALERIRNSRKnlnfrgkq 146
                                       .4899***************8544332211233444444444457********************999966666644 PP

                                       .TTTSHHHHHHHHHHHHHHHHHHHH....TTSTEEEEETTS-HHHH CS
                   Thymidylate_kin 141 .ldeeeeeqldflrkvrerylelak....ederiliidasksieev 181
                                        +  ee+e l+  + + e++l  ++    ++ +i  i+a++++e+v
  gi|518652358|ref|YP_008141878.1| 147 lSILEEKEGLKAIQDYYEYFLGNIEmftkKQIKIERINANSPMEDV 192
                                       3334555555555555555554443320233333445666666665 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   1.2   1.8e-18   2.7e-15       1     203 [.       3     200 ..       3     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 1.8e-18
                                       EEEEESTTSSHHHHHHHHHCCST.CEEEE-HHHHCCSSSSHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHCHHSSS- CS
                               dNK   1 ivveGnIgaGKstlvklLskklg.vkvfeEpvdkwtnvqknlLekfYkdpsrwsfalqtyvllsrlkqqlealatkq 76 
                                       i++eG  g+GK+tlv+ L+k ++ +++ +Ep dk++  + + L+  ++ +  + f l t     rl+ q e+ +  +
  gi|518652358|ref|YP_008141878.1|   3 ITIEGIDGSGKTTLVNSLRKIFDnIHFTREPTDKFQLANLKTLSTPFNSF--YNFFLFT---YDRLEHQDEI-NGFK 73 
                                       89*********************9***********887777777777654..5565544...4566666666.7779 PP

                                       EEEEES-HHHHHHTHHHHHHHTTSS-HHHHHHHHHHHHHHH..HHCCH....-SEEEEEE--HHHHHHHHHHCTTCC CS
                               dNK  77 vvvleRsiysdryiFakalaekgtlseeelkiykelldnll..eelak....pdlliYLkasletclerikkRgree 147
                                       +v+ +R   s+        a +g + ee +   ke   ++l  +   k    pd++iYL+a+l++ leri++  ++ 
  gi|518652358|ref|YP_008141878.1|  74 NVICDRYLASSI-------AYEGPMIEELFGDKKETVLWMLevS---KmlklPDMIIYLDAHLDVALERIRNSRKNL 140
                                       99***9999888.......4466677777777777777777332...224469*****************9755544 PP

                                       CT.......TS-HHHHHHHHHHHHHHHTSGGCS-EEEEETSS.-TTTHCCHHHHHHHHHHHHH CS
                               dNK 148 ek.......kieldYlekLhekyeewlkklnevpvlvidveeldlvaeeekredvveevkelv 203
                                       +          e++ l++++ +ye +l +++ +++  i +e+   +++++  edv+ + k+++
  gi|518652358|ref|YP_008141878.1| 141 NFrgkqlsiLEEKEGLKAIQDYYEYFLGNIEMFTKKQIKIER---INANSPMEDVLYKAKNII 200
                                       333445633446789***************************...889999999999888877 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.3   1.2e-07   0.00017       1     116 [.       3     139 ..       3     154 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.2e-07
                            AAA_18   1 IlltGtpGvGKttlakeLskrl.gf..gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssalee 73 
                                       I + G+ G+GKttl + L+k   ++   ++ +d ++  +l +  +p+  + ++  +  d+  +++d++++       
  gi|518652358|ref|YP_008141878.1|   3 ITIEGIDGSGKTTLVNSLRKIFdNIhfTREPTDKFQLANLKTLSTPFnSFYNFFLFTYDR-LEHQDEINGFK----- 73 
                                       89******************9966699777777777777777777774334444444444.55555555553..... PP

                            AAA_18  74 gknlvidghlaeleseaakdikk.........................vvLtaspeelleRlekRgye 116
                                         n++ d  la  + ++   i                           ++L+a+ ++ leR+++ +++
  gi|518652358|ref|YP_008141878.1|  74 --NVICDRYLASSIAYEGPMIEElfgdkketvlwmlevskmlklpdmiIYLDAHLDVALERIRNSRKN 139
                                       ..3344444444433333333333444444566777778999999999**************998765 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   0.0   0.00058      0.86       1      27 [.       2      28 ..       2      51 .. 0.84
   2 !    7.7   0.0    0.0018       2.7     122     161 ..     108     149 ..     102     186 .. 0.72

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00058
                               PRK  1 vIgvagsSGaGkttvarklekifgrek 27
                                      +I + g  G+Gktt+ + l+kif + +
  gi|518652358|ref|YP_008141878.1|  2 FITIEGIDGSGKTTLVNSLRKIFDNIH 28
                                      59999******************9554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0018
                               PRK 122 ydervaelldlkiyvdisidlelar..klqRDiaeRGrslea 161
                                        + ++ +l d+ iy+d+  d+ l r     +  + RG++l  
  gi|518652358|ref|YP_008141878.1| 108 EVSKMLKLPDMIIYLDAHLDVALERirNSRKNLNFRGKQLSI 149
                                       5778899*************9885420445567778887754 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.5   1.2e-05     0.018      30     173 ..       7     177 ..       2     203 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.2e-05
                                       ESTTSSHHHHHHHHHHHCS--.--HHHHHCCHHHHHHHHHHHHHHHHHHHHH....T.T.......HHHC-SS-SCC CS
                           G-alpha  30 GqseSGKsTilkqlkllykkg.fseeelatwraviqlnivrsiktileales....l.eselsesfelqelkerldp 100
                                       G ++SGK+T++++l++++++  f++e   +++    +++ + ++++ + + +    l +++ ++ f++  + + l+ 
  gi|518652358|ref|YP_008141878.1|   7 GIDGSGKTTLVNSLRKIFDNIhFTREPTDKFQLANLKTLSTPFNSFYNFFLFtydrLeHQDEINGFKNVICDRYLAS 83 
                                       8899***********99999866666445566666666666666665555553333234555566688888888888 PP

                                       CS-HCHHHH....................................HHCCHHC-HCHHHHHHHHCCSHHHHHHHCCGC CS
                           G-alpha 101 lkkveasliaklssateee..........................qeiefnpraevgedikaLwndpgiqelyerrn 151
                                       + ++e  +i++l ++++e+                                  ++++++ k L  +    +++e+++
  gi|518652358|ref|YP_008141878.1|  84 SIAYEGPMIEELFGDKKETvlwmlevskmlklpdmiiyldahldvA------LERIRNSRKNLNFRGKQLSILEEKE 154
                                       8999999999888888888887777776666555444444332220......1233333333332223334444444 PP

                                       CTT.--TTHHHHHCTHHHHCSTT CS
                           G-alpha 152 kik.lednaeyFlddleritspd 173
                                        +k ++d  eyFl ++e  t+++
  gi|518652358|ref|YP_008141878.1| 155 GLKaIQDYYEYFLGNIEMFTKKQ 177
                                       44445566666666665555544 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.5e-05     0.023      29      69 ..       5      49 ..       2     103 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.5e-05
                            AAA_16 29 lsGesGvGKsslvrellralekdggiflrgkcdqlesa......ipy 69
                                      + G  G+GK++lv++l++ + ++ ++f+r+ +d+++ a      +p+
  gi|518652358|ref|YP_008141878.1|  5 IEGIDGSGKTTLVNSLRK-IFDN-IHFTREPTDKFQLAnlktlsTPF 49
                                      67889************5.7767.9**99999999444444444555 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00021      0.31       3      21 ..       3      21 ..       1     104 [. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00021
                                      EEEEC-TTTCHHHHHHHHH CS
                             NACHT  3 vilqGeaGsGKTtLlqkla 21
                                      + ++G  GsGKTtL+ +l 
  gi|518652358|ref|YP_008141878.1|  3 ITIEGIDGSGKTTLVNSLR 21
                                      6799**********87663 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.8e-05     0.027       2      89 ..       3      88 ..       2     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                            AAA_28  2 ivitGgestGKTtlleaLaar..gypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlfc 78
                                      i i G  ++GKTtl++ L +   ++   +E+  ++   +l++     ++ +++  f + +le+q e     ++ k ++c
  gi|518652358|ref|YP_008141878.1|  3 ITIEGIDGSGKTTLVNSLRKIfdNIHFTREPTDKFQLANLKTLSTPFNSFYNFFLFTYDRLEHQDE----INGFKNVIC 77
                                      7789999************987799999******99999999887666668999999998887744....46778999* PP

                            AAA_28 79 DrglldtlaYa 89
                                      Dr l  ++aY 
  gi|518652358|ref|YP_008141878.1| 78 DRYLASSIAYE 88
                                      **999999995 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   2.6e-05     0.038      17      61 ..       3      50 ..       1      53 [. 0.76

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 2.6e-05
                                      EEEEESTTSSHHHHHHHHHH...SSCEECSSSSSEEEEEEEETTEEEE CS
                               Arf 17 illlGLDnaGKtTilkklkl...eelvttvPTigfnveeleiknlkft 61
                                      i + G+D++GKtT+++ l++   +   t  PT  f+  +l++    f+
  gi|518652358|ref|YP_008141878.1|  3 ITIEGIDGSGKTTLVNSLRKifdNIHFTREPTDKFQLANLKTLSTPFN 50
                                      5677**********9988743314455789*****9999988766666 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0     4e-05      0.06       7      51 ..       2      46 ..       1      89 [. 0.73

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4e-05
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst 51
                                      ++++ G  G+GKTtl++ l++ +d+  + +e+ +++ + +l+ ++
  gi|518652358|ref|YP_008141878.1|  2 FITIEGIDGSGKTTLVNSLRKIFDNIHFTREPTDKFQLANLKTLS 46
                                      78999****************999766666644444444444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0    0.0055       8.2       2      23 ..       7      28 ..       6      31 .. 0.83
   2 ?    5.2   0.0     0.018        26      95     123 ..     108     137 ..      74     152 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0055
                                      E-TTSSHHHHHHHHHHHHTEEE CS
                            AAA_17  2 GgPGsGKgtqceklvekygfth 23
                                      G+ GsGK+t+++ l + ++  h
  gi|518652358|ref|YP_008141878.1|  7 GIDGSGKTTLVNSLRKIFDNIH 28
                                      899********99998776555 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.018
                                       HHHHHH...SEEEEEE--HHHHHHHHHHHT CS
                            AAA_17  95 evleelk.pdaiilleadpeeilerrlkdr 123
                                       ev + lk pd+ii+l+a  ++ ler  + r
  gi|518652358|ref|YP_008141878.1| 108 EVSKMLKlPDMIIYLDAHLDVALERIRNSR 137
                                       444555526***********9999987664 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   0.00018      0.27       4     116 ..       5     134 ..       2     154 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00018
                            AAA_33   4 lvGlpGsGKstlaerllkklg.avllssdtlrrrlfgtdqqskt............dytrvldrlyqilnelarkal 67 
                                       + G  GsGK+tl+ +l k  +   + +++t +++l++ +  s+             d+ +  d+++++ n +++++l
  gi|518652358|ref|YP_008141878.1|   5 IEGIDGSGKTTLVNSLRKIFDnIHFTREPTDKFQLANLKTLSTPfnsfynfflftyDRLEHQDEINGFKNVICDRYL 81 
                                       789***********998766655556777766777763333332344555555543333333445555444454444 PP

                            AAA_33  68 sagrnv...ildatnlsr.rerarflklarrlgvpvrivvvetdeetlkeRla 116
                                       ++ +++   ++   + ++ ++  ++l++ + l+ p+ i+++++  +++ eR++
  gi|518652358|ref|YP_008141878.1|  82 ASSIAYegpMIEELFGDKkETVLWMLEVSKMLKLPDMIIYLDAHLDVALERIR 134
                                       44433222244444555534456666666677777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1528.15
//
Query:       gi|518652359|ref|YP_008141879.1|  [L=192]
Description: hypothetical protein FACI_IFERC00001G0998 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-16   60.3   2.0    1.6e-10   41.2   0.3    2.4  2  CBS             CBS domain
    8.6e-16   57.7   0.3    8.6e-16   57.7   0.3    1.7  2  HTH_3           Helix-turn-helix
    3.4e-11   43.0   0.9    8.2e-11   41.8   0.9    1.8  1  HTH_19          Helix-turn-helix domain
    7.9e-11   42.1   0.0    1.3e-10   41.4   0.0    1.3  1  HTH_31          Helix-turn-helix domain
    2.4e-05   24.2   0.3    0.00035   20.5   0.1    2.7  2  HTH_37          Helix-turn-helix domain
     0.0001   22.1   0.1    0.00019   21.2   0.1    1.4  1  HTH_25          Helix-turn-helix domain
    0.00037   20.9   0.0      0.001   19.5   0.0    1.7  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    0.00069   19.7   0.1     0.0013   18.8   0.0    1.5  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
     0.0089   15.6   0.4      0.094   12.3   0.1    2.7  3  HTH_24          Winged helix-turn-helix DNA-binding
  ------ inclusion threshold ------
      0.021   14.8   0.1       0.12   12.4   0.1    2.3  2  Pou             Pou domain - N-terminal to homeobox domain
      0.029   14.3   0.1        1.8    8.6   0.0    2.6  2  TTRAP           Putative tranposon-transfer assisting protein
      0.051   13.9   0.3       0.39   11.1   0.1    2.6  2  E3_binding      e3 binding domain
      0.082   13.1   2.1       0.97    9.7   0.1    2.8  3  YbaB_DNA_bd     YbaB/EbfC DNA-binding family
      0.089   12.8   0.0       0.16   12.0   0.0    1.4  1  PyrBI_leader    PyrBI operon leader peptide
      0.099   12.5   0.0       0.23   11.3   0.0    1.6  1  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.3   1.4e-13   1.6e-10       4      51 ..      72     119 ..      62     124 .. 0.92
   2 !   18.5   0.1   1.7e-06     0.002       5      55 ..     141     188 ..     136     190 .. 0.76

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.4e-13
                                       HSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDl 51 
                                       imt+dv t+  ++++  al++mrekg+s+lPVV +d++++G +t++ +
  gi|518652359|ref|YP_008141879.1|  72 IMTKDVDTCEMNDSIISALNRMREKGYSQLPVVTSDKRIIGTITESNI 119
                                       5********************************9999********987 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.7e-06
                                       SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       m + ++ ++ +++++ +  l+ ++  +++++Vd+  +l Gi+t+ D+l+a+
  gi|518652359|ref|YP_008141879.1| 141 MGSVLPQLDKNSPISMIYPLL-KY-SNAVLIVDGT-ELKGIITKADVLKAV 188
                                       555556778888888888899.52.368899*655.5***********997 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.7   0.3   7.2e-19   8.6e-16       1      49 [.       8      56 ..       8      59 .. 0.97
   2 ?   -3.5   0.1       9.5   1.1e+04       7      12 ..      95     100 ..      92     101 .. 0.69

  Alignments for each domain:
  == domain 1  score: 57.7 bits;  conditional E-value: 7.2e-19
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHT CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLg 49
                                      l+++Rk lg+sq+eLA+ +Gvs+s+i+r+E+Ge nP  +++ k+ ++L+
  gi|518652359|ref|YP_008141879.1|  8 LRKMRKSLGISQKELARISGVSQSYIARLEKGEINPAYDKVRKIFEYLN 56
                                      89**********************************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 9.5
                                       HTTHHH CS
                             HTH_3   7 qlglsq 12 
                                       ++g+sq
  gi|518652359|ref|YP_008141879.1|  95 EKGYSQ 100
                                       688888 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.9   6.8e-14   8.2e-11       3      57 ..       7      60 ..       5      77 .. 0.91

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 6.8e-14
                            HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidle 57
                                       L+++R+ lg++q+ela+  g+s+s+i+ +E+g++ +p +++++ki e+l+ + +
  gi|518652359|ref|YP_008141879.1|  7 ELRKMRKSLGISQKELARISGVSQSYIARLEKGEI-NPAYDKVRKIFEYLNNSGN 60
                                      69*********************************.***************9987 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   1.1e-13   1.3e-10       5      55 ..       7      56 ..       6      63 .. 0.93

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.1e-13
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55
                                      +Lr +R+  G+sq+e+A+ +gvs+s++ rlE G++ +p  + ++++ ++l+
  gi|518652359|ref|YP_008141879.1|  7 ELRKMRKSLGISQKELARISGVSQSYIARLEKGEI-NPAYDKVRKIFEYLN 56
                                      8**********************************.6*********99987 PP

>> HTH_37  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     3e-07   0.00035      22      58 ..       7      43 ..       4      68 .. 0.85
   2 ?    1.3   0.0      0.29   3.5e+02      42      54 ..      81      93 ..      55     138 .. 0.61

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 3e-07
                                      HHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT CS
                            HTH_37 22 aiaeliekrelsqseaaqllgiaqPkvsrllrgklsr 58
                                      +++++++++++sq+e+a++ g++q+ + rl++g+++ 
  gi|518652359|ref|YP_008141879.1|  7 ELRKMRKSLGISQKELARISGVSQSYIARLEKGEINP 43
                                      6899*****************************9975 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.29
                                      T--HHHHHHHHTT CS
                            HTH_37 42 giaqPkvsrllrg 54
                                      +++ + +s+l r 
  gi|518652359|ref|YP_008141879.1| 81 EMNDSIISALNRM 93
                                      3444444444433 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1   1.6e-07   0.00019       2      35 ..       8      41 ..       7      47 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.6e-07
                                      HHHHHHTTT--HHHHHHHSS--HHHHHHHHCT-- CS
                            HTH_25  2 LraaRearglsleevaketkIrkdylealEeddf 35
                                      Lr+ R+++g+s +e+a+   ++++y+ +lE++++
  gi|518652359|ref|YP_008141879.1|  8 LRKMRKSLGISQKELARISGVSQSYIARLEKGEI 41
                                      9******************************987 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   8.4e-07     0.001       2      50 ..       8      55 ..       7      57 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 8.4e-07
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaL 50
                                      Lr++ +  gi+++eLar +g+s++ ++rl kg++ ++  d   ki ++L
  gi|518652359|ref|YP_008141879.1|  8 LRKMRKSLGISQKELARISGVSQSYIARLEKGEI-NPAYDKVRKIFEYL 55
                                      999*****************************98.66666666665555 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.1e-06    0.0013      73     117 ..       7      52 ..       2      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                    MqsA_antitoxin  73 fiarvrkkleldqreaaeifGgGvnafsryekGkvrpplalv.kll 117
                                       +++++rk l+++q+e+a+i G+     +r ekG+++p    v k++
  gi|518652359|ref|YP_008141879.1|   7 ELRKMRKSLGISQKELARISGVSQSYIARLEKGEINPAYDKVrKIF 52 
                                       6889********************************9876552455 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.1   7.9e-05     0.094      17      36 ..      16      35 ..      13      38 .. 0.91
   2 ?   -0.2   0.0      0.65   7.8e+02      37      46 ..      89      98 ..      85      98 .. 0.85
   3 ?   -3.5   0.0       6.7     8e+03       5      13 ..     107     115 ..     106     117 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.9e-05
                            HTH_24 17 risqreLAerlglSpstvnr 36
                                      +isq+eLA+ +g+S+s + r
  gi|518652359|ref|YP_008141879.1| 16 GISQKELARISGVSQSYIAR 35
                                      79************998765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.65
                            HTH_24 37 rlkrLeeeGl 46
                                       l+r+ e+G+
  gi|518652359|ref|YP_008141879.1| 89 ALNRMREKGY 98
                                      699******8 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 6.7
                            HTH_24   5 drkILelLq 13 
                                       d++I+ ++ 
  gi|518652359|ref|YP_008141879.1| 107 DKRIIGTIT 115
                                       899998876 PP

>> Pou  Pou domain - N-terminal to homeobox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   9.8e-05      0.12      11      53 ..       6      42 ..       4      56 .. 0.86
   2 ?   -2.1   0.0       3.3     4e+03      29      41 ..      88     100 ..      84     104 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 9.8e-05
                               Pou 11 kefkqkRiklgltQadvglaLgklygkefSqttIcrFEkLdls 53
                                      +e+++ R +lg++Q+++++       + +Sq+ I r+Ek +++
  gi|518652359|ref|YP_008141879.1|  6 EELRKMRKSLGISQKELARI------SGVSQSYIARLEKGEIN 42
                                      6899***********99875......889*********96665 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.3
                               Pou  29 laLgklygkefSq 41 
                                       +aL+++  k +Sq
  gi|518652359|ref|YP_008141879.1|  88 SALNRMREKGYSQ 100
                                       6888888888888 PP

>> TTRAP  Putative tranposon-transfer assisting protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.078        93      21      40 ..       5      26 ..       3      38 .. 0.82
   2 ?    8.6   0.0    0.0015       1.8      31      60 ..      73     103 ..      49     105 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.078
                                      HHHHHHSTTTS...-HHHHHHH CS
                             TTRAP 21 ieelkaalkyl..eddelreLa 40
                                      ieel++++k l  + +el++++
  gi|518652359|ref|YP_008141879.1|  5 IEELRKMRKSLgiSQKELARIS 26
                                      89*********99999998875 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0015
                                       S..-HHHHHHHHHHHHHHTT--HHHHHHHSS CS
                             TTRAP  31 l.eddelreLaestlaKLkaltDaefaelel 60 
                                       + +d +  e+ +s+++ L++++++ +++l +
  gi|518652359|ref|YP_008141879.1|  73 MtKDVDTCEMNDSIISALNRMREKGYSQLPV 103
                                       368999*********************9965 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.1   2.6e+03       8      21 ..       9      25 ..       9      29 .. 0.65
   2 ?   11.1   0.1   0.00033      0.39      21      36 .]     170     185 ..     165     185 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.1
                                      HHHHHHCT-...-TTTS CS
                        E3_binding  8 RklAkelGi...dLsdv 21
                                      Rk+ k lGi   +L+ +
  gi|518652359|ref|YP_008141879.1|  9 RKMRKSLGIsqkELARI 25
                                      77888999955555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00033
                                       S---CTTTBE-HHHHC CS
                        E3_binding  21 vkGtGpgGRItkeDVl 36 
                                       v Gt  +G Itk+DVl
  gi|518652359|ref|YP_008141879.1| 170 VDGTELKGIITKADVL 185
                                       67*************7 PP

>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.3   1.6e+03       3      23 ..       7      27 ..       5      32 .. 0.80
   2 ?    9.7   0.1   0.00081      0.97      40      74 ..      60      96 ..      55     101 .. 0.80
   3 ?    1.5   0.1      0.29   3.5e+02      40      66 ..     112     138 ..     103     144 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.3
                                      HHHHHHHHHHHHHHHHTTSEE CS
                       YbaB_DNA_bd  3 qaqkmqkkmeeaqeelaekev 23
                                      +++km+k +   q+ela ++ 
  gi|518652359|ref|YP_008141879.1|  7 ELRKMRKSLGISQKELARISG 27
                                      678999999999999998765 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00081
                                      --EEEEEE-GGGG.GS-HHHHH..HHHHHHHHHHHHH CS
                       YbaB_DNA_bd 40 gevksikIdpslldpedkemLe..dlivaAvndAlkk 74
                                      ++ k+i+I+ +l+ ++d+++ e  d i++A+n+ ++k
  gi|518652359|ref|YP_008141879.1| 60 NRAKDIDIKAELIMTKDVDTCEmnDSIISALNRMREK 96
                                      5779********877777764444********98876 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.29
                                       --EEEEEE-GGGG.GS-HHHHHHHHHH CS
                       YbaB_DNA_bd  40 gevksikIdpslldpedkemLedliva 66 
                                       g++++ +I++ l++   +e L++li++
  gi|518652359|ref|YP_008141879.1| 112 GTITESNINDMLIKGTSIESLKHLIIK 138
                                       6789999*****99888********86 PP

>> PyrBI_leader  PyrBI operon leader peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013      0.16       5      30 ..     140     165 ..     136     170 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
                      PyrBI_leader   5 vRhsvLPRLkkDaGLPFFFPLltysr 30 
                                       v  svLP L k++ +   +PLl ys+
  gi|518652359|ref|YP_008141879.1| 140 VMGSVLPQLDKNSPISMIYPLLKYSN 165
                                       6779********************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00019      0.23      13      39 ..      11      38 ..       5      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00019
                            HTH_23 13 llae.GlsvreIAreLgvsrrTvyrwlk 39
                                      + +  G+s++e Ar+ gvs++ + r  k
  gi|518652359|ref|YP_008141879.1| 11 MRKSlGISQKELARISGVSQSYIARLEK 38
                                      33447******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1254.19
//
Query:       gi|518652360|ref|YP_008141880.1|  [L=185]
Description: hypothetical protein FACI_IFERC00001G0999 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-39  135.0  10.6    2.8e-39  134.9  10.6    1.0  1  CarS-like     CDP-archaeol synthase
    2.2e-08   34.2   4.3    2.2e-08   34.2   4.3    1.7  1  CTP_transf_1  Cytidylyltransferase family
  ------ inclusion threshold ------
      0.096   12.3   0.1       0.17   11.5   0.1    1.5  1  PsaL          Photosystem I reaction centre subunit XI
       0.23    9.7   1.4       0.29    9.4   1.4    1.1  1  DUF2070       Predicted membrane protein (DUF2070)


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 !  134.9  10.6   6.3e-43   2.8e-39       5     175 .]       8     185 .]       1     185 [] 0.87

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 6.3e-43
                         CarS-like   5 ilksiylllpayvanasavlvGGGtpvdlGktlvdGrrliGdGvtyrGtvaGvlvGvlvgliqg.lleklsilalds 80 
                                        l++i l+ pa++an  av+ GG   +d Gkt+  G+r++GdG+++ G+++G ++G+l g+i + ++  l+i   d+
  gi|518652360|ref|YP_008141880.1|   8 TLYAIILFAPAFIANPGAVITGGHWVIDRGKTY-KGKRILGDGKSWSGFIGGSFIGILSGIIIYyIVIVLKIPYPDY 83 
                                       367777888***********************8.7*************************98661555677777788 PP

                         CarS-like  81 sgsvlefvilalllafGallGdavGsfikrrlkierGkpalildqldfvlgalllayp.....vkllpieli..ili 150
                                         ++++ +++ + ++fG+llGd+ Gsfikrr++++rG +  ildq  fv++++ll+++     ++ l  +li  ++i
  gi|518652360|ref|YP_008141880.1|  84 GKNIIDAILVLIPMSFGSLLGDMSGSFIKRRIGMKRGARGSILDQWPFVIVSFLLVFIfargfFMQLYGDLIpvAVI 160
                                       8889999999999****************************************999875555555666777633678 PP

                         CarS-like 151 vlitlvlhlsaniiayklglkdvwy 175
                                       ++it+ +h ++ni+ayk+ +kdv++
  gi|518652360|ref|YP_008141880.1| 161 LIITPPIHRGVNILAYKFKMKDVPW 185
                                       899*********************9 PP

>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   4.3     5e-12   2.2e-08     170     234 ..      49     119 ..      37     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 5e-12
                                       --BHHHHHHHHHHHHHHHHHHHHHHHCTS......---TTSHHHHHHHHHHHHHHHHHHHHHHHHHHT-SS CS
                      CTP_transf_1 170 kKTveGfigGlvaavvvglllalvlskal......alsllhllllslllslvavfGDLveSglKRafgiKD 234
                                       +K+++GfigG+++ ++ g+++++++   +       ++++ ++l+ + +s+ + +GD+  S +KR++g K 
  gi|518652360|ref|YP_008141880.1|  49 GKSWSGFIGGSFIGILSGIIIYYIVIVLKipypdyGKNIIDAILVLIPMSFGSLLGDMSGSFIKRRIGMKR 119
                                       6***********************9987799999999********************************95 PP

>> PsaL  Photosystem I reaction centre subunit XI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   3.8e-05      0.17     114     145 ..      43      74 ..       4      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                       .-GGGSHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              PsaL 114 peelktkegWsqfasgfliGgvggavfaylll 145
                                       ++ l   ++Ws f +g +iG ++g ++ y+++
  gi|518652360|ref|YP_008141880.1|  43 KRILGDGKSWSGFIGGSFIGILSGIIIYYIVI 74 
                                       56788899*******************99875 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.4   6.5e-05      0.29      23     108 ..      63     159 ..      41     171 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 6.5e-05
                           DUF2070  23 llalligllaflssk.........lfgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllai 90 
                                       +l+ +i ++ +++ k         ++  +l+++p+ +  ll     +++++r+ +kr +  ++l ++++vi+s+l +
  gi|518652360|ref|YP_008141880.1|  63 ILSGIIIYYIVIVLKipypdygknIIDAILVLIPMSFGSLLGDMSGSFIKRRIGMKRGARGSILDQWPFVIVSFLLV 139
                                       34444444444444456778888999***********9999999999****************************99 PP

                           DUF2070  91 llsall..qalvllalvlsl 108
                                       +++a    ++l+ + + +++
  gi|518652360|ref|YP_008141880.1| 140 FIFARGffMQLYGDLIPVAV 159
                                       99852223333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 1383.16
//
Query:       gi|518652361|ref|YP_008141881.1|  [L=116]
Description: peptidyl-tRNA hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-38  132.1   0.2    1.2e-38  131.9   0.2    1.0  1  PTH2      Peptidyl-tRNA hydrolase PTH2


Domain annotation for each model (and alignments):
>> PTH2  Peptidyl-tRNA hydrolase PTH2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.2     7e-43   1.2e-38       1     117 []       2     116 .]       2     116 .] 0.97

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 7e-43
                                       EEEEEEEESSSSS-HHHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHHHTT-S CS
                              PTH2   1 lkmvlvvrkDLkmskGkiaaqcahAavalvkkllkesnekellkeWeeegqkkivlkveseeeLlelaakakalglp 77 
                                       +kmv+ vrkDL m+kGkiaaq+ahAava++   +k+ n+ ++++eW e+gqkk+v+kv++ +e+ ++++++k lg+ 
  gi|518652361|ref|YP_008141881.1|   2 VKMVIAVRKDLAMGKGKIAAQVAHAAVACTLISMKK-NK-KTFNEWYETGQKKVVVKVDNLQEIYKIKEECKILGVI 76 
                                       59*****************************99998.77.8************************************ PP

                                       EEEEEETSSSSSSTTCEEEEEEEEEEHHHHHHHHTTSEB- CS
                              PTH2  78 aalirDagrtqiepgtkTvlaigPapksivdkvtgkLkll 117
                                       +++i+Dag tqi pgt+T++++gP +++++d++tg++ ll
  gi|518652361|ref|YP_008141881.1|  77 SETITDAGFTQIIPGTVTCIGLGPDEDDLLDQITGSYGLL 116
                                       ***********************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 846.73
//
Query:       gi|518652362|ref|YP_008141882.1|  [L=352]
Description: hypothetical protein FACI_IFERC00001G1001 [Ferroplasma acidarmanus fer1]
Scores for complete 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-103  345.0   0.0   4.3e-103  344.8   0.0    1.0  1  DUF763    Protein of unknown function (DUF763)
     0.0067   16.9   0.0      0.014   15.9   0.0    1.4  1  TPR_19    Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.05   13.3   0.0      0.093   12.5   0.0    1.4  1  DUF4201   Domain of unknown function (DUF4201)


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 !  344.8   0.0  7.2e-107  4.3e-103       1     312 []       5     313 ..       5     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 344.8 bits;  conditional E-value: 7.2e-107
                            DUF763   1 GiadLpLhegkvPewllermkkLskaiveliveeygkeellerlsdPlwFqslgnvlGmdWdsSGsTtvvlgalkea 77 
                                       G++ +pLh+g++Pe+l++rm+kL+++i +l++++y+++ +le+++dP+wF+sl+ ++G+dW+sSG+Tt++l+alk++
  gi|518652362|ref|YP_008141882.1|   5 GSSIMPLHYGHPPEYLYKRMVKLGGIISDLMIQNYSENFFLEKIADPFWFHSLSLAIGFDWNSSGTTTATLSALKDH 81 
                                       77889************************************************************************ PP

                            DUF763  78 lkseelgilvaGGkGkksrktpeeleklaeklgldeek...lvkasrlvakvdnaalqdgyqlYlhalivsekgkwa 151
                                       +++ +  ++++GGkGk++ ++ +e+ k++++ +++++    ++k ++ +akvd+++lqdg++lY+++++++ kg+++
  gi|518652362|ref|YP_008141882.1|  82 INKGD-SLRIIGGKGKHMGNIGQEIAKIESEGNVEDKYlyrIKKDAKSIAKVDEKLLQDGFNLYMQFILMDYKGNYT 157
                                       *7766.79**************************9988777888999****************************** PP

                            DUF763 152 viqQGmneeerlARRYhwlseelesfveephsgiagekkeeevlnlvskeseearkaildlvkekpekllkelkelk 228
                                       +++QGmn+ ++lARRYhw  ++  s +++ ++gi+g  +e+ +l+l++k+se++r+ i+++++++p k +k+  +l+
  gi|518652362|ref|YP_008141882.1| 158 IVNQGMNTVSSLARRYHWK-NNDISLYDDKRNGISG-YEENIALDLSTKKSEKNREGIINIIQDNPLKYSKQR-SLD 231
                                       ******************8.7788999*********.88888************************8887774.566 PP

                            DUF763 229 allkgekklklpakhevlekvlekayelqpedfeellllkgvGpktlraLalvaeliygekasfkDPvkysfavGgK 305
                                       ++++++  l    + ++++++++++ye++p +f+el+ ++g+ ++t+raL+++ae++yg+k+sf+DPvkysf++GgK
  gi|518652362|ref|YP_008141882.1| 232 NFMESAPVL--DMNYKINWQKMKELYEYNPGKFDELMDMPGLSKSTIRALSYLAEIVYGNKPSFSDPVKYSFCLGGK 306
                                       677666555..5678889*********************************************************** PP

                            DUF763 306 dgvPypv 312
                                       dgvP+pv
  gi|518652362|ref|YP_008141882.1| 307 DGVPKPV 313
                                       ******8 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.3e-06     0.014       6      34 ..     317     345 ..     316     350 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.3e-06
                            TPR_19   6 dyaeAlalleqalqedpknaearllLAea 34 
                                       dy+eA+++++++l  + ++ae+  +LA+ 
  gi|518652362|ref|YP_008141882.1| 317 DYDEAIKFYKEILNGNSNYAEISKRLARM 345
                                       9**************************85 PP

>> DUF4201  Domain of unknown function (DUF4201)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05     0.093      98     167 ..     103     172 ..      69     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                           DUF4201  98 kelkekeerlaklrkelykvklerdklrkqneklkqqggllrvPaLlkDYdktkekveekrksvkkLrrk 167
                                       +e+ ++e + +  +k ly+ k++ + + k  ekl q+g +l++  +l DY+     v++  ++v +L r+
  gi|518652362|ref|YP_008141882.1| 103 QEIAKIESEGNVEDKYLYRIKKDAKSIAKVDEKLLQDGFNLYMQFILMDYKGNYTIVNQGMNTVSSLARR 172
                                       788888888888899************************************9999998888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2330.45
//
Query:       gi|518652363|ref|YP_008141883.1|  [L=157]
Description: hypothetical protein FACI_IFERC00001G1002 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1108.82
//
Query:       gi|518652364|ref|YP_008141884.1|  [L=334]
Description: hypothetical protein FACI_IFERC00001G1003 [Ferroplasma acidarmanus fer1]
Scores for complete 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   83.0   0.2    5.3e-23   81.8   0.0    1.6  2  Peptidase_M48  Peptidase family M48
     0.0044   16.3   4.4     0.0044   16.3   4.4    1.8  2  Peptidase_M56  BlaR1 peptidase M56
     0.0047   16.5   0.4      0.017   14.7   0.5    1.7  2  DUF2268        Predicted Zn-dependent protease (DUF2268)
  ------ inclusion threshold ------
       0.08   12.9   0.0       0.13   12.2   0.0    1.3  1  Peptidase_M78  IrrE N-terminal-like domain


Domain annotation for each model (and alignments):
>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.3      0.64   2.9e+03      95      95 ..      86      86 ..      38     123 .. 0.55
   2 !   81.8   0.0   1.2e-26   5.3e-23       8     195 ..     142     323 ..     135     324 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.64
                                      H CS
                                      x RF
                     Peptidase_M48 95 l 95
                                      +
  gi|518652364|ref|YP_008141884.1| 86 F 86
                                      2 PP

  == domain 2  score: 81.8 bits;  conditional E-value: 1.2e-26
                                       HHHHHHHHHHTT-..-EEEEEEE-GGGT.-EEEEESSS-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   8 kevveelakeaglpkpltkvyvvnspkr.NAFalgggknkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvs 83 
                                       ++ + +++k  ++  p +k+   ns k+ N + +      +i++t+ L+ ++ls+ el+aV +HE+GH++++h+++ 
  gi|518652364|ref|YP_008141884.1| 142 QA-ILKVFKDYNI-TPHIKIIDTNSVKIaNGYQSDKY---YIYITSYLF-SNLSQIELEAVVAHEIGHLVMKHNLKH 212
                                       43.4567788888.56666666666655666666666...*********.*************************** PP

                                       HHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTTHHHHHHHHHHHHHHHHTTT.HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  84 livsllasillllglallisraeedaagafldalavliglliillflalSRkrEyqADeagvellkrakdlvralik 160
                                       +++  la ++   g+++++  ++      +   +  ++++ iil f  l+Rk E +AD ++ +++  +++  +al+k
  gi|518652364|ref|YP_008141884.1| 213 FLIDWLALVIGINGFLFALIEKRFYILIPIS--I-AYLYIFIILIFPLLQRKDEVKADLFACKVVG-SDAVKSALVK 285
                                       ***************9877766665544443..2.2334455566679******************.********** PP

                                       HHHHTT--S---HHHH...HHS-SS--HHHHHHHHHH- CS
                                       xxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 161 lakdlerqdvsaslrs...ellstHPplleRiqalkel 195
                                       + + +++  +++ ++     l+  HP+++ Ri++++e+
  gi|518652364|ref|YP_008141884.1| 286 IDNLNKTPLKFSPKYMytfSLTLGHPSTSVRIKKINEW 323
                                       *******99999988777788889***********998 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.2      0.86   3.8e+03     103     114 ..      29      40 ..      23      62 .. 0.57
   2 !   16.3   4.4   9.8e-07    0.0044     103     220 ..     101     217 ..      79     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.86
                     Peptidase_M56 103 killliWivgal 114
                                       +++lliW++  +
  gi|518652364|ref|YP_008141884.1|  29 HFILLIWLLTLI 40 
                                       455666654433 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.8e-07
                     Peptidase_M56 103 killliWivgalilllyliaallvlkkrfvrklgklra..eelkeaLkeakeemqlkrnikirlsssidsPavlgll 177
                                       + ll+i i+ ++ lll l + + ++k     k  ++++  + + +a+ +  ++ ++  +iki   +s++        
  gi|518652364|ref|YP_008141884.1| 101 ETLLYINIAFVIFLLLVLFQPISNIK---YNKTPSIENneDPKIQAILKVFKDYNITPHIKIIDTNSVKIANGYQSD 174
                                       33444444444444444444444444...345555554002344555566677889999999999999999999999 PP

                     Peptidase_M56 178 kprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvav 220
                                       k++I++ ++++ +ls+ ele +++HE  Hl  k  l   l+  
  gi|518652364|ref|YP_008141884.1| 175 KYYIYITSYLFSNLSQIELEAVVAHEIGHLVMKHNLKHFLIDW 217
                                       *****************************97765555554444 PP

>> DUF2268  Predicted Zn-dependent protease (DUF2268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   3.9e-06     0.017       9      83 ..     141     211 ..     134     214 .. 0.78
   2 ?   -1.8   0.0      0.44     2e+03     100     123 ..     265     288 ..     263     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.9e-06
                           DUF2268   9 lekliealkkpdvdvfilpvneenrklieekgykgglaipdkiflfl.leneyskerlaallaHEyhHvvrlkqle 83 
                                       ++++ +++k  +++  i ++++++  +   +gy+++   +++i+++  l ++ s+ +l+a++aHE+ H+v  ++l+
  gi|518652364|ref|YP_008141884.1| 141 IQAILKVFKDYNITPHIKIIDTNS--VKIANGYQSD---KYYIYITSyLFSNLSQIELEAVVAHEIGHLVMKHNLK 211
                                       677888888888887889999888..5566676666...55666665488899999*************9887766 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.44
                           DUF2268 100 lAesfatelvgeeklapwtsklde 123
                                       +A+ fa ++vg + +++   k+d+
  gi|518652364|ref|YP_008141884.1| 265 KADLFACKVVGSDAVKSALVKIDN 288
                                       799**********99999888886 PP

>> Peptidase_M78  IrrE N-terminal-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     3e-05      0.13      35      60 ..     186     211 ..     159     226 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3e-05
                     Peptidase_M78  35 snhsptrqrftlaHElgHlllhherd 60 
                                       sn+s+ + + ++aHE+gHl++ h+  
  gi|518652364|ref|YP_008141884.1| 186 SNLSQIELEAVVAHEIGHLVMKHNLK 211
                                       57788888899************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1368  (0.076301); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2234.79
//
Query:       gi|518652365|ref|YP_008141885.1|  [L=340]
Description: hypothetical protein FACI_IFERC00001G1004 [Ferroplasma acidarmanus fer1]
Scores for complete 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   27.9   5.0    2.3e-06   27.9   5.0    3.1  3  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   5.0   1.3e-10   2.3e-06       1     108 [.      10     125 ..      10     154 .. 0.86
   2 ?   -0.3   7.2     0.062   1.1e+03      12      80 ..     161     256 ..     159     264 .. 0.75
   3 ?   -0.7   3.5     0.084   1.5e+03      11      61 ..     276     331 ..     266     339 .. 0.63

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.3e-10
                               RDD   1 laslgrRllAfliDlvllliislllallivall........nakasaneavagslllllllvlllvllvyqllllsk 69 
                                       +a++++R +A++iDl+ll+ i+ ++ + +  ++         +++ a+ +++++  ll++ + +++  + +++++++
  gi|518652365|ref|YP_008141885.1|  10 VATFFQRTFAYIIDLTLLICITSFILYPLHKQFelfdlvevYSYGTAGITTSYADKLLISSIIFVLVSFVYFFFEIY 86 
                                       6999***************************99*****988777777777777777777777777777788888888 PP

                               RDD  70 kgqTlGklllglkvvdedgrklglaqaliRalllllllv 108
                                          +lG++l++ k+v  ++ + ++ + l R  ++++++ 
  gi|518652365|ref|YP_008141885.1|  87 GNFSLGNKLVHGKIVLLKTNNNYISKILTRTAIKAFPIA 125
                                       999******************************999985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.062
                               RDD  12 liDlvllliislllallivall..........................nakasaneavagslllllllvlllvllvy 62 
                                       ++D++l+++i++ l l++ +++                                + ++++ l+l ++ ++ll+  ++
  gi|518652365|ref|YP_008141885.1| 161 IYDYILISAILYYLPLFTISIItlmigktyfsggsgsiapyhnptfnqLNNILIGNNTSYDLQLEIGGLFLLIPTIF 237
                                       78999999999999999888888999999999999999999999996544444555566666677777777777777 PP

                               RDD  63 qllllsk.kgqTlGklllg 80 
                                        l+ +s   g+  G+ llg
  gi|518652365|ref|YP_008141885.1| 238 VLYTSSLlEGSIMGMALLG 256
                                       7777777666666666665 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.084
                               RDD  11 fliDlvllliislllallivall.....nakasaneavagslllllllvlllvllv 61 
                                       +++ + +   ++ +++ ++   +     ++++s   a+  +  ++++++++l++++
  gi|518652365|ref|YP_008141885.1| 276 YVLGIAFAMCVVTIVTSFLENYIkgisyKKFQSILKAQIPMGVFYFATSMFLIFIA 331
                                       44444444444444333333333677777777777777777788887777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (340 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       788  (0.0439511); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2227.97
//
Query:       gi|518652366|ref|YP_008141886.1|  [L=651]
Description: hypothetical protein FACI_IFERC00001G1005 [Ferroplasma acidarmanus fer1]
Scores for complete 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-89  299.6   3.2    6.7e-88  294.7   0.3    2.1  2  Hydantoinase_A  Hydantoinase/oxoprolinase
    1.5e-47  161.6   0.0    5.7e-47  159.7   0.0    1.9  2  Hydant_A_N      Hydantoinase/oxoprolinase N-terminal region
  ------ inclusion threshold ------
      0.033   14.6   0.1      0.096   13.1   0.0    1.9  2  FtsA            Cell division protein FtsA
       0.12   11.8   0.0       0.21   11.0   0.0    1.4  1  ROK             ROK family
       0.13   10.9   0.7          2    6.9   0.0    2.2  2  MutL            MutL protein


Domain annotation for each model (and alignments):
>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.2    0.0023       8.3      82     100 ..       4      21 ..       2      33 .. 0.84
   2 !  294.7   0.3   1.9e-91   6.7e-88       1     290 [.     194     485 ..     194     486 .. 0.99

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                    Hydantoinase_A  82 ItfDmGGTstDvslikdge 100
                                       + +D+GGT tD+++i+  e
  gi|518652366|ref|YP_008141886.1|   4 VSIDIGGTFTDIIVID-EE 21 
                                       789************9.43 PP

  == domain 2  score: 294.7 bits;  conditional E-value: 1.9e-91
                    Hydantoinase_A   1 rtetavvnAylspilreylesvekslekrgakarlmvmqsdGglvsadearkkpvetilSGPaaGvvgaaatsklag 77 
                                       rt+t+vvnA+l+p+++ yl+++++ l+k g+ +++ +m+  Gglvs+de+ kkpv++i+SGPaaGv++a++++ + g
  gi|518652366|ref|YP_008141886.1| 194 RTSTTVVNAVLMPVVSGYLKRLKSVLDKFGS-PEINMMSNAGGLVSVDEVIKKPVNIIESGPAAGVIAASEFASILG 269
                                       89**************************997.9******************************************** PP

                    Hydantoinase_A  78 ekkvItfDmGGTstDvslikdgevevsletei............agvkvrlpaldirtvgagGgsilvvdeggklrv 142
                                        ++vI fDmGGT+ ++ ++++ +v ++ e+e+            +g++vr+p++d+++v+ gGg+++++d++g+l++
  gi|518652366|ref|YP_008141886.1| 270 IDHVISFDMGGTTSKAGTVINYNVDITAEYEVggsshhgrivkgSGYPVRFPFIDLSEVSSGGGTVIWKDKTGALNI 346
                                       ***************************************************************************** PP

                    Hydantoinase_A 143 gpesagadpgpacyrkGgteltvTDanlvLGrlqpedflsgpdgdqkldvelarrafeelakelnlkveevAegils 219
                                       gp sag++pgp++y++Gg+e+t+TD nlv+G ++ + ++   + d  l+++la +a+++l++++     evAe +++
  gi|518652366|ref|YP_008141886.1| 347 GPMSAGSEPGPVAYNRGGKEPTLTDSNLVMGIINDK-MS---GSDKILRKDLALKALQKLGDPY-----EVAESAIK 414
                                       **********************************98.88...8899****************99.....******** PP

                    Hydantoinase_A 220 vavenmanavrklsvergldpkeltlvvfGGaGaqhaaalaeelgvkkvivppyagvlsalGmalAdvree 290
                                       +a+ +ma+a+r ++vergldp+e+tl++fGGaG+q++  +a+elg+k+vi+pp +gv+salG++lAd++ e
  gi|518652366|ref|YP_008141886.1| 415 LANLEMARAIRLVTVERGLDPTEFTLFGFGGAGPQVTMPVADELGIKNVIIPPEPGVFSALGLMLADIKYE 485
                                       *******************************************************************9875 PP

>> Hydant_A_N  Hydantoinase/oxoprolinase N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.0   1.6e-50   5.7e-47       2     176 ..       4     174 ..       3     176 .. 0.96
   2 ?   -1.5   0.0      0.47   1.7e+03      96     132 ..     547     584 ..     537     595 .. 0.72

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 1.6e-50
                        Hydant_A_N   2 igIDvGGTfTDavaldekeeevavlKllstpdavaegirealeevleesiprtskidvvrmGTTvatNallerkg.. 76 
                                       + ID+GGTfTD++++de   e++ +K+++tp ++++++++ l++ l++      +id  +++TT+atN ll + g  
  gi|518652366|ref|YP_008141886.1|   4 VSIDIGGTFTDIIVIDE---EIHYYKVPTTPANPEQAVMDGLSKYLNK------NIDEFVHATTIATNSLLGQYGle 71 
                                       78**************5...5************************865......999******************** PP

                        Hydant_A_N  77 .ervaLittkgfrdlleigrqnrpdlfelrik..kplvlyeevvevderveadgevlkpldeeevrealkalkaagv 150
                                        +++aL+ttkgf+d++eigrqnrp+l++l ++  + l++ + ++e+der++++g++lk+++ + ++++ +++ +++v
  gi|518652366|ref|YP_008141886.1|  72 lPKTALLTTKGFKDVIEIGRQNRPELYNLDFHrpRSLIPSKLRYELDERTDVNGHILKKVETSDLESIRASMAKNNV 148
                                       ********************************88889**************************************** PP

                        Hydant_A_N 151 esiavvllhSylnpehElrvaeiare 176
                                       +s+a+++lhSyl+pe+E+ +++ +++
  gi|518652366|ref|YP_008141886.1| 149 KSLAICFLHSYLRPENEMNIKNYLSK 174
                                       *********************99876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.47
                        Hydant_A_N  96 qnrpdlfelrikkp.lvlyeevvevderveadgevlkp 132
                                       +++++ f  ++ +p ++l+ +v+ +++rv+ d++ +k+
  gi|518652366|ref|YP_008141886.1| 547 DTHNRTFGFTLDRPvEILTIRVFAIKKRVKPDMHSVKN 584
                                       555666666676552688899999*****999877765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.7e-05     0.096       2      71 ..       5     144 ..       4     197 .. 0.61
   2 ?   -3.4   0.1       3.7   1.3e+04       4      17 ..     277     290 ..     275     307 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.7e-05
                                       EEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHHHHHHHT--HHH...HHHHHH.....HH--S--....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxx...xxxxxx.....xxxxxxx....... RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigv...ggngitkdiakalrtavee...Aeriki.....kyGsala....... 60 
                                        +DiG++ td++v++++ + +++v  +   + + + ++++k l++ ++e   A  i++     +yG  l+       
  gi|518652366|ref|YP_008141886.1|   5 SIDIGGTFTDIIVIDEE-IHYYKVPTTpanPEQAVMDGLSKYLNKNIDEfvhATTIATnsllgQYGLELPktalltt 80 
                                       79**************4.55544444477999999999*****9998873335555555555556666666666665 PP

                                       .............EEEEEHHHHH................................................G CS
                                       .............xxxxxxxxxx................................................x RF
                              FtsA  61 .............ekeigrkels................................................g 71 
                                                    +                                                          
  gi|518652366|ref|YP_008141886.1|  81 kgfkdvieigrqnR--------PelynldfhrprslipsklryeldertdvnghilkkvetsdlesirasmA 144
                                       55555444443330........03333334444444444444444455555555555554444445544443 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 3.7
                                       EE-SSSEEEEEEET CS
                                       xxxxxxxxxxxxxx RF
                              FtsA   4 DiGagktdvavaed 17 
                                       D+G++++++  + +
  gi|518652366|ref|YP_008141886.1| 277 DMGGTTSKAGTVIN 290
                                       99999998876655 PP

>> ROK  ROK family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   5.9e-05      0.21       2      59 ..       4      58 ..       3      73 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.9e-05
                                      EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCHTEEEE CS
                               ROK  2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerkadelia 59
                                      ++idiGgt + ++++dee       kv+t+  ++e++++d +++ +++  +++ +  +
  gi|518652366|ref|YP_008141886.1|  4 VSIDIGGTFTDIIVIDEEIHY---YKVPTTPANPEQAVMDGLSKYLNKNIDEFVHATT 58
                                      79**************77655...5566777777777777777777766665544444 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.0   0.00056         2       2      50 ..       4      48 ..       3      69 .. 0.75
   2 ?    2.1   0.1     0.016        56     223     266 ..     249     290 ..     226     313 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00056
                              MutL  2 lviDiGSttTkvtlvdlekvderllgqaeapTtvee..edvleGleealee 50
                                      + iDiG t+T ++++d+e      ++  + pTt ++  + v++Gl++ l++
  gi|518652366|ref|YP_008141886.1|  4 VSIDIGGTFTDIIVIDEE------IHYYKVPTTPANpeQAVMDGLSKYLNK 48
                                      789**************4......344555666555558899999887654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.016
                              MutL 223 eimpTPaAvlkavellaeeeekglgdllvvDvGGaTTdvhsvae 266
                                        i   PaA + a++ +a     g++ ++ +D+GG+T+   +v++
  gi|518652366|ref|YP_008141886.1| 249 IIESGPAAGVIAASEFAS--ILGIDHVISFDMGGTTSKAGTVIN 290
                                       355667777777777777..45788***********99887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.63u 0.31s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 4164.39
//
Query:       gi|518652367|ref|YP_008141887.1|  [L=510]
Description: hypothetical protein FACI_IFERC00001G1006 [Ferroplasma acidarmanus fer1]
Scores for complete 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-161  536.0   0.0   9.7e-161  535.7   0.0    1.0  1  Hydantoinase_B  Hydantoinase B/oxoprolinase
  ------ inclusion threshold ------
       0.14   12.3   0.1       0.27   11.4   0.1    1.4  1  SLT_L           Soluble lytic murein transglycosylase L domai


Domain annotation for each model (and alignments):
>> Hydantoinase_B  Hydantoinase B/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  535.7   0.0  1.1e-164  9.7e-161       5     515 ..       4     508 ..       2     509 .. 0.96

  Alignments for each domain:
  == domain 1  score: 535.7 bits;  conditional E-value: 1.1e-164
                    Hydantoinase_B   5 levfrnrlmsiaeemgrtlqrtaiSpnikerlDfscalfdadgelvaqaphipvhlgsmseavkavlekf.eg..el 78 
                                        e++ ++ + iaeemg +l+r+aiSpni+er+D sca++d++g+++aqa+hipvhlgs++   +++++++ e+  +l
  gi|518652367|ref|YP_008141887.1|   4 WEIVGKATQFIAEEMGVALKRSAISPNIRERMDHSCAVLDSEGRIIAQAEHIPVHLGSFKIGSRNIINYMrEKkiTL 80 
                                       6999***************************************************************999522467* PP

                    Hydantoinase_B  79 kpGDvlltNdPyaggtHlpDitvitPvfhegelvffvasraHhaDiGGitpGsmppdateifeEGlrippvklveeg 155
                                       k+ ++l+tNdPy  gtHl+D+t+i+Pv+ +++l+++v ++aH +D+GG + Gs++p+a+++++EGl+ippv +    
  gi|518652367|ref|YP_008141887.1|  81 KENEMLITNDPYISGTHLNDVTIIAPVYDNNKLFCYVINKAHNVDVGGPVFGSLNPEARNLYQEGLIIPPVVITP-- 155
                                       *****************************99****************************************9976.. PP

                    Hydantoinase_B 156 eleedvlelllanvRtpednlgDlkAqiaanqvgerrlkelieeyGldtveaamdeildnaeravraalaelpdgty 232
                                           d+++++lan + pe   gDl+Aqi+an++g++r+kel+++yG d+++  ++ ++d++++    al+e++ g+y
  gi|518652367|ref|YP_008141887.1| 156 ----DIIRMILANFKDPETANGDLNAQISANRMGINRIKELMAKYGSDEIKSSWNSLIDHSRELSLMALKEWEAGEY 228
                                       ....9************************************************************************ PP

                    Hydantoinase_B 233 eaedylddg...ipikvtvtidgdeatvDftgtspqvkgniNaplavtlsaviyvlrclvdediplNeGclrpievk 306
                                       +a dyl++g   i+i+++++i+   ++ Df+gt+ +++ ++Na++ vt sav y++r+ ++  ip+N+G+++ i++k
  gi|518652367|ref|YP_008141887.1| 229 KAIDYLEKGiekINININLKISAGGVVADFDGTHGEIEYPLNAVEGVTFSAVAYAIRSAMQYSIPTNDGFYSVITIK 305
                                       ********96776888888899999**************************************************** PP

                    Hydantoinase_B 307 lpegsllnpsepaavvggnvetsqrvvdvvlkalaqalpervaAasqgtmnnltfggvderggeffgyyetiagGaG 383
                                       +pe sl+np+++ +v+ggnvet+qr++dv l+al+++l   ++Aas+gtm nl++gg+   g+++++yyeti+gG G
  gi|518652367|ref|YP_008141887.1| 306 APERSLVNPERNYPVSGGNVETTQRIADVTLRALSEFL-YYIPAASSGTMMNLMLGGKY--GNKYWSYYETIGGGNG 379
                                       ***********************************987.88***************876..5999************ PP

                    Hydantoinase_B 384 ArpgkdGasavhvhmtntrntdvEilErryPvlverfelrpdsgGaGkyrGGdGvvreieflepevtvsilserrvf 460
                                       +r++ +G+s++h++mtnt nt+vEi E++yP+ +++ +lr++s G+Gky+GG G+vr+++++++ + +s++++r  +
  gi|518652367|ref|YP_008141887.1| 380 GRYDSNGESGIHSNMTNTLNTPVEIAEKEYPFFFTKNNLRKNSYGKGKYHGGEGIVRSFKVRSR-TYISVIADRFII 455
                                       ***************************************************************7.************ PP

                    Hydantoinase_B 461 apwGlaGGepGargrvvlnllvrgeeenlggkatvelkagdvlvietpGGGGyGd 515
                                       +pwGl+GG pG++g++++  l +g+++++++k ++ l+++d +vietpGG  yG+
  gi|518652367|ref|YP_008141887.1| 456 PPWGLHGGFPGKTGKIYI--LSNGRKKSMPSKFSTVLEENDEVVIETPGGAAYGE 508
                                       ***************775..334899****************************7 PP

>> SLT_L  Soluble lytic murein transglycosylase L domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1     3e-05      0.27       4      42 ..     182     220 ..     180     225 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3e-05
                             SLT_L   4 qapalarirELralgrdaeArreWrhllkrlskeeqlal 42 
                                       ++ ++ ri+EL+a    +e ++ W +l+++  +  ++al
  gi|518652367|ref|YP_008141887.1| 182 NRMGINRIKELMAKYGSDEIKSSWNSLIDHSRELSLMAL 220
                                       667899***********************9988887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (510 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3452.11
//
Query:       gi|518652368|ref|YP_008141888.1|  [L=174]
Description: hypothetical protein FACI_IFERC00001G1007 [Ferroplasma acidarmanus fer1]
Scores for complete 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   19.0   2.5     0.0015   18.6   2.5    1.2  1  GMP_PDE_delta  GMP-PDE, delta subunit
  ------ inclusion threshold ------
      0.049   13.8   2.7        3.8    7.8   0.2    2.5  2  Cu             Cupiennin
        3.7    7.7  12.5        7.7    6.6  12.5    1.5  1  DHHC           DHHC palmitoyltransferase
          7    6.9  11.5        3.5    7.8   8.6    2.1  2  DUF4234        Domain of unknown function (DUF4234)


Domain annotation for each model (and alignments):
>> GMP_PDE_delta  GMP-PDE, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.5   3.4e-07    0.0015      51     154 ..      13     115 ..       6     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 3.4e-07
                     GMP_PDE_delta  51 ryqftpkflklktvgatveFsvgekpvknfrlierhyfkdkllksfdFefgFciPnskNtwehiyeapelseelvee 127
                                       r++  +++l+++ ++  + F   +k ++n+ li +  ++d  l s d  f  +iP ++N + +iy++   +++l ++
  gi|518652368|ref|YP_008141888.1|  13 RIKNVENILDMEFIKSFIVFIYNDKLLNNMDLIIEN-LNDGKLDSVDSLFENIIPDAENAITSIYKFLGKKDDLTKK 88 
                                       5566789************************99876.689999********************************** PP

                     GMP_PDE_delta 128 miaspfetksdsfyfvdnklvmhnkae 154
                                        +a   + +  +++fv   +v+ +  +
  gi|518652368|ref|YP_008141888.1|  89 FVAVIENFQWVKYFFVWYGIVIISLYQ 115
                                       *99999999999999865555544444 PP

>> Cu  Cupiennin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.2   0.00085       3.8       4      12 ..      74      82 ..      73      98 .. 0.84
   2 ?    5.9   0.2    0.0033        15       2      10 ..     134     142 ..     133     143 .. 0.94

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00085
                                Cu  4 sLFKFLAKK 12
                                      s +KFL+KK
  gi|518652368|ref|YP_008141888.1| 74 SIYKFLGKK 82
                                      789*****9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0033
                                Cu   2 FGsLFKFLA 10 
                                       FG+L+ FLA
  gi|518652368|ref|YP_008141888.1| 134 FGMLYSFLA 142
                                       9*******9 PP

>> DHHC  DHHC palmitoyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6  12.5    0.0017       7.7      49     127 ..     100     171 ..      91     173 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0017
                              DHHC  49 kyFllfllylllllilalvlllialvklveeekkseflavtllkkllsilllvlsllfllllgllllfhlylilrnl 125
                                       kyF  f++y ++++ l+ + +++ +++++e + ++ f ++  +     + +++ls++++  ++++ + ++ +i++n+
  gi|518652368|ref|YP_008141888.1| 100 KYF--FVWYGIVIISLYQIYYFYRFSRYMEIHGQFIFGMLYSF-----LAVFILSVIVFTTISSIRVHNINTIIKNI 169
                                       677..99************************999999988765.....77788888888777777777777888988 PP

                              DHHC 126 Tt 127
                                       ++
  gi|518652368|ref|YP_008141888.1| 170 NM 171
                                       75 PP

>> DUF4234  Domain of unknown function (DUF4234)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.55   2.5e+03      29      58 ..       7      33 ..       3      44 .. 0.55
   2 ?    7.8   8.6   0.00079       3.5      10      65 ..     107     155 ..      86     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.55
                           DUF4234 29 lnrlsgr.kkttslllvflllslitcgiysi 58
                                      ln++++r k+  +  l    + +i ++i++i
  gi|518652368|ref|YP_008141888.1|  7 LNAMDNRiKNVENI-LD---MEFIKSFIVFI 33
                                      56777773222222.22...23344444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00079
                           DUF4234  10 sivTlGIYslyWlykltrelnrlsgrkkttslllvflllslitcgiysivwayklg 65 
                                        iv  ++Y++y++y+++r +  + +        ++ +l+s+++++i+s++++ +++
  gi|518652368|ref|YP_008141888.1| 107 GIVIISLYQIYYFYRFSRYMEIHGQF-------IFGMLYSFLAVFILSVIVFTTIS 155
                                       5777899***************9999.......33345555666666555554443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1167  (0.0650901); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1119.14
//
Query:       gi|518652369|ref|YP_008141889.1|  [L=175]
Description: hypothetical protein FACI_IFERC00001G1008 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-14   53.4   7.5    1.9e-14   53.4   7.5    2.1  2  HTH_45    Winged helix-turn-helix


Domain annotation for each model (and alignments):
>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.6     0.096   1.7e+03      15      57 ..      17      58 ..      10      70 .. 0.59
   2 !   53.4   7.5     1e-18   1.9e-14       1      75 [.      97     175 .]      97     175 .] 0.96

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.096
                            HTH_45 15 isegeakkTkimykanLsykllnkYLdmLvekglikkskekYv 57
                                      +s + ++k ki+ ++n  yk+ n   ++ +  g+i+++ + Y+
  gi|518652369|ref|YP_008141889.1| 17 LSGNTNNKLKILSEVNNFYKN-NTVKKIALYSGIIDQKIKYYC 58
                                      555666777777777644432.222233344556666666665 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 1e-18
                            HTH_45   1 rRskleIiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli....kkskekYvlTekGlelleklkele 73 
                                       rR k eIi++ILe i+e + + T+i+y+ nL+yk     +d ++ek++i    ++++  Y++T  G e+++kl+ ++
  gi|518652369|ref|YP_008141889.1|  97 RRNKDEIILNILETIRETDLNITNIVYRCNLNYKYCIDLIDSMIEKKIIeateQDKTIRYKITSYGIEYMHKLESIR 173
                                       8************************************************9986668889****************99 PP

                            HTH_45  74 el 75 
                                       ++
  gi|518652369|ref|YP_008141889.1| 174 NM 175
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       992  (0.0553294); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1255.78
//
Query:       gi|518652370|ref|YP_008141890.1|  [L=308]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-17   63.0   2.8    5.2e-17   62.2   2.8    1.4  1  DDE_Tnp_1    Transposase DDE domain
    4.3e-12   46.3   0.0    8.7e-12   45.3   0.0    1.5  1  DDE_Tnp_1_5  Transposase DDE domain
    5.8e-05   23.2   0.8    0.00026   21.0   0.8    2.0  1  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
      0.011   15.2   0.3      0.027   13.9   0.1    1.7  2  PhoH         PhoH-like protein
      0.034   14.2   0.3       0.14   12.2   0.0    2.2  2  La           La domain
      0.049   13.5   0.2        3.6    7.5   0.0    2.2  2  DUF4252      Domain of unknown function (DUF4252)


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   2.8   1.7e-20   5.2e-17       7     211 ..     129     297 ..     124     300 .. 0.77

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 1.7e-20
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaD 83 
                                        i+D+t  +++  + + r+++ +++   ++klh++++++  ++ls+ it+  +hdsk+++ ll  ++  +  ++++D
  gi|518652370|ref|YP_008141890.1| 129 CIIDSTGSKITIRGDYLRHKWHRKR-NGWLKLHVIISLKDVTVLSFTITDEHTHDSKAARKLLSKMKN-NILRIFGD 203
                                       69*******9999988888777666.69**************************************98.******** PP

                         DDE_Tnp_1  84 aGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnse 160
                                       +GY+  +++  +   g++ ii+++kn+ ++++       + +r ++ + i + s ++                    
  gi|518652370|ref|YP_008141890.1| 204 RGYD-SKYIYNMF--GYNAIIPPRKNASTKSR------GSSTRARIVRYIKKNSMEQLKE----------------- 254
                                       ***9.77777777..7***********99966......3333333333333333333333................. PP

                         DDE_Tnp_1 161 llsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqlllllla 211
                                               + y +Rw +E  F+ lkr++  +  ++++ + + ++l l+   
  gi|518652370|ref|YP_008141890.1| 255 -------NNSYGKRWLVEIYFSGLKRVMT-EIIKAKKIEYIIQELALKVVN 297
                                       .......3668***************765.555565655555555555555 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.3   0.0   2.9e-15   8.7e-12      20     110 ..      52     139 ..      39     141 .. 0.89

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 2.9e-15
                       DDE_Tnp_1_5  20 ekkkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsrraktlevkipvkrksk 96 
                                       e+++ngk g+p++ +da i  +  ++ +f++p+R l+G+++sl  +a++  +   ys + rr ++++  +  ++ + 
  gi|518652370|ref|YP_008141890.1|  52 EENNNGKIGHPYKVPDALIMYLARLRSIFNVPFRSLEGMLRSLAIIANI--KSISYSEIFRRIRRIKPDLN-SNINS 125
                                       67889*****************************************999..8899*************995.44455 PP

                       DDE_Tnp_1_5  97 glhlvvdstGlkvl 110
                                        l  ++dstG k++
  gi|518652370|ref|YP_008141890.1| 126 KLDCIIDSTGSKIT 139
                                       69*********986 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.8   8.8e-08   0.00026      41     103 ..     155     218 ..     130     283 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 8.8e-08
                       DDE_Tnp_1_3  41 GWfyGfkLhliindk.GeilavkltpgnvdDrepveelakellg...klfaDkgyiskklaeellee 103
                                       GW   +kLh+ii+ k   +l++++t+  ++D + +++l +++++   ++f+D+gy sk + +++  +
  gi|518652370|ref|YP_008141890.1| 155 GW---LKLHVIISLKdVTVLSFTITDEHTHDSKAARKLLSKMKNnilRIFGDRGYDSKYIYNMFGYN 218
                                       66...5******9762589****************988887776222579********998876544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.84   2.5e+03     146     187 ..     135     174 ..     133     193 .. 0.60
   2 ?   13.9   0.1   9.2e-06     0.027      76     117 ..     264     305 ..     244     307 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.84
                                       T-EEEEEE--------------THHHHHHTTT-TTEEEEE-- CS
                              PhoH 146 nskvvvtGdvtqidlpkgkksGlaealevlknvegieivelk 187
                                       +sk+ + Gd    + +++ ++G  ++  +++  +++++++++
  gi|518652370|ref|YP_008141890.1| 135 GSKITIRGDYLRHKWHRK-RNGWLKLHVIIS-LKDVTVLSFT 174
                                       688999999888887776.566555443333.2344444443 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.2e-06
                                       --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                              PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                       v++y++ l   ++++++a+k+e+++++  ++v++ + mRG T
  gi|518652370|ref|YP_008141890.1| 264 VEIYFSGLKRVMTEIIKAKKIEYIIQELALKVVNYNIMRGMT 305
                                       789*************************************98 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.8e-05      0.14      18      48 ..     143     173 ..     140     188 .. 0.88
   2 ?   -3.7   0.1       4.4   1.3e+04       5      10 ..     264     269 ..     264     270 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.8e-05
                                       HHHHHHHTTSTTS---HHHHHTSSHHHHHHS CS
                                La  18 kFLrkkmdkdpegwVplsliasfkrmkkltk 48 
                                       ++Lr k  ++ +gw +l++i+s k +  l+ 
  gi|518652370|ref|YP_008141890.1| 143 DYLRHKWHRKRNGWLKLHVIISLKDVTVLSF 173
                                       79*******99**************998775 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                                       HHHHHH CS
                                La   5 vEfYFS 10 
                                       vE YFS
  gi|518652370|ref|YP_008141890.1| 264 VEIYFS 269
                                       899**9 PP

>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        49      68     100 ..     162     194 ..     154     207 .. 0.86
   2 ?    7.5   0.0    0.0012       3.6      81     129 ..     229     279 ..     221     281 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                           DUF4252  68 lkklksikvlttenkadaeklkkevkkilkknk 100
                                       + +lk ++vl+++ +++ +  +k+++k+l+k k
  gi|518652370|ref|YP_008141890.1| 162 IISLKDVTVLSFTITDEHTHDSKAARKLLSKMK 194
                                       4589*********99999999999999999876 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0012
                           DUF4252  81 nkadaeklkkevkkilkknkyeeLmrvkdkgek..vkiyvkekkdkvselv 129
                                       +k+  +  ++ + +++kkn++e+L + ++ g++  v+iy+ + k +++e++
  gi|518652370|ref|YP_008141890.1| 229 TKSRGSSTRARIVRYIKKNSMEQLKENNSYGKRwlVEIYFSGLKRVMTEII 279
                                       4566777889999*****************99999*****99999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 1973.50
//
Query:       gi|518652371|ref|YP_008141891.1|  [L=252]
Description: hypothetical protein FACI_IFERC00001G1010 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-19   70.4   0.0    2.1e-19   70.0   0.0    1.2  1  Exo_endo_phos    Endonuclease/Exonuclease/phosphatase family
    2.6e-06   27.2   0.1    1.6e-05   24.8   0.1    2.1  1  Exo_endo_phos_2  Endonuclease-reverse transcriptase


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0   0.0   2.4e-23   2.1e-19       1     233 []       4     243 ..       4     243 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.4e-23
                                       EEEEESTGCHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHH...TTCEEEEECCHECSSSTTSSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos   1 ltwNvngqaspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllal...ggflgasstsptgggggggng 74 
                                       l+wNvng       + +++  + + l++ ++D+++LQE++ d  +++++l       ++++           +g+ g
  gi|518652371|ref|YP_008141891.1|   4 LSWNVNGI------RAAVKNGIIKTLENENPDIILLQEAKADKMDIPEELHHTgykIYVNP--------ADKKGYSG 66 
                                       79*****8......446788899999999*************9998887776565422222........44577777 PP

                                       EEEEECSTEEEEEEEEEEETSSSSGCEEEEEEEEEEEEEEE....CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos  75 gavlsrfpltslfrrtfiefndlvaalrreplaakleqlni....ashrdhdlvrdlqllalllqvealnadrgapv 147
                                        + + +  + s   +t  + n++++++r++ l +++ +l +    +s +     +  ++        ++ +  ++pv
  gi|518652371|ref|YP_008141891.1|  67 TMAMAKQEPLSY--TTGTGENNKDVEGRIQTLEYDNFYLINsyfpNSQHGLTRLDYKIQFNREILEYMDKLKAKKPV 141
                                       777777777555..666666666666666666666666666779988888888888888888888888999999*** PP

                                       EEEEE-SSSTSGGGBSCGHHHHHHCTTTH............H...........SSCESCETTTTTTTTTTTEB-BEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx............x...........xxxxxxxxxxxxxxxxxxxxxxxx RF
                     Exo_endo_phos 148 ivaGDfNarpsdddsrvlrtrglalapap............v...........glyllgggptptyvtraggsrlDr 201
                                       i++GDfN+++ + d  ++  + + +  ++            +            +++ +++++++++ ++ g+r+D+
  gi|518652371|ref|YP_008141891.1| 142 IITGDFNVAHEEIDIARPKGNEKNAGFTIeerdsmteilshGyvdtyryfhkePGHYSWWSYRFNAREKNIGWRIDY 218
                                       ****************************988887777665516677888999************************* PP

                                       EEEECHHHCCEEEEEEECCHHEEC.......TSSCSSSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
                     Exo_endo_phos 202 ilaspalalfrsgvlppplalvrr.......ealtlSDH 233
                                        l+s+        +++               e++t+SDH
  gi|518652371|ref|YP_008141891.1| 219 FLVSD--------NFIG------KvedslilENVTGSDH 243
                                       ****6........2222......24444447789***** PP

>> Exo_endo_phos_2  Endonuclease-reverse transcriptase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.1   1.8e-09   1.6e-05       2     118 ..     102     246 ..     101     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.8e-09
                   Exo_endo_phos_2   2 liisvYippsd.......elenlestlekllselksp.kiiilGDfNakhplWgsedtds........sargeeLie 62 
                                       ++i+ Y p+s+          ++++++ +++++lk++ ++ii+GDfN+ h++ +  + +          ++ ++++e
  gi|518652371|ref|YP_008141891.1| 102 YLINSYFPNSQhgltrldYKIQFNREILEYMDKLKAKkPVIITGDFNVAHEEIDIARPKGneknagftIEERDSMTE 178
                                       678899999999998886555789999********999**************9883333255667898777777777 PP

                   Exo_endo_phos_2  63 fleehslsll...nllksgptfkssng.......sstiDltltsdnlals..kleleeedlgSDHrpi 118
                                       +l    + +    ++ + +  ++s +           iD +l+sdn   +     + e+ +gSDH p 
  gi|518652371|ref|YP_008141891.1| 179 ILSHGYVDTYryfHKEPGHYSWWSYRFnarekniGWRIDYFLVSDNFIGKveDSLILENVTGSDHAPL 246
                                       7777666655443555556777777667777555566*********99998878888999*****985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1651.49
//
Query:       gi|518652372|ref|YP_008141892.1|  [L=202]
Description: sulfite dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete 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-36  123.2   0.0    1.2e-35  122.7   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 !  122.7   0.0   6.5e-40   1.2e-35       5     172 .]      26     169 ..      22     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 6.5e-40
                                       --.GCCC-EEEEESTCSSEEEEEHHHHHHC-EEEEEEEEE-TTTTHHHHCHH--SS----TTSEEEEEEEEEEHHHH CS
                    Oxidored_molyb   5 pkvdpekwrlevdglvekplslslddLkalpavevtatlqCagnrrkelnkkkvkglqwgagavsnaeWtGvrlrdv 81 
                                       p +d++kw+l+v+glv+kp ++++++L++++  e++++++C++              +w   ++ +a+++G++l+d+
  gi|518652372|ref|YP_008141892.1|  26 PAIDENKWSLKVTGLVKKPAEYTYQELNKMDGIEYISDFNCVT--------------KW---SIKDAKFSGPSLKDL 85 
                                       67899**************************************..............8*...9************** PP

                                       HHHTTB-ETT..EEEEEEEEE-TCCTEEEEEEEHHHHCTTT-EEEEEETTEE--CCCTTT-EEE-TTB-GGGSBTTE CS
                    Oxidored_molyb  82 LekagvkkpearhvvfegadeeleeskygasiplekaleddvlLAyemngepLppdhGyPlRlvvpglvgarsvKwl 158
                                       + k ++  pea++v+f +ad      +y + ip+++a++++ +LA++++++pL ++hG+P R ++p l+g++s+Kw+
  gi|518652372|ref|YP_008141892.1|  86 IMKSEPL-PEAEWVMFVCAD------GYDTPIPFDDAVDEKSILALRIDDKPLGVKHGFPARPFMPSLYGWKSAKWV 155
                                       ******7.***********9......5***********889************************************ PP

                                       EEEEEESS---SHH CS
                    Oxidored_molyb 159 krievsdeesegyw 172
                                       ++i+++++ ++gyw
  gi|518652372|ref|YP_008141892.1| 156 TEIKLMEKYEDGYW 169
                                       *************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1533.37
//
Query:       gi|518652373|ref|YP_008141893.1|  [L=213]
Description: hypothetical protein FACI_IFERC00001G1012 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.95    8.4   5.0        1.7    7.5   5.0    1.6  1  Pex24p     Integral peroxisomal membrane peroxin
        1.6    9.2  14.7        2.9    8.4   0.3    3.1  3  MerC       MerC mercury resistance protein
        1.9    8.6   0.0        1.9    8.6   0.0    2.7  3  P5-ATPase  P5-type ATPase cation transporter


Domain annotation for each model (and alignments):
>> Pex24p  Integral peroxisomal membrane peroxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   5.0   0.00029       1.7      53     167 ..       6     213 .]       1     213 [] 0.76

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00029
                            Pex24p  53 ficlvpylelvvlplllllfv..vmvpaylyrh.plrksslik.................................. 92 
                                       +i+ ++++ l++++ll++ +v   +++a l++  p++ +s+ +                                  
  gi|518652373|ref|YP_008141893.1|   6 YIMELSHFMLMIYILLPVAIVglTILIAGLHMVaPDHWTSILSyslqkkfrtgkigtmsfslglihgifssilsfgi 82 
                                       45555666666666665544411456666777767777777668999999999999999999999999999999999 PP

                            Pex24p  93 ...............................keesknestsegptldea............................ 110
                                                                        ++k++++s+g +++++                            
  gi|518652373|ref|YP_008141893.1|  83 ailgmyflpefylkifavallvfvalyiilnAMHEKKSEDSRGGEIEKSillvsiipdpaivpiiliavvygihfvy 159
                                       999999999999999999999999999999855667788999999998899999***********999999866333 PP

                            Pex24p 111 skeivlnLrdlqnkmedllnpidalekflkelagfkdenlstllfltllltpilill 167
                                        + i+     l   + +ll ++   + ++k+la+f+ +++  l+ ++lllt++++l+
  gi|518652373|ref|YP_008141893.1| 160 ITLIIF---VLASALALLLVTLLLSKILMKKLATFTPQKIDYLVAIILLLTTLFVLF 213
                                       333333...455556666666666666789**********************99986 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.2     0.058   3.5e+02      46      81 ..      20      35 ..       5      54 .. 0.62
   2 ?    8.4   0.3   0.00048       2.9       2      59 ..      59     116 ..      58     122 .. 0.86
   3 ?    6.3   3.5    0.0022        13      45     108 ..     142     204 ..     127     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.058
                              MerC 46 vvaigllalvvgyrrhrktsvlvlgalGllillval 81
                                       +                     ++++Gl+il+++l
  gi|518652373|ref|YP_008141893.1| 20 LL--------------------PVAIVGLTILIAGL 35
                                      33....................34445555555444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00048
                              MerC   2 kiGivlSllCvvhClllPvllallpllglsflasellhqvllilvvaigllalvvgyr 59 
                                       kiG++   l ++h +   +l +  ++lg  fl++ +l+  +++l v ++l+ ++ +++
  gi|518652373|ref|YP_008141893.1|  59 KIGTMSFSLGLIHGIFSSILSFGIAILGMYFLPEFYLKIFAVALLVFVALYIILNAMH 116
                                       5677777899**************************9999999999999988777665 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0022
                              MerC  45 lvvaigllalvvgyrrhrktsvlvlgalGllillvalflgteaeetllfgslwqvltvlGaalL 108
                                        +v+i l+a+v+g +    t++++++a +l++llv l+l +  +++l +    q + +l a++L
  gi|518652373|ref|YP_008141893.1| 142 AIVPIILIAVVYGIHFVYITLIIFVLASALALLLVTLLLSKILMKKL-ATFTPQKIDYLVAIIL 204
                                       589*********************************99993333333.3334444444444444 PP

>> P5-ATPase  P5-type ATPase cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.7      0.26   1.6e+03      11      34 ..       9      32 ..       2      34 .. 0.87
   2 ?    8.6   0.0   0.00031       1.9      18      49 ..      70     101 ..      60     123 .. 0.83
   3 ?   -4.3   2.6         3   1.8e+04       7      34 ..     152     179 ..     150     181 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.26
                         P5-ATPase 11 rtsrwrlalyilgciltlGlllLl 34
                                      + s++ l++yil+ +  +Gl  L+
  gi|518652373|ref|YP_008141893.1|  9 ELSHFMLMIYILLPVAIVGLTILI 32
                                      56888999************9998 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00031
                         P5-ATPase  18 alyilgciltlGlllLlfrWlPewrvkltgkp 49 
                                       +  i+ +il++G++ L ++ lPe+++k+  ++
  gi|518652373|ref|YP_008141893.1|  70 IHGIFSSILSFGIAILGMYFLPEFYLKIFAVA 101
                                       5567889*******************997765 PP

  == domain 3  score: -4.3 bits;  conditional E-value: 3
                         P5-ATPase   7 iaGyrtsrwrlalyilgciltlGlllLl 34 
                                       ++G + +++ l++++l++ l l l+ Ll
  gi|518652373|ref|YP_008141893.1| 152 VYGIHFVYITLIIFVLASALALLLVTLL 179
                                       5666666666666666666666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); 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):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 1519.86
//
Query:       gi|518652374|ref|YP_008141894.1|  [L=81]
Description: hypothetical protein FACI_IFERC00001G1013 [Ferroplasma acidarmanus fer1]
Scores for complete 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   16.5   0.4       0.01   16.3   0.4    1.1  1  DUF3681   Protein of unknown function (DUF3681)
  ------ inclusion threshold ------
      0.065   13.3   0.1      0.099   12.7   0.1    1.4  1  GPHR_N    The Golgi pH Regulator (GPHR) Family N-terminal


Domain annotation for each model (and alignments):
>> DUF3681  Protein of unknown function (DUF3681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.4   1.1e-06      0.01      11      72 ..      10      71 ..       3      78 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.1e-06
                           DUF3681 11 agGvvkaaaalllalfrsp.ggvflrhgkallylYYgiLvavvvfGlaeasvgfWvsgdperr 72
                                      +  v+++ +  +l+  rsp  ++f    ++   + YgiL++v  fG++e + g++  ++  +r
  gi|518652374|ref|YP_008141894.1| 10 GSVVLTMMMIFYLLESRSPvYSLFF-GITCFGSAIYGILAGVYPFGAIESVWGIFSINRYVKR 71
                                      4557888889999999***888888.67778899*****************999855554444 PP

>> GPHR_N  The Golgi pH Regulator (GPHR) Family N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   1.1e-05     0.099      11      43 ..      36      70 ..      30      81 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                            GPHR_N 11 vsviGvtlmAiLSG...fGavstpyetfslfkrpvt 43
                                      ++  G  + +iL G   fGa+ +++  fs   r v+
  gi|518652374|ref|YP_008141894.1| 36 ITCFGSAIYGILAGvypFGAIESVWGIFSI-NRYVK 70
                                      566788999*******************97.66664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 570.02
//
Query:       gi|518652375|ref|YP_008141895.1|  [L=370]
Description: hypothetical protein FACI_IFERC00001G1014 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  109.7  49.7    1.4e-21   76.8  19.4    2.0  2  MFS_1           Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.023   14.2   3.0      0.046   13.2   3.0    1.5  1  Fijivirus_P9-2  Fijivirus P9-2 protein


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 !   76.8  19.4   1.6e-25   1.4e-21      20     233 ..      28     220 ..       5     226 .. 0.83
   2 !   37.7  28.5   1.2e-13   1.1e-09      13     173 ..     203     364 ..     199     370 .] 0.80

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 1.6e-25
                             MFS_1  20 plalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlq 95 
                                       p +l++ l+++  ++  ++tl+a+++  ++ ++G+++d+ G+r + +l+++l+++g +l++ f+++l+l++vl+ l 
  gi|518652375|ref|YP_008141895.1|  28 P-LLKTGLNVTLVQVEVAFTLFAIFSTGFQGIGGYFADKNGPRNIGILSAILSSIG-FLGTsFIHNLYLFYVLWSLG 102
                                       4.7888899***********************************************.55555989999********* PP

                             MFS_1  96 GlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       ++g+g+l+ ++  l+++wf++ +rg+a+gl+s+gf+lGa+++ ++ +  +   ++r +++i++i+ ++   l +ll+
  gi|518652375|ref|YP_008141895.1| 103 SIGEGILYGISTNLAVKWFKG-RRGFAVGLVSLGFGLGAAVANIFIAKAV---SFRTPMLIIGIAEIII--LPALLM 173
                                       *********************.********************88755555...9***************..888*** PP

                             MFS_1 173 peepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllply 233
                                        +++pe ++ ++++              ++ lk+  +w +l+++++ +++  ++ + ++ y
  gi|518652375|ref|YP_008141895.1| 174 KARYPETAKLTGEKT-------------SKNLKNTRFW-ILYISFILGAVPLIVISASFGY 220
                                       **********99888.............5666667799.5555555544555444444444 PP

  == domain 2  score: 37.7 bits;  conditional E-value: 1.2e-13
                             MFS_1  13 silgpalpl.alaedlg.....ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                       s+++ a+pl  ++ ++g     +   e+ +l++l+ l+++v+ ++lG++sd +Gr +v++l   +++lg  ++l+  
  gi|518652375|ref|YP_008141895.1| 203 SFILGAVPLiVISASFGylgetLPLVEFTILVSLFPLLSGVSRPILGYVSDLIGRVKVVMLIDSFLILG-SIFLI-- 276
                                       677888888888999995555555666778***************************999999999999.55552.. PP

                             MFS_1  84 slwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllggllasslgWravfyilai 159
                                        l l +++ ++ G+++ga++++  +l+ d+f  +  +  +g++++g +++  +g  ++++l++     + +f+++  
  gi|518652375|ref|YP_008141895.1| 277 -LRLYVFAIIFIGFFGGAMISMYFSLVGDIFGTRFSTANNGIFYTGKAISGFMGsTIFAALFLFDHEISFIFVLISS 352
                                       .4489*************************************************56666666655556666666666 PP

                             MFS_1 160 vsllafvlfllllp 173
                                       +++++f+l  + +p
  gi|518652375|ref|YP_008141895.1| 353 IAAIMFLL--ASVP 364
                                       66666665..4333 PP

>> Fijivirus_P9-2  Fijivirus P9-2 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   3.0   5.1e-06     0.046      61     120 ..     243     302 ..     238     332 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                    Fijivirus_P9-2  61 vsgpllnrylgsvg..kvvflifsflffgsiklvlkcfyhlfkcvfcnpltrcfcsiiftii 120
                                       vs p+l      +g  kvv+li sfl++gsi l+l+ +  +f  +f   +  ++ s+ f+++
  gi|518652375|ref|YP_008141895.1| 243 VSRPILGYVSDLIGrvKVVMLIDSFLILGSIFLILRLY--VFAIIFIGFFGGAMISMYFSLV 302
                                       667777655444443389****************9965..4566666665555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.36
# Mc/sec: 3108.07
//
Query:       gi|518652376|ref|YP_008141896.1|  [L=230]
Description: hypothetical protein FACI_IFERC00001G1015 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-20   72.3   0.1    5.2e-20   71.6   0.1    1.3  1  SBDS_C         SBDS protein C-terminal domain
    4.9e-18   65.0   0.2    8.6e-18   64.2   0.2    1.4  1  SBDS           Shwachman-Bodian-Diamond syndrome (SBDS) prote
  ------ inclusion threshold ------
      0.022   14.7   0.1      0.035   14.0   0.1    1.3  1  Cytochrome_cB  Cytochrome c bacterial


Domain annotation for each model (and alignments):
>> SBDS_C  SBDS protein C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.1   8.7e-24   5.2e-20       2     115 ..      99     216 ..      98     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 8.7e-24
                                       HHHHHHHHHHHEEBTTTTB---HHHHHHHHHHTT----TTS-CCCCHHHHHHHHTTTS--EE-EEEEEEEE-...CC CS
                            SBDS_C   2 ekeiieivaeklvnpqtkrpytttmIekalkelgtsvktnksaksQalevikaLiqeipiqrarmrlritcptsikd 78 
                                       +k++i+ + ++++npqt++p+++t+Ie a++e+++++++ ks+++Q++ v+ka++  ipi++++ r++i ++    d
  gi|518652376|ref|YP_008141896.1|  99 RKQVINEIVREAINPQTNTPIPVTRIEAAMEEAKVRIDPFKSVDEQVQAVLKAIRPLIPIRMEKARMAIRLT---GD 172
                                       79*********************************************************************9...99 PP

                                       CHHHHHHHH.HH.....S.EE.....EEEE.EEGGGHHHHHHHH CS
                            SBDS_C  79 kilklieqv.esqkvaekewe.....vvvl.iePgaykeleefv 115
                                          +l+ ++ +   + ++ew+     ++v+ i++g++ +l ++v
  gi|518652376|ref|YP_008141896.1| 173 AYGRLYGDIsRMGTILKEEWSnagdyICVIeIPAGMQGDLIDLV 216
                                       9999999995554566677777777755555********99988 PP

>> SBDS  Shwachman-Bodian-Diamond syndrome (SBDS) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.2   0.2   1.4e-21   8.6e-18       2      88 .]       7      92 ..       6      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.2 bits;  conditional E-value: 1.4e-21
                                      -EEEEEEETTEEEEEEE-HHHHHHHHCTT---HHHHBSSSS-EEETTTTEE--HHHHHHHHS---HHHHHHHHHHHSEE CS
                              SBDS  2 vsivrykkgkkrFeiavyknklleyregkeidLsevlqsekiFtnaskGetaskselekafgteskdeiikeILkkGei 80
                                      ++i+r++ ++ +Fei+v+++++ + r g +id+++ l+ ++iF++a+kGe+ +++ l+ +f+t++  +i+ eI+k+G+i
  gi|518652376|ref|YP_008141896.1|  7 AVIARFEYDSYKFEILVDPDAASRIRAG-KIDIENDLALPEIFKDARKGERTNEEILKRVFKTTDIGQIAIEIVKRGQI 84
                                      57899999999*****************.8************************************************* PP

                                      E--HHHHH CS
                              SBDS 81 qvsaeerk 88
                                      q+++e+rk
  gi|518652376|ref|YP_008141896.1| 85 QLTTEQRK 92
                                      *****997 PP

>> Cytochrome_cB  Cytochrome c bacterial
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   5.9e-06     0.035      58      95 ..     106     144 ..      98     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.9e-06
                                       -TT----TT..S-EESEEE---TT-TT-EEEEEEEEEEE CS
                     Cytochrome_cB  58 tlsdkidpa.kqpvalsepagslkdakaritPfKvmegk 95 
                                       +++++i+p+ ++p+ ++++++++++ak ri PfK    +
  gi|518652376|ref|YP_008141896.1| 106 IVREAINPQtNTPIPVTRIEAAMEEAKVRIDPFKSVDEQ 144
                                       578899988688**********************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       735  (0.040995); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); 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: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 1943.70
//
Query:       gi|518652377|ref|YP_008141897.1|  [L=222]
Description: hypothetical protein FACI_IFERC00001G1016 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-07   30.1   0.9      6e-07   29.2   0.9    1.5  1  KH_1           KH domain
      1e-05   25.8   0.4    1.6e-05   25.1   0.4    1.4  1  KH_6           KH domain
     0.0023   17.7   1.4     0.0047   16.7   0.9    1.8  2  KH_2           KH domain
  ------ inclusion threshold ------
      0.098   12.5   0.1       0.28   11.1   0.1    1.7  1  KH_4           KH domain
       0.12   12.3   1.5        0.3   11.1   0.3    2.1  2  Peptidase_S24  Peptidase S24-like


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 !   29.2   0.9   1.7e-10     6e-07       4      65 ..     142     196 ..     139     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.7e-10
                                       EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHHH CS
                              KH_1   4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkelie 65 
                                       i+v+  +v+r+IG+gG++I+ I++ t +kI v  +      +  + + G+ ++v+kA+++i+
  gi|518652377|ref|YP_008141897.1| 142 ISVKPPKVPRVIGRGGNMINIIKNYTDTKIIVG-Q------NGFIWLDGNVDNVKKAIDAIR 196
                                       5788889*****************99*****75.3......458***************996 PP

>> KH_6  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.4   4.6e-09   1.6e-05       1      44 [.     139     185 ..     139     187 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.6e-09
                              KH_6   1 GmlfeVslslvrRll...nhvLeeLgkagpfeiavGlNGriWvkses 44 
                                       G +++V++ +v+R++     ++  ++   +  i+vG+NG+iW+++++
  gi|518652377|ref|YP_008141897.1| 139 GRIISVKPPKVPRVIgrgGNMINIIKNYTDTKIIVGQNGFIWLDGNV 185
                                       66899**********777333366666699*************9876 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.9   1.3e-06    0.0047      27      69 ..     140     182 ..     114     193 .. 0.84
   2 ?   -2.2   0.0         1   3.7e+03      20      35 ..     192     203 ..     187     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.3e-06
                                       EEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
                              KH_2  27 viiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                                        ii ++  +  +vIG+gG +i+ i+     +i + +++ ++l+
  gi|518652377|ref|YP_008141897.1| 140 RIISVKPPKVPRVIGRGGNMINIIKNYTDTKIIVGQNGFIWLD 182
                                       589999**********************999998888888886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1
                                       EECCSCEEEEEEEESC CS
                              KH_2  20 Iertanrviiviresq 35 
                                       I    +++++v++e++
  gi|518652377|ref|YP_008141897.1| 192 I----DAIRLVEKEAH 203
                                       3....88999999987 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   7.8e-05      0.28      33      52 ..     142     161 ..     135     167 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 7.8e-05
                              KH_4  33 lnvegedlGrvIGkrGrtld 52 
                                       ++v+++++ rvIG+ G +++
  gi|518652377|ref|YP_008141897.1| 142 ISVKPPKVPRVIGRGGNMIN 161
                                       8999**************98 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.36   1.3e+03      49      68 ..       8      28 ..       4      30 .. 0.75
   2 ?   11.1   0.3   8.2e-05       0.3       1      65 [.      95     171 ..      95     176 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.36
                                      ETTEEEEE.SSTT.STEEEEC CS
                     Peptidase_S24 49 lpgdrvllasnne.ypplyin 68
                                       pgd++++a+ ++ ++  ++n
  gi|518652377|ref|YP_008141897.1|  8 YPGDKIEIAELKPrNGMYEYN 28
                                      599999999988657776666 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.2e-05
                                       EXXSSTTCCTXXTTXEEEEECTS.................---TTSEEEEEETTCE-EEEEEEEEETTEEEEE.SST CS
                     Peptidase_S24   1 rvpGdSMeptlldGdlilVdkfs.................epkrGdivvfrlpgeeeayiKrviglpgdrvllasnn 60 
                                       +v ++  e  l+ Gd+i  + ++                 ++++G i+ ++ p+ +     rvig++g  + + +n+
  gi|518652377|ref|YP_008141897.1|  95 HVSSGDLERYLNVGDYIYARISVsneikeswislrdngmrKLESGRIISVKPPKVP-----RVIGRGGNMINIIKNY 166
                                       6999***************96667888899*************************9.....**********999987 PP

                                       TSTEE CS
                     Peptidase_S24  61 eyppl 65 
                                       ++ ++
  gi|518652377|ref|YP_008141897.1| 167 TDTKI 171
                                       55554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1446.24
//
Query:       gi|518652378|ref|YP_008141898.1|  [L=240]
Description: hypothetical protein FACI_IFERC00001G1017 [Ferroplasma acidarmanus fer1]
Scores for 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  103.7   0.1    1.4e-29  103.3   0.1    1.2  1  RNase_PH    3' exoribonuclease family, domain 1
    4.7e-13   49.0   0.3    9.4e-13   48.0   0.3    1.5  1  RNase_PH_C  3' exoribonuclease family, domain 2


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.1   1.5e-33   1.4e-29       1     132 []      22     150 ..      22     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 1.5e-33
                                       EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG.--CCEEEECCCCECCCCEC-C...S...HHHH CS
                          RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseer.ddaegaldveveyapfasgerrregrpsdeei 76 
                                       e+R+++i+tgv+++a+GSa++e G +k++++v++     + + + d+a   ++++++++ ++ +er+r   p+++++
  gi|518652378|ref|YP_008141898.1|  22 EMRPIKIQTGVVERADGSAFIEWGANKIIVAVYVREAYPKHAQNiDRAI--VKARYNMSGYSVEERKR-PGPDRRTM 95 
                                       79********************************996644444459888..***************77.56****** PP

                                       HHHHHHHHHHCCTC-CCGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  77 elsrlleralrpsillekkpkstididitvlssdggslldalinaaslALadagip 132
                                       e+s+++ +al++ i+lek p+ +id++i+vl++d  ++  a+ +a+s+A adag+p
  gi|518652378|ref|YP_008141898.1|  96 EISKVVSEALSSAIVLEKLPRAEIDVFIQVLEADA-GTRIASLTASSVAVADAGVP 150
                                       ***********************************.******************99 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.0   0.3     1e-16   9.4e-13       1      61 [.     153     212 ..     153     218 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.0 bits;  conditional E-value: 1e-16
                                       S--EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHH CS
                        RNase_PH_C   1 apviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleai 61 
                                       ++v+++t gk d+++vlD++k+E++ +++d+++a+  +  +v+l++++g  ++ee++ ea 
  gi|518652378|ref|YP_008141898.1| 153 DLVVGCTAGKADGKIVLDLSKDEDNFGQADIPMAILPRTGKVVLLQLDGD-VTEEEFNEAT 212
                                       58************************************************.******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1584.85
//
Query:       gi|518652379|ref|YP_008141899.1|  [L=260]
Description: hypothetical protein FACI_IFERC00001G1018 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-27   95.6   0.0    5.8e-27   94.8   0.0    1.4  1  RNase_PH    3' exoribonuclease family, domain 1
    8.8e-14   51.3   0.2    1.6e-13   50.5   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 !   94.8   0.0   6.5e-31   5.8e-27       2     132 .]      35     169 ..      34     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 6.5e-31
                                       EEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CCEEEECCCCECCCCEC-C...S...HHHHHH CS
                          RNase_PH   2 lRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddaegaldveveyapfasgerrregrpsdeeiel 78 
                                       +R+++i  +++++a GSa++e+G+tkv+a+++++    p+e+++d +g++ +++e+ p+a +++++ g ps+++ie 
  gi|518652379|ref|YP_008141899.1|  35 YREIKITENFVPKAAGSAMVEIGKTKVVAGIKVEEGD-PFEDSPD-SGVMALNIELLPMAFPTFES-GPPSEQAIEY 108
                                       8**********************************98.7777544.589***************66.9********* PP

                                       HHHHHHHHCCTC-C........CGCCTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
                          RNase_PH  79 srlleralrpsill........ekkpkstididitvlssdggslldalinaaslALadagip 132
                                       sr+++r +r+s ++        ++k+ + i +di vl++dg +++da+ +aa  AL+++ +p
  gi|518652379|ref|YP_008141899.1| 109 SRVVDRGIRESKMVdtsklvieSGKRVWMIFVDIDVLNYDG-NIIDAATLAAVTALKNTVVP 169
                                       *************88888889888889**************.*****************998 PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.5   0.2   1.8e-17   1.6e-13       2      66 ..     185     249 ..     184     250 .. 0.95

  Alignments for each domain:
  == domain 1  score: 50.5 bits;  conditional E-value: 1.8e-17
                                       --EEEEEEEETTEEEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSCEEHHHHHHHHHHHHH CS
                        RNase_PH_C   2 pviavtvgkvddqfvlDptkeEedlsegdltlavagtkevvtlmkeggsqldeetlleaielAkk 66 
                                        ++++t+ k++d++v+Dp++eEe++s+g++t+++a++ ++ +++k + + ++ +++ +ai+++++
  gi|518652379|ref|YP_008141899.1| 185 TPVSITMVKIGDEIVCDPDLEEEQVSNGRITVTIAEDHNIHAMQKGDIGEFSLDEIRKAIKTSSD 249
                                       589*************************************9999999999***********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1822.48
//
Query:       gi|518652380|ref|YP_008141900.1|  [L=85]
Description: 50S ribosomal protein L37Ae [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.0   5.0    4.8e-27   93.9   5.0    1.0  1  Ribosomal_L37ae  Ribosomal L37ae protein family
     0.0002   21.3   5.0    0.00026   20.9   5.0    1.2  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
    0.00044   20.0   2.6     0.0005   19.8   2.6    1.1  1  Rep_fac-A_C      Replication factor-A C terminal domain
  ------ inclusion threshold ------
      0.038   13.9   3.7      0.064   13.2   3.7    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.062   13.2   0.3      0.091   12.7   0.3    1.3  1  Endonuclease_7   Recombination endonuclease VII
      0.097   12.8   1.4       0.41   10.8   0.1    2.1  2  Zn-ribbon_8      Zinc ribbon domain
       0.24   11.3   5.1        2.1    8.3   5.0    2.1  1  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit
       0.52   10.4   3.8        8.6    6.5   0.5    2.1  2  Mut7-C           Mut7-C RNAse domain
        2.3    8.8  12.6          3    8.4   1.0    2.8  3  zf-H2C2_2        Zinc-finger double domain


Domain annotation for each model (and alignments):
>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.9   5.0   2.4e-30   4.8e-27       1      73 [.       4      76 ..       4      84 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.9 bits;  conditional E-value: 2.4e-30
                                      XXXXXX-GGGGTTSS-HHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHH CS
                   Ribosomal_L37ae  1 rtkkvgiaGkygtrYGaslrkrvkkieisqhakytCpfcgktkvkRkavgiwkCkkcgktvaGgAytpettsa 73
                                      +t kvg  G++g+rYG+++rk ++ki +++ + ytCp+c+++kvkR+a giw+C++c++++aGg+ytpe +s+
  gi|518652380|ref|YP_008141900.1|  4 HTVKVGASGRFGPRYGVTVRKAWNKIYKQKISFYTCPSCKQKKVKRVANGIWECRHCSYKFAGGSYTPEYSSE 76
                                      689*****************************************************************97765 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 !   20.9   5.0   1.3e-07   0.00026      19      45 ..      37      62 ..      23      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.3e-07
                     Zn_Tnp_IS1595 19 fvCPhCgsrkayriktrglfqCkeCrk 45
                                       +CP C+ +k+ r+++ g ++C++C++
  gi|518652380|ref|YP_008141900.1| 37 YTCPSCKQKKVKRVAN-GIWECRHCSY 62
                                      57*************9.********97 PP

>> Rep_fac-A_C  Replication factor-A C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   2.6   2.5e-07    0.0005       4      49 ..      22      66 ..      20      82 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.5e-07
                                      EEEEEEEEETTTTEEEB--STT---B-EEE.TTTEEEETTTTEEESS CS
                       Rep_fac-A_C  4 vkatvsfikkdnlvYkACpsedCnkKvvee.edgewrCekCdkevee 49
                                      v+ + ++i+k+++ +  Cp   C++K v++ ++g w C +C  +++ 
  gi|518652380|ref|YP_008141900.1| 22 VRKAWNKIYKQKISFYTCP--SCKQKKVKRvANGIWECRHCSYKFAG 66
                                      5666788999999999***..998666666599********998865 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 ?   13.2   3.7   3.2e-05     0.064      30      56 ..      38      64 ..      16      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.2e-05
                    OrfB_Zn_ribbon 30 tCseCgsknkealsgrtfkCpnCgfea 56
                                      tC+ C +k+ +++++  ++C++C +++
  gi|518652380|ref|YP_008141900.1| 38 TCPSCKQKKVKRVANGIWECRHCSYKF 64
                                      8**********************9975 PP

>> Endonuclease_7  Recombination endonuclease VII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   4.6e-05     0.091       3      46 ..      13      59 ..      11      68 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.6e-05
                                      XHHHH.-SHHHHHH.TT---TTS..E-TTT--EEETTS--EEEEE-T CS
                    Endonuclease_7  3 rleslyeitkeerk.alleaqgg..kCaiCqerekektkalavDHdH 46
                                      r++ +y++t+++ + ++++++ +  +C  C++++ +++++  ++  H
  gi|518652380|ref|YP_008141900.1| 13 RFGPRYGVTVRKAWnKIYKQKISfyTCPSCKQKKVKRVANGIWECRH 59
                                      56779*********9***9999888******8666557666666555 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0002      0.41      27      39 ..      37      50 ..      28      51 .. 0.83
   2 ?    0.9   0.1      0.25   4.9e+02       7      15 ..      56      64 ..      54      68 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                       Zn-ribbon_8 27 taCPeCgs.evrrv 39
                                       +CP+C++ +v+rv
  gi|518652380|ref|YP_008141900.1| 37 YTCPSCKQkKVKRV 50
                                      57*********997 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.25
                       Zn-ribbon_8  7 rCeeCghef 15
                                      +C+ C  +f
  gi|518652380|ref|YP_008141900.1| 56 ECRHCSYKF 64
                                      688888776 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 ?    8.3   5.0    0.0011       2.1      17      31 ..      48      64 ..      34      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0011
                                      SCCCE..EEESSSS-EE CS
                    RNA_POL_M_15KD 17 kegkn..feCrqCgYee 31
                                      k + n   eCr C+Y++
  gi|518652380|ref|YP_008141900.1| 48 KRVANgiWECRHCSYKF 64
                                      333345689******97 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.3    0.0061        12     112     131 ..      25      44 ..      17      46 .. 0.83
   2 ?    6.5   0.5    0.0043       8.6     114     139 ..      45      70 ..      44      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0061
                            Mut7-C 112 vpekvyeeadeftrCekCrk 131
                                       + +k+y+++ +f++C++C++
  gi|518652380|ref|YP_008141900.1|  25 AWNKIYKQKISFYTCPSCKQ 44 
                                       55788999999*******98 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0043
                            Mut7-C 114 ekvyeeadeftrCekCrkvfWkGshw 139
                                       +kv+++a+ +++C++C+  f +Gs  
  gi|518652380|ref|YP_008141900.1|  45 KKVKRVANGIWECRHCSYKFAGGSYT 70 
                                       578888899********999999865 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1       1.9   3.7e+03       7      12 ..       2       7 ..       1       8 [. 0.73
   2 ?    7.3   2.2    0.0034       6.7      13      22 ..      35      44 ..      28      49 .. 0.76
   3 ?    8.4   1.0    0.0015         3      14      25 ..      54      65 ..      43      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.9
                         zf-H2C2_2  7 rkHtge 12
                                       kHt++
  gi|518652380|ref|YP_008141900.1|  2 TKHTVK 7 
                                      689976 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                         zf-H2C2_2 13 kpyeCplCdk 22
                                      ++y+Cp+C+ 
  gi|518652380|ref|YP_008141900.1| 35 SFYTCPSCKQ 44
                                      35******94 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0015
                         zf-H2C2_2 14 pyeCplCdkaFk 25
                                      ++eC  C+++F+
  gi|518652380|ref|YP_008141900.1| 54 IWECRHCSYKFA 65
                                      58*********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.46
# Mc/sec: 557.41
//
Query:       gi|518652381|ref|YP_008141901.1|  [L=43]
Description: hypothetical protein FACI_IFERC00001G1020 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00048   19.7   3.7    0.00093   18.8   3.7    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
     0.0017   18.6   2.5     0.0017   18.6   2.5    1.0  1  DUF1922         Domain of unknown function (DUF1922)
  ------ inclusion threshold ------
      0.052   13.7   2.1      0.081   13.1   2.1    1.3  1  Zn-ribbon_8     Zinc ribbon domain


Domain annotation for each model (and alignments):
>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   3.7   1.6e-07   0.00093       1      32 []       2      33 ..       2      33 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.6e-07
                                      -B-SSS--B--.--SSS----SSS-----B--- CS
                    DNA_RNApol_7kD  1 YiCgeCgaevs.lkkgdpiRCkeCGhRilYKkR 32
                                      Y+C +Cg + +    +  i C  CG+R++ K+R
  gi|518652381|ref|YP_008141901.1|  2 YKCIRCGRQLEkTFGTTDIECE-CGSRVFIKER 33
                                      9*********97666778***7.*********9 PP

>> DUF1922  Domain of unknown function (DUF1922)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   2.5   2.9e-07    0.0017       3      40 ..       1      39 [.       1      43 [] 0.88

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 2.9e-07
                                      EEEET.TS--EEEETT-SEEEETTTEEEE--SSS-BS-- CS
                           DUF1922  3 ifRCd.CGRvlYakegaktrkCvCGktikvkerrilkka 40
                                      +++C  CGR+l    g+   +C CG ++ +ker  ++k+
  gi|518652381|ref|YP_008141901.1|  1 MYKCIrCGRQLEKTFGTTDIECECGSRVFIKERPSVEKI 39
                                      799977**************************9766665 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.1   1.4e-05     0.081       6      36 ..       2      28 ..       1      29 [. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.4e-05
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgsev 36
                                      Y+C +Cg++ e+    +   +++C eCgs+v
  gi|518652381|ref|YP_008141901.1|  2 YKCIRCGRQLEKTFGTT---DIEC-ECGSRV 28
                                      9**********888766...7789.999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); 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: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 308.56
//
Query:       gi|518652382|ref|YP_008141902.1|  [L=380]
Description: hypothetical protein FACI_IFERC00001G1021 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0091   15.6   0.1      0.015   14.9   0.1    1.3  1  SatD      SatD family (SatD)
  ------ inclusion threshold ------
      0.071   13.4   0.4       0.19   12.0   0.1    1.9  2  MecA_N    NTF2-like N-terminal transpeptidase domain


Domain annotation for each model (and alignments):
>> SatD  SatD family (SatD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.7e-06     0.015       4      77 ..      84     157 ..      80     161 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-06
                              SatD   4 liGdiinskqiterskvqkklkklleelnkkyaeeliskftitlGdefqallkvekkifqiideiqlalkdvei 77 
                                       liG   +   + e  k+q+k+ +  e+++k++++e+   f+   G ef     +  +i  i d+++l +++  i
  gi|518652382|ref|YP_008141902.1|  84 LIGSKFDPETLLEEAKIQNKYGNNGESIKKEFNREFGKYFSSISGKEFSKDADIVIEINTIYDNVNLIIRPLYI 157
                                       688888999999*********************************************************99866 PP

>> MecA_N  NTF2-like N-terminal transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.62   5.6e+03      31      49 ..     129     148 ..     110     151 .. 0.61
   2 ?   12.0   0.1   2.1e-05      0.19      25      76 ..     223     275 ..     211     292 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.62
                                       BSS-H.HHHHHHHHHHCCCT CS
                            MecA_N  31 keise.keavekyqaiydgl 49 
                                       ke+s+  ++v  +++iyd++
  gi|518652382|ref|YP_008141902.1| 129 KEFSKdADIVIEINTIYDNV 148
                                       33443146777788888876 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.1e-05
                                       B--BSSBSS-HHHHHHHHHHHCCCTT-EEEEE.EEEEEEEEETTEEEEEEEEE CS
                            MecA_N  25 lseqskkeisekeavekyqaiydglqvkklki.eakkvkkdkentaeipykvs 76 
                                       ++e+++ ++s ke+ e +++  +g+++ +l+   +k vk+ ke t+   y++ 
  gi|518652382|ref|YP_008141902.1| 223 VDEPEIRNFSIKEFMEEVNNSGNGISISNLEFtGKKRVKEIKEATYDKIYRAV 275
                                       789999**************************667778888888888777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2903.81
//
Query:       gi|518652383|ref|YP_008141903.1|  [L=98]
Description: 50S ribosomal protein L21e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-28   97.1   0.8    4.9e-28   97.0   0.8    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 !   97.0   0.8   2.7e-32   4.9e-28       2      99 ..       3      96 ..       2      98 .] 0.97

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2.7e-32
                                      --S-STTTT-TTTTS--GGG-SS--SHHHH----TT-EEEE---TT--SS---GGGTT-EEEE..EEEETTEEEEEEEE CS
                    Ribosomal_L21e  2 knskglrrgtrklfskkfrkkgvpplstylreykkGdkVdikidpsvqkgmphkryhGktgrvynvtkravgvivnkkv 80
                                      ++s+g r+g+r++++kk++++g+p+++ +l++++ G++V+++i+p++qkgmp++ ++G+tg++  ++ ++ ++i+++k+
  gi|518652383|ref|YP_008141903.1|  3 RMSNGTRSGSRSKLTKKIKQRGMPKVNSLLKKFEIGETVAVVIEPAIQKGMPFHNFQGRTGKI--TGMQGSCYILKIKI 79
                                      579************************************************************..************** PP

                                      TTE..EEEEEE-GGGEEE- CS
                    Ribosomal_L21e 81 ggkileKriivriehlkks 99
                                      g+   e++ii  + hlk++
  gi|518652383|ref|YP_008141903.1| 80 GNT--ERKIISAPVHLKRL 96
                                      ***..***********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 736.28
//
Query:       gi|518652384|ref|YP_008141904.1|  [L=102]
Description: DNA-directed RNA-polymerase subunit F [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.5e-08   32.4   1.7      2e-07   31.4   1.7    1.5  1  RNA_pol_Rpb4  RNA polymerase Rpb4


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 !   31.4   1.7   1.1e-11     2e-07      42     120 ..      22     100 ..       8     102 .] 0.92

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 1.1e-11
                                       CHHHHHHHHHHHCTHHTTSSHHHHHHHHHHHTTST.STHHHHHHHHHCSTSSHHHHHHHSTTGTTTSTSHHHHHHHH CS
                      RNA_pol_Rpb4  42 nkilkktleyltnkfsrlkneekfnelvellksfe.LtkaEklqlvnlkPesavelktlieeleerfedeqleeiLd 117
                                       +   ++tl y+++ f ++++  + +++++ +++   L +  +++++++kP+s++el ++ ++ +   + + l++iLd
  gi|518652384|ref|YP_008141904.1|  22 TPSENDTLAYVEK-FLKYDKDADLKQIYNDISKVHkLPREAIVKIIDIKPSSTEELMAILNSYNVAADNKVLDSILD 97 
                                       556789******9.*****************98777***************************************** PP

                                       HHH CS
                      RNA_pol_Rpb4 118 elk 120
                                       +l+
  gi|518652384|ref|YP_008141904.1|  98 ILR 100
                                       997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1086  (0.0605723); expected 358.6 (0.02)
Passed bias filter:                      637  (0.035529); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 763.97
//
Query:       gi|518652385|ref|YP_008141905.1|  [L=182]
Description: hypothetical protein FACI_IFERC00001G1024 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-65  220.1   0.7    2.3e-65  220.0   0.7    1.0  1  DUF655    Protein of unknown function (DUF655)
    0.00016   21.9   0.0     0.0003   21.0   0.0    1.6  1  HHH_6     Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.07   11.5   0.0      0.095   11.1   0.0    1.1  1  DUF3029   Protein of unknown function (DUF3029)
      0.085   12.9   0.0       0.23   11.5   0.0    1.7  2  ULD       Ubiquitin-like oligomerisation domain of SATB


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 !  220.0   0.7     5e-69   2.3e-65       1     180 [.       1     180 [.       1     181 [. 0.98

  Alignments for each domain:
  == domain 1  score: 220.0 bits;  conditional E-value: 5e-69
                                       X--EEEEEEEETT--TT--S-GGG---EEEEEETTT--EEEEEE-TT----TT-EEE-SS..S--SSEEEEEEE--G CS
                            DUF655   1 leeeaivLDylpeGypddkhrehrdkpvvqalgereltLlelvplkevdilkldevaigk..gksdkivkikreisy 75 
                                       +ee+a+++D+lp+G++ddk+  +r+ p++ a+ge+e++Lle++p+ ++ + + d+++igk  +k+dki +ikr+i y
  gi|518652385|ref|YP_008141905.1|   1 MEEYAYIIDFLPQGRADDKN--FRKSPLILAIGESEFKLLEIIPKVDAVVTVGDKIYIGKspEKRDKIISIKRRITY 75 
                                       79****************96..************************************9855799************ PP

                                       GGS-HHHHHHHHHHHHHHHHTTHHHHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHHHST CS
                            DUF655  76 edLtdvaraeLpdvvekivkekEdrfveffneaepitiRlHaLelLpgvgkklarkileeRerrrFesFedvkkrvk 152
                                       +dLt++a +eLp+ +e+i++++ +rfv+ffn+ae+i++R+H+LelLpg+g+k ++++l+eR++ +F+sFed+++rvk
  gi|518652385|ref|YP_008141905.1|  76 KDLTSAAISELPYTIENIIDDNPQRFVDFFNNAEAINTRMHTLELLPGLGNKSMWSVLDERKKGPFKSFEDISERVK 152
                                       ***************************************************************************** PP

                                       T---HHHHHHHHHHHHHH-TTSS--SS- CS
                            DUF655 153 glkdpaeilverileEiedktekYylFv 180
                                       ++++p++++v+ri++E++++ ekY+lFv
  gi|518652385|ref|YP_008141905.1| 153 SVHNPKKMVVNRIMDELQNRYEKYKLFV 180
                                       ***************************9 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   6.8e-08    0.0003      29      66 ..     118     155 ..      84     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6.8e-08
                             HHH_6  29 LaaikglgeaaaerivaeRekegpfksledlarrvds.l 66 
                                       L+ + glg++ + ++++eR+ +gpfks+ed+++rv+s  
  gi|518652385|ref|YP_008141905.1| 118 LELLPGLGNKSMWSVLDERK-KGPFKSFEDISERVKSvH 155
                                       677789*************9.8*************9752 PP

>> DUF3029  Protein of unknown function (DUF3029)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   2.1e-05     0.095     364     432 ..      45     117 ..      41     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.1e-05
                           DUF3029 364 dkevtpgvRipvGeEPelvkhlkasak...fHkyfpsGisdi.ltldetvkknpealldiikgafklglrels 432
                                       d  vt g +i +G+ Pe  +++  +++   +    ++ is++ +t+++ + +np+  +d  + a ++++r+ +
  gi|518652385|ref|YP_008141905.1|  45 DAVVTVGDKIYIGKSPEKRDKIISIKRritYKDLTSAAISELpYTIENIIDDNPQRFVDFFNNAEAINTRMHT 117
                                       7889************9888877666511155557899***989******************99999988876 PP

>> ULD  Ubiquitin-like oligomerisation domain of SATB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.2e-05      0.23      33      65 ..      62      94 ..      37      99 .. 0.85
   2 ?   -2.0   0.0      0.85   3.8e+03      82     100 ..     152     170 ..     148     173 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.2e-05
                               ULD 33 eldsyviipkdllfsdlvetallkLgYskesaa 65
                                      + d+ + i++ ++++dl+++a+++L Y+ e++ 
  gi|518652385|ref|YP_008141905.1| 62 KRDKIISIKRRITYKDLTSAAISELPYTIENII 94
                                      67999***********************99875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.85
                               ULD  82 esitddpkatvediLgelt 100
                                       +s+ + +k+ v+ i+ el+
  gi|518652385|ref|YP_008141905.1| 152 KSVHNPKKMVVNRIMDELQ 170
                                       5677778888999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); 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:                         4  (0.000223102); expected 0.2 (1e-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: 1363.46
//
Query:       gi|518652386|ref|YP_008141906.1|  [L=239]
Description: dimethyladenosine transferase [Ferroplasma acidarmanus fer1]
Scores for 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-50  170.3   0.1    4.8e-50  170.1   0.1    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
     0.0038   17.0   0.0     0.0067   16.2   0.0    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
       0.04   13.8   0.0       0.05   13.4   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      0.081   13.6   0.0       0.15   12.8   0.0    1.4  1  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.1   0.1   1.1e-53   4.8e-50       3     233 ..       4     221 ..       2     236 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 1.1e-53
                                       CCXXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-SEEEEE-S-HHHHHHHHCHTT...TCC CS
                            RrnaAD   3 klrksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakrakqvvvlElderLakllqkkls...kde 76 
                                       ++ k+ygq fl++k+++++ ++ l +e+ + vleigpG GilT +L+    +++++E d r++++l+        ++
  gi|518652386|ref|YP_008141906.1|   4 NFAKKYGQVFLNDKNIAAKEVRLLGIEPGDHVLEIGPGHGILTGILLSEPVKLTAIEPDHRFYESLKISYHdhiVSG 80 
                                       6789***************************************************************988888899* PP

                                       CEEEE-S-CCGHHHHHHHCTTTCCCCEEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT CS
                            RrnaAD  77 klkvvhqDflkfetpeevtekdsihqeflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskk 153
                                       k +++++ fl++e  ++            +++n+Py+is++  +++l+   f+++ ++l++qkefarrl+arpg k+
  gi|518652386|ref|YP_008141906.1|  81 KFNIIKESFLDTEPSYFD----------HIIGNIPYNISSPVLFKILD---FNFKSSILMVQKEFARRLVARPGTKE 144
                                       ****************77..........69*****************8...889*********************** PP

                                       -SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S-HHHHHHHHHHHHCTTTSBCCCHCCCTST CS
                            RrnaAD 154 rsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqkdlkkyesvvrkllnrkrktlstslksllp 230
                                       +sr+++++ +   +k++ +v +++fsP p vdsa++ + +kd d+   dl+++++++ k++  +rk+lst l++++p
  gi|518652386|ref|YP_008141906.1| 145 YSRITINTSVRSTIKILFNVTRKVFSPVPDVDSAVISIMKKDVDI---DLANFDKFIAKIFSMRRKKLSTILNYNGP 218
                                       ********************************************9...*************************9998 PP

                                       CHH CS
                            RrnaAD 231 gge 233
                                        +e
  gi|518652386|ref|YP_008141906.1| 219 FSE 221
                                       665 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.5e-06    0.0067      59      91 ..      17      49 ..       7      70 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.5e-06
                                      HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHH CS
                              PCMT 59 phmvalalellelkkgarvLevGsGsGyltavl 91
                                        + a+ + ll +++g++vLe+G G G+lt +l
  gi|518652386|ref|YP_008141906.1| 17 KNIAAKEVRLLGIEPGDHVLEIGPGHGILTGIL 49
                                      567899999*********************986 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.1e-05      0.05      14      55 ..      24      64 ..      10     139 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.1e-05
                   Methyltransf_23 14 erllpklraggrvLdiGcGtGillevlrengfsvtgvDlspe 55
                                       rll+  ++g  vL+iG+G+Gil+ +l  +++++t+++++ +
  gi|518652386|ref|YP_008141906.1| 24 VRLLG-IEPGDHVLEIGPGHGILTGILLSEPVKLTAIEPDHR 64
                                      45555.788999**************************9854 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.3e-05      0.15       1      70 [.      35     102 ..      35     118 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.3e-05
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                       vL++G G+G lt  l+ + +  k+t++++++++ e  +  ++++ ++ +f   + + l+ e + fD ++ 
  gi|518652386|ref|YP_008141906.1|  35 VLEIGPGHGILTGILLSE-P-VKLTAIEPDHRFYESLKISYHDHIVSGKFNIIKESFLDTEPSYFDHIIG 102
                                       9***************99.4.*****************99988777555555555555666778999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1847.53
//
Query:       gi|518652387|ref|YP_008141907.1|  [L=281]
Description: hypothetical protein FACI_IFERC00001G1026 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-31  107.5   2.3    1.1e-30  107.0   2.3    1.2  1  Band_7    SPFH domain / Band 7 family
     0.0019   17.9   0.2     0.0036   17.0   0.2    1.5  1  Band_7_1  SPFH domain-Band 7 family
  ------ inclusion threshold ------
        9.4    7.2   7.6        2.4    9.1   2.1    2.2  2  Pilin_N   Archaeal Type IV pilin, N-terminal


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 !  107.0   2.3   1.8e-34   1.1e-30       4     174 ..      30     195 ..      27     201 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.8e-34
                            Band_7   4 eegevgvvvrfGklsrvlepGlhfilPfgrsvt.vvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklv 79 
                                       +e +++ v + G++ + ++pGl ++ P+++++t v s+r+q + ++   ++ t+D++pv++d+++++++  d+ k+v
  gi|518652387|ref|YP_008141907.1|  30 KEWQRAPVLTLGRYTGLKGPGLVYVTPIISKITvVLSTRIQAVAFKT-ESTFTQDNVPVNVDAVMYFQI-IDPDKAV 104
                                       56677778899**********************999***********.9999*****************.******* PP

                            Band_7  80 aaveresanldnlirrvlesalrevisemtleellsnreelaeelknelneqlrkyGvevldvritdidpppevaqa 156
                                       ++v    +n+++  + +++ +lrev+++ +++e+ls+re++ e +++ + e+ + +Gv v +v i+d+  p+++++a
  gi|518652387|ref|YP_008141907.1| 105 LNV----ENYAAATQLAAQTTLREVLGKSSFDEILSEREKIGESARQIIDEKTEHWGVKVSSVEIRDVLVPQTLQDA 177
                                       ***....********************************************************************** PP

                            Band_7 157 laakqaaeaeaqaeiara 174
                                       + + +aae+e++ ++  a
  gi|518652387|ref|YP_008141907.1| 178 MSRQAAAERERRSRVTLA 195
                                       ***********6665544 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 !   17.0   0.2   6.1e-07    0.0036     143     209 ..     120     184 ..      74     186 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 6.1e-07
                          Band_7_1 143 trlsdvlaeskipvldlaakseelaeklkealkeelaeyGlelekleienislpeevekaldkrasm 209
                                       t+l +vl++s     ++ ++ e+++e  ++ ++e+ ++ G++++++ei+++ +p+ ++ a++++a++
  gi|518652387|ref|YP_008141907.1| 120 TTLREVLGKSSF--DEILSEREKIGESARQIIDEKTEHWGVKVSSVEIRDVLVPQTLQDAMSRQAAA 184
                                       556666666544..46778999****************************************99976 PP

>> Pilin_N  Archaeal Type IV pilin, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   2.1    0.0004       2.4       7      42 ..       6      40 ..       3      55 .. 0.84
   2 ?    0.5   0.3       0.2   1.2e+03      14      35 ..      60      82 ..      55     108 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0004
                           Pilin_N  7 iGviLmvaitvIlaAviaafvlglasneekapqasi 42
                                      +G+++++ + +I++A+i + +  l ++ ++ap  ++
  gi|518652387|ref|YP_008141907.1|  6 VGEVILILVLIIIVAIILSGIHIL-KEWQRAPVLTL 40
                                      899**************9999988.78888887766 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                           Pilin_N 14 aitvIlaAviaafvlgl.asnee 35
                                       itv+l   i a+++ + +  ++
  gi|518652387|ref|YP_008141907.1| 60 KITVVLSTRIQAVAFKTeSTFTQ 82
                                      599**********9999322222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 1849.90
//
Query:       gi|518652388|ref|YP_008141908.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1027 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-11   43.5   0.0    8.1e-11   41.9   0.0    1.8  2  ACP_syn_III_C   3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
    5.3e-06   26.3   0.4     0.0019   17.8   0.0    2.1  2  HMG_CoA_synt_C  Hydroxymethylglutaryl-coenzyme A synthase C t
    1.2e-05   24.8   0.1    2.2e-05   24.0   0.1    1.4  1  Thiolase_N      Thiolase, N-terminal domain
    0.00075   19.3   2.9     0.0073   16.1   0.6    2.6  2  ACP_syn_III     3-Oxoacyl-[acyl-carrier-protein (ACP)] syntha
     0.0022   17.9   0.1     0.0037   17.2   0.1    1.4  1  HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N t
  ------ inclusion threshold ------
       0.14   12.5   1.5       0.16   12.4   0.1    1.8  2  WYL_3           WYL domain


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.9   1.2e+04      66      83 ..      86     103 ..      81     107 .. 0.68
   2 !   41.9   0.0   2.7e-14   8.1e-11       2      81 ..     219     298 ..     218     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.9
                                       S-TT-EEEEEEEETTTEE CS
                     ACP_syn_III_C  66 lkpgdlvllvgfGaGltw 83 
                                       +kp  +++ +++G+ l +
  gi|518652388|ref|YP_008141908.1|  86 VKPTATIVAAAIGMPLEY 103
                                       667777777777766655 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 2.7e-14
                                       HHTT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--TH..HHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEE CS
                     ACP_syn_III_C   2 ekagltpedidalvphqanlriidavakklglpeekvvvnl..deyGntsaasiplaLdeaveegklkpgdlvllvg 76 
                                       e+ g +++d d++v+hq n ++   +ak l+++ee++ + l    +Gnt + s +  L+  ++  + kpgd++l v+
  gi|518652388|ref|YP_008141908.1| 219 ERMGTKSSDYDYVVFHQPNGKFPTRAAKMLNFTEEQYKTGLltPYIGNTYSGSTMTGLSAILD--EAKPGDRILAVS 293
                                       78899******************************77766655889*****************..88********** PP

                                       EETTT CS
                     ACP_syn_III_C  77 fGaGl 81 
                                       fG G 
  gi|518652388|ref|YP_008141908.1| 294 FGSGA 298
                                       ***96 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 !    7.4   0.1   0.00098       2.9      66      96 ..     224     254 ..     205     258 .. 0.77
   2 !   17.8   0.0   6.5e-07    0.0019     150     215 ..     260     324 ..     249     338 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00098
                                       -GGG-SEEEE--SSHHHHHHHHHHHHHHHHH CS
                    HMG_CoA_synt_C  66 tlddfdyvifhsPfcklvqkslarllynDfl 96 
                                          d+dyv+fh P  k+ +++   l++++ +
  gi|518652388|ref|YP_008141908.1| 224 KSSDYDYVVFHQPNGKFPTRAAKMLNFTEEQ 254
                                       45689****************9999998765 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 6.5e-07
                                       HHHHH---GGGHHHHHHHHHHHHS-HHHHTT-EEEEEEEETTTEEEEEEEEE-S--STTSHHH...HHT CS
                    HMG_CoA_synt_C 150 vptevGnmYtaslyaalasllskvsadelagkriglfsYGsGlaaslfslrvkqdvsedsild...iak 215
                                       ++  +Gn Y  s  + l ++l    ++   g ri++ s+GsG  +  f +++++++++ +  +   ++k
  gi|518652388|ref|YP_008141908.1| 260 LTPYIGNTYSGSTMTGLSAIL----DEAKPGDRILAVSFGSGAGSDAFDITITENMKNYHRENapgVRK 324
                                       44569****************....555679***********************998866555444555 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   7.4e-09   2.2e-05      24     113 ..      51     140 ..      43     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 7.4e-09
                                       HHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHH CS
                        Thiolase_N  24 eeLlaealkallekagvdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsia 100
                                         ++ ea++++l++ +++p ++  ++vG   +  + +  a  +a ++g+p e  a   + +c  g +++ ++  ++ 
  gi|518652388|ref|YP_008141908.1|  51 ASISVEAARNALKRININPGDIGAIYVGSESHPYAVKPTATIVAAAIGMPLEYFAADYEFACKAGTAGMQNVKAMVD 127
                                       56788999********************************************************************* PP

                                       TTSHSEEEEEEEE CS
                        Thiolase_N 101 ageadvvvagGvE 113
                                       +g ++  +a+G  
  gi|518652388|ref|YP_008141908.1| 128 SGYIKYGIAIGSD 140
                                       **********975 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.6   2.5e-06    0.0073       2      64 ..     107     166 ..     106     181 .. 0.79
   2 ?    2.5   0.1     0.045   1.3e+02      37      57 ..     276     299 ..     272     310 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.5e-06
                                       EEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEE CS
                       ACP_syn_III   2 DlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleas 64 
                                       D + aC++ ++++++++a+++sg +k+ + ig++t s+       +  +  + G++A++++++
  gi|518652388|ref|YP_008141908.1| 107 DYEFACKAGTAGMQNVKAMVDSGYIKYGIAIGSDT-SQGA--PGDALEYSASAGGTAMIIGKD 166
                                       77889*****************************9.5533..335566667788888888876 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.045
                                       GGGCS-TT...THHHHTTB-EEEE CS
                       ACP_syn_III  37 lskilDwk...drstavlfGDGAg 57 
                                       ls ilD++   dr  av fG GAg
  gi|518652388|ref|YP_008141908.1| 276 LSAILDEAkpgDRILAVSFGSGAG 299
                                       789999975667***********9 PP

>> HMG_CoA_synt_N  Hydroxymethylglutaryl-coenzyme A synthase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.2e-06    0.0037       6     172 ..       3     166 ..       1     168 [. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                    HMG_CoA_synt_N   6 gilaleiylpaqyvdqaelekfdgveagkytiglgqtrmgfvsdredinslsltvvqkllertkldydaigrlevgt 82 
                                       gi++   y+p   ++  e+ +  g +  k    l     +  s  ed+ s+s+   ++ l+r +++   ig + vg+
  gi|518652388|ref|YP_008141908.1|   3 GIVSYGSYVPIYRIKPEEIARIWGDDPEKMKNNLFILSKSVPSPDEDVASISVEAARNALKRININPGDIGAIYVGS 79 
                                       677777788888888888888888888888888888888899999******************************** PP

                    HMG_CoA_synt_N  83 etiidksksvksvlmqlfeesgntdiegidtlnacyggtaalfnavnwiessawdgryalvvagdiaiydsgnarp. 158
                                       e+     k   +++   ++     +    d   ac  gta + n    ++s +   +y + +  d +  + g+a   
  gi|518652388|ref|YP_008141908.1|  80 ESHPYAVKPTATIVAAAIGM--PLEYFAADYEFACKAGTAGMQNVKAMVDSGYI--KYGIAIGSDTSQGAPGDALEy 152
                                       *9887777777777766665..5677789999******************9996..799999*****9999998652 PP

                    HMG_CoA_synt_N 159 tggagavalligpd 172
                                       +  ag  a++ig d
  gi|518652388|ref|YP_008141908.1| 153 SASAGGTAMIIGKD 166
                                       7789*******986 PP

>> WYL_3  WYL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.2       4.4   1.3e+04       9      15 ..     215     221 ..     213     229 .. 0.48
   2 ?   12.4   0.1   5.3e-05      0.16      22      59 ..     302     340 ..     297     342 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.4
                             WYL_3   9 kkmmkdg 15 
                                       k+mm+  
  gi|518652388|ref|YP_008141908.1| 215 KAMMERM 221
                                       3444432 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 5.3e-05
                             WYL_3  22 AkkLgIadkiak.aessagaleklmqTseYkKyeaYlnf 59 
                                       A +  I++++++  +++a+++ k  +  ++ +y  Y  f
  gi|518652388|ref|YP_008141908.1| 302 AFDITITENMKNyHRENAPGVRKMIENVKFIDYAIYTKF 340
                                       67889*******************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.27s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2462.25
//
Query:       gi|518652389|ref|YP_008141909.1|  [L=403]
Description: hypothetical protein FACI_IFERC00001G1028 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-25   89.2   1.8    7.2e-25   87.8   1.2    2.0  2  Thiolase_N     Thiolase, N-terminal domain
      8e-11   41.7   0.2      2e-09   37.2   0.0    2.6  3  Thiolase_C     Thiolase, C-terminal domain
    1.6e-07   31.2   0.4    5.9e-06   26.1   0.2    2.7  3  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
    0.00015   21.6   0.3       0.14   12.1   0.0    2.6  2  ACP_syn_III    3-Oxoacyl-[acyl-carrier-protein (ACP)] synthas


Domain annotation for each model (and alignments):
>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   1.2   1.6e-28   7.2e-25       1     260 []      21     243 ..      21     243 .. 0.88
   2 ?   -3.8   0.0       1.4   6.4e+03      19      45 ..     271     297 ..     266     299 .. 0.71

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 1.6e-28
                                       EEEEEEEEE--EETTSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCT..TSTSCHHHHHHHHTTS-.T CS
                        Thiolase_N   1 vvivsaartpigkfggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqa..gegqniarqaalkagip.e 74 
                                       v+i++a  t++g+    l d s ++L+ ea+ +++e+ag+ ++++d ++ +n l++  +  +ni   +a  +g++ e
  gi|518652389|ref|YP_008141909.1|  21 VYIIGAGETKFGE----LWDKSLRNLAVEAGLKAVEDAGIYSKDIDAIYGANSLAGiiNMQENIGALIADFSGLSaE 93 
                                       79***********....**************************************9844444588888888898725 PP

                                       TSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTTTGGSSSSEEEEEHHHHHHTEETTT CS
                        Thiolase_N  75 evpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvrsglklgdekakdllipdgladafn 151
                                        +p+ +v+   +Sg +a+ +a  si++ge+dvvv+gGvE+m++   ++  +  s++   + +a              
  gi|518652389|ref|YP_008141909.1|  94 GIPSLRVESSTASGGAALRDAYLSIKSGEYDVVVVGGVEKMTDIHGSDILEKSSSILDREWEAFFGAT--------P 162
                                       69*****************************************9999875544444444444333333........4 PP

                                       TSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT--HHHHHT CS
                        Thiolase_N 152 eehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevtaekLak 228
                                         +++l a+++ +++++ +e++  f v+ h +++++++a+ F+++               +  +a++s ++a++L+ 
  gi|518652389|ref|YP_008141909.1| 163 AAMAALIARKYMHDFGVEKEALSMFSVNDHLNGSKNPDAQ-FRNKL--------------TIQQAMNSTAVADPLNM 224
                                       57999***********************************.***88..............556789999******** PP

                                       S-BSSSTTSS-BTTSB--BEEEEEEEEEEEHH CS
                        Thiolase_N 229 lkpaFkkeGtvtAgnasqisDGaaavllmses 260
                                       +             ++s++sDGaaav+l+ses
  gi|518652389|ref|YP_008141909.1| 225 M-------------DCSPMSDGAAAVVLASES 243
                                       *.............***************996 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 1.4
                                       TTS-HHHHHHHHHHHHHHHHTS-GGGC CS
                        Thiolase_N  19 kdlsaeeLlaealkallekagvdpeev 45 
                                       k++ + +  + a++++l k g++ +++
  gi|518652389|ref|YP_008141909.1| 271 KSIYTLNSTKLAVEKALRKSGIKRNDI 297
                                       555555556778899999999998877 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0     0.049   2.2e+02      26      46 ..      45      65 ..      36      83 .. 0.79
   2 ?   -3.8   0.0       2.1   9.4e+03      27      49 ..     169     191 ..     160     193 .. 0.74
   3 !   37.2   0.0   4.4e-13     2e-09       5     103 ..     259     375 ..     255     400 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.049
                                      HHHHHHHHHHT--GGGESEEE CS
                        Thiolase_C 26 yaikkvlkkagltvedidlfE 46
                                       a  k++++ag+  +did++ 
  gi|518652389|ref|YP_008141909.1| 45 EAGLKAVEDAGIYSKDIDAIY 65
                                      577799************975 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2.1
                                       HHHHHHHHHT--GGGESEEEE-- CS
                        Thiolase_C  27 aikkvlkkagltvedidlfEinE 49 
                                        ++k +++ g++ e + +f +n+
  gi|518652389|ref|YP_008141909.1| 169 IARKYMHDFGVEKEALSMFSVND 191
                                       55677888888888888888875 PP

  == domain 3  score: 37.2 bits;  conditional E-value: 4.4e-13
                                       EEEEEEEEEE--GGGGGGH.HHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--G.............. CS
                        Thiolase_C   5 akirsyaevgvdpeilglg.PayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldl.............. 66 
                                       a  ++y +vg   +i +l     a++k+l k g++ +di ++E+++ F+   L  +++l++++              
  gi|518652389|ref|YP_008141909.1| 259 AVAEDYLSVGSRKSIYTLNsTKLAVEKALRKSGIKRNDISFMEVHDSFSIFGLLELEDLGFAEkgkakdlvydeikl 335
                                       56678999999998887751568****************************************************** PP

                                       ...GGBSTT--HHHH-B-TTTHHHHHHHHHHHHHHHCTTS CS
                        Thiolase_C  67 ...ekvNvnGGaialGHPlGasGaRivvtllselkkeggk 103
                                            vN  GG  a G P Ga G+ ++v + ++lk + g 
  gi|518652389|ref|YP_008141909.1| 336 ngsIPVNPSGGLKAKGDPYGAVGVGQAVDAYRQLKGKAGD 375
                                       99888****************************9976544 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 ?    1.5   0.0     0.039   1.8e+02      90     111 ..      41      62 ..      36      75 .. 0.85
   2 !   26.1   0.2   1.3e-09   5.9e-06     154     218 ..      80     147 ..      66     161 .. 0.80
   3 ?   -1.4   0.0      0.31   1.4e+03     237     250 ..     229     242 ..     203     244 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.039
                                       HHHHHHHHHHHHHHTS-HHTCT CS
                     ketoacyl-synt  90 rllleaawealedagltpeeld 111
                                        l++ea  +a+edag+  +++d
  gi|518652389|ref|YP_008141909.1|  41 NLAVEAGLKAVEDAGIYSKDID 62 
                                       5899************998875 PP

  == domain 2  score: 26.1 bits;  conditional E-value: 1.3e-09
                                       HHHHHHHHHT--S...SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---SHHHHHHHHHTT CS
                     ketoacyl-synt 154 iagrisyalglrG...psvtvdtACsSslvavhaavqslrsgeadvalaGGvellltpeavagfsaag 218
                                       i + i+ + gl +   ps+ v++  +S+ +a+  a+ s++sge dv+++GGve ++   +   +++  
  gi|518652389|ref|YP_008141909.1|  80 IGALIADFSGLSAegiPSLRVESSTASGGAALRDAYLSIKSGEYDVVVVGGVEKMTDIHGSDILEKSS 147
                                       566677775555544699************************************99988777766655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.31
                                       -BB-EEEEEEEEEC CS
                     ketoacyl-synt 237 vlGEGvGavvLkrl 250
                                        +++G++avvL ++
  gi|518652389|ref|YP_008141909.1| 229 PMSDGAAAVVLASE 242
                                       58999999999876 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 !    7.0   0.1    0.0012       5.3      11      64 ..     108     172 ..     100     185 .. 0.71
   2 !   12.1   0.0     3e-05      0.14      27      76 ..     204     260 ..     200     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TT.........THHHHTTB-E..EEEEEEEEEE CS
                       ACP_syn_III  11 vyalsvAdaliesgaakrvLvigaetlskilDwk.........drstavlfGD..GAgAvvleas 64 
                                        +al  A   i+sg++  v+v g e++++i   +         dr+    fG   +A A+++ ++
  gi|518652389|ref|YP_008141909.1| 108 GAALRDAYLSIKSGEYDVVVVGGVEKMTDIHGSDileksssilDREWEAFFGAtpAAMAALIARK 172
                                       5789999999****************998654434444455555666667887667777777666 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 3e-05
                                       SEEEEEEEEEGGG.CS-TTTHHHHTTB-EEEEEEEEEEE......SSSSCEEEEEEE CS
                       ACP_syn_III  27 krvLvigaetlsk.ilDwkdrstavlfGDGAgAvvleas......eeegarildsel 76 
                                       ++ L i     s  + D+ + + +  ++DGA+Avvl  +      + eg ril+s++
  gi|518652389|ref|YP_008141909.1| 204 RNKLTIQQAMNSTaVADPLNMMDCSPMSDGAAAVVLASEsfikknKREGVRILSSAV 260
                                       56666665556655999999****************988777554455777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.49
# Mc/sec: 2468.91
//
Query:       gi|518652390|ref|YP_008141910.1|  [L=134]
Description: hypothetical protein FACI_IFERC00001G1029 [Ferroplasma acidarmanus fer1]
Scores for complete 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   71.5   0.0    5.5e-20   71.1   0.0    1.2  1  OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
    3.5e-09   36.4   0.9    5.3e-09   35.8   0.9    1.2  1  DUF35_N        Rubredoxin-like zinc ribbon domain (DUF35_N)
  ------ inclusion threshold ------
      0.039   13.6   0.2      0.055   13.1   0.2    1.2  1  TackOD1        Thaumarchaeal output domain 1
      0.098   12.2   3.2        2.7    7.6   0.7    2.5  2  TF_Zn_Ribbon   TFIIB zinc-binding
        0.8    9.7   5.3        2.2    8.4   0.3    2.2  2  Zn_Tnp_IS1595  Transposase zinc-ribbon domain
       0.83    9.4   4.7        1.9    8.3   4.7    1.6  1  Rubredoxin_2   Rubredoxin metal binding domain
          1    9.5   5.4          5    7.3   5.4    2.1  1  Zn-ribbon_8    Zinc ribbon domain


Domain annotation for each model (and alignments):
>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.0   2.1e-23   5.5e-20       2      65 .]      50     113 ..      49     113 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 2.1e-23
                                       EEE-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc   2 velsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65 
                                       v +sg G+v s+tvvh app+f+ ++Pyv+++++L eg+ i+a++v++dp++v  G +V  vfr
  gi|518652390|ref|YP_008141910.1|  50 VKFSGNGEVISYTVVHDAPPSFKRQVPYVLALIKLSEGPVITAQIVDCDPADVDMGKKVHSVFR 113
                                       789***********************************************************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 !   35.8   0.9   2.1e-12   5.3e-09       6      34 ..      14      42 ..      12      45 .. 0.91

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2.1e-12
                           DUF35_N  6 egrLvgqrCpdCGtvqfPPravCphCgsd 34
                                      ++ L+g +C++CG  +fPPr vCp C++ 
  gi|518652390|ref|YP_008141910.1| 14 RYNLIGFKCKNCGNSYFPPRDVCPVCHRE 42
                                      7889999*******************975 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   2.1e-05     0.055      75     104 ..      21      50 ..      13      60 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.1e-05
                           TackOD1  75 lCpsCksghlnvrevCpkCkSidieeqeli 104
                                        C++C  + +  r+vCp C+   i + e +
  gi|518652390|ref|YP_008141910.1|  21 KCKNCGNSYFPPRDVCPVCHRESIGKMEKV 50 
                                       6*******************9999887766 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.7     0.001       2.7       1      10 [.      20      29 ..      20      33 .. 0.87
   2 ?    4.6   0.1    0.0091        23       2      11 ..      35      44 ..      35      59 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                                      EEETTTTCEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn 10
                                      +kC+nCg+++
  gi|518652390|ref|YP_008141910.1| 20 FKCKNCGNSY 29
                                      79*****987 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0091
                                      EETTTTCEEC CS
                      TF_Zn_Ribbon  2 kCPnCgstnl 11
                                      +CP+C+ +++
  gi|518652390|ref|YP_008141910.1| 35 VCPVCHRESI 44
                                      7****99875 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   1.2     0.024        61      19      26 ..      20      27 ..       4      33 .. 0.64
   2 ?    8.4   0.3   0.00084       2.2      15      34 ..      30      49 ..      27      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.024
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                      f C +Cg+
  gi|518652390|ref|YP_008141910.1| 20 FKCKNCGN 27
                                      67777775 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00084
                     Zn_Tnp_IS1595 15 WpngfvCPhCgsrkayrikt 34
                                      +p + vCP C+ +++ ++++
  gi|518652390|ref|YP_008141910.1| 30 FPPRDVCPVCHRESIGKMEK 49
                                      78899******888777765 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   4.7   0.00075       1.9       1      21 [.      20      40 ..      20      41 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00075
                      Rubredoxin_2  1 YvCsqCGfesakwfGrCpsCg 21
                                      + C++CG+++      Cp C+
  gi|518652390|ref|YP_008141910.1| 20 FKCKNCGNSYFPPRDVCPVCH 40
                                      89******************8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.4     0.002         5       6      34 ..      20      41 ..      12      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.002
                       Zn-ribbon_8  6 YrCeeCghefevlqsisdapltaCPeCgs 34
                                      ++C++Cg+ +        +p  +CP C+ 
  gi|518652390|ref|YP_008141910.1| 20 FKCKNCGNSYF-------PPRDVCPVCHR 41
                                      78*****6666.......55667****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 973.65
//
Query:       gi|518652391|ref|YP_008141911.1|  [L=269]
Description: hypothetical protein FACI_IFERC00001G1030 [Ferroplasma acidarmanus fer1]
Scores for complete 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-70  235.5   0.1    8.2e-70  235.4   0.1    1.0  1  VitK2_biosynth  Menaquinone biosynthesis
     0.0027   17.7   0.0      0.019   14.9   0.0    2.0  2  NMT1            NMT1/THI5 like


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.4   0.1   9.1e-74   8.2e-70       3     266 .]       3     257 ..       1     257 [. 0.97

  Alignments for each domain:
  == domain 1  score: 235.4 bits;  conditional E-value: 9.1e-74
                                       EEEESSHHHHHHHHHHHTTSS..SGCCEEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEEEES CS
                    VitK2_biosynth   3 lGhspylNdlflfyaLvegkvdsegleveivledpetlnrallegelDvakiSsaayariaddyalLpdlsisalGr 79 
                                       ++h+p+++d+f+fya++e k+++  +e++ v +d+etln++ ++ ++Dv++iS+  y++++d+y l    s++++G 
  gi|518652391|ref|YP_008141911.1|   3 IAHTPDPDDAFMFYAMFEHKIKTS-FEYDQVVKDIETLNKESVDLKYDVTAISANGYMHVSDKYDLTT--SGASFGI 76 
                                       8*********************99.9******************************************..******* PP

                                       SSSEEEEESS-CCC-SSS..T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTS.SEEEEECCH CS
                    VitK2_biosynth  80 vygvllvskvpleelegel.gkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlege.dagLlIges 154
                                        yg+ +++k++++     l gk++a pg++t++ lL+r++++e+     +l e++fd+i +a++e+e dag+lI+++
  gi|518652391|ref|YP_008141911.1|  77 SYGPQVIAKKNID-----LkGKTIASPGKYTSAELLYRMFAPEAG----TLKEIRFDKIVNAIMENEvDAGILIHDE 144
                                       ********88443.....3356**********************9....**************************** PP

                                       HHTGGGGTTEEEEEHHHHHHHHHS.S-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHCCSTTS. CS
                    VitK2_biosynth 155 altyaeeglkkvlDLgelWeeltg.lPlvlglwvvrrdlaaeaakeleealreSveyalahldevaeyaaeraqemd 230
                                       +lty+++gl+ vl L ++W++ +g lP++lg +++r+d++ e   + + ++++S++ya +h  ++++ya+++++ +d
  gi|518652391|ref|YP_008141911.1| 145 QLTYQDKGLVPVLNLYDEWKKYAGdLPIPLGFNAIRKDMPIEDKLKYKADFENSIKYAFEHETDAVKYAMKYSRYDD 221
                                       ***********************66***************************************************9 PP

                                       HHHHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHHC CS
                    VitK2_biosynth 231 devlekhlelYvnelsydlgeegragleeflelaae 266
                                        e  +k++ +Yvnels+d+ge+gr++l+ ++++aae
  gi|518652391|ref|YP_008141911.1| 222 FELERKFILMYVNELSVDFGEKGRKALDLYYKRAAE 257
                                       9*********************************86 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.046   4.1e+02      39      57 ..      68      86 ..      58      88 .. 0.84
   2 !   14.9   0.0   2.1e-06     0.019      89     160 ..      88     152 ..      81     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.046
                                      HCTS-SEEEE-HHHHHHHH CS
                              NMT1 39 asgkadfgvsyqesllaar 57
                                       +  a fg+sy ++++a++
  gi|518652391|ref|YP_008141911.1| 68 TTSGASFGISYGPQVIAKK 86
                                      466799*********9876 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.1e-06
                                       GGGTTSEEEE-S-TTHHHHHHHHHHHTT--GGG-EEEE-.TT-HHHHHHCTSSSEEECEETTTHHHHHHHTT CS
                              NMT1  89 kDLkGkrigyvgspfekallkallakdggdpsdvtlvnvggtslakalltgkvDaaiggyenwegveleseg 160
                                        DLkGk+i+ +g   +  ll ++ a + g+ +++ +     ++ ++a+++++vDa+i  + + e+++ + +g
  gi|518652391|ref|YP_008141911.1|  88 IDLKGKTIASPGKYTSAELLYRMFAPEAGTLKEIRF-----DKIVNAIMENEVDAGI-LIHD-EQLTYQDKG 152
                                       5***********999999999999999997777777.....455679*********9.6666.666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1885.55
//
Query:       gi|518652392|ref|YP_008141912.1|  [L=502]
Description: hypothetical protein FACI_IFERC00001G1031 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-83  279.5  30.1    4.3e-83  279.2  30.1    1.0  1  Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
  ------ inclusion threshold ------
      0.019   14.7   0.5      0.019   14.7   0.5    3.3  3  7TM_GPCR_Srb    Serpentine type 7TM GPCR chemoreceptor Srb
       0.66   10.0   1.4        8.9    6.3   0.3    2.2  2  DUF4501         Domain of unknown function (DUF4501)


Domain annotation for each model (and alignments):
>> Cyt_bd_oxida_I  Cytochrome bd terminal oxidase subunit I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.2  30.1   7.3e-87   4.3e-83       4     415 ..      15     468 ..      12     470 .. 0.92

  Alignments for each domain:
  == domain 1  score: 279.2 bits;  conditional E-value: 7.3e-87
                    Cyt_bd_oxida_I   4 lqfaltavfHflfvpltlGlalllailetlylrtgdekykklakfwgklfainFavGvvtGivlefqfgtnWseysr 80 
                                       ++fa+t++ H+l+v+l++Gla++++i+e+l+l+++d++y +la  ++k ++i+FavG+++G+v+++++ + W+++++
  gi|518652392|ref|YP_008141912.1|  15 AMFAYTISAHILLVSLSMGLAITVTIAEFLALKKKDKYYDTLAYKLSKALVIFFAVGTASGTVMAMELFLFWPSFMK 91 
                                       68*************************************************************************** PP

                    Cyt_bd_oxida_I  81 fvGdifgapLaiEgllAFflEstflglmlfgwdrv.skklhllatwlvaigtllSalwIlaanswmqtPvGaelnpd 156
                                       +vG++++ p+++E+ ++F+lE++ l ++++ w+ + +++ h+ ++++v+igt+lSa+ ++ +n+wm+tP+G+++ + 
  gi|518652392|ref|YP_008141912.1|  92 LVGEVAMGPFYVEV-FSFLLEAIALPMYVYFWKDFkNRWEHWGLSLAVTIGTYLSAFTVTEINAWMNTPNGFDVAKF 167
                                       *************5.********************999*********************************998643 PP

                    Cyt_bd_oxida_I 157 ..tgraeltdflavlfnpsalakflHtvlaalltaaffvagvsawyllr....rekefarkslkialvvalvaallq 227
                                         tg ++ ++++a +++ s++a+ lH+  a +++++++++g+  +++l+     ek ++r+ ++i++v++++ +++ 
  gi|518652392|ref|YP_008141912.1| 168 vtTGAVTNVNPFAPFITASTAAEELHMSGAVYYAGIAMILGYLIYKYLKttnmSEKMIYRRGINITAVFMILDIIYL 244
                                       225577778****************************************98866666******************** PP

                    Cyt_bd_oxida_I 228 allGdlsgkevaetqpaKlAAmeglwetee.......aplslfgipdeeeeknefaieiPgllsllatgsl..dgev 295
                                        ++G ++ ++++  +p K++A+e   + +        ap ++fg+  +  +k  +a + P+++slla   +  +g++
  gi|518652392|ref|YP_008141912.1| 245 GITGSNELSTLMVIEPIKYTALELDLHATIgtsfatmAPEHIFGVLIN--HKLAYAPSFPYIQSLLAFPLTfgKGSI 319
                                       ***********************9997663456777889999999555..456899***********9654357889 PP

                    Cyt_bd_oxida_I 296 kGlndlpk.......eevPpvalvfwsfrimvglgvlllllallalll..........rwllrllllaiplpfiave 355
                                       +Gl  l +         +Pp  +v+ + ++mvg+gvl+ l +l+++++          r+ l   +++++++++++e
  gi|518652392|ref|YP_008141912.1| 320 PGLIPLTTykgvtdyGVWPP-YIVHDTLDLMVGFGVLMGLYWLYVVVQyfrkkdplshRFTLLGGIAVAIMGVFTME 395
                                       999999778888887799*9.9********************998866889******988899999999******** PP

                    Cyt_bd_oxida_I 356 aGWivtevGRqPWivy...............gllrtadavspvsagevllslilflllylvLlvvevylllklik 415
                                        GW+++evGR P+i+                g +++a+a+   +++ v+   i+++++yl+++ +++y+  k++k
  gi|518652392|ref|YP_008141912.1| 396 DGWYTAEVGRVPYIIRspvpggfvvdgvkhyGTMTIAQAA--STSPLVFPLGIAIIIFYLAVFPLTFYFAGKVMK 468
                                       ***************77777777777666669*******9..78999**********************999887 PP

>> 7TM_GPCR_Srb  Serpentine type 7TM GPCR chemoreceptor Srb
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.5   3.3e-06     0.019      82     137 ..      14      70 ..      10      83 .. 0.84
   2 ?    0.1   2.3     0.096   5.7e+02       9      55 ..     104     150 ..      99     251 .. 0.73
   3 ?    0.6   0.1     0.067     4e+02      68     111 ..     406     451 ..     377     470 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 3.3e-06
                      7TM_GPCR_Srb  82 ktllkyghtsalflltlpmllplaftierfvalkmaesy.ekvrtllGpvlvlllii 137
                                       + ++ y+  + ++l++l+m l +++ti  f+alk+ ++y + +  +l   lv++  +
  gi|518652392|ref|YP_008141912.1|  14 SAMFAYTISAHILLVSLSMGLAITVTIAEFLALKKKDKYyDTLAYKLSKALVIFFAV 70 
                                       578999999************************998775166788999999988654 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.096
                      7TM_GPCR_Srb   9 qfysflvsllalpsliyflfkklfklsfhGnlktlliayfisvllfa 55 
                                       +++sfl+ ++alp  +yf      + +  G   ++ i+ ++s +  +
  gi|518652392|ref|YP_008141912.1| 104 EVFSFLLEAIALPMYVYFWKDFKNRWEHWGLSLAVTIGTYLSAFTVT 150
                                       6899*********9999865444444444555556666666666554 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.067
                      7TM_GPCR_Srb  68 vpffvksnc..dliinktllkyght.salflltlpmllplaftierf 111
                                       vp++++s+    +++++    yg + +a    t p+++pl+++i  f
  gi|518652392|ref|YP_008141912.1| 406 VPYIIRSPVpgGFVVDGV-KHYGTMtIAQAASTSPLVFPLGIAIIIF 451
                                       788888876224555554.4566551566778899999999998766 PP

>> DUF4501  Domain of unknown function (DUF4501)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3    0.0015       8.9      85     130 ..      20      66 ..       8      77 .. 0.84
   2 ?    2.3   0.0     0.025   1.5e+02      77     124 ..     179     228 ..     148     235 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0015
                           DUF4501  85 evaaslllgtlfislfLilsvasffylkrsskl.PkvfYrrnkasvl 130
                                       +++a +ll  l + l++ +++a f+ lk+ +k   ++ Y+ +ka v+
  gi|518652392|ref|YP_008141912.1|  20 TISAHILLVSLSMGLAITVTIAEFLALKKKDKYyDTLAYKLSKALVI 66 
                                       57888999999999999999*********988625789*99999886 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.025
                           DUF4501  77 vlpkvggPevaaslllg..tlfislfLilsvasffylkrssklPkvfYrr 124
                                       + p +++ ++a  l +   +++  +++il    + ylk ++ + k++Yrr
  gi|518652392|ref|YP_008141912.1| 179 FAPFITASTAAEELHMSgaVYYAGIAMILGYLIYKYLKTTNMSEKMIYRR 228
                                       44444444444444442113455678899999999**************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3656.34
//
Query:       gi|518652393|ref|YP_008141913.1|  [L=357]
Description: hypothetical protein FACI_IFERC00001G1032 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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):               0  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2198.64
//
Query:       gi|518652394|ref|YP_008141914.1|  [L=168]
Description: hypothetical protein FACI_IFERC00001G1033 [Ferroplasma acidarmanus fer1]
Scores for complete 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   31.4   0.0    2.2e-07   31.0   0.0    1.2  1  DinB      DinB family
  ------ inclusion threshold ------
      0.023   15.2   0.0      0.036   14.6   0.0    1.3  1  DinB_2    DinB superfamily


Domain annotation for each model (and alignments):
>> DinB  DinB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   2.5e-11   2.2e-07       7     145 ..       5     152 ..       1     159 [. 0.76

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.5e-11
                                       ..HHHHHHHHHHHHHHHHHCT--CCCTT--SSTTS--HHHHHHHHHHHHHHHHHHHHH.....SSSGGGT------- CS
                              DinB   7 leellqynqwardrtldaiaaLpdeelkaengegfqsvkqtlnHvldveelwlsrleg...eegapavddqterkel 80 
                                       l+e+++ ++ + + +  a+++++ e l++   ++ +s +++  H+ldv+ ++l++l+    ++ ++ + +  e  ++
  gi|518652394|ref|YP_008141914.1|   5 LREMVKTLRFHGGLIHSALESIDSECLEIIPIKNSGSFGKQFRHILDVRNSYLDALQSgtlDFYRKDINHLLENNKQ 81 
                                       349*****************************************************999995556666655566666 PP

                                       --HHHHHHHHHHHHHHHHCT--HHHHHSEE......------SS-EEHHHHHHHHHHHHHHHHHHHHHHHH CS
                              DinB  81 eeldalrealderliafldqltdleretll......dradagtvkmtlaelLaHvinHethHrGqitvllr 145
                                       e l++l   ++e    +l++ ++   + ++      +   + ++  ++ +l   + +He+ H G ++++ r
  gi|518652394|ref|YP_008141914.1|  82 ELLEELKCVMEEFSSMVLTYSSQKVSDKWIdctpsmKYLGENFRNISPLQLTGMITEHEIFHEGELALYYR 152
                                       66666655555555555555555333444422111144567788999999999************999977 PP

>> DinB_2  DinB superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     4e-06     0.036      12     127 ..      22     146 ..      12     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
                            DinB_2  12 lledlteeelnrqpspgkwsiawllaHlgnveelllerlr..geeaprpgldpltppsaaealaylaevrarllall 86 
                                       +le ++ e l  +p   + s++ +++H+ +v   +l +l      + r+  + l + + +e+l++l+ v +++ +++
  gi|518652394|ref|YP_008141914.1|  22 ALESIDSECLEIIPIKNSGSFGKQFRHILDVRNSYLDALQsgTLDFYRKDINHLLENNKQELLEELKCVMEEFSSMV 98 
                                       6778888888888999999*********************65444557777777789999***********999998 PP

                            DinB_2  87 eal.....tdadldrpltap..hpglgkltlgdvllfvlqHeqhHleq 127
                                        +      +d+  d + ++    ++++  + +++ +++++He  H ++
  gi|518652394|ref|YP_008141914.1|  99 LTYssqkvSDKWIDCTPSMKylGENFRNISPLQLTGMITEHEIFHEGE 146
                                       76623333666677777777777889999**************99775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); 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: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1100.35
//
Query:       gi|518652395|ref|YP_008141915.1|  [L=69]
Description: hypothetical protein FACI_IFERC00001G1034 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-10   40.2   2.5    9.5e-10   38.5   1.5    2.0  2  zf-CDGSH  Iron-binding zinc finger CDGSH type


Domain annotation for each model (and alignments):
>> zf-CDGSH  Iron-binding zinc finger CDGSH type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   1.5   5.3e-14   9.5e-10      16      47 ..       9      40 ..       2      41 .. 0.80
   2 ?    0.9   0.0     0.032   5.7e+02      14      26 ..      45      57 ..      41      66 .. 0.60

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 5.3e-14
                          zf-CDGSH 16 dgesvelregrevvaLCrCgrSknkPfCDgsH 47
                                      + +++ ++ g+++v +C Cg+S+nkP+CDg H
  gi|518652395|ref|YP_008141915.1|  9 RDKPYMVKVGDKEVHICACGLSENKPYCDGHH 40
                                      5566666667777******************* PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.032
                          zf-CDGSH 14 dadgesvelregr 26
                                      d+dg+ + +++++
  gi|518652395|ref|YP_008141915.1| 45 DEDGKLYVYDHNG 57
                                      5666666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 505.06
//
Query:       gi|518652396|ref|YP_008141916.1|  [L=457]
Description: hypothetical protein FACI_IFERC00001G1035 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-39  134.7   0.0    5.4e-39  134.1   0.0    1.2  1  Carb_kinase   Carbohydrate kinase
    1.2e-31  109.9   0.0    1.7e-31  109.4   0.0    1.2  1  YjeF_N        YjeF-related protein N-terminus
    0.00048   19.6   0.0    0.00077   18.9   0.0    1.3  1  HK            Hydroxyethylthiazole kinase family
  ------ inclusion threshold ------
      0.011   15.8   0.0        2.7    8.1   0.0    3.0  3  Shikimate_DH  Shikimate / quinate 5-dehydrogenase


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 !  134.1   0.0   1.2e-42   5.4e-39       1     241 [.     221     448 ..     221     451 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 1.2e-42
                                       EEEEE-BTTCHHHHHHHHHHHHCTT-SEEEEEESSTTTCCCCTTTTTCEECCTTHTTTS...--SSS-SEEEE-TT- CS
                       Carb_kinase   1 vlvigGsedytGAallaalaalrlgaglvsvateseaiavlksylpevivhplledeqakileklerldavviGpGL 77 
                                       v++++G  +++GAa+++ l+a ++g +lv+v+t++ +   +  y p ++ +p++ ++++   ++l+ l+ ++iGpG+
  gi|518652396|ref|YP_008141916.1| 221 VGILAG-WEFPGAAVMSSLSAYNVGPDLVKVFTNEVNRSIIMPYNPGLMFYPVN-GKNF---PALSGLNSMLIGPGM 292
                                       689999.89********************************************9.6777...9************** PP

                                       SSSHCHHHHCHHHCCCCS-.EEEEGGGGGSGGGG...TTTTSSEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHH CS
                       Carb_kinase  78 grdekikklleevlekdep.lviDAdgLnllaqknelserkaeviLTPhkkEfkrLlkaivkkeddrlelarelaqk 153
                                       g+ ++++ l++++ +++++ l++DAd+++l++       +  + i+TPh  Ef   +++         e a e a+k
  gi|518652396|ref|YP_008141916.1| 293 GKSKEAEDLIKYAVKNYNGqLILDADAFKLITPS---EVKDRNAIITPHSMEFTAFTGLEP-----TEENAVETAKK 361
                                       *********************************7...79999*****************99.....56667788899 PP

                                       HTTEEEEESTTSEEEECTTEEEEE----GGG-STTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHHHCCCT- CS
                       Carb_kinase 154 lnavvllkgekdvivspegevlinstgssalakGGsGDvLaGligalLaqneasyeaaiaaawlhgaasdeaaekkg 230
                                       ++ ++llkg+kd+i + + ++     g+s ++ GG+GDvLaG+++++ + + +++ +a  +++++ +++d a+ek g
  gi|518652396|ref|YP_008141916.1| 362 YGLIILLKGSKDIITD-GVNIRYSYGGNSRMTMGGTGDVLAGIVAGIASRKVSPLRSASLGSFINKKCGDIAFEKFG 437
                                       ************9998.9999******************************************************99 PP

                                       TS-HCHHHHHH CS
                       Carb_kinase 231 vgmlatelski 241
                                        ++   ++++ 
  gi|518652396|ref|YP_008141916.1| 438 SYYGIMDMIDN 448
                                       98777666665 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 !  109.4   0.0   3.8e-35   1.7e-31       3     171 .]      22     174 ..      20     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 3.8e-35
                            YjeF_N   3 eLmenagravaevlrallgnspaekkvlvlvGsgnnGgdglaaArhLaqegakVtvllleeee.kldedaeralell 78 
                                       +Lm++ag+++++++++ +   p++k++ +++G gnn gdg++ + +L  ++++V vll+++ +   +++++ra++ +
  gi|518652396|ref|YP_008141916.1|  22 KLMKQAGKSISDFVEHTI---PPGKSIAIICGTGNNAGDGICSGEYL-LKKYNVSVLLIKDVKgLKTQETRRAINDY 94 
                                       79****************...**************************.899*****999887756677777777777 PP

                            YjeF_N  79 kkaggkvveekpeedleeklsapvdlviDAllGiglrgelreelaeliewlnsseapvlavDiPSGldadtGavsgt 155
                                         a   +++ ++  +       ++d++iDA++G+g++g+ r+++ e+ie++n+s++++++vD+PSG+++   +++  
  gi|518652396|ref|YP_008141916.1|  95 NGAYYPLSSLDELIS-------RSDIIIDAIFGVGINGDPRKPYIEIIEKINNSGKTIISVDVPSGFQT---NIQ-- 159
                                       777777765555544.......69*******************************************54...466.. PP

                            YjeF_N 156 avkadvtvtfgapkrg 171
                                        vk+d+tvtf+ +k+g
  gi|518652396|ref|YP_008141916.1| 160 -VKPDYTVTFTDIKTG 174
                                       .99********99987 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.7e-07   0.00077     143     219 ..     354     429 ..     344     455 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.7e-07
                                       HHHHHHHHHTSEEEEESSSEEEEESSEEEEEE-S-GGGGGSTTHHHHHHHHHHHHHTTBSSHHHHHHHHHHHHHHHH CS
                                HK 143 avqkvAqklrvvvvvtGevDvvsdgkkvyklknGtellgkitasGCllgsvvaaflavkkdkllaaveavllykvAg 219
                                        + + A+k+++++++ G  D+++dg ++    +G++ ++ + ++G +l+ +va +++ k  +l +a  +  + k  g
  gi|518652396|ref|YP_008141916.1| 354 NAVETAKKYGLIILLKGSKDIITDGVNIRYSYGGNSRMT-MGGTGDVLAGIVAGIASRKVSPLRSASLGSFINKKCG 429
                                       56678**********************99999****998.79**************999999999855555666666 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0006       2.7      36      83 ..      71     118 ..      43     123 .. 0.78
   2 ?    3.2   0.0      0.02        88      87     123 ..     163     200 ..     159     207 .. 0.79
   3 ?    0.1   0.0      0.17   7.6e+02       5      37 ..     275     307 ..     272     309 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0006
                                       -CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-S CS
                      Shikimate_DH  36 vkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisat 83 
                                       v  +++      + +e ++ +++++  + +l++l+el++++d++i a+
  gi|518652396|ref|YP_008141916.1|  71 VSVLLIKDVKGLKTQETRRAINDYNGAYYPLSSLDELISRSDIIIDAI 118
                                       555555555566778888888999999******************986 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.02
                                       S-SB-HHHHHCCHHH.S...EEEEE--SS-SB-TTGGG CS
                      Shikimate_DH  87 epilekeeveealkkrk.kplllvDiavPRdvepevae 123
                                       ++ ++  +++  +++++  ++ + Di++P  ++++v+ 
  gi|518652396|ref|YP_008141916.1| 163 DYTVTFTDIKTGMNRENsGKITVSDIGIPEQIKSAVGP 200
                                       566777888888888777788999*********99976 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.17
                                       HHHS..TT-EEEEES-SHHHHHHHHHHHCCT-C CS
                      Shikimate_DH   5 kkleslkekkvlliGaGemaelvakhLlakgvk 37 
                                       k+++ l++ + +liG G+  ++ a+ L++  vk
  gi|518652396|ref|YP_008141916.1| 275 KNFPALSGLNSMLIGPGMGKSKEAEDLIKYAVK 307
                                       678999999********9999999988876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3321.15
//
Query:       gi|518652397|ref|YP_008141917.1|  [L=390]
Description: AMP-binding enzyme [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.8e-14   50.8   0.0    2.6e-11   42.8   0.0    2.1  2  AMP-binding  AMP-binding enzyme


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.0   1.5e-15   2.6e-11       3     134 ..      22     144 ..      20     191 .. 0.77
   2 !    6.3   0.0   0.00018       3.2     202     381 ..     221     366 ..     192     387 .. 0.75

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 1.5e-15
                                       HHHHHSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHH.HTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEE CS
                       AMP-binding   3 eqaaktpdkvalvdsgegqtlTYreldervnrlAagLr.slGvkkgdrVaillpnspewvvallailkaGavvvpln 78 
                                       ++a+ +  ++ +++   ++ +TY+ l + v+++A  L+ +l+v+kg+++ai+++ sp ++++++   k+Ga +  ++
  gi|518652397|ref|YP_008141917.1|  22 RNAEVNGSRPIIIF--YDKYITYSKLLKYVDSMAYQLEhRLNVRKGETIAIIMDFSPPYIISIISSIKIGARILIID 96 
                                       68899999******..899*******************99************************************* PP

                                       TTS-HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCC CS
                       AMP-binding  79 ptltaeelayiledseakvliatvdselleklleaaakleavklvivldadellke 134
                                        ++   ++   +++  +kv+i  + ++     +e+a+   ++ + iv+d +++l+ 
  gi|518652397|ref|YP_008141917.1|  97 GKTDDNTINGYIDKYSIKVMI--ICKKF----AEKAK--NEQIKYIVSDPNDFLTL 144
                                       *********************..43333....22222..12233555565555544 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.00018
                                       T-EEEESS-TTSCHHHHHHHHHHHHTT-EEEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHH CS
                       AMP-binding 202 ddvvlsilplahifglilelllallsGatvvllpkdaaldpklllelieklkvtviagvPrvleallesgalkaakk 278
                                       + v++s  + +  +gli+++ l+++  +t+v+ +  +        + i++  + +++g+P+++ +++e++ +     
  gi|518652397|ref|YP_008141917.1| 221 KPVFYSDIDHSTPLGLIYSIALPISFSGTIVINS--P--------ASISRNACDFVVGTPSFYSHIIEKK-I----- 281
                                       5566666666777889999999999999999944..3........36999******************62.3..... PP

                                       HCCGTT-SEEEEESS-EBHHHHHHHHHHHTCEEEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTT CS
                       AMP-binding 279 akdlsslrlvllggeplspellrffralfgeevlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeet 355
                                         + s+++++        +e+  +f++ +  +++   G +   + +t+++ + d+ ++gs G p+  ve++i  e+ 
  gi|518652397|ref|YP_008141917.1| 282 --NISGVKYC--IMPFYDREIENAFHQYTNIPLIA--GRSDQFTLTTHMN-PFDDIRVGSFGMPVNYVECMINPEN- 350
                                       ..57899995..56667788888888888767777..9999999998666.4555688999999999999994333. PP

                                       SCBEETTSEEEEEEEETTS-SEBTT- CS
                       AMP-binding 356 gepvpdgeeGellvrgpgvmkgYlkk 381
                                                 ell++ p +   Y ++
  gi|518652397|ref|YP_008141917.1| 351 ----------ELLIKTPYLPAIYENN 366
                                       ..........5666666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2479.69
//
Query:       gi|518652398|ref|YP_008141918.1|  [L=158]
Description: hypothetical protein FACI_IFERC00001G1037 [Ferroplasma acidarmanus fer1]
Scores for complete 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   17.0   1.4     0.0047   17.0   1.4    1.8  2  DUF2593        Protein of unknown function (DUF2593)


Domain annotation for each model (and alignments):
>> DUF2593  Protein of unknown function (DUF2593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   1.4   2.6e-07    0.0047      66     131 ..       8      73 ..       4      85 .. 0.88
   2 ?   -1.2   0.4      0.11   1.9e+03      20      36 ..     109     125 ..      96     145 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.6e-07
                           DUF2593  66 vlrgrnwgrWlylltqiivvlylllaslgelyPelfsisgeskaeilhslllqklPdllvllLLfv 131
                                       ++ g + g  +++++ i+ v+ l++ s ++     ++i++++ + ++  ll+ ++ dll+l L+f 
  gi|518652398|ref|YP_008141918.1|   8 IIAGLKSGFIYFIIASIVNVIILYIFSAEFAFAYGYTITSKNLSLLFTVLLVSQVRDLLILGLVFG 73 
                                       67788889999******999988888888888889****************************996 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.11
                           DUF2593  20 vvllvnelGlsglssfi 36 
                                       v+++v +lGl g+ + i
  gi|518652398|ref|YP_008141918.1| 109 VIITVYSLGLLGIYDLI 125
                                       55566666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1141  (0.0636399); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.62u 0.34s 00:00:00.96 Elapsed: 00:00:00.55
# Mc/sec: 872.45
//
Query:       gi|518652399|ref|YP_008141919.1|  [L=118]
Description: hypothetical protein FACI_IFERC00001G1038 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-05   23.4   0.1    4.3e-05   23.2   0.1    1.2  1  SMC_ScpB  Segregation and condensation complex subunit ScpB
     0.0023   18.0   0.2     0.0023   18.0   0.2    1.6  2  DUF2582   Winged helix-turn-helix domain (DUF2582)
  ------ inclusion threshold ------
      0.023   14.6   0.2       0.13   12.2   0.1    2.2  3  TrmB      Sugar-specific transcriptional regulator TrmB
      0.042   13.7   0.0      0.061   13.2   0.0    1.3  1  MarR_2    MarR family


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.1   9.5e-09   4.3e-05      67     149 ..       5      92 ..       1     113 [. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 9.5e-09
                          SMC_ScpB  67 evvkklvkekkktrLsqaaletLaiIaykqpvtraeiee...iRGvnsdsvvrtLlerglieekgrkee.pgrpil. 138
                                       e v+kl+k    +++ ++   tL +I  k  +t+ e+e+   +R  +++ +++ L ++++i +++ k+e +grp+  
  gi|518652399|ref|YP_008141919.1|   5 EEVNKLAKYLMVSDIPRSVAYTLVYIKDKGEITSVEVERetgLRQPEVSIAMQWLRRKNWIAKRNMKKEgKGRPVHg 81 
                                       4445555554456999*********************9755577888999***********998876666*****99 PP

                          SMC_ScpB 139 YgtTekFleyf 149
                                       Y++++ F e +
  gi|518652399|ref|YP_008141919.1|  82 YKLSKDFNEIL 92 
                                       *******8865 PP

>> DUF2582  Winged helix-turn-helix domain (DUF2582)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   5.2e-07    0.0023      18      56 ..      31      69 ..      27      75 .. 0.88
   2 ?   -2.9   0.1       1.8     8e+03      48      53 ..      99     104 ..      96     114 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 5.2e-07
                                      CCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEE CS
                           DUF2582 18 nengeislkelkrktglsdkelalAiGWLaREdKivier 56
                                      +++gei+  e++r+tgl + e+  A+ WL R + i+ ++
  gi|518652399|ref|YP_008141919.1| 31 KDKGEITSVEVERETGLRQPEVSIAMQWLRRKNWIAKRN 69
                                      7899****************************9997665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                                       CTTSEE CS
                           DUF2582  48 REdKiv 53 
                                       RE Ki+
  gi|518652399|ref|YP_008141919.1|  99 REKKID 104
                                       666664 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.21   9.5e+02      32      41 ..      17      26 ..       4      29 .. 0.76
   2 ?   12.2   0.1   2.8e-05      0.13      19      58 ..      32      71 ..      22      86 .. 0.84
   3 ?   -1.5   0.0      0.52   2.3e+03      16      32 ..      94     110 ..      82     113 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.21
                                      TTSSCHCHHH CS
                              TrmB 32 lgvprskvYe 41
                                      +++prs +Y 
  gi|518652399|ref|YP_008141919.1| 17 SDIPRSVAYT 26
                                      7899998886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.8e-05
                                      HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 19 klgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       +g+ t  e+ +e+g+ ++ v  +++ L +k ++ ++  +
  gi|518652399|ref|YP_008141919.1| 32 DKGEITSVEVERETGLRQPEVSIAMQWLRRKNWIAKRNMK 71
                                      689999****************************999876 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.52
                                       HHHHHCCCHHCHHCCCT CS
                              TrmB  16 aLlklgpatadeiaeel 32 
                                        ++++ ++++dei + +
  gi|518652399|ref|YP_008141919.1|  94 EIINEREKKIDEINSTI 110
                                       45566777777777665 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.061       2      54 ..      18      68 ..      17      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +++++ a  L ++ + ++  +t  e++r++gl ++ vs + + L ++ ++ +r
  gi|518652399|ref|YP_008141919.1| 18 DIPRSVAYTLVYIKDKGE--ITSVEVERETGLRQPEVSIAMQWLRRKNWIAKR 68
                                      78899999*********9..***************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1502  (0.0837749); expected 358.6 (0.02)
Passed bias filter:                      803  (0.0447878); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 848.59
//
Query:       gi|518652400|ref|YP_008141920.1|  [L=85]
Description: hypothetical protein FACI_IFERC00001G1039 [Ferroplasma acidarmanus fer1]
Scores for complete 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  105.9   0.2    9.1e-31  105.8   0.2    1.0  1  UPF0147   Uncharacterised protein family (UPF0147)
  ------ inclusion threshold ------
      0.078   12.1   0.6        0.1   11.6   0.6    1.2  1  AIP3      Actin interacting protein 3


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 !  105.8   0.2     1e-34   9.1e-31       2      80 ..       3      81 ..       2      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 1e-34
                                      HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHHHH CS
                           UPF0147  2 eekikevielLeeiiedtsvPrniRraakeakekLkdekeslavraataisiLdeisnDpnmPlhaRtliwevvskLEt 80
                                      e+ ++ev+ l++++ +d+s+Prn+R++ +eakek+kd kesl++r+a++is Ld+isnDpn+P+h R++i++++skLE+
  gi|518652400|ref|YP_008141920.1|  3 ENLFNEVLALMDDLEDDSSIPRNVRKTSSEAKEKMKDGKESLDLRCANVISELDDISNDPNVPSHGRAAIYTIISKLEA 81
                                      6889**************************************************************************8 PP

>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.6   1.2e-05       0.1     160     211 ..      11      59 ..       1      61 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.2e-05
                                       XXXXXXXXXXXXXXXXXX.XXXXXXHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              AIP3 160 eslselrekakkvkeaslastkkssnrayiekgkkkLseesdklvtkvddLq 211
                                       + + +l++  +  +  ++  +++s++++ +++gk++L+ ++ ++++++dd++
  gi|518652400|ref|YP_008141920.1|  11 ALMDDLEDDSSIPR--NV-RKTSSEAKEKMKDGKESLDLRCANVISELDDIS 59 
                                       55555555555444..55.566789999**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (85 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 635.18
//
Query:       gi|518652401|ref|YP_008141921.1|  [L=106]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   65.2   0.1    5.2e-18   64.8   0.1    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.018   15.0   0.0    1.3  1  GYD             GYD domain
       0.16   12.1   0.8       0.25   11.5   0.2    1.6  2  Mst1_SARAH      C terminal SARAH domain of Mst1


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 !   64.8   0.1   8.7e-22   5.2e-18       2      74 ..      29      98 ..      28      99 .. 0.94

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 8.7e-22
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                      +++ e ++   ++++ + + e+++V+e+++vtG+yd+++kv+++d  ale+f+++ l+s+ g+++++t++vl+
  gi|518652401|ref|YP_008141921.1| 29 GIEAEINN---VDAIGRIIGEHKNVEEVFVVTGEYDLIIKVRFPDYIALEKFIVNNLNSIQGIRKSKTMMVLS 98
                                      67777777...99***********************************************************8 PP

>> GYD  GYD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0     3e-06     0.018      36      66 ..      49      79 ..      29      99 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-06
                               GYD 36 kleslyatlGeyDvvvivEapDdetaaalsl 66
                                      ++e++++++GeyD+++ v +pD  + +++ +
  gi|518652401|ref|YP_008141921.1| 49 NVEEVFVVTGEYDLIIKVRFPDYIALEKFIV 79
                                      699********************99999876 PP

>> Mst1_SARAH  C terminal SARAH domain of Mst1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   4.1e-05      0.25      16      37 ..       1      22 [.       1      23 [. 0.95
   2 ?   -2.9   0.0       1.3   7.8e+03      24      30 ..      31      37 ..      30      39 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.1e-05
                        Mst1_SARAH 16 lasLDpeMEqEieelrkrYqaK 37
                                      +++L + ME+Ei + r+ Y +K
  gi|518652401|ref|YP_008141921.1|  1 MNNLGELMEAEITNFREYYDNK 22
                                      8999***************998 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.3
                        Mst1_SARAH 24 EqEieel 30
                                      E+Ei+++
  gi|518652401|ref|YP_008141921.1| 31 EAEINNV 37
                                      8899876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 786.17
//
Query:       gi|518652402|ref|YP_008141922.1|  [L=216]
Description: thymidine kinase related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.1e-45  153.8   0.0    4.8e-45  153.6   0.0    1.0  1  TK         Thymidine kinase
     0.0095   15.9   0.0        1.8    8.6   0.0    2.5  2  HTH_45     Winged helix-turn-helix
  ------ inclusion threshold ------
      0.034   14.2   0.6       0.22   11.6   0.0    2.2  2  Nop10p     Nucleolar RNA-binding protein, Nop10p family
       0.06   13.4   0.0      0.094   12.8   0.0    1.3  1  AAA_14     AAA domain
       0.13   10.9   0.1       0.16   10.7   0.1    1.2  1  Herpes_U5  Herpesvirus U5-like family


Domain annotation for each model (and alignments):
>> TK  Thymidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.6   0.0   1.4e-48   4.8e-45       1     177 []      21     203 ..      21     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 153.6 bits;  conditional E-value: 1.4e-48
                                TK   1 gsielilgpmfaGKsteLlrrvkryqlaekkvvvikaakdnRysegkvvthdgisleakksktssleeikeeleeed 77 
                                       g++++i+gpmf+GK++ L++  +r  la  +++++k++ d+Ry ++ v+th+g+ l a   +t++    k    +++
  gi|518652402|ref|YP_008141922.1|  21 GKLTVITGPMFSGKTSRLIELLEREILAGRNTLLFKPEMDKRYDTTFVTTHKGMRLPAIVLNTDNEGVEKMYNLSKN 97 
                                       6899*******************************************************666666555555555556 PP

                                TK  78 vdvvlvDEaqFfe.qdiv.elseklanegkivivagLdtdFerklFenilkllalaekvkklkavCmkCgkkAsftk 152
                                       vdv+++DEaqF +   i+ e+++k+a e+kiv +a+L+ ++ +++F++++ +++ a++v +l+avC kCg++A+f++
  gi|518652402|ref|YP_008141922.1|  98 VDVIGIDEAQFWNhGSILpEIADKIASENKIVYAAALNKNHLGNPFKTSMDIISRADQVYSLTAVCAKCGEDATFSQ 174
                                       *************8555439********************************************************* PP

                                TK 153 rlnke....keviliGgkekYvsvCrkcy 177
                                       r+ +     +e+i iGg e+Y++ Crkc+
  gi|518652402|ref|YP_008141922.1| 175 RILNGkeifGEQIKIGGMESYEPRCRKCF 203
                                       *995511225789***************8 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0    0.0084        30      50      65 ..      61      76 ..      36      85 .. 0.79
   2 !    8.6   0.0   0.00049       1.8      11      60 ..     114     161 ..     112     169 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0084
                            HTH_45 50 kkskekYvlTekGlel 65
                                      k  ++++v+T+kG++l
  gi|518652402|ref|YP_008141922.1| 61 KRYDTTFVTTHKGMRL 76
                                      56789********987 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00049
                            HTH_45  11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTe 60 
                                       IL  i ++ a+  ki+y+a L+ + l +  ++  + ++i+  ++ Y+lT+
  gi|518652402|ref|YP_008141922.1| 114 ILPEIADKIASENKIVYAAALNKNHLGNPFKT--SMDIISRADQVYSLTA 161
                                       9999999***************9999987664..5567888888888885 PP

>> Nop10p  Nucleolar RNA-binding protein, Nop10p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.2e-05      0.22      10      28 ..     153     171 ..     145     174 .. 0.81
   2 ?    0.1   0.2      0.24   8.7e+02       1      14 [.     192     205 ..     192     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.2e-05
                                       TT--EESSSB-TTT-SB-B CS
                            Nop10p  10 kcrvYTLkkvcpecggptk 28 
                                       +++vY L  vc +cg++++
  gi|518652402|ref|YP_008141922.1| 153 ADQVYSLTAVCAKCGEDAT 171
                                       569************9754 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.24
                                       .----EE-TTT--E CS
                            Nop10p   1 mksylrkcgkcrvY 14 
                                       m+sy  +c+kc vY
  gi|518652402|ref|YP_008141922.1| 192 MESYEPRCRKCFVY 205
                                       7788889****999 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.6e-05     0.094       3      77 ..      22     110 ..      21     150 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.6e-05
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd.......kkladpe...kllelileklke....... 62 
                                       k+ vitG+  +GKT  l +l+++++   +++l ++ + ++        +     +   +l+ ++l+  +e       
  gi|518652402|ref|YP_008141922.1|  22 KLTVITGPMFSGKTSRLIELLEREILAGRNTLLFKPEMDKRydttfvtT-----HkgmRLPAIVLNTDNEgvekmyn 93 
                                       789******************9999777777777655544422333320.....14555555555553224555666 PP

                            AAA_14  63 ..ekktylflDEiqevp 77 
                                         ++  ++ +DE+q  +
  gi|518652402|ref|YP_008141922.1|  94 lsKNVDVIGIDEAQFWN 110
                                       777888999***99875 PP

>> Herpes_U5  Herpesvirus U5-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   4.5e-05      0.16     234     285 ..       7      59 ..       1     101 [. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.5e-05
                         Herpes_U5 234 lilrvvrllraviraeldiyi.dllseevqklivllkeeakllrkGllqnpvq 285
                                       + l ++ ++++ i   l+++   ++s++  +li ll+ e+  +r+ ll +p  
  gi|518652402|ref|YP_008141922.1|   7 YELIILTIMKNIIIGKLTVITgPMFSGKTSRLIELLEREILAGRNTLLFKPEM 59 
                                       56778888999999999976637************************988843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1504.50
//
Query:       gi|518652403|ref|YP_008141923.1|  [L=253]
Description: carbamate kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.5e-08   33.0   0.0    2.9e-07   30.3   0.0    1.9  1  AA_kinase  Amino acid kinase family
  ------ inclusion threshold ------
        2.5    8.0   0.0        2.5    8.0   0.0    2.6  3  DUF2729    Protein of unknown function (DUF2729)


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 !   30.3   0.0   3.2e-11   2.9e-07     116     239 ..     112     240 ..       2     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.3 bits;  conditional E-value: 3.2e-11
                                       ..HHHTTTCEEECCHHHHHHHTT-EEEEES..EEEEETTTE....EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCE CS
                         AA_kinase 116 degsdgnvesvdaeaieelleagvvpvltg..figldeege....lgrgssDtiaallAealgAdkliiltdVdGVy 186
                                        e+  +++   +++ai++l+++g++p++ g  f ++ e +      g +++  +++ll+ +++Ad+lii++      
  gi|518652403|ref|YP_008141923.1| 112 TEEFLEPIDIPEKSAIMTLMSDGYLPIIIGagFPVVRELQYynncHGMVNNYSSSSLLGTLIEADELIIISGHK--- 185
                                       344445556666****************99435566666659**999**********************99888... PP

                                       SSTTTTCCTTCECCEEEHHHCHH..CSSS.TTTHHHHCHHHHHHHHHCTT-EEEE CS
                         AA_kinase 187 dadpkkvpdarllpeisvdeaee..saselatgGmkvkhpaalaaarrggipvvI 239
                                       d    +v +++ll++i+++ +++  +++++    +  k++a+l+++ +gg ++++
  gi|518652403|ref|YP_008141923.1| 186 DEFEGIVNSGKLLKNITFNALMDiyKSGHFNDNITGKKIKAMLDFISKGGKKAIL 240
                                       9999999999**************************************9988876 PP

>> DUF2729  Protein of unknown function (DUF2729)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.6      0.82   7.4e+03      38      48 ..       9      19 ..       8      21 .. 0.84
   2 ?    8.0   0.0   0.00028       2.5       5      41 ..      65     101 ..      62     105 .. 0.91
   3 ?   -0.2   1.7       0.1   9.1e+02      40      49 ..     148     157 ..     147     163 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.82
                           DUF2729 38 Gdryyqynnnc 48
                                      G+ y  yn  c
  gi|518652403|ref|YP_008141923.1|  9 GNNYPGYNQKC 19
                                      778999**999 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00028
                           DUF2729   5 ycklklvkGfskkfaslfcrcvvshlsdeddsdGdry 41 
                                       y ++k   G+sk   ++f r  + ++s+     Gd y
  gi|518652403|ref|YP_008141923.1|  65 YDRVKYKYGYSKEIIAVFTRVEIRKISNPSVQTGDNY 101
                                       78899999********************999999999 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.1
                           DUF2729  40 ryyqynnncn 49 
                                       r  qy nnc 
  gi|518652403|ref|YP_008141923.1| 148 RELQYYNNCH 157
                                       567******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1698.27
//
Query:       gi|518652404|ref|YP_008141924.1|  [L=160]
Description: acyl-CoA hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-14   51.8   0.0    1.2e-13   51.2   0.0    1.3  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 !   51.2   0.0   6.8e-18   1.2e-13       1      74 [.      24      96 ..      24      99 .. 0.97

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 6.8e-18
                                      TSSB-HHHHHHHHHHHHHHHHHHTTSTTEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETT CS
                              4HBT  1 gGvvhgGvylallDeaagaalrslggrgilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrded 74
                                      +G ++gG++++++D ++++ ++++ ++ ++v+++ +++ fl+p++lg  + ++  v+++ ++++++e++v +e+
  gi|518652404|ref|YP_008141924.1| 24 FGDLYGGRLVEWMDNIGSITAFKHSRK-KVVTGSIDNLFFLSPIKLGYIVHLHSFVTYTTKSTMEIEIDVSSEN 96
                                      699***********************8.******************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); 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: 1233.63
//
Query:       gi|518652405|ref|YP_008141925.1|  [L=161]
Description: hypothetical protein FACI_IFERC00001G1044 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      4e-16   58.8   0.0    5.7e-16   58.3   0.0    1.2  1  Hjc        Archaeal holliday junction resolvase (hjc)
  ------ inclusion threshold ------
      0.011   15.3   0.0      0.017   14.7   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 !   58.3   0.0   6.4e-20   5.7e-16       5      92 ..      24     115 ..      21     116 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 6.4e-20
                                       HHHHHHHHTT-EEEEBSCSSSSSSSS-SEEEEETTEEEEEEEEEESSSEEEE......EHHHHHHHHHHHHHHTCEE CS
                               Hjc   5 elvkiLrergfavvRsagSggatkplpDviAirgdvvlviEvKsskkeriyl......kkeqvekllefarkaggel 75 
                                       ++v  + ++ f+v R+agS+ga     D++A+r d +lviEvKss+++++        k++q+ kl + +  +g + 
  gi|518652405|ref|YP_008141925.1|  24 DVVYTMMDKPFYVARAAGSFGA-----DLVALRDDYSLVIEVKSSSRSQLTFseasgtKQDQALKLHNRCILSGLFI 95 
                                       6777889999************.....*******************888888************************* PP

                                       EEEEEE...TTTEEEEEEGG CS
                               Hjc  76 llavkl...qgkewkllvve 92 
                                       ++a++l   +g+ w+++++e
  gi|518652405|ref|YP_008141925.1|  96 TYAYRLknyKGDFWRFFSIE 115
                                       ******9989999****998 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-06     0.017      41      65 ..      41      65 ..      31      85 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-06
                         AHJR-like 41 ksYrpDliarkdeeaviiEvksrrs 65
                                      +s+  Dl+a +d+  ++iEvks++ 
  gi|518652405|ref|YP_008141925.1| 41 GSFGADLVALRDDYSLVIEVKSSSR 65
                                      67999****************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 1228.26
//
Query:       gi|518652406|ref|YP_008141926.1|  [L=450]
Description: hypothetical protein FACI_IFERC00001G1045 [Ferroplasma acidarmanus fer1]
Scores for complete 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-114  380.7   0.0   7.7e-114  380.5   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
      0.097   13.1   0.2        0.4   11.1   0.1    2.0  2  ZapA         Cell division protein ZapA


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 !  380.5   0.0  8.6e-118  7.7e-114       4     404 ..      34     444 ..      31     446 .. 0.95

  Alignments for each domain:
  == domain 1  score: 380.5 bits;  conditional E-value: 8.6e-118
                                       TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHH CS
                       Aminotran_3   4 reednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekll 80 
                                        + + l++v+ +++G+y++dvd++ +lD+ s+i+ +n+G+ ++ v+  v+eq++kl+h     + +++++++a+ l+
  gi|518652406|ref|YP_008141926.1|  34 TSTKSLPVVAYRGQGCYIEDVDDNVFLDFSSGISTTNIGYGNEYVISKVQEQLHKLWHFAGTDFYYSEQVEAAKALI 110
                                       5556677999******************************************************************* PP

                                       HHCT-..S.EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TS CS
                       Aminotran_3  81 klapkgld.kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpe 156
                                        + p+++d kvf+ansG+e++e++lKlar+      +t+++++i f g+fHGrt+gals t+s++ ++++f p +++
  gi|518652406|ref|YP_008141926.1| 111 GVSPGSHDkKVFYANSGAESNEASLKLARS------YTKRPQFIGFIGGFHGRTMGALSFTASQPVHHEGFFPEMAG 181
                                       ********99********************......9**************************************** PP

                                       EEEE-TTBGGGTB-HH.......HHHHHHHHHHHHHH...CHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHH CS
                       Aminotran_3 157 vvrlkypdeevlkene.......eeeaalleeleale...kkkkdevaAvivEpiqgegGvvvaspeflaklrelck 223
                                       v+++++pd+++ ++n        + ++a++ +le++       +++vaA++vEpiqgegG++v++ +f +kl el++
  gi|518652406|ref|YP_008141926.1| 182 VTHIPFPDPYRNPFNIdgyeepeDLTNAAIDYLEDYVfgkFLPSNDVAAILVEPIQGEGGYIVPPMDFHKKLMELAH 258
                                       **************987887444445555566666658866789********************************* PP

                                       HHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHH CS
                       Aminotran_3 224 khdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacav 300
                                       ++++l i+DEvqtGfGrTG +fA e++gv pD+m +aK++++G+p+ a +++ +  +  ++g h++TfgGn la + 
  gi|518652406|ref|YP_008141926.1| 259 DNEILYIMDEVQTGFGRTGYFFASEYFGVDPDIMSVAKSIASGIPMGASVVKSKY-NFEKSGLHSNTFGGNLLASVS 334
                                       ***************************************************9995.5556888************** PP

                                       HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC......HHHHHHHHHCT CS
                       Aminotran_3 301 alavleiieeekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke......keilkkakekG 371
                                       ++a++e i++++++ena+++g++l+++L+elq+ky+ i++vRg+Glm ai++++++++k        + +++a ++G
  gi|518652406|ref|YP_008141926.1| 335 SRATIEEIKNKNMVENARKVGDYLNKRLHELQEKYDNIGDVRGLGLMQAIDFVKNRKTKAhfrglrDKTIENAYKNG 411
                                       *********************************************************888*****999********* PP

                                       EE-EEETTTEEEE---TT--HHHHHHHHHHHHH CS
                       Aminotran_3 372 vlilsaGdnvirllppliitdeeidelleilkk 404
                                       +++l+aG+++ir++ppli+++++ide+++il +
  gi|518652406|ref|YP_008141926.1| 412 LILLGAGESAIRFIPPLIVNEKQIDEAIDILDN 444
                                       *****************************9976 PP

>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.57   5.1e+03      10      32 ..     195     217 ..     193     218 .. 0.81
   2 ?   11.1   0.1   4.5e-05       0.4      20      58 ..     349     388 ..     342     407 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.57
                              ZapA  10 ytlaceegeeeylreaaklvdek 32 
                                       +++ + e+ e+   +a ++++++
  gi|518652406|ref|YP_008141926.1| 195 FNIDGYEEPEDLTNAAIDYLEDY 217
                                       66778898899999999999987 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 4.5e-05
                              ZapA  20 eylreaaklvdekikeireaggnlseerll.vmaaLnlad 58 
                                       e  r++ +++++++ e++e++ n+++ r l +m a+++ +
  gi|518652406|ref|YP_008141926.1| 349 ENARKVGDYLNKRLHELQEKYDNIGDVRGLgLMQAIDFVK 388
                                       788********************99998776777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3479.89
//
Query:       gi|518652407|ref|YP_008141927.1|  [L=329]
Description: hypothetical protein FACI_IFERC00001G1046 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-22   79.2  23.8    1.9e-12   47.6   1.6    2.6  3  VIT1          VIT family
    1.4e-11   45.0   4.0    2.3e-11   44.3   4.0    1.3  1  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.014   15.0   0.2      0.051   13.2   0.0    1.8  2  DUF3231       Protein of unknown function (DUF3231)
      0.015   14.3   0.4        2.5    7.0   0.0    2.2  2  Mn_catalase   Manganese containing catalase
       0.18   11.6   0.7          4    7.2   0.7    2.4  2  COQ7          Ubiquinone biosynthesis protein COQ7


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 ?   -2.0   0.3      0.76   2.7e+03      51      77 ..      97     123 ..      96     145 .. 0.54
   2 !   47.6   1.6   5.2e-16   1.9e-12       2      69 ..     151     217 ..     150     229 .. 0.92
   3 !   43.8   7.5   7.4e-15   2.7e-11     131     214 ..     235     317 ..     216     318 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.76
                              VIT1  51 GeYlsvkserdlekaerkreeeeleed 77 
                                       GeY s ++ + ++++ +++ + + + +
  gi|518652407|ref|YP_008141927.1|  97 GEYQSIRKYKTYLESYKQEDDYKKKVN 123
                                       788888887777776554433322222 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 5.2e-16
                              VIT1   2 rdavlGanDGLvspfalvaGlsaaslgssktvllaGlaellAGaiSMgiGeYlsvkserdlekaerkr 69 
                                       rd+ +G++DGLv ++a  +Glsa+ + s+  + l+G+   ++G +SM +G+Yl+ kse+++  a+++r
  gi|518652407|ref|YP_008141927.1| 151 RDFLYGMSDGLVEVLATLVGLSAIIT-SHIDIALSGVVVGISGTFSMTLGAYLAQKSESEYKIAMLNR 217
                                       9*********************8875.9********************************98888777 PP

  == domain 3  score: 43.8 bits;  conditional E-value: 7.4e-15
                              VIT1 131 lasplkaAlssalsfliGgliPllpylfvesvglalvvsiavtllalllfGavkalltgssklvsalrmlliGalAa 207
                                         ++  +Al +a+s+++G++iP+lp++f++   +a+++s++++ +a ++   + al +++++l+s+lr  l+ ++Aa
  gi|518652407|ref|YP_008141927.1| 235 SSEATISALNTAISYITGAVIPILPFVFFQ-KYMAVALSVILVFIAQMISNSIVALSLNTPILKSGLRASLLALGAA 310
                                       245667**********************99.9********************************************* PP

                              VIT1 208 aaaylig 214
                                       aa+++ g
  gi|518652407|ref|YP_008141927.1| 311 AATFAAG 317
                                       ****987 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   4.0   6.3e-15   2.3e-11       8     135 ..      15     138 ..      14     140 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 6.3e-15
                                       HHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHH CS
                      Rubrerythrin   8 agEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttakn 84 
                                       + E +++ +Y+++++k++   p+++e F++lA  E eHa++  + l++ + + + ++  +  +++++k+  ++  kn
  gi|518652407|ref|YP_008141927.1|  15 RDELTDMIFYTYMYRKTE--DPELKENFKQLATIENEHANFWGQSLKSSNVDIN-KITYRRTKFFFMKIIRVIVGKN 88 
                                       569999************..**********************************.6666677777778777788888 PP

                                       HH.HHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHHHHHHHHHHHH CS
                      Rubrerythrin  85 Le.eaiegayaeeeemyrfyeelaekegneeakklfkklaeaEkkHeerlrk 135
                                       L+ +++e ++++ +  y++y e +++  +++ kk + +l+  E +Hee++++
  gi|518652407|ref|YP_008141927.1|  89 LIiNLLEHGEYQSIRKYKTYLESYKQ--EDDYKKKVNDLISSEMQHEEIFAN 138
                                       88578888888888888888888884..4668*****************986 PP

>> DUF3231  Protein of unknown function (DUF3231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05     0.051      28      78 ..      17      67 ..      12      73 .. 0.90
   2 ?   -2.2   0.0      0.79   2.8e+03       9      31 ..     121     145 ..     112     181 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                           DUF3231 28 nslgialitgFlqvaedkeikelleralelsnkhikelkelLkeenlpiPs 78
                                      + + ++ +t+++ ++ed e+ke +++   + n+h +   + Lk++n+ i +
  gi|518652407|ref|YP_008141927.1| 17 ELTDMIFYTYMYRKTEDPELKENFKQLATIENEHANFWGQSLKSSNVDINK 67
                                      56678899**************************************99865 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.79
                           DUF3231   9 kkrpLtasEias..lwssyianslg 31 
                                       k   L +sE+ +  ++++ i++s++
  gi|518652407|ref|YP_008141927.1| 121 KVNDLISSEMQHeeIFANKISKSVK 145
                                       5556677777644466655555543 PP

>> Mn_catalase  Manganese containing catalase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0   0.00071       2.5     155     195 ..      22      62 ..      13      73 .. 0.87
   2 ?    5.4   0.1    0.0021       7.5      34      85 ..      97     148 ..      91     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.00071
                       Mn_catalase 155 lqverlyeltddpgvrdmlsfLlaRelvHqlafekAleele 195
                                       + ++ +y  t+dp++++  + L + e  H + + + l++ +
  gi|518652407|ref|YP_008141927.1|  22 IFYTYMYRKTEDPELKENFKQLATIENEHANFWGQSLKSSN 62 
                                       678999****************************9999755 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0021
                       Mn_catalase  34 GElsvalrYlfQgfnirdkekykdLlmdiatEElgHvEliatmiarllegat 85 
                                       GE   + +Y +   + +++  yk  + d+ + E+ H E+ a+ i++ +++ +
  gi|518652407|ref|YP_008141927.1|  97 GEYQSIRKYKTYLESYKQEDDYKKKVNDLISSEMQHEEIFANKISKSVKNIQ 148
                                       6666666776665566778888899*******************99888765 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.7    0.0011         4      28     139 ..      30     135 ..      19     148 .. 0.63
   2 ?    5.6   0.1    0.0035        13      12      59 ..      97     143 ..      89     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
                              COQ7  28 akkdpelkpllkemleqEkeHlatfeellkerrvrpslllplwkvagfalGaltallGkeaamacteavEtvigeHY 104
                                       +++dpelk+ +k+ ++ E+eH +++ + lk+ +v    ++   ++  f++ ++  ++Gk+ ++   e  E +  + Y
  gi|518652407|ref|YP_008141927.1|  30 KTEDPELKENFKQLATIENEHANFWGQSLKSSNVDINKITY-RRTKFFFMKIIRVIVGKNLIINLLEHGEYQSIRKY 105
                                       46777888888888888888888888888887776655543.45566777777777777777777777777777777 PP

                              COQ7 105 neqlreleeleeeedkelleiikqfrddEleHldt 139
                                       +  l++ ++     + + ++ ++ + + E++H+++
  gi|518652407|ref|YP_008141927.1| 106 KTYLESYKQ-----EDDYKKKVNDLISSEMQHEEI 135
                                       777777663.....333444444444444444433 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0035
                              COQ7  12 GElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellker 59 
                                       GE+   + Yk  l    k++ + k+ +++  + E +H ++f++ +++ 
  gi|518652407|ref|YP_008141927.1|  97 GEYQSIRKYKTYLESY-KQEDDYKKKVNDLISSEMQHEEIFANKISKS 143
                                       7888888888888885.7777889*****************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1679  (0.0936472); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); 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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2206.15
//
Query:       gi|518652408|ref|YP_008141928.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G1047 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-25   89.4   0.0    4.5e-25   88.7   0.0    1.3  1  ABC_tran      ABC transporter
    5.8e-16   59.2   0.4    2.7e-07   30.7   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
    6.4e-05   22.4   0.0     0.0001   21.7   0.0    1.3  1  Mg_chelatase  Magnesium chelatase, subunit ChlI
    0.00069   19.6   0.0     0.0024   17.8   0.0    1.8  2  Rad17         Rad17 P-loop domain
     0.0013   19.3   2.8     0.0018   18.8   1.2    1.9  2  AAA_23        AAA domain
     0.0018   17.8   0.6       0.21   11.0   0.2    2.2  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0044   16.7   1.2     0.0089   15.7   0.7    1.8  1  AAA_29        P-loop containing region of AAA domain
     0.0083   15.9   1.8       0.24   11.1   0.1    2.1  2  AAA_15        AAA ATPase domain
  ------ inclusion threshold ------
       0.01   16.3   0.5      0.071   13.5   0.5    2.2  1  AAA           ATPase family associated with various cellular 
      0.011   14.4   1.3       0.56    8.8   0.1    2.1  2  AAA_13        AAA domain
      0.019   15.4   0.0      0.057   13.8   0.0    1.8  1  AAA_16        AAA ATPase domain
      0.021   14.8   0.2      0.092   12.6   0.1    2.0  2  ATPase_2      ATPase domain predominantly from Archaea
      0.031   14.0   0.1       0.11   12.2   0.0    1.8  2  AAA_30        AAA domain
      0.044   13.4   0.0       0.21   11.2   0.0    1.8  2  PrkA          PrkA serine protein kinase C-terminal domain
       0.05   13.5   0.5        3.5    7.5   0.1    2.2  2  NTPase_1      NTPase
      0.057   14.0   0.2       0.16   12.5   0.2    2.0  2  AAA_18        AAA domain
       0.11   12.8   0.1       0.51   10.6   0.1    2.0  2  AAA_22        AAA domain
       0.12   12.3   0.1       0.28   11.1   0.1    1.6  1  NACHT         NACHT domain
       0.14   11.9   0.2       0.68    9.6   0.1    1.9  2  AAA_24        AAA domain
       0.21   11.8   0.1       0.41   10.9   0.1    1.4  1  AAA_28        AAA domain
       0.33   10.0   1.9       0.39    9.7   0.4    1.7  2  T2SSE         Type II/IV secretion system 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 !   88.7   0.0   5.3e-28   4.5e-25       1     136 [.      19     162 ..      19     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 5.3e-28
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l+ +sl++  g++++i+G+nG+GK+tLlk+lag l p +Ge+ +dg +l+  +    ++  g++p++p l + lt  
  gi|518652408|ref|YP_008141928.1|  19 LNGISLSIAGGQIYGILGPNGSGKTTLLKILAGILPPSSGEVVIDGMNLTG-NSDNIKSITGYIPETPALYESLTPI 94 
                                       789************************************************.99999******************66 PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                                       e                +e+i+++ + l++ +  ++ +     sLS G kq+va+  +l+ +pk++++DE +
  gi|518652408|ref|YP_008141928.1|  95 EYfnflasvfkiedsVLKERINAFSNALEIGKYLNEFI----GSLSFGTKQKVAIIGSLIHDPKIIVMDEGM 162
                                       6669******9988888888************999999....****************************65 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.8   2.9e-09   2.5e-06       2     101 ..      32     129 ..      31     132 .. 0.65
   2 !   30.7   0.0   3.2e-10   2.7e-07     224     299 ..     122     194 ..     104     198 .. 0.85

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.9e-09
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        ++ GpNgsGK++LL++l ++    +++    ++  +  g+++ ++++++y pe p+ +e   ++++  ++  ++  
  gi|518652408|ref|YP_008141928.1|  32 YGILGPNGSGKTTLLKILAGIL--PPSSGEVVIDGMNLTGNSDNIKSITGYIPETPALYESL-TPIEYFNFLASVFK 105
                                       689***************9995..33333333333333455566666666666666666666.77777777777666 PP

                            AAA_21  79 ersqv.eeklssvetllesgllld 101
                                        ++ v +e++ ++ + le+g +l+
  gi|518652408|ref|YP_008141928.1| 106 IEDSVlKERINAFSNALEIGKYLN 129
                                       666667777777777777777666 PP

  == domain 2  score: 30.7 bits;  conditional E-value: 3.2e-10
                            AAA_21 224 lengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHSp 299
                                       le g++ +  + +lS Gtk+  a++ +l+ ++   ++++ DE  ngL+Pk  + + ellk+ +++g  vi++TH  
  gi|518652408|ref|YP_008141928.1| 122 LEIGKYLNEFIGSLSFGTKQKVAIIGSLIHDP---KIIVMDEGMNGLDPKSSKIIKELLKDMTAKGKTVIFSTHIM 194
                                       5666666666889*****************99...9*************9999999******************65 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.2e-07    0.0001       7      56 ..      14      63 ..       9      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.2e-07
                      Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeale 56
                                      G ++a + + +++aGg    ++Gp GsGKt l k l+++lpp s e +++
  gi|518652408|ref|YP_008141928.1| 14 GTTTALNGISLSIAGGQIYGILGPNGSGKTTLLKILAGILPPSSGEVVID 63
                                      7778889999********************************99877766 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.8e-06    0.0024      33      88 ..      17      73 ..      11     101 .. 0.81
   2 ?   -0.8   0.0       1.4   1.2e+03     131     165 ..     151     186 ..      95     205 .. 0.64

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.8e-06
                             Rad17 33 ewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrew.lnpvslkepdnq 88
                                      ++l+  +L  +  +i  i GP G gk+t +k+L+ +l ++  e  +++++l   + +
  gi|518652408|ref|YP_008141928.1| 17 TALNGISLSIAGGQIYGILGPNGSGKTTLLKILAGILPPSSGEVvIDGMNLTGNSDN 73
                                      67888888889999***********************99988752788888765544 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.4
                             Rad17 131 tdkklilvedlPnkfyrds.dalrevirkylrssea 165
                                        d k+i++++  n     s + ++e+++ +   +++
  gi|518652408|ref|YP_008141928.1| 151 HDPKIIVMDEGMNGLDPKSsKIIKELLKDMTAKGKT 186
                                       355666666655555544425566666655555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   1.2   2.1e-06    0.0018      20      42 ..      30      52 ..      14      60 .. 0.85
   2 ?   -1.0   0.0       2.5   2.2e+03     146     172 ..     106     132 ..      64     181 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.1e-06
                            AAA_23 20 gltlItGpNGaGKTTildAikla 42
                                       ++ I GpNG+GKTT+l  +  +
  gi|518652408|ref|YP_008141928.1| 30 QIYGILGPNGSGKTTLLKILAGI 52
                                      6889*************987655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.5
                            AAA_23 146 felkdkkerleelekeleeledekkll 172
                                       +e++  ker+++++++le  +  ++++
  gi|518652408|ref|YP_008141928.1| 106 IEDSVLKERINAFSNALEIGKYLNEFI 132
                                       455666777777777777666555544 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 !   11.0   0.2   0.00024      0.21      25      42 ..      30      47 ..       2      72 .. 0.83
   2 ?    5.2   0.0     0.015        13     161     205 ..     155     200 ..     134     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00024
                                      SEEEEEESTTSSHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                             SMC_N 25 sftaivGpNGSGKsnlld 42
                                      ++  i+GpNGSGK+ ll 
  gi|518652408|ref|YP_008141928.1| 30 QIYGILGPNGSGKTTLLK 47
                                      46679*********9986 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.015
                                       EEEECTTTTTS-HHHHHHHHHHHHHHCTT.SEEEEE-SSHHHCCC- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                             SMC_N 161 lyllDeidaaLDeknvkkvaellkekskn.aQfivislreemleka 205
                                       + ++De    LD k  k++ ellk  + +   +i  ++  e+ e +
  gi|518652408|ref|YP_008141928.1| 155 IIVMDEGMNGLDPKSSKIIKELLKDMTAKgKTVIFSTHIMEIAETV 200
                                       689*********************8887725555556655555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.7     1e-05    0.0089      20      49 ..      25      56 ..      13      63 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1e-05
                            AAA_29 20 dlkg..atlltGpsGsGKSTllDAiqalLvpa 49
                                      + +g  ++ + Gp+GsGK+Tll  ++ +L p+
  gi|518652408|ref|YP_008141928.1| 25 SIAGgqIYGILGPNGSGKTTLLKILAGILPPS 56
                                      444446888************97776666665 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   0.00028      0.24      28      50 ..      34      56 ..      22      78 .. 0.76
   2 ?    3.9   0.7     0.043        37     184     364 ..      89     192 ..      59     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                            AAA_15 28 liGkNnsGKSsilealdlFlnnk 50
                                      + G+N+sGK+++l++l  +l  +
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILAGILPPS 56
                                      67*************97666555 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.043
                            AAA_15 184 e.....elknvlksaiiklllisakRnvsdedsekkssllgklkekileealqekl..............eeeltek 241
                                       e     e +n+l s ++  +   ++R +  ++  ++ ++l++ + +++   +q+ +              +      
  gi|518652408|ref|YP_008141928.1|  89 EsltpiEYFNFLASVFKIEDSVLKERINAFSNALEIGKYLNEFIGSLSFGTKQKVAiigslihdpkiivmD------ 159
                                       35555555666666666666666666666666666666666666665554444333566666555544443...... PP

                            AAA_15 242 lkeiqeklkeidkklaeelkkilkkkidkikkfnykgkkneeieikddeelplnknGsGvqrllllillileaekkd 318
                                                                                                                    
  gi|518652408|ref|YP_008141928.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                            AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTH 364
                                                   E  + L p+  k++ +llk++  ++k  vi++TH
  gi|518652408|ref|YP_008141928.1| 160 ------------EGMNGLDPKSSKIIKELLKDMTAKGK-TVIFSTH 192
                                       ............33333333344444444444444443.3444444 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 ?   13.5   0.5   8.3e-05     0.071       3      38 ..      34      80 ..      32     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-05
                                      EESSTTSSHHHHHHHHHHHH..THEEEEEETTTCSSS.........S CS
                               AAA  3 lyGppGtGKTllakavakel..gvefleisgsellsk.........y 38
                                      + Gp G GKT+l k +a  l  ++  + i+g++l+ +         y
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILAGILppSSGEVVIDGMNLTGNsdniksitgY 80
                                      57****************98554555777777777332455555552 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00066      0.56      21      38 ..      34      51 ..      29      72 .. 0.87
   2 ?    4.7   0.1     0.012       9.9     524     573 ..     150     196 ..     141     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00066
                            AAA_13 21 iYGwNGaGKTtLSrllrs 38
                                      i G NG+GKTtL ++l+ 
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILAG 51
                                      6689********999986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.012
                            AAA_13 524 igkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnlef 573
                                       i   ki+v+D  +  LD +s+ i+  l+k+ +   +k k ++ +TH +e 
  gi|518652408|ref|YP_008141928.1| 150 IHDPKIIVMDEGMNGLDPKSSKIIKELLKDMT---AKGKTVIFSTHIMEI 196
                                       56789**************************9...99*********8776 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.7e-05     0.057      25     164 ..      30     182 ..      15     189 .. 0.48

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.7e-05
                            AAA_16  25 elvllsGesGvGKsslvrellralekd......ggiflrgkcdqlesaipy...sa.laqalareellrqllde..a 89 
                                       ++  + G+ G+GK++l++ l+  l  +      +g  l+g+ d  +s + y    + l + l+  e+++ l++    
  gi|518652408|ref|YP_008141928.1|  30 QIYGILGPNGSGKTTLLKILAGILPPSsgevviDGMNLTGNSDNIKSITGYipeTPaLYESLTPIEYFNFLASVfkI 106
                                       566699***********999988888876444433338888888866655533322233333333333333333221 PP

                            AAA_16  90 esaeleawrekleeala...avpelagaeasrllellkrllallsrder..........plvlvlD.dlqwadeasl 152
                                       e++ l +   ++  al+     +e  g+++            + ++ ++          p ++v+D  +  +d+ s 
  gi|518652408|ref|YP_008141928.1| 107 EDSVLKERINAFSNALEigkYLNEFIGSLS------------FGTK-QKvaiigslihdPKIIVMDeGMNGLDPKSS 170
                                       111111111111111111111112222211............1111.112222222222434444436777777777 PP

                            AAA_16 153 qllaaLlrlles 164
                                       +++++Ll+++++
  gi|518652408|ref|YP_008141928.1| 171 KIIKELLKDMTA 182
                                       777777776666 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00011     0.092      20      41 ..      29      50 ..      17     147 .. 0.87
   2 ?    0.3   0.0      0.66   5.6e+02      34      63 ..     170     199 ..     154     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00011
                          ATPase_2 20 neiyfiYGpegsGKtaLlkeii 41
                                       +iy i Gp gsGKt+Llk ++
  gi|518652408|ref|YP_008141928.1| 29 GQIYGILGPNGSGKTTLLKILA 50
                                      57999*************9765 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.66
                          ATPase_2  34 taLlkeiienledkdkyviyyialreesis 63 
                                       ++++ke+++    k+k vi+ + + e++++
  gi|518652408|ref|YP_008141928.1| 170 SKIIKELLKDMTAKGKTVIFSTHIMEIAET 199
                                       567888888888888888888887777665 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   0.00013      0.11      18      50 ..      29      61 ..      22      73 .. 0.81
   2 ?   -1.1   0.0       1.6   1.3e+03      88     121 ..     152     189 ..     110     199 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_30 18 drvavltGpAGtGKttalkalreaweaaggrvi 50
                                       ++  + Gp G+GKtt+lk l+ ++  + g+v+
  gi|518652408|ref|YP_008141928.1| 29 GQIYGILGPNGSGKTTLLKILAGILPPSSGEVV 61
                                      4578899**************999887755554 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.6
                            AAA_30  88 pgtllivDEagmv.....dtkqlaallkaaekagakvil 121
                                       + ++++ DE gm      ++k +++llk ++++g +vi+
  gi|518652408|ref|YP_008141928.1| 152 DPKIIVMDE-GMNgldpkSSKIIKELLKDMTAKGKTVIF 189
                                       446677777.44435555666677777777777777775 PP

>> PrkA  PrkA serine protein kinase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.79   6.7e+02      58      92 ..      88     122 ..      64     134 .. 0.78
   2 ?   11.2   0.0   0.00025      0.21      31      76 ..     159     203 ..     146     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.79
                              PrkA  58 ekcinpldvlealeeglkeheviseeerekylefl 92 
                                       ++ ++p++ +++l++++k + ++ +e+ + + + l
  gi|518652408|ref|YP_008141928.1|  88 YESLTPIEYFNFLASVFKIEDSVLKERINAFSNAL 122
                                       56799999999999999998888866656555555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00025
                              PrkA  31 reGmsGispRyvikilsealssseakeekcinpldvlealeeglke 76 
                                       +eGm+G++p++  ki++e+l + +ak +++i  ++++e  e +++ 
  gi|518652408|ref|YP_008141928.1| 159 DEGMNGLDPKS-SKIIKELLKDMTAKGKTVIFSTHIMEIAETVCDT 203
                                       7********87.58*******9999*************99999976 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1    0.0041       3.5       4      24 ..      34      54 ..      32      75 .. 0.77
   2 ?    4.4   0.1     0.038        33      85     144 ..     142     204 ..     104     214 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0041
                                      EE--TTSSHHHHHHHHHHHH. CS
                          NTPase_1  4 iTGppGvGKtTlvkkvlellk 24
                                      i Gp G+GKtTl+k ++  l 
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILAGILP 54
                                      669**********99888874 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.038
                                       HHHHHHHHHHHH-EEEE--.-STTGGG-HHHHHHHHHHHT.TTSEEEEE--SS-.-SHHHHHH CS
                          NTPase_1  85 alealrkalseadviviDE.iGkmElkskkfkeaveevLk.sekpvlavihrrk.dlalveei 144
                                        ++++   ++++ +iv+DE    +  ks k+++++ + ++ ++k v++  h  +  + + ++i
  gi|518652408|ref|YP_008141928.1| 142 KVAIIGSLIHDPKIIVMDEgMNGLDPKSSKIIKELLKDMTaKGKTVIFSTHIMEiAETVCDTI 204
                                       4667777789999******55568888888877766666659999999999887666666655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   0.00019      0.16       3      22 ..      34      53 ..      33     174 .. 0.79
   2 ?   -1.2   0.0       3.3   2.8e+03      69      81 ..     170     191 ..     110     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00019
                            AAA_18  3 ltGtpGvGKttlakeLskrl 22
                                      + G+ G+GKttl k L+  l
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILAGIL 53
                                      89**************7554 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 3.3
                            AAA_18  69 s.........aleegknlvidg 81 
                                       s           ++gk+++++ 
  gi|518652408|ref|YP_008141928.1| 170 SkiikellkdMTAKGKTVIFST 191
                                       2333333333334555555555 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   0.00059      0.51       6      28 ..      30      52 ..      26      81 .. 0.81
   2 ?   -1.0   0.0       2.2   1.9e+03      92     113 ..     153     178 ..     136     198 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                            AAA_22  6 gilvvtGesGtGKTtllrrlleq 28
                                      +i  + G+ G+GKTtll+ l+  
  gi|518652408|ref|YP_008141928.1| 30 QIYGILGPNGSGKTTLLKILAGI 52
                                      667799***********988765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.2
                            AAA_22  92 ielliiDEaqh.lr..seealeeL.r 113
                                       +++++ DE  + l+  s ++++eL +
  gi|518652408|ref|YP_008141928.1| 153 PKIIVMDEGMNgLDpkSSKIIKELlK 178
                                       46888888877786654555555523 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00033      0.28       5      21 ..      34      50 ..      30      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00033
                                      EEC-TTTCHHHHHHHHH CS
                             NACHT  5 lqGeaGsGKTtLlqkla 21
                                      + G++GsGKTtLl+ la
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILA 50
                                      78***********9876 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00079      0.68       5      22 ..      32      49 ..      29      92 .. 0.84
   2 ?   -0.0   0.0      0.72   6.1e+02      34     131 ..     161     193 ..     146     232 .. 0.59

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00079
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + i Gp+g+GKTtl+k l
  gi|518652408|ref|YP_008141928.1| 32 YGILGPNGSGKTTLLKIL 49
                                      5699**********9987 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.72
                            AAA_24  34 GlksldadkfpdieswedfldevvelaaeladyktlviDtideleelclaevirqnekaeskedkgdgkGygelaee 110
                                       G++ ld++  + i                                                                
  gi|518652408|ref|YP_008141928.1| 161 GMNGLDPKSSKII---------------------------------------------------------------- 173
                                       5555555554433................................................................ PP

                            AAA_24 111 frrllkklqelrknvifiahe 131
                                        ++llk++++ +k+vif  h 
  gi|518652408|ref|YP_008141928.1| 174 -KELLKDMTAKGKTVIFSTHI 193
                                       .23333344444444444443 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00048      0.41       4      20 ..      34      50 ..      32      66 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00048
                            AAA_28  4 itGgestGKTtlleaLa 20
                                      i+G+ ++GKTtll+ La
  gi|518652408|ref|YP_008141928.1| 34 ILGPNGSGKTTLLKILA 50
                                      89*************99 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   0.4   0.00045      0.39     134     161 ..      34      61 ..      11      65 .. 0.86
   2 ?   -1.5   0.1       1.2     1e+03     138     156 ..     181     199 ..     174     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00045
                             T2SSE 134 vsGgTgsGKttllyallkeinksderiv 161
                                       + G+ gsGKttll +l  +++ s+ ++v
  gi|518652408|ref|YP_008141928.1|  34 ILGPNGSGKTTLLKILAGILPPSSGEVV 61 
                                       569*************999998866665 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.2
                             T2SSE 138 TgsGKttllyallkeinks 156
                                       T  GKt++  + + ei+++
  gi|518652408|ref|YP_008141928.1| 181 TAKGKTVIFSTHIMEIAET 199
                                       889*****99999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      622  (0.0346924); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); 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 0.28s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 1931.03
//
Query:       gi|518652409|ref|YP_008141929.1|  [L=530]
Description: hypothetical protein FACI_IFERC00001G1048 [Ferroplasma acidarmanus fer1]
Scores for complete 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-68  230.4  85.1    5.5e-68  230.1  85.1    1.0  1  12TM_1    Membrane protein of 12 TMs


Domain annotation for each model (and alignments):
>> 12TM_1  Membrane protein of 12 TMs
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.1  85.1   3.1e-72   5.5e-68       1     445 [.      43     512 ..      43     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 230.1 bits;  conditional E-value: 3.1e-72
                            12TM_1   1 nirlsvllqsimftvlglvlvgpsliserasflSslliLlfvlslfitalnslyfassl...dllepLrsLPvkfkd 74 
                                       ni ++++++ i ft++ ++l ++++ +++++ l s+ +++f+++++i+++ns++f++s+   +++ pL+s P+k+++
  gi|518652409|ref|YP_008141929.1|  43 NILMTYIANAILFTMIFVLLDSVYFEEKDTAALASFGLIVFLYLFIIGIYNSIVFFNSVysnNIMAPLKSIPIKVNV 119
                                       6999************************************************************************* PP

                            12TM_1  75 rvlavfllieslsvlaFlv..sillavllvgnltagllglLwailaillGfslvlllfilfGsrisgrkslskallr 149
                                       +v++++++i++ s+++F+v  s ++ +ll+++  ++ l +++a+l ++  f++++llfi     +sg+k+ ++++++
  gi|518652409|ref|YP_008141929.1| 120 NVPFISWFIYNSSSYIFVVfpSAIFFYLLTHDYETIFLAIIYAFLVLMVSFIISSLLFI-----YSGKKAKTHTSIK 191
                                       ********************9999***********************************.....************* PP

                            12TM_1 150 iaglilflvlifglyliiqyaanil...ylvikeipeaykyifP...........ffflsIeepffslllsllYtal 212
                                       ++  il l+l++g +++ + ++ +    +  i+ +p+++ ++++           +  + I++   ++llsll++a+
  gi|518652409|ref|YP_008141929.1| 192 NVIKILVLFLFLGAFYLLIEDPSYFgyvSSAIAALPYYVRIFAFpinleyivylnYTLPLIYR-IIEILLSLLFLAI 267
                                       *********************9998888999********999888*******9*999999999.99*********** PP

                            12TM_1 213 lsfaykyslkrlfkrleeiakvkgrvktkykikvrspltamliKDfkillRksqalvlllvPivivlpnvfsivsea 289
                                       + f+y+ ++++++  l  ++++++++k    ik +  l a+l+KD k ++Rk+q+l ++ +P+++v+p+++++    
  gi|518652409|ref|YP_008141929.1| 268 VVFIYFALREKIYNILMTSEENESSEKVYSNIKGNKMLAAFLKKDAKSTFRKPQNLSYIFLPVLFVIPFFLGVGIGD 344
                                       ****************99*********9****************************************999887444 PP

                            12TM_1 290 qpvlltifiialiivlSsvylilllaievsgfsllkaLPlerreillsKlltilliylvvsvvlvllvliykgsnal 366
                                         +   ++ + l++ +Ss+y i+ll++e++g+++l++LP+++++i+++K +++l+i++v+ +   ++ ++++ +  l
  gi|518652409|ref|YP_008141929.1| 345 GFSSSFFTLLYLVEFVSSFYAIFLLVVEGKGIEVLNSLPIKKQSIAFYKSIFGLIIFSVIAIAFTVVTIVISHKIGL 421
                                       44558899999***********************************************9999888888888887778 PP

                            12TM_1 367 ylliilpspilvvliallislnrl......gaetinlpsfgvlktivlfilslvivgivaipslilsepls...... 431
                                         l+ l + i+ ++i l ++ nrl      g++++n++sfg ++++ +fils +  gi  ++ l ls +l       
  gi|518652409|ref|YP_008141929.1| 422 IDLFELIDAITLFYIILTVNINRLlkklppGTSNLNYYSFGTYPMLFIFILSILLLGISVGLALGLSFLLFysilyy 498
                                       8888899*******************************************998777665555444444333222222 PP

                            12TM_1 432 flvslvitliiall 445
                                          +l+  +i++l+
  gi|518652409|ref|YP_008141929.1| 499 AYTDLIVNIIMLLF 512
                                       33344444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (530 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1570  (0.0875676); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.49
# Mc/sec: 3275.17
//
Query:       gi|518652410|ref|YP_008141930.1|  [L=150]
Description: 30S ribosomal protein S19e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-48  164.4   0.1    1.3e-48  164.2   0.1    1.0  1  Ribosomal_S19e  Ribosomal protein S19e
  ------ inclusion threshold ------
      0.021   14.6   0.2       0.04   13.7   0.2    1.4  1  BRX_N           Transcription factor BRX N-terminal domain
      0.036   14.0   0.1       0.15   12.1   0.0    2.0  2  HTH_12          Ribonuclease R winged-helix domain


Domain annotation for each model (and alignments):
>> Ribosomal_S19e  Ribosomal protein S19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.2   0.1   2.2e-52   1.3e-48       2     136 ..       4     137 ..       3     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 164.2 bits;  conditional E-value: 2.2e-52
                                       SSSHHHHHHHHHS--S---S-SSS-SSSS-SS-S-SS-SSTTTHHHHHHHHHHHTS--TTSGGGGS----SS-SSS- CS
                    Ribosomal_S19e   2 vkdVpaeelikalaeeLkksgklevPewadlvKtgsakelapededWfyvRaAsilRkvylrgpvGverlrkvYGgk 78 
                                       vk+Vpa+ l ++la+e+k++ ++e+P+w+++ K g +ke+a+ ++dW+y+R+Asi+Rkvyl+ ++G++rl+++YG++
  gi|518652410|ref|YP_008141930.1|   4 VKEVPADLLLNKLASEFKEK-NVEIPDWVNYLKDGIGKERAWVQDDWYYTRLASIMRKVYLNTNIGISRLSQEYGSR 79 
                                       99****************97.7******************************************************* PP

                                       ------THHHHHHHHHTTSSS--SSS---SS-HHHHHTHHHHH--SS--S--XXXXXX CS
                    Ribosomal_S19e  79 krrgvrpshfvkasgsvirkilqqLeklglvkkekkkgrrltkkGqrlldriaeevak 136
                                       ++rg++++h v++s+ +ir+ilq+Le+lg++kk++++gr lt++Gq++ld+ a+ev+k
  gi|518652410|ref|YP_008141930.1|  80 QDRGTKRYHPVQGSRFIIRNILQSLEALGYLKKDTRTGRSLTPAGQSMLDKAAKEVMK 137
                                       *******************************999999*******************97 PP

>> BRX_N  Transcription factor BRX N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   6.7e-06      0.04       6      18 ..     129     141 ..     125     142 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.7e-06
                             BRX_N   6 tkaakEvIKSLTa 18 
                                        kaakEv+KSL++
  gi|518652410|ref|YP_008141930.1| 129 DKAAKEVMKSLAE 141
                                       59*********97 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.4e-05      0.15      35      66 .]      97     128 ..      92     128 .. 0.94
   2 ?   -1.7   0.0      0.49   2.9e+03       2      13 ..     134     145 ..     133     147 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.4e-05
                            HTH_12  35 vRyrLrkleergltrrvgyagreltEkGleeL 66 
                                       +R  L++le  g+ ++  + gr lt  G ++L
  gi|518652410|ref|YP_008141930.1|  97 IRNILQSLEALGYLKKDTRTGRSLTPAGQSML 128
                                       7999************************9997 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.49
                            HTH_12   2 eILkilaesdkp 13 
                                       e++k lae+dk+
  gi|518652410|ref|YP_008141930.1| 134 EVMKSLAEKDKV 145
                                       689999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1082.44
//
Query:       gi|518652411|ref|YP_008141931.1|  [L=113]
Description: hypothetical protein FACI_IFERC00001G1050 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.7e-26   91.6  15.3    4.1e-26   91.4  15.3    1.0  1  dsDNA_bind  Double-stranded DNA-binding domain
  ------ inclusion threshold ------
       0.19   12.0   6.3       0.31   11.3   6.3    1.4  1  DUF4355     Domain of unknown function (DUF4355)
        2.2    8.7   9.8         16    5.9   5.9    2.2  2  CCDC-167    Coiled-coil domain-containing protein 167


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 !   91.4  15.3   6.9e-30   4.1e-26       1     109 [.      10     111 ..      10     113 .] 0.90

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.9e-30
                                       XXXXXXXXXXXXXXXXXXXX...XXXX--SS..S--SSHHHHTTS--HHHHHHHHHHTTT-HHHHHHHHHHHHHHHH CS
                        dsDNA_bind   1 irkarlaelqaqagsssgsggaseqqeqqqeaseeeakqaiLsqiLepeAreRLsrirlvkperaeavenrLiqlaq 77 
                                       ir+++l+e+q+++++++    ++e+++q qe  ee+++q+iL+qiL++eAreRLs+++lv+p+ +++ven+Liqla 
  gi|518652411|ref|YP_008141931.1|  10 IRQRKLEEMQRNQQQGQY---DEENRKQIQE--EEARRQQILRQILSTEARERLSTLKLVRPDLVSNVENQLIQLAG 81 
                                       9**********9998775...3444444444..99****************************************** PP

                                       --SS-----HHHHHHHHHHHS---XXXXX..X CS
                        dsDNA_bind  78 sGqlrskvteeqLkeLLeqvaekkketkivis 109
                                       +G++++ + +e+Lk +L+++  +++etki  +
  gi|518652411|ref|YP_008141931.1|  82 MGRINRVIGDEELKGILSRLIGNTRETKI--E 111
                                       ****************************9..4 PP

>> DUF4355  Domain of unknown function (DUF4355)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   6.3   5.2e-05      0.31      36      93 ..      12      73 ..       2      76 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.2e-05
                           DUF4355 36 akklakmnaeekae...yeleklqkeleelkaelarkelkaearkvlaekkipi.ellnlvv 93
                                      ++kl++m++ + +    +e  k+ +e e+++++  r+ l +ear+ l++ k+   +l+++v 
  gi|518652411|ref|YP_008141931.1| 12 QRKLEEMQRNQQQGqydEENRKQIQEEEARRQQILRQILSTEARERLSTLKLVRpDLVSNVE 73
                                      68999999999988444444444455555566778999********9999987778888875 PP

>> CCDC-167  Coiled-coil domain-containing protein 167
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   5.9    0.0026        16      12      45 ..       6      40 ..       2      49 .. 0.81
   2 ?    4.8   0.1    0.0059        35      29      64 ..      47      82 ..      42      90 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0026
                          CCDC-167 12 klascr.erLeaverrlrkeelseeeResleeEea 45
                                      +l ++r ++Le++ r+ ++ +  ee+R++++eEea
  gi|518652411|ref|YP_008141931.1|  6 ELNRIRqRKLEEMQRNQQQGQYDEENRKQIQEEEA 40
                                      556655167**********************9987 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0059
                          CCDC-167 29 keelseeeResleeEeaslkeqleenekeLksLrke 64
                                      ++ ls+e+Re+l + +      +++ e++L +L + 
  gi|518652411|ref|YP_008141931.1| 47 RQILSTEARERLSTLKLVRPDLVSNVENQLIQLAGM 82
                                      56799*******98887778889999****999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2262  (0.126164); expected 358.6 (0.02)
Passed bias filter:                      814  (0.0454013); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
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 0.30s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 732.59
//
Query:       gi|518652412|ref|YP_008141932.1|  [L=51]
Description: 50S ribosomal protein L39e [Ferroplasma acidarmanus fer1]
Scores for complete 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   68.9  13.0    2.6e-19   68.6  13.0    1.1  1  Ribosomal_L39  Ribosomal L39 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L39  Ribosomal L39 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6  13.0   1.4e-23   2.6e-19       1      42 []       9      50 ..       9      50 .. 0.99

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 1.4e-23
                     Ribosomal_L39  1 kKlrLaKalkqNrpvPaWvrlktdrkvrynpkrRhWRrtkLk 42
                                      kK+rL+K +++Nr+vP Wv++ktdrk+++npkr++WRr++Lk
  gi|518652412|ref|YP_008141932.1|  9 KKIRLMKHVNSNRRVPGWVMMKTDRKMTQNPKRKNWRRSNLK 50
                                      7****************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.44
# Mc/sec: 347.49
//
Query:       gi|518652413|ref|YP_008141933.1|  [L=90]
Description: 50S ribosomal protein L31e [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   25.8   0.1    1.1e-05   25.6   0.1    1.1  1  Ribosomal_L31e  Ribosomal protein L31e


Domain annotation for each model (and alignments):
>> Ribosomal_L31e  Ribosomal protein L31e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.1   5.9e-10   1.1e-05      12      70 ..      17      77 ..       6      83 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 5.9e-10
                    Ribosomal_L31e 12 hkrihgvgfkkraprAlkeikkfamkemg..tpdvridtrLnkavwakgirnvpyrirvrl 70
                                       +  ++ ++++ra  A+  ik+ + + ++  ++   id+++n+ +w +g +++p++i  ++
  gi|518652413|ref|YP_008141933.1| 17 LRGARSSSRRRRADTAIGIIKEAVSRYTKseVEKIWIDNKVNELIWDRGREHIPTKISLKI 77
                                      5666778899***************999954666699********************8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 656.19
//
Query:       gi|518652414|ref|YP_008141934.1|  [L=218]
Description: translation initiation factor IF-6 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-61  204.8   0.7      1e-60  204.5   0.7    1.1  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 !  204.5   0.7   5.8e-65     1e-60       1     197 []       4     199 ..       4     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 204.5 bits;  conditional E-value: 5.8e-65
                                       .E-BTTB--HHHH-EE-SSEEEE-TTS-HHHHHHHHHHHT-EEEE--BTTBS-HHHH-EE-SSEEEEETT--HHHHH CS
                             eIF-6   1 rlsiegsseiGvfarltnkyalvpegveeefvkaieeeLkvevvettiagsrlvGslvvgNsngllvpstvtdeele 77 
                                       +lsi++s+ iGv+a++ n++a++p++++ee+   iee+L+v++  + + + +l+G+++v Nsng++v+ + ++e+++
  gi|518652414|ref|YP_008141934.1|   4 KLSIFESDFIGVYAKVFNDFAFLPRNIPEETRLSIEETLEVKTAGVIVDNFSLIGTMLVFNSNGIVVSGLSSKEDFS 80 
                                       6899************************************************************************* PP

                                       HHHHHHH---EEE--SS--HHHHEEE-SSEEEE-GGGGG.GHHHHHHHHTSEEEE--BTTBS-TTTSEEE-SSEEEE CS
                             eIF-6  78 klkeslkleverleekltAlGNvilaNDkvAlvhpdlsketveiiadvLgvevvrgtiagiktvGsaavvtnkgllv 154
                                        l+    ++   l+++l+A+GN i++ D++A++hp+++++++++iad+Lgvev+++ iag++tvGs+av++nkg+lv
  gi|518652414|ref|YP_008141934.1|  81 GLDLG-GRRLVFLKDRLNAIGNNIITSDRAAVIHPSFTESSEKAIADTLGVEVIKTPIAGVSTVGSVAVLNNKGMLV 156
                                       **966.57777****************************************************************** PP

                                       -TT--HHHHHHHHHHHT-SEEE--BTTTBS-GGGTEEE-SS-E CS
                             eIF-6 155 hpkateeeleeleellkveveagTvNrGsklvgsglvaNdkga 197
                                       +p+a+eee+++l+++++++v++gT N+Gs ++g++++aN++g+
  gi|518652414|ref|YP_008141934.1| 157 SPEASEEEIKNLSDIFHLPVKTGTANYGSYYIGASILANSSGI 199
                                       ****************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       246  (0.0137208); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1458.91
//
Query:       gi|518652415|ref|YP_008141935.1|  [L=166]
Description: orotate phosphoribosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-10   40.8   0.6    1.9e-10   40.5   0.6    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 !   40.5   0.6   1.1e-14   1.9e-10      31     132 ..      55     147 ..      33     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 1.1e-14
                                       EEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHH CS
                      Pribosyltran  31 dvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaal 107
                                       d+v+g + g+vp+   ++ + + p+ ++rk  ++++++ ++            ++ g+++ +++D+++tG++ll+++
  gi|518652415|ref|YP_008141935.1|  55 DTVAGMELGAVPLIVGISLKTGKPYIIIRKGEREHGTKKQI---------VGNIISGSRIDLIEDVVTTGNSLLKTA 122
                                       69***************************************.........5789*********************** PP

                                       HHHHCC-BSEEEEEEEEE-HHHHHH CS
                      Pribosyltran 108 elLkekgpeevriavlvdkpateee 132
                                       ++L++ g+ + +++++vd+ ++ ee
  gi|518652415|ref|YP_008141935.1| 123 KILRDNGAIVDHAVCVVDRESGGEE 147
                                       ********98899999999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1183.23
//
Query:       gi|518652416|ref|YP_008141936.1|  [L=227]
Description: orotidine 5''''-phosphate decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   95.6   0.0      4e-27   95.3   0.0    1.1  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil
      0.005   15.9   0.2      0.031   13.3   0.1    1.9  2  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 !   95.3   0.0   4.5e-31     4e-27       1     223 [.      19     215 ..      19     217 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 4.5e-31
                                       SEEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHH CS
                         OMPdecase   1 snLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqat 77 
                                       s+++ alDv + + ++ela++vg+++  +K++++++ + g      k+++ + k  + i++D+K+aDI ntv+++ t
  gi|518652416|ref|YP_008141936.1|  19 SKIIFALDVYDYNTAMELARTVGEKVFAIKINWPVILENG-----IKIVRDLSKY-ANIICDFKLADIDNTVSMITT 89 
                                       67999***********************************.....********99.6*******************9 PP

                                       STCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHHTTESE CS
                         OMPdecase  78 agsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkaedfvmG 154
                                             + +   ++ h + G  s+ka+++ a  +   +++ ++ ms +  l++      +++++  re    ++v G
  gi|518652416|ref|YP_008141936.1|  90 ---KVKEYGGYGIISHSFTGLNSLKAVVKSAGNM---KVFSVVSMSQESYLDNIT----EELIKISRE----AGVYG 152
                                       ...56799999*******************9666...7*********99988877....777777777....56*** PP

                                       EECCCHTH...HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHHHHH CS
                         OMPdecase 155 fvaqetln...ateed.addfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpveeae 223
                                       +va  +++   ++ ++  + ++++ pg+g+    +g+++     +++    g+d++i+GR+I+++ dp  ++e
  gi|518652416|ref|YP_008141936.1| 153 LVAPGNRPyylKKVKElSEGLKIISPGVGA----QGGDIV----NAML--LGSDYVIIGRSIYNSLDPLGTLE 215
                                       ******997653333356677777777775....444444....3343..37***************987766 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.021   1.9e+02      79     122 ..     112     159 ..     100     173 .. 0.70
   2 !   13.3   0.1   3.5e-06     0.031     270     307 ..     171     208 ..     160     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.021
                                       HHHHHHHHHTS-EEEETT-SS-HHHHHHH....HTT-EEEEEE-CSSH CS
                            FMN_dh  79 alaraaakagipfvlstvastsleevaaa....aegplwfqlyvpkdr 122
                                       a+++ a ++++  v+s  +++ l++++++    +++  ++ l  p +r
  gi|518652416|ref|YP_008141936.1| 112 AVVKSAGNMKVFSVVSMSQESYLDNITEElikiSREAGVYGLVAPGNR 159
                                       678888899999999999888888888843333445666666666555 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.5e-06
                                       .SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHHH CS
                            FMN_dh 270 grievlvDgGirrGsDvlkAlalGAdavllGRpflygl 307
                                       + ++++  g   +G D++ A+ lG d v++GR +   l
  gi|518652416|ref|YP_008141936.1| 171 EGLKIISPGVGAQGGDIVNAMLLGSDYVIIGRSIYNSL 208
                                       4566666666689*******************987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1597.75
//
Query:       gi|518652417|ref|YP_008141937.1|  [L=239]
Description: hypothetical protein FACI_IFERC00001G1056 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-42  144.3   0.0    3.7e-42  143.9   0.0    1.1  1  Peptidase_S49  Peptidase family S49
    3.3e-10   40.1   1.4    7.4e-07   29.2   0.3    2.2  2  CLP_protease   Clp protease
  ------ inclusion threshold ------
       0.02   14.2   0.8        1.2    8.4   0.0    2.4  2  ECH_1          Enoyl-CoA hydratase/isomerase
      0.078   12.5   0.0       0.18   11.4   0.0    1.7  1  Rap_GAP        Rap/ran-GAP
        0.1   12.9   0.0       0.16   12.2   0.0    1.2  1  DUF3416        Domain of unknown function (DUF3416)


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.9   0.0     1e-45   3.7e-42       4     151 ..      61     208 ..      58     211 .. 0.98

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1e-45
                                       HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS- CS
                     Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrel 80 
                                       ++kkPv+a++e++ aSg+Y+la+ a+ki+a  +++vgsiGvi + ++++++ld lg+++ + k+G+yk++ s++r++
  gi|518652417|ref|YP_008141937.1|  61 SSKKPVYALIEGIGASGAYWLACSAEKIFAMRTSLVGSIGVISMSPDFSEFLDTLGIKMRINKVGKYKDINSPFRPM 137
                                       789************************************************************************** PP

                                       -HHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHHHC CS
                     Peptidase_S49  81 teeereilqrlldetyqqFvqtVaknRnlsveqvdkiAegrvltgqqAlklgLvdelgtvddavaeleela 151
                                       teee +i+++ + ++y+ F + V+k Rnl  + +++iA+g v++++qA+k+gL+d + +++++v+el+ + 
  gi|518652417|ref|YP_008141937.1| 138 TEEENAIYNNIMKDVYSVFREEVKKRRNLGEDIMEEIATGLVFSAEQAKKNGLIDGIANLETVVDELKAKT 208
                                       ******************************************************************99865 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.3   2.1e-10   7.4e-07      31     105 ..      18      92 ..       4     106 .. 0.83
   2 !   10.3   0.0   0.00014      0.49     146     179 ..     162     195 ..     116     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 2.1e-10
                                       HHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHHHHTS-TTGEEEET CS
                      CLP_protease  31 nkiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgslllaagekgkRfalp 105
                                        + +  L ++e++++ k +ll+ins GG+ +a+  +y+ +  i  k +v+ +  G++aS +  l++++ek   fa+ 
  gi|518652417|ref|YP_008141937.1|  18 GTYMPALRYIEKKNKVKALLLIINSGGGDANATEILYNQLMKIssKKPVYALIEGIGASGAYWLACSAEKI--FAMR 92 
                                       56788999******************************9888835556666667**************996..5544 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00014
                                       HHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE- CS
                      CLP_protease 146 htgqslekiekdldrdtflsaeeAveyGLidevi 179
                                       +  +  e+i +++    ++sae+A++ GLid + 
  gi|518652417|ref|YP_008141937.1| 162 KRRNLGEDIMEEIATGLVFSAEQAKKNGLIDGIA 195
                                       3334458899999999***************997 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0096        34      74     118 ..      50      93 ..      39     105 .. 0.79
   2 ?    8.4   0.0   0.00034       1.2     142     182 ..     164     203 ..     159     209 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0096
                                       HCCHHHHHHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETT CS
                             ECH_1  74 keevlelwtklytvpkpviaavnGaaigGGlelalacDiviaadn 118
                                        e +++ ++k+ +++kpv a ++G ++ G   la  +  + a ++
  gi|518652417|ref|YP_008141937.1|  50 TEILYNQLMKI-SSKKPVYALIEGIGASGAYWLACSAEKIFAMRT 93 
                                       45556666666.579***************999999887777665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00034
                                       HHHHHHHHHHHHHHT-EEEHHHHHHCTSSSEEESGGGHHHH CS
                             ECH_1 142 rkvGkskAeeilllgkkisaqealkvGlvdkvvpeeqllee 182
                                       r++G+ + eei  +g  +sa+ a+k Gl+d +   e++++e
  gi|518652417|ref|YP_008141937.1| 164 RNLGEDIMEEI-ATGLVFSAEQAKKNGLIDGIANLETVVDE 203
                                       66777776666.59********************9999987 PP

>> Rap_GAP  Rap/ran-GAP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   4.9e-05      0.18       7      31 ..     104     128 ..     101     187 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.9e-05
                           Rap_GAP   7 vSkrfeeFlelLGekvelkgfkgYs 31 
                                        S++f eFl++LG k++++++ +Y+
  gi|518652417|ref|YP_008141937.1| 104 MSPDFSEFLDTLGIKMRINKVGKYK 128
                                       49********************998 PP

>> DUF3416  Domain of unknown function (DUF3416)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   4.5e-05      0.16      88     141 ..     150     207 ..     148     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 4.5e-05
                           DUF3416  88 vDpfatWrhdlekkveagqdveleleeGarlleraaeraea.....aalraaaaalrdd 141
                                       +D ++ +r++++k+ + g+d+ +e+++G  + ++ a+++       a+l++++++l+++
  gi|518652417|ref|YP_008141937.1| 150 KDVYSVFREEVKKRRNLGEDIMEEIATGLVFSAEQAKKN-GlidgiANLETVVDELKAK 207
                                       6999***************************99999776.4699999999999999655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); 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: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1676.63
//
Query:       gi|518652418|ref|YP_008141938.1|  [L=336]
Description: hypothetical protein FACI_IFERC00001G1057 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   12.8   0.0      0.078   12.3   0.0    1.2  1  DctP      Bacterial extracellular solute-binding protein, fam


Domain annotation for each model (and alignments):
>> DctP  Bacterial extracellular solute-binding protein, family 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-06     0.078      63     120 ..     246     301 ..     234     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-06
                                       GGGTTTSGGGGGGGSTTTSCSHHHHHH.HHHSHHHHHHHHHHHHHTEEEEEEEEEEEEE CS
                              DctP  63 akleglvpeigvldlPFlfedeealkk.vlegevgekllkslekkglkvLafwenGfrq 120
                                        +l + + +  v+ + ++++d+++l + + +++    l++ ++  g+++L+++++G+++
  gi|518652418|ref|YP_008141938.1| 246 DRLINGNNNRYVFTTGYIMKDKDKLMRkLAGQS---VLYANMNFSGITGLKYYDEGYVK 301
                                       556666677789***************565555...7*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2558.61
//
Query:       gi|518652419|ref|YP_008141939.1|  [L=318]
Description: cobalamin biosynthesis protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-69  232.9   1.0    3.9e-69  232.9   1.0    1.2  1  CobD_Cbib  CobD/Cbib protein
  ------ inclusion threshold ------
      0.054   13.7   0.2       0.38   11.0   0.0    2.3  3  NusG_add   NusG additional domain
        1.2    8.1   4.9        4.9    6.0   0.0    2.3  2  DUF3488    Domain of unknown function (DUF3488)


Domain annotation for each model (and alignments):
>> CobD_Cbib  CobD/Cbib protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.9   1.0   6.5e-73   3.9e-69       1     275 [.      12     289 ..      12     299 .. 0.87

  Alignments for each domain:
  == domain 1  score: 232.9 bits;  conditional E-value: 6.5e-73
                         CobD_Cbib   1 lllAlllDlllgdprrllhPvvligklisalekrlrkakkerlaGvllalllvllallvalllllla.laa.ll... 72 
                                       l++++l+D+++g+p++++hPvv+ig +is+l++r+ +++++ +aG+++++ ++l+ ++ ++++l+l+ +a+ ++   
  gi|518652419|ref|YP_008141939.1|  12 LFFSILFDVVIGEPPNRIHPVVFIGITISKLKTRFISKNNKIAAGCFFLISIILINTVPLVAVLYLLyIAKnTIlli 88 
                                       57899****************************9975578999*******999999998888888776333322444 PP

                         CobD_Cbib  73 .glvlealllkltlalrsLleevrkvakal.kgdleaaReavsmiVgRdtseldeeeiarAavEsvaENlsDgvvaP 147
                                          v+ +++lk+t+++r + ++v+++ +al k+dl++a++++sm+V+Rdts++d e+ia+AavE++aE ++Dg++ P
  gi|518652419|ref|YP_008141939.1|  89 lFAVIYIYFLKSTFSIRGMGTHVNRIINALeKSDLDSAKKYTSMVVRRDTSSMDSEKIASAAVETIAEGFVDGYLTP 165
                                       444888************************669******************************************** PP

                         CobD_Cbib 148 lfyflllglpgalaykavnTlDsmvGYkneryedfGwaaArlDDllnyiPARltalllalaaa...lriarrd.ark 220
                                       +f+++++g++ga++ +++nT+Ds + Y+++ + +fG++ A  D + n+i +R++ +++ ++a+   ++ a+    ++
  gi|518652419|ref|YP_008141939.1| 166 MFFYAFFGIAGAMVARVINTMDSNIAYRDNTHYEFGRCTAIGDSITNFITSRMAPFMFSISAFllgIKYAKTRiINT 242
                                       *********************************************************99984444466665441566 PP

                         CobD_Cbib 221 hpSpNsgwpeaalAgalgvrLggpnvY.lgkleekptlgdkkrpleaedieralrl 275
                                       ++S N+g++++a+A +lg+rL++ + Y  +   ++p          ++di++a+++
  gi|518652419|ref|YP_008141939.1| 243 TDSLNAGYSIGAMAKVLGIRLEKSGEYiINPDAKSP---------GVNDIKKAMHI 289
                                       67*************************555233333.........45666666655 PP

>> NusG_add  NusG additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.83     5e+03      32      46 ..      42      56 ..      32      71 .. 0.81
   2 ?   -1.1   0.0      0.37   2.2e+03       5      39 ..     132     166 ..     128     185 .. 0.77
   3 ?   11.0   0.0   6.3e-05      0.38      30      80 ..     233     284 ..     229     294 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.83
                          NusG_add 32 lktyvipekaklvtG 46
                                      lkt +i +++k+ +G
  gi|518652419|ref|YP_008141939.1| 42 LKTRFISKNNKIAAG 56
                                      688999999999888 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.37
                          NusG_add   5 irarrsGvvsevknfrkvvietvdrkylktyvipe 39 
                                       + +rr+    +   +    +et+   ++  y+ p 
  gi|518652419|ref|YP_008141939.1| 132 MVVRRDTSSMDSEKIASAAVETIAEGFVDGYLTPM 166
                                       55677777777777778889999999999998875 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 6.3e-05
                          NusG_add  30 kylktyvipekaklvtGlkigarvkq.GmplaadgeyiceldGkiveveklk 80 
                                       ky+kt +i  +  l +G  iga+ k+ G+ l + geyi + d k   v+ +k
  gi|518652419|ref|YP_008141939.1| 233 KYAKTRIINTTDSLNAGYSIGAMAKVlGIRLEKSGEYIINPDAKSPGVNDIK 284
                                       9**********************9955************9999876666666 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   2.4    0.0094        56     101     136 ..      54      89 ..       2     120 .. 0.72
   2 ?    6.0   0.0   0.00082       4.9     149     170 ..     291     312 ..     226     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0094
                           DUF3488 101 llgffllatsflfsqsllfalylllalllllaalva 136
                                       + g+f l++  l+++ +l+a+++ll+++ +++ l++
  gi|518652419|ref|YP_008141939.1|  54 AAGCFFLISIILINTVPLVAVLYLLYIAKNTILLIL 89 
                                       456666666666666666666666666666666665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.00082
                           DUF3488 149 alrlalkllllalPlalvLFll 170
                                        l  +l+ll+  +P++lvLF+l
  gi|518652419|ref|YP_008141939.1| 291 YLSSILTLLIFVIPVMLVLFVL 312
                                       567789999***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2058.35
//
Query:       gi|518652420|ref|YP_008141940.1|  [L=473]
Description: hypothetical protein FACI_IFERC00001G1059 [Ferroplasma acidarmanus fer1]
Scores for 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-41  140.5   0.1    6.9e-41  140.0   0.1    1.2  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    4.7e-17   62.2   0.0    8.9e-17   61.3   0.0    1.4  1  CbiA       CobQ/CobB/MinD/ParA nucleotide binding domain
    1.2e-11   44.8   0.0    4.3e-11   43.0   0.0    1.8  1  AAA_26     AAA domain
     0.0063   16.4   0.1      0.012   15.5   0.1    1.3  1  SNO        SNO glutamine amidotransferase family
  ------ inclusion threshold ------
      0.041   13.8   0.0       0.19   11.6   0.0    2.1  2  MobB       Molybdopterin guanine dinucleotide synthesis prote
       0.11   12.3   0.0       0.22   11.3   0.0    1.4  1  DJ-1_PfpI  DJ-1/PfpI family


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  140.0   0.1   2.3e-44   6.9e-41       1     195 [.     247     431 ..     247     432 .. 0.89

  Alignments for each domain:
  == domain 1  score: 140.0 bits;  conditional E-value: 2.3e-44
                          GATase_3   1 kiavirlpaisnytdldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggp 77 
                                       +i++i++p++++y+d+dp     ++ + fv+  + +  + +d++ilpG+k + +dl ++++ g++ ++ + ++a ++
  gi|518652420|ref|YP_008141940.1| 247 RICIIKYPHMEVYSDFDPFYL-LNIGFTFVDKDNIDALDRCDVIILPGSKLVGEDLHYMEKYGIASKLIA-LQATKT 321
                                       69*****************55.668889998666665578*****************************9.5679** PP

                          GATase_3  78 vlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel..aaegeevkGyEiHsGrtilk 152
                                       ++giCGG+qmLG++++d ++ve++++e++ l +Ldietef+++k+tg v  +++    + + + +GyEiH+G +i +
  gi|518652420|ref|YP_008141940.1| 322 IIGICGGYQMLGKRVIDTDNVESAEKEIKCLEILDIETEFKNKKITGAVSYTLNDkiFPGEIHGEGYEIHYG-SIVR 397
                                       **********************************************9999997778766679999*******.5555 PP

                          GATase_3 153 ekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnrn 195
                                       + + pl+ +     +g+ +G v +    n++Gt +Hg+f+nr+
  gi|518652420|ref|YP_008141940.1| 398 NMEPPLAYI-----DGKPEGSVRG----NIYGTNIHGIFENRA 431
                                       666776666.....34999*9966....************986 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.3   0.0     3e-20   8.9e-17       3     115 ..       7     226 ..       5     231 .. 0.94

  Alignments for each domain:
  == domain 1  score: 61.3 bits;  conditional E-value: 3e-20
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH........................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx........................ RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep........................ 54 
                                       + +t++++GK+tla +L+ +++ +g+rV++++a +++ n+ +  + +e+ +++                        
  gi|518652420|ref|YP_008141940.1|   7 VLGTSSDSGKSTLAMSLCYYFSGKGYRVAPFKAVNMSLNSISlKDSSEISRAQwlqaiaagaepskymnpflikpeg 83 
                                       889*****************************999888876444455555555************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|518652420|ref|YP_008141940.1|  84 mgksqiivegksigsmkieeyysylknnaqaiikgaidrlsgeydiiisegagsaaeinmqdrdfansyvssmygtp 160
                                       ***************************************************************************** PP

                                       .....CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE-- CS
                                       .....xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 .....dlkrllellealgkkkall...lkiagvvlnrvdgeneetllkealeelkqrygvpvlgviprd 115
                                            d++r ++++++l+++++l     +++ +v+nr +g+  +++l+ ++ +l++ +g +v+gvip++
  gi|518652420|ref|YP_008141940.1| 161 ailisDIER-GGVFASLYGTVKLMpdsNLVKYLVINRMRGN--SEMLSPGILKLEELTGKKVIGVIPYS 226
                                       *********.**********9988*****************..***********9999*********96 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   1.4e-14   4.3e-11       3     191 ..       5     226 ..       3     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 1.4e-14
                            AAA_26   3 ifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgie........ededselikellgldqtyelpeplalsa 71 
                                       i v gt+ ++GK+++++ L+++++ kg++v+ fK ++  ++        e +++++++ ++   +++++++p++++ 
  gi|518652420|ref|YP_008141940.1|   5 IQVLGTSSDSGKSTLAMSLCYYFSGKGYRVAPFKAVNMSLNsislkdssEISRAQWLQAIAAGAEPSKYMNPFLIKP 81 
                                       6799*********************************9999777766555559999999****************98 PP

                            AAA_26  72 plspelaarqegedid...lekiv...............kelekdadivvVEGagglgvpitee..llnadiaknlg 128
                                       +   + +   eg++i    +e++                ++l+ ++di++ EGag+  +   ++    n ++  + g
  gi|518652420|ref|YP_008141940.1|  82 EGMGKSQIIVEGKSIGsmkIEEYYsylknnaqaiikgaiDRLSGEYDIIISEGAGSAAEINMQDrdFANSYVSSMYG 158
                                       7655555555566665222555559999******************************76554432789******** PP

                            AAA_26 129 apvilVarggl.gtinqllltiealrqknvrvlGvilNkvrnpe.....nvetlekksgipvlGvvPyl 191
                                        p il+  +++ g ++ l+ t++++ +  + v+ +++N++r         + +le+ +g +v+Gv+Py+
  gi|518652420|ref|YP_008141940.1| 159 TPAILISDIERgGVFASLYGTVKLMPDS-NLVKYLVINRMRGNSemlspGILKLEELTGKKVIGVIPYS 226
                                       *********994588999*****99884.56999*****99884577779*****************96 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   3.9e-06     0.012      28     100 ..     280     359 ..     270     365 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
                                       GGGGCC-SEEEE-SS-HHHHH.HHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTB........SS-SS-- CS
                               SNO  28 kedlaevdaliiPGGestams.kliertglyedllefvknsekvvlGtCaGlillskelene........lvktlel 95 
                                        + l+++d +i+PG        + +e++g+  +l +   ++ k+++G C G  +l k++           ++k le+
  gi|518652420|ref|YP_008141940.1| 280 IDALDRCDVIILPGSKLVGEDlHYMEKYGIASKLIAL--QATKTIIGICGGYQMLGKRVIDTdnvesaekEIKCLEI 354
                                       5689**********99877652589*****9999875..6779************9986433233444567888888 PP

                                       CCEEE CS
                               SNO  96 lkvkv 100
                                       l+++ 
  gi|518652420|ref|YP_008141940.1| 355 LDIET 359
                                       88865 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   6.4e-05      0.19       2      51 ..       5      54 ..       4      75 .. 0.77
   2 ?   -1.4   0.0      0.67     2e+03      77      98 ..     112     134 ..      84     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.4e-05
                              MobB  2 lgivgk.sgsGKTtLleklipelkarglrvgtiKhahhgfdvdkpgkDsyr 51
                                      +++ g+ s+sGK tL   l   ++ +g+rv+  K  + +++     kDs +
  gi|518652420|ref|YP_008141940.1|  5 IQVLGTsSDSGKSTLAMSLCYYFSGKGYRVAPFKAVNMSLN-SISLKDSSE 54
                                      566665489**********************9997665554.234455555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.67
                              MobB  77 aelsleellarl.sevDlvlvEG 98 
                                       a+  ++  ++rl  e+D+++ EG
  gi|518652420|ref|YP_008141940.1| 112 AQAIIKGAIDRLsGEYDIIISEG 134
                                       34556667777745699999998 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 ?   11.3   0.0   7.5e-05      0.22      58     109 ..     282     334 ..     269     342 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.5e-05
                                       TCCG-SEEEE--BHHHHHHHHTSHHHHHHHHHHH.HTT-EEEEETTTHHHHHH CS
                         DJ-1_PfpI  58 kaaeyDalvlpGGragperlrenekvvelvkefa.ekgklvaaICagpqlLaa 109
                                       + ++ D+++lpG +   e+l+  ek++   k  a ++ k++  IC g q+L +
  gi|518652420|ref|YP_008141940.1| 282 ALDRCDVIILPGSKLVGEDLHYMEKYGIASKLIAlQATKTIIGICGGYQMLGK 334
                                       45689**************************9987999***********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 3089.85
//
Query:       gi|518652421|ref|YP_008141941.1|  [L=37]
Description: hypothetical protein FACI_IFERC00001G1060 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); 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 0.27s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 273.14
//
Query:       gi|518652422|ref|YP_008141942.1|  [L=324]
Description: histidinol-phosphate aminotransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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   63.1   0.0    4.2e-17   62.4   0.0    1.4  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
       0.14   12.7   0.4         11    6.6   0.1    2.4  2  DUF2418        Protein of unknown function (DUF2418)


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 !   62.4   0.0   4.7e-21   4.2e-17      61     315 ..      59     286 ..      18     316 .. 0.79

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 4.7e-21
                                       TTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHH CS
                     Aminotran_1_2  61 eklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplyseedfhldlealee 137
                                        + ++++  ++ + sG +a i ++ + +k   g ++++ +p++++y +     +  ++++++       +d  +++ 
  gi|518652422|ref|YP_008141942.1|  59 AGNEFNPA-NISLVSGLTAFIHTFLASIK---G-NVIIISPSFTEYLKPQIEGKRIIIPFNV------VNDHPEILS 124
                                       44567788.99999999998888777774...4.7777789999887654444444777772......355555555 PP

                                       HHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEE CS
                     Aminotran_1_2 138 alkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnll 214
                                          ++   n     +++  p +PtG++++   +  ++++a k+n  +f+De +  fv + +   + r ++e++ n++
  gi|518652422|ref|YP_008141942.1| 125 ---NF---NF--EALFLVYPDSPTGQLMSSSSIYSIIEIAMKKNSTVFLDESFIWFVNNRE-IME-RELIEKYNNVI 191
                                       ...43...33..799*******************************************954.334.*********** PP

                                       EEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 215 ivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrkelrde 291
                                       i +s+ K ++++G+R+Gyi++n+  +  ++    p+ +     +a++a ++   +   +l++ +   +++r +l ++
  gi|518652422|ref|YP_008141942.1| 192 IGRSMTKILSIPGLRLGYIASNSTTIHNIEEKLEPWRI----NQAALAYIDGNIQ---DLSNVALSTETERNYLIKS 261
                                       ***********************999999999999654....4555566666665...899999999********** PP

                                       HHHSTEEEECCS.CSSEEEEEETHH CS
                     Aminotran_1_2 292 Laelglkvlasq.sgmflltdlsae 315
                                       L+++g+  ++++ ++++++++    
  gi|518652422|ref|YP_008141942.1| 262 LKNIGFRTVGKPrANYITFQLPASI 286
                                       ******9999997889888876655 PP

>> DUF2418  Protein of unknown function (DUF2418)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.008        72      46      79 ..      68     101 ..      36     110 .. 0.85
   2 ?    6.6   0.1    0.0013        11      35      83 ..     145     193 ..     123     200 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.008
                           DUF2418  46 vllslqlylliskfeqqikDkkiiqkevleEYne 79 
                                       + l   l+ +i+ f   ik + ii +  + EY +
  gi|518652422|ref|YP_008141942.1|  68 ISLVSGLTAFIHTFLASIKGNVIIISPSFTEYLK 101
                                       5566778999**********************66 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0013
                           DUF2418  35 sesvlktlllvvllslqlylliskfeqqikDkkiiqkevleEYnekfVk 83 
                                       s+s++  ++ +++ +  + +l ++f   +++++i+ +e++e Yn+ ++ 
  gi|518652422|ref|YP_008141942.1| 145 SSSSIYSIIEIAMKKNSTVFLDESFIWFVNNREIMERELIEKYNNVIIG 193
                                       6777788888888888889999**********************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2433.67
//
Query:       gi|518652423|ref|YP_008141943.1|  [L=314]
Description: hypothetical protein FACI_IFERC00001G1062 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.014   15.6   9.9       0.42   10.9   1.3    3.3  2  DUF948        Bacterial protein of unknown function (DUF948)
        1.4    9.4  37.5        0.3   11.5   7.3    4.5  4  Syntaxin_2    Syntaxin-like protein


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   1.1   0.00028       2.5      23      73 ..      55     105 ..      49     118 .. 0.84
   2 ?   10.9   1.3   4.7e-05      0.42      29      75 ..     181     227 ..     138     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00028
                            DUF948  23 klkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdpl 73 
                                       k +k+ de+++  +e+++++++ + e ++l++k+++l ++ + + +++ +l
  gi|518652423|ref|YP_008141943.1|  55 KYAKIRDELNQKTHEMREHAKEKIAEKNELIEKIKTLRDEKEVHYKNLSEL 105
                                       568999******************************988877777776665 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 4.7e-05
                            DUF948  29 deaaatieelekqvdpilkevedllakvnelledvneklekvdplte 75 
                                       +e+++ i+e +   +++ ke+edl + + +l +++n++l+k+d++ +
  gi|518652423|ref|YP_008141943.1| 181 KELTDKINEERTVGEGYKKEIEDLSNRISQLSDEINDELQKLDEVRK 227
                                       566666666666678899*************************9865 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   7.2    0.0029        26      28      77 ..      60     107 ..      11     111 .. 0.78
   2 ?    2.1   5.0     0.027   2.5e+02       8      45 ..     102     159 ..      99     166 .. 0.48
   3 ?   11.5   7.3   3.3e-05       0.3       4      77 ..     155     230 ..     152     245 .. 0.78
   4 ?    4.6   1.1    0.0045        40       5      53 ..     257     305 ..     253     311 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0029
                        Syntaxin_2  28 teelreklhelieeinelikktnellkklsqldnsssdsqqklqkekLkk 77 
                                        +el++k he++e+++e i + nel++k+++l + ++   ++   + Lkk
  gi|518652423|ref|YP_008141943.1|  60 RDELNQKTHEMREHAKEKIAEKNELIEKIKTLRDEKE--VHYKNLSELKK 107
                                       468889999999999999999********99999886..44444455555 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.027
                        Syntaxin_2   8 insnvstleklvkqLgtkkdteelr....................eklhelieeinel 45 
                                       ++++ ++l++++++Lgt+ d ++++                    ++ +++i ei++l
  gi|518652423|ref|YP_008141943.1| 102 LSELKKQLREYRSSLGTNIDIKDIKakekelqylerrqqttelkkDEENKIIVEIRRL 159
                                       5556678888888899997755555333222222222222222233334444444444 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 3.3e-05
                        Syntaxin_2   4 nlqkinsnvstleklvkq.Lgtkkdteelreklhelieeinelikktnellkklsqldnsssdsqqkl.qkekLkk 77 
                                       ++ ++n+ +++ + l++q L +++d +el +k++e ++      k++++l +++sql++  +d+ qkl +  k ++
  gi|518652423|ref|YP_008141943.1| 155 EIRRLNNEIKKSKTLREQeLLKNGDVKELTDKINEERTVGEGYKKEIEDLSNRISQLSDEINDELQKLdEVRKVAD 230
                                       688999999999999999999999*999998888888888888888888888888888888888777744444444 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.0045
                        Syntaxin_2   5 lqkinsnvstleklvkqLgtkkdteelreklhelieeinelikktnell 53 
                                       l+ + + + +++++ k  + k    el+ek+ el e+ +   + t+e+l
  gi|518652423|ref|YP_008141943.1| 257 LKDMEKAIYSIRNKSKVTKRKEKESELQEKASELYEKFKAGEQLTTEDL 305
                                       6677788888999999999999999999999999999988888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      3896  (0.217302); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                       126  (0.00702772); expected 17.9 (0.001)
Passed Fwd filter:                        51  (0.00284455); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 1.13u 0.34s 00:00:01.47 Elapsed: 00:00:00.53
# Mc/sec: 1788.75
//
Query:       gi|518652424|ref|YP_008141944.1|  [L=371]
Description: transposase, IS605 OrfB family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-21   75.5   0.1      4e-21   74.7   0.1    1.4  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.7e-08   33.0   0.1    1.3e-07   31.9   0.1    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.018   14.5   0.3      0.036   13.6   0.3    1.4  1  TF_Zn_Ribbon    TFIIB zinc-binding
       0.39   10.7   3.1       0.81    9.7   3.1    1.5  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.62   10.3   1.9        1.2    9.4   1.9    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.1   1.1e-24     4e-21       1      69 []     277     346 ..     277     346 .. 0.97

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 1.1e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++eyka e+Gi+v++++p++TS +C++C  ++k+ ++++ +fkC +Cg++  +D+ A++Ni +r
  gi|518652424|ref|YP_008141944.1| 277 FYQLRLFIEYKAMEAGIPVIVIDPHNTSRECPNCHTISKKnRPERSVFKCISCGLKGEADYIASLNIRNR 346
                                       7899************************************999************************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.1   3.6e-11   1.3e-07       9     105 ..     158     245 ..     145     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.6e-11
                        OrfB_IS605   9 elpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarlhrkrs 85 
                                       e+p+ ++++++g+D+Gi n+ + +t++    +y+g ++k+  +     + +lqs   ks     a+r l++l+ k  
  gi|518652424|ref|YP_008141944.1| 158 EQPVIEPKNVIGVDMGIVNISVDSTGK----YYSGDEIKNVREHNLDLRSRLQSVNTKS-----AKRHLKKLSGKEH 225
                                       388999*********************....************************7776.....7************ PP

                        OrfB_IS605  86 rrrkhllhklathliktlke 105
                                       r+ ++  h ++++++++   
  gi|518652424|ref|YP_008141944.1| 226 RFATNTNHIISKEIVNKARG 245
                                       **************997654 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.3     1e-05     0.036       2      34 ..     306     338 ..     305     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34 
                                        CPnC++ +  + per  + C +CGl  e ++i
  gi|518652424|ref|YP_008141944.1| 306 ECPNCHTISKKNRPERSVFKCISCGLKGEADYI 338
                                       5******555899*************9998888 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   3.1   0.00023      0.81      19      44 ..     305     330 ..     300     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00023
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                       + CP+C+   k  r + r +f+C +C+
  gi|518652424|ref|YP_008141944.1| 305 RECPNCHTIsKKNRPE-RSVFKCISCG 330
                                       78*****665555555.6********7 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   1.9   0.00032       1.2      15      40 .]     304     330 ..     303     330 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00032
                     Auto_anti-p27  15 aetCpvCgvPLmrdr.kggkvyCvaCd 40 
                                       +  Cp+C ++  ++r ++    C++C+
  gi|518652424|ref|YP_008141944.1| 304 SRECPNCHTISKKNRpERSVFKCISCG 330
                                       678************9889999****6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       777  (0.0433376); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.45
# Mc/sec: 2481.95
//
Query:       gi|518652425|ref|YP_008141945.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G1064 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.7   0.0      0.042   14.4   0.0    1.1  1  Plug      TonB-dependent Receptor Plug Domain


Domain annotation for each model (and alignments):
>> Plug  TonB-dependent Receptor Plug Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   2.3e-06     0.042      47      92 ..      24      73 ..      10      75 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-06
                                      EEEEETTB-GGCSEEEETTEEESC....CCCSCTCGCSSBGGGEEEEEEE CS
                              Plug 47 ssisiRGlgsnrvlvlvDGvpian....ggsgagdlssidpedierievl 92
                                      +++ i G++++  l++++G         ++s+a+ +++ +p++i+ri  +
  gi|518652425|ref|YP_008141945.1| 24 EKMRINGINARGLLLTINGKKSKKpalaSPSTARVNNMANPDNIRRIPAY 73
                                      45699****************9889999999999999*********9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       222  (0.0123822); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 698.06
//
Query:       gi|518652426|ref|YP_008141946.1|  [L=360]
Description: hypothetical protein FACI_IFERC00001G1065 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-46  157.7   0.0    4.5e-46  157.4   0.0    1.1  1  NTP_transferase  Nucleotidyl transferase
    3.5e-07   30.7   0.0    4.9e-07   30.2   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    1.5e-05   24.5   9.4     0.0004   20.0   0.8    3.7  4  Hexapep          Bacterial transferase hexapeptide (six repea
    0.00057   18.2   2.6    0.00085   17.6   2.6    1.2  1  DUF4954          Domain of unknown function (DUF4954)
     0.0033   16.4   2.9      0.006   15.6   1.2    2.2  2  Fucokinase       L-fucokinase
  ------ inclusion threshold ------
        7.5    6.4   7.9        5.2    6.9   0.3    3.5  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 !  157.4   0.0   1.5e-49   4.5e-46       1     243 [.       4     229 ..       4     234 .. 0.92

  Alignments for each domain:
  == domain 1  score: 157.4 bits;  conditional E-value: 1.5e-49
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       kav++aGG+GtRL+P+t +++k+ vp++gk + + + l    n+gi++ ++++t ++  ++ + + e+ + +  +l+
  gi|518652426|ref|YP_008141946.1|   4 KAVVMAGGKGTRLRPITYSIPKPVVPIAGK-PCMLYLLDSYYNAGIKD-VIITTGYKFSSLITSIIENRHNDQAILF 78 
                                       79****************************.*****************.7777777766666666666667779*** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       ++e+e+ gtA++v+ + ++++d+      +v +gD+l + +++++++++++++a  +vt+++++ve+++++G++e++
  gi|518652426|ref|YP_008141946.1|  79 SVEKEPAGTAGSVKMVSNFIDDTL-----IVGSGDILSDFNISDIINFHKKNKA--MVTIVLTEVEDPRQFGIVEME 148
                                       ********************9655.....9************************..********************9 PP

                                       TTSBEEEEECS-SSHSH.CSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EE CS
                   NTP_transferase 155 eegrverfvEKPkeaka.selassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWs 230
                                       ++ r+ rf EKP++++  s++as+GiYv ++e+l+++       +   d+ +d++p+++++  + + ++ k+   W 
  gi|518652426|ref|YP_008141946.1| 149 NN-RIVRFLEKPDRDQTfSHIASTGIYVIEPEILDYIT------TMPYDFAKDLFPELMKRNIDIYGYMGKG--VWL 216
                                       95.9*********99888*******************3......4567************************..7** PP

                                       EXSSHHHHHHHHH CS
                   NTP_transferase 231 DvGtldslleane 243
                                       D+G +++l++an+
  gi|518652426|ref|YP_008141946.1| 217 DTGRPNDLITANQ 229
                                       **********997 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.6e-10   4.9e-07       1      77 [.       5      92 ..       5     139 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.6e-10
                                      EEEEEESS-TTTT..T...THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHC...HHHHHHTTC...TS-EEE-TTS CS
                      NTP_transf_3  1 aviLAGGrSsRmg..g...dKallplggkpllervldalraagvdevvvvggde...evlaalarl...gvrvvededp 68
                                      av++AGG+++R+   +   +K+ +p++gkp + ++ld+   ag+++v++ +g++    +++ ++ +   ++ +++ e++
  gi|518652426|ref|YP_008141946.1|  5 AVVMAGGKGTRLRpiTysiPKPVVPIAGKPCMLYLLDSYYNAGIKDVIITTGYKfssLITSIIENRhndQAILFSVEKE 83
                                      79**********8551559*********************************963332222222221113333333444 PP

                                      S-SHHHHHH CS
                      NTP_transf_3 69 gkgplasla 77
                                       +g+++s++
  gi|518652426|ref|YP_008141946.1| 84 PAGTAGSVK 92
                                      566666665 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2     0.011        34      13      28 ..     263     278 ..     247     283 .. 0.69
   2 !    5.3   1.6    0.0058        17       5      28 ..     273     295 ..     263     298 .. 0.78
   3 !   10.8   1.2   0.00011      0.32       3      32 ..     288     316 ..     283     317 .. 0.89
   4 !   20.0   0.8   1.4e-07    0.0004       1      28 [.     303     329 ..     303     331 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.011
                                       TEEEETTEEE-TTEEE CS
                           Hexapep  13 faviggnVkIGdnvkI 28 
                                        ++ig n+k Gdnv+I
  gi|518652426|ref|YP_008141946.1| 263 KCYIGRNIKAGDNVYI 278
                                       4566666666666666 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0058
                                       ETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   5 GsnvlIgpfaviggnVkIGdnvkI 28 
                                       G+nv+I  ++ +++n +IG+nv I
  gi|518652426|ref|YP_008141946.1| 273 GDNVYIK-YSALYDNEVIGNNVEI 295
                                       7788888.8888888888888877 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 0.00011
                                       EEETTEEE-TTEEEETTEEE-TTEEEETTE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkIgagv 32 
                                       vIG+nv I  ++ +++nV++ +n+kI + v
  gi|518652426|ref|YP_008141946.1| 288 VIGNNVEIT-NSLLMDNVTVRENTKIRNSV 316
                                       799999999.****************7754 PP

  == domain 4  score: 20.0 bits;  conditional E-value: 1.4e-07
                                       TEEEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       ++++ +n++I+ ++vi+ n++IG+n+ I
  gi|518652426|ref|YP_008141946.1| 303 NVTVRENTKIR-NSVIMKNCVIGENSEI 329
                                       57899******.*************998 PP

>> DUF4954  Domain of unknown function (DUF4954)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6   2.8e-07   0.00085     159     266 ..     229     335 ..     220     344 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.8e-07
                           DUF4954 159 kelidkyaeekksevGeigekvkilnaglikNvkigdyatiegasklengtin.SskeapveiGegViledfiissG 234
                                       + +++ky++   s+v  i+ k  il+   i+N+ i+++   ++ +  +n  i+ S+  +   iG++V++++++++  
  gi|518652426|ref|YP_008141946.1| 229 QIMVEKYGKP--SNVDFIKGKNIILDMAGIHNTGIDKCYIGRNIKAGDNVYIKySALYDNEVIGNNVEITNSLLMDN 303
                                       6678888764..66778999999999999999999998888999999999997355667788999999999999999 PP

                           DUF4954 235 skikdgavisrcfvGqavklkkqfsaedsllf 266
                                        ++ + ++i ++++ +++ ++++  + ds++ 
  gi|518652426|ref|YP_008141946.1| 304 VTVRENTKIRNSVIMKNCVIGENSEIVDSIIA 335
                                       99999999999999999999999999999875 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.23   6.9e+02     289     317 ..      88     117 ..      46     163 .. 0.65
   2 !   15.6   1.2     2e-06     0.006     267     335 ..     286     351 ..     256     357 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
                        Fucokinase 289 egsviehsslk.gnvsigsnsivsgleles 317
                                       +gsv + s++  + + +gs+ i+s+ +++ 
  gi|518652426|ref|YP_008141946.1|  88 AGSVKMVSNFIdDTLIVGSGDILSDFNISD 117
                                       566666666663444577777777776654 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 2e-06
                        Fucokinase 267 kekkkesavvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtilqtlsl 335
                                       +e + +++ ++nS+l  +v+v e++ i +s + +n+ ig+ns +++  ++ + +   l+ ++ + ++sl
  gi|518652426|ref|YP_008141946.1| 286 NEVIGNNVEITNSLLMDNVTVRENTKIRNSVIMKNCVIGENSEIVDSIIAPDMD---LRGKSRIYNVSL 351
                                       344588999*********************************999999988644...666665555555 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.2      0.12   3.5e+02      14      26 ..     264     278 ..     260     279 .. 0.77
   2 ?    0.5   0.2      0.18   5.4e+02      22      33 ..     285     296 ..     283     297 .. 0.78
   3 ?    6.9   0.3    0.0017       5.2       6      16 ..     319     329 ..     316     334 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.12
                                       -EES..EEE-TT-EE CS
                         Hexapep_2  14 agiG..vslGdncvv 26 
                                       ++iG  ++ Gdn+ +
  gi|518652426|ref|YP_008141946.1| 264 CYIGrnIKAGDNVYI 278
                                       788777888888876 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.18
                                       TT-EE-TT-EE- CS
                         Hexapep_2  22 dncvvgaGvvit 33 
                                       dn v+g++v it
  gi|518652426|ref|YP_008141946.1| 285 DNEVIGNNVEIT 296
                                       677899998777 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0017
                                       TT-EE-TT-EE CS
                         Hexapep_2   6 dnCliGanagi 16 
                                       +nC+iG n++i
  gi|518652426|ref|YP_008141946.1| 319 KNCVIGENSEI 329
                                       8********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       430  (0.0239835); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2420.67
//
Query:       gi|518652427|ref|YP_008141947.1|  [L=806]
Description: ABC-type peptide transport system, solute-binding component [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.1e-22   78.3   3.5    5.1e-22   78.3   3.5    1.8  2  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 ?   -3.1   0.4      0.16   2.8e+03     106     129 ..     216     239 ..     181     294 .. 0.58
   2 !   78.3   3.5   2.9e-26   5.1e-22      17     232 ..     332     597 ..     317     606 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.16
                                       CTCTTTTTGTTTSE-BSSSEEEEE CS
                         SBP_bac_5 106 ekeddkdkdtnekpvgtGPYklke 129
                                        +++ + +++++ +v tG Y+lk 
  gi|518652427|ref|YP_008141947.1| 216 LNKTLSPGNNDTLTVNTGYYMLKL 239
                                       344444555555666666666654 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 2.9e-26
                                       TTEEEEEE-TT-B-TTSSB-SHHHHHHH..HHHHHTGGGHCTTHHHHHC............TCTEEEEEEEET..TE CS
                         SBP_bac_5  17 gktytfkLRkgvkFsDGtpltAeDvvfs..ferlldpdtasgyasllee............dqdikkveavdd..yt 77 
                                       g +ytf++   +kFs G+p+tA Dv +s  ++ ll++++++++ +ll++            +++ik++ + d+  +t
  gi|518652427|ref|YP_008141947.1| 332 GNSYTFNISSKAKFSTGQPVTAYDVYYSlvMDLLLENKEPQTPGWLLAQyllpgnyhstdnYTNIKNAITYDNstQT 408
                                       789************************98899**************999************5555555554441144 PP

                                       EEEEESSE.TT.TTTTHCHHHHHHHGC.................CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTTE CS
                         SBP_bac_5  78 vrftlkkp.na.lfltllaavpasiak.................kaaekeddkdkdtnekpvgtGPYklkefkpgqk 135
                                       v++++++  ++ + +++l+ +   i +                 + + ++++ +++t+   ++ GPY++ + +pg++
  gi|518652427|ref|YP_008141947.1| 409 VTLNFTAKlQPdTVFSILSSPGTFISSysyllqngenltlssagVRTFENSN-KTYTMSGAISDGPYMILSSVPGEY 484
                                       44444444333357777777777777799**************877766666.9*********************** PP

                                       EEEEE-TTST...TTSCSSSSEEEEEE-.SHHHHHHHH..HTTSSSEEESTTCCTHCHHHHHTTEEEEEEEEEEEEE CS
                         SBP_bac_5 136 ivlernpdYw...gggkpkldriefkvipdsdaraaal..qsGeiddvaepppsdieqlkeakglkvlyespgggvt 207
                                       i+++rnp +    +++ p ++++++ +i++  +  + l  ++ ++ ++ + +p       +++     y+  ++ +t
  gi|518652427|ref|YP_008141947.1| 485 ITMVRNPFFIgnaNNSVPTINSVTIDYISQYPSIYQDLrfNTSQLAIFPNTYPYTSYLTTVKP-----YNNSYNVST 556
                                       ********9888889999**********99888888884466666444222222222222222.....244566666 PP

                                       EEEETTT................STGGGSHHHHHHHHHHS- CS
                         SBP_bac_5 208 ylafNtk................kppfddkrvRqAlsyAiD 232
                                        + fN +                 + f+++ vR+A++ A++
  gi|518652427|ref|YP_008141947.1| 557 IYDFNANvnktilgkytdnvnfpANLFSNITVREAFMEAYP 597
                                       6666666667788888888889999***********98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (806 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       818  (0.0456244); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.66u 0.27s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 5390.37
//
Query:       gi|518652428|ref|YP_008141948.1|  [L=385]
Description: hypothetical protein FACI_IFERC00001G1067 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2382.59
//
Query:       gi|518652429|ref|YP_008141949.1|  [L=273]
Description: ABC-type peptide transporter, permease component [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1905.60
//
Query:       gi|518652430|ref|YP_008141950.1|  [L=338]
Description: oligopeptide ABC transporter Dpp2, permease protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      6e-05   22.8  21.9      6e-05   22.8  21.9    3.3  3  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.29   10.9   1.1       0.63    9.8   0.7    1.8  1  IncD          Inclusion membrane protein D


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 ?   -4.5   8.5       1.6   1.5e+04     121     171 ..      16     107 ..       7     121 .. 0.54
   2 ?   -2.3  10.3      0.35   3.1e+03     102     171 ..      81     150 ..      72     157 .. 0.70
   3 !   22.8  21.9   6.7e-09     6e-05       4     181 ..     111     332 ..     108     336 .. 0.78

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 1.6
                      BPD_transp_1 121 llggavlleflgswpGlgtllleailgydyseis........................................... 154
                                       ++ g+++l+f++       ++  +il +dy+ +s                                           
  gi|518652430|ref|YP_008141950.1|  16 IFIGFTILLFII-----YKFVPITILKKDYPGTSinvlglrendffqyfyflyalitgkmgnvntllysgtvksavs 87 
                                       556666666666.....556666666666666666666666666666555555555555555555555555555533 PP

                      BPD_transp_1 155 ...nggvlalviavlllnlv 171
                                            ++++lvi +l+  ++
  gi|518652430|ref|YP_008141950.1|  88 iilPETIFFLVITFLISYAL 107
                                       33333333333333333333 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.35
                      BPD_transp_1 102 vlPnalppiitglilafggl.lggavlleflgswpGlgtllleailgydyseisnggvlalviavlllnlv 171
                                       ++++a++ i++  i+ +++  l  ++l++++g ++G + ++++ ++++ +++    +++ ++ +v +++ +
  gi|518652430|ref|YP_008141950.1|  81 TVKSAVSIILPETIFFLVITfLISYALAYLIGFYSGTTFRTVRRLSMSIFPLLF-LYMVSGLTLVTVFSGI 150
                                       567777777777766666554778888888898999999999999999999777.4444444444444433 PP

  == domain 3  score: 22.8 bits;  conditional E-value: 6.7e-09
                      BPD_transp_1   4 lGilaa..lnrnkkldkllrpliivllslPsfvlail.....lvlvf.............................. 43 
                                       +G++++  +   +++++l++ +        +++++ +     lv vf                              
  gi|518652430|ref|YP_008141950.1| 111 IGFYSGttF---RTVRRLSMSI-------FPLLFLYMvsgltLVTVFsgilgwfpsgsilsihsiighswisysgqg 177
                                       555555322...2333333332.......222222221222233333444466699999999999999999999999 PP

                      BPD_transp_1  44 .....................vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifr 99 
                                                            v++++l+h++lp i+ll+ +++ + ++i  +a  + ++++++a +++ a r   + 
  gi|518652430|ref|YP_008141950.1| 178 lfitsptniiildsiihnspvVLFDYLKHMVLPFIALLVPTTIYLSVYISHEASIEYNSSFMRAGTTRDAFRDN-YI 253
                                       9999999999999********999**************************************************.56 PP

                      BPD_transp_1 100 kvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis.nggvlalviavlllnlvadil 175
                                        +v + + + ++  l  +f +++gg vl++f++s+  lg + + + ++y++ ++    +v++l+i+v+++ +++d+l
  gi|518652430|ref|YP_008141950.1| 254 LYVKRGIRSRLLEELKPVFLIFMGGLVLISFIFSYMNLGEFAVYSFMNYNFGFMGgLYSVFMLAIIVIIFDAIIDLL 330
                                       6********************************************99999997775555555555555555555555 PP

                      BPD_transp_1 176 qrlldp 181
                                           ++
  gi|518652430|ref|YP_008141950.1| 331 ----NR 332
                                       ....54 PP

>> IncD  Inclusion membrane protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.7     7e-05      0.63      53      87 ..      73     108 ..      63     133 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7e-05
                              IncD  53 vagllfsgvlcspvsv.laaslffgvgafllggalv 87 
                                       v  ll+sg + s vs+ l  ++ff v +fl+  al 
  gi|518652430|ref|YP_008141950.1|  73 VNTLLYSGTVKSAVSIiLPETIFFLVITFLISYALA 108
                                       789************736789**********99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1037  (0.0578393); 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:                         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: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 2375.99
//
Query:       gi|518652431|ref|YP_008141951.1|  [L=176]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-15   55.3   0.1      9e-15   54.9   0.1    1.2  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.6e-14   53.3   0.2    3.1e-14   53.0   0.2    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.4e-11   44.0   0.2      3e-11   43.7   0.2    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    1.7e-07   31.6   0.1    2.7e-07   30.9   0.1    1.3  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    5.4e-06   27.1   0.0    6.9e-06   26.8   0.0    1.2  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.012   15.5   0.1       0.02   14.8   0.1    1.3  1  FR47             FR47-like protein
      0.025   14.8   0.0      0.042   14.0   0.0    1.4  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
      0.042   13.5   0.0      0.058   13.0   0.0    1.1  1  DUF4821          Domain of unknown function (DUF4821)


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1     4e-18     9e-15      25     117 .]      52     144 ..      29     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 4e-18
                                       HHHHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEE CS
                    Acetyltransf_1  25 eesfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlav 101
                                       +e++ + ++ +lv+e +g+++G  ++      k+++++  ++a+++eyr++G G+ ++++++ + +++gi+ki l+v
  gi|518652431|ref|YP_008141951.1|  52 RERLKNKDDLTLVCELNGKIAGVTTIQRGMYRKNRHVASLGIAIRKEYRHMGMGTGMIQDAISWSKQQGIEKINLEV 128
                                       23333466688999**********7766666666667777************************************* PP

                                       ETTEHHHHHHHHH.TTE CS
                    Acetyltransf_1 102 eedndaairlYek.lGF 117
                                       +++n  ai  Y + lGF
  gi|518652431|ref|YP_008141951.1| 129 FSSNINAIQAY-RnLGF 144
                                       ***********.66**9 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.2   1.4e-17   3.1e-14      20     110 ..      49     148 ..      28     161 .. 0.86

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.4e-17
                   Acetyltransf_10  20 ealrerieegealllvaeeggkivGvielrdgs.....hisll..fVdpeyrgqGigkaLleaveeeaekdgikl.e 88 
                                          rer+++++ l+lv+e +gki+Gv ++++g      h++ l  ++++eyr+ G+g+ +++++++  +++gi++  
  gi|518652431|ref|YP_008141951.1|  49 RGERERLKNKDDLTLVCELNGKIAGVTTIQRGMyrknrHVASLgiAIRKEYRHMGMGTGMIQDAISWSKQQGIEKiN 125
                                       556788899******************666655566679999989******************************** PP

                   Acetyltransf_10  89 ltvnasp.yavpfYeklGFkavg 110
                                       l+v +s+ +a++ Y++lGF+  g
  gi|518652431|ref|YP_008141951.1| 126 LEVFSSNiNAIQAYRNLGFQYEG 148
                                       *******************9775 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.2   1.4e-14     3e-11       6     154 ..      19     164 ..      14     165 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.4e-14
                    Acetyltransf_4   6 eeDakeilaiyaeyvvntaitfeyevssveefe..kflealdsekeyvflvae.sdrivGyaylgqfkkrakdwkae 79 
                                       +eDak i + ++  v+ ++i   +e + ++e     +l++    k  + lv e +++i+G  +++   +r  ++ a 
  gi|518652431|ref|YP_008141951.1|  19 PEDAKGIIECMQS-VMDEKIYLVSEYYLLTERGerERLKN----KDDLTLVCElNGKIAGVTTIQRGMYRKNRHVAS 90 
                                       6888888888875.45444443333333333221144444....5566677777***********999999999999 PP

                    Acetyltransf_4  80 lsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDmi 154
                                       l + + ++  +++g+g  +i+  +   k+q+ie+++ e++s+n+n+iq + +lGF+ +g  k+ + ++ r+ D +
  gi|518652431|ref|YP_008141951.1|  91 LGIAI-RKEYRHMGMGTGMIQDAISWSKQQGIEKINLEVFSSNINAIQAYRNLGFQYEGVRKRQFLIGDRYVDDV 164
                                       99999.599**************************************************************9976 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.1   1.2e-10   2.7e-07       4      75 ..      61     145 ..      57     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 1.2e-10
                                       EEEEEEETTEEEEEEEEEEES...TCTEE......EEE-GGGTTSSHHHHHHH.H....TTSEEEEE.EEEE..THH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitr......laVdpeyrgkGiGraLle.a....aekgiile.qlel..nae 63 
                                        ++V+e +gki G   +++         r      +a+++eyr  G G+ +++ a    +++gi+ + +le+  + +
  gi|518652431|ref|YP_008141951.1|  61 LTLVCELNGKIAGVTTIQRGMyrkN---RhvaslgIAIRKEYRHMGMGTGMIQdAiswsKQQGIE-KiNLEVfsS-N 132
                                       5789*********888777776541...2445678*****************9764543228865.334445523.3 PP

                                       .HHHHHHHHTTEE CS
                    Acetyltransf_7  64 .kaikfYeklGFe 75 
                                        +ai+ Y+ lGF+
  gi|518652431|ref|YP_008141951.1| 133 iNAIQAYRNLGFQ 145
                                       599*********8 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   3.1e-09   6.9e-06       9     138 .]      19     145 ..      12     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 3.1e-09
                    Acetyltransf_3   9 eeDlealfelrsdpevmr...y.lpe..pltleeaeewlerawaeeseeegygwaivlkdtgviGsvglr..dleee 77 
                                       +eD++++ e ++   vm    y ++e   lt+  ++e+l+       ++++++ ++++ ++++ G+  ++   + ++
  gi|518652431|ref|YP_008141951.1|  19 PEDAKGIIECMQ--SVMDekiYlVSEyyLLTERGERERLK-------NKDDLT-LVCELNGKIAGVTTIQrgMYRKN 85 
                                       666666666555..23321122322233444444444444.......235665.55565554889988884444455 PP

                    Acetyltransf_3  78 deeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                                       ++ a lg+ ++++++  G +t + + ++ +  +++g+e++  ++  +N + i+ ++ lGf+
  gi|518652431|ref|YP_008141951.1|  86 RHVASLGIAIRKEYRHMGMGTGMIQDAISWS-KQQGIEKINLEVFSSNINAIQAYRNLGFQ 145
                                       555***************************9.8888************************6 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   9.1e-06      0.02      27      80 ..      93     147 ..      80     154 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.1e-06
                                       EEE-GGG-SSSHHHHHHHHHHHHHHHS-S.-EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  27 lqvlpehrrrGlgsrlvkalakeiaergk.tvllvvvasNtpsirlyeklGfeki 80 
                                       + +++e r +G+g+ +++  +    ++g+ ++ l v  sN ++i+ y  lGf+  
  gi|518652431|ref|YP_008141951.1|  93 IAIRKEYRHMGMGTGMIQDAISWSKQQGIeKINLEVFSSNINAIQAYRNLGFQYE 147
                                       789**************99999999988725778899***************965 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.9e-05     0.042      77     133 ..      66     126 ..      46     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.9e-05
                    Acetyltransf_6  77 rldgrpvAva....lglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrrfdl 133
                                       +l+g++++v      ++r+++++  + ++++ e+++++ g+ +++++i + +++G+++++l
  gi|518652431|ref|YP_008141951.1|  66 ELNGKIAGVTtiqrGMYRKNRHVASLGIAIRKEYRHMGMGTGMIQDAISWSKQQGIEKINL 126
                                       5666666666555578999*************************************99976 PP

>> DUF4821  Domain of unknown function (DUF4821)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.6e-05     0.058     168     240 ..       2      78 ..       1      81 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.6e-05
                           DUF4821 168 ickreallpklhiRkArvEDhDDlveiferqseelreefGdyflaelieaqd...eenkai.VaevegkavGllsls 240
                                       i kr+  ++++ iR+ ++ED   ++e +++ ++e      +y+l  +  + +   ++ +   V+e +gk++G+ +++
  gi|518652431|ref|YP_008141951.1|   2 ILKRDGAVQNYAIRRGVPEDAKGIIECMQSVMDEKIYLVSEYYLLTERGERErlkNKDDLTlVCELNGKIAGVTTIQ 78 
                                       789999************************99999999999998655444445874445545**********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       440  (0.0245412); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1105.47
//
Query:       gi|518652432|ref|YP_008141952.1|  [L=107]
Description: ribosomal protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0033   17.3   0.0     0.0061   16.4   0.0    1.6  2  TrmB            Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.022   14.6   0.0    1.5  2  HTH_5           Bacterial regulatory protein, arsR family
      0.018   14.8   0.1      0.027   14.2   0.1    1.3  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.036   14.2   0.8        4.3    7.6   0.1    2.1  2  Transposase_22  L1 transposable element RBD-like domain
      0.049   13.6   2.3      0.065   13.2   0.0    2.2  3  HTH_12          Ribonuclease R winged-helix domain
      0.081   13.3   0.3       0.16   12.3   0.1    1.6  2  Rrf2            Transcriptional regulator
      0.086   13.1   0.0       0.14   12.4   0.0    1.3  1  PaaX            PaaX-like protein
      0.095   12.8   0.0       0.21   11.7   0.0    1.7  2  HTH_20          Helix-turn-helix domain
       0.12   12.1   0.6       0.23   11.1   0.1    1.9  2  GntR            Bacterial regulatory proteins, gntR family
       0.13   12.4   0.0        0.2   11.8   0.0    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.4e-06    0.0061      15      57 ..      25      67 ..      18      98 .. 0.92
   2 ?   -1.8   0.0       1.6   2.9e+03      37      45 ..      94     102 ..      81     105 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.4e-06
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESS CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekg 57
                                      ++Ll+++p+ + + ++++g+p+ k+  +Lr Le  G++e +++
  gi|518652432|ref|YP_008141952.1| 25 KTLLMEQPLGIIKMSQQTGIPEHKIRYSLRILEHEGIIEASRE 67
                                      689************************************9986 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
                                       HCHHHHHHH CS
                              TrmB  37 skvYevLrs 45 
                                        k+Y+ L++
  gi|518652432|ref|YP_008141952.1|  94 EKIYRELKN 102
                                       577777766 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.2e-05     0.022      10      46 ..      27      63 ..      23      64 .. 0.94
   2 ?   -2.9   0.0       3.7   6.7e+03       6      24 ..      81      99 ..      81     101 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                                      HHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5 10 lLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      lL+e++l +   + ++g+++ ++++ L++L+ +G++e
  gi|518652432|ref|YP_008141952.1| 27 LLMEQPLGIIKMSQQTGIPEHKIRYSLRILEHEGIIE 63
                                      7999999999*************************97 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.7
                                      HHHHHHTTSSEEHHHHHHH CS
                             HTH_5  6 kILklLaegelcvcelaee 24
                                      +ILk+ +e++  +  + +e
  gi|518652432|ref|YP_008141952.1| 81 QILKAARESSEGIEKIYRE 99
                                      5777766666555555555 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.5e-05     0.027       1      54 [.      19      72 ..      19      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                          HTH_DeoR  1 RieqilellkqqgklsveelvellgvSeaTiRRDLneLeeqglltRthGGavsi 54
                                      R+  i++ l  ++ l + + +++ g+ e  iR  L++Le++g+++  + Ga + 
  gi|518652432|ref|YP_008141952.1| 19 RHMTIIKTLLMEQPLGIIKMSQQTGIPEHKIRYSLRILEHEGIIEASREGAILT 72
                                      999*****************************************9999888775 PP

>> Transposase_22  L1 transposable element RBD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0024       4.3      26      85 ..       8      70 ..       2      77 .. 0.83
   2 ?    5.9   0.0     0.008        14      71      84 ..      77      90 ..      69      98 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0024
                                      HHHHHH-HHHHHHT---EEEEEEES...SSS-TSSSS--EEEEEESSHHHHHHHHHHHHHHS- CS
                    Transposase_22 26 diieenfpnlkkeanviiqeiqrtp...qrqdskrassrhiivrttkvenkekilkavrekGr 85
                                      + i+en+  l++++++i   +   p    + +++   + h i    +++ +e i+ a re   
  gi|518652432|ref|YP_008141952.1|  8 KEIRENIETLERHMTIIKTLLMEQPlgiIKMSQQTGIPEHKIRYSLRILEHEGIIEASREGAI 70
                                      45799*********9998777777733358999999*****99999*************9765 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.008
                                      HHHHHHHHHHHHHS CS
                    Transposase_22 71 enkekilkavrekG 84
                                       nk++ilka+re  
  gi|518652432|ref|YP_008141952.1| 77 GNKDQILKAARESS 90
                                      58*********975 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4   2.4e+03      26      40 ..      10      22 ..       4      27 .. 0.62
   2 ?   13.2   0.0   3.6e-05     0.065      30      59 ..      44      72 ..      35      76 .. 0.82
   3 ?   -1.5   0.2       1.4   2.5e+03       3      26 ..      82     103 ..      81     106 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                            HTH_12 26 rgydigeravRyrLr 40
                                      + ++i  +++ +++ 
  gi|518652432|ref|YP_008141952.1| 10 IRENI--ETLERHMT 22
                                      35566..66666665 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.6e-05
                            HTH_12 30 igeravRyrLrkleergltrrvgyagrelt 59
                                      i e  +Ry Lr+le +g+++  +  g+ lt
  gi|518652432|ref|YP_008141952.1| 44 IPEHKIRYSLRILEHEGIIEASRE-GAILT 72
                                      67889*************996554.47776 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.4
                            HTH_12   3 ILkilaesdkpigakeiaeeLkkr 26 
                                       ILk   es++  g ++i  eLk++
  gi|518652432|ref|YP_008141952.1|  82 ILKAARESSE--GIEKIYRELKNI 103
                                       6777777777..777788888765 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   9.2e-05      0.16      12      59 ..      19      66 ..       9      70 .. 0.89
   2 ?   -1.9   0.0       2.4   4.3e+03      31      50 ..      82     101 ..      78     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.2e-05
                                      HHHHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET CS
                              Rrf2 12 hallyLakeeeeepvsseeiaerqnispsylekilakLrkaglvksvr 59
                                      + ++++++   e+p+ + +++++++i+++ ++  l+ L+++g++++ r
  gi|518652432|ref|YP_008141952.1| 19 RHMTIIKTLLMEQPLGIIKMSQQTGIPEHKIRYSLRILEHEGIIEASR 66
                                      56888888888999******************************9765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.4
                                       HHHHHTS-HHHHHHHHHHHH CS
                              Rrf2  31 iaerqnispsylekilakLr 50 
                                       i +    s + +eki ++L+
  gi|518652432|ref|YP_008141952.1|  82 ILKAARESSEGIEKIYRELK 101
                                       55555556677888888887 PP

>> PaaX  PaaX-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   7.7e-05      0.14      26      60 ..      35      69 ..      32      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 7.7e-05
                              PaaX 26 LirllaelGiseslvRaalsRlakaGwlvrekegr 60
                                       i++ ++ Gi e+ +R +l  l+ +G + +++eg+
  gi|518652432|ref|YP_008141952.1| 35 IIKMSQQTGIPEHKIRYSLRILEHEGIIEASREGA 69
                                      58999****************************95 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       2.2     4e+03      41      51 ..      10      20 ..       8      27 .. 0.65
   2 ?   11.7   0.0   0.00011      0.21      32      60 ..      40      68 ..      21      69 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
                                      HHHHHHHHHHC CS
                            HTH_20 41 lsyHLrvLeea 51
                                      ++ ++++Le++
  gi|518652432|ref|YP_008141952.1| 10 IRENIETLERH 20
                                      56677777773 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00011
                                      HHHTS-HHHHHHHHHHHHHCTTEEEECTE CS
                            HTH_20 32 erldlskntlsyHLrvLeeagLvevvreg 60
                                      ++ +++   ++y Lr+Le  g++e  reg
  gi|518652432|ref|YP_008141952.1| 40 QQTGIPEHKIRYSLRILEHEGIIEASREG 68
                                      55679999******************998 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00013      0.23      17      60 ..      26      68 ..       5      71 .. 0.85
   2 ?   -2.2   0.1       1.9   3.3e+03       3      13 ..      94     104 ..      93     106 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00013
                                      SS-TTSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTC CS
                              GntR 17 elrpGdkLPsereLaaefgVsrttvReALrrLeaeglverrqgr 60
                                      +l  +++L    + +++ g+  + +R +Lr Le eg++e+ + +
  gi|518652432|ref|YP_008141952.1| 26 TLLMEQPL-GIIKMSQQTGIPEHKIRYSLRILEHEGIIEASREG 68
                                      56677888.888999999********************997765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                                       HHHHHHHHHHH CS
                              GntR   3 eqvyerLredI 13 
                                       e++y++L++ +
  gi|518652432|ref|YP_008141952.1|  94 EKIYRELKNIL 104
                                       68999998755 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00011       0.2      17      58 ..      22      63 ..      18      67 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHTTSEE CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqhrlVq 58
                                      ++++tLl +  l + +++++t+++  +++ sL +L + +++ 
  gi|518652432|ref|YP_008141952.1| 22 TIIKTLLMEQPLGIIKMSQQTGIPEHKIRYSLRILEHEGIIE 63
                                      89******************************9997777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 723.93
//
Query:       gi|518652433|ref|YP_008141953.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G1072 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.034   13.9   0.2      0.038   13.7   0.2    1.1  1  HEPN_DZIP3  DZIP3/ hRUL138-like HEPN


Domain annotation for each model (and alignments):
>> HEPN_DZIP3  DZIP3/ hRUL138-like HEPN
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   2.1e-06     0.038      39      90 ..      12      59 ..       3      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.1e-06
                        HEPN_DZIP3 39 ssedfDitLLvlLlRnicglkppstgWdklPaatdtskeadivrikyfrnel 90
                                      + ++f i L + Ll n  ++k++    +k+P++ d+  e+ i++i+ + ++ 
  gi|518652433|ref|YP_008141953.1| 12 ERKQFEIRLQIALLHNTLKIKAN----SKNPDKYDEYIEERIEKIRVLVDTT 59
                                      6789**************99988....678999*************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 544.80
//
Query:       gi|518652434|ref|YP_008141954.1|  [L=475]
Description: hypothetical protein FACI_IFERC00001G1073 [Ferroplasma acidarmanus fer1]
Scores for 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-141  472.9   0.4   1.1e-141  472.7   0.4    1.0  1  RtcB            tRNA-splicing ligase RtcB
  ------ inclusion threshold ------
       0.08   12.9   0.5       0.24   11.4   0.5    1.9  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4


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 !  472.7   0.4  1.3e-145  1.1e-141       1     412 []      44     475 .]      44     475 .] 0.97

  Alignments for each domain:
  == domain 1  score: 472.7 bits;  conditional E-value: 1.3e-145
                                       HHHHHTTSTTB-S-EEEEEEEE--SSS-EEEEEEE-...-EE-HHHC-SST.-EEEEEEEEEEHHHHGGGHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB   1 qlknvaslpgivkhvaamPDvHlGkgapiGsViatk...gviiPaaVGvDI.CGvrllktnltaeeleeklkelvke 73 
                                       q+++vaslpgivk ++amPD+HlG+g+piG+V+a++   g+i+P++VG+DI CGv+l++tn++++e ++k++ l++e
  gi|518652434|ref|YP_008141954.1|  44 QVMHVASLPGIVKSSMAMPDIHLGYGFPIGGVAAFDyddGIISPGGVGYDInCGVSLITTNIDYDEARDKINILLDE 120
                                       899************************************************************************** PP

                                       HHHHS-------------HHHHHHHHHHTHHHHHHTTSS-GGGGGGBGGGG--TT--GGGS-HHHHHHHGGGTT--- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB  74 lekavpvglgskkkvklskkeleevleegakwaveeglgeeedlekieeegalkeadlekvskkakerarkqlGtlG 150
                                       ++k+vp+g++ k++ ++s ++ +e+l++g +wa ++g+++ ed+e++ee+g++ + d + vs+ka +r++++lGtlG
  gi|518652434|ref|YP_008141954.1| 121 INKTVPAGIDYKSSFRISIDDENEILSSGIEWAYNNGYATREDIERTEENGKMLS-DISGVSEKAIKRGKNELGTLG 196
                                       *********9999*****99*********************************87.8999***************** PP

                                       STT-EEEEEEEEEES-HHHHHHHT-.-TTEEEEEEEE--HHHHHHHHHHHHHHHHCCHHHCT---SSGGG--EETTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 151 sGNHFiEvqlveeildeeaakalgl.eegqvvvmlHsGSRglGhqiaedylkiakkalkkkgiklpdrdLaylpags 226
                                       +GNHF+E+   e+i+de+ ak++g+ +++++++m+H+GSRglGhq+a+dyl  ++++ +    +  dr+L+ + ++s
  gi|518652434|ref|YP_008141954.1| 197 AGNHFLEMDRIESIMDEAKAKKFGInNKNNLAIMVHTGSRGLGHQVATDYLMRLNEEDS-SIKSEDDRQLISAYIHS 272
                                       *************************889************************9994443.4458899********** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.T--HHHH--EEEEEEESEEEEEEEE..T...EEEEEEEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x...xxxxxxxxxx RF
                              RtcB 227 eegqaYlkamqaaanyAkaNRqvitervreilekvlkkekedlelelvvdvaHNiakkEehe.d...ekvlVhRKGA 299
                                       + gq+Yl+am+aaan++++NRq+it ++r+++ek+++++ e+l++e+++ +aHN+ak E h+ d   +k++VhRKGA
  gi|518652434|ref|YP_008141954.1| 273 RTGQDYLNAMNAAANFGFVNRQIITYKIRKAFEKIFGEDFEHLGIETLYSLAHNMAKAEIHNvDgnkRKLMVHRKGA 349
                                       ************************************9999**********************95689********** PP

                                       EE-...........TT--EEEE--STTS-EEEEE--HHHH..SSSEE---S-----------------TTTTTCCCT CS
                                       xxx...........xxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 300 trA...........kvgqpviipGsmgtkSyivkGkgnae..sfgStsHGAGRlmsRakakkkfkleevkkdleeqg 363
                                       trA           ++g+pviipG+mg  Sy+++G   +e  +f+S++HGAGR++sR++a+++f++e+v+ +l+++g
  gi|518652434|ref|YP_008141954.1| 350 TRAlpayassgyfnETGHPVIIPGNMGGPSYVMVGMPGNEeiTFSSSCHGAGRVLSRKRANEQFNAEDVEMELKSRG 426
                                       ***********************************9765559*********************************** PP

                                       -EEEE------------------HHHHHHHHCTS-EEEEEEEEEEEEE- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              RtcB 364 igvearkkegvleEapeaYKdideVveaqaeaglvevvarlkpvlvvkg 412
                                       i+++a++k+ ++eE p++YK+ideVv++++ a+++  varl pv+v+kg
  gi|518652434|ref|YP_008141954.1| 427 IYLRATTKKAIIEESPGSYKNIDEVVRVINGAKIAAPVARLMPVAVMKG 475
                                       ***********************************************98 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 ?   11.4   0.5   2.7e-05      0.24      27      61 ..     208     237 ..     164     249 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                                       HHHHHHHHHHHHHHHHHCSTT.....TSHHHHHHHCTSSS CS
                    RNA_pol_Rpb1_4  27 nkilnkardkagkiaskslaa.....sNsiliMvksGaKG 61 
                                       ++i ++       +  k   +     +N++ iMv++G++G
  gi|518652434|ref|YP_008141954.1| 208 ESIMDE-------AKAK---KfginnKNNLAIMVHTGSRG 237
                                       222222.......2222...1233457************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3453.93
//
Query:       gi|518652435|ref|YP_008141955.1|  [L=260]
Description: hypothetical protein FACI_IFERC00001G1074 [Ferroplasma acidarmanus fer1]
Scores for complete 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-70  237.0   0.0    2.2e-70  236.6   0.0    1.0  1  DAHP_synth_1  DAHP synthetase I family
    4.6e-06   26.3   0.0    3.4e-05   23.4   0.0    2.1  1  NeuB          NeuB family
  ------ inclusion threshold ------
       0.15   11.2   0.0       0.31   10.2   0.0    1.5  2  IGPS          Indole-3-glycerol phosphate synthase


Domain annotation for each model (and alignments):
>> DAHP_synth_1  DAHP synthetase I family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.6   0.0   3.7e-74   2.2e-70      15     268 ..      13     250 ..       2     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 236.6 bits;  conditional E-value: 3.7e-74
                                       TTCSEEEEEEESC-S-HHHHHHHHHHHHHHHHHHTTTEEEEEESSSC-S.SSTTS-SHTTHHHTHHHHHHHHHHHT- CS
                      DAHP_synth_1  15 kddrllviaGPCsiedpeaaleyAerlkklgeklkddleiimrayfeKpRrstvgfkGlindpdlkilsrikkelgl 91 
                                        dd++l+iaGPCs+e++e+++ +A++l k+g +     +++++a+  KpR+ + +f+Gl++++ lk l+++ + +g+
  gi|518652435|ref|YP_008141955.1|  13 TDDKFLMIAGPCSVESEEQIIRVATQLRKIGVN-----VLRGGAF--KPRTCPDSFQGLGEEG-LKLLAKARDATGM 81 
                                       7999*****************************.....9******..****************.************* PP

                                       EEEEEESSCCTHHHHHHHESEEEE-CTCTTBHHHHHHHHTTSSEEEEEE-TTHHHHHHHHHHHHHHHTTEEE--EEE CS
                      DAHP_synth_1  92 piatevldpisvqyladvvdiiqiGArttesqdllelasglskpvglKngtdvaidemkaaaekilflgvetkgiil 168
                                        i+tev+d++++  +a+++di+q+G r++++++ll+++s+++kpv+lK+g+ +++de+ ++++++ + g  +k+i +
  gi|518652435|ref|YP_008141955.1|  82 AIITEVMDMDELPLVAEYADILQVGSRNSQNFSLLKKISRYDKPVLLKRGFGNTVDELISSSKYLSMNG--NKRIMF 156
                                       *********************************************************************..7***** PP

                                       EEEEEEESTSSSSSCHCHHHHHHHHHHCTSS-EEEESCHHHTTCGGGGHHHHHHHHHHHHHTTESEEEEEBBSSCCC CS
                      DAHP_synth_1 169 cerglrggkktnrdvedvaavkilkeetgklpvmvDvsHansrkdykrqkkvlklakaaiaaGiaGvmiEshlnpgk 245
                                       +erg+r++++++r ++d++a+++l e+t + pv++D+sH ++        +v +la  + aaG++G+miE+h++p k
  gi|518652435|ref|YP_008141955.1| 157 SERGIRTFEQSTRFTLDISAIPVLHEKT-EYPVIIDPSHPAGVNR-----YVEPLALGGTAAGADGLMIEVHPDPPK 227
                                       ****************************.79************99.....*************************** PP

                                       -SSTGGGGBBCTCBHHHHHHHHH CS
                      DAHP_synth_1 246 alsdgkqalkygksetdacilke 268
                                       alsd++q+l++ +++++   +k+
  gi|518652435|ref|YP_008141955.1| 228 ALSDSAQQLTVPQFQNLYTKVKN 250
                                       ***********888887776665 PP

>> NeuB  NeuB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   5.6e-09   3.4e-05      53     238 ..      64     257 ..      59     259 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 5.6e-09
                                       --HHHHHHHHHHHHHTT-EEEEEE-SHHHHHHHHHHT-S-EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT-.-HHHH CS
                              NeuB  53 lseeehkelkeyceekgieflstpfdlesvdlleslgveayKiaSgeltnlpllekiaktgkpvilStGma.tleei 128
                                       l ee  k l++  +  g+++++  +d +++ l++++  +++ ++S + +n+ ll+ki +++kpv+l  G   t++e+
  gi|518652435|ref|YP_008141955.1|  64 LGEEGLKLLAKARDATGMAIITEVMDMDELPLVAEY-ADILQVGSRNSQNFSLLKKISRYDKPVLLKRGFGnTVDEL 139
                                       567778889999999******************888.9*******************************96268999 PP

                                       HHHHHHH.HHHT--EEEEE.----SS--GG.G--THHHHHHHHH-TSEE.EEE--SSSSHHHHHHHHHT--...... CS
                              NeuB 129 eeavevlreagaeklvllh.CtseYPaple.dvnLkaietlkeafgvpv.GySDHtlgiavaiaAvalGAk...... 196
                                        ++ ++l+ +g+++++  +  + ++  ++   + ++ai+ l+e+ ++pv     H  g++  +  +alG +      
  gi|518652435|ref|YP_008141955.1| 140 ISSSKYLSMNGNKRIMFSErGIRTFEQSTRfTLDISAIPVLHEKTEYPViIDPSHPAGVNRYVEPLALGGTaagadg 216
                                       99999998888888877542445554444324666777777776665552223466666655444444432222224 PP

                                       .EEEEEB-S-TT--STTGGG-B-HHHHHHHHHHHHHHHHHSS- CS
                              NeuB 197 .viEkHftldrnlegpDhkaSlepeelkelveairnvekalge 238
                                        +iE H    ++l  +D++  l+  ++++l ++++n++++lg+
  gi|518652435|ref|YP_008141955.1| 217 lMIEVHPDPPKAL--SDSAQQLTVPQFQNLYTKVKNINAVLGK 257
                                       4677765544443..5666667777777777777777777765 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   5.2e-05      0.31     142     194 ..      64     115 ..      61     125 .. 0.86
   2 ?   -3.9   0.0      0.99   5.9e+03     205     223 ..     148     166 ..     139     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 5.2e-05
                                       S-HHHHHHHHHHHCCTT-EEEEEESSHHHHHHHHHTT-SEEEEESEETTTTEE CS
                              IGPS 142 ledeeleelaeaakslglevLvEvhdeeeleralklgakiiGvNnRnLktlev 194
                                       l +e l+ la+a   +g+ +++Ev d +el  +    a+i+ v +Rn ++++ 
  gi|518652435|ref|YP_008141955.1|  64 LGEEGLKLLAKARDATGMAIITEVMDMDELPLVA-EYADILQVGSRNSQNFSL 115
                                       667888999999999***************8765.5699********999975 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 0.99
                                       CC-TTSEEEEESSS-SHHH CS
                              IGPS 205 lvpkdvllvaeSGiktred 223
                                       +  +++++ +e Gi+t e+
  gi|518652435|ref|YP_008141955.1| 148 MNGNKRIMFSERGIRTFEQ 166
                                       4456788999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1773.05
//
Query:       gi|518652436|ref|YP_008141956.1|  [L=237]
Description: indole-3-glycerol-phosphate synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-43  148.5   0.0    2.4e-43  148.1   0.0    1.0  1  IGPS          Indole-3-glycerol phosphate synthase
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.22   11.6   0.0    1.5  1  Internalin_N  Bacterial adhesion/invasion protein N terminal


Domain annotation for each model (and alignments):
>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.1   0.0   2.7e-47   2.4e-43      15     245 ..       9     233 ..       2     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 148.1 bits;  conditional E-value: 2.7e-47
                                       HHCCS-GGCCCCG..-SS-SS-HHHHCHCHTTS-EEEEEE-SEETTTEESBSS--HHHHHHHHTTT.-SEEEEE--C CS
                              IGPS  15 akkrqsladleaavklakpkrsfaeaLresekklaliaEvKkaSPskgliredfdpaeiAkkyeeagAsaiSVLtee 91 
                                       +++++   +l++  ++++  +s+++aL+++++ +++iaE+K++SPs    + ++d+ ++    ++   + iS+Lte+
  gi|518652436|ref|YP_008141956.1|   9 KNSER---KLQEFNMRERGIISLKDALEKNQNGPGIIAEYKRKSPSGFSNKSNTDILKYFDGIQRI-IAGISILTEP 81 
                                       44444...45555567899**********************************************9.899******* PP

                                       CCC---CCHHHHHHHH-SS-EEEES---SHHHHHHHHHCT-SEEEEECCCS-HHHHHHHHHHHCCTT-EEEEEESSH CS
                              IGPS  92 kyFqGsledLrevrqavslpvlrKdFiideyqieearalgadaiLLivkvledeeleelaeaakslglevLvEvhde 168
                                       +yF G+  d ++v q  + p+l KdFi +e++i+ +++ g da LLi  +l+ + +++l+++ k+lg+++LvEvhd 
  gi|518652436|ref|YP_008141956.1|  82 QYFGGTPLDAEAV-QCYNKPILIKDFISSESMIKSSYMSGGDAFLLICDFLDYASIKKLVQYGKKLGMDALVEVHDP 157
                                       ******9997666.78999********************************************************** PP

                                       HHHHHHHHTT-SEEEEESEETTTTEE-CHHHHHHCHCC-TT.SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC- CS
                              IGPS 169 eeleralklgakiiGvNnRnLktlevdlntteeLaklvpkd.vllvaeSGiktredveklkeegvnafLvGeslmrq 244
                                       + ++ +   +  i+G N RnLktl+++ +++ee+ + +++    +v eSGi+ +e+++kl+ e+ +++L+G+sl++ 
  gi|518652436|ref|YP_008141956.1| 158 ASVKNIFPDENVILGYNRRNLKTLKME-DNSEEMYDNLKSYgLPVVLESGIN-HENINKLHIEKYQGLLIGSSLLSG 232
                                       *************************98.6788888989977699*******6.688******************986 PP

                                       T CS
                              IGPS 245 e 245
                                       +
  gi|518652436|ref|YP_008141956.1| 233 D 233
                                       5 PP

>> Internalin_N  Bacterial adhesion/invasion protein N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.5e-05      0.22      36      50 ..     153     167 ..     135     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.5e-05
                                       S-SSSEEHHHHSSSH CS
                      Internalin_N  36 sitpPaPIneiFpDp 50 
                                       ++  Pa+++ iFpD+
  gi|518652436|ref|YP_008141956.1| 153 EVHDPASVKNIFPDE 167
                                       6899**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1605.64
//
Query:       gi|518652437|ref|YP_008141957.1|  [L=186]
Description: anthranilate synthase component II [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-35  120.6   0.0    7.5e-35  120.4   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
    0.00012   21.9   0.0    0.00038   20.3   0.0    1.7  1  Peptidase_C26  Peptidase C26
     0.0027   16.8   0.1      0.019   14.0   0.0    1.9  2  GATase_5       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   1.2e-38   7.5e-35       2     187 ..       6     183 ..       5     186 .] 0.92

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 1.2e-38
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT....TTTHHHHHHHHCTSTS-E CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg....vegkieaikearenkiPi 74 
                                       +iDnyds+++n+ +++ + ++ v+++ +d   ++    l+ +dg ++s+Gpg+p+    ++g  e+i +  e    +
  gi|518652437|ref|YP_008141957.1|   6 IIDNYDSFVYNIYQYISSPEIHVDIRTNDN--LTD---LEPYDGYIISPGPGNPKnsedRGGLYEFIDRNKE--AKF 75 
                                       89*************************995..333...4579**************8888888888887555..779 PP

                                       EEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETT CS
                            GATase  75 LGICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtaksedd 151
                                       LG+C+G+Q+l++ +g ++   k + +hg+   + + ++ l+++ ++++++ ++H+++++p     ++++v a+se+d
  gi|518652437|ref|YP_008141957.1|  76 LGVCFGNQILGYYLGSDITLSK-RLMHGQPDTISHGDSLLYRDVPEKFTAIRYHSLVLEP----GSNIIVDAVSETD 147
                                       *******************999.9***********888999999***************9....899********** PP

                                       EEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 152 eelmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       +e+m++  k+ +f+gvQ+HPEs  ++ g+++++nf+
  gi|518652437|ref|YP_008141957.1| 148 GEIMGFHSKDGRFFGVQYHPESYYSEYGKQIFKNFV 183
                                       *********************************995 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   6.4e-08   0.00038     108     216 .]      75     168 ..      63     168 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.4e-08
                     Peptidase_C26 108 ilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHhqaikelaee 184
                                        lg+C G q+l    G  l +di   s++  h +++    s     + +sll++ +  e++    +H+  + e +++
  gi|518652437|ref|YP_008141957.1|  75 FLGVCFGNQIL----GYYLGSDITL-SKRLMHGQPD--TIS-----HGDSLLYRDVP-EKFTAIRYHSL-VLEPGSN 137
                                       58999999999....5555566663.2333343333..323.....36889999888.67777777775.7789*** PP

                     Peptidase_C26 185 lrveAvae.DgviEaieseeakafvlgvQwHPE 216
                                       + v Av+e Dg i  ++s++    ++gvQ+HPE
  gi|518652437|ref|YP_008141957.1| 138 IIVDAVSEtDGEIMGFHSKD--GRFFGVQYHPE 168
                                       ********9**999999988..569*******9 PP

>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1     0.034     2e+02      83     103 ..      64      85 ..      55      91 .. 0.77
   2 !   14.0   0.0   3.3e-06     0.019     161     238 ..     101     179 ..      87     184 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.034
                          GATase_5  83 ekflnr.edtlaLGiCnGfqlL 103
                                        +f++r ++   LG+C G q+L
  gi|518652437|ref|YP_008141957.1|  64 YEFIDRnKEAKFLGVCFGNQIL 85 
                                       567766356678********98 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 3.3e-06
                          GATase_5 161 hGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplN.PNgSpegiagitspdGRvlalmpHpervveavqks 236
                                       hG+     + ++ l + + ++ +a+rY+    +p +++ +    +   +i g  s+dGR++++  Hpe ++ ++ k+
  gi|518652437|ref|YP_008141957.1| 101 HGQPDTISHGDSLLYRDVPEKFTAIRYHSLVLEPGSNIIVDaVSETDGEIMGFHSKDGRFFGVQYHPESYYSEYGKQ 177
                                       5555555555666666666777788888888888777666524677889*********************9998887 PP

                          GATase_5 237 ii 238
                                       i+
  gi|518652437|ref|YP_008141957.1| 178 IF 179
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1369.16
//
Query:       gi|518652438|ref|YP_008141958.1|  [L=383]
Description: hypothetical protein FACI_IFERC00001G1077 [Ferroplasma acidarmanus fer1]
Scores for complete 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-77  258.2   0.0    1.1e-76  257.9   0.0    1.1  1  Chorismate_bind  chorismate binding enzyme


Domain annotation for each model (and alignments):
>> Chorismate_bind  chorismate binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.9   0.0   5.9e-81   1.1e-76       8     258 .]     124     368 ..     117     368 .. 0.97

  Alignments for each domain:
  == domain 1  score: 257.9 bits;  conditional E-value: 5.9e-81
                                       HHHHHHHHHHTTS-SEEEEEEEEEECESS-B-HHHHHHHHHCTBSSSEEEEEEETTEEEEEEESSEEEEEETTSEEE CS
                   Chorismate_bind   8 avekvkeeiragdlykvvlsrrlkaeleaavdplalyralrarnpapysflleledsellgaSPElllkveggrrie 84 
                                       ++  ++++i++gdl ++vlsrr+++      dpl + +++ ++ ++ y+++++++d e++g+SPE ll+v++g +i+
  gi|518652438|ref|YP_008141958.1| 124 KIGDAIKRIKNGDLLQIVLSRRFDLD---VYDPLYVAKKFLKNDKSLYVYYYKFGDLEVIGSSPENLLSVQNG-TIT 196
                                       6788999*******************...56899*************************************66.*** PP

                                       EECEEEEEEHSSSHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCBSCCEEEEECCEEEEEETTEEEEEEEEEE CS
                   Chorismate_bind  85 tepiaGTrargktpeedealeeelledeKeraEhlmivdlirndLgkvakpgsvkvpelfkverysevlhlvstieg 161
                                       ++p+aGTr+rgk++ ed++le++l +d+Ke+ Eh+m+vdl+rndLg+++ pgsv+v ++++++++++v+h+vst++g
  gi|518652438|ref|YP_008141958.1| 197 IYPVAGTRKRGKSESEDKDLENDLKTDQKELLEHRMLVDLARNDLGRICYPGSVDVLSSMEIRKFASVMHIVSTVSG 273
                                       ***************************************************************************** PP

                                       EESTT--HHHHHHHCSS-CCCSEESHHHHHHHHHHHSSS--TTTTSEEEEEETTS-EEEEEE-SEEEEETTEEEEEE CS
                   Chorismate_bind 162 elkedvslldllkalfPtgavtGaPkkrameiidelEearRgvYaGavgyldadgeaelavvIRtavvkdkelrlga 238
                                       +l+ +  + ++l+++fP+g+v+GaPkk+a+++i+ +E ++Rg+YaGa+g+++ +g ++la++IR+++ +++e + +a
  gi|518652438|ref|YP_008141958.1| 274 KLE-EYAPGNILRSVFPAGTVSGAPKKKAITLINGYEDMPRGAYAGALGIIGNNG-MDLALLIRSLFKSKNENYTQA 348
                                       **8.799*********************************************887.************9999***** PP

                                       EEEEETT--HHHHHHHHHHH CS
                   Chorismate_bind 239 GaGIvadSdpeaEyeEtlaK 258
                                       GaGIv+dS p +E++E+  K
  gi|518652438|ref|YP_008141958.1| 349 GAGIVKDSVPSSEIAEMYSK 368
                                       *****************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2661.12
//
Query:       gi|518652439|ref|YP_008141959.1|  [L=199]
Description: N-(5''''-phosphoribosyl)anthranilate isomerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-17   63.6   0.0    5.4e-17   62.2   0.0    1.6  1  PRAI         N-(5'phosphoribosyl)anthranilate (PRA) isomerase
  ------ inclusion threshold ------
       0.02   15.1   0.0       0.11   12.8   0.0    2.0  2  OKR_DC_1_N   Orn/Lys/Arg decarboxylase, N-terminal domain
      0.023   14.4   0.0       0.83    9.3   0.0    2.1  2  4HFCP_synth  4-HFC-P synthase


Domain annotation for each model (and alignments):
>> PRAI  N-(5'phosphoribosyl)anthranilate (PRA) isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2   0.0     9e-21   5.4e-17       1     193 [.       3     187 ..       3     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 9e-21
                                       TCE----SHHHHHHHHHHTSSEEEEE--TTBTTB--HHHHHHHCCCS--E.EEEEESSS-HHHHHHHHHHCTECEEE CS
                              PRAI   1 akicgltrasdvkaavkagadelglifaesskrevseeqaqellekvpak.lVGVfvNqpieevlriaqelgldvvQ 76 
                                       +k+cg+tr++d+  a+k gad +g+i +++  r+ s+  ++e+++k p + + GV    p             d++Q
  gi|518652439|ref|YP_008141959.1|   3 VKVCGITRIEDAEYAIKMGADLIGVILDPEVGRHGSQALIREIKTKYPSTpIAGVYTSMPEH-------AGYEDYIQ 72 
                                       699*********************************************77799999877743.......333589** PP

                                       E-CGG.-HHHHHHHHH.HS-TTSEEEEEEE.-SSS--S-SSTT-SEEEEESSS-SSSXXXXGGGGTTSXX.TTEEEE CS
                              PRAI  77 LHGdedeqeyeellkt.elpvikalkvaes.vdevkearradhvdllllDsgaGGtGelldwsliskllkslkviLA 151
                                       LH + + ++++ ++k+ + ++i  + ++e+ + ++ + +++  ++++ll       G     + +++l + +++ +A
  gi|518652439|ref|YP_008141959.1|  73 LHFNHSGEDIIAAKKAfNKKIISVVDFHEEgIADKVDSHMKSGAEIILLEDRS---GIINRIDQVKELPR-ERLGIA 145
                                       ***99666666666641334444444444213356666666666888887743...44444556899997.9***** PP

                                       SSXXTTTHHHHHT.TXXSEEEEXGGGEEE.TEEXHHHHHHHHH CS
                              PRAI 152 GGLtpeNvaeaiklegvlgvDvssGVEtn.GvkDlekirkfvq 193
                                       G+++ +Nv++++  +++++vDvss+ E++ G+k  +ki +f++
  gi|518652439|ref|YP_008141959.1| 146 GKIDSNNVQKLLA-TEPYLVDVSSSLEEYtGKKSFKKIDEFFN 187
                                       *************.***************************97 PP

>> OKR_DC_1_N  Orn/Lys/Arg decarboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.9e-05      0.11      18      66 ..       3      54 ..       1      71 [. 0.93
   2 ?   -0.2   0.1       0.2   1.2e+03       3      59 ..      79     133 ..      77     137 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.9e-05
                        OKR_DC_1_N 18 fevvgvtstdDllsvieqnsriaavvlsvd...deaaelldeirernedlPv 66
                                      ++v g+t+ +D++ +i++ +++ +v+l+ +   + +++l++ei+ + +  P+
  gi|518652439|ref|YP_008141959.1|  3 VKVCGITRIEDAEYAIKMGADLIGVILDPEvgrHGSQALIREIKTKYPSTPI 54
                                      68999*************************99999999*****999999998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.2
                        OKR_DC_1_N   3 gaairelaealekegfevvgvtstdDllsvieqnsriaavvlsvddeaaelldeire 59 
                                       g+ i +  +a++k+ ++vv+ ++ + +   + ++ + +a ++ ++ +++++++ i++
  gi|518652439|ref|YP_008141959.1|  79 GEDIIAAKKAFNKKIISVVDFHEEG-IADKVDSHMKSGAEIILLE-DRSGIINRIDQ 133
                                       5566667778888888888888777.6666666666666666664.55566666665 PP

>> 4HFCP_synth  4-HFC-P synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0    0.0089        53       7      49 ..      10      51 ..       6      86 .. 0.80
   2 ?    9.3   0.0   0.00014      0.83     148     207 ..     108     168 ..      88     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.0089
                                      SHHHHHHHHHHT-SEEEE.--GGG-TT----HHHHHHHHHHS-T CS
                       4HFCP_synth  7 nleEaelalaggadiiDv.KnPaeGsLGalfpevireivevvpg 49
                                       +e ae a++ gad+i v  +P+ G  G    + irei++  p+
  gi|518652439|ref|YP_008141959.1| 10 RIEDAEYAIKMGADLIGViLDPEVGRHGSQ--ALIREIKTKYPS 51
                                      6899************97369999988865..467888776665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00014
                                       EE-SS-SS--HHHHS-HHHHHHHHHHHHHTT-.EEEE-SS--GGGHHHHHHTT-SEEEESG CS
                       4HFCP_synth 148 lDTadKdgkslldflseeelaefveeareagl.ltaLAGslkledlpaLkklkpdilGvRg 207
                                       +D+  K+g +++   + + + + +++++e+    +++AG+++ +++++L + +p ++ v +
  gi|518652439|ref|YP_008141959.1| 108 VDSHMKSGAEIILLEDRSGIINRIDQVKELPReRLGIAGKIDSNNVQKLLATEPYLVDVSS 168
                                       79999999999999999999999999999866259*******************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); 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: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1384.28
//
Query:       gi|518652440|ref|YP_008141960.1|  [L=324]
Description: hypothetical protein FACI_IFERC00001G1079 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-64  218.5   0.0    1.3e-64  218.2   0.0    1.1  1  Glycos_transf_3  Glycosyl transferase family, a/b domain
    0.00023   20.9   0.1    0.00046   20.0   0.1    1.5  1  Glycos_trans_3N  Glycosyl transferase family, helical bundle 
  ------ inclusion threshold ------
      0.026   13.5   0.0      0.039   13.0   0.0    1.4  1  MT               Microtubule-binding stalk of dynein motor


Domain annotation for each model (and alignments):
>> Glycos_transf_3  Glycosyl transferase family, a/b domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.2   0.0   2.2e-68   1.3e-64       3     252 ..      68     315 ..      66     316 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.2 bits;  conditional E-value: 2.2e-68
                                       TBEEEEESS-SSSTHHHHHHHHHHHHHHTT-BEEEEE-STCTTCS-HHHHHCTST--ST--HHHHHHHHHHHSEEEE CS
                   Glycos_transf_3   3 dlvDivgTGGdgantfNiStaaaivvAaaGvkvakhgnrsvssksGsaDvLealgvnleltpeeveklleevgvgfl 79 
                                       +l D+vgTGGdg+nt+N+St  +i++A++G+k akhgn +v+ + GsaD +  +++n +++++++ + + +++ + +
  gi|518652440|ref|YP_008141960.1|  68 ELTDVVGTGGDGKNTVNVSTGVSILLASMGIKTAKHGNFGVTGHHGSADFMKYMNYNFKMDKNTIIENISRKNYVYI 144
                                       578************************************************************************** PP

                                       EHHSSSSHHHHHHHHHHHHTT.-SSHHHCHHHHHT..SEEEEHHHHHHHHTCHSEEEEEEEESTTSSCCS.TSHHHH CS
                   Glycos_transf_3  80 fapeyhkamkhvapvrrelgirTvfnlLGPLinparvkkqllgvyskelaeklaevlkelgveralvvhg.dGldev 155
                                       +apey+k++ +++++r+++ +rTvfn+LGPL+np ++ + +lg ys++lae +a+v+ke + + +++vhg dG+de+
  gi|518652440|ref|YP_008141960.1| 145 LAPEYNKSFAKFSAARKQISFRTVFNILGPLTNPLNPARVVLGTYSEDLAELYAKVIKE-EKKTGFIVHGsDGMDEI 220
                                       ***********************************************************.99*************** PP

                                       HHHHHHHHHHHHTTEEEEEEEEEGSSTSSSEEESHHHHSSHHHHHHHHTTHHTSCHHHHHHHHHHHHHHHHHHHTTS CS
                   Glycos_transf_3 156 sllakttvaelkdgeiteytlepedfglkraelealeggepkenaeilkavlegkksaakrdlvllnagaalvlagk 232
                                       s+ +k+t++++ dg+++++t++pe++  ++ + e++   ++ ++ e+l + l+gk++++ ++ +++na  a++l++k
  gi|518652440|ref|YP_008141960.1| 221 SPSSKSTLYRV-DGHLDKITIDPEKLIGHSINPEDISTTDSIKSFEMLLNGLSGKNKDV-MEFIAINALPAVILNQK 295
                                       *********99.69********************************************9.***************** PP

                                       SSSHHHHHHHHHHHHHTSHH CS
                   Glycos_transf_3 233 adslkegvakaeevidsGkA 252
                                       a+s +e+ +   + i+sGkA
  gi|518652440|ref|YP_008141960.1| 296 AESFEEAYDLSVDFIQSGKA 315
                                       *******************9 PP

>> Glycos_trans_3N  Glycosyl transferase family, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   7.8e-08   0.00046      37      61 ..      34      58 ..      16      60 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.8e-08
                                      HHHHHHHHH---HHHHHHHHHHHHH CS
                   Glycos_trans_3N 37 AfLmAlrlkGetaeEiaalaeAmre 61
                                      +fL+ ++ +Get++Eia++a A+re
  gi|518652440|ref|YP_008141960.1| 34 SFLTEIHNRGETPAEIAGFAMALRE 58
                                      7**********************98 PP

>> MT  Microtubule-binding stalk of dynein motor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-06     0.039     100     237 ..      63     200 ..      41     284 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-06
                                MT 100 tlnktnltelksfgsppdavvnvaaavmvllaprg.kvpkdrswkaa.kivmakvdafldslinfdkenihenclka 174
                                        ln  +lt++   g   +  vnv++ v +lla  g k  k   +  + +   a    +++   ++dk+ i en  + 
  gi|518652440|ref|YP_008141960.1|  63 NLNYPELTDVVGTGGDGKNTVNVSTGVSILLASMGiKTAKHGNFGVTgHHGSADFMKYMNYNFKMDKNTIIENISRK 139
                                       3667799*************************999567777777654144456666788999999************ PP

                                MT 175 ikeylndpefepefikskslaaaglcsw..vinivrfyevycdvepkrqalekanaelaaaqekl 237
                                          y+  pe++  f k    aa    s+  v ni+    +   ++p r+ l   +++la+   k+
  gi|518652440|ref|YP_008141960.1| 140 NYVYILAPEYNKSFAKF--SAARKQISFrtVFNIL--GPLTNPLNPARVVLGTYSEDLAELYAKV 200
                                       *************9764..4444444441144544..3344556666666666666666655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 2174.74
//
Query:       gi|518652441|ref|YP_008141961.1|  [L=244]
Description: hypothetical protein FACI_IFERC00001G1080 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-25   88.8   0.0    3.3e-25   88.4   0.0    1.1  1  Trp_syntA     Tryptophan synthase alpha chain
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.043   13.3   0.0    1.3  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   3.7e-29   3.3e-25      10     235 ..       2     225 ..       1     240 [. 0.87

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 3.7e-29
                                       -EEEEEEETTSS-HHHHHHHHHHHHHCT-SSEEEE---S--TTS-HHHHHHHHCCCCTT--HHHHHHHHHHHHHHCS CS
                         Trp_syntA  10 aafvpyvtagdpdleqsleilkalekagadviElGlpfsdPladGPvIqaanlraLakgvtlekvlelveevrkkev 86 
                                       ++++py t+g+p+ e+  + l+ +     + iE G+p  dP  dGPvI+++++++ + + + +   +  ++++  + 
  gi|518652441|ref|YP_008141961.1|   2 KNLIPYFTLGYPNNETLSHFLDLIPVDKINYIEFGFPSNDPRYDGPVIRKTHNVG-NINFSDDFYKKYFDHFH--KN 75 
                                       689***********************************************99987.44555555556667777..45 PP

                                       SS-EEEEE-CHHHCCC-HHHHCHHHHHCTEEEEEETTSB...CCCHHHHHHHHHHTT-EEEEEE-TTS-HHHHHHHH CS
                         Trp_syntA  87 evPivlltylnlvlsygeerflaelkeagvdglivpDlP...leeaeelveaakkkglelvflvapttsderlkevv 160
                                       +v +  l+y+  + ++  ++f++ l++ +  g+i+pDl    + e +e+ + +++ g e+++  +p+t+d+ +k v+
  gi|518652441|ref|YP_008141961.1|  76 HVKMYSLSYYSDIKAR-FDEFIDYLQKRNFSGIIIPDLIidyYSEGKEIINKLNDRGFEYIPFFSPSTPDSIIKDVS 151
                                       567899******9776.599******************72225688999999************************* PP

                                       HH--S-EEEESTTC-SSTTSSB-TTHHHHHHHHHHCT.SS-EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHHHC CS
                         Trp_syntA 161 eqaegfvYvvsraGvTgaenavaaevdelverlkklt.avPvavGFGistkeqvkqva.kvadGvivGSalvkkiee 235
                                       + +++++Y+   +  Tg    +  e+d + er+++l     +  GFGi+t ++++ ++ ++ +Gv +G  l+k  e+
  gi|518652441|ref|YP_008141961.1| 152 SMTNSWIYY-GLQPSTGID--IPYELDYTTERINELLpGREITYGFGIKTDDDIRDLMkNGGSGVAIGTYLIKMTEA 225
                                       ********8.455667765..677899999999998868899*************99989************99884 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   4.8e-06     0.043      75     110 ..     189     224 ..     173     229 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-06
                                       EEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-TH CS
                      His_biosynth  75 pvqvGGGIrsledveelleagadkviigtaavknpe 110
                                       +++ G GI++ +d+++l+++g + v igt  +k  e
  gi|518652441|ref|YP_008141961.1| 189 EITYGFGIKTDDDIRDLMKNGGSGVAIGTYLIKMTE 224
                                       799**************************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1928.12
//
Query:       gi|518652442|ref|YP_008141962.1|  [L=424]
Description: hypothetical protein FACI_IFERC00001G1081 [Ferroplasma acidarmanus fer1]
Scores for complete 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-40  137.2   0.1    9.1e-40  136.9   0.1    1.1  1  PALP      Pyridoxal-phosphate dependent enzyme


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.9   0.1   5.1e-44   9.1e-40       4     294 .]      80     411 ..      77     411 .. 0.84

  Alignments for each domain:
  == domain 1  score: 136.9 bits;  conditional E-value: 5.1e-44
                                       CSSS--EEEECCTCCCCCCE..EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBS.SHHHHHHHHHHHHH CS
                              PALP   4 gigpTPlvrlprlskelgvp..lflKlEslnptgSfKdRgaeyllarlkegtgaktvveass.GNhgralAaaaall 77 
                                         +pTPl+r+++l+k+lg    +++K+E+ + tgS+K+++a    +++ ++ g k+v++ ++ G++g a+A+aa+l+
  gi|518652442|ref|YP_008141962.1|  80 IGRPTPLIRARNLEKKLGYSgkIYYKYEGATATGSHKINTAIPQAYYAMKE-GVKGVTTETGaGQWGSATALAASLY 155
                                       679****************99*********************999996666.55555555544************** PP

                                       T-EEEEEEETTS-...HHHHHHHHHTT-EEEEE..................CCH....HHHHHHHHHHHHHHSTTCE CS
                              PALP  78 Glkvtivvpadas...pekvallrllGaevvev..................ggd....ydeavaaaaelaaegegay 129
                                       Gl++ i++ + +    p ++  + l++ +vv +                  +g+      eav    e+a +++ +y
  gi|518652442|ref|YP_008141962.1| 156 GLPSQIFMVKISFeqkPLRKTVMNLYNGNVVASpstltaygrkilkehpdtPGTlgigISEAV----EYALDNDYRY 228
                                       ********99999777899**************666666666666554444333333344444....4444455666 PP

                                       E--TTTSHHHHHHHHTHHHHHHHHTT...TTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS CS
                              PALP 130 lvsqfdnptviegygtiglEileqlg...gkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslr 203
                                       +v +  n+  ++ ++ ig+E ++ql    +  d+++ +vGgG++++G+ +++  ++ d+++i+  +++++++ ++  
  gi|518652442|ref|YP_008141962.1| 229 MVASVMNVSLTH-QSVIGQETKKQLEligEHADVLIGCVGGGSNFGGFTFPFIPDGDDTEIIATTANEVPKFSKGD- 303
                                       666666555555.********97777777**********************************************9. PP

                                       ..S.SS..B...................SSS.CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB- CS
                              PALP 204 agrrvtvpvs..................dtiadglavgspselafelldrlvdeivtvsdeealeamrllarregiv 262
                                         +++ ++++                  +  a gl+ + +s+    l+ +   +  +v++ee+ ea+r++a+++gi+
  gi|518652442|ref|YP_008141962.1| 304 -YKYDLMDSAgilpqvrmyslgadfvppTIYAGGLRYHGASPSLSLLINKGRIKSDEVTEEEVKEALRTFANTQGII 379
                                       .444444444889999999********899999*****888888889999999999********************* PP

                                       B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE-B CS
                              PALP 263 vepssaaalaalklreagelkegdrvvviltg 294
                                       + p s++a+a +    +++++e++++vv ++g
  gi|518652442|ref|YP_008141962.1| 380 AAPESGHAIASAIKYVKAHINEKKTIVVNVSG 411
                                       ***999999999677888888888*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3185.23
//
Query:       gi|518652443|ref|YP_008141963.1|  [L=216]
Description: triosephosphate isomerase [Ferroplasma acidarmanus fer1]
Scores for complete 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   47.3   0.2    1.6e-11   44.0   0.0    1.9  2  TIM           Triosephosphate isomerase
    9.3e-05   22.0   0.1    0.00018   21.1   0.0    1.4  1  His_biosynth  Histidine biosynthesis protein
     0.0044   16.4   0.1     0.0073   15.6   0.1    1.3  1  ThiG          Thiazole biosynthesis protein ThiG
     0.0087   15.1   0.6      0.028   13.4   0.7    1.6  2  FMN_dh        FMN-dependent dehydrogenase
  ------ inclusion threshold ------
      0.059   12.2   0.1      0.093   11.6   0.1    1.3  1  Trp_syntA     Tryptophan synthase alpha chain
       0.14   11.7   0.0       0.49    9.9   0.0    1.7  1  EAL           EAL domain


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   5.4e-15   1.6e-11       4     131 ..       6     126 ..       4     132 .. 0.78
   2 ?    2.5   0.0     0.026        79     153     175 ..     128     150 ..     122     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 5.4e-15
                                       EEE-TBTS-H..HHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSECEEES--BSSSSBS-TT--BHHH CS
                               TIM   4 agNwKmnktl..eeakellkklkaklkeekvevviappflylekvkklleesklklgaqnvsaeksGafTGevsaem 78 
                                       + N+K + +   ++ ++ll+ +k+ +k++ + +++a + lyl+k         l+++ q v+ +  GafTG+vs+e 
  gi|518652443|ref|YP_008141963.1|   6 FINFKHYDNAvgTNSEKLLTDFKSIKKQNGLYYCMAETDLYLQKS-----FPGLHIYGQHVDSNGYGAFTGSVSIES 77 
                                       567777665411455677777777666667777777777777753.....346789********************* PP

                                       HHHTT-SEEEES-HHHHHHST--HHHHHHHHHHHHHTT-EEEEEE---HHHHH CS
                               TIM  79 lkdlgvkyviiGHsErrqlfkEtdelvakKvkaalksglkpilCvGEtleere 131
                                       l dlgvk  ++ HsE+r     ++++++  vk+ ++ g+k+ilCv++  e+++
  gi|518652443|ref|YP_008141963.1|  78 LLDLGVKGSLLNHSEKRV----DSSIIESVVKKSKELGFKIILCVENLDEAEK 126
                                       *****************8....578999999**************76555544 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.026
                                       CCGGCEEEEE--GGGSSSS---- CS
                               TIM 153 ealknvviAYePvWAiGtgktat 175
                                       ++l+  +iAYeP   iG + +++
  gi|518652443|ref|YP_008141963.1| 128 SKLEPAYIAYEPPELIGGDISVS 150
                                       4578899*****99999865544 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   5.9e-08   0.00018      37     121 ..     133     215 ..     118     216 .] 0.76

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.9e-08
                                       HHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH-THHHH CS
                      His_biosynth  37 ryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGGIrsledveelleagadkviigtaavknpelik 113
                                       +y + +  el+  D++ + + r++ +   +ei++  + ++ vG G+++ edv++ + +ga  v i++  +kn + i+
  gi|518652443|ref|YP_008141963.1| 133 AYIAYEPPELIGGDISVS-SARPEIIGQAAEICKG-RTKLLVGAGVKTKEDVDTSMALGAAGVLIASGIIKNAKPIN 207
                                       555555666666666555.3555555555666666.79*************************************** PP

                                       HHHHHHCG CS
                      His_biosynth 114 elaekfgs 121
                                       +l++ +g+
  gi|518652443|ref|YP_008141963.1| 208 RLVSLMGN 215
                                       99987775 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.5e-06    0.0073     177     215 ..     169     207 ..     153     213 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.5e-06
                                       -BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHH CS
                              ThiG 177 PvivDAGigspsdaaqamelGadavllntavaeakdpva 215
                                        ++v AG+ + +d+ ++m lGa +vl+++ + + + p++
  gi|518652443|ref|YP_008141963.1| 169 KLLVGAGVKTKEDVDTSMALGAAGVLIASGIIKNAKPIN 207
                                       5899***************************99999986 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.32   9.5e+02     120     141 ..      95     116 ..      69     119 .. 0.80
   2 !   13.4   0.7   9.5e-06     0.028     261     301 ..     157     197 ..     145     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.32
                                       SSHHHHHHHHHHHHHCTESEEE CS
                            FMN_dh 120 kdrelteellkraeaagykalv 141
                                        d++++e+++k+ +++g+k ++
  gi|518652443|ref|YP_008141963.1|  95 VDSSIIESVVKKSKELGFKIIL 116
                                       5888999999999999999875 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 9.5e-06
                                       HHHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESH CS
                            FMN_dh 261 LpeiveavggrievlvDgGirrGsDvlkAlalGAdavllGR 301
                                       + + +e ++gr+++lv  G+++ +Dv   +alGA +vl++ 
  gi|518652443|ref|YP_008141963.1| 157 IGQAAEICKGRTKLLVGAGVKTKEDVDTSMALGAAGVLIAS 197
                                       445589999*****************************986 PP

>> Trp_syntA  Tryptophan synthase alpha chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   3.1e-05     0.093     201     233 ..     170     203 ..     151     210 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.1e-05
                                       EEEESSS-SHHHHHHHH.TT-SEEEE-HHHHHHH CS
                         Trp_syntA 201 vavGFGistkeqvkqva.kvadGvivGSalvkki 233
                                       ++vG G++tke+v++ +  +a+Gv++ S ++k+ 
  gi|518652443|ref|YP_008141963.1| 170 LLVGAGVKTKEDVDTSMaLGAAGVLIASGIIKNA 203
                                       689**********976659************975 PP

>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00017      0.49     138     227 ..     101     190 ..      88     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00017
                                       .HHHHHHHCTT-EEEEEEETSSTCCCHHHCCC--SEEEE-HHHH..TTTTTSCHHHHHHHHCHHHHCCCT-EEEE-S CS
                               EAL 138 eevlarLralGirialddfgtgysslsylarlppdiiKldrsll..adleedeeaqalvkalialakelgikvvaeg 212
                                       e+v+++ ++lG++i l       +  ++ ++l+p +i      l   d+  ++ + +++ + ++++k     +v  g
  gi|518652443|ref|YP_008141963.1| 101 ESVVKKSKELGFKIILCVE--NLDEAEKYSKLEPAYIAYEPPELigGDISVSSARPEIIGQAAEICKGRTKLLVGAG 175
                                       5788889999999999876..5678899999****9999876666999***************************** PP

                                       --SHHHHHHHHHHT- CS
                               EAL 213 Veteeqlealrelgc 227
                                       V+t+e++++ ++lg+
  gi|518652443|ref|YP_008141963.1| 176 VKTKEDVDTSMALGA 190
                                       ***********9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1747.92
//
Query:       gi|518652444|ref|YP_008141964.1|  [L=226]
Description: hypothetical protein FACI_IFERC00001G1083 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0045   16.6   6.3     0.0074   15.9   6.3    1.2  1  Bac_rhodopsin  Bacteriorhodopsin-like protein


Domain annotation for each model (and alignments):
>> Bac_rhodopsin  Bacteriorhodopsin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   6.3   4.2e-07    0.0074     107     174 ..      43     113 ..      38     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-07
                                       HHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHH...THHHHHHTTSTHHHHHHHHHHHHHHHHHHHH CS
                     Bac_rhodopsin 107 vvmivgglvgaliestyrwvyftisvaallvvlylll...gelaraakslsserrslfntLrnlvvvlwil 174
                                        v+i g l+g l++ +  ++y+ is++  +vv+y+l    + ++ a+ + +s    +++ L++  +v wi+
  gi|518652444|ref|YP_008141964.1|  43 SVFITGALIGLLSGELEIYGYWYISIILIIVVIYFLRsiiTLFKIAIPKQTSHKLLMYLELIITWLVFWII 113
                                       58999******************************972212233333333333345555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1523.25
//
Query:       gi|518652445|ref|YP_008141965.1|  [L=111]
Description: hypothetical protein FACI_IFERC00001G1084 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-11   44.0   0.0    2.8e-11   43.8   0.0    1.1  1  DrsE      DsrE/DsrF-like family
  ------ inclusion threshold ------
       0.11   12.5   0.0       0.13   12.2   0.0    1.1  1  DUF5311   Family of unknown function (DUF5311)


Domain annotation for each model (and alignments):
>> DrsE  DsrE/DsrF-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   3.2e-15   2.8e-11      14     116 ..       9     110 ..       2     111 .] 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 3.2e-15
                                       BSHHHHHHHHHHHHHTTT....-EEEEEE-GGGGGGGBS---TGGGTS---GGGGGGCGGGT-EEEEEHHHHHHTT- CS
                              DrsE  14 seaarealelalaaaalg....hevsvffygdGvllllkgqtanpadeknlaellkalkeygvklyvCgqaakargl 86 
                                       ++++     l+++ ++++    + ++v+f  ++v++llkg+        ++ +++k+ ++ gvk+ +C++++k+ +l
  gi|518652445|ref|YP_008141965.1|   9 NDYSIMKTILKQIGNLKNsmpdANIEVVFNRSAVKALLKGD--------EFMPKIKEIIDSGVKINACKNTLKELKL 77 
                                       55555555666666666688899****************33........4889************************ PP

                                       -GGG..E-.T--EEEE-HHHHHHHHHH-SEEEE CS
                              DrsE  87 dede..dl.gvgvevsglgelaelqnegdrvit 116
                                       +ed+  +  g+g++ +++ e++++q+eg+ +++
  gi|518652445|ref|YP_008141965.1|  78 SEDDvdKGsGIGIVTAAVEEIVRKQAEGYFYLQ 110
                                       *9885533778******************9987 PP

>> DUF5311  Family of unknown function (DUF5311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.4e-05      0.13       9      76 ..       9      76 ..       2      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.4e-05
                           DUF5311  9 sereiLlevlrCvssisqqlGkaasaifyeslvskpvisseeivsrllkiLetGysssvasllvselg 76
                                       +  i+  +l+ + ++++ +  a   + ++    k+ +  +e ++++ +i+++G   ++ +++++el 
  gi|518652445|ref|YP_008141965.1|  9 NDYSIMKTILKQIGNLKNSMPDANIEVVFNRSAVKALLKGDEFMPKIKEIIDSGVKINACKNTLKELK 76
                                      588999******************999999888888******************99999888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 852.10
//
Query:       gi|518652446|ref|YP_008141966.1|  [L=668]
Description: hypothetical protein FACI_IFERC00001G1085 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.0    2.7e-31  108.9   0.0    1.5  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 
    9.2e-18   64.2   0.4    1.8e-17   63.3   0.4    1.5  1  HGTP_anticodon   Anticodon binding domain
    2.2e-13   50.1   0.1    2.3e-12   46.8   0.0    2.4  2  tRNA_SAD         Threonyl and Alanyl tRNA synthetase second a
    8.8e-05   22.5   1.7    0.00021   21.3   1.7    1.6  1  Zn-ribbon_8      Zinc ribbon domain
    0.00095   19.1   0.3     0.0022   17.9   0.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.002   18.1   0.2     0.0039   17.2   0.2    1.4  1  HypA             Hydrogenase/urease nickel incorporation, met
     0.0055   16.1   0.8       0.45   10.0   0.1    2.4  2  zf-ribbon_3      zinc-ribbon domain
  ------ inclusion threshold ------
      0.011   15.8   0.6      0.019   15.0   0.6    1.3  1  DZR              Double zinc ribbon
       0.08   13.0   0.0       0.16   12.1   0.0    1.5  1  Ribosomal_L37ae  Ribosomal L37ae protein family
       0.13   12.6   1.0       0.26   11.6   1.0    1.4  1  C1_2             C1 domain
       0.15   11.6   1.8       0.64    9.6   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
       0.18   11.7   1.1       0.32   10.9   1.1    1.3  1  C1_1             Phorbol esters/diacylglycerol binding domain
        0.4   11.2   3.7        4.5    7.9   0.2    2.5  2  zf-H2C2_2        Zinc-finger double domain
        5.1    7.0   5.4        7.1    6.5   0.5    2.5  2  zinc_ribbon_2    zinc-ribbon 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 !  108.9   0.0   2.1e-34   2.7e-31       3     178 ..     310     556 ..     308     557 .. 0.92

  Alignments for each domain:
  == domain 1  score: 108.9 bits;  conditional E-value: 2.1e-34
                                       EEETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   3 ledrndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeasld 77 
                                       +   n+++y LkP+n+++++++++   + s+r +P+k+++ +t+yR+Eks ++ GL+R r+F+ +dg+ f+ e+++ 
  gi|518652446|ref|YP_008141966.1| 310 FTLPNGDNYGLKPMNCPGHIAIFQRS-VYSYRdMPVKYSEAGTVYRYEKSgEMGGLTRPRGFTIDDGHGFVREDQIF 385
                                       566899******************99.888655*****************8888*********************** PP

                                       HHHHHHHHHHHHHHHHT.T.SCEEEEEE..GTTSC.......................................... CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxx..xxxxx.......................................... RF
                      tRNA-synt_2b  78 dslrdlikaisriferl.glefraiiel..msaks.......................................... 109
                                       d+   l+k i  if+++ g e+     l  m++++                                          
  gi|518652446|ref|YP_008141966.1| 386 DETISLLKIIPSIFKTIlGTEEITYD-LsvMDKQHpenylmsyecsscgekfmlraasqeykcpacgsenlnsdfsm 461
                                       ****************9455544333.34555444899*************************************** PP

                                       ..........................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEE CS
                                       ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 110 ..........................adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvi 160
                                                                 a+y++k ++ + +  l++ ++++tiq + + ++  +++ ++d+n+ + +++
  gi|518652446|ref|YP_008141966.1| 462 wdnatenlrraleelklkyteypgeaAFYGPKIDVHIKDA-LGRLWQLSTIQID-FFMPANFDLYYIDKNDTKVRPV 536
                                       ************************************9999.*************.********************** PP

                                       EEEEE.EE.HHHHHHHHHHH CS
                                       xxxxx.xx.xxxxxxxxxxx RF
                      tRNA-synt_2b 161 micaa.ig.veRllsaileq 178
                                       +i++a  g  eR+++++le+
  gi|518652446|ref|YP_008141966.1| 537 IIHRAiYGsYERFIAILLEH 556
                                       *****9899*********98 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.3   0.4   1.4e-20   1.8e-17       1      87 [.     569     651 ..     569     658 .. 0.90

  Alignments for each domain:
  == domain 1  score: 63.3 bits;  conditional E-value: 1.4e-20
                                       SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTC CS
                    HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtr 77 
                                       q+++ip++e   ++ eya ++ ++Lr++gir ++d s+++i kki+  +++   +++vvGekel +++v+vr+r+++
  gi|518652446|ref|YP_008141966.1| 569 QAYIIPVSE---AYNEYATEINKKLREKGIRSKVDISDGTISKKIKLIRTMRPSYILVVGEKELANNSVSVRNRKDK 642
                                       89*******...9*************************************************************666 PP

                                       EEEEEETTHH CS
                    HGTP_anticodon  78 eqervsldel 87 
                                        + +  +de+
  gi|518652446|ref|YP_008141966.1| 643 TR-EYGMDEF 651
                                       44.5555555 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 !   46.8   0.0   1.8e-15   2.3e-12       2      44 .]     160     208 ..     159     208 .. 0.91
   2 ?    0.4   0.0      0.55     7e+02      23      38 ..     216     231 ..     209     236 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 1.8e-15
                                       EEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
                          tRNA_SAD   2 rvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                                       +++ +G+ ++e+C+G+Hvp+Tg+Igafk+l       +++ +++ + RIy
  gi|518652446|ref|YP_008141966.1| 160 SIYIQGN-YKEFCRGPHVPSTGYIGAFKLLsisstnyEGDVNKDKMIRIY 208
                                       5788999.**********************99999999999999999998 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.55
                                       GGC-SEEEECCECCCT CS
                          tRNA_SAD  23 geIgafkilseesiak 38 
                                       ++++af + +ee+i+ 
  gi|518652446|ref|YP_008141966.1| 216 KQLKAFLLRREEAIKR 231
                                       799**********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 !   21.3   1.7   1.7e-07   0.00021       6      36 ..     427     455 ..     425     458 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 1.7e-07
                       Zn-ribbon_8   6 YrCeeCghefevlqsisdapltaCPeCgs.ev 36 
                                       Y+C +Cg++f  ++++    + +CP+Cgs ++
  gi|518652446|ref|YP_008141966.1| 427 YECSSCGEKFMLRAASQ---EYKCPACGSeNL 455
                                       *******9999776444...556*****9665 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   1.7e-06    0.0022      25      60 ..     422     459 ..     414     471 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.7e-06
                    OrfB_Zn_ribbon  25 ay.TSktCseCgsknkealsgrtfkCpnCgfe.adrDv 60 
                                       +y  S +Cs Cg+k   + +++++kCp+Cg e ++ D+
  gi|518652446|ref|YP_008141966.1| 422 NYlMSYECSSCGEKFMLRAASQEYKCPACGSEnLNSDF 459
                                       455799*********999************99788886 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.2     3e-06    0.0039      69      98 ..     425     456 ..     400     459 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 3e-06
                                       -EEEETTTS-EEECHH.H.HHS-TTTSSS-EE CS
                              HypA  69 vkvrCreCgkefelee.k.alrCpkCgsadve 98 
                                       ++++C++Cg++f l++ + +++Cp+Cgs++++
  gi|518652446|ref|YP_008141966.1| 425 MSYECSSCGEKFMLRAaSqEYKCPACGSENLN 456
                                       7899*********87743699*******9875 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   0.0     0.028        36       3      10 ..     427     434 ..     426     439 .. 0.81
   2 !   10.0   0.1   0.00035      0.45       1      14 [.     443     457 ..     443     459 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.028
                       zf-ribbon_3   3 vrCPnCGa 10 
                                       ++C++CG+
  gi|518652446|ref|YP_008141966.1| 427 YECSSCGE 434
                                       57999997 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00035
                       zf-ribbon_3   1 stvrCPnCGa.plss 14 
                                       ++++CP+CG+ +l s
  gi|518652446|ref|YP_008141966.1| 443 QEYKCPACGSeNLNS 457
                                       589******999866 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   1.5e-05     0.019      13      38 ..     427     454 ..     419     461 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.5e-05
                               DZR  13 rfCseCgtk..lkavaaedrCpsCgekv 38 
                                         Cs Cg+k  l+a+++e++Cp+Cg+++
  gi|518652446|ref|YP_008141966.1| 427 YECSSCGEKfmLRAASQEYKCPACGSEN 454
                                       56*******99999999********984 PP

>> Ribosomal_L37ae  Ribosomal L37ae protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00012      0.16      32      60 ..     425     453 ..     412     477 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                                       S-BEESSSSSSEEEEEETTEEEETTTTEE CS
                   Ribosomal_L37ae  32 akytCpfcgktkvkRkavgiwkCkkcgkt 60 
                                        +y+C++cg++ + R a   +kC  cg +
  gi|518652446|ref|YP_008141966.1| 425 MSYECSSCGEKFMLRAASQEYKCPACGSE 453
                                       57************************975 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.0    0.0002      0.26      11      38 ..     419     450 ..     408     459 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0002
                              C1_2  11 kgedssesfnCsaCgrk....idgffYsCseC 38 
                                        +e++  s++Cs Cg+k      + +Y+C+ C
  gi|518652446|ref|YP_008141966.1| 419 HPENYLMSYECSSCGEKfmlrAASQEYKCPAC 450
                                       47788889*********886544444***999 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1       0.5   6.4e+02      22      28 ..     429     435 ..     427     444 .. 0.76
   2 ?    9.6   0.1    0.0005      0.64       1      12 [.     445     461 ..     445     470 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.5
                                       ESSSSBE CS
                      TF_Zn_Ribbon  22 CtdCGlV 28 
                                       C++CG+ 
  gi|518652446|ref|YP_008141966.1| 429 CSSCGEK 435
                                       8888864 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0005
                                       EEETTTTCEEC.....H CS
                      TF_Zn_Ribbon   1 ykCPnCgstnl.....v 12 
                                       ykCP Cgs+nl      
  gi|518652446|ref|YP_008141966.1| 445 YKCPACGSENLnsdfsM 461
                                       8********99555555 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 ?   10.9   1.1   0.00025      0.32       7      35 ..     422     451 ..     417     453 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                                       --SS--B-TTT-SB--S.SSS-EEEETTT- CS
                              C1_1   7 nfkqptfCkhCgeflwg.kekqglkCswCk 35 
                                       n+ ++  C+ Cge +    ++q +kC +C+
  gi|518652446|ref|YP_008141966.1| 422 NYLMSYECSSCGEKFMLrAASQEYKCPACG 451
                                       7889999********778***********7 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2    0.0035       4.5       8      24 ..     417     436 ..     415     436 .. 0.80
   2 ?    3.8   0.3     0.069        89      14      21 ..     444     451 ..     442     453 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                         zf-H2C2_2   8 kHtgekp...yeCplCdkaF 24 
                                       k ++e+    yeC++C+ +F
  gi|518652446|ref|YP_008141966.1| 417 KQHPENYlmsYECSSCGEKF 436
                                       77889955569******998 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.069
                         zf-H2C2_2  14 pyeCplCd 21 
                                       +y+Cp+C+
  gi|518652446|ref|YP_008141966.1| 444 EYKCPACG 451
                                       59*****8 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.5      0.13   1.7e+02       2       8 ..     429     435 ..     427     436 .. 0.65
   2 ?    6.5   0.5    0.0056       7.1       1      11 [.     446     456 ..     446     458 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.13
                     zinc_ribbon_2   2 CpnCGae 8  
                                       C++CG++
  gi|518652446|ref|YP_008141966.1| 429 CSSCGEK 435
                                       6666654 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0056
                     zinc_ribbon_2   1 fCpnCGaelqd 11 
                                       +Cp CG e+ +
  gi|518652446|ref|YP_008141966.1| 446 KCPACGSENLN 456
                                       79999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      686  (0.038262); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4413.79
//
Query:       gi|518652447|ref|YP_008141967.1|  [L=124]
Description: glycine cleavage system protein H [Ferroplasma acidarmanus fer1]
Scores for complete 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  127.0   0.6    3.7e-37  126.9   0.6    1.0  1  GCV_H     Glycine cleavage H-protein


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 !  126.9   0.6   2.1e-41   3.7e-37       1     117 [.       8     120 ..       8     124 .] 0.92

  Alignments for each domain:
  == domain 1  score: 126.9 bits;  conditional E-value: 2.1e-41
                                       -EE-TTSEEEEEETT.EEEEEE-HHHHHHH-SEEEEE---TT-EE-TT-EEEEEEESS-EEEEE-SSSEEEEEE-GG CS
                             GCV_H   1 lyytkehewvkveedgvatvGitdfaqeelgdvvfvelpevgtkvkkgeslaavEsvKaasevyapvsGevvevNek 77 
                                       l+ytk+hew+k ++d vatvGitdfaq++l d+v+v++p++gt  k+g++l ++EsvK+a +v+ pvsGev+e Ne+
  gi|518652447|ref|YP_008141967.1|   8 LKYTKSHEWFKIDGD-VATVGITDFAQHQLTDIVYVDMPKKGTVKKAGDTLLTIESVKSAEDVFFPVSGEVIETNEE 83 
                                       79************9.************************************************************* PP

                                       GTT-TTHHHH-TTTTT--EEEEES-GGGGGGSEEHHHHHH CS
                             GCV_H  78 leeepeliNkdpyeegWliklklsnleeleeLlsaeeyek 117
                                       l+++pel+N+d+y e Wl+k+kl++++ ++  ++a ey+ 
  gi|518652447|ref|YP_008141967.1|  84 LDKKPELVNSDCY-ENWLVKIKLTDNKYDS--MTAAEYKS 120
                                       *************.78*******9965443..55556655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 921.85
//
Query:       gi|518652448|ref|YP_008141968.1|  [L=194]
Description: FtsJ-like protein methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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  152.7   0.0    1.0  1  FtsJ      FtsJ-like methyltransferase
  ------ inclusion threshold ------
      0.072   13.0   0.0       0.13   12.1   0.0    1.4  1  UPF0146   Uncharacterised protein family (UPF0146)


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.7   0.0   1.1e-48     1e-44       1     176 [.      16     192 ..      16     193 .. 0.96

  Alignments for each domain:
  == domain 1  score: 152.7 bits;  conditional E-value: 1.1e-48
                                       CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       +rsR++yKLlei++kf+++ +++ v++ g++PGgw+qv+ + ++  + v+a+D+ pm+p+++vt++qg+i+dpe  e
  gi|518652448|ref|YP_008141968.1|  16 FRSRASYKLLEIQSKFNVIWKTDYVIEFGSSPGGWTQVVQKLTE--KPVIAIDISPMDPIENVTFVQGNINDPELSE 90 
                                       79***************999*******************88864..56***************************** PP

                                       HHCHCHHH...SSEEEEEE--S-SS-CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHHHHHHHHHCC CS
                              FtsJ  78 kikealse...rkvdlvvsDgapdvsgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeeteallkqlkkf 151
                                       kik a++    + v+ v+sD   ++sg+ d d++ +  L+++ ++l+++ll+ gg++vlk f+g++t a++++ k +
  gi|518652448|ref|YP_008141968.1|  91 KIKIAMDSlgiSSVSTVLSDAMIKTSGNYDRDHMGSYLLCDNVMNLSIDLLSSGGNVVLKQFQGDSTMAFVNKWKVY 167
                                       ***7776677799**************************************************************** PP

                                       EEEEEEEE-SS--CCG-EEEEEEEE CS
                              FtsJ 152 FekvsvvkPkssrsesseeflvcrg 176
                                       F++ +v+kP++sr+ s+e++++ ++
  gi|518652448|ref|YP_008141968.1| 168 FNYYKVTKPNASRQHSREVYIIFKD 192
                                       *********************9886 PP

>> UPF0146  Uncharacterised protein family (UPF0146)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.5e-05      0.13       4      66 ..      27      89 ..      24      97 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHS-SSEEEEET-..TT--HHHHHHHHHS-EEEEE-SS-S....STTEE---SSS--HH CS
                           UPF0146  4 lakkiaeenargkvvEvGi..GrkldvaealakrgvdlvatDikekkakegvrivrDDvtdPnle 66
                                      + +k+ +  ++  v+E G   G  ++v ++l+++   ++a+Di +    e+v +v+ ++ dP+l+
  gi|518652448|ref|YP_008141968.1| 27 IQSKFNVIWKTDYVIEFGSspGGWTQVVQKLTEK--PVIAIDISPMDPIENVTFVQGNINDPELS 89
                                      55566666677788898865588999******99..9*********888*************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        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 0.28s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1419.98
//
Query:       gi|518652449|ref|YP_008141969.1|  [L=205]
Description: hypothetical protein FACI_IFERC00001G1088 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00038   20.5   2.4    0.00058   19.9   2.4    1.3  1  Rad10          Binding domain of DNA repair protein Ercc1 (ra
    0.00056   19.9   0.9     0.0009   19.2   0.9    1.4  1  Thioredoxin_6  Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> 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 !   19.9   2.4   6.5e-08   0.00058       2      86 ..     111     201 ..     110     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 6.5e-08
                             Rad10   2 ilvserqkgnplLks.lk..nvp.wey.kdivpDyvigsttcvlflslkyhklhp.eYieerlkklkkkyklrvlLv 72 
                                       i+ s+  k   lL++ ++  +v+ +++ +++  ++v + +  v   s k  + +  +Yi er+ +l+k+y+ r +++
  gi|518652449|ref|YP_008141969.1| 111 IIYSKYVKTTDLLRHsMRkkKVSkYKFdAETPEEFVESWNNVVDLKSFKKVNAERkKYIIERIDSLQKEYSDRNIFC 187
                                       777888888999998876323334777555666777755555555588776666559******************** PP

                             Rad10  73 lvDvedseevlkeL 86 
                                       +vD + +++vl+++
  gi|518652449|ref|YP_008141969.1| 188 IVDYDYYKDVLNHF 201
                                       **********9976 PP

>> Thioredoxin_6  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.9     1e-07    0.0009      82     145 ..     137     201 ..     105     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1e-07
                                       -SHHHHHHHHTSS--EEEE.EEE-TTSTTHHHHHHHHHHHHHHTTTT-EEEEEETTGGHHHHHHT CS
                     Thioredoxin_6  82 ltpenaeelfeeglpplll.lflkkddeeteklkkaiekvakefkdkinfaladaksfkrpleyl 145
                                       ++ e+ ee+ e+  +++ l  f k + e+++++ ++i ++ ke++d+ +f+++d +++k++l+++
  gi|518652449|ref|YP_008141969.1| 137 FDAETPEEFVESWNNVVDLkSFKKVNAERKKYIIERIDSLQKEYSDRNIFCIVDYDYYKDVLNHF 201
                                       5666666666666443333145666789999*********************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1076  (0.0600145); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1604.38
//
Query:       gi|518652450|ref|YP_008141970.1|  [L=306]
Description: hypothetical protein FACI_IFERC00001G1089 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-09   36.6   0.5    1.4e-08   34.7   0.3    2.0  2  HTH_3         Helix-turn-helix
    2.1e-05   24.4   0.2    6.4e-05   22.9   0.2    1.9  1  HTH_19        Helix-turn-helix domain
    0.00037   20.4   0.0     0.0025   17.7   0.0    2.4  2  HTH_11        HTH domain
  ------ inclusion threshold ------
      0.045   14.1   0.0      0.077   13.4   0.0    1.3  1  HTH_31        Helix-turn-helix domain
      0.086   12.8   0.1       0.19   11.7   0.1    1.7  1  Ribosomal_S8  Ribosomal protein S8
       0.16   11.8   0.5       0.47   10.2   0.1    2.0  2  HTH_38        Helix-turn-helix domain
       0.19   11.6   0.0       0.81    9.6   0.0    2.1  2  HTH_23        Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.3   5.3e-12   1.4e-08       2      50 ..     133     180 ..     132     184 .. 0.92
   2 ?   -1.3   0.0      0.93   2.4e+03      41      49 ..     256     264 ..     253     268 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 5.3e-12
                                       HHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTS CS
                             HTH_3   2 kelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgv 50 
                                       + lR+q+++s+ ++A+klGvsr+++s +E+G ++ ++++ +kl+  L  
  gi|518652450|ref|YP_008141970.1| 133 RILREQNNYSIGYIAQKLGVSRRSVSLYESG-SSATIDIYLKLESILRG 180
                                       789****************************.77*********999875 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.93
                                       HHHHHHHHT CS
                             HTH_3  41 lkklakaLg 49 
                                       +kk++++Lg
  gi|518652450|ref|YP_008141970.1| 256 IKKISEVLG 264
                                       789999998 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   2.5e-08   6.4e-05       1      45 [.     129     174 ..     129     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.5e-08
                            HTH_19   1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvps.aell 45 
                                       G++ + +Re++++++  +a++lg+sr++ s +E+g++ +++ + +l
  gi|518652450|ref|YP_008141970.1| 129 GQKMRILREQNNYSIGYIAQKLGVSRRSVSLYESGSSATIDiYLKL 174
                                       6777889****************************88787754444 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.7e-07    0.0025       6      32 ..     132     157 ..     130     160 .. 0.82
   2 ?   -1.7   0.0       1.1   2.8e+03      11      26 ..     248     264 ..     246     264 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.7e-07
                            HTH_11   6 lelLleargpisgeeLAeeLnvSrrtv 32 
                                       +++L +++++ s+ ++A++L+vSrr v
  gi|518652450|ref|YP_008141970.1| 132 MRIL-REQNNYSIGYIAQKLGVSRRSV 157
                                       6788.555569**************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                            HTH_11  11 eargp.isgeeLAeeLn 26 
                                       e+++  +s+++++e L+
  gi|518652450|ref|YP_008141970.1| 248 ENTNRiVSIKKISEVLG 264
                                       67778899999999875 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     3e-05     0.077       3      39 ..     129     165 ..     129     179 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3e-05
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrr 39 
                                       G+  r lRe+ + s    A+ lgvs+  +s +E+G  
  gi|518652450|ref|YP_008141970.1| 129 GQKMRILREQNNYSIGYIAQKLGVSRRSVSLYESGSS 165
                                       7889******************************975 PP

>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   7.5e-05      0.19      23      77 ..     198     261 ..     180     292 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                                       E.E--HHHHHHHHHHHHCTSEEEEEEECCC.......CCC....EEEEE-BSSS-SBSSSEEEE-SB CS
                      Ribosomal_S8  23 v.pasklkeeilkvLkeeGyikdfeveeek.......kkk....ikielkynkkkksvikklkrvsk 77 
                                       v  as +++e+l+v+++ Gyi+++    +        +      i    ++n+ +++ i ++k++s+
  gi|518652450|ref|YP_008141970.1| 198 VnAASGFINEVLTVMNNIGYISEYISR-NPfdglsynS-DshliIGAFNNVNE-NTNRIVSIKKISE 261
                                       4478999*****************993.3345666441.14333333444444.5677777777776 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       3.3   8.5e+03       8      18 ..      41      51 ..      41      53 .. 0.85
   2 ?   10.2   0.1   0.00019      0.47      15      38 ..     134     158 ..     131     158 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3.3
                            HTH_38  8 eeReeIerlla 18
                                      +eR+ + +l++
  gi|518652450|ref|YP_008141970.1| 41 DERYILKILYN 51
                                      69999999997 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00019
                            HTH_38  15 rllaeG.lslreIArrLgrspsTIs 38 
                                       +l++++ +s+  IA++Lg+s+ ++s
  gi|518652450|ref|YP_008141970.1| 134 ILREQNnYSIGYIAQKLGVSRRSVS 158
                                       6787666**************9987 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00032      0.81      23      35 ..     146     158 ..     134     166 .. 0.81
   2 ?   -2.9   0.0       2.6   6.6e+03      19      28 ..     255     264 ..     254     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00032
                            HTH_23  23 IAreLgvsrrTvy 35 
                                       IA++Lgvsrr v+
  gi|518652450|ref|YP_008141970.1| 146 IAQKLGVSRRSVS 158
                                       9**********98 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.6
                            HTH_23  19 svreIAreLg 28 
                                       s+++I++ Lg
  gi|518652450|ref|YP_008141970.1| 255 SIKKISEVLG 264
                                       8999***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2249.96
//
Query:       gi|518652451|ref|YP_008141971.1|  [L=197]
Description: hypothetical protein FACI_IFERC00001G1090 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   1.0      0.035   14.2   1.0    1.6  1  DUF1938   Domain of unknown function (DUF1938)


Domain annotation for each model (and alignments):
>> DUF1938  Domain of unknown function (DUF1938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   1.0     2e-06     0.035      28      85 ..      96     153 ..      69     157 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2e-06
                                       EEESSHHHHHH.HHHHHHHHHHHT------B--..-SHHHHHHHHHT.TSS-GGGGGG. CS
                           DUF1938  28 ifaidegelikhripdlieflekrlskklevkegnsdysekvfkvli.Gkldneealef 85 
                                          id+g  +k  ip++i  lek++s   e+   nsdy     + +   ++++e + +f
  gi|518652451|ref|YP_008141971.1|  96 TVFIDKGMYFK-VIPEIIRILEKQMSNIKEIYSINSDYETSFIRLIFyNEVEEEVFRKF 153
                                       3459******9.9*************************877665443256666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       937  (0.0522617); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1317.20
//
Query:       gi|518652452|ref|YP_008141972.1|  [L=300]
Description: hypothetical protein FACI_IFERC00001G1091 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-47  161.8   0.1    5.9e-47  159.3   0.0    1.9  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    8.5e-35  119.3   0.2      1e-34  119.1   0.2    1.0  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0053   17.3   2.0        3.9    8.1   0.3    2.9  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0079   16.3   1.2      0.061   13.4   0.0    2.4  2  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
  ------ inclusion threshold ------
       0.31   11.4   3.5        0.3   11.4   0.7    2.6  3  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 


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 ?    0.2   0.0      0.11   4.1e+02      72     110 ..      23      60 ..      11      73 .. 0.70
   2 !  159.3   0.0   1.6e-50   5.9e-47       1     178 []     106     278 ..     106     278 .. 0.95

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.11
                                       HHCHHHHTCEECSHHHHHHH-SEEEE-S--STTTTTSBS CS
                      2-Hacid_dh_C  72 eeeeeelgvelvsleellaesDivslhlpltpetrhlin 110
                                        e + + +++ ++l e++++ D+v++    t+ t+++i+
  gi|518652452|ref|YP_008141972.1|  23 FEIDYKPKISSQELLEVIKDYDVVVVRSR-TKITKDVIS 60 
                                       4445566778899999******9998765.666666554 PP

  == domain 2  score: 159.3 bits;  conditional E-value: 1.6e-50
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       la+++  +r l ++ e++r++++   ++l+g el+gkt+Gi+G+GrIG+a+ +  + f+mk iayd+ + +      
  gi|518652452|ref|YP_008141972.1| 106 LAMMVIGARSLYKGMENTRKNDF---TKLKGMELEGKTLGILGFGRIGKAIVDASRTFKMKFIAYDPMPVE----YP 175
                                       5789999****************...99****************************************883....44 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       + v++vsl+el+++sD++s+++ + ++   ++n++el+k+k+g+i++Nt+R+  ++ +++l+ Lk+gki++++ Dvf
  gi|518652452|ref|YP_008141972.1| 176 EYVKKVSLDELMEQSDVISINVTMRKDSPYILNDNELSKLKEGVIIVNTSRARAINGKDMLKYLKNGKISAFVSDVF 252
                                       567899*********************************************************************** PP

                                       SSSSSGTCHHH..HHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspl..lelpnviltPHia 178
                                       ++ep++e+ ++  l+l+nv++tPH++
  gi|518652452|ref|YP_008141972.1| 253 WNEPAKEEYEMemLKLDNVMITPHLG 278
                                       ******9964444***********97 PP

>> 2-Hacid_dh  D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.1   0.2   2.8e-38     1e-34       1     121 [.       5     297 ..       5     299 .. 0.99

  Alignments for each domain:
  == domain 1  score: 119.1 bits;  conditional E-value: 2.8e-38
                                       EEEEST.CHHHHHHHHHTTEEEEEESCSSHHHCHHHHTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh   1 vlileplreeelellkeegvevevkdellteellekakdadalivrsntkvtaevlealpkLkviaragvGvDnvDl 77 
                                       vli++p+++ + + lk+ ++e+++k +++++elle +kd+d+++vrs+tk+t++v+++ +kLk+iarag+GvDn+D 
  gi|518652452|ref|YP_008141972.1|   5 VLICDPVDTVMTDKLKD-KFEIDYKPKISSQELLEVIKDYDVVVVRSRTKITKDVISNGKKLKIIARAGIGVDNIDT 80 
                                       79***************.66********************************************************* PP

                                       HHHHHTT-EEEE-TTTTHHHHHHHH.................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.................................................... RF
                        2-Hacid_dh  78 daakerGilVtnvpgystesvAElt.................................................... 102
                                       d+a+e+ i+V+ +pg+stesv E t                                                    
  gi|518652452|ref|YP_008141972.1|  81 DYAEEKHIKVVYAPGSSTESVVEITlammvigarslykgmentrkndftklkgmelegktlgilgfgrigkaivdas 157
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|518652452|ref|YP_008141972.1| 158 rtfkmkfiaydpmpveypeyvkkvsldelmeqsdvisinvtmrkdspyilndnelsklkegviivntsraraingkd 234
                                       ***************************************************************************** PP

                                       ............................................T-BHHHHHHHHHHHHHHHH CS
                                       ............................................xxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ............................................aaTeeaqeniaeeaaenlv 121
                                                                                   a T+eaq++ia ++a+n++
  gi|518652452|ref|YP_008141972.1| 235 mlkylkngkisafvsdvfwnepakeeyememlkldnvmitphlgAQTKEAQKRIAIMTADNII 297
                                       *******************************************99****************97 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0015       5.2      41      81 ..      22      62 ..      12      69 .. 0.84
   2 !    8.1   0.3    0.0011       3.9       2      34 ..     141     169 ..     140     226 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0015
                                      HHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHC CS
                     F420_oxidored 41 elaeelgvkvtavdneeaaeeadvvvlavkpedveevlsel 81
                                      +++ ++++k+++ +  e++++ dvvv+  +++ +++v+s+ 
  gi|518652452|ref|YP_008141972.1| 22 KFEIDYKPKISSQELLEVIKDYDVVVVRSRTKITKDVISNG 62
                                      455567799****************************9987 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0011
                                       EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEES CS
                     F420_oxidored   2 igiiGaGnmgealasgllaagaqpheivvansr 34 
                                       +gi+G+G++g+a++    +      +++ a ++
  gi|518652452|ref|YP_008141972.1| 141 LGILGFGRIGKAIVDASRTFK---MKFI-AYDP 169
                                       89***********98665554...5555.4455 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.11   3.8e+02      71     126 ..      35      88 ..      30     106 .. 0.73
   2 !   13.4   0.0   1.7e-05     0.061      21     111 ..     136     226 ..     123     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.11
                                       -HHHCTTT-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT- CS
                     AdoHcyase_NAD  71 tleevvkkadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanal 126
                                       +l ev+k+ d+vv  +     it++ +++ k+  i++  G    +id++  e++ +
  gi|518652452|ref|YP_008141972.1|  35 ELLEVIKDYDVVVVRSR--TKITKDVISNGKKLKIIARAGIGVDNIDTDYAEEKHI 88 
                                       56689999999887654..4477777777777778777777777777776665554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.7e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTTT-SEE.EE-SSSSS...SB- CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvkkadiv.vtttGnkd...iit 93 
                                       l Gk+  + G+G +Gk   ++ +++  + i    dP+       e  + v l+e+++++d++ + +t  kd   i++
  gi|518652452|ref|YP_008141972.1| 136 LEGKTLGILGFGRIGKAIVDASRTFKMKFIAY--DPMPV--EYPEYVKKVSLDELMEQSDVIsINVTMRKDspyILN 208
                                       78*********************998887765..66654..345777889999999999987566777776666899 PP

                                       HHHHCCS-TTEEEEE-SS CS
                     AdoHcyase_NAD  94 lehlkkmkddaivcniGh 111
                                        ++l+k+k+ +i+ n   
  gi|518652452|ref|YP_008141972.1| 209 DNELSKLKEGVIIVNTSR 226
                                       99***********99765 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 ?   -1.9   0.0       1.2   4.3e+03      53      73 ..      51      68 ..      23      91 .. 0.62
   2 ?   11.4   0.7   8.5e-05       0.3       3      20 ..     141     158 ..     139     244 .. 0.83
   3 ?   -2.8   0.0       2.3   8.1e+03      34      51 ..     257     274 ..     251     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                                      SS-EEEETTEEEETTEEEEEE CS
                           Gp_dh_N 53 kgeveaeeealvvngkkikvl 73
                                      +++++   ++++ ngkk+k++
  gi|518652452|ref|YP_008141972.1| 51 RTKIT---KDVISNGKKLKII 68
                                      33333...3344455555554 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.5e-05
                                       EEEESTSHHHHHHHHHHH CS
                           Gp_dh_N   3 vainGfGRIGrlvlrall 20 
                                       ++i GfGRIG+ ++ a  
  gi|518652452|ref|YP_008141972.1| 141 LGILGFGRIGKAIVDASR 158
                                       79**********998865 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                                       S-HHHHHHHHHEETTTEC CS
                           Gp_dh_N  34 tdletlayllkyDsvhgr 51 
                                       ++ e+ + +lk D v+ +
  gi|518652452|ref|YP_008141972.1| 257 AKEEYEMEMLKLDNVMIT 274
                                       556677778888877432 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2054.47
//
Query:       gi|518652453|ref|YP_008141973.1|  [L=371]
Description: hypothetical protein FACI_IFERC00001G1092 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.6   0.3    5.2e-25   88.2   0.3    1.0  1  Aminotran_5      Aminotransferase class-V
      6e-07   28.3   0.2    9.7e-07   27.6   0.2    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
      1e-06   28.2   0.0    3.2e-06   26.5   0.0    1.7  1  Aminotran_1_2    Aminotransferase class I and II
  ------ inclusion threshold ------
      0.081   13.2   0.1        0.3   11.3   0.1    2.0  2  TA0956           Thermoplasma acidophilum protein TA0956


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 !   88.2   0.3   1.2e-28   5.2e-25      33     359 ..      21     324 ..      10     332 .. 0.82

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 1.2e-28
                                       SSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHH CS
                       Aminotran_5  33 svhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqela 109
                                          h++ e+++ v+e ++ + ++ +a +  ++++t ++t a+++++ sl   +++ d+++  + +  +++  +  +a
  gi|518652453|ref|YP_008141973.1|  21 VSNHRSPEFKNVVKENESLLNKFSGAYK--TVMVTGSGTLAVETMVFSL---INNNDRVLSISYGNFGER-LIDSIA 91 
                                       4579999*******************95..8888888888*********...9*****************.899999 PP

                                       HHHTEEEEEEEBETTSCBEGGGHHHH--.TTEEEEEEESBETTTTE.B--HHHHHHHHHHTT-EEEEE-TTTTTTS- CS
                       Aminotran_5 110 krtgakvkvipldeegeldldeleklln.ektklvaithvsnvtGt.iqpveeigklakkkgalvlvDaaqavghip 184
                                       k+ + + ++i+     +l++++l + ++  + + +++ h++++ Gt i ++ ei+k++k+kga +lvD ++++  ++
  gi|518652453|ref|YP_008141973.1|  92 KK-TTNTQFITH---DQLNIETLLEEIRsRDFDKLFLVHNETSNGTaIRDLTEIIKIVKEKGAKLLVDDVSGFAGYN 164
                                       55.677788887...5677777766665499********************************************** PP

                                       --HHHHTESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET.TEEEEHCTTGGGS.SS--HHHHH CS
                       Aminotran_5 185 idvkklgvDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl.eettfaeapskfeaGTpnvagii 259
                                       +d++ + +  ++ +++K l   +GiG+++ + e+ + +   ++++++    +l  + +f e+     a Tp + ++i
  gi|518652453|ref|YP_008141973.1| 165 MDMNGIYA--MVTGSQKnLASIPGIGIIFLSIEAYNDV-MSQVSTNTPFYLDLkTSLKFLEKNE--TAYTPSTGAFI 236
                                       ****9999..*******667789*********999988.5666666555555544444444444..4559******* PP

                                       HHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEE CS
                       Aminotran_5 260 glgaaleyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavr 336
                                       +l+ al++le+ g+++  k+ ++ a+ +++ l++ +gv+++g  k   ++++  + f + +  d+++ L+e+gI v+
  gi|518652453|ref|YP_008141973.1| 237 SLNFALKILEKEGFANRVKRITSSADFIRSSLSD-NGVEIFGN-KGTYSSTV--VCFYNND-PDMVNKLAEHGITVS 308
                                       ********************************98.57888894.44444444..4444444.5788889******** PP

                                       EE-TTTHHHHHHTT.S-EEEEE.- CS
                       Aminotran_5 337 sGhhcaqplmkrlalegtvRaS.l 359
                                        G   +         + t+R++ +
  gi|518652453|ref|YP_008141973.1| 309 KGMGKL--------ANTTLRVGtM 324
                                       *97666........4555555555 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   2.2e-10   9.7e-07      58     175 ..      37     157 ..      28     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.2e-10
                                       HHHHHHHHT-.SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHH.HHHHHHHTHHH.TTCEEEEESTTSHHHHH CS
                   Cys_Met_Meta_PP  58 eeriaaLegg.eaalavssGmaAiaaailallkaGdeivvsddlYgg.tqrllkkvlkk.lgievkfvdtsdleele 131
                                       e+ +++  g+ + ++++ sG+ A+++++++l+++ d++++ +  Yg   +rl+++++kk ++ ++   d+ ++e l 
  gi|518652453|ref|YP_008141973.1|  37 ESLLNKFSGAyKTVMVTGSGTLAVETMVFSLINNNDRVLSIS--YGNfGERLIDSIAKKtTNTQFITHDQLNIETLL 111
                                       566788888856778899********************9987..554258999999988567778888999999999 PP

                                       HHCCT..TEEEEEEESS-TTTT----HHHHHHHHHHTT-EEEEEGT CS
                   Cys_Met_Meta_PP 132 kaike..ntklvylEtptnpllkvvDiekiaklakkagvlvvvDnt 175
                                       + i++    kl+++   t+    + D+++i+k++k++g+ ++vD +
  gi|518652453|ref|YP_008141973.1| 112 EEIRSrdFDKLFLVHNETSNGTAIRDLTEIIKIVKEKGAKLLVDDV 157
                                       99998334799999999999************************85 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   7.2e-10   3.2e-06      50     348 ..      37     323 ..      15     338 .. 0.72

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 7.2e-10
                                       HHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBEETT CS
                     Aminotran_1_2  50 eealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryplysee 126
                                       e+ l kf g     ++k+    v+gsG+ a+  +++ l+  n  d++l+   +y+++ + l  s ++  +      +
  gi|518652453|ref|YP_008141973.1|  37 ESLLNKFSG-----AYKTV--MVTGSGTLAVETMVFSLI--NNNDRVLS--ISYGNFGERLIDSIAKKTTNT----Q 98 
                                       444455555.....23333..566666666666666666..56667664..667777777777666644444....3 PP

                                       TTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHH CS
                     Aminotran_1_2 127 dfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavat 203
                                         + d  ++e++l+e  +++  + +++++  +N t       +l+++++++k++++ l+vD++ +gf+  ++     
  gi|518652453|ref|YP_008141973.1|  99 FITHDQLNIETLLEEIRSRDFDKLFLVHNETSNGTA----IRDLTEIIKIVKEKGAKLLVDDV-SGFAGYNM----- 165
                                       445666666666666666777666888888888664....5789999999************9.55554433..... PP

                                       HGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEEEH.....................HHHHHHHHHHHHHTSSHHHHH CS
                     Aminotran_1_2 204 ranveeepnllivgslsKaf.GlaGeRvGyilgna.....................avvsqlrklsrpflsssllqa 258
                                           ++++  + v++  K++ +++G  +G+i+ +                        ++ l+k  ++ + +s ++ 
  gi|518652453|ref|YP_008141973.1| 166 ---DMNGIY-AMVTGSQKNLaSIPG--IGIIFLSIeayndvmsqvstntpfyldlkTSLKFLEKNETA-YTPSTGAF 235
                                       ...356667.555555699857899..9998886667999*************555555555555554.45777888 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEG CS
                     Aminotran_1_2 259 avaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpg 335
                                       + ++ + + l+k + + ++++r+ ++++++r++L + g++++++++++ + +++   ++ ++  kL+e+ g+ v++g
  gi|518652453|ref|YP_008141973.1| 236 ISLNFALKILEK-EGFANRVKRITSSADFIRSSLSDNGVEIFGNKGTYSSTVVCFYNNDPDMVNKLAEH-GITVSKG 310
                                       887777777765.599******************999********99999999999999*********9.******8 PP

                                       GGGTSTTEEEEEC CS
                     Aminotran_1_2 336 tsftvpgrlRitv 348
                                           + + lR+  
  gi|518652453|ref|YP_008141973.1| 311 MGKLANTTLRVGT 323
                                       8888888899876 PP

>> TA0956  Thermoplasma acidophilum protein TA0956
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   6.7e-05       0.3      64     101 ..      61      98 ..      27     105 .. 0.86
   2 ?   -3.3   0.0       2.3     1e+04      34      49 ..     324     339 ..     301     342 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.7e-05
                                       EEEEEEEEETTTTEEEEEE-S--CCHHHHHHHHHHHHH CS
                            TA0956  64 ktvGfviinsdkkvlslsfselkeelkksikeiaekfk 101
                                       +t+ f +in++ +vls+s+ +  e l++si +++++ +
  gi|518652453|ref|YP_008141973.1|  61 ETMVFSLINNNDRVLSISYGNFGERLIDSIAKKTTNTQ 98 
                                       6899**************************99887665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.3
                                       HHHTTS-.-CCHHHHH CS
                            TA0956  34 advldselieesleef 49 
                                       + ++++++ie+ l+ +
  gi|518652453|ref|YP_008141973.1| 324 MGMINNHYIEKFLNSY 339
                                       4577777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2415.50
//
Query:       gi|518652454|ref|YP_008141974.1|  [L=238]
Description: alanyl-tRNA synthetase [Ferroplasma acidarmanus fer1]
Scores for complete 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   59.4   0.1    3.9e-16   58.7   0.1    1.3  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.9e-10   40.7   0.2    3.3e-10   39.9   0.2    1.4  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.1   4.3e-20   3.9e-16     472     551 ..      12      90 ..       2      91 .. 0.94

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 4.3e-20
                                       XSEEEEEEEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEE CS
                      tRNA-synt_2c 472 dkefveeveegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaev 548
                                       ++ef ++v ++++++vvLd+T fY++sGGq +D+G+++++++e+++ dv +++g + h+++   ++++ g +v++++
  gi|518652454|ref|YP_008141974.1|  12 GREFDASVISVKDNYVVLDKTLFYPTSGGQPNDTGILKTSNGEMKIIDVIQEDGEIRHIADKI-ENVTPGANVHGVI 87 
                                       67999******************************************************9996.9************ PP

                                       XHH CS
                      tRNA-synt_2c 549 dee 551
                                       d++
  gi|518652454|ref|YP_008141974.1|  88 DWD 90 
                                       *96 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 !   39.9   0.2   3.6e-14   3.3e-10       1      43 [.     191     233 ..     191     234 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 3.6e-14
                                       EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEE CS
                          tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRI 43 
                                       vr+++i++++ ++ gGtHv+nTge+g +  l+ e+++kg  R+
  gi|518652454|ref|YP_008141974.1| 191 VRIIEIENFDFQADGGTHVKNTGEVGRIEMLKIENKGKGHKRL 233
                                       8**************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1639.52
//
Query:       gi|518652455|ref|YP_008141975.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G1094 [Ferroplasma acidarmanus fer1]
Scores for complete 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-13   48.3   0.0    2.7e-12   46.8   0.0    1.8  1  DDE_Tnp_1     Transposase DDE domain
  ------ inclusion threshold ------
      0.043   12.9   0.0      0.069   12.2   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0     3e-16   2.7e-12      21     213 ..     181     398 ..     160     399 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 3e-16
                         DDE_Tnp_1  21 edarwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       ++  +g++ ++ + + +++ ++++    l++ +++ pg+  d+ ++  ++d++ + ++++++aD+G++sa+++++l+
  gi|518652455|ref|YP_008141975.1| 181 SFLEPGHNSKEiHLPQINVMMLFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGI-EKCVIVADKGFFSADNIKKLR 256
                                       666778887777889999999999998999999999******************9.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrk................................gaeskrrgrlrkhdrnkiltksqkrr 141
                                       +++++yii+l+ n+ +                                    +e++r+  +r hd+ ++ + +    
  gi|518652455|ref|YP_008141975.1| 257 KRHLSYIIPLRRNSSIIPEngdflnvfmyngkpvkcwkpengvyvfedpvlKSEEERDYLIRIHDNIRPKSSY---- 329
                                       **********999999888766666666665555555554444444333332333333333333333333333.... PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllaln 213
                                           ++ gd   ++++++   ++e + +ly+ R  +E  F   k+++  dr + r+      +++l ll+l 
  gi|518652455|ref|YP_008141975.1| 330 ---YDHSGDFGKLYLLSDINDEPERIYRLYKEREYVEYAFNVYKNDLETDRSYIRDDHMLSSYMFLNLLSLY 398
                                       ...3333444455566666669********************************************999986 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 ?   12.2   0.0   7.7e-06     0.069      71     141 ..     190     257 ..     180     279 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-06
                                       CCTT-EEEESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH CS
                      ANF_receptor  71 nlfkiPvisygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee 141
                                       ++ ++P+i ++     +s+++  ptf+r+ p + + + A+++++ + g  k +++++++      +++l++
  gi|518652455|ref|YP_008141975.1| 190 KEIHLPQINVMM---LFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGIEKCVIVADKGFFSADNIKKLRK 257
                                       567899996544...8999**************************************99666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.20s 00:00:00.71 Elapsed: 00:00:00.36
# Mc/sec: 3808.38
//
Query:       gi|518652456|ref|YP_008141976.1|  [L=220]
Description: hypothetical protein FACI_IFERC00001G1095 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-25   87.3   0.8    2.5e-16   59.5   0.1    2.2  2  Thioredoxin_3   Thioredoxin domain
    1.3e-11   44.5   2.9    5.7e-06   26.5   0.3    2.7  2  Glutaredoxin    Glutaredoxin
    8.5e-09   35.3   1.2    6.5e-05   22.9   0.1    2.2  2  Thioredoxin     Thioredoxin
    2.1e-06   27.4   0.4    0.00091   18.8   0.0    2.1  2  ABC_transp_aux  ABC-type uncharacterized transport system
    0.00091   19.1   0.0       0.11   12.3   0.0    3.0  2  TraF            F plasmid transfer operon protein
     0.0022   18.4   7.1       0.83   10.1   0.7    3.7  2  Thioredoxin_2   Thioredoxin-like domain
     0.0061   16.7   3.7        3.2    7.9   0.0    3.3  3  Thioredoxin_4   Thioredoxin
     0.0065   16.2   0.1       0.35   10.6   0.1    2.1  2  Thioredoxin_9   Thioredoxin
     0.0066   16.2   0.2      0.013   15.2   0.1    1.6  1  MafB19-deam     MafB19-like deaminase
  ------ inclusion threshold ------
      0.043   13.8   0.0       0.08   12.9   0.0    1.4  1  HyaE            Hydrogenase-1 expression protein HyaE
      0.087   13.2   0.0       0.47   10.8   0.0    2.0  2  ArsD            Arsenical resistance operon trans-acting repr
       0.13   12.0   0.0       0.54   10.0   0.0    2.0  2  DSBA            DSBA-like 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 !   26.5   0.0   3.2e-09   4.7e-06       7      76 .]      33     109 ..      24     109 .. 0.78
   2 !   59.5   0.1   1.6e-19   2.5e-16       2      72 ..     137     210 ..     136     214 .. 0.94

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 3.2e-09
                                       SSSSTTCHHHHHHHHHHCHCCT.CEC.EEECCTTHHHH.HHCT-SSSSEEECT......TCEEEESS---CCHHHHH CS
                     Thioredoxin_3   7 gpgCakCpklekavkeaaaekg.ika.evekvtdfeei.ekygVmsvPalvid......gkvvvsGkvpseeeirkl 74 
                                       ++ C++C+++ ++v e+ a ++ i++ +++  ++ +e+ ekygV++ Pa+++       g++ + G +ps++e+ +l
  gi|518652456|ref|YP_008141976.1|  33 SSDCKYCKDTISLVDEVGALSDkINIvKYVY-EKDKEMvEKYGVEKYPATIVArhddkdGRIIYYG-IPSGYEFGSL 107
                                       577*************999885266633334.4445555***********996666666*******.*****99988 PP

                                       HH CS
                     Thioredoxin_3  75 le 76 
                                       +e
  gi|518652456|ref|YP_008141976.1| 108 IE 109
                                       75 PP

  == domain 2  score: 59.5 bits;  conditional E-value: 1.6e-19
                                       EEEE.ESSSSTTCH.HHHHHHHHHCHCCTCECEEECCTTHHHH.HHCT-SSSSEEECTTCEEEESS---CCHHH CS
                     Thioredoxin_3   2 eikv.lgpgCakCp.klekavkeaaaekgikaevekvtdfeei.ekygVmsvPalvidgkvvvsGkvpseeeir 72 
                                       +ikv ++p+C++Cp ++ +a+k a+ +k+ik e+++  +f++  ++ gV +vP++vi++ v++ G+ p+ ++ +
  gi|518652456|ref|YP_008141976.1| 137 TIKVyVTPTCQYCPkAVITAHKFALMNKNIKSEMIESLEFDKEaSDAGVSAVPHIVINDDVTFPGAYPDDQFAE 210
                                       69************99*************************999************************999876 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2   1.9e-06    0.0029       2      53 ..      27      81 ..      26      86 .. 0.91
   2 !   26.5   0.3   3.8e-09   5.7e-06       1      59 [.     138     197 ..     138     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.9e-06
                                      EEEES..TSSHHHHHHHHHHHHTTGGEEEEEGCCSH.HHHHHHHHHHTSSSSSEE CS
                      Glutaredoxin  2 vlftk..ptCpyCkkakrlLkelgvkfeeidvdkde.eireelkelsgvrtvPqv 53
                                      v+f++  + C yCk ++ l +e g+  + i++ k   e  +e+ e+ gv++ P  
  gi|518652456|ref|YP_008141976.1| 27 VVFSSesSDCKYCKDTISLVDEVGALSDKINIVKYVyEKDKEMVEKYGVEKYPAT 81
                                      8999999****************************779999999999***99975 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 3.8e-09
                                       EEEEESTSSHHHHHHHHHHHHTTGGEEEEEGCCSH..HHHHHHHHHHTSSSSSEEEETTEE CS
                      Glutaredoxin   1 vvlftkptCpyCkkakrlLkelgvkfeeidvdkde..eireelkelsgvrtvPqvfidgkh 59 
                                       + ++++ptC yC+ka+ +++++ +  + i  ++ e  e+ +e  +  gv++vP+++i++++
  gi|518652456|ref|YP_008141976.1| 138 IKVYVTPTCQYCPKAVITAHKFALMNKNIKSEMIEslEFDKEASDA-GVSAVPHIVINDDV 197
                                       689****************999855444444444343445555444.***********975 PP

>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.1   4.4e-08   6.5e-05       7      84 ..      13      89 ..       8      97 .. 0.88
   2 !   11.4   0.1   0.00016      0.24      14      81 ..     129     196 ..     117     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.4e-08
                                      HHHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEETTEE CS
                       Thioredoxin  7 kenFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkngke 84
                                       e+F+++++++ +lv+    ++ C  Ck   + ++++  +l+dk+ ++k   ++ +++++ky+ve +P+ ++++++++
  gi|518652456|ref|YP_008141976.1| 13 REDFDKKLKNTVDLVVFSSESSDCKYCKDTISLVDEVG-ALSDKINIVKYVYEKDKEMVEKYGVEKYPATIVARHDDK 89
                                      688*******8888888888999************997.5777*************************9999888775 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00016
                                       HTTTSSEEEEEEE.-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTTSHHHHHHTT-SSSSEEEEEET CS
                       Thioredoxin  14 vakekklvlveFy.ApwCghCkalaPeleklaeelkdkvklakvdvdenedlakkyevegiPtlklfkn 81 
                                       ++k +k++ ++ y  p C  C +   + +k+a   k ++k   ++  e ++ a++ +v+++P +++  +
  gi|518652456|ref|YP_008141976.1| 129 ISKIDKPITIKVYvTPTCQYCPKAVITAHKFALMNK-NIKSEMIESLEFDKEASDAGVSAVPHIVINDD 196
                                       66677888888763689****988888888887777.9**************************87654 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 !    7.0   0.1    0.0023       3.5      21     109 ..      18      98 ..      14     105 .. 0.76
   2 !   18.8   0.0   6.1e-07   0.00091      12      95 ..     121     193 ..     119     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0023
                    ABC_transp_aux  21 knleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygitpvqisveek 97 
                                       k+l++ v + v+ se+ +      ++ k++ +l +e  a s+ ki++  + ++   +++e+ e+yg+++ + + + +
  gi|518652456|ref|YP_008141976.1|  18 KKLKNTVDLVVFSSESSD-----CKYCKDTISLVDEVGALSD-KINIVKYVYE---KDKEMVEKYGVEKYPATIVAR 85 
                                       789999*********973.....3679**************9.7776555555...456799999999888776644 PP

                    ABC_transp_aux  98 delkt.krvymgl 109
                                          k   ++y g+
  gi|518652456|ref|YP_008141976.1|  86 HDDKDgRIIYYGI 98 
                                       4444557777765 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 6.1e-07
                    ABC_transp_aux  12 LsdatkellknleepvtikvylsenlalppelkalekevkdlLeeyaaysggkisvefidpspneeeeeeaeaygit 88 
                                        s+++++l++++++p+tikvy+++         ++  ++  + +++a  ++ +i+ e+i+  ++    +ea+++g++
  gi|518652456|ref|YP_008141976.1| 121 VSKKAVDLISKIDKPITIKVYVTPTC-------QYCPKAVITAHKFALMNK-NIKSEMIESLEFD---KEASDAGVS 186
                                       58999********************5.......44566677899****988.**********998...556666888 PP

                    ABC_transp_aux  89 pvqisve 95 
                                       +v+  v 
  gi|518652456|ref|YP_008141976.1| 187 AVPHIVI 193
                                       8775554 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   7.3e-05      0.11     121     215 ..      14     100 ..       4     104 .. 0.75
   2 ?    2.2   0.0     0.088   1.3e+02     121     155 ..     126     160 ..     115     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.3e-05
                              TraF 121 eaalkklakeygLlfFyr..gkcpyceaqapilqafadkyglevraVsvdgrplpelpnarvdkgqaarlgvkrtPa 195
                                       e++ kkl++ + L++F +  ++c+yc+  +  ++    + g     +++ + +       ++dk+  +++gv+  Pa
  gi|518652456|ref|YP_008141976.1|  14 EDFDKKLKNTVDLVVFSSesSDCKYCKDTISLVD----EVGALSDKINIVKYVY------EKDKEMVEKYGVEKYPA 80 
                                       5555789999999999986678999999887654....4444445555555444......346777789******** PP

                              TraF 196 lvlvdpksqkvvpvaaGlls 215
                                       +++++ + ++  ++ +G+ s
  gi|518652456|ref|YP_008141976.1|  81 TIVARHDDKDGRIIYYGIPS 100
                                       ********999999999866 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.088
                              TraF 121 eaalkklakeygLlfFyrgkcpyceaqapilqafa 155
                                        + ++k+ k   + + + ++c+yc +++ +  +fa
  gi|518652456|ref|YP_008141976.1| 126 VDLISKIDKPITIKVYVTPTCQYCPKAVITAHKFA 160
                                       56788888889999999999****99988877776 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.9    0.0028       4.1      10      86 ..      27      83 ..      19     107 .. 0.57
   2 !   10.1   0.7   0.00056      0.83      42     108 ..     166     211 ..     130     212 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0028
                     Thioredoxin_2 10 vvft..dpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivf 86
                                      vvf+  ++dC yCk    +++ +d+v         +++  + +v+  ++k+k           e ++kygv+  P++++
  gi|518652456|ref|YP_008141976.1| 27 VVFSseSSDCKYCKD---TISLVDEVGAL------SDK--INIVKYVYEKDK-----------EMVEKYGVEKYPATIV 83
                                      444434677777776...55555555444......222..333333444443...........5677777777777554 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00056
                     Thioredoxin_2  42 lkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtivfldgkeivarlpGyvpaeeleal 108
                                       +k++ ++++ +++++++                  gv+++P iv+ d      + pG++p ++++++
  gi|518652456|ref|YP_008141976.1| 166 IKSE-MIESLEFDKEASD----------------AGVSAVPHIVINDDV----TFPGAYPDDQFAEY 211
                                       3222.3333333333333................4**************....9**********986 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.2      0.29   4.3e+02      22      52 ..      33      63 ..      21      95 .. 0.56
   2 !    7.1   0.2    0.0037       5.5      12      48 ..     133     171 ..     128     174 .. 0.78
   3 !    7.9   0.0    0.0021       3.2     128     164 ..     175     212 ..     170     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.29
                                      -TT-HHHHHHHHHHH..HHHHHHHHTTSEEEEE CS
                     Thioredoxin_4 22 dlrCphCakfeeeve..klleeyidtGkvkfii 52
                                      + +C +C++    v     l++      vk+++
  gi|518652456|ref|YP_008141976.1| 33 SSDCKYCKDTISLVDevGALSDK--INIVKYVY 63
                                      56666666655555412223332..22333333 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0037
                                       T-SEEEEEEE-TT-HHHHH..HHHHHHHHHHHHHHTTSE CS
                     Thioredoxin_4  12 dApvtvieyedlrCphCak..feeeveklleeyidtGkv 48 
                                       d p+t+ +y+  +C +C k     + ++l+++ i+++ +
  gi|518652456|ref|YP_008141976.1| 133 DKPITIKVYVTPTCQYCPKavITAHKFALMNKNIKSEMI 171
                                       5699*************7742334444999999998765 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHT--SS-EEEETTEE.E-TT--HHHHHHHH CS
                     Thioredoxin_4 128 aeskeakkagiestPtfiingek.veepqtyeelkali 164
                                       +++kea  ag++++P ++in+ + + ++ + +++ +++
  gi|518652456|ref|YP_008141976.1| 175 EFDKEASDAGVSAVPHIVINDDVtFPGAYPDDQFAEYV 212
                                       578999*************9999789999999988876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.033        50      53     105 ..      36      85 ..       6      97 .. 0.77
   2 !   10.6   0.1   0.00023      0.35      27     105 ..     120     195 ..     112     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                                       -HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE- CS
                     Thioredoxin_9  53 CgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliild 105
                                       C  +  ++  ++++  l+++i++   + ++++e++++y   g ++ P+ i+  
  gi|518652456|ref|YP_008141976.1|  36 CKYCKDTISLVDEVGALSDKINIVKYVYEKDKEMVEKY---GVEKYPATIVAR 85 
                                       6667788899999999999999999999999*****99...778888887765 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00023
                                       HHH---HHHHHT--S-EEEEEE--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEE CS
                     Thioredoxin_9  27 elseeteekiksiekklkilvltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtlii 103
                                        +s++  + i++i+k+++i v  ++ C  +   v   +k+a  n+ni+ +++   e le+ ++ +  g  a+P ++i
  gi|518652456|ref|YP_008141976.1| 120 DVSKKAVDLISKIDKPITIKVYVTPTCQYCPKAVITAHKFALMNKNIKSEMI---ESLEFDKEASDAGVSAVPHIVI 193
                                       577888889***************************************9987...5666666666677788887777 PP

                                       E- CS
                     Thioredoxin_9 104 ld 105
                                        d
  gi|518652456|ref|YP_008141976.1| 194 ND 195
                                       66 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   8.9e-06     0.013      53     118 ..     117     182 ..      75     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.9e-06
                       MafB19-deam  53 aEiaalqqAakklkskrlddat.lyvtlepCdmCagaivqaglkklvygagnpkslnkLkvkekngr 118
                                       +E+++ ++A++ ++++ +  ++ +yvt ++C++C +a++ a    l+ +  + + +++L++ ++   
  gi|518652456|ref|YP_008141976.1| 117 GEADVSKKAVDLISKIDKPITIkVYVT-PTCQYCPKAVITAHKFALMNKNIKSEMIESLEFDKEASD 182
                                       799999999999999854433315666.79***********99999999888888****99988665 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.4e-05      0.08      20      97 ..      17      91 ..       7      95 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.4e-05
                                      HHHHHHHSEEEEEESS-SS-SSSSS-HCHHHHHHHCT-TTS-EEEEEETHHHHHHHHHCCT-TSSSEEEEEETTEEEE CS
                              HyaE 20 ddflkaagdavlllagDpkrfpEvsDvaVvlpEllkaFpnalraavvadreqeealaerfgvlktPsllflrdgeylg 97
                                      d+ lk++ d v++ +++ +    + D+  ++ E+ +   +      v   e+++++ e++gv k+P++++ r+++  g
  gi|518652456|ref|YP_008141976.1| 17 DKKLKNTVDLVVF-SSESSDCKYCKDTISLVDEVGALSDKINIVKYV--YEKDKEMVEKYGVEKYPATIVARHDDKDG 91
                                      5555555565555.455666667888888888876554444444444..599999***************99887666 PP

>> ArsD  Arsenical resistance operon trans-acting repressor ArsD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.86   1.3e+03      62      78 ..      67      83 ..      52      95 .. 0.76
   2 ?   10.8   0.0   0.00031      0.47      40      95 ..     153     209 ..     137     220 .] 0.75

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.86
                              ArsD 62 kellekkgaeaLPlvlv 78
                                      ke++ek g+e+ P ++v
  gi|518652456|ref|YP_008141976.1| 67 KEMVEKYGVEKYPATIV 83
                                      56778888888888877 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00031
                              ArsD  40 gveveRynlaqep..qaFvenkavkellekkgaeaLPlvlvdgeivktgrYptreela 95 
                                        ++ +++ l+++   ++ +e+ + ++  +++g+ a+P ++++++++  g+Yp+++ +a
  gi|518652456|ref|YP_008141976.1| 153 VITAHKFALMNKNikSEMIESLEFDKEASDAGVSAVPHIVINDDVTFPGAYPDDQ-FA 209
                                       556666666665322567788888889999**********************875.44 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.71   1.1e+03      30     173 ..      56      83 ..      29      97 .. 0.58
   2 ?   10.0   0.0   0.00036      0.54     155     191 ..     175     211 ..     146     213 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.71
                                       EEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHHHHHHHGHHHHH CS
                              DSBA  30 vkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarlllaagaeglaekvv 106
                                       +++v                                                                         
  gi|518652456|ref|YP_008141976.1|  56 INIV------------------------------------------------------------------------- 59 
                                       3333......................................................................... PP

                                       HHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEE CS
                              DSBA 107 relfealwsegqaitddqellevaekaGldaeeldealeseavkeavrentaaaqslgvtGvPtvvv 173
                                                                                  k  ++++ ++ +++gv   P+++v
  gi|518652456|ref|YP_008141976.1|  60 -------------------------------------------KYVYEKDKEMVEKYGVEKYPATIV 83 
                                       ...........................................444555555555566655555555 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00036
                                       HHHHHHHHTT-SSSSEEEETTCEEEESSSSHHHHHHH CS
                              DSBA 155 entaaaqslgvtGvPtvvvdgkrmvfGadrldtlada 191
                                       e +++a + gv+ vP +v+++ ++++Ga + d++a++
  gi|518652456|ref|YP_008141976.1| 175 EFDKEASDAGVSAVPHIVINDDVTFPGAYPDDQFAEY 211
                                       56799**************9999**********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:01.11
# Mc/sec: 599.48
//
Query:       gi|518652457|ref|YP_008141977.1|  [L=402]
Description: SoxB-like protein sarcosine oxidase, beta subunit related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-52  179.0   0.0    2.1e-52  178.8   0.0    1.0  1  DAO              FAD dependent oxidoreductase
    4.3e-10   39.3   1.3    3.1e-05   23.3   0.1    2.3  2  Pyr_redox_2      Pyridine nucleotide-disulphide oxidoreductas
    1.4e-08   34.4   0.0      2e-05   24.0   0.0    2.2  2  Pyr_redox_3      Pyridine nucleotide-disulphide oxidoreductas
    1.9e-07   30.1   0.3     0.0018   17.0   0.2    2.4  2  HI0933_like      HI0933-like protein
      5e-07   30.2   0.2    5.2e-05   23.7   0.1    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
    1.8e-06   27.3   0.2    0.00028   20.1   0.0    2.2  2  GIDA             Glucose inhibited division protein A
    2.5e-06   27.6   0.4    6.4e-06   26.3   0.4    1.7  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
    1.1e-05   24.7   1.0    2.8e-05   23.4   0.3    1.8  2  FAD_binding_2    FAD binding domain
    1.3e-05   24.8   0.4    6.5e-05   22.4   0.4    1.9  1  FAD_oxidored     FAD dependent oxidoreductase
    1.8e-05   24.8   0.1        1.1    9.3   0.1    3.1  3  NAD_binding_9    FAD-NAD(P)-binding
    0.00029   20.2   0.3    0.00052   19.3   0.3    1.3  1  Thi4             Thi4 family
    0.00045   19.6   0.0     0.0032   16.8   0.0    2.0  2  Amino_oxidase    Flavin containing amine oxidoreductase
     0.0031   16.8   0.1     0.0054   16.0   0.1    1.3  1  FAD_binding_3    FAD binding domain
     0.0064   16.1   0.4      0.022   14.4   0.2    1.9  2  ApbA             Ketopantoate reductase PanE/ApbA
     0.0065   15.7   0.3      0.021   14.0   0.1    1.8  2  K_oxygenase      L-lysine 6-monooxygenase (NADPH-requiring)
  ------ inclusion threshold ------
      0.015   15.2   0.1      0.027   14.4   0.1    1.4  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.019   14.9   0.1      0.047   13.7   0.1    1.7  1  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      0.024   13.5   0.2       0.16   10.8   0.1    1.9  2  Trp_halogenase   Tryptophan halogenase
      0.025   14.0   0.4        3.3    7.0   0.1    2.4  2  GMC_oxred_N      GMC oxidoreductase
      0.057   13.7   0.9       0.57   10.5   0.2    2.3  2  TrkA_N           TrkA-N domain
       0.11   11.7   0.0       0.19   10.9   0.0    1.3  1  Methyltransf_20  Putative methyltransferase
       0.16   12.4   0.0       0.34   11.4   0.0    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.23   10.5   0.1       0.39    9.7   0.1    1.3  1  Lycopene_cycl    Lycopene cyclase protein


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 !  178.8   0.0   2.7e-55   2.1e-52       2     352 .]      10     364 ..       9     364 .. 0.84

  Alignments for each domain:
  == domain 1  score: 178.8 bits;  conditional E-value: 2.7e-55
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHHSTHHHHHHHHHHHHHHHHHHHHHS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylpeaselarlslealeelreleeelg 76 
                                       v+++GGG  G s+Ay La rg  V l+e+g+ia+ g +g++s+l++ +++  +    +  l+l++++e+  + ++ g
  gi|518652457|ref|YP_008141977.1|  10 VIVVGGGSSGTSIAYNLANRGkkVKLIERGNIAS-GNTGKSSALVRTHYS-NE---LISSLALYSIREFMNFGNT-G 80 
                                       9*******************99********7776.************775.55...788**********999987.8 PP

                                       STTSEEEEEEEEEESSHHHHHHHHHHHHHHHHTTTTEEEEEHHHHHHHSTT..STTTSEEEEETTEEEEEHHHHHHH CS
                               DAO  77 ididyrrtGllslaadeeelealdkllallleagldaelldaeevrelepa..lpgllgalfypdtgqvdpakltaa 151
                                          ++ +tG+++ + +++ lea+ k++++l+++g+ ++ ++ +ev+e +p   ++g+   l++pd+g +dp +  +a
  gi|518652457|ref|YP_008141977.1|  81 Y-SGFTKTGMVFPFNGSNALEAS-KNFKMLKSLGINEKEISLKEVKEFFPDisTEGYDYILYEPDSGYADPVATSNA 155
                                       7.89***********99999999.99****99***887788888******8654499999***************** PP

                                       HHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.HH.HTT....CTTT.SEEEEE CS
                               DAO 152 laraaealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.ll.gll....keld.lpispv 220
                                       +a+aa++lG+ei++g  v+ ++  d++ ++v  +t  ge+++ada+V+a++ w++ ll +         d lpi++ 
  gi|518652457|ref|YP_008141977.1| 156 YASAAKNLGAEIVTGKSVKTVSS-DNGMAHV--ETYnGEKFSADAIVLATNTWTNdLLqR-SgvssA--DlLPIYAS 226
                                       ***************99999966.4566899..6666999777************87753.334443..44899999 PP

                                       EEEEEEEEECCTHSTGSG.CSEEEEEEEETTTTEEEEEETTSEEEE.EESSE........EETTCSS..TSCSHHHH CS
                               DAO 221 rgqvlvlkplseklvspa.ailpvpetdddgrgvyvtprkdgrvlv.Ggtad........eesgddd..pevdeedi 285
                                        +  + l++++e     +  i p++ +d ++ ++y +   + ++ + G+ +         +   d+d    +++e i
  gi|518652457|ref|YP_008141977.1| 227 VHDTIYLRRPEE-----YtGIKPTL-WDPQNSSYYKME--GASITAiGSLDPaidtrefdP---DGDieNHITDEYI 292
                                       999999966666.....33788888.777766655544..455665266655999985533...333457******* PP

                                       HHHHHHHHHHSGGG..CGEEEEEEEEEEE.TTSSEEEEEEE..TEEEEEEEEECTTTHHHHHHHHHHHHHHH CS
                               DAO 286 dellealrklfPql..gdvlrkwaGlrpl.pdglpligetp..gvkglylatGhsghGltlapatGkllael 352
                                       +++l +l +++P+   ++v ++ +Gl+++ pdg  +i+  +  g +++y+++G sghG++l+pa G+++a++
  gi|518652457|ref|YP_008141977.1| 293 EQYLGKLTDRLPGManASVISTVSGLYDMsPDGQAIIDSLSgiGLDNVYVCAGLSGHGFKLSPAYGRIVADM 364
                                       *************73466889*******769*******94478999************************97 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1     4e-08   3.1e-05       2      58 ..       9      80 ..       8     140 .. 0.72
   2 !   14.8   0.0   1.7e-05     0.013     185     241 ..     152     208 ..     145     219 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4e-08
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH................H CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................x RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias................e 58
                                      +v+v+GgG  G++ a +la+ g kv l+ ++g++  g    s+al+++    e +s                 
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANRGKKVKLI-ERGNIASGNTGKSSALVRTHYSNELISslalysirefmnfgntG 80
                                      79**************************.88888888888888888777777666666666665455444440 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.7e-05
                                       HHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 185 lsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpst 241
                                        s+a++ a ++ G e+++g+svk++ +++  ++v++ +ge++ ad +v+a+    ++
  gi|518652457|ref|YP_008141977.1| 152 TSNAYASAAKNLGAEIVTGKSVKTVSSDNGMAHVETYNGEKFSADAIVLATNTWTND 208
                                       5788999999*******************9777****************98555554 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 !   24.0   0.0   2.5e-08     2e-05     165     220 ..       8      63 ..       2     112 .. 0.88
   2 !    8.3   0.0    0.0016       1.2      87     133 ..     156     203 ..     143     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2.5e-08
                       Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrlee 220
                                       + v+V+Gg+ S+  +A++l+++g++V+++ rg+  + +  + s+ ++ ++ n+l +
  gi|518652457|ref|YP_008141977.1|   8 NSVIVVGGGSSGTSIAYNLANRGKKVKLIERGNIASGNTGKSSALVRTHYSNELIS 63 
                                       689*****************************987777788888999999888855 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0016
                       Pyr_redox_3  87 lrevaksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtG 133
                                       +++ ak+   +i + ++V++v+++++  +vet ++ +++A+ +++At 
  gi|518652457|ref|YP_008141977.1| 156 YASAAKNLGAEIVTGKSVKTVSSDNGMAHVETYNGeKFSADAIVLATN 203
                                       56677778889999999********9****998866999**9999995 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.2   2.3e-06    0.0018       2      33 ..       9      40 ..       8      45 .. 0.93
   2 !   10.7   0.0   0.00019      0.15     114     162 ..     155     202 ..     142     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 2.3e-06
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                                      +viv+GgG +G   A ++a+rgk+V l+e+++
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANRGKKVKLIERGN 40
                                      69***************************986 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00019
                                       HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE-- CS
                       HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAt 162
                                       a+ +++k+ g ++ + ++vk+v++ ++g  +v+t ++e+++ad++vlAt
  gi|518652457|ref|YP_008141977.1| 155 AYASAAKNLGAEIVTGKSVKTVSS-DNGMAHVETYNGEKFSADAIVLAT 202
                                       6778999***************76.5666999999*************7 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.1   6.6e-08   5.2e-05       1      32 [.       9      40 ..       9      61 .. 0.90
   2 ?    4.0   0.0     0.096        75      44      78 ..     154     187 ..     145     191 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.6e-08
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSS CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversd 32
                                      +v+vvGgG +g   A +la+ gkkV+++er++
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANRGKKVKLIERGN 40
                                      699***************************86 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.096
                                       HHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEEE CS
                         Pyr_redox  44 kilqeklekngievllntkveeiegsedgvesvkl 78 
                                       ++ +   +++g e++++++v+ +  ++ g+ +v++
  gi|518652457|ref|YP_008141977.1| 154 NAYASAAKNLGAEIVTGKSVKTVSSDN-GMAHVET 187
                                       4555566777**************666.4788876 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.6e-07   0.00028       2      36 ..      10      53 ..       9      75 .. 0.79
   2 ?    5.2   0.0     0.012       9.5     116     154 ..     171     208 ..     153     218 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.6e-07
                                      EEEE-SSHHHHHHHHHHHHTT--EEEE.........ES-GGGTT CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLi.........thkldtia 36
                                      viV+GgG +G+  A+++a++G kv+Li         t k + ++
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIergniasgnTGKSSALV 53
                                      9**************************77777766654544444 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.012
                                       S-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT- CS
                              GIDA 116 eeveeliveekkvkgvvtedgetikakavviatGtflkg 154
                                       ++v+ +  +++ ++ v t +ge+++a+a+v+at t+ + 
  gi|518652457|ref|YP_008141977.1| 171 KSVKTV-SSDNGMAHVETYNGEKFSADAIVLATNTWTND 208
                                       345555.66899999******************997765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.4   8.2e-09   6.4e-06       1      35 [.      12      46 ..      12      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.2e-09
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGra 35
                                      +vG+G sG ++Ay La++g++v l+e+++  +G+ 
  gi|518652457|ref|YP_008141977.1| 12 VVGGGSSGTSIAYNLANRGKKVKLIERGNIASGNT 46
                                      8******************************9986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.3   3.6e-08   2.8e-05       2      45 ..      10      53 ..       9      61 .. 0.93
   2 ?   -0.9   0.0      0.83   6.5e+02     183     208 ..     186     211 ..     155     220 .. 0.65

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 3.6e-08
                                      EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-E CS
                     FAD_binding_2  2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgi 45
                                      viV+G+G +G + A+++a++G+kv ++e ++  +g+t  s++ +
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIERGNIASGNTGKSSALV 53
                                      9************************************9999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.83
                                       TTTCEEEEEESEEEE-----GG.... CS
                     FAD_binding_2 183 esgrevrirakavvlatgGfgrallk 208
                                       e+ + +++ a+a+vlat  + ++ll+
  gi|518652457|ref|YP_008141977.1| 186 ETYNGEKFSADAIVLATNTWTNDLLQ 211
                                       33344578999*****9999975544 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.4   8.4e-08   6.5e-05       2      67 ..      10      77 ..       9     218 .. 0.57

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 8.4e-08
                      FAD_oxidored  2 vvVvGGgpaGvaAAiaAaraGakvlLveergvlGGll..tsglvatdignkaeeqvvtgiareflerl 67
                                      v+VvGGg++G+  A+  a++G+kv L+e+ +   G++  +s+lv t   n+  ++++   +ref++  
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIERGNIASGNTgkSSALVRTHYSNELISSLALYSIREFMNFG 77
                                      9**********************************975566777776666655555555555555544 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0019       1.4       2      33 ..      12      38 ..      11      66 .. 0.79
   2 !    9.3   0.1    0.0014       1.1     108     153 ..     156     202 ..     150     204 .. 0.73
   3 ?    3.0   0.0      0.12        93      83     154 ..     275     345 ..     250     347 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0019
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                      +vG+G +G++++ +L++r       +++l+++
  gi|518652457|ref|YP_008141977.1| 12 VVGGGSSGTSIAYNLANRG-----KKVKLIER 38
                                      8***************995.....55666666 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.0014
                     NAD_binding_9 108 larlpegvtvevhra.evvdleeradgqavlladgaslaadaVvLAl 153
                                        a++ +++  e++++ +v  ++ +++ ++v + +g+++ ada+vLA+
  gi|518652457|ref|YP_008141977.1| 156 YASAAKNLGAEIVTGkSVKTVSSDNGMAHVETYNGEKFSADAIVLAT 202
                                       45555666677776625555665555569*9***************8 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.12
                     NAD_binding_9  83 eeldpddfvpRalyGrYlrdlfeellarlpegvtvevhraevvdlee.radgqavlladgaslaadaVvLAlG 154
                                       +e+dpd  +   +  +Y+++++ +l++rlp  +    + ++v  l + ++dgqa+  ++ + + +d+V ++ G
  gi|518652457|ref|YP_008141977.1| 275 REFDPDGDIENHITDEYIEQYLGKLTDRLPG-MANASVISTVSGLYDmSPDGQAI-IDSLSGIGLDNVYVCAG 345
                                       567777777778889**************86.55666666777765526677655.67777788888888877 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.3   6.7e-07   0.00052      19      51 ..       9      40 ..       2      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 6.7e-07
                                      EEEEE--SHHHHHHHHHHHHCTTS-EEEEESSS CS
                              Thi4 19 DvvivGaGssGLtaayylakkpdlkvailersv 51
                                       v++vG+GssG + ay la++ + kv ++er  
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANR-GKKVKLIERGN 40
                                      69*******************.********953 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.34   2.6e+02       2      23 ..      18      39 ..      17      45 .. 0.90
   2 !   16.8   0.0   4.1e-06    0.0032     206     261 ..     143     203 ..      47     212 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.34
                                      HHHHHHHHHHHTTEEEEEEESS CS
                     Amino_oxidase  2 aGLaaArqLlsaGfdVtvlEar 23
                                      +G + A+ L+++G +V ++E  
  gi|518652457|ref|YP_008141977.1| 18 SGTSIAYNLANRGKKVKLIERG 39
                                      78899***************86 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.1e-06
                                       TTHTHHHHHHHHH.....TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
                     Amino_oxidase 206 rgGlsqlpealae.....elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                                       + G++ ++ +  +     + +g +i +++ Vk ++ +++   v++ +ge+++aDa+v+++ 
  gi|518652457|ref|YP_008141977.1| 143 DSGYADPVATSNAyasaaKNLGAEIVTGKSVKTVSSDNGMAHVETYNGEKFSADAIVLATN 203
                                       55555555554445556689**************************************986 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   6.9e-06    0.0054       3      39 ..       9      45 ..       8      62 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.9e-06
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCS CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvl 39
                                      +V++VG+G +G + a  L+++G +v l+e+ + ++ +
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANRGKKVKLIERGNIASGN 45
                                      69****************************8766655 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.2   2.9e-05     0.022       1      34 [.      10      42 ..      10      61 .. 0.88
   2 ?   -1.5   0.0       2.2   1.7e+03      95     111 ..     172     188 ..     151     210 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHHHH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsrrle 34
                                      + ++G G+ G+ +a++La+ g +v li r++ ++
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIERGN-IA 42
                                      579**************************99.44 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                                       CEEEEEESSSSCHHHHH CS
                              ApbA  95 ntvvlllqNGlgheeel 111
                                         ++++  NG+ h e+ 
  gi|518652457|ref|YP_008141977.1| 172 SVKTVSSDNGMAHVETY 188
                                       35677788888887765 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 !   14.0   0.1   2.7e-05     0.021     189     225 ..       5      39 ..       1      69 [. 0.73
   2 ?   -0.9   0.0       0.9     7e+02     117     338 ..     171     202 ..     155     206 .. 0.50

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
                       K_oxygenase 189 lakkriaVvGsGqSaaeifedllrrqkkvelklvtrs 225
                                       ++ ++++VvG+G S+  i+++l++r k  ++kl+ r+
  gi|518652457|ref|YP_008141977.1|   5 KHINSVIVVGGGSSGTSIAYNLANRGK--KVKLIERG 39 
                                       56789********************99..55666555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.9
                       K_oxygenase 117 eeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkr 193
                                       ++v++v+ d+                                                                   
  gi|518652457|ref|YP_008141977.1| 171 KSVKTVSSDNG------------------------------------------------------------------ 181
                                       33333333332.................................................................. PP

                       K_oxygenase 194 iaVvGsGqSaaeifedllrrqkkvelklvtrsealeplddspfvneifsPeyvdyfyslpeekreallkeqkatnyk 270
                                                                                                                    
  gi|518652457|ref|YP_008141977.1|   - -----------------------------------------------------------------------------   -
                                       ............................................................................. PP

                       K_oxygenase 271 gvdaelieelyeelyeqkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdavvlAT 338
                                                                                      + + e+ + e+ ++da+vlAT
  gi|518652457|ref|YP_008141977.1| 182 -----------------------------------------------MAHVETYNGEKFSADAIVLAT 202
                                       ...............................................334444445555555555555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   3.5e-05     0.027       2      32 ..      10      40 ..       9      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 3.5e-05
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                                      v v+G G  G++ia+ +a++g +V+l+++ +
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIERGN 40
                                      88*************************9854 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1     6e-05     0.047       2      31 ..      10      39 ..       9      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-05
                                      EEEE--SHHHHHHHHHHHTTT--EEEE-S- CS
                    NAD_Gly3P_dh_N  2 iavlGaGswGtalAkvlaenghevrlwvre 31
                                      + v+G+Gs Gt++A  la++g++v+l+ r 
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIERG 39
                                      88***********************99875 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00021      0.16       2      45 ..      10      50 ..       9      70 .. 0.86
   2 ?    0.3   0.0       0.3   2.4e+02     163     204 ..     159     199 ..     149     211 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00021
                                      EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE- CS
                    Trp_halogenase  2 ivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeat 45
                                      +++vGGG++G   A  la+ +    +v+l+e  +i   + G+++
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRG---KKVKLIERGNIASGNTGKSS 50
                                      89*****************99...46*********999999954 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.3
                                       HHHHCT-EEEE--EEEEEE-TTS-EEEEEETTS-EEE-SEEE CS
                    Trp_halogenase 163 vaearGvtrvegkvvevqldedgrveslrledgreveadlfi 204
                                        a++ G ++v gk+v+++  ++g  +++++ +g++++ad ++
  gi|518652457|ref|YP_008141977.1| 159 AAKNLGAEIVTGKSVKTVSSDNG-MAHVETYNGEKFSADAIV 199
                                       57788*********998877766.6899999******99776 PP

>> GMC_oxred_N  GMC oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0043       3.3       3      36 ..      10      42 ..       8      73 .. 0.79
   2 ?    4.6   0.0     0.023        18     151     202 ..     151     203 ..     144     216 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                       GMC_oxred_N  3 elveggGsagsvvAaRLsedpstsvlvleaggre 36
                                       +v+ggGs g+ +A+ L++ ++ +v ++e g   
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGK-KVKLIERGNIA 42
                                      599***************9875.68888888654 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.023
                       GMC_oxred_N 151 plnkallkaaeelGlp.vprdlngk..hqcGvcllgvtcrtgarqstarawLrpa 202
                                       ++++a  +aa++lG + v+  + +   ++ G+ +++  + +g+++s++  +L  +
  gi|518652457|ref|YP_008141977.1| 151 ATSNAYASAAKNLGAEiVTGKSVKTvsSDNGMAHVE--TYNGEKFSADAIVLATN 203
                                       56789999********85555555567999999999..9******9998777654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.2   0.00073      0.57       1      29 [.      10      38 ..      10      42 .. 0.92
   2 ?    1.2   0.0      0.54   4.2e+02      32      66 ..     183     221 ..     155     231 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00073
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEES CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidk 29
                                      +i++G G  G+s+a +L ++gk+v +i++
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNLANRGKKVKLIER 38
                                      79*****************7778****96 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.54
                                       HHHHHHHHTTSE....EEES-TTSHHHHHHTTGGGESEE CS
                            TrkA_N  32 erveelreegle....vvvgdatdeevLeeagiekadav 66 
                                       ++ve++  e++     v+  +    ++L++ g+++ad++
  gi|518652457|ref|YP_008141977.1| 183 AHVETYNGEKFSadaiVLATNTWTNDLLQRSGVSSADLL 221
                                       456666655533344466677778899999999999987 PP

>> Methyltransf_20  Putative methyltransferase
   #    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     204     234 ..     306     336 ..     299     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00024
                   Methyltransf_20 204 lePrptlaivsGlyelfpdndlvkrslaGla 234
                                       ++ ++ ++ vsGly++ pd +++ +sl+G++
  gi|518652457|ref|YP_008141977.1| 306 MANASVISTVSGLYDMSPDGQAIIDSLSGIG 336
                                       566778999********************96 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 ?   11.4   0.0   0.00044      0.34       9      39 ..       9      39 ..       2     105 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00044
                     NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvape 39
                                      +v+vvGgG+ +++ +++l++ g+kv+++   
  gi|518652457|ref|YP_008141977.1|  9 SVIVVGGGSSGTSIAYNLANRGKKVKLIERG 39
                                      799************************8776 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1    0.0005      0.39       2      34 ..      10      40 ..       9      47 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0005
                     Lycopene_cycl  2 vvviGaGpAglslAarlteakpglkvvlieasp 34
                                      v+v+G+G  g s+A +l  a+ g kv lie ++
  gi|518652457|ref|YP_008141977.1| 10 VIVVGGGSSGTSIAYNL--ANRGKKVKLIERGN 40
                                      8****************..99999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); 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: 0.64u 0.33s 00:00:00.97 Elapsed: 00:00:00.52
# Mc/sec: 2319.54
//
Query:       gi|518652458|ref|YP_008141978.1|  [L=88]
Description: hypothetical protein FACI_IFERC00001G1097 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       277  (0.0154498); 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: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 698.72
//
Query:       gi|518652459|ref|YP_008141979.1|  [L=229]
Description: 3-dehydroquinate dehydratase [Ferroplasma acidarmanus fer1]
Scores for 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   62.2   0.0      1e-16   61.9   0.0    1.1  1  DHquinase_I  Type I 3-dehydroquinase
  ------ inclusion threshold ------
      0.037   13.6   0.0      0.065   12.9   0.0    1.4  1  DAGK_cat     Diacylglycerol kinase catalytic domain


Domain annotation for each model (and alignments):
>> DHquinase_I  Type I 3-dehydroquinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.0   1.1e-20     1e-16      27     228 ..      43     219 ..      32     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 1.1e-20
                                       EEEGGG-.TT.THHHHHHHHHHHHHHTTS-EEEE---GGGT-S.SSS-HHHHHHHHHHHHHCT-SEEEEEGG-.HHG CS
                       DHquinase_I  27 ElRlDllketseaedvseeleelrstsdlpliftlrtkaeggrfkrkseeeylellrtaielgadyvDvElteapee 103
                                       E+R Dl++++ + +++++ l  l s +++  ift+r++          ++e ++++ ta+++ + ++D+++      
  gi|518652459|ref|YP_008141979.1|  43 EIRYDLFNDK-SLKNLEDMLMYLNS-HKVDYIFTFRSAD---------KNEIEKVYGTALKFSPPVIDIDIK----- 103
                                       9******766.6799********99.8*********744.........456799*****************3..... PP

                                       HHHHHHHHHHHTT-EEEEEEEESS----HHHHHHHHHHHHHTT-SEEEEEE--SSHHHHHHHHHHHHHHHHHT-SS- CS
                       DHquinase_I 104 skkrlieekreggtkvIvSyhdfegtpsaeelkallekmqalgaDivKiavmaksieDvlrllsltseakeekdeap 180
                                       s  +  +++  +++k+++S+h  ++    +++ alle m +++ Di+Kia   ++ie  l+ l+  +  ++ k+ ++
  gi|518652459|ref|YP_008141979.1| 104 SF-TFNRNM-FNNSKLMISFHGDNN----DDVPALLEDMSEFNPDIYKIALAYTDIEKFLKDLNYLYAYRK-KNGIK 173
                                       23.556666.8********996664....56899**************************99999876666.578** PP

                                       EEEEE-TTTTGHHHCHHHHHTB-EEEEESSS-..SSTT-EEHHHHHHH CS
                       DHquinase_I 181 lIamamGelGkiSRilgevfGspvtfasleeakasapGqltarelrei 228
                                       l  + mG++  + R+++ ++ s +++as +++  +apGq++ ++ + +
  gi|518652459|ref|YP_008141979.1| 174 LAYIPMGSENSFLRVVSAYLVSDYSYASYTQP--TAPGQISKEQFQAV 219
                                       ****************************8888..******99987765 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.3e-06     0.065      74     100 ..     162     189 ..     156     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.3e-06
                                       HHCT.HHCTTSEEEEEE-SS--HHHHHC CS
                          DAGK_cat  74 glle.elatkpplgiiPlGtgNdlaral 100
                                        l   ++++ ++l++iP+G+ N++ r +
  gi|518652459|ref|YP_008141979.1| 162 YLYAyRKKNGIKLAYIPMGSENSFLRVV 189
                                       5555678899***************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); 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 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1788.78
//
Query:       gi|518652460|ref|YP_008141980.1|  [L=209]
Description: multiple antibiotic resistance protein marC [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  187.1  16.7    2.7e-55  186.9  16.7    1.0  1  MarC      MarC family integral membrane protein
     0.0023   16.9   1.1     0.0023   16.9   1.1    1.6  2  MscS_TM   Mechanosensitive ion channel inner membrane domain 


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 !  186.9  16.7     3e-59   2.7e-55       3     203 .]       6     207 ..       4     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 186.9 bits;  conditional E-value: 3e-59
                              MarC   3 aiikafvsLlaiinplgnvpvflslleevskeerkrialkasilallillvfllfGelilklfgisidalkiaGgil 79 
                                        +i +fv L+ai+np+g+vp++++l+  +s +erk+++++ + +a  +++ f+++G +i++++gisi  + iaGgil
  gi|518652460|ref|YP_008141980.1|   6 LFITVFVALFAIMNPIGAVPILITLTDGYSLKERKEVIRRSVYMASGMVFGFMFLGVYIFDILGISIYDFEIAGGIL 82 
                                       5899************************************************************************* PP

                              MarC  80 lfliaidmlkakqkkekkkkseeeeseekdeiavvPLAlPliaGPgaittvlvlasea.ssivekvavvlaillaal 155
                                       lf++++dml++k++++k  + e+++s++++ ia+ P+ +Pl+aGPg+itt ++  ++a  +i ++++vvla++l+++
  gi|518652460|ref|YP_008141980.1|  83 LFKVGFDMLQGKTSTTKITNAEQQDSADREGIAIAPIGTPLLAGPGTITTAIIYFNRAgIDIFSRLMVVLAVILVLV 159
                                       **************************************************99988776157**************** PP

                              MarC 156 itllilllsslilrllgktginaleRlmGllLvalavqlivdGikeil 203
                                       ++++il++s  i +++gktg  +++R+mGllL+a+av+li +Gi +i+
  gi|518652460|ref|YP_008141980.1| 160 LAFIILRYSLPIFQKIGKTGSIVISRIMGLLLTAIAVDLITTGIIHIF 207
                                       ********************************************8875 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 ?   -1.8   0.3      0.12   1.1e+03     165     174 ..       8      17 ..       1      62 [. 0.59
   2 !   16.9   1.1   2.6e-07    0.0023     130     211 ..     117     199 ..     103     204 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.12
                           MscS_TM 165 lllavflarl 174
                                       ++++v l+ +
  gi|518652460|ref|YP_008141980.1|   8 ITVFVALFAI 17 
                                       2222222222 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.6e-07
                           MscS_TM 130 ilvllplll...vlilaealsdalardvlGrlaflllllllavflarllrpalglyankkeeeknslrlrrllylll 203
                                       + + +pll+   ++++a  + +++  d ++rl+++l+++l++v+++ +lr +l+ +++    ++ s+++ r++ lll
  gi|518652460|ref|YP_008141980.1| 117 APIGTPLLAgpgTITTAIIYFNRAGIDIFSRLMVVLAVILVLVLAFIILRYSLPIFQKIG--KTGSIVISRIMGLLL 191
                                       567778888888999999****************************************93..334459********9 PP

                           MscS_TM 204 vlaPlala 211
                                       +++ + l+
  gi|518652460|ref|YP_008141980.1| 192 TAIAVDLI 199
                                       99887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1267  (0.0706676); expected 358.6 (0.02)
Passed bias filter:                      541  (0.0301746); 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):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 1307.41
//
Query:       gi|518652461|ref|YP_008141981.1|  [L=493]
Description: hypothetical protein FACI_IFERC00001G1100 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.1e-15   54.6   0.0      4e-09   36.1   0.0    2.5  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
      5e-13   48.7   0.0    4.7e-06   25.7   0.0    3.1  3  AAA_32           AAA domain
    9.4e-11   41.7   0.0    3.7e-05   23.5   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    5.2e-09   36.2   0.0    0.00027   20.9   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    3.6e-07   30.1   0.0      0.028   14.2   0.0    2.3  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    1.4e-05   25.5   0.0     0.0077   16.6   0.0    2.6  2  AAA              ATPase family associated with various cellul
    0.00011   21.3   0.0      0.058   12.5   0.0    2.3  2  MCM              MCM P-loop domain
    0.00024   21.4   0.0      0.038   14.3   0.0    3.1  3  AAA_22           AAA domain
    0.00073   19.3   0.0     0.0013   18.5   0.0    1.3  1  IstB_IS21        IstB-like ATP binding protein
     0.0032   17.9   0.0     0.0069   16.8   0.0    1.5  1  AAA_16           AAA ATPase domain
      0.005   17.0   0.0       0.24   11.5   0.0    2.3  2  Sigma54_activ_2  Sigma-54 interaction domain
     0.0061   16.9   0.0        1.9    8.8   0.0    2.4  2  AAA_19           AAA domain
     0.0062   16.1   0.0      0.014   15.0   0.0    1.5  1  AAA_7            P-loop containing dynein motor region
  ------ inclusion threshold ------
      0.015   15.3   0.6      0.026   14.5   0.6    1.3  1  DZR              Double zinc ribbon
      0.016   15.2   0.0        3.9    7.5   0.0    2.9  3  AAA_14           AAA domain
      0.018   14.9   2.9      0.034   14.0   2.9    1.4  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.025   14.0   0.0       0.12   11.8   0.0    2.0  2  TniB             Bacterial TniB protein
      0.026   13.8   0.1       0.54    9.4   0.0    2.5  3  TIP49            TIP49 P-loop domain
      0.026   15.0   0.0      0.067   13.7   0.0    1.7  1  ABC_tran         ABC transporter
      0.032   13.9   0.0      0.053   13.2   0.0    1.3  1  TackOD1          Thaumarchaeal output domain 1
      0.054   13.2   0.0        0.2   11.3   0.0    1.9  2  AAA_30           AAA domain
      0.059   13.5   0.0        5.8    7.0   0.0    2.7  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.067   12.6   6.8       0.13   11.7   6.8    1.4  1  zf-ribbon_3      zinc-ribbon domain
      0.069   12.6   0.0       0.13   11.7   0.0    1.4  1  SMC_N            RecF/RecN/SMC N terminal domain
      0.088   12.7   0.0       0.48   10.3   0.0    2.0  2  Rad17            Rad17 P-loop domain
       0.11   12.3   0.0       0.27   11.0   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
       0.14   11.2   0.0       0.24   10.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.17   11.6   2.0       0.43   10.4   0.2    2.1  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.58   10.0   7.7        1.1    9.0   7.7    1.5  1  zinc_ribbon_2    zinc-ribbon domain
        1.9    7.9   4.9        3.4    7.1   4.9    1.4  1  zf-RanBP         Zn-finger in Ran binding protein and others


Domain annotation for each model (and alignments):
>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   6.8e-12     4e-09       2      49 ..      23      70 ..      22      94 .. 0.90
   2 !   15.8   0.0   1.2e-05     0.007      97     158 ..     265     333 ..     257     345 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.8e-12
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllppl 49
                                      l  v+Gqeea r   iaa  + nlllvGppG GK+m+a++++  +++ 
  gi|518652461|ref|YP_008141981.1| 23 LDRVIGQEEAVRLALIAAKQRRNLLLVGPPGVGKSMIAQAMSFYISRP 70
                                      6789************************************98776654 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 1.2e-05
                      Mg_chelatase  97 pkpGeislahnGvLfLDElpef...krkvlevLRe...Pledgevtisrakakv.efparfqlvaamNp 158
                                       +  G + +ah+GvLf+DE++++   +r +l ++ e   P+  ++ + + a+ kv + p++f lvaa N 
  gi|518652461|ref|YP_008141981.1| 265 VVAGSVHMAHEGVLFIDEITHLgnlQRFILTAMQErkfPIVGRNPQSAGASVKVdDVPTDFILVAACNI 333
                                       6789**************987521156666666543447766666666666666468888888888885 PP

>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00025      0.15       5      76 ..      21      86 ..      19      88 .. 0.74
   2 !    8.5   0.0    0.0012      0.73     291     341 ..     228     281 ..     174     304 .. 0.87
   3 !   25.7   0.0   7.8e-09   4.7e-06     421     509 ..     356     448 ..     352     450 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                            AAA_32  5 epleeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeeP 76
                                      +pl+++igqe    a++++l   k+  N+ ++G++g+G++++++ +   i++     +++  v+n + pe+P
  gi|518652461|ref|YP_008141981.1| 21 NPLDRVIGQEE---AVRLALIAAKQRRNLLLVGPPGVGKSMIAQAMSFYISRP---EEEIRVVHNPSYPERP 86
                                      588999**985...67899999999***************9998876544322...3345556666655555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                            AAA_32 291 gaPVvvednptyanLfGkieyesemg..alvt.dftlIkaGaLhkAnGGyLild 341
                                         P v  +  + ++L+G + ++ + g   l t  ++++ aG++h A+ G+L +d
  gi|518652461|ref|YP_008141981.1| 228 RNPFVLATGASETELLGDVRHDPYGGhpQLGTmPYERVVAGSVHMAHEGVLFID 281
                                       578999999999***********999654444269****************987 PP

  == domain 3  score: 25.7 bits;  conditional E-value: 7.8e-09
                            AAA_32 421 Fddemerteenekkyarfiasivk.kekllpfdrsavarlieyssrlaedqek...lstrfseiadllrEAdywakk 493
                                       ++++++ t+en  ky++fia+ ++ + k+++++ +a   +i+++ r a +++k   l+++++e+  l+r +  ++ +
  gi|518652461|ref|YP_008141981.1| 356 MENSIPDTKENRMKYLQFIAQEINvDGKIPHMTMDAADLIINEGRRRALEEHKsnaLTLKLRELGGLIRASGDMSIE 432
                                       7899***************9877626789*****************98554443349******************** PP

                            AAA_32 494 egaevveaehVekAle 509
                                       +g++++e+++V++Al+
  gi|518652461|ref|YP_008141981.1| 433 NGHKLIEKSDVKEALS 448
                                       **************85 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.5e-05     0.009      11      59 ..      32      80 ..      27      90 .. 0.78
   2 !   23.5   0.0   6.2e-08   3.7e-05      86     130 ..     267     310 ..     262     333 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.5e-05
                                      HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETT CS
                   Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavnca 59
                                      +++ +  +ak++ ++l++G  G+GK+++a+a+    +r e+++  v   
  gi|518652461|ref|YP_008141981.1| 32 AVRLALIAAKQRRNLLLVGPPGVGKSMIAQAMSFYISRPEEEIRVVHNP 80
                                      566677788999********************88777776666555555 PP

  == domain 2  score: 23.5 bits;  conditional E-value: 6.2e-08
                                       EHHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  86 kGlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       +G ++ a++G+lf+Dei++l  +lQ  +l+++qe+++  vG + +
  gi|518652461|ref|YP_008141981.1| 267 AGSVHMAHEGVLFIDEITHLG-NLQRFILTAMQERKFPIVGRNPQ 310
                                       599*****************7.79*****************8743 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   4.6e-07   0.00027       1      29 [.      45      73 ..      45     104 .. 0.78
   2 !   12.8   0.0   0.00015     0.089      63     137 ..     272     346 ..     231     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 4.6e-07
                                      EEEEE--SSSSHHHHHHHGGGGBS--EEE CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaalnrevey 29
                                      ++lLvGppG+gKs++a+ ++  + r+ e+
  gi|518652461|ref|YP_008141981.1| 45 NLLLVGPPGVGKSMIAQAMSFYISRPEEE 73
                                      69*******************99554443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00015
                                       --G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-TTH CS
                             AAA_5  63 aregeilvlDEverae.sevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnelsp 132
                                       + +  +l++DE++  +  + +   l+ + er++++  ++ +   ++ +          f ++a++n +d  l+ + +
  gi|518652461|ref|YP_008141981.1| 272 MAHEGVLFIDEIT--HlGNLQRFILTAMQERKFPIVGRNPQSAGASVK---VddvptdFILVAACNIQD--LQYILS 341
                                       347789*******..448999999**********77666666555532...2356799***********..99**** PP

                                       HHHTT CS
                             AAA_5 133 alrsR 137
                                       +lrsR
  gi|518652461|ref|YP_008141981.1| 342 PLRSR 346
                                       ***99 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   8.2e-05     0.049       7      54 ..      24      64 ..      19      83 .. 0.80
   2 !   14.2   0.0   4.7e-05     0.028      80     153 ..     270     347 ..     262     351 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-05
                            RuvB_N  7 eeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiia 54
                                      +  igqe   e +++++ aak+r++    +ll+GpPG+Gk+ +a+ ++
  gi|518652461|ref|YP_008141981.1| 24 DRVIGQE---EAVRLALIAAKQRRN----LLLVGPPGVGKSMIAQAMS 64
                                      5667776...467888999999986....79***********999776 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 4.7e-05
                            RuvB_N  80 tnleekdvlfideihrlsraveevlysamedfrldivigkGpsa.rsikld.lp.kftlvgattragl..lssPlrd 151
                                       +++ ++ vlfidei  l +  + ++ +am++ ++ iv  + +sa  s+k+d +p  f lv+a   + l  + sPlr+
  gi|518652461|ref|YP_008141981.1| 270 VHMAHEGVLFIDEITHLGNL-QRFILTAMQERKFPIVGRNPQSAgASVKVDdVPtDFILVAACNIQDLqyILSPLRS 345
                                       5678899**********875.667779*******987555544424556642433699**99876543228899999 PP

                            RuvB_N 152 rf 153
                                       r+
  gi|518652461|ref|YP_008141981.1| 346 RI 347
                                       96 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   1.3e-05    0.0077       1      22 [.      46      67 ..      46     101 .. 0.83
   2 ?    6.0   0.0     0.025        15      59     123 ..     275     346 ..     262     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.3e-05
                                      EEEESSTTSSHHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavakel 22
                                      +ll+GppG+GK+++a+a+   +
  gi|518652461|ref|YP_008141981.1| 46 LLLVGPPGVGKSMIAQAMSFYI 67
                                      69**************987665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.025
                                       SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..GGGS CS
                               AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..pdkl 115
                                         +lfiDEi  l++ +              +lt++++ k                      ++i+++a+n    + +
  gi|518652461|ref|YP_008141981.1| 275 EGVLFIDEITHLGNLQ------------RFILTAMQERKFPivgrnpqsagasvkvddvPTDFILVAACNIqdLQYI 339
                                       48*********97666............6677777766666677777777777777777666888888888555556 PP

                                       THHHHSTT CS
                               AAA 116 dpallrgR 123
                                        ++l+ +R
  gi|518652461|ref|YP_008141981.1| 340 LSPLR-SR 346
                                       66666.56 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0062       3.7      54      78 ..      40      64 ..      25      71 .. 0.81
   2 !   12.5   0.0   9.6e-05     0.058      82     149 ..     227     301 ..     220     338 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0062
                                      BCSS-EEEEEESSTSTHHHHHHHHH CS
                               MCM 54 lrgdinvllvgdpgtaKsqlLkyve 78
                                       + + n+llvg pg++Ks + ++++
  gi|518652461|ref|YP_008141981.1| 40 AKQRRNLLLVGPPGVGKSMIAQAMS 64
                                      566789************9988776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 9.6e-05
                                       SSEEEEESSSSSSSHSSSEEEEESSSSS........EEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSE CS
                               MCM  82 pravytsgkgssaagLtaavvrdeetge........fvleaGalvladkGvcciDefdkmkeedrsalhEamEqqt 149
                                       +r+ ++ ++g+s+++L   v++d+  g+          + aG + +a++Gv+ iDe+ +  +  +  ++ am + +
  gi|518652461|ref|YP_008141981.1| 227 DRNPFVLATGASETELLGDVRHDPYGGHpqlgtmpyERVVAGSVHMAHEGVLFIDEITHLGN-LQRFILTAMQERK 301
                                       6778888999999999999999988776555554434578********************99.8888888997766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   6.3e-05     0.038       3      25 ..      41      63 ..      38      93 .. 0.89
   2 ?    2.5   0.0      0.27   1.6e+02      86     108 ..     270     293 ..     228     335 .. 0.76
   3 ?    0.0   0.0       1.6   9.3e+02      38      73 ..     442     475 ..     426     491 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.3e-05
                            AAA_22  3 ktagilvvtGesGtGKTtllrrl 25
                                      k+++ l+++G++G+GK++ ++ +
  gi|518652461|ref|YP_008141981.1| 41 KQRRNLLLVGPPGVGKSMIAQAM 63
                                      48899*************99875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.27
                            AAA_22  86 lraravielliiDEaqhlr..seea 108
                                       ++ ++  ++l iDE+ hl   +  +
  gi|518652461|ref|YP_008141981.1| 270 VHMAHE-GVLFIDEITHLGnlQRFI 293
                                       444444.9**********4332333 PP

  == domain 3  score: 0.0 bits;  conditional E-value: 1.6
                            AAA_22  38 erpevvfvtlpsstsskdllrellralglelkaerl 73 
                                         +e ++ ++p++++ k+ +  + +alg+e+ +   
  gi|518652461|ref|YP_008141981.1| 442 DVKEALSLYVPVEEKIKKYYGSMNNALGEEATG--S 475
                                       456778999*******************99988..3 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 !   18.5   0.0   2.2e-06    0.0013      45      72 ..      41      68 ..      29      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-06
                         IstB_IS21 45 ekkenivllGpsGvGKshlaialgveav 72
                                      +++ n++l+Gp+GvGKs +a a++    
  gi|518652461|ref|YP_008141981.1| 41 KQRRNLLLVGPPGVGKSMIAQAMSFYIS 68
                                      5678******************987655 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.1e-05    0.0069      21      51 ..      40      70 ..      26     124 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.1e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd 51
                                      + + +++ll+G++GvGKs ++++   ++++ 
  gi|518652461|ref|YP_008141981.1| 40 AKQRRNLLLVGPPGVGKSMIAQAMSFYISRP 70
                                      344499***************9988777766 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.0    0.0004      0.24      13      42 ..      34      64 ..      29      92 .. 0.80
   2 ?    2.9   0.0      0.19   1.1e+02      64      89 ..     269     294 ..     232     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0004
                                      HHHHHH.T-SS-EEEEEETT--HHHHHHCC- CS
                   Sigma54_activ_2 13 rLeqaa.qsklpvfltGekGsgkelvArlLh 42
                                      rL+ +a ++  +++l+G++G gk+++A++++
  gi|518652461|ref|YP_008141981.1| 34 RLALIAaKQRRNLLLVGPPGVGKSMIAQAMS 64
                                      66666547889*****************987 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.19
                                       HHHHTTTSEEEEEE-TT--HHHHHHH CS
                   Sigma54_activ_2  64 lleqakggtLylkdiadlskaeqkeL 89 
                                       ++  a++g+L++ +i +l++ +   L
  gi|518652461|ref|YP_008141981.1| 269 SVHMAHEGVLFIDEITHLGNLQRFIL 294
                                       566799************98765544 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0    0.0032       1.9       6      30 ..      39      63 ..      29      94 .. 0.78
   2 ?    5.5   0.0     0.033        20     100     141 ..     272     311 ..     254     314 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0032
                            AAA_19  6 ealkekvllvtaGpGtGKTrvlkhi 30
                                      +a ++++ll++++pG GK+ + +++
  gi|518652461|ref|YP_008141981.1| 39 AAKQRRNLLLVGPPGVGKSMIAQAM 63
                                      267899************9876554 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.033
                            AAA_19 100 lqeeellivDEfqdvdelqyrLlkallgekkklllvGDpdQl 141
                                       + +e +l++DE+  +  lq  +l a+  e+k + +vG + Q+
  gi|518652461|ref|YP_008141981.1| 272 MAHEGVLFIDEITHLGNLQRFILTAMQ-ERK-FPIVGRNPQS 311
                                       434449*******************99.556.8899987776 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 !   15.0   0.0   2.3e-05     0.014      29      53 ..      39      63 ..      29      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.3e-05
                             AAA_7 29 llknkkpvllvGptGtGKtviikdl 53
                                        k+++++llvGp G+GK++i++ +
  gi|518652461|ref|YP_008141981.1| 39 AAKQRRNLLLVGPPGVGKSMIAQAM 63
                                      57899****************9984 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   4.4e-05     0.026      28      48 ..     125     145 ..      99     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-05
                               DZR  28 edrCpsCgekvdpearfCpeC 48 
                                        ++Cp+Cg   +p++++Cp+C
  gi|518652461|ref|YP_008141981.1| 125 GYKCPHCGFYSSPTESVCPNC 145
                                       689****************** PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.072        43       2      23 ..      43      64 ..      42     107 .. 0.76
   2 ?   -1.5   0.0         4   2.4e+03      90     117 ..     227     254 ..     180     265 .. 0.76
   3 ?    7.5   0.0    0.0065       3.9      64      92 ..     274     301 ..     259     319 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.072
                            AAA_14  2 rkilvitGaRrvGKTtllkqli 23
                                      r+ l+++G+  vGK+++++ + 
  gi|518652461|ref|YP_008141981.1| 43 RRNLLLVGPPGVGKSMIAQAMS 64
                                      57789************86553 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4
                            AAA_14  90 gknldvivtGSnskllskeiatslagrv 117
                                       ++n  v++tG +   l+ ++++++ g +
  gi|518652461|ref|YP_008141981.1| 227 DRNPFVLATGASETELLGDVRHDPYGGH 254
                                       3466788999999999988888877755 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0065
                            AAA_14  64 kktylflDEiqevpewekalkslvdegkn 92 
                                       ++ +lf+DEi ++ ++++++   ++e+ +
  gi|518652461|ref|YP_008141981.1| 274 HEGVLFIDEITHLGNLQRFILTAMQER-K 301
                                       5678****************9999987.4 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 ?   14.0   2.9   5.7e-05     0.034      11      31 ..     125     145 ..     124     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.7e-05
                           DUF35_N  11 gqrCpdCGtvqfPPravCphC 31 
                                       g +Cp CG +  P + vCp+C
  gi|518652461|ref|YP_008141981.1| 125 GYKCPHCGFYSSPTESVCPNC 145
                                       789********9999****** PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.12      32      54 ..      41      62 ..      31     101 .. 0.79
   2 ?   -1.4   0.0       2.1   1.3e+03     117     131 ..     272     286 ..     259     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                              TniB 32 rkrmpnlllvGdsnnGKtmivek 54
                                      ++r +nlllvG++ +GK+mi++ 
  gi|518652461|ref|YP_008141981.1| 41 KQR-RNLLLVGPPGVGKSMIAQA 62
                                      455.8***************975 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.1
                              TniB 117 elkvrvLiiDEihnl 131
                                         +  vL iDEi +l
  gi|518652461|ref|YP_008141981.1| 272 MAHEGVLFIDEITHL 286
                                       556679******998 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0    0.0009      0.54      27      75 ..      27      68 ..      17      78 .. 0.78
   2 ?    0.9   0.0      0.34     2e+02     279     308 ..     275     303 ..     266     318 .. 0.72
   3 ?   -1.9   0.0       2.5   1.5e+03      70     118 ..     374     423 ..     373     465 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0009
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 27 vGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelg 75
                                      +Gq++a     v + li +k+   r +Ll+Gp+g Gk+ +a a+s  ++
  gi|518652461|ref|YP_008141981.1| 27 IGQEEA-----VRLALIAAKQ--RRNLLLVGPPGVGKSMIAQAMSFYIS 68
                                      666655.....3455666666..589*****************997766 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.34
                                       XXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhml.DiecfsylnraleselaP 308
                                        GvlfiDe+  l ++    ++  a+ +   P
  gi|518652461|ref|YP_008141981.1| 275 EGVLFIDEITHLgNLQ--RFILTAMQERKFP 303
                                       69******85551444..3445555555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.5
                                       XXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-S-EE CS
                             TIP49  70 iskelg..edvpfvalsgsevyslevkktevltqalrksigvrikeekevl 118
                                       i++e++   ++p +++ ++++  +e +   +l +    ++ ++++e   ++
  gi|518652461|ref|YP_008141981.1| 374 IAQEINvdGKIPHMTMDAADLIINEGR-RRALEEHKSNALTLKLRELGGLI 423
                                       677776546899999999999988865.56889999999999999876665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00011     0.067      10      51 ..      42      83 ..      37     141 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                                      TTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 10 egekvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                                      + + + +vG+ G GKS ++++++   +  e+ei++  +++  
  gi|518652461|ref|YP_008141981.1| 42 QRRNLLLVGPPGVGKSMIAQAMSFYISRPEEEIRVVHNPSYP 83
                                      567789******************999999999877666655 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05     0.053      12     100 ..      61     152 ..      55     155 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                           TackOD1  12 kllayllsrdeeklepvldpkske..lysypllealskekeeseelleelvkrglleeelvdri.rlCpsCksghln 85 
                                       + +++ +sr+ee+++ v++p+ +e  +++ + +  +++ek+e++++  e+ + +   +++++r+   Cp+C  ++  
  gi|518652461|ref|YP_008141981.1|  61 QAMSFYISRPEEEIRVVHNPSYPErpFIEVRTIAEIENEKHEMNSIEGEIIEPKDAPDNVAQRLgYKCPHCGFYSSP 137
                                       5677788889999999999988887788999999988888899999999999888888888887468********** PP

                           TackOD1  86 vrevCpkCkSidiee 100
                                          vCp+C+  ++ +
  gi|518652461|ref|YP_008141981.1| 138 TESVCPNCNNPKVVN 152
                                       ********9988765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00034       0.2       5      39 ..      28      64 ..      27      79 .. 0.77
   2 ?   -2.0   0.0       4.3   2.6e+03      84     104 ..     270     290 ..     245     312 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00034
                            AAA_30  5 eQaaavea..lltsgdrvavltGpAGtGKttalkalr 39
                                      +Q++av+   ++++++r  +l+Gp+G GK+++ +a+ 
  gi|518652461|ref|YP_008141981.1| 28 GQEEAVRLalIAAKQRRNLLLVGPPGVGKSMIAQAMS 64
                                      6888887622568889999***********9988875 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4.3
                            AAA_30  84 arlepgtllivDEagmvdtkq 104
                                       ++++++ +l +DE+  +++ q
  gi|518652461|ref|YP_008141981.1| 270 VHMAHEGVLFIDEITHLGNLQ 290
                                       566777899999999988765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0097       5.8       4      38 ..      44      77 ..      41     109 .. 0.80
   2 ?    3.4   0.0      0.13        76      62      77 ..     268     283 ..     263     288 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0097
                                      --EEEE--TTSSHHHHHHHHHHHTT-....-EEEE CS
                             AAA_2  4 isilllgptgvGktelakalaellfvkkekklira 38
                                       ++ll+gp gvGk+++a+a++ +++ + e+++ ++
  gi|518652461|ref|YP_008141981.1| 44 RNLLLVGPPGVGKSMIAQAMSFYIS-RPEEEIRVV 77
                                      5899***************999988.666666655 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.13
                                       T-HHHHTTSEEEEETG CS
                             AAA_2  62 gyvgaeegGivllDEi 77 
                                       g v  + +G++++DEi
  gi|518652461|ref|YP_008141981.1| 268 GSVHMAHEGVLFIDEI 283
                                       6788999********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 ?   11.7   6.8   0.00022      0.13       3      22 ..     126     145 ..     125     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00022
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       ++CP+CG    s+  +vCp+C
  gi|518652461|ref|YP_008141981.1| 126 YKCPHCGFyS-SPTESVCPNC 145
                                       68********.********** 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 ?   11.7   0.0   0.00021      0.13      26      57 ..      45      75 ..      35     110 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00021
                                      EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 26 ftaivGpNGSGKsnlldAilFvLGersakklr 57
                                         +vGp G GKs + +A++F+++    +++r
  gi|518652461|ref|YP_008141981.1| 45 NLLLVGPPGVGKSMIAQAMSFYISR-PEEEIR 75
                                      5579*******************94.444665 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0    0.0008      0.48      38      66 ..      36      64 ..      26     113 .. 0.81
   2 ?   -0.7   0.0       1.9   1.1e+03     110     146 ..     290     326 ..     279     346 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0008
                             Rad17 38 dvLesrkkriLLisGPsGCgkstvvkvLs 66
                                        +  +++r LL+ GP+G gks + + +s
  gi|518652461|ref|YP_008141981.1| 36 ALIAAKQRRNLLLVGPPGVGKSMIAQAMS 64
                                      45566678899***********9999887 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.9
                             Rad17 110 keleLkdakylklqklGddlrtdkklilvedlPnkfy 146
                                       + + L + +  k+   G + ++    + v+d+P  f 
  gi|518652461|ref|YP_008141981.1| 290 QRFILTAMQERKFPIVGRNPQSAGASVKVDDVPTDFI 326
                                       6688999999999999999999999999*****9986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00046      0.27      21      44 ..      42      65 ..      34      77 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00046
                            AAA_29 21 lkgatlltGpsGsGKSTllDAiqa 44
                                      ++ + ll+Gp G+GKS +  A+++
  gi|518652461|ref|YP_008141981.1| 42 QRRNLLLVGPPGVGKSMIAQAMSF 65
                                      44489************9999875 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 ?   10.4   0.0    0.0004      0.24     116     164 ..      31      78 ..      15      92 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0004
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvE 164
                                       e+++ +l +a ++r ++l+ G+ g GK+ ++ a+  +i   +e+i +v 
  gi|518652461|ref|YP_008141981.1|  31 EAVRLALIAA-KQRRNLLLVGPPGVGKSMIAQAMSFYISRPEEEIRVVH 78 
                                       5566667777.899*************************9999998776 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 ?    0.0   0.1       1.3   7.6e+02      22      29 ..     126     133 ..     123     135 .. 0.84
   2 ?   10.4   0.2   0.00071      0.43       3      20 ..     139     156 ..     138     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.3
                     A2L_zn_ribbon  22 lvCieCga 29 
                                       + C+ Cg+
  gi|518652461|ref|YP_008141981.1| 126 YKCPHCGF 133
                                       66****97 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00071
                     A2L_zn_ribbon   3 lkvCsvCggngilnseqg 20 
                                       ++vC +C++++++n +qg
  gi|518652461|ref|YP_008141981.1| 139 ESVCPNCNNPKVVNNTQG 156
                                       579***********9997 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   7.7    0.0019       1.1       1      20 [.     127     146 ..     127     149 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0019
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyCG 20 
                                       +Cp+CG   ++++  Cp+C 
  gi|518652461|ref|YP_008141981.1| 127 KCPHCGFYSSPTESVCPNCN 146
                                       8******************5 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 ?    7.1   4.9    0.0057       3.4       6      28 ..     127     149 ..     127     150 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0057
                                       E-SSS--EEESSSSB-TTT--BT CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqapk 28 
                                       +C++C+++ +++ ++C +C +pk
  gi|518652461|ref|YP_008141981.1| 127 KCPHCGFYSSPTESVCPNCNNPK 149
                                       7*********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (493 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      615  (0.034302); expected 358.6 (0.02)
Passed Vit filter:                       144  (0.00803168); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.49
# Mc/sec: 3053.29
//
Query:       gi|518652462|ref|YP_008141982.1|  [L=428]
Description: hypothetical protein FACI_IFERC00001G1101 [Ferroplasma acidarmanus fer1]
Scores for 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   45.7   0.3    2.2e-11   44.0   0.1    2.0  2  Toprim_4        Toprim domain
    2.3e-06   27.9   0.0    7.9e-06   26.2   0.0    2.0  1  Toprim_2        Toprim-like
      6e-05   23.2   0.1     0.0004   20.6   0.0    2.5  2  Toprim          Toprim domain
  ------ inclusion threshold ------
        9.3    6.9   6.3          6    7.5   0.5    3.0  3  YtxH            YtxH-like protein


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 ?   -2.3   0.0       1.5   6.5e+03      27      44 ..      86     103 ..      84     122 .. 0.66
   2 !   44.0   0.1     5e-15   2.2e-11       2      76 ..     173     256 ..     172     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.5
                          Toprim_4  27 lggalspldgirpeklkt 44 
                                       l  al++ d i+p k k 
  gi|518652462|ref|YP_008141982.1|  86 LAAALETIDRIGPCKAKV 103
                                       677889999999988887 PP

  == domain 2  score: 44.0 bits;  conditional E-value: 5e-15
                          Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklkt.enlve....aekkvkevilaldgDa.....eGe 68 
                                        ii+VEg++Dvl+l ++gikn++av g+++ p+   +++k +t + +v+    +e ++ke++++ d D      +G 
  gi|518652462|ref|YP_008141982.1| 173 SIIVVEGRNDVLNLLRYGIKNTIAVQGTSV-PKTVKELSKARTvTLFVDgdhgGELIIKEMLQVADVDFiarapPGT 248
                                       69****************************.7777777788887788888888888999999999988877777777 PP

                          Toprim_4  69 ataerlae 76 
                                       ++ e  ++
  gi|518652462|ref|YP_008141982.1| 249 EVEELTYK 256
                                       77766666 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.8e-09   7.9e-06       1      69 [.     175     237 ..     175     254 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.8e-09
                          Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellr 69 
                                       +v+Eg  D+l l+++gik   n +a+ Gt + ++ +k+l++   ++v l +D D  G+  +k++ +++ 
  gi|518652462|ref|YP_008141982.1| 175 IVVEGRNDVLNLLRYGIK---NTIAVQGT-SVPKTVKELSKA--RTVTLFVDGDHGGELIIKEMLQVAD 237
                                       69***************9...********.889999999999..89**************999887774 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   4.9e+03       4      14 ..      21      31 ..      21      60 .. 0.83
   2 !   20.6   0.0   8.9e-08    0.0004       2      98 ..     174     248 ..     173     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
                                      EESSHHHHHHH CS
                            Toprim  4 ivEgpsdakti 14
                                      +vE+p  +++i
  gi|518652462|ref|YP_008141982.1| 21 VVEKPDVVGAI 31
                                      79999999887 PP

  == domain 2  score: 20.6 bits;  conditional E-value: 8.9e-08
                                       EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHH CS
                            Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGea 78 
                                       +++vEg +d+ ++ ++   g ++++a++G+ +  +                     +++++a  + l  D+D  Ge 
  gi|518652462|ref|YP_008141982.1| 174 IIVVEGRNDVLNLLRY---GIKNTIAVQGTSVPKTV--------------------KELSKARTVTLFVDGDHGGEL 227
                                       89**************...9**********997776....................6667***************** PP

                                       HHHHHHHHHT.HHHTTTEEEE CS
                            Toprim  79 iawellevlk.ellenkigrv 98 
                                       i +e+l+v++ +++ ++ + +
  gi|518652462|ref|YP_008141982.1| 228 IIKEMLQVADvDFIARAPPGT 248
                                       ******999876666655555 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0013         6      35      69 ..     117     151 ..     109     155 .. 0.90
   2 ?   -1.0   0.6      0.58   2.6e+03      32      56 ..     279     305 ..     256     335 .. 0.64
   3 ?    0.5   0.0      0.21   9.3e+02      40      66 ..     350     380 ..     337     385 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0013
                              YtxH  35 ddlkekakelleeakekakekaedlkekvkekade 69 
                                       d++ ++a+el++++  ++k+ +e + ++v+e++++
  gi|518652462|ref|YP_008141982.1| 117 DKVIQRAEELYKKMGTNGKSLSESIIQSVREEVEK 151
                                       78999**************************9998 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.58
                              YtxH  32 ekaddlkekakelleeakeka..keka 56 
                                       e+++++ ek ++++ +++ ++  ke+ 
  gi|518652462|ref|YP_008141982.1| 279 EELKEFTEKNNKAIADMNVNTtvKEEP 305
                                       344444555555555544444443333 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.21
                              YtxH  40 kakelleeakeka........kekaedlkekvkek 66 
                                       ka e++++    a        ++ a++l+++vk++
  gi|518652462|ref|YP_008141982.1| 350 KAVEIYDD----AgnpiarypVSDAAELMQSVKNG 380
                                       33344433....24555888899999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1641  (0.0915277); expected 358.6 (0.02)
Passed bias filter:                      840  (0.0468515); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 2768.43
//
Query:       gi|518652463|ref|YP_008141983.1|  [L=337]
Description: hypothetical protein FACI_IFERC00001G1102 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.2e-10   39.1   0.0    7.9e-10   38.5   0.0    1.2  1  AP_endonuc_2  Xylose isomerase-like TIM barrel
  ------ inclusion threshold ------
       0.13   12.9   0.1       0.42   11.2   0.0    1.9  2  MCM_N         MCM N-terminal domain


Domain annotation for each model (and alignments):
>> AP_endonuc_2  Xylose isomerase-like TIM barrel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   8.8e-14   7.9e-10      13     184 ..      92     257 ..      91     286 .. 0.85

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 8.8e-14
                                       EEECCTCSHHHHCHHHHHHHHHHHHHHTTSEEEEEEECCCHSTCTHCHTTCSHHHHHHHHHHHHHHHHHHTBSEEEE CS
                      AP_endonuc_2  13 ElfgrdlvpvselsdeelrelrkaldelglriaslslftrfgypdederearreesvdalkraielaaaLGapllvl 89 
                                       E+f+  +++++     el+e  ++++el++ i+++ +++ +   + +      e+s+++l+  + + +a+Ga+ +++
  gi|518652463|ref|YP_008141983.1|  92 EIFWNMARNYD-----ELKEGSEIARELDVDISMHAPYYMDLLNGGEMA----EKSLNHLRWSLLIGKAMGAKRIIT 159
                                       77888888887.....58**********************999776433....567********************* PP

                                       EBCCGBCTTTSGHHHHHHHHHHHHHHHHHHHH.HHT.SEEEEE--TTTTSSSTCHHHHHHHHHHTTTTEEEEEEHHH CS
                      AP_endonuc_2  90 hpGtagagpkgseeeawerlaeslneladyae.keg.vklalEtlagsgvelgdeelarlldavdspnvgvclDtgH 164
                                       h+G     + + + e ++++ +   ++a+++  ++g   +++E   +++ +   +el +l d+++   v   l++ H
  gi|518652463|ref|YP_008141983.1| 160 HTG----FYTRKKSESLKNALDIYADVAKKFShENGyPYIGVEASGKKDLFGTQKELFYLADRIPE--VEPILNFPH 230
                                       ***....44555566888888888888888884555777**********98888***********7..********* PP

                                       HHHH.......TTTHHHHHHHHHGGEE CS
                      AP_endonuc_2 165 llia.......eedvddalraladrik 184
                                       ++           +++d+++a+a++ k
  gi|518652463|ref|YP_008141983.1| 231 IHSInngslidAKNFEDVVAAFAKYAK 257
                                       ***********7777777777777644 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.7e-05      0.42      21      64 ..      15      58 ..      10      68 .. 0.82
   2 ?   -3.0   0.0       1.3   1.2e+04      21      29 ..     122     130 ..      97     142 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                             MCM_N 21 ekkYrdqlqemaerekttLevdlddLaafdeeLaeailenpkey 64
                                       ++Y+d +qe+a+ + ++Lev+l  ++  ++   e +  +pk++
  gi|518652463|ref|YP_008141983.1| 15 GRTYMDSIQEVANLGLNSLEVQLLRVNVSEDPAIEYVDMYPKDV 58
                                      589*******************9988887777666666666665 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
                             MCM_N  21 ekkYrdqlq 29 
                                        ++Y+d l+
  gi|518652463|ref|YP_008141983.1| 122 APYYMDLLN 130
                                       378888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); 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:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2333.14
//
Query:       gi|518652464|ref|YP_008141984.1|  [L=95]
Description: hypothetical protein FACI_IFERC00001G1103 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-23   83.6   1.1    1.7e-23   83.4   1.1    1.0  1  DUF5611   Domain of unknown function (DUF5611)


Domain annotation for each model (and alignments):
>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.4   1.1   9.4e-28   1.7e-23       1     103 []       1      95 []       1      95 [] 0.97

  Alignments for each domain:
  == domain 1  score: 83.4 bits;  conditional E-value: 9.4e-28
                                       -EEE---SSS--SH.HHHHHHHHHHT.-EEEEETTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHH CS
                           DUF5611   1 mreYkiKrGfkkeeeerlkelleeyfggeveeegdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaald 77 
                                       mr Y++K+++k +e  ++ e+l++    e+++eg+++++s++++kk+e+++  ++kkl+v+te+ d   +++ ++ +
  gi|518652464|ref|YP_008141984.1|   1 MRTYPVKKTIKINE-TYVMETLKSRN-LEFQQEGNHIISSYPGLKKIELWT--DGKKLYVETET-D---TQYSNPGE 69 
                                       9***********99.9********99.9***********************..***********.7...79****** PP

                                       HHHHHHHHHHHHH---GGGHHHHH-- CS
                           DUF5611  78 tvkkfndFLeeaTGydaKeRkkkakk 103
                                       t+k fn++Le++TGy++KeRkk ++k
  gi|518652464|ref|YP_008141984.1|  70 TIKFFNNLLEALTGYTTKERKKLISK 95 
                                       **********************8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 687.04
//
Query:       gi|518652465|ref|YP_008141985.1|  [L=121]
Description: hypothetical protein FACI_IFERC00001G1104 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-14   53.7   2.3    1.9e-14   53.3   2.3    1.2  1  DUF3198       Protein of unknown function (DUF3198)
  ------ inclusion threshold ------
        3.7    7.9   6.8       0.36   11.2   1.0    2.0  2  Wzz           Chain length determinant protein


Domain annotation for each model (and alignments):
>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   2.3   2.1e-18   1.9e-14       5      50 .]      75     120 ..      71     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 2.1e-18
                                       HHHHHHHS--HHHHHHHHHHHHHHHHHH-SHHHHHHHHHHHHH--- CS
                           DUF3198   5 kFeelInSdSKstFvknlkeLekiarklGssYqqrLeeakekWkvk 50 
                                        F++l  S SK+tF+ n+ +Le+i+++lG+ Y + L +ak kW +k
  gi|518652465|ref|YP_008141985.1|  75 TFKKLLKSSSKKTFIDNMPSLERISKRLGKNYDELLKQAKHKWGIK 120
                                       7******************************************987 PP

>> Wzz  Chain length determinant protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5      0.13   1.1e+03      17      31 ..      11      25 ..       6      35 .. 0.71
   2 ?   11.2   1.0     4e-05      0.36      16      56 ..      49      90 ..      35     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.13
                                      XXXXXXXXXXXXXXX CS
                               Wzz 17 klIilvtllfallav 31
                                      ++I +v l+f+++++
  gi|518652465|ref|YP_008141985.1| 11 IIISIVSLFFLIISL 25
                                      466677777777765 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 4e-05
                                      XXXXXXXXXXXXXXXXXXXXXXXX-EEEEEEEES--CHHH.H CS
                               Wzz 16 kklIilvtllfallaviyaflatpkYtataqilvpekkqv.e 56
                                       +++i+ t++f+ +a++   ++ ++Yt + ++  ++kk   +
  gi|518652465|ref|YP_008141985.1| 49 YWILIASTIVFIYFAYLTYSILNDIYTFKKLLKSSSKKTFiD 90
                                      69999**********************999999999887553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1334  (0.0744046); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 862.43
//
Query:       gi|518652466|ref|YP_008141986.1|  [L=273]
Description: hypothetical protein FACI_IFERC00001G1105 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  185.8   0.0    7.6e-55  185.2   0.0    1.2  1  Spermine_synth   Spermine/spermidine synthase domain
    2.3e-15   56.2   0.1      4e-15   55.4   0.1    1.4  1  Spermine_synt_N  Spermidine synthase tetramerisation domain
    5.1e-05   23.9   0.0     0.0001   22.9   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
     0.0096   15.8   0.0      0.017   15.0   0.0    1.4  1  Methyltransf_30  S-adenosyl-L-methionine-dependent methyltran
  ------ inclusion threshold ------
      0.091   13.8   0.0       0.21   12.6   0.0    1.6  2  Methyltransf_24  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 !  185.2   0.0   2.1e-58   7.6e-55       2     181 ..      62     238 ..      61     246 .. 0.97

  Alignments for each domain:
  == domain 1  score: 185.2 bits;  conditional E-value: 2.1e-58
                                       HHHHHHHHHHHHCCSSST-EEEEESSTTSHHHHHHTTSTT-SEEEEEES-HHHHHHHHHHSHHHHTTCGGCTTEEEE CS
                    Spermine_synth   2 faykemiahvplmlhknpkevLiiGGgDGgvlrevvkhntvekitlvdiDqkvidfskkflpslaisafndarvklv 78 
                                        +y+emi+ vp  ++++p +vLiiGGgDGg++r+++ +    kit v+iD +v+++ kk++p+++ s f+d+rvkl+
  gi|518652466|ref|YP_008141986.1|  62 YVYHEMITMVPHYFNSRPSNVLIIGGGDGGAARRLLDLG-TDKITNVEIDGNVVEIAKKYFPDISSS-FKDSRVKLI 136
                                       68*************************************.9**************************.********* PP

                                       ESTCHHHHCTCSS-EEEEEEECCSTTCSSCGCSSHHHHHHHHHTEEEEEEEEEEEEETTTCHHHHHHHHHHHHTTSS CS
                    Spermine_synth  79 lgdgfkflkayekkfdvvivdsldpvgpaenlFskeffdllkkvlkedGviilqaekpelekelvinvdksgkqvfa 155
                                       +gdg+k++k++e+kfd +i ds+dpvgpae lFs++f++ +k  l++dG++++q+ +p ++ + +  ++k +++vf+
  gi|518652466|ref|YP_008141986.1| 137 VGDGIKYIKETENKFDRIIIDSTDPVGPAEGLFSRDFYEDIKAHLTDDGIVVTQSGSPYYQPAALAMAHKGMSEVFK 213
                                       ****************************************************************************9 PP

                                       CEEEEEEEETTTSCSCEEEEEEEESS CS
                    Spermine_synth 156 lqvepsavlvPtylsgminfvveskk 181
                                        +v+ + + +Pty+sg+++f+++s  
  gi|518652466|ref|YP_008141986.1| 214 -SVKTYCAFIPTYPSGLWSFTMASSG 238
                                       .********************99865 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 !   55.4   0.1   1.1e-18     4e-15       2      53 .]       7      58 ..       6      58 .. 0.99

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.1e-18
                                      EEEEEEETTEEEEEEEEEEEEEEEESSSEEEEEEETTTEEEEEETTEEEEET CS
                   Spermine_synt_N  2 WfteisdpglalelkVekvLyeekSeyQdieifesktfGkvLvLDgvvqltE 53
                                      Wf+e+++++l l+++V++ L+ +k++yQ i +f++++fGk L +Dg+vqltE
  gi|518652466|ref|YP_008141986.1|  7 WFSERYSDNLQLSFRVKDQLLSVKTDYQRIDLFDTYDFGKLLSIDGTVQLTE 58
                                      ***************************************************9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   2.8e-08    0.0001       1      70 [.      82     156 ..      82     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 2.8e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHH..TTT...TEEEEESBC.CGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraee..egl...nvefvqgda.edlpfedgsfDlvvs 70 
                                       vL +G G G  +++l++  g  k+t v+i+ + +e+a++ + +  +++   +v++++gd  + +++ +++fD +++
  gi|518652466|ref|YP_008141986.1|  82 VLIIGGGDGGAARRLLDL-GTDKITNVEIDGNVVEIAKKYFPDisSSFkdsRVKLIVGDGiKYIKETENKFDRIII 156
                                       789**************9.68******************998876333666********9555899********98 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 !   15.0   0.0   4.8e-06     0.017      26      91 ..     126     192 ..     111     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 4.8e-06
                                       ETTTTEEEEEEES-HHHHHHHC-T-EEEEEE-SS-TTTSGG.GCSHHHHHHHHHHEEEEEEEEES-- CS
                   Methyltransf_30  26 laaeevtlklligdarealkeldekadawFlDgFsPaknPe.lwseellkelarllkkkgtlatyss 91 
                                        + ++ ++kl++gd  + +ke ++k+d +  D   P    e l+s ++++ +++ l + g ++t s 
  gi|518652466|ref|YP_008141986.1| 126 SSFKDSRVKLIVGDGIKYIKETENKFDRIIIDSTDPVGPAEgLFSRDFYEDIKAHLTDDGIVVTQSG 192
                                       44567899****************************876655*******************999775 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       3.7   1.3e+04      71      79 ..      43      54 ..      13      70 .. 0.64
   2 ?   12.6   0.0   5.9e-05      0.21      18     102 ..      96     188 ..      85     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.7
                   Methyltransf_24 71 D...llfiDggh 79
                                      D   ll iDg  
  gi|518652466|ref|YP_008141986.1| 43 DfgkLLSIDGTV 54
                                      233356666654 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 5.9e-05
                   Methyltransf_24  18 lrrngagrlvavdhdpgaeeaaalare.......aglddrvrlikadseealaslaagsiDllfiDg.ghaa....e 82 
                                       l + g+ +++ v+ d    ++ ++a++       +  d+rv+li++d  +++++ +  ++D ++iD  ++++     
  gi|518652466|ref|YP_008141986.1|  96 LLDLGTDKITNVEIDG---NVVEIAKKyfpdissSFKDSRVKLIVGDGIKYIKETE-NKFDRIIIDStDPVGpaegL 168
                                       4556667889999999...888888887777887778889****************.99*******85333322113 PP

                   Methyltransf_24  83 avledleallprlapggvvl 102
                                         ++++e +  +l+++g+v+
  gi|518652466|ref|YP_008141986.1| 169 FSRDFYEDIKAHLTDDGIVV 188
                                       567778999999**999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1990.17
//
Query:       gi|518652467|ref|YP_008141987.1|  [L=90]
Description: DNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-21   75.5   5.4    3.5e-21   75.2   5.4    1.0  1  Bac_DNA_binding  Bacterial DNA-binding protein
    1.2e-05   25.4   0.2    1.3e-05   25.3   0.2    1.1  1  HU-HIG           HU domain fused to wHTH, Ig, or Glycine-rich
  ------ inclusion threshold ------
      0.021   14.7   0.2      0.035   14.0   0.2    1.3  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
      0.051   13.7   0.1      0.059   13.5   0.1    1.1  1  HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
      0.071   13.4   0.3      0.098   13.0   0.3    1.4  1  FERM_f0          N-terminal or F0 domain of Talin-head FERM


Domain annotation for each model (and alignments):
>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.2   5.4   9.7e-25   3.5e-21       4      86 ..       5      87 ..       3      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.2 bits;  conditional E-value: 9.7e-25
                                      HHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEEEEEE- CS
                   Bac_DNA_binding  4 keLieeiaektgltkkdakrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvvkFkps 82
                                      +eL +++a  t+ t+k++++++ afl+++ e++++g+kv+l +FG f+ ke+k+r +rnpkT+e++k+pa+ +  F++s
  gi|518652467|ref|YP_008141987.1|  5 SELSKKVASTTNTTQKKTAEIITAFLKETVESVNAGNKVNLADFGIFERKEQKERVARNPKTREEIKVPAKDKFVFRAS 83
                                      7999*************************************************************************** PP

                                      HHHH CS
                   Bac_DNA_binding 83 kelk 86
                                      +++k
  gi|518652467|ref|YP_008141987.1| 84 SAIK 87
                                      9987 PP

>> HU-HIG  HU domain fused to wHTH, Ig, or Glycine-rich motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.2   3.6e-09   1.3e-05      32     115 ..       2      87 ..       1      89 [. 0.83

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 3.6e-09
                            HU-HIG  32 vdfeeLceeiskrstlsrgdvkavldaledelkeaLadGerVeLgelGyFslslkskgvedekev..ransikkkki 106
                                       v ++eL++++++ +  ++ + + ++ a+ +e++e+ + G+ V+L ++G F  + + + v  + +   + +   k+k 
  gi|518652467|ref|YP_008141987.1|   2 VGISELSKKVASTTNTTQKKTAEIITAFLKETVESVNAGNKVNLADFGIFERKEQKERVARNPKTreEIKVPAKDKF 78 
                                       7789**********************************************999998777664444113345567888 PP

                            HU-HIG 107 nfrpgkklk 115
                                       +fr+++++k
  gi|518652467|ref|YP_008141987.1|  79 VFRASSAIK 87 
                                       888888776 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 ?   14.0   0.2   9.7e-06     0.035       4      53 ..       8      57 ..       7      60 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.7e-06
                   HU-CCDC81_bac_2  4 ansiaeaegisyeeAlqkiekeveelkqeLeeegrveleniGeLslneeg 53
                                       + +a++ +++ ++  + i  + +e  +  + +++v+l + G + ++e++
  gi|518652467|ref|YP_008141987.1|  8 SKKVASTTNTTQKKTAEIITAFLKETVESVNAGNKVNLADFGIFERKEQK 57
                                      567899**************************************999875 PP

>> HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.6e-05     0.059      11      69 ..      11      67 ..       4      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                   HU-CCDC81_euk_1 11 tssalkplltteqllliWdalgeyieeqlekgkgvhipnfGtFtfeapdldlkadknel 69
                                        s++  + t+++  +i+ a+ +   e ++ g+ v++ +fG+F  + ++  ++ + +++
  gi|518652467|ref|YP_008141987.1| 11 VASTT--NTTQKKTAEIITAFLKETVESVNAGNKVNLADFGIFERKEQKERVARNPKTR 67
                                      33444..68889999999999999999*****************998888877766554 PP

>> FERM_f0  N-terminal or F0 domain of Talin-head FERM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   2.7e-05     0.098      10      57 ..      12      59 ..       6      90 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.7e-05
                           FERM_f0 10 knvtktiqFdpettVydacklirekiaeaelgnakdygLFladedpkk 57
                                      +++t t+q +  +++   +k+  e ++ ++  n  d+g+F ++e++++
  gi|518652467|ref|YP_008141987.1| 12 ASTTNTTQKKTAEIITAFLKETVESVNAGNKVNLADFGIFERKEQKER 59
                                      5688999999999*****************9**********9977655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1067  (0.0595125); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 740.15
//
Query:       gi|518652468|ref|YP_008141988.1|  [L=531]
Description: hypothetical protein FACI_IFERC00001G1107 [Ferroplasma acidarmanus fer1]
Scores for 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-82  276.9   0.0    2.7e-82  276.5   0.0    1.2  1  Peptidase_M22   Glycoprotease family
      2e-09   37.1   0.0    3.6e-09   36.3   0.0    1.4  1  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
    1.7e-08   34.3   0.2    4.1e-08   33.0   0.1    1.5  1  RIO1            RIO1 family
    0.00068   19.1   0.2     0.0012   18.2   0.2    1.3  1  Pkinase         Protein kinase domain
  ------ inclusion threshold ------
      0.035   13.4   0.2      0.052   12.8   0.2    1.3  1  EcKinase        Ecdysteroid kinase
      0.041   13.8   0.1      0.063   13.2   0.1    1.3  1  APH             Phosphotransferase enzyme family
      0.058   13.0   0.3       0.16   11.5   0.2    1.7  1  Choline_kinase  Choline/ethanolamine kinase


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 !  276.5   0.0   1.1e-85   2.7e-82       2     270 ..      23     290 ..      22     291 .. 0.96

  Alignments for each domain:
  == domain 1  score: 276.5 bits;  conditional E-value: 1.1e-85
                                       CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHH CS
                     Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglal 78 
                                       +++n+ +++   ++k GG++P++a+ +H+ ++lp++++a++e+gls+ +++ +a++ gPGl+++Lrv++++A+++++
  gi|518652468|ref|YP_008141988.1|  23 IISNFSSTY---IPKNGGIHPREAAIHHADNILPVMKKAFEESGLSPGQINLVAFSMGPGLGPCLRVVATAARAFSI 96 
                                       566666666...59*************************************************************** PP

                                       HCT--EEEEEHHHHHHHCCHCTSECSSCEEEEESSSTEEEEEECTTEEEEEEEESSSEHHHHHHHHHHHHT..SSCC CS
                     Peptidase_M22  79 alnkPlvgVnhleahalaarleekeefPvvllvsGghtqvylvkegryeilgetlddaagealdkvarllglpypgg 155
                                       ++++Pl+gVnh  +h++ +r  ++ ++P++l++sGg+tq+++ +e+ y++lget+d+ +g+ ldk+ar +g+p+pgg
  gi|518652468|ref|YP_008141988.1|  97 KYGIPLIGVNHPLGHVEIGRKLSGAKDPIMLYISGGNTQIIAHEENSYKVLGETMDIGLGNLLDKLARDVGIPFPGG 173
                                       *******************9557779*****************99******************************** PP

                                       HHHHHHHCTC.S.......EETTEEE.CHHHHHHHHHHST.THHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEE CS
                     Peptidase_M22 156 pkieklakeg.kkiefprplkgldfsfsGlktavlkelek.evedlaasfqeavvdhlvekteralklpkakelvil 230
                                       pkie++a +g k +++p+ +kg+d sfsG+ ta+++ + + ++e++++s+qe+ +++lve++eral +++++e++++
  gi|518652468|ref|YP_008141988.1| 174 PKIEEFALKGdKLLDLPYSVKGMDTSFSGIYTAARNYIGReSIENICYSVQETTFSMLVEVLERALYYTDKREILLA 250
                                       **********666*************************4437*********************************** PP

                                       SGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHH CS
                     Peptidase_M22 231 GGvaankrLrealeeeaeelglkliiPplkyctdnaamia 270
                                       GGva n rLr++++++a+  g+  + +++kyc dn+amia
  gi|518652468|ref|YP_008141988.1| 251 GGVARNDRLRSMVSHMAKSSGYVAYLTDKKYCMDNGAMIA 290
                                       *****************99********************8 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.0   1.4e-12   3.6e-09      25     165 ..     343     465 ..     323     481 .. 0.84

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 1.4e-12
                               Kdo  25 aekvnaalrkyyrggllgklskdlyrfk.lgrtravrEfrllkrLeeagvavpkpvaagavkvgleyrAlllterle 100
                                        +  + ++rk   ++ ++k ++++   + + + r+ +Ef+l+ rL++ g++ p  + +   k+++     l++ +l+
  gi|518652468|ref|YP_008141988.1| 343 ES--QFYGRKTITKQRVEKEYRNQELDRkIRTERMKNEFNLIFRLKSNGINSP--ILYDFDKYNF----TLVMQKLD 411
                                       33..4799999999999999999755555*********************976..7777777665....7******* PP

                               Kdo 101 gaqdLedllakwaelaeelkrallkavgrliaklhragvnHadlyaknillqqeeeeeaeiwliD 165
                                       g+  L++l+++     +    a ++++g++i ++h++ + H+dl++ ni++   +     i+liD
  gi|518652468|ref|YP_008141988.1| 412 GI-TLNKLIRS-----GDNYMAVINKLGQIIGEMHNLLISHGDLNPNNIMVVGPD-----IYLID 465
                                       *7.6******8.....99999*****************************98776.....77776 PP

>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.0   0.1   1.6e-11   4.1e-08      23     149 ..     344     466 ..     340     469 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.0 bits;  conditional E-value: 1.6e-11
                                       -SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEEETT..EEEEE--EETTEEGGB CS
                              RIO1  23 teFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpielkrh..vlvmefigedgvaapk 97 
                                       ++F  rk  +++  + k+ +++   rk+     ++Ef+ + rl++ g++ P  +++ +    lvm+ ++  g+ + k
  gi|518652468|ref|YP_008141988.1| 344 SQFYGRKTITKQRVE-KEYRNQELDRKIRTERMKNEFNLIFRLKSNGINSPILYDFDKYnfTLVMQKLD--GITLNK 417
                                       566666665555555.44456777899999999**********************9864338*******..****** PP

                                       HHHCG.-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--G CS
                              RIO1  98 lkdve.eeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDv 149
                                       l     +     + + +++ em+ l+    + H+DL+  N++v   ++++ID 
  gi|518652468|ref|YP_008141988.1| 418 LIRSGdNYMAVINKLGQIIGEMHNLL----ISHGDLNPNNIMVVGPDIYLIDP 466
                                       *9999445566666777777877777....99********************5 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2   4.8e-07    0.0012      32     138 ..     361     462 ..     341     471 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 4.8e-07
                                       EECHCHCHHHH......HHHHHHHHHHHHHSCTTB--EEEEEEESSEEEEEEE--TTEBHHHHHHHHSS--HHHHHH CS
                           Pkinase  32 ikkekakkkke......kkvlrEikilkklkhpnivrlyevfeekdelylvleyveggeladllerkgslseeeakk 102
                                        ++++            +++ +E +++ +lk++ i   + +  +k +++lv++ ++g +l++l++     s ++   
  gi|518652468|ref|YP_008141988.1| 361 YRNQE-----LdrkirtERMKNEFNLIFRLKSNGINSPILYDFDKYNFTLVMQKLDGITLNKLIR-----SGDNYMA 427
                                       33332.....03333359999**************999998889********************8.....7888999 PP

                                       HHHHHHHHHHHHHHTTEE-SS-SGGGEEEETTTEEE CS
                           Pkinase 103 iakqilegleylHskgiiHrDlKpeNiLidekgelK 138
                                       +++++ + +  +H+  i H Dl p+Ni++    ++ 
  gi|518652468|ref|YP_008141988.1| 428 VINKLGQIIGEMHNLLISHGDLNPNNIMVV-GPDIY 462
                                       9999************************98.44555 PP

>> EcKinase  Ecdysteroid kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2     2e-05     0.052     140     229 ..     356     456 ..     347     509 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                          EcKinase 140 evfkelkkglleedyvssalkeafeelleellkaalealreelpelekea..........ekleklkenlferllel 206
                                        v ke++++ l+++++ +++k++f+ +++   + +   +  ++++++ +           +kl +  +n+++ + +l
  gi|518652468|ref|YP_008141988.1| 356 RVEKEYRNQELDRKIRTERMKNEFNLIFRLKSNGINSPILYDFDKYNFTLvmqkldgitlNKLIRSGDNYMAVINKL 432
                                       56678888888888888888888888888777777777777777775444777778888899999999********* PP

                          EcKinase 207 ve.ekeeefnvlnHGDlwvnNimf 229
                                        +   e +   + HGDl+ nNim+
  gi|518652468|ref|YP_008141988.1| 433 GQiIGEMHNLLISHGDLNPNNIMV 456
                                       *987888888999**********7 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   2.5e-05     0.063     167     193 ..     443     466 ..     404     479 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                                       EEE-SS-SGGGEEEC..TTEEEEE--- CS
                               APH 167 vllHgDlhpgNllvdpddgrvtGviDf 193
                                        + HgDl+p+N++v   ++ + ++iD 
  gi|518652468|ref|YP_008141988.1| 443 LISHGDLNPNNIMVV--GPDI-YLIDP 466
                                       688************..5555.89996 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   6.2e-05      0.16     120     184 ..     411     479 ..     347     491 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                                       CCCTHHHHHHHHHTHHHHHH......CHGG-EEEE-S--SGGGEEE.-CTTEEEE--GTT-EEEEHHHHHH CS
                    Choline_kinase 120 klinledlekelekleklle......elespvvfcHnDlqegNillnkeekklvlIDFEYagynyrgfDla 184
                                       + i+l++l +  ++++++++         +++  +H Dl ++Ni++    ++++lID     +n+   D+a
  gi|518652468|ref|YP_008141988.1| 411 DGITLNKLIRSGDNYMAVINklgqiiGEMHNLLISHGDLNPNNIMV--VGPDIYLIDPSMGKFNCEIEDMA 479
                                       5556666666666666666523333333345999************..9********77777777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      512  (0.0285571); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3834.07
//
Query:       gi|518652469|ref|YP_008141989.1|  [L=182]
Description: nucleoside-triphosphatase [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  147.5   0.0    4.7e-43  147.3   0.0    1.0  1  Ham1p_like     Ham1 family
  ------ inclusion threshold ------
      0.028   13.9   0.1      0.038   13.5   0.1    1.1  1  Nab6_mRNP_bdg  RNA-recognition motif


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 !  147.3   0.0   5.3e-47   4.7e-43       1     186 [.       2     174 ..       2     175 .. 0.88

  Alignments for each domain:
  == domain 1  score: 147.3 bits;  conditional E-value: 5.3e-47
                                       EEEC-S-HHHHHHHHHHTTTECCCE.EECCCCEE----BS.SSHHHHHHHHHHHHHH.HTS-EEEEEEEEEEGGGTT CS
                        Ham1p_like   1 ivfaTgNkgKlrevkeilaeellevkslkelelpeveEtq.gtfeenalkKaraaae.aglpvladDsgLevdaLng 75 
                                       i f+T+N +K++e+k++++++++e++ +    + e+eE+q ++ e + ++ + ++ e ++ p+++dD+gL+++ Lng
  gi|518652469|ref|YP_008141989.1|   2 IKFVTSNSHKYEEAKALFKSKNIELSWV----KMEYEEIQaEDNELICRDSCMKLTEkIDSPFFIDDTGLYIKSLNG 74 
                                       669***************9888888744....45889***78888899****9999746888*************** PP

                                       TBGGGTTTTTHTTCHHHHHHHHHHHHCTHTTS--EEEEEEEEEEEETTTTEEEEEEEEEEEEE-SS.--SSSSTTGG CS
                        Ham1p_like  76 lPGvysarfagegaedeenlaklleeleeeeedrsArfvcvlaladpeeeeellfeGeveGeiveeprgeggfGyDp 152
                                       +PG+y +++++     + ++ +++e  +      +A+f++v++++   e+e+++f+G+++G+i++++ g+++fGyDp
  gi|518652469|ref|YP_008141989.1|  75 FPGPYASYVQS-----TLGNSRIMEIGA--G--SEAHFKTVIGFSM--ESEIYTFTGILNGHIAKKESGTNKFGYDP 140
                                       *********53.....457789998886..3..57*********98..57779************************ PP

                                       GEEETT-SSBTTTS.CHHHHHHSHHHHHHHHHHH CS
                        Ham1p_like 153 iFvpeegektfaelskeeknaiShRgkAleklle 186
                                       iF+pe+ +kt+aels+eekn iShRg+Al+k+++
  gi|518652469|ref|YP_008141989.1| 141 IFIPEGYDKTLAELSTEEKNIISHRGRALDKFMD 174
                                       ****76567***********************87 PP

>> Nab6_mRNP_bdg  RNA-recognition motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   4.2e-06     0.038      80     112 ..      10      43 ..       2      65 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.2e-06
                     Nab6_mRNP_bdg  80 qrlaefKtklksesLklsFVslkyk.kesedeee 112
                                        +++e K+  ks++++ls+V+++y+  ++ed+e 
  gi|518652469|ref|YP_008141989.1|  10 HKYEEAKALFKSKNIELSWVKMEYEeIQAEDNEL 43 
                                       589*********************6245555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1239.89
//
Query:       gi|518652470|ref|YP_008141990.1|  [L=129]
Description: 30S ribosomal protein S6e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-29  100.5   0.6      8e-29  100.2   0.6    1.0  1  Ribosomal_S6e  Ribosomal protein S6e


Domain annotation for each model (and alignments):
>> Ribosomal_S6e  Ribosomal protein S6e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.2   0.6   4.5e-33     8e-29       4     121 ..       5     118 ..       2     120 .. 0.96

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 4.5e-33
                                       EEEETTTTEEEEEE-CHHHCTTCTT-BSSEEEECCTTTSSSTS-EEEEEEEEETTC-BB-TTS-SSSEEEEEEETTS CS
                     Ribosomal_S6e   4 nisdpatgkqklievdekklrtligkrigeevdgdalGeelkgyvlkitggsdkqGfpmkqgvltpgrvrlLlskgg 80 
                                       +i+d ++gk+++ +++e  l +l g++igee+dg ++   ++gy++k+tggs ++Gfpmk++++  g++r+L++   
  gi|518652470|ref|YP_008141990.1|   5 VIADRNSGKTYKKDISEDVLGSLAGRKIGEEIDGIFFE--MPGYKMKLTGGSANDGFPMKKDLSIMGKKRILITY-- 77 
                                       89************************************..*********************************99.. PP

                                       SSS-SSSSS-EEEEEEE-SB--SSEEEEEEEEEE--SS--T CS
                     Ribosomal_S6e  81 vgyrprrkGerkrksvrGcivsadisqlnlvivkkgekdie 121
                                          r+ ++G rkr++ rG+++ +disqlnlvi+++g k+++
  gi|518652470|ref|YP_008141990.1|  78 NKGRKGKNGVRKRVTFRGNTIGSDISQLNLVITQYGTKPLD 118
                                       4458889******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 888.78
//
Query:       gi|518652471|ref|YP_008141991.1|  [L=406]
Description: hypothetical protein FACI_IFERC00001G1110 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-32  113.1   2.6    3.5e-32  111.5   2.6    1.7  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.3e-29  102.2   0.1    3.3e-29  101.0   0.1    1.7  1  eIF2_C        Initiation factor eIF2 gamma, C terminal
    4.3e-05   23.6   0.1    0.00011   22.2   0.1    1.7  1  MMR_HSR1      50S ribosome-binding GTPase
    0.00031   21.1   0.1     0.0008   19.8   0.1    1.8  1  GTP_EFTU_D2   Elongation factor Tu domain 2
     0.0013   18.7   2.2      0.024   14.5   0.2    2.5  2  RsgA_GTPase   RsgA GTPase
     0.0065   16.2   0.9       0.81    9.4   0.3    2.4  2  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0091   15.5   1.1        3.9    7.0   0.1    2.6  2  FeoB_N        Ferrous iron transport protein B
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.023   14.7   0.1    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.075   13.4   0.0       0.14   12.5   0.0    1.5  1  DUF4124       Domain of unknown function (DUF4124)
      0.084   11.8   0.9       0.26   10.2   0.1    2.0  2  MeaB          Methylmalonyl Co-A mutase-associated GTPase Mea


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.5   2.6   1.9e-35   3.5e-32       3     193 ..       5     193 ..       3     194 .. 0.88

  Alignments for each domain:
  == domain 1  score: 111.5 bits;  conditional E-value: 1.9e-35
                                       EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE............... CS
                          GTP_EFTU   3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle............... 64 
                                        +nig++ghvDhGK+TLt +L+ k                +D ++eE +rgi+ik   + +                
  gi|518652471|ref|YP_008141991.1|   5 SVNIGMVGHVDHGKSTLTFALTGK---------------KTDVHSEEVKRGISIKLGYADTPiyrctdetgkefysn 66 
                                       68*******************922...............27888899999999999999988899999999999999 PP

                                       .....TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTE.EEEEEESCGS CS
                          GTP_EFTU  65 .....ketkkylinliDtPGHvdFskevirglrvlDgavlvvdaveG.vepqteevlrlalkegvp.iivfiNKmDr 134
                                            + + ++ i+++D+PGH+  + ++ +g ++++ga+lv++a+e  ++pqt+e+l  +  +g++ iiv+ NK+D 
  gi|518652471|ref|YP_008141991.1|  67 kknsdNCQLSRVISIVDAPGHETLMATMLAGSAIMNGAILVIAANEEcPQPQTREHLTALEIMGIKeIIVVQNKIDL 143
                                       877644667899*********************************9879**************************** PP

                                       T.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
                          GTP_EFTU 135 l.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                                       + +++  e+ +e+k+ l       +   ++   + pv+++Sa+++ +++ ++ea+ + ++
  gi|518652471|ref|YP_008141991.1| 144 VtRERAMESYKEIKDFL-------KGSIAE---NAPVIPVSAYHNTNIDVVFEAIEKIIK 193
                                       *8888999999999666.......444333...46*******************998775 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 !  101.0   0.1   1.8e-32   3.3e-29       2      86 .]     318     402 ..     317     402 .. 0.98

  Alignments for each domain:
  == domain 1  score: 101.0 bits;  conditional E-value: 1.8e-32
                                       EEEEEEEE-SBESSSSSCCC-----TTEEEEEEETTEEEEEEEEEEESSEEEEEEEEEEE-STTEEEEEEEEETTSE CS
                            eIF2_C   2 eleieyellerlvgvkeekkveklkkkEvLmlniGsastggvvtsvkkdeakvkLkkPvcaekgekialsRrvekrW 78 
                                       ++e++++ll+r+vg +ee +ve+lk++E++ml++G+a+t+g+vts+k++ + v+Lk Pv+a+++++ a+ Rr+++rW
  gi|518652471|ref|YP_008141991.1| 318 NMEMDIHLLNRVVGFDEEVNVEPLKSNEMIMLTVGTANTIGTVTSIKDKRVGVSLKYPVAASINDRMAIGRRISNRW 394
                                       689************************************************************************** PP

                                       EEEEEEEE CS
                            eIF2_C  79 rLiGwGei 86 
                                       rLiG+G+i
  gi|518652471|ref|YP_008141991.1| 395 RLIGYGSI 402
                                       ******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 !   22.2   0.1   6.2e-08   0.00011       1     113 [.       7     139 ..       7     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 6.2e-08
                                       EEEEEESTTSSHHHHHHHHHTSTEEE.SSSTTSSSSEEEEEEE......ETTEE.....................EE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaiv.sdkpgtTrdinegrvk......lkgke.....................ie 49 
                                       +++ vG+   GKStL  altg+k  v s++    + i+ g  +      +   +                     i 
  gi|518652471|ref|YP_008141991.1|   7 NIGMVGHVDHGKSTLTFALTGKKTDVhSEEVKRGISIKLGYADtpiyrcT---DetgkefysnkknsdncqlsrvIS 80 
                                       5899*****************86666455555555555554443332220...0334446666667778888888** PP

                                       EEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHH.TTSEEEEEEE CS
                          MMR_HSR1  50 lvDtpGliegaseekglgkaflalee.adlillvvdaseeklkpldeeleellee.akkplilvln 113
                                       +vD pG  e       l  ++la    ++ ++lv+ a+ee  +p+ +e    le    k++i+v n
  gi|518652471|ref|YP_008141991.1|  81 IVDAPG-HE------TLMATMLAGSAiMNGAILVIAANEECPQPQTREHLTALEImGIKEIIVVQN 139
                                       ******.54......788999987776799999999886666666666555554422344555655 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 !   19.8   0.1   4.4e-07    0.0008       1      62 [.     225     293 ..     225     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 4.4e-07
                                       EEEEEEEEEESEEETTEEEEEEC.TCTTSEE.......EEEEEEEEEEETEEESEEETTSEEEEEEEESS CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke.......ivtrissletfhededeavaganaGvivaikg 62 
                                       G+v +g +++G+l +Gde++i + ++  k +        +t+i+sl +    ++   +g+ a v++ +++
  gi|518652471|ref|YP_008141991.1| 225 GGVLGGALIRGKLTVGDEIEIAPgVQITK-GnkttwdnVTTKITSLMAGSSSYESILPGGLAAVGTELDP 293
                                       8899*******************765444.348***************9999999999999999887765 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.045        80     104     136 ..      10      39 ..       4      44 .. 0.74
   2 !   14.5   0.2   1.4e-05     0.024      17      98 ..     102     189 ..      87     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.045
                                       EECSTTSSHHHHHHHHCTT-----S-------- CS
                       RsgA_GTPase 104 lvGqSGvGKStLinallpelelktgevseklgr 136
                                       +vG+   GKStL  al+++   kt   se+ +r
  gi|518652471|ref|YP_008141991.1|  10 MVGHVDHGKSTLTFALTGK---KTDVHSEEVKR 39 
                                       6888999**********97...34444444444 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.4e-05
                                       -EEEEEEESTTTT--HHHHHHHHHHHHHTT-.EEEEEEE-GGG--HHH......HHHHHHHHHHHTTSEEEE--TTT CS
                       RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgi.epvivlnKiDlleeee......eleelkeelealgyevllvsakt 86 
                                       + +++v++++ +e+ + +    L+++e  gi e+++v nKiDl+++e+      e++++ +   a + +v+ vsa +
  gi|518652471|ref|YP_008141991.1| 102 NGAILVIAAN-EECPQPQTREHLTALEIMGIkEIIVVQNKIDLVTRERamesykEIKDFLKGSIAENAPVIPVSAYH 177
                                       5678999999.77777788889*********55566679*******9967755555555555556678888888888 PP

                                       HTTHHHHHHHCT CS
                       RsgA_GTPase  87 kegleelkellk 98 
                                       +++++ + e+++
  gi|518652471|ref|YP_008141991.1| 178 NTNIDVVFEAIE 189
                                       877777766665 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0      0.01        19       4      26 ..       8      30 ..       5      51 .. 0.83
   2 !    9.4   0.3   0.00045      0.81      40     142 ..      81     189 ..      68     190 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.01
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeel 26
                                      i ++G+v+ GK tLt al+g++ 
  gi|518652471|ref|YP_008141991.1|  8 IGMVGHVDHGKSTLTFALTGKKT 30
                                      6689**************99865 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
                         PduV-EutP  40 viDtPGeylenrklysalivtsaeadvialvqdateeesvfp.pgfasvfnkeviGiitkidlaedeeniea...ve 112
                                       ++D+PG      ++    +++     via   ++ ++++     ++  +  ke+i +  kidl++ e ++e     +
  gi|518652471|ref|YP_008141991.1|  81 IVDAPGHETLMATMLAGSAIMNGAILVIAANEECPQPQTREHlTALEIMGIKEIIVVQNKIDLVTRERAMESykeIK 157
                                       6788886666666666666666666667776776665554330444445579***********98776665511156 PP

                         PduV-EutP 113 elLksaGaek..ifevsavekegieellkyle 142
                                       ++Lk   ae+  ++ vsa+++++i+ +++ +e
  gi|518652471|ref|YP_008141991.1| 158 DFLKGSIAENapVIPVSAYHNTNIDVVFEAIE 189
                                       67876655552279*************99987 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0028       4.9       2      27 ..       7      32 ..       6      34 .. 0.91
   2 !    7.0   0.1    0.0022       3.9      99     156 .]     126     188 ..      65     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                                      EEEEEESTTSSHHHHHHHHHTTSEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkv 27
                                      ++ +vG  + Gk+tl  altg+k++v
  gi|518652471|ref|YP_008141991.1|  7 NIGMVGHVDHGKSTLTFALTGKKTDV 32
                                      6889******************9987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0022
                                       HHHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHT......S-EEEEBTTTTBTHHHHHHHH CS
                            FeoB_N  99 lqllelgvpvvlalnmideaekkgieidlkkLsekLg......vpvvktsakkkegieellkai 156
                                       l+++ + ++++++ n+id +++++     k++++ L+       pv+++sa ++++i+ + +ai
  gi|518652471|ref|YP_008141991.1| 126 LEIMGI-KEIIVVQNKIDLVTRERAMESYKEIKDFLKgsiaenAPVIPVSAYHNTNIDVVFEAI 188
                                       344433.5688889**********999999999999544334489************9988775 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 ?   14.7   0.1   1.3e-05     0.023      57     100 ..     133     188 ..      87     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.3e-05
                      MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare............pnsvviSaekelnldeLkeki 100
                                       + ++v NKiDl++ e   e ++e              ++++Sa +++n+d + e+i
  gi|518652471|ref|YP_008141991.1| 133 EIIVVQNKIDLVTRERAMESYKEikdflkgsiaenAPVIPVSAYHNTNIDVVFEAI 188
                                       568999*****98887766666557788899987668999**********999987 PP

>> DUF4124  Domain of unknown function (DUF4124)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.9e-05      0.14      12      30 ..      50      68 ..      47     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.9e-05
                           DUF4124 12 aevYkWvDanGvvhysdqP 30
                                        +Y+++D+ G+  ys+  
  gi|518652471|ref|YP_008141991.1| 50 TPIYRCTDETGKEFYSNKK 68
                                      579*************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 ?   -0.5   0.1      0.27   4.9e+02      31      50 ..       7      26 ..       4      32 .. 0.86
   2 ?   10.2   0.1   0.00015      0.26     165     228 ..     128     191 ..      76     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.27
                                      EEEEEE-TTSSHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealg 50
                                       +G+ G    Gkstl+ al+
  gi|518652471|ref|YP_008141991.1|  7 NIGMVGHVDHGKSTLTFALT 26
                                      69*************98886 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00015
                                       CHHH-SEEEE.E---HHHHHHHHHHHHHHHHHCSTTBTTB--EEEEEBCCCTBSHHHHHHHHHHH CS
                              MeaB 165 ileiaDiivv.nkaDkkeaekaarelraaleleeekekeWrpkvlktsavegeGidelvdaieeh 228
                                       i+ i +iivv nk D+   e+a + ++ + + ++ + +e +++v+ +sa ++  id +++aie+ 
  gi|518652471|ref|YP_008141991.1| 128 IMGIKEIIVVqNKIDLVTRERAMESYKEIKDFLKGSIAE-NAPVIPVSAYHNTNIDVVFEAIEKI 191
                                       788899888879***************999998877655.789*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2697.93
//
Query:       gi|518652472|ref|YP_008141992.1|  [L=94]
Description: hypothetical protein FACI_IFERC00001G1111 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-23   82.3   1.7    2.2e-23   82.1   1.7    1.1  1  DUF357    Protein of unknown function (DUF357)


Domain annotation for each model (and alignments):
>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.1   1.7   1.2e-27   2.2e-23       1      73 []       9      81 ..       9      81 .. 0.99

  Alignments for each domain:
  == domain 1  score: 82.1 bits;  conditional E-value: 1.2e-27
                                      HHHHHHHHHHHHHH.....TS---HHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTSTS CS
                            DUF357  1 rYirlleealekvkiapdeesplgeaaeevlemaesYleDakyflekgdlvnAlasfsYaeGwLDagarlgll 73
                                      +Y+++ + al+k++i ++ +s ++  a++ ++m+ +Y++Dakyf++k+d++nA+a+++Y++Gw+D+ +r+gl+
  gi|518652472|ref|YP_008141992.1|  9 KYFEIEKAALDKIRIIAPVDSYIYGIAKDHMDMVLNYYNDAKYFYSKNDFINAFAALNYSYGWIDSAIRIGLF 81
                                      7**********************************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (94 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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 0.30s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 623.35
//
Query:       gi|518652473|ref|YP_008141993.1|  [L=384]
Description: hypothetical protein FACI_IFERC00001G1112 [Ferroplasma acidarmanus fer1]
Scores for complete 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-71  238.8   0.0    8.8e-71  238.4   0.0    1.1  1  RmuC             RmuC family
     0.0019   18.5   0.5      0.077   13.3   0.0    2.9  2  DUF2383          Domain of unknown function (DUF2383)
     0.0048   17.1   3.6       0.47   10.6   0.5    2.4  2  Fib_alpha        Fibrinogen alpha/beta chain family
     0.0083   16.5   9.8      0.026   14.9   0.9    3.1  4  Syntaxin_2       Syntaxin-like protein
     0.0087   16.3   1.9          3    8.2   0.1    2.5  2  BLOC1_2          Biogenesis of lysosome-related organelles co
  ------ inclusion threshold ------
      0.012   14.8   2.8          2    7.5   0.1    2.2  2  DUF2232          Predicted membrane protein (DUF2232)
      0.029   14.1   1.2        3.3    7.6   0.0    3.0  2  DASH_Duo1        DASH complex subunit Duo1
      0.032   14.3   0.3        1.6    8.8   0.1    2.3  2  ApoLp-III        Apolipophorin-III precursor (apoLp-III)
      0.038   14.2   1.5       0.62   10.4   0.2    3.1  3  DUF948           Bacterial protein of unknown function (DUF94
       0.04   13.0   0.7          4    6.5   0.1    2.2  2  APG17            Autophagy protein Apg17
      0.042   13.5   0.1       0.11   12.2   0.0    1.6  2  BCAS2            Breast carcinoma amplified sequence 2 (BCAS2
      0.048   13.7   4.8       0.29   11.2   0.6    2.3  2  Baculo_PEP_C     Baculovirus polyhedron envelope protein, PEP
      0.048   13.2   0.7        5.6    6.5   0.1    2.7  3  PI3K_P85_iSH2    Phosphatidylinositol 3-kinase regulatory sub
      0.052   13.6   2.0        1.8    8.6   0.0    2.7  3  DUF4460          Domain of unknown function (DUF4460)
      0.061   13.4   0.7          1    9.4   0.0    2.3  2  DHR10            Designed helical repeat protein 10 domain
       0.12   12.8   2.0        5.4    7.5   0.1    2.5  2  H-kinase_dim     Signal transducing histidine kinase, homodim
       0.13   12.8   0.2        2.2    8.8   0.2    2.4  2  APG6_N           Apg6 coiled-coil region
       0.13   12.8   0.9        9.1    6.9   0.3    2.5  2  Syntaxin-6_N     Syntaxin 6, N-terminal
       0.19   11.8   0.6        2.8    8.0   0.1    2.3  2  DUF1664          Protein of unknown function (DUF1664)
       0.26   11.4   3.9        7.8    6.7   0.6    2.7  2  IFT20            Intraflagellar transport complex B, subunit 
       0.33   11.1   3.6       0.99    9.6   1.8    2.2  2  Tropomyosin_1    Tropomyosin like
       0.52   10.3   3.9          6    6.9   0.1    2.9  3  P4Ha_N           Prolyl 4-Hydroxylase alpha-subunit, N-termin
       0.89    9.6   5.1        1.6    8.7   2.4    2.2  2  CENP-F_leu_zip   Leucine-rich repeats of kinetochore protein 


Domain annotation for each model (and alignments):
>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.4   0.0   1.1e-73   8.8e-71       2     287 ..      79     361 ..      78     364 .. 0.96

  Alignments for each domain:
  == domain 1  score: 238.4 bits;  conditional E-value: 1.1e-73
                              RmuC   2 qleellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLknsktrGnwGEvqLeril 78 
                                       +l+ l +plk++l+++++ +e+ ++e+++e ++lk +l +l++  ++l++++ +L+ aLkn+ +rG+wGE++L+r++
  gi|518652473|ref|YP_008141993.1|  79 KLNGLIEPLKDSLKTYQTYIENIERERKSESGALKDNLDTLSRKITDLEHDTIKLSGALKNPSIRGKWGEITLRRTV 155
                                       58899************************************************************************ PP

                              RmuC  79 essgleegeeyetqvslkdeege.lrpDvvvklpggkklviDsKvpleaYerlveaeddeereealkahaksvkkhi 154
                                       e +g++  +++ +q+    e ++  +pD+++klp+++++v+DsKvpl+ Y + ++ e+d   +++l+++  ++++h+
  gi|518652473|ref|YP_008141993.1| 156 EIAGMTPYCDFIEQAVS--E-DRlTKPDMIIKLPNRRTIVVDSKVPLSGYFEHMNGEED---KTFLDKYMLAFNSHV 226
                                       ***************94..3.34459*****************************9885...79************* PP

                              RmuC 155 keLseKdYeel.e.sldyvlmFiPiEsayaealeadpeLleealrkkVvlasPttLlalLrtvamlwrqeaqeknae 229
                                       ++L++K+Y+e  + s+d+v+mF+P+Es+++++++++pe++e+a++kkV++a+P tL+ lL tv+m+w++ +  +n +
  gi|518652473|ref|YP_008141993.1| 227 RDLASKKYWEKfDgSVDFVVMFLPMESLLSLVMSNKPEIIEDAISKKVIIATPVTLISLLLTVHMGWKDINTVENFN 303
                                       ***********648*************************************************************** PP

                              RmuC 230 eiaellgelydkfekfgedleklgkklekaqksydkavkklegnilrkaeklkelgvk 287
                                        +  +++e+y+++++f+ dl+++ k+l+k+ +s++++    ++++   +e+l + +v+
  gi|518652473|ref|YP_008141993.1| 304 GLIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNKLEPVIENLIKTDVA 361
                                       ************************************9999999999999999887776 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   9.9e-05     0.077       5      30 ..      79     104 ..      75     133 .. 0.90
   2 ?    2.2   0.0      0.28   2.2e+02       5      32 ..     322     348 ..     286     370 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.9e-05
                                       HHHHHHHHHHHHHHHHHHHHHT--SH CS
                           DUF2383   5 aLndLietlkdgeegykeaaekvkdp 30 
                                       +Ln Lie lkd+ ++y++++e+++++
  gi|518652473|ref|YP_008141993.1|  79 KLNGLIEPLKDSLKTYQTYIENIERE 104
                                       8**********************976 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.28
                                       HHHHHHHHHHHHHHHHHHHHHT--SHHH CS
                           DUF2383   5 aLndLietlkdgeegykeaaekvkdpql 32 
                                        Ln+  ++l  +++ ++++ +++k ++l
  gi|518652473|ref|YP_008141993.1| 322 DLNETSKNLSKSIDSFNRMTRDIK-NKL 348
                                       344444445555555555555555.333 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.5    0.0006      0.47      67     128 ..      72     133 ..      29     140 .. 0.71
   2 !    7.0   0.2    0.0082       6.4      36      92 ..     298     354 ..     291     369 .. 0.62

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.0006
                                       HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCH.HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  67 ekqkskkdndnvikksskeleeeilrlketidaqe.snirvLqnvlesneqkiqkLeqdidqk 128
                                       e++++  + + +i+ ++++l+  ++++ e+i ++  s+  +L+++l+++++ki++Le d  ++
  gi|518652473|ref|YP_008141993.1|  72 ERENTGLKLNGLIEPLKDSLK-TYQTYIENIERERkSESGALKDNLDTLSRKITDLEHDTIKL 133
                                       22222233388999999****.666666667766669********************998766 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0082
                                       HHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH CS
                         Fib_alpha  36 dlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilr 92 
                                       ++e+ +  +++i++ ++++++ v +++++ ++  ks +  ++++++++++le  i++
  gi|518652473|ref|YP_008141993.1| 298 TVENFNGLIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNKLEPVIEN 354
                                       556666666667777777777777777666666666666666666666666643333 PP

>> Syntaxin_2  Syntaxin-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.4     0.066        51      29      98 ..      37     106 ..      27     109 .. 0.77
   2 ?    4.7   0.5     0.049        38      11      50 ..      90     131 ..      78     142 .. 0.61
   3 ?    0.7   0.1      0.87   6.8e+02       3      31 ..     114     142 ..     112     153 .. 0.60
   4 !   14.9   0.9   3.3e-05     0.026       4      54 ..     298     349 ..     296     362 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.066
                        Syntaxin_2  29 eelreklhelie.einelikktnellkklsqldnsssdsqqklqkekLkkdfkealqeFqkiqrqyaekek 98 
                                       ++l+ ++he ie e ++l+++ +  +k+  ++++s+   +  l+ + L + +k++l+ +q + +++++ +k
  gi|518652473|ref|YP_008141993.1|  37 DKLKASMHEFIEsESRNLLNTGTIAFKNALEIERSERE-NTGLKLNGLIEPLKDSLKTYQTYIENIERERK 106
                                       56666677666514555556669999999999999865.8888999****************999987776 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.049
                        Syntaxin_2  11 nvstleklvkqLgtkkd..teelreklhelieeinelikktn 50 
                                       +++t + +++ ++  +   +  l+++l++l  +i++l ++t 
  gi|518652473|ref|YP_008141993.1|  90 SLKTYQTYIENIERERKseSGALKDNLDTLSRKITDLEHDTI 131
                                       444555555555555433366777777777777777777664 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.87
                        Syntaxin_2   3 snlqkinsnvstleklvkqLgtkkdteel 31 
                                       +nl +++++++ le+ + +L+ +  ++ +
  gi|518652473|ref|YP_008141993.1| 114 DNLDTLSRKITDLEHDTIKLSGALKNPSI 142
                                       45566666666666665555555555555 PP

  == domain 4  score: 14.9 bits;  conditional E-value: 3.3e-05
                        Syntaxin_2   4 nlqkinsnvstleklvkqLgtk.kdteelreklhelieeinelikktnellk 54 
                                        + ++n+++ +++++ +  +t  +d  e+ ++l ++i++ n++ ++++++l+
  gi|518652473|ref|YP_008141993.1| 298 TVENFNGLIAKIKEFYNNMQTFvGDLNETSKNLSKSIDSFNRMTRDIKNKLE 349
                                       6899******************88***********************99986 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 !    7.2   0.2    0.0082       6.4      39      81 ..      87     130 ..      73     139 .. 0.84
   2 !    8.2   0.1    0.0039         3      27      75 ..     301     345 ..     287     357 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0082
                           BLOC1_2  39 lkdvaaslekkleklnekye.elqpylqqidqiekqvteLeeav 81 
                                       lkd+++  ++ +e+++++ + e   +++++d + +++t+Le+  
  gi|518652473|ref|YP_008141993.1|  87 LKDSLKTYQTYIENIERERKsESGALKDNLDTLSRKITDLEHDT 130
                                       78888999999999998777799999**************9755 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0039
                           BLOC1_2  27 klNeaasekykklkdvaaslekkleklnekyeelqpylqqidqiekqvt 75 
                                       + N      ++k+k+  +++++++ +lne++++l++ +++ +++ ++++
  gi|518652473|ref|YP_008141993.1| 301 NFNG----LIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIK 345
                                       4443....34566666666666666666666666666666666666553 PP

>> DUF2232  Predicted membrane protein (DUF2232)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0026         2      87     132 ..       4      49 ..       1      67 [. 0.92
   2 ?    7.5   0.1    0.0026         2      65     153 ..     246     340 ..     236     352 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0026
                           DUF2232  87 tliagtlafllgillafallalllgvnllaqvekeikesveealkl 132
                                       +l++g++a +++  + +++++ +++ ++   ve+++k+s++e +++
  gi|518652473|ref|YP_008141993.1|   4 VLVIGIIAGFISGFALAIVIYSMINRKMSGNVEDKLKASMHEFIES 49 
                                       799**************************************99875 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0026
                           DUF2232  65 ilfgllGlvlGyllkkkksaert.....liagtlafllgillafallalllg.vnllaqvekeikesveealklyee 135
                                       ++f+++  +l+  +++k ++ +      +i++t ++l+++ll++ +  + ++ v+ ++ ++ +ike ++++++++ +
  gi|518652473|ref|YP_008141993.1| 246 VMFLPMESLLSLVMSNKPEIIEDaiskkVIIATPVTLISLLLTVHMGWKDINtVENFNGLIAKIKEFYNNMQTFVGD 322
                                       5555555555555555544332222223788888888888888888888888877799999**************99 PP

                           DUF2232 136 aGmsedelkelqklleee 153
                                        + +++ l++  ++++ +
  gi|518652473|ref|YP_008141993.1| 323 LNETSKNLSKSIDSFNRM 340
                                       976555555555555555 PP

>> DASH_Duo1  DASH complex subunit Duo1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0042       3.3      11      39 ..      79     107 ..      72     121 .. 0.88
   2 ?    3.9   0.3     0.056        44       6      50 ..     296     340 ..     294     362 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0042
                         DASH_Duo1  11 kinevienviesLkkaksniervketves 39 
                                       k+n  ie +++sLk+ +++ie++++  +s
  gi|518652473|ref|YP_008141993.1|  79 KLNGLIEPLKDSLKTYQTYIENIERERKS 107
                                       79*********************997666 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.056
                         DASH_Duo1   6 leqLrkinevienviesLkkaksniervketvestntLLdkWirI 50 
                                       +++++++n  i +++e  +++++ +  ++et ++ ++ +d++ r+
  gi|518652473|ref|YP_008141993.1| 296 INTVENFNGLIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRM 340
                                       556666666666666666666666666667766666666666655 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.12        93      38      69 ..      94     125 ..      82     142 .. 0.74
   2 ?    8.8   0.1    0.0021       1.6      84     130 ..     308     357 ..     296     366 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.12
                         ApoLp-III  38 lkqvikslqeelkkksdeleealkevkkkiee 69 
                                        +++i++++ e k +s++l+  l+ +  ki+ 
  gi|518652473|ref|YP_008141993.1|  94 YQTYIENIERERKSESGALKDNLDTLSRKITD 125
                                       56777888888888888888888877777765 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0021
                         ApoLp-III  84 kaqelqekvQsgvqslvkesqklaeslke...nsqeakeklakaikqayd 130
                                       k++e  +++Q+ v  l + s++l +s+++    ++ +k+kl++ i++++ 
  gi|518652473|ref|YP_008141993.1| 308 KIKEFYNNMQTFVGDLNETSKNLSKSIDSfnrMTRDIKNKLEPVIENLIK 357
                                       67777788888888888888888887754111556666777777666654 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 ?   -0.3   0.0       1.7   1.3e+03       1      18 [.      10      27 ..      10      54 .. 0.71
   2 ?    0.5   0.0      0.93   7.2e+02      24      41 ..     112     129 ..      78     139 .. 0.55
   3 ?   10.4   0.2   0.00079      0.62      35      70 ..     306     351 ..     274     370 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                            DUF948  1 IAglIaAiAFvvLvifli 18
                                      IAg+I   A+++++  +i
  gi|518652473|ref|YP_008141993.1| 10 IAGFISGFALAIVIYSMI 27
                                      899999999887665554 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.93
                            DUF948  24 lkktldeaaatieelekq 41 
                                       lk+ ld +++ i++le++
  gi|518652473|ref|YP_008141993.1| 112 LKDNLDTLSRKITDLEHD 129
                                       233333333333333333 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00079
                            DUF948  35 ieele..........kqvdpilkevedllakvnelledvneklekv 70 
                                       i++++           ++++++k++ + ++  n+++ d+++kle v
  gi|518652473|ref|YP_008141993.1| 306 IAKIKefynnmqtfvGDLNETSKNLSKSIDSFNRMTRDIKNKLEPV 351
                                       4444444444445558888899999999999999999999998866 PP

>> APG17  Autophagy protein Apg17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1    0.0051         4      35      95 ..      74     134 ..      39     233 .. 0.78
   2 ?    5.3   0.1     0.012       9.1     120     161 ..     308     354 ..     295     377 .. 0.59

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0051
                                       HHHHHHHHHHHHHHHHHHHHHHHIIIIIIIIIIIIIIIIIHHHHHHHHHHHHHHHHHHHHH CS
                             APG17  35 vkllakteflrdglkqQlkllekirkslerklekgkeefkdlikeldaanerLektlekLr 95 
                                       ++   k++ l++ lk+ lk+ ++  +++er++++ +  +kd +++l+++   Le+   kL+
  gi|518652473|ref|YP_008141993.1|  74 ENTGLKLNGLIEPLKDSLKTYQTYIENIERERKSESGALKDNLDTLSRKITDLEHDTIKLS 134
                                       4555566666777777777777777777777777777777777777777777776655555 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.012
                                       TTTHHHHHHHHHHHHHHHHHHHHHTTHH..HHHHHHHHHHH.....- CS
                             APG17 120 sveelkealkesidelqaaqkkldssllefdtdlrelkkel.....s 161
                                       +++e  +++++   +l+++ k+l++s+ +f++  r++k++l     +
  gi|518652473|ref|YP_008141993.1| 308 KIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNKLepvieN 354
                                       34444455555555555555555555555555555555555443330 PP

>> BCAS2  Breast carcinoma amplified sequence 2 (BCAS2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00014      0.11     132     185 ..      80     133 ..      74     139 .. 0.87
   2 ?   -2.7   0.0         5   3.9e+03     135     169 ..     319     353 ..     313     368 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                             BCAS2 132 leaelkklekeleetkeeieevnrqRkseQeeageeLksleekWrelvsknlei 185
                                       l+  ++ l++ l+++++ ie+++r+Rkse  +++++L +l++k ++l   ++++
  gi|518652473|ref|YP_008141993.1|  80 LNGLIEPLKDSLKTYQTYIENIERERKSESGALKDNLDTLSRKITDLEHDTIKL 133
                                       6677888999********************************999887777665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5
                             BCAS2 135 elkklekeleetkeeieevnrqRkseQeeageeLk 169
                                        + +l+++ +++++ i++ nr  ++ +++++  ++
  gi|518652473|ref|YP_008141993.1| 319 FVGDLNETSKNLSKSIDSFNRMTRDIKNKLEPVIE 353
                                       55556666666666666666665555555555554 PP

>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.056        43      36      80 ..      87     127 ..      54     139 .. 0.52
   2 ?   11.2   0.6   0.00038      0.29      40      94 ..     296     355 ..     286     368 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.056
                      Baculo_PEP_C  36 latlldaietqLnalsedlksllaeldtrldtlltnLtdalnalq 80 
                                       l+  l++ +t +++++ + ks +     +l+++l++L++++  l+
  gi|518652473|ref|YP_008141993.1|  87 LKDSLKTYQTYIENIERERKSESG----ALKDNLDTLSRKITDLE 127
                                       333333334444444444444333....44444444444444444 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00038
                      Baculo_PEP_C  40 ldaietqLnalsedlksllaeldt...rldtlltnLtdalnalq...dtlrneLtnlnsil 94 
                                       ++++e+ +n l +++k+  ++++t   +l+++++nL++++ +++    +++n+L+ +  +l
  gi|518652473|ref|YP_008141993.1| 296 INTVEN-FNGLIAKIKEFYNNMQTfvgDLNETSKNLSKSIDSFNrmtRDIKNKLEPVIENL 355
                                       566666.88899999999999999999************9999966667777776654443 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 ?    6.5   0.1    0.0071       5.6      65     113 ..      88     139 ..      60     144 .. 0.82
   2 ?   -2.5   0.0       4.2   3.3e+03     116     138 ..     210     232 ..     184     234 .. 0.60
   3 ?    4.3   0.0     0.035        27      17      50 ..     314     347 ..     298     384 .] 0.69

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0071
                     PI3K_P85_iSH2  65 eeqiklqekfskea...qehEieklqenleqlksrlkelhsskekLeedlkq 113
                                       ++ +k+  +++++     + E   l++nl+ l +++  l+    kL+ +lk+
  gi|518652473|ref|YP_008141993.1|  88 KDSLKTYQTYIENIereRKSESGALKDNLDTLSRKITDLEHDTIKLSGALKN 139
                                       556666666666663334678889**********************999997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.2
                     PI3K_P85_iSH2 116 eeereleReinalkpellqLqkr 138
                                       e++  l++ + a ++++  L+ +
  gi|518652473|ref|YP_008141993.1| 210 EDKTFLDKYMLAFNSHVRDLASK 232
                                       44555666666666666655544 PP

  == domain 3  score: 4.3 bits;  conditional E-value: 0.035
                     PI3K_P85_iSH2  17 eklrevskqlqekskeydqlkeeynkiseeiqlk 50 
                                       ++ + +  +l+e+sk++ +  +++n+++ +i+ k
  gi|518652473|ref|YP_008141993.1| 314 NNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNK 347
                                       4555555666667777777777777777666654 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.079        62      38      57 ..      89     111 ..      87     143 .. 0.75
   2 ?    8.6   0.0    0.0023       1.8      22      68 ..     178     223 ..     176     259 .. 0.83
   3 ?   -2.8   0.1       8.1   6.3e+03      41      49 ..     328     336 ..     307     354 .. 0.51

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.079
                           DUF4460  38 eSLklLnsyleelkkeekk...s 57 
                                       +SLk  + y+e++++e+k+    
  gi|518652473|ref|YP_008141993.1|  89 DSLKTYQTYIENIERERKSesgA 111
                                       79************998764333 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0023
                           DUF4460  22 hPDlfgqyPkekkvNeeSLklLnsyleelkkeekksikpekkkLtFy 68 
                                       +PD++ ++P+ +++  +S   L++y+e+++ ee  +++ +k+ L F 
  gi|518652473|ref|YP_008141993.1| 178 KPDMIIKLPNRRTIVVDSKVPLSGYFEHMNGEED-KTFLDKYMLAFN 223
                                       7******************************976.777779999995 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 8.1
                           DUF4460  41 klLnsylee 49 
                                       k L+  +++
  gi|518652473|ref|YP_008141993.1| 328 KNLSKSIDS 336
                                       233333333 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 ?    1.9   0.3      0.28   2.2e+02      52      78 ..     102     128 ..      66     139 .. 0.66
   2 ?    9.4   0.0    0.0013         1       5      37 ..     314     346 ..     311     355 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.28
                             DHR10  52 leeakkklkelrdaleekeielreler 78 
                                       ++e k++  +l+d+l++++++  +le+
  gi|518652473|ref|YP_008141993.1| 102 ERERKSESGALKDNLDTLSRKITDLEH 128
                                       334445555566666666666666655 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0013
                             DHR10   5 aeekeelaelErkarelqakidalqvvekdlrs 37 
                                       +++++ + +l + +++l+++id+++++++d+++
  gi|518652473|ref|YP_008141993.1| 314 NNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKN 346
                                       56778889999*******************997 PP

>> H-kinase_dim  Signal transducing histidine kinase, homodimeric domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.3     0.063        49      36      66 ..      81     130 ..      26     133 .. 0.73
   2 ?    7.5   0.1    0.0069       5.4      21      61 ..     298     336 ..     297     348 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.063
                      H-kinase_dim  36 r...................fenglkasvtelksslqnlgrisgeLQegv 66 
                                       +                   +e ++k+   +lk+ l+ l+r +++L    
  gi|518652473|ref|YP_008141993.1|  81 NglieplkdslktyqtyienIERERKSESGALKDNLDTLSRKITDLEHDT 130
                                       0555555555555566666678899999999**************97655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0069
                      H-kinase_dim  21 lVitkarLnqsleefrfenglkasvtelksslqnlgrisge 61 
                                       +V + + L  +++ef   n++++ v +l+++++nl++ ++ 
  gi|518652473|ref|YP_008141993.1| 298 TVENFNGLIAKIKEFY--NNMQTFVGDLNETSKNLSKSIDS 336
                                       5667789999999999..88889999988888888875543 PP

>> APG6_N  Apg6 coiled-coil region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.2    0.0029       2.2      19      71 ..      85     138 ..      78     140 .. 0.83
   2 ?    1.3   0.0       0.6   4.7e+02      18      74 ..     306     359 ..     297     384 .] 0.63

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0029
                            APG6_N  19 eqaekerdaYeeflkklkkekkeeek.qdeeleeleeeleklekeeeelleeLk 71 
                                       e +++  ++Y+++ +++++e+k+e+   +++l+ l +++ +le +  +l   Lk
  gi|518652473|ref|YP_008141993.1|  85 EPLKDSLKTYQTYIENIERERKSESGaLKDNLDTLSRKITDLEHDTIKLSGALK 138
                                       66788899***********98887658899999999999999999888877776 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.6
                            APG6_N  18 leqaekerdaYeeflkklkkekkeeekqdeeleeleeeleklekeeeelleeLkele 74 
                                       +++ ++  +++++f   l++++k+ +   +++++ ++  ++++++ e  +e+L +++
  gi|518652473|ref|YP_008141993.1| 306 IAKIKEFYNNMQTFVGDLNETSKNLS---KSIDSFNRMTRDIKNKLEPVIENLIKTD 359
                                       55566666777777778887766655...4666666666666666666666665554 PP

>> Syntaxin-6_N  Syntaxin 6, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.3     0.012       9.1      30      62 ..      96     128 ..      63     157 .. 0.75
   2 ?    4.0   0.0     0.097        75      10      56 ..     309     354 ..     296     374 .. 0.60

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.012
                      Syntaxin-6_N  30 dtssstseeldetrteLrkalrsiewdledLee 62 
                                       + +++ + e ++ +  L+ +l++++ ++ dLe+
  gi|518652473|ref|YP_008141993.1|  96 TYIENIERERKSESGALKDNLDTLSRKITDLEH 128
                                       223357889999999999999999999999997 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.097
                      Syntaxin-6_N  10 VqkslnkaeslyrrwerlledtssstseeldetrteLrkalrsiewd 56 
                                       +++  n++++ ++  +++ ++ s ++ +++++ +++++++l+ + ++
  gi|518652473|ref|YP_008141993.1| 309 IKEFYNNMQTFVGDLNETSKNLS-KSIDSFNRMTRDIKNKLEPVIEN 354
                                       44444555555555554333332.23566666666666666655544 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.33   2.6e+02      61     100 ..      91     127 ..      61     140 .. 0.45
   2 ?    8.0   0.1    0.0037       2.8      68     120 ..     299     351 ..     283     363 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.33
                           DUF1664  61 krhLssridrvdkkldeqkeiskeikeevtevredlseig 100
                                        +  +  i++++++    k  s ++k++++++++++++++
  gi|518652473|ref|YP_008141993.1|  91 LKTYQTYIENIERE---RKSESGALKDNLDTLSRKITDLE 127
                                       22222222222221...12222222222333333332222 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0037
                           DUF1664  68 idrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskleri 120
                                       +++ +  + + ke  ++++  v +++e  +++++ ++s +++ +++++kle +
  gi|518652473|ref|YP_008141993.1| 299 VENFNGLIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNKLEPV 351
                                       55566667777888888888888888888888888888888888888888754 PP

>> IFT20  Intraflagellar transport complex B, subunit 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.6      0.01       7.8      63     109 ..      59     105 ..      37     127 .. 0.90
   2 ?    5.1   0.2      0.03        24      31      58 ..     312     336 ..     295     357 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.01
                             IFT20  63 AigarnllkseakqreaeqqqlqaliaekkaeleRlrvelesLqkve 109
                                        i+ +n+l+ e+ +re+   +l+ li+  k  l  +++ +e +++  
  gi|518652473|ref|YP_008141993.1|  59 TIAFKNALEIERSERENTGLKLNGLIEPLKDSLKTYQTYIENIERER 105
                                       6999****************************999999888887755 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.03
                             IFT20  31 Fvkkinefqklvkelievleelakkvek 58 
                                       F    n++q++v++l e+ ++l+k++++
  gi|518652473|ref|YP_008141993.1| 312 FY---NNMQTFVGDLNETSKNLSKSIDS 336
                                       22...23344455555555555555544 PP

>> Tropomyosin_1  Tropomyosin like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.8    0.0013      0.99      25      88 ..      65     129 ..      37     140 .. 0.88
   2 ?    0.8   0.0      0.63   4.9e+02      66     103 ..     325     355 ..     299     381 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0013
                     Tropomyosin_1  25 eleqenlekeqeiksLtkknqqleeevekleeklkeak.ekaeesekkktnnealtrkiqlLEee 88 
                                       +le e+ e+e+   +L+  ++ l + + ++++ +++ + e ++es  +k n ++l+rki  LE +
  gi|518652473|ref|YP_008141993.1|  65 ALEIERSERENTGLKLNGLIEPLKDSLKTYQTYIENIErERKSESGALKDNLDTLSRKITDLEHD 129
                                       68999999**************************998625678888999999***********88 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.63
                     Tropomyosin_1  66 eesekkktnnealtrkiqlLEeeleesdkkLkettekL 103
                                       e s++++++ ++++r  + +        +kL+  +e L
  gi|518652473|ref|YP_008141993.1| 325 ETSKNLSKSIDSFNRMTRDIK-------NKLEPVIENL 355
                                       223333333333333333333.......3333333333 PP

>> P4Ha_N  Prolyl 4-Hydroxylase alpha-subunit, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.5   2.7e+03      10      32 ..      34      56 ..      28      78 .. 0.76
   2 ?    3.4   0.3     0.091        71      18      48 ..      79     109 ..      64     124 .. 0.83
   3 ?    6.9   0.1    0.0078         6       5      59 ..     302     356 ..     298     358 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.5
                            P4Ha_N 10 klErelveeLesyieeeekklek 32
                                      ++E++l   ++++ie e ++l +
  gi|518652473|ref|YP_008141993.1| 34 NVEDKLKASMHEFIESESRNLLN 56
                                      68999999999999998877654 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.091
                            P4Ha_N  18 eLesyieeeekkleklkrfleeleeehesak 48 
                                       +L+  ie ++  l++ + ++e++e+e++s++
  gi|518652473|ref|YP_008141993.1|  79 KLNGLIEPLKDSLKTYQTYIENIERERKSES 109
                                       6788899999****************97643 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0078
                            P4Ha_N   5 lekLlklErelveeLesyieeeekkleklkrfleeleeehesakedkeeylsnPl 59 
                                        + L+   +e+ +++++++ ++++  ++l++ ++++++ +++ k++ e +++n +
  gi|518652473|ref|YP_008141993.1| 302 FNGLIAKIKEFYNNMQTFVGDLNETSKNLSKSIDSFNRMTRDIKNKLEPVIENLI 356
                                       566777778999**************************99888888888888866 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 ?    8.7   2.4    0.0021       1.6      23     111 ..      44     138 ..      30     140 .. 0.70
   2 ?    0.9   0.0      0.56   4.4e+02      56      87 ..     304     332 ..     296     359 .. 0.56

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0021
                    CENP-F_leu_zip  23 kdkvenLerelemseenqekvileaEtskaevet..lkeeieelaeelreleldLvalr....sekeeLekelqkkq 93 
                                       ++ +e+  r+l + +    k  le E s  e  +  l+  ie l+ +l+  ++ ++++     se   L+ +l +  
  gi|518652473|ref|YP_008141993.1|  44 HEFIESESRNLLNTGTIAFKNALEIERSERENTGlkLNGLIEPLKDSLKTYQTYIENIErerkSESGALKDNLDTLS 120
                                       55555555666666666666677778777777763355669999999999999999998444444556999999999 PP

                    CENP-F_leu_zip  94 ervseLeslnsslenlle 111
                                       +++ +Le    +l+  l+
  gi|518652473|ref|YP_008141993.1| 121 RKITDLEHDTIKLSGALK 138
                                       999999988777776665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.56
                    CENP-F_leu_zip  56 tlkeeieelaeelreleldLvalrsekeeLek 87 
                                       +l ++i+e  ++++ +  dL+++++   +L k
  gi|518652473|ref|YP_008141993.1| 304 GLIAKIKEFYNNMQTFVGDLNETSK---NLSK 332
                                       5666666666666666666665553...2333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1337  (0.0745719); expected 358.6 (0.02)
Passed bias filter:                      960  (0.0535445); expected 358.6 (0.02)
Passed Vit filter:                       132  (0.00736237); 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):              23  [number of targets reported over threshold]
# CPU time: 0.67u 0.33s 00:00:01.00 Elapsed: 00:00:00.47
# Mc/sec: 2443.49
//
Query:       gi|518652474|ref|YP_008141994.1|  [L=131]
Description: hypothetical protein FACI_IFERC00001G1113 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   12.5   0.0       0.16   11.6   0.0    1.4  1  NAT       NAT, N-acetyltransferase, of N-acetylglutamate synt


Domain annotation for each model (and alignments):
>> NAT  NAT, N-acetyltransferase, of N-acetylglutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.1e-06      0.16      26     116 ..       3     125 ..       1     128 [. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-06
                                       SSCCCS....SXCCHHHHHHTTSTTTSSXHHHHHHHHHTSXEEEEEETTXSEEEEE.....EXSS............ CS
                               NAT  26 kslkel....idlekLksliedsfkrkldvkdYldrlkgkiakiyiaedyeglAivtwedpkeek............ 86 
                                       ++++e+    idl+kL++++e+ f++++ + +  ++ +g+++++  ++ ++++A +    +   +            
  gi|518652474|ref|YP_008141994.1|   3 TKDREFngknIDLDKLSNVVEQYFQNEKFKTQLGKHPNGTLIQATKEGLLRSIAGMDR--SY--Sitisgtpdnvki 75 
                                       55556666678*************8888787877888888888888888888886622..22..233556667777* PP

                                       ....................SSXEEEEEEEXHHHHHTTHHHHHHHHHHHH CS
                               NAT  87 ....................evayLdkFavlkssqgsgvsdvvfkalkkd 116
                                                            ++ L  F v +s +g ++ d+ +k + ++
  gi|518652474|ref|YP_008141994.1|  76 sigmgkwlqnlgvaaiesflLTPELAFFEVPESLWGFEIEDKFWKYIENQ 125
                                       *****************99999**********************999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); 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 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 954.79
//
Query:       gi|518652475|ref|YP_008141995.1|  [L=165]
Description: hypothetical protein FACI_IFERC00001G1114 [Ferroplasma acidarmanus fer1]
Scores for 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   23.0   1.5     0.0013   18.4   0.3    2.3  2  Phage_holin_2_3  Bacteriophage holin family HP1
  ------ inclusion threshold ------
      0.023   14.9   3.5       0.33   11.1   0.1    2.1  2  DUF2371          Uncharacterised conserved protein (DUF2371)
       0.04   14.1   3.8       0.62   10.3   0.1    2.4  2  DUF2905          Protein of unknown function (DUF2905)
       0.12   12.1   0.1       0.12   12.1   0.1    1.6  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
       0.24   11.2   0.5       0.69    9.8   0.0    1.9  2  DUF4307          Domain of unknown function (DUF4307)
       0.31   11.3   3.1        3.4    7.9   0.3    2.3  2  DUF2964          Protein of unknown function (DUF2964)
        0.4   10.8   4.0          4    7.6   0.1    2.2  2  DUF2614          Zinc-ribbon containing domain
          6    7.2   5.8         14    6.0   0.4    2.2  2  DUF3040          Protein of unknown function (DUF3040)


Domain annotation for each model (and alignments):
>> Phage_holin_2_3  Bacteriophage holin family HP1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.028        62      25      43 ..       3      21 ..       1      31 [. 0.85
   2 !   18.4   0.3     6e-07    0.0013       5      49 ..     119     164 ..     116     165 .] 0.91

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.028
                   Phage_holin_2_3 25 eWAiviGIicgvvTfliNw 43
                                       W +v G+++ +v + + +
  gi|518652475|ref|YP_008141995.1|  3 KWILVLGVVMLIVGVSMYV 21
                                      7*********999887755 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 6e-07
                   Phage_holin_2_3   5 slaAYisSavavvlGll.sLseWAiviGIicgvvTfliNwyykrke 49 
                                       + + Y + + +v++G+    s   i+iGIi++++ +l+N  ++ ++
  gi|518652475|ref|YP_008141995.1| 119 TSITYGPTGYLVYIGYVaDFSTFLILIGIIVAIAGILLNNKFRLRD 164
                                       6789***********87799**********************9887 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00015      0.33      42      71 ..       4      33 ..       1      65 [. 0.64
   2 ?    4.6   0.6     0.015        34      39      57 ..     138     156 ..     133     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00015
                           DUF2371 42 lvlllGllvllvGiamavlgywpkkaklas 71
                                       +l+lG+++l+vG++m v +   k + +++
  gi|518652475|ref|YP_008141995.1|  4 WILVLGVVMLIVGVSMYVYSGMEKPKISEN 33
                                      5899************99766655532222 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.015
                           DUF2371  39 vsglvlllGllvllvGiam 57 
                                        s++++l+G++v + Gi +
  gi|518652475|ref|YP_008141995.1| 138 FSTFLILIGIIVAIAGILL 156
                                       5899************976 PP

>> DUF2905  Protein of unknown function (DUF2905)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00028      0.62       2      21 ..       3      22 ..       2      32 .. 0.89
   2 ?    4.3   0.6      0.02        45       3      18 ..     141     156 ..     140     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00028
                           DUF2905  2 klLivlglvlvvlgllllll 21
                                      k+++vlg+v++++g+ +++ 
  gi|518652475|ref|YP_008141995.1|  3 KWILVLGVVMLIVGVSMYVY 22
                                      9**************99986 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.02
                           DUF2905   3 lLivlglvlvvlglll 18 
                                       +Li++g++++++g+ll
  gi|518652475|ref|YP_008141995.1| 141 FLILIGIIVAIAGILL 156
                                       59***********997 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.5       3.1     7e+03      36      47 ..       6      17 ..       3      23 .. 0.72
   2 ?   12.1   0.1   5.5e-05      0.12      22      53 ..     128     160 ..     109     164 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.1
                   Phage_holin_2_4 36 alvGlavAliGl 47
                                       ++G+++ ++G+
  gi|518652475|ref|YP_008141995.1|  6 LVLGVVMLIVGV 17
                                      567888888886 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 5.5e-05
                   Phage_holin_2_4  22 vvsfaGflas.selialvGlavAliGlLvnWyY 53 
                                          ++G++a  s ++ l+G++vA++G+L+n  +
  gi|518652475|ref|YP_008141995.1| 128 YLVYIGYVADfSTFLILIGIIVAIAGILLNNKF 160
                                       4567899885488999************99666 PP

>> DUF4307  Domain of unknown function (DUF4307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00031      0.69       3      43 ..       3      39 ..       1      53 [. 0.53
   2 ?   -1.3   0.2      0.84   1.9e+03       5      19 ..     141     155 ..     139     159 .. 0.60

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00031
                           DUF4307  3 rllvillvvlvvvalalvawigysqgsadvsaevvgfevvd 43
                                      +++++l+vv+++v++ + ++ g+++  +++s  + +f+v  
  gi|518652475|ref|YP_008141995.1|  3 KWILVLGVVMLIVGVSMYVYSGMEK--PKIS--ENNFTVKG 39
                                      5666666666666666666666655..4444..44444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.84
                           DUF4307   5 lvillvvlvvvalal 19 
                                       ++il++++v++a++l
  gi|518652475|ref|YP_008141995.1| 141 FLILIGIIVAIAGIL 155
                                       455666666666554 PP

>> DUF2964  Protein of unknown function (DUF2964)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.2     0.033        74      37      52 ..       6      21 ..       2      27 .. 0.86
   2 ?    7.9   0.3    0.0015       3.4      11      33 ..     136     158 ..     134     163 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.033
                           DUF2964 37 lrygvialliGiaafV 52
                                      l  gv+ l++G+ + V
  gi|518652475|ref|YP_008141995.1|  6 LVLGVVMLIVGVSMYV 21
                                      6789********9888 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0015
                           DUF2964  11 AtiavFiaLagiaaaihGlLfde 33 
                                       A  ++F+ L gi++ai G+L  +
  gi|518652475|ref|YP_008141995.1| 136 ADFSTFLILIGIIVAIAGILLNN 158
                                       7789***************9876 PP

>> DUF2614  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0018         4      40      62 ..       5      27 ..       1      41 [. 0.87
   2 ?    4.4   0.8     0.018        40       8      32 ..     134     158 ..     128     163 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                           DUF2614 40 flllGlllvlastvvyfwiGlls 62
                                      +l+lG++++++ + +y++ G+  
  gi|518652475|ref|YP_008141995.1|  5 ILVLGVVMLIVGVSMYVYSGMEK 27
                                      689*****************965 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.018
                           DUF2614   8 kirtfalllvfiglivmyigllfke 32 
                                        +  f+ +l++ig+iv   g+l+++
  gi|518652475|ref|YP_008141995.1| 134 YVADFSTFLILIGIIVAIAGILLNN 158
                                       56789999*********99999876 PP

>> DUF3040  Protein of unknown function (DUF3040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4    0.0062        14      51      65 ..       5      19 ..       2      26 .. 0.76
   2 ?    3.6   0.7     0.036        80      58      83 ..     129     155 ..     120     157 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0062
                           DUF3040 51 lfvaGllllvlGvaa 65
                                      ++v+G+++l++Gv+ 
  gi|518652475|ref|YP_008141995.1|  5 ILVLGVVMLIVGVSM 19
                                      678899999999764 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.036
                           DUF3040  58 llvlG.vaaaavvlgvvGfvvmlagvv 83 
                                       l+ +G va  ++ l+++G++v++ag++
  gi|518652475|ref|YP_008141995.1| 129 LVYIGyVADFSTFLILIGIIVAIAGIL 155
                                       456775666668899999999988865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1014  (0.0565564); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1364.65
//
Query:       gi|518652476|ref|YP_008141996.1|  [L=403]
Description: hypothetical protein FACI_IFERC00001G1115 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-35  122.2  49.8    6.6e-34  117.4  37.1    2.2  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 !  117.4  37.1   3.7e-38   6.6e-34       4     353 .]      32     356 ..      29     356 .. 0.83
   2 !   18.5   4.8   4.2e-08   0.00075     105     175 ..     323     391 ..     316     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 117.4 bits;  conditional E-value: 3.7e-38
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       ++ l +l+ ++++p+++ +++e ++ s   ig++l++y++++a+++  lGrlsdr+Gr+ ++ +g+++f++g l+++
  gi|518652476|ref|YP_008141996.1|  32 TIGLRTLGLFMVLPIFT-LYGEKFTGSYLLIGTALGAYGITMALFQTSLGRLSDRYGRKLIISIGIATFIIGNLICA 107
                                       5667889999*******.9*****************************************************77777 PP

                             MFS_1  81 .fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                          ++++ l+++r++ G+ga  + +ag+al+ + +p ++r+   ++++++++l+++lg ++g+lla+ ++++++f+i
  gi|518652476|ref|YP_008141996.1| 108 dP-INIYGLILGRLVEGAGA--VSSAGIALVHESVPVNRRNISDAIIGVAIGLSFMLGVIVGPLLATIFNYSSIFVI 181
                                       43.89999**********95..******************************************************* PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..lltllp 231
                                       +ai+++++f+   l+ + e +++k ++                +ka   ++   +++i++++ff+ f++  ++ +lp
  gi|518652476|ref|YP_008141996.1| 182 AAIIGAISFI--PLWKVKETKKEKMFK----------------IKAHIDSK---LAVISIISFFIYFYMivFYLYLP 237
                                       ********88..244444444444442................55556666...26666666665666667888888 PP

                             MFS_1 232 lylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll.vl 307
                                       ++  + +  s +++ +  +++++++g+i+ l ++r +d+    ++ l++l++l+++++++ l+ + ++ + + + +l
  gi|518652476|ref|YP_008141996.1| 238 VFSLKYFPVSRFYEFL--IPVVFIAGIIG-LAIARPADK---NKTVLFSLVSLIVLLISVPLFFLNTHVTDVTYfAL 308
                                       8877777777666666..88888887666.677888888...78888888888888888888888855555555477 PP

                             MFS_1 308 vliGf..glgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                        ++Gf  g+ +  + + +l+++lap++  g  +g++++++++g ++g+
  gi|518652476|ref|YP_008141996.1| 309 SVAGFysGYIISETVFPTLITRLAPKNSYGGNLGFYTSMQHAGVFFGA 356
                                       779995455555********************************9995 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 4.2e-08
                             MFS_1 105 agaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                       +  +li++++pk+  g  +g+++++  +G+ +g+++ggll+  ++   + +i+ + ++++ ++  ll++ +
  gi|518652476|ref|YP_008141996.1| 323 VFPTLITRLAPKNSYGGNLGFYTSMQHAGVFFGAVVGGLLIIKVNHDIPIMIIIFTLFVFSIV--LLYFIT 391
                                       66789************************************9999888877777777777664..555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1263  (0.0704445); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.35s 00:00:01.03 Elapsed: 00:00:00.48
# Mc/sec: 2535.68
//
Query:       gi|518652477|ref|YP_008141997.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518652477|ref|YP_008141997.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518652477|ref|YP_008141997.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518652477|ref|YP_008141997.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518652477|ref|YP_008141997.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518652477|ref|YP_008141997.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518652477|ref|YP_008141997.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518652477|ref|YP_008141997.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518652477|ref|YP_008141997.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2306.99
//
Query:       gi|518652478|ref|YP_008141998.1|  [L=53]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.5   1.0    1.6e-24   85.3   1.0    1.0  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   9.1e-29   1.6e-24       1      50 []       4      53 .]       4      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.1e-29
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++d+
  gi|518652478|ref|YP_008141998.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITRDE 53
                                      8**********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.45
# Mc/sec: 357.59
//
Query:       gi|518652479|ref|YP_008141999.1|  [L=214]
Description: hypothetical protein FACI_IFERC00001G1118 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.3e-11   43.3   0.0    4.6e-11   42.3   0.0    1.5  1  HTH_10     HTH DNA binding domain
     0.0083   16.0   0.5      0.013   15.4   0.5    1.3  1  REPA_OB_2  Replication protein A OB domain


Domain annotation for each model (and alignments):
>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   5.1e-15   4.6e-11       8      52 ..     165     209 ..     161     210 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 5.1e-15
                            HTH_10   8 vlklAyemGYFdyPRrvtlkeLAkelGIskstlsehLrkaeskli 52 
                                       +lk+A+e GYFd+P+++ lkeL+ +l+I ++tl   Lr+  +++i
  gi|518652479|ref|YP_008141999.1| 165 ILKEAFERGYFDVPKKIGLKELSSTLDIPPTTLDLLLRRQLRQVI 209
                                       89*************************************999987 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 !   15.4   0.5   1.4e-06     0.013       3      91 ..      72     162 ..      70     168 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-06
                         REPA_OB_2   3 elenvekdsivDvigvvksveevseitskstekelkkreltlvDesga...svevtlWgkeaekfesseepvvalkg 76 
                                       +++ vek++    + vv +  ++ e+++k+ +++ +k +l+ +D sg    +++v  ++k  ++++ + +++  +k 
  gi|518652479|ref|YP_008141999.1|  72 DVTIVEKGANFVTLNVVAKSCPLVEVMKKKLMNSDSKIKLERIDYSGNlfwELNVSNYNK-IRHIDDTLREIYDIKD 147
                                       67788999999999*********************************8555677777776.677899********** PP

                         REPA_OB_2  77 vkvsdFggrslslls 91 
                                         ++ F+gr +s+ s
  gi|518652479|ref|YP_008141999.1| 148 SNIKTFNGRRISIKS 162
                                       ***********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1535.70
//
Query:       gi|518652480|ref|YP_008142000.1|  [L=258]
Description: cytochrome c oxidase assembly factor [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1279  (0.0713369); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 1883.10
//
Query:       gi|518652481|ref|YP_008142001.1|  [L=742]
Description: hypothetical protein FACI_IFERC00001G1120 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.9  10.6      0.054   14.1   0.4    3.1  4  Fer4_7    4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.023   14.6   0.9      0.049   13.5   0.9    1.5  1  DUF4428   Domain of unknown function (DUF4428)
       0.04   13.9   0.5       0.04   13.9   0.5    5.5  5  Fer4_5    4Fe-4S binding domain
      0.045   13.8   0.6      0.045   13.8   0.6    2.6  3  Fer4_6    4Fe-4S binding domain
       0.09   13.2   0.0       0.21   12.0   0.0    1.6  1  DUF5060   Domain of unknown function (DUF5060)
       0.16   12.1   4.7      0.084   13.0   1.9    1.9  2  Fer4_11   4Fe-4S dicluster domain
       0.31   11.2   8.6        2.3    8.5   6.6    2.5  2  Fer4_9    4Fe-4S dicluster domain
       0.45   10.7  12.8       0.16   12.1   0.3    2.9  3  Fer4_10   4Fe-4S dicluster domain
        4.5    7.9  11.6         74    4.0   0.0    3.1  2  Fer4_17   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 ?    2.6   0.0       0.1   2.1e+02       7      28 ..     520     541 ..     518     554 .. 0.72
   2 ?    2.4   3.4      0.12   2.4e+02      34      52 .]     652     672 ..     631     672 .. 0.78
   3 !    7.6  11.5    0.0028       5.6       2      51 ..     656     703 ..     655     704 .. 0.87
   4 !   14.1   0.4   2.7e-05     0.054       1      22 [.     689     710 ..     689     728 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.1
                            Fer4_7   7 aCvaaCpvkaieldeeenekgt 28 
                                       +C   Cp+ +++     ++ g+
  gi|518652481|ref|YP_008142001.1| 520 YCSTLCPSAVMYGGTLGQAMGR 541
                                       8999999999988766655555 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.12
                            Fer4_7  34 dpekClgCga..CvavCPtga 52 
                                       d + C +C+   C++ C +g+
  gi|518652481|ref|YP_008142001.1| 652 DKNVCRTCETkaCATSCEVGI 672
                                       456799998666999999885 PP

  == domain 3  score: 7.6 bits;  conditional E-value: 0.0028
                            Fer4_7   2 CigC..gaCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtg 51 
                                       C  C  +aC+  C v+  +l+ +  ekg     +++ kC+g g C ++CP++
  gi|518652481|ref|YP_008142001.1| 656 CRTCetKACATSCEVGISTLPGQFIEKG----SFKSVKCVGAGDCKRACPYD 703
                                       8888446*************99865555....9*****************86 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 2.7e-05
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee 22 
                                       +C+g g C +aCp++ i++ ++
  gi|518652481|ref|YP_008142001.1| 689 KCVGAGDCKRACPYDNIYFYDV 710
                                       7****************99765 PP

>> DUF4428  Domain of unknown function (DUF4428)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.9   2.5e-05     0.049      11      42 ..     645     674 ..     642     682 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                           DUF4428  11 llkrlkleDgyvCkdClkKlseflsdvkikki 42 
                                        +k lk++D +vC +C  K++  + +v+i ++
  gi|518652481|ref|YP_008142001.1| 645 FFK-LKVKDKNVCRTCETKACATSCEVGI-ST 674
                                       555.****************998888777.44 PP

>> Fer4_5  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   4.4         9   1.8e+04       6      18 ..      13      25 ..       8      31 .. 0.55
   2 ?   -3.9   1.8       6.9   1.4e+04       5      12 ..     219     226 ..     216     230 .. 0.51
   3 ?   -1.4   4.6       1.2   2.3e+03       2      17 ..     270     285 ..     268     292 .. 0.64
   4 ?   13.9   0.5     2e-05      0.04      14      30 ..     510     527 ..     498     533 .. 0.79
   5 ?   -5.3   6.2         9   1.8e+04       2      25 ..     607     632 ..     606     646 .. 0.75

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 9
                            Fer4_5  6 lilflaivlvtll 18
                                       i+ +++++++++
  gi|518652481|ref|YP_008142001.1| 13 GIMTIIFMVTYII 25
                                      3455555555554 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 6.9
                            Fer4_5   5 llilflai 12 
                                       ++i+++++
  gi|518652481|ref|YP_008142001.1| 219 MIIFMIIF 226
                                       34444444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 1.2
                            Fer4_5   2 allllilflaivlvtl 17 
                                       +++++++++ai++ ++
  gi|518652481|ref|YP_008142001.1| 270 GFAWIFFAVAILFGMW 285
                                       5677777776655444 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 2e-05
                            Fer4_5  14 lvtllfGR.afCgWiCPf 30 
                                       +++llfGR  +C+ +CP 
  gi|518652481|ref|YP_008142001.1| 510 FLALLFGRrSYCSTLCPS 527
                                       566778888********5 PP

  == domain 5  score: -5.3 bits;  conditional E-value: 9
                            Fer4_5   2 allllilfl.aivlvtllfGR.afCg 25 
                                       ++l++++f+ + ++ +   ++  +C+
  gi|518652481|ref|YP_008142001.1| 607 NILWYVFFFsIPFVGMSPCRKyGWCS 632
                                       56788777745555555577779997 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.3         9   1.8e+04      15      21 ..     521     527 ..     520     529 .. 0.75
   2 ?   -0.6   2.8       0.8   1.6e+03       6      21 ..     653     670 ..     650     672 .. 0.62
   3 ?   13.8   0.6   2.3e-05     0.045       4      23 ..     685     704 ..     684     705 .. 0.85

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 9
                            Fer4_6  15 CvrvCPe 21 
                                       C + CP 
  gi|518652481|ref|YP_008142001.1| 521 CSTLCPS 527
                                       8888996 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.8
                            Fer4_6   6 pdkCigCgd..CvrvCPe 21 
                                       ++ C  C+   C++ C  
  gi|518652481|ref|YP_008142001.1| 653 KNVCRTCETkaCATSCEV 670
                                       566666755567777765 PP

  == domain 3  score: 13.8 bits;  conditional E-value: 2.3e-05
                            Fer4_6   4 idpdkCigCgdCvrvCPega 23 
                                       ++  kC+g gdC r+CP++ 
  gi|518652481|ref|YP_008142001.1| 685 FKSVKCVGAGDCKRACPYDN 704
                                       56679************975 PP

>> DUF5060  Domain of unknown function (DUF5060)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00011      0.21      36      65 ..     361     392 ..     352     395 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       TEEEEEE-EE-ST..TEEEEEE---S-EEEEE CS
                           DUF5060  36 gksltvpGFYdGd..gayrvrFaPdeeGeWtY 65 
                                        + ++v GFY +d  +++   F P  +G++++
  gi|518652481|ref|YP_008142001.1| 361 FHGVSVAGFYAHDvlREFVSPFVPASTGTYNF 392
                                       56789*****9998899*************99 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.4   2.8e+03      81      98 ..     516     533 ..     515     535 .. 0.83
   2 ?   13.0   1.9   4.2e-05     0.084       8      62 ..     654     708 ..     650     716 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                           Fer4_11  81 Gllpacvescptgalnfg 98 
                                       G+   c++ cp+ +++ g
  gi|518652481|ref|YP_008142001.1| 516 GRRSYCSTLCPSAVMYGG 533
                                       667889*****9999876 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 4.2e-05
                           Fer4_11   8 eqCrhCleppCvasapse.aivkdeetGaVlldektkkeevrevveacPykivrkn 62 
                                       + Cr C++++C++s++++ + +  +      +++ ++  ++ ++++acPy+ ++  
  gi|518652481|ref|YP_008142001.1| 654 NVCRTCETKACATSCEVGiSTLPGQFIEKGSFKSVKCV-GAGDCKRACPYDNIYFY 708
                                       57**************9876655555555567788885.9**********988765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.15   2.9e+02       7      27 ..     520     540 ..     519     554 .. 0.81
   2 ?    8.5   6.6    0.0012       2.3       2      49 ..     656     703 ..     654     705 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.15
                            Fer4_9   7 aCveaCpagvvvedaaerkar 27 
                                       +C + Cp+ v+ +   ++ + 
  gi|518652481|ref|YP_008142001.1| 520 YCSTLCPSAVMYGGTLGQAMG 540
                                       7*******9998887777765 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0012
                            Fer4_9   2 CtgC..gaCveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkg 49 
                                       C  C  +aC ++C+ g+ +    +++++   ++  +C+g g+C  aCp +
  gi|518652481|ref|YP_008142001.1| 656 CRTCetKACATSCEVGISTL--PGQFIEKGSFKSVKCVGAGDCKRACPYD 703
                                       77773334777777766644..34444444445579************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 ?    0.9   0.0      0.26   5.2e+02      14      30 ..     520     532 ..     517     553 .. 0.67
   2 ?    5.0  12.8     0.014        27       3      56 .]     650     701 ..     648     701 .. 0.85
   3 ?   12.1   0.3   7.8e-05      0.16       6      30 ..     687     706 ..     682     735 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.26
                           Fer4_10  14 kCvkaCPadltsvgakg 30 
                                        C + CP+     + +g
  gi|518652481|ref|YP_008142001.1| 520 YCSTLCPSA----VMYG 532
                                       6******93....3333 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                           Fer4_10   3 vidddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       v+d++ C  C+  +C ++C         +     +e+ + k+ kC g g C +aCP
  gi|518652481|ref|YP_008142001.1| 650 VKDKNVCRTCEtkACATSCE----VGISTLPGQFIEKGSFKSVKCVGAGDCKRACP 701
                                       7899******9999*****3....3556667777888888999************9 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7.8e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadltsvgakg 30 
                                       + +C++ g+C++aCP+d+     ++
  gi|518652481|ref|YP_008142001.1| 687 SVKCVGAGDCKRACPYDN-----IY 706
                                       569************944.....33 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.037        74       6      32 ..     519     545 ..     518     560 .. 0.71
   2 ?    1.2   8.9      0.27   5.3e+02      42      59 ..     686     703 ..     655     704 .. 0.75

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.037
                           Fer4_17   6 gyClpeCpsyeaydnepkkllraaklg 32 
                                       +yC   Cps   y+    + + +++++
  gi|518652481|ref|YP_008142001.1| 519 SYCSTLCPSAVMYGGTLGQAMGRYNWE 545
                                       59*******999999877777777773 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.27
                           Fer4_17  42 kaslCieCgeCerkCPqg 59 
                                       k  +C++ g C+r+CP++
  gi|518652481|ref|YP_008142001.1| 686 KSVKCVGAGDCKRACPYD 703
                                       5668************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (742 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.73u 0.30s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 4793.86
//
Query:       gi|518652482|ref|YP_008142002.1|  [L=512]
Description: hypothetical protein FACI_IFERC00001G1121 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (512 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1274  (0.0710581); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.46
# Mc/sec: 3336.11
//
Query:       gi|518652483|ref|YP_008142003.1|  [L=51]
Description: hypothetical protein FACI_IFERC00001G1122 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      212  (0.0118244); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 362.39
//
Query:       gi|518652484|ref|YP_008142004.1|  [L=73]
Description: hypothetical protein FACI_IFERC00001G1123 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   12.5   0.4      0.082   12.3   0.4    1.1  1  Jiraiya          Jiraiya
        1.3    7.7   5.7        1.6    7.4   5.7    1.0  1  DUF2207          Predicted membrane protein (DUF2207)
        2.1    8.8   5.5        2.8    8.4   5.5    1.2  1  DUF202           Domain of unknown function (DUF202)
        3.7    7.6   8.1        4.5    7.3   8.1    1.1  1  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe


Domain annotation for each model (and alignments):
>> Jiraiya  Jiraiya
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.4   1.8e-05     0.082     120     153 ..      28      61 ..      22      72 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                           Jiraiya 120 lilytlllfestpaivtsiilgvGivllllalvh 153
                                       l++y ll fe  +ai+++++ ++G  + +la+++
  gi|518652484|ref|YP_008142004.1|  28 LSIYSLLPFEAYTAILGVAVFIIGLGITALASTK 61 
                                       78*************9999988888777777665 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   5.7   0.00035       1.6     382     433 ..      10      61 ..       7      68 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00035
                           DUF2207 382 klsalglgliilglilillallllvlllvfllilllillliaiivlllfsrl 433
                                       kl a g gl++ g+  ++l++++l ++  + +il++++++i++++++l+s+ 
  gi|518652484|ref|YP_008142004.1|  10 KLLATGMGLLLGGFGTAILSIYSLLPFEAYTAILGVAVFIIGLGITALASTK 61 
                                       67899999**************************************998765 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   5.5   0.00063       2.8      16      57 ..      16      57 ..      14      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00063
                            DUF202 16 tslalialglallrffltgepsalgkilglilivlgiltllv 57
                                      ++l+l+++g a+l + +    +a+++ilg++ +++g+ + ++
  gi|518652484|ref|YP_008142004.1| 16 MGLLLGGFGTAILSIYSLLPFEAYTAILGVAVFIIGLGITAL 57
                                      799***********9887777777899998866666655444 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.1     0.001       4.5      36      89 ..       8      60 ..       4      68 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.001
                   Phage_holin_3_6 36 gagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglk 89
                                      g+ ll+ ++ l+l +++++++ +  +l    + + i++++++++++   +++  
  gi|518652484|ref|YP_008142004.1|  8 GVKLLATGMGLLLGGFGTAILSIYSLLP-FEAYTAILGVAVFIIGLGITALAST 60
                                      4445555555555555555555543331.1233445776666666555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 531.15
//
Query:       gi|518652485|ref|YP_008142005.1|  [L=72]
Description: hypothetical protein FACI_IFERC00001G1124 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 491.06
//
Query:       gi|518652486|ref|YP_008142006.1|  [L=43]
Description: hypothetical protein FACI_IFERC00001G1125 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.31s 00:00:00.73 Elapsed: 00:00:00.50
# Mc/sec: 257.96
//
Query:       gi|518652487|ref|YP_008142007.1|  [L=252]
Description: hypothetical protein FACI_IFERC00001G1126 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-42  143.8   5.2    6.3e-42  143.6   5.2    1.0  1  DUF929    Domain of unknown function (DUF929)


Domain annotation for each model (and alignments):
>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   5.2   3.5e-46   6.3e-42       5     248 ..      12     249 ..       8     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 3.5e-46
                            DUF929   5 viaiivliivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdlasng.kvevyfvswegCPvgaaesWaL 80 
                                       ++++iv+ +v++++ ++ a ++na+        +s++l  +++kvs+  l +++ ++ vy+++w g+P g a sWaL
  gi|518652487|ref|YP_008142007.1|  12 LAFFIVFFVVIAFLAIYGAEHYNAH-------DESIELE-TYCKVSDSALIKDNtSTFVYYITWGGSPTGDAGSWAL 80 
                                       4556666666777777777778888.......5888999.8********987651677******************* PP

                            DUF929  81 yiaLsryGnl...nlephySdpsdeypniPgLiFknftpnskvefysiY.........iyneylnasrngtpinsel 145
                                       y  L + G     ++++++S +  +y n+PgLiF+ ++     ++++ Y         +y ++ n + n tp     
  gi|518652487|ref|YP_008142007.1|  81 YDFLHSNGFNmngTFNETQSMSGYQYNNTPGLIFNTSY-----TYSVTYdhrntivvpVYLYGENLNNNTTPA---- 148
                                       ******99666667778888889************995.....555555555555555555555555567887.... PP

                            DUF929 146 vsvglqeLkeelpssvynlvkkYetesliqetsepsaylvsppHivttiiitGpkGtyilvgysinPsllsgyspey 222
                                         +gl++Lk+ +pssvyn+vk Y+te+++++ s +s +++s pHi+++ +itGp+G y ++gy+++P +  + +p  
  gi|518652487|ref|YP_008142007.1| 149 --AGLKVLKADVPSSVYNVVKGYTTEAIVGGLSISSDNMSSIPHINSVTLITGPSGAYLFNGYIVDPADYTNDTPGE 223
                                       ..9************************************************************************** PP

                            DUF929 223 vlkqlengnsksaIlsaanlitqiIq 248
                                       vl++++n++  + I ++ + ++++I+
  gi|518652487|ref|YP_008142007.1| 224 VLHDVNNNTNDNGINTGMEGLEATIK 249
                                       ********998889999998888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       859  (0.0479112); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1768.32
//
Query:       gi|518652488|ref|YP_008142008.1|  [L=835]
Description: hypothetical protein FACI_IFERC00001G1127 [Ferroplasma acidarmanus fer1]
Scores for complete 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-101  339.5  65.9   2.8e-101  339.5  65.9    3.2  3  COX1            Cytochrome C and Quinol oxidase polypeptide I
  ------ inclusion threshold ------
       0.13   11.6   0.3       0.23   10.7   0.3    1.4  1  Chordopox_A33R  Chordopoxvirus A33R protein
       0.95    9.6   5.4       0.98    9.5   0.5    3.4  2  DUF2752         Protein of unknown function (DUF2752)
        6.6    6.9   8.7        6.6    6.9   0.2    3.8  3  DUF2371         Uncharacterised conserved protein (DUF2371)


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.5  65.9  6.3e-105  2.8e-101       2     432 .]      32     485 ..      31     521 .. 0.96
   2 !    5.0  11.3    0.0021       9.4      51     178 ..     568     709 ..     563     719 .. 0.69
   3 !    5.5  11.3    0.0015       6.6      80     173 ..     731     833 ..     714     835 .] 0.63

  Alignments for each domain:
  == domain 1  score: 339.5 bits;  conditional E-value: 6.3e-105
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTCT...............-HHCHHHHHHHHHHHHHHHHHHHHCHHHHHHH CS
                              COX1   2 igllylilalvlllvggllgllirlqlafp...............dletynqlrtlHgnlmiflfatpfilgfgnyl 63 
                                       +glly++++lv+++ gg+l+ll+r+qla p               d+++ynql+t+Hg  m+++f++p+ +g+g+yl
  gi|518652488|ref|YP_008142008.1|  32 VGLLYILTSLVFFIGGGVLALLMRVQLAIPrydlvhyglfsgrflDALQYNQLVTIHGFPMLIWFLGPLGFGLGIYL 108
                                       799************************99888777777777777777****************************** PP

                                       HHHHHCTSS-S-HHHHHHHHHHHHHHHHHHHHHHH...CSS-STTTTTTTC.........SHHHHHHHHHHHHHHHH CS
                              COX1  64 vplllgardlafprlnalsfwlvvlgvvllllsll...gaattgwteYapls........evdlwllglllvvvssl 129
                                       vpl lg+rd+ fpr+nal++wl++++++ll+++++   g+ +tgwt Y pls        + d++  ++++  ++++
  gi|518652488|ref|YP_008142008.1| 109 VPLALGSRDMIFPRINALGYWLYLFSGILLWIGFFlpgGNLDTGWTVYQPLSsfkftpylGADTAAAAVVVRSLGTI 185
                                       ***********************************9*888********************9999************* PP

                                       HHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHCT.-SS.SC.E-HHHHHHHHH CS
                              COX1 130 lgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalalllllldrslg.kff.sp.gdplldqhlfW 203
                                       +++  +i+t++k ra+g  ++++plfvwavl ++++   ++p + + + +l++  +lg + f s+ g +l++++lfW
  gi|518652488|ref|YP_008142008.1| 186 IASTEVIATVFKARARGFRLMNMPLFVWAVLWVSMISWYVFPEIGAMFFTLVVSNVLGlSGFiSTyGGALMWENLFW 262
                                       **************************************************9999999997774558*********** PP

                                       HHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHHTHH CS
                              COX1 204 ffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfslliav 280
                                       +fgHpeVy l+lp++g++  +l+++  r  + +k++++a+ +i + s++v +HH f+tg+   + +  svf+  i +
  gi|518652488|ref|YP_008142008.1| 263 YFGHPEVYLLLLPGTGAMFDYLSNLGHRAPYLKKWMIAAMGAISVDSVMVFLHHTFMTGIVFAWLMATSVFTETISI 339
                                       *************************88************************************************** PP

                                       HHHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHH CS
                              COX1 281 PsglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfa 357
                                       P+g+ +++++atl + + +f+tp+lf+l+++  f+igG+tGv++++ +++ +vh+ y+vvaHfH+ ++g++v++l++
  gi|518652488|ref|YP_008142008.1| 340 PTGMLIVGLIATLLGAKHKFQTPILFALAASTSFMIGGITGVTQSSLAIDTIVHGDYYVVAHFHYFMVGVAVMGLMG 416
                                       *************999999********************************************************** PP

                                       HHHHHHHHHHSB--HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
                              COX1 358 aiyyllpkltgrmlserlaklhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                                        +yy++pk+tg+m+se+++++h+ ++ iG++++++pm++l    +prr+++y++       ++ +  ++t g+++
  gi|518652488|ref|YP_008142008.1| 417 NLYYYFPKFTGKMYSETWGRIHWAIAYIGVNVLYFPMFFLY--DLPRRVYTYPA-G---YGYTIFSEISTAGAFI 485
                                       **************************************986..9*******954.2...3778888888888875 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0021
                                       HHHHHCHHHHHHHHHHHHCTSS-S-HHHHHHHHHHHHHHHHHHHHHHHCSS-STTTTTTTC................ CS
                              COX1  51 fatpfilgfgnylvplllgardlafprlnalsfwlvvlgvvllllsllgaattgwteYapls............... 112
                                       + ++++l+f+  +v l+  ++  + p  ++l++ +++++++++l++       gw +Y +++               
  gi|518652488|ref|YP_008142008.1| 568 IGVGVVLAFIGAAVTLMGYKPYAFGPAYAYLGYGIIAFAAAIFLWGT-----IGW-MYDDFKlrspnvppmykkepv 638
                                       55667888999999999767777778889999999999999988777.....798.9999999999999999999** PP

                                       ..SHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHTT-CCGS-HHHHHHHHHHHH.HHHHCHHHHHHHH CS
                              COX1 113 ..evdlwllglllvvvssllgainf..ivtilkrrapgmtvaklplfvwavlatail.illalpvlalall 178
                                         + +   lg+l++ ++ +++++ f  +v +lk ++  ++v     ++w++ ++a++ i+++++++ +a l
  gi|518652488|ref|YP_008142008.1| 639 mkGFNNTRLGMLMFLAGNMIWMATFygMVEWLKLQSASPYVDGNDPTTWFFPTMATVyIVISIVAIGIAAL 709
                                       **555556666666666666555551267789999999****77777788533333202333333333322 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHHHHHH..CS....S-STTTTTTTC.SHHHHHHHH..HHHHHHHHHHHHHHHHHHHH..HHHHT CS
                              COX1  80 alsfwlvvlgvvllllsll..ga....attgwteYaplsevdlwllgl..llvvvssllgainfivtilk..rrapg 146
                                       +++++l+v+++++ llsl+  +a       g t+  p++   +wl++l  ll+ +++++++in++v + +  +  +g
  gi|518652488|ref|YP_008142008.1| 731 TAGVVLAVISLITSLLSLIviNAhpalSYGGATANNPIAS-MYWLISLmdLLFSIGVIAVMINYVVHLKRgkKILWG 806
                                       2333345555555444443552233444445566666554.447776622577799999999999999995433346 PP

                                       T-CCGS-HHHHHHHHHHHHHHHHCHHH CS
                              COX1 147 mtvaklplfvwavlatailillalpvl 173
                                        t ++  +++w+v++++++++++++++
  gi|518652488|ref|YP_008142008.1| 807 RTATRADVVMWFVAFVFLTGIFTTIAF 833
                                       6777999***************99986 PP

>> Chordopox_A33R  Chordopoxvirus A33R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.3   5.2e-05      0.23      21      70 ..     713     762 ..     695     772 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 5.2e-05
                    Chordopox_A33R  21 GstiyGnklkkktkkkkskclsillr.vaiitsilsllaiattlalqyskc 70 
                                       Gst yG   k ++k+       ++l  +++its+lsl+ i +  al y   
  gi|518652488|ref|YP_008142008.1| 713 GST-YGAIRKERNKSANYMTAGVVLAvISLITSLLSLIVINAHPALSYGGA 762
                                       555.89888877777777777777762689***************999755 PP

>> DUF2752  Protein of unknown function (DUF2752)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.5   0.00022      0.98      23      48 ..      70      96 ..      66      97 .. 0.87
   2 ?   -0.2   0.5      0.25   1.1e+03      22      46 ..     390     414 ..     386     416 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00022
                           DUF2752 23 llhgdfaaAfrynplgv.lllplllll 48
                                      l+ g+f++A++yn l+    +p+l+++
  gi|518652488|ref|YP_008142008.1| 70 LFSGRFLDALQYNQLVTiHGFPMLIWF 96
                                      889************995689999998 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.25
                           DUF2752  22 allhgdfaaAfrynplgvlllplll 46 
                                        ++hgd    ++++ ++v ++++ l
  gi|518652488|ref|YP_008142008.1| 390 TIVHGDYYVVAHFHYFMVGVAVMGL 414
                                       689***99999*****997777655 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.5      0.12   5.4e+02     105     119 ..      95     109 ..      80     113 .. 0.84
   2 ?    6.9   0.2    0.0015       6.6      38      66 ..     562     590 ..     557     627 .. 0.89
   3 ?    1.6   0.2     0.063   2.8e+02      44      78 ..     693     727 ..     689     748 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.12
                           DUF2371 105 kvlGPlimGiGiflf 119
                                         lGPl  G+Gi+l+
  gi|518652488|ref|YP_008142008.1|  95 WFLGPLGFGLGIYLV 109
                                       579*********985 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0015
                           DUF2371  38 svsglvlllGllvllvGiamavlgywpkk 66 
                                       s+  l++ +G+++ ++G a++++gy p +
  gi|518652488|ref|YP_008142008.1| 562 STRPLLIGVGVVLAFIGAAVTLMGYKPYA 590
                                       67789999*****************9965 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.063
                           DUF2371  44 lllGllvllvGiamavlgywpkkaklaseekssss 78 
                                       + + +++++v i++a l  w ++  + ++e+++s+
  gi|518652488|ref|YP_008142008.1| 693 ATVYIVISIVAIGIAALLAWGSTYGAIRKERNKSA 727
                                       677899**********9999998555444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (835 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1063  (0.0592894); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.77u 0.29s 00:00:01.06 Elapsed: 00:00:00.46
# Mc/sec: 5504.88
//
Query:       gi|518652489|ref|YP_008142009.1|  [L=73]
Description: hypothetical protein FACI_IFERC00001G1128 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 523.49
//
Query:       gi|518652490|ref|YP_008142010.1|  [L=204]
Description: sulfocyanin [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.8e-21   74.5   6.1    1.8e-20   72.9   6.1    1.9  1  SoxE      Sulfocyanin (SoxE) domain


Domain annotation for each model (and alignments):
>> SoxE  Sulfocyanin (SoxE) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   6.1     1e-24   1.8e-20      28     148 ..      80     202 ..      51     203 .. 0.77

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 1e-24
                              SoxE  28 lfnfnGtsnGqlkiyiPagwsvlvklvneeslphnlvlvqnntaiPnsleissdGki.llivGattsnyavsGissG 103
                                        fnfnGts G ++iy+Pa+ ++  +++n e  ph l   +   +  ++  i ++  + +  v a+t+    + i  G
  gi|518652490|ref|YP_008142010.1|  80 PFNFNGTSYGAMTIYLPANADIHANMTNYEVKPHTLKFELPYSSQWSTGPIWAHTSVhVKKVIASTGT--IDPIWYG 154
                                       59**********************************98765544444444433333314455555554..4455555 PP

                              SoxE 104 qsa...sGlledlsaGtywlacgilGhaesGmWvdlivssnvtvPyai 148
                                       + a   s  ++d ++G+yw++cg++ hae+Gm++ +ivss+vt+Py +
  gi|518652490|ref|YP_008142010.1| 155 NVAhyrSIWWNDTASGHYWVVCGLTTHAEAGMYAFVIVSSSVTTPYYT 202
                                       54411145689***********************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       678  (0.0378158); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); 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 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1421.43
//
Query:       gi|518652491|ref|YP_008142011.1|  [L=276]
Description: hypothetical protein FACI_IFERC00001G1130 [Ferroplasma acidarmanus fer1]
Scores for complete 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   52.4   2.3    3.6e-12   46.2   0.0    2.6  3  COX2          Cytochrome C oxidase subunit II, periplasmic do
     0.0045   15.5   0.0     0.0057   15.2   0.0    1.1  1  DcuC          C4-dicarboxylate anaerobic carrier
  ------ inclusion threshold ------
      0.057   12.1   0.0      0.077   11.7   0.0    1.1  1  Lactate_perm  L-lactate permease


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.47   2.8e+03      77      88 ..      71      82 ..      50     115 .. 0.76
   2 !    5.0   0.5    0.0035        21       2      18 ..     133     149 ..     132     156 .. 0.86
   3 !   46.2   0.0     6e-16   3.6e-12      47     113 ..     156     221 ..     151     224 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.47
                              COX2 77 kvdavpGrlnqv 88
                                       +d  pGr++++
  gi|518652491|ref|YP_008142011.1| 71 DMDMRPGRIENL 82
                                      456666766543 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0035
                              COX2   2 tikaiGhqwywsyeytd 18 
                                        i+ +G+qw w + y++
  gi|518652491|ref|YP_008142011.1| 133 DINVVGYQWQWVFIYPN 149
                                       6889*********9997 PP

  == domain 3  score: 46.2 bits;  conditional E-value: 6e-16
                              COX2  47 rvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfyGqcselcGvnhssm 113
                                        +vlp +t+i++ vt+ dv+hsf +  +  kvda pG  n v+  i+ +G +  +c elcG  h++m
  gi|518652491|ref|YP_008142011.1| 156 FLVLPADTPIQFNVTSVDVMHSFYLINV-TKVDAFPGHYNYVWSNITLTGEYQFECVELCGLGHAHM 221
                                       589********************99886.6***********************************99 PP

>> DcuC  C4-dicarboxylate anaerobic carrier
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   9.6e-07    0.0057     188     271 ..      20     104 ..      18     142 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 9.6e-07
                              DcuC 188 iAgvsiadgivlrllv.lviltlisiaflyfYakkikkdpvysekdeskelfskekseseesfskrqkvvlilfvlp 263
                                       i g +i++ +  ++l+ + i+  ++++++y++ k +k +   + ++e+++  ++      e+++ ++k +  +fvl 
  gi|518652491|ref|YP_008142011.1|  20 ITGAEITSIFLAYVLPgILIGGGFALWYVYVFLKSYKPKNADEFEKEKYNKDMDMRPGRIENLERGNKTIFKIFVLF 96 
                                       67888999999999974668889****************977777777888888888888889************** PP

                              DcuC 264 lilvllgl 271
                                       ++l+ll+l
  gi|518652491|ref|YP_008142011.1|  97 VVLILLSL 104
                                       *****993 PP

>> Lactate_perm  L-lactate permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.3e-05     0.077     225     290 ..      25     100 ..       2     121 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.3e-05
                      Lactate_perm 225 lisnvlGpelpsi.lgalvslvilalflkafqpkeifrfagkeeskeksel.........kaakilkAlsPfvllv 290
                                       ++s +l + lp i +g+ ++l  + +flk ++pk+  +f++++ +k    +          +  i+k ++ fv+l+
  gi|518652491|ref|YP_008142011.1|  25 ITSIFLAYVLPGIlIGGGFALWYVYVFLKSYKPKNADEFEKEKYNKDMDMRpgrienlerGNKTIFKIFVLFVVLI 100
                                       678899999**973699**********************9999888777667777766642333444444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (276 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2063.27
//
Query:       gi|518652492|ref|YP_008142012.1|  [L=288]
Description: hypothetical protein FACI_IFERC00001G1131 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-44  150.4  25.5    6.9e-44  150.0  25.5    1.1  1  UbiA      UbiA prenyltransferase family
  ------ inclusion threshold ------
      0.097   12.5   1.5       0.19   11.5   1.5    1.4  1  PHBC_N    Poly-beta-hydroxybutyrate polymerase N terminal


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 !  150.0  25.5   7.7e-48   6.9e-44       5     246 ..      23     268 ..      21     284 .. 0.87

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 7.7e-48
                              UbiA   5 alvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgl 81 
                                       a+ ++ l  g+ +++l+l+ll+l ++la+ +a ++N+++D +iD +m+rt+ R    +  ++   + +a++++++++
  gi|518652492|ref|YP_008142012.1|  23 AITAFILVPGSFSHPLILFLLILSGTLASMSASMFNNIYDMDIDTKMKRTRSRSSTLNPGTRGLIFSIAAAMIVVSF 99 
                                       56778999999999***************************************8888888888888899999999*9 PP

                              UbiA  82 lllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltw 157
                                       +l+ +++n+ltal+++ ++l y ++Yt + lKrrt +++v+ggia+g+p+l+gwaa t+s+s++ l+la++vf++t 
  gi|518652492|ref|YP_008142012.1| 100 VLSSVFINLLTALFIFGGFLSYvFLYT-ILLKRRTTWNIVIGGIAGGFPALAGWAALTNSVSFTSLFLAFLVFMWTP 175
                                       999************************.************************************************* PP

                              UbiA 158 aialandlrdregDrkagiktlpvvlGrkaaril...lalllavlllallllllalllllylllalllaalallraa 231
                                       ++++  ++  ++++++ ++++lp++ G k++ ++    +++l++ +l++l+++   l+l+y  +a+++ +++l++ +
  gi|518652492|ref|YP_008142012.1| 176 THFWNLSINNVDDYKASQVPMLPAIVGIKKTEFWiviNTVILIFYSLIPLFVPSIKLGLPYIPIAIIMDIILLYYVL 252
                                       *******************************9875663333333333367888888888888888888888888866 PP

                              UbiA 232 r.lvrrrdakkaakff 246
                                       +  ++++d+k  +k+f
  gi|518652492|ref|YP_008142012.1| 253 KpAFKSYDKKYFRKAF 268
                                       5245556666666665 PP

>> PHBC_N  Poly-beta-hydroxybutyrate polymerase N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.5   2.2e-05      0.19      12      31 ..     150     169 ..     147     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.2e-05
                            PHBC_N  12 AalArlTgGlSPaslalAyl 31 
                                       A +A lT+++S +sl+lA+l
  gi|518652492|ref|YP_008142012.1| 150 AGWAALTNSVSFTSLFLAFL 169
                                       899***************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1023  (0.0570584); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.46
# Mc/sec: 1878.32
//
Query:       gi|518652493|ref|YP_008142013.1|  [L=192]
Description: beta-lactamase, type II [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-11   42.8   0.0    7.4e-11   42.4   0.0    1.1  1  Lactamase_B  Metallo-beta-lactamase superfamily


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 !   42.4   0.0   4.1e-15   7.4e-11       4     197 .]       6     185 ..       3     185 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.1e-15
                                       CSSEEEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHH CS
                       Lactamase_B   4 dpvnsyliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeap 80 
                                       + vn+y+i   g+vi iD+G+ ++a++        +  ++++d++++T  ++ H+G+l+++ + ++ ++++ + e  
  gi|518652493|ref|YP_008142013.1|   6 TVVNVYVIKYMGTVIQIDAGIKSDANKVI---NFYKDSGLNPDYILITAVDYIHVGALRDIYDVYNPKIYVPKREMG 79 
                                       579************************95...7999***************************************** PP

                                       CCHCHHHHHHHHHCCHHTTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTS.SHH CS
                       Lactamase_B  81 alfmeeaddaasrkglllagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDall.age 156
                                       ++++    ++         ++     +  ++++  n +++ +l+v+g+pg + + +++++++++ lf+GD +   ++
  gi|518652493|ref|YP_008142013.1|  80 SMKNGPTLRGILEV-----EGKGLQFEGIQHVYSYNKMDIDFLEVIGTPGYTMDNVSIYFRDKNSLFVGDSIIiKRN 151
                                       *******8888886.....58999999*********************************************94555 PP

                                       CCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 157 tgridltlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                        ++id        ++++  + +++sl+k+++  +++l+p+H
  gi|518652493|ref|YP_008142013.1| 152 KIKIDS-------MFTQNMQMARSSLDKIKEFCPATLFPSH 185
                                       555555.......***************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1509.27
//
Query:       gi|518652494|ref|YP_008142014.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G1133 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-13   50.8   0.0    3.5e-13   49.7   0.0    1.6  1  DDE_Tnp_1     Transposase DDE domain
      0.006   16.0   0.0      0.009   15.4   0.0    1.2  1  DDE_5         DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.043   12.9   0.0       0.07   12.2   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
      0.093   11.0   0.0        3.9    5.6   0.0    2.0  2  DDE_Tnp_1_4   Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   7.7e-17   3.5e-13      21     214 .]     181     399 ..     160     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 7.7e-17
                         DDE_Tnp_1  21 edarwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       ++  +g++ ++ + + +++ ++++    l++ +++ pg+  d+ ++  ++d++ + ++++++aD+G++sa+++++l+
  gi|518652494|ref|YP_008142014.1| 181 SFLEPGHNSKEiHLPQINVMMLFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGI-EKCVIVADKGFFSADNIKKLK 256
                                       666778887777889999999999998999999999******************9.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrk................................gaeskrrgrlrkhdrnkiltksqkrr 141
                                       +++++yii+l+ n+ l  +                                 +e++r+  +r hd+ ++ + +  + 
  gi|518652494|ref|YP_008142014.1| 257 KRHLSYIIPLRRNSSLVPDtddflgvfmyngkpvkywkpengvymfedpvlKSEEERDYLIRIHDNIRPKSSYYDHS 333
                                       ****************9999999988888877777766665555554444434444444444444444444443333 PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       +           ++++++   ++e + +ly+ R  +E  F   k+++  dr + r+     a+++l ll+l l
  gi|518652494|ref|YP_008142014.1| 334 GD-------FGKLYLLSDINDEPERIYRLYKDREYVEYAFNVYKNDLEADRSYIRDDHMLSAYMFLNLLSLYL 399
                                       33.......4445555555559*********************************************999865 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-06     0.009     167     219 ..     226     277 ..     205     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                             DDE_5 167 lldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdralyppga 219
                                       + + +  ag++  v+vaD g+ +a+ + + l+ + l y++ +r++++l+p  +
  gi|518652494|ref|YP_008142014.1| 226 MANTIDMAGIEKCVIVADKGFFSADNI-KKLKKRHLSYIIPLRRNSSLVPDTD 277
                                       5556666899999**************.********************99765 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 ?   12.2   0.0   1.6e-05      0.07      71     141 ..     190     257 ..     180     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       CCTT-EEEESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH CS
                      ANF_receptor  71 nlfkiPvisygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee 141
                                       ++ ++P+i ++     +s+++  ptf+r+ p + + + A+++++ + g  k +++++++      +++l++
  gi|518652494|ref|YP_008142014.1| 190 KEIHLPQINVMM---LFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGIEKCVIVADKGFFSADNIKKLKK 257
                                       567899996544...8999**************************************99666666666665 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0   0.00087       3.9     217     254 ..     237     274 ..     222     283 .. 0.87
   2 ?    3.2   0.0    0.0049        22     313     354 ..     345     384 ..     329     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00087
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlea 254
                                       k ++ +D +f + + +k +++r+++Y+i l++ns l  
  gi|518652494|ref|YP_008142014.1| 237 KCVIVADKGFFSADNIKKLKKRHLSYIIPLRRNSSLVP 274
                                       567889****************************9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0049
                       DDE_Tnp_1_4 313 laklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfa 354
                                       ++  +pe++y +lY+ R  +E  +   k+dl+adr   ++ +
  gi|518652494|ref|YP_008142014.1| 345 IN-DEPERIY-RLYKDREYVEYAFNVYKNDLEADRSYIRDDH 384
                                       44.799****.***********************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2854.17
//
Query:       gi|518652495|ref|YP_008142015.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G1134 [Ferroplasma acidarmanus fer1]
Scores for complete 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-70  237.4   3.0      1e-68  232.0   3.0    2.0  1  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.0   3.0   5.8e-73     1e-68       7     369 .]       5     329 ..       1     329 [. 0.92

  Alignments for each domain:
  == domain 1  score: 232.0 bits;  conditional E-value: 5.8e-73
                                       XXXXSSXCCCTTXSBXSXSSXXXSX.XXSBTTTTTXBSEEEEEEEEEEEEEEECHHTTSCCCCCEEEEEEEEEEC-- CS
                      Ribosomal_L3   7 eaprhgslGflprkRaerergkvksfPkddtskpvkltaflGyKaGmthiVrevdkpgskldkkevveavtvvetpp 83 
                                       ++ r+gs+ + pr Ra++  ++++s+P+ + +   k++af+GyK Gmthi  ++ + +s + +k ++++vtvve pp
  gi|518652495|ref|YP_008142015.1|   5 HHSRRGSMAYYPRVRAKKIGAEIRSWPEIEGK--SKIQAFAGYKVGMTHIQVTDYRKTSVTAGKTIMVPVTVVEVPP 79 
                                       56899**********************98887..789**************************************** PP

                                       EEEEEEEEEEEETTEEEEEEEEESSS.SHHHHCCCSTSTTTSSSSSSHCCCCHCSSCCCCCCHHHHHHHHHHSCSCE CS
                      Ribosomal_L3  84 mvivgvvgyvetprGlrslktvwaehlseevkrrlyknwykskkkaftkyskkyeskdvkklieadleeikkeasvv 160
                                       + +++++ y++   Gl+ + ++ ae++++ev +r+                 +  ++++ k+   +++ +++    v
  gi|518652495|ref|YP_008142015.1|  80 INVIAIRYYEDGDNGLQVFAEKRAEQIEKEVFKRI----------------PEI-KNKEPKN--IEIKDVAD----V 133
                                       *************************9999998888................122.1223334..45667777....* PP

                                       EEEEEEECCCSS-SCCSSHHEEEEECHCSCHHHHHHHHHHCCTCEEECCCCS-TTSEEEEEEEE---EEE-HHHHCT CS
                      Ribosomal_L3 161 rviahtvirktkslaqKkahllEiqvngGtiaekldfarealektvavaavFrqgeliDvigvtkGkGfeGvvkRWg 237
                                       r+++ t  + ++++  K +++ E+++ g tia+++ +a+e+l k  ++++    g ++Dvi+vtkGkGf+GvvkR+g
  gi|518652495|ref|YP_008142015.1| 134 RLLVNTNPQLVTGIPTKTPEIFEVRISGSTIADRIKLAEEKLGKELHFDDFNSTGSFVDVISVTKGKGFQGVVKRFG 210
                                       ***************************************************************************** PP

                                       ----STTTSSSSSS-S-SS-SSSSS--TTS--SEEESCCEEEEEEEEEEEEETTTSSTTTSSTTT.SS..SS.TTTC CS
                      Ribosomal_L3 238 vkklprkthrglRkvaaigawdparVsstvaraGqkGyhhRtelnkkiyrigkgedaknastefdltekeitPmGGf 314
                                       vk lpr   + +R ++++g+w+p  V+ tv++aGq G h+Rt  n +i++  +               +ei+ +GGf
  gi|518652495|ref|YP_008142015.1| 211 VKLLPRSNRKHRRMIGTLGPWHPDWVRNTVPQAGQVGLHQRTIHNIRIMKTAT-----------KEQVDEINVKGGF 276
                                       *************************************************9999...........334689******* PP

                                       TTCB..TSCEEEEES--SSSTTEEEEEEE-SSGGGSCCCSS-EEEEEE-TTCTSS CS
                      Ribosomal_L3 315 vhyGevkndfilvkGsvpGpkkrlvklrkslltqtsrkaeeevslkfidtaskfg 369
                                        +yG v+nd+il+ Gs+ Gp krl+k+r+  + +  + +  +v+  +i+  sk+g
  gi|518652495|ref|YP_008142015.1| 277 LKYGLVRNDYILLYGSISGPSKRLIKMRDPARQAVPNTD--KVDITYISRESKQG 329
                                       *****************************9998887665..56669******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.31s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2100.34
//
Query:       gi|518652496|ref|YP_008142016.1|  [L=256]
Description: hypothetical protein FACI_IFERC00001G1135 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-32  112.7   0.1    1.9e-32  112.5   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family
  ------ inclusion threshold ------
       0.11   12.2   0.0       0.16   11.6   0.0    1.2  1  PAS_12        UPF0242 C-terminal PAS-like domain


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 !  112.5   0.1   2.1e-36   1.9e-32       1     191 [.      16     254 ..      16     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 2.1e-36
                                       EEE-HHHHSS---HHHHHHHHHHHHHSS-EE-----.-TTTSS---S-SS-SSSSSS---S-TT.......STTSTT CS
                      Ribosomal_L4   1 veLspkvFaapirrdlihravvaylanrrqgtastk.arsevsgsgrklwkQKGtGrARvgsir.......spiarg 69 
                                       +eL p+vF+++ r+dlih+a++a + + rq+++s++ a+ +  g  ++l++   +G +R++++         + ++g
  gi|518652496|ref|YP_008142016.1|  16 IEL-PQVFEIETREDLIHKAFRAISLSMRQPYGSSPlAGTRRVG--HNLGP--NHGISRIPRLAsgsrgvlLASMVG 87 
                                       789.********************************77777777..7****..***********999999999**** PP

                                       ---SS---S.EEHHHHHHHHHHHHHHHHHHHHHHHTT-EEEES......---.-S..............S--HHHHH CS
                      Ribosomal_L4  70 GgvahgpkperdystklnkKvrrlAlrsaLsakakqglllvvd......nleple..............esktkelv 126
                                       G+ a  p+ ++  ++k+nkK+rrlA  sa++ +a+++++l ++      +   +e              + k k++v
  gi|518652496|ref|YP_008142016.1|  88 GRSALSPRSDKVLYKKINKKERRLAKLSAIAFTANKERILQRGhriseeS---IEkltfpvvveddiesITKVKDAV 161
                                       *******************************************8665542...3355566889999999999***** PP

                                       HHHHHTT-..........................TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSS CS
                      Ribosomal_L4 127 ellkklgl..........................ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkad 177
                                       ++l++lg+                          ++ks+Liv s  + + ++a++ lpgv++++++sl++ +l+++ 
  gi|518652496|ref|YP_008142016.1| 162 QVLSNLGVyddvlrskdgkkiragrgkmrnrtykQPKSLLIVGS--SVESLRAFASLPGVDLASLNSLSITKLAPGG 236
                                       *****999999999999999999999999999988888888887..58899************************** PP

                                       E....EEEEHHHHHHHHH CS
                      Ribosomal_L4 178 k....vvitksaveklee 191
                                       +    +++t s +e+l+e
  gi|518652496|ref|YP_008142016.1| 237 NpgrlTIYTASTIENLRE 254
                                       ***************987 PP

>> PAS_12  UPF0242 C-terminal PAS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.8e-05      0.16      63     139 ..      93     171 ..      86     176 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.8e-05
                            PAS_12  63 sqkenkllf..aNaqirallGwssdkflqdfseivqegleeWkralaklsskteskirlvlKtKagqevllncllgi 137
                                       s++ +k+l+  +N++ r+l  +s+  f+ + + i+q g    ++ ++kl+  + ++  ++  tK  ++v++   lg+
  gi|518652496|ref|YP_008142016.1|  93 SPRSDKVLYkkINKKERRLAKLSAIAFTANKERILQRGHRISEESIEKLTFPVVVEDDIESITKVKDAVQVLSNLGV 169
                                       78899***9778***************************************99999999999999999999999988 PP

                            PAS_12 138 ip 139
                                        +
  gi|518652496|ref|YP_008142016.1| 170 YD 171
                                       65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1916.46
//
Query:       gi|518652497|ref|YP_008142017.1|  [L=82]
Description: 50S ribosomal protein L23 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-14   53.1   3.4      6e-14   52.2   3.4    1.4  1  Ribosomal_L23  Ribosomal protein L23
     0.0081   16.0   0.0     0.0092   15.8   0.0    1.1  1  SIS            SIS domain
  ------ inclusion threshold ------
      0.066   13.3   0.1      0.071   13.2   0.1    1.0  1  Med28          Mediator complex subunit 28


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   3.4     1e-17     6e-14       1      61 [.       2      63 ..       2      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1e-17
                                      SSEEEE--SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHHT--EEEEEEEEE--EBESS CS
                     Ribosomal_L23  1 dvilkPvitEkstklaek.nkyvFeVakdanKleikkaveklFgVkVekVntlnvkgkkkrv 61
                                      d +++Pv+tEk+t ++ek nk++F V+++  K +ikk +e+ F+VkV   n+l+ k+ kk +
  gi|518652497|ref|YP_008142017.1|  2 DYVISPVVTEKTTLMMEKeNKLTFIVDRRGRKKDIKKEIEERFDVKVIGLNILITKKGKKAI 63
                                      5789*************988**********************************99988854 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.5e-06    0.0092      48      99 ..      15      68 ..       3      73 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.5e-06
                                      GGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSEE.EEEESSTTSHHHHHSS CS
                               SIS 48 lalideddlvilisfsgetkdlvaaae.lakergaki.iaITdskgsplaread 99
                                      l++ +e+ l ++++++g++kd ++ +e     +   + i+IT++ + ++a+ +d
  gi|518652497|ref|YP_008142017.1| 15 LMMEKENKLTFIVDRRGRKKDIKKEIEeRFDVKVIGLnILITKKGKKAIAKLSD 68
                                      777799*********************88888887779*************996 PP

>> Med28  Mediator complex subunit 28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.2e-05     0.071      13      73 ..       3      69 ..       1      78 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                             Med28 13 FvllDviRekktfvlekrneLsa......svsdlkkelerkaekykvapeellmkHlqktseqlatq 73
                                      +v+  v+ ek t ++ek+n+L           d+kke+e++ +   +  + l+ k  +k+  +l+ +
  gi|518652497|ref|YP_008142017.1|  3 YVISPVVTEKTTLMMEKENKLTFivdrrgRKKDIKKEIEERFDVKVIGLNILITKKGKKAIAKLSDD 69
                                      66777999*************99999999999********977777888999999988877777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       919  (0.0512577); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 567.53
//
Query:       gi|518652498|ref|YP_008142018.1|  [L=232]
Description: hypothetical protein FACI_IFERC00001G1137 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.7e-38  131.0   3.9    4.2e-38  130.4   3.9    1.3  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
     0.0014   18.6   0.0     0.0055   16.6   0.0    2.1  2  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   3.9   4.7e-42   4.2e-38       2     117 ..      86     205 ..      85     219 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 4.7e-42
                                       SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT CS
                    Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehke 78 
                                       +G ++ l++i  Gt+v+nie +pg+ggk++r+aG+++ ++++  + v +klpSg++r+++ +c At+Gvv++++ ++
  gi|518652498|ref|YP_008142018.1|  86 NGTTTTLSKIEDGTYVYNIENHPGDGGKFCRTAGSSGLIISHG-NSVSIKLPSGKTRELNPNCKATVGVVAGSGARD 161
                                       7999*************************************96.********************************* PP

                                       ----STTHHHHT.....TBS----SSSS-TTTSSS--SSSS--S CS
                    Ribosomal_L2_C  79 kklgkAgrkrwl.....grrpkvrGvamnpvdHphGGGeGktks 117
                                        +++kAg++ +      +r  +vrGvamn+v+HphGGG+ ++++
  gi|518652498|ref|YP_008142018.1| 162 IPILKAGKHIKYlqskaKRPYTVRGVAMNAVNHPHGGGNHQHVG 205
                                       *******998888898555559*****************54433 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 !   16.6   0.0   6.2e-07    0.0055      36      76 ..      37      77 ..       5      78 .. 0.85
   2 ?   -3.6   0.0       1.3   1.2e+04      43      55 ..     144     156 ..     142     160 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 6.2e-07
                                      EEEEEE--TT-SS-EEEEEETTTEEEEEE--SS--SS-EE- CS
                      Ribosomal_L2 36 kVveieyDpgRsApiAlvkyedgekryiiapeglkvGdtvv 76
                                       + +i++ pgR+Ap+  +k e++e +y+ia +g   G++++
  gi|518652498|ref|YP_008142018.1| 37 SIDDIIQAPGRNAPLLSLKNEQNEISYMIAFNGAFKGQKLY 77
                                      5789*******************************999987 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 1.3
                                       -TT-SS-EEEEEE CS
                      Ribosomal_L2  43 DpgRsApiAlvky 55 
                                       +p+ +A ++ v+ 
  gi|518652498|ref|YP_008142018.1| 144 NPNCKATVGVVAG 156
                                       7899999998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1661.94
//
Query:       gi|518652499|ref|YP_008142019.1|  [L=151]
Description: 30S ribosomal protein S19P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.4e-26   89.8   0.4    1.2e-25   89.1   0.1    1.5  2  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.36   6.5e+03       4      11 ..      13      20 ..       6      31 .. 0.50
   2 !   89.1   0.1   6.9e-30   1.2e-25       6      81 .]      63     134 ..      53     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.36
                                      HSSTTCCC CS
                     Ribosomal_S19  4 kkgpfvqe 11
                                      k+ +++++
  gi|518652499|ref|YP_008142019.1| 13 KRRSRKAQ 20
                                      33333322 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 6.9e-30
                                       S.TTCCCHHHHHHHHHHTS-----EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
                     Ribosomal_S19   6 g.pfvqesllkkvrkakaekkkevikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81 
                                       + +++q++l++++      ++ke++kth+Rd++IlP++vg +++ ynG ++ ++eik+em+Gh+LgEF+pTrk vkh
  gi|518652499|ref|YP_008142019.1|  63 EmNHEQQKLFDDLL-----GDKETLKTHVRDVIILPQFVGKKIELYNGTSYLKFEIKPEMIGHYLGEFAPTRKEVKH 134
                                       33344444444332.....37899****************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1041.59
//
Query:       gi|518652500|ref|YP_008142020.1|  [L=149]
Description: 50S ribosomal protein L22P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-17   62.9   0.0    3.8e-17   62.4   0.0    1.2  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 !   62.4   0.0   2.1e-21   3.8e-17       2     102 ..      17     143 ..      16     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 2.1e-21
                                       EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT.-SST..........................THHHHHHHHHHHH CS
                     Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkf.skkk..........................aakfvlklLknae 51 
                                       + ++  +s k + +va+ Ir+m++e A++ L+   +kk                          a k + klL  + 
  gi|518652500|ref|YP_008142020.1|  17 QVKETDISLKDAVNVAHFIRNMDLEAAKNALNLvVEKKmavpyfryldsvshrkgigpgrypvkAVKSFQKLLDDVS 93 
                                       568899***************************955556************************************** PP

                                       HHHH..HT-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEEEEEEEE CS
                     Ribosomal_L22  52 anaelkgldvdslvIeeiqvnkgpklkrrtyrArGrinpirkspchievvl 102
                                       anae kgl  d+l I +i ++kg+++k++t++A Gr++   k  +++ +v+
  gi|518652500|ref|YP_008142020.1|  94 ANAEFKGL-TDDLKIFHISASKGRMIKKFTPKAYGRAGANFKDLINLDIVV 143
                                       ********.9****************************9999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1055.56
//
Query:       gi|518652501|ref|YP_008142021.1|  [L=222]
Description: 30S ribosomal protein S3P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-17   63.0   1.5    2.8e-17   63.0   1.5    1.5  2  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    1.6e-10   40.6   0.0    3.6e-10   39.5   0.0    1.6  1  KH_2            KH domain
  ------ inclusion threshold ------
      0.021   14.7   0.0      0.051   13.4   0.0    1.7  1  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 ?   -3.5   0.0       2.7   1.6e+04      62      75 ..      60      73 ..      57      74 .. 0.75
   2 !   63.0   1.5   4.7e-21   2.8e-17       1      82 [.      98     180 ..      98     181 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 2.7
                                      H-EEEEEEEEETTE CS
                    Ribosomal_S3_C 62 didyavaeaktkyG 75
                                      +i+  ++  +tkyG
  gi|518652501|ref|YP_008142021.1| 60 KIKAMTSILETKYG 73
                                      67777888888888 PP

  == domain 2  score: 63.0 bits;  conditional E-value: 4.7e-21
                                       HHHHHHTT--HHHHHHHHHHHHHHCC-SEEEEEEEC-SS.TTT--EEEEEEC----..TCHHHH-EEEEEEEEETTE CS
                    Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramkagakGikiqvsGrLggaeiarsekykeGrvpl..htlradidyavaeaktkyG 75 
                                       ia +lek++++R+a ++++rr+++++a+G+ i++ G+++ +e+ar++k++ G+++   +++ra + ++++ a +k G
  gi|518652501|ref|YP_008142021.1|  98 IALSLEKGWNYRKAGNTTLRRIIDQHARGVLIRIGGKIS-GERARTQKFMYGEIKYsgEPARAGVITGYSVAMLKTG 173
                                       8999***********************************.9***************9******************** PP

                                       EEEEEEE CS
                    Ribosomal_S3_C  76 iiGvkVw 82 
                                        iG+ V+
  gi|518652501|ref|YP_008142021.1| 174 AIGIYVR 180
                                       ****997 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.0     6e-14   3.6e-10       4      75 ..      18      86 ..      15      89 .. 0.90

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 6e-14
                                      HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETT CS
                              KH_2  4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkk 75
                                      e+l+ e  +ag ++++ +rt+ +++i++++++pg+vIG+ Gs+ik++++ l+ + + le  +++  +++V++
  gi|518652501|ref|YP_008142021.1| 18 EYLQSENDSAGFGGMDMKRTPFGTNITLYVNRPGLVIGRHGSKIKAMTSILETKYG-LESPQIE--VKEVEN 86
                                      67777778999********************************************8.9999999..667766 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06     0.051      35      58 ..      45      68 ..      34      82 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
                              KH_4 35 vegedlGrvIGkrGrtldAlqylv 58
                                      +  +  G+vIG++G  ++A+  ++
  gi|518652501|ref|YP_008142021.1| 45 LYVNRPGLVIGRHGSKIKAMTSIL 68
                                      445668*************97776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1637.17
//
Query:       gi|518652502|ref|YP_008142022.1|  [L=65]
Description: 50S ribosomal protein L29 [Ferroplasma acidarmanus fer1]
Scores for complete 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-17   61.4   0.5    6.8e-17   61.2   0.5    1.1  1  Ribosomal_L29  Ribosomal L29 protein
     0.0087   16.2   2.5     0.0087   16.2   2.5    1.8  2  cwf21          cwf21 domain


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 !   61.2   0.5   7.6e-21   6.8e-17       1      57 []       6      63 ..       6      63 .. 0.98

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 7.6e-21
                                      HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHT.SSS-CHHHHHHHHHHHHHHHHHHHH CS
                     Ribosomal_L29  1 kelrelsdeeLkeklkelkkeLfnLrfqkatg.qlenpsrirkvRkdIARikTvlrer 57
                                      kelr++sdee++eklk lk+ L++ r + a+g ++  p+ +  ++k+IARi+Tv+ e+
  gi|518652502|ref|YP_008142022.1|  6 KELRAMSDEEINEKLKALKESLLKERSAIAMGgAPASPGTMHSIKKQIARILTVMEEK 63
                                      7*******************************9999*******************997 PP

>> cwf21  cwf21 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   2.5   9.7e-07    0.0087      25      44 .]      11      30 ..       1      30 [. 0.82
   2 ?   -1.8   0.1      0.41   3.7e+03      12      17 ..      58      63 ..      57      65 .] 0.63

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 9.7e-07
                             cwf21 25 lseeeIeervdelRekLlke 44
                                      +s+eeI e++++l+e Llke
  gi|518652502|ref|YP_008142022.1| 11 MSDEEINEKLKALKESLLKE 30
                                      69****************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.41
                             cwf21 12 kvlelr 17
                                       v+e+ 
  gi|518652502|ref|YP_008142022.1| 58 TVMEEK 63
                                      678775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 453.99
//
Query:       gi|518652503|ref|YP_008142023.1|  [L=99]
Description: translation initiation factor Sui1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-19   68.8   0.3    5.2e-19   68.5   0.3    1.1  1  SUI1      Translation initiation factor SUI1
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.13   12.6   0.1    1.2  1  Img2      Mitochondrial large subunit ribosomal protein (Img2
       0.14   11.5   0.0       0.15   11.3   0.0    1.1  1  HEM4      Uroporphyrinogen-III synthase HemD


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 !   68.5   0.3   8.7e-23   5.2e-19       3      76 ..      24      94 ..      22      95 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 8.7e-23
                              SUI1  3 pkihirleqrggrKkvTtvsgleafgidlkklakelkkkfacsgsvvkdggeeiqvQGdqrkkvaelLtekygv 76
                                      + i+i++++r+ +K vT++ g++++  +++++ak+lkkk a++g+v kdg   i++QGd+r+  ++ L+++ g+
  gi|518652503|ref|YP_008142023.1| 24 ELIKISVDKRRYGKLVTVIDGIDPKTENINDIAKTLKKKAASGGTV-KDG-RSIELQGDHRDVMKKELESM-GF 94
                                      569******************************************9.888.79****************98.87 PP

>> Img2  Mitochondrial large subunit ribosomal protein (Img2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.2e-05      0.13      36      80 .]      51      94 ..      24      94 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.2e-05
                              Img2 36 DiaalredLrkaleelvkvnevtgkieikGdrveevkkfLeskgF 80
                                      +i+++++ L+k  + +    +  ++ie++Gd+++  kk Les gF
  gi|518652503|ref|YP_008142023.1| 51 NINDIAKTLKKKAA-SGGTVKDGRSIELQGDHRDVMKKELESMGF 94
                                      34455555555555.67788899*********************9 PP

>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.15      98     145 ..      46      98 ..      32      99 .] 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                                       -..SSSHHHHGGGS-.---E.EE.....EEE-SS.S--HHHHHHHHHTTEEEEE CS
                              HEM4  98 pseegtaegLaeelaeslag.kr.....vlllrgeiarddlaegLeergaevde 145
                                        +++++  + a++l+++ a+ ++      + l+g ++rd ++++Le++g++v++
  gi|518652503|ref|YP_008142023.1|  46 DPKTENINDIAKTLKKKAASgGTvkdgrSIELQG-DHRDVMKKELESMGFKVQM 98 
                                       45599999999999994444344233326669**.5****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 732.55
//
Query:       gi|518652504|ref|YP_008142024.1|  [L=100]
Description: ribonuclease P protein component 1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.7e-18   63.9   0.0    1.1e-17   63.7   0.0    1.1  1  UPF0086         Domain of unknown function UPF0086
    0.00069   19.4   0.5      0.021   14.6   0.6    2.2  2  KcnmB2_inactiv  KCNMB2, ball and chain domain
  ------ inclusion threshold ------
      0.083   13.3   0.7       0.12   12.8   0.7    1.3  1  DUF5607         Domain of unknown function (DUF5607)


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 !   63.7   0.0   1.9e-21   1.1e-17       5      83 ..       8      85 ..       4      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 1.9e-21
                                      CSXXSS-EEEEEECSSTTTTTEEEEEEEEETTEEEEEECTTEEEEEESTTCEEEEEE.TTEEEEEECCCCSSXHHHHHC CS
                           UPF0086  5 kadlhGaeveVvrsknpslvgikGiVvkEtkntlkivtkksrvktvpKegsvFefevkdvlevevdGsqlryrpadRae 83
                                       ++++G +++V +s+n + vgikG  ++Etkn++ i    s++  ++K+g++F +e+++ ++++++G+ ++++p+dR++
  gi|518652504|ref|YP_008142024.1|  8 LMEFIGKNITVKNSHNIKNVGIKGKLIDETKNMMYIWN-GSKICSIQKSGTIFGIEFNEGAHYDINGDAILIKPEDRTK 85
                                      68***********************************8.9*****************99******************97 PP

>> KcnmB2_inactiv  KCNMB2, ball and chain domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.024   1.4e+02       1       9 [.      41      49 ..      41      55 .. 0.89
   2 !   14.6   0.6   3.5e-06     0.021      16      29 ..      85      98 ..      83      98 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.024
                    KcnmB2_inactiv  1 MFlvvGgRt 9 
                                      M ++ G+++
  gi|518652504|ref|YP_008142024.1| 41 MYIWNGSKI 49
                                      99******8 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.5e-06
                    KcnmB2_inactiv 16 teqRsIYQKiRehD 29
                                       e+R IY+K+R+++
  gi|518652504|ref|YP_008142024.1| 85 KEKRKIYKKLRGYE 98
                                      69*********987 PP

>> DUF5607  Domain of unknown function (DUF5607)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7     2e-05      0.12       3      46 ..      13      56 ..      11      75 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2e-05
                                      TT-TT-EEE--STT---EEEEEEE-SSEEEEE-SSEEEEEESSS CS
                           DUF5607  3 tnkiGcnvssplkhvdivGeiveeavynflidaGdkmcvGnkiG 46
                                         i    s  +k v i G++++e+   + i  G k+c  +k G
  gi|518652504|ref|YP_008142024.1| 13 GKNITVKNSHNIKNVGIKGKLIDETKNMMYIWNGSKICSIQKSG 56
                                      56678888999***************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 730.55
//
Query:       gi|518652505|ref|YP_008142025.1|  [L=106]
Description: 30S ribosomal protein S17P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-22   79.4   6.2    1.9e-22   79.1   6.2    1.1  1  Ribosomal_S17  Ribosomal protein S17


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 !   79.1   6.2   1.1e-26   1.9e-22       1      68 []      35     103 ..      35     103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 1.1e-26
                                       EEEEE--STTEEEEEEEEEEEETTTTEEEEEEEEEEEE-TTTS.--TT-EEEEEEECECSSSEEEEEEE CS
                     Ribosomal_S17   1 GvVvsdkmdkTvvVrverlvkhpkykkyvkrrkkylahdenns.vkvGDiVrieecrPlSktkrfvvve 68 
                                       G+Vvs km+++vv+r+e +v+ +ky++y+++ +ky+ah ++++ vkvGD V+ +ecr+l+kt+ fvv+e
  gi|518652505|ref|YP_008142025.1|  35 GKVVSVKMKRSVVIRREAKVYVKKYERYITKFTKYHAHLPDCIdVKVGDSVKAAECRKLAKTIDFVVIE 103
                                       99*****************************************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); 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: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 813.72
//
Query:       gi|518652506|ref|YP_008142026.1|  [L=132]
Description: 50S ribosomal protein L14P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-32  111.0   0.1    4.3e-32  110.8   0.1    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 !  110.8   0.1   2.4e-36   4.3e-32       4     122 .]      14     132 .]      12     132 .] 0.93

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 2.4e-36
                                       SS-EEE--SSSSBSEEEEEEETT-.....---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-E CS
                     Ribosomal_L14   4 lktrlkvaDNsgakevecikvlggk....krkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsv 76 
                                       l++++ +aDN+gak + +i v   +    + +aa vG   ++sv+k++p   +++ +vv+avvvr+++++rr+dG +
  gi|518652506|ref|YP_008142026.1|  14 LGAVIPCADNTGAKMISLIGVKDLHtvarRIPAAGVGTLFIASVRKGTP---EMRAKVVYAVVVRQRRPYRRADGNI 87 
                                       568899***************98875553449*****************...8999********************* PP

                                       EEESS-EEEEB-TTS-BSS-.B-SBEEHHHHHH.-HHHHHTBSBE. CS
                     Ribosomal_L14  77 irfddnaaVllnkkgeplGtrifgpvarelrekkflkivslApevl 122
                                       i+f+dnaaVl++ +ge++G++i+gpvare++e+ +++i+++A++++
  gi|518652506|ref|YP_008142026.1|  88 IEFEDNAAVLVTPEGEVRGSEIKGPVAREAAER-WPRIAAIASTIV 132
                                       ********************************9.********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1066.65
//
Query:       gi|518652507|ref|YP_008142027.1|  [L=166]
Description: 50S ribosomal protein L24P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-11   44.7   0.1    4.5e-11   43.1   0.1    1.7  1  Ribosomal_L26  Ribosomal proteins L26 eukaryotic, L24P archae
    0.00035   20.4   2.4    0.00074   19.4   2.4    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 !   43.1   0.1     5e-15   4.5e-11      23      75 ..       6      91 ..       2      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 5e-15
                                      xxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Ribosomal_L26 23 msapLskeLrekygvrslpir................................gvtrekangttvpvgihpSkvvItkl 69
                                      ++ +L ++L++kyg+r++p+                                 g+t  ka+g++v++ i+ S++v+tkl
  gi|518652507|ref|YP_008142027.1|  6 INVSLNRDLKKKYGIRRFPVVkgdivkivsgsrkgesgkvigvshktkkiaieGITIAKADGKQVEYYIDHSNLVVTKL 84
                                      56789************************************************************************** PP

                                      xx.xxxx RF
                     Ribosomal_L26 70 kl.Dkdr 75
                                      +l  + r
  gi|518652507|ref|YP_008142027.1| 85 DLsIEGR 91
                                      *965666 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   2.4   8.3e-08   0.00074       1      25 [.      27      51 ..      27      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 8.3e-08
                                      TTSEEEESSSTTTTCEEEEEEEETT CS
                               KOW  1 pGdhVkVvsGphkGktGkVvkvdqh 25
                                      +Gd+Vk+vsG  kG+ GkV  v  +
  gi|518652507|ref|YP_008142027.1| 27 KGDIVKIVSGSRKGESGKVIGVSHK 51
                                      7******************999766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       761  (0.0424452); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1240.16
//
Query:       gi|518652508|ref|YP_008142028.1|  [L=238]
Description: 30S ribosomal protein S4e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-16   59.5   1.1    4.5e-16   58.5   1.1    1.6  1  Ribosomal_S4e  Ribosomal family S4e
    0.00025   20.7   0.1    0.00059   19.5   0.1    1.7  1  S4             S4 domain
    0.00041   20.2   0.1     0.0012   18.7   0.1    1.9  1  KOW            KOW motif
  ------ inclusion threshold ------
      0.085   13.0   0.6       0.15   12.2   0.6    1.4  1  RS4NT          RS4NT (NUC023) domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4e  Ribosomal family S4e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   1.1     1e-19   4.5e-16       3      75 .]      91     163 ..      89     163 .. 0.96

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 1e-19
                                       EEEEEEE-TTSSEEEEEE-TTCCCEEEEEECEEEEECCCEEEEEETTS-EEEESSTT-STTEEEEEETTTTEE CS
                     Ribosomal_S4e   3 enyrllydtkgrfalhkItseeakyKLcKikkkttvkkgipqlvthdGrtirypdpdikvnDtvkidleenkI 75 
                                       + y ++yd+kg++++ +  + ++ +KL K+ kkt++ +g++ql +hdG+ti ++ +di++ D++++++++ +I
  gi|518652508|ref|YP_008142028.1|  91 NDYIIVYDRKGKLVIRQNAPGNKGLKLFKVVKKTIIGTGKIQLGFHDGKTIVTDRKDINTSDVLLMKIPDLEI 163
                                       679*****************************************************************99776 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.1   1.3e-07   0.00059      17      48 .]      53      84 ..      45      84 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-07
                                      HHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
                                S4 17 reArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48
                                      re+ ++ +   V+V+G++vkd  ++V+++Dv+
  gi|518652508|ref|YP_008142028.1| 53 REITRILNNNMVKVDGRIVKDRRFPVGFMDVL 84
                                      89999999999*******************85 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   2.7e-07    0.0012       1      27 [.     171     201 ..     171     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.7e-07
                                       TTSEEEESSSTTTTCEEEEEEEETTT....T CS
                               KOW   1 pGdhVkVvsGphkGktGkVvkvdqhk....v 27 
                                       +Gd V +++G h G+ +++++++ +k    +
  gi|518652508|ref|YP_008142028.1| 171 EGDKVFITGGSHVGELATIKSIEVKKssvkN 201
                                       59*********************99955444 PP

>> RS4NT  RS4NT (NUC023) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.6   3.4e-05      0.15       8      37 .]       4      33 ..       1      33 [. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                                      ETTTS-TTS---SSSSSEE----SSSS-TT CS
                             RS4NT  8 KrlaAPkhWpldkkegvfavkPspGPHklr 37
                                      K ++A +   +++k++ + v+P p  H+++
  gi|518652508|ref|YP_008142028.1|  4 KIMMASRKLKIPRKTNFWSVTPTPATHSKE 33
                                      778999999******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 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:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.45
# Mc/sec: 1580.74
//
Query:       gi|518652509|ref|YP_008142029.1|  [L=175]
Description: 50S ribosomal protein L5P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-21   75.8   0.0    4.8e-21   74.7   0.0    1.6  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    5.5e-21   74.7   0.8    9.4e-21   73.9   0.8    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.7   0.0   5.4e-25   4.8e-21       1      78 [.      64     135 ..      64     164 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.7 bits;  conditional E-value: 5.4e-25
                    Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivtta 77 
                                       +iG+kvtLr++++y+fl++++ ++ +++        +sfd++Gn  fGi+++++f++++yd+d+gifGmdi+i++++
  gi|518652509|ref|YP_008142029.1|  64 NIGAKVTLRKDDAYKFLKEAFYAKDYKIP------VYSFDKQGNAYFGITDYTDFKGMKYDPDIGIFGMDIAIILKR 134
                                       59***************************......9**************************************998 PP

                    Ribosomal_L5_C  78 k 78 
                                        
  gi|518652509|ref|YP_008142029.1| 135 A 135
                                       6 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.8     1e-24   9.4e-21       1      57 []       7      60 ..       7      60 .. 0.99

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1e-24
                                      SCTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
                      Ribosomal_L5  1 NvMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                                      N+M+++ ++K+vin+gvG age+   l+ka k+++ +tG kPv+t+akk+i++F+iR
  gi|518652509|ref|YP_008142029.1|  7 NPMRKIAIDKVVINIGVGAAGER---LTKATKVIELLTGHKPVITSAKKTIRDFNIR 60
                                      9**********************...******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1253.26
//
Query:       gi|518652510|ref|YP_008142030.1|  [L=156]
Description: 30S ribosomal protein S8P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-24   86.8   0.1    1.4e-24   86.4   0.1    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 !   86.4   0.1   7.8e-29   1.4e-24       1     127 []      31     156 .]      31     156 .] 0.90

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 7.8e-29
                                       -HHHHHHHHHHHHHHTT-SEEEE.E--HHHHHHHHHHHHCTSEEEEEEE.CCCCCCEEEEE-BSSS-SBSSSEEEE- CS
                      Ribosomal_S8   1 DpiadmltrirNaekakkeevev.pasklkeeilkvLkeeGyikdfeve.eekkkkikielkynkkkksvikklkrv 75 
                                       Dp++d++++i+ a++ +++e+++ pas+++ ++lkv+++ +yik+fev  ee+  k+++ l  + ++++vik    v
  gi|518652510|ref|YP_008142030.1|  31 DPLNDVINTIKMASRIGENEITIsPASRIIGRVLKVMQDYNYIKSFEVIeEERGGKFSVVLSDTINNCGVIKPRLSV 107
                                       9***********************************************9666666677777666667*****99999 PP

                                       SBTTC--EE-CCC---CGGGTSEEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
                      Ribosomal_S8  76 skpgrrvYakvkelpkvlnglGiaivsTskGvmtdkeArkkkvGGevlayvw 127
                                        +++   Y + + lp   + +Gi+i++T+kGvm++ eArk ++GG++layv+
  gi|518652510|ref|YP_008142030.1| 108 TRSSIGRYES-RYLP--AQDFGIIILTTTKGVMSHLEARKFGIGGKLLAYVY 156
                                       9999987765.5666..589*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.94
# Mc/sec: 503.31
//
Query:       gi|518652511|ref|YP_008142031.1|  [L=181]
Description: 50S ribosomal protein L6P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-16   59.3   3.1    4.8e-07   30.4   0.1    2.1  2  Ribosomal_L6  Ribosomal protein L6
  ------ inclusion threshold ------
      0.087   13.0   0.6        1.4    9.1   0.0    2.8  3  HSP20         Hsp20/alpha crystallin family


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 !   29.7   0.6   8.8e-11   7.9e-07       1      76 []      12      84 ..      12      84 .. 0.92
   2 !   30.4   0.1   5.3e-11   4.8e-07       1      76 []      96     169 ..      96     169 .. 0.97

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 8.8e-11
                                      CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHHHHHHHHHHHHHHHHHHHHTC CS
                      Ribosomal_L6  1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekvAligtvrslinnmikGVteg 76
                                      iP+g +  i+g  +++v+G+ ge +r++++   v+v +++n++  +v ++++ ++   igt+ s  +   +GV+ g
  gi|518652511|ref|YP_008142031.1| 12 IPEGISLDIDG-TVINVKGKLGEASRNFRDK-YVKVYKKENSIIIAVSKENKFTNG-IIGTWYSELKLVFHGVSNG 84
                                      8*********8.*******************.7777799*****************.****999888888888876 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5.3e-11
                                       CSTTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
                      Ribosomal_L6   1 iPvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                                       +P+ v+v +++  ++++lG k ++ ++i+   +v vk     ++ ++++gidk ++    A+i+ ++ ++  + +++
  gi|518652511|ref|YP_008142031.1|  96 FPMRVSVRGNELHVENFLGGKAPRIAKIKNC-KVSVK-----GDRVIIEGIDKRDMgdtaANIERATYIKHFDARVF 166
                                       79****************************8.9**98.....*********************************** PP

                                       HTC CS
                      Ribosomal_L6  74 teg 76 
                                       ++g
  gi|518652511|ref|YP_008142031.1| 167 QDG 169
                                       998 PP

>> HSP20  Hsp20/alpha crystallin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1       0.1   8.9e+02      21      39 ..      14      32 ..       6      63 .. 0.58
   2 ?   -0.5   0.0      0.15   1.4e+03       8      34 ..      86     109 ..      81     111 .. 0.68
   3 ?    9.1   0.0   0.00015       1.4      21      71 ..     124     180 ..     116     181 .] 0.83

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                                      CCEEEEEETTEEEEEEE-- CS
                             HSP20 21 eelkvkvednrvlvkgehe 39
                                      e + ++++++++ vkg+  
  gi|518652511|ref|YP_008142031.1| 14 EGISLDIDGTVINVKGKLG 32
                                      5566666666666666654 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.15
                                       EEEEEEE-TT--CCCEEEEEETTEEEE CS
                             HSP20   8 efevkldvpglkkeelkvkvednrvlv 34 
                                       ++e+k+d  ++    ++v+v++n++ v
  gi|518652511|ref|YP_008142031.1|  86 KYEMKIDFTHFP---MRVSVRGNELHV 109
                                       688888888875...566777776665 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00015
                                       CCEEEEEETTEEEEEEE--........---TT----SS---EEEEEE--STTB-TTT CS
                             HSP20  21 eelkvkvednrvlvkgehe......eeeedekglikerssrkFsrkftLPenvdadk 71 
                                       ++ kv+v+++rv+++g  +        + ++  +ik   +r F+  + L ++v++d+
  gi|518652511|ref|YP_008142031.1| 124 KNCKVSVKGDRVIIEGIDKrdmgdtAANIERATYIKHFDARVFQDGIYLLKGVNPDE 180
                                       6899************99988887666777888888899999999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.32s 00:00:00.82 Elapsed: 00:00:00.52
# Mc/sec: 1043.44
//
Query:       gi|518652512|ref|YP_008142032.1|  [L=134]
Description: 50S ribosomal protein L32e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-34  118.4   0.0    2.7e-34  117.8   0.0    1.2  1  Ribosomal_L32e  Ribosomal protein L32


Domain annotation for each model (and alignments):
>> Ribosomal_L32e  Ribosomal protein L32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.8   0.0   1.5e-38   2.7e-34       3     108 .]      27     130 ..      25     130 .. 0.99

  Alignments for each domain:
  == domain 1  score: 117.8 bits;  conditional E-value: 1.5e-38
                                       ----TTTTT-TTS-SS------TT-TTTTT-TTS-----GGG---TTTTT--TTS-EEEEESSGGGGTT--TTTE.. CS
                    Ribosomal_L32e   3 kFirhqsdryvklkeswrkprGidnrvrrrfkgqilmpkiGYgspkktrgllpsGfkkvlVhnvkeLevllmenksy 79 
                                       +F+r+++ ry+k+++swr+prG+++++r ++  + +++  GY++p+++rgl+psGf++vlVhnv+eL+++++  +  
  gi|518652512|ref|YP_008142032.1|  27 EFHRQEWFRYKKFDDSWRRPRGKHSKLRTHLGYRSPVVGPGYRTPRAVRGLHPSGFREVLVHNVNELSKINPDLE-- 101
                                       8**************************************************************************.. PP

                                       EEEE-TTS-HHHHHHHHHHHHHTT-EBSS CS
                    Ribosomal_L32e  80 aaeiahsVsskkrkeiverAaelgikVtN 108
                                        a+ia+sV+ +kr++i+++A++lgi+++N
  gi|518652512|ref|YP_008142032.1| 102 GARIASSVGYRKRIDIESEADNLGIHIFN 130
                                       ***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); 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: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 953.98
//
Query:       gi|518652513|ref|YP_008142033.1|  [L=158]
Description: 50S ribosomal protein L19e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-45  154.0  10.3    2.9e-45  153.9  10.3    1.0  1  Ribosomal_L19e  Ribosomal protein L19e


Domain annotation for each model (and alignments):
>> Ribosomal_L19e  Ribosomal protein L19e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9  10.3   1.6e-49   2.9e-45       2     142 ..       3     143 ..       2     145 .. 0.98

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 1.6e-49
                                       THHHHHHHHHHTTS-GGGEEE-GGGHHHHHH--SHHHHHHHHHTTSEEE-------THHHHHHHHHHHTT-S-SGGG CS
                    Ribosomal_L19e   2 lklqkrlaasvlkvGknrvwldpeeleeiaeAitredirklikdglIikkpkkgnsrararerkekkrkgrrrgsGk 78 
                                       ++++k+++a+ lkvG +rvw+d+++l+++ +A++redi+kli  ++I++++kk +s++r+++r ++  kgrrrg+G+
  gi|518652513|ref|YP_008142033.1|   3 MSSVKEISADELKVGISRVWIDTNNLDRVLDATSREDIKKLIGLNIIQRRDKKNHSNQRLKKRINQLTKGRRRGPGS 79 
                                       6789************************************************************************* PP

                                       --S-HHHHS-HHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHTT--SSHHHHHHHHT- CS
                    Ribosomal_L19e  79 rkGtkeaRlpekelWikriRalRrlLkelrekkkidkktYrelYrkakGgefknkavLkeyiek 142
                                        +Gtk aR p+k++Wi++iRalR++Lk+l+ek++idk+tYr++Yr +k+g+f+++a+L +++++
  gi|518652513|ref|YP_008142033.1|  80 VRGTKYARYPRKRRWITTIRALRDELKTLKEKESIDKTTYRKYYRTIKSGSFSSRAQLVSHLKT 143
                                       *************************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1282  (0.0715043); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1212.38
//
Query:       gi|518652514|ref|YP_008142034.1|  [L=157]
Description: 50S ribosomal protein L18P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-11   44.9   1.7    6.3e-07   29.5   0.5    2.2  2  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 
    3.6e-06   27.3   0.1    4.5e-06   27.0   0.1    1.1  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L5e  Ribosomal large subunit proteins 60S L5, and 50S L18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.5     7e-11   6.3e-07       7      99 ..       7      91 ..       4      95 .. 0.89
   2 !   15.0   0.0     2e-06     0.018     130     162 ..      95     127 ..      88     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 7e-11
                     Ribosomal_L5e  7 frrrregktdYyarkrliiqdknkyntpkyRlvVrvtnkdiicqiayakiegdkvlaaayskelp.kygvkvgltnyaa 84
                                      ++rr  g tdY++r rl+  +         R vVr tnk ++++++  + +gd v ++++ k l+ +ygv    +n +a
  gi|518652514|ref|YP_008142034.1|  7 LKRRNLGITDYQKRYRLLKSN-------VTRAVVRPTNKGLMIEFVDYSPSGDLVKVTVTDKTLQkEYGVY--GNNIQA 76
                                      5899*************8654.......4599***********************9999999987479988..579*** PP

                     Ribosomal_L5e 85 aYatglllarrllkk 99
                                       Y+ g+l ++++ +k
  gi|518652514|ref|YP_008142034.1| 77 MYLAGYLAGKKAAEK 91
                                      ********9998765 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 2e-06
                     Ribosomal_L5e 130 kaiLdvGLartttgakvfgalkgavdgglsiph 162
                                        ai+d G  +  +g ++ +alkg+vd+g++ip 
  gi|518652514|ref|YP_008142034.1|  95 SAIFDTGRYKFIHGGRLAAALKGIVDSGIEIPA 127
                                       68999**************************97 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 !   27.0   0.1     5e-10   4.5e-06      24     115 ..      28     124 ..       8     125 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 5e-10
                                       S-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCT...S-SSSCHHHHHHHHHHHHHHHCHHCHTC-EE--TTSS CS
                    Ribosomal_L18p  24 rprlvvfrsnrhiyaQviddvkgktlasastlekelk...lkstknkeaakkvgeliAerakekgiekvvfDrggyk 97 
                                         r vv  +n+ +++  +d + +  l+++   +k+l+   + +++n++a    g l  ++a ekgie+++fD+g yk
  gi|518652514|ref|YP_008142034.1|  28 VTRAVVRPTNKGLMIEFVDYSPSGDLVKVTVTDKTLQkeyGVYGNNIQAMYLAGYLAGKKAAEKGIESAIFDTGRYK 104
                                       45888999*********************999999996666677888888888888889*****************9 PP

                                       S..-CHHHHHHHHHHCTSSB CS
                    Ribosomal_L18p  98 Y..hGrvaalAdaaReaGlk 115
                                       +   Gr+aa  +++ + G++
  gi|518652514|ref|YP_008142034.1| 105 FihGGRLAAALKGIVDSGIE 124
                                       86358998887777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1091.99
//
Query:       gi|518652515|ref|YP_008142035.1|  [L=221]
Description: hypothetical protein FACI_IFERC00001G1154 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   87.1   1.4      1e-24   86.3   1.4    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain
    4.7e-19   67.6   0.3    8.1e-19   66.9   0.3    1.4  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.3   1.4   1.1e-28     1e-24       1      64 [.      46     109 ..      46     110 .. 0.98

  Alignments for each domain:
  == domain 1  score: 86.3 bits;  conditional E-value: 1.1e-28
                                       XEEEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE- CS
                      Ribosomal_S5   1 lkekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvpv 64 
                                       l+++v++i r q++t++Grr+++s+++vvG+gnG+vG+G gkake a AirkAi++Ak n++++
  gi|518652515|ref|YP_008142035.1|  46 LQDEVINIERAQRMTDSGRRMNYSITAVVGNGNGYVGIGRGKAKEAAPAIRKAINNAKTNIIEI 109
                                       799***********************************************************98 PP

>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.9   0.3     9e-23   8.1e-19       2      66 ..     132     197 ..     131     201 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.9 bits;  conditional E-value: 9e-23
                                       EEETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS.-SSHHHHHHHHHHHHHHTTTT- CS
                    Ribosomal_S5_C   2 gkfgavkvllkpaprGtGiiaggavravlelaGikDvlakslg.srnpinvvkAtfeALkklrspe 66 
                                       gk g+v v+lk+ap+G G+ +g++v+ +l++aGi+D +  + g +++++n + Atf+ALkk+ s++
  gi|518652515|ref|YP_008142035.1| 132 GKSGSVVVKLKSAPQGVGLAVGDVVKIILKMAGIEDAWGFASGhTKTTVNYALATFDALKKTVSMK 197
                                       99***********************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); 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 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1627.53
//
Query:       gi|518652516|ref|YP_008142036.1|  [L=164]
Description: 50S ribosomal protein L30P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-12   46.4   0.0    5.7e-12   45.3   0.0    1.6  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 !   45.3   0.0   3.2e-16   5.7e-12       2      51 .]       3      52 ..       2      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 45.3 bits;  conditional E-value: 3.2e-16
                                      EEEE-S-STTS-HHHHHHHHHTT-SSTTEEEE--SSHHHHHHHHHCCCGE CS
                     Ribosomal_L30  2 fVtrirsiigvppkvrktLqlLgLrkingtvvklntpsirGmLkkVkhlV 51
                                      +++rir+  g++p   kt +lL L++in+ v    + s++GmL+ Vk++V
  gi|518652516|ref|YP_008142036.1|  3 AIIRIRGSTGIKPFAGKTAELLNLNRINHMVLFQESESLNGMLNRVKDYV 52
                                      79**************************99999999*************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1167.54
//
Query:       gi|518652517|ref|YP_008142037.1|  [L=135]
Description: 50S ribosomal protein L15P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.6e-11   43.8   0.3    5.4e-11   43.3   0.3    1.3  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.3     3e-15   5.4e-11       1     126 [.      24     132 ..      24     134 .. 0.86

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 3e-15
                                       GGGGTSSTTTTTTTTT-...S--.......S--.........---.GGG..---EEEEHHHHHHTTTTGTTS.---- CS
                    Ribosomal_L27A   1 kGktgGrGhkGqkkrsg...vkk.kpgfeGGqmplyrrlpkrGfk.nskfkkeykvvnlkdLdelideerle.lade 71 
                                       kGk+gG G++G   +++   + + k+ +  G +         Gf+ +s+  + ++++ l++L++ ++ ++ +    e
  gi|518652517|ref|YP_008142037.1|  24 KGKRGGSGMAGLGGHKKiwlIIHdKNHY--GVH---------GFTsHST--TYENPITLRQLNDRYEVLKASgY-VE 86 
                                       6**************9998634334558..***.........**96655..999*********87777777644.59 PP

                                       --EEEGGGTTTTSSS....SE.EEE--S---.--EEEESEE-HHHHHHHHHTT-EE CS
                    Ribosomal_L27A  72 aeeidleelaeaglikkkdgv.KvlgkgeltkklkvkaskfSkkAkekIeaaGGkv 126
                                       +++idle+           g+ K+l++g+++ k k+k  k+++k ++k  + G ++
  gi|518652517|ref|YP_008142037.1|  87 NDVIDLESA----------GYtKLLASGNFEIKCKIKIPKATEKSINKLSNHGITI 132
                                       9********..........*****************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 902.42
//
Query:       gi|518652518|ref|YP_008142038.1|  [L=586]
Description: hypothetical protein FACI_IFERC00001G1157 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-69  234.9  18.3    1.2e-69  234.9  18.3    2.1  2  SecY             SecY translocase
    6.9e-12   45.0   1.6    3.2e-11   42.9   0.6    2.9  2  Plug_translocon  Plug domain of Sec61p
  ------ inclusion threshold ------
       0.16   12.4   0.1       0.16   12.4   0.1    3.4  4  Phage_holin_5_1  Bacteriophage A118-like holin, Hol118


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 ?    1.3   1.3     0.027   1.6e+02     174     199 ..       7      77 ..       2     128 .. 0.48
   2 !  234.9  18.3   2.1e-73   1.2e-69       1     306 []     133     564 ..     133     564 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.027
                                       TCCCSCHHHHHHHHHHH.....................HHCCCCS.........................T CS
                              SecY 174 nyagviPiIfassllal.....................pstiaqfl........................l 199
                                       n    iP+If  +l+++                     p +i+ +l                        +
  gi|518652518|ref|YP_008142038.1|   7 NKGAAIPVIFIFALFIVvfyyfshytglklfilgllssPLFIIAYLllsykgpkksrlyglenltaklpaI 77 
                                       67778999999999985333333333333333333333333333335555555555555554444443330 PP

  == domain 2  score: 234.9 bits;  conditional E-value: 2.1e-73
                                       BTTSSTCHHHHHHHHHHHHH.HHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC........... CS
                              SecY   1 sifaLGImPyitasIilqLl.tvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg........... 65 
                                       s++ LGI+P++tasI++qL+ ++   k+ +l+  + ++++ +++++++l++++++v+a+  a+++            
  gi|518652518|ref|YP_008142038.1| 133 SLMDLGIGPIVTASIVMQLFaGA---KIFNLDLSDSSDKAIYQGFQKLLVIIMIFVEAIPQAFGFLvpdaglvsnia 206
                                       89******************999...4445554499************************88877799********* PP

                                       .........HH.HHHHHHHHHHHHHHHHHHHHHHHHSSTTHHHHHHHHHHHHHHC.CHSS................. CS
                              SecY  66 .........lalllivlqltagtvllmwLgEqitekGiGnGisllifagivarlp.kals................. 115
                                                la  +i+lql++g++l+++++E+++++GiG+Gisl+i+ag++++l+ ++++                 
  gi|518652518|ref|YP_008142038.1| 207 hvvpgygefLAQSIIILQLFFGSYLVFLMDEVVSKYGIGSGISLFIAAGVSQQLFtGTFNwipstitsplslsnppa 283
                                       *********8899******************************************6666666655555555555555 PP

                                       -HHHH................SS..........THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBS.TT....S.S- CS
                              SecY 116 gliel................ale........gilallllllvtllvillvvyveeaerripvqya.krgrkggqss 167
                                       g                    + +        +  + +++l+ tll++++v +++++++++p+ ++  r    g+++
  gi|518652518|ref|YP_008142038.1| 284 G---AipkalylfinapgsylT-NtgmeqilfAQPNPMIALVGTLLIFFVVAFFQSSKIELPIAHErVR----GARG 352
                                       1...044445555555555441.144443444223789999*************************666....9*** PP

                                       EEEEETTCCCSCHHHHHHHHHH....................................................... CS
                              SecY 168 ylPlklnyagviPiIfasslla....................................................... 189
                                       ++Pl+l+ya++iP+I+a++lla                                                       
  gi|518652518|ref|YP_008142038.1| 353 RYPLQLLYASNIPVILATALLAnismwtllfwdspvlskipilghshllgsyasaaqisalgissttptgglayyly 429
                                       **********************7777777777777777777777777777777777766666666666666665555 PP

                                       HHHCCCCS..........TCCCS........THHHHHHHHHHHHHH....HHHHHHTCT.THHHHHHHCCHHTBSSS CS
                              SecY 190 lpstiaqfl.........lalls........psvlyvvlyvlliif....Fayfyteit.fnpkevaenlkksggfi 244
                                       +p+ +  +l         +   s        ++++++v++++++++    Fa+f++e+t + p+ va++++ sg++i
  gi|518652518|ref|YP_008142038.1| 430 TPNGLSDWLfpilqpsvsQ---SvllghtpvEELIHIVVFMVFLVGfsilFAKFWIETTnMGPDAVAKQIRSSGMQI 503
                                       3444444445554444431...0333445555566777777777666777*************************** PP

                                       CTTT.TCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.TT.TTHHHHHHHHHHHHHHH CS
                              SecY 245 pgir.pgketakyLekvlsritliGalflaliavlpdllgasligafggtslLivVgvaletv 306
                                       pg+r + + +ak+L+k+++ it++++++++++a  +dl+g+  +g  +gt+lL++Vg++++++
  gi|518652518|ref|YP_008142038.1| 504 PGFRrDPRIMAKVLSKYIPAITIFSGAIVGILAGAADLIGT--VGDTSGTGLLLAVGIVIQFY 564
                                       ****999**********************************..8999*************986 PP

>> Plug_translocon  Plug domain of Sec61p
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.6   5.3e-15   3.2e-11       1      35 []      98     132 ..      98     132 .. 0.98
   2 ?   -3.0   0.0       1.2     7e+03       5      13 ..     388     396 ..     388     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 5.3e-15
                                       HHHHHHCCSB-TT--SSS-TCCHTTTCCCCTSSTT CS
                   Plug_translocon   1 llYlvlsqiPLyGissssssDpfywlRaifAsnrG 35 
                                       l+Y+ l++i++yG+ +s++ D f+ +RaifA+++G
  gi|518652518|ref|YP_008142038.1|  98 LIYFALTNIYIYGLNTSKTVDVFASFRAIFAGASG 132
                                       7*******************************998 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                                       HHCCSB-TT CS
                   Plug_translocon   5 vlsqiPLyG 13 
                                       vls iP+ G
  gi|518652518|ref|YP_008142038.1| 388 VLSKIPILG 396
                                       79****988 PP

>> Phage_holin_5_1  Bacteriophage A118-like holin, Hol118
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.97   5.8e+03      38      67 ..     144     173 ..     141     179 .. 0.84
   2 ?   -1.7   0.1      0.67     4e+03      14      27 ..     177     190 ..     166     203 .. 0.69
   3 ?   -1.3   0.1      0.48   2.9e+03       7      23 ..     463     479 ..     459     492 .. 0.75
   4 ?   12.4   0.1   2.6e-05      0.16      30      71 ..     515     556 ..     503     571 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.97
                   Phage_holin_5_1  38 tvsilvgailgalatsldgsgslatmiwag 67 
                                       t si++    ga    ld s s    i+ g
  gi|518652518|ref|YP_008142038.1| 144 TASIVMQLFAGAKIFNLDLSDSSDKAIYQG 173
                                       789999999999999999999988888776 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.67
                   Phage_holin_5_1  14 lvvvtpvfvqaikk 27 
                                       l+v+  +fv+ai +
  gi|518652518|ref|YP_008142038.1| 177 LLVIIMIFVEAIPQ 190
                                       66777788888755 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.48
                   Phage_holin_5_1   7 llvymtflvvvtpvfvq 23 
                                       ++v+m flv  + +f +
  gi|518652518|ref|YP_008142038.1| 463 IVVFMVFLVGFSILFAK 479
                                       6899***9988888876 PP

  == domain 4  score: 12.4 bits;  conditional E-value: 2.6e-05
                   Phage_holin_5_1  30 lvpskwlptvsilvgailgalatsldgsgslatmiwagalag 71 
                                        v sk++p+++i+ gai+g la + d  g++     +g l  
  gi|518652518|ref|YP_008142038.1| 515 KVLSKYIPAITIFSGAIVGILAGAADLIGTVGDTSGTGLLLA 556
                                       5789*******************9999988877666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.27s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3785.68
//
Query:       gi|518652519|ref|YP_008142039.1|  [L=180]
Description: adenylate kinase [Ferroplasma acidarmanus fer1]
Scores for complete 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-30  104.5   0.0    7.1e-30  104.2   0.0    1.1  1  AAA_17           AAA domain
    2.6e-10   40.9   0.1    4.6e-10   40.2   0.1    1.4  1  AAA_18           AAA domain
     0.0014   18.8   0.1     0.0049   17.0   0.0    1.7  2  AAA_33           AAA domain
     0.0048   16.7   0.0      0.011   15.5   0.0    1.6  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
     0.0082   15.4   0.1      0.011   14.9   0.1    1.2  1  NB-ARC           NB-ARC domain
     0.0098   15.9   0.2      0.021   14.9   0.0    1.6  2  AAA_14           AAA domain
  ------ inclusion threshold ------
      0.011   15.9   0.0       0.02   15.1   0.0    1.5  1  AAA_28           AAA domain
      0.017   15.1   0.1      0.029   14.3   0.1    1.5  1  NTPase_1         NTPase
      0.026   15.0   0.1       0.03   14.9   0.1    1.3  1  ABC_tran         ABC transporter
      0.037   13.8   0.1      0.077   12.8   0.1    1.5  1  AAA_29           P-loop containing region of AAA domain
      0.044   13.5   0.1      0.073   12.8   0.1    1.4  1  AAA_24           AAA domain
      0.053   12.5   0.0      0.083   11.9   0.0    1.3  1  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
       0.06   13.1   0.4       0.19   11.5   0.0    1.8  2  Cytidylate_kin   Cytidylate kinase
      0.065   13.7   0.0      0.096   13.1   0.0    1.4  1  AAA              ATPase family associated with various cellul
       0.12   12.8   0.0       0.17   12.2   0.0    1.3  1  AAA_16           AAA ATPase domain
       0.13   12.3   0.1       0.31   11.1   0.1    1.6  1  MMR_HSR1         50S ribosome-binding GTPase


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 !  104.2   0.0   6.3e-33   7.1e-30       2     136 .]       7     138 ..       6     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 6.3e-33
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeeakkkgvlvdg 78 
                                       G+PG+GK+t+++ + +k  ++++++G+l++++a++  l+k+rd++r+l+ + ++ lqk+  +++ ++   +++++d+
  gi|518652519|ref|YP_008142039.1|   7 GIPGVGKSTILDMVSKKSMYEIINFGSLMFDMARDLDLVKSRDDIRRLDVDTQRNLQKKTSNQLGKM---DNIIIDT 80 
                                       9***************************************************************986...89***** PP

                                       -SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-SHHHHH CS
                            AAA_17  79 hprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddneesik 136
                                       h++ik +ag+l+glp++vl+el ++  +l+e  p ei +rr +d tr+rd+d++++i+
  gi|518652519|ref|YP_008142039.1|  81 HMSIKSPAGYLPGLPAWVLNELMVSSYFLIESTPAEIKRRRDNDSTRSRDEDTINDIE 138
                                       ******************************************************9985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   4.1e-13   4.6e-10       1     121 [.       3     132 ..       3     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 4.1e-13
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf......gvnlrdvakenglllevdpealdeskrldedkldklldaleenssal 71 
                                       ++++G+pGvGK+t+ + +sk+  +      g    d+a++ +l+ ++d+      +rld d + +l+++  ++   l
  gi|518652519|ref|YP_008142039.1|   3 VVISGIPGVGKSTILDMVSKKS-MyeiinfGSLMFDMARDLDLVKSRDDI-----RRLDVDTQRNLQKKTSNQ---L 70 
                                       78******************94.4478999********************.....444444444555554443...5 PP

                            AAA_18  72 eegknlvidghlaeleseaakdikk............vvLtaspeelleRlekRgyeeakik 121
                                       ++ +n++id h++   ++ +  +              + ++  p e ++R  ++++++++  
  gi|518652519|ref|YP_008142039.1|  71 GKMDNIIIDTHMSIKSPAGYLPGLPawvlnelmvssyFLIESTPAEIKRRRDNDSTRSRDED 132
                                       67899999999999999988887778888888888877777777777777777666665544 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   4.4e-06    0.0049       2      76 ..       3      79 ..       3      86 .. 0.79
   2 ?   -0.7   0.0       1.3   1.5e+03      31      49 ..     114     132 ..      97     152 .. 0.55

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 4.4e-06
                            AAA_33  2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg..tdqqsktdytrvldrlyqilnelarkalsagrnvild 76
                                      v++ G pG+GKst ++ + kk  +++++  +l++ ++   + ++s  d  r+  ++ + l++     l +  n+i+d
  gi|518652519|ref|YP_008142039.1|  3 VVISGIPGVGKSTILDMVSKKSMYEIINFGSLMFDMARdlDLVKSRDDIRRLDVDTQRNLQKKTSNQLGKMDNIIID 79
                                      6789******************************9998765555655545555557777777777777777777777 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 1.3
                            AAA_33  31 dtlrrrlfgtdqqsktdyt 49 
                                       +++++r + +d ++ +d  
  gi|518652519|ref|YP_008142039.1| 114 PAEIKRRRDNDSTRSRDED 132
                                       4455555544444433322 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   9.4e-06     0.011       2      69 ..       4      79 ..       3      91 .. 0.72
   2 ?   -1.9   0.0         2   2.2e+03     200     221 ..     126     147 ..     101     150 .. 0.59

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9.4e-06
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts..liltvnrptaelltegk.....pklpnlsvrtvdsflmalvks.tkgkililD 69
                                      v++G+pG GKSt++  + ++s   i++ ++  + ++++       ++  +l+v t + ++++ +++  k + +i+D
  gi|518652519|ref|YP_008142039.1|  4 VISGIPGVGKSTILDMVSKKSmyEIINFGSLMFDMARDLDlvksrDDIRRLDVDTQRNLQKKTSNQlGKMDNIIID 79
                                      9***********8888888889988888888888888877666665555555555555555555555556666666 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2
                   Viral_helicase1 200 tlvllketdlelisesrenllv 221
                                       t  ++++t +++ ++++ n++ 
  gi|518652519|ref|YP_008142039.1| 126 TRSRDEDTINDIEEHQQVNRYY 147
                                       3345566666666666666655 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1     1e-05     0.011      23      83 ..       3      69 ..       1      84 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1e-05
                                      EEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE......EEESXXHHHHHHHXXHHHHHCCCTTS CS
                            NB-ARC 23 valvGmgGvGKttlakqilnksdeveg.rFdsvawv......vvsktdkseeiletilkeLslseddl 83
                                      v ++G +GvGK+t++  + +k ++ e  +F s+++        v   d+++++  +  ++L+++ +++
  gi|518652519|ref|YP_008142039.1|  3 VVISGIPGVGKSTILDMVSKK-SMYEIiNFGSLMFDmardldLVKSRDDIRRLDVDTQRNLQKKTSNQ 69
                                      789******************.5555449998887666666767777777777777777777665554 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.9e-05     0.021       5      71 ..       3      79 ..       1      94 [. 0.62
   2 ?   -2.5   0.0       4.4     5e+03      51      57 ..     132     138 ..      98     154 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.9e-05
                            AAA_14  5 lvitGaRrvGKTtllkqlikellvkkesilyinldderd.......kkladpe......kllelileklke..ekktyl 68
                                      +vi+G+  vGK+t+l  + k+++ +  ++  + +d  rd       +     +      +  + +++k ++   k+  +
  gi|518652519|ref|YP_008142039.1|  3 VVISGIPGVGKSTILDMVSKKSMYEIINFGSLMFDMARDldlvksrD-----DirrldvDTQRNLQKKTSNqlGKMDNI 76
                                      79*************99999999555556666666666633332221.....122332333344444422234455556 PP

                            AAA_14 69 flD 71
                                      ++D
  gi|518652519|ref|YP_008142039.1| 77 IID 79
                                      666 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 4.4
                            AAA_14  51 kllelil 57 
                                       + ++ i 
  gi|518652519|ref|YP_008142039.1| 132 DTINDIE 138
                                       2233333 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   1.8e-05      0.02       1     134 [.       2     134 ..       2     162 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.8e-05
                            AAA_28   1 kivitGgestGKTtlleaLaargypvvpEaareileeklakgedalpwvedllafaervleeqleeeaaaaankvlf 77 
                                       ++vi+G ++ GK+t+l   +++ +  +  ++  +++   + +  +      + +++++ ++ q +++++ ++n++  
  gi|518652519|ref|YP_008142039.1|   2 RVVISGIPGVGKSTILDMVSKKSMYEIINFGSLMFDMARDLDLVK-----SRDDIRRLDVDTQ-RNLQKKTSNQLGK 72 
                                       79******************9987777889998886655544433.....3445555555555.3455557888888 PP

                            AAA_28  78 cDrglldtlaYarayggeaeaelea.aarekrydlvfllppap.ei....dddgeRredleer 134
                                       +D  ++dt + ++   g   + l a  ++e     +fl + +p ei    d+d +R  d++  
  gi|518652519|ref|YP_008142039.1|  73 MDNIIIDTHMSIKSPAGY-LPGLPAwVLNELMVSSYFLIESTPaEIkrrrDNDSTRSRDEDTI 134
                                       888888888877777776.66677645556666778888876665555566666665555444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   2.6e-05     0.029       1      25 [.       2      26 ..       2      83 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.6e-05
                                      EEEEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1  1 kvfiTGppGvGKtTlvkkvlellks 25
                                      +v+i+G pGvGK+T+++ v+++   
  gi|518652519|ref|YP_008142039.1|  2 RVVISGIPGVGKSTILDMVSKKSMY 26
                                      689**************99987655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   2.6e-05      0.03      13      67 ..       2      57 ..       1     159 [. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.6e-05
                                      EEEEEESTTSSHHHHHHHHTTSS--...SEEEEEET.TCEGGGB-HHHCCHCEEEE-SS CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp...teGeilld.gkdlkeqeleslrkeigvlpqe 67
                                      +v+i G  G GKSt+l ++++++     + G++ +d  +dl+   l ++r  i+ l  +
  gi|518652519|ref|YP_008142039.1|  2 RVVISGIPGVGKSTILDMVSKKSMYeiiNFGSLMFDmARDLD---LVKSRDDIRRLDVD 57
                                      6899****************9988755566777666333333...45555555555444 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 ?   12.8   0.1   6.8e-05     0.077      26      41 ..       4      19 ..       2      22 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                            AAA_29 26 lltGpsGsGKSTllDA 41
                                      +++G  G+GKST+lD 
  gi|518652519|ref|YP_008142039.1|  4 VISGIPGVGKSTILDM 19
                                      799************6 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   6.6e-05     0.073       4      73 ..       2      80 ..       1      89 [. 0.64

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.6e-05
                            AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie.........swedfldevvel........aaelad 65
                                      +++i G +g+GK+t++ +  +k  +  ++ G+   d ++  d+           ++                 + +l +
  gi|518652519|ref|YP_008142039.1|  2 RVVISGIPGVGKSTILDMVSKKSMYEIINFGSLMFDMARDLDLVksrddirrlDVD--------TqrnlqkktSNQLGK 72
                                      89*****************4444444445566666666555433222222233333........245555555888889 PP

                            AAA_24 66 yktlviDt 73
                                       + ++iDt
  gi|518652519|ref|YP_008142039.1| 73 MDNIIIDT 80
                                      99999998 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   7.4e-05     0.083      31      51 ..       2      22 ..       1      32 [. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.4e-05
                                      EEEEEE-TTSSHHHHHHHHHH CS
                              MeaB 31 vvGltGvPGaGkstlvealgl 51
                                      +v + G+PG+Gkst+++ +  
  gi|518652519|ref|YP_008142039.1|  2 RVVISGIPGVGKSTILDMVSK 22
                                      7889***********998765 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.19       3      70 ..       5      76 ..       3      86 .. 0.82
   2 ?   -0.7   0.1      0.85   9.6e+02     165     179 ..     115     129 ..     104     144 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                      EE-STTSSHHHHHHHHHHHHT-EEEEHHH....HHHHHHHHHHHTT--TT-HHHHHHHHHT--EEEEEEEEE CS
                    Cytidylate_kin  3 iDGPagsGKssvaralaeklglkyldtga....lYRalalaalrrkvdlldeaalvelakevelsfeaekvl 70
                                      i G  g GKs++  ++++k  +++++ g+    + R l l+  r ++  ld+++  +l k+++ ++ +   +
  gi|518652519|ref|YP_008142039.1|  5 ISGIPGVGKSTILDMVSKKSMYEIINFGSlmfdMARDLDLVKSRDDIRRLDVDTQRNLQKKTSNQLGKMDNI 76
                                      778889*********************9743335699999***************99999999888776544 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.85
                                       HHHHHHHHHHHCTSS CS
                    Cytidylate_kin 165 aeikeRDklDkerev 179
                                       aeik+R + D++r+ 
  gi|518652519|ref|YP_008142039.1| 115 AEIKRRRDNDSTRSR 129
                                       677777777777754 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   8.5e-05     0.096       1      29 [.       3      31 ..       3      80 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.5e-05
                                      EEEESSTTSSHHHHHHHHHHHHTHEEEEE CS
                               AAA  1 vllyGppGtGKTllakavakelgveflei 29
                                      v+++G pG+GK+++   v k++  e++++
  gi|518652519|ref|YP_008142039.1|  3 VVISGIPGVGKSTILDMVSKKSMYEIINF 31
                                      5789****************987666654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00015      0.17      27      46 ..       3      22 ..       2      71 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
                            AAA_16 27 vllsGesGvGKsslvrellr 46
                                      v++sG +GvGKs++++++ +
  gi|518652519|ref|YP_008142039.1|  3 VVISGIPGVGKSTILDMVSK 22
                                      79*************99986 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00028      0.31       1      22 [.       2      23 ..       2      33 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00028
                                      EEEEEESTTSSHHHHHHHHHTS CS
                          MMR_HSR1  1 evaivGrpNvGKStLinaltge 22
                                      +v+i G p vGKSt++   +++
  gi|518652519|ref|YP_008142039.1|  2 RVVISGIPGVGKSTILDMVSKK 23
                                      699************9877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 1231.13
//
Query:       gi|518652520|ref|YP_008142040.1|  [L=228]
Description: hypothetical protein FACI_IFERC00001G1159 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-25   89.1  12.5    2.6e-25   89.1  12.5    1.5  2  EMC3_TMCO1     Integral membrane protein EMC3/TMCO1-like
    4.2e-05   23.9   4.8      0.007   16.6   2.4    2.1  2  EI24           Etoposide-induced protein 2.4 (EI24)
     0.0047   17.2   0.2        0.3   11.4   0.1    2.5  2  Orf78          Orf78 (ac78)
  ------ inclusion threshold ------
      0.026   14.7   2.6      0.026   14.7   2.6    2.0  2  DPM3           Dolichol-phosphate mannosyltransferase subunit
      0.049   13.0  12.8      0.086   12.2   1.2    2.4  2  Polysacc_synt  Polysaccharide biosynthesis protein


Domain annotation for each model (and alignments):
>> EMC3_TMCO1  Integral membrane protein EMC3/TMCO1-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.8       1.4   4.9e+03      91     104 ..      14      27 ..       8      37 .. 0.55
   2 !   89.1  12.5   7.2e-29   2.6e-25       2     159 ..      50     218 ..      49     220 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.4
                        EMC3_TMCO1  91 qmkpmivtmipqil 104
                                       ++k m++ ++++++
  gi|518652520|ref|YP_008142040.1|  14 MTKFMMIEFVFMFA 27 
                                       44445544444443 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 7.2e-29
                        EMC3_TMCO1   2 lvldplirdwvllPivivillvgiltgllsellqkllidkkkmekeqkrekelqkrarelqkngdklklkklekrqe 78 
                                        v++pl+ +++ lPi ++++l+gi+ gl+s++ +++++d+ km k+q+++k++qk++re+ ++gd+ +++kl+k ++
  gi|518652520|ref|YP_008142040.1|  50 YVFMPLLGFNYELPI-LTLMLTGIVLGLISSIPRYFFTDWLKMGKTQMISKAYQKAMREAYRSGDRARQQKLQKLSM 125
                                       6899***********.999********************************************************** PP

                        EMC3_TMCO1  79 elmedqsemmmdqmkpmivtmipqiliffwlnsffs...............gfvvaklp.fpltgrfksllqrgles 139
                                       + + dq  ++m++mkp +vt i+++lif+wl+ f+                ++v+ k+  +pl++ +++l     + 
  gi|518652520|ref|YP_008142040.1| 126 QRQMDQAALSMNTMKPLMVTEIFFFLIFIWLYVFMLtihyqyvsmpwdlnlNIVTSKIYiMPLWMALYTLG----NL 198
                                       ***************************************************9999999879*******888....99 PP

                        EMC3_TMCO1 140 ldvrfvssiswYflcsfgls 159
                                       ++++fv+si+ +  ++  l+
  gi|518652520|ref|YP_008142040.1| 199 AVGYFVTSIMKFVDFTYKLR 218
                                       9********99988777766 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 !    7.8   0.0   0.00098       3.5      10      76 ..       9      80 ..       2     113 .. 0.68
   2 !   16.6   2.4     2e-06     0.007      10      79 ..     129     213 ..     122     228 .] 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00098
                                      TS.TTTHHHHHHHHHHHHHHHHHHHHHHH..........-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              EI24 10 lsspkllallllplllnlllfllllvlll..........wvllasllvllllllplwlfplvalllaapfygllaek 76
                                      +++p++ +++++ ++  ++ ++l+ ++++               + +v++ ll + + +p+++l+l ++++gl++ +
  gi|518652520|ref|YP_008142040.1|  9 AQNPQMTKFMMIEFVFMFAGLGLI-FIISdpsirnplghY----LNYVFMPLLGFNYELPILTLMLTGIVLGLISSI 80
                                      578999999999999999998833.333356544332211....334444444455555599999999999999865 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 2e-06
                                       TS.TTTHHHHHHHHHHHHHHHHHHHHHHH..............-TTHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHH CS
                              EI24  10 lsspkllallllplllnlllfllllvlll..............wvllasllvllllllplwlfp.lvalllaapfyg 71 
                                       +++++l +++++pl ++ ++f+l++++l+              w l   +++  ++++plw+   ++ +l ++ f+ 
  gi|518652520|ref|YP_008142040.1| 129 MDQAALSMNTMKPLMVTEIFFFLIFIWLYvfmltihyqyvsmpWDLNLNIVTSKIYIMPLWMALyTLGNLAVGYFVT 205
                                       4568999**********99999776666689999998888888777789***************9************ PP

                                       HHHHHHHH CS
                              EI24  72 llaekvek 79 
                                        + + v+ 
  gi|518652520|ref|YP_008142040.1| 206 SIMKFVDF 213
                                       99999965 PP

>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.026        92      53      83 ..       5      35 ..       1      37 [. 0.82
   2 !   11.4   0.1   8.3e-05       0.3      36      84 ..     112     160 ..      89     171 .. 0.71

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.026
                             Orf78 53 esnaaekaqalnillisllavvcvlvllyvi 83
                                      +++ a++ q+++ ++i ++ +++ l l+++i
  gi|518652520|ref|YP_008142040.1|  5 NNRPAQNPQMTKFMMIEFVFMFAGLGLIFII 35
                                      444578889999************9999999 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 8.3e-05
                             Orf78  36 nkkekksaaeknditekesnaaekaqalnillisllavvcvlvllyviy 84 
                                        ++ ++++ +k +++ + ++aa ++++++ l+++ + ++ +++ lyv +
  gi|518652520|ref|YP_008142040.1| 112 GDRARQQKLQKLSMQRQMDQAALSMNTMKPLMVTEIFFFLIFIWLYVFM 160
                                       3344455556666666666678889999999999999999999999864 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 ?   -1.9   0.2       1.1     4e+03      41      53 ..      62      74 ..      51      77 .. 0.86
   2 ?   14.7   2.6   7.2e-06     0.026      11      76 ..     148     222 ..     136     226 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                              DPM3 41 lPlwalvlfGays 53
                                      lP++ l+l G+ +
  gi|518652520|ref|YP_008142040.1| 62 LPILTLMLTGIVL 74
                                      8999999999865 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 7.2e-06
                              DPM3  11 allllalwlalllrlvslpl.skvqdev.......vpvlPlw.alvlfGayslatlgygvltfndcpeaakeLqk 76 
                                       +++l+ +wl++++ +++ ++ s ++d         + ++Plw al ++G  ++   ++++++f d   + ++L +
  gi|518652520|ref|YP_008142040.1| 148 FFFLIFIWLYVFMLTIHYQYvSMPWDLNlnivtskIYIMPLWmALYTLGNLAVGYFVTSIMKFVDFTYKLRKLDD 222
                                       3333444444443333333123333332444455599***984699*******************9988888765 PP

>> Polysacc_synt  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   1.2   2.4e-05     0.086      72     141 ..      13      94 ..       4     105 .. 0.85
   2 ?    5.5   4.1    0.0026       9.3     135     185 ..     136     186 ..     131     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
                     Polysacc_synt  72 elvslillnvllvllvlvllfllllliaa..........flglpelavlylilalmll..llvgvasfrrglfqgle 136
                                       + ++ ++++ ++++  l l+f+++++  +          f+ l  +++ ++il+lml+  +l  ++s +r +f+++ 
  gi|518652520|ref|YP_008142040.1|  13 QMTKFMMIEFVFMFAGLGLIFIISDPSIRnplghylnyvFMPLLGFNYELPILTLMLTgiVLGLISSIPRYFFTDWL 89 
                                       6778889999999999999999999999999999**99988888888888888777777799*************** PP

                     Polysacc_synt 137 rmkya 141
                                       +m  +
  gi|518652520|ref|YP_008142040.1|  90 KMGKT 94 
                                       99765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0026
                     Polysacc_synt 135 lermkyaavsqvveqlsrvilvliavflfldivaavlgavlaalvggivsl 185
                                       ++ mk+++v+ +  +l+++ l ++++++++++v++++ + l  +++ i+ +
  gi|518652520|ref|YP_008142040.1| 136 MNTMKPLMVTEIFFFLIFIWLYVFMLTIHYQYVSMPWDLNLNIVTSKIYIM 186
                                       789******************9999999999**********9999999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1241  (0.0692175); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1503.71
//
Query:       gi|518652521|ref|YP_008142041.1|  [L=180]
Description: cytidylate kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-15   57.4   2.1      2e-08   34.6   0.0    2.1  2  Cytidylate_kin2  Cytidylate kinase-like family
    4.5e-13   49.9   0.0    5.8e-13   49.5   0.0    1.2  1  AAA_18           AAA domain
    6.8e-10   39.3   0.1    1.2e-09   38.5   0.1    1.4  1  SKI              Shikimate kinase
    9.7e-10   38.5   0.9    9.6e-07   28.7   0.0    2.9  3  Cytidylate_kin   Cytidylate kinase
    1.2e-06   28.9   0.0    3.1e-06   27.7   0.0    1.6  1  AAA_17           AAA domain
    3.8e-05   24.1   0.0    3.9e-05   24.1   0.0    1.2  1  AAA_16           AAA ATPase domain
     0.0003   20.7   2.1      0.012   15.5   0.1    2.4  2  dNK              Deoxynucleoside kinase
     0.0012   19.2   0.0     0.0036   17.6   0.0    1.8  2  AAA_22           AAA domain
      0.003   17.3   2.8     0.0079   16.0   0.4    2.1  2  PRK              Phosphoribulokinase / Uridine kinase family
     0.0084   16.3   0.0      0.072   13.2   0.0    2.0  1  AAA_33           AAA domain
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.021   15.2   0.0    1.4  1  AAA              ATPase family associated with various cellul
      0.021   15.2   0.3      0.043   14.2   0.3    1.6  1  RNA_helicase     RNA helicase
      0.029   14.9   0.6      0.034   14.7   0.6    1.4  1  ABC_tran         ABC transporter
       0.04   14.0   0.2       0.29   11.2   0.0    2.2  2  ADK              Adenylate kinase
      0.043   13.5   1.8        1.6    8.4   0.5    2.3  2  CoaE             Dephospho-CoA kinase
      0.052   13.2   0.2        1.2    8.8   0.1    2.3  2  Thymidylate_kin  Thymidylate kinase
       0.11   12.4   0.3       0.42   10.5   0.1    1.8  2  APS_kinase       Adenylylsulphate kinase
       0.12   12.5   0.6       0.25   11.4   0.6    1.5  1  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
       0.21   10.8   0.8        0.6    9.4   0.8    1.9  1  Zeta_toxin       Zeta toxin
       0.27   11.7   1.7        0.4   11.1   1.7    1.4  1  AAA_23           AAA domain
       0.41   11.0   4.3       0.38   11.1   1.7    2.0  2  RNaseH_C         T4 RNase H, C terminal


Domain annotation for each model (and alignments):
>> Cytidylate_kin2  Cytidylate kinase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.6   0.0   2.4e-11     2e-08       1      63 [.       2      66 ..       2      73 .. 0.89
   2 !   23.3   1.5     7e-08     6e-05      82     179 .]      60     156 ..      56     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 34.6 bits;  conditional E-value: 2.4e-11
                   Cytidylate_kin2  1 iITIsreyGsgGetigeaLAekLglpfydr.eiieevakelglseeeveevde.rsrlssflskl 63
                                      iITIs+e Gsg++t+g+ LA  L+++f++    +++ a+e +++   + ++ e ++ +++  +++
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNYKFFSGgYFFRKKAEEYNMDLIDFSNYAEhHPEIDKEEDRM 66
                                      8****************************9899******************99777777666655 PP

  == domain 2  score: 23.3 bits;  conditional E-value: 7e-08
                   Cytidylate_kin2  82 feaqervirela.aeesvVivGRgadliLkdrp.nvlrvfltapledrvkrvaere.glseeearekiketDkrrak 155
                                        + + r+i e +  ++++++  R + ++  ++  n+++++l  + + rv+r+a+r  g++    r  i ++ + +  
  gi|518652521|ref|YP_008142041.1|  60 DKEEDRMIVEFMqHNDDIILESRLSGYMAYKNNiNAIKIYLNTDIATRVDRLASRDkGVD----RAGIMTRARSEFL 132
                                       556677788887677789999**99888766555*****************999994554....4556666666666 PP

                   Cytidylate_kin2 156 yykkytgqdwgdaenYdlvlntsk 179
                                       +y  ++g d+   +nYd +++t++
  gi|518652521|ref|YP_008142041.1| 133 RYMIFYGIDYRVFTNYDYIIDTDH 156
                                       677789***************986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   6.8e-16   5.8e-13       1     119 [.       3     120 ..       3     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 6.8e-16
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssale 72 
                                       I ++G +G+GKtt++k L+++l++     g+  r+ a e ++ l ++ + + e++ + ++  d+ + ++++++    
  gi|518652521|ref|YP_008142041.1|   3 ITISGESGSGKTTVGKLLASSLNYkffsgGYFFRKKAEEYNMDLIDFSN-YAEHHPEIDKEEDRMIVEFMQHN---- 74 
                                       89********************999*****************9999999.77777777777799999999997.... PP

                            AAA_18  73 egknlvidghlaeleseaakdikk.vvLtaspeelleRlekRgyeeak 119
                                         ++++++++l+ +  +++ ++   ++L ++  ++ +Rl+ R++  ++
  gi|518652521|ref|YP_008142041.1|  75 --DDIILESRLSGYMAYKNNINAIkIYLNTDIATRVDRLASRDKGVDR 120
                                       ..699**********9988877768*****************987555 PP

>> SKI  Shikimate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   1.4e-12   1.2e-09       1     156 [.       9     169 ..       9     171 .. 0.73

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 1.4e-12
                                       TTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHTS-HHHHHH....HHHHHHHHHHHHHHHHHHCCCSSEEEEE-..TT CS
                               SKI   1 mGaGKstvGkllAkklglefiDlDeliekrtgksiaeife....eegeegFrelEsevlkelleeeglViatG..GG 71 
                                       +G+GK+tvGkllA +l+++f+    ++ k+++    ++++     e   +  ++E +++ e++++++ +i      G
  gi|518652521|ref|YP_008142041.1|   9 SGSGKTTVGKLLASSLNYKFFSGGYFFRKKAEEYNMDLIDfsnyAEHHPEIDKEEDRMIVEFMQHNDDIILESrlSG 85 
                                       59*************************88777444444332113345567889999*********966664321145 PP

                                       GGGSHHHHHHHHHHSEEEEEE--HHHHHHHHHHTTS...SGGGCSCHHHHHHHHHHH..HHHHHHCCSSCEEEECTS CS
                               SKI  72 avlseenrellkekgiviyLdvsleellerlkadke...RPllqekskeeelleela..ereplyeeaadvvvdese 143
                                        +  ++n +++k     iyL++++ + ++rl+++++   R+ + ++ ++e l+  ++     +++++++ + +d+++
  gi|518652521|ref|YP_008142041.1|  86 YMAYKNNINAIK-----IYLNTDIATRVDRLASRDKgvdRAGIMTRARSEFLRYMIFygIDYRVFTNYDYI-IDTDH 156
                                       555566666666.....**************9998889999888888877777777765556666666555.55555 PP

                                       SHHHHHHHHHHHH CS
                               SKI 144 eskeevaeeilea 156
                                        s+e++++ i+++
  gi|518652521|ref|YP_008142041.1| 157 ISPENIVNDIVDF 169
                                       5559***999975 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.0   1.1e-09   9.6e-07       1      38 [.       3      40 ..       3      63 .. 0.85
   2 ?    5.9   0.0     0.011       9.6      96     149 ..      57     113 ..      43     129 .. 0.76
   3 ?    1.6   0.0      0.24     2e+02     190     209 ..     151     170 ..     144     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 1.1e-09
                                      EEEE-STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHH CS
                    Cytidylate_kin  1 iaiDGPagsGKssvaralaeklglkyldtgalYRalal 38
                                      i+i G +gsGK +v+++la+ l++k+++ g ++R  a 
  gi|518652521|ref|YP_008142041.1|  3 ITISGESGSGKTTVGKLLASSLNYKFFSGGYFFRKKAE 40
                                      89********************************8764 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.011
                                       HHHHHHHHHHHHTT-B.SSBEEEEESSIIIIISTT-..SEEEEEE--HHHHHHHHHH CS
                    Cytidylate_kin  96 pavRailvkklrelvk.karvvveGRDigtvvfpda..elKifldAsveeRakRRlk 149
                                       p++ ++  + + e+++ ++++++e R  g +  ++    +Ki+l+  + +R+ R ++
  gi|518652521|ref|YP_008142041.1|  57 PEIDKEEDRMIVEFMQhNDDIILESRLSGYMAYKNNinAIKIYLNTDIATRVDRLAS 113
                                       5555555666666666689999999999999888843379************99654 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.24
                                       EEETTTS-HHHHHHHHHHHH CS
                    Cytidylate_kin 190 iidtskltieevvekileli 209
                                       iidt++++ e++v+ i++ +
  gi|518652521|ref|YP_008142041.1| 151 IIDTDHISPENIVNDIVDFY 170
                                       89**************9876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   3.6e-09   3.1e-06       2     122 ..       7     114 ..       6     125 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 3.6e-09
                                       E-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTS.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHSSEEEEE CS
                            AAA_17   2 GgPGsGKgtqceklvekygfthlsaGdllreeakrggl.akardemrklpleekkelqkeaaekiaeeakkkgvlvd 77 
                                       G  GsGK+t+ + l+  ++++++s G  +r+ a++ ++   +++++++   e++ke ++++ e +++   +++++++
  gi|518652521|ref|YP_008142041.1|   7 GESGSGKTTVGKLLASSLNYKFFSGGYFFRKKAEEYNMdLIDFSNYAEHHPEIDKEEDRMIVEFMQH---NDDIILE 80 
                                       678******************************9998854567777788888888888888776666...4677776 PP

                                       E-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  78 ghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkd 122
                                          +     g+++ ++    +++   + i+l++d  + ++r++++
  gi|518652521|ref|YP_008142041.1|  81 SRLS-----GYMA-YK----NNI-NAIKIYLNTDIATRVDRLASR 114
                                       6653.....3321.22....222.234577777777777777766 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   4.6e-08   3.9e-05      26      84 ..       2      61 ..       1     135 [. 0.77

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.6e-08
                            AAA_16 26 lvllsGesGvGKsslvrellralekd...ggiflrgkcdqlesaipysalaqalareellrq 84
                                      ++ +sGesG+GK+++ + l+ +l+ +   gg+f+r k++++ ++  ++ + ++++ +  + +
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNYKffsGGYFFRKKAEEYNMD--LIDFSNYAEHHPEIDK 61
                                      5789************************99***********666..3334444433344444 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.4e-05     0.012       1      28 [.       3      30 ..       3      42 .. 0.94
   2 ?    4.7   0.1     0.028        24     101     147 ..      78     118 ..      58     138 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-05
                                      EEEEESTTSSHHHHHHHHHCCSTCEEEE CS
                               dNK  1 ivveGnIgaGKstlvklLskklgvkvfe 28
                                      i+++G  g+GK+t+ klL+  l++k+f+
  gi|518652521|ref|YP_008142041.1|  3 ITISGESGSGKTTVGKLLASSLNYKFFS 30
                                      89*********************99986 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.028
                                       S-HHHHHHHHHHHHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCC CS
                               dNK 101 lseeelkiykelldnlleelakpdlliYLkasletclerikkRgree 147
                                       + e+ l  y +  +n++       + iYL++++ t + r+  R++  
  gi|518652521|ref|YP_008142041.1|  78 ILESRLSGYMAYKNNIN------AIKIYLNTDIATRVDRLASRDKGV 118
                                       44444444444444444......455*****************9765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   4.2e-06    0.0036       7      30 ..       2      25 ..       1      73 [. 0.84
   2 ?   -0.8   0.0       1.9   1.6e+03     100     117 ..     154     171 ..     103     177 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.2e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlleqld 30
                                      i+++ GesG+GKTt+ + l+++l+
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLN 25
                                      799****************99984 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.9
                            AAA_22 100 aqhlrs.eealeeLrslln 117
                                        +h+ s e++++++++++n
  gi|518652521|ref|YP_008142041.1| 154 TDHI-SpENIVNDIVDFYN 171
                                       4677.55889999999998 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.4   9.3e-06    0.0079       1      25 [.       2      26 ..       2      56 .. 0.89
   2 ?    1.7   0.1      0.22   1.9e+02     104     157 ..      68     118 ..      47     137 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.3e-06
                               PRK  1 vIgvagsSGaGkttvarklekifgr 25
                                      +I ++g+SG+Gkttv + l ++++ 
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNY 26
                                      8*******************99984 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.22
                               PRK 104 eeliegadvlviEGlhalydervaelldlkiyvdisidlelarklqRDiaeRGr 157
                                        e+++ +d +++E  +++y     +   +kiy+ ++i  ++ r  +RD+   G 
  gi|518652521|ref|YP_008142041.1|  68 VEFMQHNDDIILESRLSGYMAYKNNINAIKIYLNTDIATRVDRLASRDK---GV 118
                                       567778888888888888888888888999***9999999999999985...44 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   8.5e-05     0.072       3      77 ..       4      81 ..       2     135 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.5e-05
                            AAA_33  3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfg...tdqqsktdytrvldrlyqilnelarkalsagrnvilda 77
                                       + G +GsGK+t+ + l+  l + + s  +++r+ ++    d  + ++y++  +++ +   +++ + ++++ ++il +
  gi|518652521|ref|YP_008142041.1|  4 TISGESGSGKTTVGKLLASSLNYKFFSGGYFFRKKAEeynMDLIDFSNYAEHHPEIDKEEDRMIVEFMQHNDDIILES 81
                                      56799*****************99999999888666645555557777788777788888888888888888888764 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.5e-05     0.021       3      28 ..       5      30 ..       3      81 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.5e-05
                                      EESSTTSSHHHHHHHHHHHHTHEEEE CS
                               AAA  3 lyGppGtGKTllakavakelgvefle 28
                                      ++G  G GKT++ k +a++l+ +f++
  gi|518652521|ref|YP_008142041.1|  5 ISGESGSGKTTVGKLLASSLNYKFFS 30
                                      79*****************9988763 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.3     5e-05     0.043       1      42 [.       3      41 ..       3      92 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5e-05
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkkl......klkkkdsvysrnpedd 42
                                      i ++G+sg GK+t+ k La++l  k+                r+++++
  gi|518652521|ref|YP_008142041.1|  3 ITISGESGSGKTTVGKLLASSLNYKFfsggyfF---------RKKAEE 41
                                      6799******************98874444430.........444333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.6     4e-05     0.034      13      37 ..       2      26 ..       1     131 [. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4e-05
                                      EEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagllkp 37
                                      ++ i Ge+G+GK+t+ klla  l+ 
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNY 26
                                      57899**************987765 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00034      0.29       2      36 ..       6      40 ..       5      55 .. 0.92
   2 ?    0.8   0.0      0.56   4.8e+02     133     133 ..     101     101 ..      50     175 .. 0.59

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00034
                                      EESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               ADK  2 lGaPgaGKGtqaeklvkkyglahlstGdllRaevk 36
                                       G  g+GK t+ + l+++++++  s G ++R++ +
  gi|518652521|ref|YP_008142041.1|  6 SGESGSGKTTVGKLLASSLNYKFFSGGYFFRKKAE 40
                                      7999***************************9876 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.56
                                       H CS
                                       x RF
                               ADK 133 e 133
                                       +
  gi|518652521|ref|YP_008142041.1| 101 N 101
                                       2 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.5    0.0018       1.6       1      22 [.       1      22 [.       1      32 [. 0.88
   2 ?    3.9   0.0     0.044        38      87     156 ..      56     129 ..      52     133 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0018
                                      EEEEEEESTTSSHHHHHHHHHH CS
                              CoaE  1 livgltGgiasGKstvanlfad 22
                                      +i+ ++G  +sGK+tv +l+a+
  gi|518652521|ref|YP_008142041.1|  1 MIITISGESGSGKTTVGKLLAS 22
                                      699***************9987 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.044
                                       HHHHHHHHHHHHHH--S..SEEEEE-TTTTTTTGGGGSSEE.EEEE--HHHHHHHHHHCC.TSTHHHHHHHHHH CS
                              CoaE  87 hPlirreikkelakles..kyvlldvPLLvEkqleklierv.lvvdvelelqveRlvard.gvseeevkaiiaa 156
                                       hP i +e  + + ++ +    ++l+  L     +++ i+ + + ++ +  ++v+Rl +rd gv+++ + ++ ++
  gi|518652521|ref|YP_008142041.1|  56 HPEIDKEEDRMIVEFMQhnDDIILESRLSGYMAYKNNINAIkIYLNTDIATRVDRLASRDkGVDRAGIMTRARS 129
                                       77777776666666655555666777776666777777766466889999*********999999999888765 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0014       1.2       3      25 ..       7      29 ..       5      90 .. 0.89
   2 ?    3.0   0.0     0.085        73     121     143 ..      97     122 ..      87     166 .. 0.73

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0014
                                      ESTTSSHHHHHHHHHHHHHHTTE CS
                   Thymidylate_kin  3 GlDGaGKttqaellkerlkeegi 25
                                      G  G+GKtt+ +ll++ l+ +  
  gi|518652521|ref|YP_008142041.1|  7 GESGSGKTTVGKLLASSLNYKFF 29
                                      677*************9987765 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.085
                                       EEEEESSHHHHHTSCCTTSS...TTT CS
                   Thymidylate_kin 121 tflldvdpevalkRlakrde...lde 143
                                        ++l++d ++++ Rla rd+   ++ 
  gi|518652521|ref|YP_008142041.1|  97 KIYLNTDIATRVDRLASRDKgvdRAG 122
                                       69****************99644333 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1   0.00049      0.42       4      28 ..       2      26 ..       1      38 [. 0.89
   2 ?   -0.1   0.0      0.89   7.6e+02      88     115 ..      89     108 ..      52     157 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00049
                                      EEEEESSTTSSHHHHHHHHHHHHHH CS
                        APS_kinase  4 vvwltGlsgsGKstianalekkLve 28
                                      ++ ++G sgsGK+t+ + l+++L+ 
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNY 26
                                      7899**************9999975 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.89
                                       HHHHHHHHHHCHTEEEEEEEE--HHHHH CS
                        APS_kinase  88 eReaarelleealkfievfvdtplevce 115
                                        ++++        + i+++++t+++++ 
  gi|518652521|ref|YP_008142041.1|  89 YKNNI--------NAIKIYLNTDIATRV 108
                                       43333........334444444433332 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.6   0.00029      0.25       1      25 [.       2      26 ..       2      30 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00029
                                      EEEEESSTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  1 iaiastkGGvGKTtlaanLaralar 25
                                      i+ +s+ +G+GKTt+   La +l+ 
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLNY 26
                                      7889***********9999999876 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.8    0.0007       0.6      18      41 ..       2      25 ..       1     129 [. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0007
                        Zeta_toxin 18 lillgGqpGAGKselaellkdele 41
                                      +i ++G +G+GK+++ +ll+ +l+
  gi|518652521|ref|YP_008142041.1|  2 IITISGESGSGKTTVGKLLASSLN 25
                                      6889**************999983 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.7   0.00047       0.4      22      83 ..       3      75 ..       2     172 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00047
                            AAA_23 22 tlItGpNGaGKTTildAiklaL.ygetprlsrks............grgfeksdveiesegkvkayveltfenkd 83
                                        I+G+ G+GKTT+   +   L y ++++    +             +++ ++ +ei +e +++ +ve+   n d
  gi|518652521|ref|YP_008142041.1|  3 ITISGESGSGKTTVGKLLASSLnYKFFSGGYFFRkkaeeynmdlidFSNYAEHHPEIDKE-EDRMIVEFMQHN-D 75
                                      569**********99999999977766555444445666666666555555555565554.555556665433.2 PP

>> RNaseH_C  T4 RNase H, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2      0.89   7.6e+02      44      79 ..      61      70 ..      36     111 .. 0.50
   2 ?   11.1   1.7   0.00044      0.38      17      99 ..      90     175 ..      88     179 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.89
                                      HHHHHHH.HH-GGGHHHHS-HHHHHHHHHHHHHH-G CS
                          RNaseH_C 44 keileallasdreelkkllteeeyarykenlklldf 79
                                      ke+ + +                          ++f
  gi|518652521|ref|YP_008142041.1| 61 KEEDRMI--------------------------VEF 70
                                      3333333..........................333 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00044
                                       GGTBE-TTS..-TTHHHH--TT-------HHH.HHHH.HH-GGGH.HH.HS-HHHHHHHHHHHHHH-GGGS.-HHHH CS
                          RNaseH_C  17 kdnvaslkv..rsdfyftrveGerapsvkkei.leallasdreel.kk.llteeeyarykenlklldfdyi.penia 87 
                                       k+n+ ++k+  ++d   trv+  r  s  k +    +++  r e  +  ++   +y  + +   ++d d+i peni 
  gi|518652521|ref|YP_008142041.1|  90 KNNINAIKIylNTDIA-TRVD--RLASRDKGVdRAGIMTRARSEFlRYmIFYGIDYRVFTNYDYIIDTDHIsPENIV 163
                                       5666666652133433.5555..3444434330345788777665133144578999999999*******989**** PP

                                       HHHHHHHHT--- CS
                          RNaseH_C  88 dsiveqyesqkl 99 
                                       ++iv++y+ + +
  gi|518652521|ref|YP_008142041.1| 164 NDIVDFYNKFEP 175
                                       *******98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 1202.01
//
Query:       gi|518652522|ref|YP_008142042.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1161 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-28   99.3   0.9    3.9e-25   89.0   0.9    3.2  1  TruB_N           TruB family pseudouridylate synthase (N term
    3.2e-18   65.6   0.0    5.7e-18   64.8   0.0    1.4  1  TruB_C_2         tRNA pseudouridylate synthase B C-terminal d
    2.5e-11   43.4   0.0    5.1e-11   42.4   0.0    1.5  1  PUA              PUA domain
    4.1e-06   27.0   0.2    1.6e-05   25.1   0.1    2.1  2  UPF0113          UPF0113 PUA domain
    0.00047   20.2   0.1     0.0015   18.5   0.1    1.9  2  DKCLD            DKCLD (NUC011) domain
     0.0007   19.7   0.0     0.0013   18.9   0.0    1.6  1  PseudoU_synth_2  RNA pseudouridylate synthase


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.0   0.9   1.3e-28   3.9e-25       1     149 []      33     146 ..      33     146 .. 0.97

  Alignments for each domain:
  == domain 1  score: 89.0 bits;  conditional E-value: 1.3e-28
                                       HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHH CS
                            TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekl 77 
                                       +++++ k+vGh GtLDp+++GvLv+a+g+aTkl+++++e +KeY+ ++rl  + dt++                  +
  gi|518652522|ref|YP_008142042.1|  33 REITGEKRVGHIGTLDPNVSGVLVMALGKATKLIDIVHERPKEYISVMRLYSTADTDN------------------I 91 
                                       688999********************************************99999887..................7 PP

                                       HHHHHHC-EEE---------------------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
                            TruB_N  78 eevlkkftGeieqvppmySAvkvnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                                        +v+k+ftG+i+q pp+ SAv                  r+ r+ tiy++++le++e+ + ++v+c++GtYi
  gi|518652522|ref|YP_008142042.1|  92 MKVFKEFTGKIYQLPPVRSAVS-----------------RQVRERTIYNMDVLEIQEKLILFRVKCESGTYI 146
                                       789******************9.................999*****************************9 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.0   1.9e-21   5.7e-18       1      63 [.     147     211 ..     147     212 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 1.9e-21
                                       HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHHHHHHHHHT.--H.HHHHEEEGGGGG CS
                          TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLedavllyke.dee.LdrlllPlesal 63 
                                       RtLc+D+G ++g+gA++++LRR+++g+f+e++++tl++L d+v l k+ d +  d++++P++ ++
  gi|518652522|ref|YP_008142042.1| 147 RTLCTDMGYVIGTGAQMADLRRLSTGQFNESHIHTLQELSDSVVLKKQgDTSlFDNMVIPMDFVF 211
                                       9****************************************999888888889*********776 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.0   1.7e-14   5.1e-11       1      57 [.     215     271 ..     215     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.7e-14
                                       CEEEE-HHHHHHHHTT-EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HH CS
                               PUA   1 grvvvddgAvkallsgasLlapGvvevegdfeegdvVaivdedgelvavGlanysse 57 
                                       ++vvv++ A+k +++g+++++ G+    gd+++g  Vai+++d+el+a G ++++s 
  gi|518652522|ref|YP_008142042.1| 215 PKVVVKNTAIKNIMHGSDIYPSGIKALIGDIHKGSRVAIYSGDNELLAFGTMLVDSL 271
                                       69***************************************************9985 PP

>> UPF0113  UPF0113 PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       2.2   6.7e+03      58      75 ..     130     147 ..     120     148 .. 0.69
   2 !   25.1   0.1   5.2e-09   1.6e-05       1      56 [.     216     272 ..     216     283 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.2
                           UPF0113  58 spgkivvknlaDiGeYlR 75 
                                       +++ i+++  +  G+Y+R
  gi|518652522|ref|YP_008142042.1| 130 QEKLILFRVKCESGTYIR 147
                                       556666777788899999 PP

  == domain 2  score: 25.1 bits;  conditional E-value: 5.2e-09
                           UPF0113   1 kvvvkekaeklFLYGrdvlkesilkitesvkenqvvvVlnengeplGiGkirkdt.k 56 
                                       kvvvk  a k+++ G d++ ++i+ + +++ ++ +v++++ ++e+l++G +  d+ +
  gi|518652522|ref|YP_008142042.1| 216 KVVVKNTAIKNIMHGSDIYPSGIKALIGDIHKGSRVAIYSGDNELLAFGTMLVDSlN 272
                                       79*************************************************998753 PP

>> DKCLD  DKCLD (NUC011) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1     5e-07    0.0015      42      57 ..      13      28 ..      11      29 .. 0.93
   2 ?   -4.0   0.0       5.4   1.6e+04      13      28 ..     216     231 ..     209     232 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5e-07
                                      EEEEEEE-SSS-HHHH CS
                             DKCLD 42 GvinLDKPsnPsSHEV 57
                                      G+i +DKP++P+SH++
  gi|518652522|ref|YP_008142042.1| 13 GFIVIDKPKGPTSHQI 28
                                      9*************97 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 5.4
                                       -EEESS-----TTSS- CS
                             DKCLD  13 kllvrtehytplpaGs 28 
                                       k++v++++  ++ +Gs
  gi|518652522|ref|YP_008142042.1| 216 KVVVKNTAIKNIMHGS 231
                                       7788888888888886 PP

>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   4.3e-07    0.0013       2      86 ..      14      82 ..      13     185 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 4.3e-07
                   PseudoU_synth_2  2 lvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkY 80
                                      ++v++KP+g ++++ +            +  r+ + +k++++++ LD ++sG+l++A     a kl +    ++  K+Y
  gi|518652522|ref|YP_008142042.1| 14 FIVIDKPKGPTSHQID------------AWVREITGEKRVGHIGTLDPNVSGVLVMALG--KATKLID--IVHERPKEY 76
                                      7999999999999999............5566679**********************83..3455556..556677777 PP

                   PseudoU_synth_2 81 lalvfg 86
                                      + + + 
  gi|518652522|ref|YP_008142042.1| 77 ISVMRL 82
                                      777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.36
# Mc/sec: 2886.50
//
Query:       gi|518652523|ref|YP_008142043.1|  [L=144]
Description: Nop56p-related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.4   0.0    9.1e-31  107.1   0.0    1.0  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 !  107.1   0.0   5.1e-35   9.1e-31      90     228 ..       4     140 ..       2     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 5.1e-35
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHCHHHHHHHHHHHHSSHHHHHCS-HHHHTTTT-HHHHCCCHH.T CS
                               Nop  90 elcdrvleleelrkelleYlesrmsaiAPNlsaLvGeevaarLishaGgLtnLakmPastiqilGaekalfralk.k 165
                                       +++++ +++ ++r+ l +Yl +++++  P   +L+G+++a  ++ + G+L+nL k+Pa t+qilGaeka+f++++ +
  gi|518652523|ref|YP_008142043.1|   4 AAAEMGINMCSFRSYLDNYLGNEIEKYMPHTVSLIGKTLALDFLLKSGSLENLVKYPAGTLQILGAEKAFFNHMRkG 80 
                                       578999*********************************************************************66 PP

                                       ---SSSCHHHCSHHHHHTS-CCCHHHHHHHHHHHHHHHHHHHHTT----SHHHHHHHHHHHHH CS
                               Nop 166 kntpkyGliyhselvqkatppklkkkiaRllaaKvalaaRiDafsekdgslGkklreeiekkl 228
                                       +  pk+G+i++ + ++ a+pp++++k+aR++a+K+a+  ++D f+ + ++ G  + +ei+kk+
  gi|518652523|ref|YP_008142043.1|  81 TPPPKHGIIFNYPGLS-ALPPNQRGKVARAIANKMAITLKMDFFKTDGDTEG--MVNEIKKKM 140
                                       69*************9.99***********************8854445555..666777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1059.23
//
Query:       gi|518652524|ref|YP_008142044.1|  [L=474]
Description: hypothetical protein FACI_IFERC00001G1163 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-22   78.5   0.0    5.9e-22   77.9   0.0    1.3  1  GATase_7      Glutamine amidotransferase domain
    3.6e-21   75.8   0.0      7e-21   74.8   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    6.8e-08   32.2   0.1    1.4e-07   31.1   0.1    1.5  1  Pribosyltran  Phosphoribosyl transferase domain
    6.6e-06   25.2   0.0    1.2e-05   24.3   0.0    1.4  1  GATase_4      Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.033   13.7   0.0      0.064   12.7   0.0    1.5  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   1.7e-25   5.9e-22      10     122 ..     104     222 ..      93     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 1.7e-25
                          GATase_7  10 eagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtev.llallea.......ewgeealerlnGm 77 
                                        ++a P+v  s+ g + i +nGe++N ++lre+L++kg+ f ++sDtev l++++++       +++++a+ +++G 
  gi|518652524|ref|YP_008142044.1| 104 VENAGPFVIsSSMGYIGISHNGEVTNAHDLREKLKEKGYIFYSSSDTEVmLTEIVSEinkygirDGIKKAMLKIKGA 180
                                       55677888878899999********************************444555559******************* PP

                          GATase_7  78 fAfaiwdeeekrlllaRDrlGikPLyygedkgdallfaSelkall 122
                                       +A+ai+ +++  l++ RD++G++PL++g+++ d++++aSe  a+ 
  gi|518652524|ref|YP_008142044.1| 181 YALAILINDT--LYALRDPFGFRPLILGKNN-DGYIVASESAAID 222
                                       *******999..******************6.7*******99985 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.0   1.9e-24     7e-21       9     134 .]      84     217 ..      76     217 .. 0.90

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 1.9e-24
                          GATase_6   9 lvedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevlla.ll. 81 
                                       + e++++++H+R ++ g +  e a Pf  +s+ g + ++hNGe+ n+++lre+l++ kg+ f s sDtev+l+ ++ 
  gi|518652524|ref|YP_008142044.1|  84 FLEGRIGIGHNRYSTAGSKGVENAGPFviSSSMGYIGISHNGEVTNAHDLREKLKE-KGYIFYSSSDTEVMLTeIVs 159
                                       56778*************977777***9888889999*******************.****************6668 PP

                          GATase_6  82 ..eelG.....eevlerlrGmfafaiwdkrentlilardrlgvkplyyavdesglafase 134
                                         +++G     ++++ +++G++a ai    ++tl  +rd +g +pl+ + +++g ++ase
  gi|518652524|ref|YP_008142044.1| 160 eiNKYGirdgiKKAMLKIKGAYALAILI--NDTLYALRDPFGFRPLILGKNNDGYIVASE 217
                                       8877779999999999*****9999875..7788888**********************8 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.1     4e-11   1.4e-07      26     120 ..     292     393 ..     272     396 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4e-11
                                       --GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE-S CS
                      Pribosyltran  26 yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVDD 95 
                                       ++ + dvvv+++  G   a  ++ + ++p+   +++ +++d++   + + s  +       +  + + gk+V++VDD
  gi|518652524|ref|YP_008142044.1| 292 NPVNADVVVPVPDSGRSQALGYSVYSKIPYSEGLIKNRYSDRTFILPDQESRYNaikiklnTIKSVINGKRVVLVDD 368
                                       566778999999999999999999999998844444444444444444444444688899899999*********** PP

                                       EESSSHHHHHHHHHHHCC-BSEEEE CS
                      Pribosyltran  96 ildtGgTllaalelLkekgpeevri 120
                                        +  G+T+++++ +L++ g++ev++
  gi|518652524|ref|YP_008142044.1| 369 SIVRGNTMRHIIGILRKDGATEVHV 393
                                       **********************986 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   3.4e-09   1.2e-05      10     145 ..      38     165 ..      29     185 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.4e-09
                          GATase_4  10 nvptdisfsftgfaarggltdahadGwGiafyegkaarvfkdpepsaesplaelvreypiksknvvaHiRkatqGev 86 
                                       n+ t+i f ++++++rg++        Gia ++gk               ++e+ r+  ++ ++ + H R  t G+ 
  gi|518652524|ref|YP_008142044.1|  38 NAYTNIIFALRALQHRGQE------SSGIATFDGKIH------IKKGMGFVSEVFRDEFLEGRIGIGHNRYSTAGSK 102
                                       6778999999999999888......458999999863......234567899*****99****************** PP

                          GATase_4  87 klenthpFvRelwgrewifAHnGdlke...ykpkl.egrfePvGsTDsElafCelleelasrf 145
                                         en+ pFv +    ++ + HnG++++   +++kl e+ +    s D+E+++ e+++e++++ 
  gi|518652524|ref|YP_008142044.1| 103 GVENAGPFVISSSMGYIGISHNGEVTNahdLREKLkEKGYIFYSSSDTEVMLTEIVSEINKYG 165
                                       *************************6633356666777899999*************999876 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05     0.064     117     149 ..     356     388 ..     309     397 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
                          PRTase_2 117 llaaakelvLvDDEistGktalnliralqeklp 149
                                        + + k++vLvDD i  G+t+ ++i  l+++  
  gi|518652524|ref|YP_008142044.1| 356 SVINGKRVVLVDDSIVRGNTMRHIIGILRKDGA 388
                                       4567789******************99988754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.22s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 3901.92
//
Query:       gi|518652525|ref|YP_008142045.1|  [L=84]
Description: small nuclear ribonucleoprotein [Ferroplasma acidarmanus fer1]
Scores for complete 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   74.0   1.3    6.4e-21   73.8   1.3    1.0  1  LSM       LSM domain
     0.0017   18.4   0.0     0.0021   18.2   0.0    1.2  1  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   1.3   7.2e-25   6.4e-21       2      67 .]      16      80 ..      15      80 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 7.2e-25
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlisl 67
                                       lk++++k++ +  k++r ++G+L+g+D +mNlvL++++et++++ +k   +++l+RG+ni+++s+
  gi|518652525|ref|YP_008142045.1| 16 TLKNSLEKNIMIDVKGNRMYSGILEGYDIYMNLVLKNATETINNE-NKGTFSMMLLRGDNIIFVSP 80
                                      79******************************************9.*****************986 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.0   2.3e-07    0.0021      14      55 ..      23      61 ..      14      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.3e-07
                                      SEEEEEETTS-EEEEEEEEE-T..T--EEEEEEEETTS.... CS
                            SM-ATX 14 kevevtvknGevyeGifstvslekdfsvvLkmarkvkkansk 55
                                      k++ + vk    y+Gi+ +++    +++vLk+a ++ + n++
  gi|518652525|ref|YP_008142045.1| 23 KNIMIDVKGNRMYSGILEGYDI--YMNLVLKNATETIN-NEN 61
                                      678999****************..*********99988.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.31s 00:00:00.71 Elapsed: 00:00:00.46
# Mc/sec: 543.40
//
Query:       gi|518652526|ref|YP_008142046.1|  [L=149]
Description: hypothetical protein FACI_IFERC00001G1165 [Ferroplasma acidarmanus fer1]
Scores for complete 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   17.6   7.5     0.0037   17.6   7.5    2.1  2  PsiE      Phosphate-starvation-inducible E


Domain annotation for each model (and alignments):
>> PsiE  Phosphate-starvation-inducible E
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4      0.14   2.6e+03      30      40 ..      19      29 ..      11      38 .. 0.65
   2 !   17.6   7.5     2e-07    0.0037       2      68 .]      63     134 ..      62     134 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.14
                              PsiE 30 lvieaaiiava 40
                                       ++++a +av+
  gi|518652526|ref|YP_008142046.1| 19 SLLLIAFVAVI 29
                                      45555555554 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 2e-07
                              PsiE   2 gdiLllLillEllrtivaylkehriavrlvieaaiiavaRklIil.dlkdggy....ltllglaaailaLgl 68 
                                       +d Ll  +++E+++++v+ +    + + ++i  ai + aR++I+  ++ ++       +++g++++i+aL++
  gi|518652526|ref|YP_008142046.1|  63 EDSLLAVVIFEIYESVVEFFHGEGDTILYIINGAISFTAREIIVTvFTVHIFRivnvYEIIGFSILIFALVA 134
                                       6789999**************************************84444433566699**********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       962  (0.0536561); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1075.80
//
Query:       gi|518652527|ref|YP_008142047.1|  [L=325]
Description: Met-10+ protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-36  125.4   0.3    3.7e-36  124.8   0.3    1.3  1  Met_10           Met-10+ like-protein
    2.2e-09   37.1   0.0    3.5e-09   36.4   0.0    1.3  1  MTS              Methyltransferase small domain
    2.3e-09   37.0   0.0    4.9e-09   35.9   0.0    1.5  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    6.3e-07   30.0   0.0    1.5e-06   28.8   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    2.4e-06   27.4   0.0    1.4e-05   24.9   0.0    2.0  2  Methyltransf_31  Methyltransferase domain
    2.5e-05   24.3   0.0    6.6e-05   22.9   0.0    1.6  1  Methyltransf_18  Methyltransferase domain
    0.00027   21.6   0.0    0.00053   20.7   0.0    1.5  1  Methyltransf_12  Methyltransferase domain
    0.00044   19.9   0.1    0.00081   19.0   0.1    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
     0.0006   19.1   0.0      0.002   17.4   0.0    1.5  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
  ------ inclusion threshold ------
      0.027   14.1   0.0      0.047   13.3   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
      0.046   13.6   0.0      0.075   12.9   0.0    1.2  1  PRMT5            PRMT5 arginine-N-methyltransferase
      0.059   12.8   0.0      0.094   12.1   0.0    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.068   12.2   0.0       0.11   11.6   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase


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 !  124.8   0.3   2.7e-39   3.7e-36      21     187 ..      94     258 ..      84     272 .. 0.93

  Alignments for each domain:
  == domain 1  score: 124.8 bits;  conditional E-value: 2.7e-39
                                       HHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEETTTS---GGGHHHHHHHHTT CS
                            Met_10  21 ykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDvskvyfsskleaErerlakl 97 
                                       +++++++ ++ + kv  v+ ++++++g  R+++l++++G++  et+++E+ +++ +D++kv+fs+++++ r+++  +
  gi|518652527|ref|YP_008142047.1|  94 ISQKVAHEYASRLKVDNVYVETGKIQGIKREPSLKLIYGNG-GETVVRESEVSYIMDLQKVMFSPGNINTRSKMKFI 169
                                       6678888888899***************************9.9********************************** PP

                                       --TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---TT-EEEEEE CS
                            Met_10  98 veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevireqladrvvm 174
                                          g +++d+f GiG+f++ i k s++ r++  d+nP+s++ylk+n++ N+++++v  +++D+r v++  +ad ++m
  gi|518652527|ref|YP_008142047.1| 170 DFTGMIILDMFCGIGYFSLQILKNSRPARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPAMQADYIIM 246
                                       99*************************************************************************** PP

                                       --TTTGGGGHHHH CS
                            Met_10 175 nlpksaieFldkv 187
                                       +   ++i+F+ ++
  gi|518652527|ref|YP_008142047.1| 247 GNF-NSINFMVAA 258
                                       *98.567777654 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.0   2.5e-12   3.5e-09      34     103 ..     175     246 ..     151     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.5e-12
                                       EEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  34 kvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                        +lD+ cG+G+ +++++k+s  a+++++d++  +++  k+nl+ n+++  v++++ d  + ++ ++ d+i++
  gi|518652527|ref|YP_008142047.1| 175 IILDMFCGIGYFSLQILKNSRPARMVMCDINPDSIHYLKKNLQVNRIKskVDIYTGDSRAVLPAMQADYIIM 246
                                       489*********************************************999*******************97 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.0   3.6e-12   4.9e-09       1      45 [.       5      49 ..       5      51 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 3.6e-12
                                      EEEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S--HH CS
                            Trm5_N  1 cikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkeepeg 45
                                      ci+ +k  + +++kk +++glLd +y I +d++y+yIP++++++g
  gi|518652527|ref|YP_008142047.1|  5 CIRFSKISADDAIKKYRALGLLDTTYHIEQDENYVYIPLIRHIDG 49
                                      9999**************************************998 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.1e-09   1.5e-06       1      76 [.     176     251 ..     176     262 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.1e-09
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       +Ld+ cG G ++l+++k+   a+++++Di+++ + + +++++ +++  +v++++gd +++  ++ + D++++ g+++
  gi|518652527|ref|YP_008142047.1| 176 ILDMFCGIGYFSLQILKNSRPARMVMCDINPDSIHYLKKNLQVNRIksKVDIYTGDSRAVL-PAMQADYIIM-GNFN 250
                                       8*****************868********************9999999999*****99964.5668999999.5665 PP

                                       G CS
                   Methyltransf_25  76 h 76 
                                        
  gi|518652527|ref|YP_008142047.1| 251 S 251
                                       4 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.46   6.3e+02      42      67 ..      97     122 ..      92     152 .. 0.89
   2 !   24.9   0.0     1e-08   1.4e-05       4      80 ..     173     246 ..     170     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.46
                   Methyltransf_31  42 elArenaqklgldnveFeqgdieele 67 
                                       ++A e a++l++dnv +e g i+ ++
  gi|518652527|ref|YP_008142047.1|  97 KVAHEYASRLKVDNVYVETGKIQGIK 122
                                       67899999**********99998765 PP

  == domain 2  score: 24.9 bits;  conditional E-value: 1e-08
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee.leklledekfDli 78 
                                       g+ +lD  CG G++++++ ++ +p a++v  Di++++i + ++n+q + ++  v    gd  + l+      + D+i
  gi|518652527|ref|YP_008142047.1| 173 GMIILDMFCGIGYFSLQILKNSRP-ARMVMCDINPDSIHYLKKNLQVNRIKsKVDIYTGDSRAvLPA----MQADYI 244
                                       7889***************77666.9*************************99*********99994....346666 PP

                   Methyltransf_31  79 ls 80 
                                       + 
  gi|518652527|ref|YP_008142047.1| 245 IM 246
                                       55 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.8e-08   6.6e-05      15      88 ..     173     246 ..     164     257 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklkeeevdtvvi 88 
                                       g +++D  +  gy ++ ++k+++  +++++Din+ +++  k+n++ +++++k++++ +d  ++l + ++d++++
  gi|518652527|ref|YP_008142047.1| 173 GMIILDMFCGIGYFSLQILKNSRPARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPAMQADYIIM 246
                                       55899999*****************************************************9998888999885 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   3.9e-07   0.00053       1      76 [.     177     250 ..     177     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.9e-07
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       L+  cG G ++  +l++ ++++ + +Di+p++i +  +k  + + +  ++v++ + d+    +  + D++++ n+ 
  gi|518652527|ref|YP_008142047.1| 177 LDMFCGIGYFSLQILKNSRPARMVMCDINPDSI-HYLKKNLQVN-RIKSKVDIYTGDSRAVLPAMQADYIIMGNFN 250
                                       5667*****************************.4444444444.46679999999999899999*******9875 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 !   19.0   0.1   5.9e-07   0.00081       3      68 ..     175     242 ..     173     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 5.9e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv..fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklkle 68 
                                       +ilD+f+G G  + q+ ++    +++  +in++ +   ++N +v  +++k+++ +gd   +l  ++ +
  gi|518652527|ref|YP_008142047.1| 175 IILDMFCGIGYFSLQILKNsrPARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPAMQAD 242
                                       79*********99998666465689999*****************************99977666655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.5e-06     0.002      51     121 ..     174     243 ..     137     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.5e-06
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-E CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrf 121
                                       + +ld + + G  ++  ++    ++ v+  Di++  ++ +k+N ++n ++  v i ++d +++l +++  +
  gi|518652527|ref|YP_008142047.1| 174 MIILDMFCGIGYFSLQILKNSRPARMVM-CDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPAMQADY 243
                                       789*****************66666655.9********************************998666554 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.047      41     106 ..     172     238 ..     160     246 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                                       CC-EEEETT-TTSHHHHHHH..HTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCT CS
                     Cons_hypoth95  41 egarvLDlfaGsGalglEAl..SRgakkavlvekdkeavkilkenleelkleeetaelkedaleallk 106
                                       +g  +LD+f+G G  +l  l  SR  +++v+ + ++  ++ lk+nl+  +++++++++  d+   l+ 
  gi|518652527|ref|YP_008142047.1| 172 TGMIILDMFCGIGYFSLQILknSRP-ARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPA 238
                                       67789********888888766999.578999*******************99999999988777665 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.5e-05     0.075      87     142 ..     192     245 ..     182     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.5e-05
                                       HHHCCCEEEEEEEES-HHHHHHHHHHHHHHTTCCGCEEEES-CCCCCHCC-ECEEE CS
                             PRMT5  87 eetkvtkvkivavEKnpnavvtLqkkvneekWeekveviksdmrelkaeekvdllv 142
                                       ++   +  ++v+ + np+++ +L+k++++++ ++kv++ + d r++   +++d ++
  gi|518652527|ref|YP_008142047.1| 192 KN--SRPARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTGDSRAVLPAMQADYII 245
                                       33..3588999999**************************************9987 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   6.8e-05     0.094     162     231 ..     173     245 ..     165     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
                              PrmA 162 geevlDvGtGSGiLaiaaakLg.akkvvavDiDevAvkvakeNaelNkveakleval..seellkeekadviv 231
                                       g  +lD+ +G G  ++  +k    +++v  Di++ +++  k+N+++N++++k+++++  s+ +l + +ad i+
  gi|518652527|ref|YP_008142047.1| 173 GMIILDMFCGIGYFSLQILKNSrPARMVMCDINPDSIHYLKKNLQVNRIKSKVDIYTgdSRAVLPAMQADYII 245
                                       56789***********9999762689999************************99862223333357888776 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.8e-05      0.11      32     127 ..     174     279 ..     158     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.8e-05
                                       SEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTT...TCCCEEEE-S-CCGHHHHHHHCT....TTC CS
                            RrnaAD  32 ltvleigpGkGilTeeLakra..kqvvvlElderLakllqkkls...kdeklkvvhqDflkfetpeevte....kds 99 
                                       + +l++  G G ++ +++k +    +v+  + ++ +  l+k+l+    ++k+ ++  D        ++ +       
  gi|518652527|ref|YP_008142047.1| 174 MIILDMFCGIGYFSLQILKNSrpARMVMCDINPDSIHYLKKNLQvnrIKSKVDIYTGDSRAVLPAMQA-DyiimGNF 249
                                       779**************99998899****************999888889999999998876554433.35677666 PP

                                       CCCEEEEEEE--TTTHHHHHHHHHH..GGG CS
                            RrnaAD 100 ihqeflvvanlPyeistqlvkqlle..esr 127
                                          +f+v+a l   i+tq+ +++l   es 
  gi|518652527|ref|YP_008142047.1| 250 NSINFMVAALLRSRIGTQISMHYLTptESM 279
                                       7899********************866444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2103.84
//
Query:       gi|518652528|ref|YP_008142048.1|  [L=314]
Description: hypothetical protein FACI_IFERC00001G1167 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.7e-17   62.2   0.0    2.4e-16   60.1   0.0    1.7  1  Esterase       Putative esterase
  ------ inclusion threshold ------
      0.047   12.9   0.0       0.11   11.7   0.0    1.5  2  Hydrolase_4    Serine aminopeptidase, S33
       0.12   12.0   0.0        0.2   11.3   0.0    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0     4e-20   2.4e-16       7     238 ..      25     298 ..      23     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 4e-20
                                       EEEEEEEE.CC.GGTTTEEEEEEE--TTHHCCHHHHHCHHCCCCHCCT.EEEEEECCCSS-TTTTTSBTTSBB.TTE CS
                          Esterase   7 eikvqvyLPedyspgrkypvvylldGltgwdqnfrakelleslaregeiaeviivvvprggessfysdwdlgarfye 83 
                                       e+k+ v+ Pe+     + p+++ l Gl+g+ +  + ++++ +  +++++   ++++ p+  ++     +++     +
  gi|518652528|ref|YP_008142048.1|  25 ERKILVFHPEE--LVPGAPLLIELAGLNGTPKLNNRFSQVLNKLYKKNMLGNAVIINPDFSTK-----YHV-----N 89 
                                       56777777777..4456799***********99998888888888888988899999998888.....553.....6 PP

                                       EETTCCCCCCHCHHHHTHHHHHHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEE...S--S-CC.... CS
                          Esterase  84 nategpgaeayetfltqeLlplldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssf...Spivnps.... 153
                                       + t+ p a +ye+f+ +e+ p++ ++++t ++  a++G S GG+gA +la+++p+     + +   S++        
  gi|518652528|ref|YP_008142048.1|  90 QYTNSPAAGNYEDFIIKEIIPFISERYKTGKT--ALFGKSSGGFGAYTLAARNPEIINGFADHfgdSGF---Eyvyi 161
                                       999************************99988..********************985333333122555...15569 PP

                                       ..................................................................HCHHHCTTCCH CS
                          Esterase 154 ..................................................................namWgqeekea 164
                                                                                                         + +Wg+     
  gi|518652528|ref|YP_008142048.1| 162 pdipvtyrelgdkdineyvnekslkedlndneirtlniigmsafysynnsesgfdlpfdrktgmfrDDIWGR----- 233
                                       9************************************************************99999999988..... PP

                                       HHCC-CCCCHCHHCHTTSEEE.EEEEECTTBCCCHTSCHHHHHHHHHHHCCHHHHCCCCCCTT-SCCCC--SSHH CS
                          Esterase 165 wqendpvllakelsaslkalr.iyldvGtseddlgeqlsveilevlarnrelkeqlaargvegedheydGghswe 238
                                       w + dp+ ++++++++lk+l+ iyldvG +++               ++r+l+ ++++ +++++++e+dGgh ++
  gi|518652528|ref|YP_008142048.1| 234 WSSFDPARNVDNNIENLKKLDaIYLDVGIKDE----------YNLYMGMRSLHRKMENFNISHRYNEFDGGHFYN 298
                                       ****************999855*********9..........667789************************776 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.37   2.2e+03     115     162 ..      47      95 ..      35     101 .. 0.66
   2 ?   11.7   0.0   1.9e-05      0.11      63     104 ..     106     147 ..      99     148 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.37
                       Hydrolase_4 115 aklk.appllklllkllgkllpklqvsnnlkadslsrdpevvaayeadp 162
                                       a l+ +p+l + ++++l+kl++k  + n +  +   + + +v +y + p
  gi|518652528|ref|YP_008142048.1|  47 AGLNgTPKLNNRFSQVLNKLYKKNMLGNAVIINPDFSTKYHVNQYTNSP 95 
                                       4556677788888888888888877766666666666666666666655 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 1.9e-05
                       Hydrolase_4  63 aafvekvkeehpelplfllGhSmGGliallyllrypdkvagl 104
                                       ++++  + e++++ +  l+G S GG+ a ++++r+p+ ++g+
  gi|518652528|ref|YP_008142048.1| 106 KEIIPFISERYKTGKTALFGKSSGGFGAYTLAARNPEIINGF 147
                                       5667789999999***********************988775 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.4e-05       0.2      52     101 ..      98     147 ..      78     148 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.4e-05
                                       CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEE CS
                     Abhydrolase_1  52 ddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyperVkal 101
                                        +y+++ + +++ +i ++++ +k +l G S GG+ a ++aa++pe ++++
  gi|518652528|ref|YP_008142048.1|  98 GNYEDFIIKEIIPFISERYKTGKTALFGKSSGGFGAYTLAARNPEIINGF 147
                                       5677777899999********************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2170.11
//
Query:       gi|518652529|ref|YP_008142049.1|  [L=175]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.7e-14   52.1   0.1      1e-13   51.0   0.0    1.6  2  PadR      Transcriptional regulator PadR-like family
     0.0004   20.2   0.2    0.00055   19.7   0.2    1.3  1  DUF4364   Domain of unknown function (DUF4364)
    0.00054   20.6   0.0    0.00085   19.9   0.0    1.4  1  RTP       Replication terminator protein
     0.0083   16.6   0.2      0.024   15.1   0.0    1.9  2  HTH_27    Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.047   13.5   0.1      0.093   12.6   0.1    1.5  1  DUF1495   Winged helix DNA-binding domain (DUF1495)
      0.076   12.9   0.9      0.076   12.9   0.9    1.7  2  DUF3116   Protein of unknown function (DUF3116)
       0.12   12.5   0.0       0.23   11.7   0.0    1.3  1  HTH_34    Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.0   3.9e-17     1e-13       1      74 [.      51     119 ..      51     120 .. 0.95
   2 ?   -3.6   0.0       4.6   1.2e+04      37      43 ..     138     144 ..     137     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 3.9e-17
                                       HHHHHCCS-EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHHHH CS
                              PadR   1 iLalleeqpsyGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrrela 74 
                                       iL++++ ++  G+++i+++++++eg + +s+G +YpaL++L +eg++e ++++     ++kyY+ T++G++ ++
  gi|518652529|ref|YP_008142049.1|  51 ILNMASSEEITGVDVIDRVDRRTEGRWVPSPGVIYPALRKLYEEGYLEMREDN-----NKKYYKATEKGKEVVK 119
                                       899999********************************************886.....7***********9865 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.6
                                       HHHHHHH CS
                              PadR  37 aLkrLek 43 
                                       +L+r+e+
  gi|518652529|ref|YP_008142049.1| 138 ILERMED 144
                                       5666665 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   2.1e-07   0.00055      39      72 ..      87     120 ..      84     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.1e-07
                           DUF4364  39 alseLvesglieeeekenktlykiTekGketlel 72 
                                       al +L e+g++e++e++nk++yk TekGke+++ 
  gi|518652529|ref|YP_008142049.1|  87 ALRKLYEEGYLEMREDNNKKYYKATEKGKEVVKD 120
                                       799***************************9974 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   3.3e-07   0.00085      10      77 ..      47     118 ..      41     153 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT.----HHHHHHHHHHHHHTTSEEEEEEEB.....TSSSSSEEE CS
                               RTP  10 lklylitlvekkklyglklldelkkeFkelg.ykPnhseiyralhelvedgilkrrkelk.....ekaklqevv 77 
                                       lk  +++++ +++  g+ ++d++ ++  + g + P++  iy al+ l+e+g+l+ r+  +       +k +evv
  gi|518652529|ref|YP_008142049.1|  47 LKYLILNMASSEEITGVDVIDRVDRR--TEGrWVPSPGVIYPALRKLYEEGYLEMREDNNkkyykATEKGKEVV 118
                                       788999***************88654..4445*********************876544412222444444544 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   0.1       2.7     7e+03      49      61 ..      31      43 ..      24      43 .. 0.79
   2 !   15.1   0.0   9.6e-06     0.024      38      68 .]      87     114 ..      80     114 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.7
                            HTH_27 49 ertgdeadrrekr 61
                                      +r+g+ ++rr ++
  gi|518652529|ref|YP_008142049.1| 31 HRMGSGENRRGMH 43
                                      6889999999875 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 9.6e-06
                            HTH_27  38 slkkLtekGLvertgdeadrrekrvrlTdkG 68 
                                       +l+kL e G++e+ +d      k +++T+kG
  gi|518652529|ref|YP_008142049.1|  87 ALRKLYEEGYLEMREDN---NKKYYKATEKG 114
                                       89*********999665...8899******9 PP

>> DUF1495  Winged helix DNA-binding domain (DUF1495)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.6e-05     0.093      58      88 ..      90     119 ..      82     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.6e-05
                           DUF1495  58 sLielGLveeeeeseglklYklteeGieive 88 
                                        L e G  e + e+++ k+Yk+te+G+e+v+
  gi|518652529|ref|YP_008142049.1|  90 KLYEEGYLE-MREDNNKKYYKATEKGKEVVK 119
                                       577788885.78999*************997 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.9     3e-05     0.076      53      81 ..      93     119 ..      89     122 .. 0.84
   2 ?   -2.7   0.0       2.1   5.3e+03      10      21 ..     136     147 ..     129     167 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3e-05
                           DUF3116  53 lkgyilRkeekannkkrYelTekGellyk 81 
                                       ++gy+  +e   nnkk+Y++TekG+++ k
  gi|518652529|ref|YP_008142049.1|  93 EEGYLEMRED--NNKKYYKATEKGKEVVK 119
                                       5788877777..7************9876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.1
                           DUF3116  10 levLelvkdpnf 21 
                                         +Le ++d   
  gi|518652529|ref|YP_008142049.1| 136 DTILERMEDYAQ 147
                                       555555544332 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 ?   11.7   0.0     9e-05      0.23      29      71 ..      82     120 ..      79     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9e-05
                            HTH_34  29 gnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                       g ++  l+kL + gY+e++ + ++k     ++ T++G+e  k+
  gi|518652529|ref|YP_008142049.1|  82 GVIYPALRKLYEEGYLEMREDNNKK----YYKATEKGKEVVKD 120
                                       789999*************999998....9********98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1217.52
//
Query:       gi|518652530|ref|YP_008142050.1|  [L=420]
Description: hypothetical protein FACI_IFERC00001G1169 [Ferroplasma acidarmanus fer1]
Scores for complete 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-66  224.4   0.0    2.4e-66  224.1   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
     0.0002   20.7   0.0    0.00024   20.4   0.0    1.1  1  Aminotran_1_2  Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  224.1   0.0   2.6e-70   2.4e-66      10     376 ..      29     389 ..      21     416 .. 0.90

  Alignments for each domain:
  == domain 1  score: 224.1 bits;  conditional E-value: 2.6e-70
                                       CEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-. CS
                       Aminotran_3  10 llvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkg 86 
                                       +++  +++G+ + dv+gk+y+D   ++ +++lGha+P+v++ +k+q++k   + fg ++ e+ +kl + + ++++  
  gi|518652530|ref|YP_008142050.1|  29 PVMFAQGHGSKILDVNGKEYIDYSLGFGPMILGHANPDVSNHIKSQVDKG--ILFGSIS-ENEIKLGKTIKNAVGS- 101
                                       4778899*******************************************..6666665.5567899999998888. PP

                                       .SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TT CS
                       Aminotran_3  87 ldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkyp 163
                                       ++++ + nsG+eA++ A++lar        t k++i++++g++HG   +al  +gs  +  t   p++++v+     
  gi|518652530|ref|YP_008142050.1| 102 IERLRFTNSGTEATMHAIRLARG------FTGKKYIVKMEGGYHGAHDYALIKSGS--GTMTFGVPSSAGVPEEVSR 170
                                       ***********************......***************************..6666666777777777777 PP

                                       BGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTT.. CS
                       Aminotran_3 164 deevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtGf.. 238
                                          v  +n+      +e +e+l k++ +e+aAvi+Ep+ g+ Gv+ ++++fl+ lre+++k+  lli+DEv tGf  
  gi|518652530|ref|YP_008142050.1| 171 TVLVGRYND------AESIEKLFKEHRNEIAAVITEPVLGNIGVINPENDFLNSLREITEKYSSLLIFDEVITGFrf 241
                                       778888898......899********************************************************944 PP

                                       TTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTS...B--TTTT-HHHHHHHHHHHHHHHHTT CS
                       Aminotran_3 239 GrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgs...hgsTfgGnplacavalavleiieeek 312
                                       G  G     + ag++pDl+t++K ++gG p+  + +++++m  +ap++    ++Tf+Gnpl +a+ +a+l+ ++ ++
  gi|518652530|ref|YP_008142050.1| 242 GFKG---YQDIAGIKPDLTTMGKIIGGGAPVGMFGGREDIMAHVAPQGdvyEAGTFSGNPLTMAAGIATLDQLKSKD 315
                                       5555...24556**********************************99999************************** PP

                                       HHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC............HHHHHHHHHCTEE-EE CS
                       Aminotran_3 313 llenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke............keilkkakekGvlils 376
                                       +   + +  a+l+e+L++l ++y+  +++ +   m+ i ++++++v++            +++++ ++ekG+ + +
  gi|518652530|ref|YP_008142050.1| 316 YS-AITNYAARLEEKLNSLISEYNIDATINRCHSMFQI-FFNKNKVTDykgatasdtekfNKMFHTLLEKGIFFPP 389
                                       96.5778999*************9999***********.666666677799******999999********98755 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 !   20.4   0.0   2.7e-08   0.00024      79     357 ..     113     407 ..      91     413 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-08
                                       HHHHHHHHHHHHTTT-E..EEEEESS-THHHHHHHHTTSEEEEEEBEET............TTTEE-HHHHHHHHTT CS
                     Aminotran_1_2  79 aliealifllklnpgde..ilvpdptyasyknilrlsggevvryplyse............edfhldlealeealke 141
                                       ++   +i+l++ ++g++  + +   +++ ++ +l  sg+  +++ + s+             ++ +d+e++e++ ke
  gi|518652530|ref|YP_008142050.1| 113 EATMHAIRLARGFTGKKyiVKMEGGYHGAHDYALIKSGSGTMTFGVPSSagvpeevsrtvlVGRYNDAESIEKLFKE 189
                                       555555555554444442233445566666666666777777776666667777777777677889********999 PP

                                       HHCTTETEEEEEEESS-TTT--B--HHH.HHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEE CS
                     Aminotran_1_2 142 apegnkktkvilvesphNPtGtvatlee.leklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivg 217
                                       +  +++    +++e +  + G++ ++++ l  l ++++ky  ll++De+  gf fg ++++  +a+++++       
  gi|518652530|ref|YP_008142050.1| 190 H-RNEI--AAVITEPVLGNIGVINPENDfLNSLREITEKYSSLLIFDEVITGFRFGFKGYQD-IAGIKPDLT----- 257
                                       4.4444..7************99776543899************************555444.999999755..... PP

                                       ESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHH..HHHH...HHHHHHHHHHHHHHHH CS
                     Aminotran_1_2 218 slsKafGlaGeRvGyilgnaavvsqlrklsrpfls.ssllqaavaaalsdal..lkqs...eleemrqrlqkrrkel 288
                                       +++K  G     vG++ g +++  +++     +   + ++ ++++aa  ++l  lk +    +++ ++rl+++  +l
  gi|518652530|ref|YP_008142050.1| 258 TMGKIIGGGA-PVGMFGGREDIMAHVAPQGDVYEAgTFSGNPLTMAAGIATLdqLKSKdysAITNYAARLEEKLNSL 333
                                       ******8644.89*****99888888766665555544444444443333330022223555666666666666666 PP

                                       HHHHHHSTEEEECCS.CSSEEEEEETHH..........CHHHHHHH....HHHTCTEEEEEGGGGTSTTEEEEECTT CS
                     Aminotran_1_2 289 rdeLaelglkvlasq.sgmflltdlsae..........takelskk....LleevgvyvtpgtsftvpgrlRitvAg 350
                                        +e    +++ +++  + mf +   +++          + +e + k    Lle+ g+   p ++f+++    +++ +
  gi|518652530|ref|YP_008142050.1| 334 ISEY---NIDATINRcHSMFQIFFNKNKvtdykgatasD-TEKFNKmfhtLLEK-GIFFPP-SQFETEF---VSF-A 400
                                       5555...88888888788888877777788888888842.33333346668888.888877.7777655...556.5 PP

                                       S-HHHHH CS
                     Aminotran_1_2 351 lteeele 357
                                       ++e +le
  gi|518652530|ref|YP_008142050.1| 401 HSETDLE 407
                                       5555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2742.77
//
Query:       gi|518652531|ref|YP_008142051.1|  [L=285]
Description: hypothetical protein FACI_IFERC00001G1170 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-64  217.4   0.0    4.7e-64  215.7   0.1    1.7  2  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
     0.0015   18.9   0.0     0.0045   17.3   0.0    1.9  1  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.7   0.1   5.2e-68   4.7e-64       2     199 ..       4     201 ..       3     205 .. 0.94
   2 ?   -1.0   0.0      0.12   1.1e+03     140     165 ..     244     269 ..     237     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 215.7 bits;  conditional E-value: 5.2e-68
                    Porphobil_deam   2 rigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDl 77 
                                       +igtR+SkLAl+qa+ v++aL++   ev+i++ ++ GD +++ pL++++++g+F++el+e++l+geidlaVhS+KD+
  gi|518652531|ref|YP_008142051.1|   4 TIGTRNSKLALIQANSVKDALESrGYEVNIKSYTSAGDSNKNIPLYRMSSTGVFVDELNERVLKGEIDLAVHSAKDI 80 
                                       7********************6645669************************************************* PP

                    Porphobil_deam  78 ptelpeglelaavlkredprDvlvvkssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegey 154
                                       p+++++gle++av+ r+d rDvl+ ++ lee+ +g+v+gTsS+RR  q  ++ p+++v+d+RGn+dtR++k  e++y
  gi|518652531|ref|YP_008142051.1|  81 PSNIQKGLEITAVTGRDDFRDVLISRTPLEEMTAGSVIGTSSMRRIRQAMTVNPEITVSDIRGNIDTRISKYTEKKY 157
                                       ************************8779************************************************* PP

                    Porphobil_deam 155 daiiLAaAGLkRlgleerisev.lspeellpavgQGalavevrked 199
                                       ++ii+A+A+ kR++l  +i+++ ls+e++lpa+ QG++a+  ++++
  gi|518652531|ref|YP_008142051.1| 158 TGIIIAMAAYKRMKL--DIEHFiLSEEQFLPAPNQGIIAIVGKSNS 201
                                       *************94..554434*****************999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.12
                    Porphobil_deam 140 GnvdtRlrkldegeydaiiLAaAGLk 165
                                       G ++tR+  ld++e   ++++a  L+
  gi|518652531|ref|YP_008142051.1| 244 GKIKTRFYSLDSDEHRDMVFSAENLD 269
                                       9999******9999888888776665 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0     5e-07    0.0045       5      57 ..     220     269 ..     216     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 5e-07
                                       HHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE CS
                   Porphobil_deamC   5 laERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakg 57 
                                       + ER + + L+ GCs+P+G  ++  +++ +k ++  l+ d+ + +v+ ae  +
  gi|518652531|ref|YP_008142051.1| 220 KNERFIATSLNLGCSMPVGILSK--DGK-IKTRFYSLDSDEHRDMVFSAENLD 269
                                       56999999***********9999..666.*************99999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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 0.27s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1835.28
//
Query:       gi|518652532|ref|YP_008142052.1|  [L=239]
Description: uroporphyrinogen-III synthase [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   75.4   0.0      5e-21   75.1   0.0    1.1  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.1   0.0   2.8e-25     5e-21      14     220 ..      26     215 ..      19     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.1 bits;  conditional E-value: 2.8e-25
                                       EEE---EECCECCHHHHHHHHH.T.....--SEEEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHH CS
                              HEM4  14 plelPlieiepaedraelraal.ddleagkydwliftSanavealfealkreeedvkalaslkvaavGpaTaraLee 89 
                                        l +Pl  i++    ++ ++ + ++l + k+ ++++tS+ +   +f++        k   +   +a+G++Ta  +++
  gi|518652532|ref|YP_008142052.1|  26 ILNIPLTSIQA----RNFDENIgKELIQAKPGVIVLTSSFGAMEFFKNYY------KFTVNPDFVAIGEKTAGIIRK 92 
                                       56789999999....556666666677889***********999999998......33336689************* PP

                                       TT---SEE-..SSSHHHHGGGS-.---EEEEEE-SS.S--HHHHHHHHHTTEEEEEE-SEEEEE-HHHHHHHHHHHH CS
                              HEM4  90 lglrvdlvpseegtaegLaeelaeslagkrvlllrgeiarddlaegLeergaevdevevYetvpaeeepeelkealk 166
                                       +  +v+ vp    ++ g++++l     ++ + l+r++++++++ e L +rg++++e +vY+    + e+  lk+ + 
  gi|518652532|ref|YP_008142052.1|  93 YAGNVK-VPT-VKDSYGVLDLLS-GYENTDIALFRSNESNNIIRESLTRRGVKYHEYHVYDV--IQLENTGLKDSFL 164
                                       *99997.999.9999*****887.777789********************************..7778999****** PP

                                       TT--SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SE CS
                              HEM4 167 agevdavvftSpstvrnllellkdegdelkevkvaaiGptTaealkklglkvdv 220
                                       +++++++++tS+ ++r + e ++      ++ k+++iG++T+ +l++lg kv++
  gi|518652532|ref|YP_008142052.1| 165 SSSCNGILVTSSMEARIFRETIGT---YTGGKKIYSIGKITTSTLESLGYKVSL 215
                                       ***********************8...69**********************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1757.09
//
Query:       gi|518652533|ref|YP_008142053.1|  [L=185]
Description: hypothetical protein FACI_IFERC00001G1172 [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   42.2   3.9    7.5e-05   22.5   1.2    2.4  2  KH_1      KH domain
    0.00014   22.2   0.4       0.72   10.3   0.1    2.2  2  NfeD      NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
      0.014   15.6   0.2      0.039   14.2   0.1    1.7  2  Nab2      Nuclear abundant poly(A) RNA-bind protein 2 (Nab2)
      0.051   13.4   2.9        3.5    7.6   0.1    2.9  2  KH_4      KH domain
      0.071   13.2   0.0       0.18   11.9   0.0    1.7  1  KH_8      Krr1 KH1 domain
       0.25   11.2   9.7        1.4    8.8   2.7    3.1  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 !   20.1   0.1   1.4e-07   0.00041       4      50 ..       7      47 ..       5      61 .. 0.83
   2 !   22.5   1.2   2.5e-08   7.5e-05      10      64 ..     104     150 ..      94     152 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1.4e-07
                                      EEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEE CS
                              KH_1  4 ilvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevti 50
                                      i+vP   +g +IGk G +  +I+ee +ak +++ se+      +vt+
  gi|518652533|ref|YP_008142053.1|  7 IKVPFARIGVLIGKEGTVKAKIEEEGKAKLDID-SEN-----AIVTV 47
                                      799*999*****************55*****87.654.....46666 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 2.5e-08
                                       HHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEESHHHHHHHHHHH CS
                              KH_1  10 lvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisGspeavekAkeli 64 
                                         gr+IGk G +   I+e tg++I +  +       ++v i G+  +++ A+e++
  gi|518652533|ref|YP_008142053.1| 104 IRGRLIGKEGHTREIIEELTGTYISIS-G-------NTVSILGDFISIQYAREAV 150
                                       57**********99999999*****76.4.......49*******99****9987 PP

>> NfeD  NfeD-like C-terminal, partner-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00026      0.78      33      58 ..      17      47 ..       8      65 .. 0.71
   2 !   10.3   0.1   0.00024      0.72      10      57 ..      87     135 ..      82     147 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00026
                                      GTTSEEEEEE-B.S-EEEEET....TEEEEE CS
                              NfeD 33 liGkegvvledi.gtGrvkvd....GeeWsa 58
                                      liGkeg+v ++i ++G++k+d    +++ ++
  gi|518652533|ref|YP_008142053.1| 17 LIGKEGTVKAKIeEEGKAKLDidseNAIVTV 47
                                      9***********648**99885444455555 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00024
                                       XXXXXXXS---SSS--S.S---GGTTSEEEEEE-B.S.-EE.EEETTEEEE CS
                              NfeD  10 lvllrplllkklkkkekktnaealiGkegvvledi.g.tGr.vkvdGeeWs 57 
                                       ++ ++ ++ k+ k+   k  +++liGkeg++ e i + tG+ + + G++ s
  gi|518652533|ref|YP_008142053.1|  87 VISIKEFVNKDAKR-I-KEIRGRLIGKEGHTREIIeElTGTyISISGNTVS 135
                                       44444566665533.2.244559**********998455665889888766 PP

>> Nab2  Nuclear abundant poly(A) RNA-bind protein 2 (Nab2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.1   3.2e+03      46      70 ..      26      50 ..      12      70 .. 0.54
   2 ?   14.2   0.1   1.3e-05     0.039      24      94 ..      93     169 ..      81     174 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
                              Nab2 46 esvvqelstlfdsvskealadvvqt 70
                                       ++ +e  + +d  s++a+  v q+
  gi|518652533|ref|YP_008142053.1| 26 AKIEEEGKAKLDIDSENAIVTVYQK 50
                                      4444555566666666666666654 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.3e-05
                              Nab2  24 f.nedvnyvaeyivlllsnGgtvesvvqelstlfdsvskea...ladvvqtaf..falealqqGetvesivsklrgv 94 
                                       f n d + + e    l+   g++ ++++el++ + s+s ++   l d +++++   a++++ qG + ++++s l+++
  gi|518652533|ref|YP_008142053.1|  93 FvNKDAKRIKEIRGRLIGKEGHTREIIEELTGTYISISGNTvsiLGDFISIQYarEAVNMILQGRKHKTVYSYLEKN 169
                                       4378999999999999*********************98762225677766652279**************998865 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.2    0.0054        16      34      49 ..       8      23 ..       4      26 .. 0.79
   2 ?    7.6   0.1    0.0012       3.5      40      55 ..     105     120 ..      81     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0054
                              KH_4 34 nvegedlGrvIGkrGr 49
                                      +v    +G++IGk+G 
  gi|518652533|ref|YP_008142053.1|  8 KVPFARIGVLIGKEGT 23
                                      5555679********6 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0012
                              KH_4  40 lGrvIGkrGrtldAlq 55 
                                        Gr+IGk+G t   + 
  gi|518652533|ref|YP_008142053.1| 105 RGRLIGKEGHTREIIE 120
                                       6********9965555 PP

>> KH_8  Krr1 KH1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.1e-05      0.18      27      81 .]      30      81 ..      14      81 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.1e-05
                              KH_8 27 eekklklevdlkerslkvsTtekTrDPyiilkardlikLisrgvpleeakkvleD 81
                                      ee k kl++d ++    + T  +  DP   l a ++++ i+rg + e+a+ +++D
  gi|518652533|ref|YP_008142053.1| 30 EEGKAKLDIDSENA---IVTVYQKNDPLKALMALNVVQAIARGFNPEKAMLLFDD 81
                                      44456666666655...44667789*************************99998 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   2.7   0.00047       1.4      34      59 ..      12      37 ..       6      50 .. 0.80
   2 ?    5.0   0.4    0.0074        22      37      66 ..     106     134 ..     101     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00047
                                      SCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2 34 sqpgivIGkgGsnikkigkelrkdie 59
                                      ++ g++IGk+G    ki++e + +++
  gi|518652533|ref|YP_008142053.1| 12 ARIGVLIGKEGTVKAKIEEEGKAKLD 37
                                      799***************99877774 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0074
                                       HHHHTGGGHHHHHHHHHHHHHHHHHHTTCE CS
                              KH_2  37 givIGkgGsnikkigkelrkdieklegkkV 66 
                                       g++IGk+G + + i++  +  i  + g  V
  gi|518652533|ref|YP_008142053.1| 106 GRLIGKEGHTREIIEELTGTYIS-ISGNTV 134
                                       99********9999999998884.666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       625  (0.0348597); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1266.92
//
Query:       gi|518652534|ref|YP_008142054.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G1173 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-58  197.3   0.0    2.4e-58  196.9   0.0    1.1  1  RIO1            RIO1 family
  ------ inclusion threshold ------
      0.018   13.8   0.0      0.019   13.7   0.0    1.2  1  Pkinase_fungal  Fungal protein kinase
      0.031   13.8   0.0        4.4    6.8   0.0    2.3  2  Choline_kinase  Choline/ethanolamine kinase
       0.06   12.7   0.0        2.2    7.6   0.0    2.1  2  Kdo             Lipopolysaccharide kinase (Kdo/WaaP) family
      0.073   13.0   0.0        1.3    8.9   0.0    2.0  2  APH             Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> RIO1  RIO1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.9   0.0   6.7e-62   2.4e-58       2     181 ..      66     241 ..      65     247 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.9 bits;  conditional E-value: 6.7e-62
                                       EEEEEETTTEEEEEEEE-S---SS-HHHHCTTTSTTSTCG--GS-HHHHHHHHHHHHHHHHHHHHHTT--S--EEEE CS
                              RIO1   2 VyhavsedgkevaiKiyktstteFkkrkkyvsgekrfkdrksktnprklvklwaekEfrnLkrleeagvpvPkpiel 78 
                                       ++++  ++g   a+Kiyk+st++F +  +y++g++rf+++  k+n+ +lv +wa+kEf+nL+ l+++gv++Pkp+ +
  gi|518652534|ref|YP_008142054.1|  66 IFNVKLRNGITRALKIYKMSTLKFSNTMEYIKGDYRFDKE--KINRSNLVFVWAQKEFTNLQSLRDSGVHAPKPYGF 140
                                       78888889999**************************966..9********************************** PP

                                       ETTEEEEE--EETTEEGGBHHHCG-HHHHHHHHHHHHHHHHHHHHTSTEEESS-STTSEEEETTEEEE--GTTEEET CS
                              RIO1  79 krhvlvmefigedgvaapklkdveeeeeaeelyeevleemrklykeaglvHaDLSeyNvlvdedkvviIDvsQavel 155
                                        +++l+m+++g+ + +a ++kd++     +e+y ++ e++ k+y++ag+vHaDLSeyN+l+++++++iIDv+Q+v++
  gi|518652534|ref|YP_008142054.1| 141 YKNILLMSYLGSSKGPALQIKDLN--GGFDEIYVKLREAIWKMYNKAGIVHADLSEYNILYYRNNPYIIDVGQSVST 215
                                       ************************..999************************************************ PP

                                       TSTTHHHHHHHHHHHHHHHHHTTC-- CS
                              RIO1 156 dhpnalefLerDveniikfFrrkgve 181
                                       +hp+alefL+rD++ni++fF +kgv+
  gi|518652534|ref|YP_008142054.1| 216 KHPMALEFLKRDIKNISTFFIKKGVK 241
                                       ************************98 PP

>> Pkinase_fungal  Fungal protein kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.4e-06     0.019     318     341 ..     177     200 ..      83     223 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.4e-06
                    Pkinase_fungal 318 ghrsLflkagiLHrDiSenNilit 341
                                       + +++++kagi+H D Se+Nil +
  gi|518652534|ref|YP_008142054.1| 177 AIWKMYNKAGIVHADLSEYNILYY 200
                                       56899****************988 PP

>> Choline_kinase  Choline/ethanolamine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0057        20      20      61 ..     117     162 ..     101     166 .. 0.79
   2 ?    6.8   0.0    0.0012       4.4     130     169 ..     170     207 ..     165     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0057
                                       HHHHHHHHHHHHHTTS.SS-EEEEETTEEEEE--TCE...E--TTG CS
                    Choline_kinase  20 retElvvfallsergl.gpklygifenGrieefiesr...tlsted 61 
                                        ++E  +++ l + g+ +pk yg+ +n  +  ++ s+   +l+ +d
  gi|518652534|ref|YP_008142054.1| 117 AQKEFTNLQSLRDSGVhAPKPYGFYKNILLMSYLGSSkgpALQIKD 162
                                       578999999999998648****************665111455555 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0012
                                       HHHTHHHHHHCHGG-EEEE-S--SGGGEEE.-CTTEEEE- CS
                    Choline_kinase 130 elekleklleelespvvfcHnDlqegNillnkeekklvlI 169
                                          kl++ + +++++    H Dl e Nil+    ++ ++I
  gi|518652534|ref|YP_008142054.1| 170 IYVKLREAIWKMYNKAGIVHADLSEYNILYYR--NNPYII 207
                                       556788889999999999************44..444445 PP

>> Kdo  Lipopolysaccharide kinase (Kdo/WaaP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0   0.00061       2.2      57      81 ..     116     140 ..      89     146 .. 0.80
   2 ?    3.0   0.0     0.016        57     131     155 ..     178     203 ..     168     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00061
                               Kdo  57 ravrEfrllkrLeeagvavpkpvaa 81 
                                        a +Ef +l+ L++ gv++pkp  +
  gi|518652534|ref|YP_008142054.1| 116 WAQKEFTNLQSLRDSGVHAPKPYGF 140
                                       4779*****************9766 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.016
                               Kdo 131 iakl.hragvnHadlyaknillqqee 155
                                       i k+ ++ag+ Hadl   nil   ++
  gi|518652534|ref|YP_008142054.1| 178 IWKMyNKAGIVHADLSEYNILYYRNN 203
                                       55553789************987665 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.04   1.4e+02      38      60 ..     118     140 ..      58     159 .. 0.88
   2 ?    8.9   0.0   0.00036       1.3     164     194 ..     183     210 ..     156     219 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.04
                                       HHHHHHHHHHHHTT-B--B-CTT CS
                               APH  38 rrevallrlLakagvpvPevlag 60 
                                       ++e+  l+ L+++gv++P+++ +
  gi|518652534|ref|YP_008142054.1| 118 QKEFTNLQSLRDSGVHAPKPYGF 140
                                       5778889*************985 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00036
                                       S-EEEE-SS-SGGGEEEC..TTEEEEE---T CS
                               APH 164 lptvllHgDlhpgNllvdpddgrvtGviDfe 194
                                        +++++H Dl+  N+l   ++++   +iD +
  gi|518652534|ref|YP_008142054.1| 183 NKAGIVHADLSEYNILYY-RNNPY--IIDVG 210
                                       5789**************.99997..***76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); 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: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1968.77
//
Query:       gi|518652535|ref|YP_008142055.1|  [L=110]
Description: translation initiation factor IF-1A [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   86.5   0.3    1.4e-24   85.6   0.2    1.5  2  eIF-1a    Translation initiation factor 1A / IF-1
  ------ inclusion threshold ------
      0.064   13.1   0.8       0.68    9.8   0.0    2.7  3  Myosin_N  Myosin N-terminal SH3-like domain


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 ?   -2.3   0.0      0.44     4e+03      12      24 ..       9      20 ..       5      22 .. 0.65
   2 !   85.6   0.2   1.6e-28   1.4e-24       1      64 []      23      85 ..      23      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.44
                                      TTTEEEEEE.SSS CS
                            eIF-1a 12 gnnlfrVelpdng 24
                                      g n  rV +p n+
  gi|518652535|ref|YP_008142055.1|  9 GENITRVITP-NK 20
                                      6677777776.54 PP

  == domain 2  score: 85.6 bits;  conditional E-value: 1.6e-28
                                      EEEEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHHCT----TT-EEEEEE-TT-TTEEEEES- CS
                            eIF-1a  1 gevigkViealgnnlfrVelpdngkevlaeipgkfRnkiwikrGdyVlVelspydltkGrIvyr 64
                                      ge++g+V+++ g ++ +V ++ +g ++ ++ipgk+++++wi++Gd V+V++++++++kG+I+yr
  gi|518652535|ref|YP_008142055.1| 23 GEIYGIVEKLSGASRLTVMCE-DGSTRNCRIPGKMKKRMWIREGDLVIVKPWDFQDEKGDIIYR 85
                                      689*****************7.6****************************************8 PP

>> Myosin_N  Myosin N-terminal SH3-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   7.6e-05      0.68      18      38 ..      29      50 ..      18      51 .. 0.81
   2 ?   -1.1   0.1       0.2   1.8e+03       1       7 [.      57      63 ..      57      68 .. 0.81
   3 ?    0.2   0.1     0.077   6.9e+02      21      30 ..      63      72 ..      61      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7.6e-05
                                      EEEEES.SEEEEEETTSEEEEE CS
                          Myosin_N 18 IkeeeG.dkvtVetedGktvtV 38
                                      + + +G   +tV +edG+t+ +
  gi|518652535|ref|YP_008142055.1| 29 VEKLSGaSRLTVMCEDGSTRNC 50
                                      556677566**********976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.2
                                      SEEEEET CS
                          Myosin_N  1 KklVWVp 7 
                                      Kk+ W++
  gi|518652535|ref|YP_008142055.1| 57 KKRMWIR 63
                                      8999996 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.077
                                      EESSEEEEEE CS
                          Myosin_N 21 eeGdkvtVet 30
                                      +eGd v+V+ 
  gi|518652535|ref|YP_008142055.1| 63 REGDLVIVKP 72
                                      5899999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 851.26
//
Query:       gi|518652536|ref|YP_008142056.1|  [L=582]
Description: hypothetical protein FACI_IFERC00001G1175 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-40  138.5  57.1    2.8e-40  138.5  57.1    2.1  2  AA_permease_2    Amino acid permease
    5.8e-29  101.0  65.8    3.6e-27   95.1  59.2    2.1  2  AA_permease      Amino acid permease
     0.0022   16.9   1.7     0.0022   16.9   1.7    4.0  4  Spore_permease   Spore germination protein
     0.0032   17.5  12.2     0.0032   17.5  12.2    5.1  5  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


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 !  138.5  57.1   6.2e-44   2.8e-40       1     398 [.      25     461 ..      25     482 .. 0.81
   2 ?   -1.4   9.2      0.18   7.9e+02      85     175 ..     457     558 ..     447     579 .. 0.73

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 6.2e-44
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+++++ +l++g +igsg +++   +a+++gpa+il+++i+ +i+ l  +lvyaEl+s++pr g i+ y+++  g +
  gi|518652536|ref|YP_008142056.1|  25 LNTWDLYFLSLGGIIGSGWLFAAaaSAGTTGPAAILSWIIGGVIV-LFIALVYAELGSMIPRTGAISRYGHYSHGGV 100
                                       789***************98888899******************9.89********999****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlas....ilsvaasyllnalgpdlqgn...........twltyliaiaililvalinirgi 137
                                       ++ +++w++++++v v a+    ++++a sy+ ++ ++   +n           t l +l+a+++++ ++++n+ g+
  gi|518652536|ref|YP_008142056.1| 101 AGLFFGWTYFLSAVSVPAIeaeaVITYASSYIKGLSYS--APNpinpsatvallTGLGILLAAILIVAFFALNYAGV 175
                                       ************99988876665677777777544333..122344557777778899999**************** PP

                     AA_permease_2 138 kesakiqnilgilkillpliiliilglitvdgggfsslstetdtffpngwp.gvllglli..vlwsfdGfesaanvs 211
                                       ++++k ++ ++++k+++p i+++ l++++++ + f+s+  + + f+p+ ++ +++ + ++  +++sf Gf  a  + 
  gi|518652536|ref|YP_008142056.1| 176 RIMGKTNTGMTWWKLIIPSITIVMLAFLVFHTSNFTSP--ALGGFLPGNNSaTIFEAVSTdgIVFSFLGFRQALDYG 250
                                       *****************************988888744..3333555533313455555566*************** PP

                     AA_permease_2 212 eevkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsv................aalffeavg.. 268
                                        e+k+  k +p+a+++++l+ +v+y+l++++f+g++ + ++a  +++ ++                +a +++ +g  
  gi|518652536|ref|YP_008142056.1| 251 GEAKTpqKSIPRATIFSVLTGIVVYVLLQVVFIGAIDPTKLAAAGGWFGLvsstpttyaasvvaapFAFLAKSSGif 327
                                       **8766599********************************777776665566777788888755555555555544 PP

                     AA_permease_2 269 gk.vvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllas 343
                                       +  v+++++++ + +s +g +n +  +s+r+l+ la+ g++P+ ++ v+ k++ p+  iil++i+ +i+l  f    
  gi|518652536|ref|YP_008142056.1| 328 ALvVLTYVLYADAYVSPAGTLNVYAGTSTRTLFGLAEIGYFPKQLSVVSkKTHVPVLPIILSVIIGIIFLAPFP--- 401
                                       224666677777777**********************************9****************77765553... PP

                     AA_permease_2 344 saaynfllsvsslgliisyllliigalilrkkrphlkrpgk.......ilvaiigalfllfl 398
                                         + ++l+ + + +  + y++   ++++lr+    lkrp k       +++a+iga ++++ 
  gi|518652536|ref|YP_008142056.1| 402 --SWYALVGLITGATAFTYIVGGSALMVLRREADALKRPFKlpfakilAPIAFIGATLIVYW 461
                                       ..589*********************************555344433334444444444443 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.18
                     AA_permease_2  85 wfayvpvlasilsvaasyllnalgp...........dlqgntwltyliaiaililvalinirgikesakiqnilgil 150
                                       ++ y+ ++++i ++a++ +l+++              ++++++ + + + +++++++l++++g   ++  ++    +
  gi|518652536|ref|YP_008142056.1| 457 LIVYWSGWPTIPYLAIGIFLGIVVYliilathkvenVFTKENIKAGWWVPGFILVLTLLSYLGEGDYGGTNTLPYPY 533
                                       67777778887777777777765224555556666655667888899999999999999999999999999999999 PP

                     AA_permease_2 151 killpliiliilglitvdgggfssl 175
                                        +++++i++ii+ li ++ g+ +++
  gi|518652536|ref|YP_008142056.1| 534 DFVVVIIVAIIFYLISIRSGYRTEE 558
                                       9999999999999988888888765 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1  59.2   8.1e-31   3.6e-27       2     416 ..      30     453 ..      29     490 .. 0.77
   2 !    5.8   5.5   0.00097       4.3      79     169 ..     463     558 ..     460     573 .. 0.70

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 8.1e-31
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       + + +lgg+iG g +++ +  +++ Gp +a+l+++++gv++++++l  +e+ +++p++g+++ y + ++g  +G + 
  gi|518652536|ref|YP_008142056.1|  30 LYFLSLGGIIGSGWLFAAAASAGTTGP-AAILSWIIGGVIVLFIALVYAELGSMIPRTGAISRYGHYSHGGVAGLFF 105
                                       56899**********************.888********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwel.vtdlpkawvt.....................gavflvvlliinlvgvk 133
                                       G+ y++s + v a+e   a+ +i+++++ ++ l+   +                      +a+++v+++++n++gv+
  gi|518652536|ref|YP_008142056.1| 106 GWTYFLSAVSVPAIE---AEAVITYASSyIKGLS---YSapnpinpsatvalltglgillAAILIVAFFALNYAGVR 176
                                       *************99...7777777744233333...33457888999999************************** PP

                       AA_permease 134 vygeaefilalikiiaiiafiivg..iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfviv 208
                                         g++ + +++ k+i+  ++i+++   +++++  ++++         g     +lp++   ++   f ++      +
  gi|518652536|ref|YP_008142056.1| 177 IMGKTNTGMTWWKLIIPSITIVMLafLVFHTSNFTSPA--------LG----GFLPGN---NSATIFEAV--STDGI 236
                                       **************999999999976666666666666........23....345555...222233332..34569 PP

                       AA_permease 209 vfaftGielvaiiagEvkdPeksiPkailqvviritifYv..............lsllligllvprndlgllndsas 271
                                       vf+f G+      +gE+k P+ksiP+a+++ v++ +++Yv              l+++   ++++ + ++  ++s++
  gi|518652536|ref|YP_008142056.1| 237 VFSFLGFRQALDYGGEAKTPQKSIPRATIFSVLTGIVVYVllqvvfigaidptkLAAAGGWFGLVSSTPTTYAASVV 313
                                       9***************************************7777777777777666666666666666666666665 PP

                       AA_permease 272 aaspfvifikesgvsvlapl...inaviltaalssansslysasRvlyslakdglaPkvlkkvskr.gvPlraills 344
                                       a  pf    k+sg+ +l +l   ++a  +++  +++n +  +++R+l+ la+ g++Pk l++vsk+ +vP+  i+ls
  gi|518652536|ref|YP_008142056.1| 314 A-APFAFLAKSSGIFALVVLtyvLYADAYVSPAGTLNVYAGTSTRTLFGLAEIGYFPKQLSVVSKKtHVPVLPIILS 389
                                       5.9**********97776651115566788888899999999***************99988875439********* PP

                       AA_permease 345 miisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvi 416
                                        ii+ ++l  a + +        l+ + + ++ +++++   +++++R++  + +r   +l+f   l+p  +i
  gi|518652536|ref|YP_008142056.1| 390 VIIGIIFL--APFPSW-----YALVGLITGATAFTYIVGGSALMVLRREADALKRPF-KLPFAKILAPIAFI 453
                                       ********..333333.....333444444555667777777777777766666633.44444444444333 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00097
                       AA_permease  79 Gln...ylfswitvlaleltaasiliqfwel.vtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaii 151
                                       G+    yl  +i+  ++ + ++  + +  +  +++++ka  ++  f++vl++++++g   yg + ++  ++ ++ +i
  gi|518652536|ref|YP_008142056.1| 463 GWPtipYLAIGIFLGIVVYLIILATHKVENVfTKENIKAGWWVPGFILVLTLLSYLGEGDYGGTNTLPYPYDFVVVI 539
                                       555444666666666666555544444444448999999999999**********************7777666666 PP

                       AA_permease 152 afiivg.iillaggkpnkg 169
                                       ++ i++  i++ +g ++++
  gi|518652536|ref|YP_008142056.1| 540 IVAIIFyLISIRSGYRTEE 558
                                       6655555666666666655 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.7   4.9e-07    0.0022       3      66 ..      26      89 ..      24     123 .. 0.80
   2 ?    0.0   4.5     0.066     3e+02     130     234 ..     172     286 ..     149     294 .. 0.62
   3 ?   -2.9   0.3      0.52   2.3e+03      74      80 ..     389     395 ..     370     427 .. 0.59
   4 ?    1.2   1.8      0.03   1.3e+02     189     232 ..     475     519 ..     466     545 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.9e-07
                    Spore_permease  3 stkqlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektli 66
                                      +t  l +l    ++G+g l+++++ a +++p + +s +++g+i+l+++l++ +l + +p    i
  gi|518652536|ref|YP_008142056.1| 26 NTWDLYFLSLGGIIGSGWLFAAAASAGTTGPAAILSWIIGGVIVLFIALVYAELGSMIPRTGAI 89
                                      5666778888899*****************************************9998876555 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.066
                    Spore_permease 130 vkGieslar......eflfiivilliilllillfslklaeiknlrPvl.gngikpvlks..lkttslsflgveilll 197
                                       + G++ + +         +ii+ ++i++l++l+f+++ +    l   l gn    ++++  +  +++sflg+  +l 
  gi|518652536|ref|YP_008142056.1| 172 YAGVRIMGKtntgmtWWKLIIPSITIVMLAFLVFHTSNFTSPALGGFLpGNNSATIFEAvsTDGIVFSFLGFRQALD 248
                                       55666666653322223345555666666666666665555555544423445556666656778999999999998 PP

                    Spore_permease 198 lvpflkdkkk.vkkaallgvlistllyllttlivilvl 234
                                       +    k ++k + +a++ +vl+ +++y+l+ ++ i++ 
  gi|518652536|ref|YP_008142056.1| 249 YGGEAKTPQKsIPRATIFSVLTGIVVYVLLQVVFIGAI 286
                                       88888876541568888899999999999988888775 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.52
                    Spore_permease  74 gkwLGsl 80 
                                         ++G +
  gi|518652536|ref|YP_008142056.1| 389 SVIIGII 395
                                       1111111 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.03
                    Spore_permease 189 flgveillllvpflkdkkkvkkaal.lgvlistllyllttlivil 232
                                       flg++++l+++   k ++ + k  +  g ++++++++lt+l +++
  gi|518652536|ref|YP_008142056.1| 475 FLGIVVYLIILATHKVENVFTKENIkAGWWVPGFILVLTLLSYLG 519
                                       888899999888888888877765515567788888888877765 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 ?   -3.3   6.2       1.9   8.6e+03      95     140 ..      32      75 ..      15      78 .. 0.51
   2 ?   -7.9  17.0         4   1.8e+04      53     137 ..     155     278 ..     103     282 .. 0.62
   3 ?    0.1   7.2      0.17   7.6e+02      28      85 ..     261     319 ..     259     363 .. 0.63
   4 !   17.5  12.2   7.2e-07    0.0032      26     139 ..     377     486 ..     370     490 .. 0.77
   5 ?   -1.2   0.8      0.42   1.9e+03     122     137 ..     534     549 ..     501     553 .. 0.66

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 1.9
                   Polysacc_synt_C  95 llaalvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                       +l+  ++ +  +l++      ++++  a +l+ ++g+++ l+++l+
  gi|518652536|ref|YP_008142056.1|  32 FLSLGGIIGSGWLFAAAASAGTTGP--AAILSWIIGGVIVLFIALV 75 
                                       3333333333332222222222222..6666666777777666664 PP

  == domain 2  score: -7.9 bits;  conditional E-value: 4
                   Polysacc_synt_C  53 fgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla.......... 119
                                       +gi+ aai +v+ +++  +   ++ +  +g+ +  ++ ++ p +  ++++ +v++  +++ +    a          
  gi|518652536|ref|YP_008142056.1| 155 LGILLAAILIVAFFALNYAGVRIMGKTNTGMTW--WKLII-PSITIVMLAFLVFHTSNFTSP----Alggflpgnns 224
                                       333334444444444444444444444444444..44443.222222222223333333333....22334667777 PP

                   Polysacc_synt_C 120 ..................................al..alllavlvgalvYlll 137
                                                                         ++  a++++vl g++vY+ll
  gi|518652536|ref|YP_008142056.1| 225 atifeavstdgivfsflgfrqaldyggeaktpqkSIprATIFSVLTGIVVYVLL 278
                                       777777777777777777777777778888777766678888888888888876 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.17
                   Polysacc_synt_C  28 qkialkalvigalvklilnllliplfgivG.aaiatvlallvvavlnlyalrrllgikl 85 
                                       +++++ +++ g++v ++l++++i  +  +  aa++  ++l+ ++   + a      + +
  gi|518652536|ref|YP_008142056.1| 261 PRATIFSVLTGIVVYVLLQVVFIGAIDPTKlAAAGGWFGLVSSTPTTYAASVVAAPFAF 319
                                       57889999999999999999999777654435555555555555555555555555555 PP

  == domain 4  score: 17.5 bits;  conditional E-value: 7.2e-07
                   Polysacc_synt_C  26 grqkialkalvigalvklilnllliplfgivG.aaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvm 101
                                       ++++ +++ +++++++ +i+  ++  ++ +vG +  at+++++v+   ++++ r    +k  +   + k+l+  +++
  gi|518652536|ref|YP_008142056.1| 377 KKTHVPVLPIILSVIIGIIFLAPFPSWYALVGlITGATAFTYIVGGSALMVLRREADALKRPFKLPFAKILAPIAFI 453
                                       6889999999**********************889999999999988776666666666664455555766666666 PP

                   Polysacc_synt_C 102 givvylllllllgllllaalalllavlvgalvYlllll 139
                                       g+ ++ +++   ++++     l++++++g++vYl++l 
  gi|518652536|ref|YP_008142056.1| 454 GATLI-VYWSGWPTIP----YLAIGIFLGIVVYLIILA 486
                                       66633.5555555444....89************9986 PP

  == domain 5  score: -1.2 bits;  conditional E-value: 0.42
                   Polysacc_synt_C 122 alllavlvgalvYlll 137
                                        +++ ++v++++Yl+ 
  gi|518652536|ref|YP_008142056.1| 534 DFVVVIIVAIIFYLIS 549
                                       4566666777777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.36s 00:00:01.04 Elapsed: 00:00:00.47
# Mc/sec: 3726.04
//
Query:       gi|518652537|ref|YP_008142057.1|  [L=143]
Description: transcription elongation factor NusA-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-08   33.3   0.9      2e-06   27.8   0.0    2.2  2  KH_5      NusA-like KH domain
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.049   13.5   0.0    1.4  1  KH_4      KH domain
       0.13   11.7   0.0       0.16   11.4   0.0    1.2  1  Sp38      Zona-pellucida-binding protein (Sp38)


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 !   27.8   0.0   3.4e-10     2e-06       2      68 ..      32      92 ..      31      93 .. 0.96
   2 !    4.4   0.2    0.0066        39      18      37 ..     110     129 ..      96     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 3.4e-10
                              KH_5  2 GertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68
                                      +e++ ++V +h+     ++ i++k   +i  ++ ++ +++i   e+s+Dl +f +n+++++ v++++
  gi|518652537|ref|YP_008142057.1| 32 EEMVLFVVGEHK-----LADIFKKHENIIADLKAKI-NKRIVMAEFSPDLLTFTKNLFYRYGVNEIN 92
                                      68999*******.....*******************.****************************98 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0066
                              KH_5  18 pvGaivgkkGsrikavsseL 37 
                                        +G+++gk  ++ik   + +
  gi|518652537|ref|YP_008142057.1| 110 NIGKAIGKDSRNIKLMRDAI 129
                                       49***********9666555 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.3e-06     0.049       6      60 ..      77     131 ..      74     137 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.3e-06
                              KH_4   6 dilkalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAlqylvsa 60 
                                       ++ k+l+      e+++  +++ ++i + +++e++G+ IGk+ r+++ ++  +s+
  gi|518652537|ref|YP_008142057.1|  77 TFTKNLFYRYGVNEINLIWKDNITNIFVGIAPENIGKAIGKDSRNIKLMRDAISR 131
                                       56677776667778888889999*******************9999988876665 PP

>> Sp38  Zona-pellucida-binding protein (Sp38)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.6e-05      0.16      23     105 ..      52     142 ..      32     143 .] 0.76

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.6e-05
                              Sp38  23 dklisdlscevselsykchsvkiqrrglqselfiafqvnpfapgwkdlcns...sldtedt......tnkrllkakd 90 
                                       +++i+dl  ++++      +   +   ++++lf  + vn +   wkd  ++    +  e+        +++++  +d
  gi|518652537|ref|YP_008142057.1|  52 ENIIADLKAKINKRI-VMAEFSPDLLTFTKNLFYRYGVNEINLIWKDNITNifvGIAPENIgkaigkDSRNIKLMRD 127
                                       667788877765543.33445556678999****************98776433445566599999999******** PP

                              Sp38  91 rieeffrkqveilkk 105
                                        i ++f+ +  i+k+
  gi|518652537|ref|YP_008142057.1| 128 AISRYFKIKNVIIKQ 142
                                       *******99888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1084.52
//
Query:       gi|518652538|ref|YP_008142058.1|  [L=505]
Description: hypothetical protein FACI_IFERC00001G1177 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-57  195.5   0.7    1.6e-57  195.0   0.7    1.3  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0   0.7   8.7e-62   1.6e-57      66     265 ..     118     450 ..       9     452 .. 0.87

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 8.7e-62
                                       S........................................................B--TT-BHHHHHHHHHHHHH CS
                                       x........................................................xxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5  66 g........................................................lvepGeavGiiaaQSiGePg 86 
                                       +                                                         ++p eavGiiaaQSiGePg
  gi|518652538|ref|YP_008142058.1| 118 EafhlsteatsimedaesrgykipvsianklvkyrkafpdskyekllervdrelrkrEIDPFEAVGIIAAQSIGEPG 194
                                       155555555555555566666666666666666666667777777777777777777899***************** PP

                                       HCCCSSTTSSTCSSTSSSSSSHHHHHHHHTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE............. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
                    RNA_pol_Rpb1_5  87 TQltlnTFHfaGvasknvtlGvprlkeilnvskniksksltvllvdeeakelekakkvkkaiek............. 150
                                       TQ+t++TFHfaGv ++nvtlG+prl ei+++ ++ +++s+t++l++++ k+ +k++++ k++e+             
  gi|518652538|ref|YP_008142058.1| 195 TQMTMRTFHFAGVVEMNVTLGLPRLIEIVDARRIPSTPSMTIYLTEKYRKDENKVRELIKNLENttiidvaeivtdv 271
                                       ********************************************************999999999************ PP

                                       .....................................................................CBTTEEEE CS
                                       .....................................................................xxxxxxxx RF
                    RNA_pol_Rpb1_5 151 .....................................................................gikkikri 158
                                                                                                            g++ki+r+
  gi|518652538|ref|YP_008142058.1| 272 gnmeltirmdsnksrdrlvsigdilsalekrkgiifaqvddsnisiklqqesfkslyqvqeqlkstpikGVNKISRA 348
                                       ***************************************************************99955555555555 PP

                                       EEEEEEEEEEETEEEEEEECS--HHHHTTSTTTBETTTEEESSHHHHHHHHCHHHHHHHHHHHHHHHHHHTTS---H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 159 lvkeaekgkeeekelvletegvnlsevlkveevvdageilsndiaeileilgieaarkallkeiqevykvqgvsvnd 235
                                       + +     +++e+ +v+ t+g nl+evl++e+ vd +++++ndi ei +++gieaar+a+++e ++++++qg++v++
  gi|518652538|ref|YP_008142058.1| 349 IAR----IDPKEDAWVIYTQGSNLREVLNIEG-VDSNRTTTNDIIEIENVFGIEAARNAIYREAENTLSEQGLNVDK 420
                                       554....3344468******************.******************************************** PP

                                       HHHHHHHHHHTTTSS---SSTTCHCCSSSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5 236 rHlelivdqmtkkgeivavnrsGinkaels 265
                                       rHl+l++d+mt+ g + av+r+Gi  +++s
  gi|518652538|ref|YP_008142058.1| 421 RHLMLVADMMTFSGAVRAVGRQGISGRKSS 450
                                       ************************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      572  (0.0319036); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3679.51
//
Query:       gi|518652539|ref|YP_008142059.1|  [L=887]
Description: hypothetical protein FACI_IFERC00001G1178 [Ferroplasma acidarmanus fer1]
Scores for complete 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-98  328.4   0.0    6.5e-98  327.9   0.0    1.2  1  RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
    6.3e-60  202.2   0.0    9.6e-60  201.6   0.0    1.3  1  RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
    4.5e-31  107.9   0.0    7.9e-31  107.1   0.0    1.4  1  RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
    4.2e-24   85.4   0.1    8.4e-24   84.4   0.1    1.5  1  RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
    6.8e-23   80.7   0.0    1.5e-22   79.6   0.0    1.6  1  RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
  ------ inclusion threshold ------
        1.4    9.0   3.3         22    5.3   0.1    3.1  3  Zn-ribbon_8     Zinc ribbon domain


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 !  327.9   0.0  2.2e-101   6.5e-98       2     312 .]       8     315 ..       7     315 .. 0.90

  Alignments for each domain:
  == domain 1  score: 327.9 bits;  conditional E-value: 2.2e-101
                                       E---EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTTT-----EEEEEEC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1   2 kkikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkkeCeghfGhieLak 78 
                                       k+i++i+f ++sp+eirk+S+++v +++t++++   P e Gl+D ++g+i+  l+C+tCg k  eC+ghfGhieLa+
  gi|518652539|ref|YP_008142059.1|   8 KRIEKIKFALLSPDEIRKMSQIRVITPDTYDDDG-YPIERGLMDLHMGVIEPGLKCATCGGKVDECPGHFGHIELAM 83 
                                       89******************************95.9***************************************** PP

                                       EEE-HHHHHHHHHHCTTCETTTTEBSS-TT.....SH....HHHHHHCSSSCCCCHHHHHHHHCCS-BE-SSSSB-E CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1  79 Pvfhigffklilkilecvckecskllldee.....kkkllsklkkrekleelkkrlkaieelckkinlcekCgavqp 150
                                       Pv+higf+k+i+++l+  ckec+++ l++      + +++s + +++  e + + lk+i ++  + n+c +C  ++p
  gi|518652539|ref|YP_008142059.1|  84 PVVHIGFIKEIKTMLDASCKECGRIKLTDDeinnyRTQISSVDFETTDPEIIDMTLKKILDVAIQRNICPHCSSESP 160
                                       ***************************99833333222333333444444455999999999999999999997776 PP

                                       EEEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 151 kleeegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldgg 227
                                       k+      + ++  + +e    k++++++++ l+ri+d+d+ + g++s  +rPew+iltvlPVpP ++RPs++l++g
  gi|518652539|ref|YP_008142059.1| 161 KV------ILDKPTTFRE-GGIKITPKEIRERLERIPDNDLLFFGINSTAARPEWMILTVLPVPPIDVRPSITLETG 230
                                       66......2222222222.456899**************************************************** PP

                                       SEEBECCCCHHHHHHHHHHHHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_1 228 rrsedDlteklrdiikrNnrLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGK 304
                                       +rsedDlt+kl+dii++ +rL++ +++g p+liie+ ++lLQ+h++t+fdn+ +g++pa+++s+r lk+l qrLkGK
  gi|518652539|ref|YP_008142059.1| 231 ERSEDDLTHKLVDIIRISQRLRESRDNGSPQLIIEDLWDLLQYHITTYFDNQTAGIPPARHRSGRALKTLVQRLKGK 307
                                       ***************************************************************************** PP

                                       SSCCCCCT CS
                                       xxxxxxxx RF
                    RNA_pol_Rpb1_1 305 eGrfRgnL 312
                                       eGrfR nL
  gi|518652539|ref|YP_008142059.1| 308 EGRFRANL 315
                                       *******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 !  201.6   0.0   3.2e-63   9.6e-60       1     166 []     317     490 ..     317     490 .. 0.93

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 3.2e-63
                                       SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTT.SSS......SEEEEESTTSS CS
                    RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpe.vyP......gasyvkredgs 70 
                                       Gkrv++s+Rsvisp+p l+++evg+P + a+ ltvp  ++++ni+k+++ +++g     P      g +y++r dg+
  gi|518652539|ref|YP_008142059.1| 317 GKRVNFSSRSVISPEPFLSMNEVGIPEVAARELTVPVLINSFNIDKMKEWIKRGTApRTPdgkylaGINYLIRPDGR 393
                                       9***************************************************99752233222222889999***** PP

                                       EEETTTT-SC.HHCCTTTTSEEEEE--TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EE CS
                    RNA_pol_Rpb1_2  71 ekklkakkrk.lakelekgdiverhvkdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDem 146
                                       + kl+ ++++  ++++ +g++ver++++gd+vl+NRqPsLh++s+mah v+vl++ t+r+nls +t+yNaDFDGDem
  gi|518652539|ref|YP_008142059.1| 394 RIKLTDQNAEiNSDRIDIGWTVERQMTEGDIVLFNRQPSLHRMSMMAHAVRVLPGMTFRFNLSDCTPYNADFDGDEM 470
                                       *******99538899************************************************************** PP

                                       EEE--SSHHHHHHHHHCSBT CS
                    RNA_pol_Rpb1_2 147 nlhlpqseearaEaeelllv 166
                                       nlh+ qsee+raEa+ ++ v
  gi|518652539|ref|YP_008142059.1| 471 NLHVIQSEESRAEARIIMKV 490
                                       ***************99975 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 !  107.1   0.0   2.6e-34   7.9e-31       1     156 [.     493     657 ..     493     658 .. 0.91

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 2.6e-34
                                       CSEETTTTEESSS--THHHHHHHHHSSTTEEEEHHHHHHHHHHSSSCCSSSSSSSSSBESS.SEBEEHHHHHHCCCH CS
                    RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTkedvfidreeaqqllykgvgsdsktvtlrpailkp.kelwtgkqtfsrilp 76 
                                       +i+sp+ g P+ig ++D++++++llT+++ +i++++ ++ ++++       ++l+ +++k  k+ + g+++fs+ilp
  gi|518652539|ref|YP_008142059.1| 493 QIMSPRFGGPIIGAIHDHITSLFLLTHNNPLISEDDTLHTVSYIE-----FDRLPEPVIKDgKKYYHGRDIFSLILP 564
                                       79******************************************4.....455666666666*************** PP

                                       CCCCEEEE.....SSSS...........STSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHH CS
                    RNA_pol_Rpb1_3  77 neinyerk.....neek...........dgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldsl 137
                                       + +n++ k                    d++v+i +g l++G+id+++vg    g +++ ++++ g++++++f+ds+
  gi|518652539|ref|YP_008142059.1| 565 EGLNVKFKshlcaG--AkdkceyeddpaDTYVVITDGKLVHGTIDDEAVG-PFSGVIVDKIFRNIGPQAAAKFIDSV 638
                                       *9999998765551..0456778999************************.777*********************** PP

                                       HHHHHHHHHHHCEB-TGGG CS
                    RNA_pol_Rpb1_3 138 qrlgfkyllqsgftigigD 156
                                       +rl+ ++l ++gf++gi+D
  gi|518652539|ref|YP_008142059.1| 639 TRLAVGFLSHRGFSTGIKD 657
                                       ******************9 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 !   84.4   0.1   2.8e-27   8.4e-24       1      66 [.     796     861 ..     796     875 .. 0.97

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 2.8e-27
                                       B--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb1_5   1 GLkvkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg 66 
                                       GL+++e+ffh+ ggReGL+D Av+T++sGY+qRrl++a ed+ v++ + v ++ g++vqf+ygedg
  gi|518652539|ref|YP_008142059.1| 796 GLNPTEYFFHSIGGREGLVDIAVRTSRSGYMQRRLINAFEDLKVNETRRVEDTIGSVVQFKYGEDG 861
                                       9****************************************************************8 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 !   79.6   0.0   4.9e-26   1.5e-22       6     108 .]     687     789 ..     682     789 .. 0.96

  Alignments for each domain:
  == domain 1  score: 79.6 bits;  conditional E-value: 4.9e-26
                                       THTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBS CS
                    RNA_pol_Rpb1_4   6 rygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkr 82 
                                       r+g+l++lpg+s+e+++e +i +    +rd++gkias++l  + + +iM++sGa+  ++ni+ +ag++Gqq+v+g r
  gi|518652539|ref|YP_008142059.1| 687 RSGQLQPLPGRSVEDTLEVEILSSTGGVRDESGKIASQYLGLNDPSVIMARSGARAKMLNIAEVAGMVGQQSVRGGR 763
                                       569***************999999999**************879********************************* PP

                                       S--SSTSCSSTTSSSSESSTTTSSEE CS
                    RNA_pol_Rpb1_4  83 ipkgfsgrtlphfkkidespesrGFv 108
                                        ++g+ +rtl hfk++d ++ +rGF+
  gi|518652539|ref|YP_008142059.1| 764 LNRGYANRTLSHFKENDLGAYARGFI 789
                                       *************************8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.3      0.23   6.8e+02      25      36 ..      58      69 ..      50      74 .. 0.70
   2 ?    1.6   0.0       0.1   3.1e+02      28      35 ..     100     109 ..      87     112 .. 0.70
   3 ?    5.3   0.1    0.0074        22      28      40 .]     150     163 ..     139     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.23
                       Zn-ribbon_8 25 pltaCPeCgsev 36
                                      p  +C +Cg++v
  gi|518652539|ref|YP_008142059.1| 58 PGLKCATCGGKV 69
                                      555688888765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.1
                       Zn-ribbon_8  28 a.CPeCgs.e 35 
                                       a C+eCg  +
  gi|518652539|ref|YP_008142059.1| 100 AsCKECGRiK 109
                                       3399998765 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0074
                       Zn-ribbon_8  28 a.CPeCgsevrrvi 40 
                                         CP+C se  +vi
  gi|518652539|ref|YP_008142059.1| 150 NiCPHCSSESPKVI 163
                                       34****99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (887 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:                        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: 0.67u 0.25s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 6292.68
//
Query:       gi|518652540|ref|YP_008142060.1|  [L=1195]
Description: hypothetical protein FACI_IFERC00001G1179 [Ferroplasma acidarmanus fer1]
Scores for complete 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-127  423.7   0.0     1e-126  423.1   0.0    1.3  1  RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
    2.6e-35  121.8   0.0    1.6e-33  116.0   0.0    2.4  1  RNA_pol_Rpb2_1  RNA polymerase beta subunit
    3.2e-26   91.6   0.2    2.1e-25   89.0   0.0    2.5  3  RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
    1.5e-25   89.9   0.3    3.3e-25   88.9   0.3    1.6  1  RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
    1.8e-25   88.9   0.1    3.9e-25   87.8   0.1    1.6  1  RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
      5e-22   78.0   0.5    1.3e-21   76.6   0.5    1.8  1  RNA_pol_Rpb2_4  RNA polymerase Rpb2, domain 4
    5.4e-11   42.9   0.2    1.5e-10   41.4   0.2    1.8  1  RNA_pol_Rpb2_5  RNA polymerase Rpb2, domain 5
  ------ inclusion threshold ------
      0.017   15.0   2.9          5    7.1   0.8    2.6  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.057   13.4   1.3        1.6    8.7   0.1    2.8  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.097   12.6   0.1       0.42   10.6   0.0    2.0  2  gpD             Bacteriophage scaffolding protein D
       0.18   11.4   6.3       0.32   10.6   1.7    2.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.18   11.9   1.6        2.4    8.3   0.1    2.8  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain
       0.43   10.6   3.6         10    6.2   0.1    3.3  3  Ogr_Delta       Ogr/Delta-like zinc finger
       0.86    9.1   5.7         12    5.4   0.1    3.2  3  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.1   0.0  8.2e-130    1e-126       1     390 []     724    1096 ..     724    1096 .. 0.95

  Alignments for each domain:
  == domain 1  score: 423.1 bits;  conditional E-value: 8.2e-130
                                        HHHT-SS-TTB-HHHHHHHHHHGGGB-S---TTTTT---SSEEEESS----SSB-S.TTTTTS........GGGS CS
                    RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqalgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvldgpatekgel 75  
                                        va+l+p++eh++spri+i +am kq++g+ ++n+  r++++ +ll+++q Plv+t+  +++++        + + 
  gi|518652540|ref|YP_008142060.1|  724 VASLIPYPEHNSSPRITIASAMIKQSIGLPQANYRIRTDTRGHLLHYPQIPLVTTK-VMDFIK--------YRRK 789 
                                        699*****************************************************.999999........**** PP

                                        -SEEEEEBBBS--TTTTTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..-.....-SS-GGG CS
                    RNA_pol_Rpb2_6   76 alGqnavVAvmsyeGYniEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnv.....seealkk 145 
                                        ++Gqn+vVA++sy+GYn+ Daii+n+++++r++ +s ++++y+ e r++++g+e+ ++ ++++      ee +k+
  gi|518652540|ref|YP_008142060.1|  790 PAGQNFVVAIVSYHGYNMQDAIIMNKASIERGLGRSSFFRTYTAEERRYPGGQEDKFEIPSHDvlgarAEEYYKN 864 
                                        *****************************************************88787777768***99****** PP

                                        S-TTSB--SS-EEETT-EEE---..B-----...-----------..-B---EE--TT-EEEEEEEEE....... CS
                    RNA_pol_Rpb2_6  146 LdedGivrvgaevkegdilvgkvtkgeteltpeekllraifgekarevkdtslrvksgeegvVdkvkvfsrekgd 220 
                                        Lde+Gi+ ++++v+  d+lvgk+  ++ ++ +ee+    + g  +   +++s++v+++e+g+Vd+v +       
  gi|518652540|ref|YP_008142060.1|  865 LDENGIIFPESKVEGSDVLVGKT--SPPRFLEEENAD--KLGPLR--RRESSVTVRPTESGYVDNVFL------- 926 
                                        **********************8..888887554432..233333..589******************....... PP

                                        EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEEB-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHH CS
                    RNA_pol_Rpb2_6  221 elkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvslilpqeDmPfledGivvDivlNPlgvPSRmtigqllEt 295 
                                        + +++ ++++kv+v++ R +q GDKfasrhGqKGv+++++ qeDmPf+edGi++D+++NP++vPSRmt+g++lE+
  gi|518652540|ref|YP_008142060.1|  927 TVSESNSRIIKVKVRSDRIPQPGDKFASRHGQKGVIGYVAAQEDMPFTEDGIIPDLLFNPHSVPSRMTLGHVLEM 1001
                                        8899999******************************************************************** PP

                                        HHHHCCCSSSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS-- CS
                    RNA_pol_Rpb2_6  296 llgkaaalegkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKih 370 
                                        +  k++ ++g+++d+t+Fdg+ e  ++e+L++ g+++sG+ev+ydG+tG+k+e +if+GviYy+kL+h+v+ K+h
  gi|518652540|ref|YP_008142060.1| 1002 MGAKVSTMSGENIDSTIFDGEPERSLREQLKKYGFRESGNEVMYDGITGKKFEVDIFMGVIYYQKLHHMVASKFH 1076
                                        *************************************************************************** PP

                                        --SS--B-TTT--B-SCGGG CS
                    RNA_pol_Rpb2_6  371 aRstGpyslltqQPlgGkaq 390 
                                        aRs+Gp++ lt+QP++G+++
  gi|518652540|ref|YP_008142060.1| 1077 ARSRGPVQILTRQPTEGRSR 1096
                                        ******************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 !  116.0   0.0   1.2e-36   1.6e-33       4     201 ..      16     436 ..      13     438 .. 0.86

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 1.2e-36
                                       HHHHHHHHHH............................HHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEES CS
                                       xxxxxxxxxx............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1   4 sqqldSFnkf............................veqdlekiikeeaaieseeeiqssgeelelkfvsirlgk 52 
                                       + q+dS n+f                            ++ d+ k  +++ +i    e q+           i+++k
  gi|518652540|ref|YP_008142060.1|  16 NYQIDSMNYFyasknnpdnimqqivdetkisddatpgvIDLDPSKTKGKDIKIYFGRERQNG---KATGDPTIWVDK 89 
                                       56666666666666665555555544444444444443444444444444444433333321...22333579**** PP

                                       CSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCCTCCEEEEEEEEEEEEEXBTTSTTSSSTTS....... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...... RF
                    RNA_pol_Rpb2_1  53 PvvdesdasereiyPkearlrnltYsaplyvklklvvyekdnkeeikeeevyiGelPlMlrskacvlseas...... 123
                                       P ++e+++++++i+P+earlr+l Y ap++++l+ v     ++ e + + ++iGe+P+M+rsk c+lse++      
  gi|518652540|ref|YP_008142060.1|  90 PEIKEASGATNQITPQEARLRDLNYMAPIMLRLRIVE----DGIERDANTIKIGEIPVMVRSKICTLSEQNldlyie 162
                                       ************************************9....899**********************98653222222 PP

                                       ..........HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE................................... CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................... RF
                    RNA_pol_Rpb2_1 124 ..........eeelvelkEcpldqGGyFiinGtekvivaqek................................... 155
                                                 e++l  ++E+p+d+GGyFii G+e+viv++e+                                   
  gi|518652540|ref|YP_008142060.1| 163 knngpidetrENKLRYVDEDPTDPGGYFIIGGSERVIVSLEDlapnkilveyeekydsrvevakifsqksgfralis 239
                                       2223333333789999************************************************************* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                    RNA_pol_Rpb2_1 156 ............................................................................. 155
                                                                                                                    
  gi|518652540|ref|YP_008142060.1| 240 mekgsdgiinvsiptvagtiplvilmkalgidkdvdiheaiytdprmdpliyaniedsrnlkilppnginnnedals 316
                                       ***************************************************************************** PP

                                       ..........................................................................XHH CS
                                       ..........................................................................xxx RF
                    RNA_pol_Rpb2_1 156 ..........................................................................laG 158
                                                                                                                 l G
  gi|518652540|ref|YP_008142060.1| 317 ylekrfaagqakefrdkkitqmldrallphlgddvsdrlkkaiylgrmarsllelnlgmrhvddkdhyankrikLSG 393
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                    RNA_pol_Rpb2_1 159 eLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpi 201
                                       +Ll +lfr++++++ +d+k +l+k+ +k++ + l+ +v+ + +
  gi|518652540|ref|YP_008142060.1| 394 DLLDELFRNAFQSVMKDLKYQLEKTYNKKRGIRLRPAVRQDLL 436
                                       ****************************998888888876655 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 ?   -2.6   0.0       6.1   7.8e+03      49      81 ..     509     541 ..     499     544 .. 0.80
   2 ?   -2.0   0.0         4   5.1e+03       3      22 ..     627     646 ..     627     649 .. 0.90
   3 !   89.0   0.0   1.6e-28   2.1e-25       1      85 [.    1098    1190 ..    1098    1192 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 6.1
                                       EBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBE CS
                    RNA_pol_Rpb2_7  49 eCkivkseekiekveipeafklLlqeLqslgia 81 
                                       +C +vk+ + i +v+      ++++eLq + i+
  gi|518652540|ref|YP_008142060.1| 509 NCGLVKNASLIINVTQGIDPDIVMEELQNMDIH 541
                                       688888888888888888888999999999885 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 4
                                       EEEEHHHHHHHHHHTBHHHH CS
                    RNA_pol_Rpb2_7   3 lrfGEMErdaliayGaaalL 22 
                                       lr+GE  +  li+ Ga + L
  gi|518652540|ref|YP_008142060.1| 627 LRMGEYTVNDLISSGAIEWL 646
                                       79**************8877 PP

  == domain 3  score: 89.0 bits;  conditional E-value: 1.6e-28
                                        BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESS..SSSCCCEE......EBTTTTCSSSEEEEEEEHH CS
                    RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgr..ckllaaan......eCkivkseekiekveipea 67  
                                        GGlrfGEMErd+lia+Ga++++k+rl+++SD + ++vcg+  c+++a+++      +C+ + ++ +i ++e+++a
  gi|518652540|ref|YP_008142060.1| 1098 GGLRFGEMERDTLIAHGASMVIKDRLLDQSDGTILYVCGNptCGHIAIYDfrkgtlRCPACGNTGNIYPIETSYA 1172
                                        9*************************************965599999999************************* PP

                                        HHHHHHHHHHTTBEEEEE CS
                    RNA_pol_Rpb2_7   68 fklLlqeLqslgialkll 85  
                                        fkl+ +eL s+gi ++l+
  gi|518652540|ref|YP_008142060.1| 1173 FKLMRDELSSMGIVMRLE 1190
                                        **************9986 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 !   88.9   0.3   2.5e-28   3.3e-25       2     190 .]     207     390 ..     206     390 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 2.5e-28
                                       TSCEEEEE-SSSSSE..SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHTS. CS
                    RNA_pol_Rpb2_2   2 sngiyvekekdknki..satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIlericy. 75 
                                        n+i+ve e++ +++  +a+  s ++  r++++ ++ +++++ ++ +++   ip+vi++kAlg+ +d +I e+i   
  gi|518652540|ref|YP_008142060.1| 207 PNKILVEYEEKYDSRveVAKIFSQKSGFRALISMEKGSDGIINVSIPTVAGTIPLVILMKALGIDKDVDIHEAIYTd 283
                                       68999999999999966666667777777778888888899999******************************964 PP

                                       ...SSTTHHHHHHHH.HHHHHHCTSSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHHCHHHHHHHTTTTSSTTTTTS CS
                    RNA_pol_Rpb2_2  76 ...dsedsqlleell.eeleekeeiqtqeealdyigkvvalrrgeearlqsareilqkrydlgeigreklnkhlgls 148
                                          d+  ++ +e+ +  +    + i + e+al+y+ k++a+++ +e r ++  ++l         +r  l+ hlg +
  gi|518652540|ref|YP_008142060.1| 284 prmDPLIYANIEDSRnLKILPPNGINNNEDALSYLEKRFAAGQAKEFRDKKITQML---------DRALLP-HLGDD 350
                                       44444333333333313445557799***********9999999999999999998.........8*****.***** PP

                                       SSTCHH...HHHHHHHHHHHHHHHHTTSSSS--TTSGGGEEEE CS
                    RNA_pol_Rpb2_2 149 eslenkr.lkaqdilymidrLlslklgrrevDDiDhlgnkRvr 190
                                        s   +r +ka +++ m++ Ll+l lg+r vDD+Dh++nkR++
  gi|518652540|ref|YP_008142060.1| 351 VS---DRlKKAIYLGRMARSLLELNLGMRHVDDKDHYANKRIK 390
                                       **...5667********************************96 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.1   3.1e-28   3.9e-25       1      68 []     458     522 ..     458     522 .. 0.97

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 3.1e-28
                    RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvsslrgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                                       q+ldr++ +s+lshlrr+ s+   l++++ ++e+Rdlhp++wGriCp eTPEG+ncGlvk+ +l ++v
  gi|518652540|ref|YP_008142060.1| 458 QLLDRTSNMSTLSHLRRIISP---LTRSQPHFEARDLHPTQWGRICPNETPEGQNCGLVKNASLIINV 522
                                       89*******************...*************************************9998765 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 !   76.6   0.5     1e-24   1.3e-21       1      62 []     552     613 ..     552     613 .. 0.99

  Alignments for each domain:
  == domain 1  score: 76.6 bits;  conditional E-value: 1e-24
                                       EECTT-BEEE-S-HCCHHHHHHHHCCTTSS-TT-EEEE-TTT--EEEE-SSEEB-EEEEE-S CS
                    RNA_pol_Rpb2_4   1 VfvNGrllGvtrdpkklvetlRelRRkgkiseevsivlnekqkevkiatDgGRvcRPliiVe 62 
                                       +++NG+ +G+++dp+ l++t+R+lRR+gk+s+ev++ ++++++ev i++D GR++RPl++V+
  gi|518652540|ref|YP_008142060.1| 552 IYLNGDFIGYHNDPAILTDTIRNLRRSGKLSNEVNVKYDSNTNEVIINCDRGRLRRPLFVVN 613
                                       7***********************************************************95 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 !   41.4   0.2   1.2e-13   1.5e-10       3      57 ..     636     716 ..     635     716 .. 0.89

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.2e-13
                                       HHHHTTSEEEEEHHHHTT--EESSTTTCSST.-SSTTTSS-.........................-TTSSSST-SE CS
                    RNA_pol_Rpb2_5   3 dLlregvvEylDaeEEetamIamtpedleks.reekealee.........................kenskshtyTH 53 
                                       dL+++g +E+lDaeEEe+a+I + p +++++ +++++ l +                          +n+ s  +TH
  gi|518652540|ref|YP_008142060.1| 636 DLISSGAIEWLDAEEEENAYISVFPFEFPDNcPDCGKVLYRdnvtwinpgnsdvtlecdechahfkGTNNLSMDHTH 712
                                       9************************999999999998777799999***********9999999994555555**** PP

                                       EES- CS
                    RNA_pol_Rpb2_5  54 cEIh 57 
                                       cEI+
  gi|518652540|ref|YP_008142060.1| 713 CEID 716
                                       ***7 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0043       5.5      27      56 ..     663     700 ..     645     702 .. 0.78
   2 ?    7.1   0.8    0.0039         5      32      55 ..    1138    1161 ..    1135    1163 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0043
                    OrfB_Zn_ribbon  27 TSktCseCgsknke........alsgrtfkCpnCgfea 56 
                                          +C+ Cg+++++         +s+ t++C++C +++
  gi|518652540|ref|YP_008142060.1| 663 FPDNCPDCGKVLYRdnvtwinpGNSDVTLECDECHAHF 700
                                       5568999**99999999999998999999999998875 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0039
                    OrfB_Zn_ribbon   32 seCgsknkealsgrtfkCpnCgfe 55  
                                        + Cg++  ++  + t++Cp+Cg +
  gi|518652540|ref|YP_008142060.1| 1138 PTCGHIAIYDFRKGTLRCPACGNT 1161
                                        78********************87 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 ?    2.6   0.1      0.11   1.4e+02      20      45 ..     666     698 ..     649     699 .. 0.67
   2 ?    8.7   0.1    0.0013       1.6      18      34 ..    1152    1169 ..    1138    1176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.11
                     Zn_Tnp_IS1595  20 vCPhCgsrkayrikt........rglfqCkeCrk 45 
                                        CP Cg+  +yr +            ++C eC++
  gi|518652540|ref|YP_008142060.1| 666 NCPDCGKV-LYRDNVtwinpgnsDVTLECDECHA 698
                                       59***965.3332223556677777788888876 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0013
                     Zn_Tnp_IS1595   18 gfvCPhCgsr.kayrikt 34  
                                        + +CP+Cg++  +y i+t
  gi|518652540|ref|YP_008142060.1| 1152 TLRCPACGNTgNIYPIET 1169
                                        367999999999998887 PP

>> gpD  Bacteriophage scaffolding protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8   3.6e+03      37      52 ..     593     608 ..     583     615 .. 0.83
   2 ?   10.6   0.0   0.00033      0.42      60      99 ..     780     816 ..     773     822 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                                       SSS---GGGHHHHHHH CS
                               gpD  37 snkvwiatdrsrarrc 52 
                                       +n v i  dr r rr 
  gi|518652540|ref|YP_008142060.1| 593 TNEVIINCDRGRLRRP 608
                                       689**********996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00033
                                       HHHHTT--SSSBBHHHHHHHHHHHS-HHHHHHHHHHHTTS CS
                               gpD  60 tldfvgyprfpapvefiaaviayyvhpvniqtaclimega 99 
                                        +df+ y r pa  +f+ a+++y  h  n+q a  im+ a
  gi|518652540|ref|YP_008142060.1| 780 VMDFIKYRRKPAGQNFVVAIVSY--HGYNMQDAI-IMNKA 816
                                       68********************9..788999885.55555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.12   1.5e+02      22      29 ..     667     674 ..     666     680 .. 0.68
   2 ?   10.6   1.7   0.00025      0.32       4      27 ..    1138    1160 ..    1133    1161 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.12
                                       ESSSSBEE CS
                      TF_Zn_Ribbon  22 CtdCGlVl 29 
                                       C+dCG Vl
  gi|518652540|ref|YP_008142060.1| 667 CPDCGKVL 674
                                       77777766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00025
                                        TTTTCEEC.HEETSTTCEEESSSSB CS
                      TF_Zn_Ribbon    4 PnCgstnl.veDpergelvCtdCGl 27  
                                        P Cg+  + ++D+  g+l+C++CG+
  gi|518652540|ref|YP_008142060.1| 1138 PTCGH--IaIYDFRKGTLRCPACGN 1160
                                        45665..159**************6 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   0.1    0.0019       2.4       3      14 ..     666     677 ..     666     679 .. 0.88
   2 ?    1.6   0.1      0.24   3.1e+02       3       9 ..    1154    1160 ..    1153    1161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0019
                            zf-ACC   3 KCpsCgemlykk 14 
                                       +Cp Cg +ly+ 
  gi|518652540|ref|YP_008142060.1| 666 NCPDCGKVLYRD 677
                                       6*********96 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.24
                            zf-ACC    3 KCpsCge 9   
                                        +Cp+Cg+
  gi|518652540|ref|YP_008142060.1| 1154 RCPACGN 1160
                                        6*****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 ?    6.2   0.1     0.008        10       1      40 [.     666     703 ..     666     711 .. 0.88
   2 ?    2.6   0.0       0.1   1.3e+02      24      35 ..    1131    1142 ..    1115    1145 .. 0.85
   3 ?    0.2   0.3      0.59   7.6e+02       1       8 [.    1154    1161 ..    1154    1164 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.008
                         Ogr_Delta   1 rCPhCgapaaartsrnlskdvreryyqCsnfeCgatfvaa 40 
                                       +CP Cg+  +  +++ + +   ++  +C+   C+a f+  
  gi|518652540|ref|YP_008142060.1| 666 NCPDCGKVLYRDNVTWINPGNSDVTLECDE--CHAHFKGT 703
                                       6******************99*******98..99999864 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.1
                         Ogr_Delta   24 ryyqCsnfeCga 35  
                                        + y+C n+ Cg+
  gi|518652540|ref|YP_008142060.1| 1131 ILYVCGNPTCGH 1142
                                        679********9 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.59
                         Ogr_Delta    1 rCPhCgap 8   
                                        rCP Cg+ 
  gi|518652540|ref|YP_008142060.1| 1154 RCPACGNT 1161
                                        7*****86 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.1    0.0097        12      18      26 .]     666     674 ..     665     677 .. 0.82
   2 ?   -2.7   0.1       3.6   4.6e+03       6      11 ..    1138    1143 ..    1138    1144 .. 0.80
   3 ?    5.0   0.3     0.013        17       2      10 ..    1152    1160 ..    1151    1161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0097
                       zf-ribbon_3  18 vCpyCGtkl 26 
                                       +Cp CG++l
  gi|518652540|ref|YP_008142060.1| 666 NCPDCGKVL 674
                                       788888876 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.6
                       zf-ribbon_3    6 PnCGap 11  
                                        P CG++
  gi|518652540|ref|YP_008142060.1| 1138 PTCGHI 1143
                                        889986 PP

  == domain 3  score: 5.0 bits;  conditional E-value: 0.013
                       zf-ribbon_3    2 tvrCPnCGa 10  
                                        t rCP+CG+
  gi|518652540|ref|YP_008142060.1| 1152 TLRCPACGN 1160
                                        569****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        75  (0.00418317); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.44
# Mc/sec: 8090.51
//
Query:       gi|518652541|ref|YP_008142061.1|  [L=86]
Description: DNA-directed RNA polymerase subunit H [Ferroplasma acidarmanus fer1]
Scores for 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   90.7   0.6    4.7e-26   90.5   0.6    1.0  1  RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb5_C  RNA polymerase Rpb5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.6   2.6e-30   4.7e-26       1      73 []       4      81 ..       4      81 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 2.6e-30
                                      ..-TSSSS--EEEEE-HHHHHHHHHHTT--TTCSS-EETTSHHHHCC.....T--TTSEEEEEEEETTTEEEEEEEEE CS
                    RNA_pol_Rpb5_C  1 vnitkHelvPkhevlseeekkellkklkikeeqLPkisksDpvaryl.....glkkGdvvkItrksetageavtYRlV 73
                                      +n+++He+vP+h+++  ee++++l+kl++++++LPki  +Dp +++l     +l +G+vvkI+rks+tag +++YR++
  gi|518652541|ref|YP_008142061.1|  4 FNVLEHEIVPEHHLVPVEEEESVLTKLNVTKDDLPKIGINDPTIKALeeihgKLVPGRVVKIIRKSPTAGYYEYYRVI 81
                                      7*********************************************999999************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 617.41
//
Query:       gi|518652542|ref|YP_008142062.1|  [L=338]
Description: hypothetical protein FACI_IFERC00001G1181 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-72  243.4   0.0      5e-72  242.5   0.0    1.4  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 !  242.5   0.0   2.8e-76     5e-72       2     282 .]      54     321 ..      53     321 .. 0.97

  Alignments for each domain:
  == domain 1  score: 242.5 bits;  conditional E-value: 2.8e-76
                                       S-SHHHHHHHHHHHHHHHHHHCCCSTHHHHHHHHHHHHHHHHTSSTS-HHHHHHHHHHHHHHHCCTTTSSHHHHHHH CS
                             IF-2B   2 vrGspaiaiaalevllevikdaktskvaeLkeelrkaidlLkkarPtavslgnairrllkeiselksssdvkeakks 78 
                                       vrG+pai+++a+++l+++ k+ +         +++ka++++ ++rPta +l+ ai+++++           +++++s
  gi|518652542|ref|YP_008142062.1|  54 VRGAPAIGVTAAYGLAMASKNME---------DMEKAVKTISSSRPTAYDLFKAIDFMKA-----------NNFSES 110
                                       89**************9999887.........9***************************...........455554 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTTC-TTEEEEEES--SH........HHHHHHHHHHTTEEEEEEEEEXTTTTHH CS
                             IF-2B  79 liekikelikeieeadekigdiaaelikdgdtilTicnskt........vlevlraaakekkkfkVivvEsrPrlqG 147
                                          ++++++ ei e  +kig+++ +li+ +d ilT+cn+++        +l+ +r a++++kk+ V+v E+rPrlqG
  gi|518652542|ref|YP_008142062.1| 111 ---AARRYALEITERSRKIGEYGNTLIQANDHILTHCNAGAlavvdwgtALAPMRIAHDSGKKIFVYVDETRPRLQG 184
                                       ...578899******************************************************************** PP

                                       .HTHHHHHHHTTXEEEEEEGGGHHHHHHC.TESEEEEEXSEEETTSEEEEETTHHHHHHHHHHTTXEEEEEXXGGGB CS
                             IF-2B 148 .rltakeLvqagipvtlitdsavayvmse.evdkvivGAdrilenGaiankiGTsslAvlAkefnipvlvvaeslkf 222
                                        +lta+eL+q+gi+  +i d+a++y+m++ +++ +ivGAdri++nG+ ankiGT++ AvlAk  nip++v+a+ ++f
  gi|518652542|ref|YP_008142062.1| 185 aKLTAWELQQEGIDYSIIADNAAGYFMKNgDINLAIVGADRIAANGDFANKIGTYEKAVLAKVNNIPFYVAAPGSTF 261
                                       ***************************************************************************** PP

                                       ESTSSSGGGSSXXBEXTHHHHEETTEESSTTTEEEEEBSEEEEEGGGXSEEEETTEEEXC CS
                             IF-2B 223 servqldedifieerdpeellnitgeriaeeelkvvnpafDvtPpelItliITevGvlpp 282
                                       +  ++++e i ieerd++e+l +++ r  ++e +  npafDvtP+e++t++ITe+G++ p
  gi|518652542|ref|YP_008142062.1| 262 DFSLKTGEGIPIEERDENEVLMVNNSRLGPAEGHAKNPAFDVTPHEYVTAFITEYGIFRP 321
                                       *********************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2168.61
//
Query:       gi|518652543|ref|YP_008142063.1|  [L=430]
Description: hypothetical protein FACI_IFERC00001G1182 [Ferroplasma acidarmanus fer1]
Scores for complete 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  135.6   0.1    8.4e-24   84.4   0.0    2.2  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.0   4.7e-28   8.4e-24       5     177 ..      57     222 ..      53     253 .. 0.84
   2 !   49.2   0.0   2.4e-17   4.3e-13     174     292 ..     292     407 ..     284     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.7e-28
                                       --EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHH.HHHHHHHTC CS
                      tRNA-synt_1b   5 plrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlena.ikaqlakgl 80 
                                       ++ +++G +P+g++HlG+ +++ +++++q+ g +v++ +aDl+ + ++        ++k++e + n  i ++++ gl
  gi|518652543|ref|YP_008142063.1|  57 KFNAMTGLMPSGQMHLGNKLSIDQIIYFQSLGADVYIAVADLESYATRGV-----GFKKAREIAINEyIANYISMGL 128
                                       67899*********************************************.....5555555555555666****** PP

                                       HTTTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSS.SC--BHHHHHHHHHHHHHHHHTCHS.... CS
                      tRNA-synt_1b  81 dpekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrlee.gegislgeftYplLqaaDilllkad.... 152
                                       +p   ++++qse +++++l  +l++ +++++l+ ++   + ++++ + +          p+ qaaD+l+ + +    
  gi|518652543|ref|YP_008142063.1| 129 KP--CKIYFQSENYDTQSLSFVLSNETNMNELKAIYGLTD-SSSILHvN---------SPIIQAADVLHTQLKhlgg 193
                                       **..99**********************************.55555533.........4666666666666666666 PP

                                       ....EEEEEGGGHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 153 ....lvpgGsDQkqnielgrdlarrfnkk 177
                                           +vp+G DQ+ +i+l rd+a+r++  
  gi|518652543|ref|YP_008142063.1| 194 pratIVPVGVDQDPHIRLMRDIAKRLRVY 222
                                       6666*********************9755 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 2.4e-17
                                       HHHHSTTSS-EEEEET-BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTC..SHHHHHHHHHTHHHCHH CS
                      tRNA-synt_1b 174 fnkkevfkkpegltvplltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsde..evekllklktelsneli 248
                                       +n+  +f +p+++  +l tgl+G+ KmS+S + s I L+d+ e++  ki+ avt  ++  e +k + +++ +++ ++
  gi|518652543|ref|YP_008142063.1| 292 INDF-AFIEPSATFQKLETGLKGG-KMSSSIPDSLISLNDSGEEATRKIKHAVTGGKQtiEEQKKYGGNPDICP-VF 365
                                       4555.899****************.*********************************99999999********.** PP

                                       HHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 249 erleavsgkkpkreaeellaeevtklvhggdlkkalaealnell 292
                                       e ++++s+ ++   +  ++ e++ +  ++g++k+++ae++  +l
  gi|518652543|ref|YP_008142063.1| 366 ELYKYHSTDDK--YVTRVYDECKGGVRMCGACKSEAAENISGML 407
                                       *9999888777..9*************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2859.57
//
Query:       gi|518652544|ref|YP_008142064.1|  [L=442]
Description: hypothetical protein FACI_IFERC00001G1183 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-46  159.8  35.3    1.2e-46  159.5  35.3    1.0  1  Sugar_tr       Sugar (and other) transporter
    7.7e-25   87.6  52.7    4.7e-23   81.7  40.6    2.2  2  MFS_1          Major Facilitator Superfamily
  ------ inclusion threshold ------
        7.9    6.2  17.3       0.62    9.8   0.3    2.7  3  FA_desaturase  Fatty acid desaturase


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.5  35.3     2e-50   1.2e-46      47     445 ..      53     441 ..      19     442 .] 0.85

  Alignments for each domain:
  == domain 1  score: 159.5 bits;  conditional E-value: 2e-50
                                       HHHHHHHTHHHHH.HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGa.iiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                       +   i++i ++G+ +iGs+++g+++d++GR+ +++   +l++i ++l+++a+   ++  + +  ++vGig+G+ + +
  gi|518652544|ref|YP_008142064.1|  53 YEISIMGISSIGGvLIGSFISGYIADIYGRRFIYIYDLFLVSIFIFLTGLAT---NYINFSILELIVGIGIGADYPV 126
                                       3355677777765279************************************...999999**************** PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHH CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylv 199
                                       ++  ++E++p+k Rg+++ ++ ++ ++G l+  +f + l  +++ + wr++  + +v+++l+l+ +  +PESP++  
  gi|518652544|ref|YP_008142064.1| 127 SSSIQAEFSPTKSRGKFMFFNIFSFSIGSLIFLGFAVPLVLFTGVNAWRYMYMIGAVFPILVLYSRKKIPESPYWVQ 203
                                       ****************************8877777777766666679****************************** PP

                                       HTT-HHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHH CS
                          Sugar_tr 200 ekgkeeeakevlaklrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyy 276
                                       +k  + + +e   k + +++ + e   e++  +         ++ +++ k   + ++i ++  +   +++   i  y
  gi|518652544|ref|YP_008142064.1| 204 HKYGKVAGEEAKDKFEASTGYSIENLPEISPGKTR-------LRDVFKGKYAAYIIFISIAWFSYDIVSY--GIWTY 271
                                       **************999999999999999999999.......8899999775556666666666666665..9**** PP

                                       TTTHHHHSS-THH....HHHHHHHHHHHHHH.HHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS... CS
                          Sugar_tr 277 sptifenlglsks....llvtiivgvvnfva.tfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaa 348
                                       sp if++   s      +++t++   + +v+  ++ai+ vdr+GRR ll++G++g +++++++      +v++  + 
  gi|518652544|ref|YP_008142064.1| 272 SPLIFSTEITSYYadlyVVFTGMAESIPVVIgFLIAIYYVDRIGRRFLLIIGFLGSFAVLILFF-----FVNQYMVV 343
                                       *******99999999887777777666665516688**********999999999877766663.....44444688 PP

                                       CHHHHHHHHHHHHHH.HTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHH CS
                          Sugar_tr 349 sivaivfialfialf.algwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfag 424
                                       + ++++  + f+ +f ++g+ p+ + +  E+fp+++R++a+ +a+ v+ + +++  + fpii+  +g   + ++fa+
  gi|518652544|ref|YP_008142064.1| 344 GLLMTFSAFGFVHFFhNVGPSPITYTYPVEIFPTRIRGTAMGFATSVSRIGSIVAVFSFPIIDALYGLKAIIIFFAI 420
                                       999999999999766379*************************************************999******* PP

                                       HHHHHHHHHHHHS--STT--C CS
                          Sugar_tr 425 lavlfiifvfffvpetkgrtl 445
                                       +  +++  ++   petkg+ l
  gi|518652544|ref|YP_008142064.1| 421 FEFIGLALTLKYAPETKGKAL 441
                                       ******************987 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7  40.6   7.9e-27   4.7e-23      10     352 ..      32     398 ..      19     399 .. 0.73
   2 !   19.7   4.2   5.4e-08   0.00032     104     175 ..     365     436 ..     357     441 .. 0.89

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 7.9e-27
                             MFS_1  10 larsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw 86 
                                       ++ ++++ al  +l +   +   ei+++      g +++s++ G+++d +Grr +++  l+l +++++l  +a+++ 
  gi|518652544|ref|YP_008142064.1|  32 YTLTVFSYALL-YLINVMSLKSYEISIMGISSIGGVLIGSFISGYIADIYGRRFIYIYDLFLVSIFIFLTGLATNYI 107
                                       33333333333.454554455556777666666688******************************44444765555 PP

                             MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaiv 160
                                        + +l ++ G+g ga +p++ ++ a+ +p + rg+ + +   +fs+G+++  +++  l+   g   Wr++++i a++
  gi|518652544|ref|YP_008142064.1| 108 NFSILELIVGIGIGADYPVSSSIQAEFSPTKSRGKFMFFNIFSFSIGSLIFLGFAVPLVLFTGvnaWRYMYMIGAVF 184
                                       7***********************************************998888887776666789*********** PP

                             MFS_1 161 sllafvlfllllpeepperkrkspkeee..................kgtgpaplvp....awkallkdpvlw...il 212
                                        +l++         ++++ + + +  +                   +     p ++     ++ ++k ++     ++
  gi|518652544|ref|YP_008142064.1| 185 PILVLY---SRKKIPESPYWVQHKYGKVageeakdkfeastgysieN----LPEISpgktRLRDVFKGKYAAyiiFI 254
                                       ***933...44455555555555555546666666777767743331....33333444566777777744222234 PP

                             MFS_1 213 lialllfffgfsglltllplylqevlgls....glllaglllallalvgailallagrlsdrlgrrrrlllalllll 285
                                        ia+++  ++ +g+ t++pl+  +   ++      l+++++ ++ ++ ++i++l+a +++dr+grr+ l++++l+ +
  gi|518652544|ref|YP_008142064.1| 255 SIAWFSYDIVSYGIWTYSPLI--FSTEITsyyaD-LYVVFTGMAESIPVVIGFLIAIYYVDRIGRRFLLIIGFLGSF 328
                                       444444444444488888884..44444445643.6666666666666666699*********************** PP

                             MFS_1 286 laalglallavtssavllll.vlvliGfglgfv....fpsllalasdlappeeagtasglfntagslggalg 352
                                       ++++++++++ +   v++ll  +  +Gf ++f     +p+  ++ ++ +p++ +gta+g++++++ +g++++
  gi|518652544|ref|YP_008142064.1| 329 AVLILFFFVNQY--MVVGLLmTFSAFGFVHFFHnvgpSPITYTYPVEIFPTRIRGTAMGFATSVSRIGSIVA 398
                                       ************..44444414444888888889***********************************997 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 5.4e-08
                             MFS_1 104 pagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpee 175
                                       p+ +++ +++fp + rg a+g++++ + +G+i++    +++ +++g  a+ +++ai+ ++++ l l + pe+
  gi|518652544|ref|YP_008142064.1| 365 PITYTYPVEIFPTRIRGTAMGFATSVSRIGSIVAVFSFPIIDALYGLKAIIIFFAIFEFIGLALTLKYAPET 436
                                       77889999*****************************************************77655555544 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.45   2.7e+03     136     163 ..      78     105 ..      34     124 .. 0.57
   2 ?    9.8   0.3    0.0001      0.62     145     202 ..     156     225 ..      91     236 .. 0.70
   3 ?    1.1   9.6      0.05     3e+02     135     202 ..     298     373 ..     232     404 .. 0.64

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.45
                     FA_desaturase 136 rllawlllllawlglwlalllllglall 163
                                        +++ ++++++ l+l+  +++l gla++
  gi|518652544|ref|YP_008142064.1|  78 DIYGRRFIYIYDLFLVSIFIFLTGLATN 105
                                       3444444444444555555554444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0001
                     FA_desaturase 145 lawlglwlalllllglalllwlvplllllfllalvl..........nyveHyg....gdwgerqvetsasir 202
                                       l++lg++++l+l+ g+   +w +++++++++  lvl           +v+H +    g+ +++ +e s+ ++
  gi|518652544|ref|YP_008142064.1| 156 LIFLGFAVPLVLFTGVN--AWRYMYMIGAVFPILVLysrkkipespYWVQHKYgkvaGEEAKDKFEASTGYS 225
                                       12244444444444444..888888888887777777789************98888666666666666555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.05
                     FA_desaturase 135 wrllawlllllaw.......lglwlalllllglall.lwlvplllllfllalvlnyveHyggdwgerqvetsasir 202
                                         ++  +l+++++        +l++++l+ ++++ l +++ ++++++ l+++ ++ + H++++ g  ++ +++ ++
  gi|518652544|ref|YP_008142064.1| 298 IPVVIGFLIAIYYvdrigrrFLLIIGFLGSFAVLILfFFVNQYMVVGLLMTFSAFGFVHFFHNVGPSPITYTYPVE 373
                                       4444555555545566666656666666666666667888888888888888888888999888888888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); 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:                         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: 0.72u 0.37s 00:00:01.08 Elapsed: 00:00:00.59
# Mc/sec: 2238.83
//
Query:       gi|518652545|ref|YP_008142065.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1184 [Ferroplasma acidarmanus fer1]
Scores for complete 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-99  331.4   0.0      5e-99  331.2   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 !  331.2   0.0  2.8e-103     5e-99       2     286 ..      27     309 ..      26     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 331.2 bits;  conditional E-value: 2.8e-103
                                DS   2 llesyeki.gfqatslgeaidilnkmrkdekctiflgltsnlissGlreiiadlvkeklvdvivtTaggieeDlika 77 
                                       l+e ++++ gf++++++e+++il++    ++ t+fl++ + +is+G+r+ii +lvk+klvdvi+tT g++++D+++ 
  gi|518652545|ref|YP_008142065.1|  27 LMEMFGTSgGFTSKKIYEGYQILKEEF-TSDETTFLSFPADIISTGTRGIINQLVKNKLVDVIITTNGTLDHDIARV 102
                                       899999999****************96.56779******************************************** PP

                                DS  78 lgkktylgdfelddeeLrekginRignllvpneny.ckfedwvreildkleeeqkvwspselikelGkeindeeSil 153
                                       + + +y g+f++ de+L++ +inR+gn++vp+e+y   +e+ +++++++l +++k+w+p +li+e+G ++n+e+Sil
  gi|518652545|ref|YP_008142065.1| 103 YTD-YYAGTFNFGDEKLKDMNINRLGNVFVPDESYgVIIEEKLMPMIEELYSKKKEWAPVDLIREVGLKLNNENSIL 178
                                       *99.*******************************999*************************************** PP

                                DS 154 ywAykndipvfcpaltDgslGdqlllfhsvkekkklkldivkDirelndialkakktgaiilGGGvpKhhilnanlm 230
                                       y A+kn+ipvf+p++tDgs+G ql+ f+  ++++++++++++D ++l+di+++akktga+++GGG++Khh++++n++
  gi|518652545|ref|YP_008142065.1| 179 YNAAKNGIPVFVPGITDGSFGSQLWSFY--EMHHDFRINLLEDEHRLSDIVFDAKKTGALMIGGGISKHHTIWWNQF 253
                                       ****************************..58899****************************************** PP

                                DS 231 rngadyavyittaqefdGslsgatldEavSwgkikaeaksvkvyaDaTivlPLlva 286
                                       r+g++ avyittaqe+dGslsga+l+Ea++w k++++ak v++y+DaT +lP++va
  gi|518652545|ref|YP_008142065.1| 254 RDGLNEAVYITTAQEYDGSLSGAKLEEAITWKKVRKDAKFVNIYGDATAILPIMVA 309
                                       ******************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.51
# Mc/sec: 1845.35
//
Query:       gi|518652546|ref|YP_008142066.1|  [L=186]
Description: ribosomal protein L11 methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-12   47.5   0.0    2.1e-12   47.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.1e-09   38.0   0.0    1.6e-09   37.6   0.0    1.1  1  MTS              Methyltransferase small domain
    5.6e-08   33.4   0.0    9.2e-08   32.7   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    7.1e-08   32.4   0.0    8.8e-08   32.1   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    3.4e-06   27.0   0.0    4.3e-06   26.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    6.1e-05   22.8   0.0    0.00011   21.9   0.0    1.5  1  UPF0020          Putative RNA methylase family UPF0020
    0.00016   22.4   0.0    0.00025   21.7   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
      0.001   19.7   0.0     0.0017   19.0   0.0    1.4  1  Methyltransf_11  Methyltransferase domain
     0.0019   17.9   0.0     0.0023   17.6   0.0    1.2  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 !   47.0   0.0   1.1e-15   2.1e-12     162     233 ..      37     105 ..      22     111 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 1.1e-15
                              PrmA 162 geevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvivaN 233
                                       g++v+D+GtG+Gi ai++  Lga++++++DiD+  ++++++Nae   +++ ++   s + ++ +++d ++ N
  gi|518652546|ref|YP_008142066.1|  37 GKTVIDLGTGTGIFAIGSCYLGASHATGIDIDPAMIEISRRNAEPFPCAEFIN--SSISEVH-GNYDTVIMN 105
                                       689*****************************************999998774..3334444.678888877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   7.8e-13   1.6e-09      19     112 ..      22     113 ..      17     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 7.8e-13
                                       HHHHHHHH.CHCC.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTS CS
                               MTS  19 GsklLlet.lpke.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleev 93 
                                       +s lL e+ ++ + l ++v+DlG+G+G+ ++       + + t +d+d + +e++++n+e   + +e+++ + ++ev
  gi|518652546|ref|YP_008142066.1|  22 ASTLLTEAyMDGNiLGKTVIDLGTGTGIFAIGSCYLGAS-HATGIDIDPAMIEISRRNAEPFPC-AEFIN-SSISEV 95 
                                       677777652555578899*************99998777.79****************987654.55555.556788 PP

                                       TTS-EEEEEE---STTTCH CS
                               MTS  94 eekkfdlivsNPPfhagka 112
                                       + +++d++++NPPf +  +
  gi|518652546|ref|YP_008142066.1|  96 H-GNYDTVIMNPPFGSVIK 113
                                       8.8***********77655 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   4.6e-11   9.2e-08       1      80 [.      40     115 ..      40     125 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 4.6e-11
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhh 76 
                                       v+dlG+GtG +++      g+++ tg+Di+++m+e+ r++ae   + +ef++ ++++++   g +D v+++   +  
  gi|518652546|ref|YP_008142066.1|  40 VIDLGTGTGIFAIGSCYL-GASHATGIDIDPAMIEISRRNAEP-FPCAEFINSSISEVH---GNYDTVIMN-PpFGS 110
                                       89**********999977.79********************53.3599*****999986...789999995.33554 PP

                                       .SSHH CS
                   Methyltransf_25  77 .lsde 80 
                                        ++++
  gi|518652546|ref|YP_008142066.1| 111 vIKHD 115
                                       34545 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   4.4e-11   8.8e-08       4      95 ..      37     125 ..      36     163 .. 0.81

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.4e-11
                   Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlils 80 
                                       g++v+DlG+GtG +++     lg  ++ +GiDi++ +ie +r na+   +  +eF  ++i e        ++D ++ 
  gi|518652546|ref|YP_008142066.1|  37 GKTVIDLGTGTGIFAIGSC-YLG-ASHATGIDIDPAMIEISRRNAE--PFPCAEFINSSISEVH-----GNYDTVIM 104
                                       579********99999888.666.5999****************99..67778*********88.....78****** PP

                   Methyltransf_31  81 nevl......naladpdkile 95 
                                       n ++      +++++  k+le
  gi|518652546|ref|YP_008142066.1| 105 NPPFgsvikhDDMPFIIKALE 125
                                       965555557777777777666 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.1e-09   4.3e-06      20      95 ..      34     111 ..      14     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.1e-09
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiae....kakkaqkdqfdeqeaaepqgkfdlIvlrev 91 
                                       +  g+ v+d+G+GtGi++    + g+ + tg+D++p+++ei +     +++a++ +    +++e  g +d+++++  
  gi|518652546|ref|YP_008142066.1|  34 NILGKTVIDLGTGTGIFAIGSCYLGAsHATGIDIDPAMIEISRrnaePFPCAEFINS---SISEVHGNYDTVIMNPP 107
                                       67789**************888888889*************8876664444444444...67777799999999877 PP

                   Methyltransf_23  92 lehv 95 
                                       +++v
  gi|518652546|ref|YP_008142066.1| 108 FGSV 111
                                       7766 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.7e-08   0.00011      79     137 ..      62     114 ..      37     119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.7e-08
                                       EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---------- CS
                           UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPYGerlgs 137
                                         g+D+d+++++ +r+Nae    +++i+ s     +++   g++d+++ npP+G  +++
  gi|518652546|ref|YP_008142066.1|  62 ATGIDIDPAMIEISRRNAEPFPCAEFINSSI---SEVH---GNYDTVIMNPPFGSVIKH 114
                                       57******************99998887665...6666...67***********98876 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.3e-07   0.00025       2      87 ..      42     122 ..      41     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.3e-07
                   Methyltransf_12   2 eiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       ++G+GtG ++          ++ tg+Di+p++i     ++++r+++ + + e+ + ++++ +g   +D+v+++  + 
  gi|518652546|ref|YP_008142066.1|  42 DLGTGTGIFAIGS--CYlGASHATGIDIDPAMI-----EISRRNAEPFPCAEFINSSISEVHG--NYDTVIMNPPFG 109
                                       7788888555554..4448899***********.....999999999**********999988..9*****995444 PP

                   Methyltransf_12  78 hl...kdirevld 87 
                                        +   +d+ ++++
  gi|518652546|ref|YP_008142066.1| 110 SVikhDDMPFIIK 122
                                       4446677766665 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   8.3e-07    0.0017       2      66 ..      42     103 ..      41     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 8.3e-07
                                       EET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEE CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvv 66 
                                       d+G+GtG++a      g ++ +g+D++++m+++++++a++ +   ef+ ++++++    + +D v+
  gi|518652546|ref|YP_008142066.1|  42 DLGTGTGIFAIGSCYLGaSHATGIDIDPAMIEISRRNAEPFPC-AEFINSSISEV---HGNYDTVI 103
                                       9*********99998889******************9998885.67777777764...34555555 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0023      39     127 ..      34     112 ..      22     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                       CHCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEE CS
                     Cons_hypoth95  39 eiegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefd 115
                                       +i g++v+Dl  G+G  ++     ga++a+ ++ d+++++i ++n e + +    ae+++++ ++++ +      +d
  gi|518652546|ref|YP_008142066.1|  34 NILGKTVIDLGTGTGIFAIGSCYLGASHATGIDIDPAMIEISRRNAEPFPC----AEFINSSISEVHGN------YD 100
                                       477899*******************************************95....57999999998666......9* PP

                                       EEEE--SSSTTC CS
                     Cons_hypoth95 116 ivflDPPyakel 127
                                        v ++PP+ ++ 
  gi|518652546|ref|YP_008142066.1| 101 TVIMNPPFGSVI 112
                                       ********9874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1233.75
//
Query:       gi|518652547|ref|YP_008142067.1|  [L=101]
Description: hypothetical protein FACI_IFERC00001G1186 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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    9.0   4.2       0.88    9.3   2.2    2.0  2  DUF3755   Protein of unknown function (DUF3755)


Domain annotation for each model (and alignments):
>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   2.2   4.9e-05      0.88      16      31 ..       5      26 ..       5      28 .. 0.91
   2 ?   -2.9   0.0      0.31   5.6e+03      26      29 ..      79      82 ..      70      84 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 4.9e-05
                           DUF3755 16 dNImaIlnd......MsdmpGi 31
                                      +NI++I+++      ++d pG+
  gi|518652547|ref|YP_008142067.1|  5 NNINKIMERtrndnsLRDIPGV 26
                                      9********9999999999997 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.31
                           DUF3755 26 sdmp 29
                                      ++mp
  gi|518652547|ref|YP_008142067.1| 79 NEMP 82
                                      6777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 711.00
//
Query:       gi|518652548|ref|YP_008142068.1|  [L=297]
Description: protoheme IX farnesyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  153.6  24.6    8.1e-45  153.1  24.6    1.3  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1  24.6   4.5e-49   8.1e-45       3     246 ..      21     268 ..      16     287 .. 0.84

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 4.5e-49
                              UbiA   3 ipalvg...lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivl 76 
                                       +++++g   la+   +  ++ ++l++++++++ + +a +l +y+D e D+ mert+nRPl++G+i++k+al+f++ l
  gi|518652548|ref|YP_008142068.1|  21 VFIAFGgaiLAVNNFSFNNIIMILVAIAAVTMGSMGAEGLTNYIDLEMDSTMERTKNRPLPTGEITKKQALMFGYSL 97 
                                       4445553333333333344466666666666********************************************** PP

                              UbiA  77 lilgllllalllnpltallgllallly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalav 152
                                       ++l++++l+++  + + +++ ++++   ++Y+ + lK+++++ ++ gg+++++p+l+gw+ +t ++s+l+++l+++v
  gi|518652548|ref|YP_008142068.1|  98 AVLSVIILLAFRRFIASIFMSIGIFDNvFIYS-YLLKKVSPYSIIYGGFSGAFPVLIGWYTITSDFSWLPWILFFLV 173
                                       ********77777888888888888888****.8******************************************* PP

                              UbiA 153 flltwaialandlrdregDrkagiktlpvvlGrkaarillalllavllla..llllllalllllylllalllaalal 227
                                       ++++  + +  ++r re+++ka+++++pv++ ++ ++i  +++  vll++  l+ ++++ ++l+yl+ +++l +  +
  gi|518652548|ref|YP_008142068.1| 174 MFWIPVHVWSLAYRYREDYKKANVPMFPVTHSDRSTAIA-ISFSSVLLIVfsLIPYFMGFYNLVYLIPVAILSIPVI 249
                                       *************************************95.4444444444456688888888888888888888888 PP

                              UbiA 228 lraarlvrrrdakkaakff 246
                                       ++++ ++++  +k+  ++f
  gi|518652548|ref|YP_008142068.1| 250 IFSYNFIKNPGRKTSFRLF 268
                                       8888888888888887777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2265.79
//
Query:       gi|518652549|ref|YP_008142069.1|  [L=191]
Description: exosome complex RNA-binding protein Csl4 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-07   31.1   0.0    2.9e-07   30.2   0.0    1.6  1  ECR1_N           Exosome complex exonuclease RRP4 N-terminal 
     0.0035   17.0   1.1     0.0069   16.0   1.1    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
     0.0076   16.4   0.6      0.012   15.7   0.6    1.2  1  FYVE             FYVE zinc finger
  ------ inclusion threshold ------
      0.016   14.7   0.6       0.03   13.9   0.6    1.5  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.03   14.1   1.4      0.077   12.7   1.4    1.6  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.035   14.7   2.3        4.1    8.1   0.1    3.1  3  EXOSC1           Exosome component EXOSC1/CSL4
      0.098   12.5   0.0       0.24   11.2   0.0    1.6  1  Bac_rhamnosid_C  Bacterial alpha-L-rhamnosidase C-terminal do
       0.14   12.8   0.4       0.24   12.0   0.4    1.6  1  Trm112p          Trm112p-like protein


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 !   30.2   0.0   1.3e-10   2.9e-07       1      37 [.       7      43 ..       7      44 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.3e-10
                                      EE-TT-EEEETTTSEE-TTEEEETTEEEESSSEEEEE CS
                            ECR1_N  1 iVtPGevlttdeefmrGhGTYvrggtiyAsvaGtvev 37
                                      iV PG++++++ee+++G++T   +g ++++  G v++
  gi|518652549|ref|YP_008142069.1|  7 IVFPGDIIAKEEEYLSGKNTQDIDGDVISTAFGRVSR 43
                                      9**********************************98 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.1   3.1e-06    0.0069       7      32 .]     147     171 ..     145     171 .. 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.1e-06
                           zf-RRN7   7 CgvCgcrsftlddGfyyCrrChtqeg 32 
                                       C +C++++++ ++G+ yCr+C+ +e+
  gi|518652549|ref|YP_008142069.1| 147 CTICRSDLVA-ENGKLYCRNCGRVEQ 171
                                       99****7766.68*********8876 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.6   5.5e-06     0.012      10      34 ..     145     169 ..     143     178 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.5e-06
                                       SB-TTT--B--SSS--EE-TTT--E CS
                              FYVE  10 kkCeiCakkFsllrrrhhCrlCGkv 34 
                                       +kC+iC++   + + + +Cr+CG+v
  gi|518652549|ref|YP_008142069.1| 145 SKCTICRSDLVAENGKLYCRNCGRV 169
                                       79*********************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   1.3e-05      0.03       2      30 ..     146     171 ..     145     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVle 30 
                                       kC +C s+  v  +e+g l+C +CG V +
  gi|518652549|ref|YP_008142069.1| 146 KCTICRSDL-V--AENGKLYCRNCGRVEQ 171
                                       899999973.3..568***********87 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 ?   12.7   1.4   3.5e-05     0.077       4      32 ..     145     171 ..     144     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.5e-05
                     A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgasfp 32 
                                       ++C+ C+++ +   e g l+C +Cg +++
  gi|518652549|ref|YP_008142069.1| 145 SKCTICRSDLVA--ENGKLYCRNCGRVEQ 171
                                       69*******987..***********8876 PP

>> EXOSC1  Exosome component EXOSC1/CSL4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.54   1.2e+03      91     104 ..       3      16 ..       1      36 [. 0.79
   2 ?    8.1   0.1    0.0018       4.1       4      30 ..      63      90 ..      60     103 .. 0.79
   3 ?    4.6   0.0     0.022        48      91     109 .]     110     128 ..     101     128 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.54
                                       -GGCTEECTTEEEE CS
                            EXOSC1  91 kviemfrpGDIvra 104
                                       +v++++ pGDI+ +
  gi|518652549|ref|YP_008142069.1|   3 QVKDIVFPGDIIAK 16 
                                       67889999999765 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0018
                                      TT-EEEEEEEEEESSEEEEEEEEE.CTB CS
                            EXOSC1  4 egdvVLarvtrlrkkqalveilsv.ege 30
                                        d+V ++++++ +k+a++ i+ v +g+
  gi|518652549|ref|YP_008142069.1| 63 RYDIVYGKIIKILNKEAVILISGVvKGN 90
                                      569******************9761444 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.022
                                       -GGCTEECTTEEEEEEEEC CS
                            EXOSC1  91 kviemfrpGDIvraqviSl 109
                                       +   ++  GD+vra++iS+
  gi|518652549|ref|YP_008142069.1| 110 MYSHIITLGDLVRAKIIST 128
                                       55566778**********7 PP

>> Bac_rhamnosid_C  Bacterial alpha-L-rhamnosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.24      28      68 ..      63     108 ..      58     113 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                                       EEEETTEEEEEEEEEE.....TTEEEEEEEE-TT-EEEEEEE-SSG CS
                   Bac_rhamnosid_C  28 sfeslyGkikvdWkre.....dgkftlnvsvPanttaeVvLpgeke 68 
                                       +++ +yGki    ++e     +g ++ n  vPant+a++ Lp  ++
  gi|518652549|ref|YP_008142069.1|  63 RYDIVYGKIIKILNKEaviliSGVVKGNALVPANTEARLKLPIPNK 108
                                       677788877777766666677888999999************8766 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.4   0.00011      0.24      47      62 ..     154     169 ..      81     169 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00011
                                       EECCCCEEEETTTTEE CS
                           Trm112p  47 ldieegeLvCpncgra 62 
                                       l+ e+g+L+C+ncgr+
  gi|518652549|ref|YP_008142069.1| 154 LVAENGKLYCRNCGRV 169
                                       57899*********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1237.34
//
Query:       gi|518652550|ref|YP_008142070.1|  [L=52]
Description: hypothetical protein FACI_IFERC00001G1189 [Ferroplasma acidarmanus fer1]
Scores for complete 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   16.4   0.3     0.0052   16.3   0.3    1.1  1  DUF4349      Domain of unknown function (DUF4349)
  ------ inclusion threshold ------
      0.016   14.6   0.1      0.018   14.4   0.1    1.0  1  Helo_like_N  Fungal N-terminal domain of STAND proteins
      0.037   14.6   0.2      0.039   14.6   0.2    1.1  1  SlyX         SlyX
      0.038   14.3   0.1      0.044   14.1   0.1    1.0  1  DUF2383      Domain of unknown function (DUF2383)
      0.083   13.4   0.9       0.12   12.9   0.8    1.4  1  COMP         Cartilage oligomeric matrix protein


Domain annotation for each model (and alignments):
>> DUF4349  Domain of unknown function (DUF4349)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   1.4e-06    0.0052     109     140 ..       1      32 [.       1      37 [. 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.4e-06
                           DUF4349 109 lekaksvedlleiereLsevqaeieslegqlr 140
                                       +++a++++d+ e++re+ + ++ei+s++  l 
  gi|518652550|ref|YP_008142070.1|   1 MKEADKIKDVQELSREVRDMRKEIDSMKELLG 32 
                                       899************************98665 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 ?   14.4   0.1   4.9e-06     0.018      26      65 ..       5      43 ..       2      48 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-06
                       Helo_like_N 26 etvksfrsrdktvreLkeeleaLeevLesLeevavaeees 65
                                      + +k+ ++ +++vr++++e+++++e L  L +v +++ ++
  gi|518652550|ref|YP_008142070.1|  5 DKIKDVQELSREVRDMRKEIDSMKELLGGLIKVMMDH-DN 43
                                      68999***************************76444.43 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.2   1.1e-05     0.039      17      56 ..       8      47 ..       1      51 [. 0.85

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXX CS
                              SlyX 17 dtieeLndvvaeqqqqidrlqrqlrllaerlkeleessga 56
                                      + ++eL+++v + +++id +++ l  l + + + +++ ++
  gi|518652550|ref|YP_008142070.1|  8 KDVQELSREVRDMRKEIDSMKELLGGLIKVMMDHDNQFND 47
                                      5699***********************9999888877664 PP

>> DUF2383  Domain of unknown function (DUF2383)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.2e-05     0.044      42      87 ..       5      50 ..       2      51 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHHHHHCT----------------------------H CS
                           DUF2383 42 ereeaaeeLqseiralggepedggslagklhrawvdlksaltsnde 87
                                      ++ + ++eL+ e+r++ +e ++   l+g l ++++d    ++++de
  gi|518652550|ref|YP_008142070.1|  5 DKIKDVQELSREVRDMRKEIDSMKELLGGLIKVMMDHDNQFNDEDE 50
                                      566789*********************************9999986 PP

>> COMP  Cartilage oligomeric matrix protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   3.3e-05      0.12      17      37 ..      10      30 ..       5      35 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.3e-05
                              COMP 17 lkeLreelrqQvkEisfLRnt 37
                                      ++eL  e+r+++kEi  ++ +
  gi|518652550|ref|YP_008142070.1| 10 VQELSREVRDMRKEIDSMKEL 30
                                      89*************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      679  (0.0378716); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 370.16
//
Query:       gi|518652551|ref|YP_008142071.1|  [L=71]
Description: snRNP Sm-like protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   71.4   2.7      4e-20   71.3   2.7    1.0  1  LSM       LSM domain


Domain annotation for each model (and alignments):
>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   2.7   2.2e-24     4e-20       2      66 ..       8      69 ..       7      70 .. 0.93

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.2e-24
                                      HHHHTTTSEEEEEETTSEEEEEEEEEEETTSEEEEEEEEEEETTETEEEEEEEEEEEGGGEEEEE CS
                               LSM  2 flkklinkkvtvelkngrelrGtLkgfDqfmNlvLedveetlkdkkekrklglvliRGnnivlis 66
                                       l++ +nkkvt+ lk++r l+GtL+g+D++mN+ L+d+ee  +    +rk+g+v+iRG+n+v i+
  gi|518652551|ref|YP_008142071.1|  8 MLEENLNKKVTLLLKDNRSLVGTLVGYDEYMNMTLDDAEENGE---VQRKIGKVIIRGSNVVRIT 69
                                      68999**********************************9664...57*************9885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 524.82
//
Query:       gi|518652552|ref|YP_008142072.1|  [L=524]
Description: hypothetical protein FACI_IFERC00001G1191 [Ferroplasma acidarmanus fer1]
Scores for complete 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-40  137.0   0.1    9.2e-40  136.0   0.1    1.5  1  DUF5591   Domain of unknown function (DUF5591)
    0.00026   20.9   0.0    0.00054   19.9   0.0    1.5  1  PUA       PUA domain
  ------ inclusion threshold ------
       0.06   13.5   0.0       0.17   12.1   0.0    1.8  1  TGT_C2    Patch-forming domain C2 of tRNA-guanine transglycos


Domain annotation for each model (and alignments):
>> DUF5591  Domain of unknown function (DUF5591)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.0   0.1   1.5e-43   9.2e-40       1     153 [.     229     374 ..     229     375 .. 0.90

  Alignments for each domain:
  == domain 1  score: 136.0 bits;  conditional E-value: 1.5e-43
                                       X-HHHHHHHHH---S..SSEEEEEE--SSSSGGGSHHHHHHHHHS---...SEEEEE-SS-.EEEGGGTT------- CS
                           DUF5591   1 vkrfrervlerYeppeekkvlvLlPcsakkPyseskshrkfaeaikkrkakvheviltsPlGvvPreleevYPaaqY 77 
                                       ++ +r+++ + Y +p+++++ +LlPcsakkPys+sk+h+k+ + i ++++ +he+i+tsP+G+vPrele+ YPa  Y
  gi|518652552|ref|YP_008142072.1| 229 IVAYRNKISS-YVKPDRRNIALLLPCSAKKPYSDSKTHKKILSGIWQYRRYLHELIVTSPVGLVPRELEKGYPARFY 304
                                       56799***97.****************************************************************** PP

                                       ---------HHHHHHHHHHHHHHHHHHT-SEEEE---THHHHHHHHHHTT-SSEEEE--.SS-TTSHHHHHHHHHH CS
                           DUF5591  78 diavtgewseeeiefvaellakylektkyekviahleeeyreiveevaeelgleiiytvvedkptskeslknLkea 153
                                       di+v g+w e+e+ ++++l++ y++k++ye via+++e+  ++v+++     +++ +  +e+k+t+++ +++L++ 
  gi|518652552|ref|YP_008142072.1| 305 DIPVIGTWYEDEKLMMKNLISAYFNKNRYEDVIAYIPED-LDFVRDAI---PDNAKI--IEGKVTDDNNIARLATV 374
                                       ***************************************.88888876...333333..35778888888877765 PP

>> PUA  PUA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.1e-08   0.00054      18      72 ..     467     520 ..     460     522 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.1e-08
                                       EEEGGGEEEEETT--TTSEEEEEETTSCEEEEEEESS-HHHHHHHCTSEEEEEEE CS
                               PUA  18 sLlapGvvevegdfeegdvVaivdedgelvavGlanysseelakikggksveier 72 
                                        ++a G+ ++  d+++ d+V i++ ++el + G a++ s  + + + g +v+++ 
  gi|518652552|ref|YP_008142072.1| 467 TVYAMGIQNATPDIKAFDEV-IMTYNNELRGTGTALMPSRAMVDLNNGAAVKVRS 520
                                       68999***************.9*******************************97 PP

>> TGT_C2  Patch-forming domain C2 of tRNA-guanine transglycosylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.8e-05      0.17       4      68 ..     393     453 ..     390     456 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.8e-05
                            TGT_C2   4 raiadYqFGagagdaLfpedvtitrsatgrirqvlvdgerlatlraqdgrltLsleGarrlhesl 68 
                                       ra++ +qFG+ +   +   +v++   ++ +   ++ +   l+ ++++ gr++++ e+++   e +
  gi|518652552|ref|YP_008142072.1| 393 RALLRFQFGDWIIPYIS--NVKLI--NSFHQDMIVEGSRILFVYNESIGRFSITPESGKFFLEND 453
                                       89999***999988888..58888..99999999999**********************988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (524 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3895.38
//
Query:       gi|518652553|ref|YP_008142073.1|  [L=375]
Description: hypothetical protein FACI_IFERC00001G1192 [Ferroplasma acidarmanus fer1]
Scores for complete 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-77  258.2   0.0    6.4e-77  257.8   0.0    1.2  1  ATP-sulfurylase  ATP-sulfurylase
    1.5e-36  125.5   0.0    2.5e-36  124.7   0.0    1.4  1  PUA_2            PUA-like domain
  ------ inclusion threshold ------
       0.18   12.0   0.0       0.52   10.5   0.0    1.7  1  PIN_11           PIN like domain


Domain annotation for each model (and alignments):
>> ATP-sulfurylase  ATP-sulfurylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.8   0.0   1.1e-80   6.4e-77       5     211 ..     162     366 ..     159     367 .. 0.98

  Alignments for each domain:
  == domain 1  score: 257.8 bits;  conditional E-value: 1.1e-80
                                       .-HHHHHHHHHHTT-SSEEEEEESS---HHHHHHHHHHHHHTSEEEEEEEB-SB-STTSTTHHHHHHHHHHHHHHHS CS
                   ATP-sulfurylase   5 ltPaevreefkekgwdkVvAfqtrnplHraHeellkraleeeadglllhplvgptkpgdvpaevrvrayealieeyl 81 
                                       l P  +r+ f e+gw++V++fqtrn++Hr+Hee++++al+  +dg++++p++g++kpgd+++e+++++y++li++y+
  gi|518652553|ref|YP_008142073.1| 162 LFPVDTRQIFLERGWKTVTGFQTRNVPHRGHEEMQRTALR-VTDGIFINPVIGKKKPGDYRDEIIMKSYDTLINNYY 237
                                       56999***********************************.8*********************************** PP

                                       -GGGEEE-BB-SB---SCHHHHHHHHHHHHHTT-SEEEE-TTTT-STCSS-TTHHHHHHHHCHHHCTSEEEE---EE CS
                   ATP-sulfurylase  82 pkdrvvlallplamryaGprEallhaiirknyGcthfivGrdhagvgdfYgpydaqellakvagelgiepvkfeeav 158
                                       p +rv+++ l+++m y+GprEa+ hai+rkn+Gcthf+vGrdhag+g+fYgpydaq+ l+ ++  lgie+++++e++
  gi|518652553|ref|YP_008142073.1| 238 PSNRVLFSPLHYEMSYGGPREAMIHAIMRKNFGCTHFVVGRDHAGIGNFYGPYDAQKNLQAFE--LGIEIMNMDEVF 312
                                       ************************************************************987..************ PP

                                       EETTTTEEEECCCC.GCCGGEEE--HHHHHCCHHTT----TTTS-HHHHHHHHH CS
                   ATP-sulfurylase 159 Yckkegevasektc.hkkeevesisgtelrkllregeeipewfsrpevlkvLre 211
                                       Yckk++++a+++ c h + +++++sgt +r++l++g  +   ++r++v++ + +
  gi|518652553|ref|YP_008142073.1| 313 YCKKCEQLATSRDCsHVDGDRVHFSGTMVRDTLKNGLSPETYLFRKDVYETINR 366
                                       ***************99********************************99876 PP

>> PUA_2  PUA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.7   0.0   4.2e-40   2.5e-36      27     157 ..      21     150 ..       4     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.7 bits;  conditional E-value: 4.2e-40
                                       TS-EEE--HHHHHHHHHHHTTTTTT-SCC--HHHHHHHHHHSEETTS-E-SS---EEEECCHCHHHTT-SEEEEEET CS
                             PUA_2  27 elpsielskrelqdlellaeGgfsPLegFmreedyesvleemrLadgllwsiPivLdvseedakklkegdrvaLkdk 103
                                          +ie+s  ++  ++ +  G+ sPL+gFm+e+d++sv+e+ rL++gl wsiP +Ld+ e++ + +++gd+v L ++
  gi|518652553|ref|YP_008142073.1|  21 AHHTIEVSYGTAIRIMNMKMGILSPLKGFMGESDFHSVVENQRLENGLPWSIPYTLDIGEKEFRCVRAGDTVRLSQN 97 
                                       34689999********************************************************************* PP

                                       TTEEEEEEEEEEEEE-HHHHHHHHHHS---TTSHHHHHHCTS-SEEEEEEEEE- CS
                             PUA_2 104 egellAileveeiyeldkeeeaekvfgttdeaHPgvkkvleqgevlvgGkvevl 157
                                          ++Ai++v++iy++d+ e ++kvfgtt+++HPgv+++ e++ + ++G+++  
  gi|518652553|ref|YP_008142073.1|  98 -SGVIAIMDVTDIYRYDRIEYCRKVFGTTSTDHPGVRNIRESTGICMAGEIKSA 150
                                       .788***********************************************965 PP

>> PIN_11  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.6e-05      0.52      71     104 ..      53      86 ..      36      96 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.6e-05
                            PIN_11  71 adfalvlhagkldeklpkqipftilsGdkgflel 104
                                       +df  v++ ++l++ lp +ip+t+  G+k f  +
  gi|518652553|ref|YP_008142073.1|  53 SDFHSVVENQRLENGLPWSIPYTLDIGEKEFRCV 86 
                                       89***************************99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2637.82
//
Query:       gi|518652554|ref|YP_008142074.1|  [L=245]
Description: phosphoadenosine phosphosulfate reductase [Ferroplasma acidarmanus fer1]
Scores for complete 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  131.4   0.1    4.1e-38  131.1   0.1    1.1  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 !  131.1   0.1   2.3e-42   4.1e-38       3     174 .]      28     201 ..      26     201 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 2.3e-42
                                       EEE--SSCTCHHHHHHHHHHCTTHEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-SCHHHHHHHHHH-S-THHH CS
                       PAPS_reduct   3 vvsvsgGkdslVllhLalkafkpvpvvfvdtghefpetiefvdeleeryglrlkvyepeeevaekinaekhgsslye 79 
                                       v++ s G +++V+ +++ +++ +v++  +dtg+  +et+++++ +++++g++lk+y pe+e  e ++  + g +l+ 
  gi|518652554|ref|YP_008142074.1|  28 VFTSSLGLEDMVITDMIARNNINVEIATIDTGRLPDETYQLMETVRSEMGIDLKIYFPEREDVEDMINSR-GINLFY 103
                                       7899******************************************************999888888887.667776 PP

                                       C......HHHHHHTHHHHHHHHHCTTECEEE----CCCTTTTTTSSSEEECTTT-SCEEE-CCCT--HHHHHHHHHH CS
                       PAPS_reduct  80 e......aaeriaKveplkkaLekldedalltGaRrdesksraklpiveidedfekslrvfPllnWteedvwqyilr 150
                                       +       +++++Kv+plk+ L+k +  +++tG+R++++ +r++ + ve  +d +++ +v+Pll+W+  ++w+y+  
  gi|518652554|ref|YP_008142074.1| 104 HsldnrhFCCNVRKVKPLKNILRKRS--VWITGIRAEQTVARKNARKVEYVRD-HNVWKVNPLLDWSRDEIWSYVSI 177
                                       66999999****************99..**********************999.88********************* PP

                                       CT--B-CCCCTT-SS--BCTTB-S CS
                       PAPS_reduct 151 enipynpLydqgfrsiGcvpctga 174
                                       +++pyn L+dq ++siGc pct+a
  gi|518652554|ref|YP_008142074.1| 178 HKVPYNILFDQNYKSIGCQPCTKA 201
                                       **********************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1594.22
//
Query:       gi|518652555|ref|YP_008142075.1|  [L=310]
Description: hypothetical protein FACI_IFERC00001G1194 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-57  195.2   0.1    1.4e-57  195.0   0.1    1.1  1  ComA       (2R)-phospho-3-sulfolactate synthase (ComA)
    0.00037   20.3   0.0    0.00092   19.0   0.0    1.6  1  MarR_2     MarR family
    0.00069   19.1   0.1     0.0022   17.5   0.0    1.9  2  HTH_24     Winged helix-turn-helix DNA-binding
    0.00098   19.0   0.0     0.0027   17.6   0.0    1.8  1  HTH_36     Helix-turn-helix domain
     0.0012   18.7   0.1     0.0083   16.0   0.0    2.3  2  TrmB       Sugar-specific transcriptional regulator TrmB
  ------ inclusion threshold ------
      0.018   15.0   0.0      0.064   13.2   0.0    1.9  1  HTH_Crp_2  Crp-like helix-turn-helix domain
      0.029   14.0   0.0      0.075   12.7   0.0    1.7  1  GntR       Bacterial regulatory proteins, gntR family
      0.058   13.3   0.0       0.17   11.9   0.0    1.7  1  MarR       MarR family
      0.069   13.2   0.1        3.9    7.6   0.0    2.4  2  HTH_29     Winged helix-turn helix
      0.094   12.3   0.0       0.24   11.0   0.0    1.7  1  HTH_CodY   CodY helix-turn-helix domain
      0.097   12.6   0.0       0.23   11.4   0.0    1.6  1  HTH_5      Bacterial regulatory protein, arsR family
       0.12   12.4   0.0       0.99    9.4   0.0    2.4  3  HTH_43     Winged helix-turn helix


Domain annotation for each model (and alignments):
>> ComA  (2R)-phospho-3-sulfolactate synthase (ComA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.0   0.1   9.2e-61   1.4e-57      14     243 .]       5     230 ..       1     230 [. 0.97

  Alignments for each domain:
  == domain 1  score: 195.0 bits;  conditional E-value: 9.2e-61
                                       EEEESS--HHHHHHHHHHHGGG-SEEEE-TTGGGGSTCHHHHHHHHHHHCTT-EEEE-HHHHHHHHHTT-HHHHHHH CS
                              ComA  14 eviDkGlglreledlletageyiDglKlgggtsallpeeilrekielahehgvyvstGgtlfEaalaqgkvdeylee 90 
                                       +++Dk  +++   d+++++ e i ++K+g+ ts+ll+e++l + i+ +++ g++vs+Ggt +E+a+a+g++++ l  
  gi|518652555|ref|YP_008142075.1|   5 MLLDKLSSVD--MDVISSLRERIYVMKIGWTTSMLLDEKTLINRIKRYRDLGIDVSPGGTTLEIAYAKGHLERTLSS 79 
                                       5566665555..6999************************************************************* PP

                                       HHHCT-SEEEE--SSS---HHHHHHHHHHHCCTTSEEEEEES-SSHHHHTT--CCHHHHHHHHHHHHTECEEEE--T CS
                              ComA  91 ckelgfdviEvsdgtlelpeeeklrliekakkeglkvlpevgkkdgelesesdveklieeakrdleaGaekviiEar 167
                                       + ++gf++ E+s+g+++lp+++k+++++ ak++++ + +evgkk++  ++++++++ ie ++rdle   ++vi+E+r
  gi|518652555|ref|YP_008142075.1|  80 LLQYGFSHLEISEGVIDLPDSQKKKIVDFAKSNNIPFTMEVGKKSE--KNQLSLDETIEGVNRDLEYEPDVVIVEGR 154
                                       *********************************************9..9**************************** PP

                                       TT--SSTTB-TTS-B-HHHHHHHHTTS-GGGEEEE--SHHHHHHHHHHH-TT--EEEEEGGGHHHHHHHHCT-SGG CS
                              ComA 168 esGitegvydekgevrtdvvekiierlgleklifEApekkqqewfikefGpnVnLgnvdpsevlaLealRlglrgd 243
                                       e+G+++gv+d +g ++ d v +++e++++ekl+fEAp ++qq++++ ++G+ VnLgn++p    aLe+ Rlglrgd
  gi|518652555|ref|YP_008142075.1| 155 ETGKGVGVFDIEGLIKWDWVTRLAENFPIEKLMFEAPVERQQVELVIRMGNTVNLGNIAPASLAALETQRLGLRGD 230
                                       ***************************************************************************8 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.0   6.2e-07   0.00092      13      61 ..     253     299 ..     251     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 6.2e-07
                                       HHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  13 aLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61 
                                       ++ ++++  l ++ + + +gl + +v+++lk+Lv+ G v+++   +D+R
  gi|518652555|ref|YP_008142075.1| 253 VISDHGP--LDQAGIMDLTGLNRKTVQNALKELVSSGIVRESFYRNDLR 299
                                       6889999..*********************************6666998 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       2.6   3.9e+03      32      46 ..      41      55 ..      38      55 .. 0.77
   2 !   17.5   0.0   1.5e-06    0.0022       8      48 .]     250     290 ..     250     290 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 2.6
                            HTH_24 32 stvnrrlkrLeeeGl 46
                                       t+  r+kr  + G+
  gi|518652555|ref|YP_008142075.1| 41 KTLINRIKRYRDLGI 55
                                      577789999998886 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.5e-06
                            HTH_24   8 ILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       I+ ++ +++ + q+ + + +gl + tv   lk+L+++G+++
  gi|518652555|ref|YP_008142075.1| 250 IYYVISDHGPLDQAGIMDLTGLNRKTVQNALKELVSSGIVR 290
                                       66789999*******************************97 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.8e-06    0.0027      28      54 ..     262     288 ..     244     289 .. 0.90

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.8e-06
                            HTH_36  28 qetlakrlglsknTvsraikeLeqlGy 54 
                                       q+ ++ ++gl+++Tv++a+keL+  G+
  gi|518652555|ref|YP_008142075.1| 262 QAGIMDLTGLNRKTVQNALKELVSSGI 288
                                       78899******************9997 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.5   2.3e+03      41      52 ..      75      86 ..      70      93 .. 0.72
   2 !   16.0   0.0   5.5e-06    0.0083      14      64 ..     251     305 ..     248     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.5
                                      HHHHHHHHCTSE CS
                              TrmB 41 evLrsLedkGlV 52
                                      ++L+sL++ G+ 
  gi|518652555|ref|YP_008142075.1| 75 RTLSSLLQYGFS 86
                                      677888887774 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 5.5e-06
                                       CHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST....TTEEEE CS
                              TrmB  14 YlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr....pklYra 64 
                                       Y ++  +gp++   i   +g+ r +v+++L++L++ G+V+ +  r    +++Y+a
  gi|518652555|ref|YP_008142075.1| 251 YYVISDHGPLDQAGIMDLTGLNRKTVQNALKELVSSGIVRESFYRndlrKRIYSA 305
                                       666668999******************************9876555665666665 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 ?   13.2   0.0   4.3e-05     0.064      21      53 ..     259     291 ..     249     302 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-05
                                       EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEE CS
                         HTH_Crp_2  21 pltqeelAsmlGltretvsrilseLkreglisr 53 
                                       pl q+ + ++ Gl+r tv  +l+eL   g+++ 
  gi|518652555|ref|YP_008142075.1| 259 PLDQAGIMDLTGLNRKTVQNALKELVSSGIVRE 291
                                       778888999*********************994 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     5e-05     0.075      28      54 ..     263     289 ..     254     292 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5e-05
                                       HHHHHHHTS-HHHHHHHHHHHHHTTSE CS
                              GntR  28 reLaaefgVsrttvReALrrLeaeglv 54 
                                         +++  g +r tv+ AL++L++ g+v
  gi|518652555|ref|YP_008142075.1| 263 AGIMDLTGLNRKTVQNALKELVSSGIV 289
                                       56889999*****************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00011      0.17      12      56 ..     254     298 ..     250     300 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       HHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTST CS
                              MarR  12 lyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDr 56 
                                       ++++gpl ++ + +  g+++ tv ++l++L+  G ++ s   +D 
  gi|518652555|ref|YP_008142075.1| 254 ISDHGPLDQAGIMDLTGLNRKTVQNALKELVSSGIVRESFYRNDL 298
                                       899********************************9876655555 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.069     1e+02      22      43 ..      36      57 ..      35      79 .. 0.74
   2 ?    7.6   0.0    0.0026       3.9      18      41 ..     265     288 ..     260     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.069
                            HTH_29 22 lglsrrtvyrwlkrfeegGlaa 43
                                      + l+++t  + +kr++  G++ 
  gi|518652555|ref|YP_008142075.1| 36 MLLDEKTLINRIKRYRDLGIDV 57
                                      66899**************976 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0026
                            HTH_29  18 iAkllglsrrtvyrwlkrfeegGl 41 
                                       i+ l+gl r+tv+++lk  +  G+
  gi|518652555|ref|YP_008142075.1| 265 IMDLTGLNRKTVQNALKELVSSGI 288
                                       6789**************999997 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   0.00016      0.24       4      34 ..     259     289 ..     256     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00016
                          HTH_CodY   4 rLtaskiaDriGitrsvivnaLrkLesaGii 34 
                                        L  + i D  G+ r  + naL+ L s+Gi+
  gi|518652555|ref|YP_008142075.1| 259 PLDQAGIMDLTGLNRKTVQNALKELVSSGIV 289
                                       56667899**********************8 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00015      0.23      12      46 ..     255     290 ..     248     291 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                                       TT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  12 ae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ++ g+l    +++ +gl++ tv   Lk L  +G+V+
  gi|518652555|ref|YP_008142075.1| 255 SDhGPLDQAGIMDLTGLNRKTVQNALKELVSSGIVR 290
                                       3478999999************************96 PP

>> HTH_43  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.1   9.2e+03      34      51 ..      40      57 ..      23      58 .. 0.70
   2 ?    0.9   0.0       0.3   4.5e+02      64      76 ..     251     263 ..     242     265 .. 0.84
   3 ?    9.4   0.0   0.00067      0.99      22      50 ..     261     289 ..     248     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.1
                                      HHHHHHHHHGGGGGT-EE CS
                            HTH_43 34 RRtlqDtlkalaeldiel 51
                                       +tl + +k   +l+i++
  gi|518652555|ref|YP_008142075.1| 40 EKTLINRIKRYRDLGIDV 57
                                      567778888888888876 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.3
                                       EEEEEE-TTB-HH CS
                            HTH_43  64 yyrisdWGpidke 76 
                                       yy isd Gp+d++
  gi|518652555|ref|YP_008142075.1| 251 YYVISDHGPLDQA 263
                                       8*********986 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00067
                                       -HHHHHHHH---HHHHHHHHHGGGGGT-E CS
                            HTH_43  22 nvpklieltgmPRRtlqDtlkalaeldie 50 
                                           +++ltg+ R+t+q++lk l   +i 
  gi|518652555|ref|YP_008142075.1| 261 DQAGIMDLTGLNRKTVQNALKELVSSGIV 289
                                       556799***************99887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       557  (0.031067); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2169.12
//
Query:       gi|518652556|ref|YP_008142076.1|  [L=527]
Description: hypothetical protein FACI_IFERC00001G1195 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       518  (0.0288917); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3650.17
//
Query:       gi|518652557|ref|YP_008142077.1|  [L=287]
Description: hypothetical protein FACI_IFERC00001G1196 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       986  (0.0549947); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2173.74
//
Query:       gi|518652558|ref|YP_008142078.1|  [L=626]
Description: hypothetical protein FACI_IFERC00001G1197 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-25   88.3   0.1      1e-24   87.0   0.1    1.7  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
    1.7e-15   57.4   0.4      3e-15   56.6   0.1    1.6  2  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    1.3e-06   28.2   0.2    0.00032   20.4   0.0    2.6  3  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    1.1e-05   25.0  15.2     0.0059   16.4   6.3    3.4  2  Fer4             4Fe-4S binding domain
    5.4e-05   23.0  11.1       0.02   14.9   2.1    2.6  2  Fer4_2           4Fe-4S binding domain
    0.00058   19.8  20.0      0.011   15.8   3.8    3.0  2  Fer4_6           4Fe-4S binding domain
     0.0015   18.4   0.0     0.0042   17.0   0.0    1.7  1  Transketolase_C  Transketolase, C-terminal domain
     0.0028   17.7  12.0        0.1   12.8  12.9    2.4  2  Fer4_10          4Fe-4S dicluster domain
     0.0045   17.6   9.5       0.39   11.3   1.8    2.5  2  Fer4_7           4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.017   14.3   1.4       0.02   14.1   0.1    1.6  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
      0.089   13.0   9.0       0.27   11.4   9.1    1.8  1  Fer4_9           4Fe-4S dicluster domain
       0.24   11.6   9.1       0.48   10.6   9.1    1.5  1  Fer4_21          4Fe-4S dicluster domain
       0.51   11.3   9.4        2.7    9.0   1.5    2.6  2  Fer4_16          4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.1   7.5e-28     1e-24       1     151 [.     406     546 ..     406     548 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 7.5e-28
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc++l      + + p     + +l +mG ++++A G ++   d++v+a++GD++f+++ ++ l++av +nl+++
  gi|518652558|ref|YP_008142078.1| 406 DIGCYSL------GTYDPFDE--ADTLISMGSSIGVANGFSMV-TDQKVIAFIGDSTFYHSgIPPLINAVHNNLNML 473
                                       8999999......65566444..459****************7.578****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpali 151
                                       v++++N++++mtg+q++p  +  + g+     + + ++ +++++G++ +  +++++++e  +++ + l++ g+++i
  gi|518652558|ref|YP_008142078.1| 474 VIIMDNGTTAMTGQQPNPGNELDYNGKP---VTGIPIEDVVRGIGVSnVSLLDPYNLKESFATINRSLHQTGVSVI 546
                                       ********************99998876...999*************77799**********************99 PP

>> POR_N  Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.6   0.1   2.2e-18     3e-15       2     188 ..      28     209 ..      27     253 .. 0.86
   2 ?   -3.6   0.0       5.4   7.4e+03      93     117 ..     533     557 ..     531     560 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.6 bits;  conditional E-value: 2.2e-18
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++ag++++++YP TPsse++e+l+  ++k ++   +++   +E  a + +  A+++G r++++    Gl  +++ 
  gi|518652558|ref|YP_008142078.1|  28 GAVEAGIEFASSYPGTPSSEVGETLSHVADKLGI---KFLYSVNEKVALESAFAASISGMRSLVFMKHVGLNVASDP 101
                                       899****************************997...9*************************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       ++ ++ + +   +v+++   ps   s +++q    +a    + ++ ++n qea d++ +Af l+ek+++Pv+     
  gi|518652558|ref|YP_008142078.1| 102 FVSIVYTGTRGGLVIMTADDPSM-FSSQNEQDNRHYADLAHIPMIEPSNPQEAKDFVKAAFELSEKYHIPVLFR-TT 176
                                       **999888888888888888999.99***********999******************************9755.57 PP

                                       HHH.HEEEEEEC-SGG.GS-----SBXXXXXXX CS
                             POR_N 156 fllshevekvelpdeedelklikekleeyerke 188
                                       +++sh++ +v++ +  +++ +++ ++ + er+ 
  gi|518652558|ref|YP_008142078.1| 177 TRVSHMRGPVNVGEIPKIKGTRRVFERDPERFV 209
                                       8888******99888766666666666665554 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 5.4
                                       EEEEE-STTBEEEEE--TTCHHHHS CS
                             POR_N  93 vvaRalpstglsirtdqsDlmaard 117
                                        ++R+l +tg+s+  +  +   +rd
  gi|518652558|ref|YP_008142078.1| 533 TINRSLHQTGVSVIISRRECAIIRD 557
                                       689********99988888877776 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 !   20.4   0.0   2.3e-07   0.00032       3     156 ..      21     187 ..      19     193 .. 0.85
   2 ?   -3.5   0.0         5     7e+03      23      41 ..     254     271 ..     251     274 .. 0.78
   3 ?    5.1   0.0     0.012        16      52     106 ..     431     485 ..     426     546 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                                       HHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHH CS
                      TPP_enzyme_N   3 vaealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGa 76 
                                       + ea++r   ++g+e +  +pG+ + ++ + ls      gi+++ +++E +a   A + + +  +  v++ ++g ++
  gi|518652558|ref|YP_008142078.1|  21 GNEAIARGAVEAGIEFASSYPGTPSSEVGETLSHVAdklGIKFLYSVNEKVALESAFAASISGMRSLVFMKHVGLNV 97 
                                       67999***************************999899*******************99877777888888889987 PP

                                       HH.CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHH..........HCCCSSEEEE-SSGGGHHHHH CS
                      TPP_enzyme_N  77 tn.altalaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlal..........frpvtkyaervtspeelpeal 140
                                       ++  + +++    +r  l+++++d p+   +q+ + +    d +++          +++++k+a++++++ ++p+++
  gi|518652558|ref|YP_008142078.1|  98 ASdPFVSIVY-TGTRGGLVIMTADDPSMFSSQNEQDNRHyaDLAHIpmiepsnpqeAKDFVKAAFELSEKYHIPVLF 173
                                       7535556544.5567789999999999999977666444666777799999999999******************** PP

                                       HHHHHHHHSSS--EEE CS
                      TPP_enzyme_N 141 rrAirtalsgrpgPvy 156
                                       r   r++  + +gPv 
  gi|518652558|ref|YP_008142078.1| 174 RTTTRVS--HMRGPVN 187
                                       *999999..9999985 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 5
                                       --CCCHHHHCCHHCT.TSE CS
                      TPP_enzyme_N  23 pGsrilplldalseeqgir 41 
                                        Gs++++l+da++ +  i+
  gi|518652558|ref|YP_008142078.1| 254 SGSGYNSLMDAVASHS-IE 271
                                       6899999999999984.65 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.012
                                       HHHHHHHHHHH.TS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  52 afaAdgyarat.gkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg 106
                                       ++ A g++++t +k+ +++  s +   ++++ l++A ++++ +lv+ +d++t+   
  gi|518652558|ref|YP_008142078.1| 431 IGVANGFSMVTdQKVIAFIGDS-TFYHSGIPPLINAVHNNLNMLVIIMDNGTTAMT 485
                                       6778999999955555555555.578899********************9998776 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.5   0.00011      0.16       1      16 [.     569     584 ..     569     585 .. 0.92
   2 !   16.4   6.3   4.3e-06    0.0059       1      24 []     598     623 ..     598     623 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       EEEETTTSSS-THHHH CS
                              Fer4   1 vvideekCigCGaCve 16 
                                       ++++++kC +C++Cve
  gi|518652558|ref|YP_008142078.1| 569 YTVNQDKCGKCMNCVE 584
                                       589************8 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 4.3e-06
                                       EEEETTTSSS-THHHH..HSTTTEEE CS
                              Fer4   1 vvideekCigCGaCve..vCPvgAIt 24 
                                       ++i+++ C gCG C+e  vCP++AI+
  gi|518652558|ref|YP_008142078.1| 598 IQINPSICDGCGVCAEplVCPFNAIE 623
                                       68*************988******96 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   1.8   7.9e-05      0.11       3      22 .]     569     590 ..     567     590 .. 0.85
   2 !   14.9   2.1   1.5e-05      0.02       3      21 ..     598     618 ..     596     619 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.9e-05
                            Fer4_2   3 vvvdtdrCigCgaCvsa..CPa 22 
                                       + v+ d+C  C  Cv +  CPa
  gi|518652558|ref|YP_008142078.1| 569 YTVNQDKCGKCMNCVENfsCPA 590
                                       789************5557**8 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.5e-05
                            Fer4_2   3 vvvdtdrCigCgaCv..saCP 21 
                                       +++++ +C gCg C    +CP
  gi|518652558|ref|YP_008142078.1| 598 IQINPSICDGCGVCAepLVCP 618
                                       799***********9888899 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   1.9   1.4e-05     0.019       3      21 ..     570     590 ..     570     593 .. 0.94
   2 !   15.8   3.8   8.1e-06     0.011       2      24 .]     598     622 ..     597     622 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.4e-05
                            Fer4_6   3 eidpdkCigCgdCvrv..CPe 21 
                                       ++++dkC  C++Cv +  CP+
  gi|518652558|ref|YP_008142078.1| 570 TVNQDKCGKCMNCVENfsCPA 590
                                       69**************99996 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.1e-06
                            Fer4_6   2 veidpdkCigCgdCvr..vCPegai 24 
                                       ++i+p+ C+gCg C+   vCP++ai
  gi|518652558|ref|YP_008142078.1| 598 IQINPSICDGCGVCAEplVCPFNAI 622
                                       78************65227***998 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.1e-06    0.0042      24      69 ..     261     303 ..     247     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                                       HHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEE CS
                   Transketolase_C  24 aleAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvvee 69 
                                        ++A    +++ i+++V+ + +++pl + +i+e ++k++++v+vee
  gi|518652558|ref|YP_008142078.1| 261 LMDA---VASHSIEIDVLKIGFTNPLPRGMIAEFLRKHDKVVIVEE 303
                                       4444...57789*********************************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 !   12.8  12.9   7.2e-05       0.1       4      53 ..     571     613 ..     568     618 .. 0.84
   2 !   11.2   1.9   0.00023      0.32       2      23 ..     598     621 ..     597     626 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                           Fer4_10   4 idddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCve 53 
                                       +++d+C +C +Cv+  +CPa            e+++++++++ C+gcg C+e
  gi|518652558|ref|YP_008142078.1| 571 VNQDKCGKCMNCVEnfSCPA---------LFIEKGEIQINPSICDGCGVCAE 613
                                       689***********777***.........66677788999**********98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00023
                           Fer4_10   2 vvidddtCirCgkCvk..aCPadl 23 
                                       ++i+++ C +Cg C +  +CP+++
  gi|518652558|ref|YP_008142078.1| 598 IQINPSICDGCGVCAEplVCPFNA 621
                                       689*************999**954 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   2.2    0.0014       1.9      24      49 ..     562     589 ..     549     592 .. 0.77
   2 !   11.3   1.8   0.00028      0.39      29      52 .]     596     621 ..     586     621 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0014
                            Fer4_7  24 nekgtekveidpekClgCgaCva..vCP 49 
                                       ++ ++e ++++++kC  C +Cv+   CP
  gi|518652558|ref|YP_008142078.1| 562 KNGEIEIYTVNQDKCGKCMNCVEnfSCP 589
                                       3445688999************966787 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                            Fer4_7  29 ekveidpekClgCgaCva..vCPtga 52 
                                        +++i+p+ C gCg+C++  vCP++a
  gi|518652558|ref|YP_008142078.1| 596 GEIQINPSICDGCGVCAEplVCPFNA 621
                                       58999************999***997 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 ?   -2.6   0.1       1.8   2.4e+03     132     160 ..     241     267 ..     229     275 .. 0.71
   2 ?   14.1   0.1   1.4e-05      0.02     104     174 ..     414     482 ..     388     489 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.8
                    DXP_synthase_N 132 ekkkvvaviGDgaltgGmafealnnigel 160
                                        ++++v+ i  ga+t+G  +++l ++ ++
  gi|518652558|ref|YP_008142078.1| 241 AQSNMVSEI--GAITSGSGYNSLMDAVAS 267
                                       455566655..699999999998877554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.4e-05
                    DXP_synthase_N 104 eyDafeagHsstsisaalGlavardlkgekkkvvaviGDgalt.gGmafealnnigelkkkllvilNdNems 174
                                       +yD f+ + +  s+  + G+a   ++  +++kv+a iGD+++  +G+    l n+ +++ ++lvi+ dN  +
  gi|518652558|ref|YP_008142078.1| 414 TYDPFDEADTLISMGSSIGVANGFSMV-TDQKVIAFIGDSTFYhSGI--PPLINAVHNNLNMLVIIMDNGTT 482
                                       799999887777777777777777765.679*********9961554..6789999999**********865 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   9.1    0.0002      0.27       1      51 []     575     622 ..     574     622 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0002
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCv..eaCpkgai 51 
                                       kC +C +Cve   Cpa  +++ + +   ++       C gCg C+   +Cp +ai
  gi|518652558|ref|YP_008142078.1| 575 KCGKCMNCVENfsCPALFIEKGEIQINPSI-------CDGCGVCAepLVCPFNAI 622
                                       799*****98777***99999999998887.......********5559998876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   9.1   0.00035      0.48       5      58 ..     573     623 ..     569     624 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00035
                           Fer4_21   5 edkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCss..vCPvedcie 58 
                                       +dk   CgkC+   e+ s  a+ i+ k  +++  + C GC +C++  vCP  ++ie
  gi|518652558|ref|YP_008142078.1| 573 QDK---CGKCMNCVENFSCPALFIE-KGEIQINPSICDGCGVCAEplVCPF-NAIE 623
                                       555...5555555556666688775.666799***********96558**7.8887 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   3.0     0.034        48       1      24 [.     575     599 ..     575     605 .. 0.76
   2 ?    9.0   1.5     0.002       2.7       2      20 ..     605     625 ..     604     626 .] 0.87

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.034
                           Fer4_16   1 rCgtCgkCae..vCPtnaikekkeke 24 
                                       +Cg+C +C+e  +CP+  i++  e +
  gi|518652558|ref|YP_008142078.1| 575 KCGKCMNCVEnfSCPALFIEKG-EIQ 599
                                       5*******97447***999988.444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.002
                           Fer4_16   2 CgtCgkCae..vCPtnaikek 20 
                                       C +Cg Cae  vCP nai+ k
  gi|518652558|ref|YP_008142078.1| 605 CDGCGVCAEplVCPFNAIEVK 625
                                       99*****98779******976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (626 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       588  (0.032796); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.47
# Mc/sec: 3992.19
//
Query:       gi|518652559|ref|YP_008142079.1|  [L=210]
Description: indolepyruvate oxidoreductase subunit beta [Ferroplasma acidarmanus fer1]
Scores for complete 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  117.8   0.1    6.3e-34  117.6   0.1    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.6   0.1   3.5e-38   6.3e-34       1     176 [.      11     189 ..      11     190 .. 0.97

  Alignments for each domain:
  == domain 1  score: 117.6 bits;  conditional E-value: 3.5e-38
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG++tag+i+++aa+r+G +v +++ +g ++rGg+++++vri+d    p i+   +dl+++l+  + ++ ++   
  gi|518652559|ref|YP_008142079.1|  11 GGQGIITAGNIISEAAMRSGQKVIMSEIHGLSQRGGSVTVDVRIGDC-YGPIISQSSCDLVIGLELIETFRAIESFE 86 
                                       9*********************************************8.88999999**********9999******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H.. CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglpl.. 147
                                       + g++++ +e+++p  l   k e++ l++       g r+y+v a +ia e+g  ++a+N+vm+G++++l  +p+  
  gi|518652559|ref|YP_008142079.1|  87 NVGTALMSTEKINPISLSMHKKEYPCLEDLMekygmGTRIYPVEAGEIAMEAGS-SKAVNIVMIGVALGLNLFPMta 162
                                       ***************************98889*******************888.***************99***99 PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragy 176
                                       +++  ++k++fp+k   +  N+ka+++g+
  gi|518652559|ref|YP_008142079.1| 163 DEVVYVLKDTFPEK--KLGINMKALELGI 189
                                       ************96..79********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1393.13
//
Query:       gi|518652560|ref|YP_008142080.1|  [L=416]
Description: hypothetical protein FACI_IFERC00001G1199 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-59  202.4   0.1    1.3e-59  202.2   0.1    1.0  1  Amidohydro_1  Amidohydrolase family
    7.2e-16   58.7   0.0    1.6e-08   34.5   0.0    2.9  3  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 !  202.2   0.1   1.5e-63   1.3e-59       1     344 []      51     397 ..      51     397 .. 0.90

  Alignments for each domain:
  == domain 1  score: 202.2 bits;  conditional E-value: 1.5e-63
                                       EEEE-EEEEEEECETTECSSS....GHHHHH.........STTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHH CS
                      Amidohydro_1   1 ivlPGlIDaHvHleqsllrga....tledwl.........vppetaaealesgiktalksGtttvadmgattstgie 64 
                                       +++PG+I++H+H+ +s ++g      l ++l          ++e ++  +  g+ ++++sGtt++ d ++    + +
  gi|518652560|ref|YP_008142080.1|  51 VIIPGFINTHTHVGMSGFKGLlddiVLSEFLdktskldsqRTDEGIYNSSLLGMNEMINSGTTSFVDLYY----SED 123
                                       689*************888887777777777999*****999999*************************....899 PP

                                       HHHHHHHTSSSEEEEEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHH CS
                      Amidohydro_1  65 alleaaeelplglrilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkea 141
                                        + +a+e++  g+r ++++  ld +++ t +      ++ a+ +i+++++g v +  +  + +  sde  + + ++a
  gi|518652560|ref|YP_008142080.1| 124 IVEKAVEKI--GMRGFLAWATLD-QEFTTQRG---DPVKNAEAFIRKEHPGTVIPMAGIQGIYVSSDENYYRVKELA 194
                                       999*****8..***********9.55444444...4444445578999999999*********************** PP

                                       HHHTTEEEEEETSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHHHHHHHHHHHHHHCEEHH CS
                      Amidohydro_1 142 kkrdlpvaiHaletkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpteaellkerlkeagvahc 218
                                       +k++++v++H++et++ev d ++ +    e+  ++e ++ +g+l + ++i+ah+v++t +e+++l ++  +++v+  
  gi|518652560|ref|YP_008142080.1| 195 EKYNVMVHTHLSETRKEVYDFVKTHN---ER--PVEHLGAIGFLSD-RIIAAHCVWITLNEIKILSKY--KTSVSWN 263
                                       **************************...99..*************.*********************..9999999 PP

                                       HHHHHHSEH.HHHHHHHHHHHTSCEEEEEECTTSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHH CS
                      Amidohydro_1 219 pfsnsilrs.grealrkaldeGvkvglgtDgaasgnslnlleelrlalklqrgllye.deegglslkealrmaTing 293
                                       + sn +l+s g++++ ++l+++v+v+lgtD+ +s+nsln++ee+++ +    + +++  +++ ++  ++ +maT n+
  gi|518652560|ref|YP_008142080.1| 264 AISNAKLSSgGIAPVPELLSNNVNVSLGTDSSGSNNSLNMFEEMKYSA---ISINNDrWSADTVKSQQIMDMATRNA 337
                                       9999997773699999********************************...444444656778************** PP

                                       HHHTT-TTTSSSS-TTSB--EEEECC...CT........CGGGTTTCTSEEEEEEEETTEEE CS
                      Amidohydro_1 294 AkalglddkvGsievGkdADlvvvdl...di........laafvglkkdgnvkkvivkGklv 344
                                        +al+    +G i +G+ ADlv++d    +          +++v+++++ nv +v+v+Gk++
  gi|518652560|ref|YP_008142080.1| 338 GIALKS--PIGIIREGYLADLVILDMnkyNTmpyndsniVNNIVFSANPENVESVMVNGKII 397
                                       *****9..9*****************7651156777788********************985 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-07    0.0021       1      21 [.      43      63 ..      43      75 .. 0.86
   2 !    2.7   0.0    0.0077        69     172     238 ..     174     254 ..     156     268 .. 0.81
   3 !   34.5   0.0   1.8e-12   1.6e-08     357     472 ..     275     397 ..     262     398 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-07
                      Amidohydro_3  1 eviDakGrlvlPGFvDsHtHl 21
                                      e+i+ak+r+ +PGF+  HtH+
  gi|518652560|ref|YP_008142080.1| 43 EEINAKNRVIIPGFINTHTHV 63
                                      68******************5 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0077
                      Amidohydro_3 172 yGitsveagggnvsslddleplfeltaeeklplrviikelldaaerlglpls...................pgseel 229
                                        Gi+++     +vss++ + ++ el+++ + +++ + +e ++ ++   ++++                     + ++
  gi|518652560|ref|YP_008142080.1| 174 AGIQGI-----YVSSDENYYRVKELAEKYNVMVHTHLSETRKEVYDFVKTHNerpvehlgaigflsdriiaAHCVWI 245
                                       477888.....9************************99999999999999997777777777777777777667777 PP

                      Amidohydro_3 230 tigavklfa 238
                                       t++ +k++ 
  gi|518652560|ref|YP_008142080.1| 246 TLNEIKILS 254
                                       777777766 PP

  == domain 3  score: 34.5 bits;  conditional E-value: 1.8e-12
                      Amidohydro_3 357 stpvkellnagvkvalgsD..apvgpfdpwprigaavmrktrrggevlrpdeelsleealalyTrgpAkalgledrk 431
                                       ++pv ell+++v+v+lg+D     ++++ + ++ +   + +    + ++    +  +++ ++ Tr++  al+ +   
  gi|518652560|ref|YP_008142080.1| 275 IAPVPELLSNNVNVSLGTDssGSNNSLNMFEEMKYSAISIN----NDRWSADTVKSQQIMDMATRNAGIALKSPI-- 345
                                       59*****************8888899999999999999999....899********************9999999.. PP

                      Amidohydro_3 432 GtLevGadADlvvld...adpldvdppelaear...........vrltvvdGrvv 472
                                       G +++G+ ADlv+ld   ++ +   ++   +++           v+ ++v+G+++
  gi|518652560|ref|YP_008142080.1| 346 GIIREGYLADLVILDmnkYNTMPYNDS---NIVnnivfsanpenVESVMVNGKII 397
                                       ***************655444444555...55555599999999********996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2630.99
//
Query:       gi|518652561|ref|YP_008142081.1|  [L=288]
Description: hypothetical protein FACI_IFERC00001G1200 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy 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:                      1099  (0.0612973); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 1889.80
//
Query:       gi|518652562|ref|YP_008142082.1|  [L=129]
Description: translation initiation factor IF-5A [Ferroplasma acidarmanus fer1]
Scores for complete 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   19.7   0.0     0.0014   18.6   0.0    1.6  1  EFP_N     Elongation factor P (EF-P) KOW-like domain
     0.0041   17.2   0.0       0.01   15.9   0.0    1.7  1  eIF-5a    Eukaryotic elongation factor 5A hypusine, DNA-bindi


Domain annotation for each model (and alignments):
>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   1.6e-07    0.0014       3      32 ..       9      38 ..       7      40 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 1.6e-07
                                      GG--TT-EEEETTEEEEEEEEEEEEETTS- CS
                             EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGq 32
                                       elk G    id+ +++++++  +kpGk +
  gi|518652562|ref|YP_008142082.1|  9 RELKVGRYMLIDDSPCKIVDITMSKPGKHG 38
                                      69**************************86 PP

>> eIF-5a  Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.2e-06      0.01       2      66 ..      70     126 ..      69     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.2e-06
                                       -EEEEEEEEEE-SS.EEEEEE.TT--EEE.EEGG..GB-HHHHTT--TT-E..EEEEEETTEEEEE CS
                            eIF-5a   2 VkrkeyqLidIqdDgflsLmd.ddgetkeDlklpegelgkqikekfeegkdvlVtVlsamGeekii 66 
                                       + +k +q+++I ++   ++md ++ et+    lp   ++ + ++k+++g +  V +++amG+ ki+
  gi|518652562|ref|YP_008142082.1|  70 IVKKNAQILSIANN-EAQMMDsESFETFI---LP---IEPEDQDKLKPGME--VPYWEAMGKRKIM 126
                                       77899******866.9*****88888876...88...8888899*******..***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 896.44
//
Query:       gi|518652563|ref|YP_008142083.1|  [L=301]
Description: hypothetical protein FACI_IFERC00001G1202 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-73  247.0   0.0    2.9e-73  246.8   0.0    1.0  1  Arginase  Arginase family
  ------ inclusion threshold ------
       0.16   12.3   0.0       0.38   11.0   0.0    1.6  1  NES_C_h   Nicking enzyme C-terminal middle helical 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 !  246.8   0.0   3.2e-77   2.9e-73       2     277 ..      34     291 ..      33     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 246.8 bits;  conditional E-value: 3.2e-77
                                       EEEEEEEE--TTTSSSGGGGGHHHHHHHHHHTSBTHCHEETTTTE.SCCSEEEEEEEEE--SSCHHHHHHHHHHHHH CS
                          Arginase   2 dvallGvPfdaagsgrpGarfGPraireasarleealeynlelgv.leelkivdlgdvavtpvdneevleqieeava 77 
                                       d +++G+Pfd + s+r+G+r +P++ir+a  +le+   y+++ g+ l ++ki+dlgd++v   d + +l +ie+a+a
  gi|518652563|ref|YP_008142083.1|  34 DYVIFGAPFDNTSSYRRGSRLAPNSIRAAYDNLES---YEVNYGInLLDAKICDLGDLPVYE-DVDYILSEIETATA 106
                                       889******************************98...67777777889***********75.9999********** PP

                                       HHHHTTCEEEEEESSGGGHHHHHHHHHHHHSTTEEEEEESSS----SSCTTTBSSSTTSHHHHHHHHTSECGCEEEE CS
                          Arginase  78 eilkagklpivlGGDHsialgilralaekygkplgvihfDAHaDlrtpetegsgnshGtpfrraaeegllkpkklvq 154
                                       +i++++k+p++lGG+Hs+++g+lr l+     +++++ +DAH D+r+++  g++n+h+++ rra+  +ll ++k++ 
  gi|518652563|ref|YP_008142083.1| 107 TIFHDKKIPVMLGGEHSLTVGALRNLK-----DITMVIIDAHSDFRDSY-MGNKNNHACVTRRAL--ELLGKNKIIS 175
                                       *********************999887.....4899*************.9**************..8999****** PP

                                       EEE-STCSHHHHHHHHTTSEEEEHHHHHHHHHHHHHHHHHHHHTCTTSEEEEEEEGGGBBTTTSTSSSS-BSS-B-H CS
                          Arginase 155 iGirsvdneeyelakelgirvitmreidelglkavveeilervgaeedpvylSfDiDvlDpavaPGtGtpepgGltl 231
                                       iG rs+++ee    +  ++r+i+++e+++ g+++v++e++e+ +   d vy S+D+D++Dpa+aPG+Gtpep Glt+
  gi|518652563|ref|YP_008142083.1| 176 IGTRSTSYEEIASGEYENVRFISANEVRASGIDEVISEVMEKTS---DRVYFSIDMDGFDPAYAPGVGTPEPYGLTS 249
                                       **********9999999************************994...69**************************** PP

                                       HHHHHHHHHHHCHSEEEEEEEE-B-GGGSSTTTHHHHHHHHHHHHH CS
                          Arginase 232 rellallrelaeklnlvgaDvvEvnPaldteaeqtarlaarlvrel 277
                                       ++++++l  +++  +++g+D+ E+ P +d+ + +t++laa+l++++
  gi|518652563|ref|YP_008142083.1| 250 YDVRSILTSISD--RIIGFDINEMTPLYDN-G-NTSMLAAKLIQDF 291
                                       **********77..9**************9.5.9*********995 PP

>> NES_C_h  Nicking enzyme C-terminal middle helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   4.3e-05      0.38      46      90 ..     186     230 ..     166     234 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.3e-05
                           NES_C_h  46 vgedktkqleeiekqeelleeAdellnkeadrlveklYpelDiee 90 
                                       +   + ++++ i+ +e   +  de+++++ +++ +++Y+ +D++ 
  gi|518652563|ref|YP_008142083.1| 186 IASGEYENVRFISANEVRASGIDEVISEVMEKTSDRVYFSIDMDG 230
                                       45556799999*******************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1962.24
//
Query:       gi|518652564|ref|YP_008142084.1|  [L=176]
Description: hypothetical protein FACI_IFERC00001G1203 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  119.2   0.8    1.3e-34  119.0   0.8    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 !  119.0   0.8   7.5e-39   1.3e-34       4     132 .]      15     163 ..      12     163 .. 0.95

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 7.5e-39
                                       SXXBSSSXXSSTSXX.XSXXXXXESX........EEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXC...EEXXSXX CS
                     Ribosomal_L16   4 kkyrKsrkryirgvs.tkgtklefgd........ygLvalekgqltaealeaariainrylkkkrgk...klwirvf 68 
                                       ++y++++  ++ gv+ +k+t++  g+        ++Lva+e++q++++aleaari inr+l ++ g     l+irv+
  gi|518652564|ref|YP_008142084.1|  15 PAYTRKE--FMGGVPyPKITTFVQGNqkrefeieMQLVAEEACQIRHTALEAARISINRKLLENVGAgnyFLHIRVY 89 
                                       7899999..99***************************************************999999999****** PP

                                       XXEEEEE-.....SS-TTTSSSS....XEEEEEEEEEXSSCEEEEE.TTXXXSHHHHHHHHHHHHTSSSXEEEE CS
                     Ribosomal_L16  69 phhpvtkk.....agedRmgkGk....Gkpegwvarvkigqiifei.kagvneeiakealrraasKlpiktkiv 132
                                       ph++++++     ag+dR+++G+    Gkp g++arv+ig+ii+    ++ +++++k+al++a+ Klp+++k++
  gi|518652564|ref|YP_008142084.1|  90 PHQVIREHkmatgAGADRISSGMrmafGKPVGTAARVHIGEIIMVGkVDRASAKTMKDALKKASIKLPTPCKVI 163
                                       ********************************************9863446999******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1277.67
//
Query:       gi|518652565|ref|YP_008142085.1|  [L=472]
Description: amino acid transporter [Ferroplasma acidarmanus fer1]
Scores for 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   88.9  63.1    4.5e-25   88.4  63.1    1.2  1  AA_permease_2  Amino acid permease
    8.8e-19   67.4  58.4    1.1e-18   67.1  58.4    1.1  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 !   88.4  63.1     5e-29   4.5e-25      17     424 ..      33     439 ..      18     456 .. 0.83

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 5e-29
                     AA_permease_2  17 sgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvla 93 
                                       +g+++      +  a+ l+++++ li+ l+ l +   +ss+  + g +++y+ + +g ++a + +w ++f+ +++ a
  gi|518652565|ref|YP_008142085.1|  33 LGGIAL----VALGATPLSILVGFLIY-LTILNTSYRFSSKYVSAGSDFTYVGKSIGGFMATFEGWNLLFGTIFAYA 104
                                       455533....34455666667777777.44555666688879********************************998 PP

                     AA_permease_2  94 silsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglitvdgg 170
                                       +   ++++ + +++++++  +  l++ i+ a+ +++++i ++gi+ s ++q i+gi+ ++  ++i+  +gl+++ g+
  gi|518652565|ref|YP_008142085.1| 105 GFGMLGLAGFFGIFDSKI-LTGGLWIPIVLALNVITFIILYKGIRFSTNYQIITGIAEFI--ILIAGGIGLVILAGK 178
                                       888899999999999887.5677************************************4..567888999998887 PP

                     AA_permease_2 171 gfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee...vkkkdvpkaifigllivlvlyllvniaflgv 244
                                        ++ +++    + ++g  g++ +l+ ++ +f+G + a    +e   ++kk+vpk + i+ +i++v  ++++ a++ +
  gi|518652565|ref|YP_008142085.1| 179 NNTLAVFS-PFIASGGIIGFAHSLTLSVVTFIGLSIALTAISEeahIPKKTVPKSLLISSIIIGVTIVFLSYAMTVA 254
                                       77743222.23444466667778888********999988888799999**************************** PP

                     AA_permease_2 245 vpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP.rffakvnkfgs 320
                                        +++ + + +n+++++ ++f+ v  +++++++ i+++ s +g+ ++  ++++r+++a++rd+++    f++++k+g+
  gi|518652565|ref|YP_008142085.1| 255 WGPSRMLSFGNSVDNGLVLFREVS-PIMFGLLFIFTVNSFMGNNISMGTSMTRIFYAFSRDNIIFpGIFSRTDKNGT 330
                                       **********************99.*************************************9877*********** PP

                     AA_permease_2 321 piraiiltaivslillllfllas..saaynfllsvsslgliisyllliigalilrkkrphl.kr..pgkilvaiiga 392
                                       p++++i+++ +s++l+++f ++    +  ++ll + +++++++  + + +++i  +k  +  k+   g+ +   i++
  gi|518652565|ref|YP_008142085.1| 331 PVYTTIFILAISVFLCMVFGIYFgpIDGGYVLLFADAFFSFLIRSISSSSLIISTFKAGKInKKtlTGYLIAPVISI 407
                                       ************88888887542233444488888888888888888888888888866552447766677788889 PP

                     AA_permease_2 393 lfllfllvalffppkgpatqssliytiiltva 424
                                       + l+ +l+ +ffp+     ++ + + i+++v+
  gi|518652565|ref|YP_008142085.1| 408 VALIAVLASNFFPLPAYPYNFASVLGIVIIVV 439
                                       99999999999997777776666666666665 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.1  58.4   1.2e-22   1.1e-18       4     472 ..      17     457 ..      14     461 .. 0.73

  Alignments for each domain:
  == domain 1  score: 67.1 bits;  conditional E-value: 1.2e-22
                       AA_permease   4 vialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGl 80 
                                       ++  g   +++ +  l   ++ + ++++ l++l+++++++ + ++ + +++++ ++g++ ty+ +++g  ++ + G+
  gi|518652565|ref|YP_008142085.1|  17 WQGWGMTAPAADIAYLLGGIALVALGATPLSILVGFLIYLTILNTSYRFSSKYVSAGSDFTYVGKSIGGFMATFEGW 93 
                                       6666666777777777788888899999************************************************* PP

                       AA_permease  81 nylfswitvla.leltaasiliqfwelvtdlpkawvt...gavflvvlliinlvgvkvygeaefilalikiiaiiaf 153
                                       n+lf  i+++a +++ +++ ++++    +++++   +   ++ + v+ +ii + g++++   ++i+ +  +i++ia 
  gi|518652565|ref|YP_008142085.1|  94 NLLFGTIFAYAgFGMLGLAGFFGIF--DSKILTGGLWipiVLALNVITFIILYKGIRFSTNYQIITGIAEFIILIAG 168
                                       *888777754437888888888888..77777666674444444445555555666666665555555555544444 PP

                       AA_permease 154 iivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGi.elvaiiagEvkdPe 229
                                        i++ ++lag++++ +                ++p    +++g + +f+  +  +v++f G  +++++i++E+  P+
  gi|518652565|ref|YP_008142085.1| 169 GIGL-VILAGKNNTLA---------------VFSPF---IASGGIIGFAHSLTLSVVTFIGLsIALTAISEEAHIPK 226
                                       4444.34444444444...............56666...66678*****************7357899********* PP

                       AA_permease 230 ksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssans 306
                                       k++Pk+ l   i+i++  v++++++++ ++ +   ++  s++   ++v+f +    ++++ l+++++  + ++  +s
  gi|518652565|ref|YP_008142085.1| 227 KTVPKSLLISSIIIGVTIVFLSYAMTVAWGPSRMLSFGNSVDN--GLVLFRE-VSPIMFGLLFIFTV-NSFMGNNIS 299
                                       ********************************99999999988..5555544.44556666666655.5789999** PP

                       AA_permease 307 slysasRvlyslakdgl.aPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwll 382
                                       + +s++R++y++++d++ +P ++++ +k+g P+   ++ ++is+++ ++ ++++++     +ll + a+  +++  +
  gi|518652565|ref|YP_008142085.1| 300 MGTSMTRIFYAFSRDNIiFPGIFSRTDKNGTPVYTTIFILAISVFLCMVFGIYFGPIDGGYVLLFADAFFSFLIRSI 376
                                       ****************7368***********************************5555555555555555555555 PP

                       AA_permease 383 iilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivl.l 458
                                       ++ s++    ++k+ +++      ++ ++   +++ ++ali++l  +++    ++++ p+++ ++  +  ++ vl +
  gi|518652565|ref|YP_008142085.1| 377 SSSSLI--ISTFKAGKINK----KTLTGYLIAPVISIVALIAVLASNFF----PLPAYPYNFASVLGIVIIVVVLaI 443
                                       544444..45554444422....23445555555555555555555554....555669888888777777665425 PP

                       AA_permease 459 fliilvgvklhvkn 472
                                       +li ++ + + vkn
  gi|518652565|ref|YP_008142085.1| 444 TLITWIKRPDTVKN 457
                                       66667766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); 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:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 3140.08
//
Query:       gi|518652566|ref|YP_008142086.1|  [L=364]
Description: hypothetical protein FACI_IFERC00001G1205 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.2      3e-05   23.8   0.2    1.3  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
     0.0028   17.5   0.8      0.084   12.8   0.1    2.2  2  Nudix_N_2        Nudix N-terminal
  ------ inclusion threshold ------
      0.022   14.5   0.6        6.6    6.5   0.0    2.4  2  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l
      0.088   12.3   1.8       0.21   11.1   1.8    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
       0.15   12.2   0.1       0.25   11.5   0.1    1.3  1  DUF2318          Predicted membrane protein (DUF2318)
       0.31   10.8   5.8        2.9    7.7   0.3    2.3  2  zinc_ribbon_2    zinc-ribbon domain
        1.8    8.1   6.5         30    4.2   6.4    2.2  1  zf-ribbon_3      zinc-ribbon domain
          5    7.8   0.0          5    7.8   0.0    3.4  4  OAD_gamma        Oxaloacetate decarboxylase, gamma chain


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 !   23.8   0.2   1.4e-08     3e-05      30      67 ..     317     354 ..     316     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.4e-08
                    OrfB_Zn_ribbon  30 tCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                        C++Cg + ++   +  ++C++Cg ++d D+ + +Ni+
  gi|518652566|ref|YP_008142086.1| 317 ACPNCGNVEYRIGPDMSLECTKCGQKLDKDYTGPYNII 354
                                       6**********99999********************96 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   3.8e-05     0.084      13      33 ..     306     326 ..     299     327 .. 0.89
   2 ?    3.1   0.1     0.042        94       3      11 ..     336     344 ..     336     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                                       E--TT-SS-EEEETTTTEEE- CS
                         Nudix_N_2  13 ripdgDnreRlvCpaCgtihY 33 
                                       ++p+++   R  Cp+Cg + Y
  gi|518652566|ref|YP_008142086.1| 306 KTPPDELWIRSACPNCGNVEY 326
                                       788999999***********9 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.042
                                       -TTT--B-E CS
                         Nudix_N_2   3 CsqCGtpve 11 
                                       C++CG+++ 
  gi|518652566|ref|YP_008142086.1| 336 CTKCGQKLD 344
                                       99***9985 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1    0.0056        13      35      48 ..      14      27 ..      10      31 .. 0.86
   2 ?    6.5   0.0     0.003       6.6      21      65 ..     240     284 ..     234     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0056
                   Phage_holin_2_4 35 ialvGlavAliGlL 48
                                      i+++G+a+A++G+ 
  gi|518652566|ref|YP_008142086.1| 14 ISYIGIAIAVLGFF 27
                                      89**********97 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.003
                   Phage_holin_2_4  21 avvsfaGflasselialvGlavAliGlLvnWyYkreanRRaaaeh 65 
                                       a  +faG +  s + +++  + A +Gl    +Y  + nR+a  e 
  gi|518652566|ref|YP_008142086.1| 240 ALTAFAGNVIVSSITSVFIFIWAFLGLYTVTFYIVDRNRKASRER 284
                                       6789************************999********998876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.8   9.4e-05      0.21       3      32 ..     318     346 ..     317     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.4e-05
                                       ETTTTCEE.CHEETSTTCEEESSSSBEEEEC CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDpergelvCtdCGlVledn 32 
                                       CPnCg+ +  + + +   l Ct+CG  l+ +
  gi|518652566|ref|YP_008142086.1| 318 CPNCGNVEyRIGPDM--SLECTKCGQKLDKD 346
                                       ******776899988..777*****999876 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00011      0.25      35      65 ..     316     347 ..     305     352 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00011
                           DUF2318  35 daCevCekkgYv.qegeelvCknCgvrfalds 65 
                                       +aC  C++ +Y    + +l C++Cg+++++d 
  gi|518652566|ref|YP_008142086.1| 316 SACPNCGNVEYRiGPDMSLECTKCGQKLDKDY 347
                                       79**********556789*********98875 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.9    0.0066        15       2       7 ..     318     323 ..     317     324 .. 0.78
   2 ?    7.7   0.3    0.0013       2.9       2      12 ..     336     346 ..     335     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0066
                     zinc_ribbon_2   2 CpnCGa 7  
                                       CpnCG+
  gi|518652566|ref|YP_008142086.1| 318 CPNCGN 323
                                       888886 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0013
                     zinc_ribbon_2   2 CpnCGaelqdn 12 
                                       C++CG +l+++
  gi|518652566|ref|YP_008142086.1| 336 CTKCGQKLDKD 346
                                       99***999875 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   6.4     0.013        30       5      26 .]     318     343 ..     316     343 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.013
                       zf-ribbon_3   5 CPnCGa.p..lssddnv.CpyCGtkl 26 
                                       CPnCG+    + +d++  C++CG+kl
  gi|518652566|ref|YP_008142086.1| 318 CPNCGNvEyrIGPDMSLeCTKCGQKL 343
                                       99999943678888887788888876 PP

>> OAD_gamma  Oxaloacetate decarboxylase, gamma chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.7         8   1.8e+04       3      19 ..      18      34 ..      18      35 .. 0.75
   2 ?   -3.2   0.2         6   1.4e+04       5      16 ..      61      72 ..      59      80 .. 0.64
   3 ?    1.5   2.7      0.21   4.6e+02       8      38 ..     136     166 ..     131     169 .. 0.80
   4 ?    7.8   0.0    0.0022         5       3      55 ..     245     297 ..     243     314 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 8
                         OAD_gamma  3 gllltllGmgvVFvvLi 19
                                      g+ +++lG+ +   +Li
  gi|518652566|ref|YP_008142086.1| 18 GIAIAVLGFFFTIPFLI 34
                                      56778888888887776 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                         OAD_gamma  5 lltllGmgvVFv 16
                                      + ++ G+++V++
  gi|518652566|ref|YP_008142086.1| 61 IFLISGIIIVLA 72
                                      455666666654 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.21
                         OAD_gamma   8 llGmgvVFvvLilLslvislfskiikkkakk 38 
                                       +  m+ VF vLi+  + i+++ +ii + +kk
  gi|518652566|ref|YP_008142086.1| 136 IYLMSSVFQVLIFEFIPITILIAIILLATKK 166
                                       55599********999999988888776665 PP

  == domain 4  score: 7.8 bits;  conditional E-value: 0.0022
                         OAD_gamma   3 gllltllGmgvVFvvLilLslvislfskiikkkakkkkkkakaaaaaaaaaaa 55 
                                       ++++ + +++ VF+++     ++++  +i+ +  k++ +  + ++a++ ++++
  gi|518652566|ref|YP_008142086.1| 245 AGNVIVSSITSVFIFIWAFLGLYTVTFYIVDRNRKASRERGTDEPAQSGEPNT 297
                                       89999***********9999999999999988877776665555555444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1127  (0.0628591); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2431.18
//
Query:       gi|518652567|ref|YP_008142087.1|  [L=240]
Description: alanyl-tRNA synthetase [Ferroplasma acidarmanus fer1]
Scores for complete 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   20.9   0.1    0.00017   20.3   0.1    1.3  1  tRNA-synt_2c     tRNA synthetases class II (A)
  ------ inclusion threshold ------
      0.058   13.8   0.4       0.23   11.9   0.1    2.0  2  CBM77            Carbohydrate binding module 77
       0.11   12.4   0.0       0.19   11.5   0.0    1.5  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP


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 !   20.3   0.1   2.8e-08   0.00017     479     551 ..      23      95 ..       6      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.8e-08
                                       EEEEETTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEETTEEEEEXSS.XSXXXTTSEEEEEEXHH CS
                      tRNA-synt_2c 479 veegeevgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkakgvvlhkgkleegklkvgdkvkaevdee 551
                                       v   e   + +d+T f+++  Gq++D+G i  +g++  ++dv   + ++  +   ++ +  vg++++ ++d++
  gi|518652567|ref|YP_008142087.1|  23 VLMCEFTDLTVDKTIFFPTMDGQQNDKGEIVIDGKTYGIVDVWTDGDYIHLISLDTYPENVVGKTIQQKLDWD 95 
                                       55555566889********************************999998888878889999*********997 PP

>> CBM77  Carbohydrate binding module 77
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   3.8e-05      0.23       4      37 ..      25      59 ..      21      61 .. 0.78
   2 ?   -1.2   0.0      0.42   2.5e+03      45      72 ..     120     147 ..     110     169 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                             CBM77  4 vcsFtakgkss.sff.tvtGnlstskgtvtinGlty 37
                                      +c+Ft  + +   ff t+ G+ +++kg+++i+G+ty
  gi|518652567|ref|YP_008142087.1| 25 MCEFTDLTVDKtIFFpTMDGQ-QNDKGEIVIDGKTY 59
                                      799999998773555355565.59***********9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.42
                             CBM77  45 SktsisFtttekmtltlvfaesdsekik 72 
                                       +k +is t ++k+ + l++++  +  +k
  gi|518652567|ref|YP_008142087.1| 120 AKSRISQTYDDKAWVDLYIDNITEDIVK 147
                                       5667777777777777777765444443 PP

>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.2e-05      0.19       8      73 ..      34     101 ..      31     155 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
                   CPSase_sm_chain   8 dGtvfeGksfgakeavGEvvfnTgmtGYqeiltDpsYagqilvltypl..iGnyGvneedvesekikv 73 
                                       d t+f  ++ g+++  GE+v+   + G  ++ tD  Y + i + typ   +G++  ++ d++ ++i++
  gi|518652567|ref|YP_008142087.1|  34 DKTIFFPTMDGQQNDKGEIVIDGKTYGIVDVWTDGDYIHLISLDTYPEnvVGKTIQQKLDWDVRSIHM 101
                                       556777777788999********************************633777777777777755443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 1819.40
//
Query:       gi|518652568|ref|YP_008142088.1|  [L=250]
Description: tRNA pseudouridine synthase A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-15   55.7   0.9    8.3e-13   48.7   0.4    3.1  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.0    0.0083   1.5e+02       5      65 ..       9      60 ..       6      94 .. 0.65
   2 !   48.7   0.4   4.6e-17   8.3e-13       4      69 ..     123     182 ..     121     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0083
                   PseudoU_synth_1  5 lvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl 65
                                      ++Gt + g f  q+ +++n+v   +   ++++       +  ++++++++d+ V a ++v+
  gi|518652568|ref|YP_008142088.1|  9 YDGTSFTG-F--QRGNGENSVEDSIIKILKKYG------IGNNIESAARTDRYVSARGNVM 60
                                      88999888.8..444444444433333333222......2357888899999998888887 PP

  == domain 2  score: 48.7 bits;  conditional E-value: 4.6e-17
                   PseudoU_synth_1   4 elvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavg 69 
                                       e+vG+hdf +fck ++  +ntvrti++++ +    ++++++ ++++g++F++hq+R m++ ++   
  gi|518652568|ref|YP_008142088.1| 123 EFVGQHDFVNFCKLDS--RNTVRTIKSINYS----TRNGFYIINIQGRSFVWHQIRSMMAFALMGK 182
                                       79*********96665..78***********....77899********************985433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1918.58
//
Query:       gi|518652569|ref|YP_008142089.1|  [L=96]
Description: hypothetical protein FACI_IFERC00001G1208 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-13   49.4   0.7    6.3e-09   35.5   0.5    2.1  2  RHH_1            Ribbon-helix-helix protein, copG family
  ------ inclusion threshold ------
      0.019   15.5   0.5        1.6    9.3   0.0    2.1  2  CopG_antitoxin   CopG antitoxin of type II toxin-antitoxin sy
      0.022   14.8   0.1      0.032   14.3   0.1    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
       0.15   12.5   3.5       0.41   11.0   0.4    2.4  2  Ca_bind_SSO6904  Calcium binding protein SSO6904


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 !   35.5   0.5   1.4e-12   6.3e-09       1      38 [.       6      44 ..       6      45 .. 0.97
   2 !   12.4   0.0   2.6e-05      0.12       4      37 ..      56      90 ..      54      91 .. 0.93

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 1.4e-12
                                      EEEEEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHHH CS
                             RHH_1  1 rvsirldeellerLdelarrrg.rSrSelIReAlreyle 38
                                      r++ir++e+l+ +L+e++++ + +S Se+IR A+ e+++
  gi|518652569|ref|YP_008142089.1|  6 RITIRVSEDLINQLQEIVEKNQySSISEAIRLAISEFIT 44
                                      8***********************************997 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.6e-05
                                      EEEEHHHHHHHHHHHHHHT.SSHHHHHHHHHHHHH CS
                             RHH_1  4 irldeellerLdelarrrg.rSrSelIReAlreyl 37
                                      ++l+++++ +L+e +  ++  S+ +lIR  lrey 
  gi|518652569|ref|YP_008142089.1| 56 LKLPRNIYTELEEEVNNGNaISVNDLIRFILREYA 90
                                      68999****************************96 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 ?    5.3   0.1    0.0064        28      43      65 ..       5      27 ..       3      42 .. 0.77
   2 ?    9.3   0.0   0.00036       1.6      39      78 ..      48      88 ..      26      89 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0064
                    CopG_antitoxin 43 ksislrlpedlLealkekAnkrd 65
                                      ++i++r++edl+++l+e  +k +
  gi|518652569|ref|YP_008142089.1|  5 YRITIRVSEDLINQLQEIVEKNQ 27
                                      57999**********98777665 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00036
                    CopG_antitoxin 39 kkktksislrlpedlLealkekAnk.rdvpyqslikellee 78
                                      +  t ++ l+lp ++ ++l e+ n+   ++++ li+ +l+e
  gi|518652569|ref|YP_008142089.1| 48 ENATSKVDLKLPRNIYTELEEEVNNgNAISVNDLIRFILRE 88
                                      567889*************998765278*********9987 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   7.2e-06     0.032      98     135 ..      43      81 ..       7      84 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.2e-06
                                       CHHH.S..EEEEE--SS-SB-TTGG.GSTTCCCEEHHHH CS
                      Shikimate_DH  98 alkkrkkplllvDiavPRdvepeva.eledvrlytvDdL 135
                                       + k+r++ +  vD+ +PR++ +e++ e+++ ++++v+dL
  gi|518652569|ref|YP_008142089.1|  43 ITKNRENATSKVDLKLPRNIYTELEeEVNNGNAISVNDL 81 
                                       44566688899*********999862689999*****99 PP

>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.5     0.023     1e+02      18      59 ..      10      49 ..       5      52 .. 0.70
   2 ?   11.0   0.4   9.1e-05      0.41      14      43 ..      49      78 ..      34      96 .] 0.76

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.023
                                      -S-HHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHTHHHHHHT CS
                   Ca_bind_SSO6904 18 kvdveevekileeieedlrksnnikssiifvyanhveevkkn 59
                                      +v+ ++++++ e +e++     +i  +i  + ++++ + ++n
  gi|518652569|ref|YP_008142089.1| 10 RVSEDLINQLQEIVEKNQYS--SISEAIRLAISEFITKNREN 49
                                      67778888877777776544..78888888888777665555 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 9.1e-05
                                      HHT--S-HHHHHHHHHHHHHHHHHSS-HHH CS
                   Ca_bind_SSO6904 14 kfkgkvdveevekileeieedlrksnniks 43
                                      +  +kvd ++ ++i +e+ee+++++n+i  
  gi|518652569|ref|YP_008142089.1| 49 NATSKVDLKLPRNIYTELEEEVNNGNAISV 78
                                      4569*********************99864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1292  (0.072062); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 684.76
//
Query:       gi|518652570|ref|YP_008142090.1|  [L=533]
Description: hypothetical protein FACI_IFERC00001G1209 [Ferroplasma acidarmanus fer1]
Scores for 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   97.0   0.0    1.4e-27   96.5   0.0    1.2  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
    4.7e-12   45.9   0.0    8.4e-12   45.1   0.0    1.3  1  B3_4             B3/4 domain
    4.8e-11   42.8   0.1      2e-10   40.8   0.1    2.1  2  B5               tRNA synthetase B5 domain
  ------ inclusion threshold ------
      0.038   14.2   0.1         12    6.2   0.1    2.6  2  PhetRS_B1        Phe-tRNA synthetase beta subunit B1 domain


Domain annotation for each model (and alignments):
>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.5   0.0   3.1e-31   1.4e-27       1     214 []     334     524 ..     334     524 .. 0.94

  Alignments for each domain:
  == domain 1  score: 96.5 bits;  conditional E-value: 3.1e-31
                   tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRts 77 
                                       Ip +  k++ t+  + + ++ ++ ++ +l++++++Ev ++ + se+ ++k       +  v + nP s ++sv+R  
  gi|518652570|ref|YP_008142090.1| 334 IPAKPLKTSGTGV-PYTPNEDENIIKGILTSINYQEVRSFILNSEDFYRKT----GYSGDVIITNPKSLEYSVIRDK 405
                                       7777778888888.456667799*************************999....778899**************** PP

                   tRNA_synthFbeta  78 LlpglLevlarNlargnedvrlFEigkvflkdseeelpeeerhlaivltgkreeeswsekaravdfydlkgiveall 154
                                       L pg++  la N +r+++ +++FEig+v+ +       ++e+hl++++ +++           + + d+ +++e ll
  gi|518652570|ref|YP_008142090.1| 406 LYPGIISLLAINKRRKLP-LKIFEIGQVVVSG------NQESHLCVLYNNSK-----------AAYSDIYAVLEYLL 464
                                       ******************.*************......89******999999...........************** PP

                   tRNA_synthFbeta 155 eslgiekvefepaehpalhpgrsAeikvdgkevGvlGelhpevleafdlkqrvyvfEldl 214
                                       ++   +  ++ + +++    gr  +i+++++++G++Ge+ p++l +f+++++v+++E++l
  gi|518652570|ref|YP_008142090.1| 465 ARTINAGAKVLQGNYNEIISGRGGDIVYENTTLGIIGEMDPSILVDFGIQNPVAFMEINL 524
                                       99877899**************************************************97 PP

>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.1   0.0   1.9e-15   8.4e-12      34     131 ..     109     232 ..      92     237 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.1 bits;  conditional E-value: 1.9e-15
                                       ---HHHHHHHHHHHHHT-.....-EEEEEGGGTBTEEE.EEE--TTEEEEBTTS-EEEE-T................ CS
                              B3_4  34 pinnvVDitNyvmlelgq.....PlhafDldkiqgdiv.vrlakegeklvtldgkerelde................ 88 
                                        ++ ++D +++++  +g+     +++++Dld+i++++    + k+  +++t d+ + +  e                
  gi|518652570|ref|YP_008142090.1| 109 YYSHIIDYQEKLHETIGKsrkkmAIGIHDLDNISPPFLfTMRDKKTLEFTTYDNFHGTAGEilekhdkgkqyhqlis 185
                                       5899******************************988845556666799999866555555788899********** PP

                                       ...TSEEEETEEEEE.EETTTEEBTTTB--TT--EEEEEEEE--HHH CS
                              B3_4  89 ...edlviadsekpv.slagvmggeeskvsedTknvfleaaafdpvs 131
                                            +vi ds++ v s++++++g +sk+ ++T++ f+ +++ d  +
  gi|518652570|ref|YP_008142090.1| 186 sdeMVPVILDSKEDVmSMPPIINGLKSKIGNNTSKLFFDITGTDYNA 232
                                       *999999******999************************9987655 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.5   1.1e+04       7      21 ..      25      39 ..      22      51 .. 0.72
   2 !   40.8   0.1   4.4e-14     2e-10       1      67 []     268     331 ..     268     331 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.5
                                      HHHHHHTS---HHHH CS
                                      xxxxxxxxxxxxxxx RF
                                B5  7 kinkllGidlseeei 21
                                       +  ++G +++ee+ 
  gi|518652570|ref|YP_008142090.1| 25 DFAGIIGYSIEEENN 39
                                      566788888888754 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 4.4e-14
                                       EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                                       ++++++++ kl+G  l++e+++ +L+++g++  e +  +++V vP  R D+  ++D+iE++a +yGY
  gi|518652570|ref|YP_008142090.1| 268 IEITHKEVTKLMG--LEPENTVILLRKMGYRC-EVTSGGYRVNVPGNRIDVMGPVDIIEDIAKAYGY 331
                                       5788999******..89999**********86.999******************************9 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 ?    6.2   0.1    0.0027        12      25      81 ..       9      66 ..       2      68 .. 0.72
   2 ?    5.1   0.0    0.0057        26      34      69 ..     282     317 ..     265     328 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0027
                         PhetRS_B1 25 edllfefGlElDeiveeeekkk.adkkseeviykidipAnryDLLcleglaralkvFl 81
                                      +dl+ e G+      ++ +     + ++e++ +k++    r+DL ++  l  ++k+F 
  gi|518652570|ref|YP_008142090.1|  9 DDLIHEIGINYYSKLSDFAGIIgYSIEEENNEVKLEFNPDRPDLFSFYALKSNMKIFY 66
                                      556666666655555555522214556778889************************7 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0057
                         PhetRS_B1  34 ElDeiveeeekkkadkkseeviykidipAnryDLLc 69 
                                       E  + v    k    ++ ++  y++++p+nr D++ 
  gi|518652570|ref|YP_008142090.1| 282 EPENTVILLRKMGYRCEVTSGGYRVNVPGNRIDVMG 317
                                       5555554444455667778888***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 3455.08
//
Query:       gi|518652571|ref|YP_008142091.1|  [L=445]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.1e-08   31.7  83.7    3.1e-07   29.6  82.9    2.1  1  AA_permease_2  Amino acid permease
    3.9e-05   22.4  50.6    3.9e-05   22.4  50.6    2.4  2  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 !   29.6  82.9   3.5e-11   3.1e-07       8     395 ..      11     390 ..       4     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 3.5e-11
                     AA_permease_2   8 alvigsv......igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaf 78 
                                       + +++s+      i ++++++  a+sg ++ +++++  ++++s+  l+++  ls    ++gG y+y+ +a g+ ++f
  gi|518652571|ref|YP_008142091.1|  11 MQSFTSIgpmldfIALFSIIS--AYSGSMLPFVVIF--SFLLSYFTLYTIYSLSRIYVTNGGYYSYVGNALGRGAGF 83 
                                       555555555566566677777..7666665555444..44444679999999************************* PP

                     AA_permease_2  79 lsawfnwfayvpvlasi..lsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkil 153
                                       ++  ++ +  v++++ i  +++++sy +  l+++  + ++l y++  +++ +v  + +rg k s +++ i g l i 
  gi|518652571|ref|YP_008142091.1|  84 FVLLLYIIYSVLTVPNIslFISGFSYSILELAGF--TAPVLKYVLLLIFIGTVYYVVSRGLKVSITYTLIAGFLEI- 157
                                       **99999999998865422677888887777655..6789************************************. PP

                     AA_permease_2 154 lpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee.vkk.kdvpkaifigll 228
                                        ++i++ i+ +i+ ++g +       + ++ +++p+++++++  +++f+G  s++ +se+ +    ++pk +f+++ 
  gi|518652571|ref|YP_008142091.1| 158 AFIILMSIIFIIYRSPGFSF------SGINFSFNPFFFGVIF-GILAFSGGGSSIFISEQtASShINTPKSLFLSFT 227
                                       69999999999997776664......4577789999999999.56788888999999999544457*********** PP

                     AA_permease_2 229 ivlvlyllvniaflgvvpddei.anlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealar 304
                                       i++++  + ++a+l+  +  ++ a  sn+ ++++l+ +++g          +++l ++++i++a+  s  +l+a++ 
  gi|518652571|ref|YP_008142091.1| 228 ISGIIMAVSAFALLMFAGFAGLrAYESNSFYITELVQARLG--------TPFLILFSFFGIMSAFNLSVSYLNAFV- 295
                                       *******************9996667777877888888877........556677778888888888888899888. PP

                     AA_permease_2 305 dgvlPrffakvn.kfgspiraiiltaivslillllfllassaayn...fllsvsslgliisyllliigalilrkkrp 377
                                         + P+f+++ n k     + +i ++ v+++ + +f+++ +  +n   +++ + s+ +ii+ ++  i+++++ ++++
  gi|518652571|ref|YP_008142091.1| 296 -HMVPKFYHDFNlKGEFNRNKLIAILSVTSAGIAIFSGYYGGFFNsfvIIAGIISFVYIIIHIISNISLIKIFRRKK 371
                                       .69*********99545555555555555555566665544444444499999999999999999999999999988 PP

                     AA_permease_2 378 hl.krpgkilvaiigalfl 395
                                        + +    i+++i ++l++
  gi|518652571|ref|YP_008142091.1| 372 FFmPVLSSIILTIAFILSF 390
                                       8744433343444333322 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  50.6   4.4e-09   3.9e-05       2     299 ..       9     283 ..       8     305 .. 0.80
   2 ?   -9.9  20.0         2   1.8e+04      85     160 ..     338     423 ..     317     429 .. 0.62

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-09
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       +++++  ++ +   f++l +++s+ ++  +  +++++++ ++++ ++++ ++ ++  +gg+y y+ + lg+ +Gf++
  gi|518652571|ref|YP_008142091.1|   9 AVMQSFTSIGPMLDFIALFSIISAYSGSMLPFVVIFSFLLSYFTLYTIYSLSRIYVTNGGYYSYVGNALGRGAGFFV 85 
                                       78888889777889*************99************************************************ PP

                       AA_permease  79 Glnylfswitvlale.ltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafi 154
                                        l+y +++++++++  l++++   +++    + ++a v   v+l+++++  ++ v    ++++ ++li++   iafi
  gi|518652571|ref|YP_008142091.1|  86 LLLYIIYSVLTVPNIsLFISGFSYSIL--ELAGFTAPVLKYVLLLIFIGTVYYVVSRGLKVSITYTLIAGFLEIAFI 160
                                       *************96133333333333..22333344458888899999999999999999999************* PP

                       AA_permease 155 ivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeks 231
                                       i+  ++++   +++g     ++++g                ++f  f+++ ++ ++af+G ++ + i++ ++++  +
  gi|518652571|ref|YP_008142091.1| 161 ILM-SIIFIIYRSPG-----FSFSGI--------------NFSFNPFFFGVIFGILAFSGGGSSIFISEQTASSHIN 217
                                       **9.45566666777.....223333..............46688******************************** PP

                       AA_permease 232 iPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavilta 299
                                        Pk+    + + +i+   s++++ +  +   l   ++      + ++++  +g ++l  +  ++i +a
  gi|518652571|ref|YP_008142091.1| 218 TPKSLFLSFTISGIIMAVSAFALLMFAGFAGLRAYESNSFY--ITELVQARLGTPFLILFSFFGIMSA 283
                                       ******99999999999999999888888777777765555..6666777777776666555555554 PP

  == domain 2  score: -9.9 bits;  conditional E-value: 2
                       AA_permease  85 switvlaleltaasiliqfwelvtdlpkawvt..........gavflvvlliinlvgvkvygeaefi.lalikiiai 150
                                       +  +v++++++  +++i  +  ++ ++ + ++          ++++l++ +i+++ g+ +y +  +i ++li +i+i
  gi|518652571|ref|YP_008142091.1| 338 FNSFVIIAGIISFVYIIIHI--ISNISLIKIFrrkkffmpvlSSIILTIAFILSFSGNTGYYA--VInYFLIGFIMI 410
                                       24445555555554444444..45555445556677778888999999999999999876554..333566666666 PP

                       AA_permease 151 iafiivg...iil 160
                                        afi+++   ii+
  gi|518652571|ref|YP_008142091.1| 411 SAFIVILvrkIIP 423
                                       6666665446665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1035  (0.0577277); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.31s 00:00:01.00 Elapsed: 00:00:00.48
# Mc/sec: 2790.05
//
Query:       gi|518652572|ref|YP_008142092.1|  [L=2061]
Description: hypothetical protein FACI_IFERC00001G1211 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-12   45.6  77.9    2.5e-06   27.7   4.0    9.6 10  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    2.2e-06   28.0   1.5    2.2e-06   28.0   1.5    4.1  3  PMT_2            Dolichyl-phosphate-mannose-protein mannosylt
  ------ inclusion threshold ------
      0.022   15.0   8.3        6.1    7.2   0.0    5.7  4  Big_6            Bacterial Ig domain
       0.13   12.3   0.4        0.4   10.7   0.4    1.9  1  Halogen_Hydrol   5-bromo-4-chloroindolyl phosphate hydrolysis
        5.9    6.5   6.9         29    4.2   0.3    3.5  3  DUF4131          Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.7      0.35   1.3e+03      30      51 ..     758     783 ..     746     801 .. 0.70
   2 !   27.7   4.0   6.9e-10   2.5e-06       2      61 ..     886     946 ..     885     972 .. 0.77
   3 !    8.8   5.2   0.00054       1.9       2      80 ..     984    1064 ..     983    1067 .. 0.79
   4 !   21.5   5.8   5.7e-08    0.0002       5      68 ..    1071    1134 ..    1069    1149 .. 0.88
   5 !    9.8   0.9   0.00026      0.94      10      70 ..    1153    1212 ..    1147    1221 .. 0.73
   6 ?   -0.3   1.6      0.37   1.3e+03       2      53 ..    1447    1505 ..    1446    1527 .. 0.69
   7 ?   -1.4   0.2       0.8   2.9e+03      27      45 ..    1575    1593 ..    1560    1609 .. 0.73
   8 !   21.0   1.2   8.4e-08    0.0003       2      81 ..    1622    1701 ..    1621    1702 .. 0.86
   9 ?   -3.3   0.1       3.2   1.1e+04      49      70 ..    1843    1863 ..    1815    1875 .. 0.62
  10 ?   -0.8   0.3      0.52   1.9e+03      49      77 ..    1942    1969 ..    1916    1972 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                   CarboxypepD_reg  30 astttdadGafrlrglpp....gtys 51 
                                         ++t++  +++l++lp+     +y 
  gi|518652572|ref|YP_008142092.1| 758 VVAVTNTGAQYTLNNLPTgvtvSNYL 783
                                       5578999999*******944444454 PP

  == domain 2  score: 27.7 bits;  conditional E-value: 6.9e-10
                   CarboxypepD_reg   2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglpp.gtysvtvsapGyat 61 
                                       i+G++t+a+g +iag++Vt++++ +     +tt+++G+++++glp  +t      + + +t
  gi|518652572|ref|YP_008142092.1| 886 IHGQITNANGIGIAGVHVTIEDQYGIPHEVVTTNSTGYYSITGLPGnDTLVYSTGSVNSDT 946
                                       99*******************87666778899************97444444444444444 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00054
                   CarboxypepD_reg    2 isGrVtda...sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagq 73  
                                        + G+Vt     s a i   t+t+tn +t     t   ++G ++l+++ p  y+ t++++G   ++++++++t g+
  gi|518652572|ref|YP_008142092.1|  984 VYGYVTVDngtSHASINSGTITLTN-STYGINVTAPITNGMYSLSNVIPYGYNATITSNGKTYTNFTTLQVT-GK 1056
                                        7899985513356799999*****6.555566677789***********99****************9**99.55 PP

                   CarboxypepD_reg   74 tttl.dit 80  
                                        +++l ++t
  gi|518652572|ref|YP_008142092.1| 1057 SQQLsNLT 1064
                                        55554655 PP

  == domain 4  score: 21.5 bits;  conditional E-value: 5.7e-08
                   CarboxypepD_reg    5 rVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevt 68  
                                        +Vt + sg +++g t  + +++++ + + +t ++G++++ g+ pgty++t+ a+G +  ++ +v+
  gi|518652572|ref|YP_008142092.1| 1071 KVTASvSGSGLSGYTAYLNSTSGNYQLTGVTSSSGTYTF-GVYPGTYNITIKANGTEDKSVATVS 1134
                                        799999*********************************.6***************999986544 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.00026
                   CarboxypepD_reg   10 sgapiagatVtvtnadt.gtvastttdadGafrlrglppgtysvtvsapGyatatreevtlt 70  
                                        sg++ ++a+++++ +++ +  +++t +a+Ga++++ +p g y++  + +    +++ ++ +t
  gi|518652572|ref|YP_008142092.1| 1153 SGNATPYAKISFYFDGQiSDYKNVTANASGAYNIS-MPYGIYTIYSTNTSGGVFAK-TINVT 1212
                                        89999******995322134699***********7.*******9886666655554.35555 PP

  == domain 6  score: -0.3 bits;  conditional E-value: 0.37
                   CarboxypepD_reg    2 isGrVtda..sgapiagatVtvtnadtgt....vastttdadG.afrlrglppgtysvt 53  
                                        ++G+V+++  s   +++ ++ +t ++++t    + +t  +++G +  l+ lp+gty++ 
  gi|518652572|ref|YP_008142092.1| 1447 LTGTVVNSsaSQSFVKNSNLYFTFKNSNTtitgSGTTLFNSTGvNVGLNHLPAGTYTLY 1505
                                        68999986456788999999988766654333356677789995566888999999875 PP

  == domain 7  score: -1.4 bits;  conditional E-value: 0.8
                   CarboxypepD_reg   27 gtvastttdadGafrlrgl 45  
                                         t+++  t+++Ga++  + 
  gi|518652572|ref|YP_008142092.1| 1575 ITSSGNFTNSTGAYTYVNT 1593
                                        4667788999999997665 PP

  == domain 8  score: 21.0 bits;  conditional E-value: 8.4e-08
                   CarboxypepD_reg    2 isGrVtdasgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtv...sapGyatatreevtltagq 73  
                                        isG V    g+ ++g++V++t +++++  +tt+ ++G f+l+ l pgty + +   +a G + a +++vtl++ +
  gi|518652572|ref|YP_008142092.1| 1622 ISGNVY-LKGTNVSGVNVILT-KNGKQIDNTTSSSTG-FNLTKLVPGTYGLYAnytTAGGNEYAYFQNVTLQPFK 1693
                                        788887.47899*********.466677888888888.9**************8888888888888********* PP

                   CarboxypepD_reg   74 tttlditL 81  
                                        + t +i L
  gi|518652572|ref|YP_008142092.1| 1694 NLTYNISL 1701
                                        *****988 PP

  == domain 9  score: -3.3 bits;  conditional E-value: 3.2
                   CarboxypepD_reg   49 tysvtvsapGyatatreevtlt 70  
                                        +y++tv +   +t+ + ++t+ 
  gi|518652572|ref|YP_008142092.1| 1843 PYNLTVPMGANKTVVV-NITIP 1863
                                        5666665555555555.34444 PP

  == domain 10  score: -0.8 bits;  conditional E-value: 0.52
                   CarboxypepD_reg   49 tysvtvsapGyatatreevtltagqtttl 77  
                                        +y++++ a+       ++vtl+ gq++t+
  gi|518652572|ref|YP_008142092.1| 1942 DYDIVAYATENGKNV-TNVTLSTGQSVTI 1969
                                        566666554444444.6899998888876 PP

>> PMT_2  Dolichyl-phosphate-mannose-protein mannosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   1.5   6.1e-10   2.2e-06      31      97 ..     122     190 ..      86     196 .. 0.88
   2 ?   -7.4  12.0         5   1.8e+04      44     112 ..     209     279 ..     202     341 .. 0.66
   3 ?    2.1   0.4     0.055     2e+02      40      78 ..     395     432 ..     381     454 .. 0.59

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.1e-10
                             PMT_2  31 agvltilllyllarrlfgkraallaalllavvplfvalsa..lftpdaplvllwalalylllraleknk 97 
                                        g+l i+ +yl+ +++fgk+a+l+aa+l +++p +++++    ++  +p + +  l++y++ +a+ + k
  gi|518652572|ref|YP_008142092.1| 122 YGALLIIPVYLITKQIFGKKAGLFAAVLFTIMPGNLTSGIltDGRAHTPELIFAFLSIYFFEMAVITAK 190
                                       6899*********************************999888999******************98766 PP

  == domain 2  score: -7.4 bits;  conditional E-value: 5
                             PMT_2  44 rrlfg.kraallaalllavvplfvalsalftpdaplvllwalalylllraleknklkyw.llagvlfGlgf 112
                                       ++++  +++a + al+ av++  +++  ++ p++  +ll+  a+ ll+ + +k+ + y+ +++ + ++++f
  gi|518652572|ref|YP_008142092.1| 209 KNYYEeNKIATIYALMSAVSLGGLIVFWQGFPYIEVILLIYVAVQLLYNLFTKKPTGYLtYISTIYVAASF 279
                                       55555456666667777777766666667777777777777777777777777777777644444444433 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.055
                             PMT_2  40 yllarrlfgkraallaalllavvplfvalsa.lftpdapl 78 
                                       +++ r l  k+ a l +++ a++ +f+   a  f++    
  gi|518652572|ref|YP_008142092.1| 395 FIIYRFLKEKKEATLLVIIFAIFSIFMSFEAaRFNIT--A 432
                                       3344444446777777777777776666665344443..3 PP

>> Big_6  Bacterial Ig domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.3     0.025        89      15      51 ..     891     927 ..     883     936 .. 0.89
   2 ?   -2.5   0.0       1.8   6.3e+03      13      39 ..     943     970 ..     933     976 .. 0.75
   3 ?    3.7   0.6     0.021        75      14      54 ..    1073    1113 ..    1045    1133 .. 0.81
   4 ?    7.2   0.0    0.0017       6.1      14      52 ..    1149    1188 ..    1139    1195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
                             Big_6  15 ttltGkaeagatVtvkdadgtvlgtgtadadGeFsvt 51 
                                       t  +G + ag  Vt+ d+ g     +t +++G +s+t
  gi|518652572|ref|YP_008142092.1| 891 TNANGIGIAGVHVTIEDQYGIPHEVVTTNSTGYYSIT 927
                                       55689999***************************97 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.8
                             Big_6  13 dgttltGkaeaga.tVtvkdadgtvlgt 39 
                                       + +tl+G+   g+ +V v++++g+ +g+
  gi|518652572|ref|YP_008142092.1| 943 NSDTLNGTNVIGTqSVAVSQNQGNRIGN 970
                                       4567888888886359999999998886 PP

  == domain 3  score: 3.7 bits;  conditional E-value: 0.021
                             Big_6   14 gttltGkaeagatVtvkdadgtvlgtgtadadGeFsvtlep 54  
                                        +++++G++  g t  +   +g+   tg+ +++G++++ + p
  gi|518652572|ref|YP_008142092.1| 1073 TASVSGSGLSGYTAYLNSTSGNYQLTGVTSSSGTYTFGVYP 1113
                                        45689999999999999999999999999999999987755 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.0017
                             Big_6   14 gttltGkaeagatVtv.kdadgtvlgtgtadadGeFsvtl 52  
                                        +++++G+a + a++    d + +  +++ta+a+G++++++
  gi|518652572|ref|YP_008142092.1| 1149 TAKVSGNATPYAKISFyFDGQISDYKNVTANASGAYNISM 1188
                                        568***********993444445569***********987 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.4   0.00011       0.4       4      55 ..     408     459 ..     407     479 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                    Halogen_Hydrol   4 wllsiliavivalvsffllgfsfflalliailggilvyvasrknkkkkhlkk 55 
                                       +ll+i++a++ +++sf +++f++ +a ++ailgg l++ ++ k++  +  kk
  gi|518652572|ref|YP_008142092.1| 408 TLLVIIFAIFSIFMSFEAARFNITAAPAYAILGGGLIMYFVDKIRHNESTKK 459
                                       6899**********************99996666666655554444444333 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.9     0.016        58       9      55 ..     299     345 ..     291     365 .. 0.68
   2 ?    4.2   0.3    0.0082        29       6      65 ..     384     439 ..     379     475 .. 0.68
   3 ?   -0.5   0.0      0.24   8.6e+02      32      65 ..     471     515 ..     430     520 .. 0.64

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.016
                           DUF4131   9 llalllllllllllllrrrprrrvllllllllllallgfalrapqpn 55 
                                        la++l+++ + +l++  ++r+ ++++ +l+l+++++ f+++  +p+
  gi|518652572|ref|YP_008142092.1| 299 PLAMGLMIIGFGILINIVARRPWIITIPALVLVTIAGLFVISKTNPA 345
                                       23333344444444443388999999999999999998888777665 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0082
                           DUF4131   6 alvllalllllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles 65 
                                        l+ll+++++ +++  +     + ++ ++ll ++++++++++ ++a++ n +  + ++ +
  gi|518652572|ref|YP_008142092.1| 384 GLFLLGIAGVPFIIYRF----LKEKKEATLLVIIFAIFSIFMSFEAARFNITAAPAYAIL 439
                                       45555555555555555....577888888888888888888888888888777777655 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.24
                           DUF4131  32 v...........llllllllllallgfalrapqpnandlsqlles 65 
                                                   +++l+l++  +++ f + +p++na +++++l+s
  gi|518652572|ref|YP_008142092.1| 471 KnisgvtigfavIVVLILIIPSGMGAFSAAVPENNAASYNHILNS 515
                                       256666666665888999999999999999999999999999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (2061 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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):               5  [number of targets reported over threshold]
# CPU time: 1.24u 0.36s 00:00:01.60 Elapsed: 00:00:00.60
# Mc/sec: 10430.96
//
Query:       gi|518652573|ref|YP_008142093.1|  [L=281]
Description: hypothetical protein FACI_IFERC00001G1212 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.4    7.7   8.2        2.7    8.4   5.9    1.9  2  DUF11     Domain of unknown function DUF11


Domain annotation for each model (and alignments):
>> DUF11  Domain of unknown function DUF11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0      0.26   4.6e+03      51      51 ..      66      66 ..      23     108 .. 0.58
   2 ?    8.4   5.9   0.00015       2.7      12      77 ..     138     211 ..     117     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.26
                             DUF11 51 s 51
                                      +
  gi|518652573|ref|YP_008142093.1| 66 G 66
                                      1 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00015
                             DUF11  12 pGdtvtytltvtNtgpasangvvvtDtlPaglayvsvsas.......qgtasaltsv.gsLeagesatlsftvr 77 
                                         + v ++ t +Nt p++ ++++vt t   g++ v +  s       ++t++ + +v  sL + ++ tl++t +
  gi|518652573|ref|YP_008142093.1| 138 VSAPVIFNSTIKNTDPVPITNITVTYTISHGTSSVVAGIShineiksNSTYKDNITVpASLVYKGKDTLTVTTN 211
                                       5556778889*********************999999999999999999*********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1901.53
//
Query:       gi|518652574|ref|YP_008142094.1|  [L=213]
Description: hypothetical protein FACI_IFERC00001G1213 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0087   15.8   0.2      0.024   14.4   0.0    1.7  2  DUF460    Protein of unknown function (DUF460)
  ------ inclusion threshold ------
        0.2   12.1   0.1       0.99    9.9   0.1    1.9  1  Tex_YqgF  Tex protein YqgF-like domain


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 !   14.4   0.0   2.6e-06     0.024      25      48 ..      76      99 ..      58     108 .. 0.84
   2 ?   -1.7   0.0      0.24   2.1e+03     105     134 ..     141     169 ..     138     178 .. 0.48

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.6e-06
                            DUF460 25 kkkrkkklivGiDPGittgiavld 48
                                      +k++ +++i+GiDPG   giav++
  gi|518652574|ref|YP_008142094.1| 76 NKSQFTRVIIGIDPGPRPGIAVMS 99
                                      4677789***************86 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.24
                            DUF460 105 PeedlsveeKeelaeklsekekvkykddHe 134
                                       P++d+ +++ +++a  +  +e+  ++++H+
  gi|518652574|ref|YP_008142094.1| 141 PNRDIIIKQLKNIAPMVIVNEEN-TSTPHK 169
                                       56666666666665554444422.344443 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 ?    9.9   0.1   0.00011      0.99       2      96 ..      83     165 ..      82     169 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00011
                                       -EEEEE--STT-EEEEEE-TTS-EEEEEEE--STTT--HHHHHHHHHHHHHHTT--EEEEESSTTHHHHHHHHHHHH CS
                          Tex_YqgF   2 vvlglDPgyrtGcKlavvdetgkvletaviyphepkkkveeakkklkklvkkykveliaiGnGtasreteklvaeli 78 
                                       v++g+DPg r G+  av++++  vl +a   p     ++   k+ + ++vk+y+ ++i i  G + r   +++ + +
  gi|518652574|ref|YP_008142094.1|  83 VIIGIDPGPRPGI--AVMSDN--VLMEAWECP-----TICGVKDDVLDVVKNYSYRYIMIKIGNGDRPNRDIIIKQL 150
                                       7899999999995..666543..333333333.....4667788899999999888777766666788888888888 PP

                                       HHGGG--EEEEE--TTHH CS
                          Tex_YqgF  79 keeelkvkyvivsEaGaS 96 
                                       k+    + +viv+E  +S
  gi|518652574|ref|YP_008142094.1| 151 KNI---APMVIVNEENTS 165
                                       876...678999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.28s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1399.36
//
Query:       gi|518652575|ref|YP_008142095.1|  [L=326]
Description: hypothetical protein FACI_IFERC00001G1214 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-23   82.5   0.0    5.5e-23   81.8   0.0    1.4  1  ALP_N     Actin like proteins N terminal domain
  ------ inclusion threshold ------
      0.061   11.9   0.0      0.083   11.5   0.0    1.1  1  MutL      MutL protein


Domain annotation for each model (and alignments):
>> ALP_N  Actin like proteins N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   0.0   6.1e-27   5.5e-23       1     147 []       5     153 ..       5     153 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 6.1e-27
                                       EEEE-SSEEEEE-GGG-EEEEES-EEEE--..SS-EETTT.EEEBBS.STTSEEEGGG--..SSSEB--SSTT-TTS CS
                             ALP_N   1 GiDiGygntKavsgeletvifPSvvapaeerslssligegdglrvev.dgekyfvGelaerqgssasrsldddkaas 76 
                                       G+D+Gyg+tK+v++  ++ +fPS + pae+r+ +++++ +   ++ v dge++++Ge+a   g++ ++   d ++++
  gi|518652575|ref|YP_008142095.1|   5 GVDLGYGDTKLVTEGNKKAKFPSRWTPAESRNWGIGGNIP---VISVnDGESFIFGEDAT--GTNLREPQGDGRLTD 76 
                                       8*************99**************8888777666...66666***********5..88888889******* PP

                                       TTTHHHHHHHHHHH.....---EEEEEEEEE-GGGHHHHHHHHHHHHTTEEEEEE.GGGEEEEEEEEEEEEEETTHH CS
                             ALP_N  77 edykalllaalall.....gkeeevvLvtGLPveqykkqkealkkrlkgehevvs.vngkersvevekvrvipQplG 147
                                       +++ +ll++al+       g++++v+L +G+ ++ ++++  + +k+l+g+   ++  +g+e  ++++k+ + pQ++G
  gi|518652575|ref|YP_008142095.1|  77 PNAIQLLAGALWTSgigheGEKTDVTLSSGVQLGSFDREVVEAAKLLEGKTLKIKsAQGTEQDFKISKLVMRPQGVG 153
                                       **************98665566*****************************88889********************9 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   9.3e-06     0.083     212     264 ..     135     186 ..     111     208 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 9.3e-06
                              MutL 212 glskleelvsaeimpTPaAvlkavellae.eeekglgdllvvDvGGaTTdvhsv 264
                                       g ++  ++ +   +  P+ v+ a+ +l++   ++++g+ +++D+G  TTdv ++
  gi|518652575|ref|YP_008142095.1| 135 GTEQDFKISKL--VMRPQGVGAAIYALNHgILKTQYGNGVIIDIGFKTTDVLTI 186
                                       44444444444..44577888888888887444569***************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2336.19
//
Query:       gi|518652576|ref|YP_008142096.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G1215 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.37
# Mc/sec: 604.94
//
Query:       gi|518652577|ref|YP_008142097.1|  [L=247]
Description: hypothetical protein FACI_IFERC00001G1216 [Ferroplasma acidarmanus fer1]
Scores for complete 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-30  104.5   5.1      1e-29  104.0   5.1    1.3  1  Cas_Cas6    CRISPR associated protein Cas6
  ------ inclusion threshold ------
      0.016   15.6   0.1      0.024   15.0   0.1    1.2  1  N_NLPC_P60  NLPC_P60 stabilising domain, N term


Domain annotation for each model (and alignments):
>> Cas_Cas6  CRISPR associated protein Cas6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   5.1   1.1e-33     1e-29       2     146 .]      96     242 ..      95     242 .. 0.81

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.1e-33
                                       HHCS-EEEETTEEEEEEEEEE----S...--TCEE.EEESS-BBEEEEEEETTCCEEEEE-TTSTTHHHHHHHHHHH CS
                          Cas_Cas6   2 llknkeirlgnnefkveevellkepe...itssevvfktlSPivvrstkkengkkktyylspddeeFsellkenlkk 75 
                                       ll +++i l+ ++++v +++    ++   ++ +  +++++SP++v+  +++n+ +kt  +sp ++eF++ + +n+  
  gi|518652577|ref|YP_008142097.1|  96 LLADENIFLNSTKINVIDIKSHSFDDekyKNIKYYMIEMISPLTVY--ITQNNHRKTF-FSPWSPEFENAISNNIST 169
                                       8999************999995544443433344569*********..6678877776.89**************** PP

                                       HHHHHHSS..SS---EEEEE.E.EEE.......TEEEEEEEEEEEEEE-HHHHHHHHHC-SCS-CCCT-S-EEE CS
                          Cas_Cas6  76 kykalygeekeeklsikpdk.k.vkkivvkkk.etyirGylgrfelegdpellklaydaGlGeknsqGFGmvev 146
                                       k++a+ +++ ++ ++i+p++ k +k+ +v+ + +t i+Gy g+f+l+ d e++k++y++G+G+kns GFG++++
  gi|518652577|ref|YP_008142097.1| 170 KFSAISNNR-NFLFNIRPNNiKnNKDEKVIYFkDTLIKGYNGIFTLKTDSEVMKMLYYTGIGSKNSEGFGCFNI 242
                                       *******98.66666666665313333444446***************************************96 PP

>> N_NLPC_P60  NLPC_P60 stabilising domain, N term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.1   2.6e-06     0.024      31     105 ..     113     187 ..     105     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.6e-06
                                       HHHHS-S-HHHHHHHH-TT--SS-HHHHHHHHHHHHHHHCGGGG-SS--S-HHHHHG...GG-G--SB-TTSSB- CS
                        N_NLPC_P60  31 dlerfpQdvdvyaeaasadrpllsaaeqaaldeefrrryFaPWnqtklsvsaedaawevrrfgkkrgYgeNlqpv 105
                                       d++ +  d + y + + +  +++s+ +    +++ r+ +F+PW+ ++ ++  ++++ +++++ ++r +  N +p 
  gi|518652577|ref|YP_008142097.1| 113 DIKSHSFDDEKYKNIKYYMIEMISPLTVYITQNNHRKTFFSPWSPEFENAISNNISTKFSAISNNRNFLFNIRPN 187
                                       6666677777775444478889999999999*******************************9999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.29s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1621.33
//
Query:       gi|518652578|ref|YP_008142098.1|  [L=614]
Description: CRISPR-associated Csh1 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-75  255.4  45.5    1.5e-75  255.2  45.5    1.0  1  Cas_TM1802  CRISPR-associated protein TM1802 (cas_TM1802)
  ------ inclusion threshold ------
        1.1    9.5   9.5          1    9.6   0.5    4.2  5  DUF1623     Protein of unknown function (DUF1623)


Domain annotation for each model (and alignments):
>> Cas_TM1802  CRISPR-associated protein TM1802 (cas_TM1802)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  255.2  45.5   1.7e-79   1.5e-75       1     607 [.       1     597 [.       1     598 [. 0.81

  Alignments for each domain:
  == domain 1  score: 255.2 bits;  conditional E-value: 1.7e-79
                        Cas_TM1802   1 MleaikeiGeillggegekdeleql.tedpkaekkhvliinfdtekekleykgveeidleefdekktakylYlkkgn 76 
                                       M+ ai  +G  l + +  ++++ ++  ++ k++  ++ i++f+ ++  + ++ ++ ++  e  +k++a++ Y ++gn
  gi|518652578|ref|YP_008142098.1|   1 MMPAISSLGSNLTE-DSLSNKINNIkFKNTKNKDFYLCILDFSSKESCITISPIKVVKN-EN-DKNIAEK-YHWVGN 73 
                                       78899999999999.4434444443034444449******************9997776.44.5589999.****** PP

                        Cas_TM1802  77 angsnssqtykttkkle...............kllskkipnl..........ldleklgveknlseeekellk.... 124
                                         g n++q+ +t+++l                k+l++ki+n+          +             +++++++    
  gi|518652578|ref|YP_008142098.1|  74 LTG-NIPQWHVTSDNLLyalnslyflykkteiKTLKDKIYNIvklyyddnpvI-----------HIKKSKIIDqpsg 138
                                       988.************9999999999999999999999999955554332222...........2233333332222 PP

                        Cas_TM1802 125 kiekelsk..nkekiakelekklkki......kne..kevvlltlkidgkylgdieeyrevllrklierlfekkkek 191
                                       k++  l +  +  + +ke++k + ++      +ne  ++ vl+t+ +dg+ ++++++y ++l    i         k
  gi|518652578|ref|YP_008142098.1| 139 KVYFFLPNnnEAHVKSKEFNKNYINKfledtkDNEyiTRAVLYTIFVDGECIAEDKDYIKMLDSREI---------K 206
                                       444444444422233444444444444555665557999***********************99643.........4 PP

                        Cas_TM1802 192 kkkskegvCsvCgeekeevtgdvstklkfkfyttDkpgFasgfnkknawknfpiCeeCarkLeaGkkyleeklsfkf 268
                                       + +  +g+Cs+Cg    +vt+++ ++lkfk+y tDk +Fas++n + + kn+++C++C++++ +G+ y+ +  s +f
  gi|518652578|ref|YP_008142098.1| 207 EDEYYDGICSLCG-SIGKVTANT-KELKFKYYNTDKSSFASNMNGSYFKKNLSLCSNCYNNIISGEDYIFKR-SASF 280
                                       566889*******.9999****9.77******************************************9876.889* PP

                        Cas_TM1802 269 yglnyyvIPkfifslekvleeiidilsslkklkkleklekklkkrldldeeeileeledekdvlllnfLFyerksqs 345
                                       +g+n+++IP+ +  +++  +  i+ + +++   ++  l          +++ei +++ + + +++++++Fy rk ++
  gi|518652578|ref|YP_008142098.1| 281 AGMNLLMIPESLP-FKDGDDLYIENIFNVN---RDIIL----------KNNEIAHIEDNLDGFYTIDLMFY-RKHNN 342
                                       **********977.5555555555555555...22332..........34567788888899*********.7**** PP

                        Cas_TM1802 346 afrilllieDVppsrlskilkakekvdekfnklileekaslkftfgslykff.pirkkkkkdddkykkfLeivnsif 421
                                       +f+il++i ++p sr+ ki k ++k+  kf++         +f++ ++  f+ +i++ +++++++    L+++ s+f
  gi|518652578|ref|YP_008142098.1| 343 SFKILEFIPEIPESRMIKISKYMYKTSLKFKN------VFDNFNYLTINGFYlSIKNTRNSNFNES---LRMLSSLF 410
                                       ******************************43......3469*********989999888888887...******** PP

                        Cas_TM1802 422 kgrpisyslLikqflelirksfkneekeekeiaykvlkanlllkFLeelnllkggkkmdegelelkvede.ekldef 497
                                       +++pi++++Li+ +l +ir ++ n++   ++i+ ++l+  + ++FLe+++l k++kk + g  +++ e   + ld  
  gi|518652578|ref|YP_008142098.1| 411 NSKPIDRNYLIRIYLDRIRTDYYNNN--INNITMYILQKYAYIEFLEKIDLTKENKKIT-GDNDMDSEIGnKTLDSG 484
                                       **********************9999..8***********************9977776.44444444331667777 PP

                        Cas_TM1802 498 fkeyietlnyteqkkalFLlGvLlgellniQykkrks.kPflkkLnglgmderdikrllnevinKlrqYkk....nl 569
                                       + ++i+++n  e+  +lF +G+ +  ++ i  kk+ + +P+l+k+n++gm+ r + +l+n++ +K++qY+     ++
  gi|518652578|ref|YP_008142098.1| 485 L-NFIKNMNLPEESEGLFCIGYAIRYIGMILFKKKINnNPLLEKINYQGMNFRAVEKLMNQIDEKVKQYDIygeeIA 560
                                       7.8****************************9999888********************************7666644 PP

                        Cas_TM1802 570 ykkkelleaiakyllesesnwklskdElnFyflsGysl 607
                                       y   +  +  +ky l s s+w++++ E++F +++Gys+
  gi|518652578|ref|YP_008142098.1| 561 YVLYKAHFVLSKYTLVS-SKWPINDAENVFLIMTGYSI 597
                                       44445556667777777.67****************97 PP

>> DUF1623  Protein of unknown function (DUF1623)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.7   6.3e+03      60      69 ..      32      42 ..      16      78 .. 0.55
   2 ?    9.6   0.5   0.00011         1      70      89 ..      99     118 ..      80     119 .. 0.85
   3 ?    1.5   0.1     0.038   3.4e+02      16      53 ..     362     401 ..     349     455 .. 0.80
   4 ?   -2.0   0.0      0.46   4.1e+03      15      39 ..     445     469 ..     433     470 .. 0.67
   5 ?    0.7   0.2     0.069   6.2e+02      69      90 .]     532     553 ..     512     553 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.7
                           DUF1623 60 kekdlevld.e 69
                                      k   l +ld +
  gi|518652578|ref|YP_008142098.1| 32 KDFYLCILDfS 42
                                      33344555532 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00011
                           DUF1623  70 yelkdvelLlekiynivemY 89 
                                       y+  ++++L +kiyniv+ Y
  gi|518652578|ref|YP_008142098.1|  99 YKKTEIKTLKDKIYNIVKLY 118
                                       55679*************99 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.038
                           DUF1623  16 qkeiYekyLkkfdVvda..vmclnGdcLAvvvssaniide 53 
                                        k++Y+++Lk   V d+  +  +nG +L +  ++++ ++e
  gi|518652578|ref|YP_008142098.1| 362 SKYMYKTSLKFKNVFDNfnYLTINGFYLSIKNTRNSNFNE 401
                                       5789*****9999999722456699999888877777776 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 0.46
                           DUF1623  15 dqkeiYekyLkkfdVvdavmclnGd 39 
                                        qk+ Y + L+k+d   +   ++Gd
  gi|518652578|ref|YP_008142098.1| 445 LQKYAYIEFLEKIDLTKENKKITGD 469
                                       5777888888888877766666666 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.069
                           DUF1623  69 eyelkdvelLlekiynivemYn 90 
                                        ++ + ve+L+++i + v++Y+
  gi|518652578|ref|YP_008142098.1| 532 GMNFRAVEKLMNQIDEKVKQYD 553
                                       567789***************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (614 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.46
# Mc/sec: 4002.71
//
Query:       gi|518652579|ref|YP_008142099.1|  [L=305]
Description: CRISPR-associated Csh2 family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-57  192.9   0.7    8.2e-57  192.6   0.7    1.1  1  Cas_Cas7  CRISPR-associated protein Cas7


Domain annotation for each model (and alignments):
>> Cas_Cas7  CRISPR-associated protein Cas7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.6   0.7   4.6e-61   8.2e-57       3     252 .]       9     268 ..       7     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 192.6 bits;  conditional E-value: 4.6e-61
                          Cas_Cas7   3 yefvllfdvkngNpNGDpdagnkPRidpetgeglvsDvclKrkiRnyvekakee..keiyvkekkvlnekkeeay.. 75 
                                        e+++l+++k  NpNGD d++n+PR+d +t ++lvsDv+lKr+iR+y+++  +e  ++i++++++v + k++  +  
  gi|518652579|ref|YP_008142099.1|   9 GEILFLYEAKLTNPNGDIDDENRPRMDYDTFTNLVSDVRLKRYIRDYLQDDLSEdkYNIFINHGDVQTAKDRLREiv 85 
                                       689**********************************************9988889**********66666655566 PP

                          Cas_Cas7  76 ..k..deekkelreamcenffDvRtFGavmst...gvn..........gqvrGpVqltfarslepv.lpeeqsitrm 134
                                         +  ++  k++r+a+ ++f+D+R+FGa ++    g n           +++GpVq+++++sl++v l ++ sit+ 
  gi|518652579|ref|YP_008142099.1|  86 sdDifKD-IKKARDAITQKFIDIRMFGAMVPIpkkG-NnsgesgsgdsIKIIGPVQFSWGYSLNKVqLLNSYSITSG 160
                                       5414333.3359*******************96653.158889999954466************************* PP

                          Cas_Cas7 135 aateekkekekkqrtmgrkhivpyglYrahgfinanlaektgfseeDlellkeallnmfehdrsaargemevrkllv 211
                                       ++++e  +   k +++g++++v y+l+ ++g+i+ + a+k +++ eD+ +l +a+++++ ++++++++++ +  ++ 
  gi|518652579|ref|YP_008142099.1| 161 FSSSE-GN---KMNSIGKDYRVYYSLIGFYGVISSSRAKKANLTSEDMRKLDDAMIKAIPSQATRSKINQMPLLYMR 233
                                       **988.32...799*****************************************************9999987777 PP

                          Cas_Cas7 212 fehesklgnapaaklfdlvkvekkdeveparsfedyeitvd 252
                                        e     +n     l d vk++ k  ++p+r+++dy+++++
  gi|518652579|ref|YP_008142099.1| 234 TES----ENGFIGDLRDYVKISIK--SDPIRNINDYKLDIN 268
                                       777....55556678888999998..68*********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       699  (0.0389871); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2062.71
//
Query:       gi|518652580|ref|YP_008142100.1|  [L=256]
Description: CRISPR-associated Cas5 family Hmari subtype protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      1e-06   28.8   0.0    2.2e-06   27.7   0.0    1.6  2  Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)


Domain annotation for each model (and alignments):
>> Cas_Cas5d  CRISPR-associated protein (Cas_Cas5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.0   1.2e-10   2.2e-06       1      47 [.       1      47 [.       1      98 [. 0.89
   2 ?   -2.0   0.0      0.15   2.7e+03     132     154 ..     138     160 ..     119     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 1.2e-10
                                      EEEEEEECCEE-EB-TTCCSCCCBESS--HHHHHHHHHHHHT--TTS CS
                         Cas_Cas5d  1 tLllrlegplasfgrpsrkveretydvPtkSavlGllaaalGirrdd 47
                                      +L++ + + +asf+  ++     ty +P+++++ G+++a++G++ d 
  gi|518652580|ref|YP_008142100.1|  1 MLIFDIKAKFASFKKLYTNSSSMTYMFPPRTTLEGIIGAIMGYDFDS 47
                                      699***************************************99775 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.15
                                       HTTSSSSESSSTTSEEEECESET CS
                         Cas_Cas5d 132 rkpvwplyLGrkecivpvepvea 154
                                        +pv+p  LG    +++++++ +
  gi|518652580|ref|YP_008142100.1| 138 NNPVYPVSLGNANMLASINYIAK 160
                                       47888999999999888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1722.35
//
Query:       gi|518652581|ref|YP_008142101.1|  [L=803]
Description: hypothetical protein FACI_IFERC00001G1220 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      8e-07   29.2   1.2      8e-07   29.2   1.2    3.3  3  ResIII      Type III restriction enzyme, res subunit
    8.6e-07   28.9   0.0    2.2e-06   27.6   0.0    1.7  1  DEAD        DEAD/DEAH box helicase
    1.4e-06   28.6   2.2      2e-06   28.1   0.4    2.2  2  Helicase_C  Helicase conserved C-terminal domain
     0.0019   18.4   0.0     0.0033   17.6   0.0    1.3  1  HD_6        HD domain
     0.0043   17.3   0.1      0.029   14.6   0.0    2.3  2  HD          HD domain
  ------ inclusion threshold ------
      0.043   14.1   0.0        2.8    8.2   0.0    2.7  2  AAA_22      AAA domain
      0.087   12.3   0.1       0.71    9.3   0.0    2.2  2  PhoH        PhoH-like protein


Domain annotation for each model (and alignments):
>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   1.2   3.1e-10     8e-07      19     170 ..     276     464 ..     256     465 .. 0.68
   2 ?    1.1   0.7      0.13   3.4e+02      54     114 ..     511     578 ..     492     592 .. 0.68
   3 ?    0.5   0.5      0.21   5.3e+02      72     118 ..     659     713 ..     638     745 .. 0.71

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 3.1e-10
                                       ..........TTSEEEEEESTTSTHHHHHHHHHHHH-S..........-EEEEESSHHHHHHHHHHGGGGTGG.... CS
                            ResIII  19 lks......krdkrglikmaTGtGKTlvaaklierllkkgkee.....kflflvprkslleqtleefkkflseayke 84 
                                       +k+       +d+ + i  +TGtGKT+  + ++ ++++k  ++     +++   p +++++q +++ +++l+++  +
  gi|518652581|ref|YP_008142101.1| 276 VKKnvqnidLNDHFFTITSPTGTGKTISGLYTAFSIRNKLFKNtgnifRIIYTLPFTTIVDQNYDTGRNILETCSGF 352
                                       2223333436666777**********765555555555554445556899999***********8887777776554 PP

                                       ................GEEEESSS-B--...............-SEEEEEHHHHHHTH........HHHTTT-S... CS
                            ResIII  85 ................igkkvsgdkkka........kekdstnkkilvttiqsldadseeeeeeseellrdrfd... 134
                                                        ++k+++    +           ++ +++i++tt  +l +++     +++++l++++    
  gi|518652581|ref|YP_008142101.1| 353 knnderyiikhhhlsiLSGKIDD----EelsadevlMLTEDWDSEIIFTTFVQLFSAL---AGYKNKNLKKYYRiin 422
                                       44445555555533443333333....255558888799999****************...6666666666666667 PP

                                       .EEEEETGGGTTS.TTTHHH...HHT---...SEEEEEESS-S CS
                            ResIII 135 .viiiDEaHrlgakkswrei...lekfke...avllglTATpe 170
                                        ++i DE   +   ++w +i   ++++ +    + + ++AT++
  gi|518652581|ref|YP_008142101.1| 423 sIVILDEIQAIDI-AKWPQIrylMNYYAKkfnIYFILMSATLP 464
                                       7*******99988.99999988855554423355566799975 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.13
                                       ..-EEEEESSHHHHHHHHHHGGGGTGG...............GEEEESSS-B--.......-SEEEEEHHHH CS
                            ResIII  54 eekflflvprkslleqtleefkkflseayke...........igkkvsgdkkkakekdstnkkilvttiqsl 114
                                       e   lf+ ++++    + + +k+  s++++            ++ ++++     ++  ++nkki+v+ +q +
  gi|518652581|ref|YP_008142101.1| 511 ETAKLFVFNTINTSIEAFNYLKENVSNDVNTyylssnivpikKKDVIDNI----NKDIKNNKKIIVVATQIF 578
                                       34668888888888888888888888887778865655442222223333....455588899998888755 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.21
                                       HHGGGGTGG....GEEEESSS-B--...............-SEEEEEHHHHHHTH CS
                            ResIII  72 eefkkflseaykeigkkvsgdkkka........kekdstnkkilvttiqsldads 118
                                       +++ k+++ +y+ei++++ g +++         +++++ + +++v++ +++d   
  gi|518652581|ref|YP_008142101.1| 659 KDYLKLIKHYYNEINQNLIGSSENLqnalnkldFNSKNRDEHYYVSNFSMIDDMD 713
                                       5777777888888555533333333346677778999999999999999998766 PP

>> DEAD  DEAD/DEAH box helicase
   #    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      16     173 ..     289     467 ..     274     470 .. 0.72

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 8.6e-10
                                       EEEEEESTTSSHHHHHHHHHHHHHHHS..TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST............SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxx RF
                              DEAD  16 dvlvaaeTGsGKTlaflipvlqivyet..kgktgpkalivePtreLaeqtlnnlkkfkkyid............lrv 78 
                                        + +  +TG+GKT   l  +++i  +   ++ +  ++++  P + ++ q +++ ++++++++               
  gi|518652581|ref|YP_008142101.1| 289 FFTITSPTGTGKTISGLYTAFSIRNKLfkNTGNIFRIIYTLPFTTIVDQNYDTGRNILETCSgfknnderyiikHHH 365
                                       566899*********99999977755575677778*********************999543455555555543445 PP

                                       EEEETTSSHHHHHHHH.....HTT..CSEEEEEHHHHHHHH...HCTSSHCTTE.....EEEEEETHHHHHHTTTHH CS
                                       xxxxxxxxxxxxxxxx.....xxx..xxxxxxxxxxxxxxx...xxxxxxxxxx.....xxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskl.....dng..vdivvgtpgrlddll...stgklnlsqv.....rflVlDEadrlldqgfsd 140
                                       l+i++g+  +++ls+       ++   +i+++t  +l++ l   ++++  l++      ++++lDE++ +      +
  gi|518652581|ref|YP_008142101.1| 366 LSILSGKIDDEELSADevlmlTEDwdSEIIFTTFVQLFSALagyKNKN--LKKYyriinSIVILDEIQAIDIA-KWP 439
                                       5666665555555544333442335699******99999777864444..44444346788*******99988.889 PP

                                       HHHHHHHHSHHHCTTSTTTSEEEEEESSBSHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 141 finrilnqlpqitcdgklqrqvivlSATlpkdv 173
                                       +i+ ++n  +   ++   +  +i++SATlp+ v
  gi|518652581|ref|YP_008142101.1| 440 QIRYLMNYYA---KK--FNIYFILMSATLPELV 467
                                       9999999994...22..33459*******9655 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 !   28.1   0.4   7.7e-10     2e-06      14     110 ..     510     609 ..     497     610 .. 0.81
   2 ?   -3.1   0.1       3.8   9.6e+03      26      71 ..     709     756 ..     688     760 .. 0.56

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 7.7e-10
                                       TTTSEEEEEESSHHHHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHH...TTSSS.EEEESGGGTSSSTSTT CS
                        Helicase_C  14 eeggkilifvntidrlekvklllekk..gikvavlhgelpqnereeileqfn...kgesd.vLiatdvaerGidipk 84 
                                       +e+ k  +f +  +++e +++l+e+   ++++ +l +++   ++++++++ n   k++ + +++at++ e G+di +
  gi|518652581|ref|YP_008142101.1| 510 SETAKLFVFNTINTSIEAFNYLKENVsnDVNTYYLSSNIVPIKKKDVIDNINkdiKNNKKiIVVATQIFEAGVDI-S 585
                                       44455555555555888899997766889*********************9988855555599************.6 PP

                                       ESEEEESSSSSSHHHHHHHHTTSSST CS
                        Helicase_C  85 vnlVinfdlprnvtsyiqriGRtgRa 110
                                        ++Vi+  +p  ++s+iq++GR+ R 
  gi|518652581|ref|YP_008142101.1| 586 FDMVIRDIAP--IDSLIQSSGRVNRN 609
                                       9999999988..89*********995 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.8
                                       HHHHHH.HHHH..HHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEE CS
                        Helicase_C  26 idrlek.vkll..lekkgikvavlhgelpqnereeileqfnkgesdvLi 71 
                                       id+++k ++++  l +++++++  + + ++ er +i++   ++ ++++i
  gi|518652581|ref|YP_008142101.1| 709 IDDMDKyISIFveLDSNAMRIIDTYINRKSYERADIIQLK-REMYNYII 756
                                       4455544344433334456665556666666666666544.33555555 PP

>> HD_6  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.3e-06    0.0033      44     157 ..      40     156 ..       8     174 .. 0.65

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.3e-06
                                       TS-HHHHHHHHHHHHHCCCGGGSSHHHHTTS----TTS-.....-GGGT----HHHHHHHHHH..........HHHH CS
                              HD_6  44 gleeealrrllaflaalHDlGKaspaFqakvpelaekleeaglelekelekarHdslgaalle..........evar 110
                                       + + e l +  +++ +lHD+GK ++ Fq+   +  ++  ++  + +  ++  +H+ ++a+             e + 
  gi|518652581|ref|YP_008142101.1|  40 NGNVELLLKSSIIISCLHDFGKYTSFFQNYLMSDKDS--KS--KSDGYSKYKSHAFISALYAAycasknnlpnEYIF 112
                                       555677888889999**************99433332..22..2222227789999999885466666777777788 PP

                                       HHHHHHHTTTS---HHHHHTSS-HHHHTTHHHHHHHHHHHHHHHHCT CS
                              HD_6 111 slaaavggHHGkppkeeeekaekkssaaedweeaqkelleaaaeflg 157
                                       ++   +  HHG   + +++   ++++     +   +e+++ a++ l+
  gi|518652581|ref|YP_008142101.1| 113 YVYLSIKHHHGNLCNLDSDIGTSTQDFL---RPKISEDIKIAKKQLE 156
                                       99999999***87777777665555543...3444455555544444 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.1e-05     0.029       3      90 ..      21     123 ..      19     128 .. 0.82
   2 ?   -1.3   0.0      0.93   2.4e+03      58      87 ..     641     667 ..     630     686 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....HTTTTHHHHTS..HHH........HHH...CTCCHHHHHHHH CS
                                HD   3 eHsleVaklarrlaedlgeeedrellllaaL....lHDiGkgpfgdafekk........eee...fekflaHekvga 64 
                                       +H +eV +      ++l+++ ++elll+  +    lHD Gk++  ++f+++        + +   + k ++H++++a
  gi|518652581|ref|YP_008142101.1|  21 THLIEVGENVYNSLNELKFNGNVELLLKSSIiiscLHDFGKYT--SFFQNYlmsdkdskS-KsdgYSKYKSHAFISA 94 
                                       799999999999999999988888887654433339*******..789999998876541.156799999******* PP

                                       HHHHHHHHHHHHH...HHHHHHHHHTTCC CS
                                HD  65 eilrevekrlgld...ledvaklirehhe 90 
                                         +      ++l+   +  v+  i++hh+
  gi|518652581|ref|YP_008142101.1|  95 LYAAYCASKNNLPneyIFYVYLSIKHHHG 123
                                       99999999998889998899999999997 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
                                HD  58 aHekvgaeilrevekrlgldledvaklire 87 
                                        H++ + +il+++++++++   d +kli++
  gi|518652581|ref|YP_008142101.1| 641 IHTDTTIKILSDRKIVEEK---DYLKLIKH 667
                                       69999999********988...67777665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.059   1.5e+02       7      21 ..     289     303 ..     284     313 .. 0.87
   2 ?    8.2   0.0    0.0011       2.8      81     128 ..     409     459 ..     400     465 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.059
                            AAA_22   7 ilvvtGesGtGKTtl 21 
                                       + ++t ++GtGKT +
  gi|518652581|ref|YP_008142101.1| 289 FFTITSPTGTGKTIS 303
                                       77899********87 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0011
                            AAA_22  81 aleqalrarav..ielliiDEaqhlrseealeeLrsllnl..srkgvqliLv 128
                                       + +++l+++++   +++i+DE+q +   + + ++r l+n   +++++ +iL+
  gi|518652581|ref|YP_008142101.1| 409 YKNKNLKKYYRiiNSIVILDEIQAI-DIAKWPQIRYLMNYyaKKFNIYFILM 459
                                       567788888889999**********.77777777777888778888888886 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00028      0.71      11      58 ..     278     331 ..     271     340 .. 0.71
   2 ?   -0.3   0.1      0.23   5.9e+02     120     133 ..     422     435 ..     419     442 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
                                       HHHHHHH.H-SEEEEE--TTSSTTHHHHHHHHHHHHT.....TS-SEEEEEE-S CS
                              PhoH  11 eylealk.kndivfaiGpaGtGKtylavalavealkk.....kkvkriiltrpa 58 
                                       + +++++ + ++ +++ p+GtGKt   + +a+++ +k     +++ rii+t p 
  gi|518652581|ref|YP_008142101.1| 278 KNVQNIDlNDHFFTITSPTGTGKTISGLYTAFSIRNKlfkntGNIFRIIYTLPF 331
                                       56777885666888999*******877777765433322225778888888775 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.23
                                       SEEEEE-SGGG--H CS
                              PhoH 120 dafvilDEAQnttk 133
                                       +++vilDE Q +  
  gi|518652581|ref|YP_008142101.1| 422 NSIVILDEIQAIDI 435
                                       89********8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (803 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1220  (0.0680462); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); 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 0.30s 00:00:01.02 Elapsed: 00:00:00.49
# Mc/sec: 4944.85
//
Query:       gi|518652582|ref|YP_008142102.1|  [L=183]
Description: CRISPR-associated Cas4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      3e-31  108.7   0.4    4.4e-31  108.2   0.4    1.2  1  Cas_Cas4   Domain of unknown function DUF83
    0.00019   20.8   0.1    0.00024   20.5   0.1    1.1  1  NucS       Endonuclease NucS
  ------ inclusion threshold ------
      0.019   15.3   0.4      0.036   14.4   0.4    1.4  1  PDDEXK_3   PD-(D/E)XK nuclease superfamily
      0.027   14.0   0.1       0.04   13.5   0.1    1.2  1  AHJR-like  REase_AHJR-like


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 !  108.2   0.4   9.9e-35   4.4e-31       1      92 [.       5      95 ..       5     102 .. 0.97

  Alignments for each domain:
  == domain 1  score: 108.2 bits;  conditional E-value: 9.9e-35
                          Cas_Cas4  1 tgtkiqyyliCkrklwlisheitleensetvelGkllheesyerekkevelsesikiDvvekekeklvvvEvKkskkke 79
                                      +gt+i+yy+iCkr++wlish+i+ +++++++ lGk+lhee+y+r++ke+++ +s +iD+v++++++l++vE+Kks+k +
  gi|518652582|ref|YP_008142102.1|  5 NGTMIWYYFICKREVWLISHGIESDQEDDNILLGKILHEEAYKRNDKEIAI-NSSRIDMVKDKGDNLIIVEIKKSSKTA 82
                                      59*************************************************.*************************** PP

                          Cas_Cas4 80 eaaklQllyYlll 92
                                      eaak+QllyY++ 
  gi|518652582|ref|YP_008142102.1| 83 EAAKMQLLYYIYE 95
                                      ***********96 PP

>> NucS  Endonuclease NucS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   5.3e-08   0.00024      87     173 ..       7      94 ..       2     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.3e-08
                              NucS  87 vehasayeledveelvldGseaelae.liiehpdLieeGfkpvareyavaiGivdiLgkdeegklvivelkrrkaev 162
                                            ++ ++ +  l+ +G e++ ++  i+    L ee +k   +e a+ +  +d++ kd+ ++l+ive+k+     
  gi|518652582|ref|YP_008142102.1|   7 TMIWYYFICKREVWLISHGIESDQEDdNILLGKILHEEAYKRNDKEIAINSSRIDMV-KDKGDNLIIVEIKKSSKTA 82 
                                       5556688899999999*****998642677777899*******************85.9***********9875555 PP

                              NucS 163 dave.qLkryve 173
                                       +a + qL  y+ 
  gi|518652582|ref|YP_008142102.1|  83 EAAKmQLLYYIY 94 
                                       554338888875 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4     8e-06     0.036      53      96 ..      51      96 ..      39     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8e-06
                          PDDEXK_3 53 kgkevgeeyrlDllv...eekvivElKaveelkeeheaqllnYlklt 96
                                      k+  +++  r+D++    ++ +ivE+K  ++ +e+ ++qll Y+  +
  gi|518652582|ref|YP_008142102.1| 51 KEIAINS-SRIDMVKdkgDNLIIVEIKKSSKTAEAAKMQLLYYIYEA 96
                                      5556666.8999998888899**********************9655 PP

>> AHJR-like  REase_AHJR-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     9e-06      0.04      41      75 ..      56      90 ..      49      99 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9e-06
                         AHJR-like 41 ksYrpDliarkdeeaviiEvksrrssaseqyLqel 75
                                      +s r D++  k+++ +i+E+k+++++a   ++q l
  gi|518652582|ref|YP_008142102.1| 56 NSSRIDMVKDKGDNLIIVEIKKSSKTAEAAKMQLL 90
                                      56699******************998887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1163.78
//
Query:       gi|518652583|ref|YP_008142103.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518652583|ref|YP_008142103.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518652583|ref|YP_008142103.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518652583|ref|YP_008142103.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518652583|ref|YP_008142103.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518652583|ref|YP_008142103.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518652583|ref|YP_008142103.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518652583|ref|YP_008142103.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518652583|ref|YP_008142103.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2353.63
//
Query:       gi|518652584|ref|YP_008142104.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G1223 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-84  283.9   4.1    1.3e-84  283.7   4.1    1.0  1  Cas_Cas1  CRISPR associated protein Cas1
  ------ inclusion threshold ------
      0.035   14.3   0.0      0.074   13.3   0.0    1.5  1  DUF5599   Domain of unknown function (DUF5599)
      0.054   14.0   0.4       0.17   12.4   0.4    1.8  1  YbaJ      Biofilm formation regulator YbaJ
       0.95    9.5   3.8       0.69    9.9   1.3    2.1  2  RL        RL domain


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 !  283.7   4.1     3e-88   1.3e-84       1     282 [.       5     284 ..       5     285 .. 0.98

  Alignments for each domain:
  == domain 1  score: 283.7 bits;  conditional E-value: 3e-88
                                       EEEESTEEEEEEETTEEEEEESSEEEEEEECCCEEEEEEESTEEEEHHHHHHHHHTT-EEEEE-TTS-EEEEEEE.S CS
                          Cas_Cas1   1 lyvteqgaylrkkgerlvvekegeekkeiplediesivifgevslstkalrllaekgipvvflsengkylgrlep.e 76 
                                       +y++++g+ +r++++++ + ++++ kk ip+e++++i++fgev+++tk+l +l+ekgi +++++++g+y g++ p +
  gi|518652584|ref|YP_008142104.1|   5 IYIFSNGT-IRRDENTISIVNDND-KKFIPIENTSEIYMFGEVTFNTKLLTYLSEKGIIIHYFNYYGYYSGTIFPrQ 79 
                                       69******.*************88.9*************************************************99 PP

                                       SSSTHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHCCHHCTTHHHHCHCHHHHHHHHHHHH-HSHHHHHH CS
                          Cas_Cas1  77 esgnvelrraQyraaddeekrlelakkivagklenqrkvlrrlkrdreeeeleeaieeleelleklekaesleeLrg 153
                                       + +++++ ++Q+  + d ekrl++ak i +g + n+ ++l+++ ++    +l+e+ie++++l +  ++ +++++L+ 
  gi|518652584|ref|YP_008142104.1|  80 HLSSGAVILNQVSYYLDMEKRLQIAKLIEHGSAINIIANLKYYYNRG--RSLAEEIEKISRLNDTFDEQTTINSLML 154
                                       99*****************************************9999..89************************** PP

                                       HHHHHHHHHHHHHHHHCSC.GGS-SS-SSSS-SSHHHHHHHHHHHHHHHHHHHHHHTSS--TT--SSS--TTSS-HH CS
                          Cas_Cas1 154 iEGeaakaYfeafdkllke.efefegRsrrppkDpvNalLsfgYtllysevlsaieavgLdPyiGfLHedrpgrpsL 229
                                       iE++++++Y+++fdk++ + +f+fe R++rpp+++vN+l+sf++++ly++vls+i+++++dP+iG+LHe++ +r++L
  gi|518652584|ref|YP_008142104.1| 155 IEANIREIYYSTFDKIIADkNFRFEHRTKRPPQNNVNSLISFINSMLYTTVLSEIYKTHMDPRIGYLHETNFRRFTL 231
                                       ******************77********************************************************* PP

                                       HHHHHHHHHHHHCHHHHHHHHHTTSS-GGGEEEETTEEEE-HHHHHHHHHHHH CS
                          Cas_Cas1 230 alDLmEefRpllvDrlvlslinkrqlkekdFekeengvlLteegrkkfleafe 282
                                        lD+ E+f+p++ Dr++++l+n++++++++F++  n v ++e+g+kk++++++
  gi|518652584|ref|YP_008142104.1| 232 NLDVSEIFKPIIGDRIIFKLLNEKIIDASNFKNIGNIVNINESGKKKIIQELD 284
                                       **************************************************986 PP

>> DUF5599  Domain of unknown function (DUF5599)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.6e-05     0.074      18      76 ..     225     286 ..     220     298 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.6e-05
                           DUF5599  18 rlasFvlpkldsgelrlvvGDelrlkykgse...aeeWegeghvvkltdssseevtleLrss 76 
                                       ++  F+l+   s+ ++ ++GD ++ k+  ++   a+++++ g++v++++s ++++  eL ++
  gi|518652584|ref|YP_008142104.1| 225 NFRRFTLNLDVSEIFKPIIGDRIIFKLLNEKiidASNFKNIGNIVNINESGKKKIIQELDNK 286
                                       566788888888999**********9998888889***********************9876 PP

>> YbaJ  Biofilm formation regulator YbaJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.4   3.9e-05      0.17      43      85 ..      98     144 ..      89     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-05
                              YbaJ  43 avnlqlneliehiaaf..vlnfkikykeesdlseqidey..lddtya 85 
                                       ++ lq+ +lieh +a+  + n k  y++   l+e i++   l+dt+ 
  gi|518652584|ref|YP_008142104.1|  98 EKRLQIAKLIEHGSAIniIANLKYYYNRGRSLAEEIEKIsrLNDTFD 144
                                       788*********988622667777789999*******8545889885 PP

>> RL  RL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.3   0.00015      0.69      27      48 ..      48      69 ..      42      75 .. 0.87
   2 ?   -2.3   0.1      0.98   4.4e+03      23      48 ..      99     124 ..      93     128 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                                RL 27 ekkllkylsqhGkinkhFfYes 48
                                      ++kll yls+ G i ++F Y  
  gi|518652584|ref|YP_008142104.1| 48 NTKLLTYLSEKGIIIHYFNYYG 69
                                      689***************9965 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.98
                                RL  23 skisekkllkylsqhGkinkhFfYes 48 
                                       ++ ++ kl+++ s    i ++ +Y +
  gi|518652584|ref|YP_008142104.1|  99 KRLQIAKLIEHGSAINIIANLKYYYN 124
                                       45555666666666655665555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2502.61
//
Query:       gi|518652585|ref|YP_008142105.1|  [L=87]
Description: CRISPR-associated protein Cas2 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-19   69.4   1.9    2.6e-19   69.2   1.9    1.1  1  CRISPR_Cas2  CRISPR associated protein Cas2
  ------ inclusion threshold ------
      0.062   13.9   0.1      0.067   13.7   0.1    1.3  1  AntA         AntA/AntB antirepressor


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 !   69.2   1.9   2.9e-23   2.6e-19       1      73 [.       1      70 [.       1      73 [. 0.96

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 2.9e-23
                                      EEEEEEEECHCHHHHHHHHHHHHHHTTEEEEETTEEEEEESHHHHHHHHHHHHHHSHTTTCEEEEEEEETCHH CS
                       CRISPR_Cas2  1 mlvlvvYDikedrkrrrkvakilkkyGfqrvQySVFegelseaqleklkkrlkkiidpeedsiriykltekqf 73
                                      m++++vYD+   +kr+ kv ki +ky  +++Q+SV ege+s+ ++ek k +++k i+peedsi++y +++ ++
  gi|518652585|ref|YP_008142105.1|  1 MYIILVYDV--SEKRVFKVLKIARKY-ITWIQNSVLEGEISKGNYEKFKVEIRKTIKPEEDSILFYIIRDLKY 70
                                      9********..9**************.***************************************9998665 PP

>> AntA  AntA/AntB antirepressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   7.5e-06     0.067       1      43 [.       9      50 ..       9      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.5e-06
                              AntA  1 VsAreLhefLevkkdFskWikerikeygfvenkDfisvakkke 43
                                      Vs ++ +++L++ +++ +Wi++ + e +  ++ ++ +++ + +
  gi|518652585|ref|YP_008142105.1|  9 VSEKRVFKVLKIARKYITWIQNSVLEGEISKG-NYEKFKVEIR 50
                                      6778899*************999999655544.5777744444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 640.62
//
Query:       gi|518652586|ref|YP_008142106.1|  [L=119]
Description: hypothetical protein FACI_IFERC00001G1225 [Ferroplasma acidarmanus fer1]
Scores for complete 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   28.9   0.0      8e-07   28.9   0.0    1.1  1  DDE_Tnp_1    Transposase DDE domain
    9.2e-05   22.5   0.0    9.4e-05   22.5   0.0    1.1  1  DDE_Tnp_1_3  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0     9e-11     8e-07      25     108 ..       4      74 ..       1     109 [. 0.89

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 9e-11
                         DDE_Tnp_1  25 wgykggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtleekgvd 101
                                       w++ ++ + y +k+h+a+d  s li+   +t gn hd ++ ++++d+++  + +++la ++Y + +++d++      
  gi|518652586|ref|YP_008142106.1|   4 WSKTTKGWSYDRKCHMAIDVDSLLIMEWLFTKGNMHDPHVSRDMVDSVK--DFSYTLAYSAYETLDIYDYVF----- 73 
                                       6566777******************************************..9******************99..... PP

                         DDE_Tnp_1 102 yiirlkk 108
                                             k
  gi|518652586|ref|YP_008142106.1|  74 ------K 74 
                                       ......2 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.0     1e-08   9.4e-05      35     102 ..       4      74 ..       1     110 [. 0.75

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 1e-08
                       DDE_Tnp_1_3  35 rGkssmGWfyGfkLhliin.dkGeilavkltpgnvdDrepveelakellgklf..aDkgyiskklaeelle 102
                                       + k++ GW y  k h+ i+ d+  i+++ +t+gn++D +  ++++ ++++  +  a  +y + ++ + +++
  gi|518652586|ref|YP_008142106.1|   4 WSKTTKGWSYDRKCHMAIDvDSLLIMEWLFTKGNMHDPHVSRDMVDSVKDFSYtlAYSAYETLDIYDYVFK 74 
                                       679*************998355678899****************999987544115566666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 812.72
//
Query:       gi|518652587|ref|YP_008142107.1|  [L=59]
Description: hypothetical protein FACI_IFERC00001G1226 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 418.64
//
Query:       gi|518652588|ref|YP_008142108.1|  [L=119]
Description: hypothetical protein FACI_IFERC00001G1227 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-29  102.1   0.1    3.2e-29  102.0   0.1    1.0  1  DUF488    Protein of unknown function, DUF488
  ------ inclusion threshold ------
      0.011   15.5   0.2        2.8    7.8   0.0    2.4  2  DUF2179   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.0   0.1   3.6e-33   3.2e-29       2     121 ..       4     110 ..       3     111 .. 0.96

  Alignments for each domain:
  == domain 1  score: 102.0 bits;  conditional E-value: 3.6e-33
                            DUF488   2 lervyd.llkkdgvrvlvDVRlwPrSrnpgfskealkedlkeagiaYvwlkelgpsrelrkwfkhdp.rweefferY 76 
                                       ++r+yd   +++g+rvlv+ RlwPr    g+ske+++ dl        w+k+++ps+elrkwf+h++ +weef +rY
  gi|518652588|ref|YP_008142108.1|   4 IKRIYDkYTPEEGFRVLVE-RLWPR----GISKEKAHIDL--------WMKDIAPSTELRKWFNHEDeKWEEFVKRY 67 
                                       89*****************.*****....***********........****************99989******** PP

                            DUF488  77 aaeleskeaakealeelkelakkg..vaLlcaekdperchrvvlaey 121
                                         el  +    e++ +lkel+k++  v++++++++ e++ +v l+++
  gi|518652588|ref|YP_008142108.1|  68 TIELSGN----EEIGKLKELVKEHtkVTFVYSARNVEHNSAVALKNI 110
                                       *****96....89999999999999******************9875 PP

>> DUF2179  Uncharacterized protein conserved in bacteria (DUF2179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0   0.00031       2.8      26      46 ..      74      94 ..      71     101 .. 0.88
   2 ?    5.8   0.0    0.0012        11      27      42 ..     102     117 ..      98     118 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00031
                           DUF2179 26 rkelsklkeiikeiDpkAFii 46
                                      + e+ klke++ke+ +  F+ 
  gi|518652588|ref|YP_008142108.1| 74 NEEIGKLKELVKEHTKVTFVY 94
                                      579***********9999986 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0012
                           DUF2179  27 kelsklkeiikeiDpk 42 
                                       + ++ lk+i+++iD +
  gi|518652588|ref|YP_008142108.1| 102 NSAVALKNIVESIDSH 117
                                       56789*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 889.05
//
Query:       gi|518652589|ref|YP_008142109.1|  [L=328]
Description: hypothetical protein FACI_IFERC00001G1228 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-26   92.5   0.2    2.8e-26   92.5   0.2    2.0  2  Peptidase_M48  Peptidase family M48
    3.2e-05   23.3  13.4     0.0001   21.6   9.3    2.8  2  Peptidase_M56  BlaR1 peptidase M56
  ------ inclusion threshold ------
      0.014   15.0   0.2      0.022   14.3   0.2    1.2  1  DUF2201_N      Putative metallopeptidase domain
       0.42   11.0   0.2       0.42   11.0   0.2    4.5  5  Nodulin_late   Late nodulin protein
       0.63   10.3   3.5         10    6.5   0.1    2.7  2  Chi-conotoxin  chi-Conotoxin or t superfamily
       0.97    8.7  26.7        0.1   11.9   2.1    3.4  3  AgrB           Accessory gene regulator B
        8.6    6.3  10.2        4.7    7.2   0.6    3.1  3  RseC_MucC      Positive regulator of sigma(E), RseC/MucC


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 ?   -0.6   0.5      0.36   9.2e+02      82     130 ..      43      94 ..      12     115 .. 0.73
   2 !   92.5   0.2   1.1e-29   2.8e-26       4     194 ..     142     325 ..     139     327 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.36
                                       HHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S...---HHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx RF
                     Peptidase_M48  82 vslivsllasillllglallisraeedaagafld...alavliglliillfl 130
                                       v++++  ++s+l++    ++  +++++++++ ++   ++ ++++l i++l +
  gi|518652589|ref|YP_008142109.1|  43 VMVSIIIINSLLFMHFKDAMRDQESDENIFQYITddlSWRYVTYLSIFFLAM 94 
                                       5667777777777777778888888877777765222456666666666555 PP

  == domain 2  score: 92.5 bits;  conditional E-value: 1.1e-29
                                       SSHHHHHHHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-E.EEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48   4 eaelkevveelakeaglpkpltkvyvvnspkrNAFalgggknk.rivltdgLlkqllseeelaaVlGHElGHikhrh 79 
                                       + +l+++  +l  ++g+  +++++yv+n + r A a  ++k++ ++++t+ L+ + l+++e+ +Vl+HEl+Hik +h
  gi|518652589|ref|YP_008142109.1| 142 DIYLNNEAADLSTQMGI--KEPEIYVINTNGRIANAFEINKREsYVFITSYLM-SILNHDEIVGVLAHELSHIKLGH 215
                                       56788888999999999..99*******9999555556666666*********.*********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHTT-SHHHHHTT--S---HHHHHHHHHHTT...HHHHHHHHHHHHHHHHTTT.HHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  80 svvslivsllasillllglallisraeedaagafldalavliglliillfl...alSRkrEyqADeagvellkrakd 153
                                       ++++++v  +  i++l +++l+i+++++   +     ++v i++l ++ fl   a+ R +E++AD  +v++++ +++
  gi|518652589|ref|YP_008142109.1| 216 NRKTTMVNFVVFIIMLNLISLAITSTNAL-LFYL---TPVFIIILFLFIFLvspAIKRHNETEADLNAVKYVN-KDY 287
                                       *9999888877777777766665554433.3333...33333333333333667*******************.*** PP

                                       HHHHHHHHHHHTT--S---HHHHHHS-SS--HHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48 154 lvraliklakdlerqdvsaslrsellstHPplleRiqalke 194
                                       l++ l ++a++ +  ++       l   HP++++Ri+ +++
  gi|518652589|ref|YP_008142109.1| 288 LINGLRRIAETDKIPENVMR---SLSLDHPSTEKRIKLIEN 325
                                       ********987665444333...67888********98876 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   9.3   3.9e-08    0.0001      98     225 ..     100     229 ..       9     234 .. 0.77
   2 ?    1.6   0.1     0.049   1.3e+02     230     257 ..     259     286 ..     238     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 3.9e-08
                     Peptidase_M56  98 wktilkillliWivgalilllyliaallvlkkrfvrklgklraeelkeaLkeakeemqlkrn..ikirlsssidsPa 172
                                         +i++  ++++i+ a i+++ +i a   + + +vrk++kl++ +l+++ ++ + +m++k +    i  +  i + +
  gi|518652589|ref|YP_008142109.1| 100 YIKIVDTYSYLVILNAFIIFIWSISANNPMVNILVRKSEKLQDIYLNNEAADLSTQMGIKEPeiYVINTNGRIANAF 176
                                       446778889999999999999*****9999977*************************99874347888999***** PP

                     Peptidase_M56 173 vlgllkprIvlPadflkklsdeeleyillHElaHlkrkDllvnllvavlqclf 225
                                        +    +++ + ++++  l+ +e+  +l+HEl+H+k +      +v+++  ++
  gi|518652589|ref|YP_008142109.1| 177 EINKRESYVFITSYLMSILNHDEIVGVLAHELSHIKLGHNRKTTMVNFVVFII 229
                                       ************************************88777777777766665 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.049
                     Peptidase_M56 230 lvhlaarkirlDqElaCDaaVLarleke 257
                                       +++l+  +i++ +E ++D +++++++k+
  gi|518652589|ref|YP_008142109.1| 259 FIFLVSPAIKRHNETEADLNAVKYVNKD 286
                                       6888888889999999998888887765 PP

>> DUF2201_N  Putative metallopeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.2   8.7e-06     0.022      53      85 ..     193     225 ..     183     231 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.7e-06
                         DUF2201_N  53 esllleeqvgvlaHevlHvalrHpeRreafdpe 85 
                                       + l  +e+vgvlaHe+ H+ l H  +   ++  
  gi|518652589|ref|YP_008142109.1| 193 SILNHDEIVGVLAHELSHIKLGHNRKTTMVNFV 225
                                       668899*****************9888777765 PP

>> Nodulin_late  Late nodulin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -7.0   9.5         7   1.8e+04       4      18 ..      34      48 ..      20      62 .. 0.62
   2 ?   -1.7   0.2       1.5   3.7e+03      14      23 ..      86      95 ..      81     104 .. 0.64
   3 ?   -4.1   0.7         7   1.8e+04       9      19 ..     109     119 ..     106     125 .. 0.54
   4 ?   -1.5   1.8       1.3   3.3e+03       4      23 ..     221     242 ..     219     245 .. 0.49
   5 ?   11.0   0.2   0.00016      0.42       8      25 ..     251     268 ..     247     276 .. 0.82

  Alignments for each domain:
  == domain 1  score: -7.0 bits;  conditional E-value: 7
                      Nodulin_late  4 ilkfvYalilflslf 18
                                      i   vY++ +++s++
  gi|518652589|ref|YP_008142109.1| 34 IPFTVYTILVMVSII 48
                                      444455555555544 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                      Nodulin_late 14 flslflvatn 23
                                       ls+f++a+ 
  gi|518652589|ref|YP_008142109.1| 86 YLSIFFLAML 95
                                      5666666654 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 7
                      Nodulin_late   9 Yalilflslfl 19 
                                       Y +il  ++++
  gi|518652589|ref|YP_008142109.1| 109 YLVILNAFIIF 119
                                       55554444433 PP

  == domain 4  score: -1.5 bits;  conditional E-value: 1.3
                      Nodulin_late   4 ilkfvYalil..flslflvatn 23 
                                       +++fv ++i+  ++sl + +tn
  gi|518652589|ref|YP_008142109.1| 221 MVNFVVFIIMlnLISLAITSTN 242
                                       4556655544014555554444 PP

  == domain 5  score: 11.0 bits;  conditional E-value: 0.00016
                      Nodulin_late   8 vYalilflslflvatnvd 25 
                                       v+++ilfl++flv+  ++
  gi|518652589|ref|YP_008142109.1| 251 VFIIILFLFIFLVSPAIK 268
                                       99***********86665 PP

>> Chi-conotoxin  chi-Conotoxin or t superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   1.0     0.038        96       1      17 [.     221     237 ..     221     244 .. 0.79
   2 ?    6.5   0.1    0.0039        10       5      29 ..     250     276 ..     247     289 .. 0.67

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.038
                     Chi-conotoxin   1 MrclpVFvILLLLiaSa 17 
                                       M  + VF+I+L Li+ a
  gi|518652589|ref|YP_008142109.1| 221 MVNFVVFIIMLNLISLA 237
                                       66678******999866 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0039
                     Chi-conotoxin   5 pVFvILLLLiaS..aPsvdaqpktkdd 29 
                                       pVF+I+L L  +   P+++ + +t+ d
  gi|518652589|ref|YP_008142109.1| 250 PVFIIILFLFIFlvSPAIKRHNETEAD 276
                                       9***99988765113445555555544 PP

>> AgrB  Accessory gene regulator B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   6.5     0.017        44     137     177 ..       6      49 ..       1      57 [. 0.47
   2 ?    5.0   2.7    0.0053        14      80     127 ..      84     131 ..      82     150 .. 0.70
   3 ?   11.9   2.1     4e-05       0.1      83     128 ..     221     269 ..     198     282 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.017
                              AgrB 137 kkkklkilsiivllilliialll...knekisnaillglllvav 177
                                       kk++l++++i++ l+l+ii++++   ++  ++ + +l ++++++
  gi|518652589|ref|YP_008142109.1|   6 KKQILQKSAILSNLSLIIIFFVYiilSEIPFTVYTILVMVSIII 49 
                                       45556666666666655555555443333333333333332222 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0053
                              AgrB  80 ilslliflllillakllslslslllillliilliisliiilllaPvdt 127
                                       ++ l if+l++l+a+   +  +++++l+++ ++ii +++i    P+ +
  gi|518652589|ref|YP_008142109.1|  84 VTYLSIFFLAMLIAQGYIKIVDTYSYLVILNAFIIFIWSISANNPMVN 131
                                       567778888888887766655566777777777777777877777755 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 4e-05
                              AgrB  83 lliflllillakllslsls...lllillliilliisliiilllaPvdtp 128
                                       ++ f+++i++++l+sl ++    ll++l  +++ii +++i+l++P+ ++
  gi|518652589|ref|YP_008142109.1| 221 MVNFVVFIIMLNLISLAITstnALLFYLTPVFIIILFLFIFLVSPAIKR 269
                                       3444444444444444444444566666666666667777777777554 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.2     0.018        45      60     122 ..       6      66 ..       4      72 .. 0.80
   2 ?   -0.0   0.3       0.3   7.8e+02      71     111 ..      83     123 ..      74     139 .. 0.72
   3 ?    7.2   0.6    0.0018       4.7      65      85 ..     241     261 ..     225     276 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.018
                         RseC_MucC  60 eksllkaallvYllPllllilgallgsallgssellaalgallglvlgflivrllskrlkkks 122
                                       +k++l+ ++++  l l+++++++++ s +    +++++l+++ ++++  l+  ++++ +++++
  gi|518652589|ref|YP_008142109.1|   6 KKQILQKSAILSNLSLIIIFFVYIILSEI--PFTVYTILVMVSIIIINSLLFMHFKDAMRDQE 66 
                                       56778888888888899999999999998..67899999999999998888888888777665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.3
                         RseC_MucC  71 YllPllllilgallgsallgssellaalgallglvlgfliv 111
                                       Y++ l +++l++l+++      ++++ l+ l ++++ ++ +
  gi|518652589|ref|YP_008142109.1|  83 YVTYLSIFFLAMLIAQGYIKIVDTYSYLVILNAFIIFIWSI 123
                                       77777778888888887776667777777766666666555 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.0018
                         RseC_MucC  65 kaallvYllPllllilgallg 85 
                                       + all+Yl+P++++il+++++
  gi|518652589|ref|YP_008142109.1| 241 TNALLFYLTPVFIIILFLFIF 261
                                       5799***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1506  (0.083998); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 2234.54
//
Query:       gi|518652590|ref|YP_008142110.1|  [L=222]
Description: ribosome biogenesis protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  147.4   0.0    4.3e-43  147.2   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 !  147.2   0.0   2.4e-47   4.3e-43       2     194 .]       5     215 ..       4     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 2.4e-47
                                       EEEEES--B--GG................SCGGSB--HHHHCGG.TT..STTGGGSS-CHHHHHHHHHHHCSCHHCT CS
                              EMG1   2 vLeeasLelvkvk................kkseqLLnsddhkkilkk..lkreakeaRpDIvHqcLlalldspLnka 60 
                                       ++++a+L++v++k                ++ e+LL+s+++++ ++k   +++++++RpDI++ +L ++++s+Lnk+
  gi|518652590|ref|YP_008142110.1|   5 IIADAELQTVPEKmakdrsirniaeknhkNPAEMLLDSNYMHTTIEKfyPGESNRRGRPDIIYIFLEMAMESILNKN 81 
                                       899*************************99**********999988877789999********************** PP

                                       T.EEEEEEETTSEEEEE-TT----SSHHHHHHHHHHHHCCSEEEETTEE.SCEEEECS-HHHHCCC..SEEEEE-TT CS
                              EMG1  61 gllqvyihttknvlIevnpqtRiPrtfkrFagLmvqLLkklsirategeekLlkviknpitdhlpp.gskiillses 136
                                       ++l+vy+ht++n +I++n+qt++Pr+++rF+gLm++L+kk+si+ +++e  Ll++ + +i  +l++ + k+++ls +
  gi|518652590|ref|YP_008142110.1|  82 NMLDVYVHTRDNFIIHINNQTKLPRSYNRFQGLMEDLFKKRSIEYNGNE--LLSMEEGKIIPFLKNlDGKTVVLSPD 156
                                       ********************************************98876..***************999******** PP

                                       SEE-..............EEEE-SSSS....---HH......EEESSSS---HHHHHHHHHHHCH CS
                              EMG1 137 aekklvdleefv.vkpvvfvigamskgsvkidykee......eisisnypLsaavvcskiltafE 194
                                       ++++  +l+ ++ ++++ +vig++s+g    d+ ++      +++i +++L+ + v ++i++++E
  gi|518652590|ref|YP_008142110.1| 157 GKES--SLSGIInDNDLNVVIGGFSQG----DFISDlygnfpSYKIFREELTIWSVGMEIISQYE 215
                                       **44..599999888************....88888888899*******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1711.89
//
Query:       gi|518652591|ref|YP_008142111.1|  [L=266]
Description: aldo/keto reductase [Ferroplasma acidarmanus fer1]
Scores for complete 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-66  222.0   0.3    3.8e-63  213.4   0.3    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 !  213.4   0.3   2.1e-67   3.8e-63       2     292 ..      12     263 ..      11     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 2.1e-67
                                       EEEE-SSS-ST....TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSS CS
                      Aldo_ket_red   2 lglGtwqlgsk...eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrda 75 
                                       +glGt  +g+k   +++++++ +e++++a+ +G+n++DtAe+Yg g+seel+G+a+k+  ++re+++i +Kv     
  gi|518652591|ref|YP_008142111.1|  12 IGLGTYGMGGKnspDYKNDAKEVEAIKYAITNGMNLIDTAEYYGHGHSEELVGKAIKD--FEREDLFIISKV----- 81 
                                       9***********9*********************************************..************..... PP

                                       TTSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HH CS
                      Aldo_ket_red  76 eiksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kk 151
                                        ++++l+ +++++s +eslkrL+tdy+Dl+l+H+p+p+ p + e+l+a+ el ++++ir+iGvSnf+++ l +a  +
  gi|518652591|ref|YP_008142111.1|  82 -WPVNLHYKDVINSAKESLKRLDTDYIDLYLIHWPNPKIP-VKETLGAMGELLDSHLIRNIGVSNFDIANLTEAiDQ 156
                                       .***************************************.**************************8887777799 PP

                                       TTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHH CS
                      Aldo_ket_red 152 kkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknlda 228
                                        k  ki+a++veynl +   e  l+++c+k+++++i yspl +G ++                              
  gi|518652591|ref|YP_008142111.1| 157 LKHGKIIANEVEYNLENYYIEDDLIPFCEKNNIKIIGYSPLNQGRIS------------------------------ 203
                                       9999****************************************999.............................. PP

                                       HHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHHH CS
                      Aldo_ket_red 229 aeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaeldel 292
                                        ++++++ak+ g+s  q +l y+    +++i+ip+as+i+++++ ++ ++++l+e e+++++e+
  gi|518652591|ref|YP_008142111.1| 204 -SKINHVAKSLGMSSIQCTLGYLK---KKSIPIPKASSISHINELVECMNIDLDENEYNRIKEA 263
                                       .6799******************9...9*********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2016.30
//
Query:       gi|518652592|ref|YP_008142112.1|  [L=144]
Description: 30S ribosomal protein S15P [Ferroplasma acidarmanus fer1]
Scores for complete 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-23   80.2   0.3    1.6e-22   79.3   0.3    1.5  1  Ribosomal_S13_N  Ribosomal S13/S15 N-terminal domain
    3.2e-12   46.5   0.2    5.1e-12   45.8   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 !   79.3   0.3   1.7e-26   1.6e-22       1      60 []       1      59 [.       1      59 [. 0.98

  Alignments for each domain:
  == domain 1  score: 79.3 bits;  conditional E-value: 1.7e-26
                                      X--SSSSSS--------S-SS--TTS---HHHHHHHHHHHHHTT--HHHHHHHHHHCCT- CS
                   Ribosomal_S13_N  1 MarmhsrgkGkSgSarPyrreapsWlklskeeveelivklakkGltpSqIGviLRDqyGv 60
                                      Marmh+r++GkS+S+r +  e+psW++ + +e++e i+k++k+Gl+ S+IG++LRDqy+v
  gi|518652592|ref|YP_008142112.1|  1 MARMHTRKRGKSRSTRLVLAEKPSWMQ-NDDEIKEEILKFRKDGLSNSMIGIKLRDQYAV 59
                                      **************************6.99****************************98 PP

>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.2   5.7e-16   5.1e-12       4      68 ..      73     133 ..      70     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 5.7e-16
                                       HHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-H CS
                     Ribosomal_S15   4 likefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdv 68 
                                       +++e++ ++    ++++++a+l +r +n+++hl  nkkD +++rg ++++sk+ +l++Y+kr+ +
  gi|518652592|ref|YP_008142112.1|  73 ILEENGIKD----EIPEDLAFLLKRYKNVSQHLALNKKDISNKRGSQLIMSKILRLMRYYKRTGR 133
                                       678888888....9************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1081.92
//
Query:       gi|518652593|ref|YP_008142113.1|  [L=443]
Description: hypothetical protein FACI_IFERC00001G1232 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   61.4   0.1    2.8e-16   60.2   0.1    1.7  1  DHHA1     DHHA1 domain
    4.1e-05   23.8   0.1    8.7e-05   22.7   0.1    1.5  1  DHH       DHH family


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   0.1   3.1e-20   2.8e-16      39     138 .]     337     436 ..     307     436 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 3.1e-20
                                       TCEEEEEECHCCHHHHHHHHHHHHHHTHGBT.TCEEEEEEEECTEEEEEEEESSH....SS-HHHHHHHHHHHTTCC CS
                             DHHA1  39 gvkvlvaevgeewdagalgiaadklksklkk.pvivfvakeegdkvkvsarskkd....gvdagelakeaaaklggg 110
                                          +++a    e+   + g +a +  +  ++ pvi f ++ ++  vk+s r ++     g++++e++k a+a+ gg+
  gi|518652593|ref|YP_008142113.1| 337 YLRYFYAPE-SEMAGPIAGAIALYTVK--PDkPVIGFNSGTDD--VKISSRGSRYsvsrGLNLSEVMKTACAAAGGS 408
                                       445555555.66666677777888888..88899999999985..********88********************** PP

                                       EEEETCEEEEEEEHCHHHHHHHHHHHHH CS
                             DHHA1 111 GGGHdlAaGagipaekleealealeeai 138
                                       GGGHd AaG+ ip+++ +++l+a++e+i
  gi|518652593|ref|YP_008142113.1| 409 GGGHDIAAGGVIPKGREKQFLDAANEMI 436
                                       *************************987 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.1   9.7e-09   8.7e-05       6      84 ..      29     142 ..      25     158 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 9.7e-09
                                       -ECSSSHHHHHH.HHHHHH.................................CECS--TCGGCGCCHHCCCSEEEEE CS
                                       xxxxxxxxxxxx.xxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH   6 ghknpDtDsigS.aialan.................................llvDhneksqavegeakeeaedvii 48 
                                          ++D+D++ S +i+l++                                 ++vD ++++  +++    +  + ii
  gi|518652593|ref|YP_008142113.1|  29 VLAHYDGDGVSSsIILLKAlerldikyhlsyiknldnegfrslyeeeadslnIIVDAGSSQIPAIA----DHSNFII 101
                                       4789********55555558888888888888888888888888888888888*****99988865....999**** PP

                                       EE-S---S......S---SS--EEEE-SSS-HHHHHHHHHHH CS
                                       xxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                               DHH  49 iDHHrlge......efetlapilflnepvgstaeivaellee 84 
                                       +DHH  ++      +++   ++ +  +  +++a++++ ++ +
  gi|518652593|ref|YP_008142113.1| 102 LDHHFYNKtetsciNINA-RDFGINGTRDACGATMAYIFALA 142
                                       *****9988888752222.24556666777888888776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3187.01
//
Query:       gi|518652594|ref|YP_008142114.1|  [L=33]
Description: hypothetical protein FACI_IFERC00001G1233 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (33 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       266  (0.0148363); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 239.02
//
Query:       gi|518652595|ref|YP_008142115.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518652595|ref|YP_008142115.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518652595|ref|YP_008142115.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518652595|ref|YP_008142115.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518652595|ref|YP_008142115.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518652595|ref|YP_008142115.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518652595|ref|YP_008142115.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518652595|ref|YP_008142115.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518652595|ref|YP_008142115.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2378.02
//
Query:       gi|518652596|ref|YP_008142116.1|  [L=53]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.5   1.0    1.6e-24   85.3   1.0    1.0  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   9.1e-29   1.6e-24       1      50 []       4      53 .]       4      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.1e-29
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++d+
  gi|518652596|ref|YP_008142116.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITRDE 53
                                      8**********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 362.57
//
Query:       gi|518652597|ref|YP_008142117.1|  [L=341]
Description: hypothetical protein FACI_IFERC00001G1236 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.6e-26   90.9   1.8    9.4e-26   90.2   1.8    1.4  1  DUF3463      Domain of unknown function (DUF3463)
    1.5e-15   58.0   0.0    2.4e-15   57.3   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
      2e-08   34.6   0.0    1.6e-07   31.6   0.0    2.1  2  Fer4_12      4Fe-4S single cluster domain
     0.0019   18.3   0.0     0.0055   16.8   0.0    1.8  1  Fer4_14      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> DUF3463  Domain of unknown function (DUF3463)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2   1.8   2.1e-29   9.4e-26       1     132 [.     188     323 ..     188     325 .. 0.90

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.1e-29
                           DUF3463   1 itvspgysYekapdqdlflerektkelfrkilelkkkkyklnesplyldflag....kqeykCtpWgnptrnvlG.w 72 
                                       i+++++y+Y++a  +++++e+ek+  +++ ++++kk    ++++ +y++++ +      +++C pW ++++++ G +
  gi|518652597|ref|YP_008142117.1| 188 INFQIEYDYSTA--EKISPEKEKLLGALNMLIDRKKADGPIMNTVQYFEAIRDswfyGYKWECRPWLTINIDPEGrV 262
                                       57899*******..9**************************************7765559***************99 PP

                           DUF3463  73 qkPCYlleegyaktfk.......elleetdwekygkgkdpkCanCmvhsgyEasavsdtvksllkal 132
                                       ++PCY++ ++y+ +         +++++ dwe y       C++C++++++E+s++++t   ++k++
  gi|518652597|ref|YP_008142117.1| 263 VTPCYII-NEYSGSDYvwnidikKMWNTFDWEPYR-----TCNKCALSCYLEPSLFKWTRPAMVKSR 323
                                       *******.6666654446666779**********9.....9******************99999875 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.3   0.0   5.2e-19   2.4e-15       7     147 ..      36     161 ..      32     180 .. 0.87

  Alignments for each domain:
  == domain 1  score: 57.3 bits;  conditional E-value: 5.2e-19
                                       ESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   7 CnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgiritve 83 
                                       CnlrC+ C+++    r+++++ ls+e+ ++ +++l +e gv ++ + ggepll+ d  e+l++ +k+    ++++++
  gi|518652597|ref|YP_008142117.1|  36 CNLRCKMCPFW----RRPDSKLLSMEQEIAMMEKL-KEGGVSYLGFEGGEPLLRNDTPEILKESHKR----FHTSMV 103
                                       ***********....6*******************.6999**************************6....****** PP

                                       ECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT.CTSHHHHHHHHHHHHHHTTSETEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  84 tngtlpdeeklerllelgvdrvslgleaaddekvlklmn.rghtfeevlealeklreagikrvvd 147
                                       tng ++ e+k+ ++    +d + ++++   +  v++ m+  +++fe+ ++++  + +++++  v 
  gi|518652597|ref|YP_008142117.1| 104 TNGWRL-EKKINEIHT-SLDFLFVSIDGSKE--VHDTMRgMQGSFEHAVRGIN-ASKHMVP--VA 161
                                       ******.*********.66********9999..888888899**********9.5555588..33 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   3.7e-11   1.6e-07      12     122 ..      33     134 ..      27     147 .. 0.87
   2 ?    0.1   0.0       0.2   8.8e+02      89     117 ..     192     219 ..     177     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 3.7e-11
                           Fer4_12  12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesiegltllGGEPllpenaeallelvkevkeekpekdi 88 
                                       +  Cnl+Ck C     w+   +k  + e +  ++e+lk+  ++ l + GGEPll   +++  e++ke  +++   + 
  gi|518652597|ref|YP_008142117.1|  33 LYECNLRCKMCP---FWRRPDSKLLSMEQEIAMMEKLKEGGVSYLGFEGGEPLL---RNDTPEILKESHKRFH--TS 101
                                       679*******76...9**************************************...8888999********9..78 PP

                           Fer4_12  89 wlytgytleelskkekeellkeidvlvdGkfees 122
                                       ++++g  le+  ++  +  l+ + v +dG  e +
  gi|518652597|ref|YP_008142117.1| 102 MVTNGWRLEKKINE-IHTSLDFLFVSIDGSKEVH 134
                                       *********99974.7777888889999976643 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.2
                           Fer4_12  89 wlytgytleelskkekeellkeidvlvdG 117
                                       ++y  +t e++s+ eke+ll  +++l+d 
  gi|518652597|ref|YP_008142117.1| 192 IEYDYSTAEKISP-EKEKLLGALNMLIDR 219
                                       7888999999998.59**********995 PP

>> Fer4_14  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.2e-06    0.0055       7      79 ..      35      99 ..      32     129 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.2e-06
                           Fer4_14  7 gCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkeeyp 79
                                       Cnl Ck+C           k  + e++ +++++lk+  +  + l + GGePL+  +++   +++k+ +++++
  gi|518652597|ref|YP_008142117.1| 35 ECNLRCKMCPFWR---RPDSKLLSMEQEIAMMEKLKEGGV--SYLGFEGGEPLLRNDTP---EILKESHKRFH 99
                                      7********8755...444555555555566766677777..789********775555...55666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       407  (0.0227007); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); 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 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2433.62
//
Query:       gi|518652598|ref|YP_008142118.1|  [L=139]
Description: type I restriction-modification system methylation subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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   50.7   1.4    3.3e-13   50.4   1.4    1.1  1  HsdM_N     HsdM N-terminal domain
     0.0024   18.2   1.4      0.023   15.1   1.4    2.0  1  Nnf1       Nnf1
  ------ inclusion threshold ------
      0.037   14.4   1.4       0.39   11.1   1.4    2.2  1  EnY2       Transcription factor e(y)2
       0.26   11.6   2.4       0.66   10.3   0.0    1.9  2  PVL_ORF50  PVL ORF-50-like family


Domain annotation for each model (and alignments):
>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   1.4   7.4e-17   3.3e-13       1     114 [.      14     126 ..      14     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 7.4e-17
                                       HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..........--..--------......S-CC CS
                            HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereeklleeyken...aleeleeklksk..eafyipee 72 
                                       l + +++aad  R +v   +yk yil LlF+Krl+d ++e+ e+++++  e+   +++e +++  s+  ++f++pe+
  gi|518652598|ref|YP_008142118.1|  14 LVKLMDNAADLVRTSV---DYK-YILILLFIKRLSDGWKEEVEDAMSKIMEEagiDESEAGKRAVSNefHNFMVPEN 86 
                                       567899*******666...687.**********************99944444675544555555555989****** PP

                                       CSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS... CS
                            HsdM_N  73 lrWkelakkkdddelgenlnkafpaleelnkslkgvfmkd.df 114
                                       +  ++++k+++  +l+en+ + +++++++nk+l ++++ + df
  gi|518652598|ref|YP_008142118.1|  87 ALCNNIRKDRE--KLKENMSRGINEIAKENKELDEIVN-RiDF 126
                                       ********655..5*****************9999995.5454 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   1.4   5.1e-06     0.023      40     105 ..      57     121 ..      39     123 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.1e-06
                                       HHHHHHH.CCHH-T..........TTS.STTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  40 dlieeAk.erreegeeeasrpevppht.LpPeeliaahlapakkeeqeeLearlqeleaenaelaeev 105
                                       +++eeA  ++ e+g+++ s+ e  +h  + Pe+++++++++ +++ +e++ + ++e+ +en+el e v
  gi|518652598|ref|YP_008142118.1|  57 KIMEEAGiDESEAGKRAVSN-E--FHNfMVPENALCNNIRKDREKLKENMSRGINEIAKENKELDEIV 121
                                       67777775445555555554.3..333145*********************************98866 PP

>> EnY2  Transcription factor e(y)2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   1.4   8.7e-05      0.39      11      49 ..      28      66 ..      19     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.7e-05
                                      TTHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHH..HTS CS
                              EnY2 11 sGererlkelLrerLeesGWrdevkelckeiirekglee 49
                                      s +++ +  lL  +    GW++ev++++++i++e g +e
  gi|518652598|ref|YP_008142118.1| 28 SVDYKYILILLFIKRLSDGWKEEVEDAMSKIMEEAGIDE 66
                                      557788888888899999***************966543 PP

>> PVL_ORF50  PVL ORF-50-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00015      0.66      15      82 ..      11      78 ..       5      86 .. 0.89
   2 ?    1.4   0.9     0.088   3.9e+02      43      71 ..      88     116 ..      71     130 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00015
                         PVL_ORF50 15 eveliekygitpelvakrvkdkleldealdarkdsrlkeekekvkskileeekkerklerqrkkeael 82
                                      +++l++  + +++lv+  v  k+ l  ++  r     kee+e  +ski+ee+  ++  + +r +  e+
  gi|518652598|ref|YP_008142118.1| 11 KNDLVKLMDNAADLVRTSVDYKYILILLFIKRLSDGWKEEVEDAMSKIMEEAGIDESEAGKRAVSNEF 78
                                      467888889999**************9999**********************9999999999988887 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.088
                         PVL_ORF50  43 ldarkdsrlkeekekvkskileeekkerk 71 
                                       l+ +     ++ ke +   i e +k++++
  gi|518652598|ref|YP_008142118.1|  88 LCNNIRKDREKLKENMSRGINEIAKENKE 116
                                       44433333333444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1208  (0.0673769); expected 358.6 (0.02)
Passed bias filter:                      646  (0.036031); 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: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 997.12
//
Query:       gi|518652599|ref|YP_008142119.1|  [L=291]
Description: cation efflux integral membrane protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-14   53.8  16.5    2.7e-14   53.4  16.5    1.2  1  Cation_efflux  Cation efflux family
     0.0065   16.6   1.9      0.026   14.6   1.9    1.9  1  ZT_dimer       Dimerisation domain of Zinc Transporter
  ------ inclusion threshold ------
       0.11   11.4   8.2       0.14   11.0   8.2    1.3  1  CstA           Carbon starvation protein CstA
       0.12   10.6  15.3       0.17   10.1  15.3    1.1  1  DUF2070        Predicted membrane protein (DUF2070)
        0.5   10.2   5.4        4.9    7.0   1.1    2.4  2  PGG            Domain of unknown function


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 !   53.4  16.5   7.4e-18   2.7e-14      34     199 .]      53     209 ..      20     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 7.4e-18
                     Cation_efflux  34 slsdlvsllllllalklsrkppderfpfGygrlevlgalvsgllllglavfllleaiqklikegereihaglalvva 110
                                        l+d++s  +++l+ ++s+kp+de +++G++r+e l  ++ + l++++ +++ + + + li      + +++  + +
  gi|518652599|ref|YP_008142119.1|  53 RLVDALSISMIFLVNRISNKPTDEFHSYGFHRVEALLNITIITLFIAISAYSAILTTELLI------HGIPISSGST 123
                                       599**********************************************************......4455555555 PP

                     Cation_efflux 111 lvslvvnlalllilrragrklrsaalkaaalhvlgDaltslgvlvsalvillfnlksgplaDpvaslligliilysa 187
                                       ++s+++ + ll+      ++ + ++++  ++h+l D++  ++vl  +l+ ++f     +++D ++s+++ +iily  
  gi|518652599|ref|YP_008142119.1| 124 ALSAIIAIPLLIVAGVTIEHDEKSNFRIMFIHTLQDLAIMIIVLAFSLLPFYFF---SQYLDYLGSYIVLFIILYGN 197
                                       55555555555555555555589*************997777766666655551...368***************** PP

                     Cation_efflux 188 lkllkeslseLl 199
                                       +++++ ++ +Ll
  gi|518652599|ref|YP_008142119.1| 198 RNMFRRNVNILL 209
                                       *********997 PP

>> ZT_dimer  Dimerisation domain of Zinc Transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   1.9   7.2e-06     0.026       6      77 ..     216     284 ..     212     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.2e-06
                                       HHHHHHHHTT-SS-EEEEEEEEE-S-.---EEEEEEEE-TTS-HHHHHHHHHHHHHHHHHH-TT--EEEEEEE CS
                          ZT_dimer   6 eeeireiiksvpgvkgvhdlrtrksG.skifvdlhievdgdlsvkeaHeiadevekrikeefpgvadvliHve 77 
                                       ++e++e+i++  +  +vh+l++ ++  +++++ lh+ ++ ++++ e   + +++e+ + +++ gv +v++  e
  gi|518652599|ref|YP_008142119.1| 216 VKEVEEMIRK--EFPSVHHLHIWDICqHQRVATLHMSIPSQMQIGELDSVRKDIERIL-SKY-GVNHVTVQFE 284
                                       6788999965..566899**99977758***************************988.578.999***9987 PP

>> CstA  Carbon starvation protein CstA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   8.2     4e-05      0.14     161     263 ..      94     199 ..      22     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4e-05
                              CstA 161 avfsviltipialll.Gvllrklrkgvleasvigvvllllavvvgseveea..laelltlsketlaivlivYvfvAs 234
                                        ++ +++    a+l   +l++ + ++   + + +++ + l +v+g ++e++   +  +++ ++   +++++ v++ s
  gi|518652599|ref|YP_008142119.1|  94 ITLFIAISAYSAILTtELLIHGIPISSGSTALSAIIAIPLLIVAGVTIEHDekSNFRIMFIHTLQDLAIMIIVLAFS 170
                                       3333344444444331344455555567777888888889999999995552233334444455556677777778* PP

                              CstA 235 vlPvwlllaPrdYlstflligtivllalg 263
                                        lP +++ +  dYl +++++ +i+     
  gi|518652599|ref|YP_008142119.1| 171 LLPFYFFSQYLDYLGSYIVLFIILYGNRN 199
                                       *******************9999876554 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1  15.3   4.8e-05      0.17      17     179 ..      24     200 ..       7     209 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.8e-05
                           DUF2070  17 sllliilla.lligllaflssk........lfgillfglpalvaflltlpvlrilggrltykrslflall.telivv 83 
                                       +ll +i+l+ +l+++l +++          l   l + + +lv+ +  +p++++ +  ++ +  ++l+++ ++l+++
  gi|518652599|ref|YP_008142119.1|  24 ALLYWIILGlFLYSYLESDNPLslsvvsdrLVDALSISMIFLVNRISNKPTDEFHSYGFH-RVEALLNITiITLFIA 99 
                                       445555554045555554444499999999999999999999999999999999655565.4445555550555555 PP

                           DUF2070  84 iisllaillsall...qalvllalvls.....lalvfalrllvlvav....sdesllkavlpaliqpllailllvly 148
                                       i  + ail++ ll            +s     l++++a++ll++  v    +++s ++++++ ++q l+++++++++
  gi|518652599|ref|YP_008142119.1| 100 ISAYSAILTTELLihgI-------PISsgstaLSAIIAIPLLIVAGVtiehDEKSNFRIMFIHTLQDLAIMIIVLAF 169
                                       55555555554446443.......33344444555666666666555111156677778899999999999999999 PP

                           DUF2070 149 fspesfllllllslifalavylfivvvdrpl 179
                                       +   ++++   l  +   +v+++i + +r++
  gi|518652599|ref|YP_008142119.1| 170 SLLPFYFFSQYLDYLGSYIVLFIILYGNRNM 200
                                       5555555555555555555555555555554 PP

>> PGG  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.2    0.0055        20      65     114 ..      57     108 ..      37     110 .. 0.76
   2 ?    7.0   1.1    0.0014       4.9      65     111 ..     125     171 ..     118     176 .. 0.69

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0055
                               PGG  65 vaSlvvvvlll.issl.vedeakslpkklrvllvllvlsllsllvaFaagly 114
                                       ++S+++++l+  is+  ++++++    ++ +ll ++++ l+  + a+ a l+
  gi|518652599|ref|YP_008142119.1|  57 ALSISMIFLVNrISNKpTDEFHSYGFHRVEALLNITIITLFIAISAYSAILT 108
                                       5677777776644533588899999999999999************998765 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0014
                               PGG  65 vaSlvvvvlllissl.vedeakslpkklrvllvllvlsllsllvaFaa 111
                                       +++++++ ll+++++ +e+++ks+  +++++++l  l+++ +++aF +
  gi|518652599|ref|YP_008142119.1| 125 LSAIIAIPLLIVAGVtIEHDEKSN-FRIMFIHTLQDLAIMIIVLAFSL 171
                                       355666667776777655554554.45888899999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1888.72
//
Query:       gi|518652600|ref|YP_008142120.1|  [L=160]
Description: hypothetical protein FACI_IFERC00001G1239 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1285  (0.0716716); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); 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):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1031.94
//
Query:       gi|518652601|ref|YP_008142121.1|  [L=560]
Description: hypothetical protein FACI_IFERC00001G1240 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.8e-05   23.2   0.0     0.0011   19.3   0.0    3.0  4  MULE             MULE transposase domain
  ------ inclusion threshold ------
      0.054   12.3   0.1        1.2    7.9   0.0    2.2  2  Transposase_mut  Transposase, Mutator family
       0.13   12.5   0.1         11    6.3   0.0    2.6  2  rve              Integrase core domain
       0.14   12.2   0.1       0.28   11.2   0.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain


Domain annotation for each model (and alignments):
>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.37   1.7e+03      24      50 ..     104     130 ..     100     156 .. 0.81
   2 !   19.3   0.0   2.5e-07    0.0011      37      94 ..     167     221 ..     136     223 .. 0.76
   3 ?   -3.6   0.0       3.5   1.6e+04      62      81 ..     268     287 ..     256     290 .. 0.75
   4 ?   -2.3   0.0       1.3     6e+03      41      58 ..     445     462 ..     443     468 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.37
                              MULE  24 ddngqlvplafalveseneesyewllq 50 
                                        + +++ ++a+ ++++ +ees++ l  
  gi|518652601|ref|YP_008142121.1| 104 SHARNVTNMALRILSRIHEESWKKLKG 130
                                       678899999999*********998755 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.5e-07
                              MULE  37 veseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClfHia 94 
                                         se+ e ++ +l +++e+ ++   p+  i+D   ++l+al+evf +++ r+Cl H+ 
  gi|518652601|ref|YP_008142121.1| 167 YASESYENIKDILMKVKERFGS---PSGSISDMRSGILTALAEVFHGMPIRICLMHFL 221
                                       4566666666666677777666...*******************************96 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 3.5
                              MULE  62 pkviitDkekallnaleevf 81 
                                       ++ + +D+ k+ + a+++++
  gi|518652601|ref|YP_008142121.1| 268 ENGFCSDRGKMEIMAIRRII 287
                                       55678899999999998776 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 1.3
                              MULE  41 neesyewllqelleevsg 58 
                                       +++++e+++++++++v +
  gi|518652601|ref|YP_008142121.1| 445 TNNGMERFFRKIRRNVRK 462
                                       78999*****99998876 PP

>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.0   0.00027       1.2     231     264 ..     192     225 ..     161     271 .. 0.78
   2 ?    1.8   0.3     0.019        85     327     354 ..     436     463 ..     392     466 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00027
                   Transposase_mut 231 vvsDahkGLvkaisavfpeaavQrCrvHllrnll 264
                                        +sD   G+  a+ +vf +     C +H+lr+l 
  gi|518652601|ref|YP_008142121.1| 192 SISDMRSGILTALAEVFHGMPIRICLMHFLRDLG 225
                                       69*****************************974 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.019
                   Transposase_mut 327 peqirrkikstNllErLNkeirRrtrvv 354
                                       +++     +++N +Er  ++irR++r++
  gi|518652601|ref|YP_008142121.1| 436 NNADGTMPRTNNGMERFFRKIRRNVRKR 463
                                       3444567899**************9986 PP

>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0    0.0024        11       5      88 ..     134     209 ..     131     236 .. 0.79
   2 ?    3.2   0.0     0.021        93     102     118 ..     443     459 ..     437     460 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0024
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrli.laealsdemdastvlalleravarfggvepervlsDngseyts 80 
                                       ++++q+D t+ +     ++  + vv d  s+++ +ae + +e + +++ ++l +  +rfg   p   +sD  s +  
  gi|518652601|ref|YP_008142121.1| 134 NYVLQIDGTTDS-----KFDMIVVVRDSISNFTlHAEKYASE-SYENIKDILMKVKERFGS--PSGSISDMRSGIL- 201
                                       778899999777.....25799*********97258888888.**********99999999..9999999888776. PP

                               rve  81 kafrefla 88 
                                        a++e+ +
  gi|518652601|ref|YP_008142121.1| 202 TALAEVFH 209
                                       56666555 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                               rve 102 pqdnGkvErfhrtlkde 118
                                       p++n  +Erf+r ++++
  gi|518652601|ref|YP_008142121.1| 443 PRTNNGMERFFRKIRRN 459
                                       99************986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.2e-05      0.28      17      35 ..      10      29 ..       1      35 [. 0.75

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                     Zn_Tnp_IS1595 17 ngfvCPhCgsr.kayriktr 35
                                      ++ vCP C+sr   y++++r
  gi|518652601|ref|YP_008142121.1| 10 DRTVCPQCHSRlVEYKTERR 29
                                      3467*******999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (560 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); 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: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 3907.37
//
Query:       gi|518652602|ref|YP_008142122.1|  [L=132]
Description: hypothetical protein FACI_IFERC00001G1241 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.032   14.5   0.2      0.082   13.2   0.1    1.7  1  B5        tRNA synthetase B5 domain
       0.14   11.1   0.1       0.14   11.1   0.1    1.1  1  TMEM151   TMEM151 family


Domain annotation for each model (and alignments):
>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   9.1e-06     0.082       7      32 ..      83     108 ..      80     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.1e-06
                                       HHHHHHTS---HHHHHHHHHHTT-E. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                                B5   7 kinkllGidlseeeiikiLkrlgcer 32 
                                       +i++ll  ++s+e+i  iLk++g+e+
  gi|518652602|ref|YP_008142122.1|  83 YIKRLLDKKISQEDIDSILKKIGIEY 108
                                       79*********************994 PP

>> TMEM151  TMEM151 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   1.6e-05      0.14     104     159 ..       6      59 ..       1      97 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.6e-05
                           TMEM151 104 vlervqrlqqatPciWWkaisyhyvrrtrqvtryrnGDaytttqvyhervnthvae 159
                                       +++ ++++++++  i W  i+ h + r ++vtr ++G++y +  v   rv  +v +
  gi|518652602|ref|YP_008142122.1|   6 LYHFLRKIRRTETFILWDVITVHMTVRPKKVTR-KDGNTYYS-LVDEKRVKGKVVQ 59 
                                       6788999**************************.68998875.4777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1038  (0.057895); expected 358.6 (0.02)
Passed bias filter:                      648  (0.0361426); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 975.10
//
Query:       gi|518652603|ref|YP_008142123.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G1242 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 605.71
//
Query:       gi|518652604|ref|YP_008142124.1|  [L=256]
Description: hypothetical protein FACI_IFERC00001G1243 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-22   78.5   0.1    8.5e-22   77.9   0.1    1.3  1  DDE_Tnp_1    Transposase DDE domain
    3.8e-05   23.7   1.4    0.00012   22.1   0.1    2.0  2  DDE_Tnp_1_3  Transposase DDE domain
     0.0063   16.5   1.7       0.01   15.8   0.2    2.2  2  HTH_19       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.013   15.9   0.1       0.05   14.0   0.0    2.0  2  HTH_26       Cro/C1-type HTH DNA-binding domain
      0.025   14.4   0.2        6.9    6.6   0.0    2.6  2  HTH_10       HTH DNA binding domain
      0.044   13.1   0.0      0.071   12.4   0.0    1.3  1  DDE_Tnp_1_7  Transposase IS4


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.1   2.8e-25   8.5e-22       3     115 ..     106     218 ..     104     250 .. 0.87

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.8e-25
                         DDE_Tnp_1   3 krevlivDattvrvpgtkedarwgykggkykygyklhiavdtrsgl..ilsvvitpgnvhdskglkqlldelrpr.. 75 
                                        +++l++D+t++++  ++   +  y++ k+++g+k+hia  t+ ++  +l++ itp+nv+dsk++++ll ++++   
  gi|518652604|ref|YP_008142124.1| 106 LYSILAIDSTFIETMVNG---SGIYQREKRRNGIKIHIAAKTN-HYalPLKAIITPANVNDSKVFDDLLWHINEYms 178
                                       589**********98888...55888**************998.4556***************************** PP

                         DDE_Tnp_1  76 kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrk 115
                                        +++++ D GY s++ l++l+e+++++++rl+kn+ +   
  gi|518652604|ref|YP_008142124.1| 179 GNTVLTFDLGYYSYDRLKELKENNINFVSRLRKNADYTVI 218
                                       ***********************************98876 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.17   5.2e+02      66     135 ..      51     118 ..       5     126 .. 0.66
   2 !   22.1   0.1   4.1e-08   0.00012      45     121 ..     135     219 ..     131     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.17
                       DDE_Tnp_1_3  66 gnvdDrepveelakellgklfaDkgy.iskklaeelleegielitklrknmkkkllslldkllLrkrslie 135
                                        +  D    + ++k+ l kl   + y is+k++ +ll++   +i   r ++ +  l +l  +l    + ie
  gi|518652604|ref|YP_008142124.1|  51 NDLTDIAYNNGISKSQLSKLNNKRPYtISEKVFYSLLNT---FIKAHRYDIYHDYLDKLYSILAIDSTFIE 118
                                       334566666777888888888888887788888777654...44455555555555555555555555555 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 4.1e-08
                       DDE_Tnp_1_3  45 GfkLhlii..ndkGeilavkltpgnvdDrepveelakellgklfa......Dkgyiskklaeelleegielitklrk 113
                                       G k+h+    n+    l++ +tp+nv+D +  ++l  ++ + + +      D gy s +  +el+e++i+++++lrk
  gi|518652604|ref|YP_008142124.1| 135 GIKIHIAAktNHYALPLKAIITPANVNDSKVFDDLLWHINEYMSGntvltfDLGYYSYDRLKELKENNINFVSRLRK 211
                                       88999875226666678889***********9888777665443322222399************************ PP

                       DDE_Tnp_1_3 114 nmkkklls 121
                                       n   ++++
  gi|518652604|ref|YP_008142124.1| 212 NADYTVIK 219
                                       *8776655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   3.4e-06      0.01      15      52 ..      53      90 ..      47      90 .. 0.91
   2 ?   -2.0   0.1       1.3   3.8e+03       3      10 ..     194     201 ..     192     218 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.4e-06
                            HTH_19 15 qeelaerlgisrskisaiEngkkdvpsaelllkiaeal 52
                                      + ++a+++gis+s++s++ n + +++s ++++++++++
  gi|518652604|ref|YP_008142124.1| 53 LTDIAYNNGISKSQLSKLNNKRPYTISEKVFYSLLNTF 90
                                      679******************999*********99986 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                            HTH_19   3 rLkeaRee 10 
                                       rLke+ e+
  gi|518652604|ref|YP_008142124.1| 194 RLKELKEN 201
                                       56666554 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.7e-05      0.05       9      42 ..      45      82 ..      41      90 .. 0.82
   2 ?   -2.9   0.0       3.2   9.5e+03      25      33 ..     204     212 ..     190     216 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.7e-05
                            HTH_26  9 rgi.tkseL...argtgisaatlsrlvkgkpervsldt 42
                                      +gi +k++L   a   gis+++ls+l +++p ++s ++
  gi|518652604|ref|YP_008142124.1| 45 KGIiKKNDLtdiAYNNGISKSQLSKLNNKRPYTISEKV 82
                                      67779999966678999**************9999766 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 3.2
                            HTH_26  25 atlsrlvkg 33 
                                       + +srl+k+
  gi|518652604|ref|YP_008142124.1| 204 NFVSRLRKN 212
                                       567777776 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0    0.0023       6.9      23      42 ..      50      69 ..      48      72 .. 0.87
   2 ?    5.0   0.0     0.007        21      13      28 ..     185     200 ..     182     200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0023
                            HTH_10 23 rvtlkeLAkelGIskstlse 42
                                      + +l ++A   GIsks ls+
  gi|518652604|ref|YP_008142124.1| 50 KNDLTDIAYNNGISKSQLSK 69
                                      56799***********9986 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.007
                            HTH_10  13 yemGYFdyPRrvtlke 28 
                                       +++GY+ y+R  +lke
  gi|518652604|ref|YP_008142124.1| 185 FDLGYYSYDRLKELKE 200
                                       799*******988876 PP

>> DDE_Tnp_1_7  Transposase IS4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.4e-05     0.071     148     240 ..     128     214 ..     111     225 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.4e-05
                       DDE_Tnp_1_7 148 pgkprkvgiklhvlcdsqtgyilalelyegearnlrlsrelgktnalvlrLleplqgkgrvvvmdnfftslellqeL 224
                                       ++  r++gik+h  +   + y l l+ +  +a  +    ++   ++l++   e + g + v+++d  + s++ l+eL
  gi|518652604|ref|YP_008142124.1| 128 QREKRRNGIKIHIAAK-TNHYALPLKAIITPANVN----DSKVFDDLLWHINEYMSG-NTVLTFDLGYYSYDRLKEL 198
                                       455599**********.********9888877733....445689999999666665.9****************** PP

                       DDE_Tnp_1_7 225 akkgtyavGtlkknrs 240
                                       +++++  v  l+kn +
  gi|518652604|ref|YP_008142124.1| 199 KENNINFVSRLRKNAD 214
                                       *************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2072.71
//
Query:       gi|518652605|ref|YP_008142125.1|  [L=301]
Description: hypothetical protein FACI_IFERC00001G1244 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-11   43.7  35.3    1.6e-11   43.7  35.3    1.5  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.25   10.3  17.0      0.048   12.7  10.5    2.3  2  PUCC      PUCC protein


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 !   43.7  35.3   1.8e-15   1.6e-11      86     347 ..       6     251 ..       1     256 [. 0.79

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 1.8e-15
                             MFS_1  86 wlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsa.gfslGailgpllggllasslg..Wravfyilai 159
                                       + l+++r++qGl++ga+   ++al+ ++       +  ++l++ ++s G+++gpllgg++a++l     +v++i  i
  gi|518652605|ref|YP_008142125.1|   6 PELFLARAMQGLASGAISGPAGALLFHYRG-----KTGAILTSfSTSSGIAVGPLLGGFMAEYLPfpLKLVYIISLI 77 
                                       4799*****************999999555.....555555553789999*************99777889****** PP

                             MFS_1 160 vsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg...lltllply 233
                                       ++++ f++  +  + ++ +  ++  + +    +++p ++   +  k+     ++++++++++++s+   +l+l+p+y
  gi|518652605|ref|YP_008142125.1|  78 ITIIPFIF--IIPVINRFRIDNNHNVFK----FHFPKLD---MEAKNL----FILSAATASIAWSItvfYLSLSPFY 141
                                       *****994..444556666666666666....8888888...444444....666666666666665558888888* PP

                             MFS_1 234 lqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvli 310
                                       + e l++s+  ++g    ll +++++++ +   ls +++  + l++++++++++ +++++  +++s +++ ++ ++i
  gi|518652605|ref|YP_008142125.1| 142 IIELLNISNIAITG----LLVFLMLVISSIMQILSMKINIFNSLTIGIISIIIGIILIIVSLPFKSILIFSAATITI 214
                                       ********434444....4444444446699999999999************************888888889999* PP

                             MFS_1 311 Gfglgfvfpsllalasdlappeeagtasglfntagsl 347
                                       G+g+gf+f+ ++  +   app ++g +++ + ++ ++
  gi|518652605|ref|YP_008142125.1| 215 GIGGGFAFTGATRGIRTIAPPLRMGNVLSNYYMILYF 251
                                       *********************9999999888876554 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.4     0.013   1.2e+02     352     399 ..      45      92 ..       8      95 .. 0.74
   2 ?   12.7  10.5   5.3e-06     0.048     256     367 ..     158     271 ..     116     294 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.013
                              PUCC 352 avllggalrdllkalaandaalayglVfaleavlliisilvlnklvrr 399
                                       ++  g a+  ll  ++a+   ++  lV+ + +++ ii  +++ ++++r
  gi|518652605|ref|YP_008142125.1|  45 STSSGIAVGPLLGGFMAEYLPFPLKLVYIISLIITIIPFIFIIPVINR 92 
                                       445555555555555554455677899999999999999999998865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 5.3e-06
                              PUCC 256 tlvGlllaglv..lsrglkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaa 330
                                       +++ l++++++  ls ++++++  ++g++ ++++++l+i++ +++++ ++ a+++ +G+++G++ ++a+  + ++a+
  gi|518652605|ref|YP_008142125.1| 158 VFLMLVISSIMqiLSMKINIFNSLTIGIISIIIGIILIIVSLPFKSILIFSAATITIGIGGGFAFTGATRGIRTIAP 234
                                       4555566666511455666777788899***********************************99999998889999 PP

                              PUCC 331 eeraglalGaWGaaQaiaaglavllggalrdllkala 367
                                       + r+g  l  + ++     g++ ++ g + ++l ++ 
  gi|518652605|ref|YP_008142125.1| 235 PLRMGNVLSNYYMILYFCMGFSDIILGLIDNMLGLFN 271
                                       8888877776666666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 2307.49
//
Query:       gi|518652606|ref|YP_008142126.1|  [L=411]
Description: DNA integration/recombination/inversion protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   70.7   0.0    2.4e-19   69.8   0.0    1.4  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.015   15.3   0.4      0.029   14.4   0.4    1.4  1  DZR              Double zinc ribbon
      0.076   12.4   2.2       0.16   11.4   2.2    1.5  1  zf-ribbon_3      zinc-ribbon domain
       0.11   12.2   0.7        0.2   11.3   0.7    1.4  1  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
       0.11   12.3   2.8        0.2   11.4   2.8    1.4  1  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.8   0.0   6.6e-23   2.4e-19       3     169 ..     127     289 ..     125     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 69.8 bits;  conditional E-value: 6.6e-23
                                       HHHHHHHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   3 ltedeverllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                       +t  +++++++++++   +rdk+++ + y++G Ri+E+l Lr+kd+  ++  +l+   +gK++  r v +      +
  gi|518652606|ref|YP_008142126.1| 127 ITRADIDEMINNCNN---ARDKAIISIPYDSGCRIGEILDLRIKDVVYDEYGALL-HVHGKTGN-RSVRIIGDSIAY 198
                                       577789999999999...***************************9888888887.44566665.555555555678 PP

                                       HHHHHHHHCHCCTTTSBSSBET....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHH CS
                   Phage_integrase  80 lkellskaleeaeksellfask....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvq 152
                                       l+++l+++   + ++e+lf        +k+l+  ++r+ f +++++agiek++ pH +Rh+ a+ L+ + v+    +
  gi|518652606|ref|YP_008142126.1| 199 LRDYLKTK---DGRDEYLFTGLqgttMHKQLQYTAIRRLFINVRRRAGIEKRIYPHLFRHTRASMLA-SKVPEAPRE 271
                                       9*******...9999*****99777788888888999999999999*****************9666.55699999* PP

                                       HHHT-SSCC.HHHHHHCC CS
                   Phage_integrase 153 kllGHssis.ttqiYthv 169
                                       + +G+ + s +t iY+h+
  gi|518652606|ref|YP_008142126.1| 272 NQMGWVHGSqMTAIYVHL 289
                                       *****9965278*****7 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.4   8.1e-06     0.029       1      22 [.     319     340 ..     304     353 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 8.1e-06
                               DZR   1 CpqCgeelppdarfCseCgtkl 22 
                                       Cp+C + + + a +C +C  + 
  gi|518652606|ref|YP_008142126.1| 319 CPRCDHLNASTALYCTNCFMPF 340
                                       7888888888888888886665 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.2   4.4e-05      0.16       3      22 ..     317     336 ..     316     338 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.4e-05
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       ++CP+C++ + +s +  C++C
  gi|518652606|ref|YP_008142126.1| 317 KKCPRCDHlN-ASTALYCTNC 336
                                       68******99.********** 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 ?   11.3   0.7   5.5e-05       0.2      11      37 ..     317     341 ..     312     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
                           zf-tcix  11 rkCpkCGtyNGtRglsCkNkaCdqvfk 37 
                                       +kCp+C   N + +l C N  C + f+
  gi|518652606|ref|YP_008142126.1| 317 KKCPRCDHLNASTALYCTN--CFMPFN 341
                                       9****************98..666665 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.8   5.5e-05       0.2       1      19 [.     318     336 ..     318     336 .. 0.99

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.5e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyC 19 
                                       +Cp+C + +  +a +C++C
  gi|518652606|ref|YP_008142126.1| 318 KCPRCDHLNASTALYCTNC 336
                                       8****************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      653  (0.0364214); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 2737.93
//
Query:       gi|518652607|ref|YP_008142127.1|  [L=97]
Description: hypothetical protein FACI_IFERC00001G1246 [Ferroplasma acidarmanus fer1]
Scores for complete 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   48.3  11.5    1.5e-07   31.1   4.3    2.4  2  Fer4_6    4Fe-4S binding domain
    2.7e-10   40.7   2.8    2.7e-10   40.7   2.8    1.5  1  Fer4_7    4Fe-4S dicluster domain
      3e-10   39.5  12.0    1.3e-07   31.1   3.9    2.6  2  Fer4      4Fe-4S binding domain
    1.4e-09   37.9   4.0      4e-05   23.7   1.2    2.3  2  Fer4_10   4Fe-4S dicluster domain
      4e-08   33.3   5.3    9.7e-08   32.1   5.3    1.8  1  Fer4_9    4Fe-4S dicluster domain
    3.8e-07   30.9   5.9    0.00041   21.2   2.7    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    2.7e-05   24.2   8.0    0.00097   19.2   1.8    2.3  2  Fer4_21   4Fe-4S dicluster domain
    3.7e-05   23.6  10.0     0.0007   19.5   3.2    2.6  2  Fer4_2    4Fe-4S binding domain
    4.6e-05   23.9   7.8    0.00015   22.2   6.8    1.9  2  Fer4_17   4Fe-4S dicluster domain
     0.0001   23.0  13.0      0.011   16.7   5.7    2.4  2  Fer4_3    4Fe-4S binding domain
    0.00011   22.6   7.2       0.13   12.8   0.1    2.3  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I
    0.00031   21.4   5.4       0.75   10.6   0.0    2.5  2  Fer4_15   4Fe-4S single cluster domain
     0.0055   16.8   4.3       0.15   12.2   0.0    2.1  2  Fer4_11   4Fe-4S dicluster domain
     0.0068   16.8  14.5       0.13   12.8   0.9    2.5  2  Fer4_4    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.018   15.5  11.6       0.13   12.7  10.2    2.2  1  Fer4_8    4Fe-4S dicluster domain
        1.2   10.0   7.2         16    6.5   7.2    2.0  1  Fer4_22   4Fe-4S dicluster domain
        1.4    9.2   8.9         17    5.6   0.7    2.2  2  Fer4_18   4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.7   1.7e-07   0.00018       1      23 [.      16      38 ..      16      39 .. 0.93
   2 !   31.1   4.3   1.5e-10   1.5e-07       3      24 .]      70      91 ..      70      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.7e-07
                            Fer4_6  1 vveidpdkCigCgdCvrvCPega 23
                                      ++ i++++C   g+Cv++CP+++
  gi|518652607|ref|YP_008142127.1| 16 IPSINRNSCEAKGECVSICPYNV 38
                                      689******************97 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.5e-10
                            Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                                      +idp +C +CgdCv++CPe+ai
  gi|518652607|ref|YP_008142127.1| 70 VIDPALCHSCGDCVKACPEKAI 91
                                      69******************98 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   2.8   2.5e-13   2.7e-10       6      52 .]      28      90 ..      20      90 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 2.5e-13
                            Fer4_7  6 gaCvaaCpvkaieldeeenek................gtekveidpekClgCgaCvavCPtga 52
                                      g Cv+ Cp++++el + ++e+                g++ ++idp  C +Cg Cv++CP +a
  gi|518652607|ref|YP_008142127.1| 28 GECVSICPYNVFELIPLKDEDkknmslvgklkarahgGKQAYVIDPALCHSCGDCVKACPEKA 90
                                      79***********99876666567778877777777677899******************876 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.1   6.6e-05      0.07      12      23 ..      28      39 ..      17      40 .. 0.75
   2 !   31.1   3.9   1.2e-10   1.3e-07       1      24 []      69      92 ..      69      92 .. 0.96

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-05
                                      THHHHHSTTTEE CS
                              Fer4 12 GaCvevCPvgAI 23
                                      G+Cv++CP+++ 
  gi|518652607|ref|YP_008142127.1| 28 GECVSICPYNVF 39
                                      9********986 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 1.2e-10
                                      EEEETTTSSS-THHHHHSTTTEEE CS
                              Fer4  1 vvideekCigCGaCvevCPvgAIt 24
                                      +vid+ +C  CG Cv++CP  AIt
  gi|518652607|ref|YP_008142127.1| 69 YVIDPALCHSCGDCVKACPEKAIT 92
                                      69*********************7 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     2e-05     0.021       3      24 ..      18      46 ..      16      67 .. 0.70
   2 !   23.7   1.2   3.7e-08     4e-05       2      21 ..      69      88 ..      68      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2e-05
                           Fer4_10  3 vidddtCirCgkCvkaCPadl.......t 24
                                       i++++C   g+Cv+ CP+++       +
  gi|518652607|ref|YP_008142127.1| 18 SINRNSCEAKGECVSICPYNVfeliplkD 46
                                      6899999999********95554444431 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.7e-08
                           Fer4_10  2 vvidddtCirCgkCvkaCPa 21
                                       vid+  C  Cg+CvkaCP 
  gi|518652607|ref|YP_008142127.1| 69 YVIDPALCHSCGDCVKACPE 88
                                      589****************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 !   32.1   5.3   9.2e-11   9.7e-08       5      51 .]      24      91 ..       2      91 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 9.2e-11
                            Fer4_9  5 C...gaCveaCpagvvvedaaerkarlraase..................eaCigCgaCveaCpkgai 51
                                      C   g+Cv+ Cp++v++    + +++ ++                       C++Cg+Cv+aCp++ai
  gi|518652607|ref|YP_008142127.1| 24 CeakGECVSICPYNVFELIPLKDEDKKNMSLVgklkarahggkqayvidpALCHSCGDCVKACPEKAI 91
                                      522256**********99999988887665448899*****************************987 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00068      0.72       2      19 ..      24      41 ..      22      69 .. 0.76
   2 !   21.2   2.7   3.8e-07   0.00041       2      18 ..      76      92 ..      75      96 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00068
                           Fer4_16  2 CgtCgkCaevCPtnaike 19
                                      C   g+C+++CP n+++ 
  gi|518652607|ref|YP_008142127.1| 24 CEAKGECVSICPYNVFEL 41
                                      788899******999875 PP

  == domain 2  score: 21.2 bits;  conditional E-value: 3.8e-07
                           Fer4_16  2 CgtCgkCaevCPtnaik 18
                                      C++Cg C+++CP++ai+
  gi|518652607|ref|YP_008142127.1| 76 CHSCGDCVKACPEKAIT 92
                                      ****************8 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.3    0.0017       1.7       3      30 ..      19      46 ..      17      59 .. 0.71
   2 !   19.2   1.8   9.2e-07   0.00097       2      28 ..      70      96 ..      69      97 .] 0.92

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                           Fer4_21  3 idedkCigCgkCliaCedtshqaieida 30
                                      i++++C   g+C+  C+ +  + i +++
  gi|518652607|ref|YP_008142127.1| 19 INRNSCEAKGECVSICPYNVFELIPLKD 46
                                      7888888888888888888888884443 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.2e-07
                           Fer4_21  2 ridedkCigCgkCliaCedtshqaiei 28
                                      +id++ C +Cg C++aC++++++ i+i
  gi|518652607|ref|YP_008142127.1| 70 VIDPALCHSCGDCVKACPEKAITLISI 96
                                      69******************9999976 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.6    0.0037       3.9       6      22 .]      20      36 ..      16      36 .. 0.71
   2 !   19.5   3.2   6.7e-07    0.0007       3      22 .]      69      88 ..      67      88 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0037
                            Fer4_2  6 dtdrCigCgaCvsaCPa 22
                                      ++++C + g Cvs CP+
  gi|518652607|ref|YP_008142127.1| 20 NRNSCEAKGECVSICPY 36
                                      5555554489******5 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 6.7e-07
                            Fer4_2  3 vvvdtdrCigCgaCvsaCPa 22
                                      +v+d++ C +Cg Cv+aCP+
  gi|518652607|ref|YP_008142127.1| 69 YVIDPALCHSCGDCVKACPE 88
                                      79*****************5 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   1.1    0.0018       1.9      42      60 ..      20      38 ..       2      39 .. 0.80
   2 !   22.2   6.8   1.4e-07   0.00015       2      58 ..      24      88 ..      22      90 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0018
                           Fer4_17 42 kaslCieCgeCerkCPqgl 60
                                      + ++C   geC++ CP+++
  gi|518652607|ref|YP_008142127.1| 20 NRNSCEAKGECVSICPYNV 38
                                      6689*************97 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.4e-07
                           Fer4_17  2 CiqCgyClpeCpsyea.......ydnepkkllraaklglleeaeke.ekaslCieCgeCerkCPq 58
                                      C   g C+  Cp++          d+++++l+ ++k+  +++ ++      lC++Cg C+++CP+
  gi|518652607|ref|YP_008142127.1| 24 CEAKGECVSICPYNVFeliplkdEDKKNMSLVGKLKARAHGGKQAYvIDPALCHSCGDCVKACPE 88
                                      556677******966666666445567889999999977777655545889*************8 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.7   0.00082      0.86       4      14 ..      24      37 ..      20      38 .. 0.77
   2 !   16.7   5.7     1e-05     0.011       1      15 []      76      90 ..      76      90 .. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00082
                            Fer4_3  4 Cg...aCvevCPvg 14
                                      C+    Cv  CP++
  gi|518652607|ref|YP_008142127.1| 24 CEakgECVSICPYN 37
                                      863337******98 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 1e-05
                            Fer4_3  1 CtgCgaCvevCPvgA 15
                                      C+ Cg Cv++CP++A
  gi|518652607|ref|YP_008142127.1| 76 CHSCGDCVKACPEKA 90
                                      999*********998 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   0.00013      0.13       1      21 [.      19      40 ..      19      56 .. 0.87
   2 !   11.4   3.5   0.00033      0.35       1      18 [.      71      88 ..      71      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                           Fer4_13  1 VDrdtCiacgaCvelaP.dvFe 21
                                      ++r++C a g Cv+++P +vFe
  gi|518652607|ref|YP_008142127.1| 19 INRNSCEAKGECVSICPyNVFE 40
                                      79***************66776 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00033
                           Fer4_13  1 VDrdtCiacgaCvelaPd 18
                                      +D   C +cg Cv+++P+
  gi|518652607|ref|YP_008142127.1| 71 IDPALCHSCGDCVKACPE 88
                                      78899************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 !   10.6   0.0   0.00071      0.75       3      33 ..      19      53 ..      18      65 .. 0.75
   2 !   10.1   3.6   0.00098         1       2      20 ..      70      88 ..      70      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00071
                           Fer4_15  3 vDrdaCigcglCvaea....pevfeldedglasvl 33
                                      ++r+ C+  g Cv  +     e++ l++++++ + 
  gi|518652607|ref|YP_008142127.1| 19 INRNSCEAKGECVSICpynvFELIPLKDEDKKNMS 53
                                      89**************6555566666666666665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                           Fer4_15  2 vvDrdaCigcglCvaeape 20
                                      v+D  +C +cg Cv+++pe
  gi|518652607|ref|YP_008142127.1| 70 VIDPALCHSCGDCVKACPE 88
                                      699**************97 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00014      0.15      32      60 ..      11      40 ..       4      66 .. 0.77
   2 ?    5.6   1.7     0.017        18       3      28 ..      69      92 ..      66      95 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
                           Fer4_11 32 etGaVl..ldektkkeevrevveacPykivr 60
                                      +tG+V+  +++++++    e+v+ cPy+++ 
  gi|518652607|ref|YP_008142127.1| 11 TTGLVIpsINRNSCE-AKGECVSICPYNVFE 40
                                      689998445677776.999*********864 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.017
                           Fer4_11  3 wlflpeqCrhCleppCvasapseaiv 28
                                      +++ p  C+ C    Cv+++p++ai+
  gi|518652607|ref|YP_008142127.1| 69 YVIDPALCHSCG--DCVKACPEKAIT 92
                                      567889999996..499999999885 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   0.9   0.00012      0.13       2      17 .]      22      37 ..      21      38 .. 0.86
   2 !   10.8   4.0   0.00056      0.59       3      16 ..      75      88 ..      73      89 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00012
                            Fer4_4  2 erCigCgsCvaaCPqg 17
                                      ++C   g Cv++CP++
  gi|518652607|ref|YP_008142127.1| 22 NSCEAKGECVSICPYN 37
                                      57888899******86 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00056
                            Fer4_4  3 rCigCgsCvaaCPq 16
                                       C  Cg Cv aCP 
  gi|518652607|ref|YP_008142127.1| 75 LCHSCGDCVKACPE 88
                                      599**********5 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7  10.2   0.00012      0.13       5      64 ..      24      89 ..      22      90 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00012
                            Fer4_8  5 CieCgaCqsaCp.......vlrrtkkhlldargeaaedvqeeqvlee..eealwsCttcgaCtevCpvg 64
                                      C   g C s Cp        l++++k +++  g+ ++  +   + ++        C++cg C+++Cp++
  gi|518652607|ref|YP_008142127.1| 24 CEAKGECVSICPynvfeliPLKDEDKKNMSLVGKLKA--RAHGG-KQayVIDPALCHSCGDCVKACPEK 89
                                      555589*****96655544344444444444444333..22222.1123456789************97 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   7.2     0.015        16      33      95 ..      27      89 ..       9      90 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                           Fer4_22 33 rvrvwdsClleeftkvaggenvrkekkerlrqrllhklsefkekfgesgCvGCgRCieacpvk 95
                                      +  +++ C ++ f+ +  +++ +k+ +   + +   +  + +  ++   C  Cg C++acp+k
  gi|518652607|ref|YP_008142127.1| 27 KGECVSICPYNVFELIPLKDEDKKNMSLVGKLKARAHGGKQAYVIDPALCHSCGDCVKACPEK 89
                                      5566677777777777777555555555445455455555555669999***********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   0.7     0.016        17      58      75 ..      21      38 ..       3      42 .. 0.80
   2 ?    4.9   6.4     0.028        30      55      73 ..      70      88 ..      27      94 .. 0.55

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.016
                           Fer4_18 58 agdcidcescvkvcPtgi 75
                                       + c + + cv++cP ++
  gi|518652607|ref|YP_008142127.1| 21 RNSCEAKGECVSICPYNV 38
                                      567888889999999765 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.028
                           Fer4_18 55 ekgagdcidcescvkvcPt 73
                                        + + c +c+ cvk cP 
  gi|518652607|ref|YP_008142127.1| 70 VIDPALCHSCGDCVKACPE 88
                                      3445679999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 657.68
//
Query:       gi|518652608|ref|YP_008142128.1|  [L=697]
Description: hypothetical protein FACI_IFERC00001G1247 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-94  315.8   0.0    1.6e-94  315.2   0.0    1.3  1  MCM              MCM P-loop domain
    4.5e-32  110.5   0.1    8.2e-32  109.7   0.1    1.4  1  MCM_OB           MCM OB domain
    9.2e-23   80.5   0.4    2.3e-22   79.2   0.4    1.6  1  MCM_lid          MCM AAA-lid domain
    1.3e-09   37.8   0.0    2.5e-06   27.0   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    2.1e-05   25.1   1.4    0.00013   22.5   0.3    2.7  2  MCM_N            MCM N-terminal domain
    2.8e-05   24.1   0.0    8.3e-05   22.6   0.0    1.9  1  AAA_5            AAA domain (dynein-related subfamily)
     0.0025   17.6   0.0     0.0076   16.0   0.0    1.7  1  Sigma54_activat  Sigma-54 interaction domain
      0.006   16.4   0.0      0.025   14.4   0.0    2.0  1  AAA_3            ATPase family associated with various cellul
  ------ inclusion threshold ------
       0.21   11.4   0.2       0.44   10.4   0.2    1.5  1  Cys_rich_CPCC    Cysteine-rich CPCC


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 !  315.2   0.0   8.2e-98   1.6e-94       1     223 [.     269     492 ..     269     493 .. 0.98

  Alignments for each domain:
  == domain 1  score: 315.2 bits;  conditional E-value: 8.2e-98
                                       HHHHHHHHHTSSTHHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTSTHHHHHHHH CS
                               MCM   1 eveeikelakekdiieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgtaKsqlLkyv 77 
                                       ++++ikela+e++ii++l+ksiapsiyg + +kk+++lqlfggv+k ++d+t++rgdi++l++gdpgtaKsqlL+y+
  gi|518652608|ref|YP_008142128.1| 269 DEKKIKELAREPNIIDRLAKSIAPSIYGLDVIKKSLVLQLFGGVRKVMKDGTHIRGDIHILMIGDPGTAKSQLLRYM 345
                                       5799************************************************************************* PP

                                       HHHSSSEEEEESSSSSSSHSSSEEEEESS.SSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM  78 eklapravytsgkgssaagLtaavvrdee.tgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       + ++pr+v++ gkgssaagLtaa vrd+  +g ++leaGalvlad+G ++iDe+dkm+++d+ ++hEamEqq+++i+
  gi|518652608|ref|YP_008142128.1| 346 TFISPRSVFAFGKGSSAAGLTAAAVRDDFgEGRWTLEAGALVLADNGFAAIDELDKMDKNDTASMHEAMEQQSVTIS 422
                                       **********************99999861556******************************************** PP

                                       SSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEEEEE-SSTTHHHHHHHHHHHHHH CS
                               MCM 154 KaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDlifvllDkvdeekDeelaehivsl 223
                                       KaGi+atL++r+s+laAanp++gryd+ k++ae+ +++++lLsrFD+if l D++++e D +laeh++++
  gi|518652608|ref|YP_008142128.1| 423 KAGIMATLKSRCSILAAANPRFGRYDPMKTIAEQTEFPPPLLSRFDIIFKLIDTPNREIDDKLAEHVLKT 492
                                       *******************************************************************985 PP

>> MCM_OB  MCM OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.1   4.1e-35   8.2e-32       2     124 ..     105     231 ..     104     233 .. 0.94

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 4.1e-35
                                       XGG--GGGTTSEEEEEEEEEEE---EEEEEEEEEEETTT-.-EEE.....S----SB-..TTT-.HHH-EEE-GGGS CS
                            MCM_OB   2 lRdlrsehigklvkveGivtrasevkpklkkavfeckkcgktvev.....eleePrkCeekeCe.skdpfkleteks 72 
                                       +R++rs+++++ ++++Gi+ + +ev p+l++a+f+c++cg+ + v     +l eP+ C  ++C+ +k+++kl +e+s
  gi|518652608|ref|YP_008142128.1| 105 IRNVRSSNVNSYISINGIIRKNTEVLPRLQNAAFKCPACGELTIVpediqKLFEPTAC--QACGwNKGKLKLIPEES 179
                                       8***************************************86666887777778****..99**8888********* PP

                                       EEEEEEEEEEE-------------EEEEEEEGGGTT---TT-EEEEEEEEEE CS
                            MCM_OB  73 kfvdfqklklQEspeevpaGelPrslevileddlvdkvkPGdrvevtGiyra 124
                                       +fvd+qkl++QE+p+++   + P+ +++i+edd++ k+ PGdrv+v Gi++a
  gi|518652608|ref|YP_008142128.1| 180 EFVDTQKLEIQENPDTIDSTSQPQRITLIIEDDITGKIYPGDRVTVYGILKA 231
                                       *************************************************986 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.4   1.1e-25   2.3e-22       2      79 ..     525     598 ..     524     605 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.1e-25
                                       HHHHHHHHHHHTT--BETCHHHHHHHHHHHHHHHHHTSSTSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHH CS
                           MCM_lid   2 llrkYiayarekikPklseeakeklseaYvelRkeeedskrksipitvRqLesliRLseAlAklrlsevvteedvee 78 
                                       l+rkY++ya+++++P+ls+ea  +l+e Yv++R +      +s+pit+RqLes iRL+eA Ak rls ++t ed+  
  gi|518652608|ref|YP_008142128.1| 525 LIRKYVSYAKNRVFPRLSDEAISILKEEYVKTRASGI----DSVPITARQLESTIRLAEAAAKARLSPIITVEDALL 597
                                       79********************************775....57*******************************876 PP

                                       H CS
                           MCM_lid  79 a 79 
                                       a
  gi|518652608|ref|YP_008142128.1| 598 A 598
                                       6 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0   0.00074       1.5      21      48 ..     324     351 ..     316     355 .. 0.88
   2 !   27.0   0.0   1.3e-09   2.5e-06      94     164 ..     377     447 ..     366     480 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00074
                      Mg_chelatase  21 GgHnlllvGppGsGKtmlakrlpsllpp 48 
                                       G  ++l++G pG+ K+ l + ++ + p+
  gi|518652608|ref|YP_008142128.1| 324 GDIHILMIGDPGTAKSQLLRYMTFISPR 351
                                       7889***************999988776 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 1.3e-09
                      Mg_chelatase  94 gs.kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgkl 164
                                       g+ + + G++ la nG   +DEl +++++   ++ e +e+++vtis+a   ++  +r+ ++aa+Np   g++
  gi|518652608|ref|YP_008142128.1| 377 GRwTLEAGALVLADNGFAAIDELDKMDKNDTASMHEAMEQQSVTISKAGIMATLKSRCSILAAANPR-FGRY 447
                                       4447889**********************************************************94.4444 PP

>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.5   0.3   6.7e-08   0.00013       2      75 ..      13      77 ..      12      96 .. 0.84
   2 ?   -0.1   0.0      0.71   1.4e+03      33      61 ..     501     533 ..     493     578 .. 0.69

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 6.7e-08
                             MCM_N  2 ekFedFLeefkddsededgekkYrdqlqemaer..ekttLevdlddLaafdeeLaeailenpkeylplleealkev 75
                                      +++ dF++ +            Y dq+++++    ++++L+++++dL+ ++ ++ e ++++p+ yl + e  +ke 
  gi|518652608|ref|YP_008142128.1| 13 RQWIDFFDRY-----------DYNDQINKLRSDypDIKSLYISYNDLSGYSTDFIEGLMKDPYYYLTIGEFYIKET 77
                                      5566666666...........7*********887899*****************************9987766665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.71
                             MCM_N  33 erekttLevdlddLaaf....deeLaeailenp 61 
                                         e+++Le+d+ d ++f    d++L ++ +++ 
  gi|518652608|ref|YP_008142128.1| 501 SLENNNLEIDIPDEENFiaelDKDLIRKYVSYA 533
                                       458899999999988884444455555444444 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   4.2e-08   8.3e-05       1     125 [.     327     454 ..     327     467 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 4.2e-08
                                       EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--............--------G-SEEEEESG CS
                             AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik...ngttslvdsplvraaregeilvlDEv 74 
                                       ++l++G+pGt+Ks+l +++     r+v+   + ++ +++ l+     +   +g+  l+ ++lv        + +DE+
  gi|518652608|ref|YP_008142128.1| 327 HILMIGDPGTAKSQLLRYMTFISPRSVFA--FGKGSSAAGLTAAAVRDdfgEGRWTLEAGALV--LADNGFAAIDEL 399
                                       789*******************9999886..5555566666655544455599999999****..66677899**** PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.......... CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpld.........r 125
                                       ++++++ ++s++  +e++ + + + g     k+       +++a+anp+           
  gi|518652608|ref|YP_008142128.1| 400 DKMDKNDTASMHEAMEQQSVTISKAGIMATLKSR-----CSILAAANPRFgrydpmktiA 454
                                       *********************8777777766664.....999999999864444444444 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   3.8e-06    0.0076      19     143 ..     322     442 ..     310     470 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 3.8e-06
                                       CTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHTTTS CS
                   Sigma54_activat  19 aktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfekadgG 95 
                                       ++ d+++l+ G+ Gt K+ l r +   s+r+   f +   aa  +     + FG   G +    + ++G++  ad+G
  gi|518652608|ref|YP_008142128.1| 322 IRGDIHILMIGDPGTAKSQLLRYMTFISPRSVFAFGKGSSAAGLTAAAVRDDFGE--GRW----TLEAGALVLADNG 392
                                       56789************************99998888888877666666667874..444....4678********* PP

                                       EEEEETGGGS-HHHHHHHHHHHHHSE..EESBTSSSEEE--EEEEEEESS CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqege..vervGsskeikvdvriiaatne 143
                                          +De+ +++ +  + + +++++++  +++ G  ++ k  + i+aa+n 
  gi|518652608|ref|YP_008142128.1| 393 FAAIDELDKMDKNDTASMHEAMEQQSvtISKAGIMATLKSRCSILAAANP 442
                                       **********************9986225799***************985 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   1.3e-05     0.025       1     112 [.     327     442 ..     327     448 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.3e-05
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfee.kekefefkkGpvf.an..llladeinr 73 
                                       h+l+ g PG+ak +l + ++ +     +   f      + ++ + v ++  e ++++++G+++ a+  +   de+++
  gi|518652608|ref|YP_008142128.1| 327 HILMIGDPGTAKSQLLRYMTFISPR--SVFAFGKGSSAAGLTAAAVRDDfGEGRWTLEAGALVlADngFAAIDELDK 401
                                       8999999999999999988755443..345677888888888888876525689999999865243236667***** PP

                             AAA_3  74 appktqsalleameerqvtvege..thklpepflvlatqnP 112
                                             +++ eame++ vt++++    +l++   +la+ nP
  gi|518652608|ref|YP_008142128.1| 402 MDKNDTASMHEAMEQQSVTISKAgiMATLKSRCSILAAANP 442
                                       *******************9876226789***********9 PP

>> Cys_rich_CPCC  Cysteine-rich CPCC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.2   0.00022      0.44       2      32 ..     139     173 ..     138     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
                     Cys_rich_CPCC   2 qCpcCgyltl...eeee.gsydiCpvCfWedDlvq 32 
                                       +Cp Cg lt+   + ++  +   C+ C W++ +++
  gi|518652608|ref|YP_008142128.1| 139 KCPACGELTIvpeDIQKlFEPTACQACGWNKGKLK 173
                                       8********97532233455589******987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (697 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.52
# Mc/sec: 4048.70
//
Query:       gi|518652609|ref|YP_008142129.1|  [L=95]
Description: hypothetical protein FACI_IFERC00001G1248 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   93.5   0.5      8e-27   93.3   0.5    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 !   93.3   0.5   4.5e-31     8e-27       3      92 .]       6      94 ..       4      94 .. 0.97

  Alignments for each domain:
  == domain 1  score: 93.3 bits;  conditional E-value: 4.5e-31
                                      ETTE.EEEEEEEGGGTT-EEEETTEEEE--HHHH--EEE-HHHHHHHHHHHEEEEEESHHHHHHHHHTTSS-GGG-EEE CS
                            DUF424  3 tddllklvavcdkellgktfkegelllnvsegfyggelaseeeaikeLekatiaNivgeeavvlavkaGlvdpdsVlvi 81
                                      ++++ +++a++d+el++k ++eg+l+l+++++fyg+ ++see+++++L+ +tiaN+vge++v+ a++a+++++d++++i
  gi|518652609|ref|YP_008142129.1|  6 INGE-VMLAAADSELINKDLREGKLHLKIKPEFYGEMKVSEETFLSSLDICTIANLVGEHVVNAAIDANYIEKDNIIKI 83
                                      6789.************************************************************************** PP

                                      TTEEEEEEEE- CS
                            DUF424 82 dgvphaqigkl 92
                                      +gvphaq+ k+
  gi|518652609|ref|YP_008142129.1| 84 AGVPHAQLAKI 94
                                      *******9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       400  (0.0223102); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 641.62
//
Query:       gi|518652610|ref|YP_008142130.1|  [L=159]
Description: 30S ribosomal protein S13P [Ferroplasma acidarmanus fer1]
Scores for complete 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-39  132.7   3.9    1.1e-38  132.5   3.9    1.1  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   3.9   6.2e-43   1.1e-38       1     127 [.      16     143 ..      16     144 .. 0.99

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 6.2e-43
                     Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwi.nrqkdi 76 
                                       Ri++ di g++++ + l+ i+G+G+r a+i++kk+++d++ +ig+l+e+e+ +i+++ve k  + +p w+ n++kd+
  gi|518652610|ref|YP_008142130.1|  16 RIANKDIRGERRMDLGLADINGVGERLANILIKKLNLDRNRQIGDLSEDEVLEIRKYVESKEYEGMPVWLlNHRKDV 92 
                                       9***********************************************************99999************ PP

                     Ribosomal_S13  77 kdGkdshvvendlrrklredieRlkkirsyrGlRHkrGlkvRGQrTkttgR 127
                                        +Gk+  +++ndl  k+++di+ +kk+rsyrGlRH++G kvRGQrT+++gR
  gi|518652610|ref|YP_008142130.1|  93 ATGKNFNLLSNDLILKINDDINLMKKMRSYRGLRHEQGHKVRGQRTRSNGR 143
                                       **************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       495  (0.0276089); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1103.30
//
Query:       gi|518652611|ref|YP_008142131.1|  [L=195]
Description: 30S ribosomal protein S4 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-13   49.5   0.0    6.3e-13   48.2   0.0    1.7  1  S4            S4 domain
    0.00079   20.3   2.2     0.0038   18.1   2.2    2.0  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
  ------ inclusion threshold ------
      0.019   14.4   0.0      0.025   14.1   0.0    1.1  1  adh_short     short chain dehydrogenase


Domain annotation for each model (and alignments):
>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0     1e-16   6.3e-13       1      46 [.     106     151 ..     106     153 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1e-16
                                       EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTC CS
                                S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgD 46 
                                       rRL++++++l +a + ++ArqlI hG+++V   +v++ps  V  g 
  gi|518652611|ref|YP_008142131.1| 106 RRLQTLVYQLNMATTMKQARQLITHGHIKVGDHIVTIPSIAVLKGQ 151
                                       8**************************************9998886 PP

>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   2.2   6.4e-07    0.0038      33      79 ..      12      59 ..       2      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6.4e-07
                                      -----CHCH.HHHHHHHHHHHHT-S.HHHHHHHHHHHHHCCSHHHHHHH CS
                      Ribosomal_S4 33 rkklseYgk.qlrekqklkrrYgll.ekqfrryfkearrirGktgenLl 79
                                      ++   +++k +++ + ++  +Ygl+ +++++++  +++++r  +++ L 
  gi|518652611|ref|YP_008142131.1| 12 STPRHPWEKeRIDSERQVVAKYGLKnKRELWKAEAILSSYR-AQARTLQ 59
                                      445569***********************************.9998885 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   4.1e-06     0.025      37     150 ..      41     158 ..      23     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4.1e-06
                                       HHHHHHHHHHTTSEEEEEE-TTT.SHHHHHHHHHHHHHHHSSESEEEE---S..S--SSGGGCSHHH.HHHHHHHHT CS
                         adh_short  37 leevakelkeegakalaiqvDvt.dreevealvekavkklgkldvLvnNAGi..tgsgpfselseee.wervievNl 109
                                       l ++ + l + +a+a ++q+ v+ +   +e+ ++   kkl+kl +L  +A++      +++++ +++    v+++N+
  gi|518652611|ref|YP_008142131.1|  41 LWKAEAILSSYRAQARTLQAKVRyNDPIAEKQFQLLLKKLDKLSLLSEGATLddILALNIENILDRRlQTLVYQLNM 117
                                       33444444444678999*****9666777999********************876667788888888444569**** PP

                                       HHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHH CS
                         adh_short 110 tgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYs 150
                                         +++ +r+++++   + + +Iv++ S+a +++ +  + Ys
  gi|518652611|ref|YP_008142131.1| 118 ATTMKQARQLITHGHIKVGDHIVTIPSIAVLKGQEDSITYS 158
                                       *************77788889************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       689  (0.0384294); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); 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 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1353.06
//
Query:       gi|518652612|ref|YP_008142132.1|  [L=127]
Description: 30S ribosomal protein S11P [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.3e-40  136.5   0.9    5.7e-40  136.1   0.9    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 !  136.1   0.9   3.2e-44   5.7e-40       1     110 []       5     123 ..       5     123 .. 0.99

  Alignments for each domain:
  == domain 1  score: 136.1 bits;  conditional E-value: 3.2e-44
                     Ribosomal_S11   1 GvahiqasfnntiititdlkGaevlvksaGglgvkasr.kssPyaaqlaaekaaekvldkGikavevkvkg...... 70 
                                       G+ahi+as+nntii itd++G e+++ks+Gg++vk++r +ssPyaa++a++ + ek+ +k i+ + ++v++      
  gi|518652612|ref|YP_008142132.1|   5 GIAHIYASQNNTIILITDQTGSETIAKSTGGMVVKNDReESSPYAAMKASDIITEKLREKEITDLIIRVRApggsrs 81 
                                       9*************************************99************************************* PP

                     Ribosomal_S11  71 ..pGpGreaalralaraGlkigriedvtPiPhdgirrpkkrr 110
                                         pGpG+++a+r+l raG+ki rie+vtP+Phdg+++++++r
  gi|518652612|ref|YP_008142132.1|  82 riPGPGAQSAIRTLSRAGFKILRIEEVTPTPHDGTKKKGGKR 123
                                       *************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 927.09
//
Query:       gi|518652613|ref|YP_008142133.1|  [L=270]
Description: hypothetical protein FACI_IFERC00001G1252 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-20   72.7   0.0    7.9e-20   71.3   0.0    1.7  2  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
    1.8e-17   62.6   0.0    2.3e-17   62.2   0.0    1.2  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.0   8.9e-24   7.9e-20       5     112 .]      59     163 ..      56     163 .. 0.90
   2 ?   -1.9   0.0      0.47   4.2e+03      35      68 ..     215     248 ..     193     257 .. 0.60

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 8.9e-24
                                       ECTSSS.HHHHHCHHHCSTCBSSCHHHHHHHHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGGCBES.SSSCEESS CS
                     RNA_pol_A_bac   5 entsvlqDEvvaHrlgliplvsedvleillnlkelveeeeegeeeksvelkLnvkgpgevtagdlkle.dadveivn 80 
                                       + +  l DE++a r+glipl+++  ++   ++ e+ +   +g++ ++v+ ++n+ gpg v+++d++ + +++ ++ +
  gi|518652613|ref|YP_008142133.1|  59 DSSLPLFDEILASRIGLIPLKTDLSMN---FRDEC-SCGGKGCDLCTVTYSINKLGPGMVYSSDIMPVnNPELTVTD 131
                                       5556789**************777666...99999.44689*************************9868899999* PP

                                       TTSEEEEEETT-EEEEEEEEEEESSEECTTT- CS
                     RNA_pol_A_bac  81 pdilIakLrkgqeleleakvkkGiGkehakfs 112
                                       p i+I++L+k+q + +++++  G+Gkehak++
  gi|518652613|ref|YP_008142133.1| 132 PLIPIVELKKNQAMLVTCEAILGRGKEHAKWQ 163
                                       *******************************6 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.47
                                       HHCTT-ETSSSSTTCSEEEEEEEEESSECEEGGG CS
                     RNA_pol_A_bac  35 nlkelveeeeegeeeksvelkLnvkgpgevtagd 68 
                                       +l +l e +    ee+s+++  +++  g   a+d
  gi|518652613|ref|YP_008142133.1| 215 YLSQLMERDGVVVEEDSTKFIFKFETDGSLKASD 248
                                       4444432333444566666666666666666555 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 !   62.2   0.0   2.6e-21   2.3e-17       1      69 []      13     261 ..      13     261 .. 0.79

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 2.6e-21
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................... RF
                         RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea............................................... 30 
                                       +f ++g++++++N++Rr+l++++p++aie+                                               
  gi|518652613|ref|YP_008142133.1|  13 RFSIDGITPAIANSIRRTLINDIPKLAIENviyhhgeirdadgnvydsslplfdeilasrigliplktdlsmnfrde 89 
                                       599***********************************************999999999999999999999999999 PP

                                       ..........................................................................xx. RF
                         RNA_pol_L  31 ..........................................................................pv. 32 
                                                                                                                 ++ 
  gi|518652613|ref|YP_008142133.1|  90 cscggkgcdlctvtysinklgpgmvyssdimpvnnpeltvtdplipivelkknqamlvtceailgrgkehakwqATs 166
                                       99999999999999999999999999999887777777777777766666666655555555555555555555005 PP

                                       ..........................................................xxxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  33 ..........................................................vkvntdkdklilevetdgs 51 
                                                                                                 v v++d +k+i++ etdgs
  gi|518652613|ref|YP_008142133.1| 167 gvsykyhrnfhvnkaaldnwqfykdtcpksvlsendttilftddipcsylsqlmerdgVVVEEDSTKFIFKFETDGS 243
                                       55555555555555566666666666666667777777777777777777777777777899*************** PP

                                       xxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  52 lkPeealkeAlkiLkekl 69 
                                       lk+ ++l++Al  L++++
  gi|518652613|ref|YP_008142133.1| 244 LKASDVLSYALHRLENRF 261
                                       *************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1971.20
//
Query:       gi|518652614|ref|YP_008142134.1|  [L=283]
Description: hypothetical protein FACI_IFERC00001G1253 [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  149.2  41.2    1.7e-43  149.0  41.2    1.0  1  TauE           Sulfite exporter TauE/SafE
     0.0022   18.0   0.2     0.0022   18.0   0.2    5.4  4  Colicin_V      Colicin V production protein
  ------ inclusion threshold ------
        3.4    6.2  14.2      0.058   12.0   5.3    2.0  2  EMP70          Endomembrane protein 70


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0  41.2   2.8e-47   1.7e-43       2     235 ..      13     267 ..      11     268 .. 0.88

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 2.8e-47
                              TauE   2 llagllaGfvagllGiGggliavPlLllll...ppavavatsllavvatslsgalahrrrgnvdwrlllllllgsli 75 
                                       ++ g+++Gf  gl+G+Gg+++avPl+++++   +p++a++t++lav++t+ +++++h+r++n +++l+ +++l++++
  gi|518652614|ref|YP_008142134.1|  13 IISGIAVGFSLGLIGGGGSILAVPLFIYFVginHPHLAIGTTALAVGITAYINFAQHLRKKNANIKLGGVFALVGIV 89 
                                       799*************************74568******************************************** PP

                              TauE  76 GallGallllllpsellkllfgvlllllallmllrkkr....srak..grerrptaillvligglvGllsGllGiGg 146
                                       G+l+G+ + l +++  l+++f+ l+++++++m+++k r    +  +  +  +++++  +    ++vG++sG++GiGg
  gi|518652614|ref|YP_008142134.1|  90 GVLIGSTIGLIIKGGELLFFFSMLMIIIGIYMYISKCRavpnE--DckELAKQTKYGKVSGYSLIVGFASGFFGIGG 164
                                       ********************************88555435541..15433333444444555577************ PP

                              TauE 147 Gfllvpllllllglplkkavatslllilvislagalgy..al..........agavdwpllllllpgallGallGar 211
                                       Gfl+vp ll   ++ +  a++tsll++ ++++++a+ y  ++           g+v + +++++++g+++G++lG++
  gi|518652614|ref|YP_008142134.1| 165 GFLIVPGLLASSKIKINMAIGTSLLAVGTFGIVTAIRYsiVApglqfissgmIGDVLFLVAIVYVIGGIFGGYLGTK 241
                                       *************************************97511666677888888888999999************** PP

                              TauE 212 larrlsert..lrrlfallllvlgvk 235
                                       l+  l  r+  lr++f ++++++g++
  gi|518652614|ref|YP_008142134.1| 242 LSVNLGGRKgtLRKVFSIIIILVGIY 267
                                       *****988888*************98 PP

>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8  16.2         3   1.8e+04      27      84 ..      48     103 ..       3     146 .. 0.74
   2 ?   -3.3   6.2       1.4   8.1e+03      89      89 ..     147     147 ..     104     214 .. 0.59
   3 ?   -7.3   9.9         3   1.8e+04      33      33 ..     194     194 ..     145     245 .. 0.50
   4 !   18.0   0.2   3.7e-07    0.0022      12      49 ..     243     280 ..     240     281 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 3
                         Colicin_V  27 sllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgallsk 84 
                                       +l+    a++v++  y  +a++l++  +++ +  +  f+l+ ++++li+s +g ++++
  gi|518652614|ref|YP_008142134.1|  48 HLAIGTTALAVGITAYINFAQHLRK--KNANIKLGGVFALVGIVGVLIGSTIGLIIKG 103
                                       3444555666666666666666666..7999999999999999999999999999986 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.4
                         Colicin_V  89 t 89 
                                       +
  gi|518652614|ref|YP_008142134.1| 147 S 147
                                       1 PP

  == domain 3  score: -7.3 bits;  conditional E-value: 3
                         Colicin_V  33 v 33 
                                       +
  gi|518652614|ref|YP_008142134.1| 194 F 194
                                       1 PP

  == domain 4  score: 18.0 bits;  conditional E-value: 3.7e-07
                         Colicin_V  12 sallGlrrGfvrevlsllgwvvafvvasllypslaell 49 
                                       s+ lG r+G +r v+s++ ++v+++va+  yp l+++l
  gi|518652614|ref|YP_008142134.1| 243 SVNLGGRKGTLRKVFSIIIILVGIYVAYESYPALVHML 280
                                       667899***************************99886 PP

>> EMP70  Endomembrane protein 70
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   1.6     0.071   4.2e+02     319     380 ..      61     124 ..      17     130 .. 0.59
   2 ?   12.0   5.3   9.8e-06     0.058     274     346 ..     196     269 ..     177     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.071
                             EMP70 319 rlyktfgge..kwkkntlltalllpgllflvffllnlilwakessgalpfgtlvlllllwflis 380
                                         y  f ++  k + n+ l +++  + ++ v++   + l++k+    + f++l++++ +++ is
  gi|518652614|ref|YP_008142134.1|  61 TAYINFAQHlrKKNANIKLGGVFALVGIVGVLIGSTIGLIIKGGELLFFFSMLMIIIGIYMYIS 124
                                       3344443332122222223333333334444444455555566666666666666666666655 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 9.8e-06
                             EMP70 274 lllmalvtlllallgflspsnrgslltvalllyvllgliaGYvsarlyktfgge.kwkkntlltalllpgllfl 346
                                       +++ +  +++   l+f+s    g++l ++ ++yv+ g+++GY++++l   +gg+    ++++   ++l g+ ++
  gi|518652614|ref|YP_008142134.1| 196 IVTAIRYSIVAPGLQFISSGMIGDVLFLVAIVYVIGGIFGGYLGTKLSVNLGGRkGTLRKVFSIIIILVGIYVA 269
                                       33444456666699*************************************98767888888888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (283 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 1888.74
//
Query:       gi|518652615|ref|YP_008142135.1|  [L=188]
Description: hypothetical protein FACI_IFERC00001G1254 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       846  (0.0471861); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1345.61
//
Query:       gi|518652616|ref|YP_008142136.1|  [L=271]
Description: inorganic polyphosphate/ATP-NAD kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.9e-50  171.1   3.5      6e-50  170.1   3.5    1.6  1  NAD_kinase  ATP-NAD kinase
  ------ inclusion threshold ------
      0.018   14.7   0.8      0.038   13.6   0.8    1.6  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 !  170.1   3.5   6.6e-54     6e-50      69     291 ..      43     252 ..       2     253 .. 0.94

  Alignments for each domain:
  == domain 1  score: 170.1 bits;  conditional E-value: 6.6e-54
                                       CCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHHT-SEEEEEEEEE CS
                        NAD_kinase  69 kaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaellekllegeirvekrevld 145
                                       ++  +f d ++d+iivvGGDGT+l+ a+l +     +lg+n+G +gfl+e+e+ ++ e + +l++g++++ + ++l+
  gi|518652616|ref|YP_008142136.1|  43 RKGVNFKDIDADIIIVVGGDGTILRTAQLSRG---KILGINVGGLGFLSEVEIGNIEESIYNLIKGNYKTYEVMKLN 116
                                       556788999*********************97...9***************************************** PP

                                       EEEEETTE......EEEEEEESSEEEEEESSSSS-EEEEEEETTEEEEEEEESEEEEE-TGGGGTHHHHTT--EE-T CS
                        NAD_kinase 146 avimrskgeediadiviensvlnevviirgpgstlielelyvdtelleadqldglivstPtGstayslsaGgplisP 222
                                       ++++++          ++   +n+vvi+++++s++ ++ +y++++++e+  +dg+iv+tP+Gst ys saGgp++ P
  gi|518652616|ref|YP_008142136.1| 117 VYVNDQLF--------GKG--INDVVIHTARISKIRKFSVYINDRFMENTSADGVIVATPIGSTSYSYSAGGPILIP 183
                                       88877665........344..9******************************************************* PP

                                       T---EEEEEESESSS----EEE-TT-EEEEEE-SS--EEEEETTTEEEEE-TT-EEEEEEESSEEEEEE CS
                        NAD_kinase 223 gvlailivpicPhslssrpiVvssssklrirvasrseallaldGseelelspgdevrvtasdkkfklir 291
                                       +++a++i+ i P+  + rpiV +++sk++i++  r + l+++dG++e  ++ +d++ +++sd+   +i+
  gi|518652616|ref|YP_008142136.1| 184 SLKAMVISYIAPFGSRLRPIVCPDDSKITIKIIGRFSSLVIIDGQREAVVNGNDRIDIRVSDERLTFIE 252
                                       ****************************************************************99997 PP

>> DAGK_cat  Diacylglycerol kinase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.8   4.3e-06     0.038      54      70 ..      51      67 ..      28     115 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-06
                                      CC-SEEEEEESHHHHHH CS
                          DAGK_cat 54 egvdlivvaGGDGtvse 70
                                       ++d+i+v+GGDGt+  
  gi|518652616|ref|YP_008142136.1| 51 IDADIIIVVGGDGTILR 67
                                      2679**********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2138.24
//
Query:       gi|518652617|ref|YP_008142137.1|  [L=120]
Description: Mov34/MPN/PAD-1 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-10   38.7   0.3    1.6e-09   37.5   0.3    1.5  1  Prok-JAB  Prokaryotic homologs of the JAB domain
    0.00078   19.4   0.2     0.0012   18.8   0.2    1.5  1  RadC      RadC-like JAB domain


Domain annotation for each model (and alignments):
>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.3   1.8e-13   1.6e-09       2     112 ..       6     102 ..       5     109 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 1.8e-13
                          Prok-JAB   2 esvlsalvaharrahpeEtcGlllgkeseseevivvplvnewsnrfeipdpedslarlkfearerglevvgiwHSHp 78 
                                       e++l  ++++ r a p+E ++ll  + ++  e+++vp             p + + r    ++  + ++vg +HSHp
  gi|518652617|ref|YP_008142137.1|   6 ERTLKMIMEASRDALPNEFGALLRAEHQIIYEIALVPGSI--------NGPVHVIFRT--YTMPLDFSYVGSVHSHP 72 
                                       56778899999999*****999999985555566666553........3444444443..68999************ PP

                          Prok-JAB  79 ggsarPSetDrrdaaalarvkalliivgdkaeel 112
                                        g + PS++D+++++ +   ++++iivg  ++++
  gi|518652617|ref|YP_008142137.1|  73 SGNTHPSDADLHMFSNT---GPVHIIVGY-PYNM 102
                                       ****************9...677777774.4544 PP

>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.3e-07    0.0012      29      88 ..      29      86 ..       5      99 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-07
                                      -TTSBEEEEEEEEESTT-GGGCSHHHHHHHH.HHTT-SEEEEEEE-TTS--S--HHHHHHH CS
                              RadC 29 dsknrliadeelseGtlnstlvdprevfkea.lklnAaavilaHnhPsgdlepSeeDielt 88
                                       +++++i + +l  G++n     +  +f++  + l+ + v  +H hPsg+++pS++D+++ 
  gi|518652617|ref|YP_008142137.1| 29 RAEHQIIYEIALVPGSING---PVHVIFRTYtMPLDFSYVGSVHSHPSGNTHPSDADLHMF 86
                                      5566666666666666662...33445554425566777888***************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 880.94
//
Query:       gi|518652618|ref|YP_008142138.1|  [L=342]
Description: RNA-binding protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-16   59.7   0.6    4.1e-16   59.1   0.6    1.2  1  eRF1_1    eRF1 domain 1
    1.4e-14   54.5   0.4    6.1e-13   49.2   0.4    2.8  1  eRF1_3    eRF1 domain 3


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 !   59.1   0.6   4.6e-20   4.1e-16      13     119 ..      12     115 ..       3     125 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.1 bits;  conditional E-value: 4.6e-20
                                       CCEEEEEE-SCHHHHHHHHHCHTTHEEEEEEEECHHH........--CEEEEEEEEEEEEEEECTTSSEEEEEEEEE CS
                            eRF1_1  13 sgsvtLipeddedlwhlynliapgdsvrastvrkvqr.esstgsreservklkLtikvekvdfdkdagvlrisGkvi 88 
                                       ++ + L++++ +dlw+l n+++ gd++ +s +r+ ++    + s+ +er+k++++++vek+df + ++ l+i G++ 
  gi|518652618|ref|YP_008142138.1|  12 ESKLVLMINTIDDLWYLKNILDRGDQIITSVFRRQEQnADLNRSKATERKKINIKLNVEKIDFLPYTDNLKILGEIL 88 
                                       66788*****************************988346788888******************************* PP

                                       EGGGG--TTSEEEEEE-TTSEEEEEECEESH CS
                            eRF1_1  89 eenehvklgafhtldlelkrpftiikeewds 119
                                       e+++    g++ ++ + + +++tiik   ds
  gi|518652618|ref|YP_008142138.1|  89 EGEN---SGSHQSVMIGVDDEITIIKTL-DS 115
                                       **99...8******************54.44 PP

>> eRF1_3  eRF1 domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.4   6.8e-17   6.1e-13       2     112 ..     253     341 ..     252     342 .] 0.91

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 6.8e-17
                                       HHHHHHHHHHHHHHHCTCSSEEESHHHHHHHHHTT-EEEEEEEHCHHTSSSHHHHHS-HHH-HHHHHHHHHHHHHHH CS
                            eRF1_3   2 iqekklleefleelakdtgkavYGveevlkalemgAvetLLvseelersrdtlkekvketgeelelvelieelvenv 78 
                                       + ++kl+e+fl +l+k  g+ +YG +e  k+ +m++ve++L+se+ +++                    +++l++  
  gi|518652618|ref|YP_008142138.1| 253 AADEKLIENFLINLNKT-GLSIYGYDELVKYSRMNMVEDILISESKFKDPE------------------TRKLLN-- 308
                                       6789***********87.******************************962..................456766.. PP

                                       HHTT-EEEEE-TTSHHHHHHHHHTTTEEEEESS- CS
                            eRF1_3  79 eesgakveiisseseeGeqlvkafgGiaaiLRyk 112
                                       e +g ++++is+ +e+G  + k+fgG+ +iLRyk
  gi|518652618|ref|YP_008142138.1| 309 EATGINIHVISDYTESGDII-KQFGGYCGILRYK 341
                                       56899***************.************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 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:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2493.20
//
Query:       gi|518652619|ref|YP_008142139.1|  [L=156]
Description: hypothetical protein FACI_IFERC00001G1258 [Ferroplasma acidarmanus fer1]
Scores for complete 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  119.1   0.0    1.8e-34  119.0   0.0    1.0  1  Mut7-C          Mut7-C RNAse domain
    1.8e-05   24.4   0.0    3.2e-05   23.6   0.0    1.4  1  DUF5615         Domain of unknown function (DUF5615)
     0.0083   15.8   4.2       0.14   11.9   0.5    2.8  3  zinc_ribbon_2   zinc-ribbon domain
     0.0087   16.0   1.4       0.52   10.3   0.3    2.6  2  zinc-ribbons_6  zinc-ribbons
  ------ inclusion threshold ------
      0.014   15.6   0.8        2.2    8.5   0.2    2.6  2  zf-RING_7       C4-type zinc ribbon domain
      0.039   13.8   3.2        3.9    7.4   0.0    3.1  3  DUF35_N         Rubredoxin-like zinc ribbon domain (DUF35_N)
      0.049   13.1   2.5        4.1    6.9   0.1    2.6  2  zf-ribbon_3     zinc-ribbon domain
      0.072   13.1   0.2      0.072   13.1   0.2    2.3  2  DZR             Double zinc ribbon
       0.12   12.6   3.9         13    6.1   0.1    3.1  3  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.16   12.2   0.0       0.26   11.5   0.0    1.3  1  PIN_10          PIN like domain
        1.7    8.8   0.1        1.7    8.8   0.1    2.9  3  zf-ACC          Acetyl-coA carboxylase zinc finger domain
        2.1    8.2   6.4         10    6.0   0.0    3.5  4  A2L_zn_ribbon   A2L zinc ribbon 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 !  119.0   0.0   1.2e-37   1.8e-34       2     143 ..      11     147 ..      10     150 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.0 bits;  conditional E-value: 1.2e-37
                            Mut7-C   2 rfllDamlgklakyLRllGydalyasdvedeellalaakekrillTrdreLlkraklkkgvlltsrdveeqlrevia 78 
                                       +f++D mlg+  k++R++Gyd+ y +  +d+++l+++++e+ illTrd e++kr +++  ++l+s d++eql++v+ 
  gi|518652619|ref|YP_008142139.1|  11 KFMADHMLGRTCKWMRIMGYDTGYPQCHSDNDILKKCKEENLILLTRDYEFYKRYSNS--IFLDSPDFKEQLKQVVT 85 
                                       8*************************99**************************9988..***************88 PP

                            Mut7-C  79 rlglklslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerve 143
                                        +   ++ +  +srC +Cn+ l++v+ e++ +   + v++++d++  C+ C+k +W+Gsh++r+ 
  gi|518652619|ref|YP_008142139.1|  86 MFP--PDRELFFSRCPECNTILQTVKTETM-GPGYDLVKSRYDTVKFCPGCGKYYWEGSHYSRIL 147
                                       886..5667779************999887.888999************************9986 PP

>> DUF5615  Domain of unknown function (DUF5615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.1e-08   3.2e-05       2      62 ..      11      65 ..      10      74 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.1e-08
                           DUF5615  2 klllDenlsprlvellreaghdvlhvrelglegasDeeileyAkeedriivTkDkDFgell 62
                                      k+ +D+ l  r ++++r  g+d+ +      ++ sD++il+ +kee++i++T+D  F++++
  gi|518652619|ref|YP_008142139.1| 11 KFMADHMLG-RTCKWMRIMGYDTGYP-----QCHSDNDILKKCKEENLILLTRDYEFYKRY 65
                                      677777776.6778888888844444.....3589**********************9874 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.4   5.1e+03       3       9 ..      35      41 ..      35      42 .. 0.62
   2 ?    4.4   0.0     0.022        32       1      10 [.      97     106 ..      90     108 .. 0.82
   3 !   11.9   0.5   9.5e-05      0.14      11      20 ..     125     134 ..     121     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.4
                     zinc_ribbon_2  3 pnCGael 9 
                                      p+C+  +
  gi|518652619|ref|YP_008142139.1| 35 PQCHSDN 41
                                      6777665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.022
                     zinc_ribbon_2   1 fCpnCGaelq 10 
                                       +Cp+C + lq
  gi|518652619|ref|YP_008142139.1|  97 RCPECNTILQ 106
                                       5999987665 PP

  == domain 3  score: 11.9 bits;  conditional E-value: 9.5e-05
                     zinc_ribbon_2  11 dnakFCpyCG 20 
                                       d++kFCp CG
  gi|518652619|ref|YP_008142139.1| 125 DTVKFCPGCG 134
                                       89******** PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.039        58      33      49 ..      35      51 ..      14      54 .. 0.85
   2 !   10.3   0.3   0.00035      0.52       2      37 ..      97     135 ..      96     138 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.039
                                      SSS-S---EEEETTEEE CS
                    zinc-ribbons_6 33 peCeqelevlkaCgavd 49
                                      p+C++  ++lk+C  ++
  gi|518652619|ref|YP_008142139.1| 35 PQCHSDNDILKKCKEEN 51
                                      89999999999997665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00035
                                       --SSS-S--EE-SSEEE-...TTT--EEEEEEE-SSS-S CS
                    zinc-ribbons_6   2 kCpeCqqelekrgeqyhC...eaCqedlkkealCpeCeq 37 
                                        CpeC++ l++ ++++     +  +++++ +++Cp C++
  gi|518652619|ref|YP_008142139.1|  97 RCPECNTILQTVKTETMGpgyDLVKSRYDTVKFCPGCGK 135
                                       6*****999966644443111567889**********86 PP

>> zf-RING_7  C4-type zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.2    0.0015       2.2      24      33 .]      96     105 ..      90     105 .. 0.90
   2 ?    5.1   0.0     0.018        27      20      30 ..     123     134 ..     117     136 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                                       EE-TTT--EE CS
                         zf-RING_7  24 vtCpeCGRIL 33 
                                        +CpeC+ IL
  gi|518652619|ref|YP_008142139.1|  96 SRCPECNTIL 105
                                       69*****998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                                       S.TB-EE-TTT- CS
                         zf-RING_7  20 g.devvtCpeCG 30 
                                         d v +Cp CG
  gi|518652619|ref|YP_008142139.1| 123 RyDTVKFCPGCG 134
                                       457899*****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 ?   -0.8   0.1         1   1.5e+03      29      35 ..      35      41 ..      35      42 .. 0.86
   2 ?    7.4   0.0    0.0026       3.9       6      19 ..      90     103 ..      88     105 .. 0.85
   3 ?    5.2   0.4     0.013        19      14      22 ..     130     138 ..     128     139 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                           DUF35_N 29 phCgsdd 35
                                      p C+sd+
  gi|518652619|ref|YP_008142139.1| 35 PQCHSDN 41
                                      89***97 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0026
                           DUF35_N   6 egrLvgqrCpdCGt 19 
                                       + +L ++rCp C t
  gi|518652619|ref|YP_008142139.1|  90 DRELFFSRCPECNT 103
                                       569*********76 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.013
                           DUF35_N  14 CpdCGtvqf 22 
                                       Cp CG++++
  gi|518652619|ref|YP_008142139.1| 130 CPGCGKYYW 138
                                       999999998 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    0.0028       4.1       4      13 ..      97     106 ..      95     107 .. 0.84
   2 ?    5.2   0.4    0.0095        14      17      23 ..     128     134 ..     125     136 .. 0.63

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0028
                       zf-ribbon_3   4 rCPnCGapls 13 
                                       rCP+C+++l+
  gi|518652619|ref|YP_008142139.1|  97 RCPECNTILQ 106
                                       8*****9776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0095
                       zf-ribbon_3  17 nvCpyCG 23 
                                       ++Cp CG
  gi|518652619|ref|YP_008142139.1| 128 KFCPGCG 134
                                       5666666 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       1.4   2.1e+03       2       9 ..      35      42 ..      35      51 .. 0.62
   2 ?   13.1   0.2   4.8e-05     0.072      14      36 ..      97     135 ..      78     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1.4
                               DZR  2 pqCgeelp 9 
                                      pqC+++++
  gi|518652619|ref|YP_008142139.1| 35 PQCHSDND 42
                                      56666554 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.8e-05
                               DZR  14 fCseCgtklkavaa................edrCpsCge 36 
                                        C+eC+t l+ v++                 ++Cp Cg+
  gi|518652619|ref|YP_008142139.1|  97 RCPECNTILQTVKTetmgpgydlvksrydtVKFCPGCGK 135
                                       5********9988899*********************97 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.82   1.2e+03      13      19 ..      17      23 ..      16      28 .. 0.90
   2 ?    6.0   0.1    0.0089        13      17      26 ..      97     106 ..      93     114 .. 0.82
   3 ?    6.1   0.1    0.0085        13      25      40 .]     119     134 ..     116     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.82
                     Auto_anti-p27 13 MLaetCp 19
                                      ML+ tC+
  gi|518652619|ref|YP_008142139.1| 17 MLGRTCK 23
                                      9*****5 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0089
                     Auto_anti-p27  17 tCpvCgvPLm 26 
                                        Cp+C+++L 
  gi|518652619|ref|YP_008142139.1|  97 RCPECNTILQ 106
                                       6*******95 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0085
                     Auto_anti-p27  25 LmrdrkggkvyCvaCd 40 
                                       L+++r+++ ++C+ C+
  gi|518652619|ref|YP_008142139.1| 119 LVKSRYDTVKFCPGCG 134
                                       7899977777*****6 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.26      30      65 ..      29      64 ..      11      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                            PIN_10 30 hlrdkfaagtkDeeWiaalaeggwvvltkDrrirkr 65
                                       +   +++  +D++ +++ +e++ ++lt+D ++ kr
  gi|518652619|ref|YP_008142139.1| 29 GYDTGYPQCHSDNDILKKCKEENLILLTRDYEFYKR 64
                                      4555568889*********************99988 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         6   8.9e+03       6       9 ..      46      49 ..      45      52 .. 0.61
   2 ?    8.8   0.1    0.0011       1.7       1      11 [.      95     105 ..      95     107 .. 0.89
   3 ?   -0.2   1.9      0.76   1.1e+03       4       8 ..     130     134 ..     130     135 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6
                            zf-ACC  6 sCge 9 
                                      +C+e
  gi|518652619|ref|YP_008142139.1| 46 KCKE 49
                                      4554 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0011
                            zf-ACC   1 WtKCpsCgeml 11 
                                       +++Cp+C+++l
  gi|518652619|ref|YP_008142139.1|  95 FSRCPECNTIL 105
                                       689*****997 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.76
                            zf-ACC   4 CpsCg 8  
                                       Cp+Cg
  gi|518652619|ref|YP_008142139.1| 130 CPGCG 134
                                       ****9 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.6   2.3e+03       9      15 ..      37      43 ..      34      46 .. 0.79
   2 ?    6.0   0.0    0.0067        10       4      23 ..      45      61 ..      39      61 .. 0.77
   3 ?    3.0   0.2     0.058        87      24      32 ..      98     106 ..      97     107 .. 0.84
   4 ?    0.1   0.3      0.46   6.9e+02      23      28 ..     129     134 ..     126     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.6
                     A2L_zn_ribbon  9 Cggngil 15
                                      C++++++
  gi|518652619|ref|YP_008142139.1| 37 CHSDNDI 43
                                      9999987 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0067
                     A2L_zn_ribbon  4 kvCsvCggngilnseqgylv 23
                                      k   +C+ ++++  +++y++
  gi|518652619|ref|YP_008142139.1| 45 K---KCKEENLILLTRDYEF 61
                                      4...566777777*****98 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.058
                     A2L_zn_ribbon  24 CieCgasfp 32 
                                       C+eC+++ +
  gi|518652619|ref|YP_008142139.1|  98 CPECNTILQ 106
                                       *****9865 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.46
                     A2L_zn_ribbon  23 vCieCg 28 
                                       +C+ Cg
  gi|518652619|ref|YP_008142139.1| 129 FCPGCG 134
                                       677777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 1114.54
//
Query:       gi|518652620|ref|YP_008142140.1|  [L=184]
Description: aromatic acid decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.2   0.2      8e-25   87.4   0.2    1.4  1  Flavoprotein    Flavoprotein
  ------ inclusion threshold ------
      0.037   14.5   0.0      0.052   14.0   0.0    1.3  1  Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domai


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 !   87.4   0.2   8.9e-29     8e-25       1     125 [.       2     162 ..       2     177 .. 0.85

  Alignments for each domain:
  == domain 1  score: 87.4 bits;  conditional E-value: 8.9e-29
                                       EEEEEEE-SSCGGGCHHHHHHHHHHTTEEEEEEESCHHHHCCHHG.GS........TCSSHHHHHHCT......... CS
                      Flavoprotein   1 kkillgiTGsvaaikalellekLkkegievqvvltkaAkkfiske.klklaa....redpilhielrr......... 63 
                                       kki++giTG++++  ++++le++k+  +e+++v++++Akk+++ e +++++                +         
  gi|518652620|ref|YP_008142140.1|   2 KKIVVGITGASGTALGVKFLENIKD--MEIHLVMSESAKKVMKLEsDYSIDYikslA----------Dyyyhdsdia 66 
                                       79**********************7..****************99533333344441..........1333334444 PP

                                       ........TESEEEEEEEEHHHHHHHHTT--SSHH..............................HHHHHTHCCTTE CS
                      Flavoprotein  64 ........wadllviaPasantlakianGiadnll..............................tlilratakkpi 102
                                                +d +v++P+s  tlaki +Gi+d+l+                              +l+l   +  ++
  gi|518652620|ref|YP_008142140.1|  67 arissgsfLFDTFVVIPCSSSTLAKISAGISDTLItrvatvamkerrrfivvprempfstimlenMLKL---SMNNV 140
                                       56677778**************************************************98888777777...8889* PP

                                       EEEE.--HHCCTCSTCHHHHHHH CS
                      Flavoprotein 103 liaPamnpamyenpqtlknlekl 125
                                       ++aP + p +y++p ++++l ++
  gi|518652620|ref|YP_008142140.1| 141 IVAP-AVPGYYNKPSSVEDLLNF 162
                                       ****.**************9888 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 ?   14.0   0.0   5.8e-06     0.052       4      46 ..       5      48 ..       2      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.8e-06
                                      EETTTSHHHHHH.HHHHHCTSSEEEEEEEESTTTTTSBHHHHSG CS
                    Semialdhyde_dh  4 ivGatGyvGqel.lrlLeehpevelvvllsssrsaGkklaeavk 46
                                      +vG tG+ G++l ++ Le+ +++e++ ++s+s ++  kl++ ++
  gi|518652620|ref|YP_008142140.1|  5 VVGITGASGTALgVKFLENIKDMEIHLVMSESAKKVMKLESDYS 48
                                      8*****************************99977777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 1147.23
//
Query:       gi|518652621|ref|YP_008142141.1|  [L=182]
Description: hypothetical protein FACI_IFERC00001G1260 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1324.24
//
Query:       gi|518652622|ref|YP_008142142.1|  [L=1102]
Description: hypothetical protein FACI_IFERC00001G1261 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00011   22.4   0.8    0.00011   22.4   0.8    6.3  7  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
     0.0008   19.7   0.1      0.004   17.5   0.1    2.2  1  fn3              Fibronectin type III domain
     0.0035   17.3   0.4     0.0035   17.3   0.4    4.8  5  CarbopepD_reg_2  CarboxypepD_reg-like domain


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3     0.029   1.8e+02       5      39 ..     155     191 ..     152     198 .. 0.81
   2 ?   -3.1   0.2       1.6   9.7e+03      29      40 ..     524     535 ..     516     536 .. 0.76
   3 ?   -0.2   0.3       0.2   1.2e+03      11      72 ..     560     621 ..     557     628 .. 0.67
   4 ?   -2.4   0.1         1     6e+03      40      64 ..     709     733 ..     692     748 .. 0.55
   5 ?   -1.4   0.2      0.48   2.9e+03      28      43 ..     782     797 ..     769     803 .. 0.80
   6 !   22.4   0.8   1.9e-08   0.00011      18      81 ..     816     879 ..     811     880 .. 0.85
   7 ?    1.6   0.5     0.059   3.5e+02       2      42 ..     889     925 ..     888     941 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.029
                   CarboxypepD_reg   5 rVtdasgapiagatVtvtnadtgt..vastttdadGa 39 
                                        ++da g p  +  V+v+++ tg      t+t ++Ga
  gi|518652622|ref|YP_008142142.1| 155 VIVDAYGDPTLNYDVSVFDNKTGLppINLTVTTPEGA 191
                                       5899**************9999864467777877776 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.6
                   CarboxypepD_reg  29 vastttdadGaf 40 
                                       + +  t+++G++
  gi|518652622|ref|YP_008142142.1| 524 KFGISTNSTGYY 535
                                       67889******9 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.2
                   CarboxypepD_reg  11 gapiagatVtvtna.dtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltag 72 
                                       g  i+ga++ +t + +t ++ ++    +G++      +++ + ++ + +   at++++++t+ 
  gi|518652622|ref|YP_008142142.1| 560 GIKISGAEIYFTVNnSTVKELNVPVSFSGDYHAV-AGAQQDNAKINFVNISKATYSNIDITNA 621
                                       5678899999875313445688889999999864.4446666666667777777777777754 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1
                   CarboxypepD_reg  40 frlrglppgtysvtvsapGyatatr 64 
                                       f+  +l  g y++ ++ +   t+ r
  gi|518652622|ref|YP_008142142.1| 709 FNPVSLSGGYYNISATESSGVTFYR 733
                                       3334455566666666655555554 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 0.48
                   CarboxypepD_reg  28 tvastttdadGafrlr 43 
                                        + ++t +++G+f+ +
  gi|518652622|ref|YP_008142142.1| 782 GNNNATINSTGYFTAN 797
                                       567899999***9975 PP

  == domain 6  score: 22.4 bits;  conditional E-value: 1.9e-08
                   CarboxypepD_reg  18 tVtvtna.dtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqtttlditL 81 
                                        V v+n  +t t  +++t++ G + +  ++p+t  + ++ +Gy +++++ + lt+gq+  + ++L
  gi|518652622|ref|YP_008142142.1| 816 DVFVSNGnATVTLNGVKTNSIGGYHFLYVTPDTTYINATDTGYTSQNQS-MNLTPGQNIHISLVL 879
                                       577777413445689********************************85.*******98887776 PP

  == domain 7  score: 1.6 bits;  conditional E-value: 0.059
                   CarboxypepD_reg   2 isGrVtd.asgapiagatVtvtnadtgtvastttdadGafrl 42 
                                       ++G+V + + g +++++++t        ++   t+++G+f l
  gi|518652622|ref|YP_008142142.1| 889 VQGTVENvQYGYGLSNVNITSD-----GKTIGYTNSSGQFVL 925
                                       8999999447999999999988.....555568999999986 PP

>> fn3  Fibronectin type III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   6.7e-07     0.004      15      77 ..     981    1042 ..     976    1049 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 6.7e-07
                                        EEEEEEE-CSSSSSTEEEEEEEEEETTSTS.TEEEEEECSTSSEEEEESSSTTEEEEEEEEEEE CS
                               fn3   15 sltvsWeppkdgggpitgYeveyrekgsee.ewneftvprtttsvtltgLkpgteYevrVqavn 77  
                                        ++ vsW++ +  + ++  Y v y++ + +  +++e+  +r t+   ++gL+pg++Y v V a++
  gi|518652622|ref|YP_008142142.1|  981 YAFVSWDKYP--STNFAEYVVAYSNNSLMLnPHTEVISSRGTDFGFIPGLTPGKTYYVIVDAYT 1042
                                        5679****96..***********99999888999999999999*******************98 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.3       0.8   4.8e+03      25      36 ..     524     535 ..     519     539 .. 0.87
   2 ?   -2.2   0.1       0.7   4.2e+03      10      23 ..     599     612 ..     569     630 .. 0.52
   3 ?    1.7   0.1     0.042   2.5e+02      45      66 ..     757     779 ..     752     798 .. 0.71
   4 !   17.3   0.4   5.9e-07    0.0035      24      83 ..     827     886 ..     813     889 .. 0.88
   5 !    4.7   1.8     0.005        30       1      39 [.     889     926 ..     889     955 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.8
                   CarbopepD_reg_2  25 kkgtvTdenGnF 36 
                                       k+g +T++ G++
  gi|518652622|ref|YP_008142142.1| 524 KFGISTNSTGYY 535
                                       6899*******9 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.7
                   CarbopepD_reg_2  10 tkeplpgatVyvkg 23 
                                       ++ ++ +++++   
  gi|518652622|ref|YP_008142142.1| 599 DNAKINFVNISKAT 612
                                       23344444444444 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.042
                   CarbopepD_reg_2  45 kytLvv.syvGyktqekkvtvsk 66 
                                       +ytL v  y Gy++ +k+++v +
  gi|518652622|ref|YP_008142142.1| 757 QYTLLVdHYFGYTSSSKTIDVYE 779
                                       5676662579*********9854 PP

  == domain 4  score: 17.3 bits;  conditional E-value: 5.9e-07
                   CarbopepD_reg_2  24 tkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeealel 83 
                                       t +g+ T++ G +++ ++++++  ++++  Gy++q+++++++ ++++ +++ l++++ + 
  gi|518652622|ref|YP_008142142.1| 827 TLNGVKTNSIGGYHFLYVTPDTTYINATDTGYTSQNQSMNLTPGQNIHISLVLSPKNSSF 886
                                       45899*****************99****************************99998765 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.005
                   CarbopepD_reg_2   1 isGtVvdketkeplpgatVyvkgtkkgtvTdenGnFelk 39 
                                       ++GtV + + +  l  ++++  g++ g +T+++G+F l 
  gi|518652622|ref|YP_008142142.1| 889 VQGTVENVQYGYGLSNVNITSDGKTIG-YTNSSGQFVLF 926
                                       68999999999***********99998.8*******994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); 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: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:01.02
# Mc/sec: 3263.39
//
Query:       gi|518652623|ref|YP_008142143.1|  [L=342]
Description: hypothetical protein FACI_IFERC00001G1262 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-34  120.2   0.0    4.8e-34  118.1   0.0    1.9  1  Meth_synt_2  Cobalamin-independent synthase, Catalytic domain


Domain annotation for each model (and alignments):
>> Meth_synt_2  Cobalamin-independent synthase, Catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   2.7e-38   4.8e-34      18     321 ..      18     333 ..       5     336 .. 0.87

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.7e-38
                                       -------------HHHHHHHHHHHHHHHHHHTT--S.CBE-B-TT-SSTTHHHHTTSTTEE--SS--EEEETTEEE- CS
                       Meth_synt_2  18 araevkkgelseeeyekaireeiekvvrrqeelgvD.vlvhgepeRgdmveyfgealdgfaftkngwvqsygsrcvr 93 
                                          +v ++  + eey+k  ++++e+ ++   ++g+D + v ge+ R +m e+ ++++dg+ f   g v s+ +r+++
  gi|518652623|ref|YP_008142143.1|  18 YLSTVFHKIYGTEEYYKLSEKATEETIDLFRHAGLDnIGVGGEMFRWEMYEHQANRVDGIKF--YGPVRSFDNRYYK 92 
                                       4444455556779***********************5669*******************976..689********** PP

                                       --EE-SS---SS-SSTHHHHHHTTS-SS-BEEEEE-HHHHHHTSEE-TTS-HHHHHHHHHHHHHHHHHHHHH..... CS
                       Meth_synt_2  94 ppiivgdvsrpaamtvkesalaqsltdkpvkglltGpvtilnwsfvrddvdraeaaaqialalrdevkdLea..... 165
                                        + iv+d+s ++     e  +  s    ++k  +tGp t+++wsf +   dr e+a+  a  l  e+k+L++     
  gi|518652623|ref|YP_008142143.1|  93 KGSIVEDISIKESFHSDELEYLLSKGYDNIKIPVTGPYTMMDWSFNEHYSDRYETAMAFASLLNSEMKNLKKlwdsk 169
                                       ************************9999****************************************997655555 PP

                                       .TT-SE.EEEE-TTSSTT--SSGGGHHHHHHHHHHHHHHHHTTS-TTSEEEEEES-S--CCCH.HHHHTT--SEEEE CS
                       Meth_synt_2 166 .aGikv.iQiDepalreGlplkkadwaayldwaveafrldtiaaaddtqvhtHlCyselndil.saiaaldvDviti 239
                                        +G k+ iQ+Depa  +  p++ +  +  l+ +ve+  +d++      +   H+Cys    +l + ++++++D +++
  gi|518652623|ref|YP_008142143.1| 170 yPGRKLeIQLDEPATTT-HPDEMNIVVDSLNKSVEG--IDNC------EFTIHVCYSTDYRLLyDVMNDIKIDGLNL 237
                                       5899988******9865.677777888889988887..5666......8899*****98888868899********* PP

                                       SBSSS-S.............SGGGGTTT.T---SEEEEBSS-TTSSS--THHHHHHHHHCHHCTS-STSB-BB-SS- CS
                       Meth_synt_2 240 easrsde.............ellealee.vkygrgvglGvydihsprvpsmeeiaalikkaldvapkerlwvnPdCG 302
                                       e++++d+             e l+++++  + ++ +glGv d+h + ++ +  i+++i+ +l+++p e + vnPdCG
  gi|518652623|ref|YP_008142143.1| 238 EFANRDKlepgtsdaarpgyEELKYFQQlNTKKKFIGLGVTDVHIDYIEPVRLIKDRINYTLNIMPPELVRVNPDCG 314
                                       ***999544444444444447899****6677788****************************************** PP

                                       STTS-HHHHHHHHHHHHHH CS
                       Meth_synt_2 303 Lktrkreearaalknmvda 321
                                       L+tr+ e   ++lknm  a
  gi|518652623|ref|YP_008142143.1| 315 LRTRSIETGYEKLKNMDTA 333
                                       ****************765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); 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: 00:00:00.46
# Mc/sec: 2231.40
//
Query:       gi|518652624|ref|YP_008142144.1|  [L=293]
Description: hypothetical protein FACI_IFERC00001G1263 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      246  (0.0137208); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2063.02
//
Query:       gi|518652625|ref|YP_008142145.1|  [L=310]
Description: hypothetical protein FACI_IFERC00001G1264 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-39  134.6   0.0    2.7e-39  134.0   0.0    1.3  1  Peptidase_S66   LD-carboxypeptidase N-terminal domain
    3.7e-26   92.1   0.0    5.9e-26   91.4   0.0    1.3  1  Peptidase_S66C  LD-carboxypeptidase C-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_S66  LD-carboxypeptidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.0   0.0     3e-43   2.7e-39       1     121 []      16     134 ..      16     134 .. 0.93

  Alignments for each domain:
  == domain 1  score: 134.0 bits;  conditional E-value: 3e-43
                                       EEEE-SSS-GGGSSH.HHHHHHHHHHHHCTEEEEEGCTC..--TTTTCSS-HHHHHHHHHHHHC-TTECEEEES--S CS
                     Peptidase_S66   1 iaivapSsglkkeeekeeleraievleelglevvlgksa..aksagylagtdeeRaadLnealadpeikaiicarGG 75 
                                       i+++ap+s+ +      +l r+i+ l++lg++v++gk++   +++++la+ +++Ra++L+ a++d+++kai+carGG
  gi|518652625|ref|YP_008142145.1|  16 IRVIAPASAPD----MIKLSRGISKLKKLGYKVTVGKNIkkLNQRNDLAAPAKDRAEELMSAFRDDNVKAIFCARGG 88 
                                       89*****7653....349*******************6655566679****************************** PP

                                       S-CHHCHHHH-HCCHHCS--EEEE-CCHHHHHHHHHHCHTBSEEE- CS
                     Peptidase_S66  76 ygaarllpyldfdaikknpkiliGySDiTalhlalyaktglvtlhg 121
                                       yg++++l  ld++ai++npki++GySDiTalhla++++ +l+t+hg
  gi|518652625|ref|YP_008142145.1|  89 YGSIHILSLLDYEAIRENPKIFMGYSDITALHLAINRNSNLITFHG 134
                                       *********************************************8 PP

>> Peptidase_S66C  LD-carboxypeptidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.0   6.6e-30   5.9e-26       1     122 [.     180     293 ..     180     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 6.6e-30
                                       EEEEEEEEHHHHHCCTTSTTS---TT..EEEEEE--TTHHHHHHHHHHHHCTSTTGGG--EEEEEE--...G...CC CS
                    Peptidase_S66C   1 eGrliGGnlsvlasllgtpylpekdlkgkILflEdvsespyridrmLtqlkeagvldkvkGivlGrftkp.eekeee 76 
                                       eG  +G n+s++asllgt+y+p  +++++I+f+Ed++ +  +idr++ ++k+a+++++++G+v+G+f+ + +   + 
  gi|518652625|ref|YP_008142145.1| 180 EGYSMGTNISLVASLLGTNYIP--ETTNRIFFIEDTDVTSGDIDRYFFSMKLAHIIEQFNGFVFGDFKAIfD---K- 250
                                       6999******************..899********888*****************************94432...3. PP

                                       ...---HHHHHHHHHT-GGGTTS-EEEEESESSSBS---EEETSEE CS
                    Peptidase_S66C  77 eekeeykealeevlaeiledlkiPvlynldiGHtspnltlplGaka 122
                                          ee+   +e+v+++++++ + P ly+ ++GH++++++lpl+a++
  gi|518652625|ref|YP_008142145.1| 251 ---EEPMPSIEDVVQKFMNEINKPSLYGAPFGHGEEQMVLPLNARI 293
                                       ...466778**********************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.33s 00:00:00.89 Elapsed: 00:00:00.52
# Mc/sec: 1779.57
//
Query:       gi|518652626|ref|YP_008142146.1|  [L=387]
Description: hypothetical protein FACI_IFERC00001G1265 [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   33.6   0.1    3.2e-07   30.2   0.0    2.3  2  M20_dimer  Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   1.8e-11   3.2e-07       9     102 ..     165     256 ..     155     262 .. 0.84
   2 ?    0.6   0.0     0.029   5.2e+02      13      38 ..     332     367 ..     324     383 .. 0.54

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 1.8e-11
                                       EEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEEEEEH CS
                         M20_dimer   9 gkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeakidiRl 84 
                                       ++  ++g+++H +  p  g+NA+ +l+   +++++ +++ +     +   +   + +gG a+nv+pd+a +++d+R 
  gi|518652626|ref|YP_008142146.1| 165 MEFIFHGRSAHMAaSPCYGINALDALVTTYSAINNMRDRAK---GDKNIVVGMVIRDGGKASNVVPDRAAMEVDLRS 238
                                       4555*******************************987755...4445555555559999***************** PP

                                       HHHHHHHHHHHHHHHHHT CS
                         M20_dimer  85 lpgedpeevleeieeile 102
                                       ++ + + e +e+i+++++
  gi|518652626|ref|YP_008142146.1| 239 SDSSFLVEFIEKIKKLAK 256
                                       **************9987 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.029
                                       EE-B-EEGG-TTTTB-HHH..........HHHHHHH CS
                         M20_dimer  13 vkgkagHsgapgagaNAie..........klarlla 38 
                                        +g  gHs     +aN+ +          +++ ++ 
  gi|518652626|ref|YP_008142146.1| 332 GTGLPGHSDQFREAANPARagenlmiairAASSAIL 367
                                       566677777555566766633332222224444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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 0.23s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2747.89
//
Query:       gi|518652627|ref|YP_008142147.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G1266 [Ferroplasma acidarmanus fer1]
Scores for complete 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-71  239.6   1.4    5.8e-71  239.4   1.4    1.0  1  ROK       ROK family


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 !  239.4   1.4   3.3e-75   5.8e-71       2     269 ..       4     288 ..       3     307 .. 0.89

  Alignments for each domain:
  == domain 1  score: 239.4 bits;  conditional E-value: 3.3e-75
                                       EEEEE-SSEEEEEEEETTS-EEEEEEEEEHCCHHCCHHHHHHHHHHCCCHCCH..TEEEEEEEEESSEEETTCCEBS CS
                               ROK   2 igidiGgtkialalvdeegeilarekvetptetteetlvdaiaelvdeaerka..deliavgigspGlisdksgkiv 76 
                                       +g d+Ggtki + ++d  g i+++    t ++  + +++d + ++ de+ +ka  +++ ++gi+++G++++k g+i+
  gi|518652627|ref|YP_008142147.1|   4 LGYDVGGTKISAVIGDGTGRIMKKITRRTMKDYGKSGITDQLISMGDELIKKAgiEKVSKIGIIFAGPVDSKTGTII 80 
                                       588*********************99967666667777777777777765554116788****************** PP

                                       SGGCGCC.CCTTHHHHHHHHHTS-EEEEEHHHHHHHHHHHHCTTTTTS-EEEEEESSSEEEEEEETTEEE--TTS-T CS
                               ROK  77 stpnitw.enfdlvekleerlnvpvevenDvnaaalaEavfgaskdvenviyvtvgtGvGaGviingklitGrnGva 152
                                       s pni + +n+++ +++ +++nv v+++nD+ a++ aE+  ga+k+ +n++y+t++tG+G+G+ i++kl++G++G+a
  gi|518652627|ref|YP_008142147.1|  81 SSPNIIGlKNYNITDSIRKHFNVDVYLQNDASASTIAEKLYGAAKNFSNFVYITLSTGIGGGIFIDNKLYKGSHGMA 157
                                       ****8888********************************************************************* PP

                                       T-GGGSBS-TTS-B-TTS-BSBHHHCCSHHHHHHCHTC..............CGTTS-HHHHHHHHCTT-HHHHHHH CS
                               ROK 153 gelGHiqldpegekcgCGnqgClEtlasgralekraqq..............kgekleakeiiklaekgdevaeevv 215
                                       gelGH+ + p+g++cgCG++gClE++asg+++++r+ +              ++++++ak+i+ + + gd  a+ +v
  gi|518652627|ref|YP_008142147.1| 158 GELGHMVILPNGPICGCGRRGCLEAIASGKGMARRVIEnisevknstifsdmNPADIDAKKIFAARRAGDMFAQLIV 234
                                       ***********************************9999************************************** PP

                                       HHHHHHHHHHHHHHHHHH--SEEEEEHCCCTST.THHHHHHHHHHHCCTTTTCCC CS
                               ROK 216 erlaeylakaiadlinlfdpqaivlgGgvsead.klleairklvkkylnkklevp 269
                                       e+  +yla +i+++in+fdpqai++gGg+s +  +l++++r +v + + +  ++p
  gi|518652627|ref|YP_008142147.1| 235 EETIYYLAVGIVNIINIFDPQAIIIGGGLSLEGeDLFHPLRLAVREEMKSM-KRP 288
                                       *****************************9875155599998888765543.334 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2067.89
//
Query:       gi|518652628|ref|YP_008142148.1|  [L=436]
Description: hypothetical protein FACI_IFERC00001G1267 [Ferroplasma acidarmanus fer1]
Scores for complete 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   3.3    3.8e-12   46.4   1.1    2.5  2  NfeD      NfeD-like C-terminal, partner-binding
  ------ inclusion threshold ------
        5.1    7.1   7.4        2.1    8.3   0.6    3.2  3  ODV-E18   Occlusion-derived virus envelope protein ODV-E18
        7.9    6.0   6.0       0.85    9.1   0.1    2.3  3  DUF5385   Family of unknown function (DUF5385)


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 ?    0.1   0.0      0.17     1e+03       3      42 ..       8      44 ..       6      69 .. 0.52
   2 !   46.4   1.1   6.4e-16   3.8e-12       2      84 .]     350     435 ..     347     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                                      XXXXXXXXXXXXXXS---SSS--S.S---.GGTTSEEEEEE CS
                              NfeD  3 avvsvlllvllrplllkklkkkekktnae.aliGkegvvle 42
                                      ++v +++++ll+ ++  + +++ + t  e ++    g+v+ 
  gi|518652628|ref|YP_008142148.1|  8 IIVLIIFIFLLM-VASSAGHSTGQ-T--EnSYKAGNGKVVL 44
                                      445555555555.44444433221.1..1234444444444 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 6.4e-16
                                       XXXXXX.XXXXXXXXXS---SSS--S..S---GGTTSEEEEEE-B..S.-EEEEETTEEEEEE-.SS.B-TT-EEEE CS
                              NfeD   2 favvsv.lllvllrplllkklkkkek.ktnaealiGkegvvledi..g.tGrvkvdGeeWsarsege.iekgerVrV 72 
                                       ++++   ll++ + + +lk++++  +  t+ae+l G  + v++++  + +G v++dG +W+a+  g  +++ e+V++
  gi|518652628|ref|YP_008142148.1| 350 AIILIGiLLIIYISK-ILKSQRR--EiYTGAESLKGHSADVVTPMkrNeKGFVMIDGVQWEAINIGVdVNRSEKVVI 423
                                       444444044444445.5554434..346*****************97348*************97667********* PP

                                       EEE-SSSEEEEE CS
                              NfeD  73 veveGltliVep 84 
                                       +e++GltliV++
  gi|518652628|ref|YP_008142148.1| 424 IERKGLTLIVKK 435
                                       **********98 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.6   0.00035       2.1      32      63 ..       8      42 ..       5      59 .. 0.52
   2 ?   -3.8   0.2         2   1.2e+04      51      71 ..     186     208 ..     180     211 .. 0.58
   3 ?    1.6   0.0     0.043   2.6e+02      25      45 ..     343     363 ..     321     370 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00035
                           ODV-E18 32 vvlviiillvllvqss....stGsdssssnannart 63
                                      + +v+ii++ ll+ +s    stG+   s  a n ++
  gi|518652628|ref|YP_008142148.1|  8 I-IVLIIFIFLLMVASsaghSTGQTENSYKAGNGKV 42
                                      3.4444455444444402224455555555555555 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 2
                           ODV-E18  51 sdssssnannart..GfvnPlna 71 
                                       s+ ss++a+n ++  G +  +na
  gi|518652628|ref|YP_008142148.1| 186 SEYSSAQASNIKLsdGNFASMNA 208
                                       44566677776543355556665 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.043
                           ODV-E18  25 sllltilvvlviiillvllvq 45 
                                       s+++  +++++i ill++++ 
  gi|518652628|ref|YP_008142148.1| 343 SFYMFSIAIILIGILLIIYIS 363
                                       567777888889899998875 PP

>> DUF5385  Family of unknown function (DUF5385)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.48   2.8e+03       7      23 ..       8      18 ..       6      38 .. 0.51
   2 ?   -3.0   1.0      0.71   4.2e+03       2      22 ..     282     300 ..     281     305 .. 0.77
   3 ?    9.1   0.1   0.00014      0.85       4      52 ..     343     391 ..     341     399 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.48
                           DUF5385  7 iiliiiiiiilvivfll 23
                                      ii++i      + +fll
  gi|518652628|ref|YP_008142148.1|  8 IIVLI------IFIFLL 18
                                      22222......222322 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 0.71
                           DUF5385   2 ngnfliiliiiiiiilvivfl 22 
                                       n +++++++++++ il+  fl
  gi|518652628|ref|YP_008142148.1| 282 NASIFGLILLLLAGILI--FL 300
                                       78999*****9999554..44 PP

  == domain 3  score: 9.1 bits;  conditional E-value: 0.00014
                           DUF5385   4 nflii.liiiiiiilvivfllrkkkkqkeeekaggkikersdkdEVWkti 52 
                                       +f+++ + ii+i il+i+++ +k  k+++ e  +g+ + + +  +V + +
  gi|518652628|ref|YP_008142148.1| 343 SFYMFsIAIILIGILLIIYI-SKILKSQRREIYTGAESLKGHSADVVTPM 391
                                       45554266788888999998.99999999998888877776666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       943  (0.0525964); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.63u 0.30s 00:00:00.93 Elapsed: 00:00:00.45
# Mc/sec: 2933.61
//
Query:       gi|518652629|ref|YP_008142149.1|  [L=381]
Description: hypothetical protein FACI_IFERC00001G1268 [Ferroplasma acidarmanus fer1]
Scores for complete 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-124  413.8   0.0   5.3e-124  413.6   0.0    1.0  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
    1.8e-05   23.9   0.0     0.0016   17.4   0.0    2.1  2  Aminotran_5      Aminotransferase class-V
     0.0022   17.4   0.1      0.084   12.2   0.0    2.5  3  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0068   15.6   0.0      0.012   14.8   0.0    1.3  1  Aminotran_1_2    Aminotransferase class I and II


Domain annotation for each model (and alignments):
>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  413.6   0.0  1.2e-127  5.3e-124       3     382 .]       9     379 ..       7     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 413.6 bits;  conditional E-value: 1.2e-127
                                       HHHHTTTTCHTTTTBSS--B---SBBBESSHHHHCTTCSSS-SBTTT--HHHHHHHHHHHHHHT-SEEEEESSHHHH CS
                   Cys_Met_Meta_PP   3 llvhagqekdeqtgavavpiyltstykfkdvdeafageekgyeYsRsgnptrsvleeriaaLeggeaalavssGmaA 79 
                                        +vh+g  + e  g+v++pi++ st++f        g + +y+YsR gnpt++ +e++ a+Le++e+a+a+s+GmaA
  gi|518652629|ref|YP_008142149.1|   9 RCVHSGDMEIEGVGNVVTPIFENSTFEFP-----ESGVAGKYIYSRWGNPTVESFEKKYADLEKTEHAFAFSTGMAA 80 
                                       579999999999*****************.....8888888************************************ PP

                                       HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCTTEEEEEEESS-TTTT----H CS
                   Cys_Met_Meta_PP  80 iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaikentklvylEtptnpllkvvDi 156
                                       i+++i+  lk+Gd +++ ++lYg t+ +++kvl++ +i+v+f+ ++dl++l  + ++n kl+ylE++tnpll+v+Di
  gi|518652629|ref|YP_008142149.1|  81 ITSSIMPYLKSGDSVLALNELYGQTFGFFSKVLPQYKINVDFTSVNDLNRLDFK-NKNYKLLYLESITNPLLEVPDI 156
                                       *************************************************99755.779******************* PP

                                       HHHHHHHHHTT-EEEEEGTTTHTTTS-GGGGT-SEEEEETTTTTTCSSS--EEEEEESSCHHHHHHHHHHHHHHT-B CS
                   Cys_Met_Meta_PP 157 ekiaklakkagvlvvvDntfaspllqrplklgaDivvhSaTKylgGhsdvvaGvivvkgkeelkkelkflqnalGav 233
                                        ++++++k++g+ ++vD+tfa+p++q+p++lgaD+ +hS+TKy++Ghsd+++G++  ++     ++l f  +++G +
  gi|518652629|ref|YP_008142149.1| 157 VNLSRICKEEGIKLMVDATFATPYNQNPVSLGADMALHSGTKYISGHSDLLIGLAGFND---NYDNLDFYRKTFGGT 230
                                       ******************************************************99877...6677999******** PP

                                       --HHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHTSTTEEEEE-TTSTTSTTHHHHHHHSSSG-SEEEEEESSHHH CS
                   Cys_Met_Meta_PP 234 lspfdawlllrGlkTLslRlerhqenAlkvAefLekhpkvekvyYpglpshpqhelakkqlkgaggvlsFelkseee 310
                                        ++f+a+l  rGlkTL+lR+erh++nA+++A+ L+++ ++e+vyYpgl++++ +++a+k+lkg+gg++sF++k++ e
  gi|518652629|ref|YP_008142149.1| 231 PDAFQAFLAYRGLKTLGLRMERHNKNAMELAKVLNESSRIEEVYYPGLKNSEYFDVAEKNLKGYGGMVSFKVKGGIE 307
                                       ***************************************************************************** PP

                                       HHHHHHHC-SSSEECSS-SSSS-EEEETTTTTTTTSCHHHHHHTTS-TTEEEEE--SS-HHHHHHHHHHHHH CS
                   Cys_Met_Meta_PP 311 kakkfvdnlklfslaeslGgveslielpasmthasipkeereaagvtddliRlsvGiEdvdDliaDlkqale 382
                                       +++k+++nl++ + a+slGgvesli++p+  th+++++eer+a+g+td+l+RlsvGiEd +Dl++D+++ale
  gi|518652629|ref|YP_008142149.1| 308 NSHKLIKNLNIPKYAVSLGGVESLISIPVEGTHKALSPEERKASGITDNLVRLSVGIEDSEDLLQDFENALE 379
                                       **********************************************************************96 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   3.6e-07    0.0016     137     203 ..     135     200 ..      69     204 .. 0.78
   2 !    4.7   0.0    0.0027        12     269     338 ..     256     326 ..     213     374 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.6e-07
                                       -TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESEEEEETTTTT CS
                       Aminotran_5 137 nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDflafsghKll 203
                                       n+++kl+++  + n +  + ++ ++ +++k++g+ ++vDa+ a +  +  v  lg+D++  sg K++
  gi|518652629|ref|YP_008142149.1| 135 NKNYKLLYLESITNPLLEVPDIVNLSRICKEEGIKLMVDATFATPYNQNPV-SLGADMALHSGTKYI 200
                                       689*************************************99999777666.6************65 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0027
                                       HCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTC..SHHHHHHHHHHTTEEEEEE CS
                       Aminotran_5 269 eeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgv..haedvatlLdeegIavrsG 338
                                       ++++l+++ +++ +  e  + +lk+++ + +++ ++ +   ++vsf++kg   +++++ + L+  + av+ G
  gi|518652629|ref|YP_008142149.1| 256 NAMELAKVLNESSRIEEVYYPGLKNSEYFDVAE-KNLKGYGGMVSFKVKGGieNSHKLIKNLNIPKYAVSLG 326
                                       6789999************************88.69999*********875334577777777777777765 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   1.9e-05     0.084      22      56 ..      52      86 ..      38     106 .. 0.82
   2 ?    1.8   0.0     0.026   1.1e+02     126     155 ..     155     182 ..     152     198 .. 0.75
   3 ?   -1.8   0.0      0.32   1.4e+03     234     318 ..     243     284 ..     232     292 .. 0.50

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.9e-05
                                      SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLr 56
                                      +p+ve+FEk+ a+  +++ha a+s+G aA+  +++
  gi|518652629|ref|YP_008142149.1| 52 NPTVESFEKKYADLEKTEHAFAFSTGMAAITSSIM 86
                                      799**************************987665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.026
                                       -HHHHHHHHHHCT-EEEEE-TT-TT-EETT CS
                   DegT_DnrJ_EryC1 126 dmdalkaiaakhglkvieDaAhAlGatykg 155
                                       d+ +l +i+++ g+k++ Da  A    y++
  gi|518652629|ref|YP_008142149.1| 155 DIVNLSRICKEEGIKLMVDATFAT--PYNQ 182
                                       788999*************98664..4455 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.32
                                       HCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SGSC CS
                   DegT_DnrJ_EryC1 234 LerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhypn 310
                                       L+ l   ++r +++a  + + L+e   +                                           +v+yp 
  gi|518652629|ref|YP_008142149.1| 243 LKTLGLRMERHNKNAMELAKVLNESSRI------------------------------------------EEVYYP- 276
                                       5555555555555555555555544443..........................................444442. PP

                                       HGGGSCCH CS
                   DegT_DnrJ_EryC1 311 plhrqpvy 318
                                        l++ +++
  gi|518652629|ref|YP_008142149.1| 277 GLKNSEYF 284
                                       44444444 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   2.7e-06     0.012      46     196 ..      55     182 ..      37     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEE....SS-THHHHHHHHTTSEEE CS
                     Aminotran_1_2  46 lpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpd....ptyasyknilrlsggevv 118
                                         ++e++ a++ +        +e a  +++G  a+ + ++  lk   gd +l+ +    +t++ ++++l  +++ v 
  gi|518652629|ref|YP_008142149.1|  55 VESFEKKYADLEK--------TEHAFAFSTGMAAITSSIMPYLK--SGDSVLALNelygQTFGFFSKVLPQYKINVD 121
                                       5678888888888........88899999999999999999998..8999988762333556666666666666666 PP

                                       EEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBS CS
                     Aminotran_1_2 119 ryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvf 195
                                         +        +dl+ l+        +nk  k++++es+ NP   v++   l  +   +k+ ++ l+vD ++a+ + 
  gi|518652629|ref|YP_008142149.1| 122 FTS-------VNDLNRLDF-------KNKNYKLLYLESITNPLLEVPDIVNLSRI---CKEEGIKLMVDATFATPYN 181
                                       666.......556666665.......344679**********9877777777777...************9997665 PP

                                       S CS
                     Aminotran_1_2 196 g 196
                                       +
  gi|518652629|ref|YP_008142149.1| 182 Q 182
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2784.55
//
Query:       gi|518652630|ref|YP_008142150.1|  [L=427]
Description: hypothetical protein FACI_IFERC00001G1269 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-87  293.8   0.9    1.7e-87  293.5   0.9    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
      4e-13   49.2   0.5    7.2e-13   48.3   0.5    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
     0.0007   19.2   0.1       0.27   10.7   0.0    2.5  2  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    0.00077   19.5   1.5     0.0014   18.7   1.5    1.3  1  BOF              Bacterial OB fold (BOF) protein
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.21   11.6   0.1    1.5  1  DUF4539          Domain of unknown function (DUF4539)
       0.12   12.4   0.3       0.68   10.0   0.2    2.2  2  MIT              MIT (microtubule interacting and transport) 
       0.16   11.5   0.4       0.28   10.8   0.4    1.3  1  tRNA_anti-like   tRNA_anti-like


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 !  293.5   0.9   6.4e-91   1.7e-87       3     313 ..     114     421 ..     112     422 .. 0.95

  Alignments for each domain:
  == domain 1  score: 293.5 bits;  conditional E-value: 6.4e-91
                                       CHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-S CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2   3 elrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqsp 79 
                                       ++rl+nr+ldlr+++   ++++ s+++  +r+++++++fie++tP ++ ++te+ga lF v+  ek  + f L+qsp
  gi|518652630|ref|YP_008142150.1| 114 DTRLNNRFLDLRKPEHLLIFQFESQLLFGIREFMNKENFIEVHTPKIVAAATEGGADLFRVEYFEK--NAF-LNQSP 187
                                       79***********************************************************44443..555.***** PP

                                       HHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  80 qlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefv 156
                                       qly+e+li++g+d+vf++++aFRaE+ +t rhl+EFt+i++e +fi++++ m++le+ i++ v++ ++ +++++e+ 
  gi|518652630|ref|YP_008142150.1| 188 QLYKEILIASGFDKVFEVGPAFRAEKENTVRHLNEFTSIDMEAAFIDDKKAMEYLENAISYAVNRNIDLMHTKLEEY 264
                                       ****************************************************************9977776666665 PP

                                       TTTTSEE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 157 irrnskdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkl 227
                                         +  +++++pf+r++y++ ie ln++      g+d + +  ++l + + n ++f+t +P+ ++pFy+  +++ ++l
  gi|518652630|ref|YP_008142150.1| 265 GYH-LEKIETPFPRISYEDGIEYLNDHglklnfGDDFSPEANKILAE-KFNGFYFITGWPSDMRPFYTHPDTN-PAL 338
                                       555.479**************************9***********99.99********************999.9** PP

                                       BSEEEEEETTEEEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 228 tesyDllingvElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesI 304
                                       t+s+Dl +n++E+++G++Ri+++++le+++ +kgl+   ++ f++y +a+++G+pph+G+glGl+Rlvm ll+++++
  gi|518652630|ref|YP_008142150.1| 339 TKSFDLQLNDIEVTSGAQRIHNYKMLEDNFMKKGLN---KNDFEFYEKAFKFGMPPHAGWGLGLERLVMNLLHLNNV 412
                                       ************************************...************************************** PP

                                       GGCSSS-XX CS
                                       xxxxxxxxx RF
                       tRNA-synt_2 305 rdviaFPkl 313
                                       r+ ++FP+ 
  gi|518652630|ref|YP_008142150.1| 413 RESTLFPRD 421
                                       *******96 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.5   2.8e-16   7.2e-13       1      76 []      17      94 ..      17      94 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 2.8e-16
                                      EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET..HHHHHHHTTS-TTSEEEEEEEEEEC...TTSSEEEEEEEEE CS
                   tRNA_anti-codon  1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr..eeatklaenlkeGdvvrvtGrvkrr...pggelelkveeie 74
                                      Vt++G+v+ +  r++++++fi+ rD+tg+iqv++ +   + ++++ ++++++v+ v+G++++    + g +e++  eie
  gi|518652630|ref|YP_008142150.1| 17 VTIKGWVQET--RKIKNLMFIIMRDNTGSIQVTAKKdsMKNYDQLYDITRESVISVYGTLNKKsisKSG-MEIQGIEIE 92
                                      9*********..************************6655555556688****************9999.999999999 PP

                                      EE CS
                   tRNA_anti-codon 75 ll 76
                                      +l
  gi|518652630|ref|YP_008142150.1| 93 IL 94
                                      86 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 !    5.9   0.0     0.003       7.6     103     146 ..     201     247 ..     194     264 .. 0.80
   2 !   10.7   0.0   0.00011      0.27     212     233 ..     393     414 ..     357     423 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.003
                                       EEEEEEEEEBSST.-SSSB-SEEEEE..EEEEEETT--HHHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqv..eglvvdenvsladlkgvle 146
                                       k++ +g +fR ++    +hl eF+++  e  ++d++  ++ l   ++
  gi|518652630|ref|YP_008142150.1| 201 KVFEVGPAFRAEKeNTVRHLNEFTSIdmEAAFIDDKKAMEYLENAIS 247
                                       8999********966789*****998335678888888888877665 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
                                       EEEEEEHHHHHHHHHT-SSGHH CS
                      tRNA-synt_2d 212 fafGlGveRlamlkygieDiRe 233
                                       +++GlG+eRl m  + ++++Re
  gi|518652630|ref|YP_008142150.1| 393 AGWGLGLERLVMNLLHLNNVRE 414
                                       68*******************7 PP

>> BOF  Bacterial OB fold (BOF) protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   1.5   5.4e-07    0.0014      28      98 ..       8      86 ..       2      91 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.4e-07
                                      HTTS-SSEEEEEEEEE..EEEEETTEEE.EEETTEEEEEE--G...GGSTT.----TTSEEEEEEEEEEET.TEEEEEE CS
                               BOF 28 AlsaaDdasvslrGni..vkriddDeyv.FrDasGeikveidd...rvfng.levqpkdkvkiqGkvDkel.ekaeidv 98
                                       +++ D++ v+++G +  +++i++  ++  rD++G+i+v  ++   ++++   +++ +  + ++G ++k++ +k  +++
  gi|518652630|ref|YP_008142150.1|  8 IKTLDDGSDVTIKGWVqeTRKIKNLMFIiMRDNTGSIQVTAKKdsmKNYDQlYDITRESVISVYGTLNKKSiSKSGMEI 86
                                      6899**********9944678888888536**********99822244555348**************76514555555 PP

>> DUF4539  Domain of unknown function (DUF4539)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   8.3e-05      0.21      11      47 ..      24      58 ..       5      74 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.3e-05
                           DUF4539 11 ksintlnslgdalvtlkDptGeidgtihrkvleeygk 47
                                      ++ +  ++l  ++++++D+tG+i+ t +++ +++y +
  gi|518652630|ref|YP_008142150.1| 24 QETRKIKNL--MFIIMRDNTGSIQVTAKKDSMKNYDQ 58
                                      444444444..9********************99865 PP

>> MIT  MIT (microtubule interacting and transport) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00027      0.68      28      64 ..     236     272 ..     227     273 .. 0.88
   2 ?   -0.7   0.0      0.59   1.5e+03      27      35 ..     280     288 ..     278     312 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00027
                               MIT  28 kealelLlqalke.kneerrellrekieeYleRaeeLk 64 
                                       k+a+e+L  a++   n +  +l+++k+eeY  + e+++
  gi|518652630|ref|YP_008142150.1| 236 KKAMEYLENAISYaVN-RNIDLMHTKLEEYGYHLEKIE 272
                                       79**********6488.*************88888875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.59
                               MIT  27 YkealelLl 35 
                                       Y++++e+L+
  gi|518652630|ref|YP_008142150.1| 280 YEDGIEYLN 288
                                       9******96 PP

>> tRNA_anti-like  tRNA_anti-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.4   0.00011      0.28      86     152 ..      14      79 ..       6      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
                                       T-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGHHHHHH--TTSEEEEEEE-----S CS
                    tRNA_anti-like  86 GkiieVeGvvsdikkieassvvvlardddgltnVrclledeateasaakiskGqkvtivGqvngvsi 152
                                       G+ ++++G v++++ki++  +++ +rd+ g+ +V +  ++ ++  ++  i + +++ + G+ n +si
  gi|518652630|ref|YP_008142150.1|  14 GSDVTIKGWVQETRKIKN-LMFIIMRDNTGSIQVTAKKDSMKNYDQLYDITRESVISVYGTLNKKSI 79 
                                       7889***********555.5677788889999999998888889999***************99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      513  (0.0286129); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 3025.04
//
Query:       gi|518652631|ref|YP_008142151.1|  [L=43]
Description: hypothetical protein FACI_IFERC00001G1270 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      213  (0.0118802); 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 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 298.27
//
Query:       gi|518652632|ref|YP_008142152.1|  [L=93]
Description: hypothetical protein FACI_IFERC00001G1271 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       638  (0.0355848); 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:                         0  (0); expected 0.2 (1e-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: 700.04
//
Query:       gi|518652633|ref|YP_008142153.1|  [L=220]
Description: fibrillarin [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-59  201.4   0.1    1.2e-59  201.2   0.1    1.0  1  Fibrillarin  Fibrillarin


Domain annotation for each model (and alignments):
>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.2   0.1   6.6e-64   1.2e-59      29     221 ..      29     217 ..       6     220 .] 0.93

  Alignments for each domain:
  == domain 1  score: 201.2 bits;  conditional E-value: 6.6e-64
                                       T--SSSSEEEEETTEEEEEE-TTTSHHHHHHHTT-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSH CS
                       Fibrillarin  29 gekvYgEklikveeeEyRvWnpfrsKlaaailkglkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsp 105
                                       ++++YgEk+ k+++   R+W+p+rsKl+aa+lkg k++p+k +s+vLYlGa++GttvsHvsDi+  +g+v+avefs 
  gi|518652633|ref|YP_008142153.1|  29 NQSIYGEKIKKSGGFYLREWDPRRSKLGAALLKGFKSMPLKDDSSVLYLGASTGTTVSHVSDICF-RGMVFAVEFSY 104
                                       689*************************************************************9.9********** PP

                                       HHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHHHHS CS
                       Fibrillarin 106 rvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpdqarilaknaklflkeggyllisikarsidv 182
                                        ++ +l ++a+kR+ni+PileDA+ PekY+ l++  Dvi++D+aq +q++i+ +n+k f  +  + +++ikar+i +
  gi|518652633|ref|YP_008142153.1| 105 DSFVKLYTLAEKRNNIYPILEDANLPEKYEFLIDGPDVIYQDIAQRNQIQIFNENSKKFK-NAEKAMLIIKARAISS 180
                                       **********************************************************95.55678889******** PP

                                       SSSHHHHHHHHHHHHHHTTEEEEEEEE-TTTSTTEEEEE CS
                       Fibrillarin 183 tkepeevfkeeveklkeeglkvleqvklepyekdhalvv 221
                                        +  +++ ++ ++++k  ++kv+e ++l+py+    +v+
  gi|518652633|ref|YP_008142153.1| 181 NRPEKSIVNSAIREIK--DFKVKEIIDLKPYDIGNYFVY 217
                                       *************997..69***********98877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1650.77
//
Query:       gi|518652634|ref|YP_008142154.1|  [L=150]
Description: transcription factor [Ferroplasma acidarmanus fer1]
Scores for 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-13   48.2   0.9    1.3e-12   47.5   0.9    1.4  1  HTH_3           Helix-turn-helix
    4.5e-05   23.4   2.3    7.9e-05   22.6   1.6    1.8  2  HTH_19          Helix-turn-helix domain
    0.00089   19.4   0.1     0.0013   18.9   0.1    1.2  1  Thioredoxin_4   Thioredoxin
     0.0033   17.7   0.0     0.0058   16.9   0.0    1.4  1  HTH_31          Helix-turn-helix domain
      0.005   16.7   0.5     0.0089   15.9   0.5    1.4  1  HTH_25          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.024   14.7   0.4      0.048   13.8   0.4    1.5  1  Zn-ribbon_8     Zinc ribbon domain
      0.045   13.7   0.7       0.16   11.9   0.1    2.1  2  DUF723          Protein of unknown function (DUF723)
       0.11   12.3   1.2         12    5.8   0.1    3.1  3  zf-Nse          Zinc-finger of the MIZ type in Nse subunit
       0.16   12.1   2.9          1    9.5   2.9    2.3  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito


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 !   47.5   0.9   6.7e-16   1.3e-12       1      54 [.      94     147 ..      94     148 .. 0.97

  Alignments for each domain:
  == domain 1  score: 47.5 bits;  conditional E-value: 6.7e-16
                                       HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHH CS
                             HTH_3   1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvslde 54 
                                       +k++R++ +++q eLA+k+   ++ +s+iE+Ge  P++ t+ kl+k+L+++l e
  gi|518652634|ref|YP_008142154.1|  94 IKAKREEMNMTQDELAKKIFERKNVLSNIERGELLPDIATARKLEKVLNIKLLE 147
                                       8*************************************************9865 PP

>> HTH_19  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       3.3   6.6e+03      43      50 ..      39      46 ..      31      52 .. 0.67
   2 !   22.6   1.6     4e-08   7.9e-05       3      54 ..      93     143 ..      91     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.3
                            HTH_19 43 elllkiae 50
                                      ++l+ki+e
  gi|518652634|ref|YP_008142154.1| 39 KKLNKISE 46
                                      45666665 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 4e-08
                            HTH_19   3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgi 54 
                                        +k+ Ree ++tq+ela+++  +++ +s+iE g+   p++ + +k+ + l+i
  gi|518652634|ref|YP_008142154.1|  93 LIKAKREEMNMTQDELAKKIFERKNVLSNIERGEL-LPDIATARKLEKVLNI 143
                                       68999****************************77.7776666555555554 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   6.6e-07    0.0013      25     138 ..      26     143 ..      24     145 .. 0.77

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.6e-07
                                       -HHHHHHHHHHHHHHHHHHHTT.SEEEEEEE-..---S.TTTHHHHHHHTT--TT...HHHHHHHHHHHHTHHHHTT CS
                     Thioredoxin_4  25 CphCakfeeeveklleeyidtG.kvkfiirdfpldkek.eslkaamaarcagees...peaflaikallysqqeewa 96 
                                       Cp Cakf e ve+ +   i++   +kf  ++ +  ++k   +k ++  + +  e+      ++++ +l++ ++ee +
  gi|518652634|ref|YP_008142154.1|  26 CPQCAKFGEPVEEKKLNKISENvTIKFPEKKINVVTYKkPFKKPVTTKKPVHRENveeLDVVEDYADLIKAKREEMN 102
                                       ************66666677777888888888777777555666666666666553123477999999********9 PP

                                       S-HHHHH.....HHHHHTS-------HHHHHHHHHHHHHHT- CS
                     Thioredoxin_4  97 eslkelaaealdkdekfeacleeekldalveaeskeakkagi 138
                                        +++ela++ + +++++ +++e+++l ++++++ k  k ++i
  gi|518652634|ref|YP_008142154.1| 103 MTQDELAKK-IFERKNVLSNIERGELLPDIATARKLEKVLNI 143
                                       999999966.8889999999**********999887666665 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   2.9e-06    0.0058       3      55 ..      91     142 ..      89     148 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.9e-06
                            HTH_31   3 GalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralg 55 
                                       ++l +a Re+ +++q+e+A+ +   +  ls +E+G+  +p  a+ ++l  +l+
  gi|518652634|ref|YP_008142154.1|  91 ADLIKAKREEMNMTQDELAKKIFERKNVLSNIERGEL-LPDIATARKLEKVLN 142
                                       6788999******************************.9*9999999988887 PP

>> HTH_25  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.5   4.5e-06    0.0089       3      39 ..      95     129 ..      93     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.5e-06
                                       HHHHHTTT--HHHHHHHSS--HHHHHHHHCT--TTSS CS
                            HTH_25   3 raaRearglsleevaketkIrkdylealEeddfdalp 39 
                                       +a+Re+++++ +e+ak++  rk++l  +E++  ++lp
  gi|518652634|ref|YP_008142154.1|  95 KAKREEMNMTQDELAKKIFERKNVLSNIERG--ELLP 129
                                       899***************************9..5566 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.4   2.4e-05     0.048       8      33 ..       3      30 ..       1      35 [. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                       Zn-ribbon_8  8 CeeCghefevlqsis.daplta.CPeCg 33
                                      Ce+Cg   ++l +++   +    CP+C 
  gi|518652634|ref|YP_008142154.1|  3 CEMCGVSSDKLIKVKiSGAILNvCPQCA 30
                                      *********99999988886666****6 PP

>> DUF723  Protein of unknown function (DUF723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.71   1.4e+03      56      60 .]      26      30 ..      16      30 .. 0.91
   2 ?   11.9   0.1     8e-05      0.16       3      39 ..      39      78 ..      37      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.71
                            DUF723 56 CPeCa 60
                                      CP+Ca
  gi|518652634|ref|YP_008142154.1| 26 CPQCA 30
                                      ****7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 8e-05
                            DUF723  3 ltfeeaasrleekFph..lklveFeg.vakPvvinCPlHG 39
                                      + ++++  +++ kFp+  +++v +++  +kPv+ + P+H 
  gi|518652634|ref|YP_008142154.1| 39 KKLNKISENVTIKFPEkkINVVTYKKpFKKPVTTKKPVHR 78
                                      568889999******98899****985689*********5 PP

>> zf-Nse  Zinc-finger of the MIZ type in Nse subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.046        92      12      39 ..      24      50 ..      14      53 .. 0.73
   2 ?    5.8   0.1    0.0062        12      18      32 ..      63      77 ..      54      87 .. 0.90
   3 ?    0.8   0.0      0.22   4.4e+02      33      45 ..     112     124 ..      99     136 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.046
                                      SB-TTTSSB-SSEEEESSS--EEEHHHH CS
                            zf-Nse 12 lkCPltlqpfeePvtskkCpHvFEreaI 39
                                        CP  + +f ePv +kk + + E+ +I
  gi|518652634|ref|YP_008142154.1| 24 NVCP-QCAKFGEPVEEKKLNKISENVTI 50
                                      4577.5789999**99998877777666 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0062
                                      SSB-SSEEEESSS-- CS
                            zf-Nse 18 lqpfeePvtskkCpH 32
                                      ++pf++Pvt kk  H
  gi|518652634|ref|YP_008142154.1| 63 KKPFKKPVTTKKPVH 77
                                      589********9888 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.22
                                       EEEHHHHHHHCTT CS
                            zf-Nse  33 vFEreaIlelikr 45 
                                       +FEr+++l+ i+r
  gi|518652634|ref|YP_008142154.1| 112 IFERKNVLSNIER 124
                                       89**999999865 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 ?    9.5   2.9   0.00051         1      67     117 ..      87     137 ..       1     148 [. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00051
                    MqsA_antitoxin  67 elvdpafiarvrkkleldqreaa.eifGgGvnafsryekGkvrpplalvkll 117
                                       +   ++ i+  r++++++q e+a +if   +n +s  e+G+  p++a+ + l
  gi|518652634|ref|YP_008142154.1|  87 VEDYADLIKAKREEMNMTQDELAkKIFE-RKNVLSNIERGELLPDIATARKL 137
                                       333467788999*********7625776.89*************99987544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1306  (0.0728429); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 982.09
//
Query:       gi|518652635|ref|YP_008142155.1|  [L=172]
Description: hypothetical protein FACI_IFERC00001G1274 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-05   24.8   9.1    2.8e-05   24.2   9.1    1.2  1  DUF2269         Predicted integral membrane protein (DUF2269)
    0.00079   19.8   3.0    0.00079   19.8   3.0    1.6  2  CopD            Copper resistance protein D
  ------ inclusion threshold ------
       0.23   11.8   6.5       0.12   12.7   1.9    2.2  2  DUF4149         Domain of unknown function (DUF4149)
        2.2    7.2   8.4        3.7    6.5   8.4    1.6  1  SHR3_chaperone  ER membrane protein SH3


Domain annotation for each model (and alignments):
>> DUF2269  Predicted integral membrane protein (DUF2269)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   9.1   6.2e-09   2.8e-05       2     148 ..      18     167 ..      17     168 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 6.2e-09
                           DUF2269   2 llkllHilsavlllgtgigiafyllrasrtrdaaviaevarlvvladwlf.tatavillpvtGlwlvhlagwplkqs 77 
                                       +l  +H+lsa+ ++g+ i i+++l+ as + + + +   +  +v   + f t +++ ll++tGl++++   +  +  
  gi|518652635|ref|YP_008142155.1|  18 ILLSIHVLSAITFVGGSIFIWLILWPASYKMNDDKLRTRLLGFVGHRFAFwTNLTLGLLILTGLLMTYRYVLNPSLY 94 
                                       6889************************999998888888888888887615556668899*****99776555554 PP

                           DUF2269  78 Wl.llslvLyllagalwlpVvw.l..qirlrrlaeaaeeegaalpeeyvrlfriwfalgvlaflaliaifvLMva 148
                                       +   ++ +L+ +++++ ++V++ +  +i   +l  + +e+g+   ee+ ++ +++ ++ ++++++li+i++LMv+
  gi|518652635|ref|YP_008142155.1|  95 FQsTGGELLFSAEILIIAMVIImYgnNIYHGKLIVRLNEQGK--LEEVKKIRKVTHIYSMITMVLLIIIVLLMVS 167
                                       431466799*99999999999843113444455555555554..788999999********************95 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.1   4.9e+03      49      63 ..      23      37 ..      15      52 .. 0.54
   2 !   19.8   3.0   1.8e-07   0.00079       5     105 .]      63     164 ..      60     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.1
                              CopD 49 alllvllalaalnrf 63
                                       +l +++ +++ +  
  gi|518652635|ref|YP_008142155.1| 23 HVLSAITFVGGSIFI 37
                                      333333333333333 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 1.8e-07
                              CopD   5 rrFsrlalaavavvlvtGvvnallrvg.lagllttayGrlllaKlalllvllalaalnrf...rlvprleaatgagg 77 
                                        rF+ +  + ++++++tG++++ ++v  ++  ++++ G ll    +l ++++++   n      l+ rl   +++g+
  gi|518652635|ref|YP_008142155.1|  63 HRFAFWTNLTLGLLILTGLLMTYRYVLnPSLYFQSTGGELLFSAEILIIAMVIIMYGNNIyhgKLIVRL---NEQGK 136
                                       69999****************999988789999999999999998888888888888888788899999...56777 PP

                              CopD  78 qalrhrlrrsaalelvlalvvlllaaal 105
                                        +  +++r++ ++  ++  v l+++++l
  gi|518652635|ref|YP_008142155.1| 137 LEEVKKIRKVTHIYSMITMVLLIIIVLL 164
                                       7777789999888888888888777654 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.9   2.8e-05      0.12       1     101 [.      25     136 ..      25     137 .. 0.84
   2 ?    1.2   0.2      0.11   4.7e+02      39      56 ..     148     165 ..     139     171 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.8e-05
                           DUF4149   1 lslglllGsqlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevavg...........seklas 66 
                                       ls+ + +G+ +++  +  p  ++  + +   +l + +  +++ + +++++ll+lt +++            +   ++
  gi|518652635|ref|YP_008142155.1|  25 LSAITFVGGSIFIWLILWPASYKMNDDKLRTRLLGFVGHRFAFWTNLTLGLLILTGLLMTyryvlnpslyfQSTGGE 101
                                       688999******************88888888888888888877777777777777766677778****87666666 PP

                           DUF4149  67 eellqlllllvvllltllnafylepritslkeqre 101
                                         +++ +l+++++++   n+ y +  i++l eq++
  gi|518652635|ref|YP_008142155.1| 102 LLFSAEILIIAMVIIMYGNNIYHGKLIVRLNEQGK 136
                                       679999999**********************9986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.11
                           DUF4149  39 plyfglglalsvllllte 56 
                                        +y ++ ++l+++++l+ 
  gi|518652635|ref|YP_008142155.1| 148 HIYSMITMVLLIIIVLLM 165
                                       444444444444444433 PP

>> SHR3_chaperone  ER membrane protein SH3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   8.4   0.00083       3.7      79     148 ..      95     163 ..      15     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00083
                    SHR3_chaperone  79 ykpsednllFdgaSLvLyvvgvvvyitnivkglrtvtegawgevdredslkvlaasntilalvLvGVlvL 148
                                       ++ +  +llF  a +++  + +++y  ni +g  +v  +++g++++ ++++ +     ++ +vL+ ++vL
  gi|518652635|ref|YP_008142155.1|  95 FQSTGGELLFS-AEILIIAMVIIMYGNNIYHGKLIVRLNEQGKLEEVKKIRKVTHIYSMITMVLLIIIVL 163
                                       34445556665.6666777789*******************************99999999999988887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1180.06
//
Query:       gi|518652636|ref|YP_008142156.1|  [L=187]
Description: hypothetical protein FACI_IFERC00001G1275 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-38  130.9   1.7    3.5e-38  130.6   1.7    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.6   1.7     2e-42   3.5e-38      18     149 .]      47     187 .]      40     187 .] 0.95

  Alignments for each domain:
  == domain 1  score: 130.6 bits;  conditional E-value: 2e-42
                                       TTSBHHHHHHHHHSB....TTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEE CS
                      Ribosomal_S7  18 ynselveklinklmk....dGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpve 90 
                                        n +++e+l n+lm+    +Gkk  A+k++++a+dii++ktk++p+++l++A+en++Pr+ev+++++GG++++ +v+
  gi|518652636|ref|YP_008142156.1|  47 RNVNTIERLLNNLMRtekwTGKKYSAYKVMSQAFDIIATKTKQNPVQILVSAIENSAPREEVTRLKYGGIAVPKSVD 123
                                       57789************************************************************************ PP

                                       E-HHHHHHHHHHHHHHHH...STSSSS-HHHHHHHHHHHHHTT-..SHHHHHHHHHHHHHHHTG CS
                      Ribosomal_S7  91 vrpkRrqalAlrwiieaa...rkrkeksmaekLaeElidAaege..gaavkkreethrmAeanr 149
                                       v+p+Rr + Alr+i+++a   +++++ +++++La+E++ Aa+++  + a++k+ee++r+A ++r
  gi|518652636|ref|YP_008142156.1| 124 VSPSRRLDEALRNIARGAtkaSFKHKIHIQDCLANEILLAARNDanSFAISKKEEIERVAASAR 187
                                       ******************76666777789**************999**************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1394.78
//
Query:       gi|518652637|ref|YP_008142157.1|  [L=138]
Description: hypothetical protein FACI_IFERC00001G1276 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-47  159.4   0.6    2.6e-47  159.1   0.6    1.1  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.1   0.6   1.5e-51   2.6e-47       1     113 [.      23     136 ..      23     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 159.1 bits;  conditional E-value: 1.5e-51
                                       --------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE- CS
                   Ribosom_S12_S23   1 rkelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGi 77 
                                       r+ l ++ ksd+leg+pq++G+v+ekv++eak+Pns +Rk+v+++Likng+++ af+pg+ga+n++dEhdev+v+Gi
  gi|518652637|ref|YP_008142157.1|  23 RRMLDLRRKSDPLEGSPQAKGIVIEKVGIEAKQPNSGIRKCVKIQLIKNGRQLSAFAPGDGAINYIDEHDEVMVEGI 99 
                                       56778899********************************************************************* PP

                                       -......BTTSTTEEEEBETS---TSSSTTTTT---- CS
                   Ribosom_S12_S23  78 rrk.gkavkDlpGvrykvvkvagvslkalskykkekp 113
                                       +++ g++++D+pGvr+kv+kv+g+sl++l++++kek 
  gi|518652637|ref|YP_008142157.1| 100 GGRmGRSKGDIPGVRFKVIKVNGISLNELVRGRKEKT 136
                                       9999*******************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       252  (0.0140554); expected 358.6 (0.02)
Passed bias filter:                      211  (0.0117686); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1055.21
//
Query:       gi|518652638|ref|YP_008142158.1|  [L=391]
Description: hypothetical protein FACI_IFERC00001G1277 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-22   79.0   0.0      1e-21   77.1   0.0    2.0  2  MMR_HSR1       50S ribosome-binding GTPase
    2.9e-12   47.2   0.1    5.2e-12   46.3   0.1    1.4  1  MMR_HSR1_C     GTPase of unknown function C-terminal
    1.9e-10   40.7   0.0    3.2e-10   39.9   0.0    1.4  1  TGS            TGS domain
    8.2e-10   38.4   0.0    1.5e-07   31.1   0.0    2.3  2  FeoB_N         Ferrous iron transport protein B
    8.3e-05   22.7   0.4      0.002   18.3   0.0    2.8  3  YchF-GTPase_C  Protein of unknown function (DUF933)
     0.0013   18.9   0.0       0.94    9.5   0.0    2.5  2  Dynamin_N      Dynamin family
  ------ inclusion threshold ------
      0.015   15.3   0.1       0.04   13.9   0.1    1.7  1  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain
       0.13   12.7   0.1       0.44   11.1   0.1    1.8  1  ABC_tran       ABC transporter


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 !   77.1   0.0   4.6e-25     1e-21       1      87 [.       3     127 ..       3     158 .. 0.78
   2 ?   -2.3   0.0         2   4.5e+03      45      72 ..     268     294 ..     257     328 .. 0.57

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 4.6e-25
                                       EEEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE.........................EEEEE CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke.........................ielvD 52 
                                       +++++G+pN+GKStL++a+t   + ++++p+tT+++n g   +k+ +                         +e++D
  gi|518652638|ref|YP_008142158.1|   3 KIGLIGKPNAGKSTLFSAITSIDVDIANYPFTTIKPNVGISFVKD-KcpeneinakcnpregkcldgiryipVEIID 78 
                                       699************************************754332.23455666777777777888888888***** PP

                                       CGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT.............T CS
                          MMR_HSR1  53 tpGliegaseekglgkaflalee.adlillvvdas.............e 87 
                                       +pGliegase+kg+g++fl++++ adli+ ++das             +
  gi|518652638|ref|YP_008142158.1|  79 VPGLIEGASEGKGMGNEFLDNIRdADLIINLFDASgmtdmegnpsesgH 127
                                       ********************8888*********9877666655554331 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2
                                       TEEEEEEECGGCSSHHHHHH..HHHHHHHH CS
                          MMR_HSR1  45 gkeielvDtpGliegaseek..glgkafla 72 
                                         +++++D  G  e a++    ++++++++
  gi|518652638|ref|YP_008142158.1| 268 AIDFTFTDKSG--E-AQKTVlnRIKEKYRN 294
                                       46677777777..2.222222344444443 PP

>> MMR_HSR1_C  GTPase of unknown function C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1   2.3e-15   5.2e-12       3     111 ..     224     320 ..     222     321 .. 0.88

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 2.3e-15
                        MMR_HSR1_C   3 NKaDlpaadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfeikedklkeldekqkkaLekird 79 
                                       NK Dl  +d+ i++lke+++   k++++sA++El ++ka ++g+i+ +    df+ +++      e+qk+ L++i++
  gi|518652638|ref|YP_008142158.1| 224 NKLDL-LTDDSIKALKEREN---KMYLISAEYELLIEKAYNNGYISSDAI--DFTFTDK----SGEAQKTVLNRIKE 290
                                       *****.9***********99...69********************98765..6777666....569*********** PP

                        MMR_HSR1_C  80 lvlkrygsTGVqealnaavfelldlivVYPVe 111
                                          ++ +     ++l++++ + l++ivVYPV 
  gi|518652638|ref|YP_008142158.1| 291 K-YRNGEIMRFYDVLTSII-KSLGYIVVYPVL 320
                                       4.4555778899*******.***********6 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.0   1.4e-13   3.2e-10       4      59 ..     332     387 ..     328     388 .. 0.89

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.4e-13
                                       EETTSSEEEEETTB-HHHHHHHHSTTHHHHEEEEEECS...EEEETTSBB-SSEEEEEE CS
                               TGS   4 ytPdGkvpdlprgatveDfAykIhrslakkfiyAlVnG...qrvgldhvLedgdvveIv 59 
                                       ++Pd+ +  ++ g t+ D AykIh++++k+fi A VnG   +  g d++L ++dv++I+
  gi|518652638|ref|YP_008142158.1| 332 VLPDAYL--MKDGDTALDMAYKIHTDIGKNFIRA-VNGrtkRVIGKDYKLLNNDVIKII 387
                                       4555555..99**********************9.7888*8899**************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 !   31.1   0.0   6.5e-11   1.5e-07       2      41 ..       3      42 ..       2      51 .. 0.89
   2 !    4.9   0.0    0.0074        17      49      91 ..      74     115 ..      63     118 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 6.5e-11
                                      EEEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEE CS
                            FeoB_N  2 tvalvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegk 41
                                      ++ l+G+pn+Gk+tlf a+t  + +++N+p +t++ + g 
  gi|518652638|ref|YP_008142158.1|  3 KIGLIGKPNAGKSTLFSAITSIDVDIANYPFTTIKPNVGI 42
                                      689******************************9987775 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0074
                                       EEEEE----SSSSSSSHHHHHHHHHHHC.TSSSEEEEEEEGGGH CS
                            FeoB_N  49 veivDlPGiYslsayseeekvardflle.eepdvvvnvvdatnl 91 
                                       vei+D+PG   ++  se + + ++fl + +++d+++n+ da+ +
  gi|518652638|ref|YP_008142158.1|  74 VEIIDVPGL--IEGASEGKGMGNEFLDNiRDADLIINLFDASGM 115
                                       79******8..78999**********963679********9865 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       4.7     1e+04      38      54 ..     135     151 ..     133     184 .. 0.63
   2 !   18.3   0.0     9e-07     0.002      14      41 ..     336     363 ..     330     369 .. 0.92
   3 ?    1.2   0.0      0.19   4.3e+02      65      82 ..     370     387 ..     364     389 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 4.7
                     YchF-GTPase_C  38 Firaevikyedlvelgs 54 
                                       F++ e+i++ + +  + 
  gi|518652638|ref|YP_008142158.1| 135 FVNNEIISWMNGKISKD 151
                                       67777777744333333 PP

  == domain 2  score: 18.3 bits;  conditional E-value: 9e-07
                     YchF-GTPase_C  14 aWtikkgttapqaAgviHsDfekgFira 41 
                                       a+ +k+g ta + A +iH+D+ k+Fira
  gi|518652638|ref|YP_008142158.1| 336 AYLMKDGDTALDMAYKIHTDIGKNFIRA 363
                                       677899*********************9 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.19
                     YchF-GTPase_C  65 rlegkdyvvqdgDiilfk 82 
                                       r+ gkdy + ++D+i + 
  gi|518652638|ref|YP_008142158.1| 370 RVIGKDYKLLNNDVIKII 387
                                       677***********9875 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0    0.0026       5.8       1      34 [.       4      37 ..       4      58 .. 0.83
   2 !    9.5   0.0   0.00042      0.94     103     139 ..      74     113 ..      67     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0026
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrr 34
                                      i ++G+ ++GKS++  a++  d+       tT +
  gi|518652638|ref|YP_008142158.1|  4 IGLIGKPNAGKSTLFSAITSIDVDIANYPFTTIK 37
                                      789***************9999876666666655 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00042
                                       EEEEE---B-SSSGTTS...HHHHHHHSTTEEEEEEEETT CS
                         Dynamin_N 103 ltlvDlPGldsvnkrdq...elvkeyikkadiilavtsan 139
                                       ++++D+PGl++ + + +   +     i++ad+i+ + +a+
  gi|518652638|ref|YP_008142158.1|  74 VEIIDVPGLIEGASEGKgmgNEFLDNIRDADLIINLFDAS 113
                                       89***********999977777777788999999999886 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.8e-05      0.04      53      95 ..     213     257 ..     168     263 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.8e-05
                      MMR_HSR1_Xtn  53 rvYi.pclyvlNKiDlisleeldelarep.nsvviSaekelnlde 95 
                                        +Y+ p++ + NK Dl++++++++l++++ ++  iSae el +++
  gi|518652638|ref|YP_008142158.1| 213 LKYVkPVFSIGNKLDLLTDDSIKALKEREnKMYLISAEYELLIEK 257
                                       46761456677***************97538888****9998886 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00019      0.44      13      34 ..       3      24 ..       2      31 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00019
                                      EEEEEESTTSSHHHHHHHHTTS CS
                                      xxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 13 kvaivGenGaGKStLlkllagl 34
                                      k++++G+  aGKStL+++++  
  gi|518652638|ref|YP_008142158.1|  3 KIGLIGKPNAGKSTLFSAITSI 24
                                      689****************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2753.40
//
Query:       gi|518652639|ref|YP_008142159.1|  [L=146]
Description: hypothetical protein FACI_IFERC00001G1278 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.5e-39  135.1   5.2    1.7e-39  134.9   5.2    1.0  1  UPF0179    Uncharacterised protein family (UPF0179)
  ------ inclusion threshold ------
      0.038   13.0   0.1      0.052   12.6   0.1    1.2  1  RE_HindVP  HindVP restriction endonuclease


Domain annotation for each model (and alignments):
>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9   5.2   1.9e-43   1.7e-39       1     139 [.       6     145 ..       6     146 .] 0.97

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 1.9e-43
                           UPF0179   1 kitLigkklAkeGteFiylgeae.eCekCklkkvClnLekgrkYrivevrekteheCavheeg.vvaveveeapiea 75 
                                       ki+Lig +lAk++  F++ g+++ +C++Ck+++vC+nLe+g++Yri+ev+e+  ++C++++++ v++++vee++ + 
  gi|518652639|ref|YP_008142159.1|   6 KISLIGVNLAKKDLVFTFRGPLAgKCDECKIRNVCFNLEPGKSYRIKEVKEQ-INPCFIYDTNkVSTIDVEEVENTY 81 
                                       69*******************8769***************************.*********99************* PP

                           UPF0179  76 lie.skkavegskitleseeCdevecesyelcepeglkegekvkivevlgeieeckkgrslkkve 139
                                       +++  k+++egs+++l+s++Cd+++c+++e+c+  +lk ++k+++++++g+i+ c+kg+++++ve
  gi|518652639|ref|YP_008142159.1|  82 NVQnGKRLMEGSSMELRSMKCDYLTCPNIEKCNLLNLKGNKKIVVKKIIGKIS-CPKGYDMREVE 145
                                       **9789***********************************************.********997 PP

>> RE_HindVP  HindVP restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   5.8e-06     0.052     249     305 ..      63     117 ..      60     128 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 5.8e-06
                         RE_HindVP 249 LydfakkgkinvkkiideltyntknDKafavsGkitrkymkseeltkprikkeeikn 305
                                       +yd  k + i+v+++    tyn +n K      ++  + mk++ lt p i+k ++ n
  gi|518652639|ref|YP_008142159.1|  63 IYDTNKVSTIDVEEVE--NTYNVQNGKRLMEGSSMELRSMKCDYLTCPNIEKCNLLN 117
                                       5778888888888885..58*********9999999****************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1162.10
//
Query:       gi|518652640|ref|YP_008142160.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-21   76.3   0.0    3.8e-21   75.5   0.0    1.4  1  rve          Integrase core domain
    4.1e-06   26.5   1.1    0.00019   21.1   1.1    2.6  1  rve_3        Integrase core domain
     0.0011   19.6   0.1     0.0032   18.1   0.1    1.9  1  HTH_32       Homeodomain-like domain
     0.0072   16.1   0.2      0.019   14.8   0.2    1.7  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.072   13.6   4.3        0.2   12.1   4.2    1.8  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.1e-24   3.8e-21       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ +  e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518652640|ref|YP_008142160.1| 125 KHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYGEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l + +i++ + r+ +p++nGk Er + t+k+
  gi|518652640|ref|YP_008142160.1| 195 FSNgkngipgdhnKFQEYLDNSNIKHILGRVKHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   5.3e-08   0.00019       2      63 ..     217     268 ..     216     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518652640|ref|YP_008142160.1| 217 NIKHILGRVKHPETNGKLERLNYTIKRLRPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       589999********************965554444..........799************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0032       3      73 .]      36     101 ..      33     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+    + +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518652640|ref|YP_008142160.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDIEIVKKIRYEYPMSGPERIRKYL-KRKGIIIAKNNIYRIL 101
                                       556778888876666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.3e-06     0.019      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518652640|ref|YP_008142160.1| 11 IIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.2   5.7e-05       0.2      40     111 ..       3      75 ..       1     127 [. 0.79
   2 ?   -1.6   0.0      0.93   3.3e+03      44     126 ..     217     243 ..     167     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vk+++ + ++
  gi|518652640|ref|YP_008142160.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNGEyTIGKRKHRELNSKDIEIVKKIRYEYPM 75 
                                       8999****************************88888888776663346678899999999999999874444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                       Terminase_2  44 kIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseevdkeilrevkegke....gvkvklkDk 116
                                       +Ik                                                                 +++++++ k
  gi|518652640|ref|YP_008142160.1| 217 NIK------------------------------------------------------------HilgrVKHPETNGK 233
                                       222............................................................13333455555555 PP

                       Terminase_2 117 lkAlellakh 126
                                       l+ l+ ++k+
  gi|518652640|ref|YP_008142160.1| 234 LERLNYTIKR 243
                                       5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2139.08
//
Query:       gi|518652641|ref|YP_008142161.1|  [L=350]
Description: hypothetical protein FACI_IFERC00001G1280 [Ferroplasma acidarmanus fer1]
Scores for complete 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-63  212.8   4.5      8e-63  212.5   4.5    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    1.8e-21   76.4   4.2    2.6e-20   72.6   4.1    1.9  2  Fe-ADH        Iron-containing alcohol dehydrogenase
    0.00011   21.5   2.3    0.00023   20.4   0.5    2.2  2  DHQ_synthase  3-dehydroquinate synthase
  ------ inclusion threshold ------
      0.084   12.9   0.0        4.4    7.5   0.0    3.2  3  Sulf_coat_C   Sulfolobus virus coat protein C terminal


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 !  212.5   4.5   1.8e-66     8e-63       2     250 .]      17     272 ..      16     272 .. 0.86

  Alignments for each domain:
  == domain 1  score: 212.5 bits;  conditional E-value: 1.8e-66
                          Fe-ADH_2   2 igegaleklgellkelelk.kvllvadentkkaagekveeslkeagikvevveeveeeadleeveklvealreketd 77 
                                       ig++a+++++ + +++  + ++l++++++t+++age+v ++l+  +    v+  ++++a+++++++  e+++  ++ 
  gi|518652641|ref|YP_008142161.1|  17 IGHNAIDSMRIVAEKNLKSgTILVITGQKTYRIAGEAVVNKLEGLK--HYVL--FSGNATMDAIKSAREEIADIKVG 89 
                                       899******99999886545**********************7764..3322..679***************9**** PP

                          Fe-ADH_2  78 lvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfaspgaslvvdgkkrtvakaaaPlaviaDldvlaeAPrrll 154
                                       lv++vGgG+ iD++k +++ lnvp++s+pTa+S+DG+asp as++  ++  ++ +aa+P+a++aD++++a+AP r+ 
  gi|518652641|ref|YP_008142161.1|  90 LVIGVGGGSKIDMGKKIAFDLNVPFISFPTAPSHDGIASPRASIYDGKSFLSI-EAAMPTAIVADTEIMAKAPYRFA 165
                                       *********************************************99999998.9********************** PP

                          Fe-ADH_2 155 asGvGDllgkytaladwklan........evseplaklsaamvqeaaeklve.dkke.tealeel.lealalsgigi 220
                                       a+G  D+++++ta++dwk+an         +++ +++ s +++ e+a+++    +++   +++++ +++ a++++g+
  gi|518652641|ref|YP_008142161.1| 166 AAGASDVIANITAVMDWKMANrikgeifsTTAAVISEYSSRELIENANMIQPgLEASiWMITKQIlASGTAMAIAGS 242
                                       *********************6666665555667777777777777777765212232333344404556******* PP

                          Fe-ADH_2 221 srpaSGsEHliSHaldmlalkqalHGeqVG 250
                                       srpaSGsEHl++Hal+ l + +a+HGeqV+
  gi|518652641|ref|YP_008142161.1| 243 SRPASGSEHLFAHALEILGSGNAMHGEQVA 272
                                       *******************9********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 !   72.6   4.1   5.8e-24   2.6e-20       1     264 [.      12     259 ..      12     281 .. 0.83
   2 ?    1.8   0.0     0.019        84     316     342 ..     289     316 ..     285     332 .. 0.80

  Alignments for each domain:
  == domain 1  score: 72.6 bits;  conditional E-value: 5.8e-24
                                       -SEEEEETTGGGGHHHHHTTT.-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTT CS
                            Fe-ADH   1 Ptrivfgkgaleelgellkkl.gakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaal 76 
                                       P+ +++g +a++++   ++k  +   +l++t+++++    + + v+++l  +g+++ v   +++n t + ++ a + 
  gi|518652641|ref|YP_008142161.1|  12 PNDVYIGHNAIDSMRIVAEKNlKSGTILVITGQKTY--RIAGEAVVNKL--EGLKHYV--LFSGNATMDAIKSAREE 82 
                                       8899*******999888755425559********88..4478999****..6665553..4679************* PP

                                       S-TT.--EEEEEESHHHHHHHHHHHHHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEE CS
                            Fe-ADH  77 areegadvviavGGGsviDtAKaialllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegek 153
                                       + + ++ +vi+vGGGs iD++K ia+ l+                  +p+i  PT ++ +  ++p a i+d +    
  gi|518652641|ref|YP_008142161.1|  83 IADIKVGLVIGVGGGSKIDMGKKIAFDLN------------------VPFISFPTAPSHDGIASPRASIYDGK--SF 139
                                       *****************************..................***********************333..34 PP

                                       EEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHT---TTSSB--HHHHHHHHHHHHHHHHHHHH CS
                            Fe-ADH 154 lsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvskkanplsdalaleairliaknleravadgedl 230
                                       lsi     +P++++ D+e+++++P r++aa++ D++a     +  k+an +   +    +  i ++  r + + +++
  gi|518652641|ref|YP_008142161.1| 140 LSIE--AAMPTAIVADTEIMAKAPYRFAAAGASDVIANITAVMDWKMANRIKGEIFSTTAAVISEYSSRELIENANM 214
                                       4555..99******************************9998888********988888888888877666665565 PP

                                       .....HHHHHHHHHHHH.HHHHHHSS---.....HHHHHHHHHHC CS
                            Fe-ADH 231 .....eareqmllastl.aglafsnaglg.....avHalahalga 264
                                            ea   m+  ++l +g a++ ag +       H +ahal  
  gi|518652641|ref|YP_008142161.1| 215 iqpglEASIWMITKQILaSGTAMAIAGSSrpasgSEHLFAHALEI 259
                                       677889999999999998888888888777677777777777654 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.019
                                       HHHHHHHTT---SHHHHT-TT-.HHHHH CS
                            Fe-ADH 316 lrellkelglptsLselgvdee.dldkl 342
                                       l + +k++g+ t+ +++g+++e ++++l
  gi|518652641|ref|YP_008142161.1| 289 LYDTYKKIGVSTKAKDYGIPDEiAIKAL 316
                                       56789*************9996555443 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.15   6.9e+02      32      50 ..      89     107 ..      70     120 .. 0.74
   2 !   20.4   0.5   5.1e-08   0.00023      94     215 ..     146     282 ..     143     317 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.15
                                       -EEEEEESHHHHHHHHHHH CS
                      DHQ_synthase  32 sllialGGGvvgDlaGfvA 50 
                                        l+i +GGG   D+   +A
  gi|518652641|ref|YP_008142161.1|  89 GLVIGVGGGSKIDMGKKIA 107
                                       5799******999976655 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 5.1e-08
                                       --SEEEEEGGGGGGS-HHHHHHHHHHHH.HHHHHT-HHHHHHHHHHHHHHHC...........TTTHHHHHHHHHHH CS
                      DHQ_synthase  94 qPkavlidlevLktLperelraGlaEvi.Kyalikdeelfelleenaeallk...........eeeeealeeliars 158
                                       +P+a+++d+e+++  p r  +aG ++vi  +++++d ++ ++++ +  ++++            e+++ ++  +++s
  gi|518652641|ref|YP_008142161.1| 146 MPTAIVADTEIMAKAPYRFAAAGASDVIaNITAVMDWKMANRIKGEIFSTTAaviseyssrelIENANMIQPGLEAS 222
                                       79************************994578899****99999999888778888888655522333333333444 PP

                                       HHH.HHHHHHHCCTT...TTGGGGGGTTHHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHH CS
                      DHQ_synthase 159 iev.kaevveeDeke...kglralLnlGHtigHaiEallgyekllHGeaVaiGmvlaaels 215
                                       i +  ++++++        + r +    H ++Ha+E l +  + +HGe Va+G ++ ++l 
  gi|518652641|ref|YP_008142161.1| 223 IWMiTKQILASGTAMaiaGSSRPASGSEHLFAHALEILGSG-NAMHGEQVAMGSLVSMYLH 282
                                       4330223333332211225667778888********88766.***********99988775 PP

>> Sulf_coat_C  Sulfolobus virus coat protein C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0   0.00097       4.4      34      56 ..      50      72 ..      31      83 .. 0.84
   2 ?    0.2   0.0      0.18   7.9e+02       6      21 ..     122     137 ..     119     147 .. 0.81
   3 ?   -0.0   0.0      0.21   9.3e+02      25      38 ..     253     266 ..     236     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00097
                       Sulf_coat_C 34 sGpalvnminGlksyyisafnan 56
                                      +G a+vn ++Glk y + + na 
  gi|518652641|ref|YP_008142161.1| 50 AGEAVVNKLEGLKHYVLFSGNAT 72
                                      699************99888876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.18
                       Sulf_coat_C   6 sqyGitGpnraiyqGf 21 
                                       s  Gi+ p  +iy+G 
  gi|518652641|ref|YP_008142161.1| 122 SHDGIASPRASIYDGK 137
                                       6679*********995 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.21
                       Sulf_coat_C  25 iaralnriGsGpal 38 
                                        a al+ +GsG a+
  gi|518652641|ref|YP_008142161.1| 253 FAHALEILGSGNAM 266
                                       6899*******997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2258.67
//
Query:       gi|518652642|ref|YP_008142162.1|  [L=142]
Description: hypothetical protein FACI_IFERC00001G1281 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    0.00076   18.6   1.0     0.0008   18.5   0.4    1.3  1  PalH       PalH/RIM21
  ------ inclusion threshold ------
      0.017   14.9   0.0      0.028   14.2   0.0    1.4  1  Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
      0.027   15.0   2.6      0.036   14.5   2.6    1.3  1  MerC       MerC mercury resistance protein
       0.41   10.3   4.9        1.2    8.8   4.4    2.0  1  DUF4131    Domain of unknown function (DUF4131)
        7.9    7.0   8.2        2.9    8.4   1.6    2.7  3  DUF202     Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> PalH  PalH/RIM21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.4   2.2e-07    0.0008     138     235 ..      28     132 ..      24     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.2e-07
                              PalH 138 selekeivsstelkvlelisnlllnlaqvqivirlfs....rqkekriiilvGlaliildtilsalllfsk....kf 206
                                       ++l k + s+ ++ ++  i+ ++l++  v++v  l       +k+k + ++++ ++i++ +++  +l++ +    ++
  gi|518652642|ref|YP_008142162.1|  28 NSLSKYFQSGYYYGIIPRIFPIFLIFGDVFVVAGLLFplrnFNKHKDYLVTAAAIFIVAGVLFALVLHV-SpldgSQ 103
                                       567788888999999999999999999999998754447765578888888999999999999999999.3366799 PP

                              PalH 207 ldalpalsylfelalvtlyaalviyYlis 235
                                          l+a + ++e ++ + + ++++yY+  
  gi|518652642|ref|YP_008142162.1| 104 DNGLKAGYLIVEGVILLFFTLIISYYISA 132
                                       9*************************975 PP

>> Claudin_2  PMP-22/EMP/MP20/Claudin tight junction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.8e-06     0.028      91     142 ..      46      96 ..      26     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.8e-06
                         Claudin_2  91 fvqvlliLslvlivlavvlgllallkqsvlllkaagilfllagvlgllavvv 142
                                        + ++li++ v++v ++++ l  + k +++l++aa  +f++agvl++l++ v
  gi|518652642|ref|YP_008142162.1|  46 IFPIFLIFGDVFVVAGLLFPLRNFNKHKDYLVTAA-AIFIVAGVLFALVLHV 96 
                                       456799*************************9999.67999*****998765 PP

>> MerC  MerC mercury resistance protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.6     1e-05     0.036      17     111 ..      17     123 ..       7     129 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1e-05
                              MerC  17 llPvllallpllglsf.lasel.......lhqvllil...vvaigllalvvgyrrhrktsvlvlgalGllillvalf 82 
                                       l+ ++++llp  +ls  ++s +       +  ++li+   +v+ gll  ++++ +h++++v++ +++ ++ +l+al+
  gi|518652642|ref|YP_008142162.1|  17 LTYLFIFLLPGNSLSKyFQSGYyygiiprIFPIFLIFgdvFVVAGLLFPLRNFNKHKDYLVTAAAIFIVAGVLFALV 93 
                                       4667778888888888788888888877644444444666899999999**************************** PP

                              MerC  83 lgteaeetl....lfgslwqvltvlGaalLaia 111
                                       l+    + l    + g  + +l+v G++lL+ +
  gi|518652642|ref|YP_008142162.1|  94 LH---VSPLdgsqDNGLKAGYLIVEGVILLFFT 123
                                       **...3444555566678889999999998765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   4.4   0.00034       1.2      13      75 ..      56     118 ..       3     120 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00034
                           DUF4131  13 llllllllllllrrrprrrvllllllllllallgfalrapqpnandlsqlles.gqeviveGvv 75 
                                       +++++ ll+ l ++++++ +l+++++++++a++ fal  +  + +  ++   +   + iveGv+
  gi|518652642|ref|YP_008142162.1|  56 VFVVAGLLFPLRNFNKHKDYLVTAAAIFIVAGVLFALVLHVSPLDGSQDNG-LkAGYLIVEGVI 118
                                       4444444444444499******99999999999999877766664444443.448899999988 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.11   3.9e+02      41      56 ..       8      23 ..       2      38 .. 0.70
   2 ?    8.4   1.6   0.00081       2.9      30      58 ..      66      94 ..      47      99 .. 0.67
   3 ?   -1.0   0.1      0.72   2.6e+03      50      60 ..     116     126 ..      99     132 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.11
                            DUF202 41 kilglilivlgiltll 56
                                      + +gl+++vl+ l+++
  gi|518652642|ref|YP_008142162.1|  8 FSAGLAIVVLTYLFIF 23
                                      5567777777766665 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00081
                            DUF202 30 ffltgepsalgkilglilivlgiltllvg 58
                                      + + + ++++ + +++i+iv+g+l++lv 
  gi|518652642|ref|YP_008142162.1| 66 LRNFNKHKDYLVTAAAIFIVAGVLFALVL 94
                                      22256777777999***********9986 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.72
                            DUF202  50 lgiltllvglv 60 
                                         il++++ ++
  gi|518652642|ref|YP_008142162.1| 116 GVILLFFTLII 126
                                       33333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 825.17
//
Query:       gi|518652643|ref|YP_008142163.1|  [L=280]
Description: hypothetical protein FACI_IFERC00001G1282 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-45  154.8   0.1    2.6e-45  154.3   0.1    1.2  1  Phage_integrase  Phage integrase family
    9.1e-10   38.9   5.2    2.9e-09   37.3   4.0    2.1  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0024   18.0   0.1     0.0041   17.2   0.1    1.3  1  Integrase_1      Integrase
     0.0029   17.9   0.8     0.0069   16.7   0.8    1.6  1  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.044   12.7   0.1       0.08   11.9   0.1    1.4  1  DUF3435          Protein of unknown function (DUF3435)
        3.3    8.1  11.2       0.97    9.8   6.2    2.4  2  Phage_int_SAM_5  Phage integrase SAM-like domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.1   8.9e-49   2.6e-45      10     171 ..     110     266 ..     102     267 .. 0.95

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 8.9e-49
                                       HHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHH CS
                   Phage_integrase  10 rllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellsk 86 
                                        l++ +++   ird +++ + + tG+R+sEl +L+++d+d+++++i++  + gKg k+r+v +++   e +k ++++
  gi|518652643|ref|YP_008142163.1| 110 VLINGAKS---IRDIAVISVFLYTGIRVSELTNLQIGDVDFDENIIYI--HAGKGDKDRIVVMPDICREHIKSYMKE 181
                                       55555555...*************************************..*************************** PP

                                       HCHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHH CS
                   Phage_integrase  87 aleeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssistt 163
                                       + + ++++++lf+s ++ +  ++tv++++kr++++agi+k++tpH lRh+fat  l++g d+r++q++lGHss++tt
  gi|518652643|ref|YP_008142163.1| 182 RIRIKSSNNYLFISNKKTKFDTSTVERMVKRVAKNAGITKNVTPHVLRHTFATSILRNGGDIRFIQQILGHSSLATT 258
                                       ***************************************************************************** PP

                                       HHHHCCCH CS
                   Phage_integrase 164 qiYthvak 171
                                       qiYth ++
  gi|518652643|ref|YP_008142163.1| 259 QIYTHIDD 266
                                       *****986 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   4.0   9.6e-13   2.9e-09       2      76 ..       7      80 ..       7      85 .. 0.97
   2 ?   -0.5   0.0       0.6   1.8e+03      41      56 ..     170     184 ..     167     196 .. 0.76

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 9.6e-13
                   Phage_int_SAM_4  2 lerfrealrlaglserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffyk 76
                                      l++f +++  +++s+ Tik Y++ i  fl +++ k  ++++ +d+e Y n  ++e+++s+++q  a++al+ +yk
  gi|518652643|ref|YP_008142163.1|  7 LKSFERFMITERKSYYTIKEYKFLISGFLSYCN-KDLSSIDFDDVENYKNFIVTEKQYSKASQYLAMKALRLYYK 80
                                      57899****************************.****************************************8 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.6
                   Phage_int_SAM_4  41 ltkedieaYlnyLane 56 
                                       + +e+i++Y+   + +
  gi|518652643|ref|YP_008142163.1| 170 ICREHIKSYMKERI-R 184
                                       56899999999887.3 PP

>> Integrase_1  Integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.4e-06    0.0041      71     148 ..     151     234 ..     140     235 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.4e-06
                       Integrase_1  71 lrvvfGTKGgrpRevtile..realksavalaikvaeernGkLidkpdlslipdryreilrr....lgltgessphs 141
                                       +  +   KG ++R v + +  re +ks +++ i++ +++n   i +++ +  + + + +++r    +g+t ++ ph 
  gi|518652643|ref|YP_008142163.1| 151 IIYIHAGKGDKDRIVVMPDicREHIKSYMKERIRIKSSNNYLFISNKKTKFDTSTVERMVKRvaknAGITKNVTPHV 227
                                       5556667*************************************99988887775555555544448********** PP

                       Integrase_1 142 lRyayaq 148
                                       lR+++a 
  gi|518652643|ref|YP_008142163.1| 228 LRHTFAT 234
                                       *****96 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.8   2.3e-06    0.0069       1      80 [.       7      82 ..       7      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 2.3e-06
                                      HHHHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS-----.-----HHHHHHHHHHHHH CS
                   Phage_int_SAM_1  1 leqfleyLikerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeg.lsatslarrlsalrsFfq 78
                                      l++f++  i+er  s  T+ +Y+  ++ fl + ++    +l +++ +dv ++ +  + e+ +s +s  +++ alr +++
  gi|518652643|ref|YP_008142163.1|  7 LKSFERFMITERK-SYYTIKEYKFLISGFLSYCNK----DLSSIDFDDVENYKNFIVTEKqYSKASQYLAMKALRLYYK 80
                                      689**********.*********************....8888888888555555544444****************** PP

                                      HH CS
                   Phage_int_SAM_1 79 fl 80
                                      f+
  gi|518652643|ref|YP_008142163.1| 81 FK 82
                                      96 PP

>> DUF3435  Protein of unknown function (DUF3435)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.7e-05      0.08     167     229 ..     194     256 ..     183     277 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.7e-05
                           DUF3435 167 il.kdealtastlnsrlkrlgeiagfeepitpYklRrgaakal.neSgevseaqrnlilqHassr 229
                                       i+ k+++ ++st++  +kr++++ag+ + +tp+ lR   a  +  + g++     ++il+H+s +
  gi|518652643|ref|YP_008142163.1| 194 ISnKKTKFDTSTVERMVKRVAKNAGITKNVTPHVLRHTFATSIlRNGGDIR--FIQQILGHSSLA 256
                                       565788999***************************987765413333333..334567776655 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 ?    9.8   6.2   0.00032      0.97      16      81 ..      18      80 ..       7      86 .. 0.89
   2 ?   -0.2   0.2      0.43   1.3e+03       6      26 ..     171     192 ..     166     215 .. 0.53

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00032
                                      TS-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHH CS
                   Phage_int_SAM_5 16 kgskgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavln 81
                                      ++s+ t++ yk ++  +  ++   +  ++ id + +e++++++ ++k++s+++++  +k l+ +++
  gi|518652643|ref|YP_008142163.1| 18 RKSYYTIKEYKFLISGFLSYC---NKDLSSIDFDDVENYKNFIVTEKQYSKASQYLAMKALRLYYK 80
                                      34689999*************...8899***************9*****************98875 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.43
                                       HHHHTHHHHTTS.-HHHHHHHH CS
                   Phage_int_SAM_5   6 fkeyiekkkkkg.skgtlrnyk 26 
                                       ++e+i+ + k++ + ++ +ny 
  gi|518652643|ref|YP_008142163.1| 171 CREHIKSYMKERiRIKSSNNYL 192
                                       5555555554443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.50
# Mc/sec: 1691.07
//
Query:       gi|518652644|ref|YP_008142164.1|  [L=352]
Description: hypothetical protein FACI_IFERC00001G1283 [Ferroplasma acidarmanus fer1]
Scores for complete 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-52  176.5   0.0    6.5e-52  176.1   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.1   0.0   3.6e-56   6.5e-52       9     251 ..      48     298 ..      40     303 .. 0.88

  Alignments for each domain:
  == domain 1  score: 176.1 bits;  conditional E-value: 3.6e-56
                                       HHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHC........ CS
                   polyprenyl_synt   9 eylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrl........ 77 
                                       + ++ +gGKrlRp+l+++ +++++ ++   e+  ++   +el +++ L+hDDimD+s++RRG+p+ h++        
  gi|518652644|ref|YP_008142164.1|  48 DFTL-NGGKRLRPILMIMGYNMFSGQD---ERIIKASISIELAQSFLLIHDDIMDQSDMRRGKPSFHKAvegsldgn 120
                                       4555.9******************555...899**********************************6666666666 PP

                                       ....TCHHHHHHHHHHHHHHHHHHHHHHH..STT.HHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHH CS
                   polyprenyl_synt  78 ....vGnklAindgdfllarafellaklf..eks.lellelfsevllqtveGqlldleeekdddlskfsleeyleiv 147
                                           + ++lAi +gd++ + + e l +     ++ l++   fs+++ +t +Gq+ld++++  ++l   s+e+  + +
  gi|518652644|ref|YP_008142164.1| 121 datrIAENLAISAGDLIDTFSHEALLRSGfeLENlLDADFEFSRIIEDTGKGQILDIYSSI-ENLY--SEERLTKLH 194
                                       666788899*************9998776673445999999****************7774.5555..7******** PP

                                       HHHTH.HHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-HHHHSS-TSHHHHTT---HHHHHH CS
                   polyprenyl_synt 148 kyKTa.ylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlfgdpevlgKpagtDiqegkctlpilka 223
                                         KTa y++  p+ ++a+l+g  ++ ++++kd+g++ G+aFQ+ DD+l +fg +e++gKp+  D++egk tl+i+ka
  gi|518652644|ref|YP_008142164.1| 195 FLKTArYTVQGPLLMGAYLSGN-KKYIQEIKDFGKYAGIAFQLYDDMLGIFGVEEKTGKPVKGDVNEGKKTLLIIKA 270
                                       *********************5.6778************************************************** PP

                                       HHCT-HHHHHHHHHHTTSSHHHHHHHHH CS
                   polyprenyl_synt 224 lelaspeqrkvlkeilgkkaekeedvke 251
                                       +e++ +e+r+ ++++l+    +++d ++
  gi|518652644|ref|YP_008142164.1| 271 YENSGKEDREFIESCLKCGDVSDSDFNR 298
                                       **************99965556666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2265.27
//
Query:       gi|518652645|ref|YP_008142165.1|  [L=228]
Description: hypothetical protein FACI_IFERC00001G1284 [Ferroplasma acidarmanus fer1]
Scores for complete 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-35  115.9  13.1    8.8e-07   28.6   0.5    6.1  6  TPR_2       Tetratricopeptide repeat
      6e-32  108.2  20.6    1.2e-08   34.4   1.1    6.2  6  TPR_1       Tetratricopeptide repeat
      9e-23   78.5  17.6    2.5e-07   30.4   0.3    6.2  6  TPR_8       Tetratricopeptide repeat
    1.3e-20   72.8  20.8    3.5e-08   33.0   0.1    6.4  6  TPR_11      TPR repeat
    1.7e-16   60.1   0.1    1.5e-05   25.1   0.0    4.9  5  TPR_9       Tetratricopeptide repeat
    3.8e-16   59.4   0.2    1.4e-08   35.2   0.1    4.1  4  TPR_16      Tetratricopeptide repeat
    6.2e-15   55.3   3.2    0.00012   22.3   0.1    4.8  4  TPR_12      Tetratricopeptide repeat
    3.2e-11   42.7   7.4       0.24   11.3   0.0    6.1  6  TPR_10      Tetratricopeptide repeat
    1.5e-10   40.4   4.0        0.1   12.6   0.0    6.4  7  TPR_7       Tetratricopeptide repeat
    2.9e-10   39.4   0.5       0.25   10.8   0.0    5.4  5  SHNi-TPR    SHNi-TPR
    6.9e-10   38.9   0.4       0.72   10.8   0.0    5.4  6  TPR_14      Tetratricopeptide repeat
    4.1e-08   33.3   7.2        1.5    9.6   0.1    6.1  6  TPR_6       Tetratricopeptide repeat
    1.1e-07   32.3   6.4      0.006   17.1   0.1    3.6  3  TPR_19      Tetratricopeptide repeat
    1.3e-07   31.5  16.8       0.19   12.2   0.2    6.5  6  TPR_17      Tetratricopeptide repeat
    1.9e-07   30.4   7.2     0.0006   18.9   0.1    3.1  3  NARP1       NMDA receptor-regulated protein 1
    6.9e-07   29.4   5.4     0.0089   16.2   0.1    3.2  3  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    7.7e-07   28.6   0.1      0.054   12.7   0.0    3.2  3  TPR_15      Tetratricopeptide repeat
    1.6e-06   28.1   6.7    0.00021   21.3   0.2    4.0  4  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
    6.8e-05   22.9   0.2          3    8.0   0.0    3.8  3  ANAPC5      Anaphase-promoting complex subunit 5
     0.0004   20.1   4.4       0.17   11.6   0.3    2.8  3  TPR_21      Tetratricopeptide repeat-like domain
      0.004   17.5   0.8        4.3    7.7   0.0    3.4  4  TPR_20      Tetratricopeptide repeat
     0.0083   15.7   0.7       0.51    9.9   0.9    2.1  2  Cas_DxTHG   CRISPR-associated (Cas) DxTHG family
  ------ inclusion threshold ------
       0.04   13.6   4.7        4.7    6.9   0.4    3.4  3  RPN7        26S proteasome subunit RPN7
       0.24   11.5   7.7        4.1    7.5   0.2    3.7  4  DUF357      Protein of unknown function (DUF357)


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 !   17.1   0.0   5.4e-06     0.004       2      32 ..      14      44 ..      13      46 .. 0.90
   2 !   21.1   0.2   2.9e-07   0.00021       1      31 [.      47      77 ..      47      79 .. 0.94
   3 !   17.8   0.0   3.2e-06    0.0024       2      31 ..      82     111 ..      81     113 .. 0.93
   4 !   28.6   0.5   1.2e-09   8.8e-07       1      32 [.     115     146 ..     115     148 .. 0.93
   5 !   15.1   0.1   2.5e-05     0.019       3      33 ..     151     181 ..     149     182 .. 0.93
   6 !   20.6   0.3   4.1e-07   0.00031       1      34 []     182     215 ..     182     215 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 5.4e-06
                             TPR_2  2 ealynlGlayyklgdyeeAleafekAleldP 32
                                      + ++++G +y++  +y +A++ f kA+ l  
  gi|518652645|ref|YP_008142165.1| 14 DDYNERGISYFNVTQYPDAVKEFTKAINLIK 44
                                      6799***********************9965 PP

  == domain 2  score: 21.1 bits;  conditional E-value: 2.9e-07
                             TPR_2  1 aealynlGlayyklgdyeeAleafekAleld 31
                                      ++++ n++layy +  y+eA+++++ A++l 
  gi|518652645|ref|YP_008142165.1| 47 PDYYINRALAYYSMHMYNEAIKDCKSAIALS 77
                                      579*************************985 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.2e-06
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleld 31 
                                       ++++ lG +y  ++++++Al  f++A++++
  gi|518652645|ref|YP_008142165.1|  82 DYHNTLGSIYDDMNRFDDALGEFDAAIKIE 111
                                       689*************************97 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 1.2e-09
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldP 32 
                                       ++++yn+G++y+++gd + Ale+++kA+ l+ 
  gi|518652645|ref|YP_008142165.1| 115 PDYYYNRGNVYWRKGDKDLALEDYNKAVYLNS 146
                                       589*************************9985 PP

  == domain 5  score: 15.1 bits;  conditional E-value: 2.5e-05
                             TPR_2   3 alynlGlayyklgdyeeAleafekAleldPn 33 
                                        ly + ++y ++ +ye+Al ++e +++l+ n
  gi|518652645|ref|YP_008142165.1| 151 FLYKRSQIYTEMEKYEDALGDLEDCIKLARN 181
                                       69**************************976 PP

  == domain 6  score: 20.6 bits;  conditional E-value: 4.1e-07
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       +e++   +++y+k+gd ++Al+a + Al+  P+n
  gi|518652645|ref|YP_008142165.1| 182 PEYYKDEANIYIKMGDKAKALQAVDNALKNSPEN 215
                                       689999*************************997 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00072      0.53       2      30 ..      14      42 ..      13      46 .. 0.90
   2 !   29.2   0.6     7e-10   5.3e-07       2      30 ..      48      76 ..      47      79 .. 0.93
   3 !   14.8   0.0   2.5e-05     0.019       3      31 ..      83     111 ..      81     113 .. 0.91
   4 !   34.4   1.1   1.7e-11   1.2e-08       2      32 ..     116     146 ..     115     148 .. 0.94
   5 !   12.3   0.2   0.00015      0.11       9      33 ..     157     181 ..     151     182 .. 0.92
   6 !   17.8   0.6   2.7e-06     0.002       2      34 .]     183     215 ..     182     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00072
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALel 30
                                      + ++ +G  yf+  +y +A++ + kA+ l
  gi|518652645|ref|YP_008142165.1| 14 DDYNERGISYFNVTQYPDAVKEFTKAINL 42
                                      569***********************976 PP

  == domain 2  score: 29.2 bits;  conditional E-value: 7e-10
                                      HHHHHHHHHHHHTT-HHHHHHHHHHHHHH CS
                             TPR_1  2 kalynlGnayfklgkydeAleyyekALel 30
                                      + + n+++ay+++ +y+eA+++++ A+ l
  gi|518652645|ref|YP_008142165.1| 48 DYYINRALAYYSMHMYNEAIKDCKSAIAL 76
                                      789************************98 PP

  == domain 3  score: 14.8 bits;  conditional E-value: 2.5e-05
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHS CS
                             TPR_1   3 alynlGnayfklgkydeAleyyekALeln 31 
                                        ++ lG +y  ++++d+Al  ++ A++++
  gi|518652645|ref|YP_008142165.1|  83 YHNTLGSIYDDMNRFDDALGEFDAAIKIE 111
                                       6899*******************999986 PP

  == domain 4  score: 34.4 bits;  conditional E-value: 1.7e-11
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnP 32 
                                       + +yn+Gn+y ++g+ d Ale+y+kA+ ln 
  gi|518652645|ref|YP_008142165.1| 116 DYYYNRGNVYWRKGDKDLALEDYNKAVYLNS 146
                                       78**************************995 PP

  == domain 5  score: 12.3 bits;  conditional E-value: 0.00015
                                       HHHHHTT-HHHHHHHHHHHHHHSTT CS
                             TPR_1   9 nayfklgkydeAleyyekALelnPn 33 
                                       ++y +++ky++Al + e +++l  n
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLEDCIKLARN 181
                                       69********************987 PP

  == domain 6  score: 17.8 bits;  conditional E-value: 2.7e-06
                                       HHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1   2 kalynlGnayfklgkydeAleyyekALelnPnn 34 
                                       + ++  +n+y k+g+  +Al++ + AL+  P+n
  gi|518652645|ref|YP_008142165.1| 183 EYYKDEANIYIKMGDKAKALQAVDNALKNSPEN 215
                                       678888**********************99987 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0      0.21   1.6e+02       4      32 ..      16      44 ..      16      46 .. 0.81
   2 !   13.9   0.7   6.5e-05     0.048       2      33 ..      48      79 ..      47      80 .. 0.93
   3 !   12.6   0.0   0.00017      0.12       3      31 ..      83     111 ..      81     113 .. 0.90
   4 !   30.4   0.3   3.3e-10   2.5e-07       2      33 ..     116     147 ..     115     148 .. 0.94
   5 !   14.1   0.1   5.5e-05     0.041       4      33 ..     152     181 ..     150     182 .. 0.94
   6 !   12.5   0.7   0.00019      0.14       8      34 .]     189     215 ..     183     215 .. 0.92

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.21
                                      HHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8  4 yynlgsiylklgdyeeAkeyyekaleldp 32
                                      y+  g  y++  +y  A++ + ka+ l +
  gi|518652645|ref|YP_008142165.1| 16 YNERGISYFNVTQYPDAVKEFTKAINLIK 44
                                      5667778888888999*********9865 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 6.5e-05
                                      CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  2 eayynlgsiylklgdyeeAkeyyekaleldpd 33
                                      ++y n +++y ++  y+eA++ ++ a+ l+ d
  gi|518652645|ref|YP_008142165.1| 48 DYYINRALAYYSMHMYNEAIKDCKSAIALSAD 79
                                      68*************************99876 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00017
                                       HHHHHHHHHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleld 31 
                                       +++ lgsiy+++++++ A   +  a++++
  gi|518652645|ref|YP_008142165.1|  83 YHNTLGSIYDDMNRFDDALGEFDAAIKIE 111
                                       6789***************9999999997 PP

  == domain 4  score: 30.4 bits;  conditional E-value: 3.3e-10
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       ++yyn g++y+ +gd++ A e y+ka++l+ +
  gi|518652645|ref|YP_008142165.1| 116 DYYYNRGNVYWRKGDKDLALEDYNKAVYLNSA 147
                                       69***************************976 PP

  == domain 5  score: 14.1 bits;  conditional E-value: 5.5e-05
                                       HHHHHHHHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8   4 yynlgsiylklgdyeeAkeyyekaleldpd 33 
                                       +y+ ++iy ++++ye A   +e +++l+++
  gi|518652645|ref|YP_008142165.1| 152 LYKRSQIYTEMEKYEDALGDLEDCIKLARN 181
                                       799************************987 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 0.00019
                                       HHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   8 gsiylklgdyeeAkeyyekaleldpdn 34 
                                       ++iy+k+gd+ +A ++   al+ +p+n
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQAVDNALKNSPEN 215
                                       89********************99986 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.1   7.3e-08   5.5e-05       9      40 ..      28      59 ..      13      60 .. 0.95
   2 !   11.3   0.1   0.00028      0.21      10      38 ..      63      91 ..      62      95 .. 0.95
   3 !   33.0   0.1   4.7e-11   3.5e-08       1      42 []      88     129 ..      88     129 .. 0.96
   4 !   14.5   0.3   2.9e-05     0.022       7      38 ..     128     159 ..     128     162 .. 0.89
   5 ?    3.4   0.1     0.084        63       2      18 ..     157     173 ..     156     185 .. 0.81
   6 ?    4.8   0.1      0.03        23       2      27 ..     190     215 ..     189     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 7.3e-08
                            TPR_11  9 kyeeAieaYkkAlkldPdnaeayynLGlayyk 40
                                      +y++A++++ kA++l  ++++ y n++layy 
  gi|518652645|ref|YP_008142165.1| 28 QYPDAVKEFTKAINLIKTDPDYYINRALAYYS 59
                                      8******************************7 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                            TPR_11 10 yeeAieaYkkAlkldPdnaeayynLGlay 38
                                      y+eAi++ k A++l+ d  + ++ LG +y
  gi|518652645|ref|YP_008142165.1| 63 YNEAIKDCKSAIALSADRGDYHNTLGSIY 91
                                      9*************************998 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 4.7e-11
                            TPR_11   1 GdayyeqGkyeeAieaYkkAlkldPdnaeayynLGlayykqG 42 
                                       G +y + +++++A+ ++ +A+k+  d ++ yyn+G++y+++G
  gi|518652645|ref|YP_008142165.1|  88 GSIYDDMNRFDDALGEFDAAIKIEDDVPDYYYNRGNVYWRKG 129
                                       7789999*********************************98 PP

  == domain 4  score: 14.5 bits;  conditional E-value: 2.9e-05
                            TPR_11   7 qGkyeeAieaYkkAlkldPdnaeayynLGlay 38 
                                       +G+ + A+e+Y+kA+ l++ ++ ++y++ ++y
  gi|518652645|ref|YP_008142165.1| 128 KGDKDLALEDYNKAVYLNSADPVFLYKRSQIY 159
                                       577789*********************98888 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.084
                            TPR_11   2 dayyeqGkyeeAieaYk 18 
                                       ++y+e  kye+A+ +++
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLE 173
                                       58**********96665 PP

  == domain 6  score: 4.8 bits;  conditional E-value: 0.03
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPdn 27 
                                       ++y + G+  +A++a  +Alk +P+n
  gi|518652645|ref|YP_008142165.1| 190 NIYIKMGDKAKALQAVDNALKNSPEN 215
                                       9********************99998 PP

>> TPR_9  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.0     0.036        27      27      63 ..      11      47 ..       5      50 .. 0.84
   2 !   11.6   0.0   0.00033      0.24      28      65 ..      46      83 ..      41      87 .. 0.91
   3 ?    2.4   0.0      0.23   1.7e+02      35      64 ..      87     116 ..      83     121 .. 0.88
   4 !   25.1   0.0   1.9e-08   1.5e-05       3      60 ..     123     180 ..     122     184 .. 0.94
   5 !   11.7   0.0   0.00028      0.21      29      72 ..     182     225 ..     178     226 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.036
                             TPR_9 27 ddpeerrdRGlllaqlGclsaAladLeaylalapdap 63
                                      d+++++ +RG+ ++ + ++  A++++  ++ l   +p
  gi|518652645|ref|YP_008142165.1| 11 DEADDYNERGISYFNVTQYPDAVKEFTKAINLIKTDP 47
                                      78999*********************99986655555 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
                             TPR_9 28 dpeerrdRGlllaqlGclsaAladLeaylalapdapda 65
                                      dp+ +  R+l+++ +  +++A++d   ++al+ d+ d 
  gi|518652645|ref|YP_008142165.1| 46 DPDYYINRALAYYSMHMYNEAIKDCKSAIALSADRGDY 83
                                      7888999*************************999885 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.23
                             TPR_9  35 RGlllaqlGclsaAladLeaylalapdapd 64 
                                        G ++  ++++  Al +++a++ +++d pd
  gi|518652645|ref|YP_008142165.1|  87 LGSIYDDMNRFDDALGEFDAAIKIEDDVPD 116
                                       58899999**************99988776 PP

  == domain 4  score: 25.1 bits;  conditional E-value: 1.9e-08
                             TPR_9   3 aiaireedweralavverllllaPddpeerrdRGlllaqlGclsaAladLeaylalap 60 
                                       ++++r+ d + al+ ++  ++l++ dp  ++ R +++ +++ ++ Al dLe ++ la 
  gi|518652645|ref|YP_008142165.1| 123 NVYWRKGDKDLALEDYNKAVYLNSADPVFLYKRSQIYTEMEKYEDALGDLEDCIKLAR 180
                                       689**************************************************98875 PP

  == domain 5  score: 11.7 bits;  conditional E-value: 0.00028
                             TPR_9  29 peerrdRGlllaqlGclsaAladLeaylalapdapdaeairaqL 72 
                                       pe + d + ++ ++G+ ++Al++ + +l ++p++     +++++
  gi|518652645|ref|YP_008142165.1| 182 PEYYKDEANIYIKMGDKAKALQAVDNALKNSPENLSLKELKSRI 225
                                       7778899*************************999998888886 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.0     0.016        12       3      45 ..      19      58 ..      17      80 .. 0.85
   2 ?    1.8   0.0      0.53     4e+02       2      43 ..      52      90 ..      51      91 .. 0.86
   3 !   35.2   0.1   1.9e-11   1.4e-08       3      66 ..      87     147 ..      85     149 .. 0.89
   4 !   12.5   0.0   0.00023      0.17       5      66 ..     157     214 ..     153     215 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.016
                            TPR_16  3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaal 45
                                      ++ ++++  +y+dA++ ++ a+ + + +Pd    + ++++a++
  gi|518652645|ref|YP_008142165.1| 19 RGISYFNVTQYPDAVKEFTKAINLIKTDPD---YYINRALAYY 58
                                      68899****************999999998...7777777776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.53
                            TPR_16  2 alaraalragdyddAaaaleaalkrdpssPdaaeAllllgda 43
                                      ++a+a++    y +A++  + a+++     d+ + ++ lg +
  gi|518652645|ref|YP_008142165.1| 52 NRALAYYSMHMYNEAIKDCKSAIALS---ADRGDYHNTLGSI 90
                                      68999999999******999999999...9999998888765 PP

  == domain 3  score: 35.2 bits;  conditional E-value: 1.9e-11
                            TPR_16   3 laraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       l+ ++ + +++ddA+  ++aa+k      d ++ ++++g++++r+g+ ++A++ y++a+   + 
  gi|518652645|ref|YP_008142165.1|  87 LGSIYDDMNRFDDALGEFDAAIKIE---DDVPDYYYNRGNVYWRKGDKDLALEDYNKAVYLNSA 147
                                       788999*******************...99**********************888888755554 PP

  == domain 4  score: 12.5 bits;  conditional E-value: 0.00023
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapd 66 
                                       +++ +  +y+dA+  le  +k++     ++e +   ++++ + g+ a+A+++++ al+++p 
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLEDCIKLA---R-NPEYYKDEANIYIKMGDKAKALQAVDNALKNSPE 214
                                       56667888999999999999999...3.8889999999999999999999888888888885 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   0.00014       0.1       6      67 ..      16      69 ..      11      76 .. 0.82
   2 !   19.5   0.3   1.2e-06    0.0009       6      72 ..      50     108 ..      48     113 .. 0.82
   3 !   22.3   0.1   1.5e-07   0.00012       7      71 ..      84     141 ..      83     144 .. 0.90
   4 !   13.4   0.3   9.8e-05     0.073       8      67 ..     154     204 ..     150     214 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00014
                            TPR_12  6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67
                                      +n+++  ++   +y +A + + ka+++++    pd+      ++n + +y+ +  y eA++ 
  gi|518652645|ref|YP_008142165.1| 16 YNERGISYFNVTQYPDAVKEFTKAINLIKTD--PDY------YINRALAYYSMHMYNEAIKD 69
                                      5669999999******************433..665......99999999999999999875 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.2e-06
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleeal 72 
                                       + n+a++++ +  y eA++ ++ a+++     G++        ++Lg +y+ ++r+++Al  +  a+
  gi|518652645|ref|YP_008142165.1|  50 YINRALAYYSMHMYNEAIKDCKSAIALSA-DRGDY-------HNTLGSIYDDMNRFDDALGEFDAAI 108
                                       569************************93.33444.......5889999999999999987666665 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.5e-07
                            TPR_12   7 nn.laavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlelleea 71 
                                       +n l++++  + r+d+Al  +++a+ i   +  pd+      ++n g +y++ g+ + Ale +++a
  gi|518652645|ref|YP_008142165.1|  84 HNtLGSIYDDMNRFDDALGEFDAAIKIEDDV--PDY------YYNRGNVYWRKGDKDLALEDYNKA 141
                                       555*********************9999666..665......**********************99 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 9.8e-05
                            TPR_12   8 nlaavlrrlgrydeAlellekaleiarrllGpdhpltattlrnLgrlyralgryeeAlel 67 
                                       ++ ++++++++y++Al  le ++ +ar   +p++      + + + +y ++g+ ++Al++
  gi|518652645|ref|YP_008142165.1| 154 KRSQIYTEMEKYEDALGDLEDCIKLAR---NPEY------YKDEANIYIKMGDKAKALQA 204
                                       67789*********************4...3554......55555555555555555554 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.067        50       5      31 ..      16      42 ..      16      45 .. 0.91
   2 ?    5.1   0.3     0.029        22       5      31 ..      50      76 ..      48      78 .. 0.91
   3 !   11.3   0.0   0.00032      0.24       6      31 ..      85     110 ..      85     112 .. 0.94
   4 !    9.2   0.2    0.0015       1.2       5      29 ..     118     142 ..     116     145 .. 0.91
   5 !   10.0   0.1   0.00082      0.61      10      33 ..     157     180 ..     155     181 .. 0.91
   6 ?    1.6   0.0      0.36   2.7e+02       9      28 ..     189     208 ..     189     210 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.067
                            TPR_10  5 lnNLanalrqrgrydeAealleealai 31
                                      +n  ++ ++++ +y +A++ + +a+++
  gi|518652645|ref|YP_008142165.1| 16 YNERGISYFNVTQYPDAVKEFTKAINL 42
                                      78899*******************987 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.029
                            TPR_10  5 lnNLanalrqrgrydeAealleealai 31
                                      + N a a++++  y+eA ++++ a+a+
  gi|518652645|ref|YP_008142165.1| 50 YINRALAYYSMHMYNEAIKDCKSAIAL 76
                                      7799********************996 PP

  == domain 3  score: 11.3 bits;  conditional E-value: 0.00032
                            TPR_10   6 nNLanalrqrgrydeAealleealai 31 
                                       n L+ ++ +++r+d+A+  ++ a+ i
  gi|518652645|ref|YP_008142165.1|  85 NTLGSIYDDMNRFDDALGEFDAAIKI 110
                                       89*****************9999976 PP

  == domain 4  score: 9.2 bits;  conditional E-value: 0.0015
                            TPR_10   5 lnNLanalrqrgrydeAealleeal 29 
                                       + N +n++++ g+ d A++++ +a+
  gi|518652645|ref|YP_008142165.1| 118 YYNRGNVYWRKGDKDLALEDYNKAV 142
                                       7799*****************9997 PP

  == domain 5  score: 10.0 bits;  conditional E-value: 0.00082
                            TPR_10  10 nalrqrgrydeAealleealairr 33 
                                        +++++ +y++A+ +le+++ + r
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLEDCIKLAR 180
                                       58******************9876 PP

  == domain 6  score: 1.6 bits;  conditional E-value: 0.36
                            TPR_10   9 analrqrgrydeAealleea 28 
                                       an++ ++g+ ++A++  + a
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQAVDNA 208
                                       899**********9876655 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       2.5   1.9e+03      14      27 ..       9      20 ..       8      23 .. 0.80
   2 ?    2.5   0.0      0.24   1.8e+02       6      26 ..      20      40 ..      16      48 .. 0.74
   3 ?    2.3   0.1      0.29   2.1e+02       4      33 ..      52      81 ..      50      83 .. 0.81
   4 !   12.6   0.0   0.00014       0.1       3      32 ..      85     114 ..      83     116 .. 0.85
   5 ?    6.6   0.2     0.012       9.1       2      24 ..     118     140 ..     118     148 .. 0.88
   6 ?    5.6   0.1     0.024        18       7      32 ..     157     182 ..     152     183 .. 0.87
   7 ?    5.2   0.0     0.034        26       6      34 ..     189     215 ..     189     217 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 2.5
                             TPR_7 14 dyeeAielyeqsLa 27
                                      + +eA +++e+  +
  gi|518652645|ref|YP_008142165.1|  9 KDDEADDYNER--G 20
                                      6799******9..6 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.24
                             TPR_7  6 arlysrlGdyeeAielyeqsL 26
                                      +  y+++ +y +A++ +++++
  gi|518652645|ref|YP_008142165.1| 20 GISYFNVTQYPDAVKEFTKAI 40
                                      677999999******999955 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.29
                             TPR_7  4 nLarlysrlGdyeeAielyeqsLaltkdpe 33
                                      n a +y ++  y eAi+ ++ ++al  d +
  gi|518652645|ref|YP_008142165.1| 52 NRALAYYSMHMYNEAIKDCKSAIALSADRG 81
                                      77888999999********99888877765 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00014
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       + L+++y +++++++A++ + +++ +++d 
  gi|518652645|ref|YP_008142165.1|  85 NTLGSIYDDMNRFDDALGEFDAAIKIEDDV 114
                                       67****************999977777765 PP

  == domain 5  score: 6.6 bits;  conditional E-value: 0.012
                             TPR_7   2 LlnLarlysrlGdyeeAielyeq 24 
                                       ++n +++y r Gd + A+e y +
  gi|518652645|ref|YP_008142165.1| 118 YYNRGNVYWRKGDKDLALEDYNK 140
                                       7899**************98876 PP

  == domain 6  score: 5.6 bits;  conditional E-value: 0.024
                             TPR_7   7 rlysrlGdyeeAielyeqsLaltkdp 32 
                                       ++y ++ +ye+A++ +e ++ l++ p
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLEDCIKLARNP 182
                                       79************999988888776 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.034
                             TPR_7   6 arlysrlGdyeeAielyeqsLaltkdped 34 
                                       a++y ++Gd ++A++      al ++pe+
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQAVDN--ALKNSPEN 215
                                       89************99888..88888875 PP

>> SHNi-TPR  SHNi-TPR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00034      0.25      16      30 ..      28      42 ..      27      43 .. 0.96
   2 ?    3.9   0.0      0.05        37      17      30 ..      63      76 ..      61      77 .. 0.92
   3 ?    5.7   0.0     0.014        10      15      30 ..      95     110 ..      83     112 .. 0.91
   4 ?    2.2   0.0      0.17   1.3e+02      20      29 ..     134     143 ..     133     145 .. 0.89
   5 !    9.7   0.0   0.00074      0.55      13      30 ..     161     178 ..     158     181 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00034
                          SHNi-TPR 16 nFpqAveDlrkaLeL 30
                                      ++p+Av++++ka++L
  gi|518652645|ref|YP_008142165.1| 28 QYPDAVKEFTKAINL 42
                                      7************98 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.05
                          SHNi-TPR 17 FpqAveDlrkaLeL 30
                                      +++A++D ++a++L
  gi|518652645|ref|YP_008142165.1| 63 YNEAIKDCKSAIAL 76
                                      89*********987 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.014
                          SHNi-TPR  15 enFpqAveDlrkaLeL 30 
                                       ++F++A+ ++++a+++
  gi|518652645|ref|YP_008142165.1|  95 NRFDDALGEFDAAIKI 110
                                       79***********997 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.17
                          SHNi-TPR  20 AveDlrkaLe 29 
                                       A+eD++ka+ 
  gi|518652645|ref|YP_008142165.1| 134 ALEDYNKAVY 143
                                       99******95 PP

  == domain 5  score: 9.7 bits;  conditional E-value: 0.00074
                          SHNi-TPR  13 EnenFpqAveDlrkaLeL 30 
                                       E e++++A+ Dl+ +++L
  gi|518652645|ref|YP_008142165.1| 161 EMEKYEDALGDLEDCIKL 178
                                       77**************98 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       9.3     7e+03      19      36 ..      31      48 ..      23      56 .. 0.61
   2 ?    2.3   0.0      0.53     4e+02       7      33 ..      53      79 ..      47      85 .. 0.83
   3 !    8.4   0.0    0.0056       4.2       7      37 ..      87     117 ..      82     120 .. 0.86
   4 ?    6.4   0.0     0.025        19       2      28 ..     116     142 ..     115     152 .. 0.87
   5 ?    6.0   0.0     0.034        26       4      31 ..     152     179 ..     149     185 .. 0.82
   6 !   10.8   0.0   0.00097      0.72       2      42 ..     183     223 ..     182     225 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 9.3
                            TPR_14 19 eAiallrralalaPddae 36
                                      +A++ + +a+ l  +d++
  gi|518652645|ref|YP_008142165.1| 31 DAVKEFTKAINLIKTDPD 48
                                      566666666554444444 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.53
                            TPR_14  7 laeallalGdpdeAiallrralalaPd 33
                                      +a a++    + eAi+ ++ a+al  d
  gi|518652645|ref|YP_008142165.1| 53 RALAYYSMHMYNEAIKDCKSAIALSAD 79
                                      788999999999****99999998766 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.0056
                            TPR_14   7 laeallalGdpdeAiallrralalaPddaea 37 
                                       l++++    ++d+A+  +++a++   d +++
  gi|518652645|ref|YP_008142165.1|  87 LGSIYDDMNRFDDALGEFDAAIKIEDDVPDY 117
                                       88999999**************998877665 PP

  == domain 4  score: 6.4 bits;  conditional E-value: 0.025
                            TPR_14   2 eallalaeallalGdpdeAiallrral 28 
                                       + ++ ++ ++++ Gd d A++ +++a+
  gi|518652645|ref|YP_008142165.1| 116 DYYYNRGNVYWRKGDKDLALEDYNKAV 142
                                       568889**************9999885 PP

  == domain 5  score: 6.0 bits;  conditional E-value: 0.034
                            TPR_14   4 llalaeallalGdpdeAiallrralala 31 
                                       l+++ +++ + +++++A+  l+++++la
  gi|518652645|ref|YP_008142165.1| 152 LYKRSQIYTEMEKYEDALGDLEDCIKLA 179
                                       7899999****************98865 PP

  == domain 6  score: 10.8 bits;  conditional E-value: 0.00097
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       e +++ a ++   Gd ++A+++ + al+  P+++ +  l  
  gi|518652645|ref|YP_008142165.1| 183 EYYKDEANIYIKMGDKAKALQAVDNALKNSPENLSLKELKS 223
                                       66788899*************************98877665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.051        38       6      28 ..      19      41 ..      18      42 .. 0.88
   2 ?    1.8   0.1       0.6   4.5e+02       5      21 ..      52      68 ..      48      79 .. 0.77
   3 ?    1.0   0.0       1.1   8.5e+02       6      28 ..      87     109 ..      86     112 .. 0.82
   4 !    9.6   0.1    0.0021       1.5       3      27 ..     118     142 ..     116     144 .. 0.90
   5 ?    6.1   0.1     0.026        19       3      28 ..     152     177 ..     151     181 .. 0.92
   6 !    7.8   0.0    0.0077       5.7       7      32 ..     189     214 ..     188     215 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.051
                                      HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6  6 lalsyrklgdtdkAlealerlik 28
                                      ++ sy++ +++ +A++ + + i+
  gi|518652645|ref|YP_008142165.1| 19 RGISYFNVTQYPDAVKEFTKAIN 41
                                      689****55*********99986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.6
                                      HHHHHHHHHHHHHHHHH CS
                             TPR_6  5 klalsyrklgdtdkAle 21
                                      ++al+y+++  + +A++
  gi|518652645|ref|YP_008142165.1| 52 NRALAYYSMHMYNEAIK 68
                                      689****9549999987 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   6 lalsyrklgdtdkAlealerlik 28 
                                       l+  y  +++ d+Al  ++  ik
  gi|518652645|ref|YP_008142165.1|  87 LGSIYDDMNRFDDALGEFDAAIK 109
                                       67788889999999998888776 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.0021
                                       HHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerli 27 
                                       +y+++  y + gd+d Ale +++ +
  gi|518652645|ref|YP_008142165.1| 118 YYNRGNVYWRKGDKDLALEDYNKAV 142
                                       8*********99*********9975 PP

  == domain 5  score: 6.1 bits;  conditional E-value: 0.026
                                       HHHHHHHHHHHHHHHHHHHHHHHHHH CS
                             TPR_6   3 lyklalsyrklgdtdkAlealerlik 28 
                                       lyk+ + y ++ ++++Al  le++ik
  gi|518652645|ref|YP_008142165.1| 152 LYKRSQIYTEMEKYEDALGDLEDCIK 177
                                       8*********88**********9998 PP

  == domain 6  score: 7.8 bits;  conditional E-value: 0.0077
                                       HHHHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   7 alsyrklgdtdkAlealerlikeYPd 32 
                                       a  y+k+gd++kAl+a ++ +k+ P+
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQAVDNALKNSPE 214
                                       678*************9999999886 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0064       4.8       6      62 ..      28      84 ..      24      88 .. 0.86
   2 !   17.1   0.1     8e-06     0.006       5      61 ..      61     117 ..      57     122 .. 0.91
   3 !   14.1   1.9   6.8e-05     0.051       3      64 ..     161     221 ..     133     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0064
                            TPR_19  6 dyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddarya 62
                                      +y +A++ +++a+     +++  ++ A a++++  ++eA++ ++ + +  +d  +y+
  gi|518652645|ref|YP_008142165.1| 28 QYPDAVKEFTKAINLIKTDPDYYINRALAYYSMHMYNEAIKDCKSAIALSADRGDYH 84
                                      7999***********9***********************987777776666666555 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 8e-06
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddary 61 
                                         y eA++  ++a++ +++ ++    L  ++  ++++d+A    da+ + + d ++y
  gi|518652645|ref|YP_008142165.1|  61 HMYNEAIKDCKSAIALSADRGDYHNTLGSIYDDMNRFDDALGEFDAAIKIEDDVPDY 117
                                       5799********************************************999996665 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 6.8e-05
                            TPR_19   3 aegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasL 64 
                                       ++++y++Al  le  ++  + n+e   + A++++++g+ ++A +++d +++  p +  ++ L
  gi|518652645|ref|YP_008142165.1| 161 EMEKYEDALGDLEDCIKL-ARNPEYYKDEANIYIKMGDKAKALQAVDNALKNSPENLSLKEL 221
                                       789999********8777.6699999************************999986555555 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0         1   7.5e+02      12      33 ..      11      33 ..       7      34 .. 0.81
   2 !   12.2   0.2   0.00025      0.19       2      34 .]      36      68 ..      35      68 .. 0.93
   3 ?    5.2   0.0     0.042        31       5      33 ..      73     101 ..      69     102 .. 0.86
   4 !    9.8   0.0    0.0015       1.1       2      33 ..     104     135 ..     103     136 .. 0.90
   5 !    7.8   0.1    0.0066       4.9       2      33 ..     138     169 ..     137     177 .. 0.89
   6 ?    3.0   0.1      0.22   1.6e+02      20      34 .]     189     203 ..     178     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 1
                            TPR_17 12 n.adaynnLAelllknGdlmtAr 33
                                      + ad yn+++  + +  ++ +A+
  gi|518652645|ref|YP_008142165.1| 11 DeADDYNERGISYFNVTQYPDAV 33
                                      45888********9999998886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00025
                            TPR_17  2 ylkaleldPnnadaynnLAelllknGdlmtArq 34
                                      ++ka+ l ++++d y n+A ++++ + + +A++
  gi|518652645|ref|YP_008142165.1| 36 FTKAINLIKTDPDYYINRALAYYSMHMYNEAIK 68
                                      899***********************9999985 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.042
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                       a++l  +  d +n L+ ++   +++++A+
  gi|518652645|ref|YP_008142165.1|  73 AIALSADRGDYHNTLGSIYDDMNRFDDAL 101
                                       77777888899*************99995 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.0015
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       +  a++++ + +d y+n+++++ ++Gd++ A+
  gi|518652645|ref|YP_008142165.1| 104 FDAAIKIEDDVPDYYYNRGNVYWRKGDKDLAL 135
                                       67899999999***********9999999987 PP

  == domain 5  score: 7.8 bits;  conditional E-value: 0.0066
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtAr 33 
                                       y ka+ l+  ++++++ + +++ +  ++++A+
  gi|518652645|ref|YP_008142165.1| 138 YNKAVYLNSADPVFLYKRSQIYTEMEKYEDAL 169
                                       99*********************888888774 PP

  == domain 6  score: 3.0 bits;  conditional E-value: 0.22
                            TPR_17  20 AelllknGdlmtArq 34 
                                       A+++ k Gd+++A+q
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQ 203
                                       99**********987 PP

>> NARP1  NMDA receptor-regulated protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1       0.4     3e+02     210     247 ..      31      68 ..      16      86 .. 0.54
   2 !   18.9   0.1     8e-07    0.0006     198     259 ..      87     148 ..      83     152 .. 0.94
   3 !   13.2   0.4   4.2e-05     0.031     198     252 ..     155     208 ..     150     214 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.4
                                       HHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHH CS
                             NARP1 210 kAleyidkaiehtptlvelyltKarilkhaGdlkkAae 247
                                        A++   kai+   t  ++y+++a  +  +   ++A++
  gi|518652645|ref|YP_008142165.1|  31 DAVKEFTKAINLIKTDPDYYINRALAYYSMHMYNEAIK 68 
                                       44444455555555555555555444444433333333 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 8e-07
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHHCTTT- CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeearklDlaD 259
                                       l   yd +++ + Al   d+ai+ ++ + ++y+++++++ ++Gd + A e  ++a  l  aD
  gi|518652645|ref|YP_008142165.1|  87 LGSIYDDMNRFDDALGEFDAAIKIEDDVPDYYYNRGNVYWRKGDKDLALEDYNKAVYLNSAD 148
                                       5667***************************************************9999988 PP

  == domain 3  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHT-SHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHTT-HHHHHHHHHHH CS
                             NARP1 198 lAqhydklgsrekAleyidkaiehtptlvelyltKarilkhaGdlkkAaevmeea 252
                                        +q y +++++e Al  ++ +i+      e+y   a+i+ ++Gd  kA +++++a
  gi|518652645|ref|YP_008142165.1| 155 RSQIYTEMEKYEDALGDLEDCIKLA-RNPEYYKDEANIYIKMGDKAKALQAVDNA 208
                                       57899999**************986.5689******************9999988 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   0.00013     0.098       4      79 ..      28     104 ..      25     107 .. 0.86
   2 !   16.2   0.1   1.2e-05    0.0089       2      81 ..      94     174 ..      93     175 .. 0.84
   3 ?    3.9   0.1     0.083        62      27      56 ..     184     216 ..     177     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                                       -HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHHH CS
                            ANAPC3   4 nyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaaL 79 
                                       +y +A+  + ++ +  + +p+     Al++y++  y++A++ +++a  l      ++ +++  + +++++++A+  +
  gi|518652645|ref|YP_008142165.1|  28 QYPDAVKEFTKAINLIKTDPDYYINRALAYYSMHMYNEAIKDCKSAiALSADRGDYHNTLGSIYDDMNRFDDALGEF 104
                                       88899999999998788888887778********************8888888899999999999999999998766 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 1.2e-05
                                       TT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3   2 qnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAia 77 
                                       +n++++A+  ++ + + e + p+  y  + ++ + g+ + A+e ++ka  lns ++  +y   q + +++kye+A+ 
  gi|518652645|ref|YP_008142165.1|  94 MNRFDDALGEFDAAIKIEDDVPDYYYNRGNVYWRKGDKDLALEDYNKAvYLNSADPVFLYKRSQIYTEMEKYEDALG 170
                                       6788888888888886666666666777********************9999999988888889999********98 PP

                                       HH-S CS
                            ANAPC3  78 aLek 81 
                                        Le 
  gi|518652645|ref|YP_008142165.1| 171 DLED 174
                                       7776 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.083
                                       HHH..HHHHHHTT-HHHHHHHHHCT.SHHHC-H CS
                            ANAPC3  27 yll..AlclylngqykrAyellrka.klnsksl 56 
                                       y++  A  + ++g+  +A++ +++a k  +++l
  gi|518652645|ref|YP_008142165.1| 184 YYKdeANIYIKMGDKAKALQAVDNAlKNSPENL 216
                                       44455999***************9966666655 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.075        56     133     179 ..      33      80 ..      21      87 .. 0.81
   2 !   10.6   0.0   0.00031      0.23     125     179 ..      93     148 ..      82     154 .. 0.82
   3 !   12.7   0.0   7.2e-05     0.054     109     183 ..     148     219 ..     143     221 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.075
                            TPR_15 133 lksleeeea.aeqsaafllaraelyrqegqtdaAlrdyreAlalapds 179
                                       +k+ ++  +  + ++ +++ ra +y      ++A++d + A+al++d 
  gi|518652645|ref|YP_008142165.1|  33 VKEFTKAINlIKTDPDYYINRALAYYSMHMYNEAIKDCKSAIALSADR 80 
                                       55666555547899*****************************99886 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00031
                            TPR_15 125 dydriaellksleeeeaae.qsaafllaraelyrqegqtdaAlrdyreAlalapds 179
                                       d++r ++ l +  +  + e + + +++ r+++y ++g++d Al+dy +A+ l+ ++
  gi|518652645|ref|YP_008142165.1|  93 DMNRFDDALGEFDAAIKIEdDVPDYYYNRGNVYWRKGDKDLALEDYNKAVYLNSAD 148
                                       66666677777777777774558899************************998876 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 7.2e-05
                            TPR_15 109 sprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselr 183
                                       +p +L++  ++++++++y+   + l  le   ++++++ ++   a++y + g++++Al+++ +Al+ +p++ +l+
  gi|518652645|ref|YP_008142165.1| 148 DPVFLYKRSQIYTEMEKYE---DALGDLEDCIKLARNPEYYKDEANIYIKMGDKAKALQAVDNALKNSPENLSLK 219
                                       6677777777777777775...66777777999************************************998887 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.4    0.0087       6.5       7      28 ..      53      74 ..      47      80 .. 0.82
   2 ?   -0.7   0.0       2.1   1.5e+03      14      32 ..      94     112 ..      92     114 .. 0.85
   3 ?   -1.3   0.1       3.1   2.3e+03      11      29 ..     159     177 ..     151     181 .. 0.71
   4 !   21.3   0.2   2.8e-07   0.00021      11      46 ..     192     227 ..     190     228 .] 0.96

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0087
                                      HHHHHHHHT-HHHHHHHHHHHH CS
                        Fis1_TPR_C  7 lAlGhyklgeYseArryvdalL 28
                                       Al++y ++ Y+eA + ++  +
  gi|518652645|ref|YP_008142165.1| 53 RALAYYSMHMYNEAIKDCKSAI 74
                                      59************99998766 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.1
                                       HT-HHHHHHHHHHHHHHTT CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEP 32 
                                       + ++++A+   da ++iE 
  gi|518652645|ref|YP_008142165.1|  94 MNRFDDALGEFDAAIKIED 112
                                       5689999999999999995 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 3.1
                                       HHHHT-HHHHHHHHHHHHH CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLe 29 
                                       ++ + +Y++A+  ++ +++
  gi|518652645|ref|YP_008142165.1| 159 YTEMEKYEDALGDLEDCIK 177
                                       5567889999877776665 PP

  == domain 4  score: 21.3 bits;  conditional E-value: 2.8e-07
                                       HHHHT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHH CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaqsLkelied 46 
                                       ++k+g+  +A++ vd  L+  Pen   ++Lk+ ie+
  gi|518652645|ref|YP_008142165.1| 192 YIKMGDKAKALQAVDNALKNSPENLSLKELKSRIEK 227
                                       689*******************************98 PP

>> ANAPC5  Anaphase-promoting complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.1    0.0063       4.7      45      80 ..      51      87 ..      21     101 .. 0.85
   2 !    8.0   0.0     0.004         3      44      73 ..     152     181 ..     135     188 .. 0.86
   3 ?    2.9   0.0      0.15   1.1e+02      48      76 ..     189     217 ..     187     225 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0063
                            ANAPC5 45 LnlaslhadfghneeAvkaleeairlArenkD.kscL 80
                                      +n a   ++++ ++eA+k  + ai+l+ +++D +++L
  gi|518652645|ref|YP_008142165.1| 51 INRALAYYSMHMYNEAIKDCKSAIALSADRGDyHNTL 87
                                      78899999******************99999944555 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
                            ANAPC5  44 lLnlaslhadfghneeAvkaleeairlAre 73 
                                       l +   + ++++++e+A+  le++i+lAr+
  gi|518652645|ref|YP_008142165.1| 152 LYKRSQIYTEMEKYEDALGDLEDCIKLARN 181
                                       5566778899******************97 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.15
                            ANAPC5  48 aslhadfghneeAvkaleeairlArenkD 76 
                                       a++  ++g++++A++a+ +a + + en +
  gi|518652645|ref|YP_008142165.1| 189 ANIYIKMGDKAKALQAVDNALKNSPENLS 217
                                       667889**************998777765 PP

>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.41   3.1e+02     129     174 ..      63     109 ..      54     116 .. 0.73
   2 !    9.0   0.2    0.0014         1     124     174 ..      92     143 ..      86     155 .. 0.73
   3 !   11.6   0.3   0.00022      0.17     121     179 ..     157     215 ..     150     226 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.41
                            TPR_21 129 ydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                       y+eA+k  +++   +a ++ + +  G i+  ++++d+A  +++aA++
  gi|518652645|ref|YP_008142165.1|  63 YNEAIKDCKSAiALSADRGDYHNTLGSIYDDMNRFDDALGEFDAAIK 109
                                       55666665433134555678888999999999999999999999986 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                            TPR_21 124 laekkydeAlktLeak.keeafaalvaelrGDilvaqgkldeAraaYqaAla 174
                                        +++ +d+Al + +a+ k e     +   rG+++ ++g++d A + Y++A+ 
  gi|518652645|ref|YP_008142165.1|  92 DDMNRFDDALGEFDAAiKIEDDVPDYYYNRGNVYWRKGDKDLALEDYNKAVY 143
                                       56666777777775441334444566778*********************85 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00022
                            TPR_21 121 rvllaekkydeAlktLeakkeeafaalvaelrGDilvaqgkldeAraaYqaAlaaleek 179
                                       +++ +++ky++Al  Le+  + a + ++   + +i++++g++++A +a ++Al++  e+
  gi|518652645|ref|YP_008142165.1| 157 QIYTEMEKYEDALGDLEDCIKLARNPEYYKDEANIYIKMGDKAKALQAVDNALKNSPEN 215
                                       78999************************************************998877 PP

>> TPR_20  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.055        41       8      45 ..      33      70 ..      27     103 .. 0.82
   2 ?   -0.9   0.0       2.8   2.1e+03       8      43 ..     101     136 ..      92     141 .. 0.81
   3 !    7.7   0.0    0.0058       4.3       7      54 ..     134     181 ..     128     193 .. 0.83
   4 ?    1.6   0.1      0.46   3.5e+02       4      25 ..     198     219 ..     195     224 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.055
                            TPR_20  8 laeleaalaanpddldarldlAlallaagryeeAleqL 45
                                      ++e+ +a++  ++d d  ++ Ala+++   y eA++  
  gi|518652645|ref|YP_008142165.1| 33 VKEFTKAINLIKTDPDYYINRALAYYSMHMYNEAIKDC 70
                                      6788888889999*********************9865 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.8
                            TPR_20   8 laeleaalaanpddldarldlAlallaagryeeAle 43 
                                       l e++aa++ + d  d  ++  +++  +g+++ Ale
  gi|518652645|ref|YP_008142165.1| 101 LGEFDAAIKIEDDVPDYYYNRGNVYWRKGDKDLALE 136
                                       556777888888888888999999999999998887 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0058
                            TPR_20   7 elaeleaalaanpddldarldlAlallaagryeeAleqLleilkrdrk 54 
                                        l++  +a+  n +d    ++ ++ + + ++ye+Al  L + +k  r+
  gi|518652645|ref|YP_008142165.1| 134 ALEDYNKAVYLNSADPVFLYKRSQIYTEMEKYEDALGDLEDCIKLARN 181
                                       5677778888899999999********************999987666 PP

  == domain 4  score: 1.6 bits;  conditional E-value: 0.46
                            TPR_20   4 dapelaeleaalaanpddldar 25 
                                       +a+ l+++++al+++p++l ++
  gi|518652645|ref|YP_008142165.1| 198 KAKALQAVDNALKNSPENLSLK 219
                                       67889*************9765 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 ?    3.6   0.0     0.055        41     212     262 ..      28      83 ..       5     126 .. 0.61
   2 !    9.9   0.9   0.00068      0.51     208     279 ..     160     227 ..     131     228 .] 0.60

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.055
                         Cas_DxTHG 212 klkkeleefskalelirp.lell.ekaekleke...ivek.lkeeleei.esleeees 262
                                       ++ ++++ef ka++li++ ++++ + a  +  +   + ++ +k+ +++i  s+++  +
  gi|518652645|ref|YP_008142165.1|  28 QYPDAVKEFTKAINLIKTdPDYYiNRALAY--YsmhMYNEaIKDCKSAIaLSADRGDY 83 
                                       46789************8888886633222..12343333344444444444444333 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00068
                         Cas_DxTHG 208 klkeklkkeleefskalelirplell.ekaeklekeiveklkeeleei.esleeeesakplellldeikkklek 279
                                       +  ek++++l  + ++++l r++e++ ++a ++  + + ++ + l+++ + l++  s  p +l l+e+k ++ek
  gi|518652645|ref|YP_008142165.1| 160 TEMEKYEDALGDLEDCIKLARNPEYYkDEA-NIYIK-MGDKAKALQAVdNALKN--S--PENLSLKELKSRIEK 227
                                       33455999******************5544.44444.22222344444222222..2..334467777777665 PP

>> RPN7  26S proteasome subunit RPN7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1      0.51   3.8e+02      32      62 ..      50      80 ..      25      97 .. 0.53
   2 ?    5.8   0.0     0.014        10      30      63 ..     109     142 ..      89     151 .. 0.82
   3 ?    6.9   0.4    0.0063       4.7      38      64 ..     184     210 ..     153     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.51
                                      HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTC CS
                              RPN7 32 keeirrakldlaehYlkigdleeAlkaysri 62
                                       ++ + a++    +   i d+++A+++ +  
  gi|518652645|ref|YP_008142165.1| 50 YINRALAYYSMHMYNEAIKDCKSAIALSADR 80
                                      3333444444444444555666666555555 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.014
                                       T-HHHHHHHHHHHHHHHHHCT-HHHHHHHHHTCC CS
                              RPN7  30 lgkeeirrakldlaehYlkigdleeAlkaysrir 63 
                                        ++ ++ + ++++++ Y + gd++ Al+ y++++
  gi|518652645|ref|YP_008142165.1| 109 KIEDDVPDYYYNRGNVYWRKGDKDLALEDYNKAV 142
                                       4788999999*********************974 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0063
                                       HHHHHHHHHHHCT-HHHHHHHHHTCCC CS
                              RPN7  38 akldlaehYlkigdleeAlkaysrire 64 
                                        ++d a+ Y+k+gd+++Al+a+  +++
  gi|518652645|ref|YP_008142165.1| 184 YYKDEANIYIKMGDKAKALQAVDNALK 210
                                       577899***************988765 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       5.8   4.3e+03      34      57 ..      13      36 ..      11      44 .. 0.71
   2 ?   -0.3   0.1       1.6   1.2e+03      41      41 ..      61      61 ..      26      91 .. 0.59
   3 ?    7.5   0.2    0.0055       4.1      35      57 ..     116     138 ..      82     141 .. 0.83
   4 ?    6.1   0.2     0.015        11      28      57 ..     176     205 ..     159     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.8
                                      HHHHHHHHHHHHHTT-HHHHHHHH CS
                            DUF357 34 aesYleDakyflekgdlvnAlasf 57
                                      a  Y e +  +++   + +A+  f
  gi|518652645|ref|YP_008142165.1| 13 ADDYNERGISYFNVTQYPDAVKEF 36
                                      677888888888777777766554 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.6
                                      H CS
                            DUF357 41 a 41
                                       
  gi|518652645|ref|YP_008142165.1| 61 H 61
                                      2 PP

  == domain 3  score: 7.5 bits;  conditional E-value: 0.0055
                                       HHHHHHHHHHHHTT-HHHHHHHH CS
                            DUF357  35 esYleDakyflekgdlvnAlasf 57 
                                        +Y++ ++ + +kgd   Al  +
  gi|518652645|ref|YP_008142165.1| 116 DYYYNRGNVYWRKGDKDLALEDY 138
                                       589****************9865 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.015
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHH CS
                            DUF357  28 eevlemaesYleDakyflekgdlvnAlasf 57 
                                       +++ ++ e+Y  +a+ +++ gd  +Al ++
  gi|518652645|ref|YP_008142165.1| 176 IKLARNPEYYKDEANIYIKMGDKAKALQAV 205
                                       4455566789999*************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (228 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        25  (0.00139439); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.63u 0.33s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1219.65
//
Query:       gi|518652646|ref|YP_008142166.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G1285 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-16   58.6   0.1    6.9e-16   58.1   0.1    1.3  1  ADH_N         Alcohol dehydrogenase GroES-like domain
    3.8e-14   52.8   0.0    3.9e-13   49.5   0.0    2.1  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.6e-06   29.2   0.0    2.7e-06   28.5   0.0    1.3  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
     0.0045   16.4   0.0     0.0075   15.6   0.0    1.3  1  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.016   14.5   0.0    1.2  1  AlaDh_PNT_C   Alanine dehydrogenase/PNT, C-terminal domain
      0.026   14.0   0.0      0.036   13.5   0.0    1.2  1  PALP          Pyridoxal-phosphate dependent enzyme
      0.029   13.6   0.0      0.047   12.9   0.0    1.3  1  Pyr_redox_2   Pyridine nucleotide-disulphide oxidoreductase
      0.082   13.4   0.0       0.13   12.8   0.0    1.4  1  XdhC_C        XdhC Rossmann domain


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 !   58.1   0.1   3.1e-19   6.9e-16       4     108 ..      31     133 ..      28     134 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 3.1e-19
                                       EEEEEEEEEE-HHHHHHHTTS.TTTTSSSSEE---EEEEEEEEESTT-CS--TT-EEEE-SEEE-SSSHHHHTT-GG CS
                             ADH_N   4 vlikvkaagiCgsDlhilkgg.kelevklplilGHEivGeveevgpevkklkvGdrVvvepliscgeCaaCkegeen 79 
                                       + +k+  ag++  D+ ++ g+     +++p i+G E++G+  e g++   +++GdrV+v+  i ++ C+ C +g+e+
  gi|518652646|ref|YP_008142166.1|  31 IKVKIVKAGLNPLDYNLIAGNiVYNVNPMPHIPGSEVMGIAMEDGKR---IRKGDRVIVYNRIFDNGCDMCYSGNEH 104
                                       88******************855566789************999965...689************************ PP

                                       G-TTBEETTTSS-SSSBSEEEECGGGEEE CS
                             ADH_N  80 lCeeakllgvsldGgfaeyvvvpekklvk 108
                                       lC +++++gv ++Gg+a+y+ + e++l++
  gi|518652646|ref|YP_008142166.1| 105 LCYNGGIWGVITNGGYADYIKIGEQNLFR 133
                                       **********************9999886 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   1.7e-16   3.9e-13       3     129 ..     177     286 ..     176     287 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 1.7e-16
                                       HHHHHHHHHHTT-EEEEEESSHHHHHHHHHTTESEEEETTTCHHHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCE CS
                        ADH_zinc_N   3 GlaavqlAkalGaeviavdsseeklelakklGadevinykeadlverikeltggegvdvvfecvGsgatleaalkll 79 
                                       G+++vq+A+ +G+ v++ ++++e    +++lG   v+++        + +   + ++d++++ +G g+ + +++k l
  gi|518652646|ref|YP_008142166.1| 177 GIFTVQIARQMGMDVYVYSRNRE----LESLGI-KVLDS--------VPD---DFKADIIVNPLG-GKLFGDSIKHL 236
                                       67777777777777777777776....777773.34444........334...448*********.*********** PP

                                       EEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSCHHHHHHHHHHHHH CS
                        ADH_zinc_N  80 kpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgslreefkealdlla 129
                                       k++G++v++G+  + + ++d++n+  +e+ i+Gs++g+ r+++ e+l++l+
  gi|518652646|ref|YP_008142166.1| 237 KRRGKIVTYGVlTGRNADLDIANVYTNELEIIGSTGGT-RKDLTELLQILE 286
                                       ***********7555555********************.********9986 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 !   28.5   0.0   1.2e-09   2.7e-06      14     123 ..     215     311 ..     188     319 .. 0.78

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.2e-09
                                       HHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----.S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHH CS
                      ADH_zinc_N_2  14 feaatggegvDvvldtvggealleaslkvlpggGrlvsiggpplsaallkpakkrkgrsvkyeflfsmkasaqadil 90 
                                       f       + D++++ +gg+ +  +s+k+l+ +G++v++g   l+ + +++   ++  +  +e + s + + ++d l
  gi|518652646|ref|YP_008142166.1| 215 F-------KADIIVNPLGGKLF-GDSIKHLKRRGKIVTYGV--LTGRNADLDI-ANVYTNELEIIGS-TGGTRKD-L 278
                                       3.......47**********99.*******777******95..3444444444.6666666666664.3336888.* PP

                                       HHHHHHHHHHH----EEEEEEGGGHHHHHHHHH CS
                      ADH_zinc_N_2  91 eelaalieeGklrpvvdrvfpleeaaeAhryle 123
                                       +el++ +e+ ++r +v ++++l ++++A+ + +
  gi|518652646|ref|YP_008142166.1| 279 TELLQILEKSNFRLPVYKEYSLWDIKDALHAFK 311
                                       ****************************98775 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.3e-06    0.0075      37      81 ..     166     206 ..     153     224 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.3e-06
                                       SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCE CS
                      2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgve 81 
                                        ++ + G+G+ G  + ++++++gm+v++y+r+++     e+lg++
  gi|518652646|ref|YP_008142166.1| 166 DKILVYGAGNTGIFTVQIARQMGMDVYVYSRNRE----LESLGIK 206
                                       67899**************************977....3445554 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   7.2e-06     0.016      30      67 ..     167     200 ..     154     236 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.2e-06
                                       EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHH CS
                       AlaDh_PNT_C  30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleql 67 
                                       k+lv G+G  G+  +++a+++g +V+v+  + +    l
  gi|518652646|ref|YP_008142166.1| 167 KILVYGAGNTGIFTVQIARQMGMDVYVYSRNRE----L 200
                                       89*************************976654....4 PP

>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.6e-05     0.036      43      85 ..     154     195 ..     139     218 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHHHT-EEEEEE CS
                              PALP  43 eyllarlkegtgaktvveassGNhgralAaaaallGlkvtivv 85 
                                       +  l+r++ g  ++ +++ ++GN+g+ +  +a+ +G++v+++ 
  gi|518652646|ref|YP_008142166.1| 154 YRSLKRARAG-INDKILVYGAGNTGIFTVQIARQMGMDVYVYS 195
                                       5556678888.999***************************95 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   2.1e-05     0.047     128     182 ..     149     204 ..     126     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2.1e-05
                                       SECHHHHHHCCSS-T..SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS- CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 128 rtldsaealklkllp..krivvvGgGyiGvElAaalaklgkevtlveardrllrald 182
                                        +l+s + lk++     ++i+v G+G++G+ + + ++++g +v+ v+ r+r l++l+
  gi|518652646|ref|YP_008142166.1| 149 GALTSYRSLKRARAGinDKILVYGAGNTGIFTVQIARQMGMDVY-VYSRNRELESLG 204
                                       456666666666666778*************************8.777777666655 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   5.7e-05      0.13       2      76 ..     169     272 ..     168     296 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.7e-05
                                       EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.........-GGG-TT-SE......................... CS
                            XdhC_C   2 vifGaghvaqalarlaaalgfrvtvvdpreefa.........tkerfpeade......................... 44 
                                       +++Gag+ +   +++a+++g++v+v+  ++e++          +++f+   +                         
  gi|518652646|ref|YP_008142166.1| 169 LVYGAGNTGIFTVQIARQMGMDVYVYSRNRELEslgikvldsVPDDFK---Adiivnplggklfgdsikhlkrrgki 242
                                       799***********************9999887788886666333333...13355556666666666666666666 PP

                                       .-EEEE--S-HHHHHHHHHHHSSS--SEEEESS CS
                            XdhC_C  45 .tavvvlthdhklDaealeaalrkkaayigllG 76 
                                        t+ v+  ++ +lD +   ++ +++++ ig  G
  gi|518652646|ref|YP_008142166.1| 243 vTYGVLTGRNADLDIA---NVYTNELEIIGSTG 272
                                       6666666666555532...22323455555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 2139.69
//
Query:       gi|518652647|ref|YP_008142167.1|  [L=213]
Description: hypothetical protein FACI_IFERC00001G1286 [Ferroplasma acidarmanus fer1]
Scores for complete 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  218.5   0.0    6.2e-65  218.3   0.0    1.0  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
  ------ inclusion threshold ------
      0.097   12.6   0.0       0.36   10.8   0.0    1.8  2  AhpC-TSA        AhpC/TSA family


Domain annotation for each model (and alignments):
>> 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 !  218.3   0.0   6.9e-69   6.2e-65       1     198 []       2     199 ..       2     199 .. 0.99

  Alignments for each domain:
  == domain 1  score: 218.3 bits;  conditional E-value: 6.9e-69
                                       EEEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHH CS
                    Ribul_P_3_epim   1 kiapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefa 77 
                                       +i+pS++s +  +lg ++k+ ++aga ++H+D+mDghfv+N+t+gp  v a+rk t+l ld+HLm+e++dr+ ++f+
  gi|518652647|ref|YP_008142167.1|   2 EISPSIISSNLLELGTQIKECQDAGAGSFHLDIMDGHFVDNITMGPDLVAAIRKGTNLRLDCHLMIERPDRYYKSFI 78 
                                       599************************************************************************** PP

                                       HCT-SEEEEE-ST-TTHHHHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHH CS
                    Ribul_P_3_epim  78 eagasiisvHaEalehlkrtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekik 154
                                       +aga+++ +H+E+  ++ ++i++ ++  ++ g+v+np t ++ + +l++  ++vl+msv Pgf+GQkFi++ lek+k
  gi|518652647|ref|YP_008142167.1|  79 NAGADVLLIHYETPIEVINLIKKFQDENIRYGIVINPDTDVKKIYKLIPGSEIVLVMSVFPGFSGQKFIEKSLEKVK 155
                                       ***************************************************************************** PP

                                       HHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEESHHHH CS
                    Ribul_P_3_epim 155 kvrklidekeldlkievDGGvkldnieqiaeagadvlVagsavf 198
                                       ++r+ ide++++++ie+DGG+++++ + ++eagad+lV++s++f
  gi|518652647|ref|YP_008142167.1| 156 ALREFIDENNYSTRIEIDGGINNETGKLAVEAGADILVSASYIF 199
                                       ******************************************98 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     4e-05      0.36      41     101 ..      63     126 ..      61     138 .. 0.85
   2 ?   -0.8   0.0      0.15   1.3e+03      66      89 ..     150     173 ..     129     184 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4e-05
                                       HHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H....SSEEEE-TTSHHHHHTT-E CS
                          AhpC-TSA  41 Cttelpalaklyeefkergvevigvsvdspeshkkfiekes...lnfpllsDeegkvakaygvl 101
                                       C   +++  ++y+ f ++g++v+ +  ++p ++ + i+k +   + + ++  ++ +v k y+++
  gi|518652647|ref|YP_008142167.1|  63 CHLMIERPDRYYKSFINAGADVLLIHYETPIEVINLIKKFQdenIRYGIVINPDTDVKKIYKLI 126
                                       77777778899********************6666666655555****************9986 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.15
                                       ESSSCHHHHHHHHH-H.SSEEEE- CS
                          AhpC-TSA  66 svdspeshkkfiekeslnfpllsD 89 
                                       s ++++++++fi+++++  ++  D
  gi|518652647|ref|YP_008142167.1| 150 SLEKVKALREFIDENNYSTRIEID 173
                                       778888999999999887776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1388.44
//
Query:       gi|518652648|ref|YP_008142168.1|  [L=508]
Description: hypothetical protein FACI_IFERC00001G1287 [Ferroplasma acidarmanus fer1]
Scores for complete 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   81.8   0.0    8.4e-23   80.8   0.0    1.5  1  ABC1      ABC1 family
  ------ inclusion threshold ------
      0.027   13.9   0.3      0.027   13.9   0.3    1.6  2  Pkinase   Protein kinase domain
       0.15   12.0   0.1       0.31   10.9   0.1    1.5  1  APH       Phosphotransferase enzyme family


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.8   0.0   1.4e-26   8.4e-23       6     118 ..     108     219 ..     103     220 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.8 bits;  conditional E-value: 1.4e-26
                              ABC1   6 kleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelr.ldleelvd 81 
                                       k+e++F++fde++i  AS++qV+rAk k g++ avKv r ++++ +k+Dl ++k l++++k+f+ ++   ++ +++ 
  gi|518652648|ref|YP_008142168.1| 108 KMETVFESFDENAISGASLGQVYRAKYK-GRDAAVKVNRHNIDNVLKRDLIIIKKLLNMFKRFIDNYLyISISNVLS 183
                                       899**********************986.999***********************************999******* PP

                              ABC1  82 efskslleEldferEAknaekfrenfaklkevkvPkv 118
                                       +fs +++ E +++ EA+n +++ +n++k++ + +P+v
  gi|518652648|ref|YP_008142168.1| 184 DFSARIYDETNYLVEAENIKRIGNNIKKYD-IIIPEV 219
                                       ***************************986.557776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.79   4.7e+03      12      35 ..     126     147 ..     124     162 .. 0.76
   2 ?   13.9   0.3   4.4e-06     0.027     111     153 ..     262     304 ..     190     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.79
                                       SEEEEEEEETTTTEEEEEEEEECH CS
                           Pkinase  12 fGkVykaveketgkivAvKkikke 35 
                                        G+Vy+a+   +g+  AvK+ +++
  gi|518652648|ref|YP_008142168.1| 126 LGQVYRAK--YKGRDAAVKVNRHN 147
                                       69999999..68899999976554 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.4e-06
                                       HHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
                           Pkinase 111 leylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                                       ++ l ++ i+H D  p Ni i+++g++ + DFG++ +l+ +++
  gi|518652648|ref|YP_008142168.1| 262 IRMLLRNDIFHADPHPGNIAISDEGKIILYDFGMVGKLDDDTR 304
                                       56777899***************************99988765 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   5.2e-05      0.31     157     197 ..     262     297 ..     238     300 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 5.2e-05
                                       HHH--SSS-EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
                               APH 157 aallpgelptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                                        + l+   +  + H D+hpgN+ +  d+g++  + Df+++g
  gi|518652648|ref|YP_008142168.1| 262 IRMLL---RNDIFHADPHPGNIAIS-DEGKI-ILYDFGMVG 297
                                       44444...78899************.55665.488999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); 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: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.44
# Mc/sec: 3441.65
//
Query:       gi|518652649|ref|YP_008142169.1|  [L=126]
Description: hsp 20 family small heat shock protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.5e-15   54.6   0.2    1.1e-14   54.4   0.2    1.1  1  HSP20       Hsp20/alpha crystallin family
    4.1e-08   32.6   0.0    6.5e-08   32.0   0.0    1.3  1  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 !   54.4   0.2   1.3e-18   1.1e-14       4      91 ..      35     121 ..      32     126 .] 0.88

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.3e-18
                                       SSEEEEEEEEE-TT--CCCEEEEEETTEEEEEEE--..---TT----SS---EEEEEE--STTB-TTT.-EEEEETT CS
                             HSP20   4 eeeeefevkldvpglkkeelkvkvednrvlvkgeheeeeedekglikerssrkFsrkftLPenvdadk.vkaslkdG 79 
                                       e++  + +++d+pg++++++kv++e+n +++++ +e  + +++++ ++r ++ F+r ++LP +vd+++  +a+++dG
  gi|518652649|ref|YP_008142169.1|  35 EDNGYIGIEADLPGFARDDIKVTLEKNAIVIRADRE-IKPEGTVFENQRPEKVFKR-MSLPMEVDTEQdFSAKYNDG 109
                                       45555679****************************.9999******9******97.69******875489999*** PP

                                       EEEEEEEBSS-- CS
                             HSP20  80 vLtvtvpkkepe 91 
                                       vL++++p k+ +
  gi|518652649|ref|YP_008142169.1| 110 VLSLKIPVKNVK 121
                                       *******98765 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 !   32.0   0.0   7.2e-12   6.5e-08       4      61 ..      40     113 ..      37     115 .. 0.92

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 7.2e-12
                        ArsA_HSP20   4 yvlkldLPfvdkeeidlsrsgdeLtIkig................nfrRqitLPsvlarkevtsAkfedgvLeI 61 
                                       + + +dLP++ +++i+++ + + ++I+++                +  ++++LP+ ++ ++  sAk++dgvL  
  gi|518652649|ref|YP_008142169.1|  40 IGIEADLPGFARDDIKVTLEKNAIVIRADreikpegtvfenqrpeKVFKRMSLPMEVDTEQDFSAKYNDGVLSL 113
                                       56789***********************************9998877788**********************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 887.83
//
Query:       gi|518652650|ref|YP_008142170.1|  [L=527]
Description: hypothetical protein FACI_IFERC00001G1289 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (527 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       856  (0.0477439); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3718.82
//
Query:       gi|518652651|ref|YP_008142171.1|  [L=567]
Description: hypothetical protein FACI_IFERC00001G1290 [Ferroplasma acidarmanus fer1]
Scores for complete 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-217  721.4   0.0   6.2e-217  721.2   0.0    1.0  1  MM_CoA_mutase  Methylmalonyl-CoA mutase


Domain annotation for each model (and alignments):
>> MM_CoA_mutase  Methylmalonyl-CoA mutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  721.2   0.0  3.5e-221  6.2e-217       3     513 .]      47     559 ..      44     559 .. 0.98

  Alignments for each domain:
  == domain 1  score: 721.2 bits;  conditional E-value: 3.5e-221
                     MM_CoA_mutase   3 aegievkplYtaedleek.klgeslPGefPftRGvkatmyrgrpWtirqyagfstaeetnerykklLeaGqtglsva 78 
                                       ++ ++vk+lYt+ dl+++ +     PGe+PftRGv+++myrgr+Wt+r++ gf+t+ +tn+r+k+l+e+G tgls+a
  gi|518652651|ref|YP_008142171.1|  47 SSSMPVKELYTRGDLPDNiDSILGNPGEYPFTRGVYPNMYRGRNWTMRMFSGFGTPDDTNKRLKYLIENGETGLSIA 123
                                       46799**********6666666789**************************************************** PP

                     MM_CoA_mutase  79 fdlptlrgyDsdhpraegevGkaGvaidsledmetlldgidldkvsvsmtinaaalpllamylaaaeeqgvdlekls 155
                                       fd+ptl+g+D+d++raegevGk+Gv+++sl+dme+++dgidl+kvs+smtina+a++l+amy+++aee+g++lek+ 
  gi|518652651|ref|YP_008142171.1| 124 FDMPTLYGFDCDNKRAEGEVGKCGVNVSSLHDMERIFDGIDLSKVSTSMTINAPAAILTAMYFVLAEEKGIPLEKIA 200
                                       ***************************************************************************** PP

                     MM_CoA_mutase 156 gtiqnDiLkellargtyiyppepslrliadiieyaakevpkfntisvsgyhireaGatavqElAftladGveYvral 232
                                       gt+q+DiLke++a+++++yppe +lrli d++ y +++vpk+n isvsgyhireaG++avqElAftladG+ Y++ +
  gi|518652651|ref|YP_008142171.1| 201 GTVQADILKEYIAQKEWMYPPEAHLRLIRDMLTYSTEHVPKWNYISVSGYHIREAGSSAVQELAFTLADGFYYIEMG 277
                                       ***************************************************************************** PP

                     MM_CoA_mutase 233 leaGldvdefaprlsFffaigsdffeeiAklRAaRrlWarivkekfgakeekslklrvhaqTsgvsltaqdpyvNil 309
                                       ++aGl+vd+fapr+sFff+ + +ffeeiAk+RAaRr+Wa+++kek++ak+++s++l++h+qTsg++lt q+p +Ni+
  gi|518652651|ref|YP_008142171.1| 278 MNAGLNVDDFAPRMSFFFNSSINFFEEIAKFRAARRIWATVLKEKYHAKNPRSMELKFHTQTSGYTLTWQQPLNNIV 354
                                       ***************************************************************************** PP

                     MM_CoA_mutase 310 RttlealaAvlggtqslhtnsfDealalPtefsariArntqlilaeEsgvakvvDPlgGSyyvEaLTdelaekawkl 386
                                       Rtt+ea+aAvlggtqslhtns+Dea+alPt++++++A++tq+i+aeE+g+a+v+DPlgGSyy+E+LT e++ +a k+
  gi|518652651|ref|YP_008142171.1| 355 RTTIEAMAAVLGGTQSLHTNSYDEAWALPTDNAVKVALRTQQIIAEETGIADVIDPLGGSYYLERLTCEMEIEAYKY 431
                                       ***************************************************************************** PP

                     MM_CoA_mutase 387 fqeieeaGGmlkaiesGlvqeeiaesaarrqkaiesrkevivGvNkfrpneeekelevlkideeveerqaerlealr 463
                                       f eie++GG+l a++sG++q+eia++++++q +ie+++++ivGvN++  +++ek++++lki++ +e+ q++ l++++
  gi|518652651|ref|YP_008142171.1| 432 FSEIEKMGGILDAVKSGYIQKEIADTSYKKQLKIENEDDIIVGVNRY-VDKDEKPINTLKITDIAENGQINSLKNIK 507
                                       ***********************************************.78889*********999************ PP

                     MM_CoA_mutase 464 aerdeaavkaaLaalgeaarse..nllaraveaaralatlGeisdaleevfg 513
                                       ++rde++v + L++l++a+++e  nl++++++++r ++tl eis++ ++ fg
  gi|518652651|ref|YP_008142171.1| 508 SKRDESKVAESLEKLKNAMEDEsvNLMPYIMDCVRNYCTLEEISNIGRDIFG 559
                                       ********************889**********************9999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.24s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 4046.93
//
Query:       gi|518652652|ref|YP_008142172.1|  [L=246]
Description: hypothetical protein FACI_IFERC00001G1291 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-26   91.7   0.3    7.6e-26   91.4   0.3    1.1  1  GDPD      Glycerophosphoryl diester phosphodiesterase family


Domain annotation for each model (and alignments):
>> GDPD  Glycerophosphoryl diester phosphodiesterase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.4   0.3   4.2e-30   7.6e-26       1     259 []      16     240 ..      16     240 .. 0.90

  Alignments for each domain:
  == domain 1  score: 91.4 bits;  conditional E-value: 4.2e-30
                                       TTTTTTTSSTTSHHHHHHHHHTT-SEEEEEEEE-TTS-EEE-SSSBSTTTCSCCCH.BGGGS-HHHHHTSTECCTTC CS
                              GDPD   1 HRGasgnlpEnTlesfakAaelGadyiEfDvqlTkDgvpVvlHDfnldrttdvagrldvkdltleelkrldkiaken 77 
                                       HRG+++++ EnT+esf++A++   + +E+Dv+l++D+ + v+HDfnl+r+   ++  d++++  +e+++        
  gi|518652652|ref|YP_008142172.1|  16 HRGLPSEYVENTIESFENAFKYT-NIVELDVHLSRDNEVYVIHDFNLNRLASIDK--DIENIESAEIDKIM------ 83 
                                       ********************998.*******************************..9***9999999888...... PP

                                       CCCSCCCSSGCCB...BHHHHHHHHHHCCSEEEEEEECCCCCCCHHHHHHTCHHHCCCCCSCHHTT..STTCSCEEE CS
                              GDPD  78 kaqlsenrvrlefpfptleevlkkpqnvglnieikipmlseakeeeelqivkeilksvdeilkkvlkkadkrkvifs 154
                                          ++++++      p l +++k  ++  + +e k+ + + +  + e    k +l++v  ++        ++ v + 
  gi|518652652|ref|YP_008142172.1|  84 ---VRGHNI------PKLRDLFKLFRDKYFLVELKTVHDDGYLVKNE--LTKYTLQVVESMG-------MEDHVCII 142
                                       ...567887......9******9877777777777777777777776..8999999999998.......78999999 PP

                                       ESTHHHHHHHHHTCTCTEEEEEEHHHHHHC-E.EECHCCCCCCCTCCCCHHCCCHCCCEB.CHHHHHHHTT-EEEEB CS
                              GDPD 155 sfnpdilkllrekqpklpllflteggteaeadssleraakfakadallgevsavaeglgdpdlVkraksrglvvhvy 231
                                       sf+p +l++  e++ ++ l f +++ +e++  + + +++++++ + +l+e ++           k++++ g  v+++
  gi|518652652|ref|YP_008142172.1| 143 SFDPYALRRAGELSRTIMLGFDYDQHSEKYIGKIDCKDLRSMGVSLFLPEYKKEYMK-----KFKEIQEDGYFVVPW 214
                                       ***************999999999999999998888899999999999998888877.....8************** PP

                                       SB-THSHHHHHHHHCCC-SEEEES-HHH CS
                              GDPD 232 tvnnedeeemkrlleagvdgvitDfpdt 259
                                       tv+ e  e++ +  + g +g it+ +d+
  gi|518652652|ref|YP_008142172.1| 215 TVDRE--EDSMFITDSGLNGYITNMVDK 240
                                       *****..6666************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1763.42
//
Query:       gi|518652653|ref|YP_008142173.1|  [L=106]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete 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   30.8   0.0    2.5e-07   30.2   0.0    1.3  1  HTH_33         Winged helix-turn helix
     0.0016   19.0   0.0      0.002   18.7   0.0    1.2  1  HTH_32         Homeodomain-like domain
  ------ inclusion threshold ------
      0.012   15.9   0.0      0.018   15.2   0.0    1.3  1  HTH_Tnp_Tc3_2  Transposase
      0.037   14.3   0.2      0.061   13.6   0.2    1.4  1  TFIIE_beta     TFIIE beta subunit core domain
      0.045   13.7   0.0      0.054   13.5   0.0    1.1  1  DUF2001        Phage tail tube protein


Domain annotation for each model (and alignments):
>> HTH_33  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   6.9e-11   2.5e-07       4      38 ..      49      83 ..      46      84 .. 0.92

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 6.9e-11
                            HTH_33  4 rWtlarlaqlieerfgvsysvsgvyrlLkrlGfsy 38
                                        t+++++++iee+f+v+ys++ v+++L++  ++y
  gi|518652653|ref|YP_008142173.1| 49 VCTVHEIQEYIEEEFNVTYSSKEVREILRKFNLTY 83
                                      579**************************988887 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   5.7e-07     0.002      23      73 .]      26      76 ..      12      76 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.7e-07
                            HTH_32 23 rgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                       grp+kl++ ++ ++++ ++++   +  +++++++e++ v++S   v+ iL
  gi|518652653|ref|YP_008142173.1| 26 MGRPSKLHENQMIALKNCVENKKVCTVHEIQEYIEEEFNVTYSSKEVREIL 76
                                      49*****************777799*********9999**********998 PP

>> HTH_Tnp_Tc3_2  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   5.1e-06     0.018       5      48 ..      41      85 ..      38      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.1e-06
                     HTH_Tnp_Tc3_2  5 vrlvrkdPritlreLanelkee.GksvsreTirrrLrkaglkkrk 48
                                        +v+++   t  e+++ ++ee +++ s++ +r +Lrk++l  + 
  gi|518652653|ref|YP_008142173.1| 41 KNCVENKKVCTVHEIQEYIEEEfNVTYSSKEVREILRKFNLTYYP 85
                                      5678888889*******************************9875 PP

>> TFIIE_beta  TFIIE beta subunit core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.7e-05     0.061      15      67 ..      46      97 ..      39      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
                        TFIIE_beta 15 kdgplsleeIlsylslqldlsdknwllleaLknnpkieyDpkkgkfsfkPlyn 67
                                      +++  +++eI++y+  +++++   ++++e+L++ +  +y p  +k+ + + yn
  gi|518652653|ref|YP_008142173.1| 46 NKKVCTVHEIQEYIEEEFNVTYSSKEVREILRKFNLTYY-PLLRKYTYPSYYN 97
                                      44589**********999***999********9886666.4556777766665 PP

>> DUF2001  Phage tail tube protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.5e-05     0.054      78     136 ..      12      71 ..       3      74 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
                           DUF2001  78 iktGkdprfelivkleDPda.vGkervvlknvnfdeltlakfeagklleeevpFtFedye 136
                                       +++Gk++r+ + + +  P+    ++ ++lkn++ ++   +  e ++++eee++ t++  e
  gi|518652653|ref|YP_008142173.1|  12 VENGKEKRVLVRTYMGRPSKlHENQMIALKNCVENKKVCTVHEIQEYIEEEFNVTYSSKE 71 
                                       678999999999999999998899*******************************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       965  (0.0538234); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.35s 00:00:00.91 Elapsed: 00:00:00.56
# Mc/sec: 565.58
//
Query:       gi|518652654|ref|YP_008142174.1|  [L=245]
Description: hypothetical protein FACI_IFERC00001G1293 [Ferroplasma acidarmanus fer1]
Scores for complete 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   21.5   0.0     0.0002   21.2   0.0    1.1  1  SBP_bac_11  Bacterial extracellular solute-binding protein


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 !   21.2   0.0   1.1e-08    0.0002     100     170 ..     120     207 ..      86     244 .. 0.72

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.1e-08
                                       HHSS--EEEE--T-TTTTHH.HHHHG.GG--HHHHHHHHHTEEEEESSHHHHHHHHHTTT-SEEEEEHHHH...... CS
                        SBP_bac_11 100 lkpglklavadPttspsGlaalalle.aagaqellkalekkvvklgessrqlltaveageadagivyesea...... 169
                                       +  +l++a+++P+ts++G a ++++e + g   ++ +l+++++      r +++ + +g++d+gi  +sea      
  gi|518652654|ref|YP_008142174.1| 120 K--NLRFAIPNPRTSSTGIAFKNYYEeKCG---YYGELKENTAICDVPNREIPKKLINGDVDYGIMLKSEAihwkfr 191
                                       3..78*********************5558...********99888888**********************666555 PP

                                       ...............H CS
                        SBP_bac_11 170 ...............k 170
                                                      +
  gi|518652654|ref|YP_008142174.1| 192 hyfpdvvkekfswllL 207
                                       5555555555544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); 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: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1308.01
//
Query:       gi|518652655|ref|YP_008142175.1|  [L=272]
Description: hypothetical protein FACI_IFERC00001G1294 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.004   17.4   1.3      0.016   15.5   0.2    2.6  3  Ish1      Putative stress-responsive nuclear envelope protein


Domain annotation for each model (and alignments):
>> Ish1  Putative stress-responsive nuclear envelope protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.22   3.9e+03       6      19 ..     164     177 ..     164     181 .. 0.81
   2 ?   -3.9   0.1         1   1.8e+04      22      33 ..     205     216 ..     200     216 .. 0.65
   3 !   15.5   0.2   8.8e-07     0.016       6      32 ..     234     259 ..     233     266 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.22
                              Ish1   6 dsdLkkWLdshGip 19 
                                       +++++ ++   Gi 
  gi|518652655|ref|YP_008142175.1| 164 EENMRTFWLYKGIN 177
                                       58999999999997 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 1
                              Ish1  22 kaastRdeLlkl 33 
                                       k+   R +Llkl
  gi|518652655|ref|YP_008142175.1| 205 KKSEERGKLLKL 216
                                       666678888885 PP

  == domain 3  score: 15.5 bits;  conditional E-value: 8.8e-07
                              Ish1   6 dsdLkkWLdshGipvskaastRdeLlk 32 
                                        ++Lk++L++ Gi+v +  ++ d++ +
  gi|518652655|ref|YP_008142175.1| 234 REQLKNYLSDKGIKV-QNSKNIDYMYE 259
                                       59************8.99999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       982  (0.0547716); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1762.02
//
Query:       gi|518652656|ref|YP_008142176.1|  [L=608]
Description: hypothetical protein FACI_IFERC00001G1295 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.6e-19   68.9   0.0    1.3e-18   67.9   0.0    1.6  1  Radical_SAM     Radical SAM superfamily
    9.2e-06   25.8   0.0    9.2e-06   25.8   0.0    2.3  3  Fer4_14         4Fe-4S single cluster domain
      7e-05   23.1   0.0    0.00021   21.6   0.0    1.8  1  Fer4_12         4Fe-4S single cluster domain
  ------ inclusion threshold ------
      0.028   14.5   0.0      0.072   13.2   0.0    1.6  1  DUF2059         Uncharacterized protein conserved in bacteria
       0.14   12.8   0.0        8.5    7.0   0.0    2.6  2  Arg_decarbox_C  Arginine decarboxylase C-terminal helical ext


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 !   67.9   0.0   3.7e-22   1.3e-18       1     166 [.     149     307 ..     149     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 3.7e-22
                                       EEEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH..HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   1 vvvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk..aekgvkevilgggepllypdfvellerlaklav 75 
                                       vv+t+ C l C++C ++ +   +++ ++ s+++i   +++++  +  g++ v ++ggep+l++d+++ ++ ++++  
  gi|518652656|ref|YP_008142176.1| 149 VVITNRCDLSCWYCFFYAK--ENEPIYEPSLDQIRLMLRRMRneKPVGANAVQITGGEPTLRDDIIDVIRIAREE-- 221
                                       689**************96..*********************845555*****************9999999999.. PP

                                       CTEEEEEEECSSCHG..HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEE CS
                                       xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  76 pgiritvetngtlpd..eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdriv 150
                                          ++ + tn ++    +++++r +++g ++v+ + + ++++      n+ ++f e+  ale +++a +  vv + +
  gi|518652656|ref|YP_008142176.1| 222 GYEHVQMNTNSVRAAydPDFVKRARDAGSNVVYTSFDGPTPR-----SNP-KNFWEIPMALEHYKQAPMG-VVLVPT 291
                                       9************88**************************9.....546.67777779********999.****** PP

                                       EBTTTSHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxx RF
                       Radical_SAM 151 glpGendeeleellel 166
                                       ++ G nd+ l +++++
  gi|518652656|ref|YP_008142176.1| 292 VIGGINDQYLGDMIKF 307
                                       ***********99998 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 ?   -2.6   0.1       1.6   5.7e+03      12      23 ..      54      65 ..      52     112 .. 0.73
   2 ?   -3.3   1.1       2.6   9.3e+03       8      19 ..     130     141 ..     129     144 .. 0.83
   3 !   25.8   0.0   2.6e-09   9.2e-06       3      91 ..     150     234 ..     149     248 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.6
                           Fer4_14 12 CkgCdnketwks 23
                                      C+ C ++e++++
  gi|518652656|ref|YP_008142176.1| 54 CPLCADEEKFDQ 65
                                      888888887765 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
                           Fer4_14   8 CnlsCkgCdnke 19 
                                       C+ +C  C +++
  gi|518652656|ref|YP_008142176.1| 130 CPTHCGLCVKHK 141
                                       9*******9776 PP

  == domain 3  score: 25.8 bits;  conditional E-value: 2.6e-09
                           Fer4_14   3 vrlsgCnlsCkgCdnketwkselgkpqtee..lleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       v +++C lsC  C+  ++ ++   +p+ ++  l+ +++   +++ + ++ + +tGGeP +    ++++++++  +ee
  gi|518652656|ref|YP_008142176.1| 150 VITNRCDLSCWYCFFYAKENEPIYEPSLDQirLMLRRM--RNEKPVGANAVQITGGEPTL---RDDIIDVIRIAREE 221
                                       559***********888778876666544411444555..88888999**********94...489*********** PP

                           Fer4_14  78 ypekkiwletngtl 91 
                                       +   +++++tn + 
  gi|518652656|ref|YP_008142176.1| 222 G-YEHVQMNTNSVR 234
                                       9.668999999875 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   5.8e-08   0.00021       4      92 ..     144     231 ..     141     243 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 5.8e-08
                           Fer4_12   4 eGvrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkkesi......egltllGGEPllpenaealle 74 
                                       +G+  ++ +++C+lsC +Cf       k+++++ ++ l++i   l   ++      + + ++GGEP l   ++++++
  gi|518652656|ref|YP_008142176.1| 144 TGLGNVVITNRCDLSCWYCFF----YAKENEPIYEPSLDQIRLMLRRMRNekpvgaNAVQITGGEPTL---RDDIID 213
                                       5666788899*********93....34444444444444443333221111234559***********...9999** PP

                           Fer4_12  75 lvkevkeekpekdiwlyt 92 
                                       +++  +ee++e + + ++
  gi|518652656|ref|YP_008142176.1| 214 VIRIAREEGYEHVQMNTN 231
                                       ********9986666665 PP

>> DUF2059  Uncharacterized protein conserved in bacteria (DUF2059)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05     0.072      13      40 ..     562     589 ..     558     591 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
                                       HHS-HHHHHHHHHHHHSHHHHHHHHHHH CS
                           DUF2059  13 ktfteaelkailaFYkSPlGkkllekep 40 
                                       + +t +e k+i+ FY+  lG+ l++ke+
  gi|518652656|ref|YP_008142176.1| 562 RKYTVEEKKRIISFYERSLGRNLTSKEI 589
                                       789**********************997 PP

>> Arg_decarbox_C  Arginine decarboxylase C-terminal helical extension
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0024       8.5       3      30 ..     313     340 ..     312     352 .. 0.86
   2 ?    3.0   0.0     0.044   1.6e+02      30      45 ..     565     580 ..     562     583 .. 0.90

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0024
                    Arg_decarbox_C   3 dVLryVqYdpeeLlerlrrqveaagrLt 30 
                                       dV r V+++p  L+ r+ ++++a +r+t
  gi|518652656|ref|YP_008142176.1| 313 DVVRGVNFQPVSLVGRMSDRARARQRIT 340
                                       899******************9996666 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.044
                    Arg_decarbox_C  30 tpeerqalleeleagL 45 
                                       t ee++++++ +e++L
  gi|518652656|ref|YP_008142176.1| 565 TVEEKKRIISFYERSL 580
                                       689************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (608 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 3756.14
//
Query:       gi|518652657|ref|YP_008142177.1|  [L=133]
Description: hypothetical protein FACI_IFERC00001G1296 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-26   93.5   0.0    1.4e-26   93.4   0.0    1.0  1  Archease    Archease protein family (MTH1598/TM1083)
  ------ inclusion threshold ------
      0.096   12.7   0.7        0.2   11.7   0.5    1.6  2  Pallilysin  Pallilysin beta barrel domain
      0.097   13.0   0.1       0.17   12.2   0.1    1.5  1  Mnd1        Mnd1 HTH domain
       0.11   12.7   0.0       0.17   12.1   0.0    1.3  1  DUF1229     Protein of unknown function (DUF1229)


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 !   93.4   0.0   3.2e-30   1.4e-26       1     137 [.       3     132 ..       3     133 .] 0.91

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 3.2e-30
                                       EEE---SSEEEEEEE-SSSHHHHHHHHHHHHHHHS--TT---S-EEEEEEEESSSHHHHHHHHHHHHHHHHHT--S- CS
                          Archease   1 yeyldhtADviieawGksleeafesaalalfeymtdlskvepkeekeieveaedledlLfdfLdellylfdteyfvf 77 
                                       y +ldhtAD++i+++G+sl+++fe+ + a+ +++t  +++e+  ++++e+++++++d+L+++L++++++++te+++f
  gi|518652657|ref|YP_008142177.1|   3 YDILDHTADLKIKVYGNSLNSIFENSVAAISDLITGSKSMENAIKRKVEITKQSVDDMLVQLLNDVIFYLETENVLF 79 
                                       889************************************************************************** PP

                                       ---EEEE.E-SSSEEEEEEEE----.-TT----.----B--S---EEEEETTEEEEEEEEE CS
                          Archease  78 kevkvdeeeeeeeleleaeargekfdkekhevq.tevKAvTyhelrieeeddgweayvvvD 137
                                       ++++     + ++ +l++++ g k+ ++   +  + +KAvTy +l+i+ e+    a +v+D
  gi|518652657|ref|YP_008142177.1|  80 QRAE----INISGNRLNGILFGTKLPDN--PCYsNAIKAVTYYNLKISPEE--GFAILVLD 132
                                       ***4....455899***********666..3444**************988..33445555 PP

>> Pallilysin  Pallilysin beta barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   4.4e-05       0.2      72     110 ..      37      76 ..      19      81 .. 0.86
   2 ?    2.3   0.0     0.035   1.6e+02      44      73 ..      67      99 ..      66     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.4e-05
                        Pallilysin  72 tknksitn.lkrrldielesldeirvkvidDvrlkigees 110
                                       t  ks++n +kr+++i  +s+d++ v++ +Dv + +++e+
  gi|518652657|ref|YP_008142177.1|  37 TGSKSMENaIKRKVEITKQSVDDMLVQLLNDVIFYLETEN 76 
                                       55677765499*********************98887765 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.035
                        Pallilysin 44 eiifllddteevyewen...sslrrnGiylstk 73
                                      ++if+l++ + +++ ++   s  r nGi++ tk
  gi|518652657|ref|YP_008142177.1| 67 DVIFYLETENVLFQRAEiniSGNRLNGILFGTK 99
                                      799999999999986551115568899999875 PP

>> Mnd1  Mnd1 HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   3.7e-05      0.17      15      42 ..      40      67 ..      38      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.7e-05
                              Mnd1 15 KeleklapkekgivsqsVkdvlqsLvdD 42
                                      K +e  ++++  i++qsV d+l +L++D
  gi|518652657|ref|YP_008142177.1| 40 KSMENAIKRKVEITKQSVDDMLVQLLND 67
                                      7889999999****************99 PP

>> DUF1229  Protein of unknown function (DUF1229)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05      0.17      16      73 ..      67     123 ..      55     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                           DUF1229  16 flilllssseiyfflketyiGqriinsi.aseklnehvdywnavkkdffvypkitigse 73 
                                        +i+ l + ++ f++ e+ i  + +n+i +  kl +++ y na+k   + y ++ i  e
  gi|518652657|ref|YP_008142177.1|  67 DVIFYLETENVLFQRAEINISGNRLNGIlFGTKLPDNPCYSNAIK--AVTYYNLKISPE 123
                                       589*****************9999999845799************..555656665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       612  (0.0341346); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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 0.29s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 949.46
//
Query:       gi|518652658|ref|YP_008142178.1|  [L=902]
Description: hypothetical protein FACI_IFERC00001G1297 [Ferroplasma acidarmanus fer1]
Scores for complete 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-63  213.8   1.1    6.8e-62  209.6   1.1    2.5  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    3.3e-23   82.1   0.1    4.4e-11   42.2   0.0    3.3  3  tRNA-synt_1g   tRNA synthetases class I (M)
    1.9e-13   50.7   0.1      5e-13   49.3   0.1    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    9.4e-09   35.0   0.2    5.5e-08   32.5   0.2    2.2  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
      1e-08   34.9   0.0    9.9e-05   21.8   0.0    2.7  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
    0.00074   18.5   0.0      0.003   16.5   0.0    2.0  1  tRNA-synt_1f   tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.6   1.1   2.3e-65   6.8e-62       2     595 ..       9     645 ..       8     652 .. 0.79

  Alignments for each domain:
  == domain 1  score: 209.6 bits;  conditional E-value: 2.3e-65
                       tRNA-synt_1   2 lyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaiea 78 
                                       + ++W ++ +f+++   +++k++f ++++ Py +GslH+Gh  + tl di+ rykr++G++vl+ +G+   G +i a
  gi|518652658|ref|YP_008142178.1|   9 WRDEWAKSHIFEPS--IDDTKPKFFVTVPWPYSNGSLHVGHGRTYTLGDIIARYKRLTGFNVLFPMGFHESGTPILA 83 
                                       6789**********..8889*****************************************************9977 PP

                       tRNA-synt_1  79 kvek.............k.lgakekkerkklgreefrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkelee 141
                                         e+             + l + e+ +  +   e f ++ ++++++++  i k++ +lG s+D+ r+    d+ ++e
  gi|518652658|ref|YP_008142178.1|  84 FSERirngdpgtiklyrNyLMEYENPSDIDGIIESF-KNPQNIADYFSRVIVKDFMDLGYSIDWTRKFTSADPFYQE 159
                                       665521122111100001011112222222223333.34567899999***************************** PP

                       tRNA-synt_1 142 avkevfvrladkgliyrgkklvnwstklktalselEveykdkkdalih.vafpladkeevklviaTTtPeTllgdta 217
                                        vk+ f++l  kgli +gk+++ +s + + a+ e +++  d++ ++i+ ++  l ++++ +l++a  +PeTl+g t 
  gi|518652658|ref|YP_008142178.1| 160 IVKWQFMQLESKGLIKKGKYPILYSINDENAVGEDDIKDGDTDKVTIEeFTGVLFKGDKYYLIAASLRPETLFGVTN 236
                                       *************************************99998877764244444555555***************** PP

                       tRNA-synt_1 218 vavnpeldyv...itkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGv 291
                                       + +n + +y+    ++  +++  +   ++  +++  +    ++ +e++g +++ p++++ + +i  d+vd ++GtGv
  gi|518652658|ref|YP_008142178.1| 237 LWINSDAQYAmvrYNNMDVVMSADGYTKFSLQHDGIEYIGSVNPEEIIGEKFNVPFQDTPVDVIGADFVDPDNGTGV 313
                                       **********87545555555555555555555666999************************************** PP

                       tRNA-synt_1 292 VkiaPahdedDyevgkkynl..evinildedgtlteea..................................aefeg 332
                                       V   P+h   Dy    ++n+  ++  +++ + +++ e                                   + ++g
  gi|518652658|ref|YP_008142178.1| 314 VYSVPGHSIFDYLYYGRNNIknSIKKVVEVKSKMSVESlvkkyglehnesklkeatqelykdefyngvlinsGPYSG 390
                                       ********************764556677777777666679999999999*************************** PP

                       tRNA-synt_1 333 lkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvke..ladaalkavekvqfvpkskek 407
                                       ++v + r+++ ++l  k++ +   +++ +  ++  +  +i+  +++qWf+  ++  l+++a +++++++f+p+ ++k
  gi|518652658|ref|YP_008142178.1| 391 MNVAAGREAIKNDLISKNMAVIFYETTRKA-VTRSGSRVIVAVLKDQWFIDYSPewLKNKAHEVINSMRFYPELYRK 466
                                       ***************998766665555443.4444556778899*******99999*****************9888 PP

                       tRNA-synt_1 408 ryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekde 484
                                        +++ +   ++    R+r  G+r+p+       e  v e+l++ +  + +   ++k++ k++ d+l       + ++
  gi|518652658|ref|YP_008142178.1| 467 LMMDAIDWLKERPCARKRGIGTRLPFD------ENWVIESLSDSTIYMLAY--TNKKELKDIYDRL-------HSIP 528
                                       877777777777899**********72......223333444444322222..2222234455555.......4443 PP

                       tRNA-synt_1 485 .dvlDvWFsSgswpfs....tlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgse.Pfkevlvhgl 555
                                        d+lD       + +     +++   + ++e++  +  d+ ++    i   +a  i+   a++  +     ++++gl
  gi|518652658|ref|YP_008142178.1| 529 gDILDYVLLGKETRNRyddyIMENARSAKKEFDYWYGNDLRITAPPHISNHLAFFIMNHAAIFSGNkLPGGLMISGL 605
                                       388888776666655511114455556689999999***************99999998887654424468999999 PP

                       tRNA-synt_1 556 vrdeeGrKmSKslgNvidpldvikkygadalRltli.lsdv 595
                                       v+ ++G K+SKs+gNvi+ l++i++y+ad+ Rl+++  +d 
  gi|518652658|ref|YP_008142178.1| 606 VI-SNGAKISKSKGNVISLLEIINRYSADIYRLFMAaGADI 645
                                       98.68******************************966665 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 !   42.2   0.0   1.5e-14   4.4e-11       2      53 ..      31      82 ..      30      93 .. 0.95
   2 !    9.9   0.0   9.3e-05      0.28      62     135 ..     121     196 ..     115     229 .. 0.86
   3 !   26.1   0.0   1.1e-09   3.4e-06     269     371 ..     557     656 ..     545     662 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.5e-14
                                      EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHH CS
                      tRNA-synt_1g  2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpie 53
                                      +vt+++pY+ng+lH+Gh +++  +Di+aRykrl+g +vlf  g  e Gtpi 
  gi|518652658|ref|YP_008142178.1| 31 FVTVPWPYSNGSLHVGHGRTYTLGDIIARYKRLTGFNVLFPMGFHESGTPIL 82
                                      8*************************************************97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 9.3e-05
                                       -HHHHHHHHHHHHHHHHHHTT---SEEEETTS..HHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
                      tRNA-synt_1g  62 tpeelvekvheeikelfkklnisfdkygrtts..eehkelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                                       +p+++++ +++ i ++f +l+ s d   + ts     +e+v+  f +l++kgli+++++  ly+ +de+   +  +
  gi|518652658|ref|YP_008142178.1| 121 NPQNIADYFSRVIVKDFMDLGYSIDWTRKFTSadPFYQEIVKWQFMQLESKGLIKKGKYPILYSINDENAVGEDDI 196
                                       799999999**********9999886655444115579****************************9988776655 PP

  == domain 3  score: 26.1 bits;  conditional E-value: 1.1e-09
                                       SGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHH..TT----S-EEEE--EEE--------------HHHHHH CS
                      tRNA-synt_1g 269 eekwkeyWakdkevelvhfigkdiikFHtifwPaillg..aelklpkkvvaheyltvegkKlSkSrgvvvkakeale 343
                                       +++++ ++   ++     + +   i  H  f+ +   +  ++ klp  ++ ++ +  +g+K+SkS+g+v+   e+++
  gi|518652658|ref|YP_008142178.1| 557 KKEFDYWYG--ND---LRITAPPHISNHLAFFIMNHAAifSGNKLPGGLMISGLVISNGAKISKSKGNVISLLEIIN 628
                                       556664442..23...3344555666777777665555778899********************************* PP

                                       HH-HHHHHHHHHHHS-TTS-EEE-HHHH CS
                      tRNA-synt_1g 344 rldadllRYylaaeapekkDldfswedf 371
                                       r++ad+ R ++aa a+ ++ ld++++d+
  gi|518652658|ref|YP_008142178.1| 629 RYSADIYRLFMAAGADISSLLDWNEKDI 656
                                       ************9998888888887776 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 !   49.3   0.1   1.7e-16     5e-13       3     147 ..     686     814 ..     685     819 .. 0.82

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1.7e-16
                       Anticodon_1   3 wilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaP 79 
                                       w+ s ++k +k +  ++e++++++a+ ++++ ++ndl    +e +  +++           ++l+ +l  +l+ l+P
  gi|518652658|ref|YP_008142178.1| 686 WFRSSFYKNLKNYLGYMESMNIRDACISIFYNVMNDL--KNVENHGGDIN-----------SALKPILADWLKALSP 749
                                       99***********************************..44566666663...........68************** PP

                       Anticodon_1  80 fmPfitEelwqreeeelgkkesimlaewpekaeel.ekeleeeevellkeivkairklrselkikpsse 147
                                       ++Pf +Ee w+   +++++k+++++++   + e   +  +  ++ ++l ++++ ir++ +++ ikp + 
  gi|518652658|ref|YP_008142178.1| 750 VIPFSCEEYWH---RHIDNKTFVSVQPIDTNIESRiDSGI-IKSETYLNRVISDIREIIKIIRIKPEKA 814
                                       **********5...88999*******99954433355555.7788886677777777777777777655 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 !   32.5   0.2   1.8e-11   5.5e-08      29     183 ..     227     403 ..     221     405 .. 0.73

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 1.8e-11
                     tRNA-synt_1_2  29 rpdtlfGvtfvalapehplveklaekkkel...aafieevkkksesereletkekeGvftglkaihPitgekipiwv 102
                                       rp+tlfGvt + + ++ + +    ++ + +   + +++   +++ +e  + + + e    g k   P++++ +++  
  gi|518652658|ref|YP_008142178.1| 227 RPETLFGVTNLWINSDAQYAMVRYNNMDVVmsaDGYTKFSLQHDGIEY-IGSVNPEE-IIGEKFNVPFQDTPVDVIG 301
                                       899999999999999988876654444333111234444444444443.33333333.35777888*********** PP

                     tRNA-synt_1_2 103 anyvlmeygtgavmavPahdqrDfeFakkynlp..ikqvikpedee..kklee.................seeayte 158
                                       a++v  + gtg+v +vP+h   D+ +  + n++  ik+v++ + +   +   +                 ++e y++
  gi|518652658|ref|YP_008142178.1| 302 ADFVDPDNGTGVVYSVPGHSIFDYLYYGRNNIKnsIKKVVEVKSKMsvE---SlvkkyglehnesklkeaTQELYKD 375
                                       *****************************99865599***966554222...1233566777777777777777877 PP

                     tRNA-synt_1_2 159 ...egilvnsgefdglkskeakekiakk 183
                                          +g+l+nsg ++g+++++ +e+i + 
  gi|518652658|ref|YP_008142178.1| 376 efyNGVLINSGPYSGMNVAAGREAIKND 403
                                       5668*****************9999876 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0   0.00011      0.34      22      50 ..      42      70 ..      25     171 .. 0.91
   2 !   21.8   0.0   3.3e-08   9.9e-05     220     299 ..     574     659 ..     552     661 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00011
                                      --BHHHHHHHHHHHHHHHHHHHTT-EEEE CS
                      tRNA-synt_1e 22 ashlGhaRslvafDilrrilqalgYdvqf 50
                                        h+Gh+R++   Di++r+ + +g++v f
  gi|518652658|ref|YP_008142178.1| 42 SLHVGHGRTYTLGDIIARYKRLTGFNVLF 70
                                      68*************************98 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 3.3e-08
                                       THHHHHHH....HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS.S-TTS-EE CS
                      tRNA-synt_1e 220 Phhenela....qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls.ahyrsqld 290
                                       Ph  n la     + a f  ++l    + +g +  +g k+sks +n+i++ ++++++++ + Rl+++  a+  s ld
  gi|518652658|ref|YP_008142178.1| 574 PHISNHLAffimNHAAIFSgNKLPGGLMISGLVISNGAKISKSKGNVISLLEIINRYSADIYRLFMAAgADISSLLD 650
                                       666666653332355555547777788999***********************************9862689999** PP

                                       E-HHHHHHH CS
                      tRNA-synt_1e 291 fkeelleea 299
                                       ++e++++++
  gi|518652658|ref|YP_008142178.1| 651 WNEKDISSV 659
                                       ****99876 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 !   16.5   0.0     1e-06     0.003     262     310 ..     593     641 ..     584     667 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-06
                      tRNA-synt_1f 262 ggeaPekvvYelillkggekmssSkGnvltledwlevaepevlrflilr 310
                                       g + P +++   + +++g+k+s+SkGnv++l ++++ ++ ++ r++++ 
  gi|518652658|ref|YP_008142178.1| 593 GNKLPGGLMISGLVISNGAKISKSKGNVISLLEIINRYSADIYRLFMAA 641
                                       45569999999999*******************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (902 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 6190.18
//
Query:       gi|518652659|ref|YP_008142179.1|  [L=179]
Description: pyruvoyl-dependent arginine decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-57  193.9   0.0    1.7e-57  193.7   0.0    1.0  1  PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC
  ------ inclusion threshold ------
      0.041   14.8   0.0      0.061   14.2   0.0    1.3  1  CwfJ_C_2  Protein similar to CwfJ C-terminus 2


Domain annotation for each model (and alignments):
>> PvlArgDC  Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.7   0.0   1.9e-61   1.7e-57       1     162 []       3     178 ..       3     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 193.7 bits;  conditional E-value: 1.9e-61
                          PvlArgDC   1 vPkkvfltkGvgeskeelasFdlALldAgIenfNLvkvSSilPpeaeivsveeglkelppGsivevvmarassnepg 77 
                                       +Pkk+f+t+G+g+++++l+sF++AL+dA+I+ +NLv+vSSilPp aeiv ++eg k+l+ G+i+++v+ar+ssne +
  gi|518652659|ref|YP_008142179.1|   3 LPKKIFFTRGIGRGETQLQSFENALRDADIAAYNLVSVSSILPPYAEIVDKSEGIKLLSYGQILFTVLARNSSNELN 79 
                                       59*************************************************************************** PP

                          PvlArgDC  78 rliaaavgvaipkdekkgGyiaEysgfgeseeeaeeeaeelaaemlattrgl..............leekiietkei 140
                                       r+i++a+gva+p+d++k+Gy++E++ fg++e+++++ ae+laaemla+t+gl              l++ki++tk+i
  gi|518652659|ref|YP_008142179.1|  80 RMISSAIGVAVPSDRSKWGYLSEHHTFGQTENDSGHFAEKLAAEMLASTMGLddhlkwedkkneyvLDDKILTTKNI 156
                                       *****************************************************************9899******** PP

                          PvlArgDC 141 evaaveakvekygtvlaaavfv 162
                                        +++v+ k ++++tv+aaav+v
  gi|518652659|ref|YP_008142179.1| 157 AATTVVLKPDEWATVIAAAVLV 178
                                       ********************96 PP

>> CwfJ_C_2  Protein similar to CwfJ C-terminus 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   6.9e-06     0.061      18      77 ..      83     143 ..      71     154 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 6.9e-06
                                       HHHS-SSS--EEEEET.TT-..-EEE----HHHH-TTHHHHHHHHHTT--TTT.SS----- CS
                          CwfJ_C_2  18 rrslvknlpyfyvqfd.ykgekgyghviedeerfdlqFareviaglLdlekrrkwrkpkrq 77 
                                        +++  ++p +  +++  +++  +g+  +d+++f  + a e +a+ ++l+++ kw+++k++
  gi|518652659|ref|YP_008142179.1|  83 SSAIGVAVPSDRSKWGyLSEHHTFGQTENDSGHFAEKLAAEMLASTMGLDDHLKWEDKKNE 143
                                       55666677778888875567789****9999*************************97665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 1380.42
//
Query:       gi|518652660|ref|YP_008142180.1|  [L=899]
Description: hypothetical protein FACI_IFERC00001G1299 [Ferroplasma acidarmanus fer1]
Scores for complete 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-32  110.3   0.3    2.9e-31  108.6   0.1    2.0  2  DEAD            DEAD/DEAH box helicase
    5.1e-19   68.7   4.3    4.4e-17   62.4   0.1    3.7  3  Helicase_C      Helicase conserved C-terminal domain
    9.6e-11   42.0   0.1    4.7e-10   39.7   0.0    2.1  2  ResIII          Type III restriction enzyme, res subunit
      7e-10   39.0   0.0    2.3e-09   37.3   0.0    1.9  2  DEAD_assoc      DEAD/H associated
     0.0057   16.5   3.6      0.012   15.6   3.6    1.4  1  Zn_ribbon_SprT  SprT-like zinc ribbon domain
  ------ inclusion threshold ------
      0.014   15.4   0.1      0.051   13.6   0.1    2.0  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.023   14.8   0.2      0.047   13.8   0.2    1.5  1  Zn-ribbon_8     Zinc ribbon domain
      0.033   14.2   0.6       0.89    9.6   0.1    2.6  2  DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domai
        0.1   12.4   1.1        1.3    8.8   0.1    2.6  3  AAA_11          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 !  108.6   0.1   1.5e-34   2.9e-31       1     171 [.      27     195 ..      27     199 .. 0.86
   2 ?   -3.1   0.0       2.9   5.9e+03     130     157 ..     328     355 ..     328     364 .. 0.70

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 1.5e-34
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t+ Q+ aip+il+g++ l+  +TGsGKT+a+l+p+l+++y  ++ +    l+++P+r+L +++l+++  ++ ++d+r
  gi|518652660|ref|YP_008142180.1|  27 TEAQKMAIPEILSGENTLLISPTGSGKTEAALVPLLNKIYL-EKPQSIALLYITPLRALNRDMLSRVFDYCRTLDIR 102
                                       689************************************98.8999999**************************** PP

                                       EEEEETTSSHHHHHHHHHTT.CSEEEEEHHHHHHHH..HCTSSH..CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx..xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldng.vdivvgtpgrlddll..stgkln..lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                       v++  ++ ++  ++++++++ ++i+++tp+ l+ l+  +  +l+  +++++++++DE++++ +++++ +    +++l
  gi|518652660|ref|YP_008142180.1| 103 VQVRHSDISQ-AERNEISRNpAQILITTPESLQLLMmgK--RLRehIKNIKYVIVDEVHEMAQNERGSQFAIAMERL 176
                                       *977665555.5555664444*************88552..44444******************************* PP

                                       HHHCTTSTTTSEEEEEESSBS.H CS
                                       xxxxxxxxxxxxxxxxxxxxx.x RF
                              DEAD 150 pqitcdgklqrqvivlSATlp.k 171
                                       +     g+   qvi lSAT++ +
  gi|518652660|ref|YP_008142180.1| 177 KVL--AGN--FQVIGLSATAKnE 195
                                       544..334..55*******9844 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                                       HHHHHHTTTHHHHHHHHHHSHHHCTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 130 adrlldqgfsdfinrilnqlpqitcdgk 157
                                       ad++ + +  ++in++++++ ++ ++ +
  gi|518652660|ref|YP_008142180.1| 328 ADMVVQFNSPRQINKMVQRIGRAGHSLQ 355
                                       5667777888999****99987777665 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.016        32      28      62 ..      88     122 ..      57     131 .. 0.63
   2 !   62.4   0.1   2.2e-20   4.4e-17       6     108 ..     250     351 ..     245     353 .. 0.87
   3 ?   -0.3   0.2      0.66   1.3e+03       6      52 ..     772     817 ..     767     850 .. 0.72

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.016
                                       HHHH.HHHHHHHTTSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  28 rlek.vklllekkgikvavlhgelpqnereeileqf 62 
                                       +l++ +++  ++ +i+v v h++++q er+ei ++ 
  gi|518652660|ref|YP_008142180.1|  88 MLSRvFDYC-RTLDIRVQVRHSDISQAERNEISRNP 122
                                       332233333.3338*****************98876 PP

  == domain 2  score: 62.4 bits;  conditional E-value: 2.2e-20
                                       HHHHHHHTTTTSEEEEEESSHHHHHH..HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSS CS
                        Helicase_C   6 llellkleeeggkilifvntidrlek..vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGi 80 
                                       +  ++   ee++ +++fvn++  +e+  ++l l  k+  + v+hg+l+ + re +  +f++++++ Li+t+ +e Gi
  gi|518652660|ref|YP_008142180.1| 250 IHSIV---EENKGTIVFVNRRYVAEDisFRLRLWLKDPDIEVHHGSLSRETRETAEMDFKENRVKALICTSSLELGI 323
                                       44454...89999*********88766634444455778888*********************************** PP

                                       TSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  81 dipkvnlVinfdlprnvtsyiqriGRtg 108
                                       d+ ++++V++f+ pr++ +++qriGR+g
  gi|518652660|ref|YP_008142180.1| 324 DVGSADMVVQFNSPRQINKMVQRIGRAG 351
                                       ***************************8 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.66
                                       HHHHHHHTTTTSEEEEEESSHH..HHHHHHHHHHHTTSTEEEESTTSTH CS
                        Helicase_C   6 llellkleeeggkilifvntid..rlekvklllekkgikvavlhgelpq 52 
                                       +le + ++  +++++++++++   r   ++ ++   +i++ v+h++l +
  gi|518652660|ref|YP_008142180.1| 772 ILESIRKRLMNEEVILYCTSCGnkR---TRKIKDITEIRCPVCHSRLVA 817
                                       5666677888999999999998444...466655568999999998644 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   2.4e-13   4.7e-10       3     170 ..      25     193 ..      23     194 .. 0.78
   2 ?   -1.3   0.0      0.92   1.8e+03      48      93 ..     754     799 ..     748     848 .. 0.51

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 2.4e-13
                                       EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHH.HHHHHHH-S......-EEEEESSHHHHHHHHHHGGGG CS
                            ResIII   3 elreyQeeaienlleklkskrdkrglikmaTGtGKTlva.aklierllkkgkee.kflflvprkslleqtleefkkf 77 
                                       ++ e Q+ ai ++l        ++ l+  +TG+GKT  a + l  +++ +++++   l + p ++l   +l+++ ++
  gi|518652660|ref|YP_008142180.1|  25 NPTEAQKMAIPEIL------SGENTLLISPTGSGKTEAAlVPLLNKIYLEKPQSiALLYITPLRALNRDMLSRVFDY 95 
                                       66778888888887......45688999*********9966666666655555559999************888777 PP

                                       TGG.......GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T... CS
                            ResIII  78 lseayke...igkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk... 148
                                         + + +      ++s+ ++++  ++++ ++il+tt +sl+  +     ++ +   ++++++i+DE+H +++++   
  gi|518652660|ref|YP_008142180.1|  96 CRTLDIRvqvRHSDISQAERNE--ISRNPAQILITTPESLQLLM---MGKRLREHIKNIKYVIVDEVHEMAQNErgs 167
                                       7665433444333343333333..699*****************...889999999****************85666 PP

                                       ....TTHHHHHT---SEEEEEESS-S CS
                            ResIII 149 ....swreilekfkeavllglTATpe 170
                                           ++++++    ++ ++gl+AT +
  gi|518652660|ref|YP_008142180.1| 168 qfaiAMERLKVLAGNFQVIGLSATAK 193
                                       66678888777778899*******76 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.92
                                       H-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS- CS
                            ResIII  48 llkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdk 93 
                                       ++ +++ e+++ l p+k++le  ++++++     y   +++++ +k
  gi|518652660|ref|YP_008142180.1| 754 IFLSHYSERVMPLKPTKTILESIRKRLMNEEVILYCTSCGNKRTRK 799
                                       6677788889999999999999888774444333332222222222 PP

>> DEAD_assoc  DEAD/H associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.8   3.5e+03     156     189 ..     364     397 ..     363     399 .. 0.84
   2 !   37.3   0.0   1.2e-12   2.3e-09       5     181 ..     586     746 ..     582     753 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.8
                        DEAD_assoc 156 ledqlDlerlaellrriaageirvvevetprpSp 189
                                        +d+++le++++++ +i+ ge++ v ++ ++ S 
  gi|518652660|ref|YP_008142180.1| 364 CNDVIELEEAKAIVGNIKLGELENVMIKKNSLST 397
                                       6899*****************9999887777775 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.2e-12
                        DEAD_assoc   5 rtllvErfrdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlpllldellell 81 
                                       +++++E  +      ++++  ++G+  n +la +l+  l++ +g +v++  +++ i + ++ + ++ + +++l+  +
  gi|518652660|ref|YP_008142180.1| 586 DKIIIEAHNS-----EIIIQILLGSLGNFTLAQILSGLLTSITGESVEMDYSPYHIYMRVSRNISA-EDVKNLIMNI 656
                                       6788888876.....67*****************************************88655555.4678999*** PP

                        DEAD_assoc  82 spdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavrevled 158
                                       + ++l+  ++++  +s  f+  F   A++++++  + +         r+r ++++d +    ++++++  +r+ + d
  gi|518652660|ref|YP_008142180.1| 657 DINNLDGYVKSSARRSRFFNNVFLYEARKFGIITNEADI-------TRIRFEKIVDSYY---NTVVYEDSIRKLIFD 723
                                       ***********************************9988.......9*******99988...*************** PP

                        DEAD_assoc 159 qlDlerlaellrriaageirvve 181
                                       ++D++ l+++l+++ +++  +++
  gi|518652660|ref|YP_008142180.1| 724 YMDINVLHDYLENLDDSNFILKN 746
                                       **************998877765 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 !   15.6   3.6   5.8e-06     0.012       6      35 ..     788     816 ..     788     818 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 5.8e-06
                    Zn_ribbon_SprT   6 rCtgCgreythhlsi.rrhnYrCrrCkgtLr 35 
                                       +Ct+Cg   +++++i +    rC+ C+++L+
  gi|518652660|ref|YP_008142180.1| 788 YCTSCG--NKRTRKIkDITEIRCPVCHSRLV 816
                                       7*****..59*****88888********997 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.6e-05     0.051      54      98 ..     770     817 ..     735     829 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.6e-05
                                       C.TTTT-EEEEEEE--EEEETTTS-EEECHH.H..HHS-TTTSSS-EE CS
                              HypA  54 gtvlegaeLeieevpvkvrCreCgkefelee.k..alrCpkCgsadve 98 
                                       +t+le+ + ++ +++v ++C++Cg++ + +  +  ++rCp C+s+ v 
  gi|518652660|ref|YP_008142180.1| 770 KTILESIRKRLMNEEVILYCTSCGNKRTRKIkDitEIRCPVCHSRLVA 817
                                       567777777888999*********9888544345688******98664 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.2   2.4e-05     0.047       8      36 ..     789     815 ..     786     819 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.4e-05
                       Zn-ribbon_8   8 CeeCghefevlqsisdapltaCPeCgsev 36 
                                       C++Cg++ +  ++i+d  ++ CP C+s++
  gi|518652660|ref|YP_008142180.1| 789 CTSCGNKRT--RKIKDITEIRCPVCHSRL 815
                                       *****6666..67888899*******965 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 ?    2.0   0.0      0.11   2.1e+02      14      21 ..     783     790 ..     771     793 .. 0.86
   2 ?    9.6   0.1   0.00045      0.89       1      11 [.     807     817 ..     807     827 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.11
                    DNA_ligase_ZBD  14 geaiyRCt 21 
                                       +e+i++Ct
  gi|518652660|ref|YP_008142180.1| 783 EEVILYCT 790
                                       8******9 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00045
                    DNA_ligase_ZBD   1 hCPvCGsavvR 11 
                                       +CPvC+s +v 
  gi|518652660|ref|YP_008142180.1| 807 RCPVCHSRLVA 817
                                       5*******995 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1   0.00064       1.3       4      43 ..      28      94 ..      25     131 .. 0.64
   2 ?    1.9   0.0      0.08   1.6e+02     194     225 ..     121     156 ..     102     162 .. 0.65
   3 ?   -2.6   0.1       1.9   3.8e+03     148     148 ..     812     812 ..     759     852 .. 0.53

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00064
                            AAA_11  4 dsqreaiksalseseitliqGPPGtgKT.ktivellsqll...........................s 43
                                      + q+ ai ++ls ++ tl+  P G+gKT  ++v ll++++                            
  gi|518652660|ref|YP_008142180.1| 28 EAQKMAIPEILSGEN-TLLISPTGSGKTeAALVPLLNKIYlekpqsiallyitplralnrdmlsrvfD 94
                                      7899**********9.99999*******8899999999976655555555555555554444444440 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.08
                            AAA_11 194 deaeivltTlsga....gsklleklakkfdvviIDE 225
                                       + a+i +tT  +       k+l++  k++++vi+DE
  gi|518652660|ref|YP_008142180.1| 121 NPAQILITTPESLqllmMGKRLREHIKNIKYVIVDE 156
                                       557778888665411112355555556********* PP

  == domain 3  score: -2.6 bits;  conditional E-value: 1.9
                            AAA_11 148 e 148
                                       +
  gi|518652660|ref|YP_008142180.1| 812 H 812
                                       1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (899 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 6084.09
//
Query:       gi|518652661|ref|YP_008142181.1|  [L=296]
Description: hypothetical protein FACI_IFERC00001G1300 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   28.7   0.0    0.00017   21.7   0.1    2.4  2  CCG       Cysteine-rich domain


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.7   0.0     0.002        36      19      80 ..     102     164 ..      91     169 .. 0.82
   2 !   21.7   0.1   9.6e-09   0.00017       1      84 [.     196     281 ..     196     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.002
                               CCG  19 kalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpgC 80 
                                       k+++  l+a+g+++ +l ++e   Ga    sg+ ++ ++++k+ ++ ++e g++ i+t +p+ 
  gi|518652661|ref|YP_008142181.1| 102 KNITSMLTAHGLNFGYLyDEEPYSGALLLESGFINEYKEYGKKLYNFFKERGVKQIITVDPHT 164
                                       55666677777888777777777899999999999999*********************9985 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 9.6e-09
                               CCG   1 vayfdgChllraa..ypevrkalkk..llealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadai 73 
                                       ++++d+C + ra+  y++ r ++k   + + ++  +  ++  sCCG +    +++  +e++ k ++e + ++ ++ +
  gi|518652661|ref|YP_008142181.1| 196 YVIHDSCLYSRAMgmYDNIRAKIKDsgISASENYLITGKDMGSCCGGPLALVSTK-DSEDISKSRAEKLLSV-NENV 270
                                       5789***55555599888888888644666667666777889********99999.6**************9.5559 PP

                               CCG  74 vtacpgCllql 84 
                                       ++ cp C+ +l
  gi|518652661|ref|YP_008142181.1| 271 LVMCPLCYQNL 281
                                       99*****9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2276.28
//
Query:       gi|518652662|ref|YP_008142182.1|  [L=378]
Description: hypothetical protein FACI_IFERC00001G1301 [Ferroplasma acidarmanus fer1]
Scores for 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  154.3   0.1    4.2e-45  153.8   0.1    1.2  1  LUD_dom       LUD domain
    1.6e-09   38.0   2.1    3.2e-09   37.1   1.2    1.9  2  Fer4_8        4Fe-4S dicluster domain
    3.6e-08   33.4   1.2    0.00088   19.3   0.1    2.4  2  Fer4_10       4Fe-4S dicluster domain
    1.3e-07   32.1   2.6    2.7e-07   31.0   2.6    1.6  1  Fer4_17       4Fe-4S dicluster domain
    9.6e-07   29.3   1.7    1.9e-06   28.4   1.7    1.5  1  Fer4_7        4Fe-4S dicluster domain
    0.00015   21.8   2.7     0.0031   17.6   4.2    2.1  2  Fer4_9        4Fe-4S dicluster domain
    0.00053   19.9   4.2      0.005   16.9   1.0    2.3  2  Fer4_2        4Fe-4S binding domain
    0.00085   19.3   6.9     0.0054   16.8   0.9    2.3  2  Fer4_6        4Fe-4S binding domain
     0.0013   18.5   7.1     0.0059   16.4   1.2    2.4  2  Fer4          4Fe-4S binding domain
     0.0043   18.0   4.5      0.029   15.3   4.5    2.3  1  Fer4_16       4Fe-4S double cluster binding domain
     0.0072   16.1   1.9      0.018   14.8   0.1    2.3  2  Fer4_20       Dihydroprymidine dehydrogenase domain II, 4Fe-4
     0.0083   16.2   0.2      0.016   15.3   0.2    1.5  1  ApoLp-III     Apolipophorin-III precursor (apoLp-III)
  ------ inclusion threshold ------
      0.017   15.6   5.9      0.072   13.6   1.0    2.2  2  Fer4_4        4Fe-4S binding domain
       0.02   15.0   7.1       0.31   11.2   7.1    2.3  1  Fer4_21       4Fe-4S dicluster domain
      0.063   13.2   0.9       0.12   12.2   0.9    1.4  1  DUF2972       Protein of unknown function (DUF2972)
      0.093   12.9   1.5        4.6    7.5   0.1    2.5  2  Fer4_18       4Fe-4S dicluster domain
       0.15   12.9   4.0        2.1    9.3   0.6    2.4  2  Fer4_22       4Fe-4S dicluster domain
        4.7    7.6   7.0        5.9    7.3   1.4    2.9  2  ATP-synt_E_2  ATP synthase epsilon subunit
        4.8    8.3   9.7        5.3    8.2   2.2    2.3  2  Fer4_3        4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> LUD_dom  LUD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.8   0.1   4.4e-48   4.2e-45       1     189 []      52     283 ..      52     283 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.8 bits;  conditional E-value: 4.4e-48
                           LUD_dom   1 leefienleangaevyyaktaeealelilellkeksv.....................vseggstdlgeigl..... 51 
                                       + +++e++++ g++ +yak++e+a+++++e+l eks                      +   ++td+ge+ +     
  gi|518652662|ref|YP_008142182.1|  52 ISKTEESVKRTGGHFHYAKDGEQAMDIVREILGEKSKivlsksnvlyeiklreelekeGKDIWETDMGEYLVqinnd 128
                                       5799*******************************989*************************************** PP

                           LUD_dom  52 ......apalhsgreevldlfeekl.............treareelrekfltadvgitganfaiAetGtlvlvdneg 109
                                             apa+h ++ ++ +l++e+l             ++  r+ l+ek l a+vgitgan+  A+tG++ l++neg
  gi|518652662|ref|YP_008142182.1| 129 mpshlvAPAIHLTKDKIGKLLHENLdsainentspeemVSIVRKFLMEKYLGAEVGITGANAIAADTGSVLLIENEG 205
                                       *************************************************************999************* PP

                           LUD_dom 110 nrraltflpkvhivvvginkivpdledavkrlktaprnatrlqkktpyvsfisgpsrtadielvlvygvhgpkrihv 186
                                       n r+ t+lp+vhi+++gi+kivp+l+da++ +    ++  +  + + y+++ sgps t+diel+ v+ + gpk++h+
  gi|518652662|ref|YP_008142182.1| 206 NIRMDTVLPQVHIAITGIDKIVPTLKDAFNEVIV-QASYAG-FYPPAYINVTSGPSATGDIELKHVSPATGPKEFHL 280
                                       *********************************9.334444.89********************************* PP

                           LUD_dom 187 ilv 189
                                       i++
  gi|518652662|ref|YP_008142182.1| 281 IVL 283
                                       *85 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       3.4   3.3e+03      17      35 ..      58      77 ..      57     114 .. 0.66
   2 !   37.1   1.2   3.4e-12   3.2e-09       5      65 .]     301     362 ..     297     362 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 3.4
                            Fer4_8 17 vlrrtkkhlldargeaae.d 35
                                      +++rt+ h ++a+++ ++ d
  gi|518652662|ref|YP_008142182.1| 58 SVKRTGGHFHYAKDGEQAmD 77
                                      57888866666666655532 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 3.4e-12
                            Fer4_8   5 CieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvlee.eealwsCttcgaCtevCpvgi 65 
                                       Ci+Cg+C  +Cp+++  + ++  +++ + ++   ++  +++ ++    C++ g C evCp++i
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPSYKLYGkDFGDSPYTGPTG-IMWSAITMKkYDKSMLCMHSGGCHEVCPMDI 362
                                       ******************7788888888888.66666666668999**************987 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.1   9.4e-07   0.00088       5      33 ..     297     321 ..     293     334 .. 0.78
   2 !   12.7   0.1   0.00011      0.11       7      27 ..     346     366 ..     339     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 9.4e-07
                           Fer4_10   5 dddtCirCgkCvkaCPadltsvgakgeas 33 
                                       ++  CirCg+C  +CP+    ++ +g++ 
  gi|518652662|ref|YP_008142182.1| 297 ESLLCIRCGRCYFSCPS----YKLYGKDF 321
                                       5667*************....55555555 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00011
                           Fer4_10   7 dtCirCgkCvkaCPadltsvg 27 
                                         C++ g C ++CP+d++  +
  gi|518652662|ref|YP_008142182.1| 346 MLCMHSGGCHEVCPMDINIPQ 366
                                       46*************774333 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   2.6   2.9e-10   2.7e-07       2      61 .]     301     363 ..     300     363 .. 0.78

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 2.9e-10
                           Fer4_17   2 CiqCgyClpeCpsyeaydn....epkkllraaklglleeaekeekaslCieCgeCerkCPqgld 61 
                                       Ci+Cg C  +Cpsy+ y++     p +    ++++ + +++k +k  lC++ g+C ++CP++++
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPSYKLYGKdfgdSPYTGPTGIMWSAI-TMKKYDKSMLCMHSGGCHEVCPMDIN 363
                                       ****************887333246665555566544.4567799****************985 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   1.7     2e-09   1.9e-06       2      51 ..     301     361 ..     300     362 .. 0.71

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 2e-09
                            Fer4_7   2 CigCgaCvaaCpvkaieldeeenek..........gtekv....eidpekClgCgaCvavCPtg 51 
                                       Ci Cg+C   Cp++ ++ +++ + +              +    + +++ C++ g C +vCP +
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPSYKLYGKDFGDSPytgptgimwsA---ItmkkYDKSMLCMHSGGCHEVCPMD 361
                                       *****************9988766644444333320...13331334678************87 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.5   9.2e-05     0.087      20      48 ..     284     313 ..     277     317 .. 0.66
   2 !   17.6   4.2   3.3e-06    0.0031       2      49 ..     301     361 ..     300     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.2e-05
                            Fer4_9  20 daaerkarlraase.eaCigCgaCveaCpk 48 
                                       d+++++a     +e   Ci Cg+C+  Cp+
  gi|518652662|ref|YP_008142182.1| 284 DNGRKEAIDSDIREsLLCIRCGRCYFSCPS 313
                                       555555444444445689999999999996 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 3.3e-06
                            Fer4_9   2 CtgCgaCveaCpagvvvedaaerkarlraase.............eaCigCgaCveaCpkg 49 
                                       C++Cg+C  +Cp+    +++++       ++                C++ g C e+Cp +
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPSYKLYGKDFGDSPYTGPTGImwsaitmkkydksMLCMHSGGCHEVCPMD 361
                                       ***********888888888888888777766888888888888889************98 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   5.3e-06     0.005       8      21 ..     299     312 ..     290     313 .. 0.85
   2 ?    3.8   0.1     0.074        70       9      21 ..     347     359 ..     340     360 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 5.3e-06
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                         Ci+Cg C+ +CP
  gi|518652662|ref|YP_008142182.1| 299 LLCIRCGRCYFSCP 312
                                       48************ PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.074
                            Fer4_2   9 rCigCgaCvsaCP 21 
                                        C++ g C  +CP
  gi|518652662|ref|YP_008142182.1| 347 LCMHSGGCHEVCP 359
                                       6999999****** PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.9   5.7e-06    0.0054       8      21 ..     300     313 ..     298     317 .. 0.91
   2 ?    5.4   0.6     0.022        21       9      22 ..     348     361 ..     346     367 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.7e-06
                            Fer4_6   8 kCigCgdCvrvCPe 21 
                                       +Ci Cg+C+  CP 
  gi|518652662|ref|YP_008142182.1| 300 LCIRCGRCYFSCPS 313
                                       7************5 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.022
                            Fer4_6   9 CigCgdCvrvCPeg 22 
                                       C + g C  vCP++
  gi|518652662|ref|YP_008142182.1| 348 CMHSGGCHEVCPMD 361
                                       666677******86 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.2   6.2e-06    0.0059       7      19 ..     300     312 ..     297     314 .. 0.93
   2 ?    5.2   0.5     0.022        20      12      21 ..     352     361 ..     346     362 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.2e-06
                                       TSSS-THHHHHST CS
                              Fer4   7 kCigCGaCvevCP 19 
                                       +Ci+CG+C+  CP
  gi|518652662|ref|YP_008142182.1| 300 LCIRCGRCYFSCP 312
                                       7************ PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.022
                                       THHHHHSTTT CS
                              Fer4  12 GaCvevCPvg 21 
                                       G C evCP +
  gi|518652662|ref|YP_008142182.1| 352 GGCHEVCPMD 361
                                       77******87 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   4.5     3e-05     0.029       2      66 ..     301     360 ..     300     361 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 3e-05
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisyntaekkdlaedeekck.kqeaitgCdiCqdvCPa 66 
                                       C++Cg+C  +CP+  + +k     +  ++  +  +    ++  + k++ k + ++  + C +vCP+
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPSYKLYGK-----DFGDSPYT-GPTGIMWSAITMKKYdKSMLCMHSGGCHEVCPM 360
                                       ******************9.....33333333.23333333333333314466788899******7 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.89   8.4e+02      18      38 ..     295     313 ..     282     316 .. 0.78
   2 !   14.8   0.1   1.9e-05     0.018      23      53 ..     344     375 ..     333     378 .] 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.89
                                       HHHHTT----TT-HHHHCSTT CS
                           Fer4_20  18 leeAsRClqCkkapcvkgCPv 38 
                                       ++e+  C++C    c  +CP 
  gi|518652662|ref|YP_008142182.1| 295 IRESLLCIRC--GRCYFSCPS 313
                                       6777789999..678888985 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.9e-05
                                       T----TT-H.HHHCSTT---HHHHHHHHHTT- CS
                           Fer4_20  23 RClqCkkap.cvkgCPveidipefikkiaegn 53 
                                       + + C ++  c++ CP++i+ip+ i+ki+ + 
  gi|518652662|ref|YP_008142182.1| 344 KSMLCMHSGgCHEVCPMDINIPQVIEKIKFRY 375
                                       5567875444******************9765 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   1.7e-05     0.016       4      57 ..      13      67 ..      10      87 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.7e-05
                         ApoLp-III  4 ieelqksvkkqln.lpsqeevvetiKensenlvdqlkqvikslqeelkkksdele 57
                                      i + ++ v++ l   p  ++v  ++++  ++++d+++++i++++e++k++ + + 
  gi|518652662|ref|YP_008142182.1| 13 IVNNAPRVQQILDdNPYIKDVASELRKTKNTVLDNIETYISKTEESVKRTGGHFH 67
                                      5566777888887778999******************************998875 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   1.0   7.6e-05     0.072       4      16 ..     301     313 ..     296     322 .. 0.91
   2 ?    4.1   0.3     0.088        83       4      16 ..     348     360 ..     342     361 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 7.6e-05
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       Ci+Cg+C+ +CP+
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPS 313
                                       ************5 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.088
                            Fer4_4   4 CigCgsCvaaCPq 16 
                                       C + g C+ +CP+
  gi|518652662|ref|YP_008142182.1| 348 CMHSGGCHEVCPM 360
                                       777788******7 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   7.1   0.00033      0.31       7      54 ..     300     361 ..     294     366 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
                           Fer4_21   7 kCigCgkCliaCedtshqai...............eidaktvlkvv.edeCvGCnlCssvCPve 54 
                                        Ci Cg+C+ +C+  s++                   +a t+ k+  +  C+    C++vCP++
  gi|518652662|ref|YP_008142182.1| 300 LCIRCGRCYFSCP--SYKLYgkdfgdspytgptgiMWSAITMKKYDkSMLCMHSGGCHEVCPMD 361
                                       5************..5666655555555444443223333444554255899999999999985 PP

>> DUF2972  Protein of unknown function (DUF2972)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.9   0.00013      0.12      70     172 ..      13     118 ..       2     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                           DUF2972  70 yik.....kqaleedinltditkelfnkqkcfyeriiiyikkkdfeilkeneklleqvkeyllelieeLkkqkeiek 141
                                       +++     +q+l+++  ++d+ +el +++++  ++i  yi+k + e++k++   ++  k+   + +  ++++   + 
  gi|518652662|ref|YP_008142182.1|  13 IVNnaprvQQILDDNPYIKDVASELRKTKNTVLDNIETYISKTE-ESVKRTGGHFHYAKDG-EQAMDIVREILGEKS 87 
                                       3333555489******************************9876.6777777677766665.334455555666667 PP

                           DUF2972 142 kkklsekdvLeylkkhkkvaleaKaildeeL 172
                                       k  ls+++vL  +k  +++ +e K+i + ++
  gi|518652662|ref|YP_008142182.1|  88 KIVLSKSNVLYEIKLREELEKEGKDIWETDM 118
                                       77899*********************99887 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.066        62      76      95 ..     294     311 ..     286     319 .. 0.68
   2 ?    7.5   0.1    0.0049       4.6      54      78 ..     341     365 ..     328     371 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.066
                           Fer4_18  76 dirkGlqleciscllcidac 95 
                                       dir+   l ci c++c  +c
  gi|518652662|ref|YP_008142182.1| 294 DIRES--LLCIRCGRCYFSC 311
                                       55554..3577777776666 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0049
                           Fer4_18  54 kekgagdcidcescvkvcPtgidir 78 
                                       k +++  c++ + c +vcP++i+i 
  gi|518652662|ref|YP_008142182.1| 341 KYDKSMLCMHSGGCHEVCPMDINIP 365
                                       55666779**************996 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.6    0.0022       2.1      78      94 ..     297     313 ..     286     315 .. 0.74
   2 ?    4.1   0.1      0.09        85      78      95 ..     344     361 ..     332     362 .. 0.67

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0022
                           Fer4_22  78 gesgCvGCgRCieacpv 94 
                                       ++  C+ CgRC  +cp+
  gi|518652662|ref|YP_008142182.1| 297 ESLLCIRCGRCYFSCPS 313
                                       55678888888888875 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.09
                           Fer4_22  78 gesgCvGCgRCieacpvk 95 
                                       +++ C+  g C+e+cp++
  gi|518652662|ref|YP_008142182.1| 344 KSMLCMHSGGCHEVCPMD 361
                                       456688888888888876 PP

>> ATP-synt_E_2  ATP synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2      0.27   2.5e+02      12      32 ..      29      49 ..      23      56 .. 0.84
   2 ?    7.3   1.4    0.0062       5.9      13      44 ..      76     107 ..      72     111 .. 0.90

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.27
                      ATP-synt_E_2 12 YlniLkskLdeKKsElLkkiN 32
                                      Y++ + s+L + K+ +L +i 
  gi|518652662|ref|YP_008142182.1| 29 YIKDVASELRKTKNTVLDNIE 49
                                      888889999999****99997 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0062
                      ATP-synt_E_2  13 lniLkskLdeKKsElLkkiNmEYEKlLKqRLd 44 
                                       ++i+++ L eK   +L+k N+ YE  L++ L+
  gi|518652662|ref|YP_008142182.1|  76 MDIVREILGEKSKIVLSKSNVLYEIKLREELE 107
                                       689*********************99998886 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   2.2    0.0057       5.3       1      13 [.     301     313 ..     301     315 .. 0.93
   2 ?    4.5   0.9     0.089        84       4      13 ..     348     360 ..     346     362 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0057
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg+C  +CP+
  gi|518652662|ref|YP_008142182.1| 301 CIRCGRCYFSCPS 313
                                       ************6 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.089
                            Fer4_3   4 Cg...aCvevCPv 13 
                                       C+    C evCP 
  gi|518652662|ref|YP_008142182.1| 348 CMhsgGCHEVCPM 360
                                       532225******6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (378 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2863.29
//
Query:       gi|518652663|ref|YP_008142183.1|  [L=416]
Description: hypothetical protein FACI_IFERC00001G1302 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-28   99.2   0.4    2.1e-27   96.7   0.4    1.9  1  Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosp
    2.1e-07   31.2   0.0      0.024   14.7   0.0    2.2  2  PglZ          PglZ domain


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 !   96.7   0.4   2.3e-31   2.1e-27       1     355 [.      60     394 ..      60     396 .. 0.72

  Alignments for each domain:
  == domain 1  score: 96.7 bits;  conditional E-value: 2.3e-31
                                       EEEEEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEE........ CS
                      Phosphodiest   1 vlvislDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfy........ 69 
                                       v++i +DGl  d   ++ ++   ++++ + g+ +p +++ fP++T+++  ++ TGl+P+eHG +  + y        
  gi|518652663|ref|YP_008142183.1|  60 VVFIYIDGLGYDSWINYLGKYRAFKEINESGIVSP-ITSLFPSTTAAASNTINTGLTPAEHGLFEWRLYidrydmvm 135
                                       799*******9999996689***************.*****************************666698887777 PP

                                       ........ETTTTEEEEEETTTTGGGGGCTTS-HHHHHHHTHTTCEEEESETTTTSEBTTCT.SC.TBHHSBTCT.C CS
                      Phosphodiest  70 ........drktgeyvvfvtededaprwwqgepiwdtaakarglkaaalfwpgsevdystyyylvsetppryleddf 138
                                                ++++e  +f ++++d p ++ +++++ +  k++g+k +++    se  +s+y        +r ++   
  gi|518652663|ref|YP_008142183.1| 136 kslpfipvYKQDRE--KFIEANPD-PSVLFHGKTFYETLKENGIKPYVV--SRSELLKSSY--------SRIMYSGA 199
                                       77777654444444..66666666.777666555555555559987777..5678888744........34443444 PP

                                       STTSCHHHHHH.HHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHH CS
                      Phosphodiest 139 nakvpledkvd.kavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlea 214
                                       ++k  ++  +    +l+++l++           ++  ++++y+ee+D++ H++Gp spe+++ l+++    + L+e+
  gi|518652663|ref|YP_008142183.1| 200 KEKKRYDFLFEgFLILKKLLEKI----------KDNSYVFFYIEEPDKMEHRYGPGSPEHLESLHYIAGLFNTLFES 266
                                       55555555554112333333333..........677***************************************** PP

                                       HHHTTGTTTEEEEEEES---EEEH.TTSEEEGGGTSTGGHGEEEEECBHHS.SSEEEEEESTEEE.CCCTTHHHHHH CS
                      Phosphodiest 215 lderglsaetniilvSDHGmadvs.ddkvielndlleekgllhlkdegkggakaliainpkarelnrvaeaeaeevy 290
                                       l  +    + +ii++SDHG+++v+ + +v  +++l++ k   ++ ++++  ++a++  np+  +l+   e++ +  +
  gi|518652663|ref|YP_008142183.1| 267 LSGQ----DISIIISSDHGFTPVNnKIYVSGVENLMPIKNGKRMPETWSPRDMAMYSDNPE--KLKLFLEHQLDGKA 337
                                       **99....9**************74466666999999997777777774444444444443..12222222222222 PP

                                       HHHHTCHHCCHSTHTTTEEEEEGG.GS-GGGCHSTTS-SEEEEE-TTEEEESSTTCS.SBS-SEE-- CS
                      Phosphodiest 291 aelkakleelrkkegealavylke.aipkrlhykkrapdlvlvadpgwsitskdkpd.eyeikgthG 355
                                       + + +            +   l + ++++ +   +r++d+++++  g+++ +k+ +d   ++ g+hG
  gi|518652663|ref|YP_008142183.1| 338 DVITKQ--------ELLTSGILGSrNVDEKYA--SRIGDVIVLPYSGNTVWYKYYEDdIIKDRGMHG 394
                                       222222........224444444446888777..9************99999999997677788887 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   3.3e-06     0.029       1      56 [.      58     115 ..      58     123 .. 0.80
   2 !   14.7   0.0   2.7e-06     0.024     103     174 ..     216     287 ..     161     289 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.3e-06
                              PglZ   1 ekvfvIisDalryeawee.lkqlLnkedrfeael.savlgvlPslTklgraallpgkk 56 
                                       +kv++I +D+l+y+ w + l ++ + +++ e  + s++ ++ Ps T  + + +  g  
  gi|518652663|ref|YP_008142183.1|  58 KKVVFIYIDGLGYDSWINyLGKYRAFKEINESGIvSPITSLFPSTTAAASNTINTGLT 115
                                       69**************76266666666666666669***********99998866655 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.7e-06
                              PglZ 103 derrellkdkevvyivhnkvDalgdkasteqksfeaveeslkelkelvksllee.ngyk..vlltaDHGfiyqrg 174
                                       ++ +e +kd+ +v  ++++ D++ +   +   ++    esl+ ++ l++ l e+ +g+   +++ +DHGf  +++
  gi|518652663|ref|YP_008142183.1| 216 KKLLEKIKDNSYVFFYIEEPDKMEH---RYGPGSPEHLESLHYIAGLFNTLFESlSGQDisIIISSDHGFTPVNN 287
                                       456789*******************...8888888889999999999999999998876116778****976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 3069.11
//
Query:       gi|518652664|ref|YP_008142184.1|  [L=787]
Description: hypothetical protein FACI_IFERC00001G1303 [Ferroplasma acidarmanus fer1]
Scores for complete 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-75  251.9   1.7      8e-75  251.1   1.7    1.4  1  Peptidase_M1    Peptidase family M1 domain
    5.8e-32  111.4   0.9    2.3e-31  109.4   0.9    2.0  1  Peptidase_M1_N  Peptidase M1 N-terminal domain
    3.4e-21   76.1   0.6    5.1e-21   75.5   0.6    1.2  1  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
       0.34   11.8   2.2          2    9.3   0.1    3.0  2  DUF4744         Domain of unknown function (DUF4744)


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.1   1.7   1.8e-78     8e-75       1     218 []     200     416 ..     200     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 251.1 bits;  conditional E-value: 1.8e-78
                                       HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHH CS
                      Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaH 77 
                                       y +e +kk le+le+y++++Y lpkl+l+ +p+f+agAMEnwg+it+re ll +d +++++++++++aevi+HEl+H
  gi|518652664|ref|YP_008142184.1| 200 YPIECAKKSLEYLENYTGIDYMLPKLNLISVPEFAAGAMENWGAITFREILLNID-KSTTSRSYKRTAEVITHELVH 275
                                       567999*************************************************.7777789999*********** PP

                                       HHBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTS CS
                      Peptidase_M1  78 qWfGnlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevF 154
                                       +WfG+lVtmkwW+dlwLnE+fat+++++ +d+++p+w++  ++ll+++  a  +dal++shpi+  v++p+ i+++ 
  gi|518652664|ref|YP_008142184.1| 276 MWFGDLVTMKWWNDLWLNESFATFFAFKTVDSTNPDWKFFGDFLLDQTDGAYTMDALKNSHPINADVTDPRSISQLS 352
                                       ***************************************************************************** PP

                                       SHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                      Peptidase_M1 155 dsiaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                        +i Y KG+++lrm+e+++g++vF+k++++Ylkef+y+na+ +dlw+a+e++++  is++m++w
  gi|518652664|ref|YP_008142184.1| 353 YEIRYGKGSNVLRMIEAYVGKDVFMKAMRNYLKEFSYSNASGSDLWNAIEKESGMGISTIMEQW 416
                                       **************************************************************** PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.4   0.9   5.1e-35   2.3e-31       4     186 .]       5     166 ..       3     166 .. 0.85

  Alignments for each domain:
  == domain 1  score: 109.4 bits;  conditional E-value: 5.1e-35
                                       EEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEE CS
                    Peptidase_M1_N   4 hYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkesl 80 
                                       +Y+++l++d++ k+++G  +i+++ +  +++i+ld ++++i++++++      + +++f+  + ++    +++++  
  gi|518652664|ref|YP_008142184.1|   5 NYNIKLDVDFSGKKYSGIEKIKITDA--EKKITLDLNKIDIHKIKVN------GADVKFE--AGEDG---VTFPT-- 66 
                                       7******************9988755..9************666666......5444443..32333...34555.. PP

                                       ETTCEEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEE CS
                    Peptidase_M1_N  81 qqtskytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalS 157
                                        + + +  e++++++    l+G+y        ek+++++Tqfe  dAR+afPC+D+P++KAtf+i+++ +k+  a+S
  gi|518652664|ref|YP_008142184.1|  67 -NGGDIVAEVQFSSDNDRGLKGFYV----AGTEKEYILSTQFEESDARRAFPCIDNPNYKATFDITMAIDKDLQAIS 138
                                       .3688999******77777777776....457889****************************************** PP

                                       SSECCCEEEETTCEEEEEEEEEESBEGGG CS
                    Peptidase_M1_N 158 nmpeeeseklengqkiteFeqtpkmstYL 186
                                       nmp++  e+len++k+++Feqtp+m tYL
  gi|518652664|ref|YP_008142184.1| 139 NMPVK-FETLENNKKVVQFEQTPVMATYL 166
                                       ****9.8888899***************9 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.6   1.1e-24   5.1e-21       4     278 ..     483     742 ..     480     763 .. 0.85

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                                       ESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHHHHH CS
                           ERAP1_C   4 lNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvwsqal 80 
                                       lN ++ G+yrV Yd+++++++++ +ls+ ++++++ gl +d++a+  +g++++++++  l+++  + ++ +v +++ 
  gi|518652664|ref|YP_008142184.1| 483 LNFNHNGFYRVLYDDSMFENISR-NLSQ-ITAEEKWGLANDLYAFLLSGKINMTTYVRRLEKL-YGINENIVIDEIS 556
                                       8**********************.6677.***************999**************66.4899********* PP

                                       HHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHHT.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHCS CS
                           ERAP1_C  81 sqlatlksllsadplyaalkaflrklleplaeklgwepgeshldaqlrslllsaacaagdpevveearklfkawleg 157
                                         l +l+++  + +    +k++++  ++  +e + ++ +++++ +   s l++ +++ +++     ++ l+k++ + 
  gi|518652664|ref|YP_008142184.1| 557 KELFNLYTIT-DNN---YFKDLANFYIKDKMEYVEANRKDDFNFKITLSGLYTKLAYINND----FCKSLLKKYSSY 625
                                       ******9998.656...9**************99876678999999999999999888855....667777777332 PP

                                       TT-S-HHHHHHHHHHHHHHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-GGGHHH CS
                           ERAP1_C 158 ddlippdlrwavycalaanggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrnqdlra 234
                                        ++++pd+r a + a a+    +++    ++  +t++ + k++a++a +a +  +   ++++fv  s++ ++qd+ +
  gi|518652664|ref|YP_008142184.1| 626 -ENVDPDFRLAYLVAEAKI--NQDFSYFADIITNTKNDEDKTKAITASGALEGDKNHSAIMEFVK-SGKAKKQDMDS 698
                                       .26**********999987..5667777777766666488************************5.99********* PP

                                       HHHHH.HSTTHHHHHHHHHHHCHCCHHHHTSSTS.CHHHHHHHHH CS
                           ERAP1_C 235 llaglannpegrellwefvkenwdalakrwsgge.ildrivkgll 278
                                        + ++a+n + r+   + +k+  d l+k ++ +   ++r v++++
  gi|518652664|ref|YP_008142184.1| 699 FFVAMASNTPSRQFIIDNLKDIVDMLYK-FELSPlRINRCVQSMI 742
                                       *****99999999888888888888877.6633336666666655 PP

>> DUF4744  Domain of unknown function (DUF4744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00045         2      49      65 ..     376     392 ..     373     395 .. 0.85
   2 ?    0.4   0.2      0.27   1.2e+03      39      59 ..     702     719 ..     648     721 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00045
                           DUF4744  49 FdlaidnYLKDFgYgnq 65 
                                       F  a +nYLK F Y+n 
  gi|518652664|ref|YP_008142184.1| 376 FMKAMRNYLKEFSYSNA 392
                                       66799**********96 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
                           DUF4744  39 esepnkpsssFdlaidnYLKD 59 
                                         + n+ps+ F  +idn LKD
  gi|518652664|ref|YP_008142184.1| 702 AMASNTPSRQF--IIDN-LKD 719
                                       45668888887..9***.**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (787 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       740  (0.0412739); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 6034.87
//
Query:       gi|518652665|ref|YP_008142185.1|  [L=141]
Description: hypothetical protein FACI_IFERC00001G1304 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.085   11.9  11.0       0.56    9.2   4.4    2.1  2  COX15-CtaA  Cytochrome oxidase assembly protein
        4.9    5.2   9.8        5.5    5.0   9.8    1.2  1  UPF0182     Uncharacterised protein family (UPF0182)
        6.5    6.6  11.9       0.44   10.3   5.7    1.8  2  DUF2238     Predicted membrane protein (DUF2238)


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.4   0.00037       2.2     283     315 ..      13      46 ..       4      50 .. 0.85
   2 ?    9.2   4.4   9.3e-05      0.56     145     203 ..      54     103 ..      47     125 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00037
                        COX15-CtaA 283 vllaallllQvalGi.stvllavplslavaHqlg 315
                                       ++++all++Q++lG+ +++++++p    vaH +g
  gi|518652665|ref|YP_008142185.1|  13 TAIMALLFIQFILGMyVNLYVSFPPLNNVAHLAG 46 
                                       44599*********95699999**999****987 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 9.3e-05
                        COX15-CtaA 145 yrlaaHLllaflllalllwlalrllakeaesaeeeaaakklrllallllallllqialG 203
                                       +++++H++++fl+l++ ++l+l  ++          +++kl l  +++l+ +++  ++G
  gi|518652665|ref|YP_008142185.1|  54 IVVMVHMMFGFLILIVAFILLLLSVKI---------RNSKLVLSSAISLVFVIVAGISG 103
                                       577888888888887777776664444.........33444444444444444444444 PP

>> UPF0182  Uncharacterised protein family (UPF0182)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   9.8   0.00093       5.5     192     272 ..      12      99 ..       3     135 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.00093
                           UPF0182 192 lallllllalsywLdryellys......krgvvtGagYtdvnavlpaktilavialvvavlllvai.vlkklklpli 261
                                       ++++++ll ++++L +y  ly       +  +++G ++    +v+++ +++ ++ l+va++ll+   + ++ kl+l 
  gi|518652665|ref|YP_008142185.1|  12 ITAIMALLFIQFILGMYVNLYVsfpplnNVAHLAGKSFPSNYIVVMVHMMFGFLILIVAFILLLLSvKIRNSKLVLS 88 
                                       456788888899999988777767776333479**************999999999998877765547788777777 PP

                           UPF0182 262 alallvllail 272
                                       +++ lv+++++
  gi|518652665|ref|YP_008142185.1|  89 SAISLVFVIVA 99 
                                       77766666663 PP

>> DUF2238  Predicted membrane protein (DUF2238)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   5.7   7.3e-05      0.44      12      97 ..       3      92 ..       1     111 [. 0.68
   2 ?   -0.2   0.9      0.13   7.7e+02      20      40 ..     113     133 ..      95     137 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.3e-05
                           DUF2238 12 rrfrlsnlayllillflvlhlvGghYt..Yaevplddwlkelfg..lernkYDrlvHfaqGlllalvvrelllrkkkl. 85
                                      +++++  l ++ i+++l++ ++ g Y+  Y   p  + + +l g  +  n    +vH+++G+l+ +v++ lll + k+ 
  gi|518652665|ref|YP_008142185.1|  3 EKYSFAYLGITAIMALLFIQFILGMYVnlYVSFPPLNNVAHLAGksFPSNYIVVMVHMMFGFLILIVAFILLLLSVKIr 81
                                      6778888889999999999999999963376666666777775511556777789************999988888884 PP

                           DUF2238 86 .rkwllllavlvv 97
                                       +   l+l+ ++ 
  gi|518652665|ref|YP_008142185.1| 82 nS--KLVLSSAIS 92
                                      42..222222222 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.13
                           DUF2238  20 ayllillflvlhlvGghYtYa 40 
                                       +y li+++ ++++v +++ Y 
  gi|518652665|ref|YP_008142185.1| 113 LYSLIMAVSFIIIVLSEFYYL 133
                                       566777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1313  (0.0732333); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1097.60
//
Query:       gi|518652666|ref|YP_008142186.1|  [L=154]
Description: hypothetical protein FACI_IFERC00001G1305 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.069   13.5   0.2       0.16   12.3   0.1    1.6  2  CpxA_peri  Two-component sensor protein CpxA, periplasmic dom
       0.11   11.9   0.0       0.12   11.7   0.0    1.1  1  DUF5309    Family of unknown function (DUF5309)
       0.15   11.1   0.1       0.19   10.8   0.1    1.3  1  TelA       Toxic anion resistance protein (TelA)


Domain annotation for each model (and alignments):
>> CpxA_peri  Two-component sensor protein CpxA, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   2.7e-05      0.16      20      75 ..      20      75 ..      11      79 .. 0.91
   2 ?   -1.9   0.0      0.66     4e+03       6      27 ..     109     130 ..      88     141 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
                                      HHHHHHTSS---HHHHHHHHHH..T---TT--S-EEEEE-TTS-EE----S-HHHH CS
                         CpxA_peri 20 dkiekrfseeedlkkilkrleerknrkkkkderlrlfltdldgeilttkkradfkl 75
                                        i+  f +e dl++ l+rl + ++ + ++ +++  f+  l+  i+t +k adf++
  gi|518652666|ref|YP_008142186.1| 20 SGIQMYFMKEYDLAELLNRLMKVDEPRMEEYKKMVEFIKSLENYIITGEKAADFSF 75
                                      56888999*****************99999999999*****************985 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.66
                                       E--HHHHHHHHHHHHHHHHHTS CS
                         CpxA_peri   6 dipaeelerlleirdkiekrfs 27 
                                       +i    + rl++ ++ ++ rf+
  gi|518652666|ref|YP_008142186.1| 109 TIEVMYYYRLVSRKEGFSGRFN 130
                                       3444455556665655555555 PP

>> DUF5309  Family of unknown function (DUF5309)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0     2e-05      0.12      88     146 ..      42     121 ..      33     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2e-05
                           DUF5309  88 kdelayqvakklkElkrdvEkalingnkasvdgskttarqmgGllawiksnnsvgaag................... 145
                                        de + +  kk++E  + +E+ +i+g+ka++    ++  +m+G + w+++ +  ++++                   
  gi|518652666|ref|YP_008142186.1|  42 VDEPRMEEYKKMVEFIKSLENYIITGEKAAD---FSFLEKMEGERGWANDYKILSSENraahvafracrktievmyy 115
                                       578889999*******************887...5699*********998877766655555555555555555555 PP

                           DUF5309 146 .....a 146
                                            +
  gi|518652666|ref|YP_008142186.1| 116 yrlvsR 121
                                       555555 PP

>> TelA  Toxic anion resistance protein (TelA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   3.2e-05      0.19     121     168 ..      48      92 ..      31     119 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
                              TelA 121 qlyeknleyfkeLekyiaaGekkleeldekllpeleakaeasgdpeda 168
                                       ++y+k++e++k Le yi+ Gek     d   l+++e ++  ++d +  
  gi|518652666|ref|YP_008142186.1|  48 EEYKKMVEFIKSLENYIITGEK---AADFSFLEKMEGERGWANDYKIL 92 
                                       68********************...66767777777776656665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); 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: 0.37u 0.20s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1284.05
//
Query:       gi|518652667|ref|YP_008142187.1|  [L=224]
Description: lipoate-protein ligase B [Ferroplasma acidarmanus fer1]
Scores for complete 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-05   22.6   0.0    0.00013   21.9   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 !   21.9   0.0     7e-09   0.00013      28     111 ..      68     142 ..      58     162 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 7e-09
                                       EEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH........HHTT-TTEEEETTTEEE CS
                     BPL_LplA_LipB  28 vvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealg.y.rdskpgiegipvfikwpnDly 102
                                        ++ ++gG  ++h+p++ +ty ++ +++ +++    l  ++ ++v++ l+a+g + + +  + +g++v         
  gi|518652667|ref|YP_008142187.1|  68 AIKVNRGGYMTYHGPGQLVTYYIVNMKR-RNINALGLIKMIQDSVISLLDAYGiEgKPMLNEKTGVWVG-------- 135
                                       6789*******************99977.5777666666699999*******86566688888888888........ PP

                                       ETTEEEEEE CS
                     BPL_LplA_LipB 103 vngrKlaGi 111
                                         ++K+ +i
  gi|518652667|ref|YP_008142187.1| 136 --DKKICSI 142
                                       ..5666444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 1812.00
//
Query:       gi|518652668|ref|YP_008142188.1|  [L=307]
Description: pirin protein [Ferroplasma acidarmanus fer1]
Scores for complete 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  118.1   0.1    1.4e-33  115.1   0.0    2.1  2  Pirin     Pirin
    9.9e-25   86.9   0.0    1.3e-23   83.3   0.0    2.2  2  Pirin_C   Pirin C-terminal cupin domain


Domain annotation for each model (and alignments):
>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.06   5.4e+02      49      64 ..       7      22 ..       2      26 .. 0.85
   2 !  115.1   0.0   1.6e-37   1.4e-33       2     107 ..      27     141 ..      26     142 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.06
                                      BSEEEEEEEECSEEEE CS
                             Pirin 49 rgletvtylleGeveh 64
                                      ++++++ y+++G+ +h
  gi|518652668|ref|YP_008142188.1|  7 HDFKIIDYIIKGNETH 22
                                      5899********9988 PP

  == domain 2  score: 115.1 bits;  conditional E-value: 1.6e-37
                                       EEECCGTCC.TTCCEECTCEECCEEESS.S.ETTEEEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT- CS
                             Pirin   2 vrvrralgkaaelqsvdpFlfldefdpaelevgeedvigagfpphphrgletvtylleGevehrDslGnkgvirpGd 78 
                                       v+++r +g+ +++q +dpFl+ld+f+++++    ed+i agfp+hphrg+et+tyll+G+vehrDs+ ++g+i+p +
  gi|518652668|ref|YP_008142188.1|  27 VKLKRIFGGPNTVQLTDPFLLLDHFGSDRI----EDYI-AGFPWHPHRGIETITYLLSGKVEHRDSTDHRGTIYPDE 98 
                                       6889999999********************....79**.************************************** PP

                                       EEEEE-TT-EEEEEEE-SS..............SS-EEEEEEE CS
                             Pirin  79 vqwmtAgsGivhsEmneee..............eesleglqlW 107
                                       +qwmtAgsGi+h+Em+++                + ++g+qlW
  gi|518652668|ref|YP_008142188.1|  99 LQWMTAGSGIFHEEMPKPLdeknpeelikaygmPTLVSGFQLW 141
                                       ****************998788888888888777778888888 PP

>> Pirin_C  Pirin C-terminal cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.053   4.7e+02      18      55 ..      69     109 ..      63     117 .. 0.80
   2 !   83.3   0.0   1.5e-27   1.3e-23       1     103 [.     197     298 ..     197     299 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.053
                                       TT-EEEEEEEES-EEESSTT...EEE-TTEEEEE-SSSEEE CS
                           Pirin_C  18 egleaavyvleGelevgger...seieeeqlavlgdgdslv 55 
                                        g e++ y l+G++e  +++    +i +++l ++++g+ ++
  gi|518652668|ref|YP_008142188.1|  69 RGIETITYLLSGKVEHRDSTdhrGTIYPDELQWMTAGSGIF 109
                                       5789999*******988877777889999998888887765 PP

  == domain 2  score: 83.3 bits;  conditional E-value: 1.5e-27
                                       EEEEEE-TT-EEEEE--TT-EEEEEEEES-EEESSTTEEE-TTEEEEE-.SSSEEEEE--SS-EEEEEEEE----S- CS
                           Pirin_C   1 yldltleagaelelplpegleaavyvleGelevggerseieeeqlavlg.dgdslvvkaeekgarvlLlaGePlgep 76 
                                       yld+t+++++++  ++++g++ +++ ++Ge+  +g++  +e+++ a+++ +g+ +++++++++ r++Ll+G+Pl+ep
  gi|518652668|ref|YP_008142188.1| 197 YLDITMDEDSDFVYRVKDGYTSLIFSITGEGISNGQK--LEPDTAAIMSrNGNFIKIHTGNSKYRFILLSGKPLNEP 271
                                       89******************************99996..**********99************************** PP

                                       -EEETTEEESSHHHHHHHHHHHHTT-T CS
                           Pirin_C  77 vvqyGpfVmntkeeieqafedyregrf 103
                                       + +yGp+Vmnt e+i++a++d ++++f
  gi|518652668|ref|YP_008142188.1| 272 IKWYGPIVMNTDEQIREAISDLNNNNF 298
                                       ***********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 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:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 2484.43
//
Query:       gi|518652669|ref|YP_008142189.1|  [L=278]
Description: hypothetical protein FACI_IFERC00001G1308 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0013   18.0  20.5     0.0033   16.8  20.5    1.7  1  ABC2_membrane_2  ABC-2 family transporter protein
  ------ inclusion threshold ------
      0.032   13.4  34.0       0.08   12.0  34.0    1.7  1  ABC2_membrane_3  ABC-2 family transporter protein
       0.11   12.1  31.3       0.02   14.5  18.6    3.0  3  ABC2_membrane_5  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> ABC2_membrane_2  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8  20.5   5.5e-07    0.0033      63     284 ..      42     272 ..       7     276 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.5e-07
                   ABC2_membrane_2  63 asdeaedtdqdlkv..........vstimavlipviaalfgadaiagEkergTlkllLskPvsRdeillgKfiggla 129
                                          ++ d + +lk+          +s++ a l+++i+a fg d+i+ +         L +Pv R+ + +g f + l+
  gi|518652669|ref|YP_008142189.1|  42 TALMLHDEYSMLKAgtpllyfykyLSGFSADLVVIIGAFFGGDIISTDTGTNAAYYTLVQPVRRSILFVGRFTAALI 118
                                       44555666666666777777788789999*****************99999999999******************** PP

                   ABC2_membrane_2 130 igla.iavallatvllalaiilalgivlaledllllvvasvlllllvvflalglllSsvarssreaaalalglfvvl 205
                                       ++ + ++v ++++  ++  + l++++ + + + l ++v+++  ++   ++a++ l+S +++ +++ + +++ l+++ 
  gi|518652669|ref|YP_008142189.1| 119 SSFIiVLVYFVVG--VGSSLYLYGKVTPVIFESLGILVLFL--AA---AIAFASLFSGIFKGQSSGIIVSVLLLFIG 188
                                       *777666666666..44455555565555555555555555..33...4799*********8888888888888887 PP

                   ABC2_membrane_2 206 ailvpivlygvaellagpavpqeindflsllsptsayntllneilagsdlna.......lgstatnllilllllavl 275
                                       + +++ ++  ++ +   ++   +    + +l    +y ++ ++ +  ++          +   +  l++l++++++ 
  gi|518652669|ref|YP_008142189.1| 189 FPIIDEFVGSIGGIDPLFSL--NFAGEIMYLIFEKPYPAVKASGSGFGPGAGagafytfSPTVMQGLGVLIAYIIIC 263
                                       77777777777777777777..6666666777777766666665555543336666544333334445555555555 PP

                   ABC2_membrane_2 276 lvlgyvlFk 284
                                        ++++ l+ 
  gi|518652669|ref|YP_008142189.1| 264 GIIAIILYS 272
                                       555555555 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 ?   12.0  34.0   1.3e-05      0.08     159     345 .]      62     269 ..       3     269 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.3e-05
                   ABC2_membrane_3 159 vasflvgliliilifitasfiavsiveEkesrikelqlvsgvsplqywlskilgdflvyllqlllilllafglgipf 235
                                       +  +l g+ + ++++i+a+f    i ++  +++    lv +v+++ ++++++++ ++ +++++l+++++ +g+  + 
  gi|518652669|ref|YP_008142189.1|  62 FYKYLSGFSADLVVIIGAFFGGDIISTDTGTNAAYYTLVQPVRRSILFVGRFTAALISSFIIVLVYFVVGVGS--SL 136
                                       444566677777788888888888899999999999********************************98885..33 PP

                   ABC2_membrane_3 236 g....nlglll...llfllfglayialgyllsslfknsetaqilifivilllsgffgglfpledlpsalkwifsiiP 305
                                       +       +++     ++lf+ a+ia++ l+s +fk +++++i+ +++++    + +++     +++++  i+ i P
  gi|518652669|ref|YP_008142189.1| 137 YlygkVTPVIFeslGILVLFLAAAIAFASLFSGIFKGQSSGIIVSVLLLF----IGFPI-----IDEFVGSIGGIDP 204
                                       32232223344555999999999999999999999999999875544433....22222.....3567777777777 PP

                   ABC2_membrane_3 306 ffapglg..llrli....tgdplwe........................illsliilalfavvylllall 345
                                       +f++  +  ++ li    +     +                        +++ l++l++ +++++++a++
  gi|518652669|ref|YP_008142189.1| 205 LFSLNFAgeIMYLIfekpY-----PavkasgsgfgpgagagafytfsptVMQGLGVLIAYIIICGIIAII 269
                                       7775555222233323331.....245566666777788888888889899****************985 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 ?    5.0   0.3    0.0026        16      59     103 ..       2      46 ..       1      60 [. 0.76
   2 ?   14.5  18.6   3.3e-06      0.02      42     166 ..      72     193 ..      51     219 .. 0.69
   3 ?    0.8   0.6     0.052   3.1e+02     124     135 ..     257     268 ..     238     275 .. 0.42

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0026
                   ABC2_membrane_5  59 DekskwnkylltLPvtrkeiVksKYlfvlililiailitllllii 103
                                       +  s+ n+y ++L ++ k + + K +++lil++  i i++ +l++
  gi|518652669|ref|YP_008142189.1|   2 ENDSDANQYMISLKYQFKSYLRTKRFLGLILFTTIISIGITALML 46 
                                       567899999999999999999988777777776666666666544 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3.3e-06
                   ABC2_membrane_5  42 ilslvisiililttlsyDekskwnkylltLPvtrkeiVksKYlfvlililiailitllllii.avlikgnvtisevl 117
                                        l+++i ++    ++s D   +  +y+l  Pv+r+ +   ++  +li ++i +l+++++++  + +++g+vt  +v+
  gi|518652669|ref|YP_008142189.1|  72 DLVVIIGAFFGGDIISTDTGTNAAYYTLVQPVRRSILFVGRFTAALISSFIIVLVYFVVGVGsSLYLYGKVT--PVI 146
                                       467777788899*********************************************999864788****98..555 PP

                   ABC2_membrane_5 118 lsiliglvialiflaivlPlyfkfgvekgrivliiiifgiifllvaifs 166
                                       + +l +lv++l + ai +  +f  g  kg+   ii+++++ f+++ i+ 
  gi|518652669|ref|YP_008142189.1| 147 FESLGILVLFL-AAAIAFASLFS-GIFKGQSSGIIVSVLLLFIGFPIID 193
                                       55555544443.33333333332.3345555555555555555554443 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.052
                   ABC2_membrane_5 124 lvialiflaivl 135
                                       +++++i+++i +
  gi|518652669|ref|YP_008142189.1| 257 IAYIIICGIIAI 268
                                       111111111111 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); 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):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 2167.50
//
Query:       gi|518652670|ref|YP_008142190.1|  [L=304]
Description: hypothetical protein FACI_IFERC00001G1309 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-24   86.9   0.0    3.5e-24   85.9   0.0    1.5  2  ABC_tran  ABC transporter
      8e-11   42.3   1.3    5.5e-07   29.7   0.0    2.5  3  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
      0.008   15.9   0.0      0.015   15.0   0.0    1.4  1  AAA_29    P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.023   15.4   0.1      0.042   14.6   0.1    1.4  1  DUF4162   Domain of unknown function (DUF4162)
      0.026   15.0   0.1       0.11   13.0   0.0    1.9  2  AAA_23    AAA domain
      0.032   14.5   0.1      0.087   13.1   0.0    1.8  2  AAA_22    AAA domain
       0.14   11.7   0.0       0.31   10.6   0.0    1.5  1  AAA_27    AAA domain
       0.16   12.4   0.6        1.3    9.4   0.2    2.5  2  AAA       ATPase family associated with various cellular acti
       0.17   11.6   0.1       0.25   11.1   0.1    1.4  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 !   85.9   0.0   1.7e-27   3.5e-24       1     137 []      18     161 ..      18     161 .. 0.92
   2 ?   -2.5   0.0       3.4   6.7e+03      87      87 ..     241     241 ..     194     282 .. 0.51

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.7e-27
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l++vs++ +    ++ +G+nGaGK+t lk++++ll+p eG+ +l+g d+++   +++ +++g + ++p+  p ltv+
  gi|518652670|ref|YP_008142190.1|  18 LDDVSFNYRDHGAIGYLGPNGAGKTTTLKVMTNLLRPSEGHAELNGIDVNK-YPKKALANVGSMIETPTPYPFLTVK 93 
                                       799************************************************.5556667889999999********* PP

                                       HH.............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en.............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       e+             + +++i+++ + l+l+   ++++     +LS+Gq+qr + a +l+++p++++lDEpt+
  gi|518652670|ref|YP_008142190.1|  94 ESmqfvgelrgidkkTINSKIDEFYDALKLPP-LTSKM----GQLSKGQRQRAVFASVLISDPDVVILDEPTS 161
                                       **********9998888888999999999999.44444....9****************************96 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.4
                                       H CS
                                       x RF
                          ABC_tran  87 k 87 
                                       k
  gi|518652670|ref|YP_008142190.1| 241 K 241
                                       2 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 !   11.2   0.0   0.00012      0.23       6      24 ..      35      53 ..      34      76 .. 0.79
   2 !   29.7   0.0   2.7e-10   5.5e-07     234     298 ..     130     190 ..     101     195 .. 0.89
   3 ?   -3.1   0.0       2.6   5.2e+03      40      71 ..     213     244 ..     202     275 .. 0.60

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00012
                            AAA_21  6 GpNgsGKSnLLdaldllar 24
                                      GpNg+GK++ L+ +  l r
  gi|518652670|ref|YP_008142190.1| 35 GPNGAGKTTTLKVMTNLLR 53
                                      *************988865 PP

  == domain 2  score: 29.7 bits;  conditional E-value: 2.7e-10
                            AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQv.iltTHS 298
                                       + +lS G+++  a+++++l  ++  +++++DEp +gL+P   + + +++ el++  +++ ++++H 
  gi|518652670|ref|YP_008142190.1| 130 MGQLSKGQRQR-AVFASVLISDP--DVVILDEPTSGLDPFERKIFRDFILELKK--TKLvFFSSHI 190
                                       5799*******.99999999888..9*************8888888***88888..7777*****5 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 2.6
                            AAA_21  40 ggirkipslldlydpeipfefeieeflsqgvr 71 
                                       g+i++i+ ++++++ +i+f   +++  ++++ 
  gi|518652670|ref|YP_008142190.1| 213 GKIDEIAQEFNTNAVSIEFLKPLDNNMIKNIQ 244
                                       56666666677776666666666644444444 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   0.0   7.7e-06     0.015      16      55 ..      22      62 ..      12      64 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.7e-06
                            AAA_29 16 tieidlkgatlltGpsGsGKSTllDAiqalLvpak.kvrfN 55
                                      +++ + +ga+   Gp+G+GK+T l  ++ lL p++ +++ N
  gi|518652670|ref|YP_008142190.1| 22 SFNYRDHGAIGYLGPNGAGKTTTLKVMTNLLRPSEgHAELN 62
                                      4445555567778********************99777777 PP

>> DUF4162  Domain of unknown function (DUF4162)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.1e-05     0.042       1      68 [.     213     287 ..     213     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.1e-05
                                       E-HHHHHTTS-SSEEEEE....-------..--.-EEE.E-TTS-EEEEE--.---------------EEEEEEE CS
                           DUF4162   1 GtleeiKrsygknrieve....adaeelleepg.veev.eeeggelelkled.eeaanellkaltsgveirsFee 68 
                                       G+++ei +++ +n + +e     d+  ++++++  + v +++g+++++k ++ e+ + ++l+ + + ++i s++ 
  gi|518652670|ref|YP_008142190.1| 213 GKIDEIAQEFNTNAVSIEflkpLDNNMIKNIQSlGSGVlKTDGKYAVIKFSGkEDERAQILENAIKLAPIISYTS 287
                                       99*****************88755555555544444444888899******98***********99999998876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   5.6e-05      0.11       7      39 ..      15      48 ..      11      53 .. 0.78
   2 ?   -0.5   0.0      0.77   1.5e+03     173     173 ..     233     233 ..     126     300 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.6e-05
                            AAA_23  7 frsfrdqeidF.skgltlItGpNGaGKTTildAi 39
                                      f+ ++d++++  ++g     GpNGaGKTT l  +
  gi|518652670|ref|YP_008142190.1| 15 FMALDDVSFNYrDHGAIGYLGPNGAGKTTTLKVM 48
                                      66667777777788888889*********99765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.77
                            AAA_23 173 e 173
                                       +
  gi|518652670|ref|YP_008142190.1| 233 K 233
                                       1 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   4.4e-05     0.087      11     111 ..      34     173 ..      25     194 .. 0.65
   2 ?   -3.3   0.0       5.1     1e+04      97     118 ..     215     238 ..     214     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.4e-05
                            AAA_22  11 tGesGtGKTtllrrlleqldeeakaee......................erpevvfvtlpsst....sskdl.lrel 60 
                                        G+ G+GKTt+l+ +++ l   + ++e                       + ++ f t+++s+    +++ +  + +
  gi|518652670|ref|YP_008142190.1|  34 LGPNGAGKTTTLKVMTNLLRPSEGHAElngidvnkypkkalanvgsmieTPTPYPFLTVKESMqfvgELRGIdKKTI 110
                                       59*****************9998888899999999888888666666542222224444444433444444433444 PP

                            AAA_22  61 lralglelkaerlsseellealeqalrarav...........ielliiDEaqh.lr..seealee 111
                                        +++++  +a  l++  l +++ q ++ ++            + ++i+DE    l+  + +++++
  gi|518652670|ref|YP_008142190.1| 111 NSKIDEFYDA--LKLPPLTSKMGQLSKGQRQravfasvlisdPDVVILDEPTSgLDpfERKIFRD 173
                                       4444443334..77777778888888888777788888888888888888666665443555554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 5.1
                            AAA_22  97 iDEaqh.lr.seealeeLrsllnl 118
                                       iDE+   ++ ++  +e+L+ l n+
  gi|518652670|ref|YP_008142190.1| 215 IDEIAQeFNtNAVSIEFLKPLDNN 238
                                       677655476558888888888775 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00016      0.31      31      50 ..      33      52 ..      10      61 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00016
                            AAA_27 31 iyGpNEAGKstalrAisdll 50
                                       +GpN AGK+t+l+ +++ll
  gi|518652670|ref|YP_008142190.1| 33 YLGPNGAGKTTTLKVMTNLL 52
                                      57***************998 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2   0.00067       1.3       4      49 ..      34      80 ..      32     161 .. 0.67
   2 ?   -2.0   0.0       2.2   4.4e+03      18      28 ..     218     228 ..     190     276 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00067
                                      ESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSSSTTHHHHHHHHH CS
                               AAA  4 yGppGtGKTllakavakelg..vefleisgsellskyvgesekkirel 49
                                       Gp G GKT++ k + + l       e++g ++  ky +++ +++  +
  gi|518652670|ref|YP_008142190.1| 34 LGPNGAGKTTTLKVMTNLLRpsEGHAELNGIDVN-KYPKKALANVGSM 80
                                      59***********999998532334555555554.5444444444333 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.2
                                       HHHHHTHEEEE CS
                               AAA  18 vakelgvefle 28 
                                       +a+e++++ ++
  gi|518652670|ref|YP_008142190.1| 218 IAQEFNTNAVS 228
                                       22222222222 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00012      0.25      24      45 ..      34      55 ..      26     160 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00012
                            AAA_30 24 tGpAGtGKttalkalreaweaa 45
                                       Gp G+GKtt+lk+++++++ +
  gi|518652670|ref|YP_008142190.1| 34 LGPNGAGKTTTLKVMTNLLRPS 55
                                      69*************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 2257.19
//
Query:       gi|518652671|ref|YP_008142191.1|  [L=474]
Description: beta-glucosidase [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  186.2  15.9    8.5e-49  166.2   7.3    2.3  2  Glyco_hydro_1  Glycosyl hydrolase family 1


Domain annotation for each model (and alignments):
>> Glyco_hydro_1  Glycosyl hydrolase family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.4   2.7e-10   4.8e-06      10      92 ..       1      88 [.       1     115 [. 0.80
   2 !  166.2   7.3   4.8e-53   8.5e-49      93     451 ..     118     464 ..     101     466 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.7e-10
                                      EEEEE--HHHHH.--TTSTT---BHHHHHHHHGGGS....TTS---SSTT-HHHHHHHHHHHHHHTT-SEEEEE--HHH CS
                     Glyco_hydro_1 10 lwgaataayqiE.GawnedGkgesiwDtftetpgkv....legsngdvacdsYhrykeDvallkelgvkayrfSisWpR 83
                                      ++g+at+ +q+E G  ++    es w ++++  + +    ++g+  d + d+++ yk+ ++   ++g +++r+ i W+R
  gi|518652671|ref|YP_008142191.1|  1 MFGTATSPFQVEmGRSDNSISSESDWYKWSHDSNIIqktyVSGDFPDDGPDFWNNYKRFIDASIDMGNNSIRIGIDWAR 79
                                      7***********44455556788999999987544400014555677899***************************** PP

                                      HSTTSTT-- CS
                     Glyco_hydro_1 84 ilPkGegei 92
                                      i+ + + ++
  gi|518652671|ref|YP_008142191.1| 80 IFKTSTESV 88
                                      **9886554 PP

  == domain 2  score: 166.2 bits;  conditional E-value: 4.8e-53
                                       -HHHHHHHHHHHHHHHHTT-EEEEEEESS--BHHHHH..H-..........GGG-SHHHHHHHHHHHHHHHHHTTT- CS
                     Glyco_hydro_1  93 nekGlayYerLidelleagieplvTlyHwdlPqaLqd..eG..........gwenrsiidafkeyaevvfkrfgdkv 157
                                       +++ +++Y ++++ +++++++ ++T yHw lP +L+d  +           gw +++++++f +y  +++++f+  v
  gi|518652671|ref|YP_008142191.1| 118 DNDAVKHYVEIMEYIKAKNLKLILTAYHWPLPLWLHDpvKCnqdfancrekGWGDKATVEEFGKYIYYIYNKFHRYV 194
                                       57789******************************98642233333344448888********************** PP

                                       -EEEEEE-HHHHHHHHHTSS-...STT-S-TTTHHHHHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEEEEEESSSS CS
                     Glyco_hydro_1 158 klwlTfnEpnvvallgyltge...faPgkkdleaayeaaHnlllaharavklykevaqkgkigivlnlslaeplses 231
                                       ++w T+nEpn++a+ gy++g+   f+Pg ++++ a +++ nl  ah  a+k +k   +++++gi +++ + +p  + 
  gi|518652671|ref|YP_008142191.1| 195 DIWNTLNEPNIIAINGYVYGNlegFPPGLSNFSIAVSVMRNLAYAHNIAYKIIKALDHSSQVGINVAVPYFQPEMDT 271
                                       ******************9965559**************************************************** PP

                                       HHHHHHHHHHHHHHTHHHHHHHHHSS--HHHHHHHGGG..S----HHHHHHHTT--SEEEEEEEEEEEEEE--...- CS
                     Glyco_hydro_1 232 eedkeaaeraleflngwfldpvvkGdYpeemkellrergalpeiteedkellkgkadflglnyYtsrlvknkeseea 308
                                       +e+   ++  +++  + +l+  + G++ +++  +++e  +  e+         + +df+g++yY++  v+  ++++ 
  gi|518652671|ref|YP_008142191.1| 272 PENRFIVNYVKHIFYDLYLNSALYGNFDNSLSGIFNES-RPSEF---------AGTDFIGIDYYSRIRVRYVDNDNV 338
                                       ****99999*********************99999888.33333.........3579****************6666 PP

                                       STT---SSGGGGG-SBSS-B-SSSS-B-HHHHHHHHHHHHHTS----EEEEE----EE-BSSSHHH--HHHHHHHHH CS
                     Glyco_hydro_1 309 slskteekkleeevdpslpktdigwiiepeglrkllellkkeYqklpiyiteNGlgakdeieegkveDdkRidYlke 385
                                        l++              + +d++w i peg+r++ + + ++Y  +p++i eNG+++ +         + R +++++
  gi|518652671|ref|YP_008142191.1| 339 DLRYRFAFLP------CSKCSDNYWDIFPEGIRNVSRSVFNHYR-KPVMILENGVADAEG--------SLRKEFIEK 400
                                       6665554444......4556***********************9.9*********99885........68******* PP

                                       HHHHHHHHH.HTT--EEEEEEE-SB----GGGTTSEE--SEEEETTTTTEEEE-HHHHHHHHHHH-S CS
                     Glyco_hydro_1 386 hlnevkkai.edgvdlkgYvawsllDnfewaegyskrfGlvyvdrnetleRtpkkSakwykeviekn 451
                                       hl e++kai ed + +kgY+ ws++Dn+ewa+gy+++fGl+ ++   + e  + +   +y+++ + +
  gi|518652671|ref|YP_008142191.1| 401 HLIELHKAIkEDYIPVKGYFHWSIVDNYEWARGYKDKFGLYKIN---NGEFVKTEASEFYSKICHDH 464
                                       *********9999*******************************...55666667888998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 3325.87
//
Query:       gi|518652672|ref|YP_008142192.1|  [L=204]
Description: transcriptional activator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.2e-22   78.7   1.4    6.6e-22   78.4   1.4    1.1  1  TENA_THI-4  TENA/THI-4/PQQC family


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.4   3.7e-26   6.6e-22       4     206 ..      12     198 ..       9     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 3.7e-26
                                       CHHHHHHHHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCHHHHHH CS
                        TENA_THI-4   4 lrpiwkeyinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgeeielhl 80 
                                       + ++++ +++  Fv+a+++Gt++ e+f++y++qd  y+k +  +  +i+ ++ d   r el + i    +ee e h+
  gi|518652672|ref|YP_008142192.1|  12 VMELIDHIVHSDFVEAMKDGTIEDERFRYYLKQDHIYVKYYKAAGEVIGKNTGDDNIR-ELYNEI---GSEEPEFHR 84 
                                       667788888899*************************997766666999999999888.776655...456799*** PP

                                       HHHHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHH CS
                        TENA_THI-4  81 rlaealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvke 157
                                       ++ +++G+++  +++++   +t++y+++ll+++++ s+   + ++ pc ++y +iae  + + +      y  w++ 
  gi|518652672|ref|YP_008142192.1|  85 NMLKQFGIDEAGIKESEINYTTYSYINHLLRWSKDSSI-NGMLSMFPCQWSYGYIAEATAAPSE-----KYLFWFDF 155
                                       *********************************98876.5799*************88885544.....8******* PP

                                       HCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        TENA_THI-4 158 yaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltm 206
                                       y s+++r+  +++ ++l   +++ + +    +++i +  le+e ++++ 
  gi|518652672|ref|YP_008142192.1| 156 YRSKDYRSITDKYLEIL---QKE-PLS--TYQEQIIKFGLEYELNYWKE 198
                                       ********999855443...222.332..33456777789999999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       744  (0.041497); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 1585.50
//
Query:       gi|518652673|ref|YP_008142193.1|  [L=428]
Description: hypothetical protein FACI_IFERC00001G1312 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.4e-16   59.4   0.3    6.7e-16   58.9   0.3    1.3  1  Mur_ligase_M  Mur ligase middle domain
      9e-08   32.3   0.0    3.5e-07   30.4   0.0    2.0  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain
  ------ inclusion threshold ------
      0.096   12.5   0.0       0.23   11.3   0.0    1.6  1  DUF1317       Protein of unknown function (DUF1317)


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.3   1.1e-19   6.7e-16       1     191 [.      43     266 ..      43     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.1e-19
                                       EESSS-HHHHHHHHHHHHHCT..EEEEETTC.........................................SS-TH CS
                      Mur_ligase_M   1 vTGtnGKTTtteliaaileka..gkvigtvg.........................................ttnne 34 
                                       ++GtnGK ++++++++il+++  ++++++                                           t+ ++
  gi|518652673|ref|YP_008142193.1|  43 IAGTNGKGSIASYVYNILRQKykTGMYTSPHlldfneriildlnmipdsyiidfmnsnrdyienlatiyrnpTFFET 119
                                       89****************9995555666666***************************************9777776 PP

                                       HHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCH..CBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETT CS
                      Mur_ligase_M  35 iglpktlaemekkeaeyavlEvsshglgekrlegl..lkpdvavitnispdHldfh.gtlenyaeaKaelferlkee 108
                                       +++ ++ + +++++a+ya++Ev+      +rl+++  ++p+v vi  i+ +H +++  +l  +a++K  ++++ k+ 
  gi|518652673|ref|YP_008142193.1| 120 TTVMAFKY-FADNNADYAAIEVGLG----GRLDSTniINPEVSVIAQIGYEHYQRLgCSLTSIAHEKGGIIKNGKP- 190
                                       66666555.5555************....55555444*******************55899***********8885. PP

                                       CEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHH CS
                      Mur_ligase_M 109 giavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNa 185
                                        ++++ +  ++++e++k ++ +++k+v+++          ++++ + +g +++l  ++ +e++i+++ lG +++ N+
  gi|518652673|ref|YP_008142193.1| 191 -VVLLDNKPEVVAEITKIASVRNSKLVKISDYCSI-----TDLKFNLDGMSFKLQ-TPVEEYHITTSNLGLFQLGNI 260
                                       .5555556666777777777777777777766655.....689*********999.99******************* PP

                                       HHHHHH CS
                      Mur_ligase_M 186 laaiaa 191
                                         a+a 
  gi|518652673|ref|YP_008142193.1| 261 STAVAS 266
                                       ***986 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.88   5.3e+03      14      55 ..     125     168 ..     117     170 .. 0.61
   2 !   30.4   0.0   5.9e-11   3.5e-07       1      84 [.     289     364 ..     289     371 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.88
                                       EEEEEET--SHHHHHHHHHHHHHHSS..SSEEEEEEEESTT.CC CS
                      Mur_ligase_C  14 vtvidDyahnpdslsaalkalreiap..dkrlilvfgpggelge 55 
                                       ++++ D ++  ++++ +l +  ++ +  + ++ ++++ g e ++
  gi|518652673|ref|YP_008142193.1| 125 FKYFADNNADYAAIEVGLGGRLDSTNiiNPEVSVIAQIGYEHYQ 168
                                       66677777777777777665544444555666677766666565 PP

  == domain 2  score: 30.4 bits;  conditional E-value: 5.9e-11
                                       CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSE.EE CS
                      Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasalads.lv 76 
                                       ++ R+ev+++   ++vi D  hnp ++ a+++++ +++++k ++l+ +   +    +++ ++    ++ +l ds ++
  gi|518652673|ref|YP_008142193.1| 289 WPSRFEVISR--EPLVIMDSSHNPPAAHALVETFSNFVTQKPVLLIGM--LD----DKD-YFSYMSILRKLSDSvIL 356
                                       689*******..9************************99766655555..45....333.56677777778888566 PP

                                       EEESS-TT CS
                      Mur_ligase_C  77 vlgdypra 84 
                                       +++d+p++
  gi|518652673|ref|YP_008142193.1| 357 TTPDEPSR 364
                                       66666643 PP

>> DUF1317  Protein of unknown function (DUF1317)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   3.8e-05      0.23      23      48 ..     376     399 ..     373     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.8e-05
                           DUF1317  23 GWvfPGlkviknPlkAqrlAEEknnk 48 
                                       G +fP  ++ik+P++A++ A  + n+
  gi|518652673|ref|YP_008142193.1| 376 GHMFPSIRIIKDPVEAYNFA--IQNY 399
                                       889***************99..5666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3035.79
//
Query:       gi|518652674|ref|YP_008142194.1|  [L=422]
Description: hypothetical protein FACI_IFERC00001G1313 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-17   63.3   0.1    4.1e-17   61.9   0.1    1.8  1  Cdc6_C      CDC6, C terminal winged helix domain
    7.2e-10   39.5   0.0    6.1e-07   30.0   0.0    2.7  3  AAA_16      AAA ATPase domain
    9.8e-09   35.7   0.2    4.4e-08   33.6   0.1    2.2  2  AAA         ATPase family associated with various cellular ac
    5.9e-08   33.1   0.1    4.6e-07   30.2   0.0    2.1  2  AAA_22      AAA domain
    0.00075   18.7   0.0     0.0013   18.0   0.0    1.3  1  DUF815      Protein of unknown function (DUF815)
    0.00079   19.4   1.3      0.011   15.7   1.3    2.3  1  ATPase_2    ATPase domain predominantly from Archaea
      0.006   16.1   1.5      0.015   14.8   1.5    1.6  1  Pox_A32     Poxvirus A32 protein
  ------ inclusion threshold ------
      0.012   15.7   0.1      0.056   13.6   0.1    2.0  1  AAA_2       AAA domain (Cdc48 subfamily)
      0.022   14.6   0.4        3.4    7.4   0.0    2.7  3  DEAD        DEAD/DEAH box helicase
      0.032   13.6   0.1      0.094   12.1   0.1    1.7  1  TniB        Bacterial TniB protein
      0.068   12.4   1.8          5    6.3   0.1    2.3  2  KAP_NTPase  KAP family P-loop domain
      0.073   12.8   0.7       0.25   11.0   0.7    1.9  1  AAA_24      AAA domain


Domain annotation for each model (and alignments):
>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.9   0.1   2.7e-20   4.1e-17       3      81 ..     303     379 ..     301     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.9 bits;  conditional E-value: 2.7e-20
                                       HHHHHHCHCSSS-EEHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESSSCH CS
                            Cdc6_C   3 alvlllrksgkeevttgevyevYkslCesegvdpltqrevsdllseLemlgileleksskGrregrtrkisLnvdpd 79 
                                       +++l  + ++ +   tge+ye Y ++C ++g++plt+r++sdlls+Le+ g+l+++++s Gr +gr++ i++  + +
  gi|518652674|ref|YP_008142194.1| 303 SACLTQE-TDADLSVTGEIYENYGNICTELGFQPLTMRRISDLLSDLEDTGLLTTNTRSLGR-YGRMKFIRVMGSIQ 377
                                       5554444.7778889**********************************************9.*******9977666 PP

                                       HH CS
                            Cdc6_C  80 dv 81 
                                       +v
  gi|518652674|ref|YP_008142194.1| 378 NV 379
                                       55 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   4.1e-10   6.1e-07       2      66 ..      31      99 ..      30     116 .. 0.77
   2 !    6.3   0.0    0.0078        12     126     165 ..     131     171 ..     126     178 .. 0.74
   3 ?   -1.2   0.0       1.5   2.3e+03     112     149 ..     243     279 ..     179     302 .. 0.62

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 4.1e-10
                            AAA_16  2 lvGReeeleqLlsalervrsgrp.elvllsGesGvGKsslv....rellralekdggiflrgkcdqlesa 66
                                      ++ Re++++ ++++l+++ +g+  +++ll+G sG+GK+s v     +l++ l+++ +  ++ +c+ ++s+
  gi|518652674|ref|YP_008142194.1| 31 FPHREKQIDSIARVLSSIVTGGLsSNLLLYGKSGSGKTSSViyvtGMLKETLKGN-INIIYINCEIYDSQ 99
                                      899*******************9****************9966655555555555.55677777766433 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0078
                            AAA_16 126 llallsrderplvlvlDdlq.wadeaslqllaaLlrllesk 165
                                       l+++l + +r +v++lD+++  ++ +  ++l+ Ll+ + ++
  gi|518652674|ref|YP_008142194.1| 131 LVKRLNKSGRYTVIILDEIDkLIQKSGSDALYVLLKIMADS 171
                                       66677777999*********545556666699999887664 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.5
                            AAA_16 112 agaeasrllellkrllallsrderplvlvlDdlqwade 149
                                       +  +a+   +ll+ +++ + +d++   +++Dd+  a++
  gi|518652674|ref|YP_008142194.1| 243 EHGDARKSIDLLRIAIDSALKDGK-DCVTIDDVYLARD 279
                                       222234555555555566666566.7888888876665 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 !   33.6   0.1   2.9e-11   4.4e-08       1     125 [.      57     197 ..      57     203 .. 0.80
   2 ?   -1.9   0.0       2.9   4.3e+03      46      69 ..     254     276 ..     233     305 .. 0.66

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 2.9e-11
                                       EEEESSTTSSHHHHHHHHHHHH......THEEEEEETTTCSSS...................STTHHHHHHH.HHHH CS
                               AAA   1 vllyGppGtGKTllakavakel......gvefleisgsellsk...................yvgesekkir.elfk 51 
                                       +llyG  G GKT+ +  v   l      +++++ i++    s+                   ++g  ++ki  el+k
  gi|518652674|ref|YP_008142194.1|  57 LLLYGKSGSGKTSSVIYVTGMLketlkgNINIIYINCEIYDSQysilvyltnainsgdapipILGLPQDKIYfELVK 133
                                       69*******************954454449999999988887799***************88777777776425555 PP

                                       HHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHSTTSS CS
                               AAA  52 eakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnr...pdkldpallrgRfd 125
                                       ++ ++ + +++++DEid+l++++       +++++ +Ll+ + + ++      +ig+tn+   ++ ld  +  +R++
  gi|518652674|ref|YP_008142194.1| 134 RLNKSGRYTVIILDEIDKLIQKS-------GSDALYVLLKIMADSNT-----SLIGITNDasfVNALDARVQ-SRLN 197
                                       55555456**************9.......88899999999988877.....6******9666666666666.6665 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.9
                                       HHHHHHHHHHTSTSEEEEEETGGG CS
                               AAA  46 irelfkeakekakpsilfiDEida 69 
                                       +r  +++a +   + ++ iD+++ 
  gi|518652674|ref|YP_008142194.1| 254 LRIAIDSALKDG-KDCVTIDDVYL 276
                                       444555544443.57777777764 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   3.1e-10   4.6e-07       7     125 ..      56     175 ..      53     183 .. 0.78
   2 ?    0.2   0.0      0.55   8.2e+02      59     111 ..     234     288 ..     228     346 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 3.1e-10
                            AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka....erlsseell 79 
                                        l+++G sG+GKT ++  ++  l+e  k    +  ++++++    s+ ++l  l +a++++          + + ++
  gi|518652674|ref|YP_008142194.1|  56 NLLLYGKSGSGKTSSVIYVTGMLKETLK---GNINIIYINCEIYDSQYSILVYLTNAINSGDAPipilGLPQDKIYF 129
                                       689*******************965433...499999**********************87777***6555666666 PP

                            AAA_22  80 ealeqalraravielliiDEaqhlr..s.eealeeL.rsllnlsrkgvql 125
                                       e++ +  ++ +   ++i+DE+++l+  s  +al  L +++++   ++++l
  gi|518652674|ref|YP_008142194.1| 130 ELVKRLNKSGRY-TVIILDEIDKLIqkSgSDALYVLlKIMAD---SNTSL 175
                                       777777777777.**********9987355555555155555...44333 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.55
                            AAA_22  59 ellralglelkaerlsseellealeqalraravielliiDEaqhlr...seealee 111
                                       +l+ alg + ++   +s +ll+   + + + ++  ++ iD++   r   ++++l+e
  gi|518652674|ref|YP_008142194.1| 234 NLCAALGAQEHGDARKSIDLLRIAIDSALKDGK-DCVTIDDVYLARdrfEMNVLKE 288
                                       577788877777334444444444444444444.6999999866654333444444 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   8.6e-07    0.0013      32      88 ..      33      92 ..       8     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 8.6e-07
                            DUF815 32 gidkqkealventeqfleglpannvLLwGarGtGKSslv...kallneyaeegLrlieve 88
                                        +kq +++ +  +  ++g  ++n+LL+G+ G+GK s v     +l+e+ + ++ +i ++
  gi|518652674|ref|YP_008142194.1| 33 HREKQIDSIARVLSSIVTGGLSSNLLLYGKSGSGKTSSViyvTGMLKETLKGNINIIYIN 92
                                      568999999999***********************9976111455666666668888765 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 !   15.7   1.3   7.1e-06     0.011       3     147 ..      33     166 ..      31     179 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.1e-06
                          ATPase_2   3 dRekelkelee....ilerepneiyfiYGpegsGKtaLlkeiienledkdk..yviyyialreesiskldefieeee 73 
                                        Rek ++++ +    i+  + ++ +++YG  gsGKt+ +  +   l++  k    i yi+ + +++++         
  gi|518652674|ref|YP_008142194.1|  33 HREKQIDSIARvlssIVTGGLSSNLLLYGKSGSGKTSSVIYVTGMLKETLKgnINIIYINCEIYDSQYSILV----- 104
                                       689999887651111556799999*************99988888866544337777788887777776666..... PP

                          ATPase_2  74 ekkklekal...giavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLln 147
                                          +l++a+     ++p   l         + + ++e l + ++k+g+  +ii+De+ kli  ++    + ++ Ll+
  gi|518652674|ref|YP_008142194.1| 105 ---YLTNAInsgDAPIPILGL--------PQDKIYFE-LVKRLNKSGRYTVIILDEIDKLI-QKSG--SDALYVLLK 166
                                       ...344444222345555555........44344555.56789*****************9.4444..344444444 PP

>> Pox_A32  Poxvirus A32 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   1.5   9.9e-06     0.015      15     132 ..      56     176 ..      53     188 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.9e-06
                           Pox_A32  15 rlalvGgsGsGkt...vyLlsLlrtlvkky.khifLltpvknseYdkyvwPdhinkvtseeeleYsLsatkekiekl 87 
                                       +l l G+sGsGkt   +y+  +l++  k+    i++   +++s+Y   v+    n + s +     L   ++ki   
  gi|518652674|ref|YP_008142194.1|  56 NLLLYGKSGSGKTssvIYVTGMLKETLKGNiNIIYINCEIYDSQYSILVYLT--NAINSGDAPIPILGLPQDKIYF- 129
                                       68899*******966679999998666655499****************954..5566666644455555555543. PP

                           Pox_A32  88 akkeknqkeaerfLlilDDlGdkqtks..ktLlellnvgRhlnvsii 132
                                         +++ +k+   +++ilD++ ++  ks    L  ll +   +n+s+i
  gi|518652674|ref|YP_008142194.1| 130 ELVKRLNKSGRYTVIILDEIDKLIQKSgsDALYVLLKIMADSNTSLI 176
                                       33346666678899999999887666422567778887777777776 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   3.7e-05     0.056      63     108 ..     132     173 ..      53     188 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.7e-05
                                       -HHHHTTS...EEEEETGGG-------------HHHHHHHHHHHH--EE CS
                             AAA_2  63 yvgaeegG...ivllDEidKihpkessgadvSregVqrdLLqileggtl 108
                                        ++ +++G   ++ lDEidK  +        S+ + + +LL+i+ +++ 
  gi|518652674|ref|YP_008142194.1| 132 VKRLNKSGrytVIILDEIDKLIQ-------KSGSDALYVLLKIMADSNT 173
                                       34444555888*********999.......7999**********99875 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.021        31      10      34 ..      47      73 ..      35      94 .. 0.64
   2 ?    7.4   0.0    0.0023       3.4     119     149 ..     138     168 ..     118     179 .. 0.77
   3 ?   -2.3   0.0       2.2   3.2e+03     153     172 ..     290     309 ..     279     312 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.021
                                      HHHTT...CEEEEEESTTSSHHHHHHHH CS
                                      xxxxx...xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 10 lilgg...gdvlvaaeTGsGKTlaflip 34
                                       i++g    ++l+ ++ GsGKT    i 
  gi|518652674|ref|YP_008142194.1| 47 SIVTGglsSNLLLYGKSGSGKTSSV-IY 73
                                      333333446999**********873.33 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0023
                                       CTTEEEEEEETHHHHHHTTTHHHHHHHHHHS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinrilnql 149
                                         + ++++lDE+d+l +++ sd +  +l+ +
  gi|518652674|ref|YP_008142194.1| 138 SGRYTVIILDEIDKLIQKSGSDALYVLLKIM 168
                                       566789************9988887777666 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.2
                                       CTTSTTTSEEEEEESSBSHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 153 tcdgklqrqvivlSATlpkd 172
                                         + + ++++++lSA l+++
  gi|518652674|ref|YP_008142194.1| 290 IRTLPIHSKMVLLSACLTQE 309
                                       344455567999***99965 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   6.3e-05     0.094      35     182 ..      54     199 ..      30     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.3e-05
                              TniB  35 mpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealg...aplkara.rvskl 107
                                        +nlll+G+s  GKt+ v   + + +++    + +++++++++    ++  +   + +a++   ap+       +k+
  gi|518652674|ref|YP_008142194.1|  54 SSNLLLYGKSGSGKTSSVIYVTGMLKET---LKGNINIIYINCEIYDSQYSILVYLTNAINsgdAPIPILGlPQDKI 127
                                       479************9998777666554...4678999999999999998888888777762225565554355677 PP

                              TniB 108 eqqvlrllrel.kvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealralrtDpqlasRFepi 182
                                       + + ++ l++  +  v+i+DEi++l++ s      +l +l +++ + + +++++ t++a  +   D+ ++sR++++
  gi|518652674|ref|YP_008142194.1| 128 YFELVKRLNKSgRYTVIILDEIDKLIQKSG---SDALYVLLKIMADSNTSLIGI-TNDASFVNALDARVQSRLNQE 199
                                       777777776652689***********5444...445566666677778899988.778888888899999998876 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 ?    5.5   0.3    0.0059       8.8       2      59 ..      35      92 ..      34     110 .. 0.76
   2 ?    6.3   0.1    0.0034         5     146     226 ..     113     193 ..      97     202 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0059
                        KAP_NTPase  2 dlyasaladilseptl.atpivvgLygkWGsGKssllnkledelkefakpvrflfaefn 59
                                      ++ ++++a +ls+    + ++ + Lygk GsGK+s +  +   lke   +  + ++++n
  gi|518652674|ref|YP_008142194.1| 35 EKQIDSIARVLSSIVTgGLSSNLLLYGKSGSGKTSSVIYVTGMLKET-LKGNINIIYIN 92
                                      67788888888865335888999***********9888777777777.66667776666 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0034
                        KAP_NTPase 146 eeaplkklqteveelladmektLdalqkrlVvviDdLDrceteevlqlleavkllfslkpvvfilavDphviakaie 222
                                        +ap+  l+   ++++ +++k L ++ +  V+++D++D + ++     l+++  ++  +++++i ++++     a+ 
  gi|518652674|ref|YP_008142194.1| 113 GDAPIPILGLPQDKIYFELVKRLNKSGRYTVIILDEIDKLIQKSGSDALYVLLKIMADSNTSLIGITNDASFVNALD 189
                                       56666677777788888999*******************98887777666665555558888888888877777776 PP

                        KAP_NTPase 223 anse 226
                                       a  +
  gi|518652674|ref|YP_008142194.1| 190 ARVQ 193
                                       6655 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00017      0.25       4      77 ..      56     152 ..      53     161 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                            AAA_24   4 kiliyGpsgiGKTtlakel..........gpkplfidtek..Glksldadkfpdie...........swedfldevv 57 
                                       ++l+yG+sg+GKT+++               ++++i++e   +  s+ +   + i+             ++++ e+v
  gi|518652674|ref|YP_008142194.1|  56 NLLLYGKSGSGKTSSVIYVtgmlketlkgNINIIYINCEIydSQYSILVYLTNAINsgdapipilglPQDKIYFELV 132
                                       789***********987776666666655555566666642122222222222222555555555443344444444 PP

                            AAA_24  58 elaaeladyktlviDtidel 77 
                                       +   +  +y ++++D id+l
  gi|518652674|ref|YP_008142194.1| 133 KRLNKSGRYTVIILDEIDKL 152
                                       44555555677777776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 2972.03
//
Query:       gi|518652675|ref|YP_008142195.1|  [L=96]
Description: hypothetical protein FACI_IFERC00001G1314 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 670.65
//
Query:       gi|518652676|ref|YP_008142196.1|  [L=189]
Description: hypothetical protein FACI_IFERC00001G1315 [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   42.3   0.1    1.5e-10   41.7   0.1    1.3  1  AAA_18           AAA domain
    5.6e-09   36.5   0.1    8.4e-09   36.0   0.1    1.2  1  AAA_17           AAA domain
     0.0025   17.8   0.1     0.0058   16.6   0.0    1.6  2  P-mevalo_kinase  Phosphomevalonate kinase
  ------ inclusion threshold ------
      0.026   14.7   0.0      0.041   14.0   0.0    1.3  1  AAA_33           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 !   41.7   0.1   3.3e-14   1.5e-10       2     120 ..       5     128 ..       4     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 3.3e-14
                            AAA_18   2 lltGtpGvGKttlakeLskrlgf.....gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenssale 72 
                                       ++tG+pG+GK ++ k  +++ gf     g  ++++a e+ + l++    a+  ++r + +++  + ++ e +    +
  gi|518652676|ref|YP_008142196.1|   5 IITGMPGSGKDEFVKVAKSM-GFidahmGNTVKKNALEKKIPLDDGSIgAYATEERKKYGMDIWAKRTAELI----T 76 
                                       89***************777.8999999*************9999999855555555555544555555544....5 PP

                            AAA_18  73 egknlvidghlaeleseaakdikk....vvLtaspeelleRlekRgyeeaki 120
                                       e++  ++dg+++e e +++k +      + + a+++ +leR+ +R++e++  
  gi|518652676|ref|YP_008142196.1|  77 EPDITIVDGLRNEEELDYFKGNFQniivIAVFANENDRLERILARDREDDSH 128
                                       799**************9996666**********************988765 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.1   1.9e-12   8.4e-09       1     131 [.       7     127 ..       7     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.9e-12
                                       EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHC.TSHHHHHHHHHHHHHHHHHHHH.HSSEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemr.klpleekkelqkeaaekiaeea.kkkgvl 75 
                                       +G+PGsGK + + k+++ +gf    +G  + ++a +++   +++ +   + +e+kk  +++ a++ ae   + +  +
  gi|518652676|ref|YP_008142196.1|   7 TGMPGSGKDEFV-KVAKSMGFIDAHMGNTVKKNALEKKIPLDDGSIGaYATEERKKYGMDIWAKRTAELItEPDITI 82 
                                       7***********.************************997777777724566666667788888888875366789* PP

                                       EEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHHTTST-TS-S CS
                            AAA_17  76 vdghprikeqagfldglpkevleelkpdaiilleadpeeilerrlkdrtrgrdddn 131
                                       vdg      ++++ld ++ ++++     ++i + a++ + ler l    r+r+dd+
  gi|518652676|ref|YP_008142196.1|  83 VDGLR----NEEELDYFKGNFQNI----IVIAVFANENDRLERILA---RDREDDS 127
                                       ***97....567788888876555....5***************98...6676665 PP

>> P-mevalo_kinase  Phosphomevalonate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.5   6.8e+03       1      15 [.       6      20 ..       6      25 .. 0.73
   2 !   16.6   0.0   1.3e-06    0.0058      68     113 ..      57     100 ..      53     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.5
                   P-mevalo_kinase  1 isGkrksGKdyvtel 15
                                      i+G   sGKd +++ 
  gi|518652676|ref|YP_008142196.1|  6 ITGMPGSGKDEFVKV 20
                                      578888999977655 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 1.3e-06
                   P-mevalo_kinase  68 eekrkkdpglFcraaiekieaakkdvliisDiRrktdleyfkeayg 113
                                       ee++k  + ++ ++  e i  ++ d+ i++++R++++l+yfk +++
  gi|518652676|ref|YP_008142196.1|  57 EERKKYGMDIWAKRTAELI--TEPDITIVDGLRNEEELDYFKGNFQ 100
                                       7777888899******976..8899*****************9997 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   9.2e-06     0.041       1     125 [.       3     128 ..       3     140 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 9.2e-06
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg......avllssdtlrrrlfgtdqqsktdytrvldr..lyqilnelarkalsa 69 
                                       ++++ G+pGsGK  +++ ++k  g      + ++ +++l +++  +d     + t+ +++  +  + +++a +  ++
  gi|518652676|ref|YP_008142196.1|   3 MLIITGMPGSGKDEFVK-VAKSMGfidahmGNTVKKNALEKKIPLDDGSIGAYATEERKKygMDIWAKRTA-ELITE 77 
                                       57899***********9.56666777777799999999999999877776666666554444333444444.55566 PP

                            AAA_33  70 grnvildatnlsrrerarflklarrlgvpvrivvvetdeetlkeRlakRaangddr 125
                                          +i+d ++++++e + f   ++    ++ +++v + e    eR+ +R ++ d+ 
  gi|518652676|ref|YP_008142196.1|  78 PDITIVD-GLRNEEELDYFKGNFQ----NIIVIAVFANENDRLERILARDREDDSH 128
                                       6555555.89*************9....799********************87654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1440.40
//
Query:       gi|518652677|ref|YP_008142197.1|  [L=260]
Description: hypothetical protein FACI_IFERC00001G1316 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-61  207.4   0.0    2.1e-61  207.3   0.0    1.0  1  GATase_5   CobB/CobQ-like glutamine amidotransferase domain
    5.6e-06   26.1   0.0      1e-05   25.2   0.0    1.5  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
    0.00018   21.4   0.0    0.00031   20.6   0.0    1.4  1  DJ-1_PfpI  DJ-1/PfpI family
    0.00091   19.0   0.0      0.002   17.9   0.0    1.7  1  GATase     Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.022   14.4   0.0      0.032   13.9   0.0    1.2  1  ThiJ_like  ThiJ/PfpI family-like


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  207.3   0.0   5.9e-65   2.1e-61       3     259 ..       7     254 ..       5     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 207.3 bits;  conditional E-value: 5.9e-65
                          GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklr 79 
                                       k+ ilr eG+n e+e+  +++++Gfe + vh+s++  g+++++d+  l++pGGfs+gD   +g+++a +l       
  gi|518652677|ref|YP_008142197.1|   7 KAGILRMEGTNNEEEAFLSLRRSGFESEYVHVSEI--GKKKFEDYDLLFIPGGFSAGDYVRAGAIFASRLA---PHI 78 
                                       6679*******************************..9999**************************9998...556 PP

                          GATase_5  80 ealekflnredtlaLGiCnGfqlLvklglvpggeieeaeksptltrNksgrfesrlvsvvvsekspsvflkgme..g 154
                                       ++l+kf+++ +++ +G+CnGfq+L++lg++p  + +e ++++ l  N+s rfe+r ++++  ++++ +f ++ e  +
  gi|518652677|ref|YP_008142197.1|  79 NELNKFVDS-GKILIGVCNGFQVLSELGMIPD-TGTERKRTMVLGTNDSDRFECRYTYIKY-TSKNKIFRRHFEgkI 152
                                       79*******.*********************9.88999*********************98.555556665554449 PP

                          GATase_5 155 lslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeyplNPNgSpegiagitspdGRvlalmpHpervve 231
                                       l++pvah eG++ f+s+++l+++++n q++++Y d +g+  ++yp+NPNgS+ +iag+t+++G v++lmpHperv+ 
  gi|518652677|ref|YP_008142197.1| 153 LQVPVAHMEGKVIFDSKKTLDSVIENDQMIFQYTDINGT-DSSYPWNPNGSVMDIAGLTNREGNVIGLMPHPERVYY 228
                                       ************************************776.589********************************** PP

                          GATase_5 232 avqksiipeeeeeevspwlrlFenavky 259
                                        +q+   + +++++ + +   F++ ++y
  gi|518652677|ref|YP_008142197.1| 229 GFQMM-ND-GNKHKNGTGEVFFNSLYEY 254
                                       **998.44.4444448888888888888 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.9e-09     1e-05      24      92 ..      33     105 ..       8     126 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.9e-09
                          GATase_3  24 evrvrfvplkdeslgedadlvilpGgkd.....tiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeei 92 
                                       +++v+++++ ++++ ed+dl+++pGg++     ++ ++ ++r     +++++++ +g+ ++g+C G+q+L+e  
  gi|518652677|ref|YP_008142197.1|  33 SEYVHVSEIGKKKF-EDYDLLFIPGGFSagdyvRAGAIFASRLAPHINELNKFVDSGKILIGVCNGFQVLSELG 105
                                       46778888888888.67*********972222234455567778889999********************9854 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 !   20.6   0.0   8.5e-08   0.00031      57     114 ..      44     108 ..      29     121 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 8.5e-08
                                       CTCCG-SEEEE--BHHHHHHHHTSH.......HHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTT CS
                         DJ-1_PfpI  57 vkaaeyDalvlpGGragperlrene.......kvvelvkefaekgklvaaICagpqlLaaagvlk 114
                                        k ++yD+l +pGG +  +++r+ +         ++ + +f+++gk++  +C g q+L++ g+++
  gi|518652677|ref|YP_008142197.1|  44 KKFEDYDLLFIPGGFSAGDYVRAGAifasrlaPHINELNKFVDSGKILIGVCNGFQVLSELGMIP 108
                                       56789****************9987333322233556899*******************999875 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   5.7e-07     0.002      17     113 ..      26     134 ..      16     232 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.7e-07
                                       HHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT...........TTTHHHHHHHHCTSTS-EEEETHHHH CS
                            GATase  17 lvelgvkvevvpidasaeeilellknpdgilvsgGpgspg...........vegkieaikearenkiPiLGICLGmQ 82 
                                       l++ g++ e v +++  +++    +++d ++++gG+ +                +i+ ++++ ++++ ++G+C G+Q
  gi|518652677|ref|YP_008142197.1|  26 LRRSGFESEYVHVSEIGKKK---FEDYDLLFIPGGFSAGDyvragaifasrLAPHINELNKFVDSGKILIGVCNGFQ 99 
                                       66777888888888655555...689**********99888888888877766677777777779************ PP

                                       HHHHHTTT..EEEEEECEEEEEEEEEEEETTT...C CS
                            GATase  83 llaiefgr..kvvkekekehhggtmrlgddet...a 113
                                       +l + +g   ++  e+++++  gt   +  e+    
  gi|518652677|ref|YP_008142197.1| 100 VLSE-LGMipDTGTERKRTMVLGTNDSDRFECrytY 134
                                       *975.4433433333334444444444444443332 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     9e-06     0.032      76     139 ..      27     102 ..      11     119 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-06
                         ThiJ_like  76 ssesF.............sleeydlvllpGGsdkavrelles.erlhsllveylklvkrekepskvlgaicqgvlal 138
                                       + ++F             ++e+ydl+++pGG   +  +++    +  s l+++++  ++  +  k+l  +c g  +l
  gi|518652677|ref|YP_008142197.1|  27 RRSGFeseyvhvseigkkKFEDYDLLFIPGGFSAG--DYVRAgAIFASRLAPHINELNKFVDSGKILIGVCNGFQVL 101
                                       44444555556666666689***********8765..56655166788999999999999899999999**998888 PP

                         ThiJ_like 139 a 139
                                       +
  gi|518652677|ref|YP_008142197.1| 102 S 102
                                       6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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 0.28s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1808.77
//
Query:       gi|518652678|ref|YP_008142198.1|  [L=49]
Description: 50S ribosomal protein L40E [Ferroplasma acidarmanus fer1]
Scores for complete 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   32.4   5.9    7.6e-08   32.1   5.9    1.1  1  Ribosomal_L40e  Ribosomal L40e family
     0.0017   18.0   2.6     0.0022   17.6   2.6    1.2  1  zinc_ribbon_2   zinc-ribbon domain
      0.006   16.6   1.2     0.0081   16.2   1.2    1.1  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.4   6.6      0.018   14.7   6.6    1.4  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.08   13.0   1.3      0.087   12.8   1.3    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.08   13.0   1.7       0.12   12.5   1.7    1.4  1  UPF0547         Uncharacterised protein family UPF0547


Domain annotation for each model (and alignments):
>> Ribosomal_L40e  Ribosomal L40e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   5.9   2.5e-11   7.6e-08      12      42 ..       9      37 ..       5      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 2.5e-11
                    Ribosomal_L40e 12 yncdKmiCrkCYArlpprAtnCrkkkCghsn 42
                                       +  ++iC kCYAr ++ At+Cr  kCg + 
  gi|518652678|ref|YP_008142198.1|  9 RRLTRKICMKCYARNSINATKCR--KCGYTG 37
                                      57889******************..9**985 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   2.6   7.4e-07    0.0022       2      21 ..      16      35 ..      15      37 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.4e-07
                     zinc_ribbon_2  2 CpnCGaelqdnakFCpyCGt 21
                                      C +C a ++ na+ C +CG+
  gi|518652678|ref|YP_008142198.1| 16 CMKCYARNSINATKCRKCGY 35
                                      *******************8 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.2   2.7e-06    0.0081      28      49 .]      13      34 ..       4      34 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                               DZR 28 edrCpsCgekvdpearfCpeCG 49
                                       + C++C + ++ +a+ C +CG
  gi|518652678|ref|YP_008142198.1| 13 RKICMKCYARNSINATKCRKCG 34
                                      689******************9 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   6.6   6.1e-06     0.018       2      25 ..      15      35 ..      15      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.1e-06
                                      B-SSS--B----SSS----SSS-- CS
                    DNA_RNApol_7kD  2 iCgeCgaevslkkgdpiRCkeCGh 25
                                      iC++C a++s++++   +C++CG+
  gi|518652678|ref|YP_008142198.1| 15 ICMKCYARNSINAT---KCRKCGY 35
                                      8************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 ?   12.8   1.3   2.9e-05     0.087      64     101 ..       7      42 ..       4      47 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.9e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS-EEEEE CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsadveivs 101
                                       ie+   +  C +C ++ +++  a++C kCg ++++++s
  gi|518652678|ref|YP_008142198.1|   7 IERRLTRKICMKCYARNSIN--ATKCRKCGYTGLRVKS 42 
                                       677777889*****999988..459*****99998865 PP

>> UPF0547  Uncharacterised protein family UPF0547
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   1.7     4e-05      0.12       5      22 ..      18      35 ..      14      36 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4e-05
                           UPF0547  5 eCeakvPvaaqfCphCGy 22
                                       C a  +++a +C+ CGy
  gi|518652678|ref|YP_008142198.1| 18 KCYARNSINATKCRKCGY 35
                                      56666799*********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       869  (0.048469); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.45
# Mc/sec: 326.58
//
Query:       gi|518652679|ref|YP_008142199.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518652679|ref|YP_008142199.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518652679|ref|YP_008142199.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518652679|ref|YP_008142199.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518652679|ref|YP_008142199.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518652679|ref|YP_008142199.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518652679|ref|YP_008142199.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518652679|ref|YP_008142199.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518652679|ref|YP_008142199.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.61
# Mc/sec: 1721.49
//
Query:       gi|518652680|ref|YP_008142200.1|  [L=62]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-23   82.0   1.2      2e-23   81.8   1.2    1.1  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.8   1.2   1.1e-27     2e-23       1      48 [.       4      51 ..       4      53 .. 0.98

  Alignments for each domain:
  == domain 1  score: 81.8 bits;  conditional E-value: 1.1e-27
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIld 48
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++
  gi|518652680|ref|YP_008142200.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITR 51
                                      8*********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); 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: 0.41u 0.32s 00:00:00.73 Elapsed: 00:00:00.47
# Mc/sec: 392.66
//
Query:       gi|518652681|ref|YP_008142201.1|  [L=381]
Description: hypothetical protein FACI_IFERC00001G1320 [Ferroplasma acidarmanus fer1]
Scores for complete 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-173  575.2   0.1   6.1e-173  575.1   0.1    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 !  575.1   0.1  3.4e-177  6.1e-173       1     360 [.       2     365 ..       2     366 .. 0.98

  Alignments for each domain:
  == domain 1  score: 575.1 bits;  conditional E-value: 3.4e-177
                          FBPase_3   1 kvtlsvikaDvGslaGhtkvheellekveevleeakkkgllidfyvtkvGDDielimthtkgvdneevhklawdafk 77 
                                       k+t+s+ikaD+Gsl+Ght v + ++++ve++++++++ gl++df+++++GDDi+++m ht+g+dn e+hklawdafk
  gi|518652681|ref|YP_008142201.1|   2 KTTISHIKADIGSLPGHTVVYQPVVDEVENYVKNNSE-GLISDFHISHIGDDIQITMVHTRGADNPEIHKLAWDAFK 77 
                                       79******************************99875.6************************************** PP

                          FBPase_3  78 eatevakelklygaGqDlLkdafsGnvkGlGPgvaelefeeRksepvvvfaaDktepgafnlplykifadpfntaGl 154
                                       ++tevak+++lygaGqDlLkdafsGn+kG+GPgvaele++ Rk+ep++v+++Dktepgafn+p+yk+f dpfnt+Gl
  gi|518652681|ref|YP_008142201.1|  78 AGTEVAKKIGLYGAGQDLLKDAFSGNIKGMGPGVAELEITPRKAEPFIVYMMDKTEPGAFNYPIYKMFGDPFNTPGL 154
                                       ***************************************************************************** PP

                          FBPase_3 155 vidpklheGfkfevlDvieekkillsapeelydllallgakeryvikrvysk.....kdeeiaavvsterlsliaGk 226
                                       vidp++h+Gfkfev+D+++ kki ls pe++ydlla++g+k++yvikrvy+k       +e++av++t++ls iaG+
  gi|518652681|ref|YP_008142201.1| 155 VIDPNMHMGFKFEVWDIYNGKKIYLSLPEDTYDLLAFIGSKSKYVIKRVYTKnthtkLPDENVAVITTDKLSFIAGE 231
                                       ***************************************************96665556789*************** PP

                          FBPase_3 227 YvGkDDPvaivRaqsglPavgevlepfalphlvaGwmrGshngplmPvslkdakptrfdgpprvvalgfqlkegklv 303
                                       YvGkDDP  ivR+qsglPa ge+lepfa+++lv+GwmrGs+ngp+mPv +++a++trfdgpprv+algf +kegkl+
  gi|518652681|ref|YP_008142201.1| 232 YVGKDDPAGIVRIQSGLPASGEALEPFANSYLVSGWMRGSFNGPMMPVGMDNAQMTRFDGPPRVMALGFVMKEGKLA 308
                                       ***************************************************************************** PP

                          FBPase_3 304 gpvDlfddpafdeaRekaaeiadelRrqGpfephrlpeeeleYttlpevleklkerf 360
                                       gpvD+f d afd+aR++a ++a+++Rr+G+fephrlp e++eYt+lp++lek ++ f
  gi|518652681|ref|YP_008142201.1| 309 GPVDMFRDVAFDYARNEALNMANYMRRMGVFEPHRLPDEDMEYTALPKILEKRAQDF 365
                                       ***************************************************988777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.49
# Mc/sec: 2353.79
//
Query:       gi|518652682|ref|YP_008142202.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G1321 [Ferroplasma acidarmanus fer1]
Scores for complete 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-40  136.7   2.5    1.7e-39  135.9   0.7    2.1  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    5.9e-14   52.4   2.4    3.7e-12   46.6   0.2    3.4  4  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0013   18.1  12.3     0.0026   17.1   6.0    3.7  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0019   17.9  10.3       0.72    9.4   2.6    3.9  4  DAO            FAD dependent oxidoreductase
  ------ inclusion threshold ------
      0.013   14.8   1.5        1.2    8.4   0.4    2.3  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.084   13.1   1.2         17    5.7   0.0    2.9  3  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.26   10.4   0.3       0.58    9.2   0.0    1.7  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
        1.4    7.9  10.3        9.6    5.2   2.4    3.3  3  GIDA           Glucose inhibited division protein A


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 !  135.9   0.7   7.4e-43   1.7e-39       2     294 .]       4     269 ..       3     269 .. 0.87
   2 ?   -1.1   0.0       0.4   8.9e+02     258     291 ..     292     322 ..     284     323 .. 0.79

  Alignments for each domain:
  == domain 1  score: 135.9 bits;  conditional E-value: 7.4e-43
                                       SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHHHHHHCHHHHCCCCHCCTCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeiasevvkklnqgielllgeevvki 78 
                                       +++viGgG+AG++a l+ ++      l+ +e+ ++   + +  +l+g + d   ++        ++++  +  +++i
  gi|518652682|ref|YP_008142202.1|   4 KIIVIGGGIAGISAKLRNRK----SKLM-DENPFMIMAPRIIDTLRGKSVDFPRIK-------RNLDYTGK--ATGI 66 
                                       89************666555....4578.999998888887777777666665444.......35676666..9*** PP

                                       EESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T.SEEEEES-SHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
                       Pyr_redox_2  79 dpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp.krivvvGgGyiG 154
                                       d ++k+v +      ++++iay+klv+AtG s++   i G   +++++ + l++a +l+ +l++ k+iv++GgGy G
  gi|518652682|ref|YP_008142202.1|  67 DLEEKTVNI------NGKNIAYEKLVIATGHSQKYDFINGS--KYIHGFSGLEDALYLRNQLVNrKKIVIIGGGYLG 135
                                       *********......4568***********5555555****..777777**************99************ PP

                                       HHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 155 vElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlv 231
                                       vE+A+a+ ++   +t++ea++r+l +l+ ++s+++++ lek+Gv++ lg+ v e++++      v +  ++++ d  
  gi|518652682|ref|YP_008142202.1| 136 VEVAGAMQNA--SITILEAGNRILAGLPLKFSDYATQLLEKNGVNIELGNPVDEVKKDC-----VVSGTKKFNSDIT 205
                                       ******9988..89*****************************************9555.....56666779***** PP

                                       EE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBES.STTEEE-GGGC...TECCSS--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 232 vvavGvrpstelleeklglelderggivvdeflrtn.vpgiyaiGDva...ggkggpelaqaAvqqG 294
                                       ++a G++ + +    k+ l++ ++ +ivv++fl++   p++ya+GD     +g  +p++a  A ++G
  gi|518652682|ref|YP_008142202.1| 206 LFAGGFTGNLPEM--KQELKT-KNSRIVVNSFLQSVdYPDVYAAGDSMlvdNGGFIPMSAIIARSSG 269
                                       *********8775..778998.***********9866*********99***999******9999887 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.4
                                       EE--TTSBESSTTEEE-GGGCTECCSS--HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 258 ivvdeflrtnvpgiyaiGDvaggkggpelaqaAv 291
                                       i v +++  ++ +i++ G +a   ++++ a +A 
  gi|518652682|ref|YP_008142202.1| 292 IRVGDQYFGTIGNIFVHGSIA---HIIKEAAVAL 322
                                       666666655699*********...9999999985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.065   1.5e+02       1      12 [.       4      15 ..       4      25 .. 0.90
   2 ?   -0.3   0.0      0.75   1.7e+03       8      20 ..     106     118 ..     105     123 .. 0.88
   3 !   46.6   0.2   1.6e-15   3.7e-12       1      69 [.     125     191 ..     125     199 .. 0.95
   4 ?   -2.9   0.0       4.6     1e+04      46      67 ..     218     239 ..     217     242 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.065
                                      EEEEECSSHHHH CS
                         Pyr_redox  1 kvvvvGgGyigl 12
                                      k++v+GgG  g+
  gi|518652682|ref|YP_008142202.1|  4 KIIVIGGGIAGI 15
                                      799*****9997 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.75
                                       SHHHHHHHHHHHH CS
                         Pyr_redox   8 GyiglElAgalae 20 
                                       G++glE A +l++
  gi|518652682|ref|YP_008142202.1| 106 GFSGLEDALYLRN 118
                                       9*********987 PP

  == domain 3  score: 46.6 bits;  conditional E-value: 1.6e-15
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                                       k+v++GgGy+g+E+Aga+++    +t++e+++++l +l+ ++s++ ++ lekng+++ l++ v e++++
  gi|518652682|ref|YP_008142202.1| 125 KIVIIGGGYLGVEVAGAMQNAS--ITILEAGNRILAGLPLKFSDYATQLLEKNGVNIELGNPVDEVKKD 191
                                       79*****************987..******************************************986 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 4.6
                                       HHHHHHHTTEEEECSEEEEEEE CS
                         Pyr_redox  46 lqeklekngievllntkveeie 67 
                                       ++++l+ ++ +++ n+ +++++
  gi|518652682|ref|YP_008142202.1| 218 MKQELKTKNSRIVVNSFLQSVD 239
                                       6788888999999998888876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.4     0.032        73       1      21 [.       6      26 ..       6      44 .. 0.88
   2 !    4.8   0.0    0.0064        14     229     276 ..      57     100 ..      15     123 .. 0.71
   3 !   17.1   6.0   1.2e-06    0.0026     115     305 .]      72     247 ..      69     247 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.032
                       Pyr_redox_3  1 iIiGaGPaGlaaaielkkagl 21
                                      i+iG+G aG++a +  +k++l
  gi|518652682|ref|YP_008142202.1|  6 IVIGGGIAGISAKLRNRKSKL 26
                                      89*********9988888776 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0064
                       Pyr_redox_3 229 vlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkk 276
                                       + ++ +++ i+ +e++++++ ++     ++++ v+atG + +++f++ 
  gi|518652682|ref|YP_008142202.1|  57 LDYTGKATGIDLEEKTVNINGKN----IAYEKLVIATGHSQKYDFING 100
                                       44556678888888888887777....568999*********999985 PP

  == domain 3  score: 17.1 bits;  conditional E-value: 1.2e-06
                       Pyr_redox_3 115 evetsketyeAkkviiAtGefdkPnkln....ipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkg 187
                                       +v+ + +++  +k++iAtG  +k ++ n    i+G + l    +     + ++ +k+v+iGg+  +v++A  +  ++
  gi|518652682|ref|YP_008142202.1|  72 TVNINGKNIAYEKLVIATGHSQKYDFINgskyIHGFSGLEDALYL--RNQLVNRKKIVIIGGGYLGVEVAGAM--QN 144
                                       677788888899*******74444432111113333322222222..22358999***************876..56 PP

                       Pyr_redox_3 188 aeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla 264
                                       a++t++  g+ i +       + + +  + le+    + ++++  + v+e+k++     v+ ++  k+ ++d  ++a
  gi|518652682|ref|YP_008142202.1| 145 ASITILEAGNRILAG---LPLKFSDYATQLLEK----NGVNIELGNPVDEVKKD---CVVSGTK--KF-NSDITLFA 208
                                       7********988886...455666777766665....459************86...3343333..44.45888*** PP

                       Pyr_redox_3 265 tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        G++ +l  +k + +++ +++r+v+++  ++  +p+++ aG
  gi|518652682|ref|YP_008142202.1| 209 GGFTGNLPEMK-QELKT-KNSRIVVNSFLQSVDYPDVYAAG 247
                                       **********9.66666.799******************99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   1.6    0.0042       9.5       1      14 [.       4      17 ..       4      20 .. 0.90
   2 ?    0.8   0.0      0.13   2.8e+02     166     203 ..      61      92 ..      54     107 .. 0.69
   3 !    9.4   2.6   0.00032      0.72       1      31 [.     125     155 ..     125     159 .. 0.88
   4 ?    2.8   0.0     0.033        73     145     190 ..     161     198 ..     160     260 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0042
                                      EEEEECTSHHHHHH CS
                               DAO  1 dvviiGGGiiGlst 14
                                      ++++iGGGi+G+s+
  gi|518652682|ref|YP_008142202.1|  4 KIIVIGGGIAGISA 17
                                      59*********996 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.13
                                       SECEEEEEEEETCEEEEE.EECTEEEEEEEEEEE--GGG CS
                               DAO 166 gtevtgleeedgkvwgve.rttpgendaadavVnaaGaw 203
                                       g ++tg++ e+   ++v  +   g n a++++V+a+G+ 
  gi|518652682|ref|YP_008142202.1|  61 G-KATGIDLEE---KTVNiN---GKNIAYEKLVIATGHS 92 
                                       4.677775552...344223...6666778899999975 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00032
                                       EEEEECTSHHHHHHHHHHHHTTEEEEESSSS CS
                               DAO   1 dvviiGGGiiGlstAyeLarrgVtllekgdi 31 
                                       ++viiGGG+ G+ +A + + + +t+le+g++
  gi|518652682|ref|YP_008142202.1| 125 KIVIIGGGYLGVEVAGAMQNASITILEAGNR 155
                                       59****************7777******954 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.033
                                       HHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE CS
                               DAO 145 pakltaalaraaealGveilegtevtgleeedgkvwgverttpgen 190
                                       p k+  +  + +e++Gv+i +g +v ++++ d  v+g        +
  gi|518652682|ref|YP_008142202.1| 161 PLKFSDYATQLLEKNGVNIELGNPVDEVKK-DCVVSGT-------K 198
                                       567777788889***************954.3222222.......2 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 ?    8.4   0.4   0.00055       1.2      28      43 ..       2      17 ..       1      24 [. 0.91
   2 ?    5.4   0.0    0.0045        10      25      56 ..     120     149 ..      97     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00055
                                      --EEEEESTSHHHHHH CS
                       AlaDh_PNT_C 28 pakvlviGgGvaGlqA 43
                                      ++k++viGgG+aG++A
  gi|518652682|ref|YP_008142202.1|  2 AGKIIVIGGGIAGISA 17
                                      689**********998 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0045
                                       CB---EEEEESTSHHHHHHHHHHHHTT-EEEE CS
                       AlaDh_PNT_C  25 gvepakvlviGgGvaGlqAiatakglgakVtv 56 
                                        v++ k+++iGgG  G++ + + +  +a++t+
  gi|518652682|ref|YP_008142202.1| 120 LVNRKKIVIIGGGYLGVEVAGAMQ--NASITI 149
                                       57899***********98766443..345555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0    0.0076        17       1      16 [.       7      22 ..       7      28 .. 0.81
   2 ?   -3.4   0.0       5.5   1.2e+04      44      55 ..      96     107 ..      86     118 .. 0.53
   3 ?    5.2   0.1     0.011        25       1      31 [.     128     156 ..     128     181 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0076
                                      EE--SHHHHHHHHHHH CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLa 16
                                      ++G+G++G +a  + +
  gi|518652682|ref|YP_008142202.1|  7 VIGGGIAGISAKLRNR 22
                                      8********9866555 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 5.5
                                       EECTS---EEET CS
                     NAD_binding_8  44 rvdygahifhgs 55 
                                        +  g  ++hg+
  gi|518652682|ref|YP_008142202.1|  96 DFINGSKYIHGF 107
                                       333444444444 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.011
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G  G   A ++++  +++++le+++r+
  gi|518652682|ref|YP_008142202.1| 128 IIGGGYLGVEVAGAMQN--ASITILEAGNRI 156
                                       89*******99999998..5********996 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.2       1.4   3.2e+03     193     203 ..       4      14 ..       2      25 .. 0.79
   2 ?    9.2   0.0   0.00026      0.58     143     210 ..      76     142 ..      47     171 .. 0.76

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.4
                       K_oxygenase 193 riaVvGsGqSa 203
                                       +i+V+G+G  +
  gi|518652682|ref|YP_008142202.1|   4 KIIVIGGGIAG 14 
                                       899****9765 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00026
                       K_oxygenase 143 eeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                       + +++  ++lv+++G + k  ++++  +  + +   +++l+ +++l ++k+i+++G+G  + e++  +
  gi|518652682|ref|YP_008142202.1|  76 NGKNIAYEKLVIATGHSQKY-DFINGSKYIHGFSGLEDALYLRNQLVNRKKIVIIGGGYLGVEVAGAM 142
                                       55666777888888877665.555555544455555677777888******************98665 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   2.4    0.0043       9.6       1      17 [.       4      20 ..       4      27 .. 0.83
   2 ?    2.8   0.0     0.023        52     261     330 ..      30     116 ..      18     121 .. 0.67
   3 ?    3.4   0.9     0.015        33       1      23 [.     125     147 ..     125     155 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0043
                                      CEEEE-SSHHHHHHHHH CS
                              GIDA  1 dviViGgGhAGceAAla 17
                                      ++iViGgG AG+ A l 
  gi|518652682|ref|YP_008142202.1|  4 KIIVIGGGIAGISAKLR 20
                                      69**********99765 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.023
                                       -.B--S-CCC-SSTCCCCCCST...............T-S--EEEEEESSTT--E.EEEET----S-HHHHHHHHTT CS
                              GIDA 261 c.ieelgprycpsiedkivrla...............dkeshqvfLepegletel.iylvgfstslpeevqkevlrs 320
                                            ++pr  ++++ k v ++               d e+++v ++  + + e  +   g s+++ +    + ++ 
  gi|518652682|ref|YP_008142202.1|  30 NpFMIMAPRIIDTLRGKSVDFPrikrnldytgkatgiDLEEKTVNINGKNIAYEKlVIATGHSQKYDFINGSKYIHG 106
                                       44566788888888888888887777777777777777777777777666554443666677777777777777777 PP

                                       STT-TT--EE CS
                              GIDA 321 ipGLenaeiv 330
                                         GLe+a ++
  gi|518652682|ref|YP_008142202.1| 107 FSGLEDALYL 116
                                       7777777655 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.015
                                       CEEEE-SSHHHHHHHHHHHHTT- CS
                              GIDA   1 dviViGgGhAGceAAlaaarlGa 23 
                                       ++++iGgG  G+e A a+ ++ +
  gi|518652682|ref|YP_008142202.1| 125 KIVIIGGGYLGVEVAGAMQNASI 147
                                       689************99988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       536  (0.0298957); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); 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):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 2124.51
//
Query:       gi|518652683|ref|YP_008142203.1|  [L=358]
Description: hypothetical protein FACI_IFERC00001G1322 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00052   20.0   1.9      0.099   12.7   2.3    2.3  2  DUF3939   Protein of unknown function (DUF3939)
  ------ inclusion threshold ------
      0.018   14.1   0.4        1.2    8.2   0.6    2.9  3  MCR_C     Methyl-coenzyme M reductase operon protein C
      0.079   13.5   0.4       0.16   12.6   0.4    1.5  1  HD_assoc  Phosphohydrolase-associated domain
       0.22   11.6   2.6        2.9    8.0   0.1    3.1  3  SH3_14    Dda helicase SH3 domain


Domain annotation for each model (and alignments):
>> DUF3939  Protein of unknown function (DUF3939)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   2.3   2.2e-05     0.099       8      88 ..      40     121 ..      33     131 .. 0.83
   2 !    4.4   0.0     0.008        36      18      46 ..     171     199 ..     158     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2.2e-05
                           DUF3939   8 ldevrkAvrkfeeklpkginrtvlvnddkeidlerLapyLggipkqkFymskeTfeife...eeekdivkeiDkvQk 81 
                                       l++ +kA+ k ++ + +++   v++ +d +++ e++  y++++++q    +k   +i+    + ++++ ++i++  k
  gi|518652683|ref|YP_008142203.1|  40 LENDKKAIDKMKKGMRENMDEFVVIYNDFKVNEEKIMDYISSVTDQY--YTKHSQDILStisQLQHETENYIENGVK 114
                                       566699*************************************9994..4566666655333778889999999999 PP

                           DUF3939  82 AvdqYvk 88 
                                       A++q+++
  gi|518652683|ref|YP_008142203.1| 115 AMNQFFS 121
                                       9999986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.008
                           DUF3939  18 feeklpkginrtvlvnddkeidlerLapy 46 
                                       + ++l  gi+  vl+  d ++++e+L +y
  gi|518652683|ref|YP_008142203.1| 171 YFSSLYTGIKIPVLIAGDGSVNYENLDSY 199
                                       55678899******************999 PP

>> MCR_C  Methyl-coenzyme M reductase operon protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.6   0.00026       1.2     168     229 ..       5      69 ..       2      88 .. 0.71
   2 ?    0.9   0.0     0.044     2e+02     199     251 ..      73     128 ..      66     143 .. 0.76
   3 ?    1.2   0.0     0.035   1.6e+02     147     170 ..     172     194 ..     162     203 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00026
                             MCR_C 168 kleevpgaeay.vgglGriahrlrkeeeiealdelveeveevldkkreelak..Dpllvsparvk 229
                                       +l+e++++  y v ++   ++r +k+ eie++ ++ e+ ++ +dk+++ + +  D  +v     k
  gi|518652683|ref|YP_008142203.1|   5 DLNELKYIFSYlVDSFSYEVERDKKSGEIENMTRMLENDKKAIDKMKKGMREnmDEFVVIYNDFK 69 
                                       556666666653567888899**************************999762255555554444 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.044
                             MCR_C 199 delveeveevldkkreelakDpllvspa...rvkkeieeqveeieevlsPapitlq 251
                                       +++++ +++v d+  ++ ++D l++ ++   +  + ie+ v+++++++s  p+t+ 
  gi|518652683|ref|YP_008142203.1|  73 EKIMDYISSVTDQYYTKHSQDILSTISQlqhETENYIENGVKAMNQFFSLNPLTIL 128
                                       57888999999999999999998876541115667899999999999998888875 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.035
                             MCR_C 147 keklfedievPvvvtggPeelkle 170
                                        ++l+++i++Pv++ g   +++ e
  gi|518652683|ref|YP_008142203.1| 172 FSSLYTGIKIPVLIAGDG-SVNYE 194
                                       5689**********9976.55555 PP

>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.4   3.5e-05      0.16      17      88 ..      11      89 ..       3      93 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                          HD_assoc 17 flfenvyrhpevqreeekarriireLfealled..perllpeefrarleaaedd........araRvVcDyiAgmTDry 85
                                      ++f +++++ + + e++k+   i+++ ++l +d  + +++++ +r+++++              +  ++Dyi++ TD+y
  gi|518652683|ref|YP_008142203.1| 11 YIFSYLVDSFSYEVERDKKSGEIENMTRMLENDkkAIDKMKKGMRENMDE---FvviyndfkVNEEKIMDYISSVTDQY 86
                                      56788888888888888888888888888877412223444444444422...12223334678889************ PP

                          HD_assoc 86 alr 88
                                       ++
  gi|518652683|ref|YP_008142203.1| 87 YTK 89
                                      876 PP

>> SH3_14  Dda helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.2      0.14   6.2e+02      76     105 ..      56      87 ..      32     115 .. 0.76
   2 ?    8.0   0.1   0.00065       2.9      19      73 ..     227     281 ..     223     290 .. 0.74
   3 ?    1.2   0.0     0.083   3.7e+02      17      52 ..     284     319 ..     280     325 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.14
                                       --EEEEEE--SHHH..HHHHHHHHHHHHHHHH CS
                            SH3_14  76 yyvekikvlsddee..kekfalflakaaetyk 105
                                        +++++ v+++d +   ek   +++  ++ y 
  gi|518652683|ref|YP_008142203.1|  56 ENMDEFVVIYNDFKvnEEKIMDYISSVTDQYY 87 
                                       46778888888864215788888877766664 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00065
                                       EEEETTEEEEEEEE.-TT-EEEEEEEEEEEEEE--TTSSS-EEEEEEEEEEEEESS CS
                            SH3_14  19 sykidGkpvseivi.enGelvkileaeytstfvkaktvdGellkrafdlavetved 73 
                                        yki G  +  iv+ +nGe vki +     + +  k +d  l k a +++ +t +d
  gi|518652683|ref|YP_008142203.1| 227 KYKISGPDIE-IVFaNNGEKVKITDNPDFMSHMDVKIMDDALGKLANEITGLTGKD 281
                                       5899996665.666489********8777777778888888877777777776554 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.083
                                       EEEEEETTEEEEEEEE-TT-EEEEEEEEEEEEEE-- CS
                            SH3_14  17 lksykidGkpvseivienGelvkileaeytstfvka 52 
                                       l+s kidG  +   +  +    +i++++y  ++v++
  gi|518652683|ref|YP_008142203.1| 284 LVSLKIDGEEILTTMSFEKVFFRIIKSDYIKSLVRE 319
                                       6889999997765555555678********999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1213  (0.0676558); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); 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: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.49
# Mc/sec: 2206.17
//
Query:       gi|518652684|ref|YP_008142204.1|  [L=192]
Description: precorrin-4 C11-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-29  100.8   0.0    1.1e-28  100.7   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.0   6.1e-33   1.1e-28      73     210 ..       4     143 ..       1     146 [. 0.96

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 6.1e-33
                      TP_methylase  73 aealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl....lpg 145
                                       +++ ++g d+ +l+sGDP++yg+   +++++    +g+e+e+iPG+ss+ aaaa++g++lt  g+++sv+     ++
  gi|518652684|ref|YP_008142204.1|   4 KKYYDEGLDITRLHSGDPSIYGAINDEIQFFNS--NGMEYEIIPGISSVFAAAASMGMELTSPGTTQSVIltrvPRR 78 
                                       678899***************************..9**************************************999 PP

                      TP_methylase 146 lakeeereleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtle 210
                                       ++  e +el+ l+++++ l+++ + +++  + e L++  +++d+ +++++ r++++d++++++t+ 
  gi|518652684|ref|YP_008142204.1|  79 TEHFENEELDILASHKTALAIFLSASNARAVTEKLIKGgYKGDD-RAVIAYRVSWPDQKIIETTIN 143
                                       99************************************888877.*******************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       388  (0.0216409); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1358.14
//
Query:       gi|518652685|ref|YP_008142205.1|  [L=219]
Description: precorrin-2 C20-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-30  106.3   0.0    2.5e-30  106.0   0.0    1.0  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   0.0   1.4e-34   2.5e-30       4     205 ..       6     200 ..       4     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 1.4e-34
                      TP_methylase   4 lVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.......eleapmgkekepleeayeeiaeala 73 
                                       +VG+GpGdpel+T+++++a+ +ad+v++++   l +++++l+          ele+p g e     +  +e a ++ 
  gi|518652685|ref|YP_008142205.1|   6 VVGLGPGDPELITMKGYKAIMDADIVFYPK-TSLNSAENILKSLGvnsnrmrELEFPIGSE--KISALSREYAGMIM 79 
                                       8*****************************.655555555544444445666666666655..55556999****** PP

                      TP_methylase  74 ealragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakee 150
                                       +a r+  + v++v G P++y+t+  ++      + +ie++viPG+ss++ + a+++i l+ ++e+l vl p+ +  +
  gi|518652685|ref|YP_008142205.1|  80 KASRDNLKSVYAVEGEPMLYSTFLDIMP-----YIDIEFDVIPGISSMNGISAAMKIILATKDEPLLVL-PAVK--D 148
                                       **************************93.....35578*******************************.8866..6 PP

                      TP_methylase 151 ereleallangdtlvllkaprklaelaelLkealyddttpvavveragtedervv 205
                                       ++ +e+ +   +++v++ka r + e++++++++  + +t+ ++++ ++te+e ++
  gi|518652685|ref|YP_008142205.1| 149 YSYMEEKIMSYGNVVIFKAIR-AREIIKEIIKK--NQLTNYYIMSYVSTEKEIIY 200
                                       66666666668*********9.***********..999**************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       597  (0.033298); 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 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1526.64
//
Query:       gi|518652686|ref|YP_008142206.1|  [L=411]
Description: precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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   57.0   0.0    3.7e-15   56.4   0.0    1.3  1  TP_methylase     Tetrapyrrole (Corrin/Porphyrin) Methylases
    6.8e-10   39.1   0.0    1.2e-09   38.2   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    3.7e-06   26.4   0.0    5.9e-06   25.7   0.0    1.3  1  GidB             rRNA small subunit methyltransferase G
    0.00058   19.4   0.1     0.0022   17.5   0.0    2.0  3  Methyltransf_4   Putative methyltransferase
     0.0013   18.3   0.1      0.008   15.7   0.0    2.0  2  DOT1             Histone methylation protein DOT1
  ------ inclusion threshold ------
       0.02   14.5   0.0      0.044   13.4   0.0    1.5  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.028   14.0   0.0      0.057   13.0   0.0    1.4  1  MTS              Methyltransferase small domain
      0.031   14.2   0.0      0.064   13.2   0.0    1.4  1  Methyltransf_18  Methyltransferase domain
      0.042   13.0   0.1       0.08   12.1   0.1    1.5  1  Methyltransf_3   O-methyltransferase
      0.061   12.4   0.0       0.11   11.6   0.0    1.3  1  RrnaAD           Ribosomal RNA adenine dimethylase
      0.084   12.2   0.1       0.24   10.8   0.0    1.6  2  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.14   11.4   0.0       0.28   10.5   0.0    1.6  1  CMAS             Mycolic acid cyclopropane synthetase
       0.16   11.6   0.0       0.28   10.8   0.0    1.3  1  GCD14            tRNA methyltransferase complex GCD14 subunit


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 !   56.4   0.0   2.7e-18   3.7e-15       2     212 ..      19     204 ..      18     205 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 2.7e-18
                      TP_methylase   2 lylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeeleleapmgkekepleea.yeeiaealaealr 77 
                                       + +VGv pG p  + ++A + + +++v++  + r le++ + +a             +  + + +++    la  l+
  gi|518652686|ref|YP_008142206.1|  19 INIVGVFPGMP--INPEAEKCIMESQVIFSGR-RNLELIPQTPA-------------QIFNIGsMKQFTGDLANTLA 79 
                                       66899999996..999************9888.99999954332.............33333346666777899999 PP

                      TP_methylase  78 agkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvllpglakeeerel 154
                                       + k+V ++ sGDPl++g+g +++e+        ++ ++P vsslq a +rlg++ ++   ++ +  + ++      l
  gi|518652686|ref|YP_008142206.1|  80 DNKTVTVVASGDPLFFGIGKYITEHYDS----GDIYIVPEVSSLQVALSRLGMDASHMVAISLHG-REIK-----GL 146
                                       **********************987777....35**********************888888888.4444.....55 PP

                      TP_methylase 155 eallangdtlvllkapr.klaelaelLkealyddttpvavveragtedervvrgtleel 212
                                       ++ + n++ +++++++  +++++ae +  + +  ++  +v er+g++de + + +++el
  gi|518652686|ref|YP_008142206.1| 147 AQKIRNKRKIAIFTDGNnTPSRIAEYMTSF-GLVDYSSYVLERLGYKDESISKYKIKEL 204
                                       555566799999999994588888888888.77779***************99988886 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 !   38.2   0.0   8.8e-13   1.2e-09      53     198 ..     237     384 ..     225     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 38.2 bits;  conditional E-value: 8.8e-13
                                       TEEE--HHHHHHHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEE CS
                              PCMT  53 natiSaphmvalalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivv 129
                                       n+ i +  +  + +  l+l++g+ + +vGsGsG   a+ a l++++g++ +ie+ k l++   +n++k  + ++ ++
  gi|518652686|ref|YP_008142206.1| 237 NNNITKKEIREISISELDLNNGDTMWDVGSGSGS-VAIYASLINPDGNIFAIEKDKALCNFIDENMRKFST-DINII 311
                                       566666666777778899***************5.689*****************************9876.57788 PP

                                       ES-GGGTTGGG-SEEEEEESSBB...SS--HHHHHTEEEEEEEEEEESB.SSSEEEEEEEEETTTEEEEEEEE CS
                              PCMT 130 vgDGrkGyeekaPYdaihvgaaa...peiPealidQLkeGGrlvvPvge.eeeQvlklvdkkadgkvvikkle 198
                                        g+  +  +     +a+++g ++   ++i +     Lk+GGr+v+ + + e+   ++ + k+++ ++ +k+++
  gi|518652686|ref|YP_008142206.1| 312 NGEAPEALDGIPDPEAVFIGGSSgniKNIVKYCYVRLKDGGRMVANITTmENFYAMMNYIKENNLQFDVKQVN 384
                                       8888888888777899**99887222566677889*************989999999******9999888876 PP

>> GidB  rRNA small subunit methyltransferase G
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   4.3e-09   5.9e-06      25     146 ..     235     356 ..     214     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.3e-09
                                       -SHHHHHHHCHHHHHHHGGCS-CCC-.EEEETSTTTTTHHHHHHH-TTSEEEEEES-HHHHHHHHHHHHHCT-SSEE CS
                              GidB  25 kepeellerhlldslsvlellkekrdkviDvGsGaGlPGipLaiarpelkltLleslekkiaFLeevkeelklenve 101
                                       ++ +++ ++ + + +s++el  ++ d++ DvGsG G  +i  ++++p+ ++  +e+++  ++F+ e ++++  + ++
  gi|518652686|ref|YP_008142206.1| 235 RKNNNITKKEIRE-ISISELDLNNGDTMWDVGSGSGSVAIYASLINPDGNIFAIEKDKALCNFIDENMRKFSTD-IN 309
                                       5666777777766.3444444444446***********************************************.** PP

                                       EEES-CCC.TTTTT-EEEEEEC.-SSSHHHHHHHHCCCEEEEEEEEE CS
                              GidB 102 ivearaee.kqeeekydvvtsR.Alaslnelteillkllkegglila 146
                                       i++ +a e  +   + ++v +    ++++++++++   lk+gg+++a
  gi|518652686|ref|YP_008142206.1| 310 IINGEAPEaLDGIPDPEAVFIGgSSGNIKNIVKYCYVRLKDGGRMVA 356
                                       ******886666666777766515789****************9997 PP

>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       6.6   9.2e+03     102     131 ..     145     174 ..     141     180 .. 0.71
   2 !   17.5   0.0   1.6e-06    0.0022       4      64 ..     260     319 ..     257     328 .. 0.86
   3 ?   -2.1   0.0       1.7   2.3e+03     106     135 ..     347     375 ..     338     398 .. 0.50

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.6
                                       HHHHHEEEEEEEEEEESHHHHHHHHHHHHH CS
                    Methyltransf_4 102 elarvLkkgGvlelaTDveeyaeemlkvle 131
                                        la++++++  + + TD ++   ++++ + 
  gi|518652686|ref|YP_008142206.1| 145 GLAQKIRNKRKIAIFTDGNNTPSRIAEYMT 174
                                       567788888888888887777666666655 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 1.6e-06
                                       EEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHH CS
                    Methyltransf_4   4 vvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvl 64 
                                       ++ ++G+G+G++ +  +  nPd n+++iE+ + + + + +++++   + ++i++g+a + l
  gi|518652686|ref|YP_008142206.1| 260 TMWDVGSGSGSVAIYASLINPDGNIFAIEKDKALCNFIDENMRKF-STDINIINGEAPEAL 319
                                       5789**************************999988877777665.678999999998887 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.7
                                       HEEEEEEEEEEESHHHHHHHHHHHHHCSTT CS
                    Methyltransf_4 106 vLkkgGvlelaTDveeyaeemlkvleeepl 135
                                       +Lk gG +++     e ++ m++ ++e+ +
  gi|518652686|ref|YP_008142206.1| 347 RLKDGGRMVANITTMENFYAMMNYIKEN-N 375
                                       4555555444333333333344444443.2 PP

>> DOT1  Histone methylation protein DOT1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   5.8e-06     0.008      35      93 ..     250     308 ..     240     316 .. 0.91
   2 ?   -0.3   0.1      0.47   6.5e+02     138     185 ..     338     389 ..     334     395 .. 0.62

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 5.8e-06
                                       HHHTT--TT-EEEEES-TTSHHHHHHHHHH--SEEEEEE--HHHHHHHHHHHHHHHHHH CS
                              DOT1  35 ldkvnlkkedvFvDLGSGvGnvvlqaalevgcklsvGvEimdnaselaekqkeelkkrl 93 
                                       +++++l++ d+  D GSG G v ++a+l     + + +E+ ++ +++ +++++ ++  +
  gi|518652686|ref|YP_008142206.1| 250 ISELDLNNGDTMWDVGSGSGSVAIYASLINPDGNIFAIEKDKALCNFIDENMRKFSTDI 308
                                       7899********************************************99999998765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.47
                                       HHHHHHHHTT--TT-EEE....ESS-SS-TT----SSSTT-GGGGEEEEEEE CS
                              DOT1 138 nkqlkellqdlkegtkii....slkslvpskykinsrnledivnilkveelk 185
                                       ++ +k     lk+g++++    +++++ +    i+++nl+  v+ +++++lk
  gi|518652686|ref|YP_008142206.1| 338 KNIVKYCYVRLKDGGRMVanitTMENFYAMMNYIKENNLQFDVKQVNISRLK 389
                                       5556677778899988762222456666666667777766666666666665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.2e-05     0.044       4      67 ..     253     314 ..     250     322 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES- CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaD 67 
                                       L++++++t+ D+ ++ G+   + a l+++ g+++A++++k   + + en+++++   + +++++
  gi|518652686|ref|YP_008142206.1| 253 LDLNNGDTMWDVGSGSGSVAIY-ASLINPDGNIFAIEKDKALCNFIDENMRKFSTD-INIINGE 314
                                       8999***********9997666.7788*************************9988.8887776 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.1e-05     0.057      25      89 ..     251     315 ..     247     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                       HHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-ST CS
                               MTS  25 etlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdv 89 
                                       + l+ +  +++ D+G+G G +++ +   +p+ ++ ++++d++  ++  en+++   ++++++ ++
  gi|518652686|ref|YP_008142206.1| 251 SELDLNNGDTMWDVGSGSGSVAIYASLINPDGNIFAIEKDKALCNFIDENMRKFSTDINIINGEA 315
                                       667777788999****************************************9999999887766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.6e-05     0.064      13     135 ..     256     378 ..     249     388 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.6e-05
                   Methyltransf_18  13 ekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGleklk.eeevdtvvi 88 
                                       ++g++++D+G+  g ++iy+   +   ++ a++  +  ++  +en++k   +++i+++ ++  e+l+   + ++v i
  gi|518652686|ref|YP_008142206.1| 256 NNGDTMWDVGSGSGSVAIYASLINPDGNIFAIEKDKALCNFIDENMRKF--STDINIINGEAPEALDgIPDPEAVFI 330
                                       6789******************************************996..55788888888888873334778888 PP

                   Methyltransf_18  89 aGmGgelileILeeakeklkkikkli..lqpnseaeelRkylvengfki 135
                                        G  g +i +I++ +   lk+  +++  +  +++ + + +y+ en+ ++
  gi|518652686|ref|YP_008142206.1| 331 GGSSG-NIKNIVKYCYVRLKDGGRMVanITTMENFYAMMNYIKENNLQF 378
                                       77665.6999999998888888887744678888888888888888765 PP

>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   5.8e-05      0.08      45     153 ..     255     354 ..     238     380 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
                                       HHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEEEEES-HHHHHHHHHTSSS- CS
                    Methyltransf_3  45 lvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekieliegdalkvLeelvkdkkl 121
                                       l n   + ++G   G s+   a  + +DG+i ai++d+   +   + ++k      i++i+g+a ++L+ + + +  
  gi|518652686|ref|YP_008142206.1| 255 LNNGDTMWDVGSGSG-SVAIYASLINPDGNIFAIEKDKALCNFIDENMRKF--STDINIINGEAPEALDGIPDPE-- 326
                                       556666667777777.45556777999*****************9999996..567************9876555.. PP

                                       --EEEEEE-S-GGGHHHHHHHHHHTEEEEEEE CS
                    Methyltransf_3 122 pefDfifvDaDkssyvnyyeklleLvkvGgli 153
                                            +f+     + +n  + +   +k Gg +
  gi|518652686|ref|YP_008142206.1| 327 ----AVFIGGSSGNIKNIVKYCYVRLKDGGRM 354
                                       ....3666666666666666666666666555 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.7e-05      0.11      23      83 ..     250     313 ..     235     318 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.7e-05
                                       HHHH-GGTTSEEEEES-TTTCCH..HHHHCC-SEEEEE-S-HHHHHHHHCHTT.TCCCEEEE-S CS
                            RrnaAD  23 ldklnleekltvleigpGkGilT..eeLakrakqvvvlElderLakllqkkls.kdeklkvvhq 83 
                                       +++l+l++ +t+ ++g+G G     ++L +   +  ++E+d++L+++  ++++  ++ +++++ 
  gi|518652686|ref|YP_008142206.1| 250 ISELDLNNGDTMWDVGSGSGSVAiyASLINPDGNIFAIEKDKALCNFIDENMRkFSTDINIING 313
                                       6778888************9765337888888******************99866778888875 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00017      0.24     159     207 ..     255     304 ..     246     324 .. 0.81
   2 ?   -2.0   0.0       1.3   1.8e+03      49      91 ..     345     387 ..     331     390 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                              PrmA 159 vkegeevlDvGtGSGiLaiaaakLgak.kvvavDiDevAvkvakeNaelN 207
                                       +++g+++ DvG GSG  ai a++++ + +++a+  D+   +   eN+++ 
  gi|518652686|ref|YP_008142206.1| 255 LNNGDTMWDVGSGSGSVAIYASLINPDgNIFAIEKDKALCNFIDENMRKF 304
                                       5788999*****************9754899*999999999888888765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                              PrmA  49 eeelkeevkvkalfkeeteakeliaqlkeselglekgkvkvee 91 
                                        ++lk+  ++ a  ++ +++  +++++ke++l+ + ++v+++ 
  gi|518652686|ref|YP_008142206.1| 345 YVRLKDGGRMVANITTMENFYAMMNYIKENNLQFDVKQVNISR 387
                                       5567777888888888899999999999999988888888766 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0002      0.28      52      81 ..     247     276 ..     237     383 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0002
                                       HHHHTTTT--TT-EEEEES-TTSHHHHHHH CS
                              CMAS  52 dlileklelkpGmtlLdiGcGWGslvrrav 81 
                                       ++ +  l+l++G+t+ d+G G Gs++++a 
  gi|518652686|ref|YP_008142206.1| 247 EISISELDLNNGDTMWDVGSGSGSVAIYAS 276
                                       567889*******************99874 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0002      0.28      33      86 ..     250     302 ..     235     313 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                             GCD14  33 imkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefr 86 
                                       i +L+l++G  + + G Gsgs++ + a  ++P G++f++e  ++  ++  e++r
  gi|518652686|ref|YP_008142206.1| 250 ISELDLNNGDTMWDVGSGSGSVAIY-ASLINPDGNIFAIEKDKALCNFIDENMR 302
                                       5789*****************9866.5689*********976665555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2510.86
//
Query:       gi|518652687|ref|YP_008142207.1|  [L=429]
Description: uroporphyrin-III C-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-46  158.3   0.0    3.2e-46  157.9   0.0    1.1  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.0   1.8e-50   3.2e-46       3     212 ..       5     213 ..       3     214 .. 0.91

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 1.8e-50
                      TP_methylase   3 ylVGvGpGdpellTvrAlralktadvvlgddsraleilldllaeel.eleapmgkekepleeayeeiaealaealra 78 
                                       y+VG GpG+ +llT++A++++k+ad++++d  ++   +ld++ + + +++  +++   + +  +eei+++++ ++ +
  gi|518652687|ref|YP_008142207.1|   5 YIVGCGPGNKDLLTIKAIKIIKNADAIIYDH-LVNPEILDYATPGTrKIYVGKKPY--VKRISQEEINKIIVNEALK 78 
                                       9******************************.877777788887777888888888..67778************** PP

                      TP_methylase  79 gkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl...lpglakeeer 152
                                       +++V++l++GDP+v+g+g+e++e+l +  ++ie+e+iPG+ssl+ ++ ++giplt++++++ vl     + ++ +  
  gi|518652687|ref|YP_008142207.1|  79 YRTVARLKGGDPFVFGRGGEEIEELIR--NNIEYEIIPGISSLTGVPESAGIPLTHRNVNHGVLvttGNSVENLNIP 153
                                       ***************************..9**********************************9775555666677 PP

                      TP_methylase 153 eleallangdtlvllkaprklaelaelLkea.lyddttpvavveragtedervvrgtleel 212
                                       + + +  + +tlv++++ ++l +++ +L+ + +++  +p+a++e+++++ +++++g+l+++
  gi|518652687|ref|YP_008142207.1| 154 DCRTFNCRMYTLVIFMGAHNLRDIVSRLLSSgYDP-ALPIALIENGTYNYQKTYTGKLGDI 213
                                       777777779**********************7777.55********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2756.92
//
Query:       gi|518652688|ref|YP_008142208.1|  [L=200]
Description: indolepyruvate oxidoreductase subunit beta [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-36  125.8   0.2    2.1e-36  125.6   0.2    1.0  1  POR       Pyruvate ferredoxin/flavodoxin oxidoreductase


Domain annotation for each model (and alignments):
>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.6   0.2   1.2e-40   2.1e-36       1     177 []      12     191 ..      12     191 .. 0.94

  Alignments for each domain:
  == domain 1  score: 125.6 bits;  conditional E-value: 1.2e-40
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEE CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglk 77 
                                       GGqG++tag ++++aa + G++v++++ +g ++rGg+++++vri+d    p  ++ + dl++++++ +  + l+ ++
  gi|518652688|ref|YP_008142208.1|  12 GGQGIITAGTLISEAAIKMGLNVVMSEIHGLSQRGGSVNVEVRIGDA-YGPISPRRKFDLVLGFEPIETMRILSTIN 87 
                                       9*********************************************9.7888888***********7777******* PP

                                       EEEEEEEECTCGTT-CCHHHCTS-HHHHHHH.....T-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H.. CS
                               POR  78 pggiiiynseelkpdelkkakeeerelkerl.....gvrvygvdatkiakeiggneraaNtvmlGalaallglpl.. 147
                                        +  +i+n+e++ p  +  ++ e+++++          ++y++da +i  ++g   r aNtvm+Ga++ l+ lp+  
  gi|518652688|ref|YP_008142208.1|  88 SDARVIMNKEKITPISVSLKDAEYPDVNGMAllipgIKKIYEIDAGDIGNQAGS-FRSANTVMIGAVLSLGILPVde 163
                                       *************************9998889***9999**********99877.************7776655544 PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragye 177
                                       ++++ea+++rf +k  +++ Nlka+++g+e
  gi|518652688|ref|YP_008142208.1| 164 KSIIEALNDRFSGK--MLDINLKAMKLGME 191
                                       99**********95..************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1588.07
//
Query:       gi|518652689|ref|YP_008142209.1|  [L=623]
Description: indolepyruvate oxidoreductase, alpha subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-28  100.1   0.1    1.7e-28   99.3   0.1    1.4  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
      5e-14   52.6   0.4    8.9e-14   51.8   0.4    1.3  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    4.9e-08   32.8   0.6    0.00089   18.9   0.1    2.3  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
    7.6e-05   22.6  12.6      0.011   15.8   2.3    2.6  2  Fer4_2           4Fe-4S binding domain
    0.00039   20.1  15.9       0.16   11.9   1.5    3.3  2  Fer4             4Fe-4S binding domain
     0.0012   18.6   2.1          1    9.0   0.2    3.0  2  Transket_pyr     Transketolase, pyrimidine binding domain
     0.0024   17.9  12.9       0.12   12.5  13.7    2.5  2  Fer4_10          4Fe-4S dicluster domain
     0.0033   17.4  21.1      0.022   14.8   3.0    2.9  3  Fer4_6           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.027   14.3   0.3        1.3    8.9   0.0    3.0  3  Transketolase_C  Transketolase, C-terminal domain
      0.046   13.9   8.7       0.13   12.4   8.7    1.9  1  Fer4_9           4Fe-4S dicluster domain
      0.074   13.2  11.0       0.17   12.1  11.0    1.6  1  Fer4_21          4Fe-4S dicluster domain
       0.14   12.5   0.0       0.61   10.4   0.0    2.1  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
        1.2    9.8  16.0        5.7    7.6   4.1    2.7  4  Fer4_7           4Fe-4S dicluster domain
          4    8.2  12.3        6.7    7.5   3.6    3.5  3  Fer4_15          4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.3   0.1   1.3e-31   1.7e-28       1     152 [.     403     544 ..     403     545 .. 0.93

  Alignments for each domain:
  == domain 1  score: 99.3 bits;  conditional E-value: 1.3e-31
                                       ESSHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   1 diGcltlwaarllkvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       diGc++l      +++ p++  +  ++ +mG ++++A G ++   +++v+a++GD++f+++ ++ l++av ++l+++
  gi|518652689|ref|YP_008142209.1| 403 DIGCYSL------GLYDPYEEAD--TMISMGSSIGMANGFAMS-TKQKVIAFIGDSTFFHSgIPPLINAVHNKLNML 470
                                       89****9......8888988777..9****************5.467****************************** PP

                                       EEEEE-SBCCCHHHHHHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggqqepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpalie 152
                                       v+vl+N++++mtg+q++   + + +g++   l+pv+++++a+++G+  +  v+++d++e+ +a+ +al+++  ++i+
  gi|518652689|ref|YP_008142209.1| 471 VMVLDNGTTAMTGQQPNAGENFSPAGDE---LPPVSIENIARSIGVAdVQIVDPYDIKETLKAVTKALRENTLSVIV 544
                                       ***************9999887766655...****************999******************999999986 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 !   51.8   0.4   6.9e-17   8.9e-14       2     166 ..      28     187 ..      27     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 6.9e-17
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +a++agv++++ YP TPsse++++l+  ++k ++   ++    +E  ai+++  A+++G r++++    Gl  +++ 
  gi|518652689|ref|YP_008142209.1|  28 GAVEAGVRIATTYPGTPSSEVGDTLSHIADKSGM---KFQFSINEKVAIETAFAASISGQRSMVFMKHVGLNVASDP 101
                                       899**************************99996...888899********************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHHS---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEEEEEEH CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaardtglivlasenvqeafdlalvAfnlAekvrvPvivlfDg 155
                                       ++ +a + + + +vv+    ps   s + +q    +a    + ++ ++n qea d+ + Af l+ek+++Pv+     
  gi|518652689|ref|YP_008142209.1| 102 FMSIAYTGVRAGMVVMSADDPSM-YSSQSEQDNRHYADLAHVPMIEPSNPQEAKDFLVLAFDLSEKFKLPVLFR-TT 176
                                       ***********999999889999.999999999999999999****************************9755.57 PP

                                       HHH.HEEEEEE CS
                             POR_N 156 fllshevekve 166
                                       +++sh++  v+
  gi|518652689|ref|YP_008142209.1| 177 TRVSHMRGAVT 187
                                       8888*998886 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   6.9e-07   0.00089       5     147 ..      23     164 ..      21     182 .. 0.76
   2 !   11.9   0.0   9.6e-05      0.12      50     150 ..     426     537 ..     417     548 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 6.9e-07
                                       HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHH CS
                      TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatn 78 
                                       ea++r   ++gv+ + ++pG+ + ++ d ls      g+++  + +E +a+  A + + + ++ +v++ ++g ++++
  gi|518652689|ref|YP_008142209.1|  23 EAIARGAVEAGVRIATTYPGTPSSEVGDTLSHIAdksGMKFQFSINEKVAIETAFAASISGQRSMVFMKHVGLNVAS 99 
                                       78999999******************99998766678*******************988888888888888998765 PP

                                       .CHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHH CS
                      TPP_enzyme_N  79 .altalaeAkvdriPllvlsgdrptslrgqgvlqqeldqlalfrpvtkyaervtspeelpealrrAirta 147
                                         ++++a     r  ++v+s+d p+ + +q   q++ + ++l ++v     ++++p+e++  l  A++ +
  gi|518652689|ref|YP_008142209.1| 100 dPFMSIAY-TGVRAGMVVMSADDPSMYSSQS-EQDNRHYADL-AHV--PMIEPSNPQEAKDFLVLAFDLS 164
                                       26666654.3448999999999999999833.3334444444.222..2556666666666666666655 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH.............S..TC-- CS
                      TPP_enzyme_N  50 gaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg.............qgvlqqe 113
                                       + +++A g+a++t++ ++++    + + ++++ l++A ++++ +lv++ d++t+                 + l   
  gi|518652689|ref|YP_008142209.1| 426 SSIGMANGFAMSTKQKVIAFIGDSTFFHSGIPPLINAVHNKLNMLVMVLDNGTTAMTgqqpnagenfspaGDELP-P 501
                                       5689*********666666665667899***********************999888788888877755333333.4 PP

                                       T-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSS CS
                      TPP_enzyme_N 114 ldqlalfrpvtkyaervtspeelpealrrAirtalsg 150
                                       +++++++r++  + +++ +p +++e+l+   ++al +
  gi|518652689|ref|YP_008142209.1| 502 VSIENIARSIGVADVQIVDPYDIKETLKAV-TKALRE 537
                                       588888999999999999999999988644.444344 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   2.9   0.00018      0.23       4      22 .]     567     587 ..     565     587 .. 0.88
   2 !   15.8   2.3   8.7e-06     0.011       3      21 ..     595     615 ..     593     616 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                            Fer4_2   4 vvdtdrCigCgaCv..saCPa 22 
                                        v+ d+C  C  Cv   aCPa
  gi|518652689|ref|YP_008142209.1| 567 TVNQDKCGKCMNCVenFACPA 587
                                       699***********7677**8 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.7e-06
                            Fer4_2   3 vvvdtdrCigCgaCv..saCP 21 
                                       +++d+++C gCg C    +CP
  gi|518652689|ref|YP_008142209.1| 595 IKIDSNICDGCGVCAepYVCP 615
                                       789***********99999*9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   1.5   0.00012      0.16       1      16 [.     566     581 ..     566     582 .. 0.92
   2 !   11.6   7.0   0.00015      0.19       1      24 []     595     620 ..     595     620 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                                       EEEETTTSSS-THHHH CS
                              Fer4   1 vvideekCigCGaCve 16 
                                       ++++++kC +C++Cve
  gi|518652689|ref|YP_008142209.1| 566 YTVNQDKCGKCMNCVE 581
                                       589************8 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00015
                                       EEEETTTSSS-THHHH..HSTTTEEE CS
                              Fer4   1 vvideekCigCGaCve..vCPvgAIt 24 
                                       ++id + C gCG C+e  vCP+ AI+
  gi|518652689|ref|YP_008142209.1| 595 IKIDSNICDGCGVCAEpyVCPFKAIE 620
                                       689************98899999996 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2    0.0008         1      47     171 ..      59     176 ..      20     182 .. 0.77
   2 !    7.7   0.2     0.002       2.6      49     172 ..     416     547 ..     386     550 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.0008
                                       TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGGHHGGHHHHHCHHHHHT--EE.EEESBSGGGSTTGT CS
                      Transket_pyr  47 egrvidsgisEqavlgfavGaalagpllviveaqFgdFangAqiyadqairsgeakgklkvg.vvtrlpigvgedGp 122
                                       +g  ++++i E+ ++ +a +a+++g+  + ++++  + +n   +  d++++   a  ++++g vv+      + +  
  gi|518652689|ref|YP_008142209.1|  59 SGMKFQFSINEKVAIETAFAASISGQ--RSMVFMKHVGLN---VASDPFMS--IAYTGVRAGmVVMS---ADDPSMY 125
                                       55668899999999999999999994..444444444444...56677777..66666666633333...2467778 PP

                                       TTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHS..SS.SEEEEEE- CS
                      Transket_pyr 123 ehqsaeleaflrlipglkvvrPsdpaetkhllrrairr..edrkPvvlrlp 171
                                       + qs ++ ++++ ++ + ++ Ps+p+e+k  l  a     +++ Pv +r++
  gi|518652689|ref|YP_008142209.1| 126 SSQSEQDNRHYADLAHVPMIEPSNPQEAKDFLVLAFDLseKFKLPVLFRTT 176
                                       89999999************************9999887788999999987 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.002
                                       GEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGG.....HHGGHHHHHCHHHHHT--EEEEESBSGGGST. CS
                      Transket_pyr  49 rvidsgisEqavlgfavGaalagpllviveaqFgdFangA.....qiyadqairsgeakgklkvgvvtrlpigvge. 119
                                       +  d++is    +g+a+G+a++ +++vi+ +  ++F+  +     + + ++  +  + + + ++ ++   p   +  
  gi|518652689|ref|YP_008142209.1| 416 EEADTMISMGSSIGMANGFAMSTKQKVIAFIGDSTFFHSGippliNAVHNKLNMLVMVLDNGTTAMTGQQPNAGENf 492
                                       55678888888999999999999988888888999999667754433333333334444444444554555532222 PP

                                       ..TGTTTSBSSHHHHHHTSTT..EEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-S CS
                      Transket_pyr 120 ..dGpehqsaeleaflrlipg..lkvvrPsdpaetkhllrrairredrkPvvlrlpk 172
                                          G e  ++++e++ r+i    +++v P+d  et +++ +a+r  +++ +v++  +
  gi|518652689|ref|YP_008142209.1| 493 spAGDELPPVSIENIARSIGVadVQIVDPYDIKETLKAVTKALR--ENTLSVIVARR 547
                                       22566666777777777653255999999999999999999999..55677776655 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5  13.7   9.1e-05      0.12       4      53 ..     568     610 ..     565     615 .. 0.85
   2 !   11.3   2.0   0.00022      0.28       2      22 ..     595     617 ..     594     623 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.1e-05
                           Fer4_10   4 idddtCirCgkCvk..aCPadltsvgakgeaseeeavrkkvekCtgcgaCve 53 
                                       +++d+C +C +Cv+  aCPa         +  e++ +++++  C+gcg C+e
  gi|518652689|ref|YP_008142209.1| 568 VNQDKCGKCMNCVEnfACPA---------ISIEGGNIKIDSNICDGCGVCAE 610
                                       689***********888***.........88888888899999*******97 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                           Fer4_10   2 vvidddtCirCgkCvk..aCPad 22 
                                       ++id++ C +Cg C +  +CP++
  gi|518652689|ref|YP_008142209.1| 595 IKIDSNICDGCGVCAEpyVCPFK 617
                                       789*************999**94 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.4       7.3   9.3e+03       8      12 ..     373     377 ..     371     377 .. 0.83
   2 !   14.8   3.0   1.7e-05     0.022       3      21 ..     567     587 ..     567     590 .. 0.90
   3 !   13.3   4.1   5.1e-05     0.065       2      24 .]     595     619 ..     594     619 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7.3
                            Fer4_6   8 kCigC 12 
                                       +C gC
  gi|518652689|ref|YP_008142209.1| 373 LCPGC 377
                                       8*999 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.7e-05
                            Fer4_6   3 eidpdkCigCgdCvrv..CPe 21 
                                       ++++dkC  C++Cv +  CP+
  gi|518652689|ref|YP_008142209.1| 567 TVNQDKCGKCMNCVENfaCPA 587
                                       69************9999**8 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 5.1e-05
                            Fer4_6   2 veidpdkCigCgdCvr..vCPegai 24 
                                       + id + C+gCg C+   vCP++ai
  gi|518652689|ref|YP_008142209.1| 595 IKIDSNICDGCGVCAEpyVCPFKAI 619
                                       689***********65225999997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0     0.001       1.3      14      69 ..     251     303 ..     240     307 .. 0.88
   2 ?    1.5   0.1      0.19   2.5e+02      37      61 ..     510     534 ..     503     546 .. 0.80
   3 ?   -1.2   0.0       1.3   1.7e+03      56      75 ..     555     574 ..     549     581 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.001
                                       EEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEE CS
                   Transketolase_C  14 lvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvvee 69 
                                       ++a G+  + +++++ e     ++++V+ l +++pl +  i + +   ++++++ee
  gi|518652689|ref|YP_008142209.1| 251 IIASGAAYNSVMDVISEY---DLDISVLKLGFTNPLPESAIVKFISDNKKVIIIEE 303
                                       889999999988888655...799*******************************9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                                       CEEEEE-SEEESHHHHHHHHHHHHH CS
                   Transketolase_C  37 saeVvdlrtvkplDketilesvkkt 61 
                                       s+ V d++ v+p D +  l++v k 
  gi|518652689|ref|YP_008142209.1| 510 SIGVADVQIVDPYDIKETLKAVTKA 534
                                       7889999999999998888888775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 1.3
                                       HHHHHHSEEEEEEEEESTTS CS
                   Transketolase_C  56 esvkktgrlvvveeavkrgG 75 
                                       ++++kt+r+++ + +   +G
  gi|518652689|ref|YP_008142209.1| 555 KAMQKTHRVITYTVNQDKCG 574
                                       7899*******987777776 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   8.7    0.0001      0.13       1      51 []     572     619 ..     554     619 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                            Fer4_9   1 kCtgCgaCvea..CpagvvvedaaerkarlraaseeaCigCgaCve..aCpkgai 51 
                                       kC +C +Cve   Cpa  +++ + +   ++       C gCg C+e  +Cp +ai
  gi|518652689|ref|YP_008142209.1| 572 KCGKCMNCVENfaCPAISIEGGNIKIDSNI-------CDGCGVCAEpyVCPFKAI 619
                                       799*****88666*****999999999998.......********5448998876 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1  11.0   0.00013      0.17       4      58 ..     569     620 ..     567     621 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                           Fer4_21   4 dedkCigCgkCliaCedtshqaieidaktvlkvvedeCvGCnlCss..vCPvedcie 58 
                                       ++dkC +C +C    e+ +  ai+i++ ++ k+ ++ C GC +C++  vCP  ++ie
  gi|518652689|ref|YP_008142209.1| 569 NQDKCGKCMNC---VENFACPAISIEGGNI-KIDSNICDGCGVCAEpyVCPF-KAIE 620
                                       55555555555...55556669**987765.99***********97558**7.7776 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00048      0.61       2      60 ..     248     303 ..     247     333 .. 0.83
   2 ?   -2.5   0.0       5.2   6.6e+03       3      29 ..     516     542 ..     514     546 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00048
                                       SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE- CS
                           PFOR_II   2 evvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldr 60 
                                       e+ i+a G++ +++ +++ e     +++ +l+l +  P Pe ++ +++++ kkv+ ++ 
  gi|518652689|ref|YP_008142209.1| 248 EYGIIASGAAYNSVMDVISE---YDLDISVLKLGFTNPLPESAIVKFISDNKKVIIIEE 303
                                       67788888887776666665...5677****************************9985 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 5.2
                                       EEEEE-STHHHHHHHHHHHHHHTT--E CS
                           PFOR_II   3 vvivamGsvagtaksavdelReegikv 29 
                                       v iv    + +t+k++ ++lRe+ ++v
  gi|518652689|ref|YP_008142209.1| 516 VQIVDPYDIKETLKAVTKALRENTLSV 542
                                       555555566789999999999987766 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       9.3   1.2e+04      12      27 ..     377     392 ..     375     408 .. 0.57
   2 ?    7.6   4.1    0.0045       5.7      25      49 ..     560     586 ..     545     588 .. 0.77
   3 ?    7.1  12.1    0.0066       8.5       1      52 []     572     618 ..     572     618 .. 0.84
   4 ?    7.2   2.4     0.006       7.7       2      19 ..     602     621 ..     601     623 .] 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 9.3
                            Fer4_7  12 Cpvkaieldeeenekg 27 
                                       Cp++a ++  +   k 
  gi|518652689|ref|YP_008142209.1| 377 CPHRATYYAVKRAVKM 392
                                       8888877765444443 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0045
                            Fer4_7  25 ekgtekveidpekClgCgaCva..vCP 49 
                                         ++ +++++++kC  C +Cv+  +CP
  gi|518652689|ref|YP_008142209.1| 560 THRVITYTVNQDKCGKCMNCVEnfACP 586
                                       334567899************988898 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0066
                            Fer4_7   1 rCigCgaCvaa..CpvkaieldeeenekgtekveidpekClgCgaCva..vCPtga 52 
                                       +C +C +Cv++  Cp+  ie            ++id++ C gCg+C++  vCP++a
  gi|518652689|ref|YP_008142209.1| 572 KCGKCMNCVENfaCPAISIEG---------GNIKIDSNICDGCGVCAEpyVCPFKA 618
                                       7********754499666666.........3589*************999***986 PP

  == domain 4  score: 7.2 bits;  conditional E-value: 0.006
                            Fer4_7   2 CigCgaCv..aaCpvkaiel 19 
                                       C gCg C+   +Cp kaie+
  gi|518652689|ref|YP_008142209.1| 602 CDGCGVCAepYVCPFKAIEV 621
                                       99999999555899999986 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   1.0      0.12   1.5e+02       2      17 ..     567     582 ..     567     589 .. 0.89
   2 ?    7.5   3.6    0.0052       6.7       1      16 [.     595     610 ..     595     616 .. 0.92
   3 ?    0.8   0.0      0.66   8.4e+02      58      66 .]     613     621 ..     610     621 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                           Fer4_15   2 vvDrdaCigcglCvae 17 
                                       +v++d+C  c +Cv++
  gi|518652689|ref|YP_008142209.1| 567 TVNQDKCGKCMNCVEN 582
                                       689***********86 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0052
                           Fer4_15   1 VvvDrdaCigcglCva 16 
                                       +++D + C+gcg+C++
  gi|518652689|ref|YP_008142209.1| 595 IKIDSNICDGCGVCAE 610
                                       79************97 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.66
                           Fer4_15  58 aCPvdAIrv 66 
                                       +CP +AI+v
  gi|518652689|ref|YP_008142209.1| 613 VCPFKAIEV 621
                                       7******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.64u 0.31s 00:00:00.95 Elapsed: 00:00:00.48
# Mc/sec: 3926.89
//
Query:       gi|518652690|ref|YP_008142210.1|  [L=377]
Description: hypothetical protein FACI_IFERC00001G1329 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-18   66.8   0.0    4.4e-18   65.5   0.0    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.047   13.7   0.0       0.25   11.3   0.0    2.1  3  NAD_binding_9  FAD-NAD(P)-binding
       0.18   11.0   0.0        6.8    5.8   0.0    2.1  2  FAD_binding_3  FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   7.4e-22   4.4e-18       2     286 ..       5     293 ..       4     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 7.4e-22
                                       SEEEE--SHHHHHHHHHHHH...HTS-EEEEE.TTHCHHHCSHHHHCHHHHHHHHHHHHH....HHHHCHHHHCCCC CS
                                       xxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxx RF
                       Pyr_redox_2   2 dvvviGgGpAGlaaaltlaq...agakvtlve.legtclnggcllskallgvaedaeias....evvkklnqgiell 70 
                                       +v++iG   AG+ +a +l+    + +++t+++ +e+t +    +l  +  +  + ++ ++         +n gi+++
  gi|518652690|ref|YP_008142210.1|   5 NVLIIGDANAGIITANKLRMhtgKDVNITIIGnSEKTYFKPEGVL--IPFNGIDYRDSIKptdfL----INYGIKRI 75 
                                       79******************7777999999977666666655555..333333333333333331....56699999 PP

                                       HCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T..SEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxx RF
                       Pyr_redox_2  71 lgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp..kri 145
                                       ++  +++idp+++ v+l     ++++k++yd+lv+AtG +    ++pG +++v+++   ++++ +lk+ l+      
  gi|518652690|ref|YP_008142210.1|  76 KA-MATRIDPANRSVVL-----DNGQKLTYDYLVIATGDRLVPEDVPGYNPDVYHF-YDIENVLRLKKMLRGfkGGK 145
                                       99.9*************.....8899************666655*********999.67777777766666666444 PP

                                       EEES-SHHHHHHHHH......HHHHT-.............EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEES CS
                                       xxxxxxxxxxxxxxx......xxxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 146 vvvGgGyiGvElAaa......laklgk.............evtlveardrllraldkelsaaleealekeGvevklg 203
                                       +vvG   +   +  a                         e  l+  ++ +l+   k++s+++++ +e+ ++++   
  gi|518652690|ref|YP_008142210.1| 146 IVVGPASTPFQCPVApgefmfG----LhlllrnkgirensELSLIVPMKDVLP--FKSVSDFVRKGFEEYNINFIPD 216
                                       8999999999999995544330....13344455557776999*********5..479******************* PP

                                       CEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BES.STTEEE-GGGC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxx RF
                       Pyr_redox_2 204 tsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklglelderggivvdefl.rtn.vpgiyaiGDva 278
                                        + + i+++++  + v ++ge++++d +v+    r ++ l   ++g++  + g++ vd+f  + +  ++++a+GD a
  gi|518652690|ref|YP_008142210.1| 217 FKTEYIEPEKN--SIVSSSGESLQYDKLVLIPPHRGQKFL--SDSGMAG-DSGYVDVDKFTlEYSdYDNVFAVGDAA 288
                                       ***99999998..89**************99988888655..899**97.9********9976555*********** PP

                                       TECCSS-- CS
                                       xxxxxxxx RF
                       Pyr_redox_2 279 ggkggpel 286
                                          + p+ 
  gi|518652690|ref|YP_008142210.1| 289 ---NFPMK 293
                                       ...44443 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 ?   -2.3   0.0      0.65   3.9e+03       2      33 ..       8      37 ..       7      41 .. 0.81
   2 ?   11.3   0.0   4.1e-05      0.25     117     155 ..      72     108 ..      67     109 .. 0.82
   3 ?   -1.9   0.0       0.5     3e+03     128     151 ..     223     244 ..     198     246 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.65
                     NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdp 33
                                      i+G   +G+ ++++L  +   +++++it++ +
  gi|518652690|ref|YP_008142210.1|  8 IIGDANAGIITANKLRMHT--GKDVNITIIGN 37
                                      7777788999999999996..99999999855 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 4.1e-05
                     NAD_binding_9 117 vevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                                       ++ ++a ++++++++++  v+l++g++l++d++v+A+G 
  gi|518652690|ref|YP_008142210.1|  72 IKRIKAMATRIDPANRS--VVLDNGQKLTYDYLVIATGD 108
                                       56677777778777665..899***************95 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.5
                     NAD_binding_9 128 eeradgqavlladgaslaadaVvL 151
                                       e++++   ++ ++g+sl++d++vL
  gi|518652690|ref|YP_008142210.1| 223 EPEKN--SIVSSSGESLQYDKLVL 244
                                       44433..578999*******9998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0011       6.8       2      38 ..       4      43 ..       3      51 .. 0.74
   2 ?    3.0   0.0    0.0085        51     273     303 ..     268     298 ..     262     309 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0011
                                      EEEEEE--SHHHHHHHHHHHHT.THH..EEEEESSSSSCC CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLsea.Gvr..vvlvekrsttvv 38
                                      t+VlI+G   aG+++a+ L+++ G +   +++   ++t+ 
  gi|518652690|ref|YP_008142210.1|  4 TNVLIIGDANAGIITANKLRMHtGKDvnITIIGNSEKTYF 43
                                      89*****************987454433566666666655 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0085
                                       EEEEEESSSEETTEEE-GGGTEEE-STTSHH CS
                     FAD_binding_3 273 vaqrvaekyrkgrvflaGDAaHihpPtgGqG 303
                                       v +++ e    ++vf +GDAa     +g++G
  gi|518652690|ref|YP_008142210.1| 268 VDKFTLEYSDYDNVFAVGDAANFPMKVGALG 298
                                       566677777889*********9888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2425.54
//
Query:       gi|518652691|ref|YP_008142211.1|  [L=158]
Description: hypothetical protein FACI_IFERC00001G1330 [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   31.9   0.2    2.4e-07   30.5   0.2    1.8  1  DUF1641   Protein of unknown function (DUF1641)
  ------ inclusion threshold ------
      0.012   15.9   0.1       0.02   15.2   0.1    1.3  1  DUF4806   Domain of unknown function (DUF4806)


Domain annotation for each model (and alignments):
>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.2   2.7e-11   2.4e-07       2      39 .]     115     152 ..     114     152 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 2.7e-11
                           DUF1641   2 gleepkpvGlfgLlraLrDPDVqrGLGfllalLKalGk 39 
                                       g+++p+ ++ ++Ll++L+DP+V+ G+  +++ LK lG+
  gi|518652691|ref|YP_008142211.1| 115 GASKPQTLSALKLLAMLKDPEVSSGINAVMNGLKVLGS 152
                                       7999********************************96 PP

>> DUF4806  Domain of unknown function (DUF4806)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.1   2.2e-06      0.02      11      88 ..      10      83 ..       3      85 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.2e-06
                           DUF4806 11 seeelerLEaavrtdekirqqyvnyLrkikgkkadlkkvfdklftdealvnynwtGksrkskkKkamkkykiftdcll 88
                                      s  ++  +E+a++++ ++ + +++ L k kg  a ++++++ + ++ +  n  +  k  +s  K +m+++++  ++l+
  gi|518652691|ref|YP_008142211.1| 10 SNVDIADIENAIKENADVVMAFMKLLEKLKG--AGIVDALNSINENVIPDNLDFFAKAFTS--KDSMETFARSGNTLF 83
                                      567999*************************..9999999999999999999999998876..999998887666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      521  (0.0290591); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1135.40
//
Query:       gi|518652692|ref|YP_008142212.1|  [L=420]
Description: hypothetical protein FACI_IFERC00001G1331 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.2e-06   27.4   0.0      2e-05   25.2   0.0    2.2  1  VWA_2           von Willebrand factor type A domain
  ------ inclusion threshold ------
      0.018   14.4   0.8      0.018   14.4   0.8    1.8  2  DUF1978         Domain of unknown function (DUF1978)
        1.1    9.9   6.2        1.7    9.3   1.2    3.2  3  Cytochrom_B562  Cytochrome b562


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.4e-09     2e-05       3     107 .]     265     364 ..     263     364 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.4e-09
                             VWA_2   3 fvlDtSgSmrngdygptrleaakdaveallkslpgdrvglvtfsdgpevlipltkdkakilnalrnleakgggtnla 79 
                                       ++lD SgSm +gd  +t +++  +++   +++ +g ++    f+++p+ l++   ++ ++ + +  +ea ++gt+++
  gi|518652692|ref|YP_008142212.1| 265 VLLDKSGSMYEGD--KTLWSRSVALALFRIARSRGRKYYFRFFDNKPHDLLN---SPFDVVENILTVEA-NKGTCIE 335
                                       79**********7..8888888887777777889*************97765...44456666777888.5****** PP

                             VWA_2  80 aaLqlarkalkkrr.kgekrvivlitDge 107
                                        aL++a   l++++ ++e+++i++itDge
  gi|518652692|ref|YP_008142212.1| 336 CALKTALRDLQDTKiRSETNTIIIITDGE 364
                                       ***********9999************96 PP

>> DUF1978  Domain of unknown function (DUF1978)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.8   2.9e-06     0.018      83     144 ..      55     118 ..      30     173 .. 0.76
   2 ?   -2.2   0.1      0.36   2.1e+03     195     195 ..     380     380 ..     325     412 .. 0.59

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-06
                           DUF1978  83 eelekesskkNqkeleeaekellkalkdlkdqeierveeRlke.lealYp.evseskeeteaqe 144
                                         l   +s+kN+ e+ e +  +++++++ kd+++er+ + l++ l  lY  + ++  +e+ +++
  gi|518652692|ref|YP_008142212.1|  55 SGLATVRSEKNKNEFMESVRLRMEYITETKDFKQERAYTQLNDrLSMLYSiNFMKALNENAKKN 118
                                       5566779**********************************86599999744555555554443 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.36
                           DUF1978 195 v 195
                                       +
  gi|518652692|ref|YP_008142212.1| 380 K 380
                                       2 PP

>> Cytochrom_B562  Cytochrome b562
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   1.2   0.00029       1.7      18      73 ..      94     150 ..      76     160 .. 0.84
   2 ?    1.0   0.1      0.12   6.9e+02      66     102 .]     174     210 ..     167     210 .. 0.82
   3 ?   -0.6   0.0      0.37   2.2e+03      55      67 ..     387     399 ..     337     406 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00029
                    Cytochrom_B562  18 kaddaeelkkalkelraaaedakeatpsklek.dseeqkdYqeGldklidqldkaea 73 
                                       + +d  ++  +++ ++a+ e+ak+++p++ +  ++++qk+ ++ ++   ++++ a++
  gi|518652692|ref|YP_008142212.1|  94 QLNDRLSMLYSINFMKALNENAKKNQPRNGNSsNAPDQKTIEKSMEGASKKVEMAHE 150
                                       66677778889999*************877769999999999999999999988775 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.12
                    Cytochrom_B562  66 dqldkaealakagkleeakaalkelkdlrkeyHkkfk 102
                                       + +d +++++k ++ +++ +++++l d+  +y kk++
  gi|518652692|ref|YP_008142212.1| 174 SLIDLTDKAMKVDNADKILTLANKLIDIMPRYTKKMR 210
                                       5588899999999999999999999999998888875 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.37
                    Cytochrom_B562  55 kdYqeGldklidq 67 
                                       ++Y+eGl+k+ ++
  gi|518652692|ref|YP_008142212.1| 387 NGYNEGLKKISTE 399
                                       5677777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); 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 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2823.51
//
Query:       gi|518652693|ref|YP_008142213.1|  [L=388]
Description: hypothetical protein FACI_IFERC00001G1332 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-21   74.5   0.0    1.8e-20   73.4   0.0    1.6  1  AAA_5      AAA domain (dynein-related subfamily)
    3.9e-08   33.2   0.1    1.7e-06   27.9   0.0    2.4  2  AAA_3      ATPase family associated with various cellular act
    4.3e-06   27.2   0.0    1.8e-05   25.2   0.0    2.0  2  AAA_16     AAA ATPase domain
    0.00026   21.4   0.0    0.00073   20.0   0.0    1.9  1  AAA        ATPase family associated with various cellular act
      0.003   17.1   0.0     0.0069   15.9   0.0    1.5  1  AAA_7      P-loop containing dynein motor region
     0.0086   15.4   2.6        1.3    8.4   0.6    2.3  2  ATPase     KaiC
  ------ inclusion threshold ------
      0.015   15.2   0.3      0.075   12.9   0.1    2.1  2  AAA_lid_8  AAA lid domain
      0.064   13.0   0.0       0.15   11.8   0.0    1.6  1  AAA_29     P-loop containing region of AAA domain
      0.087   12.6   0.4       0.49   10.1   0.0    2.0  2  AAA_11     AAA domain
      0.099   12.4   0.1       0.78    9.5   0.1    2.3  1  RuvB_N     Holliday junction DNA helicase RuvB P-loop domain


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 !   73.4   0.0   9.9e-24   1.8e-20       2     137 ..      38     163 ..      37     164 .. 0.91

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 9.9e-24
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEv 74 
                                        lLvGppGt+K+++++ +++++n++++y++lt++t++e+l+g+++i    t+l+++++ +  +     + i++lDE+
  gi|518652693|ref|YP_008142213.1|  38 TLLVGPPGTAKTSIIDTMSKLINARYFYYLLTKFTEPEELLGPIDI----TALKNGEYRNITKgklpDANIVFLDEI 110
                                       69*******************************************9....99999999877778899********** PP

                                       GG--HHHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
                             AAA_5  75 eraesevlnsLlslleerrllleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                                       ++ +s++ n+Ll ++ +rrl+  +gg+ ++ +       + +  ++n+ + + +e + al++R
  gi|518652693|ref|YP_008142213.1| 111 FKSSSAIRNTLLDIMLNRRLP--NGGTMINLDL------LGIYSASNEIS-DDEE-DMALYDR 163
                                       ********************9..9999998888......78888888888.5555.7777777 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 !   27.9   0.0   9.4e-10   1.7e-06       3     101 ..      39     140 ..      37     156 .. 0.88
   2 ?    2.6   0.1     0.063   1.1e+02      76     122 ..     287     335 ..     279     342 .. 0.73

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 9.4e-10
                             AAA_3   3 llegvPGlaktllvkalakaldlefkriqftpdllPsdilG.tevfeekekef.efkkGpvf.anllladeinrapp 76 
                                       ll g PG+akt ++ +++k +++++    +t    P ++lG +++   k+ e+ +++kG +  an+++ dei ++++
  gi|518652693|ref|YP_008142213.1|  39 LLVGPPGTAKTSIIDTMSKLINARYFYYLLTKFTEPEELLGpIDITALKNGEYrNITKGKLPdANIVFLDEIFKSSS 115
                                       8899*************************************457888888777258999985489************ PP

                             AAA_3  77 ktqsalleameerqvtvegethklp 101
                                        ++ +ll++m +r++  +g+  +l+
  gi|518652693|ref|YP_008142213.1| 116 AIRNTLLDIMLNRRLPNGGTMINLD 140
                                       *************999998888776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.063
                             AAA_3  76 pktqsalleameerq..vtvegethklpepflvlatqnPieqeGtyplp 122
                                       pk+++a++++  e++  +  + et+  +++ l+ +t+n i+ +  y++ 
  gi|518652693|ref|YP_008142213.1| 287 PKIEAAIIDSKLENKsdIVQKAETTMEETKSLIQSTENAINRNSPYNVV 335
                                       89999999998776611344444555556678889******99999875 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   0.0   9.9e-09   1.8e-05       2      63 ..      18      74 ..      17     129 .. 0.91
   2 ?   -1.5   0.0       1.6   2.9e+03      37      76 ..     301     339 ..     273     369 .. 0.59

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 9.9e-09
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63
                                      +vGRe+ +   + +l  + sg+p  +ll+G++G+ K+s++++  + ++++++++l +k+++ 
  gi|518652693|ref|YP_008142213.1| 18 FVGREDVI---NGVLAGLISGEP--TLLVGPPGTAKTSIIDTMSKLINARYFYYLLTKFTEP 74
                                      99*****9...999999999976..99*****************************999876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                            AAA_16  37 Ksslvrellralekdggiflrgkcdqlesaipysalaqal 76 
                                       Ks +v+++ + +e+++ +  ++++  + ++ py +++++l
  gi|518652693|ref|YP_008142213.1| 301 KSDIVQKAETTMEETKSLIQSTENAIN-RNSPYNVVLDQL 339
                                       344444444444444322222222222.455555544444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   4.1e-07   0.00073       2      87 ..      39     119 ..      38     171 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.1e-07
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGH CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk........yvgesekkirelfkeakekakpsilfiDEidal 70 
                                       ll+GppGt KT+++  + k ++++++   ++++++         +   ++ + r++ k      +  i+f+DEi + 
  gi|518652693|ref|YP_008142213.1|  39 LLVGPPGTAKTSIIDTMSKLINARYFYYLLTKFTEPeellgpidITALKNGEYRNITKGKLP--DANIVFLDEIFKS 113
                                       8*********************************6568888877777777777777765333..359******9766 PP

                                       HHHHTTCCCHHHHHHHH CS
                               AAA  71 aksrsgseseeeervvn 87 
                                        ++             n
  gi|518652693|ref|YP_008142213.1| 114 SSAI-----------RN 119
                                       4444...........44 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.9e-06    0.0069      32      69 ..      34      71 ..      27      76 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.9e-06
                             AAA_7 32 nkkpvllvGptGtGKtviikdllkkldkekylsltinf 69
                                      ++ p+llvGp Gt+Kt+ii ++ k ++ + + +l  +f
  gi|518652693|ref|YP_008142213.1| 34 SGEPTLLVGPPGTAKTSIIDTMSKLINARYFYYLLTKF 71
                                      5789****************999998877777766666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.7   0.1    0.0023       4.2      14      34 ..      30      50 ..       6      55 .. 0.86
   2 !    8.4   0.6    0.0007       1.3      73     139 ..     281     351 ..     270     357 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0023
                            ATPase 14 gGipegrvvlitGepGtGKti 34
                                       G+ +g+ +l++G pGt+Kt 
  gi|518652693|ref|YP_008142213.1| 30 AGLISGEPTLLVGPPGTAKTS 50
                                      699****************95 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0007
                            ATPase  73 dlekleeegklaiidasesaeesaee...kdkedleelieelaeaikeikakrvviDsitgl.ayeekeav 139
                                       d e++  + + aiid   +++ ++ +   ++ e++++li++ ++ai++    +vv+D+++ l  y++k + 
  gi|518652693|ref|YP_008142213.1| 281 DSEDYIPKIEAAIIDSKLENKSDIVQkaeTTMEETKSLIQSTENAINRNSPYNVVLDQLSLLeIYIKKLER 351
                                       6677777777788887766665555545588899999***********************99778777655 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.88   1.6e+03       6      25 ..     144     163 ..     141     170 .. 0.81
   2 ?   12.9   0.1   4.2e-05     0.075      16      70 ..     237     291 ..     222     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.88
                         AAA_lid_8   6 ileiknkleeeeeaiyvSDR 25 
                                       i++  n++++ ee++ ++DR
  gi|518652693|ref|YP_008142213.1| 144 IYSASNEISDDEEDMALYDR 163
                                       566678999999*******9 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 4.2e-05
                         AAA_lid_8  16 eeeaiyvSDRRwkkivkllkasAylngrdevnlsDllllkhclWnepeqkekvkk 70 
                                       ee+++++SDRR  k +k+  a  +l + + ++  D+++   +  ++++ ++k++ 
  gi|518652693|ref|YP_008142213.1| 237 EENDVILSDRRKIKLLKIAAAFSILMDSKTITGNDVAMAMRYSADSEDYIPKIEA 291
                                       6899********************************9988888888888877776 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   8.5e-05      0.15      23      47 ..      35      60 ..      25      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.5e-05
                            AAA_29 23 g.atlltGpsGsGKSTllDAiqalLv 47
                                      g  tll+Gp G+ K++++D ++ l+ 
  gi|518652693|ref|YP_008142213.1| 35 GePTLLVGPPGTAKTSIIDTMSKLIN 60
                                      4479*****************99875 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00028      0.49      17      42 ..      35      60 ..      23     103 .. 0.76
   2 ?    0.6   0.1      0.22   3.9e+02     116     145 ..     297     324 ..     170     372 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00028
                            AAA_11 17 seitliqGPPGtgKTktivellsqll 42
                                       e tl+ GPPGt KT+ i  + + ++
  gi|518652693|ref|YP_008142213.1| 35 GEPTLLVGPPGTAKTSIIDTMSKLIN 60
                                      3449***********87766655554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                            AAA_11 116 rlekeekaqlakeiskeleklakelrafee 145
                                       +le+  k +++++ + + e+ ++ ++++e+
  gi|518652693|ref|YP_008142213.1| 297 KLEN--KSDIVQKAETTMEETKSLIQSTEN 324
                                       1111..122222222222222222222222 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00044      0.78      36     108 ..      38     125 ..      32     132 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00044
                            RuvB_N  36 vllyGpPGlGkttlakiiakelgvk......lkitsgPvlekagdlaallt.........nleekdvlfideihrls 97 
                                       +ll+GpPG  kt++   ++k ++++       k t    l  + d++al +         +l + +++f+dei + s
  gi|518652693|ref|YP_008142213.1|  38 TLLVGPPGTAKTSIIDTMSKLINARyfyyllTKFTEPEELLGPIDITALKNgeyrnitkgKLPDANIVFLDEIFKSS 114
                                       699*********88877777776652222223566666677777777774322222222357778999999999999 PP

                            RuvB_N  98 raveevlysam 108
                                       +a+ + l   m
  gi|518652693|ref|YP_008142213.1| 115 SAIRNTLLDIM 125
                                       99988887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      563  (0.0314016); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.48
# Mc/sec: 2416.78
//
Query:       gi|518652694|ref|YP_008142214.1|  [L=393]
Description: mechanosensitive ion channel [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   9.9    1.4e-21   77.0   9.9    2.2  3  MS_channel    Mechanosensitive ion channel
     0.0099   16.2   0.4      0.029   14.7   0.0    1.9  2  DUF3813       Protein of unknown function (DUF3813)
  ------ inclusion threshold ------
      0.042   13.8   0.5      0.042   13.8   0.5    3.4  4  SecE          SecE/Sec61-gamma subunits of protein translocat


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 ?   -2.4   0.7      0.47   2.8e+03       5      26 ..      60      81 ..      57      84 .. 0.77
   2 !   77.0   9.9   2.4e-25   1.4e-21       3     142 ..      95     238 ..      93     278 .. 0.95
   3 ?   -3.5   0.0         1   6.1e+03      90     101 ..     326     337 ..     310     350 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.47
                                      HHHHHHHHHHHHHHTTT--SCC CS
                        MS_channel  5 kiliivvgilivlsllgvnvsa 26
                                      +++i+++g+l+v s+l +   a
  gi|518652694|ref|YP_008142214.1| 60 AVIILIIGFLVVGSFLKYLKEA 81
                                      6899999999999998876555 PP

  == domain 2  score: 77.0 bits;  conditional E-value: 2.4e-25
                                       HHHHHHHHHHHHHHHHTTT--SCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHTT-SS-TT-EEESS......SEE CS
                        MS_channel   3 ilkiliivvgilivlsllgvnvsallavlGalglalglalkdlisnlvaGiillfekpfkiGDlveig......die 73 
                                       i++i+ +++++ +v+s ++++v+ +la+ +++g++lgla++++ snl+++i+ + ++++k G+++ ++      + +
  gi|518652694|ref|YP_008142214.1|  95 IIRIVFYIIILALVMSAFHISVTGILAGSAIGGVVLGLAVQTVASNLLSSIFATSTNTIKYGEVISVNswvwsiETT 171
                                       899************************************************************************** PP

                                       EEEEEE-SSEEEEEETTSEEEEEEHHHHHTS-EEESSS.SSEEEEEEEEEE-TTS-...HHHHHHHHHH CS
                        MS_channel  74 GtVediglrttkirtfdgrivtiPnsslvtsnieNlsresgtrrikvsigvtyssdvkklekvleelke 142
                                       G+++d+++++ ++ t d++i++ Pns+++ ++++   r +++ + ++  ++t+++d   ++++l+++ke
  gi|518652694|ref|YP_008142214.1| 172 GKIIDVKTLFSQMLTKDNNIIYLPNSEILGNSVITEFR-TKNGSYTYPLNITVQAD-VPADQILSQIKE 238
                                       ******************************99987777.89999999999999999.559999999987 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1
                                       TSEEEEEEHHHH CS
                        MS_channel  90 dgrivtiPnssl 101
                                       d +i  iPns++
  gi|518652694|ref|YP_008142214.1| 326 DEAIKQIPNSEV 337
                                       445556666654 PP

>> DUF3813  Protein of unknown function (DUF3813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1       0.9   5.4e+03      34      47 ..     138     151 ..     134     152 .. 0.84
   2 !   14.7   0.0   4.8e-06     0.029      19      44 ..     262     288 ..     246     291 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.9
                           DUF3813  34 AKnAlssAYanssd 47 
                                       A n lss +a s++
  gi|518652694|ref|YP_008142214.1| 138 ASNLLSSIFATSTN 151
                                       77899******996 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.8e-06
                           DUF3813  19 aaaasee.eqqeaiqrAKnAlssAYan 44 
                                          ++e  e +e i+rA nAl+sAY n
  gi|518652694|ref|YP_008142214.1| 262 LIVFNEVtELNEKIARANNALDSAYWN 288
                                       44455556999**************87 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 ?   13.8   0.5   7.1e-06     0.042      19      51 ..      12      44 ..      11      47 .. 0.94
   2 ?    0.7   0.7     0.088   5.2e+02      23      40 ..      58      75 ..      55      84 .. 0.61
   3 ?   -2.9   3.5       1.1   6.6e+03      33      52 ..      98     117 ..      90     120 .. 0.69
   4 ?   -2.6   0.0      0.93   5.5e+03      38      54 ..     129     145 ..     117     146 .. 0.57

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 7.1e-06
                                      CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              SecE 19 rkEllkttvvVlvfvvimglflflvDlvfskli 51
                                      r+E+lk+ v V++++v+  l +f++D v++k++
  gi|518652694|ref|YP_008142214.1| 12 RNEVLKIVVEVIIGIVLALLAGFAIDIVINKFL 44
                                      89***************************9876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.088
                                      HHHHHHHHHHHHHHHHHH CS
                              SecE 23 lkttvvVlvfvvimglfl 40
                                      ++  ++ +++++++g fl
  gi|518652694|ref|YP_008142214.1| 58 VHAVIILIIGFLVVGSFL 75
                                      455555666666666554 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHHHHHHHH CS
                              SecE  33 vvimglflflvDlvfsklin 52 
                                       +v+  ++l+lv ++f + ++
  gi|518652694|ref|YP_008142214.1|  98 IVFYIIILALVMSAFHISVT 117
                                       67777888888888877664 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 0.93
                                       HHHHHHHHHHHHHHHHH CS
                              SecE  38 lflflvDlvfsklinll 54 
                                       +++ +v +v s+l++ +
  gi|518652694|ref|YP_008142214.1| 129 VLGLAVQTVASNLLSSI 145
                                       34445666777776555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      495  (0.0276089); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2413.55
//
Query:       gi|518652695|ref|YP_008142215.1|  [L=443]
Description: hypothetical protein FACI_IFERC00001G1334 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-38  132.3   0.0    3.1e-38  131.5   0.0    1.3  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    2.5e-19   69.5   5.7    4.8e-19   68.6   5.7    1.5  1  Seryl_tRNA_N    Seryl-tRNA synthetase N-terminal domain
     0.0066   16.2   0.7      0.015   15.1   0.7    1.6  1  Nsp1_C          Nsp1-like C-terminal region
  ------ inclusion threshold ------
      0.014   15.3   0.5      0.033   14.1   0.5    1.6  1  Transcrip_act   Transcriptional activator
      0.024   12.2   0.2      0.032   11.8   0.2    1.1  1  DUF3584         Protein of unknown function (DUF3584)
      0.042   14.3   2.1        0.1   13.1   2.1    1.6  1  DUF16           Protein of unknown function DUF16
      0.072   13.0   0.5       0.19   11.6   0.5    1.7  1  Myb_DNA-bind_7  Myb DNA-binding like
       0.69    9.6   3.8        1.3    8.7   0.0    2.8  2  DUF2312         Uncharacterized protein conserved in bacteria


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 !  131.5   0.0   1.4e-41   3.1e-38       7     178 ..     241     416 ..     234     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 1.4e-41
                                       TSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   7 ndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeasldds 79 
                                       ++++++L++t+e++++++ + e+l + +LPl+++ +++++R+E+     d++G++Rv++F++ ++++++ +++++d 
  gi|518652695|ref|YP_008142215.1| 241 EGDDLYLIATAEHPLASMLSGEILEESELPLRVSGVSPCFRREAGahgrDTKGIFRVHQFNKIEQFIYCRPEESWDF 317
                                       4689******************998888****************77899**************************** PP

                                       HHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  80 lrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennre 156
                                       + +l+k  ++i+++lgl++r +  + ++    +++k+++e++ +s++k++e+++++++ +++++ l++++ + ++ +
  gi|518652695|ref|YP_008142215.1| 318 FDELVKNSEDIYKSLGLPYRIVNICSGDLGSLAAKKYDIEVWYPSQGKFREVVSASNDTDYQARSLNIRY-RAKDGN 393
                                       ******************99777779999999**************************************.889999 PP

                                       EEEEEEEEE.EEHHHHHHHHHHH CS
                                       xxxxxxxxx.xxxxxxxxxxxxx RF
                      tRNA-synt_2b 157 ksvimicaa.igveRllsaileq 178
                                       k+ ++++ + i++eR+l ai+e+
  gi|518652695|ref|YP_008142215.1| 394 KFAHTLNSTaIATERVLVAIMEN 416
                                       *******999***********98 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   5.7   2.1e-22   4.8e-19       1     107 [.       1     107 [.       1     108 [. 0.99

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 2.1e-22
                                       ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCH CS
                      Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevk 77 
                                       M+Dikl+r++ e + +++++Rg d + +de+++ld k+re  + l+  ++ +N +++ I+++ kk+e+++ l+ ev+
  gi|518652695|ref|YP_008142215.1|   1 MIDIKLLRSDKERFYNSCRARGFDLNILDEFFSLDLKWRENLKILNTYKHDKNIITADISSLVKKGENIDNLKLEVE 77 
                                       9**************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCTS--- CS
                      Seryl_tRNA_N  78 elkeelkaleaelkeleaeleklllaiPNi 107
                                       +++++++ le+e++++e++ ++l++ iPN+
  gi|518652695|ref|YP_008142215.1|  78 KINKKISLLEEEQNDIESKRNELARLIPNL 107
                                       *****************************8 PP

>> Nsp1_C  Nsp1-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.7   6.7e-06     0.015      50      97 ..      60     107 ..      23     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.7e-06
                            Nsp1_C  50 rvLvengekIskLysevleaeqeqnkidqeLeyiesqqdeLeslLdny 97 
                                         Lv+ ge+I +L+ ev++++++ + +++e + ies+++eL +l+ n+
  gi|518652695|ref|YP_008142215.1|  60 SSLVKKGENIDNLKLEVEKINKKISLLEEEQNDIESKRNELARLIPNL 107
                                       67****************************************998775 PP

>> Transcrip_act  Transcriptional activator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.5   1.5e-05     0.033      17      73 ..      48     103 ..      36     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                     Transcrip_act  17 ekedeevsrsalsafkakeeeierkklevrekveaqLgrveeetkrLaeireeLeal 73 
                                        k+d+++  +++s++ +k e+i+  klev ek++++++  eee   + + r+eL  l
  gi|518652695|ref|YP_008142215.1|  48 YKHDKNIITADISSLVKKGENIDNLKLEV-EKINKKISLLEEEQNDIESKRNELARL 103
                                       567999999*******************9.8****************9999999766 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2   1.4e-05     0.032     340     396 ..      56     112 ..      30     137 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.4e-05
                           DUF3584 340 dadieklkadldqlpsirseleeleeeldaltekhqdvqekydrrkqkikeeleeel 396
                                        adi++l ++ +++++++ e+e++++++ +l+e+++d+++k +++   i + l+e++
  gi|518652695|ref|YP_008142215.1|  56 TADISSLVKKGENIDNLKLEVEKINKKISLLEEEQNDIESKRNELARLIPNLLAEDV 112
                                       689****************************************99999888777765 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   2.1   4.5e-05       0.1      23      87 ..      43     103 ..      41     112 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.5e-05
                                       HHHHHB-..BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHH CS
                             DUF16  23 kqlnefkdsnkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetlel 87 
                                       k ln +k++ +    +i   v+ +ge+i++l+ +vek ++ki+ l++eq+  + + n   e  +l
  gi|518652695|ref|YP_008142215.1|  43 KILNTYKHDKNIITADISSLVK-KGENIDNLKLEVEKINKKISLLEEEQNDIESKRN---ELARL 103
                                       6689999998888888877666.9*************************99888444...44444 PP

>> Myb_DNA-bind_7  Myb DNA-binding like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   8.5e-05      0.19      15      78 ..      10      75 ..       7      91 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.5e-05
                    Myb_DNA-bind_7 15 etekFYkaLsqfGtDFsliaklfpk....rtrrqlKlKFkkEerknpeliekalkkrkeldleefkee 78
                                      + e+FY+  +  G D++++ ++f+     r+  ++ + +k+ ++   + i++ +kk +++d  ++  e
  gi|518652695|ref|YP_008142215.1| 10 DKERFYNSCRARGFDLNILDEFFSLdlkwRENLKILNTYKHDKNIITADISSLVKKGENIDNLKL--E 75
                                      789********************988855555566689999999999999999999888664432..2 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   0.0    0.0006       1.3      19      68 ..       4      49 ..       1      53 [. 0.79
   2 ?   -0.1   1.6      0.34   7.5e+02       5      27 ..      72      98 ..      68     102 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0006
                           DUF2312 19 kkaiaedikdvyaeaKseGfdtkvlrkivklrkkdkdereEeeallelYk 68
                                      +k +  d    y+ ++++Gfd  +l++ ++l      + +E+  +l++Yk
  gi|518652695|ref|YP_008142215.1|  4 IKLLRSDKERFYNSCRARGFDLNILDEFFSLDL----KWRENLKILNTYK 49
                                      677899999*****************9998743....3455556666666 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
                           DUF2312  5 LrqfieRiEr....leeEkkaiaedik 27
                                      L+  +e+i +    leeE+++i+ +  
  gi|518652695|ref|YP_008142215.1| 72 LKLEVEKINKkislLEEEQNDIESKRN 98
                                      566666555444449999999998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3267.29
//
Query:       gi|518652696|ref|YP_008142216.1|  [L=250]
Description: diphthine synthase [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   39.1   0.0    1.1e-09   38.5   0.0    1.3  1  TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases


Domain annotation for each model (and alignments):
>> TP_methylase  Tetrapyrrole (Corrin/Porphyrin) Methylases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.0   6.2e-14   1.1e-09       6     211 ..       2     215 ..       1     217 [. 0.74

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 6.2e-14
                      TP_methylase   6 GvGpGdpellTvrAlralktadvv.......lgddsraleilldllaeeleleapmgkekepleeayeeiaealaea 75 
                                       G+G+ +++ lT++ ++alk++d+v       + ++ ++ ++l  l          +g   + ++++  e  + ++ +
  gi|518652696|ref|YP_008142216.1|   2 GLGLRGTKSLTLEEADALKESDLVyfeiytsISPG-NTVDSLSSL----------TGGMIRLADRNLIETDSEIINE 67 
                                       99**********************43332222222.344444333..........3444456777777777888888 PP

                      TP_methylase  76 lragkdVvllvsGDPlvygtgselvealrareagieveviPGvsslqaaaarlgiplteggevlsvl.......lpg 145
                                       ++++  V llv+GD l ++t+ el  ++++  ag+ev++    s+++a ++++g+  +++g ++s           +
  gi|518652696|ref|YP_008142216.1|  68 AKNKI-VTLLVTGDALSATTHNELRMEAQK--AGVEVRIFENASIITAFISKTGLFNYKFGNIVSMPfiyenffPVS 141
                                       88864.******************866666..******************************999999999886333 PP

                      TP_methylase 146 lakeeereleallangdtlvll..kapr.k..........laelaelLkealyddttpvavveragtedervvrgtl 209
                                        +   +r + + ++n +tl+ll  k  + k          l+++ ++ k+ l ++++ v+++  +g e+e ++ g l
  gi|518652696|ref|YP_008142216.1| 142 VY---DRIYINYSNNMHTLLLLdlK--DgKtmgiqdalgiLKRMEDRQKKGLIEPERTVIAGIGIGSENESIIYGEL 213
                                       33...56666667778888888442..222345444444344444444555777788**************999999 PP

                      TP_methylase 210 ee 211
                                       e+
  gi|518652696|ref|YP_008142216.1| 214 EK 215
                                       86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.31s 00:00:00.82 Elapsed: 00:00:00.50
# Mc/sec: 1514.26
//
Query:       gi|518652697|ref|YP_008142217.1|  [L=402]
Description: hypothetical protein FACI_IFERC00001G1336 [Ferroplasma acidarmanus fer1]
Scores for complete 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-64  215.5   2.7    1.2e-63  215.2   2.7    1.1  1  Enolase_C      Enolase, C-terminal TIM barrel domain
    7.1e-30  103.9   0.0    1.4e-29  103.0   0.0    1.5  1  Enolase_N      Enolase, N-terminal domain
    7.5e-07   28.9   0.0    1.1e-06   28.4   0.0    1.2  1  MR_MLE_C       Enolase C-terminal domain-like
     0.0021   17.3   0.0     0.0034   16.6   0.0    1.2  1  MAAL_C         Methylaspartate ammonia-lyase C-terminus
  ------ inclusion threshold ------
      0.068   13.2   0.1        1.2    9.3   0.0    2.5  2  HTH_54         ParA helix turn helix domain
      0.086   12.9   1.4          2    8.5   0.0    3.4  4  HET-s_218-289  Het-s 218-289


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 !  215.2   2.7   3.9e-67   1.2e-63       4     281 ..     135     401 ..     132     402 .] 0.94

  Alignments for each domain:
  == domain 1  score: 215.2 bits;  conditional E-value: 3.9e-67
                                       E-EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHH CS
                         Enolase_C   4 lPvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnk 80 
                                       +P P+ n+i GG+h+ n   +qef++   g ++f +++     v++++ + l++k   ++  +Gde  ++ +++ ++
  gi|518652697|ref|YP_008142217.1| 135 IPRPMGNIIGGGKHSKNGTTIQEFLVSSQG-KTFYDSVYYNILVHRRVGEKLSEKLKGQSVGLGDEKAWTADVS-DE 209
                                       799*********************998766.89**********************9999999**********95.78 PP

                                       HHHHHHHHHHHHCT-TC..TBEEEEE--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEE CS
                         Enolase_C  81 ealdliveaiekaGykg..kvkialdvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsie 155
                                       ea+++++ea  +   ++  k+ +++d a+  fy  +++kyd ++ +         t+++  d+ ++l k++  + ie
  gi|518652697|ref|YP_008142217.1| 210 EAIEIMKEAAGEISSENkvKIYLGVDFAADSFY--NNGKYDYKTSK--------KTQDEQIDYAVSLNKEHGFYFIE 276
                                       9**********99988844666799********..66799987655........6888899**************** PP

                                       S-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHHH-SHHHHHHHHHHHHHTT-EEE CS
                         Enolase_C 156 dpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnqiGsltesleavklakeagygvv 232
                                       dpl ++d+e+++++t+++g+   ivGddl+ tn+ r++++i+ k++na+l+kvnqiG+l++++++vkla++++  +v
  gi|518652697|ref|YP_008142217.1| 277 DPLYDNDFEGFAEITKKIGEDSLIVGDDLYTTNSARIQKGIDMKSTNAVLIKVNQIGTLSDTVKSVKLATKNSMDTV 353
                                       ***************************************************************************** PP

                                       EE--SC--S--HHHHHHHHCT-SEEE---S-SHHHHHHHHHHHHHHHHH CS
                         Enolase_C 233 vshrsGetedttiadlavglsaGqiktGaparserlakynqllrieeel 281
                                       vshrsGet d +ia+lav+ ++  iktG++   erlak+n+++r+ee+l
  gi|518652697|ref|YP_008142217.1| 354 VSHRSGETTDDFIAHLAVAFNSKFIKTGTIG-GERLAKLNEVIRLEEDL 401
                                       ****************************986.8**************97 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.0   0.0   4.5e-33   1.4e-29       2     131 .]       8     128 ..       7     128 .. 0.95

  Alignments for each domain:
  == domain 1  score: 103.0 bits;  conditional E-value: 4.5e-33
                                       EEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTT CS
                         Enolase_N   2 kkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapalig 78 
                                       ++ +  +i+dSrGnp++e++++++  a+g++++p+GaStg++e++         y  + ++++v+  n+++++al g
  gi|518652697|ref|YP_008142217.1|   8 TDSRITKIFDSRGNPAIEATIILN-YATGTSSAPAGASTGKTEVI--------AYPKNNIDNSVDFYNKHVRNALKG 75 
                                       5667789****************7.668*****************........59999******************* PP

                                       SBTT-HHHHHHHHHHHH-STT-TTT-HHHHHHHHHHHHHHHHHHHTS-HHHHH CS
                         Enolase_N  79 ldvtdqeeiDkllielDgtenksklGaNailavSlAvakaaAkakelplyryl 131
                                       +++++q+ +D+ll elDgt+n s++G+N ++a+S+A aka ++++e+plyry+
  gi|518652697|ref|YP_008142217.1|  76 FNALNQSGFDTLLHELDGTDNFSEMGGNLATALSIANAKAVSNYLEIPLYRYV 128
                                       ****************************************************7 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   3.8e-10   1.1e-06      37     173 ..     215     373 ..     186     391 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 3.8e-10
                                       HHHHHTT.....TSTSEEEEE-TTTS..............BHHHHHHHHHHHGG.GTESEEESSSSTTTHHHHHHHH CS
                          MR_MLE_C  37 vreavgp.....gddvdlmvDanqaw..............dlatAirvarelee.ldllwlEEPvppeddleglael 93 
                                       ++ea+g+     ++++ l vD+ +                ++++ i +a  l++ ++ +++E+P+   +d eg ae+
  gi|518652697|ref|YP_008142217.1| 215 MKEAAGEissenKVKIYLGVDFAADSfynngkydyktskkTQDEQIDYAVSLNKeHGFYFIEDPLYD-NDFEGFAEI 290
                                       444444444433333444455433323455666777777788999999999*665**********98.88******* PP

                                       HH.HHSSEEEESTTSSS..HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHHH CS
                          MR_MLE_C  94 ra.rasipiaagEslys..radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaasl 167
                                       ++ + +  +++g +ly+   a++++ ++ +   +v ++v+++g ++ ++k ++la ++ ++ ++ + sg  +    +
  gi|518652697|ref|YP_008142217.1| 291 TKkIGEDSLIVGDDLYTtnSARIQKGIDMKSTNAVLIKVNQIGTLSDTVKSVKLATKNSMDTVVSHRSGETTDDFIA 367
                                       *86334467777777764578888************************************96665533444444444 PP

                                       HHHHTT CS
                          MR_MLE_C 168 hlaaai 173
                                       hla+a 
  gi|518652697|ref|YP_008142217.1| 368 HLAVAF 373
                                       444444 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 !   16.6   0.0   1.1e-06    0.0034     125     220 ..     286     377 ..     250     385 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-06
                            MAAL_C 125 rlaelreklkekgikvelvaDe.WcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscn 200
                                        +ae+++k+   g +  +v D+ ++ +   i++ +d +++++v ik+  +G++++t+++v  + ++ + + +   + 
  gi|518652697|ref|YP_008142217.1| 286 GFAEITKKI---GEDSLIVGDDlYTTNSARIQKGIDMKSTNAVLIKVNQIGTLSDTVKSVKLATKNSMDTVVSHRSG 359
                                       445555544...555568887725556678*****************************************999998 PP

                            MAAL_C 201 etdvsarvsvhvalatrpaq 220
                                       et      ++h+a+a++++ 
  gi|518652697|ref|YP_008142217.1| 360 ETT--DDFIAHLAVAFNSKF 377
                                       885..467889999988765 PP

>> HTH_54  ParA helix turn helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0    0.0004       1.2       9      89 ..      48     126 ..      44     128 .. 0.85
   2 ?    0.9   0.0      0.17     5e+02      30      58 ..     246     274 ..     232     280 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0004
                            HTH_54   9 teqiqkqkkEl.kedeyyqtyskaalaklpklsrrkvdkavsemeaeGyefekkeagstekYaltiqnvidlykhrg 84 
                                       te i   k+ + ++ ++y+++ ++al+ +  l++   d+ ++e++ +  +f+    g     al+i n+  + ++ +
  gi|518652697|ref|YP_008142217.1|  48 TEVIAYPKNNIdNSVDFYNKHVRNALKGFNALNQSGFDTLLHELDGT-DNFSEM--GGNLATALSIANAKAVSNYLE 121
                                       5667777888866789**************************99754.467655..6667789************** PP

                            HTH_54  85 vPkyr 89 
                                       +P yr
  gi|518652697|ref|YP_008142217.1| 122 IPLYR 126
                                       **998 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.17
                            HTH_54  30 kaalaklpklsrrkvdkavsemeaeGyef 58 
                                       k   ++  k   +++d+avs  +++G+ f
  gi|518652697|ref|YP_008142217.1| 246 KYDYKTSKKTQDEQIDYAVSLNKEHGFYF 274
                                       55555566666677778887777777776 PP

>> HET-s_218-289  Het-s 218-289
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.33   9.9e+02      23      42 ..     180     199 ..     177     206 .. 0.86
   2 ?    8.5   0.0   0.00067         2       9      43 ..     217     251 ..     210     257 .. 0.85
   3 ?   -2.0   0.0       1.3   3.9e+03      28      46 ..     306     324 ..     291     331 .. 0.61
   4 ?   -0.3   0.1      0.37   1.1e+03      38      52 ..     341     355 ..     333     360 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.33
                                       XXXXXXXXXXXXXXXXXXXX CS
                     HET-s_218-289  23 rvGnefseealqqstgirdr 42 
                                       rvG++ se+   qs+g+ d+
  gi|518652697|ref|YP_008142217.1| 180 RVGEKLSEKLKGQSVGLGDE 199
                                       79************999876 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00067
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                     HET-s_218-289   9 NsakdikgeesarvrvGnefseealqqstgirdrt 43 
                                         a++i++e+++++ +G +f ++++ ++ + +++t
  gi|518652697|ref|YP_008142217.1| 217 EAAGEISSENKVKIYLGVDFAADSFYNNGKYDYKT 251
                                       579********************999887777776 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.3
                                       XXXXXXXXXXXXXXXXXXX CS
                     HET-s_218-289  28 fseealqqstgirdrttNs 46 
                                       +++++   ++gi+ + tN 
  gi|518652697|ref|YP_008142217.1| 306 YTTNSARIQKGIDMKSTNA 324
                                       4444555555565555555 PP

  == domain 4  score: -0.3 bits;  conditional E-value: 0.37
                                       XXXXXXXXXXXXXXX CS
                     HET-s_218-289  38 girdrttNsvdevsa 52 
                                       +++  t+Ns+d+v  
  gi|518652697|ref|YP_008142217.1| 341 SVKLATKNSMDTVVS 355
                                       5777899***99965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); 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: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2895.75
//
Query:       gi|518652698|ref|YP_008142218.1|  [L=219]
Description: hypothetical protein FACI_IFERC00001G1337 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-49  166.6   0.2    6.4e-49  166.5   0.2    1.0  1  AIM24     Mitochondrial biogenesis AIM24


Domain annotation for each model (and alignments):
>> AIM24  Mitochondrial biogenesis AIM24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.5   0.2   3.6e-53   6.4e-49       1     200 [.       4     206 ..       4     207 .. 0.97

  Alignments for each domain:
  == domain 1  score: 166.5 bits;  conditional E-value: 3.6e-53
                                       EEEESSSS-EEEEEE-TT-EEEE-CCGEEEEETTEEEEE...--------------EEEEEEES.SS-EEEEE--SS CS
                             AIM24   1 fevlgepssllsvtLspgeelyaerGalvamsgkvemet...gllkalkrlltgeslfllkftakissgtvllapkl 74 
                                       +e+ g + ++l+ tL++ge+ y+e+G l++ +++++++t   gl +a++ +l+g+ +fllk+ +   +g+   a  l
  gi|518652698|ref|YP_008142218.1|   4 YEIRGGDVQYLHATLEAGESAYIEPGHLIYKTPGARLDTgtgGLRGAFSHMLAGSAVFLLKVDG---PGNFGSAGFL 77 
                                       799************************************************************5...5********* PP

                                       SEEEEEEEGGTT.EEEEEGGGEEEEETT-EEEEEEEE--.SSGGGTS-EEEEEEESSSEEEEEEECSEEEEEEE.EE CS
                             AIM24  75 pgtivtlelgggdwlivqkdafLAatgnveldikfqkgl.kglfggeglflqkltGrGlvalsgyGaiyeielkage 150
                                       pg++++++l ++++++++ +afL++++++++++kf + + +++fggeg+fl++++G+G+v+l+g+G+++e+elk+ge
  gi|518652698|ref|YP_008142218.1|  78 PGKVFEIKL-NNNSIFAEFNAFLCMDSTIKYSTKFAG-FwQAIFGGEGIFLEEFSGTGSVMLHGHGQVIEYELKDGE 152
                                       *********.6669**********************5.569************************************ PP

                                       EEEEEGGGEEEEETTEEEEEEEETT---STTTT...S-E.EEEEEEEEEEEEES CS
                             AIM24 151 elvvdpghlvafsgslkfdiervgglkrrligG...egl.flkltGpgtvllqs 200
                                       e++++ +h++af++s+++++ r+gg+k++++gG   eg+ f+ ++Gpg+v+l s
  gi|518652698|ref|YP_008142218.1| 153 EIQAELSHVLAFESSVSYNVSRIGGIKTMVLGGmegEGFfFANMRGPGKVWLHS 206
                                       ***********************99999999988889**9************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1603.21
//
Query:       gi|518652699|ref|YP_008142219.1|  [L=657]
Description: hypothetical protein FACI_IFERC00001G1338 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-27   96.8   0.0    1.5e-19   70.2   0.0    2.3  2  AAA_32           AAA domain
    6.6e-27   94.4   5.9    1.1e-26   93.7   5.9    1.3  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    2.4e-15   56.5   0.0    2.1e-09   37.1   0.0    2.8  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    9.1e-15   54.8   0.1    9.3e-08   31.9   0.0    2.6  2  Sigma54_activat  Sigma-54 interaction domain
    1.1e-11   44.9   0.0    0.00019   21.5   0.0    3.0  3  AAA_5            AAA domain (dynein-related subfamily)
    1.4e-10   40.7   0.5    2.1e-05   23.8   0.0    2.7  3  MCM              MCM P-loop domain
    5.2e-09   36.0   0.3    1.1e-08   35.0   0.3    1.5  1  ChlI             Subunit ChlI of Mg-chelatase
      2e-07   31.5   0.0      0.054   13.9   0.0    3.2  3  AAA              ATPase family associated with various cellul
    4.8e-07   30.1   0.0    5.3e-05   23.5   0.0    3.0  3  AAA_22           AAA domain
    3.9e-06   26.8   0.0     0.0034   17.2   0.0    2.8  2  AAA_3            ATPase family associated with various cellul
    4.5e-06   26.8   0.0      0.096   12.8   0.0    2.5  2  Sigma54_activ_2  Sigma-54 interaction domain
      1e-05   25.1   0.0    0.00018   21.1   0.0    2.8  3  AAA_7            P-loop containing dynein motor region
    2.4e-05   24.1   0.0       0.37   10.5   0.0    2.8  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    6.4e-05   23.4   0.0      0.013   15.9   0.0    2.8  3  AAA_16           AAA ATPase domain
    0.00036   20.9   0.0       0.15   12.4   0.0    2.5  2  AAA_19           AAA domain
    0.00069   19.6   0.0      0.004   17.1   0.0    2.1  2  NACHT            NACHT domain
     0.0041   16.4   0.4       0.33   10.1   0.0    2.9  3  TIP49            TIP49 P-loop domain
  ------ inclusion threshold ------
      0.019   14.7   0.0       0.38   10.5   0.0    2.3  2  AAA_30           AAA domain
      0.028   13.4   0.0      0.071   12.0   0.0    1.7  1  AAA_10           AAA-like domain
      0.044   13.5   0.0       0.13   11.9   0.0    1.8  2  AAA_24           AAA domain
      0.045   12.8   0.0        0.1   11.6   0.0    1.5  1  T2SSE            Type II/IV secretion system protein
      0.061   12.1   0.7       0.11   11.2   0.7    1.3  1  DUF2207          Predicted membrane protein (DUF2207)
      0.064   13.6   0.9       0.54   10.7   0.0    2.7  2  RNA_helicase     RNA helicase
      0.087   12.2   0.1       0.19   11.1   0.1    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
       0.12   12.7   0.4       0.35   11.3   0.4    1.8  1  DUF3194          Protein of unknown function (DUF3194)
       0.12   11.5   0.0        0.3   10.2   0.0    1.6  1  DUF815           Protein of unknown function (DUF815)
       0.12   12.0   0.0       0.28   10.9   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
       0.14   11.3   0.0       0.35   10.1   0.0    1.6  2  DUF2075          Uncharacterized conserved protein (DUF2075)
       0.15   12.5   0.0       0.38   11.2   0.0    1.7  1  MCM_lid          MCM AAA-lid domain
       0.19   10.8   0.0       0.39    9.8   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1


Domain annotation for each model (and alignments):
>> AAA_32  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   2.3e-08   1.4e-05       8      95 ..      31     113 ..      24     126 .. 0.83
   2 !   70.2   0.0   2.5e-22   1.5e-19     280     508 ..     185     412 ..     173     416 .. 0.89

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 2.3e-08
                            AAA_32   8 eeiigqeRAvealefglkikkkgYNifvlGesgtGrttlvkrlleeiakkeptpdDwcYvnnfdnpeePkalsLpaG 84 
                                       +++igqe A e ++ +  +  ++ ++ ++Ge+gtG+++l++++++     ++  +D++   n ++ ++Pk+  +paG
  gi|518652699|ref|YP_008142219.1|  31 NQVIGQEHAGEVIQKAA-M--QKRHVLLIGEPGTGKSMLAQSMVDFLP--KEDLEDVLCFPNPEDSNKPKIKTFPAG 102
                                       789**********9885.4..3459*******************7764..44567888889**************** PP

                            AAA_32  85 kGkelkkdmee 95 
                                       kGke  ++ + 
  gi|518652699|ref|YP_008142219.1| 103 KGKEILRQYQI 113
                                       ***98777665 PP

  == domain 2  score: 70.2 bits;  conditional E-value: 2.5e-22
                            AAA_32 280 vnvlvdnsetegaPVvvednptyanLfGkieyesemg.alvt.dftlIkaGaLhkAnGGyLildaedlLeeplaWea 354
                                        ++lv ++++++ P +  +  +   L+G + ++  +   l t  +++++aG ++kA  G+L +d  +lL+ p   +a
  gi|518652699|ref|YP_008142219.1| 185 PKLLVGHNPNDKPPFIDSTGAHSGALLGDVRHDPFQSgGLETpAHERVEAGNMQKADKGVLFIDEINLLR-PEDQQA 260
                                       579****************************997544355553899**********************97.56679* PP

                            AAA_32 355 LkraLrskeikiesleeqlglistvsLkPepipldvKViLiGsrelYylLseyDpdfkklFkvkadFddemerteen 431
                                       L  a+++k  +i+      + ++    + ep+p+d   +  G+ +  + ++ +     + +  ++ ++d+me +++n
  gi|518652699|ref|YP_008142219.1| 261 LLTAMQEKHFSISGQ---SERSAGAMVQTEPVPCDFVLVAAGNLDAIRNMHPALRSRIRGYGYEVYMNDTMEDSDDN 334
                                       *************53...34567788999*******999999987776666666666677889************** PP

                            AAA_32 432 ekkyarfias.ivkkekllpfdrsavarlieyssrlaedqeklstrfseiadllrEAdywakkegaevveaehVekA 507
                                        kk+++fia+ i+k++k++pfd+ a+ ++++++ +  +++ +l++r++e+  l+r A  +a ++++ +v+a++V++A
  gi|518652699|ref|YP_008142219.1| 335 RKKIVQFIAQeIAKDKKIPPFDDGAIIEILKEAQKRGGRKGRLTLRLRELGGLVRVAGDIAVTNKQPIVTADDVNQA 411
                                       ********86388999************************************************************9 PP

                            AAA_32 508 l 508
                                        
  gi|518652699|ref|YP_008142219.1| 412 R 412
                                       6 PP

>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   5.9   1.8e-29   1.1e-26      25     204 ..     441     623 ..     419     624 .. 0.84

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.8e-29
                                       -BSSEEEEEEE......ETTEEEEEEEEEEEES....S-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-T CS
                             Lon_C  25 dqvGvvtGlaw......tevGGdlltieavllp....gkgklkltGklgdvmkesaqaalsyvrsraeelgidkevf 91 
                                       + +G v Gla        ++ G ++ i a +++     +g +  tGklg++ ke++q   +++++ + +      + 
  gi|518652699|ref|YP_008142219.1| 441 SAIGKVNGLAVmgssdmSDFTGVVMPIVAEVTQaqhpHNGGVYATGKLGEIAKEAVQNVSAVIKKLSGK------NV 511
                                       5677777777522222245678888776655431122789*****************998888765443......45 PP

                                       TT-EEEEEE-S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEE CS
                             Lon_C  92 ekkdihihvPeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvil 168
                                       ++ dihi +       +G sa v++ata++s l  +++++ vamtG +++rG vlp+GG+  k+ aa  +g+ kvi+
  gi|518652699|ref|YP_008142219.1| 512 SDVDIHIQFIGTYEGVEGDSASVSIATAVISSLESIPIDQTVAMTGSLSVRGDVLPVGGVTAKVEAAIDTGLAKVIV 588
                                       6789****99999999************************************************************* PP

                                       EGGGGGGTTTS-HHHHTS-B--EESBHHHHHHHHB- CS
                             Lon_C 169 PkenekdlediPeevreeleiilveevdevlkaalv 204
                                       P +n +d+  + e+ + +++ii +++++evl++al+
  gi|518652699|ref|YP_008142219.1| 589 PASNFNDII-LDEAHKGKIQIIGASRIEEVLENALI 623
                                       *******96.88999*******************96 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.1   0.0   3.6e-12   2.1e-09       2      55 ..      30      83 ..      29      89 .. 0.93
   2 !   16.1   0.0   9.2e-06    0.0055      96     158 ..     231     301 ..     222     325 .. 0.80
   3 ?   -3.0   0.0       6.6   3.9e+03     173     198 ..     494     519 ..     473     522 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.1 bits;  conditional E-value: 3.6e-12
                      Mg_chelatase  2 lkdvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeeal 55
                                      +++v+Gqe+a ++++ aa  + ++ll+G pG+GK+mla+ +   lp+ + e++l
  gi|518652699|ref|YP_008142219.1| 30 FNQVIGQEHAGEVIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLPKEDLEDVL 83
                                      689*******************************************98877765 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.2e-06
                      Mg_chelatase  96 kpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtis....rak....akvefparfqlvaamNp 158
                                       +++ G++ +a +GvLf+DE+  ++ +  ++L + +++++ +is    r++    ++   p++f lvaa N+
  gi|518652699|ref|YP_008142219.1| 231 RVEAGNMQKADKGVLFIDEINLLRPEDQQALLTAMQEKHFSISgqseRSAgamvQTEPVPCDFVLVAAGNL 301
                                       6789**************************************83222332111122347899999999886 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 6.6
                      Mg_chelatase 173 csekeierYlsklsgplldRidlqve 198
                                        + ++++  ++klsg  +  +d++++
  gi|518652699|ref|YP_008142219.1| 494 EAVQNVSAVIKKLSGKNVSDVDIHIQ 519
                                       44577788899999999999999987 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.6e-07   0.00045      12      47 ..      40      75 ..      32      85 .. 0.86
   2 !   31.9   0.0   1.6e-10   9.3e-08      81     130 ..     228     278 ..     220     308 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.6e-07
                                      HHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHST CS
                   Sigma54_activat 12 leqikkvaktdlsvlitGesGtGKellaraiheask 47
                                       e i+k+a ++ +vl+ Ge GtGK++la+++ +  +
  gi|518652699|ref|YP_008142219.1| 40 GEVIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLP 75
                                      578999***********************9987554 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.6e-10
                                       TSS-BE.HHHHHTTTSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSE CS
                   Sigma54_activat  81 Aekekk.GlfekadgGtlfLDeigelplelQekLlrvlqegevervGsske 130
                                       A+++ + G ++kad+G+lf+Dei+ l +e Q+ Ll+++qe++++  G+s+ 
  gi|518652699|ref|YP_008142219.1| 228 AHERVEaGNMQKADKGVLFIDEINLLRPEDQQALLTAMQEKHFSISGQSER 278
                                       5554444************************************99887754 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   9.3e-07   0.00056       1      25 [.      52      77 ..      52      91 .. 0.85
   2 ?   -2.3   0.0       6.8   4.1e+03     114     129 ..     167     182 ..     145     188 .. 0.69
   3 !   21.5   0.0   3.1e-07   0.00019      64     137 ..     236     314 ..     216     315 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9.3e-07
                                      EEEEE--SSSSHHHHHHHGGGGB.S- CS
                             AAA_5  1 dvlLvGppGtgKselaerlaaal.nr 25
                                      +vlL+G+pGtgKs+la+++  +l + 
  gi|518652699|ref|YP_008142219.1| 52 HVLLIGEPGTGKSMLAQSMVDFLpKE 77
                                      79*****************9998544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 6.8
                                       -EEEEEESS--.-TT- CS
                             AAA_5 114 frviatanpldrslne 129
                                       +++i+++np+ r +  
  gi|518652699|ref|YP_008142219.1| 167 LYIIMAMNPAARMERA 182
                                       789*****99855544 PP

  == domain 3  score: 21.5 bits;  conditional E-value: 3.1e-07
                                       -....G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---............-EEEEEESS--.-TT-T CS
                             AAA_5  64 r....egeilvlDEveraesevlnsLlslleerrllleeggelvkaknddller......frviatanpldrslnel 130
                                       +     + +l++DE++ +++e +++Ll+ + e++++  +g+ + +a +  +  +      f ++a++n       ++
  gi|518652699|ref|YP_008142219.1| 236 NmqkaDKGVLFIDEINLLRPEDQQALLTAMQEKHFS-ISGQSERSAGAMVQ--TepvpcdFVLVAAGNLDA--IRNM 307
                                       34456789****************************.55555555555223..24589**********988..6667 PP

                                       THHHHTT CS
                             AAA_5 131 spalrsR 137
                                        palrsR
  gi|518652699|ref|YP_008142219.1| 308 HPALRSR 314
                                       99***99 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   2.9e-05     0.018      51      83 ..      44      76 ..      14      80 .. 0.77
   2 !   23.8   0.0   3.4e-08   2.1e-05     112     153 ..     232     273 ..     204     283 .. 0.94
   3 ?   -3.8   0.0       9.1   5.5e+03       8      31 ..     328     351 ..     326     353 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.9e-05
                                      SSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSS CS
                               MCM 51 ktklrgdinvllvgdpgtaKsqlLkyveklapr 83
                                      ++    + +vll+g+pgt+Ks l +++ +++p+
  gi|518652699|ref|YP_008142219.1| 44 QKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLPK 76
                                      34467789*****************99999886 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 3.4e-08
                                       EEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEE CS
                               MCM 112 leaGalvladkGvcciDefdkmkeedrsalhEamEqqtisia 153
                                       +eaG +  adkGv+ iDe++  + ed++al+ am +++ si+
  gi|518652699|ref|YP_008142219.1| 232 VEAGNMQKADKGVLFIDEINLLRPEDQQALLTAMQEKHFSIS 273
                                       89***********************************99997 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 9.1
                                       HHTSSTHHHHHHHHSSTTSSS-HH CS
                               MCM   8 lakekdiieklvksiapsiyghed 31 
                                       +++++d  +k+v+ ia++i  +++
  gi|518652699|ref|YP_008142219.1| 328 MEDSDDNRKKIVQFIAQEIAKDKK 351
                                       667778889999999999987776 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.3   1.8e-11   1.1e-08      14     121 .]     484     592 ..     470     592 .. 0.94

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 1.8e-11
                              ChlI  14 ivGlpdtavkeskervrsalkn.sgfefpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLs 89 
                                        +G + +  ke+ + v + +k+ sg ++ +  i +         eG + + +iA +++++le+i+ ++++ + G Ls
  gi|518652699|ref|YP_008142219.1| 484 ATGKLGEIAKEAVQNVSAVIKKlSGKNVSDVDIHIQFIGTYEGVEGDSASVSIATAVISSLESIPIDQTVAMTGSLS 560
                                       568888889************999***************************************************** PP

                              ChlI  90 ldGslrpvkgvlpialaakkegikkvivpken 121
                                         G++ pv gv++ + aa ++g++kvivp++n
  gi|518652699|ref|YP_008142219.1| 561 VRGDVLPVGGVTAKVEAAIDTGLAKVIVPASN 592
                                       *****************************987 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0     9e-05     0.054       1      21 [.      53      73 ..      53     129 .. 0.77
   2 !   13.6   0.0   0.00011     0.067      56     124 ..     239     315 ..     225     319 .. 0.87
   3 ?   -1.8   0.0       6.7     4e+03      96     120 ..     601     623 ..     585     631 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9e-05
                                      EEEESSTTSSHHHHHHHHHHH CS
                               AAA  1 vllyGppGtGKTllakavake 21
                                      vll+G pGtGK++la++++  
  gi|518652699|ref|YP_008142219.1| 53 VLLIGEPGTGKSMLAQSMVDF 73
                                      79*************998765 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 0.00011
                                       TSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS..................SSTEEEEEEESS..G CS
                               AAA  56 kakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk..................eskvivigatnr..p 112
                                       ka++ +lfiDEi  l +++           +++Llt++++   +                    ++++++a+n   +
  gi|518652699|ref|YP_008142219.1| 239 KADKGVLFIDEINLLRPED-----------QQALLTAMQEKHFSisgqsersagamvqtepvPCDFVLVAAGNLdaI 304
                                       22469**************...........********9999889999************99667********9999 PP

                                       GGSTHHHHSTTS CS
                               AAA 113 dkldpallrgRf 124
                                       +++ pal+ +R+
  gi|518652699|ref|YP_008142219.1| 305 RNMHPALR-SRI 315
                                       9******9.887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 6.7
                                       TTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  96 vkkkeskvivigatnrpdkldpall 120
                                           ++k+ +iga+  ++ l++al+
  gi|518652699|ref|YP_008142219.1| 601 AH--KGKIQIIGASRIEEVLENALI 623
                                       33..367889999999998888886 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   8.8e-08   5.3e-05       4      76 ..      49     124 ..      45     135 .. 0.78
   2 ?    2.8   0.0      0.23   1.4e+02      87     112 ..     238     261 ..     219     279 .. 0.70
   3 ?   -2.2   0.0       7.9   4.7e+03      95     110 ..     596     619 ..     594     643 .. 0.64

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 8.8e-08
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.......erpevvfvtlpsstsskdllrellralglelkaerl 73 
                                       ++++++++Ge+GtGK++l++ +++ l++e    +       e++   +++    ++ k++lr+   + ++e+k+   
  gi|518652699|ref|YP_008142219.1|  49 QKRHVLLIGEPGTGKSMLAQSMVDFLPKEDLE-DvlcfpnpEDSNKPKIKTFPAGKGKEILRQYQIKAEREKKD--- 121
                                       789***********************865444.35999886666666888888888888888888888877777... PP

                            AAA_22  74 sse 76 
                                       +s+
  gi|518652699|ref|YP_008142219.1| 122 RSK 124
                                       444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
                            AAA_22  87 raravielliiDEaqhlrseealeeL 112
                                       +++++ ++l iDE+  lr +e  + L
  gi|518652699|ref|YP_008142219.1| 238 QKADK-GVLFIDEINLLR-PEDQQAL 261
                                       44455.9**********5.3333332 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.9
                            AAA_22  95 liiDEaqhlr......s..eeale 110
                                       +i+DEa++        s  ee+le
  gi|518652699|ref|YP_008142219.1| 596 IILDEAHKGKiqiigaSriEEVLE 619
                                       789999974222333214544444 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.0     0.014       8.2       1      23 [.      52      74 ..      52      83 .. 0.90
   2 !   17.2   0.0   5.7e-06    0.0034      65      98 ..     244     277 ..     231     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.014
                             AAA_3  1 hvllegvPGlaktllvkalakal 23
                                      hvll g PG++k +l++++ + l
  gi|518652699|ref|YP_008142219.1| 52 HVLLIGEPGTGKSMLAQSMVDFL 74
                                      9****************998765 PP

  == domain 2  score: 17.2 bits;  conditional E-value: 5.7e-06
                             AAA_3  65 llladeinrappktqsalleameerqvtvegeth 98 
                                       +l+ dein   p  q all am+e++ +++g++ 
  gi|518652699|ref|YP_008142219.1| 244 VLFIDEINLLRPEDQQALLTAMQEKHFSISGQSE 277
                                       8999*************************99876 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   0.00016     0.096      14      43 ..      43      72 ..      38      84 .. 0.88
   2 !   11.3   0.0   0.00047      0.28      64      96 ..     236     268 ..     216     308 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00016
                                      HHHHHT-SS-EEEEEETT--HHHHHHCC-- CS
                   Sigma54_activ_2 14 LeqaaqsklpvfltGekGsgkelvArlLhk 43
                                      +++aa +k  v+l+Ge+G+gk++ A+ + +
  gi|518652699|ref|YP_008142219.1| 43 IQKAAMQKRHVLLIGEPGTGKSMLAQSMVD 72
                                      789999*******************98765 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00047
                                       HHHHTTTSEEEEEE-TT--HHHHHHHHHHHHHH CS
                   Sigma54_activ_2  64 lleqakggtLylkdiadlskaeqkeLlellaka 96 
                                        +++a+ g+L++ +i+ l +++q+ Ll +++++
  gi|518652699|ref|YP_008142219.1| 236 NMQKADKGVLFIDEINLLRPEDQQALLTAMQEK 268
                                       5789************************99983 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.1e-07   0.00018      25      62 ..      42      79 ..      33      87 .. 0.90
   2 ?   -2.4   0.0       4.9   2.9e+03     108     129 ..      90     111 ..      88     114 .. 0.91
   3 ?   -0.1   0.0      0.97   5.8e+02     100     116 ..     241     257 ..     236     263 .. 0.82

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-07
                             AAA_7 25 llelllknkkpvllvGptGtGKtviikdllkkldkeky 62
                                      ++++   +k++vll+G+ GtGK+++++++++ l+ke++
  gi|518652699|ref|YP_008142219.1| 42 VIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLPKEDL 79
                                      6788899************************9998876 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.9
                             AAA_7 108 DlnmpakekygaqppiellRql 129
                                       D n p+  ++ a +  e+lRq+
  gi|518652699|ref|YP_008142219.1|  90 DSNKPKIKTFPAGKGKEILRQY 111
                                       8899****************97 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.97
                             AAA_7 100 kklvvFvDDlnmpakek 116
                                        k v+F+D++n+ ++e+
  gi|518652699|ref|YP_008142219.1| 241 DKGVLFIDEINLLRPED 257
                                       6789*******988876 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00067       0.4      24      53 ..      45      70 ..      26      77 .. 0.69
   2 !   10.5   0.0   0.00062      0.37      84     123 ..     241     280 ..     229     316 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00067
                            RuvB_N 24 eaakkreealdhvllyGpPGlGkttlakii 53
                                      +aa     +  hvll+G PG Gk+ la+ +
  gi|518652699|ref|YP_008142219.1| 45 KAAM----QKRHVLLIGEPGTGKSMLAQSM 70
                                      3443....346***************9855 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00062
                            RuvB_N  84 ekdvlfideihrlsraveevlysamedfrldivigkGpsa 123
                                       +k vlfidei  l+++ ++ l +am++ ++ i  ++ +sa
  gi|518652699|ref|YP_008142219.1| 241 DKGVLFIDEINLLRPEDQQALLTAMQEKHFSISGQSERSA 280
                                       567***********************99998865444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-05     0.013      22      51 ..      49      77 ..      38     123 .. 0.78
   2 ?    4.1   0.0      0.09        54     134     160 ..     240     266 ..     228     276 .. 0.79
   3 ?   -2.4   0.0       8.9   5.3e+03     117     152 ..     381     416 ..     332     426 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-05
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekd 51
                                      +  + vll+Ge+G+GKs l+++  + l k+
  gi|518652699|ref|YP_008142219.1| 49 Q-KRHVLLIGEPGTGKSMLAQSMVDFLPKE 77
                                      3.489***************9988877776 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.09
                            AAA_16 134 erplvlvlDdlqwadeaslqllaaLlr 160
                                       +++ vl++D++  ++++++q+l + ++
  gi|518652699|ref|YP_008142219.1| 240 ADKGVLFIDEINLLRPEDQQALLTAMQ 266
                                       44479***************9655554 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 8.9
                            AAA_16 117 srllellkrll.allsrderplvlvlDdlqwadeasl 152
                                        r l  l r + + + +  ++ +++ Dd+ +a+  s 
  gi|518652699|ref|YP_008142219.1| 381 LRELGGLVRVAgDIAVT-NKQPIVTADDVNQARNLSK 416
                                       44455566666555555.4458888888888877665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   0.00025      0.15       6      37 ..      45      77 ..      41      88 .. 0.82
   2 ?    5.8   0.0     0.027        16      98     129 ..     238     268 ..     150     278 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00025
                            AAA_19  6 e.alkekvllvtaGpGtGKTrvlkhivallvel 37
                                      + a++++++l+++ pGtGK+ + + +v  l ++
  gi|518652699|ref|YP_008142219.1| 45 KaAMQKRHVLLIGEPGTGKSMLAQSMVDFLPKE 77
                                      44789***************9999998877665 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.027
                            AAA_19  98 kklqeee.llivDEfqdvd.elqyrLlkallgek 129
                                       +k  + + +l++DE+  +  e q++Ll a+ + k
  gi|518652699|ref|YP_008142219.1| 238 QKA-D-KgVLFIDEINLLRpEDQQALLTAMQE-K 268
                                       222.4.359**********9*********994.3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   6.6e-06     0.004       1      32 [.      51      82 ..      51     132 .. 0.79
   2 ?   -0.8   0.0       2.1   1.2e+03      77     113 ..     237     265 ..     222     275 .. 0.73

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 6.6e-06
                                      SCEEEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
                             NACHT  1 rlvilqGeaGsGKTtLlqklalawaegklpqg 32
                                      r v+l Ge+G GK++L+q++++ + +++l+ +
  gi|518652699|ref|YP_008142219.1| 51 RHVLLIGEPGTGKSMLAQSMVDFLPKEDLEDV 82
                                      5699******************9999998874 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.1
                                       CCSCCCEEEEEE-STT-SS-TCH.........HHHHH CS
                             NACHT  77 lelperlLlilDglDelvtdlgqkekqpvrtlLseli 113
                                       ++ +++ +l +D ++ l+ +++q         L + +
  gi|518652699|ref|YP_008142219.1| 237 MQKADKGVLFIDEINLLRPEDQQ--------ALLTAM 265
                                       67889999999*******99999........333333 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00056      0.33      41      70 ..      41      70 ..      14      79 .. 0.84
   2 ?    2.7   0.0     0.098        59     279     293 ..     242     256 ..     229     271 .. 0.77
   3 ?   -1.7   0.0       2.1   1.3e+03     173     194 ..     593     614 ..     572     637 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00056
                                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49 41 elikekklaGravLlaGpsgtGktalaiai 70
                                      e+i++  +  r vLl G++gtGk+ la ++
  gi|518652699|ref|YP_008142219.1| 41 EVIQKAAMQKRHVLLIGEPGTGKSMLAQSM 70
                                      679999999*****************9776 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.098
                                       XXXXXXXXXXXXXXX CS
                             TIP49 279 pGvlfiDevhmlDie 293
                                       +GvlfiDe+++l  e
  gi|518652699|ref|YP_008142219.1| 242 KGVLFIDEINLLRPE 256
                                       7**********9766 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 2.1
                                       TT-EEEEETTT--EEE-SSS-S CS
                             TIP49 173 egDviviekesGkvkklGrsea 194
                                        +D+i  e+++Gk++ +G s+ 
  gi|518652699|ref|YP_008142219.1| 593 FNDIILDEAHKGKIQIIGASRI 614
                                       4799999999999999998865 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00063      0.38       9      45 ..      42      77 ..      35      87 .. 0.79
   2 ?    1.4   0.0      0.38   2.3e+02      84     116 ..     237     269 ..     205     275 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00063
                            AAA_30  9 avealltsgdrvavltGpAGtGKttalkalreaweaa 45
                                      ++++++++++  ++l G +GtGK+++ +++++ + ++
  gi|518652699|ref|YP_008142219.1| 42 VIQKAAMQKR-HVLLIGEPGTGKSMLAQSMVDFLPKE 77
                                      5677777775.99************999988776665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.38
                            AAA_30  84 arlepgtllivDEagmvdtkqlaallkaaekag 116
                                       ++ +++ +l +DE+ ++  ++ +all+a+++++
  gi|518652699|ref|YP_008142219.1| 237 MQKADKGVLFIDEINLLRPEDQQALLTAMQEKH 269
                                       55566789*******************999876 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00012     0.071      12      45 ..      41      74 ..      33     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00012
                            AAA_10 12 qevkgsktnasasliiGdlGnGKSvlakllvlyi 45
                                      + ++ +  +  ++l+iG++G GKS+la+ +v ++
  gi|518652699|ref|YP_008142219.1| 41 EVIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFL 74
                                      557777788899*****************99886 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.13       2      23 ..      50      74 ..      49     101 .. 0.83
   2 ?   -3.1   0.0       9.3   5.5e+03      81     123 ..     464     508 ..     458     518 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                            AAA_24  2 klkiliyGpsgiGKTtlakel...g 23
                                      k+ +l++G++g+GK++la ++    
  gi|518652699|ref|YP_008142219.1| 50 KRHVLLIGEPGTGKSMLAQSMvdfL 74
                                      6789***************994441 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 9.3
                            AAA_24  81 claevirqnekaeskedkgdgkG.ygelaeefrrllkk.lqelrk 123
                                       ++  v + ++++   +++ +++G  ge+a+e ++ + + +++l +
  gi|518652699|ref|YP_008142219.1| 464 VMPIVAEVTQAQHPHNGGVYATGkLGEIAKEAVQNVSAvIKKLSG 508
                                       556666677777777889999999999999988888776666655 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   0.00017       0.1     102     157 ..      22      78 ..      14      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00017
                             T2SSE 102 eltlddlgaeeal.kekiaevlrkavrerglilvsGgTgsGKttllyallkeinksd 157
                                       e+++ +l +++   +e+  ev++ka  ++  +l+ G  g+GK+ l+ +++ +++k+d
  gi|518652699|ref|YP_008142219.1|  22 EIEVPKLLFNQVIgQEHAGEVIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLPKED 78 
                                       55666666666541467789*****9***************************9984 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.7   0.00019      0.11     370     430 ..     110     170 ..      91     183 .. 0.48

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00019
                           DUF2207 370 gyfdkkgkkklkk...lsalglgliilglilillallllvlllvfllilllillliaiivlllf 430
                                       +y  k++++k+ +   l ++ l +i+lg il++++ ++ ++     +i +++l++i++++l+++
  gi|518652699|ref|YP_008142219.1| 110 QYQIKAEREKKDRsksLLFIVLSIILLGAILAIYLWVSGNT---AVAIEVMFLAVIGAAFLYII 170
                                       45555554444440004444444444444444444444333...33333333333332222222 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00091      0.54       1      25 [.      53      77 ..      53     116 .. 0.67
   2 ?    0.2   0.1       1.7     1e+03      48      70 ..     398     420 ..     396     436 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00091
                      RNA_helicase  1 iwlyGpsgeGKStlakeLakallkk 25
                                      ++l G++g+GKS+la+++++ l k+
  gi|518652699|ref|YP_008142219.1| 53 VLLIGEPGTGKSMLAQSMVDFLPKE 77
                                      5799*************77655533 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.7
                      RNA_helicase  48 tgqevvvidDfgqvkdeenpsdl 70 
                                       ++q++v  dD++q ++ ++p + 
  gi|518652699|ref|YP_008142219.1| 398 NKQPIVTADDVNQARNLSKPVEQ 420
                                       589**********9865333333 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00031      0.19      22      60 ..      29      71 ..      16      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00031
                                      EEEETTS-EE...EEEGGGS-..SEEEE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE 22 lgkeisgnpl...vldlkkma.shllvaGatgsGKStalntLi 60
                                      l+ +++g+ +   v++ + m   h+l++G +g+GKS   ++++
  gi|518652699|ref|YP_008142219.1| 29 LFNQVIGQEHageVIQKAAMQkRHVLLIGEPGTGKSMLAQSMV 71
                                      44444444440004444555589**************999986 PP

>> DUF3194  Protein of unknown function (DUF3194)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   0.00058      0.35      12      71 ..     488     551 ..     485     556 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00058
                                       HHHHHHHHHHH..HHHTTS-TTTEEEEEEEEEE...EESSSEEEE.EEEEEEE-TT----TTHHHH CS
                           DUF3194  12 iseflaeviek..kifkkvskkevldlditvev...keneeLdvd.veveleldelskldqelide 71 
                                        +e+++e++++   ++kk+s k+v d+di++++   +  e+ + d  +v + +  +s+l+   id+
  gi|518652699|ref|YP_008142219.1| 488 LGEIAKEAVQNvsAVIKKLSGKNVSDVDIHIQFigtY--EGVEGDsASVSIATAVISSLESIPIDQ 551
                                       6788888888744699****************98543..444333246666666666666666665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0005       0.3      52      80 ..      49      77 ..      15      82 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0005
                            DUF815 52 pannvLLwGarGtGKSslvkallneyaee 80
                                      + ++vLL+G+ GtGKS l ++++  + +e
  gi|518652699|ref|YP_008142219.1| 49 QKRHVLLIGEPGTGKSMLAQSMVDFLPKE 77
                                      4579**************99998766555 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 ?   10.9   0.0   0.00047      0.28      46      67 ..      49      70 ..      11      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00047
                         IstB_IS21 46 kkenivllGpsGvGKshlaial 67
                                      +k  ++l+G +G+GKs la ++
  gi|518652699|ref|YP_008142219.1| 49 QKRHVLLIGEPGTGKSMLAQSM 70
                                      456799*************987 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00058      0.35       3      45 ..      52      92 ..      50     128 .. 0.69
   2 ?   -3.7   0.0       8.7   5.2e+03      89      99 ..     593     603 ..     589     605 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00058
                           DUF2075  3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvl 45
                                       vl  G++GtGK++++ +++  l   +e+ + v+   N +  +
  gi|518652699|ref|YP_008142219.1| 52 HVLLIGEPGTGKSMLAQSMVDFL--PKEDLEDVLCFPNPEDSN 92
                                      46667***************999..555555555555554443 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 8.7
                           DUF2075  89 edvvivDEAhr 99 
                                       ++ +i DEAh+
  gi|518652699|ref|YP_008142219.1| 593 FNDIILDEAHK 603
                                       55689*****7 PP

>> MCM_lid  MCM AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00064      0.38      41      83 ..     373     415 ..     339     418 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00064
                                       TSSSST--HHHHHHHHHHHHHHHHHHTSSSE-HHHHHHHHHHH CS
                           MCM_lid  41 krksipitvRqLesliRLseAlAklrlsevvteedveeairll 83 
                                       ++ +++   R+L  l+R++  +A  + + +vt++dv++a +l 
  gi|518652699|ref|YP_008142219.1| 373 RKGRLTLRLRELGGLVRVAGDIAVTNKQPIVTADDVNQARNLS 415
                                       466788889******************************9986 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00066      0.39     106     139 ..      42      75 ..      21      77 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00066
                         Parvo_NS1 106 wlskqlgkrntvwfyGpantGktnlaeaIakavp 139
                                       +++k   ++  v+++G++ tGk++la++++  +p
  gi|518652699|ref|YP_008142219.1|  42 VIQKAAMQKRHVLLIGEPGTGKSMLAQSMVDFLP 75 
                                       67888899999****************9988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (657 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1187  (0.0662056); expected 358.6 (0.02)
Passed bias filter:                      863  (0.0481343); expected 358.6 (0.02)
Passed Vit filter:                       162  (0.00903564); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.46
# Mc/sec: 4322.87
//
Query:       gi|518652700|ref|YP_008142220.1|  [L=140]
Description: hypothetical protein FACI_IFERC00001G1339 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-05   25.2   0.0    1.8e-05   24.9   0.0    1.1  1  CGI-121   Kinase binding protein CGI-121


Domain annotation for each model (and alignments):
>> CGI-121  Kinase binding protein CGI-121
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0     1e-09   1.8e-05      18      96 ..      24     100 ..       9     115 .. 0.86

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1e-09
                                       CHCTT-EEE-GGG---HHHHHHHHHHHHHHHHHS---SSSHHHHHHHHHSSSS-HHHHHHHHB--TT-S-EEEEEEE CS
                           CGI-121  18 raeldfafldaslilskehllsAvlrallaaargklktktlhsEilfsLspnnnIgealkrfgisdkttsllvvkvs 94 
                                       r++l + ++d + i s+  l  A+ ++     +++ k + + + +l++L ++n+I+ a++r+gi+++t+s +vv  +
  gi|518652700|ref|YP_008142220.1|  24 RTSL-IQLIDGNSISSELELSEAIRKTDRYL-EHNGKIHFPGTVLLMYLAHTNQINVAINRCGINPDTQSGVVVYSN 98 
                                       4444.699******************99766.588899******************************999999776 PP

                                       SS CS
                           CGI-121  95 ss 96 
                                        +
  gi|518652700|ref|YP_008142220.1|  99 RE 100
                                       54 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1017.86
//
Query:       gi|518652701|ref|YP_008142221.1|  [L=296]
Description: 6-phosphofructokinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-37  129.1   0.0    2.8e-37  128.7   0.0    1.1  1  PfkB          pfkB family carbohydrate kinase
  ------ inclusion threshold ------
      0.039   13.3   0.1       0.12   11.8   0.1    1.8  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 !  128.7   0.0   3.1e-41   2.8e-37       1     292 [.       1     275 [.       1     280 [. 0.88

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 3.1e-41
                                       EEEEEEEEEEEEEEEEECSSH..TTSEEEESEEEEEEESHHHHHHHHHHHTT-EEEEEEEEESSHHHHHHHHHHHHT CS
                              PfkB   1 mtkvvviGealidliavsekl..egelvevktveksaGGagaNvAvalarlgadvafigavGdDnfGeflleelkke 75 
                                       m+ ++ +G+++id+ + + +l  +g++  vk ++ +++G + N A ++  lg + ++ +avG     e +l++lkk 
  gi|518652701|ref|YP_008142221.1|   1 MKFLAFFGHLNIDVTLSVPSLpsPGQATGVKALREKFAGTAGNFAYVANALGLKFDLYSAVGEIS-HEKYLANLKKV 76 
                                       67899*****************777777*************************************.9********** PP

                                       TEEETTEEEESSSEEEEEEEEETTTSEEEEEEEEGGGGGHHHHHHHHHHHHHGCTSEEEEESEECTTSHHHHHHHHH CS
                              PfkB  76 gvdtdyvkidedtrtglalivvdedgertivfnrgaaadltkeeleededlleeadllyisgllsselpeavleela 152
                                       g++t++v i ++++  ++++  d+  e+  ++++g++++++ +++     + ++ ++l i++      p++ + ++ 
  gi|518652701|ref|YP_008142221.1|  77 GINTEHVDIMKEENGPICYLPSDGR-EQIAYMFQGPMNNWEASKH----FEYGNYTFLNIGT-----GPVKEYMKIL 143
                                       ***********************86.8888888888888888654....4779999999998.....6666677777 PP

                                       HHHHHTTE.EEEEECESSSHH...HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEE CS
                              PfkB 153 eaaknggt.fdpnlldplgaq...fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvv 225
                                       +  k+++  fdp +      +    ke  + ++++++ +++n++E+ +l++  ++d   a+ + +      ++++++
  gi|518652701|ref|YP_008142221.1| 144 DREKKAKVvFDPGQE--I--WytyNKESAEYMVNHSNMIIMNRKEFYHLLELLNTDS--AAVY-K-----TVNNIII 208
                                       777777744665543..2..2345688999999********************4444..3333.3.....3678*** PP

                                       EEGGGEEEEEETTEEEEEEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHTS CS
                              PfkB 226 tlGkeGalvvekdgelkvpavpkvkvvDttGAGDsfvggflaallegksleealrfanavAalvvqk 292
                                       t G++Ga + e++++  +p +++  + Dt+GAGDsf +g+  al++g +l++++ ++n +A+ ++++
  gi|518652701|ref|YP_008142221.1| 209 TEGEKGATLIENGESTLMPGIKPDRIADTIGAGDSFRAGLFTALSNGYTLKDSVSIGNITASKAIEN 275
                                       **************************************************************99975 PP

>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   1.3e-05      0.12     114     237 ..     169     278 ..     136     285 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                                       HHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEE.. CS
                      Phos_pyr_kin 114 eeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvlydgeeveelea.. 188
                                       e +++++++i+ N +E  +Ll+        +++   ++ k ++++++i+ g+   + a    +l++++e + +++  
  gi|518652701|ref|YP_008142221.1| 169 EYMVNHSNMIIMNRKEFYHLLE-------LLNTDSAAVYK-TVNNIIITEGE---KGA----TLIENGESTLMPGik 230
                                       4566677777777777777766.......22222233333.34555555554...122....466555555544411 PP

                                       .E----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-B CS
                      Phos_pyr_kin 189 .erietknthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikeale 237
                                        +ri+  +t G+G+++ + + + l++g++l+++v+ ++   ++ai+++++
  gi|518652701|ref|YP_008142221.1| 231 pDRIA--DTIGAGDSFRAGLFTALSNGYTLKDSVSIGNITASKAIENNIN 278
                                       15555..99***********************************997764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); 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 0.27s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2134.63
//
Query:       gi|518652702|ref|YP_008142222.1|  [L=525]
Description: Alpha glucosidase [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   42.2  12.3    7.2e-09   35.8   0.6    3.8  3  CarboxypepD_reg  Carboxypeptidase regulatory-like domain
    9.5e-09   35.1   1.3    9.5e-09   35.1   1.3    4.3  4  CarbopepD_reg_2  CarboxypepD_reg-like domain
      6e-06   26.1   0.2    0.00016   21.5   0.0    3.2  2  PEGA             PEGA domain
  ------ inclusion threshold ------
        1.4    9.3   8.3         13    6.1   0.1    4.1  4  AglB_L1          Archaeal glycosylation protein B long periph
        5.6    7.3   7.6        1.6    9.1   0.1    3.7  4  DUF3823          Protein of unknown function (DUF3823) N-term


Domain annotation for each model (and alignments):
>> CarboxypepD_reg  Carboxypeptidase regulatory-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.6     2e-12   7.2e-09       1      77 [.      54     126 ..      54     129 .. 0.87
   2 ?    2.0   0.1     0.071   2.5e+02      28      79 ..     200     250 ..     180     251 .. 0.74
   3 !    9.6   1.3    0.0003       1.1      10      76 ..     270     336 ..     264     340 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 2e-12
                   CarboxypepD_reg   1 tisGrVtda.sgapiagatVtvtnadtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                       t+sG V ++ ++ p++g t+tv+  +++ +++  t ++G+++++ lp+g+ys+  s pG++ +++ ++ l+ ++t++
  gi|518652702|ref|YP_008142222.1|  54 TLSGNVSNSnNNLPLSG-TITVS--NSTMSRTFNTSSNGSYNIT-LPQGNYSISSSIPGFQNYSS-TINLDSNKTQN 125
                                       79******934557776.89999..47889*************9.*******************7.59999999887 PP

                   CarboxypepD_reg  77 l 77 
                                       +
  gi|518652702|ref|YP_008142222.1| 126 I 126
                                       6 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.071
                   CarboxypepD_reg  28 tvastttdadGafrlrglpp.gtysvtvsapGyatatreevtltagqtttldi 79 
                                        +++ +t+ +G  +l +l+  g+y++ +    y ++ + +   ++++t++ ++
  gi|518652702|ref|YP_008142222.1| 200 YSYNWVTNGSGMAKL-FLKYsGNYTMSAYTLYYNSSVI-HYNTANNDTARFNM 250
                                       468889********9.68888*******8888888887.45555566666554 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0003
                   CarboxypepD_reg  10 sgapiagatVtvtna.dtgtvastttdadGafrlrglppgtysvtvsapGyatatreevtltagqttt 76 
                                       ++  +a+ t+tv+    +  + s+ ++ +G++    +p+g y+   s + y + ++ +v++t + t++
  gi|518652702|ref|YP_008142222.1| 270 DNSSVANSTLTVKGGvFSVPSLSVNSNLTGTYYKYEVPAGFYNFAYSNAHYVSKNF-GVDVTGNSTVN 336
                                       56788999999994212334899********************************9.69999666554 PP

>> CarbopepD_reg_2  CarboxypepD_reg-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   1.3   2.7e-12   9.5e-09       1      74 [.      55     128 ..      55     141 .. 0.85
   2 ?    4.0   0.2     0.014        49      27      81 ..     203     255 ..     197     262 .. 0.81
   3 !    4.5   0.4    0.0096        35      26      74 ..     291     339 ..     269     348 .. 0.85
   4 ?   -0.5   0.2      0.36   1.3e+03      30      72 ..     397     438 ..     388     447 .. 0.71

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.7e-12
                   CarbopepD_reg_2   1 isGtVvdketkeplpg.atVyvkgtkkgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvni 74 
                                       +sG+V++++++ pl g +tV+    ++   T +nG+++++ lp+g+y +  s  G+++ + +++++++kt+++++
  gi|518652702|ref|YP_008142222.1|  55 LSGNVSNSNNNLPLSGtITVSNSTMSRTFNTSSNGSYNIT-LPQGNYSISSSIPGFQNYSSTINLDSNKTQNIST 128
                                       69**************33555555567778*********7.***************************9999764 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.014
                   CarbopepD_reg_2  27 gtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvnillkeeal 81 
                                       + vT+ +G  +l  + +g+yt+ +  + y++  ++ +++++ t    ++++e+ +
  gi|518652702|ref|YP_008142222.1| 203 NWVTNGSGMAKLFLKYSGNYTMSAYTLYYNSSVIHYNTANNDTAR--FNMTERIT 255
                                       56899999999999999**************99888888887766..66776655 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0096
                   CarbopepD_reg_2  26 kgtvTdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldvni 74 
                                         + ++  G++   ++pag y +  s   y +++  v+v++++t++ +i
  gi|518652702|ref|YP_008142222.1| 291 LSVNSNLTGTYYKYEVPAGFYNFAYSNAHYVSKNFGVDVTGNSTVNKTI 339
                                       56779999*999999*************************999998665 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.36
                   CarbopepD_reg_2  30 TdenGnFelknlpagkytLvvsyvGyktqekkvtvskektldv 72 
                                       T +n +++l+ l+  +  L+++ +  ++ + ++  s++ t ++
  gi|518652702|ref|YP_008142222.1| 397 TSANPYYQLN-LTISNKNLTFNGIETDSTNLSIVYSGNVTSNF 438
                                       7777889995.77777778888777777777777766666554 PP

>> PEGA  PEGA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   4.5e-08   0.00016      28      63 ..      92     127 ..      85     131 .. 0.94
   2 ?   -0.1   0.2      0.24   8.6e+02      27      62 ..     302     337 ..     290     340 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 4.5e-08
                              PEGA  28 tlsleaGnyslrvekeGYedlektvtvtagetvkln 63 
                                       +++l++Gnys+  + +G+++++ t+++++++t++++
  gi|518652702|ref|YP_008142222.1|  92 NITLPQGNYSISSSIPGFQNYSSTINLDSNKTQNIS 127
                                       789******************************997 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                              PEGA  27 vtlsleaGnyslrvekeGYedlektvtvtagetvkl 62 
                                        +++++aG y +  +   Y   +  v+vt + tv+ 
  gi|518652702|ref|YP_008142222.1| 302 YKYEVPAGFYNFAYSNAHYVSKNFGVDVTGNSTVNK 337
                                       567799999999999999999999999999999875 PP

>> AglB_L1  Archaeal glycosylation protein B long peripheral domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.012        44      29      54 ..      78     106 ..      54     132 .. 0.67
   2 ?    0.5   0.3      0.21   7.6e+02       4      69 ..     168     239 ..     167     257 .. 0.62
   3 ?    6.1   0.1    0.0037        13       1      31 [.     326     359 ..     326     369 .. 0.84
   4 ?   -1.4   0.0       0.8   2.9e+03      28      46 ..     493     511 ..     473     521 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.012
                                       EEEEEEE.-BTTEEEEEE-...--SS... CS
                           AglB_L1  29 tYrqeaeadedGefeltvP...Ystegee 54 
                                       t +++ +++++G++++t+P   Ys + + 
  gi|518652702|ref|YP_008142222.1|  78 TMSRTFNTSSNGSYNITLPqgnYSISSSI 106
                                       44566678899******995555555444 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.21
                                       EEEEBSSSSEEEEEEEEE-TT........S-EEEEEEEEE.-BTTEEEEEE---SS......-SSSSEESS-EE CS
                           AglB_L1   4 itGsaeagatvtasveletnq........grtftYrqeaeadedGefeltvPYstegeedgetnssveaagpYe 69 
                                       itG+ +++ t+ +  +l+ +q        g  ++Y+   +++ +G  +l + Ys + + + +t +  +   +Y+
  gi|518652702|ref|YP_008142222.1| 168 ITGTFDKNITIDLGKKLNNTQfvvlmkldGAVYSYN--WVTNGSGMAKLFLKYSGNYTMSAYTLYYNSSVIHYN 239
                                       666666666666666666666666666545555554..445788999999999998666777666666666665 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0037
                                       -EEEEEEBSSSSEE...EEEEEEE-TTS-EEEEE CS
                           AglB_L1   1 GAtitGsaeagatv...tasveletnqgrtftYr 31 
                                       G  +tG+++ ++t+    +s++++ n+g tf+Y+
  gi|518652702|ref|YP_008142222.1| 326 GVDVTGNSTVNKTIdpyLISINIRNNTGNTFNYT 359
                                       78899**999966633379**************8 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.8
                                       EEEEEEEE.-BTTEEEEEE CS
                           AglB_L1  28 ftYrqeaeadedGefeltv 46 
                                         Y +  ++++dG+ ++ v
  gi|518652702|ref|YP_008142222.1| 493 LVYDNDSKVSTDGRMTVEV 511
                                       4577777777777766654 PP

>> DUF3823  Protein of unknown function (DUF3823) N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.1   0.00044       1.6      37      88 ..      79     126 ..      53     128 .. 0.77
   2 ?   -1.3   0.1      0.77   2.8e+03      43      59 ..     216     232 ..     187     255 .. 0.55
   3 ?   -0.4   0.3      0.42   1.5e+03      41      87 ..     293     336 ..     282     340 .. 0.78
   4 ?   -1.2   0.0      0.73   2.6e+03      59      69 ..     406     416 ..     384     441 .. 0.47

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00044
                                       --EEEEB-TTSEEEEEE-SEEEEEEE-TT-SSB-TT---EEEEESSSEE--E CS
                           DUF3823  37 epidvyvkqDGtfntllFdGeYklvlkegegpfvkavdtievelkgntkldf 88 
                                        + +++++++G++n  l +G+Y +       p + ++ + +++l++n+++++
  gi|518652702|ref|YP_008142222.1|  79 MSRTFNTSSNGSYNITLPQGNYSISS---SIPGF-QNYSSTINLDSNKTQNI 126
                                       5678999*****************99...46666.56777778877777766 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.77
                                       B-TTSEEEEEE-SEEEE CS
                           DUF3823  43 vkqDGtfntllFdGeYk 59 
                                       +k  G++    +   Y+
  gi|518652702|ref|YP_008142222.1| 216 LKYSGNYTMSAYTLYYN 232
                                       44444444333333333 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.42
                                       EEB-TTSEE.EEEE-SEEEEEEE-TT-SSB-TT---EEEEESSSEE-- CS
                           DUF3823  41 vyvkqDGtf.ntllFdGeYklvlkegegpfvkavdtievelkgntkld 87 
                                       v+ +  Gt+ +  + +G Y++     +  +v  +++  v++ gn +++
  gi|518652702|ref|YP_008142222.1| 293 VNSNLTGTYyKYEVPAGFYNFAYS--NAHYV--SKNFGVDVTGNSTVN 336
                                       666777999999999999999997..66777..578888888888876 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 0.73
                                       EEEE-TT-SSB CS
                           DUF3823  59 klvlkegegpf 69 
                                       +l++ +++  f
  gi|518652702|ref|YP_008142222.1| 406 NLTISNKNLTF 416
                                       23333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       830  (0.0462937); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 3581.98
//
Query:       gi|518652703|ref|YP_008142223.1|  [L=188]
Description: hypothetical protein FACI_IFERC00001G1342 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1049.44
//
Query:       gi|518652704|ref|YP_008142224.1|  [L=157]
Description: hypothetical protein FACI_IFERC00001G1343 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1751  (0.097663); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1026.20
//
Query:       gi|518652705|ref|YP_008142225.1|  [L=317]
Description: hypothetical protein FACI_IFERC00001G1344 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-62  208.6   0.1    3.5e-62  208.1   0.1    1.3  1  AAA_3            ATPase family associated with various cellul
      2e-15   57.0   0.0    4.3e-15   55.9   0.0    1.6  1  AAA_5            AAA domain (dynein-related subfamily)
    1.5e-14   53.6   0.0    2.4e-14   52.9   0.0    1.3  1  AAA_lid_2        AAA lid domain
    2.9e-07   29.8   0.0    6.1e-07   28.8   0.0    1.6  1  MCM              MCM P-loop domain
    5.1e-05   23.7   0.0    0.00052   20.4   0.0    2.2  2  AAA              ATPase family associated with various cellul
    7.5e-05   22.5   0.1     0.0011   18.7   0.0    2.5  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0001   21.7   0.0       0.13   11.6   0.0    2.2  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00037   20.2   0.0    0.00084   19.1   0.0    1.5  2  Sigma54_activat  Sigma-54 interaction domain
     0.0065   16.3   0.2      0.013   15.3   0.2    1.5  1  AAA_lid_8        AAA lid domain
  ------ inclusion threshold ------
      0.046   14.2   0.0       0.68   10.4   0.0    2.3  2  Cep57_MT_bd      Centrosome microtubule-binding domain of Cep
       0.51   10.7   5.5       0.25   11.7   2.7    1.9  2  Ca_bind_SSO6904  Calcium binding protein SSO6904


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 !  208.1   0.1   2.2e-65   3.5e-62       1     131 []      41     171 ..      41     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 2.2e-65
                             AAA_3   1 hvllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfanllladeinrappk 77 
                                       h+l+e+vPGlakt+l+++++k+l+l+fkriqftpd+lPsd++G +vf+ +++++ef++Gpvf+n++ladeinr+ppk
  gi|518652705|ref|YP_008142225.1|  41 HILMESVPGLAKTMLASEFSKHLGLQFKRIQFTPDMLPSDVTGNMVFNPETRKMEFREGPVFSNIVLADEINRTPPK 117
                                       9**************************************************************************** PP

                             AAA_3  78 tqsalleameerqvtvegethklpepflvlatqnPieqeGtyplpeaqldrfll 131
                                       +qsalleamee+qv+v g t+klp+pflv+atqnPieqeGt+pl+ea +drfl+
  gi|518652705|ref|YP_008142225.1| 118 VQSALLEAMEEKQVSVYGLTTKLPSPFLVIATQNPIEQEGTFPLAEALMDRFLF 171
                                       ****************************************************96 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.9   0.0   2.6e-18   4.3e-15       5     138 .]      45     169 ..      41     169 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.9 bits;  conditional E-value: 2.6e-18
                                       E--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--H CS
                             AAA_5   5 vGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraes 79 
                                          pG +K++la ++++ l+ ++  +q+t d+ ++d++g + ++   ++ +++++p+      + i++ DE++r ++
  gi|518652705|ref|YP_008142225.1|  45 ESVPGLAKTMLASEFSKHLGLQFKRIQFTPDMLPSDVTGNMVFNpeTRKMEFREGPVF-----SNIVLADEINRTPP 116
                                       5579***************************************9888899999*****.....9************* PP

                                       HHHHHHHHHHHSSEEE..-SSSEEE---......-EEEEEESS--..-TT-TTHHHHTT- CS
                             AAA_5  80 evlnsLlslleerrllleeggelvkaknddllerfrviatanpld.rslnelspalrsRf 138
                                       +v+++Ll  +ee+++++  +++     +      f viat np +  +  +l +al +Rf
  gi|518652705|ref|YP_008142225.1| 117 KVQSALLEAMEEKQVSVYGLTTKLPS-P------FLVIATQNPIEqEGTFPLAEALMDRF 169
                                       ****************6666666643.4......***********9999**********9 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.9   0.0   1.5e-17   2.4e-14       2      61 ..     232     290 ..     231     301 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.9 bits;  conditional E-value: 1.5e-17
                         AAA_lid_2   2 atrahlaielgvsgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepea 61 
                                       ++r++ ++ lg+s+r  ++  l+aArA+A+l gr+yV+peDv  +a+ +L+HRl+++pe 
  gi|518652705|ref|YP_008142225.1| 232 KSRESDMVYLGASTR-TAVKYLNAARANAMLSGRKYVIPEDVIFIAREILNHRLIMRPES 290
                                       6789999********.***************************************88865 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   3.7e-10   6.1e-07      52     218 ..      34     188 ..      10     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 3.7e-10
                                       SBBCSS-EEEEEESSTSTHHHHHHHHHHHS....SSEEEEESSSSSSSHSSSEEEEESSSSSEEEEETHHHHTTTSE CS
                               MCM  52 tklrgdinvllvgdpgtaKsqlLkyvekla....pravytsgkgssaagLtaavvrdeetgefvleaGalvladkGv 124
                                       ++l ++ ++l+ + pg+aK+ l  + +k +    +r ++t       ++ t  +v ++et+++ +  G +      +
  gi|518652705|ref|YP_008142225.1|  34 ISLFTNNHILMESVPGLAKTMLASEFSKHLglqfKRIQFTP--DMLPSDVTGNMVFNPETRKMEFREGPVFS---NI 105
                                       56778899***********9998888765411003333333..344567899999*************9875...49 PP

                                       EEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSCCTTS-HHHHSSSSHHHHHHSSEE CS
                               MCM 125 cciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagrydkkksvaeninlsaalLsrFDli 201
                                       ++ De+++   + +sal+EamE++++s+   G++++L++   v+a  np++    ++ +      l +al++rF l+
  gi|518652705|ref|YP_008142225.1| 106 VLADEINRTPPKVQSALLEAMEEKQVSVY--GLTTKLPSPFLVIATQNPIE----QEGT----FPLAEALMDRF-LF 171
                                       ***************************96..9*****************97....2333....35677777777.44 PP

                                       EEE-SSTTHHHHHHHHH CS
                               MCM 202 fvllDkvdeekDeelae 218
                                           D +d+e + ++ +
  gi|518652705|ref|YP_008142225.1| 172 RYYIDYPDREDEIKILK 188
                                       44456666666666655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   3.2e-07   0.00052       2     131 ..      43     176 ..      42     177 .. 0.80
   2 ?    0.7   0.0      0.42   6.8e+02      32      58 ..     235     268 ..     201     279 .. 0.57

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 3.2e-07
                                       EEESSTTSSHHHHHHHHHHHHTHEEEEEET.TTCS.SSSTTHHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHT CS
                               AAA   2 llyGppGtGKTllakavakelgvefleisg.sell.skyvgesekkirelfkeakeka.kpsilfiDEidalaksrs 75 
                                       l+   pG  KT+la+   k+lg +f +i+  +++l s++ g++  + +    e +e      i++ DEi +  ++  
  gi|518652705|ref|YP_008142225.1|  43 LMESVPGLAKTMLASEFSKHLGLQFKRIQFtPDMLpSDVTGNMVFNPETRKMEFREGPvFSNIVLADEINRTPPKV- 118
                                       66778********************9999626777677777766666666656555555449**********8888. PP

                                       TCCCHHHHHHHHHHHHHHHHTTTS........SSTEEEEEEESS.....GGGSTHHHHSTTSSEEEETT CS
                               AAA  76 gseseeeervvnqLlteldgvkkk........eskvivigatnr.....pdkldpallrgRfdrkieie 131
                                                 +++Ll+++++ + +         s+++vi++ n         l +al+ +Rf  +++i+
  gi|518652705|ref|YP_008142225.1| 119 ----------QSALLEAMEEKQVSvyglttklPSPFLVIATQNPieqegTFPLAEALM-DRFLFRYYID 176
                                       ..........*********************9888****9999855444445788888.9998888876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.42
                                       TTCSSS..STTHHHHHHHHHHHHHHHTS........T CS
                               AAA  32 sellsk..yvgesekkirelfkeakeka........k 58 
                                        +   +  y+g+s +   +++++a+++a         
  gi|518652705|ref|YP_008142225.1| 235 ES---DmvYLGASTRTAVKYLNAARANAmlsgrkyvI 268
                                       11...12266777777777777666666555554442 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   6.7e-07    0.0011      34     115 ..      40     133 ..      35     139 .. 0.72
   2 ?   -3.3   0.0       4.1   6.6e+03      84     100 ..     269     288 ..     257     300 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 6.7e-07
                            RuvB_N  34 dhvllyGpPGlGkttlakiiakelgvklkit.sgPvlekagdlaa.ll.......tnleek....dvlfideihrls 97 
                                       +h+l+   PGl kt la+  +k lg ++k    +P +  ++d+++ ++       ++++e+    ++++ dei r  
  gi|518652705|ref|YP_008142225.1|  40 NHILMESVPGLAKTMLASEFSKHLGLQFKRIqFTPDML-PSDVTGnMVfnpetrkMEFREGpvfsNIVLADEINRTP 115
                                       8**************************98651566653.4444431331111111233332223368899******* PP

                            RuvB_N  98 raveevlysamedfrldi 115
                                       ++v+  l  ame+ ++ +
  gi|518652705|ref|YP_008142225.1| 116 PKVQSALLEAMEEKQVSV 133
                                       ************999876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.1
                            RuvB_N  84 ekdvlfid.ei..hrlsrav 100
                                       ++dv+fi  ei  hrl    
  gi|518652705|ref|YP_008142225.1| 269 PEDVIFIArEIlnHRLIMRP 288
                                       57888885355556765554 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   8.1e-05      0.13       4      44 ..      21      61 ..      19      79 .. 0.91
   2 !    7.8   0.0    0.0011       1.9     109     159 ..     105     153 ..     101     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8.1e-05
                      Mg_chelatase  4 dvkGqeeakraleiaaaGgHnlllvGppGsGKtmlakrlps 44
                                       v+G ++  r + i+   + ++l+   pG  Ktmla+ +++
  gi|518652705|ref|YP_008142225.1| 21 TVIGSSRIVRFMLISLFTNNHILMESVPGLAKTMLASEFSK 61
                                      689999999***************************98765 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0011
                      Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpc 159
                                       +++ DE+     kv  +L e +e+++v++     +++ p+ f ++a+ Np 
  gi|518652705|ref|YP_008142225.1| 105 IVLADEINRTPPKVQSALLEAMEEKQVSVYGL--TTKLPSPFLVIATQNPI 153
                                       5678***********************99865..5677999********96 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       6.8   1.1e+04      22      41 ..      39      58 ..      35      63 .. 0.75
   2 !   19.1   0.0   5.1e-07   0.00084      96     146 ..     105     154 ..     100     170 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 6.8
                                      SS-EEEECSTTSSHHHHHHH CS
                   Sigma54_activat 22 dlsvlitGesGtGKellara 41
                                      + ++l++   G  K++la+ 
  gi|518652705|ref|YP_008142225.1| 39 NNHILMESVPGLAKTMLASE 58
                                      56788888888888888876 PP

  == domain 2  score: 19.1 bits;  conditional E-value: 5.1e-07
                                       EEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEEEEESS-HH CS
                   Sigma54_activat  96 tlfLDeigelplelQekLlrvlqegevervGsskeikvdvriiaatnedle 146
                                       +++ Dei++ p+++Q+ Ll++++e++v+  G +++ +  + +ia t++ +e
  gi|518652705|ref|YP_008142225.1| 105 IVLADEINRTPPKVQSALLEAMEEKQVSVYGLTTKLPSPFLVIA-TQNPIE 154
                                       5667********************************99998775.555555 PP

>> AAA_lid_8  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   8.2e-06     0.013       1      54 [.     221     275 ..     221     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 8.2e-06
                         AAA_lid_8   1 evlelileiknkleeeeea.iyvSDRRwkkivkllkasAylngrdevnlsDllll 54 
                                       e++e+i++i +k  e +   +  S R   k+++  +a+A+l+gr+ v ++D++++
  gi|518652705|ref|YP_008142225.1| 221 EIIEYIINIIRKSRESDMVyLGASTRTAVKYLNAARANAMLSGRKYVIPEDVIFI 275
                                       68888888888884444332578****************************9876 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 ?    1.0   0.0      0.37     6e+02      59      74 ..     121     136 ..     107     138 .. 0.86
   2 ?   10.4   0.0   0.00042      0.68      21      50 ..     181     210 ..     179     216 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.37
                       Cep57_MT_bd  59 elvkrlEaKadqIykL 74 
                                       +l++++E+K+ ++y L
  gi|518652705|ref|YP_008142225.1| 121 ALLEAMEEKQVSVYGL 136
                                       6899999999999876 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00042
                       Cep57_MT_bd  21 edEfehlklelqelaaqynaldpslgkrkR 50 
                                       edE++ lk ++   a++yn ld+++  + R
  gi|518652705|ref|YP_008142225.1| 181 EDEIKILKSIYRNAAKKYNTLDSATILHYR 210
                                       8*********************87655555 PP

>> Ca_bind_SSO6904  Calcium binding protein SSO6904
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.7   0.00015      0.25      26      72 ..     185     232 ..     170     238 .. 0.85
   2 ?   -2.8   0.0       5.1   8.3e+03      62      88 ..     302     311 ..     294     314 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
                                       HHHHHHHHHH.HHSS-HHHHHHHHHHHTHHHHHHTHHHHHHHHHHHHH CS
                   Ca_bind_SSO6904  26 kileeieedl.rksnnikssiifvyanhveevkknkefydliskilek 72 
                                       kil+ i  ++ +k n++ s+ i  y n v+ev  n e+ + i +i+ k
  gi|518652705|ref|YP_008142225.1| 185 KILKSIYRNAaKKYNTLDSATILHYRNLVNEVYVNEEIIEYIINIIRK 232
                                       78888877651667899****************************988 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.1
                                       HHHHHHHHHHHHHTTT-HHHHHHHHHH CS
                   Ca_bind_SSO6904  62 fydliskilekyakkiGvenvkeliln 88 
                                       +y++i +i+                 n
  gi|518652705|ref|YP_008142225.1| 302 IYNVIDSII-----------------N 311
                                       344443333.................3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); 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 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 2147.24
//
Query:       gi|518652706|ref|YP_008142226.1|  [L=431]
Description: hypothetical protein FACI_IFERC00001G1345 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-07   31.0   0.0    4.6e-07   30.0   0.0    1.6  1  DUF58     Protein of unknown function DUF58
    0.00037   21.1   0.0    0.00074   20.1   0.0    1.5  1  VWA_2     von Willebrand factor type A domain


Domain annotation for each model (and alignments):
>> DUF58  Protein of unknown function DUF58
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0   0.0   5.2e-11   4.6e-07       3      59 ..     197     255 ..     195     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5.2e-11
                             DUF58   3 dfaglReYvpgDplrrIdWkatARtge..lyvrefeaerartvllvldlspemslgstg 59 
                                       +++g+R+Y+  D++r I W  ++ ++e   +v+e+e+er+ t+++++d s  m+ g+ +
  gi|518652706|ref|YP_008142226.1| 197 NLYGVRPYTFEDDPRFIVWSRYSEGNEdsIMVKEMEEEREITTIFIIDYSIAMNYGDID 255
                                       679*********************86666***********************9998765 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 !   20.1   0.0   8.2e-08   0.00074       1      86 [.     239     327 ..     239     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 8.2e-08
                             VWA_2   1 lvfvlDtSgSmrngdygptrleaakdaveallksl.....pgdrvglvtfsdgpevliplt...kdkakilnalrnl 69 
                                       ++f++D S  m+ gd    + + + d++++          ++d+vg + +s++ +v ip+    ++ +++++ + ++
  gi|518652706|ref|YP_008142226.1| 239 TIFIIDYSIAMNYGDIDRVYDSSIVDIINS----AhfmakNRDNVGFLLYSSKINVYIPPGksgESISRLEKSVSSI 311
                                       69************8655555555555544....223333799*****************63446678888888888 PP

                             VWA_2  70 eakgggtnlaaaLqlar 86 
                                        ++ g+ ++++aL+ ++
  gi|518652706|ref|YP_008142226.1| 312 LPD-GEFRIGDALKELQ 327
                                       886.*********9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 3086.81
//
Query:       gi|518652707|ref|YP_008142227.1|  [L=290]
Description: hypothetical protein FACI_IFERC00001G1346 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1183  (0.0659825); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); 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):               0  [number of targets reported over threshold]
# CPU time: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.47
# Mc/sec: 1857.42
//
Query:       gi|518652708|ref|YP_008142228.1|  [L=104]
Description: rhodanese-related sulfurtransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      8e-17   61.7   0.1    9.2e-17   61.5   0.1    1.1  1  Rhodanese       Rhodanese-like domain
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.14   12.0   0.0    1.1  1  DEDD_Tnp_IS110  Transposase


Domain annotation for each model (and alignments):
>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.5   0.1     1e-20   9.2e-17       2     105 ..       7      97 ..       6      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 61.5 bits;  conditional E-value: 1e-20
                         Rhodanese   2 akelkellekgkvallDvRppeeYekghIpgAvnvskdtlsrakkseapllelpeellelgidnkktvvvycdgggr 78 
                                       a+e+ e+ ek++ +++DvR++ eYe ghI+++v +          ++ +  +++  ++++   ++k++v++c++g+r
  gi|518652708|ref|YP_008142228.1|   7 ADEVSEMAEKNECVIIDVREQFEYESGHIENSVPI----------PMYDIFNNISLVEKY---RDKKIVLVCSSGHR 70 
                                       799*****999999*********************..........777777777777777...899*********** PP

                         Rhodanese  79 aaaaaallkklGyknvsvldGGfkawk 105
                                       +  + ++l++ G +nv++l +G+ +w 
  gi|518652708|ref|YP_008142228.1|  71 SYYTGKFLEENGITNVYNLYNGLYGWE 97 
                                       9999999999**999***********7 PP

>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.14       9      75 ..      16      87 ..      13      93 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                    DEDD_Tnp_IS110  9 khdacvidaegkvllse.rvpndee.gleallek...laakagevlvvveatghygallvaflleagitvvv 75
                                      k+++++id  ++   +  +++n+ +  + +++++   +++  ++  v v ++gh+++   +fl+e+git v+
  gi|518652708|ref|YP_008142228.1| 16 KNECVIIDVREQFEYESgHIENSVPiPMYDIFNNislVEKYRDKKIVLVCSSGHRSYYTGKFLEENGITNVY 87
                                      678888888888766544899997654455555544377889999***********************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 703.70
//
Query:       gi|518652709|ref|YP_008142229.1|  [L=637]
Description: hypothetical protein FACI_IFERC00001G1348 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-21   76.6   0.8    1.7e-16   60.1   1.1    2.7  2  Glyco_hydro_15   Glycosyl hydrolases family 15
    6.1e-06   25.7   1.5    1.1e-05   24.9   1.4    1.5  1  DUF608           Glycosyl-hydrolase family 116, catalytic reg
  ------ inclusion threshold ------
       0.13   11.5   5.5       0.17   11.1   1.9    2.5  2  Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin gly


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   1.1   2.8e-20   1.7e-16      24     358 ..     283     576 ..     270     585 .. 0.78
   2 !   13.2   0.0   4.6e-06     0.028     408     447 ..     585     625 ..     578     626 .. 0.89

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 2.8e-20
                                       T-B-S-S-BSSS......B--SEEHHHHHHHHHHHH.......HHHHHTTT-HCCHHHHHHHHHHHHHHCTS-BTTB CS
                    Glyco_hydro_15  24 GlliASpstsdp......DYrytWvRDsvyvilavwglgyrdedrakayeleqslvklmrglleamvrqagkvekfk 94 
                                       G++ AS + sd       +Y+y W RD+++ + a+  +g + e+ +k   +++sl    +g+++  ++ +g   +  
  gi|518652709|ref|YP_008142229.1| 283 GAIAASCD-SDIlkishdGYYYMWPRDASIAAYALSIAG-HTESGRKFFSMSTSLMS-GKGYMYHKYNMDGS--PA- 353
                                       66666655.3324556669****************9666.67999999999999987.88999999999996..32. PP

                                       -TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCCCHHH.HTHHHHHHHHHHHTTS-. CS
                    Glyco_hydro_15  95 etqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiistldev.afvqnlvdYieaayktp. 169
                                          s+   +++  ++      G+ e   +Q D t+l +++l+++ ++   i +t+  + ++v    ++ +   +   
  gi|518652709|ref|YP_008142229.1| 354 ---SS---WLPHIMN------GK-EIYPIQEDETALLIYVLWEYFKKYNDIGFTAPFYeSIVIRAAEFMTGFVDADg 417
                                       ...23...7887776......33.55667***************888877777777766666665555544333222 PP

                                       ....EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHHSTTT..GGGEETTCCEC CS
                    Glyco_hydro_15 170 ....dfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklqgkygckrgfwplfntyl 242
                                           +f+lWEe+ g++ +  +     +Al  a ++a  fg+++ ++++++ +d ++n  + k + +  +   ++   
  gi|518652709|ref|YP_008142229.1| 418 lpreSFDLWEERYGIHAY--TVSTTFAALKAASNFAGVFGDQALSRKYSDAADRMVNAFDQKFYSDE-Y--RRYARA 489
                                       22359*************..999999*********************************44444222.2..223334 PP

                                       ECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHHHHHHSGGGTT-STTS-- CS
                    Glyco_hydro_15 243 ildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyildsllsegflavgeldplvr 319
                                       i++g            +  +d++l  +++ ++ ++ d          +r+l+++ +i+++l   g        + + 
  gi|518652709|ref|YP_008142229.1| 490 IINGK----------LDFTVDSALSSIAIFGMKNPTD----------SRVLSTMEAIMEKLWVNGS-------GGIA 539
                                       44444..........6899******************..........*****************99.......459* PP

                                       SBTT--CG...SSSBSCT--BHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 320 Rysedvkp...dklglsGrpyylctlwtvetlldelyekagk 358
                                       Ry++d++    ++ + +G+p+ ++tlw     +++ y + g+
  gi|518652709|ref|YP_008142229.1| 540 RYENDNYMrirEDSNITGNPWIITTLW-----MARYYIRIGN 576
                                       *******988889999***********.....6666665555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.6e-06
                                       HHHHH.S-TTS---SEE-TTT--EESSTT-HHHHHHHHHHH CS
                    Glyco_hydro_15 408 eavee.dnslgvLteevdvylgeliraqpllfsealllrig 447
                                       e v+  ++++g+++e+++ y+ge+ + +pl +s a+++ ++
  gi|518652709|ref|YP_008142229.1| 585 EWVKShRQKSGIFSEQINPYTGEPHSVSPLVWSNAEFIIAI 625
                                       5667778999**************************99876 PP

>> DUF608  Glycosyl-hydrolase family 116, catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   1.4   1.8e-09   1.1e-05     143     221 ..     410     489 ..     370     601 .. 0.81

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.8e-09
                            DUF608 143 dglienegfadqtYDaws.vkGvsaycgglwlaaLeaaiemaellgdkkdaeeykellekakkvyekkLwnGeYfky 218
                                        g+++ +g + +++D w+   G+ ay+ +   aaL+aa+++a + gd++  ++y++  ++  +++++k+++ eY +y
  gi|518652709|ref|YP_008142229.1| 410 TGFVDADGLPRESFDLWEeRYGIHAYTVSTTFAALKAASNFAGVFGDQALSRKYSDAADRMVNAFDQKFYSDEYRRY 486
                                       589999999999*****7257*****************************************************999 PP

                            DUF608 219 des 221
                                        ++
  gi|518652709|ref|YP_008142229.1| 487 ARA 489
                                       764 PP

>> Bac_rhamnosid6H  Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1     0.084     5e+02     297     316 ..     237     256 ..     231     268 .. 0.80
   2 ?   11.1   1.9   2.9e-05      0.17     103     223 ..     377     488 ..     367     495 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.084
                                       SHHHHHTT-SS--SSTTSB- CS
                   Bac_rhamnosid6H 297 wgymvknGaTtiwErWdsml 316
                                       ++  +++ +T  wE W+s  
  gi|518652709|ref|YP_008142229.1| 237 YMEKLNRRTTNYWELWSSKV 256
                                       788889999*******9865 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 2.9e-05
                                       HHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHTSBT.TB.--S-S--STT.....-SS----HHHHHHHHHHHHH CS
                   Bac_rhamnosid6H 103 ivivpwelyetygDkeilkkqYesmkryldylkqrsddgleelskfqlgDWldpeardgaaktekalvataylvrsl 179
                                       ++ v we++++y+D  + +  Yes+     +  +   d  ++l +  +  W            + ++v+t++   +l
  gi|518652709|ref|YP_008142229.1| 377 LIYVLWEYFKKYNDIGFTAPFYESIVIRAAEFMTGFVD-ADGLPRESFDLWE------ERYGIHAYTVSTTFA--AL 444
                                       56667777777777777777777765544444444444.2344444444455......344456667777775..68 PP

                                       HHHHHHHHHTTS..--HHHHHHHHHHHHHHHHHHB.-TTS-BTT CS
                   Bac_rhamnosid6H 180 klvakiaellgkeedakkyaalaeelkaafnkkyldsetgsvan 223
                                       k ++++a ++g ++ ++ky++ a+++ +af +k++ +e +++a 
  gi|518652709|ref|YP_008142229.1| 445 KAASNFAGVFGDQALSRKYSDAADRMVNAFDQKFYSDEYRRYAR 488
                                       999********************************888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (637 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.80u 0.35s 00:00:01.14 Elapsed: 00:00:00.58
# Mc/sec: 3285.71
//
Query:       gi|518652710|ref|YP_008142230.1|  [L=610]
Description: hypothetical protein FACI_IFERC00001G1349 [Ferroplasma acidarmanus fer1]
Scores for complete 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-90  303.8   0.0    1.5e-89  300.7   0.0    2.1  2  GDE_C            Amylo-alpha-1,6-glucosidase
    5.8e-54  182.8   0.1    8.9e-54  182.2   0.1    1.2  1  GDE_N            Glycogen debranching enzyme N terminal
     0.0067   15.2   0.0        2.1    6.9   0.0    2.5  2  Glyco_hydro_100  Alkaline and neutral invertase
  ------ inclusion threshold ------
      0.013   15.3   0.1       0.32   10.9   0.0    2.5  2  CotJA            Spore coat associated protein JA (CotJA)


Domain annotation for each model (and alignments):
>> GDE_C  Amylo-alpha-1,6-glucosidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1     0.056   2.5e+02     292     310 ..      56      74 ..      50      82 .. 0.90
   2 !  300.7   0.0   3.3e-93   1.5e-89      21     383 .]     263     590 ..     248     590 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.056
                             GDE_C 292 YdgsedsrdaaYHqGtvWv 310
                                       ++g+++  d++Y  Gt+W+
  gi|518652710|ref|YP_008142230.1|  56 FQGKQYAIDTNYYPGTMWP 74 
                                       899***************7 PP

  == domain 2  score: 300.7 bits;  conditional E-value: 3.3e-93
                             GDE_C  21 gvsliAGlpwFsdWGRDtfIaLsGllLvtgrfeeAreilltFaktlrhGliPNlldegqealyntvdaslwlieaie 97 
                                        ++liAG++wF  W RDtfI+++GllL+ + f+ Arei l++a+++++ l+PN l +  +    ++da+lw+i+a++
  gi|518652710|ref|YP_008142230.1| 263 KNDLIAGFHWFGPWARDTFISMPGLLLIEKNFDMAREIFLNYAGKMKENLVPNNLYS--QSFERSADAPLWFIYALY 337
                                       6789***************************************************65..556679************ PP

                             GDE_C  98 kYleyagdaeilrriypvlqeilqkyvqGtkykigldeedglisagerlnqlTWmDakvkgepvtPRdGkaveinaL 174
                                       kY++y++d +++r  ++ +++i+++y+ G++  + ld    +i+  +   + TWmDak+ ++  tPR Gk+veinaL
  gi|518652710|ref|YP_008142230.1| 338 KYYAYSNDSSFVRSLLKNVRDIINSYISGNE-DFSLD--GKFIKVSN--APMTWMDAKNGNTSFTPRIGKPVEINAL 409
                                       *******************************.99999..99999999..9*************************** PP

                             GDE_C 175 wyaaLkileelaekalgeakkssykelaekikesfekkFwdeaaaavakreilaDvlksseekdlslRpNflialsl 251
                                       wy++Lki++ + +   ge+ +++ + + ++ +++f+ kF          ++ +aD++++    d+s+RpNfl+a+sl
  gi|518652710|ref|YP_008142230.1| 410 WYNSLKIYTYFCN-ISGEQPEKTVNDILSEFEDEFTGKFII--------NGEIADTIDP---VDTSFRPNFLFAYSL 474
                                       *************.667757888888888888888888833........5778999998...89************* PP

                             GDE_C 252 apellseekakkvlekaeeeLltplGlktLdpedpeYkgnYdgsedsrdaaYHqGtvWvwllgsyveallkfgeklg 328
                                       ++ ll++++   +leka+ eL+tp+Gl++L+p+  ++ g+Y+g+  +rd aYH+GtvW+wl+g y++a ++ g +  
  gi|518652710|ref|YP_008142230.1| 475 PFPLLNQKQ---FLEKARLELVTPYGLRSLSPRSNKFAGTYSGPVMERDRAYHNGTVWPWLAGPYITACVRNGYD-- 546
                                       *****9887...*************************************************************98.. PP

                             GDE_C 329 kskealeevkalLeglekhleeaglgslsElfdgdaellpkgciaQAWSvaellr 383
                                              +++  +++l        ++ ++E+fdg  +  p+gci+QAWS +el+r
  gi|518652710|ref|YP_008142230.1| 547 -----AGNLYRFFSDL------YSMEMVPEIFDGLSPGEPRGCIMQAWSYGELIR 590
                                       .....23333344422......25899**************************97 PP

>> GDE_N  Glycogen debranching enzyme N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.2   0.1     2e-57   8.9e-54       2     209 ..       6     209 ..       5     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.2 bits;  conditional E-value: 2e-57
                             GDE_N   2 EwllTNglGGYasgtvagantRryhGlLvaalnppsgRtlllskldeslevsgkvfeLstneypgeiepeGyeyLes 78 
                                       Ewl++N  G+Y+s+t++ antR+yhG+Lv + ++  +R+++lskl e+l ++gk++++ tn ypg++ peG++y+++
  gi|518652710|ref|YP_008142230.1|   6 EWLIANSKGSYSSSTISFANTRTYHGILVKSEQNNYNRYVILSKLYEELAFQGKQYAIDTNYYPGTMWPEGFRYIQD 82 
                                       9**************************************************************************** PP

                             GDE_N  79 FelepvptwtyrvgdvllekqivmpkgentvliaYrlenadepatLrlrpllafRdfheltkanellqksqeeglve 155
                                       ++  p+p  t+++++   +k+++++++++tv+i+Y+  +++ p t++l pllafR+fh+  k++++++   e+++  
  gi|518652710|ref|YP_008142230.1|  83 YSTTPYPSLTFNLEGNICKKSLILDPDADTVVIRYEFPEKT-PDTMNLYPLLAFRSFHNVIKSGQKEFVADEDKGS- 157
                                       ***************************************55.********************99888888774222. PP

                             GDE_N 156 iqaseaepslrlqaskegefqeepvwyynveypeEaerGlddredlyspgyfev 209
                                          s  +  ++l++sk g+f++++ wyyn+ ypeE+erG+++ edly+pg++++
  gi|518652710|ref|YP_008142230.1| 158 --YSFTDGIYSLKISKIGKFINKGLWYYNFIYPEEQERGTNSMEDLYMPGVISI 209
                                       ..334566688999999**********************************987 PP

>> Glyco_hydro_100  Alkaline and neutral invertase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.0   0.00047       2.1     113     204 ..     325     424 ..     321     462 .. 0.62
   2 !    5.4   0.0    0.0014       6.2     354     404 ..     521     569 ..     515     590 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00047
                                       -HHHHHHHHHHHHHHHHHH---HHHHSHHHHHHHHHHHHHHT-..--SSSSSS--B-SS-SS..S-S-SS-...... CS
                   Glyco_hydro_100 113 pvDsslWWiillraYvkatgdlslaeeeevqkgiklilelvla..erfdeaPtllvpdgafm..idRrlgv...... 179
                                       ++D+ lW+i  l+ Y   ++d+s++++  + k ++ i++ +++  e f+    ++    a m  +d + g       
  gi|518652710|ref|YP_008142230.1| 325 SADAPLWFIYALYKYYAYSNDSSFVRS--LLKNVRDIINSYISgnEDFSLDGKFIKVSNAPMtwMDAKNGNtsftpr 399
                                       6899*******************9986..344555555544431134444333322222222123443332111111 PP

                                       -BSBHHHHHHHHHHHHHHHHHS-ST CS
                   Glyco_hydro_100 180 ygapleiqaLlyaalrsakelleee 204
                                        g+p+ei+aL+y++l+  + + + +
  gi|518652710|ref|YP_008142230.1| 400 IGKPVEINALWYNSLKIYTYFCNIS 424
                                       5899999999999999877766655 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0014
                                       TBTTBT-B-GGGHHHHHHHHHHTT-HHHHHHHHHHHHTTHTTTT--S-EES CS
                   Glyco_hydro_100 354 wsYhngGsWpvllWllvaaalkterkelaekaielaekrlskdewaeYydg 404
                                        +Yhng  Wp l    ++a+++ + +  a + ++  ++ +s +  +e +dg
  gi|518652710|ref|YP_008142230.1| 521 RAYHNGTVWPWLAGPYITACVRNGYD--AGNLYRFFSDLYSMEMVPEIFDG 569
                                       58******************998865..45556666666666666666666 PP

>> CotJA  Spore coat associated protein JA (CotJA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1     0.056   2.5e+02      14      30 ..      59      75 ..      56      75 .. 0.83
   2 ?   10.9   0.0     7e-05      0.32      13      35 .]     514     536 ..     511     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.056
                             CotJA 14 elYepeeALkrGTiFpe 30
                                      ++Y  ++    GT++pe
  gi|518652710|ref|YP_008142230.1| 59 KQYAIDTNYYPGTMWPE 75
                                      78888888889*****8 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 7e-05
                             CotJA  13 eelYepeeALkrGTiFpeLdkPF 35 
                                        +++e ++A ++GT++p L  P+
  gi|518652710|ref|YP_008142230.1| 514 GPVMERDRAYHNGTVWPWLAGPY 536
                                       68999**************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (610 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.59u 0.30s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 4088.70
//
Query:       gi|518652711|ref|YP_008142231.1|  [L=372]
Description: hypothetical protein FACI_IFERC00001G1350 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   87.4   0.0    1.5e-24   86.5   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
      1e-20   74.5   0.0    1.6e-20   73.8   0.0    1.2  1  Glyco_transf_4   Glycosyltransferase Family 4
    6.2e-20   72.0   0.0    9.8e-20   71.4   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
    1.4e-11   45.1   0.0    1.9e-11   44.7   0.0    1.2  1  Glyco_trans_4_4  Glycosyl transferase 4-like domain
      4e-10   39.8   0.1    3.3e-08   33.5   0.0    3.0  3  Glyco_transf_5   Starch synthase catalytic domain


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.5   0.0   4.1e-28   1.5e-24      10     133 ..     191     313 ..     185     347 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.5 bits;  conditional E-value: 4.1e-28
                                       TTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSH CS
                   Glycos_transf_1  10 gknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredl 86 
                                       + +++++++l+ gr++ +Kg++ + + ++++++  ++nvk+v+aG g++  e+++ a +++ +++v+f g+v+ ++ 
  gi|518652711|ref|YP_008142231.1| 191 VSYKRERMLLYFGRVTSQKGPKFFMEMADKVNQY-EKNVKFVMAGTGDMIGEMESYAVNHGFREKVFFPGFVDFHKA 266
                                       567899*************************875.**************************************999* PP

                                       HHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHT CS
                   Glycos_transf_1  87 eellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkd 133
                                       +e++k++ +fv+p+ sE+fGi++lE+m +g pvi s++ g+ e +++
  gi|518652711|ref|YP_008142231.1| 267 IEYYKRSGVFVIPAVSEPFGITVLESMVSGSPVIMSKTTGVGEALNN 313
                                       ****************************************9998765 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   4.4e-24   1.6e-20      65     166 ..      82     182 ..      48     185 .. 0.82

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 4.4e-24
                    Glyco_transf_4  65 rrllkrekpDvv...HahspaalgaallalrrrlgiplVltvHglyekrllkarlkplsrllralerrllrradrvi 138
                                       r+++++++pD v   H+h+++++  a++ ++ + giplV+t+H++++     a+ +p+ ++  ++e+  + +ad++i
  gi|518652711|ref|YP_008142231.1|  82 RNVIENFRPDGVsviHCHDWITF-RAGIDIKEKFGIPLVVTFHSTEY--DRSAYFNPQGNIM-KIEKEGAEKADAII 154
                                       455666655544444*******7.88899999**************4..4445555555554.569999******** PP

                    Glyco_transf_4 139 avSeatadelrerygvppekitVipnGv 166
                                       +vS++t+  l+e+yg++++kit+++nGv
  gi|518652711|ref|YP_008142231.1| 155 TVSNSTKGVLVEKYGIDADKITTVYNGV 182
                                       ***************************9 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   0.0   2.7e-23   9.8e-20       2     126 ..     197     327 ..     196     335 .. 0.82

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 2.7e-23
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---...HHHHHHH.T.T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk..dvrlvivGdgp.rpeeleela.a.gleerveftGfv..edlaella 71 
                                       + +l++Gr+   +kg ++++e + ++ +   +v++v++G g+    e+e++a + g++e+v f Gfv  ++  e+++
  gi|518652711|ref|YP_008142231.1| 197 RMLLYFGRV-TSQKGPKFFMEMADKVNQYekNVKFVMAGTGDmI-GEMESYAvNhGFREKVFFPGFVdfHKAIEYYK 271
                                       579******.556**************55425*********965.5999877458************7777****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealae 126
                                       ++ vfv+P   e fg+++lE+m +g pv+++++ g+ e+++ n l v+  d++ +  
  gi|518652711|ref|YP_008142231.1| 272 RSGVFVIPAvsEPFGITVLESMVSGSPVIMSKTTGVGEALN-NVLKVDYWDTDVMSS 327
                                       **********9*********************999999552.335556666665555 PP

>> Glyco_trans_4_4  Glycosyl transferase 4-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.7   0.0   5.3e-15   1.9e-11      70     160 .]      86     181 ..      61     181 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.7 bits;  conditional E-value: 5.3e-15
                   Glyco_trans_4_4  70 rrerpd...vvhahsptaglaarlarrrrgiplvvtlhglllrrg..sgavrrlyralerrllrradavlvvseaea 141
                                       + +rpd   v+h+h++ +  a+  ++ + giplvvt+h+++++r     ++++++  +e+  +  ada+++vs++  
  gi|518652711|ref|YP_008142231.1|  86 ENFRPDgvsVIHCHDWITFRAGIDIKEKFGIPLVVTFHSTEYDRSayFNPQGNIM-KIEKEGAEKADAIITVSNSTK 161
                                       566777777********999999999899************99886655666666.9******************** PP

                   Glyco_trans_4_4 142 eelra.lgvpadrvvvvpng 160
                                         l++ +g++ad++++v ng
  gi|518652711|ref|YP_008142231.1| 162 GVLVEkYGIDADKITTVYNG 181
                                       *****9************98 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 ?    2.5   0.0     0.028        99       1      22 [.       2      22 ..       2      27 .. 0.89
   2 !   33.5   0.0   9.3e-12   3.3e-08     120     235 ..      82     169 ..      64     178 .. 0.76
   3 ?   -2.0   0.0      0.67   2.4e+03      29      77 ..     315     366 ..     297     369 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.028
                    Glyco_transf_5  1 kilfvasEvaplaktGGLadvv 22
                                      k+ +v++E +p a  GGL+ ++
  gi|518652711|ref|YP_008142231.1|  2 KVAVVGWELPP-AFSGGLGIHT 22
                                      7999*******.*******876 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 9.3e-12
                    Glyco_transf_5 120 raalelleklgwkpdvihahDWhtalvpallkel.ykerglfkkiktvftiHNlayqgrfpkdel.aalglpaedfe 194
                                       r ++e  +    ++ vih+hDW t  +++ +ke           i++v+t H+++y+++   ++  +          
  gi|518652711|ref|YP_008142231.1|  82 RNVIENFRP--DGVSVIHCHDWITFRAGIDIKEKfG--------IPLVVTFHSTEYDRSAYFNPQgN---------- 138
                                       445555555..4699******************844........*************8888544322.......... PP

                    Glyco_transf_5 195 kldglefygkvnflkagivyadavttVSptyakEiltpefg 235
                                                 ++  k g   ada++tVS++++  +++++ g
  gi|518652711|ref|YP_008142231.1| 139 ---------IMKIEKEGAEKADAIITVSNSTKGVLVEKY-G 169
                                       .........355667999999999999999987777665.3 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.67
                    Glyco_transf_5  29 LaklghdvrvilPrygaikeekkeleevaelskaaed.evevev...ekvkva 77 
                                       L+    d +v++ +  +i ++ k+l+e+ +l+ ++e+ ++++e    ++++v+
  gi|518652711|ref|YP_008142231.1| 315 LKVDYWDTDVMSSYAISILNH-KSLRETLSLYGKYEGmSFTWEKsaiKTMEVY 366
                                       444555555555444444443.4677788888777777766663234555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 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:                        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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.47
# Mc/sec: 2396.07
//
Query:       gi|518652712|ref|YP_008142232.1|  [L=377]
Description: hypothetical protein FACI_IFERC00001G1351 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-53  182.5   4.8    2.5e-53  181.4   4.8    1.5  1  Glyco_hydro_57   Glycosyl hydrolase family 57
    1.2e-06   28.4   0.0    2.1e-06   27.6   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase
  ------ inclusion threshold ------
      0.075   12.7   0.0       0.12   12.0   0.0    1.3  1  dCache_3         Double sensory domain of two-component senso


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 !  181.4   4.8   4.2e-57   2.5e-53       1     323 [.       5     281 ..       5     283 .. 0.93

  Alignments for each domain:
  == domain 1  score: 181.4 bits;  conditional E-value: 4.2e-57
                                       EEEEEE-----TTS-SSSSSHHHHHHHHHHTHHHHHHHHHHHHHTT----EEEEE-HHHHHHHT-HHHHHHHHHHHH CS
                    Glyco_hydro_57   1 afvfhqHqplykkpgkgeytlpwvrehaaedYiklalilekfpkvhvtfeLsgsLiaqLeeylngekksylpateel 77 
                                       af+f+ Hqpl+ +p       +  +       ++ + +  +f++++                    + sy+pat++l
  gi|518652712|ref|YP_008142232.1|   5 AFYFELHQPLRLRPL------KIQDRPDKMGIFWEEQNRDIFKRIS--------------------EISYIPATKLL 55 
                                       688888888888887......3333333334577888888888888....................99999999999 PP

                                       HHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHT.TT-HHHHHHHHHHCTSEEEEEE-TT-B-GGG-S-HHHHH CS
                    Glyco_hydro_57  78 lelieeglerctelkldlavlfnlaisgplleqiqkwlnkevlelfrelqesgqvElltspyyHpllpllpdsedie 154
                                       +e+          +k       ++++sg+++eq+ k+  +e+++ ++++++sg +El++++y H+l++++++ ++++
  gi|518652712|ref|YP_008142232.1|  56 MES---------GIK------STFSLSGTFIEQALKY-SPETIDVIDDYVKSGLCELMGETYFHSLASIWNE-DEFK 115
                                       999.........799......****************.**********************************.**** PP

                                       HHHHHHHHHHHHHHSS--SBEE-GGG-B--SHHHHHHHTT--EEEE-C------------TTS-EE-TTS.-EEEE- CS
                    Glyco_hydro_57 155 aqvkkarelyeeyfgqePrgfwlpElavspeileilaelGfeylftdelaeiledkskespyrpyllknggiavffR 231
                                        qv+++   ++++f+++P+ f+++El+++++i+e+ +++Gf+ +++++++ei++++   sp+ +yl++ g +++++R
  gi|518652712|ref|YP_008142232.1| 116 YQVNEQMHSIKSIFNYSPVSFRNTELIYNNRIAEMARDMGFRNILAEGTEEISRRY---SPNFRYLSPSG-VNLYLR 188
                                       ********************************************************...*********88.****** PP

                                       -CHH-TTTSGGG-................TTSB..........-TT---TTT-..-BB-TT-S---HHHHHHHHHHH CS
                    Glyco_hydro_57 232 dreLsddigFrys....eqypleavddfinwlkkvkkaksevvtialdgEnwg..hypetgkkeFleklyeeleeng 302
                                       ++ +sd+i+Fr+s    + ypl ++d++i+w++++   +++++++++d+E++g  +++etg+++F+ +l +++e+ g
  gi|518652712|ref|YP_008142232.1| 189 NYPMSDNISFRFSntawSGYPL-TADKYIQWIQNS---PGDIMNLYMDYETFGehQRKETGIFDFVHYLGKYIEQYG 261
                                       *****************99***.**********88...***************9*********************** PP

                                       HHHHHHHHHHHHHHSS-EEEE CS
                    Glyco_hydro_57 303 lielvtpsefikklkpkglik 323
                                        +e++++ e+  k+  k++++
  gi|518652712|ref|YP_008142232.1| 262 -METLKIDEIQAKFSVKDTVS 281
                                       .*********99998888766 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   3.6e-10   2.1e-06      24     123 ..      51     158 ..      47     159 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 3.6e-10
                                       HHHHHHHCT--EEEEE-HHHHCH-.......HHHHHHHHHTT.EEEEE--SS--EGGGSHHHHHHHHHHHHHHHHHH CS
                   Polysacc_deac_1  24 ilpvLkkykvkatffvigglvedy.......pdevremaasG.veignHtinhsnlkrlseeevrreierakdalrk 92 
                                       + ++L + ++k tf ++g+ +e+         d +   ++sG +e+   t+ hs  + + e+e++ ++++  + +++
  gi|518652712|ref|YP_008142232.1|  51 ATKLLMESGIKSTFSLSGTFIEQAlkyspetIDVIDDYVKSGlCELMGETYFHSLASIWNEDEFKYQVNEQMHSIKS 127
                                       56899***************9999999*9999********************************************* PP

                                       HHS----EEE-GGGEE-HHHHHHHHHTT.EE CS
                   Polysacc_deac_1  93 algreprlfryPygsasatvlevarelgfay 123
                                       +++  p+ fr   + +++++ e+ar++gf+ 
  gi|518652712|ref|YP_008142232.1| 128 IFNYSPVSFRNTELIYNNRIAEMARDMGFRN 158
                                       *****************************85 PP

>> dCache_3  Double sensory domain of two-component sensor kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0     2e-05      0.12       2      73 ..     119     189 ..     118     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2e-05
                          dCache_3   2 nqvkeqLeaslqtaenlleqeedqllallelvasspgvaeaisegdreqlerlldsiwndlgleqivlldad 73 
                                       n+++++++++++ + +++ + e ++ +++  +a+++g+++++ +  +e+++r  ++++ +l ++++ l+ ++
  gi|518652712|ref|YP_008142232.1| 119 NEQMHSIKSIFNYSPVSFRNTELIYNNRIAEMARDMGFRNIL-AEGTEEISRRYSPNFRYLSPSGVNLYLRN 189
                                       567889999999999*************************77.8899***************9999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       531  (0.0296168); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2602.32
//
Query:       gi|518652713|ref|YP_008142233.1|  [L=77]
Description: hypothetical protein FACI_IFERC00001G1352 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.021   15.0   0.0      0.028   14.6   0.0    1.4  1  zinc_ribbon_13   Nucleic-acid-binding protein containing Zn-r
      0.044   13.4   0.2      0.088   12.5   0.2    1.5  1  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.2e-06     0.028      30      50 ..      43      63 ..      14      69 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.2e-06
                    zinc_ribbon_13 30 nkkfitvsCknCgYtelYkae 50
                                      +++f++  C++Cg +elY+++
  gi|518652713|ref|YP_008142233.1| 43 TQTFTLYKCNTCGKVELYEPQ 63
                                      578***************987 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   9.8e-06     0.088       3      15 ..      45      57 ..      43      61 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-06
                                      TT-EEE-TTT--E CS
                   Desulfoferrod_N  3 klevYkCevCGni 15
                                      +   YkC+ CG +
  gi|518652713|ref|YP_008142233.1| 45 TFTLYKCNTCGKV 57
                                      5678*******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 536.54
//
Query:       gi|518652714|ref|YP_008142234.1|  [L=79]
Description: hypothetical protein FACI_IFERC00001G1353 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       870  (0.0485247); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); 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 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 536.35
//
Query:       gi|518652715|ref|YP_008142235.1|  [L=196]
Description: methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-10   39.4   0.0    4.1e-10   39.2   0.0    1.1  1  RrnaAD           Ribosomal RNA adenine dimethylase
    1.9e-06   27.8   0.1    2.3e-06   27.5   0.1    1.1  1  Methyltransf_31  Methyltransferase domain
    9.3e-06   25.5   0.1    1.8e-05   24.6   0.1    1.4  1  Met_10           Met-10+ like-protein
      2e-05   25.2   0.0    3.6e-05   24.4   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    0.00022   20.8   0.0    0.00032   20.3   0.0    1.2  1  Methyltransf_5   MraW methylase family
    0.00043   19.9   0.0    0.00059   19.4   0.0    1.1  1  MTS              Methyltransferase small domain
    0.00074   20.1   0.0     0.0018   18.9   0.0    1.6  2  Methyltransf_11  Methyltransferase domain
    0.00097   19.8   0.0     0.0015   19.3   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
     0.0015   18.6   0.0     0.0023   17.9   0.0    1.3  1  Methyltransf_32  Methyltransferase domain
     0.0031   17.4   0.4      0.008   16.0   0.3    1.9  1  PRMT5            PRMT5 arginine-N-methyltransferase
     0.0033   17.1   0.0     0.0041   16.8   0.0    1.1  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0085   15.9   0.0      0.012   15.4   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.021   13.9   0.0      0.028   13.5   0.0    1.2  1  DREV             DREV methyltransferase
      0.043   12.9   0.0       0.07   12.2   0.0    1.3  1  Fibrillarin      Fibrillarin
      0.064   13.4   0.0      0.092   12.9   0.0    1.3  1  FtsJ             FtsJ-like methyltransferase
       0.16   11.8   0.0        0.5   10.2   0.0    1.7  2  Methyltransf_23  Methyltransferase domain


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   3.7e-13   4.1e-10      19      91 ..      35     109 ..      26     144 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.7e-13
                                       HHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHH CS
                            RrnaAD  19 ineIldklnleekltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklskdeklkvvhqDflkfetp 91 
                                       +n+I++k++l++++ ++++g+G G+ ++ +a+ +   +v ++E  ++ + +lq +l + ++ +vv++++   +++
  gi|518652715|ref|YP_008142235.1|  35 YNKIVEKMDLKPDDVIIDMGAGDGFYSKLFADKLknGKVYAIERNPDVLPHLQRNLMEMKNFEVVNENMCHVDIK 109
                                       79********************************6668******************************9887765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.1   2.1e-09   2.3e-06       3     113 ..      46     149 ..      44     182 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 2.1e-09
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                        + +++D G+G G++++ +a++l ++++v+ i+++++++ + + n+   + +n+e+  +++ + +  ++   f+ i+
  gi|518652715|ref|YP_008142235.1|  46 PDDVIIDMGAGDGFYSKLFADKL-KNGKVYAIERNPDVLPHLQRNL--MEMKNFEVVNENMCHVD--IK--GFNKIF 115
                                       56789***************765.79****************9995..5999**********999..55..7***** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedpr 113
                                          v++++   ++i+  ++r+ k+   + + +++
  gi|518652715|ref|YP_008142235.1| 116 FSTVFHDIECREDIIDFMIRNSKKPLNVYLIEFN 149
                                       *********************9998888888777 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   1.6e-08   1.8e-05      96     149 ..      41      95 ..      28     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1.6e-08
                                       TT.--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT- CS
                            Met_10  96 kl.veegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkv 149
                                       k+  ++++v++d+ AG G+++   a   k+ +v+ai+ nP+    l++n+   k 
  gi|518652715|ref|YP_008142235.1|  41 KMdLKPDDVIIDMGAGDGFYSKLFADKLKNGKVYAIERNPDVLPHLQRNLMEMKN 95 
                                       345799***************9999999999*****************9865554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   3.2e-08   3.6e-05       1      78 [.      50     124 ..      50     141 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 3.2e-08
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       ++d+G+G G +++ +a++l+++kv++++ +++ l + ++++ e   n+e+v+ ++ +++ +   f+ ++ s ++h +
  gi|518652715|ref|YP_008142235.1|  50 IIDMGAGDGFYSKLFADKLKNGKVYAIERNPDVLPHLQRNLME-MKNFEVVNENMCHVDIKG--FNKIFFSTVFHDI 123
                                       79*****************99********************64.44*********9998765..8888887667765 PP

                                       S CS
                   Methyltransf_25  78 s 78 
                                       +
  gi|518652715|ref|YP_008142235.1| 124 E 124
                                       4 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   2.9e-07   0.00032      10      80 ..      36     105 ..      28     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.9e-07
                                       HHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EEEEES-GGG CS
                    Methyltransf_5  10 qevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrltlvkgnfke 80 
                                       +++ve ++ k+d v iD+  G+g  s+ + ++l++ ++++i+r +++l + +++L e+++ +++v++n  +
  gi|518652715|ref|YP_008142235.1|  36 NKIVEKMDLKPDDVIIDMGAGDGFYSKLFADKLKNGKVYAIERNPDVLPHLQRNLMEMKN-FEVVNENMCH 105
                                       678999*************************************************99976.8888887755 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.2e-07   0.00059      24     130 ..      39     142 ..      36     144 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.2e-07
                                       HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEE CS
                               MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdl 100
                                       +e+++ + ++ ++D+G+G G+ +  +a++ ++ +v +++ +   l   ++nl + k + evv++++ +    k f+ 
  gi|518652715|ref|YP_008142235.1|  39 VEKMDLKPDDVIIDMGAGDGFYSKLFADKLKNGKVYAIERNPDVLPHLQRNLMEMK-NFEVVNENMCHVDI-KGFNK 113
                                       67888888999*****************************************9887.58888888876544.79999 PP

                                       EEE---STTTCHCHHHHHHHHHHHHHHHEE CS
                               MTS 101 ivsNPPfhagkatelavaeeliaeAkeaLk 130
                                       i     fh+ +  ++++++ +i+++k+ L+
  gi|518652715|ref|YP_008142235.1| 114 IFFSTVFHDIEC-REDIIDFMIRNSKKPLN 142
                                       999999998765.88899999999988775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.6e-06    0.0018       2      82 ..      52     131 ..      51     139 .. 0.87
   2 ?   -2.4   0.0         7   7.9e+03      52      64 ..     179     191 ..     164     194 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.6e-06
                                       EET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   2 dvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       d+G+G G +++ +a++   ++v++++ ++ +l   +++  e ++ +e+v +++ ++ ++   f  ++ s v+h +e 
  gi|518652715|ref|YP_008142235.1|  52 DMGAGDGFYSKLFADKLknGKVYAIERNPDVLPHLQRNLMEMKN-FEVVNENMCHVDIKG--FNKIFFSTVFHDIEC 125
                                       99************777789************999999999985.999******987776..999********9987 PP

                                       HHHHHH CS
                   Methyltransf_11  77 pekalk 82 
                                       +e++++
  gi|518652715|ref|YP_008142235.1| 126 REDIID 131
                                       777765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7
                                       CCCTSS-TT-EEE CS
                   Methyltransf_11  52 aeklpfednsfDl 64 
                                       a ++ fe n+fD 
  gi|518652715|ref|YP_008142235.1| 179 ALHMDFEYNYFDS 191
                                       4567899999996 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.3e-06    0.0015       2      87 ..      52     131 ..      51     143 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.3e-06
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhh 78 
                                       + G+G+G +++ +++kl++ ++++++ +p+++++ ++ l + +n     +e+ +++    d +  f  ++ s v+h 
  gi|518652715|ref|YP_008142235.1|  52 DMGAGDGFYSKLFADKLKNGKVYAIERNPDVLPHLQRNLMEMKN-----FEVVNENMCHVDIK-GFNKIFFSTVFHD 122
                                       89******************************999999999885.....44444444433333.9999********* PP

                   Methyltransf_12  79 lkdirevld 87 
                                       ++ +++++d
  gi|518652715|ref|YP_008142235.1| 123 IECREDIID 131
                                       *55544444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0     2e-06    0.0023      15      75 ..      37      94 ..      24     117 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2e-06
                   Methyltransf_32 15 kllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklg 75
                                      k++++ ++ +++  ++D+GaG g+ s   a+  k ++ kv++i+ + ++  + ++   +++
  gi|518652715|ref|YP_008142235.1| 37 KIVEK-MDLKPDDVIIDMGAGDGFYSKLFAD--KLKNGKVYAIERNPDVLPHLQRNLMEMK 94
                                      45555.46688999*****************..4489*********998877766555554 PP

>> PRMT5  PRMT5 arginine-N-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   7.2e-06     0.008      30     143 ..      22     117 ..       4     144 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 7.2e-06
                                       HHHHCC-CCHHHHHHHHHHHHHHHHCTCCGTCC.-EEEEEEES-TTSHHHHHHHHHHHHHCCCEEEEEEEES-HHHH CS
                             PRMT5  30 YevFEkdkvKYelYeeAiekalsdlkkekkkksekklvilvvGaGRGplvdralkaleetkvtkvkivavEKnpnav 106
                                       Ye   + + KY  Y++ +ek           + + + vi+ +GaG G   +  l a +    ++ k++a+E+np+ +
  gi|518652715|ref|YP_008142235.1|  22 YERIKEFREKYIPYNKIVEK----------MDLKPDDVIIDMGAGDGFYSK--LFADK---LKNGKVYAIERNPDVL 83 
                                       44444444444444444433..........233344578888999985443..33322...23469*********** PP

                                       HHHHHHHHHHTTCCGCEEEES-CCCCCHCC-ECEEEE CS
                             PRMT5 107 vtLqkkvneekWeekveviksdmrelkaeekvdllvs 143
                                        +Lq+++ e    ++ ev++++m +++++    +  s
  gi|518652715|ref|YP_008142235.1|  84 PHLQRNLMEM---KNFEVVNENMCHVDIKGFNKIFFS 117
                                       ***9885433...458999999999988876666655 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   3.7e-06    0.0041       4      89 ..      42     125 ..      39     144 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 3.7e-06
                                       H---TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHH.HCC.. CS
                   Methyltr_RsmB-F   4 LapqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkv.lggel 79 
                                       +++++++ i+D+ a+ G    + a+ + ++g+v+A+++n   l ++++nl  +  +n  v++  + ++d     +++
  gi|518652715|ref|YP_008142235.1|  42 MDLKPDDVIIDMGAGDGFYSKLFADKL-KNGKVYAIERNPDVLPHLQRNLMEM--KNFEVVNENMCHVDIKgFNKIF 115
                                       67899************9999999874.6799*****************9654..4555555555555422123355 PP

                                       EEEEEEEE-- CS
                   Methyltr_RsmB-F  80 fDriLlDaPC 89 
                                       f  +  D  C
  gi|518652715|ref|YP_008142235.1| 116 FSTVFHDIEC 125
                                       6666666666 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 !   15.4   0.0   1.1e-05     0.012      64     123 ..      37      95 ..      32     122 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                                       HHHHHTT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTT CS
                              PCMT  64 lalellelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldl 123
                                       +++e ++lk+ + ++++G+G G+ + ++a  ++ +g+v +ier +++  + +rnl + + 
  gi|518652715|ref|YP_008142235.1|  37 KIVEKMDLKPDDVIIDMGAGDGFYSKLFADKLK-NGKVYAIERNPDVLPHLQRNLMEMKN 95 
                                       5688899***********************997.688***********999999976654 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.5e-05     0.028      89     143 ..      40     102 ..      26     125 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.5e-05
                              DREV  89 pasdqe.dkklldlGaGdGeitkrvaptfee..vyatelsetm.....rdrlkkkkynvlsal 143
                                        + d + d  ++d+GaGdG  +k  a+ +++  vya e    +     r+ ++ k+++v+ ++
  gi|518652715|ref|YP_008142235.1|  40 EKMDLKpDDVIIDMGAGDGFYSKLFADKLKNgkVYAIERNPDVlphlqRNLMEMKNFEVVNEN 102
                                       444444145679****************99888*****8766511111455567888888776 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   6.3e-05      0.07      62     114 ..      38      93 ..      25     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.3e-05
                                       T-S--S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHH....HHHHHH CS
                       Fibrillarin  62 glkelpikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvl....reliev 114
                                        ++++ +k+++ ++ +Ga+ G      +D ++ +g+vya+e  p vl    r+l+e+
  gi|518652715|ref|YP_008142235.1|  38 IVEKMDLKPDDVIIDMGAGDGFYSKLFADKLK-NGKVYAIERNPDVLphlqRNLMEM 93 
                                       578999************************99.********9887651111555554 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.2e-05     0.092      11      70 ..      37     103 ..      35     137 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.2e-05
                                       HHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS.........HHHTTEEEECS-C CS
                              FtsJ  11 eidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm.........aplpgvttiqgdi 70 
                                       +i ek++ +kp++ ++D ga+ G +s+  + +l++ gkv+a+  +p            +++ ++++ + 
  gi|518652715|ref|YP_008142235.1|  37 KIVEKMD-LKPDDVIIDMGAGDGFYSKLFADKLKN-GKVYAIERNPDvlphlqrnlMEMKNFEVVNENM 103
                                       5789999.99***********************86.******999987666665333336666665554 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00045       0.5       7      62 ..      23      95 ..      17     157 .. 0.66
   2 ?   -1.0   0.0       1.2   1.4e+03     149     161 ..     165     177 ..     160     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00045
                   Methyltransf_23  7 eelsdklerllpk........lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.......k 62
                                      e++++++e+  p+        l+++  ++d+G+G+G  +++++++ +  +v++++ +p   + ++       +
  gi|518652715|ref|YP_008142235.1| 23 ERIKEFREKYIPYnkivekmdLKPDDVIIDMGAGDGFYSKLFADKLKngKVYAIERNPDVLPHLQrnlmemkN 95
                                      55666666666554444446578888****************9988877999999998766655454444330 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
                   Methyltransf_23 149 rslkelleeaGle 161
                                       ++l++++ e+G++
  gi|518652715|ref|YP_008142235.1| 165 DELNKIFTESGFQ 177
                                       79**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       653  (0.0364214); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.67u 0.35s 00:00:01.02 Elapsed: 00:00:00.58
# Mc/sec: 1018.39
//
Query:       gi|518652716|ref|YP_008142236.1|  [L=307]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-17   63.1   3.0    4.6e-17   62.4   3.0    1.3  1  DDE_Tnp_1     Transposase DDE domain
    1.6e-12   47.7   0.1    1.7e-11   44.4   0.0    2.1  2  DDE_Tnp_1_5   Transposase DDE domain
      2e-05   24.7   0.8    9.5e-05   22.4   0.8    2.0  1  DDE_Tnp_1_3   Transposase DDE domain
  ------ inclusion threshold ------
      0.017   14.6   0.1      0.037   13.5   0.1    1.5  1  PhoH          PhoH-like protein
        0.1   12.6   0.3        0.4   10.8   0.0    2.2  2  La            La domain
        0.1   12.5   1.1        2.4    8.1   0.2    2.8  3  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.4   3.0   1.5e-20   4.6e-17       7     191 ..     128     276 ..     123     299 .. 0.80

  Alignments for each domain:
  == domain 1  score: 62.4 bits;  conditional E-value: 1.5e-20
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvla 82 
                                        i+D+t  +++  +   + g+k ++k+k ++klh++++++   +ls+ it+  +hdsk+++ ll  ++  +  ++++
  gi|518652716|ref|YP_008142236.1| 128 CIIDSTGYKITIRG--DYLGHKwHKKRKGWLKLHVIISLKDVNVLSFTITDEHTHDSKAARKLLSKMKN-NILRIFG 201
                                       68999998886666..6669999999*****************************************98.******* PP

                         DDE_Tnp_1  83 DaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntns 159
                                       D+GY+  +++  +   g++ +i+++kn+ ++++   s +r ++ + ++++ ++++++ +                  
  gi|518652716|ref|YP_008142236.1| 202 DRGYD-SKYIYNMF--GYNAVIPPRKNASTKSR--GSSTRAKIVRFIKKNSMEQWKENNS----------------- 256
                                       ****9.77777777..7***********99977..2334566666666666666666444................. PP

                         DDE_Tnp_1 160 ellsaeevaelyrlRwqiErvFkwlkrkfgld 191
                                                  y +Rw +E  F+ lkr++  +
  gi|518652716|ref|YP_008142236.1| 257 -----------YGKRWIVEIYFSGLKRVMT-E 276
                                       ...........6***************764.4 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   5.7e-15   1.7e-11      19     110 ..      51     138 ..      38     140 .. 0.88
   2 ?    0.8   0.1       0.2     6e+02       3      32 ..     236     265 ..     234     280 .. 0.81

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 5.7e-15
                       DDE_Tnp_1_5  19 kekkkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsrraktlevkipvkrks 95 
                                        e+k++gk g+p++ +da i  +  ++ +f++p+R l+G+++sl  ++g+  +   ys + rr ++++ ++   ++ 
  gi|518652716|ref|YP_008142236.1|  51 LEEKNSGKIGHPYKVPDALIMYLARLRSIFNVPFRSLEGILRSLAIITGI--KSISYSEIFRRIRRIKPELNNINN- 124
                                       356788*****************************************999..8899***********999955555. PP

                       DDE_Tnp_1_5  96 kglhlvvdstGlkvl 110
                                         l  ++dstG k++
  gi|518652716|ref|YP_008142236.1| 125 -KLDCIIDSTGYKIT 138
                                       .59*********986 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.2
                       DDE_Tnp_1_5   3 RGsltiwldeeaiaawkekkkngkrgrpqv 32 
                                       R +++ ++ ++ +++wke++  gkr   + 
  gi|518652716|ref|YP_008142236.1| 236 RAKIVRFIKKNSMEQWKENNSYGKRWIVEI 265
                                       7778889999999***99999999866555 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.8   3.2e-08   9.5e-05      37     102 ..     150     216 ..     145     282 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.2e-08
                       DDE_Tnp_1_3  37 kssmGWfyGfkLhliindk.GeilavkltpgnvdDrepveelakellg...klfaDkgyiskklaeelle 102
                                       k   GW   +kLh+ii+ k  ++l++++t+  ++D + +++l +++++   ++f+D+gy sk + +++  
  gi|518652716|ref|YP_008142236.1| 150 KKRKGW---LKLHVIISLKdVNVLSFTITDEHTHDSKAARKLLSKMKNnilRIFGDRGYDSKYIYNMFGY 216
                                       666788...5******966269*****************998887776222579*******999877644 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   1.2e-05     0.037      76     117 ..     263     304 ..     256     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                              PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                       v++y++ l   ++++++a+k+e+++++  ++v++ + mRG T
  gi|518652716|ref|YP_008142236.1| 263 VEIYFSGLKRVMTEVIKAKKIEYIIQELALKVVNYNIMRGMT 304
                                       789*************************************98 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00013       0.4      18      48 ..     142     172 ..     139     187 .. 0.86
   2 ?   -3.7   0.1       4.4   1.3e+04       5      10 ..     263     268 ..     263     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00013
                                       HHHHHHHTTSTTS---HHHHHTSSHHHHHHS CS
                                La  18 kFLrkkmdkdpegwVplsliasfkrmkkltk 48 
                                       ++L  k  k+ +gw +l++i+s k ++ l+ 
  gi|518652716|ref|YP_008142236.1| 142 DYLGHKWHKKRKGWLKLHVIISLKDVNVLSF 172
                                       689999999999**************98875 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                                       HHHHHH CS
                                La   5 vEfYFS 10 
                                       vE YFS
  gi|518652716|ref|YP_008142236.1| 263 VEIYFS 268
                                       899**9 PP

>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0     0.085   2.5e+02      34     100 ..      36     130 ..      25     138 .. 0.54
   2 ?    8.1   0.2    0.0008       2.4      16      48 ..     180     212 ..     168     266 .. 0.72
   3 ?   -0.5   0.2      0.37   1.1e+03      12      37 ..     254     279 ..     216     291 .. 0.50

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.085
                                       HHHHHCTSEEEEEEE.CCC......................CCCEEEEE-BSS...S-SBSSSEEEE-SB..TTC-- CS
                      Ribosomal_S8  34 kvLkeeGyikdfeve.eek......................kkkikielkynk...kkksvikklkrvsk..pgrrv 82 
                                       + L++  +ikd+++  eek                      ++++++  +  +   ++  +i+++k +s     rr+
  gi|518652716|ref|YP_008142236.1|  36 EYLTDLSFIKDYDTLlEEKnsgkighpykvpdalimylarlRSIFNVPFRSLEgilRSLAIITGIKSISYseIFRRI 112
                                       56788889999999865554544444444433333333332222455444444333345566666666552223555 PP

                                       EE-CCC---CGGGTSEEE CS
                      Ribosomal_S8  83 YakvkelpkvlnglGiai 100
                                          + el+++ n l ++i
  gi|518652716|ref|YP_008142236.1| 113 RRIKPELNNINNKLDCII 130
                                       555555555555555555 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0008
                                       TT-SEEEEE--HHHHHHHHHHHHCTSEEEEEEE CS
                      Ribosomal_S8  16 akkeevevpasklkeeilkvLkeeGyikdfeve 48 
                                         ++ ++   sk+k++il+++ ++Gy +++ ++
  gi|518652716|ref|YP_008142236.1| 180 HDSKAARKLLSKMKNNILRIFGDRGYDSKYIYN 212
                                       4555566678****************9888773 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.37
                                       HHHHTT-SEEEEE--HHHHHHHHHHH CS
                      Ribosomal_S8  12 NaekakkeevevpasklkeeilkvLk 37 
                                       N++  k+  ve+  s lk+ +++v+k
  gi|518652716|ref|YP_008142236.1| 254 NNSYGKRWIVEIYFSGLKRVMTEVIK 279
                                       22222223334444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.70u 0.36s 00:00:01.06 Elapsed: 00:00:00.60
# Mc/sec: 1549.46
//
Query:       gi|518652717|ref|YP_008142237.1|  [L=209]
Description: hypothetical protein FACI_IFERC00001G1356 [Ferroplasma acidarmanus fer1]
Scores for complete 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   23.9   0.6    6.3e-05   22.7   0.1    2.0  2  ACT_7     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 ?   -2.4   0.0      0.23   4.1e+03      15      15 ..      90      90 ..      76     108 .. 0.51
   2 !   22.7   0.1   3.5e-09   6.3e-05      22      62 ..     160     201 ..     139     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.23
                                      . CS
                             ACT_7 15 g 15
                                      +
  gi|518652717|ref|YP_008142237.1| 90 S 90
                                      2 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 3.5e-09
                                       -HHHHHHHHHHTTT---EEEE-SS-EEEEE.EGGGHHHHHHH CS
                             ACT_7  22 GivaklaspLaeagIsifqiStyrtdyiLV.peedlekAvea 62 
                                       G +  ++  L +agI+i+qi ++++d i++ +e+dl  A ++
  gi|518652717|ref|YP_008142237.1| 160 GYINFITMLLYRAGINILQIISFYSDTIIIlEEKDLTDAFKI 201
                                       677778999************999998877356788888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.60u 0.36s 00:00:00.96 Elapsed: 00:00:00.59
# Mc/sec: 1071.39
//
Query:       gi|518652718|ref|YP_008142238.1|  [L=339]
Description: hypothetical protein FACI_IFERC00001G1357 [Ferroplasma acidarmanus fer1]
Scores for complete 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-39  133.7   0.2      9e-39  133.0   0.2    1.3  1  NOG1_N     NOG1 N-terminal helical domain
    6.1e-17   61.8   0.0    1.2e-16   60.8   0.0    1.5  1  MMR_HSR1   50S ribosome-binding GTPase
    2.5e-16   59.2   0.0    6.5e-16   57.9   0.0    1.8  1  NOG1       Nucleolar GTP-binding protein 1 (NOG1)
    1.1e-08   34.8   0.0    1.9e-08   34.0   0.0    1.4  1  FeoB_N     Ferrous iron transport protein B
     0.0012   18.4   0.0      0.002   17.6   0.0    1.5  1  SRPRB      Signal recognition particle receptor beta subunit
  ------ inclusion threshold ------
      0.012   15.7   1.5        2.3    8.2   0.0    2.8  3  Dynamin_N  Dynamin family
      0.022   14.5   0.8       0.22   11.3   0.8    2.5  1  PduV-EutP  Ethanolamine utilisation - propanediol utilisation
      0.023   14.0   0.0      0.038   13.3   0.0    1.4  1  AIG1       AIG1 family


Domain annotation for each model (and alignments):
>> NOG1_N  NOG1 N-terminal helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0   0.2     4e-42     9e-39       1     159 [.      14     170 ..      14     170 .. 0.96

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 4e-42
                            NOG1_N   1 FekiptvptseelidkalrrakraakttkkkkneikrlrnlearkvrtasntlsdkLeeivkkfPnldelhpFyrel 77 
                                       F  iptv+ s+e+idk++ +a+ + +    kk e +++r+  + ++ t++ +    L +i++kfP +++lhpFy +l
  gi|518652718|ref|YP_008142238.1|  14 FDYIPTVLRSQEIIDKSFHKASNIVEPYFPKK-E-MKIRKEVTDRISTIESISTGHLDKIIRKFPTIETLHPFYFDL 88 
                                       889*********************98888873.4.4789999999******999*********************** PP

                            NOG1_N  78 ldvlvdkdelkksLaqvkwarklirkigkeyvnklkkaddkkeakelrreafgrvasvlkkvdkaldfLedvrkkLr 154
                                       +d++ d+d++k sL++v+w+ ++i++ +  y++klk  ++++e+++++++ +gr +s++k+++k+l +L + r+ Lr
  gi|518652718|ref|YP_008142238.1|  89 IDLMFDVDKYKLSLGNVQWTTDKIKDFSTVYIKKLKGVKTINEMNNIMKQYYGRFSSLIKNINKDLLYLGECRNYLR 165
                                       ***************************************************************************** PP

                            NOG1_N 155 kLpai 159
                                       +Lp i
  gi|518652718|ref|YP_008142238.1| 166 RLPGI 170
                                       ***87 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.8   0.0   5.3e-20   1.2e-16       2      94 ..     177     273 ..     176     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.8 bits;  conditional E-value: 5.3e-20
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS..HHHHHHHHHHHHHHHHCT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgkeielvDtpGlie..gaseekglgkaflaleea 76 
                                       ++i+G pN+GKS+Li++ltg++  ++++p+tT++i  g  +++ ++++++DtpG+++  +++++  +++a+ al + 
  gi|518652718|ref|YP_008142238.1| 177 FIIAGIPNSGKSSLIQKLTGTTPDIASYPFTTKEILIGYKNIGTRRVQFIDTPGILDrpMDDRNDIERRAIIALSKI 253
                                       579*********************************99988989**********98654444445899999999996 PP

                                       .SEEEEEEETT..TTCSHHHH CS
                          MMR_HSR1  77 .dlillvvdas..eeklkpld 94 
                                          il+++d s  + ++++++
  gi|518652718|ref|YP_008142238.1| 254 eGTILFLFDYSgtS-SYTEDQ 273
                                       377******88642.343332 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 !   57.9   0.0   2.9e-19   6.5e-16       1      58 []     241     297 ..     241     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.9e-19
                              NOG1   1 eIEkqAiaALkhladavlFllDpseecgysleeQlsLleeikelfankpvivvlnKiD 58 
                                       +IE++Ai+AL ++++++lFl+D+s+++ y+ ++Q +L++ei   f+ +++i + +KiD
  gi|518652718|ref|YP_008142238.1| 241 DIERRAIIALSKIEGTILFLFDYSGTSSYTEDQQNNLFNEISGSFP-NKIIRIQTKID 297
                                       6*********************************************.57********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 !   34.0   0.0   8.6e-12   1.9e-08       3      59 ..     177     233 ..     175     259 .. 0.89

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 8.6e-12
                                       EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETTEEEEEEE----SS CS
                            FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkgkeveivDlPGiYs 59 
                                       ++++G pn+Gk++l+ +ltg++ +++ +p +t e   g+ ++ +++v+++D PGi +
  gi|518652718|ref|YP_008142238.1| 177 FIIAGIPNSGKSSLIQKLTGTTPDIASYPFTTKEILIGYKNIGTRRVQFIDTPGILD 233
                                       6799**************************************************965 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 !   17.6   0.0   8.9e-07     0.002       4      58 ..     175     230 ..     172     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 8.9e-07
                                       -EEEEE-STTSSHHHHHHHHHHSS---B---S.S-EEETTG...GGTT-SEEEETT CS
                             SRPRB   4 pavllvGlsdsGKTslftrLttdsvkktvtSq.essaalkvksekgskltliDfPG 58 
                                       p+++++G+ +sGK sl+++Lt  +   +      +++   +k+    ++++iD PG
  gi|518652718|ref|YP_008142238.1| 175 PTFIIAGIPNSGKSSLIQKLTGTTPDIASYPFtTKEILIGYKNIGTRRVQFIDTPG 230
                                       89******************9886655554444777777888899999999***99 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.6     8e+03      65      79 ..      50      64 ..      23      92 .. 0.56
   2 ?    6.1   0.2    0.0047        11       5      22 ..     181     198 ..     178     217 .. 0.73
   3 ?    8.2   0.0     0.001       2.3      93     140 ..     213     265 ..     204     296 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.6
                                      CHHHHHHHHHHHHHH CS
                         Dynamin_N 65 fsevreeieketeki 79
                                       +ev++ i+  ++ +
  gi|518652718|ref|YP_008142238.1| 50 RKEVTDRISTIESIS 64
                                      233333333333333 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0047
                                       EBTTTTHHHHHHHHHTS- CS
                         Dynamin_N   5 GsqSsGKSSvlnaLlged 22 
                                       G  +sGKSS++ +L+g  
  gi|518652718|ref|YP_008142238.1| 181 GIPNSGKSSLIQKLTGTT 198
                                       6668***********987 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.001
                                       EEEEETTS-SEEEEE---B-SSSGTTS.....HHHHHHHSTTEEEEEEEETTS CS
                         Dynamin_N  93 lkilsllvkgltlvDlPGldsvnkrdq.....elvkeyikkadiilavtsanh 140
                                       +  +++   ++ ++D+PG+ +++  d      + +  + k +  il++ +++ 
  gi|518652718|ref|YP_008142238.1| 213 IGYKNIGTRRVQFIDTPGILDRPMDDRndierRAIIALSKIEGTILFLFDYSG 265
                                       555666778999*********99999865554333333355556777777765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.8   9.8e-05      0.22       5     111 ..     178     308 ..     175     328 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 9.8e-05
                         PduV-EutP   5 lliGkvgsGKttLtqalkg..............eelkYkktqaiefsdeviDtPGey...lenrkl..ysalivtsa 62 
                                       ++ G  +sGK +L q+l+g                + Yk         ++iDtPG     ++ r+    +a+i++s 
  gi|518652718|ref|YP_008142238.1| 178 IIAGIPNSGKSSLIQKLTGttpdiasypfttkeILIGYKNIG--TRRVQFIDTPGILdrpMDDRNDieRRAIIALSK 252
                                       566778899999999999977766665555532222343322..223467888885433366665411456776665 PP

                         PduV-EutP  63 eadvialvqda.......teeesvfppgfasvfnkeviGiitkidlaedeenieav 111
                                           i ++ d        +++++ + ++++  f  ++i i tkid++e +eni ++
  gi|518652718|ref|YP_008142238.1| 253 IEGTILFLFDYsgtssytEDQQNNLFNEISGSFPNKIIRIQTKIDISERKENICIS 308
                                       555555555541111111234444556677788899***********999999764 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   1.7e-05     0.038      42     117 ..     214     291 ..     176     302 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
                                       EEEEETTEEEEEEE--SCCCTTC..CHHCHHHHHHHHHHHCTT-ESEEEEEEETT.B-SHHHH.HHHHHHHHHHCGG CS
                              AIG1  42 ksrtwdgkkinViDTPglfdlsv..sadkiskeivrclllseegihalllvlslg.rfteede.kalktlkelFGek 114
                                         +    ++++ iDTPg++d     ++d  ++ i+   l + eg   +l++ s +  +te+ + ++++++   F +k
  gi|518652718|ref|YP_008142238.1| 214 GYKNIGTRRVQFIDTPGILDRPMddRNDIERRAII--ALSKIEGTILFLFDYSGTsSYTEDQQnNLFNEISGSFPNK 288
                                       555566789***********875214554455555..4666788999999998886888654415789999999999 PP

                                       GGG CS
                              AIG1 115 ilk 117
                                       i++
  gi|518652718|ref|YP_008142238.1| 289 IIR 291
                                       975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.54
# Mc/sec: 1906.78
//
Query:       gi|518652719|ref|YP_008142239.1|  [L=547]
Description: hypothetical protein FACI_IFERC00001G1358 [Ferroplasma acidarmanus fer1]
Scores for 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-62  210.3   0.1    3.9e-62  209.9   0.1    1.1  1  tRNA-synt_1c    tRNA synthetases class I (E and Q), catalytic
    6.1e-12   45.8   0.0    2.7e-11   43.7   0.0    2.0  1  tRNA-synt_1c_C  tRNA synthetases class I (E and Q), anti-codo


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.9   0.1   4.4e-66   3.9e-62       2     312 ..      95     397 ..      94     399 .. 0.95

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 4.4e-66
                                       -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGH CS
                      tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrf 78 
                                       V+ R aP+P+G LHiGh++ a+ln  + k+++Gk+ilRieDT+p   +++a + i edlkwlg++   + + qs r+
  gi|518652719|ref|YP_008142239.1|  95 VVMRMAPSPSGPLHIGHSRMAILNDEYVKRYGGKLILRIEDTNPGNIDPDAYTMIPEDLKWLGVDV-TETVIQSSRM 170
                                       899***************************************************************.778999**** PP

                                       HHHHHHHHHHHHTTSEEEE-STHHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSS CS
                      tRNA-synt_1c  79 delkkyaeeLikkGkAYvcectkeeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideess 155
                                       + +++ a+++i++G+ Yv e+++ e ++++ +  k+  kerd   + nl+ f ++m +g++++++a + +k d +++
  gi|518652719|ref|YP_008142239.1| 171 EFYYSEAKRMISEGYMYVIEENQQEFHDLKLK--KVPVKERDADPSVNLEKF-DKMISGHYSEGEAALVMKTDINHP 244
                                       ******************************98..777779************.89********************** PP

                                       .GGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEE CS
                      tRNA-synt_1c 156 .vefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfi 231
                                          +rD ++ ri+ ++   h+l+++k+ +yPt +f v +dD+  ++thv+r+ ++l nt+k+  ++ + ++++p++ 
  gi|518652719|ref|YP_008142239.1| 245 nPSIRDWIAFRINTTE---HPLTGSKYSVYPTMNFSVSVDDHYLGLTHVIRGIDHLVNTEKQKYVFMYNNWKIPEYF 318
                                       9***************...*****************************************************88887 PP

                                       EEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHH CS
                      tRNA-synt_1c 232 heylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafd 308
                                       h y  +++ ++ l    ++  +++ ++ +wdd r+ +l++l ++G++pe  r+   r ++ ks   + +++ + ++d
  gi|518652719|ref|YP_008142239.1| 319 H-YGFITIPDTILKTTIIKEGIKSGKYSGWDDIRLGTLKALKKRGYNPETFRKYWVRSGMNKSN-ATFSWEIFDSMD 393
                                       7.5667788888888888888889***************************************9.999999999998 PP

                                       HHHH CS
                      tRNA-synt_1c 309 rkkL 312
                                       r+ +
  gi|518652719|ref|YP_008142239.1| 394 REII 397
                                       8866 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 !   43.7   0.0     3e-15   2.7e-11       2     174 .]     402     538 ..     401     538 .. 0.83

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 3e-15
                    tRNA-synt_1c_C   2 pRymaVldpvkvtienlpegkeeelevplhpknpelgtrkvpfs..keiyiereDakrlkpgeevrLkelynikvee 76 
                                       +Ry +V +p  ++++n +   + + ++ lhp++p+ g r++ +    ++y   + ++++ +ge +rLk+l+++  + 
  gi|518652719|ref|YP_008142239.1| 402 ERYSFVPHPELISLQNAE---PLKSHALLHPQRPDSGFREYSIPaqASVYFPGDEIDKINEGEVIRLKDLCVAVKKG 475
                                       7**************876...899**************997655227***********************9986654 PP

                    tRNA-synt_1c_C  77 vekdesgevtelkleydgesleearkkkgiihWvsaeeaveaevrlYdrLfkeeededfllnpdslkvleeglaepa 153
                                              + +    ++++e +       +ii+W ++ ++ +                 +++ pd++  +++g +ep 
  gi|518652719|ref|YP_008142239.1| 476 N------KLVY--SNIEPEGR------VKIIQWAPE-NSGDL----------------QIFYPDGN--IDKGKLEPL 519
                                       3......3333..45555333......35******6.66777................7899***9..59******8 PP

                    tRNA-synt_1c_C 154 lanlkkgdivQfeRiGyfrvd 174
                                       +++  k  +vQ+eR+Gy+++d
  gi|518652719|ref|YP_008142239.1| 520 ATE--KRGVVQLERYGYVNLD 538
                                       766..89***********987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (547 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3989.11
//
Query:       gi|518652720|ref|YP_008142240.1|  [L=79]
Description: hypothetical protein FACI_IFERC00001G1359 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (79 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); 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 0.31s 00:00:00.77 Elapsed: 00:00:00.51
# Mc/sec: 462.35
//
Query:       gi|518652721|ref|YP_008142241.1|  [L=230]
Description: hypothetical protein FACI_IFERC00001G1360 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1611.81
//
Query:       gi|518652722|ref|YP_008142242.1|  [L=677]
Description: hypothetical protein FACI_IFERC00001G1361 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-51  174.1   0.1    4.3e-51  172.8   0.1    1.7  1  DNA_gyraseB    DNA gyrase B
    2.9e-31  107.4   0.1    5.1e-31  106.6   0.1    1.4  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    9.8e-20   71.1   0.4    7.8e-18   65.0   0.1    2.9  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    9.8e-20   70.7   0.1    2.7e-19   69.3   0.1    1.8  1  Toprim         Toprim domain
    3.8e-05   24.1   0.2    0.00014   22.2   0.1    2.0  2  Toprim_4       Toprim domain
     0.0016   18.3   0.1     0.0035   17.2   0.1    1.6  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.8   0.1   1.4e-54   4.3e-51       1     173 [.     267     435 ..     267     436 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.8 bits;  conditional E-value: 1.4e-54
                       DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktln 77 
                                       Gl ++v++l+++k+ + ke++++++e+  +e   ve+alq+ ++ + + +sFvNni+tpeGGtH++gf ++l +++ 
  gi|518652722|ref|YP_008142242.1| 267 GLVEYVQFLDQGKDIVNKEPIYCREEY--KE-YVVEFALQYIDNVTGTEESFVNNIKTPEGGTHITGFHTGLSRAVL 340
                                       899************************..88.***********9999****************************** PP

                       DNA_gyraseB  78 eyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakki 154
                                       eyak k+l+k     + g+d regltav++vk+ +pqFeGQTKekLgns vksiv++++++ l+ ++e+ + +a++i
  gi|518652722|ref|YP_008142242.1| 341 EYAKAKNLVKGVS-GLIGDDTREGLTAVLHVKMFNPQFEGQTKEKLGNSVVKSIVSSITEKYLKDYFESYPPIADAI 416
                                       *******988866.*************************************************************** PP

                       DNA_gyraseB 155 lekaveaakareaarkare 173
                                       ++++++aa area+rka++
  gi|518652722|ref|YP_008142242.1| 417 IKRVLAAAIAREASRKAKD 435
                                       *****************97 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.1   1.7e-34   5.1e-31       2      63 .]     605     666 ..     604     666 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.7e-34
                     DNA_gyraseB_C   2 kkveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefie 63 
                                       k+v iqRfKGLGEmnpeqLweTTm+pe+R+L+qv+ieda  ad+lf++LmG+kvepRr+fie
  gi|518652722|ref|YP_008142242.1| 605 KNVVIQRFKGLGEMNPEQLWETTMNPESRKLVQVSIEDALYADQLFNILMGEKVEPRRKFIE 666
                                       7899*********************************************************8 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   0.1   2.6e-21   7.8e-18       3      94 ..      65     174 ..      63     222 .. 0.73
   2 ?    3.3   0.1     0.038   1.1e+02      43      86 ..     358     395 ..     312     405 .. 0.88

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.6e-21
                                       HHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT..............GTCSTTCH CS
                         HATPase_c   3 ekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk..............klfekfsq 63 
                                       +++L++++ ++vdN +++  a+ +++i + i   + d +isveD+G+Gip+++++              ++++kf++
  gi|518652722|ref|YP_008142242.1|  65 PDGLHHMVYEVVDNCIDEamAGFGSDINIVIY--K-DGSISVEDDGRGIPVDIHPkykrpgleivmtelHSGAKFDK 138
                                       689***************6656**********..7.9******************************888888**** PP

                                       HCSTCHTSTSSSHHHHHHHHHHH.H.....TTTEEEE CS
                         HATPase_c  64 ddstkrggggtGlGlsivkklve.l.....mgGeiwv 94 
                                        + +k++gg +G+G+ +v++l++ l      g +i++
  gi|518652722|ref|YP_008142242.1| 139 -KVYKVTGGLHGVGVHVVNALSDyLvavvkKGTKIYY 174
                                       .********************9955444441224443 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.038
                                       EESSSSSTTHHHTGTCS.TTCHHCSTCHTSTSSSHHHHHHHHHHH CS
                         HATPase_c  43 eDnGiGipkedlkklfe.kfsqddstkrggggtGlGlsivkklve 86 
                                        D+  G++   + k+f   f         +  + lG s+vk++v+
  gi|518652722|ref|YP_008142242.1| 358 DDTREGLTAVLHVKMFNpQFEG-------QTKEKLGNSVVKSIVS 395
                                       58899************66666.......8899999999999776 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.3   0.1     9e-23   2.7e-19       1     102 [.     464     575 ..     464     576 .. 0.86

  Alignments for each domain:
  == domain 1  score: 69.3 bits;  conditional E-value: 9e-23
                                       EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH.....HHHHHHHHSEEEEE CS
                            Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka.....lkelakradeiila 69 
                                       e++ivEg+s+ +++++a+++++qa+++++G+il++e+ + ++++e  ei++ ++++++     ++   +r+ +ii++
  gi|518652722|ref|YP_008142242.1| 464 EVYIVEGDSAGGSAKQARNREYQAILPLRGKILNVEKsNDNKALEneEIKNLITAIGTnikdkFEIKNLRYGKIIIM 540
                                       589**********************************53333333677777777777787777777789******** PP

                                       CSSSHHHHHHHHHHHHHHTHHHTT..TEEEEEESS CS
                            Toprim  70 tDpDreGeaiawellevlkellen..kigrvefse 102
                                       tD+D++G +i+++ll++++++ ++  ++g+++f++
  gi|518652722|ref|YP_008142242.1| 541 TDADVDGAHIRTLLLTFFYRFMNEliQGGHIYFAQ 575
                                       *******************777777888****997 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.8   1.4e+04      60      75 ..     356     371 ..     355     383 .. 0.75
   2 !   22.2   0.1   4.7e-08   0.00014       6      69 ..     498     549 ..     493     557 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.8
                          Toprim_4  60 aldgDaeGeataerla 75 
                                        +d + eG ++ ++++
  gi|518652722|ref|YP_008142242.1| 356 IGDDTREGLTAVLHVK 371
                                       5789999999988765 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 4.7e-08
                          Toprim_4   6 VEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGea 69 
                                       VE  +D  ale+ +ikn++   g+++  +d+ ++++l++           ++i+++d+D++G  
  gi|518652722|ref|YP_008142242.1| 498 VEKSNDNKALENEEIKNLITAIGTNI--KDKFEIKNLRY----------GKIIIMTDADVDGAH 549
                                       9*************************..7777777****..........99**********965 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   1.2e-06    0.0035       6      47 ..      71     112 ..      67     168 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.2e-06
                       HATPase_c_3   6 AlaelvdNsld.Adaen...vkievnknrgktgeivieDdGkGmse 47 
                                        + e+vdN++d A a     ++i++ k+    g+i++eDdG G++ 
  gi|518652722|ref|YP_008142242.1|  71 MVYEVVDNCIDeAMAGFgsdINIVIYKD----GSISVEDDGRGIPV 112
                                       689********75554466799999996....69*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (677 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4494.54
//
Query:       gi|518652723|ref|YP_008142243.1|  [L=791]
Description: hypothetical protein FACI_IFERC00001G1362 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.5e-150  501.9   0.7   1.5e-150  501.9   0.7    1.6  2  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    2.1e-50  168.0  23.0    3.1e-10   39.4   0.2    7.4  7  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
        0.8   10.6   5.6        1.8    9.4   5.0    1.9  2  FliT           Flagellar protein FliT


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.9   0.7  2.5e-154  1.5e-150       1     421 [.      25     456 ..      25     461 .. 0.98
   2 ?   -1.8   0.1      0.19   1.1e+03     318     389 ..     552     625 ..     530     641 .. 0.72

  Alignments for each domain:
  == domain 1  score: 501.9 bits;  conditional E-value: 2.5e-154
                     DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGn 76 
                                       RaiP+ rDGlKPvqRri+y+m++l  ++dk++kK+a+++Ge++gkYhPHGd+s+y+a+ r+aqdf+++++l+d+qGn
  gi|518652723|ref|YP_008142243.1|  25 RAIPDFRDGLKPVQRRIIYSMYELgVTHDKPYKKSARIIGETMGKYHPHGDSSIYEALARMAQDFSLRYTLIDGQGN 101
                                       9**************************************************************************** PP

                     DNA_topoisoIV  77 fGsildgdkdAaaRYietrLskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipp 153
                                       fGsi dgd +Aa+RY+e+rL k+a+e++++i+ketv +++n+Dgs +EP+++p++iP lL+nG++GIavGmat++ p
  gi|518652723|ref|YP_008142243.1| 102 FGSI-DGDAPAAMRYTEARLGKMAEEMVRDIEKETVPFSPNFDGSLDEPVYFPSRIPQLLINGTSGIAVGMATNMVP 177
                                       ****.************************************************************************ PP

                     DNA_topoisoIV 154 hnlkeiidaliallkgeea...ellelvlgPdfptgggiigkeeikeayetgrGkikvrakveiee.ktivitElPi 226
                                       hnl+ei da+++ ++++++   +ll++v+gPdfp+gg+i++++++ + y+tg+Gk+  +++++ ee k+i+i+ lP+
  gi|518652723|ref|YP_008142243.1| 178 HNLSEISDAIMYGIDHPDCsveDLLKFVQGPDFPGGGMIYRNSDLLNIYRTGHGKVFCQGEIDDEEkKKIIIKTLPY 254
                                       **************************************************************99978********** PP

                     DNA_topoisoIV 227 gvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvleklykktkLessisvnnlvlfdkkpk 301
                                       gvn++ +i++++e vk++ i+ isdirdesdr g+r+vi++k++ s+  ++++ly++t Le++i vnnlvl +++pk
  gi|518652723|ref|YP_008142243.1| 255 GVNKALYIQNVAEQVKNGIISnISDIRDESDRnGIRVVIKIKNDDSKGLTINQLYEHTPLETTIGVNNLVLLNNEPK 331
                                       *****************************9999******************************************** PP

                     DNA_topoisoIV 302 ylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeq 376
                                       +++l e++  f+++rle++++r+ ++++kl +r +il+gl++al++id+vi++ir+s+++++ak++L+++  lse+q
  gi|518652723|ref|YP_008142243.1| 332 VMTLDEMILGFIDFRLEIIRKRSVFEVNKLMDREHILSGLVIALENIDRVIKIIRSSDNADMAKTSLMDQlsLSEKQ 408
                                       **********************************************************************999**** PP

                     DNA_topoisoIV 377 aeyllemrlrrLtkeeveklekeieelekeikelekllak...lkkli 421
                                       a ++l+mrl+rLt +e++k+++e+ +++++i++l++++++    ++++
  gi|518652723|ref|YP_008142243.1| 409 ALAILDMRLQRLTGLEIKKINDELISIKENIERLNEIINNeskRRDVL 456
                                       *************************************99955555555 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.19
                     DNA_topoisoIV 318 evyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee..lseeqaeyllemrlrrLt 389
                                       +v++ +  +  +k + +l  + g   ++n+ +++++++++  + k+    + ++  ++++ ++ +l+mr   L+
  gi|518652723|ref|YP_008142243.1| 552 RVLRTKAYTIEKKSRTSLGSVGGTFLKMNENEKIKQIMKSPASPKNFLIIITKKgfIKRTPVKEILDMRESGLK 625
                                       44444444444455667778888899999999999999999887777777777788888888899988866555 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.3     0.023   1.4e+02      12      40 ..     272     300 ..     271     300 .. 0.91
   2 !   29.1   0.1   8.4e-11     5e-07       2      46 ..     494     537 ..     493     539 .. 0.89
   3 !   22.1   0.2   1.3e-08   7.5e-05       1      42 [.     542     586 ..     542     591 .. 0.93
   4 !   38.3   0.1   1.1e-13   6.8e-10       2      45 ..     598     639 ..     597     642 .. 0.94
   5 !   21.9   0.0   1.5e-08   8.9e-05       3      43 ..     647     687 ..     645     691 .. 0.83
   6 !   27.1   0.1   3.6e-10   2.2e-06       1      47 [.     694     741 ..     694     742 .. 0.95
   7 !   39.4   0.2   5.2e-14   3.1e-10       1      46 [.     745     790 ..     745     791 .] 0.96

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.023
                                       EEEEEGGGS-B.T-TTSCTEEGS.ETTTTSS CS
                     DNA_gyraseA_C  12 vkrfplselpe.qgRgakGvkgi.klkegdk 40 
                                       ++  ++s+++  + R+  G++++ k+k++d+
  gi|518652723|ref|YP_008142243.1| 272 GIISNISDIRDeSDRN--GIRVViKIKNDDS 300
                                       788899**********..***********95 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 8.4e-11
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                        +++ ++nG  kr++ +e+ +q+Rg+kG +   ++++d + s+l 
  gi|518652723|ref|YP_008142243.1| 494 SIMILSENGLLKRVSSEEYNVQKRGGKGTIT-ATRKEDTVRSILS 537
                                       69***************************54.5999999999886 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 1.3e-08
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklv 42 
                                       d++ ++T+ G+v+r++++++  ++R++ G  g    k++e++k+ 
  gi|518652723|ref|YP_008142243.1| 542 DMIYFFTNTGRVLRTKAYTIEKKSRTSLGSVGGtflKMNENEKIK 586
                                       8999**************************999999999999985 PP

  == domain 4  score: 38.3 bits;  conditional E-value: 1.1e-13
                                       EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEE CS
                     DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvl 45 
                                        l++iT++G++kr+p+ e+  ++   +G k+ikl++ d++vsv+
  gi|518652723|ref|YP_008142243.1| 598 FLIIITKKGFIKRTPVKEILDMR--ESGLKIIKLDDQDEVVSVM 639
                                       599********************..88*******999*****98 PP

  == domain 5  score: 21.9 bits;  conditional E-value: 1.5e-08
                                       EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEE CS
                     DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvs 43 
                                       ++++ sn ++  f  +e++++gR+++Gvk ++l+  + + s
  gi|518652723|ref|YP_008142243.1| 647 IFVAASNNKAAVFLSDEVSSTGRASRGVKSMRLNGAEVINS 687
                                       89999****************************55454444 PP

  == domain 6  score: 27.1 bits;  conditional E-value: 3.6e-10
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvlvv 47 
                                       d ++ iT+nG +kr+++ +++  +Rg++G+ + k +e+ ++lv++l+v
  gi|518652723|ref|YP_008142243.1| 694 DTVMSITENGLGKRTKITDFSIHHRGSSGNLIFKESERtGSLVTALPV 741
                                       789***************************999999999***999998 PP

  == domain 7  score: 39.4 bits;  conditional E-value: 5.2e-14
                                       SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEE CS
                     DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlv 46 
                                       +e+l++T+n + +r++ +e++ q+R ++Gvk+i+ +++d +v++ v
  gi|518652723|ref|YP_008142243.1| 745 QEVLIVTRNNKTIRLNSDEIKIQSRVTSGVKLINVDDDDLVVAASV 790
                                       589****************************************988 PP

>> FliT  Flagellar protein FliT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.51   3.1e+03      33      68 ..     385     420 ..     371     429 .. 0.74
   2 ?    9.4   5.0    0.0003       1.8      28      83 ..     418     478 ..     391     479 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.51
                                       ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FliT  33 aplspaereekrellrrilandaeirallqprldel 68 
                                        + s+++  +k+ l+ ++   +++  a+l+ rl++l
  gi|518652723|ref|YP_008142243.1| 385 IRSSDNADMAKTSLMDQLSLSEKQALAILDMRLQRL 420
                                       455667788889999999999999999999999888 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0003
                                       HCS-.....-ST--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHTHHHHHHHH CS
                              FliT  28 reld.....aaplspaereekrellrrilandaeirallqprldelqkllgalrrqrkann 83 
                                       ++l+       + +    +e  e l++i+ n+ + r+ l+++  e++k++g++rr++ +n+
  gi|518652723|ref|YP_008142243.1| 418 QRLTgleikKINDELISIKENIERLNEIINNESKRRDVLKQETLEIKKQFGDVRRTKVLNR 478
                                       33334333333344444567778888*******************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (791 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       940  (0.052429); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.71u 0.30s 00:00:01.01 Elapsed: 00:00:00.46
# Mc/sec: 5220.09
//
Query:       gi|518652724|ref|YP_008142244.1|  [L=215]
Description: cyclase family protein [Ferroplasma acidarmanus fer1]
Scores for 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   99.4   0.0    2.4e-28   99.0   0.0    1.1  1  Cyclase   Putative cyclase


Domain annotation for each model (and alignments):
>> Cyclase  Putative cyclase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   1.4e-32   2.4e-28       1     136 []       7     157 ..       7     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 1.4e-32
                           Cyclase   1 idLshplsedtpvwp.dp...................islsehtGTHlDapgHfae..ktidelpleelvgpavvld 55 
                                       +dLs++l++++p+wp +p                   +++ +htGTH+Dap+H++   +t+d++pl++++gp+ ++ 
  gi|518652724|ref|YP_008142244.1|   7 FDLSVELKPNMPCWPtNPivridpigvlsrdgysvekFETVTHTGTHIDAPYHMIDngMTVDKIPLSQIIGPGYCIR 83 
                                       59************7444777888******************************99888****************** PP

                           Cyclase  56 vsakaaaedyeiitaedleaalakqgveikpgdivlirTgwskrl..edkekyrnpglseeaaewlaekgvkavGvD 130
                                          ++  +++ei + + l++  + +     +++i+li+T w+k++  +++ +y+ pgl  +++++l+e++ k++G+D
  gi|518652724|ref|YP_008142244.1|  84 P--EV--DGTEI-KLNALKKIWKPEY----DNKIILINTNWDKKRgfTKEFQYDFPGLADDTVDFLIEHHPKVIGID 151
                                       9..44..56755.*****99887776....699***********98766677899********************** PP

                           Cyclase 131 tlsvDa 136
                                       tl++D+
  gi|518652724|ref|YP_008142244.1| 152 TLGIDP 157
                                       ****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (215 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); 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: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1710.81
//
Query:       gi|518652725|ref|YP_008142245.1|  [L=168]
Description: OsmC family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   42.2   0.0    1.3e-10   41.6   0.0    1.3  1  OsmC      OsmC-like protein


Domain annotation for each model (and alignments):
>> OsmC  OsmC-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   7.4e-15   1.3e-10       2      99 ..      69     165 ..      67     166 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 7.4e-15
                                       TXSSB-HHHHHHHHHHHHHHHHHHHHTCCCT---SCEEEEEEEEEECCECT......CEEEEE.EEEEEE-SS-H.. CS
                              OsmC   2 dgsgpsPeelllaalasCfaitlravakkkgikledleveveaerdpegak......giteir.lkvevkipgadse 71 
                                       +g   +P  +l+++++sCfa+t+++ a+k+gi l++l+ + ++  d  +         i   + lk+ev+   ad  
  gi|518652725|ref|YP_008142245.1|  69 QGVHATPLNYLMMGVMSCFASTVAIQAAKRGIVLKKLKFKGHLYYDIGPVVvesdfpII---KsLKIEVE---AD-- 137
                                       555889*******************************9999886666544455533223...23455553...33.. PP

                                       HHHHHHHHHHHHHSHHHHHHCT-SSSEE CS
                              OsmC  72 eklkkllekaekrCpvsntlkngvkvel 99 
                                       +++k +le+++k Cp + ++ n+++ e+
  gi|518652725|ref|YP_008142245.1| 138 QDIKVVLEHSRKACPALYAIMNPIPTEI 165
                                       789**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); 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 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1193.23
//
Query:       gi|518652726|ref|YP_008142246.1|  [L=531]
Description: amino acid transporter related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-42  144.9  55.4    3.2e-42  144.9  55.4    2.0  2  AA_permease_2  Amino acid permease
    1.6e-29  102.9  51.2    1.6e-29  102.9  51.2    2.1  2  AA_permease    Amino acid permease
  ------ inclusion threshold ------
        1.5    8.9   0.0        1.5    8.9   0.0    3.3  4  Vma12          Endoplasmic reticulum-based factor for assembl


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 !  144.9  55.4   5.4e-46   3.2e-42       1     398 [.      19     425 ..      19     438 .. 0.82
   2 ?   -8.2  15.0         3   1.8e+04      76     164 ..     416     507 ..     412     527 .. 0.56

  Alignments for each domain:
  == domain 1  score: 144.9 bits;  conditional E-value: 5.4e-46
                     AA_permease_2   1 lsllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       l+l+s+++l++g ++g ++  ++   +a++gp+ il + ia++++ ++ +lvyaEl++++p+ gG+  y ++  g+ 
  gi|518652726|ref|YP_008142246.1|  19 LGLWSVIMLALGGILGPAVAYAPvyTLAYAGPIGILAWPIAMVMI-IPIGLVYAELGTTWPKAGGVAYYPSKSNGPI 94 
                                       79**************6666677778999***************9.9*********999****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgn...twltyliaiaililvalinirgikesakiqnilgi 149
                                       v+ +++w+++++y++v ++i+ ++++yl +  +p+l+ n   t+l +++a ++lilv+l+ni+ ik+++ i+ il+ 
  gi|518652726|ref|YP_008142246.1|  95 VGAINGWSSMVGYLFVGPVIVFAVVEYLSF-YFPSLYANgtlTYLGIIVAEIVLILVFLVNILRIKHMGAINLILTA 170
                                       ************************999988.5699999944444555555679************************ PP

                     AA_permease_2 150 lkillpliiliilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaif 224
                                       +++ll+ +++i+l++++   ++ s      + + p g +g++++++ +++ ++Gf   + +seevk+  k +p+ai+
  gi|518652726|ref|YP_008142246.1| 171 ITLLLIGVVIIALAFYFKLSNITS----TAGGVIPYGFTGFFGAITLTVFGYGGFRQPIDYSEEVKNpgKSIPIAII 243
                                       ***988888888888888888887....34468999******************************99899****** PP

                     AA_permease_2 225 igllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavg....gk.vvaiivvilialsllg....aintav 292
                                       ++ll++++++ l +++f+g+++ +++  + +  +  alf+  +     +k  v  ++vi++++++l+     +  ++
  gi|518652726|ref|YP_008142246.1| 244 VALLVSGLVFSLESLVFAGAINFSKLGISTG--NWSALFAYSSPyatlSKvLVLPAIVIIAIIVALIatfkDGVIYY 318
                                       *************************965444..12222222222222223233333333333333332333788899 PP

                     AA_permease_2 293 igssrvlealard.gvlPrffakvnkfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliig 368
                                        g++rv e lar+ ++lP+ f ++n +g+p+++i+l++i++ i+  l++l  + ++ ++  + + g+++sy+  +i+
  gi|518652726|ref|YP_008142246.1| 319 GGTARVGEVLAREdKFLPKLFDRMNVRGIPVYSIVLVLIIT-IV--LVAL--GRSLATIIGIMVDGFLLSYAPGAIS 390
                                       99*********8549*************************9.54..3455..468********************** PP

                     AA_permease_2 369 alilrkkrphlkr.....pgkilvaiigalfllfl 398
                                       +++ rk+  + kr     ++kil  i +++ +l++
  gi|518652726|ref|YP_008142246.1| 391 LMVFRKTDMVTKRpfklpFAKILAPIAFIVANLLV 425
                                       *******9999995555555566666666666655 PP

  == domain 2  score: -8.2 bits;  conditional E-value: 3
                     AA_permease_2  76 vaflsawfn..wfayvpvlasilsv.aasyllnalgpdlqgn..twltyliaiaililvalinir.gikesakiqni 146
                                       +af++a+++  w ++++v   i+++ +a+ ll ++++++++   ++++y+i + ++++++li +r g +    ++ i
  gi|518652726|ref|YP_008142246.1| 416 IAFIVANLLvyWSGWAAVEI-IIPLdFAGILLVLVYSHYTKIdmKYAMYGIWMPVYLIFILIMSRiGSSLFHGLNYI 491
                                       56666655443666666554.44445888888888875544344667788877777777776554255555555566 PP

                     AA_permease_2 147 lgilkillpliiliilgl 164
                                        + + ++ ++ii+   ++
  gi|518652726|ref|YP_008142246.1| 492 AFPYDTI-VFIIVT-MVF 507
                                       6555552.322222.222 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.9  51.2   2.6e-33   1.6e-29       2     418 ..      24     421 ..      23     428 .. 0.89
   2 ?   -7.2  12.3         3   1.8e+04     116     163 ..     463     514 ..     417     529 .. 0.48

  Alignments for each domain:
  == domain 1  score: 102.9 bits;  conditional E-value: 2.6e-33
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       v++ algg+ G ++  +  ++l+ aGp+g+ la+ +a+v+i+ ++l  +e+ t  pk+gg ++y s++ gp +G   
  gi|518652726|ref|YP_008142246.1|  24 VIMLALGGILGPAVAYAPVYTLAYAGPIGI-LAWPIAMVMIIPIGLVYAELGTTWPKAGGVAYYPSKSNGPIVGAIN 99 
                                       89*************************777.********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt........gavflvvlliinlvgvkvygeaefilaliki 147
                                       G++ ++ +++v ++ ++a++ +++f   +++l  a +t        + ++l++++++n++ +k  g++ +il+ i +
  gi|518652726|ref|YP_008142246.1| 100 GWSSMVGYLFVGPVIVFAVVEYLSFY--FPSLY-ANGTltylgiivAEIVLILVFLVNILRIKHMGAINLILTAITL 173
                                       **************************..99999.8888899*9988778999999********************** PP

                       AA_permease 148 iaiiafiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                       + i  +ii + + +  +  ++ +         g+     +p g        f++f++++   vf++ G+   +  ++
  gi|518652726|ref|YP_008142246.1| 174 LLIGVVIIALaFYFKLSNITSTA---------GG----VIPYG--------FTGFFGAITLTVFGYGGFRQPIDYSE 229
                                       99999999996555555555555.........67....56666........************************** PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa....aspfvifikesgvsvlaplinavi 296
                                       Evk+P ksiP+ai+ +++  ++++ l +l+    ++ + lg+ ++  sa    +sp+ +  k + ++++  + ++v 
  gi|518652726|ref|YP_008142246.1| 230 EVKNPGKSIPIAIIVALLVSGLVFSLESLVFAGAINFSKLGISTGNWSAlfaySSPYATLSKVLVLPAIVIIAIIVA 306
                                       ********************************************99999***99****9999999999999999999 PP

                       AA_permease 297 ltaalssansslysasRvlyslak.dglaPkvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllais 372
                                       l+a++  ++ +   + Rv   la+ d+ +Pk +++++ rg P+ +i+l++ii  +++ + + +la  +++ ++    
  gi|518652726|ref|YP_008142246.1| 307 LIATFKDGVIYYGGTARVGEVLAReDKFLPKLFDRMNVRGIPVYSIVLVLIITIVLV-ALGRSLA--TIIGIM---- 376
                                       99999999999999*********8355679*********************998887.4444444..444444.... PP

                       AA_permease 373 aliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilv 418
                                          +l+ +   ++s+++fRk+  + +r   +l+f   l+p  +i++
  gi|518652726|ref|YP_008142246.1| 377 VDGFLLSYAPGAISLMVFRKTDMVTKRPF-KLPFAKILAPIAFIVA 421
                                       44688889999999999999966666644.7888887777777765 PP

  == domain 2  score: -7.2 bits;  conditional E-value: 3
                       AA_permease 116 t...gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg.iillag 163
                                       +     v l+++li++ +g  ++    +i++++  i +i++  v+ ++++  
  gi|518652726|ref|YP_008142246.1| 463 YgiwMPVYLIFILIMSRIGSSLFHGLNYIAFPYDTIVFIIVTMVFyFVGVNL 514
                                       1444555666666666666666666666666665444443333333443333 PP

>> Vma12  Endoplasmic reticulum-based factor for assembly of V-ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00025       1.5      68     132 ..     159     264 ..     149     269 .. 0.93
   2 ?    3.2   0.5     0.014        83     104     136 ..     289     325 ..     264     327 .. 0.76
   3 ?   -1.9   0.7      0.55   3.3e+03     105     135 ..     402     433 ..     351     435 .. 0.61
   4 ?   -4.5   0.4         3   1.8e+04      81      92 ..     499     510 ..     494     517 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00025
                             Vma12  68 qelkevnrqlilvlNiliSvvavffavwialrsartp........................................ 104
                                       +++ ++n  l+++  +li vv+ + a+++ l+++++                                         
  gi|518652726|ref|YP_008142246.1| 159 KHMGAINLILTAITLLLIGVVIIALAFYFKLSNITSTaggvipygftgffgaitltvfgyggfrqpidyseevknpg 235
                                       5688899999************************888**************************************** PP

                             Vma12 105 .slpvrvllslvvallVgvAEvvvyakyl 132
                                        s p+ ++++l+v+ lV+  E +v+a+ +
  gi|518652726|ref|YP_008142246.1| 236 kSIPIAIIVALLVSGLVFSLESLVFAGAI 264
                                       *********************99999876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.014
                             Vma12 104 p....slpvrvllslvvallVgvAEvvvyakylrkve 136
                                       +     lp+ v+++++val+  + + v+y ++  +v 
  gi|518652726|ref|YP_008142246.1| 289 LskvlVLPAIVIIAIIVALIATFKDGVIYYGGTARVG 325
                                       1444478999********************9988875 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.55
                             Vma12 105 slpvrvllslvva.llVgvAEvvvyakylrkv 135
                                       + p+++ ++ + a +   vA ++vy +++  v
  gi|518652726|ref|YP_008142246.1| 402 KRPFKLPFAKILApIAFIVANLLVYWSGWAAV 433
                                       55666655543331556678888888877666 PP

  == domain 4  score: -4.5 bits;  conditional E-value: 3
                             Vma12  81 lNiliSvvavff 92 
                                       + i++++v+ f+
  gi|518652726|ref|YP_008142246.1| 499 VFIIVTMVFYFV 510
                                       334444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1243  (0.069329); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.70u 0.34s 00:00:01.04 Elapsed: 00:00:00.46
# Mc/sec: 3497.80
//
Query:       gi|518652727|ref|YP_008142247.1|  [L=401]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.4e-24   84.2   0.2    2.4e-23   82.7   0.1    1.8  2  DEDD_Tnp_IS110  Transposase
    2.4e-13   50.2   0.0    4.5e-13   49.3   0.0    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
  ------ inclusion threshold ------
      0.034   14.4   2.0          2    8.7   0.3    2.4  2  DUF2072         Zn-ribbon containing protein
       0.14   12.3   3.2         15    5.8   0.1    3.8  4  SecIII_SopE_N   Salmonella type III secretion SopE effector N


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.1   5.5e-27   2.4e-23       1     155 []       4     162 ..       4     162 .. 0.91
   2 ?   -1.6   0.0       0.5   2.2e+03      27      69 ..     343     386 ..     337     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 5.5e-27
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeegleallek....laakagevlvv.veatghygallvaflleagit 72 
                                       vGiD +++ h+a ++d+++++l++ ++ n +e++e+l++k    + ++ ++v+++ +  tg+y+ +l +fl+++++t
  gi|518652727|ref|YP_008142247.1|   4 VGIDTHERIHYAEIQDEKENKLWHGKIRNIKEDFESLIDKikkiENSNNDKVEFIfMNPTGNYHIPLKYFLENNNFT 80 
                                       8***************************************554222456888876589******************* PP

                    DEDD_Tnp_IS110  73 vvvvnplavkrlrkly.lrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlra 148
                                       v++v ++++ +lrk+  l+  K+D+ DA+++A + ++  ++r ++ +  + ++L++++r+r+ +vk++t+ kn +++
  gi|518652727|ref|YP_008142247.1|  81 VYMVDARKTLNLRKMInLNTIKSDSEDAHILAATPWHDPKYREYTGH--NRSSLSSISRERSIVVKSITAIKNYIHS 155
                                       *************99736889***************88899999776..569************************* PP

                    DEDD_Tnp_IS110 149 lLdqvfp 155
                                        L  vfp
  gi|518652727|ref|YP_008142247.1| 156 DLAAVFP 162
                                       ****998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.5
                    DEDD_Tnp_IS110  27 vpndeegleallek.laakagevlvvveatghygallvafllea 69 
                                       v n+ +++ +++++ +++k+++v+  +  +++   +++++++++
  gi|518652727|ref|YP_008142247.1| 343 VMNKNKEFYDIFNReIGKKKSNVQAYIAVSKRLLFHIYSIMKNH 386
                                       56777788888888788888999988888888877777777765 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0     1e-16   4.5e-13       3      83 ..     270     351 ..     268     355 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1e-16
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.ra 78 
                                        L+ + G G + +a +++eig++++f+sa +l++yaG +p  + SG+k ++++i++  n+ l +a+ye A++++ ++
  gi|518652727|ref|YP_008142247.1| 270 NLTNLRGLGIINSAIIVSEIGNIEQFESALKLQSYAGKCPDIEGSGGKTHSKGITHVRNKFLSNAVYESAISLVmNK 346
                                       7999******************************************************************9998677 PP

                    Transposase_20  79 npelr 83 
                                       n+e+ 
  gi|518652727|ref|YP_008142247.1| 347 NKEFY 351
                                       77765 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.3   0.00044         2      68     122 ..      34      87 ..       6      98 .. 0.69
   2 ?    4.7   0.1    0.0074        33      87     127 ..     195     237 ..     182     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00044
                           DUF2072  68 eeklekkekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegk 122
                                       +e  e   ++ ++ e++++d+ve + +   G+Y + l+ +le++++ + + +  +
  gi|518652727|ref|YP_008142247.1|  34 KEDFESLIDKIKKIENSNNDKVEFIFMNPTGNYHIPLKYFLENNNFTVYMVD-AR 87 
                                       233333366777888999**************************99888654.44 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0074
                           DUF2072  87 drvesvrilepGsYel.NlekLlerdelvmal.keegkYvvdl 127
                                       + + s++  ++G+Y +  +++L+e+ e  + +  +++ Y  ++
  gi|518652727|ref|YP_008142247.1| 195 NIIKSIKKASKGHYRIeDINRLMETAENSIGIpDKDDAYKFKI 237
                                       6689***********955*********9999977888998776 PP

>> SecIII_SopE_N  Salmonella type III secretion SopE effector N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.56   2.5e+03       8      23 ..       8      23 ..       5      40 .. 0.83
   2 ?    5.8   0.1    0.0032        15      25      43 ..     137     155 ..     124     171 .. 0.84
   3 ?   -4.1   0.0         4   1.8e+04       6      13 ..     204     211 ..     203     214 .. 0.78
   4 ?    4.5   0.0    0.0082        37      30      45 ..     319     334 ..     298     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.56
                     SecIII_SopE_N  8 qhyrihrsdvepvkek 23
                                       h rih ++++  ke 
  gi|518652727|ref|YP_008142247.1|  8 THERIHYAEIQDEKEN 23
                                      5999**9999988875 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0032
                     SecIII_SopE_N  25 tekdifaksitavrnsfis 43 
                                        e+ i  ksita++n + s
  gi|518652727|ref|YP_008142247.1| 137 RERSIVVKSITAIKNYIHS 155
                                       6899**********97655 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 4
                     SecIII_SopE_N   6 stqhyrih 13 
                                       s  hyri 
  gi|518652727|ref|YP_008142247.1| 204 SKGHYRIE 211
                                       5679**95 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0082
                     SecIII_SopE_N  30 faksitavrnsfisls 45 
                                        +k it vrn f+s +
  gi|518652727|ref|YP_008142247.1| 319 HSKGITHVRNKFLSNA 334
                                       5789********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1227  (0.0684366); expected 358.6 (0.02)
Passed bias filter:                      557  (0.031067); 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: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2967.97
//
Query:       gi|518652728|ref|YP_008142248.1|  [L=327]
Description: hypothetical protein FACI_IFERC00001G1367 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-30  105.4   0.1    4.6e-30  104.8   0.1    1.3  1  Homoserine_dh    Homoserine dehydrogenase
    1.7e-08   35.1   0.0      3e-08   34.3   0.0    1.4  1  NAD_binding_3    Homoserine dehydrogenase, NAD binding domain
    0.00092   19.0   0.1     0.0014   18.4   0.1    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
     0.0034   17.6   0.1     0.0076   16.5   0.1    1.6  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma


Domain annotation for each model (and alignments):
>> Homoserine_dh  Homoserine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   0.1     1e-33   4.6e-30       1     173 []     150     324 ..     150     324 .. 0.95

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1e-33
                                       --HHHHHHTCTTSEEEEEEEE--HHHHHHHHHHHCHTT-HHHHHHHHHHTTSS-SSTHHHHTTHHHHHHHHHHHHHH CS
                     Homoserine_dh   1 PiiktlkeilsgdritrieGilngtlnyiltemeeegasfsevlkeaqelGyaeaDptdDveGlDaarKlailarla 77 
                                       P+++  + +l+++++ +++G +++t+n++l+++   + +f+e++k aq++G+ae+D  dD +GlD arK +i+a+ +
  gi|518652728|ref|YP_008142248.1| 150 PLFNLNRYSLKSSKLLEFKGQVSSTINFVLNHLMG-NVDFHEAIKTAQSMGIAETDYHDDTNGLDGARKTVIIANAL 225
                                       778888999*************************6.888************************************** PP

                                       CTTT--GGGSEE--STTS-HHHHHHHHCTTEEEEEEEEE......CEEEEEEEEEETTSGGGHSSST-EEEEEEESS CS
                     Homoserine_dh  78 fgleveledvevegiskltaedikeakeegkvlklvasa......vearVkpelvpkshplasvkgsenavlvetdr 148
                                       +gl+++l+dve  gi++l++  i+++++ g+v++++  +      + ++ k+ ++++ +++a ++   ++ l +td+
  gi|518652728|ref|YP_008142248.1| 226 LGLDYTLKDVEYDGIENLDN--IEYMRNSGEVYRVLSHItagtnpI-IESKIFSIKPGDSMAAMDSLSMGYLEKTDN 299
                                       ****************9975..79**************87666543.9***************************** PP

                                       SEEEEEEES-SSHHHHHHHHHHHHH CS
                     Homoserine_dh 149 lgelviqGpgaGaepTAsavlsDll 173
                                        ++l++  +  G+ +TA+ v++D+l
  gi|518652728|ref|YP_008142248.1| 300 NDDLMVFEKHDGPLETAAQVVNDIL 324
                                       ***********************96 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   6.6e-12     3e-08       1     117 []       7     142 ..       7     142 .. 0.81

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 6.6e-12
                                       --SHHHHHHHHHHHH---S......SEEEEEEEEESS.EEE-TT...........HHHHHT--CB---HHHHHHHHS CS
                     NAD_binding_3   1 GlGaiGsavleqlkrqqse......ielelvavadrd.sllskd...........rkallasealtldlddliahld 59 
                                       GlG iG+av+ +l+++ ++       ++ +  v d++ +  +k+              +l + a +++++d+ + l+
  gi|518652728|ref|YP_008142248.1|   7 GLGHIGKAVVGILNENHEYfktrfgSDIHVISVSDSKtTVYDKNglnldkvlmykERGELDEVADVMKMEDIYS-LN 82 
                                       9*****************9****888888888888886666666999988777763334444444555555444.47 PP

                                       -EEEEE-..S--HHHHT..THHHHHHTTEEEE-S--CGGG-HHHHHHHTSSSTTS--.EE-G CS
                     NAD_binding_3  60 pdvvVEc..asseavae..lvlkaLkagkdvvtankgaladealyeeLreaaeangakiyve 117
                                        dv+V++  a ++ +a+  ++ +a  +gk+vvt+nk+ la   +++e++e +++++++i++e
  gi|518652728|ref|YP_008142248.1|  83 SDVIVDMspATKDGLAGmrMYKNAFDSGKQVVTCNKAPLA--LHWKEIMESSRKQKKNILYE 142
                                       8******77777777752279*******************..****************9997 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 !   18.4   0.1   3.2e-07    0.0014      57      93 ..      35      70 ..       7     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 3.2e-07
                                      EEEEEEESSEEEEETTEE-HHHHHHHHHCSSSSTTHS CS
                     ELFV_dehydrog 57 kvvavsDssGviydpeGldieellelkeerksvkeyk 93
                                      +v++vsDs+ ++yd++Gl+++++l +ke+ + ++e++
  gi|518652728|ref|YP_008142248.1| 35 HVISVSDSKTTVYDKNGLNLDKVLMYKERGE-LDEVA 70
                                      79**********************9988654.44444 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.1   1.7e-06    0.0076       3      98 ..       5     115 ..       3     144 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1.7e-06
                                       EE--SHHHHHHHHHHHCTCCT-G.....EEEEEESSHHHHHHHHCHHTTTCEEEEE--TT..THHHHHHHHHTTS.. CS
                   Sacchrp_dh_NADP   3 iiGaGsvGqavaellarhfdvda.....eitvadrskeklealaakalgvrfeaialdae..nyeavLaallkeg.. 70 
                                       ++G G +G+av+  l +++++++     +i+v++ s++k   ++ +++g +++++ + +e  + ++ +a ++k    
  gi|518652728|ref|YP_008142248.1|   5 LVGLGHIGKAVVGILNENHEYFKtrfgsDIHVISVSDSK--TTVYDKNGLNLDKVLMYKErgELDE-VADVMKMEdi 78 
                                       79*******************9999**************..7777777777766655443113344.4444444444 PP

                                       .....SEEEE-SSGG....GHHHHHHHHHHHT-EEEE CS
                   Sacchrp_dh_NADP  71 .....dlvvnlsppi....ssldvlkaCietgvhyvd 98 
                                            d++v++sp +     ++ + k + + g  +v+
  gi|518652728|ref|YP_008142248.1|  79 yslnsDVIVDMSPATkdglAGMRMYKNAFDSGKQVVT 115
                                       6666789999998887666666777777777777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2229.91
//
Query:       gi|518652729|ref|YP_008142249.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G1368 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   15.3   0.3      0.022   15.1   0.3    1.1  1  DUF1894   Domain of unknown function (DUF1894)
      0.052   13.4   0.1      0.052   13.4   0.1    1.1  1  ERF       ERF superfamily


Domain annotation for each model (and alignments):
>> DUF1894  Domain of unknown function (DUF1894)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.3   2.4e-06     0.022      33      63 ..      15      49 ..       4      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-06
                                      EEES--EEESSS---SS----EEEE--....S-EE CS
                           DUF1894 33 yevepgykilgvrliGvppipvgidee....kilf 63
                                      +e+ p+ +i++++ iG++ i+++i++     +i++
  gi|518652729|ref|YP_008142249.1| 15 LEFLPETTIFDATYIGIESITIAINNAiksnNIII 49
                                      57889******************998776765544 PP

>> ERF  ERF superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.7e-06     0.052      25      53 ..      25      53 ..       5      65 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.7e-06
                               ERF 25 kykYasledileaikpvlkehglilkpei 53
                                      +  Y ++e+i+ ai++++k++++i++ +i
  gi|518652729|ref|YP_008142249.1| 25 DATYIGIESITIAINNAIKSNNIIIVLYI 53
                                      567**********************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.29s 00:00:00.69 Elapsed: 00:00:00.46
# Mc/sec: 435.47
//
Query:       gi|518652730|ref|YP_008142250.1|  [L=261]
Description: pyrroline-5-carboxylate reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-30  105.9   2.0    1.2e-30  105.8   0.6    1.7  2  P5CR_dimer     Pyrroline-5-carboxylate reductase dimerisation
    1.4e-12   48.0   0.4    3.4e-12   46.8   0.2    1.8  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0057   16.8   0.1      0.018   15.2   0.0    1.8  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.042   14.1   0.1        1.7    8.9   0.0    2.2  2  DUF5055        Domain of unknown function (DUF5055)
       0.13   11.9   0.1       0.67    9.6   0.1    2.0  1  ApbA           Ketopantoate reductase PanE/ApbA


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 ?   -1.7   0.0      0.98   3.5e+03      21      34 ..      96     109 ..      66     122 .. 0.67
   2 !  105.8   0.6   3.4e-34   1.2e-30       1     102 [.     151     254 ..     151     255 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.98
                                       HHHHHHHHHHHTT- CS
                        P5CR_dimer  21 liealadagvklGl 34 
                                       + e l d+ v+ G+
  gi|518652730|ref|YP_008142250.1|  96 MQEMLKDSMVARGM 109
                                       34445555555555 PP

  == domain 2  score: 105.8 bits;  conditional E-value: 3.4e-34
                                       CCHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHHHHCHS..HHHHHHHH--TTSHHHH CS
                        P5CR_dimer   1 EkqldavtalsGsgpAyvflliealadagvklGlsreeArelaaqtvaGaaklllese..paelrdkvtspgGtTia 75 
                                       E+++davt+lsGsgpA+v+++++++++ag+ +G+++ +Arel++ t++ +++l++e++  +++lrd+v++pgGtT a
  gi|518652730|ref|YP_008142250.1| 151 ESYMDAVTGLSGSGPAFVAIMADSMINAGILAGIPKIQARELVIDTFINTMSLMREKGfsASDLRDEVMTPGGTTVA 227
                                       899**************************************************9877799***************** PP

                                       HHHHHHHTTHHHHHHHHHHHHHHHHHH CS
                        P5CR_dimer  76 glkeleegglraavieaveaaakrske 102
                                       g+ e+e+++ r+a+++av  +++r+ke
  gi|518652730|ref|YP_008142250.1| 228 GIYEMEKANARTAIANAVLGSYRRAKE 254
                                       *************************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 !   46.8   0.2   9.4e-16   3.4e-12       2      97 .]       3      90 ..       2      90 .. 0.92
   2 ?   -2.7   0.0       2.6   9.4e+03      77      94 ..     180     196 ..     166     197 .. 0.65

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 9.4e-16
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80
                                       +iiGaG +g+++ +g+  ++    e+ +  s + ek+e++ +  + k++  +n e a+  dv++la+kp   ++v++e
  gi|518652730|ref|YP_008142250.1|  3 AAIIGAGTVGRSIGEGIK-ND---FEVSFS-SGSFEKLEKWSKG-EFKIFD-NNVENAKYGDVILLAIKPGISDSVMEE 74
                                      59*************765.55...8***77.**********765.689**9.*************************** PP

                                      CGHHHHTTSEEEEESSS CS
                     F420_oxidored 81 lakdalkgklvisvlag 97
                                      + ++a kgklvis +ag
  gi|518652730|ref|YP_008142250.1| 75 I-RSAAKGKLVISFMAG 90
                                      *.9***********997 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.6
                                       HHHHCGHHHHTTSEEEEE CS
                     F420_oxidored  77 vlselakdalkgklvisv 94 
                                       +l+ + ++ ++++lvi++
  gi|518652730|ref|YP_008142250.1| 180 ILAGI-PKIQARELVIDT 196
                                       45555.667777777775 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 !   15.2   0.0     5e-06     0.018       2      88 ..       3      86 ..       2     116 .. 0.83
   2 ?   -0.9   0.0      0.47   1.7e+03      34      88 ..     131     195 ..     107     202 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5e-06
                                      EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC- CS
                     NAD_binding_2  2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglleal 80
                                       ++iG G+ G+++ + + k++++v++   + ek+e++ + ++k++++  e ++  dv+++ +k g   d+v+e++ + +
  gi|518652730|ref|YP_008142250.1|  3 AAIIGAGTVGRSIGEGI-KNDFEVSFSSGSFEKLEKWSKGEFKIFDNNVENAKYGDVILLAIKPG-ISDSVMEEIRS-A 78
                                      589*********99876.789*****************************************986.67999999655.6 PP

                                      -TT-EEEE CS
                     NAD_binding_2 81 kkgdilid 88
                                      +kg+++i 
  gi|518652730|ref|YP_008142250.1| 79 AKGKLVIS 86
                                      67888775 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.47
                                       HHHHHHHTT.......EEE-SSHHHHHHHC...SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE CS
                     NAD_binding_2  34 kveelvaeg.......akaaesieelvasl...dvvitmvkagkavdeviegllealkkgdilid 88 
                                       + ++++++        +++ es  ++v++l      ++ + a++ +++ i   ++++++ +++id
  gi|518652730|ref|YP_008142250.1| 131 EHKDVLEKVlkgfgsaVHIDESYMDAVTGLsgsGPAFVAIMADSMINAGILAGIPKIQARELVID 195
                                       44444444333345556666677777777766655556666666666666666666666666666 PP

>> DUF5055  Domain of unknown function (DUF5055)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.0     0.035   1.2e+02      19      69 ..      92     141 ..      82     157 .. 0.82
   2 ?    8.9   0.0   0.00047       1.7      12      69 ..     190     247 ..     186     258 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.035
                           DUF5055  19 trrtvkemekkgfvaadieekpmttlpalfagaflahhrfekkdvineiys 69 
                                       t   ++em k+ +va  +   pm +  ++ a +++   + e+kdv++++  
  gi|518652730|ref|YP_008142250.1|  92 TLSHMQEMLKDSMVARGMPSIPMLVQKSVTAYSYKNLDK-EHKDVLEKVLK 141
                                       5566889999************99999999999887765.66788888765 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00047
                           DUF5055  12 keytleftrrtvkemekkgfvaadieekpmttlpalfagaflahhrfekkdvineiys 69 
                                       +e +++    t++ m +kgf a+d+ +  mt   +  ag +   +   +  + n +  
  gi|518652730|ref|YP_008142250.1| 190 RELVIDTFINTMSLMREKGFSASDLRDEVMTPGGTTVAGIYEMEKANARTAIANAVLG 247
                                       6677777788999******************999999999988887777777777665 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.1   0.00019      0.67       2     106 ..       4      92 ..       3     122 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00019
                                       EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SS CS
                              ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvK 77 
                                       ai+GaG +G+ ++  + k+  +v +   s  +le+++k  +++ +++        e++           d++++++K
  gi|518652730|ref|YP_008142250.1|   4 AIIGAGTVGRSIGEGI-KNDFEVSFSSGSFeKLEKWSKGEFKIFDNN-------VENAKYG--------DVILLAIK 64 
                                       7999999999999999.779999999999889999999999888888.......4444444........89999999 PP

                                       GGGHHHHHHHHGGGECTCEEEEEESSSSC CS
                              ApbA  78 ayqteealeeikplldpntvvlllqNGlg 106
                                           ++++eei+++ + +  v+++  G+ 
  gi|518652730|ref|YP_008142250.1|  65 PGISDSVMEEIRSAAKGK-LVISFMAGIT 92 
                                       999999999999999998.7777777764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       708  (0.0394891); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); 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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 1829.15
//
Query:       gi|518652731|ref|YP_008142251.1|  [L=313]
Description: CoA-transferase family III protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-46  158.2   0.0    1.4e-45  156.1   0.0    1.9  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 !  156.1   0.0   7.6e-50   1.4e-45       5     319 ..       3     274 ..       2     285 .. 0.90

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 7.6e-50
                      CoA_transf_3   5 rVldlsqvlaGplatslLAdlGAeVIkvEppkkgDpaRkvgpseekgesayflavnrnKrsvalDlkseegrellkr 81 
                                       +V+d+++++ G + t++L+d G  VIk E+ +kgD +  ++p       ++   +n++K+s+++Dlk+ eg++++ r
  gi|518652731|ref|YP_008142251.1|   3 TVIDATRLIPGAITTRILSDRGYNVIKFEDTGKGDYMDELSP-------GANDFLNHGKKSICVDLKTSEGKKIFYR 72 
                                       6**********************************8888865.......55699*********************** PP

                      CoA_transf_3  82 LvakADVvieNfrpgvlerlglgyeelrainPrLiyasvsgyGqsGpkakrpgyDlvaqaasGlmsltgepdgpPvk 158
                                       L+++A V+ieNf+ gv erlg++y +l++ nP+L+y+s++gy    ++ + p++D+++ a sG+  +t         
  gi|518652731|ref|YP_008142251.1|  73 LIKNASVFIENFSEGVTERLGIDYLTLHRLNPQLVYCSIKGYR---ENPELPAHDINFTAFSGID-IT--------- 136
                                       *******************************************...47899************74.33......... PP

                      CoA_transf_3 159 vgvplgDivtgllaavailaallarertGkGqvidvslleaalallapqlleylatgevperqgnrdpaaapygvyr 235
                                         v+++D+ +g++aa+ i   l +r+     +++ v++ +  l + a++l +   +++v +       + ++y++y+
  gi|518652731|ref|YP_008142251.1| 137 LPVQIADAGSGIYAAMEIINHLKNRD----YSKVTVNMSDIPLYFNAYNLFT---ENNVLN------GKFPCYRIYQ 200
                                       5699******************7777....5789999999999888777744...566666......56788***** PP

                      CoA_transf_3 236 tkdgwvaiaaatdkqwaalckalgrpelaedprfatnasrlenraeldaelaewlaertaaewlellaaagvpaapv 312
                                        +dg va+++ ++k+wa++ +a+ r++l e +r++ n +         +e+++++ + +  e+lel +++++p+++v
  gi|518652731|ref|YP_008142251.1| 201 VSDGKVALGCLEQKFWANFTEAIQRKDL-ENSRLNLNIN---------KEIENIFLQYNSMEILELGRKYNFPVSAV 267
                                       ***************************9.6667766666.........8**************************** PP

                      CoA_transf_3 313 ntleevl 319
                                       +  ee++
  gi|518652731|ref|YP_008142251.1| 268 RAKEEII 274
                                       *999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.46
# Mc/sec: 2059.80
//
Query:       gi|518652732|ref|YP_008142252.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G1371 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0062   16.6   0.2     0.0089   16.1   0.2    1.3  1  SdpI      SdpI/YhfL protein family
  ------ inclusion threshold ------
      0.016   14.8   1.1      0.019   14.6   1.1    1.0  1  DUF2208   Predicted membrane protein (DUF2208)
      0.027   13.5   2.1       0.34    9.9   1.8    1.7  1  DUF973    Protein of unknown function (DUF973)
       0.18   10.5   1.7        0.2   10.4   1.7    1.0  1  DUF2207   Predicted membrane protein (DUF2207)
       0.23   11.7   3.6       0.39   11.0   3.6    1.4  1  DUF3784   Domain of unknown function (DUF3784)
       0.33   11.4   2.3        1.1    9.7   2.3    1.7  1  DUF202    Domain of unknown function (DUF202)
       0.54   10.5   2.7       0.44   10.8   0.2    1.8  2  Pro_sub2  Prodomain subtilisin 2
        1.6    8.3   4.1        4.3    6.9   4.1    1.6  1  Saf_2TM   SAVED-fused 2TM effector domain


Domain annotation for each model (and alignments):
>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2     4e-06    0.0089      21      60 ..       5      66 ..       3      70 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
                              SdpI 21 tWrkahrfagklwiiaGlilllla........................lgavvlvllvlvlllv 60
                                      tW+k  +  ++++i++G+++l+++                        + +++++++v  +llv
  gi|518652732|ref|YP_008142252.1|  5 TWEKMKKS-SRYMIVTGIVFLIISlptfldynmfptinsnigphqlssW-ISFFFSFVGFVLLV 66
                                      67777665.459*****************************99886632.23333333222222 PP

>> DUF2208  Predicted membrane protein (DUF2208)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.1   8.7e-06     0.019      83     145 ..       9      67 ..       3      70 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.7e-06
                           DUF2208  83 lkeqlkasmitllllliviilffllyryiiplassllgevleeklarflaflalFealflism 145
                                       + + +   mi +++++++i l ++l   ++p ++s++g     +l+ +++f+  F +++l+ +
  gi|518652732|ref|YP_008142252.1|   9 M-KKSSRYMIVTGIVFLIISLPTFLDYNMFPTINSNIGPH---QLSSWISFFFSFVGFVLLVV 67 
                                       3.444556788888888899989999999999****9877...99999999999999988765 PP

>> DUF973  Protein of unknown function (DUF973)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.8   0.00015      0.34       8     151 ..       9      65 ..       3      67 .. 0.50

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00015
                            DUF973   8 lregslfliiasllaliliilvlvvlftaissglsqliqssasilssvlllliaaiiliiiasvllilgllkirsgf 84 
                                       ++++s ++i++ +++li+++ +++                                                     
  gi|518652732|ref|YP_008142252.1|   9 MKKSSRYMIVTGIVFLIISLPTFLDY--------------------------------------------------- 34 
                                       55555555555555555555554322................................................... PP

                            DUF973  85 siLsstgrdvgiGitgltliligaiiiiigvilaivsllslilslillgviilligiilaliGqill 151
                                                                            ++++i s i    + + i++ + ++G++ll
  gi|518652732|ref|YP_008142252.1|  35 ------------------------------------NMFPTINSNIGPHQLSSWISFFFSFVGFVLL 65 
                                       ....................................2335555555555555555555555555555 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   1.7   9.1e-05       0.2     376     423 ..       5      68 ..       1      70 [. 0.81

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 9.1e-05
                           DUF2207 376 gkkklkklsalglgliilglilillallllvll................lvfllilllilllia 423
                                         +k+kk+s + ++ +i++li++l ++l ++++                ++f+++++++ll+++
  gi|518652732|ref|YP_008142252.1|   5 TWEKMKKSSRYMIVTGIVFLIISLPTFLDYNMFptinsnigphqlsswiSFFFSFVGFVLLVVG 68 
                                       567899999999*************99999999************7777666666666666665 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   3.6   0.00017      0.39      44      90 ..      10      69 ..       7      73 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00017
                           DUF3784 44 rfmgivllligilflllgll.............saiesealliialiviiiiviylivya 90
                                      +++ ++++++gi+fl+++l              ++  ++  ++i +++ +++ ++l+v++
  gi|518652732|ref|YP_008142252.1| 10 KKSSRYMIVTGIVFLIISLPtfldynmfptinsNIGPHQLSSWISFFFSFVGFVLLVVGF 69
                                      566778888888888888777788888999998888888888999999999999999876 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   2.3   0.00049       1.1      19      59 ..      15      69 ..      11      71 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00049
                            DUF202 19 alialglallrffl..............tgepsalgkilglilivlgiltllvgl 59
                                      ++i++g+++l + l                +p +l++++++++  +g+++l+vg+
  gi|518652732|ref|YP_008142252.1| 15 YMIVTGIVFLIISLptfldynmfptinsNIGPHQLSSWISFFFSFVGFVLLVVGF 69
                                      567777777766556677788888888888888899****************997 PP

>> Pro_sub2  Prodomain subtilisin 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2    0.0002      0.44      37      70 ..       4      38 ..       1      44 [. 0.80
   2 ?    0.1   0.2       0.4     9e+02      48      64 ..      48      64 ..      42      69 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                          Pro_sub2 37 rhfkevdk.irydisspinflcffiptifdmnnlk 70
                                      + +++++k  ry i + i fl + +pt +d n + 
  gi|518652732|ref|YP_008142252.1|  4 QTWEKMKKsSRYMIVTGIVFLIISLPTFLDYNMFP 38
                                      56667766258*******************99875 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.4
                          Pro_sub2 48 disspinflcffiptif 64
                                      ++ss i f   f+  ++
  gi|518652732|ref|YP_008142252.1| 48 QLSSWISFFFSFVGFVL 64
                                      67999999999988776 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   4.1    0.0019       4.3      18      83 ..      10      69 ..       4      70 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                           Saf_2TM 18 krsaelllftigvalllailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGa 83
                                      k+s  ++++t+ v+l+++++    +l + +      ++ + +  +  ++++++  ++g++l+vvG+
  gi|518652732|ref|YP_008142252.1| 10 KKSSRYMIVTGIVFLIISLPT---FLDYNMFPT---INSNIGPHQLSSWISFFFSFVGFVLLVVGF 69
                                      566666666666666666444...444433322...333444445557999*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 527.32
//
Query:       gi|518652733|ref|YP_008142253.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G1372 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   15.9   0.3      0.016   15.3   0.3    1.3  1  OSTbeta   Organic solute transporter subunit beta protein
       0.03   14.4   0.0      0.057   13.5   0.0    1.5  1  RAMP4     Ribosome associated membrane protein RAMP4
       0.28   10.5   0.6       0.36   10.2   0.4    1.3  1  OSTMP1    Osteopetrosis-associated transmembrane protein 1 pr


Domain annotation for each model (and alignments):
>> OSTbeta  Organic solute transporter subunit beta protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.3   2.7e-06     0.016      37      66 ..      58      87 ..      54     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.7e-06
                           OSTbeta 37 siLvLsavvvvisvvLLarsiqanRnrKiq 66
                                       +Lv++ v v++s++L a+s++ nR r  +
  gi|518652733|ref|YP_008142253.1| 58 GLLVITLVMVILSIILYAISLMHNRGRHGK 87
                                      589**********************98644 PP

>> RAMP4  Ribosome associated membrane protein RAMP4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   9.5e-06     0.057      31      54 ..      89     112 .]      78     112 .] 0.82

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 9.5e-06
                             RAMP4  31 ekkspvgpwlLglfiFVViGSaif 54 
                                       ++++ + p+lL +f F+ViG a++
  gi|518652733|ref|YP_008142253.1|  89 SSRTIIAPILLYIFTFAVIGVAVI 112
                                       5777899*************8875 PP

>> OSTMP1  Osteopetrosis-associated transmembrane protein 1 precursor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.4     6e-05      0.36     191     221 ..      59      89 ..      54      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 6e-05
                            OSTMP1 191 viavssfvlllpviFYlssflhseqkkrkli 221
                                       +++++ ++++l +i Y++s +h ++++ k+ 
  gi|518652733|ref|YP_008142253.1|  59 LLVITLVMVILSIILYAISLMHNRGRHGKIS 89 
                                       45677779***************99987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 833.13
//
Query:       gi|518652734|ref|YP_008142254.1|  [L=299]
Description: hypothetical protein FACI_IFERC00001G1373 [Ferroplasma acidarmanus fer1]
Scores for 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  133.0  17.5      1e-38  133.0  17.5    2.2  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    5.3e-07   29.9   2.4    5.3e-07   29.9   2.4    3.5  2  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
    5.9e-06   26.2  15.2    5.9e-06   26.2  15.2    2.5  2  Cytochrome_B     Cytochrome b/b6/petB


Domain annotation for each model (and alignments):
>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.0  17.5   1.7e-42     1e-38       3     165 ..       1     168 [.       1     172 [. 0.93
   2 ?   -0.4   1.6      0.17     1e+03      25      48 ..     233     258 ..     207     287 .. 0.68

  Alignments for each domain:
  == domain 1  score: 133.0 bits;  conditional E-value: 1.7e-42
                   Cytochrom_B_N_2   3 miiliyvHmlrvfftGaYk.kpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiiss......vPvvg 72 
                                       mi l+y+Hm+r+ f+G+Y+ k+R+l+Wi+Gv+l+llt+++++lGy+L  ++++++a+++g  ++++      +P   
  gi|518652734|ref|YP_008142254.1|   1 MIGLVYFHMMRQWFVGSYRgKWRWLQWILGVVLFLLTIFTAILGYMLANTAIAMAAVHIGILFMQRsvlgriLPGAL 77 
                                       9*****************************************************************9****988877 PP

                   Cytochrom_B_N_2  73 .twlvellfGgelpgeallsrlyalHilllpalllalivahlllvekkgqtpsrrkeknvvgeplvpvnavkmlllf 148
                                        +wl ++l+G++++  al+s+l+alH++++++l+la++++h++l+e++g + +  k k+ ++ p++p n+++ ++  
  gi|518652734|ref|YP_008142254.1|  78 iNWLEAILVGNYTT-PALFSHLLALHVAVFSTLMLAIFAIHFMLFERSGLASE--KPKKGEMIPWFPTNLLYAVFSG 151
                                       7************8.899********************************999..589999*************888 PP

                   Cytochrom_B_N_2 149 lvlvallialalinPvp 165
                                       +v+v +++++ +++P++
  gi|518652734|ref|YP_008142254.1| 152 IVMVGVILIISAAFPQQ 168
                                       87777766666666765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.17
                   Cytochrom_B_N_2  25 elnWii..GvllllltllegflGysL 48 
                                       e  Wi+  G+++l+   ++ + Gys 
  gi|518652734|ref|YP_008142254.1| 233 ERPWITafGIFMLIGLAVMTVWGYSQ 258
                                       44566522555555566677777774 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.8   8.4         3   1.8e+04      31      31 ..      58      58 ..       4     178 .. 0.65
   2 !   29.9   2.4   8.9e-11   5.3e-07      12      92 ..     183     264 ..     175     280 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.8 bits;  conditional E-value: 3
                                      H CS
                     Cytochrom_B_C 31 l 31
                                       
  gi|518652734|ref|YP_008142254.1| 58 H 58
                                      2 PP

  == domain 2  score: 29.9 bits;  conditional E-value: 8.9e-11
                                       ---GGGHHHHHHHHCS..SSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS- CS
                     Cytochrom_B_C  12 aPeWYflpfYaiLrai..pakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqp 86 
                                       +P WY +p+Y+++ +      ++Gv ++++++v ++llp++dr ++k +  r p+ +++ +++++ ++v+++ G ++
  gi|518652734|ref|YP_008142254.1| 183 VPDWYITPVYKLMDVAgyGLSTGGVPLIIGMLVFILLLPFIDRYHNKGVLER-PWITAFGIFMLIGLAVMTVWGYSQ 258
                                       79***********9974467899*****************************.999999999999*********987 PP

                                       SSCCHH CS
                     Cytochrom_B_C  87 peevav 92 
                                       p  + +
  gi|518652734|ref|YP_008142254.1| 259 PGLTQT 264
                                       754443 PP

>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  15.2   9.9e-10   5.9e-06      76     186 ..       4     122 ..       1     125 [. 0.73
   2 ?   -4.7   9.3         3   1.8e+04      71     119 ..     213     259 ..     141     285 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 9.9e-10
                      Cytochrome_B  76 llylhifrglllgglk.ktrelvWviGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGs....tlve 147
                                       l+y h++r  ++g++  k r l W++Gv+l+ll+i ta++Gy L+ + ++  av +   l     v+G     +l++
  gi|518652734|ref|YP_008142254.1|   4 LVYFHMMRQWFVGSYRgKWRWLQWILGVVLFLLTIFTAILGYMLANTAIAMAAVHIG-ILFMQRSVLGRilpgALIN 79 
                                       79**********99973567899***************************9888863.3333444455411116899 PP

                      Cytochrome_B 148 llwgsvsvddatLtrff....slh.fllPflllillllhllllh 186
                                       +l + + v++ t   +f    +lh  ++  l+l++  +h++l+ 
  gi|518652734|ref|YP_008142254.1|  80 WLEA-ILVGNYTTPALFshllALHvAVFSTLMLAIFAIHFMLFE 122
                                       9865.667777655554111178966778888888889998766 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 3
                      Cytochrome_B  71 sllflllylhifrglllgglkktrelvWvi..GvillllvivtafiGyvLp 119
                                        l+f+ll+  i r +     k  +e+ W++  G+ +l+ + v+++ Gy+ p
  gi|518652734|ref|YP_008142254.1| 213 MLVFILLLPFIDR-YHN---KGVLERPWITafGIFMLIGLAVMTVWGYSQP 259
                                       3444444444444.433...34445555542278888888999999**977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1069  (0.0596241); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2076.01
//
Query:       gi|518652735|ref|YP_008142255.1|  [L=132]
Description: Rieske iron-sulfur protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 907.56
//
Query:       gi|518652736|ref|YP_008142256.1|  [L=112]
Description: Sec-independent protein translocase protein TatA [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-14   50.9   0.3    8.4e-14   50.6   0.3    1.2  1  MttA_Hcf106  mttA/Hcf106 family


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.3   4.7e-18   8.4e-14       3      47 ..       5      55 ..       4     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 4.7e-18
                                      HHHHHHHHHHHHHHS-.TTTHHHHHHHHHHHHHHHHHHHHHHHH-.....- CS
                       MttA_Hcf106  3 apelliIlvValllFG.pkkLPEvaraLGktLreFkkavkeleee.....n 47
                                         +liI+vVal++FG  kk+PE+ar+LGk+  eFk  + e e+e     n
  gi|518652736|ref|YP_008142256.1|  5 YMDILIIAVVALIIFGgTKKIPEMARNLGKATGEFKRGQMEIENElrnggN 55
                                      5689***********6479*********************99999555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 00:00:00.45
# Mc/sec: 751.39
//
Query:       gi|518652737|ref|YP_008142257.1|  [L=274]
Description: hypothetical protein FACI_IFERC00001G1376 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  159.2  19.8    1.4e-46  159.0  19.8    1.1  1  TatC           Sec-independent protein translocase protein (T
  ------ inclusion threshold ------
       0.44   11.1   4.1        9.2    6.8   0.2    2.3  2  GTA_holin_3TM  Holin of 3TMs, for gene-transfer release


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.0  19.8   1.5e-50   1.4e-46       4     207 .]      14     243 ..      11     243 .. 0.86

  Alignments for each domain:
  == domain 1  score: 159.0 bits;  conditional E-value: 1.5e-50
                                       HHHHHHHHHHHHHHHHHHHHHHHTHHHHHH........HCCHHHHC.C..............TTS-EE--SSS-HHH CS
                              TatC   4 eeLrkrlirallavaiafiitfvfaeelia........fllepleeae..............eevelivlspleafl 58 
                                       +e+r+rli++l +++i f i+++f  ++i+        ++ +p+ + +               +++l+vl+p+++++
  gi|518652737|ref|YP_008142257.1|  14 DEIRVRLIKILEVFGILFGIFVIFRLQYISlfgyrfmfLYPDPYDN-IgaqvlfllkahtltSDTTLLVLKPVDGVM 89 
                                       79*******************9997776554444432122233333.133444444444443348899********* PP

                                       HHHHHHHHHHHHHSHHHHHHHHHCCCTTTTS---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT....TTTS CS
                              TatC  59 lklkvslvaglvlasPvilyqlwafvapgLykherrlvlvfliaslllfllGaafayfvvlplvlkfll....seev 131
                                       + + +++ ++l++++Pvi+y++ +f+ p+L+ +e+++++ +++ ++llf++Ga+++ ++++p+++k+++    + ++
  gi|518652737|ref|YP_008142257.1|  90 ADFYTCMAIALIISMPVIIYEVSKFIDPALKTSEKEMLRSIILPASLLFFAGAFVGIYFIAPILFKIFAsfdiGVGA 166
                                       *********************************************************************77663334 PP

                                       STTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTTHHHHHHHHHHHHHHH-S..SHHHHHHHHHH CS
                              TatC 132 epllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkkrryaivvilvvaavltP.pdvisqlllavP 207
                                         ++ +s+++sf+++ ++afg++Fe+P+++v l+r+g+v+a+t++k++rya++++lv +++++P  + ++++++a+P
  gi|518652737|ref|YP_008142257.1| 167 DVTMGISSFVSFMFMYTIAFGLSFEIPVFMVGLSRFGIVTADTWKKNWRYAVIGSLVYGMIFSPgVTGFTMVVIAIP 243
                                       667*************************************************************************9 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 ?    5.2   0.5    0.0032        29      86     121 ..     104     150 ..      92     151 .. 0.77
   2 ?    6.8   0.2     0.001       9.2      62     106 ..     206     246 ..     199     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0032
                     GTA_holin_3TM  86 i.........vldPllaaaialgl..alvPepLwwllggvvgfyfva 121
                                       +          +dP+l+++  ++l    +P +L+  +g+ vg+yf+a
  gi|518652737|ref|YP_008142257.1| 104 MpviiyevskFIDPALKTSEKEMLrsIILPASLLFFAGAFVGIYFIA 150
                                       23444444668999999999999987889****************97 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.001
                     GTA_holin_3TM  62 sddgfnrrwRPllgyvtlalllwaivldPllaaaialglalvPe.p 106
                                        +d++++ wR    y++++ l++ ++++P ++   ++++  +P+ +
  gi|518652737|ref|YP_008142257.1| 206 TADTWKKNWR----YAVIGSLVYGMIFSPGVTGFTMVVI-AIPMiA 246
                                       689*******....********************99999.666643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); 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:                         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 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2120.42
//
Query:       gi|518652738|ref|YP_008142258.1|  [L=107]
Description: hypothetical protein FACI_IFERC00001G1377 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.1       0.22   11.0   0.1    1.3  1  Transp_inhibit  Transport inhibitor response 1 protein domain


Domain annotation for each model (and alignments):
>> Transp_inhibit  Transport inhibitor response 1 protein domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1   1.2e-05      0.22       5      20 ..      89     104 ..      86     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.2e-05
                    Transp_inhibit   5 slklKGKPrfadFnLv 20 
                                       +++lKGKP    F+Lv
  gi|518652738|ref|YP_008142258.1|  89 KISLKGKPEIKGFSLV 104
                                       589************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 792.25
//
Query:       gi|518652739|ref|YP_008142259.1|  [L=164]
Description: transcriptional regulatory protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-09   35.5   6.3      2e-08   34.4   6.3    1.6  1  Arc_trans_TRASH  Archaeal TRASH domain
    4.5e-06   26.1   1.2      8e-06   25.3   1.2    1.4  1  HTH_24           Winged helix-turn-helix DNA-binding
    2.3e-05   24.2   0.3    4.4e-05   23.3   0.3    1.5  1  MarR             MarR family
    6.8e-05   22.8   0.6    0.00013   22.0   0.6    1.5  1  HTH_Mga          M protein trans-acting positive regulator (M
    0.00098   19.0   4.0     0.0015   18.4   4.0    1.3  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
     0.0015   18.3   0.0     0.0023   17.8   0.0    1.3  1  MarR_2           MarR family
     0.0034   16.9   0.0     0.0068   15.9   0.0    1.5  1  Sigma70_r4       Sigma-70, region 4
      0.004   17.7   1.2     0.0081   16.7   1.2    1.4  1  Mga              Mga helix-turn-helix domain
     0.0042   16.9   0.3     0.0087   15.9   0.3    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0079   16.0   0.0      0.015   15.1   0.0    1.4  1  HTH_23           Homeodomain-like domain
  ------ inclusion threshold ------
      0.011   15.7   0.6      0.018   15.0   0.6    1.4  1  HTH_11           HTH domain
      0.017   14.9   0.0      0.033   14.0   0.0    1.4  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
      0.037   14.0   0.1      0.066   13.2   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
      0.045   14.0   0.1      0.062   13.6   0.1    1.2  1  TerB_C           TerB-C domain
      0.074   13.4   0.1       0.15   12.4   0.1    1.5  1  Rrf2             Transcriptional regulator
        0.1   12.5   0.1       0.18   11.7   0.1    1.4  1  HTH_5            Bacterial regulatory protein, arsR family
       0.12   12.2   0.0       0.18   11.6   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
       0.12   10.8   0.6       0.14   10.6   0.6    1.1  1  GerA             Bacillus/Clostridium GerA spore germination 
        1.1    9.6   6.0        0.6   10.4   1.6    2.5  3  Ta0938           Ta0938


Domain annotation for each model (and alignments):
>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   6.3   2.2e-11     2e-08       1      33 [.     124     156 ..     124     159 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 2.2e-11
                   Arc_trans_TRASH   1 CDYCGkeivgePivyklknkvYyvCCktCksel 33 
                                       CDYC ++i g+P+++       y+CC+tCkse 
  gi|518652739|ref|YP_008142259.1| 124 CDYCDSIISGKPHILDANHNKLYFCCETCKSEY 156
                                       ***************998777889******985 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   1.2   8.4e-09     8e-06       1      42 [.       1      42 [.       1      44 [. 0.95

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 8.4e-09
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLe 42
                                      +++++ ++L+lL +n++++++e+++rl l ++tv++ + +L 
  gi|518652739|ref|YP_008142259.1|  1 MNRNESRVLKLLFENSKMPISEISDRLLLNRNTVSKIITKLN 42
                                      79999*********************************9995 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.3   4.7e-08   4.4e-05       2      50 ..       2      49 ..       1      54 [. 0.92

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 4.7e-08
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++++ ++L +l e+  + +se+ ++l +++ tv++++++L  +++ieR+
  gi|518652739|ref|YP_008142259.1|  2 NRNESRVLKLLFENSKMPISEISDRLLLNRNTVSKIITKLN-REYIERY 49
                                      78999**********************************95.6788887 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 !   22.0   0.6   1.3e-07   0.00013       9      59 ..       7      56 ..       3      57 .. 0.93

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 1.3e-07
                           HTH_Mga  9 kLlelLteneksltldelakeLglseltlqsdiseLnelFpeelsivikkg 59
                                      + l lL+e ++ ++++e++ +L l + t+ ++i++Ln +++e +++++k++
  gi|518652739|ref|YP_008142259.1|  7 RVLKLLFE-NSKMPISEISDRLLLNRNTVSKIITKLNREYIERYTVTLKER 56
                                      5699****.*************************************99985 PP

>> zf-FCS  MYM-type Zinc finger with FCS sequence motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   4.0   1.6e-06    0.0015       2      41 .]     120     156 ..     119     156 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.6e-06
                            zf-FCS   2 vkkrCwfCkkyikgkpeftyvlendgvvgqFCStsCldsY 41 
                                       v+  C++C   i+gkp    +l+ ++   +FC+++C+++Y
  gi|518652739|ref|YP_008142259.1| 120 VDLYCDYCDSIISGKPH---ILDANHNKLYFCCETCKSEY 156
                                       5778************7...******************99 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0023       3      46 ..       1      42 [.       1      52 [. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHH CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLv 46
                                      +++ + rvL  L  +    + ++e+ +rl l + +vs+i+ +L 
  gi|518652739|ref|YP_008142259.1|  1 MNRNESRVLKLLFENSK--MPISEISDRLLLNRNTVSKIITKLN 42
                                      678899*********99..***********************95 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   7.2e-06    0.0068       6      43 ..       2      40 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.2e-06
                                      -HHHHHHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHHH CS
                        Sigma70_r4  6 pererevlelrf.geglTleEIgerlgiSrerVrqiekr 43
                                      + +e +vl+l f   +++ +EI++rl + r +V+ i+++
  gi|518652739|ref|YP_008142259.1|  2 NRNESRVLKLLFeNSKMPISEISDRLLLNRNTVSKIITK 40
                                      67899*******************************986 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   1.2   8.6e-06    0.0081      19      70 ..       6      58 ..       2      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 8.6e-06
                                      HHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHH.HHCHCCT-EEETTCC CS
                               Mga 19 yqllkflfeeeevsieelaqelyiSestlkrkikeln.klLkefdleltkknl 70
                                       ++lk+lfe+ ++ i e++++l + + t+ ++i +ln ++++ +  +l+++++
  gi|518652739|ref|YP_008142259.1|  6 SRVLKLLFENSKMPISEISDRLLLNRNTVSKIITKLNrEYIERYTVTLKEREN 58
                                      5789********************************957999**999966655 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.3   9.2e-06    0.0087       7      50 ..       2      44 ..       1      67 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.2e-06
                                      HHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCT CS
                              TrmB  7 seyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkG 50
                                      + +E++v + L ++ ++ ++ei+ +l + r++v +++ +L +  
  gi|518652739|ref|YP_008142259.1|  2 NRNESRVLKLLFENSKMPISEISDRLLLNRNTVSKIITKLNR-E 44
                                      579************************************954.4 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.6e-05     0.015       9      42 ..       7      42 ..       4      49 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
                            HTH_23  9 rillllae..GlsvreIAreLgvsrrTvyrwlkryr 42
                                      r+l+ll e  +++++eI+++L  +r+Tv++++ + +
  gi|518652739|ref|YP_008142259.1|  7 RVLKLLFEnsKMPISEISDRLLLNRNTVSKIITKLN 42
                                      6788888889*********************98765 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.6   1.9e-05     0.018       3      42 ..       6      44 ..       4      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.9e-05
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeel 42
                                      + +l+lL+e+ + ++++e++++L + r tv + I +L+  
  gi|518652739|ref|YP_008142259.1|  6 SRVLKLLFENSK-MPISEISDRLLLNRNTVSKIITKLNRE 44
                                      5789***99999.9***********************865 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 ?   14.0   0.0   3.5e-05     0.033       7      36 ..       7      36 ..       6      41 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.5e-05
                     HTH_AsnC-type  7 kILeaLqedaRisyaeLAervGlSestvlr 36
                                      + L++L e+++++ +e+++r+ l ++tv +
  gi|518652739|ref|YP_008142259.1|  7 RVLKLLFENSKMPISEISDRLLLNRNTVSK 36
                                      6799***********************975 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     7e-05     0.066      23      51 ..      19      46 ..       4      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 7e-05
                                      HHHHHHHHTTSSHHHHHHHHHHHHHTTSE CS
                         HTH_Crp_2 23 tqeelAsmlGltretvsrilseLkregli 51
                                         e++++l l+r tvs+i+++L re  i
  gi|518652739|ref|YP_008142259.1| 19 PISEISDRLLLNRNTVSKIITKLNREY-I 46
                                      5579*******************9874.4 PP

>> TerB_C  TerB-C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   6.5e-05     0.062      83     147 ..       3      67 ..       1      69 [. 0.95

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6.5e-05
                            TerB_C  83 eaeaalLraLlareswpreeveslarekglmpdvliesINekafdefddtviedddppeinedyl 147
                                        +e+++L++L++++++p +e+ + +  +    + +i ++N   ++++  t+ e++ + +i+++ +
  gi|518652739|ref|YP_008142259.1|   3 RNESRVLKLLFENSKMPISEISDRLLLNRNTVSKIITKLNREYIERYTVTLKERENSLYIIAEME 67 
                                       689********************************************************999875 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00016      0.15      22      52 ..      14      44 ..       7      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00016
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHT CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrka 52
                                      e++++ ++ei++r  ++++ ++ki++kL+++
  gi|518652739|ref|YP_008142259.1| 14 ENSKMPISEISDRLLLNRNTVSKIITKLNRE 44
                                      56779***********************986 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00019      0.18       6      33 ..       7      35 ..       4      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00019
                                      HHHHHHTT.SSEEHHHHHHHHTS-HHHHH CS
                             HTH_5  6 kILklLae.gelcvcelaeelglsqstvS 33
                                      ++LklL e +++ ++e+++ l l++ tvS
  gi|518652739|ref|YP_008142259.1|  7 RVLKLLFEnSKMPISEISDRLLLNRNTVS 35
                                      89******777****************99 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00019      0.18       8      43 ..       8      42 ..       6      56 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00019
                                      HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHH CS
                          HTH_IclR  8 iLdalaeapqeltlselArrtglpkStvhRlLqtLv 43
                                      +L++l e    + +se+++r+ l++ tv+ ++  L 
  gi|518652739|ref|YP_008142259.1|  8 VLKLLFENSK-MPISEISDRLLLNRNTVSKIITKLN 42
                                      6666666666.9*****************9998885 PP

>> GerA  Bacillus/Clostridium GerA spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00015      0.14      15     108 ..      47     147 ..      32     159 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00015
                              GerA  15 irefkigakkkkallvyidglvdkelieesilkpllelkeeeeeeeee........lellellekllpvaevkeved 83 
                                         + +++ k+++  l++i ++ + + ++++i++  + ++ +     ++        ++ l+++ k++ ++++++v+ 
  gi|518652739|ref|YP_008142259.1|  47 E-RYTVTLKERENSLYIIAEMENIDGLDDDIIEYYKMANGNYLVVMNKdaisdnlqYKNLNIAYKRVLNNDMEKVDL 122
                                       3.3334456788889*****************7653333322222111344555668999999************** PP

                              GerA  84 leevveailsGktvllvdgldkall 108
                                       + + +++i+sGk  +l  +++k + 
  gi|518652739|ref|YP_008142259.1| 123 YCDYCDSIISGKPHILDANHNKLYF 147
                                       ************9999888777654 PP

>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.6   1.5e+03      61      87 ..      32      60 ..      18      80 .. 0.64
   2 ?   -0.3   0.1       1.4   1.3e+03      68      88 ..      83     103 ..      51     123 .. 0.66
   3 ?   10.4   1.6   0.00064       0.6      30      49 ..     139     158 ..     112     163 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.6
                                      HHS---E..E---TTT-S--EEEE----- CS
                            Ta0938 61 skidele..ingnyykgrnveaksgekel 87
                                      + + +++  +n +y +  +v++k+ e++l
  gi|518652739|ref|YP_008142259.1| 32 NTVSKIItkLNREYIERYTVTLKERENSL 60
                                      44444431156667776777777666655 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.4
                                       E---TTT-S--EEEE-----T CS
                            Ta0938  68 ingnyykgrnveaksgekelk 88 
                                        ngny    n  a s++ ++k
  gi|518652739|ref|YP_008142259.1|  83 ANGNYLVVMNKDAISDNLQYK 103
                                       356666666666666665555 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00064
                                       B-TT--BSSS--SSSS-TTS CS
                            Ta0938  30 evdgeklffccdicakefvn 49 
                                       + + +kl+fcc+ c  e+++
  gi|518652739|ref|YP_008142259.1| 139 DANHNKLYFCCETCKSEYIQ 158
                                       56778***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        76  (0.00423894); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1070.19
//
Query:       gi|518652740|ref|YP_008142260.1|  [L=44]
Description: hypothetical protein FACI_IFERC00001G1379 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-15   57.3   2.1    1.3e-15   57.2   2.1    1.1  1  YHS              YHS domain
    0.00035   20.5   1.2    0.00045   20.1   1.2    1.1  1  zf-FCS           MYM-type Zinc finger with FCS sequence motif
  ------ inclusion threshold ------
      0.063   13.6   4.1      0.086   13.2   4.1    1.4  1  Arc_trans_TRASH  Archaeal TRASH domain
      0.098   12.5   0.3        0.1   12.4   0.3    1.1  1  Peptidase_C97    PPPDE putative peptidase domain


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 !   57.2   2.1   2.9e-19   1.3e-15       1      45 [.       2      43 ..       2      44 .] 0.95

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 2.9e-19
                               YHS  1 vtdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFedePekYa 45
                                      +tdPvcgmk    k+e +seY+Gk+YyFc + Ck +F+++P kY 
  gi|518652740|ref|YP_008142260.1|  2 ATDPVCGMKG---KKEIESEYDGKKYYFCNDNCKKEFDANPLKYI 43
                                      59******99...789****************************5 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 !   20.1   1.2     1e-07   0.00045      13      41 .]       9      35 ..       8      35 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 1e-07
                            zf-FCS 13 ikgkpeftyvlendgvvgqFCStsCldsY 41
                                      +kgk+e  ++ e+dg+ ++FC+  C++++
  gi|518652740|ref|YP_008142260.1|  9 MKGKKE--IESEYDGKKYYFCNDNCKKEF 35
                                      578888..8999***************98 PP

>> Arc_trans_TRASH  Archaeal TRASH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   4.1   1.9e-05     0.086      17      33 ..      19      35 ..       6      38 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.9e-05
                   Arc_trans_TRASH 17 lknkvYyvCCktCksel 33
                                      +  k Yy+C  +Ck+e+
  gi|518652740|ref|YP_008142260.1| 19 YDGKKYYFCNDNCKKEF 35
                                      66799**********99 PP

>> Peptidase_C97  PPPDE putative peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   2.3e-05       0.1      92     111 ..      13      32 ..       9      40 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
                                       HHHHTT--GGG-BTTTB-HH CS
                     Peptidase_C97  92 eelsseytgdkYnLiskNCn 111
                                       +e++sey g+kY + + NC+
  gi|518652740|ref|YP_008142260.1|  13 KEIESEYDGKKYYFCNDNCK 32 
                                       589****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 297.03
//
Query:       gi|518652741|ref|YP_008142261.1|  [L=676]
Description: hypothetical protein FACI_IFERC00001G1380 [Ferroplasma acidarmanus fer1]
Scores for complete 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-51  172.6   0.4    5.7e-51  172.6   0.4    1.8  2  E1-E2_ATPase  E1-E2 ATPase
      8e-28   98.2   0.1    1.7e-27   97.1   0.1    1.6  1  Hydrolase     haloacid dehalogenase-like hydrolase
    1.6e-14   53.7   2.8    3.6e-14   52.6   2.8    1.5  1  YHS           YHS domain
    1.6e-08   34.6   3.4    0.00026   20.8   1.4    2.6  2  Hydrolase_3   haloacid dehalogenase-like hydrolase
    0.00054   20.1   1.6     0.0023   18.0   1.6    2.0  1  HAD_2         Haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.098   12.5   0.7       0.18   11.7   0.1    1.7  2  DUF5126       Domain of unknown function (DUF5126)
       0.12   12.3   1.2       0.23   11.4   1.2    1.4  1  zf-FCS        MYM-type Zinc finger with FCS sequence motif


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.3       3.7   9.4e+03     116     136 ..     114     134 ..     103     149 .. 0.46
   2 !  172.6   0.4   2.2e-54   5.7e-51       2     180 ..     173     357 ..     172     358 .. 0.97

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHHHHHHHHHHHS CS
                      E1-E2_ATPase 116 dklgkvlvpvvlliallvfli 136
                                         l+++++ ++++++  +f +
  gi|518652741|ref|YP_008142261.1| 114 GTLTAFFFSLIITLVPGLFPV 134
                                       333444444444433333333 PP

  == domain 2  score: 172.6 bits;  conditional E-value: 2.2e-54
                                       SS--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE CS
                      E1-E2_ATPase   2 llpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvs 78 
                                       l p+++++++dg  ++i++++lvpGDi+++k+g+++paDg +v+g++e+des+LTGE++ v k  g+ ++sGt +++
  gi|518652741|ref|YP_008142261.1| 173 LIPDRVHILKDGIAKDIPMENLVPGDIIQIKPGENIPADGTVVDGTSEIDESMLTGEAESVLKAPGSPITSGTLNLN 249
                                       78999************************************************************************ PP

                                       -EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT......HHHH CS
                      E1-E2_ATPase  79 geakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgksla......eall 149
                                       g + ++Vtatg++++++k+ ++++ a+  ++++qk+ d +++++vp+vl++a+  +l+++++ +s+        a+l
  gi|518652741|ref|YP_008142261.1| 250 GVLSVKVTATGKNSTVNKLYSMIQMASMGRAKIQKISDIFSSYFVPIVLAAAFSSALFWYFYLRSVSnplysiIAVL 326
                                       *****************************************************************999**9999999 PP

                                       HHHHHHHHHS-TTHHHHHHHHHHHHHHHHHH CS
                      E1-E2_ATPase 150 ralallvaaiPcaLplavplalalgarrlak 180
                                        +++++v+a+Pca++la+p++l+++ ++ ++
  gi|518652741|ref|YP_008142261.1| 327 VFVSVVVIACPCAIGLAAPITLLISSNESSR 357
                                       9*********************999887766 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.1   6.6e-31   1.7e-27       1     210 []     374     565 ..     374     565 .. 0.89

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 6.6e-31
                                       SSEEEEESBTTTBCHHHHHHHHHHHH....CHHHHHHHHHHHHCHHHHHHHHHHHHH...HHHHHHHHHETTTEHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa....alalaaaletgsehpigkalvaaakar...sgaltgfatfigrgaya 70 
                                       i+tv+fDk+GT+t+ ep+++ ++       a++l   +e gs+hp + a+v++ k++   + ++++f++++g g+y 
  gi|518652741|ref|YP_008142261.1| 374 IDTVIFDKTGTITDNEPEITAFTTTGdkhlAVSLLYSIESGSNHPVAHAIVNYLKDMnpeKLDISEFREIPGSGVYG 450
                                       79************************777777777777777****************9766677**********888 PP

                                       HTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  71 igkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpet 147
                                       +   + ++a               + ++t+   ++ +la + ++++  ++ +++  ++ L+++ i+v ++tgd+ e+
  gi|518652741|ref|YP_008142261.1| 451 KYDGKNVEAS-------------RAGDHTSLTMDGIELASINLKHK--LRSGIENDIKNLQKNHIRVLIVTGDSLEN 512
                                       8888878787.............444666666677999******99..***************************** PP

                                       HHHHHHHTTGGGESEEEEHHCES.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 148 aeraanqlGddyfdaviasdiet.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                        + +a+ l            +++     +pegk ++++e q  ++ v++VGDg+nD  a++ A+
  gi|518652741|ref|YP_008142261.1| 513 TRDVAEYLH-----------VDKyYYSIKPEGKAEIVKEEQKTGKYVMFVGDGINDTVAMQTAD 565
                                       *********...........665599***************88888***********9999887 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   2.8   1.4e-17   3.6e-14       2      40 ..       3      40 ..       2      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 1.4e-17
                               YHS  2 tdPvcgmkvdkekaeekseYkGkeYyFcSegCkdkFede 40
                                       dPvcgm+v+ + ++ +s+++G++YyFcS+gCkdkF+++
  gi|518652741|ref|YP_008142261.1|  3 VDPVCGMYVSED-SKIYSDRDGTRYYFCSQGCKDKFDKP 40
                                      7********666.***********************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 !   13.1   0.0   2.3e-05      0.06      13      59 ..     481     527 ..     476     535 .. 0.90
   2 !   20.8   1.4     1e-07   0.00026     193     247 ..     535     589 ..     529     597 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.3e-05
                                       TS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                       Hydrolase_3  13 dkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                       ++k+   + + ik+l+++ i v i TG sl+++++v+e l++d ++ 
  gi|518652741|ref|YP_008142261.1| 481 KHKLRSGIENDIKNLQKNHIRVLIVTGDSLENTRDVAEYLHVDKYYY 527
                                       67888888999*******************************98875 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 1e-07
                                       HHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE--GG CS
                       Hydrolase_3 193 kklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtksnn 247
                                        +++ke + + + v+ +GDg ND   ++ a++gvAm+++s+ + +  d +  +n+
  gi|518652741|ref|YP_008142261.1| 535 AEIVKEEQKTGKYVMFVGDGINDTVAMQTADVGVAMASGSDIATATGDIILLNND 589
                                       5677888888999******************************999999988886 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   1.6   9.1e-07    0.0023       1     177 [.     377     570 ..     377     571 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.1e-07
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey.........................glselseeelrkliglslrellrkl 52 
                                       +iFD  gT+ d e+ i +++++  ++                          ++ ++++ +++++ +++   ++ k+
  gi|518652741|ref|YP_008142261.1| 377 VIFDKTGTITDNEPEITAFTTTGDKHLavsllysiesgsnhpvahaivnylkDM-NPEKLDISEFREIPGSGVYGKY 452
                                       678888888888777766555555555777888888888888888888744322.5555567888888888888888 PP

                             HAD_2  53 geseeeee....kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvi 125
                                         ++ e +         ++ ++    + + k+ +g+++ +++L+++ +++ ivT  s e++++  e l +++y+  i
  gi|518652741|ref|YP_008142261.1| 453 DGKNVEASragdHTSLTMDGIELASINLKHKLRSGIENDIKNLQKNHIRVLIVTGDSLENTRDVAEYLHVDKYYYSI 529
                                       8876555578863333344444444445679******************************************9888 PP

                             HAD_2 126 vtsedvekkKPdpeviekaleklklkkeeviyvGDsptDieaakkagikvia 177
                                                   pe  ++++++ + + + v++vGD ++D  a + a + v++
  gi|518652741|ref|YP_008142261.1| 530 K-----------PEGKAEIVKEEQKTGKYVMFVGDGINDTVAMQTADVGVAM 570
                                       4...........5566788889999999******************998876 PP

>> DUF5126  Domain of unknown function (DUF5126)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       3.8   9.7e+03      25      54 ..     260     289 ..     252     292 .. 0.54
   2 ?   11.7   0.1     7e-05      0.18      19      82 ..     486     555 ..     473     566 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.8
                           DUF5126  25 ikNptkanlaivvlvkdsekkewkevdtlY 54 
                                        kN t ++l  ++++ +   ++ +++++++
  gi|518652741|ref|YP_008142261.1| 260 GKNSTVNKLYSMIQMASMGRAKIQKISDIF 289
                                       345555566555555555555555555555 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 7e-05
                           DUF5126  19 GGikvkikNptkanlaivvlvkdsekke.....wkevdtlY.tsakegnlsvrgleaverkfgvvvrDrw 82 
                                        Gi+ +ikN +k+++ + +++ ds +++     + +vd++Y + ++eg++++   e+++ k+ ++v D  
  gi|518652741|ref|YP_008142261.1| 486 SGIENDIKNLQKNHIRVLIVTGDSLENTrdvaeYLHVDKYYySIKPEGKAEIVKEEQKTGKYVMFVGDGI 555
                                       699*******************999998888888888887615699********************9965 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 ?   11.4   1.2   9.1e-05      0.23      24      41 .]      20      37 ..      12      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.1e-05
                            zf-FCS 24 endgvvgqFCStsCldsY 41
                                      ++dg  ++FCS+ C+d++
  gi|518652741|ref|YP_008142261.1| 20 DRDGTRYYFCSQGCKDKF 37
                                      6789999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (676 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1111  (0.0619666); expected 358.6 (0.02)
Passed bias filter:                      655  (0.036533); 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: 0.68u 0.31s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 4332.60
//
Query:       gi|518652742|ref|YP_008142262.1|  [L=150]
Description: ATP/GTP binding protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.8   0.0    4.2e-25   88.6   0.0    1.0  1  PBP       Phosphatidylethanolamine-binding protein


Domain annotation for each model (and alignments):
>> PBP  Phosphatidylethanolamine-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   2.3e-29   4.2e-25       2     102 ..      14     120 ..      13     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.3e-29
                                       --GGG..CSBGGS-EEEEES--TTSSEEEEEEEETTSCCTCTTEEEEEEEEEETTSSEE-TTC..........EE-B CS
                               PBP   2 lpkky..egentsPplswsdvpegtksyalvviDpDapkvsetflHwvvtnipasvtslpega..........vqgk 66 
                                       +p+k+  +g+n sP+++++d  ++t  y +v+ DpDap  +  f+Hw+++nipa   +l+e+            qg 
  gi|518652742|ref|YP_008142262.1|  14 IPDKFtcSGKNHSPKIEIHD-RNETGYYFIVMNDPDAP-SGL-FTHWIIYNIPAGIVTLEENIgnkeiteegyYQGL 87 
                                       89999999***********9.567**************.333.*****************9778899999999**** PP

                                       -TTSSCCCCS---B--STTS..EEEEEEEEEESSSG CS
                               PBP  67 nslgeesesgYlgpcPpkgdgkHrYvfllyaldvea 102
                                       n++ge    gY+gpcPp gdg HrY++++y  d + 
  gi|518652742|ref|YP_008142262.1|  88 NDFGE---LGYGGPCPPRGDGDHRYFIKIYRTDEAV 120
                                       *****...**********************766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1145.39
//
Query:       gi|518652743|ref|YP_008142263.1|  [L=311]
Description: aminotransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-11   43.3   0.0    1.6e-07   30.8   0.0    2.7  2  Aminotran_1_2  Aminotransferase class I and II
     0.0033   16.4   0.0     0.0052   15.8   0.0    1.3  1  Aminotran_5    Aminotransferase class-V


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   6.5e-05      0.59      37     107 ..      33      94 ..      19     104 .. 0.87
   2 !   30.8   0.0   1.8e-11   1.6e-07     150     350 ..     107     293 ..     101     307 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 6.5e-05
                                       TTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHH CS
                     Aminotran_1_2  37 lneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyk 107
                                       +n+++p +   +l+e++ +++g      ++++ +vv++ Ga+++ +++   l+  +   ++v +p y+++ 
  gi|518652743|ref|YP_008142263.1|  33 FNKSTPGH-ETDLKEQIGDLHG------VDAK-NVVLTHGATEAFSMVLYHLR-AKYNTFIVNKPEYEMIY 94 
                                       45566666.99***********......9999.*******************6.88899******999976 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.8e-11
                                       EEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSG CS
                     Aminotran_1_2 150 kvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGla 226
                                        +++  +p+NPtGt+++ ++               ++De++ +fv +        ++  ++ n  iv+++ K +G  
  gi|518652743|ref|YP_008142263.1| 107 ELFVASNPNNPTGTLIKFPDTYSS----------CLIDETFMEFVEK--------LDKYRYSNGYIVNTFTKVYGGG 165
                                       488999*******99998876555..........679*********9........556678889************* PP

                                       GG-EEEEEE.EHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHSTEEEEC CS
                     Aminotran_1_2 227 GeRvGyilg.naavvsqlrklsrpflsssllqaavaaalsdallkqseleemrq.rlqkrrkelrdeLaelglkvla 301
                                        +R+Gyi++ +++ +  l+ ++    +++ ++++ + a    l+k +el ++++  +++++k+l+ e  +l +   +
  gi|518652743|ref|YP_008142263.1| 166 DLRLGYIIApDKDEAAKLEGFKGL--ITEDVSWINVSAGYEILKKHDELLANVKeIINSNHKVLTREKGKLKFYGGK 240
                                       *********777777777777766..566666666666666666666666666505678999999999999666666 PP

                                       CSCSS.EEEEEETHH...CHHHHHHHHHHTCTEEEEEGGGGTS.TTEEEEECTT CS
                     Aminotran_1_2 302 sqsgm.flltdlsae...takelskkLleevgvyvtpgtsftv.pgrlRitvAg 350
                                        + +m ++++d+s++     +++s+kL+++ g++ +p ++f++    lR+++ g
  gi|518652743|ref|YP_008142263.1| 241 DPLAMpVSFVDYSEYiaeGSESISEKLAKK-GIIALPAKYFGIsGPYLRVCITG 293
                                       6633336666666666669999********.************7568****933 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.8e-07    0.0052      46      84 ..      42      79 ..       6     102 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.8e-07
                                      HHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC CS
                       Aminotran_5 46 eearekvaelinaeseeeiiftsGtteainlvalslars 84
                                      ++ +e++ +l++++  ++++ t+G+tea+++v++ l+++
  gi|518652743|ref|YP_008142263.1| 42 TDLKEQIGDLHGVDA-KNVVLTHGATEAFSMVLYHLRAK 79
                                      45789999******6.******************99653 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2108.68
//
Query:       gi|518652744|ref|YP_008142264.1|  [L=169]
Description: hypothetical protein FACI_IFERC00001G1383 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        4.6    7.7   8.3        7.3    7.0   0.0    3.0  2  Tim17     Tim17/Tim22/Tim23/Pmp24 family


Domain annotation for each model (and alignments):
>> Tim17  Tim17/Tim22/Tim23/Pmp24 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   2.0     0.013   2.3e+02       9      25 ..      71      87 ..      59     116 .. 0.50
   2 ?    7.0   0.0   0.00041       7.3       5      29 ..     140     164 ..     137     169 .] 0.84

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.013
                             Tim17  9 gvlGallGavfglvkgs 25
                                      ++l +++G+v g+v ++
  gi|518652744|ref|YP_008142264.1| 71 MLLHFVVGTVVGMVAAL 87
                                      33333333333333332 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00041
                             Tim17   5 tglsgvlGallGavfglvkgsrrad 29 
                                       t+  + + + +Gav+g++ g++ + 
  gi|518652744|ref|YP_008142264.1| 140 TAFYYSMHIFYGAVWGIFLGYFIPR 164
                                       677899*************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 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:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1160.10
//
Query:       gi|518652745|ref|YP_008142265.1|  [L=224]
Description: hypothetical protein FACI_IFERC00001G1384 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-10   40.9   0.0    3.8e-10   39.7   0.0    1.7  1  HTH_3     Helix-turn-helix
    7.3e-07   29.1   0.0    2.5e-06   27.4   0.0    1.9  2  HTH_19    Helix-turn-helix domain
    2.9e-05   24.3   0.0      5e-05   23.6   0.0    1.4  1  HTH_31    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.7   0.0   6.3e-14   3.8e-10       1      48 [.      21      69 ..      21      69 .. 0.97

  Alignments for each domain:
  == domain 1  score: 39.7 bits;  conditional E-value: 6.3e-14
                                      HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHH CS
                             HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaL 48
                                      +k++R++ g+sq eL++ ++vs+s is++E+G + +P    +kk+ +aL
  gi|518652745|ref|YP_008142265.1| 21 IKKWREEFGISQMELSKFMDVSPSVISDYESGrRKSPGANSIKKIVDAL 69
                                      8********************************999*********9997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.2e-10   2.5e-06       4      51 ..      21      68 ..      18      77 .. 0.92
   2 ?   -2.7   0.0       1.1   6.5e+03      29      34 ..     198     203 ..     193     220 .. 0.55

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.2e-10
                            HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaea 51
                                      +k+ Ree+g++q el++  ++s+s is +E+g+++ p+a+ ++ki+ a
  gi|518652745|ref|YP_008142265.1| 21 IKKWREEFGISQMELSKFMDVSPSVISDYESGRRKSPGANSIKKIVDA 68
                                      899*****************************999*******999865 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.1
                            HTH_19  29 isaiEn 34 
                                       +s+iEn
  gi|518652745|ref|YP_008142265.1| 198 LSEIEN 203
                                       445553 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   8.3e-09     5e-05       5      54 ..      20      69 ..      18      75 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.3e-09
                            HTH_31  5 lLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaral 54
                                      + + +Re+ G+sq e+ +   vs+s +s++E+Grr  p    + ++++al
  gi|518652745|ref|YP_008142265.1| 20 TIKKWREEFGISQMELSKFMDVSPSVISDYESGRRKSPGANSIKKIVDAL 69
                                      67889*********************************999999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.35s 00:00:00.96 Elapsed: 00:00:00.56
# Mc/sec: 1194.72
//
Query:       gi|518652746|ref|YP_008142266.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G1385 [Ferroplasma acidarmanus fer1]
Scores for complete 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-75  251.9   0.5      6e-75  251.2   0.5    1.3  1  SRP54            SRP54-type protein, GTPase domain
    5.4e-07   29.7   2.6    5.4e-07   29.7   2.6    2.2  1  SRP54_N          SRP54-type protein, helical bundle domain
    6.6e-06   26.6   1.6    2.1e-05   25.0   0.1    2.2  2  AAA_17           AAA domain
      2e-05   24.4   0.0      3e-05   23.8   0.0    1.3  1  AAA_30           AAA domain
    0.00016   21.3   3.1     0.0007   19.2   3.1    1.9  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
    0.00041   20.1   0.5      0.032   13.9   0.0    3.0  3  Thymidylate_kin  Thymidylate kinase
    0.00044   19.5   0.1    0.00073   18.8   0.1    1.3  1  PIF1             PIF1-like helicase
    0.00049   19.4   0.1    0.00085   18.7   0.1    1.4  1  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0019   17.8   0.3     0.0019   17.8   0.3    1.7  2  GTP_EFTU         Elongation factor Tu GTP binding domain
     0.0035   17.8   2.1     0.0069   16.8   0.4    2.4  2  AAA              ATPase family associated with various cellul
     0.0041   16.4   0.0     0.0079   15.5   0.0    1.6  1  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.011   15.8   1.1       0.04   14.0   0.2    2.3  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.015   15.3   0.7       0.06   13.3   0.7    2.0  1  ResIII           Type III restriction enzyme, res subunit
      0.016   14.8   0.0       0.11   11.9   0.0    2.1  2  AAA_7            P-loop containing dynein motor region
      0.034   14.5   0.0      0.084   13.2   0.0    1.6  2  AAA_16           AAA ATPase domain
      0.034   13.9   0.3      0.084   12.6   0.1    1.7  2  AAA_24           AAA domain
      0.034   13.8   0.8       0.12   12.1   0.1    2.1  2  Catalase_C       C-terminal domain found in long catalases
      0.036   13.5   0.6       0.18   11.3   0.1    2.1  2  Arf              ADP-ribosylation factor family
      0.049   13.7   0.3       0.27   11.3   0.3    2.1  1  AAA_14           AAA domain
       0.05   13.9   0.3       0.26   11.5   0.1    2.1  2  AAA_22           AAA domain
      0.057   13.6   0.0       0.11   12.6   0.0    1.7  1  AAA_33           AAA domain
       0.06   13.2   0.0       0.12   12.3   0.0    1.5  1  APS_kinase       Adenylylsulphate kinase
       0.07   13.0   3.7        1.6    8.6   0.1    2.7  3  NTPase_1         NTPase
       0.12   11.4   0.0       0.15   11.1   0.0    1.1  1  ORC3_N           Origin recognition complex (ORC) subunit 3 N
       0.15   11.9   0.7       0.37   10.6   0.1    1.9  2  Helicase_RecD    Helicase
       0.22   11.6   4.5       0.39   10.8   2.2    2.4  2  MMR_HSR1         50S ribosome-binding GTPase
       0.27   11.1   2.0        1.3    8.9   0.2    2.3  2  MobB             Molybdopterin guanine dinucleotide synthesis
          1    9.2   7.3       0.74    9.7   2.1    2.9  2  AAA_31           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 !  251.2   0.5   9.4e-78     6e-75       1     195 [.     115     309 ..     115     310 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.2 bits;  conditional E-value: 9.4e-78
                                       SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHH CS
                             SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeave 77 
                                       p vil++G++G+GKTtt++KLa +lk+++k+v+l a DtfRa+A++QL++la ++gv++ik++  +dpa+va++a+e
  gi|518652746|ref|YP_008142266.1| 115 PFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAGAIDQLNILAGNVGVEIIKHDFRSDPASVAFDAIE 191
                                       579************************************************************************** PP

                                       HHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSS CS
                             SRP54  78 kakeekidvvlvDTaGrlqndkelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgda 154
                                       +ak++k+d+vl+D+aGr+q++k+l++e+kkik+v+kpd ++lvlda++gq++++qa +F+++++ ++vi+tklD+da
  gi|518652746|ref|YP_008142266.1| 192 HAKARKMDYVLIDSAGRMQTNKNLLDEMKKIKRVAKPDMTILVLDAMIGQDVINQALTFSSEINYDSVIVTKLDTDA 268
                                       ***************************************************************************** PP

                                       STTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHH CS
                             SRP54 155 kgGaalsiaaelklPikfigvGekiedleefdperlvsrll 195
                                       kgG+++si+a +k+Pi f+g+G++++d+ +fd e+++++++
  gi|518652746|ref|YP_008142266.1| 269 KGGSIISISAGIKKPILFVGIGQEMDDIIPFDVEWYLKKIF 309
                                       **************************************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 !   29.7   2.6   8.5e-10   5.4e-07      14      72 ..      36      95 ..      22      98 .. 0.74

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 8.5e-10
                                      CSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS.....S-HHHHHHHHHH CS
                           SRP54_N 14 gkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk.....lkpkqqvkkivk 72
                                      + ++i  + le     +ee+LleaDV++++++++ie++k   +g+ k         +++k++v+
  gi|518652746|ref|YP_008142266.1| 36 KEKTIRRDELES---TIEETLLEADVSYDATEEIIEKLKA-NLGKLKrkidyPAVEEELKSVVR 95
                                      466788888998...9**********************77.77744444333114555555555 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.2       1.2   7.9e+02      59     112 ..      60     113 ..      23     117 .. 0.59
   2 !   25.0   0.1   3.3e-08   2.1e-05       1     109 [.     121     235 ..     121     249 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE--H CS
                            AAA_17  59 keaaekiaeeakkkgvlvdghprikeqagfldglpkevleelkpdaiilleadp 112
                                         a e+i e+ k +   ++ +    + +++l+ + ++v++  + da+ ll +++
  gi|518652746|ref|YP_008142266.1|  60 YDATEEIIEKLKANLGKLKRKIDYPAVEEELKSVVRDVIQHNNKDAVNLLTVEK 113
                                       344444444444444444444444445667777778888877777777777765 PP

  == domain 2  score: 25.0 bits;  conditional E-value: 3.3e-08
                                       EE-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTT.T.S.HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH. CS
                            AAA_17   1 lGgPGsGKgtqceklveky....gfthlsaGdllreeakrg.g.l.akardemrklpleekkelqkeaaekiaeea. 69 
                                       lG+ G GK+t + kl+  +    +  +lsa+d +r+ a ++ + l ++   e+ k + +   +    a ++i++++ 
  gi|518652746|ref|YP_008142266.1| 121 LGINGTGKTTTIGKLAYYLksnnKSVVLSASDTFRAGAIDQlNiLaGNVGVEIIKHDFRS--DPASVAFDAIEHAKa 195
                                       79*************955544458999********9998774322233334444444444..334555555555443 PP

                                       .HSSEEEEEE-SEEEETTEEEESSHHHHHHHH..SEEEEEE CS
                            AAA_17  70 .kkkgvlvdghprikeqagfldglpkevleelkpdaiille 109
                                        k + vl+d   r+++++ +ld+++k +++ +kpd+ il+ 
  gi|518652746|ref|YP_008142266.1| 196 rKMDYVLIDSAGRMQTNKNLLDEMKK-IKRVAKPDMTILVL 235
                                       266779*****************996.9******9977743 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   4.7e-08     3e-05       9     104 ..     105     213 ..      98     236 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 4.7e-08
                            AAA_30   9 avealltsgd.rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgieastiakllkrlk... 81 
                                       av+ l+ +++  v +  G  GtGKtt++++l+  +++++++v++ A+    A ++  +l+i a ++   + +++   
  gi|518652746|ref|YP_008142266.1| 105 AVNLLTVEKKpFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAGAID-QLNILAGNVGVEIIKHDfrs 180
                                       55555544441456678******************************999999998.88998888888888888889 PP

                            AAA_30  82 ..........grarlepgtllivDEagmvdtkq 104
                                                 ++a+ ++ + +++D ag + t++
  gi|518652746|ref|YP_008142266.1| 181 dpasvafdaiEHAKARKMDYVLIDSAGRMQTNK 213
                                       999999999966888888*********987653 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 !   19.2   3.1   1.1e-06    0.0007       2     152 ..     117     266 ..     116     273 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.1e-06
                                       EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS.-SSCHCCCCCCHCCCT.EEEETTTTECCH.CTT-HHHHHH CS
                              cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNe.fgevsiDaellretgveivelenGciCct.lredllkele 74 
                                       v+++ G  G+GKTt + +l    +++++++ +   + f   +iD+  + + +     +    i +   ++ ++ +++
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLAyyLKSNNKSVVLSASDtFRAGAIDQLNILAGN-----VGVEIIKHDfRSDPASVAFD 188
                                       567789999******9999975444444444444441444667776554442.....23334568844556888889 PP

                                       HHHHHH.TT-SEEEEEECT.TTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE- CS
                              cobW  75 aleere.erldviliEttG.laePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnK 149
                                       a+e+ + +++d++li + G + + + ++ + +++k+ ++ d+++ v+Da  + ++  +++ ++ +++++ d ++++K
  gi|518652746|ref|YP_008142266.1| 189 AIEHAKaRKMDYVLIDSAGrMQTNKNLLDEMKKIKRVAKPDMTILVLDA-MIGQDVINQALTFSSEINY-DSVIVTK 263
                                       998877789**********5555555555599*****************.6668899999999999998.7888899 PP

                                       HHH CS
                              cobW 150 tDl 152
                                        D+
  gi|518652746|ref|YP_008142266.1| 264 LDT 266
                                       996 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.35   2.3e+02      48      79 ..      41      72 ..      24      74 .. 0.85
   2 !   13.9   0.0     5e-05     0.032       3      30 ..     122     149 ..     120     161 .. 0.91
   3 ?    0.8   0.0      0.51   3.2e+02     102     124 ..     214     234 ..     203     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.35
                                      TCS---HHHHHHHHHHHHHHTTHHHHHHHHHT CS
                   Thymidylate_kin 48 keeeleeqteallfaadriehleekikpalkq 79
                                      ++ ele+  e  l+ ad+++ ++e+i+++lk 
  gi|518652746|ref|YP_008142266.1| 41 RRDELESTIEETLLEADVSYDATEEIIEKLKA 72
                                      466788888999****************9986 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 5e-05
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEE CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvlt 30 
                                       G++G+GKtt + +l+ +lk++ ++vvl+
  gi|518652746|ref|YP_008142266.1| 122 GINGTGKTTTIGKLAYYLKSNNKSVVLS 149
                                       9*********************999887 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.51
                                       TTCHHHHHHGGGTTSE-SEEEEE CS
                   Thymidylate_kin 102 vdldlvlslnedvllkPdltfll 124
                                       ++ld ++++++ +  kPd+t+l+
  gi|518652746|ref|YP_008142266.1| 214 NLLDEMKKIKRVA--KPDMTILV 234
                                       4556666666654..9****997 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   1.1e-06   0.00073      16     125 ..     109     222 ..      88     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                                       ....HCTS-EEEEESTTSSCHHHHHHHHHHCHCTCCCEEEEESSHHHHHCC.TSEECHHHHT-TTSSS-HHHH..HH CS
                              PIF1  16 avlnekgklfFvtGsgGtgKtflwkallkklrsegkivlavAssGvAalllegGrtahsrfkiplekdeestc..ki 90 
                                        ++++k+ ++ + G  GtgKt    +l  +l+s++k v+  As    a  +++  +++  +++++ k+++ +   ++
  gi|518652746|ref|YP_008142266.1| 109 LTVEKKPFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAGAIDQLNILAGNVGVEIIKHDFRSDpaSV 185
                                       36789999********************************************************9999987655588 PP

                                       HTSCCCHHHHHC-SEEEEECGGG..SBHHHHHHHHHH CS
                              PIF1  91 krgsklaellkktsliiwDEapm..verecfealdrt 125
                                       + +  +  +  k++ +++D a    +++++++++ ++
  gi|518652746|ref|YP_008142266.1| 186 AFDAIEHAKARKMDYVLIDSAGRmqTNKNLLDEMKKI 222
                                       8888888999999999999996412467888887765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.3e-06   0.00085       3     132 ..     117     237 ..     115     257 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.3e-06
                           DUF2075   3 vvlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeafeklssfinnlsefkk 79 
                                       v+l  G  GtGKt    +l++ l   ++++++v+ls +  +++    +l+  +   + + ++ k +    ++s   +
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLAYYL---KSNNKSVVLSASDTFRAGAIDQLNILA--GNVGVEIIKHDFRSDPASVAFD 188
                                       56667999***************...889999999999999998877775444..3344444443333333333355 PP

                           DUF2075  80 aeekkeepkedvvivDEAhrlltksdqaekqseenqlkelmkrakvvvalvDe 132
                                       a+e+++ +k+d v++D A r+ t+++      e + +k++ k  +++++++D 
  gi|518652746|ref|YP_008142266.1| 189 AIEHAKARKMDYVLIDSAGRMQTNKNL---LDEMKKIKRVAK-PDMTILVLDA 237
                                       8899*******************5544...555566666665.5588888885 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       7.9     5e+03     131     148 ..      80      99 ..      61     112 .. 0.64
   2 !   17.8   0.3     3e-06    0.0019       7     109 ..     119     243 ..     113     272 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 7.9
                                       SCGST..HHHHHHHHHHHHH CS
                          GTP_EFTU 131 KmDrl..kaelkeiveevkq 148
                                       K+D +  ++elk +v++v q
  gi|518652746|ref|YP_008142266.1|  80 KIDYPavEEELKSVVRDVIQ 99 
                                       55554445666666655554 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3e-06
                                       EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE................... CS
                          GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle................... 64 
                                        ++g   +GKtT++++L y+++  +k+          Dt  +    ++ i + ++ +e                   
  gi|518652746|ref|YP_008142266.1| 119 LFLGINGTGKTTTIGKLAYYLKSNNKSVVLSA----SDTFRAGAIDQLNILAGNVGVEiikhdfrsdpasvafdaie 191
                                       56666779***************999555444....78888888888888888888888888888889999999887 PP

                                       .TTCSSEEEEEEEESSSGGGHHHHHHH......HHT-SEEEEEEETTTBSTH CS
                          GTP_EFTU  65 .ketkkylinliDtPGHvdFskevirg......lrvlDgavlvvdaveGvep 109
                                        ++ +k  + liD+ G ++ +k+          +++ D+ +lv+da+ G  +
  gi|518652746|ref|YP_008142266.1| 192 hAKARKMDYVLIDSAGRMQTNKNLLDEmkkikrVAKPDMTILVLDAMIGQDV 243
                                       54999***********998777665443333557889*********988443 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   0.1         5   3.2e+03      65      96 ..      43      77 ..       7     105 .. 0.67
   2 !   16.8   0.4   1.1e-05    0.0069       1      99 [.     118     225 ..     118     308 .. 0.53

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5
                                      ETGGGHHHHH...TTCCCHHHHHHHHHHHHHHHHT CS
                               AAA 65 DEidalaksr...sgseseeeervvnqLlteldgv 96
                                      DE+++ +++     + + + +e+++++L + l ++
  gi|518652746|ref|YP_008142266.1| 43 DELESTIEETlleADVSYDATEEIIEKLKANLGKL 77
                                      66666655555544445555556666555555544 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.1e-05
                                       EEEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS...................................... CS
                               AAA   1 vllyGppGtGKTllakavakelg..vefleisgsellsk...................................... 37 
                                       +l+ G  GtGKT+++  +a  l+   + + +s+s+ +                                        
  gi|518652746|ref|YP_008142266.1| 118 ILFLGINGTGKTTTIGKLAYYLKsnNKSVVLSASDTFRAgaidqlnilagnvgveiikhdfrsdpasvafdaiehak 194
                                       699******************97335568888888885556666655555555555555533334444444433333 PP

                                       ............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  38 ............yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                                                      +++k                                            Ll e+++ k+ 
  gi|518652746|ref|YP_008142266.1| 195 arkmdyvlidsaGRMQTNK-------------------------------------------NLLDEMKKIKRV 225
                                       3444443333333333333...........................................444444444433 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.2e-05    0.0079      12      56 ..     111     156 ..      99     223 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.2e-05
                        Zeta_toxin  12 sqerPklillgGqpGAGKselaellkdelerqgnvvrld.pDdlRe 56 
                                        +++P +il  G  G GK++++ +l+ +l+++++ v+l+  D++R+
  gi|518652746|ref|YP_008142266.1| 111 VEKKPFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSaSDTFRA 156
                                       4599**************************6666666551699997 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       5.4   3.5e+03      60      99 ..      64      96 ..      26     111 .. 0.60
   2 ?   14.0   0.2   6.2e-05      0.04       9      87 ..     125     267 ..     122     305 .. 0.59

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.4
                                      CHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA 60 lellealgkkkalllkiagvvlnrvdgeneetllkealee 99
                                      +e++e+l+ +       +g +  ++d ++ e++lk+ +++
  gi|518652746|ref|YP_008142266.1| 64 EEIIEKLKAN-------LGKLKRKIDYPAVEEELKSVVRD 96
                                      4444555444.......44444444444444444444444 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.2e-05
                                       TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                              CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................... 54 
                                       G+GKTt+  +La +l+ +++ V+l   D+ +       g   +++                                
  gi|518652746|ref|YP_008142266.1| 125 GTGKTTTIGKLAYYLKSNNKSVVLSASDTFR------AGAIDQLNIlagnvgveiikhdfrsdpasvafdaiehaka 195
                                       9********************9997766652......2222222223444444445666666666666666666666 PP

                                       ........................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS. CS
                                       ........................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ........................................dlkrllellealgkkkalllkiagvvlnrvdge 87 
                                                                               d+  +  ++++   +++ ++++ +v++++ d +
  gi|518652746|ref|YP_008142266.1| 196 rkmdyvlidsagrmqtnknlldemkkikrvakpdmtilvlDAMIGQDVINQAL-TFSSEINYDSVIVTKLDTD 267
                                       66666666666666666666665555555555555555544444444443333.2333355556666666555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.7   9.4e-05      0.06      21      65 ..      72     153 ..      56     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.4e-05
                                       ..........................................TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
                            ResIII  21 s........................................krdkrglikmaTGtGKTlvaaklierllkkgkeekf 57 
                                       +                                        k+   +l+    GtGKT ++ kl+++l++++   k 
  gi|518652746|ref|YP_008142266.1|  72 AnlgklkrkidypaveeelksvvrdviqhnnkdavnlltveKKPFVILFLGINGTGKTTTIGKLAYYLKSNN---KS 145
                                       4444455555555555555556666666666678888877677778889999****************9974...45 PP

                                       EEEESSHH CS
                            ResIII  58 lflvprks 65 
                                       ++l  + +
  gi|518652746|ref|YP_008142266.1| 146 VVLSASDT 153
                                       55555555 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00018      0.11      27      69 ..     107     150 ..      84     162 .. 0.73
   2 ?    0.2   0.0      0.72   4.6e+02       3      40 ..     250     288 ..     248     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00018
                             AAA_7  27 elllknkkp..vllvGptGtGKtviikdllkkldkekylsltinf 69 
                                       +ll  +kkp  +l+ G  GtGKt++i +l   l+ ++ +s++++ 
  gi|518652746|ref|YP_008142266.1| 107 NLLTVEKKPfvILFLGINGTGKTTTIGKLAYYLK-SNNKSVVLSA 150
                                       55555555533799*************9888888.5555555554 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.72
                             AAA_7   3 ideeakfseilVptvdt.vrysyllelllknkkpvllvG 40 
                                       +++e+++++++V   dt ++   +++     kkp+l+vG
  gi|518652746|ref|YP_008142266.1| 250 FSSEINYDSVIVTKLDTdAKGGSIISISAGIKKPILFVG 288
                                       6788999999**9999956778999999999******99 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0       3.7   2.4e+03      80     139 ..      65     118 ..      38     120 .. 0.42
   2 ?   13.2   0.0   0.00013     0.084      25     143 ..     116     237 ..      93     243 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 3.7
                            AAA_16  80 ellrqlldeaesaeleawrekleealaavpelagaea....srllellkrllallsrderplvl 139
                                       e++++l++++ + ++  +  + ee+l          +      + +  k++++ll+ +++p+v+
  gi|518652746|ref|YP_008142266.1|  65 EIIEKLKANLGKLKRKIDYPAVEEEL----------KsvvrDVIQHNNKDAVNLLTVEKKPFVI 118
                                       33333333333333333333333333..........2222122222222233555555555555 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00013
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrek 100
                                        ++l+ G  G+GK++ + +l+ +l+ ++  ++    d ++++   ++  +++la +  ++ ++ + +s+ ++ + ++
  gi|518652746|ref|YP_008142266.1| 116 FVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAG---AIdQLNILAGNVGVEIIKHDFRSDPASVAFDA 189
                                       57999****************888877544444444444222...22244444444444444444333333333333 PP

                            AAA_16 101 leeala.......avpelagaea.srllellkrllallsrderplvlvlDd 143
                                       +e a a       + +++ + +  + ll+++k++ + +++ +  ++lvlD 
  gi|518652746|ref|YP_008142266.1| 190 IEHAKArkmdyvlI-DSAGRMQTnKNLLDEMKKIKRVAKP-DM-TILVLDA 237
                                       33322233433322.2222222258888888888877777.55.8999986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.3   2.8e+03      86     120 ..      71     100 ..      56     112 .. 0.52
   2 ?   12.6   0.1   0.00013     0.084       4      78 ..     117     210 ..     114     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.3
                            AAA_24  86 irqnekaeskedkgdgkGygelaeefrrllkk.lqe 120
                                       + + +k + k d      y +++ee+++++++ +q+
  gi|518652746|ref|YP_008142266.1|  71 KANLGKLKRKID------YPAVEEELKSVVRDvIQH 100
                                       333333222222......677777777777764444 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00013
                            AAA_24   4 kiliyGpsgiGKTtlakel......gpkplfi...dtekGlksldadkfpdie....swedfldevvel........ 59 
                                        il  G +g+GKTt++ +l       +k +++   dt++ + ++d  ++        ++e +++++ ++        
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLayylksNNKSVVLsasDTFR-AGAIDQLNI---LagnvGVEIIKHDFRSDpasvafda 189
                                       68899**************99999877777773333333.333333333...2366888888888888899999999 PP

                            AAA_24  60 ..aaeladyktlviDtidele 78 
                                          a+ ++ + + iD+++ + 
  gi|518652746|ref|YP_008142266.1| 190 ieHAKARKMDYVLIDSAGRMQ 210
                                       99999999********99884 PP

>> Catalase_C  C-terminal domain found in long catalases
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.6     1e+03      36      62 ..     164     190 ..     128     214 .. 0.60
   2 ?   12.1   0.1   0.00018      0.12      17      66 ..     216     263 ..     207     283 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.6
                        Catalase_C  36 vvaeklgsaegvnrTY.stadaveFDai 62 
                                       ++a ++ + e +++ + s  ++v+FDai
  gi|518652746|ref|YP_008142266.1| 164 ILAGNV-GVEIIKHDFrSDPASVAFDAI 190
                                       555555.333344443134567888887 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00018
                        Catalase_C  17 laqakalaaalaaegvdvtvvaeklgsaegvnrTYstadaveFDaivvad 66 
                                       l+++k++ +++a+ +++++v+   + +++ +n+ ++ ++ +++D+++v++
  gi|518652746|ref|YP_008142266.1| 216 LDEMKKI-KRVAKPDMTILVLDAMI-GQDVINQALTFSSEINYDSVIVTK 263
                                       4555554.46788899999997777.7999******************97 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00028      0.18       6      35 ..     107     136 ..     102     159 .. 0.84
   2 ?    0.1   0.1      0.75   4.8e+02      89     121 ..     203     235 ..     196     262 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00028
                                       HGGTT.TTEEEEEEEESTTSSHHHHHHHHH CS
                               Arf   6 aklklkkkelrilllGLDnaGKtTilkklk 35 
                                       + l+ +kk + il+lG+ ++GKtT + kl 
  gi|518652746|ref|YP_008142266.1| 107 NLLTVEKKPFVILFLGINGTGKTTTIGKLA 136
                                       55667789999*************999986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.75
                                       EETT-CTTHHHHHHHHHHHCTSGCCT..TSEEEEE CS
                               Arf  89 vDsadreRleeakeeLkalleeeelk..evallvl 121
                                       +Dsa   R+++ k+ L+++ + ++++  ++++lvl
  gi|518652746|ref|YP_008142266.1| 203 IDSA--GRMQTNKNLLDEMKKIKRVAkpDMTILVL 235
                                       5654..58899999999998888887445566665 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00042      0.27       4      83 ..     117     216 ..     114     237 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00042
                            AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderd...................kkladpekllelileklk 61 
                                       +++  G+  +GKTt + +l++ l  +++s++  + d+ r                                    ++
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAgaidqlnilagnvgveiikH--------------DFR 179
                                       57788***************8888667777776677666644444444444433333221..............121 PP

                            AAA_14  62 e...............ekktylflDEiqevpewekal 83 
                                       +               +k+ y+++D + ++++ ++ l
  gi|518652746|ref|YP_008142266.1| 180 SdpasvafdaiehakaRKMDYVLIDSAGRMQTNKNLL 216
                                       1222222333333333567777777666665554444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0       1.5   9.3e+02      53      91 ..      63     103 ..      26     113 .. 0.66
   2 ?   11.5   0.1   0.00041      0.26       8     116 ..     118     223 ..     111     244 .. 0.68

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 1.5
                            AAA_22  53 skdllrellralglelka..erlsseellealeqalrarav 91 
                                        +++ ++l  +lg  + +  +++ +eel + +++ +++  +
  gi|518652746|ref|YP_008142266.1|  63 TEEIIEKLKANLGKLKRKidYPAVEEELKSVVRDVIQHNNK 103
                                       45666777777776555577777777777777777776665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00041
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv.fvtlpsstsskdllrellralglelka...erlsseelle 80 
                                       ++  G  GtGKTt++ +l++ l+        +++vv +   +   +  d l+ l+ ++g+e  +   + +  +  ++
  gi|518652746|ref|YP_008142266.1| 118 ILFLGINGTGKTTTIGKLAYYLKSN------NKSVVlSASDTFRAGAIDQLNILAGNVGVEIIKhdfRSDPASVAFD 188
                                       677899**************99542......3443333333333366666677777777777778866677777777 PP

                            AAA_22  81 aleqalraravielliiDEaqhlr.seealeeLrsll 116
                                       a+e+a  ++++   ++iD a ++  ++++l e +++ 
  gi|518652746|ref|YP_008142266.1| 189 AIEHAKARKMD--YVLIDSAGRMQtNKNLLDEMKKIK 223
                                       77777666666..999999999954366666665554 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   0.00018      0.11       1      34 [.     117     155 ..     117     235 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00018
                            AAA_33   1 lvllvGlpGsGKstlaerllkklg....avlls.sdtlr 34 
                                       ++l+ G +G+GK+t + +l+  l+     v+ls sdt+r
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLAYYLKsnnkSVVLSaSDTFR 155
                                       89****************965555555855555145544 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   0.00019      0.12       1      49 [.     114     162 ..     114     168 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00019
                                       S-EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
                        APS_kinase   1 rgvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                                       +++v+++ G+ g+GK+t   +l+ +L+++++sv+l   d+ R g   +L
  gi|518652746|ref|YP_008142266.1| 114 KPFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAGAIDQL 162
                                       589*******************************9999*9999877666 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1         4   2.6e+03     118     160 ..      63     103 ..      55     110 .. 0.56
   2 ?    8.6   0.1    0.0025       1.6       6      30 ..     122     146 ..     117     151 .. 0.89
   3 ?    4.8   0.1     0.037        24      83     129 ..     184     233 ..     166     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4
                                       HHHHHTTTSEEEEE--SS--SHHHH.HHHT-TT-EEEE--TTTT CS
                          NTPase_1 118 veevLksekpvlavihrrkdlalve.eirerkdvkvfevteenr 160
                                        ee++++ k  l+ ++r+ d + ve e+++   v+   ++ +n+
  gi|518652746|ref|YP_008142266.1|  63 TEEIIEKLKANLGKLKRKIDYPAVEeELKS---VVRDVIQHNNK 103
                                       566777777777777777744444403333...22223334444 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0025
                                       --TTSSHHHHHHHHHHHH...GGGE CS
                          NTPase_1   6 GppGvGKtTlvkkvlellkssgvkv 30 
                                       G  G+GKtT + k++  lks++ +v
  gi|518652746|ref|YP_008142266.1| 122 GINGTGKTTTIGKLAYYLKSNNKSV 146
                                       789*****************99876 PP

  == domain 3  score: 4.8 bits;  conditional E-value: 0.037
                                       HHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHH..HHHHHHTTTSEEE CS
                          NTPase_1  83 elalealrkal.seadviviDEiGkmElkskkfke..aveevLksekpvl 129
                                       ++a +a+++a  ++ d ++iD  G+m  + + + e  ++++v k++  +l
  gi|518652746|ref|YP_008142266.1| 184 SVAFDAIEHAKaRKMDYVLIDSAGRMQTNKNLLDEmkKIKRVAKPDMTIL 233
                                       67889999998899************998887764225677766665544 PP

>> ORC3_N  Origin recognition complex (ORC) subunit 3 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00023      0.15       3     117 ..      35     148 ..      33     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00023
                                       XXXXXXXXX..XXXXXXXXX-.-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHCC-..........- CS
                            ORC3_N   3 kkkrakaedyfksllkdeeks.earfkayqrlWeqikseverlqeelnkkalds.lveFvrkqaaervekadetesk 77 
                                       +k+++ ++d ++s ++++  +    ++a +++ e++k+++ +l+ ++   a ++ l + vr   ++   ++++  + 
  gi|518652746|ref|YP_008142266.1|  35 QKEKTIRRDELESTIEETLLEaDVSYDATEEIIEKLKANLGKLKRKIDYPAVEEeLKSVVRDVIQH---NNKDAVNL 108
                                       55555566777777766665568899999***************9999888876155555555544...44455566 PP

                                       ----S--EEEEEBTT-GGGCHHHHHHHHHHHHHTTS-EEE CS
                            ORC3_N  78 lesseiptaalllGvNvddheetFesLtesLrksvtplvv 117
                                       l  ++ p ++l lG+N +  + t  +L+  L+++ ++ v 
  gi|518652746|ref|YP_008142266.1| 109 LTVEKKPFVILFLGINGTGKTTTIGKLAYYLKSNNKSVVL 148
                                       667899*************************998888774 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       4.9   3.1e+03      38      50 ..      62      74 ..      34     107 .. 0.53
   2 ?   10.6   0.1   0.00058      0.37       6     104 ..     124     211 ..     120     227 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 4.9
                     Helicase_RecD 38 nvktlfeflakgl 50
                                      ++++++e l+++l
  gi|518652746|ref|YP_008142266.1| 62 ATEEIIEKLKANL 74
                                      2233333333333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00058
                     Helicase_RecD   6 RGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyiapd 82 
                                        G+GK++++G+++  l +++k +++++a +      + + +   +++l++   +   + +k+ +r++  ++ + a +
  gi|518652746|ref|YP_008142266.1| 124 NGTGKTTTIGKLAYYLKSNNK-SVVLSASDT-----FRAGA---IDQLNILAGNVGVEIIKHDFRSDPASVAFDAIE 191
                                       59*********9999999877.555555433.....33333...233333333444556667778888888888888 PP

                     Helicase_RecD  83 ellklkeqadllvvDEAAaipl 104
                                       +++++k   d +++D A  +++
  gi|518652746|ref|YP_008142266.1| 192 HAKARK--MDYVLIDSAGRMQT 211
                                       888865..68899988876655 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       2.9   1.9e+03      58      58 ..      87      87 ..      33     120 .. 0.55
   2 ?   10.8   2.2   0.00061      0.39      47      88 ..     175     242 ..     117     269 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2.9
                                      S CS
                          MMR_HSR1 58 e 58
                                      e
  gi|518652746|ref|YP_008142266.1| 87 E 87
                                      1 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00061
                                       E........................EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETT..TT CS
                          MMR_HSR1  47 e........................ielvDtpGliegaseekglgkaflaleeadlillvvdas..ee 88 
                                       +                        ++l+D +G ++++++  ++ k+++++ + d+ +lv+da   ++
  gi|518652746|ref|YP_008142266.1| 175 KhdfrsdpasvafdaiehakarkmdYVLIDSAGRMQTNKNLLDEMKKIKRVAKPDMTILVLDAMigQD 242
                                       0333334444444444444444444********555333333777777777778********775422 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2     0.002       1.3       1      30 [.     117     146 ..     117     160 .. 0.90
   2 ?    1.4   0.1      0.42   2.7e+02      28      80 ..     169     221 ..     153     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.002
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                       v+ + g +g+GKTt + kl   lk+++ +v
  gi|518652746|ref|YP_008142266.1| 117 VILFLGINGTGKTTTIGKLAYYLKSNNKSV 146
                                       67899******************9998776 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.42
                              MobB  28 lrvgtiKhahhgfdvdkpgkDsyrhrkAG.Akevlvaskerlalikel.eeaels 80 
                                       + v +iKh+  + d  +   D+ +h+kA   + vl+ s  r++  k+l +e   +
  gi|518652746|ref|YP_008142266.1| 169 VGVEIIKHDFRS-DPASVAFDAIEHAKARkMDYVLIDSAGRMQTNKNLlDE-MKK 221
                                       556778887654.56667789999999962466888888898888887433.333 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.2       0.7   4.5e+02      40     103 ..      34      96 ..      30     112 .. 0.64
   2 ?    9.7   2.1    0.0012      0.74      12      62 ..     125     176 ..     117     261 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.7
                            AAA_31  40 pQanattglgiekneiektlyevlieeknikeaiiktkvenldlipssidLaeaeielvelekk 103
                                       pQ+  t++ +  +++ie+tl+e+ ++   ++e+i  +   nl  +  +id  ++e el ++ + 
  gi|518652746|ref|YP_008142266.1|  34 PQKEKTIRRDELESTIEETLLEADVSYDATEEIIE-KLKANLGKLKRKIDYPAVEEELKSVVRD 96 
                                       67777776665566667777776554444444444.4456777777777777777777766555 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0012
                            AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanatt.glgiekneiektlyev 62 
                                       G GKTTt  +la+ l +++k v l   D+  + ++ +l+i   ++  ++++ 
  gi|518652746|ref|YP_008142266.1| 125 GTGKTTTIGKLAYYLKSNNKSVVLSASDTFRAGAIdQLNILAGNVGVEIIKH 176
                                       89********************998888755443324455555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1165  (0.0649785); expected 358.6 (0.02)
Passed bias filter:                      729  (0.0406604); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); 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: 0.63u 0.34s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 1951.48
//
Query:       gi|518652747|ref|YP_008142267.1|  [L=133]
Description: prefoldin subunit alpha [Ferroplasma acidarmanus fer1]
Scores for complete 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   56.8   6.1    2.4e-15   56.5   6.1    1.2  1  Prefoldin       Prefoldin subunit
    6.4e-05   23.2   6.9     0.0044   17.3   0.6    2.2  2  CLZ             C-terminal leucine zipper domain of cyclic nu
     0.0011   18.9  10.7     0.0088   16.0   3.2    2.1  2  Prefoldin_2     Prefoldin subunit
     0.0037   17.5   0.8     0.0037   17.5   0.8    2.1  2  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
     0.0056   16.6   1.8      0.007   16.3   0.3    1.8  2  HrcA            HrcA protein C terminal domain
      0.006   16.5   0.8      0.013   15.4   0.8    1.6  1  Tnp_22_trimer   L1 transposable element trimerization domain
  ------ inclusion threshold ------
      0.012   15.8   5.5        2.1    8.5   3.6    2.1  2  RasGAP_C        RasGAP C-terminus
      0.015   15.6   1.7      0.015   15.6   1.7    1.8  2  Phage_Gp23      Protein gp23 (Bacteriophage A118)
       0.12   12.3   1.7       0.17   11.9   0.0    1.8  2  Borealin        Cell division cycle-associated protein 8
       0.14   12.6   1.0       0.23   11.9   1.0    1.6  1  Phage_lysozyme  Phage lysozyme
       0.18   11.4   3.1        7.6    6.0   1.5    2.1  2  SseC            Secretion system effector C (SseC) like famil
       0.22   11.7   6.3       0.13   12.4   1.3    2.2  2  KIP1            KIP1-like protein
       0.44   10.7   6.6        3.4    7.9   1.2    2.2  2  Fib_alpha       Fibrinogen alpha/beta chain family
       0.44   10.8   4.0       0.39   10.9   0.3    2.0  2  DUF2951         Protein of unknown function (DUF2951)
       0.47   10.7   2.0        2.5    8.4   0.1    2.1  2  DUF948          Bacterial protein of unknown function (DUF948
       0.71   10.2   5.2       0.23   11.8   1.6    1.9  2  YnfE            Uncharacterized YnfE-like
       0.87    8.3   9.6        2.2    6.9   1.7    2.1  2  Tektin          Tektin family
        2.7    7.2   7.2         15    4.8   7.2    1.8  1  CorA            CorA-like Mg2+ transporter protein


Domain annotation for each model (and alignments):
>> Prefoldin  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.5   6.1   2.5e-18   2.4e-15       2     118 ..      15     129 ..       5     131 .. 0.96

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.5e-18
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-TT-EEEEEEETTEEEEEE--STTEEEEEEETTEEEEEEHHHH CS
                         Prefoldin   2 keeleslqaelaqlkeaieelektletlktlkkedegkevlvplgaglyvkaevkdtdkvlvdlGagyyveksleeA 78 
                                       k  le++ ++++ l +++ee ++tl+ lk+ +  +++k v + +g+gl+ ka + dt+k++v +G+g+++e ++e+ 
  gi|518652747|ref|YP_008142267.1|  15 KNLLETIDSRMNLLLKTLEESNDTLALLKDTDY-EKSKDVKISIGSGLFSKAAL-DTSKIIVPVGSGVFIEEEKEKT 89 
                                       67799999*************************.******************99.********************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                         Prefoldin  79 iellkkkleelekqlekleeeleklkdqittleanlaqly 118
                                       i+  ++++++l+++  +l ++ + ++++++ l+  +++ +
  gi|518652747|ref|YP_008142267.1|  90 IKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSVQRAQ 129
                                       *********************************9999987 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 !    9.3   1.0    0.0014       1.4      26      61 ..       4      39 ..       1      41 [. 0.90
   2 !   17.3   0.6   4.4e-06    0.0044      27      59 ..      84     116 ..      78     122 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.0014
                               CLZ 26 qkeleekverLessLeaLqtrlarLlaeyessqrkL 61
                                      ++el e++e L++ Le+++ r++ Ll+ +e+s+ +L
  gi|518652747|ref|YP_008142267.1|  4 ENELVEQIEYLKNLLETIDSRMNLLLKTLEESNDTL 39
                                      5678899*************************9887 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 4.4e-06
                               CLZ  27 keleekverLessLeaLqtrlarLlaeyessqr 59 
                                       +e e+ ++r+e+++++Lq+ ++ Ll++ +s+q+
  gi|518652747|ref|YP_008142267.1|  84 EEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQN 116
                                       77899**************************97 PP

>> Prefoldin_2  Prefoldin subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   1.1    0.0031       3.1       2      56 ..       6      62 ..       5      71 .. 0.78
   2 !   16.0   3.2   8.8e-06    0.0088      53     103 ..      79     129 ..      64     132 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0031
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT..--EEEEETTEEE CS
                       Prefoldin_2  2 elinkfqqlqqqlqqlaqqikqletqlkelelvleelellded..tkvyklvGdvlv 56
                                      el+++ + l++ l+ +++ ++ l + l+e++++l  l++ d +  ++v  ++G  l+
  gi|518652747|ref|YP_008142267.1|  6 ELVEQIEYLKNLLETIDSRMNLLLKTLEESNDTLALLKDTDYEksKDVKISIGSGLF 62
                                      577888888888999999999999999999999988888877766777777776665 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.8e-06
                                       TEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCT CS
                       Prefoldin_2  53 dvlvkqdkeevkeeLeerketlekeiktlekqleklekeleelkeelqkkl 103
                                       +v+++++ke+++++ ee++ +l+  +++l kq+++ +++++ l  ++q ++
  gi|518652747|ref|YP_008142267.1|  79 GVFIEEEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSVQRAQ 129
                                       79************************************9999887777666 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   1.3     0.058        58      60      95 ..       5      40 ..       2      50 .. 0.85
   2 !   17.5   0.8   3.7e-06    0.0037      18      61 ..      87     130 ..      76     133 .] 0.89

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.058
                       TMF_TATA_bd 60 kelkkeleelekeleelqeryetlLellGeksEeve 95
                                      +el +++e l++ le +++r + lL+ l e ++   
  gi|518652747|ref|YP_008142267.1|  5 NELVEQIEYLKNLLETIDSRMNLLLKTLEESNDTLA 40
                                      56788999999***************9999887765 PP

  == domain 2  score: 17.5 bits;  conditional E-value: 3.7e-06
                       TMF_TATA_bd  18 sseirrlEgElaslkeelerleaerdeareeivklmkeneelke 61 
                                       +++i+r+E  ++sl++++++l +++++a++   +lm ++++ +e
  gi|518652747|ref|YP_008142267.1|  87 EKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSVQRAQE 130
                                       789*****************************999998888766 PP

>> HrcA  HrcA protein C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.3   7.1e-06     0.007     131     193 ..       3      73 ..       1      91 [. 0.71
   2 ?    0.3   0.1      0.56   5.6e+02      71     116 ..      97     110 ..      66     130 .. 0.52

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.1e-06
                              HrcA 131 Gtsnllrqpefsdd......eklrellelleekvvllkllsels..daegvsvrIGsEneleelkdcSvVt 193
                                       G ++l++q e+ ++      ++++ ll+ lee ++ l ll++++  ++++v++ IGs    ++  d+S + 
  gi|518652747|ref|YP_008142267.1|   3 GENELVEQIEYLKNlletidSRMNLLLKTLEESNDTLALLKDTDyeKSKDVKISIGSGLFSKAALDTSKII 73 
                                       555555555543222322358999999*************8888954445******988777777777655 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.56
                              HrcA  71 laklsnllneklagltlseiaerlreeklkeelseyeelleqllea 116
                                       ++ l+                                + +++ll++
  gi|518652747|ref|YP_008142267.1|  97 IQSLQ--------------------------------DTYNNLLKQ 110
                                       22222................................222222222 PP

>> Tnp_22_trimer  L1 transposable element trimerization domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   1.4e-05     0.013      25      43 .]      85     103 ..      83     103 .. 0.95

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHHHHHHHHHH CS
                     Tnp_22_trimer  25 ereKrkkileQslQviqDy 43 
                                       e+eK +k+ e ++Q +qD+
  gi|518652747|ref|YP_008142267.1|  85 EKEKTIKRMEENIQSLQDT 103
                                       79****************8 PP

>> RasGAP_C  RasGAP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0    0.0046       4.5      61     132 ..       6      74 ..       2      78 .. 0.58
   2 ?    8.5   3.6    0.0021       2.1      41      82 ..      86     127 ..      84     131 .. 0.86

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0046
                          RasGAP_C  61 tLseknnylesqlesYkayienvleqlkkkkgklpfskqyfkkrelkksgklpkfgsykysakqLeekgVLl 132
                                       +L e+ +yl++ le+ ++ ++  l++l++++ +l   k++ ++++   ++ + + gs  +s + L   ++++
  gi|518652747|ref|YP_008142267.1|   6 ELVEQIEYLKNLLETIDSRMNLLLKTLEESNDTLALLKDTDYEKS---KDVKISIGSGLFSKAALDTSKIIV 74 
                                       455555666666666666666666666666544444443333333...333345688888888888888887 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0021
                          RasGAP_C  41 kgrlrekrkeElesleetlktLseknnylesqlesYkayien 82 
                                       k++ +++++e ++sl++t+++L ++++  ++  + +   +++
  gi|518652747|ref|YP_008142267.1|  86 KEKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSVQR 127
                                       788899999******************999998887666665 PP

>> Phage_Gp23  Protein gp23 (Bacteriophage A118)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.3       1.3   1.3e+03      86     118 ..      24      54 ..       4      57 .. 0.60
   2 ?   15.6   1.7   1.5e-05     0.015      67     105 ..      83     125 ..      81     130 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.3
                        Phage_Gp23  86 kqndliksekkaidelskslvklaqkkdlleek 118
                                       + n l+k  +++ d l  +l k ++  +  + k
  gi|518652747|ref|YP_008142267.1|  24 RMNLLLKTLEESNDTL--ALLKDTDYEKSKDVK 54 
                                       4455566666777777..666666655555555 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.5e-05
                        Phage_Gp23  67 keekdktissvdks.krlldkqndliksek...kaidelsksl 105
                                       +eek+kti  ++++ ++l d  n+l+k+++   +  d l  s+
  gi|518652747|ref|YP_008142267.1|  83 EEEKEKTIKRMEENiQSLQDTYNNLLKQKQsaqNNYDALMYSV 125
                                       79*********9865999**********994444456665555 PP

>> Borealin  Cell division cycle-associated protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.3       1.3   1.3e+03      94     112 ..      15      32 ..       4      42 .. 0.58
   2 ?   11.9   0.0   0.00017      0.17      56     111 ..      55     110 ..      47     120 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.3
                          Borealin  94 deellekLdeetlkqlkkL 112
                                       + +lle++d+     lk+L
  gi|518652747|ref|YP_008142267.1|  15 K-NLLETIDSRMNLLLKTL 32 
                                       2.45555555555555555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
                          Borealin  56 ls.GSPlaegvvteevanvniPvgdGevlslq.akeldevdeellekLdeetlkqlkk 111
                                       +s GS l ++++ + + ++ +Pvg G  ++ + +k +++++ e +++L+++  + lk+
  gi|518652747|ref|YP_008142267.1|  55 ISiGSGLFSKAALD-TSKIIVPVGSGVFIEEEkEKTIKRME-ENIQSLQDTYNNLLKQ 110
                                       4569******9999.9**********666666234446666.8899999888777776 PP

>> Phage_lysozyme  Phage lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   1.0   0.00024      0.23      19      60 ..      84     125 ..      15     133 .] 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00024
                                       -EHHHHHHHHHHHHHHHHHHHHHHTTSHHSSHHHHHHHHHHH CS
                    Phage_lysozyme  19 itkeeaagryekdlktaerkikqyikvkdfepnqqdalvsla 60 
                                        +ke+  +r e++++  ++  + + k+k+  +n +dal++ +
  gi|518652747|ref|YP_008142267.1|  84 EEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSV 125
                                       57889999******************************9865 PP

>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.015        15     279     312 ..       7      40 ..       3      44 .. 0.90
   2 ?    6.0   1.5    0.0076       7.6     275     309 ..      82     116 ..      80     124 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.015
                              SseC 279 ldeaaeeikellesiqellksmsqaisqkgdtlq 312
                                       l e++e +k+lle+i++ ++ ++++++ ++dtl+
  gi|518652747|ref|YP_008142267.1|   7 LVEQIEYLKNLLETIDSRMNLLLKTLEESNDTLA 40 
                                       5588999************************986 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                              SseC 275 lqkvldeaaeeikellesiqellksmsqaisqkgd 309
                                       +++ +++ ++++ e+++s q++++++++  ++ ++
  gi|518652747|ref|YP_008142267.1|  82 IEEEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQN 116
                                       67788888889999999999988888876555444 PP

>> KIP1  KIP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.3   0.00013      0.13      11      52 ..       9      50 ..       3      56 .. 0.88
   2 ?    1.8   0.3      0.26   2.6e+02      36      51 ..      84      99 ..      80     127 .. 0.53

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                              KIP1 11 kqskwLqetlseldekvkemlklieedadsfakraemyykkr 52
                                      +q ++L++ l+ +d++++ +lk +ee +d++a  + ++y+k 
  gi|518652747|ref|YP_008142267.1|  9 EQIEYLKNLLETIDSRMNLLLKTLEESNDTLALLKDTDYEKS 50
                                      68899**************************98888888875 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.26
                              KIP1 36 edadsfakraemyykk 51
                                      e++++  kr e + + 
  gi|518652747|ref|YP_008142267.1| 84 EEKEKTIKRMEENIQS 99
                                      4444444444444332 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.4     0.013        13      86     122 ..       7      43 ..       3      54 .. 0.64
   2 ?    7.9   1.2    0.0034       3.4      94     123 ..      87     116 ..      81     131 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.013
                                       HHHCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  86 leeeilrlketidaqesnirvLqnvlesneqkiqkLe 122
                                       l e+i++lk+ + +  s+++ L ++le+ +  ++ L+
  gi|518652747|ref|YP_008142267.1|   7 LVEQIEYLKNLLETIDSRMNLLLKTLEESNDTLALLK 43 
                                       4446666666666666666666666666666666665 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0034
                                       HHHHHCCHHHHHHHHHHHHHHHHHHHHHHH CS
                         Fib_alpha  94 ketidaqesnirvLqnvlesneqkiqkLeq 123
                                       ++ti++ e+ni+ Lq++++++ ++ q  ++
  gi|518652747|ref|YP_008142267.1|  87 EKTIKRMEENIQSLQDTYNNLLKQKQSAQN 116
                                       566666667777777776666555444433 PP

>> DUF2951  Protein of unknown function (DUF2951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3      0.43   4.3e+02      21      45 ..      15      40 ..       4      59 .. 0.60
   2 ?   10.9   0.3   0.00039      0.39       2      44 ..      79     121 ..      78     132 .. 0.75

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.43
                           DUF2951 21 ktmlekld.eikdslktqekvyikld 45
                                      k +le++d ++++ lkt e+ ++ l 
  gi|518652747|ref|YP_008142267.1| 15 KNLLETIDsRMNLLLKTLEESNDTLA 40
                                      56666665356666677776666653 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00039
                           DUF2951   2 gftkkheqewrlrrleendktmlekldeikdslktqekvyikl 44 
                                       g +   e+e  ++r+een +++ ++++++ + +++ ++ y+ l
  gi|518652747|ref|YP_008142267.1|  79 GVFIEEEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDAL 121
                                       6677889*******************99866666555555555 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.2      0.24   2.4e+02      32      56 ..      18      42 ..       5      56 .. 0.51
   2 ?    8.4   0.1    0.0025       2.5      25      64 ..      87     126 ..      71     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.24
                            DUF948 32 aatieelekqvdpilkevedllakv 56
                                       +ti++ ++ + ++l+e++d+la  
  gi|518652747|ref|YP_008142267.1| 18 LETIDSRMNLLLKTLEESNDTLALL 42
                                      3333333333444444555555444 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0025
                            DUF948  25 kktldeaaatieelekqvdpilkevedllakvnelledvn 64 
                                       +kt++++++ i++l++  +++lk+ + + ++  +l+  v+
  gi|518652747|ref|YP_008142267.1|  87 EKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDALMYSVQ 126
                                       5777777777777777777777777777777777666665 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.6   3.6e+03      17      28 ..      42      52 ..      28      63 .. 0.68
   2 ?   11.8   1.6   0.00023      0.23      24      60 ..      85     125 ..      83     131 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.6
                              YnfE 17 inapDYeGkeeD 28
                                      ++ +DYe k +D
  gi|518652747|ref|YP_008142267.1| 42 LKDTDYE-KSKD 52
                                      4556665.4444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00023
                              YnfE  24 GkeeDlekqkeql....elYekqLkqesssdedfDevvdav 60 
                                        ke+ +++ +e++    ++Y+  Lkq+ s+++++D ++ +v
  gi|518652747|ref|YP_008142267.1|  85 EKEKTIKRMEENIqslqDTYNNLLKQKQSAQNNYDALMYSV 125
                                       5999999999999444447****************998765 PP

>> Tektin  Tektin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   1.2    0.0037       3.7     121     161 ..      14      54 ..       6      55 .. 0.87
   2 ?    6.9   1.7    0.0022       2.2     331     358 ..      88     115 ..      81     130 .. 0.41

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0037
                            Tektin 121 LlkEveliegvqellkrtleqaeeqlrllraakhkLekdls 161
                                       L++ +e+i + ++ll +tle+ ++ l+ll+++ ++ +kd++
  gi|518652747|ref|YP_008142267.1|  14 LKNLLETIDSRMNLLLKTLEESNDTLALLKDTDYEKSKDVK 54 
                                       66668999999999999999999999999999999999975 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0022
                            Tektin 331 etieaLkeklaeaeaslkaLertrlele 358
                                       +ti++++e+++  ++++++L +++++ +
  gi|518652747|ref|YP_008142267.1|  88 KTIKRMEENIQSLQDTYNNLLKQKQSAQ 115
                                       2333333333333333333333332222 PP

>> CorA  CorA-like Mg2+ transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   7.2     0.015        15     119     225 ..      10     121 ..       4     123 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.015
                              CorA 119 ivdrlfellekleeeldeledeledstkkeilrelaqlrrr.lvkl.......rralapnrevlkrlla.kaddkll 186
                                        +++l +lle+++++++ l ++le+s++   l + ++++++  vk+        +a++++ +++       + +  +
  gi|518652747|ref|YP_008142267.1|  10 QIEYLKNLLETIDSRMNLLLKTLEESNDTLALLKDTDYEKSkDVKIsigsglfSKAALDTSKII----VpVGSGVFI 82 
                                       5666677777777777777777766666666666666664434444544444444444444444....133456666 PP

                              CorA 187 ddedkeylrdlldelerllemlealrerleslqdtyssl 225
                                       ++e+++ ++++++++++l+++ ++l ++ +s q++y +l
  gi|518652747|ref|YP_008142267.1|  83 EEEKEKTIKRMEENIQSLQDTYNNLLKQKQSAQNNYDAL 121
                                       666666677777777777777777777777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2053  (0.114507); expected 358.6 (0.02)
Passed bias filter:                      805  (0.0448993); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 953.27
//
Query:       gi|518652748|ref|YP_008142268.1|  [L=412]
Description: hypothetical protein FACI_IFERC00001G1387 [Ferroplasma acidarmanus fer1]
Scores for complete 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-104  349.8   0.0   1.9e-104  349.6   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 !  349.6   0.0  1.1e-108  1.9e-104       1     377 [.       9     393 ..       9     394 .. 0.92

  Alignments for each domain:
  == domain 1  score: 349.6 bits;  conditional E-value: 1.1e-108
                                       GGGS--TT-EEEEEE-----EECT.TEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TTS-GGG-SHHHHHHHH CS
                               PGK   1 vkdldlkgkrvlvRvDfNvplkke.gkitddtriraalpTikyllekgakvvllsHlgrpkgekeklslkpvaerLs 76 
                                       ++d+d++gkrv +R+D+N+p++   g++ ddtr+ + l Ti++l  k+ kvv+++H+grp g+++ +sl+++a +L 
  gi|518652748|ref|YP_008142268.1|   9 MDDFDFNGKRVYLRIDINSPINPItGEVVDDTRFIHYLRTINEL--KNSKVVIIAHQGRP-GDSDFVSLRQHAGHLG 82 
                                       689******************8768*******************..8999**********.89************** PP

                                       HHHTT-EEEESSTTSHHHHHHHHT-TTT-EEEES-GGGSTTT...TTT-H...H....HHHHHHHT-SEEEE--GGG CS
                               PGK  77 ellgkeVkfvedvvgeeveeaiaelkegevllLeNvrfykeE...eknde...e....lakklasladvyVnDAFgt 143
                                       +llg++V fv++++g++ve+ai+++k+g++++LeN rfy+eE   + + +   +    ++++l++l+d+++ DAF +
  gi|518652748|ref|YP_008142268.1|  83 RLLGRDVLFVDSLIGSAVETAIRNMKNGDIIMLENSRFYSEEiliK-D-DgaaQkntfIVRNLSKLFDYFIIDAFPA 157
                                       ******************************************6531.2.2233134569****************** PP

                                       TTS--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHHHTTT-..SEEEEETCHHH CS
                               PGK 144 ahrahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvienLlekv..dkliigGgman 218
                                       +hr++++++g++++ +++aG+lme+E++ ++++++++++p +ai+GGak+ d ikv    lek   d++i gG+ an
  gi|518652748|ref|YP_008142268.1| 158 IHRDQTTLTGFKDIKPNIAGRLMETEINSIDRFMNSKSHPKLAIMGGAKIRDAIKVTGPFLEKGivDNIIFGGVAAN 234
                                       ***************88*********************************************9667*********** PP

                                       HHHHHTT-B-TTSS--G....GG.....HHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EE CS
                               PGK 219 tFlkaqgleigkslvee....dk.....lelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedema 286
                                       +Fl a+g++igk  +e     dk     le +k+ll++++   ++i+lp D++++    +  +++++ e++p+++  
  gi|518652748|ref|YP_008142268.1| 235 IFLWASGIDIGKRNMEFiekqDKnykklLEECKSLLSRFS---DRIYLPEDFMLNP--LQ--TEIKTGEKVPDGQLL 304
                                       ************9995433232244445778888888776...89**********7..33..48999********** PP

                                       EEE-HHHHHHHHHHHCC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCHTSEEEEESHHHHHHHHHTT-GGGSSE CS
                               PGK 287 lDigpktielfaeaikeaktvvwnGpmGvfeiekfakGTkaiakalaeatkgalsivGGgdsaaaveklgladkvsh 363
                                        Dig ++i++f+++i++ak +++nGpmG++ei++++ GT++i +a++++   a +ivGGg++++a++++gl+d++ +
  gi|518652748|ref|YP_008142268.1| 305 ADIGFESIKTFSSIIEKAKNIFLNGPMGMYEINEYSLGTREIFNAVSQSP--ASKIVGGGHTINAINEFGLSDSMGY 379
                                       ************************************************85..6************************ PP

                                       EESSSHHHHHHHCT CS
                               PGK 364 vStGGgAsLelLeg 377
                                       +StGGgA++++L+g
  gi|518652748|ref|YP_008142268.1| 380 ISTGGGALINYLSG 393
                                       ************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       627  (0.0349713); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2809.61
//
Query:       gi|518652749|ref|YP_008142269.1|  [L=201]
Description: protease synthase and sporulation negative regulatory protein pai 2 [Ferroplasma acidarmanus fer1]
Scores for complete 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  139.6   0.2      1e-40  139.2   0.2    1.2  1  FMN_bind_2  Putative FMN-binding domain
  ------ inclusion threshold ------
      0.027   14.2   0.8       0.22   11.2   0.1    2.2  2  DUF1251     Protein of unknown function (DUF1251)
      0.058   12.9   0.5       0.17   11.4   0.5    1.8  2  YvrJ        YvrJ protein family
       0.11   13.2   0.9       0.69   10.6   0.4    2.1  2  DUF3823_C   Domain of unknown function (DUF3823_C)
       0.13   12.9   0.0       0.63   10.6   0.0    2.2  2  SEP         SEP domain


Domain annotation for each model (and alignments):
>> FMN_bind_2  Putative FMN-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.2   0.2   2.8e-44     1e-40       1     167 [.       1     157 [.       1     158 [. 0.92

  Alignments for each domain:
  == domain 1  score: 139.2 bits;  conditional E-value: 2.8e-44
                                       XXXXXXXXX--HCHHHHHHHHS-EEEEEEEETTEEEEEEEE-EE...-TTSSEEEEEEETTSGGGGGT.TTS-EEEE CS
                        FMN_bind_2   1 MYipkefaeedleelrqlirenplgtLvtaiesglqashiPflldeeekgkgkLrgHlaraNpqakaleeeeevlvv 77 
                                       MY+p+ef+ +d+e++ ++++++++g++++  ++++  ++iP++l ++++++ +L+gH+araN q+ + ++++ v v+
  gi|518652749|ref|YP_008142269.1|   1 MYVPREFKIDDMEKIVDFVKNYGFGIVLSIYNGEIYNTQIPLML-DASGNNIVLKGHMARANMQWYHSKNNK-VAVL 75 
                                       ********************************************.7777888***************97777.**** PP

                                       EEEEEEEE-CCCSSTTS-....--EEEEEEEEEEEEEEE---HHHHHHHHHHHHHHHS---...--S--.-----HC CS
                        FMN_bind_2  78 fqgpdaYvsPswYtekkettkvvPTWnYaaVhvyGkakviedeeelrkqledltdqaEaerkkpwkved.apekyie 153
                                       f+gp++Y+sP+wY+ek    + vPTW+Y++V+  G ++ + d+ e+++ l dl++ +++    +w  +   +++y++
  gi|518652749|ref|YP_008142269.1|  76 FTGPHHYISPEWYKEK----DSVPTWDYMTVRFDGMLETM-DDIETKNFLVDLSKSYDP----EWANKGyDKKEYYA 143
                                       ***************9....67******************.8888999***********....4544432688899* PP

                                       HHHCTEEEEEEEEE CS
                        FMN_bind_2 154 kllkaIvgieieit 167
                                       k+ k+Iv++ i+++
  gi|518652749|ref|YP_008142269.1| 144 KMVKQIVAFTIKVN 157
                                       ************97 PP

>> DUF1251  Protein of unknown function (DUF1251)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   6.2e-05      0.22      57      86 ..     100     129 ..      44     154 .. 0.81
   2 ?    1.7   0.1     0.057     2e+02       4      32 ..     152     184 ..     149     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 6.2e-05
                           DUF1251  57 keivFDGFvkedDeskTvpFvvgpLkslke 86 
                                       + + FDG  ++ D+ +T+ F+v   ks + 
  gi|518652749|ref|YP_008142269.1| 100 MTVRFDGMLETMDDIETKNFLVDLSKSYDP 129
                                       6799******************87777654 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.057
                           DUF1251   4 lnvkeksivakyrielsk....kkvkvevdsfd 32 
                                        ++k ++i+ak+++++++    ++v +++d++ 
  gi|518652749|ref|YP_008142269.1| 152 FTIKVNKITAKFKLTQNHqedmENVAINLDKVG 184
                                       56889999****998877788899999999874 PP

>> YvrJ  YvrJ protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   4.8e-05      0.17       2      14 ..      19      31 ..      18      31 .. 0.94
   2 ?   -2.5   0.0       1.1     4e+03      17      26 ..     102     111 ..      99     113 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                              YvrJ  2 ignvGFPIaVavY 14
                                      + n+GF I++++Y
  gi|518652749|ref|YP_008142269.1| 19 VKNYGFGIVLSIY 31
                                      89**********9 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                              YvrJ  17 vRiEkkLdeL 26 
                                       vR+ + L+++
  gi|518652749|ref|YP_008142269.1| 102 VRFDGMLETM 111
                                       8999999876 PP

>> DUF3823_C  Domain of unknown function (DUF3823_C)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.21   7.5e+02      10      58 ..      46      93 ..      35     145 .. 0.63
   2 ?   10.6   0.4   0.00019      0.69       5      36 ..     149     177 ..     144     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.21
                                      EETTEEEEEEEEEESS--.....-EEEEEEEEESSS--SS-SGGGG-STT- CS
                         DUF3823_C 10 keggkltakfkvtrivtne.p.enieevqlfvsktsfvdntnarstklsga 58
                                       +g+++++k ++ r++ +    +n + + lf + +++++    ++ k++++
  gi|518652749|ref|YP_008142269.1| 46 ASGNNIVLKGHMARANMQWyHsKNNKVAVLFTGPHHYISP---EWYKEKDS 93
                                      5778888888888888877556666677778888888888...34433333 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00019
                                       EEEEEEETTEEEEEEEEEESS--...-EEEEE CS
                         DUF3823_C   5 nveiskeggkltakfkvtrivtnepenieevq 36 
                                       +v ++ + +k+takfk+t+++++   ++e+v 
  gi|518652749|ref|YP_008142269.1| 149 IVAFTIKVNKITAKFKLTQNHQE---DMENVA 177
                                       56668999**************9...455554 PP

>> SEP  SEP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       0.8   2.9e+03      32      73 ..      37      78 ..      25      81 .. 0.59
   2 ?   10.6   0.0   0.00018      0.63       9      53 ..     101     146 ..      98     187 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.8
                               SEP 32 kGevPeelekvekgeevevnledrrneeykppkkpkfkaFsG 73
                                      + ++P  l+   ++  ++ ++ + + + y++++++ ++ F+G
  gi|518652749|ref|YP_008142269.1| 37 NTQIPLMLDASGNNIVLKGHMARANMQWYHSKNNKVAVLFTG 78
                                      446676666444555555556655555566565555666777 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00018
                               SEP   9 svd.DGelrsyddpenaeflesikkGevPeelekvekgeevevnle 53 
                                       +v+ DG l  +dd e+++fl +++k++ Pe   k ++++e   +++
  gi|518652749|ref|YP_008142269.1| 101 TVRfDGMLETMDDIETKNFLVDLSKSYDPEWANKGYDKKEYYAKMV 146
                                       5666***********************9998886666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1092  (0.0609069); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); 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: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1525.70
//
Query:       gi|518652750|ref|YP_008142270.1|  [L=435]
Description: hypothetical protein FACI_IFERC00001G1389 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0078   16.0   0.0      0.021   14.6   0.0    1.7  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-06     0.021      34     144 ..     162     282 ..     121     299 .. 0.67
   2 ?   -3.5   0.0      0.44   7.9e+03     102     120 ..     335     353 ..     319     371 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-06
                                       T--HHHHTT-BGGG..EECTTTEEEEE.......EEECSSSSEEEEECTHHHHHHHHHHHHHH...CHCCTTTSBSS CS
                   Phage_integrase  34 GlRisEllsLrvkd..ldlengvilvh.......eregKgskeravplseealellkellska...leeaeksellf 98 
                                       Gl  s++ ++++++  +++e+             ++ +K ++     l++e +++lke+l+++    ++ + ++ lf
  gi|518652750|ref|YP_008142270.1| 162 GLKLSDFPEMKIENgkVEFEK-----IptmvnvrYTLSKARHTYFSFLGQEGTKYLKEYLEVRireGDNLKADTPLF 233
                                       334444444444443344444.....03333333666666666666777**************87766666666777 PP

                                       BETTSSB--HHHHHHHHHHHHHHCT-S...SC--TTHHHHHHHHHHHHH CS
                   Phage_integrase  99 askrgkplsrqtvrkafkraveeagie...kpltpHtlRhsfataLlea 144
                                           + ++s++ +r+ + +   + +i+     ++p  lR +fataL +a
  gi|518652750|ref|YP_008142270.1| 234 KLDSQGRISHEYIRTLLATRDIRKAITesgFSWRPYVLRAYFATALDNA 282
                                       77777777777777766655555555555556*************9876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.44
                                       TSSB--HHHHHHHHHHHHH CS
                   Phage_integrase 102 rgkplsrqtvrkafkrave 120
                                       ++k +++++++k+++ a+ 
  gi|518652750|ref|YP_008142270.1| 335 EEKGIKEEDYQKILRDAAI 353
                                       6666777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       415  (0.0231469); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3273.47
//
Query:       gi|518652751|ref|YP_008142271.1|  [L=619]
Description: hypothetical protein FACI_IFERC00001G1390 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-48  164.6   0.8    2.9e-48  164.6   0.8    2.3  3  N6_N4_Mtase      DNA methylase
     0.0016   18.2   0.1       0.47   10.3   0.0    2.6  2  Methyltransf_31  Methyltransferase domain
     0.0024   18.5   0.0      0.013   16.2   0.0    2.1  2  Methyltransf_25  Methyltransferase domain
     0.0057   17.4   0.0      0.046   14.5   0.0    2.4  2  Methyltransf_12  Methyltransferase domain
  ------ inclusion threshold ------
      0.017   15.3   0.8       0.05   13.9   0.7    1.8  2  DUF4625          Domain of unknown function (DUF4625)
      0.063   13.1   0.0       0.35   10.7   0.0    2.1  2  Methyltransf_23  Methyltransferase domain
      0.067   12.6   0.0       0.14   11.6   0.0    1.4  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 !  164.6   0.8   1.1e-51   2.9e-48       1     229 [.      92     335 ..      92     337 .. 0.85
   2 ?   -2.9   0.1       1.7   4.4e+03      24     189 ..     376     392 ..     359     405 .. 0.56
   3 ?   -1.5   0.6      0.63   1.6e+03     116     164 ..     536     579 ..     438     607 .. 0.50

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 1.1e-51
                                       EEEEEE--SSSSSCS.......................GCCGCCH..HHHHHHHHHHHHHHHHHHEEEEEEEEEEE- CS
                       N6_N4_Mtase   1 vdlivtdpPYntgkdy..................endeqyeeeds..yeeyleflekvlkevrrvLkddgsifinid 57 
                                       ++li++dpP+ tg d+                  +++  y +  s  ++ yl++++++l+++r++L+d+gsi+i+ d
  gi|518652751|ref|YP_008142271.1|  92 INLIYIDPPFYTGADFsyttqvnddtevekepsvIEQRAYRDTWSggISSYLKYMYERLSIMRDLLADNGSIYIHLD 168
                                       89*************988887777666666666644444444333779***************************** PP

                                       CCCHHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCCS-B--EEEEEEEESSTT-..---GGGSSBSS-HHHHHH CS
                       N6_N4_Mtase  58 dseikkelkaladeifggffllnvivwkkpnsmpesnkdrltsthEyilvfsknkkyllkfnldaikvpyeekdkle 134
                                        +  ++ +k+++deifg +++  +ivw++    + s+  +  + h++il+++knk+  ++fnl + k  ye+   ++
  gi|518652751|ref|YP_008142271.1| 169 WRVSHY-VKIICDEIFG-INFMADIVWHYHT-GGVSKL-NWGRKHDTILFYVKNKDSDFTFNLIKEKRYYEKPFFNS 241
                                       *****9.**********.***********94.444444.89****************88999988899999999999 PP

                                       HHHHCHHHCC-B--.....BSEEE-SCCCTTSTTS-CHH----SS---HHHHHHHHHHHS-TT-EEEETT-TTTHHH CS
                       N6_N4_Mtase 135 krgaytskkkgkki.....ediWdlseiqsnekkskgdtkkkHpaqkPvallerlIklstkkgdivlDpFaGSGtTa 206
                                        +g y+++++gk +     +d+Wd++ + ++ ++  g     +p+qkP+aller+Ik+s++kgdiv+D+F+GSGtT+
  gi|518652751|ref|YP_008142271.1| 242 TEG-YQTDENGKIYvmahpDDVWDIPAVLNVSSQFIG-----YPTQKPEALLERVIKASSNKGDIVADFFCGSGTTL 312
                                       999.999999997633333677*66666666666554.....8********************************** PP

                                       HHHHHTT-EEEEEESSHHHHHHH CS
                       N6_N4_Mtase 207 vaakelgrkfiGieieeeyvela 229
                                       ++a++lgr++iG + ++++++ +
  gi|518652751|ref|YP_008142271.1| 313 AVAEKLGRRWIGSDLSKYAIQVS 335
                                       *****************999876 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.7
                                       GCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCCHHTHHHHHHHHHTT-EEEEEEEEEEESSSTTTSTCCS-B- CS
                       N6_N4_Mtase  24 eedsyeeyleflekvlkevrrvLkddgsifiniddseikkelkaladeifggffllnvivwkkpnsmpesnkdrlts 100
                                        +                                                                           
  gi|518652751|ref|YP_008142271.1| 376 WK--------------------------------------------------------------------------- 377
                                       33........................................................................... PP

                                       -EEEEEEEESSTT-..---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS-CHH----SS--- CS
                       N6_N4_Mtase 101 thEyilvfsknkkyllkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekkskgdtkkkHpaqkP 177
                                                                                                                 + P
  gi|518652751|ref|YP_008142271.1| 378 --------------------------------------------------------------------------ENP 380
                                       ..........................................................................334 PP

                                       HHHHHHHHHHHS CS
                       N6_N4_Mtase 178 vallerlIklst 189
                                       ++ +e++Ikl+ 
  gi|518652751|ref|YP_008142271.1| 381 TDYIEFMIKLYK 392
                                       444444444443 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.63
                                       .---GGGSSBSS-HHHHHHHHHHCHHHCC-B--BSEEE-SCCCTTSTTS CS
                       N6_N4_Mtase 116 lkfnldaikvpyeekdklekrgaytskkkgkkiediWdlseiqsnekks 164
                                       +++++  i ++ +++++l   +a + + k++ + + W     qs++ k+
  gi|518652751|ref|YP_008142271.1| 536 ETPDISDIIETIKDSRQLIDYWAIDWDYKSDTFHNQW-----QSYRTKK 579
                                       3334444444444444444444444444444444444.....2222222 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00018      0.47       2      55 ..     296     347 ..     295     385 .. 0.79
   2 !    5.3   0.1    0.0061        16      24     128 ..     435     553 ..     426     589 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00018
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielAre.naqklgldn 55 
                                       +kg  v D  CG+G+ + ++  +lg   + +G D s+ ai+++r+  ++ ++++n
  gi|518652751|ref|YP_008142271.1| 296 NKGDIVADFFCGSGTTLAVAE-KLGR--RWIGSDLSKYAIQVSRKrLLDIHNSKN 347
                                       5778899******88665555.8875..8***************94334444444 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0061
                   Methyltransf_31  24 elgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl........ilsnevlnaladpdk 92 
                                         + ka+v G + + e+ elA++ a+  g++    ++ +++el+++l+d k+Dl        ++ ++++ ++++++ 
  gi|518652751|ref|YP_008142271.1| 435 SGFNKADVLGWEWNYEVNELAKKVAEGDGVELNLIQIPNVNELKSALADTKIDLkllkipdqVIEKNLIPTVKFNPL 511
                                       4556888999999999999***********9555666999999977999*****88888888888899999****** PP

                   Methyltransf_31  93 ileeiervlkpggill.iedprllaelp......akveeeska 128
                                       ++ e+++ +k + i+l ied++  +e p      + +++++++
  gi|518652751|ref|YP_008142271.1| 512 AYLEVSKKIKGKEIILkIEDFQ-ISETPdisdiiETIKDSRQL 553
                                       ****999999554443266666.44444444343555555554 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06     0.013       1      70 [.     301     368 ..     301     394 .. 0.72
   2 ?   -0.8   0.0         1   2.6e+03      12      58 ..     429     477 ..     425     492 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                                       v d+ cG+G++++ + k  g  +++g D+s+ +++  r+r+ + + + ++ + +++++  +++ f +  +
  gi|518652751|ref|YP_008142271.1| 301 VADFFCGSGTTLAVAEKL-G-RRWIGSDLSKYAIQVSRKRLLDIHNSKNLTNEEVNKYGKPARPFEIHNI 368
                                       78999****766666555.6.*******************976555666777777777777777776555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1
                                       HHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEE.SBCCGB CS
                   Methyltransf_25  12 tlalakrl.gkakvtgvDiseemleaareraeeeglnvefvq.gdaedl 58 
                                       + ++   + +ka+v+g + + e  e a++ ae +g++++++q  ++++l
  gi|518652751|ref|YP_008142271.1| 429 VSECISSGfNKADVLGWEWNYEVNELAKKVAEGDGVELNLIQiPNVNEL 477
                                       5555555446899999999999999999999999998888762444555 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0         1   2.6e+03      74      98 ..     138     162 ..     111     163 .. 0.85
   2 !   14.5   0.0   1.8e-05     0.046       2      53 ..     303     352 ..     302     384 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1
                   Methyltransf_12  74 nvlhhlkdirevldnirklLkpgGr 98 
                                       +  ++lk + e l+ +r+lL+++G 
  gi|518652751|ref|YP_008142271.1| 138 GISSYLKYMYERLSIMRDLLADNGS 162
                                       567899999999999********96 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.8e-05
                   Methyltransf_12   2 eiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvel 53 
                                       ++ cG+G++l++ ++   + + +g+D+s+ ai+  +++l +++n +n  +e 
  gi|518652751|ref|YP_008142271.1| 303 DFFCGSGTTLAVAEKL--GRRWIGSDLSKYAIQVSRKRLLDIHNSKNLTNEE 352
                                       566**********999..***********************99877655544 PP

>> DUF4625  Domain of unknown function (DUF4625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       4.2   1.1e+04      33      51 ..     102     120 ..     100     125 .. 0.81
   2 ?   13.9   0.7   1.9e-05      0.05      79     131 ..     568     619 .]     536     619 .] 0.72

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 4.2
                           DUF4625  33 kiGetlhfeaklsdneala 51 
                                       ++G +++   +++d+ +++
  gi|518652751|ref|YP_008142271.1| 102 YTGADFSYTTQVNDDTEVE 120
                                       6788999999999998876 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.9e-05
                           DUF4625  79 feksydlsgskkeyelheeieiPada.eaGdYhlvirvtDasGneteesreiki 131
                                       f+++++    +++++l++e+e  ++  ++G+Y ++++v+D  Gn t++  +++i
  gi|518652751|ref|YP_008142271.1| 568 FHNQWQS--YRTKKDLKVEYEAKHNYeNNGEYTIMVKVVDVFGNDTNKVLKVEI 619
                                       3333333..33466666677777775257******************9999887 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.65   1.7e+03     102     123 ..     150     172 ..     142     198 .. 0.79
   2 ?   10.7   0.0   0.00014      0.35       8     108 ..     282     390 ..     275     430 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.65
                   Methyltransf_23 102 lrqiatllkpgGylllse.plas 123
                                       l+ +++ll+++G ++++  + +s
  gi|518652751|ref|YP_008142271.1| 150 LSIMRDLLADNGSIYIHLdWRVS 172
                                       88999******999987634445 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00014
                   Methyltransf_23   8 elsdklerllpk.lraggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae.......kakkaqkdqfdeqea 76 
                                       ++ ++ler+ +   ++g  v d+ cG+G++l v+++ g   +g Dls  a++  +       +       + +  ++
  gi|518652751|ref|YP_008142271.1| 282 KPEALLERVIKAsSNKGDIVADFFCGSGTTLAVAEKLGRRWIGSDLSKYAIQVSRkrlldihN-------SKNLTNE 351
                                       5566777777554799999******************************99999866654441.......3333323 PP

                   Methyltransf_23  77 ae.....pqgkfdl..Ivlrevlehvpdppellrqiatl 108
                                       ++     p++ f++  I + e+ ++ ++p+ ++  + +l
  gi|518652751|ref|YP_008142271.1| 352 EVnkygkPARPFEIhnIGNYEMAYWKENPTDYIEFMIKL 390
                                       222222244444333366666666666666666655554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   5.3e-05      0.14     157     203 ..     293     338 ..     282     361 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 5.3e-05
                              PrmA 157 klvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeN 203
                                       +  ++g+ v D+ +GSG    +a kLg  + ++ D+ + A++v+++ 
  gi|518652751|ref|YP_008142271.1| 293 ASSNKGDIVADFFCGSGTTLAVAEKLGR-RWIGSDLSKYAIQVSRKR 338
                                       33566789*********86666789997.577***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (619 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 4488.22
//
Query:       gi|518652752|ref|YP_008142272.1|  [L=842]
Description: hypothetical protein FACI_IFERC00001G1391 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-18   67.5   0.1    2.9e-18   66.4   0.1    1.6  1  ResIII      Type III restriction enzyme, res subunit
     0.0031   17.2   0.0     0.0079   15.9   0.0    1.6  1  SWI2_SNF2   SWI2/SNF2 ATPase
     0.0031   17.3   0.0      0.085   12.6   0.0    2.4  2  DEAD        DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.039   13.9   0.0    1.8  1  Hjc         Archaeal holliday junction resolvase (hjc)
      0.025   14.9   0.0      0.092   13.1   0.0    2.0  1  Helicase_C  Helicase conserved C-terminal domain
      0.083   13.4   0.2       0.34   11.4   0.2    2.2  1  NERD        Nuclease-related 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 !   66.4   0.1   9.8e-22   2.9e-18       3     170 ..      62     304 ..      60     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 9.8e-22
                                       EE-HHHHHHHHHHT..............................TTSEEE.EEESTTSTHHHHH.HHHHHHH-S... CS
                            ResIII   3 elreyQeeaienll...eklks.....................krdkrgl.ikmaTGtGKTlva.aklierllkkgk 53 
                                       e+ + Q e ie l+   e +k+                     ++   ++ +kmaTG+GKT+v+ + +i+++l+ + 
  gi|518652752|ref|YP_008142272.1|  62 EFWYAQRESIETLIyiyEVMKKksfidlarefgdgpirfydpeTDLYPLYgFKMATGSGKTYVMaLTIIWQYLNYQL 138
                                       556666666666665553333355566666777777777655323334444*************999******9877 PP

                                       ........-EEEEESSH.HHHHHHHHHGGGGTGG...............GEEEESSS-B--............-SEE CS
                            ResIII  54 ee......kflflvprk.slleqtleefkkflseayke...........igkkvsgdkkka.....kekdstnkkil 107
                                       e+      kfl+++ +k ++++++++++++ +  ++              +                 +   ++ ++
  gi|518652752|ref|YP_008142272.1| 139 EDrnnytsKFLIIAGEKnIIYDRLKRDYQDGKIFTAIPlippelydsfnLK---------VilkedPFYTVPDSVLF 206
                                       76999*********87747899******77666665445444444343222.........122222335578999** PP

                                       EEEHHHHHHTH................................HHHTTT-S...........EEEEETGGGTTS..T CS
                            ResIII 108 vttiqsldadseee........................eeeseellrdrfd...........viiiDEaHrlgak.k 148
                                       +t+iq+l+++s+++                        +                       +i+ DEaH+++   k
  gi|518652752|ref|YP_008142272.1| 207 LTNIQQLQEKSNRKkesekfvddvldlkevdrtnisqeN-----------RilevlekipniMILKDEAHHIYNYeK 272
                                       ***********7778888888888887554444333222...........245666667788*********987647 PP

                                       TTHHHHHT---..........SEEEEEESS-S CS
                            ResIII 149 swreilekfke..........avllglTATpe 170
                                       +w++il  + +           + l+++ATp+
  gi|518652752|ref|YP_008142272.1| 273 KWKNILVELHRhlestfgkgiITELDFSATPK 304
                                       ****955554446678889999*********8 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.7e-06    0.0079      27     183 ..     117     325 ..     115     359 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.7e-06
                         SWI2_SNF2  27 qGSGKsltmvfla..kklleeel.....knpkvv.......vvtDRkdLdkQlsktfakageekpkqaesrkeLkel 89 
                                       +GSGK++ m+++   + l   +l        k++       ++ DR   d Q  k f+++    p +  ++ +Lk  
  gi|518652752|ref|YP_008142272.1| 117 TGSGKTYVMALTIiwQYLNY-QLedrnnYTSKFLiiageknIIYDRLKRDYQDGKIFTAIPLIPP-ELYDSFNLKVI 191
                                       79999999987651133332.21122223334441133333577999999999999998855544.44555567766 PP

                         SWI2_SNF2  90 lek......esekiifttiqKfeeeek...........................eklevlsereniivlvDEaHRsq 133
                                       l++       ++ +++t iq ++e+++                           + levl++  ni++l DEaH   
  gi|518652752|ref|YP_008142272.1| 192 LKEdpfytvPDSVLFLTNIQQLQEKSNrkkesekfvddvldlkevdrtnisqenRILEVLEKIPNIMILKDEAHHIY 268
                                       6432222225778899******955333567899*************99998755569****************974 PP

                         SWI2_SNF2 134 yg.........elakklrkalpn..aafigFTGTPilkkdkktkevFgeyidkYtikeave 183
                                                  el+++l++++ +   + + F  TP +++     + F  +i  +t+kea++
  gi|518652752|ref|YP_008142272.1| 269 NYekkwknilvELHRHLESTFGKgiITELDFSATPKSEN----GALFPWLIVDFTLKEAID 325
                                       334899999999999999999873335678888886643....457888888888888874 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.0   2.9e-05     0.085      20      62 ..     114     160 ..      81     184 .. 0.88
   2 ?    1.8   0.0     0.059   1.8e+02     125     170 ..     258     304 ..     197     309 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.9e-05
                                       EESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxx RF
                              DEAD  20 aaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeq 62 
                                       +++TGsGKT ++++ ++ + ++     +++ + k li++  + ++ +
  gi|518652752|ref|YP_008142272.1| 114 KMATGSGKTYVMALTIIWQYLNYqledRNNYTSKFLIIAGEKNIIYD 160
                                       689*************96666667998899999****9988877665 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.059
                                       EEE.ETHHHHHHT..TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS CS
                                       xxx.xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 125 lVl.DEadrlldq..gfsdfinrilnqlpqitcdgklqrqvivlSATlp 170
                                       ++l DEa+ + +   + ++ + +++++l+++  +g    + + +SAT++
  gi|518652752|ref|YP_008142272.1| 258 MILkDEAHHIYNYekKWKNILVELHRHLESTFGKGI--ITELDFSATPK 304
                                       44449***9988655677777777777766666555..33688999987 PP

>> Hjc  Archaeal holliday junction resolvase (hjc)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.3e-05     0.039      23      85 ..     761     824 ..     744     832 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.3e-05
                                       SSSSSS.SS-SEEEEETTEEEEEEEEEESSSEEEEEHHHHHHHHHHHHHHTCEEEEEEEETTTE CS
                               Hjc  23 Sggatk.plpDviAirgdvvlviEvKsskkeriylkkeqvekllefarkaggelllavklqgke 85 
                                       S g  + + pD iAi +d+  v+E K + +  ++ k + +    + a++  g+ +  v++++++
  gi|518652752|ref|YP_008142272.1| 761 SAGDLRvYNPDFIAITKDTNFVLETKGREDVDVKFKDKRIVAWCRDASNITGKSWKYVRINEED 824
                                       445555589********************99999988765555555555567777777766555 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 ?   13.1   0.0   3.1e-05     0.092      23     109 ..     383     483 ..     362     485 .. 0.58

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.1e-05
                                       ESSHHHHHH.HHHHHHHT....TSTEEEESTTSTHHHHHHHHHHHHTTS.........SSEEEESGGGTSSSTSTTE CS
                        Helicase_C  23 vntidrlek.vklllekk....gikvavlhgelpqnereeileqfnkge.........sdvLiatdvaerGidipkv 85 
                                       +++ +++++   +l   +    + k++ +h + + +  +  +e+ +k           + v+++t ++ +G d+ +v
  gi|518652752|ref|YP_008142272.1| 383 CPSNKEADElKGYLS--SlpglKDKILLIHTDSTGEVVKSDIENARKSAqnidsnanpFEVIVSTMMLNEGWDVRNV 457
                                       445555555434442..1234445566666665555555444444422223333333399***************** PP

                                       SEEEESSSSSSHHHH..HHHHTTSSS CS
                        Helicase_C  86 nlVinfdlprnvtsy..iqriGRtgR 109
                                       n+++ +   ++ +++   q iGR  R
  gi|518652752|ref|YP_008142272.1| 458 NVIVGLRSYTSERNVlpEQVIGRGLR 483
                                       ***98777766443322677777666 PP

>> NERD  Nuclease-related domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.34      24      61 ..     749     797 ..     725     840 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                              NERD  24 lhdvrlrpg....tg.....eiDhlvispkgifviEvKnwsG..wifgd 61 
                                        +++ +  +     g     + D+++i++++ fv+E+K +    + f+d
  gi|518652752|ref|YP_008142272.1| 749 VRQIHFFVEyrdsAGdlrvyNPDFIAITKDTNFVLETKGREDvdVKFKD 797
                                       444333333444411455679******************8855455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (842 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       951  (0.0530426); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.75u 0.33s 00:00:01.08 Elapsed: 00:00:00.51
# Mc/sec: 5003.82
//
Query:       gi|518652753|ref|YP_008142273.1|  [L=321]
Description: hypothetical protein FACI_IFERC00001G1392 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.75    9.6   2.4       0.99    9.2   0.1    2.2  2  Gemini_mov  Geminivirus putative movement protein


Domain annotation for each model (and alignments):
>> Gemini_mov  Geminivirus putative movement protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2       0.1   1.8e+03      33      53 ..      66      86 ..      61      93 .. 0.78
   2 ?    9.2   0.1   5.5e-05      0.99      31      59 ..     188     216 ..     173     219 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.1
                        Gemini_mov 33 pwsrvgeiailtlvavlvlYL 53
                                       +s v e +i+ ++a++ lY 
  gi|518652753|ref|YP_008142273.1| 66 SHSLVFELSIIFIIALIELYY 86
                                      566788899999999999885 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 5.5e-05
                        Gemini_mov  31 elpwsrvgeiailtlvavlvlYLlytlvl 59 
                                         +w  v  i +++l++++ +YL +++ l
  gi|518652753|ref|YP_008142273.1| 188 GSKWDLVRLIGVILLISIIPVYLYWVYSL 216
                                       5689999******************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.81 Elapsed: 00:00:00.49
# Mc/sec: 1983.42
//
Query:       gi|518652754|ref|YP_008142274.1|  [L=127]
Description: hypothetical protein FACI_IFERC00001G1393 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.3   0.2      0.076   13.1   0.1    1.5  2  XkdW      XkdW protein
      0.098   12.7   0.1       0.16   12.1   0.1    1.3  1  DUF4214   Domain of unknown function (DUF4214)


Domain annotation for each model (and alignments):
>> XkdW  XkdW protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.54   4.8e+03      18      40 ..       7      29 ..       4      34 .. 0.60
   2 ?   13.1   0.1   8.4e-06     0.076      49     104 ..      58     111 ..      53     113 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.54
                                      TTEEEEE-SS-..EEEEEE-SSS CS
                              XkdW 18 kdfilrndGdGrgsyieeWnlra 40
                                      + f+++ + d   sy    ++r 
  gi|518652754|ref|YP_008142274.1|  7 EKFKIKRKDDSYLSYYTLIRVRG 29
                                      45666666666666666555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.4e-06
                                       HHHHHHHHHS----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              XkdW  49 ktwWeelqsnpayepPvqldllaqelskeklarkqleelnktlgnelsklklella 104
                                       k++W +l +  ++++ + +++l +e+ ++   r+  eel kt+ +++s+++ e+l+
  gi|518652754|ref|YP_008142274.1|  58 KNYWGKLGKFMNTKDNQYMEILDREMEEQ--KRNIWEELKKTIVSDISEIRYEILT 111
                                       789999999999****9********9885..5999*******************96 PP

>> DUF4214  Domain of unknown function (DUF4214)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   1.7e-05      0.16      26      62 ..      73     113 ..      58     118 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.7e-05
                           DUF4214  26 tlYqnvldRepDsaGlnyw....adqLksgaetReevllgf 62 
                                       + Y ++ldRe +++  n w    ++ ++ + e R+e+l gf
  gi|518652754|ref|YP_008142274.1|  73 NQYMEILDREMEEQKRNIWeelkKTIVSDISEIRYEILTGF 113
                                       5699***************88877778888899*****999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.50
# Mc/sec: 768.74
//
Query:       gi|518652755|ref|YP_008142275.1|  [L=31]
Description: hypothetical protein FACI_IFERC00001G1394 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (31 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       128  (0.00713927); expected 358.6 (0.02)
Passed bias filter:                      104  (0.00580066); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 233.53
//
Query:       gi|518652756|ref|YP_008142276.1|  [L=100]
Description: hypothetical protein FACI_IFERC00001G1395 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 741.71
//
Query:       gi|518652757|ref|YP_008142277.1|  [L=602]
Description: hypothetical protein FACI_IFERC00001G1396 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.5   1.6       0.22   10.9   0.1    2.9  2  ABC_transp_aux  ABC-type uncharacterized transport system


Domain annotation for each model (and alignments):
>> 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 ?   10.9   0.1   1.2e-05      0.22      48      86 ..      73     120 ..      59     354 .. 0.74
   2 ?    0.0   0.2     0.026   4.7e+02      86     140 ..     408     460 ..     370     576 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.2e-05
                    ABC_transp_aux  48 kevkdlLeeyaaysggkisvefidpspneeeeeeaeay..........g 86 
                                       k +k +L++y+a+ g ++ +e+i+ +p ++  ++++++           
  gi|518652757|ref|YP_008142277.1|  73 KTAKTILRKYKAQLGANLYLEVINFTPSKK-SDKEKQEnmsaiyktrfN 120
                                       67899*******************998883.333333313433344440 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.026
                    ABC_transp_aux  86 gitpvqisveekdelkt.krvymglvieygdkeetipllkntsesnlEyeltsair 140
                                        ++p ++ ++ +d+  t  r++  +++  +d +e+ip +k++ ++ lE ++++ + 
  gi|518652757|ref|YP_008142277.1| 408 NVQPSEFLKKYEDK--TePRLFEVISF-FEDLIEIIPEIKPEITKVLEDQIIRNVE 460
                                       56666666665444..43566665555.6777888888888777778888887664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (602 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       664  (0.037035); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.39
# Mc/sec: 4685.26
//
Query:       gi|518652758|ref|YP_008142278.1|  [L=324]
Description: hypothetical protein FACI_IFERC00001G1397 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00039   20.8   0.0    0.00067   20.1   0.0    1.3  1  Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
  ------ inclusion threshold ------
      0.019   14.7   0.1      0.045   13.6   0.1    1.6  1  zf-CHC2   CHC2 zinc finger


Domain annotation for each model (and alignments):
>> Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   7.4e-08   0.00067      12     143 ..      51     170 ..      42     181 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.4e-08
                          Prim-Pol  12 vPlppggKrPlgkkwekdattdpeqirawwkkhpra.nvglatgpsglv.vlDvDgkeagaealarLareegplPet 86 
                                       + ++p++K P+  + ++   + p+  +++ +   +  n gl++ p+g+  ++D D+++  ++al+        l +t
  gi|518652758|ref|YP_008142278.1|  51 ILVSPHDKIPFE-HAWQSSCNYPASSEKIHNYLLKGgNWGLMH-PAGMSiGIDEDNEKIRNAALS--------LGDT 117
                                       556899999999.666666777778888888888888*****9.666666*******97777777........8899 PP

                          Prim-Pol  87 vtvttgstgggrhlyfraPdglalpnsagklapgldlrgeggyvvappsvhetgraY 143
                                        ++ tg++g  + l++     ++ p  +  l +g  +rg+gg+ + p+s+h++g+ Y
  gi|518652758|ref|YP_008142278.1| 118 ARFNTGTPGHFCDLFLI----KDEPVGNIPLIDGAYIRGKGGQNLGPGSIHPNGNIY 170
                                       99***************....455677777878899***************999988 PP

>> zf-CHC2  CHC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1     5e-06     0.045      25      71 ..     231     278 ..     219     290 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5e-06
                           zf-CHC2  25 LkkkgkdyvalCPFHeektp.sftvspekqfyyCfgCgagGdaikFlm 71 
                                        k++g++y++  P H   t   f v  e + +yCf  g+gG  ++++ 
  gi|518652758|ref|YP_008142278.1| 231 FKQSGSKYQGPHPIHGSATGnNFVVDFELNEWYCFRHGTGGGPLQWIA 278
                                       6899***********999852799999**************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2506.33
//
Query:       gi|518652759|ref|YP_008142279.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G1398 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       166  (0.00925874); expected 358.6 (0.02)
Passed bias filter:                      136  (0.00758548); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 414.50
//
Query:       gi|518652760|ref|YP_008142280.1|  [L=50]
Description: hypothetical protein FACI_IFERC00001G1399 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.016   15.4   0.0       0.02   15.1   0.0    1.1  1  ParB_C        Centromere-binding protein ParB C-terminal
      0.063   13.3   0.0       0.07   13.1   0.0    1.1  1  Luciferase_N  Luciferase/LBP N-terminal domain


Domain annotation for each model (and alignments):
>> ParB_C  Centromere-binding protein ParB 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-06      0.02      15      38 ..      23      46 ..      19      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.2e-06
                            ParB_C 15 hleGdqtlSdfiaaAvmaeVerlE 38
                                        e + ++Sdf+  A m e e+lE
  gi|518652760|ref|YP_008142280.1| 23 KNEAYNSVSDFARIASMKELEKLE 46
                                      6799*******************9 PP

>> Luciferase_N  Luciferase/LBP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.9e-06      0.07      17      46 ..      15      44 ..       5      48 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.9e-06
                      Luciferase_N 17 qkvvayvtkqlklesvsDfanywtsseyek 46
                                      +++ ++v k+  ++svsDfa++   +e ek
  gi|518652760|ref|YP_008142280.1| 15 DEIQKFVAKNEAYNSVSDFARIASMKELEK 44
                                      678899****************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 378.33
//
Query:       gi|518652761|ref|YP_008142281.1|  [L=100]
Description: hypothetical protein FACI_IFERC00001G1400 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 729.48
//
Query:       gi|518652762|ref|YP_008142282.1|  [L=303]
Description: hypothetical protein FACI_IFERC00001G1401 [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.1   0.0    1.2e-30  106.6   0.0    1.2  1  Endonuclease_5  Endonuclease V
    5.3e-20   71.3   0.0    9.7e-20   70.5   0.0    1.4  1  DNA_binding_1   6-O-methylguanine DNA methyltransferase, DNA 
     0.0096   15.7   0.0       0.28   11.0   0.0    2.4  2  IclR            Bacterial transcriptional regulator


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 !  106.6   0.0   2.1e-34   1.2e-30      18     193 ..     134     287 ..     115     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 2.1e-34
                                       SEEEEEEEEEEECTCEEEEEEEEEEETTTTEEEEEEEEEEE--S-SSTT-CHHHCHHHHHHHHCC-SS--SEEEEEC CS
                    Endonuclease_5  18 klvaGvDvsfvkeekkeavaalvvldlpslevvekavavvklsfpYipgfLaFRElpvllkaleklkqkpdvllvDG 94 
                                       +  a++Dvs+   e ++ ++alv +d    e + k+  ++k++fpYipg+L +RE p++ k+  +++    +ll+D 
  gi|518652762|ref|YP_008142282.1| 134 ENYAAIDVSY---EGRTGYGALVYYDS--GEYMVKN-LEMKVNFPYIPGYLGYRESPFIEKLSVNVD---ALLLIDA 201
                                       56799*****...44444999999885..5544444.4679*****************998888887...59***** PP

                                       -SSSSTTS--HHHHHHHHHTS-EEEEESS-SSSBE----SSTTEEEEEEETTEEEEEEEESSTTS--EEEEEECSS- CS
                    Endonuclease_5  95 nGiaHprrlGlAshlGvlldlptiGvaKsllvgkveepekekgsvvplvsegevigaalrtkknvkpiyvSvGhris 171
                                       nG++Hpr++GlA++ Gv+l+ +tiGvaKsll+gk++++         +v ++e++g+a+      k  +vS+G++is
  gi|518652762|ref|YP_008142282.1| 202 NGLLHPRKCGLATFAGVVLGRATIGVAKSLLMGKIDDT-------GYVVYNNEKLGYAIN-----KHTIVSPGNMIS 266
                                       *********************************88754.......4556679*******9.....5568******** PP

                                       HHHHHHHHHHCS-T-SS-HHHH CS
                    Endonuclease_5 172 letalelvlallkkyrlPepir 193
                                       le++++ ++ l  k + P  ++
  gi|518652762|ref|YP_008142282.1| 267 LESSIKKIKLLG-KNKYPAILK 287
                                       *******99886.888887655 PP

>> 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 !   70.5   0.0   1.6e-23   9.7e-20       7      81 .]      13      87 ..       8      87 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 1.6e-23
                                      HHHHTTS-TT-BEEHHHHHHHTT.TSCHHHHHHHHHTSSBTTTSGGGGEEBTTSBCCTTTTCHHHHHHHHHHTTS CS
                     DNA_binding_1  7 wellrqIpyGkvttYgeiAkllgkpkaaraVgqalaanplailvPcHRVvgadgklggyagglerkralLeaEgv 81
                                      + l++qIp G +ttYge+Ak+lg+ +aaraVg++l  n+ +  +Pc++Vv +d ++g+ya g+e+k++ L+++g+
  gi|518652762|ref|YP_008142282.1| 13 YGLVKQIPEGYITTYGELAKALGDIRAARAVGYMLSINEDPDGIPCYKVVHTDRRMGKYALGVEEKARRLRKDGI 87
                                      789*********************************************************************985 PP

>> IclR  Bacterial transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.0   4.7e-05      0.28      48     111 ..      25      87 ..      16      98 .. 0.85
   2 ?    1.9   0.0     0.031   1.9e+02      72     101 ..     114     143 ..     107     149 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 4.7e-05
                                       TS--SHHHHHHHHHHHHHHTSEEEESSSSTTEEEEEEEEE-TTSSEEEEEEEEEETTTSHHHHH CS
                              IclR  48 rTitdpeeLleeLakvReqGyavdreEeeegvrciAapifdasgevvaAvsvsgptarlteeel 111
                                       +T+ + ++ l ++ + R+ Gy+++ +E+  g+ c   +++ ++++  +A+ v  ++ rl ++++
  gi|518652762|ref|YP_008142282.1|  25 TTYGELAKALGDIRAARAVGYMLSINEDPDGIPCYK-VVHTDRRMGKYALGVEEKARRLRKDGI 87 
                                       4666677777788889999**************885.68888****************999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.031
                                       ESSSSTTEEEEEEEEE-TTSSEEEEEEEEE CS
                              IclR  72 reEeeegvrciAapifdasgevvaAvsvsg 101
                                        +Ee+e ++++A    d+ +e+ aA+ vs 
  gi|518652762|ref|YP_008142282.1| 114 LQEEQEKIASMADFAGDRDEENYAAIDVSY 143
                                       5789999*******************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2192.28
//
Query:       gi|518652763|ref|YP_008142283.1|  [L=912]
Description: hypothetical protein FACI_IFERC00001G1402 [Ferroplasma acidarmanus fer1]
Scores for complete 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-72  243.0  15.9    1.5e-37  129.3   2.7    3.1  3  MMPL             MMPL family
  ------ inclusion threshold ------
      0.039   14.0   0.1      0.039   14.0   0.1    5.0  5  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
       0.12   12.5   0.1         21    5.2   0.0    2.4  2  DcrB             DcrB


Domain annotation for each model (and alignments):
>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.4   0.0     0.005        30       4      56 ..      52     104 ..      49     127 .. 0.80
   2 !  116.4   3.2   2.1e-37   1.2e-33      80     317 ..     288     522 ..     257     536 .. 0.92
   3 !  129.3   2.7   2.4e-41   1.5e-37      76     322 ..     669     903 ..     599     909 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.005
                              MMPL   4 padaesvkamdrleaafpeeadsdkiivvvlaegdealgsaaaeaavdelvde 56 
                                        ++ +s+ka d l+a+f+++++ ++ii+v  ++  + l+ + ++ a+++ +d+
  gi|518652763|ref|YP_008142283.1|  52 TKNSQSSKANDILSAQFNGSSSDPSIIIVSNNTPIDNLTISRDMMAFQHSMDS 104
                                       67899**************5555667777666667777777888888888876 PP

  == domain 2  score: 116.4 bits;  conditional E-value: 2.1e-37
                              MMPL  80 fvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvi 156
                                       ++ + +++++++ +++    + +++++++ i+++ ++    ++   +++G++++++ l+  s + + ++ +++++v 
  gi|518652763|ref|YP_008142283.1| 288 LMNQKNSTLIMIFSYK-TNITAAQQSHIDSIEKTYSSKI--SSSSFYLAGSTVANNQLASESIHGMIVALIIGIIVS 361
                                       5556667777788888.56889999*********99999..999********************************* PP

                              MMPL 157 lviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyreelaa 232
                                       ++i  + +rS+v+a+lp l  v+s +++ g+  l+ +++ + ++s  +++ll +l++++++DY + ++sR+r el+a
  gi|518652763|ref|YP_008142283.1| 362 IIIVGLFFRSPVTAFLPFLIFVFSAVISAGInGLLYKYIFHTTISFITPTLLLILILGIASDYSVYILSRFRSELRA 438
                                       ***************************************************************************** PP

                              MMPL 233 gedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTllPAllvllGraa.la 308
                                         +   a+ +  + +g++v+ +G tva++ + L ++++p+++  G++ a++ +v++ i+ Tll A+l+  G++  ++
  gi|518652763|ref|YP_008142283.1| 439 KNKD--AIPESSKWAGHAVFTSGTTVALSYIILWISNIPIFSDAGLTNAIAAVVTIIIANTLLIAILAQWGKKTyWP 513
                                       **99..*******************************************************************8888 PP

                              MMPL 309 kprrkrkkr 317
                                       ++ ++ +k 
  gi|518652763|ref|YP_008142283.1| 514 AKIKENQKL 522
                                       776666654 PP

  == domain 3  score: 129.3 bits;  conditional E-value: 2.4e-41
                              MMPL  76 vaaafvSkDgkaaralvtlegdpgsteadesvaairaaveearpleglkvevtGpaatladlrdasdrdlklievvt 152
                                        +a  +  ++k++ ++v+l   ++s+ + + v++  ++v+      + +++v+G++ +l+     ++++   ++ + 
  gi|518652763|ref|YP_008142283.1| 669 QTATYIGHNHKSVEIVVYLSNVAWSNPSTNYVNKMPSIVNGSG---NYTAYVGGTTEYLNNAYSFTSHSFNNMVPLL 742
                                       566778899********************************99...******************************* PP

                              MMPL 153 lvvilviLlivyrSlvaallplltvvvsllaalgl.vlilalllglelstfvlgllvvlliavGtDYallLvsRyre 228
                                        + i++iLli + S ++++ ++l+v+  +++al+l  +i+ +ll+l +  f + ++++ l+avG DY ++++++ +e
  gi|518652763|ref|YP_008142283.1| 743 GITIFIILLIQLASALTPVRLILMVMAAVMLALSLtYIIFYYLLHLPVIIFLPLFVFITLLAVGLDYDIFMITKVQE 819
                                       ***********************************99**************************************** PP

                              MMPL 229 elaagedreeaviravastgkvvtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvlivlTll.PAllvllGr 304
                                        + +g +++eav + +   g+v++  Gl + +++ +L ++ l++++++Gv +alGvl+d++++  +  PA+++++ +
  gi|518652763|ref|YP_008142283.1| 820 NISKGMNTAEAVKDSIVENGGVIITLGLLLFATFGALYFSGLGIIEEIGVGLALGVLIDTFVSWMFFvPAIMTVMDK 896
                                       ***************************************************************99999*******99 PP

                              MMPL 305 aalakprrkrkkrwWrrl 322
                                                   +wW+++
  gi|518652763|ref|YP_008142283.1| 897 Y-----------NWWPSR 903
                                       9...........888654 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   5.3       0.6   3.6e+03      34      82 ..     350     392 ..     336     422 .. 0.51
   2 ?   14.0   0.1   6.5e-06     0.039      22     106 ..     432     532 ..     428     535 .. 0.76
   3 ?   -2.7   0.2         1   6.1e+03      46      81 ..     546     554 ..     539     560 .. 0.37
   4 ?   -4.8  12.2         3   1.8e+04      37      83 ..     763     807 ..     757     834 .. 0.80
   5 ?   -4.4   8.7         3   1.8e+04      35      75 ..     837     882 ..     824     900 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.6
                   Phage_holin_3_6  34 gsgagllgaagvlallalllllvalalalaalwlaalivaavllvlagv 82 
                                       ++ a+++g+ + + +++l++ +         + l +li     ++ ag+
  gi|518652763|ref|YP_008142283.1| 350 MIVALIIGIIVSIIIVGLFFRSPVT------AFLPFLIFVFSAVISAGI 392
                                       3333333333333333333333332......334444433333333333 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 6.5e-06
                   Phage_holin_3_6  22 akaElkeeakragsgagllgaagvlallalllllvala..........lalaalwlaali.vaavllvlagvlalvg 87 
                                       ++ El+++ k a+      ++ +v++  + ++l+  ++          ++l + ++aa++ + ++  +l ++la +g
  gi|518652763|ref|YP_008142283.1| 432 FRSELRAKNKDAIPESSKWAGHAVFTSGTTVALSYIILwisnipifsdAGL-TNAIAAVVtIIIANTLLIAILAQWG 507
                                       788999999999999999999999999999999888873455554444444.2444555536788889999999999 PP

                   Phage_holin_3_6  88 lk.....klkkakp.lpertieelk 106
                                       +k     k+k++++ ++e+++e ++
  gi|518652763|ref|YP_008142283.1| 508 KKtywpaKIKENQKlPFEKSMEKVA 532
                                       9999999999999989999999886 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1
                   Phage_holin_3_6  46 lallalllllvalalalaalwlaalivaavllvlag 81 
                                       +                           +++++ a+
  gi|518652763|ref|YP_008142283.1| 546 F---------------------------VIVALGAL 554
                                       1...........................11111111 PP

  == domain 4  score: -4.8 bits;  conditional E-value: 3
                   Phage_holin_3_6  37 agllgaagvlallalllllvalalalaalwlaalivaavllvlagvl 83 
                                       ++l+++a+v+++l+l+++++  +l l  + + +l ++++  +la+ l
  gi|518652763|ref|YP_008142283.1| 763 LILMVMAAVMLALSLTYIIFYYLLHL--PVIIFLPLFVFITLLAVGL 807
                                       67899999999999999999998888..6666666666666666554 PP

  == domain 5  score: -4.4 bits;  conditional E-value: 3
                   Phage_holin_3_6  35 sgagllgaagvlallalllllvalalala.a...lwlaali.vaav 75 
                                         +g+++  g+l++ ++++l +  + +++ +   l+l+ li +++ 
  gi|518652763|ref|YP_008142283.1| 837 ENGGVIITLGLLLFATFGALYFSGLGIIEeIgvgLALGVLIdTFVS 882
                                       4455555555555555555555555333333334455555543332 PP

>> DcrB  DcrB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0035        21      11      49 ..      73     109 ..      68     132 .. 0.83
   2 ?    4.7   0.1    0.0051        30      94     125 ..     286     317 ..     281     320 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                                       EE--BEEEEE--BTT-EEEEEEEE---TTS-HHHHHHHH CS
                              DcrB  11 qDrSvnvlvfpdeatgaslvIsRdeleegetleeylerq 49 
                                       +D S+ + ++ ++    +l+IsRd ++ + ++++yl++ 
  gi|518652763|ref|YP_008142283.1|  73 SDPSIIIVSNNTP--IDNLTISRDMMAFQHSMDSYLKSI 109
                                       7888989988888..89******************9875 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0051
                                       EEEE--SSSEEEEEEEE-CCCHHHHHHHHHHH CS
                              DcrB  94 qvlvevprrvLiftltspgefteeqrahweai 125
                                        +l++++++ Li+ +++++  t++q++h+++i
  gi|518652763|ref|YP_008142283.1| 286 SSLMNQKNSTLIMIFSYKTNITAAQQSHIDSI 317
                                       5688889**********************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (912 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1333  (0.0743488); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.79u 0.27s 00:00:01.06 Elapsed: 00:00:00.44
# Mc/sec: 6293.78
//
Query:       gi|518652764|ref|YP_008142284.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G1403 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.17   11.8   0.0    1.3  1  Cbl_N3    CBL proto-oncogene N-terminus, SH2-like domain


Domain annotation for each model (and alignments):
>> Cbl_N3  CBL proto-oncogene N-terminus, SH2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   9.2e-06      0.17      58      82 ..      23      47 ..       8      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 9.2e-06
                                      T--HHHHHHHHHHTTS--EETT-S- CS
                            Cbl_N3 58 nkslvqalidGereglylyPdGkek 82
                                       +sl ++li+Ge++ +y +Pd  ++
  gi|518652764|ref|YP_008142284.1| 23 LRSLGFSLIKGEQDMVYEWPDSATA 47
                                      5899****************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); 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: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 550.20
//
Query:       gi|518652765|ref|YP_008142285.1|  [L=93]
Description: hypothetical protein FACI_IFERC00001G1404 [Ferroplasma acidarmanus fer1]
Scores for complete 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   33.5   3.4      2e-07   31.2   3.5    1.8  1  Rpr2            RNAse P Rpr2/Rpp21/SNM1 subunit domain
    0.00075   19.4   3.1     0.0014   18.5   3.1    1.4  1  zinc_ribbon_4   zinc-ribbon domain
     0.0012   18.6   0.6     0.0019   17.9   0.6    1.3  1  zinc_ribbon_5   zinc-ribbon domain
     0.0027   17.7   0.5     0.0041   17.1   0.5    1.2  1  DZR             Double zinc ribbon
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.015   15.3   0.1    1.2  1  HypA            Hydrogenase/urease nickel incorporation, meta
      0.021   14.8   0.8        1.8    8.6   0.1    2.2  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
      0.022   14.8   0.2      0.033   14.2   0.2    1.4  1  WhiA_N          WhiA N-terminal LAGLIDADG-like domain
      0.031   13.6   0.0      0.036   13.3   0.0    1.1  1  Pox_RNA_pol_35  Poxvirus DNA-directed RNA polymerase, 35 kD s
      0.054   13.6   1.6       0.21   11.7   0.1    2.4  3  zf-CHCC         Zinc-finger domain
      0.063   12.7   4.3       0.19   11.2   0.1    2.2  2  zf-ribbon_3     zinc-ribbon domain
      0.086   12.6   3.9       0.53   10.1   0.0    2.3  2  zinc_ribbon_2   zinc-ribbon domain
       0.19   11.8   2.0        1.2    9.2   0.0    2.4  3  CpXC            CpXC protein
       0.76   10.0   2.9        6.9    7.0   0.1    2.1  2  DUF4798         Domain of unknown function (DUF4798)
        6.6    6.6   8.8        3.6    7.4   4.6    2.4  2  DUF4187         Domain of unknown function (DUF4187)


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 !   31.2   3.5   1.6e-10     2e-07       1      61 [.      13      71 ..      13      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 1.6e-10
                                      HHHHHHHHHH.HHHHH-HHHHHHHHHHHHHHHHHCT---SSTCCCTB-TTT--B-.-CTTTE CS
                              Rpr2  1 rlnfLyqaahlqlaeaspalsrylakqlrevskkaqlrlppsvkrtvCkkCgsvl.ipgvtc 61
                                      r++ L++ a+    +++ al+r++++ ++++ +++++++++s+k+++Ck+C++ +  pg++ 
  gi|518652765|ref|YP_008142285.1| 13 RMQTLFNEAEN---TENIALARRYIRLMEKIGMRMNISVNTSIKHSYCKHCKTPYkNPGIKL 71
                                      67777777775...8899**********************************9762355544 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   3.1   1.1e-06    0.0014       5      33 ..      57      85 ..      56      86 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                     zinc_ribbon_4  5 CpsCkakyeiddeklpakgvkvrCskCgh 33
                                      C++Ck+ y+ +  kl+ k v vrC+ Cg+
  gi|518652765|ref|YP_008142285.1| 57 CKHCKTPYKNPGIKLKNKMVQVRCPYCGE 85
                                      ***************************97 PP

>> zinc_ribbon_5  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.6   1.5e-06    0.0019       5      34 ..      57      86 ..      55      88 .. 0.97

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.5e-06
                     zinc_ribbon_5  5 CpdCdtkFklvdsklKksgkkVrCakCaev 34
                                      C  C+t +k    klK+  + VrC  C+e+
  gi|518652765|ref|YP_008142285.1| 57 CKHCKTPYKNPGIKLKNKMVQVRCPYCGEI 86
                                      9***************************98 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.5   3.2e-06    0.0041      11      37 ..      53      86 ..      47      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.2e-06
                               DZR 11 darfCseCgtklkavaa.......edrCpsCgek 37
                                      +  +C++C+t+ k++         + rCp Cge 
  gi|518652765|ref|YP_008142285.1| 53 KHSYCKHCKTPYKNPGIklknkmvQVRCPYCGEI 86
                                      567********9855558899999*******985 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   1.2e-05     0.015      41      95 ..      11      86 ..       5      90 .. 0.61

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      HHHHHHHHHHHH..............CC.TTTT-EEEEEEE--EEEETTTS-EEECHH.HHH.......S-TTTSSS CS
                              HypA 41 peaLefafella..............egtvlegaeLeieevpvkvrCreCgkefelee.kal.......rCpkCgsa 95
                                      +e +++ f+ ++               +++  + ++++++   + +C++C++ ++    k l       rCp Cg+ 
  gi|518652765|ref|YP_008142285.1| 11 KERMQTLFNEAEntenialarryirlMEKIGMRMNISVNTSIKHSYCKHCKTPYKNPGiK-LknkmvqvRCPYCGEI 86
                                      555555555555344444443333333334334666699999999*******99966542.12345666*****985 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      0.02        25      36      45 ..      53      62 ..      42      63 .. 0.78
   2 ?    8.6   0.1    0.0014       1.8      19      28 ..      78      87 ..      69      93 .] 0.71

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.02
                     Zn_Tnp_IS1595 36 glfqCkeCrk 45
                                      +   Ck+C++
  gi|518652765|ref|YP_008142285.1| 53 KHSYCKHCKT 62
                                      5678****95 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0014
                     Zn_Tnp_IS1595 19 fvCPhCgsrk 28
                                      ++CP+Cg  +
  gi|518652765|ref|YP_008142285.1| 78 VRCPYCGEIR 87
                                      67*****654 PP

>> WhiA_N  WhiA N-terminal LAGLIDADG-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   2.6e-05     0.033      30      59 ..      23      51 ..      13      60 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.6e-05
                            WhiA_N 30 qtenaaiARriykllkelYgieaellvrkk 59
                                      +ten+a+ARr+++l++++ g++ +++v ++
  gi|518652765|ref|YP_008142285.1| 23 NTENIALARRYIRLMEKI-GMRMNISVNTS 51
                                      69****************.99999999775 PP

>> Pox_RNA_pol_35  Poxvirus DNA-directed RNA polymerase, 35 kD subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.8e-05     0.036       5      59 ..      39      93 .]      35      93 .] 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.8e-05
                    Pox_RNA_pol_35  5 tlavdldPsvatlikhgfnervkwPlLnlgvvlantttavneeWltaveslPtrk 59
                                      ++ + ++ sv t ikh + ++ k P  n g+ l+n+   v   +   +  +P +k
  gi|518652765|ref|YP_008142285.1| 39 KIGMRMNISVNTSIKHSYCKHCKTPYKNPGIKLKNKMVQVRCPYCGEIRRIPFKK 93
                                      67788999****************************9999988888888888765 PP

>> zf-CHCC  Zinc-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       6.2   7.9e+03      17      25 ..       4      12 ..       3      15 .. 0.75
   2 ?    0.3   0.1      0.61   7.8e+02      28      37 .]      55      64 ..      45      64 .. 0.78
   3 ?   11.7   0.1   0.00016      0.21      21      34 ..      70      84 ..      69      86 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 6.2
                                      EEEEE--TT CS
                           zf-CHCC 17 rvyieldkk 25
                                      rv i++ k+
  gi|518652765|ref|YP_008142285.1|  4 RVLINISKE 12
                                      788999876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.61
                                      EEETTTTEEE CS
                           zf-CHCC 28 vdCgYCglrF 37
                                        C+ C + +
  gi|518652765|ref|YP_008142285.1| 55 SYCKHCKTPY 64
                                      5699998876 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 0.00016
                                      E--.TTSEEEETTTT CS
                           zf-CHCC 21 eld.kkgpvdCgYCg 34
                                      +l+ k  +v+C+YCg
  gi|518652765|ref|YP_008142285.1| 70 KLKnKMVQVRCPYCG 84
                                      66656679******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 ?    2.6   0.8     0.075        96      19      25 ..      57      63 ..      53      63 .. 0.79
   2 ?   11.2   0.1   0.00015      0.19       3      11 ..      78      86 ..      77      88 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.075
                       zf-ribbon_3 19 CpyCGtk 25
                                      C++C t+
  gi|518652765|ref|YP_008142285.1| 57 CKHCKTP 63
                                      9999875 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00015
                       zf-ribbon_3  3 vrCPnCGap 11
                                      vrCP+CG++
  gi|518652765|ref|YP_008142285.1| 78 VRCPYCGEI 86
                                      799999985 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   1.4     0.077        98       1       8 [.      56      63 ..      56      67 .. 0.74
   2 ?   10.1   0.0   0.00041      0.53      13      21 ..      77      85 ..      68      86 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.077
                     zinc_ribbon_2  1 fCpnCGae 8 
                                      +C++C ++
  gi|518652765|ref|YP_008142285.1| 56 YCKHCKTP 63
                                      79999766 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00041
                     zinc_ribbon_2 13 akFCpyCGt 21
                                      ++ CpyCG+
  gi|518652765|ref|YP_008142285.1| 77 QVRCPYCGE 85
                                      556****96 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.39     5e+02      86     103 ..      24      41 ..       2      52 .. 0.52
   2 ?    1.4   0.2      0.25   3.2e+02      19      45 ..      35      62 ..      23      68 .. 0.68
   3 ?    9.2   0.0   0.00096       1.2      31      51 ..      71      91 ..      62      92 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.39
                              CpXC  86 gytlRlvidmaelaEkil 103
                                       + ++ l+  +  l+Eki+
  gi|518652765|ref|YP_008142285.1|  24 TENIALARRYIRLMEKIG 41 
                                       222233455555666665 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.25
                              CpXC 19 dadedpelkekl.ldgslfeatCpkCga 45
                                       + e+  ++ ++ ++ s+    C +C +
  gi|518652765|ref|YP_008142285.1| 35 RLMEKIGMRMNIsVNTSIKHSYCKHCKT 62
                                      5555556666664566777778888875 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.00096
                              CpXC 31 ldgslfeatCpkCgataklea 51
                                      l++++ +++Cp+Cg+ +++++
  gi|518652765|ref|YP_008142285.1| 71 LKNKMVQVRCPYCGEIRRIPF 91
                                      5788999*******9988765 PP

>> DUF4798  Domain of unknown function (DUF4798)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0054       6.9      36      57 ..      22      43 ..       2      50 .. 0.75
   2 ?    4.8   0.4     0.026        33      32      49 ..      48      65 ..      40      86 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0054
                           DUF4798 36 ekekyyrHrrRYyqlmEKrlka 57
                                      e+       rRY +lmEK  + 
  gi|518652765|ref|YP_008142285.1| 22 ENTENIALARRYIRLMEKIGMR 43
                                      5666666789********7665 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.026
                           DUF4798 32 kelsekekyyrHrrRYyq 49
                                       + s k+ y++H++  y+
  gi|518652765|ref|YP_008142285.1| 48 VNTSIKHSYCKHCKTPYK 65
                                      567889*******87665 PP

>> DUF4187  Domain of unknown function (DUF4187)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.54   6.9e+02       5      23 ..      17      35 ..      13      37 .. 0.85
   2 ?    7.4   4.6    0.0028       3.6      25      38 ..      53      66 ..      52      84 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.54
                           DUF4187  5 efeeleaeerLeklleyLR 23
                                       f+e e +e++++  +y+R
  gi|518652765|ref|YP_008142285.1| 17 LFNEAENTENIALARRYIR 35
                                      5899999999999999988 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0028
                           DUF4187 25 eylYCfwCgtkYed 38
                                      +++YC +C+t Y++
  gi|518652765|ref|YP_008142285.1| 53 KHSYCKHCKTPYKN 66
                                      7***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1062  (0.0592336); expected 358.6 (0.02)
Passed bias filter:                      619  (0.0345251); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 673.00
//
Query:       gi|518652766|ref|YP_008142286.1|  [L=223]
Description: phosphoglycolate phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-22   80.5   0.3    1.2e-12   48.2   0.1    2.1  2  Hydrolase_3  haloacid dehalogenase-like hydrolase
    8.5e-07   28.7   0.1      3e-06   27.0   0.0    1.8  3  S6PP         Sucrose-6F-phosphate phosphohydrolase
    8.2e-05   23.1   0.1       0.39   11.1   0.0    3.0  3  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.012   15.9   0.0        3.6    7.8   0.0    2.3  2  Hydrolase    haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.0   6.7e-11     3e-07       2      96 ..       6      97 ..       5     115 .. 0.89
   2 !   48.2   0.1   2.6e-16   1.2e-12     174     245 ..     136     207 ..     114     210 .. 0.90

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6.7e-11
                                      EEEIIIIIS-TTS---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEEEEE--B- CS
                       Hydrolase_3  2 alDlDGTLlnsdkkisektkeaikklkekgikvviATGRslravlpvleelgldlpvialNGaliddekgkilykstis 80
                                      alD+DGT+ +++  i ++++  ikk +e g ++ + +G+ +  +  +   lg++ pv + NG++  +++g i   + ++
  gi|518652766|ref|YP_008142286.1|  6 ALDVDGTITDQNRIICPEAITSIKKGIESGLQISLISGNVIPVMYGLKTFLGINAPVFGENGGIM-YYNGSIE--KFFD 81
                                      89****************************************9999999****************.9999886..7888 PP

                                      HHHHHHHHHHHHHTTC CS
                       Hydrolase_3 81 kedvkeiikllkennv 96
                                      k++  e++++++++ +
  gi|518652766|ref|YP_008142286.1| 82 KTKPLEFLEYISSRSL 97
                                      8888888888877664 PP

  == domain 2  score: 48.2 bits;  conditional E-value: 2.6e-16
                                       ESTTEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                       Hydrolase_3 174 sskgyleimpkgvsKgtalkklakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                       +sk+ + im++g +Kg a++ l k++n + +e++++GD++ND +M++      + +na++++k+++dyv++ 
  gi|518652766|ref|YP_008142286.1| 136 NSKFTWHIMNPGQNKGYAVEILKKMFNANWDEILVVGDSDNDNAMFTLPVKKACPDNATDSLKSISDYVSPE 207
                                       567899***************************************************************975 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         1   4.5e+03       4      18 ..       4      18 ..       3      36 .. 0.76
   2 ?   -2.3   0.0      0.56   2.5e+03     154     178 ..      83     107 ..      76     121 .. 0.77
   3 !   27.0   0.0   6.7e-10     3e-06     158     202 ..     142     186 ..     126     204 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1
                                      EEEE-TBTTTB.S-H CS
                              S6PP  4 llvsdLDntlvdgdn 18
                                      +++ d+D+t++d+++
  gi|518652766|ref|YP_008142286.1|  4 IMALDVDGTITDQNR 18
                                      678899999986554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.56
                                       TTEEEEEETT-SHHHHHHHHHHHHT CS
                              S6PP 154 gkdlDvlPkraskgeAlryLakkle 178
                                        k l  l   +s++ A  y+ ++++
  gi|518652766|ref|YP_008142286.1|  83 TKPLEFLEYISSRSLATPYFTNQWR 107
                                       5566667777899999999999997 PP

  == domain 3  score: 27.0 bits;  conditional E-value: 6.7e-10
                                       EEEETT-SHHHHHHHHHHHHT--GGGEEEEE-SGGGHHHHTSSSE CS
                              S6PP 158 DvlPkraskgeAlryLakkleleleqilvcGdsgnDeellignvl 202
                                        ++  + +kg+A++ L k ++++ ++ilv+Gds nD+++++  v+
  gi|518652766|ref|YP_008142286.1| 142 HIMNPGQNKGYAVEILKKMFNANWDEILVVGDSDNDNAMFTLPVK 186
                                       5778899*********************************76655 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.3     0.019        87       3      14 ..       7      18 ..       5      21 .. 0.85
   2 !   11.1   0.0   8.7e-05      0.39      84     141 ..      18      75 ..      16      87 .. 0.79
   3 !    6.3   0.0    0.0025        11     129     186 ..     136     180 ..      83     182 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.019
                               HAD  3 fDfDgTLldgds 14
                                      +D+DgT++d++ 
  gi|518652766|ref|YP_008142286.1|  7 LDVDGTITDQNR 18
                                      7********986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 8.7e-05
                               HAD  84 klldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevdd....rltge 141
                                       ++++p+a + +++  + G ++ ++Sg+  p++  l  +lg    ++  +  ++    +++g 
  gi|518652766|ref|YP_008142286.1|  18 RIICPEAITSIKKGIESGLQISLISGNVIPVMYGLKTFLG----INAPVFGENggimYYNGS 75 
                                       4688********999*************************....777333333355555555 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0025
                               HAD 129 atelevddrltgelglegkpvrgegkvaalrewlaaegegidleevvayGDspsDlpl 186
                                       ++      ++t++  + ++  ++   v  l++       ++ ++e+ ++GDs +D ++
  gi|518652766|ref|YP_008142286.1| 136 NS------KFTWH--IMNPGQNKGYAVEILKK-----MFNANWDEILVVGDSDNDNAM 180
                                       33......77777..44444444333333333.....55555667**********877 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   0.0    0.0008       3.6       1      22 [.       2      24 ..       2      65 .. 0.76
   2 ?    6.3   0.0    0.0024        11     178     206 ..     153     181 ..     118     182 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0008
                                      SSEEEEESBTTTBCHH.HHHHHH CS
                                      xxxxxxxxxxxxxxxx.xxxxxx RF
                         Hydrolase  1 iktvvfDkdGTLttge.psvedv 22
                                      ik  ++D+dGT+t+ +   + ++
  gi|518652766|ref|YP_008142286.1|  2 IKIMALDVDGTITDQNrIICPEA 24
                                      78999********9985333333 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0024
                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaal 206
                                       +++ + + ++++  e+++VGD+ nD a++
  gi|518652766|ref|YP_008142286.1| 153 AVEILKKMFNANWDEILVVGDSDNDNAMF 181
                                       33344444569999***********8885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.45
# Mc/sec: 1492.78
//
Query:       gi|518652767|ref|YP_008142287.1|  [L=412]
Description: hypothetical protein FACI_IFERC00001G1406 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   61.1   0.0    1.9e-16   60.3   0.0    1.4  1  Amidohydro_1  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 !   60.3   0.0   1.1e-20   1.9e-16       2     320 ..      46     357 ..      45     392 .. 0.68

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.1e-20
                                       EEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTHHHHHHHHHHHTSSSEEE CS
                      Amidohydro_1   2 vlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattstgiealleaaeelplglr 78 
                                       ++P++ D+HvH++             +p+et +e + +g   al +Gttt+ dm++++   i+  +  +++    l 
  gi|518652767|ref|YP_008142287.1|  46 IIPAGTDTHVHFR-------------DPGETEKEDFSTGSISALFGGTTTIFDMPNNRR-KIDNYAAYSDK----LA 104
                                       89**********9.............******************************754.55555555555....45 PP

                                       EEEESSEGGSGCCCSHHHHHHHHHHHHHHHHHHCTTTCEEEEEEECGTCCSHHHHHHHHHHHHHHHTTEEEEEE... CS
                      Amidohydro_1  79 ilggkvsldrgsaetskasreklkagaaetikgkadgvvkvalapheapafsdeelkealkeakkrdlpvaiHa... 152
                                       i+  k + d g ++ +  +   +++ +   ik+  +     +++ ++ + f++ +++++      +++pv +Ha   
  gi|518652767|ref|YP_008142287.1| 105 IVRRKAFCDFGLYSMFTGTNADIISSESSGIKIYMG----ETTNAPGTVDFTEKGIQKIN----NMNIPVLFHAedg 173
                                       565666666666666666666666666555565543....6666999*********9999....59********433 PP

                                       ..TSSCHHHHHHHHHHTTTEEEETTTTSTCCHHTTTHCCEEEHCTCEEEHH.........HHHHHHHHHHHHCEE.. CS
                      Amidohydro_1 153 ..letkgevedaeaafgetiehgthlevaeslglldeiklilahgvhltpt.........eaellkerlkeagva.. 216
                                         le    ++  ++++      +t    +e+l++ +  ++ + +gv  + t         e++   ++l  +     
  gi|518652767|ref|YP_008142287.1| 174 kcLEKHSGIAKNLKEYS-----ATRPPECEDLAIDKAGNMKFSKGVITHLThdfttayvkEVTP--HHLLLNYDMpl 243
                                       33333333333333333.....445555555555555556666666666333222233222222..33222222256 PP

                                       ...HHHHHHHHSEHHHHHHHHHHHHTSCEEEEEECT....TSSCCGGHHHHHHHHHHHHHHCCTT.TTHCHCHHHHH CS
                      Amidohydro_1 217 ...hcpfsnsilrsgrealrkaldeGvkvglgtDga....asgnslnlleelrlalklqrgllye.deegglslkea 285
                                              + +++r+    l + l +G++ ++++D+a    +    ++  + ++++++++ +l    + + ++ + ++
  gi|518652767|ref|YP_008142287.1| 244 gayGKVNPPLRSRETQKELLNGLISGKFNIVSSDHAphiqNDKVDFEYSKAGIIGVETRIPLMLAlV-QKKILPFDI 319
                                       6554455555688888899999999***********9*66555555666669999977777777766.566999999 PP

                                       HHHHTH.HHHHHTT-TTTSSSS-TTSB--EEEECC....C CS
                      Amidohydro_1 286 lrmaTi.ngAkalglddkvGsievGkdADlvvvdl....d 320
                                       +++++i n+A  ++l  k+G+i++G +AD+  +d      
  gi|518652767|ref|YP_008142287.1| 320 FYKTCIlNPALLFNL--KKGEIKKGNYADFMSIDFssmeR 357
                                       9999976********..****************9854431 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (412 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2536.27
//
Query:       gi|518652768|ref|YP_008142288.1|  [L=357]
Description: hypothetical protein FACI_IFERC00001G1407 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-65  220.3   0.1    3.9e-65  219.5   0.0    1.4  2  Peptidase_M24  Metallopeptidase family M24
    1.1e-12   48.8   0.0    2.1e-12   47.8   0.0    1.5  1  Creatinase_N   Creatinase/Prolidase N-terminal domain


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0      0.66     6e+03      28      61 ..      68     101 ..      56     105 .. 0.66
   2 !  219.5   0.0   4.3e-69   3.9e-65       2     208 ..     140     340 ..     139     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.66
                                       HHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGS CS
                     Peptidase_M24  28 relaaeieattlkrhgarglafppivasgenaav 61 
                                          + +i +tt ++++  + af+  v +g n+++
  gi|518652768|ref|YP_008142288.1|  68 TGFEVLIYNTTAEKNEIIKNAFKNDVNVGLNYSA 101
                                       4455556666667777777777777777777776 PP

  == domain 2  score: 219.5 bits;  conditional E-value: 4.3e-69
                                       HHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEE CS
                     Peptidase_M24   2 lirkaariasaaleavleaikpgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrvlkegdlvl 78 
                                       ++r+aa+ias  +e + + +k+g+te elaa i ++ + ++ga g +f++iva+g+n+a++hy p++ +lk++d+vl
  gi|518652768|ref|YP_008142288.1| 140 DLREAAKIASDSFEDFTKTLKEGMTESELAANIVYA-MMKNGASGESFSTIVAFGKNSAIPHYMPGNAKLKKNDFVL 215
                                       68********************************88.7788************************************ PP

                                       EEEEEEETTEEEEEEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHTTBCCGBSSCSEE CS
                     Peptidase_M24  79 idagaeydgyasDitrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesaglakffphglGH 155
                                        d+ga y++y+sD+trTv++G+ +++q+++ye+v++aq++  +a+k+Gv++++id +ar+++ + ++   f hglGH
  gi|518652768|ref|YP_008142288.1| 216 TDYGALYHRYCSDTTRTVVFGRADEKQKDIYETVKRAQQESKNALKAGVNGKDIDMIARKIIDE-KYPGRFIHGLGH 291
                                       ***************************************************************8.577778****** PP

                                       EESSSSSEEEEEESSSTTCSSB--TTBEEEEEEEEEEETTTEEEEEBEEEEEE CS
                     Peptidase_M24 156 gvGlevhdegpsvsresndgrkleeGmvftiEpgiyfapgeggvriedtvlvt 208
                                       gvG++vhd  p +s  ++++  l+++mv+t Epgiy +pg ggvried+++++
  gi|518652768|ref|YP_008142288.1| 292 GVGMDVHDH-PALS--PSSDFILKANMVITDEPGIY-IPGFGGVRIEDDLIIK 340
                                       ********9.**99..789*****************.9************997 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 !   47.8   0.0   2.4e-16   2.1e-12      13     131 ..      12     131 ..      10     132 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 2.4e-16
                                       T-SEEEEECC......HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHH CS
                      Creatinase_N  13 gldallvtsp......enlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvealad 83 
                                       ++d++l+++       + ++YltG ++  ++  l+  v++++ ++++ al+++ a+e     +ev+ y+  +++  +
  gi|518652768|ref|YP_008142288.1|  12 NVDSVLIMNGgenqvdKTFFYLTGAKSGIFEGSLLH-VKPEKVTIITSALEEEAAKETG---FEVLIYNT-TAEKNE 83 
                                       567777887778888899*******88888877777.***********99998888888...*******8.****** PP

                                       HHHHHHHHT-EEEE-TTSSBHHHHHHHHHHCTTSEEEETHHHHHHHHS CS
                      Creatinase_N  84 llkellesekrvgveldaltvafyealkealpdaelvdaselieelRv 131
                                       ++k+++++  +vg++ +alt++ y++l + +pd+e++d+s+ i+e R 
  gi|518652768|ref|YP_008142288.1|  84 IIKNAFKNDVNVGLNYSALTLDLYKQLMKIIPDKEFIDVSQSIAESRK 131
                                       ********************************************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (357 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.31s 00:00:00.88 Elapsed: 00:00:00.51
# Mc/sec: 2103.21
//
Query:       gi|518652769|ref|YP_008142289.1|  [L=337]
Description: DNA primase large subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-29  101.7   0.8    2.1e-28   99.5   0.8    1.9  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 !   99.5   0.8   1.2e-32   2.1e-28       3     214 ..     123     313 ..     121     330 .. 0.77

  Alignments for each domain:
  == domain 1  score: 99.5 bits;  conditional E-value: 1.2e-32
                                       EEEEHHHHHHHTT-G........GS-EETTEEEE-HHHHHHHHHHHHHHHHHH...........HHGGGSSS---HH CS
                   DNA_primase_lrg   3 ykvpfedvldlvkrr........rvllkkGyaylpkeeleslllekfrkrlekalestkeslp.eleeeikederek 70 
                                       +++pf  +++  k+          + l +G++yl k+++++ll+e f ++l++ + ++   ++ ++ +++  d +++
  gi|518652769|ref|YP_008142289.1| 123 FHIPFDFFIKNNKKIsgykyrlvYQKLSRGTIYLSKNQFIHLLREDFVQKLMDVYSRMGPGDSqNIFRKFIGDLEKI 199
                                       7788888887766446677888888899************************9666655554435544445555544 PP

                                       HHHHHCT--.............TTSSTTG...GSHHHHTT--HHHHCCHHHHCCCSS--CHHHHHHHHHHHHCT--C CS
                   DNA_primase_lrg  71 leellealsesyvaedvqeeedskisakn...idklakesfPpCmrelleglkknghlkhegrlqltlFlkdiglsl 144
                                        +++le  s                  kn   ++++  ++fPpC++ ++ +++++++l+h +r++l++Fl+++g+s 
  gi|518652769|ref|YP_008142289.1| 200 KKDFLEIKS------------------KNtisLGEVDFTMFPPCIKTYITQMRDGENLAHLARFTLASFLHSAGMSN 258
                                       444444444..................3332258899**************************************** PP

                                       HHHHCCCHCHST..HHHHHH.HTHCHCHHHCC-STT--------HHHHHHS....TT---S-HHHH.HHHH CS
                   DNA_primase_lrg 145 deilelwkeaftrteekFdk.eyrynirhnyGkegkrtnyspysCekiltkpppgkgdahgCpfrhdpdkl 214
                                       ++ l+l+k a     +++++    y+++h+ G + ++t+ysp++C+++          +h C++   +d+l
  gi|518652769|ref|YP_008142289.1| 259 ENMLNLFKFA-----PDYKEdLATYQVNHITG-VISGTEYSPPKCSTL--------RSNHLCYMG--DDPL 313
                                       *********9.....*****6777********.***************........466779884..4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       697  (0.0388756); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); 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: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2387.07
//
Query:       gi|518652770|ref|YP_008142290.1|  [L=82]
Description: hypothetical protein FACI_IFERC00001G1409 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-07   29.9   0.3    8.8e-07   29.8   0.3    1.1  1  SRP19     SRP19 protein


Domain annotation for each model (and alignments):
>> SRP19  SRP19 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.3   4.9e-11   8.8e-07       2      66 ..       4      67 ..       3      82 .] 0.80

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 4.9e-11
                                      EECCCCBTTS-CCCT--S-CCCSBSS--HHHHHHHHHHCTSCEEEEEEECTTSSTTCC.EEEEEC- CS
                             SRP19  2 iYPvYldskktrkeGRrvpkelavenPtaqeiaealkalglevvvepeksyPrdwanp.GrVrvkl 66
                                      +Y +Y++   +rk GRr+++e a +n + +++ ++l+ ++l+++v  + +y+r  ++   +  ++ 
  gi|518652770|ref|YP_008142290.1|  4 LYSQYFNPAISRKYGRRISRERA-KNYSDDKLEQILRTMNLKYEVR-DAHYSRIPYEDsKMFVIDA 67
                                      8********************99.778889***************9.99***99554414444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 549.80
//
Query:       gi|518652771|ref|YP_008142291.1|  [L=126]
Description: 30S ribosomal protein S8e [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-35  122.0   1.3    2.1e-35  121.9   1.3    1.0  1  Ribosomal_S8e  Ribosomal protein S8e


Domain annotation for each model (and alignments):
>> Ribosomal_S8e  Ribosomal protein S8e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.9   1.3   1.2e-39   2.1e-35       4     137 .]       3     125 ..       1     125 [. 0.98

  Alignments for each domain:
  == domain 1  score: 121.9 bits;  conditional E-value: 1.2e-39
                                       BXXCCCSEESSTEEXXXSSXXXCCSBXXXXXXXEESSHEEEEEEETTCEEEEEEESESEEEEEETTTTEEEEEEEEE CS
                     Ribosomal_S8e   4 srdskhkrkltGgkakllrkkrkielgrkekatklgaervkvvrvrgGkrkkralrlkkanvthpeekvtkklkIlg 80 
                                         ++k+++k tGgk +  ++kr++elgr+++ t++g++  + +r++gG+rk  +l+ + an+++pe k+tkklkIl+
  gi|518652771|ref|YP_008142291.1|   3 IYQGKSTKKFTGGKLRREHSKRRYELGREPSFTRIGETERRSLRTMGGNRKLLLLKEQFANIYNPEDKTTKKLKILT 79 
                                       5799************************************************************************* PP

                                       EECSSSTCHHHHTTC--TTEEEEEESHHHHHHHHTTEEEEEEESEHHHHSSEEEEEE CS
                     Ribosomal_S8e  81 VkknpsnneyvrlgvltKgaiievdvseLgevtqsgkvvAqvtsrPgqdGcvnavlL 137
                                       Vk+n ++++yv+++++ Kg+ii+++ ++           A++tsrPgq+G +navl+
  gi|518652771|ref|YP_008142291.1|  80 VKENNADPHYVQRNIMNKGTIISTEEGN-----------ARITSRPGQSGIINAVLV 125
                                       ****************************...........****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       513  (0.0286129); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 822.13
//
Query:       gi|518652772|ref|YP_008142292.1|  [L=570]
Description: hypothetical protein FACI_IFERC00001G1411 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-33  114.2   0.0    1.1e-32  113.4   0.0    1.4  1  ABC_tran        ABC transporter
    2.4e-31  109.4  17.5    4.9e-31  108.4  17.5    1.5  1  ABC_membrane    ABC transporter transmembrane region
    1.9e-05   24.2   0.1    0.00094   18.7   0.0    2.2  2  SMC_N           RecF/RecN/SMC N terminal domain
     0.0071   16.3   0.0      0.014   15.3   0.0    1.4  1  RsgA_GTPase     RsgA GTPase
     0.0092   16.1   0.2      0.022   14.8   0.2    1.6  1  DUF87           Helicase HerA, central domain
  ------ inclusion threshold ------
      0.011   15.8   0.0      0.026   14.6   0.0    1.6  1  MMR_HSR1        50S ribosome-binding GTPase
      0.019   14.7   0.7       0.06   13.1   0.1    2.1  2  AAA_29          P-loop containing region of AAA domain
      0.022   15.3   0.1      0.022   15.3   0.1    2.2  3  AAA_23          AAA domain
       0.09   13.1   0.4        0.3   11.4   0.0    2.0  2  AAA_22          AAA domain
       0.11   12.8   0.1        1.5    9.1   0.0    2.5  2  Roc             Ras of Complex, Roc, domain of DAPkinase
       0.14   12.5   0.0       0.35   11.3   0.0    1.7  1  AAA_16          AAA ATPase domain
       0.16   11.0   0.1       0.34    9.9   0.1    1.5  1  T2SSE           Type II/IV secretion system protein
       0.17   11.3  12.6       0.28   10.5  12.6    1.2  1  ABC_membrane_2  ABC transporter transmembrane region 2
       0.18   10.6   0.1       0.27   10.0   0.1    1.3  1  DLIC            Dynein light intermediate chain (DLIC)
       0.46    9.7   7.6      0.057   12.6   2.8    1.9  2  ABC_membrane_3  ABC transporter transmembrane region


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.4   0.0   9.4e-36   1.1e-32       1     137 []     345     493 ..     345     493 .. 0.89

  Alignments for each domain:
  == domain 1  score: 113.4 bits;  conditional E-value: 9.4e-36
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvr 77 
                                       l  +++++ +ge+vaivGe+GaGK+tL+++++gl+k+  G+  ldg++lke++ +  r++ig+++q++ lf+++ +r
  gi|518652772|ref|YP_008142292.1| 345 LTGINMDIAPGERVAIVGETGAGKTTLVNIISGLYKNYTGHAYLDGTELKEIDDKLIREKIGIVSQDAILFSGT-IR 420
                                       5689*********************************************************************9.99 PP

                                       HH......HHHTC.........HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       xx......xxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  78 en......esdee.........iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                        n      + d++         +++++++l   +  dt+v++++ +LSgGqkqr+a+ar+++++p+++++D+ t+
  gi|518652772|ref|YP_008142292.1| 421 YNitmgkdYTDDQvrnaaklsmLDDFIDSLPSGY--DTPVGERGITLSGGQKQRMAIARIIIRNPQIIIFDDSTS 493
                                       9999999944444234444555777777777666..9**********************************9985 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4  17.5   4.1e-34   4.9e-31       2     273 ..      19     287 ..      17     288 .. 0.95

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 4.1e-34
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrr 78 
                                       i++i ++++   l +l+pl++g  +++l++ ++     + +++ll++++++a++i+ ++  y+ n+++++ +  lr+
  gi|518652772|ref|YP_008142292.1|  19 IVVIGASLAYAYLRLLVPLYIGDAVNNLVG-KNYII--ILHFALLIFGVTVASSIFDFAIDYYANKASQKFVYNLRK 92 
                                       5566677777888999************98.77777..9************************************** PP

                                       HHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                      ABC_membrane  79 klfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailplii 155
                                         f ++l  + ++f++ns+G++ls++t d+++lr +++++l+ +f   ++++++ i +  l   +t++ ++++  ii
  gi|518652772|ref|YP_008142292.1|  93 NEFSHLLAKNYEYFNSNSTGNILSKFTMDIETLRRLVNMSLSNLFSVTFLIIIAGIDLTRLYYGFTVIFFVVIAPII 169
                                       ******************************************99999999999998888888888************ PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 156 lvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitq 232
                                       +++ v+ ++ +k+ +   ++++ +++++++ + g r+V++f++ee+++++f+++++++   ++  a +++l ++ + 
  gi|518652772|ref|YP_008142292.1| 170 YFTLVMQRKQRKYWRALRDKYGTMNNLINQNIIGNRVVRSFTAEEEEIKRFNNSTDSYFDDYKGIAGVRSLYNPLLA 246
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 233 llgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                                       l+ +l++ ++l +G+  +i++ +svg++++ + +f++++ +
  gi|518652772|ref|YP_008142292.1| 247 LFLSLAIGFVLIYGGIESIDSIISVGSVIAAVNIFTLVLRP 287
                                       ************************************98877 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.043        51      27      44 ..     358     375 ..     331     379 .. 0.81
   2 !   18.7   0.0   7.9e-07   0.00094     121     213 ..     394     537 ..     373     542 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.043
                                       EEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAi 44 
                                        aivG+ G+GK+ l++ i
  gi|518652772|ref|YP_008142292.1| 358 VAIVGETGAGKTTLVNII 375
                                       68**********999766 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 7.9e-07
                                       HHHHHHHHCTT-STT.......................................................CS-HHHH CS
                                       xxxxxxxxxxxxxxx.......................................................xxxxxxx RF
                             SMC_N 121 kevsellesagiske.......................................................lLSgGek 142
                                       ke+ + l +++i +                                                        +LSgG+k
  gi|518652772|ref|YP_008142292.1| 394 KEIDDKLIREKIGIVsqdailfsgtirynitmgkdytddqvrnaaklsmlddfidslpsgydtpvgergiTLSGGQK 470
                                       34444444444444444777777777777777777777777777777777777888888888888888889****** PP

                                       HHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 143 tLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                                       + +a+a ++    ++   + ++D+  ++LD+   +++ + ++        i+is++   +  a++ + + k
  gi|518652772|ref|YP_008142292.1| 471 QRMAIARII----IRNPQIIIFDDSTSNLDADTETRFLNTIQGFIAGKTTIIISHKISSVMLAERAYVIEK 537
                                       ****99883....5556699*************************9***************9999988766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05     0.014      86     126 ..     341     382 ..     307     402 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
                                       THTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT---- CS
                       RsgA_GTPase  86 tkegleelkellkd.ktsvlvGqSGvGKStLinallpelelk 126
                                       +++ l+ ++  ++  + +++vG++G+GK+tL+n + +  +  
  gi|518652772|ref|YP_008142292.1| 341 NSTILTGINMDIAPgERVAIVGETGAGKTTLVNIISGLYKNY 382
                                       5555566666666658899**************998865555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.9e-05     0.022      21      43 ..     353     375 ..     334     385 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.9e-05
                             DUF87  21 lvtrHlAilgsTGsGKSntvavL 43 
                                       +  +++Ai+g+TG+GK+++v ++
  gi|518652772|ref|YP_008142292.1| 353 APGERVAIVGETGAGKTTLVNII 375
                                       55689***************976 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   2.2e-05     0.026       1      21 [.     357     377 ..     357     399 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.2e-05
                                       EEEEEESTTSSHHHHHHHHHT CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltg 21 
                                       +vaivG + +GK+tL+n ++g
  gi|518652772|ref|YP_008142292.1| 357 RVAIVGETGAGKTTLVNIISG 377
                                       69***************9987 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1     5e-05      0.06      15      39 ..     348     372 ..     338     381 .. 0.84
   2 ?   -2.7   0.0       4.2     5e+03      33      39 ..     512     518 ..     510     530 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5e-05
                            AAA_29  15 htieidlkgatlltGpsGsGKSTll 39 
                                         ++i + + + ++G++G+GK+Tl+
  gi|518652772|ref|YP_008142292.1| 348 INMDIAPGERVAIVGETGAGKTTLV 372
                                       56788888899*************8 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                            AAA_29  33 sGKSTll 39 
                                       +GK+T++
  gi|518652772|ref|YP_008142292.1| 512 AGKTTII 518
                                       69***98 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       8.3   9.9e+03     119     143 ..     191     215 ..     148     232 .. 0.59
   2 ?   15.3   0.1   1.8e-05     0.022      23      40 ..     359     376 ..     339     440 .. 0.92
   3 ?   -3.0   0.5         7   8.4e+03      30      36 ..     512     518 ..     512     518 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 8.3
                            AAA_23 119 qfisellgskkiilnlilflgqerf 143
                                        ++++l++++ i ++++  + +e++
  gi|518652772|ref|YP_008142292.1| 191 GTMNNLINQNIIGNRVVRSFTAEEE 215
                                       3344444444443333333333332 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 1.8e-05
                            AAA_23  23 lItGpNGaGKTTildAik 40 
                                       +I+G++GaGKTT+++ i 
  gi|518652772|ref|YP_008142292.1| 359 AIVGETGAGKTTLVNIIS 376
                                       7*************9885 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 7
                            AAA_23  30 aGKTTil 36 
                                       aGKTTi+
  gi|518652772|ref|YP_008142292.1| 512 AGKTTII 518
                                       8*****7 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       3.6   4.3e+03     109     129 ..     122     145 ..     113     152 .. 0.75
   2 ?   11.4   0.0   0.00025       0.3       9      32 ..     359     382 ..     355     428 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 3.6
                            AAA_22 109 leeLrsllnl...srkgvqliLvG 129
                                       +e+Lr+l+n    + ++v++++++
  gi|518652772|ref|YP_008142292.1| 122 IETLRRLVNMslsNLFSVTFLIII 145
                                       688999999887667777766665 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00025
                            AAA_22   9 vvtGesGtGKTtllrrlleqldee 32 
                                       +++Ge+G+GKTtl++ +   ++++
  gi|518652772|ref|YP_008142292.1| 359 AIVGETGAGKTTLVNIISGLYKNY 382
                                       79***********98776666655 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 ?    9.1   0.0    0.0012       1.5       1      17 [.     357     373 ..     357     390 .. 0.88
   2 ?    0.5   0.0      0.55   6.5e+02      64     118 ..     467     523 ..     466     525 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                                       EEEEESSTTSSHHHHHH CS
                               Roc   1 KvvlvGdsgvGKtsllk 17 
                                       +v +vG++g+GKt+l++
  gi|518652772|ref|YP_008142292.1| 357 RVAIVGETGAGKTTLVN 373
                                       589************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.55
                                       -SGGCTTTT-HHHHCTSCEEEEEEEGHH.H.HCHHHHHHHHHHHCSSS-EEEEEE-T CS
                               Roc  64 aGqerfrslhplylreaalailvydsrs.s.enlkeWlkelkkvagkspvilvgnki 118
                                       +Gq++  +++++ +r+ +++i+   +++ + ++  + l+ ++     +  i++  ki
  gi|518652772|ref|YP_008142292.1| 467 GGQKQRMAIARIIIRNPQIIIFDDSTSNlDaDTETRFLNTIQGFIAGKTTIIISHKI 523
                                       688888889999999998887655433313245567999999988888888777776 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   0.0   0.00029      0.35      25      50 ..     356     380 ..     345     519 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                            AAA_16  25 elvllsGesGvGKsslvrellralek 50 
                                       e v ++Ge G GK++lv+ +   l k
  gi|518652772|ref|YP_008142292.1| 356 ERVAIVGETGAGKTTLVNIIS-GLYK 380
                                       6799*************8665.3333 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 ?    9.9   0.1   0.00029      0.34     103     155 ..     330     381 ..     322     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00029
                             T2SSE 103 ltlddlgaeealkekiaevlrkavrerglilvsGgTgsGKttllyallkeink 155
                                       ++l++lg++ + + +i   ++  ++    + + G Tg GKttl++++    ++
  gi|518652772|ref|YP_008142292.1| 330 ISLENLGYKSN-NSTILTGINMDIAPGERVAIVGETGAGKTTLVNIISGLYKN 381
                                       56667776554.456666777777888888999************99877665 PP

>> ABC_membrane_2  ABC transporter transmembrane region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5  12.6   0.00024      0.28       6     174 ..       8     174 ..       4     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00024
                    ABC_membrane_2   6 ipklkskeallllvlllllvlrtllsvlvaqldgklvkalvaknvraFvlsllkfallavpasfvnsalkYltqkLa 82 
                                       + k+ + ++ l++v++ + ++  +l +lv    g+ v++lv kn+   +   l ++ + v++s+   a++Y+ +k +
  gi|518652772|ref|YP_008142292.1|   8 F-KNIKSVWYLIIVVIGASLAYAYLRLLVPLYIGDAVNNLVGKNYIIILHFALLIFGVTVASSIFDFAIDYYANKAS 83 
                                       4.44566788889999999999******************************************************* PP

                    ABC_membrane_2  83 lafRkrLtkhllseYlknr.tyYkvsnlderidnpDqritqDvekFtsslssLlsglvkpildvilftfiLwslsgt 158
                                        +f  +L k   s+ l ++  y++ sn  +   n+    t D+e+  + ++  ls+l++  + +i+  + L++l   
  gi|518652772|ref|YP_008142292.1|  84 QKFVYNLRKNEFSHLLAKNyEYFN-SNSTG---NILSKFTMDIETLRRLVNMSLSNLFSVTFLIIIAGIDLTRLYYG 156
                                       **********99999998867777.44444...78899************999********************9988 PP

                    ABC_membrane_2 159 lgl..lllllyvllatvi 174
                                        ++  +++++ ++  t++
  gi|518652772|ref|YP_008142292.1| 157 FTVifFVVIAPIIYFTLV 174
                                       888443333333333333 PP

>> DLIC  Dynein light intermediate chain (DLIC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00023      0.27      22      63 ..     352     389 ..     337     450 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00023
                              DLIC  22 lPsgksvlvlGedgsGkttliaklqGveeekkGrGleylyld 63 
                                       +  g  v ++Ge g+Gkttl+  + G+ ++  G+    +yld
  gi|518652772|ref|YP_008142292.1| 352 IAPGERVAIVGETGAGKTTLVNIISGLYKNYTGH----AYLD 389
                                       55678899******************98877764....3444 PP

>> ABC_membrane_3  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   2.8   4.8e-05     0.057      10      62 ..      16      68 ..       5      76 .. 0.85
   2 ?   -1.9   0.2       1.4   1.6e+03     136     157 ..     153     174 ..     104     205 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.8e-05
                    ABC_membrane_3 10 krlavtfllvlaenvlllayPlligfaiddllagkvaqlliyalvvlllilig 62
                                      + ++v+    la + l l++Pl ig a+++l+ +++  +l +al+++++++ +
  gi|518652772|ref|YP_008142292.1| 16 YLIIVVIGASLAYAYLRLLVPLYIGDAVNNLVGKNYIIILHFALLIFGVTVAS 68
                                      557888888899999********************************998865 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                    ABC_membrane_3 136 lefslglsallillllllllpr 157
                                       l    ++ ++++++ ++ +  +
  gi|518652772|ref|YP_008142292.1| 153 LYYGFTVIFFVVIAPIIYFTLV 174
                                       3333333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (570 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); 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):              15  [number of targets reported over threshold]
# CPU time: 0.64u 0.27s 00:00:00.91 Elapsed: 00:00:00.42
# Mc/sec: 4046.57
//
Query:       gi|518652773|ref|YP_008142293.1|  [L=585]
Description: hypothetical protein FACI_IFERC00001G1412 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-39  135.0  18.8    5.1e-39  134.6  18.8    1.2  1  ABC_membrane     ABC transporter transmembrane region
    1.5e-30  106.5   0.0    2.4e-30  105.8   0.0    1.4  1  ABC_tran         ABC transporter
    8.8e-05   21.8  18.8    0.00012   21.4  13.7    2.9  2  ABC_membrane_3   ABC transporter transmembrane region
    0.00015   21.2   1.5     0.0029   17.1   0.1    2.1  2  SMC_N            RecF/RecN/SMC N terminal domain
    0.00041   20.3   0.7       0.21   11.5   0.0    2.4  2  NTPase_1         NTPase
     0.0011   18.9   0.0     0.0021   18.0   0.0    1.4  1  RsgA_GTPase      RsgA GTPase
     0.0013   18.4   0.0     0.0027   17.4   0.0    1.5  1  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
     0.0076   16.5   0.3      0.058   13.7   0.3    2.3  1  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.016   15.3   0.8      0.054   13.6   0.6    2.0  1  DUF87            Helicase HerA, central domain
      0.026   14.3   1.0      0.083   12.6   0.5    2.2  2  AAA_24           AAA domain
      0.029   13.9   0.1      0.059   12.9   0.1    1.5  1  AAA_7            P-loop containing dynein motor region
       0.03   13.4   0.1      0.061   12.4   0.1    1.4  1  T2SSE            Type II/IV secretion system protein
      0.042   13.0   0.2       0.13   11.5   0.1    1.7  2  NB-ARC           NB-ARC domain
      0.044   13.9   0.0       0.11   12.6   0.0    1.7  1  MMR_HSR1         50S ribosome-binding GTPase
      0.048   14.1   0.2       0.28   11.6   0.2    2.1  1  AAA              ATPase family associated with various cellul
      0.059   13.1   0.0       0.12   12.1   0.0    1.4  1  Sigma54_activat  Sigma-54 interaction domain
      0.076   13.5   0.2       0.19   12.2   0.2    1.7  1  AAA_23           AAA domain
       0.13   12.3   0.3       0.47   10.4   0.0    2.0  2  ResIII           Type III restriction enzyme, res subunit
       0.17   11.7   0.3        4.6    7.0   0.1    2.5  2  DEAD             DEAD/DEAH box helicase
       0.25   11.1   0.7       0.51   10.1   0.1    1.8  2  AAA_29           P-loop containing region of AAA domain


Domain annotation for each model (and alignments):
>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6  18.8   5.7e-42   5.1e-39       2     273 ..      36     304 ..      35     305 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 5.7e-42
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane   2 iliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrr 78 
                                       ++ii +++++ v++++ p+++g  +d+++   + +   l+++++l+l++++++ i++  ++ ++++t++ ++k lr 
  gi|518652773|ref|YP_008142293.1|  36 TIIISAILASSVIAMIGPYIIGIATDSIIA-LKFKI--LIILAVLYLGIYIINYIAENRRTKYMMNTSQAVIKGLRD 109
                                       58899999*********************9.88888..*************************************** PP

                                       HHHHHHHCSTHHHHHHSCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHH CS
                      ABC_membrane  79 klfkkilrqpmsffdtnsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailplii 155
                                       ++f+++ + p++++  +++G+++sr+tnd+++l+d+l+++l +++  ++ +++++ +m+yl + lt+  ++i+p+++
  gi|518652773|ref|YP_008142293.1| 110 RAFRNLQYVPLKYYAGKNAGQIISRITNDAETLSDFLTFQLPQVVAGIAGIIASIFIMIYLDPLLTVYAVIIIPMLL 186
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 156 lvsaviakilkklkkkeqkavakassvaeEslsgirtVkafgreeyflekfekaleeakkagikkaianglligitq 232
                                          ++++k++k +  +   ++a+++  + Es++g++ +k+ g e+ f+++fe  + ++++a+i++ ++++l+++i q
  gi|518652773|ref|YP_008142293.1| 187 ATVFLMNKRIKFNYMNVRRRIAELTGNVGESINGVKAIKSSGTEDVFNDNFETVNSNNYEANIRAVRLTSLFSSIVQ 263
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
                      ABC_membrane 233 llgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                                       ++  l ++++l+ G++ v    +s+g lv f+++   +f++
  gi|518652773|ref|YP_008142293.1| 264 IIEGLGIMIVLYEGGAEVFGRVISIGILVSFIVYVQSFFNP 304
                                       ************************************99987 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   2.7e-33   2.4e-30       2     137 .]     365     511 ..     364     511 .. 0.95

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 2.7e-33
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvre 78 
                                       +n+s+ +++g+++ai+G++GaGK+t+ +l+++ +kp+ G+i++dg d+++ ++ ++rk +gv+ q+p+lf+++ + e
  gi|518652773|ref|YP_008142293.1| 365 DNLSMVIEKGKRIAIIGKTGAGKTTISNLILNFYKPDTGTITMDGVDINNFNTMEYRKLFGVILQDPFLFDGT-ILE 440
                                       89***********************************************************************.999 PP

                                       H.......HHHTCHHHHHHHSTTGG.....TTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       x.......xxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  79 n.......esdeeiekalsklglke.....lkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                       n         +eei++ +s+lgl+          +v++++s+LS+Gq+q v++ ra +++p+++++DE+t+
  gi|518652773|ref|YP_008142293.1| 441 NirfadysIPEEEIKEKISSLGLDSiigplGLYANVGERGSNLSEGQRQAVSILRAAVNNPQIIIMDEATS 511
                                       99***99988888999999999999888886777889999*****************************96 PP

>> ABC_membrane_3  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4  13.7   1.4e-07   0.00012      13     162 ..      36     196 ..      25     209 .. 0.75
   2 ?   -0.6   0.2      0.71   6.4e+02     118     172 ..     256     315 ..     253     335 .. 0.67

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
                    ABC_membrane_3  13 avtfllvlaenvlllayPlligfaiddllagkvaqlliyalvvllliligaarrivDTR....aysrIyael..... 80 
                                       +++ + +la  v+ +  P++ig+a d+++a k++ l+i+a++ l++ +i  +     T+    +  +++  l     
  gi|518652773|ref|YP_008142293.1|  36 TIIISAILASSVIAMIGPYIIGIATDSIIALKFKILIILAVLYLGIYIINYIAENRRTKymmnTSQAVIKGLrdraf 112
                                       56778999*************************************99998765544444111133444444411111 PP

                    ABC_membrane_3  81 .avevvleqrqqdldtSkvaarlal.srelvdFlEkhlPtlitavvsivgavvmllvlefslglsallillllllll 155
                                          ++v  +   +++  ++ +r++  ++ l dFl  +lP++++ +  i++++ ++  l   l++ a++i+ +ll ++
  gi|518652773|ref|YP_008142293.1| 113 rNLQYVPLKYYAGKNAGQIISRITNdAETLSDFLTFQLPQVVAGIAGIIASIFIMIYLDPLLTVYAVIIIPMLLATV 189
                                       134455566678899999999997626779**********************************9999988777776 PP

                    ABC_membrane_3 156 prFarrn 162
                                          ++r 
  gi|518652773|ref|YP_008142293.1| 190 FLMNKRI 196
                                       6555554 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                    ABC_membrane_3 118 tlitavvsivgavvmllvl.....efslglsallillllllllprFarrnerlnikLNne 172
                                        l++++v+i+ ++ ++ vl     e+   + +++il+++++ ++ F +   +l    N+ 
  gi|518652773|ref|YP_008142293.1| 256 SLFSSIVQIIEGLGIMIVLyeggaEVFGRVISIGILVSFIVYVQSFFNPIVQLSQFYNSY 315
                                       578888998877644333312222455567788999999999999988888887777765 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 ?    2.5   0.2     0.095        85      26      44 ..     376     394 ..     347     399 .. 0.78
   2 !   17.1   0.1   3.2e-06    0.0029     135     211 ..     466     553 ..     405     559 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.095
                                       EEEEEESTTSSHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAi 44 
                                         ai+G+ G+GK+ + + i
  gi|518652773|ref|YP_008142293.1| 376 RIAIIGKTGAGKTTISNLI 394
                                       469*********9987655 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 3.2e-06
                                       T...............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE- CS
                                       x...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 135 e...............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivis 196
                                                       +LS G+++ v++ L+ A   v+   + ++De  ++LD kn +++ + + +  +   +i+i+
  gi|518652773|ref|YP_008142293.1| 466 IigplglyanvgergsNLSEGQRQAVSI-LRAA---VNNPQIIIMDEATSQLDMKNESIIQSAIFKFMEGKTIIIIA 538
                                       3555555555555555899999985554.3433...4455689********************************** PP

                                       SSHHHCCC-SCEEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 197 lreemlekadklvgv 211
                                       ++ +++ ++d ++ +
  gi|518652773|ref|YP_008142293.1| 539 HHLQTIIHSDYIYYI 553
                                       **9999988887765 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1    0.0066       5.9       1      26 [.     376     401 ..     376     429 .. 0.68
   2 !   11.5   0.0   0.00023      0.21      70     135 ..     475     542 ..     470     559 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0066
                                       EEEEE--TTSSHHHHHHHHHHHH... CS
                          NTPase_1   1 kvfiTGppGvGKtTlvkkvlellkss 26 
                                       +++i G+ G GKtT+ + +l+  k +
  gi|518652773|ref|YP_008142293.1| 376 RIAIIGKTGAGKTTISNLILNFYKPD 401
                                       58999***********9999876644 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00023
                                       EETTEEE-HHHHHHHHHHHHHHHHHHH-EEEE---.STTGGG-HHHHH.HHHHHHTTTSEEEEE--SS CS
                          NTPase_1  70 rvgkyvvdvesfeelalealrkalseadviviDEi.GkmElkskkfke.aveevLksekpvlavihrr 135
                                       +vg+   ++ + ++ a+++lr a++++++i++DE   ++ +k +++++ a+ + ++ ++++++  h +
  gi|518652773|ref|YP_008142293.1| 475 NVGERGSNLSEGQRQAVSILRAAVNNPQIIIMDEAtSQLDMKNESIIQsAIFKFMEGKTIIIIAHHLQ 542
                                       6888888999999*********************7257999988875427888888888888776655 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.4e-06    0.0021      72     130 ..     346     405 ..     312     410 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.4e-06
                                       HHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT-----S-- CS
                       RsgA_GTPase  72 lealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallpelelktgev 130
                                       + +l ++ ++ s  +++ +++l+ ++++ k ++++G++G+GK+t+ n +l+  +  tg +
  gi|518652773|ref|YP_008142293.1| 346 TDKLKFNNVTFSYGKERIIDNLSMVIEKgKRIAIIGKTGAGKTTISNLILNFYKPDTGTI 405
                                       566777778888999999********999*******************998777777776 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 !   17.4   0.0   3.1e-06    0.0027       3      65 ..     362     492 ..     361     545 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.1e-06
                                       HHHHHH.S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEE.............................. CS
                                       xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
                       ATP-synt_ab   3 rvlDal.fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvg.............................. 48 
                                       r++D l + i +G+r++i+g+ g Gkt+is+ +++  + d+ +i +                               
  gi|518652773|ref|YP_008142293.1| 362 RIIDNLsMVIEKGKRIAIIGKTGAGKTTISNLILNFYKPDTGTITMDgvdinnfntmeyrklfgvilqdpflfdgti 438
                                       678877245679**********************9988886444443477888888888888888888888888888 PP

                                       .....................................ESEEHHHHHHHHHHCHH CS
                                       .....................................xxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  49 .....................................iGergnevaevleefpe 65 
                                                                            +Gerg++++e  ++  +
  gi|518652773|ref|YP_008142293.1| 439 lenirfadysipeeeikekisslgldsiigplglyanVGERGSNLSEGQRQAVS 492
                                       888888888888888888888888888888888888888888777776665555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   6.5e-05     0.058       6     103 ..     375     513 ..     371     545 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.5e-05
                            AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee.................................erpevvfvtlps 49 
                                       + ++++G +G+GKTt  + +l+ ++ +    +                                 e+ +++ + +p+
  gi|518652773|ref|YP_008142293.1| 375 KRIAIIGKTGAGKTTISNLILNFYKPDTGTITmdgvdinnfntmeyrklfgvilqdpflfdgtilENIRFADYSIPE 451
                                       5589*******************953222222444444444444444444444433333333333333333333333 PP

                            AAA_22  50 st...sskdllrellralglelka....................erlsseellealeqalrarav.ielliiDEaqh 102
                                       ++   +                                      ++ +++e  ++    lra+   ++++i DEa  
  gi|518652773|ref|YP_008142293.1| 452 EEikeK-----------------IsslgldsiigplglyanvgeRGSNLSEGQRQAVSILRAAVNnPQIIIMDEATS 511
                                       333333.................033333333333333334454444444444444444444444666666666665 PP

                            AAA_22 103 .l 103
                                        l
  gi|518652773|ref|YP_008142293.1| 512 qL 513
                                       55 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.6     6e-05     0.054      24      45 ..     375     396 ..     367     408 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 6e-05
                             DUF87  24 rHlAilgsTGsGKSntvavLle 45 
                                       +++Ai+g+TG+GK++   ++l+
  gi|518652773|ref|YP_008142293.1| 375 KRIAIIGKTGAGKTTISNLILN 396
                                       789************9999986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.4   2.2e+03     106     130 ..      16      42 ..      12      46 .. 0.84
   2 ?   12.6   0.5   9.3e-05     0.083       2      46 ..     374     415 ..     373     524 .. 0.63

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.4
                            AAA_24 106 elaeefrrllkklqelrk..nvifiah 130
                                       +l++ f+rllk + +++   ++i+ a 
  gi|518652773|ref|YP_008142293.1|  16 RLNNYFIRLLKEILAYKRnsTIIISAI 42 
                                       78999********99999888888876 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.3e-05
                            AAA_24   2 klkiliyGpsgiGKTtlakel....gpkplfidtekGlksldadkfpdi 46 
                                       +++i+i+G+ g+GKTt+ + +    +p++  i        +d+ ++++ 
  gi|518652773|ref|YP_008142293.1| 374 GKRIAIIGKTGAGKTTISNLIlnfyKPDTGTIT-------MDGVDINNF 415
                                       789*************99988444444444444.......444443333 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   6.6e-05     0.059      26      60 ..     367     401 ..     348     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.6e-05
                             AAA_7  26 lelllknkkpvllvGptGtGKtviikdllkkldke 60 
                                       l+++++++k + ++G+tG GKt+i + +l+ ++++
  gi|518652773|ref|YP_008142293.1| 367 LSMVIEKGKRIAIIGKTGAGKTTISNLILNFYKPD 401
                                       78899******************999988877755 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.8e-05     0.061     116     160 ..     361     405 ..     337     413 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.8e-05
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderi 160
                                       e+i + l+  +++ + i + G Tg GKtt+ + +l++ + ++  i
  gi|518652773|ref|YP_008142293.1| 361 ERIIDNLSMVIEKGKRIAIIGKTGAGKTTISNLILNFYKPDTGTI 405
                                       5556667777888899999*****************988875554 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   0.00014      0.13       5      42 ..     360     396 ..     357     404 .. 0.85
   2 ?   -2.0   0.0       1.8   1.6e+03      80     108 ..     510     537 ..     504     538 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00014
                                       HHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC   5 vekviekLlekdelqslvvalvGmgGvGKttlakqiln 42 
                                       +e++i++L+   e +   +a+ G+ G GKtt+++ iln
  gi|518652773|ref|YP_008142293.1| 360 KERIIDNLSMVIEKG-KRIAIIGKTGAGKTTISNLILN 396
                                       799999999766666.789**************99987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.8
                                       CTTSSSS-STTSHHHHHHHHCCCTTEEEE CS
                            NB-ARC  80 eddleekeeveslkrklvrlLltkrfllv 108
                                        ++l+ k+e+  ++  +++++++k  +++
  gi|518652773|ref|YP_008142293.1| 510 TSQLDMKNESI-IQSAIFKFMEGKTIIII 537
                                       56788888888.9*********9988876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.11       1      27 [.     376     403 ..     376     434 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                                       EEEEEESTTSSHHHHHHHHHTS.TEEES CS
                          MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivs 27 
                                       ++ai+G++ +GK+t+ n +++  k  ++
  gi|518652773|ref|YP_008142293.1| 376 RIAIIGKTGAGKTTISNLILNFyKPDTG 403
                                       69****************9985444444 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00031      0.28       3      98 ..     379     534 ..     377     547 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00031
                                       EESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS........................................ CS
                               AAA   3 lyGppGtGKTllakavakelg..vefleisgsellsk........................................ 37 
                                       ++G  G GKT++ + + +  +  +  ++++g ++ +                                         
  gi|518652773|ref|YP_008142293.1| 379 IIGKTGAGKTTISNLILNFYKpdTGTITMDGVDINNFntmeyrklfgvilqdpflfdgtilenirfadysipeeeik 455
                                       7899***************8533333444444444224445555788899999999999999999999999999999 PP

                                       ...................STTHHHHHHHHHHHHHHHTS.....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
                               AAA  38 ...................yvgesekkirelfkeakeka.....kpsilfiDEidalaksrsgseseeeervvnqLl 90 
                                                           vge+ ++++e  ++a +       +p i+++DE+ +    +      +e+ ++++++
  gi|518652773|ref|YP_008142293.1| 456 ekisslgldsiigplglyaNVGERGSNLSEGQRQAVSILraavnNPQIIIMDEATSQLDMK------NESIIQSAIF 526
                                       99***************99555555555555555433333344459********9998888......7888999999 PP

                                       HHHHHTTT CS
                               AAA  91 teldgvkk 98 
                                       ++++g + 
  gi|518652773|ref|YP_008142293.1| 527 KFMEGKTI 534
                                       99998765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00013      0.12       9      62 ..     361     413 ..     355     428 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS- CS
                   Sigma54_activat   9 kelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaip 62 
                                       +++++++++v+++  ++ i G++G+GK++++++i +  k +++  ++++  +i+
  gi|518652773|ref|YP_008142293.1| 361 ERIIDNLSMVIEKGKRIAIIGKTGAGKTTISNLILNFYKPDTG-TITMDGVDIN 413
                                       567899999*************************998776555.4555555554 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   0.00021      0.19      22      39 ..     377     394 ..     315     398 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00021
                            AAA_23  22 tlItGpNGaGKTTildAi 39 
                                        +I+G++GaGKTTi + i
  gi|518652773|ref|YP_008142293.1| 377 IAIIGKTGAGKTTISNLI 394
                                       58************7765 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 ?   10.4   0.0   0.00052      0.47       6      44 ..     358     394 ..     342     403 .. 0.78
   2 ?   -1.8   0.0         3   2.7e+03     132     141 ..     500     509 ..     481     546 .. 0.61

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                                       HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHH CS
                            ResIII   6 eyQeeaienlleklkskrdkrglikmaTGtGKTlvaakl 44 
                                       +  e++i+nl   +  ++ kr+ i   TG+GKT ++  +
  gi|518652773|ref|YP_008142293.1| 358 YGKERIIDNLSMVI--EKGKRIAIIGKTGAGKTTISNLI 394
                                       45556666665444..799**************998554 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 3
                                       T-SEEEEETG CS
                            ResIII 132 rfdviiiDEa 141
                                       + ++ii+DEa
  gi|518652773|ref|YP_008142293.1| 500 NPQIIIMDEA 509
                                       3345555554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0052       4.6      10      32 ..     370     392 ..     361     407 .. 0.80
   2 ?    2.0   0.0      0.17   1.5e+02     119     145 ..     498     524 ..     451     547 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0052
                                       HHHTTCEEEEEESTTSSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  10 lilgggdvlvaaeTGsGKTlafl 32 
                                        i +g+ + + ++TG+GKT++  
  gi|518652773|ref|YP_008142293.1| 370 VIEKGKRIAIIGKTGAGKTTISN 392
                                       466899*************9854 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.17
                                       CTTEEEEEEETHHHHHHTTTHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 119 lsqvrflVlDEadrlldqgfsdfinri 145
                                       +++ +++++DEa   ld++ +  i++ 
  gi|518652773|ref|YP_008142293.1| 498 VNNPQIIIMDEATSQLDMKNESIIQSA 524
                                       678899***********9888888765 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       8.7   7.8e+03      43      55 ..     187     199 ..     186     200 .. 0.83
   2 ?   10.1   0.1   0.00057      0.51      17      38 ..     369     390 ..     361     396 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 8.7
                            AAA_29  43 qalLvpakkvrfN 55 
                                       +++++ +k+++fN
  gi|518652773|ref|YP_008142293.1| 187 ATVFLMNKRIKFN 199
                                       688888999***9 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00057
                            AAA_29  17 ieidlkg.atlltGpsGsGKSTl 38 
                                       + i+ kg  + ++G++G+GK+T+
  gi|518652773|ref|YP_008142293.1| 369 MVIE-KGkRIAIIGKTGAGKTTI 390
                                       5555.555899***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.71u 0.36s 00:00:01.06 Elapsed: 00:00:00.54
# Mc/sec: 3277.69
//
Query:       gi|518652774|ref|YP_008142294.1|  [L=125]
Description: hypothetical protein FACI_IFERC00001G1413 [Ferroplasma acidarmanus fer1]
Scores for 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   0.2    1.4e-07   31.6   0.2    1.3  1  MazG-like  MazG-like family
     0.0047   17.1   0.5     0.0076   16.4   0.4    1.5  1  MazG       MazG nucleotide pyrophosphohydrolase domain


Domain annotation for each model (and alignments):
>> MazG-like  MazG-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.2   1.6e-11   1.4e-07       4      76 ..      34     110 ..      31     123 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.6e-11
                         MazG-like   4 nlkaiElLkaellksveelfkallk....gseeeildeLAdviiylylLAdrlGidfee.ideklkkklkkypveke 75 
                                       +++  ElL++ l+ +  e+ + +l+    +s e+i++e +d++ +++  Ad l++++ee  ++k+++  k+y  +k 
  gi|518652774|ref|YP_008142294.1|  34 SVESNELLEILLWRDK-EFENNILNgkdnKSLEMIKNEVSDILFSCFAIADHLHFNLEEaYRQKMTELDKRYDPDKV 109
                                       78999*********99.566656655788999***********************************9999987775 PP

                         MazG-like  76 h 76 
                                       +
  gi|518652774|ref|YP_008142294.1| 110 K 110
                                       5 PP

>> MazG  MazG nucleotide pyrophosphohydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.4   8.5e-07    0.0076      24      70 ..      62     104 ..      24     106 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 8.5e-07
                                       T-HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH- CS
                              MazG  24 edrdeleeELGDvLlqvlflaniaeeeggidledvaetileKlerRh 70 
                                       +  + +++E+ D+L+  + +a      ++++le++ ++ ++ l +R+
  gi|518652774|ref|YP_008142294.1|  62 KSLEMIKNEVSDILFSCFAIADH----LHFNLEEAYRQKMTELDKRY 104
                                       44559*****************6....*********99999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 971.99
//
Query:       gi|518652775|ref|YP_008142295.1|  [L=507]
Description: hypothetical protein FACI_IFERC00001G1414 [Ferroplasma acidarmanus fer1]
Scores for complete 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-101  338.0   0.0   7.4e-101  337.5   0.0    1.2  1  N6_Mtase         N-6 DNA Methylase
    5.1e-18   66.0   4.4    5.1e-18   66.0   4.4    2.1  3  HsdM_N           HsdM N-terminal domain
    5.6e-06   26.2   0.1    3.9e-05   23.4   0.0    2.4  2  UPF0020          Putative RNA methylase family UPF0020
    0.00082   19.2   0.0     0.0015   18.3   0.0    1.5  1  Methyltransf_31  Methyltransferase domain
  ------ inclusion threshold ------
      0.012   16.0   1.7       0.32   11.4   1.7    2.6  1  Nnf1             Nnf1
      0.053   13.6   0.1       0.18   11.9   0.1    1.9  2  Katanin_con80    con80 domain of Katanin


Domain annotation for each model (and alignments):
>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  337.5   0.0  2.5e-104  7.4e-101       3     306 ..     158     466 ..     156     472 .. 0.96

  Alignments for each domain:
  == domain 1  score: 337.5 bits;  conditional E-value: 2.5e-104
                          N6_Mtase   3 kdllGdvYEyllrkfaeeegksgGeffTPrevsklivellepksgesvyDpacGsggllvqaekvlkee..dgktke 77 
                                        d++Gd+YE +l +fa e++k+ Ge++TPrev++l+v++l+p++g svyDpacGsgg+l++a +++k++   +k+++
  gi|518652775|ref|YP_008142295.1| 158 GDAMGDAYEHILMRFAPEKAKE-GEVYTPREVVRLMVDILDPQPGMSVYDPACGSGGMLIEAYEHVKSRmgVDKANR 233
                                       699******************9.********************************************997778999* PP

                          N6_Mtase  78 lsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfe...kdkkfdvvvaNppfnqkewkektlekde.. 149
                                       + +yG e  +tty+LakmN +lh+i  +  + + gd+l  pkf+     ++fd+v+aNpp++qk++ e+tl++ e  
  gi|518652775|ref|YP_008142295.1| 234 VGLYGEERSPTTYALAKMNTILHDISES--HLEVGDSLLYPKFKtasGLRHFDFVLANPPWSQKGYGEDTLKQAEfk 308
                                       **************************99..7999**********888899****************99888887655 PP

                          N6_Mtase 150 .rfreavapksnadlafllhiieslkpkGraavvlangvLfrggkegkIrkalvekdlveavialpeklFyntsipt 225
                                        r+++++ p++  d+a++ h++++ k   ++av++++g+Lfr++ e+ Ir+++v+++l+++v  lpek+Fynt++++
  gi|518652775|ref|YP_008142295.1| 309 dRYAYGFVPQRYGDWAWIEHMLYTSKS--KVAVIMDQGALFRSNSEKIIRQKIVDEKLLDSVTLLPEKIFYNTGAAG 383
                                       688888*****************9988..9*********************************************** PP

                          N6_Mtase 226 cilvlkkekae.rkgkvlfidaseefkkkd..rkknklteediekildtykekskevdkfskvveleeiaendynln 299
                                       +il+++kek+e  ++kvlfidas+e+ k++  rk n++t+++i++i+ +yk++ + +d+fskvv+++ei+e+dynln
  gi|518652775|ref|YP_008142295.1| 384 AILIFNKEKQEeYRDKVLFIDASREYGKHPdmRKLNIITNDNIDRIVSAYKKF-ESIDGFSKVVSVDEIKEKDYNLN 459
                                       *********9989****************999*********************.*********************** PP

                          N6_Mtase 300 vgryvet 306
                                       v  +v +
  gi|518652775|ref|YP_008142295.1| 460 VTTFVIP 466
                                       *999866 PP

>> HsdM_N  HsdM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.0   4.4   1.7e-21   5.1e-18       1     136 [.      14     145 ..      14     146 .. 0.81
   2 ?   -2.2   0.1         2   5.9e+03      65      82 ..     313     332 ..     292     401 .. 0.61
   3 ?   -2.3   0.1       2.1   6.2e+03      58      76 ..     393     410 ..     346     459 .. 0.53

  Alignments for each domain:
  == domain 1  score: 66.0 bits;  conditional E-value: 1.7e-21
                                       HHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHHHHHHHHHCC..........--..--------......S-CC CS
                            HsdM_N   1 lesklwkaadiLRgkvdaseykeyilgLlFlKrlddveeereeklleeyken...aleeleeklksk..eafyipee 72 
                                       l + +++aad +R +v   +yk yil LlF+Krl+d+++e+ e++++e  e+   +++e +++  s+  + f++pe+
  gi|518652775|ref|YP_008142295.1|  14 LVKLVDNAADLIRTSV---DYK-YILVLLFIKRLSDRWKEEIEDAMSEIMEEtgiDESEAAKRAVSNefHSFMVPEN 86 
                                       57899********666...688.**********************99944444675544444444445889****** PP

                                       CSHHHHHHS--HHHHHHHHHHCHHHHCT--STHHHHHHHS.......S-----SSHHHHHHHHHH CS
                            HsdM_N  73 lrWkelakkkdddelgenlnkafpaleelnkslkgvfmkd.dfnafalgeitkkspalLskviek 136
                                         W++++k+   d+l en+ +a+++++++nk+l gv++ + df +f++   t ++  lL ++   
  gi|518652775|ref|YP_008142295.1|  87 VLWNNIRKD--RDKLTENMSRAINEIAKQNKELDGVVN-RiDFIDFTK---TRENRILLEQLFAL 145
                                       ********5..556***********************5.667777755...56788888888765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2
                                       ....S-CCCSHHHHHHS..- CS
                            HsdM_N  65 eafyipeelrWkelakk..k 82 
                                       ++f+ +    W+++ ++   
  gi|518652775|ref|YP_008142295.1| 313 YGFVPQRYGDWAWIEHMlyT 332
                                       34444445566666666542 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 2.1
                                       -------....S-CCCSHH CS
                            HsdM_N  58 eeklkskeafyipeelrWk 76 
                                       +e++++k  ++i++   ++
  gi|518652775|ref|YP_008142295.1| 393 QEEYRDK-VLFIDASREYG 410
                                       2223222.34444433333 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.3e-08   3.9e-05      19      58 ..     191     229 ..     186     305 .. 0.65
   2 ?   -2.8   0.0       1.5   4.4e+03      58      91 ..     396     432 ..     384     457 .. 0.61

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                                       HHHHHTT--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT CS
                           UPF0020  19 alvrlagwkpgepllDPmCGsGtilIEaallganiapgll 58 
                                        +v + + +pg + +DP CGsG++lIEa   +++++ g  
  gi|518652775|ref|YP_008142295.1| 191 LMVDILDPQPGMSVYDPACGSGGMLIEAYEHVKSRM-GVD 229
                                       699999*********************987777776.333 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.5
                                       T----SSHHHHHHHHHH...HH--EEEEES-HHHHHH CS
                           UPF0020  58 lrefvlelkaeaeeear...aelklygsDldrrvvqg 91 
                                       +r++vl++ a  e  ++   ++l+++  D++ r+v +
  gi|518652775|ref|YP_008142295.1| 396 YRDKVLFIDASREYGKHpdmRKLNIITNDNIDRIVSA 432
                                       5666666333333333322455567777777777765 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.2e-07    0.0015       2      82 ..     199     305 ..     198     398 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-07
                   Methyltransf_31   2 dkglrvlDlGCGtGeltfelae....elgp.kae....vvGiDiseeaielArenaqklgldnveFeqgdieelekl 69 
                                       + g++v+D++CG+G  ++e++e    ++g  k      ++G ++s++   lA+ n+  + +++ ++e+gd    +k 
  gi|518652775|ref|YP_008142295.1| 199 QPGMSVYDPACGSGGMLIEAYEhvksRMGVdK-AnrvgLYGEERSPTTYALAKMNTILHDISESHLEVGDSLLYPK- 273
                                       5789******************8876555433.3588899*********************************998. PP

                   Methyltransf_31  70 led....ekfDlilsn...............e 82 
                                       ++     + fD++l+n               +
  gi|518652775|ref|YP_008142295.1| 274 FKTasglRHFDFVLANppwsqkgygedtlkqA 305
                                       4445699*******996666666666444440 PP

>> Nnf1  Nnf1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   1.7   0.00011      0.32       8     106 ..      41     122 ..      38     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHCCHH-T..........TTSSTTTHHHHHHHHHHHHHHH CS
                              Nnf1   8 kqmvefleesiraefeeIleerdvvekLneLDdlieeAkerreegeeeasrpevpphtLpPeeliaahlapakkeeq 84 
                                       k++ ++++e+i++  +eI+ee ++ e         +eA++r+ ++e            + Pe+++ +++++ + + +
  gi|518652775|ref|YP_008142295.1|  41 KRLSDRWKEEIEDAMSEIMEETGIDE---------SEAAKRAVSNEFH--------SFMVPENVLWNNIRKDRDKLT 100
                                       56778888888888889999988887.........5777777763221........2334***************** PP

                                       HHHHHHHHHHHHHHHHHHHHHH CS
                              Nnf1  85 eeLearlqeleaenaelaeeve 106
                                       e++ + ++e+ ++n+el   v+
  gi|518652775|ref|YP_008142295.1| 101 ENMSRAINEIAKQNKELDGVVN 122
                                       ****************988775 PP

>> Katanin_con80  con80 domain of Katanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   5.9e-05      0.18      59     137 ..       9      86 ..       3     119 .. 0.77
   2 ?   -3.6   0.0       3.5     1e+04     132     150 ..     248     266 ..     232     269 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                     Katanin_con80  59 itLdlcvallplleeLLkskyesyvkvglevlrlilknFgseiksalsapsssvgvdlsreeRlekcsecfkeLqki 135
                                       it    v l++ + +L++++ +   ++ l +++ + +++++ei++a+s+  +++g+d s+    + +s+ f++++  
  gi|518652775|ref|YP_008142295.1|   9 ITKNDLVKLVDNAADLIRTSVDYKYILVLLFIKRLSDRWKEEIEDAMSEIMEETGIDESEAA-KRAVSNEFHSFMVP 84 
                                       555667999**************************************8888899**988877.45555555555554 PP

                     Katanin_con80 136 rk 137
                                       ++
  gi|518652775|ref|YP_008142295.1|  85 EN 86 
                                       44 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 3.5
                     Katanin_con80 132 Lqkirkllkklarrsgkvg 150
                                       L k++++l+ +++ + +vg
  gi|518652775|ref|YP_008142295.1| 248 LAKMNTILHDISESHLEVG 266
                                       5555555555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1061  (0.0591779); expected 358.6 (0.02)
Passed bias filter:                      702  (0.0391544); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.43
# Mc/sec: 3554.73
//
Query:       gi|518652776|ref|YP_008142296.1|  [L=427]
Description: hypothetical protein FACI_IFERC00001G1415 [Ferroplasma acidarmanus fer1]
Scores for complete 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-66  223.5  10.5    1.2e-38  133.0   0.8    2.1  2  Methylase_S   Type I restriction modification DNA specificity
  ------ inclusion threshold ------
      0.037   13.3   0.1      0.071   12.4   0.1    1.4  1  Orthopox_A47  Orthopoxvirus A47 protein
       0.51   10.6   2.4         44    4.4   0.1    3.4  3  DUF3006       Protein of unknown function (DUF3006)


Domain annotation for each model (and alignments):
>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.3   3.2   7.8e-31   4.7e-27       1     160 [.      15     189 ..      15     199 .. 0.84
   2 !  133.0   0.8     2e-42   1.2e-38       1     167 [.     227     408 ..     227     409 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 7.8e-31
                                       ETT-EEEEHHHHEEEEE-----TTGGTTT--EEEE-HH.HCCT........EE-HHHHCCTT---B-TT-EEEE-S. CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkkelkengkypyirag.ilnn........kvvkdglgykkkyilpkgdilissr. 67 
                                       p +w +vkLgdv  + k+    k ++k++g yp+ r++ i+++         +    ++++++y+l +gdil+s + 
  gi|518652776|ref|YP_008142296.1|  15 PQEWGFVKLGDVLSLIKNGVTYKQNKKDSG-YPVTRIEtISEEkidtakvgYIDNIKTENINDYRLIEGDILFSHIn 90 
                                       789************777777775655555.6******66666***777654555556778888888999999999* PP

                                       ..SSTT-EEEESS.-BEE-TTEEEEEEST.TT--HHHHHHHHHHCHHHHHHH.....CCSSTTT---HHHHCC-EEE CS
                       Methylase_S  68 ..atiGkvayrdk.kyylnqsvivlipkn.kkkineflylylllklkklksl.....svgstqpkltkenlkkikIp 135
                                         ++iGk+a+ +  +  l ++++ l +++ k ki e+ yl ++lk  + k l     +++++q+++++++lk ikIp
  gi|518652776|ref|YP_008142296.1|  91 slEHIGKTAIYEGePELLLHGMNLLLLRSdKSKI-EPSYLVYSLKFYRAKELfksmaKRAVNQASINQTELKRIKIP 166
                                       *********9998578*************99999.9999999988887777777789******************** PP

                                       E--HHHHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 136 lPpleeQkkIakiLsqldntielek 160
                                       lPpl+eQ+kIa+iLs+ d+  e+ k
  gi|518652776|ref|YP_008142296.1| 167 LPPLPEQQKIAEILSTADD--EIQK 189
                                       *******************..6665 PP

  == domain 2  score: 133.0 bits;  conditional E-value: 2e-42
                                       ETT-EEEEHHHHEEEEE-----TT..GGTTT--EEEE-HHHCCT............EE-HHHHCCTT---B-TT-EE CS
                       Methylase_S   1 pedwevvkLgdvfeikkgktpkkk..elkengkypyiragilnn............kvvkdglgykkkyilpkgdil 63 
                                       pe+w+++ Lg++f+  +g+tp++k  +++ +g++ ++++++ln+            kv++++l+  + +ilp+++il
  gi|518652776|ref|YP_008142296.1| 227 PEEWDTFGLGEIFKTITGTTPSTKvkDYWHGGTIEWLTPKDLNKlnntitlppserKVTEKALKENNLNILPENSIL 303
                                       89*************************************************************************** PP

                                       EE-SSSTT-EEEESS-BEE-TTEEEEEEST.TT--HHHHHHHHHHCHHHHHHHCCSSTTT---HHHHCC-EEEE--H CS
                       Methylase_S  64 issratiGkvayrdkkyylnqsvivlipkn.kkkineflylylllklkklkslsvgstqpkltkenlkkikIplPpl 139
                                       is+ra++G+v +++ k+++nq+++ l p n +     f+++yl+ k+  l+sls gst+++l+ke l+ + +plPpl
  gi|518652776|ref|YP_008142296.1| 304 ISTRAPVGYVGINNTKITFNQGCKGLVPLNrDVSFPFFYAYYLKSKTTFLNSLSTGSTFKELSKEGLDDVVVPLPPL 380
                                       *****************************8555558888899999999***************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                       Methylase_S 140 eeQkkIakiLsqldntielekkikneie 167
                                       +eQ+kI +iLs++dn++el  ++ ++++
  gi|518652776|ref|YP_008142296.1| 381 PEQQKIGEILSTVDNKLELLGNKREKLN 408
                                       ********************99999885 PP

>> Orthopox_A47  Orthopoxvirus A47 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   1.2e-05     0.071     162     208 ..      76     123 ..      57     148 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.2e-05
                      Orthopox_A47 162 eys.isndllyahinaleyiikntfnvperqlilrgqyltpifsdllk 208
                                       +y  i  d+l++hin+le+i k ++   e +l+l g  l  + sd  k
  gi|518652776|ref|YP_008142296.1|  76 DYRlIEGDILFSHINSLEHIGKTAIYEGEPELLLHGMNLLLLRSDKSK 123
                                       5542678*****************************999988888766 PP

>> DUF3006  Protein of unknown function (DUF3006)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.17     1e+03      32      50 ..      21      39 ..      13      43 .. 0.74
   2 ?    3.2   0.3     0.017     1e+02      20      66 ..     162     208 ..     154     209 .. 0.80
   3 ?    4.4   0.1    0.0074        44      20      66 ..     372     418 ..     364     419 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
                           DUF3006 32 akeGdvLeieddeieldpe 50
                                      +k GdvL++ ++++++ ++
  gi|518652776|ref|YP_008142296.1| 21 VKLGDVLSLIKNGVTYKQN 39
                                      788******9555555554 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.017
                           DUF3006  20 tidiprsdLpegakeGdvLeieddeieldpeetekrkeriqelldrL 66 
                                        i+ip+  Lpe  k   +L+  ddei+ + e+ + +++  + l+++L
  gi|518652776|ref|YP_008142296.1| 162 RIKIPLPPLPEQQKIAEILSTADDEIQKMDEQIALAEQLKKGLMQKL 208
                                       488*******************9999999888777766666666665 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0074
                           DUF3006  20 tidiprsdLpegakeGdvLeieddeieldpeetekrkeriqelldrL 66 
                                        + +p+  Lpe  k G +L+  d+++el  +++ek     + l+++L
  gi|518652776|ref|YP_008142296.1| 372 DVVVPLPPLPEQQKIGEILSTVDNKLELLGNKREKLNVLKKGLMNDL 418
                                       46799***************997788888887777766666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (427 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       802  (0.044732); expected 358.6 (0.02)
Passed bias filter:                      597  (0.033298); 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: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3068.06
//
Query:       gi|518652777|ref|YP_008142297.1|  [L=994]
Description: hypothetical protein FACI_IFERC00001G1416 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-56  191.3   0.0    5.3e-56  189.8   0.0    1.8  1  SWI2_SNF2       SWI2/SNF2 ATPase
    9.9e-37  126.8   3.5    1.1e-36  126.6   0.9    2.5  2  HSDR_N          Type I restriction enzyme R protein N terminu
    8.5e-23   81.2   2.0    1.7e-22   80.2   0.0    2.5  3  ResIII          Type III restriction enzyme, res subunit
    0.00023   21.1   0.1    0.00079   19.4   0.0    1.9  2  HSDR_N_2        Type I restriction enzyme R protein N terminu
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.083   13.2   0.0    2.4  2  Helicase_C      Helicase conserved C-terminal domain
      0.034   13.9   0.0       0.18   11.6   0.0    2.3  1  DEAD            DEAD/DEAH box helicase
      0.043   14.7   3.9       0.11   13.3   1.4    2.8  2  DUF5611         Domain of unknown function (DUF5611)
       0.19   11.7   3.7        6.7    6.7   0.1    3.1  3  Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis 
        0.2   10.9   1.0       0.27   10.4   0.0    1.6  2  DUF4106         Protein of unknown function (DUF4106)


Domain annotation for each model (and alignments):
>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.8   0.0   2.7e-59   5.3e-56       2     219 ..     255     497 ..     254     501 .. 0.85

  Alignments for each domain:
  == domain 1  score: 189.8 bits;  conditional E-value: 2.7e-59
                         SWI2_SNF2   2 Qyravekavervke.......gdrkgGviWHtqGSGKsltmvflakklleeelknpkvvvvtDRkdLdkQlsktfak 71 
                                       Q+ra+ek+++r+++       + +k G+iWH qGSGK+l m+++a +l++ +l ++++++v+DRkdLd+Q  + f++
  gi|518652777|ref|YP_008142297.1| 255 QFRATEKILNRIHNnmdknlkEPKKTGLIWHWQGSGKTLIMAYTAYQLRK-TLPDATILIVVDRKDLDNQALSSFSD 330
                                       9***********999999987779**************************.************************** PP

                         SWI2_SNF2  72 a.geekpkqaesrkeLkell...e.kesekiifttiqKfeee.ekeklevlsereniivlvDEaHRsqygelakklr 142
                                       + g e +k +++++eL +l+   + ++ ++i+++tiqKf++e  k+ ++  + ++n+i lvDE+HR+qyg +a + r
  gi|518652777|ref|YP_008142297.1| 331 IqGLELTKDIKNTTELGDLIaynNgNAMPGIFIVTIQKFSPEnFKSIVKDSTLNNNVICLVDESHRTQYGLMAGTFR 407
                                       8556667899**********6532244889**********763334568888899********************** PP

                         SWI2_SNF2 143 kalpnaafigFTGTPilkkd....kktkevF...g.eyidkYtikeaveDgavvpilYesrlaklelkeeek..... 206
                                       +a+p+a ++gFTGTPi kk+    ++t e+F   g  y+d+Yt+k+a eDg +vpi Ye + a  ++k++       
  gi|518652777|ref|YP_008142297.1| 408 NAFPDAFVFGFTGTPIRKKSggniRNTFEEFcppGeVYLDRYTMKDAQEDGFTVPIAYEYNAAIPAVKDHIIneale 484
                                       ******************8777779999999555246**********************988766666544222223 PP

                         SWI2_SNF2 207 ldeefeeiteele 219
                                       ldee e +te+++
  gi|518652777|ref|YP_008142297.1| 485 LDEEAEGLTENEK 497
                                       6676666666654 PP

>> HSDR_N  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.9   5.7e-40   1.1e-36       2     182 ..       3     183 ..       2     190 .. 0.91
   2 ?   -2.4   0.1         2   3.9e+03      38      68 ..     732     777 ..     698     810 .. 0.64

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 5.7e-40
                                       SSHHHHHH.HHHHHHHHTT-EE................----SHHHHHHHHHHHHHHHH.......-HHHHHHHH.. CS
                            HSDR_N   2 lsEaeleqelidellrelGyqvlskkdveiegrrpe.vrkskaevaleknlreqlgaln.......ikkltkrla.. 68 
                                       + Ea +e+  i+e l+elG+++ ++++ e ++++++ +r+          l ++l ++n       +++++k+    
  gi|518652777|ref|YP_008142297.1|   3 FDEASSEK-WIIEKLQELGWTYNTPEELEDMEDNKYfLRET---------LLNSLRKMNsipdsliSDAVSKLEElt 69 
                                       67897777.********************999999987776.........6667777788888**977777777778 PP

                                       .TT--HHHHHHHHHTS.-EEEETS-EEEEESS-SSSGGGS-EEEEE----SSSS---EEEEEEETTEEEEEEEE--T CS
                            HSDR_N  69 .lsdgnkefyellkeg.kvkfkegrkknikLiDkknlenNrfqvvnQvtvtgnqkrrpDivlfvnglplvviElKrp 143
                                          dgn +f+++lk+g +v  +  ++ +++Li   n  nN+f v+nQ+++ g++++rpDi+lfvng+p+v++E K+p
  gi|518652777|ref|YP_008142297.1|  70 pSKDGNSKFLNFLKNGiNVIDEHRQIHTVRLIAQSNKYNNSFIVTNQLSIHGKSNKRPDILLFVNGIPVVIMENKNP 146
                                       79**************999967899**************************************************** PP

                                       ...T-HHHHHHHHTSS---.---SSSGGGGG--EEEEE-SS- CS
                            HSDR_N 144 ...gtieeAinQikryrkeksdvsipqlfrYlqfgvisngke 182
                                          g+i eA+nQik y+ e+    i+ lf Ylq+ vi ng +
  gi|518652777|ref|YP_008142297.1| 147 ynaGSIDEAYNQIKGYE-ES----IEGLFTYLQIAVINNGIN 183
                                       9866*************.66....****************86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2
                                       .----SHHHHHHHHHHHHHHHH...............-HHHHHHHH CS
                            HSDR_N  38 vrkskaevaleknlreqlgaln...............ikkltkrla 68 
                                       + k++++  + +++++++ +l                i+k +++++
  gi|518652777|ref|YP_008142297.1| 732 LIKILSNPEISDRFEKNFRKLTamlnlprakayltlhIDKYRQLAK 777
                                       5566677777777777777776665566665555555444444443 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.6   3.2e+03      96     120 ..      96     125 ..      56     159 .. 0.61
   2 !   80.2   0.0   8.5e-26   1.7e-22       4     170 ..     251     423 ..     248     424 .. 0.87
   3 ?   -2.6   0.1       2.5   4.9e+03      65     103 ..     580     613 ..     576     622 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                                       -............-SEEEEEHHHHHHTH.. CS
                            ResIII  96 a.....kekdstnkkilvttiqsldadsee 120
                                       +      ++++ n++++vt+  s++ +s++
  gi|518652777|ref|YP_008142297.1|  96 HtvrliAQSNKYNNSFIVTNQLSIHGKSNK 125
                                       244444466777777778887777777733 PP

  == domain 2  score: 80.2 bits;  conditional E-value: 8.5e-26
                                       E-HHHHHHHHHHT.............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHH CS
                            ResIII   4 lreyQeeaienlleklks.......krdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtlee 73 
                                        r++Q +a e++l+ +++       + +k gli++  G+GKTl++a ++++l+k  +   +l++v+rk+l +q+l+ 
  gi|518652777|ref|YP_008142297.1| 251 ARYMQFRATEKILNRIHNnmdknlkEPKKTGLIWHWQGSGKTLIMAYTAYQLRKTLPDATILIVVDRKDLDNQALSS 327
                                       6899*********8888877777767788************************************************ PP

                                       GGGGTGG....GEEEESSS-B--........-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TT CS
                            ResIII  74 fkkflseaykeigkkvsgdkkka.kekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakks 149
                                       f++++  + ++  k++++ ++ + +++ +    i+++tiq+++ ++   ++  ++   +++ + ++DE+Hr+++   
  gi|518652777|ref|YP_008142297.1| 328 FSDIQGLELTKDIKNTTELGDLIaYNNGNAMPGIFIVTIQKFSPEN--FKSIVKDSTLNNNVICLVDESHRTQYGLM 402
                                       ******999887777777777775666777778**********999..5667777777888899**********765 PP

                                       THHHHHT---SEEEEEESS-S CS
                            ResIII 150 wreilekfkeavllglTATpe 170
                                            ++f++a+++g+T+Tp 
  gi|518652777|ref|YP_008142297.1| 403 AGTFRNAFPDAFVFGFTGTPI 423
                                       5566779*************6 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.5
                                       HHHHHHHHHGGGGTGG....GEEEESSS-B--....... CS
                            ResIII  65 slleqtleefkkflseaykeigkkvsgdkkkakekdstn 103
                                       ++++  ++e++k + +++k+++k++++  +++      n
  gi|518652777|ref|YP_008142297.1| 580 DIISEYRDELQKRTGKDAKQACKEFTESFNIS-----GN 613
                                       67777778888888888888888877777666.....44 PP

>> HSDR_N_2  Type I restriction enzyme R protein N terminus (HSDR_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     4e-07   0.00079       5      79 ..      92     167 ..      90     189 .. 0.73
   2 ?   -3.1   0.0         4   7.9e+03      80     109 ..     777     806 ..     769     806 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4e-07
                          HSDR_N_2   5 vRq.klikyLveelgypkeliavekelq.lgskkkraDivvykkdkkpllivecKapsvki.seevleqlksYleal 78 
                                        Rq ++++ + +  +y+++ + v  +l+ +g+++kr+Di+++ +   p++i e K+p  +   +e+++q+k Y e +
  gi|518652777|ref|YP_008142297.1|  92 HRQiHTVRLIAQSNKYNNS-FIVTNQLSiHGKSNKRPDILLFVNG-IPVVIMENKNPYNAGsIDEAYNQIKGYEESI 166
                                       5773555556666666665.55666666477************88.9*********976654789********9975 PP

                          HSDR_N_2  79 k 79 
                                       +
  gi|518652777|ref|YP_008142297.1| 167 E 167
                                       4 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 4
                          HSDR_N_2  80 aeylvvtNglehivykvdkkkkkfeelkdi 109
                                         y++  N l+   ++ +k ++ +e +k+i
  gi|518652777|ref|YP_008142297.1| 777 KAYGIYVNNLKLGAVNGEKVQEAYERVKKI 806
                                       459999999999999999999999998876 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       5.3   1.1e+04      12      35 ..     122     141 ..     112     159 .. 0.67
   2 ?   13.2   0.0   4.2e-05     0.083      52     109 ..     598     655 ..     526     656 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 5.3
                                       HTTTTSEEEEEESSHHHHHHHHHH CS
                        Helicase_C  12 leeeggkilifvntidrlekvkll 35 
                                       +++++ +il+fvn i  +    ++
  gi|518652777|ref|YP_008142297.1| 122 KSNKRPDILLFVNGIPVV----IM 141
                                       467888999999998744....44 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.2e-05
                                       HHHHHHHHHHHH.TTSSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  52 qnereeileqfn.kgesdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       ++  +e  e+fn +g+ ++Li td++ +G d pk+ ++    +    +++ q+iGRt R
  gi|518652777|ref|YP_008142297.1| 598 KQACKEFTESFNiSGNPKILIVTDMLLTGFDSPKLWVMYLAKPL-FEERLLQAIGRTDR 655
                                       44456788999999999****************98666555555.5599********88 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     9e-05      0.18      24     133 ..     288     397 ..     258     408 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9e-05
                                       TSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTT... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
                              DEAD  24 GsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldng... 97 
                                       GsGKTl+++  ++q     k+ +   +liv+  + L +q l+ ++ +     l++   i+++++  +l + +ng   
  gi|518652777|ref|YP_008142297.1| 288 GSGKTLIMAYTAYQLR---KTLPDATILIVVDRKDLDNQALSSFSDIQG---LELTKDIKNTTELGDLIAYNNGnam 358
                                       9************877...789999*******************99988...4444444444443333333344455 PP

                                       CSEEEEEH.....HHHHHHHHCTSSHCTTEEEEEEETHHHH CS
                                       xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  98 vdivvgtp.....grlddllstgklnlsqvrflVlDEadrl 133
                                       + i++ t      + + +++++ +  l++  +  +DE +r 
  gi|518652777|ref|YP_008142297.1| 359 PGIFIVTIqkfspENFKSIVKDST--LNNNVICLVDESHRT 397
                                       666666652222255556666555..777777778888876 PP

>> DUF5611  Domain of unknown function (DUF5611)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   5.7e-05      0.11       8     101 ..     509     604 ..     506     606 .. 0.82
   2 ?   -0.4   0.0         1   2.1e+03       9      36 ..     793     821 ..     792     837 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.7e-05
                                       SSS--SH..HHHHHHHHHHT.-EEEEE.TTEEEEE-TTBS-EEEEE..-SS-EEEEE--.B...-TTS-HHHHHHHH CS
                           DUF5611   8 rGfkkeee.erlkelleeyfggeveee.gdllvvsfgaikklevkisskkkklvvdteerdaeeeddeaaldtvkkf 82 
                                         +k++ + +++ + + ++f+ eve++ ++l  +   +  +  v ++ k +kl++  +++   +   ++  d+++ +
  gi|518652777|ref|YP_008142297.1| 509 ELYKTDANvDTIARDVANHFKNEVENTnSGLKAMLVAVDREACVMYKRKLDKLLAPETSEIVMTFGHNESSDIISEY 585
                                       55778888899*********98888885555555777778888999999999998777756666899999******* PP

                                       HHHHHHHH---GGGHHHHH CS
                           DUF5611  83 ndFLeeaTGydaKeRkkka 101
                                       +d L++ TG daK+  k++
  gi|518652777|ref|YP_008142297.1| 586 RDELQKRTGKDAKQACKEF 604
                                       *************988876 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1
                                       SS--SH..HHHHHHHHHHT.-EEEEETTE CS
                           DUF5611   9 Gfkkeee.erlkelleeyfggeveeegdl 36 
                                       G+k +e  er+k++++e f  +ve++g+ 
  gi|518652777|ref|YP_008142297.1| 793 GEKVQEAyERVKKIISENFFLDVENRGNF 821
                                       777788889******99997777766554 PP

>> Halogen_Hydrol  5-bromo-4-chloroindolyl phosphate hydrolysis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.016        31     127     175 ..     225     276 ..     223     279 .. 0.89
   2 ?   -1.6   0.1       1.2   2.3e+03     117     138 ..     758     779 ..     745     809 .. 0.74
   3 ?    6.7   0.1    0.0034       6.7     133     168 ..     864     899 ..     859     903 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                    Halogen_Hydrol 127 yLdsaveltekYaeLskqpvksket...realeetrqlLdelaealekdlqk 175
                                        +d+ v+l+  Y+ ++k+  +++++   +++ + t+++L+++  ++ k+l++
  gi|518652777|ref|YP_008142297.1| 225 NIDNFVKLLLNYTHIRKKGDRNEKIlarYMQFRATEKILNRIHNNMDKNLKE 276
                                       68*******************99986668899999999*****999999975 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
                    Halogen_Hydrol 117 lkkarrFlysyLdsaveltekY 138
                                       l +a+ +l+ ++d+ ++l++ Y
  gi|518652777|ref|YP_008142297.1| 758 LPRAKAYLTLHIDKYRQLAKAY 779
                                       6789999999999999999998 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0034
                    Halogen_Hydrol 133 eltekYaeLskqpvksketrealeetrqlLdelaea 168
                                       ++++ Y +L +++  ++e+ +++++++ ++d +ae+
  gi|518652777|ref|YP_008142297.1| 864 RIVDAYQKLLNAKAVNDEILQQIKSIKDTMDSIAES 899
                                       589******************************986 PP

>> DUF4106  Protein of unknown function (DUF4106)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00013      0.27     257     303 ..     692     738 ..     683     751 .. 0.87
   2 ?   -3.9   0.2         3     6e+03      16      58 ..     871     915 ..     866     930 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00013
                           DUF4106 257 qghkrsreqenqeflkmlkeeygypdsldfsdrykeairkfkegntd 303
                                       qg   sre+ +++f+k+l e y    ++dfsd  ++ + k+ +  ++
  gi|518652777|ref|YP_008142297.1| 692 QGIVISREEIEKDFIKLLDETYAIFGNFDFSDNSHDNLNKLIKILSN 738
                                       78889****************************99999987665555 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 3
                           DUF4106  16 dwldaqa.nakaaqligsirtkiqa.eedssnealmnadfknafe 58 
                                         l+a+a n    q i si+  +++  e  s e   +a f++a++
  gi|518652777|ref|YP_008142297.1| 871 KLLNAKAvNDEILQQIKSIKDTMDSiAESESTEGETKAAFREAIK 915
                                       556666536667788888887765425666778888888887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (994 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       959  (0.0534888); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); 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: 0.80u 0.29s 00:00:01.09 Elapsed: 00:00:00.46
# Mc/sec: 6535.57
//
Query:       gi|518652778|ref|YP_008142298.1|  [L=145]
Description: hypothetical protein FACI_IFERC00001G1417 [Ferroplasma acidarmanus fer1]
Scores for complete 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-06   25.8   0.0    1.4e-05   25.2   0.0    1.3  1  WLM            WLM domain
     0.0001   22.4   0.1     0.0035   17.4   0.0    2.0  2  DUF45          Protein of unknown function DUF45
     0.0097   15.8   0.0      0.012   15.4   0.0    1.4  1  SprT-like      SprT-like family
  ------ inclusion threshold ------
      0.054   13.3   0.4      0.078   12.7   0.4    1.2  1  Peptidase_M48  Peptidase family M48


Domain annotation for each model (and alignments):
>> WLM  WLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.2e-09   1.4e-05      79     116 ..     103     140 ..      89     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.2e-09
                               WLM  79 pyesimgtllHELaHnvygpHdakFyallkeLekevee 116
                                       +  +i+++l+HELaH+  + Hd+kF   +  + +++ +
  gi|518652778|ref|YP_008142298.1| 103 SRVDIREILIHELAHIFSSHHDEKFLMAMRYIGGKQRR 140
                                       56689********************9888777766655 PP

>> DUF45  Protein of unknown function DUF45
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.014        62      62     118 ..       6      58 ..       2      82 .. 0.63
   2 !   17.4   0.0   7.9e-07    0.0035     160     190 ..     101     131 ..      85     140 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                             DUF45  62 pllGkkyrlkvekgkeasvklkreelelavkkeeeeeklrkaleewlrkeakeelee 118
                                        ++Gkk+ +   + k    + k+  + l+ +++ +e++l++ l+  lr+ +k+e+++
  gi|518652778|ref|YP_008142298.1|   6 TIMGKKLTVIKSERK----RPKQSGNILYIPVSFDEHALKEYLRMRLRRIIKSEFSK 58 
                                       556666665555555....44555555555555555555555555555555555544 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 7.9e-07
                             DUF45 160 kappevidYVvvHElaHlleknHskrFwalv 190
                                       k+++  i+ +++HElaH++ ++H ++F   +
  gi|518652778|ref|YP_008142298.1| 101 KLSRVDIREILIHELAHIFSSHHDEKFLMAM 131
                                       55555567799****************7655 PP

>> SprT-like  SprT-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   2.7e-06     0.012      47     109 ..      91     143 ..      34     145 .] 0.83

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.7e-06
                         SprT-like  47 asIeLseklldsrsedrllntLaHElcHlalfvisgvrnnpHGaeFkawaakvekalaarlei 109
                                        +I   e  ++  s+ +++++L+HEl+H+      +    +H+++F   ++ ++  + +rl+i
  gi|518652778|ref|YP_008142298.1|  91 STILVREDTIKL-SRVDIREILIHELAHIFS----S----HHDEKFLMAMRYIGGKQ-RRLPI 143
                                       677777888888.899************865....3....59999999999988775.66665 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.4   1.7e-05     0.078      44      87 ..      89     130 ..      84     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.7e-05
                                       S-EEEEEEHHHH-SSB-HHHHHHHHHHHHHHHHTTHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  44 knkrivltdgLlkqllseeelaaVlGHElGHikhrhsvvslivs 87 
                                       k ++i + ++ +  +ls+ +++ +l HEl+Hi + h+ ++++++
  gi|518652778|ref|YP_008142298.1|  89 KGSTILVREDTI--KLSRVDIREILIHELAHIFSSHHDEKFLMA 130
                                       455888999999..999*******************98886554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); 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: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1008.08
//
Query:       gi|518652779|ref|YP_008142299.1|  [L=417]
Description: hypothetical protein FACI_IFERC00001G1418 [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   74.7   0.1    1.1e-20   74.1   0.1    1.3  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
      0.013   15.5   0.3      0.023   14.7   0.3    1.3  1  DZR              Double zinc ribbon
        0.1   12.3   3.0       0.19   11.5   3.0    1.4  1  zinc_ribbon_2    zinc-ribbon domain
       0.42   10.1   1.8        0.8    9.2   1.8    1.4  1  zf-ribbon_3      zinc-ribbon domain


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   0.1   2.5e-24   1.1e-20       8     170 ..     132     290 ..     126     292 .. 0.85

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 2.5e-24
                                       HHHHHHCCGCHHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHH CS
                   Phage_integrase   8 verllaaleeslkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkell 84 
                                       ++++++ + +    rdk+++ +ly++G Ri+E+lsLr++d++ ++  +++ + +gK++  r v +  +   +l+e+l
  gi|518652779|ref|YP_008142299.1| 132 IDKMVDSCTN---SRDKAFVSILYDSGCRIGEILSLRISDVRYDEYGAIL-NVHGKTGN-RSVRIIGNSIAYLREYL 203
                                       5666666666...9*****************************9998888.45666654.66666666677899*** PP

                                       HHHCHCCTTTSBSSBET....TSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT- CS
                   Phage_integrase  85 skaleeaeksellfask....rgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGH 157
                                       + +   ++k+e+lf        +k+++  ++rk++ +++ +agiek++  H +Rh+ a+ L+ + v+   +++ +G+
  gi|518652779|ref|YP_008142299.1| 204 KSK---DDKDEFLFTGMkadtMHKQMQYTSARKILLSLKARAGIEKKIYAHLFRHTRASMLA-SKVPEAPLENQMGW 276
                                       999...9*******99988889999*********************************8666.567*********** PP

                                       SSCC.HHHHHHCCC CS
                   Phage_integrase 158 ssis.ttqiYthva 170
                                        + s +t +Y+h++
  gi|518652779|ref|YP_008142299.1| 277 IHGSkMTGVYVHLS 290
                                       8865278*****86 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.3   5.1e-06     0.023       1      18 [.     320     337 ..     299     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.1e-06
                               DZR   1 CpqCgeelppdarfCseC 18 
                                       Cp+C++ + + a +C +C
  gi|518652779|ref|YP_008142299.1| 320 CPRCEHLNASTALYCTNC 337
                                       566666666666666666 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.0   4.2e-05      0.19       1      19 [.     319     337 ..     319     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.2e-05
                     zinc_ribbon_2   1 fCpnCGaelqdnakFCpyC 19 
                                       +Cp+C + +  +a +C++C
  gi|518652779|ref|YP_008142299.1| 319 KCPRCEHLNASTALYCTNC 337
                                       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 ?    9.2   1.8   0.00018       0.8       3      22 ..     318     337 ..     317     339 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00018
                       zf-ribbon_3   3 vrCPnCGa.plssddnvCpyC 22 
                                       ++CP+C + + +s +  C++C
  gi|518652779|ref|YP_008142299.1| 318 KKCPRCEHlN-ASTALYCTNC 337
                                       68******99.********** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (417 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      727  (0.0405488); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 2884.28
//
Query:       gi|518652780|ref|YP_008142300.1|  [L=391]
Description: hypothetical protein FACI_IFERC00001G1419 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 2604.63
//
Query:       gi|518652781|ref|YP_008142301.1|  [L=93]
Description: hypothetical protein FACI_IFERC00001G1420 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0096   16.3   0.1      0.013   15.9   0.1    1.2  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   7.1e-07     0.013      28      56 ..      57      86 ..      44      90 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 7.1e-07
                              ZapA 28 lvdekikeireagg.nlseerllvmaaLnl 56
                                      ++d+kik +r+ag+  +s +rl+vmaaL++
  gi|518652781|ref|YP_008142301.1| 57 RLDDKIKIMRKAGKmGVSVSRLMVMAALDY 86
                                      69************77************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       489  (0.0272742); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); 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 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 670.66
//
Query:       gi|518652782|ref|YP_008142302.1|  [L=57]
Description: hypothetical protein FACI_IFERC00001G1421 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       250  (0.0139439); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 440.48
//
Query:       gi|518652783|ref|YP_008142303.1|  [L=980]
Description: virulence-associated protein E [Ferroplasma acidarmanus fer1]
Scores for 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    5.4e-21   75.6   0.0    1.3  1  Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
    4.4e-07   30.3   0.3    1.3e-06   28.8   0.3    1.9  1  D5_N      D5 N terminal like
     0.0012   19.3   0.1     0.0012   19.3   0.1    3.1  3  Pox_D5    Poxvirus D5 protein-like
  ------ inclusion threshold ------
      0.093   12.8   0.0        0.2   11.7   0.0    1.5  1  PCSK9_C2  Proprotein convertase subtilisin-like/kexin type 9 


Domain annotation for each model (and alignments):
>> Prim-Pol  Bifunctional DNA primase/polymerase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.6   0.0   1.2e-24   5.4e-21       1     156 [.      14     188 ..      14     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 75.6 bits;  conditional E-value: 1.2e-24
                          Prim-Pol   1 aleyaergwpvvPlppggKrPlgkkwekdattdpeqirawwkkhpranvglatgpsglvvlDvDgke.......... 67 
                                       a +y+++g+p++P++pg+K P + +++kdat+d ++  ++ +  p  +++++tg+s ++++D D  +          
  gi|518652783|ref|YP_008142303.1|  14 AKKYTKAGLPIFPTKPGSKEPDTVHGFKDATNDFNKFMQMHR--PGDGIAMPTGASTYIIIDPDVAKdenkkpikkd 88 
                                       568999*******************************98888..***********************9999999988 PP

                          Prim-Pol  68 .....agaealarLareeg....plPe..tvtvttgstgggrhlyfraPdglalpnsagklapg....ldlrgeggy 129
                                                 l++L+++ +    +  +  t++++t+s  gg h++fr+P+g+   ++ + + ++    +d+++eg y
  gi|518652783|ref|YP_008142303.1|  89 gkvirI---GLDNLCKQFNllglEDSKlqTLVTETQS--GGDHFWFRNPKGKPPLKKMQGNENNgidkVDIQAEGAY 160
                                       885552...3444554444442333334466666677..********998777666666655557888********* PP

                          Prim-Pol 130 vvappsvhetgraYrwledp..reiaelP 156
                                       vv+pp+   + ++Y++++d   +ei+e+P
  gi|518652783|ref|YP_008142303.1| 161 VVLPPTEG-KFGKYKFITDVpfDEIPEMP 188
                                       ********.7888****995666666665 PP

>> D5_N  D5 N terminal like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.3   2.9e-10   1.3e-06      29     151 .]     411     536 ..     381     536 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.9e-10
                              D5_N  29 Weedekeaireladkvaeaiaeeaeeaksalkalkkfakssrskkkvdnvlreaaelprldleideldadplllafa 105
                                       W++   e + +la k+ e++    ++ +++++ +kk+ ++  +++ ++++l++++       ++d+++ d   ++f 
  gi|518652783|ref|YP_008142303.1| 411 WNKA-LELANKLAPKTDELSPDTTKAIFEIRESMKKVIERGPTRSQINETLAQLRLA--TYTNPDKFNPD-SHIPFL 483
                                       4444.6677788888888888888999***************************866..88889999888.679*** PP

                              D5_N 106 NGvldlktgelrdhepedyltkitpvdydpd.......adcptfkewlddilp 151
                                       NG l+ kt +l +h+p+ ++ ++++ + + d        d+p+f ++++++++
  gi|518652783|ref|YP_008142303.1| 484 NGYLNTKTWKLEPHNPDLIYLWRIEANLNADkldvvrlQDSPKFSKFINETFE 536
                                       ****************************99888887766***********985 PP

>> Pox_D5  Poxvirus D5 protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.31   1.4e+03       8      33 ..     529     554 ..     524     560 .. 0.88
   2 !   19.3   0.1   2.6e-07    0.0012      18      73 ..     760     810 ..     744     820 .. 0.82
   3 ?   -3.0   1.1       2.4   1.1e+04      59      83 ..     890     915 ..     857     924 .. 0.61

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.31
                            Pox_D5   8 dFveelfeeekstrvpsdvlYeaYka 33 
                                       +F++e fe+ +++ +  ++ Y  Y  
  gi|518652783|ref|YP_008142303.1| 529 KFINETFEDRDIPLILQYFGYTMYPD 554
                                       699999**999999999999999965 PP

  == domain 2  score: 19.3 bits;  conditional E-value: 2.6e-07
                            Pox_D5  18 kstrvpsdvlYeaYkafcekngykpvlskrtFqkrlkkileegfekkkkkkgqqpn 73 
                                           +p++ +Y+ +k + +++g+   + ++tF+k ++k+    ++kk+ + +++  
  gi|518652783|ref|YP_008142303.1| 760 PEMEIPVNTVYDSFKRWSKAKGIPL-MAQQTFTKYFGKN----YIKKRIRGENKER 810
                                       56679********************.***********99....8999999766655 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 2.4
                            Pox_D5  59 eg.fekkkkkkgqqpneyleyified 83 
                                       ++   ++++ ++ +++e++e+i++ +
  gi|518652783|ref|YP_008142303.1| 890 QEkVLNNNTHNECKNTEKVEKILFYK 915
                                       22355666666666666666666655 PP

>> PCSK9_C2  Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.6e-05       0.2      20      42 ..     809     831 ..     800     835 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.6e-05
                          PCSK9_C2  20 eedhVLTGCssHsevedlsdqvr 42 
                                       e  +V TGCs+H+  ++++++++
  gi|518652783|ref|YP_008142303.1| 809 ERIYVFTGCSFHKGNGEIENNIK 831
                                       5569*************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (980 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.78u 0.31s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 6047.18
//
Query:       gi|518652784|ref|YP_008142304.1|  [L=50]
Description: hypothetical protein FACI_IFERC00001G1423 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 397.88
//
Query:       gi|518652785|ref|YP_008142305.1|  [L=137]
Description: hypothetical protein FACI_IFERC00001G1424 [Ferroplasma acidarmanus fer1]
Scores for complete 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-05   22.5   0.0    0.00011   21.8   0.0    1.3  1  Hfq       Hfq protein
     0.0028   17.3   0.1      0.006   16.3   0.1    1.5  1  LSM       LSM domain
     0.0052   16.9   0.2     0.0052   16.9   0.2    1.8  2  SM-ATX    Ataxin 2 SM domain


Domain annotation for each model (and alignments):
>> Hfq  Hfq protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.9e-08   0.00011      17      60 ..      89     132 ..      85     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.9e-08
                                       EEEETTS-EEEEEEEEE-SSEEEEEETTEEEEEEGGGEEEEEES CS
                               Hfq  17 tifLvnGiklkGviksfDnftvlLesdgkqqlvYKhaistivpa 60 
                                        i L+nG  l+Gv+++f ++ +lLes gk  ++ K+ i  i  +
  gi|518652785|ref|YP_008142305.1|  89 NITLLNGEILSGVLRGFGQYDILLESGGKNVILMKSGIVKIEVQ 132
                                       799**************************999999999888665 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     1e-06     0.006       4      31 ..      81     108 ..      78     108 .. 0.92

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1e-06
                                       HHTTTSEEEEEETTSEEEEEEEEEEETT CS
                               LSM   4 kklinkkvtvelkngrelrGtLkgfDqf 31 
                                       k+li+k++++ l ng+ l+G+L+gf q+
  gi|518652785|ref|YP_008142305.1|  81 KNLIGKTMNITLLNGEILSGVLRGFGQY 108
                                       89***********************775 PP

>> SM-ATX  Ataxin 2 SM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       0.6   3.6e+03      45      45 ..      49      49 ..      22      66 .. 0.60
   2 !   16.9   0.2   8.7e-07    0.0052       9      42 ..      81     111 ..      78     132 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.6
                                      E CS
                            SM-ATX 45 m 45
                                      +
  gi|518652785|ref|YP_008142305.1| 49 H 49
                                      2 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.7e-07
                                       HTTTTSEEEEEETTS-EEEEEEEEE-T..T--EE CS
                            SM-ATX   9 tslvGkevevtvknGevyeGifstvslekdfsvv 42 
                                       ++l+Gk+ ++t+ nGe+ +G+++++     +++ 
  gi|518652785|ref|YP_008142305.1|  81 KNLIGKTMNITLLNGEILSGVLRGFGQ---YDIL 111
                                       69*********************9977...4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1014.13
//
Query:       gi|518652786|ref|YP_008142306.1|  [L=68]
Description: hypothetical protein FACI_IFERC00001G1425 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); 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:                         0  (0); expected 0.2 (1e-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: 482.28
//
Query:       gi|518652787|ref|YP_008142307.1|  [L=67]
Description: hypothetical protein FACI_IFERC00001G1426 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.2   0.0      0.093   12.7   0.0    1.2  1  HTH_Crp_2  Crp-like helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-06     0.093      31      56 ..      31      56 ..      30      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-06
                                      TTSSHHHHHHHHHHHHHTTSEEETEE CS
                         HTH_Crp_2 31 lGltretvsrilseLkreglisrgrr 56
                                      lG++ + ++ il+ +++ ++i+ gr+
  gi|518652787|ref|YP_008142307.1| 31 LGISEQKLNEILQSMEQLKIIREGRG 56
                                      89********************7754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       836  (0.0466284); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 484.71
//
Query:       gi|518652788|ref|YP_008142308.1|  [L=87]
Description: hypothetical protein FACI_IFERC00001G1427 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.47
# Mc/sec: 560.47
//
Query:       gi|518652789|ref|YP_008142309.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G1428 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------

   [No hits detected that satisfy 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:                       132  (0.00736237); expected 358.6 (0.02)
Passed bias filter:                       80  (0.00446204); 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):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 521.53
//
Query:       gi|518652790|ref|YP_008142310.1|  [L=84]
Description: hypothetical protein FACI_IFERC00001G1429 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 577.99
//
Query:       gi|518652791|ref|YP_008142311.1|  [L=175]
Description: hypothetical protein FACI_IFERC00001G1430 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.33   10.9   0.0    1.5  1  DUF3907   Protein of unknown function (DUF3907)


Domain annotation for each model (and alignments):
>> DUF3907  Protein of unknown function (DUF3907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   1.8e-05      0.33      74      95 ..      17      38 ..       3      44 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.8e-05
                           DUF3907 74 ekaLykvyHqcveefftPkkdv 95
                                      e ++y+ y +c+e ff+P  d+
  gi|518652791|ref|YP_008142311.1| 17 EVVVYNTYGECIEGFFSPVIDT 38
                                      6789**************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1204.78
//
Query:       gi|518652792|ref|YP_008142312.1|  [L=113]
Description: hypothetical protein FACI_IFERC00001G1431 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 846.04
//
Query:       gi|518652793|ref|YP_008142313.1|  [L=220]
Description: hypothetical protein FACI_IFERC00001G1432 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.041   13.4   1.0       0.99    8.9   0.2    2.3  2  4HB_MCP_1  Four helix bundle sensory module for signal transd
       0.15   12.6   0.2       0.85   10.2   0.0    2.2  2  DUF2408    Protein of unknown function (DUF2408)


Domain annotation for each model (and alignments):
>> 4HB_MCP_1  Four helix bundle sensory module for signal transduction
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.2   0.00011      0.99      91     122 ..      43      74 ..      26      78 .. 0.90
   2 ?    3.0   0.0    0.0075        67     119     160 ..     162     204 ..     158     206 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00011
                         4HB_MCP_1  91 idkllekyektilteeEkelleefkeqlnaYr 122
                                       + +l++++ +t l +e ++ +e+f+  l+ Yr
  gi|518652793|ref|YP_008142313.1|  43 FYSLMKNFANTQLLDENQNTMEKFEALLKSYR 74 
                                       6689***************************8 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0075
                         4HB_MCP_1 119 naYrevrkkvlelakegkkdeAyq.lyetegrpareklieale 160
                                       + Yr +++++++ a+e  + e ++ ly + +r+++e +i+ l+
  gi|518652793|ref|YP_008142313.1| 162 TDYRLIKDQLVKIANEPGYSEDREfLYVKALRQYFEIMIQWLN 204
                                       78999*************9988874799999********9887 PP

>> DUF2408  Protein of unknown function (DUF2408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.21   1.9e+03     107     117 ..       8      18 ..       3      21 .. 0.76
   2 ?   10.2   0.0   9.4e-05      0.85      64     118 ..     101     174 ..      51     177 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.21
                           DUF2408 107 slqpiYdrLle 117
                                       +l++iYd+Ll 
  gi|518652793|ref|YP_008142313.1|   8 DLKKIYDKLLY 18 
                                       68889998875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 9.4e-05
                           DUF2408  64 FkseegkevvekgqavlngLlddcfdlvedlkaqd....................geekkvasslqpiYdrLlei 118
                                       F+ +   + +e+g+a++++++++cfd+v++ + ++                      ek  +++++ i d+L++i
  gi|518652793|ref|YP_008142313.1| 101 FHANG-LMNSEQGKAIIHDMINKCFDFVQNNRIDNnssiflwechldglnalligFGEKAYSTDYRLIKDQLVKI 174
                                       64444.368899*****************9888876777777777777777777744477777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1494.61
//
Query:       gi|518652794|ref|YP_008142314.1|  [L=380]
Description: hypothetical protein FACI_IFERC00001G1433 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   27.7   0.0    5.3e-06   26.1   0.0    1.8  1  HTH_23           Homeodomain-like domain
    8.7e-05   22.2   0.6    0.00023   20.8   0.1    2.0  2  HTH_38           Helix-turn-helix domain
    0.00022   21.0   0.0    0.00043   20.0   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
    0.00043   20.3   0.6      0.013   15.6   0.0    2.6  2  ResIII           Type III restriction enzyme, res subunit
    0.00044   20.3   0.1    0.00099   19.1   0.1    1.5  1  HTH_7            Helix-turn-helix domain of resolvase
    0.00068   19.5   0.1     0.0018   18.2   0.1    1.7  1  HTH_11           HTH domain
     0.0011   18.9   0.0     0.0025   17.8   0.0    1.5  1  HTH_29           Winged helix-turn helix
     0.0015   18.1   0.2      0.004   16.7   0.2    1.6  1  CENP-B_N         CENP-B N-terminal DNA-binding domain
     0.0019   18.2   0.0     0.0066   16.5   0.0    1.9  1  HTH_3            Helix-turn-helix
     0.0024   17.7   0.0     0.0052   16.6   0.0    1.5  1  TrmB             Sugar-specific transcriptional regulator Trm
     0.0025   17.5   0.0       0.84    9.2   0.0    2.7  3  Zot              Zonular occludens toxin (Zot)
     0.0039   17.3   0.0      0.008   16.3   0.0    1.6  1  HTH_28           Helix-turn-helix domain
      0.007   15.5   0.0      0.012   14.7   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
     0.0084   15.8   0.0      0.025   14.2   0.0    1.8  1  Sigma70_r4_2     Sigma-70, region 4
  ------ inclusion threshold ------
      0.024   15.0   2.2      0.048   14.0   2.2    1.5  1  BRF1             Brf1-like TBP-binding domain
      0.025   15.2   0.5       0.05   14.3   0.5    1.5  1  RPA_C            Replication protein A C terminal
      0.028   14.3   0.0      0.057   13.3   0.0    1.4  1  MarR_2           MarR family
      0.042   13.4   0.1        0.1   12.2   0.1    1.7  1  HTH_24           Winged helix-turn-helix DNA-binding
      0.068   13.6   0.3       0.25   11.7   0.0    2.2  2  AAA              ATPase family associated with various cellul
      0.069   13.0   0.2       0.18   11.6   0.2    1.8  1  LacI             Bacterial regulatory proteins, lacI family
      0.071   13.4   0.0       0.23   11.7   0.0    1.9  2  AAA_22           AAA domain
      0.096   12.4   0.0       0.33   10.7   0.0    1.9  1  IstB_IS21        IstB-like ATP binding protein
      0.097   12.4   0.0       0.39   10.5   0.0    2.0  2  AAA_29           P-loop containing region of AAA domain
       0.12   12.7   0.0       0.27   11.6   0.0    1.9  1  AAA_16           AAA ATPase domain
       0.14   12.7   0.5       0.76   10.3   0.0    2.4  2  HTH_40           Helix-turn-helix domain
       0.16   12.1   8.9       0.21   11.6   6.1    2.5  1  DUF87            Helicase HerA, central domain
       0.17   11.8   0.0       0.39   10.7   0.0    1.6  1  HTH_Crp_2        Crp-like helix-turn-helix domain
        0.2   11.9   0.5        1.8    8.8   0.0    2.7  2  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   8.3e-09   5.3e-06       9      40 ..     342     373 ..     341     378 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 8.3e-09
                            HTH_23   9 rillllaeGlsvreIAreLgvsrrTvyrwlkr 40 
                                       +i++l  +Glsvr+IA+  gv+r+Tv+r+++ 
  gi|518652794|ref|YP_008142314.1| 342 KIIKLKMKGLSVRDIAKSTGVPRSTVQRVISE 373
                                       79***************************986 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       5.4   3.5e+03      20      27 ..     135     142 ..     134     144 .. 0.89
   2 !   20.8   0.1   3.6e-07   0.00023       7      41 ..     337     371 ..     333     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 5.4
                            HTH_38  20 GlslreIA 27 
                                       G+s+++IA
  gi|518652794|ref|YP_008142314.1| 135 GKSYSAIA 142
                                       99*****9 PP

  == domain 2  score: 20.8 bits;  conditional E-value: 3.6e-07
                            HTH_38   7 leeReeIerllaeGlslreIArrLgrspsTIsREl 41 
                                        ++  +I +l  +Gls+r+IA+  g+ +sT++R +
  gi|518652794|ref|YP_008142314.1| 337 NNDIIKIIKLKMKGLSVRDIAKSTGVPRSTVQRVI 371
                                       567778899999*********************98 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.7e-07   0.00043       8      39 ..     340     371 ..     339     373 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.7e-07
                                       HHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHH CS
                          HTH_IclR   8 iLdalaeapqeltlselArrtglpkStvhRlL 39 
                                       i++++     +l+++++A+ tg+p+Stv R +
  gi|518652794|ref|YP_008142314.1| 340 IIKIIKLKMKGLSVRDIAKSTGVPRSTVQRVI 371
                                       77888888999******************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 !   15.6   0.0     2e-05     0.013      13      59 ..     112     158 ..     107     167 .. 0.87
   2 ?    1.6   0.6      0.39   2.5e+02      70     105 ..     302     339 ..     283     354 .. 0.45

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-05
                                       HHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEE CS
                            ResIII  13 enlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflf 59 
                                       + +++ +k++r+  +l+  +TG+GK++ a++l+e+l   ++ ++++f
  gi|518652794|ref|YP_008142314.1| 112 RWTKQRIKENRNCSMLFSGETGSGKSYSAIALAEKLDPGFNVDRIVF 158
                                       5567889989999***********************99999888888 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.39
                                       HHHHGGGGTGG.........GEEEESSS-B--............-S CS
                            ResIII  70 tleefkkflseayke.....igkkvsgdkkka.....kekdstnkk 105
                                         +ef + ++ea+ e     ++k        +      +k++tn++
  gi|518652794|ref|YP_008142314.1| 302 VNKEFLHEIQEAQREkkeklNKK--------NgtgkgDNKKETNND 339
                                       22333333333332222212111........133334222333333 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 !   19.1   0.1   1.6e-06   0.00099       8      42 ..     337     371 ..     329     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 1.6e-06
                                       HHHHGGGGSSTTTT--STTTSSSS---SSSS--SS CS
                             HTH_7   8 kndinrvvkLleeGisiskIAkevnisRsTvYRyl 42 
                                        ndi  ++kL  +G s+++IAk +++ RsTv R+ 
  gi|518652794|ref|YP_008142314.1| 337 NNDIIKIIKLKMKGLSVRDIAKSTGVPRSTVQRVI 371
                                       458999*************************9996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.9e-06    0.0018       3      41 ..     338     376 ..     336     377 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                            HTH_11   3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLee 41 
                                       ++i+++++ + + +s  ++A+ ++v r+tv+r I ++++
  gi|518652794|ref|YP_008142314.1| 338 NDIIKIIKLKMKGLSVRDIAKSTGVPRSTVQRVISEINS 376
                                       79*****999999**********************9986 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   3.8e-06    0.0025       3      38 ..     342     376 ..     341     378 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 3.8e-06
                            HTH_29   3 qallllaeGvstvsqiAkllglsrrtvyrwlkrfee 38 
                                       +++ l  +G+s v++iAk +g+ r+tv+r++   + 
  gi|518652794|ref|YP_008142314.1| 342 KIIKLKMKGLS-VRDIAKSTGVPRSTVQRVISEINS 376
                                       67888889998.******************988776 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.2   6.3e-06     0.004      10      43 ..     338     371 ..     336     373 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 6.3e-06
                                       HHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHH CS
                          CENP-B_N  10 reKievIqrleegeSkaelarrfnvpestlsdil 43 
                                       ++ i++I++   g S++++a+  +vp+st+ +++
  gi|518652794|ref|YP_008142314.1| 338 NDIIKIIKLKMKGLSVRDIAKSTGVPRSTVQRVI 371
                                       56699*************************9986 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0     1e-05    0.0066       5      31 ..     346     372 ..     342     376 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 1e-05
                                       HHHTTHHHHHHHHHHTSSHHHHHHHHT CS
                             HTH_3   5 RkqlglsqeeLAeklGvsrstisriEn 31 
                                       +k +gls +++A+ +Gv+rst++r ++
  gi|518652794|ref|YP_008142314.1| 346 LKMKGLSVRDIAKSTGVPRSTVQRVIS 372
                                       6789*******************9876 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   8.1e-06    0.0052      18      45 ..     346     373 ..     343     377 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 8.1e-06
                                       HHHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  18 lklgpatadeiaeelgvprskvYevLrs 45 
                                       lk + +++++ia+ +gvprs+v++v+++
  gi|518652794|ref|YP_008142314.1| 346 LKMKGLSVRDIAKSTGVPRSTVQRVISE 373
                                       5778899******************975 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.021        13       4      20 ..     127     143 ..     125     165 .. 0.69
   2 !    9.2   0.0    0.0013      0.84      78     141 ..     171     234 ..     151     252 .. 0.81
   3 ?   -2.9   0.0         7   4.5e+03      34      55 ..     346     368 ..     333     376 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.021
                               Zot   4 lvtGapGsgKtsgavkk 20 
                                       l+ G+ GsgK++ a+  
  gi|518652794|ref|YP_008142314.1| 127 LFSGETGSGKSYSAIAL 143
                                       789*********99865 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.0013
                               Zot  78 idkgallviDEcqeifpvrakegrkdpevi..naftehRhlgwDivlltqdiskihkevralaeka 141
                                        +kg+++++D ++   +++ ++  +  ++i  ++ ++ R l+   + +++ +++i+k+ r+l+++ 
  gi|518652794|ref|YP_008142314.1| 171 LPKGSVIIFDDAGVGASNKEWN--SLSGRIigKFSQNSRYLNLINIYTVPSLNYIEKQSRELINLY 234
                                       57****************9998..566665545556778899999****************99865 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 7
                               Zot  34 tnidGlrlerieqvlgekvs.ta 55 
                                        +++Gl ++ i++ +g   s  +
  gi|518652794|ref|YP_008142314.1| 346 LKMKGLSVRDIAKSTGVPRStVQ 368
                                       47889999999998876666334 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.2e-05     0.008       3      35 ..     341     373 ..     341     380 .] 0.91

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-05
                            HTH_28   3 leiikllaaGhsvreaArelgisrrtvyrWikr 35 
                                       ++iikl ++G svr++A+  g+ r+tv+r i+ 
  gi|518652794|ref|YP_008142314.1| 341 IKIIKLKMKGLSVRDIAKSTGVPRSTVQRVISE 373
                                       58***************************9976 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   1.8e-05     0.012     121     166 ..     117     163 ..      82     176 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.8e-05
                             T2SSE 121 vlrkavrerglilvsGgTgsGKttllyallkeinks...derivtvEDp 166
                                        +++   +++++l+sG TgsGK+ ++ al ++++     d+ +  vED 
  gi|518652794|ref|YP_008142314.1| 117 RIKEN--RNCSMLFSGETGSGKSYSAIALAEKLDPGfnvDRIVFNVEDF 163
                                       44444..7899*******************9999877745555578885 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.0   3.9e-05     0.025      18      45 ..     343     369 ..     342     372 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.9e-05
                                       HHHHHHTS---HHHHHHHHT--HHHHHH CS
                      Sigma70_r4_2  18 ifllryleglsykEIAellgisegtVks 45 
                                       i+ l  ++gls ++IA+ +g++ +tV++
  gi|518652794|ref|YP_008142314.1| 343 IIKL-KMKGLSVRDIAKSTGVPRSTVQR 369
                                       5666.589******************86 PP

>> BRF1  Brf1-like TBP-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   2.2   7.5e-05     0.048      18      62 ..     292     337 ..     284     376 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.5e-05
                              BRF1  18 vkiKeriWvelnkeyLee.qeekrlkeeaeeaeadkkkkkkkrkrk 62 
                                        ++K++  +++nke+L e qe++r+k+e+ ++++ + k  +k++++
  gi|518652794|ref|YP_008142314.1| 292 ENAKQTYMNRVNKEFLHEiQEAQREKKEKLNKKNGTGKGDNKKETN 337
                                       5788999999*******77777776666666663444444444333 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.5   7.9e-05      0.05      32      91 ..     318     374 ..     288     377 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.9e-05
                                       XXXXXXXXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHSTSXHHHHHHHHHHH CS
                             RPA_C  32 dgalsgnqaklankgltalaqqvlnlikqspeseeGvhvdeiaqklrlsvndvkqavdeL 91 
                                       + +l++ ++    ++++++++ ++ +ik    + +G++v+ ia++++++ ++v++++ e 
  gi|518652794|ref|YP_008142314.1| 318 KEKLNKKNGTGKGDNKKETNNDIIKIIKL---KMKGLSVRDIAKSTGVPRSTVQRVISEI 374
                                       3333333333333778999999******9...778*********************9886 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   8.9e-05     0.057      19      44 ..     350     373 ..     343     377 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.9e-05
                                       TSEEEHHHHHHHHTSSHHHHHHHHHH CS
                            MarR_2  19 grdltvgelarrlglsksavsrilkr 44 
                                       g  l+v+++a+ +g+++s+v+r++ +
  gi|518652794|ref|YP_008142314.1| 350 G--LSVRDIAKSTGVPRSTVQRVISE 373
                                       5..9******************9865 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016       0.1      17      39 ..     350     372 ..     334     373 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
                            HTH_24  17 risqreLAerlglSpstvnrrlk 39 
                                       ++s r++A+ +g+++stv r + 
  gi|518652794|ref|YP_008142314.1| 350 GLSVRDIAKSTGVPRSTVQRVIS 372
                                       69****************99875 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    0.0004      0.25       1      36 [.     126     165 ..     126     239 .. 0.75
   2 ?   -1.5   0.2       4.9   3.1e+03      76      99 ..     293     316 ..     282     352 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0004
                                       EEEESSTTSSHHHHHHHHHHHH....THEEEEEETTTCSS CS
                               AAA   1 vllyGppGtGKTllakavakel....gvefleisgsells 36 
                                       +l++G  G GK++ a a+a++l    +v+ + +++ ++l+
  gi|518652794|ref|YP_008142314.1| 126 MLFSGETGSGKSYSAIALAEKLdpgfNVDRIVFNVEDFLK 165
                                       89*******************9553335545555555552 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 4.9
                                       TCCCHHHHHHHHHHHHHHHHTTTS CS
                               AAA  76 gseseeeervvnqLlteldgvkkk 99 
                                       +++++  +rv +++l+e+++ +++
  gi|518652794|ref|YP_008142314.1| 293 NAKQTYMNRVNKEFLHEIQEAQRE 316
                                       456667777888888888777765 PP

>> LacI  Bacterial regulatory proteins, lacI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00029      0.18       3      21 ..     354     372 ..     352     376 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00029
                                       HHHHHHCTS-HHHHHHHCT CS
                              LacI   3 kDVArlAGVSkaTVSrvLn 21 
                                       +D+A+  GV  +TV rv++
  gi|518652794|ref|YP_008142314.1| 354 RDIAKSTGVPRSTVQRVIS 372
                                       8****************97 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00036      0.23       8      37 ..     126     155 ..     119     232 .. 0.80
   2 ?   -2.0   0.0       6.1   3.9e+03      54      70 ..     304     320 ..     283     359 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee 37 
                                       ++  Ge+G+GK++++  l+e+ld   + ++
  gi|518652794|ref|YP_008142314.1| 126 MLFSGETGSGKSYSAIALAEKLDPGFNVDR 155
                                       6778*****************986655544 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 6.1
                            AAA_22  54 kdllrellralglelka 70 
                                       k++l+e+ +a  +++++
  gi|518652794|ref|YP_008142314.1| 304 KEFLHEIQEAQREKKEK 320
                                       33333443333333333 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 ?   10.7   0.0   0.00051      0.33      48      70 ..     124     146 ..     112     204 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00051
                         IstB_IS21  48 enivllGpsGvGKshlaialgve 70 
                                        ++++ G +G GKs+ aial+ +
  gi|518652794|ref|YP_008142314.1| 124 CSMLFSGETGSGKSYSAIALAEK 146
                                       235678**************986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   0.00061      0.39      17      36 ..     118     137 ..     112     147 .. 0.80
   2 ?   -2.7   0.0       8.2   5.3e+03      51      59 ..     277     285 ..     274     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00061
                            AAA_29  17 ieidlkgatlltGpsGsGKS 36 
                                       i+ +++ ++l++G++GsGKS
  gi|518652794|ref|YP_008142314.1| 118 IKENRNCSMLFSGETGSGKS 137
                                       444434489**********9 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 8.2
                            AAA_29  51 kvrfNkaan 59 
                                       k++fN a++
  gi|518652794|ref|YP_008142314.1| 277 KLHFNLASR 285
                                       589****97 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   0.0   0.00043      0.27      18      51 ..     117     150 ..     111     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00043
                            AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                                       r++++r +++l+sGe G+GKs  + +l++ l   
  gi|518652794|ref|YP_008142314.1| 117 RIKENRNCSMLFSGETGSGKSYSAIALAEKLDPG 150
                                       67788889*************9999988877765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.2       5.2   3.3e+03      34      63 ..     288     316 ..     283     325 .. 0.57
   2 ?   10.3   0.0    0.0012      0.76       7      35 ..     345     373 ..     341     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 5.2
                            HTH_40  34 aelieegeeidlerlvseeeekeIeeaiek 63 
                                       +e++e+ ++  ++r v++e   eI+ea ++
  gi|518652794|ref|YP_008142314.1| 288 LEAYENAKQTYMNR-VNKEFLHEIQEAQRE 316
                                       55555554344444.466666777776665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0012
                            HTH_40   7 elleeglsieeIAkerglkesTIegHLae 35 
                                       +l ++gls+ +IAk  g+ +sT+++ + e
  gi|518652794|ref|YP_008142314.1| 345 KLKMKGLSVRDIAKSTGVPRSTVQRVISE 373
                                       66789******************987766 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   6.1   0.00033      0.21      30     223 ..     130     374 ..     124     377 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                             DUF87  30 gsTGsGKSntvavLleelle.....................kkgatililDpHGEYgkal................. 68 
                                       g+TGsGKS+ +  L e+l                        ++++++i+D  G  +  +                 
  gi|518652794|ref|YP_008142314.1| 130 GETGSGKSYSAIALAEKLDPgfnvdrivfnvedflklstsnLPKGSVIIFDDAGVGA--Snkewnslsgriigkfsq 204
                                       89****************888889999999999999999988999999999877222..233555666***999999 PP

                             DUF87  69 ekllsekvkvitpspsakdkelkinpwsldpeelldlleeddkpaaavqrsvleealdqaka............... 130
                                       ++++ + ++++t++        ++n+ + + +el++l++e++k + +++     ++++ a+                
  gi|518652794|ref|YP_008142314.1| 205 NSRYLNLINIYTVP--------SLNYIEKQSRELINLYFESTKIQGDAKVFHPFRVFRGADTlgfkypklwignipi 273
                                       99999999999998........9*****************6666666666666777777777988888888888844 PP

                             DUF87 131 ..keekeklssdepveklleelk.....kekeelrklknqaiarlldkledllrkggsf..snsstdlialllekle 198
                                          ++   l s++++e     ++     ++++ +++  ++++++  +k+e+l +k+g+   +n+++++++ +  ++ 
  gi|518652794|ref|YP_008142314.1| 274 tiSKLHFNLASRDLLE----AYEnakqtYMNRVNKEFLHEIQEAQREKKEKLNKKNGTGkgDNKKETNNDIIKIIKL 346
                                       4444444444444444....444555555556888888899999999999999999999985555555555555588 PP

                             DUF87 199 kegkitiidlsg...vdelaqqlvvsvi 223
                                       k + +++ d+++   v+ +++q v+s i
  gi|518652794|ref|YP_008142314.1| 347 KMKGLSVRDIAKstgVPRSTVQRVISEI 374
                                       8888888888877779999999999887 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00062      0.39      22      45 ..     351     374 ..     331     378 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00062
                                       HHHHHHHHHTTSSHHHHHHHHHHH CS
                         HTH_Crp_2  22 ltqeelAsmlGltretvsrilseL 45 
                                       l+ +++A   G+ r+tv r++se 
  gi|518652794|ref|YP_008142314.1| 351 LSVRDIAKSTGVPRSTVQRVISEI 374
                                       7899*****************986 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    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      57      74 ..      10      27 ..       6      28 .. 0.84
   2 ?    8.8   0.0    0.0028       1.8       2      28 ..     348     374 ..     347     376 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.2
                   HU-CCDC81_euk_2 57 rkvkmkFyesfleslegs 74
                                      +  + kF e+f+es +g+
  gi|518652794|ref|YP_008142314.1| 10 NERQQKFKEDFPESFNGI 27
                                      566779********9997 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0028
                   HU-CCDC81_euk_2   2 vvplnytelaaaaglsrdvVescvqet 28 
                                       ++ l+  ++a+ +g++r +V++ ++e+
  gi|518652794|ref|YP_008142314.1| 348 MKGLSVRDIAKSTGVPRSTVQRVISEI 374
                                       67789999****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1439  (0.080261); expected 358.6 (0.02)
Passed bias filter:                      774  (0.0431703); expected 358.6 (0.02)
Passed Vit filter:                       141  (0.00786435); 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: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 2509.96
//
Query:       gi|518652795|ref|YP_008142315.1|  [L=188]
Description: hypothetical protein FACI_IFERC00001G1434 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00027   20.8   0.0     0.0055   16.5   0.0    2.0  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.1e-07    0.0055      13      74 ..      21      89 ..      13     172 .. 0.68

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.1e-07
                                      HCCGC.HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEE......EEECSSSSE......EEEECTH CS
                   Phage_integrase 13 aalee.slkirdklllellyetGlRisEllsLrvkdldlengvilvh......eregKgske......ravplse 74
                                      +al+e s+k+ +++ l  ++ tG+R  El++L+     ++ g+i  +      +      k+      r+++ls 
  gi|518652795|ref|YP_008142315.1| 21 HALREgSKKLSNQIWLDAMLLTGMRYEELRRLQQYPSWFKGGYIDMPkgngnkT------KKyarqreRTIHLST 89
                                      445555677****************************9******9974443222......223333336666663 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); 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 0.30s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 1230.68
//
Query:       gi|518652796|ref|YP_008142316.1|  [L=326]
Description: hypothetical protein FACI_IFERC00001G1435 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.26   11.5   0.2       0.26   11.5   0.2    3.4  3  Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
        1.3    8.8   7.5       0.17   11.7   2.7    1.8  2  FA_desaturase  Fatty acid desaturase
          9    6.6  15.7        4.4    7.6   4.0    2.4  2  DUF2304        Uncharacterized conserved protein (DUF2304)


Domain annotation for each model (and alignments):
>> Pox_EPC_I2-L1  Poxvirus entry protein complex L1 and I2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4     0.086   5.2e+02      49      69 ..      43      63 ..      11      65 .. 0.80
   2 ?   11.5   0.2   4.4e-05      0.26      30      68 ..     174     214 ..     172     217 .. 0.65
   3 ?   -1.6   2.1      0.57   3.4e+03      51      69 ..     226     244 ..     215     246 .. 0.56

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.086
                     Pox_EPC_I2-L1 49 ltlliiliavlilvlllflyl 69
                                      +t+ + +i+v+i ++  f yl
  gi|518652796|ref|YP_008142316.1| 43 VTFTFQFIIVMINSFTGFGYL 63
                                      347888899999998888887 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.4e-05
                     Pox_EPC_I2-L1  30 VLtdek.askktassgtklwltllii.liavlilvlllfly 68 
                                       +Ltd++ + +  ++ +++ w  l+++ l++++  v l + y
  gi|518652796|ref|YP_008142316.1| 174 ILTDSSqRIRYEIKGNKWYWASLIVLiLFIAITPVYLYYTY 214
                                       69999845666677778889886655055555556666655 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.57
                     Pox_EPC_I2-L1  51 lliiliavlilvlllflyl 69 
                                        li+++++ i+  ++++ l
  gi|518652796|ref|YP_008142316.1| 226 QLIVFFTAFIICAYVTIAL 244
                                       3555555555555555555 PP

>> FA_desaturase  Fatty acid desaturase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   1.0       0.2   1.2e+03     136     163 ..      46      73 ..      22     126 .. 0.58
   2 ?   11.7   2.7   2.8e-05      0.17      59     179 ..     119     240 ..      71     251 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.2
                     FA_desaturase 136 rllawlllllawlglwlalllllglall 163
                                       ++  + +++ +++g+ +++++ ++ ++l
  gi|518652796|ref|YP_008142316.1|  46 TFQFIIVMINSFTGFGYLTYFQSPASGL 73 
                                       2333333333334444444444444443 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.8e-05
                     FA_desaturase  59 sawrisH.lrHHaytngpdeDpdlaplalsrfeglfryllrlllgllvlg..wllalvlglwlrrlarrrapsksrr 132
                                       + ++  H  +H +++ ++   + +       + ++  ++++ll ++ + +   ++ +++++++   +r r+ +k+ +
  gi|518652796|ref|YP_008142316.1| 119 EFYSNLHiVSHPNHILND-NQILIK----YDKNSFIPWFFGLLAISKRKKlkKNYDRDFIILTDSSQRIRYEIKGNK 190
                                       458888988888885555.777777....777777777777777777777888999999999999999999999999 PP

                     FA_desaturase 133 rkwrllawlllllaw..lglwlalllllglall.lwlvplllllfllalv 179
                                       ++w  l +l+l++a+  + l++ ++   +l ll + l+++++++++ a+v
  gi|518652796|ref|YP_008142316.1| 191 WYWASLIVLILFIAItpVYLYYTYYIYRSLELLiIQLIVFFTAFIICAYV 240
                                       99999999999999888888888888888887765555555555555554 PP

>> DUF2304  Uncharacterized conserved protein (DUF2304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   3.9    0.0069        41      27      88 ..      33      94 ..      22     100 .. 0.86
   2 ?    7.6   4.0   0.00074       4.4      31      94 ..     190     250 ..     173     253 .. 0.84

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0069
                           DUF2304 27 kleysllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfslslklsk 88
                                       ++y+ ++ ++ +   +++++ + +t +  l  ++++++ l +++i+ l+ + + l+ +++k
  gi|518652796|ref|YP_008142316.1| 33 IFKYTSFFAVVTFTFQFIIVMINSFTGFGYLTYFQSPASGLSVIFIFSLIGLYIGLTRAIRK 94
                                      56889999999999999999999************************999999999999887 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00074
                           DUF2304  31 sllwlllalilivlslfpqiltvlanllGvgrgtnllfllgivfllvilfslslklskleekik 94 
                                       +  w  l+++++++++ p    +l     ++r + ll++ +ivf+  +++  ++++    e+++
  gi|518652796|ref|YP_008142316.1| 190 KWYWASLIVLILFIAITP---VYLYYTYYIYRSLELLIIQLIVFFTAFIICAYVTIALKTEDVN 250
                                       567888899999999999...78888899*********99999999999999998876666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1344  (0.0749624); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2175.26
//
Query:       gi|518652797|ref|YP_008142317.1|  [L=301]
Description: hypothetical protein FACI_IFERC00001G1436 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.2e-63  212.7  10.1    9.3e-63  212.3  10.1    1.1  1  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
     0.0046   16.9   0.3      0.024   14.6   0.1    2.2  2  HHH_4            Helix-hairpin-helix containing domain
  ------ inclusion threshold ------
      0.021   14.5   0.1      0.047   13.3   0.1    1.6  1  Cons_hypoth95    Conserved hypothetical protein 95


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 !  212.3  10.1   1.6e-66   9.3e-63       1     260 []      35     280 ..      35     280 .. 0.96

  Alignments for each domain:
  == domain 1  score: 212.3 bits;  conditional E-value: 1.6e-66
                                       STTTSCTTHHHHHCCS-..--SEEEETT-TTSCCHHCS.....SSCEEEEES-HHHHHHHHHHCCHSHHHHHHHHH. CS
                   MethyltransfD12   1 YiGgKrkllpeIkelipkdkgktfvepFaGggaVffeakk..qgkkvlinDinedlinlykaliknnveelikelek 75 
                                       ++GgKr+ll+ + ++ip+ + ++++epF+Ggg++ +++ +  ++ +++i+D+n+dl+nly  +ik n+ +li+el+ 
  gi|518652797|ref|YP_008142317.1|  35 WAGGKRQLLNDLIKYIPN-NFNEYYEPFIGGGSFLIKLYSmdKISNAVISDLNTDLYNLYV-TIKSNPYALINELKD 109
                                       9****************9.7789***************9999*******************.88888*********9 PP

                                       TCTTGGC.TSHHHHHHHHHHHH...HHH-HHHHHHHHHHHHCCBGGG---B-TTS-B---B-S-SS-....HHHHHH CS
                   MethyltransfD12  76 llekeelenereyfyelreefnkkidaireaeeaidflylnrllfsglervnkkgnfnvpygaykkpkkvaekelkl 152
                                       +++k    n+++ +y+ re fn    + + + ++++++yln+++++gl+rvn++++fnvpyg+y++p    e ++  
  gi|518652797|ref|YP_008142317.1| 110 IEFK----NNSKDYYKARELFN---STGNLVSRSALLIYLNKHCYNGLYRVNSQNKFNVPYGKYANPGMPIESDILG 179
                                       9988....99************...99999*************************************8888889999 PP

                                       HHHHHHHCCEEEC-CHHHHTT--TTE.EEEE--S-T.S...TS--GGGG.CS-HHHHHHHHHHHHHH.HHTT-EEEE CS
                   MethyltransfD12 153 rseklknakiecgdfdavllkakieddivYlDPPYnprqytanytlyetlafsdedevrlaevlkslsskfgvkvll 229
                                       +s+ +++ +i+++df+++ ++a  ++d+vY+DPPY p ++t+n+t+y+ ++f+++d+ rl +v+k l s++gv+v+ 
  gi|518652797|ref|YP_008142317.1| 180 LSNLFQKCTILNEDFEEAVKTA-SKGDFVYFDPPYMPVNKTSNFTGYTSNGFYEKDQERLYKVFKRL-SSKGVYVME 254
                                       9999999**************9.6677****************************************.6******** PP

                                       EEESEESHHHHHHCTT...SEEEEECCCCHH CS
                   MethyltransfD12 230 snsfkdtklfrelyksYnnesileveelrai 260
                                       sns  dt+++++lyk+   ++++ev ++r+i
  gi|518652797|ref|YP_008142317.1| 255 SNS--DTDFIKNLYKD---FNLIEVTARRSI 280
                                       ***..***********...*********987 PP

>> HHH_4  Helix-hairpin-helix containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1     4e-06     0.024      33      56 ..      92     115 ..      67     149 .. 0.74
   2 ?   -0.8   0.0      0.26   1.5e+03      14      31 ..     227     244 ..     221     273 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4e-06
                             HHH_4  33 aleilkenPYrliedvegigFkta 56 
                                       ++ ++k+nPY li+++++i+Fk  
  gi|518652797|ref|YP_008142317.1|  92 LYVTIKSNPYALINELKDIEFKNN 115
                                       4557*****************975 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.26
                             HHH_4  14 eygisaklaekiykkyge 31 
                                       + g+ +k  e++yk ++ 
  gi|518652797|ref|YP_008142317.1| 227 SNGFYEKDQERLYKVFKR 244
                                       567777777777777753 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   7.9e-06     0.047      92     128 ..     186     218 ..     174     276 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7.9e-06
                                       TTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH CS
                     Cons_hypoth95  92 etaelkedaleallklakkkeefdivflDPPyakell 128
                                       ++++l+ed +ea+++     ++ d+v++DPPy+ ++ 
  gi|518652797|ref|YP_008142317.1| 186 KCTILNEDFEEAVKTA----SKGDFVYFDPPYMPVNK 218
                                       5666666666666555....4569********97764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2050.94
//
Query:       gi|518652798|ref|YP_008142318.1|  [L=138]
Description: hypothetical protein FACI_IFERC00001G1437 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.023   14.1   0.3       0.03   13.7   0.3    1.1  1  DUF4566   Domain of unknown function (DUF4566)
      0.026   14.9   0.2      0.048   14.0   0.2    1.5  1  PDDEXK_3  PD-(D/E)XK nuclease superfamily


Domain annotation for each model (and alignments):
>> DUF4566  Domain of unknown function (DUF4566)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.3   3.4e-06      0.03     146     211 ..      21      86 ..      13      95 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.4e-06
                           DUF4566 146 fefdhedyekqll...rllarkdktgliinnpkqsvflfvdrhhlktpknkavvfklsslclylpqeql 211
                                       +ef+h dy+kq+    +l++++ k+ ++++n   s+++ +  +++  + ++ v++ ++sl   ++++++
  gi|518652798|ref|YP_008142318.1|  21 LEFNHYDYKKQVFigkQLFNNRYKADFVVDN---SIIVSLKWQQVAGTAEQKVIYEIASLIKIIENDNF 86 
                                       79*********8544489***********87...899999*******************9988888765 PP

>> PDDEXK_3  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   5.3e-06     0.048      49      82 ..      31      64 ..      14      82 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5.3e-06
                          PDDEXK_3 49 pvvYkgkevgeeyrlDllveekvivElKaveelk 82
                                      +v+   + ++++y +D++v++++iv lK  +   
  gi|518652798|ref|YP_008142318.1| 31 QVFIGKQLFNNRYKADFVVDNSIIVSLKWQQVAG 64
                                      566777888999****************876554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.46
# Mc/sec: 900.22
//
Query:       gi|518652799|ref|YP_008142319.1|  [L=68]
Description: hypothetical protein FACI_IFERC00001G1438 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); 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 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 482.83
//
Query:       gi|518652800|ref|YP_008142320.1|  [L=311]
Description: hypothetical protein FACI_IFERC00001G1439 [Ferroplasma acidarmanus fer1]
Scores for 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-40  135.7   4.2    1.3e-19   70.0   0.4    2.3  2  TFIIB            Transcription factor TFIIB repeat
    1.8e-21   75.4   1.3      3e-21   74.6   1.3    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
    2.4e-05   24.4   0.0      0.026   14.6   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
    0.00044   20.3   0.2     0.0013   18.7   0.0    1.8  2  RB_B             Retinoblastoma-associated protein B domain
     0.0014   18.1   0.5      0.017   14.6   0.4    2.6  2  Sigma70_r4       Sigma-70, region 4
     0.0034   17.2   0.2     0.0092   15.8   0.2    1.8  1  HTH_AsnC-type    AsnC-type helix-turn-helix domain
     0.0091   16.0   3.9        0.1   12.7   2.6    2.5  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
  ------ inclusion threshold ------
      0.012   14.9   2.5      0.079   12.4   2.5    2.1  1  zf-ribbon_3      zinc-ribbon domain
      0.018   15.3   0.1       0.49   10.7   0.1    2.4  2  UPF0253          Uncharacterised protein family (UPF0253)
      0.018   15.0   0.4      0.039   13.9   0.4    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.029   14.1   1.5      0.067   12.9   0.1    2.1  2  Cyclin_N         Cyclin, N-terminal domain
      0.033   13.9   0.1       0.06   13.1   0.1    1.3  1  Ribosomal_S27e   Ribosomal protein S27
      0.049   14.0   0.1       0.11   12.9   0.1    1.6  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.051   13.7   1.1      0.092   12.9   1.1    1.4  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
      0.057   13.2   2.6        2.5    7.9   2.7    2.4  1  A2L_zn_ribbon    A2L zinc ribbon domain
      0.063   13.0   0.8       0.11   12.1   0.8    1.4  1  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.07   13.1   0.3       0.19   11.8   0.3    1.7  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.088   12.9   1.4       0.83    9.8   0.2    2.4  2  Zn-ribbon_8      Zinc ribbon domain
      0.094   12.7   0.4       0.26   11.2   0.4    1.8  1  HTH_11           HTH domain
       0.13   11.7   0.3        0.3   10.5   0.3    1.7  1  HTH_Tnp_ISL3     Helix-turn-helix domain of transposase famil
       0.14   11.7   0.1       0.26   10.9   0.1    1.4  1  DUF3053          Protein of unknown function (DUF3053)
       0.14   12.3   0.3       0.27   11.4   0.3    1.5  1  DUF2318          Predicted membrane protein (DUF2318)
       0.26   11.1   1.3       0.54   10.1   1.3    1.5  1  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
        1.5    8.8   4.2        4.9    7.2   4.2    1.8  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
        4.4    7.1   6.9         21    5.0   0.0    2.9  3  zinc_ribbon_2    zinc-ribbon domain


Domain annotation for each model (and alignments):
>> TFIIB  Transcription factor TFIIB repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.2   0.3   1.3e-21   9.6e-19       2      71 .]     131     200 ..     130     200 .. 0.98
   2 !   70.0   0.4   1.9e-22   1.3e-19       1      71 []     224     294 ..     224     294 .. 0.99

  Alignments for each domain:
  == domain 1  score: 67.2 bits;  conditional E-value: 1.3e-21
                                       HHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   2 krfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       +r+a++l +p+ V++    ++++a++++++ Grs +g++A ++y Acr  +v rt+ ei+sv++V++k+i
  gi|518652800|ref|YP_008142320.1| 131 ERMASNLSIPNDVRETSAVIYRKAVKQNMIRGRSIEGVVAGSIYAACRITNVPRTLDEIASVTRVKKKEI 200
                                       79******************************************************************98 PP

  == domain 2  score: 70.0 bits;  conditional E-value: 1.9e-22
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++rf+++l L+ + +++A+e++k a ++++++G+ p+g+aAA++yiA++  +++rtq+ i++v+ V+e+ti
  gi|518652800|ref|YP_008142320.1| 224 VNRFCSKLRLSMEARKRAEEILKMAIDNDLTSGKGPTGVAAAAIYIASLITGERRTQRAIAEVAGVTEVTI 294
                                       68*******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   1.3   4.2e-24     3e-21       2      43 .]      14      55 ..      14      55 .. 0.99

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 4.2e-24
                                      EETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      kCP+Cgs++lv+D+ergelvC++CGlV++d +idegpewr+f
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVRDYERGELVCSNCGLVIDDSYIDEGPEWRAF 55
                                      8***************************************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 !    7.3   0.0    0.0069         5      49      90 ..     170     211 ..     167     219 .. 0.92
   2 !   14.6   0.0   3.6e-05     0.026       5      89 ..     222     304 ..     219     308 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0069
                                       HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                       a+++++a+++ n p   +++ ++t+++k+++   ++ ++ +l
  gi|518652800|ref|YP_008142320.1| 170 AGSIYAACRITNVPRTLDEIASVTRVKKKEIGRTYRIMARYL 211
                                       899***********************************9987 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.6e-05
                                       HHHHHH.HCCSSHT.-HCCHHCHHCHHHHHHCSCCHCCS-HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHH CS
                          Cyclin_C   5 sFlrrf.lkaadasedselrtlakylleltlldydflsyppSliAaaalllarstlnspewtetlehytgyskedlk 80 
                                       ++++rf +k      ++e r++a+ +l +++ +  + +  p  +Aaaa+++a+ + ++   ++++ ++ g+++  ++
  gi|518652800|ref|YP_008142320.1| 222 DYVNRFcSKL--R-LSMEARKRAEEILKMAIDNDLTSGKGPTGVAAAAIYIASLITGERRTQRAIAEVAGVTEVTIR 295
                                       7899997888..3.34699**********998888999*************************************** PP

                                       HHHHHHHHH CS
                          Cyclin_C  81 pcvelilel 89 
                                       + ++ + e 
  gi|518652800|ref|YP_008142320.1| 296 NRYKELTEK 304
                                       999998875 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 !   18.7   0.0   1.9e-06    0.0013      10      94 ..     123     205 ..     114     213 .. 0.87
   2 ?   -2.3   0.0       5.9   4.2e+03      18      42 ..     225     249 ..     223     255 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.9e-06
                              RB_B  10 yklaavrlrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqp 86 
                                       ++ a   l+++ ++L++ +++re    + ++++  ++++++ R ++ ++  ++Y+ +++t+  +++ ei +  r ++
  gi|518652800|ref|YP_008142320.1| 123 LSQALQELERMASNLSIPNDVRETSAVIYRKAV--KQNMIRGRSIEGVVAGSIYAACRITNVPRTLDEIASVTRVKK 197
                                       66788899999*********9999877777766..5689*******************************9999999 PP

                              RB_B  87 qasskvyr 94 
                                       ++  ++yr
  gi|518652800|ref|YP_008142320.1| 198 KEIGRTYR 205
                                       88888877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.9
                              RB_B  18 rdLcerLklsselrekiwtlfehvl 42 
                                       ++ c++L+ls e r+++ ++++ ++
  gi|518652800|ref|YP_008142320.1| 225 NRFCSKLRLSMEARKRAEEILKMAI 249
                                       6789999999999888777666665 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.86   6.2e+02      20      29 ..     183     192 ..     177     206 .. 0.81
   2 !   14.6   0.4   2.4e-05     0.017      18      48 ..     275     305 ..     267     306 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.86
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       ++Tl EI+ +
  gi|518652800|ref|YP_008142320.1| 183 PRTLDEIASV 192
                                       6899999976 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.4e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       ge +T+  I+e+ g+++ ++r + k+  +kL
  gi|518652800|ref|YP_008142320.1| 275 GERRTQRAIAEVAGVTEVTIRNRYKELTEKL 305
                                       899**********************998887 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.2   1.3e-05    0.0092      15      41 ..     275     301 ..     269     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-05
                     HTH_AsnC-type  15 daRisyaeLAervGlSestvlrRvrrL 41 
                                         R++ +++Ae  G++e t+++R++ L
  gi|518652800|ref|YP_008142320.1| 275 GERRTQRAIAEVAGVTEVTIRNRYKEL 301
                                       569*********************998 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 !   12.7   2.6   0.00014       0.1       3      26 .]      14      37 ..      14      37 .. 0.99
   2 ?    1.9   0.0      0.34   2.4e+02       9      20 ..     148     159 ..     147     159 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00014
                            zf-ACC  3 KCpsCgemlykkeLernlyVCPkC 26
                                      KCp+Cg++ + ++ er   VC +C
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVRDYERGELVCSNC 37
                                      9*********************** PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.34
                            zf-ACC   9 emlykkeLernl 20 
                                       +++y+k + +n+
  gi|518652800|ref|YP_008142320.1| 148 AVIYRKAVKQNM 159
                                       89******9996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   2.5   0.00011     0.079       4      26 .]      14      41 ..      12      41 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00011
                       zf-ribbon_3  4 rCPnCGa.pl....ssddnvCpyCGtkl 26
                                      +CP+CG+ +l    + +  vC +CG ++
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSsQLvrdyERGELVCSNCGLVI 41
                                      7******99546666799*******986 PP

>> UPF0253  Uncharacterised protein family (UPF0253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00068      0.49      27      52 ..     123     148 ..     115     151 .. 0.90
   2 ?    1.7   0.0      0.44   3.2e+02      27      45 ..     179     197 ..     166     203 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00068
                           UPF0253  27 iscalktLdevaanealpeevrekAA 52 
                                       +s al+ L+++a+n ++p++vre  A
  gi|518652800|ref|YP_008142320.1| 123 LSQALQELERMASNLSIPNDVRETSA 148
                                       77899******************987 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.44
                           UPF0253  27 iscalktLdevaanealpe 45 
                                       i+ + +tLde+a+  ++ +
  gi|518652800|ref|YP_008142320.1| 179 ITNVPRTLDEIASVTRVKK 197
                                       777889******9998876 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 ?   13.9   0.4   5.5e-05     0.039      30      57 ..      14      42 ..       3      44 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.5e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke.alsgrtfkCpnCgfead 57
                                      +C+eCgs +   + ++ +++C+nCg+++d
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVrDYERGELVCSNCGLVID 42
                                      8*****98777699***********9977 PP

>> Cyclin_N  Cyclin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   9.3e-05     0.067      32     126 ..     124     215 ..      98     216 .. 0.86
   2 ?   -0.3   0.1       1.2   8.4e+02      74      86 ..     260     272 ..     222     306 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
                                       HHHHHHHHHHHHHTT--TTHHHHHHHHHHHHHHHS---CCCHHHHHHHHHHHHHHHHSSS---HHHHHHHTTTSS-H CS
                          Cyclin_N  32 ailidwlvevaekfkltpetlflavnyldRflskksvpkdklqlvgatcLllAaKveeisppkledlvyitdeafte 108
                                       +++++ l ++a+++++ +++  ++++++ + ++++ ++ + ++ v+a++++ A+++ ++ p +l++++ +t   +++
  gi|518652800|ref|YP_008142320.1| 124 SQALQELERMASNLSIPNDVRETSAVIYRKAVKQNMIRGRSIEGVVAGSIYAACRITNV-PRTLDEIASVTR--VKK 197
                                       5566668889999999999999**********************************999.9*********76..889 PP

                                       HHHHHHHHHHHHHTTT-- CS
                          Cyclin_N 109 eeilemErliLetLnfdl 126
                                       +ei +  r + ++L+ ++
  gi|518652800|ref|YP_008142320.1| 198 KEIGRTYRIMARYLKLNI 215
                                       999998888888888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 1.2
                                       HHHHHHHHHHHHH CS
                          Cyclin_N  74 qlvgatcLllAaK 86 
                                         v+a+++++A+ 
  gi|518652800|ref|YP_008142320.1| 260 TGVAAAAIYIASL 272
                                       4466777777765 PP

>> Ribosomal_S27e  Ribosomal protein S27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   8.3e-05      0.06       9      36 ..      14      41 ..      10      43 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.3e-05
                                      E-TTTS-EEEEESS-SS-EEESSSTCEE CS
                    Ribosomal_S27e  9 kCpdCenetvvFshaatvvkCisCgkvL 36
                                      kCp+C+  + v +       C  Cg v+
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVRDYERGELVCSNCGLVI 41
                                      9************************875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   0.00016      0.11       2      40 ..      11      43 ..      10      65 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00016
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigqcvyCadCgastpw 40
                                      e+  CP Cg+ + +   +r+         C +Cg + ++
  gi|518652800|ref|YP_008142320.1| 11 EIDKCPECGSSQLVRDYERGE------LVCSNCGLVIDD 43
                                      6789********999998885......89*****93222 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 ?   12.9   1.1   0.00013     0.092      17      40 .]      14      38 ..      12      38 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00013
                     Auto_anti-p27 17 tCpvC.gvPLmrdrkggkvyCvaCd 40
                                       Cp+C ++ L+rd ++g+++C +C+
  gi|518652800|ref|YP_008142320.1| 14 KCPECgSSQLVRDYERGELVCSNCG 38
                                      6****99******999********6 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 ?    7.9   2.7    0.0035       2.5       5      30 ..      14      40 ..      14      41 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0035
                     A2L_zn_ribbon  5 vCsvCggngiln.seqgylvCieCgas 30
                                      +C  Cg+  ++   e+g+lvC +Cg++
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVRdYERGELVCSNCGLV 40
                                      5777888888877799********986 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.8   0.00016      0.11       6      31 ..      14      41 ..      13      42 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
                           zf-RRN7  6 pCgvCgc.rsftl.ddGfyyCrrChtqe 31
                                       C++Cg+  +++  + G  +C +C+ ++
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSsQLVRDyERGELVCSNCGLVI 41
                                      6******99****************887 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 ?   11.8   0.3   0.00026      0.19      20      44 ..      14      38 ..      11      39 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00026
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCr 44
                                       CP Cgs+++ r   rg + C+ C+
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVRDYERGELVCSNCG 38
                                      5*******66665557********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 ?    9.8   0.2    0.0012      0.83      26      38 ..      11      25 ..       3      27 .. 0.79
   2 ?    1.6   0.1      0.43   3.1e+02       5      14 ..      31      40 ..      26      51 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                       Zn-ribbon_8 26 lta.CPeCgs.evrr 38
                                      +++ CPeCgs ++ r
  gi|518652800|ref|YP_008142320.1| 11 EIDkCPECGSsQLVR 25
                                      4555******99988 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.43
                       Zn-ribbon_8  5 eYrCeeCghe 14
                                      e  C +Cg +
  gi|518652800|ref|YP_008142320.1| 31 ELVCSNCGLV 40
                                      4469999865 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.4   0.00037      0.26      16      47 ..     278     310 ..     266     311 .] 0.83

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                            HTH_11  16 isgeeLAeeLnvSrrtvrrdIkaLeelg.vpIe 47 
                                        +   +Ae  +v++ t+r++ k+L+e++ + Ie
  gi|518652800|ref|YP_008142320.1| 278 RTQRAIAEVAGVTEVTIRNRYKELTEKLnLTIE 310
                                       57889*******************887756665 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00042       0.3      18      51 ..     267     301 ..     263     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00042
                      HTH_Tnp_ISL3  18 ayilellles.rsvkavArqlgvSwtTVwrildry 51 
                                        yi+ l +   r+ +a+A+  gv++ T++++++++
  gi|518652800|ref|YP_008142320.1| 267 IYIASLITGErRTQRAIAEVAGVTEVTIRNRYKEL 301
                                       58999999999********************9976 PP

>> DUF3053  Protein of unknown function (DUF3053)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00036      0.26      93     147 ..     103     157 ..      93     169 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                           DUF3053  93 ltrrdelrqaagalneleqqlqnakaqadkaraaLkqpddlkavydkayektVtq 147
                                       l r  ++++  +  n++e +l +a ++ +   + L  p+d+++  + +y k+V q
  gi|518652800|ref|YP_008142320.1| 103 LYRLRKWQKRIKVSNAAERNLSQALQELERMASNLSIPNDVRETSAVIYRKAVKQ 157
                                       567788999999****************************************987 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   0.00037      0.27      31      67 ..       9      47 ..       1      51 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00037
                           DUF2318 31 rvaldaCevCekkgYv..qegeelvCknCgvrfaldsig 67
                                         +d C  C++++ v   e  elvC nCg +++ + i+
  gi|518652800|ref|YP_008142320.1|  9 IYEIDKCPECGSSQLVrdYERGELVCSNCGLVIDDSYID 47
                                      4578******8888875567889*******999888776 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   1.3   0.00075      0.54       2      15 ..      13      27 ..      12      38 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00075
                                      EE-SSS-.-EEEEEE CS
                    zf-C4_Topoisom  2 ekCPkCg.gdLvlkr 15
                                       kCP+Cg ++Lv+ +
  gi|518652800|ref|YP_008142320.1| 13 DKCPECGsSQLVRDY 27
                                      59*****99999755 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.2    0.0068       4.9       4      26 ..      14      38 ..      12      39 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0068
                    PhnA_Zn_Ribbon  4 kCplCaSeytY..edgallvCpeCa 26
                                      kCp+C+S+      ++  lvC++C+
  gi|518652800|ref|YP_008142320.1| 14 KCPECGSSQLVrdYERGELVCSNCG 38
                                      9******976577677779*****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 ?    4.4   1.0     0.045        32       1       7 [.      14      20 ..      14      21 .. 0.71
   2 ?    5.0   0.0     0.029        21       2      11 ..      34      43 ..      33      45 .. 0.75
   3 ?   -1.6   0.1       3.5   2.5e+03      13      18 ..     225     230 ..     224     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.045
                     zinc_ribbon_2  1 fCpnCGa 7 
                                      +Cp+CG 
  gi|518652800|ref|YP_008142320.1| 14 KCPECGS 20
                                      6888884 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.029
                     zinc_ribbon_2  2 CpnCGaelqd 11
                                      C+nCG  ++d
  gi|518652800|ref|YP_008142320.1| 34 CSNCGLVIDD 43
                                      9999977766 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.5
                     zinc_ribbon_2  13 akFCpy 18 
                                       ++FC++
  gi|518652800|ref|YP_008142320.1| 225 NRFCSK 230
                                       589986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1077  (0.0600703); expected 358.6 (0.02)
Passed bias filter:                      772  (0.0430587); expected 358.6 (0.02)
Passed Vit filter:                       109  (0.00607954); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 1979.80
//
Query:       gi|518652801|ref|YP_008142321.1|  [L=70]
Description: H/ACA RNA-protein complex component Gar1 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0014   18.4   0.1     0.0017   18.2   0.1    1.1  1  Gar1      Gar1/Naf1 RNA binding region


Domain annotation for each model (and alignments):
>> Gar1  Gar1/Naf1 RNA binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   9.5e-08    0.0017      25      81 ..       6      57 ..       2      69 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 9.5e-08
                                      EEEEEETTEEEEEE---S--B--BTT-EEEETT--EEEE--EEES-SSS-EEEEE-- CS
                              Gar1 25 tvssivenevviksttsgekkvldfnsilflenktqiGkVdEifGpvnepyysVkln 81
                                      t+ + ++nev+ +++     + +     l +e   +iGkV+ i+Gpv+ py    + 
  gi|518652801|ref|YP_008142321.1|  6 TIVHKFNNEVLLRVN-----DCIGLHNKLVNEYDAVIGKVTKILGPVSGPYALAYIA 57
                                      566667777777776.....567778888899999**************99665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); 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 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 526.43
//
Query:       gi|518652802|ref|YP_008142322.1|  [L=305]
Description: hypothetical protein FACI_IFERC00001G1441 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-37  127.4   1.7    1.9e-18   66.3   0.0    2.3  2  TFIIB            Transcription factor TFIIB repeat
    6.2e-17   60.8   0.9      1e-16   60.1   0.9    1.3  1  TF_Zn_Ribbon     TFIIB zinc-binding
    0.00046   20.3   0.0        1.5    9.0   0.0    2.4  2  Cyclin_C         Cyclin, C-terminal domain
     0.0055   17.1   0.4      0.033   14.6   0.2    2.1  2  Lar_restr_allev  Restriction alleviation protein Lar
     0.0056   16.2   0.1      0.032   13.7   0.1    2.3  2  Sigma70_r4       Sigma-70, region 4
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.022   14.8   0.0    1.5  1  DNA_pol_D_N      DNA polymerase delta subunit OB-fold domain
      0.013   15.1   0.6       0.11   12.1   0.1    2.7  3  Sigma70_r4_2     Sigma-70, region 4
      0.015   15.2   0.2      0.033   14.2   0.2    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
      0.018   15.1   0.1      0.044   13.8   0.0    1.7  1  RB_B             Retinoblastoma-associated protein B domain
      0.021   14.2   3.1       0.13   11.7   3.0    2.2  1  zf-ribbon_3      zinc-ribbon domain
      0.062   13.2   0.5        2.7    7.9   0.1    2.9  3  TrmB             Sugar-specific transcriptional regulator Trm
      0.093   12.7   0.3       0.22   11.5   0.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.098   12.8   0.3       0.64   10.2   0.0    2.3  2  Zn-ribbon_8      Zinc ribbon domain
       0.21   11.8   1.5        0.4   10.9   1.5    1.5  1  Auto_anti-p27    Sjogren's syndrome/scleroderma autoantigen 1
       0.23   11.6   4.5         13    6.0   2.0    2.7  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
       0.26   11.0   4.1        1.9    8.3   0.0    2.9  3  A2L_zn_ribbon    A2L zinc ribbon domain
       0.66    9.8   4.0        9.8    6.1   0.1    3.1  2  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 !   60.3   0.3   1.3e-19   1.4e-16       6      71 .]     129     194 ..     128     194 .. 0.97
   2 !   66.3   0.0   1.8e-21   1.9e-18       1      71 []     218     288 ..     218     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 1.3e-19
                                       HHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   6 daleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       ++l++p+ +++ A  ++++a+e++++ Grs ++i+ A++y  cr+ +  rt+ eis+v++V++k i
  gi|518652802|ref|YP_008142322.1| 129 AKLGIPKDIKESAALIYRKAVEKNLIRGRSIESIVCASIYASCRMINIPRTLDEISKVSEVNKKKI 194
                                       68************************************************************9986 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 1.8e-21
                                       HHHHHHHTT--HHHHHHHHHHHHHHTTSTTTTSGCTTHHHTTHHHHHHTTTTSS--HHHHHHHSS--SHHH CS
                             TFIIB   1 ikrfadaleLpekVadaAkelaklaleekvlkGrspagiaAAclyiAcrkeevkrtqkeissvlqVsekti 71 
                                       +++f+++l+L ++V  + +++++la e ++  G+ p+giaAA++yiA+ k++ +rtqk+++ v+ V+e+ti
  gi|518652802|ref|YP_008142322.1| 218 VSQFCNKLDLDKQVIMDSEHIIRLAGESGLSTGKGPTGIAAAAIYIAAMKNGKQRTQKDVARVSGVTEVTI 288
                                       679******************************************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.9   9.8e-20     1e-16       3      43 .]       9      49 ..       8      49 .. 0.98

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 9.8e-20
                                      ETTTTCEECHEETSTTCEEESSSSBEEEECCCCCCCHHHHH CS
                      TF_Zn_Ribbon  3 CPnCgstnlveDpergelvCtdCGlVlednsidegpewref 43
                                      CP+Cgs +lv D++rgel+C dCG V+ed  id gpewr+f
  gi|518652802|ref|YP_008142322.1|  9 CPECGSIHLVKDYDRGELTCYDCGIVIEDSLIDQGPEWRAF 49
                                      ******99*******************************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 !    8.8   0.0    0.0015       1.6      49      90 ..     164     205 ..     160     221 .. 0.87
   2 !    9.0   0.0    0.0014       1.5      44      88 ..     253     297 ..     212     302 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0015
                                       HHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHHHH CS
                          Cyclin_C  49 aaalllarstlnspewtetlehytgyskedlkpcvelilell 90 
                                        a+++++++++n p   +++ ++++++k+++ + ++++++ l
  gi|518652802|ref|YP_008142322.1| 164 CASIYASCRMINIPRTLDEISKVSEVNKKKIGKAYRHLAKEL 205
                                       699**********************************99877 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHHCCHHHHS--S-HHHHHHC---HHHHHHHHHHHHH CS
                          Cyclin_C  44 pSliAaaalllarstlnspewtetlehytgyskedlkpcvelile 88 
                                       p  iAaaa+++a    +++  ++ +  ++g+++  +++ ++ i +
  gi|518652802|ref|YP_008142322.1| 253 PTGIAAAAIYIAAMKNGKQRTQKDVARVSGVTEVTIRNRYKEISK 297
                                       556999999999988899999******************999987 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 !   14.6   0.2   3.1e-05     0.033       2      36 ..       5      33 ..       4      56 .. 0.80
   2 ?   -0.1   0.0       1.2   1.3e+03      28      38 ..     161     177 ..     134     198 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.1e-05
                   Lar_restr_allev  2 eLkpCPfCggravlersqrvvaeigqcvyCadCga 36
                                      e+k CP Cg+   ++   r+        +C dCg 
  gi|518652802|ref|YP_008142322.1|  5 EVKNCPECGSIHLVKDYDRGE------LTCYDCGI 33
                                      79**********999998885......8******9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 1.2
                   Lar_restr_allev  28 cvyCad....Cga..st 38 
                                        + Ca     C +    
  gi|518652802|ref|YP_008142322.1| 161 SIVCASiyasCRMinIP 177
                                       78886666679996533 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       2.1   2.2e+03      20      29 ..     177     186 ..     175     191 .. 0.84
   2 !   13.7   0.1   3.1e-05     0.032      18      48 ..     269     299 ..     260     300 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.1
                                       T--HHHHHHH CS
                        Sigma70_r4  20 glTleEIger 29 
                                       ++Tl EI+++
  gi|518652802|ref|YP_008142322.1| 177 PRTLDEISKV 186
                                       68*****975 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 3.1e-05
                                       TTT--HHHHHHHHTS-HHHHHHHHHHHHHHH CS
                        Sigma70_r4  18 geglTleEIgerlgiSrerVrqiekrAlrkL 48 
                                       g+ +T+++++++ g+++ ++r + k+  +kL
  gi|518652802|ref|YP_008142322.1| 269 GKQRTQKDVARVSGVTEVTIRNRYKEISKKL 299
                                       6789*********************999988 PP

>> DNA_pol_D_N  DNA polymerase delta subunit OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.1e-05     0.022       3     115 ..      95     260 ..      95     275 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.1e-05
                       DNA_pol_D_N   3 aniYfaRleqlkprlleaakekw...skeelk..........................vnrildlkegeecivvGti 50 
                                       ++iY++R    + r+ +aa+++         +                          v++ l   ++ e+iv++ i
  gi|518652802|ref|YP_008142322.1|  95 SQIYRVRKWHQRIRVSNAAERNLalaL----QvlnedgaklgipkdikesaaliyrkaVEKNLIRGRSIESIVCASI 167
                                       578999999999999999999995540....2344555557777777788888877766666656666889999999 PP

                       DNA_pol_D_N  51 y..kemklkpsvlkeiak.......................edesapqaerkkyvse..kdellLEDesgrvrLsgs 100
                                       y  ++m + p+ l+ei+k                        + ++p +  ++++++   d+ ++ D++  +rL g+
  gi|518652802|ref|YP_008142322.1| 168 YasCRMINIPRTLDEISKvsevnkkkigkayrhlakelalnLQPTTPYSYVSQFCNKldLDKQVIMDSEHIIRLAGE 244
                                       844568899*************************99865443334444445555555878999999*********98 PP

                       DNA_pol_D_N 101 .gieseklvtGvvvav 115
                                        g++ +k  tG+  a+
  gi|518652802|ref|YP_008142322.1| 245 sGLSTGKGPTGIAAAA 260
                                       7999999999998775 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       6.6     7e+03      15      29 ..     145     159 ..     144     162 .. 0.59
   2 ?   12.1   0.1   0.00011      0.11      27      54 .]     272     299 ..     266     299 .. 0.89
   3 ?    4.4   0.0     0.028        30      29      40 ..     292     303 ..     291     304 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 6.6
                                       HHHHHHHHHTS---H CS
                      Sigma70_r4_2  15 qreifllryleglsy 29 
                                       +r++++   + g s+
  gi|518652802|ref|YP_008142322.1| 145 YRKAVEKNLIRGRSI 159
                                       677776655555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00011
                                       --HHHHHHHHT--HHHHHHHHHHHHHHH CS
                      Sigma70_r4_2  27 lsykEIAellgisegtVksrlsRArkkL 54 
                                        ++k++A++ g++e+t+++r++   kkL
  gi|518652802|ref|YP_008142322.1| 272 RTQKDVARVSGVTEVTIRNRYKEISKKL 299
                                       689******************9888887 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.028
                                       HHHHHHHHT--H CS
                      Sigma70_r4_2  29 ykEIAellgise 40 
                                       ykEI+++lgi +
  gi|518652802|ref|YP_008142322.1| 292 YKEISKKLGIDD 303
                                       9********986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   3.1e-05     0.033      20      44 ..       8      32 ..       3      33 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.1e-05
                     Zn_Tnp_IS1595 20 vCPhCgsrkayriktrglfqCkeCr 44
                                       CP Cgs ++ +  +rg + C++C+
  gi|518652802|ref|YP_008142322.1|  8 NCPECGSIHLVKDYDRGELTCYDCG 32
                                      5*****999999999*********6 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 ?   13.8   0.0   4.2e-05     0.044      17      95 ..     124     200 ..     109     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.2e-05
                              RB_B  17 lrdLcerLklsselrekiwtlfehvlveetellkdRhlDqillcavYvvakvtkeelsFkeiikaYrkqpqasskvy 93 
                                       l++  ++L + ++++e++  + ++++  e++l++ R ++ i+ +++Y+ +++ +  +++ ei k  + ++++  k y
  gi|518652802|ref|YP_008142322.1| 124 LNEDGAKLGIPKDIKESAALIYRKAV--EKNLIRGRSIESIVCASIYASCRMINIPRTLDEISKVSEVNKKKIGKAY 198
                                       55555666777777776655555554..578*******************************999888888888877 PP

                              RB_B  94 rs 95 
                                       r+
  gi|518652802|ref|YP_008142322.1| 199 RH 200
                                       76 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   3.0   0.00012      0.13       3      26 .]       7      35 ..       5      35 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00012
                       zf-ribbon_3  3 vrCPnCGa.p.l...ssddnvCpyCGtkl 26
                                      ++CP+CG+ + +   + +  +C+ CG ++
  gi|518652802|ref|YP_008142322.1|  7 KNCPECGSiHlVkdyDRGELTCYDCGIVI 35
                                      79******985555556888******986 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.1    0.0026       2.7      22      62 ..     177     217 ..     173     219 .. 0.83
   2 ?    2.1   0.1      0.16   1.7e+02      12      39 ..     260     288 ..     258     298 .. 0.78
   3 ?   -2.2   0.0       3.8     4e+03      25      35 ..     292     302 ..     289     303 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0026
                                       CCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTEE CS
                              TrmB  22 patadeiaeelgvprskvYevLrsLedkGlVerekgrpklY 62 
                                       p t dei++ ++v + k+ ++ r L +    + ++ +p+ Y
  gi|518652802|ref|YP_008142322.1| 177 PRTLDEISKVSEVNKKKIGKAYRHLAKELALNLQPTTPYSY 217
                                       7899*****************99999877777777777666 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.16
                                       CHCHHHHHHC.CCHHCHHCCCTTSSCHCH CS
                              TrmB  12 kvYlaLlklg.patadeiaeelgvprskv 39 
                                        +Y+a +k+g + t +++a+ +gv + ++
  gi|518652802|ref|YP_008142322.1| 260 AIYIAAMKNGkQRTQKDVARVSGVTEVTI 288
                                       6788888776156889*******988776 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.8
                                       HCHHCCCTTSS CS
                              TrmB  25 adeiaeelgvp 35 
                                        +ei+++lg++
  gi|518652802|ref|YP_008142322.1| 292 YKEISKKLGID 302
                                       589****9997 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   0.3    0.0002      0.22      29      55 ..       7      34 ..       6      37 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0002
                    OrfB_Zn_ribbon 29 ktCseCgsknke.alsgrtfkCpnCgfe 55
                                      k+C+eCgs++   + ++ +++C +Cg +
  gi|518652802|ref|YP_008142322.1|  7 KNCPECGSIHLVkDYDRGELTCYDCGIV 34
                                      79*******9887899**********87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00061      0.64      25      38 ..       4      19 ..       1      21 [. 0.73
   2 ?   -0.6   0.0       1.4   1.5e+03       7      14 ..      27      34 ..      22      45 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00061
                       Zn-ribbon_8 25 plta.CPeCgs.evrr 38
                                      ++++ CPeCgs ++ +
  gi|518652802|ref|YP_008142322.1|  4 DEVKnCPECGSiHLVK 19
                                      35556******99987 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.4
                       Zn-ribbon_8  7 rCeeCghe 14
                                       C +Cg +
  gi|518652802|ref|YP_008142322.1| 27 TCYDCGIV 34
                                      57777755 PP

>> Auto_anti-p27  Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   1.5   0.00038       0.4      16      40 .]       7      32 ..       6      32 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00038
                     Auto_anti-p27 16 etCpvC.gvPLmrdrkggkvyCvaCd 40
                                      ++Cp+C ++ L++d ++g++ C  C+
  gi|518652802|ref|YP_008142322.1|  7 KNCPECgSIHLVKDYDRGELTCYDCG 32
                                      68****66667777799********6 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 ?    6.0   2.0     0.012        13       3      18 ..       8      23 ..       7      31 .. 0.83
   2 ?    5.3   0.0      0.02        21       9      20 ..     142     153 ..     141     153 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.012
                            zf-ACC  3 KCpsCgemlykkeLer 18
                                      +Cp+Cg++ + k+ +r
  gi|518652802|ref|YP_008142322.1|  8 NCPECGSIHLVKDYDR 23
                                      6*******99999877 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.02
                            zf-ACC   9 emlykkeLernl 20 
                                       +++y+k +e+nl
  gi|518652802|ref|YP_008142322.1| 142 ALIYRKAVEKNL 153
                                       68*********7 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 ?    8.3   0.0    0.0018       1.9      17      31 ..       2      16 ..       1      18 [. 0.83
   2 ?    3.5   0.2      0.06        63      18      30 ..      22      34 ..      19      36 .. 0.87
   3 ?   -2.4   0.1       4.1   4.4e+03      16      22 ..      79      85 ..      77      85 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0018
                     A2L_zn_ribbon 17 seqgylvCieCgasf 31
                                      +++   +C+eCg+++
  gi|518652802|ref|YP_008142322.1|  2 KTDEVKNCPECGSIH 16
                                      6777789******97 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.06
                     A2L_zn_ribbon 18 eqgylvCieCgas 30
                                      ++g+l C +Cg +
  gi|518652802|ref|YP_008142322.1| 22 DRGELTCYDCGIV 34
                                      6899*******75 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 4.1
                     A2L_zn_ribbon 16 nseqgyl 22
                                      +s+++y+
  gi|518652802|ref|YP_008142322.1| 79 WSNKDYY 85
                                      99***98 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.7      0.11   1.2e+02      29      40 ..      92     103 ..      91     113 .. 0.86
   2 ?    6.1   0.1    0.0093       9.8      18      39 ..     272     293 ..     263     303 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.11
                            HTH_23  29 vsrrTvyrwlkr 40 
                                        +r+++yr++k+
  gi|518652802|ref|YP_008142322.1|  92 KNRSQIYRVRKW 103
                                       689******998 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0093
                            HTH_23  18 lsvreIAreLgvsrrTvyrwlk 39 
                                        +++++Ar  gv++ T+++  k
  gi|518652802|ref|YP_008142322.1| 272 RTQKDVARVSGVTEVTIRNRYK 293
                                       5889999999999999994433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      652  (0.0363657); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2182.81
//
Query:       gi|518652803|ref|YP_008142323.1|  [L=246]
Description: protein-L-isoaspartate O-methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-27   96.5   0.0    2.6e-27   96.1   0.0    1.1  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    1.9e-10   40.7   0.0    2.7e-10   40.2   0.0    1.1  1  Methyltransf_31  Methyltransferase domain
    6.8e-09   36.3   0.0    1.1e-08   35.6   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    1.8e-06   28.6   0.0      6e-06   26.9   0.0    1.9  1  Methyltransf_12  Methyltransferase domain
    5.5e-05   22.6   0.0    8.7e-05   22.0   0.0    1.4  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    8.8e-05   22.1   0.0    0.00014   21.5   0.0    1.4  1  MTS              Methyltransferase small domain
     0.0003   21.4   0.0    0.00081   20.0   0.0    1.7  1  Methyltransf_11  Methyltransferase domain
     0.0022   17.8   0.0     0.0027   17.5   0.0    1.2  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
     0.0034   17.5   0.0      0.021   14.9   0.0    1.9  2  FtsJ             FtsJ-like methyltransferase
     0.0077   16.1   0.0      0.027   14.3   0.0    1.7  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.016   14.9   0.0    1.4  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
      0.023   14.1   0.0      0.035   13.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.059   13.3   0.0      0.099   12.6   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
       0.11   11.8   0.0       0.15   11.3   0.0    1.1  1  Glyco_hydro_98M  Glycosyl hydrolase family 98
       0.18   11.4   0.0       0.29   10.8   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020


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 !   96.1   0.0   2.2e-30   2.6e-27      20     185 ..      65     225 ..      50     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 2.2e-30
                             GCD14  20 rtqilytaDisliimkLelkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehelsqlvtv 96 
                                        tq +   D s ii+   + pG+ ++e+G+G+gsls +i+++++ +G+l t++  ++ ++ ar + ++  l ++   
  gi|518652803|ref|YP_008142323.1|  65 NTQAVLPLDTSYIIHAAGILPGTCILEAGAGTGSLSYSILKAIGSKGKLVTMDINKSTIDIARGNVERFMLPDNWET 141
                                       69*********************************************************************998888 PP

                             GCD14  97 thrDvckeGfdeevsgkvDavfLDlPaPweaiphaakalkkeggrlCsfsPCieqvqrtceaLrelgfteietlevl 173
                                        h D+ ++ +     gk Da  LD+P Pw+a+++++k++   gg l ++sP  +q  + + a+++l+f  +et+e+ 
  gi|518652803|ref|YP_008142323.1| 142 IHGDIRSDNL----PGKYDAAILDIPDPWDAVENMKKHI-VPGGYLVTYSPNFNQAEKNVIAMKKLNFYVLETVELI 213
                                       999**98866....8899*********************.9************************************ PP

                             GCD14 174 lrtyevrkskle 185
                                        r+  vr++  +
  gi|518652803|ref|YP_008142323.1| 214 KRNIIVRENATR 225
                                       ****99997665 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   2.3e-13   2.7e-10       6     128 ..      88     202 ..      84     233 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 2.3e-13
                   Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdiee..leklledekfDlil 79 
                                        +l++G+GtG l++ + + +g+k+++v  Di++  i  Ar n ++  l  n e  +gdi +  l+      k+D  +
  gi|518652803|ref|YP_008142323.1|  88 CILEAGAGTGSLSYSILKAIGSKGKLVTMDINKSTIDIARGNVERFMLPdNWETIHGDIRSdnLP-----GKYDAAI 159
                                       589*****************************************999877**********94344.....99***77 PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlkpggilliedprllaelpakveeeska 128
                                             +++dp ++ e++++ + pgg+l++ +p+   +  ++v ++ k+
  gi|518652803|ref|YP_008142323.1| 160 L-----DIPDPWDAVENMKKHIVPGGYLVTYSPN-FNQAEKNVIAMKKL 202
                                       7.....6***************************.33333333333333 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   9.5e-12   1.1e-08       1      97 []      89     180 ..      89     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 9.5e-12
                                       EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgal 74 
                                       +L++G+GtG l+  ++k++g k+k++ +Di+++ +++ar ++e+  l  n+e ++gd+++ +++ g++D+ ++    
  gi|518652803|ref|YP_008142323.1|  89 ILEAGAGTGSLSYSILKAIGsKGKLVTMDINKSTIDIARGNVERFMLpdNWETIHGDIRSDNLP-GKYDAAILD--- 161
                                       8******************779********************9876789*********987776.69***9992... PP

                                       GGSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  75 hhlsdedlekalkeiarvLkpgG 97 
                                            +d  +a++++++++ pgG
  gi|518652803|ref|YP_008142323.1| 162 ----IPDPWDAVENMKKHIVPGG 180
                                       ....3466789999999999998 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   5.1e-09     6e-06       1      99 []      90     182 ..      90     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 5.1e-09
                   Methyltransf_12   1 LeiGcGtGsllrallekl.pdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvl 76 
                                       Le G+GtGsl+  +l+++ +  +++ +Di++s i+ a+    +    +  n+e  + d+ ++  ++++D+ ++    
  gi|518652803|ref|YP_008142323.1|  90 LEAGAGTGSLSYSILKAIgSKGKLVTMDINKSTIDIARGNVERFMLPD--NWETIHGDIRSDNLPGKYDAAIL---- 160
                                       89********************************99999999988754..4444444444444446***9875.... PP

                   Methyltransf_12  77 hhlkdirevldnirklLkpgGrl 99 
                                         ++d+ ++++n++k+++pgG+l
  gi|518652803|ref|YP_008142323.1| 161 -DIPDPWDAVENMKKHIVPGGYL 182
                                       .579*****************87 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   7.3e-08   8.7e-05      38      94 ..      76     132 ..      71     208 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.3e-08
                                       HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHH CS
                   Ubie_methyltran  38 fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklke 94 
                                       ++++  + ++g+ +l+  +Gtg l++++++++g+kgk+v +Din++ +++++  +++
  gi|518652803|ref|YP_008142323.1|  76 YIIHAAGILPGTCILEAGAGTGSLSYSILKAIGSKGKLVTMDINKSTIDIARGNVER 132
                                       5677788899****************************************9988876 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.2e-07   0.00014      35     103 ..      89     160 ..      78     197 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.2e-07
                                       EEEET-TTSHHHHHHHHHTTC.E.EEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTSTTS-EEEEEE CS
                               MTS  35 vlDlGcGaGvlgaalakespeae.vtlvdvdarAlesakenleankle..vevvasdvleeveekkfdlivs 103
                                       +l  G+G+G l+ +++k+  +   ++ +d+++  +++a+ n+e+  l    e+++ d+ ++  ++k+d+ + 
  gi|518652803|ref|YP_008142323.1|  89 ILEAGAGTGSLSYSILKAIGSKGkLVTMDINKSTIDIARGNVERFMLPdnWETIHGDIRSDNLPGKYDAAIL 160
                                       7889*********99998766544**********************9999**********9999****8775 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.7e-07   0.00081       1      95 [.      90     183 ..      90     184 .. 0.89

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.7e-07
                                       EEET-TTSHHHHHHHHTT...SEEEEEES-HHHHHHHHHHCCHHT-..EEEETTEECCCTSS-TT-EEEEEEES-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg...arvvgvDlskemlklakekaseegl..kvefvvadaeklpfednsfDlvvssevlh 72 
                                       L++G+GtG+l+  + k+    +++v++D++k ++++a+ ++++  l  + e +++d+++ +++  ++D+ ++     
  gi|518652803|ref|YP_008142323.1|  90 LEAGAGTGSLSYSILKAIgskGKLVTMDINKSTIDIARGNVERFMLpdNWETIHGDIRSDNLPG-KYDAAILD---- 161
                                       799*******999996666999***************999999888998899******866666.99998776.... PP

                                       C-CCHHHHHHHHHHHEEEEEEEE CS
                   Methyltransf_11  73 hvedpekalkeiaRvLkpgGllv 95 
                                        ++dp +a++++++   pgG+lv
  gi|518652803|ref|YP_008142323.1| 162 -IPDPWDAVENMKKHIVPGGYLV 183
                                       .79******************98 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.3e-06    0.0027      69     132 ..      81     145 ..      57     202 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.3e-06
                                       TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC.SEEEEES- CS
                              PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle.nvivvvgD 132
                                         + +g+ +Le G+G+G l+  + + +g+kg++v+++  k+ ++ a+ n+++  l  n  +++gD
  gi|518652803|ref|YP_008142323.1|  81 AGILPGTCILEAGAGTGSLSYSILKAIGSKGKLVTMDINKSTIDIARGNVERFMLPdNWETIHGD 145
                                       45789999*******************************************98764488888887 PP

>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.8e-05     0.021      17      73 ..      82     149 ..      56     161 .. 0.84
   2 ?   -0.0   0.0      0.68   8.1e+02      32      77 ..     178     224 ..     175     236 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-05
                                       T-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSS............HHH.TTEEEECS-CCCS CS
                              FtsJ  17 klfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpm............apl.pgvttiqgditdp 73 
                                       +++ pg+ +++ ga++G+ s  +l+ +g kgk+v +D+++               l ++ +ti+gdi++ 
  gi|518652803|ref|YP_008142323.1|  82 GIL-PGTCILEAGAGTGSLSYSILKAIGSKGKLVTMDINKStidiargnverfM-LpDNWETIHGDIRSD 149
                                       434.778899****************************9998999888876533.25999*******986 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.68
                                       TSHHHHHHCCT.T..-SEEEEEESSSSHHHTTEEEECS-CCCSSHHH CS
                              FtsJ  32 PGgwsqvllqrlga.kgkvvavDlqpmaplpgvttiqgditdpetie 77 
                                       PGg+    + ++++ +++v+a+   +   l+ v++i+ +i   e++ 
  gi|518652803|ref|YP_008142323.1| 178 PGGYLVTYSPNFNQaEKNVIAMKKLNFYVLETVELIKRNIIVRENAT 224
                                       77777777777765468899999988877788888888875555544 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   2.2e-05     0.027      23     121 ..      86     188 ..      54     205 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.2e-05
                   Methyltransf_23  23 ggrvLdiGcGtGillevl.rengf..svtgvDlspeaveiae..........kakkaqkdqfdeqeaaepqgkfdlI 86 
                                       g  +L+ G+GtG+l+ ++ ++ g   +++ +D++   ++ia+          +  + + d       ++  gk+d +
  gi|518652803|ref|YP_008142323.1|  86 GTCILEAGAGTGSLSYSIlKAIGSkgKLVTMDINKSTIDIARgnverfmlpdNWETIHGDIR----SDNLPGKYDAA 158
                                       4489********988777688898899*************9877555544442222222222....444677***98 PP

                   Methyltransf_23  87 vlrevlehvpdppellrqiatllkpgGylllsepl 121
                                       +l      +pdp  ++ ++++++ pgGyl+   p+
  gi|518652803|ref|YP_008142323.1| 159 IL-----DIPDPWDAVENMKKHIVPGGYLVTYSPN 188
                                       87.....79*******************9876665 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.3e-05     0.016      11      88 ..      88     163 ..      83     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.3e-05
                                       EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--.SEEEEES-CTCCHHHHCC..EEEEEEE CS
                   Methyltr_RsmB-F  11 tilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvt.ntivleaDarkidkvlggelfDriLlD 86 
                                        il++ a+ G+    i++ + +kg++v +d+nk+ ++    n++r+ +  n   +++D+r   +  g+  +D ++lD
  gi|518652803|ref|YP_008142323.1|  88 CILEAGAGTGSLSYSILKAIGSKGKLVTMDINKSTIDIARGNVERFMLPdNWETIHGDIRSD-NLPGK--YDAAILD 161
                                       6999*****************************************99976999******975.78886..******* PP

                                       E- CS
                   Methyltr_RsmB-F  87 aP 88 
                                        P
  gi|518652803|ref|YP_008142323.1| 162 IP 163
                                       99 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-05     0.035     161     281 ..      85     208 ..      74     220 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                              PrmA 161 egeevlDvGtGSGiLaiaaak.Lgak.kvvavDiDevAvkvakeNaelNkveaklevalseellk...eekadviva 232
                                       +g+ +l  G+G+G L+   +k +g k k v +Di++ ++++a+ N+e+  + ++ e+ +++++ +    +k+d  + 
  gi|518652803|ref|YP_008142323.1|  85 PGTCILEAGAGTGSLSYSILKaIGSKgKLVTMDINKSTIDIARGNVERFMLPDNWET-IHGDIRSdnlPGKYDAAIL 160
                                       56778999*****9998887735554389********************99999886.4444443233478898777 PP

                              PrmA 233 NILaevlielaedikklvkeggllil.SGilkekaeevaealeqgfelee 281
                                        I  ++  + +e++kk++ +gg+l++ S   ++ +++v++  + +f + e
  gi|518652803|ref|YP_008142323.1| 161 DIP-DP-WDAVENMKKHIVPGGYLVTySPNFNQAEKNVIAMKKLNFYVLE 208
                                       763.44.4668899999999999875477777777777776665555544 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.3e-05     0.099      15      74 ..      86     146 ..      78     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.3e-05
                   Methyltransf_18  15 gsrvaDiGtDHgylpiylvke.gkakkviasDinegplekakeniekagledkievrlsdG 74 
                                       g+ ++  G+  g l++ ++k  g   k + +Din++ ++ a+ n+e+  l d++e++ +d 
  gi|518652803|ref|YP_008142323.1|  86 GTCILEAGAGTGSLSYSILKAiGSKGKLVTMDINKSTIDIARGNVERFMLPDNWETIHGDI 146
                                       5666677777888888877652667799*****************************9985 PP

>> Glyco_hydro_98M  Glycosyl hydrolase family 98
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00013      0.15     163     211 ..     179     226 ..     168     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00013
                   Glyco_hydro_98M 163 GgyldisfcaniWsaalnpiallkkspefkeavekYaenlileekytqe 211
                                       Ggyl ++++ n+ +a+ n ia++k +    e ve  ++n+i+ e  t  
  gi|518652803|ref|YP_008142323.1| 179 GGYL-VTYSPNFNQAEKNVIAMKKLNFYVLETVELIKRNIIVRENATRP 226
                                       9***.**************************************999853 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   0.00025      0.29      75     130 ..     109     163 ..      78     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       HH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE--- CS
                           UPF0020  75 aelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpP 130
                                        + kl+ +D++++ ++ ar N e+  + d +e    d+++ +   g++d+ + + P
  gi|518652803|ref|YP_008142323.1| 109 SKGKLVTMDINKSTIDIARGNVERFMLPDNWETIHGDIRSDN-LPGKYDAAILDIP 163
                                       556799*******************************99766.5568998888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); 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: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 1599.77
//
Query:       gi|518652804|ref|YP_008142324.1|  [L=193]
Description: GMP synthase subunit A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-35  123.2   0.0    1.3e-35  123.0   0.0    1.0  1  GATase         Glutamine amidotransferase class-I
      5e-12   46.0   0.3    4.8e-10   39.6   0.3    2.3  1  Peptidase_C26  Peptidase C26
      4e-05   23.6   0.3    0.00054   19.9   0.3    2.0  1  SNO            SNO glutamine amidotransferase family


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   2.1e-39   1.3e-35       2     187 ..      10     188 ..       9     190 .. 0.88

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 2.1e-39
                                       EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCT.STS-EEE CS
                            GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikeare.nkiPiLG 76 
                                       +iDn+ + t+   + ++++gv+ e++p++ ++       ++ dg+++sgGp s     gk+  ik+++e +  PiLG
  gi|518652804|ref|YP_008142324.1|  10 VIDNGGQWTHREWRVIRSFGVDSEIYPNTVDNTSL----DGLDGLVLSGGPASIDsEVGKLGYIKQYIEtHSYPILG 82 
                                       79*************************99765555....79**************8556777777666669****** PP

                                       ETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEE CS
                            GATase  77 ICLGmQllaiefgrkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddee 153
                                       IC G Q +a+ +g++v k+ + e+ +++  + + ++++++g +++++++ +H++e+++   ++++ +  a s d+++
  gi|518652804|ref|YP_008142324.1|  83 ICVGAQFIALNSGATVSKAIHPEYGKKKVTFIK-SESIFTGIPETINAWESHNDEIKN---LSDEYVLCASS-DTCK 154
                                       ********************6555555555555.88**********************...99998776666.789* PP

                                       EEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHH CS
                            GATase 154 lmeiiekknpfvgvQFHPEststpegpellfnfl 187
                                       + ++ +k++ +++vQFHPE+  t++g+e+++nf+
  gi|518652804|ref|YP_008142324.1| 155 VQAFYHKTKDIFAVQFHPEVNNTEHGTEIFKNFI 188
                                       *******************************983 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.3     8e-14   4.8e-10      98     216 .]      69     173 ..      24     173 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 8e-14
                     Peptidase_C26  98 iraale.rgvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnsl 173
                                       i++ +e ++ PilgiC G q+++   G t+ ++i+            ++ +++   ++++s++  + +  +i+    
  gi|518652804|ref|YP_008142324.1|  69 IKQYIEtHSYPILGICVGAQFIALNSGATVSKAIHP-----------EYGKKKVTFIKSESIFTGIPE--TINAWES 132
                                       5555541578************************94...........344344445888999999887..8888899 PP

                     Peptidase_C26 174 HhqaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                                       H+  ik+l++e+  +A ++   + a+ +++++  +++vQ+HPE
  gi|518652804|ref|YP_008142324.1| 133 HNDEIKNLSDEYVLCASSDTCKVQAFYHKTKD--IFAVQFHPE 173
                                       ******************************77..99******9 PP

>> SNO  SNO glutamine amidotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.3     9e-08   0.00054      28     187 ..      41     192 ..      22     193 .] 0.76

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 9e-08
                                       GGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEEETHHHHHHCCEETTBSS-SS--CCEEEETTT CS
                               SNO  28 kedlaevdaliiPGGestamskliertglyedllefvknsekvvlGtCaGlillskelenelvktlellkvkvkrna 104
                                       +  l+++d+l++ GG + ++   + + g    ++++++  + ++lG C G  +++ + +    k             
  gi|518652804|ref|YP_008142324.1|  41 NTSLDGLDGLVLSGGPA-SIDSEVGKLG---YIKQYIETHSYPILGICVGAQFIALNSGATVSK--------AIHPE 105
                                       56899**********76.5666667777...567788889999*******99999888777666........23467 PP

                                       T-SCCGEEEE.EEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEECTTEEEEEE..ETTEEEESS-GGG..STTHC CS
                               SNO 105 fGrqvdsfek.eldfknliekftavfiraPvieeilddeavkvlyeldgeivvak..qkkilatsfhPel..aeddi 176
                                       +G++  +f k e  f ++ e ++a       i+++  de v  ++    ++ +     k+i+a+ fhPe+  +e+++
  gi|518652804|ref|YP_008142324.1| 106 YGKKKVTFIKsESIFTGIPETINAWESHNDEIKNLS-DEYVLCASSDTCKVQAFYhkTKDIFAVQFHPEVnnTEHGT 181
                                       998776665516668888899999999999998876.66666666666666554421679*********94457788 PP

                                       HHHHHHHHHHC CS
                               SNO 177 rvhdyfveevv 187
                                        + + f+e + 
  gi|518652804|ref|YP_008142324.1| 182 EIFKNFIEVCR 192
                                       99999*99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 1391.32
//
Query:       gi|518652805|ref|YP_008142325.1|  [L=201]
Description: hypothetical protein FACI_IFERC00001G1444 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1439.58
//
Query:       gi|518652806|ref|YP_008142326.1|  [L=132]
Description: iron-dependent repressor [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-17   63.0   0.0    7.5e-17   61.2   0.0    1.8  2  Fe_dep_repr_C   Iron dependent repressor, metal binding and d
    3.8e-05   23.5   0.0    5.8e-05   22.9   0.0    1.3  1  MarR            MarR family
     0.0001   22.1   0.0    0.00016   21.5   0.0    1.2  1  MarR_2          MarR family
    0.00014   22.0   0.0    0.00024   21.2   0.0    1.4  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
    0.00046   20.0   0.0    0.00071   19.4   0.0    1.4  1  TrmB            Sugar-specific transcriptional regulator TrmB
    0.00049   19.6   0.0    0.00096   18.7   0.0    1.4  1  HTH_24          Winged helix-turn-helix DNA-binding
     0.0098   16.1   0.0      0.017   15.3   0.0    1.3  1  HTH_17          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.4   0.0       0.02   14.8   0.0    1.3  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.019   14.7   0.0      0.031   14.0   0.0    1.3  1  LexA_DNA_bind   LexA DNA binding domain
      0.039   14.0   0.0      0.085   12.9   0.0    1.5  2  HTH_29          Winged helix-turn helix
      0.043   13.5   0.0      0.073   12.7   0.0    1.3  1  GntR            Bacterial regulatory proteins, gntR family
      0.052   13.4   0.0      0.091   12.6   0.0    1.4  1  HTH_10          HTH DNA binding domain
      0.099   12.8   0.0       0.21   11.8   0.0    1.5  1  HTH_28          Helix-turn-helix domain
       0.13   12.0   0.0       0.25   11.2   0.0    1.4  1  HTH_IclR        IclR helix-turn-helix domain
       0.14   12.1   0.0       0.35   10.8   0.0    1.7  1  HTH_1           Bacterial regulatory helix-turn-helix protein


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 ?   -1.0   0.0       1.7     2e+03      24      41 ..      31      48 ..      29      55 .. 0.78
   2 !   61.2   0.0   6.3e-20   7.5e-17       1      67 [.      63     128 ..      63     130 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.7
                                      HHCT--CCCHHHHCCCCG CS
                     Fe_dep_repr_C 24 dvlgvdweeaheeAerlE 41
                                      ++l++++  a+e  +rlE
  gi|518652806|ref|YP_008142326.1| 31 EILNIKPPTAYELIKRLE 48
                                      678888888888888888 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 6.3e-20
                                       -HHHHHHHHHHHHHHHHHHHHHHHHCT--CCCHHHHCCCCGGGS-HHHHHHHHHHCT-.SB-TTS-B CS
                     Fe_dep_repr_C   1 TekGrelAkrlvrrhrllerfLvdvlgvdweeaheeAerlEhalseelierldellgfpeecPhgdp 67 
                                       T+ G+ +  +++  hr+le++L++  gv+ ++a+e+ e++++ +++ +i++l + lg+p++cPhg+p
  gi|518652806|ref|YP_008142326.1|  63 TPYGNTIYSEIIMAHRTLEVMLTK-SGVNSDRACEQIEKIDYLMDDTSIQKLFTSLGNPQTCPHGKP 128
                                       999*******************77.****************************************99 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.8e-08   5.8e-05       2      50 ..       6      56 ..       5      58 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.8e-08
                                      -HHHHHHHHHHHHSTTEEHH..HHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  2 tltqfviLrilyeqgplsvs..eLakklgvskstvtrvldrLekkGlieRs 50
                                      t+ + ++++ ++++ +  +    +a+ l+++++t+ ++++rLe k+ ieR+
  gi|518652806|ref|YP_008142326.1|  6 TRKERDCIVAIHDSSGFPLRlfNIAEILNIKPPTAYELIKRLESKEIIERK 56
                                      55566666777777776666669***************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.4e-07   0.00016       3      54 ..       5      56 ..       3      58 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.4e-07
                                      --HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2  3 ltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      +t+ +++ + a++++ g +l+   +a+ l+++++++  ++krL+++  +er+
  gi|518652806|ref|YP_008142326.1|  5 ITRKERDCIVAIHDSSGFPLRLFNIAEILNIKPPTAYELIKRLESKEIIERK 56
                                      7999*************888******************************97 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     2e-07   0.00024      26      53 ..      27      54 ..      12      58 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2e-07
                                      HHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 26 kdlaerLnvspssVsemlkkLekdGyve 53
                                       ++ae+Ln++p+++ e +k+Le+++ +e
  gi|518652806|ref|YP_008142326.1| 27 FNIAEILNIKPPTAYELIKRLESKEIIE 54
                                      57********************998765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   5.9e-07   0.00071      27      58 ..      28      59 ..       4      73 .. 0.89

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 5.9e-07
                                      HHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB 27 eiaeelgvprskvYevLrsLedkGlVerekgr 58
                                       iae+l++  +++Ye +++Le+k ++er+ g 
  gi|518652806|ref|YP_008142326.1| 28 NIAEILNIKPPTAYELIKRLESKEIIERKNGV 59
                                      69**************************9875 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0     8e-07   0.00096      23      48 .]      29      54 ..      27      54 .. 0.96

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 8e-07
                            HTH_24 23 LAerlglSpstvnrrlkrLeeeGlIk 48
                                      +Ae l++ p+t  + +krLe++++I+
  gi|518652806|ref|YP_008142326.1| 29 IAEILNIKPPTAYELIKRLESKEIIE 54
                                      9************************7 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.5e-05     0.017       7      31 ..      29      56 ..      28      63 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.5e-05
                            HTH_17  7 aAelLgvsrstvyrlir...rgelpaak 31
                                      +Ae+L++++ t+y+li+   ++e++  k
  gi|518652806|ref|YP_008142326.1| 29 IAEILNIKPPTAYELIKrleSKEIIERK 56
                                      69**************755577776655 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   1.7e-05      0.02      21      58 ..      23      60 ..       5      64 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.7e-05
                                      EHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEEETEEEE CS
                         HTH_Crp_2 21 pltqeelAsmlGltretvsrilseLkreglisrgrrir 58
                                      pl    +A++l++ + t   ++++L+ + +i+r+++++
  gi|518652806|ref|YP_008142326.1| 23 PLRLFNIAEILNIKPPTAYELIKRLESKEIIERKNGVI 60
                                      6666679*************************764444 PP

>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   2.6e-05     0.031      14      61 ..      12      58 ..       5      59 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.6e-05
                                      HHHHHHHHHSS---HHHHHHHHTS-.HHHHHHHHHHHHHTTSEE-GGG CS
                     LexA_DNA_bind 14 likasieetgypPsireiaralglkSpsaveehLkaLerKGyierdpg 61
                                       i+a  ++ g+p    +ia+ l++k p ++ e  k+Le K +ier++g
  gi|518652806|ref|YP_008142326.1| 12 CIVAIHDSSGFPLRLFNIAEILNIK-PPTAYELIKRLESKEIIERKNG 58
                                      577777899999999**********.8899999************997 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   7.1e-05     0.085      14      41 ..      25      52 ..      14      59 .. 0.86
   2 ?   -3.2   0.0       7.5     9e+03       6      21 ..      83      97 ..      82      98 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGl 41
                                      +  +iA++l++ ++t y  +kr e +++
  gi|518652806|ref|YP_008142326.1| 25 RLFNIAEILNIKPPTAYELIKRLESKEI 52
                                      5679*******************99985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 7.5
                            HTH_29  6 lllaeGvstvsqiAkl 21
                                      +l + Gv +  +++++
  gi|518652806|ref|YP_008142326.1| 83 MLTKSGV-NSDRACEQ 97
                                      5667788.78888875 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.1e-05     0.073      21      59 ..      21      58 ..      10      59 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
                                      TSB---HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT CS
                              GntR 21 GdkLPsereLaaefgVsrttvReALrrLeaeglverrqg 59
                                      G +L +   +a+ ++++ +t  e ++rLe++ ++er++g
  gi|518652806|ref|YP_008142326.1| 21 GFPL-RLFNIAEILNIKPPTAYELIKRLESKEIIERKNG 58
                                      5567.77789***************************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 ?   12.6   0.0   7.6e-05     0.091      28      50 ..      28      50 ..      24      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.6e-05
                            HTH_10 28 eLAkelGIskstlsehLrkaesk 50
                                       +A++l+I+++t++e +++ esk
  gi|518652806|ref|YP_008142326.1| 28 NIAEILNIKPPTAYELIKRLESK 50
                                      79*******************98 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00017      0.21      18      38 ..      29      49 ..      18      55 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
                            HTH_28 18 aArelgisrrtvyrWikryee 38
                                      +A++l+i + t y +ikr+e+
  gi|518652806|ref|YP_008142326.1| 29 IAEILNIKPPTAYELIKRLES 49
                                      8*****************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00021      0.25      18      50 ..      23      55 ..      14      56 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00021
                                      S-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR 18 eltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +l+l  +A+ + + ++t++ l++ L+   ++e+
  gi|518652806|ref|YP_008142326.1| 23 PLRLFNIAEILNIKPPTAYELIKRLESKEIIER 55
                                      699**********************98877775 PP

>> HTH_1  Bacterial regulatory helix-turn-helix protein, lysR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0003      0.35      20      59 ..      30      66 ..      30      67 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                                      HHHHTS-HHHHHHHHHHHHHHHTS-SEEESSSEEEE-HHH CS
                             HTH_1 20 AeeLglsqpavsrqikrLEeelgvpLfeRtgrglrLTeaG 59
                                      Ae L++ +p++   ikrLE+    +++eR+++ + LT++G
  gi|518652806|ref|YP_008142326.1| 30 AEILNIKPPTAYELIKRLES---KEIIERKNGVIYLTPYG 66
                                      889****************8...5999**77789999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       629  (0.0350828); expected 358.6 (0.02)
Passed bias filter:                      561  (0.0312901); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 912.44
//
Query:       gi|518652807|ref|YP_008142327.1|  [L=189]
Description: phosphoglycerate mutase/fructose-2,6-bisphosphatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-31  107.9   0.0    2.4e-30  105.7   0.0    1.8  1  His_Phos_1  Histidine phosphatase superfamily (branch 1)


Domain annotation for each model (and alignments):
>> His_Phos_1  Histidine phosphatase superfamily (branch 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   1.4e-34   2.4e-30       1     185 [.       4     171 ..       4     176 .. 0.90

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 1.4e-34
                                       EEEEE---BTTB--.....TT----B-HHHHHHHHHHHHHHTTS---EEEE-SSHHHHHHHHHHHHCTT--EEE-GG CS
                        His_Phos_1   1 lyLvRHGetewnaegr.lqgrtdvpLteeGreqAealaerlagepidaiysSplkRarqTaeliaealglpveldeg 76 
                                       ++L+RHGe+  n++g+  +  +   LteeG+eqA+ ++e l+g ++d i+sSp+ Ra++Ta++i + l+l++++d +
  gi|518652807|ref|YP_008142327.1|   4 VILIRHGESYTNRNGIlSSELNRYRLTEEGIEQARFTGEQLNGLKFDGIISSPILRAVETANIINQYLNLEIKTDNR 80 
                                       69**************555567789**************************************************** PP

                                       GS----GGGTT-B.HHHHHH..HSHHHHHHHHH-GGG-BS-BHHHHHHHHHHHHHHHHHHTTTSEEEEEE-HHHHHH CS
                        His_Phos_1  77 LrEidfGdweglttaeiaeeypeeleawlrdpadvrppggEsledvaaRvaaaleelaarhegetvlvVsHggvira 153
                                         E dfG++ g+   +i ++        +++       g Es+e  ++R+ + ++  +    g + +vVsH  +ir+
  gi|518652807|ref|YP_008142327.1|  81 AIESDFGEYNGKRIVDIPDK-------SRDE------LGMESFESQTSRMIDLINSYT----G-NYIVVSHSFPIRC 139
                                       ************88888777.......2222......259**********98876544....4.479********** PP

                                       HHHHHHT--GGGGGGB---TT-EEEEEE-SS- CS
                        His_Phos_1 154 llarllglpleelrrleldnaslsvlefdegg 185
                                       +la +l+l   e   l++ +as+sv+++++++
  gi|518652807|ref|YP_008142327.1| 140 VLANYLKLGEIESFGLDIRHASMSVINVEKEK 171
                                       ********9999999999*********99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1494.40
//
Query:       gi|518652808|ref|YP_008142328.1|  [L=638]
Description: hypothetical protein FACI_IFERC00001G1447 [Ferroplasma acidarmanus fer1]
Scores for complete 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-71  239.1   0.1    3.8e-71  238.3   0.1    1.4  1  Thioredox_DsbH  Protein of unknown function, DUF255
    1.4e-10   41.2   0.0    2.7e-10   40.3   0.0    1.6  1  Thioredoxin_7   Thioredoxin-like
    0.00069   19.0   0.1      0.043   13.1   0.2    2.4  2  GlcNAc_2-epim   N-acylglucosamine 2-epimerase (GlcNAc 2-epime
     0.0007   19.2   5.9       0.12   11.9   0.2    2.5  2  Glyco_hydro_76  Glycosyl hydrolase family 76
     0.0065   16.9   0.0      0.018   15.4   0.0    1.8  1  Thioredoxin_2   Thioredoxin-like domain


Domain annotation for each model (and alignments):
>> Thioredox_DsbH  Protein of unknown function, DUF255
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.3   0.1     1e-74   3.8e-71       2     162 ..       2     162 ..       1     163 [. 0.98

  Alignments for each domain:
  == domain 1  score: 238.3 bits;  conditional E-value: 1e-74
                    Thioredox_DsbH   2 nrlaeekspYllqhaknpvdWypwgeealekakeedkpillsiGysachWChvmekesfedeevaallnesfvsvkv 78 
                                       n+la+e+spYll+h++npvdW pw++ea++ ak+edkp++lsiGys+chWChvme+esf+d+eva+ +n++fv++kv
  gi|518652808|ref|YP_008142328.1|   2 NKLANENSPYLLEHSNNPVDWNPWSDEAFNLAKKEDKPVFLSIGYSSCHWCHVMEQESFTDPEVAKRMNSTFVCIKV 78 
                                       9**************************************************************************** PP

                    Thioredox_DsbH  79 DreerPdldkiymeavqaltgsggWPlnvfltpdlkpffggtYfpkeeregrpgflevlekiaelweeereeleeea 155
                                       Dree Pd+d++ym+++q++tg+ggWPlnv+ltpd+kp+f+ tY+p+ +r+++ g++e++e+i+ lw+++r e+e++ 
  gi|518652808|ref|YP_008142328.1|  79 DREEMPDVDSLYMTFSQVMTGTGGWPLNVILTPDRKPIFAFTYIPRVSRNNMIGIMELAENIDYLWKNKRGEMEKNG 155
                                       ***************************************************************************99 PP

                    Thioredox_DsbH 156 eelleal 162
                                       +e +++l
  gi|518652808|ref|YP_008142328.1| 156 DEAISRL 162
                                       9988776 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.0   7.7e-14   2.7e-10       1      65 [.      21      85 ..      21     111 .. 0.82

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 7.7e-14
                                      ---SSHHHHHHHHHHHT--EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-G CS
                     Thioredoxin_7  1 ewlsdldealakaaergkpvlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterda 65
                                      +w  + dea+  a+++ kpv++ +g s c+ C+++e++  +d+ev++ +++ fv+ +vd +e  +
  gi|518652808|ref|YP_008142328.1| 21 DWNPWSDEAFNLAKKEDKPVFLSIGYSSCHWCHVMEQESFTDPEVAKRMNSTFVCIKVDREEMPD 85
                                      7999*******************************9998888888888***********988765 PP

>> GlcNAc_2-epim  N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.2   1.2e-05     0.043      34     121 ..     219     310 ..     211     325 .. 0.76
   2 ?    3.2   0.0     0.012        44     146     181 ..     471     506 ..     452     512 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.2e-05
                                       HHTT-TTHHHHHHHHHHHTTTTTB.-TTTSSB-SEEETT..EEEE--EEHHHHHHHHHHHHHHH.TTT-TTHHHHHH CS
                     GlcNAc_2-epim  34 aqlgrpgwldlvehGlkflekvlr.daehggyfsalrdg..gvldaskdaYdhaFvllalasal.aageeeakdlld 106
                                       +++g +++l++v+h l+++   +  d+  gg+ +  +d   +    +k  Yd+a +++a++ a+  +g++ +k+++ 
  gi|518652808|ref|YP_008142328.1| 219 KAHGKEEALEMVKHSLRMMYIGGMyDHVGGGFHRYSTDPffRIPHFEKMTYDQAMAIIAYSYAYdVTGDTFYKNVVY 295
                                       5699************9997655526666666555544411456678899************8735799999***** PP

                                       HHHHHHHHHTEETTT CS
                     GlcNAc_2-epim 107 etlavlekhlweeka 121
                                       e++++l++++ ++  
  gi|518652808|ref|YP_008142328.1| 296 EIYKFLKQEMFSRGF 310
                                       ******999877654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.012
                                       HHHHHHHHTT-BTHHHHHHHHHHHHHTTTTGGGGTT CS
                     GlcNAc_2-epim 146 eAmLalaeatgdkeyleraeeiaelvisefadaesg 181
                                         +L l+ea+ ++ yl+ a  + ++++++f+d++sg
  gi|518652808|ref|YP_008142328.1| 471 SGLLSLYEASLNDIYLDYARDLQKTIMDTFYDKTSG 506
                                       5679999***********************999887 PP

>> Glyco_hydro_76  Glycosyl hydrolase family 76
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   1.4   0.00026      0.93     216     258 ..     266     308 ..     262     333 .. 0.86
   2 !   11.9   0.2   3.3e-05      0.12      59     163 ..     436     536 ..     418     548 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00026
                                       -HHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCEEC CS
                    Glyco_hydro_76 216 qwtYnqGtylsgaaylynaTgdekWldrvkgllnatlstffpd 258
                                       + tY q++ + +  y y +Tgd+ +++ v+++ +  ++ +f+ 
  gi|518652808|ref|YP_008142328.1| 266 KMTYDQAMAIIAYSYAYDVTGDTFYKNVVYEIYKFLKQEMFSR 308
                                       68**********************************9999887 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHCCCTCEE-SSSTTCTCSSEHHHHHHHHHHHHHHHHH.....H--HHHHHHHHHHHHHHHHC.B-SCSCC CS
                    Glyco_hydro_76  59 dlitqallaqagenydympanqsrtegnDDqafwglaamtaaernfpeptdepswLalAqavfntqasr.wdeetcg 134
                                       d i ++++ +++  ++y + + s + + DD  f++   ++ +e+     + ++ +L++A+ +++t++++ +d++   
  gi|518652808|ref|YP_008142328.1| 436 DFIMNDMYTDKKLMHSYRNGKSSINGMLDDYSFMVSGLLSLYEA-----SLNDIYLDYARDLQKTIMDTfYDKT--S 505
                                       77889999999999999999999999*****************9.....56666***************66665..4 PP

                                       S-BBSEC..ES..S--SEEEHHHHHHHHHHH CS
                    Glyco_hydro_76 135 GGlrWqiftwn..sgydyknsisngplfqla 163
                                       GG +  + ++    + +y n+i  g +f+++
  gi|518652808|ref|YP_008142328.1| 506 GGFYNGMGNLLvrLKESYDNAIPSGFSFEIG 536
                                       7766555322222566777888777777776 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   5.1e-06     0.018       1      51 [.      33      76 ..      33     119 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.1e-06
                     Thioredoxin_2  1 akgngkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkav 51
                                      ak++ kpv++ +  ++C  C+ +++e +++++v +r     +++ f+   +
  gi|518652808|ref|YP_008142328.1| 33 AKKEDKPVFLSIGYSSCHWCHVMEQESFTDPEVAKR-----MNSTFV--CI 76
                                      6899*******************************9.....555533..33 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (638 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); 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:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.44
# Mc/sec: 4312.01
//
Query:       gi|518652809|ref|YP_008142329.1|  [L=330]
Description: NMD protein affecting ribosome stability and mRNA decay [Ferroplasma acidarmanus fer1]
Scores for 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-36  124.4   3.9    6.5e-36  124.0   3.9    1.1  1  NMD3           NMD3 family
     0.0075   16.4   3.8      0.088   12.9   1.6    2.7  2  Zn-ribbon_8    Zinc ribbon domain
  ------ inclusion threshold ------
      0.046   13.9   0.9       0.42   10.8   0.1    2.4  2  NOB1_Zn_bind   Nin one binding (NOB1) Zn-ribbon like
      0.049   13.1   2.3        1.5    8.3   0.1    2.7  2  zf-ribbon_3    zinc-ribbon domain
       0.11   12.1   0.5         21    4.9   0.1    2.6  2  zf-RRN7        Zinc-finger of RNA-polymerase I-specific TFIIB
       0.16   12.0   2.9       0.72    9.9   1.5    2.2  2  DZR            Double zinc ribbon
        1.2    9.2  10.3        2.5    8.1   4.8    2.9  2  Prok-RING_1    Prokaryotic RING finger family 1


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.0   3.9   2.5e-39   6.5e-36       1     243 []       3     226 ..       3     226 .. 0.83

  Alignments for each domain:
  == domain 1  score: 124.0 bits;  conditional E-value: 2.5e-39
                              NMD3   1 CcrCGkeieelinglCedCllkevditegiekievevCkeCgrylpkgkWvkaeleseellaeclkklvekgLkvse 77 
                                       C+ CG+++     glC++Cl +++++ +  ++++++vC++Cg+++ ++kW        +  + ++k+++++ +    
  gi|518652809|ref|YP_008142329.1|   3 CILCGENEA-YKLGLCRSCLSDKIHLKS--DNMDLTVCPKCGAVRLNKKWH-----YDNADKYIIKSATSHVIM--- 68 
                                       ********6.6588********998766..78*************999**3.....334445566666555565... PP

                              NMD3  78 eveevkvelvdaefiwtephskrikvkvtvqgevrgenetilqqevevevkvkrqqCprCsriaggyyeaivQvRqk 154
                                         +e k+  v++    +   +++i +++ v+ +  g  +  +++e+++++k+ ++ Cp C++++g+yye+++Q+R+ 
  gi|518652809|ref|YP_008142329.1|  69 -DKEDKISSVTSY---NIG-ENEISMELVVEDRNLG--D--VEKEISINLKTYKESCPVCNKVTGSYYESVIQLRTY 136
                                       .345577666666...444.7889*******99966..3..67*********************************9 PP

                              NMD3 155 relteeehkrtfelleqli...lkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedk 228
                                        +   +  +++++ + +++   +khd ++fis+i++ keGlD+y+g+k++A k+ + ++  + +++k +++l+++ k
  gi|518652809|ref|YP_008142329.1| 137 TTAYGKILEEAKDTIVKFMknlNKHDPNSFISRIDTLKEGLDIYLGKKEDAVKIDKLMELDYFCNMKITKSLAGR-K 212
                                       55555555555555555556668****************************************************.7 PP

                              NMD3 229 ksgkevyrltysvrl 243
                                       + +k+ +r+t +vr+
  gi|518652809|ref|YP_008142329.1| 213 D-SKDLFRYTHLVRI 226
                                       7.9***********8 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   1.6   3.4e-05     0.088       8      38 ..      17      47 ..       2      49 .. 0.73
   2 ?    2.6   0.0     0.058   1.5e+02      23      34 ..     110     121 ..      99     124 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.4e-05
                       Zn-ribbon_8  8 CeeCghefevlqsis.dapltaCPeCgs.evrr 38
                                      C++C +  ++++  s   +lt+CP+Cg+ ++ +
  gi|518652809|ref|YP_008142329.1| 17 CRSCLS--DKIHLKSdNMDLTVCPKCGAvRLNK 47
                                      888884..45554552455777*****998877 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.058
                       Zn-ribbon_8  23 dapltaCPeCgs 34 
                                       +  ++ CP C++
  gi|518652809|ref|YP_008142329.1| 110 KTYKESCPVCNK 121
                                       444556****86 PP

>> NOB1_Zn_bind  Nin one binding (NOB1) Zn-ribbon like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   0.00017      0.42      11      38 ..      17      49 ..      10      81 .. 0.76
   2 ?    0.8   0.1      0.22   5.6e+02       4      18 ..     109     123 ..     107     129 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00017
                      NOB1_Zn_bind 11 ChaCfk.....vtkdmtkkFCpkCGnktLkrva 38
                                      C++C +        +m+   CpkCG   L++  
  gi|518652809|ref|YP_008142329.1| 17 CRSCLSdkihlKSDNMDLTVCPKCGAVRLNKKW 49
                                      999998665422366*************99954 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.22
                      NOB1_Zn_bind   4 vkswvlrChaCfkvt 18 
                                       +k++   C  C kvt
  gi|518652809|ref|YP_008142329.1| 109 LKTYKESCPVCNKVT 123
                                       788889999999887 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.1   0.00059       1.5      18      24 ..      36      42 ..      33      45 .. 0.62
   2 ?    3.5   0.5     0.019        49       3      11 ..     114     122 ..     113     125 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00059
                       zf-ribbon_3 18 vCpyCGt 24
                                      vCp+CG+
  gi|518652809|ref|YP_008142329.1| 36 VCPKCGA 42
                                      5666654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.019
                       zf-ribbon_3   3 vrCPnCGap 11 
                                        +CP C+++
  gi|518652809|ref|YP_008142329.1| 114 ESCPVCNKV 122
                                       58****997 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0    0.0092        24       6      14 ..      36      44 ..      33      53 .. 0.74
   2 ?    4.9   0.1    0.0081        21       3      12 ..     112     121 ..     110     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.0092
                           zf-RRN7  6 pCgvCgcrs 14
                                      +C+ Cg+++
  gi|518652809|ref|YP_008142329.1| 36 VCPKCGAVR 44
                                      799999943 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0081
                           zf-RRN7   3 kgppCgvCgc 12 
                                       +++ C+vC+ 
  gi|518652809|ref|YP_008142329.1| 112 YKESCPVCNK 121
                                       7899****96 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.5   0.00028      0.72       1      41 [.       3      48 ..       3      51 .. 0.78
   2 ?    0.6   0.0      0.22   5.7e+02      28      36 ..     113     121 ..      91     126 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00028
                               DZR  1 CpqCgeelppdarfCseCgtklkavaa....edrCpsCgek.vdpe 41
                                      C  Cge+   +   C  C ++    ++     ++Cp+Cg+  ++++
  gi|518652809|ref|YP_008142329.1|  3 CILCGENEAYKLGLCRSCLSDKIHLKSdnmdLTVCPKCGAVrLNKK 48
                                      88899999999999****99954444456799*******9855555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                               DZR  28 edrCpsCge 36 
                                       ++ Cp C++
  gi|518652809|ref|YP_008142329.1| 113 KESCPVCNK 121
                                       567777776 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 ?    8.1   4.8   0.00096       2.5       7      29 ..      17      43 ..       1      54 [. 0.72
   2 ?    2.9   0.2      0.04     1e+02       3      12 ..     112     121 ..     110     125 .. 0.84

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00096
                       Prok-RING_1  7 CpvC.gke..lkee.dDiVvCpeCgtp 29
                                      C  C +++  lk++ +D+ vCp+Cg++
  gi|518652809|ref|YP_008142329.1| 17 CRSClSDKihLKSDnMDLTVCPKCGAV 43
                                      5555322311333359*********97 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.04
                       Prok-RING_1   3 tgkkCpvCgk 12 
                                       ++++CpvC+k
  gi|518652809|ref|YP_008142329.1| 112 YKESCPVCNK 121
                                       6899****97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1151  (0.0641977); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        94  (0.0052429); 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: 0.52u 0.29s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2167.59
//
Query:       gi|518652810|ref|YP_008142330.1|  [L=415]
Description: hypothetical protein FACI_IFERC00001G1449 [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  160.5   0.0    8.6e-47  159.9   0.0    1.3  1  Amidinotransf  Amidinotransferase


Domain annotation for each model (and alignments):
>> Amidinotransf  Amidinotransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.9   0.0   4.8e-51   8.6e-47       1     338 [.      15     412 ..      15     414 .. 0.87

  Alignments for each domain:
  == domain 1  score: 159.9 bits;  conditional E-value: 4.8e-51
                                       E----HHHHT--TTTTTTTT-SS---HHHHHHHHHHHHHHHHTTT-EEEEHHHHHHHHCTSHHHHHHHHHHHSSTT. CS
                     Amidinotransf   1 mvrPgrflenltetasdnllqddeiilekaqkEHdafvqvLrekGveVlvledllaealeaeearkekldeklles. 76 
                                       m+rPg +++  + ++   l+ +++++ + a kEH+++ ++Lre+Gv+V +le+l  +  e++  +++kl ek+++  
  gi|518652810|ref|YP_008142330.1|  15 MHRPGTEITYAMLAPKPFLF-ERPFNYSIANKEHQNLEDTLRENGVKVDLLENLIVDEAEKKASFRQKLEEKIMALv 90 
                                       9*********8888888766.*********************************99777777777777777766541 PP

                                       TTITTT.......................GGGS-S-HHHHHHHHHHHHH----EEE---GGGG-TTTTEEEEBSEEE CS
                     Amidinotransf  77 elgikl.......................gvklseeikiekleladkatsnnsflipplpnlvFtrdwfstigggvv 130
                                       ++                              l +e  i+ +e +   +  + +   pl nl+F+rd+++  + gv+
  gi|518652810|ref|YP_008142330.1|  91 NFYG-TmesveeakkdmeknikyvdplslFQALIMEPSIDLKEYVPGIQYPRVYSNLPLANLYFMRDQQAV-SSGVL 165
                                       3333.2599******************975566666677778888888899999999************97.679** PP

                                       E---SSGGGHHHHHHHHHHHHHSHTSB-EEEEE-TTS--TT----GGGEEEEETTEEEEEESSSS-HHHHHHHHHHH CS
                     Amidinotransf 131 lnpmaapnRrrErllaeliykkhpgvkvakvldisgkeeesktlEGGdfvvlskgvvaigvssRtdeegieelakkl 207
                                       l++m+ ++Rr+E+  + + + +        +l+ ++k+++ +++EGGdf++ +++ ++ g ++Rtde g+ e  ++ 
  gi|518652810|ref|YP_008142330.1| 166 LGKMKMQQRRKETDITSFVFSE--------ILGAKTKKITEGYFEGGDFIPCGDFCLI-GTGNRTDETGAMEAINSG 233
                                       ********************99........89*********************99876.*********987777665 PP

                                       HHT....TS-SEEEEEE--GGSS..TS-GGGTEEEEETTEEEE-HHHH.TT-E...........SS-HHHHHHHHTT CS
                     Amidinotransf 208 fyk....tvafkviaieipkgra..imHldtvftvvdddavvclpsildaegv...........kakereavaqaLk 267
                                        ++     ++   + + ++ +     mHldt f++ ++  ++   +  + +++           +++ ++++++ Lk
  gi|518652810|ref|YP_008142330.1| 234 IFNfptvAIITNPLYDFMDGHDVmvNMHLDTYFNIPAKGMAITSVELARVARAkiytrdreghyAQETETTLYDFLK 310
                                       444244423333333333333331259***********999999999999888999********999********** PP

                                       -SS-EEEE-CS-SS-B---S-EEEETTEEEEETTGHHHHHHHHHT...............................T CS
                     Amidinotransf 268 ekgleiIeigeeeqwnfggNvLelkpgvvvaydrntvtnekleea...............................g 313
                                        +g+e+I  g  eq  + +N+L+l++ ++va d+ +v +++l e                                g
  gi|518652810|ref|YP_008142330.1| 311 GEGYEFINLGISEQLSYSSNFLTLSDRKIVAIDSSKVIKKLLAENvfdtdtrqkiikdmelksgkmfpdsdamaksG 387
                                       ******************************************999******************************** PP

                                       -EEEEE-HTTTGGGS--TTTT-EEE CS
                     Amidinotransf 314 ievievpiselerGgGgarCmsapl 338
                                       i+vi++++se++ G+Gga+Cm+  +
  gi|518652810|ref|YP_008142330.1| 388 IDVIKIDLSEITGGYGGAHCMTSAI 412
                                       **********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (415 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       874  (0.0487478); expected 358.6 (0.02)
Passed bias filter:                      626  (0.0349155); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3017.92
//
Query:       gi|518652811|ref|YP_008142331.1|  [L=209]
Description: 30S ribosomal protein S3Ae [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-47  160.8   2.3    3.4e-47  160.7   2.3    1.0  1  Ribosomal_S3Ae  Ribosomal S3Ae family
  ------ inclusion threshold ------
        1.8    8.3   9.9      0.058   13.1   3.9    1.6  2  Cas9-BH         Bridge helix of CRISPR-associated endonucleas


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 !  160.7   2.3   3.8e-51   3.4e-47       4     200 ..       7     192 ..       4     194 .. 0.97

  Alignments for each domain:
  == domain 1  score: 160.7 bits;  conditional E-value: 3.8e-51
                                       ---S-TCCSEEEEEEEB-TTSSSSEEEEEEEE--BSSSESHHSHTT-EEEEESHHHHTCSHTSSSEEEEEEEEEEES CS
                    Ribosomal_S3Ae   4 kkvvDkfkkKeWydvkaPslfgkreiGktlvnrtqgtkiaseklkgrvvevslaDLtndekeqafrklklkieevqg 80 
                                         ++Dk+k+K+Wy++ aPs+fg++eiG  +         +++ +++r++ v ++ +t+++ ++a   + ++i++++g
  gi|518652811|ref|YP_008142331.1|   7 STTKDKWKEKSWYTIVAPSYFGEKEIGLSPS-------ADPKYMINRTIAVPVSTFTGNF-KKASSMVLFQIDNCEG 75 
                                       5789***************************.......**********************.568************* PP

                                       SEEEEEEEEEEE-HHHHHHH--SSB-EEEEEEEEEESSSEEEEEEEEEEE-STTB---HHHHHHHHHHHHHHHHHHH CS
                    Ribosomal_S3Ae  81 knaltnFkgmeltrDklrslvrkwsslIeaivdvktkDgyllrvfvvafTkkrnsYakssqkkaIrkkmveilteea 157
                                       k+++t+F g+e+++D +r++vr+++++ ++++dvkt+D y + v+ v + +++   ++ ++ ++Ir ++v+++ ++a
  gi|518652811|ref|YP_008142331.1|  76 KRCTTKFIGHEVSDDTIRRMVRRRRERLDIVTDVKTSDLYNVAVKLVLVADQK---LTGTKRSEIRSTAVDYILNKA 149
                                       *****************************************************...********************* PP

                                       HHS-HHHHHHHHTTTHHHHHHHHHHTTTS-EEEEEEEEEEEEE CS
                    Ribosomal_S3Ae 158 seldlkelvkklipeslgkeiekeakkIyplrnveirKvkvlk 200
                                       +e+dl ++ +++i + +  +  ++ k++yp++++e+rK+++ k
  gi|518652811|ref|YP_008142331.1| 150 KEMDLGTFANYVIGDAVYGDFVNSLKDVYPIKKIEVRKTEIGK 192
                                       **************99***********************9876 PP

>> Cas9-BH  Bridge helix of CRISPR-associated endonuclease Cas9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.3      0.95   8.5e+03      12      15 ..       3       6 ..       2       7 .. 0.61
   2 ?   13.1   3.9   6.5e-06     0.058       6      23 ..      91     108 ..      91     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 0.95
                                      HHHH CS
                           Cas9-BH 12 eRRR 15
                                      +RRR
  gi|518652811|ref|YP_008142331.1|  3 DRRR 6 
                                      5665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.5e-06
                                       HHHHHHHHHHHHHHHHHH CS
                           Cas9-BH   6 gsRRRleRRReRLhlLqe 23 
                                       + RR+  RRReRL+++ +
  gi|518652811|ref|YP_008142331.1|  91 TIRRMVRRRRERLDIVTD 108
                                       67999999******9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1510.76
//
Query:       gi|518652812|ref|YP_008142332.1|  [L=631]
Description: hypothetical protein FACI_IFERC00001G1451 [Ferroplasma acidarmanus fer1]
Scores for 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-68  229.2  26.0      4e-68  229.2  26.0    3.6  3  DUF3494   Protein of unknown function (DUF3494)


Domain annotation for each model (and alignments):
>> DUF3494  Protein of unknown function (DUF3494)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.5     0.025   4.5e+02      40      58 ..      60      87 ..      25     141 .. 0.44
   2 !  229.2  26.0   2.2e-72     4e-68       1     209 []     144     349 ..     144     349 .. 0.98
   3 ?  -10.1  12.4         1   1.8e+04       9     150 ..     417     559 ..     409     617 .. 0.40

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.025
                                      TEES--......EE-TT--........H CS
                           DUF3494 40 estsglvl.tGkvyaadaa........a 58
                                      + t  +v+ +G+  +++ +         
  gi|518652812|ref|YP_008142332.1| 60 SGTQWNVVlNGTSRTSTSSsivfsevnN 87
                                      3333333335554444444222222220 PP

  == domain 2  score: 229.2 bits;  conditional E-value: 2.2e-72
                                       EEESSEEE-TT-EEESSEEEESSS-.GGEES--B-STT.BTTEES--.....EE-TT--HH...HHHHHHHHHHHHH CS
                           DUF3494   1 ilaksgvtntGstvitGdiGvspas.taitGfadelat.gtestsglvltGkvyaadaaaatpatltqAvadletAy 75 
                                       ilak+g++ntG+t+i G+iGvspas t+itG+++++++ g++sts++v tG+vyaa++a++tp+tlt+Av d++tAy
  gi|518652812|ref|YP_008142332.1| 144 ILAKTGISNTGTTSIVGNIGVSPASsTYITGLSLTMNSsGQFSTSSMV-TGNVYAATYASPTPSTLTTAVGDMQTAY 219
                                       79*********************************9666*********.8*************************** PP

                                       HHHHSSS-TT-EEE--SB-TTEEEESEEEEESS-EEE-SS-EEEE-TT-TT--EEEEESS-EEE-TT--EEEETT-- CS
                           DUF3494  76 nalagrslpditelgagelggrtLapGvYkstsavtittgdltLDaqGdanavwiFqiagtLtvasgssvvLinGAq 152
                                       +++agr++p++ +lgag+l+g+tL pG+Yk+ ++v+i+t  +tL  +G++++vwiFqi+g Lt ++g++++L +GAq
  gi|518652812|ref|YP_008142332.1| 220 TNAAGRTNPNYVNLGAGDLNGMTLVPGLYKWGTGVSIST-SITL--TGNSSSVWIFQISGGLTFGNGAHIILSGGAQ 293
                                       **********99*************************66.****..******************************* PP

                                       GGGEEEEESS-EEE-TT-EEEEEEEESS-EEE-TT-EEEEEEEESSSEEEESS-EEE CS
                           DUF3494 153 aknvfWqvggsatlgtgstfeGtilaqtsitlstgatvnGrllaqtgaVtLdnntit 209
                                       ++n+fWqv++ at+gtg+tf Gtil+qt+it++tg++++G +laqt aVtL+++tit
  gi|518652812|ref|YP_008142332.1| 294 PQNIFWQVASGATIGTGATFYGTILSQTAITIATGSSMTGLALAQT-AVTLQSDTIT 349
                                       **********************************************.9*******96 PP

  == domain 3  score: -10.1 bits;  conditional E-value: 1
                                       -TT-EEESSEEEESSS-.GGEES--B-STTBTTEES--.....EE-TT--HH...HHHHHHH.HHHHHHHHHHSSS- CS
                           DUF3494   9 ntGstvitGdiGvspas.taitGfadelatgtestsglvltGkvyaadaaaatpatltqAva.dletAynalagrsl 83 
                                       +tGs +++G+i  + ++ +a +     + t ++ +sgl+ +G+    +    t++t+ ++v+  ++ A    + +++
  gi|518652812|ref|YP_008142332.1| 417 STGSIIVNGEIAYQGITfAAPNQA---TYTVAFNESGLA-SGTQWGVTLDGITTTTISSSVNfTMTNASYPFSIIVP 489
                                       566666777776666632221111...222333333333.3433333322222222222222123333333333322 PP

                                       TT-EEE--.SB-TTEEEESEEEEE.SS-EEE-SS-EEEE-TT-TT-.-EEEEESS-EEE-TT-....-EEEETT CS
                           DUF3494  84 pditelga.gelggrtLapGvYks.tsavtittgdltLDaqGdana.vwiFqiagtLtvasgs....svvLinG 150
                                       +d++   a  + g +t +    ++  +av i    +t+  +G +++ +w ++i++  + +  +    +v L nG
  gi|518652812|ref|YP_008142332.1| 490 ADYS---AtPSTGTETVNGNNITVlVTAVLI-VYPVTFKETGLPSGtTWYLNITSMASSGPLTgttyTVSLLNG 559
                                       2211...111222222222222222334444.335555555544331455555544433321122335555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (631 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4500.70
//
Query:       gi|518652813|ref|YP_008142333.1|  [L=163]
Description: hypothetical protein FACI_IFERC00001G1452 [Ferroplasma acidarmanus fer1]
Scores for complete 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   99.6  13.0    6.7e-27   93.4   9.4    2.2  2  DUF2250   Uncharacterized protein conserved in archaea (DUF22
     0.0028   17.4   0.6     0.0033   17.1   0.6    1.2  1  DUF3242   Protein of unknown function (DUF3242)


Domain annotation for each model (and alignments):
>> DUF2250  Uncharacterized protein conserved in archaea (DUF2250)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.4   9.4   7.5e-31   6.7e-27       2      93 .]       8      99 ..       7      99 .. 0.97
   2 !    7.9   0.1   0.00038       3.4      36      56 ..     122     142 ..     103     148 .. 0.82

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 7.5e-31
                           DUF2250  2 eeleedelalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlervegktikrteaklKkksevhkhHtYY 80
                                      ++l  d+++l+vl+h++ a+ dYak++  ++ ip+e+v+ ++++L+++ Lle+++g+++krt+aklKk +evhkhHtYY
  gi|518652813|ref|YP_008142333.1|  8 KKLAMDHQMLMVLEHFQLAKLDYAKNVKIYTSIPQENVEIYIERLYSMELLEKYSGSSVKRTQAKLKKTNEVHKHHTYY 86
                                      5788899************************************************************************ PP

                           DUF2250 81 rltreGelllrel 93
                                      +lt++G+++l+++
  gi|518652813|ref|YP_008142333.1| 87 ELTNKGHYILKDM 99
                                      **********986 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00038
                           DUF2250  36 leevrellkkLeelGLlerve 56 
                                       ++e re++ kL+++GL+++  
  gi|518652813|ref|YP_008142333.1| 122 RKENREKCAKLYDMGLMDKNY 142
                                       578899***********9865 PP

>> DUF3242  Protein of unknown function (DUF3242)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   3.7e-07    0.0033      18      93 ..      27     102 ..      10     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 3.7e-07
                                       EEEEEEEEEEETTEEEEEEEEEE.EETTEEEEEEEEESTTHHHHHHHHHT-------EEEEE-SSEEEEEEEETTEE CS
                           DUF3242  18 rLvdveeidgygdvegkGvvavf.dnkngllyvfkykdeeakksWkkivkkvgivskrkyldlldsGlfsvkkegkd 93 
                                       +L   +++  y  +  +  v ++ +  + + ++ ky++++ k++  k++k  ++  + +y++l+++G + +k  + +
  gi|518652813|ref|YP_008142333.1|  27 KLDYAKNVKIYTSIPQEN-VEIYiERLYSMELLEKYSGSSVKRTQAKLKKTNEVHKHHTYYELTNKGHYILKDMTEK 102
                                       344567788898887665.556659999999999***********************************99875544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1170  (0.0652574); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1114.83
//
Query:       gi|518652814|ref|YP_008142334.1|  [L=416]
Description: hypothetical protein FACI_IFERC00001G1453 [Ferroplasma acidarmanus fer1]
Scores for complete 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-75  253.2   0.3    4.2e-75  252.6   0.3    1.3  1  ELFV_dehydrog    Glutamate/Leucine/Phenylalanine/Valine dehyd
      2e-55  186.2   0.0    4.3e-55  185.1   0.0    1.6  1  ELFV_dehydrog_N  Glu/Leu/Phe/Val dehydrogenase, dimerisation 
     0.0059   16.0   0.8      0.011   15.1   0.3    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas


Domain annotation for each model (and alignments):
>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.6   0.3     7e-79   4.2e-75       1     243 []     180     413 ..     180     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 252.6 bits;  conditional E-value: 7e-79
                                       T--TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHHHHHHHHHHHHC.T-EEEEEEESSEEEEETTEE-H CS
                     ELFV_dehydrog   1 GGsldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnvgsyaallltel.gakvvavsDssGviydpeGldi 76 
                                       GGsl+r +aT+ G +y+++e +k+ ++d l+++++a++G+Gn g++a+++++e+ gakvvavsDssG iy+++G+d 
  gi|518652814|ref|YP_008142334.1| 180 GGSLGRGDATAKGGMYVLREGAKYKGID-LTKAKFAVQGFGNAGQFAVKFVKEMfGAKVVAVSDSSGGIYKESGIDY 255
                                       9***********************7777.************************99********************** PP

                                       HHHHHHHHCSSSSTTHSHHSTSTSEEESHHSHHHHSS-SEEEE-SSTTSB-HHHHTHTHHTT-SEEE-SSSS-B-HH CS
                     ELFV_dehydrog  77 eellelkeerksvkeykkssekkaeyieneeellelkvdilvPcAtqneideenakalikngvklvvEgANlpttqe 153
                                       +ell++ke+++sv++++       + i+ne elle +vd+l+P+A++++++++na+ ++k  +k+v+E AN+p+t+e
  gi|518652814|ref|YP_008142334.1| 256 AELLAHKEKHGSVENFPG-----SKNISNE-ELLESDVDVLIPSAIEDQLTGANAS-KVK--AKIVLELANGPSTPE 323
                                       *****************3.....478***7.*************************.999..*************** PP

                                       HHHHHHHTT-EEE-HHHHTTHHHHHHHHHHHHHHCT----HHHHHHHHHHHHHHHHHHHHHHHHHCT-THHHHHHHH CS
                     ELFV_dehydrog 154 AkeileeagvlvvpdkaaNaGGVtvSslEmlqnlarlswteeevdeklkkimkeifkavveeaeeykqelvkgania 230
                                       A+ei+ +++vl++pd+++NaGGVtvS++E++qn+++ +wte+ v +kl+++m+ ++k+v+++ e+y+++ +++a+i+
  gi|518652814|ref|YP_008142334.1| 324 ADEIFYKNNVLLLPDFLSNAGGVTVSYFEWVQNITGDYWTEDVVYSKLDEKMTFATKDVLATHEKYQTDPRTAAYII 400
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHCT CS
                     ELFV_dehydrog 231 gfekvaeamkaqG 243
                                       ++++v +amka+G
  gi|518652814|ref|YP_008142334.1| 401 AIQRVLDAMKARG 413
                                       ***********99 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 !  185.1   0.0   7.2e-59   4.3e-55       1     129 [.      34     161 ..      34     162 .. 0.99

  Alignments for each domain:
  == domain 1  score: 185.1 bits;  conditional E-value: 7.2e-59
                                       -SEEEEEEEEEE-TTSBEEEEEEEEEEEE-TTSSEEEEEEEETT--HHHHHHHHHHHHHHHHHTTSS-EEEEEEEES CS
                   ELFV_dehydrog_N   1 pervlqvtvpvkrdnGelevikgyraqhssalgPakGGiRfhpsvnldevkaLaalmtyKnalvdlpfGGakggvki 77 
                                       p+++lqv++pvk+dnG++ev++g+r+++++a+gP+kGGiR+  + nl+evkaL+a+mt+K+al++lpfGGakgg+++
  gi|518652814|ref|YP_008142334.1|  34 PREILQVSIPVKMDNGTTEVFTGFRVHYNNARGPMKGGIRYYIKENLSEVKALSAWMTWKTALLGLPFGGAKGGIIC 110
                                       6789************************************************************************* PP

                                       -GGGS-HHHHHHHHHHHHHHHG.GG-BTTTEEEEBBTTB-HHHHHHHHHHHH CS
                   ELFV_dehydrog_N  78 dpkklseeeleritrrfvrelakkfiGpgiDvpApDvgtgaremawladeyk 129
                                       dpkk+s+ eler+ r +++++a +fiGp+iDvpApDv+t+++ m+w++dey+
  gi|518652814|ref|YP_008142334.1| 111 DPKKMSKMELERLSRGYIDAIA-NFIGPEIDVPAPDVYTTPQIMGWMMDEYE 161
                                       **********************.****************************8 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       1.2   7.1e+03     136     155 ..      13      32 ..      11      39 .. 0.81
   2 !   15.1   0.3   1.9e-06     0.011      15      82 ..     187     255 ..     179     263 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 1.2
                                       HHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C 136 aLleaLksgkiagaalDvfe 155
                                        L +a k  k+  a +Dv++
  gi|518652814|ref|YP_008142334.1|  13 QLNKAAKVMKLDKASIDVLS 32 
                                       57788888899999999976 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.9e-06
                                       HHHHHTTCC..HTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHH.HTT-EEEEESSSHHHHHCHHHHTCEE CS
                      2-Hacid_dh_C  15 deevregew..ksekallgkelsgktvGiiGlGrIGqavakrlk.afgmkviaydrskkkeeeeeelgvel 82 
                                       d+  + g +  ++ ++++g +l++ + ++ G+G+ Gq + k +k  fg+kv+a++ s       +e g+++
  gi|518652814|ref|YP_008142334.1| 187 DATAKGGMYvlREGAKYKGIDLTKAKFAVQGFGNAGQFAVKFVKeMFGAKVVAVSDSSG--GIYKESGIDY 255
                                       55556666676778899**************************989********98854..2345555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2949.57
//
Query:       gi|518652815|ref|YP_008142335.1|  [L=246]
Description: hypothetical protein FACI_IFERC00001G1454 [Ferroplasma acidarmanus fer1]
Scores for complete 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-14   51.8   0.3    1.8e-11   43.8   0.2    2.2  2  PCNA_N    Proliferating cell nuclear antigen, N-terminal doma
    7.5e-06   26.1   0.1    8.2e-05   22.8   0.0    2.3  2  PCNA_C    Proliferating cell nuclear antigen, C-terminal doma


Domain annotation for each model (and alignments):
>> PCNA_N  Proliferating cell nuclear antigen, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.2     2e-15   1.8e-11      12      95 ..      11      94 ..       4     107 .. 0.92
   2 !    5.9   0.0    0.0011       9.6      14     112 ..     138     235 ..     131     241 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 2e-15
                                      HHHHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEE CS
                            PCNA_N 12 lkklleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtl 90
                                      l+ +++ +  +v+ea f++ ++Gis+ a+D +hva+vsle+ +    +y  + +  l+++l+ +  ilk+a  +ds ++
  gi|518652815|ref|YP_008142335.1| 11 LRDVVDMLGTVVTEAKFKIGQQGISVNAVDPAHVAMVSLEIPKGILLEYDVESEEELSLDLEKVKGILKLASGNDSFII 89
                                      77899*******************************************************************9999988 PP

                                      EEETT CS
                            PCNA_N 91 kaede 95
                                        + e
  gi|518652815|ref|YP_008142335.1| 90 TKDKE 94
                                      76544 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0011
                                       HHHHHHTTTCSEEEEEEETTEEEEEEE-TTSSEEEEEEEEGGGSSEEEESS-EEEEEEHHHHHHHHTTSTTTSEEEE CS
                            PCNA_N  14 klleaikdlvneanfdcddsGislqalDsshvaLvslelrsegfekyrCDrnlalgvnlnslskilkcannedsvtl 90 
                                       k l a  d+ + + f ++ + +s++++ ++  +  ++ l  +  ++ +C   +  +  l+ l k ++    ++ v l
  gi|518652815|ref|YP_008142335.1| 138 KGLKAAEDVSDAIRFTMNPDSFSAKSMSDADES--EMILPGDKLKEIQCHESIKSSYPLEYLLKFMRSISPNEEVKL 212
                                       556777788888889999999999999777655..78899999**************************99999999 PP

                                       EEE.TTSSEEEEEEEECTSSEEE CS
                            PCNA_N  91 kae.deadtlalvfesekkdkia 112
                                       + + d + t+ + + se++d+i+
  gi|518652815|ref|YP_008142335.1| 213 SFKsDYPLTIEFNLGSESADRIK 235
                                       86526788999999999999987 PP

>> PCNA_C  Proliferating cell nuclear antigen, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.1     0.056     5e+02      25      50 ..      80     104 ..      68     127 .. 0.72
   2 !   22.8   0.0   9.2e-09   8.2e-05      59     118 ..     170     229 ..     144     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.056
                                       HTTT-SEEEEEEETTEEEEEEEETTE CS
                            PCNA_C  25 lsqlsdsvvisvtkegvkfsasGdiG 50 
                                       l++ +ds +i+  ke ++f   G+i 
  gi|518652815|ref|YP_008142335.1|  80 LASGNDSFIITKDKEKLRFEI-GNII 104
                                       666789999999999999975.4444 PP

  == domain 2  score: 22.8 bits;  conditional E-value: 9.2e-09
                                       BEESSSGGGCBEEEESS-EEEEEEHHHHHHHGGGGGC-SEEEEEEETTSEEEEEEEETTC CS
                            PCNA_C  59 vkdvdkeeeavklelkepvtltfalkYlaeftkatsLservtlslssevPlvveykikdv 118
                                        +++   ++  +++ +e+++  + l+Yl++f+++ s  e+v+ls+ s+ Pl +e+++ + 
  gi|518652815|ref|YP_008142335.1| 170 SEMILPGDKLKEIQCHESIKSSYPLEYLLKFMRSISPNEEVKLSFKSDYPLTIEFNLGSE 229
                                       334445677889*******************************************99664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1675.67
//
Query:       gi|518652816|ref|YP_008142336.1|  [L=430]
Description: hypothetical protein FACI_IFERC00001G1455 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-53  180.5   0.0    6.1e-27   94.5   0.0    2.0  2  AdoHcyase      S-adenosyl-L-homocysteine hydrolase
    1.2e-51  174.9   2.3    2.2e-51  174.1   2.3    1.4  1  AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD bindi
      2e-06   27.3   0.2    3.3e-06   26.6   0.2    1.3  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
    0.00014   21.5   0.1    0.00024   20.7   0.1    1.4  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
      0.003   17.6   0.1     0.0071   16.4   0.1    1.6  1  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
     0.0047   17.3   0.2      0.014   15.8   0.2    1.7  1  NAD_binding_7  Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.039   14.2   0.1        0.1   12.9   0.1    1.7  1  TrkA_N         TrkA-N domain


Domain annotation for each model (and alignments):
>> AdoHcyase  S-adenosyl-L-homocysteine hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.5   0.0   2.4e-30   6.1e-27       2     138 ..      16     148 ..      15     153 .. 0.95
   2 !   84.8   0.0   2.3e-27   5.8e-24     175     291 ..     151     429 ..     147     430 .] 0.99

  Alignments for each domain:
  == domain 1  score: 94.5 bits;  conditional E-value: 2.4e-30
                                       -B-S-GGGHHHHHHHHHHHHCC-HHHHHHHHHCTTT-TTTT-EEEEES--SHHHHHHHHHHHHTT-EEEEE-SSTTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase   2 ykvkdislaefGrkeielaekempglmalreeyaeekplkgariaGslhmtiqtavLietLvalGaevrWasCnifs 78 
                                       y ++ i + + G  +++ a   mp   ++re++ +ekp+kg +ia +lh+ ++t +    L++ Gaevr asCn  s
  gi|518652816|ref|YP_008142336.1|  16 YYIHIIMTDNNGFLRLKWARDHMPVCANIRERFLKEKPFKGIKIAMALHVEAKTGIFALLLTEGGAEVRLASCNPLS 92 
                                       777778888999999************************************************************** PP

                                       --HHHHHHHCCT.TEEEE--TT--HHHHHHHHHHCHS-SSTS-S-SEEEESSSHHHHHHHH CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase  79 tqdeaaaaiaea.gvpvfawkgetleeywwcieqalkwaedekepnlilDdGGDltllvhk 138
                                        +d +  +++++ +  v+a kge+++ey + i+++++       p++i+DdGGDlt+lv +
  gi|518652816|ref|YP_008142336.1|  93 SDDSVVQSLSKDyNYMVYAKKGESEKEYYENINKTIEA-----APDIIIDDGGDLTNLVAS 148
                                       **********999***********************55.....7**************976 PP

  == domain 2  score: 84.8 bits;  conditional E-value: 2.3e-27
                                       CCHCC--EEEE-SHHHHHHHHHHHHTT---SEEEESTTSHHHCTTH............................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................... RF
                         AdoHcyase 175 ellkkikGvseetttGvhrLyelakkgkLlvpainvndsvtkskfD............................... 220
                                       el+kk+ G  eetttGv rL+ ++k+g L++p ++vnd+  k  fD                               
  gi|518652816|ref|YP_008142336.1| 151 ELVKKVIGGNEETTTGVVRLKAMEKAGALKFPMFDVNDAQMKHFFDnrygsgqsaldgfmnatniliagknalvagy 227
                                       789999*********************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                         AdoHcyase 221 ............................................................................. 220
                                                                                                                    
  gi|518652816|ref|YP_008142336.1| 228 gyvgkgvamrlkgmgarvtvtevdpvkaieavmdgftvdtmnsairycdliftatgmknvvsyddmlvakkgiimgn 304
                                       ***************************************************************************** PP

                                       ......................................................S-HHHHHHHHHHHHHHHHHHHHT CS
                                       ......................................................xxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 221 ......................................................hpsfvmsasftnqvlaqielfkk 243
                                                                                             hp  +m+ sf+ q+l+   + k+
  gi|518652816|ref|YP_008142336.1| 305 vghfnneidysslekknigktpvrnlvteyklengntvnlisdgrllnlaagqgHPVEIMDLSFALQALTAEYIVKN 381
                                       ***************************************************************************** PP

                                       TSSS-SSEEE--CHHHHHHHHHCCCCCT-------HHHHHCCTSXTTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         AdoHcyase 244 ekkyekkvyvlpkklDekvarlhleklgaklteltkeqaeyigveveG 291
                                       + k ++kvy +p ++D +va++ le+l+ k+++ t+eq +y++  +eG
  gi|518652816|ref|YP_008142336.1| 382 KGKLSNKVYPVPAEIDTEVAKIALESLNFKIDTYTEEQLKYLDSYQEG 429
                                       ******************************************988887 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 !  174.1   2.3   8.6e-55   2.2e-51       1     161 [.     197     357 ..     197     358 .. 0.98

  Alignments for each domain:
  == domain 1  score: 174.1 bits;  conditional E-value: 8.6e-55
                                       HHHHHCCCCCHHHHHHH-S--TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--HHHCTT CS
                     AdoHcyase_NAD   1 nlygcreslvdgikratdvllaGkvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvtleevvk 77 
                                       n yg  +s +dg + at++l+aGk+a+vaGyG vGkG a  lkg+Garv+vtevdP+ a+ a+m+Gf v t++ +++
  gi|518652816|ref|YP_008142336.1| 197 NRYGSGQSALDGFMNATNILIAGKNALVAGYGYVGKGVAMRLKGMGARVTVTEVDPVKAIEAVMDGFTVDTMNSAIR 273
                                       789************************************************************************** PP

                                       T-SEEEE-SSSSSSB-HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEEEE-TTS-EEEEEGGGSB CS
                     AdoHcyase_NAD  78 kadivvtttGnkdiitlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdrvtlkdgkkiillaeGrl 154
                                        +d++ t+tG k++++ +++   k+  i++n+Ghf++eid ++le++++ k+ v+  v +++l++g+++ l+++Grl
  gi|518652816|ref|YP_008142336.1| 274 YCDLIFTATGMKNVVSYDDMLVAKKGIIMGNVGHFNNEIDYSSLEKKNIGKTPVRNLVTEYKLENGNTVNLISDGRL 350
                                       ***************************************************************************** PP

                                       CHHHTS- CS
                     AdoHcyase_NAD 155 lnlgcat 161
                                       lnl++ +
  gi|518652816|ref|YP_008142336.1| 351 LNLAAGQ 357
                                       ***9865 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.2   1.3e-09   3.3e-06      33      99 ..     216     282 ..     193     307 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 1.3e-09
                                       -GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHHH-SEEEE-S CS
                      2-Hacid_dh_C  33 elsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleellaesDivslhl 99 
                                        ++gk   + G+G +G+ va rlk++g++v+++++ + k  e+   g+++++++ +++ +D ++ ++
  gi|518652816|ref|YP_008142336.1| 216 LIAGKNALVAGYGYVGKGVAMRLKGMGARVTVTEVDPVKAIEAVMDGFTVDTMNSAIRYCDLIFTAT 282
                                       5899*******************************99988889999****************98765 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 !   20.7   0.1   9.4e-08   0.00024       2      66 ..     217     280 ..     216     294 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.4e-08
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmi 66 
                                       + gk+  v GyG  G+  a+ l+  g  v+v+  +   ++ +A  +gf+v t++ a++  d++++
  gi|518652816|ref|YP_008142336.1| 217 IAGKNALVAGYGYVGKGVAMRLKGMGARVTVTEVDPV-KAIEAVMDGFTVDTMNSAIRYCDLIFT 280
                                       6789999************************998887.677899******************986 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.8e-06    0.0071      10      94 ..     217     293 ..     211     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.8e-06
                                       .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatase 86 
                                       +++k++l+ G G +++ va  L   g++ v+v+    + +k++   ++g      +++ ++++++ +d++++at+ +
  gi|518652816|ref|YP_008142336.1| 217 IAGKNALVAGYGYVGKGVAMRLKGMGAR-VTVTEV--DPVKAIEAVMDGF-----TVDTMNSAIRYCDLIFTATGMK 285
                                       57899**********************9.999865..5555565555444.....899******************9 PP

                                       S-SB-HHH CS
                      Shikimate_DH  87 epilekee 94 
                                       +++   ++
  gi|518652816|ref|YP_008142336.1| 286 NVVSYDDM 293
                                       98876665 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   0.2   5.4e-06     0.014       5      73 ..     217     286 ..     214     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.4e-06
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeelekdlegadlviaatddre 73 
                                       + gk+ lv+G G v+   + +l   ga+vtv   +  +++e  ++ ++ +++++ +   dl+++at  ++
  gi|518652816|ref|YP_008142336.1| 217 IAGKNALVAGYGYVGKGVAMRLKGMGARVTVTEVDPVKAIEAVMDgFTVDTMNSAIRYCDLIFTATGMKN 286
                                       679****************************777755677766665677777888999999999998765 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     4e-05       0.1       2      43 ..     223     264 ..     222     271 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4e-05
                                       EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHHTTSE CS
                            TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelreegle 43 
                                       +++G+G vG+ +a +L+  g  +v+v + d+ ++ e+  +g++
  gi|518652816|ref|YP_008142336.1| 223 LVAGYGYVGKGVAMRLKGmGA-RVTVTEVDPVKAIEAVMDGFT 264
                                       79****************666.6********999888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2870.42
//
Query:       gi|518652817|ref|YP_008142337.1|  [L=274]
Description: fumarylacetoacetate hydrolase family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-57  195.0   0.0    1.5e-57  194.8   0.0    1.1  1  FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
     0.0084   15.5   0.0      0.012   15.0   0.0    1.1  1  NolX           NolX protein


Domain annotation for each model (and alignments):
>> FAA_hydrolase  Fumarylacetoacetate (FAA) hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.8   0.0   1.7e-61   1.5e-57       3     217 ..      70     273 ..      68     274 .] 0.94

  Alignments for each domain:
  == domain 1  score: 194.8 bits;  conditional E-value: 1.7e-61
                                       EEEEEE--SHHHHHTTT.-SS-EEEEEEGGGE.EETTE..EE-TTSSSS-EE......EEEEEEEESS-B--T--HH CS
                     FAA_hydrolase   3 vcdglnyaehvreagkaaeeppdrhiplepvfflkrasslvgpgdpirrPagsekldyEvELavvigkplrevlsve 79 
                                       +c+glny++hv e      + p+     +pv+f k +++++g  + ++  +g  ++dyE+EL v+igk +r+v   +
  gi|518652817|ref|YP_008142337.1|  70 LCIGLNYKSHVSEHAGG--KIPE-----TPVVFSKANNAFTGNHSIVQTGNG-MHMDYEGELCVMIGKTARNV-GEA 137
                                       79***********7644..5656.....899***********9988888888.569*****************.99* PP

                                       HHHTTEEEEEEEEEEE-SBGGG---.HHHHHHTGGGEEEEEE-B--B-.STT---SS-EEEEEETTEEEEEEEGGGT CS
                     FAA_hydrolase  80 eAedaiaGytllnDvsaRdlqaeekaplgwflgksfdtftpiGpwivtpdeledpedlelrlrvngeevqdsntkdm 156
                                       +A ++++Gy ++nDvs R +q +     ++flgksfd+f p Gp i +  e+ dp++l++++rvnge +qdsnt  m
  gi|518652817|ref|YP_008142337.1| 138 NALNYVLGYFIGNDVSSRLMQYKTT---QFFLGKSFDNFYPNGPYI-SIGEINDPQNLTIQTRVNGELRQDSNTGLM 210
                                       *********************8888...9*****************.****************************** PP

                                       TTSHHHHHHHHHHHH-B-TT-EEEEEES.........S--EE--TT-EEEEEETTTEEEEEEE CS
                     FAA_hydrolase 157 ifspaeliahlsagltLepGdliltGTpsgv..gaeeeslkflkdgDeveveieglGelrnrV 217
                                       if++ +li+++s+++tL+pGd i+tGTp+gv  g  e+++k+l +gD vev+i+glG+l++++
  gi|518652817|ref|YP_008142337.1| 211 IFPVNKLISYISQFMTLRPGDCISTGTPAGVimGMPESNQKWLGKGDKVEVQITGLGKLETTF 273
                                       ******************************9886678899*******************9985 PP

>> NolX  NolX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-06     0.012     185     262 ..      31     112 ..      22     124 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-06
                              NolX 185 kasssvkLtadekktletinenqdvffgdgkltrdkLakiadDkklspevre.AAkqllsdplLfglldNaktGykt 260
                                       ka+s  +L++d+   l+ in+ qd  f  +++ ++k + +    + + +v e A  ++ + p++f++ +Na tG++ 
  gi|518652817|ref|YP_008142337.1|  31 KATSVAELSHDDFAKLKDINRFQDYTFSYNSIIDQKSSLLCIGLNYKSHVSEhAGGKIPETPVVFSKANNAFTGNHS 107
                                       788999****************************99999998888888887626679*****************954 PP

                              NolX 261 k...G 262
                                           G
  gi|518652817|ref|YP_008142337.1| 108 IvqtG 112
                                       35433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       329  (0.0183502); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1864.62
//
Query:       gi|518652818|ref|YP_008142338.1|  [L=179]
Description: hypothetical protein FACI_IFERC00001G1457 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-11   42.7   0.0    7.3e-11   42.2   0.0    1.2  1  2_5_RNA_ligase2  2'-5' RNA ligase superfamily
    2.3e-07   30.9   0.0       0.02   15.1   0.0    2.2  2  LigT_PEase       LigT like Phosphoesterase
  ------ inclusion threshold ------
       0.17   11.6   0.0       0.23   11.2   0.0    1.2  1  CPDase           Cyclic phosphodiesterase-like protein


Domain annotation for each model (and alignments):
>> 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 !   42.2   0.0   1.2e-14   7.3e-11      16     141 ..      29     172 ..       9     178 .. 0.76

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 1.2e-14
                   2_5_RNA_ligase2  16 lydkayprwppHitLlypfvededladlaellsrlaketepfevrldgfgvFeh....kks.vvylsvsdsealqal 87 
                                        y ++ ++  +Hit++y+        d++  + +l+  t+pf+ + + +g+Fe     k s +v+l+v +s+++ ++
  gi|518652818|ref|YP_008142338.1|  29 GYTGSLSNKGVHITMAYLRNSRF--LDVNP-IITLCGKTAPFTYEMGEVGYFEKvrkgKISyIVFLNVIPSPEMYEF 102
                                       46666888889******999886..56655.556788*******************997778*************** PP

                   2_5_RNA_ligase2  88 raallealpeagdkedsgeftPHlTiaqsadstsa...............aellekl...aqalpplefevd 141
                                       ++ l +al+  ++    g+f PH+T+ +++ ++                 ++l ++l   ++ +++ +++ +
  gi|518652818|ref|YP_008142338.1| 103 HEGLIKALGDNTTEA--GKFIPHITLIRKNVNENNlneivkfcenlkidcKFLSTYLilgKRSSEYSRWHFE 172
                                       ***********9988..*********9999888765555555544444444444444555555555555555 PP

>> LigT_PEase  LigT like Phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.4e-06      0.02       8      83 ..      14      83 ..       7      87 .. 0.75
   2 !   14.1   0.0   6.9e-06     0.041      31      61 ..     118     147 ..      95     156 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.4e-06
                                      HHHHHHHHHHHHHHHCCTTEEET.SGGGSEEEEEEEEEESHHHHHHHHHHHHHHHHTSBEEEEEEEEEEEEEECCSC CS
                        LigT_PEase  8 aeelarlaaeleralaklglkpv.rpfnpHiTLaflgevdeekvpellealaeiasgaepfelkvdgvglfpsrlrp 83
                                      ++++++ +++le +l +  +     +  +HiT a l++ +  +v+ ++  +++     +pf+++  +vg+f+  +++
  gi|518652818|ref|YP_008142338.1| 14 RRKITAKKKRLE-KLYGYTG--SlSNKGVHITMAYLRNSRFLDVNPIITLCGKT----APFTYEMGEVGYFEKVRKG 83
                                      566667777777.3333333..3458889**********9999****9999955....7************976554 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 6.9e-06
                                       SGGGSEEEEEEEEEESHHHHHHHHHHHHHHH CS
                        LigT_PEase  31 rpfnpHiTLaflgevdeekvpellealaeia 61 
                                        +f pHiTL +  +v+e +++e+++ ++++ 
  gi|518652818|ref|YP_008142338.1| 118 GKFIPHITLIRK-NVNENNLNEIVKFCENLK 147
                                       589********9.89**********999984 PP

>> CPDase  Cyclic phosphodiesterase-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.23       7      57 ..      93     139 ..      88     172 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                            CPDase   7 lcPpanspeyetlktlIqsLqtlfpdsevFePHvTltselsvdskddvekv 57 
                                        +P++   +ye  + lI+ L     ++  F PH+Tl+ + +  ++++++++
  gi|518652818|ref|YP_008142338.1|  93 VIPSP--EMYEFHEGLIKALGDNTTEAGKFIPHITLIRKNV--NENNLNEI 139
                                       56777..88999***********************975422..33334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        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 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1293.77
//
Query:       gi|518652819|ref|YP_008142339.1|  [L=402]
Description: hypothetical protein FACI_IFERC00001G1458 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-53  180.0   0.0    4.9e-53  179.5   0.0    1.2  1  PhosphMutase     2,3-bisphosphoglycerate-independent phosphog
    1.1e-38  133.0   0.0    1.3e-38  132.8   0.0    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    8.4e-07   28.9   0.0    6.4e-06   26.0   0.0    2.0  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    0.00074   18.6   0.4     0.0012   17.9   0.0    1.5  2  Alk_phosphatase  Alkaline phosphatase
  ------ inclusion threshold ------
      0.095   12.1   0.0       0.32   10.3   0.0    1.8  2  Sulfatase        Sulfatase


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 !  179.5   0.0   1.4e-56   4.9e-53       2     170 .]      39     203 ..      38     203 .. 0.97

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.4e-56
                                       HTSEEEEEE-----------TCHHHHTT--HHCH---HHHHHHHHTT----TT-EEEEEEEEEEC..TTCEEETTGG CS
                      PhosphMutase   2 kkGetGlldtvpegiapgSdvAnlsilGydpkkyytGRGplEAlgiGlelkpgdvafRcnlvtvdeedgiiidrrag 78 
                                       ++G+tGl+++v+ gi++gSd+++lsilGydp+kyytGRGp+EAlg+Glelkpgd+afR+n++++   dg+i+drrag
  gi|518652819|ref|YP_008142339.1|  39 SHGTTGLMSPVASGIRAGSDTSHLSILGYDPNKYYTGRGPFEALGVGLELKPGDIAFRANYASII--DGKIVDRRAG 113
                                       68**************************************************************5..8********* PP

                                       G-.-TTHHHHHHHT-EEE.TTEEEEEEE-STTEEEEEE....--S-B--S--..SSTTS------BS.SGGGHHHHH CS
                      PhosphMutase  79 risteeakeLikalneeleegvevkfypgveyrhllvl....lsdkitdtdpphdkegkeikellplkseeaketae 151
                                       ri  ++++eL +al++e+ +gv++ +++gve+r+++v+    lsdk+++tdp  + ++ ++++  pl ++ea+ t++
  gi|518652819|ref|YP_008142339.1| 114 RI--QNTAELSSALETEI-DGVKFIVKSGVEHRAAVVMrgpnLSDKVSETDP--HSVDSSPMDTEPL-APEANFTSA 184
                                       **..999***********.59*******************************..8888889999998.79******* PP

                                       HHHHHHHHHHHHHHHSHHH CS
                      PhosphMutase 152 llnelieksqeiLedhpvN 170
                                       ++n+++e+s++iL++hp+N
  gi|518652819|ref|YP_008142339.1| 185 VINKFLERSRKILASHPLN 203
                                       *****************99 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.8   0.0   3.5e-42   1.3e-38       1     244 [.       2     389 ..       2     393 .. 0.95

  Alignments for each domain:
  == domain 1  score: 132.8 bits;  conditional E-value: 3.5e-42
                                       -EEEEEEETTBB----GGGTT...HHHS--HHHHHHHHH.......SEEEEEESSSTT----HHHHHHHH....... CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
                     Metalloenzyme   1 kkvvlvvlDGlGeapadelna...ihvAktPtldkLkkeaPerwlikahgtavglpeddmgnsevgHlel....... 67 
                                       kk++l+++DGlG++p++el++   ++ A+ P+l+ L  +       +++g++ +++ +++++s+++Hl++       
  gi|518652819|ref|YP_008142339.1|   2 KKIILIIMDGLGDRPNKELDGltaLQAANRPNLNYLSSH-------GTTGLMSPVASGIRAGSDTSHLSIlgydpnk 71 
                                       799*************99999999*************99.......89***************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Metalloenzyme  68 ............................................................................. 67 
                                                                                                                    
  gi|518652819|ref|YP_008142339.1|  72 yytgrgpfealgvglelkpgdiafranyasiidgkivdrragriqntaelssaleteidgvkfivksgvehraavvm 148
                                       ***************************************************************************** PP

                                       ........................................................HHHHTT-----EEEEEEEE-S CS
                                       ........................................................xxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  68 ........................................................lrisetvkfahvtffwnggrs 88 
                                                                                               + ise++ +a+ + +++ g++
  gi|518652819|ref|YP_008142339.1| 149 rgpnlsdkvsetdphsvdsspmdteplapeanftsavinkflersrkilashplnrKLISEGKLPANEIMLRGVGKM 225
                                       *******************************************************9779****************** PP

                                       ---SSHHHHHT--EEEE--SHH....................STT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme  89 gyfnpleereeipsdtvitfdl....................qpemkavevaekaldailsgkfdlvvvniknaDmv 145
                                       + ++++ e+++++++++  + l                      ++++++++ +a++ +  +k+d++++n+k +D +
  gi|518652819|ref|YP_008142339.1| 226 PAIPSFHEKYGMKAACISGTPLirgiaglagfdvlsvegmngRVDTNYENIISSAIKSL--EKYDFILINFKGTDIA 300
                                       ******************************************9****************..78************** PP

                                       HHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS........-----EEEEEESTT----S-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 146 GHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdkqplTsHtlepVPilivgkglapdkvk 222
                                       GH++++  + ++ie +D+ ++ +l+ ++  d+++vvt+DH+++ ++ +        Ht +pVPi+++ +g+ +d+v+
  gi|518652819|ref|YP_008142339.1| 301 GHDRKPRLKKQVIESVDSVIAPLLKLLQ--DTLIVVTGDHSTPCSFGD--------HTGDPVPIMFATDGIINDNVR 367
                                       ************************8864..458***************........****************99999 PP

                                       S.SHHHHTT-TTEEEEGGGHHHH CS
                                       x.xxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 223 e.gakfrekggLanvaatllnll 244
                                       + + ++  ++g  ++ ++ ++ +
  gi|518652819|ref|YP_008142339.1| 368 SfD-ELSVSDGYYKITSEDIMPI 389
                                       954.4444555556666666655 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.071   2.5e+02       2      40 ..       5      49 ..       4      55 .. 0.81
   2 !   26.0   0.0   1.8e-09   6.4e-06     144     234 ..     265     340 ..     136     379 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.071
                                      EEEEETT-B......TTHHHHHG.STSHHHHHHHHHSEEESEEE-S CS
                      Phosphodiest  2 lvislDGlr......adlldrla.ellpnlaaLakegvsapnlrpv 40
                                      ++i++DGl        d l +l+    pnl++L ++g+++  + pv
  gi|518652819|ref|YP_008142339.1|  5 ILIIMDGLGdrpnkeLDGLTALQaANRPNLNYLSSHGTTGL-MSPV 49
                                      678888888888877666777776799***********998.8776 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 1.8e-09
                                       HHHHHHHHHHHHHHHCHTHSHHHHHCTSSESEEEEEECCCHHHHHHH-TTSHHHHHH.HHHHHHHHHHHHHHHHHTT CS
                      Phosphodiest 144 ledkvdkavlqtwldaafakvvlekelekpdlllvyleetDtvgHkfGpdspeveda.lrrvDkaigdLlealderg 219
                                       ++++vd+    + ++ a +      +lek+d++l+++ +tD +gH     +p ++++ +++vD++i+ Ll++l+++ 
  gi|518652819|ref|YP_008142339.1| 265 MNGRVDTNYE-NIISSAIK------SLEKYDFILINFKGTDIAGHDR---KPRLKKQvIESVDSVIAPLLKLLQDT- 330
                                       5555555344.55554442......359*****************66...77776662689*************86. PP

                                       GTTTEEEEEEES--- CS
                      Phosphodiest 220 lsaetniilvSDHGm 234
                                             i++++DH  
  gi|518652819|ref|YP_008142339.1| 331 -----LIVVTGDHST 340
                                       .....8*******76 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.6      0.93   3.4e+03       2      14 ..       2      14 ..       1      15 [. 0.90
   2 !   17.9   0.0   3.3e-07    0.0012     240     331 ..     278     363 ..     266     399 .. 0.77

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 0.93
                                      SEEEEEEETT-SH CS
                   Alk_phosphatase  2 knvilligDGmgv 14
                                      k +il+i DG+g+
  gi|518652819|ref|YP_008142339.1|  2 KKIILIIMDGLGD 14
                                      89*********97 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHTTSTT-EEEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTT CS
                   Alk_phosphatase 240 evAiklLsknekGFFLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyt 316
                                       ++Aik L+k +   F+l+     D a+H+ ++  + + +  +d+ ++  l++ +   +tl+vvT DHs+ +sfg +t
  gi|518652819|ref|YP_008142339.1| 278 SSAIKSLEKYD---FILINFKGTDIAGHDRKPRLKKQVIESVDSVIAPLLKLLQ---DTLIVVTGDHSTPCSFGDHT 348
                                       56666666554...6666666679999999999999999999999999999999...*******************9 PP

                                       STT..TTSEECCEET CS
                   Alk_phosphatase 317 trgesvlglepllaa 331
                                         +  +++++    +
  gi|518652819|ref|YP_008142339.1| 349 GDPVPIMFATDGIIN 363
                                       998888777665444 PP

>> Sulfatase  Sulfatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.26   9.4e+02       2      37 ..       3      42 ..       2      44 .. 0.66
   2 ?   10.3   0.0     9e-05      0.32     219     251 ..     314     340 ..     273     373 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.26
                                      EEEEEEESSE-TT.GSGGGTTTS...CSSHHHHHHHHTSE CS
                         Sulfatase  2 nvvliladdlgag.dlglyggkt...attpnldrlaeegl 37
                                       ++li++d lg+  + +l g      a+ pnl +l  +g+
  gi|518652819|ref|YP_008142339.1|  3 KIILIIMDGLGDRpNKELDGLTAlqaANRPNLNYLSSHGT 42
                                      5899999999998844444443311155788888888776 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 9e-05
                                       HHHHHHHHHHHHHHHHTTTGGGEEEEEEESSSS CS
                         Sulfatase 219 eyvDdligrvlaaLeenglldntlvvftSDhga 251
                                       e+    +++v+a L  ++ll++tl+v+t+Dh  
  gi|518652819|ref|YP_008142339.1| 314 ES----VDSVIAPL--LKLLQDTLIVVTGDHST 340
                                       44....55666666..6666***********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2808.49
//
Query:       gi|518652820|ref|YP_008142340.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1459 [Ferroplasma acidarmanus fer1]
Scores for complete 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-19   68.2   0.0    9.1e-17   61.2   0.0    2.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    4.1e-07   30.2   0.0    6.4e-05   23.0   0.0    2.2  2  Lactamase_B    Metallo-beta-lactamase superfamily
    1.6e-05   24.5   0.0    3.7e-05   23.3   0.0    1.7  1  Lactamase_B_4  tRNase Z endonuclease


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   1.5e-20   9.1e-17       4     201 .]      38     270 ..      37     270 .. 0.82

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.5e-20
                                       EES--TTHHHH.HTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC.....C--EEEEEEEEHHHHHHCCTTC CS
                     Lactamase_B_2   4 LiDagpdlrqq.alralqPvelrdelppidaVllthaHyDHlaglltlre.....lrpkklplyapkgvlavleanf 74 
                                       L+D+g ++ +q +++         ++ ++  ++++h H+DH+ gl+ l       +r +++++++p g    +++ +
  gi|518652820|ref|YP_008142340.1|  38 LFDCGEGTQKQfMKSGV-------SFMSLSNIFISHFHADHFLGLPGLLNslsfmGRTEDINIFGPVGAVNFIRNAI 107
                                       89*****8888555444.......799************************997655555**********9999997 PP

                                       GHHHCHTTTTEEEEEE-TTSEEEECSTTEEEEEEEE-EE--C..................................T CS
                     Lactamase_B_2  75 vylaleeepavnvheldwgesfelgdggleitatparhksgr..................................r 117
                                                ++nv e+ +g+s  lg  +++i++ + +h+ +                                   +
  gi|518652820|ref|YP_008142340.1| 108 TLGYGRISYNINVYEVIPGTSYNLG--KFTIRTLANNHTVPSisysleekdltkidrkkvdeigfpvyrleelrknG 182
                                       7766666689**************9..689***********9*****999999777666666666666665443330 PP

                                       CCE-TT........TSEEEEEE.CTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSH CS
                     Lactamase_B_2 118 ldrnag........dtlGlrie.gggkrvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeea 184
                                            +        +   ++++ ++g++v+y+gDt  +pe+  e  ++ad+l++d t+ ++ e++  + gH++ ++a
  gi|518652820|ref|YP_008142340.1| 183 -----KvelngkeyLLNDVAMGiKKGRKVVYTGDTRPVPEM-PEFAKNADVLIHDTTMDSSMEPMVnEYGHSSARQA 253
                                       .....03333343333333333557888***********66.889*************999999989********** PP

                                       HHHCTTSSSSEEEEESB CS
                     Lactamase_B_2 185 veaaadlgakrlvliHi 201
                                       +e+a + g+k+l+l+H+
  gi|518652820|ref|YP_008142340.1| 254 AEIALKGGVKKLFLFHY 270
                                       ****************7 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   1.1e-08   6.4e-05      18      67 ..      37      81 ..      26      96 .. 0.86
   2 !    4.9   0.0    0.0039        23     142     162 ..     203     223 ..     198     269 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 1.1e-08
                                      EEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTH CS
                       Lactamase_B 18 iLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglvea 67
                                       L+D+G +t+++ ++      g+    ++ ++++H+H+DH+ gl+gl + 
  gi|518652820|ref|YP_008142340.1| 37 NLFDCGEGTQKQFMK-----SGVSFMSLSNIFISHFHADHFLGLPGLLNS 81
                                      599**********98.....6**************************876 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0039
                                       TCCEEEECTTTSSHHCCCCCC CS
                       Lactamase_B 142 ggkvlftGDallagetgridl 162
                                       g+kv++tGD+ +++e +++ +
  gi|518652820|ref|YP_008142340.1| 203 GRKVVYTGDTRPVPEMPEFAK 223
                                       79*************999988 PP

>> Lactamase_B_4  tRNase Z endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   6.2e-09   3.7e-05      13      56 ..      26      68 ..      17      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 6.2e-09
                     Lactamase_B_4 13 PlllLqldskrYlfGkvgEgtQRavneqkvrlsklesiFLtgkv 56
                                      P +++q d+   lf ++gEgtQ+ +++++v++  l++iF+++ +
  gi|518652820|ref|YP_008142340.1| 26 PAVAIQVDDILNLF-DCGEGTQKQFMKSGVSFMSLSNIFISHFH 68
                                      7788888888889*.*************************9866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 2133.22
//
Query:       gi|518652821|ref|YP_008142341.1|  [L=95]
Description: hypothetical protein FACI_IFERC00001G1460 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-20   71.7   0.3    6.9e-20   71.1   0.3    1.3  1  DUF1805   Domain of unknown function (DUF1805)
  ------ inclusion threshold ------
      0.065   13.2   0.0      0.076   13.0   0.0    1.1  1  IMS       impB/mucB/samB family


Domain annotation for each model (and alignments):
>> DUF1805  Domain of unknown function (DUF1805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.1   0.3   7.7e-24   6.9e-20       1      63 []      37      95 .]      37      95 .] 0.98

  Alignments for each domain:
  == domain 1  score: 71.1 bits;  conditional E-value: 7.7e-24
                                      E-TT--HHHHHHTT--EEE-....-S--SHHHHHHSB-SEE-HHHHHTT--TT-BHHHHGGGG CS
                           DUF1805  1 mCGaLdvealeklgdlaarvivagsGVrtledllaapvesvteaAeelGikeGmtgkeaLekl 63
                                      mCG+L+++a+++lgd+a+rv    sGV+++ d+l+  v + t +A+elGik+G +  ++++kl
  gi|518652821|ref|YP_008142341.1| 37 MCGYLNIDAANSLGDVAVRV----SGVNDINDVLNTSVNACTDKAKELGIKPGDSIMDIVQKL 95
                                      9*******************....**********************************99987 PP

>> IMS  impB/mucB/samB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.5e-06     0.076      16      58 ..      18      93 ..      12      95 .] 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.5e-06
                                      .T-.TTS-EEEEET....................................TEEEEE-HHHHTTT--TTSBHHHHHT CS
                               IMS 16 peL.kgkPvvvaqgsek................................rgiviavsyeArayGvkrgmrikeakk 58
                                      +++ k+ P+++++g++                                 + +v a++ +A++ G+k g++i ++ +
  gi|518652821|ref|YP_008142341.1| 18 EKIgKKAPLIIVKGENGyimcgylnidaanslgdvavrvsgvndindvlNTSVNACTDKAKELGIKPGDSIMDIVQ 93
                                      467788999999996669999999999999999999999999999*************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       490  (0.02733); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); 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: 00:00:00.43
# Mc/sec: 659.98
//
Query:       gi|518652822|ref|YP_008142342.1|  [L=156]
Description: hypothetical protein FACI_IFERC00001G1461 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.079   13.3   0.0       0.24   11.8   0.0    1.9  1  Styelin   Styelin


Domain annotation for each model (and alignments):
>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.3e-05      0.24      26      51 ..      40      64 ..      23      67 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                           Styelin 26 siakhlLGDmtDeefqefmkeveqar 51
                                      + +k  +G +tD+ ++ fm  ve a+
  gi|518652822|ref|YP_008142342.1| 40 DTGK-TIGQVTDDAYKSFMGTVENAK 64
                                      5567.89****************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1243.37
//
Query:       gi|518652823|ref|YP_008142343.1|  [L=181]
Description: hypothetical protein FACI_IFERC00001G1462 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       928  (0.0517597); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1353.53
//
Query:       gi|518652824|ref|YP_008142344.1|  [L=60]
Description: hypothetical protein FACI_IFERC00001G1463 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       236  (0.013163); expected 358.6 (0.02)
Passed bias filter:                      207  (0.0115455); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 448.91
//
Query:       gi|518652825|ref|YP_008142345.1|  [L=128]
Description: hypothetical protein FACI_IFERC00001G1464 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.9   2.6      0.054   13.5   2.6    1.3  1  DUF892        Domain of unknown function (DUF892)
      0.048   13.6   3.7       0.13   12.2   3.7    1.7  1  Ferritin      Ferritin-like domain
      0.057   12.7   0.8       0.12   11.7   0.5    1.5  2  Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase famil
      0.081   13.2   0.0         20    5.6   0.0    2.4  2  A_thal_3526   Plant protein 1589 of unknown function (A_thal_


Domain annotation for each model (and alignments):
>> DUF892  Domain of unknown function (DUF892)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   2.6   1.2e-05     0.054      66     148 ..      43     123 ..       8     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.2e-05
                                       ----.-HHHHTTT-----------THHHHHHH...HHHHHHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHH CS
                            DUF892  66 sekkcdamegliaegqelieeaaedeslkdaaliaaaqavehyEiAsYgtLialAeqlgekeaaklLeqtleeekat 142
                                       +e k d ++  +   ++++ + ++ e lk+++  +a  + e+  ++ Y+ ++++A++ g++++ ++L +  e+ek  
  gi|518652825|ref|YP_008142345.1|  43 RELK-DKANVELGHFNAIFATLVKYEGLKGLVNDMAKEETEQ-HVSEYTNVANAAKAEGHDDIEAMLCAFSEQEKGI 117
                                       5555.5555556667788888888888888884444444444.489******************************* PP

                                       HHHHHH CS
                            DUF892 143 deklte 148
                                       +e+l++
  gi|518652825|ref|YP_008142345.1| 118 AETLKR 123
                                       ***986 PP

>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   3.7   2.8e-05      0.13       4     101 ..      12     123 ..       9     127 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHH......... CS
                          Ferritin   4 LneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraelee......... 71 
                                       L e+l++  + ++   a + y++ +g  + a +++++a  e++h+ +++  + + +g      + l +         
  gi|518652825|ref|YP_008142345.1|  12 LKELLTANAEDHMRLNAASNYFEKIGDLETARELKDKANVELGHFNAIFATLVKYEG-----LKGLVNdmakeeteq 83 
                                       6667777777777788999**************************************.....665555555567777 PP

                                       .........C-SSSS.CSSHHHHHHHHHHHHHHHHHHHHH CS
                          Ferritin  72 .........ieapke.fgsveevleaalehekkvteslre 101
                                                 +a+ e  +++e++l a  e+ek + e+l++
  gi|518652825|ref|YP_008142345.1|  84 hvseytnvaNAAKAEgHDDIEAMLCAFSEQEKGIAETLKR 123
                                       8888887654444445569999999999999999988876 PP

>> Oxidored_FMN  NADH:flavin oxidoreductase / NADH oxidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.23     1e+03     264     303 ..      19      58 ..       2      75 .. 0.65
   2 ?   11.7   0.5   2.6e-05      0.12     140     172 ..      74     106 ..      64     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.23
                                       SSSTTS-TTTTHHHCCTTHHHHHHCCCHSSEEEE-SS--S CS
                      Oxidored_FMN 264 haaeprkrgagsvrteqekntefvkevwkkplitvgriad 303
                                       +a+   + +a s  +e+ +++e  +e+ +k+ +  g+++ 
  gi|518652825|ref|YP_008142345.1|  19 NAEDHMRLNAASNYFEKIGDLETARELKDKANVELGHFNA 58 
                                       4555556666666677447888888888888888887765 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 2.6e-05
                                       EE--HHHHHHHHHHHHHHHHHHHHTT-SEEEEE CS
                      Oxidored_FMN 140 keltkeeikqliqefveAAkraieAgfDgVeih 172
                                         + kee +q++ e+++ A+ a++ g D +e +
  gi|518652825|ref|YP_008142345.1|  74 NDMAKEETEQHVSEYTNVANAAKAEGHDDIEAM 106
                                       579*************************99965 PP

>> A_thal_3526  Plant protein 1589 of unknown function (A_thal_3526)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0    0.0044        20      17      41 ..      40      64 ..      35      67 .. 0.88
   2 ?    5.2   0.0    0.0057        26       9      29 ..      72      92 ..      70      96 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0044
                       A_thal_3526 17 evvraLeeqanIepeftslVWkkLe 41
                                      e+ r L+++an+e    ++++  L 
  gi|518652825|ref|YP_008142345.1| 40 ETARELKDKANVELGHFNAIFATLV 64
                                      99************99999998886 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0057
                       A_thal_3526  9 LqlymskeevvraLeeqanIe 29
                                      L + m kee+ ++++e  n+ 
  gi|518652825|ref|YP_008142345.1| 72 LVNDMAKEETEQHVSEYTNVA 92
                                      6678************99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 919.47
//
Query:       gi|518652826|ref|YP_008142346.1|  [L=141]
Description: MutT family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.8e-14   51.7   0.0    1.1e-13   51.3   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 !   51.3   0.0   6.3e-18   1.1e-13       3     119 ..       6     114 ..       5     126 .. 0.73

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 6.3e-18
                                       EEEEEEEEEETTSEEEEEEESSSSTTT..EESSEEECBTTSHHHHHHHHHHHHHHSEEEEEEEEEEEEEEEEEEEEE CS
                             NUDIX   3 rravgvvllnekgevLlvrrskkpfpg..WelPgGkvepgEtpeeAArREleEEtGleaellellgrlhylapydgp 77 
                                       ++avg v++ +++ +Ll +r+ + ++   W++PgGk+e +Et+ee + RE+ EEtGl++e   llg       ++ +
  gi|518652826|ref|YP_008142346.1|   6 KVAVGGVITLGNK-ILLGKRR-DEPDRykWAIPGGKLELNETIEEGLKREMLEETGLTVEVENLLG------ISEII 74 
                                       5899999999994.*******.3333358***************************9887778888......44555 PP

                                       EEEEEEEEEEEE.EEECSGCSSTSTTTEEEEEEEEHHHHHHHH CS
                             NUDIX  78 ygdeheilyvfl.eevegelepndenevsevrwvpleellkek 119
                                        +d h+i++ +  ++v+g  + +   +   ++++++e l +  
  gi|518652826|ref|YP_008142346.1|  75 RKDFHYIILDYKcRPVKGIEHAG--SDALRLKYFDMESL-DNS 114
                                       55566666666655555555544..66677788888888.444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (141 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1003.59
//
Query:       gi|518652827|ref|YP_008142347.1|  [L=475]
Description: amino acid permease related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   93.4  55.6    1.8e-26   92.8  55.6    1.3  1  AA_permease    Amino acid permease
      1e-25   90.5  60.7    1.3e-25   90.2  60.7    1.1  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
       0.24   11.5   9.6         18    5.5   2.3    3.9  3  DUF962         Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8  55.6   3.1e-30   1.8e-26      27     471 ..      41     450 ..      13     458 .. 0.81

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 3.1e-30
                       AA_permease  27 GplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasiliqf 103
                                         +++ la+l+a++  ++ +++ ++ +t++ ++ggfyt+ ++ +gp+ G + Gl+yl+++ + la+ +   s ++  
  gi|518652827|ref|YP_008142347.1|  41 AKGALPLAILIAVISGLIWVNTPYQYSTKIASAGGFYTFTRKAIGPKYGLFDGLIYLMFEYAILANTTLFFSGVLIP 117
                                       344579*************************************************9999999999987666655544 PP

                       AA_permease 104 welvtdlpkawvt.......gavflvvlliinlvgvkvygeaefilalikiiaiiafiivg...iillaggkpnkga 170
                                       +  ++d + + v         +vf++++++++++g+k + +    +al+  +  ia +i++   ii+++g k++ + 
  gi|518652827|ref|YP_008142347.1| 118 A-IFSDFFGITVSkylwipiLIVFVLIFTVLPYIGIKPSVK----YALFGSLLEIAILIILsaaIIIISGPKNTGA- 188
                                       4.488888666668888**999*******************....6666665555555555574444444444444. PP

                       AA_permease 171 gfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviritifY 247
                                                      + p      +g ++  + + v   f +tG +  ++i++E+k P+ +i+ka+   +++++ ++
  gi|518652827|ref|YP_008142347.1| 189 --------------VFLPE----LSGGISPLFEGVVLGTFLMTGASGAVYIGEEAKMPRTNIKKAMAVSFVITGALF 247
                                       ..............33333....4556************************************************** PP

                       AA_permease 248 vlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasRvlyslakdgla 324
                                       +l++++ +++++ +  g+++  + +  ++++  k++g ++l + i+++++ +++ s++s l +  R+ ys+++dg++
  gi|518652827|ref|YP_008142347.1| 248 LLVAYAFTIGWGPTKMGNFATELIP--GLILSDKFLGFPFLVV-IVILLFNSVFVSMVSPLNVLGRISYSFSRDGVM 321
                                       ********************99977..9999999999998865.56678899************************* PP

                       AA_permease 325 P.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsylrfRkalkyqgrs 400
                                       P +++k + k++ P +ai+++ i s ++ ++ +l  ++++ + +l++i+ l+ ++ ++++ ++++ +  +       
  gi|518652827|ref|YP_008142347.1| 322 PpWFVKIHPKYKTPSNAIAFMGISSIVVSVIVGLVYGPFYGYIILITIASLALFAGHIMSDFALPFLYHK-----L- 392
                                       *****************************************************************44444.....3. PP

                       AA_permease 401 ieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvgvklhvk 471
                                               + l+ g+ ++l + ++i+l+ ++y +++ +  p++        a + +l+ li +++ ++++k
  gi|518652827|ref|YP_008142347.1| 393 --------HELNIGLHIILPITSLIVLVFGVYFSVIPPVFPYS----LATTATV-ILIALIGIFVAHFAKK 450
                                       ........33566888899999999999999988885555533....3333333.3333344444444444 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.2  60.7   2.1e-29   1.3e-25      10     420 ..      30     439 ..      11     446 .. 0.78

  Alignments for each domain:
  == domain 1  score: 90.2 bits;  conditional E-value: 2.1e-29
                     AA_permease_2  10 vigsvigsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwf 86 
                                       v++s++g       +a+++  al l ++iav+ g l+ + +  ++s+++ + gG y++t++a+g+k + + + ++++
  gi|518652827|ref|YP_008142347.1|  30 VVTSLTG-------AALYAKGALPLAILIAVISG-LIWVNTPYQYSTKIASAGGFYTFTRKAIGPKYGLFDGLIYLM 98 
                                       2222222.......45556666777777777777.5566666779999***************************77 PP

                     AA_permease_2  87 ayvpvlasilsvaasyllnalgpdlqgn...twltyliaiaililvalinirgikesakiqnilgilkillpliili 160
                                       +  + la ++  + + l+ a+++d++g    ++l++ i i+++++++++ ++gik s k++ ++ +l i  +liil 
  gi|518652827|ref|YP_008142347.1|  99 FEYAILANTTLFFSGVLIPAIFSDFFGItvsKYLWIPILIVFVLIFTVLPYIGIKPSVKYALFGSLLEIA-ILIILS 174
                                       777767677777777777777776666423377888999******************************5.544444 PP

                     AA_permease_2 161 ilglitvdgggfsslstetdtffpngwpgv...llgllivlwsfdGfesaanvseevkk..kdvpkaifigllivlv 232
                                        +++i+++g  ++     +  f+p+ + g+   + g    ++ ++G ++a+++ ee+k   ++++ka+ ++++i++ 
  gi|518652827|ref|YP_008142347.1| 175 -AAIIIISGPKNT-----GAVFLPELSGGIsplFEGVVLGTFLMTGASGAVYIGEEAKMprTNIKKAMAVSFVITGA 245
                                       .666666666666.....556888866653344999999*****************6655279************** PP

                     AA_permease_2 233 lyllvniaflgvvpddeianlsn.lgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvl 308
                                       l+llv+ af+++ ++ ++ n ++ l+ ++ ++ +++ g  + +++vil++ s++ ++ + +    r+ ++++rdgv+
  gi|518652827|ref|YP_008142347.1| 246 LFLLVAYAFTIGWGPTKMGNFATeLI-PGLILSDKFLGFPFLVVIVILLFNSVFVSMVSPLNVLGRISYSFSRDGVM 321
                                       ******************99888444.899999999988899999999999************************** PP

                     AA_permease_2 309 Prffakvn.kfgspiraiiltaivslillllfllassaayn...fllsvsslgliisyllliigalilrkkrphlkr 381
                                       P +f k++ k+++p++ai +  i s+++++++ l+ +  ++   +l +++sl+l+   ++  +++ +l+ k ++l+ 
  gi|518652827|ref|YP_008142347.1| 322 PPWFVKIHpKYKTPSNAIAFMGISSIVVSVIVGLV-YGPFYgyiILITIASLALFAGHIMSDFALPFLYHKLHELNI 397
                                       *************************9999988865.33333444888888888888888888888888888777655 PP

                     AA_permease_2 382 pgkilvaiigalfllfllvalffppkgp...atqssliytii 420
                                          i++ i+++++l+f +++  +pp+ p   at+ ++i+  +
  gi|518652827|ref|YP_008142347.1| 398 GLHIILPITSLIVLVFGVYFSVIPPVFPyslATTATVILIAL 439
                                       334778888888888888888888776632245555554422 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.034   2.1e+02      43      66 ..     183     269 ..     114     292 .. 0.70
   2 ?    5.5   2.3    0.0031        18      22      64 ..     338     380 ..     329     388 .. 0.90
   3 ?    3.9   2.0    0.0093        56      17      64 ..     393     448 ..     387     457 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.034
                            DUF962  43 k...............................................................lklllalfvvgyi 56 
                                       +                                                               + l++++f++g++
  gi|518652827|ref|YP_008142347.1| 183 PkntgavflpelsggisplfegvvlgtflmtgasgavyigeeakmprtnikkamavsfvitgalFLLVAYAFTIGWG 259
                                       25666666666666666666666666666666666666666666666666666666666666667778888999998 PP

                            DUF962  57 fafvGHfvfE 66 
                                          +G f  E
  gi|518652827|ref|YP_008142347.1| 260 PTKMGNFATE 269
                                       8888877666 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0031
                            DUF962  22 llHfigvplilltvlllllraklklllalfvvgyifafvGHfv 64 
                                       ++ f+g++ i+++v++ l+++++   + l +++  + f+GH +
  gi|518652827|ref|YP_008142347.1| 338 AIAFMGISSIVVSVIVGLVYGPFYGYIILITIASLALFAGHIM 380
                                       56799************************************75 PP

  == domain 3  score: 3.9 bits;  conditional E-value: 0.0093
                            DUF962  17 npinrllHfigvplilltvlllllrak........lklllalfvvgyifafvGHfv 64 
                                       ++ n+ lH+i  ++ l+++++ ++++         l++ +++ +++ i+ fv+Hf 
  gi|518652827|ref|YP_008142347.1| 393 HELNIGLHIILPITSLIVLVFGVYFSVippvfpysLATTATVILIALIGIFVAHFA 448
                                       4578888988655554444444444444578887788999999999********93 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); 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):               3  [number of targets reported over threshold]
# CPU time: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 3379.11
//
Query:       gi|518652828|ref|YP_008142348.1|  [L=429]
Description: hypothetical protein FACI_IFERC00001G1467 [Ferroplasma acidarmanus fer1]
Scores for 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-105  354.1   0.0   1.2e-105  353.9   0.0    1.0  1  GDC-P          Glycine cleavage system P-protein
     0.0079   15.4   0.0      0.012   14.8   0.0    1.2  1  Aminotran_1_2  Aminotransferase class I and II
  ------ inclusion threshold ------
       0.01   14.8   0.0      0.016   14.2   0.0    1.2  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 !  353.9   0.0  1.9e-109  1.2e-105      10     430 .]       3     427 ..       1     427 [. 0.91

  Alignments for each domain:
  == domain 1  score: 353.9 bits;  conditional E-value: 1.9e-109
                                       HHHHHHHHHT-SSHHHHHHHHS-GGGB--S---------HHHHHHHHHHHHTTB--.-EE--BTTB------HHHHH CS
                             GDC-P  10 dqkemLetlGlkslddliekavPkeiklkkelkleapksEeellaelekiasknkv.vksfiGaGyydtilPaviqr 85 
                                       ++ e+L+ l +ks+d l+ +++P+++  k +l l +p++E   ++ +e    knk    +f+G+G+yd+ +P+ ++ 
  gi|518652828|ref|YP_008142348.1|   3 ETDEILDYLNVKSVDGLF-SDIPDRL--KVSLDLGKPMDEFSTIRAIEDTGRKNKAgNMNFLGNGIYDRFVPPLVDE 76 
                                       7889**************.9****99..567889**********************99******************9 PP

                                       HTTT-HHHHS--S-SSGGG-HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHHHHHH-SSS--EEEEETT CS
                             GDC-P  86 nilenpewytaYtPYqaEisqGrLeallnfqtlvadltGldianasllDegtAaaEAvllaaraskkkakkvvvdkk 162
                                        i+ + e++t+YtPYq+EisqG L++l+++q++++dlt +di+n+s++D+ t +aEAv +a+r++ k   +v++ ++
  gi|518652828|ref|YP_008142348.1|  77 -IIGRNEFLTSYTPYQPEISQGILHSLFEYQSIISDLTEMDITNSSMYDGFTSLAEAVRMAYRINGKS--EVLIPEN 150
                                       .**************************************************************99888..9****** PP

                                       S-HHHHHHHHHHHGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB----HHHHHHHHHTT-EEEE CS
                             GDC-P 163 vhpqtlevlktrakglgieivevdlteekvtd.......kekevagvlvqypnteGriedlkelvekakkkkslvvv 232
                                       +++ +l+++k +++gl+++i++    +++  d       +++++++++v  pn++G i +    v+++kk +s+++ 
  gi|518652828|ref|YP_008142348.1| 151 IYKSQLSIIKNYTEGLNLKIITYGFGTDGLLDledlkskVTSDTSAIIVENPNVFGLIDENAFHVSEIKK-DSILIT 226
                                       **********************99999988888889888999****************997777777766.566778 PP

                                       EE-TTGGGTB--HHHHT-SEEEEE-TTTT---GGG----EEEEE-GGGGGG--S-EEEEEEBTTS-EEEEEE-CCGS CS
                             GDC-P 233 aadllaLtllkpPgelgaDivvGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRlvGvskDaegkralrlalqtRE 309
                                         d+++L+ + pPge+g+Di+v ++q++G+ + yGGP  g f  k++++ + PGRl+G+skD+egk+a++++lq+RE
  gi|518652828|ref|YP_008142348.1| 227 YYDPVSLGFIIPPGEYGTDIAVAEGQQLGIHMNYGGPLLGLFSFKKEYVHRSPGRLIGLSKDSEGKKAFVMTLQARE 303
                                       89*************************************************************************** PP

                                       HHCCHHHCS-S--S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT..T-EE--SSBSSEEEEE--T CS
                             GDC-P 310 qHirRdkAtsniCtaqaLlAnlaalyavyhGkeglkeiarrihkkteilakelkkk.leeelkkkkffdtllievee 385
                                       qHirR +A sniC++qaLlA+++  y  + G+egl++ia  +++k+  l++++k++ ++ ++++ +f d l      
  gi|518652828|ref|YP_008142348.1| 304 QHIRRSRAMSNICSNQALLAVASLAYLSIMGSEGLRKIALITMNKSRKLKNNMKSAgIKPVFDGINFSDNLFYFDRL 380
                                       *******************************************************9999999999999998874442 PP

                                       ..TTHHHHHHHHHHTTEE-EEESTTEEEEE--TT--HHHHHHHHHHH CS
                             GDC-P 386 ..kaaekvlkkaekeglnlrkvelktvgialdEtvtkedieallkvl 430
                                           ++++      + +  ++   ++   +++E++ +e+ie+l k+l
  gi|518652828|ref|YP_008142348.1| 381 eiLESNNISGGIRLSSISEYNGYGNASFFSVTEKTGDENIEKLAKIL 427
                                       11222223333333334444444557778999999999999998875 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0     2e-06     0.012      70     158 ..     119     203 ..      64     204 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                                       GEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTT....SEEEEEEBEETTTTEE-HHHHHHHHTTH CS
                     Aminotran_1_2  70 avvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsg....gevvryplyseedfhldlealeealkea 142
                                       +  +  G+++l+ea+ ++ ++n ++e+l+p+  y s   i+++++    +++++y +    d  ldle+l+ ++++ 
  gi|518652828|ref|YP_008142348.1| 119 NSSMYDGFTSLAEAVRMAYRINGKSEVLIPENIYKSQLSIIKNYTeglnLKIITYGFG--TDGLLDLEDLKSKVTS- 192
                                       556778*****************************98888887642222566666655..9***************. PP

                                       HCTTETEEEEEEESS- CS
                     Aminotran_1_2 143 pegnkktkvilvesph 158
                                             t  i+ve+p+
  gi|518652828|ref|YP_008142348.1| 193 -----DTSAIIVENPN 203
                                       .....8999*****96 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.7e-06     0.016      79     172 ..     135     225 ..     124     262 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.7e-06
                                       HHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB CS
                       Aminotran_5  79 lslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGti 155
                                       ++  ++++ + e+++ e+ ++++l  +++  +  ++k+  + +  +g+ldl++l+++++ +t++++   + nv G i
  gi|518652828|ref|YP_008142348.1| 135 MA--YRINGKSEVLIPENIYKSQLSIIKNYTEGLNLKIITYGFGTDGLLDLEDLKSKVTSDTSAII-VENPNVFGLI 208
                                       33..35999*********************9999999999999********************975.5789*****9 PP

                                       --HHHHHHHHHHTT-EE CS
                       Aminotran_5 156 qpveeigklakkkgalv 172
                                       ++ +  ++ +kk  +l+
  gi|518652828|ref|YP_008142348.1| 209 DENAFHVSEIKKDSILI 225
                                       99887777777765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.31s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2796.56
//
Query:       gi|518652829|ref|YP_008142349.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G1468 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-12   45.7   0.5      1e-10   41.1   0.1    2.0  2  GDC-P            Glycine cleavage system P-protein
    5.2e-11   42.1   0.0    9.1e-11   41.3   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
    7.7e-05   22.0   0.0    0.00051   19.3   0.0    1.9  2  Aminotran_1_2    Aminotransferase class I and II
    0.00034   20.0   0.0    0.00054   19.3   0.0    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0049   16.2   0.1     0.0078   15.6   0.1    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.11   12.6   0.8       0.27   11.4   0.8    1.6  1  Mad3_BUB1_I_2    Putative Mad3/BUB1 like region 1 protein


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 !   41.1   0.1   3.4e-14     1e-10     105     288 ..     103     297 ..      95     305 .. 0.79
   2 ?    2.8   0.1     0.014        41     334     429 ..     332     433 ..     325     434 .. 0.67

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 3.4e-14
                                       -HHHHHHHHHHHHHHHHHHT-SEE-S-BS-HHHHHHHHHHH.HHHH...-S...SS--EEEEETTS-HHHHHHHHHH CS
                             GDC-P 105 sqGrLeallnfqtlvadltGldianasllDegtAaaEAvll.aara...sk...kkakkvvvdkkvhpqtlevlktr 174
                                       +qG+Le + n q++++ + G+d a   l   + A +E   + ++r+   ++    k++++++  + h  +       
  gi|518652829|ref|YP_008142349.1| 103 TQGTLEVMYNMQQFLVKISGMDYA--TLQPSAGAHGELTGIlIVRKyfeTRgeiDKRNEIIIPDSAHGTN----PAS 173
                                       6*********************85..78999999999754403332111221113345555555555443....356 PP

                                       HGGGT-EEEEE-GGG--S-..........S-EEEEEEEES-TTSB---.-HHHHHHHHHTT-EEEE.EE-TTGGGTB CS
                             GDC-P 175 akglgieivevdlteekvtd.......kekevagvlvqypnteGried.lkelvekakkkkslvvv.aadllaLtll 242
                                       a   g+++vev++ e++  d       +++++a+ ++  pnt G   d ++e++  ++++ sl+    a+  a+  +
  gi|518652829|ref|YP_008142349.1| 174 AVMAGFKVVEVPSNENGLVDlealkaaVNENTAAFMITNPNTLGIFDDqISEIATIIHNNGSLLYYdGANFNAILGI 250
                                       77789999999999999998999999999***************998779***********998763689999999* PP

                                       --HHHHT-SEE.EEE-TTTT---GGG----EEEEE-GGGGGG--S-E CS
                             GDC-P 243 kpPgelgaDiv.vGsaqrfGvPlgyGGPhagffAvkeklkRkiPGRl 288
                                       ++Pg++g Div +   + f  P g GGP ag +Avk+ l+  +P  +
  gi|518652829|ref|YP_008142349.1| 251 TTPGKMGFDIVhFNLHKTFATPHGGGGPGAGPVAVKSFLMDFLPVPI 297
                                       **********94566789******************88887777655 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT....T-EE--SSBSSEEEEE--TTT..HHH.HHHHHHHTTEE-EE CS
                             GDC-P 334 lyavyhGkeglkeiarrihkkteilakelkkk...leeelkkkkffdtllieveeka..aek.vlkkaekeglnlrk 404
                                       +  v++  + l + a+r   +++++ak+l k     +++lkk++f    + +++ ka  ++k +l+ ++++   ++ 
  gi|518652829|ref|YP_008142349.1| 332 FSYVLKNGNNLSANAKRAVMNSNYMAKKLSKYykiPYKQLKKHEFV-LSTENTGRKAldISKfILDYGIHSPTTYFP 407
                                       44455556779999***************99733223455555543.222333334411345688998888877776 PP

                                       ESTT.EEEEE--TT--HHHHHHHHHH CS
                             GDC-P 405 velk.tvgialdEtvtkedieallkv 429
                                          k ++ i  +E vtk+d++  ++v
  gi|518652829|ref|YP_008142349.1| 408 LIVKeAMMIEPTESVTKKDMDYYIDV 433
                                       655549999*********99877665 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.3   0.0     3e-14   9.1e-11      84     207 ..     151     274 ..     139     278 .. 0.83

  Alignments for each domain:
  == domain 1  score: 41.3 bits;  conditional E-value: 3e-14
                                       C..-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTE.B-- CS
                       Aminotran_5  84 s..lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGt.iqp 157
                                       +  +++++ei++ ++ h  n   + +++   g+kv+ +p +e+g++dl++l++++ne+t++ +it + n++G+  ++
  gi|518652829|ref|YP_008142349.1| 151 RgeIDKRNEIIIPDSAHGTNP--ASAVM--AGFKVVEVPSNENGLVDLEALKAAVNENTAAFMIT-NPNTLGIfDDQ 222
                                       245889999999999998887..66665..69*****************************9998.57889**4456 PP

                                       HHHHHHHHHHTT-EEEEE-TTTTTTS--.-HHHHTESEEEEETTT.TTSSTT CS
                       Aminotran_5 158 veeigklakkkgalvlvDaaqavghipi.dvkklgvDflafsghK.llgPtG 207
                                       + ei+++++++g l+  D+a       i    k+g D++ f  hK +  P G
  gi|518652829|ref|YP_008142349.1| 223 ISEIATIIHNNGSLLYYDGANFNAILGItTPGKMGFDIVHFNLHKtFATPHG 274
                                       ********************8555444404579************7777887 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 !   19.3   0.0   1.7e-07   0.00051      38     186 ..      98     239 ..      67     247 .. 0.68
   2 ?    0.4   0.0     0.099     3e+02     260     344 ..     328     414 ..     311     433 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.7e-07
                                       TST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH.......HTTT-EEEEEESS-THHH CS
                     Aminotran_1_2  38 neygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk.......lnpgdeilvpdptyasyk 107
                                        + ++++g  e+ +++ +fl    k++    a+++ + Ga+  +  +  + k       +++  ei++pd  ++   
  gi|518652829|ref|YP_008142349.1|  98 ESQLKTQGTLEVMYNMQQFLV---KISGMDYATLQPSAGAHGELTGILIVRKyfetrgeIDKRNEIIIPDSAHGTNP 171
                                       555556666666666666666...3333333355555555443333333333444444489999************* PP

                                       HHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEE CS
                     Aminotran_1_2 108 nilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlll 184
                                         + ++g++vv++p  s e+  +dleal++a++e       t  + +++p+   G  +  +++ +++++++ ++ ll
  gi|518652829|ref|YP_008142349.1| 172 ASAVMAGFKVVEVP--SNENGLVDLEALKAAVNE------NTAAFMITNPN-TLG--IFDDQISEIATIIHNNGSLL 237
                                       **************..77****************......66788888874.333..33455555555566666555 PP

                                       EE CS
                     Aminotran_1_2 185 fv 186
                                       + 
  gi|518652829|ref|YP_008142349.1| 238 YY 239
                                       55 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.099
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS.TEEEECCS.CSSEEEEEETHHCHHHHHHHHHHTCTEEEEE CS
                     Aminotran_1_2 260 vaaalsdallkqseleemrqrlqkrrkelrdeLael.glkvlasq.sgmflltdlsaetakelskkLleevgvyvtp 334
                                       v+ a s +l+  ++l+++++r   ++ ++ ++L +   +++ + + + ++l t+ +  +a ++sk +l++ g++   
  gi|518652829|ref|YP_008142349.1| 328 VLRAFSYVLKNGNNLSANAKRAVMNSNYMAKKLSKYyKIPYKQLKkHEFVLSTENTGRKALDISKFILDY-GIHSPT 403
                                       5666677777777999999999999999999998887777766665788888888888888888888888.887666 PP

                                       GGGGTS.TTEE CS
                     Aminotran_1_2 335 gtsftv.pgrl 344
                                          + + ++  
  gi|518652829|ref|YP_008142349.1| 404 TYFPLIvKEAM 414
                                       33333365555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.8e-07   0.00054      70     205 ..     156     274 ..     103     286 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.8e-07
                                       TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB--- CS
                   Beta_elim_lyase  70 rgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvs 146
                                       + +e+i+ + ah+   ++ a a++ag k+++++++e+G +dle+l+aa++e      ++++ ++t+ n    G  + 
  gi|518652829|ref|YP_008142349.1| 156 KRNEIIIPDSAHG---TNPASAVMAGFKVVEVPSNENGLVDLEALKAAVNE------NTAAFMITNPNTL--G--IF 219
                                       4456666666665...56788999**************************9......5777777777776..4..57 PP

                                       HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS- CS
                   Beta_elim_lyase 147 leelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG 205
                                        +++ e+a i +++g  l +DgA f na   +  + k    ++D+v + l K   ++ G
  gi|518652829|ref|YP_008142349.1| 220 DDQISEIATIIHNNGSLLYYDGANF-NAILGITTPGK---MGFDIVHFNLHKTFATPHG 274
                                       89*********************64.55533333322...3566666666666666655 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   2.6e-06    0.0078      60     181 ..     154     275 ..     148     277 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.6e-06
                                       TTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-..GGGB--.-HHHHHHH CS
                   DegT_DnrJ_EryC1  60 vgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVh..lyGqva.dmdalkai 133
                                       +++++e+I+p     +  ++++ +g k+v v  + +   +d +a++aa++e+t+a ++ +  ++G +  +++++  i
  gi|518652829|ref|YP_008142349.1| 154 IDKRNEIIIPDSAHGTNPASAVMAGFKVVEVPSN-ENGLVDLEALKAAVNENTAAFMITNpnTLGIFDdQISEIATI 229
                                       7899***************************887.8899***************98887533788888789999999 PP

                                       HHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-E CS
                   DegT_DnrJ_EryC1 134 aakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGG 181
                                        ++ g  +  D A+ + a +     G++g + ++ F   K+++t  GG
  gi|518652829|ref|YP_008142349.1| 230 IHNNGSLLYYDGAN-FNAILGITTPGKMG-FDIVHFNLHKTFATPHGG 275
                                       99999999999986.56666666666777.555556666666665555 PP

>> Mad3_BUB1_I_2  Putative Mad3/BUB1 like region 1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.8     9e-05      0.27      38     106 ..     357     431 ..     351     440 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9e-05
                     Mad3_BUB1_I_2  38 lKkIskfyyfvYlelsry.Flkkgkk......eaalfiLqegiknkvydkeilkeelksikklekklseeeakkll 106
                                       +Kk+sk+y+  Y +l+++ F+ + ++      ++++fiL  gi+       ++ +e + i+ +e +++++++  ++
  gi|518652829|ref|YP_008142349.1| 357 AKKLSKYYKIPYKQLKKHeFVLSTENtgrkalDISKFILDYGIHSPTTYFPLIVKEAMMIEPTE-SVTKKDMDYYI 431
                                       79*************9997765543222223389*********998766666666666888888.77777766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.45
# Mc/sec: 3159.76
//
Query:       gi|518652830|ref|YP_008142350.1|  [L=369]
Description: hypothetical protein FACI_IFERC00001G1469 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.3e-11   42.1   0.8     0.0016   18.4   0.2    3.6  3  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
       0.15   12.0   0.3        2.5    8.0   0.0    2.6  3  UPF0179          Uncharacterised protein family (UPF0179)


Domain annotation for each model (and alignments):
>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   0.0   1.6e-05      0.15      25      65 ..      60     105 ..      29     125 .. 0.79
   2 !   18.4   0.2   1.8e-07    0.0016       1      71 [.     135     204 ..     135     210 .. 0.86
   3 !    8.1   0.0   0.00028       2.5      18      73 ..     278     350 ..     264     353 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.6e-05
                                       ETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTS.........S CS
                   tRNA_anti-codon  25 DgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpgg.........e 65 
                                       D+tg +  +++      +   +k+Gdvv+++  + k ++++         e
  gi|518652830|ref|YP_008142350.1|  60 DETGVLPYTAWE-----FPAPIKPGDVVQIKyAKTKVYNDRmrlyfdsktE 105
                                       788888888888.....999******************9994444444440 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 1.8e-07
                                       EEEEEEEEEEE....EEEETTEEEEE..EEETTEEEEEEEETHHHHHHHTTS-TTSEEEEE.EEEEECTTSSEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsis....drsggkvifid..lrDgtgriqvvlfreeatklaenlkeGdvvrvt.Grvkrrpggelelkv 70 
                                       V v G+++++s     ++g+ +  +   ++D+t r++++ f        + l++G+v+r+   rv++++++ le+++
  gi|518652830|ref|YP_008142350.1| 135 VAVTGKISNMSgkeyNKAGKTFTIYNgfIEDDTSRVRISSFG-------KPLENGKVYRIVgARVSEFNKQ-LEISI 203
                                       6799*********765555555555599**************.......************99*****999.99987 PP

                                       E CS
                   tRNA_anti-codon  71 e 71 
                                        
  gi|518652830|ref|YP_008142350.1| 204 G 204
                                       5 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.00028
                                       EEEEEEEETTEEEEEEEET..................HHHHHHHTTS-TTSEEEEEEEEEECTTSSEEEEEEEE CS
                   tRNA_anti-codon  18 vifidlrDgtgriqvvlfr..................eeatklaenlkeGdvvrvtGrvkrrpggelelkveei 73 
                                       +++++l+Dgt  iq+++ +                  +e ++++e+   G  v++     + ++  l+l v++i
  gi|518652830|ref|YP_008142350.1| 278 FSYFTLDDGTKYIQCIAGKnaimpfigikeeelphyaGEIYRMLEEKLYGHAVKINADFIKNEED-LSLRVNSI 350
                                       679************99887777666666666666665555555555566666666666666655.66666665 PP

>> UPF0179  Uncharacterised protein family (UPF0179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.042   3.8e+02      37      75 ..       9      46 ..       6      55 .. 0.80
   2 ?    8.0   0.0   0.00028       2.5       6      52 ..     146     194 ..     141     221 .. 0.73
   3 ?   -3.1   0.1      0.75   6.7e+03      94     106 ..     252     264 ..     242     281 .. 0.57

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.042
                           UPF0179 37 LekgrkYrivevrekteheCavheegvvaveveeapiea 75
                                      L+k + Y+i++++e  + + +  e++v+  +v++ +i++
  gi|518652830|ref|YP_008142350.1|  9 LNKHKGYEIMKINEM-QGNLNNVEGKVKILSVDKREITT 46
                                      889999*******99.55555666779999998888765 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.00028
                           UPF0179   6 gkklAkeGteFiylgeaeeCekCklkkvCln..LekgrkYrivevrekt 52 
                                       gk++ k G++F+ ++   e ++ +++   +   Le+g+ Yriv+ r ++
  gi|518652830|ref|YP_008142350.1| 146 GKEYNKAGKTFTIYNGFIEDDTSRVRISSFGkpLENGKVYRIVGARVSE 194
                                       89999******8777665555555555555445**********999775 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.75
                           UPF0179  94 eCdevecesyelc 106
                                       +C+e++ +  + +
  gi|518652830|ref|YP_008142350.1| 252 RCSECNKPLSNGV 264
                                       3444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2503.47
//
Query:       gi|518652831|ref|YP_008142351.1|  [L=298]
Description: hypothetical protein FACI_IFERC00001G1470 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00084   19.3   0.0     0.0016   18.4   0.0    1.4  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
      0.011   16.1   0.0      0.025   15.0   0.0    1.5  1  RuvA_C           RuvA, C-terminal domain
      0.019   14.3   0.0       0.05   12.9   0.0    1.6  2  Pho88            Phosphate transport (Pho88)
      0.068   13.8   0.0        0.3   11.8   0.0    1.9  2  RPA_C            Replication protein A C terminal
      0.083   12.8   0.0        1.4    8.9   0.0    2.5  2  UBA_6            UBA-like domain
        0.1   12.5   0.0       0.24   11.3   0.0    1.6  1  TrmB             Sugar-specific transcriptional regulator Trm


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 !   18.4   0.0   5.4e-07    0.0016       3      64 ..      45     108 ..      43     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 5.4e-07
                                       EEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS CS
                   tRNA_anti-codon   3 vaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg 64 
                                       +aG +t +   s  +++ +++ D  g++ +++f+    +e+ + ++++ ++d+v v G+v+++++ 
  gi|518652831|ref|YP_008142351.1|  45 FAGAITYK--NSDDRMVKVTVADYIGSFYLTAFKtgfsSEMAEELDKFNVNDIVMVMGKVSSFKTD 108
                                       57888888..89999**********************999**********************9765 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.5e-06     0.025       7      25 ..     158     176 ..     157     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.5e-06
                                       HHHHHHCTS-HHHHHHHHH CS
                            RuvA_C   7 veALlaLGYkekeaekAva 25 
                                       v +Ll LGY++ eae A++
  gi|518652831|ref|YP_008142351.1| 158 VDTLLKLGYSQDEAEDAIR 176
                                       789**************97 PP

>> Pho88  Phosphate transport (Pho88)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.2   3.6e+03      75      87 ..      54      66 ..      45      70 .. 0.73
   2 ?   12.9   0.0   1.7e-05      0.05      25     118 ..     127     215 ..     120     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.2
                             Pho88 75 eeeklvttTvkdY 87
                                        +++v++Tv dY
  gi|518652831|ref|YP_008142351.1| 54 SDDRMVKVTVADY 66
                                      3567778888888 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.7e-05
                             Pho88  25 dpevllyvRilYvvsqliillvylyikskikkknDlttlkyvepasplskeeeklvttTvkdYDlaelkkllksilm 101
                                        + + + vR+ Yv+   i l++   ik  +     l  l y + +++         +  + dYD+++ ++++ si +
  gi|518652831|ref|YP_008142351.1| 127 TERYFWGVRASYVAKRKI-LAITEAIKDDVATVDTLLKLGYSQDEAE----DAIRAKEYYADYDFNSYMDAISSINF 198
                                       567889999999988776.5567778888887777666666444444....4445577899**************** PP

                             Pho88 102 gvammafmhlymkytnP 118
                                          +m + h  m + nP
  gi|518652831|ref|YP_008142351.1| 199 DSPVMTVAHREMDIENP 215
                                       **************998 PP

>> RPA_C  Replication protein A C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.4   4.1e+03      72      89 ..      82     100 ..      75     115 .. 0.73
   2 ?   11.8   0.0   9.9e-05       0.3      33      98 ..     221     288 ..     200     290 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.4
                                       HHHHHS.TSXHHHHHHHHH CS
                             RPA_C  72 eiaqkl.rlsvndvkqavd 89 
                                       e+a++l +++vnd+  ++ 
  gi|518652831|ref|YP_008142351.1|  82 EMAEELdKFNVNDIVMVMG 100
                                       6788888999999976654 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.9e-05
                                       XXXXXXXXXXXX.XSXHHHHHHHHHHHH.SXSTTTEEHHHHHHHS...TSXHHHHHHHHHHHHHTTSEE CS
                             RPA_C  33 galsgnqaklankgltalaqqvlnlikqspeseeGvhvdeiaqkl...rlsvndvkqavdeLsneGiiY 98 
                                        ++s+nq+++  +   + ++ vl +ik+   s  G + d i  +    ++s ++v +++++L + G iY
  gi|518652831|ref|YP_008142351.1| 221 EGNSSNQQNTGAPQTFNIEEFVLAYIKN-NDSGPGCKYDDIIISCsnaGISREKVDEILNSLGSRGEIY 288
                                       444444444444667889**********.78888****9987444456********************* PP

>> UBA_6  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00047       1.4       5      19 ..     158     172 ..     156     177 .. 0.82
   2 ?    0.5   0.0       0.2     6e+02      12      26 ..     268     282 ..     268     286 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00047
                             UBA_6   5 ldfflKLGYseeqvq 19 
                                       +d  lKLGYs+++ +
  gi|518652831|ref|YP_008142351.1| 158 VDTLLKLGYSQDEAE 172
                                       8999*******9865 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                             UBA_6  12 GYseeqvqavLekLG 26 
                                       G s e v+ +L+ LG
  gi|518652831|ref|YP_008142351.1| 268 GISREKVDEILNSLG 282
                                       558899********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 ?   11.3   0.0     8e-05      0.24      31      60 ..     266     293 ..     264     298 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8e-05
                                       CTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB  31 elgvprskvYevLrsLedkGlVerekgrpk 60 
                                       ++g++r kv e+L+sL ++G ++ +  + k
  gi|518652831|ref|YP_008142351.1| 266 NAGISREKVDEILNSLGSRGEIYEV--SLK 293
                                       689*****************88877..344 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.48
# Mc/sec: 1861.41
//
Query:       gi|518652832|ref|YP_008142352.1|  [L=202]
Description: hypothetical protein FACI_IFERC00001G1471 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.27   11.3   0.0    1.6  2  YbjN      Putative bacterial sensory transduction regulator


Domain annotation for each model (and alignments):
>> YbjN  Putative bacterial sensory transduction regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.5e-05      0.27      28     115 ..      35     127 ..      28     139 .. 0.78
   2 ?   -2.0   0.0       0.2   3.5e+03      99     117 ..     160     178 ..     131     187 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.5e-05
                                       EEEEETTEEEEEEE--SSTT-EEEEEEEEES-.....-TTHHHHHHHHHHHTTTTTTT-EEE.EETTEEEEEEEEE- CS
                              YbjN  28 vvgtwggyrftiallgeseelllvlafvarvp.....eedreallellnrwNrellfgkayl.dedgdvlvehdldl 98 
                                       + ++++ ++f i l+ +++   ++l +  +          r  +++ l+ +N++  ++k+ l   + +v+++ d+dl
  gi|518652832|ref|YP_008142352.1|  35 IALENNKIPFDILLYADDQKKSCSLIVRTGIEtatveNQPRLTIYRTLLLLNQKVEMVKFMLdGINEEVVAREDFDL 111
                                       6667777777788888887777766666666677776778999*******************888888889999999 PP

                                       .TT--HHHHHHHHHHHH CS
                              YbjN  99 dagltpeqldrllalvl 115
                                          lt++ l + l++ l
  gi|518652832|ref|YP_008142352.1| 112 -SVLTKDVLNTGLNTIL 127
                                       .7788877766666555 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.2
                                       .TT--HHHHHHHHHHHHHH CS
                              YbjN  99 dagltpeqldrllalvlea 117
                                        ag t+e+++++l  +l +
  gi|518652832|ref|YP_008142352.1| 160 SAGKTKEEIKDYLVSSLGL 178
                                       5677788888777776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1312.19
//
Query:       gi|518652833|ref|YP_008142353.1|  [L=117]
Description: hypothetical protein FACI_IFERC00001G1472 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-11   44.2   1.5    2.5e-11   43.8   1.5    1.1  1  NfeD             NfeD-like C-terminal, partner-binding
     0.0062   15.9   1.9     0.0075   15.6   1.9    1.1  1  DUF929           Domain of unknown function (DUF929)
  ------ inclusion threshold ------
      0.012   16.2   2.5      0.016   15.8   2.5    1.2  1  DUF3139          Protein of unknown function (DUF3139)
      0.084   12.8   0.0       0.12   12.3   0.0    1.2  1  UPF0542          Uncharacterised protein family UPF0542
       0.23   11.7   0.2       0.27   11.4   0.2    1.1  1  Shisa            Wnt and FGF inhibitory regulator
       0.23   10.9   0.9       0.27   10.6   0.9    1.1  1  TMEM156          TMEM156 protein family
        9.8    6.7   7.4         24    5.4   7.4    1.7  1  FeoB_associated  FeoB-associated Cys-rich membrane protein


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 !   43.8   1.5   9.7e-15   2.5e-11       3      84 .]      26     114 ..      19     114 .. 0.73

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 9.7e-15
                                       XXXXXXXXXXXXXXS---SSS--S....S---GGTTSEEEEEE-B....S-EEEEETTEEEEEE-.SS..B-TT-EE CS
                              NfeD   3 avvsvlllvllrplllkklkkkek...ktnaealiGkegvvledi....gtGrvkvdGeeWsarsege..iekgerV 70 
                                       ++v v+++ +++ +l k ++++ +    t++e++   +g++  +i    g G +k+dG +W+++ +g+  iek ++V
  gi|518652833|ref|YP_008142353.1|  26 IIVLVVIITVTVYYLYKIISSQ-RgrkYTGSESMTNIIGIASNNIdknaG-GFIKIDGVSWEVINNGDepIEKYDKV 100
                                       2333333333334455544332.234469999*************97644.*************975567******* PP

                                       EEEEE-SSSEEEEE CS
                              NfeD  71 rVveveGltliVep 84 
                                       +V+++ Gl+l+V++
  gi|518652833|ref|YP_008142353.1| 101 VVTGRIGLKLMVKK 114
                                       ************98 PP

>> DUF929  Domain of unknown function (DUF929)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.9   2.9e-06    0.0075       3      69 ..      18      86 ..      16      91 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                            DUF929  3 liviaiivliivvivvvslsaivsnalvelskqvyaseplstkfvkvsnqdlasn..gkvevyfvsweg 69
                                      l++++i+v+i++v+++++  +++++ +++   + y+ +++ t+++ + ++++++n  g +++  vswe 
  gi|518652833|ref|YP_008142353.1| 18 LVFAVILVIIVLVVIITVTVYYLYKIISSQRGRKYTGSESMTNIIGIASNNIDKNagGFIKIDGVSWEV 86
                                      677888888888888888888888888888899999999999999999999888744678888888875 PP

>> DUF3139  Protein of unknown function (DUF3139)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.8   2.5   6.4e-06     0.016       6      81 ..      23      97 ..      19      98 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.4e-06
                           DUF3139  6 iililliillvivkvfl..glvgskpikkylankkldkylqekgykeddIksikpkydskkgsyyakVvFKDepnleY 81
                                      i++i++++++++v+v+   +++ s+   ky++ +   + +   g+ +++I +    +   +g+    +   Dep ++Y
  gi|518652833|ref|YP_008142353.1| 23 ILVIIVLVVIITVTVYYlyKIISSQRGRKYTGSESMTNII---GIASNNIDKNAGGFIKIDGVSWEVINNGDEPIEKY 97
                                      5666666666666666668999999999**********99...99999999988888777777766666777776666 PP

>> UPF0542  Uncharacterised protein family UPF0542
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.8e-05      0.12      13      65 ..       8      60 ..       2      64 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.8e-05
                           UPF0542 13 vlyvakdPweFlttvlliltPllllsaflsyKLakelkkqekekklkakrkan 65
                                      v y +  P++ +  v+l++  l+++  +  y L k +  q+ +k   +   +n
  gi|518652833|ref|YP_008142353.1|  8 VDYTTAVPGSLVFAVILVIIVLVVIITVTVYYLYKIISSQRGRKYTGSESMTN 60
                                      7899************************************9998766655555 PP

>> Shisa  Wnt and FGF inhibitory regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00011      0.27      92     131 ..      21      60 ..       6      74 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                             Shisa  92 ifivfvivgvvvivcccgclkkkqrekrpgrenlssalae 131
                                       ++i+ +iv vv+i++ +  l+k  +++r ++ + s + ++
  gi|518652833|ref|YP_008142353.1|  21 AVILVIIVLVVIITVTVYYLYKIISSQRGRKYTGSESMTN 60 
                                       45777888889999999999**999999444444444444 PP

>> TMEM156  TMEM156 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.9   0.00011      0.27     177     213 ..      23      58 ..      13      71 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
                           TMEM156 177 tWyvlvllvfifliiliihKileehrrvqkwqshkyk 213
                                       +  ++vl+v+i + +  ++Ki+ ++r  +k++     
  gi|518652833|ref|YP_008142353.1|  23 ILVIIVLVVIITVTVYYLYKIISSQR-GRKYTGSESM 58 
                                       3345555555555566679***9998.8888866555 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   7.4    0.0095        24       3      23 ..      26      46 ..      17      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0095
                   FeoB_associated  3 iIVgliiaaavafvirrlikk 23
                                      iIV+++i+ + ++ ++++i +
  gi|518652833|ref|YP_008142353.1| 26 IIVLVVIITVTVYYLYKIISS 46
                                      677777777777778887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1522  (0.0848904); expected 358.6 (0.02)
Passed bias filter:                      838  (0.0467399); expected 358.6 (0.02)
Passed Vit filter:                       156  (0.00870099); expected 17.9 (0.001)
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: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 773.08
//
Query:       gi|518652834|ref|YP_008142354.1|  [L=34]
Description: hypothetical protein FACI_IFERC00001G1473 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (34 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       116  (0.00646996); expected 358.6 (0.02)
Passed bias filter:                      110  (0.00613531); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.26s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 253.10
//
Query:       gi|518652835|ref|YP_008142355.1|  [L=99]
Description: hypothetical protein FACI_IFERC00001G1474 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-24   84.5   0.1    5.3e-24   84.4   0.1    1.0  1  DUF2175   Uncharacterized protein conserved in archaea (DUF21
  ------ inclusion threshold ------
      0.091   13.0   0.1       0.13   12.5   0.1    1.3  1  LIM       LIM domain


Domain annotation for each model (and alignments):
>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.1   5.9e-28   5.3e-24       2      96 ..       2      96 ..       1      98 [. 0.93

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 5.9e-28
                           DUF2175  2 kwkCyiCgkeivegekFTftkkgvvHyeClvekarkklkesedaaaLleleevlneeivklkelervaedee.vkkvle 79
                                      ++ Cy C+k i +gekFTftk+g+vH++C+v+  rkk+ e e+++ L++l+ vl++e+++l el  +++d++   + ++
  gi|518652835|ref|YP_008142355.1|  2 EYGCYTCNKIIKTGEKFTFTKEGPVHLDCFVATQRKKVPE-EKQEYLRNLSMVLDYELTYLVELLGLKSDDKpTSEFIK 79
                                      899***********************************98.9*************************666652789999 PP

                           DUF2175 80 qkrkelEkaaakltkkl 96
                                       +   +Ek+a+++t  +
  gi|518652835|ref|YP_008142355.1| 80 RRITAIEKQAGETTGLI 96
                                      9999*********9877 PP

>> LIM  LIM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   1.4e-05      0.13       1      30 [.       5      34 ..       5      53 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                                      -TTT--BE-TTTEEEEETTEEEETTTSB-T CS
                               LIM  1 CagCnkkiadrelvlkaldkvwHeeCFtCs 30
                                      C+ Cnk i+  e ++  ++   H +CF+ +
  gi|518652835|ref|YP_008142355.1|  5 CYTCNKIIKTGEKFTFTKEGPVHLDCFVAT 34
                                      9********888888899*********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       661  (0.0368676); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.45
# Mc/sec: 655.22
//
Query:       gi|518652836|ref|YP_008142356.1|  [L=51]
Description: 30S ribosomal protein S27ae [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.9e-20   72.1   4.0    3.2e-20   72.0   4.0    1.1  1  Ribosomal_S27   Ribosomal protein S27a
     0.0011   19.1   0.5     0.0013   18.9   0.5    1.1  1  IBR             IBR domain, a half RING-finger domain
     0.0026   17.8   1.1      0.003   17.6   1.1    1.1  1  DZR             Double zinc ribbon
     0.0029   17.5   5.0     0.0043   17.0   4.9    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
  ------ inclusion threshold ------
      0.023   14.6   1.0      0.023   14.6   1.0    1.2  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      0.044   13.9   0.2      0.044   13.9   0.2    1.2  1  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.085   12.9   1.3      0.085   12.9   1.3    1.1  1  DUF1451         Zinc-ribbon containing domain
        0.1   12.7   0.9        0.1   12.7   0.9    1.1  1  HypA            Hydrogenase/urease nickel incorporation, meta
       0.11   12.5   4.3       0.61   10.1   0.7    2.2  2  ADK_lid         Adenylate kinase, active site lid
       0.14   12.1   8.2       0.94    9.5   0.3    2.1  2  Nudix_N_2       Nudix N-terminal
        0.5    9.9   2.1         12    5.6   0.3    2.1  2  zf_C2H2_10      C2H2 type zinc-finger
       0.66   10.2   5.2        1.4    9.1   1.3    2.2  2  zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ri
       0.82    9.3   8.1        1.1    8.9   1.2    2.6  2  zf_UBZ          Ubiquitin-Binding Zinc Finger


Domain annotation for each model (and alignments):
>> Ribosomal_S27  Ribosomal protein S27a
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.0   4.0   2.3e-23   3.2e-20       3      45 .]       5      45 ..       3      45 .. 0.96

  Alignments for each domain:
  == domain 1  score: 72.0 bits;  conditional E-value: 2.3e-23
                                      SSCCESSSSSEEESS-B-SS-S-TTSBEEECTTEEEESSTTTE CS
                     Ribosomal_S27  3 kyYkvddsgkverlrkeCpreCGaGvfMAehkdRkyCGkCglT 45
                                      ++Y v+  +k+ r+r+ Cpr CGaGvfMAeh dR++CGkC +T
  gi|518652836|ref|YP_008142356.1|  5 ELYAVEA-DKIVRKRRTCPR-CGAGVFMAEHSDRYTCGKCKYT 45
                                      5799*99.9***********.********************99 PP

>> IBR  IBR domain, a half RING-finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.5   9.3e-07    0.0013      15      46 ..      15      44 ..       2      47 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.3e-07
                               IBR 15 dpnlkwCprpdCeaiieksegcksvtCskCgf 46
                                       ++++ Cp   C+a +   e++++ tC kC++
  gi|518652836|ref|YP_008142356.1| 15 VRKRRTCP--RCGAGVFMAEHSDRYTCGKCKY 44
                                      35699***..9*****999999999*****97 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.1   2.2e-06     0.003       8      37 ..      14      45 ..      11      51 .] 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.2e-06
                               DZR  8 lppdarfCseCgtklkavaa..edrCpsCgek 37
                                      +  + r+C++Cg+ +  +++   ++C +C++ 
  gi|518652836|ref|YP_008142356.1| 14 IVRKRRTCPRCGAGVFMAEHsdRYTCGKCKYT 45
                                      667889********87666688*******986 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   4.9   3.1e-06    0.0043      17      46 .]      17      45 ..      11      45 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                     Zn_Tnp_IS1595 17 ngfvCPhCgsrkayriktrglfqCkeCrkq 46
                                       +++CP+Cg + ++  ++  ++ C +C+++
  gi|518652836|ref|YP_008142356.1| 17 KRRTCPRCG-AGVFMAEHSDRYTCGKCKYT 45
                                      5799*****.7777777789********95 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   1.0   1.7e-05     0.023      29      55 ..      19      45 ..       2      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-05
                    OrfB_Zn_ribbon 29 ktCseCgsknkealsgrtfkCpnCgfe 55
                                       tC++Cg+ +  a ++++++C +C+++
  gi|518652836|ref|YP_008142356.1| 19 RTCPRCGAGVFMAEHSDRYTCGKCKYT 45
                                      59*******99999**********986 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   3.2e-05     0.044      36      60 ..      20      44 ..       3      51 .] 0.78

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.2e-05
                    MqsA_antitoxin 36 fCarCGegvldeeeedrlseellef 60
                                       C+rCG gv+ +e++dr++    ++
  gi|518652836|ref|YP_008142356.1| 20 TCPRCGAGVFMAEHSDRYTCGKCKY 44
                                      6*****************9765544 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   1.3   6.2e-05     0.085     116     146 ..      20      50 ..       2      51 .] 0.89

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.2e-05
                           DUF1451 116 vCekCgkelalkkteeippCpkCgateFrRe 146
                                       +C +Cg+ + + + +   +C kC+ teF+ +
  gi|518652836|ref|YP_008142356.1|  20 TCPRCGAGVFMAEHSDRYTCGKCKYTEFKKK 50 
                                       7***************************975 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.9   7.3e-05       0.1      67      98 ..      15      48 ..       2      51 .] 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                                      E--EEEETTTS-EEECHH.H.HHS-TTTSSS-EE CS
                              HypA 67 vpvkvrCreCgkefelee.k.alrCpkCgsadve 98
                                      v+ + +C +Cg+ + ++e + +++C+kC+ ++++
  gi|518652836|ref|YP_008142356.1| 15 VRKRRTCPRCGAGVFMAEhSdRYTCGKCKYTEFK 48
                                      566789*****999877643689*****988765 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   0.7   0.00044      0.61       1       9 [.      18      26 ..      18      30 .. 0.93
   2 ?    4.0   0.2     0.036        49       1       8 [.      36      43 ..      36      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00044
                                      EEE-TTT-- CS
                           ADK_lid  1 RrvCpkCGr 9 
                                      Rr+Cp CG+
  gi|518652836|ref|YP_008142356.1| 18 RRTCPRCGA 26
                                      9*******8 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.036
                                      EEE-TTT- CS
                           ADK_lid  1 RrvCpkCG 8 
                                      R +C kC+
  gi|518652836|ref|YP_008142356.1| 36 RYTCGKCK 43
                                      99*****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 ?    6.8   2.5    0.0047       6.5      20      30 ..      16      26 ..       8      28 .. 0.88
   2 ?    9.5   0.3   0.00068      0.94      18      31 ..      32      45 ..      26      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0047
                                      S-EEEETTTTE CS
                         Nudix_N_2 20 reRlvCpaCgt 30
                                      r R +Cp+Cg+
  gi|518652836|ref|YP_008142356.1| 16 RKRRTCPRCGA 26
                                      78999****95 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00068
                                      -SS-EEEETTTTEE CS
                         Nudix_N_2 18 DnreRlvCpaCgti 31
                                      ++  R++C +C ++
  gi|518652836|ref|YP_008142356.1| 32 EHSDRYTCGKCKYT 45
                                      6788*******997 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 ?    4.2   0.1     0.022        31       4       9 ..      20      25 ..      18      28 .. 0.85
   2 ?    5.6   0.3    0.0084        12       3      10 ..      37      44 ..      36      46 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.022
                        zf_C2H2_10  4 sCPKCq 9 
                                       CP+C+
  gi|518652836|ref|YP_008142356.1| 20 TCPRCG 25
                                      6****7 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0084
                        zf_C2H2_10  3 fsCPKCqe 10
                                      + C KC++
  gi|518652836|ref|YP_008142356.1| 37 YTCGKCKY 44
                                      79*****9 PP

>> zinc_ribbon_13  Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.085   1.2e+02       1       9 [.      20      28 ..      20      36 .. 0.75
   2 ?    9.1   1.3     0.001       1.4      37      49 ..      38      50 ..      35      51 .] 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.085
                    zinc_ribbon_13  1 kCpKCgnte 9 
                                      +Cp+Cg   
  gi|518652836|ref|YP_008142356.1| 20 TCPRCGAGV 28
                                      599999765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.001
                    zinc_ribbon_13 37 sCknCgYtelYka 49
                                      +C +C+Yte+ k+
  gi|518652836|ref|YP_008142356.1| 38 TCGKCKYTEFKKK 50
                                      7********9665 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   1.2   0.00082       1.1       4      22 ..      20      35 ..      17      35 .. 0.78
   2 ?    4.1   1.6     0.026        36       1       9 [.      35      43 ..      35      45 .. 0.88

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00082
                            zf_UBZ  4 lCerCgkeipeselqEHeD 22
                                      +C+rCg+ + +   +EH+D
  gi|518652836|ref|YP_008142356.1| 20 TCPRCGAGVFM---AEHSD 35
                                      8*****99874...57766 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.026
                            zf_UBZ  1 dtylCerCg 9 
                                      d y+C +C+
  gi|518652836|ref|YP_008142356.1| 35 DRYTCGKCK 43
                                      68******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      269  (0.0150036); 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: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 390.32
//
Query:       gi|518652837|ref|YP_008142357.1|  [L=105]
Description: 30S ribosomal protein S24e [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   70.7   1.9      1e-19   70.3   1.9    1.3  1  Ribosomal_S24e   Ribosomal protein S24e
  ------ inclusion threshold ------
      0.041   13.7   0.1      0.042   13.7   0.1    1.2  1  Ribosomal_L13e   Ribosomal protein L13e
      0.066   12.7   0.0      0.075   12.6   0.0    1.2  1  Glyco_hydro_67C  Glycosyl hydrolase family 67 C-terminus
      0.069   13.0   0.0      0.095   12.5   0.0    1.1  1  DarT             ssDNA thymidine ADP-ribosyltransferase, DarT


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 !   70.3   1.9   2.3e-23     1e-19       4      78 ..      30     104 ..      27     105 .] 0.94

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 2.3e-23
                                       EE-SSS-S--HHHHHHHHHHHHTS-CTTEEEEEEEE-SSSSEEEEEEEEES-HHHHHHHS-HHHHHHTTSS---S CS
                    Ribosomal_S24e   4 vlHpgkatpskteireklakmykvdpdlvvvfgfrthfGggkttGfakiYdsleaakkfEpkhrlaRnglaekkk 78 
                                       + +   +t+s++ei++ l   yk+++++++v++  ++ G+   +G++kiYd++e+a+ +Ep++ l Rngl+ek+ 
  gi|518652837|ref|YP_008142357.1|  30 IDFRSGKTVSRNEIKKLLMDYYKAKEEVIIVDHNIQETGKDSLKGYVKIYDTKEHAMLYEPDYELLRNGLKEKES 104
                                       5566679******************************************************************96 PP

>> Ribosomal_L13e  Ribosomal protein L13e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   9.4e-06     0.042      55     107 ..      25      77 ..      11     103 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 9.4e-06
                    Ribosomal_L13e  55 tvrYntkvraGrGFtleElkaagiskklArtiGIavDhRrknkseeslkaNve 107
                                        ++Y +  r G+  + +E+k+  ++   A+   I vDh  +++ ++slk  v+
  gi|518652837|ref|YP_008142357.1|  25 EIKYTIDFRSGKTVSRNEIKKLLMDYYKAKEEVIIVDHNIQETGKDSLKGYVK 77 
                                       58*****************************************9999987665 PP

>> Glyco_hydro_67C  Glycosyl hydrolase family 67 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.7e-05     0.075     125     172 ..      12      63 ..       3      89 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.7e-05
                                       TTTS-GGGGGGT-EEETT-B-TTS-BH....HHHHHHHHHHHHHHHHHHHHH CS
                   Glyco_hydro_67C 125 letcpeelLLwfHhvpythklksGktl....iqelydayfegveeveelqkt 172
                                       +++  ++ LL+   + yt  ++sGkt+    i++l + y+++ eev  + ++
  gi|518652837|ref|YP_008142357.1|  12 VDSERDNKLLFRKEIKYTIDFRSGKTVsrneIKKLLMDYYKAKEEVIIVDHN 63 
                                       56667999*******************6666678999999999998665554 PP

>> DarT  ssDNA thymidine ADP-ribosyltransferase, DarT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.1e-05     0.095      14      73 ..      33      89 ..      30      93 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.1e-05
                              DarT 14 asggllsdnkveeeginytnigdsgikqrrlk.kevpippggtlgdYvpfYfaprspmlyr 73
                                      +sg+ +s+n+++++ ++y +  ++ i+ + +   +     + +l+ Yv +Y +  + mly+
  gi|518652837|ref|YP_008142357.1| 33 RSGKTVSRNEIKKLLMDYYKAKEEVIIVDHNIqET----GKDSLKGYVKIYDTKEHAMLYE 89
                                      78999**********************99998333....457******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 755.26
//
Query:       gi|518652838|ref|YP_008142358.1|  [L=168]
Description: hypothetical protein FACI_IFERC00001G1477 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-33  115.7   1.0    1.3e-33  115.3   1.0    1.1  1  DUF359        Protein of unknown function (DUF359)
  ------ inclusion threshold ------
      0.016   14.9   0.6      0.021   14.5   0.6    1.3  1  BppU_N        BppU N-terminal domain
       0.12   12.4   0.0       0.19   11.8   0.0    1.3  1  Pyridox_ox_2  Pyridoxamine 5'-phosphate oxidase


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 !  115.3   1.0   2.2e-37   1.3e-33       1     125 [.      48     163 ..      48     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 115.3 bits;  conditional E-value: 2.2e-37
                            DUF359   1 vtknllkagikPdlaivDgktkReeveeeekeeekekekekevievkNpaGtiteelieaikealeseekvlilVdG 77 
                                       +t+nl +agik +l ivD  tkR+          k   +e+ +i+v+Np+G+i+ +l+++i e ++++ + +i+VdG
  gi|518652838|ref|YP_008142358.1|  48 TTENLKNAGIKLNLQIVDLVTKRD---------GKRFMHEEGSITVSNPPGIISIDLMNKIYEFISTGVHGRIEVDG 115
                                       79**********************.........334578999*********************************** PP

                            DUF359  78 EEDLavlpaillapegsvvvYGqpdeGvvlvkvteeakeeaeellekf 125
                                       EEDLav+p+i++a++++v+vYG+pd G++ +kv++e+ke+++e++ ++
  gi|518652838|ref|YP_008142358.1| 116 EEDLAVIPIIFYADKNTVIVYGVPDVGMAYIKVNDEIKERIKEMIMEM 163
                                       ********************************************9887 PP

>> BppU_N  BppU N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.6   3.5e-06     0.021      43     148 .]      49     158 ..       9     158 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.5e-06
                            BppU_N  43 pldLtgltarlefkke....kaedgsgvhdelaiieDavnGilkyvlpdeilk.yvGkveaslyidkndeslittgr 114
                                         +L+++ ++l+++      k +++ ++h+e +i ++   Gi++++l ++i + ++  v++ +++d   e+ ++   
  gi|518652838|ref|YP_008142358.1|  49 TENLKNAGIKLNLQIVdlvtKRDGKRFMHEEGSITVSNPPGIISIDLMNKIYEfISTGVHGRIEVDG--EEDLAVIP 123
                                       55664444444444444476788999*************************994467799*****99..88999999 PP

                            BppU_N 115 FtFeikksl.iddsipevesyyfndfedliekiee 148
                                       + F+ +k++ i  ++p v   y++  ++++e+i+e
  gi|518652838|ref|YP_008142358.1| 124 IIFYADKNTvIVYGVPDVGMAYIKVNDEIKERIKE 158
                                       *********9*********************9997 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 ?   11.8   0.0   3.1e-05      0.19       5      44 ..      99     138 ..      97     164 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.1e-05
                                       HHHHHHC-SEEEEEEEETTEEEEEEEEEEEETTEEEEEEE CS
                      Pyridox_ox_2   5 ilalLdegevgrlafvddgepvilPvnyvvdgdslyfhga 44 
                                       i++++++g +gr+ +  +++ +++P+++  d +++++ g 
  gi|518652838|ref|YP_008142358.1|  99 IYEFISTGVHGRIEVDGEEDLAVIPIIFYADKNTVIVYGV 138
                                       789*******************************999775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1228.22
//
Query:       gi|518652839|ref|YP_008142359.1|  [L=63]
Description: DNA-directed RNA polymerase subunit E'' [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.3e-09   36.0   0.1    7.2e-09   35.6   0.1    1.2  1  Spt4      Spt4/RpoE2 zinc finger
     0.0031   17.0   0.4     0.0043   16.6   0.4    1.2  1  RecR      RecR protein


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 !   35.6   0.1     8e-13   7.2e-09       2      77 .]       6      62 ..       5      62 .. 0.95

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 8e-13
                              Spt4  2 rACllCklvktedqFeeegCpnCeilelkgdkekvsectseefeGlvaildpekSwvAkwqrldkkvpglYAlkve 77
                                      +AC+ Ck+++ted      Cp++           ++e t  ++ G+++i d + S++A++   + +++g+YA+kv+
  gi|518652839|ref|YP_008142359.1|  6 KACKICKRLTTEDV-----CPVH-----------GEERTKVDWFGFLIINDIN-SQIAQK--AGITEKGIYAIKVR 62
                                      9***********99.....***9...........9************998888.******..9***********96 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.4   4.8e-07    0.0043      13      33 ..       2      22 ..       1      22 [. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.8e-07
                                      HHH-EE-TTT--EESSSS-CC CS
                              RecR 13 kekvrhCsrCgnlteedlCaI 33
                                      k+  + C++C  lt+ed+C++
  gi|518652839|ref|YP_008142359.1|  2 KKAYKACKICKRLTTEDVCPV 22
                                      777899*************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 432.25
//
Query:       gi|518652840|ref|YP_008142360.1|  [L=191]
Description: DNA-directed RNA polymerase subunit E' [Ferroplasma acidarmanus fer1]
Scores for complete 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   48.4   2.0    1.5e-12   47.7   0.3    1.9  2  S1             S1 RNA binding domain
    5.1e-12   46.0   0.1    1.1e-11   44.9   0.0    1.6  2  SHS2_Rpb7-N    SHS2 domain found in N terminus of Rpb7p/Rpc25
  ------ inclusion threshold ------
      0.038   14.2   1.3       0.46   10.7   0.5    2.4  2  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.23   1.4e+03      42      68 ..      38      64 ..      27      69 .. 0.72
   2 !   47.7   0.3   2.5e-16   1.5e-12       3      64 ..      88     158 ..      87     167 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.23
                                      EESCHHHCEETTEEEEEEEEEEETTTT CS
                                S1 42 rvedpdevlkvGdevkvkvlkvdkdrr 68
                                       v+  + +  +G+ + v v  ++++ +
  gi|518652840|ref|YP_008142360.1| 38 LVDIQEGQKNIGKSYIVSVNSIEMKGE 64
                                      555666677889999999988888766 PP

  == domain 2  score: 47.7 bits;  conditional E-value: 2.5e-16
                                       TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSS..........CEESCHHHCEETTEEEEEEEEEEE CS
                                S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrd..........arvedpdevlkvGdevkvkvlkvd 64 
                                       + +evv+G+V+ v k+Gaf+ +g + eg++++s++++d            ++d++ +lkvGd+++v++  ++
  gi|518652840|ref|YP_008142360.1|  88 KMHEVVDGIVVAVQKFGAFIKFG-PFEGLLHISQIMDDainidmenqrIVGKDSKMELKVGDKIRVRIVALN 158
                                       6689*******************.**********************997799****************9876 PP

>> 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 !   44.9   0.0   1.9e-15   1.1e-11       1      70 []       8      85 ..       8      85 .. 0.95
   2 ?   -3.5   0.0       2.3   1.4e+04      35      41 ..      93     100 ..      88     102 .. 0.68

  Alignments for each domain:
  == domain 1  score: 44.9 bits;  conditional E-value: 1.9e-15
                                      EEEEEE-GGGTTSTHHHHHHHHHHHHHTTBEETTT.E.......EEEEEEEEEEECCEEE-TTTSSEEEEEEEEEEEE CS
                       SHS2_Rpb7-N  1 edtvrlePsylgstledallerllekyegkvvpsl.G.......vivavldiaeysegkvlggsGsvyvrVtfralvF 70
                                      e+++r++P+ l++++ da++e+ ++ +egk+v+   G       +iv+v+ i+  +eg++++g+G+vy+ +++ al +
  gi|518652840|ref|YP_008142360.1|  8 EYVIRVPPELLNDNYSDAVAEASKSTLEGKLVDIQeGqknigksYIVSVNSIEMKGEGTIVHGDGGVYQSIKYSALAY 85
                                      689******************************98888888899******************************9975 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                                       T.EEEEEE CS
                       SHS2_Rpb7-N  35 l.Gvivav 41 
                                       + G++vav
  gi|518652840|ref|YP_008142360.1|  93 VdGIVVAV 100
                                       55889988 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 ?    1.2   0.0     0.067     4e+02      63     125 ..       5      66 ..       1      68 [. 0.69
   2 ?   10.7   0.5   7.7e-05      0.46       1      80 [.      87     163 ..      87     186 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.067
                                       TTSEEEEEEEEEEE-------HHHHHCHHHCCTS-SS--SSTTS--S-SCEE.EEEB-STTTCE CS
                     RNA_pol_Rbc25  63 vgeeirfrveeeifvdvkpkspkeaeleeeeaseeeaeeeeeekekkspyev.lgsiqedGlGl 125
                                        ++e  +rv  e  +d    + +  e+++++ + +  + +e +k+  ++y v + si+ +G G 
  gi|518652840|ref|YP_008142360.1|   5 LEDEYVIRVPPELLNDNYSDAVA--EASKSTLEGKLVDIQEGQKNIGKSYIVsVNSIEMKGEGT 66 
                                       56777788888888666665555..445567888888888888888888888346888888776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.7e-05
                                       -STTSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTTEEEECCCTCEEEEESSSEEEEE-TTSEEEEEEEEEEE- CS
                     RNA_pol_Rbc25   1 PfvgevltgkiksstregikvslgffddifvpkelLfepsefdeeeqawvweveeeeelyldvgeeirfrveeeifv 77 
                                       P + ev+ g + + ++ g +++ g f+ ++   + + +  + d e+q  v +   +++++l+vg++ir+r++  + +
  gi|518652840|ref|YP_008142360.1|  87 PKMHEVVDGIVVAVQKFGAFIKFGPFEGLLHISQIMDDAINIDMENQRIVGK---DSKMELKVGDKIRVRIVALNLS 160
                                       6678999999999999999999999999888888999999999999987765...69**************988776 PP

                                       --- CS
                     RNA_pol_Rbc25  78 dvk 80 
                                         +
  gi|518652840|ref|YP_008142360.1| 161 SAS 163
                                       555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1314.49
//
Query:       gi|518652841|ref|YP_008142361.1|  [L=437]
Description: hypothetical protein FACI_IFERC00001G1480 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-84  281.2   0.0    1.1e-83  280.9   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    2.2e-14   53.2   0.0    5.4e-14   51.9   0.0    1.7  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.005   16.3   0.0        0.1   12.1   0.0    2.2  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 !  280.9   0.0   1.8e-87   1.1e-83       2     313 ..     118     431 ..     117     432 .. 0.95

  Alignments for each domain:
  == domain 1  score: 280.9 bits;  conditional E-value: 1.8e-87
                                       CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE....- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
                       tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeff....a 74 
                                       ee++l+nr+l lr+++  +vl++rstv ka+ +y+ ++++++++ P++++++te+g+ lF v       ++f     
  gi|518652841|ref|YP_008142361.1| 118 EEFLLDNRHLWLRSREFTAVLKIRSTVFKAFADYFYKEDYYQVQAPMFVSTATEGGSSLFNV-------DYFgekvN 187
                                       6899**********************************************************.......77778889 PP

                                       E-S-SHHHHHHHHHCTHSEEEEEEEEE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  75 LtqspqlylellivagidrvfqiaraFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessak 151
                                       Ltqs+q+yle+li + +++vf+ia++FRaE+srt+rhl+E+++ e e ++ ++ed+m   e++ik++++evl+++ +
  gi|518652841|ref|YP_008142361.1| 188 LTQSSQFYLETLIYS-LEKVFTIAPSFRAEKSRTRRHLTEYWHAEGEAAWYSNEDMMADEEKMIKYIIDEVLKNNLE 263
                                       ***************.***********************************************************99 PP

                                       CCCHTTTTTS..EE-SSS-EEEEHHHHHHHHHTS......-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBB CS
                                       xxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 152 diefvirrns..kdlkkpfkrltykeaieklnei......gkdldkaderalvkkeknepvfvtdfPaelkpFyark 220
                                       d+e  +r     k++k pf+r++yk+ iek +e       g+dl  ade + +  +  +p+fvtd+P++lk Fy+r 
  gi|518652841|ref|YP_008142361.1| 264 DLEIIKRDINkiKNIKIPFERIKYKDLIEKSKEFgmnlkyGDDL-GADEEYGIMVHFDNPIFVTDYPESLKTFYHRP 339
                                       99988887666799999*************76668888765555.467777777899******************** PP

                                       STTSTTBBSEEEEEET.TE.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHH CS
                                       xxxxxxxxxxxxxxxx.xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 221 eeddkkltesyDllin.gv.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlv 295
                                       + d++      Dll + g+ E++gG  Ri d ++l +++k+++l+   +e ++wy+++++yG+ ph+G+glGldRlv
  gi|518652841|ref|YP_008142361.1| 340 DPDNPGEILCHDLLAPeGYgEVLGGGERIYDLQQLLDRIKENNLN---PEDYYWYVDLRKYGSIPHSGFGLGLDRLV 413
                                       ***************9889**************************...***************************** PP

                                       HHHCT-SSGGGCSSS-XX CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 296 mlllgsesIrdviaFPkl 313
                                       m+++g++++r++i++P++
  gi|518652841|ref|YP_008142361.1| 414 MWICGLSNVRETIPYPRT 431
                                       ****************97 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.9   0.0     9e-18   5.4e-14       1      75 [.      25     103 ..      25     104 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.9 bits;  conditional E-value: 9e-18
                                       EEEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET....HHHHHHHTTS-TTSEEEEEEEEEECTTS..SEEEEEE CS
                   tRNA_anti-codon   1 VtvaGrvtsisdrsggkvifidlrDgtgriqvvlfr....eeatklaenlkeGdvvrvtGrvkrrpgg..elelkve 71 
                                       V+++G+v +i  rs+gk+ fi+ rD tg+iq+++ +    +e++k  ++l++++ ++ +G++++ p+    +e++ +
  gi|518652841|ref|YP_008142361.1|  25 VSIRGWVYRI--RSSGKITFIVMRDSTGIIQCIASSenlnDEQMKEISSLTIESSIELSGKLRKEPRAvtGYEISLQ 99 
                                       89********..*****************************************************777775777777 PP

                                       EEEE CS
                   tRNA_anti-codon  72 eiel 75 
                                       ++++
  gi|518652841|ref|YP_008142361.1| 100 SYKI 103
                                       7665 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 ?    1.7   0.0     0.024   1.4e+02     103     148 ..     205     253 ..     184     264 .. 0.74
   2 !   12.1   0.0   1.7e-05       0.1     211     234 ..     402     425 ..     393     434 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.024
                                       EEEEEEEEEBSST.-SSSB-SEEEEEEE..EEEETT--HHHHHHHHHHH CS
                      tRNA-synt_2d 103 kiisigrvfRrda.vDathlaeFhqveg..lvvdenvsladlkgvleel 148
                                       k+++i   fR ++   ++hl e+  +eg   +  ++  +ad  ++++ +
  gi|518652841|ref|YP_008142361.1| 205 KVFTIAPSFRAEKsRTRRHLTEYWHAEGeaAWYSNEDMMADEEKMIKYI 253
                                       899999******978999*****99998223344455555555555555 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.7e-05
                                       EEEEEEEHHHHHHHHHT-SSGHHH CS
                      tRNA-synt_2d 211 gfafGlGveRlamlkygieDiRel 234
                                         +fGlG++Rl m  +g++++Re 
  gi|518652841|ref|YP_008142361.1| 402 HSGFGLGLDRLVMWICGLSNVRET 425
                                       568*******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2776.36
//
Query:       gi|518652842|ref|YP_008142362.1|  [L=335]
Description: hypothetical protein FACI_IFERC00001G1481 [Ferroplasma acidarmanus fer1]
Scores for complete 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-86  290.7   0.0    1.6e-86  290.6   0.0    1.0  1  URO-D      Uroporphyrinogen decarboxylase (URO-D)
  ------ inclusion threshold ------
      0.079   11.5   0.0       0.11   11.0   0.0    1.1  1  DUF1744    Domain of unknown function (DUF1744)
      0.089   12.8   0.4       0.65   10.0   0.0    2.3  2  DPPIV_rep  Dipeptidyl peptidase IV (DPP IV) low complexity re


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  290.6   0.0   2.7e-90   1.6e-86       5     346 .]       3     334 ..       1     334 [. 0.94

  Alignments for each domain:
  == domain 1  score: 290.6 bits;  conditional E-value: 2.7e-90
                                       HHHHHHTT---SS--B--TT-SSTTSHHHHHHHTSSSHHHHHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGG CS
                             URO-D   5 rllralrgekvdrvPvwlmRqaGrylpeyraeragvsflelcknpelaaevtlqpvrrfglDaailfsdilveaeal 81 
                                       +++ al++e+ d++Pvw+mRqaGry+ ey + r+ ++++++c +pe   ++t++pv+ +g+Daai+f di +++ea+
  gi|518652842|ref|YP_008142362.1|   3 NFIPALKQEPHDHIPVWFMRQAGRYMDEYKELRKLYNIRQMCMDPEITEKITYAPVKLLGVDAAIIFADIILPLEAM 79 
                                       7999************************************************************************* PP

                                       T-EEEEETTTEEEEE--S-....GGGS----GGG.G..HH.HHHHHHHHHHH.--SS-EEEEEE-HHHHHHHHHCTT CS
                             URO-D  82 GlevefeegegPvvekpvrtaedveklevpddveegrlpy.vleaikllkkelggevpligfvgaPftlasylveGg 157
                                       G +++f++  gP + +  r  + +e +++ +  +   l+y +++ai+l+k+    e+pligf+g+ +t++sy++ G 
  gi|518652842|ref|YP_008142362.1|  80 GYKIDFNS-SGPDIGNGYRHNKSMEGIHEFNTGD---LKYrTYDAIRLFKQNH-PETPLIGFSGGIITVMSYIIAGV 151
                                       *******8.77********999*9*999998754...44439*********85.7********************** PP

                                       .-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHHHHTHHHHHHHHHHHHH CS
                             URO-D 158 .skgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifDswagllspedfeefvlpylkrivdevka 233
                                         ++   ++k ++ dp  +  + +++ +++ +y+ +q++ag+daiqifDsw g+lsp  fe++  + + ++v+ +k+
  gi|518652842|ref|YP_008142362.1| 152 sDNNLVYTKKVMLNDPS-FGIMKKMIKNMILDYVTMQVKAGVDAIQIFDSWLGALSPYTFEKYLKNDIIELVESIKS 227
                                       999**********9995.6777777889999********************************************** PP

                                       .H--S-EEEEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGGS-HHHHHHHHHHHHT CS
                             URO-D 234 egpkvpvilfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLlgspeeiekevkeile 310
                                          kvpvi+f +g++  ++e++++++ d+ls+dw+++l  a+  ++ ++ +qGnldP  l   s+e+  +e+ +il 
  gi|518652842|ref|YP_008142362.1| 228 ---KVPVIYFSTGSS-GMIEQFNDIKPDILSVDWRIKLSHARTILNGSIGMQGNLDPY-LVQYSREAALEETGRILG 299
                                       ...68*********9.8*********************66666888***********4.555*************** PP

                                       .T---SSSEEB-BSS---TTS-HHHHHHHHHHHHT- CS
                             URO-D 311 kgaggkkgyilnlGhgippetppenvkalveavkey 346
                                        +ag+  +yi+nlGhg++pet+p+++k ++++v++y
  gi|518652842|ref|YP_008142362.1| 300 -EAGKDDNYIFNLGHGVLPETDPDTLKSITDTVHSY 334
                                       .6999*****************************97 PP

>> DUF1744  Domain of unknown function (DUF1744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   1.9e-05      0.11     258     319 ..     158     220 ..     145     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 1.9e-05
                           DUF1744 258 sldesalssaafrvLrslvkswlddal.kgnkladllvqhlvrWvespsslLyDpaLrrlvqn 319
                                         ++ +l +++f ++++++k+ + d +  + k    ++q + +W+   s + ++++L++ + +
  gi|518652842|ref|YP_008142362.1| 158 YTKKVMLNDPSFGIMKKMIKNMILDYVtMQVKAGVDAIQIFDSWLGALSPYTFEKYLKNDIIE 220
                                       4455567999***************99677778899**********99999999999876554 PP

>> DPPIV_rep  Dipeptidyl peptidase IV (DPP IV) low complexity region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.15   9.2e+02      14      21 .]     111     118 ..     111     118 .. 0.89
   2 ?   10.0   0.0   0.00011      0.65       3      16 ..     205     218 ..     203     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.15
                         DPPIV_rep  14 ntfrYKsY 21 
                                       ++ +Y++Y
  gi|518652842|ref|YP_008142362.1| 111 GDLKYRTY 118
                                       6899***9 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                         DPPIV_rep   3 rRtfTLeDYlNntf 16 
                                         ++T+e Yl+n++
  gi|518652842|ref|YP_008142362.1| 205 LSPYTFEKYLKNDI 218
                                       679**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2531.77
//
Query:       gi|518652843|ref|YP_008142363.1|  [L=182]
Description: hypothetical protein FACI_IFERC00001G1482 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.3e-10   41.3   0.5    1.7e-10   40.9   0.5    1.2  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.5   9.7e-15   1.7e-10      82     206 ..       1     137 [.       1     144 [. 0.73

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 9.7e-15
                         DDE_Tnp_1  82 aDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnk............... 143
                                       +D+GY   +++d++++++++yii++k+n+k+ +     k + +++k+  ++ +     r+n                
  gi|518652843|ref|YP_008142363.1|   1 MDRGYLDSSVMDAVDSMKLKYIIPAKDNHKVIKF---KKMDLKYCKDVYGNEFPFMVLRDNIgsskrvnanfvhivy 74 
                                       7****************************99755...4444455555555555555555555555555555555665 PP

                         DDE_Tnp_1 144 skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqll 206
                                         + k+d ++ tn+n ++  + e+aelyr+Rw+iE+   + k + +   ++++   r +++++
  gi|518652843|ref|YP_008142363.1|  75 YSHKKHDFSFYTNINVNENNVIELAELYRKRWGIENGYQERKIDIREKTHSSHMAIRQFLYFF 137
                                       55667777****************************999888777766666655555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (182 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.48
# Mc/sec: 1151.50
//
Query:       gi|518652844|ref|YP_008142364.1|  [L=190]
Description: hypothetical protein FACI_IFERC00001G1483 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 1271.37
//
Query:       gi|518652845|ref|YP_008142365.1|  [L=294]
Description: ferrochelatase [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  161.4   0.0    3.5e-47  161.1   0.0    1.0  1  Ferrochelatase  Ferrochelatase
  ------ inclusion threshold ------
      0.018   14.5   0.4      0.037   13.5   0.4    1.5  1  DUF576          Csa1 family


Domain annotation for each model (and alignments):
>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.1   0.0   3.8e-51   3.5e-47       4     313 ..       4     283 ..       2     286 .. 0.95

  Alignments for each domain:
  == domain 1  score: 161.1 bits;  conditional E-value: 3.8e-51
                                       EEEEE----SSCCCHHHHHHHHCT-TTTS-S-TTTHHHHHHHHHHHHHHHHHHHHHHTTSS-SHHHHHHHHHHHHHH CS
                    Ferrochelatase   4 vLLlnlGgPekpedvrpflenllsdrrvielplllqkllaklilkerlekvaekYekigggSPlneitrkqaealek 80 
                                       v+Ll++G+Pe  +dv ++l+ +++++ v+e               + +e+  +kYe ++g SP n+i ++++++l k
  gi|518652845|ref|YP_008142365.1|   4 VILLSYGSPERIDDVPEYLSGIFNGKPVPE---------------KIMEENIKKYEMVNGISPSNQIIKNLKNKLGK 65 
                                       89****************************...............78899999************************ PP

                                       HHHHH---EEEEEEESSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT-SSEEEEE--- CS
                    Ferrochelatase  81 elaergidvkvylamrywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkreapevrvirqf 157
                                        la+ + d+++  a+++w+P ie+++  l a ++e++++lpl++ +s    +s+   +++a++   +++++r+i+  
  gi|518652845|ref|YP_008142365.1|  66 LLAR-YGDFEIIDAYKHWHPGIEETVSSLDA-DYEEIIALPLFAFKSNNIRKSYEIPVKKAMEG--KNMKLRFING- 137
                                       **85.79***********************7.59***************************977..589*****98. PP

                                       TT-HHHHHHHHHHHHHHHTTS-HC.C-EEEEEEE--BHHHHT.TT-SHHHHHHHHHHHHHHHTTT-S-EEEEEE--- CS
                    Ferrochelatase 158 ydhpgyiealaesikealeelpeekkakllfsaHglPeravkkkgdpYqqqveetarlvaealglkeevelayqSrv 234
                                        d   + ++++++i +++ ++     +++lf+aH+lP  ++ +    Yq+ +e+ a  + + lg+++ + +a+ S+ 
  gi|518652845|ref|YP_008142365.1| 138 LDYSILASMWVSEISKYVYDF-----DNFLFTAHSLPLIDD-E-S-DYQASLERNAGKISDMLGIEK-YYTAFYSQG 205
                                       6999***************99.....78*********9996.3.3.6*******************9.********9 PP

                                       SSS-BSSSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIITTSTT..CCCEEE----TT-HHHHHHHHH CS
                    Ferrochelatase 235 GpeeWlePdtddtleelaekgvkaivvvpigFvsDhlEtleeldiearelaeeaggekfvrvptlndspafiealad 311
                                          +W+eP++ ++++ ++e+++++++v pigF  +hlE+l++ld++++e +e  g+ k++r++t+ ds+ ++ +l++
  gi|518652845|ref|YP_008142365.1| 206 PHGKWIEPSIYSKIDLFKEDKINNLLVSPIGFLYEHLEILYDLDVKYKEFLESRGI-KYARARTPSDSDGMAILLKN 281
                                       99******************************************************.************99988887 PP

                                       HH CS
                    Ferrochelatase 312 lv 313
                                        +
  gi|518652845|ref|YP_008142365.1| 282 AI 283
                                       66 PP

>> DUF576  Csa1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   4.1e-06     0.037      92     182 ..      37     125 ..      27     143 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 4.1e-06
                                       ETTEEEEEEEEETTEEEESS--SSHHHHHHHHC---HHHC-----GGGSSCEEEEEETTTTEEEEEEE....--TTS CS
                            DUF576  92 eskekkypvklennkiiltkkikdeklkkeienfkFfvqygnfkdlkdykdgdvsynpnvpsYsaeyq....lsndd 164
                                       e++ kky +    n i ++++i  ++lk+++   k ++ yg+f+ ++ yk+ +  ++++v s +a+y+    l    
  gi|518652845|ref|YP_008142365.1|  37 EENIKKYEMV---NGISPSNQII-KNLKNKLG--KLLARYGDFEIIDAYKHWHPGIEETVSSLDADYEeiiaLPLFA 107
                                       5555666543...6777777775.56888775..89*****************************997444455566 PP

                                       HHHHHHHHHS--S--S-- CS
                            DUF576 165 envkqlrkrYdiptnkap 182
                                          +++rk Y+ip++ka 
  gi|518652845|ref|YP_008142365.1| 108 FKSNNIRKSYEIPVKKAM 125
                                       677889*******99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (294 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2046.84
//
Query:       gi|518652846|ref|YP_008142366.1|  [L=299]
Description: hypothetical protein FACI_IFERC00001G1485 [Ferroplasma acidarmanus fer1]
Scores for complete 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   37.2   0.0    5.7e-09   36.2   0.0    1.5  1  GTP_EFTU_D2  Elongation factor Tu domain 2
      0.005   16.7   0.1      0.012   15.5   0.1    1.7  1  GTP_EFTU_D4  Elongation factor Tu domain 4


Domain annotation for each model (and alignments):
>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.2   0.0   6.3e-13   5.7e-09       1      73 [.     154     220 ..     154     221 .. 0.96

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 6.3e-13
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                                       Gtvalg v sG + k +++++  +d +++   ++++s++++ ed+d a ag ++G+ ++ ++  d +++G+ l
  gi|518652846|ref|YP_008142366.1| 154 GTVALGFVLSGSISKHQKLVL--SDLDRE---VEVRSIQMNDEDVDSAGAGSRVGLALKNIEPTD-MERGMFL 220
                                       9********************..988899...*********************************.8***977 PP

>> GTP_EFTU_D4  Elongation factor Tu domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.4e-06     0.012      21      72 ..     158     208 ..     140     217 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.4e-06
                                       EEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEES CS
                       GTP_EFTU_D4  21 vGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisieg 72 
                                        G  vl+G i    kl+ +d  +  e+++iq +++ ++ a aG++v++++++
  gi|518652846|ref|YP_008142366.1| 158 LG-FVLSGSISKHQKLVLSDLDREVEVRSIQMNDEDVDSAGAGSRVGLALKN 208
                                       55.69***************99999**********************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1888.61
//
Query:       gi|518652847|ref|YP_008142367.1|  [L=425]
Description: hypothetical protein FACI_IFERC00001G1486 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-49  168.6   0.4    1.8e-49  168.2   0.4    1.2  1  GARS_A        Phosphoribosylglycinamide synthetase, ATP-grasp
      4e-20   72.4   0.0    9.6e-20   71.2   0.0    1.7  1  GARS_N        Phosphoribosylglycinamide synthetase, N domain
    1.6e-08   34.7   0.1    3.1e-07   30.6   0.0    2.4  2  GARS_C        Phosphoribosylglycinamide synthetase, C domain
  ------ inclusion threshold ------
      0.088   12.6   0.1        0.3   10.8   0.0    1.9  2  ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter 
      0.096   13.2   0.0       0.27   11.7   0.0    1.7  1  YxiJ          YxiJ-like protein


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   0.4   5.1e-53   1.8e-49       1     193 [.     100     293 ..     100     294 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 5.1e-53
                                       HBHHHHHHHHHHTT--B-.-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEE....SSHHHHHHHHHHHCT CS
                            GARS_A   1 asKsfakdllkkagipta.eyeaftdpeeakeyieeatakalVvKadglaagKgviva....kseeealkavkeile 72 
                                       +sK+++++l+++++i++  e + ++d e +k+++e+ +++   vK+ gl++gKgv+v+    ++++ea+++++ei++
  gi|518652847|ref|YP_008142367.1| 100 TSKEYMRNLMERHHIKGNiENKLISDKEVLKTFFENNDTEY-AVKPIGLTGGKGVKVMglqlSNVAEAIAYASEIID 175
                                       79***************989999***************999.9**************999999*************7 PP

                                       S-TTCCCCSSEEEEE---SEEEEEEEEECTTEEEE---BEEEEEEECCCEEEEECECEEEE....S-TTS-HHHHHH CS
                            GARS_A  73 kkkfGeagekvviEelleGeEvsllalvdgktvkplplaqdhkrvlegDkgpnTGGmGays....papvvteellek 145
                                         + G    kv++E++  GeE+s++a++d k+v+ +p++qd+kr++e D gpnTGGmG++s     +p+++ +++++
  gi|518652847|ref|YP_008142367.1| 176 --RDG----KVLLEKREIGEEFSIQAFTDSKNVVFMPVVQDYKRLYEDDLGPNTGGMGSISdknfILPFLSIDVVNE 246
                                       ..445....9***************************************************7777788889999999 PP

                                       HHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTC CS
                            GARS_A 146 ikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpe 193
                                       ++  il+ +v ++++e++pfkGv+y+++m +++g +v+e+n Rf+Dpe
  gi|518652847|ref|YP_008142367.1| 247 ARG-ILNDIVTAMREENNPFKGVIYGQFMSTAQGVRVIEINSRFADPE 293
                                       888.*******************************************9 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   2.7e-23   9.6e-20       1      90 []       1      99 [.       1      99 [. 0.93

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 2.7e-23
                                      EEEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG...........TTHHHHHHHHHHCTESEEEE-SHHHHHTTHH CS
                            GARS_N  1 mkvLvvGsGGRehalawklaqspkvekvyvapgNagt...........edlealvefakeekidlvvvGpeapLvaGva 68
                                      m+vL+vGsGGRe a+a+k+++ +++ +v v  +N+++           ++++++v+fak++++d++++Gp++ L ++++
  gi|518652847|ref|YP_008142367.1|  1 MNVLLVGSGGREDAIARKIRETDNLYSV-VSNENPSIlglsrnvikynKNTQEIVNFAKKNRVDIAFIGPDDILNTDLV 78
                                      9*******************99887754.567899999***999999877889************************** PP

                                      HHHHHHHT-EEES--CCCCHHH CS
                            GARS_N 69 daleeekgikvfGpskeaAqlE 90
                                      d l e+ +i+v +p ++aA++E
  gi|518652847|ref|YP_008142367.1| 79 DSLIEN-HIPVASPGQKAAMIE 99
                                      ***888.**************9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0       0.1   3.6e+02      10      64 ..     103     175 ..      95     185 .. 0.65
   2 !   30.6   0.0   8.7e-11   3.1e-07       2      79 ..     329     415 ..     328     416 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.1
                                       TTTSS--ST-EEBS..........TTEEEEESSEE.......EEE-SSEEEEEEEE.ESSHHHHHHHHHHHHT CS
                            GARS_C  10 GYPgsyekgkeitg..........egvkvfhagtk.......lvtsGGRvlavvav.getleeArakayeavk 64 
                                        Y  +  + ++i+g          e  k f            +  +GG+ + v+++  ++++eA+a a e ++
  gi|518652847|ref|YP_008142367.1| 103 EYMRNLMERHHIKGnienklisdkEVLKTFFENNDteyavkpIGLTGGKGVKVMGLqLSNVAEAIAYASEIID 175
                                       5555555566666665555554442223333332245666667889999999999845799999999988876 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 8.7e-11
                                       EEEEEEETTTTSS--.ST-EEBS....TTEEEEESSEE.....EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB- CS
                            GARS_C   2 vgvvlaskGYPgsye.kgkeitg....egvkvfhagtk.....lvtsGGRvlavvavgetleeArakayeavkkikf 68 
                                       v  ++++ GY  ++  ++ +i+     ++ kv++++++     + t+ +R la++++g+++ eA + +++++k i+ 
  gi|518652847|ref|YP_008142367.1| 329 VLKYIVPPGYGIKPVeTELTIKDrietDNFKVYYSSVSgtlnhVTTTKSRSLALIGIGDSIYEASDIVEDNLKYIT- 404
                                       5678889999755442555664466668899****988888999*******************************5. PP

                                       TTEE--STTTH CS
                            GARS_C  69 eglfyRkDIGa 79 
                                        + ++R+DIG+
  gi|518652847|ref|YP_008142367.1| 405 GDYYIRHDIGT 415
                                       58********7 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       2.9     1e+04      13      28 ..     188     203 ..     187     208 .. 0.74
   2 ?   10.8   0.0   8.3e-05       0.3      63     125 ..     266     329 ..     246     334 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 2.9
                      ATPgrasp_Ter  13 gpEySvDvlaekgevl 28 
                                       g+E+S+  ++++ +v+
  gi|518652847|ref|YP_008142367.1| 188 GEEFSIQAFTDSKNVV 203
                                       7999999998855554 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 8.3e-05
                      ATPgrasp_Ter  63 dglvnvQvrededgpkLLEiNpRas..GGlgysalaGvnlpylalklllgleteeveepeeglrv 125
                                       +g++  Q+  +++g +++EiN+R++   G+++ +l   n+++++l+   g   ++  + +++++v
  gi|518652847|ref|YP_008142367.1| 266 KGVIYGQFMSTAQGVRVIEINSRFAdpEGINVLTLLQSNIVDIFLDIYSG-TLKNNIKFKSKATV 329
                                       666677999999************83359******************999.44444455555554 PP

>> YxiJ  YxiJ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.5e-05      0.27      32      63 ..     349     380 ..     335     386 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.5e-05
                              YxiJ  32 tkddclsaDfneyfmliagtLsyvlngkeqki 63 
                                        kd + +++f+ y++ ++gtL+ v + k++ +
  gi|518652847|ref|YP_008142367.1| 349 IKDRIETDNFKVYYSSVSGTLNHVTTTKSRSL 380
                                       466688999*****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); expected 358.6 (0.02)
Passed bias filter:                      533  (0.0297284); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2677.26
//
Query:       gi|518652848|ref|YP_008142368.1|  [L=162]
Description: thiosulfate sulfurtransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-20   73.2   0.4      2e-20   73.0   0.4    1.0  1  SMC_ScpB        Segregation and condensation complex subunit 
    7.8e-05   22.5   0.5    0.00051   19.9   0.2    2.4  2  HTH_11          HTH domain
  ------ inclusion threshold ------
      0.033   14.7   0.3        0.3   11.6   0.0    2.3  3  HTH_27          Winged helix DNA-binding domain
       0.04   13.8   0.6         11    6.0   0.0    2.4  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.078   13.2   1.2        2.3    8.5   0.0    2.4  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
       0.17   12.0   0.0        1.1    9.4   0.0    2.2  2  HTH_20          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SMC_ScpB  Segregation and condensation complex subunit ScpB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.0   0.4   6.6e-24     2e-20       2     153 ..      10     154 ..       9     159 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.0 bits;  conditional E-value: 6.6e-24
                          SMC_ScpB   2 iiEAiLfvageplsleeLakilelskeeveealeeLkeeyeeedrglelvevaggyrlvtkpelaevvkklvkekkk 78 
                                       +iEAiLf+++ep++++e+a++l+++++e+ +a++e++++ye+ ++ l + ++++ y++ +++e+ +vv  ++++   
  gi|518652848|ref|YP_008142368.1|  10 RIEAILFSSKEPVKASEIAEYLNITNAEFIKAIKEISRNYENIESSLIVGQFGNSYKIKLSEEFVPVVDPFIEK--- 83 
                                       7*************************************************************************... PP

                          SMC_ScpB  79 trLsqaaletLaiIa.ykqpvtraeieeiRGvnsdsvvrtLlerglieekgrkeepgrpilYgtTekFleyfglks 153
                                        ++++ +l +L++I  ++    + ++ +  G + ++ +++L + g++++++ ++    +  Y++T +F+++f++++
  gi|518652848|ref|YP_008142368.1|  84 -EFTEKQLAMLSYIYkMNGEAISGNLRDNFGYAYKEDLEKLKKGGMVSSRKYRN----THKYKVTTEFHRKFNINK 154
                                       .*************736779*******************************775....567*************87 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   1.7e-07   0.00051       5      48 ..      11      54 ..       8      55 .. 0.88
   2 ?   -0.9   0.0      0.56   1.7e+03      20      33 ..     145     158 ..     135     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.7e-07
                            HTH_11  5 ilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgvpIes 48
                                      i  +L+++++p+ ++e+Ae+Ln++ +   + Ik+++     Ies
  gi|518652848|ref|YP_008142368.1| 11 IEAILFSSKEPVKASEIAEYLNITNAEFIKAIKEISRNYENIES 54
                                      557899********************999999999888777776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.56
                            HTH_11  20 eLAeeLnvSrrtvr 33 
                                       e  +++n+ +rt r
  gi|518652848|ref|YP_008142368.1| 145 EFHRKFNINKRTLR 158
                                       56679999999987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   9.9e-05       0.3      16      43 ..      19      46 ..       9      50 .. 0.89
   2 ?    0.2   0.0      0.36   1.1e+03      18      40 ..      87     109 ..      81     110 .. 0.82
   3 ?   -3.0   0.0       3.7   1.1e+04      39      50 ..     120     131 ..     118     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.9e-05
                            HTH_27 16 rrrkkladlcgrlnvedshisyslkkLt 43
                                       +++k+++++++ln++ + +++++k+  
  gi|518652848|ref|YP_008142368.1| 19 KEPVKASEIAEYLNITNAEFIKAIKEIS 46
                                      68999********************975 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.36
                            HTH_27  18 rkkladlcgrlnvedshisyslk 40 
                                       +k la+l+  ++++  +is +l+
  gi|518652848|ref|YP_008142368.1|  87 EKQLAMLSYIYKMNGEAISGNLR 109
                                       78899999999999999886665 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 3.7
                            HTH_27  39 lkkLtekGLver 50 
                                       l+kL + G v +
  gi|518652848|ref|YP_008142368.1| 120 LEKLKKGGMVSS 131
                                       688999898833 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0036        11      19      38 ..      18      37 ..      12      48 .. 0.78
   2 ?    5.9   0.1    0.0039        12      43      64 ..     120     142 ..     115     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0036
                                      HHCCCHHCHHCCCTTSSCHC CS
                              TrmB 19 klgpatadeiaeelgvprsk 38
                                      +++p +a+eiae l++  + 
  gi|518652848|ref|YP_008142368.1| 18 SKEPVKASEIAEYLNITNAE 37
                                      789************98776 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0039
                                       HHHHHHCTSEEEES.STTTEEEE CS
                              TrmB  43 LrsLedkGlVerek.grpklYra 64 
                                       L++L++ G+V  +k +++++Y++
  gi|518652848|ref|YP_008142368.1| 120 LEKLKKGGMVSSRKyRNTHKYKV 142
                                       99*********999555999996 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 ?    8.5   0.0   0.00078       2.3      19      47 ..      18      46 ..       3      48 .. 0.78
   2 ?    3.1   0.2     0.036   1.1e+02      42      58 ..     119     135 ..     117     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00078
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHH CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLe 47
                                      +k++vk +++ae Ln+  +   + +k+ +
  gi|518652848|ref|YP_008142368.1| 18 SKEPVKASEIAEYLNITNAEFIKAIKEIS 46
                                      6999************9887777766665 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.036
                                       HHHHHHHTTSEEEETTT CS
                    Fe_dep_repress  42 mlkkLekdGyveyekyk 58 
                                        l+kL+k G v   ky+
  gi|518652848|ref|YP_008142368.1| 119 DLEKLKKGGMVSSRKYR 135
                                       599************98 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.0   0.00036       1.1       9      40 ..       5      37 ..       2      45 .. 0.89
   2 ?   -0.9   0.0      0.58   1.7e+03      45      58 ..     120     133 ..     118     135 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00036
                                      -HHHHHHHHHH.STCTTB-HHHHHHHHTS-HHH CS
                            HTH_20  9 hPvRrrilraL.araegltaselaerldlsknt 40
                                      ++  rri++ L +++e++ ase+ae l ++ ++
  gi|518652848|ref|YP_008142368.1|  5 NEISRRIEAILfSSKEPVKASEIAEYLNITNAE 37
                                      7788*********************99998776 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                                       HHHHHHCTTEEEEC CS
                            HTH_20  45 LrvLeeagLvevvr 58 
                                       L++L + g v +++
  gi|518652848|ref|YP_008142368.1| 120 LEKLKKGGMVSSRK 133
                                       89*******99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (162 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1144.34
//
Query:       gi|518652849|ref|YP_008142369.1|  [L=449]
Description: hypothetical protein FACI_IFERC00001G1488 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-28  100.3  34.9    5.4e-28   97.9  34.9    1.9  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 !   97.9  34.9     3e-32   5.4e-28       1     422 [.      20     402 ..      20     426 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 3e-32
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       pvpee R+ +  +lf++W+++n+ i  ++ig +++ lgL+++ s+++ ++g+++g i+va++++ G+ +Glp+++l 
  gi|518652849|ref|YP_008142369.1|  20 PVPEEMRKNNSSELFTLWFASNMTIGDFAIGFIPVLLGLSLGMSLFSMLLGSVMGSILVAFMSRTGTLTGLPQMVLG 96 
                                       8**************************************************************************** PP

                    Transp_cyt_pur  78 RasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivll 154
                                       R  fG  + ++  +l ++  ++w +v+ +++s a++l                     +  ++++  +++ ++i+  
  gi|518652849|ref|YP_008142369.1|  97 RRAFGKNFGIFMTVLQWINTLGWLTVNLILASFAFSLAFHVP----------------YYEISIILMGIIIFLISNS 157
                                       ********************************9998865554................455778888899999999* PP

                    Transp_cyt_pur 155 gvskirkffviaallvpvaafgfliwalvkaegGpvld.kavklgkselflsavagvlagfatlilnapDFtryakt 230
                                       g ++i  f+++ ++++++++  + i + +  ++ +++  k++++g+  +f  ++a+  +  +++ + a+D++ry kt
  gi|518652849|ref|YP_008142369.1| 158 GRKSISYFEKAMSVILGILF-TI-IILNAGLHINDIYAyKPSSFGFGVAFGITLATSFSYLMSWGPYAADYSRYNKT 232
                                       *****************995.33.3333344555555504555555559999**********************999 PP

                    Transp_cyt_pur 231 kkssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdetagvllililvalaqlgvnisanllsa 307
                                       k++    +++++ ++++ ++++ i+++ +a +  + +  +p + l++++    + +i +++ + +     ++nl+s 
  gi|518652849|ref|YP_008142369.1| 233 KNA----FIYTFSGGLIATFWAEIAGVFVAIMSLDPS-GNPASDLNHVLGP--YGIIGLIAIFLGGIAADALNLYSN 302
                                       986....788999999999999999988877665544.4444456666666..334444444445555567778888 PP

                    Transp_cyt_pur 308 gldlaallPkkinikrgsliaavialvivpwkllssssklftaflsllavflspvagviiadyfvvrrgylklaaly 384
                                          l+     ki +   +++  via++ +++ l+ ++ +    fl+ll++ ++p+ g+++ad+f+v r +    +++
  gi|518652849|ref|YP_008142369.1| 303 SISLKSTGL-KIRRIYSVIFGIVIAIALAVA-LYTKFYSFYEDFLFLLDYWITPWLGIMLADFFIVNRNEKFNIKTI 377
                                       888877666.9999999999999***99999.99999995557***********************99877666666 PP

                    Transp_cyt_pur 385 trrrgsaYwyrkgvNwravaayivGiaaglvgvagsvg 422
                                                   g N   + ay ++++a++++++  +g
  gi|518652849|ref|YP_008142369.1| 378 P-----------GLNISGISAYFIALIASVPFMD--PG 402
                                       6...........8888888888888888888855..34 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3381.96
//
Query:       gi|518652850|ref|YP_008142370.1|  [L=147]
Description: deoxycytidine triphosphate deaminase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-12   44.8   0.0    1.2e-11   44.4   0.0    1.1  1  dUTPase   dUTPase
  ------ inclusion threshold ------
      0.032   13.0   0.0       0.45    9.3   0.0    2.0  2  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 !   44.4   0.0   1.3e-15   1.2e-11      14     125 ..      29     140 ..      15     142 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 1.3e-15
                                       SSEEEE-SSS..EEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-E CS
                           dUTPase  14 AgyDlsaakd..ltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdv 88 
                                        gyD++  +    ++k ++   +++  ++ +pd++ a +  +S  a++g++   g +d+ + G++   ++n+++ ++
  gi|518652850|ref|YP_008142370.1|  29 NGYDIRIGDHelDIIKTNSLFFISSLEKFNIPDNIVASLHIKSKYARRGVFASFGFVDAGFIGNLTMAFYNFGE-EF 104
                                       5999999865224788899*******************************************************.** PP

                                       EE-TT-EEEEEEEEEBECGEEEEESSTTTESSBTTXT CS
                           dUTPase  89 kikkgdRiAqLifariltaeleevetlkatergeggf 125
                                       +ik+g ++ q++f +i+t + +++   + t++ ++g+
  gi|518652850|ref|YP_008142370.1| 105 RIKRGMKFVQIVFYEIKT-PEKNYPGRSGTYQNSEGI 140
                                       ******************.666666678888888876 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 ?    2.0   0.0    0.0078        70       5      42 ..       2      38 ..       1      42 [. 0.86
   2 ?    9.3   0.0     5e-05      0.45      77     163 ..      42     120 ..      38     136 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.0078
                               DCD  5 lpdqeiealieegaikaeepleeeqiqPaslDLrLgkk 42
                                      l d+eie  +++g+i  +e+++++ + P+  D+r+g++
  gi|518652850|ref|YP_008142370.1|  2 LNDREIEYNVAAGKII-SENYSRDSLTPNGYDIRIGDH 38
                                      788999999******5.56799999**********975 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 5e-05
                               DCD  77 vlekgcvYivplleslaLpadlsaaanpksstGRlDvftRvitdkgeefdeveagYkGplyleisprsFsilvrkGs 153
                                       +++++ ++ +  le++++p+++ a+   ks   R  vf+        +f  v+ag+ G+l +         ++++G+
  gi|518652850|ref|YP_008142370.1|  42 IIKTNSLFFISSLEKFNIPDNIVASLHIKSKYARRGVFA--------SFGFVDAGFIGNLTMAFYNFGEEFRIKRGM 110
                                       688999999999**********************99995........799999999999999999999999999999 PP

                               DCD 154 rLsqirfrrg 163
                                       +  qi f + 
  gi|518652850|ref|YP_008142370.1| 111 KFVQIVFYEI 120
                                       9999999765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 945.57
//
Query:       gi|518652851|ref|YP_008142371.1|  [L=172]
Description: nicotinamide-nucleotide adenylyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-16   61.0   0.0    1.8e-16   60.6   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like
    0.00011   21.6   0.8      0.022   14.0   0.9    2.1  2  HIGH_NTase1      HIGH Nucleotidyl Transferase
  ------ inclusion threshold ------
      0.077   12.7   0.4        5.6    6.6   0.0    2.6  3  Citrate_ly_lig   Citrate lyase ligase C-terminal domain


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.6   0.0   3.1e-20   1.8e-16       2     142 ..       5     132 ..       4     133 .. 0.92

  Alignments for each domain:
  == domain 1  score: 60.6 bits;  conditional E-value: 3.1e-20
                                       EEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHH CS
                   CTP_transf_like   2 agGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlelakevdevisvdpweltrevlk 78 
                                       + G+F+p+H+GHl++++ ++++ e+ +++g+ s++ ++    ++++a eR+ m+    e++    ++ +++++  ++
  gi|518652851|ref|YP_008142371.1|   5 IIGRFQPFHNGHLAIIKHILEHNEY-VVIGIGSAQLSHTI-MNPFTAGERYLMILNTLENNG---ISNYYIVP--IE 74 
                                       68***********************.************87.*************99988888...89999998..77 PP

                                       HTTTTEEEEEEEHHHHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
                   CTP_transf_like  79 klkpdklylvigadvledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                                       + +++  ++v+  ++l+       ++++++n++lv + + ekq++vl +++ ++n  S+t+ir+
  gi|518652851|ref|YP_008142371.1|  75 DVNSN-PMWVAHVESLTP-----PFHRVYTNNPLVRRLFYEKQYEVLSLPMINRNSWSGTRIRQ 132
                                       77775.578888888887.....69**************************************8 PP

>> HIGH_NTase1  HIGH Nucleotidyl Transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.9   3.7e-06     0.022       6      34 ..       5      32 ..       1      40 [. 0.79
   2 !    5.7   0.0    0.0012         7     201     237 ..     122     155 ..     104     168 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 3.7e-06
                       HIGH_NTase1  6 iIaEYNPfHnGHlyhlekakeltgadvvi 34
                                      iI  + PfHnGHl  ++++ e+ ++ vvi
  gi|518652851|ref|YP_008142371.1|  5 IIGRFQPFHNGHLAIIKHILEH-NEYVVI 32
                                      88999**************996.555555 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0012
                       HIGH_NTase1 201 eeiaSAtaiRkalkeekkleelkklvPestleilkee 237
                                       ++  S t iR+ + +    e+ ++ vP+++++i+k+ 
  gi|518652851|ref|YP_008142371.1| 122 RNSWSGTRIRQKILKG---EDWRSDVPDTVYNIMKDL 155
                                       5788*********655...69************9986 PP

>> Citrate_ly_lig  Citrate lyase ligase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1    0.0071        42       6      33 ..       7      34 ..       2      44 .. 0.81
   2 ?    6.6   0.0   0.00094       5.6       8      27 ..      44      63 ..      39      81 .. 0.71
   3 ?   -1.5   0.0      0.28   1.7e+03     135     178 ..     109     148 ..      93     152 .. 0.55

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0071
                    Citrate_ly_lig  6 mnanPftlGhryLvekaakendvvhlfv 33
                                          Pf +Gh  ++++  ++n++v + +
  gi|518652851|ref|YP_008142371.1|  7 GRFQPFHNGHLAIIKHILEHNEYVVIGI 34
                                      5568******************998866 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00094
                    Citrate_ly_lig  8 anPftlGhryLvekaakend 27
                                       nPft G ryL+   + en+
  gi|518652851|ref|YP_008142371.1| 44 MNPFTAGERYLMILNTLENN 63
                                      49********9755444444 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.28
                    Citrate_ly_lig 135 kaeievveierkekeeelisaskvrkllkeknleklaelvPktt 178
                                       +++ ev  ++ +  + +  s +++r+ + +++  + ++ vP t 
  gi|518652851|ref|YP_008142371.1| 109 EKQYEVLSLPMI--NRNSWSGTRIRQKILKGE--DWRSDVPDTV 148
                                       444444444444..344568888887654432..2344455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        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 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1219.30
//
Query:       gi|518652852|ref|YP_008142372.1|  [L=777]
Description: hypothetical protein FACI_IFERC00001G1491 [Ferroplasma acidarmanus fer1]
Scores for complete 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-66  223.7   0.2    9.1e-66  222.4   0.2    1.6  1  DNA_pol_B       DNA polymerase family B
    5.9e-16   58.5  10.1    8.6e-12   44.8   0.1    2.8  3  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
    1.3e-06   27.3   0.0    2.1e-06   26.6   0.0    1.3  1  DUF1744         Domain of unknown function (DUF1744)
     0.0018   18.3   0.2     0.0063   16.5   0.2    2.0  1  RNase_H_2       RNase_H superfamily
     0.0034   16.3   1.7      0.009   14.9   0.1    2.2  2  DNA_pol_B_2     DNA polymerase type B, organellar and viral
  ------ inclusion threshold ------
      0.021   15.0   2.3       0.13   12.5   0.1    3.0  3  DNA_pol_B_3     DNA polymerase family B viral insert


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 !  222.4   0.2     3e-69   9.1e-66       3     415 ..     345     709 ..     343     745 .. 0.88

  Alignments for each domain:
  == domain 1  score: 222.4 bits;  conditional E-value: 3e-69
                                       HHHHHHS-HHHHHHHHHHHHHHHTTBE-B-----.--SS.-S----BE----EEESS-EEEEEETTHHHHHHHHTT- CS
                         DNA_pol_B   3 lsrvledgqqirveslLlrlakeegfilpdrtekkgkeeegYqGatVlePkkglydkpvlvlDFaSLYPsiiqahNl 79 
                                       l  v ++g ++ v slL+r a++e++ +p ++++k +++ +Y+G+ V   + glyd  ++vlDF+S+YPs+i+++N+
  gi|518652852|ref|YP_008142372.1| 345 LDDVTNGGTSTYVDSLLIRRADRENIGVP-MSSSKFSND-TYAGGYVHTMDPGLYD-MIVVLDFKSMYPSMIIKYNI 418
                                       5567889**********************.777756666.7**************7.6889**************** PP

                                       STTTCE-HCCHCCT--BTT...TEEE-TCC-EEE-TTS---HHHHHHHHHHHHHHHHHHHHHCS--HHHHHHHHHHH CS
                         DNA_pol_B  80 cyttlvaseeeakeleaedeyleveveprlvefvkksvregllpklLkdllakRkaikkelkeekdefekalldkqQ 156
                                       c+ttl  + +               v+p++ +f+ + v++g++p lL++l+++R ++kk++ke+k++  +  ld  Q
  gi|518652852|ref|YP_008142372.1| 419 CFTTLSPEGTI--------------VAPNGARFLDPGVKKGIIPDLLEQLMKNRDEVKKQMKEDKSN--HDYLDGLQ 479
                                       *****988776..............5678899******************************99998..9******* PP

                                       HHHHHHHHHHHHHHTSTTSTT--HHHHHHHHHHHHHHHHHHHHHHHHT...SSGGGT-SS.....T-EEEEEBSSEE CS
                         DNA_pol_B 157 lalKvtaNsvYGftGvansrlpclalAasvTtiGRemLektkelvekkaellskllalpeeaeeeklkviYGDTDSv 233
                                       +a+Kv++N++YG++G +  r+   ++++ +T++ R++++++ + ++k                  + kviYGDTDS+
  gi|518652852|ref|YP_008142372.1| 480 AAIKVLMNTFYGVLGTSFYRFTNREISSAITAYARNTITSIIADLDKS-----------------GNKVIYGDTDSI 539
                                       ***************************************999999987.................89********** PP

                                       EEE-S-SSHHHHHHHHHHHHHHHHT.TSTTT--EEEEEEEEEEEEE.ETTEEEEEEEEESSTTSEEEEESSGGGSTT CS
                         DNA_pol_B 234 fielkvkdveellkigkelaeevseklfkkplklefekvykkllLi.sKKkYaglkvektskanklliKGvdlvRrd 309
                                       fie + k+++e+++ g+ l + +s+   k++l lefek+  +l  + +KK+Yag +v  +s+a+++l++G ++ R d
  gi|518652852|ref|YP_008142372.1| 540 FIESGKKTLDEAIEYGNRLSSDISR---KENLVLEFEKIMDPLFSHgAKKRYAGKIVYPPSSAGEILVRGYETRRTD 613
                                       *************************...999************98747***************************** PP

                                       S-HHHHHHHHHHHHHHSSS....S-HHHHHHHHHHHHHHHHHHHHTT-S-GGGG-EEEEESS.CCCS.SGCCSHHHH CS
                         DNA_pol_B 310 ncklvkevikkvlelllkdeteersleeglealksilkdvleeleenkvplekfvlskelskepeny.ksknlphle 385
                                       + +l++e  ++v +l+l+      ++e + ++ ++++    +e++++k++ +k+v+s+++++  + y ++ ++++++
  gi|518652852|ref|YP_008142372.1| 614 SFDLQSEALSTVFDLILSR-----DVEGAKQYAEDLV----KEVATGKIDTSKLVISRSVKN-FSTYkNAGSMANVN 680
                                       *****************99.....7777766666666....9******************99.666648889***** PP

                                       HHHHHHHHCSS---TTCEEEEEEBETSS.. CS
                         DNA_pol_B 386 vakrlkkrneeapevgdrisYvivekkkev 415
                                       +ak+l    +e+  +g ++s++++ + k++
  gi|518652852|ref|YP_008142372.1| 681 AAKKLIDA-GETFIPGMKVSWIVTDAGKTP 709
                                       ******99.688888999999998887633 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 !   18.8   1.8   2.3e-07   0.00069       2     168 ..      25     165 ..      24     184 .. 0.77
   2 !   44.8   0.1   2.9e-15   8.6e-12     237     283 ..     193     238 ..     178     282 .. 0.83
   3 ?   -3.3   0.1       1.3   3.7e+03      17      55 ..     726     767 ..     721     771 .. 0.59

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.3e-07
                                       ECTTSEEEEEEEE---EE.EEEESSCGGHHHHHHHHHHHCCTTCCCEEEEEEEECCCCEECCTSSCCHHCEEEEEES CS
                    DNA_pol_B_exo1   2 teegksvcvnvfgfkpyf.Yceapdgkeleevkeelkelyeelskkvtkivkvelvlkkslygyekkpvpylkvsvs 77 
                                       te++ks+    +gfkpyf Y+e+      e++++e+k   +++           +++  + + +e k+v++ +++++
  gi|518652852|ref|YP_008142372.1|  25 TEDNKSITALYYGFKPYFdYVEPD-----EKCITEIK---NNPE---------FIKMEDKKLFLEGKDVNVKRIYIK 84 
                                       678888888888888888555554.....23444444...3332.........14566788888888899******* PP

                                       STCHHHHHHHHHHHCCCCCCCCSSS--HHHHHHHHCTS-TTCEEEEETEEEEGCC--C-.SEEEEEETTTSCEETTT CS
                    DNA_pol_B_exo1  78 npnelkkirkelspleeivdvyeydvdylerflidnkivgfgwysvkkylvraegkisncdveidcdvddliakpke 154
                                       +p +++++rk+   +   ++   +d++++ rf++d ++ +    +++ ++ + e+   ++d+ i++   + ++k+++
  gi|518652852|ref|YP_008142372.1|  85 SPWKVPELRKIC--Q---CQALAADIPFHHRFIYDFDLGST--VEIEGEPAEGEKGNYTTDLVIKI---NTVKKTDD 151
                                       ***********9..5...9****************999877..67776677766666666777777...66777777 PP

                                       CCS-EEEEEEEEEE CS
                    DNA_pol_B_exo1 155 sepplrvlsFDIec 168
                                        +p+l++ sFDIe 
  gi|518652852|ref|YP_008142372.1| 152 FNPQLKIFSFDIEN 165
                                       78**********95 PP

  == domain 2  score: 44.8 bits;  conditional E-value: 2.9e-15
                                       SHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHC CS
                    DNA_pol_B_exo1 237 sEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvkls 283
                                       +E e+L++f ++++++dPd+itgYNid +D+p +++R+k  +kv++s
  gi|518652852|ref|YP_008142372.1| 193 TEPEMLEDFNKLVQREDPDIITGYNIDGYDMPLLEERMK-FNKVRFS 238
                                       799************************************.6666654 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.3
                                       -EEEEEESSCGGHHHHHHHHHHHCCTTCCCEE...EEEEEEC CS
                    DNA_pol_B_exo1  17 pyfYceapdgkeleevkeelkelyeelskkvt...kivkvel 55 
                                        y+Y++ + +++l+ v e+l++    ++++ +   + +++++
  gi|518652852|ref|YP_008142372.1| 726 DYVYYSKRLQETLNRVLESLDKEIAVFKNPQSkitDAFEEKP 767
                                       588988887777777777777655555544442114444444 PP

>> DUF1744  Domain of unknown function (DUF1744)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   7.1e-10   2.1e-06     291     374 ..     483     566 ..     461     580 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 7.1e-10
                           DUF1744 291 dllvqhlvrWvespsslLyDpaLrrlvqnlmkKvflqLlaefkrlgskvvyAdfnkillkTsKksvenayaYveyil 367
                                       ++l+++++  + ++  ++ ++ + + +    + +++ ++a++ + g kv+y+d+  i+++++Kk++++a+ Y + + 
  gi|518652852|ref|YP_008142372.1| 483 KVLMNTFYGVLGTSFYRFTNREISSAITAYARNTITSIIADLDKSGNKVIYGDTDSIFIESGKKTLDEAIEYGNRLS 559
                                       56677777777777777888889999999************************************************ PP

                           DUF1744 368 kairske 374
                                       + i++ke
  gi|518652852|ref|YP_008142372.1| 560 SDISRKE 566
                                       *999987 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.2   2.1e-06    0.0063       3      85 ..     161     239 ..     159     329 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
                         RNase_H_2   3 fDiEttGlspkknliyliGvldvdekeiekltqllaeepeeekailelflellekkkalvtfngksFDvpflkrlf. 78 
                                       fDiE   +s   + i++iG+ ++   ei++   l   epe  + + +  l + e+ + +  +n  ++D+p+l++++ 
  gi|518652852|ref|YP_008142372.1| 161 FDIENS-IST--REIFVIGYSVFFNGEITEG-ALTGTEPEMLEDFNK--LVQREDPDIITGYNIDGYDMPLLEERMk 231
                                       9***99.655..99*******9999888752.233444444444444..223566667778***************7 PP

                         RNase_H_2  79 .kkyklde 85 
                                        +k++++ 
  gi|518652852|ref|YP_008142372.1| 232 fNKVRFSI 239
                                       76666665 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 !   14.9   0.1     3e-06     0.009     197     248 ..     371     418 ..     274     429 .. 0.64
   2 ?   -0.2   0.1      0.11   3.4e+02     371     400 ..     479     509 ..     461     580 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3e-06
                       DNA_pol_B_2 197 ellapskeldkyiRkayrGGrcypsvlgiyeeniyvyDvnSlYPsamthypm 248
                                        +++ s+++       y GG++  +  g y + i+v D++S+YPs+  +y +
  gi|518652852|ref|YP_008142372.1| 371 GVPMSSSKFS---NDTYAGGYVHTMDPGLY-DMIVVLDFKSMYPSMIIKYNI 418
                                       4444444444...468******66666666.***************999765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.11
                       DNA_pol_B_2 371 rsiaKlllNsLYGrFatnpd.ntkivildee 400
                                       +  +K l+N+ YG  +t+    t+  i++  
  gi|518652852|ref|YP_008142372.1| 479 QAAIKVLMNTFYGVLGTSFYrFTNREISSAI 509
                                       5678999999999988876544444444444 PP

>> DNA_pol_B_3  DNA polymerase family B viral insert
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.48   1.4e+03      66      97 ..      52      83 ..      43     100 .. 0.81
   2 ?   12.5   0.1   4.3e-05      0.13      72     123 ..     276     326 ..     243     330 .. 0.77
   3 ?   -0.3   0.1      0.38   1.1e+03       7      54 ..     461     507 ..     455     547 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.48
                       DNA_pol_B_3 66 tvkvkaeneiaigdtytlsfgkDDvdlsdlYk 97
                                        ++k++ e+   +  +l +   Dv+++++Y 
  gi|518652852|ref|YP_008142372.1| 52 ITEIKNNPEFIKMEDKKLFLEGKDVNVKRIYI 83
                                      456778888888888999999999****9996 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 4.3e-05
                       DNA_pol_B_3  72 eneiaigdtytlsfgkDDvdlsdlYknynlevaleiarYClhDacLCkylwk 123
                                       +++++  +++ l  gk+Dv+  d+ ++++ +  +++ +YC+ Da L   +++
  gi|518652852|ref|YP_008142372.1| 276 HETLNYVSNMLLNEGKEDVNRLDIENEWK-NRRDDVIKYCIKDARLALLIYR 326
                                       55666778889999*********999886.678999**********999986 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.38
                       DNA_pol_B_3   7 ctakveeaenealtlegdetkdakdkisiFsevlstgnYvtiddnvlk 54 
                                       ++ +++e ++++  l g  +++ k  ++ F+ vl t+ Y + + ++  
  gi|518652852|ref|YP_008142372.1| 461 VKKQMKEDKSNHDYLDGL-QAAIKVLMNTFYGVLGTSFYRFTNREISS 507
                                       555555555554444443.34566677888888888888887777654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (777 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       747  (0.0416643); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.72u 0.30s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 5336.05
//
Query:       gi|518652853|ref|YP_008142373.1|  [L=411]
Description: hypothetical protein FACI_IFERC00001G1492 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.4e-29  101.2  41.2    1.7e-20   73.3  17.8    2.0  2  MFS_1       Major Facilitator Superfamily
    2.6e-05   23.3  25.7    2.6e-05   23.3  25.7    2.0  2  MFS_1_like  MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3  17.8   1.9e-24   1.7e-20      13     241 ..      22     256 ..       8     260 .. 0.79
   2 !   35.0  15.9     8e-13   7.2e-09      30     181 ..     255     404 ..     251     410 .. 0.77

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.9e-24
                             MFS_1  13 silgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalg.lllll..fa..s 83 
                                       ++l+p+l  +++   ++s +++g ++ +y l+++++ + +G l+dr+ r   +++lg+ll a++ + ++   f+  +
  gi|518652853|ref|YP_008142373.1|  22 FLLFPTLIAYYKVIPHVSIAFLGVMAIIYNLLSGLLGPSIGKLADRIDRDGaLIFLGILLEAISaI-FFGlaFVftA 97 
                                       23444444466666779*******************************9999************33.3334654667 PP

                             MFS_1  84 slw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.Wravfyila 158
                                        +  ++lv+ v+ G+g++++ p+ga+++a  + k++ + a+g+ +++ slG +l p +  + +  +g + ++  ++a
  gi|518652853|ref|YP_008142373.1|  98 YVNyIILVAAVILGIGQAFYHPIGASILAFTYGKKDSSTAMGINGSFGSLGRALIPSVLVYAIVFFGkFYGLVAVAA 174
                                       77779**************************************************8888888878887777777777 PP

                             MFS_1 159 ivsllafv.lfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsglltllply 233
                                         ++ a++ l++l ++ + +  k +++k   k t+++++++  ++ +k   ++ il +++++ +f+++g++t++p y
  gi|518652853|ref|YP_008142373.1| 175 YTTIAAVIiLGGLSFFKRSKYIKIDTKKHA-KNTEESKASE--SEYKKYGKFLyILTAIVFIRSFFLMGTVTFTPDY 248
                                       777777555777777777777777766666.6788888888..66666666654788888888999999******** PP

                             MFS_1 234 lqevlgls 241
                                       +   ++ +
  gi|518652853|ref|YP_008142373.1| 249 FDNIFHSK 256
                                       99999876 PP

  == domain 2  score: 35.0 bits;  conditional E-value: 8e-13
                             MFS_1  30 spseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.lllllfasslwlllvlrvlqGlgagalfpa 105
                                       s+  +g llt+ +lga+v+++ +Gr++  +G + ++ ++ +++ ++ +l+ll + +++l+ v  +l + +a ++fp+
  gi|518652853|ref|YP_008142373.1| 255 SKVIMGDLLTISFLGAVVGQPYFGRVVKDHGGKFTIAVTTIASTVFfGLMLL-TDNVYLVTVIYLLYATFAFTSFPV 330
                                       56667889**************************777777777777355555.58888999**************** PP

                             MFS_1 106 gaaliadwfpkeergraigl.lsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkr 181
                                        + ++a+  p++  +r ++l +s g+ +G ++g ++  +l+     +++ y   +v+l++ v+ ++ lp  p+++k 
  gi|518652853|ref|YP_008142373.1| 331 LLGYVAQTIPQKFSTRSNALvWSFGNIVGGAIGIAIVTILL---YVHVALYTSLVVMLIFSVISIIMLPLLPSKKKQ 404
                                       ***********988888875266677788899966666666...466666666666666666555666666665554 PP

>> MFS_1_like  MFS_1 like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3  25.7   2.9e-09   2.6e-05      36     369 ..      43     366 ..      36     379 .. 0.77
   2 !    2.1   0.7    0.0077        69     154     208 ..     360     406 ..     356     410 .. 0.56

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 2.9e-09
                        MFS_1_like  36 igiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfl..sllfippskerqeesklevsvaqdvdaekt 110
                                        g++  i  l+s l  p +g laDr+ +  +++ l++ll+a++ +  +l                 ++  +   + +
  gi|518652853|ref|YP_008142373.1|  43 LGVMAIIYNLLSGLLGPSIGKLADRIDRDGALIFLGILLEAISAIffGL-----------------AFVFTAYVNYI 102
                                       5778888888998889999*********************998761133.................44445567889 PP

                        MFS_1_like 111 fwilfllvvlasfflaailvlldaatlkelgedrkdyGrqrlfGsvGyaifafitGilidhysvnllp..ysallyv 185
                                       + + ++++ ++++f ++i + + a t+ + ++ ++  G    fGs+G a++  ++ ++i ++   + +   +a+  +
  gi|518652853|ref|YP_008142373.1| 103 ILVAAVILGIGQAFYHPIGASILAFTYGK-KDSSTAMGINGSFGSLGRALIPSVLVYAIVFFGK-FYGlvAVAAYTT 177
                                       999999999*********99998888877.5666779*************99999999888877.556543344445 PP

                        MFS_1_like 186 laallvisllvvlilne.tekesklkvtksl............qvllnilknpeviifllvalilgmswgiienFlf 249
                                       +aa++++  l++ +  +  +  +k +    +            ++  + l    +i     ++i  ++     +F  
  gi|518652853|ref|YP_008142373.1| 178 IAAVIILGGLSFFKRSKyIKIDTKKHA---KnteeskaseseyKKYGKFLYILTAI-----VFIRSFFLMGTVTFTP 246
                                       555555444443322220222222222...12345555444443333444444444.....4444455555667888 PP

                        MFS_1_like 250 lYLkelgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgis 326
                                        Y+++   s+ ++G l+++  ++ ++   +  ++++  G  + + ++ +a ++ f l+ +++n+ lv +i +L++  
  gi|518652853|ref|YP_008142373.1| 247 DYFDNIFHSKVIMGDLLTISFLGAVVGQPYFGRVVKDHGGKFTIAVTTIASTVFFGLMLLTDNVYLVTVIYLLYATF 323
                                       88888888********************************************************************* PP

                        MFS_1_like 327 fgllwaaaveyvskiapksleatgqgllsglyfglGralGsli 369
                                         + + ++  yv++ +p++  ++  +l+ ++   +G+a+G  i
  gi|518652853|ref|YP_008142373.1| 324 AFTSFPVLLGYVAQTIPQKFSTRSNALVWSFGNIVGGAIGIAI 366
                                       ****************************999999999999654 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.0077
                        MFS_1_like 154 GsvGyaifafitGilidhysvnllpysallyvlaallvisllvvlilnetekesk 208
                                       G++G ai+++++ + +  y+         l+v++++ vis++++  l+ ++k+++
  gi|518652853|ref|YP_008142373.1| 360 GAIGIAIVTILLYVHVALYT--------SLVVMLIFSVISIIMLPLLPSKKKQEE 406
                                       44444444444444444333........356677777777777666777666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.32s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 2645.57
//
Query:       gi|518652854|ref|YP_008142374.1|  [L=485]
Description: hypothetical protein FACI_IFERC00001G1493 [Ferroplasma acidarmanus fer1]
Scores for complete 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-79  266.4   0.0    3.1e-79  265.9   0.0    1.2  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
    2.4e-09   37.0   0.0    3.9e-08   33.0   0.0    2.2  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
     0.0068   15.5   0.0        1.6    7.7   0.0    3.3  4  tRNA-synt_2      tRNA synthetases class II (D, K and N)
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.029   14.3   0.0    1.8  1  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.9   0.0   6.8e-83   3.1e-79       2     244 ..     212     480 ..     211     481 .. 0.97

  Alignments for each domain:
  == domain 1  score: 265.9 bits;  conditional E-value: 6.8e-83
                                       .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-.. CS
                      tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpeka.. 76 
                                       +d++   ++++ ++lhplt ++e++++ifle+gf+e++g+ +e   +n d+L++pqdhpaRd+qdt+y+++++    
  gi|518652854|ref|YP_008142374.1| 212 YDLNSRVEPLNGAGLHPLTYLIEKVRKIFLEMGFTEMHGHFIEYTGWNMDMLFIPQDHPARDLQDTYYVESKNPVef 288
                                       8999999999***********************************************************5555449* PP

                                       ..............................ECESEEE-SSTHHHHHHHH.TTS-SSEEEEEEEEEEBSST-SSSB-S CS
                      tRNA-synt_2d  77 ..............................veekllLRthttavqirtl.ekkkppikiisigrvfRrdavDathla 122
                                                                     +++kl+LRthtt  +ir+l +++++p++i+si++vfR+++vD +hl 
  gi|518652854|ref|YP_008142374.1| 289 enpeildkvkrvhehgygkysgwnykwsedEAKKLILRTHTTVNTIRYLyNHRDKPQYIFSIEKVFRHESVDWKHLS 365
                                       ******************************999****************88889*********************** PP

                                       EEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE-HHH CS
                      tRNA-synt_2d 123 eFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmvrpev 199
                                       e +q+eg v +++v+l++lk++l+e++++l g++ ++r+ psy+p+tePs++v+v +   ++k +El+g+G++rpev
  gi|518652854|ref|YP_008142374.1| 366 ELYQIEGAVYGSDVNLSTLKWLLTEFYSRL-GFK-NIRLIPSYYPYTEPSMDVAVDI---NGKEVELGGSGIFRPEV 437
                                       ******************************.***.********************99...9999************* PP

                                       HHHTT-.TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHHHGG CS
                      tRNA-synt_2d 200 leavgideevsgfafGlGveRlamlkygieDiRelvendlrflrq 244
                                       ++++g+  + +++afGlG+eRlaml y+++DiRe++++dl++l++
  gi|518652854|ref|YP_008142374.1| 438 TKPMGL--KEPVLAFGLGLERLAMLYYNFNDIREIYNSDLDWLKN 480
                                       ******..9*********************************997 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.041   1.8e+02       9      37 ..     220     248 ..     217     256 .. 0.87
   2 !   33.0   0.0   8.7e-12   3.9e-08      83     212 ..     331     452 ..     323     454 .. 0.92

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.041
                   tRNA_synthFbeta   9 pttegelnkeqklrrklrdllagaGlnEv 37 
                                       p++++ l++   l +k+r++  ++G++E+
  gi|518652854|ref|YP_008142374.1| 220 PLNGAGLHPLTYLIEKVRKIFLEMGFTEM 248
                                       5566678999999***************7 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 8.7e-12
                   tRNA_synthFbeta  83 LevlarNlargnedvrlFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslg 158
                                       ++++++ ++++ +   +F i kvf+ +  + +   e  ++ ++++g++           v+  +lk ++ ++ ++lg
  gi|518652854|ref|YP_008142374.1| 331 VNTIRYLYNHRDKPQYIFSIEKVFRHEsVDWKHLSELYQIEGAVYGSD-----------VNLSTLKWLLTEFYSRLG 396
                                       5677888888888899***********777788***************...........****************** PP

                   tRNA_synthFbeta 159 iekvefepaehpalhpgrsAeikvdgk..evGvlGelhpevleafdlkqrvyvfEl 212
                                       ++++++ p+ +p+ +p     + ++gk  e+G  G + pev + ++lk++v +f l
  gi|518652854|ref|YP_008142374.1| 397 FKNIRLIPSYYPYTEPSMDVAVDINGKevELGGSGIFRPEVTKPMGLKEPVLAFGL 452
                                       ************************9987799*********************9976 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.12   5.4e+02      14      66 ..     164     217 ..     155     243 .. 0.69
   2 ?   -2.1   0.0      0.35   1.6e+03      28      45 ..     232     249 ..     216     254 .. 0.89
   3 !    7.7   0.0   0.00037       1.6      94     119 ..     347     371 ..     343     387 .. 0.89
   4 ?    3.0   0.0      0.01        46     287     307 ..     450     470 ..     445     472 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.12
                                       CSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS-..-SSSS--EEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                       tRNA-synt_2  14 rtekvskvlrlrstvtkavrkyleengfieietPiLsksd..teegarlFkvksr 66 
                                       +++ +++++++ ++  +a+ +y  +++++e+ tP L+ s     ++ r++ ++sr
  gi|518652854|ref|YP_008142374.1| 164 KRKYTKRIININESGKEALESY-GKDDYFEMLTPSLIASGkwRDAKFRPYDLNSR 217
                                       5555666666666666665555.5889*********9985333444456666555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.35
                                       HHHHHHHHHHHTT-EE-- CS
                                       xxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  28 vtkavrkyleengfieie 45 
                                       +++ vrk++ e gf+e++
  gi|518652854|ref|YP_008142374.1| 232 LIEKVRKIFLEMGFTEMH 249
                                       67899**********987 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00037
                                       EEEEEEEE--S--BTTB-S-CEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  94 vfqiaraFRaEdsrtdrhlaEFtqie 119
                                       +f+i ++FR E+++  +hl+E +qie
  gi|518652854|ref|YP_008142374.1| 347 IFSIEKVFRHESVD-WKHLSELYQIE 371
                                       79************.67899*****9 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.01
                                       EEEEHHHHHHHHCT-SSGGGC CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 287 lglGldRlvmlllgsesIrdv 307
                                       +glGl+Rl ml  + ++Ir++
  gi|518652854|ref|YP_008142374.1| 450 FGLGLERLAMLYYNFNDIREI 470
                                       89*****************97 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.6e-06     0.029       1     133 [.     313     429 ..     313     465 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-06
                                       EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld 77 
                                       Yk ++++ +++iL+   +   ++   ++  r+k  P++++ i  ++R+E  d +    + e+ q +g v++++    
  gi|518652854|ref|YP_008142374.1| 313 YKWSEDEAKKLILRTHTTVNTIRYLYNH--RDK--PQYIFSIEKVFRHESVDWKH---LSELYQIEGAVYGSDV--- 379
                                       788888899*****99999999999989..888..***************98887...7899999999999865... PP

                                       HHHHHHHHHHHHHHHHTT.SCEEEEEEGTTSCBTTSEEEEEEEEETTTSEEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b  78 dslrdlikaisriferlglefraiielmsaksadykdkkefeavsesltkgieigt 133
                                         l+ l  +  ++++rlg++   i+++ s   +  +++ +  + + + +k++e+g 
  gi|518652854|ref|YP_008142374.1| 380 -NLSTLKWLLTEFYSRLGFKN--IRLIPSY-YPYTEPSMD--VAVDINGKEVELGG 429
                                       .57778888899999999764..4444441.122333333..33444466666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (485 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 3308.30
//
Query:       gi|518652855|ref|YP_008142375.1|  [L=607]
Description: hypothetical protein FACI_IFERC00001G1494 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-06   27.8   0.2    1.6e-06   27.8   0.2    2.4  1  KH_1             KH domain
    2.5e-06   26.7   0.1    5.7e-06   25.6   0.1    1.6  1  T2SSE            Type II/IV secretion system protein
    2.6e-05   23.9   0.0    0.00088   18.9   0.0    2.2  2  AAA_25           AAA domain
    0.00014   21.7   0.2    0.00053   19.8   0.2    2.0  1  KH_4             KH domain
    0.00026   20.8   0.5      0.001   18.8   0.5    2.1  1  KH_2             KH domain
     0.0016   17.8   0.0     0.0032   16.8   0.0    1.4  1  Zeta_toxin       Zeta toxin
     0.0026   18.2   0.4       0.14   12.5   0.1    2.4  2  DUF1890          Domain of unknown function (DUF1890)
     0.0031   17.5   0.2      0.051   13.6   0.0    2.6  3  AAA_14           AAA domain
     0.0037   16.7   0.2      0.029   13.7   0.0    2.5  3  DnaB_C           DnaB-like helicase C terminal domain
     0.0038   17.6   0.0      0.013   15.9   0.0    1.9  1  AAA_16           AAA ATPase domain
      0.006   17.1   0.0      0.015   15.8   0.0    1.6  1  ABC_tran         ABC transporter
     0.0084   15.9   0.1      0.022   14.5   0.1    1.7  1  ATP_bind_1       Conserved hypothetical ATP binding protein
     0.0088   16.6   0.1      0.055   14.0   0.0    2.2  2  AAA_18           AAA domain
     0.0096   14.9   0.1      0.035   13.1   0.0    1.9  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
  ------ inclusion threshold ------
      0.016   15.1   0.1       0.19   11.6   0.0    2.5  2  NTPase_1         NTPase
       0.02   14.6   0.0      0.078   12.7   0.0    1.9  2  AAA_29           P-loop containing region of AAA domain
      0.026   14.6   0.0      0.075   13.1   0.0    1.9  1  MMR_HSR1         50S ribosome-binding GTPase
      0.028   14.1   0.0      0.064   12.9   0.0    1.6  1  Thymidylate_kin  Thymidylate kinase
      0.031   14.0   0.0       0.11   12.2   0.0    1.9  2  AAA_30           AAA domain
      0.031   13.4   0.0      0.057   12.6   0.0    1.4  1  DUF815           Protein of unknown function (DUF815)
      0.051   12.9   0.0       0.12   11.8   0.0    1.5  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.057   13.6   0.0       0.11   12.6   0.0    1.5  1  AAA_33           AAA domain
      0.061   13.4   0.1       0.21   11.7   0.1    1.9  1  HTH_Tnp_IS630    Transposase
      0.073   13.0   0.0       0.19   11.6   0.0    1.7  1  RsgA_GTPase      RsgA GTPase
      0.074   11.8   0.0       0.58    8.9   0.0    2.0  2  Peptidase_M29    Thermophilic metalloprotease (M29)
      0.079   12.6   0.5       0.21   11.2   0.1    1.9  2  SRP54            SRP54-type protein, GTPase domain
      0.081   13.2   0.1       0.45   10.8   0.0    2.2  2  AAA_22           AAA domain
      0.085   13.3   0.1       0.44   11.0   0.0    2.3  1  AAA              ATPase family associated with various cellul
       0.13   12.3   0.0       0.25   11.3   0.0    1.5  1  AAA_5            AAA domain (dynein-related subfamily)
       0.13   12.0   0.0       0.36   10.5   0.0    1.8  2  Viral_helicase1  Viral (Superfamily 1) RNA helicase
       0.14   11.9   0.0       0.34   10.6   0.0    1.6  1  IstB_IS21        IstB-like ATP binding protein


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 !   27.8   0.2   2.8e-09   1.6e-06       3      47 ..     484     530 ..     482     549 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.8e-09
                                       EEEEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEES.STT....T.-E CS
                              KH_1   3 rilvPsslvgriIGkgGsnIkeIreetgakIkvpk.sedeg.sdere 47 
                                        i+vP  +++r+IG++G+++  +++ +g kI+v+  s+d    ++  
  gi|518652855|ref|YP_008142375.1| 484 IIKVPDAKIPRLIGRKGETVTALEKSYGLKIDVDTlSDDVNvMQDAL 530
                                       589**********************66*****997666655733333 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 !   25.6   0.1   9.9e-09   5.7e-06      43     243 ..     174     366 ..     135     385 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 9.9e-09
                             T2SSE  43 ekaalerlisriaalak...ldiseerplqdarlpekgvrlrvvllPvvag.ealviRkksakeltlddlgaeealk 115
                                       ++++ler++++i +  k   ++  e  +     ++ k+ r+ +  +P +   e  ++R     + +++d+  ++++ 
  gi|518652855|ref|YP_008142375.1| 174 SNDELERIAYNIVQRGKfedQSFIEMDMFGATVIQLKNLRIVITRPPFSDImEITAVRPVV--KTSIEDYKLDKRVM 248
                                       4556666666665544311123333333333344478889989999999888889999443..34678887665544 PP

                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiqleganqvqlnakkakvtfadll 192
                                       +     l++     + ilv+G  g GK+t++ al ++ +++++ + t+E p+ +q+++   +q  +   + ++++  
  gi|518652855|ref|YP_008142375.1| 249 D----RLQNK---AYGILVAGSPGAGKSTFVTALAEYYASQNKIVKTMEKPRDLQVNDSI-TQYTTL--EGDMEKTG 315
                                       3....34444...589*************************88899*********97643.333333..23444444 PP

                             T2SSE 193 raaLRlrPDrimvGEiRdketlei.lkAvnTGHlgslsTlHansaagalerL 243
                                         +L  r D  +  E+R +  +++       G  g ++ +H+  a++a++r 
  gi|518652855|ref|YP_008142375.1| 316 DILLLVREDYTVFDEMRVTSDFKVySDLRLAG-VGMVGVVHSTRAVDAIQRF 366
                                       44556666888888888888888843334444.4447788888888888886 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.16        94      49      88 ..      96     133 ..      95     179 .. 0.78
   2 !   18.9   0.0   1.5e-06   0.00088      32     157 ..     254     388 ..     239     392 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.16
                            AAA_25  49 laldlalavatGkpwlgpvap.eqgkVlyvsaEdsedelrr 88 
                                       +ald a++++tG++   ++a+ + ++V+y+ +E++    +r
  gi|518652855|ref|YP_008142375.1|  96 IALDNAATLVTGDHIQSIIASiKGINVIYIKGEEKD---AR 133
                                       589999999****998855566***********986...33 PP

  == domain 2  score: 18.9 bits;  conditional E-value: 1.5e-06
                            AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwlg......pvapeqgkVlyvsaEdsedelrrRlravgealrddar 102
                                       +   +l+aG pg+GK+t+++ la  +a+  +  +      ++++    + y  +E++ + +   l  v+e+++  ++
  gi|518652855|ref|YP_008142375.1| 254 KAYGILVAGSPGAGKSTFVTALAEYYASQNKIVKtmekprDLQVNDSITQYTTLEGDMEKTGDILLLVREDYTVFDE 330
                                       44446789*******************8888888888877666677778899*****99*************99999 PP

                            AAA_25 103 llvldlagv.eslpLfakdrggtl.ltadvdaleaaieevegvrlv..viDplsralgg 157
                                        +v++  +v  +l+L+  +  g +  t++vda+++ + ++e ++l+  v+D++ ++ gg
  gi|518652855|ref|YP_008142375.1| 331 MRVTSDFKVySDLRLAGVGMVGVVhSTRAVDAIQRFVGRIE-LGLIpqVVDTVLFIDGG 388
                                       99999999999*****9999999999*************87.99998899999888777 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   9.2e-07   0.00053       9      54 ..     465     506 ..     458     508 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 9.2e-07
                              KH_4   9 kalvddpeevevteeeeeeeveielnvegedlGrvIGkrGrtldAl 54 
                                        +l+ + + v+v++    +e ++ ++v   ++ r+IG++G+t++Al
  gi|518652855|ref|YP_008142375.1| 465 MKLL-ETDHVDVQIV---SEGRVIIKVPDAKIPRLIGRKGETVTAL 506
                                       4455.4789999998...6789***********************9 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.5   1.8e-06     0.001      17      59 ..     474     515 ..     459     542 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.8e-06
                                       EEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHH CS
                              KH_2  17 kveIertanrviiviresqpgivIGkgGsnikkigkelrkdie 59 
                                       +v I  ++ rvii + +++  ++IG++G+++ +++k  + +i+
  gi|518652855|ref|YP_008142375.1| 474 DVQI-VSEGRVIIKVPDAKIPRLIGRKGETVTALEKSYGLKID 515
                                       3444.3679***************************9999885 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   5.4e-06    0.0032      18      47 ..     257     286 ..     240     290 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 5.4e-06
                        Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvv 47 
                                        il++G+pGAGKs+  ++l+++ ++q+++v
  gi|518652855|ref|YP_008142375.1| 257 GILVAGSPGAGKSTFVTALAEYYASQNKIV 286
                                       589*******************99988888 PP

>> DUF1890  Domain of unknown function (DUF1890)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   0.00024      0.14      26     111 ..      43     132 ..      28     157 .. 0.79
   2 ?    3.2   0.0      0.18   1.1e+02      20      56 ..     248     284 ..     245     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00024
                                       TTEEEEEEE-HHHHHHHHHHSTT-SS-SEE..EEHHHHHHH--TTS-SEEEEEESSHHHHHHHHH..HHHHH-.SEE CS
                           DUF1890  26 kgievvvagnpaalkLlkvaDpekhYvkel..vdldkaleeieekdvdlllgfvhnDagvsyavt..lkavlnkakl 98 
                                       +g ++  ++ +  +kL +++D  k+Y++ +  + ++  +++ +++++d ++  +  D +++ +    +++++ + k 
  gi|518652855|ref|YP_008142375.1|  43 EGRSIGFTALEELKKLRELSDSGKIYIDIMgnRPMEWQIKNAHSGEIDNIIRNIALDNAATLVTGdhIQSIIASIKG 119
                                       555556666677789************9998799***********************99998764447888888999 PP

                                       EEEEE-S-HHHHH CS
                           DUF1890  99 iaivfgkdaeela 111
                                       i +++ k +e+ a
  gi|518652855|ref|YP_008142375.1| 120 INVIYIKGEEKDA 132
                                       9999977666533 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                                       HHHHHCTTEEEEEEE-HHHHHHHHHHSTT-SS-SEEE CS
                           DUF1890  20 anklkkkgievvvagnpaalkLlkvaDpekhYvkelv 56 
                                       +++l++k++ ++vag p a k   v    ++Y ++ +
  gi|518652855|ref|YP_008142375.1| 248 MDRLQNKAYGILVAGSPGAGKSTFVTALAEYYASQNK 284
                                       789****************999988888888877653 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       2.5   1.5e+03      50      90 ..      85     127 ..      50     139 .. 0.64
   2 ?    0.2   0.0       1.2   6.9e+02      32      88 ..     121     157 ..      81     168 .. 0.58
   3 !   13.6   0.0   8.8e-05     0.051       5      79 ..     258     337 ..     254     344 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 2.5
                            AAA_14  50 e..kllelileklkeekktylflDEiqevpewekalkslvdeg 90 
                                       +  +++++i++ + ++  t++  D iq +    k ++ ++ +g
  gi|518652855|ref|YP_008142375.1|  85 HsgEIDNIIRNIALDNAATLVTGDHIQSIIASIKGINVIYIKG 127
                                       1346777777774445788888888888888888888777766 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.2
                            AAA_14  32 silyinldderdkkladpekllelileklkeekktylflDEiqevpewekalkslvd 88 
                                       +++yi+ ++++ ++                       f+DE   + +++  +k l++
  gi|518652855|ref|YP_008142375.1| 121 NVIYIKGEEKDARD--------------------IQEFFDEYTSSVHLKAGMKPLIK 157
                                       33333333333333....................33455555555555555555555 PP

  == domain 3  score: 13.6 bits;  conditional E-value: 8.8e-05
                            AAA_14   5 lvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklke.......ekktylflDEiq 74 
                                       +++ G   +GK+t++  l++ +   +++ +  +++++rd + +d+ + ++ +   +++        ++ y ++DE+ 
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYA--SQNKIVKTMEKPRDLQVNDSITQYTTLEGDMEKtgdilllVREDYTVFDEMR 332
                                       57889999**********96655..888888999*****9888763222222222322567888888999*****98 PP

                            AAA_14  75 evpew 79 
                                         +++
  gi|518652855|ref|YP_008142375.1| 333 VTSDF 337
                                       77766 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 ?    0.4   0.0      0.56   3.3e+02      73     139 ..     180     252 ..     174     257 .. 0.69
   2 !   13.7   0.0   5.1e-05     0.029      12      82 ..     247     315 ..     234     346 .. 0.74
   3 ?   -2.8   0.0       5.5   3.2e+03      84     112 ..     519     546 ..     509     554 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.56
                                       TXXHHHHHHTTSXHHHHHHHHH...HHHHHHHSEEEEEEXSSXCHHHHHHHHHHHHHH....TTEEEEEEEEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxx RF
                            DnaB_C  73 eidskklrtgklkeedweklte...aieelseaklfiddtpaltvseirskarrlkke....kglgliviDyLq 139
                                       +i  + +++gk++++ + ++     ++ +l++++++i   p   ++ei + +r + k+     +l+  v+D Lq
  gi|518652855|ref|YP_008142375.1| 180 RIAYNIVQRGKFEDQSFIEMDMfgaTVIQLKNLRIVITRPPFSDIMEITA-VRPVVKTsiedYKLDKRVMDRLQ 252
                                       677777888888877655444322178999*********99998888866.33322222444777777777777 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 5.1e-05
                                       HCTSBXTTXE.EEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT CS
                                       xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  12 ltsGlqkgdl.iiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtg 82 
                                       ++  lq+    i++A+ p+ Gk+++++ +ae  a ++k   +v  +e +++  v+  +++ ++++ +  +tg
  gi|518652855|ref|YP_008142375.1| 247 VMDRLQNKAYgILVAGSPGAGKSTFVTALAEYYASQNK---IVKTMEKPRDLQVNDSITQYTTLEGDMEKTG 315
                                       45556665543789******************997554...6677888877777777777666666555555 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 5.5
                                       SXHHHHHHHHHHHHHHHHSEEEEEEXSSX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaB_C  84 lkeedweklteaieelseaklfiddtpal 112
                                       l+ +d++ +++a+ e+++  +fid  ++ 
  gi|518652855|ref|YP_008142375.1| 519 LS-DDVNVMQDALIEIKNKTIFIDVGSRN 546
                                       44.48889999999999999999976665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.2e-05     0.013      26      76 ..     257     305 ..     242     387 .. 0.64

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.2e-05
                            AAA_16  26 lvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqal 76 
                                        +l+ G +G GKs+ v++l++++  ++ i+ + +k ++l+ +   + ++q+ 
  gi|518652855|ref|YP_008142375.1| 257 GILVAGSPGAGKSTFVTALAEYYASQNKIVkTMEKPRDLQVN---DSITQYT 305
                                       79*******************988887555577777777433...2233333 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   2.6e-05     0.015      15      86 ..     259     361 ..     252     392 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 2.6e-05
                                       EEEESTTSSHHHHHHHHTTSS--SEEEE.........EETTCEGGG...........B-HHHCCHCEEEE-SS--S- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  15 aivGenGaGKStLlkllagllkpteGei.........lldgkdlke...........qeleslrkeigvlpqepqlf 71 
                                        + G+ GaGKSt++ +la+ +  ++  +         +                    ++e++   +  + ++ ++f
  gi|518652855|ref|YP_008142375.1| 259 LVAGSPGAGKSTFVTALAEYYASQNKIVktmekprdlQ-------VndsitqyttleGDMEKTGDILLLVREDYTVF 328
                                       467****************9998877776555555432.......13333335666678888888888888888888 PP

                                       TTSBHHHH..................HHHTCHH CS
                                       xxxxxxxx..................xxxxxxx RF
                          ABC_tran  72 peltvren..................esdeeie 86 
                                       +e++v +                   +s++ ++
  gi|518652855|ref|YP_008142375.1| 329 DEMRVTSDfkvysdlrlagvgmvgvvHSTRAVD 361
                                       888877777776666666666666654444444 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.8e-05     0.022       1      27 [.     260     286 ..     260     291 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.8e-05
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsv 27 
                                       v+G +G+GK+tfv al+e++ ++++ v
  gi|518652855|ref|YP_008142375.1| 260 VAGSPGAGKSTFVTALAEYYASQNKIV 286
                                       89*****************99987655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       3.1   1.8e+03      15      67 ..      52     104 ..      49     150 .. 0.71
   2 !   14.0   0.0   9.6e-05     0.055       1      21 [.     258     278 ..     258     331 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 3.1
                            AAA_18  15 akeLskrlgf...gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                        +eL+k+ ++   g +++d+  ++ +++   ++    s ++d   ++ +ld+    
  gi|518652855|ref|YP_008142375.1|  52 LEELKKLRELsdsGKIYIDIMGNRPMEWQIKNA---HSGEIDNIIRNIALDNAATL 104
                                       566655555566688888888777777777666...78888888777777776665 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 9.6e-05
                            AAA_18   1 IlltGtpGvGKttlakeLskr 21 
                                       Il++G pG+GK+t+  +L++ 
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEY 278
                                       99****************886 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.3   1.3e+03     153     193 ..     105     146 ..      96     154 .. 0.69
   2 !   13.1   0.0   6.1e-05     0.035      27      57 ..     253     283 ..     228     289 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.3
                                       STTTTTTT--CCCHHH-SEEEEE.---HHHHHHHHHHHHHHH CS
                              MeaB 153 eaGDelqgikkGileiaDiivvn.kaDkkeaekaarelraal 193
                                        +GD++q+i + i  i  i++     D +++++   e+++ +
  gi|518652855|ref|YP_008142375.1| 105 VTGDHIQSIIASIKGINVIYIKGeEKDARDIQEFFDEYTSSV 146
                                       589*****9999999888877431334555555555555555 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 6.1e-05
                                       S-SEEEEEEE-TTSSHHHHHHHHHHHHHCTT CS
                              MeaB  27 GraqvvGltGvPGaGkstlvealglelrrrG 57 
                                        +a  + + G+PGaGkst+v al++ ++++ 
  gi|518652855|ref|YP_008142375.1| 253 NKAYGILVAGSPGAGKSTFVTALAEYYASQN 283
                                       35777889***************98877665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0       1.3   7.3e+02      73     104 ..     170     202 ..     146     219 .. 0.72
   2 ?   11.6   0.0   0.00033      0.19       2      31 ..     258     287 ..     257     297 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 1.3
                                       TEEE-HHHHHHHHHHHHHHHH.HHH-EEEE--- CS
                          NTPase_1  73 kyvvdvesfeelalealrkal.seadviviDEi 104
                                        yvv  +++e++a +++++   +++  i +D  
  gi|518652855|ref|YP_008142375.1| 170 DYVVSNDELERIAYNIVQRGKfEDQSFIEMDMF 202
                                       699999*********999865454446666655 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00033
                                       EEEE--TTSSHHHHHHHHHHHH...GGGEE CS
                          NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkvg 31 
                                       +++ G+pG GK+T+v  ++e  +s++  v+
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYASQNKIVK 287
                                       789******************999998775 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 ?   -2.6   0.0       8.4   4.9e+03      17      30 ..      96     108 ..      85     109 .. 0.68
   2 ?   12.7   0.0   0.00014     0.078      23      43 ..     255     276 ..     240     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 8.4
                            AAA_29  17 ieidlkg.atlltGp 30 
                                       i +d  + atl+tG+
  gi|518652855|ref|YP_008142375.1|  96 IALD--NaATLVTGD 108
                                       4444..447999997 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00014
                            AAA_29  23 g.atlltGpsGsGKSTllDAiq 43 
                                          +l++G  G+GKST++ A++
  gi|518652855|ref|YP_008142375.1| 255 AyGILVAGSPGAGKSTFVTALA 276
                                       2459*************98876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00013     0.075       2      36 ..     258     292 ..     257     403 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00013
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSE CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdi 36 
                                       ++++G p +GKSt++ al +  a  +++  t  ++
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYASQNKIVKTMEKP 292
                                       789***************98644444444444444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011     0.064       3      55 ..     262     314 ..     260     329 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
                                       ESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HH CS
                   Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeq 55 
                                       G  GaGK+t++ +l+e++ ++ + v +   p++ ++ ++i ++ + e ++e+ 
  gi|518652855|ref|YP_008142375.1| 262 GSPGAGKSTFVTALAEYYASQNKIVKTMEKPRDLQVNDSITQYTTLEGDMEKT 314
                                       6679******************6577777799**********99977766655 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.8     4e+03     104     127 ..      88     111 ..      84     113 .. 0.84
   2 ?   12.2   0.0   0.00019      0.11      21      48 ..     258     285 ..     245     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.8
                            AAA_30 104 qlaallkaaekagakvilvGDerQ 127
                                       +++++++ ++ ++a  ++ GD+ Q
  gi|518652855|ref|YP_008142375.1|  88 EIDNIIRNIALDNAATLVTGDHIQ 111
                                       5678899999999999*****988 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00019
                            AAA_30  21 avltGpAGtGKttalkalreaweaaggr 48 
                                        ++ G +G+GK+t ++al+e ++++++ 
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYASQNKI 285
                                       5789******************998644 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.9e-05     0.057      51      82 ..     253     286 ..     228     310 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.9e-05
                            DUF815  51 lpannvLLwGarGtGKSslvkallneyaeeg..L 82 
                                       ++a  +L+ G+ G+GKS+ v al + ya+++  +
  gi|518652855|ref|YP_008142375.1| 253 NKAYGILVAGSPGAGKSTFVTALAEYYASQNkiV 286
                                       67999******************99999887444 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0002      0.12      40      59 ..     256     275 ..     221     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0002
                                       .SEEEE--TTSSHHHHHHHH CS
                      FtsK_SpoIIIE  40 shllvaGatgsGKStalntL 59 
                                         +lvaG++g GKSt++ +L
  gi|518652855|ref|YP_008142375.1| 256 YGILVAGSPGAGKSTFVTAL 275
                                       579**************998 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    0.0002      0.11       2      39 ..     258     291 ..     258     319 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.0002
                            AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg 39 
                                       +l+ G pG+GKst+++ l++    +  s++++ +++++
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAE----YYASQNKIVKTMEK 291
                                       6789************9984....33455555555555 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   0.00036      0.21      11      81 ..     464     539 ..     456     550 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00036
                     HTH_Tnp_IS630  11 vidyiesGg....gitkaskvfkvgratvyrWlkreelaatkvetrkr.kidrkelkedvkknpdallkerakkfg 81 
                                       +++ +e+ +     + + + + kv  a + r ++r+  + t  e+    kid + l +dv+   dal+  + k   
  gi|518652855|ref|YP_008142375.1| 464 MMKLLETDHvdvqIVSEGRVIIKVPDAKIPRLIGRKGETVTALEKSYGlKIDVDTLSDDVNVMQDALIEIKNKTIF 539
                                       5556666542221356778899***************999999887666****************98877777655 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   0.00033      0.19      78     123 ..     232     279 ..     221     298 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00033
                                       EEEE--TTTHTTHHHHHHHCTTSE..EEEECSTTSSHHHHHHHHCTT- CS
                       RsgA_GTPase  78 evllvsaktkegleelkellkdkt..svlvGqSGvGKStLinallpel 123
                                       +v+++s ++ +  +++ ++l++k   ++++G+ G+GKSt++ al++  
  gi|518652855|ref|YP_008142375.1| 232 PVVKTSIEDYKLDKRVMDRLQNKAygILVAGSPGAGKSTFVTALAEYY 279
                                       577788888888888889998865225779*************99853 PP

>> Peptidase_M29  Thermophilic metalloprotease (M29)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.38   2.2e+02      45     107 ..      18      80 ..      15     117 .. 0.85
   2 ?    8.9   0.0     0.001      0.58      51     199 ..     168     318 ..     163     339 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.38
                                       HHTT-SEEEEEEE-HHHHHHHHHHS-TT-TT---HHHHHHHHHHHHTT-EEEEEE---GGGST CS
                     Peptidase_M29  45 ykagakkvvvewsdeeltkerlknaseeqleevpeweaekleelveegaarlsilaedpkllk 107
                                       y ag ++v+v + +  + ++  + ++  ++ +++  e +kl+el ++g+ ++ i+++ p+  +
  gi|518652855|ref|YP_008142375.1|  18 YVAGKNDVRVILAEAMIAEIEHQANEGRSIGFTALEELKKLRELSDSGKIYIDIMGNRPMEWQ 80 
                                       778999999999999999999999999999999999999*****************9887655 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.001
                                       EEEEEEE-HHHHHHHHHHS-TT-TT---HHHHHHH.HHHHHTT-EEEEEE--.-GGGSTTS-HHHHHHHHHHHHHHH CS
                     Peptidase_M29  51 kvvvewsdeeltkerlknaseeqleevpeweaekl.eelveegaarlsilae.dpkllkgvdpekiaaaqkarskal 125
                                       ++   +s++el+++ ++  +  ++e+ + +e++++ +++++ ++ r+ i+ +   + ++ +  + + + +    k+ 
  gi|518652855|ref|YP_008142375.1| 168 ELDYVVSNDELERIAYNIVQRGKFEDQSFIEMDMFgATVIQLKNLRIVITRPpFSDIMEITAVRPVVKTSIEDYKLD 244
                                       55667899************************99967788999*********88888888888999*********** PP

                                       HHHHHHHHTTSS-B-BEE---TTTHHHH---S-HHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHHHHH CS
                     Peptidase_M29 126 keyreriasgklrWcvvavPteawAkkvfpdleaeealeklwdaifkavrldeedpvaaWeehnaelekrakyL 199
                                       k++++r +++++   v+  P +     v   +e  ++ +k  + + k   l+ +d + ++ + + ++ek  ++L
  gi|518652855|ref|YP_008142375.1| 245 KRVMDRLQNKAYGILVAGSPGAGKSTFVTALAEYYASQNKIVKTMEKPRDLQVNDSITQYTTLEGDMEKTGDIL 318
                                       ***********999999999999988777666777888888888888888999999999999999999988877 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00037      0.21       4      31 ..     258     285 ..     255     290 .. 0.90
   2 ?   -2.6   0.0         6   3.4e+03      69     131 ..     523     583 ..     511     594 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00037
                                       EEEEESTTSSHHHHHHHHHHHHHHTTS- CS
                             SRP54   4 illvGlqGaGKTttlaKLaallkkegkk 31 
                                       il++G  GaGK t ++ La+++ +++k 
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYASQNKI 285
                                       899********************99875 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                                       HHHHHHHHHHHHHTTSSEEEEEE--SSTTHHHHHHHHHHHHHHH.SSSEEEEEEETTBHTHHHH CS
                             SRP54  69 aavakeavekakeekidvvlvDTaGrlqndkelmeelkkikkvv.kpdevllvldattgqeavk 131
                                       ++v+++a+ + k++   ++++D   r++  k +++ ++ ++    ++  + l +++ tg++++k
  gi|518652855|ref|YP_008142375.1| 523 VNVMQDALIEIKNK---TIFIDVGSRNRPVKLYVDGIAMLSARSsAKGMIKLRINSDTGNTVYK 583
                                       55555555555553...35555555555555555555544444312222334444444444444 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       9.3   5.4e+03      72     112 ..     142     181 ..     101     191 .. 0.62
   2 ?   10.8   0.0   0.00078      0.45       4      38 ..     254     298 ..     250     327 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 9.3
                            AAA_22  72 rlsseellealeqalraravielliiDEaqhlrseealeeL 112
                                         ss +l + +   +++ +  + +++ E +++ s++ le +
  gi|518652855|ref|YP_008142375.1| 142 YTSSVHLKAGMKPLIKTGKP-GEVVLKELDYVVSNDELERI 181
                                       23455555555555555555.66777777774366666655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00078
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee..........e 38 
                                       +a+ ++v G +G+GK+t +  l+e +  ++k+ +          +
  gi|518652855|ref|YP_008142375.1| 254 KAYGILVAGSPGAGKSTFVTALAEYYASQNKIVKtmekprdlqvN 298
                                       567799**********99888888776555444455444444332 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 ?   11.0   0.0   0.00075      0.44       1      23 [.     258     280 ..     258     314 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00075
                                       EEEESSTTSSHHHHHHHHHHHHT CS
                               AAA   1 vllyGppGtGKTllakavakelg 23 
                                       +l+ G pG GK++++ a+a+   
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYA 280
                                       699****************9864 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 ?   11.3   0.0   0.00044      0.25       2      52 ..     258     311 ..     257     332 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00044
                                       EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..... CS
                             AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngtt 52 
                                       +l+ G pG gKs+++  la+ +   n+ v ++  +rd++ +d + ++ + +g+ 
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEYYasqNKIVKTMEKPRDLQVNDSITQYTTLEGDM 311
                                       7889******************98888888888888888888777766655555 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 ?   -2.5   0.0       6.1   3.5e+03      75     100 ..      85     112 ..      83     150 .. 0.61
   2 ?   10.5   0.0   0.00063      0.36       1      39 [.     258     291 ..     258     330 .. 0.61

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 6.1
                   Viral_helicase1  75 haGyilllaalskaklv..ilfGDplQi 100
                                       h+G+i+ ++++  ++++  +++GD+ Q+
  gi|518652855|ref|YP_008142375.1|  85 HSGEIDNIIRNIALDNAatLVTGDHIQS 112
                                       6666666655555544311567777774 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00063
                   Viral_helicase1   1 ivvhGvpGcGKStlirkllrtsliltvnrptaelltegk 39 
                                       i+v+G pG+GKSt +  l++     ++n    ++ t+ k
  gi|518652855|ref|YP_008142375.1| 258 ILVAGSPGAGKSTFVTALAEY--YASQN---KIVKTMEK 291
                                       68************9999977..32222...33333333 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00059      0.34      45      82 ..     253     290 ..     231     340 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00059
                         IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavraglsvlfvr 82 
                                       +k+ +i++ G +G+GKs + +al+   + +++ v  + 
  gi|518652855|ref|YP_008142375.1| 253 NKAYGILVAGSPGAGKSTFVTALAEYYASQNKIVKTME 290
                                       4566899*****************99888887776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       710  (0.0396006); expected 358.6 (0.02)
Passed bias filter:                      549  (0.0306208); expected 358.6 (0.02)
Passed Vit filter:                       102  (0.00568911); 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: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.45
# Mc/sec: 4063.79
//
Query:       gi|518652856|ref|YP_008142376.1|  [L=124]
Description: hypothetical protein FACI_IFERC00001G1495 [Ferroplasma acidarmanus fer1]
Scores for complete 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-16   59.1   0.1    4.5e-16   58.5   0.1    1.3  1  DUF302    Domain of unknown function DUF302
  ------ inclusion threshold ------
      0.082   13.0   0.0      0.082   13.0   0.0    1.1  1  DUF3479   Domain of unknown function (DUF3479)


Domain annotation for each model (and alignments):
>> DUF302  Domain of unknown function DUF302
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.5   0.1     5e-20   4.5e-16       1      63 []      34      95 ..      34      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.5 bits;  conditional E-value: 5e-20
                                      EEHHHHHHCTT-S--S-EEEEEEE-HHHHHHHHCC-GGGGGG-SEEEEEEEETTEEEEEEE-H CS
                            DUF302  1 iDvqatlkkklgedlrpykilgaCnPklatealqadpeiglllPcrvvVyekdgkttvsyvdP 63
                                      iD+++ + +k++++++py+il +C P++a+e+++ + +ig+++Pc+vv+ + +++t++ + +P
  gi|518652856|ref|YP_008142376.1| 34 IDLKEIF-SKMQKEIEPYYILDVCFPPAAAELVKDNEDIGAFIPCKVVLIQHGNTTKILMPKP 95
                                      8******.**************************************************99887 PP

>> DUF3479  Domain of unknown function (DUF3479)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   9.1e-06     0.082      39     105 ..       9      74 ..       1     118 [. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.1e-06
                           DUF3479  39 lrekpealeelaaavaeAdifiasllfdedqvealrealeaarekldavlvfeSapelmrltk.vGsF 105
                                        ++++e +  l++ ++eA+ +i s + ++++++++++++e+    +  v+  ++a el++ +  +G F
  gi|518652856|ref|YP_008142376.1|   9 NKSAEEVFGGLHKLLKEANWLIISYIDLKEIFSKMQKEIEPYY--ILDVCFPPAAAELVKDNEdIGAF 74 
                                       455566677888999**************************44..56677778999999877438887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (124 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 823.18
//
Query:       gi|518652857|ref|YP_008142377.1|  [L=500]
Description: hypothetical protein FACI_IFERC00001G1496 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-10   41.4  27.1      1e-10   41.4  27.1    3.2  2  Polysacc_synt    Polysaccharide biosynthesis protein
    4.5e-07   30.0  17.6    4.5e-07   30.0  17.6    4.3  6  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai


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 !   41.4  27.1   1.2e-14     1e-10       8     270 ..       2     275 ..       1     279 [. 0.72
   2 ?  -18.7  24.4         2   1.8e+04      43     132 ..     322     405 ..     292     493 .. 0.42

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 1.2e-14
                     Polysacc_synt   8 lllsqlitkllafvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek......kelvslil 78 
                                       l+ +q+++ l++++ l+ + r++g    G +++ la+++ l+i+ dlG+++a  ++ +  + +      + l+  ++
  gi|518652857|ref|YP_008142377.1|   2 LVFGQVTNSLFGYIGLFFIIRFVGLQSWGYLSFSLAFIGVLSIIGDLGYGTAHLKYLSSGEYEegvctgTFLTIRTV 78 
                                       67899***************************************************997665554544322233333 PP

                     Polysacc_synt  79 lnvllvllvlvllfllllliaa..flglpelavlylilalmll.llvgvasfrrglfqglermkyaavsqvveqlsr 152
                                         ++++++vl  lf+ + ++ +    + +++a+++l+  ++++ l    ++++++ ++  ++  ++  + vv++  +
  gi|518652857|ref|YP_008142377.1|  79 QTLITISIVLGSLFIWINVLHRgfQSNVEIYAIILLLPYFFFArLKDVPIIYYNSKLKSARMSIPQITEAVVRNSLF 155
                                       33334444444444444444335444455555555555555555556666666666666666666666666666666 PP

                     Polysacc_synt 153 vilvliavflfldivaavlgavlaalvggivslavlrkkf..rprfvils.lklvrellsfsapltisslaillyty 226
                                       +il ++ ++ +  + ++ ++++la + ++ +++++l   f  rp +v++   +l+++  + + pl + s++++++ +
  gi|518652857|ref|YP_008142377.1| 156 IILGAVYILRIPGYNTVSAAILLAIIYSISYFIYFLLSVFlgRPWKVNRPsMELFKKYTKLAYPLALASIIGSVSGN 232
                                       666666666665566666666666666666666666666654598999888************************** PP

                     Polysacc_synt 227 idsillglllgaeavGiYnaayqllvaisgllapivtaalfPvf 270
                                       id +l+ ++  a+a G +   +++++ i+ +  +i     +P++
  gi|518652857|ref|YP_008142377.1| 233 IDKVLIEFYWHAVATGAFASLQRIASPITTFSGTISI-FFIPLL 275
                                       *******************999999988888777766.556655 PP

  == domain 2  score: -18.7 bits;  conditional E-value: 2
                     Polysacc_synt  43 aivtllviltdlGlnaalvreiakyrekkelvslillnvllvl.lvlvllfllllliaaflglpelavlylilalml 118
                                       a++ ++ il+ l l a+lv   + y++  +lv+ +l n +  + ++++++ + l+    +l  p +++ ++i++l +
  gi|518652857|ref|YP_008142377.1| 322 ALIPYADILIFLTLAAYLVAINSAYSS--SLVARGLTNKIGKItVIALIINISLD----LLLIPPDVFEIRIFSLGV 392
                                       333344444444444444444444444..22222222221111011111111111....123333333333333322 PP

                     Polysacc_synt 119 lllvgvasfrrglf 132
                                       l   +v++f+++lf
  gi|518652857|ref|YP_008142377.1| 393 L-GGAVSTFVAMLF 405
                                       2.223333333332 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.5      0.44   3.9e+03       5      14 ..      32      41 ..       7      60 .. 0.48
   2 ?   -2.1   1.0      0.41   3.7e+03      94     113 ..      81      98 ..      66     124 .. 0.45
   3 ?   -0.6   5.3      0.14   1.3e+03     101     141 ..     157     196 ..     129     198 .. 0.57
   4 ?   -1.6   7.7      0.28   2.5e+03      48     104 ..     164     229 ..     146     253 .. 0.49
   5 ?    0.7   1.3     0.055     5e+02      83     117 ..     286     319 ..     257     327 .. 0.61
   6 !   30.0  17.6     5e-11   4.5e-07       1     140 [.     329     472 ..     329     475 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
                   Polysacc_synt_C  5 lalsiiflsl 14
                                      l++s+ f+++
  gi|518652857|ref|YP_008142377.1| 32 LSFSLAFIGV 41
                                      1222222222 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.41
                   Polysacc_synt_C  94 pllaalvmgivvylllllll 113
                                       ++ +++v+g +   ++  +l
  gi|518652857|ref|YP_008142377.1|  81 LITISIVLGSLF--IWINVL 98 
                                       333333333331..222222 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.14
                   Polysacc_synt_C 101 mgivvylllllllgllllaalalllavl..vgalvYlllllll 141
                                       + ++vy+l     ++    + a+lla++  +  ++Y+ll ++l
  gi|518652857|ref|YP_008142377.1| 157 ILGAVYILRIPGYNT-V--SAAILLAIIysISYFIYFLLSVFL 196
                                       222333222222222.2..236666664446666666666665 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 0.28
                   Polysacc_synt_C  48 lliplfgivGaaiatvlallvvavlnlyalrrllgikl..........ellrrllkpllaalvmgiv 104
                                       l ip +++v aai  ++ + ++ ++ +++l+  lg ++          + +++l  pl++a ++g v
  gi|518652857|ref|YP_008142377.1| 164 LRIPGYNTVSAAILLAIIYSISYFI-YFLLSVFLGRPWkvnrpsmelfKKYTKLAYPLALASIIGSV 229
                                       2245555555555555544444433.23333344444444445664443344444555555555555 PP

  == domain 5  score: 0.7 bits;  conditional E-value: 0.055
                   Polysacc_synt_C  83 ikl..ellrrllkpllaalvmgivvylllllllglll 117
                                       +k   +l+ r++ ++++ lv+  v   +l++ +  l+
  gi|518652857|ref|YP_008142377.1| 286 FKTdiSLFERIISIFILPLVIIFV---VLRVYVANLW 319
                                       333446688898888888888888...3333333333 PP

  == domain 6  score: 30.0 bits;  conditional E-value: 5e-11
                   Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnlllip.........lfgivGaaiatvlallv 68 
                                       +L +l+l++ + ++++ +ss L + g + ++ k++vi++++++ l lllip         ++g++G a++t +a+l+
  gi|518652857|ref|YP_008142377.1| 329 ILIFLTLAAYLVAINSAYSSSLVARGLTNKIGKITVIALIINISLDLLLIPpdvfeirifSLGVLGGAVSTFVAMLF 405
                                       6899**********************************************77877777667788************* PP

                   Polysacc_synt_C  69 vavlnlyalrrllgikl..ellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYllllll 140
                                        +v   + + r  ++k+   ++ +ll +l+ ++++++++ ++  + + l+ +       +v + ++v+l++++l
  gi|518652857|ref|YP_008142377.1| 406 ETVAYRVTVIRAEKMKPdlRIFYQLLPILAQSMFLFGITSYIKIYSILLFIPV------SV-ASVIVFLGVAVL 472
                                       *****************998888888999999999999777777776655544......33.555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (500 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); 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):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 3574.72
//
Query:       gi|518652858|ref|YP_008142378.1|  [L=108]
Description: methionyl-tRNA synthetase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-28   98.5   0.3      2e-28   98.3   0.3    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 !   98.3   0.3   1.1e-32     2e-28       1      96 []      14     106 ..      14     106 .. 0.98

  Alignments for each domain:
  == domain 1  score: 98.3 bits;  conditional E-value: 1.1e-32
                                       EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTSTHHHHTTEEEEEETTSESEEETTEEESSEE-EEECC CS
                         tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvyepeelvakkvvvvanlkpkklrGveSeGMilsaeel 77 
                                       +rvGkv+e+ +++++++Ll+++vd+G+++ +qi+s ++n+y+pe++++k++vv++nl p+k++G eS+GM+l++e  
  gi|518652858|ref|YP_008142378.1|  14 IRVGKVIECTKVEKSRNLLKIIVDLGDQQ-KQIISSISNCYSPEDMMGKQLVVINNLAPAKFMGLESQGMLLAVE-- 87 
                                       79***************************.*********************************************.. PP

                                       ESSCEEEEEESST--TTCE CS
                         tRNA_bind  78 dekevgilelpadveaGek 96 
                                       de+ v++l+++++v +G+k
  gi|518652858|ref|YP_008142378.1|  88 DENGVSLLKPDREVSPGTK 106
                                       8****************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 725.34
//
Query:       gi|518652859|ref|YP_008142379.1|  [L=419]
Description: hypothetical protein FACI_IFERC00001G1498 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-16   60.7   0.0    3.9e-16   59.7   0.0    1.6  1  AAA           ATPase family associated with various cellular 
    0.00024   21.4   0.1     0.0065   16.7   0.1    2.4  1  AAA_22        AAA domain
    0.00043   20.2   0.1       0.08   12.9   0.2    2.5  2  Rad17         Rad17 P-loop domain
     0.0014   17.9   0.0     0.0087   15.2   0.0    2.0  2  DUF815        Protein of unknown function (DUF815)
     0.0018   18.4   0.0     0.0038   17.4   0.0    1.5  1  AAA_2         AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.017   14.3   0.1      0.052   12.7   0.0    1.7  2  TIP49         TIP49 P-loop domain
      0.026   13.9   0.0      0.057   12.8   0.0    1.5  1  IPT           Isopentenyl transferase
      0.046   13.7   0.0      0.095   12.7   0.0    1.6  1  AAA_5         AAA domain (dynein-related subfamily)
       0.11   12.9   0.0       0.17   12.2   0.0    1.4  1  AAA_16        AAA ATPase domain
       0.12   12.1   0.0       0.26   11.0   0.0    1.6  1  RuvB_N        Holliday junction DNA helicase RuvB P-loop doma
       0.13   11.9   0.0       0.25   10.9   0.0    1.5  1  AAA_25        AAA domain
       0.13   12.0   0.0         11    5.8   0.0    2.4  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
       0.13   12.1   0.0       0.36   10.7   0.0    1.7  2  RsgA_GTPase   RsgA GTPase


Domain annotation for each model (and alignments):
>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   2.8e-19   3.9e-16       1     120 [.      42     158 ..      42     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.8e-19
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS....STTHHHHHHHHHHHH.HHHTSTS.EEEEEETGGGHH CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk....yvgesekkirelfke.akekakp.silfiDEidala 71 
                                       ++l+G  G+GKT++a a+a+ +g +++e+++se ++k     +  ++++ r+lf++ a+    p + ++iDE+d+++
  gi|518652859|ref|YP_008142379.1|  42 LILWGQQGIGKTSAAYALASYAGLPVVEMNASEQRNKesmkKIALMASQYRNLFDDdARM---PdKLILIDEADNIF 115
                                       589********************************8867777777777777777773333...55************ PP

                                       HHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  72 ksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                       +sr +++s+ ++  +++Ll+ +++ k+      vi++ n++ +++++  
  gi|518652859|ref|YP_008142379.1| 116 ESR-SRSSGGDTGGMSELLEIIKNTKN-----PVIITMNDYYSFKSKNN 158
                                       ***.889999999************99.....57888887777766665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.1   4.7e-06    0.0065       5     120 ..      39     139 ..      34     150 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 4.7e-06
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellea 81 
                                       +++l+++G+ G+GKT  +  l++ +         + +vv+++++++ + +++ ++++              ++++++
  gi|518652859|ref|YP_008142379.1|  39 KNSLILWGQQGIGKTSAAYALASYA---------GLPVVEMNASEQRNKESM-KKIALMA-----------SQYRNL 94 
                                       7899*******************99.........9************66655.5554433...........46999* PP

                            AAA_22  82 leqalraravielliiDEaqhlr...s.......eealeeLrsllnlsr 120
                                       + + +r  ++  l++iDEa++++   s         + e L ++ n  +
  gi|518652859|ref|YP_008142379.1|  95 FDDDARMPDK--LILIDEADNIFesrSrssggdtGGMSELLEIIKN--T 139
                                       ********99..*********8877614567776444444444444..3 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0      0.01        14      11      75 ..       5      69 ..       2      77 .. 0.84
   2 !   12.9   0.2   5.8e-05      0.08      99     151 ..      71     121 ..      65     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.01
                             Rad17 11 ekykPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklre 75
                                      + y+P  ++ l +  +  +++  w+++ +  s+ k+ L++ G  G gk+ +   L+   g  + e
  gi|518652859|ref|YP_008142379.1|  5 DDYRPSDLNSLLLSNEARQAMISWIDSWMNHSEVKNSLILWGQQGIGKTSAAYALASYAGLPVVE 69
                                      6788888888888888888888899988888888889**************99999888776665 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.8e-05
                             Rad17  99 esrflsqiesfkeleLkdakylklqklGddlrtdkklilvedlPnkfyrdsda 151
                                       + + +   es k + L++++y  l    dd+r   klil+++  n f+  s++
  gi|518652859|ref|YP_008142379.1|  71 NASEQRNKESMKKIALMASQYRNLF--DDDARMPDKLILIDEADNIFESRSRS 121
                                       55557778999**********8887..9*******************876543 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   6.3e-06    0.0087      23      91 ..       8      74 ..       2     100 .. 0.75
   2 ?   -0.1   0.0      0.31   4.3e+02      95     124 ..     129     159 ..     124     173 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 6.3e-06
                            DUF815 23 devklddLvgidkqkealventeqfleglpann.vLLwGarGtGKSslvkallneyaeegLrlieveked 91
                                      ++ +l++L   ++ ++a+++ +  ++++ + +n ++LwG++G GK s   al +    +gL ++e++ ++
  gi|518652859|ref|YP_008142379.1|  8 RPSDLNSLLLSNEARQAMISWIDSWMNHSEVKNsLILWGQQGIGKTSAAYALAS---YAGLPVVEMNASE 74
                                      56788999999999************99887762679**********8888764...4567777776555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.31
                            DUF815  95 lpklvellrerperfilfvDD.LsFeeeeee 124
                                       +++l+e+++++++ +i+ + D  sF++++++
  gi|518652859|ref|YP_008142379.1| 129 MSELLEIIKNTKNPVIITMNDyYSFKSKNNA 159
                                       78999***********999883589887654 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   2.8e-06    0.0038       5     103 ..      41     136 ..      37     141 .. 0.75

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 2.8e-06
                                       -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS..EEEEETGGG CS
                             AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG..ivllDEidK 79 
                                       s++l g++g+Gkt +a ala++  +    +++ ++ase   +e ++++  +  + ++     +      +l+DE d 
  gi|518652859|ref|YP_008142379.1|  41 SLILWGQQGIGKTSAAYALASYAGL----PVVEMNASEQRNKESMKKIALMASQYRNLFDDDARMPdkLILIDEADN 113
                                       78899*******************8....999999999999888888777766666655555555499********* PP

                                       ----..---------HHHHHHHHHHH CS
                             AAA_2  80 ihpk..essgadvSregVqrdLLqil 103
                                       i ++  +ssg d   +g +  LL i+
  gi|518652859|ref|YP_008142379.1| 114 IFESrsRSSGGD---TGGMSELLEII 136
                                       *99544444444...34455555555 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.8e-05     0.052      28     101 ..      17      88 ..       3      95 .. 0.79
   2 ?   -1.9   0.1         1   1.4e+03     123     165 ..     169     211 ..     155     218 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.8e-05
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  28 GqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkktevltq 101
                                         ++ar+a+   ++   ++     +++l G++g Gkt+ a a++   g  +p v +++se    e  k  +l+ 
  gi|518652859|ref|YP_008142379.1|  17 LSNEARQAMISWIDSWMNHSEVKNSLILWGQQGIGKTSAAYALASYAG--LPVVEMNASEQRNKESMKKIALMA 88 
                                       56789999887777655555556999******************9987..9*********99998776666654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1
                                       EEEEE...-SSS-..TTS--EEEEEE-SS-EEEEEE-HHHHHH CS
                             TIP49 123 veleveeaenplskekkikevkitlktakeekklklgskiaee 165
                                       +e+++ +++n+++++  ++ v+ +lk    +++++++ + ++ 
  gi|518652859|ref|YP_008142379.1| 169 IEMTPYKRKNEVNYKIFTSGVHSVLKNIAIKENIHINDHEIDG 211
                                       6777888888888888888888888888888888887665555 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.1e-05     0.057       5      32 ..      43      70 ..      39      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.1e-05
                               IPT  5 lifGatttGKtaeaiklaketgapvivl 32
                                      +++G  ++GKt+ a +la   g+pv+ +
  gi|518652859|ref|YP_008142379.1| 43 ILWGQQGIGKTSAAYALASYAGLPVVEM 70
                                      68***********************965 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 ?   12.7   0.0   6.9e-05     0.095       2      48 ..      42      88 ..      41     118 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
                                      EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--. CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreik 48
                                      ++L G++G+gK++ a  la+  + +v++++ +++ ++e +k    ++
  gi|518652859|ref|YP_008142379.1| 42 LILWGQQGIGKTSAAYALASYAGLPVVEMNASEQRNKESMKKIALMA 88
                                      89********************************9999999887776 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   0.00013      0.17      22      66 ..      35      80 ..      20     150 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_16 22 grp..elvllsGesGvGKsslvrellralekdggiflrgkcdqlesa 66
                                      +++  ++++l G++G+GK+s + +l+ ++    ++ +++  ++++++
  gi|518652859|ref|YP_008142379.1| 35 HSEvkNSLILWGQQGIGKTSAAYALASYAGLP-VVEMNASEQRNKES 80
                                      4445699***************9999766655.33355555555333 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 ?   11.0   0.0   0.00019      0.26       2      61 ..       8      67 ..       7     104 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00019
                            RuvB_N  2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvkl 61
                                      rP+ l+  +  ++ ++ +   i++  + +e  + ++l G  G+Gkt+ a  +a+  g  +
  gi|518652859|ref|YP_008142379.1|  8 RPSDLNSLLLSNEARQAMISWIDSWMNHSEVKNSLILWGQQGIGKTSAAYALASYAGLPV 67
                                      8999999999999*************************************9998776655 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   0.00018      0.25      33     145 ..      39     144 ..       9     168 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00018
                            AAA_25  33 gelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal........rdda 101
                                       +   +l+G++g GKt +a+ la ++a G p+          V + + E++++e  ++++ +  ++        r ++
  gi|518652859|ref|YP_008142379.1|  39 KNSLILWGQQGIGKTSAAYALA-SYA-GLPV----------VEMNASEQRNKESMKKIALMASQYrnlfdddaRMPD 103
                                       56689*************9887.455.7765..........457788888888888888888887777777666667 PP

                            AAA_25 102 rllvldlagveslpLfakdrggtl.ltadvdaleaaieevegvrl 145
                                       +l ++d a+     +f+++++++   t+ + +l + i+ +++++ 
  gi|518652859|ref|YP_008142379.1| 104 KLILIDEADN----IFESRSRSSGgDTGGMSELLEIIKNTKNPVI 144
                                       7777765553....4555555555567777777777777665544 PP

>> TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0076        11      11      48 ..      38      73 ..      36     100 .. 0.85
   2 ?    3.6   0.0     0.036        49       2      19 ..     130     147 ..     129     169 .. 0.75

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0076
                                      -SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG CS
                      TPP_enzyme_M 11 akrpvilvGggvarsgaseelrelaeklgiPvvttlmg 48
                                       k+ +il G++ +  g + ++ +la   g+Pvv++ + 
  gi|518652859|ref|YP_008142379.1| 38 VKNSLILWGQQGI--GKTSAAYALASYAGLPVVEMNAS 73
                                      58899********..******************98765 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.036
                                       HHHHHHHHH-SSEEEEE- CS
                      TPP_enzyme_M   2 ekaaellkaakrpvilvG 19 
                                       ++++e++k+ k+pvi+  
  gi|518652859|ref|YP_008142379.1| 130 SELLEIIKNTKNPVIITM 147
                                       5789***********975 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00026      0.36      72     148 ..       7      88 ..       2      97 .. 0.72
   2 ?   -2.4   0.0       2.9     4e+03      39      81 ..     133     175 ..     126     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00026
                                       HHHTTSEEEE--TTTH.TTHHHHHHHCTT....SEEEEECSTTSSHHHHHHHHCTT-----S--------------S CS
                       RsgA_GTPase  72 lealgyevllvsaktk.egleelkellkd....ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTta 143
                                       ++  +++ ll+s++ + + ++ + +++++    +  +l Gq G+GK++   al++ + l + e+ ++ +r k   ++
  gi|518652859|ref|YP_008142379.1|   7 YRPSDLNSLLLSNEARqAMISWIDSWMNHsevkNSLILWGQQGIGKTSAAYALASYAGLPVVEMNASEQRNKESMKK 83 
                                       5666666666665544144555666665432225679*******************999999999999998887777 PP

                                       EEEEE CS
                       RsgA_GTPase 144 velle 148
                                         l++
  gi|518652859|ref|YP_008142379.1|  84 IALMA 88 
                                       76665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.9
                                       HHHHHHTT-EEEEEEE-GGG--HHHHHHHHHHHHHHTTSEEEE CS
                       RsgA_GTPase  39 LvlaeekgiepvivlnKiDlleeeeeleelkeelealgyevll 81 
                                       L ++++++ +++i +n     +++++++e+ ++  ++++++++
  gi|518652859|ref|YP_008142379.1| 133 LEIIKNTKNPVIITMNDYYSFKSKNNAREIVSRSVEIEMTPYK 175
                                       5556666667777777776666666666666666666655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       948  (0.0528752); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.45
# Mc/sec: 2773.02
//
Query:       gi|518652860|ref|YP_008142380.1|  [L=195]
Description: hypothetical protein FACI_IFERC00001G1499 [Ferroplasma acidarmanus fer1]
Scores for complete 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-74  249.6   7.2    2.1e-74  249.4   7.2    1.0  1  Ribosomal_L15e  Ribosomal L15


Domain annotation for each model (and alignments):
>> Ribosomal_L15e  Ribosomal L15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  249.4   7.2   1.2e-78   2.1e-74       2     191 .]       4     190 ..       3     190 .. 0.99

  Alignments for each domain:
  == domain 1  score: 249.4 bits;  conditional E-value: 1.2e-78
                                       SHHHHHHHTTSTTSHHHHHHHHHHHHHHTTS-SEEEESS-SSHHHHHHHT--SSTTEEEEEEEEE-SS---..---S CS
                    Ribosomal_L15e   2 aykylrelwkkkqsdvlrellrerlweyrqepavvrverptrldrArrLGYkakqGivvvrvrvrrGgrkkkvskgk 78 
                                        y+ +r+ wk+ +++ +  l++er++++r+ ++++rv+rptrld+Ar++GYkak+G++vvr+rvrrGg++k  +k++
  gi|518652860|ref|YP_008142380.1|   4 SYSLIRNEWKHLKKSSIYGLQKERMISWRRGNSIERVDRPTRLDKARNVGYKAKEGYIVVRARVRRGGQHK--PKIM 78 
                                       5899*******************************************************************..**** PP

                                       S---GGGG-SSS---SS-HHHHHHHHHHHHSTTSEEEEEEEEEEESSEEEEEEEEE-TTSHHHHT-TTTGGGGSGGG CS
                    Ribosomal_L15e  79 tgrkpkrqgvnklkpakslqaiaeervgrklpnlrvLnSYwvgeDgtykyyEvilvDpshkairndkkinwickkvh 155
                                        gr+p+r +++k++ +k++q iaeerv++k+pn +vLnSY+vgeDg ykyyEvilvD++ +ai nd+ki+wi+++++
  gi|518652860|ref|YP_008142380.1|  79 GGRRPRRLAYTKMTLKKNIQVIAEERVADKYPNTEVLNSYYVGEDGLYKYYEVILVDKATPAIYNDSKISWIVEPQN 155
                                       ***************************************************************************** PP

                                       TTGGGGT-SHHHHHHTT-S-SS.TT-TTTSS-TGGG CS
                    Ribosomal_L15e 156 khRelrGltsagkksRGlrkkglkgaekirgsrran 191
                                       k+R++rGltsa+ k+RGl ++g  g++k r+s+ran
  gi|518652860|ref|YP_008142380.1| 156 KGRAYRGLTSAAYKNRGL-GHGRLGSDKSRPSIRAN 190
                                       ******************.8898***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); 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: 00:00:00.39
# Mc/sec: 1515.58
//
Query:       gi|518652861|ref|YP_008142381.1|  [L=208]
Description: hypothetical protein FACI_IFERC00001G1500 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.054   12.8   0.2       0.07   12.4   0.2    1.2  1  SLATT_5   SMODS and SLOG-associating 2TM effector domain fami


Domain annotation for each model (and alignments):
>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   3.9e-06      0.07     114     185 ..      88     164 ..      66     171 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.9e-06
                           SLATT_5 114 seedlkekykeiskeYeeiLdkyeNHdeiDyklfraknak....kseelekskklkwfl.rrylivifllylliill 185
                                       ++ +  + ++ ++++Y++iL+k++N + i  +  r+++++      ++ e+  ++++ + +  l+++++l+ + i+ 
  gi|518652861|ref|YP_008142381.1|  88 DDPENFDDVDFYMEKYSDILEKNDNVSLINIIPLRTNRKEtflaLFDRTEFNGIITFDYiINTLFKSYILPVINIIK 164
                                       66666677778999***********************8889998444444444444433346777777776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); 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 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1515.57
//
Query:       gi|518652862|ref|YP_008142382.1|  [L=149]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-16   58.3   0.0    9.8e-16   58.0   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      8e-11   42.0   0.0    9.8e-11   41.7   0.0    1.1  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    5.8e-09   36.3   0.0    8.1e-09   35.8   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.1e-08   34.4   0.1    2.6e-08   34.1   0.1    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    4.6e-08   32.9   0.0    6.7e-08   32.4   0.0    1.2  1  FR47             FR47-like protein
    3.5e-05   23.9   0.0    0.00052   20.1   0.0    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain
     0.0076   16.4   0.0      0.012   15.8   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
      0.059   13.0   0.0      0.079   12.6   0.0    1.3  1  MOZ_SAS          MOZ/SAS family


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 !   58.0   0.0   4.4e-19   9.8e-16      27     117 .]      35     122 ..       7     122 .. 0.87

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 4.4e-19
                                       HHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEET CS
                    Acetyltransf_1  27 sfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlavee 103
                                       ++  ++++++v  ++ +l G++++ + ++   + + ies+ V pe + +G+Gs+L++a+e +ar +g+  i l+v+e
  gi|518652862|ref|YP_008142382.1|  35 ILNSINGFTYVLDDGSKLHGYATMGPLNE---QAIDIESIGVLPEDQDMGYGSMLITAIEAEARARGYSIIILEVRE 108
                                       34558889999999999************...9******************************************** PP

                                       TEHHHHHHHHH.TTE CS
                    Acetyltransf_1 104 dndaairlYek.lGF 117
                                        nd+ai++Y k +G+
  gi|518652862|ref|YP_008142382.1| 109 KNDHAIKFY-KaHGY 122
                                       *********.55998 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.7   0.0   4.4e-14   9.8e-11      22     109 ..      32     125 ..       7     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 41.7 bits;  conditional E-value: 4.4e-14
                   Acetyltransf_10  22 lrerieegealllvaeeggkivGviel.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvna 93 
                                       l+  +++ + +++v+++g k+ G++++   ++    i+ + V pe +  G+g++L+ a+e+ea+ +g+++  l+v++
  gi|518652862|ref|YP_008142382.1|  32 LKGILNSINGFTYVLDDGSKLHGYATMgPLNEqaiDIESIGVLPEDQDMGYGSMLITAIEAEARARGYSIiILEVRE 108
                                       444456667899*************9974444689****************************************** PP

                   Acetyltransf_10  94 sp.yavpfYeklGFkav 109
                                       ++ +a++fY+ +G+++ 
  gi|518652862|ref|YP_008142382.1| 109 KNdHAIKFYKAHGYETF 125
                                       **************986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.0   3.6e-12   8.1e-09       4      75 ..      42     123 ..      39     124 .. 0.74

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.6e-12
                                       EEEEEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHHHHTT.....SE..EEEE.EEEETHHHHHHHH CS
                    Acetyltransf_7   4 evfVaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLleaae.....kg..iile.qlelnaekaikfY 69 
                                        ++V++d+ k  G++ + +l+    +i+ + V+pe +  G+G+ L++a+e     +g  ii + +++ ++++aikfY
  gi|518652862|ref|YP_008142382.1|  42 FTYVLDDGSKLHGYATMGPLNeqaIDIESIGVLPEDQDMGYGSMLITAIEaearaRGysII-IlEVREKNDHAIKFY 117
                                       579998889999*9999999987666666*****************982234566773322.2333333349***** PP

                                       HHTTEE CS
                    Acetyltransf_7  70 eklGFe 75 
                                       + +G+e
  gi|518652862|ref|YP_008142382.1| 118 KAHGYE 123
                                       *****8 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   1.2e-11   2.6e-08      33     138 ..      28     126 ..       7     134 .. 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 1.2e-11
                    Acetyltransf_4  33 sveefekflealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeq 109
                                       s  +++ +l+++   + + +  ++  ++ Gya++g ++   +    e    l    ++++g+g+ li+a+e  +++ 
  gi|518652862|ref|YP_008142382.1|  28 SNFMLKGILNSI---NGFTYVLDDGSKLHGYATMGPLNE--QAIDIESIGVLP--EDQDMGYGSMLITAIEAEARAR 97 
                                       445555555554...99999999999*************..888888777774..59******************** PP

                    Acetyltransf_4 110 nienllaeiaspnensiqfhkalGFelvg 138
                                       ++  +  e+  +n+ +i+f+ka+G+e   
  gi|518652862|ref|YP_008142382.1|  98 GYSIIILEVREKNDHAIKFYKAHGYETFE 126
                                       *************************9765 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0     3e-11   6.7e-08      22      79 ..      66     124 ..      51     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 3e-11
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EE.EEEETT-HHHHHHHHHHT-EE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergktvl.lvvvasNtpsirlyeklGfek 79 
                                         + ++ vlpe + +G+gs l+ a+ +e ++rg+ ++ l v+++N+ +i++y++ G+e 
  gi|518652862|ref|YP_008142382.1|  66 IDIESIGVLPEDQDMGYGSMLITAIEAEARARGYSIIiLEVREKNDHAIKFYKAHGYET 124
                                       5688999**************************98751669***************986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   2.3e-07   0.00052       2     127 ..       3     124 ..       2     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 2.3e-07
                                       EEEE-GGGHHHHHHHHHHHTT----H..HHHHHHHHHHT..TSEEEEEEETTEEEEEEEEEEEEEEETTEEEEEEEE CS
                    Acetyltransf_9   2 irelteedldevlellkyaFqdeespleeireyfrklle..esrvlgaedngelvgqlallplelnvpGktlkaagv 76 
                                       +r+++++d+++v  + k+aF+de        + ++ +l+  ++ ++++ d+ +l g +++ pl         +a  +
  gi|518652862|ref|YP_008142382.1|   3 VRPYRKSDFHGVSIIEKMAFGDEAYSN----FMLKGILNsiNGFTYVLDDGSKLHGYATMGPLNE-------QAIDI 68 
                                       799999999999999999999999983....7788999844478999999999999888888754.......45568 PP

                                       EEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--.....SSHHHHHTTT-EE CS
                    Acetyltransf_9  77 tgVavapehrgrgvlskLlaraleemreegqplsllfP.....ssipiYrrfGyei 127
                                        +++v pe +  g+ s L+++  +e+r++g+++++l        +i++Y+  Gye+
  gi|518652862|ref|YP_008142382.1|  69 ESIGVLPEDQDMGYGSMLITAIEAEARARGYSIIILEVrekndHAIKFYKAHGYET 124
                                       99************************************77777668********97 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.2e-06     0.012       9      62 ..      50     103 ..      41     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.2e-06
                   Acetyltransf_CG   9 geevafleYevrkegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvvp 62 
                                        +  ++++    +e+ +d++ + V +e +  G+++ L++a+  +ar++g+++++
  gi|518652862|ref|YP_008142382.1|  50 SKLHGYATMGPLNEQAIDIESIGVLPEDQDMGYGSMLITAIEAEARARGYSIII 103
                                       4455666665678899***********************************986 PP

>> MOZ_SAS  MOZ/SAS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   3.5e-05     0.079      59     100 ..      47      88 ..      25     110 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
                           MOZ_SAS  59 eegahivGyFskekesaeeynlaCilvlPpyqrkgyGkllie 100
                                       ++g+++ Gy      +++   +  i vlP  q  gyG++li 
  gi|518652862|ref|YP_008142382.1|  47 DDGSKLHGYATMGPLNEQAIDIESIGVLPEDQDMGYGSMLIT 88 
                                       46788899999999999999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.28s 00:00:00.77 Elapsed: 00:00:00.48
# Mc/sec: 935.55
//
Query:       gi|518652863|ref|YP_008142383.1|  [L=230]
Description: hypothetical protein FACI_IFERC00001G1502 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.035   13.7   0.1      0.045   13.4   0.1    1.3  1  DFF40            DNA fragmentation factor 40 kDa
        2.6    8.2   7.3    1.4e+02    2.6   7.3    2.7  1  RNase_H2-Ydr279  Ydr279p protein family (RNase H2 complex com


Domain annotation for each model (and alignments):
>> DFF40  DNA fragmentation factor 40 kDa
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   5.1e-06     0.045      49     113 ..      47     110 ..      36     189 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.1e-06
                             DFF40  49 fktkeevmkrraqsRirgYlkkvkeeltkvknakarellkevleelrelLkaakyfgsyFdRsek 113
                                       +k k + ++++ +  ir+ lk++++ l++ ++a++++ ++++   l++++++++ f++yFdR++ 
  gi|518652863|ref|YP_008142383.1|  47 TKVKIKDLQMNLKRAIRALLKRAQS-LEESRKAAQERNYNDIERGLEKQIEDVRAFTTYFDRTNI 110
                                       46677778999999*****999987.5555688888899***********************954 PP

>> RNase_H2-Ydr279  Ydr279p protein family (RNase H2 complex component) wHTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   7.3     0.015   1.4e+02      74     120 ..      56     122 ..      12     227 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
                   RNase_H2-Ydr279  74 lseekllefLlsKverladeaglpesleekfvrkaleapllsvkre....................e 120
                                       ++ ++ ++ Ll+++++l ++ +  ++++ + + ++le+++ +v+                       
  gi|518652863|ref|YP_008142383.1|  56 MNLKRAIRALLKRAQSLEESRKAAQERNYNDIERGLEKQIEDVRAFttyfdrtnilldsissqldmY 122
                                       4445555666666666665555555566666666666666555333555555555555555555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1659  (0.0925317); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1686.60
//
Query:       gi|518652864|ref|YP_008142384.1|  [L=158]
Description: hypothetical protein FACI_IFERC00001G1503 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-07   30.1   0.1      7e-07   28.7   0.1    1.8  1  HTH_24           Winged helix-turn-helix DNA-binding
    3.4e-06   26.9   0.1    6.5e-06   26.0   0.1    1.5  1  MarR             MarR family
    0.00047   20.1   0.1    0.00073   19.5   0.1    1.4  1  HTH_Crp_2        Crp-like helix-turn-helix domain
     0.0021   17.9   0.0     0.0034   17.3   0.0    1.3  1  MarR_2           MarR family
     0.0046   16.7   0.0     0.0082   15.9   0.0    1.4  1  HTH_IclR         IclR helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.8   0.0      0.025   15.0   0.0    1.4  1  Penicillinase_R  Penicillinase repressor
      0.016   14.9   0.0      0.027   14.1   0.0    1.4  1  Crp              Bacterial regulatory proteins, crp family
      0.027   14.3   0.0      0.046   13.6   0.0    1.4  1  TrmB             Sugar-specific transcriptional regulator Trm
      0.056   13.4   1.0       0.21   11.5   0.0    2.3  2  HTH_36           Helix-turn-helix domain
      0.061   13.4   0.0       0.11   12.6   0.0    1.4  1  DprA_WH          DprA winged helix domain
      0.062   13.0   0.1       0.12   12.1   0.1    1.5  1  HTH_DeoR         DeoR-like helix-turn-helix domain
      0.064   13.2   0.1       0.13   12.3   0.1    1.5  1  Cdc6_C           CDC6, C terminal winged helix domain


Domain annotation for each model (and alignments):
>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.7   0.1   4.7e-10     7e-07       3      47 ..      97     142 ..      95     143 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.7 bits;  conditional E-value: 4.7e-10
                            HTH_24   3 etdrkILelLqk.nprisqreLAerlglSpstvnrrlkrLeeeGlI 47 
                                       + + +I ++L+k n+ri q+ L  ++g S +t++r l  Lee+G+I
  gi|518652864|ref|YP_008142384.1|  97 DSESAIVSILEKnNGRIMQNSLTGKTGYSAPTISRILTTLEEKGVI 142
                                       5667899*****9999*****************************9 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   0.1   4.3e-09   6.5e-06       1      52 [.      95     147 ..      95     148 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 4.3e-09
                                       --HHHHHHHHHHHHSTT.EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE CS
                              MarR   1 ltltqfviLrilyeqgp.lsvseLakklgvskstvtrvldrLekkGlieRsks 52 
                                       lt ++  i+ il+ +++ + +  L  k g s +t++r+l++Le+kG i+R+++
  gi|518652864|ref|YP_008142384.1|  95 LTDSESAIVSILEKNNGrIMQNSLTGKTGYSAPTISRILTTLEEKGVIDRRRH 147
                                       6777777888887666548899****************************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 !   19.5   0.1   4.9e-07   0.00073      31      56 ..     122     147 ..      93     157 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 4.9e-07
                                       TTSSHHHHHHHHHHHHHTTSEEETEE CS
                         HTH_Crp_2  31 lGltretvsrilseLkreglisrgrr 56 
                                        G +  t+sril+ L+++g+i+r+r+
  gi|518652864|ref|YP_008142384.1| 122 TGYSAPTISRILTTLEEKGVIDRRRH 147
                                       688999****************7653 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   2.3e-06    0.0034      22      55 ..     113     146 ..      94     149 .. 0.78

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 2.3e-06
                                       EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE CS
                            MarR_2  22 ltvgelarrlglsksavsrilkrLvaaGLverrp 55 
                                       + ++ l+ ++g+s +++sril  L+++G + rr+
  gi|518652864|ref|YP_008142384.1| 113 IMQNSLTGKTGYSAPTISRILTTLEEKGVIDRRR 146
                                       55666677899********************997 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   5.5e-06    0.0082      12      50 ..     106     144 ..     101     146 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                                       -CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  12 laeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50 
                                       l++ +++     l  +tg + +t +R+L tL+e G + +
  gi|518652864|ref|YP_008142384.1| 106 LEKNNGRIMQNSLTGKTGYSAPTISRILTTLEEKGVIDR 144
                                       5555666666667779*******************9876 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   1.6e-05     0.025       1      58 [.      95     149 ..      95     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.6e-05
                                       ---S-SHHHHHHHHHS-EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEETT CS
                   Penicillinase_R   1 lgelEaevmeilwekgeatvkevveeleeekelaysTVktllrrLvkKgllsrekegr 58 
                                       l+++E+++  il +++       ++ l  ++  +  T+  +l+ L++Kg+++r+++g 
  gi|518652864|ref|YP_008142384.1|  95 LTDSESAIVSILEKNNGR---IMQNSLTGKTGYSAPTISRILTTLEEKGVIDRRRHGM 149
                                       578888888888777653...3355688999999********************9985 PP

>> Crp  Bacterial regulatory proteins, crp family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.8e-05     0.027      18      32 .]     128     142 ..     123     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.8e-05
                                       HHHHHHHHHHHTTSE CS
                               Crp  18 TVSRlLtrLrekGLI 32 
                                       T+SR Lt L+ekG+I
  gi|518652864|ref|YP_008142384.1| 128 TISRILTTLEEKGVI 142
                                       9*************9 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   3.1e-05     0.046       5      56 ..      94     146 ..      90     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 3.1e-05
                                       HHHHHCCCHCHHHH.HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB   5 GLseyEakvYlaLl.klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56 
                                        L++ E+ +   L  ++g+   + +  ++g + +++ ++L  Le+kG+++r++
  gi|518652864|ref|YP_008142384.1|  94 ELTDSESAIVSILEkNNGRIMQNSLTGKTGYSAPTISRILTTLEEKGVIDRRR 146
                                       56666666655555667777778889999*********************987 PP

>> HTH_36  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.81   1.2e+03       8      18 ..      38      48 ..      36      55 .. 0.91
   2 ?   11.5   0.0   0.00014      0.21      30      55 .]     117     142 ..      96     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.81
                            HTH_36  8 klllgslasfa 18
                                      k+ll+++ s+a
  gi|518652864|ref|YP_008142384.1| 38 KILLLYIISYA 48
                                      8999****998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00014
                            HTH_36  30 tlakrlglsknTvsraikeLeqlGyi 55 
                                        l  ++g s  T+sr++  Le++G i
  gi|518652864|ref|YP_008142384.1| 117 SLTGKTGYSAPTISRILTTLEEKGVI 142
                                       455567******************76 PP

>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   7.3e-05      0.11       9      58 ..      94     145 ..      82     148 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7.3e-05
                           DprA_WH   9 plddlerrvLaaL..gpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58 
                                       +l+d e ++++ L   +  +    L  +tg +a ++s++L+ LE +G + r+
  gi|518652864|ref|YP_008142384.1|  94 ELTDSESAIVSILekNNGRIMQNSLTGKTGYSAPTISRILTTLEEKGVIDRR 145
                                       5677777777777333357777888999*******************99886 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     8e-05      0.12      11      50 ..     109     148 ..     100     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-05
                          HTH_DeoR  11 qqgklsveelvellgvSeaTiRRDLneLeeqglltRthGG 50 
                                       + g +  + l+   g+S  Ti R L++Lee+g++ R + G
  gi|518652864|ref|YP_008142384.1| 109 NNGRIMQNSLTGKTGYSAPTISRILTTLEEKGVIDRRRHG 148
                                       45677778889999*******************9876544 PP

>> Cdc6_C  CDC6, C terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   8.4e-05      0.13      39      76 ..     126     157 ..     116     158 .] 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.4e-05
                                       HHHHHHHHHHHHHTTSEEEEEEE-CC.C-EEEEEEESS CS
                            Cdc6_C  39 qrevsdllseLemlgileleksskGrregrtrkisLnv 76 
                                         ++s++l+ Le +g+++++      r+g+t++isL+ 
  gi|518652864|ref|YP_008142384.1| 126 APTISRILTTLEEKGVIDRR------RHGMTNEISLKE 157
                                       557999*************8......569******985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1182  (0.0659267); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.52u 0.34s 00:00:00.86 Elapsed: 00:00:00.53
# Mc/sec: 900.68
//
Query:       gi|518652865|ref|YP_008142385.1|  [L=120]
Description: hypothetical protein FACI_IFERC00001G1504 [Ferroplasma acidarmanus fer1]
Scores for complete 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-08   31.7   0.9    1.4e-07   31.0   0.9    1.2  1  SHOCT            Short C-terminal domain
     0.0017   18.1   5.0     0.0021   17.8   5.0    1.1  1  Yip1             Yip1 domain
  ------ inclusion threshold ------
      0.011   14.6   1.4       0.01   14.7   1.4    1.1  1  DUF2207          Predicted membrane protein (DUF2207)
      0.012   15.6   0.0      0.018   15.1   0.0    1.2  1  DUF1707          Domain of unknown function (DUF1707)
      0.026   14.4   0.1      0.045   13.6   0.1    1.4  1  VbhA             Antitoxin VbhA
      0.029   13.2   0.1      0.033   13.0   0.1    1.1  1  DUF2254          Predicted membrane protein (DUF2254)
      0.068   13.0   0.2      0.086   12.7   0.2    1.1  1  CdvA             CdvA-like coiled-coil domain
       0.15   12.0   5.4       0.18   11.7   5.4    1.1  1  DctQ             Tripartite ATP-independent periplasmic trans
       0.39   11.2   5.1       0.53   10.8   5.1    1.2  1  DUF202           Domain of unknown function (DUF202)
        1.6    8.7   7.4        1.2    9.1   0.8    2.2  2  DUF2474          Protein of unknown function (DUF2474)


Domain annotation for each model (and alignments):
>> SHOCT  Short C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.9   7.6e-11   1.4e-07       4      24 ..      94     114 ..      92     117 .. 0.89

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 7.6e-11
                             SHOCT   4 ekLkeLyarGeIteEEFeakK 24 
                                       ++L+e+ya+GeI+eEE+ ++ 
  gi|518652865|ref|YP_008142385.1|  94 AILRERYAKGEISEEEYKTRL 114
                                       79***************9987 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   5.0   1.2e-06    0.0021      23      94 ..      12      81 ..       1      87 [. 0.69

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                              Yip1 23 dlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhliakllggk 94
                                      +la++++al ++ ++l++   +++  ++    ++ t++   +a+i+ +++ ++++l+l l++ +i++++gg+
  gi|518652865|ref|YP_008142385.1| 12 GLAIFVVALSMVSFFLYGRPDIATRYSGV--YPSATGFPGRFAFIIMPVMAIISILILILFVRFIMRMAGGS 81
                                      45566666666666666665555555555..444566666666777777779******************96 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   1.4   5.6e-06      0.01     388     436 ..       6      76 ..       1     112 [. 0.73

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.6e-06
                           DUF2207 388 lgliilglilillallllvll.......................lvfllilllillliaiivlllfsrllgr 436
                                       ++++i+gl+ i++++l++v++                         f++i++ + ++i+i++l+lf r++ r
  gi|518652865|ref|YP_008142385.1|   6 IIWLIIGLA-IFVVALSMVSFflygrpdiatrysgvypsatgfpGRFAFIIMPVMAIISILILILFVRFIMR 76 
                                       222222222.22333333333355578999**************8888888888888888888888876654 PP

>> DUF1707  Domain of unknown function (DUF1707)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0     1e-05     0.018      13      34 ..      94     115 ..      90     117 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1e-05
                           DUF1707  13 elLrealaeGrLtldEfdeRle 34 
                                       ++Lre +a G ++ +E+ +Rl 
  gi|518652865|ref|YP_008142385.1|  94 AILRERYAKGEISEEEYKTRLN 115
                                       78******************96 PP

>> VbhA  Antitoxin VbhA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   2.5e-05     0.045      28      44 ..      98     114 ..      96     116 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                              VbhA  28 eayvrGeIdadElvrrv 44 
                                       e+y++GeI+ +E++ r+
  gi|518652865|ref|YP_008142385.1|  98 ERYAKGEISEEEYKTRL 114
                                       89***********9987 PP

>> DUF2254  Predicted membrane protein (DUF2254)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.8e-05     0.033      96     166 ..      11      95 ..       3     119 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                           DUF2254  96 LGtfigtfvYsllvlrairteee..............vpq.lsvlvalllaivsvllLiyFihhlarsiqvsnviar 157
                                       +G+ i  ++ s+++++ ++   +               p+ +++++  ++ai+s+l+Li+F++ ++r+   s+  ++
  gi|518652865|ref|YP_008142385.1|  11 IGLAIFVVALSMVSFFLYGRP-DiatrysgvypsatgFPGrFAFIIMPVMAIISILILILFVRFIMRMAGGSSCRRD 86 
                                       555555555555555555533.23555568766655544479999999**************999988766666666 PP

                           DUF2254 158 veeelrkai 166
                                       +  + ++ai
  gi|518652865|ref|YP_008142385.1|  87 MIYDNSEAI 95 
                                       666666666 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   4.8e-05     0.086      68      89 ..      98     119 ..      91     120 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                              CdvA  68 isyasGEidEeaYksaieaire 89 
                                        +ya GEi+Ee+Yk+  + +++
  gi|518652865|ref|YP_008142385.1|  98 ERYAKGEISEEEYKTRLNNLKN 119
                                       58*************9999886 PP

>> DctQ  Tripartite ATP-independent periplasmic transporters, DctQ component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   5.4    0.0001      0.18      62     124 ..       4      69 ..       2      79 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
                              DctQ  62 rrlleliadllallfaa.vliwagw..levaaalfeettpvlglplwwvylvlpigaallalvala 124
                                       ++++ li+ l+++++a+ +++++++   + a ++++   ++ g+p  + ++++p++a++ +l+++ 
  gi|518652865|ref|YP_008142385.1|   4 KKIIWLIIGLAIFVVALsMVSFFLYgrPDIATRYSGVYPSATGFPGRFAFIIMPVMAIISILILIL 69 
                                       56667777776666555344444446669999*************************666665543 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   5.1    0.0003      0.53      13      63 ..       8      74 ..       6      79 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
                            DUF202 13 WlRtslalialglallrffl.................tgepsalgkilglilivlgiltllvglvryl 63
                                      Wl ++la+++++l ++ ffl                 tg p ++++i+  ++++++il+l++ +vr++
  gi|518652865|ref|YP_008142385.1|  8 WLIIGLAIFVVALSMVSFFLygrpdiatrysgvypsaTGFPGRFAFIIMPVMAIISILILIL-FVRFI 74
                                      9999****************888888888888877777777777888888899999999987.55554 PP

>> DUF2474  Protein of unknown function (DUF2474)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.8   0.00065       1.2       5      28 ..       4      27 ..       2      28 .. 0.92
   2 ?    3.2   0.9     0.047        84      26      36 ..      69      79 ..      58      82 .. 0.78

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00065
                           DUF2474  5 kRlgWLvlIWaaSVlaLgvvAlll 28
                                      k++ WL++  a+ V+aL +v+++l
  gi|518652865|ref|YP_008142385.1|  4 KKIIWLIIGLAIFVVALSMVSFFL 27
                                      99******************9876 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.047
                           DUF2474 26 lllRllMtaAG 36
                                      l++R++M++AG
  gi|518652865|ref|YP_008142385.1| 69 LFVRFIMRMAG 79
                                      678*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      618  (0.0344693); 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):              10  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 820.88
//
Query:       gi|518652866|ref|YP_008142386.1|  [L=365]
Description: hypothetical protein FACI_IFERC00001G1505 [Ferroplasma acidarmanus fer1]
Scores for complete 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  141.5   0.0    4.3e-41  140.4   0.0    1.6  1  AAA              ATPase family associated with various cellul
    1.9e-09   37.2   0.0    5.3e-09   35.7   0.0    1.8  1  AAA_lid_3        AAA+ lid domain
    3.7e-06   27.4   0.0    8.7e-06   26.2   0.0    1.6  1  AAA_16           AAA ATPase domain
    6.8e-06   26.3   0.0    4.6e-05   23.6   0.0    2.3  2  AAA_2            AAA domain (Cdc48 subfamily)
    2.1e-05   24.5   0.0    8.4e-05   22.6   0.0    2.1  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00015   21.6   0.0    0.00036   20.3   0.0    1.7  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00057   19.9   0.0     0.0018   18.3   0.0    1.8  1  AAA_14           AAA domain
    0.00096   19.0   0.0     0.0067   16.3   0.0    2.3  2  Bac_DnaA         Bacterial dnaA  protein
     0.0015   18.4   0.0     0.0035   17.2   0.0    1.6  1  AAA_3            ATPase family associated with various cellul
     0.0018   17.5   0.0     0.0038   16.5   0.0    1.5  1  TIP49            TIP49 P-loop domain
      0.002   17.9   0.0     0.0048   16.6   0.0    1.7  1  IstB_IS21        IstB-like ATP binding protein
     0.0026   18.3   0.0       0.01   16.3   0.0    1.9  2  ABC_tran         ABC transporter
     0.0037   17.1   0.7      0.037   13.8   0.0    2.1  2  AAA_11           AAA domain
     0.0041   17.4   0.0       0.02   15.2   0.0    2.0  1  AAA_22           AAA domain
     0.0046   17.3   0.0      0.015   15.7   0.0    1.9  1  RNA_helicase     RNA helicase
      0.005   16.9   3.8     0.0095   16.0   3.1    1.9  1  MIT              MIT (microtubule interacting and transport) 
     0.0053   16.3   0.0     0.0095   15.5   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0064   16.2   0.0       0.29   10.8   0.0    2.4  2  Sigma54_activat  Sigma-54 interaction domain
  ------ inclusion threshold ------
       0.01   15.0   0.0      0.032   13.4   0.0    1.9  1  DUF815           Protein of unknown function (DUF815)
      0.013   15.2   0.0      0.032   14.0   0.0    1.6  1  AAA_30           AAA domain
      0.015   15.7   0.0      0.029   14.7   0.0    1.4  1  AAA_19           AAA domain
      0.017   15.7   0.8       0.27   11.7   0.0    2.4  2  AAA_23           AAA domain
      0.017   15.2   0.0      0.033   14.4   0.0    1.5  1  AAA_33           AAA domain
      0.021   14.5   0.1       0.07   12.8   0.0    1.8  2  AAA_24           AAA domain
      0.023   14.7   0.0      0.065   13.2   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.037   14.0   0.0      0.095   12.7   0.0    1.8  1  ResIII           Type III restriction enzyme, res subunit
      0.052   12.6   0.0      0.095   11.8   0.0    1.3  1  MCM              MCM P-loop domain
      0.058   12.8   0.0       0.13   11.7   0.0    1.5  1  Mg_chelatase     Magnesium chelatase, subunit ChlI
      0.069   12.3   0.1       0.21   10.7   0.0    1.8  2  PIF1             PIF1-like helicase
      0.077   13.4   1.5          1    9.8   0.0    2.7  2  AAA_17           AAA domain
      0.079   12.7   0.0       0.15   11.8   0.0    1.4  1  AAA_29           P-loop containing region of AAA domain
      0.082   12.6   0.0       0.16   11.6   0.0    1.5  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
        0.1   13.1   2.0       0.25   11.9   1.2    2.0  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain
       0.11   12.5   0.0       0.23   11.3   0.0    1.7  1  Rad17            Rad17 P-loop domain
       0.11   11.7   0.0       0.17   11.0   0.0    1.2  1  Aminotran_1_2    Aminotransferase class I and II
       0.12   11.4   0.0       0.21   10.6   0.0    1.3  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.13   12.2   0.0        0.7    9.8   0.0    2.0  2  NACHT            NACHT domain
       0.14   12.1   5.4        1.2    9.0   0.0    3.2  4  ATPase_2         ATPase domain predominantly from Archaea
       0.15   11.0   0.0       0.31   10.0   0.0    1.5  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
       0.18   12.4   1.3        1.2    9.9   0.3    2.6  2  DUF4665          Domain of unknown function (DUF4665)


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 !  140.4   0.0   9.6e-44   4.3e-41       1     131 [.     138     269 ..     138     270 .. 0.97

  Alignments for each domain:
  == domain 1  score: 140.4 bits;  conditional E-value: 9.6e-44
                                       EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTC CS
                               AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgs 77 
                                       +llyGppGtGKT ++ka+a+e++++f++++ s+l s+++g+ ek+i+ lf++a   + psilf+DEid l+++rsgs
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKANFINVNPSTLYSQWFGQFEKNISLLFRAAYLLS-PSILFFDEIDTLVPKRSGS 213
                                       89**************************************************99998.******************* PP

                                       CCHHHHHHHHHHHHHHHHTTTS.SSTEEEEEEESSGGGSTHHHHS.TTSSEEEETT CS
                               AAA  78 eseeeervvnqLlteldgvkkk.eskvivigatnrpdkldpallr.gRfdrkieie 131
                                       es+ ++r v+qLlte+ g++++ +++v++i+atn+p+ +d+a++r gRfd+ki+i+
  gi|518652866|ref|YP_008142386.1| 214 ESDAARRGVSQLLTEVGGLTSQkDRNVFIIAATNNPWGIDEAIMRpGRFDVKIYIP 269
                                       *******************9986788****************************97 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.2e-11   5.3e-09       2      43 ..     293     339 ..     292     341 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-11
                         AAA_lid_3   2 vdlkeLAerTeGySGADlaalcreAa....llAlrrgike.itmedf 43 
                                       +d++eLA +Te ySGAD++ +c++A+    ++ ++ g+k  ++++d+
  gi|518652866|ref|YP_008142386.1| 293 IDYDELANKTERYSGADIEFICKKAVqnvfMEVIKTGNKIdVSTDDL 339
                                       79************************444444555555556777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2   0.0   1.9e-08   8.7e-06      25     138 ..     136     241 ..     126     244 .. 0.65

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.9e-08
                            AAA_16  25 elvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysalaqalareellrqllde..aesaeleawre 99 
                                       + +ll+G++G+GK+ +v++++++++++   f++ +   l     ys++  ++++   +  l ++  +  +    + +
  gi|518652866|ref|YP_008142386.1| 136 GGMLLYGPPGTGKTFIVKAIANEVKAN---FINVNPSTL-----YSQWFGQFEK--NISLLFRAayLL-SPSILFFD 201
                                       679*******************99999...899988888.....9999999944..444444442222.23344444 PP

                            AAA_16 100 kleealaavpelagaeasrllellkrll.allsrderplv 138
                                       ++++ +   +  ++++a+r   +l   +  l+s+++r + 
  gi|518652866|ref|YP_008142386.1| 202 EIDTLVPKRSGSESDAARRGVSQLLTEVgGLTSQKDRNVF 241
                                       4555555333344444444444444444477777666544 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0     1e-07   4.6e-05       6     128 ..     138     247 ..     135     256 .. 0.85
   2 ?   -1.9   0.0       7.2   3.2e+03      85     102 ..     329     346 ..     298     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1e-07
                                       EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---..----THHHHHHHHHTTT-HHHHTTSEEEEETGGG- CS
                             AAA_2   6 illlgptgvGktelakalaellfvkkekkliradaselle..eeevehlvsrligappgyvgaeegGivllDEidKi 80 
                                       +ll gp g+Gkt++ ka+a+  ++    ++i ++ s+l      + e+ +s l  a+          i+++DEid  
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKA----NFINVNPSTLYSqwFGQFEKNISLLFRAAYLLS----PSILFFDEIDTL 206
                                       6899****************9995....999999999999454678888888877776665....56********** PP

                                       ---.---------HHHHHHHHHHHH--EE-------EE-TT-EEEEEE- CS
                             AAA_2  81 hpk.essgadvSregVqrdLLqileggtltdkqgrkvdtknilfImtga 128
                                        pk + s++d  r gV ++L      g lt +++     +n+ +I++++
  gi|518652866|ref|YP_008142386.1| 207 VPKrSGSESDAARRGVSQLLTE---VGGLTSQKD-----RNVFIIAATN 247
                                       ***999************9975...588888888.....7777777776 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 7.2
                                       --------HHHHHHHHHH CS
                             AAA_2  85 ssgadvSregVqrdLLqi 102
                                        ++ dvS ++ ++++ qi
  gi|518652866|ref|YP_008142386.1| 329 GNKIDVSTDDLLEVISQI 346
                                       445566666666666555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   1.9e-07   8.4e-05       2      79 ..     138     208 ..     137     256 .. 0.81
   2 ?   -2.2   0.0       8.5   3.8e+03     113     130 ..     315     339 ..     288     345 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 1.9e-07
                                       EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------..G-SEEEEESGGG CS
                             AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar..egeilvlDEver 76 
                                       +lL GppGtgK+++++ +a  +++++  ++ + +t +++ +g+ e          s l raa   +++il++DE+++
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKANF--INVNPSTLYSQWFGQFE-------KNISLLFRAAYllSPSILFFDEIDT 205
                                       89*****************9887776..77889999999999999.......4567777777788**********98 PP

                                       --H CS
                             AAA_5  77 aes 79 
                                       + +
  gi|518652866|ref|YP_008142386.1| 206 LVP 208
                                       755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8.5
                                       ........-EEEEEESS--.-TT-T CS
                             AAA_5 113 r.......frviatanpldrslnel 130
                                       +       + vi t+n+ d s  +l
  gi|518652866|ref|YP_008142386.1| 315 KkavqnvfMEVIKTGNKIDVSTDDL 339
                                       1355566677888888888666665 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 !   20.3   0.0     8e-07   0.00036      35      96 ..     137     206 ..      98     212 .. 0.71

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 8e-07
                            RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgPvl........ekagdlaalltnleekdvlfideihrl 96 
                                        +llyGpPG Gkt + k ia+e+++++      +l        ek+  l    + l +  +lf dei  l
  gi|518652866|ref|YP_008142386.1| 137 GMLLYGPPGTGKTFIVKAIANEVKANFINVNPSTLysqwfgqfEKNISLLFRAAYLLSPSILFFDEIDTL 206
                                       589*********************9986654444311111111333333333455667778888887766 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   4.1e-06    0.0018       6      76 ..     139     206 ..     136     249 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 4.1e-06
                            AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelilek.lkeekktylflDEiqev 76 
                                       ++ G+  +GKT+++k +++e      +++ +n  +   + + ++ek+++l+++  +     ++lf+DEi  +
  gi|518652866|ref|YP_008142386.1| 139 LLYGPPGTGKTFIVKAIANEVK---ANFINVNPSTLYSQWFGQFEKNISLLFRAaY-LLSPSILFFDEIDTL 206
                                       7899*************98877...9999999999999999999988888777733.34789*******876 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   1.5e-05    0.0067      37     179 ..     138     284 ..     124     303 .. 0.61
   2 ?   -2.4   0.0       7.5   3.4e+03     105     124 ..     309     327 ..     307     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.5e-05
                                       EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHT.T-SEEEEE-GGGGTT- CS
                          Bac_DnaA  37 lfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklr.kvDvLliDDiqflagk 112
                                       +++yg+ G Gkt ++kai+nev++n+ +   + l ++ F        +++    f+  +  +  +L  D+i  l  k
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKANFINVNPSTLYSQWFG-----QFEKNISLLFRAAYLlSPSILFFDEIDTLVPK 209
                                       79***********************999887777776664.....34555566677776546677777777777766 PP

                                       HHHHHH.........HHHHHHHHH.TTT-EE.EEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHH CS
                          Bac_DnaA 113 ektqee.........lfhtfnall.eegkqv.vlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkk 178
                                        +  e          l++ +  l+ +++++v ++++  +P+ ++e   r   rf+  + + i ppd+e r +i + k
  gi|518652866|ref|YP_008142386.1| 210 RSGSESdaarrgvsqLLTEVGGLTsQKDRNVfIIAATNNPWGIDEAIMR-PGRFD--VKIYIPPPDYESRKKIFQLK 283
                                       5543321111111112222223331233333134555666655443333.23443..45566666666666666655 PP

                                       H CS
                          Bac_DnaA 179 i 179
                                       +
  gi|518652866|ref|YP_008142386.1| 284 L 284
                                       5 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.5
                                       -GGGGTT-HHHHHHHHHHHH CS
                          Bac_DnaA 105 Diqflagkektqeelfhtfn 124
                                       Di+f+ +k  +q+ ++ ++ 
  gi|518652866|ref|YP_008142386.1| 309 DIEFICKKA-VQNVFMEVIK 327
                                       888888777.7777766543 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   7.7e-06    0.0035       2     113 ..     138     250 ..     137     259 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 7.7e-06
                             AAA_3   2 vllegvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeekekefefkkGpvfa.nllladeinrappk 77 
                                       +ll g PG++kt +vka+a+ ++++f  i + p  l s   G+  fe k+ ++ f++  +++ ++l+ dei+   pk
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKANF--INVNPSTLYSQWFGQ--FE-KNISLLFRAAYLLSpSILFFDEIDTLVPK 209
                                       6899*****************99998..677899999999996..44.45567777777665378889***999999 PP

                             AAA_3  78 tqsalleamee...rqvt.vegethklp.epflvlatqnPi 113
                                          +  +a +    + +t v+g t + + + f++ at+nP 
  gi|518652866|ref|YP_008142386.1| 210 RSGSESDAARRgvsQLLTeVGGLTSQKDrNVFIIAATNNPW 250
                                       88877777654111223325566655551567777899985 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.4e-06    0.0038      52      96 ..     137     179 ..     125     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.4e-06
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                             TIP49  52 avLlaGpsgtGktalaiaiskelgedvpfvalsgsevyslevkkt 96 
                                       ++Ll Gp+gtGkt +  ai++e+     f+ ++ s +ys+   + 
  gi|518652866|ref|YP_008142386.1| 137 GMLLYGPPGTGKTFIVKAIANEVK--ANFINVNPSTLYSQWFGQF 179
                                       689*******************97..78**********9866555 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 !   16.6   0.0   1.1e-05    0.0048      33      72 ..     121     160 ..      98     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 1.1e-05
                         IstB_IS21  33 rkvkeLatlsfiekkenivllGpsGvGKshlaialgveav 72 
                                        + keL +   ie + +++l Gp+G+GK+++  a++ e  
  gi|518652866|ref|YP_008142386.1| 121 MRYKELSQEYNIEFSGGMLLYGPPGTGKTFIVKAIANEVK 160
                                       55678888888999999*****************998754 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       5.3   2.4e+03      76      80 ..      64      73 ..      12     139 .. 0.50
   2 !   16.3   0.0   2.3e-05      0.01      14      80 ..     138     214 ..     128     240 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 5.3
                                      HHHH.....H CS
                                      xxxx.....x RF
                          ABC_tran 76 vren.....e 80
                                      ++e+      
  gi|518652866|ref|YP_008142386.1| 64 IYESiggeaV 73
                                      2222333331 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 2.3e-05
                                       EEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS.--S-TTSBHHHH.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx.......... RF
                          ABC_tran  14 vaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqe.pqlfpeltvren.......... 79 
                                       + + G+ G+GK+ ++k++a+++k  +  i+++   l +q   +++k+i+ l+     l p +   ++          
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVK--ANFINVNPSTLYSQWFGQFEKNISLLFRAaYLLSPSILFFDEidtlvpkrsg 212
                                       5689*****************98..6889999999999**************9955666666566556777776665 PP

                                       .H CS
                                       .x RF
                          ABC_tran  80 .e 80 
                                        e
  gi|518652866|ref|YP_008142386.1| 213 sE 214
                                       52 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.9      0.77   3.5e+02     134     195 ..      14      75 ..       2      90 .. 0.58
   2 !   13.8   0.0   8.2e-05     0.037      20      42 ..     138     160 ..     124     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.77
                            AAA_11 134 eklakelrafeeeeekeklkkskekskskleqerrklkkerkelskeleeaeesleeevlde 195
                                       +k  +e ++ +++e+ ++ k ++++  + ++++  k+k++r e   +l+++ es+  e ++e
  gi|518652866|ref|YP_008142386.1|  14 RKAIEEESSGNKNEAARTYKAAYKEVLEIASRSTGKIKQKRLEQAANLKKIYESIGGEAVEE 75 
                                       33333333344444446666666666666777777777777777777777766666544444 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 8.2e-05
                            AAA_11  20 tliqGPPGtgKTktivellsqll 42 
                                        l+ GPPGtgKT+ + ++ +++ 
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVK 160
                                       699**********9999999883 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.5e-05      0.02       8      46 ..     138     167 ..     135     175 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.5e-05
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvt 46 
                                       ++++G++GtGKT+ ++ ++++          ++ ++ v+
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEV---------KANFINVN 167
                                       789****************998.........55555554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   3.4e-05     0.015       2      36 ..     139     173 ..     138     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.4e-05
                      RNA_helicase   2 wlyGpsgeGKStlakeLakallkklklkkkdsvys 36 
                                       +lyGp+g+GK+ ++k +a+++  ++ + + +++ys
  gi|518652866|ref|YP_008142386.1| 139 LLYGPPGTGKTFIVKAIANEVKANFINVNPSTLYS 173
                                       79*******************98874444455554 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 !   16.0   3.1   2.1e-05    0.0095       7      54 ..      12      59 ..      10      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.1e-05
                               MIT  7 lvkkAveeDnagnyeeAlelYkealelLlqalkekneerrellrekie 54
                                      l++kA+ee+++gn  eA + Yk a +  l++ ++++ + +++  e+++
  gi|518652866|ref|YP_008142386.1| 12 LIRKAIEEESSGNKNEAARTYKAAYKEVLEIASRSTGKIKQKRLEQAA 59
                                      799**********************99999998644466666666655 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 !   15.5   0.0   2.1e-05    0.0095      32      63 ..     134     164 ..     110     185 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                             AAA_7  32 nkkpvllvGptGtGKtviikdllkkldkekyl 63 
                                        +  +ll+Gp GtGKt i+k + ++++  +++
  gi|518652866|ref|YP_008142386.1| 134 FSGGMLLYGPPGTGKTFIVKAIANEVK-ANFI 164
                                       55679*****************99999.3333 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   0.00064      0.29      24      61 ..     137     171 ..     121     182 .. 0.80
   2 ?    2.6   0.0      0.21        94      96     143 ..     197     248 ..     192     267 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00064
                                       -EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  24 svlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                        +l+ G  GtGK+++ +ai ++ k   ++f++vn + +
  gi|518652866|ref|YP_008142386.1| 137 GMLLYGPPGTGKTFIVKAIANEVK---ANFINVNPSTL 171
                                       589****************88765...78999886654 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.21
                                       EEEEETGGGS-HHHH...HHHHHHHHHSEEESBTS.SSEEE--EEEEEEESS CS
                   Sigma54_activat  96 tlfLDeigelplelQ...ekLlrvlqegevervGs.skeikvdvriiaatne 143
                                       +lf+Dei +l ++     +   r   ++ ++ vG+ +++++ +v iiaatn+
  gi|518652866|ref|YP_008142386.1| 197 ILFFDEIDTLVPKRSgseSDAARRGVSQLLTEVGGlTSQKDRNVFIIAATNN 248
                                       6777777776655431113333333445677888735678899999999997 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-05     0.032      53      82 ..     135     164 ..      85     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-05
                            DUF815  53 annvLLwGarGtGKSslvkallneyaeegL 82 
                                       +  +LL+G  GtGK  +vka+ ne++++ +
  gi|518652866|ref|YP_008142386.1| 135 SGGMLLYGPPGTGKTFIVKAIANEVKANFI 164
                                       4468********************998754 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.1e-05     0.032      21      44 ..     138     161 ..     132     172 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.1e-05
                            AAA_30  21 avltGpAGtGKttalkalreawea 44 
                                       ++l Gp+GtGKt+++ka+++ ++a
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKA 161
                                       5789**************887665 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   6.5e-05     0.029      12      37 ..     137     162 ..     130     174 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 6.5e-05
                            AAA_19  12 vllvtaGpGtGKTrvlkhivallvel 37 
                                        +l+ ++pGtGKT ++k+i ++++++
  gi|518652866|ref|YP_008142386.1| 137 GMLLYGPPGTGKTFIVKAIANEVKAN 162
                                       589**************999887764 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.5      0.89     4e+02     149     189 ..      23      65 ..       4     109 .. 0.58
   2 ?   11.7   0.0   0.00061      0.27      12      39 ..     129     155 ..     121     156 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.89
                            AAA_23 149 kdkkerleelekeleeledekkllekl..eqekekekeleele 189
                                        +k+e+ + ++ +++e  ++++    +  ++++e+ ++l+++ 
  gi|518652866|ref|YP_008142386.1|  23 GNKNEAARTYKAAYKEVLEIASRSTGKikQKRLEQAANLKKIY 65 
                                       3333444444444444333333211111223333333333333 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 0.00061
                            AAA_23  12 dqeidFskgltlItGpNGaGKTTildAi 39 
                                       + +i+Fs g+ l++Gp G+GKT i+ Ai
  gi|518652866|ref|YP_008142386.1| 129 EYNIEFSGGM-LLYGPPGTGKTFIVKAI 155
                                       446****999.****************9 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.0   7.3e-05     0.033       3      44 ..     139     182 ..     138     248 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 7.3e-05
                            AAA_33   3 llvGlpGsGKstlaerllkklg..avllssdtlrrrlfgtdqqs 44 
                                       ll G+pG+GK++ ++ ++++ +  ++ ++  tl+++ fg+ +++
  gi|518652866|ref|YP_008142386.1| 139 LLYGPPGTGKTFIVKAIANEVKanFINVNPSTLYSQWFGQFEKN 182
                                       688***************99996677777778777777743333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.8   2.2e+03      77     109 ..       9      41 ..       5      52 .. 0.56
   2 ?   12.8   0.0   0.00016      0.07       5      32 ..     138     167 ..     137     206 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.8
                            AAA_24  77 leelclaevirqnekaeskedkgdgkG.ygelae 109
                                       +  l+ + +i+  + ++++e + + k+ y+e+ e
  gi|518652866|ref|YP_008142386.1|   9 VSLLI-RKAIEEESSGNKNEAARTYKAaYKEVLE 41 
                                       43333.3444444444666565555555887755 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00016
                            AAA_24   5 iliyGpsgiGKTtlakel..gpkplfidte 32 
                                       +l+yGp+g+GKT ++k +  + k+ fi+++
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIanEVKANFINVN 167
                                       79*************999776666666655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00015     0.065      21      49 ..     134     167 ..     106     178 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00015
                                       E...EEEEESTTSSHHHHHHHHHHHTT--..--- CS
                              TsaE  21 v...ilLeGdLGaGKTtlvrglakalgve..evk 49 
                                       +   +lL+G+ G+GKT +v+++a++++ +  +v+
  gi|518652866|ref|YP_008142386.1| 134 FsggMLLYGPPGTGKTFIVKAIANEVKANfiNVN 167
                                       134499******************9988766665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   0.00021     0.095      26      79 ..     137     184 ..     105     246 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
                                       EEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTG CS
                            ResIII  26 rglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfls 79 
                                        +l+  + GtGKT++  +++ +++ +     f+  v+  +l++q+  +f+k +s
  gi|518652866|ref|YP_008142386.1| 137 GMLLYGPPGTGKTFIVKAIANEVKAN-----FIN-VNPSTLYSQWFGQFEKNIS 184
                                       56688899************999995.....555.55668*********98776 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021     0.095      20      88 ..      97     165 ..      89     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
                                       HHSSTTSSS-HHHHHHHHHHHH---E.BBBSSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                               MCM  20 ksiapsiyghedvkkaillqlfggvk.kkledktklrgdinvllvgdpgtaKsqlLkyveklapravyts 88 
                                       k  ++ + g e+vk+ i+ +++ +++ k+l+++ ++  +  +ll g pgt+K+ ++k++++ + +a++++
  gi|518652866|ref|YP_008142386.1|  97 KVTFQDVAGLENVKTEIMSKIIYPMRyKELSQEYNIEFSGGMLLYGPPGTGKTFIVKAIANEV-KANFIN 165
                                       5678899***************999857788889999999*******************9655.455555 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00028      0.13      25      43 ..     138     156 ..     129     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                      Mg_chelatase  25 lllvGppGsGKtmlakrlp 43 
                                       +ll+GppG+GKt + k+++
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIA 156
                                       89************99885 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00048      0.21      22      49 ..     135     162 ..     123     170 .. 0.83
   2 ?   -2.1   0.0       3.6   1.6e+03     263     306 ..     273     316 ..     267     335 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00048
                                       TS-EEEEESTTSSCHHHHHHHHHHCHCT CS
                              PIF1  22 gklfFvtGsgGtgKtflwkallkklrse 49 
                                       ++ + ++G  GtgKtf+ ka+ + ++++
  gi|518652866|ref|YP_008142386.1| 135 SGGMLLYGPPGTGKTFIVKAIANEVKAN 162
                                       556789*****************99876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 3.6
                                       .....EEEESSCCHHHHHHHHHHCCSSS--EEEE-EEE...... CS
                              PIF1 263 yleerailcptnedvdeiNnyvlsklpgeekeylssDsisksse 306
                                       y +++ i   + ++v++i     ++l ++ ++y  +D    +++
  gi|518652866|ref|YP_008142386.1| 273 YESRKKIFQLKLSEVKHIDHIDYDELANKTERYSGADIEFICKK 316
                                       55566667777789999999999999999999999886444444 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.6       0.8   3.6e+02      20      68 ..       5      50 ..       1      83 [. 0.70
   2 ?    9.8   0.0    0.0023         1       1      25 [.     141     165 ..     141     168 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.8
                                      TEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHH CS
                            AAA_17 20 gfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaee 68
                                      ++ h+s   l+r+ +++++++ +++e ++ ++   ke++++a ++  + 
  gi|518652866|ref|YP_008142386.1|  5 KIDHVS--LLIRKAIEEESSG-NKNEAARTYKAAYKEVLEIASRSTGKI 50
                                      566777..5777777777665.455555666677777777777655443 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0023
                                       EE-TTSSHHHHHHHHHHHHTEEEEE CS
                            AAA_17   1 lGgPGsGKgtqceklvekygfthls 25 
                                       +G+PG GK+++++ ++ +++  +++
  gi|518652866|ref|YP_008142386.1| 141 YGPPGTGKTFIVKAIANEVKANFIN 165
                                       7***************999877765 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   0.00034      0.15      16      43 ..     129     156 ..     123     169 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00034
                            AAA_29  16 tieidlkgatlltGpsGsGKSTllDAiq 43 
                                       +++i+ +g +ll Gp G+GK+ ++ Ai+
  gi|518652866|ref|YP_008142386.1| 129 EYNIEFSGGMLLYGPPGTGKTFIVKAIA 156
                                       455666688**************99987 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 ?   11.6   0.0   0.00037      0.16       5      71 ..     142     203 ..     138     208 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00037
                   Viral_helicase1   5 GvpGcGKStlirkllrts.liltvnrptaelltegk.pklpnlsvrtvdsflmalvkstkgkililDEy 71 
                                       G pG GK+ +++ ++++   ++  ++p   l++ ++ ++++n s     ++l +  +s    il++DE+
  gi|518652866|ref|YP_008142386.1| 142 GPPGTGKTFIVKAIANEVkANFINVNP-STLYSQWFgQFEKNISLLFRAAYLLS--PS----ILFFDEI 203
                                       78***************9977777777.79******766666655544444443..33....8999997 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 ?   11.9   1.2   0.00055      0.25       5      63 ..       9      72 ..       6      74 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00055
                                      HHHHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHH.....HHHGGGHTXS.SHHHHHHHHHHHH CS
                     Ribosomal_L11  5 tsylLkkaagiekgsgkpgketvGtvslkqvyeIA.....kiKksdlnaalsleaavksilgtA 63
                                      +s l+ ka+ +e+  +k +   + +   k+v eIA     kiK++ l++a +l+++  si g A
  gi|518652866|ref|YP_008142386.1|  9 VSLLIRKAIEEESSGNKNEAARTYKAAYKEVLEIAsrstgKIKQKRLEQAANLKKIYESIGGEA 72
                                      688999999887644444444568899********888888*****99777*********9988 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00052      0.23      48      87 ..     138     176 ..     105     206 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00052
                             Rad17  48 LLisGPsGCgkstvvkvLskelgiklrewlnpvslkepdn 87 
                                       +L+ GP+G gk+ +vk ++ e   +++ ++np +l +  +
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKANFI-NVNPSTLYSQWF 176
                                       6999*****************999887.678888776655 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 ?   11.0   0.0   0.00037      0.17      62     153 ..     231     314 ..     213     321 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00037
                                       TCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-...EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHH CS
                     Aminotran_1_2  62 klklkreaavvvgsGagaliealifllklnpgd...eilvpdptyasyknilrlsggevvryplyseedfhldleal 135
                                       +l+ +++++v  +  ++    + +++++  pg+   +i++p p y+s k+i++l  +ev  +        h+d ++l
  gi|518652866|ref|YP_008142386.1| 231 GLTSQKDRNVFIIAATNNPWGIDEAIMR--PGRfdvKIYIPPPDYESRKKIFQLKLSEVKHID-------HIDYDEL 298
                                       5555666566666555554444445554..4432226**************************.......******* PP

                                       HHHHTTHHCTTETEEEEE CS
                     Aminotran_1_2 136 eealkeapegnkktkvil 153
                                        ++ ++ +  ++   +i+
  gi|518652866|ref|YP_008142386.1| 299 ANKTERYSGADI--EFIC 314
                                       **9998766666..6666 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00048      0.21     118     139 ..     139     160 ..     132     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00048
                         Parvo_NS1 118 wfyGpantGktnlaeaIakavp 139
                                       ++yGp+ tGkt + +aIa+ v+
  gi|518652866|ref|YP_008142386.1| 139 LLYGPPGTGKTFIVKAIANEVK 160
                                       79****************9875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0    0.0016       0.7       3      27 ..     138     162 ..     137     194 .. 0.90
   2 ?   -0.2   0.0       1.8     8e+02      85     114 ..     198     227 ..     170     256 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0016
                                       EEEEC-TTTCHHHHHHHHHHHHCTS CS
                             NACHT   3 vilqGeaGsGKTtLlqklalawaeg 27 
                                       ++l G++G GKT  ++ +a + +++
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKAN 162
                                       6899***************998865 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.8
                                       EEEE-STT-SS-TCH.........HHHHHC CS
                             NACHT  85 lilDglDelvtdlgqkekqpvrtlLselir 114
                                       l +D +D lv + + +e  ++r+  s+l++
  gi|518652866|ref|YP_008142386.1| 198 LFFDEIDTLVPKRSGSESDAARRGVSQLLT 227
                                       567777777766555444444444444433 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 ?   -0.6   0.1       2.3     1e+03     211     225 ..      53      70 ..       9     118 .. 0.58
   2 ?    9.0   0.0    0.0027       1.2      23      46 ..     138     161 ..     122     243 .. 0.90
   3 ?   -1.4   0.0       4.1   1.8e+03     121     202 ..     197     281 ..     162     302 .. 0.64
   4 ?    3.9   0.6     0.099        45      97     131 ..     309     343 ..     264     364 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.3
                          ATPase_2 211 l...skedfeeiyryvGG 225
                                       +   +  ++++iy+ +GG
  gi|518652866|ref|YP_008142386.1|  53 KrleQAANLKKIYESIGG 70 
                                       112233334444444444 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0027
                          ATPase_2  23 yfiYGpegsGKtaLlkeiienled 46 
                                       +++YGp g GKt ++k i+++ + 
  gi|518652866|ref|YP_008142386.1| 138 MLLYGPPGTGKTFIVKAIANEVKA 161
                                       689***************998754 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.1
                          ATPase_2 121 iiiiDelqklidlgln....gaellvkeLlnliesltkekhl.cvviclsSeglfiervyneselegrhky.ilvdd 191
                                       i+++De+  l+   +      a+  v++Ll+ +  lt++k+  +++i+++ +   i+   +  ++ gr +  i++ +
  gi|518652866|ref|YP_008142386.1| 197 ILFFDEIDTLVPKRSGsesdAARRGVSQLLTEVGGLTSQKDRnVFIIAATNNPWGID---EAIMRPGRFDVkIYIPP 270
                                       666666666552211122225556666666666666666554145566666666665...55566666666666666 PP

                          ATPase_2 192 ldketalnflk 202
                                        d+e+ +++++
  gi|518652866|ref|YP_008142386.1| 271 PDYESRKKIFQ 281
                                       66666666555 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.099
                          ATPase_2  97 eksklvfkaielllekikkkgkkiiiiiDelqkli 131
                                       +     +ka++++++++ k+g ki +  D+l ++i
  gi|518652866|ref|YP_008142386.1| 309 DIEFICKKAVQNVFMEVIKTGNKIDVSTDDLLEVI 343
                                       335677899*********************98887 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00069      0.31      22      66 ..     123     169 ..     109     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00069
                             AAA_6  22 yltltqAlklklgg..apaGpagtGKtEtvkdLakalakqvvvfncs 66 
                                       y  l q +++++ g   ++Gp gtGKt  vk +a+++   ++ +n s
  gi|518652866|ref|YP_008142386.1| 123 YKELSQEYNIEFSGgmLLYGPPGTGKTFIVKAIANEVKANFINVNPS 169
                                       5556666666655412579****************999888877755 PP

>> DUF4665  Domain of unknown function (DUF4665)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.3    0.0026       1.2      11      66 ..      36      97 ..      23     117 .. 0.82
   2 ?   -0.1   0.0       3.4   1.5e+03       8      19 ..     234     245 ..     232     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0026
                           DUF4665 11 qknVFkvAsakslKaKaKAkpVttnLKkinav......kkekvenldkalvdiqkdlkslsk 66
                                       k+V ++As+ + K K+K      nLKki         +++++++  k+l  ++ ++ +++k
  gi|518652866|ref|YP_008142386.1| 36 YKEVLEIASRSTGKIKQKRLEQAANLKKIYESiggeavEEDRISEGKKILGTLNIEPPEIPK 97
                                      589******9999****************655566666999999999999999888887777 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 3.4
                           DUF4665   8 gkkqknVFkvAs 19 
                                        +k +nVF +A 
  gi|518652866|ref|YP_008142386.1| 234 SQKDRNVFIIAA 245
                                       5899******97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                       101  (0.00563333); expected 17.9 (0.001)
Passed Fwd filter:                        40  (0.00223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              40  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2433.54
//
Query:       gi|518652867|ref|YP_008142387.1|  [L=150]
Description: hypothetical protein FACI_IFERC00001G1506 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1038.88
//
Query:       gi|518652868|ref|YP_008142388.1|  [L=297]
Description: hypothetical protein FACI_IFERC00001G1507 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.087   11.5   0.0        2.1    7.0   0.0    2.0  2  DUF3525   Protein of unknown function (DUF3525)


Domain annotation for each model (and alignments):
>> DUF3525  Protein of unknown function (DUF3525)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0    0.0027        49     275     324 ..      25      74 ..       8      81 .. 0.85
   2 ?    7.0   0.0   0.00012       2.1      56     102 ..     200     248 ..     185     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.0027
                           DUF3525 275 kdeaisewwmsddsvktvendvlyllsflkdtaipedvklelvelvyaqi 324
                                        de  ++   s +s+  v +++ y   ++  t ip dvk + ++++   +
  gi|518652868|ref|YP_008142388.1|  25 ADEISDQMKKSLESIINVAEEIGYPYELVITTHIPVDVKSDKIKFINEAF 74 
                                       5677777888999**************************99988876655 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00012
                           DUF3525  56 lkagavvhlvpfhvq..klldsmddkalpysashncttvilesimyrsv 102
                                       lk  +++h+ pf+v    ll s   +++py  + n   +++e+im   +
  gi|518652868|ref|YP_008142388.1| 200 LKDIKIFHIEPFYVSfiSLLLSKLSRTKPYKFKENNRIIVMEGIMESLI 248
                                       677789*******974468999999********************7655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (297 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2159.22
//
Query:       gi|518652869|ref|YP_008142389.1|  [L=165]
Description: hypothetical protein FACI_IFERC00001G1508 [Ferroplasma acidarmanus fer1]
Scores for complete 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-12   45.7   0.0    8.2e-12   45.4   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
    2.6e-11   43.9   0.0    3.1e-11   43.7   0.0    1.0  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    3.4e-09   37.0   0.0      5e-09   36.5   0.0    1.2  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    1.7e-06   28.0   0.0    2.3e-06   27.5   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.022   15.4   0.0      0.029   15.0   0.0    1.3  1  Acetyltransf_3   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   2.3e-15   8.2e-12      13     117 .]      33     139 ..      22     139 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 2.3e-15
                                       HHHHHHHHHHHHHHHHHSTTCEEEE..EEETTEEEEEEEEEEEET.TSTTEEEEEEEEESGGGTTSSHHHHHHHHHH CS
                    Acetyltransf_1  13 fppnedaseeefeesfsleaegllv..aeedgeliGfisllkipd.ekggvayieslaVspeyrgkGlGsaLleale 86 
                                       f+ +++++++   +++ + +++++v  a   ++++G++sl++    e+++ ++ +s++V  +y+g+G+Gs Ll++ +
  gi|518652869|ref|YP_008142389.1|  33 FEIKKRDPVWT-SDWLVKRDPRYVVlvAGNRNNILGWLSLNPFSSrEAYRFVADISIYVENSYHGRGIGSGLLDHGI 108
                                       45566777777.666666777666644555578*************888888889********************** PP

                                       HHHHHTTESEEEEEEETTEHHHHHHHHHTTE CS
                    Acetyltransf_1  87 erareegikkivlaveedndaairlYeklGF 117
                                        +a+ +g++k+vl+   dn+ a++lY   GF
  gi|518652869|ref|YP_008142389.1| 109 IEAKINGFHKLVLTMLRDNEIARKLYISRGF 139
                                       **************************66887 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   8.5e-15   3.1e-11       2     153 ..       8     158 ..       7     160 .. 0.94

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.5e-15
                    Acetyltransf_4   2 raateeDakeilaiyaeyvvntaitfeyevssveefekflealdsekeyvflvae.sdrivGyaylgqfkkr.akdw 76 
                                       r a ++D   i +i ++       tfe +     ++  +l ++  + +yv lva    +i G + l+ f +r a++ 
  gi|518652869|ref|YP_008142389.1|   8 RKASLDDVPYIADIWNQGIDSGNATFEIKKRDPVWTSDWLVKR--DPRYVVLVAGnRNNILGWLSLNPFSSReAYRF 82 
                                       667889999999999987777799999999999*********9..99999999999********************* PP

                    Acetyltransf_4  77 kaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFelvgifkkcikkngrwiDm 153
                                        a +s+y+  +    +g+g+ l+d+ +  +k +++++l+     +ne++ +++ + GF+ vgi ++ +  n++wiD 
  gi|518652869|ref|YP_008142389.1|  83 VADISIYVE-NSYHGRGIGSGLLDHGIIEAKINGFHKLVLTMLRDNEIARKLYISRGFSTVGIMHEQGILNNKWIDT 158
                                       ********5.99**************999**********************************************95 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   1.4e-12     5e-09       3      75 ..      54     140 ..      51     141 .. 0.73

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 1.4e-12
                                       EEEEEEEETTEEEEEEEEEEES....TCTEE......EEE-GGGTTSSHHHHHHHH...TT..SEEEEE.EEEE.TH CS
                    Acetyltransf_7   3 gevfVaeddgkivGfialslld....aeitr......laVdpeyrgkGiGraLlea...ae..kgiile.qlel.na 62 
                                       + v+Va + ++i+G ++l + +    +   r      ++V  +y+g+GiG+ Ll++   ++  +g++    + l ++
  gi|518652869|ref|YP_008142389.1|  54 YVVLVAGNRNNILGWLSLNPFSsreaY---RfvadisIYVENSYHGRGIGSGLLDHgiiEAkiNGFHKLvLTMLrDN 127
                                       568899999*****9999999886641...2346678******************9654114566432222233544 PP

                                       HHHHHHHHHTTEE CS
                    Acetyltransf_7  63 ekaikfYeklGFe 75 
                                       e a+k+Y + GF 
  gi|518652869|ref|YP_008142389.1| 128 EIARKLYISRGFS 140
                                       599*********6 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   6.5e-10   2.3e-06      28     112 ..      51     145 ..      18     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 6.5e-10
                   Acetyltransf_10  28 egealllvaeeggkivGvielrdgs......hisll.....fVdpeyrgqGigkaLleaveeeaekdgikl.eltvn 92 
                                       ++++++lva + ++i+G ++l   s          +     +V+++y+g+Gig+ Ll++ + ea+ +g ++  lt+ 
  gi|518652869|ref|YP_008142389.1|  51 DPRYVVLVAGNRNNILGWLSLNPFSsreayrF---VadisiYVENSYHGRGIGSGLLDHGIIEAKINGFHKlVLTML 124
                                       78899999999999999998844444755542...033355**********************99999999988887 PP

                   Acetyltransf_10  93 asp.yavpfYeklGFkavgee 112
                                        ++  a+++Y + GF +vg +
  gi|518652869|ref|YP_008142389.1| 125 RDNeIARKLYISRGFSTVGIM 145
                                       7777************99755 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   8.2e-06     0.029      34     137 ..      40     139 ..       5     140 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 8.2e-06
                    Acetyltransf_3  34 leeaeewlerawaeeseeegygwaivlkdtgviGsvglrdleeedee...aelgymlapsfwgkGyateavralley 107
                                       +  + +wl +      ++  y  ++  + ++++G+ +l++++ ++     a++++++  s++g+G+++  +   +  
  gi|518652869|ref|YP_008142389.1|  40 PVWTSDWLVK------RDPRYVVLVAGNRNNILGWLSLNPFSSREAYrfvADISIYVENSYHGRGIGSGLLDHGIIE 110
                                       4444444442......2244555554455559*******99988666999*****************9998886666 PP

                    Acetyltransf_3 108 afeelglerlvavidkeNeaSirvleklGf 137
                                       a +  g ++lv ++  +Ne  ++++ + Gf
  gi|518652869|ref|YP_008142389.1| 111 A-KINGFHKLVLTMLRDNEIARKLYISRGF 139
                                       6.5667899999999999999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1244.59
//
Query:       gi|518652870|ref|YP_008142390.1|  [L=376]
Description: hypothetical protein FACI_IFERC00001G1509 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-25   90.3   0.0    1.8e-25   89.9   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    1.8e-19   69.6   0.0    5.8e-19   68.0   0.0    1.8  2  M20_dimer      Peptidase dimerisation domain
    4.1e-05   23.4   0.0    6.3e-05   22.7   0.0    1.3  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.049   12.6   0.0       0.13   11.3   0.0    1.6  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.9   0.0     4e-29   1.8e-25       2     206 ..      80     371 ..      79     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 4e-29
                                       EEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       l  H+D+V +e t   ++ pf+ +  +Gk yG+G  dmk+g++  ++al+al +++ ++k++ivll++ dEE+ +g+
  gi|518652870|ref|YP_008142390.1|  80 LLCHYDTVFPEGT--IKSrPFKVE--NGKGYGPGRFDMKTGLVQTVYALKALVKNK-ELKYSIVLLITSDEEIESGS 151
                                       668******6666..6777*****..8999*************************7.779*************9777 PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHST.ETEEEE...................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx...................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagk.laigvv...................................... 115
                                       +k l+      e+ + +f + ++ep++  a k    gv+                                      
  gi|518652870|ref|YP_008142390.1| 152 SKDLII----SEAKKSIFTF-VMEPSLDGALKtERSGVGtitlkiygkashaglepekginaiyemaymipviekln 223
                                       7*****....6677777744.45466655444333333377888888888888888888888888888888888888 PP

                                       .........................................................EEEEEEEEEESHEEEC...C CS
                                       .........................................................xxxxxxxxxxxxxxxx...x RF
                     Peptidase_M20 116 .........................................................kvevelleggapvtln...d 132
                                                                                                + e+e     +p+ ++   +
  gi|518652870|ref|YP_008142390.1| 224 dkqkgtsinldvinggtrsnvipdycegimdiryklpeeseriiealentplrfhgsRKELE--YKLRPPLVKsedS 298
                                       999999999*********************************************99746666..3344555555799 PP

                                       HHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTT.EEEEEEE.SSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 133 splvkalaeaaeelfgekvelivsgpggtdarffagi.ptvmifg.pgsglaHspnEyvdledlekgikvlarlle 206
                                       ++l+ +++e+ e+l g++ ++   + gg+d +f     p ++++g  g ++aHs+nEy+ ++ +++ +++l+ +l+
  gi|518652870|ref|YP_008142390.1| 299 KELFLKVREIGENL-GLDLDEASVA-GGSDGNFCSYYcPVIDGLGaVG-AGAHSENEYIVVDKIPERTALLYLALK 371
                                       999*******9998.*888887777.9*******44469999***888.**********************98876 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.82   3.7e+03      49      82 ..     104     137 ..      57     161 .. 0.54
   2 !   68.0   0.0   1.3e-22   5.8e-19       2      99 ..     180     272 ..     179     275 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.82
                                       ...TCCTCCCCCEECCE-CCCCEESSEEEEEEEE CS
                         M20_dimer  49 eerslprttlnvtgiegGsaknvipdeaeakidi 82 
                                       +++ ++r  +  + ++  +a  +++   e+k++i
  gi|518652870|ref|YP_008142390.1| 104 KGYGPGRFDMKTGLVQTVYALKALVKNKELKYSI 137
                                       4555555555555555555555555555555554 PP

  == domain 2  score: 68.0 bits;  conditional E-value: 1.3e-22
                                       EB-EEEEEEEEEE-B-EEGG.-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEE CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsg.apgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeae 77 
                                       ++ G+ + ++++ gka H+g  p++g+NAi+++a ++  +e++++++      ++t++n+ +i+gG+ +nvipd++e
  gi|518652870|ref|YP_008142390.1| 180 ERSGVGTITLKIYGKASHAGlEPEKGINAIYEMAYMIPVIEKLNDKQ------KGTSINLDVINGGTRSNVIPDYCE 250
                                       789****************************8888888888886654......59********************** PP

                                       EEEEEEHHHHHHHHHHHHHHHH CS
                         M20_dimer  78 akidiRllpgedpeevleeiee 99 
                                         +diR    e+ e+++e++e+
  gi|518652870|ref|YP_008142390.1| 251 GIMDIRYKLPEESERIIEALEN 272
                                       ********99********9986 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.0   1.4e-08   6.3e-05       5     102 ..      69     238 ..      66     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.4e-08
                                       EESTTCESEEEEEEEE--B-TTT...............TCCT---TTTTHHHHHHHHHHHHHCHHGGCCSSEEEEEE CS
                     Peptidase_M28   5 tlegkatdevlllgAHyDsvgvg...............rgpifvGAdDnAsgvaalLelarvlaasgsrpkrgvrfl 66 
                                        ++gk+ d+++ll +HyD+v  +                gp   G  D  +g +  ++ +++l++++ ++k+++++l
  gi|518652870|ref|YP_008142390.1|  69 AIKGKS-DNRILLLCHYDTVFPEgtiksrpfkvengkgYGP---GRFDMKTGLVQTVYALKALVKNK-ELKYSIVLL 140
                                       578999.**************989***99999997766666...********************855.99******* PP

                                       EESSCSGSSHHHHHHHHHHCCCTTE.................................................... CS
                     Peptidase_M28  67 ffdaEEagllGSkafakakpelkki.................................................... 91 
                                       +++ EE     Sk ++  ++++k i                                                    
  gi|518652870|ref|YP_008142390.1| 141 ITSDEEIESGSSKDLI-ISEAKKSIftfvmepsldgalktersgvgtitlkiygkashaglepekginaiyemaymi 216
                                       ******9888888888.555666665555555555555555555555555555555555555555555555555555 PP

                                       ...........EEEEEECS-SS CS
                     Peptidase_M28  92 ...........aavlnlDmvgs 102
                                                   + +nlD ++ 
  gi|518652870|ref|YP_008142390.1| 217 pvieklndkqkGTSINLDVING 238
                                       5555555555555555555555 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.44     2e+03       7      25 ..      70      87 ..      66      89 .. 0.82
   2 ?   11.3   0.0   2.9e-05      0.13     115     174 ..      92     153 ..      87     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.44
                                      EESSTTSSEEEEEEE--B- CS
                     Peptidase_M42  7 kkgkekepkvmiaAHmDei 25
                                      +kg +++ ++++  H D++
  gi|518652870|ref|YP_008142390.1| 70 IKG-KSDNRILLLCHYDTV 87
                                      567.67899********98 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 2.9e-05
                                       EES---EEETTEC.EEETTHHHHHHHHHHHHHHHHH.CTSS-SSEEEEEEESTCTTTSHHHH CS
                     Peptidase_M42 115 vfdkefvelangk.ivskalDdragvavllellkel.keeeleatvylvatvqEEvGlrGak 174
                                       ++++++  ++ngk +    +D ++g++  +++lk+l k++el++ ++l++t  EE+  + +k
  gi|518652870|ref|YP_008142390.1|  92 TIKSRPFKVENGKgYGPGRFDMKTGLVQTVYALKALvKNKELKYSIVLLITSDEEIESGSSK 153
                                       6778888888888777789***************983566788*************877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 2391.40
//
Query:       gi|518652871|ref|YP_008142391.1|  [L=352]
Description: hypothetical protein FACI_IFERC00001G1510 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-32  112.7   0.0    2.2e-32  112.4   0.0    1.1  1  MR_MLE_C   Enolase C-terminal domain-like
      6e-08   32.9   0.0    1.2e-07   31.9   0.0    1.6  1  MR_MLE_N   Mandelate racemase / muconate lactonizing enzyme, 
  ------ inclusion threshold ------
      0.013   14.7   0.0      0.036   13.3   0.0    1.7  1  Enolase_C  Enolase, C-terminal TIM barrel domain
      0.046   12.9   0.0      0.079   12.1   0.0    1.3  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus
        0.1   11.6   0.0       0.25   10.3   0.0    1.7  2  DuoxA      Dual oxidase maturation factor


Domain annotation for each model (and alignments):
>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.4   0.0   6.2e-36   2.2e-32       6     219 ..     134     339 ..     130     341 .. 0.91

  Alignments for each domain:
  == domain 1  score: 112.4 bits;  conditional E-value: 6.2e-36
                                       HHHHHHHHT-SEEEEETSSSHHHHHHHHHHHHHHHHTTTSTSEEEEE-TTTSBHHHHHHHHHHHGGGTESEEESSSS CS
                          MR_MLE_C   6 arelvaeqgfravKlkvggddvaedvervravreavgpgddvdlmvDanqawdlatAirvareleeldllwlEEPvp 82 
                                       ++e+++ +g++++K+k+ ++   +++  + avr+ + p  d+ l  Dan  ++  +   ++++++ ++l +lE+P+ 
  gi|518652871|ref|YP_008142391.1| 134 IQEALD-RGYKRIKVKIMKG---KEIGILSAVRDNF-P--DIVLSADANSDYTE-KDFDLIKKIDRYNLVYLEQPLY 202
                                       556566.5********8886...99***********.6..46**********95.578******88*********** PP

                                       TTTHHHHHHHHHHHH.SSEEEESTTSSSHHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCS CS
                          MR_MLE_C  83 peddleglaelrara.sipiaagEslysradfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgs 158
                                       + dd+  + +l+ +  s+p++++Es++s++ +++++e ga+ +++++ +r gGi +++kv+ ++++f   v+++++ 
  gi|518652871|ref|YP_008142391.1| 203 H-DDIIYHSRLA-KGlSTPLCLDESITSPEKAQKAFEMGACKVINIKEGRLGGIGNSLKVMGIVKEFKGHVWIGGML 277
                                       9.77999*****.77899*********************************************************96 PP

                                       .SHHHHHHHHHHHHTTTTBEEEEEEGGGGHTSGCSBSSSSEEETTEEECTSSSBTSSEB-HH CS
                          MR_MLE_C 159 .gglglaaslhlaaaipnllileyfldaelleeelleeplevedGrvtvpdgpGlGveldee 219
                                        +g+g+  ++++a+  +     + +  +++++++++++p+++e+G+++  +g G+Gve+ ee
  gi|518652871|ref|YP_008142391.1| 278 eTGIGRSFNVSMASLSDINYPGDTSPNDKYFKNDIVKNPFTMENGTIKPNKGTGIGVEISEE 339
                                       59**********988876666666666666*****************************965 PP

>> MR_MLE_N  Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   3.4e-11   1.2e-07      14     117 .]       5     110 ..       1     110 [. 0.89

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 3.4e-11
                                       CEEEETTEEEEEEEEEEEEEEECTTEEEEEEEE-STT......GHHHHHHHHHHHHHHHHTTSBTTHHHHHHHHHHH CS
                          MR_MLE_N  14 rPvqlavttvqkqslvlvkietseGvvGigeatsvgg......raetikaelddhlapllvgkdaanisdlaqllkr 84 
                                        P+ ++++t  ++ + + k+e ++G++  +e ++          + t+  +++++lap + g +     d+ ++  +
  gi|518652871|ref|YP_008142391.1|   5 SPFTTSFGTDVNKDVYVFKLE-HNGITAYSESVTDENpfygseDNYTVFHIVKQYLAPVVKGLPE---PDEFNEQVK 77 
                                       4********999999999***.*********988766688877888999**********999874...567777889 PP

                                       HCSSCHHHHHHHHHHHHHHHHHHTTSBHHHHTT CS
                          MR_MLE_N  85 avlgnmsAkaaidmAlwDlkakalnlpladLlG 117
                                       +++gn +Aka ++m l+D  aka + +l+d +G
  gi|518652871|ref|YP_008142391.1|  78 FIKGNNMAKASMEMLLYDYYAKANKKSLVDYIG 110
                                       9*****************************998 PP

>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.036     134     224 ..     179     264 ..      97     274 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                       EHHHHHHHHHHHHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--SEEEE-HHH CS
                         Enolase_C 134 tseqladlykelvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaanalllkvnq 210
                                       t++++ dl k+ +++y +v +e pl +dd   +++l + l   +     d  +t p++ ++a e +a+  + +k  +
  gi|518652871|ref|YP_008142391.1| 179 TEKDF-DLIKK-IDRYNLVYLEQPLYHDDIIYHSRLAKGLSTPL--C-LDESITSPEKAQKAFEMGACKVINIKEGR 250
                                       43333.55554.688***********************999444..3.36789************************ PP

                                       H-SHHHHHHHHHHH CS
                         Enolase_C 211 iGsltesleavkla 224
                                       +G + +sl+ + + 
  gi|518652871|ref|YP_008142391.1| 251 LGGIGNSLKVMGIV 264
                                       *******9987655 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 ?   12.1   0.0   2.2e-05     0.079     137     203 ..     215     280 ..     208     294 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.2e-05
                            MAAL_C 137 gikvelvaDeWcntledirefvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetd 203
                                       g +  l  De   + e  ++  + +a++++ ik   lGgi n+++ + + ke   ++++GG   et 
  gi|518652871|ref|YP_008142391.1| 215 GLSTPLCLDESITSPEKAQKAFEMGACKVINIKEGRLGGIGNSLKVMGIVKEFKGHVWIGGML-ETG 280
                                       5566677899999999999999******************************99999999964.555 PP

>> DuoxA  Dual oxidase maturation factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       0.8   2.9e+03     130     145 ..      54      69 ..      47      70 .. 0.86
   2 ?   10.3   0.0   6.8e-05      0.25      87     108 ..     115     136 ..      71     148 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.8
                             DuoxA 130 leeeyrealekGlPeP 145
                                       + ++y + + kGlPeP
  gi|518652871|ref|YP_008142391.1|  54 IVKQYLAPVVKGLPEP 69 
                                       678999999*****99 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 6.8e-05
                             DuoxA  87 eakiglkiGLegvNiTLkgepv 108
                                        a++g+ +G++++N+TLk+ ++
  gi|518652871|ref|YP_008142391.1| 115 YANVGISLGMDDINVTLKKIQE 136
                                       599**************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (352 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2163.72
//
Query:       gi|518652872|ref|YP_008142392.1|  [L=607]
Description: glucoamylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      1e-46  159.6   0.0    3.5e-45  154.6   0.0    2.0  2  Glyco_hydro_15  Glycosyl hydrolases family 15


Domain annotation for each model (and alignments):
>> Glyco_hydro_15  Glycosyl hydrolases family 15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.6   0.0   1.9e-49   3.5e-45       4     358 ..     237     552 ..     234     565 .. 0.92
   2 !    4.4   0.0   0.00073        13     401     447 ..     550     597 ..     546     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: 154.6 bits;  conditional E-value: 1.9e-49
                                       HHHHHHCBCSTTSSBTTS-TT-B-S-S-BSSS.........B--SEEHHHHHHHHHHHH.......HHHHHTTT-HC CS
                    Glyco_hydro_15   4 ldlylrnvktlilleqnpvtGlliASpstsdp.........DYrytWvRDsvyvilavwglgyrdedrakayeleqs 71 
                                        d++ r++ tl  l++ p tG+++A+p+ts+p         DYrytW+RD +yv++a+  +g  d + ++ y++   
  gi|518652872|ref|YP_008142392.1| 237 YDHVIRSALTLRGLFYDP-TGMMVAAPTTSLPeiiggernwDYRYTWIRDTAYVVEALSLIGLNDVATKFLYDIMSI 312
                                       68999*************.****************************************99999*********9999 PP

                                       CHHHHHHHHHHHHHHCTS-BTTB-TTSCGGGG--EE-TTS-B--S-..-S--BTTHHHHHHHHHHHHHCTTHCHCCC CS
                    Glyco_hydro_15  72 lvklmrglleamvrqagkvekfketqstkgLhakyftktgstvvGddewghlQlDatslyllalaqmtasglqiist 148
                                       ++k  +  +++++  +g+  k++e +      +++++ + ++++G+++  +lQ+D+++ ++ a+ +++++g  ++ +
  gi|518652872|ref|YP_008142392.1| 313 VQKDKK--VKTIYPVNGD-SKLEEKKV----NLSGYMDSIPVRIGNEASEQLQIDQYGSIVNAVFRFHEAGGLVTTY 382
                                       998666..9999999998.55555455....59**************************************999999 PP

                                       CHHHHTHHHHHHHHHHHTTS-EE-TTS--ECEEHH..HHHHHHHHHHHHHHHHHHCT-HHHHCCHHHHHHHHHHHHH CS
                    Glyco_hydro_15 149 ldevafvqnlvdYieaayktpdfglWEenqgeselnassvgmakAlleaideadlfgakgdaqlvektkdeilnklq 225
                                       l+ +    +++d ++  +k pd+ +WE + + +++ +s++ ++ A+ +ai++ +++g ++  ++++k ++ei n++ 
  gi|518652872|ref|YP_008142392.1| 383 LWDF--LIEILDTLKDIWKLPDSSIWEFRSEPKHYLYSKLISWSAFNRAIKMGRELGYSAPYRTWHKIREEIKNEI- 456
                                       9988..89********************************************************************. PP

                                       STTT..GGGEETTCCECECSCH.....HHHTTS--S-BCHHHHHHHHCS-TTS-TT-TT-TTTSHHHHHHHHHHHHH CS
                    Glyco_hydro_15 226 gkygckrgfwplfntylildgsfaedkeqvqeyrealdasllllpelyfvpaddvdeeyqnpqsprllaqslyilds 302
                                           +++g+ p+   +++++gs            +++das+l +p  + ++a d          pr+++++  ++++
  gi|518652872|ref|YP_008142392.1| 457 ----MEKGYNPDVKAFTQYYGS------------DQMDASVLRMPLTGIISAKD----------PRFVSTLARVEAE 507
                                       ....******************............********************..........************* PP

                                       HHHHSGGGTT-STTS--SBTT--CGSSSBSCT--BHHHHHHHHHHHHHHHHHHHHH CS
                    Glyco_hydro_15 303 llsegflavgeldplvrRysedvkpdklglsGrpyylctlwtvetlldelyekagk 358
                                       l++           ++ Ry +d   d+l++  ++++l ++w ve+l  +   ++ k
  gi|518652872|ref|YP_008142392.1| 508 LKNPCG--------MFIRYHSD---DGLKGHDNAFLLLSFWYVEDLILSGRIMEAK 552
                                       ***877........499****9...68*****************997655555555 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.00073
                                       HHHHHHHHHHHHS-TTS---SEE-T.TT--EESSTT-HHHHHHHHHHH CS
                    Glyco_hydro_15 401 eladliveaveednslgvLteevdv.ylgeliraqpllfsealllrig 447
                                       e ++++ ++   +n+l +++ee++  ++ e+++++p++  ++  +r++
  gi|518652872|ref|YP_008142392.1| 550 EAKETFENILDHSNHLMLFSEEINFnDCREMLGNFPQAITHLGVIRAA 597
                                       677889999999***********9636777**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (607 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); 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: 0.64u 0.30s 00:00:00.94 Elapsed: 00:00:00.50
# Mc/sec: 3676.36
//
Query:       gi|518652873|ref|YP_008142393.1|  [L=450]
Description: hypothetical protein FACI_IFERC00001G1512 [Ferroplasma acidarmanus fer1]
Scores for complete 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-99  331.7   4.5    1.3e-98  330.8   4.5    1.4  1  Glyco_transf_20  Glycosyltransferase family 20
     0.0011   18.5   0.8       0.67    9.5   0.1    2.5  2  Glycos_transf_1  Glycosyl transferases group 1
  ------ inclusion threshold ------
       0.12   12.7   0.0        0.3   11.5   0.0    1.8  1  Glyco_trans_1_4  Glycosyl transferases group 1
       0.32   10.7   1.2       0.85    9.3   0.1    2.2  2  DUF3755          Protein of unknown function (DUF3755)


Domain annotation for each model (and alignments):
>> Glyco_transf_20  Glycosyltransferase family 20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  330.8   4.5  2.9e-102   1.3e-98      31     472 ..      33     441 ..       8     443 .. 0.93

  Alignments for each domain:
  == domain 1  score: 330.8 bits;  conditional E-value: 2.9e-102
                                       SSHHHHHCCCHHCCC-EEEEEEECCES-CCC..HCCCCHHHCCCCCEEEEEE-HHHHHHHCCCHHHHCHHHHHTT-G CS
                   Glyco_transf_20  31 sgglvsalkglkeetevvwvgwlgvevdeseeakekvskeleekfsvvpvflsdekveeyyngfsksvLWpllHYkl 107
                                        gg+++al+ + + t ++wv w   ++d  +      ++e  + +++++vfl++++   +yn +s++vLWpl+HY  
  gi|518652873|ref|YP_008142393.1|  33 VGGVATALSTMLKGTGGTWVCWGDGKNDMAH------QEETTDGYKIARVFLNKTEKFGFYNSYSNRVLWPLFHYFR 103
                                       4789999***************988888877......4556689999***************************988 PP

                                       G....G----HHHHHHHHHHHHHHHHHHHCC--TT-EEEEESGGGTTHHHHHHHCCTTSEEEEEE-S----HHHHTT CS
                   Glyco_transf_20 108 pdsseekefersawdaYvkvnklFAdkiveeikdgdliwvhDYhLmllPellRkkledakigfflHiPFPsseifri 184
                                       +    + +f+++a++ Y  +n++FA+ki e+i ++ +iwvhDY+Lm++P++lR +   + i f  HiP+ s e f i
  gi|518652873|ref|YP_008142393.1| 104 N----NIHFDSTAFKYYYIANEKFAKKIKENITPDTIIWVHDYQLMMIPSILRTMDISNYIIFSWHIPWISPEFFSI 176
                                       8....9*********************************************************************** PP

                                       STTHHHHHHHHTTSSEEEESSHHHHHHHHHHHHHHSSEEEECTTEEEEETTEEEEEEE------HHHHHHHCCSCHH CS
                   Glyco_transf_20 185 LpvreeilegllgadliGFhtedyarhFlsccsrllgleveskrggveykgrkvsvkalpigidverlesalkkesv 261
                                       Lp  + + +++ +++l+ Fht+ y ++F+++++    ++v+          ++ ++ a+p gid + ++        
  gi|518652873|ref|YP_008142393.1| 177 LPEAKFLAQSISKSNLVTFHTRLYEKNFFNTLEYHE-IKVK----------NRLKTLAIPLGIDKNFFHL------- 235
                                       *****************************9976432.3333..........3467889******988864....... PP

                                       HHHHHHHHHHT.TTSEEEEEEEEC-GGG-HHHHHHHHHHHHHH-GGGTTTEEEEEEEEB-STTSHHHHHHHHHHHHH CS
                   Glyco_transf_20 262 sekvkelkerfenkkklilgvDrlDyikGvkqkllaferfLeeypelrgkvvlvqiavpsredveeyqelekeveel 338
                                        +k+  +k + e+  ++i++ DrlDy+kG+ q+ +a e++L+ ++ l+gk v++  ++psr+ ++ey e+++++e  
  gi|518652873|ref|YP_008142393.1| 236 -SKTMAIKPKKEK-ASIIFSIDRLDYTKGLLQRVKAIEKILSYRKDLIGKLVYLMNVTPSRTGIPEYDEIKEQLEME 310
                                       .356778888877.59************************************************************* PP

                                       HHHHHHHH-BTTB-SEEEEES---HHHHHHHHHH-SEEEE--SSBSS-CHHHHHHHCSTTT--EEEEETTBGGGGT- CS
                   Glyco_transf_20 339 vgrINgefgtldytPvvylersldfeeliallaaadvllvtslRdGmnlvakeyvvcqqekkgvLiLSeFaGaaqsL 415
                                       vgr+Ng ++t +++P++y++r+++++ l++l+a++d++l+t+l dG+nlv+ke+v++ ++  gvLiLS+FaGaa+ +
  gi|518652873|ref|YP_008142393.1| 311 VGRVNGLYSTTSWVPIIYIYRKISQKYLVSLYARSDIALITPLMDGLNLVSKEFVATTDK--GVLILSKFAGAAEYM 385
                                       ********************************************************9887..**************9 PP

                                       TTTSEEE-TT-HHHHHHHHHHHHC--HHHHHHHHHHHHHHHHHT-HHHHHHHHHHHH CS
                   Glyco_transf_20 416 kdaailvNPwdieevaeaikeaLkmseeerkkrekkllkqvskhdvqsWaesflsel 472
                                         +a++vNP +i+e+a+ai +a++m+ ee+ +r k++ k+v  ++++ W + +l+ +
  gi|518652873|ref|YP_008142393.1| 386 D-GALIVNPNNINELASAIVRAMEMDGEEKMSRLKRMKKDVYVKNSNWWYKRILTTA 441
                                       9.88**********************************************9988765 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 !    9.5   0.1   0.00015      0.67       7      41 ..     240     274 ..     236     283 .. 0.87
   2 !    7.0   0.0   0.00085       3.8      77     167 ..     329     420 ..     326     425 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00015
                                       HHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCC CS
                   Glycos_transf_1   7 kklgknekkkiilsvgrlekeKgvdllikafallk 41 
                                       + ++k+ek  ii+s+ rl+++Kg+ + +ka++++ 
  gi|518652873|ref|YP_008142393.1| 240 AIKPKKEKASIIFSIDRLDYTKGLLQRVKAIEKIL 274
                                       667899*************************9986 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.00085
                                       EEECCHSSSHHHHHHCESEEEEEESSBSS-HHHHH..HHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHH CS
                   Glycos_transf_1  77 flgevsredleellknadifvlpsisEgfGivllE..AmaaglpviasnaggpaevvkdgetGllvkpnnaealaea 151
                                       ++ ++s++ l +l+ ++di++++  ++g+ +v  E  A + +   i s+  g+ae+   g   l+v pnn+ +la a
  gi|518652873|ref|YP_008142393.1| 329 IYRKISQKYLVSLYARSDIALITPLMDGLNLVSKEfvATTDKGVLILSKFAGAAEYMD-GA--LIVNPNNINELASA 402
                                       567788999*************************954555578888999999999975.44..588888******** PP

                                       HHHHHHSH..HHHHHHHH CS
                   Glycos_transf_1 152 irkllede..elrerlge 167
                                       i +++e +  e+  rl++
  gi|518652873|ref|YP_008142393.1| 403 IVRAMEMDgeEKMSRLKR 420
                                       *99999887766666655 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   6.6e-05       0.3      65     133 ..     336     408 ..     248     409 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.6e-05
                                       H.HHHHHHH-SEEEE--..---SHHHHHHHHT..T-EEEE-TGGGTTT--TTSS.EE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  65 d.laellaaadvfvaPs..egfglkllEamaa..glpvVatdvggiaevvgeng.llvppgdpealaeailrLle 133
                                       + l +l+a++d+++++    g++l+  E  a   +   + ++ +g+ae++  +g l+v+p++ ++la ai+r +e
  gi|518652873|ref|YP_008142393.1| 336 KyLVSLYARSDIALITPlmDGLNLVSKEFVATtdKGVLILSKFAGAAEYM--DGaLIVNPNNINELASAIVRAME 408
                                       258899******96654499*******99997433456666777989966..443888*************9875 PP

>> DUF3755  Protein of unknown function (DUF3755)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.1   0.00019      0.85      10      18 ..      98     106 ..      97     107 .. 0.94
   2 ?   -1.6   0.1       0.5   2.2e+03       2       8 ..     125     131 ..     124     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00019
                           DUF3755  10 LFcqtRdNI 18 
                                       LF+++R+NI
  gi|518652873|ref|YP_008142393.1|  98 LFHYFRNNI 106
                                       9*******9 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.5
                           DUF3755   2 fklqeNi 8  
                                        k+ eNi
  gi|518652873|ref|YP_008142393.1| 125 KKIKENI 131
                                       699***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 3210.49
//
Query:       gi|518652874|ref|YP_008142394.1|  [L=243]
Description: trehalose-phosphatase [Ferroplasma acidarmanus fer1]
Scores for 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-21   74.2   0.0    9.9e-21   73.9   0.0    1.1  1  Trehalose_PPase  Trehalose-phosphatase
    1.2e-05   25.2   1.1    0.00038   20.3   0.3    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.12   11.8   0.0       0.36   10.3   0.0    1.7  2  S6PP             Sucrose-6F-phosphate phosphohydrolase


Domain annotation for each model (and alignments):
>> Trehalose_PPase  Trehalose-phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.9   0.0   1.7e-24   9.9e-21       1     199 [.      22     206 ..      22     222 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.9 bits;  conditional E-value: 1.7e-24
                                       EEETBTTTB---SSGGG--B-TTHHHHHHHHHTTS-..EEEE-SS-HHHHHHHH---SSEEEEGGGTEEE-TT--EE CS
                   Trehalose_PPase   1 flDydGTlspivedpdaavpssellslLkkLasdpknvvaivSGrslkeeellvkvpelglaaeHGaeirspsgedw 77 
                                       flDydGTl+pi+++p+    + +ll+l+++L s+++  ++iv+Gr++++  ++ + ++  +++ HG+     ++ + 
  gi|518652874|ref|YP_008142394.1|  22 FLDYDGTLVPIIKNPEINQADYDLLKLISHLDSRFE--MYIVTGREVSDIIRFLGEYN--IIGLHGSIFHIDGQ-TI 93 
                                       8***********************************..***************77776..69****98887777.44 PP

                                       E-HHHHTTHHHHHHHHHHHHHHHTTSTT-EEEEETTEEEEE-TT--TT..THHHHHHHHHHHHHHH.--EEEE-SSE CS
                   Trehalose_PPase  78 enqaevedlewlkevkeileektertpGsyiEekkfalsvHyrnaddeelqakelaehlesvltdkpdlevtqgkkv 154
                                       +  + +  +e ++++ +   +  e++ G  i +k  ++ +H  n +++  + +e   + ++ l   +++e+++g ++
  gi|518652874|ref|YP_008142394.1|  94 NIPEFAPYVELFNQIYQNTVYIQEKFHGLRIYNKTGSILFHMGNIKNQ--RSRETVHKIINFLAFRYNIELYTGIDI 168
                                       44455566788899999999999*************************..*************************** PP

                                       EEEE-S---HHHHHHHHHHTS--------EEEEEE-SSTTHHHHT CS
                   Trehalose_PPase 155 vevrpqgvsKGkaverlleslgsadseddfvlciGDdrtDedmFs 199
                                       +e+r    +KG a++++ + ++ a       + iGDdrtDed F 
  gi|518652874|ref|YP_008142394.1| 169 IELRIPHINKGTAIKQIRNLNRPA-------IIIGDDRTDEDSFI 206
                                       *****************8887776.......99*********995 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.3   6.3e-08   0.00038       1     111 [.      21     135 ..      21     162 .. 0.67
   2 ?    3.0   0.0     0.012        71     177     212 ..     167     198 ..     163     203 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.3e-08
                                       EEEEIIIIIS-..TTS---HHHHHHHHHHHH..TTSEEEEE-SS-HHHHHHHHHHCCCCSEEEEGGGTEEECTTTEE CS
                       Hydrolase_3   1 ialDlDGTLln..sdkkisektkeaikklke..kgikvviATGRslravlpvleelgldlpvialNGaliddekgki 73 
                                       ++lD DGTL+   ++ +i++   + +k ++     ++  i TGR++++++++l e++    +i+l+G++  + +g++
  gi|518652874|ref|YP_008142394.1|  21 LFLDYDGTLVPiiKNPEINQADYDLLKLISHldSRFEMYIVTGREVSDIIRFLGEYN----IIGLHGSIF-HIDGQT 92 
                                       689******88779999999999999988874467888****************999....889999998.888888 PP

                                       EEE--B-.....HHHHHHHHHHHHHTTCEEEEEESSEEEESTT CS
                       Hydrolase_3  74 lykstis.....kedvkeiikllkennveillytedkvyvlnk 111
                                       +   ++       +++ +   +++e+ + + +y++ + +  ++
  gi|518652874|ref|YP_008142394.1|  93 INIPEFApyvelFNQIYQNTVYIQEKFHGLRIYNKTGSILFHM 135
                                       8555555342222222222234444445555555544444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.012
                                       TEEEEEETT-SHHHHHHHHHHHCT--GGGEEEEESS CS
                       Hydrolase_3 177 gyleimpkgvsKgtalkklakelnisleeviafGDg 212
                                        ++e+  ++++Kgta+k++ + ln      i +GD+
  gi|518652874|ref|YP_008142394.1| 167 DIIELRIPHINKGTAIKQIRN-LN---RPAIIIGDD 198
                                       68999999*********9983.22...234556665 PP

>> S6PP  Sucrose-6F-phosphate phosphohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   6.1e-05      0.36       5      59 ..      21      79 ..      18     111 .. 0.90
   2 ?   -1.6   0.0      0.25   1.5e+03     184     206 ..     192     214 ..     173     220 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.1e-05
                                      EEE-TBTTTB......S-HHHHHHHHHHHH.GGGGGEEEEEE-SS-HHHHHHHHHHHT-- CS
                              S6PP  5 lvsdLDntlv.....dgdnealarlnelleaeerkdvllvfaTGRsldsakellkeknll 59
                                      l  d D+tlv     ++ n+a  +l +l++ + ++++ + ++TGR++++  + l e+n++
  gi|518652874|ref|YP_008142394.1| 21 LFLDYDGTLVpiiknPEINQADYDLLKLIS-HLDSRFEMYIVTGREVSDIIRFLGEYNII 79
                                      67899******9997667888889999999.89999*******************99986 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.25
                                       EEEEE-SGGGHHHHTSSSEEEE- CS
                              S6PP 184 ilvcGdsgnDeellignvlgVvV 206
                                        ++ Gd   De+ +i+n  ++ +
  gi|518652874|ref|YP_008142394.1| 192 AIIIGDDRTDEDSFIANQDAITI 214
                                       57889999999999998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1618.22
//
Query:       gi|518652875|ref|YP_008142395.1|  [L=266]
Description: nucleoside-diphosphate-sugar epimerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   37.4   0.0    1.9e-09   37.0   0.0    1.1  1  RmlD_sub_bind  RmlD substrate binding 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 !   37.0   0.0   1.1e-13   1.9e-09     114     229 ..     105     214 ..      85     228 .. 0.89

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 1.1e-13
                                       -TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHH CS
                     RmlD_sub_bind 114 eeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakereelkvvaDqlgsPTsardlA 190
                                       +e+++t P + YG++Kl+ E+  +  ++++li+R +  yg+   n  + +l   +++ ++k+ +D + +P    dl+
  gi|518652875|ref|YP_008142395.1| 105 NEESATIPETEYGKAKLKAEELAK-GNEHYLIIRRGMTYGKCTYNIYTDILAAIRSKMPIKLNNDIIINPVLNSDLS 180
                                       68899***************9765.8999************************************************ PP

                                       HHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHH CS
                     RmlD_sub_bind 191 evllqllekaaeekelagvyHlanegetswlefArailk 229
                                         + ++++ + +     g+  +a+e++++ +ef+r+   
  gi|518652875|ref|YP_008142395.1| 181 IGVYKAMRDMDR-----GIINIAGEETMTLYEFGRKLYY 214
                                       *********997.....****************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1778.57
//
Query:       gi|518652876|ref|YP_008142396.1|  [L=402]
Description: hypothetical protein FACI_IFERC00001G1515 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-24   86.3  49.5    2.2e-14   53.2  23.9    2.2  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.34   10.9   6.1        1.3    9.0   1.9    3.1  2  DUF3290   Protein of unknown function (DUF3290)


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 !   53.2  23.9   2.4e-18   2.2e-14       1     259 [.      15     252 ..      15     262 .. 0.76
   2 !   38.9  17.6   5.4e-14   4.9e-10      64     168 ..     268     373 ..     262     400 .. 0.87

  Alignments for each domain:
  == domain 1  score: 53.2 bits;  conditional E-value: 2.4e-18
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltl.yalgaavaslplGrlsdrfGrrrvlllglllfalgl 76 
                                       l++++f + ++ +++++++pl+ + dlg+s  ++g++ ++ y +++ v+ ++  r+  r+ rr +++ + ++ +++ 
  gi|518652876|ref|YP_008142396.1|  15 LMIMTFSMRATNNMIITTVPLLAKIDLGFSSFFVGIISAViYLFTFTVTFYVNPRINARL-RRQLFIGANFAILFS- 89 
                                       57899999************9999************999956667777777779999999.999999999999999. PP

                             MFS_1  77 llll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWr 151
                                       l++  f++    +++   +l+Gl++g+++p+ ++  + +  ++er r i+l+s+g sl+ ilgp +  ++++ +++r
  gi|518652876|ref|YP_008142396.1|  90 LIAYyFTN--GiAIWGISALAGLAYGIMMPNLITSSTLLKDQKERERLISLYSVGLSLSLILGPTIEDYILTFVSYR 164
                                       77775643..44699************************************************************** PP

                             MFS_1 152 avfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsgllt 228
                                        vf+++ ++ + +++   +  + + p  k+++ +                 +++d    + l+++ +  + f++l++
  gi|518652876|ref|YP_008142396.1| 165 DVFLLFIPIVIAGVI---VSTMIKFPHTKNETRANV---------------MKNDGLR-ASLLTITTYNIPFAALSI 222
                                       ***********9966...344444444444433333...............2222211.133333333347777888 PP

                             MFS_1 229 llplylqevlgls.glllaglllallalvgai 259
                                       +l+ly+  +++ s ++ ++   +  ++ +++ 
  gi|518652876|ref|YP_008142396.1| 223 FLTLYAIARFHVSgAVAYSP--YIYFFSISFL 252
                                       88888888888885333333..3333333333 PP

  == domain 2  score: 38.9 bits;  conditional E-value: 5.4e-14
                             MFS_1  64 vlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpl 139
                                        ll+++ +++++ l+++ f ++++ +l+l +l G+  g++fp++ ++ia+ ++ e+r+ a+++++a +++ +++ pl
  gi|518652876|ref|YP_008142396.1| 268 PLLFSIMITGFA-LIMFpFLTTFTSFLLLMMLLGIPHGSIFPMSTIMIARGTSVEQRSAANSYFMAYNNILFMVIPL 343
                                       789999999999.777766578779**************************************************** PP

                             MFS_1 140 lggllasslgWravfyilaivsllafv.lf 168
                                       + g+++  +g++++f+il +  +l++v lf
  gi|518652876|ref|YP_008142396.1| 344 AFGYIVKFIGYEYSFLILIAPVILSAVaLF 373
                                       *************************99333 PP

>> DUF3290  Protein of unknown function (DUF3290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   1.9   0.00014       1.3      18      62 ..      46      91 ..      41      97 .. 0.83
   2 ?    2.0   0.1     0.021   1.9e+02       6      45 ..     155     194 ..     153     198 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00014
                           DUF3290 18 lryililvlllllivvlilylrnrldtkyR.dLsiilllllllllg 62
                                      + +++i +++ l+ +++++y+  r++ + R  L i + + +l+ l 
  gi|518652876|ref|YP_008142396.1| 46 FFVGIISAVIYLFTFTVTFYVNPRINARLRrQLFIGANFAILFSLI 91
                                      56789***********************963788888888877654 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.021
                           DUF3290   6 dYlqsqqslndllryililvlllllivvlilylrnrldtk 45 
                                       dY+ +  s  d++ +++ +v++ +++ ++i++ + + +t+
  gi|518652876|ref|YP_008142396.1| 155 DYILTFVSYRDVFLLFIPIVIAGVIVSTMIKFPHTKNETR 194
                                       6888889999999999999************999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       972  (0.0542138); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.33s 00:00:00.93 Elapsed: 00:00:00.50
# Mc/sec: 2435.34
//
Query:       gi|518652877|ref|YP_008142397.1|  [L=783]
Description: hypothetical protein FACI_IFERC00001G1516 [Ferroplasma acidarmanus fer1]
Scores for complete 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-49  166.4   2.1    4.7e-49  166.4   2.1    3.6  4  E1-E2_ATPase     E1-E2 ATPase
    2.8e-27   96.4   0.0    4.2e-27   95.8   0.0    1.3  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.2e-13   50.6   0.0    4.8e-13   48.6   0.0    2.1  2  Cation_ATPase_N  Cation transporter/ATPase, N-terminus
    1.1e-05   25.4   1.1     0.0001   22.2   0.1    2.6  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.014   15.5   0.0       0.12   12.5   0.0    2.3  2  Cation_ATPase    Cation transport ATPase (P-type)
       0.08   13.1   0.1       0.24   11.6   0.1    1.8  1  FMP23            Found in mitochondrial proteome


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       0.2     6e+02     108     143 ..      44      75 ..      36      91 .. 0.58
   2 !  166.4   2.1   1.6e-52   4.7e-49       3     181 .]     110     287 ..     108     287 .. 0.98
   3 ?   -0.4   3.0      0.24   7.3e+02      83     156 ..     565     639 ..     550     644 .. 0.55
   4 ?   -3.0   0.5       1.5   4.4e+03     146     166 ..     738     758 ..     724     767 .. 0.69

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.2
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSS CS
                      E1-E2_ATPase 108 ktplqkkldklgkvlvpvvlliallvflialllgks 143
                                       ++     + k+ k +++ + +++ l+++i+++lgk 
  gi|518652877|ref|YP_008142397.1|  44 ES----SILKFLKKFWTPISWMLELTIIITFILGKY 75 
                                       44....455555666666666666666665555554 PP

  == domain 2  score: 166.4 bits;  conditional E-value: 1.6e-52
                                       S--EEEEE-TTS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE- CS
                      E1-E2_ATPase   3 lpptakvirdgteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsg 79 
                                       l+++a+v+rdg++  i++k lvpGDiv l+ gd+vpaD++i++ + e+d+saLTGEsl v+++kgd+++s++vv++g
  gi|518652877|ref|YP_008142397.1| 110 LSAQARVLRDGKWNVIETKFLVPGDIVHLRLGDVVPADIKIIDDELEIDQSALTGESLSVTRKKGDTIYSSSVVKRG 186
                                       5789************************************************************************* PP

                                       EEEEEEEE-TTTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHH CS
                      E1-E2_ATPase  80 eakavVtatgedtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallv 156
                                       e+++ Vt+tg++t++gk ++lve a ++k+++++ + k++k l+++ ++++++++l+ +++g +++e + +al++l+
  gi|518652877|ref|YP_008142397.1| 187 ECNGLVTETGSKTYFGKTTELVEIA-KTKSHIEELIMKIIKDLIAIDTILVIALILFSIYRGVDITEVIPFALVILI 262
                                       *************************.9************************************************** PP

                                       HHS-TTHHHHHHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 157 aaiPcaLplavplalalgarrlakk 181
                                       a+iP aLp+++++a++lga  ++k+
  gi|518652877|ref|YP_008142397.1| 263 ASIPVALPATFTIAMSLGALHMSKR 287
                                       **********************986 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.24
                                       EEEEE-TTTSTTTTTSTTS----.----HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTT.HHHHHHHHHHH CS
                      E1-E2_ATPase  83 avVtatgedtelgkiarlveeak.skktplqkkldklgkvlvpvvlliallvflialllgksla.eallralallv 156
                                       a +  +  ++ l  i++ +++ +   +  l+  l+k++kv+  +v++++l +f++ ++++       l++a ++++
  gi|518652877|ref|YP_008142397.1| 565 ASASVVLTHSGLTDIVDGIKSGRrIYQRMLTYTLNKIIKVIQ-IVFFLTLSFFVVGFFVTTAFDvILLIFANDFVT 639
                                       444555556666666666666663344455566677776654.455555555666655555444333444444444 PP

  == domain 4  score: -3.0 bits;  conditional E-value: 1.5
                                       HHHHHHHHHHHHHS-TTHHHH CS
                      E1-E2_ATPase 146 eallralallvaaiPcaLpla 166
                                        ++++  ++lv aiP  ++l+
  gi|518652877|ref|YP_008142397.1| 738 ISFISYYGILVTAIPLKFILI 758
                                       456667778888888777554 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.8   0.0   1.4e-30   4.2e-27       1     209 [.     303     550 ..     303     551 .. 0.80

  Alignments for each domain:
  == domain 1  score: 95.8 bits;  conditional E-value: 1.4e-30
                                       SSEEEEESBTTTBCHHHHHHHHHHHH....CHHHHHHHHHH....HHCHHHHHHHHHHHHH........HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx....xxxxxxxxxxxxxxxx........xxxxxxxx RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsa....alalaaaletg....sehpigkalvaaakar........sgaltgfa 61 
                                       ++t+++Dk+GT+t+ +  +++    +    +l+l +   ++    se pi  a+  +a+          +   ++f+
  gi|518652877|ref|YP_008142397.1| 303 MDTLCMDKTGTITENKLTIKTPK--VytgdELSLIKYASYAsqrkSEDPIDDAILDYADLKsvkidyanR---SKFT 374
                                       79***********8883333322..23344667777667778899*********9999999444443331...2222 PP

                                       HETTTE.................HHHHTHHHHHHHH..HCHHHHHHHHHHHHHHCHHHHHH.....TTHHHHHHHHH CS
                                       xxxxxx.................xxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxx RF
                         Hydrolase  62 tfigrg.................ayaigkpewltal..dippdlgaaigsaqsqgrtvall.....qaralavftia 114
                                           +                  ++ +g p+ + +l  ++p+ ++++i    sqg   + +     + ++l+v+ + 
  gi|518652877|ref|YP_008142397.1| 375 P---FDpsikrteaiineagksvKIVKGAPQVISELtgNVPETYENDIKYFSSQGFRIISVaagtdKLEILGVIPLY 448
                                       2...223345556777777899***************************************7777666********* PP

                                       HTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.......GGGESEEEEHHCES.......STTTSHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxx.......xxxxxxx RF
                         Hydrolase 115 dplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.......ddyfdaviasdiet.......vakpspe 177
                                       dp  ++++ ++++ +Lk+  +  v++tgdn+  ae++a ++G       +     +i +   +       +a++ pe
  gi|518652877|ref|YP_008142397.1| 449 DP--PRKDSRDLITELKQLSVSPVMITGDNSLIAEEVAGEIGlekklcnA----ENIKGNY-AgasdcsvFAEVFPE 518
                                       **..**************************************96433331....2233333.24777789******* PP

                                       HHHHHHHHHTSTGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 178 gkvaaireLqgkpeevamVGDgvnDaaalaaA 209
                                       +k ++++ Lq +++ v m GDgvnD++al++A
  gi|518652877|ref|YP_008142397.1| 519 DKYYIVKALQKSGHIVGMTGDGVNDSPALKQA 550
                                       **********99999***************99 PP

>> Cation_ATPase_N  Cation transporter/ATPase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.6e-16   4.8e-13       3      68 ..       5      68 ..       3      69 .. 0.93
   2 ?   -2.6   0.0       1.5   4.5e+03      10      38 ..     571     601 ..     564     611 .. 0.75

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.6e-16
                   Cation_ATPase_N  3 alsleevlekLetdlenGLtqaeaaerlkkyGpNelkekkkkslwvkllkqftnplvilLlvaalv 68
                                      + sle++++kL+ +++ GL+  ea  rl +yG Ne+  +kk+s + k+lk+f+ p+ ++L+   ++
  gi|518652877|ref|YP_008142397.1|  5 SDSLEDLFKKLN-TSKAGLSGNEASSRLHTYGYNEV-SEKKESSILKFLKKFWTPISWMLELTIII 68
                                      679********9.9**********************.999999999**************987776 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.5
                   Cation_ATPase_N  10 lekLe.tdlenGLtq.aeaaerlkkyGpNel 38 
                                       l++ + td  +G+++   + +r  +y  N++
  gi|518652877|ref|YP_008142397.1| 571 LTHSGlTDIVDGIKSgRRIYQRMLTYTLNKI 601
                                       5555557888888666889999999999987 PP

>> Hydrolase_3  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.1      0.13   3.8e+02     122     189 ..     371     439 ..     322     443 .. 0.73
   2 !   22.2   0.1   3.4e-08    0.0001     195     245 ..     523     573 ..     519     578 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.13
                                       HCHCTCEEEESHHHHHCHCSESEEE..EES-HHHHHHHHHHHHHHCTTTEEEEEESTTEEEEEETT-SHH CS
                       Hydrolase_3 122 ektkkkkeeidseeeledeeiakil..ilkdkekldelekelksklnklltitssskgyleimpkgvsKg 189
                                        k++ ++++i+  e + + e+ k +  +   ++ ++el  ++++ ++++++++ss+++ +  +++g++K 
  gi|518652877|ref|YP_008142397.1| 371 SKFTPFDPSIKRTEAIIN-EAGKSVkiVKGAPQVISELTGNVPETYENDIKYFSSQGFRIISVAAGTDKL 439
                                       333344444444444444.44444456888999999**************99999999998888888886 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 3.4e-08
                                       HHHHCT--GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEEE-- CS
                       Hydrolase_3 195 lakelnisleeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyvtks 245
                                       ++k l+ s   v   GDg ND + L++a++gvA+++a++ +k+ A+ v ++
  gi|518652877|ref|YP_008142397.1| 523 IVKALQKSGHIVGMTGDGVNDSPALKQAEFGVAVASATDVAKASASVVLTH 573
                                       556666677777788*******************************99876 PP

>> Cation_ATPase  Cation transport ATPase (P-type)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.39   1.2e+03      18      35 ..      37      54 ..      17      84 .. 0.80
   2 ?   12.5   0.0   3.9e-05      0.12      13      86 ..     339     406 ..     312     411 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.39
                     Cation_ATPase 18 kllGnktEsALlvlaekl 35
                                      + + +k Es++l++ +k+
  gi|518652877|ref|YP_008142397.1| 37 NEVSEKKESSILKFLKKF 54
                                      5678999********998 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.9e-05
                     Cation_ATPase  13 ekdevkllGnktEsALlvlaeklgldteelreetkkvqeipFnssrKrmsvvlklepekkvrlyvKGApeiilk 86 
                                       +++ + ++ ++ + A+l +a+ ++ +++ ++    + +  pF+ s Kr   ++++   +k + +vKGAp++i +
  gi|518652877|ref|YP_008142397.1| 339 SYASQRKSEDPIDDAILDYADLKSVKIDYAN----RSKFTPFDPSIKRTEAIINE--AGKSVKIVKGAPQVISE 406
                                       5566667778888888888888866555554....45789**************5..5999**********987 PP

>> FMP23  Found in mitochondrial proteome
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     8e-05      0.24     104     141 ..     667     704 ..     634     714 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8e-05
                             FMP23 104 slsdklvieryldfikgvkltlrlnGGhtfifdvllqa 141
                                        l+  lv+e ++ +  g+   lr+   htfifd+l+ +
  gi|518652877|ref|YP_008142397.1| 667 ILAAFLVVESFIFLYIGLYAGLRISQIHTFIFDMLVFS 704
                                       467789****************************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (783 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.46
# Mc/sec: 5095.51
//
Query:       gi|518652878|ref|YP_008142398.1|  [L=193]
Description: isochorismatase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.3e-40  138.6   0.0    2.6e-40  138.5   0.0    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
       0.09   12.5   0.0       0.26   11.0   0.0    1.7  2  4HPAD_g_N        4-Hydroxyphenylacetate decarboxylase subunit


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 !  138.5   0.0   2.9e-44   2.6e-40       1     173 [.      12     186 ..      12     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 2.9e-44
                   Isochorismatase   1 talvviDmqndfv.eegvkeseeisavveninkllkaarkagipviftrdvhe.leevkgdlderkaaphfkpgttg 75 
                                       talvviD+q++++ ++ +    +++ v++n+++l++++rk+++pv+ +  v++   + +  +d+  +++  +  +  
  gi|518652878|ref|YP_008142398.1|  12 TALVVIDLQKGIAsMGRNLVPYDANTVIKNASELAESFRKNDMPVFLVHVVPDkRAMLNVLADDSAWSGPAEMPPDF 88 
                                       8************99999999********************************98888899999999999999999* PP

                   Isochorismatase  76 aelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaals 152
                                       +++vpel p+ +dvv+ K++++af+gtdl+  L++ giktivl+Gi+t  +Ve+tar a++ G++ + ++DA+ a++
  gi|518652878|ref|YP_008142398.1|  89 SDIVPELGPRDNDVVISKKQWGAFYGTDLELRLRRGGIKTIVLCGISTTHGVESTARFAYEMGFQQIFAEDAMTAMT 165
                                       ***************************************************************************** PP

                   Isochorismatase 153 pelhdaalkrlkqafatvitt 173
                                       +e h+  +++++++++ v +t
  gi|518652878|ref|YP_008142398.1| 166 KEMHESTINNVFKKMGRVRKT 186
                                       **************9999877 PP

>> 4HPAD_g_N  4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   2.9e-05      0.26      12      30 ..      17      35 ..      14      36 .. 0.91
   2 ?   -2.5   0.0       0.5   4.5e+03      18      25 ..     161     168 ..     158     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.9e-05
                         4HPAD_g_N 12 lDceKGiCrltkeivpiDg 30
                                      +D  KGi  + + +vp+D 
  gi|518652878|ref|YP_008142398.1| 17 IDLQKGIASMGRNLVPYDA 35
                                      89****************6 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.5
                         4HPAD_g_N  18 iCrltkei 25 
                                       + ++tke+
  gi|518652878|ref|YP_008142398.1| 161 MTAMTKEM 168
                                       6789**98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1351.86
//
Query:       gi|518652879|ref|YP_008142399.1|  [L=120]
Description: hypothetical protein FACI_IFERC00001G1518 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.063   14.0   1.3       0.39   11.5   0.5    2.2  2  CsgA           Minor curli fiber component A
      0.065   12.1   3.7      0.066   12.1   3.7    1.0  1  VPS38          Vacuolar protein sorting 38
      0.069   13.1   3.3      0.099   12.6   1.7    2.1  2  Rho_N          Rho termination factor, N-terminal domain
      0.079   12.2   0.3       0.11   11.7   0.3    1.5  1  tRNA-synt_His  Histidyl-tRNA synthetase


Domain annotation for each model (and alignments):
>> CsgA  Minor curli fiber component A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.5   8.8e-05      0.39      23      58 ..      41      76 ..      29      86 .. 0.90
   2 ?    1.3   0.0      0.13   5.9e+02      16      48 ..      89     120 .]      82     120 .] 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.8e-05
                              CsgA 23 keiykkleekeykseeefvkdLseeEiefLnkiLee 58
                                      k +  k++ + y++ee++ ++L+++ i+ L +i++e
  gi|518652879|ref|YP_008142399.1| 41 KPVAMKIDLSGYDTEEKLYNALKKKNIKELKSIIKE 76
                                      5688899**************************987 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.13
                              CsgA  16 teesevgkeiykkleekeykseeefvkdLseeE 48 
                                       t +s+  k i+k+++ ++y++ ++f +++ e+E
  gi|518652879|ref|YP_008142399.1|  89 TTRSDLIKFIIKRVN-DRYHKGDSFSRSMPEKE 120
                                       566677777888875.57899999999998887 PP

>> VPS38  Vacuolar protein sorting 38
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   3.7   1.5e-05     0.066     177     257 ..       6      85 ..       1     114 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
                                       --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHS--S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH....H CS
                             VPS38 177 slLKLnklleYtsqveeElqeisekveelikseekkelwslkelqkaieqlkksiekkklklkrLessleee....n 249
                                       +++ L+ +l Y+++  eE+  i+e++  ++k ++ k + ++  l+ +  + k  +  kk ++k+L+s ++e+    +
  gi|518652879|ref|YP_008142399.1|   6 KAVALSDILRYMADKIEETPDIAENLKIDVKLKQDKPVAMKIDLSGYDTEEKLYNALKKKNIKELKSIIKENklgkD 82 
                                       6778999*****************************************9999999999*********9998643332 PP

                                       HHHHHH-- CS
                             VPS38 250 skteesse 257
                                       s     s+
  gi|518652879|ref|YP_008142399.1|  83 S-----ST 85 
                                       2.....22 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.53   2.4e+03      12      19 ..      26      33 ..      20      36 .. 0.84
   2 ?   12.6   1.7   2.2e-05     0.099       2      37 ..      62     101 ..      61     105 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.53
                                      HHHHHTT- CS
                             Rho_N 12 aiAkelgi 19
                                      +iA+ l+i
  gi|518652879|ref|YP_008142399.1| 26 DIAENLKI 33
                                      79999998 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.2e-05
                                       HHHS-HHHHHHHHHHTT-.T..TGGGS.-HHHHHHHHHHG CS
                             Rho_N   2 LkektlseLraiAkelgi.e..nysrl.RKqdLIfaIlka 37 
                                       Lk+k+++eL+ i ke ++ +   +s+l +++dLI +I+k+
  gi|518652879|ref|YP_008142399.1|  62 LKKKNIKELKSIIKENKLgKdsSTSKLtTRSDLIKFIIKR 101
                                       9*****************878888888459********96 PP

>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.3   2.4e-05      0.11     169     199 ..      53      83 ..       3     108 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 2.4e-05
                                       HHHHHHHHHHHCT-HHHHHHHHHCCTTHHHC CS
                     tRNA-synt_His 169 sleeallaalarkdlaelkelaaeaglkeal 199
                                       ++ee+l++al++k+++elk++++e++l ++ 
  gi|518652879|ref|YP_008142399.1|  53 DTEEKLYNALKKKNIKELKSIIKENKLGKDS 83 
                                       6799********************9998664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1316  (0.0734006); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); 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 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 905.93
//
Query:       gi|518652880|ref|YP_008142400.1|  [L=285]
Description: hypothetical protein FACI_IFERC00001G1519 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      1e-47  162.3   1.7    1.4e-47  161.9   1.7    1.2  1  AAA_31       AAA domain
    7.5e-16   58.4   0.0    9.7e-16   58.0   0.0    1.1  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    8.5e-07   28.7   0.0     0.0035   16.8   0.0    2.2  2  ParA         NUBPL iron-transfer P-loop NTPase
    1.2e-05   24.9   0.1    3.4e-05   23.4   0.1    1.7  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
    2.5e-05   23.6   0.4    0.00017   20.9   0.4    2.0  1  ArsA_ATPase  Anion-transporting ATPase
    3.8e-05   23.1   0.0      0.047   13.0   0.0    2.2  2  MipZ         ATPase MipZ
    0.00064   19.3   0.0       0.57    9.6   0.0    2.3  2  CBP_BcsQ     Cellulose biosynthesis protein BcsQ


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 !  161.9   1.7   5.6e-51   1.4e-47       2     172 ..       3     198 ..       2     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 161.9 bits;  conditional E-value: 5.6e-51
                            AAA_31   2 kvIaianqKGGvGKTTtsvnlaaala.klgkkvLlvDlDpQanatt.....glgiekneiektlyev........l. 63 
                                       ++I+i+n KGGvGKT ts++++++la ++ kkvL++DlDpQ+nat+     +l +e++++ +t++++          
  gi|518652880|ref|YP_008142400.1|   3 HIISIINLKGGVGKTQTSIAVSEFLAtNYAKKVLIIDLDPQTNATVslmdeNLWLEHDKKGNTIFQLfsdkvyntEl 79 
                                       79************************999*****************5555533344444555666663333333223 PP

                            AAA_31  64 ..ieeknikeaii.ktkvenldlipssidLaeaeielvelekk.......eeilkellekvkdeYDyiiiDcpPsLg 130
                                         +e++ +k++ +  + ++nldl+pss+ L++++++l  ++++        +ilke+++++ ++YDy+iiDcpP+Lg
  gi|518652880|ref|YP_008142400.1|  80 fnVESSIVKNVSNiGSGIKNLDLLPSSLRLIDIQDKLPLVSNSgyfvrtpITILKEAVSSIIKNYDYVIIDCPPNLG 156
                                       32244444444331345899******************999998888776677************************ PP

                            AAA_31 131 lltenaLvasdsviipvqaeayaleGleqllktieevkkkln 172
                                       l+t +++++sd+++ip+ ++ ++++G++q+l++i+ +k++  
  gi|518652880|ref|YP_008142400.1| 157 LITLSGIFISDYYLIPTIPDILSTYGIPQILTRINAFKEDAG 198
                                       *************************************99854 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.0   0.0   3.8e-19   9.7e-16       1     127 [.       5     257 ..       5     258 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.0 bits;  conditional E-value: 3.8e-19
                                       EEEEESSTTSSHHHHHHHHHHHHHH.TT--EEEEEEEESSCCCCHHTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralar.rglrVllvDaDpqannlaileglendiep...................... 54 
                                       i+i++ kGGvGKT ++++    la    ++Vl +D+Dpq+n++     + +d++                       
  gi|518652880|ref|YP_008142400.1|   5 ISIINLKGGVGKTQTSIAVSEFLATnYAKKVLIIDLDPQTNATV----SLMDENLwlehdkkgntifqlfsdkvynt 77 
                                       789*********************9679***********99998....44444445555666799999********* PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                              CbiA  55 ............................................................................. 54 
                                                                                                                    
  gi|518652880|ref|YP_008142400.1|  78 elfnvessivknvsnigsgiknldllpsslrlidiqdklplvsnsgyfvrtpitilkeavssiiknydyviidcppn 154
                                       ***************************************************************************** PP

                                       ...........................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC CS
                                       ...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  55 ...........................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry 104
                                                                  ++ ++l  ++a+++    ++k++g+++ +++ +  ++l+k+ ++ lk+r 
  gi|518652880|ref|YP_008142400.1| 155 lglitlsgifisdyyliptipdilstyGIPQILTRINAFKEDAGINIKPLGILISMFRAN--NRLHKSIIDSLKYRE 229
                                       ************************************9999998888************99..788888888887666 PP

                                       ....TS-EEE.EEE--CCHCCCCHHTS- CS
                                       ....xxxxxx.xxxxxxxxxxxxxxxxx RF
                              CbiA 105 ....gvpvlg.viprdeavaeapargep 127
                                            +++++  ip + +++ea++ + +
  gi|518652880|ref|YP_008142400.1| 230 rrgdYPRIFDtYIPLSIKISEAAEFQSS 257
                                       8888899999************998765 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.4e-06    0.0035       3      41 ..       2      41 ..       1      74 [. 0.87
   2 !   10.1   0.0   0.00015      0.39     110     224 ..     142     257 ..     104     281 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-06
                              ParA  3 kkviavlSgKGGVGKStvavnlAlaLa.kkglkvgllDaD 41
                                      +++i ++  KGGVGK+ +++ ++  La +  +kv ++D+D
  gi|518652880|ref|YP_008142400.1|  2 THIISIINLKGGVGKTQTSIAVSEFLAtNYAKKVLIIDLD 41
                                      799***********************95668899****99 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00015
                              ParA 110 gelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladv....kkaiemfkk..vkvkvlGvveNmsgfvcp 180
                                       ++ Dy+iiD+PP  g ++l+ +  +  +  +i t p  +++  +    ++  ++ ++  +++k lG++  m  f  +
  gi|518652880|ref|YP_008142400.1| 142 KNYDYVIIDCPPNLGLITLSGI--FISDYYLIPTIPDILSTYGIpqilTRINAFKEDagINIKPLGILISM--FRAN 214
                                       678************8777654..44467888888888887544111133333444422444556666444..4444 PP

                              ParA 181 kcgekteifgkgggeklaeelgvpllgeipldpeireasdegkp 224
                                       +   +++i  + + ++   ++   + + ipl+ +i+ea++ +++
  gi|518652880|ref|YP_008142400.1| 215 NRL-HKSIIDSLKYRERRGDYPRIFDTYIPLSIKISEAAEFQSS 257
                                       433.3356666666777777777777777777777777776665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.1   1.3e-08   3.4e-05       7      77 ..      10      89 ..       4      99 .. 0.78
   2 ?   -2.1   0.0       0.8     2e+03      96     122 ..     122     150 ..     117     160 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.3e-08
                         Fer4_NifH  7 GkGGiGksttsqnlsaalaemg.kkvlivGCDPkaDstrlll.......ggkaqetvldtlrekgav.edvkvedvvkk 76
                                       kGG+Gk+ ts  +s  la++  kkvli+  DP++++t  l+       + k+ +t+++++ +k +  e  +ve+ + k
  gi|518652880|ref|YP_008142400.1| 10 LKGGVGKTQTSIAVSEFLATNYaKKVLIIDLDPQTNATVSLMdenlwleHDKKGNTIFQLFSDKVYNtELFNVESSIVK 88
                                      59****************98755***************87773333333567789999999999988677777776665 PP

                         Fer4_NifH 77 G 77
                                       
  gi|518652880|ref|YP_008142400.1| 89 N 89
                                      4 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.8
                         Fer4_NifH  96 aGrgvitaielleel..gayddlDfvlyD 122
                                       +G+ v t i +l+e   ++ +++D+v+ D
  gi|518652880|ref|YP_008142400.1| 122 SGYFVRTPITILKEAvsSIIKNYDYVIID 150
                                       78999999999998622456689999988 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.4   6.6e-08   0.00017       8      47 ..      10      50 ..       3     163 .. 0.59

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.6e-08
                                      ESTTSSHHHHHHHHHHHHHHT.TS-EEEEE-STTTHHHHHH CS
                       ArsA_ATPase  8 GKGGVGKttvsaatavklsek.gkkvllistDPAhslsDsf 47
                                       KGGVGKt  s a++  l+ +  kkvl+i +DP  +   s+
  gi|518652880|ref|YP_008142400.1| 10 LKGGVGKTQTSIAVSEFLATNyAKKVLIIDLDPQTNATVSL 50
                                      59**************999763799********88765444 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   1.8e-05     0.047       1      48 [.       3      51 ..       3      66 .. 0.82
   2 !    7.8   0.0   0.00068       1.7      87     111 ..     131     155 ..      99     178 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.8e-05
                                      EEEEE--SSTTSSHHHHHHHHHHHHHTT.T--EEEEE--TTT-HHHHHH CS
                              MipZ  1 hvivlgnekGGsGksttavhvavaLlkk.Garvaaidldlrqrtlaryl 48
                                      h+i + n kGG Gk+ t++ v   L+++  ++v  idld + ++    +
  gi|518652880|ref|YP_008142400.1|  3 HIISIINLKGGVGKTQTSIAVSEFLATNyAKKVLIIDLDPQTNATVSLM 51
                                      79999*****************9998762678*******8877665555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00068
                                       HHHHHHHHHHHHH-SEEEEE--SS- CS
                              MipZ  87 aeleelvadleaeldfividtPGsd 111
                                       + l+e+v+++ +++d+++id+P + 
  gi|518652880|ref|YP_008142400.1| 131 TILKEAVSSIIKNYDYVIIDCPPNL 155
                                       46899*****************765 PP

>> CBP_BcsQ  Cellulose biosynthesis protein BcsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.0   0.00022      0.57       3      41 ..       4      43 ..       1      55 [. 0.85
   2 !    7.6   0.0   0.00094       2.4     104     148 ..     132     176 ..      99     196 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00022
                          CBP_BcsQ  3 vlalqGvRGGvGttsllaaLawalhe.lgesvlviDlspd 41
                                      ++ +  ++GGvG+t  + a +  l +   ++vl+iDl p+
  gi|518652880|ref|YP_008142400.1|  4 IISIINLKGGVGKTQTSIAVSEFLATnYAKKVLIIDLDPQ 43
                                      6778889**************9997526899*****9986 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00094
                          CBP_BcsQ 104 allaalkelkeqyrwillDlpagasaltrellaladlvllvvepd 148
                                        l++a++++ ++y+++++D+p +   +t + +  +d  l  + pd
  gi|518652880|ref|YP_008142400.1| 132 ILKEAVSSIIKNYDYVIIDCPPNLGLITLSGIFISDYYLIPTIPD 176
                                       5778899999**************999999999999887766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); 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: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2162.83
//
Query:       gi|518652881|ref|YP_008142401.1|  [L=375]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-28  100.1   0.3    2.2e-28   99.1   0.1    1.6  2  DEDD_Tnp_IS110  Transposase
    3.5e-22   78.5   0.0    5.7e-22   77.8   0.0    1.3  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.1   0.1   2.5e-32   2.2e-28       1     155 []       4     159 ..       4     159 .. 0.94
   2 ?   -2.9   0.0       0.6   5.4e+03      46      90 ..     294     338 ..     286     341 .. 0.65

  Alignments for each domain:
  == domain 1  score: 99.1 bits;  conditional E-value: 2.5e-32
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       vGiD+ak+k+d c+id+e +v+++  + n+  g++++l    +k ++++ ++e+tg y+ +l+++l +++++++++n
  gi|518652881|ref|YP_008142401.1|   4 VGIDMAKKKFDYCIIDSELSVIKRGILINNIYGFSEFLRI-IKKYKNIKLGIESTGIYHVNLYTYLINNNCNIILLN 79 
                                       8***********************99999999******99.999********************************* PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllr.drgrlrpl.klddeayaeLrqltrqredlvkertrlknrlralLdq 152
                                       p+ +k l+++ +rk+KtD++DA+ IA++++ + +++ ++ k+++++y++Lr+ +  +  + ++++ +kn+l+  Ld 
  gi|518652881|ref|YP_008142401.1|  80 PMETKLLKSSRIRKNKTDKIDAEAIAKYIIiRKNNIITMeKDTENTYTNLREYVYTYVRINRKIAMAKNQLIRDLDL 156
                                       ****************************987666665552778899****************************999 PP

                    DEDD_Tnp_IS110 153 vfp 155
                                       ++p
  gi|518652881|ref|YP_008142401.1| 157 LYP 159
                                       887 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.6
                    DEDD_Tnp_IS110  46 gevlvvveatghygallvaflleagitvvvvnplavkrlrklylr 90 
                                       g+ ++  +++++  +l+ ++l    i+ +  np++ +++ + ++ 
  gi|518652881|ref|YP_008142401.1| 294 GDYNITSKISKRGNPLIRYALYLSTIPAIKFNPVIKRYYTRKKND 338
                                       555666666666677777777777777777788777777655444 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.8   0.0   6.3e-26   5.7e-22       3      86 ..     249     332 ..     247     333 .. 0.98

  Alignments for each domain:
  == domain 1  score: 77.8 bits;  conditional E-value: 6.3e-26
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                        +++ipGiG++t + +l+ igd+++f+s  +l ay G++pv++qSG+++  ++iskrGn+ +R aLy  ++ ai++n
  gi|518652881|ref|YP_008142401.1| 249 KIKTIPGIGTITGSIILSSIGDINKFDSVLKLRAYSGMDPVVKQSGDYNITSKISKRGNPLIRYALYLSTIPAIKFN 325
                                       589*********************************************99*************************** PP

                    Transposase_20  80 pelrayy 86 
                                       p++++yy
  gi|518652881|ref|YP_008142401.1| 326 PVIKRYY 332
                                       ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1224  (0.0682693); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2821.74
//
Query:       gi|518652882|ref|YP_008142402.1|  [L=261]
Description: 3-oxoacyl-[acyl-carrier-protein] reductase [Ferroplasma acidarmanus fer1]
Scores for complete 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-46  157.3   0.0      6e-46  156.9   0.0    1.1  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    8.8e-38  129.7   0.2      1e-37  129.5   0.2    1.1  1  adh_short        short chain dehydrogenase
    9.7e-07   28.9   0.0    1.3e-06   28.4   0.0    1.3  1  KR               KR domain
     0.0089   16.4   0.1      0.024   15.0   0.0    1.8  2  PsbR             Photosystem II 10 kDa polypeptide PsbR
  ------ inclusion threshold ------
      0.021   15.1   0.1      0.034   14.4   0.1    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.026   14.3   0.8        4.7    7.1   0.1    3.0  2  ACT              ACT domain
      0.058   14.0   0.1       0.11   13.0   0.1    1.5  1  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
      0.065   13.1   0.1       0.12   12.3   0.1    1.3  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
       0.11   12.4   0.0        0.2   11.7   0.0    1.6  1  ADH_zinc_N       Zinc-binding dehydrogenase
       0.14   12.1   0.0       0.22   11.4   0.0    1.3  1  Polysacc_deac_1  Polysaccharide deacetylase


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 !  156.9   0.0   3.4e-49     6e-46       4     233 ..      16     257 ..      12     258 .. 0.93

  Alignments for each domain:
  == domain 1  score: 156.9 bits;  conditional E-value: 3.4e-49
                                       TSHHHHHHHHHHHTT-EEEEEESSGGH.HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   4 sgIGraiAkalaeeGaevvltdlneea.kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnna 77 
                                        gIG+++   la+ Ga++    + +e+ ++  ee+ +e+g +v  + +D ++++++ ++v+ + e++gk+D+lv n 
  gi|518652882|ref|YP_008142402.1|  16 TGIGKGVISVLAKYGANITTFSRTKENvESLKEEIRKETGVTVnaMCADLSKKDDLMRVVDSAHEQYGKIDFLVMNY 92 
                                       7*********************99999899999999999988667******************************** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealt 152
                                       g  +    pf++++++++d  +d+ ++s+++++  ++  ++k++ g+i+ ++s+  +  ++n ++ +  + +++al 
  gi|518652882|ref|YP_008142402.1|  93 GDPRV--DPFMQLNESDWDYNIDMIFKSTIRMVDMCATdMIKSNsGRIIFITSMTTKNPLENFAISNSLRSGVVALG 167
                                       *9999..******************************99888878******************************** PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTT.........HHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGT CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikg.........fdelleelearaplgrlgtpeevaeaalfLasdeas 220
                                       ++l  elg+++i vN++s+g+  T+  ++i +          +e++++l +++plgr+g+peev+++++fL+s ++s
  gi|518652882|ref|YP_008142402.1| 168 KTLSIELGKYNINVNSISQGYFYTRRLENIIKknsvssgkpVEEVESQLMKEIPLGRFGKPEEVGNLVAFLCSGMSS 244
                                       **********************9999777644345555555678999****************************** PP

                                       T--SEEEEESTTG CS
                      adh_short_C2 221 yitGqtlvvDgGl 233
                                       yitG ++ +DgG+
  gi|518652882|ref|YP_008142402.1| 245 YITGINIPIDGGV 257
                                       ************7 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.5   0.2   5.8e-41     1e-37       1     192 [.       7     199 ..       7     202 .. 0.98

  Alignments for each domain:
  == domain 1  score: 129.5 bits;  conditional E-value: 5.8e-41
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklg 76 
                                       k ++v  +s GIG+ +   lak Ga+++ ++r++e++e +++e+++e g ++ a+ +D+++++++ ++v+ a +++g
  gi|518652882|ref|YP_008142402.1|   7 KNAIVCAGSTGIGKGVISVLAKYGANITTFSRTKENVESLKEEIRKEtGVTVNAMCADLSKKDDLMRVVDSAHEQYG 83 
                                       689********************************************9***************************** PP

                                       SESEEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHH CS
                         adh_short  77 kldvLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsK 153
                                       k+d Lv N G  ++ pf +l+e++w+  i++ +++++ ++ ++++ m+k++sGrI++++S+++k+p++++a   +  
  gi|518652882|ref|YP_008142402.1|  84 KIDFLVMNYGDPRVDPFMQLNESDWDYNIDMIFKSTIRMVDMCATDMIKSNSGRIIFITSMTTKNPLENFAISNSLR 160
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCT CS
                         adh_short 154 aavagltrslakelaptgirvnavaPGlvdTdmakelre 192
                                        +v++l ++l+ el +++i+vn++  G++ T   +++ +
  gi|518652882|ref|YP_008142402.1| 161 SGVVALGKTLSIELGKYNINVNSISQGYFYTRRLENIIK 199
                                       *******************************98887765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   7.3e-10   1.3e-06       4     108 ..      10     111 ..       8     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.3e-10
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaee 79 
                                       +++ G  g+G+ ++  la+ ga ++  +sR++++    ++l +e+++  g++v+++ aD+s+kd++ +++++++++ 
  gi|518652882|ref|YP_008142402.1|  10 IVCAGSTGIGKGVISVLAKYGA-NITTFSRTKENV---ESLKEEIRKEtGVTVNAMCADLSKKDDLMRVVDSAHEQY 82 
                                       57778999*************8.79******5444...44555555544**************************** PP

                                       S---EEEE---------TTT--HHHHHHH CS
                                KR  80 ppikGvihaAgvlrdklleemtaedleqv 108
                                       ++i   +   g  r +++++++++d++  
  gi|518652882|ref|YP_008142402.1|  83 GKIDFLVMNYGDPRVDPFMQLNESDWDYN 111
                                       ****9999999999999999999999865 PP

>> PsbR  Photosystem II 10 kDa polypeptide PsbR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.3e-05     0.024      17      52 ..       3      38 ..       1      60 [. 0.90
   2 ?   -2.5   0.0       3.7   6.6e+03      28      52 ..     162     186 ..     156     191 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                              PsbR 17 dlelkegvdasGrkakGkGvyqfvdkyGanvdGysp 52
                                      dl+ k+ +  +G ++ GkGv     kyGan+  +s 
  gi|518652882|ref|YP_008142402.1|  3 DLKNKNAIVCAGSTGIGKGVISVLAKYGANITTFSR 38
                                      688999999**********************99986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.7
                              PsbR  28 GrkakGkGvyqfvdkyGanvdGysp 52 
                                       G +a Gk +     ky  nv+  s 
  gi|518652882|ref|YP_008142402.1| 162 GVVALGKTLSIELGKYNINVNSISQ 186
                                       5555566666666788888887765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   1.9e-05     0.034       1      67 [.      10      75 ..      10      94 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.9e-05
                                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH...TTTCEEEEE--TTTHHHHHHHHH CS
                   Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka...lgvrfeaialdaenyeavLaall 67
                                      +++ G+ ++G++v+ +la+ +    +it  +r+ke++e l++++   +gv+++a+  d +++++ L +++
  gi|518652882|ref|YP_008142402.1| 10 IVCAGSTGIGKGVISVLAKYGA---NITTFSRTKENVESLKEEIrkeTGVTVNAMCADLSKKDD-LMRVV 75
                                      67778989***********987...6************99999988899999999999998888.76655 PP

>> ACT  ACT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.018        32      17      30 ..      22      35 ..      10      37 .. 0.83
   2 ?    7.1   0.1    0.0026       4.7      21      34 ..     174     187 ..     170     187 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.018
                                      HHHHHHHTTSEEEE CS
                               ACT 17 vfgaladrgiNids 30
                                      v ++la++g Ni+ 
  gi|518652882|ref|YP_008142402.1| 22 VISVLAKYGANITT 35
                                      779*********96 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0026
                                       HHHTTSEEEEEEEE CS
                               ACT  21 ladrgiNidsieqr 34 
                                       l++++iN+ si+q+
  gi|518652882|ref|YP_008142402.1| 174 LGKYNINVNSISQG 187
                                       89**********96 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   6.3e-05      0.11       6      55 ..      14      59 ..       7      70 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.3e-05
                                      TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECH CS
                     F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdn 55
                                      G+  +g++++s l++ g    +i+ + sr++e +e+l+ee+  ++  + n
  gi|518652882|ref|YP_008142402.1| 14 GSTGIGKGVISVLAKYG---ANIT-TFSRTKENVESLKEEIRKETGVTVN 59
                                      444599***********...****.66*************9843333223 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.6e-05      0.12       3      67 ..      11      75 ..       9      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.6e-05
                                      EEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCE CS
                           3HCDH_N  3 aviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalari 67
                                       + G+  +G+g+ +v+a+ g +++ + +++e +e+ +e+i+k++   v++  ++ ++ ++++  +
  gi|518652882|ref|YP_008142402.1| 11 VCAGSTGIGKGVISVLAKYGANITTFSRTKENVESLKEEIRKETGVTVNAMCADLSKKDDLMRVV 75
                                      45566679**********************************88888887777766666666655 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   0.00011       0.2       1      32 [.      17      48 ..      17     168 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00011
                                      HHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                        ADH_zinc_N  1 gvGlaavqlAkalGaeviavdsseeklelakk 32
                                      g+G  ++ +++ +Ga++++ ++++e++e +k+
  gi|518652882|ref|YP_008142402.1| 17 GIGKGVISVLAKYGANITTFSRTKENVESLKE 48
                                      8*************************998887 PP

>> Polysacc_deac_1  Polysaccharide deacetylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.22      23      61 ..      21      58 ..      13      81 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                                      HHHHHHHHCT--EEEEE-HH.HHCH-HHHHHHHHHTTEEE CS
                   Polysacc_deac_1 23 eilpvLkkykvkatffvigg.lvedypdevremaasGvei 61
                                       +++vL+ky++++t f  ++ +ve++++e+r+    Gv++
  gi|518652882|ref|YP_008142402.1| 21 GVISVLAKYGANITTFSRTKeNVESLKEEIRKET--GVTV 58
                                      6899*************99978****99999754..5555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       946  (0.0527637); expected 358.6 (0.02)
Passed bias filter:                      754  (0.0420548); expected 358.6 (0.02)
Passed Vit filter:                        89  (0.00496402); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.30s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1800.03
//
Query:       gi|518652883|ref|YP_008142403.1|  [L=123]
Description: cupin 2 protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-13   49.0   0.0    4.6e-13   48.7   0.0    1.2  1  Cupin_2       Cupin domain
      1e-07   32.0   0.0    1.3e-07   31.6   0.0    1.2  1  AraC_binding  AraC-like ligand binding domain
    0.00014   21.7   0.2    0.00036   20.3   0.1    1.5  2  EutQ          Ethanolamine utilisation protein EutQ
    0.00035   20.8   0.1    0.00046   20.4   0.1    1.2  1  ARD           ARD/ARD' family
     0.0038   16.8   0.0     0.0058   16.2   0.0    1.3  1  Cupin_1       Cupin
     0.0062   16.5   0.0     0.0073   16.3   0.0    1.2  1  Pirin         Pirin
     0.0094   15.6   0.0      0.016   14.9   0.0    1.4  1  Cupin_3       Protein of unknown function (DUF861)
  ------ inclusion threshold ------
      0.014   15.0   0.1      0.018   14.7   0.1    1.3  1  DMSP_lyase    Dimethlysulfonioproprionate lyase
      0.089   12.7   0.0       0.12   12.3   0.0    1.3  1  Cupin_7       ChrR Cupin-like domain


Domain annotation for each model (and alignments):
>> Cupin_2  Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   2.3e-16   4.6e-13       5      62 ..      43      99 ..      39     107 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 2.3e-16
                                      EETTEEEEEECSSSEEEEEEEEESEEEEEECTEEEEEETTEEEEE-TT-EEEEEE-SS CS
                           Cupin_2  5 lppGesapshrHpgedeffyVleGegeltvdgeeveleaGdsvyfpagtpHrfrNtgd 62
                                      + +G   p+h+H++e ++  + +G+++++++g+e++++aG+++++p++t H+ +  +d
  gi|518652883|ref|YP_008142403.1| 43 IRKGSIVPEHSHENE-QITWIMKGKLHFKIGGKEMDVGAGEVLIIPSNTKHEAIALED 99
                                      778999*********.***********************************9987766 PP

>> AraC_binding  AraC-like ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   6.7e-11   1.3e-07      16      63 ..      49      96 ..      37     108 .. 0.90

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.7e-11
                                      EEEETT-SEEEEEEEEE-EEEEETTEEEEE-TT-EEEE-TTS-EEEEE CS
                      AraC_binding 16 fpphvhdeyvihyvteGtgrlrlngrtydlgpGdlfLlppgepHdyes 63
                                      +p+h h++ +i  +++G+  ++++g++ d+g+G+++++p ++ H+  +
  gi|518652883|ref|YP_008142403.1| 49 VPEHSHENEQITWIMKGKLHFKIGGKEMDVGAGEVLIIPSNTKHEAIA 96
                                      699*****************************************9876 PP

>> EutQ  Ethanolamine utilisation protein EutQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       1.5   2.9e+03      16      33 ..      20      30 ..       4      45 .. 0.50
   2 !   20.3   0.1   1.8e-07   0.00036      96     131 ..      57      92 ..      51     100 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.5
                              EutQ 16 eklglekaeqsesfkkkv 33
                                      e       + se f++++
  gi|518652883|ref|YP_008142403.1| 20 E-------KLSETFYRQM 30
                                      2.......2344444444 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.8e-07
                              EutQ  96 deidyvieGrldvlidGrkvvaeaGdviliPkgski 131
                                       ++i +++ G+l+  i G+++  +aG+v++iP ++k 
  gi|518652883|ref|YP_008142403.1|  57 EQITWIMKGKLHFKIGGKEMDVGAGEVLIIPSNTKH 92 
                                       67999**************************99885 PP

>> ARD  ARD/ARD' family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   2.3e-07   0.00046      53     133 ..      18      92 ..       3     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.3e-07
                               ARD  53 kilktkeeekkdidvevlkestpnfdeklekFfeEhlhedeeirliveGtgyFdvrskdeawirvlvekGDLivlPa 129
                                       k  k+ e++++++ v  +k   +++d    +   Eh+he+e+i  i++G+  F +  k+     + v +G+ +++P 
  gi|518652883|ref|YP_008142403.1|  18 KKEKLSETFYRQM-VYGDKVMVAQLDIRKGSIVPEHSHENEQITWIMKGKLHFKIGGKE-----MDVGAGEVLIIPS 88 
                                       4455666666666.8888889999999999*************************9997.....5688********* PP

                               ARD 130 giyh 133
                                       +++h
  gi|518652883|ref|YP_008142403.1|  89 NTKH 92 
                                       ***9 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   2.9e-06    0.0058      32     103 ..      35      98 ..      27     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.9e-06
                                       TEEEEEEEE.TTEEEEEEEESSS-EEEEEEESEEEEEEEETTSS.EEEEEEEETTEEEEE-TT-EEEEEEES CS
                           Cupin_1  32 gisaarvdlepgglllPhyhpnateiayvlqGegrvgfvvpgngnrdfhkklreGdvfvvPaglvhfqynsg 103
                                       ++ +a +d+++g++++ h h   ++i+ +++G++++ +   +        ++ +G+v+++P++  h +++ +
  gi|518652883|ref|YP_008142403.1|  35 KVMVAQLDIRKGSIVPEHSH-ENEQITWIMKGKLHFKIGGKEM-------DVGAGEVLIIPSNTKHEAIALE 98 
                                       5778999*************.99************55544444.......7999999999999988777765 PP

>> Pirin  Pirin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   3.7e-06    0.0073      19      82 ..      29      86 ..       8     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.7e-06
                                      TCEECCEEESS.S.ETTEEEET-EEEEEEEBSEEEEEEEECSEEEEEETTS-EEEEETT-EEEE CS
                             Pirin 19 pFlfldefdpaelevgeedvigagfpphphrgletvtylleGevehrDslGnkgvirpGdvqwm 82
                                      + ++ d++  a+l++ +    g  +p+h h++ e +t++++G+++++   G++  + +G+v ++
  gi|518652883|ref|YP_008142403.1| 29 QMVYGDKVMVAQLDIRK----GSIVPEHSHEN-EQITWIMKGKLHFK-IGGKEMDVGAGEVLII 86
                                      34445555555555555....7779*****98.789********887.78999*******9876 PP

>> Cupin_3  Protein of unknown function (DUF861)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     8e-06     0.016      24      63 ..      54      93 ..      42     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8e-06
                                      SS.EEEEEEEECEEEEEETTTEEEEEETTEEEEE-TTEEEC CS
                           Cupin_3 24 ee.dEfcyileGevkvtpeggetvelraGDlvvlpkglsgt 63
                                       e +++  i++G+ +++  gg+++ ++aG ++ +p +++ +
  gi|518652883|ref|YP_008142403.1| 54 HEnEQITWIMKGKLHFKI-GGKEMDVGAGEVLIIPSNTKHE 93
                                      45266669**********.****************998655 PP

>> DMSP_lyase  Dimethlysulfonioproprionate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   9.1e-06     0.018     109     154 ..      50      94 ..      11     101 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.1e-06
                        DMSP_lyase 109 PdHhhaaeelYlvlsggaefrqgeaewlsrgiGevifnepgikham 154
                                       P+H+h++e +  +++g   f+ g++e +++g+Gev+  +++ kh  
  gi|518652883|ref|YP_008142403.1|  50 PEHSHENEQITWIMKGKLHFKIGGKE-MDVGAGEVLIIPSNTKHEA 94 
                                       9************************9.*****************75 PP

>> Cupin_7  ChrR Cupin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   5.9e-05      0.12      23      83 ..      35      99 ..      13     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                                      -EEEEEEEE-TTEE---EE-TT-EEEEEEEEEEEETTE....EEETTEEEEE-TT-EE--EESS- CS
                           Cupin_7 23 aratslvryapgsafsahkHpggeeilVLeGvfsdeeg....dypaGsylrnppgsshapvseeG 83
                                      + +++ + + +gs  ++h+H++   +++++G+++ + g    d +aG+ l  p +++h+ ++ e+
  gi|518652883|ref|YP_008142403.1| 35 KVMVAQLDIRKGSIVPEHSHENEQITWIMKGKLHFKIGgkemDVGAGEVLIIPSNTKHEAIALED 99
                                      45677788999********************9876533222267999999999999999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.29s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 792.32
//
Query:       gi|518652884|ref|YP_008142404.1|  [L=57]
Description: hypothetical protein FACI_IFERC00001G1523 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-05   24.6   0.8      0.029   14.3   0.0    2.1  2  zinc_ribbon_4    zinc-ribbon domain
     0.0015   18.0   1.0      0.002   17.6   1.0    1.2  1  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0074   16.2   1.2      0.012   15.6   1.2    1.4  1  Prok-RING_1      Prokaryotic RING finger family 1
     0.0079   16.1   0.2     0.0079   16.1   0.2    1.2  1  PHD              PHD-finger
  ------ inclusion threshold ------
      0.013   15.3   1.7       0.12   12.2   0.0    2.1  2  zf-C2H2_3        zinc-finger of acetyl-transferase ESCO
      0.019   14.9   1.0        3.9    7.5   0.0    2.2  2  ADK_lid          Adenylate kinase, active site lid
      0.033   14.2   0.5      0.035   14.1   0.5    1.0  1  HypA             Hydrogenase/urease nickel incorporation, met
      0.037   14.4   0.4      0.043   14.2   0.4    1.2  1  Lar_restr_allev  Restriction alleviation protein Lar
      0.045   13.7   0.2      0.055   13.4   0.2    1.2  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.064   13.2   0.3      0.087   12.7   0.3    1.2  1  C1_1             Phorbol esters/diacylglycerol binding domain
      0.076   12.4   0.7      0.098   12.1   0.7    1.2  1  Vps36-NZF-N      Vacuolar protein sorting 36 NZF-N zinc-finge
      0.076   13.1   0.9       0.12   12.5   0.9    1.3  1  DUF2318          Predicted membrane protein (DUF2318)
       0.18   11.9   1.4       0.92    9.6   1.4    1.9  1  Elf1             Transcription elongation factor Elf1 like
       0.21   11.3   3.0        8.2    6.2   0.0    2.5  3  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.2   0.00088       1.1       1      20 [.       1      20 [.       1      22 [. 0.89
   2 !   14.3   0.0   2.2e-05     0.029       3      27 ..      24      46 ..      23      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00088
                     zinc_ribbon_4  1 MkitCpsCkakyeiddeklp 20
                                      M + C+ C+ k +++d+ ++
  gi|518652884|ref|YP_008142404.1|  1 METKCKICGEKINVPDDSMA 20
                                      999*************9765 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 2.2e-05
                     zinc_ribbon_4  3 itCpsCkakyeiddeklpakgvkvr 27
                                      i+C sC+  yei++  ++a+gv+++
  gi|518652884|ref|YP_008142404.1| 24 IECGSCGMSYEIAS--IKADGVEIK 46
                                      9************9..888888876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   1.0   1.6e-06     0.002       2      34 ..       4      38 ..       3      44 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.6e-06
                                      EETTTTCEE.CHEETSTTCE.EESSSSBEEEECCC CS
                      TF_Zn_Ribbon  2 kCPnCgstn.lveDpergel.vCtdCGlVlednsi 34
                                      kC++Cg +  +  D + gel  C++CG   e  si
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEKInVPDDSMAGELiECGSCGMSYEIASI 38
                                      9*****98768999******77*****87776666 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   1.2   9.2e-06     0.012       4      30 ..       2      33 ..       1      43 [. 0.82

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 9.2e-06
                       Prok-RING_1  4 gkkCpvCgkelkeedD.....iVvCpeCgtpy 30
                                      ++kC++Cg++++  dD     ++ C  Cg +y
  gi|518652884|ref|YP_008142404.1|  2 ETKCKICGEKINVPDDsmageLIECGSCGMSY 33
                                      68*********9887644444899*****999 PP

>> PHD  PHD-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.2   6.2e-06    0.0079       2      25 ..       5      33 ..       4      55 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.2e-06
                                      BTTTTS.....TTSTTSCEEEETTTSCEE CS
                               PHD  2 CavCkk.....ksdeeeelvqCdgCkrwf 25
                                      C++C++     ++   +el+ C +C+ ++
  gi|518652884|ref|YP_008142404.1|  5 CKICGEkinvpDDSMAGELIECGSCGMSY 33
                                      ******999877777**********9887 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 ?    2.6   0.5     0.093   1.2e+02      14      20 ..       3       9 ..       1       9 [. 0.83
   2 ?   12.2   0.0   9.2e-05      0.12      13      26 ..      22      36 ..      12      41 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.093
                         zf-C2H2_3 14 sqCkeCg 20
                                      ++Ck Cg
  gi|518652884|ref|YP_008142404.1|  3 TKCKICG 9 
                                      67****8 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 9.2e-05
                         zf-C2H2_3 13 a.sqCkeCgMvYnpg 26
                                      +  +C  CgM+Y   
  gi|518652884|ref|YP_008142404.1| 22 ElIECGSCGMSYEIA 36
                                      4467********765 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 ?    6.4   0.4    0.0068       8.7      21      31 ..       2      12 ..       1      17 [. 0.83
   2 ?    7.5   0.0     0.003       3.9       4      14 ..      26      36 ..      24      51 .. 0.69

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0068
                                      TTB-TTT--.- CS
                           ADK_lid 21 eglCDkCGepL 31
                                      e +C  CGe+ 
  gi|518652884|ref|YP_008142404.1|  2 ETKCKICGEKI 12
                                      789*****985 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.003
                                      -TTT--EEETT CS
                           ADK_lid  4 CpkCGrsYhvv 14
                                      C +CG sY ++
  gi|518652884|ref|YP_008142404.1| 26 CGSCGMSYEIA 36
                                      99******855 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   0.5   2.7e-05     0.035      70     108 ..       2      46 ..       1      50 [. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.7e-05
                                       EEEETTTS-EEECHHHHH.....S-TTTSSS.-EEEEESSSEEEE CS
                              HypA  70 kvrCreCgkefeleekal.....rCpkCgsa.dveivsGeellvk 108
                                       +++C+ Cg+++++ ++++     +C++Cg + ++  ++ +++++k
  gi|518652884|ref|YP_008142404.1|   2 ETKCKICGEKINVPDDSMageliECGSCGMSyEIASIKADGVEIK 46 
                                       689*********77643345667*****97658888888888887 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 ?   14.2   0.4   3.4e-05     0.043       5      40 ..       4      35 ..       3      54 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3.4e-05
                   Lar_restr_allev  5 pCPfCggravlersqrvvaeigqcvyCadCgastpw 40
                                       C  Cg++  +  +    +     ++C  Cg+s   
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEKINVPDDSMAGE----LIECGSCGMSYEI 35
                                      5999****99999999998....9********3222 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 ?   13.4   0.2   4.3e-05     0.055      30      56 ..       4      33 ..       3      43 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.3e-05
                    OrfB_Zn_ribbon 30 tCseCgsknke...alsgrtfkCpnCgfea 56
                                      +C  Cg+k +    + +g++ +C +Cg+++
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEKINVpddSMAGELIECGSCGMSY 33
                                      8*******9999999************986 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.8e-05     0.087      10      38 ..       1      33 [.       1      35 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-05
                                      S--B-TTT-SB-...-S.SSS-EEEETTT--EE CS
                              C1_1 10 qptfCkhCgefl...wg.kekqglkCswCkllv 38
                                      ++t+Ck Cge +       +   + C  C++++
  gi|518652884|ref|YP_008142404.1|  1 METKCKICGEKInvpDDsMAGELIECGSCGMSY 33
                                      589*********998444888899*****9986 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 ?   12.1   0.7   7.6e-05     0.098      12      49 ..       5      39 ..       3      53 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.6e-05
                       Vps36-NZF-N 12 CpICsfsNevpsnfdpnastplPpClaCGvkpdlelik 49
                                      C IC  + +vp +   +   +l  C +CG   +++ ik
  gi|518652884|ref|YP_008142404.1|  5 CKICGEKINVPDD---SMAGELIECGSCGMSYEIASIK 39
                                      *******999994...458999*******999988887 PP

>> DUF2318  Predicted membrane protein (DUF2318)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.9   9.4e-05      0.12      36      70 ..       4      41 ..       2      50 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.4e-05
                           DUF2318 36 aCevCekkgYv....qegeelvCknCgvrfaldsigekk 70
                                       C++C++k  v    + ge + C +Cg++ +++si+  +
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEKINVpddsMAGELIECGSCGMSYEIASIK-AD 41
                                      599**776655333378999***************9.44 PP

>> Elf1  Transcription elongation factor Elf1 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   1.4   0.00072      0.92      23      58 ..       4      36 ..       1      46 [. 0.72

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00072
                              Elf1 23 dCpfCnheksvevkldkkekiaevsCkvCgesfetk 58
                                      +C  C+++  ++v  d +     ++C++Cg s+e+ 
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEK--INVP-DDSMAGELIECGSCGMSYEIA 36
                                      68899988..4443.3333345689******99964 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 ?    5.1   0.4     0.014        19      19      27 ..       4      12 ..       2      13 .. 0.88
   2 ?    6.2   0.0    0.0064       8.2      18      25 ..      24      31 ..      18      38 .. 0.63
   3 ?   -1.7   0.0       1.9   2.5e+03       9      17 ..      42      50 ..      40      51 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.014
                                      --SSS---- CS
                    DNA_RNApol_7kD 19 RCkeCGhRi 27
                                      +Ck CG +i
  gi|518652884|ref|YP_008142404.1|  4 KCKICGEKI 12
                                      7*****987 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0064
                                      ---SSS-- CS
                    DNA_RNApol_7kD 18 iRCkeCGh 25
                                      i C  CG+
  gi|518652884|ref|YP_008142404.1| 24 IECGSCGM 31
                                      55555553 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 1.9
                                      B----SSS- CS
                    DNA_RNApol_7kD  9 evslkkgdp 17
                                       v++k+ + 
  gi|518652884|ref|YP_008142404.1| 42 GVEIKPAEN 50
                                      589999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 381.93
//
Query:       gi|518652885|ref|YP_008142405.1|  [L=347]
Description: hypothetical protein FACI_IFERC00001G1524 [Ferroplasma acidarmanus fer1]
Scores for complete 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-37  127.5   0.0    7.7e-37  126.4   0.0    1.5  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    9.6e-11   42.1   0.0    1.5e-10   41.5   0.0    1.3  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
     0.0028   17.9   0.0     0.0047   17.2   0.0    1.4  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
     0.0094   16.1   0.0       0.02   15.0   0.0    1.6  1  DapB_N           Dihydrodipicolinate reductase, N-terminus
  ------ inclusion threshold ------
      0.051   14.4   0.0       0.09   13.6   0.0    1.3  1  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.4   0.0   2.2e-40   7.7e-37       1     121 []       2     141 ..       2     141 .. 0.96
   2 ?   -3.1   0.0       2.9   1.1e+04      51      73 ..     208     231 ..     195     237 .. 0.60

  Alignments for each domain:
  == domain 1  score: 126.4 bits;  conditional E-value: 2.2e-40
                                       EEEEETTTSHHHHHHHHHHHCTSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGC.TT-SEEEE-SCH CS
                    Semialdhyde_dh   1 kvaivGatGyvGqellrlLeehpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeel.kevdivflalpa 76 
                                       kv+ivGa+GyvG el+rlL +hpe+e++ ++s+++  G+k+++ ++ l++ +dlk+ed+++ ++  +vd++flalp+
  gi|518652885|ref|YP_008142405.1|   2 KVGIVGASGYVGGELMRLLVRHPEIEITSVSSTRH-SGEKVSRIHPDLYGLTDLKFEDITPLDMaGKVDLIFLALPH 77 
                                       7****************************999999.**********************6665555************ PP

                                       HHHHHHHHHHHHTTSEEEESSSTTTTST...................TSEBE-HHHHGGGGGGH CS
                    Semialdhyde_dh  77 gvskelapklaeagvkviDlssdfRlkd...................davyvlpevnreaikka 121
                                       g+s +++p l+e+gvk+iD+s+dfRlk+                   + vy++pe++re+ik+a
  gi|518652885|ref|YP_008142405.1|  78 GTSIKYVPGLVETGVKIIDMSADFRLKNpelykpwygyehgypdlikKFVYGMPELHREQIKNA 141
                                       *************************************************************986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                                       TECEBEEE.GGGGGCTT-SEEEE- CS
                    Semialdhyde_dh  51 gkdlkved.vdeeelkevdivfla 73 
                                       +++ ++e+  + ++ k+v+i+++a
  gi|518652885|ref|YP_008142405.1| 208 RHTPEIEQeLEYASGKKVKIALSA 231
                                       444444443444555777777766 PP

>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5   0.0   4.2e-14   1.5e-10      14     184 .]     171     317 ..     161     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 4.2e-14
                                       EEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTE CS
                   Semialdhyde_dhC  14 vivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkilef 90 
                                       ++v+++ + SG+G                   +++ +  ++  +++ +y+    ++++pe+++el     +k++++ 
  gi|518652885|ref|YP_008142405.1| 171 INVDAKVGSSGSGSG-----------------LDESKVFSERFDSIRAYKPV-NHRHTPEIEQELEYASGKKVKIAL 229
                                       789999999999995.................77788888889*********.9**********************9 PP

                                       SCSEEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCSTTEEEEESS....HCHHSSHHHHTTCSSSEEEEEE CS
                   Semialdhyde_dhC  91 tekvsatcvrVPvlrGhseavtiklklkdveveeveellaaapevkvvvne....eedrPtpaavaggtnsvsVGRi 163
                                       ++      + V ++rG++++ +i  + +++++   + +++   e++++       + ++P p+ v+g +n++++G +
  gi|518652885|ref|YP_008142405.1| 230 SA------HSVNMVRGILTTSSIYSEGDEITLWSLLRKFYGN-EKFIRLIMdrksNYKYPDPKTVIG-SNFADIG-F 297
                                       98......89***************999**************.66665444456999*********9.9******.* PP

                                       EEETTCTTEEEEEEEEETTTT CS
                   Semialdhyde_dhC 164 rkdemgdeglklvvvgDNllk 184
                                         d+ +++ ++ + ++DNl+k
  gi|518652885|ref|YP_008142405.1| 298 AIDKYVKR-VVSFGAIDNLIK 317
                                       *******8.**********97 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.3e-06    0.0047       1      66 [.       3      62 ..       3     125 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.3e-06
                                      EEEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHH CS
                   Sacchrp_dh_NADP  1 vliiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaal 66
                                      v i+Ga G+vG  +++ll+rh ++  eit ++ ++++ e++     ++  + + l+  + e+ +++l
  gi|518652885|ref|YP_008142405.1|  3 VGIVGAsGYVGGELMRLLVRHPEI--EITSVSSTRHSGEKVS----RIHPDLYGLTDLKFED-ITPL 62
                                      689*********************..9**********99985....4444555555555555.4444 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   5.7e-06      0.02       1      41 [.       1      38 [.       1      59 [. 0.87

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 5.7e-06
                                      EEEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTT CS
                            DapB_N  1 ikvavvGasGrmGkevvkaveeaedlelvaavdrkeseleg 41
                                      +kv++vGasG +G e+++++ +++++e++++ ++++s   g
  gi|518652885|ref|YP_008142405.1|  1 MKVGIVGASGYVGGELMRLLVRHPEIEITSVSSTRHS---G 38
                                      89****************************9998873...3 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05      0.09       1      90 [.       1      95 [.       1      95 [. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                                      EEEEEETT.SHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHH...HHHTTHE..EESSHHHHHTCTTESEEEE-S-GG CS
                      GFO_IDH_MocA  1 lrvaiiGa.Gkigskhlrplnesqrleevvalldpdaeraeav...aesfgve..aysdleelladpeidavivatpng 73
                                      ++v+i+Ga G++g + +r l ++ ++ e++ + +++ +  +      + +g+    ++d+  l    ++d+++ a p g
  gi|518652885|ref|YP_008142405.1|  1 MKVGIVGAsGYVGGELMRLLVRH-PEIEITSVSSTRHSGEKVSrihPDLYGLTdlKFEDITPLDMAGKVDLIFLALPHG 78
                                      69******999999999666666.99****9999988777766556666666689999999888888***********9 PP

                                      GHHHHHHHHHHTT-EEE CS
                      GFO_IDH_MocA 74 theelakaaleagkhvl 90
                                      t  +++  ++e g++++
  gi|518652885|ref|YP_008142405.1| 79 TSIKYVPGLVETGVKII 95
                                      99998888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 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:                        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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2437.75
//
Query:       gi|518652886|ref|YP_008142406.1|  [L=254]
Description: acetylglutamate/acetylaminoadipate kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.2e-28  100.4   0.4    1.3e-28  100.2   0.4    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 !  100.2   0.4   7.4e-33   1.3e-28       3     240 ..       2     238 ..       1     239 [. 0.89

  Alignments for each domain:
  == domain 1  score: 100.2 bits;  conditional E-value: 7.4e-33
                                       EEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC........E..HHHHH CS
                         AA_kinase   3 vVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaa....glrstleeage 75 
                                        V+K+GGs+l++  e   ++l  +i+++   + +l++VhGgg++ d +++   ++++++ ++    + r+t++ ++e
  gi|518652886|ref|YP_008142406.1|   2 KVLKIGGSVLDNFLE--NDNLYSIIQQF---DCPLAIVHGGGNYLDTHADS-FNYTKKFVTSpegiRSRYTDKNTLE 72 
                                       69*********9999..8**********...99******************.999999999899999********** PP

                                       HHHHHHHHHHHHHHHHHHHHTTHGEEEE-GGGTCEECCCE...............HHHTTTCEEECCHHHHHHHTT- CS
                         AA_kinase  76 vatrdalaslgerlvaallaaglpavglsaaaldateagr.............degsdgnvesvdaeaieelleagv 139
                                       + t   +  ++++lv +l ++g++av l++  ++a+++++             d g++g+ves d+  i+  +++g+
  gi|518652886|ref|YP_008142406.1|  73 IFT-MVMNLINQKLVLNLKEHGIKAVTLNGI-INARRKEKliimneknrkmiiDGGYTGRVESADSIPIRAVIDEGY 147
                                       ***.578999******************977.555666666************************************ PP

                                       EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCCTTCECCEEEHHHCHHCSSS.TT CS
                         AA_kinase 140 vpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvpdarllpeisvdeaeesaselat 216
                                       +pv+++ +    +g  +++++D++aa++A  +g d+l++lt+V+G+y +d       r++++ +v  +++   + + 
  gi|518652886|ref|YP_008142406.1| 148 IPVISPVA--YGNGNYLNVDADRAAAYVAGSMGSDSLVFLTNVSGLYYKD-------RVIEKADVAYIKS-ILNEIG 214
                                       ******66..4455566********************************9.......5555555555555.222566 PP

                                       THHHHCHHHHHHHHHCTT-EEEEE CS
                         AA_kinase 217 gGmkvkhpaalaaarrggipvvIt 240
                                        Gm  k+ a ++a++ g+ +v I 
  gi|518652886|ref|YP_008142406.1| 215 TGMDKKLMASIEALEMGVRQVTIS 238
                                       69****************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 1606.26
//
Query:       gi|518652887|ref|YP_008142407.1|  [L=393]
Description: hypothetical protein FACI_IFERC00001G1526 [Ferroplasma acidarmanus fer1]
Scores for complete 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-97  326.6   0.1      2e-97  326.4   0.1    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 !  326.4   0.1  1.1e-101     2e-97       3     404 ..       9     382 ..       7     384 .. 0.94

  Alignments for each domain:
  == domain 1  score: 326.4 bits;  conditional E-value: 1.1e-101
                                       -TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHH CS
                       Aminotran_3   3 areednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekl 79 
                                       a+ ++ l++++  ++G++l d +gkry+D+++++ v++lG+ + k+ +av  q +++ +   +   ++  +++ + l
  gi|518652887|ref|YP_008142407.1|   9 ANTYQRLPVNVLNGNGAILHDINGKRYIDMMGGYGVAILGYGNKKIKEAVCRQFDTIPIAH-ASEYTAAREEFIKNL 84 
                                       556677789999*********************************************8777.5555566789***** PP

                                       HHHCT-..SEEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB.-T CS
                       Aminotran_3  80 lklapkgldkvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpf.lp 155
                                       + ++p gldk+ l n+G+eA+e+A+K+ +k      + + +kiia+++++HG+t gals+t s +ky++ fg++ + 
  gi|518652887|ref|YP_008142407.1|  85 TGIVPAGLDKFYLGNTGAEAIEAAIKVVIK------SSKNHKIIAMTNSYHGKTAGALSITYS-EKYRQSFGDLlIK 154
                                       ******************************......9999***********************.*********9789 PP

                                       SEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE CS
                       Aminotran_3 156 evvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivD 232
                                       +v ++ y+               +e l ++  +k+++++Av +Ep+qgegG+++++ +++++lr+++++++++l++D
  gi|518652887|ref|YP_008142407.1| 155 NVEFIRYNN--------------MEDLDKI--RKDNDISAVFFEPVQGEGGINIPDRDYVRELRQITEEKGIILVAD 215
                                       9999***96..............2335555..599****************************************** PP

                                       -TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHH CS
                       Aminotran_3 233 EvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiie 309
                                       E+q+G+GrTGk++A+eh+g++pD++t++K+++gG+pls+++++ e m+ la+g+++sT gGnp+a+a   av+e + 
  gi|518652887|ref|YP_008142407.1| 216 EIQSGLGRTGKMWAHEHFGIKPDIITIGKGIGGGIPLSVTAGKPEFMDNLAKGEQSSTTGGNPIAMASGSAVIEQLT 292
                                       **************************************************************************997 PP

                                       HTTHHHHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETTTEEEE-- CS
                       Aminotran_3 310 eekllenaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGdnvirllp 386
                                        ++l+++++ +g+ +++ L+e  +++  +ke+Rg+Glm aiel  +       ++    + Gvl l +G n++r+lp
  gi|518652887|ref|YP_008142407.1| 293 -DDLINEVAVKGELFRNTLKEYLADSRIVKEIRGLGLMDAIELRVKFL----PVFMDIINRGVLPLYSGINILRMLP 364
                                       .58***************************************998887....89999******************** PP

                                       -TT--HHHHHHHHHHHHH CS
                       Aminotran_3 387 pliitdeeidelleilkk 404
                                       p++i+d+ei e+ +i+++
  gi|518652887|ref|YP_008142407.1| 365 PYVISDAEITEAAKIMSE 382
                                       ************999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2810.26
//
Query:       gi|518652888|ref|YP_008142408.1|  [L=282]
Description: hypothetical protein FACI_IFERC00001G1527 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   95.6   0.0    3.4e-27   95.3   0.0    1.1  1  RimK         RimK-like ATP-grasp domain
    1.6e-12   47.1   0.0    2.8e-12   46.4   0.0    1.4  1  GSH-S_ATP    Prokaryotic glutathione synthetase, ATP-grasp do
    0.00011   21.6   0.0    0.00028   20.2   0.0    1.7  2  ATPgrasp_ST  Sugar-transfer associated ATP-grasp
    0.00022   21.3   0.0     0.0003   20.8   0.0    1.3  1  R2K_3        ATP-grasp domain, R2K clade family 3
     0.0013   18.8   0.0     0.0035   17.4   0.0    1.6  1  ATP-grasp_3  ATP-grasp domain
  ------ inclusion threshold ------
       0.07   13.2   0.3       0.12   12.4   0.3    1.3  1  DUF2420      Protein of unknown function (DUF2420)
      0.095   12.6   0.0       0.18   11.7   0.0    1.4  1  R2K_2        ATP-grasp domain, R2K clade family 2


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 !   95.3   0.0   1.3e-30   3.4e-27       3     187 ..      87     275 ..      85     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 95.3 bits;  conditional E-value: 1.3e-30
                                       -HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--... CS
                              RimK   3 dKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai... 76 
                                       +K+ +  lL +++i +p+t ++ ++e   k  ++  ++   v K v gs G  + l +++ ++ +v +  k  +   
  gi|518652888|ref|YP_008142408.1|  87 NKMFTSLLLSQKRIRIPKTFVSFSNERFLKSFKED-FNGRAVTKPVTGSWGRMISLLNDYYAAMDV-SEYKDYMypl 161
                                       78888899***************999866555443.67999************************9.5556655565 PP

                                       ....EEEEE--SS-SEEEEEEEETTEEEEEEEEE--SSS----TTTT-EEEE----HHHHHHHHHHHHHCT-SEEEE CS
                              RimK  77 ....lvqeyieeaenediRvlvvddevvaalrrvskeGdFRsnlhrGgvaeklqlseeekelAikaakamelvvaGv 149
                                             qey++   ++d+Rv++v+d+v+a++ r     d+R+n  +Gg ae+l+++ e +e+A k++ a++  + G+
  gi|518652888|ref|YP_008142408.1| 162 yqinYTQEYVNDF-GRDLRVFIVNDQVIAGIYRYKSGEDWRTNTALGGRAEPLKITGEVEEIAQKVSAALGPGIYGM 237
                                       4445677777654.59*****************977779************************************** PP

                                       EEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHHHH CS
                              RimK 150 DllrakrgllvlEvnsspglekiektlgidiakkliea 187
                                       D+l++k+g++v Evn + + ++    +gi+i   ++++
  gi|518652888|ref|YP_008142408.1| 238 DILESKDGYFVNEVNGNTEFKNTVPVTGINIPDYIADY 275
                                       *******************************9999887 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 !   46.4   0.0   1.1e-15   2.8e-12      11     154 ..     101     242 ..      87     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.1e-15
                                       CS--EEEES-.HHHHHHHHHHH.SSEEEEESS--TTTT-EEE-TT..-TTHHHHHHHHTTTTTS-EEEEE--GGGGG CS
                         GSH-S_ATP  11 lipktlvskd.keeirafleeq.gdvilKPldgkgGegvfrvkks..dpnlksilellteegkepviaqrylpeike 83 
                                        ipkt vs + ++ +++f e+  g+++ KP+ g+ G+ +  +++    ++++   + +    +     q+y+++  +
  gi|518652888|ref|YP_008142408.1| 101 RIPKTFVSFSnERFLKSFKEDFnGRAVTKPVTGSWGRMISLLNDYyaAMDVSEYKDYMYPLYQ-INYTQEYVNDFGR 176
                                       479****965055689999875156*************9999886446777777777777666.6679*******98 PP

                                       -EEEEEEETTEE-SEEEEEE--SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETT CS
                         GSH-S_ATP  84 GDkRillvdGepigyalaRvpaegevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigd 154
                                        D R+++v+ + i   + R  + ++ R+n a ggrae  ++t + +eia++++ +L   G  + G+D++++
  gi|518652888|ref|YP_008142408.1| 177 -DLRVFIVNDQVIA-GIYRYKSGEDWRTNTALGGRAEPLKITGEVEEIAQKVSAAL---GPGIYGMDILES 242
                                       .************9.**************************************998...444568888765 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 !   20.2   0.0   1.1e-07   0.00028      10      87 ..      76     145 ..      70     171 .. 0.85
   2 ?   -2.8   0.0       1.1   2.9e+03     230     265 ..     221     254 ..     218     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 1.1e-07
                       ATPgrasp_ST  10 yNpraefplvddKlkfkelalraglkvpkllgvikeqaeiseleafvkeleegvviKpakgsgGkGilviteredqd 86 
                                       +N+ +   +  +K+ ++ l++++ + +pk+++++++++ ++++++  +++    v Kp+ gs+G+ i+ +++     
  gi|518652888|ref|YP_008142408.1|  76 INDFNSTIVTGNKMFTSLLLSQKRIRIPKTFVSFSNERFLKSFKEDFNGR---AVTKPVTGSWGRMISLLND----- 144
                                       67788888899**************************9999999877777...79***********999966..... PP

                       ATPgrasp_ST  87 y 87 
                                       y
  gi|518652888|ref|YP_008142408.1| 145 Y 145
                                       3 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
                       ATPgrasp_ST 230 elaakaaeklpglgylGwDivldeekgplllElNar 265
                                       e+a k+++  +g g+ G+Di   +++   + E+N +
  gi|518652888|ref|YP_008142408.1| 221 EIAQKVSA-ALGPGIYGMDILESKDG-YFVNEVNGN 254
                                       77888888.88899999999655555.888888866 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 !   20.8   0.0   1.2e-07    0.0003     111     182 ..     169     252 ..     110     255 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                             R2K_3 111 evv.rfsaEwRvFvvdGevva.asrYrkanddpdl.............epdlaafaeavralvgappfyvlDvavta 172
                                       e+v +f+   RvF+v+++v+a + rY+ +  d+ +               +++++a+ v+a+   p  y +D+  ++
  gi|518652888|ref|YP_008142408.1| 169 EYVnDFGRDLRVFIVNDQVIAgIYRYK-SGEDWRTntalggraeplkiTGEVEEIAQKVSAAL-GPGIYGMDILESK 243
                                       556589*********887765267896.55555555556886666666666666777777777.6************ PP

                             R2K_3 173 dGrwkVVEvn 182
                                       dG + V Evn
  gi|518652888|ref|YP_008142408.1| 244 DG-YFVNEVN 252
                                       **.***9999 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.4e-06    0.0035       2     155 ..      86     252 ..      85     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.4e-06
                                       TSHHHHHHHHTTT.S---..........-EESS--.....SSSEEEEESS-------B--SS--TTE.......... CS
                       ATP-grasp_3   2 sdKlktykkLkeagvkvP......tkleaeeleee.....ekklvvKprdGaggesvrvveekeeaeaaieeve... 64 
                                        +K++t   L+++ +++P      +   +e++ ++     + + v Kp++G+ g  +++ ++  +a    e++    
  gi|518652888|ref|YP_008142408.1|  86 GNKMFTSLLLSQKRIRIPktfvsfS---NERFLKSfkedfNGRAVTKPVTGSWGRMISLLNDYYAAMDVSEYKDymy 159
                                       6999999***********7774441...333333355556899********************88887777766544 PP

                                       .EEEE---SEEEEEEEEE..SSSEEEEEEEEEEEET.............TEEEEEEES----HHHHHHHHHHHHHTT CS
                       ATP-grasp_3  65 .lvqefieGkplSvsllsd.gekvlvlavnrqliekaeke.........fvyaGnvtpietelkeevvelaeevvek 130
                                        l        +++ + + d g + +v+ vn+q+i    +           +  G   p +   + ev+e+a++v ++
  gi|518652888|ref|YP_008142408.1| 160 pL-----YQINYTQEYVNDfGRDLRVFIVNDQVIAGIYRYksgedwrtnTALGGRAEPLK--ITGEVEEIAQKVSAA 229
                                       42.....33555555555534677788888888864333356777777566666666666..799************ PP

                                       STT--EEEEEEEEESS.SEEEEEEE CS
                       ATP-grasp_3 131 leglaGyvGvDlvlkdeepyviEvN 155
                                       l    G+ G D++ ++++  v EvN
  gi|518652888|ref|YP_008142408.1| 230 L--GPGIYGMDILESKDGYFVNEVN 252
                                       *..68*********99999999**9 PP

>> DUF2420  Protein of unknown function (DUF2420)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3   4.6e-05      0.12      11      92 ..       2      87 ..       1      95 [. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.6e-05
                           DUF2420 11 slselfaalRsfleekegelvsaekElvL.eipeLdltltEdnvynkdislndilsifkiLkens...kseedvpesLs 85
                                      ++s lf  +R  +    + l  ++ E+ L +++e++l l   n    disl++ + ++++L++       ++++ + ++
  gi|518652888|ref|YP_008142408.1|  2 KISMLFDIMRWEERAILKALQDKNVEVQLyNVKEMNLDLQDPNYDFGDISLQRSTGYYRNLHSTAyveFTGNRIINDFN 80
                                      689999****999999999999999998768*******************************98876555666777777 PP

                           DUF2420 86 itlslqp 92
                                       t+ +  
  gi|518652888|ref|YP_008142408.1| 81 STIVTGN 87
                                      7666655 PP

>> R2K_2  ATP-grasp domain, R2K clade family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   6.9e-05      0.18      60     124 ..     171     248 ..     157     256 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.9e-05
                             R2K_2  60 vvsfasEyRlfvldgeiit.vsrYagegrldpdp............evaeeavaalksa.lpsayvlDvgvtedget 122
                                       v +f +  R+f++++++i+ + rY+   + ++++              +ee++++++ a  p  y +D+ +++d + 
  gi|518652888|ref|YP_008142408.1| 171 VNDFGRDLRVFIVNDQVIAgIYRYKSGEDWRTNTalggraeplkitGEVEEIAQKVSAAlGPGIYGMDILESKD-GY 246
                                       56789999******99886379**976666555556999999999977788888888877799******99888.44 PP

                             R2K_2 123 al 124
                                        +
  gi|518652888|ref|YP_008142408.1| 247 FV 248
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2120.65
//
Query:       gi|518652889|ref|YP_008142409.1|  [L=355]
Description: hypothetical protein FACI_IFERC00001G1528 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.7e-22   79.1   0.0    4.5e-22   78.8   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    4.3e-11   42.7   0.0    7.4e-11   41.9   0.0    1.4  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 !   78.8   0.0     5e-26   4.5e-22       2     203 ..      60     345 ..      59     349 .. 0.90

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 5e-26
                                       EEEES-BSS.TTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTTTH CS
                                       xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20   2 lgsHlDvVp.eeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggrgG 77 
                                       l +H D+Vp   e        +++   +++yGrGa+d k ++la++  +r+  d+g+  kg++ + +   EE+ ++G
  gi|518652889|ref|YP_008142409.1|  60 LCGHEDTVPgILEV-------KSD--GNMVYGRGAVDAKSSLLALILGARKAMDNGF--KGKLLVSAASGEESDSKG 125
                                       569******43333.......333..459***************************7..89***********989** PP

                                       HHHHHHHHHTTTCESEEEEEEEESSSBTCHSTETEEEE....................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................................... RF
                     Peptidase_M20  78 akallegleerekvdavfelhieepgileagklaigvv....................................... 115
                                       +++++e+    ++ d+   ++ +epg++   +  i+ +                                       
  gi|518652889|ref|YP_008142409.1| 126 INNIMEN---YHGYDY---AIFGEPGGSM--N--ITAGykgrllmkvdvktathhassswmesnaidllmglwvkir 192
                                       ******3...445666...5688888887..3..3333559999999999*************************** PP

                                       ...............................................................EEEEEEEEEESHEE CS
                                       ...............................................................xxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ...............................................................kvevelleggapvt 129
                                                                                                      +++++ +++ +p+ 
  gi|518652889|ref|YP_008142409.1| 193 eqygnnkdfnsvsagitrfnggeydnmtpehasmyidirypksvsedeltgelksymeellvkNYSYTIESRTYPYI 269
                                       **************************************************************86888888******* PP

                                       EC.CHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEEEEEEESSG.GCTTSTTTEEEHHHHHHHHHHH CS
                                       xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 130 ln.dsplvkalaeaaeelfgekvelivsgpggtdarff...agiptvmifgpgs.glaHspnEyvdledlekgikvl 201
                                       ++  s lvk +++ +++  g +++li ++ g+ d++ +   ++ip++  +gpg+ +l+H+ nE +d++dl+k i+v+
  gi|518652889|ref|YP_008142409.1| 270 SDmKSSLVKSFKSGISRN-GMAPRLIFKS-GSGDMNNLghvWKIPAI-TYGPGDtQLSHTQNEVIDIRDLYKSIDVI 343
                                       *****************7.*99****888.99999999888999866.7****88********************98 PP

                                       HH CS
                                       xx RF
                     Peptidase_M20 202 ar 203
                                        +
  gi|518652889|ref|YP_008142409.1| 344 SD 345
                                       76 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.0   8.3e-15   7.4e-11       4     106 ..     155     254 ..     152     256 .. 0.95

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 8.3e-15
                                       -EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-CCCCEESSEEEEEE CS
                         M20_dimer   4 kGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGsaknvipdeaeaki 80 
                                       kG + +k+ vk    H++      NAi +l+ l  ++++++g+   ++++   +  +t ++gG   n++p++a+++i
  gi|518652889|ref|YP_008142409.1| 155 KGRLLMKVDVKTATHHASSSWMESNAIDLLMGLWVKIREQYGN---NKDFNSVSAGITRFNGGEYDNMTPEHASMYI 228
                                       899999*************************************...56***************************** PP

                                       EEEHHHHHHHHHHHHHHHHHHTSCCS CS
                         M20_dimer  81 diRllpgedpeevleeieeilekeap 106
                                       diR ++  + +e+  e+++++e++++
  gi|518652889|ref|YP_008142409.1| 229 DIRYPKSVSEDELTGELKSYMEELLV 254
                                       **********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2706.24
//
Query:       gi|518652890|ref|YP_008142410.1|  [L=258]
Description: hypothetical protein FACI_IFERC00001G1529 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.09   11.9   0.0       0.14   11.2   0.0    1.2  1  Lipoprotein_9  NLPA lipoprotein


Domain annotation for each model (and alignments):
>> Lipoprotein_9  NLPA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   7.9e-06      0.14      71     130 ..      35      94 ..      23     100 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.9e-06
                                       EEEEEEEE---EEE-SS-SSGGG--TT-EEEEESSHHHHHHHHHHHHHTTSSEE-TT-CT CS
                     Lipoprotein_9  71 vavgnthvepiglYSkkykslselkeGatiavpndpsnegRaLllLekagLikLkdgkgl 130
                                       +a +++h+ p+++Y    +s+++++  + i+ ++  +n   aL + +   Li+ k+ k++
  gi|518652890|ref|YP_008142410.1|  35 IAGIRGHIMPLHFYRGMARSIKNISGDSPISYTDSCINWLQALAVYKYSSLIYWKKHKNA 94 
                                       566789*************************************************88765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); 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: 1898.36
//
Query:       gi|518652891|ref|YP_008142411.1|  [L=642]
Description: hypothetical protein FACI_IFERC00001G1530 [Ferroplasma acidarmanus fer1]
Scores for complete 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-56  189.5   1.3    1.1e-55  188.3   1.3    1.6  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    1.5e-47  162.0   0.0    2.7e-47  161.2   0.0    1.4  1  ECH_1           Enoyl-CoA hydratase/isomerase
      3e-30  104.7   0.0    8.1e-21   74.5   0.0    2.6  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
    4.9e-26   92.0   0.0    7.2e-24   84.9   0.0    2.3  2  ECH_2           Enoyl-CoA hydratase/isomerase
    0.00011   22.5   0.9    0.00044   20.4   0.9    2.0  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
    0.00015   21.8   1.1    0.00047   20.2   0.4    2.2  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
      0.019   14.5   1.2      0.047   13.3   1.2    1.8  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.062   12.7   0.1       0.13   11.6   0.1    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.073   12.3   0.2       0.13   11.4   0.2    1.4  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      0.074   13.6   1.0       0.38   11.4   1.0    2.3  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
        0.1   12.5   4.4       0.06   13.3   1.4    2.1  2  Vip3A_N         Vegetative insecticide protein 3A N terminal


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   1.3     7e-59   1.1e-55       1     179 [.       4     182 ..       4     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 7e-59
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaalarisfttdleeav 77 
                                       +vaviGaG+mG++ia+vfa +g++V+l d  +e +eka+  i+ sl+kl+++gk++++  +aal++i+f +++ eav
  gi|518652891|ref|YP_008142411.1|   4 QVAVIGAGVMGHSIAEVFALNGYKVNLEDFYPEVIEKAKVGINGSLDKLIASGKINDAAKKAALDNIKFFNNIGEAV 80 
                                       69*************************************************************************** PP

                                       .C-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-T CS
                           3HCDH_N  78 .dadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrge 153
                                        ++dl iE v+E +++K kv++e+++ +  d i+asnTS+++i+e+ e++k+per++g+HFfnPp lmkLvEv++g+
  gi|518652891|ref|YP_008142411.1|  81 kNVDLSIEVVPEIYNIKVKVLKEIAENT--DKIIASNTSNIRITEMGEEIKNPERLVGMHFFNPPILMKLVEVIKGD 155
                                       ************************9986..89********************************************* PP

                                       T--HHHHHHHHHHHHHTT-EEEEE.CS CS
                           3HCDH_N 154 kTseetvatvvelakkigktpvvv.kd 179
                                       kTs e v++++ela kigk+p++v kd
  gi|518652891|ref|YP_008142411.1| 156 KTSMEYVEEIYELAGKIGKKPIKVlKD 182
                                       ***********************9887 PP

>> ECH_1  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.0   1.6e-50   2.7e-47       4     250 ..     401     641 ..     398     642 .] 0.91

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 1.6e-50
                                       TTEEEEEE--CGCTTEE-HHHHHHHHHHHHHHHHSTTECEEEEEEBTSEEEEEB-HHHHHHHHCHHHHHHHCCHHHH CS
                             ECH_1   4 agvaviklnrPeavNalsaelltEliqalekleddksvravvLtGgdkaFaaGadlkemaeeekakqallkeevlel 80 
                                         v vi++++  ++N +s ell+ l + l  +e+ + v +vv+ G ++aF+aGadl +   +      +++++ ++ 
  gi|518652891|ref|YP_008142411.1| 401 GKVGVITIKNG-KNNLMSFELLKALDKQLDAIEEANDVNVVVIKGNERAFSAGADLSQFISNP-YMFMKISNTGESI 475
                                       5799*******.9************************************************75.5556778899*** PP

                                       HHHHHHSSSEEEEEE-SEEETHHHHHHHHSSEEEEETTTEEE-GGGGGTS--CTTCHHHHHHHHHHHHHHHHHHHT- CS
                             ECH_1  81 wtklytvpkpviaavnGaaigGGlelalacDiviaadnasfglnelklGlipgaggtqilarkvGkskAeeilllgk 157
                                       +++++ ++k+ ia ++G+++gGG+el lacDi+    ++++g +e+ lGlipg gg+q+l++ +G s+A+ ++l+++
  gi|518652891|ref|YP_008142411.1| 476 FDRITRMNKIFIAQLRGYVLGGGFELSLACDIRTSLPDSVIGFPETSLGLIPGYGGSQRLPNLIGISRAMDMILTCE 552
                                       ***************************************************************************** PP

                                       EEEHHHHHHCTSSSEEESGGGHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSHHHH CS
                             ECH_1 158 kisaqealkvGlvdkvvpeeqlleealelaeklaekspaalrqlkealnakledalaeqleaeaklfestfskddik 234
                                       +is++ a + G++ + + +e+l+e++++la+ l ek++ a + + + l  ++        ++   ++++    +d+k
  gi|518652891|ref|YP_008142411.1| 553 RISGEKAYEYGIITRLF-KEELEENTMKLAKDLSEKISPASVYVAKRLIYNTATINLDEEALSMGMLYA---GNDMK 625
                                       ***************98.679***************988888887777666655444455566666654...56679 PP

                                       HHHHHHHTCSH----- CS
                             ECH_1 235 eGlqaflEkrkpefed 250
                                       eG++aflEkrkp++++
  gi|518652891|ref|YP_008142411.1| 626 EGVKAFLEKRKPDYKG 641
                                       **************97 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0     5e-24   8.1e-21       1      97 []     185     279 ..     185     279 .. 0.97
   2 !   27.5   0.0   2.2e-09   3.6e-06      10      88 ..     303     381 ..     299     386 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 5e-24
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GFvvnR+ ap +   ++++ +++ +pe iD+ ++   GlpmGp++l+d+vgld++ + l+++ +el+ + y ++  +
  gi|518652891|ref|YP_008142411.1| 185 GFVVNRISAPEMLLLCNAYGNKIDRPEAIDKYFKS-QGLPMGPYQLFDYVGLDTVVDSLQYYGKELSPD-YGKCHAF 259
                                       9**********************************.*****************************9888.556**** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       ++++ea++lg ktg+g+yk+
  gi|518652891|ref|YP_008142411.1| 260 DSFIEAKHLGLKTGSGIYKW 279
                                       ******************97 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 2.2e-09
                                       HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT-- CS
                             3HCDH  10 pllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapsplleklveagrl 86 
                                         +nea +l+e+gva p di+  +++gl+ p Gp++++  +  d ++  l+ l+++++ + ++ps+ +e+   ++ +
  gi|518652891|ref|YP_008142411.1| 303 LEINEATKLIEDGVAVPDDIEIGVKYGLNRPFGPITVANGLSNDEVLETLNNLYKQYKIEVFKPSKTIESHKMKESF 379
                                       568*********************************************************99999998876666555 PP

                                       BG CS
                             3HCDH  87 gr 88 
                                        +
  gi|518652891|ref|YP_008142411.1| 380 NK 381
                                       55 PP

>> ECH_2  Enoyl-CoA hydratase/isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.9   0.0   4.4e-27   7.2e-24       2     177 ..     404     573 ..     403     587 .. 0.88
   2 !    7.5   0.0    0.0015       2.4     246     317 ..     574     639 ..     564     642 .] 0.70

  Alignments for each domain:
  == domain 1  score: 84.9 bits;  conditional E-value: 4.4e-27
                                       EEEEE--GGGTT-B-HHHHHHHHHHHHHHCC-TT-SEEEEEESSSSECE--B--HHHHHHHHCS-THHHHHHHHHHH CS
                             ECH_2   2 gvitLnrpkalNaLslemvralkealkewekddevklvvlkgagekafCAGgDvralyeaakegkkeeeeffreeYk 78 
                                       gvit+ +  + N +s e+++al+++l+++e+ ++v++vv+kg +e+af+AG D+ ++ ++         ++ ++  +
  gi|518652891|ref|YP_008142411.1| 404 GVITIKNG-KNNLMSFELLKALDKQLDAIEEANDVNVVVIKG-NERAFSAGADLSQFISNPYMFM----KISNTGES 474
                                       56666554.4599*****************************.56***********998877743....46677778 PP

                                       HHHHHHC-SS-EEEEE-BEEETHHHHHHTTSSEEEE-TT-EEE--GGGGT----TTHHHHHHCSST.THHHHHHHH- CS
                             ECH_2  79 lnyliatypkpvvalmdGivmGgGvGlsvhgsfrvvtertvfAmPEtaIGlfPDvGgsyfLsrlpg.elGlylalTG 154
                                       +  +i +++k ++a + G+v+GgG  ls+ + +r    ++v+  PEt++Gl+P  Ggs  L+ l g + ++ + lT 
  gi|518652891|ref|YP_008142411.1| 475 IFDRITRMNKIFIAQLRGYVLGGGFELSLACDIRTSLPDSVIGFPETSLGLIPGYGGSQRLPNLIGiSRAMDMILTC 551
                                       8899************************************************************88799******** PP

                                       --B-HHHHHHTTS--EE--GGGH CS
                             ECH_2 155 arlkgadalaaglathyvpsekl 177
                                       +r++g+ a++ g+ t ++++e l
  gi|518652891|ref|YP_008142411.1| 552 ERISGEKAYEYGIITRLFKEE-L 573
                                       ****************99876.3 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0015
                                       SHHHHHHHHHH.HHS-HHHHHHHHHHHHHHTTT--HHHHHHHHHHHHHHHHHHSSHHHHHHHHTTS------- CS
                             ECH_2 246 dewakktletl.kkrsPtslkvtleqlrrgrklsslaevlrmElrlalrllaekDfveGvrallvdkdkkPkW 317
                                       +e   k ++ l +k sP s+ v+ +++ ++++ +     l++E   +  l a +D+ eGv+a l ++  kP +
  gi|518652891|ref|YP_008142411.1| 574 EENTMKLAKDLsEKISPASVYVAKRLIYNTATIN-----LDEEALSMGMLYAGNDMKEGVKAFLEKR--KPDY 639
                                       333444444441578****************997.....77777777777778*********98554..5665 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.9   2.7e-07   0.00044       1      97 [.       4     122 ..       4     145 .. 0.69

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 2.7e-07
                                       EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT........................EEE-SSHHHHH CS
                     NAD_binding_2   1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaeg........................akaaesieelv 53 
                                       ++++iG GvMG+++a+ ++ +gykv + +  +e +e++                            +k +++i e+v
  gi|518652891|ref|YP_008142411.1|   4 QVAVIGAGVMGHSIAEVFALNGYKVNLEDFYPEVIEKAKVGIngsldkliasgkindaakkaaldnIKFFNNIGEAV 80 
                                       589*****************************999998765356889977777777777777777777777777777 PP

                                       HHCSEEEE-SSSHHHHH.HHHHSHCCC--TT-EEEE-S---HHHH CS
                     NAD_binding_2  54 asldvvitmvkagkavd.eviegllealkkgdilidgstsspedt 97 
                                       +++d+ i +v++  +++ +v+++++e   + d +i + ts+++ t
  gi|518652891|ref|YP_008142411.1|  81 KNVDLSIEVVPEIYNIKvKVLKEIAE---NTDKIIASNTSNIRIT 122
                                       77777777777766655223333444...4455555555555444 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.4   2.9e-07   0.00047       1      98 [.       4     117 ..       4     127 .. 0.74
   2 ?   -3.0   0.0       3.8   6.2e+03      55     104 ..     422     443 ..     409     453 .. 0.55

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 2.9e-07
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H...........HHHHHHHHHSSBTTTBTT----TTEEEES-HHHH CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvree...........elieeineehenvkyLpgiklpenlvattdlaea 66 
                                       ++av+GaG  G ++A v+a ng +v l  + +             ++++ ++ + ++  ++ +l +n+++ +++ ea
  gi|518652891|ref|YP_008142411.1|   4 QVAVIGAGVMGHSIAEVFALNGYKVNLEDFYPeviekakvginGSLDKLIASGKINDAAKKAAL-DNIKFFNNIGEA 79 
                                       59********************999999999978888888887445555555444455666555.699********* PP

                                       HTT--EEEE---H......HHHHHHHHHHCCC--TT-E CS
                    NAD_Gly3P_dh_N  67 lkgadiivlvvPs......qalrevlkklkgllkkkai 98 
                                       +k++d+ + vvP       ++l+e++++ +++++ ++ 
  gi|518652891|ref|YP_008142411.1|  80 VKNVDLSIEVVPEiynikvKVLKEIAENTDKIIASNTS 117
                                       ***********963222225566666666666666555 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.8
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-EEEE--- CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkailvsliK 104
                                       ++l  + d  e +++++++v                            iK
  gi|518652891|ref|YP_008142411.1| 422 KALDKQLDAIEEANDVNVVV----------------------------IK 443
                                       44444444444444444444............................44 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.2   2.9e-05     0.047       2      85 ..       4      91 ..       3     130 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.9e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT.....S-SS--TTHHHHHHHHCHTTTEEEES-HHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsg.....kipiyepgLeelvkkavesgrlsfttdvekave 75
                                      +++viG+G +G   a v+a  g +v + D   e ++k + g     +  i   ++++  kka+  ++++f +++ +av+
  gi|518652891|ref|YP_008142411.1|  4 QVAVIGAGVMGHSIAEVFALNGYKVNLEDFYPEVIEKAKVGingslDKLIASGKINDAAKKAA-LDNIKFFNNIGEAVK 81
                                      79***************************9988888877651111144577778888888888.79************* PP

                                      C-SEEEE--- CS
                    UDPG_MGDP_dh_N 76 eadvifiaVg 85
                                      + d+ + +V+
  gi|518652891|ref|YP_008142411.1| 82 NVDLSIEVVP 91
                                      ***9998886 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1     8e-05      0.13      37      90 ..       3      54 ..       2      58 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 8e-05
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEECSHHHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelvsleella 90
                                      k+v++iG+G +G+++a++++  g kv   d +++  e ++++g+   sl++l+a
  gi|518652891|ref|YP_008142411.1|  3 KQVAVIGAGVMGHSIAEVFALNGYKVNLEDFYPEVIE-KAKVGI-NGSLDKLIA 54
                                      789*****************************99777.555565.458888876 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 ?   11.4   0.2   8.1e-05      0.13       2      47 ..       4      54 ..       3     129 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
                                      SEEEE--SHHHHHHHHHHHHHTS-EEEEE.....TTHCHHHCSHHHHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  2 dvvviGgGpAGlaaaltlaqagakvtlve.....legtclnggcllskall 47
                                      +v+viG+G+ G++ a+  a +g+kv l +      e++ ++   +l k ++
  gi|518652891|ref|YP_008142411.1|  4 QVAVIGAGVMGHSIAEVFALNGYKVNLEDfypevIEKAKVGINGSLDKLIA 54
                                      677777777777777777777777777666666655555555555555444 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 ?   11.4   1.0   0.00023      0.38       2      29 ..       5      29 ..       4     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00023
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEE CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheiv 29
                                      +++iGaG mg+++a+ ++ +g   +++ 
  gi|518652891|ref|YP_008142411.1|  5 VAVIGAGVMGHSIAEVFALNG---YKVN 29
                                      8********************...7665 PP

>> Vip3A_N  Vegetative insecticide protein 3A N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   1.4   3.7e-05      0.06      54     112 ..      42     100 ..      28     129 .. 0.85
   2 ?   -1.9   0.1       1.6   2.6e+03     128     144 ..     421     437 ..     395     456 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                           Vip3A_N  54 ldgvngslndliaqgnlntelskeilkianeqnqvlndvnnkldaintmlrvylpkits 112
                                         g+ngsl+ lia g++n    k  l   +  n++ + v+n   +i+ + ++y  k+  
  gi|518652891|ref|YP_008142411.1|  42 KVGINGSLDKLIASGKINDAAKKAALDNIKFFNNIGEAVKNVDLSIEVVPEIYNIKVKV 100
                                       459********************999999999999999999888999999999888754 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                           Vip3A_N 128 ieylskqlqeisdkldi 144
                                       ++ l kql+ i +  d+
  gi|518652891|ref|YP_008142411.1| 421 LKALDKQLDAIEEANDV 437
                                       34444555555444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (642 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.42
# Mc/sec: 4625.41
//
Query:       gi|518652892|ref|YP_008142412.1|  [L=525]
Description: hypothetical protein FACI_IFERC00001G1531 [Ferroplasma acidarmanus fer1]
Scores for complete 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-80  270.8   0.3    7.5e-80  268.6   0.0    1.8  2  AMP-binding    AMP-binding enzyme
    6.9e-14   52.6   0.0      2e-13   51.1   0.0    1.8  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
     0.0011   18.7   0.3      0.069   12.9   0.0    3.0  3  ubiquitin      Ubiquitin family


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.6   0.0   1.2e-83   7.5e-80       7     422 ..      18     429 ..      12     430 .. 0.85
   2 ?    0.0   0.0     0.042   2.5e+02     384     412 ..     474     504 ..     469     508 .. 0.81

  Alignments for each domain:
  == domain 1  score: 268.6 bits;  conditional E-value: 1.2e-83
                                       HSTTSEEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-H CS
                       AMP-binding   7 ktpdkvalvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlta 83 
                                        + d+  +++  ++ +lTY+ ++++v+++Aa L ++Gvk+gdr+a++   ++ ++  ++ i ++Gav+ ++n ++++
  gi|518652892|ref|YP_008142412.1|  18 ANGDQK-IIY--KNLQLTYNSFYKNVKNFAANLVKIGVKPGDRIAVIDYDTINYMYCYYSIPMIGAVIHMVNIRYPP 91 
                                       444444.558..899************************************************************** PP

                                       HHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS....-TSCCCS- CS
                       AMP-binding  84 eelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae....kpeeeeel 156
                                       e l y +++se ++++  v+s+ ++ l + +   e  k  iv+++ + +++ +l++    +++ +    ++    ++
  gi|518652892|ref|YP_008142412.1|  92 EILYYTIKNSEDTYIV--VNSDFMPLLMQFKNMFEFIKGFIVYSEHGHENY-QLDNVY--YAD-DllkdTDYNITPP 162
                                       ****************..888888877777776677777777776665544.333322..222.123455667779* PP

                                       BTTSEEEEEEE--SSSS-EEEEEEHHHH.HHHHHHHH.HHHCSC.CTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 157 kpddlayiiYTSGTTGkPKGVmlshrnl.vanvaslk.letrfk.lkeddvvlsilplahifglilelllallsGat 230
                                       +++d+a+++YTSGTTG PKGV + hr+l ++++a+++ l+++   l++++ +l  +p++h+ ++    ++a+++G +
  gi|518652892|ref|YP_008142412.1| 163 DENDMATLFYTSGTTGLPKGVYYNHRQLvLHSMATAEgLSDDPIlLNKTSILLPLVPMFHVHAW-GMPYFAIMKGLK 238
                                       *************************887577778877877775547778899999*********.************ PP

                                       EEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEE.EEESS-EBHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlv.llggeplspellrffra 305
                                        vl+ k + +d  +++e++ek++vt  a vP++l  ll+ ++ ++       l++l+l  ++gg++l++ l+r +++
  gi|518652892|ref|YP_008142412.1| 239 YVLPGKYE-WD--RIVETMEKEHVTNSAMVPSILYLLLQaKRGPE------VLGKLKLKsVIGGAALNEGLARSAES 306
                                       ***88665.45..689***********************676666......78888887456*************** PP

                                       HHTCEEEEEEEEGGGSSECEE.........CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETT CS
                       AMP-binding 306 lfgeevlegYGlTEttgvvtv.........lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpg 373
                                       ++   ++ gYG++Et++++t          l +e ++k++ ++G p+p v +++v + +     d e Ge+ v+ p+
  gi|518652892|ref|YP_008142412.1| 307 IGMS-LVTGYGMSETCPILTLasytndilpLSEEIKEKYRRKTGVPVPMVNLRVVYQGKDVAKDDTEIGEIIVQAPW 382
                                       *876.**************7777799**99777888889999*************9864444446666********* PP

                                       S-SEBTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 374 vmkgYlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       ++ gYlk+pe+ta+ ++  ++wl+TGDl+++d+ Gy++iv+R  d +k+
  gi|518652892|ref|YP_008142412.1| 383 LTAGYLKDPEKTAKLWI--DGWLHTGDLATMDKYGYIKIVDRESDAVKS 429
                                       ****************9..57***********99*************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.042
                                       HHHHHEEET.CCEEEEEEEEE.EETTSEEEE CS
                       AMP-binding 384 ataeafdse.grwlrTGDlgr.ldedGylei 412
                                       at ea++++ ++++ TG +++ + +d y+++
  gi|518652892|ref|YP_008142412.1| 474 ATVEAIKEHmQQFVDTGRIAKfWLPDDYIFV 504
                                       788888854557*********669****987 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         3   1.8e+04      42      55 ..     336     349 ..     325     361 .. 0.72
   2 !   51.1   0.0   3.3e-17     2e-13       2      76 .]     439     514 ..     438     514 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHT- CS
                     AMP-binding_C  42 leeeLkahvrkelg 55 
                                       l ee+k++ r++ g
  gi|518652892|ref|YP_008142412.1| 336 LSEEIKEKYRRKTG 349
                                       67899999988766 PP

  == domain 2  score: 51.1 bits;  conditional E-value: 3.3e-17
                                       HHHHHHSSTTEEEEEEE-----TTS---EEEEEE------HHHHHHHHH.HHHT-TTTS-SEEEE-S---B-TTS- CS
                     AMP-binding_C   2 vEsalvshpaVaeaaVvGvpdevkGealvafVvlkdgsealeeeLkahv.rkelgpyavpkkvvfvdelpktrsGK 76 
                                       +E  ++++p+V e+aV  ++de++Ge++vaf+   + +ea++e+ +++v + ++++++ p++ +fvd+++kt +GK
  gi|518652892|ref|YP_008142412.1| 439 LEDLISTVPGVGEVAVTKKSDEKWGERPVAFIKGTATVEAIKEHMQQFVdTGRIAKFWLPDDYIFVDDFEKTGTGK 514
                                       59999**************************986323455777777777555***********************9 PP

>> ubiquitin  Ubiquitin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1      0.56   3.3e+03      38      51 ..      21      34 ..      17      42 .. 0.80
   2 !   12.9   0.0   1.2e-05     0.069      22      57 ..     338     376 ..     337     380 .. 0.86
   3 ?    2.1   0.0     0.028   1.7e+02      15      32 ..     470     487 ..     463     494 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.56
                                      GEEEEETTEEE-TT CS
                         ubiquitin 38 qqrLiysGkvLede 51
                                       q++iy+  +L  +
  gi|518652892|ref|YP_008142412.1| 21 DQKIIYKNLQLTYN 34
                                      699***99998766 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 1.2e-05
                                       HHHHHHHHHHHT..SSGGGEEEEETTEEE.-TTSBHGGH CS
                         ubiquitin  22 eelKekiaekeg..ipaeqqrLiysGkvL.edertleey 57 
                                       ee+Kek+ +k+g  +p+ ++r++y+Gk   +d+  ++e+
  gi|518652892|ref|YP_008142412.1| 338 EEIKEKYRRKTGvpVPMVNLRVVYQGKDVaKDDTEIGEI 376
                                       69**********77888899*******998888888876 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.028
                                       EETTSBHHHHHHHHHHHH CS
                         ubiquitin  15 veesdtveelKekiaeke 32 
                                       ++ + tve +Ke+ ++  
  gi|518652892|ref|YP_008142412.1| 470 IKGTATVEAIKEHMQQFV 487
                                       67899*********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (525 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.38
# Mc/sec: 4124.80
//
Query:       gi|518652893|ref|YP_008142413.1|  [L=391]
Description: hypothetical protein FACI_IFERC00001G1532 [Ferroplasma acidarmanus fer1]
Scores for 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-59  200.5   0.0    9.7e-59  198.8   0.0    1.7  2  Thiolase_N     Thiolase, N-terminal domain
    5.3e-45  152.0   0.1    1.1e-44  151.1   0.1    1.5  1  Thiolase_C     Thiolase, C-terminal domain
    0.00029   20.5   0.8     0.0013   18.3   0.4    2.2  2  ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
  ------ inclusion threshold ------
       0.11   11.2   0.0       0.48    9.1   0.0    1.9  2  SpoVAD         Stage V sporulation protein AD (SpoVAD)


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 !  198.8   0.0   2.2e-62   9.7e-59       1     258 [.       4     259 ..       4     261 .. 0.89
   2 ?   -1.1   0.0      0.22   9.7e+02      30      47 ..     294     311 ..     293     328 .. 0.87

  Alignments for each domain:
  == domain 1  score: 198.8 bits;  conditional E-value: 2.2e-62
                                       EEEEEEEEE--EET......TSTTTTS-HHHHHHHHHHHHHHHHTS-GGGCCEEEEEHSSCTTSTSC.HHHHHHHHT CS
                        Thiolase_N   1 vvivsaartpigkf......ggslkdlsaeeLlaealkallekagvdpeevdevivGnvlqagegqn.iarqaalka 70 
                                       v+iv+  r+p+ +       + +++dl+++++l+e++++ +++++++p+e+++vi G+  qage+++   r+ +l a
  gi|518652893|ref|YP_008142413.1|   4 VYIVDYRRIPFSRArprdpeKDVYNDLRMDKMLSELIRHSVSETKINPAEIEDVITGCAFQAGENWTyGGRHPVLLA 80 
                                       6788888888876422222267999******************************************999******* PP

                                       TS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEESTTS-EEETCTTT..TGGSSSSEEEEEHHHHHH CS
                        Thiolase_N  71 gipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEsmsnaptaestdvr..sglklgdekakdllipdg 145
                                       ++p +vpa+ ++++csS+l+a   +a +i+ag+a +++ gG+E+m+++p  ++ +++  +   + + k +++     
  gi|518652893|ref|YP_008142413.1|  81 DLPVSVPAMSLDRACSSSLNATGIGALEIMAGKAGIIISGGMEHMTHVPLGVDNQFIkpNMELMANPKYSKFN---- 153
                                       ****************************************************977664322223333333333.... PP

                                       TEETTTTSEHHHHHHHHHHHHT--HHHHHHHHHHHHHHHHHHHHTTTTTTTBE-EEEEESSSEEEE-S-TTS-TT-- CS
                        Thiolase_N 146 ladafneehmGltaenlakkykisReeqdefAvkshqkaaaaqkagkFkdeivPvkvkgkkgkktvdkdeairsevt 222
                                          +   + mGltae+lak  +isR+e de+  +sh++aa+a ++g  k ei+Pv+v+g    +t+++d +ir+++t
  gi|518652893|ref|YP_008142413.1| 154 ---MNVSYNMGLTAEKLAKLRNISRDEMDEYSYNSHKRAAKAYEDGFMKGEIMPVTVNG----NTITSDLGIRKDTT 223
                                       ...34589**************************************99*********99....58************ PP

                                       HHHHHTS-BSSSTTSS-BTTSB--BEEEEEEEEEEE CS
                        Thiolase_N 223 aekLaklkpaFkkeGtvtAgnasqisDGaaavllms 258
                                       +e++++lkpa++++G +tA+n+s+++DGa++v+lms
  gi|518652893|ref|YP_008142413.1| 224 LEQIKSLKPAYSEDGIITAANSSSLNDGASMVMLMS 259
                                       ***********************************8 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.22
                                       HHHHHHHHHTS-GGGCCE CS
                        Thiolase_N  30 alkallekagvdpeevde 47 
                                       a k++le+++++pe++d+
  gi|518652893|ref|YP_008142413.1| 294 ATKKVLERNNLKPEDIDY 311
                                       6799***********997 PP

>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.1   2.4e-48   1.1e-44       1     123 []     268     390 ..     268     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 2.4e-48
                                       ---SEEEEEEEEEE--GGGGGGHHHHHHHHHHHHHT--GGGESEEEE--SBHHHHHHHHHHHT--GGGBSTT--HHH CS
                        Thiolase_C   1 lkplakirsyaevgvdpeilglgPayaikkvlkkagltvedidlfEinEAFaaqaLavakaldldlekvNvnGGaia 77 
                                       lkp+a+i+++a +gvdp+i+g gP++a+kkvl+++ l+ edid++EinEAFa+++L +++a++ldl++vN++GG ++
  gi|518652893|ref|YP_008142413.1| 268 LKPMARIVDFAAAGVDPTIMGEGPVPATKKVLERNNLKPEDIDYWEINEAFAVVVLNAVHAFNLDLNRVNIHGGGLS 344
                                       589************************************************************************** PP

                                       H-B-TTTHHHHHHHHHHHHHHHCTTSEEEEEEEETTTEEEEEEEEE CS
                        Thiolase_C  78 lGHPlGasGaRivvtllselkkeggklgvaalCigggqgvalviek 123
                                       +GHPlGa+GaRi+ tl+++l+ ++g lg+a+lC gggqg ++++e+
  gi|518652893|ref|YP_008142413.1| 345 IGHPLGATGARIAGTLARTLEDKKGDLGIATLCVGGGQGYSMLLER 390
                                       *******************************************985 PP

>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.4     3e-07    0.0013     167     207 ..      87     127 ..      81     132 .. 0.93
   2 ?   -1.3   0.0       0.3   1.3e+03     220     240 ..     181     201 ..     163     204 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3e-07
                                       SEEEEESGGGHHHHHHHHHHHHHHTTS-SEEEEEEEE---S CS
                     ketoacyl-synt 167 psvtvdtACsSslvavhaavqslrsgeadvalaGGvelllt 207
                                       p++++d ACsSsl a      ++++g+a +++ GG+e +++
  gi|518652893|ref|YP_008142413.1|  87 PAMSLDRACSSSLNATGIGALEIMAGKAGIIISGGMEHMTH 127
                                       899**********************************9887 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.3
                                       B-TTSGGGTTBTTB-SB-BB- CS
                     ketoacyl-synt 220 lspdgrckafdpkadGfvlGE 240
                                        s + + +a +++ dGf+ GE
  gi|518652893|ref|YP_008142413.1| 181 YSYNSHKRAAKAYEDGFMKGE 201
                                       344556777777779999887 PP

>> SpoVAD  Stage V sporulation protein AD (SpoVAD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00011      0.48      53     138 ..      34     127 ..      24     162 .. 0.76
   2 ?   -0.8   0.0      0.11   4.9e+02      58      75 ..     294     311 ..     249     330 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00011
                                       HHHHHHHHHHHHHTT--GGG-SEEEEEESSGGGHHHHHHHHH........H---EEEB--GGGHHHHHHHHHHHHHH CS
                            SpoVAD  53 klleeavkkalkkanlkkedidfllaGDLlnqlisssfaare........lkiPflglygaCstsaeslalaallvd 121
                                       k+l+e +++++++++++  +i+ +++G   +     +++ r+        +++P ++l  aCs+s ++  ++al + 
  gi|518652893|ref|YP_008142413.1|  34 KMLSELIRHSVSETKINPAEIEDVITGCAFQAGENWTYGGRHpvlladlpVSVPAMSLDRACSSSLNATGIGALEIM 110
                                       67777777777777777777777777777766666666655433333333789************************ PP

                                       TTS-SEEEEEEEE-CCH CS
                            SpoVAD 122 ggfakrvlaatsshfaa 138
                                       +g a  ++++   h + 
  gi|518652893|ref|YP_008142413.1| 111 AGKAGIIISGGMEHMTH 127
                                       *********99999864 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.11
                                       HHHHHHHHTT--GGG-SE CS
                            SpoVAD  58 avkkalkkanlkkedidf 75 
                                       a+kk+l+++nlk edid+
  gi|518652893|ref|YP_008142413.1| 294 ATKKVLERNNLKPEDIDY 311
                                       567778888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2705.37
//
Query:       gi|518652894|ref|YP_008142414.1|  [L=359]
Description: hypothetical protein FACI_IFERC00001G1533 [Ferroplasma acidarmanus fer1]
Scores for complete 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-32  110.2   0.1    1.4e-31  109.7   0.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.4e-28   97.3   0.1    9.1e-28   96.3   0.1    1.5  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
    4.4e-09   36.7   0.0    1.2e-08   35.3   0.0    1.8  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    5.5e-09   36.7   0.1      5e-08   33.6   0.1    2.3  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.7   0.1   3.2e-35   1.4e-31       1     149 [.     215     355 ..     215     356 .. 0.95

  Alignments for each domain:
  == domain 1  score: 109.7 bits;  conditional E-value: 3.2e-35
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       gkGf+++m  +n +R+ vaa++lg+ar a++ + +y+++   +       +   ++l ++ +++ea+r ++y+aa  
  gi|518652894|ref|YP_008142414.1| 215 GKGFYYIMMFFNISRIYVAAQSLGIARGAFDKIKSYIKENNIKD------EESMFRLSDVGTRIEATRQMTYNAATY 285
                                       79*************************************99855......66789********************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                       l + kp++  +smaK+++se+a+++a++am++lG ++  e+  v+r++r+a++++i+eGtsei +++iar +
  gi|518652894|ref|YP_008142414.1| 286 LFEFKPKPELTSMAKAYGSETAVYAAESAMEILGDHSAYED--VQRIFRNAKIMEIWEGTSEIEKLVIARYI 355
                                       ************************************99555..7*************************976 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.1     2e-31   9.1e-28       1      96 [.     107     202 ..     107     203 .. 0.95

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 2e-31
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS---.----EEEEEEE..GGGEEE- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpd.rarglslflvprdapgvsvr 76 
                                       ++++TEp++Gsdva++kt +a+++g++y+lnG+K++itn+ ia++++vlart +++  ++gls+flv+++ +g++ +
  gi|518652894|ref|YP_008142414.1| 107 GLGVTEPSGGSDVAGLKT-TAKKQGNKYILNGSKMFITNGSIADYLVVLARTSEDSnPHHGLSTFLVNTKLKGFKAN 182
                                       589***************.88888889************************6666689******************* PP

                                       ----BSS-TTS-EEEEEEE. CS
                     Acyl-CoA_dh_M  77 rieeklGlrglptgelvfed 96 
                                       ++ +klG+r ++t+el+f++
  gi|518652894|ref|YP_008142414.1| 183 KLVDKLGVRATNTAELQFNN 202
                                       ******************98 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.0   2.7e-12   1.2e-08       2     133 ..     231     344 ..     230     345 .. 0.87

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 2.7e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----HH CS
                     Acyl-CoA_dh_2   2 giaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtve 78 
                                        +aa+ lG+Ar+a++++ ++++e            d+  +++l ++ +r++A r+++++aa+   +     k+    
  gi|518652894|ref|YP_008142414.1| 231 YVAAQSLGIARGAFDKIKSYIKENNI--------KDEESMFRLSDVGTRIEATRQMTYNAATYLFEF----KP---- 291
                                       689*****************998777........566678**********************95542....22.... PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  79 draearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                       +    ++a+a+ +e+a+ a+++++e+ G ++ +++  +qR++R+a++++++++++
  gi|518652894|ref|YP_008142414.1| 292 KPELTSMAKAYGSETAVYAAESAMEILGDHSAYED--VQRIFRNAKIMEIWEGTS 344
                                       1245799*************************987..9*********99998876 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.6   0.1   1.1e-11     5e-08       2     103 ..       3      94 ..       3     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 33.6 bits;  conditional E-value: 1.1e-11
                                       HHHHHHHHHHHHHHHHHT.HHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeel.aphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradag 77 
                                       ee +++r ++refa +e  +++aa++d+++++p+el+kk   lG++ ++ p ++          +i +eel r+dag
  gi|518652894|ref|YP_008142414.1|   3 EEYDEYRNKIREFALKEFtEDVAADYDRKEAYPDELRKKSLSLGIVDMQNPAKV----------MIGIEELCRVDAG 69 
                                       67899*************788999999999****************99999776..........6889********* PP

                                       HHHHHHHHHHTTHHHHHHHS-HHHHH CS
                     Acyl-CoA_dh_N  78 lalllgvhsslvapailrfGteeqkr 103
                                       l+++l +    ++++i+ fG+++qk+
  gi|518652894|ref|YP_008142414.1|  70 LGIALTTP-YFGSEVIMLFGNDAQKA 94 
                                       *9988775.57889**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (359 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2682.66
//
Query:       gi|518652895|ref|YP_008142415.1|  [L=328]
Description: acyl-CoA dehydrogenase, short-chain specific [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-12   45.6   0.0    2.1e-11   44.5   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    1.2e-10   41.8   0.0    1.4e-08   35.1   0.0    2.3  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    4.2e-06   27.1   0.0      0.012   15.9   0.0    2.4  2  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.5   0.0   3.5e-15   2.1e-11       2      89 ..       3      87 ..       2      98 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.5 bits;  conditional E-value: 3.5e-15
                                      HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHHHH CS
                     Acyl-CoA_dh_N  2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradaglal 80
                                      ee   l++tv+ef+e++l   ++++++eg + +++ + la +G+lg t+p +y G++ld++++ i++ee+++++ ++a+
  gi|518652895|ref|YP_008142415.1|  3 EENNILKETVAEFCEKNLD--EKKIENEG-ISKATTELLASQGFLGATIPAKYSGSELDNTSYEIILEEISKYSPSVAM 78
                                      78999*************6..68886655.678899999**************************************99 PP

                                      .HHHHHHHTT CS
                     Acyl-CoA_dh_N 81 .llgvhsslv 89
                                       ++ + +sl 
  gi|518652895|ref|YP_008142415.1| 79 kIF-ILNSLY 87
                                      544.555555 PP

>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.1   0.0   2.4e-12   1.4e-08      19     140 ..     202     313 ..     199     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 35.1 bits;  conditional E-value: 2.4e-12
                                       -..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHH CS
                     Acyl-CoA_dh_1  19 aaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaealdagkpdraeasmaKlfa 95 
                                        a alg++  al+ a++y   rkafg  l d++ ++++l +++    ++r+++y  +               a ++a
  gi|518652895|ref|YP_008142415.1| 202 SAIALGMISGALQKAIDYTSVRKAFGNYLKDFEPISFRLSRFRSIESVLRSALYGGVD-----------PYYAFNLA 267
                                       6789**************************************************9884...........34566788 PP

                                       HHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHH.HHSSS-HHH CS
                     Acyl-CoA_dh_1  96 selaqevadlamqllGgaGyleeypverlyrdarvl.rigeGtsei 140
                                        e ++e+a+  +  +Gg+Gy ++ +ve++yrd+ v+ +i+ G++e 
  gi|518652895|ref|YP_008142415.1| 268 MESMVEIARYSVNTHGGYGYFQDFGVEKFYRDSIVMkSIFYGNQEL 313
                                       9*******************************99883577799886 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-06     0.012       4      47 ..     202     243 ..     200     256 .. 0.93
   2 !    8.7   0.0   0.00032       1.9      90     125 ..     267     302 ..     259     308 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHH CS
                     Acyl-CoA_dh_2   4 aavalGaAraalaefvelarervrassgekladdpatqlalaea 47 
                                       +a+alG+  +al+++++++  r+   +g+ l+d++ + ++l + 
  gi|518652895|ref|YP_008142415.1| 202 SAIALGMISGALQKAIDYTSVRKA--FGNYLKDFEPISFRLSRF 243
                                       89**********************..**************9886 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00032
                                       HHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHH CS
                     Acyl-CoA_dh_2  90 avelaiaavdalfeaaGgsalrkesplqRlwRDaha 125
                                       a e  +++++  ++++Gg++++++  ++ ++RD  +
  gi|518652895|ref|YP_008142415.1| 267 AMESMVEIARYSVNTHGGYGYFQDFGVEKFYRDSIV 302
                                       66777888888999*******************866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       589  (0.0328518); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2327.29
//
Query:       gi|518652896|ref|YP_008142416.1|  [L=158]
Description: potassium-transporting ATPase subunit C [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  113.0   0.9    2.1e-17   63.5   0.2    2.0  2  KdpC      K+-transporting ATPase, c chain


Domain annotation for each model (and alignments):
>> KdpC  K+-transporting ATPase, c chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.2   1.2e-21   2.1e-17       3      62 ..       9      68 ..       7      74 .. 0.93
   2 !   48.8   0.0     4e-17   7.2e-13     118     180 ..      74     135 ..      69     137 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 1.2e-21
                                      HHHHHHHHHHHHHHTHHHHHHHHHHHHH-HHHHTT-EEE.ETEEEEETTT------SSS- CS
                              KdpC  3 kalrlllvltvllgliYplavtgiaqllfpeqAnGslieadgkvvGseligqeftsdkYf 62
                                      ++lr++++l++++gl+Yp++vtgi+q +fp qAnG+l + d+++vGs ligq+ ++++Y+
  gi|518652896|ref|YP_008142416.1|  9 SSLRMAVILVLICGLLYPAVVTGIGQGVFPYQANGELAKLDNTTVGSYLIGQSTNNSQYL 68
                                      789***************************************************888885 PP

  == domain 2  score: 48.8 bits;  conditional E-value: 4e-17
                                       -BSSS---EE-HHHHHHTHHHHHHHHT--HHHHHHHHHHTEE--SSTTT---EEEHHHHHHHH CS
                              KdpC 118 aSgSGLDPhIspeaAelQvarvakarglseeeveklvaentegrllgilGeprVnVlklNlaL 180
                                       +S+SG+DP+I++++A +Q++ + +a+++s + +  l+++nt++  l ++G+ +Vn lkl +++
  gi|518652896|ref|YP_008142416.1|  74 NSASGVDPDITVASALIQAQVIHNATNISLSYLDGLIHNNTRHT-LFFFGTAYVNALKLDIQI 135
                                       7****************************************986.5699**********9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      409  (0.0228122); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1094.22
//
Query:       gi|518652897|ref|YP_008142417.1|  [L=720]
Description: hypothetical protein FACI_IFERC00001G1536 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-36  124.8   2.6    2.6e-36  124.8   2.6    2.9  3  E1-E2_ATPase     E1-E2 ATPase
    9.1e-31  107.8   0.3    1.6e-30  107.0   0.3    1.4  1  Hydrolase        haloacid dehalogenase-like hydrolase
    1.6e-05   24.7   2.7    0.00024   21.0   1.0    2.3  2  Hydrolase_3      haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
      0.085   12.8   0.0       0.48   10.4   0.0    2.1  2  Intein_splicing  Intein splicing domain


Domain annotation for each model (and alignments):
>> E1-E2_ATPase  E1-E2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.8      0.57   2.6e+03     149     166 ..      52      69 ..      38      89 .. 0.55
   2 !  124.8   2.6   5.8e-40   2.6e-36      13     181 .]     130     296 ..     115     296 .. 0.94
   3 ?    3.2   1.8     0.013        57     114     167 ..     619     673 ..     590     681 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.57
                                       HHHHHHHHHHS-TTHHHH CS
                      E1-E2_ATPase 149 lralallvaaiPcaLpla 166
                                        ++++ll+a++P a+p +
  gi|518652897|ref|YP_008142417.1|  52 SFFVVLLMAIVPGAFPHL 69 
                                       334445555555444433 PP

  == domain 2  score: 124.8 bits;  conditional E-value: 5.8e-40
                                       TS-EEEEGGG--TTSEEEEETT-B--SEEEEEEE-SEEE-TTTS---S-EE-G-TTEE-TT-EEEE-EEEEEEEE-T CS
                      E1-E2_ATPase  13 gteeeidakelvpGDivllkagdrvpaDgrivegsaevdesaLTGEslpvekekgdmvfsGtvvvsgeakavVtatg 89 
                                        t+e+++++el+ GD++l+++gd+vp+D+++ eg a vdes+LTGEs  v+k+kgd+v++G++v+s++++a+V    
  gi|518652897|ref|YP_008142417.1| 130 RTIESVKSSELRKGDVILIEKGDQVPIDAEVTEGIAMVDESLLTGESAGVKKSKGDTVIGGSTVISDSIVAIVNVNP 206
                                       38899************************************************************************ PP

                                       TTSTTTTTSTTS--------HHHHHHHHHHHHHHHHHHHHHHHHHHS-STTTSSTTHHHHHHHHHHHHHS-TTHHHH CS
                      E1-E2_ATPase  90 edtelgkiarlveeakskktplqkkldklgkvlvpvvlliallvflialllgkslaeallralallvaaiPcaLpla 166
                                        +t+++k++++ve++++ ktp +  l+ l   l+ v ++i++ ++++ lll+ +    l   +al v+ +P  ++++
  gi|518652897|ref|YP_008142417.1| 207 DETYISKLVKMVESSERPKTPNELALSILLIGLTGVFTIILISLIAFSLLLNLG--ADLSVLIALYVCLLPTTIGAL 281
                                       ******************************************999999999998..599999*************** PP

                                       HHHHHHHHHHHHHHT CS
                      E1-E2_ATPase 167 vplalalgarrlakk 181
                                       +p + + g++r++k+
  gi|518652897|ref|YP_008142417.1| 282 LPAIGISGITRMSKN 296
                                       ************996 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.013
                                       HHHHHHHHHHHHHHHHHHHHHHS-S.TTTSSTTHHHHHHHHHHHHHS-TTHHHHH CS
                      E1-E2_ATPase 114 kldklgkvlvpvvlliallvflial.llgkslaeallralallvaaiPcaLplav 167
                                       + + ++k++++v +++a + +l al +lg s+  a+l+al +  a+iP  +pla+
  gi|518652897|ref|YP_008142417.1| 619 ITNDVAKYFAIVPIMFASIPALGALnILGLSPHIAVLSALIFNAAVIPALIPLAL 673
                                       45778888777655555554444431567777799999**********9999987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.3   3.5e-34   1.6e-30       2     210 .]     313     569 ..     312     569 .. 0.84

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 3.5e-34
                                       SEEEEESBTTTBCHHHHHHHHHHHH...CHHHHHHHHHH...HHCHHHHHH.HHHHHHH..........HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx...xxxxxxxxx.xxxxxxx..........xxxxxxxx RF
                         Hydrolase   2 ktvvfDkdGTLttgepsvedvivsa...alalaaaletg...sehpigkal.vaaakar..........sgaltgfa 61 
                                       +t+++Dk+GT+t g++   ++i+     +++la+a +++    ++p gk +   a+k+           +g  ++f 
  gi|518652897|ref|YP_008142417.1| 313 DTILLDKTGTITVGNRLAYEFIPLGthtERELAEAAFLSswnDDTPEGKSIlELAYKKKfvpreydalrEGVQEEFS 389
                                       79***********************8887777777777788**********76677777898887777544447777 PP

                                       HETTTE.......................................HHHHTHHHHHHHH.....HCHHHHHHHHHHHH CS
                                       xxxxxx.......................................xxxxxxxxxxxxx.....xxxxxxxxxxxxxx RF
                         Hydrolase  62 tfigrg.......................................ayaigkpewltal.....dippdlgaaigsaq 94 
                                       +++ +                                        ++++g pe +++      d    +++ ++   
  gi|518652897|ref|YP_008142417.1| 390 AVTRKSgitltdaddftllkggrdilqrhrfrrkfelqtpmtqetTIQKGAPESIKESakicpDG---YDDVVTRIT 463
                                       75555589999999998888888999999999999999999999999999999999999844444...444455555 PP

                                       HHCHHHHHH..TTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTTGGGESEEEEHHCE CS
                                       xxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  95 sqgrtvall..qaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlGddyfdaviasdie 169
                                       s+g t + +  ++++l+++ ++d   +k +++e +  Lk +gi+ v++tgd+p ta+ +a ++G           ie
  gi|518652897|ref|YP_008142417.1| 464 SEGGTPISVsmDGDILGIIYFKDV--IKRGIKEKILGLKTMGIRPVMITGDHPLTAKNIAGEVG-----------IE 527
                                       5555555555569***********..**************************************...........66 PP

                                       S.STTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHHHHHTT CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 170 t.vakpspegkvaaireLqgkpeevamVGDgvnDaaalaaAg 210
                                         va ++pe k ++++  q++ + vam+GDg nDa+alaaA+
  gi|518652897|ref|YP_008142417.1| 528 DyVAQAKPETKYQKVKDEQAENRIVAMIGDGTNDAPALAAAD 569
                                       66*****************99999*****************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 ?    3.1   0.0     0.014        65      15      59 ..     487     531 ..     470     534 .. 0.84
   2 !   21.0   1.0   5.2e-08   0.00024     203     242 ..     549     588 ..     537     599 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.014
                                       ---HHHHHHHHHHHHTTSEEEEE-SS-HHHHHHHHHHCCCCSEEE CS
                       Hydrolase_3  15 kisektkeaikklkekgikvviATGRslravlpvleelgldlpvi 59 
                                        i+  +ke i  lk  gi  v  TG ++ ++++++ e+g++ +v 
  gi|518652897|ref|YP_008142417.1| 487 VIKRGIKEKILGLKTMGIRPVMITGDHPLTAKNIAGEVGIEDYVA 531
                                       478889999999*****************************9986 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 5.2e-08
                                       GGGEEEEESSGGGHHHHHHSSEEEEETTS-HHHHHHSSEE CS
                       Hydrolase_3 203 leeviafGDgeNDieMLeaaglgvAmgnaseevkkaAdyv 242
                                       +  v+ +GDg ND + L aa++g Am++++  +k aA++v
  gi|518652897|ref|YP_008142417.1| 549 NRIVAMIGDGTNDAPALAAADVGLAMASGTLAAKDAANMV 588
                                       556889********************************98 PP

>> Intein_splicing  Intein splicing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.26   1.2e+03      79      96 ..     135     152 ..     128     327 .. 0.70
   2 ?   10.4   0.0   0.00011      0.48      19     109 ..     465     549 ..     440     553 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
                                       EECCC--TT-EEEEEHSC CS
                                       xxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  79 kradeLkegdliavpdad 96 
                                       ++ +eL++gd+i + ++d
  gi|518652897|ref|YP_008142417.1| 135 VKSSELRKGDVILIEKGD 152
                                       567888888888877433 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00011
                                       CTTEEEEEETTTTEEEEEEEEEEEEEEEE.EEEEEEETTS-EEEEETT-EEEECCTTEEEEEECCC--TT-EEEEEH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Intein_splicing  19 egeevlslnledlklevksvkkliklklk.elyeiklesgrkikaTpeHkllvvrdegivEkradeLkegdliavpd 94 
                                       eg + +s++++   l     k +ik ++k +++ +k+   r + +T++H+l +    +i    a e+  +d++a ++
  gi|518652897|ref|YP_008142417.1| 465 EGGTPISVSMDGDILGIIYFKDVIKRGIKeKILGLKTMGIRPVMITGDHPLTAK---NI----AGEVGIEDYVAQAK 534
                                       66666666666666666667899999***9********************8776...56....89999********* PP

                                       SCEEEEEEEEEEEEE CS
                                       xxxxxxxxxxxxxxx RF
                   Intein_splicing  95 advvwdkvksieved 109
                                        +  ++kvk+ + e+
  gi|518652897|ref|YP_008142417.1| 535 PETKYQKVKDEQAEN 549
                                       ********9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (720 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.49
# Mc/sec: 4399.99
//
Query:       gi|518652898|ref|YP_008142418.1|  [L=553]
Description: hypothetical protein FACI_IFERC00001G1537 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.4e-184  614.3  34.3     2e-184  613.8  34.3    1.2  1  KdpA       Potassium-transporting ATPase A subunit
  ------ inclusion threshold ------
        4.9    6.8   7.3        1.2    8.7   0.6    2.7  2  Kinocilin  Kinocilin protein


Domain annotation for each model (and alignments):
>> KdpA  Potassium-transporting ATPase A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  613.8  34.3  2.2e-188    2e-184       2     547 .]      12     546 ..      11     546 .. 0.97

  Alignments for each domain:
  == domain 1  score: 613.8 bits;  conditional E-value: 2.2e-188
                                       HHHHHHHHHHHHHHHHHHHHHTT-...--SS-SHHHHHHHHHHT---.----HHHHHHHHHHHHHHHHHHHHHHHHT CS
                              KdpA   2 lllllllllalplgkylakvfegektlldkllkpverllyrllgvdeeeemtwkeYalalllfnlvlllllylllrl 78 
                                       l++++++lla++l+kyl+ v+++ kt++dk+++pv++++y++lg+d+++em wkeY+l+l++f+++++++ +l+l +
  gi|518652898|ref|YP_008142418.1|  12 LVWAIVVLLAWILAKYLQGVYDSGKTIFDKIMDPVDNVIYKILGIDKNQEMGWKEYFLSLFIFSIFTAIISFLVLSF 88 
                                       6789************************************************************************* PP

                                       TTTSS--SS------HHHHHHHHHHHHTT-----S-HHHH--HHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHS-.. CS
                              KdpA  79 qgvlplnpeglealspdlafntavSFvtntnlQhYsgestlsylsqmlgltvlnFvsaatGlavavalirglark.. 153
                                       qgvlplnp ++++l++ la+nta S  +ntnlQhY+g s+lsyl qm+g+  l+F+saatGlavava++rg+++k  
  gi|518652898|ref|YP_008142418.1|  89 QGVLPLNPMKFAGLKWPLALNTALSISSNTNLQHYAGGSSLSYLGQMAGIQSLQFTSAATGLAVAVAIFRGFVGKkd 165
                                       ************************************************************************87622 PP

                                       S-S----HHHHHHHHHHHTHHHHHHHHHHHHHHHT--------EEEE-SSS-EEEE--SSHHHHHHHHHHTT----S CS
                              KdpA 154 etkelGnfyvdlvrailrvLLPlslvvalllvaqGvpqtlsgkaevttlegakqtialGpvAsleaIkqlGtnGGGf 230
                                       e+++lGnfyvdl+r+i+rvLLPls++ a++++a Gvpq+lsg++ +t l+g +q i++Gpv sl++I qlGtnGGG+
  gi|518652898|ref|YP_008142418.1| 166 EKSKLGNFYVDLIRSITRVLLPLSIIGAIIVIALGVPQSLSGYDLTTSLSGISQIIKVGPVGSLVSIMQLGTNGGGY 242
                                       5689************************************************************************* PP

                                       SSSTTTSTTTS-SHHHHHHHHHHHHHHHHHHHHHHHHHTS-THHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHH. CS
                              KdpA 231 fgaNsahpfenptaltnlleilaillipaalvftfGrmvkdkrqglailavmlvlflvllvvvvvaeaagnpalaee 307
                                       fgaNsa+p++np +l+n++e+ +++lip++++f fG m++++ +g++il + ++l+++ l+++++  ++    l   
  gi|518652898|ref|YP_008142418.1| 243 FGANSAYPLQNPGPLSNYVELGMMMLIPTSMPFLFGGMLRNRNEGRTILLASYTLYAIDLAIALIPVTT----L--- 312
                                       ***********************************************************9999874322....2... PP

                                       .-----TTB-SSS-HHHHHHHHHHHHHTT----SS-GGGS-HHHHHHHHHHHHTS-TT-TTTHHHHHHHHHHHHHHH CS
                              KdpA 308 qaggnmeGkEvrfGiaasalfavvttatstGavnamhdsltplgglvpllnmmlevvfGGvGvGllnllvfvilavF 384
                                              G E+rfG  +  l++v+tta++tG+vn+++ +++pl +l++++ m++++++GG+GvG +++l+++i++vF
  gi|518652898|ref|YP_008142418.1| 313 -----GAGMETRFGGFSPVLWTVTTTAFTTGSVNTSLAAMHPLVILAAFMGMIIQATPGGIGVGAMYMLMYIIITVF 384
                                       .....3599******************************************************************** PP

                                       HHHHHHTS--EETTEE--HHHHHHHHHHHHHHHHHHHHHHHHHTTSHHHTT.--S-THHHHHHHHHHHHHHHTT--- CS
                              KdpA 385 iagLmvGrtPeylgkkiearevklaalaiLvhpllilvgtalalalpalas.lsnpgahglsevLYeftSaaanNGS 460
                                       i+gLm GrtPeylg ki a +vkla++a+L+hp++ilv+tala a+ a +     +g+ g++++LYeftS+aanNGS
  gi|518652898|ref|YP_008142418.1| 385 IVGLMAGRTPEYLGGKITAGDVKLAVIAFLAHPIIILVPTALAYATGAVHGiGLGSGPVGFTQILYEFTSSAANNGS 461
                                       **********************************************9777747899********************* PP

                                       --S-S---SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS------TT---SSHHHHHHHHHHHHHHHHHHHHHHH CS
                              KdpA 461 afeGlgdntvfwnltlglamllgRflpiiavlaiAgslaakkkvpesagtlktdtplFvvllvgvilivgaLtFlPa 537
                                        + G ++nt+f+n+++g++m++gRf+pi+++laiAg +++kk+   s+ +l+td+ +F ++l++ i+i+++LtF+P+
  gi|518652898|ref|YP_008142418.1| 462 DYLGTQANTTFFNVSTGIVMWAGRFIPILIMLAIAGRMHEKKRS--SEAALRTDGLVFPAILIVSIFILAVLTFFPF 536
                                       ******************************************97..7789*************************** PP

                                       HHTTHHHHHH CS
                              KdpA 538 laLGPiaehl 547
                                       la+GPi+ hl
  gi|518652898|ref|YP_008142418.1| 537 LAIGPILMHL 546
                                       ******8776 PP

>> Kinocilin  Kinocilin protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   1.1     0.061   5.5e+02      32      58 ..     339     365 ..     327     386 .. 0.82
   2 ?    8.7   0.6   0.00014       1.2      18      65 ..     409     458 ..     401     471 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.061
                         Kinocilin  32 svskaaaavggifigaaglgllllayp 58 
                                       sv  + aa+  + i aa +g+++ a p
  gi|518652898|ref|YP_008142418.1| 339 SVNTSLAAMHPLVILAAFMGMIIQATP 365
                                       788888999999999999999988766 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00014
                         Kinocilin  18 valsllagsiiigv..svskaaaavggifigaaglgllllaypflkarfn 65 
                                       + +++la  iii v  +++ a+ av gi +g+  +g+  + y f  +  n
  gi|518652898|ref|YP_008142418.1| 409 AVIAFLAHPIIILVptALAYATGAVHGIGLGSGPVGFTQILYEFTSSAAN 458
                                       456789999999983245667789********************987655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (553 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 3457.19
//
Query:       gi|518652899|ref|YP_008142419.1|  [L=53]
Description: hypothetical protein FACI_IFERC00001G1538 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 351.27
//
Query:       gi|518652900|ref|YP_008142420.1|  [L=98]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-16   60.2   0.7    1.6e-16   60.0   0.7    1.1  1  AsnC_trans_reg  Lrp/AsnC ligand binding 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 !   60.0   0.7     9e-21   1.6e-16       2      74 ..      18      87 ..      17      88 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.0 bits;  conditional E-value: 9e-21
                                      EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74
                                       v ++  +   +e++  +l++l+ V+e+y vtG++d+   + + ++e++++fl++k++++pg++++ +sivl 
  gi|518652900|ref|YP_008142420.1| 18 DVFVDTTK---IEDVVNELCRLDRVEEVYEVTGEFDIATVISSTNIEDFRDFLKNKIMKIPGIKSVVSSIVLT 87
                                      57778778...9***********************************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 650.13
//
Query:       gi|518652901|ref|YP_008142421.1|  [L=64]
Description: hypothetical protein FACI_IFERC00001G1540 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   11.0   0.0       0.15   11.0   0.0    1.0  1  MukE      MukE-like family


Domain annotation for each model (and alignments):
>> MukE  MukE-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.3e-06      0.15      26      65 ..      10      49 ..       2      63 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.3e-06
                              MukE 26 hisldeldnhaflldfqeeleefyrrynvelirapeGffy 65
                                      +i  ++l+++ + ++ +++ + fy r ++++i a + f y
  gi|518652901|ref|YP_008142421.1| 10 KIDRESLEKFNVYIERKDSPDPFYPRLRIKIIYAKDRFIY 49
                                      578899********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (64 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); 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 0.25s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 456.47
//
Query:       gi|518652902|ref|YP_008142422.1|  [L=271]
Description: hypothetical protein FACI_IFERC00001G1541 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-60  205.2   0.1    1.2e-60  205.0   0.1    1.0  1  Memo      Memo-like protein


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 !  205.0   0.1   6.6e-65   1.2e-60       1     270 [.       6     267 ..       6     268 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 6.6e-65
                              Memo   1 eaavAGsfYpedeeelkkqleeflekntgkkeiarviis...PHagyvysgevaakayaelesskvervvilGpsHt 74 
                                       e+ v G fYp+d e+l + ++ ++  ++++ + ++++i    PH +y+ys+++aa+ay+ +++sk  +++i+Gp+H 
  gi|518652902|ref|YP_008142422.1|   6 EPHVSGGFYPDDYEALMDSIKGSMDITMPDIR-YKKLIGaivPHGQYMYSSHTAAYAYKIIQESKKRTFLIIGPNHS 81 
                                       58899****************99999999876.555554567*********************************** PP

                              Memo  75 ilgskvsvlaaseleTPlGdlkvDeelveeLvkkeeiadldetaalaEHSlEvqlpfLkellkekkfkivPilvsaq 151
                                        +  + ++++ + ++TPlG +kv +el e+L  k++i++ d+ a+  EHS+EvqlpfL++l+k++ f+  P++++ q
  gi|518652902|ref|YP_008142422.1|  82 KFPAYPAIYPDGYWSTPLGYAKVNSELSERLLLKSDIIHDDKEAHITEHSIEVQLPFLQYLFKSN-FTFTPLILGNQ 157
                                       ****************************************************************6.*********** PP

                              Memo 152 seetakevgealakvikdesnlviiSsDlsHygrrFgspqeiaesieDrevikaleelneeelkeylektnnticGe 228
                                          +a++++e +++    e+  v+iSs ++Hy      p +  ++  D+++i++++e+++ ++++ +ek+++t cG+
  gi|518652902|ref|YP_008142422.1| 158 GAAIARNIAETIESLE--EKPFVLISSNFNHYL-----PYDKNNEL-DQILINDIQEMRTLKFYQDIEKYGITACGY 226
                                       ***********99875..4578999********.....87777777.****************************** PP

                              Memo 229 kpiavilkalkklgakkakllkYaqssdvtsdtdsvVsyasl 270
                                       + ia+++ + k+++  k  ll++++s+d + d++ vV+y ++
  gi|518652902|ref|YP_008142422.1| 227 GAIAILMLITKNMK-GKIALLNHSNSGDYSKDRKRVVGYSAM 267
                                       **************.9***********************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1941.77
//
Query:       gi|518652903|ref|YP_008142423.1|  [L=83]
Description: hypothetical protein FACI_IFERC00001G1542 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   0.1      0.016   14.9   0.1    1.3  1  DUF4325   STAS-like domain of unknown function (DUF4325)


Domain annotation for each model (and alignments):
>> DUF4325  STAS-like domain of unknown function (DUF4325)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1     9e-07     0.016       6      48 ..      24      63 ..      21      75 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9e-07
                           DUF4325  6 rdkilkpllkegekvelDFdgvesigssFldeaFgglirefge 48
                                      +dki+++     ++v++DF  v+ i+  F d+ + +  +++++
  gi|518652903|ref|YP_008142423.1| 24 FDKIERLD---DNEVIIDFLLVYYISNEFIDAYIANRHMSMKH 63
                                      78999966...*********************99876666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.43
# Mc/sec: 584.80
//
Query:       gi|518652904|ref|YP_008142424.1|  [L=271]
Description: carbon-nitrogen hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-42  144.5   0.0    4.2e-42  144.3   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 !  144.3   0.0   2.4e-46   4.2e-42       1     260 [.      14     255 ..      14     256 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.3 bits;  conditional E-value: 2.4e-46
                                       EEEEEEBB-STTHHHHHHHHHHHHHHHHHHTTESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEE CS
                      CN_hydrolase   1 rvAvvQlpqkaadleanlqklleliaeAarkgadLivlPElfitgykeeahfleaAeaglgetlallaalarkngia 77 
                                       ++A+ Ql+++ ad++  l +++ ++  Aa + adLiv+PE+  +  ++++ ++ +Ae ++g+ ++++++++r+n+i 
  gi|518652904|ref|YP_008142424.1|  14 KIALTQLKPV-ADKDVSLRNIEYYAGTAAANSADLIVFPEYYMFYSQYKDAIIRNAEVLNGNYIKRIKEISRTNKIG 89 
                                       69*******7.8********************************99******************************* PP

                                       EEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-SS--EECTTSCECCGHHTSCS-SS.S-EEEETTEEEEEEEG CS
                      CN_hydrolase  78 vvigliereltngklqayntavlldldgklvgkyrKlhLfpgeprpptaverelfepgdg.ipvfdtpvgkiGaaiC 153
                                       +++g+ e   ++ ++  y tav++ +dg+l+  yrK+hL    ++  +++e+ ++  g+g +++ +   +++G++iC
  gi|518652904|ref|YP_008142424.1|  90 IITGINEV--YDHNY--YDTAVYV-NDGELLNYYRKSHL----YDAFGYRESDIYTYGNGpFKISKIGNINFGMLIC 157
                                       ********..99999..*******.788899*******8....799*************99999999999******* PP

                                       GGGGSHHHHHHHHHTT-SEEEEBH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE- CS
                      CN_hydrolase 154 yeigfpellralalkgaeilvnlserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiid 230
                                       y+i+fpe+ r ++l++a++++ +s  a++ + + ++qw+ l  +ralen  +++ +n +gg       + g + ++d
  gi|518652904|ref|YP_008142424.1| 158 YDIRFPEVFRNYSLNDADMVILIS--AWFAGPIKEEQWLSLVSTRALENTTYLATSNMIGG------GFTGITTFTD 226
                                       **********************77..***********************************......9********* PP

                                       TTS-EEEECCSSSTEEEEEEEEHHHHHHHH CS
                      CN_hydrolase 231 pdGrilaglgeeeegvliaeidladvratr 260
                                       p G i+ ++ e+e ++++  id +++  +r
  gi|518652904|ref|YP_008142424.1| 227 PIGAIINRAAEDE-DIIYSIIDTNRISTVR 255
                                       ***********99.6*******99998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (271 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1907.19
//
Query:       gi|518652905|ref|YP_008142425.1|  [L=288]
Description: hypothetical protein FACI_IFERC00001G1544 [Ferroplasma acidarmanus fer1]
Scores for 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-54  183.6   0.1    5.7e-54  183.4   0.1    1.0  1  VitK2_biosynth  Menaquinone biosynthesis


Domain annotation for each model (and alignments):
>> VitK2_biosynth  Menaquinone biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.4   0.1   3.2e-58   5.7e-54       1     265 [.       4     274 ..       4     275 .. 0.91

  Alignments for each domain:
  == domain 1  score: 183.4 bits;  conditional E-value: 3.2e-58
                                       EEEEEESSHHHHHHHHHHHTTSS..SGCC.EEEEEE-HHHHHHHHHTTS-SEEEEEHHHHTTCTTTEEEESEESCEE CS
                    VitK2_biosynth   1 lrlGhspylNdlflfyaLvegkvdsegle.veivledpetlnrallegelDvakiSsaayariaddyalLpdlsisa 76 
                                       l++G++++++dl++f++L+e+kv+s+ ++   +++ +++++n++++++++D+++ S+a+y++i++dy++L+++++sa
  gi|518652905|ref|YP_008142425.1|   4 LKIGALADSGDLYPFIPLLEKKVKSDDFNlEFEFIPTVQEVNDKIVKKDVDISVPSAALYPYIQNDYFILSSAVASA 80 
                                       68************************8886667899***************************************** PP

                                       EESSSSEEEEESS-CCC-SSS..T.EEEESTTTSHHHHHHHHHHCSTS----EEEEE-GGGHHHHHHTTSSEEEEEC CS
                    VitK2_biosynth  77 lGrvygvllvskvpleelegel.gkrvalpgestTsvlLlrlllaeryglkprlvevpfdeieaavlegedagLlIg 152
                                       ++ ++g+ +++ ++++ +e    +++++++g +tT+++L++ll+ ++   k  +v+  +de+++ + ++  ++++++
  gi|518652905|ref|YP_008142425.1|  81 VDGITGMPILAMKKMDIDE--IkNSKIIVHGLNTTAFNLYKLLIGKYK--KLIVVHRVLDEVNS-MVNEDGVMVAVH 152
                                       ***********55444443..2488**********************7..55556666889998.6666699***** PP

                                       CHHHTGGGGTT....EEEEEHHHHHHHHH.SS-EEEEEEEEECCCHHHHHHHHHHHHHHHHHHHHHSHHHHHHH... CS
                    VitK2_biosynth 153 esaltyaeegl....kkvlDLgelWeelt.glPlvlglwvvrrdlaaeaakeleealreSveyalahldevaey... 221
                                       e + +y+ +++    +++++++e+W++l+ + P+++g +v++ ++++e a +++e + +S++ya++h++e+++    
  gi|518652905|ref|YP_008142425.1| 153 ELKAMYDLRKMgvepVRLASMWEMWKQLSgNRPMPMGTVVINSEIGEEYALKFKELYNKSKKYAESHMEEILPVdvk 229
                                       ****999999888999*************55*****************************************98888 PP

                                       HHCCSTTS.H..HHHHHHHHHHCSHHHHS-CHHHHHHHHHHHHHHH CS
                    VitK2_biosynth 222 aaeraqemdd..evlekhlelYvnelsydlgeegragleeflelaa 265
                                       ++++ q  d   ev++ ++ ++v+e+++++ ++ ++gle f+e+++
  gi|518652905|ref|YP_008142425.1| 230 IMREVQNSDIslEVIKGTIGADVKEYNVSI-DDVKSGLEFFYEIMH 274
                                       999999987789******************.999********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1889.83
//
Query:       gi|518652906|ref|YP_008142426.1|  [L=115]
Description: hypothetical protein FACI_IFERC00001G1545 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.7   0.1      0.064   13.2   0.1    1.2  1  DUF5067   Domain of unknown function (DUF5067)
      0.056   13.5   0.0      0.072   13.1   0.0    1.4  1  DUF2561   Protein of unknown function (DUF2561)
       0.14   12.4   0.0       0.18   11.9   0.0    1.3  1  DUF2615   Protein of unknown function (DUF2615)
       0.48   10.4   1.6        2.3    8.2   1.6    2.0  1  CcmE      CcmE


Domain annotation for each model (and alignments):
>> DUF5067  Domain of unknown function (DUF5067)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.4e-05     0.064      79     121 ..      34      75 ..      27      79 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                                       -B---S--TTHHHCCCCSEE-TTSEEEEEEEEE-TTTTS-EEE CS
                           DUF5067  79 etailaddekdkldnldkeikpgktvevviaYeLqdtdspvtv 121
                                       +t+ +a  ++ ++  l ++i  + tv+++ a++L+d+ + +tv
  gi|518652906|ref|YP_008142426.1|  34 NTSPSAMKDN-NSYYLAGKITQDVTVNGQSAFTLNDNGKSITV 75 
                                       4444444444.88999**********************99998 PP

>> DUF2561  Protein of unknown function (DUF2561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.072      54      94 ..       2      42 ..       1      84 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
                           DUF2561 54 aksaedshttwvLyavivvsalvivgavPlLLrarrvaeae 94
                                      +k+a + h + ++ ++i+v al+i g +P +L     a ++
  gi|518652906|ref|YP_008142426.1|  2 SKMARNKHKGIIVLVIIIVLALLIYGLIPTILNTSPSAMKD 42
                                      6899***************************9887666555 PP

>> DUF2615  Protein of unknown function (DUF2615)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.1e-05      0.18      50      89 ..       5      44 ..       1      55 [. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.1e-05
                           DUF2615 50 keggsslfliallwlvvaavlfllrPsslrnasaknkpsr 89
                                       +++++ ++++++++v+a++++ l P  l  + +  k+++
  gi|518652906|ref|YP_008142426.1|  5 ARNKHKGIIVLVIIIVLALLIYGLIPTILNTSPSAMKDNN 44
                                      56788999*******************9988766666655 PP

>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   1.6   0.00052       2.3      47      90 ..      42      81 ..       5     107 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00052
                                      TTSEEEEEEEE-TTT-EE-TTSSEEEEEEE-T.-EEEEEEES-- CS
                              CcmE 47 egrrlrvgGlVkegsvkrdpesleveFvvtdlekelkVeYegil 90
                                       +++  + G+++++  ++     +  F++ d+ k+++V Y+g  
  gi|518652906|ref|YP_008142426.1| 42 DNNSYYLAGKITQDVTVN----GQSAFTLNDNGKSITVLYNGTA 81
                                      445566677776655443....3458*****99********975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1101  (0.0614089); expected 358.6 (0.02)
Passed bias filter:                      603  (0.0336327); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 775.72
//
Query:       gi|518652907|ref|YP_008142427.1|  [L=35]
Description: hypothetical protein FACI_IFERC00001G1546 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (35 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 271.07
//
Query:       gi|518652908|ref|YP_008142428.1|  [L=49]
Description: hypothetical protein FACI_IFERC00001G1547 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       376  (0.0209716); 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: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 361.49
//
Query:       gi|518652909|ref|YP_008142429.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1548 [Ferroplasma acidarmanus fer1]
Scores for 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   23.7   0.0    7.6e-05   23.2   0.0    1.2  1  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.2e-09   7.6e-05       4     153 ..      50     203 ..      47     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-09
                                       ESEESS-....-TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC. CS
                                       xxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Radical_SAM   4 trgCnlr....CsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlakla. 74 
                                       t gC+      Cs C        ++++ ++  e+++++v+ l+   +++k++ ++    +l+p++v  + r   ++ 
  gi|518652909|ref|YP_008142429.1|  50 TTGCAWYkftaCSMCGYF-----NDTSPEIVDENLMRQVDTLYdSLNDTKVLKIFTSGSFLDPNEVHPAVRDYFIDr 121
                                       67888877888****999.....79*****************96444466666665556666666666666555555 PP

                                       ..CCTEEEEEEECSSCHGHHHHHHHHHTT.-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEE CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  75 ..vpgiritvetngtlpdeeklerllelg.vdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdr 148
                                         ++  ++ ve+    + +e l+ ++++    r+++gle+add   +  +n+g t++++++a ++l +  i+  ++ 
  gi|518652909|ref|YP_008142429.1| 122 mkDKVDKLLVESRTEYIKPETLQPFKKAKiDLRIAIGLESADDYIMKYSVNKGSTLKKFIDAAKILQQEKIELRTYL 198
                                       6646666777776666669**********888************6666667****************9988866666 PP

                                       EEEBT CS
                                       xxxxx RF
                       Radical_SAM 149 ivglp 153
                                       ++ +p
  gi|518652909|ref|YP_008142429.1| 199 LFKPP 203
                                       66555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2497.69
//
Query:       gi|518652910|ref|YP_008142430.1|  [L=212]
Description: prephenate dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-10   38.7   0.0    1.2e-09   37.6   0.0    1.6  1  PDH       Prephenate dehydrogenase


Domain annotation for each model (and alignments):
>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   6.8e-14   1.2e-09      35     244 ..      29     209 ..      23     212 .] 0.72

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 6.8e-14
                                       EEES-.GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEEE--S--CHHHHHHHHHCC..GCEEEEEES---S- CS
                               PDH  35 eatdd.ieavkeadivvlavPvevilevlkelaphlkedalitDvgsvKekvvreleellkegksfvgghPmaGtek 110
                                       e++d+ ++++ +ad+++lavP e + ++++   +     +  +D++s+K    +++ee+     ++++ hP++G+  
  gi|518652910|ref|YP_008142430.1|  29 ENEDQlQSELTKADFALLAVPLEETVNIIRSFPE----YRGFVDLTSMK----YNMEEFSG---HIISIHPLFGP-- 92 
                                       344445899********************98876....88899****99....57999999...9**********.. PP

                                       SSGGG--TTTTTT-EEEEEE-TTS-HHHHHHHHHHHHHCT-EEEE--HHHHHHHHHHHTHHHHHHHHHHHHHHHCHH CS
                               PDH 111 sGvdaareelfenavviLtPtektdkealekvkelleevgarvilmspeeHDrvvavvshlphvvaialaatlkekk 187
                                               e+++ ++ i+  ++ + +  l+kvkel++  g r+i m++ eHD+ ++   + p ++++   a    ++
  gi|518652910|ref|YP_008142430.1|  93 --------ESYKTNKTIIFINDISTPDSLDKVKELFN--GYRIISMNAREHDYLMSELLVKPYILSYISEA----SN 155
                                       ........66665555554444455599********8..569**************999999998874322....33 PP

                                       CCCCHHHHCGTCCHHHHHCGG.GS-HHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHH CS
                               PDH 188 ndekeirklasggfrdvtRia.ksnPelwadilleNkeavlealdkfikelkklkeli 244
                                       +d+      +  +f  + +i  + n e++ d +++N++  +e++ + +k+l++lk+li
  gi|518652910|ref|YP_008142430.1| 156 TDIV---TGSYIKFLEIEKIKhNENTEIFLDTIKYNER-AMEIIINIEKKLDELKKLI 209
                                       3332...3333455555566413456666666666666.5666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1628.50
//
Query:       gi|518652911|ref|YP_008142431.1|  [L=191]
Description: chorismate mutase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-09   36.1   0.2    1.1e-08   35.3   0.2    1.4  1  CM_2      Chorismate mutase type II


Domain annotation for each model (and alignments):
>> CM_2  Chorismate mutase type II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.3   0.2   6.2e-13   1.1e-08       2      74 ..      13      81 ..      12      82 .. 0.88

  Alignments for each domain:
  == domain 1  score: 35.3 bits;  conditional E-value: 6.2e-13
                                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTSGSS-HHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHH CS
                              CM_2  2 keIdeiDdeileLLaeRaelakevgeyKkeeglpvydpeReaevlerleegaldeeaierifreiisasralq 74
                                      +e+ +  ++i++LL+eR e+a ++ge K ++gl++++ eRe e+l+ l+     +++ e +++ +++ s++++
  gi|518652911|ref|YP_008142431.1| 13 NELYNNSRDIIKLLEERREIAGKIGECKVAGGLKIRNREREIEILKSLSY----DHFTEFVLNLLFEFSINYE 81
                                      555666689********************9999****************9....7888888888888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.31s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1231.98
//
Query:       gi|518652912|ref|YP_008142432.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G1551 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-16   59.4   0.0    1.5e-15   57.6   0.0    1.8  2  AIRS      AIR synthase related protein, N-terminal domain
      5e-08   33.2   0.0    7.8e-08   32.6   0.0    1.3  1  AIRS_C    AIR synthase related protein, C-terminal domain


Domain annotation for each model (and alignments):
>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.6   0.0   1.6e-19   1.5e-15       1      93 [.      26     135 ..      26     136 .. 0.87
   2 ?   -1.5   0.0      0.48   4.3e+03      53      71 ..     265     287 ..     241     309 .. 0.61

  Alignments for each domain:
  == domain 1  score: 57.6 bits;  conditional E-value: 1.6e-19
                                       SSSEE........EEEEEEEE.EECCTCCCC........HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HH CS
                              AIRS   1 dDaav........vvttdshnrpvlvepvhf........iGakavavnlsDlaamGArPlalllslalp......wl 55 
                                       dD+a+        +++td   r++               +G+  +a nlsD+aam + P ++l sl+++       l
  gi|518652912|ref|YP_008142432.1|  26 DDCAIigfgnyyaLLSTDLITRETH-----LpegaepflAGKFFAAINLSDIAAMAGIPSGFLISLSVSpeydisYL 97 
                                       89**55666666699***6666665.....3333444777************************************* PP

                                       HHHHHHHHHHHHHTT-EEEEEEEEEESSEEEEEEEEEE CS
                              AIRS  56 eevvrglaeaaeelgvplvgGdtsfsneptisvtavGl 93 
                                       ee++rg+++ +++++v+++gGdt++++++t + t++G 
  gi|518652912|ref|YP_008142432.1|  98 EEFYRGVRHELDKFNVSIIGGDTKEGSDFTAAGTIIGK 135
                                       **************************99*******995 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.48
                                       C....HHHHHHHHHHHHHHHTT- CS
                              AIRS  53 p....wleevvrglaeaaeelgv 71 
                                             lee+++ +++   e+ +
  gi|518652912|ref|YP_008142432.1| 265 TveknSLEEFMAAMSHENIEVHC 287
                                       14466777888777766544444 PP

>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.0   8.7e-12   7.8e-08       1     150 [.     148     296 ..     148     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 8.7e-12
                                       STTEEEEEEETSSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHH CS
                            AIRS_C   1 kpGdvliltgslGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgala 77 
                                       kpG+ l++t slG  +ag+     ++++e l      +  +  e  +i+++ ++ a+  ++k + D+++ G+  +++
  gi|518652912|ref|YP_008142432.1| 148 KPGQFLMVTNSLGSSAAGYIYYMYGINRE-LG----IRKMLDVE-PRINEAIKISAS--GAKFMMDLSD-GVYASIH 215
                                       79****************65555555554.55....35555555.667777777775..**********.8****** PP

                                       HHHHTTTEEEEEECGTHHHHHHHH........HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEE CS
                            AIRS_C  78 emapasgvgaeidldkvpifdele........splemllsensGrllvavppeea.davlaileeeglpeaavIGev 145
                                       ++  + gvg++++ dk+p+   +e        s ++++ls+     l++ +++++ ++++a+++ e++ e+  IGe+
  gi|518652912|ref|YP_008142432.1| 216 QISTDFGVGFKLYGDKIPFDRDVEkaasisnfSVSDIALSFGGDYELMFTVEKNSlEEFMAAMSHENI-EVHCIGET 291
                                       ******************99999989999999888888887665555555555555************.8******* PP

                                       EESSS CS
                            AIRS_C 146 takee 150
                                        ++++
  gi|518652912|ref|YP_008142432.1| 292 YNGDN 296
                                       99874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2355.10
//
Query:       gi|518652913|ref|YP_008142433.1|  [L=171]
Description: GrpE protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-31  107.1   6.1    2.9e-30  105.1   6.1    1.9  1  GrpE          GrpE
  ------ inclusion threshold ------
      0.085   12.9   3.2       0.12   12.4   3.2    1.3  1  DUF2532       Protein of unknown function (DUF2532)
        2.2    8.2   7.2        1.1    9.3   0.4    2.7  3  pRN1_helical  Primase helical domain


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.1   6.1   4.9e-34   2.9e-30       6     166 .]      22     170 ..       5     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: 105.1 bits;  conditional E-value: 4.9e-34
                                       .CTTTHHHHCCCCCCTTCHHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC. CS
                              GrpE   6 eeeeeedeeeeleeeleelekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksa 82 
                                       ++ + ++e ++ ++  ++  + ++++k+ + r++ e+en+ k  e+e+e+++k a ++++k+LLpvlD l+  +++ 
  gi|518652913|ref|YP_008142433.1|  22 NKMKDREEMKKYKQLYTDTMSDLNDYKSLYVRQRSEMENYSKYKEREIENIRKNASSDLIKELLPVLDTLDAGIAHD 98 
                                       444555555666666677777999***************************************************82 PP

                                       .HHH-HHHHHHHHHHHHHHHHHHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE- CS
                              GrpE  83 keneeekslleGvemtlkqllkiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRp 159
                                                   +e ++ qllk+L++hg++++e kg ++Dpnl eav + ++ e  +gtv+e+vqkGY+l++ vlR+
  gi|518652913|ref|YP_008142433.1|  99 ---P-------KLEPVRSQLLKVLQSHGLQVLEVKGTKYDPNLEEAVGVLDQGE--DGTVLEEVQKGYTLNGDVLRT 163
                                       ...3.......3567899********************************9999..********************* PP

                                       EEEEEEE CS
                              GrpE 160 AmVkVsk 166
                                       ++V+Vsk
  gi|518652913|ref|YP_008142433.1| 164 SKVIVSK 170
                                       *****97 PP

>> DUF2532  Protein of unknown function (DUF2532)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   3.2   2.1e-05      0.12      47      98 ..       4      60 ..       1      77 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.1e-05
                           DUF2532 47 hkfleeklffseqqikkenkihe.....kykqfylqhnnklsdfsmqflekkseins 98
                                      hk  +  l f  +q++k nk+++     kykq+y +    l d+   ++ ++se++ 
  gi|518652913|ref|YP_008142433.1|  4 HKEYNRPLEFDIEQVRKRNKMKDreemkKYKQLYTDTMSDLNDYKSLYVRQRSEMEN 60
                                      7777888999999*******974334449************************9975 PP

>> pRN1_helical  Primase helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   1.1     0.044   2.6e+02      10      29 ..      25      44 ..      16      49 .. 0.75
   2 ?    9.3   0.4   0.00018       1.1      11      41 ..      54      84 ..      45      98 .. 0.86
   3 ?   -1.3   0.0      0.32   1.9e+03      85     100 ..     107     122 ..      94     130 .. 0.82

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.044
                      pRN1_helical 10 klkeemakydrykgktleai 29
                                      k +eem+ky +    t+  +
  gi|518652913|ref|YP_008142433.1| 25 KDREEMKKYKQLYTDTMSDL 44
                                      55799****99888887655 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00018
                      pRN1_helical 11 lkeemakydrykgktleaireelckeikkkl 41
                                       + em +y +yk + +e ir++   ++ k+l
  gi|518652913|ref|YP_008142433.1| 54 QRSEMENYSKYKEREIENIRKNASSDLIKEL 84
                                      578******************9999988887 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.32
                      pRN1_helical  85 allyvllshgatdldv 100
                                       +ll+vl shg   l+v
  gi|518652913|ref|YP_008142433.1| 107 QLLKVLQSHGLQVLEV 122
                                       5788999999877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1378  (0.0768587); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); 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: 1260.73
//
Query:       gi|518652914|ref|YP_008142434.1|  [L=628]
Description: hypothetical protein FACI_IFERC00001G1553 [Ferroplasma acidarmanus fer1]
Scores for complete 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-217  721.6  13.8   1.9e-197  657.2  13.2    2.1  2  HSP70          Hsp70 protein
    2.7e-15   56.0   9.1    4.5e-15   55.3   0.1    3.1  3  MreB_Mbl       MreB/Mbl protein
  ------ inclusion threshold ------
      0.058   13.2   2.2       0.24   11.2   1.9    2.1  2  TRAF_BIRC3_bd  TNF receptor-associated factor BIRC3 binding d
          3    8.2  10.4        2.7    8.4   5.2    2.4  2  Rubrerythrin   Rubrerythrin
        5.2    7.8   7.6        1.5    9.5   1.3    2.7  2  DUF4404        Domain of unknown function (DUF4404)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.8   0.0   2.4e-21   8.6e-18       1      75 [.       4      83 ..       4      86 .. 0.91
   2 !  657.2  13.2  5.2e-201  1.9e-197     102     598 ..      84     579 ..      82     580 .. 0.99

  Alignments for each domain:
  == domain 1  score: 63.8 bits;  conditional E-value: 2.4e-21
                                      EEEEEEXSSEEEEEEEETTEEEEEXXTTS....XSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTT CS
                             HSP70  1 viGiDLGttnsvvavmeggkievianeeg....nrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfs 74
                                      +iGiDLGt ns+ av+ +gk+e+i  +eg     ++ Ps+vaFtk+ + lvGe+A+rqa  np+ t++ +Kr +G++f+
  gi|518652914|ref|YP_008142434.1|  4 IIGIDLGTSNSAAAVVISGKPETIPAAEGvslgGKSFPSYVAFTKDgQLLVGEPARRQALLNPEGTIYGAKRKMGTDFK 82
                                      69***********************999622226899*********9999***************************98 PP

                                      S CS
                             HSP70 75 d 75
                                       
  gi|518652914|ref|YP_008142434.1| 83 Y 83
                                      5 PP

  == domain 2  score: 657.2 bits;  conditional E-value: 5.2e-201
                                       EETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHH CS
                             HSP70 102 eaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYG 178
                                       ++ g+++tp+qisa++L+k+k++aea+lg++v+davitvPaYfnd+qRqatkdAg+iAGLnv Ri+NepTAa +aYG
  gi|518652914|ref|YP_008142434.1|  84 KIFGKEYTPQQISAFILQKIKKDAEAFLGEPVNDAVITVPAYFNDNQRQATKDAGAIAGLNVKRIINEPTAACMAYG 160
                                       5679************************************************************************* PP

                                       TCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHH CS
                             HSP70 179 ldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqr 255
                                       +dk ++  ++l+yD+Gggt dv ++++++Gvfev +T+gDt+lGG d+Dea+v++l+++fk+kegidl+kdk a+ r
  gi|518652914|ref|YP_008142434.1| 161 IDKLNETLKILIYDFGGGTLDVTVMDFGQGVFEVMSTSGDTKLGGSDMDEAIVNFLADDFKSKEGIDLRKDKSAYIR 237
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEE CS
                             HSP70 256 lkeaaekaKkeLSsskqteinleietvdedg.kdlseklsRakfeelvedllertlepvekalkdaklkkeeidevv 331
                                       l++aaekaK+eLS++ +++inl+++t+++dg k+l+ kl+Rak+eel+++++ +   ++ kal+ akl+k +i++++
  gi|518652914|ref|YP_008142434.1| 238 LRDAAEKAKIELSTVLESDINLPYITATQDGpKHLEFKLTRAKLEELIAPIVGKSAASLDKALEGAKLSKGDINKII 314
                                       ***************************************************************************** PP

                                       EESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEES CS
                             HSP70 332 lvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslgietlggvmtklie 408
                                       l+GG tR+P v++ v+++fgk+ + +v+p +ava+GAA+q+gvl g  ++kd++llDvtpL+lgiet ggvmt li+
  gi|518652914|ref|YP_008142434.1| 315 LIGGPTRMPYVKKYVEDYFGKKSEGGVDPMQAVATGAAIQGGVLMG--DIKDIVLLDVTPLTLGIETVGGVMTPLIN 389
                                       **********************************************..***************************** PP

                                       TTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEE CS
                             HSP70 409 rnttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakd 485
                                        n tiptkk+qvfstaad qt+vei+++qger lvkd  +lg+f l+gi paprGvpqieVtfdidanGil+vsakd
  gi|518652914|ref|YP_008142434.1| 390 ANATIPTKKTQVFSTAADMQTSVEIHIVQGERPLVKDDVSLGNFVLTGIAPAPRGVPQIEVTFDIDANGILNVSAKD 466
                                       ***************************************************************************** PP

                                       TTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHH CS
                             HSP70 486 ketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekves 562
                                       k+tgk+++i+i+as++ls++eiekm k+ae++aeedkk+ke+ie+ n+ e+l+y++ek+++e+++k+++++k+k++ 
  gi|518652914|ref|YP_008142434.1| 467 KGTGKSQSISISASNKLSKDEIEKMKKEAEQYAEEDKKEKETIETLNNGESLAYTVEKTINEAGDKLDNETKDKIKG 543
                                       ***************************************************************************** PP

                                       HHHHHHCHTTSSCHHHHHHHHHHHHHHHHHHHHHHH CS
                             HSP70 563 aieeLkeeleeeekeeieakteelkkvvekiaekly 598
                                        i++Lk+++e+++++++++ te+l+k+++++ +k+ 
  gi|518652914|ref|YP_008142434.1| 544 IIKDLKDAVEKKDVDKVKEITENLTKEMTEVYTKMA 579
                                       ******************************999986 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0     0.048   1.7e+02       2      16 ..       3      17 ..       2      59 .. 0.86
   2 !   55.3   0.1   1.2e-18   4.5e-15      83     316 ..     101     352 ..      84     358 .. 0.71
   3 ?    0.9   3.6     0.043   1.6e+02     199     275 ..     486     566 ..     479     578 .. 0.80

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.048
                                      SEEEEEE-SSEEEEE CS
                          MreB_Mbl  2 kdlgiDLGtantlvy 16
                                      k +giDLGt n  + 
  gi|518652914|ref|YP_008142434.1|  3 KIIGIDLGTSNSAAA 17
                                      569******998654 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 1.2e-18
                                       HHHHT..SS-S..S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--.TTSSS-EEEEEE-S CS
                          MreB_Mbl  83 kkvkk..kksl..skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglp.veepsgnmvvdiGg 154
                                       +k+kk  + +l  + +  vi+vP   ++ +r+A k+a   aG +   +i+ep aA +  g++ ++e+   ++ d Gg
  gi|518652914|ref|YP_008142434.1| 101 QKIKKdaEAFLgePVNDAVITVPAYFNDNQRQATKDAGAIAGLNVKRIINEPTAACMAYGIDkLNETLKILIYDFGG 177
                                       444442112222255679*******************************************847788888999**** PP

                                       S-EEEEEEETTEEE.....EEEEES-SHHHHHHHHHHHHHHHHSEE--H..HHHHHHHHHH-BSS--HHHH...... CS
                          MreB_Mbl 155 gttevavislggiv.....tsksvrvaGdeldeaiikyirkkynlliGe..rtaekikieigsavkeeeee...... 218
                                       gt +v+v+ +g+ v     ts   +++G ++deai++++  +++   G   r+ ++  i++  a+++++ e      
  gi|518652914|ref|YP_008142434.1| 178 GTLDVTVMDFGQGVfevmsTSGDTKLGGSDMDEAIVNFLADDFKSKEGIdlRKDKSAYIRLRDAAEKAKIElstvle 254
                                       *********997442222255669***************99998765541144444555555555555444222221 PP

                                       .EEEEEEEETTTTCEEE..EEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHH CS
                          MreB_Mbl 219 .kmeikGrdlvtglpke..vevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkl 292
                                         +++     ++  pk+  ++++ ++++e ++  v +   ++ ++Le   + L++  +++ i+l GG + +  ++k+
  gi|518652914|ref|YP_008142434.1| 255 sDINLPYITATQDGPKHleFKLTRAKLEELIAPIVGKSAASLDKALEG--AKLSKGDINK-IILIGGPTRMPYVKKY 328
                                       122222223344456541145667777777777777777777777775..5687665555.7788************ PP

                                       HHHHHSS-EEE-SSTTTHHHHHHH CS
                          MreB_Mbl 293 lseetglpvkvaedpltcvakGtg 316
                                       +++ +g + + + dp+++va+G++
  gi|518652914|ref|YP_008142434.1| 329 VEDYFGKKSEGGVDPMQAVATGAA 352
                                       **********************97 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.043
                                       HHHHHHHHHH-BSS--HHHH....EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHH CS
                          MreB_Mbl 199 rtaekikieigsavkeeeee....kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaad 271
                                        + ek+k+e  + ++e+++e    ++  +G  l+  + k+++   +++ +  k++++ i++ +k + ek   + +++
  gi|518652914|ref|YP_008142434.1| 486 DEIEKMKKEAEQYAEEDKKEketiETLNNGESLAYTVEKTINEAGDKLDNETKDKIKGIIKDLKDAVEKKDVDKVKE 562
                                       56788888887777766666332333347999999999999999999999999999999999999999999888888 PP

                                       HHHH CS
                          MreB_Mbl 272 ivdr 275
                                       i+++
  gi|518652914|ref|YP_008142434.1| 563 ITEN 566
                                       8775 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 ?   -3.1   0.0       1.9   6.8e+03      37      54 ..     129     146 ..     125     146 .. 0.84
   2 ?   11.2   1.9   6.6e-05      0.24      26      53 ..     487     514 ..     483     516 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.9
                     TRAF_BIRC3_bd  37 verqrrldqekieaLekK 54 
                                        +rq  +d   i++L+ K
  gi|518652914|ref|YP_008142434.1| 129 NQRQATKDAGAIAGLNVK 146
                                       579999999999999876 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.6e-05
                     TRAF_BIRC3_bd  26 EverssttieaverqrrldqekieaLek 53 
                                       E+e+++ ++e++++  ++++e+ie+L++
  gi|518652914|ref|YP_008142434.1| 487 EIEKMKKEAEQYAEEDKKEKETIETLNN 514
                                       9*************************87 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   5.2   0.00075       2.7      52     125 ..     479     551 ..     474     555 .. 0.84
   2 ?    2.3   0.4     0.056     2e+02      82     111 ..     554     583 ..     551     588 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00075
                                       HHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTSHHHHHHHHHHHHH CS
                      Rubrerythrin  52 lleklepelelevkekvreyaeakpkflttaknLeeaiegayaeeeemyrfyeelaekegneeakklfkklaea 125
                                       + +kl +++  ++k+++ +yae ++k+++t + L + + +ay++e+++ +   +l + e+++++k ++k+l +a
  gi|518652914|ref|YP_008142434.1| 479 ASNKLSKDEIEKMKKEAEQYAEEDKKEKETIETLNNGESLAYTVEKTINEAGDKLDN-ETKDKIKGIIKDLKDA 551
                                       5677888888999***********************************666666555.5566699999998775 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.056
                                       HHHHHHHHHHHHHHHHCHHHHHHHHHHHTT CS
                      Rubrerythrin  82 aknLeeaiegayaeeeemyrfyeelaekeg 111
                                       +k+++++ e+ +   +em ++y+++a+ ++
  gi|518652914|ref|YP_008142434.1| 554 KKDVDKVKEITENLTKEMTEVYTKMAQAQQ 583
                                       578889999*****************9775 PP

>> DUF4404  Domain of unknown function (DUF4404)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.9      0.24   8.7e+02       3      30 ..     486     513 ..     479     529 .. 0.78
   2 ?    9.5   1.3   0.00042       1.5      16      58 ..     531     572 ..     516     582 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.24
                           DUF4404   3 elLekLheeLeqnesldeetralLesla 30 
                                       +++ek ++e eq  + d+++++++e+l+
  gi|518652914|ref|YP_008142434.1| 486 DEIEKMKKEAEQYAEEDKKEKETIETLN 513
                                       5677888888888888888888887775 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00042
                           DUF4404  16 esldeetralLeslaedieellaeedaaaeeeelaerlneave 58 
                                       ++ld+et+++++ +++d++ +++++d  + +e ++e+l++ ++
  gi|518652914|ref|YP_008142434.1| 531 DKLDNETKDKIKGIIKDLKDAVEKKDVDKVKE-ITENLTKEMT 572
                                       789***********************999997.6666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (628 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2815  (0.157008); expected 358.6 (0.02)
Passed bias filter:                      714  (0.0398237); expected 358.6 (0.02)
Passed Vit filter:                       106  (0.00591221); 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):               5  [number of targets reported over threshold]
# CPU time: 0.90u 0.34s 00:00:01.24 Elapsed: 00:00:00.54
# Mc/sec: 3481.55
//
Query:       gi|518652915|ref|YP_008142435.1|  [L=367]
Description: hypothetical protein FACI_IFERC00001G1554 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-34  118.2   0.0    3.9e-34  117.9   0.0    1.1  1  DnaJ_C         DnaJ C terminal domain
    1.6e-28   98.6   2.4    2.9e-28   97.8   2.4    1.5  1  DnaJ           DnaJ domain
    3.5e-12   46.5  14.1    5.8e-12   45.8  14.1    1.4  1  DnaJ_CXXCXGXG  DnaJ central domain
    1.1e-05   25.3  14.3     0.0011   18.9   1.8    2.4  2  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi
  ------ inclusion threshold ------
      0.011   15.0  11.0        1.1    8.5   2.2    3.1  3  DUF1356        Protein of unknown function (DUF1356)
      0.046   13.8   0.3       0.13   12.4   0.2    1.7  2  DUF148         Domain of unknown function DUF148
      0.093   12.7   0.6      0.093   12.7   0.6    2.1  3  Prok-RING_1    Prokaryotic RING finger family 1
       0.13   12.4   0.2       0.13   12.4   0.2    2.0  2  zf-RING_10     zinc RING finger of MSL2
        5.1    7.2   9.3        1.6    8.8   1.1    2.2  2  HypA           Hydrogenase/urease nickel incorporation, metal


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.0     2e-37   3.9e-34       1     148 []     127     341 ..     127     341 .. 0.98

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 2e-37
                                       EEEEEEE-HHHHHH-.EEE.EEEE..................................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx.................................................. RF
                            DnaJ_C   1 ieveleisleelykGktkkikikrnvi.................................................. 27 
                                       i v+l++++e++y G++k ik+krn +                                                  
  gi|518652915|ref|YP_008142435.1| 127 IYVKLNVTMEDAYYGASKPIKFKRNAMcevcngtgaeggvlvtcptchgtgqerisrgqgffnfvqvivcrtcmgkg 203
                                       5689*********************99************************************************** PP

                                       ...................TEEEEEE-TT--TT-EEEETT-SSSS..S---EEEEEEE---SS-EEETTEEEEEEEE CS
                                       ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  28 ...............kkekktlevkipaGikdgqkirlegeGdeeggepGDlivtikvkphpvFkrkgndlyvevei 89 
                                                      + + ++++++ip+G+++++++r ++ G++ gg +GDl+ ++ v+p+p+ kr+g++lyv+  i
  gi|518652915|ref|YP_008142435.1| 204 kipktpckacagkgyIPKMENISITIPKGVDTNTRLRTQKLGNSFGGVTGDLYAVVYVQPNPNIKRTGDNLYVKEAI 280
                                       *************98777889**********************999**************************999** PP

                                       EHHHHHHTEEEEEE-SS-EEEEEE...--TT-EEEETT-S-EET...TEE--EEEEEEEE-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            DnaJ_C  90 slaeallGgklevptldgkvklki...tqpgevlrikgkGmpklkkpgkrGdlyvevkvefP 148
                                       ++ +a+lGg++e+p +++k +l+i   +qp++vlrikg Gmpkl  +++ Gdl+v +k ++P
  gi|518652915|ref|YP_008142435.1| 281 DFPTAALGGSVEIPLFKEKFTLNIpagSQPEDVLRIKGAGMPKLT-SRGSGDLLVVLKLQVP 341
                                       ********************************************7.**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   2.4   1.5e-31   2.9e-28       1      63 []       4      66 ..       4      66 .. 0.99

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 1.5e-31
                                      HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
                              DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                                      dyY+iLgv+k+as++eI++++r+la+kyHPD n++++eae+kFkei+eAyevLsdp+kR+qYD
  gi|518652915|ref|YP_008142435.1|  4 DYYQILGVDKTASQEEIRSKFRELAKKYHPDVNSGSKEAEQKFKEIAEAYEVLSDPQKRQQYD 66
                                      8*************************************************************9 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8  14.1   2.9e-15   5.8e-12       1      67 []     154     217 ..     154     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.9e-15
                     DnaJ_CXXCXGXG   1 CkkCkGsgakkgkkktCktCkGsGvvreeqkt.lgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                                       C+ C+G+ga+ g   tC+tC+G+G++r ++ + + +fv  +   C++C G+Gk+   k++Ck+C Gkg
  gi|518652915|ref|YP_008142435.1| 154 CEVCNGTGAEGGVLVTCPTCHGTGQERISRGQgFFNFV--QVIVCRTCMGKGKIP--KTPCKACAGKG 217
                                       ********9888899*********88777643354555..5679*********88..889******97 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 !   18.9   1.8   5.3e-07    0.0011      12      55 ..     153     192 ..     150     195 .. 0.93
   2 !   11.8   4.8   9.2e-05      0.18      13      43 ..     196     220 ..     193     224 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 5.3e-07
                                       E-TTTTTTSEETTE......E-TTTTTSSEEE-HHHHHHHHHHH CS
                         Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkglipTaqGqkLldFik 55 
                                        C+ Cng+G + +      + CP C G g      Gq   +F++
  gi|518652915|ref|YP_008142435.1| 153 MCEVCNGTGAEGGV----LVTCPTCHGTGQERISRGQGFFNFVQ 192
                                       6********98887....89**********************98 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 9.2e-05
                                       -TTTTTTSEETTE......E-TTTTTSSEEE CS
                         Anti-TRAP  13 CdaCngsGkiepeeprasleCPkCsGkglip 43 
                                       C +C g Gki+ +      +C +C Gkg ip
  gi|518652915|ref|YP_008142435.1| 196 CRTCMGKGKIPKT------PCKACAGKGYIP 220
                                       *************......**********99 PP

>> DUF1356  Protein of unknown function (DUF1356)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   2.2   0.00056       1.1      19      43 ..     154     178 ..     142     186 .. 0.75
   2 ?    7.9   0.5   0.00081       1.6      31      47 ..     192     208 ..     179     211 .. 0.88
   3 ?    3.8   0.1     0.015        29      35      58 ..     210     231 ..     207     247 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00056
                           DUF1356  19 vsqvpyveatgrdsvtCptCqGtGe 43 
                                       +     + a g   vtCptC GtG+
  gi|518652915|ref|YP_008142435.1| 154 CEVCNGTGAEGGVLVTCPTCHGTGQ 178
                                       44455667888899**********6 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00081
                           DUF1356  31 dsvtCptCqGtGeiPre 47 
                                       + ++C tC G+G+iP+ 
  gi|518652915|ref|YP_008142435.1| 192 QVIVCRTCMGKGKIPKT 208
                                       6799***********85 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.015
                           DUF1356  35 CptCqGtGeiPreqekqLvaLiPy 58 
                                       C +C G+G+iP+    ++   iP 
  gi|518652915|ref|YP_008142435.1| 210 CKACAGKGYIPKME--NISITIPK 231
                                       9**********853..33344555 PP

>> DUF148  Domain of unknown function DUF148
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.3e-05      0.13       5      46 ..       4      48 ..       2      57 .. 0.85
   2 ?    0.6   0.1       0.3     6e+02       1      25 [.      41      66 ..      41      70 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.3e-05
                            DUF148  5 effaIl.knenltiaeieeqleawaeky..gvtdeykefeakvka 46
                                      ++++Il  +++ +++ei ++++++a+ky  +v++  ke e+k k+
  gi|518652915|ref|YP_008142435.1|  4 DYYQILgVDKTASQEEIRSKFRELAKKYhpDVNSGSKEAEQKFKE 48
                                      79****88999*****************88888888887777665 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.3
                            DUF148  1 earkeffaIlknen.ltiaeieeqle 25
                                      ea ++f++I++  + l+++++ +q +
  gi|518652915|ref|YP_008142435.1| 41 EAEQKFKEIAEAYEvLSDPQKRQQYD 66
                                      68899999995555499999988876 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.6   4.7e-05     0.093       3      27 ..     150     175 ..     148     181 .. 0.87
   2 ?   -1.7   0.1       1.5   2.9e+03      20      26 ..     193     199 ..     184     201 .. 0.79
   3 ?   -3.9   0.5       7.1   1.4e+04       5      11 ..     208     214 ..     207     216 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.7e-05
                       Prok-RING_1   3 tgkkCpvCgkelkeedDiVvCpeC.g 27 
                                        +  C+vC+ + +e+  +V+Cp+C g
  gi|518652915|ref|YP_008142435.1| 150 RNAMCEVCNGTGAEGGVLVTCPTChG 175
                                       6789********************44 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.5
                       Prok-RING_1  20 iVvCpeC 26 
                                       ++vC +C
  gi|518652915|ref|YP_008142435.1| 193 VIVCRTC 199
                                       8899999 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 7.1
                       Prok-RING_1   5 kkCpvCg 11 
                                       + C++C 
  gi|518652915|ref|YP_008142435.1| 208 TPCKACA 214
                                       5688885 PP

>> zf-RING_10  zinc RING finger of MSL2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.4      0.99     2e+03      25      44 ..     153     174 ..     146     180 .. 0.63
   2 ?   12.4   0.2   6.5e-05      0.13      23      55 ..     193     227 ..     189     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.99
                        zf-RING_10  25 vCrlCvgk..kkklkpsCsqCk 44 
                                       +C +C g   +  +  +C++C+
  gi|518652915|ref|YP_008142435.1| 153 MCEVCNGTgaEGGVLVTCPTCH 174
                                       5777765411344666777776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 6.5e-05
                        zf-RING_10  23 HyvCrlCvgkkkklkpsCsqCk..dyekyeenkql 55 
                                         vCr+C+gk k  k+ C+ C    y    en ++
  gi|518652915|ref|YP_008142435.1| 193 VIVCRTCMGKGKIPKTPCKACAgkGYIPKMENISI 227
                                       57*******************85567666666665 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   1.1   0.00078       1.6      69     105 ..     150     187 ..     146     190 .. 0.77
   2 ?    2.6   1.5     0.067   1.3e+02      70      96 ..     193     217 ..     188     228 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00078
                                       -EEEETTTS-EEECHHHHHS-TTTSSS.-EEEEESSSE CS
                              HypA  69 vkvrCreCgkefeleekalrCpkCgsa.dveivsGeel 105
                                        +++C++C+ ++ +    ++Cp+C+++ + +i +G+++
  gi|518652915|ref|YP_008142435.1| 150 RNAMCEVCNGTGAEGGVLVTCPTCHGTgQERISRGQGF 187
                                       5789*****99987755679****99845667777765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.067
                                       EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  70 kvrCreCgkefeleekalrCpkCgsad 96 
                                       ++ Cr+C  ++++ +  + C++C +++
  gi|518652915|ref|YP_008142435.1| 193 VIVCRTCMGKGKIPK--TPCKACAGKG 217
                                       578*****9999884..48****8865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2315.04
//
Query:       gi|518652916|ref|YP_008142436.1|  [L=307]
Description: hypothetical protein FACI_IFERC00001G1555 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.4e-137  457.6   1.2   1.6e-137  457.4   1.2    1.0  1  SOR       Sulphur oxygenase reductase
    1.5e-05   25.0   0.1      0.072   13.2   0.0    2.7  2  ABM       Antibiotic biosynthesis monooxygenase
  ------ inclusion threshold ------
      0.013   15.2   0.1          6    6.5   0.0    2.5  2  DUF3291   Domain of unknown function (DUF3291)


Domain annotation for each model (and alignments):
>> SOR  Sulphur oxygenase reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  457.4   1.2  2.7e-141  1.6e-137       2     302 .]       4     301 ..       3     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 457.4 bits;  conditional E-value: 2.7e-141
                               SOR   2 vyvainkakvenepktlelmakvgpkvClvtarhpGFlGFqalvqvGvlPlggRyGaakvdmaeelnplellqytlW 78 
                                       +yvain++++ n+++t++++++vgpkvC vtarhpGF+GFq+++q+G++P+g+R+G++++dm++ +++++++qyt+W
  gi|518652916|ref|YP_008142436.1|   4 PYVAINEVEMLNNDTTMQMFQQVGPKVCQVTARHPGFVGFQNHMQFGIIPMGTRWGGGSMDMTK-MDTMNVYQYTMW 79 
                                       8**************************************************************9.************ PP

                               SOR  79 kdledheemheenfdrifelCssCleqvveGPwePvyeiveanlPevvsltdvpkvlGkkfaqakevdipkvslasg 155
                                       k+++dhe+mh+enf++if+lCssCl+qvv+GPweP+yeiv+a +P +++++d+++++Gkkfa++++ ++p +s+++g
  gi|518652916|ref|YP_008142436.1|  80 KSIKDHEDMHRENFSSIFRLCSSCLSQVVYGPWEPLYEIVDASMPLNTEMADFTTMFGKKFAAGDPAGVPPISMPYG 156
                                       ***************************************************************************** PP

                               SOR 156 krvvalgehtvkeGkekeFeegavetlellkeapGllGymilkkiGvsalgsfqlkpegiaealetlgavppkkket 232
                                       +r++al+ehtvk+ kekeFe+++ve+++ +++apG+lGymilk++Gvsa+gsfqlk++gi+e+le+ g+vp  ++e+
  gi|518652916|ref|YP_008142436.1| 157 QRTIALSEHTVKKDKEKEFESTIVEVMKDFEKAPGFLGYMILKEVGVSAVGSFQLKSKGIHETLESGGEVP-TQQEG 232
                                       *****************************************************************999995.556** PP

                               SOR 233 afevleaaetPkeylvhveWesleaaqfGlarvlvkpelrkihdekvlatlvkgPyirllnplmedtlwr 302
                                        f+++ea++tP+ey vh+eW+s+++a+fG++rvl+ +  r+ihd kvl+tl++gPyirllnp+me+t+wr
  gi|518652916|ref|YP_008142436.1| 233 SFKPEEARPTPPEYKVHMEWASPNDAMFGIGRVLFAHPAREIHD-KVLDTLIRGPYIRLLNPMMEGTTWR 301
                                       ********************************************.************************8 PP

>> ABM  Antibiotic biosynthesis monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0   0.00022       1.3       5      66 ..       8      88 ..       4      92 .. 0.77
   2 !   13.2   0.0   1.2e-05     0.072       7      44 ..     164     200 ..     159     259 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00022
                                      EEEEE.ESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEE..................EEETSTTEEEEEEEESSHHHHH CS
                               ABM  5 iaeir.vkpgqaeafldafaeavesllaeepGclgyell..................rstedpdevvvieeWeseaale 64
                                      i+e++    +   +  +++   v +++a++pG+ g++ +                    ++d+  v+ ++ W+s+ ++e
  gi|518652916|ref|YP_008142436.1|  8 INEVEmLNNDTTMQMFQQVGPKVCQVTARHPGFVGFQNHmqfgiipmgtrwgggsmdMTKMDTMNVYQYTMWKSIKDHE 86
                                      555555555555445555555556799*************9***999999998888735899999**********9999 PP

                                      HH CS
                               ABM 65 ah 66
                                      + 
  gi|518652916|ref|YP_008142436.1| 87 DM 88
                                      75 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                                       EEEESTTGHHHHHHHHHHHHHHHHHTSTTEEEEEEEEE CS
                               ABM   7 eirvkpgqaeafldafaeavesllaeepGclgyellrs 44 
                                       e +vk++++++f+    e+ ++  ++ pG+lgy +l++
  gi|518652916|ref|YP_008142436.1| 164 EHTVKKDKEKEFESTIVEVMKDF-EKAPGFLGYMILKE 200
                                       668******************9*.9********98864 PP

>> DUF3291  Domain of unknown function (DUF3291)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0     0.001         6      11      43 ..      13      45 ..       5      96 .. 0.62
   2 ?    6.1   0.0    0.0014       8.3       3      41 ..     157     195 ..     156     213 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.001
                           DUF3291 11 aplddpeladFvaaldeinalaeaspGfvwrle 43
                                         +d +++ F++  +++ ++  ++pGfv   +
  gi|518652916|ref|YP_008142436.1| 13 MLNNDTTMQMFQQVGPKVCQVTARHPGFVGFQN 45
                                      4456778*********************96544 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0014
                           DUF3291   3 qvniarlkaplddpeladFvaaldeinalaeaspGfvwr 41 
                                       q +ia   + +++++ ++F + + e+ +  e++pGf+  
  gi|518652916|ref|YP_008142436.1| 157 QRTIALSEHTVKKDKEKEFESTIVEVMKDFEKAPGFLGY 195
                                       5689999999**************************865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.23s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2108.10
//
Query:       gi|518652917|ref|YP_008142437.1|  [L=192]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   37.9   0.1    2.3e-09   36.9   0.1    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    7.2e-09   35.1   0.6    1.9e-08   33.7   0.6    1.8  1  HTH_24          Winged helix-turn-helix DNA-binding
    1.5e-06   28.1   0.2    2.7e-06   27.2   0.2    1.4  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
  ------ inclusion threshold ------
      0.067   13.1   0.0        0.2   11.6   0.0    1.7  1  MarR            MarR family


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 !   36.9   0.1   5.2e-13   2.3e-09       1      42 []      43      85 ..      43      85 .. 0.97

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 5.2e-13
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGl.SestvlrRvrrLe 42
                                      +D +D++IL+++ +d+R + +e+++++G+ S+s++ rR++ ++
  gi|518652917|ref|YP_008142437.1| 43 MDSFDLRILKEISRDSRKPLKEIGKAIGIySASAISRRIKEMQ 85
                                      9***************************98**********995 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.6   4.2e-12   1.9e-08       1      48 []      43      91 ..      43      91 .. 0.97

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 4.2e-12
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlgl.SpstvnrrlkrLeeeGlIk 48
                                      +d  d++IL+++ +++r + +e+ +++g+ S s+++rr+k+++e+ +Ik
  gi|518652917|ref|YP_008142437.1| 43 MDSFDLRILKEISRDSRKPLKEIGKAIGIySASAISRRIKEMQENNIIK 91
                                      7999************************9899****************7 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.2   6.1e-10   2.7e-06      11      74 ..     119     181 ..     111     182 .. 0.93

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 6.1e-10
                                       THHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  11 eqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       e+++ ++e++ +++ V+ +  + Gd d+ + ++++  +++  +l+e l ++ +++r++t+ vl+
  gi|518652917|ref|YP_008142437.1| 119 EYHDIVAEKIMKIKGVIDVLFLLGDIDFYILCATKTKDDYVIILNE-LEKITEIERSDTHTVLN 181
                                       7899******************************************.***************97 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.6e-05       0.2       6      48 ..      48      91 ..      47      95 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
                                      HHHHHHHHHSTTEEHHHHHHHHTS.-HHHHHHHHHHHHHTTSEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgv.skstvtrvldrLekkGlie 48
                                      ++iL  +++     ++e++k++g+ s s+++r ++++ +++ i+
  gi|518652917|ref|YP_008142437.1| 48 LRILKEISRDSRKPLKEIGKAIGIySASAISRRIKEMQENNIIK 91
                                      689999999999***********967899***********9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1397.98
//
Query:       gi|518652918|ref|YP_008142438.1|  [L=437]
Description: aminotransferase class-III [Ferroplasma acidarmanus fer1]
Scores for complete 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-85  287.4   0.0    1.8e-85  287.1   0.0    1.0  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.32   10.8   0.0    1.5  1  NifZ         NifZ domain


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  287.1   0.0     2e-89   1.8e-85       9     406 .]      42     434 ..      37     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 287.1 bits;  conditional E-value: 2e-89
                                       SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT- CS
                       Aminotran_3   9 lllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapk 85 
                                       ++++i++ae++ ++d dg+ ++D vs+i+v+nlG++  k+ +avk+q+++++h     + +e  +++ e l + +p 
  gi|518652918|ref|YP_008142438.1|  42 FPIAIKRAENSLIEDLDGNIFIDWVSGISVMNLGFN-DKIRDAVKAQLDDIWHAL--EIPTEVRINFLEALRNSFPP 115
                                       6699******************************96.69***************9..8888999************9 PP

                                       ..S..EEEEESSHHHHHHHHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE CS
                       Aminotran_3  86 gld..kvflansGseAvetAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrl 160
                                       ++   k+++  sG++A etA+ +a +      +++ + +iaf+ga+HG   g +++t+   ky++ + +   +++r+
  gi|518652918|ref|YP_008142438.1| 116 EMRnyKTIFGISGADACETAINIAHA-----IRKKNAPTIAFEGAYHGVSGGIIAATAG-RKYREAVYSDGFKIIRV 186
                                       998899******************99.....45567889********************.***************** PP

                                       -TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTT CS
                       Aminotran_3 161 kypdeevlkeneeeeaalleelealekkkkdevaAvivEpiqgegGvvvaspeflaklrelckkhdvllivDEvqtG 237
                                       +yp+e   ++  +   ++++++ +  ++  d    vivEpiqgegG++v++++fl+++re+c+++d  +ivDEvq+G
  gi|518652918|ref|YP_008142438.1| 187 PYPYELWYDYDVSDIISIMKKIMDDGEAGYDRPDSVIVEPIQGEGGYIVPPDGFLKAIREFCTEYDLTMIVDEVQSG 263
                                       ********9999888888888888789999*********************************************** PP

                                       TTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHHHHHHHHHHHHTTHH CS
                       Aminotran_3 238 fGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacavalavleiieeekll 314
                                       +GrTGk++A e+ +++pD+++++K+++gGlp+s v  +++  + l +  h +T+ +npla+a+ + v++ +   k+ 
  gi|518652918|ref|YP_008142438.1| 264 VGRTGKMWAFEYENITPDIVCVSKSIGGGLPVSLVYYRDDYDKKLPKPFHLGTYRANPLAMAAGITVINEV--PKYF 338
                                       *********************************************9999**************99999866..79** PP

                                       HHHHHHHHHHHHHHHHHCTT-TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETT..TEEEE- CS
                       Aminotran_3 315 enaqelgaalkegLeelqkkyevikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGd..nvirll 385
                                       ++++  g+++ ++ ++++++   i+evRgkG mi+iel+++ +  +     e+ ++++++G+l+ ++G+  nv r++
  gi|518652918|ref|YP_008142438.1| 339 DKVKSSGKEMLNKFNKIDSN--LIGEVRGKGYMIGIELVDNGKPMNskrmMELKHELLQNGLLMHTCGHygNVFRFM 413
                                       *****************955..8*****************99854478898999*********************** PP

                                       --TT--HHHHHHHHHHHHHHH CS
                       Aminotran_3 386 ppliitdeeidelleilkkal 406
                                        +l + de i+ +++i+ k+l
  gi|518652918|ref|YP_008142438.1| 414 GALNMPDELINTGINIFGKVL 434
                                       ****************98875 PP

>> NifZ  NifZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.5e-05      0.32       3      46 ..     195     240 ..     194     251 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.5e-05
                              NifZ   3 kfevgdkVraakdirNDGtfpgkeigelLvk..kGdvGvvvsvGtf 46 
                                        ++v d + + k+i +DG+    ++++++v+  +G+ G++v    f
  gi|518652918|ref|YP_008142438.1| 195 DYDVSDIISIMKKIMDDGEAGYDRPDSVIVEpiQGEGGYIVPPDGF 240
                                       59999*************************9667******976555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2688.38
//
Query:       gi|518652919|ref|YP_008142439.1|  [L=465]
Description: cationic amino acid transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-28  100.0  50.5    1.6e-28   99.6  50.5    1.1  1  AA_permease    Amino acid permease
    3.2e-27   95.4  57.3      4e-27   95.1  57.3    1.1  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6  50.5   1.8e-32   1.6e-28      11     467 ..      26     449 ..      14     459 .. 0.81

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 1.8e-32
                       AA_permease  11 iGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswi 87 
                                        +++ f+ +gv++  +   ++ l y++a++ ++ +m++ + +a  ++++gg+y++++  lg +lG   ++ yl+  i
  gi|518652919|ref|YP_008142439.1|  26 ASVASFFTTGVAAIGG---SLPLTYIIATFGVLSAMYMDYSFAKRISHAGGYYAFVRSGLGNKLGTLSAWFYLYDMI 99 
                                       3345555555554444...56**************************************************999888 PP

                       AA_permease  88 tvla..leltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiivg...ii 159
                                       +++a    l   +i+  ++ ++   p+ w       ++ ++i ++ +    + +++++li  +a i+f+++g   ii
  gi|518652919|ref|YP_008142439.1| 100 AAIAgfSTLYFGAIVAPYIPFLNTSPYGWLPL---SLIPFAIVFFFLWNGLRPSLWYTLISSVAEISFLVIGaiiII 173
                                       87764223334455555665555556555554...3333444444445566779******************86444 PP

                       AA_permease 160 llaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkai 236
                                       +l g k++ +        + +     l++         +++   + v +v++f G ++v+++++E+k+P+k+iPka 
  gi|518652919|ref|YP_008142439.1| 174 ILLGSKNTLA--------PFT-----LTGH-------PISALGLATVYSVLSFVGAGSVIALSEEIKNPRKNIPKAL 230
                                       4444443333........333.....3333.......477888899999**************************** PP

                       AA_permease 237 lqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssansslysasR 313
                                         v ++ + +Y+l++++++++++ ++ ++++ s ++  ++ ++ +++g  +l  ++++v   + +s +++   ++sR
  gi|518652919|ref|YP_008142439.1| 231 VIVALLAAAVYILASYAVVVGWGLSNISSFATSTNP--GITVYARYLGPVGLVIFVVLVA-NSFISNGIAQGNAGSR 304
                                       *******************************99988..**************88877765.5899************ PP

                       AA_permease 314 vlyslakdglaP..kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliilsyl 388
                                       + ys+a+d+++   +++k+ ++ g P + i +++i+ ++++++ +l +++++  ++l+++ a+   i+++l  +s++
  gi|518652919|ref|YP_008142439.1| 305 TAYSMARDNILFssRWAKVNERTGAPRMVIGIMIIVTFILMIVFGLIFGPFEGGTILITAEAALLYIIHILGDISLP 381
                                       **********9889*************************************************************** PP

                       AA_permease 389 rfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvg 465
                                        +       +r   +l++++  +  ++   l a i ++ ++ +  ++++++ p ++ +++  +a ++v ++l+i + 
  gi|518652919|ref|YP_008142439.1| 382 IY------AKR---KLKYRLKAYLPLLLGPLPATIVYA-VAEYGVFIPIPAYP-NSIYVYGTLALIGVGIVLAITIR 447
                                       33......333...789999999999999999876665.55677789999999.77889999999988888888776 PP

                       AA_permease 466 vk 467
                                       +k
  gi|518652919|ref|YP_008142439.1| 448 HK 449
                                       65 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.1  57.3   4.5e-31     4e-27      14     418 ..      22     436 ..      10     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 95.1 bits;  conditional E-value: 4.5e-31
                     AA_permease_2  14 v...igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfa 87 
                                       v   +++++f+++++a+ g +l l+++ia++ + l+ ++    ++ ++++ gG y +++ + g+k++ lsawf++++
  gi|518652919|ref|YP_008142439.1|  22 VapaASVASFFTTGVAAIGGSLPLTYIIATFGV-LSAMYMDYSFAKRISHAGGYYAFVRSGLGNKLGTLSAWFYLYD 97 
                                       2445788899999999************99988.4555444445666****************************** PP

                     AA_permease_2  88 yvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilgl 164
                                        ++++a+ +++ +++++    p+l+++++ ++ +  + +++v+++   g + s +++ i  ++ i  +l+i   + +
  gi|518652919|ref|YP_008142439.1|  98 MIAAIAGFSTLYFGAIVAPYIPFLNTSPYGWLPLSLIPFAIVFFFLWNGLRPSLWYTLISSVAEIS-FLVIGA-III 172
                                       *****9999999****999999998887777666666666666666778888*************5.544433.333 PP

                     AA_permease_2 165 itvdgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllv 237
                                       i++ g+ ++        f+ +g p+++lgl++  +++sf+G  s++  see+k+  k++pka++i++l+++ +y+l 
  gi|518652919|ref|YP_008142439.1| 173 IILLGSKNT-----LAPFTLTGHPISALGLATvySVLSFVGAGSVIALSEEIKNprKNIPKALVIVALLAAAVYILA 244
                                       333444444.....3478889****9999999556****************8888689******************* PP

                     AA_permease_2 238 niaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP.rffa 313
                                       + a++ + + ++i++ +++ +++  +++++ g+v+ +i+v+l+a s + +++++  + sr+++++ard++l  +++a
  gi|518652919|ref|YP_008142439.1| 245 SYAVVVGWGLSNISSFATSTNPGITVYARYLGPVGLVIFVVLVANSFISNGIAQGNAGSRTAYSMARDNILFsSRWA 321
                                       *************99999999**999999999********************************************* PP

                     AA_permease_2 314 kvn.kfgspiraiiltaivslillllfl..lassaaynfllsvsslgliisyllliigalilrkkrphlkrpgk... 384
                                       kvn ++g+p  +i +  iv++il+++f   +++ +  ++l ++ + +l+i+ +l  i++ i+ k++ +++ +++   
  gi|518652919|ref|YP_008142439.1| 322 KVNeRTGAPRMVIGIMIIVTFILMIVFGliFGPFEGGTILITAEAALLYIIHILGDISLPIYAKRKLKYRLKAYlpl 398
                                       ***99***999999999999999888883333345556999999999999999999999999999777644332233 PP

                     AA_permease_2 385 ...ilvaiigalfllfllvalf.fppkgpatqssliyt 418
                                          +l+a+i   ++ + +++++  +p+ + ++ +l++ 
  gi|518652919|ref|YP_008142439.1| 399 llgPLPATIVYAVAEYGVFIPIpAYPNSIYVYGTLALI 436
                                       33333333333333333333332444555566655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.48
# Mc/sec: 2941.72
//
Query:       gi|518652920|ref|YP_008142440.1|  [L=439]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.7e-79  267.9   0.4    6.9e-78  262.6   0.4    2.1  1  Amidase     Amidase
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.23   11.5   0.0    1.3  1  Phage_RpbA  Phage RNA polymerase binding, RpbA


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  262.6   0.4   7.7e-82   6.9e-78      41     451 .]      52     411 ..      24     411 .. 0.88

  Alignments for each domain:
  == domain 1  score: 262.6 bits;  conditional E-value: 7.7e-82
                                       ......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE--SGGG-SSSSTT-TT-- CS
                           Amidase  41 rgkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkTnmdefamgsstensvfgp 117
                                       ++++ +pL+G+P svKD id+k+++t +Gs++++++++++Da v++ L + G v+ gkTn++efamg+ t       
  gi|518652920|ref|YP_008142440.1|  52 HKHSSSPLYGIPYSVKDIIDTKNLRTEYGSEFFKGHVPQEDADVIRALDEYGPVLQGKTNTHEFAMGIVTPV----- 123
                                       67889***************************************************************9987..... PP

                                       -BBTTCTCCB--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEE CS
                           Amidase 118 trNPwdksrtpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGpla 194
                                        +NPw+ s++ GGSSGGsAAav++gl+++++GtDt+GSiRiP+s+cg+ GlKPt+g +S +g+ + ++sld+vGp++
  gi|518652920|ref|YP_008142440.1| 124 CNNPWNVSKITGGSSGGSAAAVSSGLSLFSLGTDTAGSIRIPSSMCGVSGLKPTTGSLSVKGIFPEAWSLDTVGPIT 200
                                       9**************************************************************************** PP

                                       SSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT. CS
                           Amidase 195 rsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaG. 270
                                       r+++d+ +++ ++  + p+                 +k+++++   G++ ++  +s d +v+ a+ ++ +++ ++  
  gi|518652920|ref|YP_008142440.1| 201 RYASDIPAIVTAMGFKSPR-----------------AKSQRRKPLLGIIGNLT-ESSDTNVKFAFYSFMDHMVSEDl 259
                                       ******9999988744433.................3455667789***9999.799******************99 PP

                                       -EEEEEE-CCGGGHHHHHHHHHHHHHHHHTTT-SSSSS---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCC CS
                           Amidase 271 hevvevelpsleealslyylilvaeassnlarylgvryerlsetkvlsellpksraellgeevkrrielgnyalsae 347
                                       + ++e+++ ++e+++s   ++ + ++ +n                ++++   ++ +el++ e +++i+  +  l+ +
  gi|518652920|ref|YP_008142440.1| 260 VDIKEIHIDNMESMAS---AADMIDGCENA---------------TIHRSRYENNPELFSVESRNQIKYYS-SLKPM 317
                                       9999999888888888...55555665552...............24444455677888888887777777.66666 PP

                                       CCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCCCCCHHHCSHHHHHGCCTTT...HHHHHTT--EEE CS
                           Amidase 348 asskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlgekdktidsytvlynlldftavvvpvnlaglpals 424
                                       +    y++a + r +   ef+ +f+++D+l+sPt pt ap+++e +           ++++++++ p+nl g pals
  gi|518652920|ref|YP_008142440.1| 318 D----YIEAKRLRMRQGMEFNSLFNQYDFLVSPTLPTIAPDKKEIE-----NVPFDYFMKYIKFTNPFNLFGVPALS 385
                                       6....************************************88775.....45677788899999************ PP

                                       EECCCCT.TECEEEEEEESTT-HHHHH CS
                           Amidase 425 vpagksedglPvGvqvigkafqeetlL 451
                                       +++g+s  ++PvG+q++g ++++ +++
  gi|518652920|ref|YP_008142440.1| 386 ITCGFSR-DMPVGLQIVGGKLRDIEVC 411
                                       *****96.9*************98875 PP

>> Phage_RpbA  Phage RNA polymerase binding, RpbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.6e-05      0.23      39      80 ..     240     283 ..     233     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.6e-05
                        Phage_RpbA  39 eqevrfelYkeiDkeVsdkwielmrkhre..dslaagakvvkak 80 
                                         +v+f++Y  +D++Vs+  +++   h +  +s+a  a ++ + 
  gi|518652920|ref|YP_008142440.1| 240 DTNVKFAFYSFMDHMVSEDLVDIKEIHIDnmESMASAADMIDGC 283
                                       5679*****************99988865336888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.50
# Mc/sec: 2652.10
//
Query:       gi|518652921|ref|YP_008142441.1|  [L=496]
Description: hypothetical protein FACI_IFERC00001G1560 [Ferroplasma acidarmanus fer1]
Scores for complete 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-154  512.8   0.0     8e-154  512.6   0.0    1.0  1  Aldedh    Aldehyde dehydrogenase family
    0.00022   20.4   0.0    0.00035   19.7   0.0    1.3  1  LuxC      Acyl-CoA reductase (LuxC)
     0.0046   16.4   0.0      0.034   13.6   0.0    2.1  1  DUF1487   Protein of unknown function (DUF1487)


Domain annotation for each model (and alignments):
>> Aldedh  Aldehyde dehydrogenase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.6   0.0  1.3e-157    8e-154       6     462 .]      16     475 ..      12     475 .. 0.97

  Alignments for each domain:
  == domain 1  score: 512.6 bits;  conditional E-value: 1.3e-157
                                       S.SEEEEEETTTCEEEEEEE-B-HHHHHHHHHHHHHHHHH.HTTS-HHHHHHHHHHHHHHHHHTHHHHHHHHHHHH- CS
                            Aldedh   6 s.etievinPatgeviakvpaataedvdaavaaAkeafka.waklpaeeRaeiLrkaadlleerkeelaeletletG 80 
                                       + e+ie  +P++g+ i+ + + ++++v++a+++++eaf++ + + +++ R+e++ k+ d+++e++   a+le+++tG
  gi|518652921|ref|YP_008142441.1|  16 GgERIELKSPVDGSLIGYIIDTDKDTVERAIQSSREAFNKfYLESTIKSRQELIGKLTDIVQEKATIYADLESKNTG 92 
                                       4378***********************************637799******************************** PP

                                       --HHHHHH.HHHHHHHHHHHHHHHHHH.HSEEEEEE.CTTEEEEEEEEE-SEEEEEE-SSSCCHHHHHHHHHHHHTT CS
                            Aldedh  81 kplaeara.eveeaidvlryyaelaek.legevlps.segklalvrrePlGvvgaItPWNfPlllaawklapalaaG 154
                                       k++++++  +++ ai+++ry+ae  e   + +++    +g++ +v++ P+Gvv++I+PWN+P+l+a+wk++p ++aG
  gi|518652921|ref|YP_008142441.1|  93 KTIRQSTFmDIPLAISHIRYFAETDEFkFQRKITHPeYPGTEGIVQNAPMGVVASIAPWNVPFLMAVWKIIPPVLAG 169
                                       ***********************977746666655535*************************************** PP

                                       -EEEEEE-TTSHHHHHHHHHHHHHTTS-TTSEEE--SSTCCHHHHHHH-TTESEEEEES-HHHHHHHHHHHHCTTSE CS
                            Aldedh 155 NtvvlKPaeetplsalllaelfeeaglPkgvlnvvtgsgsevgealvehpevdkvsftGstevgrkiakaaaknlkr 231
                                       N+vv+KP+  tpl+a+ l++ +++ag+P+g++n+v+g+g+++g+ lv++++vd+vsftGst++g +i+++aakn+k+
  gi|518652921|ref|YP_008142441.1| 170 NAVVIKPSHYTPLTAIELVKDMKAAGFPDGLVNLVNGTGRTTGNLLVNSDHVDMVSFTGSTPTGSRIMEQAAKNIKK 246
                                       ***************************************************************************** PP

                                       EEEEE---EEEEE-TTSHHHHHHHHHHHHHHGGGGTSTTSEEEEEEEHHHHHHHHHHHHHHHHT--BS-TTSTT-SB CS
                            Aldedh 232 vtlElGGknplivledaDldkaveaivkgafgnaGQvCiaasrllvqesiydefveklveaakklkvgdpldedtdv 308
                                       v+lElGGk+p+iv++daDld+av+++++g+f+naGQ C +asrl+++esi+d+f++k++  + ++k g+p+d +td+
  gi|518652921|ref|YP_008142441.1| 247 VSLELGGKSPNIVFADADLDHAVKGVIFGIFLNAGQLCESASRLIIEESIMDKFLQKVKTYLDSMKSGNPMDFETDI 323
                                       ***************************************************************************** PP

                                       ---SSHHHHHHHHHHHHHHHHTTSEEEE-TTE.SB-SSSTTEE--EEEES-TTTSHHHHS---SSEEEEEEESSHHH CS
                            Aldedh 309 GPliseaqlekvekyveeakeegaklllGgereeaglekgyfvePtvlanvtpdmriaqeEiFGPVlsvikfkdeee 385
                                        ++++++q ek+e++++++++ g ++ +   + +  ++kg ++ Pt+l+++tp  +i  eEiFGPVl+v++fk+e+e
  gi|518652921|ref|YP_008142441.1| 324 SAITTKEQKEKIESLISQTVKSGGNIFYSK-NMQGTPDKGTYFPPTLLTGLTPGQQISDEEIFGPVLTVYPFKSEKE 399
                                       ****************************77.56899***************************************** PP

                                       HHHHHHSSSEESEEEEE-SBHHHHHHHHHHS-SSEEEESSSST--TTTSEB--CGGGEES-BSHHHHHHHTEEEEEE CS
                            Aldedh 386 aieiaNdteyGLaagvftkdleraervaerleaGnvyiNdsttgaaealpfgGvkqSglGreggkegleeytevktv 462
                                       ai++aN+t+yGLaag++tkd+e+a rva+ +eaG+v++N+++  +a a p gG+k+Sg+Gre g eg+ eyt+++++
  gi|518652921|ref|YP_008142441.1| 400 AIDLANSTKYGLAAGIWTKDIEKAGRVASMIEAGTVWVNEYHLLSAAA-PRGGFKKSGIGRELGLEGILEYTQTRHI 475
                                       ***********************************************9.*************************986 PP

>> LuxC  Acyl-CoA reductase (LuxC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   5.8e-08   0.00035      83     272 ..     135     316 ..     116     358 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 5.8e-08
                              LuxC  83 syekaqprglvlhvlsgNvp.llpvmsilqglLvknvnllkvSssdpflaaallksladvdenhtladslsvvyfks 158
                                       +  +  p g+v  + + Nvp l++v+ i+  +L++n+ ++k+S   p +a++l+k ++       l++    v+  +
  gi|518652921|ref|YP_008142441.1| 135 GIVQNAPMGVVASIAPWNVPfLMAVWKIIPPVLAGNAVVIKPSHYTPLTAIELVKDMKAAGFPDGLVN---LVN--G 206
                                       5667889************94569**********************************9988755554...442..2 PP

                              LuxC 159 gdtkleeeiv..qnaDvvvawGgeeaikaiseklkpgkqlik..fGakvSfavvdkealeeealdkaaeraAkDiiv 231
                                          +  + +v  +++D v+  G+  + + i e+++ + + ++   G k    +v  +a    +ld+a++ +   i  
  gi|518652921|ref|YP_008142441.1| 207 TGRTTGNLLVnsDHVDMVSFTGSTPTGSRIMEQAAKNIKKVSleLGGKS-PNIVFADA----DLDHAVKGVIFGIFL 278
                                       2333333333348999999999999999999977777665431134443.33333333....677777777777777 PP

                              LuxC 232 fdQqAClspqvvfvekddkieidefaeaLaaaLekrarilp 272
                                          q C s+  + +e   +  +d+f +++   L+      p
  gi|518652921|ref|YP_008142441.1| 279 NAGQLCESASRLIIE---ESIMDKFLQKVKTYLDSMKSGNP 316
                                       777777777777777...34667777777666666555555 PP

>> DUF1487  Protein of unknown function (DUF1487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   5.7e-06     0.034       9     167 ..     258     438 ..     254     443 .. 0.59

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
                           DUF1487   9 vifedgDlnsalealves..lkePfaegavatvlveesirdefvervrsklkplseev.aeHpsylkal......ek 76 
                                       ++f+d+Dl++a++ ++    l+    +++   +++eesi d+f+++v++ l  +++    +  + ++a+      ek
  gi|518652921|ref|YP_008142441.1| 258 IVFADADLDHAVKGVIFGifLNAGQLCESASRLIIEESIMDKFLQKVKTYLDSMKSGNpMDFETDISAIttkeqkEK 334
                                       89**********99886522566777899999*******************99986320222222222210011123 PP

                           DUF1487  77 idelkaktisa........ksesakakas...PilVldvt.hsflgd..kptgvvTlhtFrnakEvvkllakeslkf 139
                                       i+ l  +t++         +++ ++ k++   P l +++t  + ++d      v+T+  F++ kE++ l++  +  +
  gi|518652921|ref|YP_008142441.1| 335 IESLISQTVKSggnifyskNMQGTPDKGTyfpPTLLTGLTpGQQISDeeIFGPVLTVYPFKSEKEAIDLANSTKYGL 411
                                       33333344433677666655555555544444666665542344444222345677777777777777766555554 PP

                           DUF1487 140 asvsvwneklaavyelvarlnvdvftiN 167
                                       a+  +w + + ++  ++ +++  ++ +N
  gi|518652921|ref|YP_008142441.1| 412 AA-GIWTKDIEKAGRVASMIEAGTVWVN 438
                                       43.5666666666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.61u 0.29s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3186.54
//
Query:       gi|518652922|ref|YP_008142442.1|  [L=134]
Description: sterol carrier protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-12   47.5   0.0    2.4e-12   47.2   0.0    1.1  1  SCP2      SCP-2 sterol transfer family


Domain annotation for each model (and alignments):
>> SCP2  SCP-2 sterol transfer family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.3e-16   2.4e-12       5     100 ..      14     120 ..      10     121 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.3e-16
                                       HHHHHHH.HHHHHHCCH-EEEEEEECTC.T.....EEEEEETTSTEEE......SSCTT.BS-SEEEEEEHHHHHHH CS
                              SCP2   5 lerlkdp.ekkealkklagvlrfdltdlkg.....sltldlkegqldv......aakde.gkadvtlslsledllel 68 
                                        e+l+++ +++ea k +   l f +++ ++     +l+l+lk g  ++      +a+++  ka ++  ++++++++l
  gi|518652922|ref|YP_008142442.1|  14 TEKLNSNpAYAEAGKTWDDSLTFVVQPDETyndswYLYLNLKAG--KCidskvgKAESDvPKATFKYMGKYSNWVKL 88 
                                       55664444********************99***55555555544..444469997777779**************** PP

                                       HCTSS-HHHHHHTTSSEEEC-HHHHHHHHHHH CS
                              SCP2  69 aegklnpqkafmqgkLkieGDielaqkleall 100
                                       ++g+++p + +m+gk k++G +++ +++ +++
  gi|518652922|ref|YP_008142442.1|  89 IKGEIDPIQGLMTGKFKLDGSMMKIMRYTNAA 120
                                       ****************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (134 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      233  (0.0129957); 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 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 923.04
//
Query:       gi|518652923|ref|YP_008142443.1|  [L=513]
Description: hypothetical protein FACI_IFERC00001G1562 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-34  118.7   0.0    1.1e-32  113.0   0.0    2.2  2  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    7.2e-22   77.8   0.1    6.2e-21   74.8   0.0    2.5  3  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    2.3e-12   46.8   0.0    6.2e-12   45.4   0.0    1.8  2  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.0   0.0   1.8e-36   1.1e-32       1     169 [.       1     163 [.       1     165 [. 0.96
   2 !    3.4   0.0    0.0088        52      51     123 ..     391     474 ..     388     490 .. 0.76

  Alignments for each domain:
  == domain 1  score: 113.0 bits;  conditional E-value: 1.8e-36
                                       EEHHHHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHH CS
                      TPP_enzyme_N   1 mtvaealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGat 77 
                                       m++ e+l ++L+al+ + vfg+pG+++ p+l+ +++      +l++h   a ++Adgya+  +   +v++++ pG+ 
  gi|518652923|ref|YP_008142443.1|   1 MKGYEILEKTLAALKLDPVFGNPGTTEIPMLRGIRNY-----YLTLHDSIALGMADGYAQYNNTASIVNLHTLPGLG 72 
                                       78999*****************************997.....9********************************** PP

                                       HCHHHHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS- CS
                      TPP_enzyme_N  78 naltalaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrp 152
                                       n++  + +Ak +r+P+++ +g+++t+++    + + l  d l+ +  ++ky++++++p+++p a+rrA ++a+++++
  gi|518652923|ref|YP_008142443.1|  73 NTMSFVNTAKWNRSPVVITAGQQDTRHIV---FDPLLsgDLLNTVSGLVKYSYEIKNPSDIPTAFRRAKAIAMTPPM 146
                                       *****************************...886668899************************************ PP

                                       -EEEEEEEHHHCC-EEE CS
                      TPP_enzyme_N 153 gPvylelpkdvlleevd 169
                                       gPv++++p+d+++ +++
  gi|518652923|ref|YP_008142443.1| 147 GPVFISVPMDMMDYTAE 163
                                       ************98765 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH.............S..TC--T CS
                      TPP_enzyme_N  51 aafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg.............qgvlqqel 114
                                       a++aA g+ +  +k  v++     +++ ++ +l +Ak+ +iP+ +l+ +++ + +              ++++q +l
  gi|518652923|ref|YP_008142443.1| 391 ATAAALGIGMNNKKTLVIIGDG--AFMYTVQGLWTAKHYNIPVKFLVLNNSGYNILksfsksyypdmekKDYFQLNL 465
                                       7788888888888887777755..8999******************9998887777677777777777666666666 PP

                                       -CCHHHCCC CS
                      TPP_enzyme_N 115 dqlalfrpv 123
                                       d++++++ +
  gi|518652923|ref|YP_008142443.1| 466 DIESVAKGF 474
                                       666666655 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       0.2   1.2e+03      14      56 ..      55      95 ..      47     105 .. 0.74
   2 ?   -2.8   0.0      0.81   4.9e+03     126     151 ..     173     198 ..     159     198 .. 0.83
   3 !   74.8   0.0     1e-24   6.2e-21      21     141 ..     380     490 ..     369     502 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.2
                                      TTSSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHH CS
                      TPP_enzyme_C 14 kvkrprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDG 56
                                      ++++  s+++  +l  +G+++++   ak    +++vv ++G  
  gi|518652923|ref|YP_008142443.1| 55 QYNNTASIVNLHTLPGLGNTMSFVNTAKWN--RSPVVITAGQQ 95
                                      445566777777899999999999999996..46999988865 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.81
                                       EESSH.HHHHHHHHHHHHCSSSEEEE CS
                      TPP_enzyme_C 126 rvekadveeleealkealekkgpali 151
                                        v+++d+e + e++++  + k+pal+
  gi|518652923|ref|YP_008142443.1| 173 NVSSYDPEAVFEIVERINKAKHPALV 198
                                       68899999999999999999999987 PP

  == domain 3  score: 74.8 bits;  conditional E-value: 1e-24
                                       EECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHHHHTC CS
                      TPP_enzyme_C  21 yltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqepfgg 97 
                                       y+t +  g +G++ +aA+G+ +   +++  +i+GDG+f++++q l+ta  +n+p++++vlnN+gy+  +  +++++ 
  gi|518652923|ref|YP_008142443.1| 380 YYT-AKSGQLGWATAAALGIGMN--NKKTLVIIGDGAFMYTVQGLWTAKHYNIPVKFLVLNNSGYNILKSFSKSYYP 453
                                       555.45799*************7..479************************************************9 PP

                                       CTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHH CS
                      TPP_enzyme_C  98 krksgpagkdlkpvdfaklaealGakgarvekadveeleealke 141
                                       + + +++   + ++d++ +a+++G++  +      +e    l++
  gi|518652923|ref|YP_008142443.1| 454 DMEKKDY--FQLNLDIESVAKGFGVETHT-----ADENLSDLEW 490
                                       8877766..699*************9444.....2444444455 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 !   45.4   0.0     1e-15   6.2e-12       3     113 ..     184     294 ..     182     316 .. 0.82
   2 ?   -3.3   0.0       1.1   6.8e+03      11      23 ..     402     414 ..     399     431 .. 0.70

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1e-15
                                       HHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EEEEEGGG.TTSS-TTSTTEEEESGGGSCHHHHHHHHH- CS
                      TPP_enzyme_M   3 kaaellkaakrpvilvGggvarsgaseelrelaeklgiPvvttlmg.kgvipedhplylgmlglhgskaanealeea 78 
                                       +++e++++ak p++++G +++  +a +e++++a++lg+ v + + + +g+++  +++y+g l  + s+  n  + + 
  gi|518652923|ref|YP_008142443.1| 184 EIVERINKAKHPALVFGYEIDVYNAYAEAEAFADRLGVEVYSEPLAsRGTFNTANEHYAGDLLPA-STLMNLKFVNN 259
                                       689*************************************6666665*************77776.89999999*** PP

                                       SEEEEES-SSSTCCCTT..TTTTTTTT-.EEEEEESSC CS
                      TPP_enzyme_M  79 DlvlalGarfddirttg..sepefapea.kiihididp 113
                                       Dl++++G + ++   +   ++ +f+ ++  +i  di++
  gi|518652923|ref|YP_008142443.1| 260 DLIVFIGGDITF---YPylPSLPFPGKDvIFIGTDISH 294
                                       *******77655...44213336766655555556655 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                                       -SSEEEEE-CHHC CS
                      TPP_enzyme_M  11 akrpvilvGggva 23 
                                        k+ ++++G g+ 
  gi|518652923|ref|YP_008142443.1| 402 NKKTLVIIGDGAF 414
                                       6888899998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (513 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3658.63
//
Query:       gi|518652924|ref|YP_008142444.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1563 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  186.5   0.0    3.7e-55  186.1   0.0    1.2  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
    4.1e-23   81.5   0.0    4.9e-23   81.3   0.0    1.0  1  2-Hacid_dh      D-isomer specific 2-hydroxyacid dehydrogenase
    1.4e-05   25.4   0.0    2.6e-05   24.5   0.0    1.4  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.012   16.3   0.2        0.2   12.4   0.1    2.4  2  PTS_IIB         PTS system, Lactose/Cellobiose specific IIB s
      0.019   15.4   0.0       0.39   11.1   0.0    2.3  2  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,
      0.046   13.3   0.0       0.09   12.3   0.0    1.5  1  IlvN            Acetohydroxy acid isomeroreductase, NADPH-bin


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 !  186.1   0.0   1.2e-58   3.7e-55       2     178 .]     104     277 ..     103     277 .. 0.98

  Alignments for each domain:
  == domain 1  score: 186.1 bits;  conditional E-value: 1.2e-58
                                       HHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHH CS
                      2-Hacid_dh_C   2 alllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeel 78 
                                       ++ lall+++  +d+++++g+w  +  + ++el+gkt GiiG+G+IG ++ ++l +f++ +++yd+++ k e+ee +
  gi|518652924|ref|YP_008142444.1| 104 GMSLALLKNFIPFDQQIKSGNW--PLLTNSRELQGKTFGIIGMGAIGIKLVQKLIPFNVGIVYYDPRRLKPEDEEFY 178
                                       789*******************..999******************************************9999**** PP

                                       TCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES--S CS
                      2-Hacid_dh_C  79 gvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvfe 155
                                       g+++  l+el++ sDi+s+h+pl++etr ++n++++++mk+++i+iN +RG++vde+aL++a+k+++i  aa+Dvf+
  gi|518652924|ref|YP_008142444.1| 179 GLTYLPLDELVKVSDIISIHTPLSKETRSMFNESRFNLMKENSIFINSSRGEIVDEKALVKAIKEKNIY-AAIDVFS 254
                                       ********************************************************************8.999**** PP

                                       SSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 156 eeplpedspllelpnviltPHia 178
                                        ep++ +s+l++l+nvi++PHia
  gi|518652924|ref|YP_008142444.1| 255 VEPPDFSSELFHLDNVIFSPHIA 277
                                       **********************8 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 !   81.3   0.0   1.6e-26   4.9e-23      37     133 ..      37     308 ..      12     309 .. 0.97

  Alignments for each domain:
  == domain 1  score: 81.3 bits;  conditional E-value: 1.6e-26
                                       HTTESEEEE-TTS-BSHHHHHHHTT--EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH........... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........... RF
                        2-Hacid_dh  37 akdadalivrsntkvtaevlealpkLkviaragvGvDnvDldaakerGilVtnvpgystesvAElt........... 102
                                        +dad++++++ t++ ++ ++++p+Lk+i+ a++G++nvDl+  ++r il++nvp +++++vAE++           
  gi|518652924|ref|YP_008142444.1|  37 KNDADVVVITTFTPFGKKEMDKFPELKYIQVASTGYNNVDLKEVRRRKILLCNVPVANKDAVAEHVigmslallknf 113
                                       367************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|518652924|ref|YP_008142444.1| 114 ipfdqqiksgnwplltnsrelqgktfgiigmgaigiklvqklipfnvgivyydprrlkpedeefygltylpldelvk 190
                                       ***************************************************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|518652924|ref|YP_008142444.1| 191 vsdiisihtplsketrsmfnesrfnlmkensifinssrgeivdekalvkaikekniyaaidvfsveppdfsselfhl 267
                                       ***************************************************************************** PP

                                       ..........T-BHHHHHHHHHHHHHHHHHHHTTCCGTTBC CS
                                       ..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 ..........aaTeeaqeniaeeaaenlvaflkgespanav 133
                                                 ++T e+qe+  +e++ n++++ +g +p + v
  gi|518652924|ref|YP_008142444.1| 268 dnvifsphiaGVTMESQERFITETIGNVIRYSQGIDPLYKV 308
                                       **********************************9887766 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 !   24.5   0.0   8.7e-09   2.6e-05       2     109 ..     139     246 ..     138     252 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 8.7e-09
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHS.HC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieg.ll 77 
                                       +g+iG+G +G +++++l+  +  ++ y+ ++ k e+    g++ +  + elv+  d++ +  + +k+++++ ++  +
  gi|518652924|ref|YP_008142444.1| 139 FGIIGMGAIGIKLVQKLIPFNVGIVYYDPRRLKPEDEEFYGLTYL-PLDELVKVSDIISIHTPLSKETRSMFNEsRF 214
                                       89**************************88888877776777554.567899**********************999 PP

                                       CC--TT-EEEE-S---HHHHHHHHHHHHHTT- CS
                     NAD_binding_2  78 ealkkgdilidgstsspedtrelakelkekgl 109
                                       + +k+++i+i++s  ++ d + l k++kek++
  gi|518652924|ref|YP_008142444.1| 215 NLMKENSIFINSSRGEIVDEKALVKAIKEKNI 246
                                       *****************************986 PP

>> PTS_IIB  PTS system, Lactose/Cellobiose specific IIB subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   6.6e-05       0.2      41      86 ..      33      79 ..       9      83 .. 0.71
   2 ?    1.4   0.0      0.18   5.4e+02      18      66 ..     235     288 ..     232     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                                      HHHHHHT-SEEEEEESSGG..CTHHHHTTSEEEEECTTH.HHCCHCHHH CS
                           PTS_IIB 41 aeeiaddaDlvllapqvrv..kdlarfagkpvavinikd.algimdgek 86
                                       e +++daD+v++++ +++  k++++f++ +   i+++   +++ d ++
  gi|518652924|ref|YP_008142444.1| 33 TEFEKNDADVVVITTFTPFgkKEMDKFPELK--YIQVAStGYNNVDLKE 79
                                      3445678**********************43..3333331355556555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.18
                                       HHHHHHHHHCT....EEEEETTEEGGGHHHHHHT-SEEEEEESSGG...CTHHHHT CS
                           PTS_IIB  18 eklekaakelg....ieaegeagveleaeeiaddaDlvllapqvrv...kdlarfa 66 
                                       ++l ka ke++    i++ +++ +  + + +    D v+ +p+++    ++ +rf 
  gi|518652924|ref|YP_008142444.1| 235 KALVKAIKEKNiyaaIDVFSVEPP--DFSSELFHLDNVIFSPHIAGvtmESQERFI 288
                                       688899999996554444444444..666666668889999888833456666665 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.11   3.4e+02      51      75 ..      24      48 ..      11      79 .. 0.79
   2 ?   11.1   0.0   0.00013      0.39      20      94 ..     149     220 ..     145     228 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
                                      BTCCEEES-CHHHHTT-SEEEE-S- CS
                    UDPG_MGDP_dh_C 51 ekgvevvdsleealkgadaivilte 75
                                        g+e++++ e + ++ad++vi+t 
  gi|518652924|ref|YP_008142444.1| 24 MPGLEIATNTEFEKNDADVVVITTF 48
                                      4678888899999999*****9985 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
                                       HHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--.GGGGGS-HHHHHHCCSS- CS
                    UDPG_MGDP_dh_C  20 ldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaivilteh.defkeldlaklkelmkpa 94 
                                       ++++++L   ++ +++yDP+  + + e+    +g++++ +l+e +k +d+i i+t+  +e +++  ++  +lmk++
  gi|518652924|ref|YP_008142444.1| 149 IKLVQKLIPFNVGIVYYDPRRLKPEDEE---FYGLTYL-PLDELVKVSDIISIHTPLsKETRSMFNESRFNLMKEN 220
                                       7899***************777666666...689****.7***************874667776555555666544 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     3e-05      0.09       2      91 ..     134     223 ..     133     253 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHH.HHHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDel.qkevy 77 
                                       l+gk+  +iG+G+ G    ++l    + +v+   +   + +  +  g++ l ++e+vk +d++ i +P +   ++++
  gi|518652924|ref|YP_008142444.1| 134 LQGKTFGIIGMGAIGIKLVQKLIPFNVGIVYYDPRR-LKPEDEEFYGLTYLPLDELVKVSDIISIHTPLSKeTRSMF 209
                                       89******************9988777766544433.367888899**********************655156777 PP

                                       HHHTGGG--TT-EE CS
                              IlvN  78 eeeiepnlkegkal 91 
                                       +e+  + +ke+++ 
  gi|518652924|ref|YP_008142444.1| 210 NESRFNLMKENSIF 223
                                       77766666666644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.36
# Mc/sec: 2586.42
//
Query:       gi|518652925|ref|YP_008142445.1|  [L=386]
Description: transposase (04) [Ferroplasma acidarmanus fer1]
Scores for complete 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-84  282.2   0.2    7.3e-84  281.8   0.2    1.1  1  Transposase_mut  Transposase, Mutator family
    1.6e-06   28.5   0.0    3.1e-06   27.5   0.0    1.5  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  281.8   0.2   8.2e-88   7.3e-84      22     368 ..      16     351 ..       3     362 .. 0.93

  Alignments for each domain:
  == domain 1  score: 281.8 bits;  conditional E-value: 8.2e-88
                   Transposase_mut  22 kddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspalleryk 97 
                                        d +lke++k  +e+l+e el+++l        ee+ + +nG+++r+l+T++g++ +l+iPrdR+ +F+++++e y+
  gi|518652925|ref|YP_008142445.1|  16 IDRILKEAIKEKIEKLMETELNAYL--------EENPGIKNGKYKRDLKTKYGEIkQLNIPRDRDSNFHTKVIEPYN 84 
                                       5556666666666666666666665........6677889*************9957******************** PP

                   Transposase_mut  98 RrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkv 174
                                       R+   +e+ ++++y +G+str+++ ++e++ g +++Sks++S+it+ + e+v +f +R+L++  y ++flD+l   +
  gi|518652925|ref|YP_008142445.1|  85 RSI-GIEDLIVSMYSNGISTRRIAGIMEDILG-NKYSKSTISRITDLTIEEVYKFVNRPLDKR-YIAIFLDGLFFYL 158
                                       *86.69**************************.66***************************9.************* PP

                   Transposase_mut 175 ReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaa 251
                                       R  g v  ++v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L +rGlk+  l+v+D+ k L + + + +p ++
  gi|518652925|ref|YP_008142445.1| 159 R-RGNVDKEPVIFALGIKETGEYEVLGFYLTVKESHNSYKEVLEDLYSRGLKEPLLIVADGIKNLDEEVMEIYPRSE 234
                                       *.788999********************************************************************* PP

                   Transposase_mut 252 vQrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldeaaedvlaflafpe 328
                                        Q C++H+ r l ++v   + ++++ +  +++k  + ee+  ++++f  k+ +kypkv    +++  ++l f+++p+
  gi|518652925|ref|YP_008142445.1| 235 FQLCTIHYTRGLKSNVRERDIEEISIDANKMFKCDSKEEGIIKFNDFKYKWESKYPKVIYNTEKNLGKLLRFYNYPS 311
                                       ***************************************************************************** PP

                   Transposase_mut 329 qirrkikstNllErLNkeirRrtrvvgiFPneesilrlvg 368
                                        i+r++kstN++ErLN e+rRr++++  FP+e+s++++ +
  gi|518652925|ref|YP_008142445.1| 312 SIWRSLKSTNAIERLNGEVRRRVKTISSFPDEDSAMKVFY 351
                                       *************************************977 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   3.5e-10   3.1e-06      15      93 ..     166     242 ..     149     244 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 3.5e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ +sy+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518652925|ref|YP_008142445.1| 166 EPVIFALGIKETGEYEVLGFYLTVKESHNSYKEVLEDLYSRGL--KEPLLIVADGIKNLDEEVMEIYPRSEFQLCTI 240
                                       5777899*******************************99644..6******************************9 PP

                              MULE  92 Hi 93 
                                       H 
  gi|518652925|ref|YP_008142445.1| 241 HY 242
                                       96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       817  (0.0455686); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.50
# Mc/sec: 2344.06
//
Query:       gi|518652926|ref|YP_008142446.1|  [L=401]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-23   83.2   0.1    5.2e-23   81.6   0.1    1.8  2  DEDD_Tnp_IS110  Transposase
    2.4e-13   50.2   0.0    4.5e-13   49.3   0.0    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family
  ------ inclusion threshold ------
      0.034   14.4   1.5        2.6    8.3   0.2    2.4  2  DUF2072         Zn-ribbon containing protein
      0.055   13.5   1.1         15    5.8   0.1    3.4  3  SecIII_SopE_N   Salmonella type III secretion SopE effector N


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.6   0.1   1.2e-26   5.2e-23       1     155 []       4     162 ..       4     162 .. 0.91
   2 ?   -1.6   0.0       0.5   2.2e+03      27      69 ..     343     386 ..     337     389 .. 0.77

  Alignments for each domain:
  == domain 1  score: 81.6 bits;  conditional E-value: 1.2e-26
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeegleallek....laakagevlvv.veatghygallvaflleagit 72 
                                       vGiD +++ h+a ++d+++++l++ ++ n +e++e l++k    ++++ ++v+++ +  tg+y+ +l +fl+++++t
  gi|518652926|ref|YP_008142446.1|   4 VGIDTHERMHYAEIQDEKENKLWHGKIRNIKEDFEFLIDKiskiEKSNNDKVEFIfMNPTGNYHVPLKYFLENNNFT 80 
                                       8*************************************996654445668888765899****************** PP

                    DEDD_Tnp_IS110  73 vvvvnplavkrlrkly.lrkaKtDakDAkvIAdllrdrgrlrplklddeayaeLrqltrqredlvkertrlknrlra 148
                                       v++v ++++ +lrk+  l+  K+D+ DA+++A + ++  ++r ++ +  + ++L++++r+r+ +vk++t+ kn +++
  gi|518652926|ref|YP_008142446.1|  81 VYMVDARKTLNLRKMInLNTIKSDSEDAHILAATPWHDPKYREYTGH--NRSSLSSISRERSIVVKSITAIKNYIHS 155
                                       *************99736889***************88899999776..569************************* PP

                    DEDD_Tnp_IS110 149 lLdqvfp 155
                                        L  vfp
  gi|518652926|ref|YP_008142446.1| 156 DLAAVFP 162
                                       ****998 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.5
                    DEDD_Tnp_IS110  27 vpndeegleallek.laakagevlvvveatghygallvafllea 69 
                                       v n+ +++ +++++ +++k+++v+  +  +++   +++++++++
  gi|518652926|ref|YP_008142446.1| 343 VMNKNKEFYDIFNReIGKKKSNVQAYIAVSKRLLFHIYSIMKNH 386
                                       56777788888888788888999988888888877777777765 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.3   0.0     1e-16   4.5e-13       3      83 ..     270     351 ..     268     355 .. 0.93

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 1e-16
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaai.ra 78 
                                        L+ + G G + +a +++eig++++f+sa +l++yaG +p  + SG+k ++++i++  n+ l +a+ye A++++ ++
  gi|518652926|ref|YP_008142446.1| 270 NLTNLRGLGIINSAIIVSEIGNIEQFESALKLQSYAGKCPDIEGSGGKTHSKGITHVRNKFLSNAVYESAISLVmNK 346
                                       7999******************************************************************9998677 PP

                    Transposase_20  79 npelr 83 
                                       n+e+ 
  gi|518652926|ref|YP_008142446.1| 347 NKEFY 351
                                       77765 PP

>> DUF2072  Zn-ribbon containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.2   0.00059       2.6      67     122 ..      33      87 ..       6      98 .. 0.69
   2 ?    4.7   0.1    0.0074        33      87     127 ..     195     237 ..     182     243 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00059
                           DUF2072  67 eeeklekkekekaekekeeedrvesvrilepGsYelNlekLlerdelvmalkeegk 122
                                        +e  e   ++ ++ ek+++d+ve + +   G+Y + l+ +le++++ + + +  +
  gi|518652926|ref|YP_008142446.1|  33 IKEDFEFLIDKISKIEKSNNDKVEFIFMNPTGNYHVPLKYFLENNNFTVYMVD-AR 87 
                                       333344447778888999***************************99888654.44 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0074
                           DUF2072  87 drvesvrilepGsYel.NlekLlerdelvmal.keegkYvvdl 127
                                       + + s++  ++G+Y +  +++L+e+ e  + +  +++ Y  ++
  gi|518652926|ref|YP_008142446.1| 195 NIIKSIKKASKGHYRIeDINRLMETAENSIGIpDKDDAYKFKI 237
                                       6689***********955*********9999977888998776 PP

>> SecIII_SopE_N  Salmonella type III secretion SopE effector N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.1    0.0032        15      25      43 ..     137     155 ..     124     171 .. 0.84
   2 ?   -4.1   0.0         4   1.8e+04       6      13 ..     204     211 ..     203     214 .. 0.78
   3 ?    4.5   0.0    0.0082        37      30      45 ..     319     334 ..     298     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0032
                     SecIII_SopE_N  25 tekdifaksitavrnsfis 43 
                                        e+ i  ksita++n + s
  gi|518652926|ref|YP_008142446.1| 137 RERSIVVKSITAIKNYIHS 155
                                       6899**********97655 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 4
                     SecIII_SopE_N   6 stqhyrih 13 
                                       s  hyri 
  gi|518652926|ref|YP_008142446.1| 204 SKGHYRIE 211
                                       5679**95 PP

  == domain 3  score: 4.5 bits;  conditional E-value: 0.0082
                     SecIII_SopE_N  30 faksitavrnsfisls 45 
                                        +k it vrn f+s +
  gi|518652926|ref|YP_008142446.1| 319 HSKGITHVRNKFLSNA 334
                                       5789********9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.46
# Mc/sec: 2631.70
//
Query:       gi|518652927|ref|YP_008142447.1|  [L=349]
Description: hypothetical protein FACI_IFERC00001G1566 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.2e-26   91.6   0.2    7.3e-26   89.9   0.2    2.0  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
      1e-05   25.7   0.3    2.2e-05   24.6   0.3    1.5  1  OrfB_IS605      Probable transposase
  ------ inclusion threshold ------
      0.011   15.8   0.1       0.18   11.8   0.0    2.4  2  HypA            Hydrogenase/urease nickel incorporation, meta
      0.012   15.2   0.3       0.02   14.5   0.3    1.4  1  Zn_ribbon_17    Zinc-ribbon, C4HC2 type
      0.026   14.8   0.3      0.066   13.5   0.3    1.7  1  C1_2            C1 domain
       0.23   11.1   3.0       0.42   10.3   2.6    1.8  1  TackOD1         Thaumarchaeal output domain 1
       0.38   10.2   3.5        4.7    6.7   0.2    2.4  2  zf-ribbon_3     zinc-ribbon domain
        2.7    8.0   5.5        2.3    8.2   0.5    2.6  2  zinc_ribbon_4   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 !   89.9   0.2   3.3e-29   7.3e-26       1      69 []     243     309 ..     243     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 89.9 bits;  conditional E-value: 3.3e-29
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++lk+++eyka+  Gi+v +v+p++TSk+Cs+Cg+++++  sg+ fkC+nCg++ ++D nA++Ni+ r
  gi|518652927|ref|YP_008142447.1| 243 FYQLKTMIEYKARLPGIPVAYVDPYNTSKECSRCGQIGNR--SGKSFKCNNCGHVDHADANASFNIALR 309
                                       899*************************************..************************976 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.3     1e-08   2.2e-05      14     108 ..     128     215 ..     116     224 .. 0.84

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 1e-08
                        OrfB_IS605  14 kgnkaagiDlGinnLatvvtedgtwflyk.grrlksdykylakeiaelqsklkksknykkasrklarlhrkrsrrrk 89 
                                       ++n  +g+D +    ++v+ + +t +++k g+++    k+++k +++lq+k  ++       rk +r+ ++ sr++k
  gi|518652927|ref|YP_008142447.1| 128 EPNGYLGVDRNTTGHIAVAGNPETGKIIKlGKEAGHVHKKYSKTRKNLQKK--GK------NRKAKRIKNRESRIVK 196
                                       678888899988888888888877755552799999*************99..44......3899************ PP

                        OrfB_IS605  90 hllhklathliktlkevgv 108
                                       +  hk+a++++++ k++g 
  gi|518652927|ref|YP_008142447.1| 197 DINHKVARKIVQEAKDNGM 215
                                       *************999875 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0      0.15   3.3e+02       8      34 ..      45      72 ..      40      79 .. 0.80
   2 ?   11.8   0.0   8.1e-05      0.18      64      96 ..     264     296 ..     191     306 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.15
                                      HHHHHHHHHHH.CCTT..EEEEEEEEEE CS
                              HypA  8 esivevveeea.keaaarkvtkvkvevG 34
                                      ++i +++ ++  ++++a+ v+k+k++v 
  gi|518652927|ref|YP_008142447.1| 45 SAISNQILRKYsRNSKAKDVHKIKLTVP 72
                                      677788888885668999******9985 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.1e-05
                                       EEEE--EEEETTTS-EEECHHHHHS-TTTSSS- CS
                              HypA  64 ieevpvkvrCreCgkefeleekalrCpkCgsad 96 
                                       ++  + + +C++Cg+ ++ + k+++C++Cg+ d
  gi|518652927|ref|YP_008142447.1| 264 VDPYNTSKECSRCGQIGNRSGKSFKCNNCGHVD 296
                                       556677889*******99887789******876 PP

>> Zn_ribbon_17  Zinc-ribbon, C4HC2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.3   9.1e-06      0.02       4      32 ..     270     300 ..     267     306 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 9.1e-06
                      Zn_ribbon_17   4 lksCayCela..vkgrvvlcgvCeHvlHasC 32 
                                        k+C+ C       g+ + c++C+Hv Ha+ 
  gi|518652927|ref|YP_008142447.1| 270 SKECSRCGQIgnRSGKSFKCNNCGHVDHADA 300
                                       68899997541146789************96 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.3   2.9e-05     0.066      13      41 ..     265     295 ..     245     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.9e-05
                              C1_2  13 edssesfnCsaCgrkidgff..YsCseCdfs 41 
                                       ++++ s++Cs Cg+ ++ +   ++C+ C  +
  gi|518652927|ref|YP_008142447.1| 265 DPYNTSKECSRCGQIGNRSGksFKCNNCGHV 295
                                       578899*********7777778******765 PP

>> TackOD1  Thaumarchaeal output domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.6   0.00019      0.42      85     115 ..     268     298 ..     182     305 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                           TackOD1  85 nvrevCpkCkSidieeqelihhftCgnvgpe 115
                                       n  ++C+ C+ i  ++ +++++ +Cg+v+  
  gi|518652927|ref|YP_008142447.1| 268 NTSKECSRCGQIGNRSGKSFKCNNCGHVDHA 298
                                       6678899999999999999999999988765 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.3     0.015        33       3      11 ..     271     279 ..     270     284 .. 0.87
   2 ?    6.7   0.2    0.0021       4.7       4      11 ..     288     295 ..     285     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.015
                       zf-ribbon_3   3 vrCPnCGap 11 
                                       ++C++CG++
  gi|518652927|ref|YP_008142447.1| 271 KECSRCGQI 279
                                       68*****85 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0021
                       zf-ribbon_3   4 rCPnCGap 11 
                                       +C+nCG++
  gi|518652927|ref|YP_008142447.1| 288 KCNNCGHV 295
                                       7*****97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.5      0.14   3.2e+02      28      34 ..     273     279 ..     268     279 .. 0.84
   2 ?    8.2   0.5     0.001       2.3      22      34 ..     283     295 ..     278     295 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.14
                     zinc_ribbon_4  28 CskCghv 34 
                                       Cs+Cg++
  gi|518652927|ref|YP_008142447.1| 273 CSRCGQI 279
                                       9999985 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.001
                     zinc_ribbon_4  22 kgvkvrCskCghv 34 
                                       +g++ +C +Cghv
  gi|518652927|ref|YP_008142447.1| 283 SGKSFKCNNCGHV 295
                                       7999********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1298  (0.0723967); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); 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):               8  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 2218.98
//
Query:       gi|518652928|ref|YP_008142448.1|  [L=133]
Description: transposase IS200-family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-38  131.5   0.9    1.8e-38  131.3   0.9    1.0  1  Y1_Tnp    Transposase IS200 like
     0.0034   17.1   0.1     0.0039   16.9   0.1    1.1  1  PRD_Mga   M protein trans-acting positive regulator (MGA) PRD


Domain annotation for each model (and alignments):
>> Y1_Tnp  Transposase IS200 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.3   0.9     2e-42   1.8e-38       1     121 []      13     130 ..      13     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.3 bits;  conditional E-value: 2e-42
                            Y1_Tnp   1 vsnlkyhivlvtkyRrkvltgeveerlkeiikeiaekkevkilelelmpDHvHllvelppklsiskivkalkgassr 77 
                                       v+nl yhi++++kyRr+vl + ++ rlke+++  a++ +++i e+e+mpDH+H++++++p ls++ i++++kg++sr
  gi|518652928|ref|YP_008142448.1|  13 VYNLGYHIIWCPKYRRNVLVNGIDVRLKELLNYKAQELKIEIKEMEVMPDHIHIFIKADPVLSPHYIIQQFKGYTSR 89 
                                       689************************************************************************** PP

                            Y1_Tnp  78 linkefpelkkkklkkeslWqrgYfvstvgeasletvkrYIenq 121
                                       ++++efp lk+k    ++lW+r+Y++ +vg+ s+++v++YIe+q
  gi|518652928|ref|YP_008142448.1|  90 ILRQEFPVLKRKL---PTLWTRSYYIESVGHISESVVRKYIEEQ 130
                                       **********996...46************************98 PP

>> PRD_Mga  M protein trans-acting positive regulator (MGA) PRD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.1   4.4e-07    0.0039     124     189 ..      40     104 ..      24     127 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 4.4e-07
                           PRD_Mga 124 kllldelsallkievenkdelikilHNtaffkrqelfn.qyllfdfkgltikkykgnkPkLykslkk 189
                                       k+ll+   + lkie+++ + +++++H   f+k   + + +y++ +fkg+t++ +++++P L  +l +
  gi|518652928|ref|YP_008142448.1|  40 KELLNYKAQELKIEIKEMEVMPDHIH--IFIKADPVLSpHYIIQQFKGYTSRILRQEFPVLKRKLPT 104
                                       589999999****************6..9999999999*********************99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); 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:                         2  (0.000111551); expected 0.2 (1e-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: 944.77
//
Query:       gi|518652929|ref|YP_008142449.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G1568 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-13   50.8   0.0    3.5e-13   49.7   0.0    1.6  1  DDE_Tnp_1     Transposase DDE domain
      0.006   16.0   0.0      0.009   15.4   0.0    1.2  1  DDE_5         DDE superfamily endonuclease
  ------ inclusion threshold ------
      0.043   12.9   0.0       0.07   12.2   0.0    1.2  1  ANF_receptor  Receptor family ligand binding region
      0.093   11.0   0.0        3.9    5.6   0.0    2.0  2  DDE_Tnp_1_4   Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   7.7e-17   3.5e-13      21     214 .]     181     399 ..     160     399 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 7.7e-17
                         DDE_Tnp_1  21 edarwgykggk.ykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       ++  +g++ ++ + + +++ ++++    l++ +++ pg+  d+ ++  ++d++ + ++++++aD+G++sa+++++l+
  gi|518652929|ref|YP_008142449.1| 181 SFLEPGHNSKEiHLPQINVMMLFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGI-EKCVIVADKGFFSADNIKKLK 256
                                       666778887777889999999999998999999999******************9.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrk................................gaeskrrgrlrkhdrnkiltksqkrr 141
                                       +++++yii+l+ n+ l  +                                 +e++r+  +r hd+ ++ + +  + 
  gi|518652929|ref|YP_008142449.1| 257 KRHLSYIIPLRRNSSLVPDtddflgvfmyngkpvkywkpengvymfedpvlKSEEERDYLIRIHDNIRPKSSYYDHS 333
                                       ****************9999999988888877777766665555554444434444444444444444444443333 PP

                         DDE_Tnp_1 142 nkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                       +           ++++++   ++e + +ly+ R  +E  F   k+++  dr + r+     a+++l ll+l l
  gi|518652929|ref|YP_008142449.1| 334 GD-------FGKLYLLSDINDEPERIYRLYKDREYVEYAFNVYKNDLEADRSYIRDDHMLSAYMFLNLLSLYL 399
                                       33.......4445555555559*********************************************999865 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0     2e-06     0.009     167     219 ..     226     277 ..     205     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2e-06
                             DDE_5 167 lldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdralyppga 219
                                       + + +  ag++  v+vaD g+ +a+ + + l+ + l y++ +r++++l+p  +
  gi|518652929|ref|YP_008142449.1| 226 MANTIDMAGIEKCVIVADKGFFSADNI-KKLKKRHLSYIIPLRRNSSLVPDTD 277
                                       5556666899999**************.********************99765 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 ?   12.2   0.0   1.6e-05      0.07      71     141 ..     190     257 ..     180     275 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                                       CCTT-EEEESS---GGGG-TTTTTTEEESS--CHHHHHHHHHHHHHTT--EEEEEEESSHHHHHHHHHHHH CS
                      ANF_receptor  71 nlfkiPvisygstspelsdknryptflrtvpsdtsqaqAivdilkhfgWkkvaliysdddygesglqalee 141
                                       ++ ++P+i ++     +s+++  ptf+r+ p + + + A+++++ + g  k +++++++      +++l++
  gi|518652929|ref|YP_008142449.1| 190 KEIHLPQINVMM---LFSSTRTLPTFIRVLPGSIRDVSAMANTIDMAGIEKCVIVADKGFFSADNIKKLKK 257
                                       567899996544...8999**************************************99666666666665 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.0   0.00087       3.9     217     254 ..     237     274 ..     222     283 .. 0.87
   2 ?    3.2   0.0    0.0049        22     313     354 ..     345     384 ..     329     408 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.00087
                       DDE_Tnp_1_4 217 kilvRgDSafarpellkwceergvdYviglaknsrlea 254
                                       k ++ +D +f + + +k +++r+++Y+i l++ns l  
  gi|518652929|ref|YP_008142449.1| 237 KCVIVADKGFFSADNIKKLKKRHLSYIIPLRRNSSLVP 274
                                       567889****************************9865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.0049
                       DDE_Tnp_1_4 313 laklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfa 354
                                       ++  +pe++y +lY+ R  +E  +   k+dl+adr   ++ +
  gi|518652929|ref|YP_008142449.1| 345 IN-DEPERIY-RLYKDREYVEYAFNVYKNDLEADRSYIRDDH 384
                                       44.799****.***********************98766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.45
# Mc/sec: 3048.33
//
Query:       gi|518652930|ref|YP_008142450.1|  [L=243]
Description: hypothetical protein FACI_IFERC00001G1569 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.9   0.5       0.14   12.2   0.1    1.9  2  SAWADEE   SAWADEE domain


Domain annotation for each model (and alignments):
>> SAWADEE  SAWADEE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.8e-06      0.14       3      44 ..      17      66 ..      15      81 .. 0.87
   2 ?   -0.6   0.0     0.067   1.2e+03      13      44 ..     143     172 ..     136     185 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.8e-06
                                      --EEEE-TTTS-EEEEEEEEEEEE-........EEEETTC-GGGEEEEEH CS
                           SAWADEE  3 lelEarsskDeaWYdvrvflekral........rvkfegfgeeedewvnv 44
                                      l+lE + s+ +aWY+v++ +++++l        + kf +  +++de+v+v
  gi|518652930|ref|YP_008142450.1| 17 LSLEDQFSRLDAWYKVDFLIDNNILtkeyvienKTKFLDLLTTTDEMVKV 66
                                      6789999999***************9999999999999999999999998 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.067
                                       S-EEEEEEEEEEEE-EEEETTC-GGGEEEEEH CS
                           SAWADEE  13 eaWYdvrvflekralrvkfegfgeeedewvnv 44 
                                       +aW+ v + l+ +++  + +++++++  ++nv
  gi|518652930|ref|YP_008142450.1| 143 DAWHMVPLLLKAGVI--SNADYDDNKKYLFNV 172
                                       799999999998876..345666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1632.84
//
Query:       gi|518652931|ref|YP_008142451.1|  [L=374]
Description: hypothetical protein FACI_IFERC00001G1570 [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.1    1.2e-23   84.0   0.1    1.3  1  DNA_primase_S  DNA primase small subunit


Domain annotation for each model (and alignments):
>> DNA_primase_S  DNA primase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.0   0.1   6.9e-28   1.2e-23       1     175 [.      84     306 ..      84     308 .. 0.82

  Alignments for each domain:
  == domain 1  score: 84.0 bits;  conditional E-value: 6.9e-28
                                       EEEEEETTT-.TT--HHHHHHHHHHHHHHHHHHHH-----GG..GEEEEE--SEEEEEEE--TTEEES-HHHHHHHH CS
                     DNA_primase_S   1 FDiDmddyddcseatvcekcwkfvsvavkvldellredfgfk..dilwvfsgrrGfHcwvsdkdarpltdeeraaiv 75 
                                       FD+D+d+ ++ +++t+ e+++++ + + ++l+ l+ +dfgf+  +i ++fsg+rG+H++v  +++ ++++  r++i 
  gi|518652931|ref|YP_008142451.1|  84 FDLDADHIEGADKMTYMEILAEVKKHTLRLLEMLM-DDFGFEekNIRLYFSGGRGYHVHVESDRIYTMDSDSRREIG 159
                                       9******************************8777.***************************************** PP

                                       HH....................................................................HCHHHHC CS
                     DNA_primase_S  76 nylnly.......................rplhpflsrs.mlkivkpvveeiileeqdpf..........eikkllr 118
                                       +y+ +                        +   + + r+ + +  k+v+ +       ++            +k+++
  gi|518652931|ref|YP_008142451.1| 160 DYIKIEglnmedlkllddsyfeygilkkfNIYISNFYRNlDENYIKKVFPKS------WWnyleylekyyNGEKIRD 230
                                       ******9999988888888888877776644666666666777777777654......6666666666665555555 PP

                                       T--------.........................................-----------------....------ CS
                     DNA_primase_S 119 llpdkslrekkkw.......................eakedivlvllyprldeqvtkgikhllkapfcihgktgnvc 172
                                        l++++  +   +                       +   +++++    ++de+vt++i++l++ p+++hgktg  +
  gi|518652931|ref|YP_008142451.1| 231 FLSNEKGNK---FkllikqnksnenasidydriilgK-ILEDFKSNALAEIDEPVTTDIHRLIRFPYSLHGKTGLMV 303
                                       555555444...244577777888999999999*965.555666677789************************999 PP

                                       --- CS
                     DNA_primase_S 173 vpl 175
                                        p+
  gi|518652931|ref|YP_008142451.1| 304 KPV 306
                                       887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       624  (0.0348039); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 2632.09
//
Query:       gi|518652932|ref|YP_008142452.1|  [L=337]
Description: hypothetical protein FACI_IFERC00001G1571 [Ferroplasma acidarmanus fer1]
Scores for 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   85.9   0.3    2.8e-24   85.5   0.3    1.2  1  Gp_dh_C       Glyceraldehyde 3-phosphate dehydrogenase, C-ter
    3.7e-08   33.5   0.0    8.5e-08   32.4   0.0    1.6  1  DapB_N        Dihydrodipicolinate reductase, N-terminus
    5.1e-05   23.5   0.5    0.00021   21.6   0.0    2.2  2  Gp_dh_N       Glyceraldehyde 3-phosphate dehydrogenase, NAD b
  ------ inclusion threshold ------
      0.015   14.7   0.4        1.1    8.6   0.0    2.3  2  2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, 


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 !   85.5   0.3   6.1e-28   2.8e-24       1     158 []     144     297 ..     144     297 .. 0.98

  Alignments for each domain:
  == domain 1  score: 85.5 bits;  conditional E-value: 6.1e-28
                                       HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTT.CSSEEEE-THHHHHHHHSGGGTTTEEEEE CS
                           Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaa.eniiptstgaakavglVlpelkgkldglA 76 
                                       La+ +  l++kfg++++ +t+ +++t++         +d ++++++a e  +  ++++a+++++V++   ++++++A
  gi|518652932|ref|YP_008142452.1| 144 LARSVSPLKEKFGVQEVNATIMRRATDP---------NDNKKGPINAiEPSMSYPSHHAEDLKTVMD--GINVETSA 209
                                       7999************************.........9*********99999***************..799***** PP

                                       EEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH....TTTTTTEEEEHSHHHGGGGTTGCS..SEEEEGGGCEEE CS
                           Gp_dh_C  77 vrVPtpnvsvvdlvvelekevtveevnaalkeaae....galkgilsyteeelvssDlvgdph..ssifdaketivv 147
                                       ++VPt+ ++v+ + +el++e   +ev++ l++  +    ++ +g+ s+++ + ++++l +++   ++i  +k +i++
  gi|518652932|ref|YP_008142452.1| 210 IKVPTTLMHVHVINLELKSEPGIDEVISELSTKRRliliNDKEGVNSTAQVMDYARELSRNRSdlYEIAIWKGSINI 286
                                       ************************************************************99999************ PP

                                       TTTEEEEEEEE CS
                           Gp_dh_C 148 eenlvkvvawy 158
                                        +n+v++++++
  gi|518652932|ref|YP_008142452.1| 287 YKNKVHYIQAV 297
                                       ********986 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.4   0.0   1.9e-11   8.5e-08       2      96 ..       3     106 ..       2     118 .. 0.91

  Alignments for each domain:
  == domain 1  score: 32.4 bits;  conditional E-value: 1.9e-11
                                       EEEEETTTSHHHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHH...........HHSSSS--S-BEBSSHHHHHHH CS
                            DapB_N   2 kvavvGasGrmGkevvkaveeaedlelvaavdrkeselegkdag...........ellglgklgvavtddleevlek 67 
                                        va++G+ G++G++v++ v+ ++d+ +++ v++++ +++ k a+           +  +++ +g+ v+ +le++l +
  gi|518652932|ref|YP_008142452.1|   3 GVAINGY-GTIGRRVAYGVSIQDDMYVTGIVKNSP-DYVTKLASrnfniytpdmdKKREFEAHGIRVKGTLEDLLSE 77 
                                       69*****.*************************99.67766666778899999988888889*************** PP

                                       -SEEEE-S-HHHHHHHHHHHHHTT-EEEE CS
                            DapB_N  68 advliDFTtpeavlenlklalekgvklVi 96 
                                       +d+++D T      +nlkl+ ++g+k+++
  gi|518652932|ref|YP_008142452.1|  78 SDIVVDGTPEGNGEKNLKLYRQYGIKAIL 106
                                       ********999999**********99885 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 !   21.6   0.0   4.7e-08   0.00021       2      74 ..       3      76 ..       2      87 .. 0.82
   2 ?   -1.5   0.1      0.74   3.3e+03      26      73 ..     244     294 ..     234     304 .. 0.61

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 4.7e-08
                                      EEEEESTSHHHHHHHHHHHHHTTCEEEEEE-.TS-HHHHHHHHHEETTTEC-SS-EEEETTEEEETTEEEEEE- CS
                           Gp_dh_N  2 kvainGfGRIGrlvlralleekelevvaind.ltdletlayllkyDsvhgrfkgeveaeeealvvngkkikvla 74
                                       vainG+G IGr v+  +  ++++ v  i + + d  t     +++     ++++ e+e + + v+g+   +l+
  gi|518652932|ref|YP_008142452.1|  3 GVAINGYGTIGRRVAYGVSIQDDMYVTGIVKnSPDYVTKLASRNFNIYTPDMDKKREFEAHGIRVKGTLEDLLS 76
                                      59****************************95566656556666777889999999999999999997555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.74
                                       EEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEE...TTEEEETTEEEEEE CS
                           Gp_dh_N  26 evvaindltdletlayllkyDsvhgrfkgeveae...eealvvngkkikvl 73 
                                       +++ ind   +++ a+++ y     r ++++ +    + ++ + ++k++++
  gi|518652932|ref|YP_008142452.1| 244 RLILINDKEGVNSTAQVMDYARELSRNRSDLYEIaiwKGSINIYKNKVHYI 294
                                       567788877777777777776655555444332223355566666665555 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 ?    3.7   0.3    0.0077        34      39      54 ..       4      19 ..       3      39 .. 0.82
   2 ?    8.6   0.0   0.00025       1.1      64     100 ..      49      86 ..      36      96 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0077
                                      EEEES-SHHHHHHHHH CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakr 54
                                      v+i G+G IG++va  
  gi|518652932|ref|YP_008142452.1|  4 VAINGYGTIGRRVAYG 19
                                      7899*********965 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00025
                                       EESSSHHHHHCHHHHTCEEC.SHHHHHHH-SEEEE-S- CS
                      2-Hacid_dh_C  64 aydrskkkeeeeeelgvelv.sleellaesDivslhlp 100
                                       +y +  +k++e+e++g+++  +le+ll+esDiv+  +p
  gi|518652932|ref|YP_008142452.1|  49 IYTPDMDKKREFEAHGIRVKgTLEDLLSESDIVVDGTP 86 
                                       344444555679999**8888************86555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2156.12
//
Query:       gi|518652933|ref|YP_008142453.1|  [L=331]
Description: hypothetical protein FACI_IFERC00001G1572 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-81  270.9   0.0    1.1e-80  270.6   0.0    1.1  1  Rad51            Rad51
    4.6e-11   42.7   0.1    7.4e-11   42.0   0.1    1.3  1  RecA             recA bacterial DNA recombination protein
    1.5e-09   38.3   1.6    3.1e-09   37.3   1.6    1.6  1  HHH_5            Helix-hairpin-helix domain
    9.1e-08   31.7   0.4    2.6e-07   30.2   0.4    1.7  1  ATPase           KaiC
    1.4e-06   28.1   0.0    2.1e-06   27.4   0.0    1.3  1  AAA_25           AAA domain
    0.00011   21.8   0.2      0.036   13.9   0.0    2.6  2  HHH              Helix-hairpin-helix motif
    0.00025   21.1   0.3    0.00084   19.4   0.1    2.0  2  HHH_2            Helix-hairpin-helix motif
     0.0037   17.5   0.0     0.0069   16.6   0.0    1.4  1  Cdd1             Pathogenicity locus
     0.0057   17.1   0.1      0.037   14.5   0.0    2.3  3  BAF              Barrier to autointegration factor
     0.0066   16.2   0.0      0.013   15.3   0.0    1.4  1  AAA_24           AAA domain
     0.0069   16.7   0.0      0.029   14.7   0.0    2.1  2  IMS_HHH          IMS family HHH motif
  ------ inclusion threshold ------
      0.028   14.7   0.0      0.065   13.5   0.0    1.6  1  AAA_22           AAA domain
      0.032   14.6   1.3       0.12   12.8   0.1    2.4  2  HHH_8            Helix-hairpin-helix domain
        0.1   12.5   0.1       0.66    9.8   0.0    2.3  2  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda


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 !  270.6   0.0   8.7e-84   1.1e-80       3     254 ..      82     329 ..      80     330 .. 0.99

  Alignments for each domain:
  == domain 1  score: 270.6 bits;  conditional E-value: 8.7e-84
                                       -EBHHHHHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEES CS
                             Rad51   3 fvsavellekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidt 79 
                                       f ++ e+l++r+e+ +l+tG++ lD+l+gGG+et+site fGef+sGktq+  +l+v + +p e+gG ++ ++ idt
  gi|518652933|ref|YP_008142453.1|  82 FETGEEILKRRKEVRKLSTGAQGLDNLIGGGLETQSITEFFGEFGSGKTQIMLQLAVNATMPEEQGGLNSDVLIIDT 158
                                       78999************************************************************************ PP

                                       SS---GGGGHHHHHHTT--HHHHGGGEEEEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGGCH-------TH CS
                             Rad51  80 egtfrperlveiaerykldkeevlenvayaRaytiehqeellqqaaallaedkfallivDsvtalyRtdfsgrgela 156
                                       e tfrper++++a+  +ld++e+l+++ +aRay++ hq  l ++a+   +e  ++llivDs+t+++R+++ grg la
  gi|518652933|ref|YP_008142453.1| 159 ENTFRPERVIQMAKAKNLDPDETLKRIHVARAYNAHHQILLAEKASDIAKEFPIKLLIVDSLTSHFRSEYVGRGSLA 235
                                       ***************************************9999********************************** PP

                                       HHHHHHHHHHHHHHHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEE CS
                             Rad51 157 kRqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvv 233
                                       +Rqq l+k+++ L k+   f++ + +tnqv+a++      f +dp+ PigG++++h++t Rl+lrk k  +Ri++++
  gi|518652933|ref|YP_008142453.1| 236 ERQQLLNKHMHDLLKFGTIFNAVIAVTNQVSANPAV----FFGDPMTPIGGNIVGHTATFRLYLRKAKAGKRIARLI 308
                                       ********************************9977....9************************************ PP

                                       S-SSS-S-EEEEEEETTEEE- CS
                             Rad51 234 dsPnlpeleavfaigeeGied 254
                                       dsP lpe eav++++e+Gi+d
  gi|518652933|ref|YP_008142453.1| 309 DSPYLPEGEAVITLTEDGIID 329
                                       *******************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 !   42.0   0.1   5.8e-14   7.4e-11      27     226 ..      91     302 ..      66     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.8e-14
                                       .-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHH...HHTT--...EEEEESS----HH. CS
                              RecA  27 eklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaea...qkkggv...aafidaehaldpk. 96 
                                       ++++v  +s+G+ +ld+ +G GGl    i+e +G   sGkt + l++ ++a   +++gg+   +  id+e ++ p+ 
  gi|518652933|ref|YP_008142453.1|  91 RRKEVRKLSTGAQGLDNLIG-GGLETQSITEFFGEFGSGKTQIMLQLAVNAtmpEEQGGLnsdVLIIDTENTFRPEr 166
                                       46899***************.*********************9998776652234677763225689***9998852 PP

                                       ...HHHHTT--....GGG-EEE--SSHHHHH...HHHHHHHTTT--SEEEEE-TTT---STT-----------HHHH CS
                              RecA  97 ...yakklGvd....idellvsqpdtGeqal...eiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqar 163
                                           ak+  +d    ++ + v++  +  + +   e a  + +   i l++vds+++   ++e    +g  +++ + +
  gi|518652933|ref|YP_008142453.1| 167 viqMAKAKNLDpdetLKRIHVARAYNAHHQIllaEKASDIAKEFPIKLLIVDSLTSHF-RSEY---VGRGSLAERQQ 239
                                       222455555551133455679998887766613344556889999********98865.5554...44566777778 PP

                                       HHHHHHHHHHHHHTTT--EEEEEEE-----------------HHHHHHH-SEEEEEEEES--- CS
                              RecA 164 lmsqalrkltgaisksntvvifinqirekiGvmfgnpetttGGralkfyasvrldvrrieeik 226
                                       l+ + +  l    +  n+v+   nq+     v fg+p t  GG+ +   a+ rl +r++++ k
  gi|518652933|ref|YP_008142453.1| 240 LLNKHMHDLLKFGTIFNAVIAVTNQVSANPAVFFGDPMTPIGGNIVGHTATFRLYLRKAKAGK 302
                                       8888888888888888999999************************************98765 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   1.6   2.4e-12   3.1e-09       4      57 .]      22      75 ..      18      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.4e-12
                                      HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHHH CS
                             HHH_5  4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelkd 57
                                      + +++G+G++tA +l ++G++ + ++a a++++La+i Gi +  A +ii ++++
  gi|518652933|ref|YP_008142453.1| 22 IEDLPGVGEATAEKLRENGYDDIMAIAVASPKDLADISGIAEGAAVKIINAARK 75
                                      4689***********************************************997 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.4   2.1e-10   2.6e-07       2     143 ..      99     233 ..      98     249 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.1e-10
                            ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaeky.....gepgvfvtveepa..edlrenakslG 71 
                                       +tg +glD+++ gG+  ++++   Ge G+GKt + lq +++  +       +  ++++ +e +   e +++ ak+  
  gi|518652933|ref|YP_008142453.1|  99 STGAQGLDNLIGGGLETQSITEFFGEFGSGKTQIMLQLAVNATMPEeqgglNSDVLIIDTENTFrpERVIQMAKAKN 175
                                       79***************************************98763111113457899999975669********** PP

                            ATPase  72 wdlekleeegklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitglayeekeavaRei 143
                                        d ++  ++  + +  a++  ++            l+e+  ++ ke+ +k +++Ds+t++    +e v R  
  gi|518652933|ref|YP_008142453.1| 176 LDPDETLKR--IHVARAYNAHHQ----------ILLAEKASDIAKEFPIKLLIVDSLTSH--FRSEYVGRGS 233
                                       **9999999..555555554433..........358899999999999999999999998..4455555555 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   1.7e-09   2.1e-06      11     156 ..      94     225 ..      85     243 .. 0.78

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.7e-09
                            AAA_25  11 svadlaapppprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr 87 
                                       +v++l +  + ++ l++g l  ++++ ++G  g+GKt + l+la+  +  ++  g     +  Vl++++E++  + +
  gi|518652933|ref|YP_008142453.1|  94 EVRKLSTGAQGLDNLIGGGLETQSITEFFGEFGSGKTQIMLQLAVNATMPEEQGG----LNSDVLIIDTENTF-R-P 164
                                       67777888888999****9*****************************5443333....5779*********9.4.5 PP

                            AAA_25  88 rRlravg..ealrddarllvldlagveslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralg 156
                                       +R+ ++   ++l++d++l  +++a+       ++ +++ ll+++     + ++e   ++l+++D+l++ ++
  gi|518652933|ref|YP_008142453.1| 165 ERVIQMAkaKNLDPDETLKRIHVARA------YNAHHQILLAEK---ASDIAKE-FPIKLLIVDSLTSHFR 225
                                       55555553455599999999999886......545555456665...5666788.56*********98665 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   2.8e-05     0.036      13      28 ..      22      37 ..      11      38 .. 0.89
   2 ?    5.1   0.1     0.018        23       5      19 ..      47      61 ..      46      71 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.8e-05
                                      HHTSTT-SHHHHHHHH CS
                               HHH 13 LlalPGVGpktAeaIl 28
                                      +++lPGVG++tAe+ +
  gi|518652933|ref|YP_008142453.1| 22 IEDLPGVGEATAEKLR 37
                                      689**********975 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.018
                                      HHTSSHHHHHTSTT- CS
                               HHH  5 lipasreeLlalPGV 19
                                      +  as+++L++++G+
  gi|518652933|ref|YP_008142453.1| 47 IAVASPKDLADISGI 61
                                      678***********9 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   6.6e-07   0.00084       9      53 ..      26      71 ..      24      77 .. 0.92
   2 ?   -2.8   0.0       5.6   7.2e+03      49      55 ..     116     122 ..     113     124 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 6.6e-07
                             HHH_2  9 rhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53
                                      + VGe+tA++L ++ ++++ a++ as ++L+ + +i+e  A +i++
  gi|518652933|ref|YP_008142453.1| 26 PGVGEATAEKLRENgYDDIMAIAVASPKDLADISGIAEGAAVKIIN 71
                                      78*********9866*************************999987 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 5.6
                             HHH_2  49 qsivefF 55 
                                       qsi+efF
  gi|518652933|ref|YP_008142453.1| 116 QSITEFF 122
                                       89****9 PP

>> Cdd1  Pathogenicity locus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.4e-06    0.0069       7      43 ..      21      57 ..      16      67 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.4e-06
                              Cdd1  7 elqdiPniGkalaedlvelGirsveelkgedpeelye 43
                                      +++d+P++G+a+ae+l+e G+ ++  ++  +p++l +
  gi|518652933|ref|YP_008142453.1| 21 TIEDLPGVGEATAEKLRENGYDDIMAIAVASPKDLAD 57
                                      679*****************************99965 PP

>> BAF  Barrier to autointegration factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.9e-05     0.037      12      42 ..      12      44 ..       2      50 .. 0.78
   2 ?   -2.4   0.0       5.2   6.6e+03      18      40 ..      53      75 ..      51      79 .. 0.74
   3 ?   -2.2   0.0       4.5   5.8e+03      33      57 ..     181     205 ..     179     212 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.9e-05
                               BAF 12 sepmgdKe..vtalaGigevlgkkLeekGfdkA 42
                                         +++K+  +++l+G+ge  ++kL+e+G+d  
  gi|518652933|ref|YP_008142453.1| 12 DSELENKKltIEDLPGVGEATAEKLRENGYDDI 44
                                      5567777533789*****************975 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 5.2
                               BAF 18 KevtalaGigevlgkkLeekGfd 40
                                      K+  +++Gi e  + k+ ++  +
  gi|518652933|ref|YP_008142453.1| 53 KDLADISGIAEGAAVKIINAARK 75
                                      78889999999888887766555 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 4.5
                               BAF  33 kLeekGfdkAyvvlgqfLvlkkdee 57 
                                        L++  + +Ay+   q L+ +k ++
  gi|518652933|ref|YP_008142453.1| 181 TLKRIHVARAYNAHHQILLAEKASD 205
                                       5677778899999999999988765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   9.8e-06     0.013       8      79 ..     122     225 ..     120     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 9.8e-06
                            AAA_24   8 yGpsgiGKTtlakel.............gpkplfidtekGlksldadkfpdie...................swedf 52 
                                       +G+ g+GKT ++++l               ++l+idte+ ++   ++++ +++                     + +
  gi|518652933|ref|YP_008142453.1| 122 FGEFGSGKTQIMLQLavnatmpeeqgglNSDVLIIDTENTFRPERVIQMAKAKnldpdetlkrihvaraynaHHQIL 198
                                       79**************************9**********99877777777777777888777776666665555555 PP

                            AAA_24  53 ldevvelaaeladyktlviDtidelee 79 
                                       l e +++ a++ ++k l++D+++   +
  gi|518652933|ref|YP_008142453.1| 199 LAEKASDIAKEFPIKLLIVDSLTSHFR 225
                                       5555555888888*********97655 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   2.3e-05     0.029      10      31 ..      19      40 ..      18      41 .. 0.89
   2 ?   -2.4   0.0         6   7.7e+03       8      18 ..     113     123 ..     109     123 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.3e-05
                           IMS_HHH 10 plpitkipGiGgklgekLeklG 31
                                      +l i ++pG+G  ++ekL+  G
  gi|518652933|ref|YP_008142453.1| 19 KLTIEDLPGVGEATAEKLRENG 40
                                      789**************99766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6
                           IMS_HHH   8 LwplpitkipG 18 
                                       L+  +it++ G
  gi|518652933|ref|YP_008142453.1| 113 LETQSITEFFG 123
                                       45567777766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-05     0.065       4     100 ..     115     220 ..     113     261 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka.........e 71 
                                       t++i+  +Ge G+GKT  + +l+ +++  +++   +++v+ ++  +   ++ + ++   +  ++ ++         +
  gi|518652933|ref|YP_008142453.1| 115 TQSITEFFGEFGSGKTQIMLQLAVNATMPEEQGGLNSDVLIIDTENTFRPERVIQMAKAKNLDPDETlkrihvaraY 191
                                       7899999******************98877777799**999999999988888777666655566668666666666 PP

                            AAA_22  72 rlsseellealeqalraravielliiDEa 100
                                       ++  + ll+  +  + + + i+lli+D  
  gi|518652933|ref|YP_008142453.1| 192 NAHHQILLAEKASDIAKEFPIKLLIVDSL 220
                                       66666666555555555555899999965 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.4e-05      0.12      37      65 ..      10      38 ..       5      39 .. 0.80
   2 ?   -0.5   0.1       1.3   1.6e+03      42      64 ..      49      70 ..      45      73 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.4e-05
                                      C-SS-HHHHTT.HCTTSTT--HHHHHHHHH CS
                             HHH_8 37 alpeeitslee.eltklpgiGkkiaakiee 65
                                      +l+ e+++ ++ ++++lpg+G+++a+k++e
  gi|518652933|ref|YP_008142453.1| 10 ELDSELEN-KKlTIEDLPGVGEATAEKLRE 38
                                      46667777.55678*************998 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1.3
                                      HHHHTTHCTTSTT--HHHHHHHH CS
                             HHH_8 42 itsleeeltklpgiGkkiaakie 64
                                      ++s ++ l ++ gi ++ a ki 
  gi|518652933|ref|YP_008142453.1| 49 VASPKD-LADISGIAEGAAVKII 70
                                      566555.99*****999999985 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.0   0.00052      0.66       8      26 ..      27      45 ..      23      57 .. 0.88
   2 ?   -1.1   0.0       1.3   1.7e+03      32      49 ..     231     248 ..     220     249 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00052
                   DNA_pol_lambd_f  8 GVGpktAkkwyakGirtle 26
                                      GVG +tA+k+ ++G+ ++ 
  gi|518652933|ref|YP_008142453.1| 27 GVGEATAEKLRENGYDDIM 45
                                      9**************9875 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                   DNA_pol_lambd_f  32 rakLtreqqiGlkyyeDl 49 
                                       r +L + qq+  k+ +Dl
  gi|518652933|ref|YP_008142453.1| 231 RGSLAERQQLLNKHMHDL 248
                                       567889999999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      560  (0.0312343); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2616.29
//
Query:       gi|518652934|ref|YP_008142454.1|  [L=259]
Description: hypothetical protein FACI_IFERC00001G1573 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 1853.97
//
Query:       gi|518652935|ref|YP_008142455.1|  [L=1156]
Description: hypothetical protein FACI_IFERC00001G1574 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-32  112.0  81.7    2.5e-31  108.8  81.7    2.9  1  SMC_N           RecF/RecN/SMC N terminal domain
    2.4e-29  102.0   0.2    1.5e-28   99.4   0.1    2.3  2  SMC_hinge       SMC proteins Flexible Hinge Domain
    6.2e-13   49.2   1.8    2.3e-07   30.9   0.2    5.0  5  AAA_21          AAA domain, putative AbiEii toxin, Type IV TA
    8.1e-07   28.7   0.1      2e-06   27.4   0.1    1.7  1  AAA_29          P-loop containing region of AAA domain
    1.9e-06   27.8  29.6    1.9e-06   27.8  29.6    4.4  2  AAA_15          AAA ATPase domain
      1e-05   26.2  43.0      1e-05   26.2  43.0    7.0  1  AAA_23          AAA domain
    4.7e-05   23.7  14.5    4.7e-05   23.7  14.5    7.0  7  ATG16           Autophagy protein 16 (ATG16)
     0.0015   18.5  60.4      0.011   15.8   3.2    8.6  8  DUF1664         Protein of unknown function (DUF1664)
     0.0091   15.8  14.3     0.0091   15.8  14.3    6.7  4  TACC_C          Transforming acidic coiled-coil-containing pr
  ------ inclusion threshold ------
       0.13   11.9   0.0        0.4   10.4   0.0    1.7  1  DUF2937         Protein of unknown function (DUF2937)
          3    8.1  14.3      0.037   14.3   2.7    3.7  4  OrfB_IS605      Probable transposase
        4.5    7.3 111.9      0.038   14.0  22.5    7.9  8  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        9.5    5.5  67.7        3.7    6.8  10.5    6.0  6  DUF4407         Domain of unknown function (DUF4407)


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8  81.7   1.8e-34   2.5e-31       2     218 ..       3    1141 ..       2    1143 .. 0.99

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 1.8e-34
                                        EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N    2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkk 76  
                                        + ++e+enFksy  ++++++++k+ft+i+GpNGSGKsn+ d++lFvLG r++k++r +kl+d ihk  + +  k+
  gi|518652935|ref|YP_008142455.1|    3 VDSIEMENFKSYG-DKQSIKINKGFTVIIGPNGSGKSNIGDSMLFVLGIRANKTVRVDKLEDFIHK--TDPPKKH 74  
                                        679*********5.9999***********************************************8..89999** PP

                                        EEEEEEE.EETTEESSSSSSCEEEEEEEETTSE...EEEEETTEEE-HHHHHHHHHCTT-STT............ CS
                                        xxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx............ RF
                             SMC_N   77 aeveitf.dnedkklkiekeevsisrrvkrkge...seykingkevtkkevsellesagiske............ 135 
                                        ++v + + +ne+++       +si+r+++ +     s+y+in+k++++++v +l+ s +i+ +            
  gi|518652935|ref|YP_008142455.1|   75 CYVVLNViSNENNR-------YSIKRELVYNHGeykSNYYINDKRASRTDVLKLIDSFHIYLDaysfvlqgdinn 142 
                                        **999763555555.......999998655543378*************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  143 lvkmtgtekrklfesiagiesykeriesaqndinglnenlnsmdavlleiksmldtlevdrenalkynklnkevn 217 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  218 elkfflkvkdrdrinqelamyngnieksqsdidnlenenknlsiqrdeainrikeiedkldamggqevkgirkri 292 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  293 eelnigiaelktkigstgesktnsearlktsreaynfnreqlenklkekknyesylkgtensiakinrelekfrq 367 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  368 enyenskltreindrlaaidvemqqandqiindydirtieqelsgfsrentmneekikeesikvkdlkwkidnlk 442 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  443 knikeyseeinevnkkfltvrnklnelvtmksnndveirnkekelrglnyrgtaspalreinsmmetesgihgpl 517 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  518 gklieyedkyanavivaaggrlnsivvdndsvaqmciqaikakklgrltfiplnkiatspdrqkaaelinsgnai 592 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  593 dfvrnlitcdpafekaikyafgdtvlmdtlenarkhmtgvrivtldgdvldpsgamtggsikndeilanritkai 667 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  668 aeleeqneilkseisfkekenseisskladltrkrdistsninnyetqlqesensieaaktrieeiklkikdaed 742 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  743 rksnfefkknevkmqlftldkerkelfkklkelapenveiekqmeeelgnemksrenyssklaqietefkhftek 817 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  818 sqeleekitgleneitkftgmvaefknkveamekeleenrakeneidsrsrelyteknqvstardklfenirknd 892 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  893 dlisnkkaiiaglktkienlafqletinyeientgmeyiefnmsisevkqkidensreieklgavnmkaieqydm 967 
                                        *************************************************************************** PP

                                        ........................................................................... CS
                                        ........................................................................... RF
                             SMC_N  136 ........................................................................... 135 
                                                                                                                   
  gi|518652935|ref|YP_008142455.1|  968 elnkynsteekyktllsekndlidlqnqiiedekriflelfdtinsqfqkiyarlseggeanleitsrddplnse 1042
                                        *************************************************************************** PP

                                        ................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEE CS
                                        ................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  136 ................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfiv 194 
                                                        +LSgGek+++ laL+++ q  +p+p+y+lDe+d+ LD +n + v el+ e+sk++Q+++
  gi|518652935|ref|YP_008142455.1| 1043 vyikvkprgkhmikidALSGGEKSVAVLALILSFQIKNPSPIYYLDEVDMFLDGHNAEHVGELFMENSKTSQVVM 1117
                                        *************************************************************************** PP

                                        E-SSHHHCCC-SCEEEEEEEETTE CS
                                        xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  195 islreemlekadklvgvtkvengv 218 
                                        +sl+  +++ ad+l+ vt+ ++g 
  gi|518652935|ref|YP_008142455.1| 1118 VSLKGAVTKFADNLIAVTTDKHGN 1141
                                        ******************977765 PP

>> SMC_hinge  SMC proteins Flexible Hinge Domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.5   2.1e+03      17      92 ..     127     204 ..     118     209 .. 0.64
   2 !   99.4   0.1   1.1e-31   1.5e-28       2     115 ..     511     627 ..     510     629 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.5
                         SMC_hinge  17 gyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldr.ikqknkadgandkns.gavplidlvevdd 91 
                                        y  A + +l +++++lv  +  + +k++e +   ++ +  + ++++ i+  n++    d     +++++d +evd 
  gi|518652935|ref|YP_008142455.1| 127 IYLDAYSFVLQGDINNLVKMTGTEKRKLFESIAGIESYKERIESAQNdINGLNENLNSMDAVLlEIKSMLDTLEVDR 203
                                       67778888899999999988888888888877766655555554422244444444443333367777777777776 PP

                         SMC_hinge  92 e 92 
                                       e
  gi|518652935|ref|YP_008142455.1| 204 E 204
                                       5 PP

  == domain 2  score: 99.4 bits;  conditional E-value: 1.1e-31
                         SMC_hinge   2 kgvlGrladlievdegyekAveaalgnrlqalvvedeetakkiieflkkknagratflpldrikqknkadgandkns 78 
                                       +g++G+l+ lie +++y  Av +a+g+rl+++vv+++ +a+ +i+ +k+k++gr+tf+pl++i +++++ +a +  +
  gi|518652935|ref|YP_008142455.1| 511 SGIHGPLGKLIEYEDKYANAVIVAAGGRLNSIVVDNDSVAQMCIQAIKAKKLGRLTFIPLNKIATSPDRQKAAELIN 587
                                       79************************************************************888877776665554 PP

                         SMC_hinge  79 ...gavplidlvevddelrkalryllgdtlvvdsldeAee 115
                                           + ++ +l+++d++++ka++y++gdt++ d+l++A++
  gi|518652935|ref|YP_008142455.1| 588 sgnAIDFVRNLITCDPAFEKAIKYAFGDTVLMDTLENARK 627
                                       59999*********************************97 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2   0.1   2.4e-09   3.3e-06       1      83 [.      26      96 ..      26     133 .. 0.67
   2 ?    0.5   1.1       0.3   4.2e+02     103     203 ..     180     281 ..     161     295 .. 0.76
   3 ?   -2.1   0.3       1.9   2.6e+03     195     195 ..     382     382 ..     301     481 .. 0.57
   4 ?   -2.2   3.6         2   2.7e+03      72     173 ..     705     802 ..     668     836 .. 0.62
   5 !   30.9   0.2   1.7e-10   2.3e-07     183     296 ..    1006    1119 ..     850    1119 .. 0.90

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 2.4e-09
                            AAA_21  1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrle 79
                                      ++v+iGpNgsGKSn+ d + ++ +             + +++  +++l d+++++ p + +++ +l+  ++ + ++ ++
  gi|518652935|ref|YP_008142455.1| 26 FTVIIGPNGSGKSNIGDSMLFVLG------------IRANKTVRVDKLEDFIHKTDPPKKHCYVVLNVISNENNRYSIK 92
                                      8********************965............5666666666666666666666666665555555555555555 PP

                            AAA_21 80 rsqv 83
                                      r+ v
  gi|518652935|ref|YP_008142455.1| 93 RELV 96
                                      5555 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.3
                            AAA_21 103 rsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsllllldglrke.rigllnifadyfgf 178
                                       ++l+++d++  e +   +++ v ++ +l +++ n++ ++  + + +++ ++++++l +   + ++++ +i + +   
  gi|518652935|ref|YP_008142455.1| 180 ENLNSMDAVLLEIKSMLDTLEVDRENALKYNKLNKEVNELKFFLKVKDRDRINQELAMYNGNiEKSQSDIDNLENEN 256
                                       56777888888888888999999999999999999999999999999999999999554444666666666666666 PP

                            AAA_21 179 akekrllqrlvrslklveielsdlg 203
                                       +++  ++++ ++++k++e++l+++g
  gi|518652935|ref|YP_008142455.1| 257 KNLSIQRDEAINRIKEIEDKLDAMG 281
                                       6666666666666666666666655 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 1.9
                            AAA_21 195 v 195
                                       +
  gi|518652935|ref|YP_008142455.1| 382 R 382
                                       1 PP

  == domain 4  score: -2.2 bits;  conditional E-value: 2
                            AAA_21  72 yryglrlersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltdit 148
                                        + +++ ++ q    l+++e+  e   ++ ++++ ++++  ++++++   + + + + +++ ++ ++ f+k+  + +
  gi|518652935|ref|YP_008142455.1| 705 STSNINNYETQ----LQESENSIEAAKTRIEEIKLKIKDAEDRKSNFEFKKNEVKMQLFTLDKERKELFKKLKELAP 777
                                       33333333333....46777777777777777777777777777777777777777777777777777777777777 PP

                            AAA_21 149 srawsllllldglrkerigllnifa 173
                                       +  +  +++ ++l++e++++ n++ 
  gi|518652935|ref|YP_008142455.1| 778 ENVEIEKQMEEELGNEMKSRENYSS 802
                                       7777777777777777444444333 PP

  == domain 5  score: 30.9 bits;  conditional E-value: 1.7e-10
                            AAA_21  183 rllqrlvrslklveielsdlgegeeliasvderlrergvvflengdgqelparelSdGtkrllalltallralkk 257 
                                        +l++   ++++++ ++ls  ge++ +i+s+d++l+ + ++ +++ + + + ++ lS G k++ a+l+++l+   k
  gi|518652935|ref|YP_008142455.1| 1006 ELFDTINSQFQKIYARLSEGGEANLEITSRDDPLNSEVYIKVKPRGKHMIKIDALSGGEKSV-AVLALILSFQIK 1079
                                        55666677889999999999999999**********9*************************.555555555555 PP

                            AAA_21  258 g..sllliDEpEngLHPkllrrllellkelsrngaQviltT 296 
                                        +  +++ +DE++ +L+ +  +++ el+ e+s+  +Qv++++
  gi|518652935|ref|YP_008142455.1| 1080 NpsPIYYLDEVDMFLDGHNAEHVGELFMENSK-TSQVVMVS 1119
                                        555************************99999.9***9976 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 !   27.4   0.1   1.5e-09     2e-06       3      46 ..       5      48 ..       3      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 1.5e-09
                            AAA_29  3 rlqlvNWgtfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                      ++++ N  ++ + ++i+i+ kg+t+++Gp+GsGKS + D++ ++L
  gi|518652935|ref|YP_008142455.1|  5 SIEMENFKSYGDkQSIKIN-KGFTVIIGPNGSGKSNIGDSMLFVL 48
                                      789999999*999*****9.889******************9998 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8  29.6   1.4e-09   1.9e-06       1     282 [.       1     288 [.       1     317 [. 0.43
   2 ?   -2.6  34.0       2.5   3.4e+03      69     360 ..     797    1116 ..     794    1119 .. 0.64

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 1.4e-09
                            AAA_15   1 MkIkkikikNFRslkd.veidlseeltvliGkNnsGKSsilealdlFlnnkekkn................kkviki 60 
                                       M++++i+ +NF+s+ d  +i++++ +tv+iG+N+sGKS+i + + + l    +k                 kk  ++
  gi|518652935|ref|YP_008142455.1|   1 MIVDSIEMENFKSYGDkQSIKINKGFTVIIGPNGSGKSNIGDSMLFVLGIRANKTvrvdkledfihktdppKKHCYV 77 
                                       999************999**************************999996655556666555555444444222222 PP

                            AAA_15  61 ekedleifeniseskdikIdvefaekekakeyektlkskekkkadl.llkkkesdlkktikdkklklkknelsdeki 136
                                         + +++++n++  k+  +  +   + k+++y+  ++ ++ +  +l +  +++ d ++++ + ++++  + + +ek 
  gi|518652935|ref|YP_008142455.1|  78 VLNVISNENNRYSIKRELVYNHG--EYKSNYYINDKRASRTDVLKLiDSFHIYLDAYSFVLQGDINNLVKMTGTEKR 152
                                       22222222222222222222111..1233333333333222222210112222333333333333333333333333 PP

                            AAA_15 137 svekkkskkelpkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsek 213
                                       ++++  +  e +ke+ e+++++++ l  + +                 +++ vl +    l++ + +R++  + ++ 
  gi|518652935|ref|YP_008142455.1| 153 KLFESIAGIESYKERIESAQNDINGLNENLN-----------------SMDAVLLEIKSMLDTLEVDRENALKYNKL 212
                                       3333333333333333333333333333333.................44455555555555555555554433333 PP

                            AAA_15 214 kssllgklkekileealqekl..........eeelteklkeiqeklkeidkklaeelkkilkkkidkikkfnykgkk 280
                                       ++++ + ++  ++++  +++           +e++++++++++++ k+++ + +e ++  +k++ dk++ ++ +++k
  gi|518652935|ref|YP_008142455.1| 213 NKEVNELKFFLKVKD--RDRInqelamyngnIEKSQSDIDNLENENKNLSIQRDEAIN-RIKEIEDKLDAMGGQEVK 286
                                       333333333333332..11111111233333333333333333333333333322222.122222222223333333 PP

                            AAA_15 281 ne 282
                                         
  gi|518652935|ref|YP_008142455.1| 287 GI 288
                                       33 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.5
                            AAA_15   69 eniseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkks 143 
                                        ++++ sk  +I+ ef           t+ks+e +++ + l+++++++  ++ ++k k++      + +++e++ +
  gi|518652935|ref|YP_008142455.1|  797 RENYSSKLAQIETEF--------KHFTEKSQELEEKITGLENEITKFTGMVAEFKNKVE-----AMEKELEENRA 858 
                                        678888999999999........223445555555566677777777777777777765.....66666667777 PP

                            AAA_15  144 kkelpkekeeklekekeelkidkedlkklikkleeslkkee....elknvlksaiiklllisakRnvsdedsekk 214 
                                        k +  ++++ +l +ek+ +++  ++l++ i+k    ++ ++     lk ++++++ +l++i+ + +++  ++ + 
  gi|518652935|ref|YP_008142455.1|  859 KENEIDSRSRELYTEKNQVSTARDKLFENIRKNDDLISNKKaiiaGLKTKIENLAFQLETINYEIENTGMEYIEF 933 
                                        666666777777777777777777777777777777766667777666666666666666666666666666666 PP

                            AAA_15  215 ssllgklkekileealqekl.......................eeelteklkeiqeklkeidkklaeelk....k 262 
                                        + +++++k+ki e++ +e                         ee+ +  l+e ++ ++ +++++ e++k    +
  gi|518652935|ref|YP_008142455.1|  934 NMSISEVKQKIDENS-REIEklgavnmkaieqydmelnkynstEEKYKTLLSEKNDLID-LQNQIIEDEKriflE 1006
                                        666666666665553.2222456665555555555556666744444444444444444.444444555525554 PP

                            AAA_15  263 ilkkkidkikkfnykgkkneeieik...................ddeelplnknGsGvqrllllillileaekkd 318 
                                         ++ + ++++k+ +  ++  e +++                    +  ++++  + G ++  +l+l + + +k+ 
  gi|518652935|ref|YP_008142455.1| 1007 LFDTINSQFQKIYARLSEGGEANLEitsrddplnsevyikvkprGKHMIKIDALSGGEKSVAVLALILSFQIKN- 1080
                                        444444444444444444444444488999999*99999999*9999*************99999999999999. PP

                            AAA_15  319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQvi 360 
                                            ++ i+ ++E +  L   + +++ +l+ e ++++  Qv+
  gi|518652935|ref|YP_008142455.1| 1081 ----PSPIYYLDEVDMFLDGHNAEHVGELFMENSKTS--QVV 1116
                                        ....999999999988777777777777777776666..555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.2  43.0   7.2e-09     1e-05       1     192 [.       5     277 ..       5     397 .. 0.62

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 7.2e-09
                            AAA_23   1 kLkienfrsf.rdqeidFskgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiese........ 68 
                                       ++++enf+s+ ++q+i  +kg+t+I+GpNG+GK+ i d + ++L+ +++++ r ++   + ++              
  gi|518652935|ref|YP_008142455.1|   5 SIEMENFKSYgDKQSIKINKGFTVIIGPNGSGKSNIGDSMLFVLGIRANKTVRVDKLEDFIHKTD---Ppkkhcyvv 78 
                                       699*******55577*******************************9999999885333322222...211222333 PP

                            AAA_23  69 .....gkvkay.veltfenkdgry............................................trsierere 95 
                                            +++++y +++++ +++g+y                                            t       +
  gi|518652935|ref|YP_008142455.1|  79 lnvisNENNRYsIKRELVYNHGEYksnyyindkrasrtdvlklidsfhiyldaysfvlqgdinnlvkmT------GT 149
                                       334455555556666666666666777777777777777777777777777766655555553333320......22 PP

                            AAA_23  96 lskkkgkttkkaklellei...deleqfisellgskki....ilnlilflgqer.........feefelkdkke... 153
                                       +++k  +++ + +  + +i   ++  + ++e+l+s ++    i ++++ l  +r         +         +   
  gi|518652935|ref|YP_008142455.1| 150 EKRKLFESIAGIESYKERIesaQNDINGLNENLNSMDAvlleIKSMLDTLEVDRenalkynklN---------Kevn 217
                                       2222222222221111111111111111111222222222212222222222223332222220.........1222 PP

                            AAA_23 154 ................rleelekeleeledekkllekl.....eqekekekeleeleeel 192
                                                       +l+ ++  +e+ + +++ le++     +q+ e  ++++e+e++l
  gi|518652935|ref|YP_008142455.1| 218 elkfflkvkdrdrinqELAMYNGNIEKSQSDIDNLENEnknlsIQRDEAINRIKEIEDKL 277
                                       333333344444444466666666666666666666665665556666666666666665 PP

>> ATG16  Autophagy protein 16 (ATG16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.7      0.67   9.3e+02     119     156 ..     162     199 ..     140     221 .. 0.64
   2 ?    2.1   3.8      0.14   1.9e+02      73     156 ..     239     323 ..     224     334 .. 0.79
   3 ?    4.0   5.6     0.038        52     109     173 ..     332     396 ..     328     399 .. 0.89
   4 !    8.8   6.0    0.0013       1.8     101     180 ..     407     486 ..     403     490 .. 0.84
   5 !    7.2  11.0    0.0039       5.4      98     177 ..     668     747 ..     659     768 .. 0.77
   6 !   23.7  14.5   3.4e-08   4.7e-05      25     156 ..     766     898 ..     751     929 .. 0.86
   7 ?    3.6   3.0      0.05        69     100     186 ..     905     991 ..     901     992 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.67
                             ATG16 119 kedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       ++ +er+++++++++ l+++l++ ++ l e + ++++l
  gi|518652935|ref|YP_008142455.1| 162 ESYKERIESAQNDINGLNENLNSMDAVLLEIKSMLDTL 199
                                       44556666666666666666666666666666555554 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.14
                             ATG16  73 sakiqsleqklaqlreelaelyksrgelaqrllelneelqkle.eklkedeerlaeleaeraaletklkdreeelre 148
                                       + +i+++++ +  l +e ++l  +r e  +r++e +++l++   ++ k  ++r++el+  +a+l+tk+ +  e    
  gi|518652935|ref|YP_008142455.1| 239 NGNIEKSQSDIDNLENENKNLSIQRDEAINRIKEIEDKLDAMGgQEVKGIRKRIEELNIGIAELKTKIGSTGESKTN 315
                                       56788888899999999999999999999999999999999862588999999999999999999998877776666 PP

                             ATG16 149 keklvqdl 156
                                        e+ +++ 
  gi|518652935|ref|YP_008142455.1| 316 SEARLKTS 323
                                       66655555 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.038
                             ATG16 109 eelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEek 173
                                       e+l+ + ++ k+ e+ l+  e+++a+++++l++ ++e  e  kl  ++ D l+a  ++++qa ++
  gi|518652935|ref|YP_008142455.1| 332 EQLENKLKEKKNYESYLKGTENSIAKINRELEKFRQENYENSKLTREINDRLAAIDVEMQQANDQ 396
                                       67888888889999999999999999999999999999999999999999999999999998776 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0013
                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrkl 177
                                       +q l   + e    eek+ke++ ++++l+ ++ +l++++k+  ee++e +k   +++  l+ L    + ++ + r+ 
  gi|518652935|ref|YP_008142455.1| 407 EQELSGFSRENTMNEEKIKEESIKVKDLKWKIDNLKKNIKEYSEEINEVNKKFLTVRNKLNELVTMKSNNDVEIRNK 483
                                       7888889999999**************************************99999998888776666666655555 PP

                             ATG16 178 ekE 180
                                       ekE
  gi|518652935|ref|YP_008142455.1| 484 EKE 486
                                       555 PP

  == domain 5  score: 7.2 bits;  conditional E-value: 0.0039
                             ATG16  98 gelaqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEekl 174
                                       +el+++   l++e++ +e++ +e +++la+l+++r   + ++++ e +l+e e+ +++ +  ++  +l+ + aE+++
  gi|518652935|ref|YP_008142455.1| 668 AELEEQNEILKSEISFKEKENSEISSKLADLTRKRDISTSNINNYETQLQESENSIEAAKTRIEEIKLKIKDAEDRK 744
                                       56666666677788888888888888888888888888888888888888888888888888888888888888887 PP

                             ATG16 175 rkl 177
                                        + 
  gi|518652935|ref|YP_008142455.1| 745 SNF 747
                                       754 PP

  == domain 6  score: 23.7 bits;  conditional E-value: 3.4e-08
                             ATG16  25 nrLldrtsaleaenaklekaaasaks.sksskksakekeasasqsnskqsakiqsleqklaqlreelaelyksrgel 100
                                       ++L+++ ++l+ en ++ek+++++   + +s+++ ++k+a+ +++ ++ ++k+q+le+k++ l +e ++     +e+
  gi|518652935|ref|YP_008142455.1| 766 KELFKKLKELAPENVEIEKQMEEELGnEMKSRENYSSKLAQIETEFKHFTEKSQELEEKITGLENEITKFTGMVAEF 842
                                       56999***************9999988666666777778887778999***************************** PP

                             ATG16 101 aqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdl 156
                                       ++++ ++++el++ ++k +e ++r +el +e+++++t+++++ e++r  + l+ + 
  gi|518652935|ref|YP_008142455.1| 843 KNKVEAMEKELEENRAKENEIDSRSRELYTEKNQVSTARDKLFENIRKNDDLISNK 898
                                       **************************************************999843 PP

  == domain 7  score: 3.6 bits;  conditional E-value: 0.05
                             ATG16 100 laqrllelneelqkleeklkedeerlaeleaeraaletklkdreeelrekeklvqdlqDElsaLqlqlnqaEeklrk 176
                                       l++++ +l  +l++ + ++++   +  e + +++++++k++++  e++ + +++ +  + ++    ++n+ Eek+++
  gi|518652935|ref|YP_008142455.1| 905 LKTKIENLAFQLETINYEIENTGMEYIEFNMSISEVKQKIDENSREIEKLGAVNMKAIEQYDMELNKYNSTEEKYKT 981
                                       6788899999999999999999999999999********************************************** PP

                             ATG16 177 lekENkeLve 186
                                       l  E ++L++
  gi|518652935|ref|YP_008142455.1| 982 LLSEKNDLID 991
                                       ********97 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.0   0.1    0.0084        12      58     114 ..     148     200 ..     125     205 .. 0.63
   2 !    7.4   1.6    0.0031       4.3      49     104 ..     251     307 ..     231     323 .. 0.64
   3 ?    2.0   0.5      0.15   2.1e+02      57     121 ..     320     387 ..     307     392 .. 0.73
   4 !    7.0   3.0    0.0041       5.7      63     113 ..     426     476 ..     402     486 .. 0.70
   5 ?    1.4   5.1      0.22     3e+02      59     102 ..     700     743 ..     660     771 .. 0.63
   6 !   15.8   3.2   7.8e-06     0.011      45     119 ..     781     855 ..     768     860 .. 0.90
   7 !   11.0   1.8   0.00023      0.32      41     121 ..     861     941 ..     855     943 .. 0.86
   8 ?    0.4   0.8      0.46   6.4e+02      43      93 ..     937     987 ..     932    1018 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0084
                           DUF1664  58 aatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegle 114
                                        + kr+L + i+     +++ ke +++ +++++ ++e+l++++  + ++k++  +le
  gi|518652935|ref|YP_008142455.1| 148 GTEKRKLFESIAG----IESYKERIESAQNDINGLNENLNSMDAVLLEIKSMLDTLE 200
                                       4455555555544....3455666666666777777777777776666666666665 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0031
                           DUF1664  49 qleqvseslaatkrhLssridrvdkkldeqk.eiskeikeevtevredlseigedve 104
                                       +le+  ++l+ ++++  +ri+++++kld++  +  k i++ ++e++ +++e+++++ 
  gi|518652935|ref|YP_008142455.1| 251 NLENENKNLSIQRDEAINRIKEIEDKLDAMGgQEVKGIRKRIEELNIGIAELKTKIG 307
                                       455556666666666666666666666666413345566666666666666665555 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.15
                           DUF1664  57 laatkrhLssridrvdkkldeqkei...skeikeevtevredlseigedvesvkeaveglesklerie 121
                                       l++ ++  + + +++++kl+e k+     k +++ +++++++l++++++  + +++ ++++ +l+ i+
  gi|518652935|ref|YP_008142455.1| 320 LKTSREAYNFNREQLENKLKEKKNYesyLKGTENSIAKINRELEKFRQENYENSKLTREINDRLAAID 387
                                       55556666666677788887776641115789999999999999999998888888888888887775 PP

  == domain 4  score: 7.0 bits;  conditional E-value: 0.0041
                           DUF1664  63 hLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegl 113
                                       + s +++ + +k+d+ k+ +ke +ee++ev+++  +++++++++ ++ ++ 
  gi|518652935|ref|YP_008142455.1| 426 EESIKVKDLKWKIDNLKKNIKEYSEEINEVNKKFLTVRNKLNELVTMKSNN 476
                                       345578888888888888888888888888888888888888877776555 PP

  == domain 5  score: 1.4 bits;  conditional E-value: 0.22
                           DUF1664  59 atkrhLssridrvdkkldeqkeiskeikeevtevredlseiged 102
                                       + ++  +s+i++ +++l+e+++ +++ k  ++e++ ++++ ++ 
  gi|518652935|ref|YP_008142455.1| 700 RKRDISTSNINNYETQLQESENSIEAAKTRIEEIKLKIKDAEDR 743
                                       33333345666666666666666666666666666555554443 PP

  == domain 6  score: 15.8 bits;  conditional E-value: 7.8e-06
                           DUF1664  45 svskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskler 119
                                       ++ kq+e+   +  + +++ ss++++++++ ++ +e s+e++e++t ++++++++   v + k+ ve +e++le+
  gi|518652935|ref|YP_008142455.1| 781 EIEKQMEEELGNEMKSRENYSSKLAQIETEFKHFTEKSQELEEKITGLENEITKFTGMVAEFKNKVEAMEKELEE 855
                                       67899988777777899******************************************************9986 PP

  == domain 7  score: 11.0 bits;  conditional E-value: 0.00023
                           DUF1664  41 davesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesvkeavegleskl 117
                                       + ++s s++l + ++++++++++L ++i + d+ + + k+i++ +k +++++  +l++i+ ++e+      ++++++
  gi|518652935|ref|YP_008142455.1| 861 NEIDSRSRELYTEKNQVSTARDKLFENIRKNDDLISNKKAIIAGLKTKIENLAFQLETINYEIENTGMEYIEFNMSI 937
                                       556677888888899************************************************99877766677777 PP

                           DUF1664 118 erie 121
                                       ++++
  gi|518652935|ref|YP_008142455.1| 938 SEVK 941
                                       6665 PP

  == domain 8  score: 0.4 bits;  conditional E-value: 0.46
                           DUF1664  43 vesvskqleqvseslaatkrhLssridrvdkkldeqkeiskeikeevtevr 93 
                                       +++v +++++ s ++++     ++ i++ d +l++ + + ++ k  ++e +
  gi|518652935|ref|YP_008142455.1| 937 ISEVKQKIDENSREIEKLGAVNMKAIEQYDMELNKYNSTEEKYKTLLSEKN 987
                                       678999999999999999999999999999999999988888776666544 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 ?   -2.8  11.9       3.2   4.4e+03      21     128 ..     282     388 ..     262     395 .. 0.68
   2 ?    1.8   8.8      0.13   1.7e+02       7      96 ..     407     492 ..     399     497 .. 0.77
   3 !   15.8  14.3   6.6e-06    0.0091       3     127 ..     797     917 ..     794     922 .. 0.88
   4 ?   -0.8   7.7      0.83   1.1e+03       9      75 ..     922     991 ..     914    1024 .. 0.62

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.2
                            TACC_C  21 eeeiqelkkkveelkkenqemk.kivaefektiaqlie..ekqkqkelakkeiqkvleekeqlladlnsveksfsdl 94 
                                        +e++  +k++eel+   +e+k ki +  e+ ++       + +  + +++++++ l+ek++  + l+ +e s++++
  gi|518652935|ref|YP_008142455.1| 282 GQEVKGIRKRIEELNIGIAELKtKIGSTGESKTNSEARlkTSREAYNFNREQLENKLKEKKNYESYLKGTENSIAKI 358
                                       568888999999999999999834556677666544331022333345678899999******************** PP

                            TACC_C  95 fkryekqkevlegykkneeslkkcaeeylarvkk 128
                                        + +ek ++  e+y +    l +++++ la +  
  gi|518652935|ref|YP_008142455.1| 359 NRELEKFRQ--ENYENS--KLTREINDRLAAIDV 388
                                       **9999988..566543..455666666666655 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.13
                            TACC_C   7 daalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeqllad 83 
                                       ++ l  + +e++ +ee+i+e + kv++lk +  ++kk ++e+ + i+++ ++        ++++++++  k+++  +
  gi|518652935|ref|YP_008142455.1| 407 EQELSGFSRENTMNEEKIKEESIKVKDLKWKIDNLKKNIKEYSEEINEVNKKF----LTVRNKLNELVTMKSNNDVE 479
                                       55566678888889999999999999999999999999999998887776665....45567788888888888888 PP

                            TACC_C  84 lnsveksfsdlfk 96 
                                       +++ ek++  l  
  gi|518652935|ref|YP_008142455.1| 480 IRNKEKELRGLNY 492
                                       8888888877765 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 6.6e-06
                            TACC_C   3 qkdldaalekvkeeveekeeeiqelkkkveelkkenqemkkivaefektiaqlieekqkqkelakkeiqkvleekeq 79 
                                        ++  ++l++++ e+++  e+ qel++k++ l++e ++   +vaef + ++ + +e ++++  +++ei+       +
  gi|518652935|ref|YP_008142455.1| 797 RENYSSKLAQIETEFKHFTEKSQELEEKITGLENEITKFTGMVAEFKNKVEAMEKELEENR-AKENEIDSR---SRE 869
                                       5677788999*****************************************9999996665.667777765...678 PP

                            TACC_C  80 lladlnsveksfsdlfkryekqkevlegykkneeslkkcaeeylarvk 127
                                       l+++ n+v ++ ++lf+ ++k  + +++ k+  + lk+++e++  +++
  gi|518652935|ref|YP_008142455.1| 870 LYTEKNQVSTARDKLFENIRKNDDLISNKKAIIAGLKTKIENLAFQLE 917
                                       99999***********************************99876665 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.83
                            TACC_C   9 alekvkeeveekeeeiqelkkkveelkkenqemkki....vaefektiaqlieekqkqkelakkeiqkvle 75 
                                        +e++ +e  e +  i+e k+k++e  +e ++++ +    +++++  +++  + ++k k+l ++  + ++ 
  gi|518652935|ref|YP_008142455.1| 922 EIENTGMEYIEFNMSISEVKQKIDENSREIEKLGAVnmkaIEQYDMELNKYNSTEEKYKTLLSE-KNDLID 991
                                       5677888899999999999999999999999999764222455555555555555554443332.222223 PP

>> DUF2937  Protein of unknown function (DUF2937)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00029       0.4      33      98 ..     240     304 ..     235     309 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00029
                           DUF2937  33 ghldelkrqlagfqatAkrffkgdlealiahyrqsedpvvradaesiqalverlerLeqelqalqq 98 
                                       g ++ ++  +++++++ k+     ++++i++ ++ ed+  +  +++++ + +r e+L+ + ++l++
  gi|518652935|ref|YP_008142455.1| 240 GNIEKSQSDIDNLENENKNLSI-QRDEAINRIKEIEDKLDAMGGQEVKGIRKRIEELNIGIAELKT 304
                                       78899999*************9.*************************************999987 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   2.7   2.7e-05     0.037      23     109 ..     297     389 ..     295     394 .. 0.89
   2 ?   -0.8   0.2       1.3   1.7e+03      44      67 ..     439     462 ..     425     481 .. 0.73
   3 ?   -1.8   0.3       2.6   3.6e+03      41      66 ..     749     774 ..     739     817 .. 0.76
   4 ?   -2.9   0.0       5.7   7.8e+03      47      66 ..     808     827 ..     785     859 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.7e-05
                        OrfB_IS605  23 lGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkkskn....ykkasrklarlhrkrsrrrkhllh.. 93 
                                       +Gi  L t   ++g+++ ++ +rlk+  ++++  + +l+ klk++kn     k + + +a++ r++ ++r++ ++  
  gi|518652935|ref|YP_008142455.1| 297 IGIAELKTKIGSTGESKTNSEARLKTSREAYNFNREQLENKLKEKKNyesyLKGTENSIAKINRELEKFRQENYEns 373
                                       6999*******************************************66643567889*************999644 PP

                        OrfB_IS605  94 klathliktlkevgve 109
                                       kl++++ ++l ++ ve
  gi|518652935|ref|YP_008142455.1| 374 KLTREINDRLAAIDVE 389
                                       7999999999988887 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                        OrfB_IS605  44 rrlksdykylakeiaelqsklkks 67 
                                         lk++ k++++ei e+ +k    
  gi|518652935|ref|YP_008142455.1| 439 DNLKKNIKEYSEEINEVNKKFLTV 462
                                       357888888888888888876554 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.6
                        OrfB_IS605  41 ykgrrlksdykylakeiaelqsklkk 66 
                                       +k +++k ++++l ke++el +klk+
  gi|518652935|ref|YP_008142455.1| 749 FKKNEVKMQLFTLDKERKELFKKLKE 774
                                       56667777788888888887777765 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.7
                        OrfB_IS605  47 ksdykylakeiaelqsklkk 66 
                                        +++k ++++ +el+ k+ +
  gi|518652935|ref|YP_008142455.1| 808 ETEFKHFTEKSQELEEKITG 827
                                       33444444444444444333 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 ?    4.3   7.6     0.027        37      22     116 ..     136     229 ..     132     260 .. 0.69
   2 ?    3.6   1.3     0.047        64      57     101 ..     231     275 ..     225     281 .. 0.83
   3 ?   -0.6  16.8       0.9   1.2e+03      10     126 ..     254     375 ..     250     395 .. 0.80
   4 ?    3.8  11.0     0.039        54      34     118 ..     404     488 ..     396     509 .. 0.82
   5 ?    2.2   0.4      0.12   1.6e+02      95     122 ..     666     693 ..     660     699 .. 0.85
   6 ?   14.0  22.5   2.8e-05     0.038       2     140 .]     685     816 ..     684     816 .. 0.94
   7 ?   10.1  11.9   0.00044      0.61       4      97 ..     803     896 ..     800     901 .. 0.94
   8 ?    5.8   5.3    0.0095        13      49     116 ..     897     968 ..     894     999 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.027
                    CENP-F_leu_zip  22 LkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervse 98 
                                       L++ ++nL +   + ++++ + i   E+ k+ +e+ ++ i+ l+e+l+ + + L +++s  ++Le +  ++  + + 
  gi|518652935|ref|YP_008142455.1| 136 LQGDINNLVKMTGTEKRKLFESIAGIESYKERIESAQNDINGLNENLNSMDAVLLEIKSMLDTLEVDR-ENALKYNK 211
                                       78889999999999999999999999999999999999999999999999999999998888885543.33345555 PP

                    CENP-F_leu_zip  99 LeslnsslenlleekEqe 116
                                       L++   +l+ +l+ k  +
  gi|518652935|ref|YP_008142455.1| 212 LNKEVNELKFFLKVKDRD 229
                                       555555555555555555 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.047
                    CENP-F_leu_zip  57 lkeeieelaeelreleldLvalrsekeeLekelqkkqervseLes 101
                                       +++e+ + + + ++ ++d+++l +e+++L  +  +  +r++e e 
  gi|518652935|ref|YP_008142455.1| 231 INQELAMYNGNIEKSQSDIDNLENENKNLSIQRDEAINRIKEIED 275
                                       567777788889999999999999999999999999999999885 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.9
                    CENP-F_leu_zip  10 ekLKeserkadsLkdkvenLerelemse.enqekvileaEtskaevetlkeeieelaeelreleldLvalr....se 81 
                                       ++ K+   + d   ++++++e  l  ++ ++   +    E+    + +lk++i    e+ ++ e+ L++ r     +
  gi|518652935|ref|YP_008142455.1| 254 NENKNLSIQRDEAINRIKEIEDKLDAMGgQEVKGIRKRIEELNIGIAELKTKIGSTGESKTNSEARLKTSReaynFN 330
                                       555666677788889999999999765515566677788999999************************99666679 PP

                    CENP-F_leu_zip  82 keeLekelqkkqervseLeslnsslenlleekEqekvqmkeeska 126
                                       +e+Le++l++k++  s L+ ++ s+ ++ +e+E+ + + +e+sk 
  gi|518652935|ref|YP_008142455.1| 331 REQLENKLKEKKNYESYLKGTENSIAKINRELEKFRQENYENSKL 375
                                       **************************9999999886666666653 PP

  == domain 4  score: 3.8 bits;  conditional E-value: 0.039
                    CENP-F_leu_zip  34 emseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenll 110
                                        ++e++++   +e   + +++++   +++ l+ +  +l+ ++++ ++e +e++k+  + +++ +eL +++s     +
  gi|518652935|ref|YP_008142455.1| 404 RTIEQELSGFSRENTMNEEKIKEESIKVKDLKWKIDNLKKNIKEYSEEINEVNKKFLTVRNKLNELVTMKSNNDVEI 480
                                       5566666666666666667777777788899999999999999999************************9999999 PP

                    CENP-F_leu_zip 111 eekEqekv 118
                                       ++kE+e +
  gi|518652935|ref|YP_008142455.1| 481 RNKEKELR 488
                                       99999954 PP

  == domain 5  score: 2.2 bits;  conditional E-value: 0.12
                    CENP-F_leu_zip  95 rvseLeslnsslenlleekEqekvqmke 122
                                        + eLe+ n+ l++ ++ kE+e+ +++ 
  gi|518652935|ref|YP_008142455.1| 666 AIAELEEQNEILKSEISFKEKENSEISS 693
                                       68999****9999999999999988765 PP

  == domain 6  score: 14.0 bits;  conditional E-value: 2.8e-05
                    CENP-F_leu_zip   2 ekkklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLval 78 
                                       ek++ ++ +kL    rk d     ++n e +l++se++ e++++  E+ k +++  ++ + + + + +e +++L +l
  gi|518652935|ref|YP_008142455.1| 685 EKENSEISSKLADLTRKRDISTSNINNYETQLQESENSIEAAKTRIEEIKLKIKDAEDRKSNFEFKKNEVKMQLFTL 761
                                       799999*********************************************************************** PP

                    CENP-F_leu_zip  79 rsekeeLekelqkkqervseLeslnsslenlleekEqekvqmkeeskaaveeLqtqlkelne 140
                                        +e++eL k+l       +eL   n+++e+++ee+  ++++ +e++ +++ +++t+ k  +e
  gi|518652935|ref|YP_008142455.1| 762 DKERKELFKKL-------KELAPENVEIEKQMEEELGNEMKSRENYSSKLAQIETEFKHFTE 816
                                       *******8877.......58999999999999999999999999999999999999998776 PP

  == domain 7  score: 10.1 bits;  conditional E-value: 0.00044
                    CENP-F_leu_zip   4 kklhvlekLKeserkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrs 80 
                                       k  +++ ++K   +k+  L++k+ +Le e+        + +  +E   +e+e+ +++ +e+ ++ rel ++ ++++ 
  gi|518652935|ref|YP_008142455.1| 803 KLAQIETEFKHFTEKSQELEEKITGLENEITKFTGMVAEFKNKVEAMEKELEENRAKENEIDSRSRELYTEKNQVST 879
                                       778999*********************************************************************** PP

                    CENP-F_leu_zip  81 ekeeLekelqkkqervs 97 
                                        +++L ++++k+ + +s
  gi|518652935|ref|YP_008142455.1| 880 ARDKLFENIRKNDDLIS 896
                                       *****999998877666 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.0095
                    CENP-F_leu_zip  49 tskaevetlkeeieelaeelreleldLvalrsekeeLekelqkkqervse....LeslnsslenlleekEqe 116
                                       ++ka + +lk++ie+la +l+ ++ +++++  e  e + ++ + +++++e     e+l     + +e+  +e
  gi|518652935|ref|YP_008142455.1| 897 NKKAIIAGLKTKIENLAFQLETINYEIENTGMEYIEFNMSISEVKQKIDEnsreIEKLGAVNMKAIEQYDME 968
                                       678889999999999999999999999999977777777777777776541111344444444444444444 PP

>> DUF4407  Domain of unknown function (DUF4407)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   2.9     0.017        23     131     239 ..     164     276 ..     134     281 .. 0.61
   2 ?    6.8  10.5    0.0027       3.7     106     227 ..     271     398 ..     270     419 .. 0.78
   3 ?    5.2   3.7    0.0082        11     107     173 ..     378     476 ..     376     546 .. 0.68
   4 ?    5.0  11.2    0.0098        14     127     208 ..     659     761 ..     648     789 .. 0.73
   5 ?    4.8  15.2     0.011        15     114     230 ..     783     913 ..     769     988 .. 0.75
   6 ?    0.2   0.6      0.27   3.7e+02     131     197 ..     933     995 ..     914    1027 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.017
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaake........kkaqldaaqael 199
                                       ++++++ ++++i+ l++++++ +a l + +  ++  l+ ++ +  +    + +  ke        k ++ d++++el
  gi|518652935|ref|YP_008142455.1| 164 YKERIESAQNDINGLNENLNSMDAVLLEIKSMLD-TLEVDRENALK----YNKLNKEvnelkfflKVKDRDRINQEL 235
                                       7777777777777777777777776655444444.33322222211....111111122344555788888888888 PP

                           DUF4407 200 aelkakld.atarlaalraelaeleaerakeraasqaaaaa 239
                                       a ++++++ +++++++l++e + l  +r++++++ ++ +++
  gi|518652935|ref|YP_008142455.1| 236 AMYNGNIEkSQSDIDNLENENKNLSIQRDEAINRIKEIEDK 276
                                       88888887788888888888888888888887776665554 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0027
                           DUF4407 106 keIdaelaeeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkg 182
                                       keI+ +l+++  +e+k ++++++ +l+  +ael+++i +  +  ++ earl++ r++++ + ++   ++ + ++ ++
  gi|518652935|ref|YP_008142455.1| 271 KEIEDKLDAMGGQEVKGIRKRIE-ELNIGIAELKTKIGSTGESKTNSEARLKTSREAYNFNREQ-LENKLKEKKNYE 345
                                       79999999999999999999988.79999******************************99996.67788999**** PP

                           DUF4407 183 paakekkaqldaaqaelaelkakld........atarlaalraelaeleaera 227
                                        + k  ++ ++++++el++++++           ++rlaa + e+++++++++
  gi|518652935|ref|YP_008142455.1| 346 SYLKGTENSIAKINRELEKFRQENYenskltreINDRLAAIDVEMQQANDQII 398
                                       ***********************434444444433334444444443333333 PP

  == domain 3  score: 5.2 bits;  conditional E-value: 0.0082
                           DUF4407 107 eIdaelaeeqqeeakelkeqlaaa................................ltaelaeleaqiaalqaeida 151
                                       eI+ +la+++ e+++++++ +++                                 l+ ++++l+++i++ ++ei++
  gi|518652935|ref|YP_008142455.1| 378 EINDRLAAIDVEMQQANDQIINDYdirtieqelsgfsrentmneekikeesikvkdLKWKIDNLKKNIKEYSEEINE 454
                                       78888888888888888555555588888888888888888855555555555555666666666666666666666 PP

                           DUF4407 152 aearldalraeaqkeldgtkgt 173
                                        ++++ + r+++++ ++ ++++
  gi|518652935|ref|YP_008142455.1| 455 VNKKFLTVRNKLNELVTMKSNN 476
                                       6666666666666555554422 PP

  == domain 4  score: 5.0 bits;  conditional E-value: 0.0098
                           DUF4407 127 laaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqaelaelk 203
                                       la+  t+ +aele+q++ l++ei+ +e++ ++   ++++ +       t++++ +++  +e ++ ++aa+++++e+k
  gi|518652935|ref|YP_008142455.1| 659 LANRITKAIAELEEQNEILKSEISFKEKENSEISSKLADLTRKRD-ISTSNINNYETQLQESENSIEAAKTRIEEIK 734
                                       566799**********************99999999986655444.34456999*********************** PP

                           DUF4407 204 akld......................a 208
                                        k++                       
  gi|518652935|ref|YP_008142455.1| 735 LKIKdaedrksnfefkknevkmqlftL 761
                                       **9976666655555555544433332 PP

  == domain 5  score: 4.8 bits;  conditional E-value: 0.011
                           DUF4407 114 eeqqeeakelkeqlaaaltaelaeleaqiaalqaeidaaearldalraeaqkeldgtk...gtgttgvaGkgpaake 187
                                       e+q ee+  ++ + +++++++la++e++ +   ++ +++e++++ l++e + + +g     +++ ++++ + ++ ++
  gi|518652935|ref|YP_008142455.1| 783 EKQMEEELGNEMKSRENYSSKLAQIETEFKHFTEKSQELEEKITGLENEIT-KFTGMVaefKNKVEAMEKELEENRA 858
                                       333344444444444558888888888888777777777777777777777.4455446777777888888888888 PP

                           DUF4407 188 kkaqldaaqaelaelkakld............atarlaalraelaeleaeraker 230
                                       k++++d +++el + k++++            +++ +++++a +a+l++++++ +
  gi|518652935|ref|YP_008142455.1| 859 KENEIDSRSRELYTEKNQVStardklfenirkNDDLISNKKAIIAGLKTKIENLA 913
                                       8888888888888888888887777777777767777777777777777766654 PP

  == domain 6  score: 0.2 bits;  conditional E-value: 0.27
                           DUF4407 131 ltaelaeleaqiaalqaeidaaearldalraeaqkeldgtkgtgttgvaGkgpaakekkaqldaaqa 197
                                       ++  ++e +++i++ ++ei+++ a   ++ ++++ el+   +t+    + + +   ek++ +d +++
  gi|518652935|ref|YP_008142455.1| 933 FNMSISEVKQKIDENSREIEKLGAVNMKAIEQYDMELNKYNSTE----EKYKTLLSEKNDLIDLQNQ 995
                                       55566666666666666777666666666666666666533322....3344455555554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2700  (0.150594); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                       143  (0.0079759); expected 17.9 (0.001)
Passed Fwd filter:                       106  (0.00591221); 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: 3.01u 0.40s 00:00:03.40 Elapsed: 00:00:00.77
# Mc/sec: 4534.45
//
Query:       gi|518652936|ref|YP_008142456.1|  [L=540]
Description: hypothetical protein FACI_IFERC00001G1575 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-16   59.6   0.1    2.7e-15   57.1   0.0    2.2  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.095   1.7e+03     126     140 ..     125     139 ..      69     166 .. 0.59
   2 !   57.1   0.0   1.5e-19   2.7e-15       2     165 ..     214     394 ..     213     396 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.095
                                       HHHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxx RF
                       Radical_SAM 126 tfeevlealeklrea 140
                                        fee+ ++++kl+++
  gi|518652936|ref|YP_008142456.1| 125 YFEELADVVRKLKQK 139
                                       234444444444444 PP

  == domain 2  score: 57.1 bits;  conditional E-value: 1.5e-19
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS........TTHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly........pdfvellerl 70 
                                        vtrgC+++CsfC+++      +++r++++e++++e+  +  ++g k + +  ++ +ly         d ++ l+  
  gi|518652936|ref|YP_008142456.1| 214 QVTRGCPRGCSFCSITP-----ETYRTIPMENVEAEASLY-LKNGYKDIEFITDDIMLYgqkkltvnHDAIVNLFST 284
                                       79**************5.....9*****************.7999**************777777774444444444 PP

                                       HHTC........CCTEEEEEEECSSCHGHHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHT...CTSHHHHHHHHHHH CS
                                       xxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx RF
                       Radical_SAM  71 akla........vpgiritvetngtlpdeeklerllelgvdrvslgleaaddekvlklmn...rghtfeevlealek 136
                                       +k+         +     +++++ tl +   +  l+e+g     +gle+++ +  +k+mn    ++ +e++++++ k
  gi|518652936|ref|YP_008142456.1| 285 VKKMgaryltfpHISAPAVLVSPDTLFEISEIGGLKEYGAEAPVVGLETGSTKIMHKYMNakpYPWKPEDWKDVIVK 361
                                       4443666666555577778888888888********************************95555555777777777 PP

                                       HHHTTSET....EEEEEEEBTTTSHHHHHHHHH CS
                                       xxxxxxxx....xxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM 137 lreagikr....vvdrivglpGendeeleelle 165
                                       +++ +       ++++++g p e++e+l++ ++
  gi|518652936|ref|YP_008142456.1| 362 ATSIMNQAsvfpCYTMTIGYPEETEEDLQQSID 394
                                       777652224444*****************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (540 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      604  (0.0336884); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3708.44
//
Query:       gi|518652937|ref|YP_008142457.1|  [L=60]
Description: hypothetical protein FACI_IFERC00001G1576 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00083   19.2   0.1        0.1   12.5   0.1    2.1  1  DUF3072   Protein of unknown function (DUF3072)
  ------ inclusion threshold ------
      0.019   14.9   0.1      0.027   14.5   0.0    1.3  1  GUN4_N    ARM-like repeat domain, GUN4-N terminal


Domain annotation for each model (and alignments):
>> DUF3072  Protein of unknown function (DUF3072)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.1   1.1e-05       0.1      13      55 ..       6      48 ..       5      60 .] 0.60

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.1e-05
                           DUF3072 13 ePmTgaQaSYLktLaeeAgeedavdedltkAeASerIdeLqek 55
                                      e +T++Q S+++ L ++ +e++++ +d  k      I+eL +k
  gi|518652937|ref|YP_008142457.1|  6 ENITKKQLSFVNDLIKRGEENQKIVDDYVKSLKKGSIEELSKK 48
                                      6678888888888888888887766655444444444444333 PP

>> GUN4_N  ARM-like repeat domain, GUN4-N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-06     0.027      22      51 ..       9      38 ..       2      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-06
                                      CCCHHHHHHHHCTSHHHHHHHHHHHHHHHS CS
                            GUN4_N 22 ekkqlqaiaqLakaGeeGleiLqeFLlksq 51
                                       kkql  + +L+k Gee ++i  ++ ++ +
  gi|518652937|ref|YP_008142457.1|  9 TKKQLSFVNDLIKRGEENQKIVDDYVKSLK 38
                                      79***********************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1349  (0.0752412); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 404.71
//
Query:       gi|518652938|ref|YP_008142458.1|  [L=329]
Description: hypothetical protein FACI_IFERC00001G1577 [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  154.3   0.0    5.5e-45  153.9   0.0    1.1  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.9   0.0   3.1e-49   5.5e-45       6     290 ..      28     317 ..      25     319 .. 0.94

  Alignments for each domain:
  == domain 1  score: 153.9 bits;  conditional E-value: 3.1e-49
                                       -EEEEEEETSSS-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHT CS
                      tRNA-synt_1b   6 lrvysGidPTgklHlGylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldp 82 
                                         +y G++P+g +H++ l+ ++k+ el k g +v +l+aD+hA ++d+   +   +rk+ e l ++   +l +gl +
  gi|518652938|ref|YP_008142458.1|  28 SEAYIGFEPSGLPHIAILIYVNKINELVKLGFNVKVLLADWHARVNDKLGGDIDLIRKSGETLRKS---MLYAGL-L 100
                                       679**********************************************99***************...*****8.5 PP

                                       TTEEEEETHHHHTTHHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGG CS
                      tRNA-synt_1b  83 ekaevvlqsewlehlelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsD 159
                                       e +++++ ++  ++ +++ell + +k  sl r+ +   ++ r ee+ +  ++  +Ypl+q  D+++l++d+ +gG+D
  gi|518652938|ref|YP_008142458.1| 101 EGVQFIWATDLVANPDYWELLLQTAKNSSLLRIRRSLPIMGRTEEDADKDFSKYIYPLMQVTDVFYLNSDIAIGGTD 177
                                       68*******************************************76889*************************** PP

                                       GHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSS......SBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTT CS
                      tRNA-synt_1b 160 QkqnielgrdlarrfnkkevfkkpegltvplltgldGe......kKmSKSagnsaIfLddekesvkkkiqkavtdsd 230
                                       Q+    l+rd+a+++++k    kp  l +pl+ +l+G+      kKmSKS++ sa+fL+d++e+++ ki++a++  +
  gi|518652938|ref|YP_008142458.1| 178 QRHAYMLARDIAEKMGRK----KPILLEMPLIASLKGKgrmddfKKMSKSDPDSALFLTDSEEDIRRKIKNAFCPMG 250
                                       *****************9....*********99999987777778*****************************998 PP

                                       C..SHHHHHHHHHTHHH.....CHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHHHHHH CS
                      tRNA-synt_1b 231 e..evekllklktelsn.....elierleavsgkkpkreaeellaeevtklvhggdlkkalaealne 290
                                          ++     +k+++++      +i+r e ++g  +  ++ el+ ++ + ++h++dlkkal++ l++
  gi|518652938|ref|YP_008142458.1| 251 IvdGNPVIDIIKYVIFPyyateIEINRPESHGGPYTIHSFGELESKYLNSEIHPMDLKKALTQILIN 317
                                       88899999999999999999777888888888888899***********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       426  (0.0237604); 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:                         1  (5.57756e-05); expected 0.2 (1e-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: 2289.75
//
Query:       gi|518652939|ref|YP_008142459.1|  [L=92]
Description: hypothetical protein FACI_IFERC00001G1578 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.035   14.6   0.4      0.081   13.5   0.2    1.7  2  Ribosomal_L25p  Ribosomal L25p family


Domain annotation for each model (and alignments):
>> Ribosomal_L25p  Ribosomal L25p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.095   1.7e+03      46      56 ..      17      29 ..       4      50 .. 0.51
   2 ?   13.5   0.2   4.5e-06     0.081      28      70 ..      50      91 ..      36      92 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.095
                                      HCH....CSEEEEE CS
                    Ribosomal_L25p 46 llkt...stlieLe 56
                                      l+ +   +++++++
  gi|518652939|ref|YP_008142459.1| 17 LV-KmdnNYMLTIK 29
                                      22.13444444443 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 4.5e-06
                                      ESSSCEEEEEEEHHHHHHHCH.CSEEEEEETT.CEEEEEEEEEE CS
                    Ribosomal_L25p 28 GggkepisisvdakelrkllktstlieLevdg.ekvllkdvqrh 70
                                       +g  + +++vd+k+l+k +  +++ieLe  + +kv++ + + h
  gi|518652939|ref|YP_008142459.1| 50 EEGFRNENFTVDEKDLKKTM--KEIIELEYPRsHKVMVSEQELH 91
                                      44556999************..9*******9778***9997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 689.85
//
Query:       gi|518652940|ref|YP_008142460.1|  [L=339]
Description: hypothetical protein FACI_IFERC00001G1579 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    5.9e-26   90.7   0.0    1.4e-25   89.4   0.0    1.7  1  XPG_I       XPG I-region
      4e-17   62.5   0.0      7e-17   61.8   0.0    1.4  1  XPG_N       XPG N-terminal domain
    2.9e-06   27.8   0.6      6e-06   26.8   0.0    1.9  2  5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
     0.0024   17.9   0.0     0.0057   16.7   0.0    1.6  1  HHH_2       Helix-hairpin-helix motif
  ------ inclusion threshold ------
       0.14   12.8   0.7       0.41   11.3   0.1    2.1  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 !   89.4   0.0   3.9e-29   1.4e-25       2      94 .]     141     236 ..     140     236 .. 0.92

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 3.9e-29
                                       HHT--EEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESTT..ECECTT....EEECEEEEEEHHHHHH CS
                             XPG_I   2 lmgipyvvApgEAEAqcayLqkkglvdaviseDsDlllFGapkvlrnls.kkkskkk..kekekkkvevidlekvlk 75 
                                       +mg+p+v+Ap+E+EAq++y+ k g vd vis+D+D+ll+Ga++vlrn++  +++  +   +  + ++e+idl++ l+
  gi|518652940|ref|YP_008142460.1| 141 MMGVPWVQAPSEGEAQASYMSKVGAVDSVISQDYDCLLLGARRVLRNFTmYGRRRISgtGKFINITPEIIDLKENLD 217
                                       79**********************************************954444333777778999*********** PP

                                       HHT--HHHHHHHHHHHCET CS
                             XPG_I  76 elgltreqlidlaillgcD 94 
                                       +lg+t++qli + il+g+D
  gi|518652940|ref|YP_008142460.1| 218 NLGITQDQLIGIGILVGTD 236
                                       *****************99 PP

>> XPG_N  XPG N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.8   0.0     2e-20     7e-17      13     100 ..      12     100 ..       1     101 [. 0.91

  Alignments for each domain:
  == domain 1  score: 61.8 bits;  conditional E-value: 2e-20
                                       H-GEEEEEGGGGTTEEEEEEHHHHHHHHHHHSE.ETTEE-BS.....-HHHHHHHHHHHHHHHTTEEEEEEE--S-- CS
                             XPG_N  13 vaairsvsiealegkklaiDaslwlyrfliavreqlgnalen.....tshlmglfsrllrlldfgikPifVFdgkap 84 
                                       +    + si++  g ++ iDa   +y+fl ++r ++g+ l+      tshl g+f+r+  ll+++ikP++ Fdgk+ 
  gi|518652940|ref|YP_008142460.1|  12 H----QTSIRENGGITVSIDAFNIIYQFLSSIRGEDGEPLKDehgniTSHLSGIFYRTATLLENNIKPVYSFDGKPY 84 
                                       3....4788999999************************9999999******************************* PP

                                       GGGHHHHHHHHHHHHH CS
                             XPG_N  85 dlkkeelekrserrqe 100
                                        lk e+l+ r++++++
  gi|518652940|ref|YP_008142460.1|  85 RLKDETLKERKAIKEK 100
                                       ************9976 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 ?   -2.6   0.1       2.4   8.5e+03      59      65 ..     106     112 ..      83     135 .. 0.51
   2 !   26.8   0.0   1.7e-09     6e-06      12      58 ..     232     271 ..     221     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2.4
                        5_3_exonuc  59 kLeenke 65 
                                       +L+ +++
  gi|518652940|ref|YP_008142460.1| 106 NLAMENK 112
                                       2322222 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.7e-09
                        5_3_exonuc  12 LvGDssDnipGvpgiGektAakLlkeygsleeilenldelkekklke 58 
                                       LvG  +D  pG++giG+kt  +L+k+yg++e++l++ ++     + +
  gi|518652940|ref|YP_008142460.1| 232 LVG--TDFNPGIRGIGAKTGLSLIKKYGDIESVLKQKNK-----TID 271
                                       555..4666**************************5542.....222 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.6e-06    0.0057       7      43 ..     240     276 ..     237     279 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.6e-06
                             HHH_2   7 GIrhVGektAklLakrFksldaLkkasleeLlevddi 43 
                                       GIr +G+kt   L k++++++   k + +++ ++d+i
  gi|518652940|ref|YP_008142460.1| 240 GIRGIGAKTGLSLIKKYGDIESVLKQKNKTIDNLDEI 276
                                       9**********************99999999999988 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       2.2   7.9e+03      48      51 ..     114     117 ..      93     139 .. 0.60
   2 ?   11.3   0.1   0.00011      0.41       6      41 ..     240     277 ..     239     279 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.2
                                       HHHH CS
                             HHH_5  48 Aeri 51 
                                       Ae+i
  gi|518652940|ref|YP_008142460.1| 114 AEKI 117
                                       3333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
                                       TSTT--HHHHHHHHTTT--SHHHHHHS...-HHHHHTST CS
                             HHH_5   6 svsGiGpktAlallsaGiesvedlaaa...dveeLakip 41 
                                       ++ GiG+kt l+l+++ ++ +e ++++   +++ L +i+
  gi|518652940|ref|YP_008142460.1| 240 GIRGIGAKTGLSLIKK-YGDIESVLKQknkTIDNLDEIK 277
                                       589*************.7777766554222666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       969  (0.0540465); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2406.64
//
Query:       gi|518652941|ref|YP_008142461.1|  [L=258]
Description: DNA repair and recombination protein RadB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-21   75.9   0.0    3.8e-21   75.5   0.0    1.1  1  Rad51     Rad51
    1.1e-05   24.9   1.3      7e-05   22.3   1.3    1.9  1  ATPase    KaiC
    0.00086   18.9   0.2     0.0017   17.9   0.2    1.7  1  RecA      recA bacterial DNA recombination protein
     0.0049   16.5   0.0     0.0069   16.1   0.0    1.3  1  Zot       Zonular occludens toxin (Zot)
      0.005   16.6   0.0     0.0081   15.9   0.0    1.4  1  AAA_24    AAA domain
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.055   13.0   0.0    1.7  1  AAA_25    AAA domain
      0.064   13.8   0.4       0.16   12.5   0.4    1.8  1  ABC_tran  ABC transporter


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 !   75.5   0.0   1.5e-24   3.8e-21      21     252 ..      37     254 ..      22     256 .. 0.80

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.5e-24
                                       -S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT- CS
                             Rad51  21 tGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykl 97 
                                        G   +D+l++GG+e g ite +Ge ++Gk+ l++  ++ +     ++G  + a+yid+eg f  er  +ia+    
  gi|518652941|ref|YP_008142461.1|  37 SGYPCIDKLMEGGLEPGIITEFYGEGGAGKSNLAMIYSISAL----KNG--NSAIYIDSEG-FSVERFRSIANG--- 103
                                       577789**************************9998887652....334..579*****96.9*********74... PP

                                       -HHHHGGGEEEEE--STTHHHHHHHHTHHHH.....HHS-EEEEEEETTTGGGCH-------THHHHHHHHHHHHHH CS
                             Rad51  98 dkeevlenvayaRaytiehqeellqqaaall.....aedkfallivDsvtalyRtdfsgrgelakRqqklgkllrtL 169
                                        + e+++++ + R+ + ++q+  l +  +l+     +++ f++++vDs t+ +R++ +g+ + ++R +   k l+ L
  gi|518652941|ref|YP_008142461.1| 104 -DMELINHMNIYRVKSLDDQYLALIKSDKLIgekreSKNSFGIMVVDSFTNFFRME-AGK-DASARMEGYEKQLNIL 177
                                       .5678888999999999888766665555551111145679**************9.455.5699************ PP

                                       HHHHHHH--EEEEEEE-------.------------HHHHHHHH-SEEEEEEE-STTEEEEEEES-SSS-S-E.EEE CS
                             Rad51 170 rkladefevavvitnqvvaqvdgqaalfsadpkkPigGlvlahasttRlalrkgkgeeRivkvvdsPnlpele.avf 245
                                       + +a ++++ vvitnq+ ++v+         +  P gG  + ha++    + k  g  R + v +  ++ e   + f
  gi|518652941|ref|YP_008142461.1| 178 SGIALKYKIPVVITNQIYEDVNN-------STLEPFGGFFIDHAMKAIYRIEKFSGGMRRITVEKHRSIREGSyTGF 247
                                       ********************999.......56689999999999999999999888888777777666666441346 PP

                                       EEETTEE CS
                             Rad51 246 aigeeGi 252
                                        i ++Gi
  gi|518652941|ref|YP_008142461.1| 248 RIVDSGI 254
                                       6666666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   1.3   2.7e-08     7e-05       3     209 ..      37     240 ..      35     257 .. 0.59

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.7e-08
                            ATPase   3 tgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdleklee 79 
                                       +g + +D++++gG+  g ++  +Ge G+GK+ +a+ + i+ +++ g+  +++  e  +++  +++++ +++   l +
  gi|518652941|ref|YP_008142461.1|  37 SGYPCIDKLMEGGLEPGIITEFYGEGGAGKSNLAMIYSISALKN-GNSAIYIDSEGFSVERFRSIANGDME---LIN 109
                                       577889**********************************9999.*******8887775544444444443...333 PP

                            ATPase  80 egklaiidasesaeesaeekdkedleelieelaeaikeikakrvviDsitgl..ayeekeavaR.....eilrqlvr 149
                                       + +++ +    ++          + ++li e +e  +++++  +v+Ds t++  ++  k+a aR     ++l  l  
  gi|518652941|ref|YP_008142461.1| 110 HMNIYRVKSLDDQYL-----ALIKSDKLIGEKRESKNSFGI--MVVDSFTNFfrMEAGKDASARmegyeKQLNILSG 179
                                       334444444444443.....345556666665555555554..6777777776555555666663333234444555 PP

                            ATPase 150 vlkklgvTailvsekssseeaaggygveefivdgvivLdlkeiee.elvRtleivkmRgtk 209
                                       +  k+++  ++++++ ++ ++ +      f +d +++  ++ ++     R + + k R+ +
  gi|518652941|ref|YP_008142461.1| 180 IALKYKIPVVITNQIYEDVNNSTLEPFGGFFIDHAMKAIYRIEKFsGGMRRITVEKHRSIR 240
                                       5566777777777766633333333333344444444333333222456666677766655 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   6.5e-07    0.0017      37      90 ..      38      90 ..      23     208 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.5e-07
                                      S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS CS
                              RecA 37 GslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidae 90
                                      G   +d  +  GGl  G i+e yG   +Gk+ la+    +a k+g+ a +id+e
  gi|518652941|ref|YP_008142461.1| 38 GYPCIDKLME-GGLEPGIITEFYGEGGAGKSNLAMIYSISALKNGNSAIYIDSE 90
                                      5566776555.9****************************************99 PP

>> Zot  Zonular occludens toxin (Zot)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   2.7e-06    0.0069       5     101 ..      58     163 ..      54     209 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.7e-06
                               Zot   5 vtGapGsgKtsgavkkdllpalkegRkiitnidGlrlerieqvlgekvs...tarlirid....npegaetlkefak 74 
                                       ++G++G+gK+  a+   +   +     i+ + +G+ +er++ + + +++     ++ r++    + +   +++++  
  gi|518652941|ref|YP_008142461.1|  58 FYGEGGAGKSNLAMIYSISALKNGNSAIYIDSEGFSVERFRSIANGDMElinHMNIYRVKslddQYLALIKSDKLIG 134
                                       69**************99877778899999************99988887666778888864333333344444443 PP

                               Zot  75 watidkgal..lviDEcqeifpvrakegr 101
                                        ++  k+++  +v+D   ++f  +a++++
  gi|518652941|ref|YP_008142461.1| 135 EKRESKNSFgiMVVDSFTNFFRMEAGKDA 163
                                       33334776544899999999999988654 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   3.2e-06    0.0081       8      80 ..      59     157 ..      56     195 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3.2e-06
                            AAA_24   8 yGpsgiGKTtlakel.......gpkplfidtek.Glksldadkfpdie...........swedfldevvel...... 59 
                                       yG+ g+GK+ la  +       g+++++id e+ ++ +   +   d+e           s   + d++ +l      
  gi|518652941|ref|YP_008142461.1|  59 YGEGGAGKSNLAMIYsisalknGNSAIYIDSEGfSVERFRSIANGDMElinhmniyrvkS---LDDQYLALiksdkl 132
                                       9***********99999****************777777777777776877887775552...33333333555677 PP

                            AAA_24  60 ....aaeladyktlviDtideleel 80 
                                           ++ ++ + + v+D+ + + ++
  gi|518652941|ref|YP_008142461.1| 133 igekRESKNSFGIMVVDSFTNFFRM 157
                                       7887******************987 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.055      20     107 ..      40     115 ..      25     193 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                            AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravg. 94 
                                       p+ ++l++g l  g ++ ++G +g+GK+ la+  +++ +  G              +y++ E+      +R+r +  
  gi|518652941|ref|YP_008142461.1|  40 PCIDKLMEGGLEPGIITEFYGEGGAGKSNLAMIYSISALkNGN-----------SAIYIDSEGFS---VERFRSIAn 102
                                       88999****99*********************99999884443...........56677777666...344444332 PP

                            AAA_25  95 ealrddarllvld 107
                                        ++++  +  ++ 
  gi|518652941|ref|YP_008142461.1| 103 GDMELINHMNIYR 115
                                       5555555555554 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.4   6.2e-05      0.16       7      42 ..      49      83 ..      44     233 .. 0.55

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                                      EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGei 42
                                       l++g ++ + Ge GaGKS L++ ++  +  ++G+ 
  gi|518652941|ref|YP_008142461.1| 49 GLEPGIITEFYGEGGAGKSNLAM-IYSISALKNGNS 83
                                      78999**************9875.555555555543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.47
# Mc/sec: 1639.15
//
Query:       gi|518652942|ref|YP_008142462.1|  [L=148]
Description: hypothetical protein FACI_IFERC00001G1581 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.057   13.1   0.0      0.072   12.8   0.0    1.3  1  SUD-M     Single-stranded poly(A) binding domain
        2.6    8.3   9.6        4.3    7.6   9.6    1.4  1  DUF3784   Domain of unknown function (DUF3784)


Domain annotation for each model (and alignments):
>> SUD-M  Single-stranded poly(A) binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.1e-06     0.072      64     114 ..      61     118 ..      36     139 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.1e-06
                                       EEEESSS....EEEEE-TTS-HHHHHHHHCCCTS-EEES-...TTCCCCTB-HHHHHH CS
                             SUD-M  64 givdygv....rfffytskepvasiitklnslneplvtmp...igyvthgfnleeaar 114
                                       gi++ g+    +  fy  ke   si++k+n l     tmp   +  +   fn +e+a 
  gi|518652942|ref|YP_008142462.1|  61 GIMQTGLskieKGTFYIDKEKFISIMSKINDLVSSQGTMPefgLDAIYVDFNKQESAE 118
                                       444444411114569************************9533345666788888775 PP

>> DUF3784  Domain of unknown function (DUF3784)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   9.6   0.00048       4.3      46      90 ..       1      43 [.       1      47 [. 0.64

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00048
                           DUF3784 46 mgivllligilflllgllsaieseallii..aliviiiiviylivya 90
                                      m +v l ig++f+++++l    s +l i+  a+ ++ii++i++++y 
  gi|518652942|ref|YP_008142462.1|  1 MANVYLAIGVIFFIMSAL----SFTLGIYylAIPLLIIFLILMFLYY 43
                                      678999************....3334443114446666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1139  (0.0635284); expected 358.6 (0.02)
Passed bias filter:                      636  (0.0354733); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1056.19
//
Query:       gi|518652943|ref|YP_008142463.1|  [L=401]
Description: transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-31  107.9  45.8    4.9e-31  107.9  45.8    1.9  2  MFS_1       Major Facilitator Superfamily
    4.8e-15   55.4  14.9    4.8e-15   55.4  14.9    2.3  2  Sugar_tr    Sugar (and other) transporter
  ------ inclusion threshold ------
      0.029   13.7  23.6      0.038   13.3  23.6    1.2  1  MFS_4       Uncharacterised MFS-type transporter YbfB
       0.86    8.3   5.7        1.7    7.3   5.7    1.4  1  Presenilin  Presenilin


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 !  107.9  45.8   1.1e-34   4.9e-31      11     351 ..      21     344 ..       7     346 .. 0.84
   2 ?    2.6   4.8     0.011        51     127     297 ..     331     381 ..     328     395 .. 0.49

  Alignments for each domain:
  == domain 1  score: 107.9 bits;  conditional E-value: 1.1e-34
                             MFS_1  11 arsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw. 86 
                                       + ++++ ++   l ++++is  +++ll++l  +g +++ l lG lsd++G+rrv+ ++ +++a+++ +++f s+   
  gi|518652943|ref|YP_008142463.1|  21 DLTLVTYIYA-ELEKSYHISLGVVSLLFALGLIGRFFGGLYLGNLSDKIGARRVMAFSTAGYAIFAGVMAF-SPDVi 95 
                                       4444555555.8999**************************************************666667.66666 PP

                             MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg..Wravfyilaivs 161
                                       +l+ +r++qG+++g+ +++g  l  + +p + r   +g++++g+++G++l+ ++  l++  +   Wr  f+i + + 
  gi|518652943|ref|YP_008142463.1|  96 ILFSARFIQGIFMGGEWTSGTMLGYEFSPASIRQTIFGIIQSGYGIGYALTGIAYILFLPTIAvtWR-FFLITGSIP 171
                                       ***************************************************8888888877773455.466666666 PP

                             MFS_1 162 llafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevl 238
                                       l+ +      ++  p+++k+ +++e+     + +l++ +k+ l++      +i++ +ff +++++l++ p++  + +
  gi|518652943|ref|YP_008142463.1| 172 LIIAP---YTIMKIPHDNKKIRQAEK-----KINLRD-YKIPLAKS-----MIMMSGFFSAYFAILSFYPTI-ATSF 233
                                       66655...899999999999999999.....455555.55555555.....6666677779**********7.**** PP

                             MFS_1 239 glsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglg 315
                                       g + + ++g+++ +++l +a++++l+g+l+  +  +++l++a++ ++la++ la+  ++   +l++ ++v++++g g
  gi|518652943|ref|YP_008142463.1| 234 GVP-ASQIGIIMIISSLTVAAGFILFGKLAAIFR-KKYLIMAGSMIALAFAWLAVPYFSPIRFLAVPGMVVFSLGIG 308
                                       ***.8*************************9855.688888888888888888888888777777779999999999 PP

                             MFS_1 316 fvfpsllalasdlappeeagtasglfntags.lggal 351
                                         +p++  l++d + p  +g +sg+   +g+ +gg++
  gi|518652943|ref|YP_008142463.1| 309 S-MPIIPLLLMDRINPAVRGLISGVSYNFGAlFGGLI 344
                                       7.7**********************996666266655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.011
                             MFS_1 127 sagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkal 203
                                       ++++++Ga++g l++ ll                                                           
  gi|518652943|ref|YP_008142463.1| 331 GVSYNFGALFGGLISVLLG---------------------------------------------------------- 349
                                       3444555555555555555.......................................................... PP

                             MFS_1 204 lkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrllla 280
                                                                                                      +   +g    ll++
  gi|518652943|ref|YP_008142463.1| 350 --------------------------------------------------------------TIGGIVGYSQLLLII 364
                                       ..............................................................555554444444444 PP

                             MFS_1 281 llllllaalglallavt 297
                                        + +l+++l+++++++t
  gi|518652943|ref|YP_008142463.1| 365 DATTLVCLLAVFITGAT 381
                                       44444444444444444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.4  14.9   1.1e-18   4.8e-15      47     192 ..      42     183 ..       7     202 .. 0.87
   2 ?    1.4  19.3     0.025   1.1e+02     259     419 ..     208     361 ..     184     386 .. 0.65

  Alignments for each domain:
  == domain 1  score: 55.4 bits;  conditional E-value: 1.1e-18
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                        ++l++++ l+G+++G+l++g l+d++G + +++++++ + i a ++a+++    v +l+ +R++ Gi++G++ +  
  gi|518652943|ref|YP_008142463.1|  42 VVSLLFALGLIGRFFGGLYLGNLSDKIGARRVMAFSTAGYAIFAGVMAFSP---DVIILFSARFIQGIFMGGEWTSG 115
                                       467899999******************************************...9********************** PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS- CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflP 192
                                       +m+  E++p+++R ++ ++ q+++ +G  ++ i +  +  t + ++wr++l   ++p ++  + ++ +P
  gi|518652943|ref|YP_008142463.1| 116 TMLGYEFSPASIRQTIFGIIQSGYGIGYALTGIAYILFLPTIA-VTWRFFLITGSIPLIIAPYTIMKIP 183
                                       ******************************9999999966666.7************999988888888 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.025
                                       HHHHHHHHHTTHHHHHHHTTTHHHHSS-THH.HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 259 vvlqifqqltGinaimyysptifenlglsks.llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvil 334
                                        ++++  +++ ++ai+ + pti  + g+  s + + +i++ ++++a f+ +     + R++ l++ +++ a++f+ l
  gi|518652943|ref|YP_008142463.1| 208 SMIMMSGFFSAYFAILSFYPTIATSFGVPASqIGIIMIISSLTVAAGFILFGKLAAIFRKKYLIMAGSMIALAFAWL 284
                                       57888888999999999999999999999994333444455555555666555555667777777767777777777 PP

                                       H..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHH..HHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                          Sugar_tr 335 givalllvakskaasivaivfialfialfalgwgpvpw..vlvsElfpqsvRskalaiavavnwlanflisllfpii 409
                                       +    ++ +    + ++a+ ++++f    +lg+g++p   +l+ +   ++vR++ + ++++   l+  lis+l  +i
  gi|518652943|ref|YP_008142463.1| 285 A---VPYFSP---IRFLAVPGMVVF----SLGIGSMPIipLLLMDRINPAVRGLISGVSYNFGALFGGLISVLLGTI 351
                                       5...455555...356666666555....455554443116888999999999999999999999999999887777 PP

                                       HCHHHT-HHH CS
                          Sugar_tr 410 teaigggyvf 419
                                        + +g     
  gi|518652943|ref|YP_008142463.1| 352 GGIVGYSQLL 361
                                       6655532333 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3  23.6   8.4e-06     0.038      19     356 ..      32     370 ..      24     383 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 8.4e-06
                             MFS_4  19 llaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagllatvllllamaltesfaaflliRflaGvas 95 
                                       l +  ++sl+ ++ll a  ++G + G l       +  +R ++  ++   ++ +  ma+   +++++ +Rf+ G+  
  gi|518652943|ref|YP_008142463.1|  32 LEKSYHISLGVVSLLFALGLIGRFFGGLYLGNLSDKIGARRVMAFSTAGYAIFAGVMAFSPDVIILFSARFIQGIFM 108
                                       55677899********************986666666677767777777777777899999**************** PP

                             MFS_4  96 AvvlvfgsslvlahaaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllp.. 170
                                       +     g++l  + + a+ r+++ +++ +G G+G a++g++ +l l + +      l+++ + +++    ++ +p  
  gi|518652943|ref|YP_008142463.1| 109 GGEWTSGTMLGYEFSPASIRQTIFGIIQSGYGIGYALTGIAYILFLPTIAVTWRFFLITGSIPLIIAPYTIMKIPhd 185
                                       ***************************************98777776666665689999999999999999999944 PP

                             MFS_4 171 raalreasaaaeaakaeqkslpllalllaYglaGfGYiitatFlvaiardgaggalle.allWllvGlaaivgvlvw 246
                                       +++ r+a+++ +      k+  +  ++++ g++  +Y ++  F + ia + +g+++ +   + ++  l++++g  + 
  gi|518652943|ref|YP_008142463.1| 186 NKKIRQAEKKINL--RDYKIPLAKSMIMMSGFFS-AYFAILSFYPTIATS-FGVPASQiGIIMIISSLTVAAGFILF 258
                                       4555566666555..4444444555666667775.7999***********.6666655156677789*******999 PP

                             MFS_4 247 lrvakrsglrralaaallie.avgvllsllspsplglivssvllGltflaitalvlqlarelappatrrllglmTas 322
                                        ++a+  + + ++ a  +i  a + l+     ++  l+v ++++    ++ +++   l    + pa+r l++ +   
  gi|518652943|ref|YP_008142463.1| 259 GKLAAIFRKKYLIMAGSMIAlAFAWLAVPYFSPIRFLAVPGMVVFSLGIGSMPIIPLLLMDRINPAVRGLISGVSYN 335
                                       99999999888777766665255555555556666777777665444455555444455556677777777777666 PP

                             MFS_4 323 fg.igQilGpllasllaeatgslalallvaaaalv 356
                                       fg ++  l  +l + +    g  +l l++ a  lv
  gi|518652943|ref|YP_008142463.1| 336 FGaLFGGLISVLLGTIGGIVGYSQLLLIIDATTLV 370
                                       65344445555666666666666666666666666 PP

>> Presenilin  Presenilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   5.7   0.00038       1.7      94     166 ..     210     282 ..     200     298 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00038
                        Presenilin  94 lilsslllLflvsglllaevlkaynipldyitlllllwnfgvvGviaifwkgplllqqaYlilisalmAlvfi 166
                                       +++s ++   +    ++ ++ + + +p   i +++++   +v   + +f k + + ++ Yli+ ++++Al f 
  gi|518652943|ref|YP_008142463.1| 210 IMMSGFFSAYFAILSFYPTIATSFGVPASQIGIIMIISSLTVAAGFILFGKLAAIFRKKYLIMAGSMIALAFA 282
                                       444444444555555666888899**********************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2816.41
//
Query:       gi|518652944|ref|YP_008142464.1|  [L=305]
Description: hypothetical protein FACI_IFERC00001G1583 [Ferroplasma acidarmanus fer1]
Scores for complete 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-39  133.6   0.0    8.3e-39  133.1   0.0    1.2  1  bact-PGI_C  Bacterial phospho-glucose isomerase C-terminal SI
    3.8e-08   33.3   0.2    1.6e-07   31.3   0.2    2.0  1  SIS         SIS domain
     0.0021   18.1   0.0     0.0073   16.3   0.0    1.9  2  SIS_2       SIS domain
  ------ inclusion threshold ------
       0.11   11.0   0.6       0.53    8.8   0.3    2.2  2  PGI         Phosphoglucose isomerase


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 !  133.1   0.0   1.9e-42   8.3e-39       3     152 .]     160     304 ..     158     304 .. 0.95

  Alignments for each domain:
  == domain 1  score: 133.1 bits;  conditional E-value: 1.9e-42
                                       -HHHHHHHHHTT..SEEEEE-..TT-THHHHHHHHHHHHTT----B---.SSHHHHHHHTTSS-GGGGTTEEEEEES CS
                        bact-PGI_C   3 npakqlAlelag..klpviygssellevaArRfknqlnenAKipafagvlpeanhneivgleaeeelkkrlrlvllr 77 
                                       ++ k+ A ++++  ++p+iyg s++++++A+R+k+q+nenAK++af++++pe+nhn+ + l ++   ++++ +  ++
  gi|518652944|ref|YP_008142464.1| 160 SDIKSEAFKIYEnsSIPIIYG-SKPFKSVAYRWKTQFNENAKTFAFYSYFPELNHNDTMPL-KSAYRRDEYLFYAFE 234
                                       67789999999999*******.***************************************.688999999999999 PP

                                       SHH........HHHHHHHHTTTSSEEEEE---SSSHHHHHHHHHHHHHHHHHHHHHHCT---S-TTTTHHHHH.. CS
                        bact-PGI_C  78 deeehprvkkraeivkelaeergvrvtevkaegesplerlaslillgDfvSvylAllrgvDPtpvpaIdelKeel 152
                                       +++   r+++r+ i++e++ e+   +t vk+  +   ++l++li+++D+ +++lAl r+vDPt+v++I+elK++l
  gi|518652944|ref|YP_008142464.1| 235 SDN--ARINQRIGITEEITGEQ---FTVVKSPSQDYFSKLFYLIHYADYLTYELALVRNVDPTDVSTIEELKKKL 304
                                       666..7*************977...***********************************************986 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.2   3.5e-11   1.6e-07       6      89 ..      27     103 ..      24     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 3.5e-11
                                       SEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSE CS
                               SIS   6 kriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergak 82 
                                       ++i++ G+G s+ +++ ++ ++ +i +i           +g+ + ++e++l+i++s+sg+t +++ ++e ak++ga+
  gi|518652944|ref|YP_008142464.1|  27 DNIVISGMGGSGIVGNIFQEYYTSIPVISIGD-------YGIPGFVNEKTLFIVVSYSGNTEETLSNVEDAKKKGAH 96 
                                       5899****************997665554333.......334558999***************************** PP

                                       EEEEESS CS
                               SIS  83 iiaITds 89 
                                       + aIT+ 
  gi|518652944|ref|YP_008142464.1|  97 VRAITSG 103
                                       *****64 PP

>> SIS_2  SIS domain
   #    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       2      22 ..       3      23 ..       2      39 .. 0.77
   2 !   16.3   0.0   1.6e-06    0.0073     102     138 .]      66     102 ..      63     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.57
                                      HHHHHHHHHHHHHHHSHHHHH CS
                             SIS_2  2 Ylaevteilerivetqaeaie 22
                                      +l+e++++ e+i+++++  i+
  gi|518652944|ref|YP_008142464.1|  3 FLDEIKNLKEQIKSKDKFDIN 23
                                      899999999999888877765 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 1.6e-06
                                       -TT-EEEEE-SS--SHHHHHHHHHHHHHT-EEEEEE- CS
                             SIS_2 102 kpgDvLlviSnsGnnavvveaaeaakergmkviAlts 138
                                       +++ +++v+S sGn +  +  +e ak++g+ v A+ts
  gi|518652944|ref|YP_008142464.1|  66 NEKTLFIVVSYSGNTEETLSNVEDAKKKGAHVRAITS 102
                                       56779*******************************8 PP

>> PGI  Phosphoglucose isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.3   0.00012      0.53     145     173 ..      64      92 ..       1     115 [. 0.74
   2 ?   -2.3   0.0      0.28   1.2e+03     125     140 ..     281     296 ..     273     303 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00012
                                       --GGGEEEEEE-SSS--HHHHHHHHHHHH CS
                               PGI 145 ldpettlfivasktfttaetllnaesake 173
                                       + +e+tlfiv+s    t+etl n e ak+
  gi|518652944|ref|YP_008142464.1|  64 FVNEKTLFIVVSYSGNTEETLSNVEDAKK 92 
                                       5679********************99986 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.28
                                       -EEEEE--SSHHHHHH CS
                               PGI 125 lkvafvsnvdgthiae 140
                                       +++a+v nvd+t++  
  gi|518652944|ref|YP_008142464.1| 281 YELALVRNVDPTDVST 296
                                       68999*******9963 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.30s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 1997.86
//
Query:       gi|518652945|ref|YP_008142465.1|  [L=615]
Description: hypothetical protein FACI_IFERC00001G1584 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-42  144.5  11.9    5.9e-42  144.0  11.9    1.1  1  FbpA       Fibronectin-binding protein A N-terminus (FbpA)
    9.4e-26   90.6   0.3    2.9e-25   89.0   0.0    2.1  2  NFACT-R_1  NFACT protein RNA binding domain
  ------ inclusion threshold ------
      0.035   14.1   0.0       0.09   12.7   0.0    1.6  1  DB_JBP1    Thymine dioxygenase JBP1 DNA-binding domain
       0.12   12.4   0.0       0.35   10.9   0.0    1.8  1  H2TH       Formamidopyrimidine-DNA glycosylase H2TH domain


Domain annotation for each model (and alignments):
>> FbpA  Fibronectin-binding protein A N-terminus (FbpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0  11.9   1.3e-45   5.9e-42      13     414 ..      18     401 ..       6     411 .. 0.82

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 1.3e-45
                                       HHHHTTXEEEEEEEEETTEEEEEEE.ETTEEEEEEEEXXTTTXEEEEXXXXXXXXSSXXHHHHHHHHHHTTXEEEEE CS
                              FbpA  13 qkellggridkiyqpekdelvltlr.anrgrhkLllsahpsyarihltekpkenpkeppnFcmlLRkyLkgarivsi 88 
                                        +++l++ i+k+yq++++e vl+++ ++ ++++  +s+    + i + + +k  p+e+++++ml Rk+L+ +riv i
  gi|518652945|ref|YP_008142465.1|  18 GDTILNSFIKKVYQVNQKEFVLQIYrSDVKKRDFFISL---NKGIGFYDAEK--PEEATQLSMLFRKQLSEKRIVGI 89 
                                       57899999*****************78888878*****...9*****88888..*********************** PP

                                       EEXTTSSEEEEEEEEEXTTSXEEEEEEEEEXXGGGXEEEEEETTTEEEEESSXBXXXSSXSXXBSTTXBXXXSXXXS CS
                              FbpA  89 eqlgfdRivelsiekrdElgdeeeytLivEimgrhSNiiLvdeenkIidaikhvspkqsrvReilpgekYelPpsqd 165
                                       eq++fdR+v++++ +          ++i+E++g  +N+iL+d ++kI+ a+++   k   +R+++ ge+Y +Pp+  
  gi|518652945|ref|YP_008142465.1|  90 EQINFDRVVRITLHTG--------QEIILELFGG-GNLILTD-NGKIVFAMEQHVYK---TRKVQIGEEY-IPPA-- 150
                                       ****************........999*******.******8.66899888888788...8*********.5666.. PP

                                       XBXTT.SXXH.HHHHHHHHHS.XXXHHHHHHHBTTXXHHHHHHHHTTXSSSH...............HHHHHHHHTX CS
                              FbpA 166 klnPl.eaeeleefkellskkekdlvkaLvkafqGlspllaeelleragldketsakelseedlerlyealqellee 241
                                        +nP  ++e+   f+ +l+k+++++vk+L++++ +l++++aee+l+ra+++k++  +e++ ++++ ly++++e++ e
  gi|518652945|ref|YP_008142465.1| 151 VINPVaDLET---FSGILDKSSASIVKTLATRV-NLGGEIAEEALYRANIEKDKMPSEIK-DQYQILYDSIMEIIGE 222
                                       6999856555...666666679***********.*******************9888886.58999*********99 PP

                                       XX....XXEE.....XSSSEESSXXTTXX.SSXXXXSXHHHHHHHHTTTXXX--SHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 242 leeekfepqlvlkeekpeefsvvplkslselekesfdslsealdeyYakkaerdrveqkrsdlekrveneleklekk 318
                                        +++    + +++   +e +s+v l+  ++    +f++++e +d y +   e+++ ++        ve+++e ++++
  gi|518652945|ref|YP_008142465.1| 223 SSKN---NAFYYEA--EELLSPVLLTAINKEPDVKFEDFNEGIDFYLKHYPENEKNKS-------SVERRIESQRRS 287
                                       9953...3445554..577777777777777789**********88777776665544.......566667777777 PP

                                       HHHHHHHHHCCGGH.....HHHHCCHH-----------------------.--................-------- CS
                              FbpA 319 lkklekelekaeka.....enyrligelltaylyaikkgmsevelenyydege................evtIpLdp 374
                                       +++++k ++  ++       n+ +++ l++ + +++k+++ e+   +y+d+                  +++I L+ 
  gi|518652945|ref|YP_008142465.1| 288 IEEFNKLMQVYNEFgnylkMNFPQLQKLINIIYNNVKRNTPEDF--KYMDM-DisdinpgkntfainynGTKIILNY 361
                                       77777766666655555778888999999999999988876542..23332.1223455668999999999****** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              FbpA 375 rkspsenAqkyfkkykKlkraveaveeqieetkeeleyle 414
                                       r s+ +n    f+ +k  k ++e++e++ieetk+ + + +
  gi|518652945|ref|YP_008142465.1| 362 RESAGNNINYVFNTAKDYKGKIEGAEKAIEETKKLIVKEK 401
                                       *********************************9886655 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 ?   -3.5   0.0       3.6   1.6e+04      61      87 ..     387     413 ..     377     414 .. 0.69
   2 !   89.0   0.0   6.5e-29   2.9e-25       2     104 ..     417     521 ..     416     526 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 3.6
                         NFACT-R_1  61 eelleeaaqlakanSiagnklssvdvv 87 
                                       e+++ee  +l++++ +++ k++ v+ +
  gi|518652945|ref|YP_008142465.1| 387 EKAIEETKKLIVKEKQKAGKKKRVKYW 413
                                       677888888887777774444477766 PP

  == domain 2  score: 89.0 bits;  conditional E-value: 6.5e-29
                         NFACT-R_1   2 vfwFkssdgylvimGkDkqeneelikkyleesdvwfhvdkessahvylrlsegeleeipeelleeaaqlakanSia. 77 
                                       ++wF+ss g ++++G+D+++ne+l+kk+++++d+++h+d  ++++++++ +eg   ei+ee+++ea+ + ++ S+a 
  gi|518652945|ref|YP_008142465.1| 417 YHWFISSSGNMIMAGRDAKTNEKLVKKHMSDDDIYVHADLYGAPSTVIK-HEGI--EITEETIKEACIFSISLSRAw 490
                                       69***********************************************.6666..8******************** PP

                         NFACT-R_1  78 gnklssvdvvyvpasnlsktap....ldtGs 104
                                        + + s ++++v++s++skt++    +++Gs
  gi|518652945|ref|YP_008142465.1| 491 PAGIGSGTAYWVYPSQVSKTPEsgefVSKGS 521
                                       *********************9566666665 PP

>> DB_JBP1  Thymine dioxygenase JBP1 DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0     2e-05      0.09     124     162 ..     249     286 ..     232     288 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 2e-05
                           DB_JBP1 124 lnvklkdfnfGGtrylkdmPeeeqerrlerkkrieearr 162
                                        +vk+ dfn G   ylk  Pe+e+++     +rie  rr
  gi|518652945|ref|YP_008142465.1| 249 PDVKFEDFNEGIDFYLKHYPENEKNKS-SVERRIESQRR 286
                                       579*******************99875.45668999998 PP

>> H2TH  Formamidopyrimidine-DNA glycosylase H2TH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   7.9e-05      0.35      39      81 ..     182     223 ..     157     230 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 7.9e-05
                                       --HHHHHHHHHHTT--TTSBGGGS-HHHHHHHHHHHHHHHHHH CS
                              H2TH  39 lGNiyadEvLfrakihPerlakslskeelellhqeikevlkea 81 
                                       lG  +a+E+L+ra i+ +++ ++++  +++ l+++i+e++ e+
  gi|518652945|ref|YP_008142465.1| 182 LGGEIAEEALYRANIEKDKMPSEIK-DQYQILYDSIMEIIGES 223
                                       67789******************97.589*********99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); 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: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 3944.81
//
Query:       gi|518652946|ref|YP_008142466.1|  [L=218]
Description: alpha/beta fold family hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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   52.0   0.2    3.4e-07   30.2   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    6.3e-09   35.4   0.0     0.0013   18.1   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
      1e-08   36.1   0.0     0.0018   18.9   0.0    2.0  2  Abhydrolase_6  Alpha/beta hydrolase family
    7.3e-05   22.8   0.0    0.00011   22.3   0.0    1.2  1  Abhydrolase_4  TAP-like protein
  ------ inclusion threshold ------
      0.015   15.1   0.0      0.019   14.8   0.0    1.2  1  Abhydrolase_2  Phospholipase/Carboxylesterase
      0.046   13.5   0.0      0.082   12.7   0.0    1.4  1  Abhydrolase_5  Alpha/beta hydrolase family
       0.15   11.6   0.0       0.26   10.8   0.0    1.4  1  VQ             VQ motif


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.1     7e-08   0.00018       4     116 ..      43     154 ..      41     156 .. 0.81
   2 !   30.2   0.0   1.3e-10   3.4e-07     201     257 .]     154     204 ..     147     204 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 7e-08
                                       EEE-STTTCGGGGTTGHHHHHHHHT...TSEEEEEEETTSTTSSSTTTGB....CHHSHHHHHHHHHHHHHHCTTSS CS
                     Abhydrolase_1   4 vilhGlpgssdvwaerglapaLakd...gfdvillDlrGvgySspapacin...ddygtasvaddldrildalgddk 74 
                                       ++lh  + +s++wa+   ++aL k    gf v+++D +G+g S++  + +    +  +    a +++ + ++l + +
  gi|518652946|ref|YP_008142466.1|  43 ILLHDSTTTSNSWAG---IDALRKIgqwGFNVYAPDFPGFGNSEANDSYNFgssP--SK--GALFIKDFAESLFLSS 112
                                       566666778999***...6688877888***************999885433221..22..35577788******** PP

                                       EEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHHHH CS
                     Abhydrolase_1  75 ltlvGhSmGGmialayaaeyperVkalvllgaidpaasliea 116
                                       +++vG S    +al  + +ype +++ + +g++   + l+e+
  gi|518652946|ref|YP_008142466.1| 113 INVVGPSVSAGVALKSLIDYPELINSSIIIGGLGVDHILNEL 154
                                       *******************************97666666665 PP

  == domain 2  score: 30.2 bits;  conditional E-value: 1.3e-10
                                       HHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHSH CS
                     Abhydrolase_1 201 llrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlaflegp 257
                                       l+r+++      p+l+++g+ D++vp +++ ++ +l+p+++ v+i +agH++++e+p
  gi|518652946|ref|YP_008142466.1| 154 LNRIDK------PVLILWGSRDNVVPVSHGLRYHDLIPSSTFVKINGAGHCVQIEKP 204
                                       344555......******************************************986 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   2.9e-06    0.0074      24     107 ..      61     142 ..      43     146 .. 0.83
   2 !   18.1   0.0   4.9e-07    0.0013     180     238 ..     147     203 ..     144     204 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2.9e-06
                       Hydrolase_4  24 aeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdk 100
                                        ++  + Gf+vya D  G+G+se +     +f +     a f++ ++e    + + ++G S+ + +al+ l +yp+ 
  gi|518652946|ref|YP_008142466.1|  61 LRKIGQWGFNVYAPDFPGFGNSEAND--SYNFGSSPSKGALFIKDFAESLFLSSINVVGPSVSAGVALKSLIDYPEL 135
                                       5677899***************6554..4788888888889998888888888999999999999999999999998 PP

                       Hydrolase_4 101 vaglils 107
                                       ++  i++
  gi|518652946|ref|YP_008142466.1| 136 INSSIII 142
                                       8866665 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 4.9e-07
                       Hydrolase_4 180 mkrleeraakitlPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHellnEp 238
                                       +++++++ ++i+ P+l+l G++D+vv+ +   ++++ ++s   t+  ++g+ H +  E+
  gi|518652946|ref|YP_008142466.1| 147 VDHILNELNRIDKPVLILWGSRDNVVPVSHGLRYHDLIPS--STFVKINGAGHCVQIEK 203
                                       688999*********************************7..89999999999988775 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   7.2e-07    0.0018       2      81 ..      43     127 ..      42     148 .. 0.66
   2 !   15.4   0.0   8.2e-06     0.021     165     217 ..     153     207 ..     144     210 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.2e-07
                                       EEE--GC.....GC.HHHHHHHHCCTCEEEEE--TTSTS-GGCS--HHH.......CHHH.HHHHCCTT..TTSEEE CS
                     Abhydrolase_6   2 lllHGagssassWl.vapLaallaagvhvlapDlpGhGrsdpppldled.......ladl.aalldelaagggpvvl 69 
                                       +llH + +++ sW+  + L++ +  g+ v+apD+pG+G ++ + ++++        +  +  +++++l      + +
  gi|518652946|ref|YP_008142466.1|  43 ILLHDSTTTSNSWAgIDALRKIGQWGFNVYAPDFPGFG-NSEANDSYNFgsspskgA-LFiKDFAESLF--LSSINV 115
                                       899999999999*7566777777777999*********.666666665543443331.22455555554..555578 PP

                                       EEETCHHHHHHH CS
                     Abhydrolase_6  70 vGHSlGGalala 81 
                                       vG S  + +al 
  gi|518652946|ref|YP_008142466.1| 116 VGPSVSAGVALK 127
                                       888877777777 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 8.2e-06
                                       HHTT-TTGCEEEC.TT-CHHHHCHHCCCH....STTEEETCE...SSS-HHHHSHHHH CS
                     Abhydrolase_6 165 awadlpvpllvlg.geDplvprllerlla....qagarlpvvlpgaGHlphleepdev 217
                                       ++ ++  p+l+l+ ++D +vp  + + l+    +++ ++ v + gaGH++++e+pd +
  gi|518652946|ref|YP_008142466.1| 153 ELNRIDKPVLILWgSRDNVVP--VSHGLRyhdlIPSSTF-VKINGAGHCVQIEKPDIF 207
                                       6778889999996599**999..8888884446666666.***************855 PP

>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.3   0.0   4.2e-08   0.00011      31      79 ..     155     203 ..     146     217 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 4.2e-08
                     Abhydrolase_4  31 akgaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaag 79 
                                       ++ ++pvL+l + rD+++P + + + ++ +++++ v  +g+GH++ +++
  gi|518652946|ref|YP_008142466.1| 155 NRIDKPVLILWGSRDNVVPVSHGLRYHDLIPSSTFVKINGAGHCVQIEK 203
                                       44579***************************************97755 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   7.3e-06     0.019      96     213 ..     102     215 ..      80     218 .] 0.77

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.3e-06
                                       HHHHTT--GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGGG-EEEEEEETT-SSS-H CS
                     Abhydrolase_2  96 aelkkgipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtkklpilqiHgeeDpvvpl 172
                                       +++++++  s i ++G S  a +al++ + +p+ +   ++++g  + ++  e   +++    p+l ++g+ D+vvp+
  gi|518652946|ref|YP_008142466.1| 102 KDFAESLFLSSINVVGPSVSAGVALKSLIDYPELINSSIIIGGLGVDHILNE--LNRID--KPVLILWGSRDNVVPV 174
                                       56777788899999*****************************988776544..56666..79************** PP

                                       HHHHHHHHHHHTTS-...GEEEEEETT--SS--HHHHHHHHHHH CS
                     Abhydrolase_2 173 algkaakevlkkllk...kvelksyeglaHsideeemqdikefl 213
                                       ++g + + ++ ++     ++  ++++    + +  ++++ik+f+
  gi|518652946|ref|YP_008142466.1| 175 SHGLRYHDLIPSSTFvkiNGAGHCVQ---IEKPDIFFNNIKKFI 215
                                       ****9998876544321444444444...334444555555555 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.2e-05     0.082      69     141 ..     124     198 ..      92     200 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.2e-05
                     Abhydrolase_5  69 vvasrfaaeeekiegvvflasYPe...kdelselskkvlsivgteDgvlnvkslekakkflpkdtkvvsieGgnha 141
                                       v+   ++   e i++ + ++        +el++  k+vl ++g++D+v++v++  + ++ +p   ++v+i+G  h+
  gi|518652946|ref|YP_008142466.1| 124 VALKSLIDYPELINSSIIIGGLGVdhiLNELNRIDKPVLILWGSRDNVVPVSHGLRYHDLIPSS-TFVKINGAGHC 198
                                       444455555566666666655544112367888999******************9999999975.6999***9995 PP

>> VQ  VQ motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.26      11      21 ..       3      13 ..       2      13 .. 0.92

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                                VQ 11 asnFRalVQrL 21
                                      ++nFR++VQ L
  gi|518652946|ref|YP_008142466.1|  3 PNNFRTIVQSL 13
                                      99*******87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       247  (0.0137766); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1537.17
//
Query:       gi|518652947|ref|YP_008142467.1|  [L=522]
Description: hypothetical protein FACI_IFERC00001G1586 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-26   92.6   0.0    4.9e-26   91.5   0.0    1.6  1  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
      0.074   13.4   0.0       0.16   12.3   0.0    1.5  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 !   91.5   0.0   5.5e-30   4.9e-26       4     245 ..     122     503 ..     119     512 .. 0.83

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 5.5e-30
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50   4 lllgilvvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakafl 80 
                                       + l++ vv+HE+ H++vA+++g+kv++++ +f                 ++p+G++V+ +++e            + 
  gi|518652947|ref|YP_008142467.1| 122 ASLVFAVVIHEMFHGIVARKHGIKVNSVGALF----------------FIIPIGAFVEPDEKE------------IM 170
                                       679999********************999999................99***********99............89 PP

                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXX................................................. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................. RF
                     Peptidase_M50  81 kkspwqrllivlAGplanfilailvfvv................................................. 108
                                       +++p+ r +i++AGp +n+i+a +++v+                                                 
  gi|518652947|ref|YP_008142467.1| 171 AADPVVRRRIIAAGPGINLIIAAICIVLlvfvmmpastpihsgvyvdnsttlysghaipkgmeitsygnlsgkqlnn 247
                                       99**********************99999************************************************ PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M50 109 ............................................................................. 108
                                                                                                                    
  gi|518652947|ref|YP_008142467.1| 248 lettsmitpglanitlfngktetngsvptgvaivdlisgcpaaaanvstdsiiynisdaghshiiynintlgdvldn 324
                                       ***************************************************************************** PP

                                       .........................................-EEECECTTTSCEE-SEEEC-....XXXXXXXXXXX CS
                                       .........................................xxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxx RF
                     Peptidase_M50 109 .........................................pkkskeseeekrgviGvspkp....vkkegllealk 140
                                                                                p + ++   +++++iGv+  +    +++ + l++l+
  gi|518652947|ref|YP_008142467.1| 325 itpgttinmtvltfhtgktvpayttytmktvstyhyyakndP-TANKAAYKDESFIGVQIDYsgigYESIDSLHSLV 400
                                       *****************************9999999888765.3334899999*********554444444444444 PP

                                       XXXXXXXXXXXXXXX.XXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxx.xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 141 egvektlkvvvltvk.algklitgklslk.tlggpisiaqlaseaaeaglssflqllalisvnLgilNLlPipvLDG 215
                                        g + +      t+   l +l    +sl+ +++ p   + +       g++++l+++++i + Lgi+N+lP+ +LDG
  gi|518652947|ref|YP_008142467.1| 401 FGGQLVGPNFYETLGlPLLGLSPIPASLShMFSTPFNSYIF------FGITNTLYWFFWIDFLLGIMNALPLSILDG 471
                                       44333333333222223444444444443333333333333......3567************************** PP

                                       XXXXXXXXXXXXXX..XXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxx RF
                     Peptidase_M50 216 ghllfalleairrk..plserkeevanlvgla 245
                                       g++++ +l+  +r+      r+e+ ++++ +a
  gi|518652947|ref|YP_008142467.1| 472 GQFFRDTLTIASRRdrLKFLRDENNVKKIYYA 503
                                       *****999877765113444555555555544 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.8e-05      0.16      14      71 ..     276     337 ..     252     347 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.8e-05
                                       .-EEEEEE-TTSGGGGT.--TT-EEEEETTB--....SSHHHHHHHHHTS-TT-EEEEEEEE CS
                             PDZ_2  14 ggvlvvsVkeggPaakaglkagDvilkvdgkkv....ksledlislllkkkpGdtVkltvlR 71 
                                       +gv +v+  +g Paa+a++ ++ +i+ + +        +  +l   l +  pG+t++ tvl 
  gi|518652947|ref|YP_008142467.1| 276 TGVAIVDLISGCPAAAANVSTDSIIYNISDAGHshiiYNINTLGDVLDNITPGTTINMTVLT 337
                                       699*************************9865432337778888888899999999999974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (522 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       792  (0.0441742); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.43
# Mc/sec: 3653.94
//
Query:       gi|518652948|ref|YP_008142468.1|  [L=143]
Description: MarR family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.6e-13   48.6   0.1    7.9e-13   48.1   0.1    1.2  1  MarR      MarR family
      1e-05   25.3   0.0    1.4e-05   24.8   0.0    1.2  1  MarR_2    MarR family
      5e-05   23.4   0.0    7.7e-05   22.8   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
    8.8e-05   22.9   0.0    0.00015   22.2   0.0    1.4  1  HTH_27    Winged helix DNA-binding domain
     0.0085   16.2   0.1      0.034   14.3   0.0    1.9  2  FUR       Ferric uptake regulator family
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.12   12.3   0.0    1.4  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.1   2.6e-16   7.9e-13       2      58 ..      34      90 ..      33      91 .. 0.96

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 2.6e-16
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTSTTS CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRskspeDrRe 58
                                      + ++++iL +l e+g+l ++eLa+  +v+++ +t v+d+Lek  +++R++s +DrR+
  gi|518652948|ref|YP_008142468.1| 34 STVEYRILKNLTERGALPMIELANINMVTQGWITGVIDKLEKLSYVMRERSDSDRRV 90
                                      5689****************************************************7 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   4.8e-09   1.4e-05       2      61 ..      32      89 ..      31      90 .. 0.97

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 4.8e-09
                                      T--HHHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEESSSSSS CS
                            MarR_2  2 gltpaqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverrpgpeDkR 61
                                      g++  ++r+L +L  r+   l + ela    ++++ ++ ++++L++  +v r++++ D+R
  gi|518652948|ref|YP_008142468.1| 32 GVSTVEYRILKNLTERGA--LPMIELANINMVTQGWITGVIDKLEKLSYVMRERSDSDRR 89
                                      78899************9..***********************************99**9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.0   2.6e-08   7.7e-05       5      71 ..      40     105 ..      36     114 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.6e-08
                            HTH_34   5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafkk 71 
                                       +l  L +     + el +   +t+g +   ++kLek  Y+ ++ + +++ + + +++Tp+G++ fk 
  gi|518652948|ref|YP_008142468.1|  40 ILKNLTERGALPMIELANINMVTQGWITGVIDKLEKLSYVMRERSDSDR-RVINITVTPKGKAFFKT 105
                                       6666666666677788888889***********************9999.9***********99985 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.1e-08   0.00015       3      68 .]      35      99 ..      33      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.1e-08
                            HTH_27  3 rqqalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +++  +L ++  +r+     +l+   +v++  i  +++kL++  +v+r++++ drr   +++T+kG
  gi|518652948|ref|YP_008142468.1| 35 TVEYRILKNLT-ERGALPMIELANINMVTQGWITGVIDKLEKLSYVMRERSDSDRRVINITVTPKG 99
                                      56666777777.7777777899999999*************************************9 PP

>> FUR  Ferric uptake regulator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.0   1.1e-05     0.034      27      64 ..      18      56 ..      10      63 .. 0.87
   2 ?   -0.6   0.0      0.46   1.4e+03      43      54 ..     124     135 ..      87     141 .. 0.66

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.1e-05
                                      HHHHHHHHHTTTT--HHHH.HHHHHHHHHTTSEEEEEET CS
                               FUR 27 eevykelkeedpeislaTV.YrtLklleeaglvkelefe 64
                                      +  yk+ +++  +++++TV Yr+Lk l+e+g++  +e++
  gi|518652948|ref|YP_008142468.1| 18 KTWYKASEKNLMSMGVSTVeYRILKNLTERGALPMIELA 56
                                      55699999************************9998887 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.46
                                       HHHHHHHHHHHH CS
                               FUR  43 aTVYrtLkllee 54 
                                          Y++L++l++
  gi|518652948|ref|YP_008142468.1| 124 EERYNILNFLKK 135
                                       444555555554 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.1e-05      0.12       2      58 ..      29      85 ..      28     107 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.1e-05
                                      HHCHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESST CS
                              TrmB  2 qklGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgr 58
                                        +G s  E ++ + L ++g + + e+a++  v +  +  v+ +Le+  +V+re++ 
  gi|518652948|ref|YP_008142468.1| 29 MSMGVSTVEYRILKNLTERGALPMIELANINMVTQGWITGVIDKLEKLSYVMRERSD 85
                                      57899*************************************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 984.05
//
Query:       gi|518652949|ref|YP_008142469.1|  [L=650]
Description: hypothetical protein FACI_IFERC00001G1588 [Ferroplasma acidarmanus fer1]
Scores for complete 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  185.1   0.1    2.3e-54  184.6   0.1    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
    5.1e-36  124.4   0.1    1.5e-35  122.8   0.1    1.8  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
    6.7e-12   45.6   0.0    1.7e-11   44.4   0.0    1.7  1  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    0.00093   18.8   0.3     0.0015   18.1   0.3    1.3  1  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
      0.035   14.0   0.0      0.079   12.9   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
      0.072   13.0   0.1       0.76    9.7   0.1    2.6  3  GTP_EFTU_D4      Elongation factor Tu domain 4
       0.12   12.5   0.0        7.6    6.8   0.0    2.4  2  DUF4723          Domain of unknown function (DUF4723)


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 !  184.6   0.1   8.9e-58   2.3e-54       2     221 ..     280     505 ..     279     513 .. 0.93

  Alignments for each domain:
  == domain 1  score: 184.6 bits;  conditional E-value: 8.9e-58
                                       HHHHCTEEEEEE--BTTTCCHHHHHCHCCCCCTTEE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEECCHHHHCCCC CS
                             POR_N   2 aaiaagvdviaaYPITPsseiaeelaellakgevgdvevvqmesEigaisaviGAaaaGaraaTaTSgqGllLmien 78 
                                       +ai+ag+++++aYP+TP+s+ ++ +a++ +k  v       +e+Ei+ai+a+iGA +aG+raaT +Sg G++Lm e 
  gi|518652949|ref|YP_008142469.1| 280 GAINAGMQMYFAYPMTPASSFLQFVATHGKKYHV---FLKLTEDEISAINAAIGANYAGVRAATGSSGGGFALMTEG 353
                                       799*****************99999999888775...55568*********************************** PP

                                       HHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHHHHHCTSEEE CS
                             POR_N  79 lglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnlAekvrvPvi 150
                                       +gl a++e+P+vi+ ++R +pstgl+++t+q+Dl++++     d++ ivla+++v+eafdl+ +AfnlAe++++Pv+
  gi|518652949|ref|YP_008142469.1| 354 VGLSAMTEVPLVIYEAQRPGPSTGLPTKTEQGDLNQVLgagqgDMPRIVLAPGTVKEAFDLTKEAFNLAERFQLPVF 430
                                       ***************************************************************************** PP

                                       EEEEHHHH.HEEEEEEC.-SGG..GS-----SBXXXXXXXX...SXXXBXXTXXTSSXXEEESBXBXTTSXBXXXX CS
                             POR_N 151 vlfDgfllshevekvel.pdee.delklikekleeyerkey...aldpekpiargtaanpdtglehrekgneaeda 221
                                       v++D +l+ +  e+v+l +++e d   l++  + +y+r+ey   +++ + ++ + +    + ++eh+e+g    da
  gi|518652949|ref|YP_008142469.1| 431 VVTDLYLA-EHDETVDLdLSYEmDRGLLADASEADYKRYEYtenGISKRAFPGQPGLMHNEDSDEHNEYGAVVSDA 505
                                       ********.77777776467777888888999999999988999*************************9887775 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.8   0.1     6e-39   1.5e-35       1     177 []      80     249 ..      78     249 .. 0.95
   2 ?   -2.2   0.0       1.5   3.9e+03      27      81 ..     512     567 ..     510     575 .. 0.69

  Alignments for each domain:
  == domain 1  score: 122.8 bits;  conditional E-value: 6e-39
                                       CTSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGG.E CS
                               POR   1 GGqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldg.l 76 
                                       +G+Gv++ag  l k+++r+G+y+++++ y+s irGg s+++vr+sde +v++++  + d+lval+a++l++h ++ +
  gi|518652949|ref|YP_008142469.1|  80 AGDGVQSAGLTLEKTFSRSGLYISTYNYYQSLIRGGESWYQVRASDE-KVRNQG-SGLDVLVALNADALERHTNRnI 154
                                       4**********************************************.9*****.***************8888779 PP

                                       EEE......EEEEEECTCGTT-CCHHHCTS-HHHHHHHT-EEEEE-HHHHHHHCCC.CCHHHHHHHHHHHHHHTS-H CS
                               POR  77 kpg......giiiynseelkpdelkkakeeerelkerlgvrvygvdatkiakeiggneraaNtvmlGalaallglpl 147
                                       ++g      gi+iy+++++ +  + +                ++v++++ia +   n++++Ntv+lGa++a lgl++
  gi|518652949|ref|YP_008142469.1| 155 NEGgasplnGIAIYDPGTIHNFKKYDGIT------------YCPVPMRDIALKFDANPLLKNTVALGAVIASLGLDF 219
                                       999999999*******9988877777554............68********************************** PP

                                       HHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 148 ealeeaikkrfpkkkeviekNlkafragye 177
                                       + +  +i+k f+kk++++e N+ a+++gye
  gi|518652949|ref|YP_008142469.1| 220 NVFSGVIEKVFNKKGKLVESNINAAKEGYE 249
                                       *****************************7 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.5
                                       EEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEES...SHHHHHHHGGGEEEEEE CS
                               POR  27 reygseirGghsyshvrisdepivpsievgeadllval...daetlsehldglkpggi 81 
                                       r+  +e+r+   + +++  +  ++p+++ ++a+++v+     + +++e +d ++++g+
  gi|518652949|ref|YP_008142469.1| 512 RKLSMEKRMKKLNLYIKEMP--PTPTYKMEDAEYVVIQwgsTKGAVEEAIDCMRKNGT 567
                                       66678888888888887664..567888888888887644344455577777777765 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 !   44.4   0.0   6.5e-15   1.7e-11       1      73 [.     541     612 ..     541     632 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 6.5e-15
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlvee 73 
                                       Ae+v++  Gs+ g +++a+d +R++g k+G + ++ ++P  ++++k+ll+++kk++v++ n+s   +G + +e
  gi|518652949|ref|YP_008142469.1| 541 AEYVVIQWGSTKGAVEEAIDCMRKNGTKIGAIEITHIFPM-NHDIKKLLAGKKKIIVVENNYSGQLNGLIRKE 612
                                       9**************************************9.789******************85555665555 PP

>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.3     6e-07    0.0015      13     157 ..     283     431 ..     273     443 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 6e-07
                                       HCT--EEEE---CCCHHHHCCHHCT....TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHH CS
                      TPP_enzyme_N  13 algvehvfgvpGsrilplldalseeq...girvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeA 86 
                                       ++g + +f++p +   ++l  ++ +     + + l+ +E +a++aA g   a   + ++  +sg G++ ++ ++   
  gi|518652949|ref|YP_008142469.1| 283 NAGMQMYFAYPMTPASSFLQFVATHGkkyHVFLKLTEDEISAINAAIGANYAG--VRAATGSSGGGFALMTEGVGLS 357
                                       46888899999999999999999997644444445678999999**9998885..899******************* PP

                                       HHHT--EEEEEEE--CCCHH..S..TC--T-CCHHHC..CCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEEE CS
                      TPP_enzyme_N  87 kvdriPllvlsgdrptslrg..qgvlqqeldqlalfr..pvtkyaervtspeelpealrrAirtalsgrpgPvyl 157
                                       + + +Pl++  ++rp  ++g  +++ q+ l+q+  +   ++ + +  + +++e+  + ++A+  a ++ + Pv++
  gi|518652949|ref|YP_008142469.1| 358 AMTEVPLVIYEAQRPGPSTGlpTKTEQGDLNQVLGAGqgDMPRIVLAPGTVKEAFDLTKEAFNLA-ERFQLPVFV 431
                                       ********************774444444433222212233444455555555555555666666.666666665 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.1e-05     0.079       9      71 ..     540     601 ..     535     605 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.1e-05
                                       TSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEE CS
                   Transketolase_C   9 gkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeav 71 
                                         + +++ +Gs+   + eA++  +k+g ++  + +  + p+  ++i+++++ +++++vve+++
  gi|518652949|ref|YP_008142469.1| 540 DAEYVVIQWGSTKGAVEEAIDCMRKNGTKIGAIEITHIFPMN-HDIKKLLAGKKKIIVVENNY 601
                                       567789***********************************9.88999************987 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 ?   -3.1   0.0       2.9   7.3e+03      49      80 ..     120     151 ..     119     156 .. 0.81
   2 ?    9.7   0.1    0.0003      0.76      26      76 ..     551     603 ..     534     606 .. 0.84
   3 ?   -0.8   0.0      0.59   1.5e+03      65      81 ..     632     648 ..     626     650 .] 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.9
                                       EEEETTEEESEEETT-EEEEEEESS-TTTS-- CS
                       GTP_EFTU_D4  49 qiqdkgkkleeakaGqevaisiegkivGrqik 80 
                                       q++ +++k++    G  v ++++ + + r+ +
  gi|518652949|ref|YP_008142469.1| 120 QVRASDEKVRNQGSGLDVLVALNADALERHTN 151
                                       78889999999999999999988887777655 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0003
                                       EEEEEETT-EEEETTE.EEEE..EEEEEETTEEESEEETT-EEEEEEESS-TT CS
                       GTP_EFTU_D4  26 lgGvikpgvklikedGrevGe..ilqiqdkgkkleeakaGqevaisiegkivG 76 
                                        +G ++  ++ ++++G+++G   i++i   ++ +++  aG++  i +e++  G
  gi|518652949|ref|YP_008142469.1| 551 TKGAVEEAIDCMRKNGTKIGAieITHIFPMNHDIKKLLAGKKKIIVVENNYSG 603
                                       6899999*************722579999*************99999988655 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.59
                                       EEEEEEESS-TTTS--T CS
                       GTP_EFTU_D4  65 evaisiegkivGrqike 81 
                                        +a+s+e+ i G++ik 
  gi|518652949|ref|YP_008142469.1| 632 DLALSLEEMIFGKKIKV 648
                                       6799**********986 PP

>> DUF4723  Domain of unknown function (DUF4723)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.042   1.1e+02      34      54 ..     106     126 ..      92     131 .. 0.82
   2 ?    6.8   0.0    0.0029       7.6      44      70 ..     546     573 ..     523     584 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.042
                           DUF4723  34 cikevhikggiewysikgcte 54 
                                          ++ i+gg  wy ++   e
  gi|518652949|ref|YP_008142469.1| 106 NYYQSLIRGGESWYQVRASDE 126
                                       556789**********98766 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0029
                           DUF4723  44 iewysikgctenksecfkki.ikayelr 70 
                                       i+w s kg  e++ +c++k  +k   + 
  gi|518652949|ref|YP_008142469.1| 546 IQWGSTKGAVEEAIDCMRKNgTKIGAIE 573
                                       9****************99854433333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (650 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.65u 0.33s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 3905.32
//
Query:       gi|518652950|ref|YP_008142470.1|  [L=285]
Description: hypothetical protein FACI_IFERC00001G1589 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.5e-31  107.7   0.2    9.1e-31  106.7   0.1    1.5  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    1.3e-16   60.5   1.1    2.3e-16   59.7   1.1    1.4  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.7   0.1     1e-34   9.1e-31       2     153 .]      48     195 ..      47     195 .. 0.96
   2 ?   -3.5   0.0      0.86   7.7e+03     127     143 ..     218     234 ..     212     239 .. 0.75

  Alignments for each domain:
  == domain 1  score: 106.7 bits;  conditional E-value: 1e-34
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc++           ++++++  g++g +G++lp+A G+k a+++ +v+a+ GDG+ ++   q++ +a++rn+++t
  gi|518652950|ref|YP_008142470.1|  48 IGCSSN----------MPEFINtYGFHGLHGRSLPVAEGIKWANKNLTVIAYGGDGDGFFEgSQHFYHAAKRNVNMT 114
                                       666666..........788999899******************9999**********999989************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       ++v +N+++g+t gq   ++p g  +ks+p+g++++p+++  +a ++Ga+ +ar  + ++++l+e  k+a+++kg++
  gi|518652950|ref|YP_008142470.1| 115 YMVSDNQVFGLTTGQaspTTPIGRITKSTPDGNIEPPFNPLHYALSAGATfVARGLSGNIKQLAELTKAAIQHKGFS 191
                                       **************************************************999999********************* PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +i+v
  gi|518652950|ref|YP_008142470.1| 192 FIDV 195
                                       **98 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.86
                                       ESSH.HHHHHHHHHHHH CS
                      TPP_enzyme_C 127 vekadveeleealkeal 143
                                       +++++ +++ ea+k a 
  gi|518652950|ref|YP_008142470.1| 218 LKDNNRKDFYEAFKHAS 234
                                       45677799999999885 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   1.1   2.6e-20   2.3e-16       1      65 [.     199     264 ..     199     265 .. 0.94

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.6e-20
                                       XTTTXSSSXSXXXXX-EEEGGGST---EEHHHHHHHHT----...-EEEEEEEETTS--HHHHHHT.. CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleedgyDpsdlekAlekalewgd...kiplGifYkeekptyeerleelk 65 
                                       Cvt+Nkv+ ++++++ +y+l++  ++ +d+ +A++ a ewg+   +ip+Gi+Y+ + p ye+  e+lk
  gi|518652950|ref|YP_008142470.1| 199 CVTYNKVEGYEFFRKTTYELKD--NNRKDFYEAFKHASEWGEeanSIPIGILYDVDAPVYEDVDETLK 264
                                       *********************9..69****************8877****************988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); 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 0.29s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1945.62
//
Query:       gi|518652951|ref|YP_008142471.1|  [L=48]
Description: hypothetical protein FACI_IFERC00001G1590 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0072   16.0   1.9      0.008   15.8   1.9    1.0  1  Filament        Intermediate filament protein
  ------ inclusion threshold ------
       0.61   10.3   5.5        3.4    8.0   5.5    1.9  1  XhlA            Haemolysin XhlA
       0.63   10.0   0.3       0.63   10.0   0.3    2.8  2  Pox_A_type_inc  Viral A-type inclusion protein repeat


Domain annotation for each model (and alignments):
>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.9   1.3e-06     0.008      21      65 ..       6      48 .]       5      48 .] 0.92

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.3e-06
                                      XXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXX CS
                          Filament 21 raLEqenkeLeakieeleekksaevsklkelyekeleelrkqlde 65
                                      r L ++ k++e+ki ele+k  a+++ +++  ++e+++l+k+ld+
  gi|518652951|ref|YP_008142471.1|  6 RDLNRKRKSIEMKIDELEQK--ARKNPMDKSIQTEINDLKKKLDK 48
                                      789999**************..77777899************985 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.5   0.00056       3.4       9      46 ..       8      44 ..       6      48 .] 0.72

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00056
                              XhlA  9 ietkldnleervdkleekaaeaeekiknleedlkkles 46
                                      +++k +++e+++d+le+ka++     k+++ ++++l++
  gi|518652951|ref|YP_008142471.1|  8 LNRKRKSIEMKIDELEQKARKNPM-DKSIQTEINDLKK 44
                                      57888999**********998643.3555555555554 PP

>> Pox_A_type_inc  Viral A-type inclusion protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   1.9     0.062   3.7e+02       9      15 ..      18      24 ..       6      25 .. 0.67
   2 ?   10.0   0.3   0.00011      0.63       7      19 ..      36      48 .]      33      48 .] 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.062
                    Pox_A_type_inc  9 RIsDLEr 15
                                      +I +LE+
  gi|518652951|ref|YP_008142471.1| 18 KIDELEQ 24
                                      7888887 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00011
                    Pox_A_type_inc  7 RsRIsDLErqLse 19
                                      +++I DL+++L++
  gi|518652951|ref|YP_008142471.1| 36 QTEINDLKKKLDK 48
                                      79*********85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1760  (0.098165); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); 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: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.43
# Mc/sec: 333.78
//
Query:       gi|518652952|ref|YP_008142472.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G1591 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0034   18.0   0.3     0.0041   17.7   0.3    1.1  1  DUF971         Protein of unknown function (DUF971)
     0.0058   16.6   0.2     0.0073   16.3   0.2    1.1  1  Endopep_inhib  IseA DL-endopeptidase inhibitor
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.043   13.9   0.0    1.1  1  F5_F8_type_C   F5/8 type C domain
      0.096   12.6   0.1       0.25   11.3   0.0    1.7  2  MliC           Membrane-bound lysozyme-inhibitor of c-type ly


Domain annotation for each model (and alignments):
>> DUF971  Protein of unknown function (DUF971)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.3   9.1e-07    0.0041       7      62 ..       7      62 ..       3      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.1e-07
                            DUF971  7 gkrLeiewddgkesslpaelLRdacpcaecrkp.gqrllqsgkipkdvkiesiepvg 62
                                       k+++++++d+++ +l+ae  ++ac  a+  ++  +r+l +++ pk+v+ ++i+p +
  gi|518652952|ref|YP_008142472.1|  7 IKEIRVRYADETDRELSAEEIKEACNKANEANDsIERVLMKKE-PKEVRYVEINPKK 62
                                      58899*********************99999444888888888.9********9876 PP

>> Endopep_inhib  IseA DL-endopeptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   1.6e-06    0.0073       4      54 ..      21      72 ..      18      76 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.6e-06
                                      S--HHHHHHHHHHHHHHHHHHHTTS-TT-S.---EEEETTEEEEE--TTSSS CS
                     Endopep_inhib  4 nlsdkeakkLilnadelfwkilsgkspkkk.eiksievkgkeYaklkddint 54
                                      +ls +e+k+  ++a+e+  +i ++  +k+  e++++e++ k+Y+ lk++ +t
  gi|518652952|ref|YP_008142472.1| 21 ELSAEEIKEACNKANEANDSIERVLMKKEPkEVRYVEINPKKYTTLKNEAGT 72
                                      799*****************999876655459***************99765 PP

>> F5_F8_type_C  F5/8 type C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   9.6e-06     0.043      64     117 ..       8      65 ..       4      74 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.6e-06
                                       EEEEEEEESSSSSEEEEEEECE.....EESSSSSSSEEEEEE.EEEEEEEEEEEEEEEES CS
                      F5_F8_type_C  64 ksykiqvsddgetWttvkdekv.....pgnsdnstpvtntfd.ppvkaryvrltptswng 117
                                       k+ ++++ d+ +  +++++e++     ++n  n++++++ ++ +p + ryv ++p+++++
  gi|518652952|ref|YP_008142472.1|   8 KEIRVRYADETD--RELSAEEIkeacnKANEANDSIERVLMKkEPKEVRYVEINPKKYTT 65 
                                       566666655532..344442222234588888999*********************9654 PP

>> MliC  Membrane-bound lysozyme-inhibitor of c-type lysozyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   5.6e-05      0.25       1      18 [.       2      19 ..       2      27 .. 0.80
   2 ?   -1.5   0.0      0.54   2.4e+03      13      26 ..      55      59 ..      39      73 .. 0.57

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.6e-05
                                      EEECCCEEEEEEEECTTE CS
                              MliC  1 YqCdsgaevtvtyiagdp 18
                                      Y+Cd+ +e++v+y+++++
  gi|518652952|ref|YP_008142472.1|  2 YKCDDIKEIRVRYADETD 19
                                      9*************4443 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.54
                                      EECTTEEEEEEECC CS
                              MliC 13 yiagdpsfavlrlg 26
                                      y+         +++
  gi|518652952|ref|YP_008142472.1| 55 YV---------EIN 59
                                      32.........222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1459  (0.0813765); expected 358.6 (0.02)
Passed bias filter:                      832  (0.0464053); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 591.26
//
Query:       gi|518652953|ref|YP_008142473.1|  [L=150]
Description: hypothetical protein FACI_IFERC00001G1592 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-14   54.8   6.4    1.7e-07   31.8   1.1    2.2  2  AAA_18           AAA domain
    5.4e-05   23.0   1.0        0.1   12.3   0.2    2.3  2  CoaE             Dephospho-CoA kinase
    9.5e-05   22.8   1.3      0.017   15.5   0.2    2.2  2  AAA_17           AAA domain
    0.00034   20.9   0.2    0.00051   20.3   0.2    1.5  1  AAA_28           AAA domain
     0.0028   17.4   0.6       0.58    9.8   0.1    2.1  2  Thymidylate_kin  Thymidylate kinase
     0.0042   17.4   0.5     0.0063   16.8   0.5    1.6  1  AAA_22           AAA domain
     0.0069   16.8   0.3      0.015   15.7   0.3    1.8  1  AAA              ATPase family associated with various cellul
     0.0081   16.1   1.2      0.021   14.7   1.1    1.9  1  NTPase_1         NTPase
     0.0082   15.9   0.7      0.021   14.6   0.7    1.9  1  AAA_24           AAA domain
  ------ inclusion threshold ------
      0.017   14.9   4.0       0.22   11.3   0.3    2.2  2  dNK              Deoxynucleoside kinase
      0.019   14.4   0.5       0.33   10.3   0.1    2.1  2  ATPase           KaiC
       0.03   14.5   0.1        0.2   11.8   0.1    2.0  2  AAA_33           AAA domain
      0.037   13.5   0.0      0.042   13.3   0.0    1.3  1  KTI12            Chromatin associated protein KTI12
      0.038   13.7   0.6      0.052   13.3   0.6    1.4  1  Viral_helicase1  Viral (Superfamily 1) RNA helicase
      0.052   13.7   0.6        5.4    7.1   0.1    2.1  2  ADK              Adenylate kinase
      0.084   12.5   0.8       0.15   11.6   0.7    1.5  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
        0.1   12.5   0.0       0.16   11.9   0.0    1.4  1  APS_kinase       Adenylylsulphate kinase
       0.12   12.1   0.1       0.11   12.2   0.1    1.4  1  AAA_30           AAA domain
       0.12   11.6   0.2       0.93    8.7   0.1    2.0  2  Zeta_toxin       Zeta toxin
       0.13   12.6   0.3       0.14   12.5   0.3    1.4  1  AAA_19           AAA domain
       0.14   12.7   1.2       0.17   12.4   1.2    1.5  1  ABC_tran         ABC transporter
       0.21   11.4   0.8       0.33   10.7   0.3    1.6  2  ATP_bind_1       Conserved hypothetical ATP binding protein


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 !   26.1   0.9   1.3e-08     1e-05       1      28 [.       2      29 ..       2      47 .. 0.74
   2 !   31.8   1.1   2.1e-10   1.7e-07      69     128 ..      44     104 ..      26     106 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 1.3e-08
                            AAA_18  1 IlltGtpGvGKttlakeLskrl.gf.gvnl 28
                                      I++tG+pG+GKtt++k L+  + ++ g  l
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGiKCtG--L 29
                                      9*****************887544452..2 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 2.1e-10
                            AAA_18  69 s.....aleegknlvidghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeaei 128
                                             ++e+ ++ v+++h +++++ +++    ++L+ ++e+l++R++ Rgy e kiken +a++
  gi|518652953|ref|YP_008142473.1|  44 VdvdvlRRENINSEVVESHYSHMLECKYV----IILEDNEEQLIRRMKSRGYPESKIKENIDAQR 104
                                       24555445555666************888....****************************9985 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   0.00013       0.1       3      37 ..       2      36 ..       1      51 [. 0.85
   2 !    9.6   0.0   0.00085      0.69     114     159 ..      59     105 ..      57     130 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00013
                                      EEEEESTTSSHHHHHHHHHHTT-EEEEHHHHHHHT CS
                              CoaE  3 vgltGgiasGKstvanlfadlgvpivDaDlvArqv 37
                                      + +tG  +sGK+t+++++++ g++      +A + 
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIKCTGLNDIASEC 36
                                      899*******************9998888887765 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00085
                                       TTTTGGGGSSEEEEEE-.-HHHHHHHHHHCCTSTHHHHHHHHHHS-- CS
                              CoaE 114 vEkqlekliervlvvdv.elelqveRlvardgvseeevkaiiaaQls 159
                                       vE+++++++e   v+   + e+q+ R ++ +g  e ++k+ i aQ s
  gi|518652953|ref|YP_008142473.1|  59 VESHYSHMLECKYVIILeDNEEQLIRRMKSRGYPESKIKENIDAQRS 105
                                       7888888887665555417899***********************76 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.2   2.1e-05     0.017       1      16 [.       5      20 ..       5      29 .. 0.85
   2 ?    6.4   0.1     0.014        11      88     122 ..      55      89 ..      27     102 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.1e-05
                                      EE-TTSSHHHHHHHHH CS
                            AAA_17  1 lGgPGsGKgtqceklv 16
                                      +G+PGsGK+t+c+ l 
  gi|518652953|ref|YP_008142473.1|  5 TGIPGSGKTTICKMLN 20
                                      7***********8764 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.014
                                       EEESSHHHHHHHH..SEEEEEE--HHHHHHHHHHH CS
                            AAA_17  88 fldglpkevleelkpdaiilleadpeeilerrlkd 122
                                       + + ++++  + l+ + +i+le+++e++++r++++
  gi|518652953|ref|YP_008142473.1|  55 NSEVVESHYSHMLECKYVIILEDNEEQLIRRMKSR 89 
                                       34456667777888999**********99877664 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.2   6.3e-07   0.00051       2      27 ..       2      27 ..       1      74 [. 0.85

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 6.3e-07
                            AAA_28  2 ivitGgestGKTtlleaLaargypvv 27
                                      i+itG +++GKTt+++ L+a+g+++ 
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIKCT 27
                                      9*********************9986 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1   0.00071      0.58       2      18 ..       5      21 ..       4      33 .. 0.86
   2 !    6.4   0.1    0.0079       6.4     112     164 ..      64     114 ..      48     138 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00071
                                      EESTTSSHHHHHHHHHH CS
                   Thymidylate_kin  2 EGlDGaGKttqaellke 18
                                       G+ G+GKtt++++l +
  gi|518652953|ref|YP_008142473.1|  5 TGIPGSGKTTICKMLNA 21
                                      69***********9965 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0079
                                       GGTTSE-SEEEEEESSHHHHHTSCCTTSSTTTSHHHHHHHHHHHHHHHHHHHH CS
                   Thymidylate_kin 112 edvllkPdltflldvdpevalkRlakrdeldeeeeeqldflrkvrerylelak 164
                                        + +l+  ++++l+  +e  ++R++ r+  +++++e++d +r+    y e+ +
  gi|518652953|ref|YP_008142473.1|  64 SH-MLECKYVIILEDNEEQLIRRMKSRGYPESKIKENIDAQRSGVI-YWEASD 114
                                       44.335566777776999999*******999999***999988655.444443 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.5   7.7e-06    0.0063       7      27 ..       1      21 [.       1     108 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.7e-06
                            AAA_22  7 ilvvtGesGtGKTtllrrlle 27
                                      ++++tG +G+GKTt +++l  
  gi|518652953|ref|YP_008142473.1|  1 MICITGIPGSGKTTICKMLNA 21
                                      689**************9976 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 !   15.7   0.3   1.9e-05     0.015       1      22 [.       2      27 ..       2     143 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.9e-05
                                      EEEESSTTSSHHHHHHHHHHH....H CS
                               AAA  1 vllyGppGtGKTllakavake....l 22
                                      ++++G pG GKT+++k +  +    +
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANgikcT 27
                                      5899************9977754441 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   1.1   2.6e-05     0.021       2      32 ..       2      28 ..       1      96 [. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                                      EEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
                          NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgG 32
                                      ++iTG pG+GKtT++k    +l+ +g+k +G
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICK----MLNANGIKCTG 28
                                      79***********986....45555666665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.7   2.6e-05     0.021       4      22 ..       1      19 [.       1     150 [] 0.84

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.6e-05
                            AAA_24  4 kiliyGpsgiGKTtlakel 22
                                      +i+i+G +g+GKTt++k+l
  gi|518652953|ref|YP_008142473.1|  1 MICITGIPGSGKTTICKML 19
                                      59***************99 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.3   0.00027      0.22       1      21 [.       2      22 ..       2      35 .. 0.90
   2 ?    5.1   0.4     0.023        19     113     149 ..      59      95 ..      41     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00027
                                      EEEEESTTSSHHHHHHHHHCC CS
                               dNK  1 ivveGnIgaGKstlvklLskk 21
                                      i++ G  g+GK+t+ k+L+ +
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNAN 22
                                      9*****************865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.023
                                       HHHHHHHCCH-SEEEEEE--HHHHHHHHHHCTTCCCT CS
                               dNK 113 ldnlleelakpdlliYLkasletclerikkRgreeek 149
                                        +   +++ + + +i L+ + e++ +r+k Rg  e k
  gi|518652953|ref|YP_008142473.1|  59 VESHYSHMLECKYVIILEDNEEQLIRRMKSRGYPESK 95 
                                       444444555688999****************988755 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00041      0.33      22      48 ..       2      28 ..       1      33 [. 0.86
   2 ?    2.8   0.0     0.079        64      54      90 ..      73     104 ..      64     149 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00041
                            ATPase 22 vlitGepGtGKtifalqFlikgaekyg 48
                                      + itG pG+GKt++++    +g++ +g
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIKCTG 28
                                      78*************999999988766 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.079
                            ATPase  54 vtveepaedlrenakslGwdlekleeegklaiidase 90 
                                       + +e ++e+l++++ks G    k++e+     ida +
  gi|518652953|ref|YP_008142473.1|  73 IILEDNEEQLIRRMKSRGYPESKIKEN-----IDAQR 104
                                       56899999*******999988888887.....44444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00024       0.2       2      35 ..       2      51 ..       1      90 [. 0.67
   2 ?    1.8   0.0       0.3   2.4e+02     100     132 ..      71      99 ..      27     109 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
                            AAA_33  2 vllvGlpGsGKstlaerl................lkklgavllssdtlrr 35
                                      + + G pGsGK+t  + l                + +l + +++ d+lrr
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLnangikctglndiaseCGALNGNTVDVDVLRR 51
                                      6788**********998755555554444443333333355555555555 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.3
                            AAA_33 100 rivvvetdeetlkeRlakRaangddrsevpeea 132
                                        ++++e  ee+l +R + R  ++       +e+
  gi|518652953|ref|YP_008142473.1|  71 YVIILEDNEEQLIRRMKSRGYPES----KIKEN 99 
                                       345666667777777777776532....34444 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.2e-05     0.042       4      27 ..       2      25 ..       1      99 [. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.2e-05
                                      EEEE--TTSSHHHHHHHHHHHHHH CS
                             KTI12  4 vvltGlPssGKstrakeLakalee 27
                                      + +tG+P sGK+t+ k L+    +
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIK 25
                                      89**************99876444 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   0.6   6.4e-05     0.052       2      22 ..       3      22 ..       2      76 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.4e-05
                   Viral_helicase1  2 vvhGvpGcGKStlirkllrts 22
                                       + G+pG+GK+t i k l+ +
  gi|518652953|ref|YP_008142473.1|  3 CITGIPGSGKTT-ICKMLNAN 22
                                      699*********.55555554 PP

>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.1    0.0066       5.4       1      18 [.       4      21 ..       4      33 .. 0.87
   2 ?    5.5   0.0     0.021        17      90     123 ..      57      98 ..      39     140 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0066
                                      EEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxx RF
                               ADK  1 llGaPgaGKGtqaeklvk 18
                                      + G Pg+GK t ++ l  
  gi|518652953|ref|YP_008142473.1|  4 ITGIPGSGKTTICKMLNA 21
                                      579**********99865 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.021
                                       HHHHHHHHHHTSEESEEEEEE--HHHHHHHHHT.........G CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........x RF
                               ADK  90 ealeelleeekvkldlvleldvpeevlveRltg.........D 123
                                       e +e+   ++  ++++v+ l+ +ee l++R+           +
  gi|518652953|ref|YP_008142473.1|  57 EVVES-HYSHMLECKYVIILEDNEEQLIRRMKSrgypeskikE 98 
                                       44555.3356789999*************99876655555441 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   0.7   0.00018      0.15       3      21 ..       2      20 ..       1      60 [. 0.77

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                      EEEEESTTCCHHHHHHHHH CS
                              cobW  3 tvltGflGsGKTtLlnhll 21
                                      + +tG +GsGKTt+ + l 
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLN 20
                                      689**********766554 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00019      0.16       5      40 ..       2      43 ..       1      63 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00019
                                      EEEESSTTSSHHHHHHHHHHH......HHHTT--EEEEEHHH CS
                        APS_kinase  5 vwltGlsgsGKstianalekk......LvekgisvylLdGdn 40
                                      + +tG+ gsGK+ti ++l+ +      L++   ++  L+G++
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANgikctgLNDIASECGALNGNT 43
                                      789***********9988754222222444444555555555 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.11      22      39 ..       3      20 ..       1     142 [. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                            AAA_30 22 vltGpAGtGKttalkalr 39
                                      ++tG +G+GKtt+ k l+
  gi|518652953|ref|YP_008142473.1|  3 CITGIPGSGKTTICKMLN 20
                                      79***********99884 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.1    0.0011      0.93      18      38 ..       1      21 [.       1      29 [. 0.87
   2 ?    0.7   0.0      0.32   2.6e+02      83     122 ..      58      91 ..      50     101 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                        Zeta_toxin 18 lillgGqpGAGKselaellkd 38
                                      +i + G pG+GK+++ ++l++
  gi|518652953|ref|YP_008142473.1|  1 MICITGIPGSGKTTICKMLNA 21
                                      57899***********99976 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.32
                        Zeta_toxin  83 lvekllqeaiengyniivegtlrspdvvkklaealkkaGY 122
                                       +ve+   + +e +y ii+e      d+ ++l++++k++GY
  gi|518652953|ref|YP_008142473.1|  58 VVESHYSHMLECKYVIILE------DNEEQLIRRMKSRGY 91 
                                       5555566666666666665......788889999999998 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   0.00017      0.14      13      41 ..       2      30 ..       1     128 [. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00017
                            AAA_19 13 llvtaGpGtGKTrvlkhivallvelggvk 41
                                      +++t+ pG+GKT++ k+  a  ++ +g++
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIKCTGLN 30
                                      789***********999888777776665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.2    0.0002      0.17      14      37 ..       2      25 ..       1     139 [. 0.74

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0002
                                      EEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 14 vaivGenGaGKStLlkllagllkp 37
                                      + i+G  G+GK+t++k+l  +  +
  gi|518652953|ref|YP_008142473.1|  2 ICITGIPGSGKTTICKMLNANGIK 25
                                      6799**************987666 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 ?   10.7   0.3    0.0004      0.33       1      17 [.       4      20 ..       4      27 .. 0.90
   2 ?   -2.6   0.0       4.7   3.8e+03     175     194 ..      61      80 ..      45     107 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.0004
                        ATP_bind_1  1 vvGpaGsGKttfvgals 17
                                      ++G +GsGKtt+++ l+
  gi|518652953|ref|YP_008142473.1|  4 ITGIPGSGKTTICKMLN 20
                                      68***********9886 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 4.7
                        ATP_bind_1 175 keleffedvealslllekee 194
                                        +  ++ + +++  l+++ee
  gi|518652953|ref|YP_008142473.1|  61 SHYSHMLECKYVIILEDNEE 80 
                                       34444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       722  (0.04027); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                       107  (0.00596798); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 1049.82
//
Query:       gi|518652954|ref|YP_008142474.1|  [L=438]
Description: hypothetical protein FACI_IFERC00001G1593 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.5   0.0    9.3e-27   93.4   0.0    1.6  1  DUF1743         Domain of unknown function (DUF1743)
  ------ inclusion threshold ------
      0.055   13.9   0.4        4.9    7.7   0.2    2.4  2  zf-met          Zinc-finger of C2H2 type
      0.059   13.3   1.3      0.095   12.7   1.3    1.3  1  zinc-ribbons_6  zinc-ribbons
       0.17   11.7   3.6       0.45   10.3   3.6    1.7  1  zf-RING_4       RING/Ubox like zinc-binding domain
       0.27   11.1   1.7       0.48   10.3   1.7    1.3  1  Prok-RING_4     Prokaryotic RING finger family 4
       0.73    9.9   5.3        3.4    7.7   5.5    1.9  2  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        1.2    9.7   6.2         11    6.6   6.2    2.3  1  zf-H2C2_2       Zinc-finger double domain
        2.1    9.0   5.4        2.2    8.9   1.2    2.4  2  zf-C2H2         Zinc finger, C2H2 type
        2.7    8.0   5.5        6.1    6.9   5.5    1.6  1  Zn_ribbon_SprT  SprT-like 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 !   93.4   0.0   4.7e-30   9.3e-27       1     116 []     155     268 ..     155     268 .. 0.91

  Alignments for each domain:
  == domain 1  score: 93.4 bits;  conditional E-value: 4.7e-30
                                       TTHHHHHHHHHH-..-TTS-EEEEEEEE-GGGTT---EEHHHHHHHHHHHTTCECTSEBTTTTCECCS-STTSSEEE CS
                           DUF1743   1 grgiiGAtaalganialedstyEllaYreperwgerevdeesvieadektypetfdnvDlshklvvlvPhtpdpvlf 77 
                                       g+giiG+ a+l++  + + +tyEll Yr+p++  +  + e+  i    +++ +tf+n+D+++++++++P+ ++pv+f
  gi|518652954|ref|YP_008142474.1| 155 GHGIIGSSASLAW--PGKSYTYELLDYRYPNYG-DITYGEKIDISSIPESFYSTFNNIDIKNRYPAIFPKPKTPVIF 228
                                       79***********..4457***********965.888888888888889999************************* PP

                                       EEEES-HHHHHHHHHCSEE..S-EEC.EEEEEESTTS-TT CS
                           DUF1743  78 Girgedpeallkaakeilskeeesee.mavfrtnqgtdah 116
                                       G+rg d+++l+  +++i+++++  ++ +++++tnqgtd+h
  gi|518652954|ref|YP_008142474.1| 229 GVRGVDKNDLITIYDRIKERHNIDDQgYIIYKTNQGTDDH 268
                                       *******************6666666*************9 PP

>> zf-met  Zinc-finger of C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.033        65       3      16 ..     367     380 ..     365     381 .. 0.91
   2 ?    7.7   0.2    0.0025       4.9       1      13 [.     382     394 ..     382     396 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.033
                            zf-met   3 CelCnvtfnsesql 16 
                                       C+ C+v++ s++q+
  gi|518652954|ref|YP_008142474.1| 367 CPECHVKTRSKGQM 380
                                       99**********98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0025
                            zf-met   1 fyCelCnvtfnse 13 
                                       + C++C+++++++
  gi|518652954|ref|YP_008142474.1| 382 YRCPVCKKRYKNP 394
                                       78*******9986 PP

>> zinc-ribbons_6  zinc-ribbons
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   4.8e-05     0.095       3      28 ..     367     393 ..     365     404 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.8e-05
                                       -SSS-S--E.E-SSEEE-TTT--EEEE CS
                    zinc-ribbons_6   3 CpeCqqele.krgeqyhCeaCqedlkk 28 
                                       CpeC+ +++ k +  y+C  C++++k+
  gi|518652954|ref|YP_008142474.1| 367 CPECHVKTRsKGQMDYRCPVCKKRYKN 393
                                       *********677799********9986 PP

>> zf-RING_4  RING/Ubox like zinc-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.6   0.00023      0.45      24      48 .]     366     392 ..     363     392 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00023
                         zf-RING_4  24 iClfCyhrile..eeegrCPaCreeYk 48 
                                       +C  C+ + ++  +++ rCP C+++Yk
  gi|518652954|ref|YP_008142474.1| 366 VCPECHVKTRSkgQMDYRCPVCKKRYK 392
                                       7999*999988556799*********7 PP

>> Prok-RING_4  Prokaryotic RING finger family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.7   0.00024      0.48      20      40 ..     366     391 ..     365     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                       Prok-RING_4  20 vCkeCfdskdls.....sCPlCqrri 40 
                                       vC eC  ++ ++     +CP+C++r 
  gi|518652954|ref|YP_008142474.1| 366 VCPECHVKTRSKgqmdyRCPVCKKRY 391
                                       8******9977777889******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 ?    7.7   5.5    0.0017       3.4      18      45 ..     362     389 ..     350     390 .. 0.70
   2 ?    3.2   0.3     0.045        89      20      34 ..     383     401 ..     376     409 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0017
                     Zn_Tnp_IS1595  18 g..fvCPhCgsrkayriktrglfqCkeCrk 45 
                                       +  +vCP C+++  +r k+   ++C  C+k
  gi|518652954|ref|YP_008142474.1| 362 KepPVCPECHVK--TRSKGQMDYRCPVCKK 389
                                       4459******66..45555568***99998 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.045
                     Zn_Tnp_IS1595  20 vCPhCgsr....kayrikt 34 
                                       +CP C++r    ++++i++
  gi|518652954|ref|YP_008142474.1| 383 RCPVCKKRyknpEITEITR 401
                                       7*****9985555555554 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 ?    6.6   6.2    0.0057        11       9      26 .]     376     393 ..     360     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0057
                         zf-H2C2_2   9 HtgekpyeCplCdkaFkt 26 
                                        +g+  y Cp+C+k++k+
  gi|518652954|ref|YP_008142474.1| 376 SKGQMDYRCPVCKKRYKN 393
                                       457778**********97 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.2      0.24   4.8e+02       2      14 ..     366     378 ..     366     380 .. 0.79
   2 ?    8.9   1.2    0.0011       2.2       1      13 [.     382     394 ..     382     395 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.24
                                       EETTTTEEESSHH CS
                           zf-C2H2   2 kCpdCgksFkrks 14 
                                       +Cp+C+ + ++k 
  gi|518652954|ref|YP_008142474.1| 366 VCPECHVKTRSKG 378
                                       6*****8887775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
                                       EEETTTTEEESSH CS
                           zf-C2H2   1 ykCpdCgksFkrk 13 
                                       y+Cp+C+k++k++
  gi|518652954|ref|YP_008142474.1| 382 YRCPVCKKRYKNP 394
                                       9**********98 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   5.5     0.003       6.1       6      33 ..     366     390 ..     366     392 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.003
                    Zn_ribbon_SprT   6 rCtgCgreythhlsirrhnYrCrrCkgt 33 
                                       +C+ C+     ++s+    YrC+ Ck +
  gi|518652954|ref|YP_008142474.1| 366 VCPECH---VKTRSKGQMDYRCPVCKKR 390
                                       699999...7788887778******975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); 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 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2755.63
//
Query:       gi|518652955|ref|YP_008142475.1|  [L=258]
Description: hypothetical protein FACI_IFERC00001G1594 [Ferroplasma acidarmanus fer1]
Scores for 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-76  254.9   0.0      7e-76  254.7   0.0    1.0  1  Prenyltransf  Putative undecaprenyl diphosphate synthase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.7   0.0   3.9e-80     7e-76       1     224 []      35     257 ..      35     257 .. 0.95

  Alignments for each domain:
  == domain 1  score: 254.7 bits;  conditional E-value: 3.9e-80
                                       EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHH...HHHHHH CS
                      Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellk...eellke 74 
                                       i DGNrR+A++ gl+++e Gh +G ++l+e+l++++e+g+++vtvY fS+eNfkR++eev++l++l++   + llk+
  gi|518652955|ref|YP_008142475.1|  35 ITDGNRRYAREAGLTPNE-GHVRGKDKLEEVLDWAMEVGIRIVTVYGFSSENFKRDPEEVNFLFDLINdslRGLLKD 110
                                       89***********77777.************************************************9777777777 PP

                                       HHHHHHHTTEEEEEESSGGGS-HHHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSG.GG CS
                      Prenyltransf  75 elkellkegvrvrviGdlellpedvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkk.ee 150
                                       +  ++ k+++rvr+iGd + lpe + ++++++e+ t+  +k +++nia+ Yg+r+ei++av++++++++++k k e+
  gi|518652955|ref|YP_008142475.1| 111 D--RIFKNQIRVRIIGDFKGLPEYLVNTIHDVEKITAGFKK-FKFNIAIGYGGRQEIIDAVKNIAADVVSKKLKiED 184
                                       7..9*********************************6655.**********************9999888888678 PP

                                       HSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EEEEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
                      Prenyltransf 151 ideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlayselyfldvlWPdfskedllealleyqkrerrfg 224
                                       i+e+ ++++ly  ++l dpDl++RtsGeeR+SnFllwq+ayselyf+dv WPd++k d+l+a+ +yq+r+rr+g
  gi|518652955|ref|YP_008142475.1| 185 INEKLFRNYLYD-NTLTDPDLILRTSGEERISNFLLWQSAYSELYFSDVNWPDLKKLDFLRAIYSYQSRKRRYG 257
                                       89*********6.558********************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.46
# Mc/sec: 1672.76
//
Query:       gi|518652956|ref|YP_008142476.1|  [L=460]
Description: hypothetical protein FACI_IFERC00001G1595 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  187.8   0.1    3.6e-55  187.3   0.1    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    4.3e-26   91.3   0.1    8.6e-26   90.4   0.1    1.5  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    8.2e-17   61.5   0.1    8.2e-17   61.5   0.1    2.2  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.1e-09   38.1   4.6    3.1e-09   36.5   4.6    1.8  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.3e-05   23.7   3.5    4.1e-05   22.8   0.6    2.6  3  GIDA            Glucose inhibited division protein A
    0.00021   20.6   0.0     0.0035   16.5   0.0    2.1  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
     0.0003   20.7   0.1     0.0026   17.7   0.0    2.5  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.01   14.6   7.3       0.59    8.8   1.0    3.3  4  HI0933_like     HI0933-like protein
      0.011   15.1   0.3       0.92    8.8   0.0    2.9  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.012   16.1   1.6        2.4    8.8   0.1    3.5  3  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.035   13.5   1.1       0.62    9.4   0.0    2.7  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.053   13.5   4.0        0.4   10.6   0.0    3.3  3  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
      0.071   12.7   0.3        3.1    7.3   0.0    2.4  2  DAO             FAD dependent oxidoreductase
      0.092   13.2   0.3          1    9.8   0.0    2.6  3  NAD_binding_7   Putative NAD(P)-binding
       0.22   10.6   2.0       0.94    8.5   1.1    2.1  2  FAD_binding_2   FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.3   0.1     3e-58   3.6e-55       1     293 [.       4     317 ..       4     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 187.3 bits;  conditional E-value: 3e-58
                                       CSEEEE--SHHHHHHHHHHHH...HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.............. CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq...agakvtlve...legtclnggcllskallgvaedaeias.............. 57 
                                       +d+++iG G+AG+aaa+++++   +++k++l++    +gtc+n+gc++sk l ++++++++a+              
  gi|518652956|ref|YP_008142476.1|   4 YDLAIIGWGAAGFAAAIKASEltsNQMKIALIGtgpIGGTCVNVGCVPSKFLIEASKNYKEATkpsyrgitananin 80 
                                       689******************9988*******999*************************999************** PP

                                       ..............HHHHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC CS
                                       ..............xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..............evvkklnqg.ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv 119
                                                     e     n++  +++++ e +++++g +k+ +++++  ++++i++ + ++ tGs++ ++ i+G+
  gi|518652956|ref|YP_008142476.1|  81 fsefmeslndfvstE----RNTKyADVIKNFENIDMYEGMAKFIDNNTVAVNNKDIKALNFIISTGSRTLIPEIKGL 153
                                       ********9976553....333323333343358887999************************************* PP

                                       .TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 120 aenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke 196
                                               ++++s+  ++  +lp +i+v G+G +++ElA a++++g ev++  + +r+l+++d+++ + l +al+ +
  gi|518652956|ref|YP_008142476.1| 154 -------TDYYTSDTIWNMRELPGKIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKGFDEDINNHLINALKTN 223
                                       .......4889****************************************************************** PP

                                       TEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 GvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiy 272
                                       G+ ++lg++++ei++++ k + v+e g+  + d ++va+G+ p+ + l+ +++g+ +  ++givvd++l+t+ p iy
  gi|518652956|ref|YP_008142476.1| 224 GIIFHLGQNFQEIINKNGKKSIVTEAGTFDNFDSLLVATGRVPQIDKLNlKAAGIST--DNGIVVDDSLKTTNPIIY 298
                                       *************998886669**********************************9..****************** PP

                                       E-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 273 aiGDvaggkggpelaqaAvqq 293
                                       a+GD++  +++++l + A ++
  gi|518652956|ref|YP_008142476.1| 299 AAGDCI--RQSLKLETLAGKE 317
                                       ******..6666666666665 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 !   90.4   0.1   7.2e-29   8.6e-26       1     107 [.     337     442 ..     337     443 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 7.2e-29
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p vvft+p+vasvG+te+e+k + ie++v ++++k++ +a + +  +g++K+ +  k++k+lG+h+v+p a+e i 
  gi|518652956|ref|YP_008142476.1| 337 VPWVVFTEPNVASVGYTEAELKSKNIEYDVRTVELKNVVKANILNSYDGIAKV-ISGKDKKILGVHVVAPMAAEFII 412
                                       79**************************************************9.6677******************* PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealk 107
                                       e   +i++glt + l++ +h+ Pt++e++k
  gi|518652956|ref|YP_008142476.1| 413 EGVYLIQNGLTYDNLINAMHVFPTVAESIK 442
                                       ***************************986 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.5       4.4   5.3e+03       2      22 ..       6      26 ..       5      39 .. 0.80
   2 !   61.5   0.1   6.9e-20   8.2e-17       1      79 [.     171     248 ..     171     254 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 4.4
                                      EEEECSSHHHHHHHHHHHHTT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg 22
                                      ++++G G  g  +A  ++el 
  gi|518652956|ref|YP_008142476.1|  6 LAIIGWGAAGFAAAIKASELT 26
                                      689999999999998888876 PP

  == domain 2  score: 61.5 bits;  conditional E-value: 6.9e-20
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEEEEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgvesvk 77 
                                       k++v+G+G ++lElA a++++g +V+++ rs+++l+++De++ + l + l+ ngi ++l+++ +ei  ++   +s++
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKGFDEDINNHLINALKTNGIIFHLGQNFQEIINKNG-KKSIV 246
                                       799***************************************************************95555.46777 PP

                                       EE CS
                         Pyr_redox  78 lk 79 
                                       ++
  gi|518652956|ref|YP_008142476.1| 247 TE 248
                                       65 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 !   36.5   4.6   2.6e-12   3.1e-09       2     305 .]       8     301 ..       7     301 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.6e-12
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagled..ylilEkgnignsiyrypk..emtfispsftsekleipdlnaiseetspafs.. 72 
                                       IiG G+aG aaai++ ++  ++  +  +  g ig +  +     ++ +i  s++ ++ + p    i+ +++ +fs  
  gi|518652956|ref|YP_008142476.1|   8 IIGWGAAGFAAAIKASELTSNQmkIALIGTGPIGGTCVNVGCvpSKFLIEASKNYKEATKPSYRGITANANINFSef 84 
                                       9*************99988865115679******9999975421555678888888899999999998887555421 PP

                       Pyr_redox_3  73 lk..eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGee 147
                                       ++  ++ +s++   +Y + + + +++      + e ++k  ++ +v  ++++++A + ii+tG   +   ++i+G +
  gi|518652956|ref|YP_008142476.1|  85 MEslNDFVSTERNTKYADVIKNFENI-----DMYEGMAKFIDNNTVAVNNKDIKALNFIISTGS--RTLIPEIKGLT 154
                                       11224455555555555555555444.....23356777778889******************9..999999***99 PP

                       Pyr_redox_3 148 klvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke 224
                                       +    + ++ +++++   k++V G ++ a + A+ + + g eV+++ r++ i k           di+n l +++k+
  gi|518652956|ref|YP_008142476.1| 155 D-YYTSDTIWNMREL-PGKIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKG-------FDEDINNHLINALKT 222
                                       4.4444455555444.579******************************977665.......566777777777777 PP

                       Pyr_redox_3 225 ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpgl 301
                                       + i ++  ++ +ei +k+ +  + te g ++++ d  ++atG  p+++ l+ +   +++d+ +v++++ + t  p +
  gi|518652956|ref|YP_008142476.1| 223 NGIIFHLGQNFQEIINKNGKKSIVTEAG-TFDNFDSLLVATGRVPQIDKLNLKAAGISTDNGIVVDDSLKTT-NPII 297
                                       779**************99999999997.67889999***********998877777778888888777666.5777 PP

                       Pyr_redox_3 302 flaG 305
                                       + aG
  gi|518652956|ref|YP_008142476.1| 298 YAAG 301
                                       7776 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.6   3.4e-08   4.1e-05       1     150 [.       5     143 ..       5     167 .. 0.80
   2 ?   -1.2   0.0       0.7   8.3e+02       2      29 ..     172     199 ..     171     225 .. 0.85
   3 ?   -0.5   0.0      0.42     5e+02     106     140 ..     253     287 ..     210     331 .. 0.61

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.4e-08
                                       CEEEE-SSHHHHHHHHHHHHT...T--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarl...GakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagi 72 
                                       d+ +iG G AG++AA++a++l    +k++Li   +  +t+++++C ps   i +++  +E  +       ++ +a+i
  gi|518652956|ref|YP_008142476.1|   5 DLAIIGWGAAGFAAAIKASELtsnQMKIALIgtGPIGGTCVNVGCVPSKFLIEASKNYKEATKP--SYRGITANANI 79 
                                       5789*************99762226789999988899***************888888888774..45556666667 PP

                                       EEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                              GIDA  73 qfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                       +f          +++l       + ++++ ++++n +n+++ e++++ ++         v  +++ ika +++i+tG
  gi|518652956|ref|YP_008142476.1|  80 NFS-------EFMESL-NDFVSTERNTKYADVIKNFENIDMYEGMAKFIDN------NTVAVNNKDIKALNFIISTG 142
                                       443.......345566.66778888999*********************65......5566788999********** PP

                                       T CS
                              GIDA 150 t 150
                                       +
  gi|518652956|ref|YP_008142476.1| 143 S 143
                                       9 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.7
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                       + V+G G   +e A+a ++ G +v ++ 
  gi|518652956|ref|YP_008142476.1| 172 IAVLGSGEVALELAYAFSNFGTEVHIFN 199
                                       889*********************9983 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.42
                                       HTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEE CS
                              GIDA 106 enepnleiieeeveeliveekkvkgvvtedgetik 140
                                       +n + l + +++v +++  + k +g+ t++g ++ 
  gi|518652956|ref|YP_008142476.1| 253 DNFDSLLVATGRVPQIDKLNLKAAGISTDNGIVVD 287
                                       33444455555555555555555555555555554 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.091   1.1e+02       3      29 ..       4      31 ..       2      38 .. 0.82
   2 !   16.5   0.0   2.9e-06    0.0035     134     249 ..     119     225 ..      75     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.091
                       K_oxygenase  3 lDligiGiGpsnLsLailleevk.kelk 29
                                      +Dl++iG G++  + ai ++e   +++k
  gi|518652956|ref|YP_008142476.1|  4 YDLAIIGWGAAGFAAAIKASELTsNQMK 31
                                      9*************99999887755555 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 2.9e-06
                       K_oxygenase 134 tveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                        +++++ + +++ ++a n ++++G++  iPe+   l+   + + s+++ + +   + + +iaV GsG  a e+++  
  gi|518652956|ref|YP_008142476.1| 119 FIDNNTVAVNNKDIKALNFIISTGSRTLIPEIKG-LT---DYYTSDTIWNMR---ELPGKIAVLGSGEVALELAYAF 188
                                       3555556667899*****************9755.54...577777777666...67899*******9999999987 PP

                       K_oxygenase 211 lrrqkkvelklvtrsealeplddspfvneifsPeyvdyf 249
                                        +  +  e++++ rs+++ +  d ++ n ++++  ++ +
  gi|518652956|ref|YP_008142476.1| 189 SNFGT--EVHIFNRSNRILKGFDEDINNHLINALKTNGI 225
                                       76655..9*************999999999888776665 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.9   2.2e+03       2      17 ..      32      47 ..      31     126 .. 0.56
   2 !   17.7   0.0   2.2e-06    0.0026       1      51 [.     171     221 ..     171     249 .. 0.87
   3 ?   -1.0   0.0       1.2   1.4e+03     122     148 ..     386     413 ..     381     442 .. 0.69

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.9
                                      EEEE--SCCHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaav 17
                                      +a iG+G +G    +v
  gi|518652956|ref|YP_008142476.1| 32 IALIGTGPIGGTCVNV 47
                                      6777777777665544 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 2.2e-06
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                       k+av+G+G +  ++a++f + g eV+++++s+++l+   e i++ l ++ +
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKGFDEDINNHLINALK 221
                                       69****************************************997766544 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 1.2
                                       HCCCSSSGGG.EEEEEE-SSTTT--EEE CS
                           3HCDH_N 122 laealkrper.viglHFfnPpplmkLvE 148
                                       +a++++ +++ ++g+H + P     ++E
  gi|518652956|ref|YP_008142476.1| 386 IAKVISGKDKkILGVHVVAPMAAEFIIE 413
                                       7777765544499999999987655544 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   1.0   0.00049      0.59       2      29 ..       5      35 ..       4      50 .. 0.78
   2 ?   -0.1   0.2      0.24   2.9e+02      46      84 ..      78     114 ..      52     147 .. 0.76
   3 ?   -2.2   0.0       1.1   1.3e+03       3      37 ..     172     206 ..     171     209 .. 0.90
   4 ?    7.1   0.0    0.0015       1.8     109     163 ..     210     263 ..     206     268 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00049
                                      SEEEE--SHHHHHHHHHH...HHTT--EEEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisa...akrgkrVlll 29
                                      d+++iG GaAG+ aAi+a    +++ +++l+
  gi|518652956|ref|YP_008142476.1|  5 DLAIIGWGAAGFAAAIKAselTSNQMKIALI 35
                                      899**************94434455555555 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
                                       T-EEEETT-SGGGEEES...STTTTHHHHHHS-HHHHHH CS
                       HI0933_like  46 rcNvTnlseepeellsrypenpkflksalsrftnedlia 84 
                                        +N++   e++++++s   e++++++ ++++f+n d+ +
  gi|518652956|ref|YP_008142476.1|  78 NINFSEFMESLNDFVST--ERNTKYADVIKNFENIDMYE 114
                                       67899988999999999..88888889999999988754 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.1
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       ++v+G G   l  A + ++ g +V ++++ +++++
  gi|518652956|ref|YP_008142476.1| 172 IAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILK 206
                                       899*************************9999876 PP

  == domain 4  score: 7.1 bits;  conditional E-value: 0.0015
                                       HHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 109 edivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       edi + l+++lk +g+ ++l ++ +++ +++++  ++ t+ ++  + d+l++AtG
  gi|518652956|ref|YP_008142476.1| 210 EDINNHLINALKTNGIIFHLGQNFQEIINKNGK-KSIVTEAGTFDNFDSLLVATG 263
                                       578899*********************887777.6666658888899*******9 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.1      0.05        60      32      52 ..       7      27 ..       2      33 .. 0.87
   2 ?   -1.6   0.0       1.1   1.4e+03     161     206 ..      50      94 ..      42      99 .. 0.79
   3 ?    8.8   0.0   0.00077      0.92      28      80 ..     169     222 ..     164     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.05
                                      EEESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglga 52
                                       +iG G aG +A+  a++l  
  gi|518652956|ref|YP_008142476.1|  7 AIIGWGAAGFAAAIKASELTS 27
                                      79*************999865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.1
                                       GGGGSHHHHHHHHHHHHHHHHHHHCHHHTCCHHHCTSHHHHCCEEE CS
                       AlaDh_PNT_C 161 lpgavprtasalltnntlpyleelladkglkkalkedealrkglvv 206
                                       +p++   +as+ + ++t p  + ++a+ ++ ++ +  e l+  + +
  gi|518652956|ref|YP_008142476.1|  50 VPSKFLIEASKNYKEATKPSYRGITANANI-NFSEFMESLNDFVST 94 
                                       688888899**********99999999988.777777777666655 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00077
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlks 80 
                                       p+k+ v+G G + l+ + + +++g +V +++ + + l+ +++ ++++ +++lk 
  gi|518652956|ref|YP_008142476.1| 169 PGKIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKGFDEdINNHLINALKT 222
                                       89***********************************99999888888877544 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.83   9.9e+02       2      18 ..       6      22 ..       5      29 .. 0.82
   2 ?    3.8   0.0     0.074        89       1      16 [.      31      46 ..      31     104 .. 0.77
   3 ?    8.8   0.1     0.002       2.4       1      47 [.     171     213 ..     171     227 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.83
                                      EEEETTSHHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgl 18
                                      ++iiG G  g+a a ++
  gi|518652956|ref|YP_008142476.1|  6 LAIIGWGAAGFAAAIKA 22
                                      79********9987665 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.074
                                      EEEEETTSHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealas 16
                                      ki++iG+G +g + ++
  gi|518652956|ref|YP_008142476.1| 31 KIALIGTGPIGGTCVN 46
                                      79*********87654 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.002
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg 47 
                                       ki+++G+G+++  la  +++ g   +e+ +  +r++  ++ + e+++
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFG---TEVHIF-NRSNRILKGFDEDIN 213
                                       7*********************...999977.887776666666655 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.4   1.7e+03      38      57 ..       5      24 ..       2      27 .. 0.82
   2 ?    1.2   0.4      0.17     2e+02      34      51 ..      27      44 ..      11      75 .. 0.84
   3 ?    9.4   0.0   0.00052      0.62      38      70 ..     171     203 ..     154     230 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.4
                                      EEEEES-SHHHHHHHHHHHH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlka 57
                                       ++iiG G+ G a+a ++++
  gi|518652956|ref|YP_008142476.1|  5 DLAIIGWGAAGFAAAIKASE 24
                                      589********999987765 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
                                      GTTSEEEEES-SHHHHHH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqav 51
                                       +++++++iG+G IG + 
  gi|518652956|ref|YP_008142476.1| 27 SNQMKIALIGTGPIGGTC 44
                                      568999********9765 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00052
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskk 70 
                                       +++++G G+++ ++a  ++ fg +v +++rs++
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFGTEVHIFNRSNR 203
                                       589***************************977 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 ?   -1.7   0.2       2.1   2.6e+03       3      20 ..       7      24 ..       5      46 .. 0.73
   2 ?    2.3   0.1      0.13   1.5e+02      33      73 ..      86     126 ..      31     141 .. 0.74
   3 ?   10.6   0.0   0.00034       0.4       1      44 [.     171     214 ..     171     232 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.1
                                      EEE--SHHHHHHHHHHHT CS
                    NAD_Gly3P_dh_N  3 avlGaGswGtalAkvlae 20
                                      a++G G+ G a A+  +e
  gi|518652956|ref|YP_008142476.1|  7 AIIGWGAAGFAAAIKASE 24
                                      789999988888765544 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                                       HHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EE CS
                    NAD_Gly3P_dh_N  33 elieeineehenvkyLpgiklpenlvattdlaealkgadii 73 
                                       e ++++ ++++n+ky + ik  en+ +++ +a+ +++ ++ 
  gi|518652956|ref|YP_008142476.1|  86 ESLNDFVSTERNTKYADVIKNFENIDMYEGMAKFIDNNTVA 126
                                       45556667777888888888888888888888777776665 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00034
                                       -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSB CS
                    NAD_Gly3P_dh_N   1 kiavlGaGswGtalAkvlaenghevrlwvreeelieeineehen 44 
                                       kiavlG+G     lA ++++ g ev+++ r++  ++ ++e+ +n
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFGTEVHIFNRSNRILKGFDEDINN 214
                                       7******************************9776665555444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.1     0.047        56       1      35 [.       5      42 ..       5      76 .. 0.83
   2 ?    7.3   0.0    0.0026       3.1     150     201 ..     214     263 ..     208     318 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.047
                                      EEEEECTSHHHHHHHHHHHHT.T....EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.g....Vtllekgdiagsg 35
                                      d++iiG G +G ++A  +++       ++l+  g  +g g
  gi|518652956|ref|YP_008142476.1|  5 DLAIIGWGAAGFAAAIKASELtSnqmkIALIGTG-PIG-G 42
                                      789***************8763256889999888.444.3 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0026
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--G CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaG 201
                                       + l +a++++G+ +++g + +++ +++gk + v  t++g+ d +d + +a+G
  gi|518652956|ref|YP_008142476.1| 214 NHLINALKTNGIIFHLGQNFQEIINKNGKKSIV--TEAGTFDNFDSLLVATG 263
                                       678999****************99999997777..55598777799*****9 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.91   1.1e+03      17      39 ..      16      38 ..       2     140 .. 0.69
   2 ?    9.8   0.0   0.00088         1       9      41 ..     171     206 ..     163     294 .. 0.67
   3 ?   -2.6   0.0       6.2   7.4e+03      33      56 ..     400     423 ..     393     440 .. 0.69

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.91
                     NAD_binding_7 17 evAarkvrklleagakvtvvape 39
                                        Aa k++ l +++ k+ ++   
  gi|518652956|ref|YP_008142476.1| 16 FAAAIKASELTSNQMKIALIGTG 38
                                      45667777777777777776554 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00088
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev...k 41 
                                       k+ v G GevA++ ++ + ++g +v++        k
  gi|518652956|ref|YP_008142476.1| 171 KIAVLGSGEVALELAYAFSNFGTEVHIFNRSNrilK 206
                                       6789***********************877733332 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 6.2
                     NAD_binding_7  33 vtvvapevkeeleelvklaeeele 56 
                                       v+vvap  +e++ e v l+++ l 
  gi|518652956|ref|YP_008142476.1| 400 VHVVAPMAAEFIIEGVYLIQNGLT 423
                                       899999987777676777776663 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   1.1   0.00079      0.94       1      20 [.       5      24 ..       5      44 .. 0.82
   2 ?    0.4   0.0      0.22   2.7e+02     373     403 ..     275     305 ..     218     315 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00079
                                      SEEEE--SHHHHHHHHHHHH CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae 20
                                      D+ +iG G+AG aAA++a+e
  gi|518652956|ref|YP_008142476.1|  5 DLAIIGWGAAGFAAAIKASE 24
                                      899**************988 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.22
                                       S-EEEBETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 373 mgGvetdengrvldadgqpipGLYAaGevaa 403
                                       ++G+ td    v+d+ +++ p  YAaG ++ 
  gi|518652956|ref|YP_008142476.1| 275 AAGISTDNGIVVDDSLKTTNPIIYAAGDCIR 305
                                       46777777777777777799999****9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       594  (0.0331307); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.66u 0.32s 00:00:00.98 Elapsed: 00:00:00.50
# Mc/sec: 2745.22
//
Query:       gi|518652957|ref|YP_008142477.1|  [L=76]
Description: copper chaperone [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-08   35.5   0.4    1.1e-08   35.4   0.4    1.2  1  HMA       Heavy-metal-associated domain
  ------ inclusion threshold ------
      0.012   15.7   0.0      0.013   15.6   0.0    1.1  1  CH        Calponin homology (CH) domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.4   1.2e-12   1.1e-08       2      48 ..       7      58 ..       6      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.2e-12
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVeg....daes.tk 48
                                      ++v gm+C+ C+++v   L+  +gV++v+v+l+ + ++V+     d+e  +k
  gi|518652957|ref|YP_008142477.1|  7 LKVYGMTCDDCVRHVSGGLKQAEGVTDVSVSLKDGMAVVKAmdtvDPENlLK 58
                                      6788************************************987655555444 PP

>> CH  Calponin homology (CH) 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      17      53 ..      24      60 ..      13      75 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.5e-06
                                      TSTTSSTTSCHHHHHTTSHHHHHHHHHHSTTTSSGGG CS
                                CH 17 eagpkvkvedfeedlrDGvlLckLlnklapglvdkkk 53
                                      + ++ + v+d++ +l+DG++  k ++ ++p+ + k  
  gi|518652957|ref|YP_008142477.1| 24 GLKQAEGVTDVSVSLKDGMAVVKAMDTVDPENLLKLD 60
                                      44567788**********************9865544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.28s 00:00:00.69 Elapsed: 00:00:00.45
# Mc/sec: 507.29
//
Query:       gi|518652958|ref|YP_008142478.1|  [L=113]
Description: hypothetical protein FACI_IFERC00001G1597 [Ferroplasma acidarmanus fer1]
Scores for complete 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   36.3   0.0    4.8e-09   36.0   0.0    1.1  1  HxlR          HxlR-like helix-turn-helix
      0.004   17.1   0.0     0.0066   16.4   0.0    1.3  1  HTH_45        Winged helix-turn-helix
  ------ inclusion threshold ------
      0.047   14.3   0.0      0.095   13.3   0.0    1.5  1  RTP           Replication terminator protein
       0.06   13.8   0.0      0.077   13.5   0.0    1.3  1  HTH_27        Winged helix DNA-binding domain
      0.094   12.7   0.0       0.13   12.3   0.0    1.3  1  HTH_12        Ribonuclease R winged-helix domain
        0.1   12.7   0.0       0.13   12.3   0.0    1.1  1  Replic_Relax  Replication-relaxation


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.6e-12   4.8e-09       1      75 [.      29     101 ..      29     112 .. 0.86

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.6e-12
                                       HHHSTTHHHHHHHHTTS-EE..HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHH CS
                              HxlR   1 liggkWkllilvellkgkkR..fselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepv 75 
                                       l+g++++l il  + + + R  f+++ + +p+  + ++a+rL+eL   g+++r   +     v Y+ltekG+++++ 
  gi|518652958|ref|YP_008142478.1|  29 LLGKRYTLFILGVIGNNNTRknFNDIYNSIPGSNRTIIARRLKELTDAGIVKRCRKEV----VTYELTEKGQDIRKG 101
                                       689***********996554449******************************87654....67********99864 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   2.2e-06    0.0066      38      68 ..      68     101 ..      62     109 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.2e-06
                            HTH_45  38 kYLdmLvekgli...kkskekYvlTekGlellek 68 
                                       + L+ L++ g++   +k+  +Y+lTekG+++ + 
  gi|518652958|ref|YP_008142478.1|  68 RRLKELTDAGIVkrcRKEVVTYELTEKGQDIRKG 101
                                       6699********77778999**********9875 PP

>> RTP  Replication terminator protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.2e-05     0.095      44      87 ..      62      97 ..      32     103 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                                      -HHHHHHHHHHHHHTTSEEEEEEEBTSSSSSEEEEEEESS..HH CS
                               RTP 44 nhseiyralhelvedgilkrrkelkekaklqevviYsltdeGke 87
                                      n++ i r l+el++ gi+kr         ++evv+Y+lt++G++
  gi|518652958|ref|YP_008142478.1| 62 NRTIIARRLKELTDAGIVKRC--------RKEVVTYELTEKGQD 97
                                      667789999999999999886........4799*******9998 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   2.6e-05     0.077      33      68 .]      63      95 ..      33      95 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2.6e-05
                            HTH_27 33 shis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                       +i+   lk+Lt +G v+r ++e     ++++lT+kG
  gi|518652958|ref|YP_008142478.1| 63 RTIIaRRLKELTDAGIVKRCRKE----VVTYELTEKG 95
                                      5667799**********999999....9********9 PP

>> HTH_12  Ribonuclease R winged-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.2e-05      0.13      35      64 ..      66      97 ..      41      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.2e-05
                            HTH_12 35 vRyrLrkleergltrrvgya..greltEkGle 64
                                      + +rL+ l + g+++r ++     eltEkG +
  gi|518652958|ref|YP_008142478.1| 66 IARRLKELTDAGIVKRCRKEvvTYELTEKGQD 97
                                      579*************99998889******86 PP

>> Replic_Relax  Replication-relaxation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05      0.13      23      67 ..      62      97 ..      49     103 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
                      Replic_Relax 23 hratarrrLarLrelgllsrlrkrvggarggsepyvYaLtpkGar 67
                                      +r+ + rrL++L++ g+++r rk+            Y Lt+kG++
  gi|518652958|ref|YP_008142478.1| 62 NRTIIARRLKELTDAGIVKRCRKE---------VVTYELTEKGQD 97
                                      444689**************9999.........456999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 752.89
//
Query:       gi|518652959|ref|YP_008142479.1|  [L=309]
Description: methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-50  171.6   0.0    2.3e-50  171.1   0.0    1.1  1  Met_10           Met-10+ like-protein
    1.1e-12   47.6   1.1    2.7e-12   46.4   1.1    1.6  1  Trm5_N           tRNA methyltransferase 5 N-terminal domain
    6.7e-08   32.3   0.0    1.1e-07   31.6   0.0    1.2  1  MTS              Methyltransferase small domain
    8.3e-05   22.1   0.0    0.00013   21.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    0.00017   22.2   0.0    0.00036   21.2   0.0    1.6  1  Methyltransf_25  Methyltransferase domain
    0.00024   20.7   0.0    0.00054   19.6   0.0    1.6  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
    0.00026   20.7   0.0    0.00059   19.5   0.0    1.6  2  Cons_hypoth95    Conserved hypothetical protein 95
     0.0007   19.6   0.0     0.0014   18.5   0.0    1.5  1  Methyltransf_18  Methyltransferase domain
     0.0012   18.6   0.0      0.011   15.4   0.0    2.1  1  UPF0020          Putative RNA methylase family UPF0020
     0.0033   16.8   0.1      0.017   14.5   0.0    1.8  2  DNA_methylase    C-5 cytosine-specific DNA methylase
     0.0047   16.6   0.0      0.011   15.4   0.0    1.6  2  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0065   15.7   0.1     0.0095   15.1   0.1    1.5  1  TRM              N2,N2-dimethylguanosine tRNA methyltransfera
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.24   11.1   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase


Domain annotation for each model (and alignments):
>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.1   0.0   1.6e-53   2.3e-50       2     199 .]      69     263 ..      68     263 .. 0.95

  Alignments for each domain:
  == domain 1  score: 171.1 bits;  conditional E-value: 1.6e-53
                                       EEEEETTEEEEEB-TTSSHHHHHHHHHHHHHSS-SCEEEE-S-SBTTTTB--EEEEEES-.SEEEEEETTEEEEEET CS
                            Met_10   2 kfeiiGdvvilnlreelkeykkvigevildktkvktvlrkvsevegefRtfelevlaGsdstetihkEngcrfklDv 78 
                                       +++iiG ++i++ ++  +  +k +++ +  ++++kt++ +++  +gefRt++l +++G+   +ti +Eng+r+ +Dv
  gi|518652959|ref|YP_008142479.1|  69 SYDIIGSIAIIKGKTIED--AKYLSDFLKTRKNIKTIYLDKGI-TGEFRTRQLTLIYGEPVYKTIYRENGIRLMVDV 142
                                       79********99776444..477888877788*******9987.********************************* PP

                                       TTS---GGGHHHHHHHHTT--TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEE CS
                            Met_10  79 skvyfsskleaErerlaklveegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkp 155
                                       sk yfs++l++Er r+ak v++ge +vd+fAGiGpf+i iak  +++ ++a+d+n +++ +l en+klN++   ++p
  gi|518652959|ref|YP_008142479.1| 143 SKAYFSPRLASERLRIAKEVSDGENIVDMFAGIGPFSILIAK-NRESSIVAMDKNQNAIDLLLENLKLNRLRGEITP 218
                                       *****************************************9.99999***************************** PP

                                       EES-GGG---.TT-EEEEEE--TTTGGGGHHHHHHHEEEEEEEEE CS
                            Met_10 156 ileDgrevir.eqladrvvmnlpksaieFldkvlaalkdggvihy 199
                                       + +D+ e+i+  + +dr++mnlp+ a eF++ +++ lk gg+i y
  gi|518652959|ref|YP_008142479.1| 219 VAGDSGELIQqYENVDRIIMNLPHDASEFVGVAYKSLKIGGLINY 263
                                       *********97899************************9999987 PP

>> Trm5_N  tRNA methyltransferase 5 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   1.1   1.9e-15   2.7e-12       2      42 ..       4      44 ..       4      48 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 1.9e-15
                                      EEEEGGGHHHHHHHHHHTT-B-TTS--EEETTEEEEEB-S- CS
                            Trm5_N  2 ikVpkkegEkvRkkLlekglLdrnyKIksdddylyIPvkee 42
                                      ++V k++g++++ kL++++l++r+yKI  d+ y+yIPv+++
  gi|518652959|ref|YP_008142479.1|  4 VRVDKENGQETINKLRDLDLINREYKILNDGTYVYIPVNKN 44
                                      89************************************985 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   7.7e-11   1.1e-07      31     107 ..     164     242 ..     151     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 7.7e-11
                                       TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTTTST.TS-EEEEEE- CS
                               MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvleeve.ekkfdlivsN 104
                                         ++++D+ +G+G+ ++ +ak+ ++ +++++d++ +A+++  enl+ n+l+  ++ va d  e ++  +++d i++N
  gi|518652959|ref|YP_008142479.1| 164 DGENIVDMFAGIGPFSILIAKNRES-SIVAMDKNQNAIDLLLENLKLNRLRgeITPVAGDSGELIQqYENVDRIIMN 239
                                       5678****************97666.8************************5555556666555553579******* PP

                                       --S CS
                               MTS 105 PPf 107
                                        P 
  gi|518652959|ref|YP_008142479.1| 240 LPH 242
                                       885 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   9.3e-08   0.00013     158     254 ..     161     259 ..     144     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 9.3e-08
                              PrmA 158 lvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveakleva..lseellk.eekadviv 231
                                        v  ge+++D+ +G G  +i  ak   +++va+D ++ A++   eN++lN+++ +++     s+el++  e++d i+
  gi|518652959|ref|YP_008142479.1| 161 EVSDGENIVDMFAGIGPFSILIAKNRESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVagDSGELIQqYENVDRII 237
                                       578899***********************************************9775421235666655899***** PP

                              PrmA 232 aNILaevlielaedikklvkegg 254
                                        N   +   e++  ++k +k gg
  gi|518652959|ref|YP_008142479.1| 238 MNL-PHDASEFVGVAYKSLKIGG 259
                                       995.4445666666666666666 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   2.6e-07   0.00036       1      97 []     168     259 ..     168     259 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 2.6e-07
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSSSTTTEEEEEEESTGG CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpfedgsfDlvvssgalh 75 
                                       ++d+ +G G +++ +ak+  +++++++D ++++++   e+++ ++l  +++ v gd  +l ++ + +D ++++  l 
  gi|518652959|ref|YP_008142479.1| 168 IVDMFAGIGPFSILIAKN-RESSIVAMDKNQNAIDLLLENLKLNRLrgEITPVAGDSGELIQQYENVDRIIMN--LP 241
                                       78999************9.68********************99999999999********************5..45 PP

                                       GSSHHHHHHHHHHHHHHEEEEE CS
                   Methyltransf_25  76 hlsdedlekalkeiarvLkpgG 97 
                                       h    d+ +++  +++ Lk gG
  gi|518652959|ref|YP_008142479.1| 242 H----DASEFVGVAYKSLKIGG 259
                                       5....66788888888888887 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 !   19.6   0.0     4e-07   0.00054       3      66 ..     167     231 ..     165     261 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 4e-07
                   Methyltransf_15   3 vilDlfsGaGGnviqfalv.fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklk 66 
                                        i+D+f+G G  +i +a++  ++++a+++n++ + +  +N ++     +it+v gd  el+++ +
  gi|518652959|ref|YP_008142479.1| 167 NIVDMFAGIGPFSILIAKNrESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVAGDSGELIQQYE 231
                                       689*************9985678************************************998743 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       4.9   6.7e+03       4      18 ..     109     123 ..     109     132 .. 0.72
   2 !   19.5   0.0   4.3e-07   0.00059      40     137 ..     163     256 ..     142     277 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 4.9
                                       XSCCCTTXEEEXTTX CS
                     Cons_hypoth95   4 igGkakgrkLkvleg 18 
                                       i G+++ r+L +  g
  gi|518652959|ref|YP_008142479.1| 109 ITGEFRTRQLTLIYG 123
                                       568888888876655 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 4.3e-07
                                       HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS--SS-EEEE CS
                     Cons_hypoth95  40 iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkleeetaelkedaleallklakkkeefdi 116
                                        +g++++D+faG G  ++  +    +++v+++k+++a+ +l enl+  +l++e++ +  d+ e +++     e++d 
  gi|518652959|ref|YP_008142479.1| 163 SDGENIVDMFAGIGPFSILIAKNRESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVAGDSGELIQQY----ENVDR 235
                                       578899**********98766555599******************************99999999777....56899 PP

                                       EEE--SSSTTCH.HHHHHHHH CS
                     Cons_hypoth95 117 vflDPPyakellieevlelle 137
                                       + ++ P  +++++  + ++l+
  gi|518652959|ref|YP_008142479.1| 236 IIMNLPHDASEFVGVAYKSLK 256
                                       999999888887666666666 PP

>> Methyltransf_18  Methyltransferase 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    0.0014       2      88 ..     153     238 ..     151     239 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.1e-06
                   Methyltransf_18   2 skRLkaiaslvekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsdGlekl 78 
                                       s+RL +ia+ v++g++++D  +  g  +i ++k ++ ++++a+D n+++++   en++ ++l+ +i+ + +d  e +
  gi|518652959|ref|YP_008142479.1| 153 SERL-RIAKEVSDGENIVDMFAGIGPFSILIAK-NRESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVAGDSGELI 227
                                       6788.699999*****************98875.66779************************************** PP

                   Methyltransf_18  79 keee.vdtvvi 88 
                                       ++ e vd +++
  gi|518652959|ref|YP_008142479.1| 228 QQYEnVDRIIM 238
                                       *8888999986 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   8.1e-06     0.011      73     131 ..     184     242 ..     137     246 .. 0.90

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.1e-06
                                       HHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS---EEEE---- CS
                           UPF0020  73 araelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevdvivtnpPY 131
                                       +++e +++++D+++++++   eN++  ++ ++i+ ++ d  +L ++ ++vd i+ n+P 
  gi|518652959|ref|YP_008142479.1| 184 KNRESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVAGDSGELIQQYENVDRIIMNLPH 242
                                       4567789*************************************88889*********6 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 ?   -0.2   0.0      0.35   4.9e+02     190     239 ..      50     101 ..       7     141 .. 0.63
   2 !   14.5   0.0   1.2e-05     0.017       3      66 ..     168     237 ..     167     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.35
                                       SGGGTTS-EE.BTTTB--GGGSSSTT-EE--.......S---H.HHTS--B- CS
                     DNA_methylase 190 lrdlleekse.ldeektalsdklvekeekikkttkaseegypk.elsrnrid 239
                                         d+++ +s+ ++ ek ++s +++ + + ik +t+++ +  ++   +r++i+
  gi|518652959|ref|YP_008142479.1|  50 TVDIEGAPSNrIEPEKVSFSYDIIGSIAIIKGKTIEDAKYLSDfLKTRKNIK 101
                                       4566666666667777777777777777777766666666665322222233 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                                       EEEES-TT-HHHHHHHHTT-EEEEEEE--TTTHHHHHHH-..-SEEEES-TTTS-......GS--.-SEEE CS
                     DNA_methylase   3 fidLfaGiGGfrlgleaagfecvaaseidkkaaktYeanfk.kvsigDitkidkk......klpediDlLv 66 
                                       ++d+faGiG f++  ++   + ++a +++++a++++  n k +   g+it ++ +      +++ ++D ++
  gi|518652959|ref|YP_008142479.1| 168 IVDMFAGIGPFSILIAKNRESSIVAMDKNQNAIDLLLENLKlNRLRGEITPVAGDsgeliqQYE-NVDRII 237
                                       89**************************************999999999999888776444444.277666 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         7   9.6e+03     145     162 ..      85     102 ..      84     107 .. 0.75
   2 !   15.4   0.0   7.8e-06     0.011       6      91 ..     162     244 ..     158     267 .. 0.83

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 7
                                       TTHHHHHHHHHH-TTEEE CS
                   Methyltr_RsmB-F 145 EneevieeaLkkredvel 162
                                       E+ + + ++Lk+r++++ 
  gi|518652959|ref|YP_008142479.1|  85 EDAKYLSDFLKTRKNIKT 102
                                       677788889999888775 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 7.8e-06
                                       --TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHH..HTT--SEEEEES-CTCCHHHHCC..E CS
                   Methyltr_RsmB-F   6 pqeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlk..rLgvtntivleaDarkidkvlggelf 80 
                                         ++e i+D+ a+ G    +ia+    ++ +vA+d+n++ ++ + enlk  rL  + ++ + +D  +  +      +
  gi|518652959|ref|YP_008142479.1| 162 VSDGENIVDMFAGIGPFSILIAKN--RESSIVAMDKNQNAIDLLLENLKlnRLRGE-ITPVAGDSGELIQQYE--NV 233
                                       57899**********999999875..999******************752277666.7777888888866666..4* PP

                                       EEEEEEE--CC CS
                   Methyltr_RsmB-F  81 DriLlDaPCsg 91 
                                       Dri++  P  +
  gi|518652959|ref|YP_008142479.1| 234 DRIIMNLPHDA 244
                                       *****999655 PP

>> TRM  N2,N2-dimethylguanosine tRNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   6.9e-06    0.0095      51     149 ..     166     261 ..      38     296 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 6.9e-06
                                       EEEEESS-TTSHHHHHHHHH-S-EEEEEEE-S-HHHHHHHHHHHHHTT--GGEEEE-S-HHHHHC--SS-EEEEEE- CS
                               TRM  51 ikvldaLsasGlRaiRfalEvpgvkevlaNDisekAvelikeNvklneveeivvineddAnvllaekkkrfdviDlD 127
                                        +++d +++ G  +i  a+    +++++a D +++A++l+ eN kln     +++  +d   l+++ + + d i + 
  gi|518652959|ref|YP_008142479.1| 166 ENIVDMFAGIGPFSILIAKN--RESSIVAMDKNQNAIDLLLENLKLNRLRGEITPVAGDSGELIQQYE-NVDRIIMN 239
                                       57999999999999999998..8999************************779999999999996554.45555555 PP

                                       -SS--GGGHHHHHHHEEEEEEE CS
                               TRM 128 PfGspapfldsavqsvkekglL 149
                                           +++f+  a +s+k +gl+
  gi|518652959|ref|YP_008142479.1| 240 LPHDASEFVGVAYKSLKIGGLI 261
                                       4456789999999999999987 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   0.00017      0.24      29     103 ..     144     219 ..     139     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00017
                   Methyltransf_16  29 vkylekklake...lganelsklsvlELGsGtGlvGlavaellpeakviltDleellellkknielnknalkskvkv 102
                                         y++  la+e     ++ + + +++++ +G G + + +a+  ++  v +   +++++ll +n++ln+  l+ +++ 
  gi|518652959|ref|YP_008142479.1| 144 KAYFSPRLASErlrIAKEVSDGENIVDMFAGIGPFSILIAKNRESSIVAMDKNQNAIDLLLENLKLNR--LRGEITP 218
                                       5677777777777767788999********************6665566666667***********87..8777765 PP

                   Methyltransf_16 103 e 103
                                        
  gi|518652959|ref|YP_008142479.1| 219 V 219
                                       5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 1912.24
//
Query:       gi|518652960|ref|YP_008142480.1|  [L=681]
Description: hypothetical protein FACI_IFERC00001G1599 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-20   72.4   0.0    7.9e-20   71.3   0.0    1.5  1  DEAD             DEAD/DEAH box helicase
    1.6e-11   44.5   0.1    8.2e-11   42.2   0.0    2.3  1  Helicase_C       Helicase conserved C-terminal domain
    1.7e-11   44.6   0.2    1.5e-10   41.6   0.1    2.5  2  HHH_5            Helix-hairpin-helix domain
    2.3e-10   40.7   0.0    7.6e-10   39.1   0.0    1.9  2  ResIII           Type III restriction enzyme, res subunit
    2.1e-06   27.8   0.2    0.00012   22.1   0.0    3.2  3  HHH_2            Helix-hairpin-helix motif
      0.008   16.0   0.0      0.019   14.8   0.0    1.7  1  DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
  ------ inclusion threshold ------
       0.01   15.3   0.0        1.5    8.2   0.0    2.6  2  PhoH             PhoH-like protein
      0.042   12.9   0.0       0.08   12.0   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
      0.051   13.3   0.1        4.6    7.1   0.0    3.4  4  HTH_38           Helix-turn-helix domain
       0.18   12.1   0.0       0.48   10.7   0.0    1.7  1  AAA_19           AAA domain
        0.3   10.8   2.1        4.2    7.1   0.1    2.9  3  DUF4364          Domain of unknown function (DUF4364)


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 !   71.3   0.0   4.8e-23   7.9e-20       2     174 ..      24     182 ..      23     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 4.8e-23
                                       HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   2 diQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrv 78 
                                       + Q+ea+  + ++++v+v+ +T+sGKTl+  i ++++ +     +g+k ++++P+r+La + +++l ++ + ++++v
  gi|518652960|ref|YP_008142480.1|  24 EHQEEAVAKLRENKNVIVSVPTASGKTLIGYISIYDTYL-----KGKKSMYIVPLRSLAMEKFSELLSLRN-LGVKV 94 
                                       68*********************************9884.....57899*****************99999.78888 PP

                                       EEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  79 lliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcd 155
                                        + ig+  ++   s + +++d++++t +r d++l++    l+ + ++++DE+++++d ++++ +++++++l   +  
  gi|518652960|ref|YP_008142480.1|  95 TMSIGD--YDVPPSFV-KNYDVIIATSERADSMLHRDPDILNYFGLVIIDEIHMISDPSRGPRLETVISSLLYLNP- 167
                                       888885..55577888.99***************877766*******************************43333. PP

                                       STTTSEEEEEESSBSHHHH CS
                                       xxxxxxxxxxxxxxxxxxx RF
                              DEAD 156 gklqrqvivlSATlpkdvk 174
                                          +  ++ lSAT++ +++
  gi|518652960|ref|YP_008142480.1| 168 ---EILLLGLSATVS-NIQ 182
                                       ...344999****97.555 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 !   42.2   0.0     5e-14   8.2e-11      11     110 ..     232     364 ..     225     365 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 5e-14
                                       HHTTTTSEEEEEESSHHHHHH.....HHHH................HHHT....TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  11 kleeeggkilifvntidrlek.....vkll................lekk....gikvavlhgelpqnereeileqf 62 
                                       ++ e+gg++l+f n+++++ek     v+++                +e +    +  v  +h+ l++++r  i + f
  gi|518652960|ref|YP_008142480.1| 232 ESIESGGQALVFRNSRRNAEKyaqsmVNFFdfqndfekleippdlfNEAQanmvAHGVMFHHAGLSNDQRTMIEKLF 308
                                       34489999999*999998877765554444666665555666655433336788899999***************** PP

                                       HTTSSSEEEESGGGTSSSTSTTESEEEESSSS...SSH.......HHHHHHHTTSSST CS
                        Helicase_C  63 nkgesdvLiatdvaerGidipkvnlVinfdlp...rnv.......tsyiqriGRtgRa 110
                                       ++g +++L at  ++ G+++p +++Vi+ d+    +          +++q+iGR+gR 
  gi|518652960|ref|YP_008142480.1| 309 KQGYIKILTATPTLAAGVNLP-ARTVIIRDITrfsD-GyskpisgIEIQQMIGRAGRP 364
                                       ********************9.88888888885442.035667779***********5 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.4   2.3e+03       1      18 [.      81      98 ..      81     104 .. 0.90
   2 !   41.6   0.1   8.9e-14   1.5e-10       4      56 ..     621     673 ..     618     674 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.4
                                      -HHHHTSTT--HHHHHHH CS
                             HHH_5  1 feeLlsvsGiGpktAlal 18
                                      f eLls+  +G k+ +++
  gi|518652960|ref|YP_008142480.1| 81 FSELLSLRNLGVKVTMSI 98
                                      789**********99987 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 8.9e-14
                                       HHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHHH CS
                             HHH_5   4 LlsvsGiGpktAlallsaGiesvedlaaadveeLakipGiGkktAeriilelk 56 
                                       +++++ +G+++ ++l+++G++s++d+a+a ve++++i G++ k+A+ ii+ + 
  gi|518652960|ref|YP_008142480.1| 621 IIEIPQVGRVRGRRLYNNGFKSIDDIANARVEDISRIFGFSTKLAKDIIENAG 673
                                       789**********************************************9775 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   4.6e-13   7.6e-10       2     169 ..      20     178 ..      19     180 .. 0.78
   2 ?   -2.0   0.1       1.9   3.1e+03     142     170 ..     292     321 ..     291     322 .. 0.72

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.6e-13
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                       ++l+e+Qeea+ +l+      ++k++++  +T +GKTl+ +  i+  + kgk  k + +vp +sl     +e+ ++ 
  gi|518652960|ref|YP_008142480.1|  20 FTLYEHQEEAVAKLR------ENKNVIVSVPTASGKTLIGYISIYDTYLKGK--KSMYIVPLRSLAMEKFSELLSLR 88 
                                       6899*********96......7899***************777777666666..99*****9999776666666666 PP

                                       GG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T...TTHH CS
                            ResIII  79 seaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk...swre 152
                                       +  +k   +   gd + +  ++ +n +++++t +++d+ +     +++    ++f ++iiDE H +++ +     + 
  gi|518652960|ref|YP_008142480.1|  89 NLGVK--VTMSIGDYDVP-PSFVKNYDVIIATSERADSML-----HRDPDILNYFGLVIIDEIHMISDPSrgpRLET 157
                                       65553..33333333333.5799*****************.....99*********************845554444 PP

                                       H....HHT---SEEEEEESS- CS
                            ResIII 153 i....lekfkeavllglTATp 169
                                       +    l  ++e +llgl+AT 
  gi|518652960|ref|YP_008142480.1| 158 VisslLYLNPEILLLGLSATV 178
                                       42332666688*********7 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.9
                                       GGTTS.TTTHH.HHHT---SEEEEEESS-S CS
                            ResIII 142 Hrlgakkswre.ilekfkeavllglTATpe 170
                                       H++g ++  r  i + fk+ ++  lTATp 
  gi|518652960|ref|YP_008142480.1| 292 HHAGLSNDQRTmIEKLFKQGYIKILTATPT 321
                                       78877655555477788888888899**95 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.27   4.4e+02      27      54 ..      74     101 ..      72     102 .. 0.87
   2 ?   -0.9   0.1       1.1   1.9e+03      45      56 ..     251     262 ..     250     266 .. 0.85
   3 !   22.1   0.0   7.4e-08   0.00012       6      53 ..     622     670 ..     617     678 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.27
                             HHH_2  27 daLkkasleeLlevddiGeeiAqsivef 54 
                                         L+  ++ eLl++++ G ++  si ++
  gi|518652960|ref|YP_008142480.1|  74 RSLAMEKFSELLSLRNLGVKVTMSIGDY 101
                                       678888999************9999876 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.1
                             HHH_2  45 eeiAqsivefFe 56 
                                       e+ Aqs v+fF+
  gi|518652960|ref|YP_008142480.1| 251 EKYAQSMVNFFD 262
                                       789********7 PP

  == domain 3  score: 22.1 bits;  conditional E-value: 7.4e-08
                             HHH_2   6 LGIrhVGektAklLakr.FksldaLkkasleeLlevddiGeeiAqsive 53 
                                       + I++VG    + L ++ Fks+d +++a +e+++ + +  ++ A++i+e
  gi|518652960|ref|YP_008142480.1| 622 IEIPQVGRVRGRRLYNNgFKSIDDIANARVEDISRIFGFSTKLAKDIIE 670
                                       569***********9766****************************987 PP

>> DNA_pol_lambd_f  Fingers domain of DNA polymerase lambda
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   1.2e-05     0.019       6      30 ..     624     648 ..     621     671 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.2e-05
                   DNA_pol_lambd_f   6 vyGVGpktAkkwyakGirtledlra 30 
                                       +  VG+++ +++y++G+++++d+ +
  gi|518652960|ref|YP_008142480.1| 624 IPQVGRVRGRRLYNNGFKSIDDIAN 648
                                       778********************87 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.0   0.00094       1.5       7      48 ..      24      65 ..      21      95 .. 0.80
   2 ?    4.2   0.0     0.016        26      63     137 ..     565     655 ..     549     665 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00094
                                      HHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTTS CS
                              PhoH  7 keQkeylealkkndivfaiGpaGtGKtylavalavealkkkk 48
                                      ++Q+e++  l++n+ v++  p+ +GKt++      + + k+k
  gi|518652960|ref|YP_008142480.1| 24 EHQEEAVAKLRENKNVIVSVPTASGKTLIGYISIYDTYLKGK 65
                                      68***************************9887777666633 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.016
                                       ----SS---------T..TTHHHHHHHTTTS..............-TTCHHHHHHTTSEEEEEGGGGTT--B.-SEE CS
                              PhoH  63 eelGflpgdleekvdp..ylrplydaLkdll..............gaekvekllekgkievaplaymRGrTl.ndaf 122
                                       e  G+ pgd++ k +   ++++    L +++               +e v++ +  + ie+ ++  +RGr l n+ f
  gi|518652960|ref|YP_008142480.1| 565 ETFGIGPGDIQAKASSadWISYSLYRLGSMFdkenennllhlnirIKEGVKEEI-IRIIEIPQVGRVRGRRLyNNGF 640
                                       666666666666654322555555556666666666666664444333333333.3678999999*****9956779 PP

                                       EEE-SGGG--HHHHH CS
                              PhoH 123 vilDEAQnttkeqmk 137
                                         +D+  n++ e + 
  gi|518652960|ref|YP_008142480.1| 641 KSIDDIANARVEDIS 655
                                       999999998888776 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   4.9e-05      0.08     116     149 ..      24      56 ..       3      69 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyal 149
                                       e+++e+++k  re+++++vs +T sGKt + y+ 
  gi|518652960|ref|YP_008142480.1|  24 EHQEEAVAKL-RENKNVIVSVPTASGKTLIGYIS 56 
                                       7788888888.99***************998876 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.2   6.8e+03      23      31 ..     181     189 ..     177     190 .. 0.72
   2 ?    7.1   0.0    0.0028       4.6       5      21 ..     296     312 ..     293     312 .. 0.94
   3 ?   -0.5   0.0      0.67   1.1e+03       8      30 ..     529     551 ..     527     552 .. 0.85
   4 ?    1.0   0.0      0.23   3.8e+02      14      28 ..     633     648 ..     629     649 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.2
                            HTH_38  23 lreIArrLg 31 
                                       + eIA +++
  gi|518652960|ref|YP_008142480.1| 181 IQEIAEWMN 189
                                       668888776 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0028
                            HTH_38   5 LsleeReeIerllaeGl 21 
                                       Ls ++R +Ie+l ++G+
  gi|518652960|ref|YP_008142480.1| 296 LSNDQRTMIEKLFKQGY 312
                                       9**************97 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.67
                            HTH_38   8 eeReeIerllaeGlslreIArrL 30 
                                        +R+ I +  +e ++ ++ A +L
  gi|518652960|ref|YP_008142480.1| 529 LDRHNISDFSEESMGAAKTAIIL 551
                                       69************999988666 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.23
                            HTH_38  14 erllaeG.lslreIAr 28 
                                        rl++ G +s+ +IA 
  gi|518652960|ref|YP_008142480.1| 633 RRLYNNGfKSIDDIAN 648
                                       589***********96 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00029      0.48       1     116 [.      26     149 ..      26     165 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00029
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrla 76 
                                       q+eav+   ++k+++v  +  +GKT +  + ++++    + k +++++v + + A+++ +e l+  ++  +   +++
  gi|518652960|ref|YP_008142480.1|  26 QEEAVAkLRENKNVIVSVPTASGKTLI--GYISIYDTYLKGK-KSMYIVPLRSLAMEKFSELLSLRNLGVKVTMSIG 99 
                                       899**8789999************976..5566666665554.89****************8744333333333343 PP

                            AAA_19  77 l..............ldfddlltealelleeaeeekklqeee.llivDEfqdvd.e 116
                                                      ++   + + a ++l   +++ ++ + + l+i+DE+ +++ +
  gi|518652960|ref|YP_008142480.1| 100 DydvppsfvknydviIA---TSERADSML---HRDPDILNYFgLVIIDEIHMISdP 149
                                       34556666544332121...122234443...45677779999*********9855 PP

>> DUF4364  Domain of unknown function (DUF4364)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.12   1.9e+02      15      52 ..       5      42 ..       3      53 .. 0.82
   2 ?   -2.1   0.2       1.8   2.9e+03      28      43 ..     255     270 ..     253     272 .. 0.84
   3 ?    7.1   0.1    0.0026       4.2      35      86 ..     446     493 ..     435     504 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
                           DUF4364 15 pltnsqlseiileneytnYfdlqqalseLvesglieee 52
                                      ++t s+ ++++ +n++t Y + ++a+++L e++++ ++
  gi|518652960|ref|YP_008142480.1|  5 EITPSEFLKVTDNNDFTLYEHQEEAVAKLRENKNVIVS 42
                                      578888899999999999*999******9999988764 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                           DUF4364  28 neytnYfdlqqalseL 43 
                                       + ++n+fd+q+ +++L
  gi|518652960|ref|YP_008142480.1| 255 QSMVNFFDFQNDFEKL 270
                                       5789******999888 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0026
                           DUF4364  35 dlqqalseLvesglieeeekenktlykiTekGketlelfenripksirekid 86 
                                        +++al  L ++++i+e    ++++y+ T+ G+ t +l  + +++ i +k+ 
  gi|518652960|ref|YP_008142480.1| 446 AFESALYFLKDNDFITE----ENDIYSATKFGRLTSDLYIDPVSSLILKKCL 493
                                       578999**********5....89***************99999998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (681 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.49
# Mc/sec: 4209.30
//
Query:       gi|518652961|ref|YP_008142481.1|  [L=581]
Description: hypothetical protein FACI_IFERC00001G1600 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-20   73.4  31.2    1.8e-20   73.4  31.2    4.0  4  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   5.3     0.074   1.3e+03     117     167 ..      14      67 ..      11      88 .. 0.77
   2 !   73.4  31.2   9.9e-25   1.8e-20       1     276 [.      93     356 ..      93     376 .. 0.82
   3 ?   -0.5   1.4     0.031   5.5e+02      39      89 ..     416     471 ..     399     479 .. 0.74
   4 ?   -2.8   1.8      0.16   2.9e+03     198     219 ..     556     577 ..     536     581 .] 0.51

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.074
                   Proton_antipo_M 117 sallAatlvkagvlllirllllla....vssneisqlllilaiismllgslvala 167
                                       s+l+ ++    +++ll+++ + ++    +   ++  +++++a+i  +++s+ +++
  gi|518652961|ref|YP_008142481.1|  14 SVLI-SIKYRTAGYLLTAIASAMFflftFRIYDYITYFYLIAAIVWIIASVFSIS 67 
                                       7888.77777788877765443333333777788888999999999999998875 PP

  == domain 2  score: 73.4 bits;  conditional E-value: 9.9e-25
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelgln 77 
                                       + + ll+  g+E++++p y+ ++++kk+   +eA + +f+ + ++ ++++ + ++ y +tgtl+f  l +       
  gi|518652961|ref|YP_008142481.1|  93 SPNYLLFITGWEIMSIPAYVTVAVNKKN--DMEAYIFMFF-SEISTVLIITAAVISYVYTGTLNFSILTND------ 160
                                       568899999***************9777..8888766665.679**********************99999...... PP

                   Proton_antipo_M  78 slelllllllllvgllvKsaqvpl..hlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqllli 152
                                             +ll++ +g++ K+++ p+  + Wlp a+  aP+  sa+++at+  +gv++++++ ll   +s +i ++++i
  gi|518652961|ref|YP_008142481.1| 161 -----TVLLIFAIGAMSKMGLTPFmiSEWLPIAHGSAPANTSAIFSATMTLMGVYGIVKIALLSV-VSIDIGIIFII 231
                                       .....56677889*********994457******************************8888877.*********** PP

                   Proton_antipo_M 153 laiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyere.. 227
                                       +++is+l+g+l a    ++K+l ++S+i   G ++  +++  +   +   + l  ++l+++++F++a s+ +     
  gi|518652961|ref|YP_008142481.1| 232 IGVISVLFGALYAYISENMKSLGGFSTIENNGALMATIGL--FV--AVNNTVLREFILISIAIFAMAHSIAKTGLfi 304
                                       ********************************99988887..33..3344556677788888888887775443344 PP

                   Proton_antipo_M 228 .....ktrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaav 276
                                             ++++ a++g  +k  i ++  +++l sl+Gl p +g l+ ++iLe+ +
  gi|518652961|ref|YP_008142481.1| 305 tvghtGVEYFSAVNG--EKSTINQIGKFFALSSLSGLFPSLGGLGTWMILESFF 356
                                       442224444444444..3666777777888888888888888888888888765 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 0.031
                   Proton_antipo_M  39 flltllgsliLLlgilllynltgtlefeelskal.....elglnslelllllllll 89 
                                       +l++l++ ++LL+g  ++ ++ + l f+ l+        ++gl  +   +++lll+
  gi|518652961|ref|YP_008142481.1| 416 ILVFLFAISFLLIGNEYISGIPSVLVFKGLMIESrfgpaDFGLITPLYIFIFLLLF 471
                                       57788899999999999999999999999887765555555555555555555544 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.16
                   Proton_antipo_M 198 veaaiihllthalfkallFlla 219
                                       ++++i + ++++++ + l++++
  gi|518652961|ref|YP_008142481.1| 556 MNSSISYYIIYMIIAFILVIII 577
                                       2333334444444444444333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1191  (0.0664287); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.70u 0.33s 00:00:01.03 Elapsed: 00:00:00.50
# Mc/sec: 3483.03
//
Query:       gi|518652962|ref|YP_008142482.1|  [L=199]
Description: Ni,Fe-hydrogenase III small subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.4e-17   63.8   0.3    4.3e-17   62.2   0.3    1.7  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
  ------ inclusion threshold ------
        2.7    7.9  13.9       0.54   10.2   1.6    3.8  4  Fer4         4Fe-4S binding domain


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 !   62.2   0.3   4.8e-21   4.3e-17       1     130 [.      92     194 ..      92     195 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.8e-21
                                       -SHHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEE CS
                       Oxidored_q6   1 CtGcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakavi 77 
                                       C++c++++++l ++ +d       r+++ ++++++         +ad lvv G  t +++  l+ ++++++++k+vi
  gi|518652962|ref|YP_008142482.1|  92 CGACNVEFTTLFSPQYDT-----NRFKIFMSNTPR---------HADALVVMGVYTDGMEAVLKEAYDAMPSPKIVI 154
                                       9*******99999999*9.....999899999999.........********************************* PP

                                       EESHHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  78 avGtCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                        +G+CA +GGi + +          +++   + di+++GCPp+p+ i++++ +
  gi|518652962|ref|YP_008142482.1| 155 GIGACALSGGIIGSR----------AMD---KYDIEVAGCPPTPASIINAIIK 194
                                       ************332..........233...5799**************9975 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   0.0     0.011     1e+02      18      24 .]      36      42 ..      35      42 .. 0.90
   2 ?   10.2   1.6   6.1e-05      0.54       2      14 ..      45      57 ..      45      58 .. 0.94
   3 ?    1.6   0.2      0.03   2.7e+02       3      11 ..      87      95 ..      85      97 .. 0.60
   4 ?   -1.4   0.2      0.26   2.4e+03       9      15 ..     154     160 ..     154     161 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.011
                                      STTTEEE CS
                              Fer4 18 CPvgAIt 24
                                      CP++A++
  gi|518652962|ref|YP_008142482.1| 36 CPTDALE 42
                                      *****85 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 6.1e-05
                                      EEETTTSSS-THH CS
                              Fer4  2 videekCigCGaC 14
                                      ++d+++Ci+C +C
  gi|518652962|ref|YP_008142482.1| 45 KWDMNRCIFCREC 57
                                      59*********** PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.03
                                      EETTTSSS- CS
                              Fer4  3 ideekCigC 11
                                      id   C +C
  gi|518652962|ref|YP_008142482.1| 87 IDSGTCGAC 95
                                      666666666 PP

  == domain 4  score: -1.4 bits;  conditional E-value: 0.26
                                       SS-THHH CS
                              Fer4   9 igCGaCv 15 
                                       ig GaC+
  gi|518652962|ref|YP_008142482.1| 154 IGIGACA 160
                                       7889**7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.45
# Mc/sec: 1320.14
//
Query:       gi|518652963|ref|YP_008142483.1|  [L=384]
Description: hypothetical protein FACI_IFERC00001G1602 [Ferroplasma acidarmanus fer1]
Scores for complete 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   72.0   0.0    8.9e-15   54.5   0.0    2.2  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
      0.005   15.8   0.0      0.026   13.4   0.0    1.8  2  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0   9.9e-19   8.9e-15      14     155 ..     168     295 ..     163     308 .. 0.88
   2 !   15.6   0.0   7.3e-07    0.0066     199     269 ..     309     379 ..     296     380 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 9.9e-19
                                       HHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHH CS
                    Complex1_49kDa  14 eRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskee 90 
                                        Re++ +++ ++ G R   s+  +G v+ D+++  l+        +ek+++++ + l + +if +R+++ g++++e+
  gi|518652963|ref|YP_008142483.1| 168 LREEVARIISRAFGHRYFFSVNGFGTVSGDFSTIKLN-------AIEKQFRDIYDGLLSSKIFLDRIQENGIVKNEN 237
                                       599**************************99876555.......5567778888888999**************997 PP

                                       HHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  91 alelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqa 155
                                             tGp +Ra+G+k+D Rk+++   Y +  f+ ++++ +D+++R++vr eE+ ++++Ii+  
  gi|518652963|ref|YP_008142483.1| 238 -----STGPAARAAGFKFDARKDSKSLDYRN--FTPVTESGADSFSRLVVRSEEVFEAINIIDSY 295
                                       .....59*****************9999986..78899999*********************865 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 7.3e-07
                                       --SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-S.GGGTHHHHTT---HHHH CS
                    Complex1_49kDa 199 vpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgell.aDvvailgsldivlgev 269
                                       + +g+  a++E+p G + +y+  ++  k   +++ +ps+ nl+ ++e lk++ +  D+  +  s+ i ++e+
  gi|518652963|ref|YP_008142483.1| 309 TGSGKGSARIESPAGDIFYYVNIEN-GKLNDIQMVSPSYLNLRLFREALKNNNIfTDFFFVWESFGIWISEL 379
                                       56788899************98875.4567899**************9997654389999999999988876 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0     0.046   4.1e+02      15      46 ..      95     126 ..      87     134 .. 0.85
   2 !   13.4   0.0   2.9e-06     0.026     395     458 ..     284     348 ..     274     350 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.046
                                       HHHHHHTT-SSSTTHHHHHHHHHHHHHHT--- CS
                      NiFeSe_Hases  15 awalvqRiCGVCttvHalasvravedAlgiki 46 
                                       a + v+Ri G  + + ++  + ave+Algi+ 
  gi|518652963|ref|YP_008142483.1|  95 ALLKVERINGFHAASNSIGYILAVEEALGIEN 126
                                       667799***********************985 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 2.9e-06
                                       HHHHHHHTTB---B--TT-S.GGGS-SEEEEEEEEEETTEEEEEEEEEETTEEEEEEEE-HHHHH CS
                      NiFeSe_Hases 395 elvenikkgdtetaneekld.kkevpkeakGvglveapRGaLsHwikikdgkienYqavvPsTWn 458
                                       e+ e i+  d+  +++ k++ k+e+  + kG + +e p G +  +++i++gk+++ q+v Ps  n
  gi|518652963|ref|YP_008142483.1| 284 EVFEAINIIDSYGVKNIKTRtKNELTGSGKGSARIESPAGDIFYYVNIENGKLNDIQMVSPSYLN 348
                                       55666666666666655554044555689********************************9655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2769.88
//
Query:       gi|518652964|ref|YP_008142484.1|  [L=441]
Description: hypothetical protein FACI_IFERC00001G1603 [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  162.2  26.2    1.5e-47  162.2  26.2    1.9  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0033   17.4   4.5     0.0033   17.4   4.5    4.1  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   2.1      0.39   3.5e+03     276     280 ..      61      65 ..      12     106 .. 0.56
   2 !  162.2  26.2   1.7e-51   1.5e-47       6     291 ..     112     387 ..     107     390 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.39
                   Proton_antipo_M 276 vavsl 280
                                       +  s+
  gi|518652964|ref|YP_008142484.1|  61 MVSSV 65 
                                       11111 PP

  == domain 2  score: 162.2 bits;  conditional E-value: 1.7e-51
                   Proton_antipo_M   6 llylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslell 82 
                                        +++g+E + + + lL    k++  sleA+  ++++ ++g  + +++++l+y   gtl +++++ +   +++ +++ 
  gi|518652964|ref|YP_008142484.1| 112 FMWVGIETTTITSALLLITEKSD-ISLEATWRYIIIVSAGVTFAFISVILIYYSFGTLTITTILAY--GAKDTIAVR 185
                                       69************999988666.******************************************..899999999 PP

                   Proton_antipo_M  83 lllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirlllllavssneisqlllilaiisml 159
                                       l+  + lvg+ +K++++p+h+Wlpda+ eaP+pvsa+++++l+ +++++l r+  ++      ++ l+++ ++is+l
  gi|518652964|ref|YP_008142484.1| 186 LAVAIALVGFGTKVGVFPVHTWLPDAHSEAPAPVSAMFSGVLLPVALYVLYRIYEIFP-----MRELFVWAGTISVL 257
                                       999999***************************************************9.....9************* PP

                   Proton_antipo_M 160 lgslvalaqtdiKrllAySsishlGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayg 236
                                       ++++    q ++Kr+ AyS++  + + li++++ t+ g+ +++++ll+h++ ka+ F  +g+v ye++ t++i+ ++
  gi|518652964|ref|YP_008142484.1| 258 FAAIFLGYQKNYKRMFAYSTMENMNIALIGFSTFTITGLIGSLLLLLAHSFGKAGAFYSSGNV-YEMSGTKSIDGVS 333
                                       **************************************************************9.************* PP

                   Proton_antipo_M 237 gLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvlavvasv 291
                                       gL   ++  a+ +l+  ++++G+Pp+  F+++fliL++++ ++ ++  +++v s+
  gi|518652964|ref|YP_008142484.1| 334 GLIR-NRSSAASMLLSSFAVTGTPPFGTFFGEFLILYSVFTIHFYAQFVIIVLSL 387
                                       **85.7889999********************************99988855554 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 !   17.4   4.5   3.7e-07    0.0033      16      46 ..      49      79 ..      41      95 .. 0.85
   2 ?   -2.6   1.3      0.67     6e+03      28      42 ..     152     166 ..     147     169 .. 0.83
   3 ?    0.3   0.3     0.083   7.4e+02      33      56 ..     252     275 ..     244     277 .. 0.84
   4 ?   -3.6   1.4       1.4   1.3e+04      23      40 ..     422     439 ..     419     440 .. 0.69

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 3.7e-07
                   Proton_antipo_N 16 fllDklsalmllvvtfvsllvhlYSigYMad 46
                                      f++D ++ +++l+v+ v l+ ++YS++Y ++
  gi|518652964|ref|YP_008142484.1| 49 FFIDHITYIFILMVSSVYLMSLIYSVKYVHN 79
                                      89**************************995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.67
                   Proton_antipo_N  28 vvtfvsllvhlYSig 42 
                                       +  f+s++ + YS+g
  gi|518652964|ref|YP_008142484.1| 152 TFAFISVILIYYSFG 166
                                       567999999999987 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.083
                   Proton_antipo_N  33 sllvhlYSigYMaddegyqRFfay 56 
                                       +++  l++  ++   ++y+R fay
  gi|518652964|ref|YP_008142484.1| 252 GTISVLFAAIFLGYQKNYKRMFAY 275
                                       5666789999999999*******9 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 1.4
                   Proton_antipo_N  23 almllvvtfvsllvhlYS 40 
                                       a  l +  +v +lv   +
  gi|518652964|ref|YP_008142484.1| 422 AAILSIFIGVVFLVVYHA 439
                                       667778888888887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      206  (0.0114898); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 2834.41
//
Query:       gi|518652965|ref|YP_008142485.1|  [L=213]
Description: hypothetical protein FACI_IFERC00001G1604 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.24   11.4   0.3       0.24   11.4   0.3    1.7  2  dDENN     dDENN domain


Domain annotation for each model (and alignments):
>> dDENN  dDENN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   1.4e-05      0.24      14      31 ..      24      41 ..      22      44 .. 0.92
   2 ?   -2.6   0.2      0.33   5.9e+03      29      41 ..     117     130 ..     116     141 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 1.4e-05
                             dDENN 14 hrpFlsrfletQmFarFI 31
                                      + ++l++++ tQ+F++FI
  gi|518652965|ref|YP_008142485.1| 24 SNKYLRSMVLTQAFQSFI 41
                                      578**************9 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.33
                             dDENN  29 rFIderlel.sgsd 41 
                                       +FI+ r +   +sd
  gi|518652965|ref|YP_008142485.1| 117 SFIHIRSHIfPDSD 130
                                       79998887665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1079  (0.0601818); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.30s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1470.33
//
Query:       gi|518652966|ref|YP_008142486.1|  [L=313]
Description: hypothetical protein FACI_IFERC00001G1605 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-35  121.2  21.0    6.2e-35  120.9  21.0    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 !  120.9  21.0   3.5e-39   6.2e-35       8     298 ..      13     309 ..       6     310 .. 0.89

  Alignments for each domain:
  == domain 1  score: 120.9 bits;  conditional E-value: 3.5e-39
                                       HHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTT CS
                            NADHdh   8 vvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafa 84 
                                       ++++l+  l++++  k+ A i++R+GP      +++qp++D++Kll Ke+i+ +++ + +fl +p++a+ +  l+ +
  gi|518652966|ref|YP_008142486.1|  13 LFVVLFSPLAIGIFEKLKANIESRKGP------SIFQPYYDLFKLLKKETIVTENS-SRFFLYSPYIAFGIYSLIAL 82 
                                       345556669999***************......********************999.56799*************** PP

                                       TS-SS..S.SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS- CS
                            NADHdh  85 viPfg..e.vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagsls 158
                                       +iP+   e ++   + +++   +l+sl++++ +++ ++s+s+++ +Ga R ++     E +l+++++av+l++g+ +
  gi|518652966|ref|YP_008142486.1|  83 IIPVFmtEpIIFTASGDFFAGAILFSLAAFVKIIGTLDSGSNFSSMGASRLMSFNFFGEGTLITVFFAVALISGTNN 159
                                       ***8854258888889************************************************************9 PP

                                       HHHHHHCCCTT..-C.CCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSS...SSCCCTT-HCHHHHHHHHHHHHHHH CS
                            NADHdh 159 lseiveaqeei..wf.illqllafiifliallaetnraPFDlpeaesEL...vaGfhtEYsgmkfalfflaeyanmv 229
                                         +  ++  ++   +  l++++a+++f++++l e +++P    e+++E+    +G+  EYsg  +a+  +++y++++
  gi|518652966|ref|YP_008142486.1| 160 PYTTNHYLISHplSNlTLVHIFAIFAFFMVFLYEFGKMPTQ-SEGNQEMgmiDSGIDYEYSGKALAINKWSSYMKTY 235
                                       999977665555422566679******************97.89****766589*********************** PP

                                       HHHHHHHHHCT.SS-HCCS.......HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCHHHHHHHHHHH CS
                            NADHdh 230 lvsalavllFlgGwllpfs.......gllwfllKvllllflfiwiratlpRlRydqlmklgwkvllplalanlllt 298
                                       l+ ++++ +Fl  w + f+       ++l ++ K+lll++++++i+++l++lR+ +++++   v +++++++l+lt
  gi|518652966|ref|YP_008142486.1| 236 LLGSVLINVFLIPWGM-FNtfplfflNALTMIGKWLLLIVIVLVIDTSLAKLRLFRVIDYL-AVAFTFSILFLILT 309
                                       ***********99854.33466778999*******************************95.57888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2217.05
//
Query:       gi|518652967|ref|YP_008142487.1|  [L=1136]
Description: hypothetical protein FACI_IFERC00001G1606 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
          0 1020.6   0.0          0 1018.3   0.0    1.8  1  CobN-Mg_chel  CobN/Magnesium Chelatase
  ------ inclusion threshold ------
       0.12   11.3   0.2       0.28   10.1   0.2    1.5  1  NatB_MDM20    N-acetyltransferase B complex (NatB) non cataly
        0.7   10.3   5.6         12    6.4   0.3    3.6  3  DUF3837       Domain of unknown function (DUF3837)


Domain annotation for each model (and alignments):
>> CobN-Mg_chel  CobN/Magnesium Chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1018.3   0.0         0         0       2    1087 ..     103    1119 ..     102    1121 .. 0.93

  Alignments for each domain:
  == domain 1  score: 1018.3 bits;  conditional E-value: 0
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel    2 aYlkeggveNlknllryladkllgkkeeeveppvelpeegiyhpdakelfesleeylewykkakkekaptvgilf 76  
                                        +Y+ +gg eN+kn++ ++ ++++    +++e+pve+p +giy+            y       ++e  ++vgilf
  gi|518652967|ref|YP_008142487.1|  103 NYYFYGGYENIKNMVLFIENTITP---RHYEEPVEMPFSGIYE------------YG------NTEFPKKVGILF 156 
                                        7999******************94...5789***********7............33......2355678***** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel   77 yrahllagntavidaliraleerglnvlpvfvssl..d....seaqealeelftkegeekvdalinttsfalvkg 145 
                                        yr+ +++++t++i+ +i++l+++++ ++pvf++++  +     +a+e ++++f+++g++ vda+in++sf+l k+
  gi|518652967|ref|YP_008142487.1|  157 YRTAWVDRDTKIIQYIIDNLNNNKISAIPVFTNGFgdRsrgiMSAEECINTYFYSDGKPVVDAVINLLSFSLIKK 231 
                                        ***********************************961567789999*************************976 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.x RF
                      CobN-Mg_chel  146 paeeeeeeaeeealkelnvPvlqa.ilssqsreeWeessqGlspldlamsvalpEldGriepvvisfke.eee.e 217 
                                        +++        + l +l+vPv+q+ i+++++++eW +s +Gl+ +++ ms +lpE+dG+iepv i++ +     +
  gi|518652967|ref|YP_008142487.1|  232 EDK--------STLMNLGVPVFQGlIYYYKEEKEWLDS-SGLDVVSTIMSAMLPEMDGTIEPVLIGVIKkI-YdR 296 
                                        642........23689********************99.9**************************97743.337 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  218 etevekyepipervervadlaarwarLrrkpnaekkvaiilanypp...gegrlgnavgLdvpaSlvnlLkalke 289 
                                         + +++ +p++e+++ +++++++w++Lr ++n+ekk+aiil++  +    e+++g+a+gLd+++S+ ++++ l+e
  gi|518652967|ref|YP_008142487.1|  297 GAIYRELVPVKEQAQYMINRIRKWVNLRYMKNSEKKIAIILHSGSSfkdLEANIGTATGLDTLNSVSSIMSLLRE 371 
                                        88899*************************************9887766899*********************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxx.xxxxx....xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  290 eGYdveelpesgdeLiellleggt.ndpew....eelkv.gaaallpaeeYeewfeeLpeelreeveerWgeppg 358 
                                        +GY+++ lpe+g+ Li++++e+++  + +w    e+++  g++  +p++eY ++f+eLpe+ ++ +++rWge + 
  gi|518652967|ref|YP_008142487.1|  372 NGYNIDYLPENGESLIKTIMEKKAiPEGKWtpveEIINKgGSVYGMPVKEYMKFFRELPEDSQDMIIKRWGELNT 446 
                                        *****999****************78888877643333269********************************99 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  359 emveeeksgekklvipglqlGnvfvgvQPargyeedps...klyhdpdlpPthqYlAfYlWlreefgadavvHvG 430 
                                        e  +  +  +++++ipg+  Gn+f+g+QP+r    d++   + +hd+ +p th +lAfY+W++e f+ada++HvG
  gi|518652967|ref|YP_008142487.1|  447 ERDY--MLLNGTMHIPGIISGNIFIGIQPKRITFADNDnsiRSIHDSLTPVTHYWLAFYKWIQEIFRADAIIHVG 519 
                                        6444..55678********************955443334799******************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  431 kHGtlEwlPGKqvglseecyPdillgdlPhlYpYivnnpgEGtqAKRRsyAviidHltPpmtraelygelaeLee 505 
                                        +HGtlE++PGK++gls +++P+i +g++P+lY+Y  n pgEG++AKRRsyAv++d++tPp +  ++ ++++eLe+
  gi|518652967|ref|YP_008142487.1|  520 THGTLEFTPGKGLGLSPSDFPEISIGEIPNLYLYSTNVPGEGIIAKRRSYAVLLDYITPPTAYDDVPDDIKELED 594 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  506 lideYeeaesldpe.rlkalreqilelveelnldkdlgleeakeeeeeefeellekldgyleelkeaqirdglhi 579 
                                        lid+Yee+e+++++ r + + e+i +   + +l  d +          + ++  +++++ l+  k++ i++gl+i
  gi|518652967|ref|YP_008142487.1|  595 LIDDYEETEKAENTsRETMILEKIQKISDKIGLSIDFK----------DAHKATHEIEHRLNLFKDSIISKGLYI 659 
                                        ********999777699999999999999999998882..........34556789******************* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  580 lGeapegeqlvdlvvailrleneegesltealaealgldldeleeksekelrtagdalealeeeaeelveellee 654 
                                         G+  ++++l+d+v++ +r++    esl+++  ++                            eae+ + ++l+e
  gi|518652967|ref|YP_008142487.1|  660 YGKDIDKDDLKDYVTTATRFD----ESLSKKYGKE----------------------------EAENQIMAYLNE 702 
                                        ******************875....6666666665............................678888999988 PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  655 eaeeeeaeaeeleeeeeeeeeeteeEitallraLdGeyippgpsGdptrgraevLPTGrNfysvDpraiPteaAw 729 
                                        ++   e e+ + e+ +     + e+E ++ll aL+G++i+pg sG++trgr +vLP+GrNfy+vDp +iP+++Aw
  gi|518652967|ref|YP_008142487.1|  703 GTPIPELETGIIEKLK----FSPENEKNNLLMALNGKFIEPGVSGSLTRGRYDVLPSGRNFYAVDPFKIPSHSAW 773 
                                        7766554433333332....23459************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  730 evGkklaeellerylqehgeyPekvglslwgtetmrteGediAqiLallGvrPvwdaa.grvvdlelipleeLgR 803 
                                        +vG  la++l+e+ +++++++Pe++g++lw+t++ r++Ge i+qiL+ +Gv+Pvw++  ++v+d++ ip++ L+R
  gi|518652967|ref|YP_008142487.1|  774 QVGVILANKLIENEYKKNNKFPETIGFVLWSTDAYRSDGELISQILYTIGVEPVWQEGtKKVKDVKPIPMDVLKR 848 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  804 PRiDVtvriSGffRDafpnlielldkavelvaeldEpeedNfvrkhvleeeaeleekeeaeeratyRvFgskpGa 878 
                                        PRiDV+v+ SG++RD++ n+iel+d a+++v+eldE+++ Nf+ kh ++                 R+F+skpG+
  gi|518652967|ref|YP_008142487.1|  849 PRIDVVVESSGIVRDNLFNIIELIDLAIKKVSELDEDDDVNFIVKHHKKYG------------HLDRIFSSKPGS 911 
                                        **********************************************99874............356********* PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  879 YgagvqeliessnWedeedLaeaYlnwssyaYgkgaegeeaeeafearLkrvdvvvqnqdsrehdlldsddyyqf 953 
                                        Yg+gv+++iess+We+e+dLa+++++w++y Ygk++ g+e+++ + +  k++++++++++ +e+d+ d ++ y++
  gi|518652967|ref|YP_008142487.1|  912 YGSGVNNAIESSKWENENDLADVFTEWMGYSYGKNNFGRESKDELLSISKDIETIIHKREIDEIDINDDSCNYSY 986 
                                        *************************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel  954 lGGltaavrslsgkkpeayfgdssnpenpkvrtlkeeiarelrsrvlNPkWiegmmrhGykGafelaatvdnlfg 1028
                                         GG+ +++++ sg+kp+++f d+ np++p+vrt+keei+r +  ++lN+kWie+ ++ Gy+Ga+e+ + +++l+g
  gi|518652967|ref|YP_008142487.1|  987 AGGFYLMAKK-SGSKPSLMFEDTFNPNKPQVRTMKEEIERTAIGKLLNEKWIEAQKNFGYRGATEMLKKIEHLYG 1060
                                        ******9987.9*************************************************************** PP

                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      CobN-Mg_chel 1029 wdatadvvddwvyeevaetYvlDeevrefleekNpwAlreiaerLlEaarrglWeasee 1087
                                        w at+++v+d++++++a+++vlD+e++e+++++NpwAl ei++r++Ea +r++W+as+ 
  gi|518652967|ref|YP_008142487.1| 1061 WGATTGMVNDNIFNNIADKFVLDREMKEWFKKENPWALSEITSRMIEAYKRDIWHASDS 1119
                                        ********************************************************986 PP

>> NatB_MDM20  N-acetyltransferase B complex (NatB) non catalytic subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.2   4.7e-05      0.28     266     321 ..      65     120 ..      61     123 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 4.7e-05
                        NatB_MDM20 266 llftrlstlgpfskalslleqalrfYesaeketpesiakayekgsYskieefiefq 321
                                       +++++++++ + +k++ +++++l+ Y++ +k + e +++ y +g Y++i++++ f 
  gi|518652967|ref|YP_008142487.1|  65 NILEDIESVIKGKKNVIAIDPILSNYSTVSKFVEEKVSNYYFYGGYENIKNMVLFI 120
                                       688999***********************************************985 PP

>> DUF3837  Domain of unknown function (DUF3837)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.3     0.002        12      67      94 ..     586     613 ..     576     617 .. 0.86
   2 ?   -2.7   0.0       1.4   8.2e+03      57      79 ..     680     702 ..     670     723 .. 0.65
   3 ?    4.4   0.1    0.0085        51      20      96 ..    1050    1126 ..    1041    1133 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.002
                           DUF3837  67 dekekklikllkdYepdeevdeqmkell 94 
                                       ++ +k+l  l++dYe +e+++++++e++
  gi|518652967|ref|YP_008142487.1| 586 PDDIKELEDLIDDYEETEKAENTSRETM 613
                                       56799******************99985 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.4
                           DUF3837  57 eeelkkvspkdekekklikllkd 79 
                                       +e l+k + k+e e++++  l++
  gi|518652967|ref|YP_008142487.1| 680 DESLSKKYGKEEAENQIMAYLNE 702
                                       55555555555555555554443 PP

  == domain 3  score: 4.4 bits;  conditional E-value: 0.0085
                           DUF3837   20 iltgnyElayalGllakllglpeieekeeleelkekleeelkkvspkdekekklikllkdYepde.evdeqmkel 93  
                                         ++ ++E  y+ G    +++ + ++++ + + l  +++e  kk +p    ++   ++++ Y++d  ++ + mke 
  gi|518652967|ref|YP_008142487.1| 1050 EMLKKIEHLYGWGATTGMVNDNIFNNIADKFVLDREMKEWFKKENPWA-LSEITSRMIEAYKRDIwHASDSMKEQ 1123
                                        69999************************************9999876.67777888888887742345556655 PP

                           DUF3837   94 lkl 96  
                                        l+ 
  gi|518652967|ref|YP_008142487.1| 1124 LEE 1126
                                        544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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: 0.83u 0.31s 00:00:01.13 Elapsed: 00:00:00.46
# Mc/sec: 7350.67
//
Query:       gi|518652968|ref|YP_008142488.1|  [L=615]
Description: hypothetical protein FACI_IFERC00001G1607 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-13   51.0   0.4    2.1e-12   47.6   0.1    2.3  2  VWA_2            von Willebrand factor type A domain
    1.1e-12   47.6   0.0    2.2e-12   46.6   0.0    1.4  1  AAA_lid_2        AAA lid domain
    4.7e-11   42.5   0.1    4.1e-07   29.6   0.0    2.4  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
    3.6e-09   36.7   0.2    7.7e-05   22.7   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
      4e-08   33.7   1.4    2.8e-07   31.0   0.1    2.3  2  VWA              von Willebrand factor type A domain
    5.8e-05   22.3   0.0     0.0042   16.2   0.0    2.4  2  MCM              MCM P-loop domain
    0.00016   22.2   0.1    0.00039   21.0   0.1    1.7  1  Mg_chelatase_C   Magnesium chelatase, subunit ChlI C-terminal
     0.0098   16.3   0.0      0.026   14.9   0.0    1.8  1  AAA_16           AAA ATPase domain
  ------ inclusion threshold ------
      0.015   15.5   1.0      0.048   13.8   0.0    2.4  2  AAA_2            AAA domain (Cdc48 subfamily)
      0.021   15.1   0.0       0.18   12.0   0.0    2.4  1  AAA_22           AAA domain
      0.022   14.7   0.1      0.074   13.0   0.1    1.8  1  Rad17            Rad17 P-loop domain
      0.026   14.2   0.1       0.12   12.2   0.1    2.0  2  AAA_29           P-loop containing region of AAA domain
      0.032   13.9   0.0        0.3   10.8   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.042   14.3   0.0       0.31   11.5   0.0    2.5  1  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> VWA_2  von Willebrand factor type A domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.59   7.5e+02      69      93 ..     295     317 ..     268     325 .. 0.73
   2 !   47.6   0.1   1.6e-15   2.1e-12       2     106 ..     453     553 ..     452     554 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.59
                             VWA_2  69 leakgggtnlaaaLqlarkalkkrr 93 
                                       +e   ++ +l +aLq+a ++  k++
  gi|518652968|ref|YP_008142488.1| 295 TE--VNEDDLKKALQFALNHRMKEK 317
                                       44..37899********99887765 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 1.6e-15
                             VWA_2   2 vfvlDtSgSmrngdygptrleaakdaveallksl..pgdrvglvtfsd.gpevlipltkdkakilnalrnleakggg 75 
                                       ++ +D+S Sm+ +    +r+e+a+++   llk+l   ++rv+l+ f++ ++evl +++++ ++++n+++n+   gg+
  gi|518652968|ref|YP_008142488.1| 453 IIAIDSSRSMNFS----SRIEIAREFSDMLLKKLyiMRSRVALIKFAGeRSEVLMNFSRNFTALKNIIDNISS-GGK 524
                                       799*********9....6**************8865699*********779*********************7.6** PP

                             VWA_2  76 tnlaaaLqlarkalkkrrkgekrvivlitDg 106
                                       t l +aL+   k+ + ++   k v +l+tDg
  gi|518652968|ref|YP_008142488.1| 525 TPLYDALENIYKLSSYEK--LKTVSLLVTDG 553
                                       **************9886..99999999999 PP

>> AAA_lid_2  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   1.7e-15   2.2e-12      14      60 ..     274     319 ..     264     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.7e-15
                         AAA_lid_2  14 sgrRadlallraArAlAalegrdyVtpeDvkeaaplVLaHRlrrepe 60 
                                       s  Ra + ++++A+A+Aa+ gr++V+++D+k+a +++L+HR++++ +
  gi|518652968|ref|YP_008142488.1| 274 SN-RAMISTVKTAKAIAAYYGRTEVNEDDLKKALQFALNHRMKEKGK 319
                                       44.5**************************************95443 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   0.00024       0.3      24      50 ..      32      58 ..       8      65 .. 0.78
   2 !   29.6   0.0   3.2e-10   4.1e-07      91     158 ..     117     184 ..      79     196 .. 0.94

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00024
                      Mg_chelatase 24 nlllvGppGsGKtmlakrlpsllppls 50
                                       ll++Gp G  K+ + ++l+s+lp+++
  gi|518652968|ref|YP_008142488.1| 32 GLLITGPKGIAKSTMVRALSSILPEVK 58
                                      599*********************987 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 3.2e-10
                      Mg_chelatase  91 vGggskpkpGeislahnGvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNp 158
                                       + g s  + G i  a++G+L++DE+  ++ ++++++ +   +g   ++r   + ++parf lv +mNp
  gi|518652968|ref|YP_008142488.1| 117 IKGESVLREGLIGEANRGILYIDEVNLLDDSIVDSILDSAASGINIVEREGVSYTHPARFILVGTMNP 184
                                       56788999************************************9**********************9 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.1   0.00017      0.22       2      25 ..      33      56 ..      32      64 .. 0.86
   2 !   22.7   0.0     6e-08   7.7e-05      24     138 .]      90     197 ..      83     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
                                      EEEE--SSSSHHHHHHHGGGGBS- CS
                             AAA_5  2 vlLvGppGtgKselaerlaaalnr 25
                                      +l+ Gp+G++Ks++++ l++ l  
  gi|518652968|ref|YP_008142488.1| 33 LLITGPKGIAKSTMVRALSSILPE 56
                                      899****************99854 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 6e-08
                                       S--EEEEE--TT--HHHHH--B--............--------G-SEEEEESGGG--HHHHHH.HHHHHHSSEEE. CS
                             AAA_5  24 nreveyvqltrdtteedlkgrreik...ngttslvdsplvraaregeilvlDEveraesevlns.Llslleerrlll 96 
                                       n ++ +++l+ +tt + ++g+++i+   +g+ +l+++ + +a  +  il++DEv+ +++++++s L s  +   +  
  gi|518652968|ref|YP_008142488.1|  90 NMKIRIINLPNSTTLDRVVGSLDIShaiKGESVLREGLIGEA--NRGILYIDEVNLLDDSIVDSiLDSAASGINIVE 164
                                       6678899*****************888777777777777744..457***********9999871556666777776 PP

                                       .-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
                             AAA_5  97 eeggelvkaknddllerfrviatanpldrslnelspalrsRf 138
                                        eg  +++ ++      f +++t+np +    el p+l++Rf
  gi|518652968|ref|YP_008142488.1| 165 REGVSYTHPAR------FILVGTMNPEE---GELRPQLLDRF 197
                                       67777777776......*********99...77889999999 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 ?    1.0   0.1      0.34   4.3e+02      75     103 ..     296     324 ..     268     327 .. 0.75
   2 !   31.0   0.1   2.2e-10   2.8e-07       3     126 ..     453     568 ..     452     592 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.34
                                       GGSSC-HHHHHHHHHHHHHHHHGTSSTTS CS
                               VWA  75 gggttntgkalkyaleklfkssagaRena 103
                                       + ++++++kal++al++ +k++ ++R+++
  gi|518652968|ref|YP_008142488.1| 296 EVNEDDLKKALQFALNHRMKEKGKSRPDY 324
                                       44566799********9999999999865 PP

  == domain 2  score: 31.0 bits;  conditional E-value: 2.2e-10
                                       EEEEE-STTS.CHHHHHHHHHHHHHHHHHHTBTTTTEEEEEEEESSS.EEEEEETTSHCHHHHHHHHHHTGSGGGGS CS
                               VWA   3 vfvlDgSgsm.geenfekvkefikklveklevgpegtrvglvqfsse.vktefslndysskeellsalnnlkysggg 77 
                                       ++++D+S sm   +++e ++ef   l++kl+    + rv+l++f++e  ++ +++++  + ++l++ ++n+  s+gg
  gi|518652968|ref|YP_008142488.1| 453 IIAIDSSRSMnFSSRIEIAREFSDMLLKKLY--IMRSRVALIKFAGErSEVLMNFSR--NFTALKNIIDNI--SSGG 523
                                       589*******445566688899999999999..8999*********94555577777..779********8..7777 PP

                                       SC-HHHHHHHHHHHHHHHHGTSSTTSEEEEEEEESS--CS.S.HTHHHHHH CS
                               VWA  78 ttntgkalkyaleklfkssagaRenakkviilltdGksnd.g.dpkeaane 126
                                       +t + +al++ ++ l + ++      k v +l+tdG+ n    + +e++ e
  gi|518652968|ref|YP_008142488.1| 524 KTPLYDALENIYK-LSSYEK-----LKTVSLLVTDGRGNVfPgNARENLME 568
                                       7779999999988.333333.....599*******9987653455555444 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0     0.027        34      60      88 ..      33      61 ..      14      65 .. 0.82
   2 !   16.2   0.0   3.3e-06    0.0042     105     178 ..     116     189 ..     108     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.027
                                      EEEEESSTSTHHHHHHHHHHHSSSEEEEE CS
                               MCM 60 vllvgdpgtaKsqlLkyveklapravyts 88
                                      +l+ g  g+aKs++++++++++p+   ++
  gi|518652968|ref|YP_008142488.1| 33 LLITGPKGIAKSTMVRALSSILPEVKAVK 61
                                      4666777**************99877665 PP

  == domain 2  score: 16.2 bits;  conditional E-value: 3.3e-06
                                       SSSSSEEEEETHHHHTTTSEEEEESGGGSTCHHHHHHHHHHHHSEEEEESSSCEEEEE--EEEEEEE--SSSSC CS
                               MCM 105 eetgefvleaGalvladkGvcciDefdkmkeedrsalhEamEqqtisiaKaGivatLnartsvlaAanpkagry 178
                                         +ge vl  G +  a++G+++iDe++  +++  +++++   +    + + G+ +t +ar  ++  +np++g+ 
  gi|518652968|ref|YP_008142488.1| 116 AIKGESVLREGLIGEANRGILYIDEVNLLDDSIVDSILDSAASGINIVEREGVSYTHPARFILVGTMNPEEGEL 189
                                       5678999**********************************9999999**********************9975 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 !   21.0   0.1     3e-07   0.00039      29      92 ..     245     308 ..     216     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 3e-07
                    Mg_chelatase_C  29 lsgeelrevceldeeaeelleeaierlglsaRaydrilkvArTiADLegseeieeehlaeAlqy 92 
                                       +++++l  ++++++e + ++ +++ + +ls Ra+  ++k A+ iA   g++e++e++l++Alq+
  gi|518652968|ref|YP_008142488.1| 245 VNARKLLPYVKIKREYRVFVADLVIKNSLSNRAMISTVKTAKAIAAYYGRTEVNEDDLKKALQF 308
                                       5677888899****************************************************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0     2e-05     0.026      21      51 ..      27      56 ..      17     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2e-05
                            AAA_16 21 sgrpelvllsGesGvGKsslvrellralekd 51
                                      ++  + +l++G++G+ Ks++vr+l  ++  +
  gi|518652968|ref|YP_008142488.1| 27 DSNIGGLLITGPKGIAKSTMVRALS-SILPE 56
                                      455589******************9.55555 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-05     0.048       4      78 ..      31     142 ..      28     159 .. 0.79
   2 ?   -3.2   0.9         6   7.6e+03     131     140 ..     364     373 ..     344     391 .. 0.47

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-05
                                       --EEEE--TTSSHHHHHHHHHHHTT-...................................-EEEEEGGG---.... CS
                             AAA_2   4 isilllgptgvGktelakalaellfv...............................kkekkliradaselle.... 45 
                                       + +l++gp+g+ k+ + +al+++l                                 +++ k+ +++  + ++    
  gi|518652968|ref|YP_008142488.1|  31 GGLLITGPKGIAKSTMVRALSSILPEvkavkgcrfhcdpdgdlcdeclearkkgelkTENMKIRIINLPNSTTldrv 107
                                       56788899999999999999998876788899999999999999999999666666533333333333333336688 PP

                                       ..----THHHHHHHHHTTT-HHHHTTSEEEEETGG CS
                             AAA_2  46 ..eeevehlvsrligappgyvgaeegGivllDEid 78 
                                         + +++h ++ + + ++g +g +++Gi+++DE+ 
  gi|518652968|ref|YP_008142488.1| 108 vgSLDISHAIKGESVLREGLIGEANRGILYIDEVN 142
                                       8889*****************************96 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 6
                                       THHHHTTTS- CS
                             AAA_2 131 sskisdesrs 140
                                        +k+++++++
  gi|518652968|ref|YP_008142488.1| 364 KEKQEKQQKQ 373
                                       1222221111 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   0.00014      0.18       8     130 ..      33     181 ..      27     186 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                            AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaee..........................erpevvfvtlpsstsskdllr 58 
                                       l++tG++G+ K+t +r l + l+e+++ +                           e+ ++  ++lp+st+++ +  
  gi|518652968|ref|YP_008142488.1|  33 LLITGPKGIAKSTMVRALSSILPEVKAVKGcrfhcdpdgdlcdeclearkkgelktENMKIRIINLPNSTTLDRVVG 109
                                       89*********************999999999999877775555555555555433333333444444444333322 PP

                            AAA_22  59 ellralglelkaerlsseellealeqalrarav..........ielliiDEaqhlr.s..eealeeLrsllnl.... 118
                                        l    +                + +a++  +v          +++l iDE+  l+ s  + +l    s  n+    
  gi|518652968|ref|YP_008142488.1| 110 SL----D----------------ISHAIKGESVlregligeanRGILYIDEVNLLDdSivDSILDSAASGINIvere 166
                                       22....2................222222222222223333345788999999987645555555555555556666 PP

                            AAA_22 119 ...srkgvqliLvGt 130
                                           +++ ++iLvGt
  gi|518652968|ref|YP_008142488.1| 167 gvsYTHPARFILVGT 181
                                       777788888888887 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.8e-05     0.074      48      69 ..      33      54 ..      15      62 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.8e-05
                             Rad17 48 LLisGPsGCgkstvvkvLskel 69
                                      LLi+GP G +kst+v+ Ls +l
  gi|518652968|ref|YP_008142488.1| 33 LLITGPKGIAKSTMVRALSSIL 54
                                      9******************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 ?   12.2   0.1     9e-05      0.12      20      46 ..      29      54 ..      23      60 .. 0.85
   2 ?   -2.0   0.0       2.4     3e+03      32      44 ..     521     533 ..     518     535 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-05
                            AAA_29 20 dlkgatlltGpsGsGKSTllDAiqalL 46
                                      +  g  l+tGp G  KST++ A++ +L
  gi|518652968|ref|YP_008142488.1| 29 NIGG-LLITGPKGIAKSTMVRALSSIL 54
                                      4455.9*****************9987 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 2.4
                            AAA_29  32 GsGKSTllDAiqa 44 
                                         GK+ l DA+  
  gi|518652968|ref|YP_008142488.1| 521 SGGKTPLYDALEN 533
                                       569*******976 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.44   5.7e+02      24      44 ..      32      52 ..      19      68 .. 0.80
   2 ?   10.8   0.0   0.00024       0.3      80     116 ..     119     155 ..     112     194 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.44
                                      -EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 24 svlitGesGtGKellaraihe 44
                                       +litG +G  K+++ ra+ +
  gi|518652968|ref|YP_008142488.1| 32 GLLITGPKGIAKSTMVRALSS 52
                                      579***********9999865 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00024
                                       TTSS-BEHHHHHTTTSEEEEETGGGS-HHHHHHHHHH CS
                   Sigma54_activat  80 GAekekkGlfekadgGtlfLDeigelplelQekLlrv 116
                                       G +  ++Gl+ +a+ G+l++De++ l+ ++   +l  
  gi|518652968|ref|YP_008142488.1| 119 GESVLREGLIGEANRGILYIDEVNLLDDSIVDSILDS 155
                                       5566799*****************9998877777765 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00024      0.31       1     128 [.      33     201 ..      33     204 .. 0.61

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00024
                                       EEEESSTTSSHHHHHHHHHHHH..........THE............................EEEEETTTCSSS.. CS
                               AAA   1 vllyGppGtGKTllakavakel..........gve............................fleisgsellsk.. 37 
                                       +l++Gp+G+ K+++++a+ + l            +                            ++++  s+ l+   
  gi|518652968|ref|YP_008142488.1|  33 LLITGPKGIAKSTMVRALSSILpevkavkgcrF-HcdpdgdlcdeclearkkgelktenmkirIINLPNSTTLDRvv 108
                                       5899****************9654443333330.0333333333333333333333333333366666666665566 PP

                                       ......STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEE CS
                               AAA  38 ......yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskviviga 108
                                             +  ++e+ +re +  + e +   il iDE+  l  s  +s  +++ + +n   +e   +++  +++i++g+
  gi|518652968|ref|YP_008142488.1| 109 gsldisHAIKGESVLREGL--IGEAN-RGILYIDEVNLLDDSIVDSILDSAASGINIVEREGVSYTH-PARFILVGT 181
                                       6666665556666666655..23333.69*******9997777444455555555555555555555.577999999 PP

                                       ESS.GGGSTHHHHSTTSSEEE CS
                               AAA 109 tnr.pdkldpallrgRfdrki 128
                                        n  + +l p+ll +Rf + +
  gi|518652968|ref|YP_008142488.1| 182 MNPeEGELRPQLL-DRFGISV 201
                                       9988999999999.9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (615 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1836  (0.102404); expected 358.6 (0.02)
Passed bias filter:                      784  (0.043728); expected 358.6 (0.02)
Passed Vit filter:                       115  (0.00641419); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.78u 0.33s 00:00:01.11 Elapsed: 00:00:00.48
# Mc/sec: 3850.47
//
Query:       gi|518652969|ref|YP_008142489.1|  [L=423]
Description: hypothetical protein FACI_IFERC00001G1608 [Ferroplasma acidarmanus fer1]
Scores for complete 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  117.7  62.1    1.2e-28  100.1  39.1    2.0  2  MFS_1     Major Facilitator Superfamily
    5.4e-30  104.6  29.6    1.7e-19   70.0  12.6    2.0  2  Sugar_tr  Sugar (and other) transporter
  ------ inclusion threshold ------
       0.21   11.0   0.0        0.4   10.1   0.0    1.4  1  DUF3552   Domain of unknown function (DUF3552)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.1  39.1     2e-32   1.2e-28       3     340 ..      13     359 ..      11     373 .. 0.76
   2 !   31.5  15.0   1.4e-11   8.6e-08      38     172 ..     272     402 ..     263     418 .. 0.71

  Alignments for each domain:
  == domain 1  score: 100.1 bits;  conditional E-value: 2e-32
                             MFS_1   3 laaflsalarsilgpalplalaedlgispse.....igl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfa 73 
                                       +++++  ++++i+++ +  ++a+++   +++     + l  ++l +++  v+++++G+++dr+Gr+++lll+ll+++
  gi|518652969|ref|YP_008142489.1|  13 IGTIIEWYGIFIFSSGAI-YIAHTFYPHVTVaegvlLTLlTFALGFVTRPVGAYVFGHFGDRLGRKKILLLTLLISG 88 
                                       677777788888887777.8888877444443233322223444555669*************************** PP

                             MFS_1  74 lg.lllllfa..ss.....lwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgg 142
                                       ++ +l +l++  +s     + ll++lr++ G+g g+ + +++ l+ + f+k +rg++ +++++++++G +lg ++  
  gi|518652969|ref|YP_008142489.1|  89 IStGLTGLIPseASigvfaIVLLVILRLVLGFGLGGEWGGAMLLTLETFKK-RRGFYSSFVQSTVGIGLLLGTAIFL 164
                                       **44444442342244433445*****************************.***********99999999955555 PP

                             MFS_1 143 .........llasslgWravfyilaivsllafvlfllllpeepperkrkspkeee....kgtgpaplvpawkallkd 206
                                                +++ s+gWr +f++  ++ +++     ++++ + +e + ++ ++++    k++++  ++ +wk++ + 
  gi|518652969|ref|YP_008142489.1| 165 plvaytphsFMY-SIGWRIPFVASFVIVVIG-----VFIRLKVKETPVFEAEKKKnrilKSPEKELFTRHWKKIIAG 235
                                       467778884444.888***************.....67777777777777777743333444444444488888888 PP

                             MFS_1 207 pvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllalll 283
                                            ll+++ ++  +f+++ +llp+++ +  ++s ++ +++  al++++ +i+ +++g+lsd+ grr ++  a +l
  gi|518652969|ref|YP_008142489.1| 236 T----LLAGSSGN--FFYFAISLLPVLFESLNKIS-VFDGLIGTALFGIIDVIFVFVGGQLSDKRGRRAIIAGANIL 305
                                       8....88888888..788899999**999999999.89999889********************8887777777666 PP

                             MFS_1 284 lllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasgl 340
                                       +l++++  ++l  +     ++++l l+ +++g+ +++l a++s+ +p++ + + +++
  gi|518652969|ref|YP_008142489.1| 306 ALIVLFPSIYLVGF---GYFVVFLSLFAIAHGLSYSPLGAMISEIFPTNVRYSGNSA 359
                                       66666666666666...677778888999*****************99877665554 PP

  == domain 2  score: 31.5 bits;  conditional E-value: 1.4e-11
                             MFS_1  38 ltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagalfpagaaliadw 113
                                       ++l+++  +++++++G lsd+ Grr ++  + +l ++  l+++ +  ++ +++v+  l +++ g++++  +a+i+++
  gi|518652969|ref|YP_008142489.1| 272 TALFGIIDVIFVFVGGQLSDKRGRRAIIAGANILALIV-LFPSiYLVGFGYFVVFLSLFAIAHGLSYSPLGAMISEI 347
                                       466999********************************.88885449999*************************** PP

                             MFS_1 114 fpk.eergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllll 172
                                       fp   + +   + ++ g+s+    +p ++ ll      ++++++  +++l++++++l ++
  gi|518652969|ref|YP_008142489.1| 348 FPTnVRYSGNSASYQYGNSFIGGPAPYASDLLG-----SVSYVLYPVFTLIFILIALGVI 402
                                       ***444444445555555555555555555555.....3444444444444444322332 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.0  12.6   2.9e-23   1.7e-19       5     204 ..      10     214 ..       7     218 .. 0.88
   2 !   40.6   8.9   2.4e-14   1.4e-10     276     442 ..     252     407 ..     218     415 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.0 bits;  conditional E-value: 2.9e-23
                                       HHHHH.HHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHH CS
                          Sugar_tr   5 aalgg.llfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkksll 80 
                                       a++ g ++++Y +++ ++ +  ++  +  +++++++      +l+ l++++ +v + +G++++g +gdr+GRkk+ll
  gi|518652969|ref|YP_008142489.1|  10 ASMIGtIIEWYGIFIFSSGAIYIAHTFYPHVTVAEG-----VLLTLLTFALGFVTRPVGAYVFGHFGDRLGRKKILL 81 
                                       555555999999999999999999554444554444.....56899******************************* PP

                                       HHHHHHHHHHHHHH-TTTT.....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHH CS
                          Sugar_tr  81 iaavlfvigavlqaaakgk.....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGil 152
                                        + +++ i++ l+++++++     +++ +l++ R+++G+g+G++ + + +++ E   kk Rg+  s+ q+ + +G l
  gi|518652969|ref|YP_008142489.1|  82 LTLLISGISTGLTGLIPSEasigvFAIVLLVILRLVLGFGLGGEWGGAMLLTLET-FKKRRGFYSSFVQSTVGIGLL 157
                                       *****************9977777777777888****************999996.6778***************** PP

                                       HHHHHHHHH.HTSS-....TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-H CS
                          Sugar_tr 153 vaaifglgl.nktsn....adgwrillglqlvpallllilllflPESPrylvekgke 204
                                       +++ + l l ++t      + gwri++  ++v+ ++ ++++l + E+P +  ek+k 
  gi|518652969|ref|YP_008142489.1| 158 LGTAIFLPLvAYTPHsfmySIGWRIPFVASFVIVVIGVFIRLKVKETPVFEAEKKKN 214
                                       ********95555559**********************************9999875 PP

  == domain 2  score: 40.6 bits;  conditional E-value: 2.4e-14
                                       HTTTHHHHSS-THH...HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...C CS
                          Sugar_tr 276 ysptifenlglsks...llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaas 349
                                       + p++fe+l        l++t+++g++ ++++fv+ +l+d+ GRR   + Ga + a+  ++ +    ++  +     
  gi|518652969|ref|YP_008142489.1| 252 LLPVLFESLNKISVfdgLIGTALFGIIDVIFVFVGGQLSDKRGRR-AIIAGANILALIVLFPS----IYLVG----F 319
                                       457888888777777779***************************.88999999999999998....55555....3 PP

                                       HHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHH CS
                          Sugar_tr 350 ivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfagla 426
                                       + ++vf+ lf+++++l+  p+ +++ sE+fp++vR+++ + +++     n +i+   p++ + +g  ++++++ ++ 
  gi|518652969|ref|YP_008142489.1| 320 GYFVVFLSLFAIAHGLSYSPLGAMI-SEIFPTNVRYSGNSASYQY---GNSFIGGPAPYASDLLG-SVSYVLYPVFT 391
                                       689*******************777.**************99876...5788999**********.*********** PP

                                       HHHHHHHHHHS--STT CS
                          Sugar_tr 427 vlfiifvfffvpetkg 442
                                       ++fi++ +  ++  k 
  gi|518652969|ref|YP_008142489.1| 392 LIFILIALGVIYKSKE 407
                                       *****98877666665 PP

>> DUF3552  Domain of unknown function (DUF3552)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   6.7e-05       0.4       7      47 ..     184     224 ..     179     235 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 6.7e-05
                           DUF3552   7 ivalvvglvvgylvrkkiaekkiaeAeeeAkkiieeAkkeA 47 
                                       +va +v +v+g+++r k++e+ + eAe++ ++i+++ +ke 
  gi|518652969|ref|YP_008142489.1| 184 FVASFVIVVIGVFIRLKVKETPVFEAEKKKNRILKSPEKEL 224
                                       688999*****************************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); 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:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.66u 0.28s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 2834.71
//
Query:       gi|518652970|ref|YP_008142490.1|  [L=82]
Description: hypothetical protein FACI_IFERC00001G1609 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.43
# Mc/sec: 578.68
//
Query:       gi|518652971|ref|YP_008142491.1|  [L=193]
Description: 50S ribosomal protein L7Ae [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-23   80.5   0.1      1e-22   79.7   0.1    1.5  1  Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 famil
     0.0043   15.9   9.1      0.005   15.7   9.1    1.1  1  Tim54           Inner membrane protein import complex subunit
  ------ inclusion threshold ------
       0.31   10.5   5.4        0.4   10.1   5.4    1.1  1  Endostatin      Collagenase NC10 and Endostatin
       0.51   10.6   0.1       0.51   10.6   0.1    1.9  3  DPM3            Dolichol-phosphate mannosyltransferase subuni
       0.64   10.2  12.0        0.8    9.9  12.0    1.2  1  GAGA_bind       GAGA binding protein-like family
        1.6    7.6   5.7        1.7    7.6   5.7    1.2  1  DUF913          Domain of Unknown Function (DUF913)
        2.3    7.9  21.1        2.9    7.6  21.1    1.2  1  RR_TM4-6        Ryanodine Receptor TM 4-6
        2.5    6.6   6.1        3.3    6.2   6.1    1.2  1  DUF853          Bacterial protein of unknown function (DUF853
        2.7    8.1  15.5        3.6    7.7  15.5    1.2  1  DUF2052         Coiled-coil domain containing protein (DUF205
        4.6    7.3   6.1        6.7    6.8   6.1    1.3  1  Podoplanin      Podoplanin
         10    4.8   6.8         12    4.5   6.8    1.1  1  Herpes_UL17     Herpesvirus UL17 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L7Ae  Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.1   6.2e-26     1e-22       8      93 ..      23     107 ..      16     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 6.2e-26
                                       HHHHHHTEEEESHHHHHHHHHTTTESEEEEETTSSSGGHHHHHHHHHHHTTEEEEEESCHHHHHHHTTSSSECSEEE CS
                    Ribosomal_L7Ae   8 kkakkagklvlGlkevtkalergeaklvilAedvepeekkkllealckekevpyvkvkskkeLGelvgkkrpvsala 84 
                                       +++ ++gk+++G++ev+k++ergeak+v++Aedv+p+e + ++++lc+e++vpy +vk+k +LG  vg    ++++a
  gi|518652971|ref|YP_008142491.1|  23 ENSYRSGKIKKGTNEVVKSIERGEAKVVVIAEDVSPPEVVFYIPVLCEERKVPYTYVKNKSDLGLKVGIA-SAASIA 98 
                                       667899**************************************************************99.577777 PP

                                       EEESTTTHH CS
                    Ribosomal_L7Ae  85 ikdegdskd 93 
                                       ++d g+ +d
  gi|518652971|ref|YP_008142491.1|  99 VVDFGKNED 107
                                       777776665 PP

>> Tim54  Inner membrane protein import complex subunit Tim54
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   9.1   3.1e-06     0.005     149     250 ..      82     184 ..       4     192 .. 0.55

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 3.1e-06
                             Tim54 149 leelrkklgieeeegagGviviGRh..ayKEYirGlhEGlLGPldkpeepeeeeaeeeeeeeeeekeeeeeeeeeee 223
                                       + +l  k+gi++  +   v+ +G++  ayKE i+ +     G  +k + ++++e+++ee+ e+e++e+ e+e+e+++
  gi|518652971|ref|YP_008142491.1|  82 KSDLGLKVGIASAAS-IAVVDFGKNedAYKELISSIENAKAGKEEKKKPAAKSEKPKEEAVEAEAAEAPEAEKEAKK 157
                                       555555555544443.346667764339**************99999666666666666555555555555554444 PP

                             Tim54 224 eekeeekeeekeeeeeeeekekkkkvp 250
                                       e+k+e k+++++e++e ++++kk+++ 
  gi|518652971|ref|YP_008142491.1| 158 EAKKEPKKAKTSESKETKKAPKKTTKK 184
                                       445444444444444444444443333 PP

>> Endostatin  Collagenase NC10 and Endostatin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   5.4   0.00024       0.4      25     126 ..      77     185 ..      71     193 .] 0.50

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00024
                        Endostatin  25 vyvkekgdlYlrvr....dgwrkvq....lgelipllselekkenevaavqpsPvvksskerlvllearrktksske 93 
                                       +yvk+k+dl l+v       +  v      + +++l s++ ++++  ++++++P++ks+k +++  ea++ ++ + e
  gi|518652971|ref|YP_008142491.1|  77 TYVKNKSDLGLKVGiasaASIAVVDfgknEDAYKELISSI-ENAKAGKEEKKKPAAKSEKPKEEAVEAEAAEAPEAE 152
                                       5888888888888653333333333333323344444444.266777888888****99997777766555555554 PP

                        Endostatin  94 svkakekeaskeeleekaekkveesekslttar 126
                                       ++ +ke ++++++ +++++k++++  k++t+++
  gi|518652971|ref|YP_008142491.1| 153 KEAKKEAKKEPKKAKTSESKETKKAPKKTTKKK 185
                                       444444333333333322222222222222221 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 ?   -3.6   0.1       8.3   1.4e+04      35      44 ..      59      68 ..      51      69 .. 0.77
   2 ?   10.6   0.1   0.00032      0.51      59      84 ..      97     122 ..      88     127 .. 0.85
   3 ?   -3.5   1.0       7.8   1.3e+04      68      82 ..     153     167 ..     147     169 .. 0.63

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 8.3
                              DPM3 35 devvpvlPlw 44
                                       evv+++P++
  gi|518652971|ref|YP_008142491.1| 59 PEVVFYIPVL 68
                                      5789999986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00032
                              DPM3  59 ygvltfndcpeaakeLqkeikeAkad 84 
                                       + v+ f   ++a+keL + i++Aka 
  gi|518652971|ref|YP_008142491.1|  97 IAVVDFGKNEDAYKELISSIENAKAG 122
                                       46999*******************85 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 7.8
                              DPM3  68 peaakeLqkeikeAk 82 
                                       +ea+ke +ke k+Ak
  gi|518652971|ref|YP_008142491.1| 153 KEAKKEAKKEPKKAK 167
                                       456666666666666 PP

>> GAGA_bind  GAGA binding protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9  12.0   0.00049       0.8     109     173 ..     121     188 ..      67     193 .] 0.52

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00049
                         GAGA_bind 109 sqlqeaeapelekeevasselveesavveke.eaakkrqqgkrpkepka...kkakkaarkpkeegedl 173
                                       +  +e++++   k+e+ ++e+ve +a+ + e e++ k++++k+pk++k+   k +kka++k+++++ed 
  gi|518652971|ref|YP_008142491.1| 121 AG-KEEKKKPAAKSEKPKEEAVEAEAAEAPEaEKEAKKEAKKEPKKAKTsesKETKKAPKKTTKKKEDS 188
                                       22.222223344455555555555554443334444444555666666644344555544444444432 PP

>> DUF913  Domain of Unknown Function (DUF913)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   5.7     0.001       1.7     264     316 ..     111     175 ..      36     192 .. 0.52

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.001
                            DUF913 264 d.........assasskseasssssssetkeeek......ssededvemeda.....eeetesesdeseesee 316
                                       +         a ++++k++a++s++++e+ +e++      +   e++ +++a     +      +++++++++
  gi|518652971|ref|YP_008142491.1| 111 ElissienakAGKEEKKKPAAKSEKPKEEAVEAEaaeapeA---EKEAKKEAkkepkK-----AKTSESKETK 175
                                       03333343332222222222222222222222224432221...11122222212220.....1111111111 PP

>> RR_TM4-6  Ryanodine Receptor TM 4-6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6  21.1    0.0018       2.9      84     157 ..     119     189 ..      77     193 .] 0.45

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0018
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXX..........XXXXXXXXXXXXXXXXXXXX CS
                          RR_TM4-6  84 pelkkklaeeeeaeeekeeeeepeaeaeekadaengekeekekekeeeekeseeeeeekkkkkkakskkkeeae 157
                                       +++ k+++++ +a++ek +ee  eaea e+ +ae++ k+e++ke    +k+++ e++e+kk  k+ +kkke +e
  gi|518652971|ref|YP_008142491.1| 119 AKAGKEEKKKPAAKSEKPKEEAVEAEAAEAPEAEKEAKKEAKKE---PKKAKTSESKETKKAPKKTTKKKEDSE 189
                                       22222222333444444445555555544444444444444433...333333333333333333333333332 PP

>> DUF853  Bacterial protein of unknown function (DUF853)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   6.1     0.002       3.3     345     472 ..      33     172 ..      13     190 .. 0.51

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.002
                            DUF853 345 fdveeaiteLgvGealvsvLdekGa.PsiveralvvpPasrlgplseeeraalvqespvagkydeei....dresay 416
                                         ++e++++++ Gea v v+ e  + P++v    v   + ++     +++++l  +  +a+  + ++     +e ay
  gi|518652971|ref|YP_008142491.1|  33 KGTNEVVKSIERGEAKVVVIAEDVSpPEVVFYIPVLCEERKVPYTYVKNKSDLGLKVGIASAASIAVvdfgKNEDAY 109
                                       45788999999999988887766551577777777766666555555555555544444444332221112578999 PP

                            DUF853 417 evLakkvaeaaeaaeqaaaeeeke.......eesgllgalkdtalgaaakkaeergskketvv 472
                                         L + +++a++ +e++++ ++k+        e+++ +a ++++ +++ +k+e+++ k+++ +
  gi|518652971|ref|YP_008142491.1| 110 KELISSIENAKAGKEEKKKPAAKSekpkeeaVEAEAAEAPEAEKEAKKEAKKEPKKAKTSESK 172
                                       999888877766555544443333122322222222222333333333333333333222222 PP

>> DUF2052  Coiled-coil domain containing protein (DUF2052)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7  15.5    0.0022       3.6      57     142 ..     108     187 ..      82     193 .] 0.42

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0022
                           DUF2052  57 lseiLlrreeeaaaaerleaqqeel.....eeeeeeeeeeeeeeeeeeeeeeedekekaeadeedeeeeeekeekee 128
                                         + L++++e+a+a +  +++ +++     ee++e e+ e +e+e+e+++e ++e++ka++       +e+ke+k++
  gi|518652971|ref|YP_008142491.1| 108 AYKELISSIENAKAGKEEKKKPAAKsekpkEEAVEAEAAEAPEAEKEAKKEAKKEPKKAKT-------SESKETKKA 177
                                       4556667777766666555555543222222222223333333222222222222222221.......111111111 PP

                           DUF2052 129 eeekeeeaeaevls 142
                                        ++     ++++ +
  gi|518652971|ref|YP_008142491.1| 178 PKKT----TKKKED 187
                                       1111....111111 PP

>> Podoplanin  Podoplanin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   6.1    0.0041       6.7      25     103 ..     102     184 ..      87     193 .] 0.62

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0041
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXX-----GGG-XXXXXXX..XXXXXXX CS
                        Podoplanin  25 tvrpeddivtpgvedekvtpGvednvvttgaseepyesglttlvpt..stesvtdlrledlptaestv..kakeesq 97 
                                       + ++ed  +      e++  G+e++   +++se+p+e+++ +  +   ++e+ ++++++++p ++ t   k+ +++ 
  gi|518652971|ref|YP_008142491.1| 102 FGKNEDAYKELISSIENAKAGKEEKKKPAAKSEKPKEEAVEAEAAEapEAEKEAKKEAKKEPKKAKTSesKETKKAP 178
                                       45678887777777888999999999999999999998887766553344444444444444444443004444444 PP

                                       XXXXXX CS
                        Podoplanin  98 stttln 103
                                       + tt++
  gi|518652971|ref|YP_008142491.1| 179 KKTTKK 184
                                       444433 PP

>> Herpes_UL17  Herpesvirus UL17 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   6.8    0.0076        12     178     243 ..     117     183 ..      85     192 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0076
                       Herpes_UL17 178 akeaaahleacapgafdeaaaearlkddfdeilslikraaeavnkraPvaavasgllqgal..aslla 243
                                         + a + e+ +p a+ e ++e++++++  e ++  k+a++ ++k +P +a++s++++ ++  +++ +
  gi|518652971|ref|YP_008142491.1| 117 ENAKAGKEEKKKPAAKSEKPKEEAVEAEAAEAPEAEKEAKKEAKK-EPKKAKTSESKETKKapKKTTK 183
                                       344566666669999******************999999999776.6989999999988886533333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (193 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2675  (0.1492); expected 358.6 (0.02)
Passed bias filter:                      853  (0.0475766); expected 358.6 (0.02)
Passed Vit filter:                       235  (0.0131073); expected 17.9 (0.001)
Passed Fwd filter:                        38  (0.00211947); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.67u 0.32s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 1241.57
//
Query:       gi|518652972|ref|YP_008142492.1|  [L=69]
Description: hypothetical protein FACI_IFERC00001G1611 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-30  103.4   1.9    5.1e-30  103.2   1.9    1.0  1  Ribosomal_S28e  Ribosomal protein S28e


Domain annotation for each model (and alignments):
>> Ribosomal_S28e  Ribosomal protein S28e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.2   1.9   2.9e-34   5.1e-30       2      64 .]       4      66 ..       3      66 .. 0.98

  Alignments for each domain:
  == domain 1  score: 103.2 bits;  conditional E-value: 2.9e-34
                                      --EEEEEEEEEE---SSSSEEEEEEEE-S-SS-S-EEEEEEES---TT-EEEES--S--TT-- CS
                    Ribosomal_S28e  2 eaklAeVikvlgrtGsrGevtqVrvellegkdkgriiiRnVkGPvreGDiLtLlEterEArrL 64
                                      +a++AeV++ +grtG++Ge+t V+v++l+gkd+grii RnV GPv++GDiL+L+Et+rEArrL
  gi|518652972|ref|YP_008142492.1|  4 DATPAEVVELMGRTGMTGEATTVKVRVLDGKDQGRIIARNVLGPVKVGDILMLRETAREARRL 66
                                      789***********************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      208  (0.0116013); 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: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 462.75
//
Query:       gi|518652973|ref|YP_008142493.1|  [L=65]
Description: hypothetical protein FACI_IFERC00001G1612 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-21   76.9   1.5    1.1e-21   76.8   1.5    1.0  1  Ribosomal_L24e  Ribosomal protein L24e
      5e-07   29.5   0.3    7.5e-07   29.0   0.3    1.3  1  zf-FCS          MYM-type Zinc finger with FCS sequence motif
    0.00028   20.5   1.0    0.00065   19.4   1.0    1.8  1  YacG            DNA gyrase inhibitor YacG
     0.0003   20.2   0.9    0.00048   19.5   0.9    1.3  1  zf-FLZ          zinc-finger of the FCS-type, C2-C2
  ------ inclusion threshold ------
      0.035   14.1   1.5        5.6    7.0   0.1    2.2  2  DUF2116         Uncharacterized protein containing a Zn-ribbo
      0.062   13.4   0.0      0.094   12.8   0.0    1.2  1  YHS             YHS domain
      0.082   12.9   0.1      0.086   12.8   0.1    1.2  1  Inhibitor_I24   PinA peptidase inhibitor
       0.78    9.6   5.2       0.35   10.8   2.2    1.9  2  VATC            Vms1-associating treble clef domain


Domain annotation for each model (and alignments):
>> Ribosomal_L24e  Ribosomal protein L24e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   1.5     5e-25   1.1e-21       1      63 [.       1      64 [.       1      65 [] 0.95

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 5e-25
                                      XXX-B-TTT-SB--SS--EEEE-TTS-EEEESSHHH.HHHHHTT--GGGSTTSTTT-XXXXXXX CS
                    Ribosomal_L24e  1 mktekCsFsgykiyPGhGkrfvrnDgkvfrFlssKc.eklfkqkrnPrklkWTkayRrahkkel 63
                                      m+ +kC F+g+ i+P+ G++++r+Dg++++F+s+Kc  ++++ kr +r++kWT+ y+r++++++
  gi|518652973|ref|YP_008142493.1|  1 MENRKCIFCGHDIEPASGIIYIRKDGNIMNFCSKKCrVNMIDLKRAARNVKWTNEYHRIKEMRK 64
                                      7789********************************99********************998765 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 !   29.0   0.3   3.4e-10   7.5e-07       4      38 ..       4      37 ..       2      38 .. 0.94

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 3.4e-10
                            zf-FCS  4 krCwfCkkyikgkpeftyvlendgvvgqFCStsCl 38
                                      ++C fC+++i+      +++ +dg + +FCS+ C+
  gi|518652973|ref|YP_008142493.1|  4 RKCIFCGHDIEPAS-GIIYIRKDGNIMNFCSKKCR 37
                                      79************.69*****************7 PP

>> YacG  DNA gyrase inhibitor YacG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   1.0   2.9e-07   0.00065      16      44 ..      26      62 ..       4      65 .] 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.9e-07
                              YacG 16 npfrPFCSeRCk..liDLGe......Waseeyripae 44
                                       + + FCS++C+  +iDL +      W +e +ri++ 
  gi|518652973|ref|YP_008142493.1| 26 GNIMNFCSKKCRvnMIDLKRaarnvkWTNEYHRIKEM 62
                                      56778******8668***74334444********875 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 !   19.5   0.9   2.1e-07   0.00048      14      51 ..       4      44 ..       4      47 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.1e-07
                            zf-FLZ 14 saCflCkkkLgegkDiymYrGd...kaFCSeeCRqqqield 51
                                      ++C +C  ++++   i   r d     FCS+ CR + i+l 
  gi|518652973|ref|YP_008142493.1|  4 RKCIFCGHDIEPASGIIYIRKDgniMNFCSKKCRVNMIDLK 44
                                      58***********97655554422458********999875 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 ?    6.5   0.2    0.0037       8.3       4      15 ..       4      15 ..       2      19 .. 0.86
   2 ?    7.0   0.1    0.0025       5.6      18      34 ..      30      46 ..      26      54 .. 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0037
                           DUF2116  4 kHCivCGkaIpl 15
                                      + Ci CG  I++
  gi|518652973|ref|YP_008142493.1|  4 RKCIFCGHDIEP 15
                                      67********97 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0025
                           DUF2116 18 sfCsekCqeeyekkrkk 34
                                       fCs+kC+ +    ++ 
  gi|518652973|ref|YP_008142493.1| 30 NFCSKKCRVNMIDLKRA 46
                                      59*****9876554444 PP

>> YHS  YHS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.2e-05     0.094       6      34 ..       9      37 ..       8      39 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.2e-05
                               YHS  6 cgmkvdkekaeekseYkGkeYyFcSegCk 34
                                      cg +++++    +++ +G    FcS++C+
  gi|518652973|ref|YP_008142493.1|  9 CGHDIEPASGIIYIRKDGNIMNFCSKKCR 37
                                      9***************************7 PP

>> Inhibitor_I24  PinA peptidase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.8e-05     0.086      37      65 ..       9      36 ..       3      61 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.8e-05
                     Inhibitor_I24 37 ceddiepdtgiieielsdgkiiniydkpi 65
                                      c  diep +gii i   dg+i+n   k  
  gi|518652973|ref|YP_008142493.1|  9 CGHDIEPASGIIYIR-KDGNIMNFCSKKC 36
                                      999**********97.79*****988864 PP

>> VATC  Vms1-associating treble clef domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.2   0.00016      0.35       4      31 ..       4      36 ..       2      39 .. 0.81
   2 ?   -3.4   0.1       4.3   9.6e+03      35      40 ..      57      62 ..      56      64 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
                              VATC  4 lrCsiCgesleg...kvyFekfdf..rYCstkC 31
                                      ++C +Cg+++e+   ++y +k  +   +Cs kC
  gi|518652973|ref|YP_008142493.1|  4 RKCIFCGHDIEPasgIIYIRKDGNimNFCSKKC 36
                                      79*********7666889999765237****99 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.3
                              VATC 35 HRranf 40
                                      HR +++
  gi|518652973|ref|YP_008142493.1| 57 HRIKEM 62
                                      887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.53
# Mc/sec: 369.02
//
Query:       gi|518652974|ref|YP_008142494.1|  [L=139]
Description: hypothetical protein FACI_IFERC00001G1613 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-53  180.9   0.0    1.2e-53  180.7   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.7   0.0   6.8e-58   1.2e-53       1     135 []       2     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 180.7 bits;  conditional E-value: 6.8e-58
                                       EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEEST CS
                               NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlege 77 
                                       ertlvliKPd+vkr+lig+ii+r+e+kglkiv+lk++++++++a++hY+ h+ kpffe lv+++tsgp+val+leg+
  gi|518652974|ref|YP_008142494.1|   2 ERTLVLIKPDGVKRHLIGNIIERFENKGLKIVSLKLMKVSDDKARQHYSVHSMKPFFEGLVSYLTSGPIVALILEGD 78 
                                       89*************************************************************************** PP

                                       THHHHHHHHH--SSTTTSSTTSHHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
                               NDK  78 daiekvreliGatnpaeaapgtiRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                                       +ai ++r+l+Gat+ + aa+gtiR+df+++++eN+vH+Sds+es ++e k+fF+e+ei
  gi|518652974|ref|YP_008142494.1|  79 NAIISCRNLAGATDGSAAAAGTIRGDFSLNIEENIVHASDSPESFNHEYKIFFNENEI 136
                                       *******************************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); 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: 0.59u 0.34s 00:00:00.93 Elapsed: 00:00:00.57
# Mc/sec: 735.30
//
Query:       gi|518652975|ref|YP_008142495.1|  [L=580]
Description: hypothetical protein FACI_IFERC00001G1614 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-32  112.7   1.2      3e-32  111.7   0.3    1.9  2  GTP_EFTU     Elongation factor Tu GTP binding domain
    8.1e-18   64.5   2.5    8.1e-18   64.5   2.5    2.0  2  IF-2         Translation-initiation factor 2
    2.5e-17   62.6   0.7    8.9e-17   60.8   0.0    2.4  3  GTP_EFTU_D4  Elongation factor Tu domain 4
    2.2e-08   34.2   0.5    2.2e-08   34.2   0.5    2.6  3  MMR_HSR1     50S ribosome-binding GTPase
    2.6e-06   27.7  11.5     0.0019   18.6   1.4    3.9  4  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00015   22.0   0.1    0.00073   19.7   0.0    2.2  2  Roc          Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.012   15.4   0.1      0.034   13.9   0.1    1.7  2  ATP_bind_1   Conserved hypothetical ATP binding protein
      0.019   14.5   2.3       0.86    9.2   0.8    2.4  2  cobW         CobW/HypB/UreG, nucleotide-binding domain
      0.024   14.7   1.8       0.49   10.4   0.0    3.2  3  Dynamin_N    Dynamin family
      0.045   13.5   1.3        5.2    6.8   0.1    3.0  3  PduV-EutP    Ethanolamine utilisation - propanediol utilisati


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  111.7   0.3   1.7e-35     3e-32       5     190 ..      12     217 ..       9     221 .. 0.78
   2 ?   -2.7   0.0         2   3.6e+03      51      62 ..     345     356 ..     342     372 .. 0.76

  Alignments for each domain:
  == domain 1  score: 111.7 bits;  conditional E-value: 1.7e-35
                                       EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSG CS
                          GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHv 81 
                                        ++++ghvDhGKtTL+d +  +t a +++g  +++  ++   k+  e  i    ++i++        + +iDtPGHv
  gi|518652975|ref|YP_008142495.1|  12 IVCVLGHVDHGKTTLLDDIRGTTVAKKEAGGITQKIGATEIDKNTLETNIKNYFKNIQVT----IPGLLFIDTPGHV 84 
                                       589*****************9998888877766543334444444444455555555555....889********** PP

                                       GGHHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST...........HHHHHHHHHHHH CS
                          GTP_EFTU  82 dFskevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl...........kaelkeiveevk 147
                                        F +  + g + +D+a+lv+d++eG +pqt e + +++k+++p+i++ NK+D++           k++l+++ +e+ 
  gi|518652975|ref|YP_008142495.1|  85 AFANMRSMGGALADIAILVIDVNEGLKPQTIESIDVLKKYKTPFIIAANKIDMIpyfvsskdtsfKETLSKQRKEYV 161
                                       ******************************************************99998887776666666666666 PP

                                       HHHHHH..........HHHHHHHHHTTT.............TTEEEEEEBTTTTBTHHHHHHHHHH CS
                          GTP_EFTU 148 qklsrk..........eeklekygekge.............kevpvvfgSalkgegvktllealve 190
                                       + l++k          +                        k + +v++Sa+ + gv ++l +l+ 
  gi|518652975|ref|YP_008142495.1| 162 DFLDEKiykiindlyvK----------GissdrydritdftKSFAIVPISAKLNIGVPDILMVLTG 217
                                       66655554443333330..........2455567777777799***************99988765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       HHTSCSSCEEEE CS
                          GTP_EFTU  51 ergiTiksaais 62 
                                       e+giTik++ai 
  gi|518652975|ref|YP_008142495.1| 345 ENGITIKAEAIG 356
                                       89*****99874 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       3.8   6.8e+03      90     103 ..     162     174 ..     131     175 .. 0.62
   2 !   64.5   2.5   4.5e-21   8.1e-18      12     104 ..     341     434 ..     330     435 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
                                       EEEEESSHHHHHHH CS
                              IF-2  90 kirlynvIYklidd 103
                                       + +l + IYk+i+d
  gi|518652975|ref|YP_008142495.1| 162 D-FLDEKIYKIIND 174
                                       3.345678999987 PP

  == domain 2  score: 64.5 bits;  conditional E-value: 4.5e-21
                                       S..SCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHST....EEEEEESSSCTHHHHH CS
                              IF-2  12 g..kelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasn....aiiigFnvkvskkakk 82 
                                          +e ++ ika+  GsleA++  +e+      k+ v ++++G+it++D+  +s+ n     +i+gFnv++s +ak+
  gi|518652975|ref|YP_008142495.1| 341 IklSENGITIKAEAIGSLEAIAYEMEQN-----KITVREAQIGDITKRDIINVSTLNnpldRVIVGFNVNTSGDAKE 412
                                       3458889*******************97.....7*********************544666**************** PP

                                       CCCCCTSEEEEESSHHHHHHHH CS
                              IF-2  83 laekegvkirlynvIYkliddv 104
                                       ++e+++ k+++ nvIY +idd+
  gi|518652975|ref|YP_008142495.1| 413 AMETNNAKVISGNVIYSMIDDL 434
                                       ********************97 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 ?   -3.4   0.1       5.2   9.3e+03      44      62 ..     355     377 ..     344     380 .. 0.50
   2 ?   -4.0   0.0       8.4   1.5e+04      17      26 ..     396     405 ..     390     411 .. 0.75
   3 !   60.8   0.0     5e-20   8.9e-17       2      86 .]     456     540 ..     455     540 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.2
                                       EEEEEEE....EETTEEESEEET CS
                       GTP_EFTU_D4  44 vGeilqi....qdkgkkleeaka 62 
                                       +G++ +i    ++++ +++ea+ 
  gi|518652975|ref|YP_008142495.1| 355 IGSLEAIayemEQNKITVREAQI 377
                                       55555441111444444555555 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.4
                                       CCEEEEEEEE CS
                       GTP_EFTU_D4  17 dpaivGvevl 26 
                                       d +ivG +v 
  gi|518652975|ref|YP_008142495.1| 396 DRVIVGFNVN 405
                                       6788988875 PP

  == domain 3  score: 60.8 bits;  conditional E-value: 5e-20
                                       -CEEEEEEEEEEETCCCEEEEEEEEEEEEETT-EEEETTE.EEEEEEEEEETTEEESEEETT-EEEEEEESS-TTTS CS
                       GTP_EFTU_D4   2 PgkikilpgvvfrrsdpaivGvevlgGvikpgvklikedGrevGeilqiqdkgkkleeakaGqevaisiegkivGrq 78 
                                       P+k+ i+p+++fr+ +p+ivG++vl+G++k+g kli+ + +  G+i++++d + + ++a +G+e++ +i+g ++ rq
  gi|518652975|ref|YP_008142495.1| 456 PSKLVIMPDYIFRAAKPVIVGIKVLSGRVKVGDKLINGKNKYAGTIKSLRDGDVNHQFADKGSELSCAIDGVTLNRQ 532
                                       99*************************************************************************** PP

                                       --TT-EEE CS
                       GTP_EFTU_D4  79 ikegdily 86 
                                       i  ++ ly
  gi|518652975|ref|YP_008142495.1| 533 IFPDEDLY 540
                                       *9999887 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.5   1.2e-11   2.2e-08       2     114 .]      13     134 ..      12     134 .. 0.81
   2 ?   -1.3   0.0       1.2   2.2e+03      30      71 ..     247     295 ..     236     344 .. 0.61
   3 ?   -1.3   0.1       1.3   2.3e+03      65     107 ..     413     454 ..     364     463 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 1.2e-11
                                       EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETTEE..................EEEEECGGCSSHH CS
                          MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkgke..................ielvDtpGliega 60 
                                       v+++G+   GK+tL+  + g+++  ++  g T++i   +++++                     + ++DtpG +   
  gi|518652975|ref|YP_008142495.1|  13 VCVLGHVDHGKTTLLDDIRGTTVAKKEAGGITQKIGATEIDKN--TletniknyfkniqvtipgLLFIDTPGHVA-- 85 
                                       899*****************99999999999999999999833..22355666777777888889*******443.. PP

                                       HHHHHHHHHHHHHHC.TSEEEEEEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
                          MMR_HSR1  61 seekglgkaflalee.adlillvvdaseeklkpldeeleelleeakkplilvlnk 114
                                              +++      ad+++lv+d++ e+lkp+  e  ++l++ k p+i+++nk
  gi|518652975|ref|YP_008142495.1|  86 ---FANMRSMGG--AlADIAILVIDVN-EGLKPQTIESIDVLKKYKTPFIIAANK 134
                                       ...333344443..236********88.88***********************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.2
                                       TTSSSSEEEEEEE.ETTEEEEEEECGGCS.....S..HHHHHHHHHHHHH CS
                          MMR_HSR1  30 pgtTrdinegrvk.lkgkeielvDtpGli.....e..gaseekglgkafl 71 
                                        gtT+d++ ++   +kg++i l  ++G       +   a  +kg+ ++  
  gi|518652975|ref|YP_008142495.1| 247 LGTTLDTILYQGVlHKGDKIALNTIAG-PavtkvKaiIATGKKGMVEKES 295
                                       589999977765524458888888888.3222211222222333333333 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 1.3
                                       HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHHHHHHTTSE CS
                          MMR_HSR1  65 glgkaflaleeadlillvvdaseeklkpldeeleelleeakkp 107
                                        ++ + +++++ ++i  ++d  ++ l+ +++e+ee  ++++kp
  gi|518652975|ref|YP_008142495.1| 413 AMETNNAKVISGNVIYSMIDDLTKWLEFKKNEIEEE-KKNNKP 454
                                       344444445556788888883333233333444444.344555 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0       1.8   3.3e+03      24      51 ..      33      63 ..       8      78 .. 0.72
   2 !   18.6   1.4   1.1e-06    0.0019       1      71 [.     248     316 ..     248     319 .. 0.83
   3 ?   -0.6   0.1         1   1.8e+03      35      59 ..     358     382 ..     344     391 .. 0.77
   4 !   13.5   0.2     4e-05     0.072       3      38 ..     474     504 ..     473     527 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1.8
                                      TCTTSEE...EEEEEEEEEEETEEESEEETT CS
                       GTP_EFTU_D2 24 ndtskke...ivtrissletfhededeavag 51
                                       ++ kke   i+ +i+++e  ++ +++ ++ 
  gi|518652975|ref|YP_008142495.1| 33 TTVAKKEaggITQKIGATEIDKNTLETNIKN 63
                                      4455566677888888888887777766555 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 1.1e-06
                                       EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETE..EESEEETTSEEEEEEEESSCCSGSSTTC CS
                       GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhe..dedeavaganaGvivaikgledaiivGd 71 
                                       Gt+ + ++y+G+l+kGd++ +  n t   + vt+++++ +  +   ++ +    +aG+ ++i +  d ++ G 
  gi|518652975|ref|YP_008142495.1| 248 GTTLDTILYQGVLHKGDKIAL--N-TIAGPAVTKVKAIIATGKkgMVEKESIKSAAGIRILITDKLD-VLSGT 316
                                       89999****************..7.67889*******998766223444477889999999999999.88886 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 1
                                       EEEEEEETEEESEEETTSEEEEEEE CS
                       GTP_EFTU_D2  35 issletfhededeavaganaGviva 59 
                                         ++  ++e+ ++ v +a++G+i++
  gi|518652975|ref|YP_008142495.1| 358 LEAIAYEMEQNKITVREAQIGDITK 382
                                       4556667888889999*****9986 PP

  == domain 4  score: 13.5 bits;  conditional E-value: 4e-05
                                       EEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEE CS
                       GTP_EFTU_D2   3 valgrvysGtlkkGdevrilgndtskkeivtrissl 38 
                                       +++++v sG +k+Gd++ +   + +     ++i+sl
  gi|518652975|ref|YP_008142495.1| 474 IVGIKVLSGRVKVGDKLIN--GKNKYA---GTIKSL 504
                                       7999***************..444345...788777 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 !   19.7   0.0   4.1e-07   0.00073       2     120 .]      13     137 ..      12     137 .. 0.73
   2 ?   -1.4   0.0       1.4   2.6e+03      13      36 ..     216     239 ..     216     249 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 4.1e-07
                                       EEEESSTTSSHHHHHHCHCT-CCC-EE....ETTTTEEEEEEECGGSG..GCTTBTTTTCEEEEEEEE-SGGCTTTT CS
                               Roc   2 vvlvGdsgvGKtsllkrfvedkfseke....kstigvdfltkevtkik..gvendkkvkkvklniWDtaGqerfrsl 72 
                                       v+++G    GKt+ll+ +   ++ +ke    ++ ig++ ++k++ +++  ++ ++ +v+   l + Dt G+  f ++
  gi|518652975|ref|YP_008142495.1|  13 VCVLGHVDHGKTTLLDDIRGTTVAKKEaggiTQKIGATEIDKNTLETNikNYFKNIQVTIPGLLFIDTPGHVAFANM 89 
                                       689*****************9999987233246777777777654332003223333333345789*********** PP

                                       -HHHHCTSCEEEEEEEGHHHHCHHHHHHHHHHHCS.SS-EEEEEE-TTT CS
                               Roc  73 hplylreaalailvydsrssenlkeWlkelkkvag.kspvilvgnkiDl 120
                                       +++    a++ailv+d ++  +  + +++++   + k+p+i+ +nkiD+
  gi|518652975|ref|YP_008142495.1|  90 RSMGGALADIAILVIDVNEGLK-PQTIESIDVLKKyKTPFIIAANKIDM 137
                                       ****************765543.3456677666553689********96 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.4
                                       HHHHHCHCT-CCC-EEETTTTEEE CS
                               Roc  13 tsllkrfvedkfsekekstigvdf 36 
                                       t l++rf+e++++ ++kst g  +
  gi|518652975|ref|YP_008142495.1| 216 TGLAQRFLEEHIQFESKSTRGSVI 239
                                       6799*********99999999655 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 ?   -2.5   0.0       1.9   3.4e+03       1      20 [.      15      34 ..      15      45 .. 0.79
   2 ?   13.9   0.1   1.9e-05     0.034      75     213 ..      57     177 ..      33     194 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.9
                        ATP_bind_1  1 vvGpaGsGKttfvgalseil 20
                                      v+G++  GKtt+   +  ++
  gi|518652975|ref|YP_008142495.1| 15 VLGHVDHGKTTLLDDIRGTT 34
                                      7899999****998776555 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.9e-05
                        ATP_bind_1  75 lresldwldeelekeeddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdptkfisgllsalsa 151
                                       l++++ +  ++++     +l +DtPG + + ++++++           a +++ ++D++   +p +  s     + +
  gi|518652975|ref|YP_008142495.1|  57 LETNIKNYFKNIQVTIPGLLFIDTPGHVAFANMRSMGG--------ALADIAILVIDVNEGLKPQTIES-----IDV 120
                                       4444433333442223468999**************99........66679999999999999877554.....599 PP

                        ATP_bind_1 152 mlrlelPhvvvlnkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefal 213
                                       + ++++P++++ nk+D++       +   +d+   ++l ++ +e++  l e+i +++++ + 
  gi|518652975|ref|YP_008142495.1| 121 LKKYKTPFIIAANKIDMIP-----YFVSSKDTSFKETLSKQRKEYVDFLDEKIYKIINDLYV 177
                                       99***************88.....44445555555566666669999999999999998765 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 ?    9.2   0.8   0.00048      0.86       2      51 ..      12      62 ..      11      72 .. 0.87
   2 ?    4.3   0.0     0.015        27      88     156 ..      78     141 ..      68     161 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00048
                                      EEEEEESTTCCHHHHHHHHH.CT--SS-EEEEESS-SSCHCCCCCCHCCCT CS
                              cobW  2 vtvltGflGsGKTtLlnhll.enraglklavivNefgevsiDaellretgv 51
                                      ++ + G +  GKTtLl  +  +  a+++   i+  +g ++iD++ l+++ +
  gi|518652975|ref|YP_008142495.1| 12 IVCVLGHVDHGKTTLLDDIRgTTVAKKEAGGITQKIGATEIDKNTLETNIK 62
                                      6778899999**********99999999*****************998744 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.015
                                       EEECTTTTHHHHHTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC CS
                              cobW  88 iEttGlaePapvafteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldee 156
                                       i t G      vaf + +    + +d+ + v+D+++  + ++ ++  + ++ ++  ++  nK+D++++ 
  gi|518652975|ref|YP_008142495.1|  78 IDTPG-----HVAFANMRSMGGALADIAILVIDVNEGLKPQTIESIDVLKKYKTPFIIAANKIDMIPYF 141
                                       55555.....334444456788999*********88866666666666677777778889999999976 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00027      0.49       1      35 [.      13      47 ..      13      70 .. 0.83
   2 ?    2.0   0.0      0.11     2e+02      93     115 ..      65      87 ..      49     135 .. 0.72
   3 ?   -0.4   0.2      0.57     1e+03      48      87 ..     414     453 ..     310     475 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00027
                                      EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
                         Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35
                                      ++v+G++ +GK+++l+ + g  +  ++++ +T+++
  gi|518652975|ref|YP_008142495.1| 13 VCVLGHVDHGKTTLLDDIRGTTVAKKEAGGITQKI 47
                                      78***************************999987 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.11
                                       EEEEETTS-SEEEEE---B-SSS CS
                         Dynamin_N  93 lkilsllvkgltlvDlPGldsvn 115
                                       +k+ + + +gl ++D+PG    +
  gi|518652975|ref|YP_008142495.1|  65 FKNIQVTIPGLLFIDTPGHVAFA 87 
                                       5667788899********87654 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.57
                                       CS...SSEEEET-EB--CHHHHHHHHHHHHHHHTSSSS-- CS
                         Dynamin_N  48 eravkeelkekekkledfsevreeieketekiagankgis 87 
                                        +++++++ +++  ++ ++++++ +e ++++i++++k+ +
  gi|518652975|ref|YP_008142495.1| 414 METNNAKVISGNVIYSMIDDLTKWLEFKKNEIEEEKKNNK 453
                                       3445555555544445555555555555555554444433 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0029       5.2       4      29 ..      13      38 ..      10      59 .. 0.80
   2 ?    4.9   0.0     0.012        21       7      62 ..      47     101 ..      42     138 .. 0.77
   3 ?   -1.8   0.1       1.3   2.3e+03      91     130 ..     353     392 ..     344     398 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                         PduV-EutP  4 illiGkvgsGKttLtqalkgeelkYk 29
                                      + ++G+v+ GKttL   ++g ++  k
  gi|518652975|ref|YP_008142495.1| 13 VCVLGHVDHGKTTLLDDIRGTTVAKK 38
                                      7799***************9887655 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.012
                         PduV-EutP   7 iGkvgsGKttLtqalkgeelkYkktqaiefsdeviDtPGe..ylenrklysalivtsa 62 
                                       iG+++  K tL  ++k+    +k  q +     +iDtPG   +++ r++  al+ +++
  gi|518652975|ref|YP_008142495.1|  47 IGATEIDKNTLETNIKN---YFKNIQVTIPGLLFIDTPGHvaFANMRSMGGALADIAI 101
                                       67888888888888876...34555655556667*****7558888999988887764 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 1.3
                         PduV-EutP  91 eviGiitkidlaedeenieaveelLksaGaekifevsave 130
                                       e iG +  i    ++++i++ e ++     + i++vs+++
  gi|518652975|ref|YP_008142495.1| 353 EAIGSLEAIAYEMEQNKITVREAQIGDITKRDIINVSTLN 392
                                       5666666666666777777777777777777777777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (580 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.78u 0.35s 00:00:01.12 Elapsed: 00:00:00.56
# Mc/sec: 3129.35
//
Query:       gi|518652976|ref|YP_008142496.1|  [L=260]
Description: hypothetical protein FACI_IFERC00001G1615 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-17   63.4  37.0    1.6e-09   37.9  10.8    2.0  2  Na_Ca_ex         Sodium/calcium exchanger protein


Domain annotation for each model (and alignments):
>> Na_Ca_ex  Sodium/calcium exchanger protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9  10.8   9.1e-14   1.6e-09      17     147 ..       3     124 ..       1     128 [. 0.83
   2 !   31.9  18.2   6.3e-12   1.1e-07       7     119 ..     148     258 ..     144     260 .] 0.85

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 9.1e-14
                                       HHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHHHHHHHHHHBT CS
                          Na_Ca_ex  17 adflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllviGlialigslk 93 
                                        d++ +   +++ks+  s++ +Gl+++ ++  + E+++s++aa+++++ ++ g++ Gsn++ ll    li l+    
  gi|518652976|ref|YP_008142496.1|   3 GDIFLDVSYSVGKSFSFSEKYVGLFIVGFAAIVDEIAMSVMAAVENQGAVSFGTIQGSNAITLLAFFILIPLY---- 75 
                                       678888889999**************************************************99855555555.... PP

                                       TSSCECCHHHHHHHHHHHHHHHHHHHTCHHHHHHTEEHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  94 vdseslkldlgllllvallllllvlllllplfvpgrltvleglvllllYalylv 147
                                       ++s   k+ l + +++a +++ll+l ++   f   ++ +  g+++l+++++y+v
  gi|518652976|ref|YP_008142496.1|  76 YKSGISKFRLDAYVVTATAIILLILSFY---F--IKVPYYIGFITLAVFLFYIV 124
                                       5555558888555566666666666666...3..79****************98 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 6.3e-12
                                       HHHHHHHHHHHHHHHHHHHHHHHHTTCTHHHHHHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHTHH CS
                          Na_Ca_ex   7 ilslllisvladflvssaeeiakslgisgsvlGltllAlgnslpElissiiaaltgevdlaignvlGsnifnlllvi 83 
                                       il++++i++++  ++++a  i+++l+i+  +++ +ll +++slpE+i+  i+++ +  +++ig ++Gs +   ++  
  gi|518652976|ref|YP_008142496.1| 148 ILAIIVIVLASYNMIDAALIISEVLKITAFLSSFFLLGFFGSLPEIIMLSISLKDQRKNVSIGLITGSTLYKETILF 224
                                       7899************************************************************************* PP

                                       HHHHHHHHBTTSSCECCHHHHHHHHHHHHHHHHHHH CS
                          Na_Ca_ex  84 Glialigslkvdseslkldlgllllvallllllvll 119
                                       ++ia+ig+l+ + +   ++l l+++++++l++++++
  gi|518652976|ref|YP_008142496.1| 225 SIIAFIGTLTFQDSF--FSLILMMIFSVVLIIYTFI 258
                                       ******995444444..4444455555555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1201  (0.0669864); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 1641.72
//
Query:       gi|518652977|ref|YP_008142497.1|  [L=128]
Description: S-adenosylmethionine decarboxylase proenzyme [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-32  111.8   0.0      2e-32  111.6   0.0    1.0  1  AdoMet_dc  S-adenosylmethionine decarboxylase
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.15   12.3   0.0    1.3  1  SpmSyn_N   S-adenosylmethionine decarboxylase N -terminal


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 !  111.6   0.0   2.3e-36     2e-32       1     106 []       6     112 ..       6     112 .. 0.99

  Alignments for each domain:
  == domain 1  score: 111.6 bits;  conditional E-value: 2.3e-36
                                       EEEEEEES--HHHCTSHHHHHHHHHHHHHHCT-EEEEEEEEE-SSS-EEEEEEETTEEEEEEEEGGGTEEEEEEEEE CS
                         AdoMet_dc   1 hllvdlygcdpelledaelleqilteaaeaigatvlsvafhkfepeGvsvvvliaeShlsiHtwpetgyaaiDvftc 77 
                                       h+++dlyg+d+el+++a+ +  i++ a+++ ++t +s+++++f+p G+s+++l+aeShls Htwpe+g +++D++tc
  gi|518652977|ref|YP_008142497.1|   6 HIIADLYGVDSELISSADGISPIIESAIKEGNLTEISSQYYQFRPMGASGIALLAESHLSFHTWPEHGLVTLDIYTC 82 
                                       9**************************************************************************** PP

                                       ST.HHHHHHHHHHHHHHT-SEEEEEEEEEE CS
                         AdoMet_dc  78 ge.ispekaleylieafkadrvtvdelkRG 106
                                       ge  ++++a++yl + ++++++++++l+RG
  gi|518652977|ref|YP_008142497.1|  83 GEhSNADRAFNYLLNVLHPTSIEYKKLERG 112
                                       *****************************8 PP

>> SpmSyn_N  S-adenosylmethionine decarboxylase N -terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.6e-05      0.15      45      72 ..      71      99 ..      57     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.6e-05
                          SpmSyn_N 45 phGlvlldlqsyeedekaq.evdkllnkv 72
                                       hGlv+ld+ ++ e+++a    + lln +
  gi|518652977|ref|YP_008142497.1| 71 EHGLVTLDIYTCGEHSNADrAFNYLLNVL 99
                                      5*********9999888775889999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       352  (0.019633); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 859.42
//
Query:       gi|518652978|ref|YP_008142498.1|  [L=256]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00054   19.8   0.0     0.0015   18.4   0.0    1.7  1  MarR_2         MarR family
    0.00059   19.3   0.0     0.0015   18.0   0.0    1.7  1  HTH_24         Winged helix-turn-helix DNA-binding
     0.0015   18.5   0.0     0.0028   17.7   0.0    1.5  1  HTH_20         Helix-turn-helix domain
     0.0025   17.6   0.0      0.005   16.7   0.0    1.5  1  HTH_5          Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.011   15.7   1.5      0.013   15.4   0.1    1.9  2  HTH_11         HTH domain
      0.014   15.3   0.3      0.038   14.0   0.3    1.7  1  HTH_45         Winged helix-turn-helix
      0.027   14.9   0.1       0.09   13.3   0.0    1.8  2  HTH_27         Winged helix DNA-binding domain
      0.091   13.1   0.1       0.32   11.3   0.0    1.9  1  DUF2513        Hypothetical protein (DUF2513)
      0.096   12.6   0.1       0.19   11.6   0.1    1.4  1  HxlR           HxlR-like helix-turn-helix
        0.1   12.5   0.1       0.38   10.7   0.0    1.9  2  TrmB           Sugar-specific transcriptional regulator TrmB
       0.12   12.2   0.0       0.25   11.2   0.0    1.5  1  LexA_DNA_bind  LexA 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 !   18.4   0.0   8.9e-07    0.0015       6      52 ..       9      52 ..       7      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8.9e-07
                                      HHHHHHHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2  6 aqarvLaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLve 52
                                      +q+++L+++ ++     +++e+ r+l+++ + v ++ k L  +G++ 
  gi|518652978|ref|YP_008142498.1|  9 SQLMILLNIKNGKT---RPSEISRELDITIQGVVYHMKILKNKGFID 52
                                      6999********95...****************************96 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.2e-07    0.0015      14      47 ..      18      51 ..      11      52 .. 0.95

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.2e-07
                            HTH_24 14 knprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      kn+++  +e++++l+++++ v +++k L+++G+I
  gi|518652978|ref|YP_008142498.1| 18 KNGKTRPSEISRELDITIQGVVYHMKILKNKGFI 51
                                      799999***************************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 !   17.7   0.0   1.7e-06    0.0028      21      56 ..      18      53 ..       1      56 [. 0.79

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.7e-06
                                      TCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEEE CS
                            HTH_20 21 raegltaselaerldlskntlsyHLrvLeeagLvev 56
                                       ++   +se+ ++ld++ + + yH+++L   g+++ 
  gi|518652978|ref|YP_008142498.1| 18 KNGKTRPSEISRELDITIQGVVYHMKILKNKGFIDD 53
                                      66666689********************99999975 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   3.1e-06     0.005       4      46 ..      10      52 ..       9      53 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.1e-06
                                      HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  4 RlkILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +l IL    +g++  +e+++el+++   v +H k+L++ G+++
  gi|518652978|ref|YP_008142498.1| 10 QLMILLNIKNGKTRPSEISRELDITIQGVVYHMKILKNKGFID 52
                                      5788999999******************************996 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   0.1   8.2e-06     0.013       4      44 ..      10      50 ..       8      61 .. 0.88
   2 ?   -2.8   0.1       3.9   6.4e+03      27      49 ..     135     157 ..     134     159 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 8.2e-06
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelgv 44
                                      q+++lL+ ++g+   +e+++eL+++ + v+ ++k+L+ +g+
  gi|518652978|ref|YP_008142498.1| 10 QLMILLNIKNGKTRPSEISRELDITIQGVVYHMKILKNKGF 50
                                      8899999999999**************************94 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 3.9
                            HTH_11  27 vSrrtvrrdIkaLeelgvpIese 49 
                                       ++  t +r I  ++++ + + ++
  gi|518652978|ref|YP_008142498.1| 135 CTGVTAVREIINIKKSRIVVLAV 157
                                       67788899998888887766665 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.3   2.4e-05     0.038      11      67 ..      13      66 ..       8      77 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-05
                            HTH_45 11 ILeaisegeakkTkimykanLsykllnkYLdmLvekglikkskekYvlTekGlelle 67
                                      IL +i++g++++++i  + +++ + +   +++L +kg+i++++   ++T++G ++l 
  gi|518652978|ref|YP_008142498.1| 13 ILLNIKNGKTRPSEISRELDITIQGVVYHMKILKNKGFIDDEN---RITKEGFDFLY 66
                                      8999***********************************8765...68888888774 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   5.5e-05      0.09       5      55 ..      10      54 ..       9      60 .. 0.88
   2 ?   -2.4   0.0       4.5   7.3e+03      27      44 ..     157     174 ..     149     177 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 5.5e-05
                            HTH_27  5 qalvLhlirhrrrrkkladlcgrlnvedshisyslkkLtekGLvertgdea 55
                                      q ++L +i+  +++ + +++++ l+++ + ++y +k L +kG++    d++
  gi|518652978|ref|YP_008142498.1| 10 QLMILLNIK--NGKTRPSEISRELDITIQGVVYHMKILKNKGFI----DDE 54
                                      889******..888888***************************....333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.5
                            HTH_27  27 rlnvedshisyslkkLte 44 
                                       + nve+  ++ s+++L++
  gi|518652978|ref|YP_008142498.1| 157 VNNVEKVDNMVSISQLVK 174
                                       556777777777777776 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.32      10      74 ..      13      69 ..      11      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
                           DUF2513 10 iLltleeletkeeslddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakssiislvvkrL 74
                                      iLl++++ +t++++++ e      + + + + ++yh+k+l ++g+i+ e++ +k++  ++ ++ L
  gi|518652978|ref|YP_008142498.1| 13 ILLNIKNGKTRPSEISRE------L-DITIQGVVYHMKILKNKGFIDDENRITKEG-FDFLYNGL 69
                                      788888888888887773......3.4566779***************99888877.55554444 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00012      0.19       8      52 ..      11      54 ..       9      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00012
                                      HHHHHHHTTS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEE CS
                              HxlR  8 llilvellkgkkRfselkralpkisqkmLaqrLreLeqdgliere 52
                                      l+il ++ +gk R se++r+l +i+ +  + +++ L+++g+i+ e
  gi|518652978|ref|YP_008142498.1| 11 LMILLNIKNGKTRPSEISREL-DITIQGVVYHMKILKNKGFIDDE 54
                                      78*******************.9******************9865 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00024      0.38      16      56 ..      13      55 ..       8      66 .. 0.89
   2 ?   -2.1   0.1       2.2   3.6e+03      25      39 ..     138     152 ..     134     154 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00024
                                      HHH..HHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEES CS
                              TrmB 16 aLl..klgpatadeiaeelgvprskvYevLrsLedkGlVerek 56
                                       Ll  k+g+ + +ei++el++  + v   ++ L++kG+++ e 
  gi|518652978|ref|YP_008142498.1| 13 ILLniKNGKTRPSEISRELDITIQGVVYHMKILKNKGFIDDEN 55
                                      5667799********************************9886 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 2.2
                                       HCHHCCCTTSSCHCH CS
                              TrmB  25 adeiaeelgvprskv 39 
                                       ++ + e++++ +s++
  gi|518652978|ref|YP_008142498.1| 138 VTAVREIINIKKSRI 152
                                       678999999999997 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 ?   11.2   0.0   0.00015      0.25      30      59 ..      26      54 ..      12      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00015
                                      HHHHHHTS-.HHHHHHHHHHHHHTTSEE-G CS
                     LexA_DNA_bind 30 eiaralglkSpsaveehLkaLerKGyierd 59
                                      ei+r+l ++  ++v  h+k L++KG+i+ +
  gi|518652978|ref|YP_008142498.1| 26 EISRELDIT-IQGVVYHMKILKNKGFIDDE 54
                                      9********.99***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        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 0.21s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1886.28
//
Query:       gi|518652979|ref|YP_008142499.1|  [L=219]
Description: thiamine-phosphate pyrophosphorylase [Ferroplasma acidarmanus fer1]
Scores for complete 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-48  162.0   0.0    1.1e-47  161.8   0.0    1.0  1  TMP-TENI   Thiamine monophosphate synthase
    4.3e-06   26.1   0.1    9.4e-05   21.7   0.3    2.1  2  DUF561     Protein of unknown function (DUF561)
  ------ inclusion threshold ------
      0.024   14.0   0.0      0.046   13.1   0.0    1.5  1  NMO        Nitronate monooxygenase
       0.18   11.6   0.0        0.3   10.9   0.0    1.3  1  QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   0.0   2.4e-51   1.1e-47       1     181 []      19     196 ..      19     196 .. 0.96

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 2.4e-51
                          TMP-TENI   1 lylvtdskldkneellevveealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgv 77 
                                       lylvt++ +   + ++++ e+a+k+gv+++q+R+k+ + r+ l+  +kla +c++y+vp+i++d+  l   +gadg+
  gi|518652979|ref|YP_008142499.1|  19 LYLVTPDYSG--DWIINATERAIKSGVDILQYRDKTSTFRDKLAIGKKLASICHDYSVPFIVDDDPVLMDILGADGI 93 
                                       79****6665..99*************************************************************** PP

                          TMP-TENI  78 HlgqddlpvaearellgpdliiGlSvhslee.aeeaealgadYigvGpifpTdtKkdaeplgleglkelaealeiPv 153
                                       H+g+dd p + ++    pd iiG+S+++  + a+  ++lgadY+++G++fpT+tK+da+ ++++ lk +   ++iPv
  gi|518652979|ref|YP_008142499.1|  94 HIGKDDVPFDYVKSKY-PDHIIGVSTYGSIKdALLYQKLGADYVAFGSFFPTKTKDDATICDINVLKGIGP-INIPV 168
                                       **************88.69*******988777**********************************99976.8**** PP

                          TMP-TENI 154 vaiGGitlenvaevleagadgvavvsai 181
                                       ++iGGi+ en++ vl++g++g+avvsai
  gi|518652979|ref|YP_008142499.1| 169 FVIGGISRENIDLVLKYGISGIAVVSAI 196
                                       ***************************8 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.021        96     140     206 ..      37     104 ..      30     118 .. 0.83
   2 !   21.7   0.3   2.1e-08   9.4e-05     185     231 ..     164     210 ..     155     216 .. 0.94

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.021
                            DUF561 140 kLeslgvdliqteGkitsiskakkvndliekslstlastyeiskk.vslPvicasGlsdvtvplalsl 206
                                       +  + gvd++q   k++++ ++  + + +  + + ++  + +    v + ++ a G+     ++++ +
  gi|518652979|ref|YP_008142499.1|  37 RAIKSGVDILQYRDKTSTFRDKLAIGKKLASICHDYSVPFIVDDDpVLMDILGADGIHIGKDDVPFDY 104
                                       55567999999999999999999999999999999999999976438889999999998888888876 PP

  == domain 2  score: 21.7 bits;  conditional E-value: 2.1e-08
                            DUF561 185 vslPvicasGlsdvtvplalslgasGiGigsavsklndeeemvalls 231
                                       +++Pv    G+s   ++l l++g sGi + sa+ + nd+e+ v++ +
  gi|518652979|ref|YP_008142499.1| 164 INIPVFVIGGISRENIDLVLKYGISGIAVVSAIYSHNDIEDQVSYFK 210
                                       89***************************************999975 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0     1e-05     0.046     114     225 ..      90     196 ..      42     215 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
                               NMO 114 vevvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgd..kglfaLvpqv 188
                                       ++ + +g ++ + + v+++    ++ + t +s+k+a   +++GaD +       G   +t  ++d     +++++ +
  gi|518652979|ref|YP_008142499.1|  90 ADGIHIGKDDVPFDYVKSKYPDHIIGVSTYGSIKDALLYQKLGADYVA-----FGSFFPTKTKDDatICDINVLKGI 161
                                       555666677777888889999999999999999999999999999863.....466777333332222333444443 PP

                               NMO 189 ldavdiPviAaGGiidrrgvaaaLalGAsgvqigtrf 225
                                          ++iPv   GGi  r++++ +L +G sg+++ ++ 
  gi|518652979|ref|YP_008142499.1| 162 G-PINIPVFVIGGIS-RENIDLVLKYGISGIAVVSAI 196
                                       3.356********96.789*************98886 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 ?   10.9   0.0   6.7e-05       0.3      87     162 ..     116     200 ..     102     204 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 6.7e-05
                                       ESSHHHHHHHHHHT...-SEEEEES--HHHHHHHHHHHHHHSTT......SEEEEESS--TTTHHHHHCTT-SEEEE CS
                         QRPTase_C  87 vesleeleevleae...adiimLDnfsveelkkaveelkeknkr......vlievSGgvtlenveeyaksgvdvisv 154
                                       v+++  ++ +l  +   ad + +  f ++++k+ +++ +    +      + ++v Gg++ en+  + k+g+  i+v
  gi|518652979|ref|YP_008142499.1| 116 VSTYGSIKDALLYQklgADYVAFGSFFPTKTKDDATICDINVLKgigpinIPVFVIGGISRENIDLVLKYGISGIAV 192
                                       5556666666553333399999999988888888887655555566787899***********************99 PP

                                       CHHCHTB- CS
                         QRPTase_C 155 galthsvk 162
                                        ++++s +
  gi|518652979|ref|YP_008142499.1| 193 VSAIYSHN 200
                                       99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       331  (0.0184617); 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:                         4  (0.000223102); expected 0.2 (1e-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: 1551.83
//
Query:       gi|518652980|ref|YP_008142500.1|  [L=343]
Description: hypothetical protein FACI_IFERC00001G1619 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-20   72.2   0.0    6.9e-20   71.8   0.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    1.3e-09   38.6   0.0    2.6e-09   37.6   0.0    1.4  1  AIRS      AIR synthase related protein, N-terminal domain
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.028   14.5   0.0    1.5  1  FokI_C    Restriction endonuclease FokI, catalytic 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 !   71.8   0.0   1.1e-23   6.9e-20       2     150 ..     154     310 ..     153     316 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.8 bits;  conditional E-value: 1.1e-23
                                       TTEEEEEEET.....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHH..HTTECEEEE--TTH CS
                            AIRS_C   2 pGdvliltgs.....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaal..kglvkaahDvTgGG 71 
                                       +Gd++i+t+s       + ++++ + ++ +  e+     + +   + ++t++ +  ++++   +++++++hD T+GG
  gi|518652980|ref|YP_008142500.1| 154 VGDRIIMTKScaletALILSNTFPEYVRNNIGEEN---YKSIIGKFYTMTCVGEETLAIEYgiSERITSMHDATEGG 227
                                       79********7777555555665554444444433...34588889999*******999999*************** PP

                                       HHHHHHHHHHTTTEEEEEECG......THHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEE CS
                            AIRS_C  72 Llgalaemapasgvgaeidld......kvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavI 142
                                       Ll+a+ e+  asg g+ +d++      +++ +++l + +++l+s ++G ll++v+++ a ++l il++ g+ ea+ I
  gi|518652980|ref|YP_008142500.1| 228 LLNAIYEIGIASGNGLSVDYNkiiidsDIEKLCNL-FNIDPLRSISEGTLLITVKEQYAMEFLTILQSSGI-EASLI 302
                                       *********************77666666666666.***********************************.8**** PP

                                       EEEEESSS CS
                            AIRS_C 143 Gevtakee 150
                                       Ge+ +  +
  gi|518652980|ref|YP_008142500.1| 303 GEILDNSK 310
                                       ***99765 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.6   0.0   4.3e-13   2.6e-09       5      91 ..      45     140 ..      30     143 .. 0.88

  Alignments for each domain:
  == domain 1  score: 37.6 bits;  conditional E-value: 4.3e-13
                                       EEEEEEEEE.EECCTCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC......HHHHHHHHHHHHHHHTT-E CS
                              AIRS   5 vvvttdshnrpvlvepvhf...iGakavavnlsDlaamGArPlalllslalp......wleevvrglaeaaeelgvp 72 
                                       ++vttd    p+++++  +   +++ a +  lsDl++ G    +++  l+lp      +++e+ + ++e + +++++
  gi|518652980|ref|YP_008142500.1|  45 MAVTTD----PLYIDKSFGfkkAAWFAFHILLSDLYTSGIPASYMSIDLNLPssitdnEFKEIWDVINEECIKYNIE 117
                                       599***....****998778*******************9999********************************** PP

                                       EEEEEEEEESS....EEEEEEEE CS
                              AIRS  73 lvgGdtsfsne....ptisvtav 91 
                                       +v+G+t+++n+    ++  +t +
  gi|518652980|ref|YP_008142500.1| 118 VVTGHTARYNGvefpMVGGITLM 140
                                       *********99888433344554 PP

>> FokI_C  Restriction endonuclease FokI, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   4.6e-06     0.028      69     135 ..     147     214 ..     141     215 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.6e-06
                            FokI_C  69 lksdtegssDkYvrmiaswLk.klglvkkeakvvtvdlggrkYtetitqsykitdkGrtalkkalGks 135
                                       + ++  g  D+ + + +  L+ +l l +  ++ v +++g ++Y+++i++ y++t  G ++l +  G+s
  gi|518652980|ref|YP_008142500.1| 147 ITTENAGVGDRIIMTKSCALEtALILSNTFPEYVRNNIGEENYKSIIGKFYTMTCVGEETLAIEYGIS 214
                                       5666777778877776655652678888999*******************************999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (343 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       310  (0.0172904); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2315.89
//
Query:       gi|518652981|ref|YP_008142501.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G1620 [Ferroplasma acidarmanus fer1]
Scores for complete 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-88  294.6   0.1    5.8e-88  294.4   0.1    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    6.2e-14   52.0   0.0    8.5e-14   51.5   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase
    0.00014   21.4   0.0    0.00025   20.6   0.0    1.4  1  Carb_kinase   Carbohydrate kinase
  ------ inclusion threshold ------
      0.022   14.1   0.1       0.04   13.2   0.1    1.4  1  CbiK          Cobalt chelatase (CbiK)
       0.18   12.1   0.0       0.35   11.2   0.0    1.5  1  CbiX          CbiX


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 !  294.4   0.1   1.6e-91   5.8e-88       1     244 [.       7     249 ..       7     251 .. 0.98

  Alignments for each domain:
  == domain 1  score: 294.4 bits;  conditional E-value: 1.6e-91
                                       ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHH CS
                      Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiiev 77 
                                       Ds+GGAGi ADlktf+a++v+g+svi +ltaqn+ +vk++++lp +++++q++a++ed++ da+K+Gml+sa +i+ 
  gi|518652981|ref|YP_008142501.1|   7 DSGGGAGIMADLKTFTAMKVFGTSVIVTLTAQNSVSVKSIYELPLKFINEQFDAIMEDIGTDAAKTGMLYSAPVISD 83 
                                       9**************************************************************************** PP

                                       HHHHHHHTTS.SEEEE---SSCTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHH CS
                      Phos_pyr_kin  78 vaeklkkykv.pvVlDPVmvaksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllk 153
                                       v+ek+k+y++ ++V+DPVm++k++ +ll+e+ave++ ++L+++a++itPN+pEae+++++ki++ ed k a kk+ +
  gi|518652981|ref|YP_008142501.1|  84 VTEKFKQYGIkNIVIDPVMISKTNVRLLREDAVETMITKLMKIAELITPNIPEAEKISSMKIRNSEDTKIASKKIYE 160
                                       ***************************************************************************** PP

                                       TT-SEEEEEEGGS-SSSEEEEEEEETSSEEEEEEEE----S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHH CS
                      Phos_pyr_kin 154 lgakaVlikGghlegeeavvtdvlydgeeveeleaerietknthGtGCtlssaiaaelakgesleeAvkkAkeyvte 230
                                        + ++VlikGgh+   + ++td+lydg+e++e++++ri+t+nthGtG+tls++ia++la g++l+e+++ Ak+y+  
  gi|518652981|ref|YP_008142501.1| 161 NTGSSVLIKGGHA--GSRYSTDILYDGSEYYEFPSRRINTNNTHGTGDTLSASIASYLASGKKLPESIELAKKYIDG 235
                                       999*********7..556668******************************************************** PP

                                       HHHCG-BSTSSS-B CS
                      Phos_pyr_kin 231 aikealelgkgagp 244
                                       ai++++ +gkg+g 
  gi|518652981|ref|YP_008142501.1| 236 AIENSFPMGKGYGA 249
                                       ***********987 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.0   2.4e-17   8.5e-14     172     284 ..     114     231 ..      73     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 2.4e-17
                                       H.HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEEEGGGEEEEEE.....TTEEEE CS
                              PfkB 172 q.fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvtlGkeGalvve.....kdgelk 242
                                       + +  ++ +l+  a l++pn  E+e+++++k+ + e+ + a +k+ +   + v+++ G  G+ +++     +++ ++
  gi|518652981|ref|YP_008142501.1| 114 DaVETMITKLMKIAELITPNIPEAEKISSMKIRNSEDTKIASKKIYENTGSSVLIKGGHAGSRYSTdilydGSEYYE 190
                                       24778999************************7777777777887777779*******************9999999 PP

                                       EEE.SSSS-SBGTTHHHHHHHHHHHHHHTTHHHHHHHHHHHH CS
                              PfkB 243 vpavpkvkvvDttGAGDsfvggflaallegksleealrfana 284
                                       +p+ + ++  +t G+GD+  +++++ l++gk+l e++++a +
  gi|518652981|ref|YP_008142501.1| 191 FPS-RRINTNNTHGTGDTLSASIASYLASGKKLPESIELAKK 231
                                       999.89*********************************975 PP

>> Carb_kinase  Carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0     7e-08   0.00025     119     232 ..     127     248 ..      98     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 7e-08
                                       SEEEE--HHHHHHHCTTTCHHCCSHHHHHHHHHHHHTTEEEEESTT......SEEEECTTEEEEE----GG.G-STT CS
                       Carb_kinase 119 eviLTPhkkEfkrLlkaivkkeddrlelarelaqklnavvllkgek......dvivspegevlinstgssa.lakGG 188
                                       +  +TP++ E ++++ + + + +d   + +++ ++ ++ vl+kg +      + i + + e +  +    +   + G
  gi|518652981|ref|YP_008142501.1| 127 AELITPNIPEAEKISSMKIRNSEDTKIASKKIYENTGSSVLIKGGHagsrysTDILYDGSEYYEFPSRRINtNNTHG 203
                                       5679***************99999999999**************86444444778998999998887765516788* PP

                                       HHHHHHHHHHHHHHCTS.SHHHHHHHHHHHHHHHHHHHCCCT-TS CS
                       Carb_kinase 189 sGDvLaGligalLaqne.asyeaaiaaawlhgaasdeaaekkgvg 232
                                       +GD+L+ +i++ La+ +  +    +a  ++ ga+ + ++  kg+g
  gi|518652981|ref|YP_008142501.1| 204 TGDTLSASIASYLASGKkLPESIELAKKYIDGAIENSFPMGKGYG 248
                                       ***************994456667888888888888777777765 PP

>> CbiK  Cobalt chelatase (CbiK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.1e-05      0.04     161     207 ..      57     103 ..      47     108 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.1e-05
                                       HHHHHHHHCT-S.EEEEETTSSS-HHHHHHHHHHHT--EEEEEE-SS CS
                              CbiK 161 eldkvlkekdfkqvvvgtvegyPeveevieelkkkgikevkliPlml 207
                                       + d ++++ + +    g++ + P +++v e+ k+ gik++ + P+m+
  gi|518652981|ref|YP_008142501.1|  57 QFDAIMEDIGTDAAKTGMLYSAPVISDVTEKFKQYGIKNIVIDPVMI 103
                                       678999**9999**********************************8 PP

>> CbiX  CbiX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.6e-05      0.35      15      64 ..      57     105 ..      52     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.6e-05
                                       HHHHHHHHCCSCCCEECESCCCECCSCCSSHHHHC-SBSEEEEEEESSSS CS
                              CbiX  15 laeelrekgpfkpvelgfleleepsleealrelaeqgvkrivvvPlflfa 64 
                                         +++ e  + +  ++g l +++p + ++ +++ + g+k+iv+ P+++++
  gi|518652981|ref|YP_008142501.1|  57 QFDAIMEDIGTDAAKTGML-YSAPVISDVTEKFKQYGIKNIVIDPVMISK 105
                                       5566777777777788875.599************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); 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 0.23s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1802.62
//
Query:       gi|518652982|ref|YP_008142502.1|  [L=405]
Description: hypothetical protein FACI_IFERC00001G1621 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.8e-32  110.8   0.0    1.1e-31  110.5   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    8.3e-30  103.8   0.3    1.4e-29  103.1   0.3    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
    3.9e-24   85.7   1.3    6.2e-24   85.0   1.3    1.3  1  Glyco_trans_2_3  Glycosyl transferase family group 2
    2.5e-10   40.3   1.8    1.2e-09   38.1   1.8    1.9  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    2.1e-08   33.8   0.0    2.8e-08   33.4   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    0.00021   21.8   0.0    0.00051   20.5   0.0    1.7  1  Glyco_tranf_2_4  Glycosyl transferase family 2
      0.009   14.7   7.2     0.0079   14.9   3.0    2.5  3  Chitin_synth_2   Chitin synthase
  ------ inclusion threshold ------
        1.3    9.0   4.5        8.8    6.3   0.7    3.2  3  Trm5_N           tRNA methyltransferase 5 N-terminal 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 !  110.5   0.0   4.8e-35   1.1e-31       2     230 .]      56     279 ..      55     279 .. 0.89

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 4.8e-35
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++++++Vp+ nee+v+ +++es+l+q+y ++e++vvvd+s++ t + a+e   ++ d rv+v    r  g ++k+ a
  gi|518652982|ref|YP_008142502.1|  56 PMVSIIVPAKNEETVIKRTIESILNQTYTNFELFVVVDNSSDNTYKIAKEY--ESRDKRVNVFN--RPDG-KSKASA 127
                                       469**********************************************95..44466889753..4337.6***** PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavg.tpvfllnrstlvsalgalefaerhlrflaarra 154
                                       ln  ++ +k+++++  D+Dt + P+tl+ ++  +++ +v++++  + + +++++ +++l  +     ++  l  r+ 
  gi|518652982|ref|YP_008142502.1| 128 LNFCFEKTKGEVIATYDADTMLLPNTLENAVYGMNYFNVDVLQgYNSYINREENIFTRLAVIDEILVKAT-LIGRTH 203
                                       *****************************99888888******555588899999999977765555554.555555 PP

                   Glyco_tranf_2_3 155 lg.vltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrnRwvyg 230
                                       ++ +++++Gs   + r+v + ++g+d  + lt+D+e++ r+ +a++++ay+  a    ++p+s ++y++qr+Rw++g
  gi|518652982|ref|YP_008142502.1| 204 FNlFVPVAGSNQYFKRKVIESIGGWDD-NFLTEDLESSIRISNARYKSAYLGSAKALQETPASYSEYFRQRTRWLRG 279
                                       5548***********************.**********************************************986 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 !  103.1   0.3   6.1e-33   1.4e-29       1     166 [.      59     222 ..      59     226 .. 0.84

  Alignments for each domain:
  == domain 1  score: 103.1 bits;  conditional E-value: 6.1e-33
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s+++p+ Nee  +++t+es+l+q +y +fe++vv D+S+D+t +i++e+ ++d+rv v+ r+ ++ ka+aln  +++
  gi|518652982|ref|YP_008142502.1|  59 SIIVPAKNEETVIKRTIESILNQ-TYTNFELFVVVDNSSDNTYKIAKEYESRDKRVNVFNRPDGKSKASALNFCFEK 134
                                       8**********************.***************************************************** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCHCCCCHCCCCCCSTTC CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerlyfkerkrslkgnlsfe 154
                                       ++g++i++ DaD+   p++le  v  ++  ++dv  g   +i+ e++ ++r      +  ++ +   r+ +     +
  gi|518652982|ref|YP_008142502.1| 135 TKGEVIATYDADTMLLPNTLENAVYGMNYFNVDVLQGYNSYINREENIFTRLAV-IDEILVKATLIGRTHFNLFVPV 210
                                       ****************************99999888888888877777776543.3444444444444444444445 PP

                                       STCCCEEEEHHH CS
                   Glycos_transf_2 155 igsaallrreal 166
                                        gs+  ++r+++
  gi|518652982|ref|YP_008142502.1| 211 AGSNQYFKRKVI 222
                                       555555566555 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 !   85.0   1.3   2.8e-27   6.2e-24       2     176 ..     140     353 ..     139     381 .. 0.70

  Alignments for each domain:
  == domain 1  score: 85.0 bits;  conditional E-value: 2.8e-27
                   Glyco_trans_2_3   2 illlDaDtvlppdclreiaaelaspevaivqgp.vlvmnvanwleelaalffaedhgkdilvrealgrvvpsvGsga 77 
                                       i+  DaDt+l p+ l+ +++ +   +v+++qg  +++++  n++++la++     +    + r  +  +vp++Gs+ 
  gi|518652982|ref|YP_008142502.1| 140 IATYDADTMLLPNTLENAVYGMNYFNVDVLQGYnSYINREENIFTRLAVIDEI-LVKATLIGRTHFNLFVPVAGSNQ 215
                                       8889******************9669*****983555789********98753.33334566779999********* PP

                   Glyco_trans_2_3  78 flrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc......elek 148
                                        + r++++++ggwd  + +++ED+++++r+  + y+  +  ++   +++p ++  ++rQr+Rw++G+      +   
  gi|518652982|ref|YP_008142502.1| 216 YFKRKVIESIGGWD--DNFLTEDLESSIRISNARYKSAYLGSAKALQETPASYSEYFRQRTRWLRGYhqvffhS--- 287
                                       **************..9************************99999999*****************96444331... PP

                   Glyco_trans_2_3 149 lil........................................lvrllgylgsllwsalplhlallll 176
                                                                                   ++ + y+ sl++ +l + +++l+l
  gi|518652982|ref|YP_008142502.1| 288 --KkrfskftdfdalmivlaptfsgilffgwlyisllnfynpfVHSMRTYFISLILISLIIYVVALVL 353
                                       ..033345556666667777777777444444222222222211111122222222222222221111 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 !   38.1   1.8   5.2e-13   1.2e-09       1     202 [.      59     246 ..      58     278 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 5.2e-13
                   Glyco_tranf_2_2   1 svviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGa 77 
                                       s+++p +++e    i+ ++  + ++   ++el vv d Ss+++ +  +      ++v + + +d   s+a a N  +
  gi|518652982|ref|YP_008142502.1|  59 SIIVPAKNEETV--IKRTIESILNQTYTNFELFVVVDNSSDNTYKIAKEYESRDKRVNVFNRPDG-KSKASALNFCF 132
                                       577777776666..99888555555557**********************999999988888775.59********* PP

                   Glyco_tranf_2_2  78 skaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaak 154
                                       +k++++++   DaD +  ++ +e+ +       + +  +  v   +  +++ + +++ +   ++ +++v   +  + 
  gi|518652982|ref|YP_008142502.1| 133 EKTKGEVIATYDADTMLLPNTLENAVY-----GM-NYFNVDVLQGYNSYINREENIFTRLA-VIDEILVK--ATLIG 200
                                       ***********************9998.....44.34555666666677777777776653.22333333..33333 PP

                   Glyco_tranf_2_2 155 stlvkffapss.ssilinrraflevGGyDErfrGhgaEDfdlllRlaka 202
                                        t  + f+p + s+   +r+ +  +GG+D++f    +ED +  +R+  a
  gi|518652982|ref|YP_008142502.1| 201 RTHFNLFVPVAgSNQYFKRKVIESIGGWDDNF---LTEDLESSIRISNA 246
                                       555556777665********************...78999999999753 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0   1.2e-11   2.8e-08      10     173 .]     116     278 ..     107     278 .. 0.84

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 1.2e-11
                   Glyco_transf_21  10 gdpvgvnpKvnnllqaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdak.glaaaleaafl. 84 
                                         ++  + K ++l+  +e+ k +++ + D+d+++ p++Le+ +  +   +v +++++  + +++ ++ ++l+     
  gi|518652982|ref|YP_008142502.1| 116 FNRPDGKSKASALNFCFEKTKGEVIATYDADTMLLPNTLENAVYGMNYFNVDVLQGYNSYINREeNIFTRLAVIDEi 192
                                       556677889999999*****************************************987666662666666333331 PP

                   Glyco_transf_21  85 ntlagvlqa.klsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvprrss 160
                                          a ++ + ++  +  + G+   ++r+++e+iGG       L eD++ + +++ a +k +    + a +++p   s
  gi|518652982|ref|YP_008142502.1| 193 LVKATLIGRtHFNLFVPVAGSNQYFKRKVIESIGGWDD--NFLTEDLESSIRISNARYKSAYLGSAKALQETPA--S 265
                                       3335555557889************************9..9******************999998888778885..8 PP

                   Glyco_transf_21 161 lrallaRqlrWar 173
                                       +++++++ +rW r
  gi|518652982|ref|YP_008142502.1| 266 YSEYFRQRTRWLR 278
                                       999********75 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.3e-07   0.00051       1      86 [.      65     151 ..      65     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                   Glyco_tranf_2_4   1 rneadiLpeflahhlalgfdr..ilvydndstDgtrailkelpe....vkllhvdksyederrqvellkallaryae 71 
                                       +ne+ +++++++ +l+  +++  ++v+ ++s+D+t++i ke++     v++++ ++     + + ++l+ ++++  +
  gi|518652982|ref|YP_008142502.1|  65 KNEETVIKRTIESILNQTYTNfeLFVVVDNSSDNTYKIAKEYESrdkrVNVFNRPD----GKSKASALNFCFEK-TK 136
                                       79**************99985559999999**********9744121144444443....45678888888866.57 PP

                   Glyco_tranf_2_4  72 adwvlvvDaDEflvv 86 
                                       ++ +++ DaD +l  
  gi|518652982|ref|YP_008142502.1| 137 GEVIATYDADTMLLP 151
                                       888888888877765 PP

>> Chitin_synth_2  Chitin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0       0.1   2.3e+02      27      63 ..      58      91 ..      36      96 .. 0.67
   2 ?   -1.7   0.0      0.36     8e+02     203     227 ..     138     162 ..     132     192 .. 0.72
   3 !   14.9   3.0   3.5e-06    0.0079     339     467 ..     245     371 ..     218     394 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.1
                    Chitin_synth_2 27 ticlvtaysegeeglrttldslastdyddkrklllvv 63
                                      + ++v+a  ++e  +++t++s+ +  y + +   +vv
  gi|518652982|ref|YP_008142502.1| 58 VSIIVPAK-NEETVIKRTIESILNQTYTNFEL--FVV 91
                                      33445554.4567899***********98753..333 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.36
                    Chitin_synth_2 203 eivlmvdadtkvapdsltrlvaalv 227
                                       e++ + dadt + p++l++ v  + 
  gi|518652982|ref|YP_008142502.1| 138 EVIATYDADTMLLPNTLENAVYGMN 162
                                       7888899****99999999887775 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 3.5e-06
                    Chitin_synth_2 339 fpkrktvfvpqakcktvaPdtfkvllsqrrrwinstvhnllelvlvrdlcGtfcfsmrfvvfieligtvvlPvaiaf 415
                                         ++k+ ++ +ak+   +P +++ ++ qr rw+    h ++     + +  +  f   ++v     + ++    +  
  gi|518652982|ref|YP_008142502.1| 245 NARYKSAYLGSAKALQETPASYSEYFRQRTRWLRG-YHQVFF-HSKKRFSKFTDFDALMIVLAPTFSGILFFGWLYI 319
                                       5689*****************************86.577664.4567788999999999999988888777666666 PP

                    Chitin_synth_2 416 tlylivasilksklvpviplvllaivlGlpailivltarkleyvawllvyll 467
                                        l    + +++s  +  i+l+l+++++ + a+++vl  ++ +++   l+y+ 
  gi|518652982|ref|YP_008142502.1| 320 SLLNFYNPFVHSMRTYFISLILISLIIYVVALVLVLIKKRQNFIYIPLIYIY 371
                                       666678889999999*********9998888877776677776666666653 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 ?    2.1   0.0     0.084   1.9e+02       2      18 ..      60      76 ..      59      83 .. 0.81
   2 ?   -1.1   0.0      0.83   1.9e+03      23      31 ..      97     105 ..      94     108 .. 0.87
   3 ?    6.3   0.7    0.0039       8.8      28      40 ..     356     368 ..     354     370 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.084
                                      EEEEGGGHHHHHHHHHH CS
                            Trm5_N  2 ikVpkkegEkvRkkLle 18
                                      i Vp k+ E+v+k+ +e
  gi|518652982|ref|YP_008142502.1| 60 IIVPAKNEETVIKRTIE 76
                                      78***********9776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.83
                                       -TTS--EEE CS
                            Trm5_N  23 drnyKIksd 31 
                                       d++yKI ++
  gi|518652982|ref|YP_008142502.1|  97 DNTYKIAKE 105
                                       89****986 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.0039
                                       -EEETTEEEEEB- CS
                            Trm5_N  28 IksdddylyIPvk 40 
                                       Ik+  +++yIP++
  gi|518652982|ref|YP_008142502.1| 356 IKKRQNFIYIPLI 368
                                       9**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1328  (0.0740699); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 2766.44
//
Query:       gi|518652983|ref|YP_008142503.1|  [L=201]
Description: CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete 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-14   52.6   1.7    5.7e-14   52.6   1.7    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   1.7   3.2e-18   5.7e-14       3      66 .]      26      90 ..      24      90 .. 0.90
   2 ?    1.8   1.7     0.024   4.4e+02      11      39 ..     113     160 ..      95     197 .. 0.61

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.2e-18
                                      HHHHHHHHHHHHHHHHHGGGS-H....HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
                   CDP-OH_P_transf  3 PnaiTllrlllsvlailllltyyp..lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                                      Pn+i++l+l+++ la + ++++++  l+la++++++++l+DalDGk+AR  n +s+ G++lD++ D
  gi|518652983|ref|YP_008142503.1| 26 PNTISILSLVFAALAGI-FYYLSHyfLLLAFIFIIFSALFDALDGKIARLKNISSKKGDMLDHVFD 90
                                      ***********999995.65666678999999999****************99888*******998 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.024
                                       HHHHHHHHHGGGS-H.......................HHHHHHHHHHHH CS
                   CDP-OH_P_transf  11 lllsvlailllltyyp.....................lvlailllliasl 39 
                                       l++ +l i ll +y++                     l+l i++ li+++
  gi|518652983|ref|YP_008142503.1| 113 LFA-ILGI-LLTSYMGtqsqalglkrnysgiagradrLILIIIFSLIQFF 160
                                       332.4444.23334446677777777777777777774444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1287.69
//
Query:       gi|518652984|ref|YP_008142504.1|  [L=446]
Description: hypothetical protein FACI_IFERC00001G1623 [Ferroplasma acidarmanus fer1]
Scores for complete 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-37  127.2   0.1    3.9e-36  123.8   0.1    2.1  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    8.4e-28   97.0   0.0    2.2e-27   95.7   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-26   92.5   0.0    3.8e-26   91.5   0.0    1.5  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.3e-10   41.3   0.0    2.7e-10   40.3   0.0    1.5  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.8   0.1   8.6e-40   3.9e-36       3     134 ..       6     131 ..       4     135 .. 0.95
   2 ?    0.8   0.0     0.082   3.7e+02     107     133 ..     398     425 ..     395     429 .. 0.83

  Alignments for each domain:
  == domain 1  score: 123.8 bits;  conditional E-value: 8.6e-40
                                       GBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-H CS
                         PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllpt 79 
                                       +fgt+G+Rg+ + + lt++l+  +g+ai++ ++     +k+++++DtR+s++++  a+a+ ++++G +vi +g lpt
  gi|518652984|ref|YP_008142504.1|   6 LFGTNGIRGVPN-EDLTTDLAMGIGKAIGTFFNG----GKIAIAKDTRISGDMFMLAVASAIMSTGSDVIYVGELPT 77 
                                       8********998.55******************7....9************************************** PP

                                       HHHHHHHHHCCECEEEEE--TTS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
                         PGM_PMM_I  80 PavsfairklkadagimitaSHnppeyngiKvylsnGgpispeveekIeaiieke 134
                                       P +++++++ k   g+mitaSHnpp+yngiK ++++G +i++e e kIe+i++ +
  gi|518652984|ref|YP_008142504.1|  78 PGLQYYCKS-KGIPGVMITASHNPPQYNGIKAIDKDGTEIDEESEIKIEDIYNGK 131
                                       *********.67778************************************9866 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.082
                                       CCEEEEETTTCE--CHH.HHHHHHHHCC CS
                         PGM_PMM_I 107 ngiKvylsnGgpispev.eekIeaiiek 133
                                        g+K+++++G  + ++  +ekI +i+ +
  gi|518652984|ref|YP_008142504.1| 398 DGVKIFDEDGWTLIRPSgTEKIIRIFSE 425
                                       699*******998777769999998876 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.0   4.9e-31   2.2e-27       3     103 .]     154     253 ..     153     253 .. 0.99

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 4.9e-31
                                       HHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----TT-TTTTHHHHGG CS
                        PGM_PMM_II   3 YiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpeekealkllielvk 79 
                                       Y++++++ vd++aik+++l vvid+++Ga+  + +++l +l+++vv+lna+pd++f++++++p++ e+l +li ++k
  gi|518652984|ref|YP_008142504.1| 154 YMDSIVSMVDEKAIKERRLNVVIDTGNGASYYTSPTILTKLNCHVVSLNANPDGKFSSRNSEPKP-ENLVDLISVMK 229
                                       9****************************************************************.*********** PP

                                       GGG-SEEEEE-TTS-BEEEEETTE CS
                        PGM_PMM_II  80 kegadlglafDgDaDRlgvvderG 103
                                         ++dlg+a+DgDaDR++++de+G
  gi|518652984|ref|YP_008142504.1| 230 TGKFDLGIAHDGDADRCVFIDEKG 253
                                       **********************98 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   8.5e-30   3.8e-26       1     111 [.     257     363 ..     257     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 8.5e-30
                                       HHHHHHHHHHHHHHCHCSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEET CS
                       PGM_PMM_III   1 dgdqllallakylleeklkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifl 77 
                                       dgd+ lal+ k+  +   k++  vv++v++s+ale++++++g+kl+ t+vG   v+++m +++a++GgEe+g+ii++
  gi|518652984|ref|YP_008142504.1| 257 DGDKSLALIVKHTIQ---KGDI-VVTPVSSSDALENICREKGAKLISTRVGAPIVARAMIDNNASIGGEENGGIIYG 329
                                       79*********9966...4666.****************************************************** PP

                                       TTBSS--HHHHHHHHHHHHHHHTS-HHHHHHHHH CS
                       PGM_PMM_III  78 deattkDGilaallvleilaetgkslselleell 111
                                       +++ ++DG+++++l+l++l++++k++s+llee++
  gi|518652984|ref|YP_008142504.1| 330 KHQFCRDGAMTMALMLNLLTHENKTVSSLLEEIP 363
                                       ******************************7754 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 !   40.3   0.0   5.9e-14   2.7e-10       4      68 ..     370     438 ..     360     444 .. 0.77

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 5.9e-14
                                       CCHCC-TT..EECCCCCTTH......HCCCCCCCCGCCEEEE.EEEETTCCEEEEEEEESSHHHHHHHHHH CS
                        PGM_PMM_IV   4 vrveekakvvaalaallkva......sikeglkilledGrrlavRpSGTepllrvyvEaksdeelarlaee 68 
                                       + v++k+  ++++++ll         ++ +g+ki++edG++l +RpSGTe  +r+  E++s+++++++ + 
  gi|518652984|ref|YP_008142504.1| 370 SSVARKKS-WEEIKKLLMENfsgkkmDFTDGVKIFDEDGWTL-IRPSGTEKIIRIFSESPSKSLAEEYNKT 438
                                       55666533.444444444335555557***************.*********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (446 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3434.75
//
Query:       gi|518652985|ref|YP_008142505.1|  [L=360]
Description: hypothetical protein FACI_IFERC00001G1624 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-19   69.0   0.0    4.7e-19   68.5   0.0    1.2  1  Glyco_transf_21  Glycosyl transferase family 21
    6.1e-09   35.9   0.0    2.5e-08   33.9   0.0    1.9  2  Glycos_transf_2  Glycosyl transferase family 2
    4.9e-06   26.6   0.0      8e-06   25.9   0.0    1.3  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00022   21.2   0.7    0.00043   20.3   0.7    1.4  1  Glyco_trans_2_3  Glycosyl transferase family group 2
  ------ inclusion threshold ------
        0.1   12.6   3.4       0.22   11.5   3.4    1.6  1  DUF3430          Protein of unknown function (DUF3430)


Domain annotation for each model (and alignments):
>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   0.0   1.3e-22   4.7e-19      15     169 ..     105     257 ..      95     260 .. 0.92

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 1.3e-22
                   Glyco_transf_21  15 vnpKvnnllqalea.akydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagv 90 
                                       ++ Kv ++++a++  ++y++ +++Dsd+ vk++ + +++ +l ++++gl t +p+ ++++g++a+++      ++g+
  gi|518652985|ref|YP_008142505.1| 105 CSGKVRAISTAIQLyNNYEVYLLADSDIEVKKNWILNMVMPLNQEDAGLSTTFPYFYPKNGFWAQIKEIWGFVGMGL 181
                                       6779999999998889**************************************************99999999*** PP

                   Glyco_transf_21  91 lqaklsglgfavGksmalrreaLeaiGGfealadeLAeDyalgkllraaGlkvvlspapiaqtsvpr.rsslralla 166
                                       + +  + ++f++G s+a++ e + +   +e +++++ +D+al+k+ +++G+k++ ++ +  + + p+  + ++++++
  gi|518652985|ref|YP_008142505.1| 182 MES--KLTRFGWGGSLAFKHELISDS--LEFFSEHVSDDTALTKICKQKGKKIYYVDSAQPDINSPDtFKVFAEWAN 254
                                       ***..7889***************99..88888************************98777777778778899999 PP

                   Glyco_transf_21 167 Rql 169
                                       Rq+
  gi|518652985|ref|YP_008142505.1| 255 RQT 257
                                       986 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 !   33.9   0.0   6.9e-12   2.5e-08      12     139 ..      55     175 ..      45     205 .. 0.74
   2 ?   -1.5   0.0      0.52   1.9e+03      30      40 ..     229     239 ..     217     295 .. 0.60

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 6.9e-12
                                       THHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH--SS.EEEEEE CS
                   Glycos_transf_2  12 tlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglraatgd.yilflD 87 
                                        l++ l s+++q +y++f+ ++v D++++e+ +++++l   d     ++ ++  Gk +a+ ++++  +   + l+ D
  gi|518652985|ref|YP_008142505.1|  55 SLEKNLISVKNQ-EYENFKFLCVVDSEEEEALKVIKKLD-IDYITSSYKCDKCSGKVRAISTAIQLYNNYeVYLLAD 129
                                       57788889****.*************************4.46677777777888***********998888****** PP

                                       SSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SSEEEECCH CS
                   Glycos_transf_2  88 aDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrvgenerly 139
                                       +D e++++w+  +v +l++++a +   ++p++  +++++ + k++       
  gi|518652985|ref|YP_008142505.1| 130 SDIEVKKNWILNMVMPLNQEDA-GLSTTFPYFYPKNGFWAQIKEI-----WG 175
                                       *******************666.5555555555555555555432.....22 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.52
                                       EEEEEEES-SS CS
                   Glycos_transf_2  30 eiivvDDgStD 40 
                                       +i++vD + +D
  gi|518652985|ref|YP_008142505.1| 229 KIYYVDSAQPD 239
                                       55555554433 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 !   25.9   0.0   2.2e-09     8e-06       2     207 ..      42     236 ..      41     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.2e-09
                   Glyco_tranf_2_3   2 rdlavlVptfneedvlgevlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrvrvvvna..rnlgstgks 76 
                                         ++v+ p+ +++  l++ l s+ +qey ++++  vvd +++e+l+v++ l       ++++++ +  ++ +s gk+
  gi|518652985|ref|YP_008142505.1|  42 E-TLVIMPVRGIDYSLEKNLISVKNQEYENFKFLCVVDSEEEEALKVIKKL-------DIDYITSSykCDKCS-GKV 109
                                       4.78999*****************************************985.......667777743377786.*** PP

                   Glyco_tranf_2_3  77 ralnealravk.sdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfllnrstlvsalgalefaerhlrflaar 152
                                       ra++ a++ ++ +++ ll D+D  v ++ +  ++  ++++++g  +t  +++  + ++++       ++ +    + 
  gi|518652985|ref|YP_008142505.1| 110 RAISTAIQLYNnYEVYLLADSDIEVKKNWILNMVMPLNQEDAGLSTTFPYFYPKNGFWAQIKE----IWGF--VGMG 180
                                       **********999***************98888888899*************99999998776....6666..4444 PP

                   Glyco_tranf_2_3 153 ralgvltlnGsg..slirrevlkelegldp.lflltdDyelglrlrragfrtayvpga 207
                                       ++ + lt  G+g  +++  e+  +   l + + ++ dD  l+  +++ g +++yv  a
  gi|518652985|ref|YP_008142505.1| 181 LMESKLTRFGWGgsLAFKHELISDS--LEFfSEHVSDDTALTKICKQKGKKIYYVDSA 236
                                       4444444445555577777777777..3334578888888888888888888877655 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 !   20.3   0.7   1.2e-07   0.00043      65     193 ..     183     306 ..     152     311 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.2e-07
                   Glyco_trans_2_3  65 algrvvpsvGsgaflrrsalq.evggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRw 140
                                        ++ + + +G   ++  ++++ ++ +++   ++vs+D+ +   + +kG ++++v++++    sp+t++ +   + R 
  gi|518652985|ref|YP_008142505.1| 183 ESKLTRFGWGGSLAFKHELISdSLEFFS---EHVSDDTALTKICKQKGKKIYYVDSAQPDINSPDTFKVFAEWANRQ 256
                                       4555667888888888888873566888...9*************************99*********999999998 PP

                   Glyco_trans_2_3 141 ayGceleklillvrllgylgsllwsalplhlallllfslla..lalvllllllla 193
                                       +        i +   + y+g+l+  a++++++ ++l+++++  l++++l++++++
  gi|518652985|ref|YP_008142505.1| 257 TALS-----ISASPKVYYYGLLFYGAYLFLFFSAILMGVFYnpLYFLFLIPAVMY 306
                                       8883.....7677777888888888899999999999988886555556665544 PP

>> DUF3430  Protein of unknown function (DUF3430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   3.4   6.2e-05      0.22       4     141 ..       3     146 ..       1     172 [. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.2e-05
                           DUF3430   4 lfslilllllllnflinsqyinfipyq.sekCs...........gegsssgigysieide.Citndnqnnyvfsvft 67 
                                       ++ ++l++ ++l++li+s++i ++ ++  ++              ++   gi ys e +   + n+ ++n  f+  +
  gi|518652985|ref|YP_008142505.1|   3 ILLILLIFYTVLLLLISSGFIYIESHKyHSEHIvnnyrpetlviMPV--RGIDYSLEKNLiSVKNQEYENFKFLCVV 77 
                                       333444444444444*****999988763333356777777744444..4777***999999999999999999999 PP

                           DUF3430  68 dssdgeiiktnyyedqnCegkpistftfeigsCvstpefvnnasnsssyysykvsttdepeiptnsvvtsfyng 141
                                       ds+++e +k+ ++      +  + t +++ ++C      ++ a +  ++y + ++  +++e+ +n +++ +++ 
  gi|518652985|ref|YP_008142505.1|  78 DSEEEEALKVIKKL-----DIDYITSSYKCDKCSGKVRAISTAIQLYNNYEVYLLADSDIEVKKNWILNMVMPL 146
                                       99999999999999.....677999**********888888777777777888888888********9999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (360 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      519  (0.0289475); 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: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2719.96
//
Query:       gi|518652986|ref|YP_008142506.1|  [L=84]
Description: elongation factor 1-beta [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-17   63.0   1.5    2.4e-17   62.9   1.5    1.0  1  EF1_GNE   EF-1 guanine nucleotide exchange domain
  ------ inclusion threshold ------
      0.049   12.9   0.1       0.15   11.3   0.0    1.6  2  HemX      HemX, putative uroporphyrinogen-III C-methyltransfe
        0.1   13.1   1.3        1.9    9.0   0.1    2.1  2  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> EF1_GNE  EF-1 guanine nucleotide exchange domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.9   1.5     4e-21   2.4e-17       1      88 [.       1      82 [.       1      84 [] 0.94

  Alignments for each domain:
  == domain 1  score: 62.9 bits;  conditional E-value: 4e-21
                                      .EEEEEEESSS---HHHHHHHHHH.HS-T.SEE--.--EEE-SSS-EEEEEEEEESSS-GGGGHHHHHHTTS-S..... CS
                           EF1_GNE  1 svvlevkPeddetdleelekkvksikleg.lvwgeasklepiafGlkkLqiscvieddkvstdeleekieeiegeledl 78
                                      +v l++ Pe+++++l++l  ++ + ++e+ ++++ ++k+e+i+fGl +L +s++++d+++++d +e++i+++++     
  gi|518652986|ref|YP_008142506.1|  1 MVQLRILPESVDVNLKDLRVAITA-SIEKlCTIN-EVKEEEIGFGLSALLFSVIVPDEEGKIDSVENAISSVKN----- 72
                                      5889********************.****88888.5**************************************..... PP

                                      SEEEEEEEEE CS
                           EF1_GNE 79 Vqsveivsfn 88
                                      V++v++ +++
  gi|518652986|ref|YP_008142506.1| 73 VSQVDTRDVT 82
                                      9999998776 PP

>> HemX  HemX, putative uroporphyrinogen-III C-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.5e-05      0.15     142     184 ..       6      48 ..       5      53 .. 0.89
   2 ?   -0.7   0.0      0.12   6.9e+02     159     175 ..      64      80 ..      56      83 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                              HemX 142 vLaevndpsllavRralaedlkaLravnqvDrdgiilrLeqLa 184
                                       +L e  d +l ++R a+++++++L ++n+v  + i   L++L 
  gi|518652986|ref|YP_008142506.1|   6 ILPESVDVNLKDLRVAITASIEKLCTINEVKEEEIGFGLSALL 48 
                                       67888999**********************9999999999886 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.12
                              HemX 159 aedlkaLravnqvDrdg 175
                                       ++ +++ ++v+qvD   
  gi|518652986|ref|YP_008142506.1|  64 ENAISSVKNVSQVDTRD 80 
                                       56788889999999765 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00032       1.9      27      54 ..       9      37 ..       6      42 .. 0.88
   2 ?    3.2   0.1     0.021   1.2e+02      15      30 ..      62      77 ..      58      81 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00032
                               HMA 27 esvkvdlatktvtVegdaes.tklrkiie 54
                                      esv+v+l+  +v ++ ++e+  ++++++e
  gi|518652986|ref|YP_008142506.1|  9 ESVDVNLKDLRVAITASIEKlCTINEVKE 37
                                      69******************888777776 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.021
                               HMA 15 kvekvLselpgVesvk 30
                                      +ve ++s+++ V++v+
  gi|518652986|ref|YP_008142506.1| 62 SVENAISSVKNVSQVD 77
                                      699*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 577.70
//
Query:       gi|518652987|ref|YP_008142507.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G1626 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       312  (0.017402); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); 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: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 636.13
//
Query:       gi|518652988|ref|YP_008142508.1|  [L=204]
Description: membrane metalloprotease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-05   24.7  15.2    2.4e-05   23.8   1.1    3.1  2  Peptidase_M50  Peptidase family M50
  ------ inclusion threshold ------
       0.54   10.3   0.2       0.54   10.3   0.2    2.5  3  Ac76           Orf76 (Ac76)


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   7.7     0.011        95      10     108 ..      55     133 ..      44     140 .. 0.64
   2 !   23.8   1.1   2.6e-09   2.4e-05     188     219 ..     143     174 ..     133     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.011
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX....XXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  10 vvvHElGHflvAklcgvkveefsigfGpkllsfkkgeteYaiallpLGGyVkmageepeeelseeeakaflkkspwq 86 
                                        ++HE++H  vA++ g     f +     +l     ++  +i + p  G V++ag  +                  +
  gi|518652988|ref|YP_008142508.1|  55 FLMHEMAHREVARRLGAVA-FFKLWP-VGILLALITSVFGFIFAAP--GAVQFAGLYDRD----------------S 111
                                       4578888888888888633.333322.2222222333333466666..448888877443................4 PP

                                       XXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50  87 rllivlAGplanfilailvfvv 108
                                       +  i+lAGp +n+i+++++f++
  gi|518652988|ref|YP_008142508.1| 112 EGKIALAGPGTNIIIGVIAFLA 133
                                       78999**********9999975 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 2.6e-09
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M50 188 lssflqllalisvnLgilNLlPipvLDGghll 219
                                       +s++l ++a++++ ++++NL+P+p+LDG +++
  gi|518652988|ref|YP_008142508.1| 143 ASTILIWVAWLNLWFALFNLIPFPPLDGSKVF 174
                                       56899***********************9986 PP

>> Ac76  Orf76 (Ac76)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.2     6e-05      0.54      16      42 ..       2      28 ..       1      31 [. 0.93
   2 ?   -2.2   1.4      0.49   4.4e+03       6      32 ..     127     152 ..     122     163 .. 0.42
   3 ?   -3.1   0.2      0.91   8.2e+03      10      18 ..     184     192 ..     178     197 .. 0.50

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6e-05
                              Ac76 16 ildkneklsellltllllfvlFiilln 42
                                      ++++n++ +++++ +++l + F +++n
  gi|518652988|ref|YP_008142508.1|  2 MYNRNNEGNDIIIAVIVLTIAFTLMIN 28
                                      79********************99986 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.49
                              Ac76   6 llialivlafildknek.lsellltlll 32 
                                        +ia+  la+ +   ++ +s++l+++  
  gi|518652988|ref|YP_008142508.1| 127 GVIAF--LAVTFSGITGvASTILIWVAW 152
                                       33333..333333333303444444444 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 0.91
                              Ac76  10 livlafild 18 
                                       + +la+il+
  gi|518652988|ref|YP_008142508.1| 184 VFLLAIILN 192
                                       333444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       923  (0.0514808); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.29s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1435.82
//
Query:       gi|518652989|ref|YP_008142509.1|  [L=1168]
Description: hypothetical protein FACI_IFERC00001G1628 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-07   31.4   0.2        1.1    9.8   0.0    5.9  7  TPR_19    Tetratricopeptide repeat
     0.0018   17.5   2.6       0.48    9.6   0.1    4.1  4  TPR_15    Tetratricopeptide repeat
      0.009   16.1  18.4       0.49   10.6   0.1    6.6  7  TPR_2     Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   16.0  16.1      0.054   13.7   0.1    5.3  5  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
      0.011   16.5   0.1         12    7.0   0.0    4.6  4  TPR_14    Tetratricopeptide repeat
      0.014   15.8   0.0       0.82   10.1   0.0    2.4  2  BTAD      Bacterial transcriptional activator domain
      0.015   15.5   0.0         20    5.7   0.0    4.3  3  PPR       PPR repeat
      0.016   15.8   0.0        2.1    9.1   0.0    3.3  3  TPR_16    Tetratricopeptide repeat
      0.028   14.7   0.5         23    5.4   0.2    4.4  4  TPR_12    Tetratricopeptide repeat
      0.097   12.7   7.3        2.7    8.2   1.6    5.0  4  TPR_7     Tetratricopeptide repeat
        5.8    6.8  10.8         11    5.8   0.1    4.0  3  CLTH      CTLH/CRA C-terminal to LisH motif domain


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       1.6   2.7e+03      31      51 ..     192     212 ..     185     215 .. 0.84
   2 ?    5.3   0.0     0.017        28      29      49 ..     249     269 ..     235     278 .. 0.87
   3 ?   -2.0   0.0       3.2   5.2e+03      32      67 ..     318     353 ..     308     354 .. 0.75
   4 ?   -3.1   0.0       7.2   1.2e+04      36      48 ..     420     432 ..     416     434 .. 0.81
   5 !    9.8   0.0    0.0007       1.1      32      61 ..     562     591 ..     546     597 .. 0.79
   6 ?   -0.0   0.0      0.81   1.3e+03       3      23 ..     600     620 ..     598     635 .. 0.67
   7 !    6.5   0.0    0.0073        12      12      47 ..     884     919 ..     880     920 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 1.6
                            TPR_19  31 LAeallalgqldeAealLdal 51 
                                       LA+++++ +q d+ ++lL ++
  gi|518652989|ref|YP_008142509.1| 192 LADIYVEFNQKDKLKELLHDI 212
                                       9***********988888766 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.017
                            TPR_19  29 llLAeallalgqldeAealLd 49 
                                       +lLA+a++ lg ++ A ++ +
  gi|518652989|ref|YP_008142509.1| 249 ALLADAYYHLGYYENALKIYK 269
                                       469*************99876 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.2
                            TPR_19  32 AeallalgqldeAealLdalpeedpddaryasLlAk 67 
                                       +e  + l  + eAe  L+++   + dd ++  L Ak
  gi|518652989|ref|YP_008142509.1| 318 IESEIVLDLYSEAELDLNRYRSNFGDDTEVLELFAK 353
                                       555566777889999999999999999998888776 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 7.2
                            TPR_19  36 lalgqldeAealL 48 
                                       + l+++++A++++
  gi|518652989|ref|YP_008142509.1| 420 IYLNRIEDAIEII 432
                                       55899****9986 PP

  == domain 5  score: 9.8 bits;  conditional E-value: 0.0007
                            TPR_19  32 AeallalgqldeAealLdalpeedpddary 61 
                                        +al++++++ eA  +Ld l  +dpd  +y
  gi|518652989|ref|YP_008142509.1| 562 TKALIKTKRYHEASTILDSLYSKDPDAFYY 591
                                       5899********************995333 PP

  == domain 6  score: -0.0 bits;  conditional E-value: 0.81
                            TPR_19   3 aegdyaeAlalleqalqedpk 23 
                                       ++ ++ +A+++ e+a++   +
  gi|518652989|ref|YP_008142509.1| 600 QDSNFGDAIKHVEEAISVLDN 620
                                       6678999*******9877443 PP

  == domain 7  score: 6.5 bits;  conditional E-value: 0.0073
                            TPR_19  12 alleqalqedpknaearllLAeallalgqldeAeal 47 
                                       ++l+ +++++p+   +  +L++ l+++g+l+eA ++
  gi|518652989|ref|YP_008142509.1| 884 DILKTLISYYPDENILFERLINSLIQNGNLNEALET 919
                                       6899999999987777779**************986 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0      0.37     6e+02     254     274 ..     251     271 ..     197     289 .. 0.69
   2 ?    1.5   0.0     0.089   1.4e+02      42      93 ..     343     395 ..     332     421 .. 0.86
   3 ?    2.6   0.0     0.039        64      90     163 ..     568     638 ..     552     652 .. 0.73
   4 !    9.6   0.1   0.00029      0.48      58     145 ..     877     963 ..     867    1000 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.37
                            TPR_15 254 YADaleqagradeAwrlRrqv 274
                                        ADa +  g+ ++A ++ +++
  gi|518652989|ref|YP_008142509.1| 251 LADAYYHLGYYENALKIYKYI 271
                                       344444444444444444433 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.089
                            TPR_15  42 kdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.lydaep 93 
                                       +dte+++++a+  +a+ +++   k++ qL++ g+ + e+y  ++++ ++++e+
  gi|518652989|ref|YP_008142509.1| 343 DDTEVLELFAKYFRAVDNQEMLYKIAIQLIEKGNTDHENYRIIVNYlYENQEY 395
                                       6889999***************************************4555554 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.039
                            TPR_15  90 daepkeaarlaekgwrrfrsprlLssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtd 163
                                       ++++ ea  +  + +  +++p+ +++++ ++ + +d+ + ++ +k +ee   + ++  fl++r++++++++ ++
  gi|518652989|ref|YP_008142509.1| 568 TKRYHEASTILDSLY--SKDPDAFYYYFRAYIEFQDS-NFGDAIKHVEEAISVLDNVDFLALRINIALAKNTNA 638
                                       555556665555555..46788888888888888886.578888998988888899999999988888777654 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00029
                            TPR_15  58 qqedearkAyrqLlasgkaraedyerliel.lydaepkeaarlaekgwrrfrsprlLssalellerakdydriaell 133
                                       + +++ +++++ L++    +    erli+   ++ + +ea++++++ +   ++   + +++++ ++++dy+ +a+++
  gi|518652989|ref|YP_008142509.1| 877 ELYEDEIDILKTLISYYPDENILFERLINSlIQNGNLNEALETTYDRFHEKKDISSFNRMVHIFYDLRDYSSLANIF 953
                                       55666666777777777777777899999967********************************************* PP

                            TPR_15 134 ksleeeeaaeqs 145
                                       ++    e ++ +
  gi|518652989|ref|YP_008142509.1| 954 NNNR--EFVNAE 963
                                       9944..333333 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       5.6   9.1e+03      10      19 ..     227     236 ..     226     239 .. 0.81
   2 !    8.4   2.7    0.0016       2.6       6      25 ..     250     269 ..     248     271 .. 0.91
   3 ?   -2.6   0.0       5.3   8.7e+03      10      22 ..     418     430 ..     417     431 .. 0.87
   4 ?   -1.2   0.0       1.9   3.1e+03      10      32 ..     564     586 ..     563     587 .. 0.76
   5 !   10.6   0.1    0.0003      0.49       1      29 [.     588     616 ..     588     620 .. 0.93
   6 ?    1.2   0.4      0.31     5e+02       3      27 ..     746     770 ..     744     774 .. 0.78
   7 ?    0.4   0.0      0.57   9.3e+02       9      22 ..     905     918 ..     905     919 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                             TPR_2  10 ayyklgdyee 19 
                                        y +lg+ye+
  gi|518652989|ref|YP_008142509.1| 227 YYSYLGEYEK 236
                                       5889999997 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
                             TPR_2   6 nlGlayyklgdyeeAleafe 25 
                                        l++ayy+lg ye Al+ ++
  gi|518652989|ref|YP_008142509.1| 250 LLADAYYHLGYYENALKIYK 269
                                       69**************9886 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 5.3
                             TPR_2  10 ayyklgdyeeAle 22 
                                       ++++l++ e+A+e
  gi|518652989|ref|YP_008142509.1| 418 SLIYLNRIEDAIE 430
                                       57899******97 PP

  == domain 4  score: -1.2 bits;  conditional E-value: 1.9
                             TPR_2  10 ayyklgdyeeAleafekAleldP 32 
                                       a++k ++y eA   ++   + dP
  gi|518652989|ref|YP_008142509.1| 564 ALIKTKRYHEASTILDSLYSKDP 586
                                       7899*******877666666666 PP

  == domain 5  score: 10.6 bits;  conditional E-value: 0.0003
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAle 29 
                                       a ++y ++++ ++  ++ +A+++ e+A++
  gi|518652989|ref|YP_008142509.1| 588 AFYYYFRAYIEFQDSNFGDAIKHVEEAIS 616
                                       679************************97 PP

  == domain 6  score: 1.2 bits;  conditional E-value: 0.31
                             TPR_2   3 alynlGlayyklgdyeeAleafekA 27 
                                       ++  l   yy +  +++ le+f+ A
  gi|518652989|ref|YP_008142509.1| 746 GYIILSSYYYSKRILKKSLEYFNLA 770
                                       566677778888888*******987 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 0.57
                             TPR_2   9 layyklgdyeeAle 22 
                                       ++++++g+++eAle
  gi|518652989|ref|YP_008142509.1| 905 NSLIQNGNLNEALE 918
                                       5789********97 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.6   2.6e+03       4      48 ..      55     102 ..      53     108 .. 0.67
   2 ?    9.2   0.9   0.00088       1.4      12      49 ..     234     271 ..     226     284 .. 0.77
   3 ?   -0.8   0.2       1.1   1.8e+03      23      77 ..     379     430 ..     357     433 .. 0.50
   4 ?   13.7   0.1   3.3e-05     0.054      29      81 ..     558     613 ..     542     641 .. 0.68
   5 ?   -3.8   0.2       9.5   1.6e+04      24      44 ..     682     702 ..     677     705 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.6
                                       -HHHHHHHHHHHH.HHH--HHH....HHHHHHHHHHTT-HHHHHHHHHC CS
                            ANAPC3   4 nyknAiflaerllaaetesped....ayllAlclylngqykrAyellrk 48 
                                       ++++A++ a+++  a t+ ++     + ++Al ly++g+ +  ++++ +
  gi|518652989|ref|YP_008142509.1|  55 ALRDAEISADLYS-ALTYIDDKspliLEYKALKLYSDGKIDDFIHFVTS 102
                                       5678888888888.4444444433325667******9999877777665 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00088
                                       HHHHH..HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3  12 aerlla.aetespedayllAlclylngqykrAyellrka 49 
                                       +e++++ ++ + p++a+ lA ++y++g y+ A+++++  
  gi|518652989|ref|YP_008142509.1| 234 YEKVVEfSDVNEPDNAL-LADAYYHLGYYENALKIYKYI 271
                                       57777744455555555.5****************9976 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  23 pedayllAlclylngqykrAyellrkaklnskslgcrylfAqcllkLkkyeeAia 77 
                                       +e+       ly+n++y + + ++ +++l ++       +  +l+ L+++e+Ai 
  gi|518652989|ref|YP_008142509.1| 379 HENYRIIVNYLYENQEYSKILSYVTEKNLINE---FKPEYCSSLIYLNRIEDAIE 430
                                       44444445556666666665555555522111...11122345666666666665 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 3.3e-05
                                       H...HHHHHHTT-HHHHHHHHHCTSHHHC-HHHHHHHHHHHHHT..T-HHHHHHHH-S CS
                            ANAPC3  29 l...AlclylngqykrAyellrkaklnskslgcrylfAqcllkL..kkyeeAiaaLek 81 
                                       l    ++l ++++y++A ++l+++  +sk++ + y + +++++   +++ +Ai++ e+
  gi|518652989|ref|YP_008142509.1| 558 LypiTKALIKTKRYHEASTILDSL--YSKDPDAFYYYFRAYIEFqdSNFGDAIKHVEE 613
                                       335567777777777777777777..66666666666666654335677777776665 PP

  == domain 5  score: -3.8 bits;  conditional E-value: 9.5
                                       HHHHHHHHHHHHTT-HHHHHH CS
                            ANAPC3  24 edayllAlclylngqykrAye 44 
                                       +++yl+ l  y + +yk+ ++
  gi|518652989|ref|YP_008142509.1| 682 KNVYLYRLKSYCLRDYKSVLK 702
                                       688999777888888887766 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.2      0.12     2e+02       5      25 ..     249     269 ..     247     269 .. 0.91
   2 ?    0.1   0.0       1.3   2.1e+03      10      37 ..     564     591 ..     563     595 .. 0.81
   3 ?    7.0   0.0    0.0074        12       2      38 ..     587     627 ..     586     634 .. 0.69
   4 ?   -2.7   0.0        10   1.6e+04       7      22 ..     903     918 ..     900     924 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.12
                            TPR_14   5 lalaeallalGdpdeAiallr 25 
                                       ++la+a+++lG ++ A+++++
  gi|518652989|ref|YP_008142509.1| 249 ALLADAYYHLGYYENALKIYK 269
                                       579**************9985 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 1.3
                            TPR_14  10 allalGdpdeAiallrralalaPddaea 37 
                                       al    ++ eA ++l+ + +++Pd   +
  gi|518652989|ref|YP_008142509.1| 564 ALIKTKRYHEASTILDSLYSKDPDAFYY 591
                                       66778899***************97555 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0074
                            TPR_14   2 eallalaeal..lalGdpdeAiallrrala..laPddaeaw 38 
                                       +a + + +a+  ++  ++ +Ai++ ++a++  ++ d+++++
  gi|518652989|ref|YP_008142509.1| 587 DAFYYYFRAYieFQDSNFGDAIKHVEEAISvlDNVDFLALR 627
                                       67777777772255668************954566766655 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 10
                            TPR_14   7 laeallalGdpdeAia 22 
                                       l   l ++G++ eA++
  gi|518652989|ref|YP_008142509.1| 903 LINSLIQNGNLNEALE 918
                                       67789999**999987 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00051      0.82      63     120 ..     211     269 ..     200     274 .. 0.81
   2 ?    2.9   0.0     0.082   1.3e+02      75     121 ..     876     923 ..     865     927 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00051
                                       HHHHHHHH.HHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHH CS
                              BTAD  63 ealealae.aelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYe 120
                                       ++++ ++   ++ + ++   l+e+e+ v+  +++E   ++l  A++++G  + AL+ Y+
  gi|518652989|ref|YP_008142509.1| 211 DIHKNRIHyNNIDIRKYYSYLGEYEKVVEFSDVNEPDNALLADAYYHLGYYENALKIYK 269
                                       5555555534556667788999************************************8 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.082
                                       TT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHH.HHHH CS
                              BTAD  75 lGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALe.vYer 121
                                       l+ +e+ ++ l+ l++ +P    l + l+  l + G+ +eALe +Y+r
  gi|518652989|ref|YP_008142509.1| 876 LELYEDEIDILKTLISYYPDENILFERLINSLIQNGNLNEALEtTYDR 923
                                       556677788999******************************724666 PP

>> PPR  PPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.1     0.041        67       6      24 ..     251     269 ..     250     271 .. 0.90
   2 ?   -3.1   0.0       7.9   1.3e+04       9      24 ..     564     579 ..     563     583 .. 0.83
   3 ?    5.7   0.0     0.012        20       6      21 ..     903     918 ..     900     919 .. 0.94

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.041
                               PPR   6 lIsgycknGkleeAlelfk 24 
                                       l ++y + G++e Al+++k
  gi|518652989|ref|YP_008142509.1| 251 LADAYYHLGYYENALKIYK 269
                                       669**************97 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 7.9
                               PPR   9 gycknGkleeAlelfk 24 
                                       ++ k  +++eA  +++
  gi|518652989|ref|YP_008142509.1| 564 ALIKTKRYHEASTILD 579
                                       7889999***998887 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.012
                               PPR   6 lIsgycknGkleeAle 21 
                                       lI+++ +nG+l eAle
  gi|518652989|ref|YP_008142509.1| 903 LINSLIQNGNLNEALE 918
                                       8*************97 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1      0.21   3.5e+02      39      57 ..     250     268 ..     245     275 .. 0.76
   2 ?    9.1   0.0    0.0013       2.1       6      61 ..     564     615 ..     563     621 .. 0.91
   3 ?   -1.2   0.0       2.1   3.4e+03       3      18 ..     903     918 ..     886     924 .. 0.57

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.21
                            TPR_16  39 llgdaalrqgrlaeAaaly 57 
                                       ll+da++++g ++ A+  y
  gi|518652989|ref|YP_008142509.1| 250 LLADAYYHLGYYENALKIY 268
                                       5788888888888887666 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0013
                            TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                                       a+++ ++y +A   l+ +  +d   P +a  +++++ + ++ +++ +A+  +++a+
  gi|518652989|ref|YP_008142509.1| 564 ALIKTKRYHEASTILDSLYSKD---P-DAFYYYFRAYIEFQDSNFGDAIKHVEEAI 615
                                       6788999***************...9.6999*******************999986 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 2.1
                            TPR_16   3 laraalragdyddAaa 18 
                                       l ++++++g+  +A++
  gi|518652989|ref|YP_008142509.1| 903 LINSLIQNGNLNEALE 918
                                       3445555555555553 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.28   4.6e+02      21      62 ..     167     203 ..     159     204 .. 0.74
   2 ?    5.4   0.2     0.014        23       8      26 ..     250     268 ..     242     270 .. 0.84
   3 ?    2.1   0.0      0.15   2.4e+02      45      73 ..     588     616 ..     565     630 .. 0.62
   4 ?   -2.5   0.0         4   6.5e+03       8      24 ..     902     918 ..     897     919 .. 0.78

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.28
                            TPR_12  21 eAlellekaleia.rrllGpdhpltattlrnLgrlyralgrye 62 
                                        ++  lek l i+ +++  p    ++t+++ L+++y ++++ +
  gi|518652989|ref|YP_008142509.1| 167 GSINDLEKILSICiSKI--P----YSTCYFSLADIYVEFNQKD 203
                                       56777888888883333..4....579*********9998876 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.014
                            TPR_12   8 nlaavlrrlgrydeAlell 26 
                                        la+++++lg y+ Al+++
  gi|518652989|ref|YP_008142509.1| 250 LLADAYYHLGYYENALKIY 268
                                       3999999999999999998 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.15
                            TPR_12  45 attlrnLgrlyralgryeeAlelleeala 73 
                                       a +++  + + ++  ++ +A+++ eea+ 
  gi|518652989|ref|YP_008142509.1| 588 AFYYYFRAYIEFQDSNFGDAIKHVEEAIS 616
                                       55555555555555555555555555554 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 4
                            TPR_12   8 nlaavlrrlgrydeAle 24 
                                       +l + l + g++ eAle
  gi|518652989|ref|YP_008142509.1| 902 RLINSLIQNGNLNEALE 918
                                       57788889999999987 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0       0.2   3.2e+02       1      21 [.     188     208 ..     188     210 .. 0.86
   2 ?    0.7   0.0      0.42   6.8e+02       9      21 ..     228     240 ..     224     240 .. 0.88
   3 ?    8.2   1.6    0.0016       2.7       4      23 ..     250     269 ..     249     272 .. 0.94
   4 ?   -2.0   0.0       3.1     5e+03       3      21 ..     934     952 ..     932     963 .. 0.67

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.2
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       +++ La++y++ ++ +++ el
  gi|518652989|ref|YP_008142509.1| 188 CYFSLADIYVEFNQKDKLKEL 208
                                       799********9999988666 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.42
                             TPR_7   9 ysrlGdyeeAiel 21 
                                       ys lG+ye+ +e+
  gi|518652989|ref|YP_008142509.1| 228 YSYLGEYEKVVEF 240
                                       899******9986 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0016
                             TPR_7   4 nLarlysrlGdyeeAielye 23 
                                        La++y  lG+ye+A+++y+
  gi|518652989|ref|YP_008142509.1| 250 LLADAYYHLGYYENALKIYK 269
                                       69*****************8 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 3.1
                             TPR_7   3 lnLarlysrlGdyeeAiel 21 
                                       +++ +++ +l+dy+ ++ +
  gi|518652989|ref|YP_008142509.1| 934 NRMVHIFYDLRDYSSLANI 952
                                       5666777777777766654 PP

>> CLTH  CTLH/CRA C-terminal to LisH motif domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.3   2.2e+03      47      65 ..     116     132 ..      62     234 .. 0.65
   2 ?    1.8   4.3      0.12     2e+02      55     129 ..     321     423 ..     292     619 .. 0.81
   3 ?    5.8   0.1     0.007        11       8      35 ..     904     931 ..     900    1039 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                              CLTH  47 fielirgktkdieealeya 65 
                                       f eli+ k ++ e+a+ey 
  gi|518652989|ref|YP_008142509.1| 116 FDELIN-K-SQPEKAVEYL 132
                                       555555.5.5555555554 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.12
                              CLTH  55 t....................kdieealeyarenlefendehlkelekamsLLafsdpes...........kelssp 100
                                       +                    +d +e+le + +++++    ++++l k++  L+ + +++            e+ ++
  gi|518652989|ref|YP_008142509.1| 321 EivldlyseaeldlnryrsnfGDDTEVLELFAKYFRAVD--NQEMLYKIAIQLIEKGNTDhenyriivnylYEN-QE 394
                                       033333333344444444444555666666666665443..578998888888888877788888888885444.48 PP

                              CLTH 101 lknlldpsrrekvakefnsailkllglsk 129
                                       ++++l+    +++++ef  +++++l + +
  gi|518652989|ref|YP_008142509.1| 395 YSKILSYVTEKNLINEFKPEYCSSLIYLN 423
                                       99999999999999999999999996655 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.007
                              CLTH   8 Iiklilegdlseaiewinenkpellesn 35 
                                       I +li++g+l+ea+e++ + ++e ++++
  gi|518652989|ref|YP_008142509.1| 904 INSLIQNGNLNEALETTYDRFHEKKDIS 931
                                       77899**************999999984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1168 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       883  (0.0492498); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.81u 0.28s 00:00:01.09 Elapsed: 00:00:00.48
# Mc/sec: 7350.28
//
Query:       gi|518652990|ref|YP_008142510.1|  [L=232]
Description: hypothetical protein FACI_IFERC00001G1629 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.7e-25   89.1   3.2    4.8e-25   88.2   3.2    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    1.3e-13   51.4   0.0    2.7e-13   50.4   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
    7.2e-11   42.6   0.0    2.4e-10   41.0   0.0    1.9  1  Methyltransf_25  Methyltransferase domain
    2.8e-06   27.1   0.0    4.2e-06   26.5   0.0    1.3  1  MetW             Methionine biosynthesis protein MetW
    1.8e-05   24.6   0.0    8.7e-05   22.4   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
    2.9e-05   24.7   0.0    9.6e-05   23.1   0.1    1.8  2  Methyltransf_12  Methyltransferase domain
    8.6e-05   22.4   0.0    0.00011   22.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
     0.0073   15.4   0.0     0.0094   15.1   0.0    1.2  1  DREV             DREV methyltransferase
  ------ inclusion threshold ------
       0.06   13.3   0.0        0.2   11.6   0.0    1.7  1  Methyltransf_32  Methyltransferase domain
       0.12   11.9   0.0       0.26   10.8   0.0    1.7  1  MTS              Methyltransferase small domain


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.2   3.2   2.7e-28   4.8e-25       5     233 .]       9     225 ..       5     225 .. 0.92

  Alignments for each domain:
  == domain 1  score: 88.2 bits;  conditional E-value: 2.7e-28
                                       XXXXXXXXXX-HHHHHHHHHHHHHTTTHHHHHH.HHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES CS
                   Ubie_methyltran   5 keekvkevfesvaskyDlmndvlslgihrlWkk.fveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDi 80 
                                       +++  ++v++++ ++yD  n+++s+ +  +W++  v  +    +++k+lDva+G g+l++ + ++++e+  vv+ D+
  gi|518652990|ref|YP_008142510.1|   9 DDKDLRDVYNKIPKSYDRANALISFFQDVKWRTrLVDGIFHISQPEKILDVASGKGELTYII-KQIKET-YVVMTDY 83 
                                       566699**************************9788889999*****************866.566665.5899*** PP

                                       -HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE--- CS
                   Ubie_methyltran  81 nenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskv 157
                                       +enmL+++         ++   + a+ ++Lpf d+sfD+v  +f l    +++ +++e+ rv    G++ v+ + k 
  gi|518652990|ref|YP_008142510.1|  84 SENMLNMS--------IVDSTRVLASFNNLPFRDNSFDSVMSTFALHAADNIEDVIREMVRV--SNGTVGVIAMGKS 150
                                       *****986........44455688999***********************************..579********** PP

                                       -SHHHHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHHHHHHS--HHHHHHHHHHTTEEEEEEEEEGGGTEEEEEEEE CS
                   Ubie_methyltran 158 elpllsqayelyskevlPvlGkllakdldsyryLvesirafPdqetlkeliedaGfksveyesltgGvvaihigvk 233
                                        ++ +s+    y k++ P + kl  ++ ++yr++    ++   +  ++e+i++  ++ v++e+ ++G v i ig+k
  gi|518652990|ref|YP_008142510.1| 151 DNKFYSFITGFYLKYFQPYIAKLTGEKSKDYRFIYYIYKRLTPNSSIREIIKKY-MDVVTFEEKAFGSVYIFIGTK 225
                                       ****************************************99999******985.899************999987 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.0   1.5e-16   2.7e-13       1      87 [.      57     137 ..      57     141 .. 0.93

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 1.5e-16
                                       EEET-TTSHHHHHHHHTT.SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CC CS
                   Methyltransf_11   1 LdvGcGtGrlaealakrg.arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhved 76 
                                       Ldv++G+G l+  +++   + vv +D+s++ml   ++ ++++      v a++ +lpf+dnsfD v+s+++lh  ++
  gi|518652990|ref|YP_008142510.1|  57 LDVASGKGELTYIIKQIKeTYVVMTDYSENML---NMSIVDSTR----VLASFNNLPFRDNSFDSVMSTFALHAADN 126
                                       8**************777899***********...777888773....9**************************** PP

                                       HHHHHHHHHHH CS
                   Methyltransf_11  77 pekalkeiaRv 87 
                                        e++++e++Rv
  gi|518652990|ref|YP_008142510.1| 127 IEDVIREMVRV 137
                                       **********9 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   1.3e-13   2.4e-10       1      92 [.      56     137 ..      56     139 .. 0.90

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 1.3e-13
                                       EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGS CS
                   Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhl 77 
                                       +Ld++ G+G+lt  + +  ++  v+++D+se+ml+          ++ + v +++++lpf d+sfD v+s++alh  
  gi|518652990|ref|YP_008142510.1|  56 ILDVASGKGELTYIIKQI-KETYVVMTDYSENMLNMSI-------VDSTRVLASFNNLPFRDNSFDSVMSTFALHAA 124
                                       8***********999887.79*************9754.......3557899*******************999985 PP

                                       SHHHHHHHHHHHHHH CS
                   Methyltransf_25  78 sdedlekalkeiarv 92 
                                       +  ++e++++e+ rv
  gi|518652990|ref|YP_008142510.1| 125 D--NIEDVIREMVRV 137
                                       5..899*******98 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   2.4e-09   4.2e-06      11     105 ..      50     141 ..      38     160 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 2.4e-09
                              MetW  11 ikpgsrvldlGcGdGellellkeekqvdgrGleldeegvaecvakGlsviqgdldkdlenfedksfdyvvlsqtlqa 87 
                                       i +  ++ld+ +G+Gel +++k+ k+      + +e+ ++ ++     v+          f+d+sfd v+ + +l a
  gi|518652990|ref|YP_008142510.1|  50 ISQPEKILDVASGKGELTYIIKQIKETYVVMTDYSENMLNMSIVDSTRVLASFN---NLPFRDNSFDSVMSTFALHA 123
                                       566679*********************9999************99999997643...3479**************** PP

                              MetW  88 trnpkevldellrigrra 105
                                         n + v++e++r+++ +
  gi|518652990|ref|YP_008142510.1| 124 ADNIEDVIREMVRVSNGT 141
                                       **************9754 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.9e-08   8.7e-05       3     102 ..      52     139 ..      50     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.9e-08
                   Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlil 79 
                                       +  ++lD+++G+Gelt+ + +  +++  vv  D+se++++ +   +        +   +++++l+  + d++fD ++
  gi|518652990|ref|YP_008142510.1|  52 QPEKILDVASGKGELTYIIKQ--IKETYVVMTDYSENMLNMSIVDS--------TRVLASFNNLP--FRDNSFDSVM 116
                                       6679****************4..34566*************99953........334688999**..********** PP

                   Methyltransf_31  80 snevlnaladpdkileeiervlk 102
                                       s  +l+a  + +++++e+ rv +
  gi|518652990|ref|YP_008142510.1| 117 STFALHAADNIEDVIREMVRVSN 139
                                       *******************9976 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.1   5.4e-08   9.6e-05       1      92 [.      57     137 ..      57     139 .. 0.73
   2 ?   -3.3   0.0       8.9   1.6e+04      86      97 ..     184     195 ..     179     197 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 5.4e-08
                   Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlh 77 
                                       L++ +G G+l+  + ++++++ ++ +D+s++++      + +  +  +++++l       +d  +sfD v + ++lh
  gi|518652990|ref|YP_008142510.1|  57 LDVASGKGELTYII-KQIKETYVVMTDYSENML---NMSIVDSTRVLASFNNLP-----FRD--NSFDSVMSTFALH 122
                                       899*****988777.555888888*********...333333333233333333.....233..39*********** PP

                   Methyltransf_12  78 hlkdirevldnirkl 92 
                                       + ++i++v++++ ++
  gi|518652990|ref|YP_008142510.1| 123 AADNIEDVIREMVRV 137
                                       **********99876 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.9
                   Methyltransf_12  86 ldnirklLkpgG 97 
                                       +  i+k L+p+ 
  gi|518652990|ref|YP_008142510.1| 184 IYYIYKRLTPNS 195
                                       567999999985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0   6.3e-08   0.00011      20     108 ..      50     137 ..      11     154 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 6.3e-08
                   Methyltransf_23  20 lraggrvLdiGcGtGillevlrengf.svtgvDlspeaveiaekakkaqkdqfdeqeaaepqgkfdlIvlrevlehv 95 
                                         ++ ++Ld++ G+G+l+ ++++     v++ D s+++ ++   +++ +  +f  ++ ++ +++fd + +++ l+  
  gi|518652990|ref|YP_008142510.1|  50 ISQPEKILDVASGKGELTYIIKQIKEtYVVMTDYSENMLNMSIVDSTRVLASF--NNLPFRDNSFDSVMSTFALHAA 124
                                       456789***************888662677**********9766666666666..99999***************** PP

                   Methyltransf_23  96 pdppellrqiatl 108
                                       ++ + ++r + + 
  gi|518652990|ref|YP_008142510.1| 125 DNIEDVIREMVRV 137
                                       *******999775 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   5.2e-06    0.0094      94     172 ..      52     132 ..      30     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-06
                              DREV  94 edkklldlGaGdGeitkrvaptfee.vyatelsetmrdrlkkkkynvlsale.lqetdvkldlilclnlldrcfdpl 168
                                       +++k+ld+ +G+Ge+t ++++  e  v  t+ se+m +       +vl+  + l   d  +d +++   l   ++  
  gi|518652990|ref|YP_008142510.1|  52 QPEKILDVASGKGELTYIIKQIKETyVVMTDYSENMLNMSIVDSTRVLASFNnLPFRDNSFDSVMSTFALHAADNIE 128
                                       689****************9988767899*********999999999988766887888888877766666555544 PP

                              DREV 169 klle 172
                                        +++
  gi|518652990|ref|YP_008142510.1| 129 DVIR 132
                                       4444 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   0.00011       0.2      23      91 ..      50     114 ..      34     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00011
                   Methyltransf_32  23 esgaltvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrlsfaelsiee 91 
                                        s++++++Dv++Gkg L+ ++++    ++++vv  d +e++ + +     ++   f ++l f ++s ++
  gi|518652990|ref|YP_008142510.1|  50 ISQPEKILDVASGKGELTYIIKQ---IKETYVVMTDYSENMLNMSIVDSTRVLASF-NNLPFRDNSFDS 114
                                       37899****************99...568999999999998888777777777677.667776666555 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00015      0.26      32      71 ..      53      91 ..      41     141 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                                      CSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHH CS
                               MTS 32 sgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesa 71
                                       +k+lD+++G G l+  +++ +++  v+++d + + l+++
  gi|518652990|ref|YP_008142510.1| 53 PEKILDVASGKGELTYIIKQIKET-YVVMTDYSENMLNMS 91
                                      468************999886655.7*****998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       675  (0.0376485); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.53u 0.30s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 1446.15
//
Query:       gi|518652991|ref|YP_008142511.1|  [L=117]
Description: hypothetical protein FACI_IFERC00001G1630 [Ferroplasma acidarmanus fer1]
Scores for complete 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   31.8   0.1    3.7e-07   30.6   0.1    1.6  1  Trm112p         Trm112p-like protein
  ------ inclusion threshold ------
       0.12   12.3   1.1        2.2    8.3   0.1    2.4  2  PhnA_Zn_Ribbon  PhnA Zinc-Ribbon


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 !   30.6   0.1   4.1e-11   3.7e-07       2      67 ..       3      71 ..       2      72 .. 0.72

  Alignments for each domain:
  == domain 1  score: 30.6 bits;  conditional E-value: 4.1e-11
                                      TGGCCC-B-TTTHH.C--HHHHHHHHH.TT---.S-SS----S.........CHHTTEECCCCEEEETTTTEEEEEET CS
                           Trm112p  2 llllniLaCpackg.pLdwealvevaa.lglne.lpkekpedy.........ellleldieegeLvCpncgraYpIkd 67
                                      ++l++++aCp+c+g        ++ +  ++ +  + +   e+          +    +d+++g L C+ cgr+YpI +
  gi|518652991|ref|YP_008142511.1|  3 YDLIDLIACPMCRGnSF-----SKSVIrEEGDNvIIPGHGEHTytdsnndgaN----HDMKNGILLCNTCGRWYPIIN 71
                                      789***********622.....3333333334445555555556888977764....6******************98 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.1     0.016   1.4e+02      19      26 ..       8      15 ..       6      17 .. 0.74
   2 ?    8.3   0.1   0.00025       2.2      11      26 ..      38      64 ..      36      65 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.016
                    PhnA_Zn_Ribbon 19 llvCpeCa 26
                                      l  Cp+C 
  gi|518652991|ref|YP_008142511.1|  8 LIACPMCR 15
                                      56699995 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00025
                    PhnA_Zn_Ribbon 11 eytY...........edgallvCpeCa 26
                                      e+tY             + +l+C +C+
  gi|518652991|ref|YP_008142511.1| 38 EHTYtdsnndganhdMKNGILLCNTCG 64
                                      8999999999999777799*******7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       562  (0.0313459); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.48
# Mc/sec: 739.39
//
Query:       gi|518652992|ref|YP_008142512.1|  [L=187]
Description: hypothetical protein FACI_IFERC00001G1631 [Ferroplasma acidarmanus fer1]
Scores for complete 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  152.1  16.1    1.8e-44  152.0  16.1    1.0  1  DUF981    Protein of unknown function (DUF981)


Domain annotation for each model (and alignments):
>> DUF981  Protein of unknown function (DUF981)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  152.0  16.1   9.8e-49   1.8e-44       1     186 [.       1     184 [.       1     185 [. 0.98

  Alignments for each domain:
  == domain 1  score: 152.0 bits;  conditional E-value: 9.8e-49
                            DUF981   1 MaFidyltlmlitlgagllllayyvlkaleerekkeankalaapflivGllalitGlhmtltWPlpgsYnilfgdpa 77 
                                       M F+d+l++ml  lg++  l+ +++++++    k +  k+l++p++i G + +++G+ m+  WPlpgsYn+lfgdp+
  gi|518652992|ref|YP_008142512.1|   1 MGFVDPLAVMLLSLGVSAGLISAFFYQVA----KGRDVKELVVPAFIFGGFDFMSGFEMSEFWPLPGSYNMLFGDPI 73 
                                       89***************************....8889999************************************* PP

                            DUF981  78 llfGvllllaavalykkaklkalgilalflGlilivygvailklgLtaeP..laalllyilvGLagllsplvllkld 152
                                       +++G+ll++ ++++yk+++l++l+i+ ++lG++l +  +a+++++L++ +  +aa++lyi+ G++++ s++++ k++
  gi|518652992|ref|YP_008142512.1|  74 MILGMLLIAGSIMIYKGYNLRTLSIPGVMLGVYLFIESAAMVNFKLESGDnlFAAMGLYIMSGISAVYSVVLFAKPE 150
                                       ************************************************9998999********************** PP

                            DUF981 153 ksrsvllvlaavlliiagllalliGieavyeHla 186
                                       k r++l+++a +ll++ +l+al+iG+ea+y+Hl+
  gi|518652992|ref|YP_008142512.1| 151 KDRKYLYYVAFILLALTALIALFIGYEAIYGHLQ 184
                                       ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.50
# Mc/sec: 1134.66
//
Query:       gi|518652993|ref|YP_008142513.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G1632 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.41   11.1   5.4       0.47   10.9   0.2    2.3  2  Phage_holin_3_1  Phage holin family (Lysis protein S)


Domain annotation for each model (and alignments):
>> Phage_holin_3_1  Phage holin family (Lysis protein S)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   2.6e-05      0.47      63      83 ..       4      24 ..       1      39 [. 0.81
   2 ?    2.6   0.8      0.01   1.8e+02      67      94 ..      50      77 ..      28      82 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 2.6e-05
                   Phage_holin_3_1 63 lellglpaslavviggliGfl 83
                                       +++ l++++ +vig++iGf+
  gi|518652993|ref|YP_008142513.1|  4 KKYIRLKNDIETVIGIIIGFV 24
                                      57999***************7 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.01
                   Phage_holin_3_1 67 glpaslavviggliGflGvekirelakk 94
                                      ++ a ++ ++ g+i f+G+ ++  l+ +
  gi|518652993|ref|YP_008142513.1| 50 SVYAPIIALVTGIILFFGIRTLAYLISS 77
                                      4456677788889999999888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       814  (0.0454013); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 781.00
//
Query:       gi|518652994|ref|YP_008142514.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G1633 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.5  60.8    4.7e-25   88.1  60.8    1.1  1  AA_permease    Amino acid permease
    5.2e-19   68.4  67.9    6.7e-19   68.0  67.9    1.1  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1  60.8   5.2e-29   4.7e-25       1     436 [.      14     436 ..      14     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 5.2e-29
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       +++++ +g++ ++  f g+ +v++ a++ +  la+l++ + ++l++++l++++    ++ g+y y+  +lg ++Gf 
  gi|518652994|ref|YP_008142514.1|  14 GLIFQGMGQLSPLFTFDGIISVAAFAEG-ASPLAFLIGLIASLLTGNTLYQFSKRTASARGYYGYSGYSLGNHAGFI 89 
                                       5799***********************9.778********************************************* PP

                       AA_permease  78 iGlnylfswitvlaleltaasiliqfwelvtdlpkawvt......gavflvvlliinlvgvkvygeaefilalikii 148
                                       ++++yl++   +la+ ++++s +i +   +++++++ ++      g++++++++i +++++      +f   +i+ +
  gi|518652994|ref|YP_008142514.1|  90 TSYLYLIY---QLANLIFILSFFIMIF--NPAILYLTGVkvpyyyGIILVIAISIPSFYAIYKGIVPSFKSQIIINV 161
                                       ****7765...5566666777777777..777777777777777799999999999998877776667666666666 PP

                       AA_permease 149 aiiafiivg.iillaggkpnkgagfrflgdngsifknnlppgfakeeegafkn.fisvfvivvfaftGielvaiiag 223
                                         i+f++   ii+++  + n            s     ++p      +g  kn f++++  +++a+tG+++++ +++
  gi|518652994|ref|YP_008142514.1| 162 VEIIFVVSIsIIIIVTSRDNTL----------S----VFSPI-----SG-YKNlFLGFITGSFLAYTGYGSIVPLGE 218
                                       6666665555444444444444..........2....23333.....22.35505555556788************* PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaa 300
                                       E++ P+k+i +ai  ++++i+++ +l++++++++++ ++ ++++d++ +   f+++ ++ g+ + + ++ a+ +  +
  gi|518652994|ref|YP_008142514.1| 219 EAQAPRKNIGIAIVAMLLIIGVLDLLISYALVVGFGLSNMSSFSDTVIP--AFIVIKSHIGL-YTSMFFLAFNFFII 292
                                       ***********************************************88..77777666665.55666666666667 PP

                       AA_permease 301 lssansslysasRvlyslakdglaPkvlkkvskrgvPlraillsmiisllal......llaslnlaap.ivfnflla 370
                                       +   n + ++ +R +ys+a+dg++P  ++k++k++ P +a++l + i  ++       + +s+n++ + + f f+ +
  gi|518652994|ref|YP_008142514.1| 293 YTLFNTIGTAITRNIYSMARDGYLPPAFSKLNKHNAPQNALFLLLGIFIAVGgistyvFYSSFNVNGFlNQFIFYAT 369
                                       77789999*********************************999877666666688886677776632245779999 PP

                       AA_permease 371 isaliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliii.llilalyaylt 436
                                       is+l++li++++++  + ++ k +       + + +++  + + +i++la+  ++ l+i+aly+++ 
  gi|518652994|ref|YP_008142514.1| 370 ISTLATLIIHMIVNSGLSKVHKNFTFDILIPSVSTIIILIALYYAISTLAFPFTYaLIIMALYIIIV 436
                                       ***********************99999999999999999999999999998888345666666544 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0  67.9   7.4e-23   6.7e-19      18     423 ..      31     436 ..      10     439 .. 0.71

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 7.4e-23
                     AA_permease_2  18 gifvkn.laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpvla 93 
                                       gi+ +   a+ + p+++l+++ia+l++    + ++ ++s +  + +G y+y+ +  g+ ++f++++++++ +++ l 
  gi|518652994|ref|YP_008142514.1|  31 GIISVAaFAEGASPLAFLIGLIASLLT----GNTLYQFSKRTASARGYYGYSGYSLGNHAGFITSYLYLIYQLANLI 103
                                       333331134556666666666666665....456666888889*************************988888666 PP

                     AA_permease_2  94 silsvaasyl....lnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliiliilglit 166
                                       +ils ++  +    l+++g ++    +  ++++iai i  +  +++gi  s k q i+ ++ i ++++ + i+ ++t
  gi|518652994|ref|YP_008142514.1| 104 FILSFFIMIFnpaiLYLTGVKVP--YYYGIILVIAISIPSFYAIYKGIVPSFKSQIIINVVEI-IFVVSISIIIIVT 177
                                       65555555554444777777763..3567888899999999999*******************.5666666666666 PP

                     AA_permease_2 167 vdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvlyllvniaf 241
                                        + ++ s       +  ++  +++l+ +++++++++G+ s++   ee  +++k++ +ai+ +lli++vl ll++ a+
  gi|518652994|ref|YP_008142514.1| 178 SRDNTLSV----F-SPISGYKNLFLGFITGSFLAYTGYGSIVPLGEEaqAPRKNIGIAIVAMLLIIGVLDLLISYAL 249
                                       66666552....2.3444566678888899*****************666669************************ PP

                     AA_permease_2 242 lgvvpddeianlsnlgsvaalffeavggkvvaiivvilial...sllgaintavigssrvlealardgvlPrffakv 315
                                       + + + +++++ s++   + + f    + ++ +  ++++a+   ++    nt  ++++r ++++ardg+lP  f+k 
  gi|518652994|ref|YP_008142514.1| 250 VVGFGLSNMSSFSDT---VIPAFIVIKSHIGLYTSMFFLAFnffIIYTLFNTIGTAITRNIYSMARDGYLPPAFSKL 323
                                       *********988884...345555555556666666666663336666789999*********************** PP

                     AA_permease_2 316 nkfgspiraiiltaivslillllfllassaaynfllsvsslgliisylll...iigalilrkkrphlkr....pgk. 384
                                       nk+++p +a++l + + ++++ ++++     ++  ++v  +++ +++ ++   +++++i+ + +  l +    + + 
  gi|518652994|ref|YP_008142514.1| 324 NKHNAPQNALFLLLGIFIAVGGISTY----VFYSSFNVNGFLNQFIFYATistLATLIIHMIVNSGLSKvhknFTFd 396
                                       ****************8666555544....45555555555554444333122566778888888886655343336 PP

                     AA_permease_2 385 ilvaiigalfllfllvalffppkgpatqssliyt.iiltv 423
                                       il+  ++++++l++l+ ++  ++ p t+  +i + +i++v
  gi|518652994|ref|YP_008142514.1| 397 ILIPSVSTIIILIALYYAISTLAFPFTYALIIMAlYIIIV 436
                                       6666666666666666666666666777777777633333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); expected 358.6 (0.02)
Passed bias filter:                      245  (0.013665); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.40
# Mc/sec: 3453.73
//
Query:       gi|518652995|ref|YP_008142515.1|  [L=211]
Description: isochorismatase [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  147.8   0.0      4e-43  147.6   0.0    1.0  1  Isochorismatase  Isochorismatase family
  ------ inclusion threshold ------
      0.077   12.9   0.5       0.21   11.5   0.0    1.9  2  DUF3198          Protein of unknown function (DUF3198)


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 !  147.6   0.0   4.4e-47     4e-43       1     174 [.      22     202 ..      22     203 .. 0.99

  Alignments for each domain:
  == domain 1  score: 147.6 bits;  conditional E-value: 4.4e-47
                   Isochorismatase   1 talvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvhe............leevkgdlderka 65 
                                       t+lv +D+qn++v    k++ + +++v+n++kl +  r++g+ v++t+ ++             ++++ g +d+ k 
  gi|518652995|ref|YP_008142515.1|  22 TMLVNWDIQNGLV----KNIFNKDEFVSNVKKLTATSREHGVAVLYTKITPLpfkymapsniysYMKRFGVDDPSKL 94 
                                       789**********....************************************************************ PP

                   Isochorismatase  66 aphfkpgttgaelvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevv 142
                                       +  + pg+++ae++ elap ++d+v++K++ s f gt+++++Lk +gi+t+v++Giat+++Ve+++rda+++Gy +v
  gi|518652995|ref|YP_008142515.1|  95 PVFMAPGSEDAEIYRELAPEKDDYVLNKHTASVFTGTNVENMLKGAGITTLVFTGIATEIGVESSVRDAINHGYYTV 171
                                       ***************************************************************************** PP

                   Isochorismatase 143 vvsDAvaalspelhdaalkrlkqafatvitte 174
                                       v+sD +++ s+e h+ +lk+++ a++tv++te
  gi|518652995|ref|YP_008142515.1| 172 VASDSCSSHSKEMHEISLKSMS-AVTTVMDTE 202
                                       *********************9.9*****998 PP

>> DUF3198  Protein of unknown function (DUF3198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   2.4e-05      0.21      15      33 ..      40      58 ..      39      61 .. 0.95
   2 ?   -2.3   0.1      0.49   4.4e+03      11      17 ..     178     184 ..     171     191 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.4e-05
                                      HHHHHHHHHHHHHHHHHH- CS
                           DUF3198 15 KstFvknlkeLekiarklG 33
                                      K +Fv n+k+L + +r++G
  gi|518652995|ref|YP_008142515.1| 40 KDEFVSNVKKLTATSREHG 58
                                      89****************9 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.49
                                       HS--HHH CS
                           DUF3198  11 nSdSKst 17 
                                       +S SK++
  gi|518652995|ref|YP_008142515.1| 178 SSHSKEM 184
                                       5555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); 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 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1586.90
//
Query:       gi|518652996|ref|YP_008142516.1|  [L=164]
Description: hypothetical protein FACI_IFERC00001G1635 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-19   69.6   0.1    5.4e-19   68.6   0.0    1.5  2  NAD_binding_7   Putative NAD(P)-binding
    5.6e-07   28.9   0.5    1.4e-06   27.6   0.0    1.9  2  Sirohm_synth_M  Sirohaem biosynthesis protein central


Domain annotation for each model (and alignments):
>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0     6e-23   5.4e-19       3     102 ..       5     111 ..       3     113 .. 0.91
   2 ?   -2.0   0.0      0.57   5.1e+03      38      60 ..     135     157 ..     124     160 .. 0.63

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 6e-23
                     NAD_binding_7   3 ldlkgkkvlvvGgGevAarkvrklleagakvtvvapevkeele.....elvklaeeel..ekdlegadlviaatddr 72 
                                       ++++gkkvl +GgG++A+ k++kl++++ ++ v+apev+e +      ++++++e+e+  ++  e+++lvi+at+++
  gi|518652996|ref|YP_008142516.1|   5 IKITGKKVLFAGGGKIAEAKIKKLIKESPEISVIAPEVTEYIRtlgkgGKINIIEREIriDDITENYFLVICATSNQ 81 
                                       899**********************************97777788889889999***943455789*********** PP

                     NAD_binding_7  73 elneriaeaakarrilvnvadkpelcdfif 102
                                        ln++i  ++++ +il     ++ ++d+++
  gi|518652996|ref|YP_008142516.1|  82 GLNRKISIECRKLGILHDDLSNHRNSDIMM 111
                                       ******************999999999886 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.57
                     NAD_binding_7  38 pevkeeleelvklaeeelekdle 60 
                                        ++k elee + ++++++e+d++
  gi|518652996|ref|YP_008142516.1| 135 RRLKTELEEDLIHNSNNFEEDIK 157
                                       33345555556667777888776 PP

>> Sirohm_synth_M  Sirohaem biosynthesis protein central
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.2   1.8e+03      19      27 ..      23      31 ..      23      32 .. 0.82
   2 !   27.6   0.0   1.6e-10   1.4e-06       2      27 ..     118     143 ..     118     144 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.2
                    Sirohm_synth_M 19 aliRreier 27
                                      a+i++ i++
  gi|518652996|ref|YP_008142516.1| 23 AKIKKLIKE 31
                                      789999987 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 1.6e-10
                    Sirohm_synth_M   2 GpLQIaiSTnGksPrLAaliRreier 27 
                                       G+L + iST G++P+ A++++ e+e+
  gi|518652996|ref|YP_008142516.1| 118 GNLTLSISTDGMAPAIARRLKTELEE 143
                                       899*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1221.27
//
Query:       gi|518652997|ref|YP_008142517.1|  [L=377]
Description: hypothetical protein FACI_IFERC00001G1636 [Ferroplasma acidarmanus fer1]
Scores for complete 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  164.1   1.1    3.5e-48  163.6   1.1    1.2  1  Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
    1.8e-25   89.8   0.2    2.9e-25   89.1   0.2    1.4  1  Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
    9.9e-25   87.4   0.0    2.1e-24   86.4   0.0    1.6  1  Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
    8.8e-24   83.5   0.1    1.5e-23   82.8   0.1    1.4  1  Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
  ------ inclusion threshold ------
       0.16   12.3   0.1          3    8.1   0.0    2.5  2  PucR           Purine catabolism regulatory protein-like fami


Domain annotation for each model (and alignments):
>> Acyl-CoA_dh_1  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.6   1.1   9.8e-52   3.5e-48       1     149 [.     225     373 ..     225     374 .. 0.99

  Alignments for each domain:
  == domain 1  score: 163.6 bits;  conditional E-value: 9.8e-52
                                       TBHHHHHTTTT--S-----..-SHHHHHHHHHHHHHHHTSB-CC-BGGGSHHHHHHHHHHHHHHHHHHHHHHHHHH- CS
                     Acyl-CoA_dh_1   1 gkGfrvametlnheRlavaaaalglarraleealeyarrrkafgkplidhqlvreklaemaaeleaarllvyraaea 77 
                                       +kGf v+m tl+ +R+++aa+alg+ar+a+ ealey+++rk+f+k++id+q +++++aem+ ++ a+ ll+++aae+
  gi|518652997|ref|YP_008142517.1| 225 NKGFSVIMDTLDAGRIGIAAQALGIARSAFHEALEYINTRKQFNKKIIDFQGIQFMIAEMESRIKASDLLIREAAEK 301
                                       89*************************************************************************** PP

                                       -------HHHHHHHHHHHHHHHHHHHHHHHHHHGGGTTSGGGHHHHHHHHTHHHHHSSS-HHHHHHHHHHHH CS
                     Acyl-CoA_dh_1  78 ldagkpdraeasmaKlfaselaqevadlamqllGgaGyleeypverlyrdarvlrigeGtseiqrniiarrl 149
                                        ++++++   +s+aK++as++a++va++ +ql+Gg+Gy+++   er++rda++++i+eGt+eiq+ ii+r +
  gi|518652997|ref|YP_008142517.1| 302 WQNHEDTVELSSIAKMYASDTAVYVAERSLQLFGGYGYTTDFNAERHMRDAKITQIYEGTNEIQKIIISREI 373
                                       *********************************************************************987 PP

>> Acyl-CoA_dh_2  Acyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.2     8e-29   2.9e-25       1     133 [.     240     362 ..     240     363 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 8e-29
                                       .HHHHHHHHHHHHHHHHHHHHHHHHHCTTT-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----H CS
                     Acyl-CoA_dh_2   1 lgiaavalGaAraalaefvelarervrassgekladdpatqlalaeaaarldAAralleraaaraealaaagkevtv 77 
                                       +giaa+alG+Ar+a+ e++e++++r++  +++k+ d++ +q+ +ae+++r++A  +l+++aa++ +       ++ +
  gi|518652997|ref|YP_008142517.1| 240 IGIAAQALGIARSAFHEALEYINTRKQ--FNKKIIDFQGIQFMIAEMESRIKASDLLIREAAEK-W-------QNHE 306
                                       589************************..***************************99999999.4.......4455 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGGGBTT-HHHHHHHHHHHHCTSGGG- CS
                     Acyl-CoA_dh_2  78 edraearraaalavelaiaavdalfeaaGgsalrkesplqRlwRDahaaaaHaaln 133
                                       +++  +++a+++a+++a+ ++++  +++Gg++++++   +R++RDa+++++++++n
  gi|518652997|ref|YP_008142517.1| 307 DTVELSSIAKMYASDTAVYVAERSLQLFGGYGYTTDFNAERHMRDAKITQIYEGTN 362
                                       67899************************************************998 PP

>> Acyl-CoA_dh_N  Acyl-CoA dehydrogenase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.4   0.0   5.8e-28   2.1e-24       2     112 ..       4     114 ..       3     115 .. 0.97

  Alignments for each domain:
  == domain 1  score: 86.4 bits;  conditional E-value: 5.8e-28
                                       HHHHHHHHHHHHHHHHHTHHHHHHHHHHTSGHHHHHHHHHHTTCTSTTS-GGGTS--S-HHHHHHHHHHHHHH-HHH CS
                     Acyl-CoA_dh_N   2 eeqealrdtvrefaeeelaphaaewdeegefprelwkklaelGllgitvpeeygGagldyleaaivaeelaradagl 78 
                                       e +  + + vre+ae++++p+a+e+de+ e+p+++++++ ++Gl++ ++pe+ygG gl++   + v+e ++ a+ ++
  gi|518652997|ref|YP_008142517.1|   4 ENETNVLKYVRELAETKIKPRAREIDEKMEVPEDIIQAMRDMGLFASYIPEKYGGYGLSFPFLVNVIETISEACPST 80 
                                       6778899********************99************************************************ PP

                                       HHHHHHHHHTTHHHHHHHS-HHHHHHHHHHHHTT CS
                     Acyl-CoA_dh_N  79 alllgvhsslvapailrfGteeqkrryLpklasg 112
                                       al+l    +l a++++ fG+ee  ++yL ++a+g
  gi|518652997|ref|YP_008142517.1|  81 ALVLDGALTLFAEPLIMFGSEELNKKYLTEIAKG 114
                                       ********************************98 PP

>> Acyl-CoA_dh_M  Acyl-CoA dehydrogenase, middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.8   0.1   4.3e-27   1.5e-23       1      97 []     118     213 ..     118     213 .. 0.91

  Alignments for each domain:
  == domain 1  score: 82.8 bits;  conditional E-value: 4.3e-27
                                       EEE---SS-SS-GGG---EEEEETT.EEEEEEEEEEEETTTT-SEEEEEEETS-------EEEEEEE..GGGEEE-- CS
                     Acyl-CoA_dh_M   1 afalTEpqaGsdvasvkttaaerdggeyvlnGeKiwitnaaiatlalvlartekpdrarglslflvprdapgvsvrr 77 
                                       ++a+TEp++Gsd+as++t  ae+ +g+y ++G+K++i+n++ia+++++ a t+k ++++g+++f+v+ +apg++++r
  gi|518652997|ref|YP_008142517.1| 118 GLAITEPGSGSDAASIST-RAEKCEGGYKITGTKTFISNGRIAKFFVMDASTDKSKGYKGITTFVVDGNAPGLEISR 193
                                       589***************.66666779************************555558******************77 PP

                                       ---BSS-TTS-EEEEEEE.. CS
                     Acyl-CoA_dh_M  78 ieeklGlrglptgelvfedv 97 
                                         +k+G+rg +t el f++v
  gi|518652997|ref|YP_008142517.1| 194 DIHKMGIRGSSTVELNFHEV 213
                                       779*************9876 PP

>> PucR  Purine catabolism regulatory protein-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00085         3      52      95 ..       2      47 ..       1      56 [. 0.90
   2 ?    1.2   0.0      0.12   4.3e+02      37      78 ..      81     123 ..      66     140 .. 0.66

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00085
                              PucR 52 lkddpealaelvrelaeagvaaLviklgr..eipeelieaadelgl 95
                                      l+++++++ ++vrelae ++   + ++++  e+pe++i+a + +gl
  gi|518652997|ref|YP_008142517.1|  2 LNENETNVLKYVRELAETKIKPRAREIDEkmEVPEDIIQAMRDMGL 47
                                      46799999*******************7458***********9997 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.12
                              PucR  37 ellrggeLllttglal.kddpealaelvrelaeagvaaLvikl 78 
                                       +l+  g L l     +   ++e  ++++ e+a+  v +L+i  
  gi|518652997|ref|YP_008142517.1|  81 ALVLDGALTLFAEPLImFGSEELNKKYLTEIAKGAVGGLAITE 123
                                       4555555555444444334788889***************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2813.18
//
Query:       gi|518652998|ref|YP_008142518.1|  [L=402]
Description: hypothetical protein FACI_IFERC00001G1637 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    9.5e-53  178.6   0.1    1.4e-52  178.1   0.1    1.2  1  Asparaginase    Asparaginase, N-terminal
    1.9e-19   70.0   0.0    5.9e-19   68.4   0.0    1.8  2  Asparaginase_C  Glutaminase/Asparaginase C-terminal domain
    1.9e-08   33.5   1.3      4e-08   32.5   1.3    1.6  1  GatD_N          GatD N-terminal domain


Domain annotation for each model (and alignments):
>> Asparaginase  Asparaginase, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.1   0.1   2.3e-56   1.4e-52       2     185 ..      73     260 ..      72     266 .. 0.97

  Alignments for each domain:
  == domain 1  score: 178.1 bits;  conditional E-value: 2.3e-56
                                       EEEEEEESGGGEEECTTS--CCEES-HHHHHCCTTTCCCCSEEEEEEEEEE-GGG--HHHHHHHHHHHHHHCCT-SE CS
                      Asparaginase   2 vlvlatGGTiasekdesggalapalsaeellealpelekiaeleseqlanidSsnmtpadwlklaeaieealeeydg 78 
                                       v++l+tGGTias++d+++ga++p  ++++l++ +++++++ +l +e + ni S+n++ ++w+++a++ ++a+++ + 
  gi|518652998|ref|YP_008142518.1|  73 VCILTTGGTIASSVDYTTGAVKPVKDISYLYNFVNNISQF-KLYHESIDNILSENVNAEKWVQFARKARDAMKKGNS 148
                                       89**************************************.************************************ PP

                                       EEEE--STTHHHHHHHHHHHEES.SSEEEEE--SS-TTSTT-SHHHHHHHHHHHHHCGGTTSECEEEETTE...... CS
                      Asparaginase  79 fVvlhGTDTlaytAsaLslmlknldkpvvltGsqrplselrsDgpeNlldAllvaasseriagvlvvfngk...... 149
                                       +++ hGTDT++y+AsaLs+m+++ + p+++tGsqr++++++sD++ N+ +++ +a+++    +v ++++        
  gi|518652998|ref|YP_008142518.1| 149 VIIFHGTDTMQYSASALSFMFEEQTEPIIFTGSQRSSDRPSSDAFLNIEGSIHFASTD--MGEVGIAMHTDtsddsi 223
                                       ********************************************************87..9*********99***** PP

                                       .EEETTTEEE-BSSSSS-EEETTT--SEEEETTEEEE CS
                      Asparaginase 150 .llranrvtKvhtssldaFespnlgplaevegskvkv 185
                                        l+ra+r++K+htss+daF+s++ +pl+ ++++kvk 
  gi|518652998|ref|YP_008142518.1| 224 sLYRATRARKMHTSSRDAFKSISEPPLGLYADGKVKE 260
                                       ****************************998888875 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 ?   -3.0   0.0       1.4   8.4e+03      39      57 ..     131     151 ..     126     158 .. 0.74
   2 !   68.4   0.0   9.9e-23   5.9e-19       1     103 [.     280     380 ..     280     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.4
                                       H..HHHHHHHHHHTTT-EEEE CS
                    Asparaginase_C  39 s..allealkeakargivvva 57 
                                       +  ++ + +++a+++g  v++
  gi|518652998|ref|YP_008142518.1| 131 KwvQFARKARDAMKKGNSVII 151
                                       355788889999999877775 PP

  == domain 2  score: 68.4 bits;  conditional E-value: 9.9e-23
                                       -EEEEE--TT--HHHHHHHHHTT--EEEEEEBTTTB--HHHHHHHHHHHTTT-EEEEEESSSBS-----H.....HH CS
                    Asparaginase_C   1 rVvvlklhpgmdtkvlkallkkgakGvvlegtGvGnlpsallealkeakargivvvatsqcpsgsvsnseyeagkel 77 
                                       ++ +++++pgm ++ + +l + + k+v++ gtG G+ ++ ++++++++ +r++   +tsqc++g+v++++y++g+el
  gi|518652998|ref|YP_008142518.1| 280 NIGLIYFYPGMAEEDFYNL-SYNKKAVIIMGTGLGHTSTGIIDVIRKL-SRETHFFMTSQCIYGNVNMNVYSTGREL 354
                                       5789*************88.68**************************.9*************************** PP

                                       HHHTEEE-TT--HHHHHHHHHHHCTT CS
                    Asparaginase_C  78 erlgvisaddmtpeaarikLmlllgk 103
                                        ++gvi  ++m +e+a++k m+l ++
  gi|518652998|ref|YP_008142518.1| 355 IDAGVIPLQNMLAETAMVKAMYLSAN 380
                                       **********************9776 PP

>> GatD_N  GatD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.5   1.3   6.7e-12     4e-08       3      53 ..       3      48 ..       1      49 [. 0.94

  Alignments for each domain:
  == domain 1  score: 32.5 bits;  conditional E-value: 6.7e-12
                                      TT-EEEEE-SS-EEEEEE----TTS-SSEEEEEETTS-EEEEE-TT-.--- CS
                            GatD_N  3 vGDlikvekkgreyeGilmPrselsdddiivlKLdnGYNiGikieeiekie 53
                                      +G++i + +kg+ey G+++ +     +++i++KL +GYNi ++ ++i +i+
  gi|518652998|ref|YP_008142518.1|  3 IGQKIIFSYKGQEYAGTYISSG----KNTITVKLGSGYNITVDASSI-EIK 48
                                      7999******************....*********************.887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2692.72
//
Query:       gi|518652999|ref|YP_008142519.1|  [L=617]
Description: hypothetical protein FACI_IFERC00001G1638 [Ferroplasma acidarmanus fer1]
Scores for 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-61  205.8   0.0    1.1e-60  205.3   0.0    1.2  1  GatB_N     GatB/GatE catalytic domain
      0.009   16.2   0.0      0.024   14.9   0.0    1.7  1  GAD        GAD domain
  ------ inclusion threshold ------
        1.3    8.9   9.7       0.19   11.6   0.3    3.1  3  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.3   0.0   1.9e-64   1.1e-60       1     273 []       1     426 [.       1     426 [. 0.93

  Alignments for each domain:
  == domain 1  score: 205.3 bits;  conditional E-value: 1.9e-64
                                       EEEEEEEEEEB--SB-SSSSSBSS..SSCESTTSS--TTTTTS.................................T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx.................................x RF
                            GatB_N   1 lviGlEiHaqlktksKlFssaste..eegeepnsevsevdlal.................................P 42 
                                       ++iGlEiH ql   +KlF+s+ste  e +e+ ++++++v   l                                 P
  gi|518652999|ref|YP_008142519.1|   1 MKIGLEIHFQLGG-NKLFCSCSTEgtELNESFTRKLTPVMGELgkldtaveyetirnrnflyrassnsclvekdeeP 76 
                                       58*********96.6*******7743222223333333333335555555***********************9998 PP

                                       T..--.EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SE.EEEEEEE.TEEEEEEEEEEE CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx.xxxxxxxxxxxx RF
                            GatB_N  43 GtlPv.lnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeepla.keGslel.ekkvrierihlE 116
                                          P+ +n +a++++i++++al+c++ + ++f+RK+++++++++g+Q+t     ++ ++G++++ + +vri++i lE
  gi|518652999|ref|YP_008142519.1|  77 ---PHpVNPDALKTTIAISKALHCKVLDYTSFMRKIVVDGSNTSGFQRTG----IVgMDGYVKTsRGNVRISTITLE 146
                                       ...999********************************************....666******97889********* PP

                                       E---EEEEEETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 117 eDaaksvheekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvree 193
                                       eDa+++++e++  + ++l+R+G+pLiEi+tepd+ +p++a ++++++++ + +++  +g++   s+R+DvN S+   
  gi|518652999|ref|YP_008142519.1| 147 EDACRKLSEKEGVVEYSLDRLGIPLIEISTEPDIIDPDHALETAKAIGHYVMSMQNFRGEV--DSIRQDVNFSMGF- 220
                                       *********999***********************************************99..8**********94. PP

                                       ETTSSS.--EEEEEE-SHHHHHHHHHHHHHHHHHHH......................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
                            GatB_N 194 ekgeeegtrvEiKnlnslksiekaieyeierqiell......................................... 229
                                               rvEiK++++l++i+++ieyei+rq +l                                          
  gi|518652999|ref|YP_008142519.1| 221 -------GRVEIKGVSKLSFIKDTIEYEIKRQSSLEaisrilaekpheignfiditgmftntdssmikksiasgksv 290
                                       .......5*************************99999*************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                            GatB_N 230 ............................................................................. 229
                                                                                                                    
  gi|518652999|ref|YP_008142519.1| 291 mcarvsacnglmkhgnyklgrefadvaknmglgglmhsdefpayglsdeelhsiystagkgdndavivvlgeksrie 367
                                       ***************************************************************************** PP

                                       ..................-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                            GatB_N 230 ..................qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                                                         +eTr+++++ get++lR+   +   r++pe+d+p ++i+e+++e
  gi|518652999|ref|YP_008142519.1| 368 klkpllderfdkilkmqlEETRSATPS-GETRYLRPLAGK--ERMYPETDIPAVKITEAIME 426
                                       ***************************.**********65..3**************99875 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.9e-06     0.024       4      93 ..     283     368 ..     280     369 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.9e-06
                                       HHHSTEEEEEEEETTG-TTTSHHHHHHHHHHHHHTTHSHCEEEEESSGGEETTTCCC.S-HHHHHHHHHHCT--TTE CS
                               GAD   4 alksggsvkalrvpggaaklsrkeideleefakelgakglawikvegegltgpiakf.lteeevkklleavgaeegD 79 
                                        ++sg+sv   rv   +  +   + + ++efa  ++ +     +++g  ++++ +++ l+ ee+  ++ ++g  ++D
  gi|518652999|ref|YP_008142519.1| 283 SIASGKSVMCARVSACNGLMKHGNYKLGREFADVAKNM-----GLGGLMHSDEFPAYgLSDEELHSIYSTAGKGDND 354
                                       56666666666666644444444444444444444444.....567899**************************** PP

                                       EEEEEEEEHHHHHH CS
                               GAD  80 illfvAdkkktvnk 93 
                                       +++ v ++k+ ++k
  gi|518652999|ref|YP_008142519.1| 355 AVIVVLGEKSRIEK 368
                                       *****999988776 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.1      0.24   1.4e+03      56      98 ..     241     284 ..     229     286 .. 0.80
   2 ?    1.9   0.6     0.032   1.9e+02      57      95 ..     420     459 ..     415     462 .. 0.76
   3 ?   11.6   0.3   3.1e-05      0.19       2     104 ..     465     581 ..     464     603 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.24
                                       SSGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHHHHH CS
                         GatB_Yqey  56 kIskkiakevleellee.gkspeeiieekgLkqisdeeeleklv 98 
                                       +I  ++  e +  +l+e   ++ + i+  g++  +d++ ++k +
  gi|518652999|ref|YP_008142519.1| 241 EIKRQSSLEAISRILAEkPHEIGNFIDITGMFTNTDSSMIKKSI 284
                                       66777777788778866689999999999999999999999876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.032
                                       SGHHHHHHHHHHHHHH.TXXHHHHHHHCTXXXXXXSSXHH CS
                         GatB_Yqey  57 Iskkiakevleellee.gkspeeiieekgLkqisdeeele 95 
                                       I++ i + + + + ++ +++++e+ ++ +L q++ e+ + 
  gi|518652999|ref|YP_008142519.1| 420 ITEAIMESIEKLVPKSlEETMNELTKKFKLSQVEAESLIN 459
                                       555555555455558899***************9988775 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 3.1e-05
                                       HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCS..............STTH.HHHHHHHHHHHTTSSGHHHHH CS
                         GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieel..............kltp.eqlaellkliaegkIskkiak 63 
                                       +f++++++  ++ ++++ ll+ + +  nk+g++++++              +l++  +   +l+l  ++k   ++ +
  gi|518652999|ref|YP_008142519.1| 465 LFKALAGNFDNPHILSRILLQTIPELENKKGKKLSQVqmvdifgnqylearQLPQyHNTDSILELSRREKWDRNTFE 541
                                       79999999999*************************88999999999999955553778899999************ PP

                                       HHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHHHHHT CS
                         GatB_Yqey  64 evleelleegkspeeiieekgLkqisdeeeleklveeviae 104
                                       + l   + ++  ++e+ ++++Lk+++d +e++k+++e ++ 
  gi|518652999|ref|YP_008142519.1| 542 TALSLYIIDNIPVSELEKREELKMLND-NEIKKILDELVKD 581
                                       *******9*******************.*********9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); 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: 0.69u 0.32s 00:00:01.01 Elapsed: 00:00:00.51
# Mc/sec: 3642.68
//
Query:       gi|518653000|ref|YP_008142520.1|  [L=144]
Description: NADH dehydrogenase subunit A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-21   75.9   3.2    2.1e-21   75.9   3.2    1.9  2  Oxidored_q4      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
        1.1    9.7   4.4       0.75   10.2   0.8    2.3  2  FeoB_associated  FeoB-associated Cys-rich membrane protein


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   2.6      0.31   2.8e+03      74      90 ..       5      21 ..       1      26 [. 0.56
   2 !   75.9   3.2   2.3e-25   2.1e-21      16      99 .]      59     142 ..      46     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.31
                                      HHHHHHHHHHHHHHHHH CS
                       Oxidored_q4 74 liemllFllillvglvY 90
                                      ++++++ ++il+++l+ 
  gi|518653000|ref|YP_008142520.1|  5 YASIVITIIILVLALYL 21
                                      55556666666665543 PP

  == domain 2  score: 75.9 bits;  conditional E-value: 2.3e-25
                                       --HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHH CS
                       Oxidored_q4  16 pnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYew 92 
                                       ++ + l+pYE+G  +v+ a+ +++v++y++  lF++FD+++++lfpwa+ +++lg++ +ie+l+F+++ l+ ++Y++
  gi|518653000|ref|YP_008142520.1|  59 EDDSYLQPYESGEVAVEYAEGHITVQYYVIIFLFILFDIDMLLLFPWAFDFYALGIIPFIETLIFMAMPLFVVFYAY 135
                                       5566899********************************************************************** PP

                                       HH-S-XX CS
                       Oxidored_q4  93 kkgaLeW 99 
                                       kkg ++W
  gi|518653000|ref|YP_008142520.1| 136 KKGYMRW 142
                                       ******9 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   8.4e-05      0.75       2      20 ..       7      25 ..       6      38 .. 0.86
   2 ?    0.1   0.1      0.13   1.1e+03       7      23 ..     121     137 ..     117     139 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 8.4e-05
                   FeoB_associated  2 tiIVgliiaaavafvirrl 20
                                       i++++ii+++++++++++
  gi|518653000|ref|YP_008142520.1|  7 SIVITIIILVLALYLLFKV 25
                                      699***********99986 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.13
                   FeoB_associated   7 liiaaavafvirrlikk 23 
                                       li  a  +fv+++ +kk
  gi|518653000|ref|YP_008142520.1| 121 LIFMAMPLFVVFYAYKK 137
                                       44446778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       853  (0.0475766); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 981.10
//
Query:       gi|518653001|ref|YP_008142521.1|  [L=154]
Description: NADH dehydrogenase subunit B [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.9e-21   75.7   0.2    3.6e-21   75.3   0.2    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   0.2     2e-25   3.6e-21       4     130 ..      35     143 ..      33     144 .. 0.84

  Alignments for each domain:
  == domain 1  score: 75.3 bits;  conditional E-value: 2e-25
                                       HHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEES CS
                       Oxidored_q6   4 csisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavG 80 
                                       c i+++a++   ld+      r+++++  +s         ++ d+++v G+ t+++++++++++e ++ +k+via+G
  gi|518653001|ref|YP_008142521.1|  35 CAIEMMATQAADLDM-----ARFGSEIFRNSP--------RQSDLMIVAGTTTKRMAPRVKRIYEEMPYPKYVIAMG 98 
                                       788887777777777.....666666655444........499********************************** PP

                                       HHHHH-TGGGSTT-TEE-HHHHHHHC.S-E.EEE-SSS--HHHHHHHHHH CS
                       Oxidored_q6  81 tCAafGGipaaannpsvgeevgellevvpvdinipGCPphpeailetlla 130
                                        C ++GG +   + +sv   v ++++v+pvd+++pGCPp+p+a++++l +
  gi|518653001|ref|YP_008142521.1|  99 VCVIQGGPY--VDGYSV---VLGVDKVIPVDVYVPGCPPSPQALTYGLIT 143
                                       *********..333444...569**********************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (154 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 1080.60
//
Query:       gi|518653002|ref|YP_008142522.1|  [L=151]
Description: NADH dehydrogenase subunit C [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-37  129.4   0.3    1.3e-37  129.1   0.3    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s
  ------ inclusion threshold ------
       0.02   15.2   0.0       0.15   12.3   0.0    2.0  2  DUF3303         Protein of unknown function (DUF3303)
      0.062   13.6   0.3       0.14   12.5   0.2    1.7  1  DUF2513         Hypothetical protein (DUF2513)
      0.067   13.6   1.0      0.099   13.0   0.5    1.5  2  MqsR_toxin      Motility quorum-sensing regulator, toxin of M
        0.1   11.7   0.0       0.15   11.2   0.0    1.2  1  Phosphatase     Phosphatase


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 !  129.1   0.3   3.7e-41   1.3e-37       2     120 ..      18     129 ..      17     131 .. 0.92

  Alignments for each domain:
  == domain 1  score: 129.1 bits;  conditional E-value: 3.7e-41
                                       E--HHHHHHHHHHHHH...TT--EEEEEEEEETTSSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHH CS
                    Complex1_30kDa   2 vvepedllevakflkdeeelgfdvlsdltavDekeerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgad 78 
                                        ++++dl+e+++  k +      +ls++t++D  ++++evvyh++++++n  i+vkv++  ++++vpS+++l+++ad
  gi|518653002|ref|YP_008142522.1|  18 NIDKSDLVELMEDYKGK---D-YYLSSITGIDM-KDHLEVVYHIHNFDQNDYICVKVAT--DDEKVPSLVKLWKAAD 87 
                                       57889999999999983...2.49********8.6**********************55..6688************ PP

                                       HHHHHHHHHSHHBCTTSSTSS-SSSSTTSSS-TTSTTS---- CS
                    Complex1_30kDa  79 wyEREayDmfGivfeghpdlrrillpedfeghPLRkdfplsg 120
                                       w ERE yD++G+ fegh++lrrillpe+++ghPLRkd++l++
  gi|518653002|ref|YP_008142522.1|  88 WDEREQYDLMGVIFEGHENLRRILLPEEWVGHPLRKDYDLKK 129
                                       ***************************************987 PP

>> DUF3303  Protein of unknown function (DUF3303)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.3e-05      0.15      18      73 ..      31      86 ..      18      91 .. 0.86
   2 ?    0.8   0.0      0.17   6.2e+02      34      64 ..     101     131 ..      88     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.3e-05
                           DUF3303 18 ykaferflesGaledkpegfellgrvhapgegrgfaiveaddakalfkhfapWral 73
                                      yk    +l+s +  d+ + +e++  +h+ +++  +++  a d++++   +  W+a 
  gi|518653002|ref|YP_008142522.1| 31 YKGKDYYLSSITGIDMKDHLEVVYHIHNFDQNDYICVKVATDDEKVPSLVKLWKAA 86
                                      5555567777777899*************************************985 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.17
                           DUF3303  34 pegfellgrvhapgegrgfaiveaddakalf 64 
                                       +eg e l r+  p+e  g+ + +  d k+++
  gi|518653002|ref|YP_008142522.1| 101 FEGHENLRRILLPEEWVGHPLRKDYDLKKVQ 131
                                       8999*******99999998888877777776 PP

>> DUF2513  Hypothetical protein (DUF2513)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   3.8e-05      0.14      23      80 ..      33     105 ..      20     119 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.8e-05
                           DUF2513  23 slddeeeklsaidgyskeeiiyhlkllaeagLieaekkkakss...............iislvvkrLtweGhd 80 
                                         d+  +++  id  +  e++yh++  +++++i ++  +++++                 ++      +eGh+
  gi|518653002|ref|YP_008142522.1|  33 GKDYYLSSITGIDMKDHLEVVYHIHNFDQNDYICVKVATDDEKvpslvklwkaadwdeREQYDLMGVIFEGHE 105
                                       334444445588888888****************999999888666655555555555555555555555555 PP

>> MqsR_toxin  Motility quorum-sensing regulator, toxin of MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.5   2.8e-05     0.099      23      88 ..       8      73 ..       2      81 .. 0.79
   2 ?   -3.1   0.0       2.9     1e+04       4      13 ..     125     134 ..     124     145 .. 0.63

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                                      HHHHHHHHHTT--HHHHHHHHHC--GGGEEEEE--.STTTT--EEEE--EETTE.E--EEEEEETTE CS
                        MqsR_toxin 23 rkalkgaaalGldeedvvdviasLerkdFyksmtt.yadhrvWqDvYhveteegkelYiKlklrenv 88
                                      ++  +g++ l +d++d+v+ +++ + kd+y s  t  +++   + vYh   +  ++ Yi +k+ ++ 
  gi|518653002|ref|YP_008142522.1|  8 ETDKSGMKVLNIDKSDLVELMEDYKGKDYYLSSITgIDMKDHLEVVYHI-HNFDQNDYICVKVATDD 73
                                      678899************************888886777889999***9.55555777766665554 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.9
                                       S-HHHHHHHH CS
                        MqsR_toxin   4 yaLskvkalv 13 
                                       y+L+kv+ + 
  gi|518653002|ref|YP_008142522.1| 125 YDLKKVQYVS 134
                                       6677766543 PP

>> Phosphatase  Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   4.1e-05      0.15     113     191 ..       2      80 ..       1      83 [. 0.96

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                       Phosphatase 113 yaaladalraaGcevltpaagrsveietelgarereiryvegvavveeegalaHtHsplpvravlaelaeageelPd 189
                                       y+ l++   ++G +vl+  ++  ve  ++ + ++++++ ++g+ +  + + + H H+      +  ++a + e++P 
  gi|518653002|ref|YP_008142522.1|   2 YKILSEETDKSGMKVLNIDKSDLVELMEDYKGKDYYLSSITGIDMKDHLEVVYHIHNFDQNDYICVKVATDDEKVPS 78 
                                       888999999********************************************************9***99*****9 PP

                       Phosphatase 190 Lv 191
                                       Lv
  gi|518653002|ref|YP_008142522.1|  79 LV 80 
                                       98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      436  (0.0243181); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1105.51
//
Query:       gi|518653003|ref|YP_008142523.1|  [L=367]
Description: hypothetical protein FACI_IFERC00001G1642 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-82  276.2   0.1    4.3e-80  268.7   0.0    2.8  2  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0     0.049   8.7e+02      43      90 ..      25      74 ..      22      81 .. 0.80
   2 !  268.7   0.0   2.4e-84   4.3e-80       1     271 []     118     367 .]     118     367 .] 0.96

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.049
                                      ---TTHHHHHHHHHHHHHHHHHHHHHH..HHSSSSHHHHHSSSS-BSHHH CS
                    Complex1_49kDa 43 Dlpegllekikeflkelekkldelekl..ltknrifkkRtkgvgvlskee 90
                                       l+e+++e++  ++ +l+++ +++ +l  + +n+i+ +R+  + +++ e 
  gi|518653003|ref|YP_008142523.1| 25 KLNEETVEDVDITIGYLHRNAEKICELsyYANNTIYFDRMDYIDAMNMEL 74
                                      57888999999999999999999988744579999999999887777665 PP

  == domain 2  score: 268.7 bits;  conditional E-value: 2.4e-84
                                       HTT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHH CS
                    Complex1_49kDa   1 DlGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifk 77 
                                       DlG+lt+f+ +f+eReki +++ e++G R   +y+ iGGv++D++++++e+ikef++ ++ kl+e+ k++ + ++f 
  gi|518653003|ref|YP_008142523.1| 118 DLGMLTPFFHTFHEREKIQNIFVEASGGRQEVNYMSIGGVYQDFNDTIIEEIKEFISGFKGKLEEIVKMYLDSEVFW 194
                                       99*************************************************************************** PP

                                       HHHSSSS-BSHHHHHHHTT-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHH CS
                    Complex1_49kDa  78 kRtkgvgvlskeealelgltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieq 154
                                       +R++g g+l+ e al++g+tGp+lRasG++yD+Rk++pY  Yd+++fdvpv+++ D + R+l++ eE+rqS+kIieq
  gi|518653003|ref|YP_008142523.1| 195 QRNQGTGILEPEVALDYGVTGPMLRASGIAYDVRKDSPYLFYDKVNFDVPVTNTKDNLGRFLLKAEELRQSIKIIEQ 271
                                       ***************************************************************************** PP

                                       HHHT--.S-SB---TTTS---GGGGGT-HHHHHHHHHHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEE CS
                    Complex1_49kDa 155 aleklpegpvlaedkkvalpkkeevkksmealihhfklvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlk 231
                                       +l klp+gp+ + ++k          + m  l              +g+v+++vE+  Ge+gv++  dg+ kpyr++
  gi|518653003|ref|YP_008142523.1| 272 CLAKLPDGPFFNPKAKK---------SAMLLL------------KGQGDVFTRVESESGEYGVFIRGDGGLKPYRIH 327
                                       *********88744332.........333333............479****************************** PP

                                       EE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
                    Complex1_49kDa 232 irapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                                        r+psf nl++++ +++g l+aD++a+++s+d v+gevDR
  gi|518653003|ref|YP_008142523.1| 328 ARSPSFKNLAVVPVMARGGLIADLIATIASTDAVAGEVDR 367
                                       ***************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 2981.37
//
Query:       gi|518653004|ref|YP_008142524.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1643 [Ferroplasma acidarmanus fer1]
Scores for complete 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-87  293.6  22.2    1.8e-87  293.4  22.2    1.0  1  NADHdh           NADH dehydrogenase
  ------ inclusion threshold ------
        7.6    6.7   8.1        4.2    7.5   0.2    3.4  3  PspB             Phage shock protein B


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 !  293.4  22.2   2.1e-91   1.8e-87       2     297 ..      27     342 ..      26     344 .. 0.94

  Alignments for each domain:
  == domain 1  score: 293.4 bits;  conditional E-value: 2.1e-91
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHH CS
                            NADHdh   2 klllllvvlllvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalil 78 
                                       ++++++v++ + ++ l+++ Rk++Ariq+R+GPnrvG++Gllq++aD++Kll Ke+i+p+k d l ++lap++++i 
  gi|518653004|ref|YP_008142524.1|  27 QTIVVIVFVGISFVALIYIFRKYMARIQRRVGPNRVGKFGLLQLIADLFKLLGKESIMPAKRDDLAYKLAPAIVIIG 103
                                       56788888999999*************************************************************** PP

                                       HHCTTTTS-SSS.......SSS--TTHHHHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHH CS
                            NADHdh  79 allafaviPfge.......vladlnvglllilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsll 148
                                       ++laf+++P+g+       ++++  v l+l++ l+s+ ++g +laG++++s+YallG++R +a  is+E+++++s+l
  gi|518653004|ref|YP_008142524.1| 104 TILAFILLPYGDlayfgsiAVTHSRVTLILMFGLLSILPIGEILAGISTKSNYALLGTMRGVAKDISFEIPMMISVL 180
                                       ***********55677888899999**************************************************** PP

                                       HHHHHH-SS...........-HHHHHHCCCTT-CCCCHHHHHHHHHHHHHHCCTCTTBTTTTSTTSSSSCCCTT-HC CS
                            NADHdh 149 avvllagsl...........slseiveaqeeiwfillqllafiifliallaetnraPFDlpeaesELvaGfhtEYsg 214
                                       a+v++++             sls iv++   i + ++++l+++if+i+++a ++  PFD+ e++sEL++G++tEYsg
  gi|518653004|ref|YP_008142524.1| 181 AIVMITSRSyvtgtaitgglSLSGIVSNEV-IPYGIIEPLGLLIFYISMVARASMSPFDMGESDSELISGYTTEYSG 256
                                       *****5555455555555559999998764.5667778*************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS...HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTCH CS
                            NADHdh 215 mkfalfflaeyanmvlvsalavllFlgGwllpfs...gllwfllKvllllflfiwiratlpRlRydqlmklgwkvll 288
                                       m+f+lf+++ + +++l s+++++l+lgG ++p++   g++++l+K+++l+++++++  tlpR+R+d++++lgwk+ll
  gi|518653004|ref|YP_008142524.1| 257 MRFGLFYVGLFGMVYLTSFIISILYLGGANGPYEsyvGFFYLLIKTVILVLIAFVVWVTLPRIRIDRFVNLGWKYLL 333
                                       *********************************99****************************************** PP

                                       HHHHHHHHH CS
                            NADHdh 289 plalanlll 297
                                       pl++anl+ 
  gi|518653004|ref|YP_008142524.1| 334 PLSMANLVY 342
                                       ******996 PP

>> PspB  Phage shock protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.2   0.00047       4.2       3      32 ..      27      56 ..      25      73 .. 0.86
   2 ?    0.6   0.0     0.066   5.9e+02      14      32 ..     214     232 ..     205     247 .. 0.81
   3 ?   -1.8   3.3      0.39   3.5e+03       4      23 ..     297     316 ..     294     318 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00047
                              PspB  3 vflavpliifvlfVapiWLiLHYrskkkrs 32
                                      ++++v++ + + fVa+i ++  Y+ + +r+
  gi|518653004|ref|YP_008142524.1| 27 QTIVVIVFVGISFVALIYIFRKYMARIQRR 56
                                      57899999***************9998776 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.066
                              PspB  14 lfVapiWLiLHYrskkkrs 32 
                                        ++ p++L+++Y+s+  r+
  gi|518653004|ref|YP_008142524.1| 214 GIIEPLGLLIFYISMVARA 232
                                       5899*********987665 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.39
                              PspB   4 flavpliifvlfVapiWLiL 23 
                                       +l++ ++i+vl+  ++W+ L
  gi|518653004|ref|YP_008142524.1| 297 YLLIKTVILVLIAFVVWVTL 316
                                       57777788888888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.49
# Mc/sec: 2173.28
//
Query:       gi|518653005|ref|YP_008142525.1|  [L=165]
Description: NADH dehydrogenase subunit I [Ferroplasma acidarmanus fer1]
Scores for complete 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   43.1  12.6    4.7e-06   26.2   3.5    2.2  2  Fer4      4Fe-4S binding domain
    1.1e-10   41.9  20.7    1.8e-08   34.8   9.7    1.8  2  Fer4_7    4Fe-4S dicluster domain
    2.8e-10   41.0   5.5    8.8e-05   23.4   0.9    2.3  2  Fer4_16   4Fe-4S double cluster binding domain
    8.5e-10   38.6   5.3    1.6e-05   24.9   0.6    2.2  2  Fer4_21   4Fe-4S dicluster domain
    4.9e-09   36.2   5.9    2.5e-06   27.6   9.6    2.2  2  Fer4_9    4Fe-4S dicluster domain
    1.6e-08   34.6  18.4      2e-07   31.0   9.0    1.7  2  Fer4_10   4Fe-4S dicluster domain
    5.8e-08   33.1   6.7      1e-07   32.3   6.7    1.4  1  Fer4_8    4Fe-4S dicluster domain
    1.9e-06   27.7  15.1     0.0058   16.6   4.1    2.2  2  Fer4_6    4Fe-4S binding domain
    2.5e-05   24.8  10.5    0.00015   22.2  10.5    2.1  3  Fer4_17   4Fe-4S dicluster domain
    2.8e-05   24.3   7.6      0.032   14.7   1.5    2.2  2  Fer4_4    4Fe-4S binding domain
    0.00011   22.1  13.3     0.0018   18.3   1.8    2.3  2  Fer4_2    4Fe-4S binding domain
    0.00045   21.0   2.9       0.45   11.4   0.3    2.3  2  Fer4_22   4Fe-4S dicluster domain
      0.004   18.0  15.9       0.28   12.2   4.5    2.3  2  Fer4_3    4Fe-4S binding domain
  ------ inclusion threshold ------
      0.045   14.0  10.6        0.1   12.8   1.1    2.2  2  Fer4_18   4Fe-4S dicluster domain
      0.058   13.9  13.2       0.46   11.1   2.7    2.6  2  Fer4_13   4Fe-4S single cluster domain of Ferredoxin I


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   1.7   6.2e-08   7.4e-05       4      23 ..      58      77 ..      55      78 .. 0.89
   2 !   26.2   3.5     4e-09   4.7e-06       2      24 .]     113     135 ..     112     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 6.2e-08
                                      ETTTSSS-THHHHHSTTTEE CS
                              Fer4  4 deekCigCGaCvevCPvgAI 23
                                       +e C+gC +C ++CP+  I
  gi|518653005|ref|YP_008142525.1| 58 VPEACVGCTLCSKICPNHSI 77
                                      69**************9987 PP

  == domain 2  score: 26.2 bits;  conditional E-value: 4e-09
                                       EEETTTSSS-THHHHHSTTTEEE CS
                              Fer4   2 videekCigCGaCvevCPvgAIt 24 
                                        ++   C+ C +C+e+CP++AI+
  gi|518653005|ref|YP_008142525.1| 113 DVNFGTCTVCRQCEEICPTDAIY 135
                                       589999****************6 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.8   9.7   1.5e-11   1.8e-08       1      52 []      61     133 ..      61     133 .. 0.73
   2 !   19.5   3.2   9.3e-07    0.0011       1      34 [.     118     152 ..     118     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 34.8 bits;  conditional E-value: 1.5e-11
                            Fer4_7   1 rCigCgaCvaaCpvkaield.....................eeenekgtekveidpekClgCgaCvavCPtga 52 
                                       +C+gC  C + Cp++ i+++                     +  ++k++ +++++  +C+ C++C++ CPt+a
  gi|518653005|ref|YP_008142525.1|  61 ACVGCTLCSKICPNHSIKMEhwdldrtglednvvqtargdrKNLQNKRNIYPDVNFGTCTVCRQCEEICPTDA 133
                                       5*****************99555555555444443333333233444667779999***************97 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 9.3e-07
                            Fer4_7   1 rCigCgaCvaaCpvkaieldee.enekgtekveid 34 
                                       +C+ C++C++ Cp++ai+l+ + e+++++ + +++
  gi|518653005|ref|YP_008142525.1| 118 TCTVCRQCEEICPTDAIYLTHQfEDARTRNSFTYS 152
                                       5*****************98651444444444444 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.2   8.8e-07    0.0011       2      32 ..      62      89 ..      61     115 .. 0.68
   2 !   23.4   0.9   7.4e-08   8.8e-05       1      37 [.     118     152 ..     118     165 .] 0.65

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 8.8e-07
                           Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecis 32
                                      C++C+ C ++CP + ik++    ++ +++  
  gi|518653005|ref|YP_008142525.1| 62 CVGCTLCSKICPNHSIKME---HWDLDRTGL 89
                                      ******************9...777766433 PP

  == domain 2  score: 23.4 bits;  conditional E-value: 7.4e-08
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisyntae 37 
                                       +C+ C++C e+CPt+ai  +   ++e  ++ ++ t  
  gi|518653005|ref|YP_008142525.1| 118 TCTVCRQCEEICPTDAIYLT--HQFEDARTRNSFTYS 152
                                       5*****************99..445444444432333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.6   1.3e-08   1.6e-05      37      59 .]      58      79 ..      47      79 .. 0.87
   2 !   16.0   0.4   8.2e-06    0.0098      35      57 ..     113     134 ..      90     136 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.3e-08
                           Fer4_21 37 vedeCvGCnlCssvCPvedciem 59
                                      v + CvGC+lCs++CP +  i+m
  gi|518653005|ref|YP_008142525.1| 58 VPEACVGCTLCSKICP-NHSIKM 79
                                      6799************.688887 PP

  == domain 2  score: 16.0 bits;  conditional E-value: 8.2e-06
                           Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                                        v   +C+ C  C ++CP+ d+i
  gi|518653005|ref|YP_008142525.1| 113 DVNFGTCTVCRQCEEICPT-DAI 134
                                       566679************7.887 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.3   2.7e-06    0.0032      33      50 ..      50      76 ..      25      77 .. 0.71
   2 !   27.6   9.6   2.1e-09   2.5e-06       1      51 []      61     134 ..      61     134 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.7e-06
                            Fer4_9 33 e.........eaCigCgaCveaCpkga 50
                                                eaC+gC  C ++Cp++ 
  gi|518653005|ref|YP_008142525.1| 50 RfrfriflvpEACVGCTLCSKICPNHS 76
                                      044456677789************975 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 2.1e-09
                            Fer4_9   1 kCtgCgaCveaC.................pagvvvedaaerkarlraase.......................eaCi 37 
                                       +C+gC+ C + C                 + +                                           C+
  gi|518653005|ref|YP_008142525.1|  61 ACVGCTLCSKICpnhsikmehwdldrtglEDN-----------------VvqtargdrknlqnkrniypdvnfGTCT 120
                                       6***********66666444444444444333.................233344666666666677******99** PP

                            Fer4_9  38 gCgaCveaCpkgai 51 
                                        C++C+e+Cp++ai
  gi|518653005|ref|YP_008142525.1| 121 VCRQCEEICPTDAI 134
                                       ***********997 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   9.0   1.7e-10     2e-07       4      56 .]      57     130 ..      54     130 .. 0.95
   2 !   15.6   1.9   1.1e-05     0.013       6      24 ..     116     137 ..     111     157 .. 0.74

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 1.7e-10
                           Fer4_10   4 idddtCirCgkCvkaCPadl.....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + ++ C++C+ C k CP +                      ++++++ +++++   +++ + Ct c +C e+CP
  gi|518653005|ref|YP_008142525.1|  57 LVPEACVGCTLCSKICPNHSikmehwdldrtglednvvqtaRGDRKNLQNKRNIYPDVNFGTCTVCRQCEEICP 130
                                       56899*************99*******************99999999999999999*****************9 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.1e-05
                           Fer4_10   6 ddtCirCgkCvkaCPadl...t 24 
                                         tC+ C++C + CP+d+   t
  gi|518653005|ref|YP_008142525.1| 116 FGTCTVCRQCEEICPTDAiylT 137
                                       568************9654441 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.3   6.7   8.6e-11     1e-07       3      64 ..      60     132 ..      59     133 .. 0.72

  Alignments for each domain:
  == domain 1  score: 32.3 bits;  conditional E-value: 8.6e-11
                            Fer4_8   3 ekCieCgaCqsaCpvlrr............tkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       e+C++C +C + Cp  +             +++  ++arg++++  q++++ + + ++++Ct c++C+e Cp++
  gi|518653005|ref|YP_008142525.1|  60 EACVGCTLCSKICPNHSIkmehwdldrtglEDNVVQTARGDRKN-LQNKRNIYPDVNFGTCTVCRQCEEICPTD 132
                                       68***********9666633444444444344666666666666.66666666699****************85 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   3.2   5.5e-06    0.0066       6      20 ..      59      73 ..      58      77 .. 0.90
   2 !   16.6   4.1   4.9e-06    0.0058       9      24 .]     119     134 ..     117     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 5.5e-06
                            Fer4_6  6 pdkCigCgdCvrvCP 20
                                      p++C+gC  C ++CP
  gi|518653005|ref|YP_008142525.1| 59 PEACVGCTLCSKICP 73
                                      79************* PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.9e-06
                            Fer4_6   9 CigCgdCvrvCPegai 24 
                                       C+ C+ C+ +CP++ai
  gi|518653005|ref|YP_008142525.1| 119 CTVCRQCEEICPTDAI 134
                                       **************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 !   12.0   2.3    0.0002      0.23      44      59 ..      60      75 ..      36      77 .. 0.88
   2 !   22.2  10.5   1.3e-07   0.00015       1      59 [.      61     132 ..      61     134 .. 0.63
   3 !   11.8   3.3   0.00023      0.27       2      31 ..     119     151 ..     118     162 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                           Fer4_17 44 slCieCgeCerkCPqg 59
                                      + C++C +C++ CP++
  gi|518653005|ref|YP_008142525.1| 60 EACVGCTLCSKICPNH 75
                                      78************98 PP

  == domain 2  score: 22.2 bits;  conditional E-value: 1.3e-07
                           Fer4_17   1 rCiqCgyClpeCpsyea............ydnepkkllraakl.....glleeaekeekaslCieCgeCerkCPqg 59 
                                       +C +C  C + Cp + +                 +++++ a+      + ++++  + ++++C+ C++Ce+ CP +
  gi|518653005|ref|YP_008142525.1|  61 ACVGCTLCSKICPNHSIkmehwdldrtglE----DNVVQTARGdrknlQNKRNIYPDVNFGTCTVCRQCEEICPTD 132
                                       5************97775544434332221....3333333222221344444444579***************86 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 0.00023
                           Fer4_17   2 CiqCgyClpeCpsyea...ydnepkkllraakl 31 
                                       C+ C+ C++ Cp+ ++   +++e +++++ +++
  gi|518653005|ref|YP_008142525.1| 119 CTVCRQCEEICPTDAIyltHQFEDARTRNSFTY 151
                                       777777777777644422255556666666655 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.5   9.8e-05      0.12       1      15 [.      59      73 ..      59      92 .. 0.90
   2 !   14.7   1.5   2.7e-05     0.032       3      16 ..     118     131 ..     113     137 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 9.8e-05
                            Fer4_4  1 qerCigCgsCvaaCP 15
                                      +e C+gC  C  +CP
  gi|518653005|ref|YP_008142525.1| 59 PEACVGCTLCSKICP 73
                                      689************ PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.7e-05
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       +C+ C++C+ +CP+
  gi|518653005|ref|YP_008142525.1| 118 TCTVCRQCEEICPT 131
                                       6999*********7 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.8   1.5e-06    0.0018       2      22 .]      54      74 ..      53      74 .. 0.91
   2 !    9.1   4.0    0.0012       1.4       5      22 .]     114     131 ..     111     131 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.5e-06
                            Fer4_2  2 pvvvdtdrCigCgaCvsaCPa 22
                                      +++ ++++C+gC  C + CP+
  gi|518653005|ref|YP_008142525.1| 54 RIFLVPEACVGCTLCSKICPN 74
                                      57899***************5 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.0012
                            Fer4_2   5 vdtdrCigCgaCvsaCPa 22 
                                       v+  +C+ C+ C   CP+
  gi|518653005|ref|YP_008142525.1| 114 VNFGTCTVCRQCEEICPT 131
                                       67889************7 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.3   0.00038      0.45      80      94 ..      60      74 ..      42      76 .. 0.87
   2 !   10.1   0.1   0.00098       1.2       2      18 ..     119     135 ..      85     155 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                           Fer4_22 80 sgCvGCgRCieacpv 94
                                      ++CvGC  C++ cp+
  gi|518653005|ref|YP_008142525.1| 60 EACVGCTLCSKICPN 74
                                      689999999999997 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00098
                           Fer4_22   2 ClsCgaCtlvCptCsCf 18 
                                       C  C +C  +Cpt   +
  gi|518653005|ref|YP_008142525.1| 119 CTVCRQCEEICPTDAIY 135
                                       77777777777776555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   4.5   0.00024      0.28       1      14 [.      62      75 ..      62      76 .. 0.93
   2 !   11.5   3.6   0.00039      0.47       1      15 []     119     133 ..     119     133 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00024
                            Fer4_3  1 CtgCgaCvevCPvg 14
                                      C+gC +C + CP++
  gi|518653005|ref|YP_008142525.1| 62 CVGCTLCSKICPNH 75
                                      ************86 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00039
                            Fer4_3   1 CtgCgaCvevCPvgA 15 
                                       Ct C++C+e CP++A
  gi|518653005|ref|YP_008142525.1| 119 CTVCRQCEEICPTDA 133
                                       777**********98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   2.5    0.0087        10      60      74 ..      61      75 ..      54      85 .. 0.89
   2 ?   12.8   1.1   8.6e-05       0.1      42      74 ..     100     132 ..      77     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0087
                           Fer4_18 60 dcidcescvkvcPtg 74
                                       c+ c  c k+cP +
  gi|518653005|ref|YP_008142525.1| 61 ACVGCTLCSKICPNH 75
                                      6************87 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.6e-05
                           Fer4_18  42 kekkalkekeerkekgagdcidcescvkvcPtg 74 
                                        +k+ +++++   + + g c+ c++c ++cPt+
  gi|518653005|ref|YP_008142525.1| 100 DRKNLQNKRNIYPDVNFGTCTVCRQCEEICPTD 132
                                       34555566666677899**************96 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.7   0.00039      0.46       4      19 ..      60      75 ..      58      76 .. 0.91
   2 ?    7.8   2.9    0.0041       4.9       2      17 ..     115     130 ..     114     134 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00039
                           Fer4_13  4 dtCiacgaCvelaPdv 19
                                      + C++c++C +++P++
  gi|518653005|ref|YP_008142525.1| 60 EACVGCTLCSKICPNH 75
                                      78************85 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0041
                           Fer4_13   2 DrdtCiacgaCvelaP 17 
                                       +  tC+ c +C e++P
  gi|518653005|ref|YP_008142525.1| 115 NFGTCTVCRQCEEICP 130
                                       5679************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       700  (0.0390429); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1173.07
//
Query:       gi|518653006|ref|YP_008142526.1|  [L=83]
Description: hypothetical protein FACI_IFERC00001G1645 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-14   53.7  15.8    1.7e-14   53.7  15.8    1.6  2  Oxidored_q3      NADH-ubiquinone/plastoquinone oxidoreductase
  ------ inclusion threshold ------
        6.3    6.9  20.1          5    7.2   0.9    2.0  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        6.8    6.7  14.6        7.9    6.5  14.6    1.1  1  TspO_MBR         TspO/MBR family


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.4     0.082   4.9e+02     124     137 ..       5      18 ..       1      21 [. 0.48
   2 !   53.7  15.8   2.9e-18   1.7e-14       2      63 ..      18      79 ..      17      83 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.082
                                       HHHHHHHHHHHHHH CS
                       Oxidored_q3 124 llpfelasllLLva 137
                                       +++f+la++  ++a
  gi|518653006|ref|YP_008142526.1|   5 IIFFILAAIAVIMA 18 
                                       34444444444443 PP

  == domain 2  score: 53.7 bits;  conditional E-value: 2.9e-18
                                      HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTT CS
                       Oxidored_q3  2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesa 63
                                      al +i++kn+++s +fL++++++ +++fi+lg +F++ + +lvY+GA+++l++Fv+ml+  +
  gi|518653006|ref|YP_008142526.1| 18 ALSAISTKNLIHSSIFLLILLLMFSIIFIFLGLSFVGSIELLVYAGAVVMLIVFVLMLTGGK 79
                                      7889******************************************************7444 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.9   0.00083         5      73      94 ..       4      25 ..       1      32 [. 0.69
   2 ?    5.2  12.5    0.0035        21      45      91 ..      33      81 ..      27      83 .] 0.71

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00083
                   Phage_holin_3_6 73 aavllvlagvlalvglkklkka 94
                                      ++++++la+++++++l++++ +
  gi|518653006|ref|YP_008142526.1|  4 TIIFFILAAIAVIMALSAISTK 25
                                      5677777777777777777664 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0035
                   Phage_holin_3_6 45 vlallalllllvalalala.alwlaali.vaavllvlagvlalvglkkl 91
                                      +l++l l++ +++++l+l+ +  +  l+  +av++++  vl+l g k +
  gi|518653006|ref|YP_008142526.1| 33 FLLILLLMFSIIFIFLGLSfVGSIELLVyAGAVVMLIVFVLMLTGGKDV 81
                                      5666666666677778887667777777566888888888888888765 PP

>> TspO_MBR  TspO/MBR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5  14.6    0.0013       7.9      45     103 ..       6      70 ..       1      77 [. 0.74

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0013
                                       HHHHHHHHHHHHHHHH......HHHHHHHHHHHHTSGGCTTTTTSGGGHHHHHHHHHHHHHHHHH CS
                          TspO_MBR  45 vlyilmgvaaylvwka......lalyavqlvlnllwsplffglkspvlalvdivallglvvalil 103
                                       + +il ++a +++++a      +   +  l+l l++s++f  l   +++ +++++ +g+vv+li+
  gi|518653006|ref|YP_008142526.1|   6 IFFILAAIAVIMALSAistknlIHSSIFLLILLLMFSIIFIFLGLSFVGSIELLVYAGAVVMLIV 70 
                                       444555555555555566667744556667899999999999999**************999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1390  (0.077528); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        90  (0.0050198); 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):               3  [number of targets reported over threshold]
# CPU time: 0.54u 0.34s 00:00:00.88 Elapsed: 00:00:00.50
# Mc/sec: 504.21
//
Query:       gi|518653007|ref|YP_008142527.1|  [L=73]
Description: NADH dehydrogenase subunit J [Ferroplasma acidarmanus fer1]
Scores for complete 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   36.0   3.3    5.4e-09   35.9   3.3    1.0  1  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
       0.31   11.2   2.8       0.54   10.4   2.8    1.4  1  SdpI         SdpI/YhfL protein family


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   3.3   6.1e-13   5.4e-09      75     144 .]       6      67 ..       1      67 [. 0.71

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 6.1e-13
                                       HHHHHHHHHHHHHHHHTT--......--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
                       Oxidored_q3  75 lalaalligllllalllllllessssavdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                                       + +a ++++++++ + ll++        ++ + ++++i+ ig+llf++y++pfel+s+lL + +ig++++
  gi|518653007|ref|YP_008142527.1|   6 QKIA-AIVFIIVIGINLLTIN-------KSFAIKPQDITDIGTLLFSTYIVPFELLSVLLVASIIGVMYI 67 
                                       3344.3333333333333332.......34467899*******************************987 PP

>> SdpI  SdpI/YhfL protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   2.8   6.1e-05      0.54      23      62 ..       3      62 ..       3      68 .. 0.65

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 6.1e-05
                              SdpI 23 rkahrfagklwiiaGlilllla......................lgavvlvllvlvlllviv 62
                                      +ka+++a+ ++ii+  i ll+                       +  + l++++l  ++ i+
  gi|518653007|ref|YP_008142527.1|  3 NKAQKIAAIVFIIVIGINLLTInksfaikpqditdigtllfstyIVPFELLSVLL--VASII 62
                                      69*********99888877777799999999999988887654311122222222..22222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.28s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 505.22
//
Query:       gi|518653008|ref|YP_008142528.1|  [L=99]
Description: NADH dehydrogenase subunit K [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-14   53.7  12.3    1.7e-14   53.3  12.3    1.1  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
        7.2    6.5  15.2        8.4    6.3  15.2    1.0  1  DUF5090      Domain of unknown function (DUF5090)


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 !   53.3  12.3   1.9e-18   1.7e-14       2     103 ..       6      94 ..       5      96 .. 0.96

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 1.9e-18
                                       HHHHHHHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHH CS
                       Oxidored_q2   2 lllliallfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaiviga 78 
                                       +l+l+++lf+iG+ygv +++  +kv+i+le+++na+ l +v+++ +               ++ + +++L++i+ig+
  gi|518653008|ref|YP_008142528.1|   6 ILFLSMILFTIGIYGVTTSKVGMKVIISLEIVLNAALLDVVGVATLY-------------YSTSVVVFALFVIAIGV 69 
                                       6899***************************************9997.............99*************** PP

                                       HHHHHHHHHHHHHHHHSSS-BCCG- CS
                       Oxidored_q2  79 aetavgLallvrlyreygtddvqel 103
                                        e  vg+a++  ++++yg+++++ l
  gi|518653008|ref|YP_008142528.1|  70 IESTVGIAIFTLISKKYGKINISLL 94 
                                       *********************9866 PP

>> DUF5090  Domain of unknown function (DUF5090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3  15.2   0.00094       8.4      52     140 ..       2      86 ..       1      94 [. 0.75

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.00094
                           DUF5090  52 diikitlllkavllipiyllviaengnkldflksksriifltlikivlsilvdlvvyfselsslfkvflllkii..k 126
                                       +ii+i++l+ ++++i+iy +++ + g        +s  i+l++  ++l+++  +  y+s    +f  f+++ ++  +
  gi|518653008|ref|YP_008142528.1|   2 NIIYILFLSMILFTIGIYGVTTSKVGM----KVIISLEIVLNA--ALLDVVGVATLYYSTSVVVFALFVIAIGVieS 72 
                                       6999*****************554444....466777777777..89999999999888887777777666544347 PP

                           DUF5090 127 llitlivllalsis 140
                                       +++++i++l+++  
  gi|518653008|ref|YP_008142528.1|  73 TVGIAIFTLISKKY 86 
                                       88999999998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1144  (0.0638072); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 702.62
//
Query:       gi|518653009|ref|YP_008142529.1|  [L=627]
Description: hypothetical protein FACI_IFERC00001G1648 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-74  249.0  26.8    5.4e-74  249.0  26.8    2.6  3  Proton_antipo_M  Proton-conducting membrane transporter
    2.6e-09   37.0   8.4    2.6e-09   37.0   8.4    3.4  4  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
    1.8e-07   30.9   4.2    1.8e-07   30.9   4.2    4.2  4  NADH5_C          NADH dehydrogenase subunit 5 C-terminus
  ------ inclusion threshold ------
       0.13   12.7   0.2       0.13   12.7   0.2    5.6  6  DUF983           Protein of unknown function (DUF983)


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   4.1      0.16   7.4e+02     118     166 ..      37      87 ..      30     118 .. 0.74
   2 !  249.0  26.8   1.2e-77   5.4e-74       1     281 [.     126     420 ..     126     437 .. 0.91
   3 ?   -3.9   0.3       1.4   6.1e+03     245     259 ..     473     487 ..     462     517 .. 0.49

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.16
                   Proton_antipo_M 118 all.Aatlvkagvlllirlllllavssneisqll.lilaiismllgslval 166
                                       + l + +lv ++ l l+  +++++++++++++ + + ++ ++++++ +va 
  gi|518653009|ref|YP_008142529.1|  37 MVLgSLILVILAYLYLLHHNFIYSHYTWFYNIDVgIYISHLTVIMAMMVAF 87 
                                       445566777778888888888888777777765514577777777777765 PP

  == domain 2  score: 249.0 bits;  conditional E-value: 1.2e-77
                   Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg........tlefeels 69 
                                       +++L+l++l++E+v+l++ylLig+w+ kp++++A+ k+f++t++g+l++++g+ +l++            l++++l+
  gi|518653009|ref|YP_008142529.1| 126 SSNLVLFFLFWEIVGLCSYLLIGFWFFKPNAAAAAKKAFIVTRVGDLLFIIGMGVLFAKLVnivpagtsPLSIPYLI 202
                                       78****************************************************99976433555556689999999 PP

                   Proton_antipo_M  70 kal...elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirlllllavs 142
                                        ++     +++   l l+++l+l+g+++Ksaq+plh+Wlpd+ +e+Pt vsal+ Aat+v+agv+l++rl++l+  s
  gi|518653009|ref|YP_008142529.1| 203 DNAqsiASAIGPDVLALATILFLAGAVAKSAQFPLHVWLPDS-MEGPTTVSALIhAATMVTAGVYLVARLFPLFYYS 278
                                       999665555666678899999*********************.********************************99 PP

                   Proton_antipo_M 143 sneisqlllilaiismllgslvalaqtdiKrllAySsishlGymlialavatqygveaa...iihllthalfkallF 216
                                       + +  + ++i+++ ++++++++a++ +diKr++AyS+is lGym+ a+++++++g++++   + hl++ha+fkallF
  gi|518653009|ref|YP_008142529.1| 279 ASFSLYAVAIIGSFTAFYAGILAIVVNDIKRVIAYSTISELGYMMAAIGLGGVIGYSGVtfgMYHLVVHAVFKALLF 355
                                       9*************************************************99999999833355899********** PP

                   Proton_antipo_M 217 llagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavsli 281
                                       + ag +    ++ r+i+++ggL+ kmP++a+++l+++++la++Pptag++s + i+++a+++ ++
  gi|518653009|ref|YP_008142529.1| 356 MSAGVILVMLMELRNIKDMGGLFRKMPVTAILMLIGVVTLAAIPPTAGYFSRDQIISGAYEYFVN 420
                                       ***99999999***********************************************9987554 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 1.4
                   Proton_antipo_M 245 lalvllvlllslaGl 259
                                       + l++l l+l++   
  gi|518653009|ref|YP_008142529.1| 473 MVLAFLSLTLGIIQK 487
                                       333333333333322 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 !   37.0   8.4   5.8e-13   2.6e-09      10      55 ..      66     111 ..      58     114 .. 0.92
   2 ?   -3.0   0.1       1.7   7.8e+03      30      37 ..     249     256 ..     249     257 .. 0.91
   3 ?   -2.9   0.1       1.7   7.6e+03      26      47 ..     387     408 ..     380     418 .. 0.59
   4 ?   -2.4   0.2       1.2   5.4e+03      15      41 ..     608     620 ..     598     623 .. 0.51

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 5.8e-13
                   Proton_antipo_N  10 lsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfa 55 
                                       ++i++g++++ l+++m+++v f sl++ l+++ YM+dd++++ +f+
  gi|518653009|ref|YP_008142529.1|  66 YNIDVGIYISHLTVIMAMMVAFMSLMITLFAMFYMKDDPRKNIYFS 111
                                       589*****************************************98 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.7
                   Proton_antipo_N  30 tfvsllvh 37 
                                       t+vs+l+h
  gi|518653009|ref|YP_008142529.1| 249 TTVSALIH 256
                                       89*****9 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.7
                   Proton_antipo_N  26 llvvtfvsllvhlYSigYMadd 47 
                                       l+++ +v+l  +  + gY ++d
  gi|518653009|ref|YP_008142529.1| 387 LMLIGVVTLAAIPPTAGYFSRD 408
                                       3445555555555556666555 PP

  == domain 4  score: -2.4 bits;  conditional E-value: 1.2
                   Proton_antipo_N  15 gfllDklsalmllvvtfvsllvhlYSi 41 
                                       +               ++  ++ +++i
  gi|518653009|ref|YP_008142529.1| 608 A--------------FLIIGMIVIFAI 620
                                       3..............333344444443 PP

>> NADH5_C  NADH dehydrogenase subunit 5 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   7.7       0.4   1.8e+03      58     117 ..      68     126 ..      35     134 .. 0.81
   2 ?   -1.4   1.3      0.34   1.5e+03      39     108 ..     259     322 ..     242     331 .. 0.54
   3 ?   -2.5   1.2      0.72   3.2e+03      41      90 ..     356     406 ..     335     428 .. 0.60
   4 !   30.9   4.2   4.1e-11   1.8e-07       1     120 [.     440     562 ..     440     621 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.4
                           NADH5_C  58 itlplllKllallvtilGlllglelsklslkllkkslklnlssfssslwFlpslshrlls 117
                                       i + +++  l++++ ++ ++++l+++ +++ ++k  +  +  +fs +  F   + + ++s
  gi|518653009|ref|YP_008142529.1|  68 IDVGIYISHLTVIMAMMVAFMSLMITLFAMFYMKDDPR-KNIYFSETSLFIAGMLGLVVS 126
                                       55678999999999999999******999999999998.777788777777766665555 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.34
                           NADH5_C  39 gsiiaGsllswlifp.ktpvitlplllKllallvtilGlllglelsklslkllkkslklnlssfssslwFl 108
                                         ++aG++l   +fp        ++    +   v i+G ++++    l++  +  +     +s +s l+++
  gi|518653009|ref|YP_008142529.1| 259 TMVTAGVYLVARLFPlFY--YSASF----SLYAVAIIGSFTAFYAGILAIVVNDIKRV-IAYSTISELGYM 322
                                       457788888888888222..22233....33334455555554444444433333322.455555555555 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 0.72
                           NADH5_C  41 iiaGsllswlifpktpvitlplllKl.lallvtilGlllglelsklslkll 90 
                                       + aG++l +l+       +  l+ K+ ++ +++++G+++   +  ++ ++ 
  gi|518653009|ref|YP_008142529.1| 356 MSAGVILVMLMELRNIKDMGGLFRKMpVTAILMLIGVVTLAAIPPTAGYFS 406
                                       346666666666655555556666653445556666666655555555555 PP

  == domain 4  score: 30.9 bits;  conditional E-value: 4.1e-11
                           NADH5_C   1 YSlRliyyvllgsprfsslspineenptllnpilrLalgsiiaGsllswlifp...ktpvitlplllKllallvtil 74 
                                       Y +Rl ++v+ g+pr +     ++ + ++l p+++La++s++ G++   + +     + +   p+++ +++++ ++l
  gi|518653009|ref|YP_008142529.1| 440 YAFRLYFLVFAGKPRSKLAEKAHDPKLIYLVPLMVLAFLSLTLGIIQKPFYTFldsSVKIYSPPFIIAAIPVIFSFL 516
                                       99*******************************************9664433223366777778999999******* PP

                           NADH5_C  75 GlllglelsklslkllkkslklnlssfssslwFlpslshrllskls 120
                                       G+ +++ +   ++k   + +k+ l+  +    ++  l + ++s   
  gi|518653009|ref|YP_008142529.1| 517 GIAIAYAIYRYNVKGYTNITKNPLYKIIKNKFYFDWLYTEIISERI 562
                                       ************9988888888999999999999999999888654 PP

>> DUF983  Protein of unknown function (DUF983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   6.1         4   1.8e+04      34      70 ..      48      84 ..      33     101 .. 0.49
   2 ?   -0.7   1.1      0.43   1.9e+03      24      50 ..     245     271 ..     210     302 .. 0.67
   3 ?   -1.4   2.0      0.73   3.3e+03      31      71 ..     354     394 ..     346     405 .. 0.58
   4 ?   -2.5   0.1       1.6   7.4e+03      52      72 ..     464     484 ..     457     489 .. 0.57
   5 ?   -2.5   1.2       1.6     7e+03      36      59 ..     483     508 ..     467     531 .. 0.46
   6 ?   12.7   0.2   2.9e-05      0.13      15      44 ..     592     621 ..     589     624 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 4
                            DUF983 34 ivghlvvplallvevayepplwvhlliwlpltlllsl 70
                                        + l+   +++ + ++   + v ++i  + ++++++
  gi|518653009|ref|YP_008142529.1| 48 AYLYLLHHNFIYSHYTWFYNIDVGIYISHLTVIMAMM 84
                                      4444444444444444444444444443322222222 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.43
                            DUF983  24 ddgPayfvilivghlvvplallvevay 50 
                                         gP  +  li ++ +v++ +++ +++
  gi|518653009|ref|YP_008142529.1| 245 MEGPTTVSALIHAATMVTAGVYLVARL 271
                                       355666666666666666655554444 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.73
                            DUF983  31 vilivghlvvplallvevayepplwvhlliwlpltlllsll 71 
                                       +++ +g+++v+l+ l +++    l   ++++ +l+l+ ++ 
  gi|518653009|ref|YP_008142529.1| 354 LFMSAGVILVMLMELRNIKDMGGLFRKMPVTAILMLIGVVT 394
                                       45556666666666656555555666666666666644332 PP

  == domain 4  score: -2.5 bits;  conditional E-value: 1.6
                            DUF983  52 pplwvhlliwlpltlllslll 72 
                                       p+l   ++++++  l l+l++
  gi|518653009|ref|YP_008142529.1| 464 PKLIYLVPLMVLAFLSLTLGI 484
                                       555555555555555555554 PP

  == domain 5  score: -2.5 bits;  conditional E-value: 1.6
                            DUF983  36 ghlvvplallvevayep..plwvhll 59 
                                       g++  p+  +++ ++++  p+ ++++
  gi|518653009|ref|YP_008142529.1| 483 GIIQKPFYTFLDSSVKIysPPFIIAA 508
                                       44444444444433333222222222 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 2.9e-05
                            DUF983  15 gldlsharaddgPayfvilivghlvvplal 44 
                                       g+d+++++++d P y+ +li+g++v+++++
  gi|518653009|ref|YP_008142529.1| 592 GTDFRKIETGDIPFYVAFLIIGMIVIFAII 621
                                       89************************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (627 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1134  (0.0632495); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 3992.70
//
Query:       gi|518653010|ref|YP_008142530.1|  [L=498]
Description: hypothetical protein FACI_IFERC00001G1649 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-48  165.7  32.1    1.3e-48  165.7  32.1    2.6  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 ?   -7.7   8.8         1   1.8e+04     118     160 ..      60     101 ..       1     108 [. 0.47
   2 !  165.7  32.1   7.3e-53   1.3e-48       3     288 ..     129     428 ..     127     436 .. 0.88

  Alignments for each domain:
  == domain 1  score: -7.7 bits;  conditional E-value: 1
                   Proton_antipo_M 118 allAatlvkagvlllirlllllavssneisqlllilaiismll 160
                                       +ll +  ++ g+ + i ++l l  +s  + ++ l++ + s+l+
  gi|518653010|ref|YP_008142530.1|  60 VLLTS-FSTSGITININFSLGLTGFSDLLVIIALLITMFSILM 101
                                       23312.4444555555555555555555555555555555555 PP

  == domain 2  score: 165.7 bits;  conditional E-value: 7.3e-53
                   Proton_antipo_M   3 dLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltg......tlefeelskal. 72 
                                       + l +y+++E+vl+p++++ig +++  ++ ++slk+f++t +gsl+LLl+i+ l ++        t ++ +l++++ 
  gi|518653010|ref|YP_008142530.1| 129 NFLFFYIFWEVVLIPVFFIIGKYGTG-NKEKSSLKFFIYTHIGSLFLLLSIFTLSTYYFlktsifTFQIGDLMNVAf 204
                                       7899*******************998.999**********************8876654444577778888888866 PP

                   Proton_antipo_M  73 elglnslelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisq 148
                                         g+   ++ ++l+ +l+++l+K++ +plh+Wlpday  aP +++++l++ lv++g+++l+ +l ++a  + + + +
  gi|518653010|ref|YP_008142530.1| 205 IIGIPTYAFYFILFGFLLAFLIKLPTFPLHVWLPDAYYDAPYSGTIMLSGGLVAMGGYGLLGILYPIAgLFPKYLVY 281
                                       778888889999999*********************************999*****************788888899 PP

                   Proton_antipo_M 149 lllilaiismllgslvalaqtdiKrllAySsishlGymlialav....atqy...gveaaiihllthalfkallFll 218
                                       ++++l++is+++ ++ al+q d+Kr+ Ay s + + +++ia+++    +++     +++ + ++++h ++ al+F+ 
  gi|518653010|ref|YP_008142530.1| 282 FIIFLGLISIIYFAFSALFQPDLKRMAAYGSAAEMSFITIAFGTallsTGYVrtlDLAGGMYQIIAHTFVAALIFAS 358
                                       99**************************************998865532221111467889***************9 PP

                   Proton_antipo_M 219 agsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vv 288
                                         s++y+r+ t  i ++ggL    Pil+  llv++l+  GlP +agF+++f++  +a++   +  +++ + 
  gi|518653010|ref|YP_008142530.1| 359 L-SLVYKRTGTSRIYELGGLNRELPILSSFLLVGMLASLGLPSLAGFIGEFSVTISAFQSIGLYTLFIvLG 428
                                       9.888***********************************************9888887655554444244 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (498 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3279.72
//
Query:       gi|518653011|ref|YP_008142531.1|  [L=468]
Description: hypothetical protein FACI_IFERC00001G1650 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-50  172.2  36.7    1.3e-50  172.2  36.7    3.2  3  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 ?   -2.2   2.0       0.1   1.9e+03      30      62 ..      18      55 ..       5      82 .. 0.40
   2 ?   -4.1   4.1      0.39     7e+03     127     163 ..      74     110 ..      35     111 .. 0.68
   3 !  172.2  36.7   7.4e-55   1.3e-50       2     293 .]     112     412 ..     111     412 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.1
                   Proton_antipo_M 30 ksleAslklf...lltllgsliLLlgil.llynltg.t 62
                                       +l+A++k+    +l+ +  +i++++++ +l+++++ +
  gi|518653011|ref|YP_008142531.1| 18 ITLAAGIKTDnkkILGGFTFIIMIVAFFiILFQVKNyS 55
                                      44555555431113333333444444443334444322 PP

  == domain 2  score: -4.1 bits;  conditional E-value: 0.39
                   Proton_antipo_M 127 agvlllirlllllavssneisqlllilaiismllgsl 163
                                       ++++++i  ++  ++   ++++ +l+  ++sm+++++
  gi|518653011|ref|YP_008142531.1|  74 VSIMVIIIPSMNDIKKRFDVYYAILLFTALSMIIAAF 110
                                       3444444333333356777788888888888888875 PP

  == domain 3  score: 172.2 bits;  conditional E-value: 7.4e-55
                   Proton_antipo_M   2 ndLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglns 78 
                                       ++L+ l++++E+v++++y+L +++k+k ++leAslk+f+++ +g ++ ++gi+ +y  t t +++++ ++      +
  gi|518653011|ref|YP_008142531.1| 112 YNLIILFISFEGVSIATYILTAYNKTK-RNLEASLKYFMVSTVGTSFNIMGIAFFYLSTRTFNLNAITTI----DFN 183
                                       69**********************888.******************************************....666 PP

                   Proton_antipo_M  79 lelllllllllvgllvKsaqvplhlWlpdayveaPtpvsallAatlvkagvllli.rllllla.vssneisqlllil 153
                                         lll+l+++++g+ +K+a +p+++W  d y +aP +vsa+l +t  k+ +++++ ++l+l +   +n +  +++il
  gi|518653011|ref|YP_008142531.1| 184 RSLLLALVFITIGFGFKIAIFPMQQWAIDTYDGAPNSVSAFL-STGGKLVAYMILlKFLFLGFiPDYNYVFFFFAIL 259
                                       77889999**********************************.8899987777660444443355666666678899 PP

                   Proton_antipo_M 154 aiismllgslvalaqtdiKrllAySsishlGymlialavatqy...............gveaaiihllthalfkall 215
                                       ai++m +g+l+al ++++Kr+lAySsi++ Gym++ +a+ ++                ++++a+++ l+++++ka+ 
  gi|518653011|ref|YP_008142531.1| 260 AILTMTYGNLAALMENNLKRILAYSSIAQAGYMILVFALIGYSyypavlvskeifvkfAIASAMFYALAYIFMKAGP 336
                                       *********************************99887743321222233333333347899*************** PP

                   Proton_antipo_M 216 FllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavslillvla.vvasv 291
                                       F++++ +   +++   i +++gLakk + +al l+++llslaG+P+t gF++k  ++  ++  +l++l+++ ++ s+
  gi|518653011|ref|YP_008142531.1| 337 FIAMSLF---KNDKVMIGDIAGLAKKSRYTALFLAIMLLSLAGVPLTGGFIAKYFLFFTLIIGNLWWLAVIaIINSA 410
                                       ****888...66678999*******************************************9999999999899888 PP

                   Proton_antipo_M 292 lt 293
                                       ++
  gi|518653011|ref|YP_008142531.1| 411 IS 412
                                       75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 3170.72
//
Query:       gi|518653012|ref|YP_008142532.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G1651 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0084   16.1   0.0      0.012   15.6   0.0    1.2  1  Mesd            Chaperone for wingless signalling and traffic
  ------ inclusion threshold ------
      0.085   12.8   0.2      0.096   12.7   0.2    1.1  1  Merozoite_SPAM  Merozoite surface protein (SPAM)
        0.4   10.7   5.3       0.35   10.9   3.1    2.0  2  Proho_convert   Prohormone convertase enzyme


Domain annotation for each model (and alignments):
>> Mesd  Chaperone for wingless signalling and trafficking of LDL receptor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0     2e-06     0.012      78     126 ..       2      50 ..       1      58 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 2e-06
                                       HHHHHHHHHHHHHHHTT-SEEEEEESTTEEEEEESSSTTHHHHHHHHHT CS
                              Mesd  78 eteeitklWqtslfnaniqveryvvdsnraifmlkdGsqawevkdflve 126
                                       +te++ ++++tsl+n +++    +v+ nr i+  +   +a e  ++l++
  gi|518653012|ref|YP_008142532.1|   2 NTEDVIEIFKTSLVNGDVNNAYKIVERNRKIYTKRGLKTAEEFMQYLID 50 
                                       699****************9999**********999999********97 PP

>> Merozoite_SPAM  Merozoite surface protein (SPAM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   1.6e-05     0.096     128     172 ..      20      65 ..       3      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.6e-05
                    Merozoite_SPAM 128 ekaqnLIskeykdneks.kkaaetlvntlisLleekNelDstlknL 172
                                       ++a++++ ++ k + k   k+ae++++ li+ l+++   D+  +  
  gi|518653012|ref|YP_008142532.1|  20 NNAYKIVERNRKIYTKRgLKTAEEFMQYLIDALKGDKTPDDLYNIF 65 
                                       68999*********99989*****************9988866655 PP

>> Proho_convert  Prohormone convertase enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       0.5     3e+03      29      38 ..      44      53 ..      41      54 .. 0.79
   2 ?   10.9   3.1   5.8e-05      0.35       6      24 ..      59      77 ..      55      80 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.5
                     Proho_convert 29 LLQALfdmLd 38
                                       +Q L+d L+
  gi|518653012|ref|YP_008142532.1| 44 FMQYLIDALK 53
                                      6999999887 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 5.8e-05
                     Proho_convert  6 dslYsdYsDgFYrikpYrH 24
                                      d+lY+ +sD  Y+i pY H
  gi|518653012|ref|YP_008142532.1| 59 DDLYNIFSDEKYNIFPYIH 77
                                      99***************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); 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 0.26s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 844.53
//
Query:       gi|518653013|ref|YP_008142533.1|  [L=81]
Description: hypothetical protein FACI_IFERC00001G1652 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); 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: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 618.37
//
Query:       gi|518653014|ref|YP_008142534.1|  [L=111]
Description: hypothetical protein FACI_IFERC00001G1653 [Ferroplasma acidarmanus fer1]
Scores for complete 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-45  151.5   1.9    9.3e-45  151.4   1.9    1.0  1  TA0956           Thermoplasma acidophilum protein TA0956
    0.00032   20.9   0.1    0.00043   20.5   0.1    1.2  1  Acetyltransf_19  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.51   10.1   4.1        1.4    8.7   0.3    2.8  3  Scm3             Centromere protein Scm3


Domain annotation for each model (and alignments):
>> TA0956  Thermoplasma acidophilum protein TA0956
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.4   1.9   1.6e-48   9.3e-45       1     110 []       1     109 [.       1     109 [. 0.97

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 1.6e-48
                                       --EEEEEEEESTTS--EEEEEEHHHHHHHHHHHHHHTTS-.-CCHHHHHHHHH---S---TTSEEEEEEEEETTTTE CS
                            TA0956   1 mtlcamynitlkekhPsticvvlsklreslealadvldselieesleefieefartdeimPedktvGfviinsdkkv 77 
                                       m++c+myn++++e+hPsticv  sk+++s+e l++vl+s+l +esleefie +artdeimPedkt+Gfviin++kkv
  gi|518653014|ref|YP_008142534.1|   1 MVTCVMYNLKMSETHPSTICVLASKFEDSFEDLIEVLTSPLPDESLEEFIESYARTDEIMPEDKTIGFVIINKEKKV 77 
                                       99*************************************************************************** PP

                                       EEEEE-S--CCHHHHHHHHHHHHHCCS-EEEEE CS
                            TA0956  78 lslsfselkeelkksikeiaekfkkkGykveid 110
                                        sl fse   +  k++ ei+ek+k++Gyk+e++
  gi|518653014|ref|YP_008142534.1|  78 ASLNFSEKYFDQ-KKLDEILEKYKNMGYKTEVE 109
                                       ******988775.679**************986 PP

>> Acetyltransf_19  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.1   7.2e-08   0.00043       6      77 ..      27      98 ..      23     106 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 7.2e-08
                                      HHHHHHHHHC-SS--.-HHHHTCHHH.SEEEEEEETTEEEEEEEE-TTSEEEEEEE-CCCHHHHHHHHHHHHTT CS
                   Acetyltransf_19  6 eelrkaYlkslsapl.Dgmweeiilk.skfykieendkliGyfcvndeglLlqfylkeehlklaeeiFseiiee 77
                                      e+  ++ ++ l++pl D+ +ee+i++ ++  +i+ +dk+iG++++n+e+++ ++  +e++++++   + ei+e+
  gi|518653014|ref|YP_008142534.1| 27 EDSFEDLIEVLTSPLpDESLEEFIESyARTDEIMPEDKTIGFVIINKEKKVASLNFSEKYFDQK--KLDEILEK 98
                                      6677888888899887999999998659999*****************************9865..45666665 PP

>> Scm3  Centromere protein Scm3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0       0.1   6.2e+02      21      36 ..      24      35 ..      21      41 .. 0.58
   2 ?    0.6   0.1     0.082   4.9e+02      15      28 ..      45      57 ..      43      62 .. 0.77
   3 ?    8.7   0.3   0.00023       1.4      12      26 ..      82     102 ..      71     108 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.1
                                      HHHHSG..GGSS--B- CS
                              Scm3 21 eKYeridfedqgDEID 36
                                      +K+e+  f    D I+
  gi|518653014|ref|YP_008142534.1| 24 SKFED-SF---EDLIE 35
                                      45555.55...44444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.082
                                      HHHHHHHHHHSG.. CS
                              Scm3 15 rwesifeKYeridf 28
                                      ++e+++e Y r  +
  gi|518653014|ref|YP_008142534.1| 45 SLEEFIESYART-D 57
                                      578999***994.3 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00023
                                       H......HHHHHHHHHHHHSG CS
                              Scm3  12 l......kkrwesifeKYeri 26 
                                       +      +k++++i+eKY+++
  gi|518653014|ref|YP_008142534.1|  82 FsekyfdQKKLDEILEKYKNM 102
                                       44444789***********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.36u 0.27s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 842.50
//
Query:       gi|518653015|ref|YP_008142535.1|  [L=156]
Description: AsnC family transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   38.8   0.1    1.1e-09   38.1   0.1    1.3  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.7e-09   36.4   1.2    4.2e-09   35.8   1.2    1.3  1  HTH_24          Winged helix-turn-helix DNA-binding
    2.7e-08   33.5   0.0    4.4e-08   32.8   0.0    1.3  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    5.9e-05   22.9   0.0    0.00012   21.9   0.0    1.5  1  TrmB            Sugar-specific transcriptional regulator TrmB
    7.5e-05   22.6   0.4    0.00016   21.5   0.1    1.7  2  HTH_11          HTH domain
     0.0003   20.7   1.1     0.0011   18.9   1.1    1.9  1  DUF977          Bacterial protein of unknown function (DUF977
    0.00035   20.5   0.3    0.00072   19.5   0.3    1.5  1  HTH_Mga         M protein trans-acting positive regulator (MG
    0.00049   20.1   0.1    0.00085   19.4   0.1    1.4  1  HTH_9           RNA polymerase III subunit RPC82 helix-turn-h
    0.00055   19.7   0.1     0.0012   18.5   0.1    1.5  1  HTH_23          Homeodomain-like domain
    0.00067   19.4   0.1     0.0015   18.2   0.1    1.6  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.001   18.8   0.0     0.0017   18.1   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
      0.001   18.4   0.0     0.0018   17.6   0.0    1.4  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
     0.0016   18.5   0.3     0.0033   17.5   0.1    1.6  1  SpoIIID         Stage III sporulation protein D
     0.0022   17.4   1.9     0.0028   17.1   0.6    1.7  2  RepL            Firmicute plasmid replication protein (RepL)
     0.0031   17.2   0.1     0.0071   16.0   0.1    1.5  1  Sigma70_r4_2    Sigma-70, region 4
     0.0037   17.8   0.3      0.011   16.2   0.1    1.9  2  Mga             Mga helix-turn-helix domain
     0.0054   16.6   0.0     0.0086   15.9   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
     0.0055   17.1   0.1      0.024   15.1   0.1    1.9  2  HTH_26          Cro/C1-type HTH DNA-binding domain
     0.0066   16.6   0.0      0.014   15.5   0.0    1.5  1  HTH_28          Helix-turn-helix domain
     0.0073   15.8   0.3      0.019   14.5   0.3    1.7  1  GerE            Bacterial regulatory proteins, luxR family
     0.0092   15.9   0.0      0.014   15.3   0.0    1.2  1  MarR_2          MarR family
  ------ inclusion threshold ------
      0.017   15.0   0.0      0.033   14.1   0.0    1.5  1  HTH_Crp_2       Crp-like helix-turn-helix domain
      0.018   15.4   0.2      0.074   13.4   0.1    1.9  2  Rrf2            Transcriptional regulator
      0.019   14.7   0.0      0.039   13.8   0.0    1.5  1  HTH_10          HTH DNA binding domain
      0.036   14.0   0.0      0.077   13.0   0.0    1.5  1  HTH_6           Helix-turn-helix domain, rpiR family
      0.047   13.6   0.1      0.093   12.7   0.1    1.5  1  MarR            MarR family
      0.065   13.3   0.1        0.1   12.6   0.1    1.5  1  DUF2089         Protein of unknown function (DUF2089)
      0.082   13.6   0.2       0.51   11.0   0.0    2.0  2  RPA_C           Replication protein A C terminal
      0.083   12.4   0.1       0.13   11.8   0.1    1.4  1  Sigma70_r4      Sigma-70, region 4
       0.13   12.4   1.2       0.26   11.4   0.4    1.9  1  HTH_7           Helix-turn-helix domain of resolvase


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 !   38.1   0.1   1.9e-12   1.1e-09      13      74 ..      86     146 ..      77     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.9e-12
                                       HHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg  13 leefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                        e+++++l ++ eV ++ ++tG+yd++l+ ++++ e+l ++l + ++ + g+++  t+i+++
  gi|518653015|ref|YP_008142535.1|  86 SETIARKLMKINEVYSVDMITGEYDLILRGYSKNQEDLYNVLTK-IQFVAGIEHLFTNIIIQ 146
                                       6899*************************************988.**************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 !   35.8   1.2   7.1e-12   4.2e-09       2      48 .]      11      57 ..      10      57 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 7.1e-12
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      +++d+ I++ L kn ri+ re+A ++g+S +tv++ +  + e G+Ik
  gi|518653015|ref|YP_008142535.1| 11 SKLDKTIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLERGIIK 57
                                      5789*****************************************97 PP

>> HTH_AsnC-type  AsnC-type helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   7.4e-11   4.4e-08       3      38 ..      12      47 ..      10      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 7.4e-11
                     HTH_AsnC-type  3 eiDrkILeaLqedaRisyaeLAervGlSestvlrRv 38
                                      ++D+ I++ L ++ Ri+++e+A+++G+Se+tv + +
  gi|518653015|ref|YP_008142535.1| 12 KLDKTIIKMLIKNTRITVREIAAQTGISEPTVKKKI 47
                                      79******************************9866 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   2.1e-07   0.00012       4      54 ..       8      58 ..       6      72 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2.1e-07
                                      CHHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEE CS
                              TrmB  4 lGLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVer 54
                                      + +s+ +  + + L+k+ + t++eia ++g+++++v + +  ++++G+++ 
  gi|518653015|ref|YP_008142535.1|  8 YEISKLDKTIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLERGIIKQ 58
                                      7899999999999**********************************9986 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.1   2.7e-07   0.00016       3      43 ..      15      54 ..      14      66 .. 0.88
   2 ?   -2.6   0.0       9.5   5.7e+03      19      25 ..      87      93 ..      82      99 .. 0.59

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.7e-07
                            HTH_11  3 lqilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg 43
                                      ++i+++L++++  i+  e+A ++++S+ tv + I  + e g
  gi|518653015|ref|YP_008142535.1| 15 KTIIKMLIKNTR-ITVREIAAQTGISEPTVKKKITGMLERG 54
                                      58*****99998.*******************997665555 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 9.5
                            HTH_11 19 eeLAeeL 25
                                      e++A++L
  gi|518653015|ref|YP_008142535.1| 87 ETIARKL 93
                                      4555554 PP

>> DUF977  Bacterial protein of unknown function (DUF977)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   1.1   1.8e-06    0.0011      12      59 ..      12      58 ..       5     139 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.8e-06
                            DUF977 12 elkeriiGlvkkneritisdleritGvgrtsvrkylvdvlerGdlirp 59
                                      +l + ii ++ kn rit+ ++ + tG+   +v+k +  +lerG  i++
  gi|518653015|ref|YP_008142535.1| 12 KLDKTIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLERGI-IKQ 58
                                      577899************************************94.444 PP

>> HTH_Mga  M protein trans-acting positive regulator (MGA) HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.3   1.2e-06   0.00072       4      42 ..      11      48 ..       9      58 .. 0.92

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.2e-06
                           HTH_Mga  4 ikrklkLlelLteneksltldelakeLglseltlqsdis 42
                                       k + +++  L++ + ++t+ e+a ++g+se t+++ i+
  gi|518653015|ref|YP_008142535.1| 11 SKLDKTIIKMLIK-NTRITVREIAAQTGISEPTVKKKIT 48
                                      577899*******.*********************9886 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.1   1.4e-06   0.00085      17      54 ..      16      53 ..      12      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.4e-06
                                      HHHHHHHHHSSBEHHHHHHHHSSTHHHHHHHHHHHHHT CS
                             HTH_9 17 kVvetLlrkgrltlrelvkktkLsldqVkksLvvLiqh 54
                                      +++++L++++r t+re++ +t++s   Vkk    ++ +
  gi|518653015|ref|YP_008142535.1| 16 TIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLER 53
                                      89***************************977666555 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.1e-06    0.0012      10      35 ..      17      44 ..      15      47 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-06
                            HTH_23 10 illllae..GlsvreIAreLgvsrrTvy 35
                                      i+++l +  +++vreIA++ g+s+ Tv 
  gi|518653015|ref|YP_008142535.1| 17 IIKMLIKntRITVREIAAQTGISEPTVK 44
                                      899999999*****************96 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.1   2.5e-06    0.0015       3      45 ..      15      57 ..      14      61 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.5e-06
                          HTH_DeoR  3 eqilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      + i+++l + + ++v e++++ g+Se T+ + ++ + e g+++
  gi|518653015|ref|YP_008142535.1| 15 KTIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLERGIIK 57
                                      67***************************99998888888875 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 !   18.1   0.0   2.8e-06    0.0017       9      50 ..      18      58 ..      16      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
                                      HCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE. CS
                          HTH_IclR  9 LdalaeapqeltlselArrtglpkStvhRlLqtLvelGyveq 50
                                      +++l + ++  t++e+A++tg++ +tv   +  + e+G+++q
  gi|518653015|ref|YP_008142535.1| 18 IKMLIKNTR-ITVREIAAQTGISEPTVKKKITGMLERGIIKQ 58
                                      556666666.79**************************9998 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 !   17.6   0.0   3.1e-06    0.0018      17      45 ..      14      44 ..      12      48 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 3.1e-06
                      HTH_Tnp_ISL3 17 eayilellles..rsvkavArqlgvSwtTVw 45
                                      +  i+++l+++  ++v+++A+q+g+S+ TV+
  gi|518653015|ref|YP_008142535.1| 14 DKTIIKMLIKNtrITVREIAAQTGISEPTVK 44
                                      5678888888889*****************8 PP

>> SpoIIID  Stage III sporulation protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.5e-06    0.0033      12      45 ..      19      52 ..       8      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.5e-06
                           SpoIIID 12 akyiveskatvRkaakvfgvskstvhkDvterLk 45
                                         i +++ tvR++a + g+s  tv k +t  L+
  gi|518653015|ref|YP_008142535.1| 19 KMLIKNTRITVREIAAQTGISEPTVKKKITGMLE 52
                                      45677899**********************9987 PP

>> RepL  Firmicute plasmid replication protein (RepL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.6   4.7e-06    0.0028      71     109 ..      24      60 ..       6      67 .. 0.81
   2 ?   -0.9   0.0       1.6   9.4e+02     116     132 ..     108     124 ..      59     132 .. 0.59

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 4.7e-06
                              RepL  71 nntliatnRelaeetgislktvsetlkileeanilkkka 109
                                       n t  +t+Re+a +tgis  tv++ +  + e +i+k+ +
  gi|518653015|ref|YP_008142535.1|  24 N-TR-ITVREIAAQTGISEPTVKKKITGMLERGIIKQFT 60 
                                       3.33.499****************************977 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.6
                              RepL 116 nPdllfkGddkkrlnlL 132
                                         dl+++G  k++  l 
  gi|518653015|ref|YP_008142535.1| 108 EYDLILRGYSKNQEDLY 124
                                       24677777777776554 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.2e-05    0.0071      28      47 ..      28      47 ..      26      48 .. 0.91

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.2e-05
                                      -HHHHHHHHT--HHHHHHHH CS
                      Sigma70_r4_2 28 sykEIAellgisegtVksrl 47
                                      + +EIA+++gise tVk+++
  gi|518653015|ref|YP_008142535.1| 28 TVREIAAQTGISEPTVKKKI 47
                                      679**************987 PP

>> Mga  Mga helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   1.9e-05     0.011      16      65 ..      12      63 ..       1      73 [. 0.81
   2 ?   -1.2   0.0       5.4   3.2e+03      45      57 ..      87      99 ..      82     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.9e-05
                                      SHHHHHHHHHHHHSEEEHHHHHHHCT--HHHHHHHHHHHHHH..CHCCT-EE CS
                               Mga 16 slkyqllkflfeeeevsieelaqelyiSestlkrkikelnkl..Lkefdlel 65
                                       l+  ++k l+++ ++++ e+a++  iSe t+k+ki ++ ++  +k+f  ++
  gi|518653015|ref|YP_008142535.1| 12 KLDKTIIKMLIKNTRITVREIAAQTGISEPTVKKKITGMLERgiIKQFTCNI 63
                                      5566799*****************************9987643366666555 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 5.4
                                      HHHHHHHHHHHHH CS
                               Mga 45 stlkrkikelnkl 57
                                       t+ rk+ ++n++
  gi|518653015|ref|YP_008142535.1| 87 ETIARKLMKINEV 99
                                      6888999999875 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-05    0.0086       7      35 ..      17      46 ..      15      58 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-05
                                      HHHHHTTSS.EEHHHHHHHHTS-HHHHHHH CS
                             HTH_5  7 ILklLaege.lcvcelaeelglsqstvShH 35
                                      I+k+L ++   +v e+a+++g+s++tv   
  gi|518653015|ref|YP_008142535.1| 17 IIKMLIKNTrITVREIAAQTGISEPTVKKK 46
                                      99999996659***************9765 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 !   15.1   0.1   4.1e-05     0.024       2      37 ..      18      53 ..      17      55 .. 0.91
   2 ?   -0.9   0.0       3.8   2.3e+03      19      46 ..      69      96 ..      62     104 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 4.1e-05
                            HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkper 37
                                      +++l++  +it+ e a +tgis++t+++  +g  er
  gi|518653015|ref|YP_008142535.1| 18 IKMLIKNTRITVREIAAQTGISEPTVKKKITGMLER 53
                                      67899999********************99998765 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 3.8
                            HTH_26 19 gtgisaatlsrlvkgkpervsldtLdki 46
                                      g++is  t+ r+++ + +   +  L+ki
  gi|518653015|ref|YP_008142535.1| 69 GYNISFITMVRIFNATNSETIARKLMKI 96
                                      6778888888888877666666666666 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   2.4e-05     0.014       4      30 ..      16      44 ..      15      47 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2.4e-05
                            HTH_28  4 eiiklla.aGh.svreaArelgisrrtvy 30
                                      +iik l+ + + +vre+A++ gis+ tv+
  gi|518653015|ref|YP_008142535.1| 16 TIIKMLIkNTRiTVREIAAQTGISEPTVK 44
                                      69999994566****************97 PP

>> GerE  Bacterial regulatory proteins, luxR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.3   3.2e-05     0.019      19      43 ..      28      52 ..      11      53 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                                      -HHHHHHHHTS-HHHHHHHHHHHHH CS
                              GerE 19 snkeIAeelniSekTVkvhksnimk 43
                                      ++ eIA++ +iSe TVk +++ +++
  gi|518653015|ref|YP_008142535.1| 28 TVREIAAQTGISEPTVKKKITGMLE 52
                                      789**************99998876 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   2.3e-05     0.014      21      52 ..      26      57 ..      10      62 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.3e-05
                                      EEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEE CS
                            MarR_2 21 dltvgelarrlglsksavsrilkrLvaaGLve 52
                                      ++tv+e+a+ +g+s ++v + +  + ++G + 
  gi|518653015|ref|YP_008142535.1| 26 RITVREIAAQTGISEPTVKKKITGMLERGIIK 57
                                      49***************************996 PP

>> HTH_Crp_2  Crp-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.6e-05     0.033      20      52 ..      25      57 ..       3      66 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.6e-05
                                      EEHHHHHHHHHTTSSHHHHHHHHHHHHHTTSEE CS
                         HTH_Crp_2 20 lpltqeelAsmlGltretvsrilseLkreglis 52
                                       ++t +e+A+  G++  tv + ++ + ++g+i+
  gi|518653015|ref|YP_008142535.1| 25 TRITVREIAAQTGISEPTVKKKITGMLERGIIK 57
                                      589*****************************8 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   0.00012     0.074      22      56 ..      23      57 ..      15      60 .. 0.85
   2 ?   -0.8   0.0       3.4     2e+03      26      42 ..      84     101 ..      65     106 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 0.00012
                                      TCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 22 eeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      +++ ++++eia++++is++ ++k ++ + + g++k
  gi|518653015|ref|YP_008142535.1| 23 KNTRITVREIAAQTGISEPTVKKKITGMLERGIIK 57
                                      55669*****************9999999999997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 3.4
                                       B-HHHHHHHH.TS-HHHH CS
                              Rrf2  26 vsseeiaerq.nispsyl 42 
                                        +se+ia++  +i+++y 
  gi|518653015|ref|YP_008142535.1|  84 TNSETIARKLmKINEVYS 101
                                       467777775447777765 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   6.5e-05     0.039      23      44 ..      26      47 ..      24      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.5e-05
                            HTH_10 23 rvtlkeLAkelGIskstlsehL 44
                                      r+t++e+A + GIs++t+++ +
  gi|518653015|ref|YP_008142535.1| 26 RITVREIAAQTGISEPTVKKKI 47
                                      89***************98765 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00013     0.077      15      53 ..      11      45 ..       3      50 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00013
                                      -HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHH CS
                             HTH_6 15 tksekkiaeyilaspdkaielsikalAkaaavSeativr 53
                                      +k +k+i++++ ++    ++++++++A++ ++Se+t+ +
  gi|518653015|ref|YP_008142535.1| 11 SKLDKTIIKMLIKN----TRITVREIAAQTGISEPTVKK 45
                                      55566666666555....789***************976 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016     0.093      15      49 ..      24      58 ..      16      64 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                                      STTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                              MarR 15 qgplsvseLakklgvskstvtrvldrLekkGlieR 49
                                      +  ++v e+a + g+s +tv + ++ + ++G i+ 
  gi|518653015|ref|YP_008142535.1| 24 NTRITVREIAAQTGISEPTVKKKITGMLERGIIKQ 58
                                      567999**************************975 PP

>> DUF2089  Protein of unknown function (DUF2089)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   0.00017       0.1      35      75 ..      11      52 ..       5      95 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00017
                           DUF2089 35 skeqlefvelfika.rGnlkevekelgisYpTvrnrldeile 75
                                      sk +++ ++++ik+ r  ++e++ + gis pTv++++  +le
  gi|518653015|ref|YP_008142535.1| 11 SKLDKTIIKMLIKNtRITVREIAAQTGISEPTVKKKITGMLE 52
                                      5567788999999637799*****************998876 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 ?   11.0   0.0   0.00086      0.51      68      97 ..      27      56 ..       6      60 .. 0.86
   2 ?    0.4   0.0       1.7     1e+03      45      63 ..     114     131 ..      81     149 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00086
                                      EEHHHHHHHSTSXHHHHHHHHHHHHHTTSE CS
                             RPA_C 68 vhvdeiaqklrlsvndvkqavdeLsneGii 97
                                      + v+eia+++++s+ +vk+ +  +++ Gii
  gi|518653015|ref|YP_008142535.1| 27 ITVREIAAQTGISEPTVKKKITGMLERGII 56
                                      789*************************99 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.7
                                       .XSXHHHHHHHHHHHH.SX CS
                             RPA_C  45 kgltalaqqvlnlikqspe 63 
                                        g +++++ ++n++++ ++
  gi|518653015|ref|YP_008142535.1| 114 RGYSKNQEDLYNVLTK-IQ 131
                                       4788888888888887.54 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00022      0.13      11      42 ..      16      48 ..      10      53 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00022
                                      HHHHHHH.TTT--HHHHHHHHTS-HHHHHHHHH CS
                        Sigma70_r4 11 evlelrf.geglTleEIgerlgiSrerVrqiek 42
                                      +++++       T  EI+++ giS+ +V+  ++
  gi|518653015|ref|YP_008142535.1| 16 TIIKMLIkNTRITVREIAAQTGISEPTVKKKIT 48
                                      666666667788****************98665 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 ?   11.4   0.4   0.00043      0.26      16      42 ..      20      47 ..      11      49 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00043
                                      SSTTTT.--STTTSSSS---SSSS--SS CS
                             HTH_7 16 kLleeG.isiskIAkevnisRsTvYRyl 42
                                       L+++  i++++IA +++is  Tv+++ 
  gi|518653015|ref|YP_008142535.1| 20 MLIKNTrITVREIAAQTGISEPTVKKKI 47
                                      344555799****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (156 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       953  (0.0531541); expected 358.6 (0.02)
Passed bias filter:                      536  (0.0298957); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1142.26
//
Query:       gi|518653016|ref|YP_008142536.1|  [L=472]
Description: amino acid permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-28   98.4  56.2    5.1e-28   97.9  56.2    1.2  1  AA_permease    Amino acid permease
    3.1e-17   62.5  62.2      4e-17   62.2  62.2    1.1  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.9  56.2   5.7e-32   5.1e-28       1     464 [.      16     456 ..      16     470 .. 0.81

  Alignments for each domain:
  == domain 1  score: 97.9 bits;  conditional E-value: 5.7e-32
                       AA_permease   1 hvlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfv 77 
                                       +++++a+g++ ++g+f g+   +++  ++++ l+++++ + ++l+++s+++ + ++ ++ g+y y+ + lg ++G  
  gi|518653016|ref|YP_008142536.1|  16 GLVFQAMGQLSPIGIFGGSILGAAAFALGATPLSFIIGLLASLLAGNSIYQYSKKMASARGYYGYIGDGLGMSAGSL 92 
                                       5799************************************************************************* PP

                       AA_permease  78 iGlnylfswitvlal....eltaasiliqfwelvtdlpkawvt....gavflvvlliinlvgvkvygeaefilalik 146
                                        +++y ++++++l +     + + s++++f+ +  ++p  + +    ++++ +  + + + g+k++ + ++++++i 
  gi|518653016|ref|YP_008142536.1|  93 AAFLYILYEFANLLFilsyYVLTFSPTLGFV-SGLSIP-DY-YsylyIILISIPAFYVVYRGIKLSYKSQIVANMIQ 166
                                       ****998887665441111566777778887.444555.22.2245577777777889999**************99 PP

                       AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiag 223
                                       ii +i   i  i+++ + ++ ++     + ++++      ++g           f++++  ++++f+G+++++ +++
  gi|518653016|ref|YP_008142536.1| 167 IIFVITISIAIIVFSPKIGLLPF-----TAYHVG------IKG----------VFLGFITGSYLSFAGFGSIVPLGE 222
                                       99888777766666666666666.....666666......555..........6777777899************** PP

                       AA_permease 224 EvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaa 300
                                       E++  +ksi ka+l+++++ + +Y+l++++++++++ n+  +++ s+  +++f+i++k+  ++   ++i  +  ++ 
  gi|518653016|ref|YP_008142536.1| 223 EARAGRKSIGKAVLYIILIMGAIYLLGSYAMVAGWGINAMASFSNSI--YPGFIIVGKFGHLPTDIFFILNFFVVYP 297
                                       ********************************************999..55************98888888888888 PP

                       AA_permease 301 lssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllal.............llaslnlaapi 363
                                       l++ ++  ++ sR ly++akd+++P    + ++ +++P++a+ + ++i   +              + +++  +   
  gi|518653016|ref|YP_008142536.1| 298 LFVTMG--TALSRNLYAMAKDNMLPhGLSAIHNTNRSPHVALGYILVIFTGLSlvssiiffyaekgFFNGFFDD--- 369
                                       888776..789**************999999*********9876666554444347777777555555555555... PP

                       AA_permease 364 vfnfllaisaliglivwlliilsyl.rfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkk 439
                                        f f+ a+s++ +l++++++++s++ +fRk+     r ++ +++ +++l  +  +++++l i++ +++l+ +++++ 
  gi|518653016|ref|YP_008142536.1| 370 -FLFFAAVSTITTLVIHVMVNFSLYsKFRKE-----REYSAVKVSTHVLLPTISTIIIVLAIYYSVVSLTFPIAYGP 440
                                       .99********************99678887.....77888899999999999999999999999999996666222 PP

                       AA_permease 440 gpkdwgaasfaaaylivllfliilv 464
                                       +         +++y i+ l   i++
  gi|518653016|ref|YP_008142536.1| 441 II--------ILTYGIIALAY-IFI 456
                                       21........33333333333.333 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.2  62.2   4.4e-21     4e-17       7     418 ..      18     439 ..      12     456 .. 0.73

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 4.4e-21
                     AA_permease_2   7 falvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafls 80 
                                       ++ ++g +  +gif  +   +aa +  a+ l+++i+ l+ +la+  +y  +s ++ + +G y+y   + g  +++l+
  gi|518653016|ref|YP_008142536.1|  18 VFQAMGQLSPIGIFGGSilgAAAFALGATPLSFIIGLLASLLAGNSIYQ-YSKKMASARGYYGYIGDGLGMSAGSLA 93 
                                       34444444446666666553455588899999***99999888887776.9999**************987777666 PP

                     AA_permease_2  81 awfn...wfayvpvlasilsvaasyllnalgp.dlqgntwltyliaiaililvalinirgikesakiqnilgilkil 153
                                       a+++    fa ++++ s+ ++ +s  l+++++ ++   ++ +yl +i+i i  + + +rgik s k q +   + i+
  gi|518653016|ref|YP_008142536.1|  94 AFLYilyEFANLLFILSYYVLTFSPTLGFVSGlSI--PDYYSYLYIILISIPAFYVVYRGIKLSYKSQIVANMIQII 168
                                       66553337899999999999999999999976454..468999999************************9999995 PP

                     AA_permease_2 154 lpliiliilglitvdgggfsslstetdtffpn.gwpgvllglli.vlwsfdGfesaanvseevkk..kdvpkaifig 226
                                        ++ i i +++i++++++          +  + g +gv+lg+ + + +sf+Gf s++   ee++   k + ka  ++
  gi|518653016|ref|YP_008142536.1| 169 -FV-ITISIAIIVFSPKIGL-----LPFTAYHvGIKGVFLGFITgSYLSFAGFGSIVPLGEEARAgrKSIGKAVLYI 238
                                       .43.3334677777777776.....3233344699999888755489***************9977578******** PP

                     AA_permease_2 227 llivlvlyllvniaflgvvpddeianlsnlgsvaalffeavgg.k.vvaiivvilialsllgaintavigssrvlea 301
                                       +li + +yll + a++++ +++ +a+ sn+++++ + + ++g+ +   + i++++++  l+    t  ++ sr l+a
  gi|518653016|ref|YP_008142536.1| 239 ILIMGAIYLLGSYAMVAGWGINAMASFSNSIYPGFIIVGKFGHlPtDIFFILNFFVVYPLFV---TMGTALSRNLYA 312
                                       *******************************9999999999953246667777777777776...4455689***** PP

                     AA_permease_2 302 lardgvlPrffakvn.kfgspiraiiltaiv....slillllfllassaayn.......fllsvsslgliisyllli 366
                                       +a+d++lP+ ++ ++  + sp +a+ +++++    sl+ +++f +a    +n       f ++vs++  +++  ++ 
  gi|518653016|ref|YP_008142536.1| 313 MAKDNMLPHGLSAIHnTNRSPHVALGYILVIftglSLVSSIIFFYAEKGFFNgffddflFFAAVSTITTLVIHVMVN 389
                                       ********99999987888888887776665111144555555544433333555555599******9999999999 PP

                     AA_permease_2 367 igalilrkkrphlkrpgk.......ilvaiigalfllfllvalffppkgpatqssliyt 418
                                       +++    +k++++   +         + +ii++l + + +v l fp         ++y 
  gi|518653016|ref|YP_008142536.1| 390 FSLYSKFRKEREYSAVKVsthvllpTISTIIIVLAIYYSVVSLTFP---------IAYG 439
                                       9988888888888776662332222233333333333344444444.........3333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1002  (0.0558871); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); 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):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3277.68
//
Query:       gi|518653017|ref|YP_008142537.1|  [L=372]
Description: hypothetical protein FACI_IFERC00001G1656 [Ferroplasma acidarmanus fer1]
Scores for complete 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-38  132.1   0.0    3.5e-38  131.5   0.0    1.2  1  Aminotran_5      Aminotransferase class-V
    7.6e-05   22.2   0.0    0.00011   21.7   0.0    1.1  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
  ------ inclusion threshold ------
       0.15   11.0   0.1        0.2   10.6   0.1    1.2  1  SelA             L-seryl-tRNA selenium transferase


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 !  131.5   0.0   5.8e-42   3.5e-38      38     339 ..      49     344 ..      20     361 .. 0.88

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 5.8e-42
                                       HHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTE CS
                       Aminotran_5  38 gkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtga 114
                                        +  t++ve+are +a+li+a++ ++i  + + ++a+n ++ s+  ++++++eiv++++e   +  +    + + ga
  gi|518653017|ref|YP_008142537.1|  49 WNLWTEKVEKARELFAQLIHADK-KDIAALYSVSSALNSIMSSM--EFSNRNEIVTSDMEFPTTNFALYGYS-KFGA 121
                                       556799****************7.********************..5***************9998999998.67** PP

                                       EEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHT CS
                       Aminotran_5 115 kvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklg 191
                                       k+k i+  ++ ++d+d+++ ++n++t + +  hvs+  G  q+v +i+++a+++g ++ vD  q++g  +idvkk +
  gi|518653017|ref|YP_008142537.1| 122 KIKTIKS-SGNTIDIDNYNGAINKNTLMTTAIHVSSLNGFRQDVGKIASIAHENGSYIYVDDYQSLGGVNIDVKKSK 197
                                       *****99.8899***************************************************************** PP

                                       ESEEEEETTT.TTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEET...TEEEEHCTTGGGS.SS--HHHHHHHHHH CS
                       Aminotran_5 192 vDflafsghK.llgPtGiGvlyvrkellekleplllggemveevsl...eettfaeapskfeaGTpnvagiiglgaa 264
                                       +Dfla++  K llg +G+ +lyv +e+ e l+p+ +g    +++     e+  +ae  ++fe GT  +++i++  + 
  gi|518653017|ref|YP_008142537.1| 198 IDFLASGNLKwLLGVSGVAFLYVNPEIVETLKPANIGWFSQKNPFEfgaESLNYAEGARRFENGTWAIPSIYASIEG 274
                                       ************************************98877766543336667999*****************9999 PP

                                       HHHHHCHHHHHHHHHHHHHHHHHHHHHCTSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHT.TEEEEE.E- CS
                       Aminotran_5 265 leyleeigleaiekhekelaeyllerlkslpgvrlygpdkaerrasivsfnfkgvhaedvatlLdee.gIavrs.Gh 339
                                       ++ +    ++ iek++++l +++ + l+  +  ++  p   ++ a+i+++++k+  + d + +L+++ +I  ++ G 
  gi|518653017|ref|YP_008142537.1| 275 MKAI-LDYYDYIEKEDRKLFQHAIDSLERNGIPTI-TP---DEAANIIAIPMKN--PGDAEAMLKKKyKIITSArGD 344
                                       9999.555799*****************9999988.54...89999*9999974..777778888877888877665 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.8e-08   0.00011      12     150 ..      41     187 ..      31     195 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.8e-08
                                       HHHTSS..-SSSSHHHHHHHHHHHHHHT..-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHH...H CS
                   DegT_DnrJ_EryC1  12 evlksg..wltsgpeveeFEkafaaylg..vkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanav...l 81 
                                       +v++ g  w    ++ve+  + fa+ ++  +k   a+ s ++Al  +++ ++ ++++e+++  + F +t  a    +
  gi|518653017|ref|YP_008142537.1|  41 DVIELGnpWNLWTEKVEKARELFAQLIHadKKDIAALYSVSSALNSIMSSMEFSNRNEIVTSDMEFPTTNFALygyS 117
                                       5555443233337788888888999988656778899********************************98873334 PP

                                       HTT-EEEEE-B-TTTSSB-GGGCGGG--TTE...EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT CS
                   DegT_DnrJ_EryC1  82 elgakpvfvDvdpdtynidpaaieaaitert...kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlG 150
                                       + gak   +    +t  id ++ + ai+++t    aI +  l G   d+ ++  ia++ g ++  D  ++lG
  gi|518653017|ref|YP_008142537.1| 118 KFGAKIKTIKSSGNT--IDIDNYNGAINKNTlmtTAIHVSSLNGFRQDVGKIASIAHENGSYIYVDDYQSLG 187
                                       677777776666665..677788999999998889****************************999988888 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   0.1   3.4e-05       0.2     112     186 ..     120     194 ..     116     217 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 3.4e-05
                                       TBEEEEESBS.SB--HHHHHHT--TTEEEEEEE---SEEEEES-B---HHHHHHHHHHHT--EEEE.EES..-B-S- CS
                              SelA 112 GvkLvevGtt.nkthlkDyekainentalllkvhtsnyrieGftkevelaeLvelgkekglpvleD.lGs..Gllvd 184
                                       G+k++ + ++ n   + +y+ ain+nt +   +h s  ++ Gf ++v   +++++++e g  ++ D   s  G+ +d
  gi|518653017|ref|YP_008142537.1| 120 GAKIKTIKSSgNTIDIDNYNGAINKNTLMTTAIHVS--SLNGFRQDVG--KIASIAHENGSYIYVDdYQSlgGVNID 192
                                       666666654416678999*****************9..589***9986..578888888866654413322255555 PP

                                       GG CS
                              SelA 185 ls 186
                                       ++
  gi|518653017|ref|YP_008142537.1| 193 VK 194
                                       55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (372 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.49
# Mc/sec: 2284.50
//
Query:       gi|518653018|ref|YP_008142538.1|  [L=310]
Description: hypothetical protein FACI_IFERC00001G1657 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2236.72
//
Query:       gi|518653019|ref|YP_008142539.1|  [L=497]
Description: transposase-like protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.8e-13   48.6   4.3    2.1e-12   47.1   4.3    1.7  1  DDE_Tnp_1    Transposase DDE domain
  ------ inclusion threshold ------
       0.02   15.0   0.1      0.055   13.6   0.1    1.7  2  GSH-S_N      Prokaryotic glutathione synthetase, N-terminal d
      0.022   14.9   0.2      0.043   13.9   0.2    1.5  1  DUF809       Protein of unknown function (DUF809)
      0.051   11.8   0.1      0.091   11.0   0.1    1.3  1  DDE_Tnp_1_4  Transposase DDE domain group 1


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   4.3   4.8e-16   2.1e-12       8     214 .]     167     433 ..     162     433 .. 0.72

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 4.8e-16
                         DDE_Tnp_1   8 ivDattvrvpgtk.edarwgykggkykygyklhiavdtrsgl..ilsvvitpgnvhdskglkqlldelrprkgklvl 81 
                                        +Da+++++  +  + a++g++ +k++y ++++  + + +    +l  +  pgn hds++++ +++ ++  ++++++
  gi|518653019|ref|YP_008142539.1| 167 FFDASNMYTFMEEnSIAKKGHN-KKHRYDLNQVSYYIASTYDyiPLYGEAYPGNIHDSRTFENIVKNIP--EDSTLI 240
                                       5677777765555333444444.4445666555555444322334444445******************..****** PP

                         DDE_Tnp_1  82 aDaGYasaelldtleekgvdyiirl..kkntklyrk...........gaeskrrgrlrkhdrnkiltksqkrrnk.. 143
                                        D+GY s++++d +   +  yi +l  ++n+ + +            +  + +++r++  + +   t       +  
  gi|518653019|ref|YP_008142539.1| 241 FDRGYNSKDNIDMIS--NRRYIGALkqSDNHSIMEInvkedsyieliRNVYGKDHRIILYHSKSLET-------Rkk 308
                                       ***************..89999999553343333336766655555533333344444444444444.......334 PP

                         DDE_Tnp_1 144 ........................................................skkekgdvyyvtntnsellsa 164
                                                                                               + +  g +  + +tn  + +a
  gi|518653019|ref|YP_008142539.1| 309 nkfmkhlakvmvkakkiidsgdsdsmekariylesehlnetillpsleidgermeyRISMMGKN--AIFTNIIDKDA 383
                                       44555899999999999********************************999997744444444..55566666789 PP

                         DDE_Tnp_1 165 eevaelyrlRwqiErvFkwlkrk.fgldrlryrglnrveaqllllllalnl 214
                                       e ++ely++R+++E+ F+++  k   +  +++ ++++++ ++++ l+a+++
  gi|518653019|ref|YP_008142539.1| 384 ESIVELYKKRARVEHCFRTINAKgIAFPLNHW-TPQKIKVHMFFSLMAYLF 433
                                       **********************9666555555.9**************975 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.3     1e+04      39      70 ..     163     197 ..     149     209 .. 0.58
   2 ?   13.6   0.1   1.2e-05     0.055      10      66 ..     271     326 ..     268     347 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                           GSH-S_N  39 aadLslregkatararkvevkedked...wyelge 70 
                                       ++d+ ++++++++ +++ ++ ++ ++    y+l++
  gi|518653019|ref|YP_008142539.1| 163 TGDIFFDASNMYTFMEENSIAKKGHNkkhRYDLNQ 197
                                       55666666666666666666443322122455544 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                           GSH-S_N  10 lesikikkDttfalmleaqarghevfvleaadLslr.egkatararkvevkedkedwy 66 
                                       + +i++k+D+ + l++++  ++h++++++ ++L  r ++k + ++ kv vk+  ++++
  gi|518653019|ref|YP_008142539.1| 271 IMEINVKEDSYIELIRNVYGKDHRIILYHSKSLETRkKNKFMKHLAKVMVKA--KKII 326
                                       789********************************95677888889998844..3333 PP

>> DUF809  Protein of unknown function (DUF809)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.2   9.7e-06     0.043      15      80 ..     415     481 ..     400     488 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 9.7e-06
                            DUF809  15 ltpteckvsvisffllafllmahiwlswfsnnq..hclrtmrhleklkipyefqygwlgvkitiksnv 80 
                                        tp + kv +  f l+a+l++a i+     n +    + t+ +l+ ++i y ++   +  ki  ks++
  gi|518653019|ref|YP_008142539.1| 415 WTPQKIKVHM-FFSLMAYLFLALIYNEIHRNSKtaSLISTIDYLKDININYAIKGKIVTTKIECKSDI 481
                                       5777777764.47799*********98887766115689**************************987 PP

>> DDE_Tnp_1_4  Transposase DDE domain group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.1     2e-05     0.091     307     380 ..     372     444 ..     360     456 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2e-05
                       DDE_Tnp_1_4 307 rfvvTslaklspeelyeqlYcaRGemEnrIKeakldlaadrtsshsfaaNqlrlllsalAynLlaalrelalak 380
                                       + + T++ + ++e ++ +lY++R+++E ++++   +  a  ++  + ++ ++ +++s +Ay  la + + + ++
  gi|518653019|ref|YP_008142539.1| 372 NAIFTNIIDKDAESIV-ELYKKRARVEHCFRTINAKGIAFPLNHWTPQKIKVHMFFSLMAYLFLALIYNEIHRN 444
                                       5578999999******.***************998888888888888999999********9988876665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 3115.75
//
Query:       gi|518653020|ref|YP_008142540.1|  [L=539]
Description: hypothetical protein FACI_IFERC00001G1659 [Ferroplasma acidarmanus fer1]
Scores for complete 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-69  233.5   0.0    4.6e-69  233.0   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    1.1e-20   74.4   0.2      2e-20   73.5   0.2    1.5  1  AMP-binding_C  AMP-binding enzyme C-terminal domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.0   0.0   5.2e-73   4.6e-69      10     422 ..      29     426 ..      23     427 .. 0.84

  Alignments for each domain:
  == domain 1  score: 233.0 bits;  conditional E-value: 5.2e-73
                                       TSEEEEE....CCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS- CS
                       AMP-binding  10 dkvalvd....sgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptlt 82 
                                       dk a+++    +ge ++++Yr l+e  n++ ++Lr+ G++kg+ V i++   pe  v+++++lkaG +v+p  ++lt
  gi|518653020|ref|YP_008142540.1|  29 DKDAIIYinegTGEERRISYRKLYESYNQFINFLRAEGINKGSSVYIMAGSIPEQWVVMMGALKAGFIVIPTAANLT 105
                                       55555555599999*********************88**************************************** PP

                                       HHHHHHHHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS-TSCCCS-BTT CS
                       AMP-binding  83 aeelayiledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekaekpeeeeelkpd 159
                                       + el y +++  + v+i   d++ +ekl+ +    ea klvi    +++   +e +++e ++       e++el +d
  gi|518653020|ref|YP_008142540.1| 106 EYELNYRFSQDSPDVII--SDEASAEKLEHVLN-TEALKLVIGNR-EGWISFDEIYKMEINA-------EPAELGKD 171
                                       *****************..56666777766665.35666665444.4444444555555222.......455799** PP

                                       SEEEEEEE--SSSS-EEEEEEH.HHHHHHHHHHH.HHHCSCCTTT-EE.EESS-TTSCHHHHHHHHHHHHTT-EEEE CS
                       AMP-binding 160 dlayiiYTSGTTGkPKGVmlsh.rnlvanvaslk.letrfklkeddvv.lsilplahifglilelllallsGatvvl 233
                                       dl +  +TSGTTG+PK+V +s   + + +++++  +    +++++        p +  f++ ++ +++l++Gatv  
  gi|518653020|ref|YP_008142540.1| 172 DLFIKYFTSGTTGMPKAVRHSSiLYPIGQLSTVTaI----GIRPEYIHnNLSSPGWAKFAW-SSFFAPLCAGATVLS 243
                                       *****************9776655555554444332....333323331456999999**9.*************** PP

                                       -TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHHCCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHHHTCE CS
                       AMP-binding 234 lpkdaaldpklllelieklkvtviagvPrvleallesgalkaakkakdlsslrlvllggeplspellrffralfgee 310
                                       ++   +l++ + leli+++kv++++++P++++++++ ++l+      +l++l+ ++++gepl+ e++ ++++++g+ 
  gi|518653020|ref|YP_008142540.1| 244 IDYRGRLNSSRYLELIDRYKVNTFCAPPTAWRQFISLKNLN-----IELKHLKETVSAGEPLNGEVINKWKERYGTV 315
                                       ******99999***********************9976666.....4899*************************** PP

                                       EEEEEEEGGGSSECEECHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEET....TS-SEBTT-HH CS
                       AMP-binding 311 vlegYGlTEttgvvtvlpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgp....gvmkgYlkkpe 383
                                       + + YG++E t++v++l   ++++++gs Gkpl    + +vD++ +   ++ + G + v+      g++ gY  + e
  gi|518653020|ref|YP_008142540.1| 316 IRDFYGQSESTAMVANL--AGEEPVPGSMGKPLKSYNLVLVDDDMNLITHPLNIGNIAVGDYsgtyGLFLGYSDR-E 389
                                       *************9944..555569*******************6666689999****987755568******88.* PP

                                       HHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 384 ataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       + a++f+ + +++ TGD +++d++Gy++++ R++d+ik+
  gi|518653020|ref|YP_008142540.1| 390 KDASVFV-N-GYYLTGDKAYFDDNGYFYFISRTDDVIKT 426
                                       ******9.5.7***************************8 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.5   0.2   2.2e-24     2e-20       1      76 []     435     513 ..     435     513 .. 0.95

  Alignments for each domain:
  == domain 1  score: 73.5 bits;  conditional E-value: 2.2e-24
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---..-.--HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg..s.ealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evEsa+++ +aV e aV+G+pd +k+e ++afV+lkdg  + e++++ + + v++ l++y++p+ ++f+delpkt s
  gi|518653020|ref|YP_008142540.1| 435 EVESAIIKNEAVLESAVIGIPDSMKYEKIKAFVILKDGyvKsEETAKSIHSTVKTLLPAYKCPRVIEFTDELPKTIS 511
                                       8***********************************99642345********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|518653020|ref|YP_008142540.1| 512 GK 513
                                       *9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (539 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); 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: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.44
# Mc/sec: 3651.25
//
Query:       gi|518653021|ref|YP_008142541.1|  [L=578]
Description: hypothetical protein FACI_IFERC00001G1660 [Ferroplasma acidarmanus fer1]
Scores for complete 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  121.2  60.2    4.9e-35  121.2  60.2    2.2  2  AA_permease_2  Amino acid permease
    8.4e-29  100.5  70.8    8.4e-29  100.5  70.8    2.4  3  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 !  121.2  60.2   5.4e-39   4.9e-35       6     398 ..       3     417 ..       1     430 [. 0.78
   2 ?   -3.6  18.6      0.42   3.8e+03       1     149 [.     417     575 ..     417     577 .. 0.83

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 5.4e-39
                     AA_permease_2   6 afalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvafls 80 
                                        f+++++ ++gsg +     + a++gpa+il++++a + + ++++lv+ El++++p sg ++ + +   g++  f  
  gi|518653021|ref|YP_008142541.1|   3 IFLISFSGMVGSGWLLGVlaGPAYAGPASILTWVVAGVFF-IILALVFSELGTLFPYSGSLVRFNEFSHGPVSNFYL 78 
                                       699**********87765445667*******999988887.9***********************977777777888 PP

                     AA_permease_2  81 awfnwfayvpvlasilsvaasyllnalgpdlqgn.....twltyliaiaililvalinirgikesakiqnilgilki 152
                                       +w+++++++++ ++ ++++++++ + + + ++ +     t l +++a a+l l++++++ g++  +k + +++++k+
  gi|518653021|ref|YP_008142541.1|  79 GWAYMIGAIATPPVEAAALTGFISSYVPGIYN-SsvallTPLGVIVALALLGLFIIVQYAGVNVFGKSNAVMTWFKM 154
                                       99998888887777666666666555433332.2355559999********************************** PP

                     AA_permease_2 153 llpliiliilglitv.dgggfsslstetdtffpngwpgvllglli..vlwsfdGfesaanvseevkk..kdvpkaif 224
                                         +++++i +  +++  ++ f       + f+p g ++v++++    v++s+ Gf     ++ e k+  + vp++++
  gi|518653021|ref|YP_008142541.1| 155 AAIILTIIFVFAFIFhARNFFA----LSHGFLPYGPSSVFAAMVPagVIFSYEGFRQGLDYAGETKNpkRSVPLGMI 227
                                       8444444444444441445554....46679********999966569****************7776378****** PP

                     AA_permease_2 225 igllivlvlyllvniaflgvvpddei........anlsnlgsv......aalffeavggk.....vvaiivvilial 282
                                       +++l ++  y+ ++i+f+g+v+++                  +      a +ff a++++     ++++i+ i++a+
  gi|518653021|ref|YP_008142541.1| 228 SAMLAAMATYIMLQIVFIGAVNWKAAgvpvgdwsG-------LlsstwsANPFFYAFHSTdetllIGFSIFLIIVAV 297
                                       ***********************998666655541.......22334457888888874334356666777777777 PP

                     AA_permease_2 283 sllgaintavig.ssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslg 357
                                       ++  + +++++g s+r l+ +a+ +++P ff k++ +f +p+ ++++t+i+   +ll f      + ++l+ + s +
  gi|518653021|ref|YP_008142541.1| 298 VSSASTLGVYVGsSARSLYGMAKMNYIPAFFGKIHpRFRTPWISLVVTFIIGAMFLLPFP-----SWYALVGINSSF 369
                                       777788888776156*************************************55544443.....58********** PP

                     AA_permease_2 358 liisyllliigalilrkkrphlkrpgk.......ilvaiigalfllfl 398
                                        ++ yl++ i+   lrk+ p+ +rp k       +++a+++a +l+++
  gi|518653021|ref|YP_008142541.1| 370 TVFAYLAAGITNTSLRKTAPEMERPFKtpfltvmAPLAFVIASMLVYF 417
                                       **********************99665344433334444444443333 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.42
                     AA_permease_2   1 lsllsafalvigsv.igsgifvkn.........laasggpalilwvwiavligslavllvyaElssalprsgGiyvy 67 
                                       +s +s++al + +v  g++if  +         ++ s+   ++++++i+++ig ++ +l ++ +   +      + +
  gi|518653021|ref|YP_008142541.1| 417 FSGWSTVALLLLIVdGGLPIFLLSrygretfhiNMRSASLFSAIYWVIFIFIG-IIYALSLLPFEEYFALFSATILV 492
                                       56788888888888566999999999999999999999999************.79999999886666667777777 PP

                     AA_permease_2  68 tkaafgkkvaflsawfnwfayvpvlasilsvaasyllna.lgpdlqgntwltyliaiaililvalinirgikesaki 143
                                       t ++  +  + ++++    ++++v++si+  ++sy+ ++ ++   ++ +++++ i+++ + ++a+ + +++ +++ +
  gi|518653021|ref|YP_008142541.1| 493 TPYLLYRMSGRTASIHIRASIWIVVYSIILGIMSYYGSLgINAIPFPYDYIIMAIMSLTIYFIAINTGYHTDKLKEY 569
                                       77787799999999999999999999***99*****77644544557889999999998888888888999999999 PP

                     AA_permease_2 144 qnilgi 149
                                       q+++g+
  gi|518653021|ref|YP_008142541.1| 570 QSTGGV 575
                                       988776 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5  70.8   9.4e-33   8.4e-29       2     450 ..       3     492 ..       2     503 .. 0.88
   2 ?   -5.1   9.8      0.97   8.7e+03     238     282 ..     458     501 ..     450     532 .. 0.63
   3 ?   -5.6   7.6       1.4   1.2e+04     416     463 ..     512     557 ..     484     571 .. 0.67

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 9.4e-33
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       +++i+  g++G g ++g     + aGp+  +l +++agv++++ +l ++e+ t++p sg+   + + ++gp   f+ 
  gi|518653021|ref|YP_008142541.1|   3 IFLISFSGMVGSGWLLGVLAGPAYAGPA-SILTWVVAGVFFIILALVFSELGTLFPYSGSLVRFNEFSHGPVSNFYL 78 
                                       78999**********************5.56********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt.........gavflvvlliinlvgvkvygeaefilalik 146
                                       G+ y++  i++ ++e +a+  +i+    v+ +    v          ++ +l++++i++++gv v+g+   +++++k
  gi|518653021|ref|YP_008142541.1|  79 GWAYMIGAIATPPVEAAALTGFISSY--VPGIYNSSVAlltplgvivALALLGLFIIVQYAGVNVFGKSNAVMTWFK 153
                                       ***************99999999999..9999977777999**999999999************************* PP

                       AA_permease 147 iiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvf..vivvfaftGielvaii 221
                                       + aii +ii+ + +++ ++  ++    f  ++g+     lp g         +++++++  + v+f++ G+  +   
  gi|518653021|ref|YP_008142541.1| 154 MAAIILTIIFVFAFIFHAR--NF----FALSHGF-----LPYG--------PSSVFAAMvpAGVIFSYEGFRQGLDY 211
                                       ***********88888777..55....3344444.....5555........33444443125799************ PP

                       AA_permease 222 agEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa.......aspfvifikesgvsvlapl 291
                                       agE+k+P++s+P +++++++  +  Y+++ ++ +  v++++ g+  +  s+       a pf +++++++  +l  +
  gi|518653021|ref|YP_008142541.1| 212 AGETKNPKRSVPLGMISAMLAAMATYIMLQIVFIGAVNWKAAGVPVGDWSGllsstwsANPFFYAFHSTDETLLIGF 288
                                       ***************************99999999999999877666666677777777***********9999999 PP

                       AA_permease 292 inaviltaalssanssly...sasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllal............ 352
                                        +++i++a++ssa+ + +   s+ R ly +ak +++P +++k + + + P+ ++++++ii++++l            
  gi|518653021|ref|YP_008142541.1| 289 SIFLIIVAVVSSASTLGVyvgSSARSLYGMAKMNYIPaFFGKIHPRFRTPWISLVVTFIIGAMFLlpfpswyalvgi 365
                                       999999999999987543233667*************999999********************************** PP

                       AA_permease 353 .................................llaslnlaapivfnfllaisaliglivwlliilsylrfRkalky 396
                                                                        +l+ +++ a+++  +l+ +s+ ++++++lli    l   + + +
  gi|518653021|ref|YP_008142541.1| 366 nssftvfaylaagitntslrktapemerpfktpFLTVMAPLAFVIASMLVYFSGWSTVALLLLIVDGGL---PIFLL 439
                                       *********************************999999999999999999999999999999998888...67777 PP

                       AA_permease 397 qgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfa 450
                                       ++   e + + ++ ++l++ + ++++i+i +i+al  +l++ + ++ ++a+  +
  gi|518653021|ref|YP_008142541.1| 440 SRYGRETFHINMRSASLFSAIYWVIFIFIGIIYALS-LLPFEEYFALFSATILV 492
                                       777778899999999***999999999999999998.66666666555555554 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 0.97
                       AA_permease 238 qvviritifYvlsllligllvprndlgllndsasaaspfvifike 282
                                       ++++++++++++++++++ll    +  l+++++ +  p+ ++ ++
  gi|518653021|ref|YP_008142541.1| 458 SAIYWVIFIFIGIIYALSLLPFEEYFALFSATILV-TPYLLYRMS 501
                                       68899999999999999999888888888888866.444444332 PP

  == domain 3  score: -5.6 bits;  conditional E-value: 1.4
                       AA_permease 416 ilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliil 463
                                        +++++ +iil i+++y +l + ++p    + + + a++++ ++ i +
  gi|518653021|ref|YP_008142541.1| 512 SIWIVVYSIILGIMSYYGSLGINAIPFP--YDYIIMAIMSLTIYFIAI 557
                                       4677788888888888888887777744..444444444444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (578 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       974  (0.0543254); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.75u 0.30s 00:00:01.05 Elapsed: 00:00:00.48
# Mc/sec: 3658.04
//
Query:       gi|518653022|ref|YP_008142542.1|  [L=421]
Description: diaminopimelate decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-42  145.6   0.0    1.9e-42  145.3   0.0    1.1  1  Orn_Arg_deC_N    Pyridoxal-dependent decarboxylase, pyridoxal
    6.9e-20   71.1   0.0    7.4e-20   71.0   0.0    1.3  1  Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-termina


Domain annotation for each model (and alignments):
>> Orn_Arg_deC_N  Pyridoxal-dependent decarboxylase, pyridoxal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.3   0.0   2.2e-46   1.9e-42       2     247 .]      40     287 ..      39     287 .. 0.95

  Alignments for each domain:
  == domain 1  score: 145.3 bits;  conditional E-value: 2.2e-46
                                       HHHHHHHHHHHHHCT..CCEEEEEGGG---HHHHHHHHHTTEEEEESSHHHHHHHHHCTTTGGGEEEEESS--HHHH CS
                     Orn_Arg_deC_N   2 asierklkrwkkalp..rikvfYavKansdlavlellaelGlgldcaSkaElelvlaagvsperiifanpckqreel 76 
                                       a+++++++r+++a++  +ikv++avK+n ++ +++ + ++G+g+d+a  +E++l++  g   ++ii + ++ +  el
  gi|518653022|ref|YP_008142542.1|  40 ARVRENIRRIRDAFNgiNIKVHFAVKSNYNPYIVSQIIKEGTGIDAANYNEVKLAIMCGLGSRDIIATPNNLSGTEL 116
                                       68999**********99************************************************************ PP

                                       HHHHHCTHTEEEESSHHHHHHHHHHHCCEEEEEEEE-SCCSSSSTCCCSSSTTSSSSEEHCHHHHHHHHHHHHTTEE CS
                     Orn_Arg_deC_N  77 ryalekgvkvvtvdnveeleklaklapeakvllRiktdvsaatcelistggessKFGaaleeavealleaakeenlq 153
                                       r ++e+gv  +++d + ++  l+   pe  v+ Ri++++ +++ + i+tgg++ KFG+++++a+ a+ +a+ + +++
  gi|518653022|ref|YP_008142542.1| 117 RTIKEEGVA-INFDHEGQMGLLKGSLPE-TVSFRINPGIGKGEFPGITTGGKNVKFGISVDDAISAYSAAI-KAGVK 190
                                       ********9.**************9997.79*****************************77777766665.57999 PP

                                       EEEEE---BSSC-SCHHHHHHHHHHHHHHHHHH.HHT---SEEE--S-BS-HCSTTSSSSTHHHHHHHHHHHHHHHH CS
                     Orn_Arg_deC_N 154 lvGvsfHvGSgvsdleafvkavekalklfdela.elGvklkiLdvGGGfgveyeeeeeplkleeiaekirealeeaf 229
                                         G+++  GS v + e f +     +k+ + +    G++ +++d+GGGfgv y+++e++l++ + a  i++      
  gi|518653022|ref|YP_008142542.1| 191 HFGIHMMTGSNVLEPEFFNESSGLFFKIAETISdRTGIDFDFIDIGGGFGVPYTSDEHALDIGKTAGYISDNFRASN 267
                                       99******************************99************************************9998777 PP

                                       H..TSSS-EEEE--SHHHHG CS
                     Orn_Arg_deC_N 230 p..gdkevtiiaEpGRalva 247
                                       +   +k+ ++i+EpGR++va
  gi|518653022|ref|YP_008142542.1| 268 NrgYFKDSRLIIEPGRYIVA 287
                                       6778999***********98 PP

>> Orn_DAP_Arg_deC  Pyridoxal-dependent decarboxylase, C-terminal sheet domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.0   8.2e-24   7.4e-20       2      98 .]     284     376 ..      35     376 .. 0.81

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 8.2e-24
                                       EEEEGGEEEEEEEEEEEEETCEEEEEES--TTTS-HHHHCTT-S-EESBTT-SCEEC.EEEEEEEE-SSSSTT-EEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC   2 yvydeagvLvtrViavkesekkkfvivdaGmndllrpalygsfheipvkeeeaekeeeeeeevdvvGptCesgDvla 78 
                                       y++ ++ +L+++V+++k+s++ + + +da+mn+l+r  lyg+ h i ++   ++ e+++++++d+vG++Ce +D++a
  gi|518653022|ref|YP_008142542.1| 284 YIVADSAILLSKVTSIKHSDR-ELIGIDASMNTLIRIPLYGARHGILLS---GHGENTSSSRFDIVGQVCENTDYIA 356
                                       4444999**********9975.8***********************443...3334556789*************** PP

                                       EEEEEEE--TT-EEEESS-S CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                   Orn_DAP_Arg_deC  79 kdrelpelevGdllafedaG 98 
                                       kd ++pe++vGd++++ daG
  gi|518653022|ref|YP_008142542.1| 357 KDISIPEPAVGDIVVIADAG 376
                                       ******************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); 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: 0.59u 0.28s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 2653.69
//
Query:       gi|518653023|ref|YP_008142543.1|  [L=392]
Description: hypothetical protein FACI_IFERC00001G1662 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.8e-14   51.7   0.8    1.3e-13   51.1   0.8    1.2  1  DDE_Tnp_1  Transposase DDE domain
    1.9e-12   47.1   0.0    1.3e-10   41.1   0.0    2.4  1  DDE_5      DDE superfamily endonuclease
      2e-11   43.7   0.8    3.5e-11   42.9   0.8    1.3  1  DDE_Tnp_2  Archaeal putative transposase ISC1217


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.8   2.2e-17   1.3e-13       5     194 ..      90     301 ..      86     314 .. 0.76

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 2.2e-17
                         DDE_Tnp_1   5 evlivDattvrvpgtk.edarwgyk..ggkykygy.klhiavdtrsgl.ilsvvitpgnvhdskglkqlldelrpr. 75 
                                       +vl +D t ++  g++   a+w y+  +gk  yg+     +++++ g+ +ls+++   ++ dsk   q ++++++  
  gi|518653023|ref|YP_008142543.1|  90 PVLSLDDTILQRNGKHiDGAQWIYDhsQGKTVYGMqYTTSVISGNEGIfPLSMEL---KTDDSKIDLQ-INTIKKAm 162
                                       7899*********999999999777225556666654444555555548******...6666666666.66666666 PP

                         DDE_Tnp_1  76 ....kgklvlaDaGYasaelldtleekgvdyiirlkkntklyrk........................gaeskrrgr 124
                                           + ++v+ D++Y+s +l+++le++g dy++ +k+n ++ ++                        g++++ + +
  gi|518653023|ref|YP_008142543.1| 163 gaglRFSTVVFDSWYFSSKLVKFLESMGKDYVSEAKSNRTVCIDgkwirlrdyantldlksmksytvnGKTYFMKAI 239
                                       7799****************************************777777666666666666666555566666666 PP

                         DDE_Tnp_1 125 lrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlr 194
                                       +++  +  i++ + +rr          + +++tn+++ ++++++  y +Rw iE ++ +lk+  gl +l+
  gi|518653023|ref|YP_008142543.1| 240 TTRMKNAGIVKVIVSRRIN-------SLKFFVTNRTDWKVKTIIGKYLRRWDIEVFHEELKQ-DGLKHLY 301
                                       6666666666666666665.......8889************************99999998.4444444 PP

>> DDE_5  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.1   0.0   2.2e-14   1.3e-10       2     217 ..      20     206 ..      19     216 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.1 bits;  conditional E-value: 2.2e-14
                             DDE_5   2 llealtradrrrglllylrgllldggr.ksvepmaarlehdgshqalqrflsrspwddaklrrrlarlvlpllapea 77 
                                       +++ ++r+++r+ ++ ++ g  ++++    + +++ +    ++  +l rfl + p d   + ++ + l+   +  ++
  gi|518653023|ref|YP_008142543.1|  20 FRPLFGRRQFRQFCRYIVSGIASSTRSsAHLNGIFVEH---TNQSNLNRFLRNIPAD--GIFNISCSLINRNC--SG 89 
                                       66677777777766666666555555544444444444...5677777777655544..44455555555556..45 PP

                             DDE_5  78 avlaiDdTgfpkdGkasvgvarqycgalgkadncqvavslglatervsapldwrlylpeswaqdlsarrrragvpdd 154
                                       +vl +DdT +++ Gk++ g ++ y+++ gk++ + +  +     ++  +pl+++l  +   ++d             
  gi|518653023|ref|YP_008142543.1|  90 PVLSLDDTILQRNGKHIDGAQWIYDHSQGKTVYGMQYTTSVISGNEGIFPLSMEL--K---TDD------------- 148
                                       55*********************************99999999**********96..3...333............. PP

                             DDE_5 155 vtaktkpeialelldraraagvplqvvvaDagYgdaaalrqglrelglhyvvrvrsdralypp 217
                                           +k ++ ++ +++a+ ag++++ vv+D++Y + + l + l+++g +yv++ +s+r++ + 
  gi|518653023|ref|YP_008142543.1| 149 ----SKIDLQINTIKKAMGAGLRFSTVVFDSWYFS-SKLVKFLESMGKDYVSEAKSNRTVCID 206
                                       ....5888999**********************55.5566*******************9775 PP

>> DDE_Tnp_2  Archaeal putative transposase ISC1217
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.8   5.9e-15   3.5e-11     167     292 ..     149     299 ..     133     326 .. 0.77

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 5.9e-15
                         DDE_Tnp_2 167 tkiellleile.ilkeefnvaavvfdsWyvnskllk......gnvvgelksnarvve..............gerhvp 222
                                       +ki+l +++++ ++  +++ ++vvfdsWy++skl+k       + v+e ksn+ v                  ++++
  gi|518653023|ref|YP_008142543.1| 149 SKIDLQINTIKkAMGAGLRFSTVVFDSWYFSSKLVKflesmgKDYVSEAKSNRTVCIdgkwirlrdyantlDLKSMK 225
                                       59****99997257789*****************98555443478********997768899998888874223333 PP

                         DDE_Tnp_2 223 vaelPeGeylveyldtvik...llvlddykkdgrrylfstdlnd.tdediittWenrWdievlirelkalGled 292
                                          +    y++  + t +k   +  ++  +  + +++f t+  d     ii  +  rWdiev + elk  Gl++
  gi|518653023|ref|YP_008142543.1| 226 SYTVNGKTYFMKAITTRMKnagIVKVIVSRRINSLKFFVTNRTDwKVKTIIGKYLRRWDIEVFHEELKQDGLKH 299
                                       33444446888877766663334444556778899999999877256889*******************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      472  (0.0263261); 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: 00:00:00.39
# Mc/sec: 3017.96
//
Query:       gi|518653024|ref|YP_008142544.1|  [L=57]
Description: hypothetical protein FACI_IFERC00001G1663 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       327  (0.0182386); expected 358.6 (0.02)
Passed bias filter:                      309  (0.0172346); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 443.98
//
Query:       gi|518653025|ref|YP_008142545.1|  [L=66]
Description: hypothetical protein FACI_IFERC00001G1664 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-11   43.1   0.0    3.9e-11   42.9   0.0    1.0  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 !   42.9   0.0   2.2e-15   3.9e-11      22      76 ..      10      64 ..       3      65 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.2e-15
                                      --TTTT-------TTIIIIIHHHHHHHHHHHHHS...SEEEE-S-GGGSEEEEEE CS
                            DUF167 22 daegrealkvrvaappvdGkANkalikfLakalgvpksdveivsGeksreKvvri 76
                                       + ++++lk+  +ap +++kAN  ++k La   +v+  +++++sG+ksr+K++ i
  gi|518653025|ref|YP_008142545.1| 10 IESEGDRLKIYTSAPRENNKANYDIMKQLATYYNVEFYKIKLISGQKSRKKIFSI 64
                                      3467899*********************************************988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 513.36
//
Query:       gi|518653026|ref|YP_008142546.1|  [L=126]
Description: hypothetical protein FACI_IFERC00001G1665 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.8   0.0          8    6.7   0.0    2.2  2  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0    0.0014        25      28      45 ..      33      50 ..      24      58 .. 0.82
   2 ?    6.7   0.0   0.00045         8      14      53 ..      83     114 ..      80     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0014
                          DUF150_C 28 kftGkivevdeetitlev 45
                                       +tG+i +vd ++i+ ++
  gi|518653026|ref|YP_008142546.1| 33 SYTGIIRAVDSDSIIMDI 50
                                      68***********99776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00045
                          DUF150_C  14 lVkvklklpvegrkkftGkivevdeetitlevdgkkrkke 53 
                                       ++k+k+k    +  +f G+i+ +  ++ +++ +gk    +
  gi|518653026|ref|YP_008142546.1|  83 YIKIKTK----NDGEFAGEIETAFSNRMVIDSNGK----N 114
                                       6999999....*******************99999....4 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 965.95
//
Query:       gi|518653027|ref|YP_008142547.1|  [L=318]
Description: hypothetical protein FACI_IFERC00001G1666 [Ferroplasma acidarmanus fer1]
Scores for complete 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  107.1   0.2    2.6e-15   56.5   0.0    2.1  2  PLDc_2         PLD-like domain
  ------ inclusion threshold ------
       0.08   12.5   0.3         11    5.5   0.1    2.3  2  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1


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 !   56.5   0.0   2.9e-19   2.6e-15       1     131 [.      16     146 ..      16     148 .. 0.85
   2 !   48.9   0.1   6.3e-17   5.7e-13      10     133 .]     179     290 ..     172     290 .. 0.81

  Alignments for each domain:
  == domain 1  score: 56.5 bits;  conditional E-value: 2.9e-19
                            PLDc_2   1 liqliksAkksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfet 77 
                                       l++lik+A++ ++i +y +  ++eil+a+ +a kr+v+ r+++d  ++      + + +e+++l +++g++v+v   
  gi|518653027|ref|YP_008142547.1|  16 LVNLIKKARRFVYINSYLL-DEPEILKAISDAVKRKVDTRLMVDG-RPYGINGSDGTHAEIDNL-RKTGAKVKVAPE 89 
                                       6899***************.************************9.443333345678899999.999999999763 PP

                            PLDc_2  78 .....llgslHaKlylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFer 131
                                               + HaK+++  ++ + vG+ N+t++++++n+E   +++dk+++k l+ +F +
  gi|518653027|ref|YP_008142547.1|  90 rfekpN-VFDHAKYMVS-ERQAEVGTPNFTEAAFSSNREYFTITSDKKIIKSLKTIFLA 146
                                       343330.556***9999.68999*******************************99965 PP

  == domain 2  score: 48.9 bits;  conditional E-value: 6.3e-17
                            PLDc_2  10 ksidiatyyfvsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllgslHaKl 86 
                                       +++ i t  +  d+eil   + + ++g+kv+++++s++++      +    +k+l  ++gv+v+ + + +  +HaK+
  gi|518653027|ref|YP_008142547.1| 179 RKLLIETEEMGDDKEIL---KVLMDKGRKVKLIVPSSISS------TDIDDIKQL-KKHGVKVKYMPANKLYMHAKM 245
                                       55666666665555544...55899**********95443......445789999.********87544479****9 PP

                            PLDc_2  87 ylidgktvivGSsNltkrgldlnlElnvviedkelakeleeeFerlw 133
                                       +   gk  ++GS N+t+++l++n+E+++++++   +++l++ F ++w
  gi|518653027|ref|YP_008142547.1| 246 I--AGKKIFIGSENFTRSSLNRNRETGIILSGLLKTSRLKNTFASDW 290
                                       5..6899*************************************999 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.002        18     120     158 ..     106     144 ..      75     151 .. 0.87
   2 ?    5.5   0.1    0.0012        11      81     109 ..     217     246 ..     189     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.002
                                       -EEEEEESS-SS---SS-EEEEEEEE--HHHHHHHHHHH CS
                     PP_kinase_C_1 120 rryvhlgtGnynektaklYtDlslltadeelgedveklf 158
                                       +r + +gt n+ e       ++  +t+d+++++ ++++f
  gi|518653027|ref|YP_008142547.1| 106 ERQAEVGTPNFTEAAFSSNREYFTITSDKKIIKSLKTIF 144
                                       567889******************************999 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0012
                                       HHHHHHHHHHHT-EEEE-.-TT--B--EEE CS
                     PP_kinase_C_1  81 Niewakkleeagvkvvyg.vvglkvhakll 109
                                        i+  k+l+++gvkv y   ++l +hak++
  gi|518653027|ref|YP_008142547.1| 217 DIDDIKQLKKHGVKVKYMpANKLYMHAKMI 246
                                       677789**********962678999**997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2227.06
//
Query:       gi|518653028|ref|YP_008142548.1|  [L=387]
Description: hypothetical protein FACI_IFERC00001G1667 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.8e-36  125.6   0.0    2.4e-36  125.2   0.0    1.1  1  SHMT             Serine hydroxymethyltransferase
    0.00021   20.7   0.0    0.00036   20.0   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0045   16.3   0.0     0.0056   16.0   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase


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 !  125.2   0.0     4e-40   2.4e-36       9     358 ..       6     336 ..       2     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 125.2 bits;  conditional E-value: 4e-40
                                       HHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTT CS
                              SHMT   9 aeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpak 85 
                                       a ii++  + ++++++l asen+ s+ + +al s +  +y+        yGG+ + d++ +l +d + +lf+ +   
  gi|518653028|ref|YP_008142548.1|   6 ARIIDEYDKYRNSTLNLQASENVLSPDARKALSSDMASRYSLSIGDYNAYGGTVYFDRILDLLKDNTCRLFDSK--- 79 
                                       66777777888899************************************************************... PP

                                       EEEE---SSHHHHHHHHHHHHT-TT-EEEEESCTTTSTGGG.T-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHH CS
                              SHMT  86 wgvnvqplsGsqanlavytallepgdrilgldladGGhlth.Gakveskkisassklfesveykvdketglidydel 161
                                        + + +plsG  a      ++l +++++++++  dGG+  + G +++     + +  f  ++y+    +  ++yd +
  gi|518653028|ref|YP_008142548.1|  80 -YCDPRPLSGHVAAEMSLLSVLGKNKNVMAISEEDGGYPGYsGGHLDR----VLGYKFYEAPYS----NFELEYDLV 147
                                       .************************************96542444444....455555556664....4579***** PP

                                       HHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-EEEEE-GGGHHHHHTTS.S--GCCTSSEEEEESSSTT-S- CS
                              SHMT 162 ekkakefkPklivaGtsaysrlidyarlreiadevgayllvdmahiaGlvaagv.ipsPfeyadvvtttthktlrGp 237
                                       e+k k+ +   i+ G+s + + +d +r+ ei+++ g+ +l d +h+ Gl+a++   p+ ++y+++v   thkt+ Gp
  gi|518653028|ref|YP_008142548.1| 148 EEKIKANNIGTIILGQSMFIKPYDMKRISEICEKHGTKILYDASHVMGLLAGKAfQPDALKYSNIVYGSTHKTFFGP 224
                                       ***************************************************986279******************** PP

                                       S-EEEEEC-SEEEEETTTEEEEHHHHHHH.HHHHTTTT-SS--HHHHHHHHHHHHHCTSHHHHHHHHHHHHHHHHHH CS
                              SHMT 238 rgglillrkgvksvdktgkevleelekki.nsavfPglqGGPlnhviaakavalkealepefkvyqkqvlknakala 313
                                       +gg+il+              +e+++++i ++a+f ++    l   ia++++a++e l+   kvy+  v+kn+  l+
  gi|518653028|ref|YP_008142548.1| 225 QGGIILTD-------------EEDIYNQIeDNAIFNTMDNINL-SRIASLSIAVEEMLKF-GKVYAGSVVKNTANLS 286
                                       *******9.............5788888834799999987766.579*******998865.5*************** PP

                                       HHHHHTT-EEG..GGS-SSSEEEEE...GGGGTS-HHHHHHHHHHTTEE- CS
                              SHMT 314 ealkekgyklv..sgGtdnhlvlvd...lrekgldGkraekvlekvnita 358
                                       + l e+g+ l+  s+ +++h +l+d   l+ kg+d ++  + lek  i +
  gi|518653028|ref|YP_008142548.1| 287 HSLIENGFGLLpgSENSETHQILIDpeyLKGKGFDYHSFSTQLEKNRIII 336
                                       **********855678999*****96667777777777777777766655 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 !   20.0   0.0     6e-08   0.00036      96     195 ..     139     241 ..     132     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6e-08
                                       TSSB-GGGCGGG--TTE..EEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETT...EECCCSSSEEEE CS
                   DegT_DnrJ_EryC1  96 tynidpaaieaaitert..kaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatykg...kkvGalgdaavf 167
                                        + ++ + +e++i  +     Il   ++ ++ dm+++ +i++khg k++ Da+h +G          + +++++   
  gi|518653028|ref|YP_008142548.1| 139 NFELEYDLVEEKIKANNigTIILGQSMFIKPYDMKRISEICEKHGTKILYDASHVMGLLAGKafqPDALKYSNIVYG 215
                                       577888999999999887778888999******************************75544222223334444444 PP

                                       E-BTTSSS-SSS-EEEEESTHHHHHHHH CS
                   DegT_DnrJ_EryC1 168 SFyptKnlttGeGGavvtndeelaekar 195
                                       S    K++    GG+++t++e++ ++++
  gi|518653028|ref|YP_008142548.1| 216 ST--HKTFFGPQGGIILTDEEDIYNQIE 241
                                       43..366777788888888888877765 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   9.4e-07    0.0056      21     220 ..      47     241 ..      33     352 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 9.4e-07
                                       S----C.CCT--HHHHHHHHHHHH....HTT-SEEEEES.-HHHHHHHHH.HHH--TTEEE.EEETT-HHHHSSTTH CS
                   Beta_elim_lyase  21 amlGde.sYgedktvnrLedavae....lfgkeaalfvp.qGtaAnsill.killqrgeev.ivtepahihfdetga 89 
                                       + +Gd  +Yg+   + r+ d +++    lf+ ++  + p +G  A +++l ++l + ++ + i +e++ +  +  g 
  gi|518653028|ref|YP_008142548.1|  47 LSIGDYnAYGGTVYFDRILDLLKDntcrLFDSKYCDPRPlSGHVAAEMSLlSVLGKNKNVMaISEEDGGYPGYSGGH 123
                                       56777437888666665444444333338888888887767876555555155554443331444556666666666 PP

                                       HHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEE CS
                   Beta_elim_lyase  90 iaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhl 166
                                       +  + g k+ +++ ++  +++ + +e++ik+     ++i+ i+l + + +      ++  ++++++i++k+g ++++
  gi|518653028|ref|YP_008142548.1| 124 LDRVLGYKFYEAPYSN-FELEYDLVEEKIKA-----NNIGTIILGQSMFI------KPYDMKRISEICEKHGTKILY 188
                                       6777888888888888.88999999999999.....69999999999986......5556788999*********** PP

                                       EETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH....HHH CS
                   Beta_elim_lyase 167 DgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddeledyla 220
                                       D+  ++    + ++   + ++y  +v  s  K  + + Gg+++++++++ + ++
  gi|518653028|ref|YP_008142548.1| 189 DASHVMGLL-AGKAFQPDALKYSNIVYGSTHKTFFGPQGGIILTDEEDIYNQIE 241
                                       ***999877.66666667889***********************9998844443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2761.71
//
Query:       gi|518653029|ref|YP_008142549.1|  [L=353]
Description: hypothetical protein FACI_IFERC00001G1668 [Ferroplasma acidarmanus fer1]
Scores for complete 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-34  115.7   5.2    1.6e-09   38.1   0.0    4.4  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 !   38.1   0.0   8.7e-14   1.6e-09       5      53 ..       1      48 [.       1      51 [. 0.94
   2 !   32.5   0.1   4.8e-12   8.5e-08      11      56 ..      67     111 ..      60     112 .. 0.90
   3 !   24.8   0.1   1.2e-09   2.2e-05       3      55 ..     124     175 ..     123     177 .. 0.89
   4 !   19.6   0.1   5.2e-08   0.00093      13      55 ..     209     251 ..     198     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 8.7e-14
                                      SBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS  5 mtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53
                                      m +d++t++ ++ ++ea+ +mre+++ +lPV+ +++k++G++t + +lr
  gi|518653029|ref|YP_008142549.1|  1 MKKDPITIDSNAKISEAISKMRENDIQQLPVL-SEEKYIGMLTYKNILR 48
                                      899******************988899*****.6778**********98 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 4.8e-12
                                       EEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
                               CBS  11 tvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                                        +++++++ ea++l++e+g++++PV    +klvGivt+ D++r l+
  gi|518653029|ref|YP_008142549.1|  67 RINENSNVMEAVKLLVESGLNSIPVFQ-KEKLVGIVTRLDIIRNLS 111
                                       689***********************6.666***********9886 PP

  == domain 3  score: 24.8 bits;  conditional E-value: 1.2e-09
                                       HHSBSSCEEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   3 dimtrdvvtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                       +imt dvvtv+ ++ +e   +++r  + +  +PV+ ++gkl Gi+ l+D+++ +
  gi|518653029|ref|YP_008142549.1| 124 EIMTADVVTVDANDEIEASSQKIRTLDeF-EIPVT-NNGKLAGILRLKDIINNI 175
                                       79*********************643347.*****.5**************876 PP

  == domain 4  score: 19.6 bits;  conditional E-value: 5.2e-08
                                       ETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  13 ppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       ++d t+ + + lm++++++ +P++ +d kl G+v  +D+l+ l
  gi|518653029|ref|YP_008142549.1| 209 TEDNTIVDTATLMVKNHLHIIPITGKDSKLTGVVGITDILNSL 251
                                       68999********99999888***99999***********865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       461  (0.0257125); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2596.00
//
Query:       gi|518653030|ref|YP_008142550.1|  [L=795]
Description: hypothetical protein FACI_IFERC00001G1669 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  257.3   0.2      2e-76  256.3   0.2    1.5  1  Peptidase_M1    Peptidase family M1 domain
    1.2e-36  126.6   4.2    7.4e-36  124.1   1.4    2.5  2  Peptidase_M1_N  Peptidase M1 N-terminal domain
    7.8e-24   84.8   0.3      2e-23   83.4   0.1    1.7  2  ERAP1_C         ERAP1-like C-terminal domain
  ------ inclusion threshold ------
        4.1    8.0   6.3        1.2    9.7   0.1    3.4  5  CCM2_C          Cerebral cavernous malformation protein, harm


Domain annotation for each model (and alignments):
>> Peptidase_M1  Peptidase family M1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.3   0.2   4.6e-80     2e-76       1     218 []     204     420 ..     204     420 .. 0.98

  Alignments for each domain:
  == domain 1  score: 256.3 bits;  conditional E-value: 4.6e-80
                                       HHHHHHHHHHHHHHHHHTS--SSSEEEEEEESSTTSSEEEETTEEEEEGGGC-SSTTTS-HHHHHHHHHHHHHHHHH CS
                      Peptidase_M1   1 yalevtkkllefleeyfkvpYplpkldlvalpdfsagAMEnwglityreelllvdpenssesdkrsvaeviaHElaH 77 
                                       y le++kk++ef+++yf+++Yplpk +l+ +p+f+agAMEnwg+it+re +l +  +++ +s k++v eviaHElaH
  gi|518653030|ref|YP_008142550.1| 204 YPLEIGKKAIEFYQDYFGIDYPLPKEHLISVPEFAAGAMENWGAITFREIYLNIS-SSTGSSVKKAVGEVIAHELAH 279
                                       679*************************************************999.67777899************* PP

                                       HHBTTTEEESSGGGGHHHHHHHHHHHHHHHHHHSCCCHCHHHHHHHCHHHHHHHHTSTTHHHSSGG-GSHHHHHHTS CS
                      Peptidase_M1  78 qWfGnlVtmkwWddlwLnEGfatyleylildklepewevseqllleeveealsedaldeshpitqevekpseidevF 154
                                       qWfG+lVtm+wWddlwLnE+fat+++y+ ++kle ++++ +++l++e+  al+ d+l +shpi++ev++p++i+++F
  gi|518653030|ref|YP_008142550.1| 280 QWFGDLVTMNWWDDLWLNESFATFMSYKAMNKLEVDYDMFADFLVSETAGALEGDSLVNSHPIEVEVKHPDDISQIF 356
                                       ***************************************************************************** PP

                                       SHHHHHHHHHHHHHHHHHCTHHHHHHHHHHHHHHCTTEEE-HHHHHHHHHHCCCSCHHTHHHHH CS
                      Peptidase_M1 155 dsiaYeKGasllrmlekllgeevFqkglksYlkefkyknaetedlwdaleealnkdisevmdtw 218
                                       d+i+Y KG s+lrm++++++++vF+kgl+ Yl++fkykna+ +dlw+ + ++++  +++vm+++
  gi|518653030|ref|YP_008142550.1| 357 DEISYGKGGSILRMINAFVTDDVFKKGLHLYLENFKYKNASGSDLWEFIAKVSDRPVRKVMESF 420
                                       *************************************************************986 PP

>> Peptidase_M1_N  Peptidase M1 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   1.4   1.6e-39   7.4e-36       4     186 .]       5     169 ..       2     169 .. 0.87
   2 ?    2.5   0.1     0.033   1.5e+02      86     111 ..     476     503 ..     438     513 .. 0.75

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.6e-39
                                       EEEEEEEEETTTTEEEEEEEEEEEESS-ECEEEEEESSEEEECEEEEECTTCTCEEEEEEEECTTTTCEEEEECCEE CS
                    Peptidase_M1_N   4 hYdldlkidlkektfkGsvtitlqlkeatseivldakdlkiksvslsaevksesvkidfkieqkdeelltiklkesl 80 
                                       +Y ldl+i+ k++t++ + ti+++ +  +++++l + +lkik+++++++ k+      fk+  k++e ++   +   
  gi|518653030|ref|YP_008142550.1|   5 NYILDLDINSKNYTYTCHETIKFNGN--EEKLILSSVNLKIKRIKVNNSIKN------FKEFIKNQEIVV---DG-I 69 
                                       577*****************999998..99***********88888855544......455566777333...44.3 PP

                                       ETTCEEEEEEEEEEE-BSSSSEEEEEEEEETSCEEEEEEEE-TTTTGGGTS-B--STTSEBEEEEEEEEETTSEEEE CS
                    Peptidase_M1_N  81 qqtskytLeieyegelndklaGlykstYtdkgekkvvvvTqfeatdARsafPCfDePsvKAtftisikapkeetalS 157
                                         t+  + ei+++ge+ ++l+G+y+ +     e+  +++Tqfe+t AR++fPC+D+Ps+KA f+i++++++   a+S
  gi|518653030|ref|YP_008142550.1|  70 I-TKDSIAEIDFSGEIPEELQGFYRAH----TEEGDMFTTQFESTGARRFFPCIDNPSYKAAFDITVRVDEGLEAIS 141
                                       4.688899*****************88....455579**************************************** PP

                                       SSECCCEEEETTCEEEEEEEEEESBEGGG CS
                    Peptidase_M1_N 158 nmpeeeseklengqkiteFeqtpkmstYL 186
                                       nmp+e++e+  +g+++ +F qtp+mstYL
  gi|518653030|ref|YP_008142550.1| 142 NMPVETKENV-DGKTVIKFMQTPVMSTYL 169
                                       *****66666.69***************9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.033
                                       EEEEEEEEEE-..BSSSSEEEEEEEEET CS
                    Peptidase_M1_N  86 ytLeieyegel..ndklaGlykstYtdk 111
                                        ++ei+ +g++  nd+ +G+y+  Y d+
  gi|518653030|ref|YP_008142550.1| 476 ESMEIDLQGFIklNDSETGFYRVLYSDS 503
                                       4566666666666********9999884 PP

>> ERAP1_C  ERAP1-like C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.37   1.7e+03     218     259 ..     371     411 ..     366     427 .. 0.73
   2 !   83.4   0.1   4.4e-27     2e-23       1     311 [.     485     781 ..     485     785 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.37
                                       HHHCTTT..S-GGGHHHHHHHH..HSTTHHHHHHHHHHHCHCC CS
                           ERAP1_C 218 lnfvlesdevrnqdlrallagl.annpegrellwefvkenwda 259
                                       +n  + +d+v +  l+  l+++ ++n+ g++ lwef+ +  d+
  gi|518653030|ref|YP_008142550.1| 371 INAFV-TDDVFKKGLHLYLENFkYKNASGSD-LWEFIAKVSDR 411
                                       44454.7889999999999999999888887.99999876666 PP

  == domain 2  score: 83.4 bits;  conditional E-value: 4.4e-27
                                       -EEESGGG-SSSEEEE-HHHHHHHHHHHHGGGS-HHHHHHHHHHHHHHHHTTSS-HHHHHHGGG.GGGG--SHHHHH CS
                           ERAP1_C   1 lvllNdddtGyyrVnYdeeslaalleqllskklspldRaglisdafalaragelsaadlldlllgylanEtdylvws 77 
                                       +++lNd  tG+yrV Y+++++++++++   ++l+  d +gl++d  a+  ag+l+++++l+ + +++ + +d+l+ +
  gi|518653030|ref|YP_008142550.1| 485 FIKLNDSETGFYRVLYSDSLYENIIKN--IAILDNKDIFGLLNDSHAFLMAGKLTLQEYLSRINKFM-ELNDSLIIR 558
                                       89************************5..578**********************************6.779****** PP

                                       HHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHHHHHHH.T.TTS-HHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           ERAP1_C  78 qalsqlatlksllsadplyaalkaflrklleplaeklgw.epgeshldaqlrslllsaacaagdpevveearklfka 153
                                       ++ + l +l+ +   dp ++++     + l+  ++ lg  +++e+ + ++ r ++ + +++ + +  ++e    f++
  gi|518653030|ref|YP_008142550.1| 559 EISNELFSLYLI---DPKNSEILGTNMEYLADKLKILGDkQKSENINISLARGIVANRFATINRG--YAEELSKFAG 630
                                       ******998644...4523333333333334444556643355999**********999999944..6666667999 PP

                                       HHCSTT-S-HHHHHHHHHHHH.HHS-HHHHHHHHHHHHC-SSHHHHHHHHHHHCC-S-HHHHHHHHHHCTTT..S-G CS
                           ERAP1_C 154 wlegddlippdlrwavycala.anggeaewdallerykdtsapsekeaalralaatpdpellerllnfvlesdevrn 229
                                        le+   ++pd+r av+++ a  + + +    +l ++   ++ + k + ++a+a  +  +  +++ + ++ + +++ 
  gi|518653030|ref|YP_008142550.1| 631 SLEQ---VDPDMRLAVLTSYAiVHNDSEKMLDMLSKF--KQD-EDKVKTIQAMAMLTGDNNFNAVEKAIS-ERKIKA 700
                                       9986...**********99862443333333344444..344.77*******************888886.889**9 PP

                                       GGHHHHHHHH.HSTTHHHHHHHHHHHCHCCHHHHTSSTSCHHHHHHHHHTT--SHHHHHHHHHHHCHTT--GGGHHH CS
                           ERAP1_C 230 qdlrallaglannpegrellwefvkenwdalakrwsggeildrivkgllpgftseeelaeieaffadkdtpglrrtl 306
                                       qd+       a np + e   + +++  ++++++++g+ + +r++++++p     ++ +eie  +a+ + ++ +r++
  gi|518653030|ref|YP_008142550.1| 701 QDSLRYYMLAAANPGAKEYIYNNLENIMEKIQAIFAGSGYSSRVIEMVVPFIG-LNHMEEIEGKLAKINIQEISRGI 776
                                       99988744223356666655555555555555556677799*********665.88999999999998899999999 PP

                                       HHHHH CS
                           ERAP1_C 307 kqale 311
                                       k+++e
  gi|518653030|ref|YP_008142550.1| 777 KKGME 781
                                       98877 PP

>> CCM2_C  Cerebral cavernous malformation protein, harmonin-homology
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00027       1.2      44      96 ..      16      72 ..       3      76 .. 0.77
   2 ?   -4.0   0.0         4   1.8e+04      74      90 ..     314     332 ..     313     339 .. 0.65
   3 ?   -1.9   0.1       1.1   4.8e+03      26      56 ..     538     568 ..     515     598 .. 0.59
   4 ?   -1.7   0.0      0.94   4.2e+03      26      86 ..     671     731 ..     649     739 .. 0.56
   5 ?   -3.3   0.0       3.1   1.4e+04      68      90 ..     749     771 ..     744     776 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00027
                            CCM2_C 44 eieefcsellqLYgderkfLllGlrPfi....pdkdvgvfesflesiGiregGiltd 96
                                      + +  c e  +  g+e k +l  +   i     ++ +++f++f++++ i  +Gi+t 
  gi|518653030|ref|YP_008142550.1| 16 NYTYTCHETIKFNGNEEKLILSSVNLKIkrikVNNSIKNFKEFIKNQEIVVDGIITK 72
                                      55567999999999999999977665551111578899*****************94 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 4
                            CCM2_C  74 kdvgvfesfl..esiGire 90 
                                        d+++f +fl  e+ G  e
  gi|518653030|ref|YP_008142550.1| 314 VDYDMFADFLvsETAGALE 332
                                       5899999999444455555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.1
                            CCM2_C  26 peelqkfalLlreyrlgaeieefcsellqLY 56 
                                        +e       + e+  +  i+e+  el+ LY
  gi|518653030|ref|YP_008142550.1| 538 LQEYLSRINKFMELNDSLIIREISNELFSLY 568
                                       3333333333333344444555555555555 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.94
                            CCM2_C  26 peelqkfalLlreyrlgaeieefcsel.lqLYgderkfLllGlrPfipdkdvgvfesflesi 86 
                                       ++ +q +a+L  +      +e+ +se   +     r ++l+   P   +  +++ e+ +e+i
  gi|518653030|ref|YP_008142550.1| 671 VKTIQAMAMLTGDNNF-NAVEKAISERkIKAQDSLRYYMLAAANPGAKEYIYNNLENIMEKI 731
                                       3444555554444433.344444444303444445777777888888888888888888876 PP

  == domain 5  score: -3.3 bits;  conditional E-value: 3.1
                            CCM2_C  68 rPfipdkdvgvfesflesiGire 90 
                                        Pfi  ++++  e  l +i i+e
  gi|518653030|ref|YP_008142550.1| 749 VPFIGLNHMEEIEGKLAKINIQE 771
                                       69999999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      504  (0.0281109); 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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.45
# Mc/sec: 5345.35
//
Query:       gi|518653031|ref|YP_008142551.1|  [L=348]
Description: hypothetical protein FACI_IFERC00001G1670 [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  178.5   0.0    1.2e-52  178.0   0.0    1.2  1  Sua5_yciO_yrdC  Telomere recombination
    3.6e-23   82.6   0.0    5.6e-23   82.0   0.0    1.3  1  SUA5            Putative GTP-binding controlling metal-bindin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.0   0.0   1.3e-56   1.2e-52       2     179 .]      22     195 ..      21     195 .. 0.98

  Alignments for each domain:
  == domain 1  score: 178.0 bits;  conditional E-value: 1.3e-56
                                       HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSC CS
                    Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpi 78 
                                       ++++Gg v++ptetvYgL++da n+ a+++++ +K+rp+d+pl+v+++++++l+++a   +++ + k +e++wP p+
  gi|518653031|ref|YP_008142551.1|  22 IIKSGGTVVFPTETVYGLGADAFNPGACSKIFIAKNRPADNPLIVHISNMKMLDQVAY--IDDGLRKKMENIWPSPL 96 
                                       699******************************************************9..***************** PP

                                       EEEEE..E-TS-HHHHTTTTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS- CS
                    Sua5_yciO_yrdC  79 tlllkrskeklpkevapglktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildgg 155
                                       tlllk+ ke++p+ v++gl+tv vr Pd+++a++L+ea g p++a+San+s++psi d e + eel+++vd+i+d+g
  gi|518653031|ref|YP_008142551.1|  97 TLLLKK-KESVPDIVSAGLDTVCVRFPDNKIALELIEASG-PIAAPSANISTRPSIVDSETAVEELDGRVDAIIDAG 171
                                       *****7.777****************************76.************************************ PP

                                       --SSS---EEEETTSSTSSECEXX CS
                    Sua5_yciO_yrdC 156 eiavgvdstVvdltegkpkilRrG 179
                                       +++ gv+st++d+t +++++lR G
  gi|518653031|ref|YP_008142551.1| 172 RVRYGVESTILDCTAEPYRLLRAG 195
                                       ***************9******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 !   82.0   0.0   6.2e-27   5.6e-23       2     133 ..     198     328 ..     197     328 .. 0.81

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 6.2e-27
                                       -HHHHHHHS.....---..........-------------S-SSEEEEE--GGGHHHH.....HHHHHTTS-EEEEE CS
                              SUA5   2 tleeleevl.....davek......keekpraPGmkyrHYaPkapvvlveaeeeeeaakeekleekkksgkkvgvla 67 
                                       ++e++e+++     d          +++   +PG kyrHYaP+ ++ l+e+eee+++        +++  k++ vl+
  gi|518653031|ref|YP_008142551.1| 198 SVEDIESIIgkiyvD---PlakgynQSDVALTPGLKYRHYAPSKKLFLIENEEEFKKF------ISSEISKDFLVLC 265
                                       6899****9433331...122345578888***********************99986......5788888889999 PP

                                       EGGGTGGTSEEEEE..E-TT-HHHHHHHHHHHHHHHHHS--SEEEEE----STTHHHHHHHHHHHT CS
                              SUA5  68 tseskeaassvlslslgsrsdleeaarnLFaaLrelDeegvdlilvegvpeeglglAvmnRLrkAA 133
                                       ++e+++ as + ++ lg  sd  e+a+nLF  +r lD++g  + +++g+pe+g+glAvmnR+rkA+
  gi|518653031|ref|YP_008142551.1| 266 SKENEKYASGKSIV-LG--SDIYEIAHNLFYDFRYLDNSGKLYGVIQGFPESGIGLAVMNRIRKAS 328
                                       77777764444444.56..******************878889999*******************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (348 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); 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: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.51
# Mc/sec: 2042.04
//
Query:       gi|518653032|ref|YP_008142552.1|  [L=305]
Description: hypothetical protein FACI_IFERC00001G1671 [Ferroplasma acidarmanus fer1]
Scores for complete 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   45.4   0.2    1.8e-10   40.8   0.1    2.4  2  Acetyltransf_10  Acetyltransferase (GNAT) domain
    6.3e-09   36.1   0.3    3.9e-08   33.5   0.2    2.1  2  Acetyltransf_1   Acetyltransferase (GNAT) family
    1.9e-06   28.2   1.2    7.1e-06   26.4   0.7    2.0  2  Acetyltransf_7   Acetyltransferase (GNAT) domain
     0.0036   17.2   0.0       0.51   10.3   0.0    2.7  3  FR47             FR47-like protein
  ------ inclusion threshold ------
      0.021   14.9   0.1      0.079   13.0   0.1    2.0  1  Acetyltransf_9   Acetyltransferase (GNAT) domain


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.057   2.1e+02      27      58 ..      42      74 ..      31      89 .. 0.70
   2 !   40.8   0.1     5e-14   1.8e-10      32     110 ..     209     292 ..     188     297 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.057
                   Acetyltransf_10 27 eegealllvaeeggkivGviel.rdgshisllf 58
                                      +e++  + +   ++++vG++ + +++++  +l+
  gi|518653032|ref|YP_008142552.1| 42 NENKIRYRIIMHKNELVGYAYImDSTDKSDRLY 74
                                      566666777777888888887755555666665 PP

  == domain 2  score: 40.8 bits;  conditional E-value: 5e-14
                   Acetyltransf_10  32 lllvaeeggkivGvi...el.rdgshisllfVdpeyrgqGigkaLleaveeeaekdgikl.eltvnaspyavpfYek 103
                                       ++++ +++g+i G++   +l  d+  i  +fV+++yr++G+gk Ll +++++++   ++   l vna + a++fY +
  gi|518653032|ref|YP_008142552.1| 209 VTVIIKNKGRISGAVvssRLgFDRAFIVSIFVKRAYRKTGMGKYLLFTALNRLKALSYHYvFLWVNAENFAKDFYLH 285
                                       45677788999999977777777779*********************************99**************** PP

                   Acetyltransf_10 104 lGFkavg 110
                                       +GFk  +
  gi|518653032|ref|YP_008142552.1| 286 YGFKYDD 292
                                       ***9765 PP

>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.23   8.3e+02      36      55 ..      49      68 ..      17     103 .. 0.71
   2 !   33.5   0.2   1.1e-11   3.9e-08      27     117 .]     202     288 ..     166     288 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.23
                                      EEEEETTEEEEEEEEEEEET CS
                    Acetyltransf_1 36 lvaeedgeliGfisllkipd 55
                                       ++ + +el+G++ +   +d
  gi|518653032|ref|YP_008142552.1| 49 RIIMHKNELVGYAYIMDSTD 68
                                      44566678888885554444 PP

  == domain 2  score: 33.5 bits;  conditional E-value: 1.1e-11
                                       HHHSTTCEEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTESEEEEEEET CS
                    Acetyltransf_1  27 sfsleaegllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegikkivlavee 103
                                       + +++ e +++++  g++ G +  +   +   ++a+i s++V+++yr+ G G+ Ll +++ r++   +++++l+v +
  gi|518653032|ref|YP_008142552.1| 202 YGEIIKEVTVIIKNKGRISGAVVSSRLGF---DRAFIVSIFVKRAYRKTGMGKYLLFTALNRLKALSYHYVFLWVNA 275
                                       345577778889999*******9999999...9******************************************88 PP

                                       TEHHHHHHHHHTTE CS
                    Acetyltransf_1 104 dndaairlYeklGF 117
                                        n  a  +Y   GF
  gi|518653032|ref|YP_008142552.1| 276 EN-FAKDFYLHYGF 288
                                       77.88899977888 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.46   1.7e+03      58      75 ..      61      80 ..      39      81 .. 0.51
   2 !   26.4   0.7     2e-09   7.1e-06       7      75 ..     212     289 ..     201     290 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.46
                                      EEE..THHHHHHHHHHTTEE CS
                    Acetyltransf_7 58 lel..naekaikfYeklGFe 75
                                      ++   +++k+ ++Y+  GF+
  gi|518653032|ref|YP_008142552.1| 61 AYImdSTDKSDRLYADIGFT 80
                                      22332222566788888885 PP

  == domain 2  score: 26.4 bits;  conditional E-value: 2e-09
                                       EEEETTEEEEEEEEEEES...TCTEEEEE-GGGTTSSHHHHHH.HH....TTSEEEEE..EEEETHH.HHHHHHHHT CS
                    Acetyltransf_7   7 VaeddgkivGfialslld...aeitrlaVdpeyrgkGiGraLl.ea....aekgiile..qlelnae.kaikfYekl 72 
                                       +++++g+i G ++ s+l+   a i  ++V+ +yr+ G G+ Ll +a    +   +  +   l++nae  a +fY ++
  gi|518653032|ref|YP_008142552.1| 212 IIKNKGRISGAVVSSRLGfdrAFIVSIFVKRAYRKTGMGKYLLfTAlnrlK--ALSYHyvFLWVNAEnFAKDFYLHY 286
                                       34445555565544444465556666****************943433221..1111212334444348999***** PP

                                       TEE CS
                    Acetyltransf_7  73 GFe 75 
                                       GF+
  gi|518653032|ref|YP_008142552.1| 287 GFK 289
                                       **8 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.016        56      58      79 ..      60      81 ..      45      87 .. 0.82
   2 ?   -2.4   0.0       1.4     5e+03      57      80 ..     109     132 ..      98     137 .. 0.62
   3 !   10.3   0.0   0.00014      0.51      11      79 ..     222     290 ..     212     296 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.016
                                      EEEEETT-HHHHHHHHHHT-EE CS
                              FR47 58 llvvvasNtpsirlyeklGfek 79
                                       +++  s ++s rly  +Gf+ 
  gi|518653032|ref|YP_008142552.1| 60 YAYIMDSTDKSDRLYADIGFTS 81
                                      578888999***********86 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                                       EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  57 vllvvvasNtpsirlyeklGfeki 80 
                                       +l  +  +N++s++ +   Gf+ i
  gi|518653032|ref|YP_008142552.1| 109 MLNPIINGNETSEKYLMDSGFKTI 132
                                       334577788888888877777766 PP

  == domain 3  score: 10.3 bits;  conditional E-value: 0.00014
                                       -EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EE CS
                              FR47  11 elaawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfek 79 
                                       +++  +l  d  ++ ++ v+   r+ G+g+ l     +++ +  ++ + ++v +++ +  +y   Gf+ 
  gi|518653032|ref|YP_008142552.1| 222 AVVSSRLGFDRAFIVSIFVKRAYRKTGMGKYLLFTALNRLKALSYHYVFLWVNAENFAKDFYLHYGFKY 290
                                       55666677788899****************99999999999988887777777788899***9999986 PP

>> Acetyltransf_9  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.2e-05     0.079      74     127 ..     233     290 ..     155     290 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
                                       EEEEEEEE-CCGTTS-HHHHHHHHHHHHHHHTT--EEEE--....SSHHHHHTTT-EE CS
                    Acetyltransf_9  74 agvtgVavapehrgrgvlskLlaraleemreegqplsllfP....ssipiYrrfGyei 127
                                       a ++++ v+  +r+ g+ + Ll +al+++++  +  ++l+     ++ ++Y ++G+++
  gi|518653032|ref|YP_008142552.1| 233 AFIVSIFVKRAYRKTGMGKYLLFTALNRLKALSYHYVFLWVnaenFAKDFYLHYGFKY 290
                                       7899*************************************87777789999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (305 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       706  (0.0393775); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2073.29
//
Query:       gi|518653033|ref|YP_008142553.1|  [L=314]
Description: cytidylyltransferase family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.043   14.1   0.1      0.043   14.1   0.1    3.4  4  DUF1774   Fungal protein of unknown function (DUF1774)


Domain annotation for each model (and alignments):
>> DUF1774  Fungal protein of unknown function (DUF1774)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.5      0.37   6.6e+03      54      71 ..       4      21 ..       3      35 .. 0.64
   2 ?    1.5   1.7     0.021   3.7e+02      33      79 ..      74     120 ..      44     134 .. 0.63
   3 ?   14.1   0.1   2.4e-06     0.043      15      67 ..     183     235 ..     170     254 .. 0.82
   4 ?   -2.8   0.3      0.47   8.5e+03      50      65 ..     272     287 ..     263     295 .. 0.57

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.37
                           DUF1774 54 fafviaavlfvlslvvav 71
                                      f f+  a+++++  ++++
  gi|518653033|ref|YP_008142553.1|  4 FNFAYLAIFLIAVSYILI 21
                                      555556666655555544 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.021
                           DUF1774  33 lLslalgvgQlltkvialQwifafviaavlfvlslvvavakllgree 79 
                                       ++ + l +  ++ +++ + ++fa + +++l+ + l   ++k+  +++
  gi|518653033|ref|YP_008142553.1|  74 AVDFVLIILSIFGNFVPVRFVFASISISILLSMFLDKNMRKYDVTNN 120
                                       34566677777888899999999988888888888777777777663 PP

  == domain 3  score: 14.1 bits;  conditional E-value: 2.4e-06
                           DUF1774  15 glffivaykDytlgfslslLslalgvgQlltkvialQwifafviaavlfvlsl 67 
                                        l++++  kD+ lg+ + +L+++  +   +t+ ++l +i+af+i+    ++++
  gi|518653033|ref|YP_008142553.1| 183 DLVYMMERKDTKLGLGSMYLAAGFLFVLSFTRSLQLIYISAFLIMIGDSLATI 235
                                       57889999*******************9****************975444444 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 0.47
                           DUF1774  50 lQwifafviaavlfvl 65 
                                       + +i+af  ++  f  
  gi|518653033|ref|YP_008142553.1| 272 VYFISAFYAIGGTFAE 287
                                       3456666555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (314 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2267.87
//
Query:       gi|518653034|ref|YP_008142554.1|  [L=111]
Description: dioxygenase ferredoxin reductase component [Ferroplasma acidarmanus fer1]
Scores for complete 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-15   54.9   0.2    9.1e-15   54.4   0.2    1.2  1  Rieske    Rieske [2Fe-2S] domain
    1.2e-08   34.8   0.0    1.5e-08   34.5   0.0    1.1  1  Rieske_2  Rieske-like [2Fe-2S] domain


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   0.2     1e-18   9.1e-15       4      78 ..       5      78 ..       2      82 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1e-18
                                      EEEEGGGC-TTCEEEEEETTEEEEEEE-TTS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEE.TTSBEEE CS
                            Rieske  4 avakesdvpegdpltvkvggeplvvlrdedgevyAlsdvCtHrgaplsegkidekgvleCpcHgwayd.adGkvik 78
                                      +++k+ +++eg++++++vg+++++v +  +g++yA++  C+H+g  l +gk  e+  ++Cp H ++++ ++Gkv k
  gi|518653034|ref|YP_008142554.1|  5 PLCKTTEIEEGKSREFEVGNKKILVSNV-GGKFYAIDALCSHMGGDLGKGKS-EGHDVICPKHHARFNvQTGKVDK 78
                                      799************************7.******************99999.777*****************976 PP

>> Rieske_2  Rieske-like [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   1.7e-12   1.5e-08       4     103 ..       5     109 ..       2     110 .. 0.91

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 1.7e-12
                                       EEEECCCS-TTB-EEEEETTEEEEEEE-TTS-EEEEESS-TTTSSSTCCCSEEEECTTCEEEE-TTT--EEETTT-B CS
                          Rieske_2   4 pvckledlvketgvaalvdgkqvalfrlekeevyAidnldpaseanvlsrGlvgdkkgelvvasPlykqkfdLktGe 80 
                                       p+ck++++ ++++    v++k++++  +  ++ yAid+l+       l +G+     +   v +P +  +f+ +tG+
  gi|518653034|ref|YP_008142554.1|   5 PLCKTTEIEEGKSREFEVGNKKILVSNV-GGKFYAIDALCSHM-GGDLGKGKS----EGHDVICPKHHARFNVQTGK 75 
                                       89************************99.9***********94.556666654....445799************** PP

                                       BSS...........-TTSB-BEE-EEESTSEEEE CS
                          Rieske_2  81 cle...........deevslkvypvrvedgkvev 103
                                       + +           +e+  lk y+v+ +dg++ v
  gi|518653034|ref|YP_008142554.1|  76 VDKningffkamtrKEATDLKSYEVKENDGELSV 109
                                       *99**********9999*************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 819.08
//
Query:       gi|518653035|ref|YP_008142555.1|  [L=284]
Description: carbon monoxide dehydrogenase, medium chain [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-50  169.0   0.0    1.1e-49  168.4   0.0    1.2  1  FAD_binding_5  FAD binding domain in molybdopterin dehydrogen
      8e-18   64.5   0.0    4.8e-17   62.0   0.0    2.0  2  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 !  168.4   0.0   1.2e-53   1.1e-49       2     168 ..       5     171 ..       4     171 .. 0.99

  Alignments for each domain:
  == domain 1  score: 168.4 bits;  conditional E-value: 1.2e-53
                                       EEEEEE-SSHHHHHHHHHHCTTSEEESS-TTHHHHHHHTT---SEEEEGTTSGGGS-EEEESSEEEEETTSBHHHHH CS
                     FAD_binding_5   2 kfeylrpasleealallaaepdaklvaGgtdlgvlmkekvarpehliditgipelkeieeteggleiGAavtlsela 78 
                                       kfey+ p+s+eea+++l+ ++dak++aGg++l++l+k++ +++++l+di++++ +++i+ +++ l+iG +++ +++a
  gi|518653035|ref|YP_008142555.1|   5 KFEYYAPESIEEATKFLNGHEDAKVLAGGQSLIPLLKLRFTSIPQLVDIGRLKGMDSISFQGNTLRIGPMARTHSIA 81 
                                       79*************************************************************************** PP

                                       HHHHHHHHHHHSHHHHHTSS-HHHHHH-BHHHHHHHT-TT-SSHHHHHHTTEEEEEEESSEEEEEECHHHEEETTEE CS
                     FAD_binding_5  79 aealvrerypalsealekiAspqiRnvaTiGGNlataspisDlapaLlaldAevelrsaegerevpleeflkgpgkt 155
                                       +++ +r+++p lsea+  iA+p +Rn++TiGG +++++p+ D+++++lal+A+ e++sa+g+r++++++f+++  +t
  gi|518653035|ref|YP_008142555.1|  82 EDPQIRKKFPILSEAAGLIADPLVRNMGTIGGDICHGDPSNDFPAVMLALNANFEVTSAKGKRTIKAQDFFTDTFTT 158
                                       ***************************************************************************** PP

                                       SS-TT-EEEEEEE CS
                     FAD_binding_5 156 alepgelitavei 168
                                       al+pge++t ++i
  gi|518653035|ref|YP_008142555.1| 159 ALNPGEILTGITI 171
                                       **********987 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 ?   -0.1   0.0      0.11     1e+03      10      26 ..     121     137 ..     119     152 .. 0.76
   2 !   62.0   0.0   5.4e-21   4.8e-17       3     101 ..     180     277 ..     178     279 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
                                       SSS-ESEEEEEEEEEET CS
                     CO_deh_flav_C  10 endiaivnaAfrvelee 26 
                                       +nd+++v+ A+++ +e 
  gi|518653035|ref|YP_008142555.1| 121 SNDFPAVMLALNANFEV 137
                                       5899******9999973 PP

  == domain 2  score: 62.0 bits;  conditional E-value: 5.4e-21
                                       E.EEESSSSSS-ESEEEEEEEEEETTCEECEEEEEEESSSSS-EE-HHHHHHHTTSBSSHHHHHHHHHHHHTTCHHH CS
                     CO_deh_flav_C   3 y.klsrrrendiaivnaAfrveleedgkiedariafggvaptpvraekaeaaLiGkplseelleeaakaleeelspa 78 
                                       y k+++ ++ d++i+++A+ ++++++ ki++a i+++++++t++ a++ae++L+Gk+++++ +++a ++l ++++  
  gi|518653035|ref|YP_008142555.1| 180 YmKYKKYAG-DFSILGIAVDLSIDSG-KIKEAGIGLTNCGATALKATEAEKFLVGKEVTDDNIAKAGDLLLKAADFM 254
                                       778999999.*************988.************************************************** PP

                                       TCTTC-HHHHHHHHHHHHHHHHH CS
                     CO_deh_flav_C  79 sdprasaeYRrslavsllfrfll 101
                                       +d  +s +++++l + l+ ++++
  gi|518653035|ref|YP_008142555.1| 255 DDDNGSVKFKEKLLKYLFTKAVK 277
                                       *******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       243  (0.0135535); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 2014.89
//
Query:       gi|518653036|ref|YP_008142556.1|  [L=159]
Description: carbon monoxide dehydrogenase alpha subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.3e-26   90.0   1.4      2e-25   88.6   0.0    2.0  2  Fer2_2    [2Fe-2S] binding domain
    0.00044   20.1   0.8    0.00044   20.1   0.8    2.0  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
     0.0071   16.3   1.7     0.0071   16.3   1.7    1.5  1  Fer2_3    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 ?    0.1   0.7      0.14   8.5e+02      21      32 ..      38      49 ..      29      72 .. 0.80
   2 !   88.6   0.0   3.4e-29     2e-25       1      75 [.      73     144 ..      70     145 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.14
                            Fer2_2 21 eegasqCGyCtp 32
                                       ++ + CG Ct 
  gi|518653036|ref|YP_008142556.1| 38 GCDTTNCGACTV 49
                                      567889**9995 PP

  == domain 2  score: 88.6 bits;  conditional E-value: 3.4e-29
                            Fer2_2   1 Tveglgeele.elhpvqeafveegasqCGyCtpGfvmsaaalleenepkpteeeirealsgnlCRCtgYrpivdAv 75 
                                       T+e  +   + +l++++e+fvee+++qCG+CtpG++m+   +l++n +kp+++ i+  l+gnlCRCtgY +i++ +
  gi|518653036|ref|YP_008142556.1|  73 TIENEK---DaDLKKIKESFVEENGLQCGFCTPGMIMTSLYMLRNN-KKPDDDYIKSNLAGNLCRCTGYVSIINSI 144
                                       444444...3379******************************999.77777********************9987 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 !   20.1   0.8   7.4e-08   0.00044       1      55 [.       5      59 ..       5      83 .. 0.80
   2 ?   -0.7   0.3      0.24   1.4e+03      38      44 ..      94     101 ..      67     122 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 7.4e-08
                                      EETTTEEEEEEEETTTHBHHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTT CS
                              Fer2  1 itidgkevevevadgettlldaaee.nggidipysCggggCgtClvevlegevqsd 55
                                      i+++g+e++ +v +++t+l  + ++  + ++++ +C   +Cg+C+v ++   v+s+
  gi|518653036|ref|YP_008142556.1|  5 IKVNGEEYKKDV-EPRTLLATFIRDdLKLTGTHIGCDTTNCGACTVLMDGRAVKSC 59
                                      579999999998.77888******88999*****************8776655444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.24
                                       SS.SSTTE CS
                              Fer2  38 gg.CgtCl 44 
                                       g  Cg C+
  gi|518653036|ref|YP_008142556.1|  94 GLqCGFCT 101
                                       33588886 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 !   16.3   1.7   1.2e-06    0.0071      50      83 ..      37      70 ..      10      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                            Fer2_3 50 asCregiCGscavainGkptlaCtatikdlakqk 83
                                        C  + CG+c+v ++G+    Ct    + + ++
  gi|518653036|ref|YP_008142556.1| 37 IGCDTTNCGACTVLMDGRAVKSCTVLAAQADGHE 70
                                      68**********************9988876543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       734  (0.0409393); 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:                         3  (0.000167327); expected 0.2 (1e-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: 1182.11
//
Query:       gi|518653037|ref|YP_008142557.1|  [L=668]
Description: carbon monoxide dehydrogenase beta subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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-96  323.5   0.0    9.4e-81  271.9   0.0    2.0  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    1.6e-14   54.2   0.1    4.7e-13   49.5   0.1    2.4  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 !  271.9   0.0   1.1e-84   9.4e-81      25     403 ..     143     501 ..     118     510 .. 0.92
   2 !   49.3   0.3   2.8e-17   2.5e-13     481     550 .]     541     610 ..     504     610 .. 0.90

  Alignments for each domain:
  == domain 1  score: 271.9 bits;  conditional E-value: 1.1e-84
                                       -S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHHHHHT--GGGEEEE-SB-S--TTTTS CS
                     Ald_Xan_dh_C2  25 adhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlvaevlglpenkvrvivprvGGGFGgKt 101
                                        d++v++++ + r++ +++Et++++a++   dg l+vy  +q +   ++ + + lglp++kvrv   + GG+FG+K 
  gi|518653037|ref|YP_008142557.1| 143 YDVKVTDTILLDRVSANPMETRGIVADY--RDGILNVYLPSQSIVRSKSGIVNSLGLPPEKVRVFLIDNGGAFGVKA 217
                                       4567************************..79********************************************* PP

                                       S--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS-EEEEEEEEEEEESST.HHHCHCCHC CS
                     Ald_Xan_dh_C2 102 qsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGkitaldvdlladaGay.adlspavle 177
                                         +p++++a++a++k+g+pVk++++R+e+++a   ++ ++ ++++ a+kdG+it+ld ++l d G+y  d+++  l 
  gi|518653037|ref|YP_008142557.1| 218 LFYPEYIIACYASMKFGKPVKWQETRTEHLQACHAGRGVEGTLTLYAKKDGTITGLDGEVLLDNGPYfVDAASVDLG 294
                                       *******************************************************************77999999** PP

                                       CTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHHHHHT--HHHHHHHHBCECGCC.SEE CS
                     Ald_Xan_dh_C2 178 ralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelAeelgldplelRrrNlikpgeltpyg 254
                                       +++++++gpY i+++++ g+ + tN++pn+ +RG+G+p+a +++Er+md lA++l++d +++R +N++++    p g
  gi|518653037|ref|YP_008142557.1| 295 NVIHEITGPYFIEKAHIVGKYMLTNKAPNGYYRGAGKPEASILMERMMDLLADKLNMDIADVRLKNALEKPFKSPLG 371
                                       ********************************************************************764444555 PP

                                       ETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS--S.EETTEEEEEEEEE-TTS-EEEE CS
                     Ald_Xan_dh_C2 255 qpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegiglgftakflnqegalvrvntdGsvtvs 331
                                            ++  +  l+ +++ ++y+e+ ++      +  ++Gi+l +  e +  ++       e+a++ v+ dG+v+ +
  gi|518653037|ref|YP_008142557.1| 372 LD--VNYPTKPFLEDALKYFNYRELSKK------E--HVGISLFILDEDT--AP------GESARIIVK-DGKVHTY 429
                                       44..5899999***********877443......2..59***********..44......469999886.******* PP

                                       ESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHHHHHHHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 332 tggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstdlngnAvkkAaeklrerllki 403
                                       +gg   GqG+e+ +  i ++eL ++ +++ ++ +dt++   g+gt++S s+ + g+  ++Aae+l+e++++ 
  gi|518653037|ref|YP_008142557.1| 430 MGGNVSGQGHEMFVKSILSDELSIEQDSISLELQDTETLSTGVGTWGSKSAMTHGSVLMQAAEELKEQVKEK 501
                                       ********************************************************************9986 PP

  == domain 2  score: 49.3 bits;  conditional E-value: 2.8e-17
                                       TT--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 481 etgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                       e g+++ l+v + +D Gk++N + v gQ eGG+ q+iG +l+E l+y+e+Gql+t+s +d  + ta+ +P
  gi|518653037|ref|YP_008142557.1| 541 EAGDIESLKVGCYYDLGKVLNMTNVMGQTEGGALQAIGEVLSETLRYSEEGQLMTTSITDAGVLTAEHTP 610
                                       679*************************************************************999887 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 !   49.5   0.1   5.2e-17   4.7e-13       2     109 ..      10     103 ..       9     104 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.2e-17
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G+++Y+dDi++ g+ly+ +vrS++a+Ak+++++             +t kdl++   a ++  ++e+  +la d+v+
  gi|518653037|ref|YP_008142557.1|  10 GKGRYLDDIDLDGMLYMSLVRSPYARAKVKKVE-----------GGLTSKDLKAYY-ALAEGDHKEP--VLAIDEVN 72 
                                       99**************************98765...........56899***9984.4546676765..******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeel 109
                                       ++gqavaav  ++++++++ ++ v+veYe+ 
  gi|518653037|ref|YP_008142557.1|  73 YQGQAVAAVFGKNRYESEDLLSTVNVEYEPM 103
                                       ****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (668 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4510.72
//
Query:       gi|518653038|ref|YP_008142558.1|  [L=1698]
Description: hypothetical protein FACI_IFERC00001G1677 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-44  152.1   0.0    2.4e-44  151.4   0.0    1.4  1  DEAD_assoc     DEAD/H associated
    1.8e-27   96.2   0.1    2.2e-26   92.7   0.0    2.4  2  DEAD           DEAD/DEAH box helicase
    4.2e-18   65.7   3.2    7.9e-17   61.6   0.3    3.5  3  Helicase_C     Helicase conserved C-terminal domain
    2.8e-12   47.0   0.0    8.7e-12   45.4   0.0    1.8  1  ResIII         Type III restriction enzyme, res subunit
    0.00055   20.3   0.1     0.0023   18.3   0.0    2.1  3  AAA_19         AAA domain
     0.0037   17.1   5.1     0.0086   15.9   1.7    3.2  4  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0095   15.8   6.8       0.39   10.6   0.2    3.1  2  TFIIE_alpha    TFIIE alpha subunit
  ------ inclusion threshold ------
      0.025   14.2   0.7        5.2    6.8   0.0    3.2  2  DUF2312        Uncharacterized protein conserved in bacteria 
       0.04   13.0   0.0      0.087   11.9   0.0    1.5  1  T2SSE          Type II/IV secretion system protein
        1.6    8.2   4.9          1    8.8   0.1    2.7  3  UvrD-helicase  UvrD/REP helicase 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 !  151.4   0.0   1.4e-47   2.4e-44       1     191 []     629     814 ..     629     814 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.4 bits;  conditional E-value: 1.4e-47
                        DEAD_assoc   1 lPtdrtllvErf.rdelgdwrlvvhspfGrrvnealalllaarlsrrfgidvqvaanDdgivlllpleerlplllde 76 
                                       +Pt++ l +E + +++l  + +++h p+Grrvn+al++++   +s+++g + ++++nD+g+ l+l  ++++p  +++
  gi|518653038|ref|YP_008142558.1| 629 IPTEDLLYIEGYiDNDL--YSIIFHIPLGRRVNDALSRAYGLAVSNKYGANTRISVNDNGFTLTL--NRKVP--IKD 699
                                       7***********64333..7*******************************************55..55877..679 PP

                        DEAD_assoc  77 llellspdeleedleaalnaselfkrrFrevAaralllprrypgkrkplwqqrlraaqLldvareypdfpllleavr 153
                                       ++ ll+p ++++++ +++ ++elfk rFr +A+r+l+++r+y++   ++ +q+lr+++Ll++++ +++fp+++ea++
  gi|518653038|ref|YP_008142558.1| 700 VVGLLTPSNFRDLVDRSIINTELFKQRFRYCATRSLMVLRKYKQTDISVARQQLRSDRLLRILESMDNFPVIKEAFN 776
                                       ***************************************************************************** PP

                        DEAD_assoc 154 evledqlDlerlaellrr.iaageirvvevetprpSpfA 191
                                       ev  d++D+er+a ++++ i++++ ++++  +++ Spf+
  gi|518653038|ref|YP_008142558.1| 777 EVKYDVMDVERAAWFVNDvISKKHYKIKD-YSTETSPFS 814
                                       *****************955666778887.677799996 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   1.3e-29   2.2e-26       3     169 ..      34     214 ..      32     219 .. 0.84
   2 ?    0.5   0.0      0.24   4.4e+02      45     104 ..     278     338 ..     259     363 .. 0.82

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.3e-29
                                       HHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHS....TTSTS-EEEEEESSHHHHHHHHHHHHHHTTTST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyet....kgktgpkalivePtreLaeqtlnnlkkfkkyid 75 
                                        Q++aipli ++++vlv+ +TG+GKTl  ++ ++++++++    + +++  +++++P+++La+++ +nl++ +++i 
  gi|518653038|ref|YP_008142558.1|  34 PQKKAIPLIHQKKNVLVSSPTGTGKTLTGFLSIINELFKKarnnELEDKIYCVYISPLKALANDINKNLNEPLSEIY 110
                                       69************************************999999999***************************644 PP

                                       ............SEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSH..CTTEEEEEEETHHHHHHTTT CS
                                       ............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx RF
                              DEAD  76 ............lrvlliiggvaardqlskldngvdivvgtpgrlddllstgkln..lsqvrflVlDEadrlldqgf 138
                                                   ++v +  g++a+++  + l++ ++i+++tp+ +   ++  k++  +s+v++++lDE++++++ ++
  gi|518653038|ref|YP_008142558.1| 111 alakekgldipeIKVAVRSGDTAQSERNKMLRKPPHIIITTPESFSLAITATKFKekFSSVEYVILDEIHEVSSTKR 187
                                       4666777777767776555555666666666666***********998855555555******************** PP

                                       HHHHHHHHHHSHHHCTTSTTTSEEEEEESSB CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 139 sdfinrilnqlpqitcdgklqrqvivlSATl 169
                                       +  ++  l++l++ +         i lSAT 
  gi|518653038|ref|YP_008142558.1| 188 GSLLSFNLERLENLSPGFV----RIGLSATQ 214
                                       ******9999965544433....89999995 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.24
                                       STS-EEEEEESSHHHHHHHHHHHHHHTTT.STSEEEEEETTSSHHHHHHHHHTT.CSEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx RF
                              DEAD  45 ktgpkalivePtreLaeqtlnnlkkfkky.idlrvlliiggvaardqlskldng.vdivvgt 104
                                       ++++ +li + tr+ +e ++ +lk ++ + i+   ++ +g++++ +  ++l+ng +++v++ 
  gi|518653038|ref|YP_008142558.1| 278 NSHKTTLIFTNTRSSTEHVAMRLKARGIEnIE-AHHSSLGKQTRIEVENRLKNGeLKCVITS 338
                                       456689********************997455.44478899999999999988888887765 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.13   2.3e+02      35      62 ..     113     144 ..      65     163 .. 0.78
   2 !   61.6   0.3   4.4e-20   7.9e-17       5     108 ..     268     373 ..     265     375 .. 0.88
   3 ?   -1.8   0.1       2.1   3.8e+03      14      62 ..    1089    1135 ..    1078    1215 .. 0.60

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.13
                                       HHHHT....TSTEEEESTTSTHHHHHHHHHHH CS
                        Helicase_C  35 llekk....gikvavlhgelpqnereeileqf 62 
                                        +ek     +ikvav  g++ q+er+++l++ 
  gi|518653038|ref|YP_008142558.1| 113 AKEKGldipEIKVAVRSGDTAQSERNKMLRKP 144
                                       34444667789****************99986 PP

  == domain 2  score: 61.6 bits;  conditional E-value: 4.4e-20
                                       HHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSS CS
                        Helicase_C   5 allell.kleeeggkilifvntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerG 79 
                                       +++++l +l ++++++lif+nt+++ e+v + l+ +   ++ ++h++l ++ r+e+ ++ ++ge +++i+++ +e G
  gi|518653038|ref|YP_008142558.1| 268 KMYDILvDLVNSHKTTLIFTNTRSSTEHVAMRLKARgIENIEAHHSSLGKQTRIEVENRLKNGELKCVITSTSLELG 344
                                       56777667889*************99874554555524688899********************************* PP

                                       STSTTESEEEESSSSSSHHHHHHHHTTSS CS
                        Helicase_C  80 idipkvnlVinfdlprnvtsyiqriGRtg 108
                                       idi  +++Vi+++ p++v+++ qriGR g
  gi|518653038|ref|YP_008142558.1| 345 IDIGYIDMVIQIGSPKSVSRALQRIGRSG 373
                                       ***************************87 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                                        TTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTT.STHHHHHHHHHHH CS
                        Helicase_C   14 eeggkilifvntidrlekvklllekkgikvavlhge.lpqnereeileqf 62  
                                        +++++i  f++ + ++e  +++ ek g+ + v++ +  ++  r+e le+ 
  gi|518653038|ref|YP_008142558.1| 1089 VSRKRISNFSTDVASIE--DYF-EKYGFAFDVYDIKvRTSHFRLELLEKA 1135
                                        56778888888888887..888.566666666666523333455555554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   4.8e-15   8.7e-12       8     168 ..      35     213 ..      11     215 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 4.8e-15
                                       HHHHHHHHT...........TTSEEEEEESTTSTHHHHH.HHHHHHH-S...........-EEEEESSHHHHHHHHH CS
                            ResIII   8 Qeeaienlleklks.....krdkrglikmaTGtGKTlva.aklierllkkgkee......kflflvprkslleqtle 72 
                                       Q+           +     +++k++l+  +TGtGKTl+  +++i +l+kk++++       ++ + p k+l +   +
  gi|518653038|ref|YP_008142558.1|  35 QK-----------KaipliHQKKNVLVSSPTGTGKTLTGfLSIINELFKKARNNeledkiYCVYISPLKALANDINK 100
                                       33...........1444447999****************99*********99999***99899999*********** PP

                                       HGGGGTGG.............GEEE....ESSS-B--.........-SEEEEEHHHHHHTH........HHHTTT-S CS
                            ResIII  73 efkkflseayke.........igkk....vsgdkkka..kekdstnkkilvttiqsldadseeeeeeseellrdrfd 134
                                       ++++ lse y+          +  +     sgd+ ++  ++  ++  +i++tt +s++ ++   + ++ + +     
  gi|518653038|ref|YP_008142558.1| 101 NLNEPLSEIYALakekgldipE--IkvavRSGDTAQSerNKMLRKPPHIIITTPESFSLAI---TATKFKEKF---S 169
                                       *999999888764445555441..15555666666666556667889**************...333333333...3 PP

                                       ...EEEEETGGGTTS.T.......TTHHHHHT---SEEEEEESS CS
                            ResIII 135 ...viiiDEaHrlgakk.......swreilekfkeavllglTAT 168
                                          ++i DE H +++ k       + +++ +  + +v++gl+AT
  gi|518653038|ref|YP_008142558.1| 170 sveYVILDEIHEVSSTKrgsllsfNLERLENLSPGFVRIGLSAT 213
                                       355************86777887788886666666********9 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.3e-06    0.0023       1     123 [.      35     192 ..      35     202 .. 0.72
   2 ?   -2.8   0.0         4   7.1e+03      43      80 ..     281     317 ..     269     409 .. 0.65
   3 ?   -3.9   0.0       8.8   1.6e+04      98     124 ..    1531    1556 ..    1497    1560 .. 0.60

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.3e-06
                            AAA_19   1 qreave.alkekvllvtaGpGtGKTrv..lkhivallvelggvkp...eeillvaftgrAakelrerlaalgaeatT 71 
                                       q++a+   +++k++lv  + GtGKT +  l  i +l++++++ ++     ++ +++ +  a+ ++++l   +++ + 
  gi|518653038|ref|YP_008142558.1|  35 QKKAIPlIHQKKNVLVSSPTGTGKTLTgfLSIINELFKKARNNELedkIYCVYISPLKALANDINKNL---NEPLSE 108
                                       89999889*****************865444444555554444444225677788999999*******...888888 PP

                            AAA_19  72 iHrlal..........................ldfddlltealelle..................eaeeekklqeee 104
                                       i +la                           l             +                   ++ ++k+ + e
  gi|518653038|ref|YP_008142558.1| 109 IYALAKekgldipeikvavrsgdtaqsernkmL-------------RkpphiiittpesfslaitATKFKEKFSSVE 172
                                       888888888999999999876665555555550.............3444444455555555555677888897788 PP

                            AAA_19 105 llivDEfqdvd.elqyrLlk 123
                                       ++i DE+ +v+     +Ll+
  gi|518653038|ref|YP_008142558.1| 173 YVILDEIHEVSsTKRGSLLS 192
                                       **********9777777776 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4
                            AAA_19  43 eeillvaftgrAakelrerlaalgae.atTiHrlalldf 80 
                                       ++ l+ + t+ +++ ++ rl+a g e ++  H+   l+ 
  gi|518653038|ref|YP_008142558.1| 281 KTTLIFTNTRSSTEHVAMRLKARGIEnIEAHHSS--LGK 317
                                       6778888888888888888877766644444433..222 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 8.8
                            AAA_19   98 kklqeeellivDEfqdvdelqyrLlka 124 
                                        k+  ++++ i DE+  ++  +  Ll++
  gi|518653038|ref|YP_008142558.1| 1531 KDKSKKYITITDEYTRIEAIE-ILLRE 1556
                                        222355678889998886433.35555 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       1.7   3.1e+03       8      41 ..      78     111 ..      77     114 .. 0.82
   2 ?   -0.7   0.0      0.74   1.3e+03      17      51 ..    1024    1058 ..    1020    1072 .. 0.84
   3 ?   -2.6   0.0         3   5.4e+03      19      46 ..    1182    1209 ..    1178    1212 .. 0.88
   4 !   15.9   1.7   4.8e-06    0.0086       5      60 ..    1483    1537 ..    1479    1552 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                                       HHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHH CS
                              TrmB   8 eyEakvYlaLlklgpatadeiaeelgvprskvYe 41 
                                       e E k+Y + ++  +a a++i ++l+ p s +Y 
  gi|518653038|ref|YP_008142558.1|  78 ELEDKIYCVYISPLKALANDINKNLNEPLSEIYA 111
                                       566777777777778889**************96 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.74
                                        HHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTS CS
                              TrmB   17 LlklgpatadeiaeelgvprskvYevLrsLedkGl 51  
                                        L ++gp++ de+  +l v+      +Lr++e+ G 
  gi|518653038|ref|YP_008142558.1| 1024 LSSYGPLSFDELLIRLPVDNGELETTLREMERSGS 1058
                                        4489***************************9996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3
                                        HHCCCHHCHHCCCTTSSCHCHHHHHHHH CS
                              TrmB   19 klgpatadeiaeelgvprskvYevLrsL 46  
                                        ++g  t ++++e++g +   v  v+++L
  gi|518653038|ref|YP_008142558.1| 1182 EKGVDTEEKLSEITGFDIKIVKAVIKNL 1209
                                        67888999*********99999999998 PP

  == domain 4  score: 15.9 bits;  conditional E-value: 4.8e-06
                                        HHHHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTT CS
                              TrmB    5 GLseyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpk 60  
                                         L+e E  vY++L+ + +at +e+ + l+    kv e+++sL ++  + + k++++
  gi|518653038|ref|YP_008142558.1| 1483 ELTEEEETVYKYLI-SRNATENELVKSLKMNSFKVKETVKSLYSMNAIAKDKSKKY 1537
                                        79***********9.789*********************************99954 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.2   0.00022      0.39      11      52 ..    1170    1210 ..    1161    1217 .. 0.88
   2 !    6.0   2.2    0.0057        10      10      69 ..    1483    1541 ..    1474    1560 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                        S-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHH CS
                       TFIIE_alpha   11 ygeeavlvldvLlekgevteedlakelkidlnelrklLnrLy 52  
                                         g e +++ld +  kg+ tee l++ +++d+++++ ++ +L+
  gi|518653038|ref|YP_008142558.1| 1170 NGPEEAKILDYIE-KGVDTEEKLSEITGFDIKIVKAVIKNLQ 1210
                                        5778999***987.*************************995 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0057
                                        CS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEE CS
                       TFIIE_alpha   10 fygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeeksw 69  
                                        +  ee   v + L+   + te++l k lk++  ++++ +  Ly+   +   +++   + +
  gi|518653038|ref|YP_008142558.1| 1483 ELTEEEETVYKYLI-SRNATENELVKSLKMNSFKVKETVKSLYSMNAIAKDKSKKYITIT 1541
                                        45567778888888.66789************************9999877777644444 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 ?    6.8   0.0    0.0029       5.2      20      56 ..     100     136 ..      86     142 .. 0.75
   2 ?    4.0   0.2     0.022        39      36      49 ..    1195    1208 ..    1164    1216 .. 0.70

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0029
                           DUF2312  20 kaiaedikdvyaeaKseGfdtkvlrkivklrkkdkde 56 
                                       k+++e + ++ya aK +G+d+  ++  v+     ++e
  gi|518653038|ref|YP_008142558.1| 100 KNLNEPLSEIYALAKEKGLDIPEIKVAVRSGDTAQSE 136
                                       799*****************99998666554444444 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.022
                           DUF2312   36 eGfdtkvlrkivkl 49  
                                        +Gfd+k+++ ++k 
  gi|518653038|ref|YP_008142558.1| 1195 TGFDIKIVKAVIKN 1208
                                        7***********96 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   4.9e-05     0.087     126     156 ..      42      73 ..      21      85 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.9e-05
                             T2SSE 126 vrerglilvsGgTgsGKttll.yallkeinks 156
                                       +++++++lvs +Tg+GKt +   ++++e+ k+
  gi|518653038|ref|YP_008142558.1|  42 IHQKKNVLVSSPTGTGKTLTGfLSIINELFKK 73 
                                       5889**************87524445555444 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 ?    8.8   0.1   0.00057         1       4     127 ..      34     182 ..      31     203 .. 0.66
   2 ?   -2.1   0.1       1.2   2.1e+03      46      68 ..     281     314 ..     262     339 .. 0.67
   3 ?   -1.0   0.2      0.55   9.9e+02     162     222 ..    1479    1546 ..    1441    1588 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00057
                                       HHHHHHHS..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGG....EEEEESS..HHHHHHHHHHHHH..... CS
                     UvrD-helicase   4 eqreaias..lggpilveAsAGsGKTfvlaerilrlikeeeiepdr....ilvvTFT..nkAaeElkeRiee..... 67 
                                        q++ai     ++++lv++  G+GKT +    i++ + ++   +++    i +v     ++ a+ +++ ++e     
  gi|518653038|ref|YP_008142558.1|  34 PQKKAIPLihQKKNVLVSSPTGTGKTLTGFLSIINELFKKA-RNNEledkIYCVYISplKALANDINKNLNEplsei 109
                                       56777766558999*************97777776666653.22222445655544433788999999999977777 PP

                                       ................HHHHCCHHCTT-H........HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEE CS
                     UvrD-helicase  68 ................alkkaeqessdde........rlrlalqnlseanisTlHsfcqkilkkeanrigldpnfri 120
                                                       a                      ++ l++  ++ i T  sf + i+ +++++     ++ i
  gi|518653038|ref|YP_008142558.1| 110 yalakekgldipeikvA-----------VrsgdtaqsERNKMLRKPPHIIITTPESFSLAITATKFKEKFSSVEYVI 175
                                       76666666655533331...........0333334444455667777888889999999999999999988888888 PP

                                       ECHHHHH CS
                     UvrD-helicase 121 ldeedee 127
                                       lde  e+
  gi|518653038|ref|YP_008142558.1| 176 LDEIHEV 182
                                       8888765 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.2
                                       GGEEEEESSHHHHHHHHHHHHH...........H CS
                     UvrD-helicase  46 drilvvTFTnkAaeElkeRiee...........a 68 
                                       +  l++T T+ ++e   +R+++            
  gi|518653038|ref|YP_008142558.1| 281 KTTLIFTNTRSSTEHVAMRLKArgienieahhsS 314
                                       457999*********9999998665544433332 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.55
                                        HCCCCCHHHHCCCHHHHHCHH...HHHHHHHHHTTCCTTHHCHSS....TSCSHHHHHHHHHHHHHHH CS
                     UvrD-helicase  162 sksrnikkeelslskskaeel...relvskakekqlspkelkkaf....ekasdlqkkiaeflkeyqe 222 
                                        +++r++  ee++ +k+ +      +elv+ +k + ++ ke+ k       +a+d++kk +++  ey +
  gi|518653038|ref|YP_008142558.1| 1479 IRKRELTEEEETVYKYLISRNateNELVKSLKMNSFKVKETVKSLysmnAIAKDKSKKYITITDEYTR 1546
                                        44444445555555544332201145555555565655555554467777777888888887777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       924  (0.0515366); expected 358.6 (0.02)
Passed bias filter:                      552  (0.0307881); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.95u 0.28s 00:00:01.23 Elapsed: 00:00:00.43
# Mc/sec: 11725.46
//
Query:       gi|518653039|ref|YP_008142559.1|  [L=92]
Description: hypothetical protein FACI_IFERC00001G1678 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.016   15.6   1.0          2    8.9   0.1    2.1  2  DUF2583      Protein of unknown function (DUF2583)
      0.029   14.7   1.1      0.038   14.4   1.1    1.2  1  MgtE         Divalent cation transporter
       0.19   10.5   3.5       0.21   10.3   3.5    1.0  1  DUF2207      Predicted membrane protein (DUF2207)
       0.38   10.4   2.8       0.43   10.3   2.8    1.1  1  Tetraspanin  Tetraspanin family
        1.1    9.5   7.5       0.72   10.1   0.4    2.2  2  TrbC         TrbC/VIRB2 family
        2.2    8.4  11.4       0.36   10.9   5.4    2.1  2  DUF3185      Protein of unknown function (DUF3185)
        3.1    7.4  10.6        4.3    6.9   3.3    2.1  2  Saf_2TM      SAVED-fused 2TM effector domain
        9.6    6.4   9.5        1.6    8.9   0.7    2.0  2  DUF2371      Uncharacterised conserved protein (DUF2371)


Domain annotation for each model (and alignments):
>> DUF2583  Protein of unknown function (DUF2583)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1    0.0067        15      39      60 ..       4      25 ..       1      46 [. 0.81
   2 ?    8.9   0.1   0.00091         2       7      36 ..      57      87 ..      52      91 .. 0.74

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0067
                           DUF2583 39 pellaeaallgifiGallWlaG 60
                                       +++  + ++gifiG ++ + G
  gi|518653039|ref|YP_008142559.1|  4 DKVVRIVGIIGIFIGIIIIIYG 25
                                      5566778899*****9998877 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00091
                           DUF2583  7 lllGnvlmglGlllmva.slaysvlnqlpel 36
                                      l+ G ++mg+G++lm++ ++  s+  ++ +l
  gi|518653039|ref|YP_008142559.1| 57 LYYGKIYMGIGFALMIVcAIIISISYKFKHL 87
                                      6789********9987526777777666665 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   1.1   1.7e-05     0.038      37      83 ..       4      78 ..       1      89 [. 0.64

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.7e-05
                                      HHHHHHHHHHHHHHHHHHHHHHHHHT-......................CTSHHH............HHHHHHHHHHHH CS
                              MgtE 37 lkelrvvlllgvilgllifllalllgw.....................slllalv............vglalvlvllaa 82
                                       k +r+v ++g+++g++i+++ ++l                       s     +            +g+al++v+ + 
  gi|518653039|ref|YP_008142559.1|  4 DKVVRIVGIIGIFIGIIIIIYGYYLHAdavylnifyknhafltkseidS-----IkpglyygkiymgIGFALMIVCAII 77
                                      567899***************8877777777777776666666555551.....0444445555533455444444333 PP

                                      H CS
                              MgtE 83 a 83
                                      +
  gi|518653039|ref|YP_008142559.1| 78 I 78
                                      3 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   3.5   9.4e-05      0.21     383     432 ..       7      83 ..       1      89 [. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 9.4e-05
                           DUF2207 383 lsalglgliilglilillallllvll...........................lvfllilllillliaiivlllfsr 432
                                       ++++g+++i++g+i+i+++ +l + +                             +++ ++++l+++++i++ ++++
  gi|518653039|ref|YP_008142559.1|   7 VRIVGIIGIFIGIIIIIYGYYLHADAvylnifyknhafltkseidsikpglyyGKIYMGIGFALMIVCAIIISISYK 83 
                                       56677777777777777776655444999*********************999888888888888888888888754 PP

>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.8   0.00019      0.43       6      65 ..       8      75 ..       3      84 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00019
                                      XXXXXXXXXXXXXXXXXXXXXXX........XXX.....................XXXXXXXXXXXXX CS
                                      xxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin  6 fffnllfwligivllavGvwlrl........khaeaalacllsesaedpailaillivvGvllfllgf 65
                                       ++ ++ + igi+++++G +l           ++ a l++ + +s ++  ++  +++ +G++l++++ 
  gi|518653039|ref|YP_008142559.1|  8 RIVGIIGIFIGIIIIIYGYYLHAdavylnifYKNHAFLTKSEIDSIKPGLYYGKIYMGIGFALMIVCA 75
                                      56778889999999999866655777777784444566666667777777888888888888887765 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   1.6     0.051   1.1e+02      49      65 ..      10      24 ..       2      32 .. 0.52
   2 ?   10.1   0.4   0.00032      0.72      50      75 ..      63      88 ..      59      92 .] 0.88

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.051
                              TrbC 49 ltgplakviatiaiiva 65
                                      +   ++++i++ +ii+ 
  gi|518653039|ref|YP_008142559.1| 10 VGI-IGIFIGI-IIIIY 24
                                      333.4444444.44444 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00032
                              TrbC 50 tgplakviatiaiivaGimlafgrls 75
                                        ++++++++++ i+++i + f++l+
  gi|518653039|ref|YP_008142559.1| 63 YMGIGFALMIVCAIIISISYKFKHLD 88
                                      567*******************9986 PP

>> DUF3185  Protein of unknown function (DUF3185)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   5.4   0.00016      0.36       1      22 [.       8      29 ..       8      34 .. 0.91
   2 ?    1.1   0.3      0.18   4.1e+02       3      20 ..      66      83 ..      63      87 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                           DUF3185  1 riiGiiLlvaGivLlvfGynas 22
                                      ri+Gii +++Gi+++++Gy  +
  gi|518653039|ref|YP_008142559.1|  8 RIVGIIGIFIGIIIIIYGYYLH 29
                                      8******************765 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.18
                           DUF3185  3 iGiiLlvaGivLlvfGyn 20
                                      iG++L+++ ++++   y+
  gi|518653039|ref|YP_008142559.1| 66 IGFALMIVCAIIISISYK 83
                                      899999998888877776 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   3.3    0.0019       4.3      63      86 ..       6      29 ..       2      45 .. 0.84
   2 ?    6.2   0.6    0.0033       7.3      70      90 ..      62      82 ..      29      92 .] 0.79

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0019
                           Saf_2TM 63 ipeivlaiilvigvllivvGavll 86
                                      ++ iv +i ++ig+++i+ G +l 
  gi|518653039|ref|YP_008142559.1|  6 VVRIVGIIGIFIGIIIIIYGYYLH 29
                                      67899***************7764 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0033
                           Saf_2TM 70 iilvigvllivvGavllilry 90
                                      i + ig++l++v+a+++ + y
  gi|518653039|ref|YP_008142559.1| 62 IYMGIGFALMIVCAIIISISY 82
                                      667899999999999998888 PP

>> DUF2371  Uncharacterised conserved protein (DUF2371)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.7   0.00072       1.6      42      67 ..       6      35 ..       1      58 [. 0.75
   2 ?    2.7   2.4     0.058   1.3e+02     107     124 ..      59      77 ..      44      86 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00072
                           DUF2371 42 lvlllGllvllvGiamavlgywpkk....a 67
                                      +v ++G++ +++Gi + + gy+ ++     
  gi|518653039|ref|YP_008142559.1|  6 VVRIVGIIGIFIGIIIIIYGYYLHAdavyL 35
                                      68899*****************99844440 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.058
                           DUF2371 107 lGPlimGiGiflfi.Cana 124
                                        G + mGiG  l+i Ca  
  gi|518653039|ref|YP_008142559.1|  59 YGKIYMGIGFALMIvCAII 77 
                                       58899****9887636654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       967  (0.053935); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 651.89
//
Query:       gi|518653040|ref|YP_008142560.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G1679 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-27   96.5   0.3    2.5e-27   95.7   0.3    1.5  1  DEDD_Tnp_IS110  Transposase
    2.9e-24   85.2   0.0    5.5e-24   84.3   0.0    1.5  1  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> DEDD_Tnp_IS110  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.7   0.3   2.8e-31   2.5e-27       1     155 []      16     171 ..      16     171 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.7 bits;  conditional E-value: 2.8e-31
                    DEDD_Tnp_IS110   1 vGiDvakdkhdacvidaegkvllservpndeeglealleklaakagevlvvveatghygallvaflleagitvvvvn 77 
                                       vGiD+ak+k+d c+i++e + +++  + n+  g++++l+   ++ +++++++e+t+ y+ +l+++l e+  + +++n
  gi|518653040|ref|YP_008142560.1|  16 VGIDIAKKKFDYCIINSEMNLIKRGILINNNYGFSEFLKI-IKNYRNIKIGMESTSIYHVNLYNYLIENSRSAIILN 91 
                                       8*******************999999999999******99.99********************************** PP

                    DEDD_Tnp_IS110  78 plavkrlrklylrkaKtDakDAkvIAdllr.drgrlrpl.klddeayaeLrqltrqredlvkertrlknrlralLdq 152
                                        l +k l+++ +rk+KtD++DA+ IA++++ + +++ ++ k ++++y++L++ +  +  + +++t +kn+l+  +d 
  gi|518653040|ref|YP_008142560.1|  92 SLETKLLKSSRIRKNKTDKIDAEAIAKYIIiRKNNIITMdKNTENTYTNLKEYVYTYIRINRKITMAKNQLIVDMDL 168
                                       ****************************997777776664668999*************************987777 PP

                    DEDD_Tnp_IS110 153 vfp 155
                                       ++p
  gi|518653040|ref|YP_008142560.1| 169 LYP 171
                                       666 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.3   0.0   6.1e-28   5.5e-24       3      86 ..     260     343 ..     258     344 .. 0.98

  Alignments for each domain:
  == domain 1  score: 84.3 bits;  conditional E-value: 6.1e-28
                    Transposase_20   3 lLesipGiGpvtaaallaeigdlrrfksakqlaayaGlapvenqSGkkkrrgriskrGnrrlRraLyeaAlaairan 79 
                                        +++ipGiG++t + +l+ igd++rf+s  +l ay G++pv++qSG+++  ++iskrGn+ +R aLy  +++air+n
  gi|518653040|ref|YP_008142560.1| 260 KIKTIPGIGTITGSIILSSIGDINRFDSIIKLRAYSGMDPVVKQSGDYNITSKISKRGNPLIRYALYLSTVSAIRFN 336
                                       589*********************************************99*************************** PP

                    Transposase_20  80 pelrayy 86 
                                       p++++yy
  gi|518653040|ref|YP_008142560.1| 337 PVIKRYY 343
                                       ******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1311  (0.0731218); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2639.81
//
Query:       gi|518653041|ref|YP_008142561.1|  [L=219]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-12   47.4   0.0      4e-12   46.4   0.0    1.6  2  rve       Integrase core domain
    3.6e-05   24.3   0.0    6.3e-05   23.5   0.0    1.4  1  HTH_32    Homeodomain-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0      0.98   8.8e+03      84     100 ..      84     100 ..      82     101 .. 0.79
   2 !   46.4   0.0   4.5e-16     4e-12       2      88 ..     127     216 ..     126     219 .] 0.90

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 0.98
                               rve  84 refladlgirvsftrpg 100
                                       +++l+d gi++s++  +
  gi|518653041|ref|YP_008142561.1|  84 EKYLKDKGIQISHNIIY 100
                                       78899999999987766 PP

  == domain 2  score: 46.4 bits;  conditional E-value: 4.5e-16
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ + +e++ ++++++le a++  g+  pe++l+D+g+++
  gi|518653041|ref|YP_008142561.1| 127 EHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYNEETIDNTIEALEIAIQLCGK--PEEILTDHGTQF 196
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefla 88 
                                        s+          +f+e+l 
  gi|518653041|ref|YP_008142561.1| 197 FSNgkngipgdhnKFQEYLD 216
                                       *9988888887777777765 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0     7e-09   6.3e-05       9      73 .]      42     103 ..      34     103 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 7e-09
                            HTH_32   9 yneeGlegLkdrprrgrpr.klsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       y e G e L+     gr++  ++  +++ ii+++ + p  +p  + ++l +  g+++Sh  +yriL
  gi|518653041|ref|YP_008142561.1|  42 YLEYGKEELYKT---GRKKkNIDSNTEELIINIRDNYPLSGPLPIEKYL-KDKGIQISHNIIYRIL 103
                                       666666666655...778736*************8899888888*****.5556***********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1567.28
//
Query:       gi|518653042|ref|YP_008142562.1|  [L=303]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.1e-19   71.0   0.2    1.7e-19   70.3   0.2    1.3  1  DDE_Tnp_1    Transposase DDE domain
    1.2e-11   44.9   0.1      2e-11   44.2   0.1    1.3  1  DDE_Tnp_1_3  Transposase DDE domain
    0.00013   22.3   0.4    0.00073   19.8   0.2    2.1  2  DDE_Tnp_1_5  Transposase DDE domain
     0.0037   17.3   0.1     0.0074   16.3   0.1    1.5  1  DUF772       Transposase domain (DUF772)
     0.0046   16.6   0.0       0.01   15.5   0.0    1.7  1  DDE_Tnp_4    DDE superfamily endonuclease
  ------ inclusion threshold ------
        0.1   12.7   0.0       0.29   11.3   0.0    1.8  2  Rv2175c_C    Rv2175c C-terminal domain of unknown function


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   0.2   5.7e-23   1.7e-19       2     214 .]      94     282 ..      93     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 5.7e-23
                         DDE_Tnp_1   2 skrevlivDattvrvpgtk...........edarw..gyk.ggk.ykygyklhiavdtrsglilsvvitpgnvhdsk 63 
                                       s++++ ++D+  + +++++           +d  +  g++ + k + yg+k+h+ +d  s +i+   it gn hds+
  gi|518653042|ref|YP_008142562.1|  94 SVESIAAIDSFIIHTCKHStamrrkvwsnyKD--PvsGWSkTTKgWSYGRKCHMSIDIDSLIIMEWLITKGNMHDSH 168
                                       578999*************8777776665522..25566644446******************************** PP

                         DDE_Tnp_1  64 glkqlldelrprkgklvlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqk 139
                                       + + ++d++r    +++laD++Y+  +++d++    ++ ++                  ++++r+ + nk +  +++
  gi|518653042|ref|YP_008142562.1| 169 VSHNMVDSVR--GFSYILADSAYDASDIYDYIFeNTHALPV----------------IDTNKRRGIIPNKLPVNRKI 227
                                       **********..*********************33344444................47777788887777777777 PP

                         DDE_Tnp_1 140 rrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                         +                      +e+a +y+lRw+iEr+F+ l+  ++ ++  y   +   +++ l+++a+nl
  gi|518653042|ref|YP_008142562.1| 228 GIDL--------------------RKEYASMYPLRWEIERTFSILEEILKCENIWYTVNRDYDTAIGLKAIAYNL 282
                                       7777....................7899**********************************************8 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.1   6.6e-15     2e-11       5     106 ..      96     204 ..      93     232 .. 0.82

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 6.6e-15
                       DDE_Tnp_1_3   5 tgisfiDstklavChnkrikrhkvfkg....lakrGkssmGWfyGfkLhliin.dkGeilavkltpgnvdDrepvee 76 
                                       + i+ iDs  ++ C+   + r+kv ++    ++ + k++ GW yG k h+ i+ d+  i+++ +t+gn++D +  ++
  gi|518653042|ref|YP_008142562.1|  96 ESIAAIDSFIIHTCKHSTAMRRKVWSNykdpVSGWSKTTKGWSYGRKCHMSIDiDSLIIMEWLITKGNMHDSHVSHN 172
                                       6899********************987222356789**************998355567899*************** PP

                       DDE_Tnp_1_3  77 lakellg..klfaDkgyiskklaeelleegie 106
                                       ++ ++ g   ++aD +y + ++ + ++e+  +
  gi|518653042|ref|YP_008142562.1| 173 MVDSVRGfsYILADSAYDASDIYDYIFENTHA 204
                                       ***998733688********999999887433 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   2.4e-07   0.00073      29      93 ..      22      88 ..      15     110 .. 0.83
   2 ?    0.3   0.0      0.28   8.4e+02      59      83 ..      95     119 ..      92     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 2.4e-07
                       DDE_Tnp_1_5 29 rpqvysdaaiqtcltvkvlfklplRqlqGfvqs...llklaglellvpdystlsrraktlevkipvkr 93
                                      r+++y+d  i  +l+v ++f++++R ++ f++     +++ag+ + +p + tlsrra+ ++++ + ++
  gi|518653042|ref|YP_008142562.1| 22 RKRKYTDRQILKVLIVLQIFNISYRSARIFLTNheeYIRMAGI-TEIPSFQTLSRRARMIDLHAVNNE 88
                                      7899**************************9752226889998.99*************999876554 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.28
                       DDE_Tnp_1_5  59 vqsllklaglellvpdystlsrrak 83 
                                       v+s+ ++ ++ + ++++st +rr+ 
  gi|518653042|ref|YP_008142562.1|  95 VESIAAIDSFIIHTCKHSTAMRRKV 119
                                       78999999999999********985 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.5e-06    0.0074       8      58 ..      29      75 ..      23      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-06
                            DUF772  8 elmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsr 58
                                      + +lk+l++ +++++S r +   l ++ ++ + +g+     ++p++ tlsr
  gi|518653042|ref|YP_008142562.1| 29 RQILKVLIVLQIFNISYRSARIFLTNHEEYIRMAGI----TEIPSFQTLSR 75
                                      789********************************8....67********9 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.4e-06      0.01       1     107 [.     101     210 ..     101     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.4e-06
                         DDE_Tnp_4   1 iDgteipiqrpsnleeraqtysnykkkn............tlkvlivvdpngkiifvskgypGsvsDkeilensgll 65 
                                       iD++ i + + s+ ++r++ +snyk               + k+ + +d +  ii+     +G ++D+++ +n   +
  gi|518653042|ref|YP_008142562.1| 101 IDSFIIHTCKHST-AMRRKVWSNYKDPVsgwskttkgwsyGRKCHMSIDIDSLIIMEWLITKGNMHDSHVSHNM--V 174
                                       7899998877664.7999*******98899999999999999*************999999*********8775..5 PP

                         DDE_Tnp_4  66 kalkeavkpg.dvilaDkgFklsekllvpykkkkkkqlseeev 107
                                       + ++     g ++ilaD++++ s+ +   ++  + + l   ++
  gi|518653042|ref|YP_008142562.1| 175 DSVR-----GfSYILADSAYDASDIYDYIFE--NTHALPVIDT 210
                                       5544.....448************5533332..4444444444 PP

>> Rv2175c_C  Rv2175c C-terminal domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0         3   9.1e+03      21      28 ..     154     161 ..     153     163 .. 0.84
   2 ?   11.3   0.0   9.6e-05      0.29       1      33 [.     174     206 ..     174     224 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 3
                         Rv2175c_C  21 ilrWLFte 28 
                                       i++WL t+
  gi|518653042|ref|YP_008142562.1| 154 IMEWLITK 161
                                       799**986 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 9.6e-05
                         Rv2175c_C   1 VkgLpGtltvLrDgGfddeeilrWLFteDesLp 33 
                                       V++++G   +L+D+ +d  +i +++F++   Lp
  gi|518653042|ref|YP_008142562.1| 174 VDSVRGFSYILADSAYDASDIYDYIFENTHALP 206
                                       788999999******************999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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: 00:00:00.42
# Mc/sec: 2168.65
//
Query:       gi|518653043|ref|YP_008142563.1|  [L=29]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (29 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       124  (0.00691617); expected 358.6 (0.02)
Passed bias filter:                      108  (0.00602376); expected 358.6 (0.02)
Passed Vit filter:                         2  (0.000111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 208.61
//
Query:       gi|518653044|ref|YP_008142564.1|  [L=295]
Description: hypothetical protein FACI_IFERC00001G1683 [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.8  12.5    5.3e-31  107.8  12.5    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 ?   -2.0   0.5      0.14   2.5e+03      26     123 ..      66      78 ..      56      87 .. 0.40
   2 !  107.8  12.5   2.9e-35   5.3e-31       1     184 [.      88     294 ..      88     295 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.14
                      BPD_transp_1  26 vllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvv 102
                                       + ++lP+ +l++                                                                 
  gi|518653044|ref|YP_008142564.1|  66 ISQALPYTLLLF----------------------------------------------------------------- 77 
                                       233333322222................................................................. PP

                      BPD_transp_1 103 lPnalppiitglilafggllg 123
                                                           g
  gi|518653044|ref|YP_008142564.1|  78 --------------------G 78 
                                       ....................2 PP

  == domain 2  score: 107.8 bits;  conditional E-value: 2.9e-35
                      BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf........................vilsilghli 53 
                                       g++lGi++ + ++kk    +     +l s+P+fvlai++ + +                         ++ ++++++
  gi|518653044|ref|YP_008142564.1|  88 GLPLGIYTSFLKGKKSEGGVISTATILNSIPFFVLAIVVWVYLaaylkifpitavfplryithpslgTLKVVAYDYA 164
                                       89************************************8877789999******************98888999*** PP

                      BPD_transp_1  54 lpviillllsaapyvrlirraalrslpkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavllef 130
                                       +p+++l+++ +++  + +r+a++++l +d++ +a+a+G++r+ i+ +++ +na+ p+ t ++l f++l+ gav++e 
  gi|518653044|ref|YP_008142564.1| 165 MPILTLTAIESMGHLLTMRAAMVSVLGEDFITTAEAKGVKRKNIMLHHAARNAMVPMSTRMALEFAFLMSGAVIVEV 241
                                       ***************************************************************************** PP

                      BPD_transp_1 131 lgswpGlgtllleailgydyseisnggvlalviavlllnlvadilqrlldprvr 184
                                       +++ pG+gt l e++l  dy+++  g+++++ ++v+l   ++d++++++dpr++
  gi|518653044|ref|YP_008142564.1| 242 IFGIPGMGTALYESTLKEDYPFAE-GALFIISLIVILTYSIVDFIHAWIDPRIK 294
                                       ************************.***************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.50
# Mc/sec: 1772.74
//
Query:       gi|518653045|ref|YP_008142565.1|  [L=707]
Description: hypothetical protein FACI_IFERC00001G1684 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.8e-14   53.3  22.5    2.8e-14   53.3  22.5    2.2  2  BPD_transp_1  Binding-protein-dependent transport system inne
     0.0012   18.7   0.1     0.0012   18.7   0.1    3.9  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 ?   -0.7   0.1      0.12     1e+03     150     176 ..      26      52 ..      16      59 .. 0.53
   2 !   53.3  22.5   3.1e-18   2.8e-14       2     183 ..     520     703 ..     519     705 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.12
                      BPD_transp_1 150 yseis..nggvlalviavlllnlvadilq 176
                                       y++ +  +g  + +v+++++l l++ ++ 
  gi|518653045|ref|YP_008142565.1|  26 YNSKYgkVG--FYIVLIFVVLALISPLII 52 
                                       444443333..334444455555555444 PP

  == domain 2  score: 53.3 bits;  conditional E-value: 3.1e-18
                      BPD_transp_1   2 illGilaalnrnkkldkllrpliivllslPsfvlaillvlvfvilsilghlilpviillllsaapyvrlirraalrs 78 
                                       + +G+l++ ++ ++++  + +l+ +++ +Ps+ l+i++        i+g + +++i++l+l + p++ ++  +++rs
  gi|518653045|ref|YP_008142565.1| 520 LAIGMLIG-YFAGIVSAGFETLSLAIYLIPSLPLLIVVA------AIVGPSLTGIILVLTLLSWPFAAFTLIGIVRS 589
                                       67999999.9999************************99......9********99999999999999999999997 PP

                      BPD_transp_1  79 l.pkdlveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis 154
                                       l ++ +v  a++ Ga+++qi+++++l+n+ p ++ + ++++gg++ + + l  lg   +l+ +++   l   ys + 
  gi|518653045|ref|YP_008142565.1| 590 LkNRAFVDSAKVSGAGTFQILKNHMLKNVTPILVYLTAINIGGAVAAVSTLQVLG-IAPLTVPTWGGMLDGFYSDAF 665
                                       64899**************************************************.444777777777777777777 PP

                      BPD_transp_1 155 .........nggvlalviavlllnlvadilqrlldprv 183
                                                + +++a+++++l+++++++ +  +++pr+
  gi|518653045|ref|YP_008142565.1| 666 alalapwwfMPPIIAITLFILAFIFLSRGMDNVVNPRI 703
                                       *************************************8 PP

>> OppC_N  N-terminal TM domain of oligopeptide transport permease C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   1.4e-07    0.0012       6      40 ..      21      55 ..      17      67 .. 0.86
   2 ?   -5.4   2.3         2   1.8e+04      19      31 ..     512     524 ..     510     533 .. 0.52
   3 ?    0.1   1.0     0.094   8.4e+02      24      36 ..     552     564 ..     551     582 .. 0.84
   4 ?   -0.7   0.5      0.16   1.4e+03      20      28 ..     683     691 ..     678     703 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.4e-07
                            OppC_N  6 awrrFkrNklAvvglvilllllliaifaPliaPyd 40
                                       wr F   k   vg+ i+l+++++a++ Pli+ ++
  gi|518653045|ref|YP_008142565.1| 21 NWRLFYNSKYGKVGFYIVLIFVVLALISPLIIQHS 55
                                      59*****************************7664 PP

  == domain 2  score: -5.4 bits;  conditional E-value: 2
                            OppC_N  19 glvilllllliai 31 
                                       g  ill+ l+i  
  gi|518653045|ref|YP_008142565.1| 512 GIGILLISLAIGM 524
                                       5555555444433 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.094
                            OppC_N  24 llllliaifaPli 36 
                                       ll++++ai++P +
  gi|518653045|ref|YP_008142565.1| 552 LLIVVAAIVGPSL 564
                                       5899999999988 PP

  == domain 4  score: -0.7 bits;  conditional E-value: 0.16
                            OppC_N  20 lvillllll 28 
                                       l+il++++l
  gi|518653045|ref|YP_008142565.1| 683 LFILAFIFL 691
                                       777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (707 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.71u 0.24s 00:00:00.95 Elapsed: 00:00:00.47
# Mc/sec: 4480.95
//
Query:       gi|518653046|ref|YP_008142566.1|  [L=706]
Description: hypothetical protein FACI_IFERC00001G1685 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-58  195.7   0.0    8.2e-29  100.9   0.0    2.4  2  ABC_tran         ABC transporter
    3.3e-33  114.0   0.0    4.1e-16   59.2   0.0    2.7  2  oligo_HPY        Oligopeptide/dipeptide transporter, C-termin
    1.3e-09   37.8   2.9    0.00089   18.8   0.0    2.9  2  SMC_N            RecF/RecN/SMC N terminal domain
    1.1e-08   35.5   2.3    9.7e-05   22.7   0.1    3.7  2  AAA_22           AAA domain
    7.6e-08   32.0   1.2    0.00053   19.7   0.2    2.4  2  AAA_29           P-loop containing region of AAA domain
    1.1e-07   32.4   0.0     0.0099   16.3   0.0    2.3  2  AAA_16           AAA ATPase domain
    2.5e-07   30.6   0.1     0.0093   15.7   0.0    2.3  2  PRK              Phosphoribulokinase / Uridine kinase family
      5e-06   26.5   8.4     0.0045   16.8   0.0    4.2  4  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      2e-05   24.6   0.5      0.067   13.1   0.0    2.3  2  NACHT            NACHT domain
    2.6e-05   24.2   0.7    0.00037   20.5   0.1    2.4  2  ATPase_2         ATPase domain predominantly from Archaea
    2.9e-05   23.8   0.0       0.26   10.9   0.0    2.3  2  ATP-synt_ab      ATP synthase alpha/beta family, nucleotide-b
    5.3e-05   23.2   0.1       0.22   11.5   0.0    2.5  2  AAA_5            AAA domain (dynein-related subfamily)
    5.9e-05   23.6   0.1       0.27   11.8   0.0    3.2  2  AAA_18           AAA domain
    7.1e-05   22.8   0.6       0.42   10.5   0.1    2.5  2  RsgA_GTPase      RsgA GTPase
    8.7e-05   22.7   0.2      0.063   13.4   0.1    2.6  2  AAA_33           AAA domain
    0.00022   21.1   0.5      0.016   15.1   0.1    2.4  2  MobB             Molybdopterin guanine dinucleotide synthesis
    0.00023   20.8   0.8      0.034   13.7   0.2    2.5  2  AAA_7            P-loop containing dynein motor region
    0.00024   20.4   0.3       0.66    9.1   0.0    2.4  2  NB-ARC           NB-ARC domain
    0.00067   20.0   2.3       0.42   11.0   0.1    2.8  2  RNA_helicase     RNA helicase
    0.00079   19.9   0.0       0.44   11.0   0.0    2.8  2  AAA              ATPase family associated with various cellul
     0.0011   19.1   5.9       0.27   11.3   2.1    3.1  2  DUF87            Helicase HerA, central domain
     0.0013   18.8   1.4       0.63   10.1   0.0    2.7  2  MMR_HSR1         50S ribosome-binding GTPase
     0.0013   18.5   1.0        1.4    8.7   0.0    3.0  3  AAA_24           AAA domain
     0.0027   16.9   0.2       0.74    8.9   0.1    2.4  2  G-alpha          G-protein alpha subunit
     0.0031   17.3   0.2        1.9    8.2   0.1    2.4  2  Sigma54_activat  Sigma-54 interaction domain
     0.0031   17.3   0.4      0.098   12.4   0.1    2.4  2  AAA_30           AAA domain
     0.0031   18.0  12.6       0.31   11.5   0.0    3.6  3  AAA_23           AAA domain
     0.0033   16.7   0.3       0.17   11.1   0.1    2.4  2  Septin           Septin
     0.0036   17.2   0.5        2.9    7.8   0.1    2.6  2  APS_kinase       Adenylylsulphate kinase
     0.0046   16.3   0.1        2.4    7.3   0.0    2.4  2  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0051   16.9   0.4       0.32   11.0   0.1    3.0  2  AAA_14           AAA domain
     0.0051   16.6   0.1          3    7.6   0.0    2.6  2  IstB_IS21        IstB-like ATP binding protein
      0.007   16.7   0.7        2.4    8.5   0.2    2.6  2  AAA_19           AAA domain
     0.0093   15.4   0.9       0.46    9.8   0.0    2.7  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
       0.01   16.1   1.8        3.6    7.8   0.1    3.1  3  Roc              Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.012   15.6   2.4       0.56   10.3   0.1    3.0  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
      0.016   15.3   0.2        4.8    7.3   0.0    3.1  3  tRNA_lig_kinase  tRNA ligase kinase domain
      0.022   14.1   3.1        1.7    8.0   0.3    2.6  3  FtsK_SpoIIIE     FtsK/SpoIIIE family
      0.023   14.4   1.9        3.7    7.2   0.5    3.0  3  Thymidylate_kin  Thymidylate kinase
      0.026   13.9   3.6        1.8    7.9   1.0    2.9  2  ATPase           KaiC
       0.03   14.1   0.2        1.6    8.5   0.0    2.4  2  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.039   13.5   0.3        5.7    6.5   0.1    2.7  3  AAA_25           AAA domain
      0.049   13.6   2.2        1.8    8.4   0.1    2.7  2  NTPase_1         NTPase
       0.12   11.9   0.8         20    4.6   0.0    3.0  3  PhoH             PhoH-like protein
       0.13   12.2   0.4        3.8    7.5   0.0    2.4  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
        0.5   10.6   2.6       0.57   10.4   0.0    2.4  1  IFT81_CH         Intraflagellar transport 81 calponin homolog


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 !   92.6   0.0   7.3e-29   2.8e-26       1     136 [.      34     201 ..      34     202 .. 0.85
   2 !  100.9   0.0   2.1e-31   8.2e-29       2     137 .]     394     557 ..     393     557 .. 0.91

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 7.3e-29
                                       EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--...SEEEEEETTCEGGG................B-HHHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxx................xxxxxxx RF
                          ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp...teGeilldgkdlke................qeleslr 58 
                                       l n++l+l+ege+++i+Ge+G+GKSt+++ ++ ll p     G+i+++++   +                + ++   
  gi|518653046|ref|YP_008142566.1|  34 LTNINLTLHEGETLGILGESGSGKSTIAMSIMSLLAPnaiVDGSITFKDNTYVSgsatkisrkskktlyeNLRNMRW 110
                                       689**********************************8888899966633333335666666666667745566666 PP

                                       HCEEEE-SS..--S-TTSBHHHH..........HHHTC.HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHH CS
                                       xxxxxxxxx..xxxxxxxxxxxx..........xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  59 keigvlpqe..pqlfpeltvren..........esdee.iekalsklglkelkdtvvksspssLSgGqkqrvalara 122
                                       k+i++++q   ++++p +t+r++          + dee  +k+l++++l +l+ +v++  p++LSgG+kqr ++a+a
  gi|518653046|ref|YP_008142566.1| 111 KNISMVFQGamNSFNPVYTIRKQiaeafkihtdYTDEEiDKKLLETVKLAGLNPSVLDAYPHELSGGMKQRAVIAMA 187
                                       99999999998899999999999*******9995555526789********************************** PP

                                       HHHTSSEEEEESTT CS
                                       xxxxxxxxxxxxxx RF
                          ABC_tran 123 llkkpkllllDEpt 136
                                       l+  p+++++DEpt
  gi|518653046|ref|YP_008142566.1| 188 LALGPDIVIADEPT 201
                                       *************9 PP

  == domain 2  score: 100.9 bits;  conditional E-value: 2.1e-31
                                       EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE............EETTCEGGG.....B-HHHCCHCE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxx.....xxxxxxxxxx RF
                          ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGei............lldgkdlke.....qeleslrkei 61 
                                       ++v++ l++ge+++ivGe+G+GK+tL ++l++l++ t G+i            +l      +     +e ++++++i
  gi|518653046|ref|YP_008142566.1| 394 DDVNIYLRRGEILGIVGESGSGKTTLGRTLIKLYEATGGNIyyhlnnktiditKLT-----KknrseEEYKEFKRNI 465
                                       89***************************************887666655544444.....1555559********* PP

                                       EEE-SS..--S-TTSBHHHH...............HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHH CS
                                       xxxxxx..xxxxxxxxxxxx...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  62 gvlpqe..pqlfpeltvren...............esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalar 121
                                       ++++q+  ++l+p++tv +                e+++ +++al++++l+  + + +++ p++LSgG+kqrva ar
  gi|518653046|ref|YP_008142566.1| 466 QMIFQDpyDSLDPKMTVFDIvsepviahrytnnpeEMQNMVAAALKQVNLNP-PSNYLYRFPYELSGGEKQRVATAR 541
                                       ******999**********************999888888**********99.888888999*************** PP

                                       HHHHTSSEEEEESTTT CS
                                       xxxxxxxxxxxxxxxx RF
                          ABC_tran 122 allkkpkllllDEpta 137
                                       al+ k k++++DEpt+
  gi|518653046|ref|YP_008142566.1| 542 ALILKTKFIIADEPTS 557
                                       **************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 !   52.1   0.0   1.8e-16     7e-14       1      65 []     254     318 ..     254     318 .. 0.99
   2 !   59.2   0.0   1.1e-18   4.1e-16       1      65 []     608     673 ..     608     673 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.8e-16
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekdklekikgeapslerldeGCpFapRCpfaleeC 65 
                                       +E+g+s+++  ++++PY++ Ll+s+p++ ++k+ + +i+g+ p++ +l +GC+F++RC fa++ C
  gi|518653046|ref|YP_008142566.1| 254 MEYGTSRDIYINSKNPYSIELLKSYPSISNGKKHVNGIPGTLPDPIKLIRGCRFYERCYFANDVC 318
                                       7**************************************************************99 PP

  == domain 2  score: 59.2 bits;  conditional E-value: 1.1e-18
                         oligo_HPY   1 vErgpssklfdeplHPYTkaLlrsvprldrekd.klekikgeapslerldeGCpFapRCpfaleeC 65 
                                       vE+g++++++++plHPYTkaL+r++p +++ +d    +i ge  ++ + ++GC+F+ RC + +++C
  gi|518653046|ref|YP_008142566.1| 608 VEYGNADDIINNPLHPYTKALIRAIPLPTPDWDpGDIEIIGEIGNAINVEKGCRFYGRCIYHQKIC 673
                                       8********************************98889999999********************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 !   17.1   1.3   7.3e-06    0.0028      26     210 ..      46     247 ..      17     255 .. 0.72
   2 !   18.8   0.0   2.3e-06   0.00089      27     198 ..     406     588 ..     393     604 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 7.3e-06
                                       EEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisrr 102
                                          i+G+ GSGKs +  +i+ +L  ++     s +++d  + s +  ++++ + + +++n  +     k+   + + 
  gi|518653046|ref|YP_008142566.1|  46 TLGILGESGSGKSTIAMSIMSLLAPNAI-VDGSITFKDNTYVSGSATKISRKSKKTLYENLRNM--RWKNISMVFQG 119
                                       3469***************999996544.22333444444444444444444444445555444..33444556666 PP

                                       EETTSEEEEEETTEEE-HHHHHHHHHCTT-STT....................CS-HHHHHHHHHHHHHHHHCCS-- CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 103 vkrkgeseykingkevtkkevsellesagiske....................lLSgGektLvalaLlfAiqkvkpa 159
                                       ++++ +  y+i ++ ++  +++    +++i+k+                    +LSgG k+ + +a+ +A+      
  gi|518653046|ref|YP_008142566.1| 120 AMNSFNPVYTIRKQIAEAFKIHTDYTDEEIDKKlletvklaglnpsvldayphELSGGMKQRAVIAMALALG----P 192
                                       67777789999999999999999999****9999************************99999999998875....3 PP

                                       SEEEECTTTTTS-HHHHHHHHHHHHHHCTT...SEEEEE-SSHHHCCC-.SCEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx.xxxxx RF
                             SMC_N 160 plyllDeidaaLDeknvkkvaellkekskn...aQfivislreemleka.dklvg 210
                                        +++ De    LD    +++ + lk+ +++     +i+is++ +++++  d++v 
  gi|518653046|ref|YP_008142566.1| 193 DIVIADEPTTGLDVITQAEIISQLKKLKQEnkiKSLIIISHDIGVISQLaDHIVV 247
                                       48999********98888887777754443233779*****99998876255444 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 2.3e-06
                                       EEEEESTTSSHHHHHHHHHHHC...TT.TTTTTTCHC..CCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSC CS
                                       xxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxx..xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  27 taivGpNGSGKsnlldAilFvL...Gersakklrsek..lsdlihk..skekasvkkaeveitfdnedkklkiekee 96 
                                         ivG+ GSGK+ l   +  +    G + + +l +++  +++l +k  s+e+ +  k +++++f+++ ++    +++
  gi|518653046|ref|YP_008142566.1| 406 LGIVGESGSGKTTLGRTLIKLYeatGGNIYYHLNNKTidITKLTKKnrSEEEYKEFKRNIQMIFQDPYDS---LDPK 479
                                       579***********99984322122555566776665114567777666666666778999*99999888...6777 PP

                                       EEEEEEEETTSEEEEEETTEEE-HHHHHHHHHCTT-STT.........CS-HHHHHHHHHHHHHHHHCCS--SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  97 vsisrrvkrkgeseykingkevtkkevsellesagiske.........lLSgGektLvalaLlfAiqkvkpaplyll 164
                                       +++   v++    + + n+ e  ++ v+  l+++++++          +LSgGek+ va a  + +    ++ + + 
  gi|518653046|ref|YP_008142566.1| 480 MTVFDIVSEPVIAHRYTNNPEEMQNMVAAALKQVNLNPPsnylyrfpyELSGGEKQRVATARALIL----KTKFIIA 552
                                       88887777777777788999999999***********999***************99888755433....567**** PP

                                       CTTTTTS-HHHHHHHHHHHHHHCTT..SEEEEE-SS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxx RF
                             SMC_N 165 DeidaaLDeknvkkvaellkekskn..aQfivislr 198
                                       De  + LD + ++ + ++l++ +k+    +i is++
  gi|518653046|ref|YP_008142566.1| 553 DEPTSMLDVSLRAGFMNMLNNIRKTdeLSVIYISHD 588
                                       ********************7665522667777765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.2     0.004       1.6      10      60 ..      49     105 ..      42     236 .. 0.73
   2 !   22.7   0.1   2.5e-07   9.7e-05       5     114 ..     403     576 ..     400     593 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.004
                            AAA_22  10 vtGesGtGKTtllrrlleqldeeakaee....erpevv..fvtlpsstsskdllrel 60 
                                       + GesG+GK+t +  +++ l   a  +     ++ ++v  + t  s +s k+l+++l
  gi|518653046|ref|YP_008142566.1|  49 ILGESGSGKSTIAMSIMSLLAPNAIVDGsitfKDNTYVsgSATKISRKSKKTLYENL 105
                                       78***********99999995555444477764444443333333333555555444 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 2.5e-07
                            AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaee......erpevv...fvtlpsst..sskdllrellralglelka 70 
                                         il ++GesG+GKTtl r+l + +++             + +++   + t ++ +  + k++ r++  +++++ ++
  gi|518653046|ref|YP_008142566.1| 403 GEILGIVGESGSGKTTLGRTLIKLYEAT----GgniyyhLNNKTIditKLTKKNRSeeEYKEFKRNIQMIFQDPYDS 475
                                       567889******************9644....345669966777763444443333779999999999999999999 PP

                            AAA_22  71 ...................erlsseellealeqalrarav...............................iellii 97 
                                                          ++++ ee+ ++++ al++                                  ++++i 
  gi|518653046|ref|YP_008142566.1| 476 ldpkmtvfdivsepviahrYTNNPEEMQNMVAAALKQVNLnppsnylyrfpyelsggekqrvataralilkTKFIIA 552
                                       99999999999999999997777777777777777766655555555555555555555555555555777777777 PP

                            AAA_22  98 DEaqh.lr.s.....eealeeLrs 114
                                       DE    l+ s     +++l+++r+
  gi|518653046|ref|YP_008142566.1| 553 DEPTSmLDvSlragfMNMLNNIRK 576
                                       777775546344455666666554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.2   1.4e-06   0.00053      18      50 ..      40      72 ..      29      75 .. 0.78
   2 !   10.6   0.0   0.00091      0.35      17      38 ..     398     419 ..     391     423 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.4e-06
                            AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalLvpak 50
                                      ++++ ++  + G+sGsGKST+  +i+ lL p+ 
  gi|518653046|ref|YP_008142566.1| 40 TLHEGETLGILGESGSGKSTIAMSIMSLLAPNA 72
                                      444333666*********************986 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00091
                            AAA_29  17 ieidlkgatlltGpsGsGKSTl 38 
                                       i +++ ++  ++G+sGsGK+Tl
  gi|518653046|ref|YP_008142566.1| 398 IYLRRGEILGIVGESGSGKTTL 419
                                       5555444888***********8 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   2.5e-05    0.0099      20      78 ..      42      95 ..      30     161 .. 0.77
   2 !   13.8   0.0   0.00015     0.058      23      52 ..     402     431 ..     390     465 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.5e-05
                            AAA_16 20 rsgrpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysa.laqalar 78
                                      ++  +e + + GesG+GKs+++ +++ +l + ++i+  + +++++    +y+   a+ ++r
  gi|518653046|ref|YP_008142566.1| 42 HE--GETLGILGESGSGKSTIAMSIM-SLLAPNAIVdGSITFKDN----TYVSgSATKISR 95
                                      34..4678899***************.566666888877777777....443336666644 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 0.00015
                            AAA_16  23 rpelvllsGesGvGKsslvrellralekdg 52 
                                       r+e++ ++GesG+GK++l r+l + +e++g
  gi|518653046|ref|YP_008142566.1| 402 RGEILGIVGESGSGKTTLGRTLIKLYEATG 431
                                       448999****************98777773 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.1    0.0002     0.079       2      54 ..      47      94 ..      46     152 .. 0.61
   2 !   15.7   0.0   2.4e-05    0.0093       1      62 [.     405     466 ..     405     500 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0002
                               PRK  2 IgvagsSGaGkttvarklekifgrekvkaaei.....egdsflrldraekdleleerk 54
                                      +g+ g+SG+Gk+t+a  + ++++ +++   +i     +          + + ++ + +
  gi|518653046|ref|YP_008142566.1| 47 LGILGESGSGKSTIAMSIMSLLAPNAIVDGSItfkdnT----------YVSGSATKIS 94
                                      5999*******************666664444333331..........2222222222 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.4e-05
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevs 62 
                                       ++g+ g+SG+Gktt+ r+l k+ + ++ +  +    + + +++  k+ ++ee++++++++++
  gi|518653046|ref|YP_008142566.1| 405 ILGIVGESGSGKTTLGRTLIKLYEATGGNIYYHLNNKTIDITKLTKKNRSEEEYKEFKRNIQ 466
                                       689*******************9977666444445555556666666666666666655554 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.3      0.26     1e+02       3      26 ..      48      83 ..      47     137 .. 0.66
   2 !   16.8   0.0   1.2e-05    0.0045     225     302 ..     162     238 ..      81     239 .. 0.76
   3 ?    6.9   0.5     0.013         5       2      19 ..     406     423 ..     405     468 .. 0.76
   4 ?    2.2   0.0      0.33   1.3e+02     257     298 ..     546     588 ..     520     592 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.26
                            AAA_21  3 vliGpNgsGKSnLLdaldllarl............d 26
                                      ++ G  gsGKS++   +  l               +
  gi|518653046|ref|YP_008142566.1| 48 GILGESGSGKSTIAMSIMSLLAPnaivdgsitfkdN 83
                                      5899********966554444323444333333333 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 1.2e-05
                            AAA_21 225 engdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsr..ngaQviltTHSp 299
                                        n++  +  ++elS G+k+  a++++ l++ +  ++++ DEp +gL+   +++++  lk+l++  +   +i+ +H+ 
  gi|518653046|ref|YP_008142566.1| 162 LNPSVLDAYPHELSGGMKQR-AVIAMALALGP--DIVIADEPTTGLDVITQAEIISQLKKLKQenKIKSLIIISHDI 235
                                       45555567899*********.99999998777..9********************888666666455566*****98 PP

                            AAA_21 300 lll 302
                                        ++
  gi|518653046|ref|YP_008142566.1| 236 GVI 238
                                       776 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.013
                            AAA_21   2 nvliGpNgsGKSnLLdal 19 
                                        +++G  gsGK++L ++l
  gi|518653046|ref|YP_008142566.1| 406 LGIVGESGSGKTTLGRTL 423
                                       579***********9999 PP

  == domain 4  score: 2.2 bits;  conditional E-value: 0.33
                            AAA_21 257 kgsllliDEpEngLHPkllrrllellkelsr.ngaQviltTHS 298
                                       k+++++ DEp + L+ +l + ++ +l++ ++     vi  +H+
  gi|518653046|ref|YP_008142566.1| 546 KTKFIIADEPTSMLDVSLRAGFMNMLNNIRKtDELSVIYISHD 588
                                       3378888*******************77776677999999998 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.1   0.0   0.00017     0.067       2      26 ..      46      70 ..      45      80 .. 0.87
   2 !    9.5   0.1    0.0023      0.89       5      23 ..     408     426 ..     404     437 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00017
                                      CEEEEC-TTTCHHHHHHHHHHHHCT CS
                             NACHT  2 lvilqGeaGsGKTtLlqklalawae 26
                                      ++ + Ge+GsGK+t + ++++++a 
  gi|518653046|ref|YP_008142566.1| 46 TLGILGESGSGKSTIAMSIMSLLAP 70
                                      56699****************9986 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0023
                                       EEC-TTTCHHHHHHHHHHH CS
                             NACHT   5 lqGeaGsGKTtLlqklala 23 
                                       + Ge+GsGKTtL + l+ +
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKL 426
                                       89**********9999876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.0      0.57   2.2e+02      22      45 ..      46      69 ..      31     160 .. 0.71
   2 !   20.5   0.1   9.5e-07   0.00037      14      83 ..     399     479 ..     390     517 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.57
                          ATPase_2 22 iyfiYGpegsGKtaLlkeiienle 45
                                       + i G  gsGK+++ + i++ l 
  gi|518653046|ref|YP_008142566.1| 46 TLGILGESGSGKSTIAMSIMSLLA 69
                                      556889********9999988774 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 9.5e-07
                          ATPase_2  14 ilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal........ 82 
                                       +l+r   ei+ i G  gsGKt+L + +i+  e  + ++ y  + ++++i+kl+++ + eee k++++ +        
  gi|518653046|ref|YP_008142566.1| 399 YLRR--GEILGIVGESGSGKTTLGRTLIKLYEATGGNIYYHLNNKTIDITKLTKKNRSEEEYKEFKRNIqmifqdpy 473
                                       5555..68999*************************99*****************8877888888877755555555 PP

                          ATPase_2  83 .....g 83 
                                            +
  gi|518653046|ref|YP_008142566.1| 474 dsldpK 479
                                       555441 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00066      0.26       9      47 ..      39      76 ..      33     138 .. 0.84
   2 !   10.5   0.0   0.00087      0.34       9      67 ..     398     456 ..     390     495 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00066
                                      S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab  9 fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyv 47
                                      +++ +G++++i+g++g Gk++i+ s++     + ai+  
  gi|518653046|ref|YP_008142566.1| 39 LTLHEGETLGILGESGSGKSTIAMSIMSLLAPN-AIVDG 76
                                      68899******************9999876444.66655 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00087
                                       S-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTSSEEEEEEESEEHHHHHHHHHHCHHSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       ATP-synt_ab   9 fpivqGqrtlipgafgvGktvisqslskqsnsddaiiyvgiGergnevaevleefpegt 67 
                                       + + +G+ ++i+g++g Gkt++ ++l+k  +++   iy    +++ +++++ ++ ++++
  gi|518653046|ref|YP_008142566.1| 398 IYLRRGEILGIVGESGSGKTTLGRTLIKLYEATGGNIYYHLNNKTIDITKLTKKNRSEE 456
                                       45678999********************9877779999999999888888888776643 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0033       1.3       4      23 ..      49      68 ..      47      77 .. 0.87
   2 !   11.5   0.0   0.00057      0.22       4      46 ..     408     453 ..     406     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0033
                                      EE--SSSSHHHHHHHGGGGB CS
                             AAA_5  4 LvGppGtgKselaerlaaal 23
                                      ++G++G+gKs++a+++ ++l
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMSLL 68
                                      68**************9998 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00057
                                       EE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B- CS
                             AAA_5   4 LvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrre 46 
                                       +vG++G+gK++l + l +++   + ++ y ++++ +  ++l+ + +
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYeatGGNIYYHLNNKTIDITKLTKKNR 453
                                       69***************99999999999999999988888877655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0088       3.4       3      43 ..      49      90 ..      47     149 .. 0.71
   2 !   11.8   0.0    0.0007      0.27       3      44 ..     408     461 ..     406     498 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0088
                            AAA_18  3 ltGtpGvGKttlakeLskrl.gf.....gvnlrdvakenglllevdp 43
                                      + G +G+GK+t+a  + ++l  +     +     + ++++++ +  +
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMSLLaPNaivdgS-----ITFKDNTYVSGSA 90
                                      8899************9998666554443.....3333333333333 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.0007
                            AAA_18   3 ltGtpGvGKttlakeLskrlgf............gvnlrdvakenglllevdpe 44 
                                       + G +G+GKttl++ L k+ +              + ++++ k+n++++e+ ++
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEAtggniyyhlnnkTIDITKLTKKNRSEEEYKEF 461
                                       8899************77632243224443333333333333333333333333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.1    0.0011      0.42      65     121 ..      10      66 ..       1      84 [. 0.70
   2 !   10.2   0.1    0.0013      0.52      88     125 ..     391     429 ..     358     451 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0011
                                       HHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
                       RsgA_GTPase  65 leelkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                                       ++++  ++e+l +++ +      ++l++++  l++ +t  ++G+SG GKSt+  ++++
  gi|518653046|ref|YP_008142566.1|  10 INKIPLKIENLSVTFKTF-GGMVHALTNINLTLHEgETLGILGESGSGKSTIAMSIMS 66 
                                       444444445554443333.2335678888888888799*************9877655 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0013
                                       TTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT--- CS
                       RsgA_GTPase  88 egleelkellkd.ktsvlvGqSGvGKStLinallpelel 125
                                       +++++++ +l+  ++  +vG+SG GK+tL  +l+   e+
  gi|518653046|ref|YP_008142566.1| 391 RAVDDVNIYLRRgEILGIVGESGSGKTTLGRTLIKLYEA 429
                                       6778888899887999*************9999876555 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.018       7.1       6      25 ..      51      71 ..      48     127 .. 0.72
   2 !   13.4   0.1   0.00016     0.063       4      58 ..     408     468 ..     405     585 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.018
                            AAA_33  6 GlpGsGKstlaerllkklg.a 25
                                      G +GsGKst a +++  l+  
  gi|518653046|ref|YP_008142566.1| 51 GESGSGKSTIAMSIMSLLApN 71
                                      88**********999777653 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00016
                            AAA_33   4 lvGlpGsGKstlaerl...lkklg...avllssdtlrrrlfgtdqqsktdytrvldrlyqi 58 
                                       +vG +GsGK+tl + l   ++++g   +++l+  t+  +   ++++s+++y++++ ++  i
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLiklYEATGgniYYHLNNKTIDITKLTKKNRSEEEYKEFKRNIQMI 468
                                       69************99444445559999***999976544445566777777777666554 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0      0.12        46       2      25 ..      47      70 ..      46      83 .. 0.86
   2 !   15.1   0.1     4e-05     0.016       1      30 [.     405     434 ..     405     444 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.12
                              MobB  2 lgivgksgsGKTtLleklipelka 25
                                      lgi g sgsGK t+   +++ l+ 
  gi|518653046|ref|YP_008142566.1| 47 LGILGESGSGKSTIAMSIMSLLAP 70
                                      89************9999888865 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 4e-05
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrv 30 
                                       +lgivg sgsGKTtL   li+  +a g ++
  gi|518653046|ref|YP_008142566.1| 405 ILGIVGESGSGKTTLGRTLIKLYEATGGNI 434
                                       79*******************999988665 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   8.7e-05     0.034      26      87 ..      37      98 ..      29     125 .. 0.86
   2 ?    5.0   0.0     0.041        16      29      56 ..     399     426 ..     387     446 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.7e-05
                             AAA_7 26 lelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiieskle 87
                                      ++l l+++  + + G++G+GK++i++++++ l ++ ++  +i+f+ +t  +   + i +k +
  gi|518653046|ref|YP_008142566.1| 37 INLTLHEGETLGILGESGSGKSTIAMSIMSLLAPNAIVDGSITFKDNTYVSGSATKISRKSK 98
                                      5677888888999********************************99988777766666655 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.041
                             AAA_7  29 llknkkpvllvGptGtGKtviikdllkk 56 
                                       +l+++  + +vG++G+GKt++ ++l+k 
  gi|518653046|ref|YP_008142566.1| 399 YLRRGEILGIVGESGSGKTTLGRTLIKL 426
                                       5666777779**********99887765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0017      0.66      22      42 ..      46      66 ..      30     137 .. 0.78
   2 !    9.0   0.1    0.0018       0.7      22      45 ..     405     428 ..     394     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                                      EEEEEESTTSSHHHHHHHHCC CS
                            NB-ARC 22 vvalvGmgGvGKttlakqiln 42
                                       +++ G  G+GK+t+a +i++
  gi|518653046|ref|YP_008142566.1| 46 TLGILGESGSGKSTIAMSIMS 66
                                      689**************9987 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0018
                                       EEEEEESTTSSHHHHHHHHCCSHC CS
                            NB-ARC  22 vvalvGmgGvGKttlakqilnksd 45 
                                       ++++vG  G+GKttl +  ++ ++
  gi|518653046|ref|YP_008142566.1| 405 ILGIVGESGSGKTTLGRTLIKLYE 428
                                       89*************988777655 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.0   0.1    0.0011      0.42       3      42 ..      49      92 ..      47     115 .. 0.82
   2 ?    7.8   0.4     0.011       4.3       3      27 ..     408     441 ..     406     509 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.0011
                      RNA_helicase  3 lyGpsgeGKStlakeLakallkkl....klkkkdsvysrnpedd 42
                                      + G+sg GKSt+a ++++ l+ +       + kd++y+ +++++
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMSLLAPNAivdgSITFKDNTYVSGSATK 92
                                      68*************99998844447767778888888776666 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.011
                      RNA_helicase   3 lyGpsgeGKStlakeLakallkkl.........k 27 
                                       ++G+sg GK+tl ++L+k  + +          k
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEATGgniyyhlnnK 441
                                       78*************9987764443334443332 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.042        16       3      46 ..      49      93 ..      47     128 .. 0.59
   2 !   11.0   0.0    0.0011      0.44       3      65 ..     408     484 ..     406     519 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.042
                                      EESSTTSSHHHHHHHHHHHH.............THEEEEEETTTCSSSSTTHHHHHH CS
                               AAA  3 lyGppGtGKTllakavakel.............gvefleisgsellskyvgesekki 46
                                      + G  G GK+++a ++++ l             +            + yv+ s+ ki
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMSLLapnaivdgsitfkD------------NTYVSGSATKI 93
                                      5799*************99833222222222221............33333333333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.0011
                                       EESSTTSSHHHHHHHHHHHH.........THEEEEEETTTCSSS.....STTHHHHHHHHHHHHHHHTSTSEEEEEE CS
                               AAA   3 lyGppGtGKTllakavakel.........gvefleisgsellsk.....yvgesekkirelfkeakekakpsilfiD 65 
                                       ++G  G GKT+l + ++k           + +  +i+ ++l++k       +e +++i+++f++   + +p+  ++D
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYeatggniyyHLNNKTIDITKLTKKnrseeEYKEFKRNIQMIFQDPYDSLDPKMTVFD 484
                                       689***************96334433333355667777777755777778999999999999984333345555555 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   2.1   0.00069      0.27      26      48 ..      47      69 ..      43     249 .. 0.80
   2 !    7.8   0.1    0.0082       3.2      26      45 ..     406     425 ..     389     434 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00069
                             DUF87 26 lAilgsTGsGKSntvavLleell 48
                                      l+ilg++GsGKS+ + ++++ l+
  gi|518653046|ref|YP_008142566.1| 47 LGILGESGSGKSTIAMSIMSLLA 69
                                      79****************99887 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0082
                             DUF87  26 lAilgsTGsGKSntvavLle 45 
                                       l+i+g++GsGK+++ + L++
  gi|518653046|ref|YP_008142566.1| 406 LGIVGESGSGKTTLGRTLIK 425
                                       79************999997 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.5     0.015         6       2      45 ..      47     112 ..      46     234 .. 0.79
   2 !   10.1   0.0    0.0016      0.63       3      42 ..     407     451 ..     405     515 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.015
                                       EEEEESTTSSHHHHHHHHH......................TSTEEESSSTTSSSSEEEEEEEETT CS
                          MMR_HSR1   2 vaivGrpNvGKStLinalt......................gekaivsdkpgtTrdinegrvklkg 45 
                                        +i+G + +GKSt+  +++                      g++ ++s+k  +T+  n +++++k+
  gi|518653046|ref|YP_008142566.1|  47 LGILGESGSGKSTIAMSIMsllapnaivdgsitfkdntyvsGSATKISRKSKKTLYENLRNMRWKN 112
                                       689***********9999845555555444444444333333566777777777777777777665 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0016
                                       EEEESTTSSHHHHHHHHHT....S.TEEESSSTTSSSSEEEEEEE CS
                          MMR_HSR1   3 aivGrpNvGKStLinaltg....e.kaivsdkpgtTrdinegrvk 42 
                                       +ivG + +GK+tL ++l++    +   i  + + +T+di++ + k
  gi|518653046|ref|YP_008142566.1| 407 GIVGESGSGKTTLGRTLIKlyeaTgGNIYYHLNNKTIDITKLTKK 451
                                       8*****************855431234667777788887766544 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0     0.011       4.5       5      22 ..      47      64 ..      43      76 .. 0.78
   2 !    8.7   0.0    0.0035       1.4       5      22 ..     406     423 ..     402     481 .. 0.81
   3 ?   -1.2   0.0       3.5   1.4e+03     107     130 ..     563     587 ..     561     590 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.011
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      + i G+sg+GK+t+a ++
  gi|518653046|ref|YP_008142566.1| 47 LGILGESGSGKSTIAMSI 64
                                      6799**********9887 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0035
                            AAA_24   5 iliyGpsgiGKTtlakel 22 
                                       + i+G+sg+GKTtl ++l
  gi|518653046|ref|YP_008142566.1| 406 LGIVGESGSGKTTLGRTL 423
                                       579***********9998 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.5
                            AAA_24 107 laeefrrllkklqelrk.nvifiah 130
                                       l++ f+++l++++++++  vi i+h
  gi|518653046|ref|YP_008142566.1| 563 LRAGFMNMLNNIRKTDElSVIYISH 587
                                       56779999999999999******99 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1    0.0019      0.74      26     113 ..      47     139 ..      33     273 .. 0.63
   2 ?    5.7   0.0     0.018         7      28      51 ..     408     437 ..     398     520 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0019
                                       EEEEESTTSSHHHHHHHHHHHCS--........--HHHHHCCHHHHHHHHHHHHHHHHHHHHHTT.......HHHC- CS
                           G-alpha  26 llllGqseSGKsTilkqlkllykkg........fseeelatwraviqlnivrsiktilealesleselsesfelqel 94 
                                       l +lG+s+SGKsTi  ++  l  ++        f+++   +      +   +s kt+ e+l++   + +++   q  
  gi|518653046|ref|YP_008142566.1|  47 LGILGESGSGKSTIAMSIMSLLAPNaivdgsitFKDN--TYVSGSATKISRKSKKTLYENLRNMRWKNISM-VFQGA 120
                                       568***********99998776666688888887777..44445555555556666666666643222222.45555 PP

                                       SS-SCCCS-HCHHHH.... CS
                           G-alpha  95 kerldplkkveasliakls 113
                                        ++++p++++ +++++ ++
  gi|518653046|ref|YP_008142566.1| 121 MNSFNPVYTIRKQIAEAFK 139
                                       5555555555555444333 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.018
                                       EEESTTSSHHHHHHHHHHHCS--......- CS
                           G-alpha  28 llGqseSGKsTilkqlkllykkg......f 51 
                                       ++G+s+SGK+T+ + l +ly+ +      +
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEATggniyyH 437
                                       79*************999997765566641 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.1    0.0048       1.9      11      44 ..      33      66 ..      26      76 .. 0.80
   2 ?    6.6   0.0     0.014       5.6       4      48 ..     385     429 ..     382     449 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0048
                                      HHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
                   Sigma54_activat 11 lleqikkvaktdlsvlitGesGtGKellaraihe 44
                                      +l++i+ + +   ++ i+GesG+GK+++a +i +
  gi|518653046|ref|YP_008142566.1| 33 ALTNINLTLHEGETLGILGESGSGKSTIAMSIMS 66
                                      5666666677777888*************99865 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.014
                                       -SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTT CS
                   Sigma54_activat   4 esealkelleqikkvaktdlsvlitGesGtGKellaraiheaskr 48 
                                       +s+++ ++++ ++ + +    + i+GesG+GK++l r++ +  + 
  gi|518653046|ref|YP_008142566.1| 385 RSHSFVRAVDDVNIYLRRGEILGIVGESGSGKTTLGRTLIKLYEA 429
                                       566666777777777777667779***********9998776554 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0      0.27   1.1e+02      19      39 ..      45      65 ..      35      76 .. 0.76
   2 !   12.4   0.1   0.00025     0.098      20      49 ..     405     434 ..     396     450 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.27
                            AAA_30 19 rvavltGpAGtGKttalkalr 39
                                       +  + G  G+GK+t+  ++ 
  gi|518653046|ref|YP_008142566.1| 45 ETLGILGESGSGKSTIAMSIM 65
                                      367789*********977665 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00025
                            AAA_30  20 vavltGpAGtGKttalkalreaweaaggrv 49 
                                       +  ++G  G+GKtt+ ++l +++ea gg++
  gi|518653046|ref|YP_008142566.1| 405 ILGIVGESGSGKTTLGRTLIKLYEATGGNI 434
                                       7789**********************9876 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   3.4    0.0013      0.51      14     112 ..      36     127 ..      21     229 .. 0.68
   2 !   11.5   0.0   0.00081      0.31       8      35 ..     391     419 ..     385     423 .. 0.80
   3 ?   -1.6   0.5       8.2   3.2e+03     167     195 ..     444     468 ..     429     473 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0013
                            AAA_23  14 eidF...skgltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdveiesegkvkay.veltfenkdgry 86 
                                       +i++   +     I G+ G+GK+Ti   i   L            + ++++++++++++ v+++  +++ ++k++ y
  gi|518653046|ref|YP_008142566.1|  36 NINLtlhEGETLGILGESGSGKSTIAMSIMSLLAP----------NAIVDGSITFKDNTYVSGSaTKISRKSKKTLY 102
                                       4555554334557****************999986..........23566777777776666666677776666655 PP

                            AAA_23  87 trsiererelskkkgkttkkaklell 112
                                        ++++++r+++ ++  +  ++ ++ +
  gi|518653046|ref|YP_008142566.1| 103 -ENLRNMRWKNISMVFQGAMNSFNPV 127
                                       .6666666666665555544433333 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00081
                            AAA_23   8 rsfrdqeidFsk.gltlItGpNGaGKTTi 35 
                                       r  +d++i + +  +  I+G+ G+GKTT+
  gi|518653046|ref|YP_008142566.1| 391 RAVDDVNIYLRRgEILGIVGESGSGKTTL 419
                                       34488999996626889***********8 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 8.2
                            AAA_23 167 dekkllekleqekekekeleeleeeleei 195
                                       d+     kl +++  e+e++e +++++ i
  gi|518653046|ref|YP_008142566.1| 444 DI----TKLTKKNRSEEEYKEFKRNIQMI 468
                                       23....33333344455555666555554 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   0.0       0.1        39       6      27 ..      46      67 ..      44     150 .. 0.68
   2 !   11.1   0.1   0.00045      0.17       9      72 ..     408     473 ..     404     507 .. 0.60

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.1
                                      EEEEEEBTTSSCCCCCCTTSSS CS
                            Septin  6 tlmvvGesglGkttlintlfet 27
                                      tl + Gesg Gk+t+  ++++ 
  gi|518653046|ref|YP_008142566.1| 46 TLGILGESGSGKSTIAMSIMSL 67
                                      56689*********97766543 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00045
                                       EEEBTTSSCCCCCCTTSSSS----.--------------S-E.EEEEEEEETTCEEEEEEEE---B CS
                            Septin   9 vvGesglGkttlintlfetdliee.ekleeasekkkktveik.kkkvvieedgvklnltviDtpgf 72 
                                       +vGesg Gkttl +tl++    +  + + + ++k+   ++++ k++++ e +++k n+++i  + +
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEATGgNIYYHLNNKTIDITKLTkKNRSEEEYKEFKRNIQMIFQDPY 473
                                       8***************98655555333333333333333333144444444577777777755555 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0075       2.9       3      27 ..      45      69 ..      43      78 .. 0.82
   2 ?    7.0   0.0     0.013       5.1       2      43 ..     403     445 ..     402     473 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0075
                                      EEEEEESSTTSSHHHHHHHHHHHHH CS
                        APS_kinase  3 vvvwltGlsgsGKstianalekkLv 27
                                       ++ + G sgsGKstia+ + + L 
  gi|518653046|ref|YP_008142566.1| 45 ETLGILGESGSGKSTIAMSIMSLLA 69
                                      5677889***********9987775 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
                                       -EEEEEESSTTSSHHHHHHHHHHHHHHTT.--EEEEEHHHHTT CS
                        APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekg.isvylLdGdnvRh 43 
                                       g ++ + G sgsGK+t+ ++l k  +++g    y L+  ++  
  gi|518653046|ref|YP_008142566.1| 403 GEILGIVGESGSGKTTLGRTLIKLYEATGgNIYYHLNNKTIDI 445
                                       5667789**************9999988845556777777754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.3   0.0    0.0062       2.4       6      72 ..      49     125 ..      45     145 .. 0.63
   2 ?    6.6   0.0      0.01       3.9       6      64 ..     408     461 ..     403     508 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0062
                           DUF2075   6 VtGvaGtGKtvvllnllael......eddeeertavylsvNhplvl.....vlrealakkeekkkkkeafeklssfi 71 
                                       + G++G+GK+ ++++++  l        +   + ++y+s++   +      +l+e+l++ +  k+++ +f++  +  
  gi|518653046|ref|YP_008142566.1|  49 ILGESGSGKSTIAMSIMSLLapnaivDGSITFKDNTYVSGSATKISrkskkTLYENLRNMR-WKNISMVFQGAMNSF 124
                                       679**************99988888744445555555555544443322226777765555.555555555555444 PP

                           DUF2075  72 n 72 
                                       n
  gi|518653046|ref|YP_008142566.1| 125 N 125
                                       4 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.01
                           DUF2075   6 VtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakkeekkkkkeaf 64 
                                       + G++G+GKt ++ +l+  +   e    ++y   N++ +++ + + ++++  ++  ++f
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLY---EATGGNIYYHLNNKTIDITKLTKKNRS--EEEYKEF 461
                                       78***********9998877...777777888888887776554433333..2222222 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0      0.31   1.2e+02       4      34 ..      46      74 ..      43     117 .. 0.59
   2 !   11.0   0.1   0.00081      0.32       3      58 ..     404     460 ..     402     498 .. 0.59

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.31
                            AAA_14  4 ilvitGaRrvGKTtllkqlikellvkkesil 34
                                       l i G   +GK+t++  +++ l   ++ i+
  gi|518653046|ref|YP_008142566.1| 46 TLGILGESGSGKSTIAMSIMSLLA--PNAIV 74
                                      5678888899****9999985544..33333 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00081
                            AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderd..kkladpekllelile 58 
                                       +il i+G   +GKTtl ++lik +       +y+ l++++   +kl+++++ +e+++e
  gi|518653046|ref|YP_008142566.1| 404 EILGIVGESGSGKTTLGRTLIKLYE-ATGGNIYYHLNNKTIdiTKLTKKNRSEEEYKE 460
                                       7899*****************7776.44444455555444422222222222222222 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.1     0.022       8.6      45      67 ..      42      64 ..      28      81 .. 0.82
   2 !    7.6   0.0    0.0076         3      43     101 ..     399     460 ..     386     477 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.022
                         IstB_IS21 45 ekkenivllGpsGvGKshlaial 67
                                      ++ e + +lG sG GKs +a+++
  gi|518653046|ref|YP_008142566.1| 42 HEGETLGILGESGSGKSTIAMSI 64
                                      5678999*************987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0076
                         IstB_IS21  43 fiekkenivllGpsGvGKshlaialgveavraglsvlfv...rvedLveelkrarrdgklar 101
                                       ++++ e + ++G sG GK+ l  +l +   ++g ++++    ++ d+ +  k++r+++++++
  gi|518653046|ref|YP_008142566.1| 399 YLRRGEILGIVGESGSGKTTLGRTLIKLYEATGGNIYYHlnnKTIDITKLTKKNRSEEEYKE 460
                                       788999999**************999888889999998622234444444444444444443 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.034        13       8      42 ..      42      76 ..      36     231 .. 0.72
   2 !    8.5   0.2    0.0061       2.4      10      60 ..     403     460 ..     396     583 .. 0.58

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.034
                            AAA_19  8 lkekvllvtaGpGtGKTrvlkhivallvelggvkp 42
                                      ++ ++l +++  G+GK+++ + i++ll  +  v+ 
  gi|518653046|ref|YP_008142566.1| 42 HEGETLGILGESGSGKSTIAMSIMSLLAPNAIVDG 76
                                      5678899*****************99987776654 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0061
                            AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkp.......eeillvaftgrAakelre 60 
                                        ++l +++  G+GKT++ ++ ++l++++gg           +i+ ++  +r+ +e +e
  gi|518653046|ref|YP_008142566.1| 403 GEILGIVGESGSGKTTLGRTLIKLYEATGGNIYyhlnnktIDITKLTKKNRSEEEYKE 460
                                       5678899*******************99976446666644555556666666666655 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    0.0012      0.46      11      50 ..      33      72 ..      24     108 .. 0.75
   2 ?   -2.7   0.1       7.9   3.1e+03       5      57 ..     174     227 ..     172     234 .. 0.76
   3 ?    3.2   0.0      0.13        50      27      46 ..     408     427 ..     396     468 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                      Mg_chelatase 11 akraleiaaaGgHnlllvGppGsGKtmlakrlpsllppls 50
                                      a + ++++   g  l ++G +GsGK+ +a  ++sll+p  
  gi|518653046|ref|YP_008142566.1| 33 ALTNINLTLHEGETLGILGESGSGKSTIAMSIMSLLAPNA 72
                                      555666666667778899*****************98754 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7.9
                      Mg_chelatase   5 vkGqeeakraleiaaaGgHnlllvGppGsGKtmlakr.lpsllpplseeealev 57 
                                       + G  +++ ++ +a a g +++++  p +G  ++ ++ + s l +l++e+ +++
  gi|518653046|ref|YP_008142566.1| 174 LSGGMKQRAVIAMALALGPDIVIADEPTTGLDVITQAeIISQLKKLKQENKIKS 227
                                       677888899999999999999999999999988876436677777777776665 PP

  == domain 3  score: 3.2 bits;  conditional E-value: 0.13
                      Mg_chelatase  27 lvGppGsGKtmlakrlpsll 46 
                                       +vG +GsGKt l + l +l 
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLY 427
                                       79************999876 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.032        12       4      21 ..      49      66 ..      46     157 .. 0.84
   2 ?   -1.5   0.0       7.1   2.8e+03      29      56 ..     199     228 ..     195     237 .. 0.65
   3 !    7.8   0.1    0.0092       3.6       4      25 ..     408     429 ..     406     467 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.032
                                      EESSTTSSHHHHHHCHCT CS
                               Roc  4 lvGdsgvGKtsllkrfve 21
                                      ++G+sg+GK++++ ++++
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMS 66
                                      89**********999985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 7.1
                                       ETTTTEEEEE..EECGGSGGCTTBTTTTCE CS
                               Roc  29 kstigvdflt..kevtkikgvendkkvkkv 56 
                                       ++t+g+d++t  + ++++k++++++k+k++
  gi|518653046|ref|YP_008142566.1| 199 EPTTGLDVITqaEIISQLKKLKQENKIKSL 228
                                       689999998832334566677777766655 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0092
                                       EESSTTSSHHHHHHCHCT-CCC CS
                               Roc   4 lvGdsgvGKtsllkrfvedkfs 25 
                                       +vG+sg+GKt+l + +++    
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEA 429
                                       8***********9999864333 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 ?   10.3   0.1    0.0014      0.56       6      25 ..      51      70 ..      49     245 .. 0.79
   2 ?    4.1   0.2      0.11        44       6      25 ..     410     429 ..     405     436 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0014
                                      SSTTSSHHHHHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxx RF
                              CbiA  6 tkGGvGKTtlaanLaralar 25
                                      + +G+GK+t+a +++ +la 
  gi|518653046|ref|YP_008142566.1| 51 GESGSGKSTIAMSIMSLLAP 70
                                      679***************96 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.11
                                       SSTTSSHHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              CbiA   6 tkGGvGKTtlaanLaralar 25 
                                       + +G+GKTtl  +L+++   
  gi|518653046|ref|YP_008142566.1| 410 GESGSGKTTLGRTLIKLYEA 429
                                       78********9999887766 PP

>> tRNA_lig_kinase  tRNA ligase kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.092        36       9      67 ..      54     110 ..      50     157 .. 0.65
   2 ?   -2.0   0.0       8.8   3.4e+03      27      41 ..     356     371 ..     349     392 .. 0.76
   3 ?    7.3   0.0     0.012       4.8       8      62 ..     412     472 ..     405     493 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.092
                                       TSSHHHHHHHHHHH-TTSEEEEGGGS-TT-SS-HHHHHHHTTSSTT--EEEEES---SH CS
                   tRNA_lig_kinase   9 GCGkttvaltlenlfgeWghvqnDnitgkdkkklvkealellkkdeskvvlvDrnnhqk 67 
                                       G Gk+t+a+ + +l +  + +++  it kd++  v+ + + ++++ +k ++ +  n   
  gi|518653046|ref|YP_008142566.1|  54 GSGKSTIAMSIMSLLA-PNAIVDGSITFKDNTY-VSGSATKISRKSKKTLYENLRNMRW 110
                                       8899999999999988.6788888888866554.4444444556666655555444443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 8.8
                                       EEEEGGGS-TT.-SS- CS
                   tRNA_lig_kinase  27 ghvqnDnitgk.dkkk 41 
                                        +v nDni ++ + kk
  gi|518653046|ref|YP_008142566.1| 356 YVVSNDNIIETkNLKK 371
                                       5799***966524444 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.012
                                       TTSSHHHHHHHHHHH-....TT.SEEEEGGGS.-TT.-SS-HHHHHHHTTSSTT--EEEEES CS
                   tRNA_lig_kinase   8 iGCGkttvaltlenlf....ge.WghvqnDni.tgk.dkkklvkealellkkdeskvvlvDr 62 
                                        G Gktt  +tl +l+    g+ + h+ n  i  +k +kk+  +e  +++ k ++++++ D 
  gi|518653046|ref|YP_008142566.1| 412 SGSGKTTLGRTLIKLYeatgGNiYYHLNNKTIdITKlTKKNRSEEEYKEF-KRNIQMIFQDP 472
                                       599*************6665568889999988544458999999999999.78889998885 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.3    0.0043       1.7      42      64 ..      47      69 ..      17      73 .. 0.75
   2 ?    5.8   0.1      0.02       7.7      44      60 ..     408     424 ..     393     426 .. 0.92
   3 ?   -2.5   0.0       6.9   2.7e+03      77      88 ..     476     487 ..     445     512 .. 0.57

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0043
                                      EEEE--TTSSHHHHHHHHHHHHH CS
                      FtsK_SpoIIIE 42 llvaGatgsGKStalntLilSla 64
                                      l ++G +gsGKSt  ++++  la
  gi|518653046|ref|YP_008142566.1| 47 LGILGESGSGKSTIAMSIMSLLA 69
                                      449************99765444 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.02
                                       EE--TTSSHHHHHHHHH CS
                      FtsK_SpoIIIE  44 vaGatgsGKStalntLi 60 
                                       ++G +gsGK+t  +tLi
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLI 424
                                       9**************99 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 6.9
                                       E-TTSSSCGGGT CS
                      FtsK_SpoIIIE  77 iDykgvelsale 88 
                                       +D+k++ +  ++
  gi|518653046|ref|YP_008142566.1| 476 LDPKMTVFDIVS 487
                                       455555444333 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.056        22       5      25 ..      53      73 ..      49     103 .. 0.83
   2 ?    7.2   0.5    0.0095       3.7       5      47 ..     412     454 ..     408     496 .. 0.79
   3 ?    0.2   0.0       1.3   5.1e+02      95     141 ..     458     501 ..     454     514 .. 0.79

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.056
                                      TTSSHHHHHHHHHHHHHHTTE CS
                   Thymidylate_kin  5 DGaGKttqaellkerlkeegi 25
                                       G+GK+t+a+ +++ l  ++i
  gi|518653046|ref|YP_008142566.1| 53 SGSGKSTIAMSIMSLLAPNAI 73
                                      69*************999887 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0095
                                       TTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHH CS
                   Thymidylate_kin   5 DGaGKttqaellkerlkeegikvvltrepggteiGekirelll 47 
                                        G+GKtt  ++l + +++ g +++    +++ +i ++ ++  +
  gi|518653046|ref|YP_008142566.1| 412 SGSGKTTLGRTLIKLYEATGGNIYYHLNNKTIDITKLTKKNRS 454
                                       69******************99888888888888877776655 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.3
                                       HHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSST CS
                   Thymidylate_kin  95 YqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrdel 141
                                       Y+++k+   ++++ +  +d l  P +t++  v++ v + R + + e+
  gi|518653046|ref|YP_008142566.1| 458 YKEFKR--NIQMIFQDPYDSL-DPKMTVFDIVSEPVIAHRYTNNPEE 501
                                       677777..4888888888987.9**********99999999998883 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.1      0.03        12      16      37 ..      41      62 ..      30      68 .. 0.89
   2 ?    7.9   1.0    0.0046       1.8      16      39 ..     400     423 ..     390     515 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.03
                            ATPase 16 ipegrvvlitGepGtGKtifal 37
                                      + eg++  i Ge+G+GK+++a+
  gi|518653046|ref|YP_008142566.1| 41 LHEGETLGILGESGSGKSTIAM 62
                                      67899999***********997 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0046
                            ATPase  16 ipegrvvlitGepGtGKtifalqF 39 
                                       + +g++  i+Ge+G+GKt+++ + 
  gi|518653046|ref|YP_008142566.1| 400 LRRGEILGIVGESGSGKTTLGRTL 423
                                       5789999*************9874 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 ?    3.3   0.0      0.16        62       1      19 [.      49      67 ..      49      73 .. 0.84
   2 ?    8.5   0.0    0.0041       1.6       1      28 [.     408     435 ..     408     465 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.16
                        ATP_bind_1  1 vvGpaGsGKttfvgalsei 19
                                      ++G  GsGK+t+  +++++
  gi|518653046|ref|YP_008142566.1| 49 ILGESGSGKSTIAMSIMSL 67
                                      689********99888776 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0041
                        ATP_bind_1   1 vvGpaGsGKttfvgalseilelrgrsva 28 
                                       +vG  GsGKtt+ ++l++++e++g +++
  gi|518653046|ref|YP_008142566.1| 408 IVGESGSGKTTLGRTLIKLYEATGGNIY 435
                                       79******************99987765 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.015       5.7      30      55 ..      41      66 ..      35      81 .. 0.85
   2 ?    4.0   0.0     0.084        33      30      49 ..     400     419 ..     394     424 .. 0.88
   3 ?   -2.6   0.0         9   3.5e+03     141     172 ..     476     510 ..     446     514 .. 0.66

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.015
                            AAA_25 30 lpagelallaGapgtGKttlaldlal 55
                                      l +ge+  + G +g+GK+t+a++++ 
  gi|518653046|ref|YP_008142566.1| 41 LHEGETLGILGESGSGKSTIAMSIMS 66
                                      6688888899************9875 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.084
                            AAA_25  30 lpagelallaGapgtGKttl 49 
                                       l++ge+  ++G +g+GKttl
  gi|518653046|ref|YP_008142566.1| 400 LRRGEILGIVGESGSGKTTL 419
                                       78999999***********8 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9
                            AAA_25 141 egvrlvviDplsr.algg.densnsdv.galveal 172
                                        ++++ v+D +s+ + ++   n+ +++ +++ +al
  gi|518653046|ref|YP_008142566.1| 476 LDPKMTVFDIVSEpVIAHrYTNNPEEMqNMVAAAL 510
                                       46899999999997777744444455644444444 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1    0.0047       1.8       3      35 ..      48      79 ..      46     100 .. 0.89
   2 ?    4.1   0.2       0.1        40       3      25 ..     407     429 ..     405     435 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0047
                                      EEE--TTSSHHHHHHHHHHHH...GGGEEEEEE CS
                          NTPase_1  3 fiTGppGvGKtTlvkkvlellkssgvkvgGfyt 35
                                       i G++G+GK+T+   +++ll   +  v+G +t
  gi|518653046|ref|YP_008142566.1| 48 GILGESGSGKSTIAMSIMSLL-APNAIVDGSIT 79
                                      5779*****************.67899999887 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.1
                                       EEE--TTSSHHHHHHHHHHHH.. CS
                          NTPase_1   3 fiTGppGvGKtTlvkkvlellks 25 
                                        i G++G+GKtTl + +++l + 
  gi|518653046|ref|YP_008142566.1| 407 GIVGESGSGKTTLGRTLIKLYEA 429
                                       588**********9888877655 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.1     0.066        26      18      39 ..      43      64 ..      32     103 .. 0.83
   2 ?    4.6   0.0      0.05        20      16      36 ..     400     420 ..     390     427 .. 0.86
   3 ?   -2.1   0.0       5.7   2.2e+03     119     185 ..     546     584 ..     536     589 .. 0.51

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.066
                                      H-SEEEEE--TTSSTTHHHHHH CS
                              PhoH 18 kndivfaiGpaGtGKtylaval 39
                                      + + + ++G++G+GK+ +a+++
  gi|518653046|ref|YP_008142566.1| 43 EGETLGILGESGSGKSTIAMSI 64
                                      56678899***********975 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.05
                                       HHH-SEEEEE--TTSSTTHHH CS
                              PhoH  16 lkkndivfaiGpaGtGKtyla 36 
                                       l++ +i+ ++G++G+GKt l 
  gi|518653046|ref|YP_008142566.1| 400 LRRGEILGIVGESGSGKTTLG 420
                                       5677899***********985 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 5.7
                                       -SEEEEE-SGGG--HHHHHHHHTTB-TT-EEEEEE--------------THHHHHHTTT-TTEEEEE CS
                              PhoH 119 ndafvilDEAQnttkeqmkmfltRlGenskvvvtGdvtqidlpkgkksGlaealevlknvegieive 185
                                       + +f+i DE                           +t + l ++ + G  ++l+ +++++++++++
  gi|518653046|ref|YP_008142566.1| 546 KTKFIIADE---------------------------PTSM-LDVSLRAGFMNMLNNIRKTDELSVIY 584
                                       444444444...........................4332.22333455555566555555555555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.1      0.44   1.7e+02      19      45 ..      44      70 ..      24      85 .. 0.74
   2 ?    7.5   0.0    0.0097       3.8      19      44 ..     403     428 ..     384     435 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.44
                                      TEEEEEEESTTSSHHHHHHHHHHHTT- CS
                              TsaE 19 gdvilLeGdLGaGKTtlvrglakalgv 45
                                      g+++ + G+ G+GK+t++ ++++ l  
  gi|518653046|ref|YP_008142566.1| 44 GETLGILGESGSGKSTIAMSIMSLLAP 70
                                      6778899***********999987755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0097
                                       TEEEEEEESTTSSHHHHHHHHHHHTT CS
                              TsaE  19 gdvilLeGdLGaGKTtlvrglakalg 44 
                                       g+++ + G+ G+GKTtl r l+k ++
  gi|518653046|ref|YP_008142566.1| 403 GEILGIVGESGSGKTTLGRTLIKLYE 428
                                       6678899*************998765 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 ?   10.4   0.0    0.0015      0.57      15      97 ..     461     539 ..     455     550 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0015
                          IFT81_CH  15 fnknlnlisfdslsseqlLqvLsdvlaeidekekvdireespeetalrilelLrilkykppedleleefrqglvege 91 
                                       f++n+++i  d  +s   L   + v+  ++e       +++pee++  + ++L+ ++ +pp++  l +f  +l  ge
  gi|518653046|ref|YP_008142566.1| 461 FKRNIQMIFQDPYDS---LDPKMTVFDIVSEPVIAHRYTNNPEEMQNMVAAALKQVNLNPPSNY-LYRFPYELSGGE 533
                                       566666665443333...3333445555555666666789***********************8.************ PP

                          IFT81_CH  92 keviyp 97 
                                       k+ +  
  gi|518653046|ref|YP_008142566.1| 534 KQRVAT 539
                                       *98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       782  (0.0436165); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                       105  (0.00585643); 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):              46  [number of targets reported over threshold]
# CPU time: 0.84u 0.33s 00:00:01.17 Elapsed: 00:00:00.48
# Mc/sec: 4407.60
//
Query:       gi|518653047|ref|YP_008142567.1|  [L=113]
Description: hypothetical protein FACI_IFERC00001G1686 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0059   16.3   1.5     0.0059   16.3   1.5    1.4  2  Tetraspanin  Tetraspanin family
  ------ inclusion threshold ------
       0.21   11.7   3.0        2.4    8.3   0.3    2.3  2  CBP_BcsF     Cellulose biosynthesis protein BcsF
        5.5    7.5   9.2         80    3.8   9.2    2.4  1  DUF202       Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> Tetraspanin  Tetraspanin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.6       1.2   7.3e+03      88      94 ..      17      23 ..      10      33 .. 0.49
   2 !   16.3   1.5   9.8e-07    0.0059       8      65 ..      41     108 ..      36     112 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.2
                                      XXXXXXX CS
                                      xxxxxxx RF
                       Tetraspanin 88 vlfllel 94
                                      +++++++
  gi|518653047|ref|YP_008142567.1| 17 IILIAMI 23
                                      2222222 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 9.8e-07
                                       XXXXXXXXXXXXXXXXXXXXX..........XXX.....................XXXXXXXXXXXXX CS
                                       xxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Tetraspanin   8 fnllfwligivllavGvwlrl..........khaeaalacllsesaedpailaillivvGvllfllgf 65 
                                       + +lf+++g ++++vG w+ +          ++ +    ++ ++ ++++ i++ ++i +G+l +++g+
  gi|518653047|ref|YP_008142567.1|  41 MPVLFFIAGFFVIFVGAWYDFgakkyvtslfQSRQHIEDSDFNDIYKQQLIMTLIFIGIGILYMIVGY 108
                                       6689************99999*********9555555666667788888888888**********997 PP

>> CBP_BcsF  Cellulose biosynthesis protein BcsF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   0.3   0.00041       2.4       6      20 ..      13      27 ..       1      31 [. 0.88
   2 ?    3.9   0.2      0.01        60      11      25 ..      90     104 ..      81     107 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00041
                          CBP_BcsF  6 ivqiiilcaLiflpL 20
                                      ++ iiil+a+if+pL
  gi|518653047|ref|YP_008142567.1| 13 LIPIIILIAMIFIPL 27
                                      688***********9 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.01
                          CBP_BcsF  11 ilcaLiflpLgylla 25 
                                       ++++Lif++ g l++
  gi|518653047|ref|YP_008142567.1|  90 LIMTLIFIGIGILYM 104
                                       789********9986 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   9.2     0.013        80      32      62 ..      67     111 ..      11     113 .] 0.70

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.013
                            DUF202  32 l........tgepsal......gkilglilivlgiltllvglvry 62 
                                                + e s++      + i+ li+i++gil ++vg+v +
  gi|518653047|ref|YP_008142567.1|  67 VtslfqsrqHIEDSDFndiykqQLIMTLIFIGIGILYMIVGYVIF 111
                                       04444444433333333334435899***************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1066  (0.0594567); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 799.09
//
Query:       gi|518653048|ref|YP_008142568.1|  [L=1024]
Description: tricorn protease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      5e-21   75.0   0.0    1.3e-20   73.7   0.0    1.7  1  Peptidase_S41  Peptidase family S41
    5.3e-18   64.8   0.1    1.5e-17   63.4   0.1    1.7  1  Tricorn_PDZ    Tricorn protease PDZ domain
    1.3e-14   54.0   0.2    2.6e-14   53.0   0.2    1.5  1  Tricorn_C1     Tricorn protease C1 domain
    8.6e-09   35.1   8.6     0.0016   18.3   0.1    5.4  5  PD40           WD40-like Beta Propeller Repeat
  ------ inclusion threshold ------
      0.013   15.8   0.3      0.039   14.3   0.3    1.8  1  PDZ_2          PDZ domain
      0.041   12.7   5.8       0.26   10.0   0.2    4.0  4  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
      0.069   13.0   2.7        0.2   11.5   0.1    2.8  2  eIF2A          Eukaryotic translation initiation factor eIF2A
      0.084   12.7   0.0       0.22   11.4   0.0    1.7  1  PDZ_6          PDZ domain


Domain annotation for each model (and alignments):
>> Peptidase_S41  Peptidase family S41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.0   5.7e-24   1.3e-20       1     166 []     834     989 ..     834     989 .. 0.90

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 5.7e-24
                                       EEEEEEES-BCCTHHHHHHHHHHHHHH.TTSSEEEEE-TTB-EBEHHHHHHHHHCCSSSSEEEEEECTTSEEEEEEH CS
                     Peptidase_S41   1 kiGyiripsfsektkeelakalkelkk.knvkglilDlRnNgGGlldeavelaslflddglivstrgrdgkkkkksk 76 
                                       kiGyi+ip+++ +    l+++++ + + +n +gli+DlR+NgGG +++++    +  + g+ v++rg +  +     
  gi|518653048|ref|YP_008142568.1| 834 KIGYIHIPDMGMN---GLNEFFRIFDReANRDGLIVDLRFNGGGFVSQLLLEKLSRKRLGYDVPRRGIILPYP---- 903
                                       79********555...5555555555555********************************************.... PP

                                       TCSS-STT-BSSEEEEEE-TTBBTHHHHHHHHHHHTTSEEEEES-.-SB-EEEEEEEE-TTSSEEEEEEEEEEETTS CS
                     Peptidase_S41  77 tekaseevqykgplvvLvnegsaSaseifagalkdngratlvGer.tfGkgtvqsvvelndgsalkltiakyltpdg 152
                                               + +gp++ L+ne+  S+++i + ++k +++++++G+r ++G  +++ +++l d++ ++ +    + +d 
  gi|518653048|ref|YP_008142568.1| 904 --ID----SVNGPMIALTNEYAGSDGDIGTHVFKLMKLGKVIGTRtWGGVIGINPKIKLIDDTTVTQPQFATWFKDV 974
                                       ..33....49***********************************99999*********999999999988888888 PP

                                       BC.TTTTS---SEE- CS
                     Peptidase_S41 153 rs.iekkGvePdiev 166
                                       +  +e+ G ePdi v
  gi|518653048|ref|YP_008142568.1| 975 KYgLENYGSEPDIYV 989
                                       888**********76 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.4   0.1   6.5e-21   1.5e-17       1      81 [.     721     799 ..     721     805 .. 0.93

  Alignments for each domain:
  == domain 1  score: 63.4 bits;  conditional E-value: 6.5e-21
                                       -B-SEEEEEETTEEEEEEE-BS-TTSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE CS
                       Tricorn_PDZ   1 GlLGadleldkgayriakilpGdswdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvk 77 
                                       G+LG+d+++++g y i+ki++Gd +de+++SPL  + ++  e d+i++++g++++++++++++L+++a++ ++L+v+
  gi|518653048|ref|YP_008142568.1| 721 GKLGIDYTFENGKYVITKIYNGDLSDENEKSPLLYTDIK--ENDVIKSINGVTLDEDNNPDRVLLNHAKEIITLEVE 795
                                       99*********************************9888..99*********************************9 PP

                                       -STT CS
                       Tricorn_PDZ  78 rkdg 81 
                                       ++++
  gi|518653048|ref|YP_008142568.1| 796 KGNE 799
                                       9664 PP

>> Tricorn_C1  Tricorn protease C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.2   1.2e-17   2.6e-14       2      69 ..     642     709 ..     641     710 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.2e-17
                                       HHHHHHHHHHHHHHHHHSS-HH.HHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--S---EE- CS
                        Tricorn_C1   2 aEwaqmfdeawrllrdkFydpd.mhgvDWeavkerYepllprvatrdeladllsemlgeLntsHvyvsg 69 
                                        Ew++m+ +++ l++++F+ ++ +++   ++ + +Y++ll+++++r el+dl++em+ge++tsH+y+ g
  gi|518653048|ref|YP_008142568.1| 642 NEWKNMLYDTFNLIKENFWSKEkLEKLG-DEPYFKYKRLLDKISSRFELSDLMREMQGEYSTSHSYEIG 709
                                       59*****************996377775.79999********************************866 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1     7e-07    0.0016       2      37 ..      34      71 ..      33      72 .. 0.87
   2 ?    4.3   0.0     0.018        40      22      37 ..     199     213 ..     198     214 .. 0.91
   3 ?   -0.8   0.0      0.73   1.6e+03      10      25 ..     364     379 ..     361     379 .. 0.76
   4 ?    0.5   0.1      0.28   6.2e+02      11      26 ..     407     422 ..     402     431 .. 0.82
   5 !   12.0   0.1   6.9e-05      0.15       5      30 ..     451     476 ..     449     483 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 7e-07
                                      EE--SSSS.EEEEEE-TTSSEEEEEEECT..TCEE.EE CS
                              PD40  2 krltntpgnegaPsfSPDGkrlaFsSdRg.sGkpd.Iy 37
                                      +rltn+ g++++P++SPD k+ +F    g sG++  Iy
  gi|518653048|ref|YP_008142568.1| 34 ERLTNNLGIITNPRISPDKKYVYFRLMTGkSGDSSdIY 71
                                      79**********************99988877665677 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.018
                                       EEEEEEECT.TCEEEE CS
                              PD40  22 rlaFsSdRgsGkpdIy 37 
                                        l+F Sd + G+ +Iy
  gi|518653048|ref|YP_008142568.1| 199 NLYFISDHE-GTANIY 213
                                       59******9.*****9 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.73
                                       .EEEEEE-TTSSEEEE CS
                              PD40  10 negaPsfSPDGkrlaF 25 
                                       ++++  +SPD +++a+
  gi|518653048|ref|YP_008142568.1| 364 IIFSLKVSPDNNYIAI 379
                                       5566668******985 PP

  == domain 4  score: 0.5 bits;  conditional E-value: 0.28
                                       EEEEEE-TTSSEEEEE CS
                              PD40  11 egaPsfSPDGkrlaFs 26 
                                       + ++s+S+D   la+s
  gi|518653048|ref|YP_008142568.1| 407 INDFSWSNDSMLLAYS 422
                                       6789*****9888887 PP

  == domain 5  score: 12.0 bits;  conditional E-value: 6.9e-05
                                       -SSSS.EEEEEE-TTSSEEEEEEECT CS
                              PD40   5 tntpgnegaPsfSPDGkrlaFsSdRg 30 
                                       t++ + +++P fS DG++l + S R+
  gi|518653048|ref|YP_008142568.1| 451 TTSGSVDFNPVFSIDGNYLFYLSKRS 476
                                       677779*****************998 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.3   1.7e-05     0.039       3      81 ..     723     806 ..     721     807 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.7e-05
                                       ..XX------..-EEEEE........E-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEE CS
                             PDZ_2   3 lGvsvsdeedtggvlvvs........VkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlR 71 
                                       lG+  + e++  + ++++         +e++P    ++k +Dvi +++g++++++ + ++ ll++ + + ++l+v+ 
  gi|518653048|ref|YP_008142568.1| 723 LGIDYTFENG--KYVITKiyngdlsdENEKSPLLYTDIKENDVIKSINGVTLDEDNNPDRVLLNHAK-EIITLEVEK 796
                                       5555555554..444444444555445788999999****************999999999999865.7899***99 PP

                                       TTEEEEEEEE CS
                             PDZ_2  72 dgkkktvevk 81 
                                       +++ k++ vk
  gi|518653048|ref|YP_008142568.1| 797 GNELKKYYVK 806
                                       9999999887 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.2   0.00012      0.26      23      79 ..      21      84 ..      12     102 .. 0.75
   2 ?   -0.8   0.0      0.23   5.1e+02     248     325 ..     198     226 ..     187     258 .. 0.62
   3 ?    1.5   0.1     0.044        99      28      78 ..     348     399 ..     327     415 .. 0.69
   4 ?   -1.9   0.0      0.49   1.1e+03     259     298 ..     434     471 ..     425     481 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                                      TEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEE.......EETTEEEEESTTTSEEEECE CS
                           DPPIV_N 23 aeyyiydletneveelspgeeklqlakwSPagdklaf.......vrnnnLyvrelatgkeiqlT 79
                                      ++++ y++ +++ve+l+++ + ++ +++SP++++++f         ++++y  ++++g+  ++T
  gi|518653048|ref|YP_008142568.1| 21 NDLWTYNIDDKNVERLTNNLGIITNPRISPDKKYVYFrlmtgksGDSSDIYSIDIENGNLNRIT 84
                                      6789999999999999999999999999999999999332222224567777777777777776 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.23
                                       SEEEEEEETTSSEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEESSSETTEBEEEEEESSCTTEEEES CS
                           DPPIV_N 248 sgflwisekdGfkHLylfdldgkseikqlTsGeweVtsilavdekrdlvyFtatkdsPlerhlYsvslesggeltrl 324
                                       +++++is+++G   +y  dl+g++                                                 +t+ 
  gi|518653048|ref|YP_008142568.1| 198 DNLYFISDHEGTANIYSTDLNGNN-------------------------------------------------ITKH 225
                                       444555555555555555555555.................................................3333 PP

                                       S CS
                           DPPIV_N 325 t 325
                                       t
  gi|518653048|ref|YP_008142568.1| 226 T 226
                                       3 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.044
                                       EETTTEECEEEETT.....TT.BSEEEEESSTTEEEEEET.TEEEEESTTTSEEEEC CS
                           DPPIV_N  28 ydletneveelspg.....eeklqlakwSPagdklafvrn.nnLyvrelatgkeiql 78 
                                       y++ +        +     ++ +   k+SP+++++a  +n  +L++ ++++g   ++
  gi|518653048|ref|YP_008142568.1| 348 YNIDKTLR-----NsfefrNGIIFSLKVSPDNNYIAIGNNrYELFILNIKDGGINKI 399
                                       44444333.....2344458899999***********987369**999988855544 PP

  == domain 4  score: -1.9 bits;  conditional E-value: 0.49
                                       SEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEE CS
                           DPPIV_N 259 fkHLylfdldgkseikqlTsGeweVtsilavdekrdlvyF 298
                                        + + l+dl+++++  + TsG+ +   + ++d   + +++
  gi|518653048|ref|YP_008142568.1| 434 SSSIKLYDLKSNKKYDATTSGSVDFNPVFSIDG--NYLFY 471
                                       455677788887766688888887755555553..34444 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.7      0.62   1.4e+03      82     112 ..     322     352 ..     316     362 .. 0.81
   2 ?   11.5   0.1   8.9e-05       0.2      38      98 ..     383     450 ..     362     470 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
                                       SCEEEEEECSCEEEEEEEEES--EEEE-TTS CS
                             eIF2A  82 pakvslfdlkvkviskleeqkrNtiffspkg 112
                                       ++ +++ +++  v+++++e+++N ++++   
  gi|518653048|ref|YP_008142568.1| 322 NQIIEFMNNNNVVVYNYNEDNNNILIYNIDK 352
                                       5678888999999999999999999998665 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 8.9e-05
                                       EEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEE......EESSSSC.EEEEEECSCEEEEEE CS
                             eIF2A  38 etelyliklkkkksevvelkkegpihdvaWspkskefav......iyGkmpa.kvslfdlkvkviskl 98 
                                         el+++++k++ ++ ++ +k g i d++Ws++s  +a        yG+  + +++l+dlk +++++ 
  gi|518653048|ref|YP_008142568.1| 383 RYELFILNIKDGGINKIDESKSGVINDFSWSNDSMLLAYsypeteYYGYNGSsSIKLYDLKSNKKYDA 450
                                       468*****************************998887622222246776665888888888877664 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.7e-05      0.22      12      55 ..     754     795 ..     744     796 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-05
                             PDZ_6  12 drAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvvr 55 
                                           ++ +D+i s+NG+++     +   + l ++a e+++l+v+
  gi|518653048|ref|YP_008142568.1| 754 LYTDIKENDVIKSINGVTL--DEDNNPDRVLLNHAKEIITLEVE 795
                                       5567999************..*********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1024 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       835  (0.0465726); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.76u 0.29s 00:00:01.05 Elapsed: 00:00:00.46
# Mc/sec: 6748.27
//
Query:       gi|518653049|ref|YP_008142569.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete 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-23   80.7   0.0    2.1e-22   79.5   0.0    1.6  2  rve             Integrase core domain
    2.1e-06   27.4   1.3    6.3e-05   22.7   1.3    2.6  1  rve_3           Integrase core domain
    0.00042   20.9   0.1     0.0014   19.2   0.1    1.9  1  HTH_32          Homeodomain-like domain
     0.0062   16.3   0.2      0.017   14.9   0.2    1.7  1  HTH_23          Homeodomain-like domain
  ------ inclusion threshold ------
      0.057   13.4   0.1       0.99    9.5   0.0    2.7  2  Put_DNA-bind_N  Putative DNA-binding protein N-terminus
      0.093   13.2   4.3       0.21   12.1   4.1    1.7  2  Terminase_2     Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.2   6.6e+03      82      95 ..      80      93 ..      43      99 .. 0.64
   2 !   79.5   0.0     7e-26   2.1e-22       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.2
                               rve 82 afrefladlgirvs 95
                                      ++r++l++ gi++ 
  gi|518653049|ref|YP_008142569.1| 80 RIRKYLKRKGITIA 93
                                      67778888887765 PP

  == domain 2  score: 79.5 bits;  conditional E-value: 7e-26
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ + +e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518653049|ref|YP_008142569.1| 125 EHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYNEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l +++i++ + r+++p++nGk Er + t+k+
  gi|518653049|ref|YP_008142569.1| 195 FSNgkngipgdhnKFQEYLDNNNIKHILGRVRHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   1.3   2.1e-08   6.3e-05       2      63 ..     217     268 ..     216     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 2.1e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518653049|ref|YP_008142569.1| 217 NIKHILGRVRHPETNGKLERLNYTIKRLSPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       68999*********************988776655..........89*************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   4.6e-07    0.0014       3      73 .]      36     101 ..      34     101 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.6e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+   ++ +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518653049|ref|YP_008142569.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDVEIVKEIRYEYPMSGPERIRKYL-KRKGITIAKNNIYRIL 101
                                       566778888886666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   5.7e-06     0.017      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 5.7e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518653049|ref|YP_008142569.1| 11 IIREKNKRRSSTEIAKEMKITARYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Put_DNA-bind_N  Putative DNA-binding protein N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00033      0.99      22      42 ..      13      33 ..       6      36 .. 0.82
   2 ?    0.6   0.0       0.2     6e+02       6      15 ..     240     249 ..     238     254 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00033
                                      HTT--EE-HHHHHHHCTS-HH CS
                    Put_DNA-bind_N 22 eegveriSSteLaealgvtaa 42
                                      +e+ +r SSte+a+++++ta 
  gi|518653049|ref|YP_008142569.1| 13 REKNKRRSSTEIAKEMKITAR 33
                                      5566888***********986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.2
                                       HHHHHHHHHH CS
                    Put_DNA-bind_N   6 tikRLplYlr 15 
                                       tikRL+ Y +
  gi|518653049|ref|YP_008142569.1| 240 TIKRLSPYFS 249
                                       9*****9986 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.1   6.9e-05      0.21      40     111 ..       3      75 ..       1     125 [. 0.77
   2 ?   -2.0   0.0       1.6   4.7e+03      45      45 ..     218     218 ..     163     257 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.9e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vke++ + ++
  gi|518653049|ref|YP_008142569.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITARYVNYIYKKYRDNGEyTIGKRKHRELNSKDVEIVKEIRYEYPM 75 
                                       8999****************************88888888776663346677888999888888888874433 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.6
                       Terminase_2  45 I 45 
                                       I
  gi|518653049|ref|YP_008142569.1| 218 I 218
                                       2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1030  (0.0574488); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2044.71
//
Query:       gi|518653050|ref|YP_008142570.1|  [L=1365]
Description: hypothetical protein FACI_IFERC00001G1689 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.7e-42  145.7   9.2    1.7e-42  145.7   9.2    2.4  2  SBP_bac_5  Bacterial extracellular solute-binding proteins, f
      5e-05   23.2  25.9    0.00033   20.6   0.1    6.1  5  Big_1      Bacterial Ig-like domain (group 1)
  ------ inclusion threshold ------
      0.011   15.9   0.5       0.46   10.7   0.0    3.2  2  MG4        Macroglobulin domain MG4
      0.042   14.3   0.0       0.33   11.4   0.0    2.5  2  MG2        MG2 domain
      0.092   12.6   0.1       0.64    9.9   0.0    2.5  2  DUF824     Salmonella repeat of unknown function (DUF824)


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 !  145.7   9.2   4.8e-46   1.7e-42       2     373 ..     112     621 ..     111     625 .. 0.86
   2 ?   -1.0   0.1      0.18   6.6e+02      27      87 ..    1231    1316 ..    1228    1341 .. 0.68

  Alignments for each domain:
  == domain 1  score: 145.7 bits;  conditional E-value: 4.8e-46
                                       EEESSEEEEE.................EEETTTTEEEEEE-TT-B-TTSSB-SHHHHHH.....H............ CS
                         SBP_bac_5   2 vvpaLAesww.................evsdDgktytfkLRkgvkFsDGtpltAeDvvf.....s............ 44 
                                       v p+LA+ +                  + +  + +yt+++R gvk++D+t  +A D        +            
  gi|518653050|ref|YP_008142570.1| 112 VGPWLATGVTgysvaghnittvdplngTKMNVNYIYTLHIRSGVKWQDWTSANAGDTYSypltqTflgtngkpadvn 188
                                       7899999988999999999999999998899999****************999988777343322222222222222 PP

                                       HHHHHTGGGHCTTHHHHHC..............................................TCTEEEEEEEET CS
                         SBP_bac_5  45 ferlldpdtasgyasllee..............................................dqdikkveavdd 75 
                                                                                                        + +i++++ v++
  gi|518653050|ref|YP_008142570.1| 189 N-----------------TiiydtavghnitvatknltmqtydvqsadfilsweilfesedfegeYPSIVNIVPVNN 248
                                       0.................1234557777777777777778************************************* PP

                                       TEEEEEESSETT..TTTTHCHHHHHHHGC..........................CHTCTCTTTTTGTTTSE-BSSS CS
                         SBP_bac_5  76 ytvrftlkkpna..lfltllaavpasiak..........................kaaekeddkdkdtnekpvgtGP 124
                                       +tv+++l++p +  lf ++  ++p+ +++                          + ++   ++++ +++ +vg+GP
  gi|518653050|ref|YP_008142570.1| 249 LTVEYYLSTPVPisLFKETALDTPIMPYNvwdshayssisglwnysatlpssgayNTWNLGYNPSTGYAPGLVGSGP 325
                                       ************997888888888888889999999***************************************** PP

                                       EEEEE........EETTTEEEEEE-TTST.......TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEE..ESTTCC CS
                         SBP_bac_5 125 Yklke........fkpgqkivlernpdYw.......gggkpkldriefkvipdsdaraaalqsGeiddv..aeppps 184
                                       Y++++        +   ++  l+ npdY+       ++  pk+ +i   ++++++a++a+l  G+  ++  + +p++
  gi|518653050|ref|YP_008142570.1| 326 YMMYAgfgmpkgaWISSDYWQLYVNPDYFvqyvpslSQFTPKVYSIYAAIYTSDSAAVASLSDGQT-YAmlNALPAT 401
                                       ********9999988889**********98888888888889999999999888888888888887.444799**** PP

                                       THCHHHHHTTEEEEEEEEEEEEEEEEETTT..STGGGSHHHHHHHHHHS-HHHHHHHCTTTSSEEESSSSTTTSTTC CS
                         SBP_bac_5 185 dieqlkeakglkvlyespgggvtylafNtk..kppfddkrvRqAlsyAiDreeivkavlegyatpansllppsspga 259
                                       +i+++k  ++ ++ y+++g+g++y ++ ++  ++pf+ +++R Al yAi+++ ++ +v egy +p++ ++ p s+  
  gi|518653050|ref|YP_008142570.1| 402 FIPTVKGIPSSYI-YDKAGTGYGYQQVSSYaaNAPFNITDLRVALEYAIPKTYLASVVAEGYSIPGPDTPVPDSDIL 477
                                       *************.*******************************************************99999999 PP

                                       CSCHCCCSHHSHHHHHHHHHHHTT-BCSSTSCEETC.........................EEEEEEEEETTSHHHH CS
                         SBP_bac_5 260 deeykpaykaydpekAkklLkeaGykdgdggglrek.........................klkltlllasgspaek 311
                                       ++    +y+++d++kAk ++++a + +++     ++                         +++++++ as++p+  
  gi|518653050|ref|YP_008142570.1| 478 WQASGVPYYHFDLAKAKSYIDDAINATKGM---PSAnvlsysrttpgvlsgttlyyggkpvTQTIQITSASEDPLGV 551
                                       999999999*****************9974...33347899************************************ PP

                                       HHHHHHHHHHHHTTEEEEEEEECHH........HHHHHHHHCTTESEEEEEEECTTSTTHHHHHHHHSTT CS
                         SBP_bac_5 312 aiaeliqqqlkkiGikvevktvdwa........atylervkdgdfdmillgwgadypdpdnflnpflsss 373
                                       + a+ i+ ++ ++Gi ++vk  +++        +  ++++  ++ d++l+++  +++d+ + +++ + ++
  gi|518653050|ref|YP_008142570.1| 552 EGANKIATYWTDLGISTTVKEESFStlvanlgaQSPTNPTAFQEIDLALSDIVLNPADDLSAFENSYLGA 621
                                       **********************777799998853333356667777777777777777777776666655 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.18
                                        T-B-TTSSB-SHHHHHHH......HHHHHTGGGHCTTHHHHHC...................TCTEEEEEEEETT CS
                         SBP_bac_5   27 gvkFsDGtpltAeDvvfs......ferlldpdtasgyasllee...................dqdikkveavddy 76  
                                        g+ +s+G+ +  +D +++      ++ +++p ++  +    ++                   + ++k v+++ + 
  gi|518653050|ref|YP_008142570.1| 1231 GASYSNGSYFILSDHKYTmyinstYNTAAGPSYKDLSFTASTNyghisvskgstgssgsyklTYTSKPVTTITKI 1305
                                        677899999999999995442222555555555555544444488888888888888888887788888888888 PP

                                        EEEEEESSETT CS
                         SBP_bac_5   77 tvrftlkkpna 87  
                                        tv++tl+    
  gi|518653050|ref|YP_008142570.1| 1306 TVTLTLAGSGQ 1316
                                        88888887744 PP

>> Big_1  Bacterial Ig-like domain (group 1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.1   9.1e-08   0.00033       9      52 ..     793     841 ..     791     862 .. 0.85
   2 ?   -3.8   0.4       3.7   1.3e+04      18      41 ..     922     949 ..     921     952 .. 0.66
   3 !    6.4   0.8    0.0025       9.1       2      34 ..    1081    1112 ..    1080    1132 .. 0.73
   4 !    4.6   0.8     0.009        32      33      55 ..    1136    1160 ..    1125    1163 .. 0.82
   5 !    5.2   2.3    0.0058        21      28      59 ..    1268    1301 ..    1263    1310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 9.1e-08
                             Big_1   9 ltatvkDangnpvagatVtfsvsg..gals...assgtTdanGkatvtl 52 
                                       lt+ v++++g+++++++V++   +  g ++   + sg+T++nG++ +++
  gi|518653050|ref|YP_008142570.1| 793 LTIQVRNQYGQAMPNIPVSIGYIAsdGGIVnitSVSGKTNSNGIYHFEF 841
                                       89****************985433334444588************9976 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.7
                             Big_1  18 gnpvagatVtfsvsggals....assgt 41 
                                       g+p++g + t+++ +g +     ++++ 
  gi|518653050|ref|YP_008142570.1| 922 GTPISGYQYTVESLSGLVQlvntTNQVL 949
                                       8899999888888776554445555555 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0025
                             Big_1    2 dGvdtntltatvkDangnpvagatVtfsvsg..ga 34  
                                        +G++  tltat   ++g+p+++ ++t+++ +  ga
  gi|518653050|ref|YP_008142570.1| 1081 NGTEMMTLTAT---QDGKPLSNYNITVTAQNalGA 1112
                                        66666666665...78*************996554 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.009
                             Big_1   33 gals..assgtTdanGkatvtltst 55  
                                        g++s  + ++tT++ G+a v++t +
  gi|518653050|ref|YP_008142570.1| 1136 GSTSmpEYTVTTNSAGVAYVNFTAS 1160
                                        455567789*************975 PP

  == domain 5  score: 5.2 bits;  conditional E-value: 0.0058
                             Big_1   28 fsvsg..galsassgtTdanGkatvtltstkagt 59  
                                        f++s   g +s s+g T+++G +  t ts+   t
  gi|518653050|ref|YP_008142570.1| 1268 FTASTnyGHISVSKGSTGSSGSYKLTYTSKPVTT 1301
                                        6666558*********************986555 PP

>> MG4  Macroglobulin domain MG4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00013      0.46      18      65 ..     793     844 ..     790     873 .. 0.75
   2 ?    1.4   0.1     0.098   3.5e+02      24      63 ..    1091    1158 ..    1084    1168 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00013
                               MG4  18 ikVlvkdpdgspaknvpVkiealk.....seteekeslttdedGtakfsintp 65 
                                       ++++v ++ g+ ++n+pV+i ++       + ++  s +t+++G+  f + ++
  gi|518653050|ref|YP_008142570.1| 793 LTIQVRNQYGQAMPNIPVSIGYIAsdggiVNITS-VSGKTNSNGIYHFEFLVT 844
                                       79********************433455533344.446789999999987654 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.098
                               MG4   24 dpdgspaknvpVkiealk.............................seteekeslttdedGtakfsin 63  
                                         +dg+p++n  ++++a +                             s +  + ++tt++ G+a++++ 
  gi|518653050|ref|YP_008142570.1| 1091 TQDGKPLSNYNITVTA-QnalganrglvygtstlgttsatdpnsafgSTSMPEYTVTTNSAGVAYVNFT 1158
                                        5688888888888888.3245555666666666667777777777764455556778888888877665 PP

>> MG2  MG2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.2e-05      0.33       6      68 ..     780     844 ..     775     849 .. 0.88
   2 ?   -1.7   0.0       1.2   4.2e+03      19      43 ..    1085    1109 ..    1079    1114 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.2e-05
                                       ES-SEE-TT-EEEEEEEEESTTCSB---EEEEEEEE-TTSSEEEEEEE..EE-CTTEEEEEEE-- CS
                               MG2   6 tDRglYrPgetVslkallrdetlqglaklplkltirdpdgkevkelpl..atdetggaesefalp 68 
                                       +  ++Y  g+  +l++ +r++ +q++++ p+++    +dg+ v+ +++  +t+++g++++ef + 
  gi|518653050|ref|YP_008142570.1| 780 SNSKIYYSGQYGNLTIQVRNQYGQAMPNIPVSIGYIASDGGIVNITSVsgKTNSNGIYHFEFLVT 844
                                       55689****************************99999999888888778***********9775 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.2
                                        EEEEEESTTCSB---EEEEEEEE-T CS
                               MG2   19 lkallrdetlqglaklplkltirdp 43  
                                        +  l+ ++++++l ++++++t +++
  gi|518653050|ref|YP_008142570.1| 1085 MMTLTATQDGKPLSNYNITVTAQNA 1109
                                        5556677888888888888887765 PP

>> DUF824  Salmonella repeat of unknown function (DUF824)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00018      0.64      16      36 ..     792     812 ..     791     817 .. 0.93
   2 ?   -2.8   0.0       1.6   5.7e+03      31      39 ..    1099    1107 ..    1086    1112 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00018
                            DUF824  16 pltitvkDasGnPvpnapftl 36 
                                       +lti v++  G+++pn p+++
  gi|518653050|ref|YP_008142570.1| 792 NLTIQVRNQYGQAMPNIPVSI 812
                                       69*****************98 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.6
                            DUF824   31 napftltRg 39  
                                        n  +t+t  
  gi|518653050|ref|YP_008142570.1| 1099 NYNITVTAQ 1107
                                        555555433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       881  (0.0491383); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.94u 0.30s 00:00:01.24 Elapsed: 00:00:00.51
# Mc/sec: 8059.64
//
Query:       gi|518653051|ref|YP_008142571.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G1690 [Ferroplasma acidarmanus fer1]
Scores for complete 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   46.3   1.0    1.3e-11   44.5   0.1    2.2  2  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.1      0.05   8.9e+02     143     167 ..      64     152 ..      12     156 .. 0.51
   2 !   44.5   0.1   7.5e-16   1.3e-11      22     212 ..     196     410 ..     176     412 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.05
                         DDE_Tnp_1 143 k................................................................skkekgdvyyvt 155
                                       +                                                                s ke++d +y++
  gi|518653051|ref|YP_008142571.1|  64 YigritengivsndksrsvyeygnseliysvskdiikllkkhfpdtwesiyamsvvrlisytpmkSIKERWDKLYMS 140
                                       02222222333333444334445555556666666666666666666666666666666666666667777777777 PP

                         DDE_Tnp_1 156 ntnsellsaeev 167
                                          + ++s+ ++
  gi|518653051|ref|YP_008142571.1| 141 RYINAHVSPNTL 152
                                       777777777666 PP

  == domain 2  score: 44.5 bits;  conditional E-value: 7.5e-16
                         DDE_Tnp_1  22 darwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvlaDaGYasaelldtlee 97 
                                        a +g++ +++y++ +++ +++d+    ++ ++  +g+v d+k l+ +l+e++   + ++++D+G+as++l+d++  
  gi|518653051|ref|YP_008142571.1| 196 MAEKGHNhEHEYIPQINIAMVFDLDYYKPVFLKSLDGSVRDIKSLRKVLEEIN--FNGVLVMDRGFASYSLADEIN- 269
                                       56789996777***************999999988******************..8********************. PP

                         DDE_Tnp_1  98 kgvdyiirlkkntklyrk...............gaeskrrgrlrkhdrnkiltksqkrrnk................ 143
                                          ++i++l+ n ++ +                 ++s++ g+++  + +++l  s++++++                
  gi|518653051|ref|YP_008142571.1| 270 --NKFIMPLRRNNNIIDYsiefkssfmyrdrgiLCTSYKYGKYTIYIFQDQLLMSEEANTFisliadnkksqddyns 344
                                       ..99*****88888888877777755554455544444444444444444444444444448889999999988888 PP

                         DDE_Tnp_1 144 skkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                       + k  g   +++n+++   ++e +  +y++R +iE++F  +k+ +  d+ ++++ + ++ ++++ + +l
  gi|518653051|ref|YP_008142571.1| 345 ASKVFGKIAILSNIDD---KPENIYLMYKQREEIEQSFDAMKNELENDKSYLSNDDSIRGYFFISFVSL 410
                                       7777777777777777...9****************************************999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       862  (0.0480785); expected 358.6 (0.02)
Passed bias filter:                      458  (0.0255452); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3328.50
//
Query:       gi|518653052|ref|YP_008142572.1|  [L=142]
Description: site-specific integrase/recombinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-12   47.1   0.1    2.8e-12   46.7   0.1    1.1  1  Phage_integrase  Phage integrase family
  ------ inclusion threshold ------
       0.11   13.1   0.1       0.29   11.7   0.1    1.8  1  YtxH             YtxH-like protein


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 !   46.7   0.1   3.2e-16   2.8e-12      88     170 ..      15      95 ..       4      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 3.2e-16
                                       CHCCTTTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHH CS
                   Phage_integrase  88 leeaeksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttq 164
                                       ++++++  +lf  k + +++++ +  + + +++++g+  +++ H+ Rh++a +++++ +dl+ + ++lGH++++tt 
  gi|518653052|ref|YP_008142572.1|  15 VRNNNDIPYLFTTK-KGKVTSEYMGNIAQDIKKKTGVI-EFSWHKCRHTYAHNMIKNDIDLESLRQMLGHEDLATTG 89 
                                       45666677888888.55677778889999999999999.9************************************* PP

                                       HHHCCC CS
                   Phage_integrase 165 iYthva 170
                                       iY + +
  gi|518653052|ref|YP_008142572.1|  90 IYSRMN 95 
                                       **9876 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   3.3e-05      0.29      16      42 ..      23      49 ..      21     122 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.3e-05
                              YtxH 16 lLlAPksGketRkdlkekaddlkekak 42
                                      +L++ k+Gk t + + + a+d+k+k+ 
  gi|518653052|ref|YP_008142572.1| 23 YLFTTKKGKVTSEYMGNIAQDIKKKTG 49
                                      79**********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); 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: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1040.24
//
Query:       gi|518653053|ref|YP_008142573.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G1692 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      174  (0.00970495); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.30s 00:00:00.73 Elapsed: 00:00:00.49
# Mc/sec: 328.65
//
Query:       gi|518653054|ref|YP_008142574.1|  [L=78]
Description: hypothetical protein FACI_IFERC00001G1693 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 577.14
//
Query:       gi|518653055|ref|YP_008142575.1|  [L=355]
Description: hypothetical protein FACI_IFERC00001G1694 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.013   15.2   0.0      0.034   13.9   0.0    1.6  1  LexA_DNA_bind  LexA DNA binding domain
      0.017   14.9   0.3      0.049   13.4   0.3    1.8  2  HTH_38         Helix-turn-helix domain
       0.15   12.6   0.0       0.35   11.4   0.0    1.7  1  HTH_27         Winged helix DNA-binding domain


Domain annotation for each model (and alignments):
>> LexA_DNA_bind  LexA DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.6e-06     0.034      27      56 ..      22      51 ..      20      57 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-06
                                      -HHHHHHHHTS-.HHHHHHHHHHHHHTTSE CS
                     LexA_DNA_bind 27 sireiaralglkSpsaveehLkaLerKGyi 56
                                      s rei+r +g kS  +v ++ k+L + Gy+
  gi|518653055|ref|YP_008142575.1| 22 SAREIGRIMGYKSGGTVSKKIKRLINHGYL 51
                                      78**************************97 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.3   8.2e-06     0.049      17      43 ..      17      44 ..      11      45 .. 0.82
   2 ?   -3.9   0.0       2.1   1.2e+04       9      18 ..     186     195 ..     185     196 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.2e-06
                            HTH_38 17 laeGlslreIArrLgr.spsTIsRElkR 43
                                      l  G+s reI+r++g+ s +T+s+ +kR
  gi|518653055|ref|YP_008142575.1| 17 LLTGKSAREIGRIMGYkSGGTVSKKIKR 44
                                      568************7255799999998 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
                            HTH_38   9 eReeIerlla 18 
                                       e e+Ie ll+
  gi|518653055|ref|YP_008142575.1| 186 EVEHIESLLS 195
                                       7899*99987 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.9e-05      0.35      18      68 .]      20      68 ..      14      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.9e-05
                            HTH_27 18 rkkladlcgrlnvedshis.yslkkLtekGLv..ertgdeadrrekrvrlTdkG 68
                                      +k+++++ + + + +  ++ + +k+L+++G++  + ++d      +++++T kG
  gi|518653055|ref|YP_008142575.1| 20 GKSAREIGRIMGYKSGGTVsKKIKRLINHGYLinHISPDN-----RFYSITLKG 68
                                      688999*****999998888************87777777.....999999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (355 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1204  (0.0671538); expected 358.6 (0.02)
Passed bias filter:                      550  (0.0306766); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2502.25
//
Query:       gi|518653056|ref|YP_008142576.1|  [L=200]
Description: resolvase protein [Ferroplasma acidarmanus fer1]
Scores for complete 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  132.0   0.1    2.3e-38  131.6   0.1    1.2  1  Resolvase      Resolvase, N terminal domain
    3.3e-07   30.3   2.0    7.9e-07   29.1   0.8    2.2  2  HTH_7          Helix-turn-helix domain of resolvase
    3.8e-07   29.7   0.2    1.1e-06   28.3   0.1    1.8  1  HTH_23         Homeodomain-like domain
    7.3e-06   25.9   0.2    0.00035   20.5   0.0    2.3  2  HTH_29         Winged helix-turn helix
    1.9e-05   24.7   0.0    4.7e-05   23.4   0.0    1.6  1  HTH_28         Helix-turn-helix domain
    0.00055   19.5   0.5     0.0015   18.1   0.5    1.7  1  CENP-B_N       CENP-B N-terminal DNA-binding domain
      0.001   18.8   0.0     0.0028   17.5   0.0    1.7  1  Phage_AlpA     Prophage CP4-57 regulatory protein (AlpA)
     0.0027   17.4   0.9     0.0027   17.4   0.9    2.1  2  HTH_38         Helix-turn-helix domain
     0.0036   17.2   0.1      0.011   15.5   0.1    1.8  1  TrmB           Sugar-specific transcriptional regulator TrmB
     0.0043   16.7   0.1       0.01   15.5   0.1    1.5  1  Sigma70_r4_2   Sigma-70, region 4
     0.0061   16.6   0.1      0.014   15.4   0.1    1.7  1  HTH_Tnp_IS630  Transposase
     0.0091   16.4   0.5      0.029   14.8   0.2    2.0  2  HTH_40         Helix-turn-helix domain
  ------ inclusion threshold ------
      0.014   15.4   0.3      0.055   13.5   0.3    2.0  2  HTH_3          Helix-turn-helix
      0.018   14.6   0.1      0.046   13.3   0.1    1.7  1  HTH_24         Winged helix-turn-helix DNA-binding
      0.027   14.6   0.2       0.14   12.3   0.0    2.2  2  HTH_17         Helix-turn-helix domain
      0.039   12.9   0.3      0.059   12.3   0.3    1.3  1  TnsD           Tn7-like transposition protein D
      0.056   13.2   0.0       0.12   12.2   0.0    1.5  1  HTH_10         HTH DNA binding domain
      0.094   13.0   1.1       0.45   10.8   0.2    2.3  2  UPF0122        Putative helix-turn-helix protein, YlxM / p13 


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 !  131.6   0.1   2.3e-41   2.3e-38       3     145 ..       5     146 ..       3     147 .. 0.96

  Alignments for each domain:
  == domain 1  score: 131.6 bits;  conditional E-value: 2.3e-41
                                       EEEEES-----THHHHHHHHHHHH-S--..SE...EEEE.S-TT-TT-HHHHHHHHHHTT-EE.EEEESSCCCC-S. CS
                         Resolvase   3 gYaRvSteeqddslerQkealrayakenglkivkefeDkgvSGakleRpglkrllaalregkgdvlvvekldRLaRs 79 
                                       +YaRvSt++++++ e+Q+ +lr+y+++++++  ke++D  +SG+k++Rpglk+ l++l +   d ++v +ldR++Rs
  gi|518653056|ref|YP_008142576.1|   5 LYARVSTKDKEQNPENQLIRLREYCNARKWNY-KEYIDF-ASGSKKDRPGLKQILDDLDK--LDGILVLRLDRFGRS 77 
                                       7********8888***************9999.78****.********************..*************** PP

                                       ..S-HHHHHHHHHTT-EEEESS.....SS----HHHHHHHHHHHHHHHHHHHHHCT-TTHHHHHHHHHH CS
                         Resolvase  80 vrdlltlleelrekgvslvsldeg...idtstpmgrlllqilaalaeferelirertkeglaaakakGk 145
                                       +++ll+ ++ +r++g  +  +d+g    ++++pm+ ++l+il+a aefereli+er+k+g+a+a +++k
  gi|518653056|ref|YP_008142576.1|  78 LQNLLECFNIIRSQGKFFEAIDQGlkiSEKKDPMNDFMLAILGAAAEFERELISERVKDGMARAMKENK 146
                                       **********************98889999***********************************9987 PP

>> HTH_7  Helix-turn-helix domain of resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.9   3.9e+03      13      24 ..     129     140 ..     126     141 .. 0.81
   2 !   29.1   0.8   7.9e-10   7.9e-07       1      39 [.     149     189 ..     149     194 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.9
                                       GGGSSTTTT--S CS
                             HTH_7  13 rvvkLleeGisi 24 
                                        + +++++G+++
  gi|518653056|ref|YP_008142576.1| 129 LISERVKDGMAR 140
                                       688999999987 PP

  == domain 2  score: 29.1 bits;  conditional E-value: 7.9e-10
                                       S---SS-HH..HHGGGGSSTTTT--STTTSSSS---SSSS- CS
                             HTH_7   1 GRpsklskn..dinrvvkLleeGisiskIAkevnisRsTvY 39 
                                       GRp+ l+k+  +   ++kL+e+G si++I  +v+i RsTvY
  gi|518653056|ref|YP_008142576.1| 149 GRPRILDKKniSASKIIKLRESGKSIREISQIVGIKRSTVY 189
                                       9*******9888***************************** PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.3   0.1   1.1e-09   1.1e-06       9      40 ..     163     194 ..     161     197 .. 0.93

  Alignments for each domain:
  == domain 1  score: 28.3 bits;  conditional E-value: 1.1e-09
                            HTH_23   9 rillllaeGlsvreIAreLgvsrrTvyrwlkr 40 
                                       +i++l   G+s+reI+++ g+ r+Tvy ++k 
  gi|518653056|ref|YP_008142576.1| 163 KIIKLRESGKSIREISQIVGIKRSTVYDIIKS 194
                                       59999999*********************995 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.1      0.11   1.1e+02      38      58 ..     135     155 ..     131     158 .. 0.87
   2 !   20.5   0.0   3.5e-07   0.00035       4      36 ..     164     195 ..     163     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.11
                            HTH_29  38 egGlaalld.rrrsgrprnrls 58 
                                       ++G a +++ ++  grpr  l+
  gi|518653056|ref|YP_008142576.1| 135 KDGMARAMKeNKKIGRPRI-LD 155
                                       6899999999*******95.77 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 3.5e-07
                            HTH_29   4 allllaeGvstvsqiAkllglsrrtvyrwlkrf 36 
                                       ++ l + G s +++i +++g+ r+tvy+++k  
  gi|518653056|ref|YP_008142576.1| 164 IIKLRESGKS-IREISQIVGIKRSTVYDIIKSS 195
                                       7888899997.*******************985 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   4.7e-08   4.7e-05       4      34 ..     163     193 ..     163     196 .. 0.95

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 4.7e-08
                            HTH_28   4 eiikllaaGhsvreaArelgisrrtvyrWik 34 
                                       +iikl  +G+s+re+++++gi r+tvy+ ik
  gi|518653056|ref|YP_008142576.1| 163 KIIKLRESGKSIREISQIVGIKRSTVYDIIK 193
                                       6999************************997 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   1.5e-06    0.0015      14      46 ..     163     195 ..     161     198 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.5e-06
                                       HHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH CS
                          CENP-B_N  14 evIqrleegeSkaelarrfnvpestlsdilknK 46 
                                       ++I++ e g+S +e+ +  ++ +st++di+k  
  gi|518653056|ref|YP_008142576.1| 163 KIIKLRESGKSIREISQIVGIKRSTVYDIIKSS 195
                                       79***************************9975 PP

>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   2.8e-06    0.0028       6      28 ..     174     196 ..     173     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.8e-06
                        Phage_AlpA   6 lreVeqktglsrstiYrlikdge 28 
                                       +re+ q++g++rst+Y++ik  e
  gi|518653056|ref|YP_008142576.1| 174 IREISQIVGIKRSTVYDIIKSSE 196
                                       899****************9765 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.82   8.2e+02       9      21 ..     126     138 ..     124     150 .. 0.84
   2 !   17.4   0.9   2.7e-06    0.0027      13      38 ..     164     189 ..     162     193 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.82
                            HTH_38   9 eReeIerllaeGl 21 
                                       eRe I    + G+
  gi|518653056|ref|YP_008142576.1| 126 ERELISERVKDGM 138
                                       9999999999998 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.7e-06
                            HTH_38  13 IerllaeGlslreIArrLgrspsTIs 38 
                                       I +l++ G+s+reI +++g ++sT++
  gi|518653056|ref|YP_008142576.1| 164 IIKLRESGKSIREISQIVGIKRSTVY 189
                                       6689*********************8 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   1.1e-05     0.011      19      45 ..     168     194 ..     165     197 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.1e-05
                                       HHCCCHHCHHCCCTTSSCHCHHHHHHH CS
                              TrmB  19 klgpatadeiaeelgvprskvYevLrs 45 
                                       ++  ++++ei++++g+ rs+vY++++s
  gi|518653056|ref|YP_008142576.1| 168 RESGKSIREISQIVGIKRSTVYDIIKS 194
                                       5677899*****************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 !   15.5   0.1     1e-05      0.01      16      44 ..     162     189 ..     160     191 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1e-05
                                       HHHHHHHHTS---HHHHHHHHT--HHHHH CS
                      Sigma70_r4_2  16 reifllryleglsykEIAellgisegtVk 44 
                                       ++i+ l ++ g+s++EI+++ gi+ +tV+
  gi|518653056|ref|YP_008142576.1| 162 SKIIKL-RESGKSIREISQIVGIKRSTVY 189
                                       689999.79******************95 PP

>> HTH_Tnp_IS630  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.4e-05     0.014       9      42 ..     162     195 ..     155     199 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.4e-05
                     HTH_Tnp_IS630   9 lkvidyiesGggitkaskvfkvgratvyrWlkre 42 
                                        k+i+  esG++i ++s++ ++ r+tvy  +k  
  gi|518653056|ref|YP_008142576.1| 162 SKIIKLRESGKSIREISQIVGIKRSTVYDIIKSS 195
                                       5899999*********************988765 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       5.8   5.8e+03      46      63 ..     127     144 ..     115     156 .. 0.62
   2 !   14.8   0.2     3e-05     0.029       6      31 ..     165     190 ..     160     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 5.8
                            HTH_40  46 erlvseeeekeIeeaiek 63 
                                       ++l+se+ ++ ++ a+++
  gi|518653056|ref|YP_008142576.1| 127 RELISERVKDGMARAMKE 144
                                       345566666666655555 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 3e-05
                            HTH_40   6 lelleeglsieeIAkerglkesTIeg 31 
                                       ++l e+g+si eI+++ g+k+sT+++
  gi|518653056|ref|YP_008142576.1| 165 IKLRESGKSIREISQIVGIKRSTVYD 190
                                       6889********************96 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       3.2   3.2e+03       1      14 [.      25      38 ..      25      49 .. 0.83
   2 ?   13.5   0.3   5.5e-05     0.055       4      32 ..     167     194 ..     156     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 3.2
                                      HHHHHHHTTHHHHH CS
                             HTH_3  1 lkelRkqlglsqee 14
                                      l+e+ +++++  +e
  gi|518653056|ref|YP_008142576.1| 25 LREYCNARKWNYKE 38
                                      79999999999865 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 5.5e-05
                                       HHHHTTHHHHHHHHHHTSSHHHHHHHHTT CS
                             HTH_3   4 lRkqlglsqeeLAeklGvsrstisriEnG 32 
                                       lR + g s++e+++ +G++rst+++i++ 
  gi|518653056|ref|YP_008142576.1| 167 LR-ESGKSIREISQIVGIKRSTVYDIIKS 194
                                       44.49*********************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 ?   13.3   0.1   4.6e-05     0.046      15      39 ..     169     193 ..     163     194 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.6e-05
                            HTH_24  15 nprisqreLAerlglSpstvnrrlk 39 
                                       +++ s+re+++ +g+ +stv   +k
  gi|518653056|ref|YP_008142576.1| 169 ESGKSIREISQIVGIKRSTVYDIIK 193
                                       67889***************99887 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       1.5   1.5e+03      12      25 ..     158     171 ..     140     172 .. 0.80
   2 ?   12.3   0.0   0.00014      0.14       3      24 ..     173     194 ..     173     200 .] 0.87

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.5
                            HTH_17  12 gvsrstvyrlirrg 25 
                                       ++s s++ +l+ +g
  gi|518653056|ref|YP_008142576.1| 158 NISASKIIKLRESG 171
                                       57778888877777 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00014
                            HTH_17   3 tveEaAelLgvsrstvyrlirr 24 
                                       ++ E++++ g++rstvy+ i++
  gi|518653056|ref|YP_008142576.1| 173 SIREISQIVGIKRSTVYDIIKS 194
                                       689***************9985 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3   5.9e-05     0.059     187     223 ..     160     195 ..     130     199 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.9e-05
                              TnsD 187 weerlkeLveeeglslkeiAkelgvdiktVlryakkl 223
                                         +++++L e +g+s++ei++++g++ +tV+ + k+ 
  gi|518653056|ref|YP_008142576.1| 160 SASKIIKLRE-SGKSIREISQIVGIKRSTVYDIIKSS 195
                                       4556677777.********************998865 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00012      0.12      25      49 ..     173     197 ..     170     199 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
                            HTH_10  25 tlkeLAkelGIskstlsehLrkaes 49 
                                       +++e++++ GI++st++++++++e+
  gi|518653056|ref|YP_008142576.1| 173 SIREISQIVGIKRSTVYDIIKSSEK 197
                                       789*******************998 PP

>> UPF0122  Putative helix-turn-helix protein, YlxM / p13 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.66   6.6e+02      52      84 ..      86     118 ..      77     147 .. 0.79
   2 ?   10.8   0.2   0.00046      0.45      35      59 ..     173     197 ..     153     200 .] 0.92

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.66
                           UPF0122  52 dnikrtekllekyEekLkllekykkreelleki 84 
                                       + i+   k++e  ++ Lk+ ek +  ++ +  i
  gi|518653056|ref|YP_008142576.1|  86 NIIRSQGKFFEAIDQGLKISEKKDPMNDFMLAI 118
                                       557777888888999999999988887776655 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00046
                           UPF0122  35 SlsEiAeefnvsrqavydnikrtek 59 
                                       S+ Ei +   ++r++vyd ik  ek
  gi|518653056|ref|YP_008142576.1| 173 SIREISQIVGIKRSTVYDIIKSSEK 197
                                       899******************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       693  (0.0386525); expected 358.6 (0.02)
Passed bias filter:                      540  (0.0301188); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1429.45
//
Query:       gi|518653057|ref|YP_008142577.1|  [L=167]
Description: hypothetical protein FACI_IFERC00001G1696 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
       0.11   11.9   7.4       0.16   11.3   7.5    1.2  1  NnrS          NnrS protein
        0.4    8.9  14.2       0.48    8.6  14.2    1.0  1  DUF2070       Predicted membrane protein (DUF2070)
        1.1    9.7   8.0        3.7    8.1   4.1    2.3  2  DUF4231       Protein of unknown function (DUF4231)
        2.2    7.6  10.4       0.59    9.4   3.0    2.3  2  SLATT_5       SMODS and SLOG-associating 2TM effector domain 
        5.1    7.5   9.0       0.63   10.4   4.1    1.9  2  DUF4149       Domain of unknown function (DUF4149)


Domain annotation for each model (and alignments):
>> NnrS  NnrS protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.5   4.4e-05      0.16     117     211 ..      57     149 ..      23     160 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
                              NnrS 117 laakqwrnlavlalllllalanllfhlallglatalasaglrlalllvlllillvggRvipfftanalelkarpspr 193
                                         + ++   +++a+l++la+++++f+l++l+ + +++++  +lal+++l+++l     ++pff  n+    ++ ++ 
  gi|518653057|ref|YP_008142577.1|  57 SFSYNYYTGILPAILVALAALDIFFYLDYLKSKITHKHMKSNLALWILLVVMLSLYVFILPFFPPNIE---PNIFKI 130
                                       333456667889999***************88888889999**********************99977...222333 PP

                              NnrS 194 ldr.lalallllalllell 211
                                       ++  ++++++++ ++++l+
  gi|518653057|ref|YP_008142577.1| 131 FSYsMIFIITIIPFIVSLA 149
                                       3333444444444444444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6  14.2   0.00014      0.48      17     120 ..      28     154 ..      16     165 .. 0.61

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00014
                           DUF2070  17 sllliillalligllaflssk..................lfgillfglpalvaflltlpvlrilggrltykrs..lf 73 
                                         +++i+ +++i++++++                     l +il+ +  + + f l++   +i++++++++ +  ++
  gi|518653057|ref|YP_008142577.1|  28 LRIFAIIWVFMISIVSYRLLYlgsigniisfsynyytgiLPAILVALAALDIFFYLDYLKSKITHKHMKSNLAlwIL 104
                                       55788888888899999988889999999999888444344444444444455566666666666667777776666 PP

                           DUF2070  74 lalltelivviisllaillsall...qalvllalvlslalvfalrllvlv 120
                                       l ++  l+v+i+ +++  +   +    ++++ +++  + ++++l + +++
  gi|518653057|ref|YP_008142577.1| 105 LVVMLSLYVFILPFFPPNIEPNIfkiFSYSMIFIITIIPFIVSLAIPIYL 154
                                       77777777777777777777666433222222222223344444444444 PP

>> DUF4231  Protein of unknown function (DUF4231)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.1     0.001       3.7       8      89 ..      16     101 ..      13     119 .. 0.79
   2 ?    3.7   1.1     0.024        85       7      65 ..      92     147 ..      87     163 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.001
                           DUF4231   8 kkasrakrrfrllrlitivlgallpilvs......sklgagvsvlkiltallsalvailaaleeffrykerWrryRs 78 
                                       +++++ k++   lr+++i+ +++++i++       s+ +  +    + t +l a+++ laal  ff     + + + 
  gi|518653057|ref|YP_008142577.1|  16 NRSENIKKINNYLRIFAIIWVFMISIVSYrllylgSIGNIISFSYNYYTGILPAILVALAALDIFFYLD--YLKSKI 90 
                                       677788888888*****************9988887777777777888999999999999998888553..566666 PP

                           DUF4231  79 taEsLktekwl 89 
                                       t++ +k+   l
  gi|518653057|ref|YP_008142577.1|  91 THKHMKSNLAL 101
                                       66666665555 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.024
                           DUF4231   7 ekkasrakrrfrllrlitivlgallpilvssklgagvsvlkiltallsalvailaalee 65 
                                        k+++++ ++  ll +++ + +++lp++     + + +++ki++  +  +++i+  +++
  gi|518653057|ref|YP_008142577.1|  92 HKHMKSNLALWILLVVMLSLYVFILPFFPP---NIEPNIFKIFSYSMIFIITIIPFIVS 147
                                       567777777777888888888888888888...66666666666666666666544443 PP

>> SLATT_5  SMODS and SLOG-associating 2TM effector domain family 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.8     0.021        74     160     188 ..      17      43 ..       7      75 .. 0.66
   2 ?    9.4   3.0   0.00016      0.59      24      80 ..      93     148 ..      89     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.021
                           SLATT_5 160 kskklkwflrrylivifllylliillpvi 188
                                       +s+ +k ++  ++++if+++++++++ v 
  gi|518653057|ref|YP_008142577.1|  17 RSENIKKIN--NYLRIFAIIWVFMISIVS 43 
                                       555556666..444444444444444333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00016
                           SLATT_5  24 eRlrrknklstfslsllSvylivlsllsnkssestinenlldflsiilSilvlvisl 80 
                                       + ++ +  l+++++ +lS+y+++l+ ++  ++e++i + +   +++i+ i+ +++sl
  gi|518653057|ref|YP_008142577.1|  93 KHMKSNLALWILLVVMLSLYVFILPFFP-PNIEPNIFKIFSYSMIFIITIIPFIVSL 148
                                       667888899*******************.6777777777777777777777777776 PP

>> DUF4149  Domain of unknown function (DUF4149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   4.1   0.00018      0.63      10      82 ..      33     112 ..      31     124 .. 0.72
   2 ?   -0.7   0.2      0.51   1.8e+03      40      52 ..     130     142 ..     122     162 .. 0.54

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
                           DUF4149  10 qlwvtfvvapvlfrsLprhqfgelqsklFplyfglglalsvlllltevavg........seklaseellqlllllvv 78 
                                       ++wv f+ ++v +r L     g++ s  + +y+g+  a++v l+ + ++ +        ++k  +++l++++ll+v+
  gi|518653057|ref|YP_008142577.1|  33 IIWV-FMISIVSYRLLYLGSIGNIISFSYNYYTGILPAILVALAALDIFFYldylkskiTHKHMKSNLALWILLVVM 108
                                       5666.9**********9999**************9999999999888887789996444344444444444444444 PP

                           DUF4149  79 lllt 82 
                                       l l 
  gi|518653057|ref|YP_008142577.1| 109 LSLY 112
                                       4333 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.51
                           DUF4149  40 lyfglglalsvll 52 
                                       ++ + ++++ +++
  gi|518653057|ref|YP_008142577.1| 130 IFSYSMIFIITII 142
                                       4444444333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1232  (0.0687155); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-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 0.32s 00:00:00.81 Elapsed: 00:00:00.45
# Mc/sec: 1107.37
//
Query:       gi|518653058|ref|YP_008142578.1|  [L=346]
Description: hypothetical protein FACI_IFERC00001G1697 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
       0.72    9.8   2.7        0.8    9.7   1.3    1.7  2  RseC_MucC  Positive regulator of sigma(E), RseC/MucC


Domain annotation for each model (and alignments):
>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.22     4e+03      96     109 ..      19      32 ..       6      49 .. 0.57
   2 ?    9.7   1.3   4.5e-05       0.8      75     123 ..     219     266 ..     214     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.22
                         RseC_MucC  96 aalgallglvlgfl 109
                                        +l+a ++++++f+
  gi|518653058|ref|YP_008142578.1|  19 GVLMAAVFVMIAFV 32 
                                       34444444444444 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 4.5e-05
                         RseC_MucC  75 llllilgallgsallgssellaalgallglvlgflivrllskrlkkksk 123
                                       l++ ++g+++g ++ ++s ++aa++++lg+v++f ++ +++ +++++ +
  gi|518653058|ref|YP_008142578.1| 219 LIGGVTGLAVGAVF-AASAAIAAVAGILGAVVAFSWASFVNLHTTSQDT 266
                                       77888899999999.7*********************999888666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1004  (0.0559987); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.48
# Mc/sec: 2153.23
//
Query:       gi|518653059|ref|YP_008142579.1|  [L=88]
Description: hypothetical protein FACI_IFERC00001G1698 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00046   20.3   0.1    0.00061   19.9   0.1    1.3  1  DUF150_C  RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> DUF150_C  RimP C-terminal SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.1   3.4e-08   0.00061      10      62 ..      29      74 ..      20      82 .. 0.90

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 3.4e-08
                          DUF150_C 10 flGelVkvklklpvegrkkftGkivevdeetitlevdgkkrkkettipladid 62
                                      ++G+ +k++lk    g+k+   +iv+v ++++tl+  g    + + +pl++++
  gi|518653059|ref|YP_008142579.1| 29 NQGKDIKLQLK----GEKNRYVTIVRVSQNEVTLSEPGG---EVISVPLSNVA 74
                                      78*********....********************9988...8888*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (88 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.44
# Mc/sec: 606.42
//
Query:       gi|518653060|ref|YP_008142580.1|  [L=117]
Description: hypothetical protein FACI_IFERC00001G1699 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-07   31.2   4.4    1.7e-07   30.7   4.4    1.3  1  zinc_ribbon_2    zinc-ribbon domain
    1.7e-06   27.2   3.7    2.4e-06   26.7   3.7    1.3  1  zf-ribbon_3      zinc-ribbon domain
      1e-05   25.5   2.9    1.5e-05   24.9   2.9    1.2  1  DZR              Double zinc ribbon
    5.5e-05   23.8   0.6    7.4e-05   23.4   0.6    1.3  1  zinc_ribbon_15   zinc-ribbon family
    0.00034   20.7   0.1    0.00048   20.2   0.1    1.2  1  HTH_34           Winged helix DNA-binding domain
    0.00083   19.7   0.1     0.0012   19.2   0.1    1.3  1  Penicillinase_R  Penicillinase repressor
     0.0012   18.6   0.0     0.0015   18.3   0.0    1.1  1  HxlR             HxlR-like helix-turn-helix
     0.0032   17.1   3.3     0.0061   16.2   3.3    1.4  1  zf-tcix          Putative treble-clef, zinc-finger, Zn-bindin
      0.006   17.0   0.1     0.0088   16.5   0.1    1.3  1  HTH_27           Winged helix DNA-binding domain
     0.0065   15.8   2.2       0.01   15.1   2.2    1.2  1  zf-RanBP         Zn-finger in Ran binding protein and others
  ------ inclusion threshold ------
       0.01   15.8   1.3      0.019   14.9   1.3    1.5  1  OrfB_Zn_ribbon   Putative transposase DNA-binding domain
      0.024   14.1   4.6      0.069   12.7   4.6    1.8  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.037   14.0   2.8       0.75    9.8   0.3    2.3  2  Nudix_N_2        Nudix N-terminal
      0.062   13.4   2.4          3    8.0   0.2    2.3  2  Zn-ribbon_8      Zinc ribbon domain
        0.1   12.6   1.0        7.5    6.6   0.0    2.3  2  zf-dskA_traR     Prokaryotic dksA/traR C4-type zinc finger
       0.13   11.9   0.1        0.3   10.8   0.0    1.7  1  HTH_41           Helix-turn-helix domain
       0.16   11.7   1.8        8.5    6.2   0.0    2.4  2  zf-RRN7          Zinc-finger of RNA-polymerase I-specific TFI
       0.39   10.4   2.2        5.8    6.7   2.2    2.2  1  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        1.2    9.2   7.9        2.8    8.0   0.7    2.5  2  YhfH             YhfH-like protein
        1.7    8.7   4.7        1.8    8.7   0.6    2.7  3  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma


Domain annotation for each model (and alignments):
>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   4.4   1.9e-10   1.7e-07       2      23 .]      94     115 ..      93     115 .. 0.96

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 1.9e-10
                     zinc_ribbon_2   2 CpnCGaelqdnakFCpyCGtpl 23 
                                       Cp CG++++++ak+C +CG++l
  gi|518653060|ref|YP_008142580.1|  94 CPVCGTKNDEDAKYCKNCGSKL 115
                                       *******************997 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   3.7   2.7e-09   2.4e-06       2      26 .]      91     115 ..      90     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.7e-09
                       zf-ribbon_3   2 tvrCPnCGa.plssddnvCpyCGtkl 26 
                                       ++ CP CG+ + ++d++ C++CG+kl
  gi|518653060|ref|YP_008142580.1|  91 YKICPVCGTkN-DEDAKYCKNCGSKL 115
                                       689******99.***********997 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   2.9   1.7e-08   1.5e-05       1      23 [.      94     116 ..      94     117 .] 0.96

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 1.7e-08
                               DZR   1 CpqCgeelppdarfCseCgtklk 23 
                                       Cp Cg+++++da++C++Cg+kl+
  gi|518653060|ref|YP_008142580.1|  94 CPVCGTKNDEDAKYCKNCGSKLD 116
                                       *********************97 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.6   8.3e-08   7.4e-05      47      86 .]      72     112 ..      48     112 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 8.3e-08
                    zinc_ribbon_15  47 leaskelgkeiekkesse.kkeCknCgkeveeefkyCpkCg 86 
                                       ++ + ++ +ei++++ss  +k+C+ Cg++ +e+ kyC +Cg
  gi|518653060|ref|YP_008142580.1|  72 IAGQFKNINEITNSKSSGqYKICPVCGTKNDEDAKYCKNCG 112
                                       4445555556655544435*********************9 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.2   0.1   5.4e-07   0.00048       5      69 ..      11      73 ..      10      83 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.2 bits;  conditional E-value: 5.4e-07
                            HTH_34  5 vlsyLasvdeadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreaf 69
                                      +l +L++ d+++ ++l + +  ++g + + +k Le++g i  +k++ g+ + + +++T+ G++ +
  gi|518653060|ref|YP_008142580.1| 11 ILIFLLDHDKVKKTDLLKVVP-STGTMESTVKRLEEQGVIRTEKKYIGR-RIIYISLTEYGHAIA 73
                                      788999999999999988775.77*************************.9**********9754 PP

>> Penicillinase_R  Penicillinase repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   1.3e-06    0.0012      18      79 ..      21      79 ..       4      90 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.3e-06
                                      EEHHHHHHT--GGG---HHHHHHHHHHHHHTTS-EEEEE..TTEEEEE----XXXXXXXXXXXX CS
                   Penicillinase_R 18 atvkevveeleeekelaysTVktllrrLvkKgllsreke..grafiYsplvseeeavasavkql 79
                                      ++ +++ + ++++      T  ++++rL+++g++++ek+  gr++iY +l++  +a+a++ k++
  gi|518653060|ref|YP_008142580.1| 21 VKKTDLLKVVPST-----GTMESTVKRLEEQGVIRTEKKyiGRRIIYISLTEYGHAIAGQFKNI 79
                                      5555555555554.....8999999*************99***********9999999998876 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.7e-06    0.0015       9      83 ..      10      83 ..       4      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.7e-06
                                      HHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEE.EE-TCGGGGHHHHHHHHHHH CS
                              HxlR  9 lilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveY.sltekGrslepvlqelkkwg 83
                                       il+ ll+  k + ++l + +p  s+ ++ ++ ++Le++g+i r++ + ++ ++ Y slte+G++++  ++++++  
  gi|518653060|ref|YP_008142580.1| 10 SILIFLLDhDKVKKTDLLKVVP--STGTMESTVKRLEEQGVI-RTEKKYIGRRIIYiSLTEYGHAIAGQFKNINEIT 83
                                      4666666547778889999998..5678999**********9.66778999****988*********9999988765 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 !   16.2   3.3   6.8e-06    0.0061      11      29 ..      92     110 ..      91     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 6.8e-06
                           zf-tcix  11 rkCpkCGtyNGtRglsCkN 29 
                                       + Cp CGt N   ++ CkN
  gi|518653060|ref|YP_008142580.1|  92 KICPVCGTKNDEDAKYCKN 110
                                       67****************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 !   16.5   0.1   9.8e-06    0.0088      10      68 .]      14      69 ..       6      69 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 9.8e-06
                            HTH_27 10 hlirhrrrrkkladlcgrlnvedshis.yslkkLtekGLvertgdeadrrekrvrlTdkG 68
                                      +l+   ++++k++dl +++   ++ ++ + +k+L+e+G++ ++++   rr   ++lT+ G
  gi|518653060|ref|YP_008142580.1| 14 FLLD--HDKVKKTDLLKVV--PSTGTMeSTVKRLEEQGVIRTEKKYIGRRIIYISLTEYG 69
                                      5555..6777777777764..3444444*****************************976 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 !   15.1   2.2   1.1e-05      0.01       6      27 ..      93     114 ..      93     114 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                       E-SSS--EEESSSSB-TTT--B CS
                          zf-RanBP   6 dCskClvqNfawstkCvaCqap 27 
                                       +C++C+++N   + +C +C+++
  gi|518653060|ref|YP_008142580.1|  93 ICPVCGTKNDEDAKYCKNCGSK 114
                                       5******************985 PP

>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   1.3   2.1e-05     0.019      29      57 ..      92     116 ..      74     117 .] 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.1e-05
                    OrfB_Zn_ribbon  29 ktCseCgsknkealsgrtfkCpnCgfead 57 
                                       k C++Cg kn+e    +  +C+nCg ++d
  gi|518653060|ref|YP_008142580.1|  92 KICPVCGTKNDE----DAKYCKNCGSKLD 116
                                       78**********....8889*****9987 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   4.6   7.6e-05     0.069       2      30 ..      93     116 ..      92     117 .] 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.6e-05
                                       EETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVle 30 
                                       +CP+Cg++n  eD++    +C++CG+ l+
  gi|518653060|ref|YP_008142580.1|  93 ICPVCGTKN-DEDAK----YCKNCGSKLD 116
                                       6******98.46666....*******986 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.039        35       3       8 ..      94      99 ..      92     103 .. 0.68
   2 ?    9.8   0.3   0.00083      0.75       1      10 [.     106     115 ..     106     117 .] 0.90

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.039
                                      -TTT-- CS
                         Nudix_N_2  3 CsqCGt 8 
                                      C+ CGt
  gi|518653060|ref|YP_008142580.1| 94 CPVCGT 99
                                      777776 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00083
                                       -B-TTT--B- CS
                         Nudix_N_2   1 kFCsqCGtpv 10 
                                       k+C++CG+++
  gi|518653060|ref|YP_008142580.1| 106 KYCKNCGSKL 115
                                       8*******97 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.2     0.012        10      26      34 ..      90      99 ..      74     104 .. 0.67
   2 ?    8.0   0.2    0.0033         3      23      37 ..     102     116 ..      99     117 .] 0.70

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.012
                       Zn-ribbon_8 26 lta.CPeCgs 34
                                      + + CP Cg 
  gi|518653060|ref|YP_008142580.1| 90 QYKiCPVCGT 99
                                      4455****98 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0033
                       Zn-ribbon_8  23 dapltaCPeCgsevr 37 
                                       d++ + C++Cgs++ 
  gi|518653060|ref|YP_008142580.1| 102 DEDAKYCKNCGSKLD 116
                                       555566*****9876 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 ?    4.7   0.2     0.033        30       1      10 [.      89      98 ..      89     100 .. 0.86
   2 ?    6.6   0.0    0.0084       7.5      23      35 ..     104     116 ..     101     117 .] 0.84

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.033
                      zf-dskA_traR  1 giygsCeeCG 10
                                      g y +C +CG
  gi|518653060|ref|YP_008142580.1| 89 GQYKICPVCG 98
                                      6799*****9 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0084
                      zf-dskA_traR  23 garlCveCqekae 35 
                                       +a++C++C +k +
  gi|518653060|ref|YP_008142580.1| 104 DAKYCKNCGSKLD 116
                                       799*****99876 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033       0.3      19      41 ..      32      54 ..      24      59 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
                            HTH_41 19 SvGlvQkALklLeddkaislerr 41
                                      S G++ + +k Le++++i +e++
  gi|518653060|ref|YP_008142580.1| 32 STGTMESTVKRLEEQGVIRTEKK 54
                                      89******************987 PP

>> zf-RRN7  Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4     0.033        30       5      11 ..      92      98 ..      92     101 .. 0.86
   2 ?    6.2   0.0    0.0095       8.5      23      30 ..     107     114 ..     106     116 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.033
                           zf-RRN7  5 ppCgvCg 11
                                      ++C+vCg
  gi|518653060|ref|YP_008142580.1| 92 KICPVCG 98
                                      58****9 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0095
                           zf-RRN7  23 yCrrChtq 30 
                                       yC++C+++
  gi|518653060|ref|YP_008142580.1| 107 YCKNCGSK 114
                                       9****986 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   2.2    0.0065       5.8       4      28 ..      92     112 ..      90     115 .. 0.68

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0065
                     zf-NADH-PPase   4 rFCgrCGaptepaeggwarvCpaCg 28 
                                       + C+ CG+++       a+ C +Cg
  gi|518653060|ref|YP_008142580.1|  92 KICPVCGTKNDED----AKYCKNCG 112
                                       56*****997533....44566665 PP

>> YhfH  YhfH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.4     0.015        13      13      25 ..      91     103 ..      90     105 .. 0.83
   2 ?    8.0   0.7    0.0032       2.8      13      24 ..     105     116 ..     104     117 .] 0.88

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.015
                              YhfH  13 kKkCteCGkeieE 25 
                                        K C+ CG + +E
  gi|518653060|ref|YP_008142580.1|  91 YKICPVCGTKNDE 103
                                       599*****98777 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0032
                              YhfH  13 kKkCteCGkeie 24 
                                       +K C +CG++++
  gi|518653060|ref|YP_008142580.1| 105 AKYCKNCGSKLD 116
                                       7********986 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   1.8e+03       7      17 ..      38      49 ..      37      55 .. 0.61
   2 ?    8.7   0.6     0.002       1.8       2       8 ..      94     100 ..      94     110 .. 0.93
   3 ?    0.2   0.1      0.87   7.8e+02       5       9 ..     111     115 ..     107     117 .] 0.82

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                    DNA_ligase_ZBD  7 savvReeg.eai 17
                                      s v R e+ ++i
  gi|518653060|ref|YP_008142580.1| 38 STVKRLEEqGVI 49
                                      556675541444 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.002
                    DNA_ligase_ZBD   2 CPvCGsa 8  
                                       CPvCG++
  gi|518653060|ref|YP_008142580.1|  94 CPVCGTK 100
                                       *****96 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.87
                    DNA_ligase_ZBD   5 CGsav 9  
                                       CGs++
  gi|518653060|ref|YP_008142580.1| 111 CGSKL 115
                                       9*997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                       110  (0.00613531); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.45u 0.30s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 752.91
//
Query:       gi|518653061|ref|YP_008142581.1|  [L=51]
Description: hypothetical protein FACI_IFERC00001G1700 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); 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:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.30s 00:00:00.68 Elapsed: 00:00:00.45
# Mc/sec: 338.07
//
Query:       gi|518653062|ref|YP_008142582.1|  [L=209]
Description: integrase-recombinase protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-12   46.1   0.1    8.3e-12   45.2   0.1    1.4  2  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.17     3e+03      98     135 ..      58     104 ..      41     112 .. 0.54
   2 !   45.2   0.1   4.6e-16   8.3e-12       5     103 ..     109     203 ..     105     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.17
                                       SBET.TSSB--HHHHHHHHHHHHHHCT-S........SC--TTHHHH CS
                   Phage_integrase  98 fask.rgkplsrqtvrkafkraveeagie........kpltpHtlRh 135
                                       f++k r++   +q+v++++k + +    e        ++l+ +++R+
  gi|518653062|ref|YP_008142582.1|  58 FLRKeRRNGSPKQKVNGYIKYLNRLLTFEgldkidyiPELRNNSFRK 104
                                       44444444444555665555555553333333555666666666664 PP

  == domain 2  score: 45.2 bits;  conditional E-value: 4.6e-16
                                       HHHHHHHHHCCGC..HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHH CS
                   Phage_integrase   5 edeverllaalee..slkirdklllellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealel 79 
                                        d++++l+  ++    ++ r+ +++ l+++tGlR sE+++++v+d+   n+ ++v  + gKg+k+r v l ++  ++
  gi|518653062|ref|YP_008142582.1| 109 TDQIQTLIVKSKGktIEDKRNHAMILLALNTGLRRSEICNIKVEDI--HNNFLTV--NYGKGEKSRDVFLDDNTRKV 181
                                       689999999999988889999*************************..9999999..9******************* PP

                                       HHHHHHHHCHCCTTTSBSSBETTS CS
                   Phage_integrase  80 lkellskaleeaeksellfaskrg 103
                                       + ++   +  ++++  +lf  k+g
  gi|518653062|ref|YP_008142582.1| 182 IMDYSFIR--NNNDMPYLFTTKKG 203
                                       **999998..88888899988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); 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: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1523.68
//
Query:       gi|518653063|ref|YP_008142583.1|  [L=67]
Description: site-specific integrase/recombinase [Ferroplasma acidarmanus fer1]
Scores for complete 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   0.0     0.0003   20.6   0.0    1.2  1  Phage_integrase  Phage integrase family


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.7e-08    0.0003     141     170 ..       1      30 [.       1      32 [. 0.93

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.7e-08
                                       HHHHCTSHHHHHHHHT-SSCCHHHHHHCCC CS
                   Phage_integrase 141 LleagvdlrvvqkllGHssisttqiYthva 170
                                       ++++ +dl+ + ++lGH++++tt iY + +
  gi|518653063|ref|YP_008142583.1|   1 MIKNDIDLESLRQMLGHEDLATTGIYSRMN 30 
                                       899***********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.45
# Mc/sec: 449.00
//
Query:       gi|518653064|ref|YP_008142584.1|  [L=428]
Description: hypothetical protein FACI_IFERC00001G1703 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-36  125.3  50.3    3.2e-36  124.9  50.3    1.0  1  Na_H_Exchanger  Sodium/hydrogen exchanger family
  ------ inclusion threshold ------
        8.8    5.9   6.7        2.2    7.9   2.2    2.3  2  TMEM100         Transmembrane protein 100


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 !  124.9  50.3   3.6e-40   3.2e-36       2     376 ..      15     416 ..      14     420 .. 0.88

  Alignments for each domain:
  == domain 1  score: 124.9 bits;  conditional E-value: 3.6e-40
                                       HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS............HHHCHCCHHHHCHHCCHHHHCTCGCCT CS
                    Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglglieps.......eedlevlselglilllFlaGleldlre 71 
                                       ++li++a+ +++ +r+  + +i++li++Gl++Gp  lg+i++s        + +  +  lgl+++l++ + ++++r 
  gi|518653064|ref|YP_008142584.1|  15 FILIVAAFSIPI-SRKASMVYIPILIVMGLIFGPL-LGFIKHSfaiymlsSFATIGVGMLGLVIILYYESHNFSPRI 89 
                                       577887888888.*********************9.77799998999998889999999****************** PP

                                       GCCTHHHHHHHHHHHHHHHHHHHHHHHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHH CS
                    Na_H_Exchanger  72 lrknlksilllallgvlitvvliGlllylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllges 148
                                       lrk + +i +l ++g+++t+v+ G++++l  + g p++ +++fgai+s+tdp+ +++++ ++  ++ ++  +l+ges
  gi|518653064|ref|YP_008142584.1|  90 LRKYFYKIAALDTIGMVVTAVGAGIFFSL--LTGAPMIIGFIFGAIISPTDPASLIPTF-KKLNIRDDISGTLIGES 163
                                       ****************************8..6899************************.78888************ PP

                                       HHHHHHCCCCCHHHHHHTX..XXXXTSSSTS........XHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCTHHHHH CS
                    Na_H_Exchanger 149 vlnDavavvllavllalak..eeaggetsll........lllliflvvavgglllglvigwllrlitrftdddrele 215
                                       ++nD ++++ll++ ++++    + +  ++ll          + ++l+++++  ++g+++g++  ++++++ + ++l 
  gi|518653064|ref|YP_008142584.1| 164 LFNDPLGIILLSIGIGILApnVSYSSFFTLLtshvglvlGSSSFLLLEIAIPAAVGIAFGFFIIYLNKYF-NFESLL 239
                                       *****************96553344444444888888777777888999999*****************7.****** PP

                                       HHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHH....HHHHHTTHHHH...HHHHHHHHHHHHHHHHHHHHSXHHH CS
                    Na_H_Exchanger 216 vllvlllallaallaellgvsgilgaflaGlvls....eyefsnklsek...lesfreglfnplfFvlvGlsldlkv 285
                                       ++l+l ++l+ +   e++g++   ++ + G++++    ++ f n+   +    e++  + +  ++F+l+G  l  + 
  gi|518653064|ref|YP_008142584.1| 240 IALTLGIVLFEFTSLEAVGITPFPAIIATGAIVGnfsdKSIFWNR---EtnfNENLS-FMAQSIIFILLGSILTRTQ 312
                                       **********************************64444444443...234577777.99**************888 PP

                                       HHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTX.......SSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHH. CS
                    Na_H_Exchanger 286 lnnhlsvlilvllilvaillgrilavflllrll.......glslrealiigfgglqrgavalalaalgpalgllar. 354
                                       ++   + ++  +++l++i+++r++avf+   l        ++++r+++++++ g  rg v ++l  +   lg  ++ 
  gi|518653064|ref|YP_008142584.1| 313 IF--NYIIFGFIISLIVIFVVRPVAVFISIGLAnmgkntiKFDTRTKAFMSLVGP-RGVVPVVLSTVPFVLGQANHi 386
                                       86..788888889999999*********99988**********************.********9988777544445 PP

                                       .......TT.SSTTTCSTSXHHHHHHHHHH CS
                    Na_H_Exchanger 355 .......el.yallivvvlftvlvqGlslk 376
                                              +  ya + +vvl+++++q++ ++
  gi|518653064|ref|YP_008142584.1| 387 pllieygTIiYASVSFVVLISIILQTIYVP 416
                                       5568788888*************9999876 PP

>> TMEM100  Transmembrane protein 100
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.2      0.24   2.1e+03      67      75 ..     103     111 ..      98     119 .. 0.84
   2 ?    7.9   2.2   0.00024       2.2      59     103 ..     168     213 ..     164     218 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.24
                           TMEM100  67 aGvvvtava 75 
                                       +G+vvtav 
  gi|518653064|ref|YP_008142584.1| 103 IGMVVTAVG 111
                                       89****995 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00024
                           TMEM100  59 PfgvvvLvaGvvvta..vaytfnshgsvisvlglvLLsaGlvllass 103
                                       P g++ L +G+ + a  v+y+      + s +glvL s+ ++ll ++
  gi|518653064|ref|YP_008142584.1| 168 PLGIILLSIGIGILApnVSYSSFFTLLT-SHVGLVLGSSSFLLLEIA 213
                                       8999999887665541177754444444.89************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1054  (0.0587874); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.45
# Mc/sec: 2834.23
//
Query:       gi|518653065|ref|YP_008142585.1|  [L=239]
Description: NAD synthetase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-64  217.9   0.1    1.4e-64  217.5   0.1    1.0  1  NAD_synthase   NAD synthase
  ------ inclusion threshold ------
      0.019   15.0   0.0      0.042   13.9   0.0    1.6  1  PAPS_reduct    Phosphoadenosine phosphosulfate reductase fami
      0.058   12.2   0.0       0.16   10.7   0.0    1.7  2  tRNA_Me_trans  tRNA methyl transferase
      0.075   12.7   0.0        0.1   12.2   0.0    1.2  1  Asn_synthase   Asparagine synthase
      0.083   13.4   0.2       0.16   12.5   0.2    1.4  1  DUF4830        Domain of unknown function (DUF4830)


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 !  217.5   0.1   3.9e-68   1.4e-64       2     242 .]       9     235 ..       6     235 .. 0.93

  Alignments for each domain:
  == domain 1  score: 217.5 bits;  conditional E-value: 3.9e-68
                                       HHHHHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE CS
                      NAD_synthase   2 ieelvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievkt 78 
                                       i+++ +flke++   g k +vlG+S G+DSslv +l  + +++++++a+ +P+++++++d+ed ++l e+ g+++ t
  gi|518653065|ref|YP_008142585.1|   9 IQAIREFLKEKI---GEKHAVLGISSGIDSSLVLTLLATSIDNNKIKAIFMPDKYTKQDDYEDIKKLSESTGLDIIT 82 
                                       456667777665...55678********************************************************* PP

                                       ---HHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS- CS
                      NAD_synthase  79 idikpivrafeqelkeakedlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaell 155
                                       ++i+++++++++ l+ +  +  +gN+++RiR++ily++an l+ +v+gT n++E+++Gy TkyGDga+d++pi++++
  gi|518653065|ref|YP_008142585.1|  83 VNIESVLESYRALLDTSD-KKLEGNIRSRIRANILYYHANLLGGVVIGTTNRTEYLLGYYTKYGDGACDIEPIEGIF 158
                                       ***********9998877.6779****************************************************** PP

                                       HHHHHHHHHHTT--HHHHCS--B--SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHH CS
                      NAD_synthase 156 KtevkeLakelnvPervlkkpPsAdLkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklv 232
                                       Kt+v ++a  l vP+++++k+PsA+L+++q De+eL + Y+e+D iL+         +i ++  l + + ek+++l+
  gi|518653065|ref|YP_008142585.1| 159 KTDVWKIASILKVPQSIIDKKPSAGLWENQYDEDELKMDYHEIDRILS---------DIFDNHTL-NGKYEKLMELY 225
                                       ************************************************.........77764444.467899***** PP

                                       HHTGGGGSSS CS
                      NAD_synthase 233 kksehKrklp 242
                                        ks hKr+lp
  gi|518653065|ref|YP_008142585.1| 226 LKSMHKRELP 235
                                       *******998 PP

>> PAPS_reduct  Phosphoadenosine phosphosulfate reductase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   1.2e-05     0.042       3      61 ..      26      86 ..      24     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.2e-05
                                      EEE--SSCTC.HHHHHHHHHHCTT.HEEEEEE-STB-HHHHHHHHHHHHHTT-EEEEEE-S CS
                       PAPS_reduct  3 vvsvsgGkds.lVllhLalkafkp.vpvvfvdtghefpetiefvdeleeryglrlkvyepe 61
                                      v+ +s G+ds lVl  La++++++ ++ +f+  +++ ++ +e +++l+e  gl++++++ e
  gi|518653065|ref|YP_008142585.1| 26 VLGISSGIDSsLVLTLLATSIDNNkIKAIFMPDKYTKQDDYEDIKKLSESTGLDIITVNIE 86
                                      677899999626888889999999669***************************8776655 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.4e-05      0.16       3      69 ..      25      84 ..      23      94 .. 0.66
   2 ?   -2.1   0.0      0.34   1.2e+03     167     195 ..     153     183 ..     151     195 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.4e-05
                     tRNA_Me_trans  3 vvvalSgGVDSsvaaallkeqg..yevigvflklweeedeegkeccaeedlkdaervaeklgiplevvd 69
                                       v ++S+G+DSs++++ll++     +++++f+  +          ++++d++d+++ +e  g+ + +v+
  gi|518653065|ref|YP_008142585.1| 25 AVLGISSGIDSSLVLTLLATSIdnNKIKAIFMPDKY---------TKQDDYEDIKKLSESTGLDIITVN 84
                                      5789**************998722445666664332.........244555666666655555555555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.34
                     tRNA_Me_trans 167 PlgeltKeevrkiAkeagla..vaekkdSqg 195
                                       P+  + K++v kiA+  +++  + +kk S g
  gi|518653065|ref|YP_008142585.1| 153 PIEGIFKTDVWKIASILKVPqsIIDKKPSAG 183
                                       8888889999999988887766778888776 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.9e-05       0.1      24     103 ..      29     109 ..      22     128 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.9e-05
                      Asn_synthase  24 LSGGlDSSliaalaarqsk.splktFsigfeekgsdeakyakevaehlgtehtelvlteeelldalpdviyhlee.. 97 
                                       +S G+DSSl+  l+a   + +++k+  +  +  + d+ +  k+++e  g++   + ++ e +l+ +++++   ++  
  gi|518653065|ref|YP_008142585.1|  29 ISSGIDSSLVLTLLATSIDnNKIKAIFMPDKYTKQDDYEDIKKLSESTGLD--IITVNIESVLESYRALLDTSDKkl 103
                                       69********999998876355665554445599****************9..577777778888888877777655 PP

                      Asn_synthase  98 pfadrs 103
                                          +rs
  gi|518653065|ref|YP_008142585.1| 104 EGNIRS 109
                                       444555 PP

>> DUF4830  Domain of unknown function (DUF4830)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.2   4.4e-05      0.16      15      83 ..      50     126 ..      43     127 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.4e-05
                           DUF4830  15 etkevkiPkefeev..yaeynelqkdiGldLekykgkevtrytYelknypkeene......vranllvkegkiiGad 83 
                                       + k++ +P++ +++  y++  +l+++ Gld+  ++ ++v +    l + ++++ e      +ran+l++  ++ G+ 
  gi|518653065|ref|YP_008142585.1|  50 KIKAIFMPDKYTKQddYEDIKKLSESTGLDIITVNIESVLESYRALLDTSDKKLEgnirsrIRANILYYHANLLGGV 126
                                       5566778998888888******************999986655555544444433467889***********99996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1771.36
//
Query:       gi|518653066|ref|YP_008142586.1|  [L=55]
Description: hypothetical protein FACI_IFERC00001G1705 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.27s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 389.28
//
Query:       gi|518653067|ref|YP_008142587.1|  [L=69]
Description: hypothetical protein FACI_IFERC00001G1706 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-19   67.7   0.9    7.1e-19   67.5   0.9    1.0  1  DUF3311   Protein of unknown function (DUF3311)


Domain annotation for each model (and alignments):
>> DUF3311  Protein of unknown function (DUF3311)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.9   3.9e-23   7.1e-19       1      57 [.       8      64 ..       8      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 3.9e-23
                           DUF3311  1 vlllvpvlvalllvpfynrvdpvllGlPffywwqllwvllasvvtwlayrlakreda 57
                                      +ll++p++ ++++v +y rv p l G+Pffyw+ql+w+++a+++t ++y+ +  e++
  gi|518653067|ref|YP_008142587.1|  8 ILLALPYIFMVAGVTIYTRVKPELGGIPFFYWYQLVWIFIAAALTSTVYFIENNEKK 64
                                      79************************************************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 518.66
//
Query:       gi|518653068|ref|YP_008142588.1|  [L=505]
Description: hypothetical protein FACI_IFERC00001G1707 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   96.5  31.2    2.3e-27   95.9  31.2    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 !   95.9  31.2   1.3e-31   2.3e-27       3     402 ..      41     429 ..      39     433 .. 0.85

  Alignments for each domain:
  == domain 1  score: 95.9 bits;  conditional E-value: 1.3e-31
                               SSF   3 lagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr.......nagalTlp 72 
                                       l+gr+ + +v+   l+++   a  ++ ++Ga+a+ G++++++++ a+   ++++ ++ + +        + g +T  
  gi|518653068|ref|YP_008142588.1|  41 LGGRRFGTVVMWFLLGGDLYTAYTLIAVPGAAATAGVGGGAFAMFAIAYGVMIYPIVYGTMPklwnvskRRGYITAS 117
                                       8*******************************************99988777777776665556689999******* PP

                               SSF  73 dylskRfkgkrilvylsalslllvitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdti 149
                                       d+++ Rf +++ l +l al+ +l+   +++ ++  g k++  +l+l +++++++  +l+a +t++ Gl+   +t ++
  gi|518653068|ref|YP_008142588.1| 118 DFVKDRFSSRS-LAMLIALTGVLAELPYIALQIT-GIKYVLASLSLPITISLIIAFILVAGFTFVSGLRGPALTSIL 192
                                       ***********.6666667777788899999986.67888899********************************** PP

                               SSF 150 qavlmlvgalilliivllevGgleslveklkeaapkvvdlltpdslkllrdpltalslwlglvlGvaglphilvRfl 226
                                       +  ++ v+ +++ i+  +++Gg+ +++ k+++++p    ll+   +  +   +  + l lg  l ++  ph +   l
  gi|518653068|ref|YP_008142588.1| 193 KDAIIWVAVIVIIIYIPIKLGGFGAIFGKAATISP---HLLNISPV--I--DVGYTTLALGSALALFLYPHAITGTL 262
                                       ***********************************...44443332..2..35566666799999999********* PP

                               SSF 227 aakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpnllaGlllavmlA 303
                                        akd+k+i++    l    +l+++   ++++ a  +++  p       +vs  a+p+Lv  l+p  + ++  a+++ 
  gi|518653068|ref|YP_008142588.1| 263 GAKDSKTIRRNASLLPLYNVLLMFV-AIVGIMAVVYFNKYP-------TVSSEALPRLVLDLFPASFTAFAFAAVVV 331
                                       ********99764443333333333.446777777777766.......67889***************997766554 PP

                               SSF 304 aimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasa 380
                                         +   + + l+++ ++t+ +Y + +  + a+e+ + ++sr++v+vvi  a++  + ++ +g + + +++ + +   
  gi|518653068|ref|YP_008142588.1| 332 GSIVPASIMALASANLLTRNVYLEYINPK-ASERTQTNLSRVLVIVVILAALAFSLVPAASGEIVYLQTIGGAFIMQ 407
                                       444445666789999*********99999.9*****************99999999999999999************ PP

                               SSF 381 vlavillalfwkrvneqGAlag 402
                                        l+ + lalf  ++n++   ag
  gi|518653068|ref|YP_008142588.1| 408 TLPAVYLALFTRKLNKYPVAAG 429
                                       ***************9765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.28s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 3266.63
//
Query:       gi|518653069|ref|YP_008142589.1|  [L=114]
Description: hypothetical protein FACI_IFERC00001G1708 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0086   15.9   0.0      0.015   15.1   0.0    1.3  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.068   12.9   0.2       0.15   11.8   0.0    1.7  2  HTH_38        Helix-turn-helix domain
       0.15   12.1   0.0       0.19   11.7   0.0    1.3  1  HTH_29        Winged helix-turn helix
        0.2   11.1   0.0       0.35   10.3   0.0    1.4  1  HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family I


Domain annotation for each model (and alignments):
>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   3.3e-06     0.015      13      41 ..      12      40 ..       5      44 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 3.3e-06
                            HTH_23 13 llaeGlsvreIAreLgvsrrTvyrwlkry 41
                                      l  + ++v++IA+ Lgv +  + +++k +
  gi|518653069|ref|YP_008142589.1| 12 LRCVNKPVKQIAKTLGVKKDAIEKIIKEW 40
                                      445589*********************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 ?   11.8   0.0   3.4e-05      0.15      11      42 ..       7      38 ..       2      39 .. 0.90
   2 ?   -2.2   0.1      0.81   3.6e+03      10      20 ..     103     113 ..     103     114 .] 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.4e-05
                            HTH_38 11 eeIerllaeGlslreIArrLgrspsTIsRElk 42
                                      e I+ l++ ++ +++IA+ Lg+++  I + +k
  gi|518653069|ref|YP_008142589.1|  7 EAIAGLRCVNKPVKQIAKTLGVKKDAIEKIIK 38
                                      57999999***************999998887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.81
                            HTH_38  10 ReeIerllaeG 20 
                                       R++I ++l+ +
  gi|518653069|ref|YP_008142589.1| 103 RYKIKIMLENK 113
                                       89999999865 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.19      15      37 ..      19      41 ..       7      56 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                            HTH_29 15 vsqiAkllglsrrtvyrwlkrfe 37
                                      v+qiAk lg+ ++ + +++k + 
  gi|518653069|ref|YP_008142589.1| 19 VKQIAKTLGVKKDAIEKIIKEWI 41
                                      89******************986 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   7.8e-05      0.35      21      51 ..      11      40 ..       5      41 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 7.8e-05
                      HTH_Tnp_ISL3 21 lelllesrsvkavArqlgvSwtTVwrildry 51
                                        ++ +  +vk++A+ lgv  + ++ i++++
  gi|518653069|ref|YP_008142589.1| 11 GLRCVNK-PVKQIAKTLGVKKDAIEKIIKEW 40
                                      5678888.******************99976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       725  (0.0404373); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.42
# Mc/sec: 808.59
//
Query:       gi|518653070|ref|YP_008142590.1|  [L=758]
Description: hypothetical protein FACI_IFERC00001G1709 [Ferroplasma acidarmanus fer1]
Scores for complete 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-65  219.4  15.3    5.6e-65  219.4  15.3    3.3  4  Thermopsin  Thermopsin


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.4  15.3   3.1e-69   5.6e-65       7     260 .]      83     346 ..      79     346 .. 0.95
   2 ?   -2.5   1.0      0.16   2.8e+03     109     145 ..     462     503 ..     418     549 .. 0.58
   3 ?   -1.9   0.0     0.099   1.8e+03      14      22 ..     642     650 ..     623     680 .. 0.65
   4 ?   -0.2   3.3      0.03   5.4e+02      98     129 ..     680     714 ..     670     736 .. 0.65

  Alignments for each domain:
  == domain 1  score: 219.4 bits;  conditional E-value: 3.1e-69
                        Thermopsin   7 slyssepaPmGiadyGiknnsgkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvt..ggktysy 81 
                                       + y+s+paPmGi+ yG +n+sgkl+ y+++t sv++++ i+++s++++ ++ p+s ++QLN+vl++vt  g++ty++
  gi|518653070|ref|YP_008142590.1|  83 PSYQSAPAPMGIGFYGTQNESGKLVGYNLTTPSVMASIGIQNMSQFYLLNDGPTSETFQLNSVLTNVTlfGNSTYTF 159
                                       6799************************************************************************* PP

                        Thermopsin  82 wvQnVvsfnttekqltfidNiWNftspsanlsnsai.sGnGtvyasskgefYyayateylelslPltlkLvinvslt 157
                                       w+QnV+ ++ ++++++f+ NiWNf+sp+ ++s++   s  G ++     +fYya++++ +++++P++l+L++n++++
  gi|518653070|ref|YP_008142590.1| 160 WTQNVAFYSERTQTIQFLTNIWNFSSPAVTISSNVFhSDDGILC---APTFYYAIGPT-IHVTTPFSLNLYLNSTVV 232
                                       ********************************998755667777...99*********.***************999 PP

                        Thermopsin 158 sngvpevsFgYsid....ggvvtYDnvtinstgkasa.......eilvngssltpsg.llyDaeLvlgGpgngektt 222
                                        + + +v F+Ysi      +  +YD +++nst ++ +       e+l +g++ tp+g ++yD e+++gGpg+g++t+
  gi|518653070|ref|YP_008142590.1| 233 DRDS-AVFFNYSITsdnhVQSGSYDYAIFNSTYGQPStftakapEYLASGTQITPTGyIPYDFEIMVGGPGGGSTTS 308
                                       8776.*******99998766789**********9998999999********************************** PP

                        Thermopsin 223 fnslnatlsLyYlngtnyqpvknaydfGsdTaEtaenv 260
                                       ++++nat++L Y+ ++ y++v++ayd+Gs+T+Et+e+v
  gi|518653070|ref|YP_008142590.1| 309 IYNVNATMNLRYMGSSGYVNVPSAYDVGSETGETSEGV 346
                                       **********************************9986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.16
                        Thermopsin 109 sanlsnsaisGnGtvyasskgefYyayatey.....lelslP 145
                                       +a++ n ++ GnGt ++      Y  +  ++      ++ +P
  gi|518653070|ref|YP_008142590.1| 462 NAQIANISLYGNGTAGNPYIMDNYQIMPISSlfegfNDFAFP 503
                                       456666666666666633333333222222244444444444 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.099
                        Thermopsin  14 aPmGiadyG 22 
                                       aP Gia+y 
  gi|518653070|ref|YP_008142590.1| 642 APLGIAEYS 650
                                       899999995 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.03
                        Thermopsin  98 fidNiWNftspsanlsnsaisG...nGtvy.asskg 129
                                       +  N WN+t++ a +++  ++G   +G+++ ++ +g
  gi|518653070|ref|YP_008142590.1| 680 VYINMWNITKQPAYITHY-VNGfalRGSIIgTHYQG 714
                                       5569***********987.64433367666322233 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (758 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); 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: 0.62u 0.32s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5077.54
//
Query:       gi|518653071|ref|YP_008142591.1|  [L=402]
Description: hypothetical protein FACI_IFERC00001G1710 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   93.7   0.0      3e-26   91.9   0.0    2.0  1  GlutR_N          Glutamyl-tRNAGlu reductase, N-terminal domai
    1.9e-24   86.3   3.2    2.3e-24   86.0   0.1    2.2  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
    1.8e-13   50.7   2.9    1.9e-13   50.7   1.5    1.8  2  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
    2.5e-07   31.2   0.9    5.8e-07   30.0   0.2    2.0  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0012   19.0   2.0      0.094   12.8   0.1    2.3  2  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0037   16.6   0.4     0.0082   15.5   0.1    1.7  2  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.023   14.9   0.4        0.2   11.9   0.1    2.4  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.054   13.7   0.6      0.054   13.7   0.6    2.2  2  Phage_TAC_10     Phage tail assembly chaperone
      0.059   13.8   0.1       0.17   12.3   0.0    1.8  2  NAD_binding_7    Putative NAD(P)-binding
      0.089   13.1   3.3        2.7    8.4   1.2    2.6  2  DUF1456          Protein of unknown function (DUF1456)


Domain annotation for each model (and alignments):
>> GlutR_N  Glutamyl-tRNAGlu reductase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.9   0.0   1.7e-29     3e-26      18     146 .]      24     135 ..       7     135 .. 0.79

  Alignments for each domain:
  == domain 1  score: 91.9 bits;  conditional E-value: 1.7e-29
                           GlutR_N  18 fseeelkellkeleekvkeaviLsTCNRtEiylsaeeeeeaseellellaevsleelkeklyvlegeeavrHlfrVa 94 
                                        + + +++++++  +++k++viL TCNR+Eiy++ ee          +l      +++ +ly le  e+v+Hlf Va
  gi|518653071|ref|YP_008142591.1|  24 RDYRYFESMMES--RSIKNYVILVTCNRIEIYFRPEE----------IL----MGSIEGSLY-LEYPESVKHLFMVA 83 
                                       333334444444..4899**************64432..........44....455666665.567899******** PP

                           GlutR_N  95 sGLdSlvlGEdqIlgQvkeayelakeagtlgkvLerlfqkaikvakrvrtet 146
                                       sGL+S+ +GE++Il Q+k++++ a+++g l+k+L+  f+ka++v+k+vrt t
  gi|518653071|ref|YP_008142591.1|  84 SGLESMAIGENDILRQIKSSFDIASKRGKLDKFLSYTFRKALSVGKDVRTLT 135
                                       *************************************************965 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.0   0.1   1.3e-27   2.3e-24       9     137 ..     157     275 ..     150     276 .. 0.91
   2 ?    0.1   0.5      0.43   7.7e+02      75     111 ..     310     349 ..     281     352 .. 0.66

  Alignments for each domain:
  == domain 1  score: 86.0 bits;  conditional E-value: 1.3e-27
                                       ..TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.ET-EEEEGCGHHHHHHT-SEEEE-SSS CS
                      Shikimate_DH   9 slkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeelkgeeiealkleelkellaeadvvisatas 85 
                                        l++kk ++iG+G+m++ ++++L+ ++   v+va+Rt+++a++la +++++   + ++ ++++l+++++++i+at+s
  gi|518653071|ref|YP_008142591.1| 157 GLAGKKLCIIGTGKMSTALLNYLAGSKTI-VTVAGRTIDHARDLAIKYGAN---YSDIGNIQSLIKSNEIIIAATSS 229
                                       4899********************98887.******************888...*********************** PP

                                       SS-SB-HHHHHCCHHH.S..EEEEE--SS-SB-TTGGGSTTCCCEEHHHHHH CS
                      Shikimate_DH  86 eepilekeeveealkkrkkplllvDiavPRdvepevaeledvrlytvDdLke 137
                                       +++i+++e+ + ++++    ++++D+++P ++e++++e   +  y++D +++
  gi|518653071|ref|YP_008142591.1| 230 KNYIIRAEDYSTINEN----KIMIDLSNPPNIEQAMNE--YIAFYDLDRIYS 275
                                       ***********99976....7************99888..589999998765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                                       T-SEEEE-SSSSS-SB-HHHHHCCHHH.S.....EEEEE- CS
                      Shikimate_DH  75 eadvvisataseepilekeeveealkkrk...kplllvDi 111
                                       ++d +i+a     + ++++e+ee+ +k++    ++ ++Di
  gi|518653071|ref|YP_008142591.1| 310 KSDDIIAAFYKFANQIKQDELEELARKTDikeAQMEIIDI 349
                                       3577889999999999999999999888774344578887 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       5.7     1e+04       4      24 ..      20      40 ..      19      42 .. 0.82
   2 !   50.7   1.5   1.1e-16   1.9e-13       1      87 [.     290     376 ..     290     386 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 5.7
                                      HHHHHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer  4 aiIeeeveefeawlkslevvp 24
                                      +iI++  + fe+ ++s+++++
  gi|518653071|ref|YP_008142591.1| 20 EIIKRDYRYFESMMESRSIKN 40
                                      789999999999999998865 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 1.1e-16
                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-S..--------TTHHHHHHHHHHHHHHHHH CS
                       GlutR_dimer   1 kAeaiIeeeveefeawlkslevvptIkalrekaeeireeeleralkklaldgedreelekltrslvnkllheptarL 77 
                                       kAe+i+e e+  + +++++++ +++I+a+++ a++i+++ele++ +k ++++ + e ++ +++s ++kll + t ++
  gi|518653071|ref|YP_008142591.1| 290 KAEEIVENELTLYTSKINEMKSDDIIAAFYKFANQIKQDELEELARKTDIKEAQMEIIDIMMNSFTKKLLAPYTDSI 366
                                       7************************************************99999999******************** PP

                                       HSS.-TTTTHH CS
                       GlutR_dimer  78 kea.edeeeel 87 
                                       k+  +++e ++
  gi|518653071|ref|YP_008142591.1| 367 KNFiKNNE-NY 376
                                       *9954333.33 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 !   30.0   0.2   3.2e-10   5.8e-07       1      97 []     162     254 ..     162     254 .. 0.88
   2 ?   -2.4   0.0       4.3   7.6e+03      32      48 ..     323     339 ..     306     350 .. 0.59

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 3.2e-10
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECE.CHHHHHHH-SEEEE-S-HHHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtav.dneeaaeeadvvvlavkpedvee 76 
                                       k++iiG+G+m  al++ l+ +    + ++va  r+ + a+ la ++g++ +   + + +++++++++ a   +++  
  gi|518653071|ref|YP_008142591.1| 162 KLCIIGTGKMSTALLNYLAGSK---TIVTVA-GRTIDHARDLAIKYGANYSDIgNIQSLIKSNEIIIAATSSKNYII 234
                                       689*************999997...666655.***************88776515677889**************** PP

                                       HHHHCGHHHHTTSEEEEESSS CS
                     F420_oxidored  77 vlselakdalkgklvisvlag 97 
                                        +++  +   ++k+ i+ +++
  gi|518653071|ref|YP_008142591.1| 235 RAEDY-STINENKIMIDLSNP 254
                                       **999.9**********9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.3
                                       EESSCCCHHHHHHHHC- CS
                     F420_oxidored  32 nsrnpekaeelaeelgv 48 
                                       n+ +++++eela++  +
  gi|518653071|ref|YP_008142591.1| 323 NQIKQDELEELARKTDI 339
                                       33344444455444443 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.1   5.3e-05     0.094      21     109 ..     158     251 ..     148     271 .. 0.84
   2 !    5.5   0.3    0.0089        16      93     137 ..     302     346 ..     288     360 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.3e-05
                                       -TTSEEEEE--SHHHHHHHHHHHHCT-EEEEE..-S-HHH..HHHHHCTT-EE--HHHCTTT-SEEEE-SSSSS.SB CS
                     AdoHcyase_NAD  21 laGkvavvaGyGdvGkGcaaslkglGarvivt..evdPic..alqaameGfevvtleevvkkadivvtttGnkd.ii 92 
                                       laGk+ +++G G +     + l g  ++v+v+   +d     a++   +  ++ +++ ++k+ +i++++t +k+ ii
  gi|518653071|ref|YP_008142591.1| 158 LAGKKLCIIGTGKMSTALLNYLAGSKTIVTVAgrTIDHARdlAIKYGANYSDIGNIQSLIKSNEIIIAATSSKNyII 234
                                       89**********9999999999999999998644699886224555566678999***************9998688 PP

                                       -HHHHCCS-TTEEEEE- CS
                     AdoHcyase_NAD  93 tlehlkkmkddaivcni 109
                                       ++e+ ++++++ i+ ++
  gi|518653071|ref|YP_008142591.1| 235 RAEDYSTINENKIMIDL 251
                                       99******999998765 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0089
                                       -HHHHCCS-TTEEEEE-SSTTTTBTHHHHHTTT-EEEEEETTEEE CS
                     AdoHcyase_NAD  93 tlehlkkmkddaivcniGhfdseidvaaleanalkkeevkpqvdr 137
                                        + ++++mk d i++    f ++i+ ++le+ a k++   +q++ 
  gi|518653071|ref|YP_008142591.1| 302 YTSKINEMKSDDIIAAFYKFANQIKQDELEELARKTDIKEAQMEI 346
                                       567899************************997665544456554 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.1   4.6e-06    0.0082      32     129 ..     156     254 ..     136     265 .. 0.80
   2 ?   -2.9   0.0         2   3.7e+03      79      94 ..     324     339 ..     319     361 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.6e-06
                                       S-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH.CHHHHTCEECSHHHHHHH-SEEEE-S--STTTTT CS
                      2-Hacid_dh_C  32 kelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkee.eeeelgvelvsleellaesDivslhlpltpetrh 107
                                       + l+gk+++iiG+G++ +a+ ++l++ +  v++  r+ ++ +  + ++g+++ ++ ++ +      + + +t + + 
  gi|518653071|ref|YP_008142591.1| 156 YGLAGKKLCIIGTGKMSTALLNYLAGSKTIVTVAGRTIDHARdLAIKYGANYSDIGNIQSLIKSNEIIIAATSSKNY 232
                                       5799*******************************999977765667777777665555444444445567788889 PP

                                       SBSHHHHHCSTTTEEEEESS-G CS
                      2-Hacid_dh_C 108 linaeelakmkkgailiNtaRG 129
                                       +i ae  + + ++ i+i  +  
  gi|518653071|ref|YP_008142591.1| 233 IIRAEDYSTINENKIMIDLSNP 254
                                       9999999999999999987765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2
                                       TCEECSHHHHHHH-SE CS
                      2-Hacid_dh_C  79 gvelvsleellaesDi 94 
                                       +++ ++leel +++Di
  gi|518653071|ref|YP_008142591.1| 324 QIKQDELEELARKTDI 339
                                       5677888888888887 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 ?   11.9   0.1   0.00011       0.2       2      45 ..     164     218 ..     163     267 .. 0.72
   2 ?    0.2   0.0      0.46   8.2e+02      14      65 ..     330     382 ..     327     390 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00011
                                       EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH..............T CS
                   Sacchrp_dh_NADP   2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka..............l 45 
                                        iiG G+++ a++ +la ++ +   +tva+r+ ++++ la k               +
  gi|518653071|ref|YP_008142591.1| 164 CIIGTGKMSTALLNYLAGSKTI---VTVAGRTIDHARDLAIKYganysdigniqsliK 218
                                       59******************99...**********99887554554444444444443 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.46
                                       HHHHHCTCCT-G.EEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHH CS
                   Sacchrp_dh_NADP  14 aellarhfdvda.eitvadrskeklealaakalgvrfeaialdaenyeavLaa 65 
                                       +e+lar+ d+++ ++ ++d   ++  + + +    ++++   + eny+ +L++
  gi|518653071|ref|YP_008142591.1| 330 LEELARKTDIKEaQMEIIDIMMNSFTKKLLAPYTDSIKNFIKNNENYSYILEE 382
                                       6899999***9999999999888888877776777777777777777776665 PP

>> Phage_TAC_10  Phage tail assembly chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.6     3e-05     0.054      18      76 ..     301     358 ..     286     360 .. 0.86
   2 ?   -1.5   0.4       1.6   2.9e+03      17      31 ..     381     395 ..     368     400 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3e-05
                      Phage_TAC_10  18 aYnkllNelapnnkvaPsknfLvrivaeeskealkeilatPgaalqiaekvneeytPdl 76 
                                        Y + +Ne+++++++a  ++f ++ +++++ e+l++   +  a+++i++ + + +t +l
  gi|518653071|ref|YP_008142591.1| 301 LYTSKINEMKSDDIIAAFYKFANQ-IKQDELEELARKTDIKEAQMEIIDIMMNSFTKKL 358
                                       68899****************776.57888899999999999*******9999998775 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                      Phage_TAC_10  17 eaYnkllNelapnnk 31 
                                       e+Y+++l ++++n k
  gi|518653071|ref|YP_008142591.1| 381 EEYDTMLGNMVKNGK 395
                                       778888888887766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   9.7e-05      0.17       5      73 ..     158     231 ..     156     259 .. 0.73
   2 ?   -2.4   0.1       3.7   6.6e+03      63      63 ..     318     318 ..     276     360 .. 0.51

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9.7e-05
                     NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvklaeee..l...ekdlegadlviaatddre 73 
                                       l gkk +++G G++ +  ++ l+ ++  vtv   ++  + +  +k+  ++  +   ++ ++  +++iaat+ ++
  gi|518653071|ref|YP_008142591.1| 158 LAGKKLCIIGTGKMSTALLNYLAGSKTIVTVAGRTIDHARDLAIKYGANYsdIgniQSLIKSNEIIIAATSSKN 231
                                       679**********************999999888876666666665333322333377799999******8765 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 3.7
                     NAD_binding_7  63 d 63 
                                       +
  gi|518653071|ref|YP_008142591.1| 318 F 318
                                       1 PP

>> DUF1456  Protein of unknown function (DUF1456)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.037        66       2      16 ..      94     108 ..      93     110 .. 0.88
   2 ?    8.4   1.2    0.0015       2.7      13      58 ..     308     354 ..     305     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.037
                           DUF1456   2 NdiLrrlRyaLdlkd 16 
                                       NdiLr ++  +d+ +
  gi|518653071|ref|YP_008142591.1|  94 NDILRQIKSSFDIAS 108
                                       ************975 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0015
                           DUF1456  13 dlkdedmveifklggvevtkeelsalLkkedee.gyeeckdqvLesF 58 
                                       ++k++d+++ f +   +++++el++l +k d + +  e+ d +++sF
  gi|518653071|ref|YP_008142591.1| 308 EMKSDDIIAAFYKFANQIKQDELEELARKTDIKeAQMEIIDIMMNSF 354
                                       5899*************************776615556999999999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1320  (0.0736237); expected 358.6 (0.02)
Passed bias filter:                      461  (0.0257125); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.46
# Mc/sec: 2647.30
//
Query:       gi|518653072|ref|YP_008142592.1|  [L=75]
Description: hypothetical protein FACI_IFERC00001G1711 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.2   11.0   0.6       0.23   10.8   0.6    1.0  1  DUF4191   Domain of unknown function (DUF4191)
       0.27   11.3   2.1       0.53   10.3   2.1    1.5  1  PsbL      PsbL protein
          1    9.0  12.3       0.16   11.6   1.8    2.2  2  DUF3149   Protein of unknown function (DUF3149)


Domain annotation for each model (and alignments):
>> DUF4191  Domain of unknown function (DUF4191)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.6   3.8e-05      0.23       9      68 ..       6      65 ..       2      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.8e-05
                           DUF4191  9 kqiaqvfkltrkedkkllwlllaaflvvvvvfvvlglllgslilllilgillgllvaliv 68
                                      + i++ +k  ++  ++  +++l++++++  +++++ +  +sl++ ++l ++ g+l++ ++
  gi|518653072|ref|YP_008142592.1|  6 SDIMELYKQNKRIPPEKFMIILLTVMGINSAIIIASFYQKSLFIRIVLELVSGILMVSYF 65
                                      579999******99999999999999999999999999888999999****999987654 PP

>> PsbL  PsbL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   2.1   8.9e-05      0.53      16      36 ..      46      66 ..      41      67 .. 0.95

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 8.9e-05
                              PsbL 16 SLYlGLLLvfvlalLFssYFf 36
                                      SL++ ++L +v ++L  sYF+
  gi|518653072|ref|YP_008142592.1| 46 SLFIRIVLELVSGILMVSYFL 66
                                      9*******************6 PP

>> DUF3149  Protein of unknown function (DUF3149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   3.2     0.015        88       9      27 ..      25      43 ..      22      53 .. 0.86
   2 ?   11.6   1.8   2.6e-05      0.16      21      33 ..      59      71 ..      56      74 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.015
                           DUF3149  9 vGLlSliVIvftigmgaff 27
                                      ++Ll +++I  +i++++f+
  gi|518653072|ref|YP_008142592.1| 25 IILLTVMGINSAIIIASFY 43
                                      88999************98 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.6e-05
                           DUF3149 21 igmgaffiryFir 33
                                      i+m+++f+++F+r
  gi|518653072|ref|YP_008142592.1| 59 ILMVSYFLWFFLR 71
                                      89*********87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       886  (0.0494171); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 510.73
//
Query:       gi|518653073|ref|YP_008142593.1|  [L=365]
Description: hypothetical protein FACI_IFERC00001G1712 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-08   35.2   0.0    2.2e-08   34.7   0.0    1.2  1  Radical_SAM  Radical SAM superfamily
    1.3e-06   28.8   0.2    3.1e-06   27.6   0.2    1.7  1  SPASM        Iron-sulfur cluster-binding domain
  ------ inclusion threshold ------
      0.099   12.9   0.0       0.19   12.0   0.0    1.4  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.7   0.0   3.6e-12   2.2e-08       2     153 ..      14     159 ..      13     172 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.7 bits;  conditional E-value: 3.6e-12
                                       EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHH.HHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelk.aekgvkevilgggepllypdfvellerlaklavpg 77 
                                       ++t++C l+C++C  +      + + ++  ee  + +k+++ + k    +il+gg+ + + d+ +++e + +    +
  gi|518653073|ref|YP_008142593.1|  14 ETTKACGLACRHCRASAL--EKPLPDEMNFEEASAFIKSIRdFGKPYPILILTGGDMMRRNDINKIIETANEY---E 85 
                                       6899************96..********************988888************************997...7 PP

                                       EEEEEEECSSCHG.HHHHHHHHHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBT CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM  78 iritvetngtlpd.eeklerllelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglp 153
                                       i ++++  +t +  +e ++ ++  ++   sl+l+   +   ++++++ + + ++++ +++++++++k   ++ v+++
  gi|518653073|ref|YP_008142593.1|  86 IPVSISPAATDLLtPERIDYFKAHHILSASLSLDGNRE--MHDWLRGDGVYNKTIDMIKLFNAKNMK-LQINSVVMR 159
                                       77777776666657*******************98777..89999999*******************.999999988 PP

>> SPASM  Iron-sulfur cluster-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2   5.2e-10   3.1e-06       5      64 ..     273     328 ..     270     335 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 5.2e-10
                             SPASM   5 srslfInsdGdVvpCcvdkktyveelklGnireesleeIw.nseeyqefrkskkfp.lielC 64 
                                       +  +f+ ++GdV+p  +        +klGn++++s+ +I+ n+e ++++r+sk+f  ++ +C
  gi|518653073|ref|YP_008142593.1| 273 KGIIFVGHNGDVIPSGFL------TYKLGNVKQNSIVDIYrNNETLKMLRNSKNFGgRCGIC 328
                                       5679***********433......4***************6666999999655665344444 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.2e-05      0.19      12      77 ..      16      79 ..       6      99 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.2e-05
                           Fer4_12 12 vsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk..esiegltllGGEPllpenaeallelvk 77
                                      ++ C l+C+ C + ++ ++   +e+++e +   i+++ +  +  + l+l+GG+ + ++   ++ ++++
  gi|518653073|ref|YP_008142593.1| 16 TKACGLACRHCRASALEKP-LPDEMNFEEASAFIKSIRDfgKPYPILILTGGDMMRRN---DINKIIE 79
                                      678********97776666.55667777777777777774344599*******98844...4444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (365 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2479.16
//
Query:       gi|518653074|ref|YP_008142594.1|  [L=432]
Description: hypothetical protein FACI_IFERC00001G1713 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-23   82.6  59.6    4.3e-20   71.9  40.2    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 !   71.9  40.2   2.4e-24   4.3e-20      25     347 ..      48     380 ..      29     385 .. 0.72
   2 !   24.6  11.4   6.1e-10   1.1e-05      61     172 ..     306     421 ..     297     431 .. 0.69

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 2.4e-24
                             MFS_1  25 edlgispseigllltlyalga.avaslpl.GrlsdrfGrrrvlllglllfalg.lllllf...a...sslw.lllvl 91 
                                       + lg+ +  + ll ++++++a +v+s++l  +++dr Gr+ +l +++++f++  ++++l+   +   + ++ ll++l
  gi|518653074|ref|YP_008142594.1|  48 KYLGYLALILTLLPVTFGAAArSVGSVILgNFIGDRKGRKNLLSISIIGFSVLsAAIGLLptySqagIASPiLLYAL 124
                                       445555556666666677766766666664888********************77777754332556668889**** PP

                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wravfyilaiv 160
                                        +l G++aga + +g al  + + +e+r +a +++++g++ G+ l   +  ll+ s g        Wr +++ + i 
  gi|518653074|ref|YP_008142594.1| 125 LFLDGIFAGAEYGGGTALSMESVRPEKREQAGAFVQSGYGTGYFLIVFVEILLLRSMGsaafasygWRILMLTAIIP 201
                                       *************************************************99999666669999999*********** PP

                             MFS_1 161 sllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdp...vlwillialllfffgfsglltllplyl 234
                                       +++   l  +  + ++ +   ++ k e       + +p  ++++k++   v+ ++++a llf  +++++ ++ p+  
  gi|518653074|ref|YP_008142594.1| 202 GAIT--L--IIRRLSKETAVFDRMKAE----NSIEKSP-VRKMFKNRssiVFGFMITAGLLF--MNTATASFYPV-- 265
                                       ***9..4..566777777777777777....4555555.44455555222343233333333..55556666666.. PP

                             MFS_1 235 qevlgls....glllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvl 307
                                       +   ++     gll+a+l++ +++l+g      +g l++ +  rrr +l++++++++  +l+++  ++++++   ++
  gi|518653074|ref|YP_008142594.1| 266 VGSVDFLnlgsGLLYALLVINFFSLIG---VWSGGILARSFRDRRRPMLIFSIIFTVPTALFVIFGYTTNIMDFTIV 339
                                       3333333355999999999*******9...55667777666665666666666666666655555555666666666 PP

                             MFS_1 308 vliGf.glgfvfpsllalasdlappeeagtasglfntagsl 347
                                       + i +   +++f++l ++++++++++ + ta+gl+   g++
  gi|518653074|ref|YP_008142594.1| 340 FSIQLfLEALIFSALPVFLAESFSKKFRSTAVGLIYNGGAI 380
                                       667777****************************9977775 PP

  == domain 2  score: 24.6 bits;  conditional E-value: 6.1e-10
                             MFS_1  61 rrr.vlllglllfalglllllfa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa 134
                                       rrr +l++++++++ ++l+ +f+  +++  + ++  +q + ++++f+a  +++a+ f+k+ r+ a+gl++ g ++  
  gi|518653074|ref|YP_008142594.1| 306 RRRpMLIFSIIFTVPTALFVIFGytTNIMDFTIVFSIQLFLEALIFSALPVFLAESFSKKFRSTAVGLIYNGGAIFG 382
                                       6665999999999999666667643444448888899*****************************99887555544 PP

                             MFS_1 135 ilgpllggllasslg....Wravfyilaivsllafvlfllll 172
                                         + +l  + a+ ++    W +  yi++i+++l+++   ++ 
  gi|518653074|ref|YP_008142594.1| 383 GTAIVLLTAPAHIINirtlWIVEVYIAGIILILGLI---FYK 421
                                       444444443333444334577778888888888755...443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       622  (0.0346924); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 2856.85
//
Query:       gi|518653075|ref|YP_008142595.1|  [L=37]
Description: hypothetical protein FACI_IFERC00001G1714 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      135  (0.0075297); 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: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.35
# Mc/sec: 313.52
//
Query:       gi|518653076|ref|YP_008142596.1|  [L=53]
Description: transposon-encoded protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.5e-24   85.5   1.0    1.6e-24   85.3   1.0    1.0  1  DUF2080   Putative transposon-encoded protein (DUF2080)


Domain annotation for each model (and alignments):
>> DUF2080  Putative transposon-encoded protein (DUF2080)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   1.0   9.1e-29   1.6e-24       1      50 []       4      53 .]       4      53 .] 0.98

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 9.1e-29
                           DUF2080  1 veIrkktwlkvkeilpffegkVkpfGnSAkvsiPkeylGkkvylvIlddd 50
                                      veI+++t++++k i++f+e+kV++fG++Akv++Pke+lGk+vy+vI++d+
  gi|518653076|ref|YP_008142596.1|  4 VEIHETTEVSIKGIYGFIERKVTKFGSGAKVDCPKEFLGKRVYIVITRDE 53
                                      8**********************************************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 441.74
//
Query:       gi|518653077|ref|YP_008142597.1|  [L=346]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0061   16.2   2.3      0.011   15.4   2.3    1.5  1  DDE_Tnp_1  Transposase DDE domain
  ------ inclusion threshold ------
      0.047   14.3   0.3        0.2   12.3   0.0    2.0  2  DUF488     Protein of unknown function, DUF488
       0.98   10.0   4.2        2.5    8.7   0.1    2.6  3  SF3A3      Pre-mRNA-splicing factor SF3A3, of SF3a complex, P


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   2.3   1.8e-06     0.011      21     198 ..     185     324 ..     148     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.8e-06
                         DDE_Tnp_1  21 edarwgykggkykygyklhiavdtrsglilsvvit.pgnvhdskglkqlldelrprkgklvlaDaGYasaelldtle 96 
                                       e++ +++kg++++       ++d+r+++ ++  ++    ++  + +  +++ + + + ++++ D+ Y+s++++d+l 
  gi|518653077|ref|YP_008142597.1| 185 EHKDKKSKGHRKRLFAYSFSIMDLRTRMYIASGTSmKSERNAYDNAMRIVNKIGI-NIDSIRLDRYYSSPSYVDKLG 260
                                       4555566655555555688889999987777777555555555555556666666.********************* PP

                         DDE_Tnp_1  97 ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntnsellsaeevaelyrl 173
                                       + +v   i++kkn++l+              +++  i++  + + n+                         e y++
  gi|518653077|ref|YP_008142597.1| 261 DTKV--YIIPKKNSTLH-----------GSHKWKSIIREFLNDTMNY------------------------LEKYHK 300
                                       6666..59999999997...........4577777777777777777........................777888 PP

                         DDE_Tnp_1 174 RwqiErvFkwlkrkfgldrlryrgl 198
                                       R+  E+ F+  k  + ++++  r+ 
  gi|518653077|ref|YP_008142597.1| 301 RSNSESGFAADKK-MLGWNMAQRRD 324
                                       8888888887777.55555554444 PP

>> DUF488  Protein of unknown function, DUF488
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   3.3e-05       0.2      61     121 ..      22      81 ..      15      82 .. 0.84
   2 ?   -1.0   0.1      0.44   2.6e+03      70      87 ..     161     178 ..     139     197 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.3e-05
                            DUF488  61 kwfkhdp.rweefferYaaeleskeaakealeelkelakkgvaLlcaekdperchrvvlaey 121
                                       k++ ++  ++ + ++ Y+ e+ ++   k+a++el  l++k+v ++  +k p + h  +la+ 
  gi|518653077|ref|YP_008142597.1|  22 KKYVQEHpEKGRNWRTYESEFSRR--IKTAMKELDPLIEKAVSIMHIAKRPGHPHSLLLAQR 81 
                                       5666555479999*********83..5699****9999999**************9999875 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
                            DUF488  70 eefferYaaeles.keaak 87 
                                       ++  e+Ya+ l++   +++
  gi|518653077|ref|YP_008142597.1| 161 KKNYESYAQRLKDlA-KEN 178
                                       444555666666532.222 PP

>> SF3A3  Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       2.2   1.3e+04      50      64 ..      31      45 ..      11      58 .. 0.51
   2 ?    2.4   0.2     0.039   2.3e+02       4      52 ..     124     189 ..     121     209 .. 0.53
   3 ?    8.7   0.1   0.00043       2.5      33      72 ..     254     302 ..     224     304 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                             SF3A3 50 kskeYkeYlkeLleY 64
                                      k +++++Y +e    
  gi|518653077|ref|YP_008142597.1| 31 KGRNWRTYESEFSRR 45
                                      334444444444444 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.039
                             SF3A3   4 geEqyGkylDLnelyeeylnlk.............eikldYlqYLesfdkf....seipkkqkksk 52 
                                       ++E    +++L+ l  +  n++             ++k +Y +Y ++++++    +ei k++ k k
  gi|518653077|ref|YP_008142597.1| 124 DNEVVMAIFNLHVLLLKNKNIAnsdatgdgtgyslTVKKNYESYAQRLKDLakenKEIGKEEHKDK 189
                                       555555556666666666666633333333332222235677777777666555545554444444 PP

  == domain 3  score: 8.7 bits;  conditional E-value: 0.00043
                             SF3A3  33 qYLesfdkf.........seipkkqkkskeYkeYlkeLleYLesfikrt 72 
                                       +Y++++ +          s+++ ++k ++  +e+l++ ++YLe+++kr 
  gi|518653077|ref|YP_008142597.1| 254 SYVDKLGDTkvyiipkknSTLHGSHKWKSIIREFLNDTMNYLEKYHKRS 302
                                       46666644444344443334444455555666***************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       920  (0.0513135); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2570.88
//
Query:       gi|518653078|ref|YP_008142598.1|  [L=443]
Description: hypothetical protein FACI_IFERC00001G1717 [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   38.5  35.4    2.9e-09   36.2  35.4    1.8  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 !   36.2  35.4   1.6e-13   2.9e-09       1     386 [.      22     397 ..      22     437 .. 0.80

  Alignments for each domain:
  == domain 1  score: 36.2 bits;  conditional E-value: 1.6e-13
                    Transp_cyt_pur   1 pvpeeeRtwktlnlfsiWlganlnintwvigalglalgLnwwqsvlviivgnligaifvallglaGakyGlpfpils 77 
                                       p+p+++Rt + + ++ +W  a+ +  t  +g  +  +gL +  + ++iiv+ lig i+  l + +G +  +p  ++s
  gi|518653078|ref|YP_008142598.1|  22 PIPNQARTMSSRKIMIFWAMASASALTPIVGLELYNMGLPF--ATIAIIVALLIGIIPAGLVAEMGRQIPVPSLVVS 96 
                                       8*********************************9999998..5789****************************** PP

                    Transp_cyt_pur  78 RasfGirgsllplllrvviaivwfgvqawiGsealllmlgkifgkwleiggailgtsltelvtffifwvvslvivll 154
                                       R  +G + s   +l+  ++ +++fg++ ++G++ ++ +  +                  +++  ++ +v+++v vl+
  gi|518653078|ref|YP_008142598.1|  97 RKTYGFMTSGAYSLVFTFLNLGFFGLNDTVGAAIISGLTHSN-----------------IIIWYVVMGVIQVVLVLF 156
                                       *********999***9****************9877665555.................677788999********* PP

                    Transp_cyt_pur 155 gvskirkffviaallvpvaafgfliwalvkaeg..GpvldkavklgkselflsavagvlagfatlilnapDFtryak 229
                                       g + ++ ff + a+++ v  + ++ ++l   ++  + +++ ++++++ ++++  +   + ++      ++  tr++ 
  gi|518653078|ref|YP_008142598.1| 157 GAKWLEYFFRYSAPVLIVSYIILAYFLLTTYTInfSMLMHPIGAFTWGAALNFLLGFSILAW---SYKISTQTRFGY 230
                                       ****************9999999999999988888999998888885444444444444444...444557788875 PP

                    Transp_cyt_pur 230 tkk......ssvkiqlvavpllftlllligilvaaaakaayganawspldilakfdet.agvllililvalaqlgvn 299
                                       ++       +++k ++++ ++ ++++ll+g+++ ++ ++a g    ++l++ +    + ++v+++++ v la + +n
  gi|518653078|ref|YP_008142598.1| 231 PYSehdssgKKLKYFISSPVGIMIPVLLMGLIGLVGNSVATGGWNIATLSFPGLHGLFgIVVFIAALGVSLAIIHTN 307
                                       54311111167899999999*****************99977777777756555555588999999**999999888 PP

                    Transp_cyt_pur 300 isanllsagld.laallPkkinikrgsliaavialvivpwkllsssskl...ftaflsllavflspvagviiadyfv 372
                                       + +nl++a  d laal P +    +  l+ ++++++      + + +++   + +f++ la ++ p++ ++i d fv
  gi|518653078|ref|YP_008142598.1| 308 A-MNLYPATADlLAALQPAFRKKPNEKLAQPIATILLGAGGIILAIAGIlahIETFIDDLASIIFPFTFILIFDWFV 383
                                       6.6667776662688999766667777777777777766666666666556688999*******************9 PP

                    Transp_cyt_pur 373 vrrgylklaalytr 386
                                         r   k+ + y  
  gi|518653078|ref|YP_008142598.1| 384 HLRHTTKIGDYYNI 397
                                       99988888877763 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (443 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 3025.68
//
Query:       gi|518653079|ref|YP_008142599.1|  [L=303]
Description: transposase IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   71.2   0.5    1.4e-19   70.6   0.5    1.3  1  DDE_Tnp_1    Transposase DDE domain
    2.7e-11   43.7   0.1    4.7e-11   42.9   0.1    1.3  1  DDE_Tnp_1_3  Transposase DDE domain
    0.00015   22.1   0.4    0.00065   20.0   0.2    2.1  2  DDE_Tnp_1_5  Transposase DDE domain
     0.0036   17.3   0.1     0.0074   16.3   0.1    1.5  1  DUF772       Transposase domain (DUF772)
  ------ inclusion threshold ------
      0.022   14.4   0.0       0.04   13.6   0.0    1.5  1  DDE_Tnp_4    DDE superfamily endonuclease


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.5   3.8e-23   1.4e-19       2     214 .]      94     282 ..      93     282 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 3.8e-23
                         DDE_Tnp_1   2 skrevlivDattvrvpgtk...........edarw..gyk.ggk.ykygyklhiavdtrsglilsvvitpgnvhdsk 63 
                                       s++++ ++D+  + +++++           +d  +  g++ + k + yg+k+h+ +d  s +i+   it gn hds+
  gi|518653079|ref|YP_008142599.1|  94 SVESIAAIDSFIIHTCKHStamrrkvwgnyKD--PvsGWSkTTKgWSYGRKCHMSIDIDSLIIMEWLITKGNMHDSH 168
                                       578999*************8777776665522..25566644446******************************** PP

                         DDE_Tnp_1  64 glkqlldelrprkgklvlaDaGYasaelldtle.ekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqk 139
                                       + ++++d++r  + +++laD++Y+  +++d++    ++ ++i                ++ r + +d+    +k+ +
  gi|518653079|ref|YP_008142599.1| 169 VSHDMVDSVR--DFSYILADSAYDASDIYDYIFeNTHALPVID--------------TNKRRGIVNDKLPVNRKIGI 229
                                       **********..9********************5555555663..............37777788888888888888 PP

                         DDE_Tnp_1 140 rrnkskkekgdvyyvtntnsellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllalnl 214
                                         +k                      e+a +y+lRw+iEr+F+ l+  ++ +   y   +   +++ l+++a+nl
  gi|518653079|ref|YP_008142599.1| 230 DLRK----------------------EYASMYPLRWEIERTFSILEEIMKAEYIWYTVNRDYDTAIGLKAIAYNL 282
                                       8888......................99**********************9999999999999999999999998 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.1   1.3e-14   4.7e-11       5     112 ..      96     213 ..      93     234 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 1.3e-14
                       DDE_Tnp_1_3   5 tgisfiDstklavChnkrikrhkvfkg....lakrGkssmGWfyGfkLhliin.dkGeilavkltpgnvdDrepvee 76 
                                       + i+ iDs  ++ C+   + r+kv  +    ++ + k++ GW yG k h+ i+ d+  i+++ +t+gn++D +  ++
  gi|518653079|ref|YP_008142599.1|  96 ESIAAIDSFIIHTCKHSTAMRRKVWGNykdpVSGWSKTTKGWSYGRKCHMSIDiDSLIIMEWLITKGNMHDSHVSHD 172
                                       6899********************865222367899**************998355567899*************** PP

                       DDE_Tnp_1_3  77 lakellg..klfaDkgyiskklaeellee..gieli.tklr 112
                                       ++ ++ +   ++aD +y + ++ + ++e+  ++ +i t++r
  gi|518653079|ref|YP_008142599.1| 173 MVDSVRDfsYILADSAYDASDIYDYIFENthALPVIdTNKR 213
                                       **9996522789**********9999987334444434444 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.2   1.8e-07   0.00065      29      93 ..      22      88 ..      13     111 .. 0.82
   2 ?   -0.1   0.0      0.32   1.2e+03      59      82 ..      95     118 ..      93     133 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.8e-07
                       DDE_Tnp_1_5 29 rpqvysdaaiqtcltvkvlfklplRqlqGfvqs...llklaglellvpdystlsrraktlevkipvkr 93
                                      r+++y+d  i  +l+v ++f++++R ++ f++     +++ag+ + +p + tlsrra+ ++++ + ++
  gi|518653079|ref|YP_008142599.1| 22 RKRKYTDRQILKVLIVLQIFNISYRSARIFLTNheeYIRMAGI-TEIPSFQTLSRRARMIDLHAVNNE 88
                                      7899**************************9752226889998.99*************999876554 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.32
                       DDE_Tnp_1_5  59 vqsllklaglellvpdystlsrra 82 
                                       v+s+ ++ ++ + ++++st +rr+
  gi|518653079|ref|YP_008142599.1|  95 VESIAAIDSFIIHTCKHSTAMRRK 118
                                       78999999999999********97 PP

>> DUF772  Transposase domain (DUF772)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   2.1e-06    0.0074       8      58 ..      29      75 ..      23      89 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                            DUF772  8 elmlkllllqylyglSdreleealrenlsfrwflgldleedpvpdhstlsr 58
                                      + +lk+l++ +++++S r +   l ++ ++ + +g+     ++p++ tlsr
  gi|518653079|ref|YP_008142599.1| 29 RQILKVLIVLQIFNISYRSARIFLTNHEEYIRMAGI----TEIPSFQTLSR 75
                                      789********************************8....67********9 PP

>> DDE_Tnp_4  DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.1e-05      0.04       2     131 ..     102     235 ..     101     261 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.1e-05
                         DDE_Tnp_4   2 Dgteipiqrpsnleeraqtysnykkkn............tlkvlivvdpngkiifvskgypGsvsDkeilensgllk 66 
                                       D++ i + + s+ ++r++ + nyk               + k+ + +d +  ii+     +G ++D+++ +  ++++
  gi|518653079|ref|YP_008142599.1| 102 DSFIIHTCKHST-AMRRKVWGNYKDPVsgwskttkgwsyGRKCHMSIDIDSLIIMEWLITKGNMHDSHVSH--DMVD 175
                                       666666655443.567777777776666666677777778889999999999998888889*******965..5666 PP

                         DDE_Tnp_4  67 alkeavkpgdvilaDkgFklsekllvpykkkkkkqlseeevefnraiasarihvErvigr.lkgrf 131
                                        ++      ++ilaD++++ s+ +   +  ++ + l   ++++ r i ++   v r ig  l++ +
  gi|518653079|ref|YP_008142599.1| 176 SVR----DFSYILADSAYDASDIYDYIF--ENTHALPVIDTNKRRGIVNDKLPVNRKIGIdLRKEY 235
                                       655....558************554444..478888888888888888888888888874355555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2133.03
//
Query:       gi|518653080|ref|YP_008142600.1|  [L=1019]
Description: hypothetical protein FACI_IFERC00001G1719 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-20   73.7   0.1    3.2e-20   72.4   0.0    1.8  2  Peptidase_S41  Peptidase family S41
    4.9e-17   61.7   0.1      1e-16   60.7   0.1    1.5  1  Tricorn_PDZ    Tricorn protease PDZ domain
    3.5e-15   55.8   0.2    8.6e-15   54.6   0.2    1.7  1  Tricorn_C1     Tricorn protease C1 domain
    1.6e-08   34.3  13.4        0.1   12.6   0.1    6.1  6  PD40           WD40-like Beta Propeller Repeat
     0.0048   16.8   2.5       0.21   11.4   0.0    3.0  3  eIF2A          Eukaryotic translation initiation factor eIF2A
  ------ inclusion threshold ------
      0.017   13.9   5.2        3.9    6.1   0.2    4.0  4  DPPIV_N        Dipeptidyl peptidase IV (DPP IV) N-terminal re
      0.026   14.8   0.1      0.072   13.4   0.1    1.8  1  PDZ_2          PDZ domain
       0.19   12.0   0.0        2.5    8.4   0.0    2.7  2  ANAPC4_WD40    Anaphase-promoting complex subunit 4 WD40 doma


Domain annotation for each model (and alignments):
>> Peptidase_S41  Peptidase family S41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.6   5.9e+03      77      98 ..     277     298 ..     219     299 .. 0.65
   2 !   72.4   0.0   1.4e-23   3.2e-20       1     166 []     829     984 ..     829     984 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.6
                                       TCSS-S..TT-BSSEEEEEE-TTB CS
                     Peptidase_S41  77 tekase..evqykgplvvLvnegs 98 
                                       +    +  +++y+g+l+ L+++g 
  gi|518653080|ref|YP_008142600.1| 277 DYL--TdyKINYTGNLIGLISRGQ 298
                                       222..1236779999999999886 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 1.4e-23
                                       EEEEEEES-BCCTHHHHHHHHHHHHHHTTSSEEEEE-TTB-EBEHHHHHHHHHCCSSSSEEEEEECTTSEEEEEEHT CS
                     Peptidase_S41   1 kiGyiripsfsektkeelakalkelkkknvkglilDlRnNgGGlldeavelaslflddglivstrgrdgkkkkkskt 77 
                                       kiGyi+ip+++ +  +e+ +++++ +  n +gli+D R+NgGG +++++    +  + g+ v++rg ++ +      
  gi|518653080|ref|YP_008142600.1| 829 KIGYIHIPDMGMNGFNEFFRIYDREA--NRSGLIVDFRFNGGGFVSQLLLEKLSRKRIGYDVPRRGIITPYP----- 898
                                       79********7777777777777777..**************************************999999..... PP

                                       CSS-STT-BSSEEEEEE-TTBBTHHHHHHHHHHHTTSEEEEES-.-SB-EEEEEEEE-TTSSEEEEEEEEEEETTSB CS
                     Peptidase_S41  78 ekaseevqykgplvvLvnegsaSaseifagalkdngratlvGer.tfGkgtvqsvvelndgsalkltiakyltpdgr 153
                                              + +gp+v L+ne+  S+++i + ++k +g+++++G+r ++G  +++ +++l d++ ++ +    + +d +
  gi|518653080|ref|YP_008142600.1| 899 --V---DSVNGPMVGLTNEYAGSDGDIGTHVFKLMGLGKVIGTRtWGGVVGINPKIKLLDNTTVTQPQFATWFKDVK 970
                                       ..3...359***********************************99************9999999999888888888 PP

                                       C.TTTTS---SEE- CS
                     Peptidase_S41 154 s.iekkGvePdiev 166
                                         +e+ G +Pdi v
  gi|518653080|ref|YP_008142600.1| 971 YgMENYGTDPDIYV 984
                                       88**********76 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.1   4.5e-20     1e-16       1      84 [.     716     797 ..     716     800 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.5e-20
                                       -B-SEEEEEETTEEEEEEE-BS-TTSSS-B-GGGGGS---.TT-EEEEETTEE-BTTB-HHHHHHTTTTSEEEEEEE CS
                       Tricorn_PDZ   1 GlLGadleldkgayriakilpGdswdeearSPLaepGvnvreGdlilavdgepvskekgiaelLvgkagkeveLtvk 77 
                                       G+LG+d+e++++ y i+ki++Gd+++e+++SPL  + ++  e d+i++++g+++++ +++++lL g+a++ +++++ 
  gi|518653080|ref|YP_008142600.1| 716 GKLGIDYEFKNNNYIITKIYKGDPSNENEKSPLLYTDIK--ENDIIKSINGVSLDAANNPDKLLSGHANEIITIEIG 790
                                       99*********************************9888..99********************************99 PP

                                       -STT-EE CS
                       Tricorn_PDZ  78 rkdgkar 84 
                                       + +++++
  gi|518653080|ref|YP_008142600.1| 791 NRNKTKK 797
                                       9765443 PP

>> Tricorn_C1  Tricorn protease C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   0.2   3.8e-18   8.6e-15       2      69 ..     637     704 ..     636     705 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 3.8e-18
                                       HHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHHHGGGGG--SHHHHHHHHHHHHHTT--S---EE- CS
                        Tricorn_C1   2 aEwaqmfdeawrllrdkFydpdmhgvDWeavkerYepllprvatrdeladllsemlgeLntsHvyvsg 69 
                                        Ew++m+ e++ l++++++ ++      +a + +Y++ll++v+tr el+dl++em+ge++tsH+y+ g
  gi|518653080|ref|YP_008142600.1| 637 NEWKNMLYETFNLIKENYWSKEKVEELGDAPYLKYKKLLNKVSTRFELSDLIREMQGEYSTSHSYEIG 704
                                       6*******************975555458************************************866 PP

>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.6   0.1   4.6e-05       0.1       2      37 ..      29      66 ..      28      67 .. 0.87
   2 ?    4.2   0.0      0.02        44      23      37 ..     195     208 ..     195     209 .. 0.94
   3 ?   -2.0   0.0       1.7   3.9e+03      17      26 ..     232     241 ..     231     245 .. 0.86
   4 ?    4.8   0.0     0.012        28      16      25 ..     365     374 ..     355     374 .. 0.77
   5 !    5.5   0.5    0.0073        16       8      26 ..     399     417 ..     397     426 .. 0.88
   6 !   11.3   0.0   0.00011      0.25       6      30 ..     446     471 ..     444     481 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.6e-05
                                      EE--SSSS.EEEEEE-TTSSEEEEEEECT...TCEEEE CS
                              PD40  2 krltntpgnegaPsfSPDGkrlaFsSdRg..sGkpdIy 37
                                      +rltn+ g+ ++P +SPD ++ +F    g    ++dIy
  gi|518653080|ref|YP_008142600.1| 29 ERLTNNLGIVTNPKISPDKRYVYFRLMTGksGESSDIY 66
                                      69**********************99988866666688 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.02
                                       EEEEEECT.TCEEEE CS
                              PD40  23 laFsSdRgsGkpdIy 37 
                                       l+F Sd + G+ +Iy
  gi|518653080|ref|YP_008142600.1| 195 LYFISDHE-GSANIY 208
                                       8******9.*****9 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 1.7
                                       -TTSSEEEEE CS
                              PD40  17 SPDGkrlaFs 26 
                                       S D k+++F 
  gi|518653080|ref|YP_008142600.1| 232 SSDNKKIIFQ 241
                                       89******96 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.012
                                       E-TTSSEEEE CS
                              PD40  16 fSPDGkrlaF 25 
                                        SPDGk++a+
  gi|518653080|ref|YP_008142600.1| 365 ASPDGKYIAI 374
                                       6*******95 PP

  == domain 5  score: 5.5 bits;  conditional E-value: 0.0073
                                       SS.EEEEEE-TTSSEEEEE CS
                              PD40   8 pgnegaPsfSPDGkrlaFs 26 
                                       +g + ++s+S+D + la+s
  gi|518653080|ref|YP_008142600.1| 399 SGTIDDFSWSNDSILLAYS 417
                                       677889************8 PP

  == domain 6  score: 11.3 bits;  conditional E-value: 0.00011
                                       SSSS..EEEEEE-TTSSEEEEEEECT CS
                              PD40   6 ntpg.negaPsfSPDGkrlaFsSdRg 30 
                                       +tpg +++ P fS+D ++l + S R+
  gi|518653080|ref|YP_008142600.1| 446 TTPGaIDFKPVFSNDDNYLFYLSKRS 471
                                       46666*******************98 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.017        37      78     119 ..     333     376 ..     300     378 .. 0.76
   2 !   11.4   0.0   9.4e-05      0.21      38      95 ..     378     442 ..     375     450 .. 0.73
   3 ?   -3.5   0.0       3.5   7.8e+03     122     136 ..     568     582 ..     563     597 .. 0.65

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.017
                                       ESSSSCEEEEEECS..CEEEEEEEEES--EEEE-TTSSEEEEE- CS
                             eIF2A  78 yGkmpakvslfdlk..vkviskleeqkrNtiffspkgklvllaG 119
                                       y + ++++ l++++  +k+ +++++    +++ sp gk++++++
  gi|518653080|ref|YP_008142600.1| 333 YNEENNQILLYSVDktLKKFFDFKNGIIFSLKASPDGKYIAIGN 376
                                       3466779999998555999999****99***********99986 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 9.4e-05
                                       EEEEEESSSTT--EEECCEESSS.EEEEEE-TTSS-EEE......EESSSSC.EEEEEECSCEEE CS
                             eIF2A  38 etelyliklkkkksevvelkkegpihdvaWspkskefav......iyGkmpa.kvslfdlkvkvi 95 
                                        +el++++l++++++ ++ ++ g i d++Ws++s  +a        yG+  + ++++fdlk +++
  gi|518653080|ref|YP_008142600.1| 378 RFELFILNLENGNINKIDESESGTIDDFSWSNDSILLAYsypeseYYGYNGSsSIKIFDLKTNKK 442
                                       689****************************9986665422222234555444666666666655 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 3.5
                                       SSS-EEEEEETTTTE CS
                             eIF2A 122 nlaGeleiwdvkkkk 136
                                       +  G++e++d kkkk
  gi|518653080|ref|YP_008142600.1| 568 EKTGNIELFDFKKKK 582
                                       446888888887443 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.2    0.0017       3.9      55      81 ..       8      34 ..       3      40 .. 0.89
   2 ?    4.4   0.0     0.006        13     289     332 ..      43      91 ..      36     109 .. 0.72
   3 ?   -0.9   0.1      0.24   5.4e+02     294     326 ..     193     222 ..     177     246 .. 0.59
   4 ?    1.0   0.0     0.065   1.4e+02      42      80 ..     357     396 ..     325     407 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0017
                                      TEEEEEETTEEEEESTTTSEEEECES- CS
                           DPPIV_N 55 dklafvrnnnLyvrelatgkeiqlTsd 81
                                      + ++fv++n+L+  ++ t++  +lT++
  gi|518653080|ref|YP_008142600.1|  8 NLVVFVNDNDLWKYNINTKNIERLTNN 34
                                      6699********************975 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.006
                                       EETTTTEEEEEESS.SETTEBEEEEEESSCTTEEEESSTTTSEE.....E CS
                           DPPIV_N 289 vdekrdlvyFtatk.dsPlerhlYsvslesggeltrltdeegdh.....y 332
                                       ++ +++ vyF   + +s   + +Ys++le +g+ltr+t   g++     y
  gi|518653080|ref|YP_008142600.1|  43 ISPDKRYVYFRLMTgKSGESSDIYSIDLE-RGNLTRVTYLCGKStsrrmY 91 
                                       5678899***876626666788*******.*******9877766555551 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.24
                                       TEEEEEESSSETTEBEEEEEESSCTTEEEESST CS
                           DPPIV_N 294 dlvyFtatkdsPlerhlYsvslesggeltrltd 326
                                       d++yF++  ++    ++Ys +++ gg+l++ td
  gi|518653080|ref|YP_008142600.1| 193 DELYFISDHEG--SANIYSTDFT-GGNLKKHTD 222
                                       45666665554..4566666666.666666553 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.065
                                       TT.BSEEEEESSTTEEEEEETT.EEEEESTTTSEEEECES CS
                           DPPIV_N  42 eeklqlakwSPagdklafvrnn.nLyvrelatgkeiqlTs 80 
                                       ++ +   k SP+g+++a  +n+ +L++ +l++g+  ++ +
  gi|518653080|ref|YP_008142600.1| 357 NGIIFSLKASPDGKYIAIGNNRfELFILNLENGNINKIDE 396
                                       678888999*********9987699999999997766654 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   3.2e-05     0.072       2      81 ..     717     801 ..     716     802 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.2e-05
                                       ...XX------..-EEEEEE-TTSGGGGT.--T........T-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEE CS
                             PDZ_2   2 ylGvsvsdeedtggvlvvsVkeggPaakaglka........gDvilkvdgkkvksledlislllkkkpGdtVkltvl 70 
                                       +lG+  + +++    +++++++g+P+++    +        +D+i +++g+ + + ++   +ll++ +++ +++++ 
  gi|518653080|ref|YP_008142600.1| 717 KLGIDYEFKNN--NYIITKIYKGDPSNENEKSPllytdikeNDIIKSINGVSL-DAANNPDKLLSGHANEIITIEIG 790
                                       67777777777..7788888888887776333355555555************.66666777777888999999999 PP

                                       ETTEEEEEEEE CS
                             PDZ_2  71 Rdgkkktvevk 81 
                                        ++k+k++ vk
  gi|518653080|ref|YP_008142600.1| 791 NRNKTKKYYVK 801
                                       99999998876 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0011       2.5      15      90 ..     336     408 ..     320     410 .. 0.67
   2 ?    6.7   0.0     0.004       8.9       6      60 ..     368     421 ..     363     443 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0011
                       ANAPC4_WD40  15 edgellvfRlng..qrvwtleedkedsevrsLaWkpdgklLavaysdgevrlldaesgkvvhslsvksekavtclgW 89 
                                       e++++l++ ++   ++ ++     +++ + sL+ +pdgk +a++ +  e+ +l+ e+g++ +  + +s  ++   +W
  gi|518653080|ref|YP_008142600.1| 336 ENNQILLYSVDKtlKKFFD----FKNGIIFSLKASPDGKYIAIGNNRFELFILNLENGNINKIDESESG-TIDDFSW 407
                                       4445555544432244444....4788999****************************98665555555.5777777 PP

                       ANAPC4_WD40  90 g 90 
                                       +
  gi|518653080|ref|YP_008142600.1| 408 S 408
                                       5 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.004
                       ANAPC4_WD40   6 tmDLiAlatedgellvfRlngqrvwtleedkedsevrsLaWkpdgklLavaysdg 60 
                                           iA+++++ el +  l+  ++ ++ +++e++++ +++W++d  lLa +y ++
  gi|518653080|ref|YP_008142600.1| 368 DGKYIAIGNNRFELFILNLENGNINKI-DESESGTIDDFSWSNDSILLAYSYPES 421
                                       555688888888888888988889999.788888999999999999999888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1019 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); 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:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.79u 0.30s 00:00:01.09 Elapsed: 00:00:00.49
# Mc/sec: 6196.45
//
Query:       gi|518653081|ref|YP_008142601.1|  [L=320]
Description: pantothenate kinase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-13   50.0   0.0    7.6e-13   48.6   0.0    1.7  2  PRK         Phosphoribulokinase / Uridine kinase family
     0.0024   18.4   0.1     0.0066   17.0   0.0    1.8  2  AAA_18      AAA domain
  ------ inclusion threshold ------
      0.023   14.4   0.0      0.047   13.4   0.0    1.5  1  CoaE        Dephospho-CoA kinase
      0.064   12.5   0.0        1.9    7.7   0.0    2.3  2  Zeta_toxin  Zeta toxin


Domain annotation for each model (and alignments):
>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.0   1.7e-16   7.6e-13       1     141 [.      96     237 ..      96     246 .. 0.83
   2 ?   -2.1   0.0      0.61   2.7e+03     171     196 ..     287     312 ..     280     313 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 1.7e-16
                               PRK   1 vIgvagsSGaGkttvarklekifgrekvkaaeiegdsflrldraekdleleerkrakekevsflspeandfdllyev 77 
                                       +Igv+gs + Gk+t++r l+ +++r +        + ++++d+++k+ +   +++  e++     pe  + ++l + 
  gi|518653081|ref|YP_008142601.1|  96 IIGVTGSVAVGKSTTSRLLKTLLERINPD----LRIYIVSTDNFLKSNARLMEENIMERKGF---PESYETQDLINF 165
                                       8***********************77666....56778888888887776666666655543...677777778888 PP

                               PRK  78 lkelkeg.kkvdkpiYsheteeaapdkeeliegadvlviEGlhalyder........vaelldlkiyvdisid 141
                                       l   k+g  ++++p+Ysh + ++ p +++ + ++d+l++EGl  l +++        v ++ld++i++d++++
  gi|518653081|ref|YP_008142601.1| 166 LVDIKSGvARTQIPVYSHLKYDILP-EKQDLVDPDILILEGLNILQVKNpgkkdeiyVSDFLDFSIFIDAKVE 237
                                       888888835799*************.56666789*************99999*****************9876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.61
                               PRK 171 pdyvnyikpqfseadliiqrvptvdv 196
                                       ++y + i  +  +a+lii++++t+++
  gi|518653081|ref|YP_008142601.1| 287 KNYSENIVKTRYRAELIIEKGKTHNI 312
                                       5789999999999*****99998876 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.5e-06    0.0066       1      66 [.      97     168 ..      97     230 .. 0.70
   2 ?   -2.2   0.0       1.3   5.7e+03      17      28 ..     275     289 ..     252     317 .. 0.51

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.5e-06
                            AAA_18   1 IlltGtpGvGKttlakeLskrlgf.......gvnlrdvakenglllevdpealdeskrldedkldklldalee 66 
                                       I++tG  +vGK+t ++ L+ +l+         ++++d++ +++ +l++++   +++   +   ++ l++ l  
  gi|518653081|ref|YP_008142601.1|  97 IGVTGSVAVGKSTTSRLLKTLLERinpdlriYIVSTDNFLKSNARLMEENI-MERKGFPESYETQDLINFLVD 168
                                       89****************999844599999999999999999999988888.333333333334444444444 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.3
                            AAA_18  17 eLskrl.gf..gvnl 28 
                                       eLs++   +  g n+
  gi|518653081|ref|YP_008142601.1| 275 ELSSKIwDNinGKNY 289
                                       333332211222222 PP

>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05     0.047       2      23 ..      96     117 ..      95     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                                       EEEEEESTTSSHHHHHHHHHHT CS
                              CoaE   2 ivgltGgiasGKstvanlfadl 23 
                                       i+g+tG +a GKst ++l++ l
  gi|518653081|ref|YP_008142601.1|  96 IIGVTGSVAVGKSTTSRLLKTL 117
                                       8****************99874 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0   0.00043       1.9      11      41 ..      89     119 ..      81     148 .. 0.82
   2 ?    2.4   0.0     0.018        82      69      94 ..     262     287 ..     245     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00043
                        Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdele 41 
                                       ++++ P +i + G+ + GKs++++llk+ le
  gi|518653081|ref|YP_008142601.1|  89 KPRKMPFIIGVTGSVAVGKSTTSRLLKTLLE 119
                                       47899********************998776 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.018
                        Zeta_toxin  69 pkkaseltqkdaselvekllqeaien 94 
                                        kk+selt+++a+el+ k+ + +  +
  gi|518653081|ref|YP_008142601.1| 262 FKKYSELTKEEARELSSKIWDNINGK 287
                                       4799***********99998876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2083.38
//
Query:       gi|518653082|ref|YP_008142602.1|  [L=150]
Description: hypothetical protein FACI_IFERC00001G1721 [Ferroplasma acidarmanus fer1]
Scores for complete 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   62.4   0.0    4.9e-17   62.2   0.0    1.1  1  Nuc_deoxyrib_tr  Nucleoside 2-deoxyribosyltransferase
    3.9e-09   36.8   0.0    4.8e-09   36.5   0.0    1.1  1  Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
  ------ inclusion threshold ------
      0.021   14.2   0.0      0.027   13.8   0.0    1.1  1  7TM_GPCR_Sru     Serpentine type 7TM GPCR chemoreceptor Sru


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 !   62.2   0.0   8.1e-21   4.9e-17       2     107 ..       7     114 ..       6     139 .. 0.87

  Alignments for each domain:
  == domain 1  score: 62.2 bits;  conditional E-value: 8.1e-21
                                       EEESGGGCSCCCHHHHHHHHHHHHTTTTEEE-CC....TT-TT......--SSHHHHHHHHHHHHHC-SEEEEE--S CS
                   Nuc_deoxyrib_tr   2 YLAgplvFrpdakalaarlkallaengldglaPl....dneaelel..paeetaraiyeadialirqaDavianldp 72 
                                       Y+ +pl F++ + + +++l+  l++ g++ + P+    ++e+ l++     et++ ++++d++ ++++ a+i+++d+
  gi|518653082|ref|YP_008142602.1|   7 YISAPL-FNEMELKFNRELAGFLEKRGFTTYLPQrdggEDEMLLKDpdLWPETSKRVFNRDVDALKSSSALIMVMDG 82 
                                       999***.***************************888755554444455689************************* PP

                                       SSSSS--HHHHHHHHHHHHCT-EEEEE-S-GCGHH CS
                   Nuc_deoxyrib_tr  73 frgpeaDsGtafEvGyavalgkpvlayttdarelr 107
                                            +D+G ++E+G+a+a gk ++++ td+r+++
  gi|518653082|ref|YP_008142602.1|  83 RV---PDEGACVELGMAYAFGKICIGFQTDNRRFA 114
                                       88...***************************964 PP

>> Nuc_deoxyri_tr2  Nucleoside 2-deoxyribosyltransferase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   8.1e-13   4.8e-09       2     107 ..       4     109 ..       3     110 .. 0.87

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 8.1e-13
                                       EEEEEEE---SSSST-HHHHHHHHHHTSSS-EEEEE----SS-----.HHHHH.......HHHHHHHHHHHH-SEEE CS
                   Nuc_deoxyri_tr2   2 ksvFLaGsteseaetdWredlteaLsaipklgvtvfnPqredwdsel.eedrs..kkrfreqvewelealekAdvvv 75 
                                       ++ ++++++++e e +++++l+  L++   +g+t + Pqr++ + e+  +d++   +++++ ++ + +al+++ +++
  gi|518653082|ref|YP_008142602.1|   4 YDFYISAPLFNEMELKFNRELAGFLEK---RGFTTYLPQRDGGEDEMlLKDPDlwPETSKRVFNRDVDALKSSSALI 77 
                                       67899********************77...8***********8888864544422789999**************** PP

                                       EEE-TT---HHHHHHHHHHTTSS-EEEEE-TT CS
                   Nuc_deoxyri_tr2  76 fvfdgedsatrslvElglaaakgkkvvlvpkg 107
                                       +v+dg+  +  + vElg+a+a gk +++ +++
  gi|518653082|ref|YP_008142602.1|  78 MVMDGRVPDEGACVELGMAYAFGKICIGFQTD 109
                                       *****55566689************9998875 PP

>> 7TM_GPCR_Sru  Serpentine type 7TM GPCR chemoreceptor Sru
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   4.5e-06     0.027     162     200 ..      83     121 ..      67     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 4.5e-06
                      7TM_GPCR_Sru 162 lipalgvCrqldepfqfGaiiisfegsnfglrnsiillv 200
                                        +p +g C++l+  + fG i i f+++n+++     +l+
  gi|518653082|ref|YP_008142602.1|  83 RVPDEGACVELGMAYAFGKICIGFQTDNRRFASGQNNLM 121
                                       5799******************99999997664444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); 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:                         3  (0.000167327); expected 0.2 (1e-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: 00:00:00.45
# Mc/sec: 1005.68
//
Query:       gi|518653083|ref|YP_008142603.1|  [L=293]
Description: inosine-uridine preferring nucleoside hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-57  195.6   0.0    1.6e-57  195.4   0.0    1.0  1  IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
  ------ inclusion threshold ------
       0.05   13.7   0.0      0.099   12.7   0.0    1.5  1  DUF1500       Protein of unknown function (DUF1500)


Domain annotation for each model (and alignments):
>> IU_nuc_hydro  Inosine-uridine preferring nucleoside hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.4   0.0   1.8e-61   1.6e-57       2     303 ..       3     280 ..       2     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 195.4 bits;  conditional E-value: 1.8e-61
                                       EEEEEE--SHHHHHHHHHHHCTHTTEEEEEEEE-SSSS-HHHHHHHHHHHHHHHCTTT.S-EEEE-SS-SSSSS-SH CS
                      IU_nuc_hydro   2 kvilDtDpGiDDalAlllalaespeiellgittvaGnvsleqatrnalrvlealggrddipvyaGaekpllrekaaa 78 
                                       +vil +D+GiDDa+A++l+ +   +i    i++++Gn+ le++ rn++ v  +l+   d+pvy G+++pl++++  +
  gi|518653083|ref|YP_008142603.1|   3 RVILNVDTGIDDAFAMILLKQ--YNITPEFIVASSGNSLLENTYRNTAGVA-KLL-DFDCPVYHGSARPLIKPHYYE 75 
                                       79*************999854..56999***********************.888.566****************** PP

                                       HHHTTTSSTSS-.--SSHCSCSSHHHHHHHHHHHHCHHTTTTEEEEECS-SHHHHHHHHHTCCHHHHEEEEEEE--- CS
                      IU_nuc_hydro  79 eihGedGlgdvllpeperkaesesavdalidaveaareypgevtlvatGplTNiAlalrldpelakkvkrlviMGGa 155
                                       ++hG++Glg+ + ++p +++++++ +   i++ ea +++  + t+++t plT +  ++rld+++++++++++iMGGa
  gi|518653083|ref|YP_008142603.1|  76 NFHGDKGLGTYEFNDPVQEKDHHNGI---IKMYEALKRE--KHTIICTSPLTSLGILMRLDNSIKENIEQIIIMGGA 147
                                       **********9988886666666666...4555444665..59********************************** PP

                                       SS....S--SSSSSS-HHHHHSHHHHHHHHHT.S-E.EEEE-HHHHTTSCHEECHHHHHHHHCSTCBHHHHHHHHHH CS
                      IU_nuc_hydro 156 ft....arGNvtpvaEfNifvDPeAAkiVles.apvkitlvpldvthkvqalltseeveelaalekglgafladlle 227
                                       f+    ++GN+   aEfNif DPeAAkiV+e+    + t+vpldvt++ +  l+ + + + ++ +++l+ f++++++
  gi|518653083|ref|YP_008142603.1| 148 FGitpyGKGNMG-NAEFNIFYDPEAAKIVMEEdI--NETIVPLDVTMNRE--LAIKSIPPSSS-GSPLEDFIHKTTK 218
                                       ******999994.3****************8643..55*********555..33333333222.1344449999999 PP

                                       HHHHHHHHHHHSSEEE-HHHHHHHHHH-GGGEEEEEEEEEEESSSSTTTTEEEEETSTT.....TTS--EEEEEEE- CS
                      IU_nuc_hydro 228 fyikaykeaegsdgaplhDplavavaldpelvttkrlavdveleggltrGrtvvdlrrl.....kkaknvkvatevd 299
                                       f+i+ + +      + +hDp+av+ +++p+ ++  + +++v+              +++     k+  + ++at+++
  gi|518653083|ref|YP_008142603.1| 219 FMIEEHGT------FEMHDPIAVFSFIEPDAFKFVNGEITVKP-------------DGStefieKRDGKKRIATGIN 276
                                       99996655......66*************99975555555533.............333334445556667777777 PP

                                       HHHH CS
                      IU_nuc_hydro 300 verf 303
                                        +++
  gi|518653083|ref|YP_008142603.1| 277 PQAY 280
                                       7665 PP

>> DUF1500  Protein of unknown function (DUF1500)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.1e-05     0.099       4      47 ..       7      51 ..       4      76 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.1e-05
                           DUF1500  4 svdvdiydavrafllrhyy.nkrfivygrsnailhniyrlftrca 47
                                      +vd  i da   +ll++y     fiv    n++l n yr  + +a
  gi|518653083|ref|YP_008142603.1|  7 NVDTGIDDAFAMILLKQYNiTPEFIVASSGNSLLENTYRNTAGVA 51
                                      58999*****9999999862568****************877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.46
# Mc/sec: 1901.60
//
Query:       gi|518653084|ref|YP_008142604.1|  [L=239]
Description: short-chain dehydrogenase/reductase SDR [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  181.8   0.1    1.8e-53  181.5   0.1    1.0  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    5.1e-47  159.9   0.6      6e-47  159.6   0.6    1.0  1  adh_short     short chain dehydrogenase
    4.2e-18   65.9   0.1    6.1e-18   65.4   0.1    1.2  1  KR            KR domain
     0.0019   17.7   0.1     0.0067   15.9   0.0    1.9  2  Epimerase     NAD dependent epimerase/dehydratase family


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 !  181.5   0.1   4.1e-57   1.8e-53       2     234 .]      10     238 ..       9     238 .. 0.96

  Alignments for each domain:
  == domain 1  score: 181.5 bits;  conditional E-value: 4.1e-57
                                       TTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-- CS
                      adh_short_C2   2 aasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnna 77 
                                         +gIGr iA+++a+e + ++++d++++  +++++l +++g+   ++cDV++ +++ ++++++ +k  ++ ++vnna
  gi|518653084|ref|YP_008142604.1|  10 SNRGIGRSIAEKMASEKYGIIMVDYDNAVLDSAKSLNSRYGNVeGIKCDVSSYDACVEAFSTIDKK--EIYGIVNNA 84 
                                       569*************************************97746*******************98..8******** PP

                                       ---EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHH CS
                      adh_short_C2  78 giapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaalealt 152
                                       gi ++  + f ++s +++d +++++lys+f+++k+++  m e+  g+ivn+ss  +  +  +++ y+ aKa+++++t
  gi|518653084|ref|YP_008142604.1|  85 GINRD--ALFKNMSFDQWDAVIKTDLYSMFNVTKQFVDSMIENlsGRIVNISSA-SWNGNVGQANYSSAKAGVIGFT 158
                                       *****..*******************************8877779********9.5577788899************ PP

                                       HHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEE CS
                      adh_short_C2 153 rylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqtlvv 229
                                       ++l +elg+++i+ Na+ pg+ikT+++++++  ++++e++ +++pl+r+g+ ++va+a+ fL+ ++++y++G  l v
  gi|518653084|ref|YP_008142604.1| 159 KTLSRELGRYNITSNAIVPGFIKTPMTDQMP--EKIKEKFIEKIPLKRMGSGDDVANAVSFLMKEDSNYVNGILLEV 233
                                       ******************************9..9******************************************* PP

                                       STTGG CS
                      adh_short_C2 230 DgGlt 234
                                        gG++
  gi|518653084|ref|YP_008142604.1| 234 GGGMS 238
                                       ***96 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.6   0.6   1.3e-50     6e-47       3     193 ..       5     191 ..       3     193 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.6 bits;  conditional E-value: 1.3e-50
                                       EEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSES CS
                         adh_short   3 vlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkld 79 
                                       +++tG  +GIGr ia+++a+e + +++vd+ ++ l   ak+l++   ++  i++Dv++++++ ++++++ k  +++ 
  gi|518653084|ref|YP_008142604.1|   5 IVITGSNRGIGRSIAEKMASEKYGIIMVDYDNAVL-DSAKSLNSRYGNVEGIKCDVSSYDACVEAFSTIDK--KEIY 78 
                                       89*****************************8877.778888888899*********************66..69** PP

                                       EEEE---SS--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHH CS
                         adh_short  80 vLvnNAGitgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaav 156
                                        +vnNAGi++++ f+++s ++w++vi++ l ++f++t+++++ m+++ sGrIvn+sS  + +++ g+a Ys++Ka+v
  gi|518653084|ref|YP_008142604.1|  79 GIVNNAGINRDALFKNMSFDQWDAVIKTDLYSMFNVTKQFVDSMIENLSGRIVNISSA-SWNGNVGQANYSSAKAGV 154
                                       *******************************************************995.569*************** PP

                                       HHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 157 agltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       +g+t++l++el +++i+ na++PG+++T+m+ +  ek
  gi|518653084|ref|YP_008142604.1| 155 IGFTKTLSRELGRYNITSNAIVPGFIKTPMTDQMPEK 191
                                       *******************************988765 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.4   0.1   1.4e-21   6.1e-18       1     155 [.       3     153 ..       3     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 65.4 bits;  conditional E-value: 1.4e-21
                                       SEEEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHH CS
                                KR   1 gtylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeika 77 
                                       g  +itG   g+G+++a+ +a++    ++ +  +    ++  +  ++l+++  +ve +++Dvs+ da  +++++i++
  gi|518653084|ref|YP_008142604.1|   3 GKIVITGSNRGIGRSIAEKMASEKYGIIM-VDYD----NAVLDSAKSLNSRYGNVEGIKCDVSSYDACVEAFSTIDK 74 
                                       5679*****************98766554.4444....455566789****************************95 PP

                                       HSS---EEEE---------TTT--HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-HHHHH CS
                                KR  78 eeppikGvihaAgvlrdklleemtaedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagqanYaa 151
                                       +  +i G+++ Ag+ rd+l+++m+ +++++v++  +  + n+ + + d   e+l   ++  S a+  g+ gqanY++
  gi|518653084|ref|YP_008142604.1|  75 K--EIYGIVNNAGINRDALFKNMSFDQWDAVIKTDLYSMFNVTKQFVDsmiENLSGRIVNISSASWNGNVGQANYSS 149
                                       5..5******************************************99777788877899999999*********** PP

                                       HHHH CS
                                KR 152 aNaf 155
                                       a a 
  gi|518653084|ref|YP_008142604.1| 150 AKAG 153
                                       9875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-06    0.0067       1     123 [.       5     143 ..       5     154 .. 0.71
   2 ?   -1.5   0.0      0.32   1.4e+03     216     231 ..     209     224 ..     205     234 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-06
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT-SEEEE CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl.......elveldltdrsalerlfkeeqpdavih 70 
                                       i++tG +  iG+ +++++++++y +i +d ++    +a+   l       e +++d+   +a+ ++f++ +  +++ 
  gi|518653084|ref|YP_008142604.1|   5 IVITGSNRGIGRSIAEKMASEKYGIIMVDYDNAVLDSAKS--LnsrygnvEGIKCDVSSYDACVEAFSTIDKKEIYG 79 
                                       79***************************99554444443..14589999*************99999876666666 PP

                                       --S---HHH.......HHHSHHHHHHHHTHHHHHHHHHHHHHTCT....EEEEEEEGGGGTSCS CS
                         Epimerase  71 lAavggvaa.......ssedpadfieknlqgtlnlleaarkagvk....rllflsSsevYGkda 123
                                       +   +g+++       s+++  ++i+++l  + n+ +   ++ ++    r++++sS+++ G++ 
  gi|518653084|ref|YP_008142604.1|  80 IVNNAGINRdalfknmSFDQWDAVIKTDLYSMFNVTKQFVDSMIEnlsgRIVNISSASWNGNVG 143
                                       6555555441112222556666667666666666666666555555556888888888877765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.32
                                       HHHHHHHHHHHHHHTT CS
                         Epimerase 216 eDvaeaillvlehvda 231
                                       +Dva+a+ +++++ ++
  gi|518653084|ref|YP_008142604.1| 209 DDVANAVSFLMKEDSN 224
                                       8**********99444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1743.73
//
Query:       gi|518653085|ref|YP_008142605.1|  [L=514]
Description: hypothetical protein FACI_IFERC00001G1724 [Ferroplasma acidarmanus fer1]
Scores for complete 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-64  218.0   0.0    2.1e-64  217.7   0.0    1.1  1  AMP-binding    AMP-binding enzyme
    2.2e-18   67.0   0.4    5.9e-18   65.6   0.4    1.8  2  AMP-binding_C  AMP-binding enzyme C-terminal domain
  ------ inclusion threshold ------
       0.07   13.3   0.0       0.37   11.0   0.0    2.2  3  DUF150_C       RimP C-terminal SH3 domain


Domain annotation for each model (and alignments):
>> AMP-binding  AMP-binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  217.7   0.0   3.6e-68   2.1e-64      12     422 ..      16     413 ..       7     414 .. 0.84

  Alignments for each domain:
  == domain 1  score: 217.7 bits;  conditional E-value: 3.6e-68
                                       EEEEECCSTEEEEHHHHHHHHHHHHHHHHHTTSSTT-EEEEEESSSHHHHHHHHHHHHTT-EEEEEETTS-HHHHHH CS
                       AMP-binding  12 valvdsgegqtlTYreldervnrlAagLrslGvkkgdrVaillpnspewvvallailkaGavvvplnptltaeelay 88 
                                       +++++    + +TY+e++  +n++A  +    + +gd +ai+++n p++ ++ +a +k +++ vpl+p  ++ e+  
  gi|518653085|ref|YP_008142605.1|  16 PFITY--FKNIMTYGEFEGYSNAVAVEFSM-YCDPGDIIAIIAENIPQFPIVQYASWKNSCIFVPLSPLDSENEITG 89 
                                       55555..57889****************86.89******************************************** PP

                                       HHHHHTESEEEETCTCCCHHHHHHHHSCC-EECEEEEESCCS-HCCHCCCHCCCCSCTTS...........-TSCCC CS
                       AMP-binding  89 iledseakvliatvdselleklleaaakleavklvivldadellkeeelkeeeeseekae...........kpeeee 154
                                        ++  +a+v++  ++se     +e+ ++l + ++  vl++d+  + +  ++++e++   +           k+ +  
  gi|518653085|ref|YP_008142605.1|  90 KIKFIDARVVV--ISSEF----REKFSSLMEIQSLHVLYTDPQTFGKLPDNMAEKYIT-GimkeelnlrlkKEFKGY 159
                                       ***********..76555....677777777788888898888888666666655533.256678899999555677 PP

                                       S-BTTSEEEEEEE--SSSS-EEEEEEHHHHHHHHHHHHHHHC.SCCTTT-EEEESS-TTSCHHHHHHHHHHHHTT-E CS
                       AMP-binding 155 elkpddlayiiYTSGTTGkPKGVmlshrnlvanvaslkletr.fklkeddvvlsilplahifglilelllallsGat 230
                                        ++p ++a++++TSGT G+ K++ ++h n+ ++ + +  +++  +++++d+ l+i+p++hi+gli+++ l++ls ++
  gi|518653085|ref|YP_008142605.1| 160 YPEPGSIAMLVFTSGTSGRQKAAEITHSNIYSA-SYI--YREwYSVQPHDKNLCIAPFFHITGLIFGISLTMLSHSS 233
                                       89***************************9998.443..344255999***************************** PP

                                       EEE-TTCGCCHHHHHHHHHHHHT-SEEEEEHHHHHHHHH.CCCHHCHHHHCCGTT-SEEEEESS-EBHHHHHHHHHH CS
                       AMP-binding 231 vvllpkdaaldpklllelieklkvtviagvPrvlealle.sgalkaakkakdlsslrlvllggeplspellrffral 306
                                       + l  ++++ +    le++e ++ t+++ v ++++a+++  ++ +  k +++lss+r+  +gg p++ ++  +++a 
  gi|518653085|ref|YP_008142605.1| 234 MALTYRFNPEN---ALETVESENTTITMFVATAYRAMINaWSNVD--KIKTRLSSMRMWSAGGMPMPYKTEIEWKAM 305
                                       ***99887733...47*******************9977433333..334589*****999**************** PP

                                       HTCEEEEEEEEGGGSSECEE......CHCTTTCTSTTS-BEE-TTEEEEEE-TTTSCBEETTSEEEEEEEETTS-SE CS
                       AMP-binding 307 fgeevlegYGlTEttgvvtv......lpleedkkklgsvGkplpgvevkivDeetgepvpdgeeGellvrgpgvmkg 377
                                        g+ v+ +YGlTE t  v+       ++     + + ++Gkp   +  +iv             Gel+v+gp+v + 
  gi|518653085|ref|YP_008142605.1| 306 SGKWVYMAYGLTESTSPVALweypytDN-IPLYNGIVTAGKP--ANYTRIVRAR---------GGELVVSGPQVIRR 370
                                       ***************9997556666433.3334556677777..4556777766.........4************* PP

                                       BTT-HHHHHHHEEETCCEEEEEEEEEEETTSEEEEEEECCCEEEE CS
                       AMP-binding 378 YlkkpeataeafdsegrwlrTGDlgrldedGyleivgRkkdlikl 422
                                       Y+k+pe t++af  +   l+TGD++++d++Gy++i++Rkkdli +
  gi|518653085|ref|YP_008142605.1| 371 YYKNPEDTEKAFG-K-YGLKTGDICYIDRKGYIYIIDRKKDLIDV 413
                                       ************8.6.35************************976 PP

>> AMP-binding_C  AMP-binding enzyme C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         3   1.8e+04      42      57 ..     144     159 ..     131     167 .. 0.72
   2 !   65.6   0.4   9.9e-22   5.9e-18       1      76 []     422     500 ..     422     500 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3
                                       HHHHHHHHHHHHT-TT CS
                     AMP-binding_C  42 leeeLkahvrkelgpy 57 
                                       ++eeL+ +++ke+  y
  gi|518653085|ref|YP_008142605.1| 144 MKEELNLRLKKEFKGY 159
                                       7899999999988776 PP

  == domain 2  score: 65.6 bits;  conditional E-value: 9.9e-22
                                       HHHHHHHSSTTEEEEEEE-----TTS---EEEEEE---...---HHHHHHHHHHHHT-TTTS-SEEEE-S---B-TT CS
                     AMP-binding_C   1 evEsalvshpaVaeaaVvGvpdevkGealvafVvlkdg...sealeeeLkahvrkelgpyavpkkvvfvdelpktrs 74 
                                       evE+a+ s++ V++++VvG +de kGe++va+V l++    +e++++ + + ++kel+ y+vp +++fv ++p+++s
  gi|518653085|ref|YP_008142605.1| 422 EVENAIRSCDHVEDVVVVGENDEYKGEVPVAYVKLSSVpdnYEEMKKSIYSVCKKELARYKVPARIIFVRDMPLNAS 498
                                       8*********************************9432222466********************************* PP

                                       S- CS
                     AMP-binding_C  75 GK 76 
                                       GK
  gi|518653085|ref|YP_008142605.1| 499 GK 500
                                       *9 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 ?   11.0   0.0   6.2e-05      0.37       6      45 ..      65     103 ..      62     109 .. 0.90
   2 ?   -3.3   0.0       1.7     1e+04      40      63 ..     168     191 ..     151     193 .. 0.67
   3 ?   -3.1   0.0       1.5   9.2e+03      39      61 ..     434     456 ..     425     458 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 6.2e-05
                          DUF150_C   6 dFarflGelVkvklklpvegrkkftGkivevdeetitlev 45 
                                       ++a + +  + v l+ p++ + ++tGki+ +d+  ++++ 
  gi|518653085|ref|YP_008142605.1|  65 QYASWKNSCIFVPLS-PLDSENEITGKIKFIDARVVVISS 103
                                       899999999****88.****************99999875 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                          DUF150_C  40 titlevdgkkrkkettipladidk 63 
                                       +++++    +r+k  +i+ ++i  
  gi|518653085|ref|YP_008142605.1| 168 MLVFTSGTSGRQKAAEITHSNIYS 191
                                       466777777778888888888765 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.5
                          DUF150_C  39 etitlevdgkkrkkettipladi 61 
                                       e++++  ++ ++k e+ + + ++
  gi|518653085|ref|YP_008142605.1| 434 EDVVVVGENDEYKGEVPVAYVKL 456
                                       45666666676887777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (514 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       610  (0.0340231); expected 358.6 (0.02)
Passed bias filter:                      505  (0.0281667); 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: 0.60u 0.30s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 3301.88
//
Query:       gi|518653086|ref|YP_008142606.1|  [L=363]
Description: hypothetical protein FACI_IFERC00001G1725 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
     0.0084   15.8   0.0       0.28   10.8   0.0    2.3  2  Thiolase_C  Thiolase, C-terminal domain


Domain annotation for each model (and alignments):
>> Thiolase_C  Thiolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.4   0.0    0.0063   1.1e+02      27      45 ..       4      22 ..       2      25 .. 0.89
   2 !   10.8   0.0   1.6e-05      0.28      24     100 ..     235     331 ..     215     347 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0063
                                      HHHHHHHHHT--GGGESEE CS
                        Thiolase_C 27 aikkvlkkagltvedidlf 45
                                      a +k+l+ agl+ +did f
  gi|518653086|ref|YP_008142606.1|  4 ALNKALSMAGLERKDIDGF 22
                                      889*************976 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHHT--..GGGESEEEE--SBHHHHHHHHHHHT--G..................GGBSTT--HHHH-B CS
                        Thiolase_C  24 Payaikkvlkkaglt..vedidlfEinEAFaaqaLavakaldldl..................ekvNvnGGaialGH 80 
                                        +  ++++ +  g++  ++  d++E+ + F+  ++  +++ ++ +                    +N  GG++  G 
  gi|518653086|ref|YP_008142606.1| 235 DITITPAAESSSGFRdnIKRCDFYELYDSFSITVMIQLENTGIVPpgksgefleknsisvngdFPLNTGGGSLNRGQ 311
                                       555555555566664348899**********************999************99998889*********** PP

                                       -TTTHHHHHHHHHHHHHHHC CS
                        Thiolase_C  81 PlGasGaRivvtllselkke 100
                                       P  +sG+ ++  +l +++  
  gi|518653086|ref|YP_008142606.1| 312 PAYMSGSVLLYEALLQMNGM 331
                                       ********999999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (363 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       287  (0.0160076); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2606.69
//
Query:       gi|518653087|ref|YP_008142607.1|  [L=112]
Description: hypothetical protein FACI_IFERC00001G1726 [Ferroplasma acidarmanus fer1]
Scores for 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   34.8   0.5    1.4e-08   34.4   0.5    1.1  1  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00013   21.9   0.0     0.0004   20.3   0.0    1.7  1  OB_aCoA_assoc    DUF35 OB-fold domain, acyl-CoA-associated
  ------ inclusion threshold ------
       0.01   15.8   0.2      0.015   15.3   0.2    1.2  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.11   12.6   0.0       0.16   12.1   0.0    1.3  1  Spt4             Spt4/RpoE2 zinc finger
       0.28   11.6   1.8         13    6.3   0.1    2.2  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> 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 !   34.4   0.5     4e-12   1.4e-08       7      36 ..      17      46 ..      15      47 .. 0.92

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 4e-12
                           DUF35_N  7 grLvgqrCpdCGtvqfPPravCphCgsddl 36
                                      g L +++C +CG+v+++Pr +Cp Cg +dl
  gi|518653087|ref|YP_008142607.1| 17 GILPYTKCMNCGKVYYYPRDSCPVCGKGDL 46
                                      66889*********************9987 PP

>> OB_aCoA_assoc  DUF35 OB-fold domain, acyl-CoA-associated
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   1.1e-07    0.0004       4      65 .]      51      99 ..      49      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 1.1e-07
                                      E-GG-EEEEEEEEEE-TTS-EEEEEEEEEEEE-TT...-EE-EEEEEEES..TT-B-EEE-S CS
                     OB_aCoA_assoc  4 lsgrGtvysftvvhrappgfaeeaPyvvgvVeLdegvrimarlvgvdpdevriGmrVravfr 65
                                      ++g G+vys+t ++  +          +g++ + eg r  +++ g  p+   iGm+V++ f+
  gi|518653087|ref|YP_008142607.1| 51 STGNGKVYSYTKFNNGF----------YGIISFSEGFRAYMDISGNNPQ---IGMEVEIKFK 99
                                      6899*******888888..........********************97...*******996 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.2   4.2e-06     0.015      71     102 ..      22      51 ..      11      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.2e-06
                                       EEETTTS-EEECHHHHHS-TTTSSS-EEEEES CS
                              HypA  71 vrCreCgkefeleekalrCpkCgsadveivsG 102
                                       ++C +Cgk +   ++  +Cp Cg+ d++i++ 
  gi|518653087|ref|YP_008142607.1|  22 TKCMNCGKVYYYPRD--SCPVCGKGDLKIMQS 51 
                                       79*****99997756..8**********9875 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.5e-05      0.16       4      49 ..      24      72 ..      21      81 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.5e-05
                              Spt4  4 CllCklvktedqFeeegCpnC..eilelk....gdkekvsectseefeGlva 49
                                      C++C+ v  + +   + Cp+C    l++     + k  +++++ + f G+++
  gi|518653087|ref|YP_008142607.1| 24 CMNCGKVYYYPR---DSCPVCgkGDLKIMqstgNGKVYSYTKFNNGFYGIIS 72
                                      ********9999...******7544655412112233345566677777776 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2    0.0091        33      27      36 ..      14      29 ..       3      37 .. 0.66
   2 ?    6.3   0.1    0.0036        13       5      22 ..      37      54 ..      35      63 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0091
                   Lar_restr_allev 27 q......cvyCadCga 36
                                      +      +  C++Cg 
  gi|518653087|ref|YP_008142607.1| 14 FstgilpYTKCMNCGK 29
                                      133445599*****97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0036
                   Lar_restr_allev  5 pCPfCggravlersqrvv 22
                                       CP Cg+ + ++ +  + 
  gi|518653087|ref|YP_008142607.1| 37 SCPVCGKGDLKIMQSTGN 54
                                      6*****999888876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 792.99
//
Query:       gi|518653088|ref|YP_008142608.1|  [L=290]
Description: 2-keto-3-deoxy gluconate aldolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-43  146.5   0.0    7.5e-43  146.3   0.0    1.0  1  DHDPS     Dihydrodipicolinate synthetase family
  ------ inclusion threshold ------
      0.067   13.3   0.0       0.11   12.6   0.0    1.2  1  DUF1517   Protein of unknown function (DUF1517)


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.3   0.0   8.3e-47   7.5e-43       5     287 ..       6     280 ..       2     282 .. 0.93

  Alignments for each domain:
  == domain 1  score: 146.3 bits;  conditional E-value: 8.3e-47
                                       EEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SS CS
                             DHDPS   5 iitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsns 81 
                                       +it+++tpf +d k+dk ++ k  e  i+ g+  l+ +GttG  +++   ek ql+   +++ +    vi +vGs +
  gi|518653088|ref|YP_008142608.1|   6 SITPVITPF-TDNKVDKDKAVKHGEDVIKGGMKYLFPGGTTGLGPSMASGEKLQLLDAYAHIPE---HVILQVGSLN 78 
                                       799******.5789******************************************99888776...69******** PP

                                       HHHHHHHHHCCCCCT-SEEEEE---SS---HHH.HHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHT.STT CS
                             DHDPS  82 tseaiklakkaeeaGadgvlavtPYYnkpsqeg.lyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLae.len 156
                                       ++e+i+la++a+++ +++v a++PYY    +++ l++++ +i ++   p+i+Yn p+ tg +++ + v+ + +   +
  gi|518653088|ref|YP_008142608.1|  79 LEESINLAREAKKYKIHAVAALPPYYFTGIKREwLIKYYTKISSEY--PTIIYNYPETTGYNITYDMVNDIKKaGGD 153
                                       **************************9976655499******9888..*************************7889 PP

                                       EEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT-SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHH CS
                             DHDPS 157 ivgvKeavgdleevikikkevgkdlviysGddelllsalslGadGvisvtsniagermrqlikalkeGdlaeaaeln 233
                                       ++g+Ke++ +++ + ++k +  +d+ +y G d+ +lsa  lG dG +s +sn+  + ++++i++  +   +    ++
  gi|518653088|ref|YP_008142608.1| 154 VIGIKETTFNMNDILNTKMY-VPDFKVYTGPDQYILSAYRLGLDGFVSGASNYGYKVINKIIENHDN---KDGDRYQ 226
                                       ******************99.799******************************9999999999888...7778888 PP

                                       HHHHHHHHHCCCCSCCHHHHHHHHCT.TSSSBB.--TTS--S-HHHHHHHHHHHH CS
                             DHDPS 234 ekllplikilfaepnvilvktalell.GlvveatlrkPltpleeeekeeleallk 287
                                         l++l +   + + ++ +   +e++ G+++++  r+P+ +l++ee+ +le+ ++
  gi|518653088|ref|YP_008142608.1| 227 FLLNELADLSRKYGTISSIYDMVEIMtGIDAGN-PREPFFKLSKEERSSLEKEMN 280
                                       899999999999999999999999875999999.****************99876 PP

>> DUF1517  Protein of unknown function (DUF1517)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   1.2e-05      0.11      20      91 ..     208     281 ..     198     288 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 1.2e-05
                           DUF1517  20 rdLnriaeeadtsskeglaellqevvlaLlrheeywvyaasesdqfk...edsaeakfnqlsleerskfeeetls 91 
                                       +  n+i e+ d +  + +++ll+e++  L r+  ++++++ +++ ++     +  + f +ls+eers++e+e   
  gi|518653088|ref|YP_008142608.1| 208 KVINKIIENHDNKDGDRYQFLLNELA-DLSRKYGTISSIYDMVEIMTgidAGNPREPFFKLSKEERSSLEKEMNE 281
                                       56899******************986.7****************9999999999*****************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2068.78
//
Query:       gi|518653089|ref|YP_008142609.1|  [L=837]
Description: hypothetical protein FACI_IFERC00001G1728 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.2e-153  512.5   0.0   1.7e-153  512.0   0.0    1.2  1  Aconitase    Aconitase family (aconitate hydratase)
    1.5e-36  125.6   0.0    3.4e-36  124.5   0.0    1.5  1  Aconitase_C  Aconitase C-terminal domain


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  512.0   0.0  1.9e-157  1.7e-153      12     461 .]      67     526 ..      51     526 .. 0.94

  Alignments for each domain:
  == domain 1  score: 512.0 bits;  conditional E-value: 1.9e-157
                         Aconitase  12 egiayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknledefern 83 
                                       +++a++p+rv+ qd+tgv++lvdlaa+re  ++ + +++ +++++++dlvidhs+     + ee +  n++defern
  gi|518653089|ref|YP_008142609.1|  67 SEMAFKPSRVVFQDYTGVPILVDLAAMREYYKENKLNADDVNPATKSDLVIDHSIivdsfRGEEPIILNMKDEFERN 143
                                       338999*****************************************************999999************ PP

                         Aconitase  84 keryefLksaakaf.girvvppgqGIvHqvnlEy.........glalpgktvvgtDSHTtmigglGvlaiGvGgiea 150
                                        ery+fLk+ +++f ++r+vppg+GIvHq+nlEy         + ++p+ +++g DSHTtmigg+Gvl++GvGg ea
  gi|518653089|ref|YP_008142609.1| 144 VERYDFLKWSQQSFkNVRIVPPGHGIVHQINLEYlssvaviekDEIFPE-SLIGADSHTTMIGGIGVLGWGVGGLEA 219
                                       ************************************9999998899***.*************************** PP

                         Aconitase 151 eavllgqplelkipkvvgvkltGklkegvtakDlvlavigklrkkgvvgkvvEffGegvesLsledraTiaNMaaEv 227
                                       ea +l++p+ +++p+vvgv+++G+++ gvt++D+vl+++++lr k+vvgk+vEf+G  +++L+++draTi+NMa+E+
  gi|518653089|ref|YP_008142609.1| 220 EASMLNEPYFMNVPDVVGVNIKGTMPTGVTPTDVVLYITKTLRSKNVVGKFVEFYG-NISELTAQDRATISNMAPEY 295
                                       ********************************************************.59****************** PP

                         Aconitase 228 GAttglfpvdektleYLkatgreeaavlveaydkaqalfelaadedaeydkvleldlstlepsvagpkrPqdavpls 304
                                       GAt+g+fpvd++tl+YLk t+r+ +   ve+y k+q+lf    +  ++y++++e+dls+++  vagpk+P++ ++++
  gi|518653089|ref|YP_008142609.1| 296 GATIGYFPVDSETLKYLKGTNRSTES--VEKYFKEQGLF---YNGPKKYTETVEIDLSKIKSAVAGPKNPDELINIE 367
                                       **********************9999..7********88...455679****************************5 PP

                         Aconitase 305 elvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsv 380
                                       +l+  ++++ l         + + + g  +k+g+v++ ai+SCTN+s + v + agl+a ka e++l+v++++k+s+
  gi|518653089|ref|YP_008142609.1| 368 DLKG-KIEDLL---------K-EGNDGKLVKNGAVVLSAITSCTNTSDPFVLLGAGLIAkKAIEHNLTVANTIKVSL 433
                                       5554.455544.........2.355688899********************************************** PP

                         Aconitase 381 aPGSevvkayleaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFegRqgpntra 446
                                       aPGS+vv++yle++Gl+++L+++Gfe+vg+gC+tCign+++l         +++    +v+s+NRNFegR++p    
  gi|518653089|ref|YP_008142609.1| 434 APGSKVVTEYLEKAGLMKYLNRLGFELVGYGCTTCIGNAGPLIpevqddmlKNNvktFAVLSGNRNFEGRINPYIAG 510
                                       *****************************************9767777666333788***************99999 PP

                         Aconitase 447 .yLaSPelvvaaAlaG 461
                                        +LaSP lvva+A+aG
  gi|518653089|ref|YP_008142609.1| 511 aFLASPMLVVAFAIAG 526
                                       9**************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.5   0.0   3.8e-40   3.4e-36      13     129 ..     658     773 ..     649     775 .. 0.94

  Alignments for each domain:
  == domain 1  score: 124.5 bits;  conditional E-value: 3.8e-40
                                       HHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEEEHHHHHHHHHHTT--EEEE--SSBTBS-- CS
                       Aconitase_C  13 edeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgekedvvdaaerykkegaklvviagknfGeGSS 89 
                                       ++++  ++++++++++++g + n++++n +v     ++t++ +dg++++++daa++y k++++lv+ agk++G+GSS
  gi|518653089|ref|YP_008142609.1| 658 TEMNTFGARRGNHEVMLRGGFSNTKIRNLMVS-HAGGSTIYYPDGQEMSIYDAAMKYMKNKTPLVIFAGKQYGSGSS 733
                                       678999*************************9.888999999*********************************** PP

                                       -THHHHHHHHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
                       Aconitase_C  90 RehAAkalrllGikaviaeSFerIfennliknglLplefk 129
                                       R++AAk ++llG+kav+aeSFerI+++nl+ +g++p++++
  gi|518653089|ref|YP_008142609.1| 734 RDWAAKVTALLGVKAVVAESFERIHRSNLVDMGIVPVQVD 773
                                       *************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (837 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); 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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.48
# Mc/sec: 5213.19
//
Query:       gi|518653090|ref|YP_008142610.1|  [L=155]
Description: acetyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-13   49.3   0.0    5.8e-13   49.1   0.0    1.1  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      1e-10   41.6   0.0    1.4e-10   41.2   0.0    1.2  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
    2.4e-09   37.5   0.0    4.5e-09   36.6   0.0    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    9.1e-06   25.9   0.7    1.1e-05   25.7   0.7    1.1  1  Acetyltransf_4   Acetyltransferase (GNAT) domain
    0.00037   20.4   0.0     0.0016   18.4   0.0    1.9  2  FR47             FR47-like protein
     0.0067   16.5   0.0      0.011   15.9   0.0    1.3  1  Acetyltransf_CG  GCN5-related N-acetyl-transferase
  ------ inclusion threshold ------
       0.19   12.2   1.4       0.33   11.4   0.2    2.0  3  CBS              CBS domain


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   2.3e-16   5.8e-13      16     116 ..      40     143 ..      18     144 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 2.3e-16
                                       HHHHHHHHHHHHHHSTTCEEEEEEETTEEEEEEEEEEEET...TSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHH CS
                    Acetyltransf_1  16 nedaseeefeesfsleaegllvaeedgeliGfisllkipd...ekggvayieslaVspeyrgkGlGsaLlealeera 89 
                                       +++ se + +++  +++   lvaee++++iG+i+  +i       + +a i++++V pe+r kG+G +L+ +l e a
  gi|518653090|ref|YP_008142610.1|  40 EKEISEKIIRIIEDKDNHINLVAEEGNRVIGMITSDIIFRiyyDPKYEARIREFYVMPEFRAKGIGMKLIGKLKEVA 116
                                       3333444444444446669999***********888888888868999***************************** PP

                                       HHTTESEEEEEEETT.EHHHHHHHHHTT CS
                    Acetyltransf_1  90 reegikkivlaveed.ndaairlYeklG 116
                                        +++ik + ++  ++ n  a ++Ye   
  gi|518653090|ref|YP_008142610.1| 117 AQRNIKMVSAEF-PSlNLLASKFYESID 143
                                       *****9977766.555********8665 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   5.3e-14   1.4e-10      18     109 ..      44     147 ..      27     153 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 5.3e-14
                   Acetyltransf_10  18 spealreri.eegealllvaeeggkivGvi......el.rdgs...hisllfVdpeyrgqGigkaLleaveeeaekd 83 
                                       s e++ + i ++ +++ lvaeeg++++G+i      ++ +d +   +i  ++V pe+r +Gig +L+ +++e a ++
  gi|518653090|ref|YP_008142610.1|  44 S-EKIIRIIeDKDNHINLVAEEGNRVIGMItsdiifRIyYDPKyeaRIREFYVMPEFRAKGIGMKLIGKLKEVAAQR 119
                                       4.445555536999999*************8888887777777999****************************9** PP

                   Acetyltransf_10  84 gikl.eltvnasp.yavpfYeklGFkav 109
                                       +ik  + +  + +  a +fYe++ Fk++
  gi|518653090|ref|YP_008142610.1| 120 NIKMvSAEFPSLNlLASKFYESIDFKEL 147
                                       ***9999999*999***********986 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   1.7e-12   4.5e-09       2      76 .]      56     146 ..      55     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 1.7e-12
                                       TEEEEEEEETTEEEEEEEEEEES.........TCTEEEEE-GGGTTSSHHHHHHHH.TT....SEEE....EE.EEE CS
                    Acetyltransf_7   2 kgevfVaeddgkivGfialslld.........aeitrlaVdpeyrgkGiGraLlea.ae....kgii....le.qle 59 
                                       ++  +Vae++++++G+i   ++          a i +++V pe+r kGiG +L+   +e    ++i+     +  l 
  gi|518653090|ref|YP_008142610.1|  56 NHINLVAEEGNRVIGMITSDIIFriyydpkyeARIREFYVMPEFRAKGIGMKLIGKlKEvaaqRNIKmvsaEFpSL- 131
                                       56679**********9987777799999976555555*****************6422233334443332211222. PP

                                       ETHH.HHHHHHHHTTEEE CS
                    Acetyltransf_7  60 lnae.kaikfYeklGFee 76 
                                          +  a kfYe+  F+e
  gi|518653090|ref|YP_008142610.1| 132 ---NlLASKFYESIDFKE 146
                                       ...147899*******86 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.7   4.2e-09   1.1e-05       1     135 [.       4     145 ..       4     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 4.2e-09
                    Acetyltransf_4   1 iraateeDakeila.iyaeyvvntait...feyevssveefekfleal.dsekeyvflvaesdrivGyaylgqfkkr 72 
                                       ir+++++D +   + ++  +++n++++     +e + +e  ek++  + d+++ + + ++e  r++G+ +   + +r
  gi|518653090|ref|YP_008142610.1|   4 IRLMEKKDVEMVMEqLLRLKHLNEEFDpllKVSEGNEKEISEKIIRIIeDKDNHINLVAEEGNRVIGMITSD-IIFR 79 
                                       788899998876541457778999999665444557778888999988556777777777799*******99.5555 PP

                    Acetyltransf_4  73 .akdwkael...svylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                                        ++d k e    ++y+     + +g+g +li  l++v+++ ni+   ae  s n  + +f++++ F+
  gi|518653090|ref|YP_008142610.1|  80 iYYDPKYEArirEFYVM-PEFRAKGIGMKLIGKLKEVAAQRNIKMVSAEFPSLNLLASKFYESIDFK 145
                                       58877766422389**8.68******************************************99887 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       0.5   1.3e+03      44      65 ..      45      66 ..      36      79 .. 0.77
   2 !   18.4   0.0   6.1e-07    0.0016      22      80 ..      88     147 ..      80     152 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.5
                                      HHHHHHHHHS-S-EEEEEETT- CS
                              FR47 44 kalakeiaergktvllvvvasN 65
                                      +++++ i  +++++ lv+ ++N
  gi|518653090|ref|YP_008142610.1| 45 EKIIRIIEDKDNHINLVAEEGN 66
                                      5667777778888888888877 PP

  == domain 2  score: 18.4 bits;  conditional E-value: 6.1e-07
                                       SSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-.EEEEEETT-HHHHHHHHHHT-EEE CS
                              FR47  22 gelgalqvlpehrrrGlgsrlvkalakeiaergkt.vllvvvasNtpsirlyeklGfeki 80 
                                         +   +v pe+r +G g +l+ +l +  a+r+++ v++     N  ++++ye++ f+++
  gi|518653090|ref|YP_008142610.1|  88 ARIREFYVMPEFRAKGIGMKLIGKLKEVAAQRNIKmVSAEFPSLNLLASKFYESIDFKEL 147
                                       6677889******************9999997765156778888*************987 PP

>> Acetyltransf_CG  GCN5-related N-acetyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.2e-06     0.011      21      61 ..      84     124 ..      73     126 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.2e-06
                   Acetyltransf_CG  21 kegvldfthTeVpeelrGkGiAkkLvkaalddareeglkvv 61 
                                       ++ +  +   +V +e+r kGi++kL+ +  + a +++ k+v
  gi|518653090|ref|YP_008142610.1|  84 PKYEARIREFYVMPEFRAKGIGMKLIGKLKEVAAQRNIKMV 124
                                       5556778899***************************9987 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       3.7   9.6e+03      17      24 ..      11      18 ..       4      24 .. 0.54
   2 ?   11.4   0.2   0.00013      0.33      19      52 ..      45      78 ..      39      82 .. 0.78
   3 ?   -3.6   0.0       6.3   1.6e+04      13      25 ..     139     151 ..     137     153 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 3.7
                                      BHHHHHHH CS
                               CBS 17 tleealel 24
                                      ++e ++e+
  gi|518653090|ref|YP_008142610.1| 11 DVEMVMEQ 18
                                      45555555 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00013
                                      HHHHHHHHHHTSSEE.EEEETTTBEEEEEEHHHHH CS
                               CBS 19 eealelmrekgvsrl.PVVdedgklvGivtlrDll 52
                                      e++++++++k+ +++ +V +e ++++G++t   ++
  gi|518653090|ref|YP_008142610.1| 45 EKIIRIIEDKD-NHInLVAEEGNRVIGMITSDIIF 78
                                      689999*8887.777668876669******86555 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 6.3
                                       ETTSBHHHHHHHH CS
                               CBS  13 ppdttleealelm 25 
                                       +++ + +e+++++
  gi|518653090|ref|YP_008142610.1| 139 YESIDFKELIKIY 151
                                       5677788888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1138.05
//
Query:       gi|518653091|ref|YP_008142611.1|  [L=435]
Description: hypothetical protein FACI_IFERC00001G1730 [Ferroplasma acidarmanus fer1]
Scores for complete 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-20   72.2   0.3    6.8e-15   55.3   0.4    2.7  2  malic       Malic enzyme, N-terminal domain
    1.7e-19   70.1   0.2      2e-18   66.6   0.2    2.2  1  Malic_M     Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.099   12.7   0.0       0.22   11.5   0.0    1.5  1  YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antito


Domain annotation for each model (and alignments):
>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.4   1.1e-18   6.8e-15       3     122 ..      26     123 ..      24     124 .. 0.89
   2 !   15.7   0.0   1.6e-06    0.0096     147     181 ..     122     156 ..     119     157 .. 0.92

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.1e-18
                                       TECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBT CS
                             malic   3 knetlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriL 79 
                                       k++tl + +++     +++ +YtP+++++ ++++ + + ++ +++ + ++                v++ tdg+r+L
  gi|518653091|ref|YP_008142611.1|  26 KIRTLSKVPITGM--GDFSSLYTPGIAAVSKKIQADKELVY-ELTGKWNS----------------VAILTDGTRVL 83 
                                       5666666777666..788999********************.99999999................9********** PP

                                       TTBS-G.HHHHHHHHHHHHHHHHHHS-EGGGEEEEEECS-BS.H CS
                             malic  80 GlGdlG.vagvgimvGKlaLytalagidPekvlpvvldvgtnne 122
                                       G+G++G  a++++m+GK+ L++ l+g++   ++p+ l v+ nne
  gi|518653091|ref|YP_008142611.1|  84 GIGNVGpEASIPVMEGKALLFNYLGGVN---AIPIPLVVN-NNE 123
                                       ****************************...999999888.554 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 1.6e-06
                                       HHHHHHHHHHHHGCTSEEEE-S--CCHHHHHHHHH CS
                             malic 147 vdefveavkelfppkaliqfEDfkaknafeilery 181
                                        +ef+ a+k++ p +++ ++ED++++++f +le +
  gi|518653091|ref|YP_008142611.1| 122 NEEFITAAKAIQPYFGGYNLEDIQSPRCFFLLESL 156
                                       589***************************99976 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.2   3.3e-22     2e-18       3     243 ..     171     386 ..     170     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 3.3e-22
                                       HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--- CS
                           Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekle 79 
                                       gTa++ lag+++al+i +kk +e kiv+ GaG+a i    +  +a  ++G        +i  +D+kG++  dr++++
  gi|518653091|ref|YP_008142611.1| 171 GTASIILAGVINALRILNKKKEEVKIVFNGAGAANIAAIYLFGAAGFDKG--------NIIAIDSKGIIEPDRQDID 239
                                       9*********************************9987777777666666........8*****************6 PP

                                       ..TTTGGGSBS--SS--S....SHHHHHHHH--SEEEE-S.SSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS- CS
                           Malic_M  80 ..eekkpfakkkeelkeakdkltLeevvkkvkptvliGls.gvagafteeivremaksterPiilplSNPtskaEat 153
                                          +k+p+  k + l++ k++++ + + +   ++v+i +s +++g++++e +r+m      P+i++l NP    E  
  gi|518653091|ref|YP_008142611.1| 240 alMFKNPWKYKIA-LETNKERIKGDPANAFKGADVVISASvSIPGTIKDEWIRSMN---RDPVIFALANPLP--EIW 310
                                       2257777766554.443445565555544445799999985689*********996...57*********75..889 PP

                                       HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHHHHHHTT-SS--HHHHHHHHHHHHTT--HHHH CS
                           Malic_M 154 aedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglglgvivarakritdemllaaaealaelvseeel 230
                                       + d+ k   g+ +va+G          +   ++Q NN+ +fPg+  gv+ arak ++  +++aa+ a+a++++e + 
  gi|518653091|ref|YP_008142611.1| 311 PGDAKK--AGARIVATG----------RSDFPNQINNSMVFPGVFRGVLDARAKGVNFGIMVAASYAIADFIKEPTE 375
                                       999987..589999998..........456799**************************************998764 PP

                                       HTT-SS--GGGHH CS
                           Malic_M 231 kegsllPelseir 243
                                         +++ P++++  
  gi|518653091|ref|YP_008142611.1| 376 --DHIVPSMEDFD 386
                                       ..68999998764 PP

>> YoeB_toxin  YoeB-like toxin of bacterial type II toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   3.8e-05      0.22      10      69 ..      10      69 ..       4      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.8e-05
                                      HHHHCC-HHHHHHHHHHHHHHHHSTTSSTT--EE-SGGGTTEEEEESSSSEEEEEEEESS CS
                        YoeB_toxin 10 lywqeadkkilkkineLikeikRdpfeGiGkPepLkedlsglwsRRideehRlvYlvedd 69
                                      +y+ ++  +i+kk    i+ +++ p++G+G    L +    + s++i++++ lvY ++++
  gi|518653091|ref|YP_008142611.1| 10 EYFDKTAIEISKKYRGKIRTLSKVPITGMGDFSSLYTPGIAAVSKKIQADKELVYELTGK 69
                                      789999999**********************************************98864 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 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:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3104.68
//
Query:       gi|518653092|ref|YP_008142612.1|  [L=296]
Description: glycerate dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.4e-39  134.5   0.0    3.2e-39  134.1   0.0    1.1  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      2e-07   30.7   0.0    2.4e-07   30.5   0.0    1.1  1  2-Hacid_dh     D-isomer specific 2-hydroxyacid dehydrogenase,
     0.0012   19.4   0.2      0.016   15.7   0.0    2.5  2  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
     0.0064   16.7   0.0      0.015   15.4   0.0    1.6  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd
  ------ inclusion threshold ------
      0.029   14.0   0.0      0.075   12.6   0.0    1.7  2  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind


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 !  134.1   0.0   8.9e-43   3.2e-39       1     178 []      93     260 ..      93     260 .. 0.94

  Alignments for each domain:
  == domain 1  score: 134.1 bits;  conditional E-value: 8.9e-43
                                       HHHHHHHHTTHHHHHHHHHTTCCHTTCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHH CS
                      2-Hacid_dh_C   1 lalllallrrlaeadeevregewksekallgkelsgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeee 77 
                                       +al+la ++++ e + ++r+g++   ++ l+++++g+tvGi+G+G IG++va r+kafgm+ i+  r++kk+    +
  gi|518653092|ref|YP_008142612.1|  93 VALILAKYKNICESNIAIRNGNY---NRKLSESIYGQTVGIMGYGGIGREVAIRAKAFGMHTIGLGRTEKKDP---A 163
                                       689********************...9999**************************************99666...4 PP

                                       HTCEECSHHHHHHH-SEEEE-S--STTTTTSBSHHHHHCSTTTEEEEESS-GGGB-HHHHHHHHHTTSCCEEEES-- CS
                      2-Hacid_dh_C  78 lgvelvsleellaesDivslhlpltpetrhlinaeelakmkkgailiNtaRGglvdeeaLleaLksgkiagaalDvf 154
                                       l v  ++ e + ++sD++ + lpl+ +tr++i+ + l+++k g i++N++R ++v+++++++ Lk++k + + +Dv+
  gi|518653092|ref|YP_008142612.1| 164 LDVFSMDSEYVAKNSDVILISLPLNIHTRGMIDYKFLSSVK-GNIIVNVGRSEIVNRDDMIKFLKENKNKWFLTDVW 239
                                       45556799*******************************98.889******************************** PP

                                       SSSSSGTCHHHHHSTTEEE-SS-T CS
                      2-Hacid_dh_C 155 eeeplpedspllelpnviltPHia 178
                                       + ep  +  ++   +nvi+tPH+a
  gi|518653092|ref|YP_008142612.1| 240 WGEPEIKG-EI--PENVIITPHVA 260
                                       ****9988.55..79*******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 !   30.5   0.0   6.6e-11   2.4e-07      62     134 .]      53     291 ..      20     291 .. 0.97

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 6.6e-11
                                       --EEEESSSSCTTB-HHHHHHTT-EEEE-TTTTHHHHHHHH.................................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................... RF
                        2-Hacid_dh  62 LkviaragvGvDnvDldaakerGilVtnvpgystesvAElt.................................... 102
                                         +++ +++Gv+++D++ + ++ i++++  ++ ++ vAE++                                    
  gi|518653092|ref|YP_008142612.1|  53 TVFMQSISAGVNHLDFKNIDKK-IVICSNADAWSIPVAEHAvalilakyknicesniairngnynrklsesiygqtv 128
                                       5678899**************9.999999999999****************************************** PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                        2-Hacid_dh 103 ............................................................................. 102
                                                                                                                    
  gi|518653092|ref|YP_008142612.1| 129 gimgyggigrevairakafgmhtiglgrtekkdpaldvfsmdseyvaknsdvilislplnihtrgmidykflssvkg 205
                                       ***************************************************************************** PP

                                       .......................................................T-BHHHHHHHHHHHHHHHHHHH CS
                                       .......................................................xxxxxxxxxxxxxxxxxxxxxx RF
                        2-Hacid_dh 103 .......................................................aaTeeaqeniaeeaaenlvafl 124
                                                                                              ++ ++ ++  +e+a+en+va++
  gi|518653092|ref|YP_008142612.1| 206 niivnvgrseivnrddmikflkenknkwfltdvwwgepeikgeipenviitphvaGLARNFMQVPVEKAFENVVAYI 282
                                       ***************************************************************************** PP

                                       TTCCGTTBCS CS
                                       xxxxxxxxxx RF
                        2-Hacid_dh 125 kgespanavn 134
                                       +g +p+n+vn
  gi|518653092|ref|YP_008142612.1| 283 HG-NPRNIVN 291
                                       **.9999998 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.0      0.31   1.1e+03      59      72 ..      35      48 ..      19      63 .. 0.80
   2 !   15.7   0.0   4.6e-06     0.016       1      75 [.     127     191 ..     127     212 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.31
                                      HHH-SEEEE-S-HH CS
                     F420_oxidored 59 aeeadvvvlavkpe 72
                                       ++ad+vv+a kpe
  gi|518653092|ref|YP_008142612.1| 35 SDDADIVVFAGKPE 48
                                      57899999999997 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4.6e-06
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHH CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedve 75 
                                       ++gi G+G +g+ +a ++ a g   h i ++  r+++k  +l      +v+++d e +a+++dv++++++ + ++
  gi|518653092|ref|YP_008142612.1| 127 TVGIMGYGGIGREVAIRAKAFG--MHTIGLG--RTEKKDPAL------DVFSMDSEYVAKNSDVILISLPLNIHT 191
                                       58********************..6777755..766654333......69999****************998655 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 ?   -2.9   0.0       1.8   6.6e+03      68      96 ..      91     119 ..      55     124 .. 0.64
   2 !   15.4   0.0   4.3e-06     0.015       2     111 ..     128     233 ..     127     244 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 1.8
                                       HHHHHHHSHCCC--TT-EEEE-S---HHH CS
                     NAD_binding_2  68 avdeviegllealkkgdilidgstssped 96 
                                       +  ++i    +++ +++i i  ++ + + 
  gi|518653092|ref|YP_008142612.1|  91 HAVALILAKYKNICESNIAIRNGNYNRKL 119
                                       33333333445566677777777776655 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.3e-06
                                       EEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCC CS
                     NAD_binding_2   2 igfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasldvvitmvkagkavdevieglle 78 
                                       +g++G G +G++ a + ++ g+++++  rt++k + +++   +   + e ++++ dv+++ ++ + +++ +i+  + 
  gi|518653092|ref|YP_008142612.1| 128 VGIMGYGGIGREVAIRAKAFGMHTIGLGRTEKK-DPALD---VFSMDSEYVAKNSDVILISLPLNIHTRGMIDYKFL 200
                                       89***************************9555.55543...2344556677888*******************666 PP

                                       C--TT-EEEE-S---HHHHHHHHHHHHHTT-EE CS
                     NAD_binding_2  79 alkkgdilidgstsspedtrelakelkekglkf 111
                                       +  kg+i+++++ s++ +  ++ k lke++ k+
  gi|518653092|ref|YP_008142612.1| 201 SSVKGNIIVNVGRSEIVNRDDMIKFLKENKNKW 233
                                       6779******************99999988766 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3   4.6e+03      57      82 ..      34      60 ..      23      66 .. 0.68
   2 ?   12.6   0.0   2.1e-05     0.075       2      73 ..     123     190 ..     122     206 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                                      HHHT-SEEEE-.S-HHHHHHHHHHHTG CS
                              IlvN 57 avkkadvvmil.iPDelqkevyeeeie 82
                                       +++ad+v++   P+  +k+v+ ++i+
  gi|518653092|ref|YP_008142612.1| 34 FSDDADIVVFAgKPEPGRKTVFMQSIS 60
                                      556778765542688888888888776 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.1e-05
                                       HHTS-EEEES-SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEEHHHHHHT-SEEEE-S-HHHH CS
                              IlvN   2 lkgkkiaviGyGsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevltvaeavkkadvvmiliPDelq 73 
                                       + g+++ ++GyG  G+  a   +  g++ ++gl +++   kk  +  +  ++ + ++k++dv++i +P +++
  gi|518653092|ref|YP_008142612.1| 123 IYGQTVGIMGYGGIGREVAIRAKAFGMH-TIGLGRTE---KKDPALDVFSMDSEYVAKNSDVILISLPLNIH 190
                                       5689***********************8.57877666...23333334456778899*********997776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2096.78
//
Query:       gi|518653093|ref|YP_008142613.1|  [L=430]
Description: hypothetical protein FACI_IFERC00001G1732 [Ferroplasma acidarmanus fer1]
Scores for complete 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-50  168.9   0.2    1.3e-49  168.3   0.2    1.3  1  DEAD           DEAD/DEAH box helicase
    6.5e-28   97.3   1.0    7.7e-26   90.6   0.1    3.3  3  Helicase_C     Helicase conserved C-terminal domain
    0.00011   21.5   0.0    0.00016   21.0   0.0    1.4  1  ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
    0.00021   20.7   0.1    0.00057   19.3   0.0    1.7  2  CMS1           U3-containing 90S pre-ribosomal complex subuni
    0.00032   20.7   0.0    0.00067   19.7   0.0    1.5  1  ResIII         Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.094   12.2   0.6       0.31   10.5   0.1    2.0  2  PhoH           PhoH-like protein


Domain annotation for each model (and alignments):
>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.2   4.4e-53   1.3e-49       1     175 [.      20     185 ..      20     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 4.4e-53
                                       -HHHHHHHHHHHTTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   1 tdiQaeaiplilgggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlr 77 
                                       t+iQ++aip +l+g+dv+++ +TGsGKT+a+l+pvl++v +  + +  ka+i+ PtreLa qt++ +++++k  +++
  gi|518653093|ref|YP_008142613.1|  20 TEIQEKAIPVVLTGKDVIIRSKTGSGKTAAYLLPVLNSVEK-LKGKSVKAIIILPTRELALQTHRVASRLGKISGIK 95 
                                       79*************************************55.556667************************999** PP

                                       EEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  78 vlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitc 154
                                          ++gg +  +q+++l  g div+gtpgr++dl ++++l+l++v++lVlDEad +ld+gf d+i++i++ +     
  gi|518653093|ref|YP_008142613.1|  96 STIVYGGASIIRQVEEL-PGSDIVIGTPGRILDLYNQKYLKLDHVKYLVLDEADLMLDMGFIDDIKKIISFT----- 166
                                       *****************.*****************************************************9..... PP

                                       TSTTTSEEEEEESSBSHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                              DEAD 155 dgklqrqvivlSATlpkdvkk 175
                                         ++ rq+i+lSATlp +vk+
  gi|518653093|ref|YP_008142613.1| 167 --PEGRQTILLSATLPAEVKT 185
                                       ..56678*********99987 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.088   2.6e+02       9      50 ..      57     103 ..      47     122 .. 0.73
   2 !   90.6   0.1   2.6e-29   7.7e-26       2     111 .]     221     329 ..     217     329 .. 0.93
   3 ?    1.1   0.1      0.16   4.8e+02      18      63 ..     334     381 ..     330     387 .. 0.58

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.088
                                       HH.HHTTTTSEEEEEESSHH.HHHH...HHHHHHHTTSTEEEESTTS CS
                        Helicase_C   9 ll.kleeeggkilifvntid.rlek...vklllekkgikvavlhgel 50 
                                        + kl+ +  k++i+++t++  l+    ++ l + +gik+++++g  
  gi|518653093|ref|YP_008142613.1|  57 SVeKLKGKSVKAIIILPTRElALQThrvASRLGKISGIKSTIVYGGA 103
                                       33678899999*********744334445666555699999999964 PP

  == domain 2  score: 90.6 bits;  conditional E-value: 2.6e-29
                                       HHHHHHHHHHHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTS CS
                        Helicase_C   2 kleallellkleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaer 78 
                                       k+++l+ ++ ++ + +k+++fv+t+++ + ++l+l+++g++ + +hg ++q  re+++++f++ +s +L+at+va+r
  gi|518653093|ref|YP_008142613.1| 221 KFSTLMSYI-HSYNSRKAIVFVKTQRSGDLLNLILSRSGFNNVLIHGGMKQHARERSIADFRHIDSGILVATNVAAR 296
                                       666666666.89999***********777789*******************************9999********** PP

                                       SSTSTTESEEEESSSSSSHHHHHHHHTTSSSTT CS
                        Helicase_C  79 GidipkvnlVinfdlprnvtsyiqriGRtgRag 111
                                       G+dip+++ +infd+p+++++y +r+GR gR+g
  gi|518653093|ref|YP_008142613.1| 297 GLDIPNITDIINFDAPDSTETYAHRVGRSGRMG 329
                                       *******************************86 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.16
                                       EEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHH....HHHHHHH CS
                        Helicase_C  18 kilifvntidrlekvklllekkgikvavlhgelpqnere....eileqfn 63 
                                        + if +++++l  ++ +++++ ik+ +++ +l+++  +    + ++qf+
  gi|518653093|ref|YP_008142613.1| 334 AMTIFDPSQKSL--IQSIQRRNRIKMEKINIDLETEYTDinygKLIAQFR 381
                                       556666666666..466666666666666666666555545555566665 PP

>> ERCC3_RAD25_C  ERCC3/RAD25/XPB C-terminal helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   5.4e-08   0.00016      43     151 ..     216     328 ..     155     348 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.4e-08
                     ERCC3_RAD25_C  43 pnkfracefLiky.hekrgDkiivf.....sDnvfaLkeyakklkkpyiyGetseaerlkilqkfkknpkvntifls 113
                                       ++kf     L++y h   + k ivf     s ++  L    + +++ +i+G ++++ r + + +f++ ++   ++  
  gi|518653093|ref|YP_008142613.1| 216 SEKFDKFSTLMSYiHSYNSRKAIVFvktqrSGDLLNLILSRSGFNNVLIHGGMKQHARERSIADFRHIDSG-ILVAT 291
                                       578887777776537788899999966666678999999999*************************9764.66778 PP

                     ERCC3_RAD25_C 114 kvgDtsiDlPeanvliqisshfgsrrqeaqrlGriLra 151
                                       +v+   +D+P+ + +i  ++   s    a r+Gr  r 
  gi|518653093|ref|YP_008142613.1| 292 NVAARGLDIPNITDIINFDAP-DSTETYAHRVGRSGRM 328
                                       9****************9886.4667789999997665 PP

>> CMS1  U3-containing 90S pre-ribosomal complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.9e-07   0.00057     180     230 ..     117     174 ..     108     189 .. 0.77
   2 ?   -3.3   0.0       1.5   4.6e+03     175     211 ..     233     268 ..     215     288 .. 0.56

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.9e-07
                              CMS1 180 iavGtpgRildLleeeslsvdeLkrivlD.......asfvDkknrgildiretrkevi 230
                                       i +GtpgRildL +++ l++d++k++vlD       + f+D  ++ i   +e r++++
  gi|518653093|ref|YP_008142613.1| 117 IVIGTPGRILDLYNQKYLKLDHVKYLVLDeadlmldMGFIDDIKKIISFTPEGRQTIL 174
                                       789**********************997622221115677777777777777777665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.5
                              CMS1 175 ksrigiavGtpgRildLleeeslsvdeLkrivlDasf 211
                                       +sr +i    ++R +dLl +  ls +  +++++    
  gi|518653093|ref|YP_008142613.1| 233 NSRKAIVFVKTQRSGDLL-NLILSRSGFNNVLIHGGM 268
                                       355555555666666663.455666666666655544 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   2.3e-07   0.00067      24     147 ..      33     153 ..       9     181 .. 0.72

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 2.3e-07
                                       TSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--.. CS
                            ResIII  24 dkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkkflseaykeigkkvsgdkkkake 98 
                                        k ++i   TG+GKT  ++  + +  +k k +  k++++ p+++l  qt +  +++ +    + + ++ g + +++ 
  gi|518653093|ref|YP_008142613.1|  33 GKDVIIRSKTGSGKTAAYLLPVLNSVEKLKGKsvKAIIILPTRELALQTHRVASRLGKISGIKSTIVYGGASIIRQV 109
                                       57899*************8888888877777778***************9777777666654455555555555577 PP

                                       .....-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS. CS
                            ResIII  99 kdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgak 147
                                       ++   ++i++ t  ++         +++ l+ d+ ++++ DEa  + ++
  gi|518653093|ref|YP_008142613.1| 110 EELPGSDIVIGTPGRILDLY-----NQKYLKLDHVKYLVLDEADLMLDM 153
                                       78889999999999998888.....777888888889999998776666 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.1    0.0001      0.31       6      55 ..      20      72 ..      16      92 .. 0.86
   2 ?   -1.8   0.0      0.59   1.8e+03     142     164 ..     327     350 ..     313     366 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0001
                                      SHHHHHHHHHHHH-SEEEEE--TTSSTT...HHHHHHHHHHHHTTS-SEEEEE CS
                              PhoH  6 tkeQkeylealkkndivfaiGpaGtGKt...ylavalavealkkkkvkriilt 55
                                      t+ Q++++ ++ + + v++  ++G+GKt   +l v   ve lk k+vk ii++
  gi|518653093|ref|YP_008142613.1| 20 TEIQEKAIPVVLTGKDVIIRSKTGSGKTaayLLPVLNSVEKLKGKSVKAIIIL 72
                                      56788888888888888999********6656999***************996 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.59
                                       TB-TT-EEEEEE----------.- CS
                              PhoH 142 RlGenskvvvtGdvtqidlpkg.k 164
                                       R+G++ +++   d++q+ l ++ +
  gi|518653093|ref|YP_008142613.1| 327 RMGKDGRAMTIFDPSQKSLIQSiQ 350
                                       889999999989998888775534 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (430 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); 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:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.56u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2667.65
//
Query:       gi|518653094|ref|YP_008142614.1|  [L=104]
Description: hypothetical protein FACI_IFERC00001G1733 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.4   0.9       0.65   10.4   0.2    2.1  2  FERM_C    FERM C-terminal PH-like domain


Domain annotation for each model (and alignments):
>> FERM_C  FERM C-terminal PH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.07   1.2e+03      26      44 ..      45      63 ..      35      69 .. 0.78
   2 ?   10.4   0.2   3.6e-05      0.65      18      42 ..      71      94 ..      68      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.07
                                      S-SEEEEGGGEEEEEEETT CS
                            FERM_C 26 tpklafpWreieklsfkdk 44
                                      t +++++  +i  ++++dk
  gi|518653094|ref|YP_008142614.1| 45 TDREEYKFLSIMSIKYNDK 63
                                      5567788888999999988 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 3.6e-05
                                      EEBTTBSSS-SEEEEGGGEEEEEEE CS
                            FERM_C 18 vyekqnkitpklafpWreieklsfk 42
                                      vy ++n    +++f+Wrei++++ +
  gi|518653094|ref|YP_008142614.1| 71 VYLHNNL-RVRKNFSWREIRNVNVN 94
                                      5655555.479**********9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 816.07
//
Query:       gi|518653095|ref|YP_008142615.1|  [L=278]
Description: aldo/keto reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-57  194.0   0.2    5.3e-56  190.0   0.2    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 !  190.0   0.2   2.9e-60   5.3e-56      14     291 ..      35     276 ..      15     278 .] 0.92

  Alignments for each domain:
  == domain 1  score: 190.0 bits;  conditional E-value: 2.9e-60
                                       TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSSTTSSSS-HHHHHHHH CS
                      Aldo_ket_red  14 eiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdaeiksglskeniresl 90 
                                       +  +++++++ r+ +++Gin++DtAe+Y   + e+l+G a+k+   kr+e+++a+Kv       + +ls+++++++l
  gi|518653095|ref|YP_008142615.1|  35 YSGRDQKIDAYRAGIDNGINLIDTAELY---RTEKLVGTAIKS--YKRDELFLASKV------FPTHLSPKSLEKAL 100
                                       67799***********************...************..************......************** PP

                                       HHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.HHTTT--EEEEE-B-BT CS
                      Aldo_ket_red  91 eeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.kkkkkvkivavqveynl 166
                                       ++slk+L+tdy+Dl+++H p+p+++ i ++l+++e++v++Gkir+iGvSnf+   l++a    +k++i+++q++yn+
  gi|518653095|ref|YP_008142615.1| 101 NRSLKNLDTDYIDLYQIHFPNPTVD-IKKTLRTMEKMVDKGKIRHIGVSNFTLNLLKRAqGILSKYEITSIQINYNV 176
                                       *************************.********************************976678999********** PP

                                       T-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSSCCC-------TS-HHHHHHHHHHHHHHHH.TT-- CS
                      Aldo_ket_red 167 lreleeegllelckkkgvpliaysplggGlltgkyqseedkedkeprkdlkrdertsknldaaeelselake.hgvs 242
                                       + +  ++g++++c+k+ ++++ay plg+G  t     ++                     + ++ ++++ k+  +v 
  gi|518653095|ref|YP_008142615.1| 177 FHRNSQKGMIDYCNKNHIAVMAYFPLGHGKVT-----QP---------------------QFNKYFDHVRKTiGDVP 227
                                       ********************************.....11.....................2344555566666788* PP

                                       HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 243 laqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                        a +al+y++s+++++++ip asn +++ +n++  ++ l+e+++++l++
  gi|518653095|ref|YP_008142615.1| 228 NANIALAYLISRNQNVFPIPRASNRAHVLQNAKNSDILLNEDDIKYLEK 276
                                       *********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (278 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1918.08
//
Query:       gi|518653096|ref|YP_008142616.1|  [L=366]
Description: hypothetical protein FACI_IFERC00001G1735 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-50  171.7   0.2    5.1e-50  169.9   0.1    1.8  2  ATP-grasp_2  ATP-grasp domain
    9.6e-11   41.7   0.1    2.1e-10   40.6   0.1    1.6  1  Ligase_CoA   CoA-ligase
      5e-06   26.1   0.1    0.00011   21.7   0.1    2.3  1  ATP-grasp_5  ATP-grasp domain
    7.9e-06   25.5   0.0    2.1e-05   24.1   0.0    1.7  2  CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP bindin


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 !  169.9   0.1   1.1e-53   5.1e-50       1     202 []       2     186 ..       2     186 .. 0.95
   2 ?   -0.6   0.0      0.18   7.9e+02     143     186 ..     321     362 ..     300     364 .. 0.77

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.1e-53
                                       BE-HHHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTT CS
                       ATP-grasp_2   1 nlhEyqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellg 77 
                                       nl+Ey +kei++kyg++vp g v e+  e+++    ++  + ++K+Q+l G RGKagG+k++++ +e++e+ ++ll+
  gi|518653096|ref|YP_008142616.1|   2 NLYEYMGKEIFKKYGIPVPDGYVIENVGELRK----FEYPV-AIKSQILSGKRGKAGGIKFARNSNELSEFSDKLLN 73 
                                       79**********************99988765....55566.9********************************** PP

                                       SEEE-TTS-TT-EEE--EEEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB- CS
                       ATP-grasp_2  78 kelvtkqtgkeGkkvekvlveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakgl 154
                                       +++          +v+k+l+e +l+ikkE+Ylsi+lDra+k++v+i+S++GG++iE v ++   +i+k++idp +g 
  gi|518653096|ref|YP_008142616.1|  74 STIN-------NLTVKKLLIERMLNIKKEIYLSITLDRATKEPVIILSADGGMEIESVPEE---NIHKIHIDPMVGY 140
                                       ***9.......789********************************************985...69*********** PP

                                       -HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEEE CS
                       ATP-grasp_2 155 keeqareiakklglekelvkkaakiikklyklfveldatlvEiNPLvv 202
                                       +++ are +  + +e+   k++++ ++ lyk+fv +da l EiNPLv+
  gi|518653096|ref|YP_008142616.1| 141 SDYIAREALSYIPVEN--KKQFSNLLSSLYKAFVGEDALLTEINPLVI 186
                                       ********99988876..69**************************96 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.18
                                       EEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHH CS
                       ATP-grasp_2 143 iikvaidpakglkeeqareiakklglekelvkkaakiikklykl 186
                                       i++  +    g++ee+ ++i+ + g+++  ++++++++k+l ++
  gi|518653096|ref|YP_008142616.1| 321 IKQPIVVRLSGVHEEEGQKILLESGIKA--FTNMTDAVKELSRI 362
                                       5555566678889999999999999875..77888888887765 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.1   4.8e-14   2.1e-10       2     148 ..     244     357 ..     243     362 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 4.8e-14
                                       ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEE CS
                        Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvil 78 
                                        nG++L++++md ++++              + ++ +++dlG+ +            + + +a+  ++   + k i+
  gi|518653096|ref|YP_008142616.1| 244 ANGAGLTMATMDSLTLH--------------KLKPRNFLDLGGTDN----------IEIVEDAFS-FVMRARPKLIF 295
                                       69***************..............************888..........566666665.5666788**** PP

                                       EEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHH CS
                        Ligase_CoA  79 ldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalr 148
                                       ++i++G  +++++a+++++  k+ +    + p+v+r+ G +++     e++k+l e+g++  +  + a++
  gi|518653096|ref|YP_008142616.1| 296 VNIFGGVTKADTVANGIVSSKKKFD---IKQPIVVRLSGVHEE-----EGQKILLESGIKAFTNMTDAVK 357
                                       ************************9...***************.....99*********99888777765 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   2.5e-08   0.00011      10     141 ..       3     126 ..       1     201 [. 0.79

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.5e-08
                       ATP-grasp_5  10 LteaeakelleaygipvvetrlassaeeaveaaeeigypvvlKivspdilhKtdvgGvrlnlkdaeevraaaeeile 86 
                                       L+e+  ke+++ ygipv++  +++++ e     ++++ypv++K ++ +  ++ ++gG+++  ++ +e+ +  +++l+
  gi|518653096|ref|YP_008142616.1|   3 LYEYMGKEIFKKYGIPVPDGYVIENVGE----LRKFEYPVAIKSQILS-GKRGKAGGIKF-ARNSNELSEFSDKLLN 73 
                                       899*****************99988776....7899*******98753.46889******.8899999999999999 PP

                       ATP-grasp_5  87 rvkekspeariegvlVqemakrggrElivgvteDpvF.GpvilfGl.GGtavevlkd 141
                                       +  +   +  ++++l+++m +  + E+ +++t D     pvi++ + GG+++e + +
  gi|518653096|ref|YP_008142616.1|  74 STIN---NLTVKKLLIERMLN-IKKEIYLSITLDRATkEPVIILSAdGGMEIESVPE 126
                                       8755...6789********99.88999999999965326777766547777776655 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0   4.7e-09   2.1e-05      29     104 ..      26     105 ..       7     121 .. 0.79
   2 ?   -2.4   0.0      0.63   2.8e+03     166     176 ..     226     236 ..     184     242 .. 0.65

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 4.7e-09
                                       HHHHHHHHH-SSEEEEETTCCTTT....TEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEE CS
                       CPSase_L_D2  29 ealaiakeigyPviikaafglGGk....GmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlr 101
                                       e++   +++ yPv ik+ +  G +    G ++arn++el+e   k l+ +   ++ k++l+e++l+  kei + +  
  gi|518653096|ref|YP_008142616.1|  26 ENVGELRKFEYPVAIKSQILSGKRgkagGIKFARNSNELSEFSDKLLNSTINNLTVKKLLIERMLNIKKEIYLSITL 102
                                       4455567889*******99888652233579****************************************999988 PP

                                       ETT CS
                       CPSase_L_D2 102 Dak 104
                                       D++
  gi|518653096|ref|YP_008142616.1| 103 DRA 105
                                       864 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.63
                                       TTTTEEEEEEE CS
                       CPSase_L_D2 166 pkskeyyviEv 176
                                       + sk++++iE+
  gi|518653096|ref|YP_008142616.1| 226 AASKSFTFIEM 236
                                       34566666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2560.60
//
Query:       gi|518653097|ref|YP_008142617.1|  [L=284]
Description: hypothetical protein FACI_IFERC00001G1736 [Ferroplasma acidarmanus fer1]
Scores for complete 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-26   90.4   0.7    9.2e-26   90.4   0.7    2.2  2  CoA_binding    CoA binding domain
    2.2e-17   63.3   0.4    3.7e-17   62.6   0.4    1.3  1  Ligase_CoA     CoA-ligase
    1.1e-08   34.9   0.0    1.9e-08   34.2   0.0    1.4  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain
    0.00014   22.4   0.0    0.00046   20.7   0.0    1.9  2  CoA_binding_2  CoA binding domain
     0.0014   18.2   0.8     0.0028   17.3   0.8    1.5  1  IlvN           Acetohydroxy acid isomeroreductase, NADPH-bind
     0.0023   18.7   0.1      0.024   15.4   0.0    2.4  3  GFO_IDH_MocA   Oxidoreductase family, NAD-binding Rossmann fo
  ------ inclusion threshold ------
       0.14   12.4   0.1       0.26   11.6   0.1    1.6  1  PHP            PHP 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 !   90.4   0.7   3.6e-29   9.2e-26       2      96 .]       6      97 ..       5      97 .. 0.97
   2 ?   -1.3   0.1       1.4   3.6e+03      28      47 ..     168     188 ..     144     230 .. 0.67

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 3.6e-29
                                      TTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHH CS
                       CoA_binding  2 kdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavd 80
                                      k+tkviv+G++g   +g++h+ e++k+g+++v+gv+p+k+gt+v+g+ vy++v++  +  ++d+++i vPa+++++a++
  gi|518653097|ref|YP_008142617.1|  6 KETKVIVQGMTGH--QGAFHSGEMIKFGTNVVAGVSPGKAGTKVNGVDVYNNVADTLDL-KPDASMISVPAPFVKDAAL 81
                                      89********999..**************************************999887.9****************** PP

                                      HHHHTT-SEEEEESST CS
                       CoA_binding 81 elveagikgiviiteg 96
                                      e++e+gik+i i te+
  gi|518653097|ref|YP_008142617.1| 82 EAIENGIKLIYILTEH 97
                                      *************985 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.4
                                       ECEEEEEEC-TT.TTTCEETT CS
                       CoA_binding  28 ygikavfgvnpr.kvgtevlg 47 
                                       +g + v+g +++  +gt+ ++
  gi|518653097|ref|YP_008142617.1| 168 FGESTVIGLGGDpIIGTTFSD 188
                                       555555555555455555443 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.6   0.4   1.4e-20   3.7e-17       2     150 ..     150     267 ..     149     269 .. 0.95

  Alignments for each domain:
  == domain 1  score: 62.6 bits;  conditional E-value: 1.4e-20
                                       ESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEE CS
                        Ligase_CoA   2 vnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvil 78 
                                       +++GtL+ye ++++++a              g +++++i+lG+d            +t++ + +k++ +dp++k i+
  gi|518653097|ref|YP_008142617.1| 150 SRSGTLTYEIVKAVTDA--------------GFGESTVIGLGGDPII---------GTTFSDIIKIFNEDPQTKQIV 203
                                       69***************..............***************8.........********************* PP

                                       EEEEESSSEHHHHHHHHHHHHHHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHH CS
                        Ligase_CoA  79 ldivlGygahedpaaellkaikeakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraa 150
                                       l +++G g++e++aae++k++ +        pv  +++G +a+p++ +++a+a+ e g  +a+sk +a + a
  gi|518653097|ref|YP_008142617.1| 204 LVGEIG-GSEEEKAAEYIKKYVKK-------PVTGYITGISAPPGKKMGHAGAIIEKGTGTADSKIKAFKDA 267
                                       ******.***********988655.......9*********************************9998776 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 !   34.2   0.0   7.3e-12   1.9e-08       2      94 ..     144     238 ..     143     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 7.3e-12
                      Succ_CoA_lig   2 GkialisqSGalalalldwaasrglgfskvvslGn..eadvdvadlleylaedpetkvillylEsird.grkflsaa 75 
                                       G++a+ s SG+l  ++++++++ g+g s+v+ lG    + ++++d+++ ++edp+tk i+l+ E  +   +k ++ +
  gi|518653097|ref|YP_008142617.1| 144 GNVAVASRSGTLTYEIVKAVTDAGFGESTVIGLGGdpIIGTTFSDIIKIFNEDPQTKQIVLVGEIGGSeEEKAAEYI 220
                                       9*********************************94458899********************996555378888888 PP

                      Succ_CoA_lig  76 rraarkkpvvvlksGrsea 94 
                                       ++ + kkpv  +  G s+ 
  gi|518653097|ref|YP_008142617.1| 221 KKYV-KKPVTGYITGISAP 238
                                       8887.88888777776544 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.8e-07   0.00046      32     114 ..      37     126 ..      25     128 .. 0.91
   2 ?   -2.4   0.0       2.6   6.7e+03       9      24 ..     208     225 ..     198     234 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.8e-07
                                       EESSS-..SEETTEES----T.....T--EEEE-S-HHHHGGGHHHHHHH--SEEEE-TT....---HHHHHHHHHT CS
                     CoA_binding_2  32 pVnpke..eeilgekvyaslaed.pepvdlvdvftppeatpeivkealalgakavwlqpg....sedeeaaelaeea 101
                                        V p +  +++ g++vy ++a+  + ++d+  + +p+  + + + ea++ g+k + +  +        e+++ a+++
  gi|518653097|ref|YP_008142617.1|  37 GVSPGKagTKVNGVDVYNNVADTlDLKPDASMISVPAPFVKDAALEAIENGIKLIYILTEhvpvHDTMELYHEARRK 113
                                       5778777799***********8469*********************************9999988999********* PP

                                       T-EEE.ES-HHHH CS
                     CoA_binding_2 102 girvvgdrCilve 114
                                       g+ ++g++++++ 
  gi|518653097|ref|YP_008142617.1| 114 GVFMIGPNSPGIT 126
                                       *********9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.6
                                       -..S-TTSHHHHHHHHHH CS
                     CoA_binding_2   9 s..dnpgkfgykvlryll 24 
                                          ++++k++ ++ +y++
  gi|518653097|ref|YP_008142617.1| 208 IggSEEEKAAEYIKKYVK 225
                                       333455566665555554 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 !   17.3   0.8   1.1e-06    0.0028       3     130 ..       6     133 ..       4     166 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 1.1e-06
                                       HTS-EEEES-.SHHHHHHHHHHHHTT--EEEEE-TT-HHHHHHHHTT-EEEE.HHHHH.HT-SEEEE-S-HHHHHHH CS
                              IlvN   3 kgkkiaviGy.GsqGhaqalnlrdsgldvvvglregsksvkkAkeegfevlt.vaeav.kkadvvmiliPDelqkev 76 
                                       k+ k+ v G+ G qG  ++ ++   g +vv g+  g++ +   k +g++v++ va+    k d  mi +P  + k+ 
  gi|518653097|ref|YP_008142617.1|   6 KETKVIVQGMtGHQGAFHSGEMIKFGTNVVAGVSPGKAGT---KVNGVDVYNnVADTLdLKPDASMISVPAPFVKDA 79 
                                       567888889659************************9544...4455555532333331466777778888888888 PP

                                       HHHHTGGG--TT-EEEESSSHHHHTTSS---TTSEEEEEEESS-SHHHHHHHHT CS
                              IlvN  77 yeeeiepnlkegkalafahGfnihfglikppkdvdvvlvAPkgpGhlvreeyee 130
                                         e+ie+ +k   +l+     +  ++l +  ++  v+++ P +pG +v  + + 
  gi|518653097|ref|YP_008142617.1|  80 ALEAIENGIKLIYILTEHVPVHDTMELYHEARRKGVFMIGPNSPGITVAGQAKI 133
                                       889*****99999998877788888899999999***********999876555 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   9.5e-06     0.024      33     114 ..      39     115 ..       9     119 .. 0.79
   2 ?   -1.4   0.0       1.5     4e+03      66      86 ..     146     167 ..     136     207 .. 0.75
   3 ?   -0.2   0.0      0.66   1.7e+03       8      44 ..     184     218 ..     171     226 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 9.5e-06
                                       CSSHHHHHHHHHHTTHEEESSHHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-...EEEEESSS-SSHHHHHHHH CS
                      GFO_IDH_MocA  33 dpdaeraeavaesfgveaysdleelladpeidavivatpngtheelakaaleagk...hvllEKPlattveeakelv 106
                                       +p+++      +  gv++y+++++ l+  ++da ++ +p+   ++ a++a+e+g+    +l E+ +  +v +  el+
  gi|518653097|ref|YP_008142617.1|  39 SPGKAG----TKVNGVDVYNNVADTLD-LKPDASMISVPAPFVKDAALEAIENGIkliYILTEH-V--PVHDTMELY 107
                                       444433....345899*****999998.57*************************888999999.3..568888888 PP

                                       HHHHHHTS CS
                      GFO_IDH_MocA 107 elaekkgk 114
                                       + a++kg+
  gi|518653097|ref|YP_008142617.1| 108 HEARRKGV 115
                                       88888886 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.5
                                       EEE-S-G.GGHHHHHHHHHHTT CS
                      GFO_IDH_MocA  66 vivatpn.gtheelakaaleag 86 
                                       v va+++ ++ +e++ka++ ag
  gi|518653097|ref|YP_008142617.1| 146 VAVASRSgTLTYEIVKAVTDAG 167
                                       6677777444778877777776 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.66
                                       TSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHH CS
                      GFO_IDH_MocA   8 aGkigskhlrplnesqrleevvalldpdaeraeavae 44 
                                       +    s+ ++ +ne  ++ ++v + +++ ++ e++ae
  gi|518653097|ref|YP_008142617.1| 184 T--TFSDIIKIFNEDPQTKQIVLVGEIGGSEEEKAAE 218
                                       2..3556687888888888999999999999888876 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1    0.0001      0.26      16      54 ..      75     114 ..      65     232 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0001
                                       ..HHHHHHHHHCT-SEE.EEEEEEBTTHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx RF
                               PHP  16 sieelvkkakelglkai.aiTDhgnlfgyvefykaakkky 54 
                                        +++ + +a+e g+k i  +T+h+++++ +e y++a+ k 
  gi|518653097|ref|YP_008142617.1|  75 FVKDAALEAIENGIKLIyILTEHVPVHDTMELYHEARRKG 114
                                       47999999*******87357****************6543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2200.17
//
Query:       gi|518653098|ref|YP_008142618.1|  [L=94]
Description: hypothetical protein FACI_IFERC00001G1737 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.44
# Mc/sec: 648.54
//
Query:       gi|518653099|ref|YP_008142619.1|  [L=632]
Description: hypothetical protein FACI_IFERC00001G1738 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-57  193.7   0.0    5.2e-57  193.3   0.0    1.2  1  POR_N            Pyruvate flavodoxin/ferredoxin oxidoreductas
      4e-37  128.0   0.1    3.1e-36  125.1   0.0    2.3  2  POR              Pyruvate ferredoxin/flavodoxin oxidoreductas
      1e-11   45.0   0.0    9.4e-11   41.9   0.0    2.3  2  PFOR_II          Pyruvate:ferredoxin oxidoreductase core doma
    8.1e-09   35.4   0.0    1.7e-08   34.4   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
    2.9e-05   23.8   0.1    6.9e-05   22.5   0.1    1.6  2  TPP_enzyme_N     Thiamine pyrophosphate enzyme, N-terminal TP
  ------ inclusion threshold ------
       0.16   12.0   0.7       0.53   10.3   0.1    2.1  2  SBDS_C           SBDS protein 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 !  193.3   0.0   1.7e-60   5.2e-57       3     230 ..     246     490 ..     244     491 .. 0.87

  Alignments for each domain:
  == domain 1  score: 193.3 bits;  conditional E-value: 1.7e-60
                                       HHHCTEEEEEE--BTTTCC...HHHHHCHCCCCCTT.......EE.EEEE-SSHHHHHHHHHHHHCTT-EEEEEEEC CS
                             POR_N   3 aiaagvdviaaYPITPsse...iaeelaellakgev.......gdvevvqmesEigaisaviGAaaaGaraaTaTSg 69 
                                       ++ +g++++++YPITP+s+   ++e + e ++  e+          +vvq e+E++ai+++ GAa++G+r+aTaTSg
  gi|518653099|ref|YP_008142619.1| 246 KLMGGLRFQTYYPITPASDestLLESH-EEMKFLETagkdlkkAGLVVVQCEDELSAINMANGAALTGTRTATATSG 321
                                       667899************977444444.433333335668888558******************************* PP

                                       CHHHHCCCCHHHHHHTT--EEEEEEEEE-STTBEEEEE--TTCHHHH.....S---EEEE-SSHHHHHHHHHHHHHH CS
                             POR_N  70 qGllLmienlglaageelPvvivvvaRalpstglsirtdqsDlmaar.....dtglivlasenvqeafdlalvAfnl 141
                                       +G++Lm e +g+a+++e+Pvvi+ ++R++pstgl++r+ q Dlm+a+     +++ iv++s++++e+  + ++ +n+
  gi|518653099|ref|YP_008142619.1| 322 PGFSLMAEGIGYAGMTEIPVVITFYQRGGPSTGLPTRNGQADLMFALntghgEFPKIVMSSGDMEECIYDGMKSLNY 398
                                       ***************************************************************************** PP

                                       HHHCTSEEEEEEEHHHH.HEEEEEEC-SGG..GS-----SBXXXXXXXXSXXXBXXT....XXTSSXXEEESBXBXT CS
                             POR_N 142 AekvrvPvivlfDgfllshevekvelpdee.delklikekleeyerkeyaldpekpi....argtaanpdtglehre 213
                                       A ++++Pvi+++D++l+ ++++ v+  d++ +++   +e+ ++++ k+y+l++e  i    ++g+  +++tg+eh+e
  gi|518653099|ref|YP_008142619.1| 399 AQRYQMPVIHMIDKTLA-NTMDLVPEIDVKkVKIVKYNENTDHENFKRYSLNTEDGIspygVFGKDIFWMTGDEHDE 474
                                       *****************.*********99965555666777778888898887654422234688899********* PP

                                       TSXBXXXXHHHHHHHHH CS
                             POR_N 214 kgneaedaaekvveeve 230
                                        g+ +ed  + +++++e
  gi|518653099|ref|YP_008142619.1| 475 LGHVTED-TKMRDRMME 490
                                       ******9.888888876 PP

>> POR  Pyruvate ferredoxin/flavodoxin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0     1e-39   3.1e-36       2     177 .]      15     213 ..      12     213 .. 0.94
   2 ?   -0.7   0.0      0.44   1.3e+03      56      88 ..     264     297 ..     250     306 .. 0.71

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 1e-39
                                       TSTHHHHHHHHHHHHHHTT-EEEEEEEEESSSSSSCEEEEEEEESS.-SSS--TTSEEEEEESSHHHHHHHGGGEEE CS
                               POR   2 GqGvvtagkilakaaaraGyyvqanreygseirGghsyshvrisdepivpsievgeadllvaldaetlsehldglkp 78 
                                       G G+ +a+++++ a++ aGy++++ re++s+i+G+hsy+h ri  e + +s++ +++d++vald++tl+eh+ ++ +
  gi|518653099|ref|YP_008142619.1|  15 GGGIDSAANMISMAFSLAGYNIYGIREFHSNIKGRHSYIHFRIKHE-RPKSLK-YPVDIMVALDPDTLFEHMFDVAK 89 
                                       99******************************************99.889999.*********************** PP

                                       EEEEEEECTCGTT-CCHHHCTS-HHHHHHH.........................T-EEEEE-HHHHHHHCCC.... CS
                               POR  79 ggiiiynseelkpdelkkakeeerelkerl.........................gvrvygvdatkiakeiggn... 127
                                       g+ ++y+s  ++  +lk+a++   ++                             g++v+++++ k++ e+      
  gi|518653099|ref|YP_008142619.1|  90 GSRVVYDS-AFNGFNLKNARMITSDTL--GrieeelssrnltydvqgvldyfkktGIDVIAIPFDKLINENVHGgpa 163
                                       ********.89*********9875443..146999*********************************975544678 PP

                                       CCHHHHHHHHHHHHHHTS-HHHHHHHHHCCS-CH.HHHHHHHHHHHHHHH CS
                               POR 128 eraaNtvmlGalaallglplealeeaikkrfpkkkeviekNlkafragye 177
                                        r+ Nt++ G ++allgl++ +  ++ik +f+kk +vie N+ +++a+y+
  gi|518653099|ref|YP_008142619.1| 164 NRYYNTLGAGTTLALLGLDIYHANDGIKFAFKKKPKVIESNINVIKAAYD 213
                                       *************************************************6 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.44
                                       TSEEEEEESSH.HHHHHHGGGEEEEEEEEEECTC CS
                               POR  56 geadllvalda.etlsehldglkpggiiiynsee 88 
                                       +e  ll  +++ + l++  ++lk+ g+++++ e+
  gi|518653099|ref|YP_008142619.1| 264 DESTLLESHEEmKFLETAGKDLKKAGLVVVQCED 297
                                       555566666664556689999********99865 PP

>> PFOR_II  Pyruvate:ferredoxin oxidoreductase core domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.34     1e+03      26      61 ..     245     281 ..     241     317 .. 0.76
   2 !   41.9   0.0   3.2e-14   9.4e-11       1     102 []     517     611 ..     517     611 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.34
                                       T--EEEEEES--BS-.-HHHHHHHSTT-SEEEEEE-S CS
                           PFOR_II  26 gikvGllrlrtlrPF.Peeelkellkkvkkvvvldrn 61 
                                       g  +G lr +t++P  P+ + ++ll++ +++  l+ +
  gi|518653099|ref|YP_008142619.1| 245 GKLMGGLRFQTYYPItPASDESTLLESHEEMKFLETA 281
                                       66789*********54888888888888777766665 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 3.2e-14
                                       -SEEEEE-STHHHHHHHHHHHHHHTT--EEEEEES--BS--HHHHHHHSTT-SEEEEEE-S--TT-G-HHHHHHHHH CS
                           PFOR_II   1 AevvivamGsvagtaksavdelReegikvGllrlrtlrPFPeeelkellkkvkkvvvldrnisfgseGqlveevkaa 77 
                                       A++  ++ Gs  + + +a+del+++gi++ ll lr++ PFP+e ++++lkk + +++++ n++     q ++ +++ 
  gi|518653099|ref|YP_008142619.1| 517 ADITYITWGSQKSLLLDAIDELKKQGISANLLYLRMFEPFPAEYVEKVLKKSHLIIDVESNMT----AQAAKVIRMN 589
                                       899999********************************************************4....6666666665 PP

                                       TGGGTSEEEEEE--GGG----HHHH CS
                           PFOR_II  78 lkkskvkvvnfvaglgGrditvedi 102
                                       +    +k+ nf+ + +Gr +t+++i
  gi|518653099|ref|YP_008142619.1| 590 T---GIKIENFILKYNGRHMTLDEI 611
                                       5...35799************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 !   34.4   0.0   5.6e-12   1.7e-08       8      72 ..     515     579 ..     508     603 .. 0.93

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 5.6e-12
                                       TTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEES CS
                   Transketolase_C   8 egkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDketilesvkktgrlvvveeavk 72 
                                       ++ d+t +++Gs+ +  l+A++eL+k+gisa ++ lr ++p+  e +++++kk + ++ ve +++
  gi|518653099|ref|YP_008142619.1| 515 KNADITYITWGSQKSLLLDAIDELKKQGISANLLYLRMFEPFPAEYVEKVLKKSHLIIDVESNMT 579
                                       588*******************************************************9998876 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 !   22.5   0.1   2.3e-08   6.9e-05      33     106 ..     284     354 ..     270     387 .. 0.81
   2 ?   -4.2   0.0       3.7   1.1e+04      80      96 ..     393     409 ..     389     419 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.5 bits;  conditional E-value: 2.3e-08
                                       CHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHHHHHHHHHHT--EEEEEEE--CCCHH CS
                      TPP_enzyme_N  33 alseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnaltalaeAkvdriPllvlsgdrptslrg 106
                                        l+++ g+ vv++ +E +a+++A g a        + +tsgpG+  +  ++  A  + iP+++   +r+  ++g
  gi|518653099|ref|YP_008142619.1| 284 DLKKA-GLVVVQCEDELSAINMANGAALTGT--RTATATSGPGFSLMAEGIGYAGMTEIPVVITFYQRGGPSTG 354
                                       34444.899****************988753..3556779***********************98888766665 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 3.7
                                       HHHHHHHHHHT--EEEE CS
                      TPP_enzyme_N  80 ltalaeAkvdriPllvl 96 
                                       + +l  A++ ++P++++
  gi|518653099|ref|YP_008142619.1| 393 MKSLNYAQRYQMPVIHM 409
                                       56777899999999975 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 ?   -1.0   0.0      0.59   1.8e+03      29      57 ..     491     540 ..     407     553 .. 0.73
   2 ?   10.3   0.1   0.00018      0.53      20      53 ..     554     587 ..     541     621 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.59
                                       HHH.....................HHTT----TTS-CCCCHHHHHHHHTT CS
                            SBDS_C  29 kal.....................kelgtsvktnksaksQalevikaLiq 57 
                                       k +                     k++ +   t  s ks  l++i++L++
  gi|518653099|ref|YP_008142619.1| 491 KRMqklitadneipledkvvlygdKNADITYITWGSQKSLLLDAIDELKK 540
                                       33355555555555555555555566666666677888888888888874 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00018
                                       B---HHHHHHHHHHTT----TTS-CCCCHHHHHH CS
                            SBDS_C  20 rpytttmIekalkelgtsvktnksaksQalevik 53 
                                        p++ + +ek lk+ +  ++++ ++ +Qa++vi+
  gi|518653099|ref|YP_008142619.1| 554 EPFPAEYVEKVLKKSHLIIDVESNMTAQAAKVIR 587
                                       699*****************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (632 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       601  (0.0335211); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-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 0.30s 00:00:00.95 Elapsed: 00:00:00.49
# Mc/sec: 3907.84
//
Query:       gi|518653100|ref|YP_008142620.1|  [L=316]
Description: hypothetical protein FACI_IFERC00001G1739 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-30  105.8   0.1    4.2e-30  104.5   0.0    1.6  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    4.2e-23   81.2   0.3    8.2e-23   80.3   0.3    1.5  1  PFO_beta_C    Pyruvate ferredoxin oxidoreductase beta subunit


Domain annotation for each model (and alignments):
>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.14   1.3e+03      24      54 ..      23      54 ..      13      59 .. 0.64
   2 !  104.5   0.0   4.7e-34   4.2e-30       2     153 .]      55     202 ..      54     202 .. 0.96

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.14
                                      ETTTS-TTTHHHHHHHHHH..HSTTSEEEEEEE CS
                      TPP_enzyme_C 24 sgglgtmGyglpaAiGakl..akpdrevvaivG 54
                                      + g+g +G   ++  ++++   +p ++vva++G
  gi|518653100|ref|YP_008142620.1| 23 CPGCGDFGIVSAVTQALSAmkMDP-QDVVAVSG 54
                                      456777777666666666631234.48999998 PP

  == domain 2  score: 104.5 bits;  conditional E-value: 4.7e-34
                                       SSHHHHHHHHHHTTSSSSEEEC.ETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHT.GGGHHHHHHTT-SEE CS
                      TPP_enzyme_C   2 iGcltlwaarllkvkrprsylt.sgglgtmGyglpaAiGaklakpdrevvaivGDGgflmi.lqelatavrrnlpit 76 
                                       iGc+             ++yl+ +g+++ +G+++p+A+G+kla+p+ +v ++ GDG++l i   +++   rrn  ++
  gi|518653100|ref|YP_008142620.1|  55 IGCSGK----------TPHYLNiAGTHTLHGRAIPYAVGVKLANPNLNVLVMGGDGDLLSIgAGHFVGEGRRNSGVK 121
                                       677776..........7899999**************************************99************** PP

                                       EEEEE-SBCCCHHHH...HHHHTCCTTTTSBB.BS----HHHHHHHTTSE.EEEESSH.HHHHHHHHHHHHCSSSEE CS
                      TPP_enzyme_C  77 vvvlnNegygmtggq...qepfggkrksgpagkdlkpvdfaklaealGak.garvekadveeleealkealekkgpa 149
                                       v+++nN++yg+t+gq   + p g+k ks p +++l ++++  la a G + +ar  ++++++l e +++a++++g+a
  gi|518653100|ref|YP_008142620.1| 122 VLLYNNSVYGLTKGQaapTLPLGEKVKSLPRPNILGKINPITLAMASGYSfVARAFSSEIKQLSELIQRAIKHEGSA 198
                                       *****************999******************************999999********************* PP

                                       EEEE CS
                      TPP_enzyme_C 150 liev 153
                                       +iev
  gi|518653100|ref|YP_008142620.1| 199 VIEV 202
                                       **98 PP

>> PFO_beta_C  Pyruvate ferredoxin oxidoreductase beta subunit C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.3   0.3   9.1e-27   8.2e-23       1      63 [.     206     279 ..     206     281 .. 0.97

  Alignments for each domain:
  == domain 1  score: 80.3 bits;  conditional E-value: 9.1e-27
                                       XTTTXSSSXSXXXXX-EEEGGGS.T---EE.........HHHHHHHHT-----EEEEEEEE.TTS--HHHHHHT CS
                        PFO_beta_C   1 CvtFNkvnTfdwYkervykleed.gyDpsd.........lekAlekalewgdkiplGifYk.eekptyeerlee 63 
                                       C+t+N+vnT dwY++rvykle+d ++Dp +         +++ ++k++ewgd+ip+G+fY+ ++ p+y++rl+ 
  gi|518653100|ref|YP_008142620.1| 206 CPTYNDVNTLDWYRQRVYKLEDDkSWDPVVnskeedeakFDRGYRKSMEWGDHIPIGVFYEnNTIPSYTKRLAG 279
                                       **********************99**********************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2055.18
//
Query:       gi|518653101|ref|YP_008142621.1|  [L=120]
Description: succinate dehydrogenase, subunit D [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 896.84
//
Query:       gi|518653102|ref|YP_008142622.1|  [L=291]
Description: hypothetical protein FACI_IFERC00001G1741 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-31  107.0   0.6    5.9e-15   55.2   0.1    2.3  2  CCG       Cysteine-rich domain
  ------ inclusion threshold ------
      0.092   12.6   0.0       0.23   11.3   0.0    1.6  1  DUF2024   Domain of unknown function (DUF2024)


Domain annotation for each model (and alignments):
>> CCG  Cysteine-rich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1   6.6e-19   5.9e-15       1      83 [.       3      84 ..       3      86 .. 0.97
   2 !   50.1   0.0   2.6e-17   2.3e-13       1      85 []     149     239 ..     149     239 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 6.6e-19
                               CCG  1 vayfdgChllraaypevrkalkkllealgveleelekesCCGagggrsgkeelaealakrnvetaeetgadaivtacpg 79
                                      vay++gC + ++ +++v+ a++ + + l +el+e ++ +CCG g +   +e  + +l+ rn+e +e++g+d+++t+c+ 
  gi|518653102|ref|YP_008142622.1|  3 VAYYPGC-ASHGIAKDVDIATQLIAKDLDLELMEVDDWNCCGGGFMDDKNESSHTSLNLRNLEKVEKMGYDKMATPCSV 80
                                      89*****.99999*********************************99999999************************* PP

                               CCG 80 Cllq 83
                                      Cl++
  gi|518653102|ref|YP_008142622.1| 81 CLNS 84
                                      *987 PP

  == domain 2  score: 50.1 bits;  conditional E-value: 2.6e-17
                               CCG   1 vayfdgChllraa......ypevrkalkkllealgveleel.ekesCCGagggrsgkeelaealakrnvetaeetga 70 
                                       v  ++gC+llr++      + + ++++  l++a+g++ + + +k+ CCG++ + s+ + +a+++a++ +++a++ g 
  gi|518653102|ref|YP_008142622.1| 149 VGTYYGCQLLRPSnvmgfeSAFNPHSVMDLVAATGATPVAFpMKSACCGFPLMGSNPT-VALKMANNVLSSARDNGS 224
                                       5679***************9999*****************99***********66655.9***************** PP

                               CCG  71 daivtacpgCllqlk 85 
                                       +++v++c+ C+lql+
  gi|518653102|ref|YP_008142622.1| 225 EILVHPCSLCHLQLD 239
                                       *************96 PP

>> DUF2024  Domain of unknown function (DUF2024)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.6e-05      0.23      28      73 ..     204     251 ..     200     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.6e-05
                                       -HHHHHHHHHHHHHHHT---S---TTTEEEEEEE..E--HHHHHHHHH CS
                           DUF2024  28 deekaleyakeyLkskgeeeakvtskeCkfCHse..eaeeeveeaikk 73 
                                       + + al++a++ L+s   +++++  + C+ CH +   +++++++++k+
  gi|518653102|ref|YP_008142622.1| 204 NPTVALKMANNVLSSARDNGSEILVHPCSLCHLQldVTQTKIQRQFKQ 251
                                       56678999************************9854566677777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       499  (0.027832); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2085.99
//
Query:       gi|518653103|ref|YP_008142623.1|  [L=313]
Description: hypothetical protein FACI_IFERC00001G1742 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.2e-28   98.4   0.1    5.7e-28   97.1   0.1    1.7  1  Fer2_3      2Fe-2S iron-sulfur cluster binding domain
    2.1e-11   44.1   4.9    2.1e-11   44.1   4.9    2.1  2  Fer4_8      4Fe-4S dicluster domain
    1.1e-08   35.5  15.1    1.4e-07   32.0   6.7    2.6  3  Fer4_17     4Fe-4S dicluster domain
    2.3e-08   33.5  18.6    1.3e-05   24.8   2.9    3.0  3  Fer4        4Fe-4S binding domain
    2.5e-08   33.9  28.0    3.7e-06   26.9   9.4    2.8  4  Fer4_10     4Fe-4S dicluster domain
    3.7e-07   30.6  14.2    3.8e-07   30.6   9.4    2.9  3  Fer4_7      4Fe-4S dicluster domain
    2.6e-06   27.5  14.4     0.0026   17.9   0.3    3.2  3  Fer4_9      4Fe-4S dicluster domain
    5.7e-05   23.0  16.6     0.0067   16.5   1.5    3.3  3  Fer4_2      4Fe-4S binding domain
    0.00023   21.2  13.8      0.014   15.5   0.6    3.1  3  Fer4_21     4Fe-4S dicluster domain
    0.00069   20.3   3.5       0.19   12.5   0.5    2.9  2  Fer4_15     4Fe-4S single cluster domain
    0.00072   20.0   9.4      0.025   15.1   0.6    3.0  2  Fer4_13     4Fe-4S single cluster domain of Ferredoxin I
     0.0013   19.6  15.6     0.0028   18.5  10.7    3.5  4  Fer4_16     4Fe-4S double cluster binding domain
     0.0039   17.4  11.3        0.1   12.8   1.0    2.7  3  Fer4_18     4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.011   15.8   2.8      0.011   15.8   2.8    3.0  3  Fer4_6      4Fe-4S binding domain
      0.024   15.1  20.9      0.025   15.1   1.4    3.1  3  Fer4_4      4Fe-4S binding domain
      0.031   14.2   0.2      0.031   14.2   0.2    2.7  2  Fer2        2Fe-2S iron-sulfur cluster binding domain
        0.1   13.6   4.2        0.1   13.6   4.2    3.2  3  Fer4_3      4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.1   0.1   5.4e-31   5.7e-28       1     108 [.       7     111 ..       7     112 .. 0.95

  Alignments for each domain:
  == domain 1  score: 97.1 bits;  conditional E-value: 5.4e-31
                            Fer2_3   1 tlkvkRfdprrdrgkqkvqeyeveaeeedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatik 77 
                                       t++vk++++   ++ + +++y++ +++ +++ ++L +ik+e+dp+la+rasC+ ++CGsc+++inG p laC++   
  gi|518653103|ref|YP_008142623.1|   7 TVNVKKYNE---KDGAFWKSYKLSVDKYTQMTEVLRRIKSEQDPSLAYRASCHMAVCGSCSMKINGVPSLACRTIAL 80 
                                       578999999...5579***********************************************************99 PP

                            Fer2_3  78 dlakqkseieleplpkfpvirDLvvDideml 108
                                       + +++k+ei+le+++ +p +rDL++Did ++
  gi|518653103|ref|YP_008142623.1|  81 QATDEKNEINLESMDYYPGVRDLITDIDVFY 111
                                       9999999********************9886 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.1       2.2   2.3e+03      54      58 ..      60      64 ..      28      94 .. 0.76
   2 !   44.1   4.9     2e-14   2.1e-11       2      65 .]     147     218 ..     146     218 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 2.2
                            Fer4_8 54 cgaCt 58
                                      cg+C+
  gi|518653103|ref|YP_008142623.1| 60 CGSCS 64
                                      44443 PP

  == domain 2  score: 44.1 bits;  conditional E-value: 2e-14
                            Fer4_8   2 lekCieCgaCqsaCpvlrrtkkhlldargeaae....dvqeeqvlee.....eealwsCttcgaCtevCpvgi 65 
                                       +e+Ci Cg+C saCp++++  k+l  a + +      d +++ +++e      +++++Ct+c +C evCp+++
  gi|518653103|ref|YP_008142623.1| 147 FEECIYCGLCVSACPSVKEDEKFLGPAAHAKGFrfvdD-ERDTKRQErldilMDSAYRCTSCYMCYEVCPQDV 218
                                       789****************9999888877755577642.33222233577889*****************975 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.4   1.5e+03      48      54 ..      59      65 ..      23      85 .. 0.70
   2 !   16.1   1.2   1.2e-05     0.012      40      58 ..     138     162 ..     113     165 .. 0.68
   3 !   32.0   6.7   1.3e-10   1.4e-07       1      60 [.     149     218 ..     149     219 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.4
                           Fer4_17 48 eCgeCer 54
                                       Cg C++
  gi|518653103|ref|YP_008142623.1| 59 VCGSCSM 65
                                      3555554 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 1.2e-05
                           Fer4_17  40 e....e..kaslCieCgeCerkCPq 58 
                                            e  k+++Ci Cg+C+++CP+
  gi|518653103|ref|YP_008142623.1| 138 PedqtEvwKFEECIYCGLCVSACPS 162
                                       133333348899***********96 PP

  == domain 3  score: 32.0 bits;  conditional E-value: 1.3e-10
                           Fer4_17   1 rCiqCgyClpeCpsyeaydn..epkkllraakl.......glleeaeke.......ekaslCieCgeCerkCPqgl 60 
                                       +Ci Cg C+ +Cps ++ ++   p+  ++ +++       ++      +       + a +C++C +C ++CPq++
  gi|518653103|ref|YP_008142623.1| 149 ECIYCGLCVSACPSVKEDEKflGPAAHAKGFRFvdderdtKR------QerldilmDSAYRCTSCYMCYEVCPQDV 218
                                       6*************9997764457777777777765433211......123455558*****************98 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.6       2.2   2.3e+03      11      15 ..      60      64 ..      59      65 .. 0.84
   2 !   24.8   2.9   1.2e-08   1.3e-05       2      19 ..     144     161 ..     143     163 .. 0.90
   3 !   19.1   1.5     8e-07   0.00084       7      22 ..     203     218 ..     200     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 2.2
                                      -THHH CS
                              Fer4 11 CGaCv 15
                                      CG C 
  gi|518653103|ref|YP_008142623.1| 60 CGSCS 64
                                      ****6 PP

  == domain 2  score: 24.8 bits;  conditional E-value: 1.2e-08
                                       EEETTTSSS-THHHHHST CS
                              Fer4   2 videekCigCGaCvevCP 19 
                                       v+  e Ci+CG+Cv++CP
  gi|518653103|ref|YP_008142623.1| 144 VWKFEECIYCGLCVSACP 161
                                       57789************* PP

  == domain 3  score: 19.1 bits;  conditional E-value: 8e-07
                                       TSSS-THHHHHSTTTE CS
                              Fer4   7 kCigCGaCvevCPvgA 22 
                                       +C+ C  C+evCP ++
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQDV 218
                                       8************985 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       2.2   2.3e+03      47      51 ..      57      63 ..      39      92 .. 0.76
   2 !   16.5   2.0   6.7e-06     0.007      29      56 .]     134     161 ..     122     161 .. 0.79
   3 !   26.9   9.4   3.5e-09   3.7e-06       7      56 .]     148     215 ..     143     215 .. 0.83
   4 !   16.4   1.6   6.8e-06    0.0072       8      31 ..     203     226 ..     195     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.2
                           Fer4_10 47 g..cgaC 51
                                      +  cg+C
  gi|518653103|ref|YP_008142623.1| 57 MavCGSC 63
                                      4334444 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.7e-06
                           Fer4_10  29 kgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       +  + e++++  k e+C+ cg Cv+aCP
  gi|518653103|ref|YP_008142623.1| 134 QRMTPEDQTEVWKFEECIYCGLCVSACP 161
                                       4455566677779**************9 PP

  == domain 3  score: 26.9 bits;  conditional E-value: 3.5e-09
                           Fer4_10   7 dtCirCgkCvkaCPadl..................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                                       + Ci Cg Cv+aCP+                    +  + ++ +++ +   +  ++Ct c +C+e+CP
  gi|518653103|ref|YP_008142623.1| 148 EECIYCGLCVSACPSVKedekflgpaahakgfrfvDDERDTKRQERLDILMDSAYRCTSCYMCYEVCP 215
                                       68*************77*****************95555555555555555566*************9 PP

  == domain 4  score: 16.4 bits;  conditional E-value: 6.8e-06
                           Fer4_10   8 tCirCgkCvkaCPadltsvgakge 31 
                                       +C+ C  C ++CP+d++ v a+++
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQDVQPVIAIKK 226
                                       799999999999997743333333 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   1.2       5.6   5.9e+03      33      41 ..      55      63 ..      34      79 .. 0.66
   2 !   14.3   5.2   4.5e-05     0.048      27      50 ..     138     162 ..      59     164 .. 0.77
   3 !   30.6   9.4   3.6e-10   3.8e-07       2      52 .]     150     218 ..     149     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 5.6
                            Fer4_7 33 idpekClgC 41
                                       ++  C +C
  gi|518653103|ref|YP_008142623.1| 55 CHMAVCGSC 63
                                      444445444 PP

  == domain 2  score: 14.3 bits;  conditional E-value: 4.5e-05
                            Fer4_7  27 gt.ekveidpekClgCgaCvavCPt 50 
                                       +  ++ + + e+C++Cg Cv++CP+
  gi|518653103|ref|YP_008142623.1| 138 PEdQTEVWKFEECIYCGLCVSACPS 162
                                       222334557899***********96 PP

  == domain 3  score: 30.6 bits;  conditional E-value: 3.6e-10
                            Fer4_7   2 CigCgaCvaaC...............pvkaieldeeenekgtekveidpe...kClgCgaCvavCPtga 52 
                                       Ci Cg Cv+aC                 + + +d+e + k++e+++i ++   +C++C++C +vCP ++
  gi|518653103|ref|YP_008142623.1| 150 CIYCGLCVSACpsvkedekflgpaahAKGFRFVDDERDTKRQERLDILMDsayRCTSCYMCYEVCPQDV 218
                                       ***********6666666666654422333334445555677888887764457************875 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.5         1   1.1e+03      33      42 ..      49      63 ..      27      66 .. 0.61
   2 !    9.7   9.4   0.00088      0.92      33      48 ..     135     162 ..      53     164 .. 0.77
   3 !   17.9   0.3   2.5e-06    0.0026      33      49 ..     196     217 ..     174     221 .. 0.72

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 1
                            Fer4_9 33 e...eaCig..CgaC 42
                                           +C++  Cg+C
  gi|518653103|ref|YP_008142623.1| 49 LayrASCHMavCGSC 63
                                      044446855558888 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00088
                            Fer4_9  33 e............eaCigCgaCveaCpk 48 
                                                    e+Ci Cg Cv aCp+
  gi|518653103|ref|YP_008142623.1| 135 RmtpedqtevwkfEECIYCGLCVSACPS 162
                                       023334455666689************6 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 2.5e-06
                            Fer4_9  33 e.....eaCigCgaCveaCpkg 49 
                                              +C++C  C+e+Cp++
  gi|518653103|ref|YP_008142623.1| 196 IlmdsaYRCTSCYMCYEVCPQD 217
                                       0333446899999999999997 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   0.6       1.3   1.4e+03      13      17 ..      60      64 ..      50      66 .. 0.71
   2 !   16.5   1.5   6.4e-06    0.0067       8      21 ..     148     161 ..     144     162 .. 0.86
   3 !   15.4   1.4   1.4e-05     0.014       9      22 .]     203     216 ..     195     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.3
                            Fer4_2 13 CgaCv 17
                                      Cg+C 
  gi|518653103|ref|YP_008142623.1| 60 CGSCS 64
                                      89994 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 6.4e-06
                            Fer4_2   8 drCigCgaCvsaCP 21 
                                       + Ci Cg CvsaCP
  gi|518653103|ref|YP_008142623.1| 148 EECIYCGLCVSACP 161
                                       55************ PP

  == domain 3  score: 15.4 bits;  conditional E-value: 1.4e-05
                            Fer4_2   9 rCigCgaCvsaCPa 22 
                                       rC++C  C+ +CP+
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQ 216
                                       9************6 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   1.4       5.7     6e+03      11      16 ..      60      65 ..      53      93 .. 0.55
   2 !   15.5   0.6   1.3e-05     0.014      34      52 ..     142     161 ..     129     166 .. 0.70
   3 !   14.6   0.4   2.5e-05     0.026      39      53 ..     202     216 ..     185     224 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.7
                           Fer4_21 11 CgkCli 16
                                      Cg+C +
  gi|518653103|ref|YP_008142623.1| 60 CGSCSM 65
                                      333332 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 1.3e-05
                           Fer4_21  34 lkvv.edeCvGCnlCssvCP 52 
                                       ++v   +eC+ C lC+s CP
  gi|518653103|ref|YP_008142623.1| 142 TEVWkFEECIYCGLCVSACP 161
                                       44532578888888888888 PP

  == domain 3  score: 14.6 bits;  conditional E-value: 2.5e-05
                           Fer4_21  39 deCvGCnlCssvCPv 53 
                                        +C+ C +C++vCP 
  gi|518653103|ref|YP_008142623.1| 202 YRCTSCYMCYEVCPQ 216
                                       58************3 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.5   0.00018      0.19       6      30 ..     148     173 ..     147     195 .. 0.70
   2 !    7.8   0.1    0.0054       5.7       7      20 ..     203     216 ..     196     252 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00018
                           Fer4_15   6 daCigcglCvaeapevfelde.dgla 30 
                                       ++Ci cglCv ++p v e ++  g a
  gi|518653103|ref|YP_008142623.1| 148 EECIYCGLCVSACPSVKEDEKfLGPA 173
                                       58************887777633555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
                           Fer4_15   7 aCigcglCvaeape 20 
                                       +C++c +C++++p+
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQ 216
                                       8***********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 !   15.1   0.6   2.4e-05     0.025       4      19 ..     148     163 ..     147     171 .. 0.90
   2 !    7.7   2.5     0.005       5.3       5      18 ..     203     216 ..     200     217 .. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.4e-05
                           Fer4_13   4 dtCiacgaCvelaPdv 19 
                                       ++Ci cg+Cv+++P v
  gi|518653103|ref|YP_008142623.1| 148 EECIYCGLCVSACPSV 163
                                       79************98 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.005
                           Fer4_13   5 tCiacgaCvelaPd 18 
                                       +C++c  C+e++P+
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQ 216
                                       7************6 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.1       2.5   2.6e+03      53      61 ..      56      64 ..      18      66 .. 0.66
   2 !   12.5   2.6    0.0002      0.21      44      65 ..     140     161 ..      73     163 .. 0.76
   3 !   18.5  10.7   2.7e-06    0.0028       2      65 ..     150     215 ..     149     217 .. 0.60
   4 !   11.0   3.6   0.00062      0.65       1      33 [.     203     230 ..     203     258 .. 0.65

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 2.5
                           Fer4_16 53 aitgCdiCq 61
                                      +++ C+ C 
  gi|518653103|ref|YP_008142623.1| 56 HMAVCGSCS 64
                                      347788775 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.0002
                           Fer4_16  44 deekckkqeaitgCdiCqdvCP 65 
                                       d+ +  k e++++C+ C+ +CP
  gi|518653103|ref|YP_008142623.1| 140 DQTEVWKFEECIYCGLCVSACP 161
                                       3333336677777777777777 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.7e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeiearecisy.....ntaekkdlaedeekckkqeaitgCdiCqdvCP 65 
                                       C+ Cg C+++CP+   +ek    ++  +         + + k++ + d+  +++++++t C +C +vCP
  gi|518653103|ref|YP_008142623.1| 150 CIYCGLCVSACPSVKEDEKFLGPAAHAKG--FrfvddERDTKRQERLDIL-MDSAYRCTSCYMCYEVCP 215
                                       ************97655552222222222..1334323333333333333.335799************ PP

  == domain 4  score: 11.0 bits;  conditional E-value: 0.00062
                           Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy 33 
                                       rC++C  C evCP+++     +++i+++++++y
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQDV-----QPVIAIKKTKNY 230
                                       6************875.....234455555555 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       8.5     9e+03      65      68 ..      56      59 ..      27      78 .. 0.56
   2 !   12.8   1.0   9.6e-05       0.1      46      73 ..     135     162 ..     109     168 .. 0.74
   3 !   11.5   0.7   0.00025      0.27      34      75 ..     178     218 ..     162     227 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 8.5
                           Fer4_18 65 escv 68
                                      ++ v
  gi|518653103|ref|YP_008142623.1| 56 HMAV 59
                                      2222 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 9.6e-05
                           Fer4_18  46 alkekeerkekgagdcidcescvkvcPt 73 
                                        ++ +++++  +  +ci c+ cv+ cP 
  gi|518653103|ref|YP_008142623.1| 135 RMTPEDQTEVWKFEECIYCGLCVSACPS 162
                                       4445556666778889999999999985 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 0.00025
                           Fer4_18  34 GekiagrkkekkalkekeerkekgagdcidcescvkvcPtgi 75 
                                       G + +++++ +k +++ +    ++a  c++c +c +vcP ++
  gi|518653103|ref|YP_008142623.1| 178 GFRFVDDERDTKRQERLDI-LMDSAYRCTSCYMCYEVCPQDV 218
                                       5555666666666655555.4677889************987 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.9       3.3   3.5e+03       8      15 ..      54      63 ..      52      66 .. 0.64
   2 ?    9.9   3.5   0.00077      0.81       9      20 ..     150     161 ..     148     166 .. 0.92
   3 ?   15.8   2.8     1e-05     0.011       8      20 ..     203     215 ..     201     224 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.3
                            Fer4_6  8 kCi..gCgdC 15
                                      +C    Cg C
  gi|518653103|ref|YP_008142623.1| 54 SCHmaVCGSC 63
                                      6763348888 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00077
                            Fer4_6   9 CigCgdCvrvCP 20 
                                       Ci Cg Cv++CP
  gi|518653103|ref|YP_008142623.1| 150 CIYCGLCVSACP 161
                                       999********* PP

  == domain 3  score: 15.8 bits;  conditional E-value: 1e-05
                            Fer4_6   8 kCigCgdCvrvCP 20 
                                       +C++C+ C+ vCP
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCP 215
                                       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 ?   -2.1   1.2       7.3   7.7e+03       7      10 ..      60      63 ..      53      64 .. 0.80
   2 ?   15.1   1.4   2.4e-05     0.025       2      15 ..     148     161 ..     147     171 .. 0.91
   3 ?   11.6   3.9   0.00031      0.33       3      16 ..     203     216 ..     201     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 7.3
                            Fer4_4  7 CgsC 10
                                      CgsC
  gi|518653103|ref|YP_008142623.1| 60 CGSC 63
                                      8888 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 2.4e-05
                            Fer4_4   2 erCigCgsCvaaCP 15 
                                       e Ci Cg Cv+aCP
  gi|518653103|ref|YP_008142623.1| 148 EECIYCGLCVSACP 161
                                       78************ PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00031
                            Fer4_4   3 rCigCgsCvaaCPq 16 
                                       rC+ C  C+ +CPq
  gi|518653103|ref|YP_008142623.1| 203 RCTSCYMCYEVCPQ 216
                                       9************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 ?   14.2   0.2     3e-05     0.031      26      77 ..      46      79 ..      27      87 .. 0.83
   2 ?   -1.0   0.6       1.6   1.7e+03      28      51 ..     197     217 ..     175     244 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 3e-05
                                      TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSEE CS
                              Fer2 26 nggidipysCggggCgtClvevlegevqsdetelegeeldegklrlaCqtiv 77
                                      ++ ++ ++sC+++ Cg+C  +++            g +       laC+ti+
  gi|518653103|ref|YP_008142623.1| 46 DPSLAYRASCHMAVCGSCSMKIN------------GVP-----S-LACRTIA 79
                                      55677889*************99............777.....3.8888775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.6
                                       TTTSTTSSSSSSSSTTEEEEEESC CS
                              Fer2  28 gidipysCggggCgtClvevlege 51 
                                        +d  y C   +C +C  ev   +
  gi|518653103|ref|YP_008142623.1| 197 LMDSAYRCT--SCYMCY-EVCPQD 217
                                       555666666..677776.565555 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   2.8       7.6     8e+03       1       7 [.      55      63 ..      55      66 .. 0.87
   2 ?   13.6   4.2   9.8e-05       0.1       1      13 [.     150     162 ..     150     164 .. 0.93
   3 ?    9.3   4.8    0.0023       2.4       1      14 [.     204     217 ..     204     218 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 7.6
                            Fer4_3  1 Ctg..CgaC 7 
                                      C++  Cg C
  gi|518653103|ref|YP_008142623.1| 55 CHMavCGSC 63
                                      988999999 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 9.8e-05
                            Fer4_3   1 CtgCgaCvevCPv 13 
                                       C+ Cg+Cv +CP+
  gi|518653103|ref|YP_008142623.1| 150 CIYCGLCVSACPS 162
                                       9***********5 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0023
                            Fer4_3   1 CtgCgaCvevCPvg 14 
                                       Ct C+ C evCP +
  gi|518653103|ref|YP_008142623.1| 204 CTSCYMCYEVCPQD 217
                                       ************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.52u 0.28s 00:00:00.80 Elapsed: 00:00:00.45
# Mc/sec: 2110.51
//
Query:       gi|518653104|ref|YP_008142624.1|  [L=564]
Description: hypothetical protein FACI_IFERC00001G1743 [Ferroplasma acidarmanus fer1]
Scores for complete 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-95  319.2   0.2    6.2e-95  318.7   0.2    1.2  1  FAD_binding_2   FAD binding domain
    1.7e-44  150.9   0.3    2.5e-44  150.3   0.3    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
     0.0013   18.4   0.5     0.0023   17.6   0.0    1.7  2  DAO             FAD dependent oxidoreductase
     0.0023   17.2   0.5      0.033   13.4   0.2    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0036   16.6   0.4     0.0059   15.9   0.4    1.3  1  FAD_binding_3   FAD binding domain
     0.0039   16.5   0.2       0.16   11.1   0.1    3.0  3  Thi4            Thi4 family
  ------ inclusion threshold ------
       0.01   14.6   1.9       0.03   13.0   1.7    1.8  2  HI0933_like     HI0933-like protein
       0.83    8.7   3.0        1.6    7.7   3.0    1.4  1  GIDA            Glucose inhibited division protein A
        2.7    7.3   5.3        4.4    6.5   4.4    1.7  2  FAD_oxidored    FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  318.7   0.2   3.1e-98   6.2e-95       1     417 []       7     386 ..       7     386 .. 0.98

  Alignments for each domain:
  == domain 1  score: 318.7 bits;  conditional E-value: 3.1e-98
                                       SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S CS
                     FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldela 77 
                                       D+++ G+GlAGL+AA   a  G +vavv+k++++++++ +++Ggi+a+  +++  +  +d+p+ + +d +k++d+l 
  gi|518653104|ref|YP_008142624.1|   7 DAVILGGGLAGLMAANMVAAGGFTVAVVSKVFPTRSHSSAAEGGIAAYIMGNS--D-PNDDPDFMSYDEVKGGDYLV 80 
                                       89***********************************************8888..5.5599**************** PP

                                       -HHHHHHHHHTHHHHHHHHHHTT----BCCTSSB-EEE-TT-SSTEEEE-.STT-......HHHHHHHHHHHHHHTC CS
                     FAD_binding_2  78 dqplveafveaapeavdeLeelgvpfsrtedgpvdvrelGglsatartlhdaadarretlvtghallarlvesarka 154
                                       dq+++e++ ++++e v+ L ++g+pf+r++dg++++r +Gg++ + rt +  ad+      tg all++l+e+    
  gi|518653104|ref|YP_008142624.1|  81 DQDAAELLSKKSGEIVNLLDAWGAPFNRQPDGRIALRYFGGQTYP-RTRF-IADK------TGMALLHTLFEHSTGF 149
                                       *********************************************.****.****......*************998 PP

                                       T.EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHH CS
                     FAD_binding_2 155 g.vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgrallkellgaaaeaettnapavtGdgl 230
                                       + +df+++++++++ +e++ v+G v++++++     ++++a+++a+gG+g            ++++tn  ++tGdg+
  gi|518653104|ref|YP_008142624.1| 150 KnIDFYNEYYVLDIAREGDSVNGLVAMEMKTLDPIYLKSRALLIASGGIGM----------MYKHSTNSYINTGDGH 216
                                       8*************************************************9..........9*************** PP

                                       HHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTSSBTH.......GGGS-HHHHHHHHH CS
                     FAD_binding_2 231 alalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdGrrFm.......nelasrdvvsrail 300
                                       ++alr+g+al+d  +e+vqfhPt+l+    +s iLi+ea+r eG+il +++G+rFm        +la+rd+vsr++ 
  gi|518653104|ref|YP_008142624.1| 217 GIALRSGVALKD--PEFVQFHPTGLY----PSDILISEAARAEGAILKNNKGERFMaryaphkFDLAPRDIVSRSMA 287
                                       ************..************....*********************************************** PP

                                       .HHHHTTTS..CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEEEEEEES-E CS
                     FAD_binding_2 301 ekeiaeggs..eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvpaqhytmgG 375
                                         ei+eg++  + +  ld++h l+++ + ++l   +++a+n+ +      +d+a+++ip       v+paqhy+mgG
  gi|518653104|ref|YP_008142624.1| 288 -IEIREGRGfeGGYLGLDLRH-LGKKYILERLTLAYDAAKNFSG------VDAAEEMIP-------VRPAQHYFMGG 349
                                       .********9988999*****.**********************......*********.......*********** PP

                                       EEBETTSBESTTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
                     FAD_binding_2 376 vetdengrvldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                                       + +d +g       + ++G +AaGe+a+++vhganrlg+nsl
  gi|518653104|ref|YP_008142624.1| 350 IDVDITGTN-----HDLKGVFAAGEAACVSVHGANRLGSNSL 386
                                       *******98.....**************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.3   0.3   1.3e-47   2.5e-44       2     128 .]     440     564 .]     439     564 .] 0.97

  Alignments for each domain:
  == domain 1  score: 150.3 bits;  conditional E-value: 1.3e-47
                                       HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-B CS
                    Succ_DH_flav_C   2 keLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESr 78 
                                       +eL++im+++vg+fR++++L++a++++k+lr r + + vtdks+ +N+el +ale +n++++A a+a++Al+R+E r
  gi|518653104|ref|YP_008142624.1| 440 EELRDIMWDNVGIFRDNDKLAQAISKIKDLRTRSRSMYVTDKSTNYNTELFNALETRNMIDVAYAMATGALNRTETR 516
                                       69*************************************************************************** PP

                                       TTBEBTTS-SEETTT-SEEEEE...TT-SS-EEEEEE--GGG--S---SS CS
                    Succ_DH_flav_C  79 GaHaredfperdDenwlkhtlasldaakeeveleyepveletlkpkeRsY 128
                                       GaH+r+dfper+D++w+kht+++l    +e++++y+pv+++  kp+ R+Y
  gi|518653104|ref|YP_008142624.1| 517 GAHFRDDFPERNDKDWMKHTITYLA--GDEIKISYKPVTYTRWKPEPRVY 564
                                       **********************766..569******************99 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   1.2e-06    0.0023       1      49 [.       7      58 ..       7     132 .. 0.81
   2 ?   -3.2   0.1       2.4   4.8e+03     318     341 ..     200     220 ..     187     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 1.2e-06
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSS..S CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsgl..r 49
                                      d vi GGG +Gl +A   a+ g  V+++ k  ++ +  S+++ g +++++   
  gi|518653104|ref|YP_008142624.1|  7 DAVILGGGLAGLMAANMVAAGGftVAVVSKV-FPTRSHSSAAEGGIAAYImgN 58
                                      78****************9988********9.777777777777777755441 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 2.4
                                       EEEEEETEEEEEEEEECTTTHHHH CS
                               DAO 318 ligetpgvkglylatGhsghGltl 341
                                       ++ ++  + + y++tG  ghG+ l
  gi|518653104|ref|YP_008142624.1| 200 MMYKH--STNSYINTGD-GHGIAL 220
                                       44443..6799*****9.898865 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.2   1.6e-05     0.033       1      37 [.       6      40 ..       6      69 .. 0.86
   2 ?    1.5   0.0     0.069   1.4e+02     255     278 ..     347     371 ..     315     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.6e-05
                                      CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtcln 37
                                      +d v++GgG AGl aa  +a+ g+ v++v   + +++
  gi|518653104|ref|YP_008142624.1|  6 YDAVILGGGLAGLMAANMVAAGGFTVAVV--SKVFPT 40
                                      588**************************..455554 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.069
                                       TTEEE--TTSBES.STTEEE-GGGC CS
                                       xxxxxxxxxxxxx.xxxxxxxxxxx RF
                       Pyr_redox_2 255 rggivvdeflrtn.vpgiyaiGDva 278
                                        ggi vd ++     +g++a+G  a
  gi|518653104|ref|YP_008142624.1| 347 MGGIDVDITGTNHdLKGVFAAGEAA 371
                                       59999**99954469*******998 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.4     3e-06    0.0059       2      40 ..       6      44 ..       5      49 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 3e-06
                                      EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSS CS
                     FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlp 40
                                      +d +I G+G+aGlm+a++ +  G  v +v k   t  ++
  gi|518653104|ref|YP_008142624.1|  6 YDAVILGGGLAGLMAANMVAAGGFTVAVVSKVFPTRSHS 44
                                      7899**************************987666655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.1   8.2e-05      0.16      16      50 ..       4      37 ..       1      99 [. 0.76
   2 ?   -0.4   0.0      0.27   5.5e+02     102     168 ..     141     197 ..     113     209 .. 0.73
   3 ?    0.7   0.0      0.13   2.6e+02     205     233 ..     354     383 ..     346     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 8.2e-05
                                      TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailers 50
                                       e D vi G+G +GL aa ++a   ++ va++ + 
  gi|518653104|ref|YP_008142624.1|  4 KEYDAVILGGGLAGLMAANMVAAG-GFTVAVVSKV 37
                                      588*******************99.****999765 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                                       HHHHHHHTSTTEEEEESEEEEEEEEETBTEEEEEEEEEHHHHTCTTTSS.-B-EEEEEEEEEE--GS CS
                              Thi4 102 tllskvlqlanvkllnavaveDlivregegvaGvvinwtlvelahdtqscvDPlvirakvvvdatGh 168
                                       tl  +     n+  +n   v D i reg++v+G+v    ++e++      +DP  +++++++ a+G 
  gi|518653104|ref|YP_008142624.1| 141 TLFEHSTGFKNIDFYNEYYVLD-IAREGDSVNGLV----AMEMKT-----LDPIYLKSRALLIASGG 197
                                       5555556666777778888888.568888888887....455555.....88888888888777775 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.13
                                       HHHECEEETTEEE-THHH.HHHHT-EB--S CS
                              Thi4 205 vkktrevvpnlyvaGmev.aevdganRmGp 233
                                       + +t++ ++++++aG ++   v+ganR+G+
  gi|518653104|ref|YP_008142624.1| 354 ITGTNHDLKGVFAAGEAAcVSVHGANRLGS 383
                                       567888999******7652689******96 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.7   1.5e-05      0.03       2      31 ..       7      36 ..       6      40 .. 0.92
   2 ?   -1.8   0.0      0.48   9.6e+02     124     175 ..     152     208 ..     129     225 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.5e-05
                                      SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
                       HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllek 31
                                      d +++GgG AGlmaA  +a+ g  V+++ k
  gi|518653104|ref|YP_008142624.1|  7 DAVILGGGLAGLMAANMVAAGGFTVAVVSK 36
                                      89***********************99865 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.48
                                       -EEE-S--EEEEECETTE.EEEEE......TTEEEEESEEEE----SS-GGGT--SH CS
                       HI0933_like 124 vklrletevksvekeedgkfrvkt.k....seeeleadklvlAtGGlSiPklGstgk 175
                                       ++++ e  v ++++e d++  + + +    +   l++++l++A+GG  +    st++
  gi|518653104|ref|YP_008142624.1| 152 IDFYNEYYVLDIAREGDSVNGLVAmEmktlDPIYLKSRALLIASGGIGMMYKHSTNS 208
                                       5555555666665555544332221111114446789999*****988766555555 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   3.0   0.00079       1.6       2      29 ..       8      35 ..       7      56 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00079
                                      EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA  2 viViGgGhAGceAAlaaarlGakvlLit 29
                                       +++GgG+AG+ AA  +a  G+ v+ + 
  gi|518653104|ref|YP_008142624.1|  8 AVILGGGLAGLMAANMVAAGGFTVAVVS 35
                                      689*********************9983 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   4.4    0.0022       4.4       1      30 [.       7      36 ..       7      38 .. 0.94
   2 ?   -2.2   0.0      0.99     2e+03     273     315 ..     259     300 ..     236     301 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0022
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLvee 30
                                      D v+ GGg+aG++AA   a  G +v++v++
  gi|518653104|ref|YP_008142624.1|  7 DAVILGGGLAGLMAANMVAAGGFTVAVVSK 36
                                      779***********************9975 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.99
                      FAD_oxidored 273 areltqgllkylqteewgfekaeleglapqlyvREsRRivGdy 315
                                        ++  +++++y + ++ +++   +++  + + +RE R ++G y
  gi|518653104|ref|YP_008142624.1| 259 NNKGERFMARYAP-HKFDLAPRDIVSRSMAIEIREGRGFEGGY 300
                                       5556678888887.788999999999999999*****999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (564 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.46
# Mc/sec: 3689.04
//
Query:       gi|518653105|ref|YP_008142625.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G1744 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.1e-39  134.3   0.5    5.1e-39  133.6   0.5    1.3  1  Ldh_1_N        lactate/malate dehydrogenase, NAD binding doma
    4.5e-25   88.5   0.0    8.2e-25   87.7   0.0    1.4  1  Ldh_1_C        lactate/malate dehydrogenase, alpha/beta C-ter
    5.5e-05   22.8   0.1     0.0003   20.4   0.0    2.0  2  Glyco_hydro_4  Family 4 glycosyl hydrolase
     0.0012   19.0   0.0     0.0037   17.5   0.0    1.8  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
     0.0045   16.9   0.9      0.045   13.6   0.2    2.5  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.037   14.1   0.8      0.081   13.0   0.3    1.9  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.042   13.6   0.0      0.079   12.7   0.0    1.4  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
      0.065   12.6   0.3       0.11   11.9   0.3    1.3  1  ThiF           ThiF family
      0.092   12.9   0.3        6.8    6.8   0.0    2.3  2  NAD_binding_2  NAD binding domain of 6-phosphogluconate dehyd


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.5   2.6e-42   5.1e-39       2     141 .]       4     147 ..       3     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 2.6e-42
                                       EEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE......SSGGGGTTESE CS
                           Ldh_1_N   2 kvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse......keeealkdadv 72 
                                       k++++Ga G++G+s+a  la k++ad + ++Di++ ++eG+ald+++++    +++k ++      ke++ lk++dv
  gi|518653105|ref|YP_008142625.1|   4 KISIIGA-GAVGASVAQVLAIKNIAD-ISIFDIVEGVAEGKALDIQEGAPHFGFDCKLQGfctqdpKEYANLKGSDV 78 
                                       9******.******************.*******************99998877776543322257899******** PP

                                       EEE--S-SS-TTTTHHHHHHHHHHHHHHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
                           Ldh_1_N  73 vvitagvprkpGetRddLlkvNakIvkeiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                                       +v+tag  r+pG++RddLl +N++I+k+++e+i+k++p+ i++ v+NP+di++++l+kasg++++r+ig
  gi|518653105|ref|YP_008142625.1|  79 IVVTAGLARRPGMSRDDLLVKNIGIMKDVGEQIKKYSPDSIIVAVTNPADIMAYALQKASGISPERIIG 147
                                       *******************************************************************98 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   4.1e-28   8.2e-25       2     161 ..     151     313 ..     150     318 .. 0.92

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 4.1e-28
                                       HHHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHH CS
                           Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdev 68 
                                       +LD+ R++tflae  +v+ r+v++ ViGgH++          v +ip+      ++ lse++++e+i+r+++gg e+
  gi|518653105|ref|YP_008142625.1| 151 SLDSSRFRTFLAEALNVSVRDVNAFVIGGHGDdmvpfihyssVSGIPI------SDLLSEEKIQEIIKRTRFGGGEI 221
                                       69******************************9998866666666666......77899****************** PP

                                       HHHHTTSSSS-HHHHHHHHHHHHHHHTTHTEEEEEEEEEESC.CCECCSSEEEEEEEEEEETTEEEEE-------HH CS
                           Ldh_1_C  69 vkakkGagsatlsmAvAgakfveallrdtkeilsagvyldge.vglkdqeieyfsvPvvlgknGvekvleilklndf 144
                                        +  k  g a+++   ++  +ve++++d +++++ ++yl+g+  +  + +  +++vP+ +gknGve++++ lk ++ 
  gi|518653105|ref|YP_008142625.1| 222 LNLYK-TGTAFYAPSISISVMVESVVNDQHRVIPCAAYLTGKhAENYKVSNAFIGVPIKIGKNGVEEIYD-LKFSEA 296
                                       **987.8**********************************96666666889******************.****** PP

                                       HHHHHHHHHHHHHHHHH CS
                           Ldh_1_C 145 eeekleksvkeLkkeie 161
                                         ++  ksv+  kk+ +
  gi|518653105|ref|YP_008142625.1| 297 DAKEWMKSVESVKKNNK 313
                                       *************9976 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.38   7.6e+02       1      24 [.       4      27 ..       4      50 .. 0.72
   2 !   20.4   0.0   1.5e-07    0.0003     119     160 ..      99     140 ..      96     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.38
                                      EEEEETTTSSSHHHHHHHHHHTTT CS
                     Glyco_hydro_4  1 kiviiGgGStifaklllgdlkkte 24
                                      ki iiG+G    +   +  +k+  
  gi|518653105|ref|YP_008142625.1|  4 KISIIGAGAVGASVAQVLAIKNIA 27
                                      899999998776655555555544 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 1.5e-07
                                       HHHHHHHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTT CS
                     Glyco_hydro_4 119 rtipvlleIakdieelcPdawvlnytNPaavvteallrlvpn 160
                                       ++i+++ ++ ++i++++Pd+ ++  tNPa +++ al + ++ 
  gi|518653105|ref|YP_008142625.1|  99 KNIGIMKDVGEQIKKYSPDSIIVAVTNPADIMAYALQKASGI 140
                                       68999*******************************998653 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 !   17.5   0.0   1.8e-06    0.0037       1      55 [.       7      65 ..       7      75 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
                                      EE--SHHHHHHHHHHHCCTE.EEEEE-SSSSSS.GGG-EECE..TTCEECTS---EEET CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagf.dvlllekrdrlG.Graasyev..pgvrvdygahifhgs 55
                                      I+GaG+ G++ A+ La +++ d+ +++  +++  G+a +++   p + +d+  + f++ 
  gi|518653105|ref|YP_008142625.1|  7 IIGAGAVGASVAQVLAIKNIaDISIFDIVEGVAeGKALDIQEgaPHFGFDCKLQGFCTQ 65
                                      9***************776659*********999******9966669999999999884 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 !   13.6   0.2   2.3e-05     0.045       1      38 [.       4      42 ..       4      62 .. 0.83
   2 ?    0.6   0.0      0.22   4.4e+02      88     134 ..      99     147 ..      95     148 .. 0.80
   3 ?   -3.6   0.0       4.5   8.9e+03      54      76 ..     292     314 ..     283     318 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
                                      EEEEE--SCCHHHHHHHHHHTT-.EEEEE-S-HHHHHHH CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagl.eVvlvdiseealeka 38
                                      k+ +iGaG +Ga++a+v+a +++ ++ ++di e  +e  
  gi|518653105|ref|YP_008142625.1|  4 KISIIGAGAVGASVAQVLAIKNIaDISIFDIVEGVAEGK 42
                                      689****************99753799999988777655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.22
                                       SSHHHHHHHHHHHHCCS-TTSEEE.E--SSS-HHHHCCCSS.SGGGEEE CS
                           3HCDH_N  88 EnlelKrkvfaelekiakpdaila.snTSslsiselaealk.rpervig 134
                                        n+ + ++v ++++k+ +++ i+a +n   ++  +l++a   +per+ig
  gi|518653105|ref|YP_008142625.1|  99 KNIGIMKDVGEQIKKYSPDSIIVAvTNPADIMAYALQKASGiSPERIIG 147
                                       5677778999999999999998876888999999999988658888887 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 4.5
                                       SS-HHHHCCCHHCEEEES-HHHH CS
                           3HCDH_N  54 klkeeeveaalarisfttdleea 76 
                                       k++e+++++ ++ ++  ++ +++
  gi|518653105|ref|YP_008142625.1| 292 KFSEADAKEWMKSVESVKKNNKL 314
                                       45566666666666665555554 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   4.1e-05     0.081      12      42 ..       2      32 ..       1      36 [. 0.94
   2 ?   -3.7   0.0       5.7   1.1e+04     104     117 ..     116     129 ..     102     134 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
                                      T-EEEEES-SHHHHHHHHHHHCCT-CEEEEE CS
                      Shikimate_DH 12 ekkvlliGaGemaelvakhLlakgvkkvvva 42
                                      +kk+ +iGaG ++  va+ L+ k++ ++ ++
  gi|518653105|ref|YP_008142625.1|  2 DKKISIIGAGAVGASVAQVLAIKNIADISIF 32
                                      699************************9996 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 5.7
                                       ..EEEEE--SS-SB CS
                      Shikimate_DH 104 kplllvDiavPRdv 117
                                          ++v +++P d+
  gi|518653105|ref|YP_008142625.1| 116 PDSIIVAVTNPADI 129
                                       33467777777777 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.9e-05     0.079     140     178 ..     132     170 ..     118     179 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.9e-05
                            FGGY_C 140 ealekdsgkpldrlavdGGgskndllmqllAdilgvpVe 178
                                        al+k sg+ ++r++  GG   +  ++ +lA++l+v V+
  gi|518653105|ref|YP_008142625.1| 132 YALQKASGISPERIIGLGGSLDSSRFRTFLAEALNVSVR 170
                                       589999*****************************9986 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.3   5.3e-05      0.11      18      49 ..       2      33 ..       1      35 [. 0.93

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.3e-05
                                      TSEEEEE--SHHHHHHHHHHHHHTTTEEEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              ThiF 18 dskvllvGaGglGsellknLalsGvgkltlvD 49
                                      d+k+ ++GaG++G  +++ La   +  + ++D
  gi|518653105|ref|YP_008142625.1|  2 DKKISIIGAGAVGASVAQVLAIKNIADISIFD 33
                                      6799******************9999999998 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.029        57       1      32 [.       4      36 ..       4      49 .. 0.83
   2 ?    6.8   0.0    0.0034       6.8      36     120 ..      94     180 ..      73     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.029
                                      EEEEE--SHHHHHHHHHH.HHTT-EEEEE-SSH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnl.lkagykvavynrtk 32
                                      ki +iG G  G++ a+ l +k+  ++++++  +
  gi|518653105|ref|YP_008142625.1|  4 KISIIGAGAVGASVAQVLaIKNIADISIFDIVE 36
                                      699*************99447778899998765 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0034
                                       HHHHHTTEEE-SSHHHHHHHC..SEEEE-SSSHHHHHHHHHSHCCC--TT-EEEE-S---HHHHHHHHHHHHHTT-E CS
                     NAD_binding_2  36 eelvaegakaaesieelvasl..dvvitmvkagkavdeviegllealkkgdilidgstsspedtrelakelkekglk 110
                                       ++l+ +++ +++++ e +++   d +i+ v++ +++ +   + ++ +++++i+  g++ + +  r + +e+ +  ++
  gi|518653105|ref|YP_008142625.1|  94 DDLLVKNIGIMKDVGEQIKKYspDSIIVAVTNPADIMAYALQKASGISPERIIGLGGSLDSSRFRTFLAEALNVSVR 170
                                       56667778889999999999999***************************************999999999999999 PP

                                       EEEEEEESHH CS
                     NAD_binding_2 111 fldaPVSGGe 120
                                        ++a V GG 
  gi|518653105|ref|YP_008142625.1| 171 DVNAFVIGGH 180
                                       9999888885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.46
# Mc/sec: 2098.59
//
Query:       gi|518653106|ref|YP_008142626.1|  [L=330]
Description: hypothetical protein FACI_IFERC00001G1745 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-94  313.7   1.6    1.8e-91  305.5   1.3    2.1  2  SOR_SNZ       SOR/SNZ family
    6.6e-12   45.3   2.0    1.5e-08   34.3   0.0    2.5  2  ThiG          Thiazole biosynthesis protein ThiG
    3.6e-05   23.5   0.3    9.3e-05   22.1   0.0    1.8  2  OMPdecase     Orotidine 5'-phosphate decarboxylase / HUMPS fa
    0.00028   20.1   0.0       0.03   13.4   0.0    2.3  2  Dus           Dihydrouridine synthase (Dus)
     0.0015   17.8   0.1      0.061   12.5   0.0    2.2  2  IGPS          Indole-3-glycerol phosphate synthase
     0.0017   17.6   0.4      0.014   14.5   0.0    2.5  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
       0.01   14.9   0.5      0.026   13.5   0.0    1.7  2  IMPDH         IMP dehydrogenase / GMP reductase domain
      0.015   14.7   0.4       0.26   10.6   0.0    2.3  2  NMO           Nitronate monooxygenase
      0.038   13.0   0.0      0.071   12.1   0.0    1.5  1  FMN_dh        FMN-dependent dehydrogenase
      0.044   13.2   0.2       0.45    9.9   0.0    2.5  2  His_biosynth  Histidine biosynthesis protein
       0.11   12.6   0.0       0.21   11.6   0.0    1.4  1  TetR_C_27     Tetracyclin repressor-like, C-terminal domain


Domain annotation for each model (and alignments):
>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.5   1.3   1.1e-94   1.8e-91       3     194 ..      13     204 ..      11     210 .. 0.98
   2 !    6.5   0.0    0.0039       6.4     186     207 .]     233     254 ..     218     254 .. 0.86

  Alignments for each domain:
  == domain 1  score: 305.5 bits;  conditional E-value: 1.1e-94
                                       HHHHHHHHTTTSSEEEEESSHHHHHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
                           SOR_SNZ   3 kvkaglaemlkgGvimdvvnaeqakiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                                        +k+g+a+m kgGv+mdv+naeqakiae+aGav+vmalervp+dir++ggvarmsdp ++kei ++vsipvmakvri
  gi|518653106|ref|YP_008142626.1|  13 LLKRGFAKMTKGGVVMDVTNAEQAKIAEKAGAVSVMALERVPSDIRAQGGVARMSDPLKVKEILDSVSIPVMAKVRI 89 
                                       589************************************************************************** PP

                                       T-HHHHHHHHHTT-SEEEEETTS--S-SS----GGG-SS-EEEEESSHHHHHHHHHHT-SEEEEES-TTS--THHHH CS
                           SOR_SNZ  80 GhfveaqilealgvdyiDesevltpadeeahidkkkfkvpfvcGarnlgealrriaeGaamirtkGeagtGdvveav 156
                                       Gh+ ea ile+lgvd++Desevltpad  +hi+kk +kvp+vcGar + ea+rri eGaamirtkGeagtG+++eav
  gi|518653106|ref|YP_008142626.1|  90 GHLSEASILESLGVDMLDESEVLTPADPFYHINKKMYKVPVVCGARTFPEAVRRIFEGAAMIRTKGEAGTGNIIEAV 166
                                       ***************************************************************************** PP

                                       HHHHHHHHHHHHHTTS-HHHHHHHHHHHHGGGHHHHHH CS
                           SOR_SNZ 157 rhvrkikeeirklkslseeelvalakelkaplelvkev 194
                                       rh+r++++ i  l+s++++e++a+a++++ ++  ++++
  gi|518653106|ref|YP_008142626.1| 167 RHIRTVNDGIYILNSITSDEMYAVAENISKSYTTLRNL 204
                                       ******************************99988876 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0039
                                       GGGHHHHHHHHHTTS-S---T. CS
                           SOR_SNZ 186 aplelvkevaelgrlpvvnfaa 207
                                         ++++ke+++l+rlp vnfaa
  gi|518653106|ref|YP_008142626.1| 233 QIYKVLKEIKHLKRLPLVNFAA 254
                                       55899***************98 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.4   0.00029      0.47     130     200 ..      26     105 ..       4     137 .. 0.71
   2 !   34.3   0.0   9.1e-12   1.5e-08     167     225 ..     238     298 ..     229     303 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00029
                                       E-S-HHH...HHHHHHTT-SEBEEB...SSSTTS----S...-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT CS
                              ThiG 130 vsdDlvl...arrleevGcaavmPl...aapiGsglGll...nkealkiiieeakvPvivDAGigspsdaaqamelG 197
                                       v  D+     a+  e++G+ +vm l    + i +  G++   ++ ++k i++++++Pv+    ig+ s+a     lG
  gi|518653106|ref|YP_008142626.1|  26 VVMDVTNaeqAKIAEKAGAVSVMALervPSDIRAQGGVArmsDPLKVKEILDSVSIPVMAKVRIGHLSEASILESLG 102
                                       33444430005556789999999873335788888776511167899************************999999 PP

                                       -SE CS
                              ThiG 198 ada 200
                                       +d 
  gi|518653106|ref|YP_008142626.1| 103 VDM 105
                                       994 PP

  == domain 2  score: 34.3 bits;  conditional E-value: 9.1e-12
                                       HHHHHHH-SS-BEEES..---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHHHHHHHHHHH CS
                              ThiG 167 lkiiieeakvPvivDA..GigspsdaaqamelGadavllntavaeakdpvamArafklave 225
                                       lk i +  ++P++  A  Gi +p daa  m++G+d+v++ + + +++dp +mA+a+  a+e
  gi|518653106|ref|YP_008142626.1| 238 LKEIKHLKRLPLVNFAagGIATPADAALMMKMGMDGVFVGSGIFKSRDPQKMAEAIVEATE 298
                                       5666666688988544449*************************************99987 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 ?   -2.2   0.0       1.5   2.5e+03       7      28 ..      28      49 ..      25      52 .. 0.68
   2 !   22.1   0.0   5.7e-08   9.3e-05      79     225 .]     140     293 ..     134     293 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.5
                                      E-SSSHHHHHHHHHHHGG.GSSE CS
                         OMPdecase  7 lDvatarelleladkvgp.sivv 28
                                      +Dv++a+   ++a+k+g+ s++ 
  gi|518653106|ref|YP_008142626.1| 28 MDVTNAE-QAKIAEKAGAvSVMA 49
                                      6888774.557888888866655 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 5.7e-08
                                       TCHHHHTTESEEEEEGTGHHHHHHHHHHHHHHTTS.EEEEEESTSSGGHHHHHHHSHHHHHHHHHHHHHHH...... CS
                         OMPdecase  79 gsarikewadivtvhavaGkasvkalaeaaekwgnrgllilaqmsskgnlmlqekgytqacveaarehkae...... 149
                                       ++ ri e+a ++   + aG++ + ++++ ++  +  g++il  ++s + ++++e     + +  +r+ +a+      
  gi|518653106|ref|YP_008142626.1| 140 AVRRIFEGAAMIRTKGEAGTGNIIEAVRHIRTVN-DGIYILNSITSDEMYAVAE--NISKSYTTLRNLTASdlygad 213
                                       456999***************************6.9******************..444444444444433333346 PP

                                       ......TTESEEECCCHTHHHHHHTTCSCEEEHHHTTEEEEECTTCCGGGHHHHHHHTTCSEEEESHHHHTSSSHHH CS
                         OMPdecase 150 ......dfvmGfvaqetlnateedaddfihltpgigleqggdgkgqqyntpekligiagadiiivGRgIlkagdpve 220
                                             + + G+   e  n++ +  ++++hl++     +   ++g+      +l+ + g d + vG gI+k++dp++
  gi|518653106|ref|YP_008142626.1| 214 kempydNVYYGMDFREISNQIYKVLKEIKHLKRLPL--VNFAAGGIATPADAALMMKMGMDGVFVGSGIFKSRDPQK 288
                                       666666777777777777743444677777776554..5778888888889999999******************** PP

                                       HHHHH CS
                         OMPdecase 221 eaery 225
                                        ae++
  gi|518653106|ref|YP_008142626.1| 289 MAEAI 293
                                       *9986 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.5   0.0    0.0097        16     114     133 ..      72      91 ..      31     106 .. 0.73
   2 !   13.4   0.0   1.8e-05      0.03     172     224 ..     238     290 ..     225     314 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0097
                                       HHHHHCCSSS-EEEEEESES CS
                               Dus 114 vkavvkaveiPvtvkirigi 133
                                       vk++ + v+iPv +k+rig 
  gi|518653106|ref|YP_008142626.1|  72 VKEILDSVSIPVMAKVRIGH 91 
                                       55666778888888888885 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 1.8e-05
                                       CHHHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEESCHHC..CSTTHHH CS
                               Dus 172 weaIkevkqavsipviaNGdIkdaedaqaileetGadgvmigrgal..gnPwlfa 224
                                       +++Ik++k +++++ +a G+I ++ da  +++  G+dgv +g g    ++P  +a
  gi|518653106|ref|YP_008142626.1| 238 LKEIKHLK-RLPLVNFAAGGIATPADAALMMKM-GMDGVFVGSGIFksRDPQKMA 290
                                       34444444.466777899*********999998.********9975114676666 PP

>> IGPS  Indole-3-glycerol phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.029        48      60      85 ..      22      47 ..      18      54 .. 0.86
   2 !   12.5   0.0   3.7e-05     0.061     210     252 ..     249     291 ..     226     293 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.029
                                      TTEESBSS--HHHHHHHHTTT.-SEE CS
                              IGPS 60 skgliredfdpaeiAkkyeeagAsai 85
                                      +kg + +d+  ae+Ak  e+agA  +
  gi|518653106|ref|YP_008142626.1| 22 TKGGVVMDVTNAEQAKIAEKAGAVSV 47
                                      6999****************988654 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 3.7e-05
                                       SEEEEESSS-SHHHHHHHCCTT-SEEEESHHHHC-TTHHHHHH CS
                              IGPS 210 vllvaeSGiktredveklkeegvnafLvGeslmrqedvekair 252
                                        +  a  Gi+t++d+  + + g++++ vG+ + ++ d +k+ +
  gi|518653106|ref|YP_008142626.1| 249 LVNFAAGGIATPADAALMMKMGMDGVFVGSGIFKSRDPQKMAE 291
                                       4556889******************************998765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1      0.22   3.6e+02     117     117 ..      54      54 ..      13     124 .. 0.55
   2 !   14.5   0.0   8.8e-06     0.014     137     179 ..     241     283 ..     225     299 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.22
                                       E CS
                              NanE 117 G 117
                                        
  gi|518653106|ref|YP_008142626.1|  54 P 54 
                                       1 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 8.8e-06
                                       HHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
                              NanE 137 vkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                                       +k+l+   l   a G i tP+ a+ ++++G+d v vGs i + 
  gi|518653106|ref|YP_008142626.1| 241 IKHLKRLPLVNFAAGGIATPADAALMMKMGMDGVFVGSGIFKS 283
                                       6677777778899*************************99764 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.61   9.9e+02     133     164 ..     115     146 ..      27     165 .. 0.56
   2 ?   13.5   0.0   1.6e-05     0.026     130     175 ..     232     279 ..     228     280 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.61
                                       HHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 133 leavkeikkkveeveviaGnvataegakaLie 164
                                        +   +i kk+ +v v+ G  +  e++++++e
  gi|518653106|ref|YP_008142626.1| 115 ADPFYHINKKMYKVPVVCGARTFPEAVRRIFE 146
                                       34444556666566666666666666666554 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 1.6e-05
                                       HHHHHHHHHHHH..HTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS CS
                                       xxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             IMPDH 130 ekvleavkeikk..kveeveviaGnvataegakaLieagadavkvGiG 175
                                       +++ +++keik+  +++ v+  aG +at + a+ ++++g d+v vG G
  gi|518653106|ref|YP_008142626.1| 232 NQIYKVLKEIKHlkRLPLVNFAAGGIATPADAALMMKMGMDGVFVGSG 279
                                       5555666666641134459999************************88 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3     0.083   1.4e+02     143     198 ..      30      85 ..      18      93 .. 0.64
   2 ?   10.6   0.0   0.00016      0.26     180     230 ..     233     285 ..     222     314 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.083
                               NMO 143 issvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpqvldavdiPviA 198
                                       ++ +++a+++e++Ga ++ +        + +  v+  +    v+++ld v+iPv+A
  gi|518653106|ref|YP_008142626.1|  30 VTNAEQAKIAEKAGAVSVMALERVPSDIRAQGGVARMSDPLKVKEILDSVSIPVMA 85 
                                       66677777777777655555433333333322344445555678999999999998 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00016
                               NMO 180 glfaLvpqvldavdiPvi..AaGGiidrrgvaaaLalGAsgvqigtrfLltke 230
                                       +  +++++++    +P++  AaGGi +  + a ++ +G  gv +g+      +
  gi|518653106|ref|YP_008142626.1| 233 QIYKVLKEIKHLKRLPLVnfAAGGIATPADAALMMKMGMDGVFVGSGIFKSRD 285
                                       44556666666666999777*************************98766655 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05     0.071     205     243 ..     238     276 ..     184     279 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                                       HHHHHHHHHHHSSEEEEEEE-SHHHHHHHHHTTESEEEE CS
                            FMN_dh 205 wddikwlreqtklplvvKGvltaedakraveaGvdgivv 243
                                        ++ik l++   +++   G+ t++da +++++G+dg+ v
  gi|518653106|ref|YP_008142626.1| 238 LKEIKHLKRLPLVNFAAGGIATPADAALMMKMGMDGVFV 276
                                       457888888888888999*******************98 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.36   5.9e+02     136     172 ..     149     185 ..      64     188 .. 0.59
   2 ?    9.9   0.0   0.00028      0.45      78     108 ..     253     283 ..     226     303 .. 0.60

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.36
                                       EEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTT CS
                      His_biosynth 136 vaikgwreetgldavelakkleelgageilltdidrd 172
                                        +i++  e  + +++e ++ + +++ g ++l++i +d
  gi|518653106|ref|YP_008142626.1| 149 AMIRTKGEAGTGNIIEAVRHIRTVNDGIYILNSITSD 185
                                       3444444555566777777777777777777777666 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00028
                                       EESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
                      His_biosynth  78 vGGGIrsledveelleagadkviigtaavkn 108
                                         GGI +  d++ ++++g+d v +g+  +k+
  gi|518653106|ref|YP_008142626.1| 253 AAGGIATPADAALMMKMGMDGVFVGSGIFKS 283
                                       4455555555555555555555555555544 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   0.00013      0.21      61      92 ..     277     308 ..     273     313 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00013
                                       HCT-STT--HHHHHHHHHHHSGGGTSHHHHHH CS
                         TetR_C_27  61 aaGeFkaadpeaaaravfdatarfhhPalaae 92 
                                        +G Fk++dp+++a+a+++at ++ +  l+++
  gi|518653106|ref|YP_008142626.1| 277 GSGIFKSRDPQKMAEAIVEATENYEDYKLLSD 308
                                       589********************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.57u 0.30s 00:00:00.86 Elapsed: 00:00:00.48
# Mc/sec: 2081.91
//
Query:       gi|518653107|ref|YP_008142627.1|  [L=190]
Description: glutamine amidotransferase subunit PdxT [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-52  178.6   0.1    1.4e-52  178.3   0.1    1.0  1  SNO            SNO glutamine amidotransferase family
    2.7e-08   33.6   0.1    3.4e-08   33.3   0.1    1.2  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    3.3e-05   23.6   0.4    4.1e-05   23.3   0.4    1.3  1  Peptidase_S51  Peptidase family S51
     0.0049   16.7   0.3      0.026   14.3   0.3    1.9  1  GATase         Glutamine amidotransferase class-I
  ------ inclusion threshold ------
      0.019   14.6   0.0       0.05   13.2   0.0    1.7  1  HTH_Tnp_IS1    InsA C-terminal domain


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 !  178.3   0.1   3.8e-56   1.4e-52       1     184 [.       5     186 ..       5     189 .. 0.94

  Alignments for each domain:
  == domain 1  score: 178.3 bits;  conditional E-value: 3.8e-56
                                       EESSSSSHHHHHHHHHHTTSEE....EEE-SGGGGCC-SEEEE-SS-HHHHHHHHHHTT-HHHHHHHHHTT.--EEE CS
                               SNO   1 vlalqGaveehveaikkclaen....ktvkrkedlaevdaliiPGGestamskliertglyedllefvknsekvvlG 73 
                                       +l +qG+v eh + ik+  ++      +vk+++dla++ +liiPGGest +  l+++ g+ye++ e+++ + + ++G
  gi|518653107|ref|YP_008142627.1|   5 ILDIQGDVSEHFQMIKRLPVKYhavpIMVKTVNDLAGISGLIIPGGESTVIYMLLKKSGMYEKIVEMAHSG-LHIMG 80 
                                       689*************988776668899*****************************************99.99*** PP

                                       ETHHHHHHCCEETTBSS-SS--CCEEEETTTT-SCCGEEEEEEEETTTCSEEEEEESS--EEEEE-.TTTCEEEEEC CS
                               SNO  74 tCaGlillskelenelvktlellkvkvkrnafGrqvdsfekeldfknliekftavfiraPvieeilddeavkvlyel 150
                                       tCaG il+s++++ ++v+ ++l+++++krna+Grq++sf +++++++++ +f avfiraP ie  +   + +vl   
  gi|518653107|ref|YP_008142627.1|  81 TCAGAILVSRDTGDKQVEGMNLIDISIKRNAYGRQINSFIQKINISGIG-NFDAVFIRAPEIESTG---NSEVLGLE 153
                                       ************************************************9.9************999...66677777 PP

                                       TTEEEEEEETTEEEESS-GGGSTTHCHHHHHHHH CS
                               SNO 151 dgeivvakqkkilatsfhPelaeddirvhdyfve 184
                                        g+ v ++ ++i+a++fhPel+ + + vh++fv 
  gi|518653107|ref|YP_008142627.1| 154 SGKPVIVREGNIMALTFHPELTGN-TGVHELFVS 186
                                       788899*****************9.99*****97 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 !   33.3   0.1   9.4e-12   3.4e-08      30     127 ..      33     120 ..      10     156 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 9.4e-12
                          GATase_3  30 vplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpegvegeageve 106
                                       v+ + ++l + +  +i+pGg++t+  +  l++sg+ e+i e+a +g +++g C+G ++ ++   d+        +ve
  gi|518653107|ref|YP_008142627.1|  33 VK-TVNDL-AGISGLIIPGGESTVIYML-LKKSGMYEKIVEMAHSGLHIMGTCAGAILVSRDTGDK--------QVE 98 
                                       22.34455.45999*********97765.5566**************************9998875........699 PP

                          GATase_3 107 glglLdietefek.ekltgqve 127
                                       g++l+di+++ +   +++++  
  gi|518653107|ref|YP_008142627.1|  99 GMNLIDISIKRNAyGRQINSFI 120
                                       *******999887556665544 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.4   1.2e-08   4.1e-05      76     144 ..      36     103 ..      11     166 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.2e-08
                                       HHHHHHHSSEEEE--S-HHHHHHHHHHTTHHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG CS
                     Peptidase_S51  76 ieeklleadviyvgGGntfrLlkllketgldkllreavqqglvyiGvSAGaivagesiettsysdspik 144
                                       +++ l+   ++++ GG+   +  llk+ g+ + + e  ++gl ++G+ AGai +++    ++++++  +
  gi|518653107|ref|YP_008142627.1|  36 VND-LAGISGLIIPGGESTVIYMLLKKSGMYEKIVEMAHSGLHIMGTCAGAILVSRDTGDKQVEGMNLI 103
                                       444.66678999*******************************************99888887777655 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.3   0.3   7.3e-06     0.026      17     182 ..      19     183 ..      12     189 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 7.3e-06
                                       HHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.....TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHT CS
                            GATase  17 lvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.....vegkieaikearenkiPiLGICLGmQllaief 88 
                                       + +l vk++ vpi  +  +    l ++ g++++gG  ++        g+ e i e++ +++ i+G C G  l+  + 
  gi|518653107|ref|YP_008142627.1|  19 IKRLPVKYHAVPIMVKTVND---LAGISGLIIPGGESTVIymllkKSGMYEKIVEMAHSGLHIMGTCAGAILVSRDT 92 
                                       55666777777777655555...789*********999999988888888888888999****************** PP

                                       TTEEEEEECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTT.EEEEEEEETTEEEEEEEEETTTE CS
                            GATase  89 grkvvkekekehhggtmrlgddetallyglknevierhrHryevnpkelepag.levtakseddeelmeiiekknpf 164
                                       g k v+  +  +   + +   ++ + + ++ n           +   e+e++g  ev++ + +++    i+++ n +
  gi|518653107|ref|YP_008142627.1|  93 GDKQVEGMNLIDISIKRNAYGRQINSFIQKINISGIGNFDAVFIRAPEIESTGnSEVLGLE-SGK--PVIVREGN-I 165
                                       *987766667777777777776666676665555555555555555588888867888888.443..34555555.9 PP

                                       EEESSBTTSTTSTTHHHH CS
                            GATase 165 vgvQFHPEststpegpel 182
                                       +++ FHPE t +++ +el
  gi|518653107|ref|YP_008142627.1| 166 MALTFHPELTGNTGVHEL 183
                                       ********9999886665 PP

>> HTH_Tnp_IS1  InsA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.4e-05      0.05       6      25 ..      60      82 ..      58      88 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.4e-05
                       HTH_Tnp_IS1  6 rkPGvkekIvemAfNGa...Gvr 25
                                      +k G+ ekIvemA+ G    G++
  gi|518653107|ref|YP_008142627.1| 60 KKSGMYEKIVEMAHSGLhimGTC 82
                                      5889***********95222555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-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: 00:00:00.46
# Mc/sec: 1235.33
//
Query:       gi|518653108|ref|YP_008142628.1|  [L=74]
Description: hypothetical protein FACI_IFERC00001G1747 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.01   16.1   2.7      0.011   16.0   2.7    1.0  1  BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-li
      0.061   13.2   5.2      0.075   12.9   5.2    1.0  1  DUF2975          Protein of unknown function (DUF2975)
      0.061   13.4   4.8      0.087   12.9   4.8    1.2  1  DUF2198          Uncharacterized protein conserved in bacteri
       0.74    9.7   7.8        2.7    7.9   1.0    2.1  2  DUF2976          Protein of unknown function (DUF2976)


Domain annotation for each model (and alignments):
>> BacteriocIIc_cy  Bacteriocin class IIc cyclic gassericin A-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   16.0   2.7   2.4e-06     0.011      13      74 ..      12      72 ..       2      74 .] 0.85

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.4e-06
                                      XXXXXXXXXXXXXXXXXXXXX-TTHHHHT--S---SSHHHHHHHHHHH---SSTTTTTSSSS CS
                   BacteriocIIc_cy 13 kvelfaisivlvvalllataniyfiadklGiqlatatarklldavasGaslgtafaiilGvt 74
                                      k   + i + +++ ++ +  ++ ++  ++ + la a a ++l  v   +  +t f  ++G+t
  gi|518653108|ref|YP_008142628.1| 12 KRVKNLIKVNIIIGII-TVIEVVYVISHFKLYLANALAIDILSIVLGMSFAATMFLWVVGIT 72
                                      4456789999999988.77777788889****************99888899********99 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   5.2   1.7e-05     0.075      54     108 ..      15      67 ..      13      73 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.7e-05
                           DUF2975  54 anvrrLrriglaliaaalllaagivalallaelelapgvvllllgvafaslvigl 108
                                       +n   ++ i++++ ++ +++++  + l+l+++l+++   + ++lg++fa+ +   
  gi|518653108|ref|YP_008142628.1|  15 KNLIKVNIIIGIITVIEVVYVISHFKLYLANALAIDI--LSIVLGMSFAATMFLW 67 
                                       79999***************************55554..4444445554433333 PP

>> DUF2198  Uncharacterized protein conserved in bacteria (DUF2198)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   4.8   1.9e-05     0.087      22      66 ..      21      64 ..      16      67 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.9e-05
                           DUF2198 22 nhyvGllltv.aLivasvykgYtkelyiividiiSllaGflyakkm 66
                                      n ++G++ ++ ++ v s +k Y  +   ++idi+S+++G+ +a++m
  gi|518653108|ref|YP_008142628.1| 21 NIIIGIITVIeVVYVISHFKLYLANA--LAIDILSIVLGMSFAATM 64
                                      6688987665255589*******986..689************998 PP

>> DUF2976  Protein of unknown function (DUF2976)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.9    0.0021       9.5      51      83 ..       5      37 ..       2      40 .. 0.83
   2 ?    7.9   1.0    0.0006       2.7      28      46 ..      53      71 ..      41      74 .] 0.84

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0021
                           DUF2976 51 fneisegkaewgkfgltlvvGvvllvvviwLlt 83
                                      ++e  e+k     +++ +++G++ ++ v++ + 
  gi|518653108|ref|YP_008142628.1|  5 YTESVENKRVKNLIKVNIIIGIITVIEVVYVIS 37
                                      67777777777788999***********99875 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0006
                           DUF2976 28 villgLvlaavaflaVaka 46
                                       i+lg+ +aa++fl+V+  
  gi|518653108|ref|YP_008142628.1| 53 SIVLGMSFAATMFLWVVGI 71
                                      5899************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1043  (0.0581739); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 546.33
//
Query:       gi|518653109|ref|YP_008142629.1|  [L=138]
Description: hypothetical protein FACI_IFERC00001G1748 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   61.1   0.0    1.3e-16   60.9   0.0    1.0  1  DUF296    Plants and Prokaryotes Conserved (PCC) domain
  ------ inclusion threshold ------
      0.036   14.0   0.0      0.056   13.3   0.0    1.4  1  DUF3395   Domain of unknown function (DUF3395)


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 !   60.9   0.0   1.5e-20   1.3e-16       2     107 .]       9     119 ..       8     119 .. 0.94

  Alignments for each domain:
  == domain 1  score: 60.9 bits;  conditional E-value: 1.5e-20
                                       EEEEEE-TTSBHHHHHHHHHHHHT-SSEEEEEEEEEEEEEE.EEECTTT....EE-S-EEEEEEEEEEEETT..EEE CS
                            DUF296   2 phvlrlepGediveaieefarkrgiraacvlsaiGavsnvt.rladgee....kllgrfeilslsGtilpdg..lHl 71 
                                       ++v+++e++ed+++ ++ +++k +i+ +++  +iG+++n++ ++++ ++     +++r e++++ G+i++d+  +H+
  gi|518653109|ref|YP_008142629.1|   9 IIVAKFEANEDVLSNLNLLVEKYSIKTGFIDMGIGMIKNLKiGYWNINKydelLIEDRSELVAFHGSIANDKnrFHI 85 
                                       6899**************************************999999998776679*************7789*** PP

                                       EEEEEETTSEEEEEEEEEE.EEEEEEEEEEEEE-CS CS
                            DUF296  72 hvslagedgqvvgGhlaegplvaattvevvvaefeg 107
                                       h+ +a++d+  +gGh+++g  +a   +ev +++f++
  gi|518653109|ref|YP_008142629.1|  86 HIGVARKDHGLYGGHFFSG--IADPLMEVKITKFDN 119
                                       *****************99..889*******99975 PP

>> DUF3395  Domain of unknown function (DUF3395)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   6.3e-06     0.056     117     154 ..      32      69 ..       7      71 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 6.3e-06
                           DUF3395 117 snllGFydPcpgeekqLkvrYtfrgklhevtvddeeel 154
                                       s   GF+d  +g  k+Lk+ Y+  +k+ e+ ++d++el
  gi|518653109|ref|YP_008142629.1|  32 SIKTGFIDMGIGMIKNLKIGYWNINKYDELLIEDRSEL 69 
                                       3347*******************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (138 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       294  (0.016398); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 936.19
//
Query:       gi|518653110|ref|YP_008142630.1|  [L=214]
Description: ATP binding cassette transporter, ExsD protein related protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-15   55.9   0.0      1e-14   55.3   0.0    1.4  1  Radical_SAM  Radical SAM superfamily
    3.2e-12   46.6   0.0    5.7e-12   45.8   0.0    1.4  1  Fer4_14      4Fe-4S single cluster domain
    1.9e-07   31.4   0.0    2.7e-07   30.9   0.0    1.3  1  Fer4_12      4Fe-4S single cluster domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.0   1.7e-18     1e-14       3      89 ..      25     104 ..      23     182 .. 0.76

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 1.7e-18
                                       EESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Radical_SAM   3 vtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlaklavpgir 79 
                                        t+ CnlrCs+C++++   + + g+++s++ei+e ++ +   +g+  + l+ggepll++d+ +l++rl+++    ++
  gi|518653110|ref|YP_008142630.1|  25 RTEYCNLRCSWCDTKY---SFYEGKEMSIDEIVESARNINSGHGASWICLTGGEPLLQKDISVLVDRLSEE----YN 94 
                                       7899***********9...7*******************86667**************************6....77 PP

                                       EEEEECSSCH CS
                                       xxxxxxxxxx RF
                       Radical_SAM  80 itvetngtlp 89 
                                       i +et+g l 
  gi|518653110|ref|YP_008142630.1|  95 ILLETSGSLN 104
                                       7777777764 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 !   45.8   0.0   9.5e-16   5.7e-12       1      93 [.      22     105 ..      22     125 .. 0.78

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 9.5e-16
                           Fer4_14   1 lfvrlsgCnlsCkgCdnketwkselgkpqteelleqilkdlkkseikiqglvltGGePLhyenkkellklvkrlkee 77 
                                       +f+r+  Cnl C +Cd+k ++ +  +   +e ++        +s   ++ + ltGGePL+   +k++  lv+rl ee
  gi|518653110|ref|YP_008142630.1|  22 VFIRTEYCNLRCSWCDTKYSFYEGKEMSIDEIVE--SA-RNINSGHGASWICLTGGEPLL---QKDISVLVDRLSEE 92 
                                       69**************999665544444444444..33.24566666888*********5...599*********** PP

                           Fer4_14  78 ypekkiwletngtlei 93 
                                       y   +i let+g+l+i
  gi|518653110|ref|YP_008142630.1|  93 Y---NILLETSGSLNI 105
                                       *...**********96 PP

>> Fer4_12  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   4.6e-11   2.7e-07       2      95 ..      11     103 ..      10     136 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 4.6e-11
                           Fer4_12   2 nGeG.....vrlslfvsgCnlsCkgCfnketwsfksgkeftkelleeiiedlkk.esiegltllGGEPllpenaeal 72 
                                       +GeG     + ++++++ Cnl+C+ C      sf +gke++ + + e  ++++  +  + + l+GGEPll   ++++
  gi|518653110|ref|YP_008142630.1|  11 QGEGlysgeKMVFIRTEYCNLRCSWCD--TKYSFYEGKEMSIDEIVESARNINSgHGASWICLTGGEPLL---QKDI 82 
                                       788855544557999**********87..456899999999666666666676547779***********...9999 PP

                           Fer4_12  73 lelvkevkeekpekdiwlytgyt 95 
                                         lv+++ ee+     ++++g+ 
  gi|518653110|ref|YP_008142630.1|  83 SVLVDRLSEEYN--ILLETSGSL 103
                                       999***999997..677887775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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 0.30s 00:00:00.77 Elapsed: 00:00:00.46
# Mc/sec: 1393.77
//
Query:       gi|518653111|ref|YP_008142631.1|  [L=191]
Description: GTP cyclohydrolase [Ferroplasma acidarmanus fer1]
Scores for complete 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-47  159.5   0.0    6.3e-47  159.3   0.0    1.1  1  GTP_cyclohydroI  GTP cyclohydrolase I
  ------ inclusion threshold ------
       0.05   13.7   0.0       0.13   12.4   0.0    1.7  1  QueF             QueF-like protein
       0.11   12.8   0.1        0.2   12.0   0.1    1.4  1  DUF4156          Domain of unknown function (DUF4156)


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0     1e-50   6.3e-47      17     161 ..      28     169 ..       9     189 .. 0.85

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 1e-50
                                       TSTTTTTHHHHHHHHHHHHTGGGGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEEEEEEEE-..TTE CS
                   GTP_cyclohydroI  17 ereglketpkRvakayeelfkgleedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigkahvaYiP..kkk 91 
                                       ++e+lk+tp+R+ + y+e++   + +   + +k  + +++++mv+vk+i+f+S+C+HHllpf+g++++aY+P   + 
  gi|518653111|ref|YP_008142631.1|  28 NDEELKNTPRRIENFYREWYGARNFTF--TKFK--I-TGHESMVIVKNISFYSMCSHHLLPFFGNINIAYLPrpAGY 99 
                                       789****************97776666..2232..2.4689******************************8657** PP

                                       EE-HHHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHHHSSTT--TT-EEEEEEEE CS
                   GTP_cyclohydroI  92 viGlSklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCmtmrgvkkkesktvtsalr 161
                                       ++G+Skl+R v+ +a+++q+QE++t++i++ l + l+p  v+v+ +++h+Cm+mrgvk++++++vts+++
  gi|518653111|ref|YP_008142631.1| 100 IAGVSKLVRSVNKIASKPQLQENMTSEIVNLLYDNLNPLFVMVTAKGQHMCMMMRGVKQESATMVTSSVK 169
                                       ******************************************************************9864 PP

>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.2e-05      0.13       1      61 [.      83     145 ..      83     150 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
                              QueF   1 PDfatlvirYvpdk..kvvelkslklYlisfrnrgifhEevvnrilddlvealkPkwlevvgd 61 
                                       P f+++ i Y+p++  ++     l + ++   ++ + +E+++ +i++ l++ l+P ++ v+++
  gi|518653111|ref|YP_008142631.1|  83 PFFGNINIAYLPRPagYIAGVSKLVRSVNKIASKPQLQENMTSEIVNLLYDNLNPLFVMVTAK 145
                                       669999999998763357788889999999999**************************9986 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   3.4e-05       0.2      14      62 ..     143     190 ..     139     191 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                           DUF4156  14 dskpaseCqllGevtgsqgnwlsgiftsnkelvrgaandLrneAaalGg 62 
                                       ++k ++ C ++  v+ ++   ++ +  + +++v+++++ L+neA ++ g
  gi|518653111|ref|YP_008142631.1| 143 TAKGQHMCMMMRGVKQESATMVTSS-VKYSDVVKTELESLKNEALKMMG 190
                                       5555578888888888888887777.99******************966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      475  (0.0264934); 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 0.25s 00:00:00.72 Elapsed: 00:00:01.80
# Mc/sec: 321.88
//
Query:       gi|518653112|ref|YP_008142632.1|  [L=157]
Description: 6-pyruvoyltetrahydrobiopterin synthase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-24   85.4   0.0    3.5e-24   85.1   0.0    1.0  1  PTPS      6-pyruvoyl tetrahydropterin synthase


Domain annotation for each model (and alignments):
>> PTPS  6-pyruvoyl tetrahydropterin synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.0     2e-28   3.5e-24       7     122 ..      14     156 ..      10     157 .] 0.89

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 2e-28
                                       EEEEEE--TTTTGGGGSTEEEEEEEEEEEEEC-STCTTBSS-HHHHHHHHHHHHHCTTTEEC.CCC-CCHHCCS... CS
                              PTPS   7 eFdaaHrlrkhegkcrnlHGHnykvevtvegeeldetgmvvdfgelkealkeileelDhkfl.naddpeleell... 79 
                                       + +++H+++++e kc+n HGH y+++v + ++  + +gm +df+ +k+a+k ++e++Dhkf+  +dd   +e +   
  gi|518653112|ref|YP_008142632.1|  14 TWSSGHYVPDNE-KCKNFHGHDYSIDVIIDSDGVKASGMAIDFTIVKQAIKPVIENMDHKFMiPEDDIRQNE-Npgf 88 
                                       6789*****665.*************************************************7755555554.56** PP

                                       .........................--HHHHHHHHHHHHHHHH.GCCCGCEEEEEEEEETTEEEEEEE CS
                              PTPS  80 ........................spTaEnlaklifeelkerl.qekevklskvrvwEtpnswaeyre 122
                                                                 TaE +ak++++++ ++l    e    kv+++E p+++a+y+e
  gi|518653112|ref|YP_008142632.1|  89 idiyvrgkyrgtmsrsdifafpysADTAEFIAKYCYDKIFAKLlGLMENFRLKVTIHEGPGNMATYNE 156
                                       **********************9877*****************8445555556*************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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 0.27s 00:00:00.75 Elapsed: 00:00:00.47
# Mc/sec: 1005.15
//
Query:       gi|518653113|ref|YP_008142633.1|  [L=248]
Description: hypothetical protein FACI_IFERC00001G1752 [Ferroplasma acidarmanus fer1]
Scores for 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-12   47.1   0.0      1e-11   45.4   0.0    1.7  2  XdhC_C     XdhC Rossmann domain
    3.7e-06   27.0   0.0    5.3e-06   26.5   0.0    1.2  1  XdhC_CoxI  XdhC and CoxI family


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 ?   -1.1   0.0      0.28   2.5e+03      54      98 ..      30      73 ..      10      79 .. 0.66
   2 !   45.4   0.0   1.1e-15     1e-11      10     125 .]     124     238 ..     118     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.28
                                      HHHHHHHHHHHSSS--SEEEESS-HHHHHHHCTTS.--....... CS
                            XdhC_C 54 hklDaealeaalrkkaayigllGSrkkaarrlerlraaglseeel 98
                                       ++ ++  + + ++k    g lGS +  + +l +l +a ++++e 
  gi|518653113|ref|YP_008142633.1| 30 SSIAKPGFKILASGKSILYGTLGSPSLDKVVLGEL-NASIEKQET 73
                                      55555555555545555789999999888888888.555665554 PP

  == domain 2  score: 45.4 bits;  conditional E-value: 1.1e-15
                                       HHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE.-EEEE--S-HHHHHHHHHHHSSS--SEEEESS-HHHHHHHC CS
                            XdhC_C  10 aqalarlaaalgfrvtvvdpreefatkerfpeade.tavvvlthdhklDaealeaalrkkaayigllGSrkkaarrl 85 
                                        +a++ l+  +g++ +v++ +++ +t++ + e  + ++vv+lt + + + + +++ l++k  y+ ++ S+++ ++ +
  gi|518653113|ref|YP_008142633.1| 124 LEAMMGLMDYTGMEPVVININKKEETEKLMSEDYSeDFVVLLT-KTENEIKFISHFLKNKPVYLSIVSSKNRFNKDM 199
                                       5678889999999999999999756666666444446666665.66999********99999*************** PP

                                       TTS.--.......TTEESS-S--S---SHHHHHHHHHHHH CS
                            XdhC_C  86 erlraaglseeelarlhaPiGldigaktpeeIAvsilAei 125
                                       e+++++  +  + + +++P+G+di+a t +eIA+si+Aei
  gi|518653113|ref|YP_008142633.1| 200 EQVKNQ-NPGLDTSLIKCPAGIDIKAITINEIAISIVAEI 238
                                       ***555.56778899************************8 PP

>> XdhC_CoxI  XdhC and CoxI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   5.9e-10   5.3e-06       4      63 ..      15      74 ..      12      79 .. 0.89

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 5.9e-10
                                      CT..EEEEEEEEEECSSSSGTT-EEEEETTS-EEE-SSSSCHHHHHHHHHHHHHHCT--E CS
                         XdhC_CoxI  4 agrpvalaTVvdteGsaprplGakmlvrpdgrviGsvgggclEaavideArallaagrta 63
                                      ++++ a+aTV++t+Gs+ +++G k l      ++G++g+  l+  v+ e  a +++++t+
  gi|518653113|ref|YP_008142633.1| 15 NKKDYAIATVIKTSGSSIAKPGFKILASGKSILYGTLGSPSLDKVVLGELNASIEKQETK 74
                                      67789**********************999955****************99999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       849  (0.0473534); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1730.61
//
Query:       gi|518653114|ref|YP_008142634.1|  [L=233]
Description: purine nucleoside phosphorylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-19   68.5   0.0    5.8e-19   68.3   0.0    1.0  1  PNP_UDP_1  Phosphorylase superfamily


Domain annotation for each model (and alignments):
>> PNP_UDP_1  Phosphorylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.3   0.0   3.2e-23   5.8e-19       4     215 ..      16     213 ..      13     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 68.3 bits;  conditional E-value: 3.2e-23
                                       EEESSHHHHHHHHHHEEEEEEEEEE.TTEEEEEEEETTEEEEEEE--SSHHHHHHHHHHHHHHHC--SEEEEEEEEE CS
                         PNP_UDP_1   4 iivgspgevellaespleetpfgregrgfkfvtGtlkgkpvvivstGiGkpnaavvaeirllkefgvkaiiriGtaG 80 
                                       +i+g+ ++ + + +  l++t+  +e++g++++tG+++gk+++ v +GiG p+ a + +  l+ ++ +k+i+r+G++ 
  gi|518653114|ref|YP_008142634.1|  16 VILGNLDRQKIINSY-LKNTEKVSEFAGYHTYTGEYNGKKITTVFHGIGIPSMA-LVVDDLIGMG-AKQIVRFGSSF 89 
                                       566666655555555.**************************************.********77.*********** PP

                                       ESSTTT-TT-EEEEEEEEE.SSSCCGCCTHHCCTCCCCTTSSE..E--HHHHHHHHHCHHTTTTTEEEEEEEEESES CS
                         PNP_UDP_1  81 glnpdlkvGDvvipddain.fdgrsplygpkeegqyfpdsyda..padpelrallkeaaealgikvhrGvvatadgf 154
                                       ++   +k+G+ ++p  + + f g  +        qy  d+y +  ++d +++++ +e+++a g   ++G v t+d  
  gi|518653114|ref|YP_008142634.1|  90 SVSDKVKPGTPILPIGYSYnFGGVFK--------QYLGDQYSIalTPDYQMLKAEEEKLSAAGLGPVVGNVFTSDAL 158
                                       ***************96552555444........77778777733456666666666999999999*********** PP

                                       S-CHHHHHHHHHHTC-CEEESSHHHHHHHHHHTT--EEEEEEEEETTTBETTCTCH.HCCC CS
                         PNP_UDP_1 155 yaeteaelrllrrlgadaveMEtaavaqlArelgipfaairvvsdlaaggadaeatheeve 215
                                          +++  + l++ g  ave E+a ++++A+++g++++++ +    +++   +e   +   
  gi|518653114|ref|YP_008142634.1| 159 MTHNKEFGQKLAKDGNIAVELEGAGLYFIAKLRGVKALSVHLA---YGNLVTGE---QLPA 213
                                       ****99999*****************************99887...33444444...2333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1749.35
//
Query:       gi|518653115|ref|YP_008142635.1|  [L=317]
Description: hypothetical protein FACI_IFERC00001G1754 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-19   71.3   0.2    1.7e-19   70.8   0.2    1.2  1  GFO_IDH_MocA    Oxidoreductase family, NAD-binding Rossmann f
    5.1e-06   26.5   0.2    2.1e-05   24.5   0.1    2.1  2  GFO_IDH_MocA_C  Oxidoreductase family, C-terminal alpha/beta 
  ------ inclusion threshold ------
      0.028   15.0   0.1       0.05   14.2   0.1    1.4  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent


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 !   70.8   0.2   2.9e-23   1.7e-19       1     119 [.       1     114 [.       1     115 [. 0.95

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.9e-23
                                       EEEEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHE.EESSHHHHHTCTTESEEEE-S-GGGHH CS
                      GFO_IDH_MocA   1 lrvaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgve.aysdleelladpeidavivatpngthe 76 
                                       ++++++Ga ++g+khl  +++     e+  ++++++e  e+  e+f++e +ys++e+  +d + d+v  ++p ++h+
  gi|518653115|ref|YP_008142635.1|   1 MKILVVGANNFGQKHLSGIKDM----EI-SIVERKPEVIEKTVEKFKIEnVYSSFEDAIKD-RFDIVDLVVPHYLHK 71 
                                       689*************888888....55.599************************99995.5************** PP

                                       HHHHHHHHTT-EEEEESSS-SSHHHHHHHHHHHHHHTS-EEEE CS
                      GFO_IDH_MocA  77 elakaaleagkhvllEKPlattveeakelvelaekkgklvsvg 119
                                       e+a++a+eag +vl+EKP+att+++ ++++++ +  g++++v+
  gi|518653115|ref|YP_008142635.1|  72 EMAIKAMEAGSNVLVEKPIATTLDDGEAMIRASKDYGVKFMVT 114
                                       ***************************************9996 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 !   24.5   0.1   3.6e-09   2.1e-05       3      54 ..     129     177 ..     127     186 .. 0.78
   2 ?   -1.8   0.0      0.49   2.9e+03       3      21 ..     265     283 ..     264     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 3.6e-09
                                       HHHTTTTSSEEEEEEEEECBEEECHHH.HCCGGSH.HCSTSHHHHTCHHHHHHH CS
                    GFO_IDH_MocA_C   3 lIengklGevvsvdvwtldtragaeak.krwkrrk.kksgGvlgdlgiHdiDll 54 
                                        I+++++G+++++     + r +++ +  +w+ +k +++gG+l+d giH++D l
  gi|518653115|ref|YP_008142635.1| 129 FIKENRIGRINTI-----IVRDQRFFEhGGWRTDKdQMGGGALIDGGIHFLDTL 177
                                       5999999999999.....5555555441556666699***************98 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.49
                                       HHHTTTTSSEEEEEEEEEC CS
                    GFO_IDH_MocA_C   3 lIengklGevvsvdvwtld 21 
                                       lI ng+  +v+ +dv+t +
  gi|518653115|ref|YP_008142635.1| 265 LILNGEKANVKKYDVYTAE 283
                                       8999999999999997765 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   8.4e-06      0.05       2      81 ..       3      77 ..       2      87 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 8.4e-06
                                      EEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEECECHHHHHH.H-SEEEE-S-HHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvtavdneeaae.eadvvvlavkpedveevls 79
                                      i ++Ga n+g+  +sg+      + ei ++ +r+pe +e++ e+++++   ++ e+a++ + d+v l v+ + ++e++ 
  gi|518653115|ref|YP_008142635.1|  3 ILVVGANNFGQKHLSGIK-----DMEISIV-ERKPEVIEKTVEKFKIENVYSSFEDAIKdRFDIVDLVVPHYLHKEMAI 75
                                      566777777777777554.....4679977.****************99999*******88999999999998888765 PP

                                      HC CS
                     F420_oxidored 80 el 81
                                      ++
  gi|518653115|ref|YP_008142635.1| 76 KA 77
                                      55 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2447.95
//
Query:       gi|518653116|ref|YP_008142636.1|  [L=763]
Description: hypothetical protein FACI_IFERC00001G1755 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.3   0.1       0.19   12.0   0.1    2.3  1  Pox_vIL-18BP  Orthopoxvirus interleukin 18 binding protein
       0.17   11.9   0.0       0.47   10.5   0.0    1.7  1  BiPBP_C       Penicillin-Binding Protein C-terminus Family


Domain annotation for each model (and alignments):
>> Pox_vIL-18BP  Orthopoxvirus interleukin 18 binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   2.1e-05      0.19       9      98 ..     563     651 ..     559     668 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.1e-05
                      Pox_vIL-18BP   9 fmygcvhsyvnaveikcpnldivtssgefrcsgcvkfmpkfsymywlakdmksdedakfiehlgegikedetvrtid 85 
                                       f y      +n + +k  n+ iv   g+f++    +   + + + w  +   s+    +  +lg gi +  +v+ +d
  gi|518653116|ref|YP_008142636.1| 563 FKYNNSRDLINNTVTKISNVRIVNDNGKFYVKINGNLTAN-ATIAWYVNGKYSNAGKSLTTKLGAGIDKI-SVKVTD 637
                                       788888999*********************9877666655.667888999999999999********765.677777 PP

                      Pox_vIL-18BP  86 gr.ivtlrkvlhvt 98 
                                       g+   t  k+++ t
  gi|518653116|ref|YP_008142636.1| 638 GGkTYTDSKIVYYT 651
                                       65155667777665 PP

>> BiPBP_C  Penicillin-Binding Protein C-terminus Family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   5.2e-05      0.47      31      84 ..     587     641 ..     577     647 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 5.2e-05
                           BiPBP_C  31 krqrlqlkargg.ea..plrWlldgeplaetkrgrelawqpepGrhrLtv.vDaaGrv 84 
                                       +++++ +k+ g+ +a  ++ W+++g++    ++g++l+ +++ G  +++v v + G++
  gi|518653116|ref|YP_008142636.1| 587 DNGKFYVKINGNlTAnaTIAWYVNGKYS---NAGKSLTTKLGAGIDKISVkVTDGGKT 641
                                       56778889999988889**********9...999999999999999999988888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (763 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       829  (0.0462379); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.28s 00:00:00.91 Elapsed: 00:00:00.44
# Mc/sec: 5246.81
//
Query:       gi|518653117|ref|YP_008142637.1|  [L=252]
Description: metal dependent hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-18   66.5   0.0      3e-18   66.1   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    9.3e-16   58.4   0.2    4.1e-15   56.3   0.2    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.3e-08   32.9   0.3    1.5e-07   31.5   0.3    1.7  1  Lactamase_B_3  Beta-lactamase superfamily domain
     0.0056   16.1   0.0      0.009   15.5   0.0    1.5  1  Lactamase_B_6  Metallo-beta-lactamase superfamily domain


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.0   6.6e-22     3e-18       3     200 ..      28     226 ..      27     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 6.6e-22
                                       EEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC....C--EE..EEEEEEHHHHHHCCTT CS
                     Lactamase_B_2   3 iLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre....lrpkk..lplyapkgvlavlean 73 
                                       iL+D+gp + + +l          +++++d +l++h H DH+ gl  +      +++ k  + +++pkg++++ e+ 
  gi|518653117|ref|YP_008142637.1|  28 ILLDCGPHTIESMLES------GINPAQVDKILISHMHLDHYGGLAEILWyraaREA-KdeVIILGPKGIMKNTEQL 97 
                                       9*******99884444......356789****************9999776554333.2467788************ PP

                                       CGHHHCHTT....TTEEEEEE-TTSEEEE...........CSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTE CS
                     Lactamase_B_2  74 fvylaleee....pavnvheldwgesfel...........gdggleitatparhksgrrldrnagdtlGlriegggk 135
                                       ++  +++ +     + n +e++  ++ e+           +  +  i+a++ +h+ +            +r+e  g+
  gi|518653117|ref|YP_008142637.1|  98 LKIYNTPDHymfsMKSNYVEIN--NNGEIyevktkftdkvK--NDYIEAFTGNHSIPD---------NMYRLEYRGN 161
                                       ***********66555555555..33333222445555542..224888888888888.........89******** PP

                                       EEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHH.HHT---STSHHHHCTTSSSSEEEEES CS
                     Lactamase_B_2 136 rvyyigDtgyipeeigerlggadllllditayeddemir.hmgHltpeeaveaaadlgakrlvliH 200
                                       +v+y+gDt+y +  i +  ++ad+ l+++t++++d  i+    H+t + a++ + +  ak+lv++H
  gi|518653117|ref|YP_008142637.1| 162 TVAYTGDTAYND-NISQVGEKADIFLHEMTFTDEDAEIAkLSKHSTYSSALRGFSESHAKKLVPVH 226
                                       *********766.88888899**************99998999*********************** PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.2   9.1e-19   4.1e-15      15     197 .]      25     226 ..      16     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 9.1e-19
                                       TCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHH CS
                       Lactamase_B  15 ggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaa 91 
                                       +g+iL D+G +t ++++       g++p +vd ++++H+HlDH+Ggl+++   + +  ++ + +   +++ ++++++
  gi|518653117|ref|YP_008142637.1|  25 DGHILLDCGPHTIESMLE-----SGINPAQVDKILISHMHLDHYGGLAEILWYRAAREAKDEVIILGPKGIMKNTEQ 96 
                                       79***************9.....6*****************************************999999999987 PP

                                       HHCCHH.............TTCHCGCCEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSH CS
                       Lactamase_B  92 srkgll.............lagvsadkpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallag 155
                                         k                 ++ +    ++++   ++ +  +    +tg +      +++ey+g +v++tGD+ ++ 
  gi|518653117|ref|YP_008142637.1|  97 LLKIYNtpdhymfsmksnyVEINNNGEIYEVKTKFTDKVKNDYIEAFTGNHSIPDNMYRLEYRGNTVAYTGDTAYND 173
                                       777666**********77766666666777777777777777777788888888889******************** PP

                                       HCCCCCC............TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEESS CS
                       Lactamase_B 156 etgridl...........tlrgaevrdpsdaekyldsllklaglkaevlvpgH 197
                                       ++  +++           t  +ae  + s ++ y ++l+   ++ a++lvp H
  gi|518653117|ref|YP_008142637.1| 174 NISQVGEkadiflhemtfTDEDAEIAKLSKHSTYSSALRGFSESHAKKLVPVH 226
                                       99999999999999999999999999999999999999999999999999887 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.3   3.2e-11   1.5e-07      16     133 ..      19     186 ..       2     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 3.2e-11
                     Lactamase_B_3  16 garilvDPf..........kanlgyeppaeeaDlvlisqaledHahletlkql........................ 58 
                                       +++i++D            +  l+ ++++ ++D +lis+ + dH+    l+++                        
  gi|518653117|ref|YP_008142637.1|  19 NVSIIIDGHilldcgphtiESMLESGINPAQVDKILISHMHLDHYG--GLAEIlwyraareakdeviilgpkgimkn 93 
                                       66666665566666666654467888899***************96..55566678999999999999999888888 PP

                     Lactamase_B_3  59 ...................aenvkvleegeslevggleiravat.shdavggsergenngflleqdgltiyhlGhla 115
                                                           + v++ ++ge +ev+     +v+  +++a  g++  ++n+++le +g t+++ G++a
  gi|518653117|ref|YP_008142637.1|  94 teqllkiyntpdhymfsmkSNYVEINNNGEIYEVKTKFTDKVKNdYIEAFTGNHSIPDNMYRLEYRGNTVAYTGDTA 170
                                       877777777766666655222223333356688887777777551457779999*********************** PP

                     Lactamase_B_3 116 helsseelkelgrvDvvl 133
                                       ++ + ++  e   +D++l
  gi|518653117|ref|YP_008142637.1| 171 YNDNISQVGEK--ADIFL 186
                                       *7777777554..67765 PP

>> Lactamase_B_6  Metallo-beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0     2e-06     0.009       8      67 ..      27      82 ..      22     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 2e-06
                     Lactamase_B_6  8 kiLlDvGwdeskvslesalkelekviptvdliLLshatlehlGayally.akfksklllni 67
                                      +iLlD+G +      es+l+       +vd iL+sh  l+h G++a ++ +++ ++   ++
  gi|518653117|ref|YP_008142637.1| 27 HILLDCGPHTI----ESMLES-GINPAQVDKILISHMHLDHYGGLAEILwYRAAREAKDEV 82
                                      7******9986....344442.223468****************98654044444555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       758  (0.0422779); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.29s 00:00:00.78 Elapsed: 00:00:00.45
# Mc/sec: 1673.54
//
Query:       gi|518653118|ref|YP_008142638.1|  [L=221]
Description: HAD family hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-19   70.3   0.0    3.1e-19   69.7   0.0    1.3  1  HAD_2           Haloacid dehalogenase-like hydrolase
      2e-12   47.9   0.0    3.9e-12   47.0   0.0    1.4  1  HAD             haloacid dehalogenase-like hydrolase
      7e-10   39.5   0.0    2.5e-09   37.8   0.0    1.8  1  Hydrolase       haloacid dehalogenase-like hydrolase
      3e-07   30.4   0.0    9.7e-07   28.8   0.0    1.8  2  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 !   69.7   0.0   6.9e-23   3.1e-19       1     176 [.       5     187 ..       5     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 69.7 bits;  conditional E-value: 6.9e-23
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleey........glselseeelrkliglslrellrklgeseeeeekieellrky 69 
                                       i+FD+DgTl+ +++++ +af ++++e          ++     +   ++gl  ++ + +++++ + +  ++ l+  +
  gi|518653118|ref|YP_008142638.1|   5 ILFDIDGTLMEESPTHTAAFDYVCKEIygvdtdikSFPRHGMTDTGIMYGLLKKQGIPEVEIKAKLDIAFQALIGYV 81 
                                       89************************988888776666666677777899999999999999999999********* PP

                             HAD_2  70 neekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdv.ivtsedvekkKPdpeviekal 145
                                        ++++    k++++vk++L+ +k +g+  gi T + +  +e  l++ gie+yF +  ++s+ + ++K    ++  a+
  gi|518653118|ref|YP_008142638.1|  82 STNLQPADYKLLNNVKNVLDAVKVNGHISGILTGNLQPIAEIRLQHAGIEEYFITgGYGSDSIIRSK----LVDYAI 154
                                       ***************************************************9965268899999996....999999 PP

                             HAD_2 146 ekl..klkkeeviyvGDsptDieaakkagikvi 176
                                       +++  +++++e+  +GD+p Di+aa++a + ++
  gi|518653118|ref|YP_008142638.1| 155 QRYgsNINRSEIYLIGDTPLDIKAAREASTGAV 187
                                       99977899*******************987665 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.0   0.0   8.6e-16   3.9e-12       1     188 []       5     180 ..       5     180 .. 0.69

  Alignments for each domain:
  == domain 1  score: 47.0 bits;  conditional E-value: 8.6e-16
                               HAD   1 alfDfDgTLldgdsle.lllrfllrrgaprlwralreklllal.....frellrldraglaelleallagls.eela 70 
                                       +lfD+DgTL+ +++ + + ++++ ++      + ++ +++  +     ++ ll+    g+ e++ ++  + + ++l+
  gi|518653118|ref|YP_008142638.1|   5 ILFDIDGTLMEESPTHtAAFDYVCKE-IYGVDTDIKSFPRHGMtdtgiMYGLLKK--QGIPEVEIKAKLDIAfQALI 78 
                                       79**********77775556644444.4444788888888888444442222222..23333333333333333333 PP

                               HAD  71 aelerfvaevirpk...lldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelgl 144
                                        ++     ++ +p+   ll   ++ +l+a++ +G+   +++g+l+p++e+ l++ g    + +      ++  ++ +
  gi|518653118|ref|YP_008142638.1|  79 GYVS----TNLQPAdykLL-NNVKNVLDAVKVNGHISGILTGNLQPIAEIRLQHAG----IEE------YFITGGYG 140
                                       3333....44444433233.59999999999*************************....***......99999788 PP

                               HAD 145 egkpvrgegkvaalrewlaaegegidleevvayGDspsDlpllr 188
                                       +++++r     + ++  +++ g +i ++e++ +GD+p D++++r
  gi|518653118|ref|YP_008142638.1| 141 SDSIIRS----KLVDYAIQRYGSNINRSEIYLIGDTPLDIKAAR 180
                                       8888888....555555566999999999*************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.5e-13   2.5e-09       1     209 [.       2     182 ..       2     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.5e-13
                                       SSEEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTE.......... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......... RF
                         Hydrolase   1 iktvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrg.......... 67 
                                       +k+++fD+dGTL + +p ++ +++++                       +k++ g  t++  f+ +g          
  gi|518653118|ref|YP_008142638.1|   2 VKLILFDIDGTLMEESPTHTAAFDYV-----------------------CKEIYGVDTDIKSFPRHGmtdtgimygl 55 
                                       699***********************.......................******************8888776666 PP

                                       ..HHHHTHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEES CS
                                       ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  68 ..ayaigkpewltaldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltg 142
                                         +  i ++e  ++l              + +  + +    +   +  ad  k+   ++ ++ + k +g   ++ltg
  gi|518653118|ref|YP_008142638.1|  56 lkKQGIPEVEIKAKL--------------DIAFQALIG--YVSTNLQPADY-KLLNNVKNVLDAVKVNGHISGILTG 115
                                       443333333333333..............444444444..55555555555.9***************999****** PP

                                       SEHHHHHHHHHHTT.GGGE.SEEEEHHCESSTTTSHHHHHHHHHHHT..STGGGEEEEESSHHHHHHHHHT CS
                                       xxxxxxxxxxxxxx.xxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 143 dnpetaeraanqlG.ddyf.daviasdietvakpspegkvaaireLq..gkpeevamVGDgvnDaaalaaA 209
                                       + +  ae  ++++G ++yf  + ++sd         + + +ai++++  ++ +e+  +GD++ D++a+++A
  gi|518653118|ref|YP_008142638.1| 116 NLQPIAEIRLQHAGiEEYFiTGGYGSDSII----RSKLVDYAIQRYGsnINRSEIYLIGDTPLDIKAAREA 182
                                       ***999988888**8888834444433333....667799******88899******************98 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.81   3.6e+03      32      58 ..      35      61 ..      34      73 .. 0.71
   2 !   28.8   0.0   2.2e-10   9.7e-07       9      61 ..     149     202 ..     146     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.81
                                      TTHHHHHHHCT-EEEEESSSSS-TTTH CS
                    Hydrolase_like 32 atDiagAnnaGwksvLVltGvtrpedl 58
                                      +tDi++  ++G++   +  G  +++  
  gi|518653118|ref|YP_008142638.1| 35 DTDIKSFPRHGMTDTGIMYGLLKKQGI 61
                                      789998888998888888777666554 PP

  == domain 2  score: 28.8 bits;  conditional E-value: 2.2e-10
                                       HHHHHHHHH---..GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHH CS
                    Hydrolase_like   9 mydfalevlgsd..peevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleep 61 
                                       ++d+a +++gs+  ++e+++iGD+   Di++A++a    v ++tGv+  +dl+++
  gi|518653118|ref|YP_008142638.1| 149 LVDYAIQRYGSNinRSEIYLIGDT-PLDIKAAREASTGAVGIATGVYPITDLSAA 202
                                       67999999966655999*******.99********************99998843 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1655.46
//
Query:       gi|518653119|ref|YP_008142639.1|  [L=316]
Description: hypothetical protein FACI_IFERC00001G1758 [Ferroplasma acidarmanus fer1]
Scores for 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  167.9   0.1    3.9e-37  127.9   0.0    2.2  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
    8.8e-34  116.0   0.1    1.8e-33  115.0   0.1    1.5  1  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
      3e-05   24.2   0.1    0.00019   21.6   0.1    2.1  1  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
      0.001   19.6   0.0     0.0022   18.5   0.0    1.6  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
     0.0077   16.2   0.0      0.014   15.4   0.0    1.6  1  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
  ------ inclusion threshold ------
       0.02   14.9   0.2       0.11   12.5   0.0    2.0  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.032   13.9   0.6       0.14   11.8   0.1    2.0  2  ApbA            Ketopantoate reductase PanE/ApbA
      0.045   13.1   0.0      0.075   12.4   0.0    1.3  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
      0.096   12.8   0.2       0.18   11.9   0.2    1.5  1  DUF2120         Uncharacterized protein conserved in archaea 
      0.098   11.9   0.0       0.14   11.4   0.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0     4e-13   7.2e-10       1      51 [.       4      54 ..       4      73 .. 0.85
   2 !  127.9   0.0   2.2e-40   3.9e-37      32     170 ..      64     202 ..      56     217 .. 0.92

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 4e-13
                                      EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N  1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51
                                      k+++iGaG mG++ia+vfa +g++V l d + e ++++ ++++k l+  ++
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYSVYLKDQNMEYVNRGISHVRKVLDDYQS 54
                                      69******************************************9988755 PP

  == domain 2  score: 127.9 bits;  conditional E-value: 2.2e-40
                                       HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCHHCEEEES-HHHHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTS CS
                           3HCDH_N  32 eealekalekieksleklvekgklkeeeveaalarisfttdleeavdadlviEavvEnlelKrkvfaelekiakpda 108
                                        +++e+   +++++ ++ ++k+  k+ +++ ++++i++ ++++e+ ++ lviEav+E+ e+K+++f+el+++  +++
  gi|518653119|ref|YP_008142639.1|  64 IKRIERNGIELTETQKNTIKKNLGKQLDIDGIISNIHPVESYKELSQCGLVIEAVFEKQEIKNDLFRELSSYFGENT 140
                                       5566666667888999999999999**************************************************** PP

                                       EEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE-TT--HHHHHHHHHHHHHT CS
                           3HCDH_N 109 ilasnTSslsiselaealkrperviglHFfnPpplmkLvEvvrgekTseetvatvvelakki 170
                                       ilasnTSslsi+e+a++ k pe+ i++HFfnPp++m+LvE+v++ +T ++tv+t++ l+  +
  gi|518653119|ref|YP_008142639.1| 141 ILASNTSSLSITEMAANYKYPENNIIIHFFNPPYTMPLVEIVPALQTGSKTVETAYSLISGL 202
                                       *******************************************************9998876 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.0   0.1     1e-36   1.8e-33       1      97 []     219     314 ..     219     314 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.0 bits;  conditional E-value: 1e-36
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+vnR+l++l+nea+++veeg+a+ +++D  m++g+G+pmGpfel d+vgld+++++l+ +++++g+ +  p++ l
  gi|518653119|ref|YP_008142639.1| 219 GFIVNRILIQLINEAIKIVEEGIADEKSVDIGMKKGAGFPMGPFELGDYVGLDIVYDVLKSFNKAYGDAYI-PPERL 294
                                       9*******************************************************************966.69*** PP

                                       HHHHHTT--BGGGTBSSSBC CS
                             3HCDH  78 eklveagrlgrktgkgfyky 97 
                                       +++v ag lgrktgkgfy+y
  gi|518653119|ref|YP_008142639.1| 295 KNMVIAGYLGRKTGKGFYEY 314
                                       ******************98 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.1e-07   0.00019       1      56 [.       4      59 ..       4     173 .. 0.90

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTTEEE-SSHHHHHHHC CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelvaegakaaesieelvasl 56
                                      kig+iG G MGs++a+ ++ +gy+v++ + + e v++ +++  k++++ ++ ++s+
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYSVYLKDQNMEYVNRGISHVRKVLDDYQSYMDSM 59
                                      79*******************************99999999988888888777766 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.2e-06    0.0022       1      42 [.       4      48 ..       4      72 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.2e-06
                                      EEEEETTSHHHHHHHHHHHHTTS....-GGCEEEEEESSCCCHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaaga....qpheivvansrnpekaeel 42
                                      kigiiGaG mg+++a+ ++ +g+    +++++    +r  + +++ 
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYsvylKDQNME-YVNRGISHVRKV 48
                                      7*********************55553333333.335555555555 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   7.9e-06     0.014       1      32 [.       4      35 ..       4      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 7.9e-06
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-H CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvree 32
                                      ki+++GaG+ G+++A v+a ng +v l  ++ 
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYSVYLKDQNM 35
                                      79********************9998866655 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.4e-05      0.11      14      65 ..       4      60 ..       2      85 .. 0.74
   2 ?   -0.4   0.0      0.63   1.1e+03      56      86 ..     119     149 ..     113     163 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.4e-05
                                      EEEEES-SHHHHHHHHHHHCCT-......CEEEEEESSHHHHHHHHHHHT.ET-EEEE CS
                      Shikimate_DH 14 kvlliGaGemaelvakhLlakgv......kkvvvaNRtlerakelaeelkgeeiealk 65
                                      k+ +iGaG m++ +a+ ++ +g+      +++  +NR +++++++ ++++++ +  ++
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYsvylkdQNMEYVNRGISHVRKVLDDYQSY-MDSMP 60
                                      899***************9888733333357888999999999999999766.44444 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.63
                                       HT.ET-EEEEGCGHHHHHHT-SEEEE-SSSS CS
                      Shikimate_DH  56 lkgeeiealkleelkellaeadvvisatase 86 
                                       ++++ei+   + el+++  e+ ++ s t+s 
  gi|518653119|ref|YP_008142639.1| 119 FEKQEIKNDLFRELSSYFGENTILASNTSSL 149
                                       577889999999********99999999885 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   7.7e-05      0.14       1      31 [.       5      35 ..       5      63 .. 0.82
   2 ?    0.0   0.0      0.33     6e+02      32      52 ..      63      83 ..      58     146 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.7e-05
                                      EEEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  1 iailGaGaiGsllaakLakagadvtlilrsr 31
                                      i i+GaGa+Gs +a   a +g+ v+l +++ 
  gi|518653119|ref|YP_008142639.1|  5 IGIIGAGAMGSSIAEVFAFNGYSVYLKDQNM 35
                                      89***************99***999977765 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.33
                                      HHHHHHHHCEEEEETTCEEEE CS
                              ApbA 32 rlealkknGlrltseggeeil 52
                                      +++++++nG++lt+ ++++i 
  gi|518653119|ref|YP_008142639.1| 63 EIKRIERNGIELTETQKNTIK 83
                                      578899999999988854443 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   4.2e-05     0.075      38      69 ..       4      35 ..       2      57 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 4.2e-05
                                      EEEEES-SHHHHHHHHHHHHTT-EEEEESSSH CS
                      2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydrsk 69
                                      ++GiiG+G++G+++a++++  g  v+  d++ 
  gi|518653119|ref|YP_008142639.1|  4 KIGIIGAGAMGSSIAEVFAFNGYSVYLKDQNM 35
                                      79*****************9999999988764 PP

>> DUF2120  Uncharacterized protein conserved in archaea (DUF2120)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2    0.0001      0.18       7      75 ..      17      90 ..      12     129 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0001
                           DUF2120  7 mkeldaFkGSkplldkeeiLiv.rgvsrkkeeleeleskleel....lekldaeevdleseeakkliekldesi 75
                                      + e+ aF+G    l+++++  v rg+s  ++ l++++s+++++    +++++ + ++l++ + +++ ++l++++
  gi|518653119|ref|YP_008142639.1| 17 IAEVFAFNGYSVYLKDQNMEYVnRGISHVRKVLDDYQSYMDSMpdkeIKRIERNGIELTETQKNTIKKNLGKQL 90
                                      556679999988888888866559****************9984444567888888888888888877777744 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 ?   11.4   0.0   7.9e-05      0.14       3      78 ..       5      82 ..       3     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 7.9e-05
                                      EEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH.HCHHHHHHHHHHHHH.HHHHCHHHHCCCCHCCTCEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  3 vvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll.skallgvaedaeias.evvkklnqgielllgeevvki 78
                                      + +iG+G+ G + a+  a +g+ v+l +++ + +n+g++   k+l  +++  + +  +++k+++ + + l+++++ +i
  gi|518653119|ref|YP_008142639.1|  5 IGIIGAGAMGSSIAEVFAFNGYSVYLKDQNMEYVNRGISHvRKVLDDYQSYMDSMPdKEIKRIERNGIELTETQKNTI 82
                                      568999999999999999999999999888888888888755566666555555557555555555222333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       804  (0.0448435); expected 358.6 (0.02)
Passed bias filter:                      617  (0.0344135); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.30s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2133.21
//
Query:       gi|518653120|ref|YP_008142640.1|  [L=68]
Description: hypothetical protein FACI_IFERC00001G1759 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00028   20.7   1.6      0.023   14.6   0.1    2.1  2  DUF35_N          Rubredoxin-like zinc ribbon domain (DUF35_N)
    0.00031   20.8   0.5       0.73   10.0   0.2    2.2  2  Zn-ribbon_8      Zinc ribbon domain
    0.00058   19.7   0.8      0.039   13.9   0.1    2.2  2  Nudix_N_2        Nudix N-terminal
    0.00072   18.8   0.4     0.0012   18.2   0.4    1.3  1  zf-TFIIB         Transcription factor zinc-finger
     0.0018   17.6   1.9       0.31   10.5   0.1    2.2  2  zf-ribbon_3      zinc-ribbon domain
     0.0037   16.9   3.4        1.4    8.7   0.6    2.6  2  A2L_zn_ribbon    A2L zinc ribbon domain
     0.0038   16.7   1.7      0.085   12.4   0.1    2.2  2  TF_Zn_Ribbon     TFIIB zinc-binding
     0.0043   17.2   1.2       0.81    9.9   0.1    2.2  2  zf-RING_7        C4-type zinc ribbon domain
     0.0047   17.0   0.9       0.09   12.8   1.1    2.0  2  CpXC             CpXC protein
     0.0048   17.0   0.1     0.0055   16.8   0.1    1.1  1  Mut7-C           Mut7-C RNAse domain
     0.0069   17.0   0.4        1.3    9.8   0.1    2.2  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
     0.0078   16.2   0.4      0.014   15.4   0.4    1.4  1  DZR              Double zinc ribbon
     0.0082   16.6   3.0      0.093   13.2   0.6    2.3  2  zf-C2H2          Zinc finger, C2H2 type
  ------ inclusion threshold ------
      0.012   15.4   1.7       0.89    9.4   0.2    2.3  2  zinc_ribbon_2    zinc-ribbon domain
      0.012   15.3   0.7       0.47   10.2   0.0    2.3  2  zf_C2H2_6        Zinc Finger domain
      0.014   15.5   0.1      0.016   15.3   0.1    1.2  1  TerY_C           TerY-C metal binding domain
       0.02   14.5   0.6       0.74    9.5   0.1    2.1  2  zf_UBZ           Ubiquitin-Binding Zinc Finger
      0.023   15.5   1.9        1.3   10.0   0.2    2.4  2  zf-C2H2_4        C2H2-type zinc finger
      0.024   14.7   1.2      0.046   13.8   1.2    1.4  1  zf-Mss51         Zinc-finger of mitochondrial splicing suppre
      0.025   14.3   0.2        1.8    8.4   0.0    2.2  2  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger
      0.026   14.9   1.1       0.23   11.9   0.1    2.2  2  zf-H2C2_2        Zinc-finger double domain
      0.032   15.0   0.1       0.04   14.7   0.1    1.2  1  zinc_ribbon_15   zinc-ribbon family
      0.033   14.1   1.2        4.8    7.2   0.2    2.2  2  zinc_ribbon_4    zinc-ribbon domain
      0.034   14.1   1.7       0.19   11.7   1.7    2.0  1  Ogr_Delta        Ogr/Delta-like zinc finger
      0.057   12.0   0.1      0.065   11.8   0.1    1.0  1  Terminase_GpA    Phage terminase large subunit (GpA)
      0.057   13.5   6.4        1.4    9.0   0.6    2.3  2  zf-ACC           Acetyl-coA carboxylase zinc finger domain
      0.061   13.6   5.1        2.9    8.2   0.7    2.2  2  zinc_ribbon_9    zinc-ribbon
      0.067   13.5   0.8       0.77   10.1   0.8    1.9  1  GFA              Glutathione-dependent formaldehyde-activatin
      0.073   13.1   3.6       0.13   12.3   0.2    2.1  2  ADK_lid          Adenylate kinase, active site lid
      0.074   13.2   0.1        2.8    8.1   0.0    2.2  2  DUF2256          Uncharacterized protein conserved in bacteri
      0.075   13.4   1.3       0.13   12.7   1.3    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
       0.08   12.9   2.0        1.3    9.0   0.6    2.2  2  Zn_ribbon_SprT   SprT-like zinc ribbon domain
      0.083   13.3   0.4         11    6.5   0.0    2.1  2  zf-IS66          zinc-finger binding domain of transposase IS
      0.094   12.4   5.3       0.61    9.8   0.7    2.2  2  zf-NADH-PPase    NADH pyrophosphatase zinc ribbon domain
        0.1   12.6   0.1       0.12   12.4   0.1    1.1  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.12   12.4   5.5        2.8    8.0   0.4    2.1  2  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.15   12.2   1.2        2.4    8.3   0.1    2.1  2  Spt4             Spt4/RpoE2 zinc finger
       0.18   11.4   3.9       0.27   10.8   0.2    2.1  2  Sgf11            Sgf11 (transcriptional regulation protein)
       0.21   11.6   6.0        2.3    8.2   6.0    2.1  2  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
       0.27   11.0   4.3        1.5    8.6   4.3    1.9  1  zinc_ribbon_10   Predicted integral membrane zinc-ribbon meta
       0.28   11.5   3.3        4.3    7.7   3.4    2.1  2  zf-Di19          Drought induced 19 protein (Di19), zinc-bind
       0.29   11.4   1.2         11    6.4   0.2    2.2  2  Ribosomal_L32p   Ribosomal L32p protein family
       0.36   10.8   4.0        1.4    8.9   0.2    2.2  2  zf-C2HC_2        zinc-finger of a C2HC-type
       0.48   11.0   3.0        2.6    8.7   3.0    2.0  1  Trm112p          Trm112p-like protein
        3.6    7.4   5.9        3.4    7.5   0.6    2.2  2  Rubredoxin_2     Rubredoxin metal binding domain


Domain annotation for each model (and alignments):
>> DUF35_N  Rubredoxin-like zinc ribbon domain (DUF35_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.2     0.037        15      27      31 ..      13      17 ..      11      22 .. 0.77
   2 !   14.6   0.1   5.7e-05     0.023       7      22 ..      36      51 ..      34      53 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.037
                           DUF35_N 27 vCphC 31
                                      vCphC
  gi|518653120|ref|YP_008142640.1| 13 VCPHC 17
                                      8**** PP

  == domain 2  score: 14.6 bits;  conditional E-value: 5.7e-05
                           DUF35_N  7 grLvgqrCpdCGtvqf 22
                                      g++ +  Cp+CG+v++
  gi|518653120|ref|YP_008142640.1| 36 GEFEAYVCPNCGRVFY 51
                                      899999********87 PP

>> Zn-ribbon_8  Zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.0    0.0029       1.2      21      35 ..       6      20 ..       2      23 .. 0.72
   2 !   10.0   0.2    0.0018      0.73       6      15 ..      41      50 ..      38      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0029
                       Zn-ribbon_8 21 isdapltaCPeCgse 35
                                      +s ++ t+CP+C+ +
  gi|518653120|ref|YP_008142640.1|  6 MSINNITVCPHCNLD 20
                                      66666777****865 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0018
                       Zn-ribbon_8  6 YrCeeCghef 15
                                      Y C +Cg++f
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVF 50
                                      9999999998 PP

>> Nudix_N_2  Nudix N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.064        26      24      29 ..      13      18 ..      12      31 .. 0.84
   2 !   13.9   0.1   9.8e-05     0.039      23      33 ..      41      51 ..      34      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.064
                                      EETTTT CS
                         Nudix_N_2 24 vCpaCg 29
                                      vCp+C+
  gi|518653120|ref|YP_008142640.1| 13 VCPHCN 18
                                      788886 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.8e-05
                                      EEETTTTEEE- CS
                         Nudix_N_2 23 lvCpaCgtihY 33
                                      +vCp+Cg ++Y
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVFY 51
                                      8********** PP

>> zf-TFIIB  Transcription factor zinc-finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.4   2.9e-06    0.0012       2      26 ..      14      47 ..      13      50 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2.9e-06
                          zf-TFIIB  2 CPkCqdele.........eserggveidyCpqCr 26
                                      CP C+ ++e          + +g++e ++Cp+C+
  gi|518653120|ref|YP_008142640.1| 14 CPHCNLDMElktapyeqnNVTLGEFEAYVCPNCG 47
                                      *****77777799776666666***********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 ?    6.7   0.2     0.012       4.7      17      22 ..      12      17 ..      12      21 .. 0.73
   2 !   10.5   0.1   0.00078      0.31      18      23 ..      42      47 ..      37      51 .. 0.64

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.012
                       zf-ribbon_3 17 nvCpyC 22
                                      +vCp+C
  gi|518653120|ref|YP_008142640.1| 12 TVCPHC 17
                                      589999 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00078
                       zf-ribbon_3 18 vCpyCG 23
                                      vCp+CG
  gi|518653120|ref|YP_008142640.1| 42 VCPNCG 47
                                      566666 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 !    8.3   0.1    0.0048       1.9       1      22 [.       9      29 ..       9      30 .. 0.83
   2 !    8.7   0.6    0.0036       1.4      22      31 ..      41      50 ..      37      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0048
                     A2L_zn_ribbon  1 snlkvCsvCggngilnseqgyl 22
                                      +n+ vC  C+ +++l ++  y+
  gi|518653120|ref|YP_008142640.1|  9 NNITVCPHCNLDMEL-KTAPYE 29
                                      57889999*****99.988776 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0036
                     A2L_zn_ribbon 22 lvCieCgasf 31
                                      +vC++Cg +f
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVF 50
                                      9******876 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.1     0.093        37       2       9 ..      13      20 ..      12      34 .. 0.67
   2 !   12.4   0.1   0.00021     0.085       1      10 [.      41      50 ..      39      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.093
                                      EETTTTCE CS
                      TF_Zn_Ribbon  2 kCPnCgst 9 
                                      +CP C+ +
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLD 20
                                      79999855 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00021
                                      EEETTTTCEE CS
                      TF_Zn_Ribbon  1 ykCPnCgstn 10
                                      y+CPnCg  +
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVF 50
                                      6777777764 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 ?    6.4   0.1     0.025       9.9      22      30 ..      10      18 ..       3      18 .. 0.83
   2 !    9.9   0.1     0.002      0.81      26      31 ..      43      48 ..      31      49 .. 0.91

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.025
                                      B-EE-TTT- CS
                         zf-RING_7 22 evvtCpeCG 30
                                      ++  Cp+C+
  gi|518653120|ref|YP_008142640.1| 10 NITVCPHCN 18
                                      5889****7 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.002
                                      -TTT-- CS
                         zf-RING_7 26 CpeCGR 31
                                      Cp+CGR
  gi|518653120|ref|YP_008142640.1| 43 CPNCGR 48
                                      *****9 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.2      0.14        55      38      49 ..      12      23 ..       2      30 .. 0.68
   2 !   12.8   1.1   0.00023      0.09      20      49 ..      23      52 ..      12      57 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.14
                              CpXC 38 atCpkCgatakl 49
                                      ++Cp+C+ + +l
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCNLDMEL 23
                                      458888766655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00023
                              CpXC 20 adedpelkeklldgslfeatCpkCgatakl 49
                                      +++ p  ++++  g++  ++Cp+Cg+ ++ 
  gi|518653120|ref|YP_008142640.1| 23 LKTAPYEQNNVTLGEFEAYVCPNCGRVFYT 52
                                      5566777889999************98876 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.1   1.4e-05    0.0055      83     143 ..       5      60 ..       1      63 [. 0.74

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.4e-05
                            Mut7-C  83 klslkpelsrCvaCngeleevekeevkervpekvyeeadeftrCekCrkvfWkGshwerve 143
                                       ++s+++ ++ C +Cn  +e  ++   +++v    +e    ++ C++C++vf     +e ++
  gi|518653120|ref|YP_008142640.1|   5 TMSINN-ITVCPHCNLDMELKTAPYEQNNVTLGEFE----AYVCPNCGRVFYTDKGYEGIN 60 
                                       566776.999*****988877777666666666665....567********9877777665 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0     0.056        22       4      12 ..      13      21 ..      11      31 .. 0.71
   2 !    9.8   0.1    0.0032       1.3       4      18 ..      42      56 ..      39      60 .. 0.84

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.056
                           zf-ISL3  4 rCPnCgskt 12
                                      +CP+C+  +
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLDM 21
                                      8****8665 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0032
                           zf-ISL3  4 rCPnCgsktvvkhgk 18
                                      +CPnCg++  +++g+
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGRVFYTDKGY 56
                                      7******98788886 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.4   3.6e-05     0.014      13      37 ..      12      49 ..       7      55 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.6e-05
                               DZR 13 rfCseCgtklkavaa.............edrCpsCgek 37
                                       +C++C+ +++  +a             +++Cp+Cg+ 
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCNLDMELKTApyeqnnvtlgefeAYVCPNCGRV 49
                                      58*****998766668899*****************87 PP

>> zf-C2H2  Zinc finger, C2H2 type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1      0.23        91       2       7 ..      13      18 ..      12      26 .. 0.85
   2 !   13.2   0.6   0.00023     0.093       1      12 [.      41      52 ..      41      57 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.23
                                      EETTTT CS
                           zf-C2H2  2 kCpdCg 7 
                                      +Cp+C+
  gi|518653120|ref|YP_008142640.1| 13 VCPHCN 18
                                      7****8 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00023
                                      EEETTTTEEESS CS
                           zf-C2H2  1 ykCpdCgksFkr 12
                                      y+Cp Cg++F +
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVFYT 52
                                      9*********86 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.043        17       2       5 ..      14      17 ..       9      23 .. 0.79
   2 ?    9.4   0.2    0.0022      0.89       2       7 ..      43      48 ..      39      49 .. 0.72

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.043
                     zinc_ribbon_2  2 CpnC 5 
                                      Cp+C
  gi|518653120|ref|YP_008142640.1| 14 CPHC 17
                                      7777 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0022
                     zinc_ribbon_2  2 CpnCGa 7 
                                      CpnCG+
  gi|518653120|ref|YP_008142640.1| 43 CPNCGR 48
                                      777775 PP

>> zf_C2H2_6  Zinc Finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0    0.0012      0.47       2      10 ..      11      19 ..      10      24 .. 0.88
   2 ?    3.6   0.2      0.14        55       2      12 ..      40      50 ..      39      53 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0012
                         zf_C2H2_6  2 AtVCpYCsL 10
                                       tVCp C+L
  gi|518653120|ref|YP_008142640.1| 11 ITVCPHCNL 19
                                      59******9 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.14
                         zf_C2H2_6  2 AtVCpYCsLRF 12
                                      A VCp C+  F
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGRVF 50
                                      77*****9666 PP

>> TerY_C  TerY-C metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.3   0.1   4.1e-05     0.016      66     119 ..       3      56 ..       1      67 [. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.1e-05
                            TerY_C  66 vntseLeGapgCPhCgnalafavCeCgkl.lCidgeeeatCpwCgkevkfgease 119
                                       v t++++  + CPhC   + + +    +  + +++ e  +Cp+Cg+    + ++ 
  gi|518653120|ref|YP_008142640.1|   3 VLTMSINNITVCPHCNLDMELKTAPYEQNnVTLGEFEAYVCPNCGRVFYTD-KGY 56 
                                       779999999*******99999887665541456889999******876555.333 PP

>> zf_UBZ  Ubiquitin-Binding Zinc Finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.12        48       4      10 ..      13      19 ..      10      25 .. 0.82
   2 ?    9.5   0.1    0.0018      0.74       2      14 ..      40      52 ..      39      55 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.12
                            zf_UBZ  4 lCerCgk 10
                                      +C+ C+ 
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNL 19
                                      8****96 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0018
                            zf_UBZ  2 tylCerCgkeipe 14
                                       y+C+ Cg+ + +
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGRVFYT 52
                                      69******99865 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1      0.14        57       2       7 ..      13      18 ..      12      25 .. 0.82
   2 ?   10.0   0.2    0.0034       1.3       1      14 [.      41      54 ..      41      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.14
                         zf-C2H2_4  2 kCpiCg 7 
                                       Cp+C+
  gi|518653120|ref|YP_008142640.1| 13 VCPHCN 18
                                      6****6 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0034
                         zf-C2H2_4  1 fkCpiCgksFsskk 14
                                      + Cp Cg++F + k
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRVFYTDK 54
                                      89********7655 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 ?   13.8   1.2   0.00011     0.046       2      30 ..      14      54 ..      13      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                          zf-Mss51  2 CPvpkhkqt............apkhvdfeCpdCGiptycse 30
                                      CP+++ +++              +  ++ Cp+CG + y ++
  gi|518653120|ref|YP_008142640.1| 14 CPHCNLDMElktapyeqnnvtLGEFEAYVCPNCGRVFYTDK 54
                                      ****9999999****999888778889*******9999865 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.0    0.0046       1.8       3      17 ..      13      27 ..      11      31 .. 0.85
   2 ?    4.4   0.0      0.08        32       3       9 ..      42      48 ..      40      62 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0046
                                      E-SSS--EEEEEE-S CS
                    zf-C4_Topoisom  3 kCPkCggdLvlkrgk 17
                                       CP C+ d+ lk+  
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLDMELKTAP 27
                                      6********999866 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.08
                                      E-SSS-- CS
                    zf-C4_Topoisom  3 kCPkCgg 9 
                                       CP Cg 
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGR 48
                                      5****95 PP

>> zf-H2C2_2  Zinc-finger double domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.95   3.8e+02      17      21 ..      14      18 ..       9      20 .. 0.89
   2 ?   11.9   0.1   0.00059      0.23      11      24 ..      36      50 ..      31      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.95
                         zf-H2C2_2 17 CplCd 21
                                      Cp C+
  gi|518653120|ref|YP_008142640.1| 14 CPHCN 18
                                      ****7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00059
                         zf-H2C2_2 11 gekp.yeCplCdkaF 24
                                      ge++ y Cp C+ +F
  gi|518653120|ref|YP_008142640.1| 36 GEFEaYVCPNCGRVF 50
                                      89988*******999 PP

>> zinc_ribbon_15  zinc-ribbon family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1    0.0001      0.04      31      77 ..       6      52 ..       1      56 [. 0.69

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 0.0001
                    zinc_ribbon_15 31 wkkkkpylacskCkslleaskelgkeiekkesse.....kkeCknCgkevee 77
                                      ++  + + +c +C+  +e ++   ++ +     +     +++C+nCg++   
  gi|518653120|ref|YP_008142640.1|  6 MSI-NNITVCPHCNLDMELKTAPYEQNNV----TlgefeAYVCPNCGRVFYT 52
                                      555.67999*********99944333332....234456********98765 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   0.1      0.03        12       3       9 ..      12      18 ..      11      26 .. 0.84
   2 ?    7.2   0.2     0.012       4.8      28      35 ..      43      50 ..      41      51 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.03
                     zinc_ribbon_4  3 itCpsCk 9 
                                      ++Cp+C+
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCN 18
                                      78****8 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
                     zinc_ribbon_4 28 CskCghvF 35
                                      C++Cg vF
  gi|518653120|ref|YP_008142640.1| 43 CPNCGRVF 50
                                      77777776 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 ?   11.7   1.7   0.00048      0.19       2      37 ..      14      50 ..      13      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00048
                         Ogr_Delta  2 CPhCgapaaartsrnlskdvre...ryyqCsnfeCgatf 37
                                      CPhC   +   t  +   +v+      y+C n  Cg  f
  gi|518653120|ref|YP_008142640.1| 14 CPHCNLDMELKTAPYEQNNVTLgefEAYVCPN--CGRVF 50
                                      *****************99999899999**99..98666 PP

>> Terminase_GpA  Phage terminase large subunit (GpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   0.00016     0.065     201     237 ..      14      50 ..      11      60 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
                     Terminase_GpA 201 CphCgelqelsferlkwpegeaeekaryvCphcgsli 237
                                       CphC+  +el+    + ++ +  e  +yvCp+cg + 
  gi|518653120|ref|YP_008142640.1|  14 CPHCNLDMELKTAPYEQNNVTLGEFEAYVCPNCGRVF 50 
                                       *********99666444555599***********875 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.7     0.011       4.2      18      26 .]       9      17 ..       8      17 .. 0.86
   2 ?    9.0   0.6    0.0036       1.4      20      26 .]      40      46 ..      37      46 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.011
                            zf-ACC 18 rnlyVCPkC 26
                                      +n  VCP+C
  gi|518653120|ref|YP_008142640.1|  9 NNITVCPHC 17
                                      6778***** PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0036
                            zf-ACC 20 lyVCPkC 26
                                       yVCP+C
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNC 46
                                      69***** PP

>> zinc_ribbon_9  zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   0.7    0.0072       2.9      21      28 ..      11      18 ..       2      21 .. 0.70
   2 ?    7.9   0.3    0.0091       3.6      19      31 ..      39      50 ..      20      50 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0072
                     zinc_ribbon_9 21 dvlCPhCg 28
                                      +++CPhC+
  gi|518653120|ref|YP_008142640.1| 11 ITVCPHCN 18
                                      346****8 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0091
                     zinc_ribbon_9 19 dsdvlCPhCgggF 31
                                      ++ v CP+Cg  F
  gi|518653120|ref|YP_008142640.1| 39 EAYV-CPNCGRVF 50
                                      3335.****9765 PP

>> GFA  Glutathione-dependent formaldehyde-activating enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.8    0.0019      0.77      34      63 ..      25      54 ..      10      64 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.0019
                               GFA 34 lkeykktadsgnkvtrsfCpeCgsplysee 63
                                      ++ y++++ +  +++ ++Cp+Cg  +y+++
  gi|518653120|ref|YP_008142640.1| 25 TAPYEQNNVTLGEFEAYVCPNCGRVFYTDK 54
                                      4557777778889999*******9999754 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.4      0.57   2.3e+02       3       8 ..      13      18 ..      12      19 .. 0.85
   2 ?   12.3   0.2   0.00032      0.13       3      11 ..      42      50 ..      41      68 .] 0.76

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.57
                                      E-TTT- CS
                           ADK_lid  3 vCpkCG 8 
                                      vCp C+
  gi|518653120|ref|YP_008142640.1| 13 VCPHCN 18
                                      899997 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00032
                                      E-TTT--EE CS
                           ADK_lid  3 vCpkCGrsY 11
                                      vCp+CGr++
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGRVF 50
                                      9******98 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 ?    2.9   0.0       0.3   1.2e+02       9      18 ..      13      22 ..      10      25 .. 0.85
   2 ?    8.1   0.0     0.007       2.8       9      21 ..      42      54 ..      36      58 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.3
                           DUF2256  9 iCavCgrpft 18
                                      +C++C+  ++
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLDME 22
                                      7****99886 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.007
                           DUF2256  9 iCavCgrpftwRk 21
                                      +C+ Cgr f   k
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGRVFYTDK 54
                                      8*******97655 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   1.3   0.00032      0.13       3      36 ..      11      48 ..       9      62 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00032
                   Lar_restr_allev  3 LkpCPfCggravlersqrvvaeigq....cvyCadCga 36
                                      +  CP+C+ + +l+++++ ++++         C +Cg 
  gi|518653120|ref|YP_008142640.1| 11 ITVCPHCNLDMELKTAPYEQNNVTLgefeAYVCPNCGR 48
                                      567*************9999865559999999****98 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0       0.2        82       6      11 ..      13      18 ..       7      22 .. 0.79
   2 ?    9.0   0.6    0.0032       1.3       4      12 ..      40      48 ..      40      51 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.2
                    Zn_ribbon_SprT  6 rCtgCg 11
                                      +C++C 
  gi|518653120|ref|YP_008142640.1| 13 VCPHCN 18
                                      577775 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.0032
                    Zn_ribbon_SprT  4 vYrCtgCgr 12
                                      +Y+C++Cgr
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGR 48
                                      6******95 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 ?    5.3   0.0     0.065        26       2      10 ..      12      20 ..      12      31 .. 0.68
   2 ?    6.5   0.0     0.027        11      38      46 .]      39      47 ..      32      49 .. 0.78

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.065
                           zf-IS66  2 rtCpcCGgl 10
                                      ++Cp+C+ +
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCNLD 20
                                      589999964 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.027
                           zf-IS66 38 pkyaCpcCe 46
                                      ++y Cp+C+
  gi|518653120|ref|YP_008142640.1| 39 EAYVCPNCG 47
                                      678888886 PP

>> zf-NADH-PPase  NADH pyrophosphatase zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.3     0.048        19      23      29 ..      13      19 ..      12      21 .. 0.87
   2 ?    9.8   0.7    0.0015      0.61      23      32 .]      42      51 ..      40      51 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.048
                     zf-NADH-PPase 23 vCpaCgl 29
                                      vCp+C+l
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNL 19
                                      8****97 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0015
                     zf-NADH-PPase 23 vCpaCglehY 32
                                      vCp+Cg+ +Y
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGRVFY 51
                                      9******999 PP

>> HypA  Hydrogenase/urease nickel incorporation, metallochaperone, hypA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00031      0.12      67      95 ..       8      49 ..       2      62 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00031
                                      E--EEEETTTS-EEECHHHHH.............S-TTTSSS CS
                              HypA 67 vpvkvrCreCgkefeleekal.............rCpkCgsa 95
                                      ++  + C +C+ ++el+++ +              Cp+Cg+ 
  gi|518653120|ref|YP_008142640.1|  8 INNITVCPHCNLDMELKTAPYeqnnvtlgefeayVCPNCGRV 49
                                      455678*********8874123478999***********985 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.4    0.0071       2.8      19      26 ..      12      19 ..       3      32 .. 0.80
   2 ?    7.3   0.7     0.012       4.7      19      27 ..      41      48 ..      36      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0071
                     Zn_Tnp_IS1595 19 fvCPhCgs 26
                                       vCPhC  
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCNL 19
                                      68****75 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.012
                     Zn_Tnp_IS1595 19 fvCPhCgsr 27
                                       vCP+Cg r
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCG-R 48
                                      58****9.3 PP

>> Spt4  Spt4/RpoE2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   0.1     0.042        17      19      47 ..      12      41 ..       2      42 .. 0.70
   2 ?    8.3   0.1    0.0059       2.4      14      30 ..      36      53 ..      32      66 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.042
                              Spt4 19 egCpnC.eilelkgdkekvsectseefeGl 47
                                      + Cp C   +elk +  + ++ t  efe +
  gi|518653120|ref|YP_008142640.1| 12 TVCPHCnLDMELKTAPYEQNNVTLGEFEAY 41
                                      68****555666777777777777777765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0059
                              Spt4 14 dqFeeegCpnC.eilelk 30
                                       +Fe   CpnC +++   
  gi|518653120|ref|YP_008142640.1| 36 GEFEAYVCPNCgRVFYTD 53
                                      5899*******7766544 PP

>> Sgf11  Sgf11 (transcriptional regulation protein)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.4      0.47   1.9e+02       4      11 ..      11      18 ..       9      21 .. 0.81
   2 ?   10.8   0.2   0.00067      0.27       4      12 ..      40      48 ..      38      49 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.47
                                      EEE-TTTS CS
                             Sgf11  4 yvtCpnCg 11
                                       ++Cp C+
  gi|518653120|ref|YP_008142640.1| 11 ITVCPHCN 18
                                      579****6 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00067
                                      EEE-TTTSS CS
                             Sgf11  4 yvtCpnCgR 12
                                       ++CpnCgR
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGR 48
                                      689*****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 ?    6.0   0.7     0.029        12      18      25 ..      10      17 ..       7      22 .. 0.80
   2 ?    8.2   6.0    0.0058       2.3       5      26 ..      14      47 ..      11      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.029
                    PhnA_Zn_Ribbon 18 allvCpeC 25
                                       + vCp+C
  gi|518653120|ref|YP_008142640.1| 10 NITVCPHC 17
                                      56789999 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0058
                    PhnA_Zn_Ribbon  5 CplCaSeytY............edgallvCpeCa 26
                                      Cp+C+ + ++             + + +vCp+C+
  gi|518653120|ref|YP_008142640.1| 14 CPHCNLDMELktapyeqnnvtlGEFEAYVCPNCG 47
                                      ***************999999999999******7 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 ?    8.6   4.3    0.0037       1.5      24      52 ..      13      48 ..       7      50 .. 0.69

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0037
                    zinc_ribbon_10 24 ICskChshnGlap......keeleev.kyrCpkCga 52
                                      +C++C+    l +      + +l e+  y+Cp+Cg 
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLDMELKTapyeqnNVTLGEFeAYVCPNCGR 48
                                      7999998877765535444334445558******96 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 ?    7.7   3.4     0.011       4.3       4      38 ..      13      47 ..      10      54 .. 0.82
   2 ?    5.2   0.3     0.064        26       2      14 ..      40      53 ..      39      59 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.011
                           zf-Di19  4 tCPyCgkeltvkeLveHvedeHrveskevvCPvCa 38
                                       CP+C+ +++ k+     ++    e + +vCP C 
  gi|518653120|ref|YP_008142640.1| 13 VCPHCNLDMELKTAPYEQNNVTLGEFEAYVCPNCG 47
                                      5*****99999988888888888899999999995 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.064
                           zf-Di19  2 sftCPyCgk.eltv 14
                                       + CP Cg+  +t+
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGRvFYTD 53
                                      57899999844555 PP

>> Ribosomal_L32p  Ribosomal L32p protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.1      0.16        62      22      33 ..       7      18 ..       2      24 .. 0.77
   2 ?    6.4   0.2     0.027        11      41      51 ..      42      54 ..      38      58 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.16
                                      ----EEEETTTC CS
                    Ribosomal_L32p 22 kapnlvecpncg 33
                                      + +n+++cp c+
  gi|518653120|ref|YP_008142640.1|  7 SINNITVCPHCN 18
                                      567889999996 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.027
                                      -BTTTT..BSSSB CS
                    Ribosomal_L32p 41 vcpscG..yYkgr 51
                                      vcp+cG  +Y  +
  gi|518653120|ref|YP_008142640.1| 42 VCPNCGrvFYTDK 54
                                      8888888877765 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 ?    3.2   0.5      0.21        83       5       9 ..      14      18 ..      12      18 .. 0.88
   2 ?    8.9   0.2    0.0036       1.4       5      12 ..      43      50 ..      42      53 .. 0.86

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.21
                         zf-C2HC_2  5 CpkCg 9 
                                      Cp+C+
  gi|518653120|ref|YP_008142640.1| 14 CPHCN 18
                                      ****7 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0036
                         zf-C2HC_2  5 CpkCgRsF 12
                                      Cp+CgR F
  gi|518653120|ref|YP_008142640.1| 43 CPNCGRVF 50
                                      ******55 PP

>> Trm112p  Trm112p-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   3.0    0.0066       2.6      53      68 .]      40      55 ..       7      55 .. 0.68

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0066
                                      EEEETTTTEEEEEETT CS
                           Trm112p 53 eLvCpncgraYpIkdG 68
                                      + vCpncgr+++ ++G
  gi|518653120|ref|YP_008142640.1| 40 AYVCPNCGRVFYTDKG 55
                                      559********96665 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.5      0.27   1.1e+02      17      21 ..      14      18 ..      13      19 .. 0.83
   2 ?    7.5   0.6    0.0086       3.4       1       9 [.      41      49 ..      41      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.27
                      Rubredoxin_2 17 CpsCg 21
                                      Cp+C+
  gi|518653120|ref|YP_008142640.1| 14 CPHCN 18
                                      99996 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0086
                      Rubredoxin_2  1 YvCsqCGfe 9 
                                      YvC +CG +
  gi|518653120|ref|YP_008142640.1| 41 YVCPNCGRV 49
                                      899999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       558  (0.0311228); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        95  (0.00529868); expected 17.9 (0.001)
Passed Fwd filter:                        45  (0.0025099); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              45  [number of targets reported over threshold]
# CPU time: 0.48u 0.28s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 419.32
//
Query:       gi|518653121|ref|YP_008142641.1|  [L=140]
Description: glucose/galactose transporter [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   47.5   3.9    1.3e-12   47.3   3.9    1.1  1  Sugar_tr         Sugar (and other) transporter
    7.3e-06   25.1   9.2    9.4e-06   24.8   9.2    1.1  1  MFS_1            Major Facilitator Superfamily
    7.7e-05   21.3   2.7    9.2e-05   21.0   2.7    1.1  1  MFS_3            Transmembrane secretion effector
     0.0049   15.3   0.3     0.0063   15.0   0.3    1.1  1  TRI12            Fungal trichothecene efflux pump (TRI12)
     0.0073   16.3   1.5      0.009   16.0   1.5    1.1  1  CarS-like        CDP-archaeol synthase
  ------ inclusion threshold ------
      0.028   14.3   0.1      0.034   14.0   0.1    1.3  1  Lipase_3         Lipase (class 3)
       0.13   11.4   5.5      0.035   13.3   2.5    1.5  2  FTR1             Iron permease FTR1 family
       0.14   11.9   5.1       0.36   10.6   5.0    1.7  1  Gly-zipper_YMGG  YMGG-like Gly-zipper
       0.18   12.4   2.1       0.35   11.4   2.1    1.5  1  YtxH             YtxH-like protein
       0.57   10.3   5.2        2.4    8.3   5.2    2.0  1  VMA21            VMA21-like domain
        3.3    7.8   9.7        1.8    8.6   6.1    2.3  2  Gly-zipper_Omp   Glycine zipper


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   3.9   8.1e-16   1.3e-12       1     105 [.      28     121 ..      28     137 .. 0.85

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 8.1e-16
                                       HHHHHHHHHHHHHHHHHCGGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHH CS
                          Sugar_tr   1 valvaalggllfgYdtgvigafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkk 77 
                                       v+l+a++gg+lfgYdt  ig+ l+++ fakn   +            +g + + +++Ga++G+l+a ll+d++GRk 
  gi|518653121|ref|YP_008142641.1|  28 VTLLATIGGFLFGYDTSNIGTDLSFIPFAKNLATTDPF--------VYGYLIAGASLGAAVGALIAALLTDKYGRKF 96 
                                       6899***********************77665444333........45899999*********************** PP

                                       HHHHHHHHHHHHHHHHH-TTTTSS-TGG CS
                          Sugar_tr  78 slliaavlfvigavlqaaakgknsvevl 105
                                        l++ a+++ iga+l+a++    ++ +l
  gi|518653121|ref|YP_008142641.1|  97 LLITDAAIYTIGAILSAVSV---NLVML 121
                                       *******************9...44444 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   9.2   5.8e-09   9.4e-06       3      89 ..      34     122 ..      24     127 .. 0.83

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 5.8e-09
                             MFS_1   3 laaflsalarsilgpalpl.alaedlg.ispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgll 77 
                                       +++fl +++ s++g+ l+    a++l   +p ++g l+++ +lgaav++l+++ l+d++Gr+ +l++ ++++ +g +
  gi|518653121|ref|YP_008142641.1|  34 IGGFLFGYDTSNIGTDLSFiPFAKNLAtTDPFVYGYLIAGASLGAAVGALIAALLTDKYGRKFLLITDAAIYTIG-A 109
                                       789999999999999888666666666578888******************************************.6 PP

                             MFS_1  78 lllfa.sslwlll 89 
                                       +l+ +  +l +ll
  gi|518653121|ref|YP_008142641.1| 110 ILSAVsVNLVMLL 122
                                       6663224433444 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   2.7   5.7e-08   9.2e-05     225     309 ..      34     120 ..      23     130 .. 0.80

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 5.7e-08
                             MFS_3 225 vRaalFglsasavlaLLPlv..ardqldgdalvyGillgalGvGAilgalllsrLRerlsserlvllaavalAlvll 299
                                       + ++lFg  +s + + L ++  a++   +d+ vyG+l+++  +GA +gal+ + L ++ + + l+ + a+ + + ++
  gi|518653121|ref|YP_008142641.1|  34 IGGFLFGYDTSNIGTDLSFIpfAKNLATTDPFVYGYLIAGASLGAAVGALIAALLTDKYGRKFLLITDAAIYTIGAI 110
                                       56899999999885555444338999***********************************9998887777777666 PP

                             MFS_3 300 slalasslwv 309
                                         a++ +l++
  gi|518653121|ref|YP_008142641.1| 111 LSAVSVNLVM 120
                                       6666655544 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   3.9e-06    0.0063      88     141 ..      75     128 ..      67     135 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.9e-06
                             TRI12  88 ttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtll 141
                                       ++g av  l+   ltd++gr+ ++i    +  +gai+ + + ++  ll a  ll
  gi|518653121|ref|YP_008142641.1|  75 SLGAAVGALIAALLTDKYGRKFLLITDAAIYTIGAILSAVSVNLVMLLGAYPLL 128
                                       5799*************************************9999999998776 PP

>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.5   5.5e-06     0.009      49     141 ..      29     118 ..      18     128 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 5.5e-06
                         CarS-like  49 tyrGtvaGvlvGvlvgliqglleklsilaldssgsvlefvilalllafGallGdavGsfikrrlkierGkpalil.d 124
                                       t   t++G l G  +++i     +ls   +   ++  + ++ ++l+a Ga lG avG++i   l  + G+++l++ d
  gi|518653121|ref|YP_008142641.1|  29 TLLATIGGFLFGYDTSNIG---TDLSFIPFAKNLATTDPFVYGYLIA-GASLGAAVGALIAALLTDKYGRKFLLItD 101
                                       4455566666666666655...46688888899999999****9987.9**********************976538 PP

                         CarS-like 125 qldfvlgalllaypvkl 141
                                          + +ga+l a  v+l
  gi|518653121|ref|YP_008142641.1| 102 AAIYTIGAILSAVSVNL 118
                                       89999**9998765544 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.1e-05     0.034      65     103 ..      67     108 ..       3     112 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.1e-05
                                       EEEEEEEETHHHHHHHHHHHHHHHTT-SS...---EEEEEES CS
                          Lipase_3  65 ysivvtGHSLGgalAlLaaldlvengene...kkkvtvvtfG 103
                                       y   ++G SLG+a+ +L+a+ l  ++ ++     ++ ++t+G
  gi|518653121|ref|YP_008142641.1|  67 YGYLIAGASLGAAVGALIAALLTDKYGRKfllITDAAIYTIG 108
                                       67789******************9998877777777777777 PP

>> FTR1  Iron permease FTR1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1      0.89   1.5e+03     198     216 ..      23      41 ..      12      48 .. 0.71
   2 ?   13.3   2.5   2.1e-05     0.035     168     222 ..      66     119 ..      55     126 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.89
                              FTR1 198 ffilegflLllvaagLfsv 216
                                        f+++ +lL+ + + Lf++
  gi|518653121|ref|YP_008142641.1|  23 KFYWAVTLLATIGGFLFGY 41 
                                       4778888888888888776 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 2.1e-05
                              FTR1 168 lilgvvlGaliavvlglliyrglvklslqsffilegflLllvaagLfsvgtlell 222
                                       ++   ++Ga+ + ++g+li  +l+   +++f++++   ++ + a L++v+ + l+
  gi|518653121|ref|YP_008142641.1|  66 VYGYLIAGASLGAAVGALIAALLTDKYGRKFLLITDAAIYTIGAILSAVS-VNLV 119
                                       5666799******************************************9.5554 PP

>> Gly-zipper_YMGG  YMGG-like Gly-zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   5.0   0.00022      0.36       5      22 ..      72      89 ..      70     111 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
                                      XXXXXXXXXXXXXXXXXX CS
                   Gly-zipper_YMGG  5 rGAaiGAaaGAvvGaliG 22
                                      +GA  GAa+GA++ al  
  gi|518653121|ref|YP_008142641.1| 72 AGASLGAAVGALIAALLT 89
                                      799999999999999877 PP

>> YtxH  YtxH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   2.1   0.00022      0.35       2      25 ..      72      95 ..      71      97 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00022
                              YtxH  2 lglliGaavGaaaglLlAPksGke 25
                                      +g+ +GaavGa+++ Ll+ k G++
  gi|518653121|ref|YP_008142641.1| 72 AGASLGAAVGALIAALLTDKYGRK 95
                                      7999***************99997 PP

>> VMA21  VMA21-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   5.2    0.0015       2.4      32      57 ..      96     121 ..      51     125 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0015
                             VMA21  32 vfglsnssatlysgvlAVivvnlvla 57 
                                       ++ +++ + ++++++l++++vnlv++
  gi|518653121|ref|YP_008142641.1|  96 FLLITDAAIYTIGAILSAVSVNLVML 121
                                       7788999*****************97 PP

>> Gly-zipper_Omp  Glycine zipper
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1       1.2   1.9e+03      29      35 ..      34      40 ..      28      48 .. 0.54
   2 ?    8.6   6.1    0.0011       1.8       2      18 ..      73      89 ..      72     124 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.2
                    Gly-zipper_Omp 29 avGaavG 35
                                      + G + G
  gi|518653121|ref|YP_008142641.1| 34 IGGFLFG 40
                                      3444443 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0011
                    Gly-zipper_Omp  2 GaaiGAaaGaliGgavg 18
                                      Ga +GAa+Gali++   
  gi|518653121|ref|YP_008142641.1| 73 GASLGAAVGALIAALLT 89
                                      99999999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.48
# Mc/sec: 883.17
//
Query:       gi|518653122|ref|YP_008142642.1|  [L=89]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-10   40.5   0.0    3.7e-10   40.0   0.0    1.3  1  HTH_Tnp_1    Transposase
    6.6e-06   26.0   0.0    1.2e-05   25.2   0.0    1.5  2  HTH_29       Winged helix-turn helix
    0.00045   20.3   0.0    0.00074   19.6   0.0    1.4  1  HTH_28       Helix-turn-helix domain
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.027   14.6   0.0    1.3  1  HTH_Tnp_1_2  Helix-turn-helix of insertion element transposas
      0.039   13.7   0.0      0.057   13.2   0.0    1.4  1  HTH_23       Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0     1e-13   3.7e-10       6      74 ..       3      71 ..       1      72 [. 0.83

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 1e-13
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr.egeeaspaefeltaleeenrelkrel 74
                                      ++++ +K++iV es  +  +++e++rrhgvs + +ykWr ++  +g +    + +    e+e+ +lkr++
  gi|518653122|ref|YP_008142642.1|  3 KFTADEKVAIVMES-FTANNIAELCRRHGVSVSNFYKWRDKFIeSGKKGFYGSGVNNGYEKEIDKLKRLV 71
                                      8*************.66789*********************97666666666666677788888888875 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.3e-09   1.2e-05      11      55 ..      19      63 ..       9      69 .. 0.85
   2 ?   -2.4   0.0       1.4     5e+03      41      52 ..      78      89 .]      74      89 .] 0.68

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.3e-09
                            HTH_29 11 GvstvsqiAkllglsrrtvyrwlkrfeegGlaalld.rrrsgrprn 55
                                      +  +++++++++g+s + +y+w++ f e G ++    + ++g  ++
  gi|518653122|ref|YP_008142642.1| 19 AN-NIAELCRRHGVSVSNFYKWRDKFIESGKKGFYGsGVNNGYEKE 63
                                      45.8*****************************9998888887766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.4
                            HTH_29 41 laalldrrrsgr 52
                                      ++ l++++r++r
  gi|518653122|ref|YP_008142642.1| 78 IDELKKNYRGRR 89
                                      667888888654 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.1e-07   0.00074      13      42 ..      20      49 ..       8      52 .. 0.84

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.1e-07
                            HTH_28 13 hsvreaArelgisrrtvyrWikryeegGia 42
                                      ++++e++r++g+s +  y+W+ ++ e G  
  gi|518653122|ref|YP_008142642.1| 20 NNIAELCRRHGVSVSNFYKWRDKFIESGKK 49
                                      589*********************999965 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 ?   14.6   0.0   7.6e-06     0.027      20      52 ..      13      43 ..       5      74 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 7.6e-06
                                      HHHHH--S-HHHHHHHHTS-HHHHHHHHH-HHH CS
                       HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWkkkkeF 52
                                      v + +    ++e+++  gvs s +ykW++k  F
  gi|518653122|ref|YP_008142642.1| 13 VMESFTANNIAELCRRHGVSVSNFYKWRDK--F 43
                                      55678888999*****************86..5 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.6e-05     0.057      20      45 ..      22      47 ..       6      54 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.6e-05
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                      ++e +r++gvs +  y+w+ ++ e+G
  gi|518653122|ref|YP_008142642.1| 22 IAELCRRHGVSVSNFYKWRDKFIESG 47
                                      7899******************6665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); 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: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 650.23
//
Query:       gi|518653123|ref|YP_008142643.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1762 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-18   65.9   0.0    6.2e-18   65.1   0.0    1.4  1  rve            Integrase core domain
    2.5e-17   62.4   0.2    8.3e-17   60.7   0.2    2.0  1  rve_3          Integrase core domain
    5.8e-12   45.6   0.6    1.6e-11   44.1   0.6    1.7  1  HTH_21         HTH-like domain
     0.0001   22.4   2.4    0.00018   21.6   0.9    2.3  3  rve_2          Integrase core domain
      0.006   16.8   0.1      0.016   15.4   0.1    1.8  1  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.027   15.1   0.6      0.062   13.9   0.6    1.6  1  HTH_32         Homeodomain-like domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.1   0.0   2.1e-21   6.2e-18       5     118 ..     113     227 ..     109     228 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.1 bits;  conditional E-value: 2.1e-21
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve...pervlsDngsey 78 
                                       ++lw++D+ +vr  + +g +yl +v d+fs++ l +  s+  +a+++++ +e a+a + +      +++++Dng++y
  gi|518653123|ref|YP_008142643.1| 113 NQLWETDIHYVR--THNGMCYLMAVKDCFSKRWLSYNFSRACTAKDCVKPIEDAYAIRYKDSnlnNLVLRTDNGPQY 187
                                       99**********..66667***************************************99999************** PP

                               rve  79 tskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++++f++ ++ l+i +++  ++ p+dnG +E+fh  lk++
  gi|518653123|ref|YP_008142643.1| 188 IAREFKTPARLLNIPHEYIEKQTPEDNGDIESFHNSLKTD 227
                                       *************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   0.2   2.8e-20   8.3e-17       3      67 .]     201     265 ..     199     265 .. 0.97

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 2.8e-20
                             rve_3   3 ielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLgykTP 67 
                                       i ++yi+  +P +Ng +Esf+++l++ ++  +  +s ++a+e++e ++ dYN+ RPHss+gy+TP
  gi|518653123|ref|YP_008142643.1| 201 IPHEYIEKQTPEDNGDIESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRPHSSIGYLTP 265
                                       7799************************************************************9 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.6   5.4e-15   1.6e-11      17      59 ..      56      97 ..      43      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 5.4e-15
                            HTH_21 17 skgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59
                                      ++ +YG+rriwa Lr+e gv++n k+VrR+ + ++L+ ++ + 
  gi|518653123|ref|YP_008142643.1| 56 KRVTYGHRRIWAVLRNE-GVKINIKTVRRIIKSNNLQLPYAKH 97
                                      3469*************.789***************9999875 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       3.4     1e+04      17      32 ..     192     207 ..     188     207 .. 0.74
   2 !   21.6   0.9   6.1e-08   0.00018       1      50 [.     218     271 ..     218     272 .. 0.90
   3 ?   -2.4   0.0       1.9   5.5e+03      43      52 .]     274     283 ..     273     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 3.4
                             rve_2  17 fktleeleaaiedYIe 32 
                                       fkt + l    ++YIe
  gi|518653123|ref|YP_008142643.1| 192 FKTPARLLNIPHEYIE 207
                                       7777777777789996 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 6.1e-08
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIewYNnkR....lkglsPvqYrnq 50 
                                       Esf  sLKt+ +     ++ e +++ ie   + YNn R    +++l+Pv++++q
  gi|518653123|ref|YP_008142643.1| 218 ESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRphssIGYLTPVEFEKQ 271
                                       9**************9***99998887666778*****888888********98 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.9
                             rve_2  43 sPvqYrnqsL 52 
                                       s+ ++rn+ L
  gi|518653123|ref|YP_008142643.1| 274 SSEEFRNKFL 283
                                       7899***976 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   5.5e-06     0.016       3     139 ..     115     257 ..     113     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.5e-06
                     DDE_Tnp_IS240   3 swrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrka..lkkek..lepeeivtDkasayasal 74 
                                        w+ D  yv+ +   +Yl ++ D  ++  l + +s    +k + + ++ a  ++ ++  l++ ++ tD  + y   +
  gi|518653123|ref|YP_008142643.1| 115 LWETDIHYVRTHNGMCYLMAVKDCFSKrWLSYNFSRACTAKDCVKPIEDAyaIRYKDsnLNNLVLRTDNGPQYI--A 189
                                       588888899999999999999999888899999999999999999998762244444559999999*9999884..4 PP

                     DDE_Tnp_IS240  75 kelkregelf...devshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                       +e+k   +l+   +e  + q++  n  iEs h+ lK  +   + ++s + a++ ++     +n +++h
  gi|518653123|ref|YP_008142643.1| 190 REFKTPARLLnipHEYIEKQTPEDNGDIESFHNSLKTDYIWLNDLESYEDAKELIEYAFNDYNNYRPH 257
                                       555554433323366667788999*******************************9888777777777 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.6   2.1e-05     0.062      23      73 .]      36      85 ..      15      85 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.1e-05
                            HTH_32 23 rgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      r r++++++    +++++  ++ +++ r++ a l + egvk+   tv+ri+
  gi|518653123|ref|YP_008142643.1| 36 RHRKSRIPENIINKVLEISGKRVTYGHRRIWAVL-RNEGVKINIKTVRRII 85
                                      236669*************55559**********.9999**********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2348.72
//
Query:       gi|518653124|ref|YP_008142644.1|  [L=87]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-06   26.6   0.2    5.1e-06   26.3   0.2    1.0  1  DDE_Tnp_1  Transposase DDE domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.2   2.9e-10   5.1e-06      59     142 ..       6      83 ..       3      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 2.9e-10
                         DDE_Tnp_1  59 vhdskglkqlldelrprkgklvlaDaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkilt 135
                                       +hdsk+++ ll  ++  +  ++++D+GY+  +++  +   g++ +i+++kn+ ++++   s+ r ++ + ++++ ++
  gi|518653124|ref|YP_008142644.1|   6 THDSKAARKLLSKMKN-NILRIFGDRGYD-SKYIYNMF--GYNAVIPPRKNASTKSR--GSYARAKIVRFIKKNSME 76 
                                       7*************98.***********9.77777777..7*************977..455677777777777777 PP

                         DDE_Tnp_1 136 ksqkrrn 142
                                       ++++ +n
  gi|518653124|ref|YP_008142644.1|  77 QWKENNN 83 
                                       7777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       568  (0.0316805); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.44
# Mc/sec: 588.89
//
Query:       gi|518653125|ref|YP_008142645.1|  [L=257]
Description: hypothetical protein FACI_IFERC00001G1764 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-40  139.3  16.0    1.8e-40  139.1  16.0    1.0  1  Sugar_tr  Sugar (and other) transporter
    3.9e-05   22.8  21.8    5.6e-05   22.2  21.8    1.2  1  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.097   12.1   0.2       0.18   11.2   0.2    1.5  1  NAR2      High-affinity nitrate transporter accessory
       0.41   10.5   0.0       0.41   10.5   0.0    1.8  2  TarH      Tar ligand binding domain homologue


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.1  16.0   4.1e-44   1.8e-40     243     452 .]      14     231 ..       1     231 [. 0.89

  Alignments for each domain:
  == domain 1  score: 139.1 bits;  conditional E-value: 4.1e-44
                                       TTHHHHSH.....HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH............HHHHHHHHHHHHHHHH CS
                          Sugar_tr 243 kellsskt..vrqrlligvvlqifqqltGinaimyysptifenlglsks............llvtiivgvvnfvatf 305
                                       ke +++ t  ++++++i+ + ++fqq tGin+ +yy+p+++ +l++  s            ++++ i+ ++n++at+
  gi|518653125|ref|YP_008142645.1|  14 KETKQKATpgIKRAFVIVGLFMMFQQITGINIPFYYGPVVIAKLHIFGStggtaissavfgIEASSILAIINVLATL 90 
                                       34444444547788888888899**********************9999999999**99999*************** PP

                                       HHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTT CS
                          Sugar_tr 306 vaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqs 382
                                       +++ l+d  GRR l llG +gma++ v+    a l+ +    + i++++++a fi++fa+g+g++ w++  E fp++
  gi|518653125|ref|YP_008142645.1|  91 IGFRLIDSYGRRSLALLGYSGMAFFDVLG---AVLYLSH---IDIGLLIGFAGFIIFFAFGVGGTGWIIQGEYFPTQ 161
                                       **********************9876655...5666666...49********************************* PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--STT--CCCCGGGT CS
                          Sugar_tr 383 vRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetkgrtleeieelf 452
                                        R++++++ ++v w++nf+i  lfp+++ +ig gy+ +vfa+l ++++++ f  +p tkg++ eei+ +f
  gi|518653125|ref|YP_008142645.1| 162 YRGLFASLIAVVDWISNFAIIELFPVMDLKIGLGYTMAVFAVLSIMAVVIFFYIMPKTKGKSVEEINDIF 231
                                       ******************************************************************9887 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2  21.8   1.2e-08   5.6e-05       5     185 ..      31     227 ..      21     249 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.2e-08
                             MFS_1   5 aflsalarsilgpalplal.......aedlg.........ispseigl.lltlyalgaavaslplGrlsdrfGrrrv 64 
                                       + l ++   i+g+++p ++           +         is +++g+ + ++ a+  ++a+l++ rl+d +Grr++
  gi|518653125|ref|YP_008142645.1|  31 VGLFMMFQQITGINIPFYYgpvviakL---HifgstggtaISSAVFGIeASSILAIINVLATLIGFRLIDSYGRRSL 104
                                       555566666666666632233333332...24445556668889999988999************************ PP

                             MFS_1  65 lllglllfalg.lllll.f.a.sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg 137
                                        llg+ ++a++ +l ++ + + + + ll+ +  +  ++a ++  +g ++  ++fp + rg+  +l+++   ++    
  gi|518653125|ref|YP_008142645.1| 105 ALLGYSGMAFFdVLGAVlYlShIDIGLLIGFAGFIIFFAFGVGGTGWIIQGEYFPTQYRGLFASLIAVVDWISNFAI 181
                                       ***********888888633354555555555555555545556666777899999999999999999888888888 PP

                             MFS_1 138 pllggllasslgWravfyilaivsllafvlfllllpeepperkrkspk 185
                                         l +++   +g  +++ ++a++s++a+v+  +++  ++++ k ++++
  gi|518653125|ref|YP_008142645.1| 182 IELFPVMDLKIGLGYTMAVFAVLSIMAVVI--FFYIMPKTKGKSVEEI 227
                                       88888888888999*************885..6665555555555544 PP

>> NAR2  High-affinity nitrate transporter accessory
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.2   4.1e-05      0.18     137     170 ..     183     216 ..     172     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.1e-05
                              NAR2 137 evkaitgrhasldiaaavfsvfSvvalavffvve 170
                                       e  ++   +  l  ++avf+v+S++a+++ff++ 
  gi|518653125|ref|YP_008142645.1| 183 ELFPVMDLKIGLGYTMAVFAVLSIMAVVIFFYIM 216
                                       55566777889999**************999864 PP

>> TarH  Tar ligand binding domain homologue
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.9       3.2   1.4e+04      13      26 ..      29      42 ..      27      43 .. 0.81
   2 ?   10.5   0.0   9.2e-05      0.41       6      39 ..     189     222 ..     185     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 3.2
                                      XXXXXXXXXXXXXX CS
                              TarH 13 lvlallgvLllvsg 26
                                      ++++l+++++ ++g
  gi|518653125|ref|YP_008142645.1| 29 VIVGLFMMFQQITG 42
                                      68899999999988 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 9.2e-05
                                       XXXXXXXXXXXXXXXXXXXXXSSSSSSHHHHHHH CS
                              TarH   6 sIrtrLllvlallgvLllvsgglglsglsrsnda 39 
                                        ++ +L  ++a+++vL +   +++++ + +++ +
  gi|518653125|ref|YP_008142645.1| 189 DLKIGLGYTMAVFAVLSIMAVVIFFYIMPKTKGK 222
                                       57889***********************887743 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       970  (0.0541023); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 1830.67
//
Query:       gi|518653126|ref|YP_008142646.1|  [L=261]
Description: hypothetical protein FACI_IFERC00001G1765 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-59  201.5   5.0    1.6e-59  201.3   5.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.2e-56  189.5   3.0    5.1e-56  189.2   3.0    1.1  1  adh_short        short chain dehydrogenase
    1.9e-11   44.2   0.8    2.8e-11   43.6   0.8    1.2  1  KR               KR domain
    0.00016   21.0   3.7     0.0005   19.4   3.7    1.9  1  THF_DHG_CYH_C    Tetrahydrofolate dehydrogenase/cyclohydrolas
    0.00058   19.4   3.6     0.0017   17.9   0.2    2.7  3  Epimerase        NAD dependent epimerase/dehydratase family
     0.0023   17.5   3.2       0.11   12.1   1.4    2.4  2  NmrA             NmrA-like family
     0.0042   16.3   0.5     0.0058   15.8   0.5    1.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.033   13.6   0.0    1.7  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      0.028   13.5   0.2        1.8    7.6   0.1    2.3  2  RmlD_sub_bind    RmlD substrate binding domain
       0.12   11.8   0.0       0.17   11.2   0.0    1.1  1  DUF1776          Fungal family of unknown function (DUF1776)
       0.12   12.2   0.0       0.35   10.8   0.0    1.8  1  DUF2642          Protein of unknown function (DUF2642)
       0.14   12.0   4.3       0.27   11.1   3.8    1.9  2  NAD_binding_10   NAD(P)H-binding


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 !  201.3   5.0   1.1e-62   1.6e-59       1     233 [.      15     251 ..      15     252 .. 0.96

  Alignments for each domain:
  == domain 1  score: 201.3 bits;  conditional E-value: 1.1e-62
                                       TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEE.EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaev.lecDVtdeeqvealveevvekfgklDilv 74 
                                       Ga  gIG+aiA  la++Ga+v+++  ++++  ++ v++++++ g+++ + +D +d+ +ve+++++v +++g +Dilv
  gi|518653126|ref|YP_008142646.1|  15 GASGGIGKAIAIGLASAGASVAVHFGRNKNaaDEVVNKIVAARGKAIaVSADMADPVAVEEMFRKVDSSLGPVDILV 91 
                                       8999*****************99865555547899*******999955***************************** PP

                                       E-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTTHHHHHHHHHH CS
                      adh_short_C2  75 nnagiapklkgpfletsreefdraldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnynaygaaKaale 149
                                       n+agi    ++ + + + e++++++++nly+ + +++ a++ mk++  g i+n++s + ++ +++y+ay+ +Ka+l 
  gi|518653126|ref|YP_008142646.1|  92 NSAGIDGV-RAMLGDDDIENWKKVISINLYGPYFCSRMAIQRMKKKnrGVIINITSDHVNIPWQGYSAYCSSKAGLD 167
                                       *******8.999999**************************8887779***************************** PP

                                       HHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEE CS
                      adh_short_C2 150 altrylAvelgpkgiRvNavspgpikTlaasgikgfdelleelearaplgrlgtpeevaeaalfLasdeasyitGqt 226
                                        ++++lA e +  giRv +++pg+ikT +++++ ++++ l+ l++++ +g  g++e+va+a+lf asd+a+yitG+t
  gi|518653126|ref|YP_008142646.1| 168 MMAKTLAQETATMGIRVISIAPGAIKTAINKSVWENPDTLKDLDDKIAMGFPGDAEDVADAVLFAASDMAKYITGTT 244
                                       ***************************************************************************** PP

                                       EEESTTG CS
                      adh_short_C2 227 lvvDgGl 233
                                       +vvDgG+
  gi|518653126|ref|YP_008142646.1| 245 IVVDGGM 251
                                       ******8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2   3.0   3.4e-59   5.1e-56       1     193 [.       9     203 ..       9     205 .. 0.96

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 3.4e-59
                                       SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHS CS
                         adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklg 76 
                                       kv++vtGas+GIG+aia  la++Ga+v+v ++r+++++ ev++++ +++ ka+a+++D++d  +ve++++k+ + lg
  gi|518653126|ref|YP_008142646.1|   9 KVAIVTGASGGIGKAIAIGLASAGASVAVhFGRNKNAADEVVNKIVAARGKAIAVSADMADPVAVEEMFRKVDSSLG 85 
                                       89*************************************************************************** PP

                                       SESEEEE---S.S--SSGGGCSHHHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHH CS
                         adh_short  77 kldvLvnNAGi.tgsgpfselseeewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAs 152
                                       ++d+Lvn AGi   +++  + + e+w++vi++Nl g++ ++r++++ m+k+++G I+n++S + + p+ g++aY++s
  gi|518653126|ref|YP_008142646.1|  86 PVDILVNSAGIdGVRAMLGDDDIENWKKVISINLYGPYFCSRMAIQRMKKKNRGVIINITSDHVNIPWQGYSAYCSS 162
                                       ***********55555666667777**************************************************** PP

                                       HHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTH CS
                         adh_short 153 KaavagltrslakelaptgirvnavaPGlvdTdmakelrek 193
                                       Ka++++++++la+e a+ girv+++aPG+++T+++k++ e+
  gi|518653126|ref|YP_008142646.1| 163 KAGLDMMAKTLAQETATMGIRVISIAPGAIKTAINKSVWEN 203
                                       ***********************************998876 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   0.8   1.9e-14   2.8e-11       4     176 ..      12     190 ..      10     194 .. 0.80

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.9e-14
                                       EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS CS
                                KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeep 80 
                                       ++tG+ Gg+G+++a  la+ ga+  v ++R+   ++++++ ++++ a   +  +v+aD +d+ ave+++++++++ +
  gi|518653126|ref|YP_008142646.1|  12 IVTGASGGIGKAIAIGLASAGASVAVHFGRN---KNAADEVVNKIVAARGKAIAVSADMADPVAVEEMFRKVDSSLG 85 
                                       8******************************...45556689999888888889999******************** PP

                                       ---EEEE------.---TTT--HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHH CS
                                KR  81 pikGvihaAgvlr.dklleemtaedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaa 152
                                       p+   +++Ag+    ++l + + e++++v++  + G     ++  +    ++  +++ ++S    +  +g ++Y + 
  gi|518653126|ref|YP_008142646.1|  86 PVDILVNSAGIDGvRAMLGDDDIENWKKVISINLYGPYFCSRMAIQrmkkKNRGVIINITSDHVNIPWQGYSAYCSS 162
                                       ***********885678889999*******99999966555543333333888899999999999999999999999 PP

                                       HHHHHHHHHHHHH....HHHTEEEEEE- CS
                                KR 153 NaflDalaeyrrs....qglpavsinwg 176
                                        a lD +a++ ++    +g +++si+ g
  gi|518653126|ref|YP_008142646.1| 163 KAGLDMMAKTLAQetatMGIRVISIAPG 190
                                       9999876665554000045556666655 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 !   19.4   3.7   3.4e-07    0.0005      31     103 ..       3      73 ..       1     123 [. 0.85

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 3.4e-07
                                       T---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B-GGGS-TT-E CS
                     THF_DHG_CYH_C  31 gielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelikaemvkegav 103
                                       +i+l+gk ++v G+s  +gk++a+ L++++a V v   + k+ a+ + +   +v+a Gk+  ++a+m  + av
  gi|518653126|ref|YP_008142646.1|   3 KIDLTGKVAIVTGASGGIGKAIAIGLASAGASVAVHFGRNKNAADEVVNK--IVAARGKAIAVSADMADPVAV 73 
                                       699********************************999999999888764..99************9887665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.2   1.1e-06    0.0017       2      77 ..      12      99 ..      11     117 .. 0.73
   2 ?   -1.5   0.0      0.96   1.4e+03     168     184 ..     115     128 ..     109     153 .. 0.62
   3 ?    1.5   0.1      0.12   1.7e+02     214     237 ..     221     244 ..     220     248 .. 0.76

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                                      EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.......EEEE--TT-HHHHHHHHHHHT.....-SE CS
                         Epimerase  2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl.......elveldltdrsalerlfkeeq.....pda 67
                                      +VtGa+G iG+a++  l+++g    + + r+++a  +  ++ +         v +d+ d++a+e++f++++     +d+
  gi|518653126|ref|YP_008142646.1| 12 IVTGASGGIGKAIAIGLASAGASvAVHFGRNKNAADEVVNK-IvaargkaIAVSADMADPVAVEEMFRKVDsslgpVDI 89
                                      8********************77444444444444443333.2589***999***************976422222455 PP

                                      EEE--S---H CS
                         Epimerase 68 vihlAavggv 77
                                       ++ A++ gv
  gi|518653126|ref|YP_008142646.1| 90 LVNSAGIDGV 99
                                      6666555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.96
                                       EESEEESTT...S-TTSTTS CS
                         Epimerase 168 rlfnlyGpr...ngegevsr 184
                                       +  nlyGp+   +       
  gi|518653126|ref|YP_008142646.1| 115 ISINLYGPYfcsR------M 128
                                       5678899983331......2 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                                       EHHHHHHHHHHHHHHHTT-STTEE CS
                         Epimerase 214 yveDvaeaillvlehvdagdkgei 237
                                       ++eDva+a+l+++   ++  +g +
  gi|518653126|ref|YP_008142646.1| 221 DAEDVADAVLFAASDMAKYITGTT 244
                                       689*********998766655555 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.1   1.4   7.2e-05      0.11       2      67 ..      12      82 ..      11      91 .. 0.89
   2 ?    4.9   0.0     0.011        17     177     214 ..     216     254 ..     188     258 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 7.2e-05
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEE.S-S...-SHHHHHHHHSTTEEE.ES-TT-HHHHHHHHTT-SE CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralv.Rdt...kselakslkeaGvelv.kgdlddkeslvealkgvdv 67
                                      +v+Ga+G +Gk+++  l++ag +v +   R+    ++ + k ++++G  +  ++d+ d   ++e +++vd 
  gi|518653126|ref|YP_008142646.1| 12 IVTGASGGIGKAIAIGLASAGASVAVHFgRNKnaaDEVVNKIVAARGKAIAvSADMADPVAVEEMFRKVDS 82
                                      59**********************997647778877777788999**99988****************996 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.011
                                       S-EE-HHHHHHHHHHHHHHHHHHH.TTEEEEE-SEEE-H CS
                              NmrA 177 avlldaeeDiGafvikilkdprkl.kgkriklagntlsg 214
                                       + ++++ eD++ +v+ +++d +k+  g  i + g +l +
  gi|518653126|ref|YP_008142646.1| 216 MGFPGDAEDVADAVLFAASDMAKYiTGTTIVVDGGMLIY 254
                                       3344899*************9999999999998888865 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.5   3.9e-06    0.0058       2     164 ..      12     185 ..      11     193 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 3.9e-06
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T. CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelk. 77 
                                       +vtGa+G iG+++   +++  ++  + + r+ ++ +e+ +++ + ++ k +     +v +d++d   +e+++++++ 
  gi|518653126|ref|YP_008142646.1|  12 IVTGASGGIGKAIAIGLASAGASVAVHFGRNKNAADEVVNKIVA-ARGKAI-----AVSADMADPVAVEEMFRKVDs 82 
                                       69************************************999743.333334.....455888888888888887643 PP

                                       ....-SEEEE------HHHH.....HHSHHHHHHHHHHHHHHHHHHHHHTT-SE....EEEEEEGGGSS-...-SHH CS
                   Polysacc_synt_2  78 ....vdvvfhaAAlKhVPlv.....eenpleaiktNvlgtenvieaaieagvkk....vvliStDKAvnP...tnvm 138
                                           vd+++++A +  V ++      en+ ++i+ N +g   + ++ai+   kk    ++ i +D    P    +++
  gi|518653126|ref|YP_008142646.1|  83 slgpVDILVNSAGIDGVRAMlgdddIENWKKVISINLYGPYFCSRMAIQRMKKKnrgvIINITSDHVNIPwqgYSAY 159
                                       3344899**********988444323699999*******99999999876554434437889999988773224678 PP

                                       HHHHHHHHHHHHHGGG--SSS--EEE CS
                   Polysacc_synt_2 139 GatKrlaekllqalakeseekktkfv 164
                                         +K+  ++++ +la+e+++   +++
  gi|518653126|ref|YP_008142646.1| 160 CSSKAGLDMMAKTLAQETATMGIRVI 185
                                       88999999999999888877666655 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.2e-05     0.033       1      75 [.      12      81 ..      12      84 .. 0.90
   2 ?   -1.7   0.0         1   1.5e+03     146     170 ..     152     176 ..     148     186 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.2e-05
                                      EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
                     GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75
                                      ++TG +G iG  +a  L + g  v +   r+++ + + ++++       ++++   +++D+ D  ++e+++++v+
  gi|518653126|ref|YP_008142646.1| 12 IVTGASGGIGKAIAIGLASAGASVAVHFGRNKNAADEVVNKIVA-----ARGKAIAVSADMADPVAVEEMFRKVD 81
                                      59************************999999988888888764.....4578899***************9986 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1
                                       -----SHHHHHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 146 pfyPrsPYaaaKlyadwivvnyrea 170
                                       p +  s Y  +K+  d++++   ++
  gi|518653126|ref|YP_008142646.1| 152 PWQGYSAYCSSKAGLDMMAKTLAQE 176
                                       6677899*********999987655 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 ?    7.6   0.1    0.0012       1.8       4      52 ..      12      82 ..       9      99 .. 0.80
   2 ?    3.6   0.0     0.019        29     168     202 ..     202     238 ..     188     245 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0012
                                      EEESTTSHHHHHHHHHCTTTSEEEEEE.-TT.....................T--TTSHHHHHHHHHHH-- CS
                     RmlD_sub_bind  4 lvtGanGqlGseLakqlaeeglevlal.tre.....................eldltdaeavaellkeakp 52
                                      +vtGa+G +G+++a  la++g++v    +r+                     ++d++d+ av+e++++++ 
  gi|518653126|ref|YP_008142646.1| 12 IVTGASGGIGKAIAIGLASAGASVAVHfGRNknaadevvnkivaargkaiavSADMADPVAVEEMFRKVDS 82
                                      69*******************88766645557888888888888888888888888888888888887654 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.019
                                       HH-SEEEEESS-..EE--EEHHHHHHHHHHHHHHCHH CS
                     RmlD_sub_bind 168 kereelkvvaDq..lgsPTsardlAevllqllekaae 202
                                       ++ ++lk  +D+  +g P  a+d+A+++l +++ +a+
  gi|518653126|ref|YP_008142646.1| 202 ENPDTLKDLDDKiaMGFPGDAEDVADAVLFAASDMAK 238
                                       66778888888733599************99998875 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 ?   11.2   0.0   0.00011      0.17     114     203 ..     109     195 ..     105     209 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                           DUF1776 114 sswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphni 190
                                       ++w++++  +l  p+  +   ++ +++   ++  +i+  +s   ++  + ++        l+ ++++L++e++  +i
  gi|518653126|ref|YP_008142646.1| 109 ENWKKVISINLYGPYFCSRMAIQRMKK---KNRGVIINITSDHVNIPWQGYSAYCSSKAGLDMMAKTLAQETATMGI 182
                                       78************************8...566666665555555555555555555557***************** PP

                           DUF1776 191 dvtqikLGnldla 203
                                        v+ i  G ++ a
  gi|518653126|ref|YP_008142646.1| 183 RVISIAPGAIKTA 195
                                       *****99999876 PP

>> DUF2642  Protein of unknown function (DUF2642)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00023      0.35      20      48 ..     126     154 ..     121     161 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00023
                           DUF2642  20 qevvvqttrgsvrGiLkdvkPDHivveig 48 
                                       +++++q  + + rG++ ++  DH+ +  +
  gi|518653126|ref|YP_008142646.1| 126 SRMAIQRMKKKNRGVIINITSDHVNIPWQ 154
                                       5789********************99765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   3.8   0.00018      0.27       1      62 [.      15      81 ..      15     235 .. 0.73
   2 ?   -0.6   0.0      0.72   1.1e+03      42      62 ..     224     244 ..     190     249 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      TTTSHHHHHHHHHHHHC-T-EE.EEEETTHHHCHHHH.....CTTTCEEEE--TT-CCHHHHHHTT-S CS
                    NAD_binding_10  1 GAtGkvGrllvkellargghev.talvRnpeklaele.....aeeglevvegdvtdvedlaealkgad 62
                                      GA+G++G++++  l+++g  +v + + Rn++ ++e+      a+ ++ +v++d+ d+ +++e ++ +d
  gi|518653126|ref|YP_008142646.1| 15 GASGGIGKAIAIGLASAG-ASVaVHFGRNKNAADEVVnkivaARGKAIAVSADMADPVAVEEMFRKVD 81
                                      9****************8.44415578**9999975433333567888999*********99999665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.72
                                       EEEE--TT-CCHHHHHHTT-S CS
                    NAD_binding_10  42 evvegdvtdvedlaealkgad 62 
                                       +v ++ +  ++d+a+ ++g+ 
  gi|518653126|ref|YP_008142646.1| 224 DVADAVLFAASDMAKYITGTT 244
                                       333444444444555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (261 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.54u 0.30s 00:00:00.84 Elapsed: 00:00:00.47
# Mc/sec: 1671.18
//
Query:       gi|518653127|ref|YP_008142647.1|  [L=109]
Description: aldose1-epimerase [Ferroplasma acidarmanus fer1]
Scores for complete 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-05   22.6   0.0    5.6e-05   22.6   0.0    1.0  1  Aldose_epim  Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   3.1e-09   5.6e-05     214     294 ..      22     100 ..       2     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 3.1e-09
                                       T.......EEEEEEEESSCSEEEEEETTTTEEEEEEEETTSSEEEEEECTTTTSEECCEEESSECTCETCCCECHHH CS
                       Aldose_epim 214 k.......glDhayllksklkaviidpdkksgiklevsttepalvvytgnflkkylsreglaletqmlpdepnhpef 283
                                       +        lD+++ l+s     +i+ d+k +i+++ ++++p lv+y+g    +y+  +++a+e++  + ++ h+  
  gi|518653127|ref|YP_008142647.1|  22 NgkelnkmPLDNCFYLDS----TVILKDEKHSIRIT-RKNMPYLVLYNG----QYAGNDSIAVEPMTGIPDVYHNMV 89 
                                       233333447999999999....77888888889987.55666*******....8999******************** PP

                                       T-EEEHTTTEE CS
                       Aldose_epim 284 psivlkpGesy 294
                                       ++++l+++ ++
  gi|518653127|ref|YP_008142647.1|  90 GLVTLEKNAEF 100
                                       ******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      265  (0.0147805); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 821.38
//
Query:       gi|518653128|ref|YP_008142648.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-21   76.3   0.0    3.8e-21   75.5   0.0    1.4  1  rve          Integrase core domain
    4.1e-06   26.5   1.1    0.00019   21.1   1.1    2.6  1  rve_3        Integrase core domain
     0.0011   19.6   0.1     0.0032   18.1   0.1    1.9  1  HTH_32       Homeodomain-like domain
     0.0072   16.1   0.2      0.019   14.8   0.2    1.7  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.072   13.6   4.3        0.2   12.1   4.2    1.8  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.1e-24   3.8e-21       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ +  e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518653128|ref|YP_008142648.1| 125 KHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYGEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l + +i++ + r+ +p++nGk Er + t+k+
  gi|518653128|ref|YP_008142648.1| 195 FSNgkngipgdhnKFQEYLDNSNIKHILGRVKHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   5.3e-08   0.00019       2      63 ..     217     268 ..     216     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518653128|ref|YP_008142648.1| 217 NIKHILGRVKHPETNGKLERLNYTIKRLRPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       589999********************965554444..........799************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0032       3      73 .]      36     101 ..      33     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+    + +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518653128|ref|YP_008142648.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDIEIVKKIRYEYPMSGPERIRKYL-KRKGIIIAKNNIYRIL 101
                                       556778888876666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.3e-06     0.019      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518653128|ref|YP_008142648.1| 11 IIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.2   5.7e-05       0.2      40     111 ..       3      75 ..       1     127 [. 0.79
   2 ?   -1.6   0.0      0.93   3.3e+03      44     126 ..     217     243 ..     167     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vk+++ + ++
  gi|518653128|ref|YP_008142648.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNGEyTIGKRKHRELNSKDIEIVKKIRYEYPM 75 
                                       8999****************************88888888776663346678899999999999999874444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                       Terminase_2  44 kIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseevdkeilrevkegke....gvkvklkDk 116
                                       +Ik                                                                 +++++++ k
  gi|518653128|ref|YP_008142648.1| 217 NIK------------------------------------------------------------HilgrVKHPETNGK 233
                                       222............................................................13333455555555 PP

                       Terminase_2 117 lkAlellakh 126
                                       l+ l+ ++k+
  gi|518653128|ref|YP_008142648.1| 234 LERLNYTIKR 243
                                       5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); 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 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 2017.82
//
Query:       gi|518653129|ref|YP_008142649.1|  [L=204]
Description: aldose1-epimerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.1e-26   92.9   0.6    2.5e-26   92.7   0.6    1.0  1  Aldose_epim  Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.6   1.4e-30   2.5e-26       9     177 ..       6     163 ..       1     171 [. 0.85

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.4e-30
                                       TEEEEEECTCTTEEEEEEETT.STEESB-B-STHHHHHHSC.CSSCEECSS-SEEETTEEEETTEEEECCCCBTTTC CS
                       Aldose_epim   9 aglsakislyGAtllslkvpdkeqrevllgsddaeeylkds.yfgatlgrvanRianGeFeldGkpyqlpqneegkn 84 
                                       +g++a +  +GA l +l+ ++   +++++ s+d     +++   +a+l+++ nRi+n+e+++++k+y+lp n+ gkn
  gi|518653129|ref|YP_008142649.1|   6 NGFHANFNPVGAYLEDLQKDG---TPIIRKSNDK----NSThGGAAVLFPFGNRIQNAEYSFNNKQYSLPEND-GKN 74 
                                       589*****************9...8********3....33344489***************************.*** PP

                                       EETBSGGGSB-EEEEEEETTEEEEEEEEEEETCHCSTSEEEEEEEEEEETTEEEEEEEEEEESSS-EEEEEEEEEEE CS
                       Aldose_epim  85 plHGgargreWeveevkeddgvtvslvlkpdgeegypgdlevrvtytLnednelkieyeatndgkptpfnltnHtYF 161
                                       ++HG++r  +++  +    +++++s +    ++  ypg+ +++v+y+++++  +   +++++ + + p+ +++H+YF
  gi|518653129|ref|YP_008142649.1|  75 SIHGLVRELPFDSNSGD--NYIEFSSHF---KSVFYPGEAHIKVKYEITGNM-FVTSFYVKSLTSRIPVEIGFHPYF 145
                                       ************99966..455555555...2344***************66.999********************* PP

                                       ETSSC..TCTGGEEEEEE CS
                       Aldose_epim 162 nlsge..sidshelqiea 177
                                       n+ g      ++++ ++ 
  gi|518653129|ref|YP_008142649.1| 146 NVHGSysISYNSRIVLSH 163
                                       ***998655566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); 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 0.27s 00:00:00.67 Elapsed: 00:00:00.43
# Mc/sec: 1429.09
//
Query:       gi|518653130|ref|YP_008142650.1|  [L=679]
Description: hypothetical protein FACI_IFERC00001G1769 [Ferroplasma acidarmanus fer1]
Scores for complete 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-100  336.6   1.4      1e-87  294.9   0.2    2.1  2  Ald_Xan_dh_C2  Molybdopterin-binding domain of aldehyde dehyd
    2.5e-13   50.3   0.0    5.1e-13   49.3   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 !  294.9   0.2   1.1e-91     1e-87       1     410 [.     129     516 ..     129     530 .. 0.92
   2 !   40.9   0.0   1.1e-14   9.5e-11     482     550 .]     553     621 ..     550     621 .. 0.94

  Alignments for each domain:
  == domain 1  score: 294.9 bits;  conditional E-value: 1.1e-91
                                       STTT-STTEEEEEEEE.-HHHHHHH-S.EEEEEEEEEEBE---SS--EEEEEEETCTTEEEEEES-SSHHHHHHHHH CS
                     Ald_Xan_dh_C2   1 vheeapdnvlakiekG.dveaafaeadhvvegefrtgrqehfylEtqaalavpddedgeltvysstqaphevrrlva 76 
                                       +he +++n+la++e G d+++   + d ++e++f ++r+  + +Et++++a++  +d +lt y+stq +++v++ + 
  gi|518653130|ref|YP_008142650.1| 129 IHEGTENNILAETELGeDFDENDIDFDLTMEDTFFNERIIANSMETRGCIADY--KDSKLTFYVSTQSVQSVKAGLV 203
                                       68889999999888774788888899999************************..79******************** PP

                                       HHHT--GGGEEEE-SB-S--TTTTSS--HHHHHHHHHHHHHTS-EEEE--HHHHHHHS-EEEEEEEEEEEEE-TTS- CS
                     Ald_Xan_dh_C2  77 evlglpenkvrvivprvGGGFGgKtqsvplevlaalaAkktgrpVklvldReedmlatgkrhpfkikykvgadkdGk 153
                                       ++lg+++++vrvi+ + GG+FG+K   +p++v+aa+a+kk g+pVk++++R+e++ a+  ++  k k+k+ a++dG+
  gi|518653130|ref|YP_008142650.1| 204 QALGMKPEDVRVIQADTGGAFGSKGSFYPEYVMAAYASKKYGKPVKWIETRKEHLEAAYPGRGAKGKIKIYARNDGR 280
                                       ***************************************************************************** PP

                                       EEEEEEEEEEEESST.HHHCHCCHCCTTGGGTTTB--SEEEEEEEEEE-SSS-EE-SSTTTHHHHHHHHHHHHHHHH CS
                     Ald_Xan_dh_C2 154 italdvdlladaGay.adlspavleralshldgpYkipnvrvegrvvytNtppntafRGfGgpqamfalErlmdelA 229
                                       it+++ d++ daGay a  + +    ++ +++gpY+i+++ ++++ v tN++p +++RG+G+p+a+f++Er+md lA
  gi|518653130|ref|YP_008142650.1| 281 ITGIKGDVYVDAGAYdAGTGGFASRFIAYQITGPYHIEKAYMRAYSVLTNKAPMGPYRGAGRPEAAFFMERMMDLLA 357
                                       ***************55666666667888999********************************************* PP

                                       HHHT--HHHHHHHHBCECGCC.SEEETEESSS-HHHHHHHHHHHHTHHHHHHSCCHHCCTECEEEEEEEEEEEEBS- CS
                     Ald_Xan_dh_C2 230 eelgldplelRrrNlikpgeltpygqpvydsgdlpelldklkessdyeerraeqaefnagwkkrGiglapvvegigl 306
                                       ++l++d  e+R  N+ ++  + p+g +v  +   +  l+k++++++y++        +++  k Gi++ + + ++  
  gi|518653130|ref|YP_008142650.1| 358 DRLQMDISEVRLVNASTEPFTSPTGLTV--KEATRPFLEKALAEVNYRKIS------REE--KTGIAFFVLIPAS-- 422
                                       ***************8876666777664..688999999999999995442......223..68********999.. PP

                                       -S.EETTEEEEEEEEE-TTS-EEEEESS--SSS-HHHHHHHHHHHHHT--GGGEEEE-SBTTSSS----S-TT-HHH CS
                     Ald_Xan_dh_C2 307 gftakflnqegalvrvntdGsvtvstggtemGqGletklaqiaaeeLgvpledvrvvegdtdkvpngsgtaaSrstd 383
                                                e+a++ v  +G++t ++gg  +GqG+e  +  i  +eL+v+ + + +++gdt+ + ng+g+++Sr++ 
  gi|518653130|ref|YP_008142650.1| 423 R------PGESARIDVS-NGKITAQLGGNVHGQGHELFVKSILENELQVEQNLISLENGDTAEMENGVGSWGSRTAI 492
                                       3......3479999997.8********************************************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHCTS CS
                     Ald_Xan_dh_C2 384 lngnAvkkAaeklrerllkiaaellev 410
                                        + +A +k a +++e++ k      + 
  gi|518653130|ref|YP_008142650.1| 493 AGASALMKVAGQIKEQVIKKYG---KY 516
                                       ****************988766...44 PP

  == domain 2  score: 40.9 bits;  conditional E-value: 1.1e-14
                                       T--EEEEEEEEEEE-BS-S-HHHHHHHHHHHHHHHHHHHHT---EEETTTEESS-STTTS----GGGS- CS
                     Ald_Xan_dh_C2 482 tgevkvlrvvivhDvGksiNpaivegQieGGfvqGiGlalmEelvydedGqlltasladYkiPtaadiP 550
                                        g v++++ +  +D G+++ p  v+ Qi GG+  G+G++ +E l+y+++Gql+t+s +d  + ta+ +P
  gi|518653130|ref|YP_008142650.1| 553 SGLVTMKDWYSYYDLGHVLSPVNVIAQITGGALEGVGQMFSESLRYSPEGQLMTTSISDAGLLTADYAP 621
                                       688999*****************************************************9999987665 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 !   49.3   0.0   5.7e-17   5.1e-13       2     109 ..      10     114 ..       9     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 49.3 bits;  conditional E-value: 5.7e-17
                                       T-SCCGGGCC-TTTEEEEEEE-SSSSEEEEEEE-HHHHCSTTEEEEEEHHHHCCGTECCTTSSS-EEEESS-SSEES CS
                      Ald_Xan_dh_C   2 GeavYvdDipapgalylafvrStkahAkivsidvsaalalpGVvavitakdlpkenkaigsiledeedallaedkvr 78 
                                       G+++Y+dD+ + ++ly+++ rS++ +Aki++++   + +  + +   ++ ++++ + +++s+   e   ++a d+v+
  gi|518653130|ref|YP_008142650.1|  10 GKGKYIDDMTFNDMLYMNVFRSPYGKAKIKNVKGGLNASELKLFYKSSMGEMASLGGKSNSAY-FE--PVFAIDNVN 83 
                                       99*******************************998888887888888888888877775444.34..4******** PP

                                       STT-EEEEEEESSHHHHHHHHHT-EEEEEE- CS
                      Ald_Xan_dh_C  79 svgqavaavvAedeetArkAaklvkveYeel 109
                                       + gqa+aav  ++++++++ ++ v+v+Ye+ 
  gi|518653130|ref|YP_008142650.1|  84 YEGQAIAAVFGKTRYESEDLLNTVSVDYEPM 114
                                       ****************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (679 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4798.88
//
Query:       gi|518653131|ref|YP_008142651.1|  [L=109]
Description: hypothetical protein FACI_IFERC00001G1770 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-14   53.5   0.3    3.3e-14   53.0   0.3    1.2  1  TA0956    Thermoplasma acidophilum protein TA0956


Domain annotation for each model (and alignments):
>> TA0956  Thermoplasma acidophilum protein TA0956
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.3   1.8e-18   3.3e-14       1     109 [.       1     102 [.       1     103 [. 0.93

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.8e-18
                                       --EEEEEEEESTTS--EEEEEEHHHHHHHHHHHHHHTTS-.-CCHHHHHHHHH---S---TTSEEEEEEEEETTTTE CS
                            TA0956   1 mtlcamynitlkekhPsticvvlsklreslealadvldselieesleefieefartdeimPedktvGfviinsdkkv 77 
                                       m++c+ yni+      st+cv l +l++sl+ l   +       +++ fi+++ ++  +  +d  vG +i+n  kk+
  gi|518653131|ref|YP_008142651.1|   1 MANCVAYNIRH-SLKSSTMCVPLAELNRSLDDLCANIG------KIQAFIDKYGKSAGVNKDDANVGIIIVNPGKKI 70 
                                       899******95.5678**************99987664......579****************************** PP

                                       EEEEE-S--CCHHHHHHHHHHHHHCCS-EEEE CS
                            TA0956  78 lslsfselkeelkksikeiaekfkkkGykvei 109
                                       + +sfs++    k +++ +ae+++k  ++v +
  gi|518653131|ref|YP_008142651.1|  71 VDMSFSQNLGIDKMKVNSSAEELRKNKFTVTV 102
                                       ***************************99975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.28s 00:00:00.70 Elapsed: 00:00:00.45
# Mc/sec: 722.68
//
Query:       gi|518653132|ref|YP_008142652.1|  [L=259]
Description: hypothetical protein FACI_IFERC00001G1771 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-17   62.4   0.0    6.1e-17   61.7   0.0    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.8e-15   57.6   0.0    2.6e-15   57.0   0.0    1.3  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 !   61.7   0.0   6.8e-21   6.1e-17      11     162 ..      79     221 ..      74     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 6.8e-21
                                       TTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  11 knekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredle 87 
                                        +++k  +l+v+ l+  Kg+d l+ ++++ +   n++v ++iaG+g e      la++ + ++++i++g ++++dl 
  gi|518653132|ref|YP_008142652.1|  79 VKNTKLKFLFVASLSSGKGLDILLPLIEKMN---NSEVEFHIAGGG-E------LADKIKTNKRIIYHGILNDTDLA 145
                                       5678999*********************874...9*********44.3......79999999*************** PP

                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTTSEEEE-TT.-HHHHHHHHHHHHHSH..H CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdgetGllvkpn.naealaeairkllede..e 160
                                        l++ +d+f++ps+ + f iv l A+++gl v +s+  +g+   + d e+++l   + ++e++  +++++++++   
  gi|518653132|ref|YP_008142652.1| 146 RLYRECDVFIYPSHADTFSIVTLQALSSGLYVMCSDyLKGN---FDDFENKYLEYLPlDIEQWYSRVNEIINNNsiI 219
                                       ************************************66665...667888888888889999999999999998664 PP

                                       HH CS
                   Glycos_transf_1 161 lr 162
                                       ++
  gi|518653132|ref|YP_008142652.1| 220 KH 221
                                       44 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 !   57.0   0.0   2.9e-19   2.6e-15       3     133 ..      85     214 ..      83     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 57.0 bits;  conditional E-value: 2.9e-19
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfv 77 
                                       ++lfv +l+   kg+d+ll  ++++ +++v+++i+G+g+ +++++      ++r++++G +  +dla+l++++dvf+
  gi|518653132|ref|YP_008142652.1|  85 KFLFVASLS-SGKGLDILLPLIEKMNNSEVEFHIAGGGELADKIK-----TNKRIIYHGILndTDLARLYRECDVFI 155
                                       689*****5.45**************889*******886333554.....2479*****998778************ PP

                                       E--..---SHHHHHHHHTT-EEEE-TG.GGTTT--TTSSEE-.-TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  78 aPs..egfglkllEamaaglpvVatdv.ggiaevvgengllv.ppgdpealaeailrLle 133
                                        Ps   +f++++l+a+++gl v ++d  +g  +   en +l   p d e++  ++ ++++
  gi|518653132|ref|YP_008142652.1| 156 YPShaDTFSIVTLQALSSGLYVMCSDYlKGNFDD-FENKYLEyLPLDIEQWYSRVNEIIN 214
                                       ***987*******************983353331.3455443244567777777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       691  (0.0385409); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1646.52
//
Query:       gi|518653133|ref|YP_008142653.1|  [L=178]
Description: methionine sulfoxide reductase A [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-61  206.5   0.3    2.6e-61  206.3   0.3    1.0  1  PMSR         Peptide methionine sulfoxide reductase
  ------ inclusion threshold ------
      0.054   13.3   0.1      0.099   12.4   0.1    1.4  1  DisA-linker  DisA bacterial checkpoint controller linker regi
      0.057   13.4   1.4      0.099   12.6   1.4    1.4  1  DUF4298      Domain of unknown function (DUF4298)
      0.074   13.2   0.1       0.19   11.9   0.0    1.7  1  PI_PP_I      Phosphoinositide phosphatase insertion domain
      0.075   13.2   0.2         13    6.0   0.3    2.4  2  HEPN         HEPN domain
       0.12   12.5   0.0       0.15   12.1   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> PMSR  Peptide methionine sulfoxide reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.3   0.3   8.7e-65   2.6e-61       2     152 ..       6     155 ..       5     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 206.3 bits;  conditional E-value: 8.7e-65
                                       EEEE-S-HHHHHHHHCTSTTEEEEEEEEESSS-SS--HHHHHTTTT--EEEEEEEEETTTS-HHHHHHHHHHTS-TT CS
                              PMSR   2 avlagGCFWgveklfeklkGvlstevGYagGktenptYeevcsgktghaEavevvydpekvsleellelffeihDpt 78 
                                       +v+++GCFW+ e++f+ +kGv ++  GYagG+tenptY+evc++ktghaE+v+v y+p+++sle+llelf+ +hDpt
  gi|518653133|ref|YP_008142653.1|   6 LVIGTGCFWCSEAIFKLIKGVNNVVPGYAGGHTENPTYREVCTDKTGHAEVVKVSYEPDVISLEKLLELFMATHDPT 82 
                                       589************************************************************************** PP

                                       -SSEETTEESGGG--EEEESSCCHHHHHHHHHHHHHTTHTTSSS---EEEEG-SEEE--CCCTTHHHH-TTS.-- CS
                              PMSR  79 qlnrqgnDvGtqYrsaiyytneeqkevaeevleelqkkkalkkkivteieplkefykaeeyHqqYleknpeg.yc 152
                                       +ln+qgnD+GtqYrs+i y++++++++++++l+e qk+  ++k+ivte+++l++fy+ae+yH +Y+++n+++ yc
  gi|518653133|ref|YP_008142653.1|  83 SLNKQGNDIGTQYRSIILYNDDAEEKMIKDFLKEHQKN--YSKPIVTEVQKLDRFYEAEDYHHNYFANNQSNpYC 155
                                       **************************************..******************************99999 PP

>> DisA-linker  DisA bacterial checkpoint controller linker region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   3.3e-05     0.099      70     119 ..      84     133 ..      79     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.3e-05
                                       TGGGGHHHHHHHHHHHTTHHHHHHHHHHHHSSS--HHHHHHHHHHH...H CS
                       DisA-linker  70 LGteGrlislqleeLlanveeeeellikDYlkeekeeeaeeileelkels 119
                                       L ++G  i  q++ ++   ++ ee +ikD+lke++++  + i+ e+++l+
  gi|518653133|ref|YP_008142653.1|  84 LNKQGNDIGTQYRSIILYNDDAEEKMIKDFLKEHQKNYSKPIVTEVQKLD 133
                                       6678999999************************9999999999999886 PP

>> DUF4298  Domain of unknown function (DUF4298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   1.4   3.3e-05     0.099      18      54 ..     114     151 ..     101     157 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.3e-05
                                       HHHHHHHHHH.THHHHHHHHHHHTSHHHHHHHTS--SS CS
                           DUF4298  18 Leealeqwkk.lqkklakLdeYYqseqwredleasnkg 54 
                                       L+e ++++ k + ++++kLd++Y+ e++   + a n+ 
  gi|518653133|ref|YP_008142653.1| 114 LKEHQKNYSKpIVTEVQKLDRFYEAEDYHHNYFANNQS 151
                                       667777775536899**************999998875 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 ?   11.9   0.0   6.5e-05      0.19       5      43 ..     135     173 ..     132     177 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
                                       HHCS-HHHHHHHHC--TT--SHHHHHHHHHHHHHHHHHH CS
                           PI_PP_I   5 frkLeeyqqaYflnleskeaslkklkqdlnqfllkWeei 43 
                                       f++ e+y + Yf n +s++  +  +k ++n+f++k  +i
  gi|518653133|ref|YP_008142653.1| 135 FYEAEDYHHNYFANNQSNPYCAMVIKPEVNDFIMKHGNI 173
                                       778899****************************98877 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0    0.0093        28      28      42 ..      12      26 ..       8      27 .. 0.91
   2 ?    6.0   0.3    0.0043        13      61      95 ..     111     147 ..      78     176 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0093
                                      HHHHHHHHHHHHHHH CS
                              HEPN 28 cfhaqqaaekalKAl 42
                                      cf++ +a++k++K++
  gi|518653133|ref|YP_008142653.1| 12 CFWCSEAIFKLIKGV 26
                                      *************86 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0043
                                       C.CHHHT....-HHHHHHHHHHHCCCHHCCCTSS--S CS
                              HEPN  61 e.elkkelke.seelreeleeLekayiesrYpdakee 95 
                                       + +lk++ k+ s+ + +e+++L+++y   +Y + ++ 
  gi|518653133|ref|YP_008142653.1| 111 KdFLKEHQKNySKPIVTEVQKLDRFYEAEDYHHNYFA 147
                                       335555555569*******************998774 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     5e-05      0.15      47     126 ..      56     143 ..      15     145 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5e-05
                                       TEB-HHHHCCHCCCHHHHHHCHCHHHH............EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  47 glendiepdlkrllellealgkkkall..........lkiagvvlnrvdgeneetllkealeelkqrygvpvlgvip 113
                                        ++   epd+++l++lle +  ++ +            ++ +++l   d e  e+++k++l+e+++ y  p++ ++ 
  gi|518653133|ref|YP_008142653.1|  56 VVKVSYEPDVISLEKLLELFMATHDPTslnkqgndigTQYRSIILYNDDAE--EKMIKDFLKEHQKNYSKPIVTEVQ 130
                                       344444446666666666666666655666889898888888888776666..************************ PP

                                       --CCHCCCCHHTS CS
                                       xxxxxxxxxxxxx RF
                              CbiA 114 rdeavaeaparge 126
                                       + ++++ea+  ++
  gi|518653133|ref|YP_008142653.1| 131 KLDRFYEAEDYHH 143
                                       ********99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (178 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       786  (0.0438396); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.32s 00:00:00.85 Elapsed: 00:00:00.52
# Mc/sec: 1038.75
//
Query:       gi|518653134|ref|YP_008142654.1|  [L=61]
Description: hypothetical protein FACI_IFERC00001G1775 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
       0.13   12.6   0.0       0.15   12.5   0.0    1.1  1  Chlamy_scaf  Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
       0.14   12.2   0.0       0.18   11.9   0.0    1.2  1  HicA_toxin   HicA toxin of bacterial toxin-antitoxin,


Domain annotation for each model (and alignments):
>> Chlamy_scaf  Chlamydia-phage Chp2 scaffold (Chlamy_scaf)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.6e-05      0.15      32      74 ..      18      60 ..      12      61 .] 0.90

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.6e-05
                       Chlamy_scaf 32 ssildyqdaleivakaeeafdelPanirkrfanPmellsfled 74
                                      s il + +++++  ka+ea  +lP  i k++    +l++f  d
  gi|518653134|ref|YP_008142654.1| 18 SVILTHDETVDLCLKAQEAGLDLPKYIMKNYMKDLKLIKFRYD 60
                                      67889999*************************9999999655 PP

>> HicA_toxin  HicA toxin of bacterial toxin-antitoxin,
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18       9      57 ..       4      53 ..       2      54 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                                      HHTT-EEE.EEETTEEEEE-TTSS-EEEEE.S-SSS--CCCHHHHHHHCC CS
                        HicA_toxin  9 eklGfevv.rqkGSHvrfkhpdkrgivtvppHpgkelkpgtlksIlkqaG 57
                                      e+lG+ +  +++G  v+++h+++ + +      g +l+++ +k+ +k+++
  gi|518653134|ref|YP_008142654.1|  4 EDLGYMILyNRSGRSVILTHDETVDLCLKAQEAGLDLPKYIMKNYMKDLK 53
                                      56788777455**********999999999999***********999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (61 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       397  (0.0221429); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 444.94
//
Query:       gi|518653135|ref|YP_008142655.1|  [L=320]
Description: hypothetical protein FACI_IFERC00001G1776 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-65  221.4   0.0    1.6e-65  221.2   0.0    1.0  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 !  221.2   0.0     9e-70   1.6e-65       1     291 [.      15     306 ..      15     309 .. 0.95

  Alignments for each domain:
  == domain 1  score: 221.2 bits;  conditional E-value: 9e-70
                                       .EEEE-SSS-ST..TS-HHHHHHHHHHHHHTT--EEE--TT-TTTHHHHHHHHHHHH-TTTGGG-EEEEEE--SSST CS
                      Aldo_ket_red   1 elglGtwqlgsk.eeiskeealellrraleaGinffDtAevYgkgqseellGealkksrkkreeviiatKvdlrdae 76 
                                       +l+lG++++gs  +  ++e++ +++++a+++Ginf+DtA++Y  g+se+++Gea+      r +++++tK+++   +
  gi|518653135|ref|YP_008142655.1|  15 RLCLGGMSFGSSkWMADPETSGKIIKKAIDYGINFIDTANIYSSGESEKIIGEAITG---YRPQLVLSTKGGGKVND 88 
                                       59**********9999*****************************************...***************** PP

                                       TSSSS-HHHHHHHHHHHHHHHT-S-EEEEEE-S--TTS-.HHHHHHHHHHHHHTTSEEEEEEES--HHHHHHH.... CS
                      Aldo_ket_red  77 iksglskeniresleeslkrLgtdyvDllllHrpdpslpsieevldaleelvkeGkiraiGvSnfsveqleka.... 149
                                         +g+s++ + ++ ++slk+L+tdy+D+++lH ++ +++   +++ +l  ++++Gk+ +iG+Snf   ql +     
  gi|518653135|ref|YP_008142655.1|  89 FTQGFSRAILFNEMKNSLKNLRTDYIDIYFLHTIFDNVD-FRDTVHTLSSFISSGKAGYIGLSNFMGYQLAEFstim 164
                                       ***************************************.************************9988888888999 PP

                                       HHTTT--EEEEE-B-BTT-HHHHTTHHHHHHHTT-EEEEBSTTGGGTTGTTTSS---SSS..CCC-------TS-HH CS
                      Aldo_ket_red 150 kkkkkvkivavqveynllreleeegllelckkkgvpliaysplggGlltgkyqseedked..keprkdlkrdertsk 224
                                       + ++ +k++++q++yn + +++e+  +++c+k+g++  ++sp++ G+l+gky++  + e+  +++ +++k++   + 
  gi|518653135|ref|YP_008142655.1| 165 EMQENIKPAILQNHYNAVYREDERDAIPFCEKHGIAYSPFSPIAAGFLSGKYKRGLENETvrTKTYPVMKERYFSDS 241
                                       99***************************************************98776651145557888889999* PP

                                       HHHHHHHHHHHHHHTT--HHHHHHHHHTTSTT-SEEEE--SSHHHHHHHHGGGG----HHHHHHHHH CS
                      Aldo_ket_red 225 nldaaeelselakehgvslaqlalryalsqpavgivipgasnieqlednldalelklseeevaelde 291
                                        +d +e ++++ak++gv++ qlal+y+l  +++ i+++ga+++e led ++al++kl+ ee++++d+
  gi|518653135|ref|YP_008142655.1| 242 DFDILESVEDIAKKKGVKVPQLALAYVL--NKGFIPVIGATKPEYLEDDIAALDVKLDREEMEAIDR 306
                                       ****************************..9**********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2449.46
//
Query:       gi|518653136|ref|YP_008142656.1|  [L=379]
Description: hypothetical protein FACI_IFERC00001G1777 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-20   74.0   0.2    5.2e-20   71.7   0.1    1.9  2  Glycos_transf_1  Glycosyl transferases group 1
    2.8e-19   69.9   0.0    1.4e-18   67.6   0.0    2.0  2  Glyco_trans_1_4  Glycosyl transferases group 1
    0.00025   21.1   0.0    0.00043   20.3   0.0    1.4  1  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0      0.12   7.2e+02     114     143 ..     112     139 ..     110     176 .. 0.54
   2 !   71.7   0.1   8.7e-24   5.2e-20      13     159 ..     199     335 ..     194     346 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.12
                                       HTT--EEEETTTTHCHHCHTTTSEEEE-TT CS
                   Glycos_transf_1 114 aaglpviasnaggpaevvkdgetGllvkpn 143
                                       + g+ v+  n+g + ev+ ++   +  k++
  gi|518653136|ref|YP_008142656.1| 112 KEGKTVVLGNHGTYFEVLDMYG--FASKAY 139
                                       5566677777777766666654..333333 PP

  == domain 2  score: 71.7 bits;  conditional E-value: 8.7e-24
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                       ++   ++++grl + Kgvd l+++ +      + +++l+i+G+g++ ++l+++      + n+i++g+vs e++++l
  gi|518653136|ref|YP_008142656.1| 199 NDNFSVVYLGRLMESKGVDMLLELEK------KADINLHIIGKGPYMEKLQQM-----KNQNTIIHGYVSSEEKIKL 264
                                       5566799****************999......689***********9999998.....67899************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEET.TTTHCHHCHTTT.SEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasn.aggpaevvkdge.tGllvkpnnaealaeairkllede 159
                                       l  +d++++psi+E++ i+++E +a+gl  i+s  + gp+ +v++    G+ v+  n++ ++++i+++   +
  gi|518653136|ref|YP_008142656.1| 265 LAESDVMIVPSINESLSISAIEGLASGLYLIVSStSMGPRYIVRQDNiFGVAVPR-NPKNFIKEIERIKIIK 335
                                       **********************************778888888777745555555.5********9986555 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 ?   -0.7   0.0      0.29   1.7e+03      72     108 ..      90     128 ..      64     144 .. 0.74
   2 !   67.6   0.0   2.4e-22   1.4e-18       3     130 ..     203     330 ..     201     332 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.29
                                       H-SEE..EE-----SHHHHHHHHTT-EEEE-TGGGTTT- CS
                   Glyco_trans_1_4  72 aadvf..vaPsegfglkllEamaaglpvVatdvggiaev 108
                                       + dv+  v P+  f+++ +  m  g+ vV  + g   ev
  gi|518653136|ref|YP_008142656.1|  90 DFDVYyfVSPTLLFRNVGYRLMKEGKTVVLGNHGTYFEV 128
                                       555551155556899999999999999999888555555 PP

  == domain 2  score: 67.6 bits;  conditional E-value: 2.4e-22
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---...HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp.rpeeleelaagleerveftGfv..edlaellaaadvf 76 
                                        ++++Grl e  kgvd+lle  ++     ++l+i+G+gp + e+l+++ +   ++ +++G+v  e++ +lla++dv+
  gi|518653136|ref|YP_008142656.1| 203 SVVYLGRLME-SKGVDMLLELEKKAD---INLHIIGKGPyM-EKLQQMKN---QNTIIHGYVssEEKIKLLAESDVM 271
                                       699*****55.5*******8655544...99*******977.59985554...79*******9888*********** PP

                                       EE--..---SHHHHHHHHTT-EEEE-TGG.GTTT--.TTS..SEE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  77 vaPs..egfglkllEamaaglpvVatdvg.giaevv.gen..gllvppgdpealaeailr 130
                                       ++Ps  e+++++++E +a+gl  ++++++ g++ +v ++n  g+ vp ++p+ ++++i+r
  gi|518653136|ref|YP_008142656.1| 272 IVPSinESLSISAIEGLASGLYLIVSSTSmGPRYIVrQDNifGVAVP-RNPKNFIKEIER 330
                                       **************************997798888885553367775.79******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 !   20.3   0.0   7.3e-08   0.00043       1     109 [.       6     149 ..       6     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 7.3e-08
                    Glyco_transf_4   1 vGGverhvleLaraLarrGheVtvvtpgddgpleeev...............elvvrvprvplpllkrllrslaflr 62 
                                       +GG e  ++++a+ + r+G++Vt++  g ++  e +                +  + ++ +   +l   l+ +  + 
  gi|518653136|ref|YP_008142656.1|   6 AGGGEANARDIAELFVRQGYDVTLFGAGIPKGYETKAgkysfnyvpdaftfdIMATGPVLKISHILSMGLIGIYTYN 82 
                                       59***********************7777777777767778887878866542222222222233444555666677 PP

                    Glyco_transf_4  63 rlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglye......................k 109
                                       r+ + +k  ++Dv    sp  l+  + + +++ g+ +Vl  Hg+y                       +
  gi|518653136|ref|YP_008142656.1|  83 RIYEKIK--DFDVYYFVSPTLLFRNVGYRLMKEGKTVVLGNHGTYFevldmygfaskayskilttmifH 149
                                       8888888..9********99999876555557*************888655544444443333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); 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: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2966.67
//
Query:       gi|518653137|ref|YP_008142657.1|  [L=376]
Description: glycosyltransferase family 4 protein [Ferroplasma acidarmanus fer1]
Scores for complete 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   79.4   0.1    7.1e-22   77.7   0.0    1.8  2  Glycos_transf_1  Glycosyl transferases group 1
    2.3e-16   60.5   0.0    4.2e-16   59.6   0.0    1.4  1  Glyco_trans_1_4  Glycosyl transferases group 1
    3.9e-05   24.0   0.0     0.0001   22.6   0.0    1.6  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 ?   -3.6   0.0       1.1   6.7e+03      59      75 ..     156     172 ..     152     180 .. 0.72
   2 !   77.7   0.0   1.2e-25   7.1e-22      13     170 ..     207     352 ..     196     354 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.1
                                       HHHHHHHHHHHCTTCGG CS
                   Glycos_transf_1  59 ekelkklaeelelsdnv 75 
                                        ++lk+l++++ +s ++
  gi|518653137|ref|YP_008142657.1| 156 PENLKYLSKAYSISRKI 172
                                       56778888888777766 PP

  == domain 2  score: 77.7 bits;  conditional E-value: 1.2e-25
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEEECCHSSSHHHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnviflgevsredleel 89 
                                       ++k ++l+  rl++ Kg +++i+a++l+  +  p++ +   G             +l l + ++f+ +++++ l++l
  gi|518653137|ref|YP_008142657.1| 207 KDKHLMLVPLRLNPAKGAKYAIDALKLIHNK-YPDISISAFG-----------DYNLPLPEYIQFHYNINQKSLKKL 271
                                       4566788888******************877.**********...........5799******************** PP

                                       HHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSHHHHHHHH CS
                   Glycos_transf_1  90 lknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairklledeelrerlg 166
                                       +  a  f+lpsi Eg + +l+EAm +g+ +i+++ ggp  v+++g++G+lv+ +++e++  +++kl+e++ + +r++
  gi|518653137|ref|YP_008142657.1| 272 YGDATFFILPSIEEGIPEPLIEAMVSGCVAISTACGGPETVIVHGQNGFLVPIKDPEKIFLQFAKLMEERIDLKRIS 348
                                       ****************************************************************************9 PP

                                       HHHH CS
                   Glycos_transf_1 167 enar 170
                                       e a+
  gi|518653137|ref|YP_008142657.1| 349 ESAK 352
                                       9997 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6   0.0   7.1e-20   4.2e-16       6     133 ..     214     339 ..     209     340 .. 0.85

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 7.1e-20
                                       EES---GG.GTHHHHHHHHHHHH.H..HEEEEEES---..HHHHHHHTT-T.TEEEE---..THHHHHHHH-SEEEE CS
                   Glyco_trans_1_4   6 fvGrleenvkgvdllleavpllrkk..dvrlvivGdgprpeeleelaagleerveftGfv..edlaellaaadvfva 78 
                                          rl  + kg+++ ++a++l+++k  d+ +   Gd + p  l        e ++f+  +  ++l++l+ +a+ f++
  gi|518653137|ref|YP_008142657.1| 214 VPLRL-NPAKGAKYAIDALKLIHNKypDISISAFGDYNLP--LP-------EYIQFHYNInqKSLKKLYGDATFFIL 280
                                       45578.466**************99744*******77443..43.......6788999997566************* PP

                                       --..---SHHHHHHHHTT-EEEE-TGGGTTT--...TTSSEE--TT-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  79 Ps..egfglkllEamaaglpvVatdvggiaevv...gengllvppgdpealaeailrLle 133
                                       Ps  eg++  l+Eam +g+  ++t++gg +e+v   g+ng+lvp +dpe++  + ++L+e
  gi|518653137|ref|YP_008142657.1| 281 PSieEGIPEPLIEAMVSGCVAISTACGG-PETVivhGQNGFLVPIKDPEKIFLQFAKLME 339
                                       ***88*********************99.665559**************99999888886 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 ?   -3.6   0.0       2.5   1.5e+04      44      63 ..     127     146 ..     119     147 .. 0.79
   2 !   22.6   0.0   1.7e-08    0.0001       3      91 ..     279     368 ..     276     369 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 2.5
                   Glyco_trans_1_2  44 ilfedleelaekiryllanp 63 
                                       +l+ d  +++e i +ll ++
  gi|518653137|ref|YP_008142657.1| 127 VLVPDKRNMVENIYFLLYHD 146
                                       67788899999999888775 PP

  == domain 2  score: 22.6 bits;  conditional E-value: 1.7e-08
                   Glyco_trans_1_2   3 LnpsrsespnlrlfEaaacGafaltddaegleelftpgkevilfe..dleelaekiryllanpeerraiaeaarerv 77 
                                       + ps  e++   l Ea+ +G++a++++  g+e  +  g+ ++l+   d+e +  ++++l++++ + ++i+e a++  
  gi|518653137|ref|YP_008142657.1| 279 ILPSIEEGIPEPLIEAMVSGCVAISTACGGPETVIVHGQNGFLVPikDPEKIFLQFAKLMEERIDLKRISESAKAT- 354
                                       568889999999**************88*********************************************999. PP

                   Glyco_trans_1_2  78 laehtydhraeqll 91 
                                         e++ ++ + ++l
  gi|518653137|ref|YP_008142657.1| 355 AMEYDINKTYTEFL 368
                                       45666666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 2629.81
//
Query:       gi|518653138|ref|YP_008142658.1|  [L=253]
Description: glycosyl transferase family 2 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-11   43.9   0.5    4.8e-11   42.8   0.5    1.5  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.015   15.8   0.0       0.33   11.5   0.0    2.3  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 !   42.8   0.5   5.3e-15   4.8e-11       1     108 [.       4     100 ..       4     131 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 5.3e-15
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       s+++++yN e+ + ++l   ++     + ei++v+ +StD+t ++l +++   +r+++i r+  +G ++ +  ++++
  gi|518653138|ref|YP_008142658.1|   4 SICTTVYNSEEIVNKFLSKFIDT----EHEIVIVNSCSTDNTGKLLANYH---DRIKLINRKSTRGMGKKI--AIEN 71 
                                       89*********************....**********************8...5**********9999976..5*** PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.T CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdg 108
                                       a+g  i+++D D+e+    l+++++ +e+  
  gi|518653138|ref|YP_008142658.1|  72 ASGGNIILIDFDVEILN--LKEIIDTYEAKY 100
                                       **************998..788877777744 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 ?   11.5   0.0   3.7e-05      0.33       2      50 ..      11      59 ..      10      88 .. 0.78
   2 ?    2.0   0.0     0.034   3.1e+02      42      79 ..     164     202 ..     152     203 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.7e-05
                   Glyco_tranf_2_4  2 neadiLpeflahhlalgfdrilvydndstDgtrailkel.pevkllhvdk 50
                                      n ++i ++fl    +   ++i++++  stD+t ++l+++ +++kl++ ++
  gi|518653138|ref|YP_008142658.1| 11 NSEEIVNKFLSKFIDT-EHEIVIVNSCSTDNTGKLLANYhDRIKLINRKS 59
                                      7777788888877777.677*****************9637799987665 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.034
                   Glyco_tranf_2_4  42 evkllhvdksyederrqvellkallary.aeadwvlvvD 79 
                                       ++  ++++++ +++r+++++ k++ +r+ + ad ++v D
  gi|518653138|ref|YP_008142658.1| 164 NCMKIRHVGPGRESRYENNIFKKASRRIkCAADAIFVSD 202
                                       4555678889999**********9999625678777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1729.19
//
Query:       gi|518653139|ref|YP_008142659.1|  [L=60]
Description: hypothetical protein FACI_IFERC00001G1780 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       402  (0.0224218); 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:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 467.60
//
Query:       gi|518653140|ref|YP_008142660.1|  [L=507]
Description: benzoylformate decarboxylase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-27   95.2   0.0    7.7e-27   94.0   0.0    1.6  1  TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP b
    1.5e-21   76.8   0.0    4.8e-21   75.1   0.0    1.8  2  TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP b
    6.5e-14   51.8   0.0    1.3e-13   50.9   0.0    1.5  1  TPP_enzyme_M  Thiamine pyrophosphate enzyme, central domain
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.53   10.0   0.0    2.1  2  CO_dh         CO dehydrogenase beta subunit/acetyl-CoA syntha


Domain annotation for each model (and alignments):
>> TPP_enzyme_N  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.0   1.7e-30   7.7e-27       5     167 ..       5     163 ..       1     166 [. 0.93

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 1.7e-30
                                       HHHHHHHHHCT--EEEE---CCCHHHHCCHHCT.TSEEEE-SSHHHHHHHHHHHHHHHTS-EEEEE-CHHHHHHCHH CS
                      TPP_enzyme_N   5 ealvraLkalgvehvfgvpGsrilplldalseeqgirvvlarhEqgaafaAdgyaratgkpgvvlvtsgpGatnalt 81 
                                       +++ + Lk+ +   vfg+pG+++ p+l+ +s     +++l++h    +++Adg a++t+kp  v+++s  G+ n + 
  gi|518653140|ref|YP_008142660.1|   5 TIFNKSLKNMKLFPVFGNPGTTEIPMLEGVSSD---EYILTLHDSISVGMADGRAQLTRKPSFVNLHSILGVGNSMA 78 
                                       56667788888889******************9...7**************************************** PP

                                       HHHHHHHHT--EEEEEEE--CCCHHS..TC--T..-CCHHHCCCSSEEEE-SSGGGHHHHHHHHHHHHHSSS--EEE CS
                      TPP_enzyme_N  82 alaeAkvdriPllvlsgdrptslrgqgvlqqel..dqlalfrpvtkyaervtspeelpealrrAirtalsgrpgPvy 156
                                        +++A+v r+P+++ +g+++++++      + l  ++++++ p++ky+++v+s++++++ +rrA+  +++++    +
  gi|518653140|ref|YP_008142660.1|  79 FIYSAFVHRVPVIITAGEQDSRHIF---YDPLLsgNISDMISPYVKYKFEVNSANDIERSIRRAYISSMTPPYSLSF 152
                                       *******************999998...333335699**************************************** PP

                                       EEEEHHHCC-E CS
                      TPP_enzyme_N 157 lelpkdvllee 167
                                       l +p+d+++ee
  gi|518653140|ref|YP_008142660.1| 153 LGFPMDIMEEE 163
                                       ********997 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.92   4.1e+03      16      54 ..      59      95 ..      50     102 .. 0.65
   2 !   75.1   0.0   1.1e-24   4.8e-21      17     152 ..     371     494 ..     360     495 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.92
                                      SSSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEE CS
                      TPP_enzyme_C 16 krprsyltsgglgtmGyglpaAiGaklakpdrevvaivG 54
                                      +r++s+++  +++ +G+g ++A   ++   + +v+ ++G
  gi|518653140|ref|YP_008142660.1| 59 TRKPSFVN--LHSILGVGNSMAFIYSAFVHRVPVIITAG 95
                                      55667777..78888888777765555333456666666 PP

  == domain 2  score: 75.1 bits;  conditional E-value: 1.1e-24
                                       SSSEEECETTTS-TTTHHHHHHHHHHHSTTSEEEEEEEHHHHHHTGGGHHHHHHTT-SEEEEEEE-SBCCCHHHHHH CS
                      TPP_enzyme_C  17 rprsyltsgglgtmGyglpaAiGaklakpdrevvaivGDGgflmilqelatavrrnlpitvvvlnNegygmtggqqe 93 
                                       +p+sy+  g  g +G++lpaA G++  k   +v +++GDG+f+++ q l+t+ ++nlp+++++l+N+gyg  ++ ++
  gi|518653140|ref|YP_008142660.1| 371 KPDSYFI-GKSGQIGWALPAAAGMATVK--DKVLCVIGDGAFMYTSQTLWTIQNYNLPVKIIILDNHGYGILKKFSD 444
                                       5666666.6789*************973..59********************************************* PP

                                       HHTCCTTTTSBB.BS----HHHHHHHTTSEEEEESSH.HHHHHHHHHHHHCSSSEEEEE CS
                      TPP_enzyme_C  94 pfggkrksgpagkdlkpvdfaklaealGakgarvekadveeleealkealekkgpalie 152
                                        +++++k       + ++ + k+  ++ ++     +++ +e+ e +++ ++ kgpa + 
  gi|518653140|ref|YP_008142660.1| 445 VNYNESKKYL----SFSIELKKVLDSFNIE-----SRENDETMEDIEWLRNIKGPAALI 494
                                       ***9887765....56899********888.....333489999999999999999775 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 !   50.9   0.0   2.8e-17   1.3e-13       1     118 [.     184     300 ..     184     314 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.9 bits;  conditional E-value: 2.8e-17
                                       HHHHHHHHHH-SSEEEEE-CHHCHTTGHHHHHHHHHHHT-EE.EEEGGGTTSS-TTSTTEEEESGGGSCHHHHHHHH CS
                      TPP_enzyme_M   1 iekaaellkaakrpvilvGggvarsgaseelrelaeklgiPv.vttlmgkgvipedhplylgmlglhgskaaneale 76 
                                       ++ ++e+++++k+pv++ G + +  +  e ++++a klgiPv ++ ++ +  +++ + +y+g l  + ++  n+ l 
  gi|518653140|ref|YP_008142660.1| 184 VKSIVEIINNSKNPVMVTGYELDMYEGIEYAKDFAGKLGIPVfAEPFASRAPFDSGDRNYAGDLPPV-AAVINDKLS 259
                                       5789**************************************7788888****************99.9******** PP

                                       H-SEEEEES-SSSTCCCTTTTT.TTTTT-EEEEEESSC.CCCTT CS
                      TPP_enzyme_M  77 eaDlvlalGarfddirttgsep.efapeakiihididp.aeigk 118
                                       e Dl++++G +    + + +++ +  + ++ii i  d   +ig 
  gi|518653140|ref|YP_008142660.1| 260 EYDLIIIVGGDI---NLYPYSKaDLLEGKEIIKIGMDIsGKIGD 300
                                       *********555...55555554555555899997774355555 PP

>> CO_dh  CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00012      0.53      15      70 ..     175     229 ..     170     276 .. 0.76
   2 ?   -1.8   0.0       0.5   2.2e+03     118     142 ..     411     435 ..     400     456 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                                       XXX--EEE--SHHHHHHHHHSSSEEEEE-S--.-HH.HHHHHHHHH.TSSSEEEEET CS
                             CO_dh  15 nskkatleealkvvakmikkakrPllivGpqvlkaeneeakekkil.ekklkvvata 70 
                                       ns+++++    k ++++i   k+P++++G ++   e   + +k ++ +  ++v a +
  gi|518653140|ref|YP_008142660.1| 175 NSNIVDMNAV-KSIVEIINNSKNPVMVTGYELDMYE-GIEYAKDFAgKLGIPVFAEP 229
                                       5556666555.9********************9888.44445544414466666655 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.5
                                       HHHHHHHHHHHH-TT-EEEE-SSS- CS
                             CO_dh 118 yasqalsslkkftdkittiaidkyy 142
                                       y+sq+l  ++++   +++i+ d+ +
  gi|518653140|ref|YP_008142660.1| 411 YTSQTLWTIQNYNLPVKIIILDNHG 435
                                       7899999999999888888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (507 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3436.19
//
Query:       gi|518653141|ref|YP_008142661.1|  [L=399]
Description: hypothetical protein FACI_IFERC00001G1782 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.9e-25   89.2   0.0      4e-25   88.7   0.0    1.2  1  Peptidase_M20  Peptidase family M20/M25/M40
    3.8e-06   26.8   0.0    7.1e-06   25.9   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
     0.0036   16.4   0.0       0.01   14.9   0.0    1.7  2  Peptidase_M42  M42 glutamyl aminopeptidase
  ------ inclusion threshold ------
       0.12   12.6   0.1       0.27   11.5   0.1    1.6  1  Toast_rack_N   N-terminal domain of toast_rack, DUF2154


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 !   88.7   0.0     9e-29     4e-25       1     206 [.      71     397 ..      71     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 9e-29
                                       EEEEES-BSSTTCGGGSSSTTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
                     Peptidase_M20   1 llgsHlDvVpeeetdgwttpfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.. 75 
                                       ++gsH+D+Vp    +g           G+++G       +gv++++++l+ l  +    +++i+ + +++EEg+r  
  gi|518653141|ref|YP_008142661.1|  71 AIGSHMDSVP----NG-----------GRFDGF------YGVMSGMQLLKDLGSTLK--NRKITAIDFTNEEGARfq 124
                                       589*******....88...........999999......************999973..89************9999 PP

                                       ...THHHHHHHHHH.T................................TTCESEEEEEEEESSSBTCHSTETEEEE. CS
                                       ...xxxxxxxxxxx.x................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                     Peptidase_M20  76 ...gGakallegle.e................................rekvdavfelhieepgileagklaigvv. 115
                                           G++  ++ ++ +                                ++++  ++elhie++++le ++ ++g+  
  gi|518653141|ref|YP_008142661.1| 125 pslLGSGMSTG-VFtKefaysrkdsdgitfeealeksgymgeeqnrvkNQDITRYLELHIEQGPVLELENYQVGIPk 200
                                       99966654444.22223445567777888889999999999999999999*****************9996666669 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|518653141|ref|YP_008142661.1| 201 givtmvvdnvsftgesnqagptpmkvrkdalvaasrftvavrdmakssgkeltmtvgkinnfpnaynvipgkvtmnl 277
                                       999************************************************************************** PP

                                       ..............................EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHT CS
                                       ..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 116 ..............................kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtd 162
                                                                      v+++  +  + + ++ ++++k + +++++l ++k+++  s   g+d
  gi|518653141|ref|YP_008142661.1| 278 dtrspdkktaeeyskmakeisekiaseegvPVDFKNQWTTETTIFD-EDMRKEIIKSCKSL-NLKYKELYSW-PGHD 351
                                       *************************999876888877777777777.*************9.9998888899.9*** PP

                                       HHHHTTT.EEEEEEESS.GGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxxxx.xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 163 arffagi.ptvmifgpg.sglaHspnEyvdledlekgikvlarlle 206
                                       a++++++ pt+mif p+ +g++H+ +Ey +++dl +g+ vl+r++e
  gi|518653141|ref|YP_008142661.1| 352 AQYMNRVvPTAMIFIPShNGRSHTREEYSSDQDLINGYSVLKRTVE 397
                                       ****9999*******9956************************987 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.6e-09   7.1e-06       4     107 ..     200     304 ..     199     306 .. 0.91

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.6e-09
                                       -EEEEEEEE...EE-B-EEGG.-TTTTB-.HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C.CCCEESS CS
                         M20_dimer   4 kGlaggkit...vkgkagHsg.apgagaN.AieklarllaeledeegdiaeerslprttlnvtgiegGs.aknvipd 74 
                                       kG++++ +    ++g++  +g  p +++  A+ +++r+  + +d  ++     s ++ t++v+ i+    a nvip+
  gi|518653141|ref|YP_008142661.1| 200 KGIVTMVVDnvsFTGESNQAGpTPMKVRKdALVAASRFTVAVRDMAKS-----SGKELTMTVGKINNFPnAYNVIPG 271
                                       7899999888889********988887756***************776.....55************77******** PP

                                       EEEEEEEEEHHHHHHHHHHHHHHHHHHTSCCST CS
                         M20_dimer  75 eaeakidiRllpgedpeevleeieeilekeape 107
                                       ++++++d R +++ ++ee  +  +ei ek a e
  gi|518653141|ref|YP_008142661.1| 272 KVTMNLDTRSPDKKTAEEYSKMAKEISEKIASE 304
                                       **************************9998865 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0      0.62   2.8e+03       6      25 ..      62      79 ..      51     101 .. 0.68
   2 !   14.9   0.0   2.3e-06      0.01     205     287 ..     300     386 ..     282     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 0.62
                                      EEESSTTSSEEEEEEE--B- CS
                     Peptidase_M42  6 kkkgkekepkvmiaAHmDei 25
                                      ++ +   + + +i +HmD +
  gi|518653141|ref|YP_008142661.1| 62 TLGS--GNDNTAIGSHMDSV 79
                                      3333..44556666777765 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-06
                                       S..TTS-CEEEEEETT....CCSHHHHHHHHHHHHHHTT--EEEEEESSSSSTHHHHHTSTTTSEEEEEEEEEBS.. CS
                     Peptidase_M42 205 k..lgkGpvirvkDas....giyhpklrkkllelAkknnipyqlevlsgggtDAgaihltgegvptalisiptry.. 273
                                       k   ++G+ + +k++     +i+++++rk++++ +k+ n++y+  ++s  g DA+ + +    vpta+i ip ++  
  gi|518653141|ref|YP_008142661.1| 300 KiaSEEGVPVDFKNQWttetTIFDEDMRKEIIKSCKSLNLKYKE-LYSWPGHDAQYMNRV---VPTAMIFIPSHNgr 372
                                       244677888888866556669*********************98.9*******9988776...*********98644 PP

                                       TTSTTEEEEHHHHH CS
                     Peptidase_M42 274 iHspvevahlddle 287
                                       +H+  e  + +dl 
  gi|518653141|ref|YP_008142661.1| 373 SHTREEYSSDQDLI 386
                                       78887777777765 PP

>> Toast_rack_N  N-terminal domain of toast_rack, DUF2154
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   6.1e-05      0.27       9      75 ..     251     316 ..     243     320 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 6.1e-05
                      Toast_rack_N   9 nlelgaGeltvsggaeellegkveynakewepevkyevkgkrgeitieqksskkkeiilgneknrWd 75 
                                       +l++ +G+++   +a + + gkv++n +   p+ k   + ++++ +i++k  +++ +  ++ kn+W+
  gi|518653141|ref|YP_008142661.1| 251 ELTMTVGKINNFPNAYNVIPGKVTMNLDTRSPDKKTAEEYSKMAKEISEKIASEEGV-PVDFKNQWT 316
                                       799***********************************************9999886.888899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.44
# Mc/sec: 2753.03
//
Query:       gi|518653142|ref|YP_008142662.1|  [L=140]
Description: inosine-5''''-monophosphate dehydrogenase [Ferroplasma acidarmanus fer1]
Scores for complete 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-21   74.2   0.1    6.1e-14   52.2   0.1    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 !   20.1   0.0   3.6e-08   0.00064       1      55 [.       5      58 ..       5      60 .. 0.86
   2 !   52.2   0.1   3.4e-18   6.1e-14       2      55 ..      71     123 ..      70     125 .. 0.94

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.6e-08
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTB.EEEEEEHHHHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgk.lvGivtlrDllral 55
                                      ++dim+++   ++ +t+  e  + m+ ++ + + +V +dgk + Givt+ D ++++
  gi|518653142|ref|YP_008142662.1|  5 AEDIMRKNCQIINGNTSALEGSKHMAANREGYI-IV-GDGKiPEGIVTEWDYINKV 58
                                      579**********************76667666.9*.7887699*******88765 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 3.4e-18
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +dimt ++ +v+ dt++e+++ lm++k+++rl+V+ +++kl Gi+t rD++++ 
  gi|518653142|ref|YP_008142662.1|  71 KDIMTAPLTSVTSDTPMEKVASLMAKKAIRRLLVI-DNNKLSGIITSRDIIKFF 123
                                       79**********************9999*******.6999***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 995.32
//
Query:       gi|518653143|ref|YP_008142663.1|  [L=289]
Description: hypothetical protein FACI_IFERC00001G1784 [Ferroplasma acidarmanus fer1]
Scores for 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-57  192.4   0.1    7.5e-57  192.1   0.1    1.1  1  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
      3e-25   88.7   0.1    1.5e-24   86.5   0.0    2.0  2  3HCDH           3-hydroxyacyl-CoA dehydrogenase, C-terminal d
     0.0034   17.4   0.2      0.012   15.6   0.2    2.0  2  NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogen
     0.0067   15.7   0.0       0.01   15.1   0.0    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0088   16.3   0.1      0.017   15.4   0.1    1.5  1  TrkA_N          TrkA-N domain
     0.0092   16.2   0.5      0.017   15.3   0.2    1.6  2  NAD_binding_2   NAD binding domain of 6-phosphogluconate dehy
  ------ inclusion threshold ------
      0.011   15.3   0.4      0.021   14.4   0.3    1.5  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.019   15.5   0.9      0.035   14.7   0.9    1.7  1  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
      0.045   14.3   0.1      0.096   13.3   0.1    1.5  1  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
      0.051   13.6   0.2        0.1   12.7   0.2    1.5  1  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
       0.06   12.6   0.0      0.078   12.3   0.0    1.3  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.089   12.1   0.1       0.15   11.4   0.1    1.4  1  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.12   12.6   0.0       0.55   10.5   0.0    2.0  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain


Domain annotation for each model (and alignments):
>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.1   0.1   5.4e-60   7.5e-57       1     179 [.       4     185 ..       4     186 .. 0.99

  Alignments for each domain:
  == domain 1  score: 192.1 bits;  conditional E-value: 5.4e-60
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH...HHHCCTTTTSS-HHHHCCCHHCEEEES-HH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekiek...sleklvekgklkeeeveaalarisfttdle 74 
                                       kvaviG+G+mG+gia+vf+++g+++ l+di++++le+a+++i++    l++lv +g ++e + +++++++s++td+ 
  gi|518653143|ref|YP_008142663.1|   4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAKNSIADgkfGLSRLVDRGTITEGQKAEYMKNLSVSTDYG 80 
                                       79******************************************9999***************************** PP

                                       HHHC-SEEEE-S-SSHHHHHHHHHHHHCCS-TTSEEEE--SSS-HHHHCCCSSSGGGEEEEEE-SSTTT--EEEEEE CS
                           3HCDH_N  75 eavdadlviEavvEnlelKrkvfaelekiakpdailasnTSslsiselaealkrperviglHFfnPpplmkLvEvvr 151
                                        + d ++ iEav+E + lK kv++ +ek +++++++asnTS+++ise+  ++k+++r+ig+H+fnP+p+mkL+Evv+
  gi|518653143|ref|YP_008142663.1|  81 MLNDREFAIEAVPEIMPLKLKVMESIEKNIPERSVIASNTSGIMISEIGMNIKDKSRLIGMHWFNPAPVMKLIEVVK 157
                                       ***************************************************************************** PP

                                       -TT--HHHHHHHHHHHHHTT-EEEEECS CS
                           3HCDH_N 152 gekTseetvatvvelakkigktpvvvkd 179
                                       ++ Ts +tv+ v ++a+++gk+pvvv+d
  gi|518653143|ref|YP_008142663.1| 158 TRFTSGDTVNMVLDMARSMGKEPVVVND 185
                                       **************************98 PP

>> 3HCDH  3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.8   2.5e+03      47      89 ..      26      64 ..      23      72 .. 0.73
   2 !   86.5   0.0   1.1e-27   1.5e-24       1      92 [.     188     279 ..     188     284 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.8
                                      HHHHHHHHHHHHHHHHHHHTTTHGGHH-HHHHHHHHTT--BGG CS
                             3HCDH 47 ldlvgldvakkilevlaeelgerayapsplleklveagrlgrk 89
                                      +d++ +d++ +ile  ++   + ++     l++lv+ g + + 
  gi|518653143|ref|YP_008142663.1| 26 MDTLLIDINDRILENAKNSIADGKFG----LSRLVDRGTITEG 64
                                      68888999999999888888888887....7777777766555 PP

  == domain 2  score: 86.5 bits;  conditional E-value: 1.1e-27
                                       TTTHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHSSCHHHHHHHHHHHHHHHHHHHHHHHTTTHGGHH-HHH CS
                             3HCDH   1 GFvvnRvlapllneavrlveegvaspediDaamrlglGlpmGpfelldlvgldvakkilevlaeelgerayapspll 77 
                                       GF+++  + ++l e +rl+e+g+a  ediD++++lg+G+pmGpfel+d++gld++k i ++l++e+g+ +  p+p+l
  gi|518653143|ref|YP_008142663.1| 188 GFFTTNFVHSWLVESLRLYEKGIAGKEDIDKMVKLGFGFPMGPFELMDTIGLDTMKEIGDYLYSETGDMRILPPPIL 264
                                       9**************************************************************************** PP

                                       HHHHHTT--BGGGTB CS
                             3HCDH  78 eklveagrlgrktgk 92 
                                       +++v ag  g k+ k
  gi|518653143|ref|YP_008142663.1| 265 KEMVYAGYKGSKKVK 279
                                       **********99865 PP

>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.2   8.4e-06     0.012       1      38 [.       4      41 ..       4     137 .. 0.89
   2 ?   -3.0   0.0       4.6   6.3e+03      55      87 ..     164     196 ..     160     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.4e-06
                                      -EEEE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHH CS
                    NAD_Gly3P_dh_N  1 kiavlGaGswGtalAkvlaenghevrlwvreeelieei 38
                                      k+av+G+G  G  +A+v+ +ng ++ l+  ++  +e+ 
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENA 41
                                      79********************9999999888666554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 4.6
                                       TTEEEES-HHHHHTT--EEEE---HHHHHHHHH CS
                    NAD_Gly3P_dh_N  55 enlvattdlaealkgadiivlvvPsqalrevlk 87 
                                       +++ ++ d+a+++ +  ++v   P  +++++++
  gi|518653143|ref|YP_008142663.1| 164 DTVNMVLDMARSMGKEPVVVNDYPGFFTTNFVH 196
                                       578888999999999888888888887777765 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   7.4e-06      0.01     143     186 ..       3      46 ..       1      48 [. 0.90

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 7.4e-06
                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkels 186
                                       k+++v+G+G  G  +A+++++ g ++ l++ +dr+l++ + +++
  gi|518653143|ref|YP_008142663.1|   3 KKVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAKNSIA 46 
                                       79**********************************87777665 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.1   1.2e-05     0.017       1      39 [.       5      43 ..       5      51 .. 0.91

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                                      EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH CS
                            TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelre 39
                                      +++iG G +G+ +a+ ++++g+d ++id +++ +e++++
  gi|518653143|ref|YP_008142663.1|  5 VAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAKN 43
                                      68*****************9989*********9999876 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 !   15.3   0.2   1.2e-05     0.017       1      39 [.       4      42 ..       4      74 .. 0.85
   2 ?   -3.0   0.0       5.1     7e+03      52      74 ..     149     171 ..     134     183 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.2e-05
                                      EEEEE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHH CS
                     NAD_binding_2  1 kigfiGlGvMGsnmalnllkagykvavynrtkekveelv 39
                                      k+++iG G+MG+ +a+ ++++g+++ +++ +   +e++ 
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAK 42
                                      69************************9998876655554 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 5.1
                                       HHHHCSEEEE-SSSHHHHHHHHH CS
                     NAD_binding_2  52 lvasldvvitmvkagkavdevie 74 
                                       +++ ++vv t  ++g+ v+ v++
  gi|518653143|ref|YP_008142663.1| 149 VMKLIEVVKTRFTSGDTVNMVLD 171
                                       44455666666666666666655 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.3   1.5e-05     0.021       2      55 ..       4      56 ..       3      93 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                                      EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHH CS
                    UDPG_MGDP_dh_N  2 kisviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelv 55
                                      k++viG+G +G   a v+ + g++ +++Di+++  ++ ++ +i     gL++lv
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAKN-SIADGKFGLSRLV 56
                                      89*****************************976665544.3444445555555 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.9   2.6e-05     0.035       1      24 [.       4      27 ..       4     118 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
                                      EEEEETTSHHHHHHHHHHHHTTS- CS
                     F420_oxidored  1 kigiiGaGnmgealasgllaagaq 24
                                      k+++iG+G mg+++a+ ++++g++
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMD 27
                                      79********************53 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1     7e-05     0.096       1      37 [.       4      40 ..       4      47 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 7e-05
                                      EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
                         Pyr_redox  1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrl 37
                                      kv+v+G+G  g   A+++ + g ++ +++ +d++l +
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILEN 40
                                      79*********************************33 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   0.2   7.3e-05       0.1      13      41 ..       3      31 ..       1      48 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-05
                                      -EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
                      Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvv 41
                                      kkv +iG G m++ +a+ ++++g++ +++
  gi|518653143|ref|YP_008142663.1|  3 KKVAVIGSGIMGQGIAQVFMRNGMDTLLI 31
                                      89**********************99876 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 ?   12.3   0.0   5.6e-05     0.078      30      70 ..       4      46 ..       1     117 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 5.6e-05
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH..T CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrparleqles..l 70
                                      kv viG G+ G+  +++ ++ g ++ ++D++ + le+ ++   
  gi|518653143|ref|YP_008142663.1|  4 KVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAKNsiA 46
                                      9**********************************99988544 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 ?   11.4   0.1   0.00011      0.15      37      73 ..       3      39 ..       1      57 [. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
                                      SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C 37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73
                                      k+v++iG G +Gq +a+++   gm+ + +d + +  e
  gi|518653143|ref|YP_008142663.1|  3 KKVAVIGSGIMGQGIAQVFMRNGMDTLLIDINDRILE 39
                                      89***************************99877444 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0    0.0004      0.55       1      36 [.       7      42 ..       7      73 .. 0.82
   2 ?   -0.9   0.0       1.5   2.1e+03      48      55 ..     140     147 ..     130     154 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.0004
                                      EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      ++G+G+ G  +A+   ++g d ll++ +dr+  +a+
  gi|518653143|ref|YP_008142663.1|  7 VIGSGIMGQGIAQVFMRNGMDTLLIDINDRILENAK 42
                                      8****************************9855555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.5
                                       S---EEET CS
                     NAD_binding_8  48 gahifhgs 55 
                                       g+h+f++ 
  gi|518653143|ref|YP_008142663.1| 140 GMHWFNPA 147
                                       9****994 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (289 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2044.14
//
Query:       gi|518653144|ref|YP_008142664.1|  [L=298]
Description: hypothetical protein FACI_IFERC00001G1785 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-59  200.1   0.0    5.4e-59  199.9   0.0    1.0  1  Peptidase_M19  Membrane dipeptidase (Peptidase family M19)
  ------ inclusion threshold ------
      0.088   12.6   0.0       0.13   12.1   0.0    1.2  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 !  199.9   0.0     6e-63   5.4e-59       7     318 ..       2     295 ..       1     296 [. 0.88

  Alignments for each domain:
  == domain 1  score: 199.9 bits;  conditional E-value: 6e-63
                                       .EEEEEE-HHHHHHHCTTTTT-TTTHCTSSS-HHHHHHHTEEEEEEEEE--CCCCCCCHHHHHHHHHHHHHHHHHHG CS
                     Peptidase_M19   7 iviDghndlplklrqekkeslllekdselqtdlerlraggvsavlfaifvpedasyeeavkatleqidlirrlvrkn 83 
                                       ++iD h d++++  +  ++   ++  + +q+ ++ l++   s+ +  +f++ + +y e++ + + ++ l+++ ++ +
  gi|518653144|ref|YP_008142664.1|   2 KFIDLHEDIAYS--SMYRD--VIH--GTGQSGVDMLKRFPGSIIFSVVFPHVNMQYGEEYGTSIPNTTLAYQQFNYY 72 
                                       689999999999..33443..334..455555555555555788888888889999999999999999999999988 PP

                                       TTTEEE-SSHHHHHHHHH.TT-EEEEEEEESCGGGTT-HHHHHHHHHTTEEEEES-SSS-BSSB-BCCGTT.SSSSB CS
                     Peptidase_M19  84 peqlklvrtaddierakk.egkiavllgiegaealgddlallrafyalGvrvlgltynrnnkfAdgaleekdedgGL 159
                                       +e ++  + ++ ie +k  + ++ +l+++eg+++l +  + ++ fy++G+r lglt+n+++kfA++++++  +d GL
  gi|518653144|ref|YP_008142664.1|  73 RE-ISKKYGINLIEGNKYvDSELNFLISMEGTDVL-NRPQDIDIFYSMGLRNLGLTWNYDTKFASSCYSK--KDYGL 145
                                       88.8888888888877765789*************.99*******************************9..***** PP

                                       -HHHHHHHHHHHHHT-EEE-TTB-HHHHHHHHHH-SSE.EECCEEBTTTS--TTSB-HHHHHHHHHTT-EEEE-SSH CS
                     Peptidase_M19 160 sefGkelVrelNrlgiliDlShlsektfldvlelSkaPvvaSHSnaralcdhpRNltDeqlkaiaesgGvvgvtfvp 236
                                       +  G+elV+ +N+ gi+iDl+h++++t+ld+ +++++P++ SH+n + l+dhpRN++ + +kai+++gGv+g+t++ 
  gi|518653144|ref|YP_008142664.1| 146 TGSGEELVKICNSSGIIIDLAHAGKRTILDTCNIASKPILDSHTNFKVLKDHPRNIDEDSIKAIVDTGGVMGITGIR 222
                                       ***************************************************************************** PP

                                       HHCTTTS--BHHHHHHHHHHHHHHT-GGGEEE---TTTTSS-BBTBSSGGGHHHHHHHHHHTTS-HHHHHHHHTHHH CS
                     Peptidase_M19 237 aflkekaeatledvvdhidyivelaGidhVGlGsDfdgggelpegledvsklpnltaeLlrrgyseadiekilggNf 313
                                         l++   ++++ ++++i y+ + +G++hV lG+Df g++e p+g+ dv+ +++l + +   g    + e +l +N+
  gi|518653144|ref|YP_008142664.1| 223 PSLHT---PDINGMLESITYLGDNFGWKHVSLGTDFLGIPEPPDGFADVNAIEKLKEMI---GL---HSEDVLFNNA 290
                                       ***76...**********************************************98877...33...3344577777 PP

                                       HHHHH CS
                     Peptidase_M19 314 lrvle 318
                                       +rv++
  gi|518653144|ref|YP_008142664.1| 291 FRVIK 295
                                       77765 PP

>> Amidohydro_2  Amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.4e-05      0.13     132     266 ..     150     270 ..     125     293 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.4e-05
                                       HHHHHHHHHHT-EEE.EE....CHHHCHHHHHHHHHHHHHHHCCHHHHCTTSEEEESGGGTTTTCHHHHHHHHHHHH CS
                      Amidohydro_2 132 rpifealeelglpvd.ihtGpspewlfggpqettraiqplllsgvarkfPnlkivlaHgGgpserlraalellarrp 207
                                        +++++++  g+ +d  h+G            t+  ++  +   +++ ++n k+  +H  +   +   + ++++++ 
  gi|518653144|ref|YP_008142664.1| 150 EELVKICNSSGIIIDlAHAG----------KRTILDTCNIASKPILDSHTNFKVLKDHPRNI--DEDSIKAIVDTGG 214
                                       57899999999999966766..........999999999999********************..9999999999999 PP

                                       HCCEEECCGHHHSSEEECCHHCHHHHHHHHHHH-GGGEEEE--BTSTTSTSCTTHHHHC CS
                      Amidohydro_2 208 nvyvklsglytellyfdspladppalarlieavgpdrilfGsDyPhptleaepealall 266
                                          + + g+ ++ l++ +   + +++  l + +g++++  G+D+  +++  +  a +++
  gi|518653144|ref|YP_008142664.1| 215 --VMGITGIRPS-LHTPDINGMLESITYLGDNFGWKHVSLGTDFLGIPEPPDGFADVNA 270
                                       ..6688899998.**********************************996665554433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.40
# Mc/sec: 2228.92
//
Query:       gi|518653145|ref|YP_008142665.1|  [L=166]
Description: molybdenum cofactor biosynthesis protein B [Ferroplasma acidarmanus fer1]
Scores for 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-16   58.4   0.0    7.2e-16   58.1   0.0    1.1  1  MoCF_biosynth  Probable molybdopterin binding domain


Domain annotation for each model (and alignments):
>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1   0.0     4e-20   7.2e-16       2     143 ..      26     157 ..      25     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 4e-20
                                       EEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHHH CS
                     MoCF_biosynth   2 vitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpeal 78 
                                       +itv++++++   +D +g+ + +++     + s +++++Dde+ei +++  + +++d+ i +GGtG+++ D t  +l
  gi|518653145|ref|YP_008142665.1|  26 IITVSSTRTPD--TDISGDKMESYIG----NKSSRSLIRDDEKEILSEFFLNYSDSDIFIYIGGTGVSRLDRTSLVL 96 
                                       66666666666..5666666666665....778899*************7777888********************* PP

                                       HHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EE....TTE.EEEE-SSHHHHHHHHHHHHHGGHH CS
                     MoCF_biosynth  79 aklfekelegfeeafrrvslkpgkpvgvapgailsrav....gkt.iigLPGspkavkealeeillpale 143
                                       +k+ +ke++gf+e+fr+ s        v p   ls+a     +++ i++LPGs  a + a  +i+ ++++
  gi|518653145|ref|YP_008142665.1|  97 RKIADKEMPGFGELFRQKSGG------VFPY--LSNASlfiyREKiIFTLPGSEDAQEIAYSIIK-EMVP 157
                                       ******************988......6666..777777888555499******99888888777.5554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1134.42
//
Query:       gi|518653146|ref|YP_008142666.1|  [L=146]
Description: molybdenum cofactor biosynthesis protein C [Ferroplasma acidarmanus fer1]
Scores for complete 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  160.2   3.4    3.1e-47  160.1   3.4    1.0  1  MoaC      MoaC family


Domain annotation for each model (and alignments):
>> MoaC  MoaC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.1   3.4   1.7e-51   3.1e-47       1     136 []       1     141 [.       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 160.1 bits;  conditional E-value: 1.7e-51
                                       E---TTS--EEEEEEEEEEEEE-HHHHHHHHTTSSTTB-HHHHHHHHHHHHHHHHHHHSTT-----EEEEEEEEEEE CS
                              MoaC   1 mvdvsekeetkrtAvAegrvklseetlelikekklkkGdvlavariagimaaKktseliplcHplpltkvevelele 77 
                                       m+d+++k+++kr+A+A+g++kl++et++li+ek++kkGdv+++a+iag++a+K+ts +ip+cHp+p+ ++++++e+e
  gi|518653146|ref|YP_008142666.1|   1 MIDITDKNTVKREAMATGTIKLNKETIKLIREKQVKKGDVIETAKIAGTIAVKNTSGMIPYCHPVPVMSIDFNFEVE 77 
                                       9*************************************************************************987 PP

                                       TTTTEEEEEEEEEEEESS--HHHHHHHHHHHHHHHHHHHTTTHTT.......-EEEEEEEEEEESS CS
                              MoaC  78 eeeesveieatvktegktGvemEALtavsvaaltvyDmvKavdke.......mvieevrlveKsgG 136
                                         ++++ ++++vk+  +tGvemEA+ +v+va+lt++DmvK ++k+       + i +v++v K++G
  gi|518653146|ref|YP_008142666.1|  78 --DSKIIVTCRVKAIYRTGVEMEAINGVQVALLTIWDMVKYLEKDetgnypdTSIGNVTVVYKRKG 141
                                       ..79****************************************99*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1187.31
//
Query:       gi|518653147|ref|YP_008142667.1|  [L=266]
Description: SAM-dependent methyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      566  (0.031569); 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: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1968.44
//
Query:       gi|518653148|ref|YP_008142668.1|  [L=152]
Description: hypothetical protein FACI_IFERC00001G1789 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-11   42.9   0.1    4.9e-11   42.6   0.1    1.2  1  PNK3P            Polynucleotide kinase 3 phosphatase
    9.4e-09   35.6   0.6    1.5e-06   28.4   0.6    2.2  1  HAD_2            Haloacid dehalogenase-like hydrolase
    1.8e-08   34.3   0.1    2.8e-08   33.7   0.1    1.3  1  Hydrolase_like   HAD-hyrolase-like
    0.00055   19.6   0.0     0.0012   18.4   0.0    1.5  1  PGP_phosphatase  Mitochondrial PGP phosphatase
     0.0057   16.8   0.1     0.0069   16.6   0.1    1.2  1  LytR_cpsA_psr    Cell envelope-related transcriptional attenu
  ------ inclusion threshold ------
      0.022   15.1   0.1      0.096   13.1   0.0    1.9  2  FtsH_ext         FtsH Extracellular
       0.18   12.0   0.4        1.2    9.4   0.0    2.0  2  Hydrolase        haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> PNK3P  Polynucleotide kinase 3 phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   1.9e-14   4.9e-11      22     127 ..      24     130 ..       6     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 1.9e-14
                             PNK3P  22 kdaddwkllsesvlekLkklkeegykivifsNqggvvek.ktkkslekfkekieallkel..dvpllvyaatkkd.. 93 
                                       ++ +d k++++ ++  Lk+ ++++y+i++++Nq+g+ ++  t +++e f +k+ + l +   +++ ++y+    d  
  gi|518653148|ref|YP_008142668.1|  24 HKLSDLKIYDD-IIPILKEYYDQNYIIIVVTNQSGIGREyYTVEDMEAFNNKLAEELMKYgvKIEEFFYCPHLPDqg 99 
                                       34577887765.8889**********************9889999*******9877777612555566666655567 PP

                             PNK3P  94 .kyRKPetGmweelkkdleekleidkeksfyvGDa 127
                                        k RKP tGm+ee +k+++     d ++s+ +GD 
  gi|518653148|ref|YP_008142668.1| 100 cKCRKPGTGMIEEAAKKYNI----DIKNSVVIGDR 130
                                       79**********99998875....88888999996 PP

>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.6   5.9e-10   1.5e-06      71     178 .]      24     148 ..      15     148 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 5.9e-10
                             HAD_2  71 eekkkkevkpydgvkelLeeLkeagyklgivTsks....r.......eaveekleq......lgiesyFdvivtsed 130
                                       +++    +k+yd+++ +L+e  +++y + +vT++s    +       ea+++kl++      ++ie++F      ++
  gi|518653148|ref|YP_008142668.1|  24 HKLS--DLKIYDDIIPILKEYYDQNYIIIVVTNQSgigrEyytvedmEAFNNKLAEelmkygVKIEEFFYCPHLPDQ 98 
                                       4444..599***********************985333222222111233333322222222345566655555444 PP

                             HAD_2 131 .vekkKPdpeviekaleklklkkeeviyvGDsp.tDieaakkagikviav 178
                                        ++ +KP + +ie+a +k++++ ++ +++GD +  D   a+k+gik+i v
  gi|518653148|ref|YP_008142668.1|  99 gCKCRKPGTGMIEEAAKKYNIDIKNSVVIGDRTsVDGTMARKLGIKFIKV 148
                                       24556***************************99*************976 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.1   1.1e-11   2.8e-08       2      48 ..     102     148 ..     101     150 .. 0.96

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.1e-11
                                       .STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEE CS
                    Hydrolase_like   2 lgKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLV 48 
                                       ++KP  +m+++a++++++d +++++iGDr   D  +A++ G+k++ V
  gi|518653148|ref|YP_008142668.1| 102 CRKPGTGMIEEAAKKYNIDIKNSVVIGDRTSVDGTMARKLGIKFIKV 148
                                       89******************************************977 PP

>> PGP_phosphatase  Mitochondrial PGP phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0   4.8e-07    0.0012      42     157 ..       6     142 ..       2     150 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 4.8e-07
                   PGP_phosphatase  42 kavvlDKDnclaap..kedkva..eeikekleelrevypeks.ilivSNsaGssd.dkdaekaealekktgipVlrh 112
                                       kav +D+D +l ++  +++k+   + + + +  l+e y ++  i++v N++G     ++ e+ ea+++k+  + +++
  gi|518653148|ref|YP_008142668.1|   6 KAVFVDRDGTLNYDtgYTHKLSdlKIYDDIIPILKEYYDQNYiIIVVTNQSGIGReYYTVEDMEAFNNKLAEELMKY 82 
                                       8999*******9873334455411456677788889999885156689****8775778888888888888777776 PP

                   PGP_phosphatase 113 k..................ekKPgca..eevleyfkerkvveeadeiavvgDRllTdvllanmmG 157
                                                           +KPg++  ee  + ++    ++  ++ +v+gDR   d ++a++ G
  gi|518653148|ref|YP_008142668.1|  83 GvkieeffycphlpdqgckCRKPGTGmiEEAAKKYN----ID-IKNSVVIGDRTSVDGTMARKLG 142
                                       666777889999****99999**6651155555443....33.456689************9998 PP

>> LytR_cpsA_psr  Cell envelope-related transcriptional attenuator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.7e-06    0.0069      17      95 ..       5      91 ..       2     128 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.7e-06
                                      EEEEEE-TTBEE-----....--....---EES-TTTTT-HHHHHHHHHHHHTS---EEEEE-HHHHH.HHHHHHT..- CS
                     LytR_cpsA_psr 17 vklvSipRDtlveipgg.eskat....gekkinsayalggaellvktvekllginidyYvevdfegfa.klvdalg..G 87
                                       k+v + RD + + ++g ++k +     ++ i  ++++  +++++ +v++++gi  +yY + d+e+f+ kl+++l+  G
  gi|518653148|ref|YP_008142668.1|  5 RKAVFVDRDGTLNYDTGyTHKLSdlkiYDDIIPILKEYYDQNYIIIVVTNQSGIGREYYTVEDMEAFNnKLAEELMkyG 83
                                      577888999999987553222225566788889999999****************************73699***999* PP

                                      --B----- CS
                     LytR_cpsA_psr 88 vevdvked 95
                                      v+++  + 
  gi|518653148|ref|YP_008142668.1| 84 VKIEEFFY 91
                                      *9987655 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   3.7e-05     0.096      55     105 ..      16      87 ..       2      89 .. 0.69
   2 ?   -0.7   0.0      0.72   1.8e+03      94     106 ..     111     123 ..     105     136 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 3.7e-05
                          FtsH_ext  55 s........................alirrptgdgvsttkkgnstttystptlgsvesleekLeealkskgvdve 105
                                       +                          ++++   +v t+++g +  +y++ +    e++++kL e l ++gv+ e
  gi|518653148|ref|YP_008142668.1|  16 LnydtgythklsdlkiyddiipilkEYYDQNYIIIVVTNQSGIGREYYTVED---MEAFNNKLAEELMKYGVKIE 87 
                                       4555555555555555555555775555555555888888888888888888...*****************986 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                          FtsH_ext  94 eealkskgvdves 106
                                       eea k++++d   
  gi|518653148|ref|YP_008142668.1| 111 EEAAKKYNIDIKN 123
                                       6777777777654 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.1      0.18   4.6e+02       2      13 ..       6      17 ..       5      30 .. 0.81
   2 ?    9.4   0.0   0.00045       1.2     171     209 ..     102     141 ..      26     142 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
                                      SEEEEESBTTTB CS
                                      xxxxxxxxxxxx RF
                         Hydrolase  2 ktvvfDkdGTLt 13
                                      k+v+ D dGTL 
  gi|518653148|ref|YP_008142668.1|  6 KAVFVDRDGTLN 17
                                      89********95 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00045
                                       STTTSHHHHHHHHHHHTSTGGGEEEEESSHH.HHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
                         Hydrolase 171 vakpspegkvaaireLqgkpeevamVGDgvn.DaaalaaA 209
                                       + kp   + ++a++++++++++ +++GD+   D  ++++ 
  gi|518653148|ref|YP_008142668.1| 102 CRKPGTGMIEEAAKKYNIDIKNSVVIGDRTSvDGTMARKL 141
                                       788899999********************99998888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       796  (0.0443973); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1190.74
//
Query:       gi|518653149|ref|YP_008142669.1|  [L=426]
Description: hypothetical protein FACI_IFERC00001G1790 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.4   0.0      0.039   13.7   0.0    1.3  1  Sigma54_activat  Sigma-54 interaction domain
       0.14   12.5   0.0       0.22   11.9   0.0    1.4  1  AAA_16           AAA ATPase domain


Domain annotation for each model (and alignments):
>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.3e-06     0.039      10      61 ..     241     292 ..     235     301 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.3e-06
                                       HHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS CS
                   Sigma54_activat  10 elleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaai 61 
                                       + +e+i+++a  + ++litG  G GK  la +i ++ +++ +++  +n +++
  gi|518653149|ref|YP_008142669.1| 241 TKTETINAIAGGEKTTLITGPAGDGKIGLAAKIMSSAEKTGREIAILNTGKF 292
                                       66789999******************************99999999999876 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   2.4e-05      0.22      19      99 ..     248     338 ..     218     396 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.4e-05
                            AAA_16  19 vrsgrpelvllsGesGvGKsslvrellralekd..g.giflrgkcdqlesa........ipysalaqalareellrq 84 
                                       + +g++  +l++G++G GK  l+ +++ ++ek+  + +i+ +gk+d ++s         i +  + q    ++ + +
  gi|518653149|ref|YP_008142669.1| 248 AIAGGEKTTLITGPAGDGKIGLAAKIMSSAEKTgrEiAILNTGKFDPFKSIingnssfsIKRFDISQEY-YDQRIVD 323
                                       4567779************************997655777********555444434442223333333.2244444 PP

                            AAA_16  85 lldeaesaeleawre 99 
                                        +++a++ +   w++
  gi|518653149|ref|YP_008142669.1| 324 SAADAAALASKLWAA 338
                                       444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.41
# Mc/sec: 3130.05
//
Query:       gi|518653150|ref|YP_008142670.1|  [L=565]
Description: molecular chaperone DnaK [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.2e-105  353.1   8.0     5e-103  345.3   4.3    2.0  2  HSP70           Hsp70 protein
    1.5e-08   33.8   0.4    1.5e-08   33.8   0.4    3.3  3  MreB_Mbl        MreB/Mbl protein
    2.5e-05   23.7   0.1    0.00011   21.6   0.1    2.0  2  Hydantoinase_A  Hydantoinase/oxoprolinase
     0.0091   15.3   4.7        0.2   10.8   0.0    2.5  2  StbA            StbA protein
  ------ inclusion threshold ------
      0.016   15.1   0.9      0.029   14.2   0.9    1.4  1  RMI1_C          Recq-mediated genome instability protein 1, C
      0.024   13.3   0.2      0.052   12.1   0.2    1.5  1  MutL            MutL protein
       0.04   12.9   1.3      0.048   12.7   0.1    1.8  2  DDR             Diol dehydratase reactivase ATPase-like domai
      0.066   13.1   4.7        0.1   12.5   4.7    1.3  1  WbqC            WbqC-like protein family
      0.066   13.6   9.6        2.5    8.6   4.3    3.7  2  FtsA            Cell division protein FtsA
       0.08   12.9   2.7       0.19   11.7   2.1    1.9  1  Sec20           Sec20
       0.15   12.4   0.5       0.55   10.6   0.3    2.0  2  BTB_2           BTB/POZ domain
       0.16   12.5   1.2        2.3    8.8   0.1    2.9  2  PC_rep          Proteasome/cyclosome repeat
       0.81   10.0  11.7       0.29   11.4   6.5    2.6  3  DUF5638         Family of unknown function (DUF5638)


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.1   0.00016      0.22       2      73 ..       4      82 ..       3      88 .. 0.79
   2 !  345.3   4.3  3.6e-106    5e-103     105     578 ..      87     549 ..      83     562 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                                      EEEEEXSSE..EEEEEEETTEEEEEXXTTSXSSEE....SEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBT CS
                             HSP70  2 iGiDLGttn..svvavmeggkievianeegnrttP....svvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkf 73
                                      iGiDLGt n  ++va + gg+ ++ia   + + t     s + F+       G+ A r   + p   v  +K  +G ++
  gi|518653150|ref|YP_008142670.1|  4 IGIDLGTSNtsAAVALVTGGEYKTIAIPLSGKKTGsslkSSITFGGSdIMFTGADADRMLKKYPGGNVSGFKTRMGSEY 82
                                      9*****97622578889********988777666512225789999844678999999999999999999999999887 PP

  == domain 2  score: 345.3 bits;  conditional E-value: 3.6e-106
                                       TE.EEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTC CS
                             HSP70 105 ge.kftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGld 180
                                       ge   +p ++sa +L+++k++ae+y+ ++v+davi+vPaYfn++qR+at++A++iAG++v   v ep A+a++Y   
  gi|518653150|ref|YP_008142670.1|  87 GEkFHSPVELSAIILARVKNIAEEYMHDRVKDAVIAVPAYFNNNQRNATREAAAIAGIKVKQFVSEPAAVAISYWNR 163
                                       4515689*******************************************************************876 PP

                                       CSS.SCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHH CS
                             HSP70 181 kkd.kernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrl 256
                                        ++ + +n+lv+D+G gt+dvSi++ +   f+v aT+g+t lGG d+D+++ e ++++f + +gi           l
  gi|518653150|ref|YP_008142670.1| 164 ASKaEAKNILVFDMGSGTTDVSIVRAQGKDFRVIATSGNTGLGGTDMDRRIEE-MMKSFLRINGISPYP-----PDL 234
                                       655479********************************************976.567888888886544.....469 PP

                                       HHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEE CS
                             HSP70 257 keaaekaKkeLSsskqteinleietvdedgkdlseklsRakfeelvedllertlepvekalkdaklkkeeidevvlv 333
                                       +++aek+K+ LS++ +t  +l         ++++ ++  ++++++v+d+l ++ + +  a+ ++++k +e+d v++ 
  gi|518653150|ref|YP_008142670.1| 235 RKDAEKLKIYLSNH-ETGDSL-----LG-STKIKYTMDSKQLDSIVSDMLPEIYRCIDTAILNSGIKRNELDTVIIT 304
                                       *************3.444333.....33.345889****************************************** PP

                                       SGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHH..HHCTCGCSHCCEEEEBESS-EEEEETTTEEEEEES CS
                             HSP70 334 GGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqag..vlsgeeevkdllllDvtpLslgietlggvmtklie 408
                                       GG t+iP + +++++++   + k+   D av++GAA+ a   ++ g+ e++++++ Dv+p+slg  t+ +++ ++i+
  gi|518653150|ref|YP_008142670.1| 305 GGPTKIPFLFHSIENYLSTRAVKQGKFDTAVSTGAAILASgfIHMGTGEISKIKVSDVVPISLGSVTRNDIVVTMIP 381
                                       ******************99*****************97556*********************************** PP

                                       TTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEE CS
                             HSP70 409 rnttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakd 485
                                        nt +p k ++ f+t++d+q+++e++v+qger l  dn  lg+f+l+gi+paprG+  i+Vt+++d+nGiltvsa+d
  gi|518653150|ref|YP_008142670.1| 382 ANTPVPCKATRPFTTIRDYQSEIEVKVVQGERPLGTDNIVLGHFTLSGIKPAPRGEVAIDVTYSVDKNGILTVSARD 458
                                       ***************************************************************************** PP

                                       TTTCCEEEEEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHH.HHHH CS
                             HSP70 486 ketgkeeeitieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaek.ekve 561
                                       + t   +ei+i+++ + s+eei++m +  +++ + d+++k+ +e  n++e+l+++l++  +++   +s ++k  +++
  gi|518653150|ref|YP_008142670.1| 459 NDTAAIKEIKISETMQHSQEEIKEMKEAVKKYFKVDSERKKMAEIMNRSEQLLHELKGIANKQ---LSTETKyYNIN 532
                                       *********************************************************998877...44444446777 PP

                                       HHHHHHHCHTTSSCHHH CS
                             HSP70 562 saieeLkeeleeeekee 578
                                       + i  +++++++++++ 
  gi|518653150|ref|YP_008142670.1| 533 TDILMVSRAIKNNNIKL 549
                                       77777777766666544 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.1     0.089   1.2e+02       3      15 ..       3      15 ..       1      29 [. 0.86
   2 !   33.8   0.4   1.1e-11   1.5e-08      92     301 ..     115     325 ..      94     349 .. 0.66
   3 ?   -0.7   0.3      0.36     5e+02     204     261 ..     436     491 ..     420     510 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.089
                                      EEEEEE-SSEEEE CS
                          MreB_Mbl  3 dlgiDLGtantlv 15
                                      ++giDLGt nt +
  gi|518653150|ref|YP_008142670.1|  3 SIGIDLGTSNTSA 15
                                      69********976 PP

  == domain 2  score: 33.8 bits;  conditional E-value: 1.1e-11
                                       S--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TT..SSS-EEEEEE-SS-EEEEEEETTE CS
                          MreB_Mbl  92 skprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpve..epsgnmvvdiGggttevavislgg 166
                                       + +  vi+vP   ++ +r+A +eaa  aG +  + ++ep a Ai      +  e++  +v d+G+gtt+v+++ ++g
  gi|518653150|ref|YP_008142670.1| 115 RVKDAVIAVPAYFNNNQRNATREAAAIAGIKVKQFVSEPAAVAISYWNRASkaEAKNILVFDMGSGTTDVSIVRAQG 191
                                       445689**************************************98666650155566999************9987 PP

                                       .....EEEEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEE CS
                          MreB_Mbl 167 .....ivtsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeeekmeikGrdlvtglpkevevs 238
                                            i ts    ++G ++d  i + +++  ++   +    +++++  +++   ++++   +G  l+     + +++
  gi|518653150|ref|YP_008142670.1| 192 kdfrvIATSGNTGLGGTDMDRRIEEMMKSFLRINGISPYPPDLRKDAEKLKIYLSNHE---TGDSLLGSTKIKYTMD 265
                                       66765778888999************99877765444444455555444444444443...3555555555556666 PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH...-EEEESGGGGSBTHHHHHHHHHSS-E CS
                          MreB_Mbl 239 seevrealkepvsaiveavkevLektppeLaadivdr...givltGGgallkgldkllseetglpv 301
                                       s+++ + +++++ +i  ++ +++ +      + i ++   ++++tGG +++  l + +++ ++ + 
  gi|518653150|ref|YP_008142670.1| 266 SKQLDSIVSDMLPEIYRCIDTAILN------SGIKRNeldTVIITGGPTKIPFLFHSIENYLSTRA 325
                                       6666666666666666666554422......22222211145566666666666666666555555 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.36
                                       HHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHH CS
                          MreB_Mbl 204 ikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevL 261
                                         ++i  +++ +++  ++++ rd  t   ke+++s+++  +  +e+++++ eavk+  
  gi|518653150|ref|YP_008142670.1| 436 GEVAIDVTYSVDKNGILTVSARDNDTAAIKEIKISETM--QHSQEEIKEMKEAVKKYF 491
                                       55667777778888889999999999999998887654..445677777777777654 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   8.1e-08   0.00011      47      98 ..     138     189 ..      95     203 .. 0.76
   2 ?   -1.5   0.0      0.88   1.2e+03     221     252 ..     276     307 ..     270     344 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 8.1e-08
                    Hydantoinase_A  47 adearkkpvetilSGPaaGvvgaaatsklagekkvItfDmGGTstDvslikd 98 
                                       a+++ +  v+  +S Paa ++ + + + +a++k++++fDmG+ +tDvs +++
  gi|518653150|ref|YP_008142670.1| 138 AAAIAGIKVKQFVSEPAAVAISYWNRASKAEAKNILVFDMGSGTTDVSIVRA 189
                                       4556667789999**********999**********************9985 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.88
                    Hydantoinase_A 221 avenmanavrklsvergldpkeltlvvfGGaG 252
                                       +  ++ + +++ + + g +++el +v+++G+ 
  gi|518653150|ref|YP_008142670.1| 276 MLPEIYRCIDTAILNSGIKRNELDTVIITGGP 307
                                       56678888999999999999999998887753 PP

>> StbA  StbA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.0   0.00015       0.2     145     249 ..     152     256 ..     128     283 .. 0.74
   2 ?    3.3   3.1     0.028        39     193     292 ..     446     545 ..     437     564 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00015
                              StbA 145 lPeslPagfealkeldeleslLiiDlGGttLDvakvrgklegiskvk..gdskiGvslitdavkealet.aktrtss 218
                                        P ++  ++   ++ +e  + L+ D+G  t Dv+ vr++ +++  +   g+  +G   +   ++e++++  ++++ s
  gi|518653150|ref|YP_008142670.1| 152 EPAAVAISYWNRASKAEAKNILVFDMGSGTTDVSIVRAQGKDFRVIAtsGNTGLGGTDMDRRIEEMMKSfLRINGIS 228
                                       455555566666667788899***************99988877665116666777889999999999877888877 PP

                              StbA 219 fladeliknrkdeeyLkrrindedkresvle 249
                                        +  +l   rkd e Lk ++++++  +s+l 
  gi|518653150|ref|YP_008142670.1| 229 PYPPDL---RKDAEKLKIYLSNHETGDSLLG 256
                                       777766...8899999999988888777765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.028
                              StbA 193 dskiGvslitdavkealetaktrtssfladeliknrkdeeyLkrrindedkresvlevinekvkkLkerviravsef 269
                                        +k G+  +    +++ + ++++ s+ + ++  + ++ +e++k++ + + +r+++ e++n+ ++ L+e    a +++
  gi|518653150|ref|YP_008142670.1| 446 VDKNGILTVSARDNDTAAIKEIKISETMQHSQEEIKEMKEAVKKYFKVDSERKKMAEIMNRSEQLLHELKGIANKQL 522
                                       566666666666666777788899999999988899999*************************9999877778889 PP

                              StbA 270 sgythvmvvGGGaeliaeaikka 292
                                       s  t+ + +     ++  aik+ 
  gi|518653150|ref|YP_008142670.1| 523 STETKYYNINTDILMVSRAIKNN 545
                                       99999999999999999999875 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 ?   14.2   0.9   2.1e-05     0.029      49     121 ..     456     527 ..     442     554 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-05
                            RMI1_C  49 akisDGsaildvdlssevlteligfspaelkeslalkkd....qkkrqklkealkeaqekLidleclmeielnpask 121
                                       a+ +D  ai ++++     +e +++s +e+ke+++ +k+    +++r+k+ e++++ ++ L +l+++ + +l++++k
  gi|518653150|ref|YP_008142670.1| 456 ARDNDTAAIKEIKI-----SETMQHSQEEIKEMKEAVKKyfkvDSERKKMAEIMNRSEQLLHELKGIANKQLSTETK 527
                                       55555555555555.....5789**************9999999***********************9999888843 PP

>> MutL  MutL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   3.8e-05     0.052     179     265 ..     103     188 ..      95     203 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
                              MutL 179 vtdNvlPkldelnveparkaIrevFlehiv.kakglskleelvsaeimpTPaAvlkav.ellaeeeekglgdllvvD 253
                                        ++N+  +  + +v++a  a+ + F+++     +  +++  +  ++ +  PaAv     +  +++e   + ++lv+D
  gi|518653150|ref|YP_008142670.1| 103 RVKNIAEEYMHDRVKDAVIAVPAYFNNNQRnATREAAAIAGIKVKQFVSEPAAVAISYwNRASKAE---AKNILVFD 176
                                       577888888888888888899999998888555666777777788889999999654404444444...46****** PP

                              MutL 254 vGGaTTdvhsva 265
                                       +G+ TTdv  v 
  gi|518653150|ref|YP_008142670.1| 177 MGSGTTDVSIVR 188
                                       ********8883 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   3.4e-05     0.048      78     158 ..     116     195 ..      44     205 .. 0.62
   2 ?   -3.1   0.2       2.1   2.9e+03     237     256 ..     474     493 ..     448     512 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                               DDR  78 slekavglaamvktdklqmqkiaeeleeelgvkvevggvEaemAilGalttPGtekplailDlGaGstDaalieeeg 154
                                       ++++ +++ a  + ++ + ++ a +++  ++vk  v    a +     +      k++ + D+G+G+tD ++++++g
  gi|518653150|ref|YP_008142670.1| 116 VKDAVIAVPAYFNNNQRNATREAAAIA-GIKVKQFVSEPAAVAISYWNRASKAEAKNILVFDMGSGTTDVSIVRAQG 191
                                       455555555555555544444444443.23333333333333344456777778899*****************999 PP

                               DDR 155 evka 158
                                       +   
  gi|518653150|ref|YP_008142670.1| 192 KDFR 195
                                       7544 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.1
                               DDR 237 dlslekirsvRreaKekvfv 256
                                       ++s e+i+++++++K+   v
  gi|518653150|ref|YP_008142670.1| 474 QHSQEEIKEMKEAVKKYFKV 493
                                       34444444444444443333 PP

>> WbqC  WbqC-like protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   4.7   7.6e-05       0.1      48     156 ..     452     560 ..     442     565 .] 0.82

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
                              WbqC  48 ltvPvekkasqqklineveidddekwrkkhlksleqaYkkapffeevlpllesvyeaeeenlael...nialleala 121
                                       ltv+   +++++++i+e++i+++ +  ++ +k +++a kk    +   + ++++++++e+ l el   + + l+   
  gi|518653150|ref|YP_008142670.1| 452 LTVSA--RDNDTAAIKEIKISETMQHSQEEIKEMKEAVKKYFKVDSERKKMAEIMNRSEQLLHELkgiANKQLSTET 526
                                       67776..4467788******************************************999988887221456666666 PP

                              WbqC 122 kyLgieteivlsselklegkklerlldickklgad 156
                                       ky +i+t+i + s+  +++++ ++l ++ +k++++
  gi|518653150|ref|YP_008142670.1| 527 KYYNINTDILMVSRA-IKNNNIKLLSQLLTKTDKE 560
                                       *************88.3588888888888877765 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.2     0.016        22       1      32 [.       4      36 ..       4     145 .. 0.84
   2 ?    8.6   4.3    0.0018       2.5       2      52 ..     174     242 ..     173     556 .. 0.74

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.016
                                      EEEEE-SSSEEEEEEETTEEEE.EEEES--HHH CS
                                      xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
                              FtsA  1 alvDiGagktdvavaedgalvh.lrvigvggng 32
                                      +++D+G++ t++ava   +  + +  i++ g+ 
  gi|518653150|ref|YP_008142670.1|  4 IGIDLGTSNTSAAVALVTGGEYkTIAIPLSGKK 36
                                      58************9875544446666665544 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0018
                                       EEEE-SSSEEEEEEETTEEEEEEEES-......-HHHHHHH.............HHHHHT--HHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxx.............xxxxxxxxxxxxxxxx RF
                              FtsA   2 lvDiGagktdvavaedgalvhlrvigv......ggngitkd.............iakalrtaveeAerik 52 
                                       + D+G+g+tdv++++  + +++rvi +      gg  +++              i+       ++Ae++k
  gi|518653150|ref|YP_008142670.1| 174 VFDMGSGTTDVSIVRA-QGKDFRVIATsgntglGGTDMDRRieemmksflringISPYPPDLRKDAEKLK 242
                                       56*************9.45568888887777778888888844433333333333333355566666666 PP

>> Sec20  Sec20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   2.1   0.00014      0.19      17      63 ..     469     515 ..     460     524 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00014
                             Sec20  17 lsqevqqSeenleeldastkslekleeeykqvedvlsrskklvkkle 63 
                                       +s+++q+S+e ++e+++  k+  k+++e k+++++++rs++l+  l+
  gi|518653150|ref|YP_008142670.1| 469 ISETMQHSQEEIKEMKEAVKKYFKVDSERKKMAEIMNRSEQLLHELK 515
                                       7899**************************************99876 PP

>> BTB_2  BTB/POZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.1   4.3e+03       4      50 ..      70     117 ..      70     132 .. 0.54
   2 ?   10.6   0.3    0.0004      0.55      33      90 ..     479     535 ..     458     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.1
                                       EETTEEEEEEHHHHHTSTTSTTTSSGG......GGEETTTTEEEE-S-H CS
                             BTB_2   4 nVgGtrfetskstLsrkpdtlLgkllkte.e.lddydeetneyffDRsp 50 
                                       nV+G + ++ ++ L r  +  +++ ++ +   l  +++  +ey  DR +
  gi|518653150|ref|YP_008142670.1|  70 NVSGFKTRMGSEYLYRTGEK-FHSPVELSaIiLARVKNIAEEYMHDRVK 117
                                       66666666666666643333.3333333312345555556666666655 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.0004
                                       ..GGEETTTTEEE.E-S-HHHHHHHHHHHHS.S-B---TTS-HHHHHHHHHHHT--TT- CS
                             BTB_2  33 elddydeetneyf.fDRspklFetiLnyyrtggkLhrpeevelkslleElefygleell 90 
                                       e++ ++e+ ++yf +D ++k  + i+n  ++   Lh+ + +  k+l+ E ++y++++++
  gi|518653150|ref|YP_008142670.1| 479 EIKEMKEAVKKYFkVDSERKKMAEIMNRSEQ--LLHELKGIANKQLSTETKYYNINTDI 535
                                       377777777777779***********96666..9*********************9985 PP

>> PC_rep  Proteasome/cyclosome repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.1    0.0017       2.3       1      14 [.     339     352 ..     339     356 .. 0.94
   2 ?    0.9   0.1      0.53   7.4e+02      16      31 ..     545     559 ..     542     560 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0017
                                       HHHHHHHHHCTTST CS
                            PC_rep   1 GAllALGlihaGsg 14 
                                       +A+lA G ih+G+g
  gi|518653150|ref|YP_008142670.1| 339 AAILASGFIHMGTG 352
                                       7***********98 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.53
                                       HHHHHHHHHHHHHHSS CS
                            PC_rep  16 eeaislLkpylsdtsa 31 
                                       +  i+lL+++l++t+ 
  gi|518653150|ref|YP_008142670.1| 545 N-NIKLLSQLLTKTDK 559
                                       4.699*******9986 PP

>> DUF5638  Family of unknown function (DUF5638)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.75     1e+03      23      53 ..     110     140 ..     103     168 .. 0.84
   2 ?   -2.7   0.0       5.4   7.4e+03      82     100 ..     258     276 ..     256     277 .. 0.84
   3 ?   11.4   6.5   0.00021      0.29      23      99 ..     470     546 ..     458     550 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.75
                                       ----HHHHHHHHHHHHHHHHHHHT--SHHHH CS
                           DUF5638  23 kelsekikkqlqeiktyYnesftkakkektk 53 
                                       + +++ +k  + ++ +y+n++ ++a++e ++
  gi|518653150|ref|YP_008142670.1| 110 EYMHDRVKDAVIAVPAYFNNNQRNATREAAA 140
                                       5578899999999999999998888887765 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 5.4
                                       HHHTTT---HHHHHHHHHH CS
                           DUF5638  82 eaiekktesrkidviihnl 100
                                        +i+++++s+++d i++++
  gi|518653150|ref|YP_008142670.1| 258 TKIKYTMDSKQLDSIVSDM 276
                                       5899999999999998876 PP

  == domain 3  score: 11.4 bits;  conditional E-value: 0.00021
                                       ----HHHHHHHHHHHHHHHHHHHT--SHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHTTT---HHHHHHHHH CS
                           DUF5638  23 kelsekikkqlqeiktyYnesftkakkektkeeiveeYeelvlllsqvkngeisadeAleaiekktesrkidviihn 99 
                                        e+ ++ +++++e k+  ++ f+  ++ k+ +ei++  e+l++ l+ + n+++s++  + +i++++   +  +  +n
  gi|518653150|ref|YP_008142670.1| 470 SETMQHSQEEIKEMKEAVKKYFKVDSERKKMAEIMNRSEQLLHELKGIANKQLSTETKYYNINTDILMVSRAIKNNN 546
                                       466677789999999999999**9***************************************99987777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (565 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1537  (0.085727); expected 358.6 (0.02)
Passed bias filter:                      596  (0.0332422); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.76u 0.31s 00:00:01.07 Elapsed: 00:00:00.47
# Mc/sec: 3582.62
//
Query:       gi|518653151|ref|YP_008142671.1|  [L=364]
Description: hypothetical protein FACI_IFERC00001G1792 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); 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: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.44
# Mc/sec: 2462.72
//
Query:       gi|518653152|ref|YP_008142672.1|  [L=245]
Description: carbon-nitrogen hydrolase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-17   62.0   0.0    7.3e-17   61.6   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 !   61.6   0.0     4e-21   7.3e-17      38     232 ..      27     193 ..       6     200 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 4e-21
                                       EETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTEEEEEEEEEEEETTSEEEEEEE-S CS
                      CN_hydrolase  38 lPElfitgykeeahfleaAeaglgetlallaalarkngiavvigliereltngklqayntavlldldgklvgkyrKl 114
                                       +PE  i   +++++f++  ++++ +++ +l +  +  ++++ + l++    +  +  yn+ +l+ ++ +++g ++K+
  gi|518653152|ref|YP_008142672.1|  27 FPENEII--VFPEKFIT--TKVDVNSFSRLLNSIKIKNMIILGSLSYV---DRFV--YNRSFLI-QNREIIGWQDKI 93 
                                       8888888..56888888..77899*****************9999998...5666..9999888.666778****** PP

                                       S--EECTTSCECCGHHTSCS-SSS-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEE...BH.GCCCTCHHHH CS
                      CN_hydrolase 115 hLfpgeprpptaverelfepgdgipvfdtpvgkiGaaiCyeigfpellralalkgaeilvn...lserapvpksmgp 188
                                       +L         + e++ + +g++++ f   + kiG+++Cy+  fp ++r+l +k+ ++++n   ++       +  +
  gi|518653152|ref|YP_008142672.1|  94 NLY--------KAESTKYTSGNQLKLFNIGGLKIGILVCYDLDFPDYARILFRKHCDVIFNpslIR-------RDFH 155
                                       *97........89*********999************************************88544.......8999 PP

                                       HHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TT CS
                      CN_hydrolase 189 pqwellgraralengcfviaanqvggyeqlilwpvghSaiidpd 232
                                         w+l  ++ralen +++i +n++         + g S +++p+
  gi|518653152|ref|YP_008142672.1| 156 SEWHLYVKTRALENRIPIISVNSISD------DFQGDSIVVAPE 193
                                       9*************************......999999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       542  (0.0302304); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.30s 00:00:00.79 Elapsed: 00:00:00.47
# Mc/sec: 1569.14
//
Query:       gi|518653153|ref|YP_008142673.1|  [L=197]
Description: molybdopterin-guanine dinucleotide biosynthesis protein A [Ferroplasma acidarmanus fer1]
Scores for complete 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-35  120.3   0.0    1.2e-34  120.0   0.0    1.0  1  NTP_transf_3  MobA-like NTP transferase domain
    1.6e-08   34.7   0.0      2e-08   34.5   0.0    1.1  1  CTP_transf_3  Cytidylyltransferase
    0.00012   21.3   0.0    0.00018   20.8   0.0    1.3  1  CofC          Guanylyl transferase CofC like
    0.00014   21.7   0.0    0.00017   21.4   0.0    1.1  1  IspD          2-C-methyl-D-erythritol 4-phosphate cytidylyltr
  ------ inclusion threshold ------
      0.024   14.7   0.0      0.062   13.4   0.0    1.7  1  UPF0270       Uncharacterised protein family (UPF0270)


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 !  120.0   0.0   3.2e-38   1.2e-34       1     157 [.       6     163 ..       6     167 .. 0.97

  Alignments for each domain:
  == domain 1  score: 120.0 bits;  conditional E-value: 3.2e-38
                                       EEEEEESS-TTTTTTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHH CS
                      NTP_transf_3   1 aviLAGGrSsRmggdKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplasla 77 
                                       a++LA G++ R++++K+l++++ kp++ +v+d+++ +++++ ++v +++e+ ++ ++lg++vv+++d + g++as+ 
  gi|518653153|ref|YP_008142673.1|   6 AIVLASGKALRFKSNKLLYEVNSKPIIYYVIDNVAMSNFQQRIIVLRSPEISDYSKQLGLKVVWNKDFENGMSASIV 82 
                                       79*************************************************************************** PP

                                       HHHHH.H.SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECCEEEGGGHHHHHHHCTHTTHHHC CS
                      NTP_transf_3  78 aalra.aadadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpllfrarllsalaallgdqgarrl 153
                                       +++++ +++ da++++++DmPll+ ++++ l++++++s++ +  ++y+g+ + p++f ++++s+l  l+gd+ga+++
  gi|518653153|ref|YP_008142673.1|  83 HGIENvSPEIDAAMIIPGDMPLLDNDTLNGLIEHFKSSSKGISGFEYNGTIISPVIFARKYFSELTGLSGDKGAKSI 159
                                       *****55599******************************************************************9 PP

                                       HHHH CS
                      NTP_transf_3 154 lrrl 157
                                       + ++
  gi|518653153|ref|YP_008142673.1| 160 IMKH 163
                                       9877 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.5   0.0   5.5e-12     2e-08       2     118 ..       6     120 ..       5     148 .. 0.88

  Alignments for each domain:
  == domain 1  score: 34.5 bits;  conditional E-value: 5.5e-12
                                       EEEEE-SSSSSST.TGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHHHHH CS
                      CTP_transf_3   2 aIipARsgSkRlp.gKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdterf 77 
                                       aI++A  +  R++ +K l + ++kp+i yv++++  s + ++ i+   s ei +  k++g +v+  +  ++  ++++
  gi|518653153|ref|YP_008142673.1|   6 AIVLASGKALRFKsNKLLYEVNSKPIIYYVIDNVAMSNFQQR-IIVLRSPEISDYSKQLGLKVVWNKDFENGMSASI 81 
                                       799999999999879*********************999888.555789**************99888888888889 PP

                                       HHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHS CS
                      CTP_transf_3  78 levvkaflmseneeiivnlqGdnPllqeevikkaietlken 118
                                       +  +++++++  ++ ++ + Gd Pll+  ++  +ie+ k +
  gi|518653153|ref|YP_008142673.1|  82 VHGIENVSPE--IDAAMIIPGDMPLLDNDTLNGLIEHFKSS 120
                                       99********..66677789****************99877 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0     5e-08   0.00018      45     114 ..      46     118 ..      16     137 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 5e-08
                              CofC  45 dvlvvsedeevleyaldelgvevvkek..ekdlntaveka..feeieekeviiipsdiPlikkedvkdllelek 114
                                       + ++v +  e+ +y + +lg++vv +k  e+++ +++ +    +++e +  +iip d+Pl+++++++ l+e+ k
  gi|518653153|ref|YP_008142673.1|  46 QRIIVLRSPEISDYSK-QLGLKVVWNKdfENGMSASIVHGieNVSPEIDAAMIIPGDMPLLDNDTLNGLIEHFK 118
                                       357888999******9.9******988668888888777634457899*********************99976 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   4.8e-08   0.00017       2     123 ..       5     123 ..       4     133 .. 0.85

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 4.8e-08
                                       EEEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE--SSHH CS
                              IspD   2 vvvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaGGdeRa 78 
                                       ++++ A G+  R k   +K+++e++ ++++   +d ++ s+  ++i+v+ s++  ++ +ql l+  +   +  +  +
  gi|518653153|ref|YP_008142673.1|   5 TAIVLASGKALRFK--SNKLLYEVNSKPIIYYVIDNVAMSNFQQRIIVLRSPEISDYSKQLGLK-VVWNKDFENGMS 78 
                                       67888887776665..69************************************9999999998.344445555678 PP

                                       HHHHHHHHTTSSTTSEEEE--TT-TT--HHHHHHHHHHHHTTCSE CS
                              IspD  79 esVlnglkalegeakfVLvHDaARpllkaadiaellaaaeqstqg 123
                                        s+++g++ +++e +  ++  +  pll +++++ l++  + s +g
  gi|518653153|ref|YP_008142673.1|  79 ASIVHGIENVSPEIDAAMIIPGDMPLLDNDTLNGLIEHFKSSSKG 123
                                       9999*****999999999999999999999999999988876655 PP

>> UPF0270  Uncharacterised protein family (UPF0270)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   1.7e-05     0.062       1      20 [.      96     117 ..      96     119 .. 0.97

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                                       EE--GGG..S-HHHHHHHHHHH CS
                           UPF0270   1 miIPyqq..LepetLenlieef 20 
                                       miIP ++  L+++tL+ lie+f
  gi|518653153|ref|YP_008142673.1|  96 MIIPGDMplLDNDTLNGLIEHF 117
                                       9*****999************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (197 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1392.73
//
Query:       gi|518653154|ref|YP_008142674.1|  [L=496]
Description: hypothetical protein FACI_IFERC00001G1795 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-23   81.6   0.7    1.2e-22   80.9   0.7    1.4  1  MutS_V    MutS domain V
     0.0073   16.8   1.1       0.01   16.4   0.1    1.8  2  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.7   1.3e-26   1.2e-22       2     165 ..     327     489 ..     326     495 .. 0.91

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.3e-26
                                       EEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--TT CS
                            MutS_V   2 litGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknatek 78 
                                       +itG n +Gkst+lr+++ ++l+ q G fv+ae+ + s+v  ift    ++d + ++  F  E++ ++ i +++ ++
  gi|518653154|ref|YP_008142674.1| 327 VITGTNRGGKSTFLRSIGQAQLMMQAGMFVAAESYSGSVVSGIFTHFKHEEDKTMERGKFDDELSTMNLIADHIRRN 403
                                       8**************************************************************************** PP

                                       SEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEEETTEEEEEEEEEE CS
                            MutS_V  79 slvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavkeeeedivflykvke 155
                                       sl++++E    t+t +G  +a+ +++ lle    k +f  H +e+++ ++++++ +++ l +++ ++     + v  
  gi|518653154|ref|YP_008142674.1| 404 SLILFNESFSSTNTREGAEVAMGITKALLE-SGIKIFFVSHLFEFASAMMEQNNESSVFLIAERADNGEHTYRIVDG 479
                                       *****************************9.799*************999988888887777766666555555566 PP

                                       S--SS--HHH CS
                            MutS_V 156 gaaeksyGik 165
                                       + +   yG++
  gi|518653154|ref|YP_008142674.1| 480 SPSITGYGMD 489
                                       6677889986 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1      0.62   5.6e+03     136     136 ..      90      90 ..      44     171 .. 0.55
   2 !   16.4   0.1   1.1e-06      0.01      18      42 ..     322     346 ..     304     449 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.62
                            AAA_23 136 l 136
                                       +
  gi|518653154|ref|YP_008142674.1|  90 S 90 
                                       1 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.1e-06
                            AAA_23  18 skgltlItGpNGaGKTTildAikla 42 
                                       +k+l++ItG N  GK+T+l+ i  a
  gi|518653154|ref|YP_008142674.1| 322 GKNLFVITGTNRGGKSTFLRSIGQA 346
                                       789*****************99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (496 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       659  (0.0367561); 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:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3956.22
//
Query:       gi|518653155|ref|YP_008142675.1|  [L=504]
Description: hypothetical protein FACI_IFERC00001G1796 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-23   82.0   0.0      1e-22   81.1   0.0    1.4  1  MutS_V    MutS domain V
     0.0083   16.2   0.1      0.048   13.7   0.0    2.4  2  AAA_14    AAA domain
  ------ inclusion threshold ------
      0.035   14.4   0.2         15    5.9   0.0    2.6  2  Rx_N      Rx N-terminal domain
       0.11   12.8   0.0        1.1    9.6   0.0    2.4  3  AAA_22    AAA domain
        3.4    8.1   6.6        3.4    8.1   1.2    2.4  2  AAA_23    AAA domain


Domain annotation for each model (and alignments):
>> MutS_V  MutS domain V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.1   0.0   2.8e-26     1e-22       1     142 [.     328     468 ..     328     499 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.1 bits;  conditional E-value: 2.8e-26
                                       EEEE-STTSSHHHHHHHHHHHHHHHHHT--BSSSEEEEE--SEEEEEE--------SS-HHHHHHHHHHHHHTT--T CS
                            MutS_V   1 llitGpnmaGkstylrqvalivllaqiGsfvpaekaeisivdkiftRvgasDdlakgkstFmvEmlEtasilknate 77 
                                       +++tGpn +Gk t+ r+ + +  la +G+ vp ++a+i  vd+if+    s++ +++      E++ +  il++ate
  gi|518653155|ref|YP_008142675.1| 328 IIVTGPNNGGKTTFARSFGQLHYLALLGCPVPGKEATILHVDNIFSHFEISENPENNMGRLEEELERLHGILEKATE 404
                                       59*************************************************************************** PP

                                       TSEEEEESTS-SS-HHHHHHHHHHHHHHHHHTT--EEEEEES-GGGGGHHHHSTTEEEEEEEEEE CS
                            MutS_V  78 kslvilDElGRGtstydGlaialavaeyllekikaktlfatHyheltklaekleevknlhlavke 142
                                       +sl+i++E+   t+  dG+ i   +++ + + +k+ +++ t  hel++l   ++ v++++ +  e
  gi|518653155|ref|YP_008142675.1| 405 RSLIIINEMLSSTTLKDGIEIGRNIIDKIKK-MKSICMYVTFIHELSDLPGVVSYVSQVDRKYPE 468
                                       ****************************987.9****************9999999988766554 PP

>> AAA_14  AAA 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      31      49 ..      46      64 ..      36     113 .. 0.59
   2 !   13.7   0.0   1.3e-05     0.048       2      81 ..     325     421 ..     324     444 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1
                            AAA_14 31 esilyinldderdkkladp 49
                                      e+ ly+ l + +d  ++++
  gi|518653155|ref|YP_008142675.1| 46 ERLLYMPLRNIDDIFYRQE 64
                                      6667777777777333322 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.3e-05
                            AAA_14   2 rkilvitGaRrvGKTtllkqlikell.......vkkesilyinldd..erdkkladpekllelileklke....... 62 
                                       + ++++tG+   GKTt+++ + + ++       v+ ++   + +d+   +++ +++pe+++  + e+l++       
  gi|518653155|ref|YP_008142675.1| 325 SSVIIVTGPNNGGKTTFARSFGQLHYlallgcpVPGKEATILHVDNifSHFEISENPENNMGRLEEELERlhgilek 401
                                       5799******************999999*****66666666666662144444556664444444433223334545 PP

                            AAA_14  63 .ekktylflDEiqevpewek 81 
                                         +++++++ E+  ++++++
  gi|518653155|ref|YP_008142675.1| 402 aTERSLIIINEMLSSTTLKD 421
                                       66788999999877766655 PP

>> Rx_N  Rx N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0     0.005        18      19      42 ..     150     173 ..     138     200 .. 0.75
   2 ?    5.9   0.0    0.0043        15      23      48 ..     381     406 ..     369     415 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.005
                              Rx_N  19 llkgvkeeleklkdeLesiqavLe 42 
                                        +k++k++ e+l++eL+si+ +++
  gi|518653155|ref|YP_008142675.1| 150 EFKSLKNDAEQLEEELSSIRYLIN 173
                                       57899**************98775 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0043
                              Rx_N  23 vkeeleklkdeLesiqavLedaeerq 48 
                                        ++ + +l++eLe+++++Le+a er 
  gi|518653155|ref|YP_008142675.1| 381 PENNMGRLEEELERLHGILEKATERS 406
                                       5778999***************9985 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.48   1.7e+03      76     124 ..     119     178 ..      60     184 .. 0.53
   2 ?   -1.0   0.0      0.54   1.9e+03      38      68 ..     172     202 ..     151     246 .. 0.66
   3 ?    9.6   0.0    0.0003       1.1       4     100 ..     324     413 ..     321     433 .. 0.67

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.48
                            AAA_22  76 eellealeqalrarav........ielliiDEaqhlr.s....eealeeLrsllnlsrkgvq 124
                                       e +l+ +++a  + +          + +  DE+  l       ee l+ +r l n   kgv+
  gi|518653155|ref|YP_008142675.1| 119 ENMLDNMRKAGAKSRGftgfinylDAYVASDEFKSLKnDaeqlEEELSSIRYLIN--IKGVK 178
                                       4444444444444444444444444445557777774413334555555566666..55555 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.54
                            AAA_22  38 erpevvfvtlpsstsskdllrellralglel 68 
                                        + + v++t+ ++ +skd ++e+ +a+ + l
  gi|518653155|ref|YP_008142675.1| 172 INIKGVKITVREDRDSKDYASEVKEAFSRFL 202
                                       4445567777777788888777777776544 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0003
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdl..lrellralglelka..erlsse 76 
                                       + ++++vtG+   GKTt +r + + +            +++  +p++++ +++    ++++ ++ + +   + +++e
  gi|518653155|ref|YP_008142675.1| 324 NSSVIIVTGPNNGGKTTFARSFGQLH-----------YLALLGCPVPGKEATIlhVDNIFSHFEISENPenNMGRLE 389
                                       6789******************9987...........2345555555544444245667777776555533344444 PP

                            AAA_22  77 ellealeqalraravielliiDEa 100
                                       e le+l+  l+++  ++l+ii E+
  gi|518653155|ref|YP_008142675.1| 390 EELERLHGILEKATERSLIIINEM 413
                                       444444444444444777777665 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.4     0.047   1.7e+02     153     175 ..      97     171 ..       5     205 .. 0.53
   2 ?    8.1   1.2   0.00094       3.4      18      40 ..     324     346 ..     309     448 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.047
                            AAA_23 153 e....................................................rleelekeleeledekkllekl 175
                                       +                                                    + ++l+++ e+le+e + ++ l
  gi|518653155|ref|YP_008142675.1|  97 DlydlqrerwlldsvymysrsienmldnmrkagaksrgftgfinyldayvasdEFKSLKNDAEQLEEELSSIRYL 171
                                       122344444444444444444444444444445666666666665555554444444444444444444444444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.00094
                            AAA_23  18 skgltlItGpNGaGKTTildAik 40 
                                       ++ + ++tGpN  GKTT+ + + 
  gi|518653155|ref|YP_008142675.1| 324 NSSVIIVTGPNNGGKTTFARSFG 346
                                       567899***********998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      665  (0.0370907); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.30s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3394.69
//
Query:       gi|518653156|ref|YP_008142676.1|  [L=136]
Description: hypothetical protein FACI_IFERC00001G1797 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.054   14.1   0.0      0.078   13.6   0.0    1.4  1  MMR_HSR1_C  GTPase of unknown function C-terminal


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 ?   13.6   0.0   4.3e-06     0.078       3      58 ..       3      60 ..       1      90 [. 0.84

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 4.3e-06
                        MMR_HSR1_C  3 NKaDl..paadenieklkekypkdkkvvpvsAaaElaLrkaakqglikYepgdedfei 58
                                      N +D   ++a++n++k+ e++p+ +  ++    + + + +a+k++ ++Y+ gd+ ++ 
  gi|518653156|ref|YP_008142676.1|  3 NEMDSfeNEAKKNYDKIGEDFPRGSIKILSPDIINILITNARKSKTVNYKAGDTVYTA 60
                                      7788887899************8885555556789999**************998665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (136 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); 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: 0.45u 0.29s 00:00:00.74 Elapsed: 00:00:00.47
# Mc/sec: 876.24
//
Query:       gi|518653157|ref|YP_008142677.1|  [L=404]
Description: major facilitator superfamily permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.7e-12   46.3  44.0    2.7e-12   46.3  44.0    2.2  2  MFS_1        Major Facilitator Superfamily
  ------ inclusion threshold ------
      0.092   11.1  15.5       0.16   10.3  15.5    1.3  1  MFS_3        Transmembrane secretion effector
       0.16   12.0   0.0       0.16   12.0   0.0    2.1  2  SNARE        SNARE domain


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 !   46.3  44.0   4.6e-16   2.7e-12      12     346 ..      29     345 ..      18     353 .. 0.78
   2 !    6.6  13.0   0.00052       3.1      62     166 ..     276     380 ..     271     398 .. 0.90

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 4.6e-16
                             MFS_1  12 rsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwll 88 
                                        + ++ +++  +  +++ s+  ++l+ ++ +lg+++ ++p G+++dr+ r  +++   +l++l+  +l+f+ sl+++
  gi|518653157|ref|YP_008142677.1|  29 TAYYIYFMW-EIIANYH-SVLLVSLIPGFSFLGYLIIAIPEGSIIDRYDRHLIYIGINILMVLTYSILFFGRSLFII 103
                                       333444454.5567788.******************************9999************6666676777799 PP

                             MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                       +++ +l++ ++ ++     al+ ++ p ++ ++a +  ++++++ ++ g +lgg+++    ++ v+++l ++s++a 
  gi|518653157|ref|YP_008142677.1| 104 YAVDFLSSTFMWVVSDDFRALTKEIMPADHMAKAQSADQLSSGIFTLAGIILGGAFI-FMRYSTVYVALIGISIFA- 178
                                       99999***99988888899**************************************.888999999999999999. PP

                             MFS_1 166 vlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlglsg 242
                                        l+++++p++ + ++r+  k          +++  k++++  ++  ll++lll+++++++ ++ + l+ +  ++ s+
  gi|518653157|ref|YP_008142677.1| 179 -LAIIFVPRTIKVSHRSIVKNG--------FRSTVKIMKNILPF--LLLTLLLNGMFVAIDVFASGLI-NIIMHASS 243
                                       .666999999999999987777........44433344444455..*********9999988888886.999**994 PP

                             MFS_1 243 lllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfp 319
                                        +++ ++ +++a + a++ +    + + ++r +r++   + ++++ ++++l+++   +v+  ++ +l G+ l+f+++
  gi|518653157|ref|YP_008142677.1| 244 IYYTFFIAGFPAGMLAGGLISMHGFYRPYQRNKRMM--AFYIFMTGVIFILISFNRLPVMDGILTFLSGVILAFINV 318
                                       455555555555555455445555555566644444..44445555555555555569999999999********** PP

                             MFS_1 320 sllalasdlappeeagtasglfntags 346
                                        + +++ +++p + +g+ ++l+ +++ 
  gi|518653157|ref|YP_008142677.1| 319 YIETMIINSIPSSITGKFNALTAMFSV 345
                                       ***********9999999999986654 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00052
                             MFS_1  62 rrvlllglllfalglllllfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg 137
                                       +r++ + ++++++ ++l++f + l+ +  +l +l+G+  ++++  + ++i    p +  g+ ++l ++++  ++ + 
  gi|518653157|ref|YP_008142677.1| 276 KRMMAFYIFMTGVIFILISF-NRLPvMDGILTFLSGVILAFINVYIETMIINSIPSSITGKFNALTAMFSVSSSPVM 351
                                       78999999999999555559.****999***********************************99999999999*** PP

                             MFS_1 138 pllggllasslgWravfyilaivsllafv 166
                                       + + g l+  l ++++  ++++++ll+  
  gi|518653157|ref|YP_008142677.1| 352 AFVFGELSRFLYFPYIITVVGVIMLLSSF 380
                                       ********9999****9999999999844 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3  15.5   2.7e-05      0.16      35     391 ..      37     383 ..      11     401 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 2.7e-05
                             MFS_3  35 WlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltl 111
                                       W +     s l v l+   + L  ++++i+ G + D +dr  + + + +l++l+  +l     l ++  +  l +t+
  gi|518653157|ref|YP_008142677.1|  37 WEIIANYHSVLLVSLIPGFSFLGYLIIAIPEGSIIDRYDRHLIYIGINILMVLTYSILFFGRSLFIIYAVDFLSSTF 113
                                       6566666799999*************************************999988888888887777777777777 PP

                             MFS_3 112 ligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallr 188
                                       +      + +  ++A + e+++++++ +A     +   i   +G  lgG  + +  +++  a+  +s +al ++++ 
  gi|518653157|ref|YP_008142677.1| 114 MW-----VVSDDFRALTKEIMPADHMAKAQSADQLSSGIFTLAGIILGGAFIFMRYSTVYVALIGISIFALAIIFVP 185
                                       76.....5667889************************************999998888889999999999888888 PP

                             MFS_3 189 wkrevrksslprEkllealraglRftaasreikavlvRaalFglsasavlaLLPlvardqldgdalvyGillgalGv 265
                                          +v+++s+ ++ ++++++      ++ + +  +l+   +F +       L+ ++    +++ ++ y  +++++ +
  gi|518653157|ref|YP_008142677.1| 186 RTIKVSHRSIVKNGFRSTVKIM---KNILPFLLLTLLLNGMFVAIDVFASGLINII----MHASSIYYTFFIAGFPA 255
                                       8889999998888777776542...2333344445555555555444445566666....56789************ PP

                             MFS_3 266 GAilgallls..rLRerlsserlvllaavalAlvllslalasslwvavlvlllgGaaWitalstlnvavqlavPrWv 340
                                       G ++g+l++   + R    ++r+++   +++ ++ + +++ +  ++  +   l+G         +++ +  ++P+ +
  gi|518653157|ref|YP_008142677.1| 256 GMLAGGLISMhgFYRPYQRNKRMMAFYIFMTGVIFILISFNRLPVMDGILTFLSGVILAFINVYIETMIINSIPSSI 332
                                       ******987522689999999******************99988888888888888776667778888888999999 PP

                             MFS_3 341 vgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaill 391
                                        g+  a+  + +  +    ++++G ++  l  +  +++ ++ +ll+ ++++
  gi|518653157|ref|YP_008142677.1| 333 TGKFNALTAMFSVSSSPVMAFVFGELSRFLYFPYIITVVGVIMLLSSFTVI 383
                                       999888888888888888888899888888888888888888888877665 PP

>> SNARE  SNARE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -6.1   2.9         3   1.8e+04      41      48 ..     176     183 ..     171     184 .. 0.43
   2 ?   12.0   0.0   2.6e-05      0.16      30      52 ..     272     294 ..     269     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: -6.1 bits;  conditional E-value: 3
                                       XXXXXXXX CS
                             SNARE  41 illilvii 48 
                                       i+ +++i+
  gi|518653157|ref|YP_008142677.1| 176 IFALAIIF 183
                                       33444443 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 2.6e-05
                                       HHCTXXXXXXXXXXXXXXXXXXX CS
                             SNARE  30 yqksnRklkciillilviillvv 52 
                                       yq++ R++ ++i+   vi++l+ 
  gi|518653157|ref|YP_008142677.1| 272 YQRNKRMMAFYIFMTGVIFILIS 294
                                       9********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.73u 0.26s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 2517.98
//
Query:       gi|518653158|ref|YP_008142678.1|  [L=194]
Description: hypothetical protein FACI_IFERC00001G1799 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.7e-05   24.6   0.4    3.4e-05   23.6   0.4    1.5  1  TrmB         Sugar-specific transcriptional regulator TrmB
     0.0004   20.2   0.0    0.00071   19.4   0.0    1.4  1  HTH_5        Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.019   14.9   0.2        0.1   12.5   0.0    2.0  2  MarR         MarR family
      0.044   13.9   0.0      0.066   13.3   0.0    1.3  1  HTH_20       Helix-turn-helix domain
      0.045   13.8   0.0       0.13   12.3   0.0    1.7  1  HTH_Mga      M protein trans-acting positive regulator (MGA) 
       0.05   13.5   1.4       0.12   12.2   0.2    2.1  2  TFIIE_alpha  TFIIE alpha subunit
      0.068   13.4   0.0       0.13   12.5   0.0    1.5  1  HTH_34       Winged helix DNA-binding domain
       0.13   12.3   0.1       0.26   11.3   0.1    1.4  1  PadR         Transcriptional regulator PadR-like family
       0.15   12.1   2.1       0.93    9.6   0.2    2.1  2  zf-CRD       Cysteine rich domain with multizinc binding regi
       0.16   11.6   0.2        0.4   10.3   0.0    1.8  2  HTH_24       Winged helix-turn-helix DNA-binding


Domain annotation for each model (and alignments):
>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.4   1.9e-08   3.4e-05      15      61 ..      22      68 ..      15      75 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 1.9e-08
                                      HHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEESSTTTE CS
                              TrmB 15 laLlklgpatadeiaeelgvprskvYevLrsLedkGlVerekgrpkl 61
                                      + L+++ ++t++  ++ ++  rs+ Y+v+++L++ G+V+  + rpk+
  gi|518653158|ref|YP_008142678.1| 22 TLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIVNEPEIRPKK 68
                                      5688************************************9999874 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0     4e-07   0.00071       1      46 [.      14      60 ..      14      61 .. 0.95

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 4e-07
                                      SHHHHHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5  1 dptRlkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVe 46
                                      +pt+ kI+ lL + ++++v+  +++++ ++s++ +  + L  +G+V+
  gi|518653158|ref|YP_008142678.1| 14 NPTKMKIITLLVNnNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIVN 60
                                      69***********788*****************************98 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   5.7e-05       0.1       2      48 ..      14      60 ..      14      62 .. 0.95
   2 ?   -0.3   0.0      0.57     1e+03      15      26 ..     123     134 ..     110     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 5.7e-05
                                      -HHHHHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              MarR  2 tltqfviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlie 48
                                      ++t ++i+++l +++ ++v+ + k +++++s++  v+  L+  G ++
  gi|518653158|ref|YP_008142678.1| 14 NPTKMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIVN 60
                                      68999************************************999985 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.57
                                       STTEEHHHHHHH CS
                              MarR  15 qgplsvseLakk 26 
                                        ++++++e++++
  gi|518653158|ref|YP_008142678.1| 123 IEAMTQKEIQNM 134
                                       456999999986 PP

>> HTH_20  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.7e-05     0.066       2      55 ..       7      60 ..       6      66 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.7e-05
                                      HHHHHHS-HHHHHHHHHHSTCTTB-HHHHHHHHTS-HHHHHHHHHHHHHCTTEE CS
                            HTH_20  2 qiaeALahPvRrrilraLaraegltaselaerldlskntlsyHLrvLeeagLve 55
                                      +i+eA+ +P+ ++i  +L  +  +t++   + + +++++l++ +  L++ g+v 
  gi|518653158|ref|YP_008142678.1|  7 EILEAFRNPTKMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIVN 60
                                      79*************************************************997 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 ?   12.3   0.0   7.5e-05      0.13       6      45 ..      16      54 ..      15      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                           HTH_Mga  6 rklkLlelLteneksltldelakeLglseltlqsdiseLn 45
                                      +k k+++lL   ++ +t++  +k+  ++++ l + +s+L 
  gi|518653158|ref|YP_008142678.1| 16 TKMKIITLLVN-NNKMTVTGMSKYIKTTRSNLYQVVSNLV 54
                                      589********.***********************99996 PP

>> TFIIE_alpha  TFIIE alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   6.9e-05      0.12       5      76 ..       7      77 ..       3      94 .. 0.84
   2 ?    0.4   0.1      0.33   5.9e+02      61      90 ..     127     157 ..      80     173 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.9e-05
                                      HHHHHCS-HHHHHHHHHHHCTTSEBHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEEEEEETTTEEEEEEEEE CS
                       TFIIE_alpha  5 evvrkfygeeavlvldvLlekgevteedlakelkidlnelrklLnrLyearlvkykrrrdeekswykyywri 76
                                      e++  f +   ++++  L+ + ++t   ++k +k  + +l +++ +L + ++v+    r  +  ++kyy  +
  gi|518653158|ref|YP_008142678.1|  7 EILEAFRNPTKMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIVNEPEIRPKKNYVEKYY-SL 77
                                      788888888999*****************************************9888776555555554.44 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.33
                                       EEEE.TTTEEEEEEEEEECCCHCCCHHHHHH CS
                       TFIIE_alpha  61 rrrd.eekswykyywrinyeklvdvvkrkle 90 
                                        +++ ++    + y  + y +  + v +kl+
  gi|518653158|ref|YP_008142678.1| 127 TQKEiQNMRKHEKYTVFSYGTCSNSVFEKLS 157
                                       3333433333444444555555555555555 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.1e-05      0.13       2      43 ..      17      58 ..      16      73 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.1e-05
                            HTH_34  2 RlavlsyLasvdeadfvelkealeatdgnLsvhlkkLekagY 43
                                      +++++++L+ +++++ + +++ +++t +nL+  ++ L + g 
  gi|518653158|ref|YP_008142678.1| 17 KMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGI 58
                                      5799*****************************999988875 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00014      0.26      27      67 ..      39      79 ..      27      80 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                      CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESH CS
                              PadR 27 lelseGslYpaLkrLekeglveseweesgegpprkyYrlTd 67
                                      ++   ++lY++ + L  +g+v++ + + +++   kyY l++
  gi|518653158|ref|YP_008142678.1| 39 IKTTRSNLYQVVSNLVSSGIVNEPEIRPKKNYVEKYYSLNE 79
                                      5677899****************9999999*********97 PP

>> zf-CRD  Cysteine rich domain with multizinc binding regions
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00052      0.93      63     113 ..       6      56 ..       2      81 .. 0.84
   2 ?    2.6   0.2     0.073   1.3e+02      84     127 ..      98     139 ..      69     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00052
                            zf-CRD  63 sglLkpieekliekipeevlegneveqkilkdylaekgltlqdvlkevlek 113
                                        ++L+ +++ ++ ki++ ++++n++    +++y+++ +  l +v+++ ++ 
  gi|518653158|ref|YP_008142678.1|   6 REILEAFRNPTKMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSS 56 
                                       5789999************************************99987765 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.073
                            zf-CRD  84 gneveqkilkdylaekgltlqdvlkevlekldkgelkrtrkkln 127
                                       +ne++ +il+++   ++l l+ ++ +++e++ ++e++++rk+ +
  gi|518653158|ref|YP_008142678.1|  98 DNEYR-EILSSFFMAQSLNLE-IIGKSIEAMTQKEIQNMRKHEK 139
                                       45554.488888877777765.6667789999888755555544 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00022       0.4       1      47 [.      13      59 ..      13      60 .. 0.97
   2 ?   -3.8   0.0       5.7     1e+04      18      23 ..     126     131 ..     126     133 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00022
                            HTH_24  1 ldetdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlI 47
                                      ++ t+ kI+ lL  n +++ +  ++ +  ++s++ + + +L+++G++
  gi|518653158|ref|YP_008142678.1| 13 RNPTKMKIITLLVNNNKMTVTGMSKYIKTTRSNLYQVVSNLVSSGIV 59
                                      6899*****************************************98 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.7
                            HTH_24  18 isqreL 23 
                                       ++q+e+
  gi|518653158|ref|YP_008142678.1| 126 MTQKEI 131
                                       699998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      592  (0.0330191); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1445.08
//
Query:       gi|518653159|ref|YP_008142679.1|  [L=586]
Description: hypothetical protein FACI_IFERC00001G1800 [Ferroplasma acidarmanus fer1]
Scores for complete 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-16   58.3   9.4     0.0015   19.0   0.2    6.3  7  TPR_19      Tetratricopeptide repeat
    3.8e-11   42.2  14.8      0.045   13.9   0.1    8.5  8  TPR_2       Tetratricopeptide repeat
      4e-09   37.0   0.1      0.035   14.8   0.0    5.1  5  TPR_16      Tetratricopeptide repeat
      5e-09   36.2   0.2        5.4    8.1   0.0    8.2  8  TPR_14      Tetratricopeptide repeat
    6.4e-07   29.3  15.4       0.44   11.0   0.0    7.6  7  TPR_17      Tetratricopeptide repeat
    3.1e-06   27.3  13.2       0.57   10.4   0.1    5.6  5  ANAPC3      Anaphase-promoting complex, cyclosome, subunit 3
    4.9e-05   23.2  25.7     0.0043   17.2   0.3    8.0  9  TPR_8       Tetratricopeptide repeat
    6.4e-05   22.3   0.8     0.0032   16.7   0.2    3.1  2  TPR_15      Tetratricopeptide repeat
    0.00013   22.2   8.9        1.5    9.1   0.0    6.3  6  TPR_12      Tetratricopeptide repeat
    0.00018   21.2   0.0     0.0017   18.0   0.0    2.4  2  HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
     0.0012   18.5  11.1       0.81    9.4   0.1    6.7  7  TPR_11      TPR repeat
     0.0023   18.4   0.0        9.7    6.6   0.0    3.3  3  BTAD        Bacterial transcriptional activator domain
     0.0025   17.6  14.6          4    7.4   0.1    7.3  8  TPR_1       Tetratricopeptide repeat
     0.0043   16.5   0.0      0.013   14.9   0.0    1.9  1  TPR_MalT    MalT-like TPR region
     0.0072   16.4   7.3       0.18   11.9   0.1    5.2  5  Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
  ------ inclusion threshold ------
      0.011   16.3   1.3         29    5.6   0.0    6.1  6  TPR_6       Tetratricopeptide repeat
      0.025   14.7   0.1      0.025   14.7   0.1    3.4  4  HEPN        HEPN domain
      0.059   13.4   0.3        0.9    9.6   0.3    2.9  1  DUF3856     Domain of Unknown Function (DUF3856)
      0.092   12.8   1.6         32    4.9   0.0    5.1  5  TPR_7       Tetratricopeptide repeat
       0.16   11.9  10.9        4.4    7.3   0.0    5.5  5  TPR_10      Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.2   1.4e-05     0.013       1      65 [.      94     158 ..      94     161 .. 0.93
   2 !    7.8   0.0    0.0054       4.8       1      59 [.     128     187 ..     128     195 .. 0.87
   3 !   19.0   0.2   1.7e-06    0.0015       8      57 ..     203     252 ..     200     260 .. 0.90
   4 !   13.4   0.0   9.4e-05     0.085       1      47 [.     297     343 ..     297     355 .. 0.93
   5 !    8.5   0.1    0.0031       2.8       5      58 ..     368     421 ..     364     427 .. 0.90
   6 ?    1.0   0.0      0.69   6.2e+02       5      45 ..     436     475 ..     432     478 .. 0.85
   7 ?   -1.3   0.0       3.6   3.2e+03      39      54 ..     541     556 ..     510     561 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.4e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpddaryasLl 65 
                                       l+++ dy +A ++   al+ dp n e  +  +++l++  +++ A + L    +  pd a + sL 
  gi|518653159|ref|YP_008142679.1|  94 LMENYDYSDAKKRIDMALALDPLNYEYHYIKVNLLIERRDYEGALKELHVMEKLVPDKASVYSLE 158
                                       78999*********************************************999999998888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0054
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.a 59 
                                       l+++ dy+ Al+ l  + +  p+ a +  l  ++l++lg   +A    d+++e+d++  +
  gi|518653159|ref|YP_008142679.1| 128 LIERRDYEGALKELHVMEKLVPDKASVYSLESRCLINLGKNFDAVGKADEALEHDRNYmQ 187
                                       7899*************999*********99********999999988888888888444 PP

  == domain 3  score: 19.0 bits;  conditional E-value: 1.7e-06
                            TPR_19   8 aeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpd 57 
                                        +A + + +al+ dp++ae  + L e++++++++d+A +  +++ + ++d
  gi|518653159|ref|YP_008142679.1| 203 NDAFDVYYSALKVDPQDAESYAVLSELHMEMKNFDAAHESAKKAINIEKD 252
                                       589999********************************999999888877 PP

  == domain 4  score: 13.4 bits;  conditional E-value: 9.4e-05
                            TPR_19   1 llaegdyaeAlalleqalqedpknaearllLAeallalgqldeAeal 47 
                                       l+++g+ ++A+++ e+ ++ +p+n + + +LA + +  +++++A ++
  gi|518653159|ref|YP_008142679.1| 297 LYESGNREDAVKIAEKFYKINPGNMNFAHNLAHIFILENRIQDAGKV 343
                                       6899****************************************766 PP

  == domain 5  score: 8.5 bits;  conditional E-value: 0.0031
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd 58 
                                       ++ya+ l+   ++++ +p+n+  +++   al   g+ ++A  +++ l  +++d+
  gi|518653159|ref|YP_008142679.1| 368 EQYAAVLKNVDELIARYPDNDGFLYNKFYALSRGGDHKDALIIIKLLYGQNKDS 421
                                       799*************************************99999888888875 PP

  == domain 6  score: 1.0 bits;  conditional E-value: 0.69
                            TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAe 45 
                                       g+ +e l++le+ ++e   ++++ + L  ++  l+q+d A 
  gi|518653159|ref|YP_008142679.1| 436 GNSDESLRILEN-FEELYIDPWISMSLWSLYSMLNQYDRAN 475
                                       677788888888.7888889999999999*********996 PP

  == domain 7  score: -1.3 bits;  conditional E-value: 3.6
                            TPR_19  39 gqldeAealLdalpee 54 
                                        ++d+ +++L++++ +
  gi|518653159|ref|YP_008142679.1| 541 DDYDKGRDILEQIGSA 556
                                       5788888888888765 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.1     0.025        22       7      34 .]      90     117 ..      84     117 .. 0.88
   2 ?    0.5   0.0      0.94   8.4e+02      10      24 ..     127     141 ..     121     150 .. 0.82
   3 !    7.1   0.0    0.0076       6.8       2      33 ..     153     184 ..     152     185 .. 0.87
   4 !   13.9   0.1     5e-05     0.045       1      34 []     220     253 ..     220     253 .. 0.93
   5 !   10.1   0.0   0.00082      0.74       9      34 .]     295     320 ..     295     320 .. 0.96
   6 ?    6.0   0.0     0.016        15       5      32 ..     325     352 ..     322     354 .. 0.93
   7 ?    0.1   0.1       1.3   1.1e+03      11      23 ..     465     477 ..     463     482 .. 0.86
   8 ?   -1.5   0.0       4.2   3.8e+03      10      31 ..     501     522 ..     500     524 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.025
                             TPR_2   7 lGlayyklgdyeeAleafekAleldPnn 34 
                                        +  ++++ dy +A++  + Al+ldP n
  gi|518653159|ref|YP_008142679.1|  90 KAIGLMENYDYSDAKKRIDMALALDPLN 117
                                       677899999*****************65 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.94
                             TPR_2  10 ayyklgdyeeAleaf 24 
                                       +++++ dye Al+ +
  gi|518653159|ref|YP_008142679.1| 127 LLIERRDYEGALKEL 141
                                       678999******976 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0076
                             TPR_2   2 ealynlGlayyklgdyeeAleafekAleldPn 33 
                                        ++    +++++lg+  +A+   ++Ale+d n
  gi|518653159|ref|YP_008142679.1| 153 SVYSLESRCLINLGKNFDAVGKADEALEHDRN 184
                                       57888899999****************99987 PP

  == domain 4  score: 13.9 bits;  conditional E-value: 5e-05
                             TPR_2   1 aealynlGlayyklgdyeeAleafekAleldPnn 34 
                                       ae +  l ++++++++++ A+e  +kA+ ++ +n
  gi|518653159|ref|YP_008142679.1| 220 AESYAVLSELHMEMKNFDAAHESAKKAINIEKDN 253
                                       6788999**********************99886 PP

  == domain 5  score: 10.1 bits;  conditional E-value: 0.00082
                             TPR_2   9 layyklgdyeeAleafekAleldPnn 34 
                                       +++y++g+ e+A++  ek  +++P+n
  gi|518653159|ref|YP_008142679.1| 295 NCLYESGNREDAVKIAEKFYKINPGN 320
                                       69**********************87 PP

  == domain 6  score: 6.0 bits;  conditional E-value: 0.016
                             TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                                       +nl+ + +  ++ ++A + ++ +++l+ 
  gi|518653159|ref|YP_008142679.1| 325 HNLAHIFILENRIQDAGKVYKNSIKLNK 352
                                       79************************96 PP

  == domain 7  score: 0.1 bits;  conditional E-value: 1.3
                             TPR_2  11 yyklgdyeeAlea 23 
                                       y  l++y++A e+
  gi|518653159|ref|YP_008142679.1| 465 YSMLNQYDRANEY 477
                                       8899******887 PP

  == domain 8  score: -1.5 bits;  conditional E-value: 4.2
                             TPR_2  10 ayyklgdyeeAleafekAleld 31 
                                        y+++g   +A+++ ++ +e +
  gi|518653159|ref|YP_008142679.1| 501 TYLEKGWKIQAIKFIDALIERA 522
                                       5899999999***999998865 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   3.9e-05     0.035       5      55 ..      92     140 ..      88     151 .. 0.90
   2 ?    3.0   0.1      0.19   1.7e+02       9      68 .]     164     220 ..     160     220 .. 0.88
   3 ?   -1.1   0.0       3.6   3.2e+03       6      23 ..     229     246 ..     224     248 .. 0.84
   4 ?    3.6   0.0      0.12     1e+02       7      55 ..     297     342 ..     296     353 .. 0.81
   5 !    7.7   0.0    0.0062       5.5      18      62 ..     375     416 ..     367     421 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3.9e-05
                            TPR_16   5 raalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAa.a 55 
                                         ++++ dy dA ++ + al++d   P+++e ++ + +++ ++ ++++A+ +
  gi|518653159|ref|YP_008142679.1|  92 IGLMENYDYSDAKKRIDMALALD---PLNYEYHYIKVNLLIERRDYEGALkE 140
                                       55777889***************...***********************955 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.19
                            TPR_16   9 ragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalraapdap 68 
                                       ++g+  dA+  +++al+ d       +A+ ++  a+   g   +A ++y +al+ +p+++
  gi|518653159|ref|YP_008142679.1| 164 NLGKNFDAVGKADEALEHD---RNYMQAYENKLIALQNIGLINDAFDVYYSALKVDPQDA 220
                                       5667778999999999999...99999999999999999******************985 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.6
                            TPR_16   6 aalragdyddAaaaleaa 23 
                                       ++++ +++d+A + ++ a
  gi|518653159|ref|YP_008142679.1| 229 LHMEMKNFDAAHESAKKA 246
                                       68899******9998776 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.12
                            TPR_16   7 alragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaa 55 
                                       ++++g+ +dA++ +e + k +   P +  ++ +l+ ++   +r ++A  
  gi|518653159|ref|YP_008142679.1| 297 LYESGNREDAVKIAEKFYKIN---PGNMNFAHNLAHIFILENRIQDAGK 342
                                       6899***************99...8888777777777777777777765 PP

  == domain 5  score: 7.7 bits;  conditional E-value: 0.0062
                            TPR_16  18 aaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraalr 62 
                                       +  +++++r+   Pd+  +l+++  a+ r g++++A+  ++ +++
  gi|518653159|ref|YP_008142679.1| 375 KNVDELIARY---PDNDGFLYNKFYALSRGGDHKDALIIIKLLYG 416
                                       667899****...***********************988777775 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0      0.22     2e+02       8      38 ..      91     121 ..      88     127 .. 0.87
   2 ?    0.2   0.0       2.1   1.8e+03       8      33 ..     125     150 ..     121     157 .. 0.79
   3 ?    5.7   0.0     0.037        33      11      43 ..     196     228 ..     186     229 .. 0.83
   4 !    8.1   0.0     0.006       5.4       2      42 ..     221     261 ..     220     263 .. 0.90
   5 ?    4.4   0.0     0.095        85      11      42 ..     297     328 ..     290     352 .. 0.89
   6 ?    4.0   0.0      0.13   1.1e+02       5      39 ..     358     392 ..     355     398 .. 0.88
   7 ?    0.4   0.0       1.8   1.6e+03       9      41 ..     396     428 ..     391     433 .. 0.75
   8 ?   -0.5   0.0       3.5   3.2e+03       7      27 ..     428     448 ..     422     457 .. 0.79

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.22
                            TPR_14   8 aeallalGdpdeAiallrralalaPddaeaw 38 
                                       a  l+++ d+ +A +  + alal+P + e++
  gi|518653159|ref|YP_008142679.1|  91 AIGLMENYDYSDAKKRIDMALALDPLNYEYH 121
                                       667899999****************998876 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 2.1
                            TPR_14   8 aeallalGdpdeAiallrralalaPd 33 
                                       + +l +++d+++A++ l+ + +l Pd
  gi|518653159|ref|YP_008142679.1| 125 VNLLIERRDYEGALKELHVMEKLVPD 150
                                       5679999********99877776666 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.037
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawlllaq 43 
                                       l + G   +A +++  al+ +P+dae +  l +
  gi|518653159|ref|YP_008142679.1| 196 LQNIGLINDAFDVYYSALKVDPQDAESYAVLSE 228
                                       555577789****************99888876 PP

  == domain 4  score: 8.1 bits;  conditional E-value: 0.006
                            TPR_14   2 eallalaeallalGdpdeAiallrralalaPddaeawllla 42 
                                       e ++ l e++++  ++d+A + +++a+    d+  a+ +l+
  gi|518653159|ref|YP_008142679.1| 221 ESYAVLSELHMEMKNFDAAHESAKKAINIEKDNIKANNMLV 261
                                       5678899**************************99998886 PP

  == domain 5  score: 4.4 bits;  conditional E-value: 0.095
                            TPR_14  11 llalGdpdeAiallrralalaPddaeawllla 42 
                                       l+++G+ ++A++++++  + +P++  +   la
  gi|518653159|ref|YP_008142679.1| 297 LYESGNREDAVKIAEKFYKINPGNMNFAHNLA 328
                                       7899******************9977666665 PP

  == domain 6  score: 4.0 bits;  conditional E-value: 0.13
                            TPR_14   5 lalaeallalGdpdeAiallrralalaPddaeawl 39 
                                       l++  +l + +++++ ++  ++++a++Pd++ +++
  gi|518653159|ref|YP_008142679.1| 358 LQYITFLNETEQYAAVLKNVDELIARYPDNDGFLY 392
                                       789999999*********************98764 PP

  == domain 7  score: 0.4 bits;  conditional E-value: 1.8
                            TPR_14   9 eallalGdpdeAiallrralalaPddaeawlll 41 
                                        al + Gd+++A+ + + +  ++ d+  +  ++
  gi|518653159|ref|YP_008142679.1| 396 YALSRGGDHKDALIIIKLLYGQNKDSILYKVEY 428
                                       68999*******987777776666666655555 PP

  == domain 8  score: -0.5 bits;  conditional E-value: 3.5
                            TPR_14   7 laeallalGdpdeAiallrra 27 
                                       +a  l+  G+ de++++l+  
  gi|518653159|ref|YP_008142679.1| 428 YALELALTGNSDESLRILENF 448
                                       666677889*******99865 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1      0.16   1.4e+02       5      33 ..     110     138 ..     108     139 .. 0.92
   2 ?    0.4   0.1       1.2   1.1e+03       3      27 ..     176     200 ..     174     205 .. 0.79
   3 !   11.0   0.0   0.00049      0.44       4      34 .]     211     241 ..     208     241 .. 0.92
   4 ?    0.9   0.0      0.85   7.6e+02       3      22 ..     244     263 ..     243     277 .. 0.81
   5 !    8.4   0.0    0.0034         3       2      32 ..     310     340 ..     309     342 .. 0.83
   6 !    8.1   0.0    0.0043       3.8       4      33 ..     379     408 ..     378     409 .. 0.93
   7 ?   -0.9   0.0       3.1   2.8e+03      22      32 ..     464     474 ..     463     476 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.16
                            TPR_17   5 aleldPnnadaynnLAelllknGdlmtAr 33 
                                       al+ldP n + ++ + +ll ++ d++ A+
  gi|518653159|ref|YP_008142679.1| 110 ALALDPLNYEYHYIKVNLLIERRDYEGAL 138
                                       899****************9999999986 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 1.2
                            TPR_17   3 lkaleldPnnadaynnLAelllknG 27 
                                        +ale+d n+  ay n+  +l ++G
  gi|518653159|ref|YP_008142679.1| 176 DEALEHDRNYMQAYENKLIALQNIG 200
                                       589******9999998766666655 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00049
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtArq 34 
                                        al+ dP +a++y  L el+ + ++++ A++
  gi|518653159|ref|YP_008142679.1| 211 SALKVDPQDAESYAVLSELHMEMKNFDAAHE 241
                                       599***********************99986 PP

  == domain 4  score: 0.9 bits;  conditional E-value: 0.85
                            TPR_17   3 lkaleldPnnadaynnLAel 22 
                                       +ka+ ++++n +a n+L  +
  gi|518653159|ref|YP_008142679.1| 244 KKAINIEKDNIKANNMLVSI 263
                                       79***********9999655 PP

  == domain 5  score: 8.4 bits;  conditional E-value: 0.0034
                            TPR_17   2 ylkaleldPnnadaynnLAelllknGdlmtA 32 
                                        +k+ +++P n ++ +nLA ++   ++ ++A
  gi|518653159|ref|YP_008142679.1| 310 AEKFYKINPGNMNFAHNLAHIFILENRIQDA 340
                                       589999**************99766666655 PP

  == domain 6  score: 8.1 bits;  conditional E-value: 0.0043
                            TPR_17   4 kaleldPnnadaynnLAelllknGdlmtAr 33 
                                       + ++++P+n  +++n+ ++l++ Gd+++A+
  gi|518653159|ref|YP_008142679.1| 379 ELIARYPDNDGFLYNKFYALSRGGDHKDAL 408
                                       6799**********************9995 PP

  == domain 7  score: -0.9 bits;  conditional E-value: 3.1
                            TPR_17  22 lllknGdlmtA 32 
                                       l+++++++++A
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRA 474
                                       899******98 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.2    0.0023       2.1       1      75 [.      96     171 ..      96     177 .. 0.87
   2 !    7.6   0.1    0.0049       4.4      15      57 ..     212     255 ..     195     261 .. 0.84
   3 !   10.4   0.1   0.00064      0.57      26      78 ..     290     343 ..     270     355 .. 0.71
   4 ?    3.6   0.2     0.086        77       4      49 ..     403     448 ..     367     453 .. 0.73
   5 ?    1.7   0.0      0.34     3e+02      36      81 ..     505     552 ..     499     553 .. 0.67

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0023
                                       HTT-HHHHHHHHHHHH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHH CS
                            ANAPC3   1 dqnnyknAiflaerllaaetespedayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeA 75 
                                       ++++y +A   ++ +la ++ ++e  y +   l ++ +y+ A++ l+ + kl +    +  l  +cl+ L+k  +A
  gi|518653159|ref|YP_008142679.1|  96 ENYDYSDAKKRIDMALALDPLNYEYHYIKVNLLIERRDYEGALKELHVMeKLVPDKASVYSLESRCLINLGKNFDA 171
                                       588999*******************************************666555556666666******997776 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0049
                                       HH.HHH--HHHHHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HH CS
                            ANAPC3  15 llaaetespedayllAlclylngqykrAyellrka.klnskslg 57 
                                       +l+ +++++e+   l++ + ++++++ A+e ++ka ++++ +++
  gi|518653159|ref|YP_008142679.1| 212 ALKVDPQDAESYAVLSELHMEMKNFDAAHESAKKAiNIEKDNIK 255
                                       45689******************************888877765 PP

  == domain 3  score: 10.4 bits;  conditional E-value: 0.00064
                                       HHHHHHHHHHTT-HHHHHHHHHCT.SHHHC-HHHHHHHHHHHHHTT-HHHHHHH CS
                            ANAPC3  26 ayllAlclylngqykrAyellrka.klnskslgcrylfAqcllkLkkyeeAiaa 78 
                                       +  l  cly++g+ + A ++++k+ k+n+ +++ +  +A+  +  +++++A ++
  gi|518653159|ref|YP_008142679.1| 290 IVQLTNCLYESGNREDAVKIAEKFyKINPGNMNFAHNLAHIFILENRIQDAGKV 343
                                       566778888888888888888888888888888777777766655666666544 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.086
                                       -HHHHHHHHHHHH.HHH--HHHHHH...HHHHHHHTT-HHHHHHHHHCT CS
                            ANAPC3   4 nyknAiflaerllaaetespedayl...lAlclylngqykrAyellrka 49 
                                       ++k+A++++ +l+    ++ +++++   +Al l l+g+ ++ +++l+++
  gi|518653159|ref|YP_008142679.1| 403 DHKDALIIIKLLY---GQNKDSILYkveYALELALTGNSDESLRILENF 448
                                       6788888888888...444444444233688888888877777777776 PP

  == domain 5  score: 1.7 bits;  conditional E-value: 0.34
                                       TT-HHHHHHHHHCT.SHHHC-H.HHHHHHHHHHHHTT-HHHHHHHH-S CS
                            ANAPC3  36 ngqykrAyellrka.klnsksl.gcrylfAqcllkLkkyeeAiaaLek 81 
                                        g   +A+++++ + + ++  l  +++ +  c l ++ y++++++Le 
  gi|518653159|ref|YP_008142679.1| 505 KGWKIQAIKFIDALiERAEGELqDICIACKGCILGIDDYDKGRDILEQ 552
                                       5555578888888854444444244444558889************96 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1       9.4   8.5e+03      20      29 ..      84      93 ..      83      96 .. 0.72
   2 ?   -2.2   0.2         8   7.1e+03       2      22 ..     119     139 ..     118     141 .. 0.82
   3 ?   -1.2   0.0       3.6   3.2e+03       2      22 ..     160     180 ..     159     181 .. 0.83
   4 ?    4.2   0.1     0.066        59       2      34 .]     187     219 ..     187     219 .. 0.93
   5 !   17.2   0.3   4.8e-06    0.0043       1      34 []     220     253 ..     220     253 .. 0.96
   6 ?    5.3   0.0     0.031        27      10      33 ..     296     319 ..     289     320 .. 0.88
   7 !    7.0   0.0    0.0088       7.9       5      32 ..     325     352 ..     323     354 .. 0.94
   8 ?   -1.4   0.2       4.4   3.9e+03      10      24 ..     464     478 ..     463     483 .. 0.78
   9 ?    2.6   0.1      0.22     2e+02      10      31 ..     501     522 ..     500     524 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 9.4
                                      HHHHHHHHHH CS
                             TPR_8 20 Akeyyekale 29
                                      A + +eka+ 
  gi|518653159|ref|YP_008142679.1| 84 ASKNMEKAIG 93
                                      6677888886 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 8
                                       CHHHHHHHHHHHTT-HHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAke 22 
                                       e++y + +++++  dye A +
  gi|518653159|ref|YP_008142679.1| 119 EYHYIKVNLLIERRDYEGALK 139
                                       678889999999999998866 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 3.6
                                       CHHHHHHHHHHHTT-HHHHHH CS
                             TPR_8   2 eayynlgsiylklgdyeeAke 22 
                                       + + nlg+  +  g+ +eA e
  gi|518653159|ref|YP_008142679.1| 160 RCLINLGKNFDAVGKADEALE 180
                                       678899999999999999976 PP

  == domain 4  score: 4.2 bits;  conditional E-value: 0.066
                                       CHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   2 eayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       +ay n+  ++++ g ++ A  +y  al+ dp++
  gi|518653159|ref|YP_008142679.1| 187 QAYENKLIALQNIGLINDAFDVYYSALKVDPQD 219
                                       589999999**********************86 PP

  == domain 5  score: 17.2 bits;  conditional E-value: 4.8e-06
                                       CCHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHH. CS
                             TPR_8   1 aeayynlgsiylklgdyeeAkeyyekaleldpdn 34 
                                       ae+y  l+ ++++++++++A e+ +ka+ +++dn
  gi|518653159|ref|YP_008142679.1| 220 AESYAVLSELHMEMKNFDAAHESAKKAINIEKDN 253
                                       799***************************9986 PP

  == domain 6  score: 5.3 bits;  conditional E-value: 0.031
                                       HHHHTT-HHHHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleldpd 33 
                                       ++ + g+ e A++  ek  +++p 
  gi|518653159|ref|YP_008142679.1| 296 CLYESGNREDAVKIAEKFYKINPG 319
                                       56789*****************96 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
                             TPR_8   5 ynlgsiylklgdyeeAkeyyekaleldp 32 
                                       +nl++i +  ++++ A ++y+  ++l++
  gi|518653159|ref|YP_008142679.1| 325 HNLAHIFILENRIQDAGKVYKNSIKLNK 352
                                       79************************98 PP

  == domain 8  score: -1.4 bits;  conditional E-value: 4.4
                                       HHHHTT-HHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyy 24 
                                       +y+ l++y+ A ey 
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRANEYA 478
                                       788899***998885 PP

  == domain 9  score: 2.6 bits;  conditional E-value: 0.22
                                       HHHHTT-HHHHHHHHHHHHHHH CS
                             TPR_8  10 iylklgdyeeAkeyyekaleld 31 
                                       +yl++g + +A++++   +e +
  gi|518653159|ref|YP_008142679.1| 501 TYLEKGWKIQAIKFIDALIERA 522
                                       79*************9999876 PP

>> TPR_15  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.12   1.1e+02       6      46 ..     114     155 ..     109     208 .. 0.71
   2 !   16.7   0.2   3.6e-06    0.0032      41     270 ..     217     444 ..     203     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.12
                            TPR_15   6 kplnealkl..atllykqgdvkkAlevLkeaaqkaapskdtey 46 
                                       +pln  +++   +ll +++d+++Al+ L   ++k  p+k+  y
  gi|518653159|ref|YP_008142679.1| 114 DPLNYEYHYikVNLLIERRDYEGALKEL-HVMEKLVPDKASVY 155
                                       5677778777789999**********99.67788777777666 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 3.6e-06
                            TPR_15  41 skdteyWrtladLAwalqqedearkAyrqLlasgkaraedyerliel.lydaepkeaarlaekgwrrfrsprl...L 113
                                       ++d+e +  l++L  +++++d+a + +++ ++++k +++  + l+ + + d   ++ ++   +++   +   +   L
  gi|518653159|ref|YP_008142679.1| 217 PQDAESYAVLSELHMEMKNFDAAHESAKKAINIEKDNIKANNMLVSIaRVDGGIEDYIKALSDAYVNTHYEGYivqL 293
                                       56667778899999999999999999999999999999999999999888999999999999999988877661125 PP

                            TPR_15 114 ssalellerakdydriaellksleeeeaaeqsaafllaraelyrqegqtdaAlrdyreAlalapdsselraallWll 190
                                       ++ l+   + +d+ +iae + ++ +     ++  f   +a +   e++ ++A ++y++ ++l+   +    +++ +l
  gi|518653159|ref|YP_008142679.1| 294 TNCLYESGNREDAVKIAEKFYKINP-----GNMNFAHNLAHIFILENRIQDAGKVYKNSIKLNKS-EFTNLQYITFL 364
                                       5555555566666666666666553.....444455566666777899999***********987.677889***** PP

                            TPR_15 191 iDlgrraeLrellkawkara.esdasLwgplaaAlllLgrpkkALeylrkqakenrkdplwllaYADaleqagrade 266
                                       ++++++a + + + ++ ar  ++d  L++ + a l++ g+ k AL  ++  + +n++++l ++ YA  l   g+ de
  gi|518653159|ref|YP_008142679.1| 365 NETEQYAAVLKNVDELIARYpDNDGFLYNKFYA-LSRGGDHKDALIIIKLLYGQNKDSILYKVEYALELALTGNSDE 440
                                       *******96666666666666999999999975.6788**************************************9 PP

                            TPR_15 267 Awrl 270
                                       + r+
  gi|518653159|ref|YP_008142679.1| 441 SLRI 444
                                       9886 PP

>> TPR_12  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0017       1.5      44      76 ..     158     190 ..     153     191 .. 0.88
   2 !    8.3   0.1    0.0031       2.8      39      74 ..     214     249 ..     195     252 .. 0.82
   3 ?    2.1   0.0      0.27   2.5e+02      51      70 ..     293     312 ..     258     318 .. 0.74
   4 ?    1.3   0.0      0.48   4.3e+02       6      35 ..     324     353 ..     320     366 .. 0.82
   5 ?   -0.4   0.1       1.7   1.5e+03      45      69 ..     422     446 ..     398     452 .. 0.61
   6 ?   -1.0   0.1       2.5   2.2e+03      54      67 ..     464     477 ..     463     483 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0017
                            TPR_12  44 tattlrnLgrlyralgryeeAlelleealaiae 76 
                                       ++++l+nLg  ++a g+ +eAle+ +  ++++e
  gi|518653159|ref|YP_008142679.1| 158 ESRCLINLGKNFDAVGKADEALEHDRNYMQAYE 190
                                       689********************9887777776 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0031
                            TPR_12  39 pdhpltattlrnLgrlyralgryeeAlelleealai 74 
                                       +  p+ a+++  L++l+ +++++++A+e  ++a++i
  gi|518653159|ref|YP_008142679.1| 214 KVDPQDAESYAVLSELHMEMKNFDAAHESAKKAINI 249
                                       446889***************************987 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.27
                            TPR_12  51 LgrlyralgryeeAlellee 70 
                                       L  +++++g+ e+A+++ e+
  gi|518653159|ref|YP_008142679.1| 293 LTNCLYESGNREDAVKIAEK 312
                                       55677777777777777776 PP

  == domain 4  score: 1.3 bits;  conditional E-value: 0.48
                            TPR_12   6 lnnlaavlrrlgrydeAlellekaleiarr 35 
                                       ++nla++     r ++A + ++ ++ + ++
  gi|518653159|ref|YP_008142679.1| 324 AHNLAHIFILENRIQDAGKVYKNSIKLNKS 353
                                       569999999999999999999999888755 PP

  == domain 5  score: -0.4 bits;  conditional E-value: 1.7
                            TPR_12  45 attlrnLgrlyralgryeeAlelle 69 
                                       + +   ++  + ++g+ +e l++le
  gi|518653159|ref|YP_008142679.1| 422 ILYKVEYALELALTGNSDESLRILE 446
                                       4555555566666666666666665 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 2.5
                            TPR_12  54 lyralgryeeAlel 67 
                                       ly++l++y+ A e+
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRANEY 477
                                       79999999999887 PP

>> HrpB1_HrpK  Bacterial type III secretion protein (HrpB1_HrpK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.9e-06    0.0017      23     107 ..      96     181 ..      87     189 .. 0.84
   2 ?   -0.5   0.0         1   9.2e+02      20      69 ..     295     345 ..     274     356 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.9e-06
                        HrpB1_HrpK  23 asedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLreveaeasgtpyakaLlAlcLaalrDe.eWr 98 
                                       ++ d  da++ +d   +L P + e + + ++llier+++e+Al+ L+ +e+  +  + + +L + cL +l+ + +  
  gi|518653159|ref|YP_008142679.1|  96 ENYDYSDAKKRIDMALALDPLNYEYHYIKVNLLIERRDYEGALKELHVMEKLVPDKASVYSLESRCLINLGKNfDAV 172
                                       5567788999999999***************************************************9886431444 PP

                        HrpB1_HrpK  99 ayAeevles 107
                                         A+e+le+
  gi|518653159|ref|YP_008142679.1| 173 GKADEALEH 181
                                       556666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 1
                        HrpB1_HrpK  20 lal.asedtedaellLdalrvLrPevaeldllegvlliergrweeAlrlLr 69 
                                         l +s++ eda ++ +    + P + +++   + + i ++r+++A ++ +
  gi|518653159|ref|YP_008142679.1| 295 NCLyESGNREDAVKIAEKFYKINPGNMNFAHNLAHIFILENRIQDAGKVYK 345
                                       3334888999999999999999999999999999999*99***99988765 PP

>> TPR_11  TPR repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.69   6.2e+02      20      32 ..     110     122 ..     106     122 .. 0.95
   2 ?    2.2   0.0      0.16   1.4e+02       3      32 ..     127     156 ..     126     157 .. 0.84
   3 ?   -1.6   0.1       2.4   2.2e+03      19      33 ..     177     191 ..     170     192 .. 0.81
   4 !    9.4   0.1    0.0009      0.81      10      34 ..     202     226 ..     199     234 .. 0.82
   5 ?    3.4   0.2     0.069        62       6      32 ..     232     258 ..     228     260 .. 0.81
   6 ?   -2.8   0.0       6.1   5.5e+03      14      21 ..     270     277 ..     265     278 .. 0.81
   7 ?    3.7   0.0     0.054        48       2      26 ..     329     353 ..     328     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.69
                            TPR_11  20 AlkldPdnaeayy 32 
                                       Al+ldP n e +y
  gi|518653159|ref|YP_008142679.1| 110 ALALDPLNYEYHY 122
                                       9********9999 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.16
                            TPR_11   3 ayyeqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       ++ e+ +ye+A++++    kl Pd a++y+
  gi|518653159|ref|YP_008142679.1| 127 LLIERRDYEGALKELHVMEKLVPDKASVYS 156
                                       6677889******99999999999999985 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 2.4
                            TPR_11  19 kAlkldPdnaeayyn 33 
                                       +Al+ d ++  ay n
  gi|518653159|ref|YP_008142679.1| 177 EALEHDRNYMQAYEN 191
                                       688888888888866 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0009
                            TPR_11  10 yeeAieaYkkAlkldPdnaeayynL 34 
                                       +++A  +Y  Alk dP++ae y  L
  gi|518653159|ref|YP_008142679.1| 202 INDAFDVYYSALKVDPQDAESYAVL 226
                                       5788999*************99655 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.069
                            TPR_11   6 eqGkyeeAieaYkkAlkldPdnaeayy 32 
                                       e  ++++A e+ kkA+++  dn  a +
  gi|518653159|ref|YP_008142679.1| 232 EMKNFDAAHESAKKAINIEKDNIKANN 258
                                       5667888888889*********98865 PP

  == domain 6  score: -2.8 bits;  conditional E-value: 6.1
                            TPR_11  14 ieaYkkAl 21 
                                       ie+Y kAl
  gi|518653159|ref|YP_008142679.1| 270 IEDYIKAL 277
                                       99*****8 PP

  == domain 7  score: 3.7 bits;  conditional E-value: 0.054
                            TPR_11   2 dayyeqGkyeeAieaYkkAlkldPd 26 
                                       +++   +++ +A ++Yk+ +kl+ +
  gi|518653159|ref|YP_008142679.1| 329 HIFILENRIQDAGKVYKNSIKLNKS 353
                                       67888999**************976 PP

>> BTAD  Bacterial transcriptional activator domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.21   1.9e+02      72     124 ..     162     214 ..     139     234 .. 0.80
   2 ?    5.2   0.0     0.029        26      50     117 ..     242     308 ..     230     316 .. 0.75
   3 ?    6.6   0.0     0.011       9.7      74     116 ..     366     408 ..     348     414 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.21
                                       HHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                              BTAD  72 elrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALevYerlrr 124
                                       ++ lG+  +a+++++++++++    ++++  + Al   G  ++A  vY ++ +
  gi|518653159|ref|YP_008142679.1| 162 LINLGKNFDAVGKADEALEHDRNYMQAYENKLIALQNIGLINDAFDVYYSALK 214
                                       47888888999999999999988899999999999999999999999987755 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHHH CS
                              BTAD  50 leaererleelrlealealaeaelrlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeALe 117
                                         +++  +e++ ++a   l+      G +e+ ++ l+++   + + E +  ql  +l+ sG++++A +
  gi|518653159|ref|YP_008142679.1| 242 SAKKAINIEKDNIKANNMLVSIARVDGGIEDYIKALSDAYV-NTHYEGYIVQLTNCLYESGNREDAVK 308
                                       55566667778888888888877777888888888777644.44679999****************87 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.011
                                       HTT-HHHHHHHHHHHHHHSTT-HHHHHHHHHHHHHTT-HHHHH CS
                              BTAD  74 rlGraeealaelealvaehPlrErlhrqlmrAlarsGrqaeAL 116
                                       + ++++++l+  ++l+a +P ++ +    + Al r G+  +AL
  gi|518653159|ref|YP_008142679.1| 366 ETEQYAAVLKNVDELIARYPDNDGFLYNKFYALSRGGDHKDAL 408
                                       5678999***********************************9 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       5.7   5.1e+03      24      32 ..     107     115 ..      99     115 .. 0.65
   2 ?    2.2   0.0       0.2   1.8e+02       2      23 ..     160     181 ..     159     181 .. 0.91
   3 ?    4.0   0.0     0.054        48      10      34 .]     195     219 ..     194     219 .. 0.86
   4 !    7.4   0.1    0.0045         4      10      34 .]     229     253 ..     223     253 .. 0.92
   5 ?   -1.9   0.0       3.8   3.4e+03      21      28 ..     270     277 ..     268     278 .. 0.89
   6 ?   -0.5   0.0       1.4   1.3e+03       9      32 ..     295     318 ..     295     320 .. 0.75
   7 !    6.7   0.1    0.0073       6.6       6      32 ..     326     352 ..     325     354 .. 0.95
   8 ?   -0.8   0.1       1.8   1.6e+03      10      20 ..     464     474 ..     463     477 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 5.7
                                       HHHHHHHST CS
                             TPR_1  24 yekALelnP 32 
                                        + AL l+P
  gi|518653159|ref|YP_008142679.1| 107 IDMALALDP 115
                                       567888888 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.2
                                       HHHHHHHHHHHHTT-HHHHHHH CS
                             TPR_1   2 kalynlGnayfklgkydeAley 23 
                                       ++l nlG  +   gk deAle+
  gi|518653159|ref|YP_008142679.1| 160 RCLINLGKNFDAVGKADEALEH 181
                                       6799****************97 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.054
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       a+++ g  ++A + y  AL+++P++
  gi|518653159|ref|YP_008142679.1| 195 ALQNIGLINDAFDVYYSALKVDPQD 219
                                       5677788899*************86 PP

  == domain 4  score: 7.4 bits;  conditional E-value: 0.0045
                                       HHHHTT-HHHHHHHHHHHHHHSTTH CS
                             TPR_1  10 ayfklgkydeAleyyekALelnPnn 34 
                                       ++++++++d A e  +kA+ ++ +n
  gi|518653159|ref|YP_008142679.1| 229 LHMEMKNFDAAHESAKKAINIEKDN 253
                                       6899***************998876 PP

  == domain 5  score: -1.9 bits;  conditional E-value: 3.8
                                       HHHHHHHH CS
                             TPR_1  21 leyyekAL 28 
                                       +e+y kAL
  gi|518653159|ref|YP_008142679.1| 270 IEDYIKAL 277
                                       89*****9 PP

  == domain 6  score: -0.5 bits;  conditional E-value: 1.4
                                       HHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   9 nayfklgkydeAleyyekALelnP 32 
                                       n++++ g+ ++A++  ek  ++nP
  gi|518653159|ref|YP_008142679.1| 295 NCLYESGNREDAVKIAEKFYKINP 318
                                       799999**9999986666555555 PP

  == domain 7  score: 6.7 bits;  conditional E-value: 0.0073
                                       HHHHHHHHTT-HHHHHHHHHHHHHHST CS
                             TPR_1   6 nlGnayfklgkydeAleyyekALelnP 32 
                                       nl++++   ++ ++A + y+  ++ln 
  gi|518653159|ref|YP_008142679.1| 326 NLAHIFILENRIQDAGKVYKNSIKLNK 352
                                       9************************96 PP

  == domain 8  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHHTT-HHHH CS
                             TPR_1  10 ayfklgkydeA 20 
                                       +y  l++yd A
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRA 474
                                       6999*****98 PP

>> TPR_MalT  MalT-like TPR region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.5e-05     0.013      94     262 ..     200     343 ..     153     352 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.5e-05
                          TPR_MalT  94 GrLheAletyeqalqlateqglqqlplvgfllvlladllyEwndLeeAeqhlqeGielleqlepeaaldayvllari 170
                                       G   +A+++y+ al++ ++  ++        +++l++l+ E+ ++++A++ ++++i + ++      ++a+ +l+ i
  gi|518653159|ref|YP_008142679.1| 200 GLINDAFDVYYSALKVDPQDAES--------YAVLSELHMEMKNFDAAHESAKKAINIEKDN-----IKANNMLVSI 263
                                       67778888888888866666555........7888***********************9987.....8888888888 PP

                          TPR_MalT 171 alaqGdleeAetllekaeelaresnfhvdwlanaeevrvrlwlaqgdlaaaerwleaaelpsdddnhflelelrnla 247
                                       a + G +e+  ++l  a   ++ + + v +l+n      ++    g+ ++a++ +e+  +  +++  f    ++nla
  gi|518653159|ref|YP_008142679.1| 264 ARVDGGIEDYIKALSDAYVNTHYEGYIV-QLTN-----CLY--ESGNREDAVKIAEKFYKINPGNMNF----AHNLA 328
                                       8888888887777777777777666632.2222.....223..4677777777777776666666666....44777 PP

                          TPR_MalT 248 rvllalgrydeAlel 262
                                       ++ ++++r ++A ++
  gi|518653159|ref|YP_008142679.1| 329 HIFILENRIQDAGKV 343
                                       777777777776665 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1    0.0002      0.18       8      35 ..      91     118 ..      90     121 .. 0.91
   2 ?   -0.8   0.0       1.8   1.6e+03      20      37 ..     171     188 ..     164     190 .. 0.84
   3 ?    2.4   0.0      0.19   1.7e+02      11      39 ..     230     258 ..     226     265 .. 0.86
   4 ?    0.8   0.0      0.57   5.1e+02      14      36 ..     300     322 ..     292     328 .. 0.84
   5 ?   -2.6   0.1       6.5   5.9e+03      14      24 ..     468     478 ..     467     483 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                                       HHHHHHHT-HHHHHHHHHHHHHHTTS-H CS
                        Fis1_TPR_C   8 AlGhyklgeYseArryvdalLeiEPenr 35 
                                       A+G +   +Ys+A++ +d+ L+++P n 
  gi|518653159|ref|YP_008142679.1|  91 AIGLMENYDYSDAKKRIDMALALDPLNY 118
                                       78888999*****************995 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
                                       HHHHHHHHHHHTTS-HHH CS
                        Fis1_TPR_C  20 ArryvdalLeiEPenrQa 37 
                                       A   +d  Le++ + +Qa
  gi|518653159|ref|YP_008142679.1| 171 AVGKADEALEHDRNYMQA 188
                                       66678999*********9 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.19
                                       HHHHT-HHHHHHHHHHHHHHTTS-HHHHH CS
                        Fis1_TPR_C  11 hyklgeYseArryvdalLeiEPenrQaqs 39 
                                       h+ +++++ A + ++  ++iE +n  a++
  gi|518653159|ref|YP_008142679.1| 230 HMEMKNFDAAHESAKKAINIEKDNIKANN 258
                                       6679********************88876 PP

  == domain 4  score: 0.8 bits;  conditional E-value: 0.57
                                       HT-HHHHHHHHHHHHHHTTS-HH CS
                        Fis1_TPR_C  14 lgeYseArryvdalLeiEPenrQ 36 
                                        g+ ++A + ++ + +i P+n++
  gi|518653159|ref|YP_008142679.1| 300 SGNREDAVKIAEKFYKINPGNMN 322
                                       677789***************97 PP

  == domain 5  score: -2.6 bits;  conditional E-value: 6.5
                                       HT-HHHHHHHH CS
                        Fis1_TPR_C  14 lgeYseArryv 24 
                                       l +Y++A +y+
  gi|518653159|ref|YP_008142679.1| 468 LNQYDRANEYA 478
                                       679****9997 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       6.7     6e+03       5      21 ..     164     180 ..     160     188 .. 0.71
   2 ?    5.6   0.0     0.032        29       9      32 ..     296     319 ..     290     320 .. 0.85
   3 ?    0.2   0.0       1.7   1.5e+03      25      33 .]     379     387 ..     378     387 .. 0.86
   4 ?    1.0   0.0      0.92   8.3e+02      12      30 ..     434     452 ..     426     452 .. 0.76
   5 ?   -0.2   0.0       2.2     2e+03       8      22 ..     462     477 ..     462     478 .. 0.79
   6 ?   -1.7   0.0       6.6   5.9e+03      14      26 ..     541     553 ..     534     555 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 6.7
                                       HHHHHHHHHHHHHHHHH CS
                             TPR_6   5 klalsyrklgdtdkAle 21 
                                       +l++ + + g++d+Ale
  gi|518653159|ref|YP_008142679.1| 164 NLGKNFDAVGKADEALE 180
                                       56666777458888876 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.032
                                       HHHHHHHHHHHHHHHHHHHHH-TT CS
                             TPR_6   9 syrklgdtdkAlealerlikeYPd 32 
                                       ++++ g+ ++A+++ e++ k  P+
  gi|518653159|ref|YP_008142679.1| 296 CLYESGNREDAVKIAEKFYKINPG 319
                                       888867************998886 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 1.7
                                       HHHHH-TT- CS
                             TPR_6  25 rlikeYPdS 33 
                                       +li +YPd+
  gi|518653159|ref|YP_008142679.1| 379 ELIARYPDN 387
                                       79*****95 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.92
                                       HHHHHHHHHHHHHHHHHH- CS
                             TPR_6  12 klgdtdkAlealerlikeY 30 
                                        +g++d++l++le++ + Y
  gi|518653159|ref|YP_008142679.1| 434 LTGNSDESLRILENFEELY 452
                                       358**********997665 PP

  == domain 5  score: -0.2 bits;  conditional E-value: 2.2
                                       HHHHH.HHHHHHHHHH CS
                             TPR_6   8 lsyrk.lgdtdkAlea 22 
                                       +s+++ l+++d+A e+
  gi|518653159|ref|YP_008142679.1| 462 WSLYSmLNQYDRANEY 477
                                       57777689*****886 PP

  == domain 6  score: -1.7 bits;  conditional E-value: 6.6
                                       HHHHHHHHHHHHH CS
                             TPR_6  14 gdtdkAlealerl 26 
                                       +d+dk +++le++
  gi|518653159|ref|YP_008142679.1| 541 DDYDKGRDILEQI 553
                                       599*******996 PP

>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       4.5   4.1e+03       8      27 ..      84     103 ..      83     142 .. 0.72
   2 ?   14.7   0.1   2.8e-05     0.025      71     114 ..     268     316 ..     224     320 .. 0.89
   3 ?   -1.7   0.0       3.4   3.1e+03      85      92 ..     380     387 ..     325     397 .. 0.57
   4 ?   -2.8   0.0       7.4   6.6e+03      26      39 ..     421     434 ..     413     453 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
                                       HHHHHHHHHHHHHTT-HHHH CS
                              HEPN   8 AeedleaAellleegdydla 27 
                                       A +++e+A  l+e+ dy++a
  gi|518653159|ref|YP_008142679.1|  84 ASKNMEKAIGLMENYDYSDA 103
                                       66677777777777777766 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 2.8e-05
                                       HHHHHHHHHHHCCCHHCCCTSS--S.....--HHHHHHHHHHHHHHHHH CS
                              HEPN  71 eelreeleeLekayiesrYpdakee.....yteedaeealkdaeevlel 114
                                         ++++++ L++ay+++ Y+ + ++     y++ + e+a+k+ae+++++
  gi|518653159|ref|YP_008142679.1| 268 GGIEDYIKALSDAYVNTHYEGYIVQltnclYESGNREDAVKIAEKFYKI 316
                                       468999****************************************985 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 3.4
                                       HHCCCTSS CS
                              HEPN  85 iesrYpda 92 
                                         +rYpd 
  gi|518653159|ref|YP_008142679.1| 380 LIARYPDN 387
                                       24566665 PP

  == domain 4  score: -2.8 bits;  conditional E-value: 7.4
                                       HHHHHHHHHHHHHH CS
                              HEPN  26 lacfhaqqaaekal 39 
                                       + ++++++a+e+al
  gi|518653159|ref|YP_008142679.1| 421 SILYKVEYALELAL 434
                                       56677778888776 PP

>> DUF3856  Domain of Unknown Function (DUF3856)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3     0.001       0.9      49      83 ..     214     248 ..     160     253 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.001
                                       -HHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH CS
                           DUF3856  49 dheGfdalchaglsealaklgrydealesadkalr 83 
                                         +  da  +a+lse  ++++++d+a esa+ka++
  gi|518653159|ref|YP_008142679.1| 214 KVDPQDAESYAVLSELHMEMKNFDAAHESAKKAIN 248
                                       45667999***********************9975 PP

>> TPR_7  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       4.9   4.4e+03      15      24 ..      88      97 ..      86     118 .. 0.56
   2 ?   -0.9   0.0       2.5   2.3e+03       1      21 [.     161     181 ..     161     184 .. 0.87
   3 ?    1.6   0.0       0.4   3.6e+02       4      23 ..     292     311 ..     290     313 .. 0.82
   4 ?    4.9   0.0     0.035        32       3      32 ..     325     354 ..     324     357 .. 0.91
   5 ?   -2.3   0.0       6.8   6.1e+03       8      21 ..     464     477 ..     463     488 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 4.9
                             TPR_7 15 yeeAielyeq 24
                                      +e+Ai+l e 
  gi|518653159|ref|YP_008142679.1| 88 MEKAIGLMEN 97
                                      6777777665 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 2.5
                             TPR_7   1 aLlnLarlysrlGdyeeAiel 21 
                                       +L nL+  + ++G+ +eA+e+
  gi|518653159|ref|YP_008142679.1| 161 CLINLGKNFDAVGKADEALEH 181
                                       688999999999*99*99986 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.4
                             TPR_7   4 nLarlysrlGdyeeAielye 23 
                                       +L ++  + G++e+A+++ e
  gi|518653159|ref|YP_008142679.1| 292 QLTNCLYESGNREDAVKIAE 311
                                       688888899*******8765 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.035
                             TPR_7   3 lnLarlysrlGdyeeAielyeqsLaltkdp 32 
                                       +nLa+++  +++ ++A ++y+ s+ l k++
  gi|518653159|ref|YP_008142679.1| 325 HNLAHIFILENRIQDAGKVYKNSIKLNKSE 354
                                       7*********************99988876 PP

  == domain 5  score: -2.3 bits;  conditional E-value: 6.8
                             TPR_7   8 lysrlGdyeeAiel 21 
                                       lys l++y++A e+
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRANEY 477
                                       67778999999555 PP

>> TPR_10  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       4.4   3.9e+03      11      24 ..     127     140 ..     126     142 .. 0.79
   2 ?    3.9   0.1      0.06        54       3      27 ..     160     184 ..     159     193 .. 0.84
   3 ?    7.3   0.0    0.0049       4.4       2      31 ..     220     249 ..     220     252 .. 0.93
   4 ?    3.4   0.0     0.085        76      12      27 ..     297     312 ..     292     316 .. 0.90
   5 ?   -0.6   0.1       1.5   1.4e+03      11      29 ..     464     482 ..     463     483 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.4
                            TPR_10  11 alrqrgrydeAeal 24 
                                       +l +r++y++A++ 
  gi|518653159|ref|YP_008142679.1| 127 LLIERRDYEGALKE 140
                                       6778999***9986 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.06
                            TPR_10   3 sslnNLanalrqrgrydeAeallee 27 
                                       ++l NL+    ++g+ deA+++ + 
  gi|518653159|ref|YP_008142679.1| 160 RCLINLGKNFDAVGKADEALEHDRN 184
                                       6999****************98775 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0049
                            TPR_10   2 AsslnNLanalrqrgrydeAealleealai 31 
                                       A s+  L+ ++ +++++d+A + +++a++i
  gi|518653159|ref|YP_008142679.1| 220 AESYAVLSELHMEMKNFDAAHESAKKAINI 249
                                       779999**********************98 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.085
                            TPR_10  12 lrqrgrydeAeallee 27 
                                       l++ g++++A++++e+
  gi|518653159|ref|YP_008142679.1| 297 LYESGNREDAVKIAEK 312
                                       7999*********997 PP

  == domain 5  score: -0.6 bits;  conditional E-value: 1.5
                            TPR_10  11 alrqrgrydeAealleeal 29 
                                       +++ +++yd+A ++++ a+
  gi|518653159|ref|YP_008142679.1| 464 LYSMLNQYDRANEYAILAM 482
                                       59999******99988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (586 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       760  (0.0423894); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.73u 0.31s 00:00:01.04 Elapsed: 00:00:00.54
# Mc/sec: 3266.10
//
Query:       gi|518653160|ref|YP_008142680.1|  [L=72]
Description: hypothetical protein FACI_IFERC00001G1801 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   14.3   0.1      0.042   14.0   0.1    1.1  1  DUF3408   Protein of unknown function (DUF3408)


Domain annotation for each model (and alignments):
>> DUF3408  Protein of unknown function (DUF3408)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   2.4e-06     0.042      97     128 ..      26      57 ..      24      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.4e-06
                           DUF3408  97 arIvrvlgerkmsvsayvdnilrhHLeeYkee 128
                                       ++I + +++    vs +v+n+l + L+ +k e
  gi|518653160|ref|YP_008142680.1|  26 DEIYKNIADSHSDVSKFVNNVLGQYLDAFKPE 57 
                                       5788999*********************9865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); 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: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.43
# Mc/sec: 508.45
//
Query:       gi|518653161|ref|YP_008142681.1|  [L=334]
Description: FAD-dependent pyridine nucleotide-disulfide oxidoreductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.2e-31  108.0   2.0    1.2e-30  106.8   2.0    1.6  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.6e-11   43.1   0.2    4.6e-11   43.1   0.2    2.7  3  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    3.7e-10   39.5   1.7      2e-08   33.8   1.8    2.4  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
     0.0065   16.1   0.1       0.37   10.3   0.0    2.5  2  DAO            FAD dependent oxidoreductase
     0.0075   16.2   0.0      0.013   15.4   0.0    1.4  1  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
  ------ inclusion threshold ------
      0.026   13.7   0.1      0.052   12.7   0.0    1.5  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.032   14.5   0.0        2.5    8.4   0.0    2.5  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.13   12.2   0.0       0.26   11.2   0.0    1.5  1  Pput2613-deam  Pput_2613-like deaminase


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 !  106.8   2.0   5.2e-34   1.2e-30      67     287 ..      57     261 ..       3     275 .. 0.78

  Alignments for each domain:
  == domain 1  score: 106.8 bits;  conditional E-value: 5.2e-34
                                       CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-T. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                       Pyr_redox_2  67 ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllp. 142
                                       i+  l+e+v +i +++++++       +  k +y kl++A G s +  +i+G  +n  kl +t+d+a  +++ l+  
  gi|518653161|ref|YP_008142681.1|  57 ID--LKENVKDINFENREIVTD-----N-GKHEYSKLIIALGHSYNVNNIKGS-TNIAKL-ETIDDAVNIRKRLQTs 123
                                       44..334699999999888882.....2.3689*********999999*****.666666.*********9999988 PP

                                       SEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 143 krivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevv 219
                                       k+++++GgGy GvE+A+ +   gk+vt+++  drll+   +e+s+++++ l +++v++  gt+v e++g++     v
  gi|518653161|ref|YP_008142681.1| 124 KNVTIIGGGYLGVEIASLI--NGKKVTIIDPHDRLLNHSSPEASEYVNNMLLARNVNITKGTKVMEVTGKS-----V 193
                                       *****************95..488********************************************888.....4 PP

                                       ETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE.SSTTEEE-GGGC..TECCSS--H CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx..xxxxxxxxx RF
                       Pyr_redox_2 220 ledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrt.nvpgiyaiGDva..ggkggpela 287
                                        +d+eei  dl ++a G+  ++ +   +l +++ ++ +i+v++++r+ + ++++a+GD    +gk+ p++a
  gi|518653161|ref|YP_008142681.1| 194 ITDNEEITSDLTIYAGGIYGNSII--SDLPIKT-KNSKILVNSKMRSlSYDDVFACGDSMaiDGKSFPATA 261
                                       788889***************966..7999999.***********9956*********8888444444444 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.4       1.3   2.9e+03       2      12 ..       5      15 ..       4      17 .. 0.86
   2 ?   -2.6   0.1       3.7   8.2e+03      51      71 ..      83     103 ..      60     111 .. 0.72
   3 !   43.1   0.2     2e-14   4.6e-11       1      70 [.     125     192 ..     125     198 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 1.3
                                      EEEECSSHHHH CS
                         Pyr_redox  2 vvvvGgGyigl 12
                                      + ++GgG++g+
  gi|518653161|ref|YP_008142681.1|  5 IYILGGGLSGI 15
                                      679*****997 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 3.7
                                       HHTTEEEECSEEEEEEEEETT CS
                         Pyr_redox  51 ekngievllntkveeiegsed 71 
                                       +k+ i + ++ +v++i+gs++
  gi|518653161|ref|YP_008142681.1|  83 SKLIIALGHSYNVNNIKGSTN 103
                                       455566667778888887776 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 2e-14
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEET CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegse 70 
                                       +v+++GgGy+g+E A+ ++  gkkVt+++ +d+ll+   +eas+++ + l ++++++  +tkv e++g++
  gi|518653161|ref|YP_008142681.1| 125 NVTIIGGGYLGVEIASLIN--GKKVTIIDPHDRLLNHSSPEASEYVNNMLLARNVNITKGTKVMEVTGKS 192
                                       589***************9..789*******************************************876 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 !   33.8   1.8   9.1e-12     2e-08      96     305 .]      55     247 ..      46     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 33.8 bits;  conditional E-value: 9.1e-12
                       Pyr_redox_3  96 lpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvk...efhkya.gqkvv 168
                                        +i l+e+V++++ e++  e+ t++++ e +k+iiA G     n++ni+G+++ +k    ++     + ++  ++v+
  gi|518653161|ref|YP_008142681.1|  55 RNIDLKENVKDINFENR--EIVTDNGKHEYSKLIIALGH--SYNVNNIKGSTNIAKLETIDDavnIRKRLQtSKNVT 127
                                       58999*******99875..688999999999*******9..7789999**9965544433321102233333789** PP

                       Pyr_redox_3 169 ViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeey 245
                                       +iGg+  +v++A  +  +g++Vt++++++ + +++       +p   + +++++  +++++ + ++v e++ k+   
  gi|518653161|ref|YP_008142681.1| 128 IIGGGYLGVEIASLI--NGKKVTIIDPHDRLLNHS-------SPEASEYVNNMLLARNVNITKGTKVMEVTGKS--- 192
                                       ************755..689********9887774.......67777777777777789***********9874... PP

                       Pyr_redox_3 246 kvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                                        v t++ +++++ d  ++a G   + s++++  +++ ++++++++++  +  ++++f +G
  gi|518653161|ref|YP_008142681.1| 193 -VITDN-EEITS-DLTIYAGGIYGN-SIISDLPIKT-KNSKILVNSKMRSLSYDDVFACG 247
                                       .44555.56665.677888776655.6777555655.899999*************9998 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.3   0.0   0.00016      0.37       2      41 ..     126     165 ..     125     172 .. 0.83
   2 ?    3.4   0.0     0.021        48     156     220 ..     172     225 ..     163     248 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                                       EEEECTSHHHHHHHHHHHHTTEEEEESSSSTTSSGGGSSE CS
                               DAO   2 vviiGGGiiGlstAyeLarrgVtllekgdiagsgaSgrns 41 
                                       v iiGGG+ G+ +A     ++Vt+++ +d++  ++S  +s
  gi|518653161|ref|YP_008142681.1| 126 VTIIGGGYLGVEIASLINGKKVTIIDPHDRLLNHSSPEAS 165
                                       89***************5445*******888778876666 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.021
                                       HHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHH.HHHTTCTTTSEEEEE CS
                               DAO 156 aealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsd.llgllkeldlpispv 220
                                       + a+ v+i +gt+v ++  +   ++ v  t ++e+++ d  + a G++ + ++    +l  pi+  
  gi|518653161|ref|YP_008142681.1| 172 LLARNVNITKGTKVMEV--T---GKSV-ITDNEEITS-DLTIYAGGIYGNsII---SDL--PIKTK 225
                                       46788999999999998..2...3444.233344455.99********88666...555..65544 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 !   15.4   0.0   5.7e-06     0.013       1      64 [.     125     186 ..     125     208 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 5.7e-06
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS-HHHHCCCH CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklkeeeveaal 64 
                                       +v++iG G +G +ia+++  +g +V+++d +++ l+++  ++++ ++++  +++++  +  +++
  gi|518653161|ref|YP_008142681.1| 125 NVTIIGGGYLGVEIASLI--NGKKVTIIDPHDRLLNHSSPEASEYVNNMLLARNVNITKGTKVM 186
                                       69*************986..7999*************999999988888777776654444444 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.3     3e+03     192     203 ..       3      14 ..       2      22 .. 0.85
   2 ?   12.7   0.0   2.3e-05     0.052     134     243 ..      67     174 ..      42     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.3
                       K_oxygenase 192 kriaVvGsGqSa 203
                                       k+i + G+G S+
  gi|518653161|ref|YP_008142681.1|   3 KQIYILGGGLSG 14 
                                       799*******98 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 2.3e-05
                       K_oxygenase 134 tveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedl 210
                                       + e+++   ++ ++e  +l+++ G + ++ ++  +++  +++   +++ + +++l+++k+++++G+G  + ei+  l
  gi|518653161|ref|YP_008142681.1|  67 NFENREIVTDNGKHEYSKLIIALGHSYNVNNIKGSTN-IAKLETIDDAVNIRKRLQTSKNVTIIGGGYLGVEIAS-L 141
                                       4444443445667788899999999999988877776.5777777777777779*******************85.6 PP

                       K_oxygenase 211 lrrqkkvelklvtrsealeplddspfvneifsP 243
                                       ++ +k + ++   r  +    + s+ vn+++ +
  gi|518653161|ref|YP_008142681.1| 142 INGKKVTIIDPHDRLLNHSSPEASEYVNNMLLA 174
                                       666666777777777777777777777777655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.034        77       1      11 [.       7      17 ..       7      56 .. 0.91
   2 ?    8.4   0.0    0.0011       2.5       1      31 [.     128     156 ..     128     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.034
                                      EE--SHHHHHH CS
                     NAD_binding_8  1 IvGaGlsGlva 11
                                      I+G+GlsG +a
  gi|518653161|ref|YP_008142681.1|  7 ILGGGLSGIYA 17
                                      89******987 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0011
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G  G  +A+l+   g++v++++ +drl
  gi|518653161|ref|YP_008142681.1| 128 IIGGGYLGVEIASLIN--GKKVTIIDPHDRL 156
                                       9*************98..78*********97 PP

>> Pput2613-deam  Pput_2613-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00011      0.26      57     105 ..     236     289 ..     226     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00011
                     Pput2613-deam  57 relslqqll..GdvlvidGqyaPCssCkG...kmrvaseetgakvqYtweegge 105
                                       r+ls +++   Gd + idG+  P +   G   ++ ++++ +g ++++++e++g+
  gi|518653161|ref|YP_008142681.1| 236 RSLSYDDVFacGDSMAIDGKSFPATAFTGrksAVVAMKNAMGNDIEFKYENNGN 289
                                       66666776667*************9987722145667889999*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      462  (0.0257683); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 2414.96
//
Query:       gi|518653162|ref|YP_008142682.1|  [L=186]
Description: hypothetical protein FACI_IFERC00001G1803 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.8e-48  164.4   0.0    2.3e-48  164.1   0.0    1.1  1  DJ-1_PfpI  DJ-1/PfpI family
     0.0022   17.7   0.0       0.33   10.6   0.0    2.2  2  ThiJ_like  ThiJ/PfpI family-like


Domain annotation for each model (and alignments):
>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.1   0.0   2.5e-52   2.3e-48       1     164 [.       2     178 ..       2     179 .. 0.99

  Alignments for each domain:
  == domain 1  score: 164.1 bits;  conditional E-value: 2.5e-52
                                       EEEEEEEETTBEHHHHHHHHHHHHHTTEEEEEEESS..............TSEEEETTSEEEE-SEEGGGCTCCG-S CS
                         DJ-1_PfpI   1 kkvlvlladgvedvElivpvdvlkragikvdvvsvd..............keevkgsrGlkvtvdaslddvkaaeyD 63 
                                       +k+l+l++d  e++E+++p++++k++g++vd++ ++               ++++++ G+kv +d +++dv++++yD
  gi|518653162|ref|YP_008142682.1|   2 AKILILTGDAGESLEVMYPLQRMKEEGFDVDLAAPEkkkiqlvvhdfedgFDTYTEKLGYKVQADIAFKDVDPSQYD 78 
                                       59**********************************************9999************************* PP

                                       EEEE--BHHHHHHHHTSHHHHHHHHHHHHTT-EEEEETTTHHHHHHTTTTTTSEE--SGGGHHHHHHTTSEE-SSSE CS
                         DJ-1_PfpI  64 alvlpGGragperlrenekvvelvkefaekgklvaaICagpqlLaaagvlkgrrvTsypavkdklekagakyvdkrv 140
                                       al++pGGra pe++r+++ ++ +v+ f+ek+ +va +C++p+ Laaagvl gr++++ypa+ ++++ ag ++vd  v
  gi|518653162|ref|YP_008142682.1|  79 ALIIPGGRA-PEYIRNDKDFIRIVQYFFEKNAPVAELCHAPLGLAAAGVLHGRKTAAYPALAPDVTIAGGTFVDAAV 154
                                       *********.******************************************************************* PP

                                       EEETTEEEESSGGGHHHHHHHHHH CS
                         DJ-1_PfpI 141 vvdgnlvTsrgpgaaiefalelle 164
                                       vvdgnl++sr++++++++++e+++
  gi|518653162|ref|YP_008142682.1| 155 VVDGNLISSRAWPDHPQWMREFIK 178
                                       *********************997 PP

>> ThiJ_like  ThiJ/PfpI family-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0017        15      10      33 ..      16      39 ..       8      58 .. 0.86
   2 !   10.6   0.0   3.7e-05      0.33      83     155 ..      75     138 ..      50     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0017
                         ThiJ_like 10 evaipwkvlkdagfsveFvtekgk 33
                                      ev  p++ +k++gf v+ ++++ k
  gi|518653162|ref|YP_008142682.1| 16 EVMYPLQRMKEEGFDVDLAAPEKK 39
                                      899****************99866 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 3.7e-05
                         ThiJ_like  83 eeydlvllpGGsdkavrelleserlhsllveylklvkrekepskvlgaicqgvlalafakpeldlktttlPlw 155
                                        +yd++ +pGG+ +   e++ +++    +v+y+       e++  ++  c+  l la+a   +  kt++ P+ 
  gi|518653162|ref|YP_008142682.1|  75 SQYDALIIPGGRAP---EYIRNDKDFIRIVQYF------FEKNAPVAELCHAPLGLAAAGVLHGRKTAAYPAL 138
                                       69**********98...5687777666677776......3566789999999999999999999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       382  (0.0213063); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); 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 0.23s 00:00:00.59 Elapsed: 00:00:00.41
# Mc/sec: 1371.58
//
Query:       gi|518653163|ref|YP_008142683.1|  [L=272]
Description: hypothetical protein FACI_IFERC00001G1804 [Ferroplasma acidarmanus fer1]
Scores for complete 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-62  211.1   1.3    2.3e-62  210.8   1.3    1.0  1  Asparaginase_2  Asparaginase
  ------ inclusion threshold ------
      0.035   13.6   0.1      0.066   12.7   0.1    1.5  1  NIR_SIR         Nitrite and sulphite reductase 4Fe-4S domain


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 !  210.8   1.3   2.5e-66   2.3e-62       3     278 ..       5     255 ..       3     269 .. 0.86

  Alignments for each domain:
  == domain 1  score: 210.8 bits;  conditional E-value: 2.5e-66
                                       EEEEEEEESE-G-HHHHHHHHHCHHHHHHHHHHHHHTT--HHHHHHHHHHHHHCTCCCSSSTTSS-BTTS---EEEE CS
                    Asparaginase_2   3 lvihGGAgsilktkereeavrkalkealeagykvLkeggsaldaVeaavrllEddplfnaGkGsvltedgeveldAs 79 
                                       +vihGGA s ++           l+e l++  + L+ +gs+ld  +++v ++Eddp fnaG+Gsv+  dg +++dA+
  gi|518653163|ref|YP_008142683.1|   5 IVIHGGANSPST-----------LNEKLQNILDNLDVNGSSLDLAVKSVVMMEDDPTFNAGTGSVPRIDGSIQMDAA 70 
                                       899**9976655...........78888888899******************************************* PP

                                       EEETTTTEEEEEEEESSBS-HHHHHHHHHHHCS-SEEEHHHHHHHHHHTT-----CGGG--HHHHHHHHHHHHCCCH CS
                    Asparaginase_2  80 imdgktlraGaVagvkrvknpislArlvmeksehvlLvgegAeefareqglelvdeesllteerlkelekakkekae 156
                                       +m  +   +G+V+++++vk+p+ +Ar vmeks+h++L+gegA efar++g+   + +++ te++++ ++k k++ ++
  gi|518653163|ref|YP_008142683.1|  71 VMSDS--GFGSVMCIENVKHPVMVARDVMEKSPHIMLAGEGAVEFARKLGY---EYYNPETEKSREMMDKLKASIKN 142
                                       **876..57******************************************...77777788888877777766666 PP

                                       S..B-S-BS-TTTTT---EEEEEE-TTS-EEEEEEE--STTB-TTEE-STTSTTTSEEEETTTEEEEEEE-HHHHCC CS
                    Asparaginase_2 157 kkeaknvsekelkaklgTvGaValDsegnlAaaTSTgGltnklvGRvGDspiiGaGtYAdnkvgAvsaTGkGeeiir 233
                                       ++   ++ +  +k++  TvGaVa   + ++Aaa STgG+   l GRvGDsp+iGaG Y   + gAv aTG Ge+i +
  gi|518653163|ref|YP_008142683.1| 143 NTL-PEKFKFMVKSSSDTVGAVAR-IDDKFAAAVSTGGAFPMLRGRVGDSPVIGAGIYQ-GEKGAVVATGIGEDIAK 216
                                       443.4444455679999******7.5679*****************************9.888************** PP

                                       TTHHHHHHHHHHTTT--HHHHHHHHHHCHHHHTTT-EEEEEEETT CS
                    Asparaginase_2 234 ellaadivalmeykglsleeAaekvieeklkrvkgsgGviavdkk 278
                                        ll+ +i +++     +l+    ++++++ +++k s+G+ia++ +
  gi|518653163|ref|YP_008142683.1| 217 DLLSFRIYQQIGT--DDLN----EIVKKEIDKFKVSVGIIAISDN 255
                                       ***********99..4555....55666667777789*****976 PP

>> NIR_SIR  Nitrite and sulphite reductase 4Fe-4S domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   7.3e-06     0.066      25      75 ..     126     176 ..     110     248 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHHHHHCTCCCCTSSSS-BEEEEESSTCSTSSGGGSSEEEEEEEET CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           NIR_SIR  25 telakaiedelepeygetylPrKfKiavsgcpnncvaveanDiglvgvkkd 75 
                                       te +++++d+l+  ++++ lP KfK+ v+   +  +av  +D  + + +  
  gi|518653163|ref|YP_008142683.1| 126 TEKSREMMDKLKASIKNNTLPEKFKFMVKSSSDTVGAVARIDDKFAAAVST 176
                                       56678999***********************99999999888777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.50
# Mc/sec: 1634.01
//
Query:       gi|518653164|ref|YP_008142684.1|  [L=51]
Description: hypothetical protein FACI_IFERC00001G1805 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); 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: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.49
# Mc/sec: 309.97
//
Query:       gi|518653165|ref|YP_008142685.1|  [L=460]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete 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-10   39.3   0.1    1.2e-09   38.0   0.1    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    5.3e-08   33.1   4.5    1.4e-07   31.8   4.5    1.7  1  OrfB_IS605      Probable transposase
     0.0043   17.3   2.2      0.008   16.5   2.2    1.5  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.032   14.2   0.2      0.097   12.7   0.2    1.8  1  Hormone_6       Glycoprotein hormone
      0.074   13.1   3.1      0.071   13.2   1.0    2.0  2  DUF1451         Zinc-ribbon containing domain
      0.095   12.7   0.4       0.19   11.8   0.4    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.24   11.1   2.0       0.59    9.9   2.0    1.7  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.24   11.1   8.2        0.1   12.4   4.7    2.1  2  A2L_zn_ribbon   A2L 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 !   38.0   0.1   5.2e-13   1.2e-09      16      67 ..     336     388 ..     327     390 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 5.2e-13
                    OrfB_Zn_ribbon  16 Gikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                         ++++++++  T k+Cs+C  k + +l++r ++C nCgf +drD+n+++N++
  gi|518653165|ref|YP_008142685.1| 336 ASTLILIDRFIpTTKECSKCHNKYDIKLDERIYQCHNCGFIIDRDYNSSLNMI 388
                                       447889999999********999998*************************86 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   4.5   6.2e-11   1.4e-07      10     105 ..     201     301 ..     182     310 .. 0.83

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 6.2e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn....ykkasrklarlh 81 
                                       +++++++k ++ DlGi+n +t+++++     ++k+r+  + +++l+++ +  + ++k s+     y k ++kl +  
  gi|518653165|ref|YP_008142685.1| 201 EKPVNNQKIISFDLGIKNQLTCSNGSILNyNIPKSRKEIRLQRSLSRKAKYAEGTKKLSRGqsrnYYKNKNKLNKEQ 277
                                       6788999****************998443589999999999999988877666666544434444************ PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlke 105
                                       +k  ++rk+ ++k++++l+ +++ 
  gi|518653165|ref|YP_008142685.1| 278 NKTMNKRKDTINKITHYLTSNYDI 301
                                       ******************999875 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   2.2   3.6e-06     0.008       3      44 ..     334     379 ..     332     380 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.6e-06
                              C1_2   3 Hp.HpLtlskgedssesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                       H+  +L+l  ++    +++Cs C +k     d  +  Y C  C f+++ 
  gi|518653165|ref|YP_008142685.1| 334 HKaSTLILI-DRFIPTTKECSKCHNKydikLD--EriYQCHNCGFIIDR 379
                                       777789999.999999**********885443..256*********995 PP

>> Hormone_6  Glycoprotein hormone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.2   4.3e-05     0.097      11      42 ..     349     382 ..     342     397 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
                                       S-BSEEEEETTTEBTTBEEEEEEEEEE..EEEEE CS
                         Hormone_6  11 ceecklkenkvfskldapiyqcvGccf..srayp 42 
                                        +ec+  +nk+  kld+ iyqc  c f   r y 
  gi|518653165|ref|YP_008142685.1| 349 TKECSKCHNKYDIKLDERIYQCHNCGFiiDRDYN 382
                                       57899999*****************983346665 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       1.2   2.6e+03      22      44 ..     274     296 ..     243     323 .. 0.64
   2 ?   13.2   1.0   3.1e-05     0.071     112     139 ..     347     374 ..     343     376 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.2
                           DUF1451  22 keklseaeeltkeelelvaeylk 44 
                                       +++ +++ +  k+ ++++++yl 
  gi|518653165|ref|YP_008142685.1| 274 NKEQNKTMNKRKDTINKITHYLT 296
                                       33333334444555555555554 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.1e-05
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C kC+++ ++k  e+i +C++Cg
  gi|518653165|ref|YP_008142685.1| 347 PTTKECSKCHNKYDIKLDERIYQCHNCG 374
                                       66789**********************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 ?   11.8   0.4   8.3e-05      0.19      16      44 ..     347     374 ..     338     375 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       p++  C +C+++  +++   + +qC  C+
  gi|518653165|ref|YP_008142685.1| 347 PTTKECSKCHNKYDIKLDE-RIYQCHNCG 374
                                       56678*****888888887.********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 ?    9.9   2.0   0.00027      0.59       3      25 ..     352     375 ..     351     377 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                                       -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpi.RCkeCGh 25 
                                       C +C+++  +k  + i +C +CG+
  gi|518653165|ref|YP_008142685.1| 352 CSKCHNKYDIKLDERIyQCHNCGF 375
                                       **************9989*****8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1       1.4   3.2e+03      14      23 ..     180     189 ..     178     189 .. 0.86
   2 ?   12.4   4.7   4.5e-05       0.1       4      30 ..     350     376 ..     349     377 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.4
                     A2L_zn_ribbon  14 ilnseqgylv 23 
                                       ++n++++y++
  gi|518653165|ref|YP_008142685.1| 180 LINKNSNYYI 189
                                       799*****96 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 4.5e-05
                     A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgas 30 
                                       k+Cs+C++  ++  +  +++C +Cg++
  gi|518653165|ref|YP_008142685.1| 350 KECSKCHNKYDIKLDERIYQCHNCGFI 376
                                       78***********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1847  (0.103017); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 3175.67
//
Query:       gi|518653166|ref|YP_008142686.1|  [L=329]
Description: hypothetical protein FACI_IFERC00001G1807 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-07   31.1   0.0    4.4e-07   30.1   0.0    1.5  1  GHMP_kinases_N  GHMP kinases N terminal domain
      8e-05   22.9   0.1      8e-05   22.9   0.1    1.8  2  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
        0.3   10.5   3.0        4.2    6.7   0.4    2.8  3  Cellulase       Cellulase (glycosyl hydrolase family 5)


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   7.3e-11   4.4e-07       2      44 ..      88     130 ..      87     144 .. 0.83

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 7.3e-11
                                       EEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHH CS
                    GHMP_kinases_N   2 ivikseiPvgaGLGSSAAlavalvaAllallglsleeaklale 44 
                                       + ++s++P+g+GLGSS+Al+ ++++ ++a    +++ ++la e
  gi|518653166|ref|YP_008142686.1|  88 VIMNSDVPPGSGLGSSSALINGILKMINAIKKRNVDPYELAKE 130
                                       7899************************998544544555554 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.5       2.3   1.4e+04      54      63 ..      96     105 ..      96     107 .. 0.78
   2 !   22.9   0.1   1.3e-08     8e-05       3      79 ..     230     305 ..     228     309 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.3
                    GHMP_kinases_C  54 sGaGgGptvf 63 
                                       +G+G+G++ +
  gi|518653166|ref|YP_008142686.1|  96 PGSGLGSSSA 105
                                       69****9865 PP

  == domain 2  score: 22.9 bits;  conditional E-value: 1.3e-08
                    GHMP_kinases_C   3 ealergdlellgellnlsqrs..elkavvgilppeleellealselGalgaklsGaGgGptvfalfkdkdeaeqvar 77 
                                       +a+ +++ +++ +++n++++        + + + +++e+++ ++e+Ga +akl G G+ +++  ++ +k++ + ++r
  gi|518653166|ref|YP_008142686.1| 230 KAISAHNRNEVCNIINEGWNIkkS--LGANVTNQRIDEIISYAKENGAKSAKLLGGGSEGFILLIG-EKNGIDSLQR 303
                                       78999999*************554..5*****************************9999999999.9999999888 PP

                    GHMP_kinases_C  78 al 79 
                                       ++
  gi|518653166|ref|YP_008142686.1| 304 KM 305
                                       87 PP

>> Cellulase  Cellulase (glycosyl hydrolase family 5)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0     0.037   2.2e+02      19      74 ..      67     120 ..      50     123 .. 0.73
   2 ?    6.7   0.4    0.0007       4.2     140     177 ..     213     250 ..     202     262 .. 0.74
   3 ?    1.7   0.1     0.024   1.4e+02      61      77 ..     260     276 ..     249     277 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.037
                                       CGGSHHHHHHHHHHHT-SEEEEEEECTGGTTSSTTTGCTHHHHHHHHHHHHHHHHT CS
                         Cellulase  19 npyttkalidevkdagfntvRlpvswgelvenapdykvdenslerveevvkyaken 74 
                                       n+  ++++id + ++g+nt R+ +   + v++++++   ++ ++ + ++++++k++
  gi|518653166|ref|YP_008142686.1|  67 NRTMENKIIDMFMENGINTGRVIMN--SDVPPGSGLGSSSALINGILKMINAIKKR 120
                                       3347889999999999999999888..44445666666777777777777777766 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0007
                                       TCHHHTTHHHHHHHHHHHHHHHHTTSSEEEEECHHHHT CS
                         Cellulase 140 wtseeadevkayaeeaikaIRavgpnrliivegnswsg 177
                                        t e+ +++k++a e+ kaI a++ n ++ + +++w+ 
  gi|518653166|ref|YP_008142686.1| 213 QTMENLNKIKHLALEMSKAISAHNRNEVCNIINEGWNI 250
                                       356888********************655555555875 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.024
                                       HHHHHHHHHHHHHTT-E CS
                         Cellulase  61 lerveevvkyakengly 77 
                                        +r++e++ yakeng++
  gi|518653166|ref|YP_008142686.1| 260 NQRIDEIISYAKENGAK 276
                                       6899**********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       895  (0.0499191); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); 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: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.49
# Mc/sec: 2034.00
//
Query:       gi|518653167|ref|YP_008142687.1|  [L=104]
Description: hypothetical protein FACI_IFERC00001G1808 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       750  (0.0418317); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); 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: 0.46u 0.30s 00:00:00.76 Elapsed: 00:00:00.49
# Mc/sec: 638.29
//
Query:       gi|518653168|ref|YP_008142688.1|  [L=464]
Description: hypothetical protein FACI_IFERC00001G1809 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-53  182.4  63.4    1.8e-43  148.8  39.7    2.1  2  MFS_1          Major Facilitator Superfamily
      1e-08   34.5  24.8    7.5e-05   21.8  10.4    2.9  2  MFS_1_like     MFS_1 like family
    1.3e-05   23.8   6.5    2.1e-05   23.2   6.5    1.3  1  MFS_3          Transmembrane secretion effector
  ------ inclusion threshold ------
      0.075   13.6   2.0       0.13   12.8   0.1    2.5  2  Adeno_E3_14_5  Early E3 14.5 kDa protein


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 !  148.8  39.7     4e-47   1.8e-43       3     351 ..      13     384 ..      11     386 .. 0.87
   2 !   47.6  15.7   2.5e-16   1.1e-12       2     177 ..     251     445 ..     250     454 .. 0.85

  Alignments for each domain:
  == domain 1  score: 148.8 bits;  conditional E-value: 4e-47
                             MFS_1   3 laaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgllll 79 
                                       l+++++a++++i+++alp a+++++++  s + l++++y + + v+ +p+  ++ r+G r ++++g+ +f +++l++
  gi|518653168|ref|YP_008142688.1|  13 LSTLMAAIDSTIVYLALP-AMGQTFHSGISYLTLVVAAYIISTTVMLVPAIEITKRIGNRNFYIIGFSIFTVSSLII 88 
                                       7899**************.******************************************************8888 PP

                             MFS_1  80 lfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyi 156
                                       +++ ++ +++++r++ G+gag+++++ + +i   f k erg+aigl s+++s+G+++gp+lgg+l+ +++Wr++f+i
  gi|518653168|ref|YP_008142688.1|  89 AVSLNIAMVIIFRFVEGIGAGIMTSSDIPIILGAFRKGERGKAIGLNSIAWSIGTLIGPVLGGFLV-AINWRYIFLI 164
                                       8658888***********************************************************.99******** PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeee...................................kgtgpaplvp 198
                                       + ++++  +  ++  +  +++++ +    + +                                     + ++p+++
  gi|518653168|ref|YP_008142688.1| 165 NVPIGIGTIFAGYKIIKKDKVNKLPI---KYKstismalfliplimgialineyyllialiilpvfiYVQIKQPVID 238
                                       *******9775444444444444444...444446999**********99999999999988888888888888888 PP

                             MFS_1 199 awkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrr 275
                                         ++ll +  + ++ +a++l +f+f+++l+ l ly+q++lgls  + +gl++  + ++++++++++g l dr+ +  
  gi|518653168|ref|YP_008142688.1| 239 --RKLLGNIRFSLITLASFLESFVFFSVLFALSLYFQSDLGLS-SIDTGLIIFTYPVASIVSSPIGGILYDRYRH-- 310
                                       ..455555545358888888899********************.688888888888888888**********776.. PP

                             MFS_1 276 rlllallllllaalglallavtssavllll.vlvliGfglgfvfpsllalasdlappeeagtasglfntagslggal 351
                                       + +++ ++++l ++ +++++ +   + ++  +l+++Gfg++f++++++++++d ++++ + +a+ ++ +++++g++ 
  gi|518653168|ref|YP_008142688.1| 311 PETIMAIGTILECVPVLIIGIY---LKYIPeLLLIAGFGGSFFWSPSTTMITDALGEKFRVQANNAMFILRNIGIIT 384
                                       6666666667777777777777...3444478999***************************************986 PP

  == domain 2  score: 47.6 bits;  conditional E-value: 2.5e-16
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgll 77 
                                        la fl ++ ++ +++al+l+ ++dlg+s    gl++ +y ++++v+s+++G l dr+ +   ++ +g +l ++ +l
  gi|518653168|ref|YP_008142688.1| 251 TLASFLESFVFFSVLFALSLYFQSDLGLSSIDTGLIIFTYPVASIVSSPIGGILYDRYRHPEtIMAIGTILECVPVL 327
                                       6899******************************************************86667************66 PP

                             MFS_1  78 lll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg... 149
                                       ++  +      ++  l +++G+g++++++ + ++i+d   ++ r +a+  + +  ++G+i +  + +l++ +++   
  gi|518653168|ref|YP_008142688.1| 328 IIGiY----LkYIPELLLIAGFGGSFFWSPSTTMITDALGEKFRVQANNAMFILRNIGIITAISILPLFILHFSrin 400
                                       66632....3356667778899****************************************9999999999999** PP

                             MFS_1 150 .................Wravfyilaivsllafvlfllllpeepp 177
                                                          +++++++++  l+ ++f++++ ++++
  gi|518653168|ref|YP_008142688.1| 401 vsigeifvskaridisaGIGAYLVFTAIISLSSLIFIFVYHRRAR 445
                                       ************999995555555555555555555666655544 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 !   21.8  10.4   1.7e-08   7.5e-05     263     374 ..      44     154 ..      33     164 .. 0.91
   2 !   21.4   2.2   2.2e-08   9.7e-05       9      81 ..     259     328 ..     249     356 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.7e-08
                        MFS_1_like 263 GslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvs 339
                                         +va   +++ ++++ a ++++++G ++  ii+++++++  l++a+  n  +v+++ + +gi  g++ ++ +  + 
  gi|518653168|ref|YP_008142688.1|  44 TLVVAAYIISTTVMLVPAIEITKRIGNRNFYIIGFSIFTVSSLIIAVSLNIAMVIIFRFVEGIGAGIMTSSDIPIIL 120
                                       456667778888999999*********************************************************** PP

                        MFS_1_like 340 kiapksleatgqgllsglyfglGralGsliGGllw 374
                                        ++ k+ +++ +gl s++ +++G+ +G ++GG+l 
  gi|518653168|ref|YP_008142688.1| 121 GAFRKGERGKAIGLNSIA-WSIGTLIGPVLGGFLV 154
                                       *************98776.**************96 PP

  == domain 2  score: 21.4 bits;  conditional E-value: 2.2e-08
                        MFS_1_like   9 FfffaalgsllPYltiylk.skglkaseigiitlilpltsilsppiwgvlaDrfgkrkkvvilslllsavlfls 81 
                                       F+ff++l +l    ++y++ + gl+  + g+i    p+ si+s+pi g l Dr++  +++++++++l++v +l+
  gi|518653168|ref|YP_008142688.1| 259 FVFFSVLFAL----SLYFQsDLGLSSIDTGLIIFTYPVASIVSSPIGGILYDRYRHPETIMAIGTILECVPVLI 328
                                       7777777775....67777589*********************************************9998774 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   6.5   4.6e-09   2.1e-05      35     196 ..      31     186 ..       4     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.6e-09
                             MFS_3  35 WlmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltl 111
                                        +  + ++      lv aa  + + ++ ++a  ++  +  R++ +++ ++  ++s++++v+     l+  +++++ +
  gi|518653168|ref|YP_008142688.1|  31 AMGQTFHSGISYLTLVVAAYIISTTVMLVPAIEITKRIGNRNFYIIGFSIFTVSSLIIAVS-----LNIAMVIIFRF 102
                                       5555666666778899999999999999**********************99999988886.....466789***** PP

                             MFS_3 112 ligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallr 188
                                       + giGa +++ +   ++    ++ +  +A+ Lns+ + i   +GP lgG lva+    + f +n+   +  i+a  +
  gi|518653168|ref|YP_008142688.1| 103 VEGIGAGIMTSSDIPIILGAFRKGERGKAIGLNSIAWSIGTLIGPVLGGFLVAIN-WRYIFLINVPIGIGTIFAGYK 178
                                       ****************************************************975.455677777666666666555 PP

                             MFS_3 189 wkrevrks 196
                                       + ++ + +
  gi|518653168|ref|YP_008142688.1| 179 IIKKDKVN 186
                                       55555555 PP

>> Adeno_E3_14_5  Early E3 14.5 kDa protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.4       2.6   1.2e+04      49      65 ..      68      84 ..      37     101 .. 0.51
   2 ?   12.8   0.1     3e-05      0.13      25      68 ..     252     296 ..     244     312 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 2.6
                     Adeno_E3_14_5 49 igwnaidamnhptfpvp 65
                                      ig      + +  f v 
  gi|518653168|ref|YP_008142688.1| 68 IGNRNFYIIGFSIFTVS 84
                                      44444444444444443 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3e-05
                     Adeno_E3_14_5  25 lyaiisvmvfcstifalaiypyldigwnaida.mnhptfpvpavi 68 
                                       l + +  +vf s +fal++y   d+g  +id+ +   t+pv +++
  gi|518653168|ref|YP_008142688.1| 252 LASFLESFVFFSVLFALSLYFQSDLGLSSIDTgLIIFTYPVASIV 296
                                       55667789***********************74677899998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       819  (0.0456802); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); 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):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 3059.81
//
Query:       gi|518653169|ref|YP_008142689.1|  [L=369]
Description: hypothetical protein FACI_IFERC00001G1810 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.1e-34  117.8   0.0    9.6e-27   93.8   0.1    3.0  2  p450      Cytochrome P450
  ------ inclusion threshold ------
      0.032   14.2   0.0       0.42   10.6   0.0    2.6  3  DUF1851   Domain of unknown function (DUF1851)


Domain annotation for each model (and alignments):
>> p450  Cytochrome P450
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.3e-07    0.0029      23     135 ..       3     114 ..       1     130 [. 0.84
   2 !   93.8   0.1   1.1e-30   9.6e-27     222     448 ..     166     356 ..     147     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.3e-07
                                       HHHHHHHHHHH-SEEEEEETTEEEEEEESHHHHHHHHCTSTTTTCEESSHHHHHHHHHTTTTSSSTTCGHHHHHHHH CS
                              p450  23 hevlrklqkkygpifrlklgskpvvvlsgpeavkevlikkgeefsgrpdeallatsrkpfkgkgvlfangekwkklR 99 
                                       h+v+++++k   +    + + + +  + ++++v  vl + + ++s+ p +a     +++  g + ++++ +++k+lR
  gi|518653169|ref|YP_008142689.1|   3 HDVFQYYRKMRKESPVHFNNDTGSWDVFDYKSVYFVLMNPDIYSSD-PSYAGNIPENRQGPGASFITMDNPDHKELR 78 
                                       5667777777777777788888889999************866666.67777777788999999999999******* PP

                                       HHHHHHHTSHSTTTHHHHHHHHHHHHHHHHHCCCCH CS
                              p450 100 rfltptltsfgklsleelveeeaedlveklrkkage 135
                                       ++ tp ++++++  +++++e+ +++l+e ++k++++
  gi|518653169|ref|YP_008142689.1|  79 NVTTPYFLTSKITGYRDMIESTSKRLMEGINKNSDF 114
                                       **********566******************99886 PP

  == domain 2  score: 93.8 bits;  conditional E-value: 1.1e-30
                                       HHHHHHHHCHCHCSCSSCSHHHHHHHHCTTCTCTSSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHH CS
                              p450 222 klieerretldsakksrrdfldalllakkekkgesklsdeelaatvlellfaGvdTtsstlswaLyeLaknPevqek 298
                                         + e  +t  ++  +  + ++  l  +      + ls ++    v+ l ++G +Tt++ +  +   L ++Pe+ +k
  gi|518653169|ref|YP_008142689.1| 166 STMAEIFKTNTED--NIISTINKGLFHS------EPLSINQKIGYVMLLVIGGNETTTNLIGNMVKVLSEHPEIADK 234
                                       5555555555555..4555555555555......57999999999******************************** PP

                                       HHHHHHHHCCTTTT-HHHHCCT-HHHHHHHHHHHHHSCSSTTEEEEESSSCEEETTEEE-TT-EEEEEHHHHHT-TT CS
                              p450 299 lreEidevlgdkreptyddlqklpyldavikEtLRlhpvvplllpRevtkdvvirgylipkGtevivnlyalhrdpe 375
                                       lr+E     +             ++ + +i+EtLR+++++ +l  R + +d v++g  i+kG++ +++l++ +rd +
  gi|518653169|ref|YP_008142689.1| 235 LRQE-----P-------------ELKKGFIEETLRYYSPIQFLPHRFAARDSVLNGQEIKKGQRLSIWLGSANRDGA 293
                                       ****.....2.............355789************555556677*************************** PP

                                       TSSSTTS--GGGGB-TTSCTESSCTT--TTEEGGGS-TTHHHHHHHHHHHHHHHHHHEEEEESTSTSGGEEES CS
                              p450 376 vfpnPeeFdpeRFldekgnskrksfaflPFGaGpRnCiGerlArmelklflatlLqnFevelqpetdpppile 448
                                        f++P++F+ eR +++          +l+FG+G ++C+G +lAr+e +++l  +L +F++  ++ ++  +  +
  gi|518653169|ref|YP_008142689.1| 294 KFEDPDTFNMERQNND----------HLAFGMGIHMCLGSPLARLEAEIALNDILNKFKHVKINAEKTSMLKN 356
                                       ***********97766..........79*******************************98666555554444 PP

>> DUF1851  Domain of unknown function (DUF1851)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.24   2.2e+03       5      40 ..     102     138 ..      99     139 .. 0.85
   2 ?   10.6   0.0   4.7e-05      0.42      35      59 ..     193     217 ..     188     228 .. 0.88
   3 ?   -1.0   0.0       0.2   1.8e+03      19      46 ..     336     364 ..     326     366 .. 0.65

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.24
                           DUF1851   5 deFfasledee.fledwlreplfeealeklgeLeyde 40 
                                       +++++  ++++ f+ d+     ++ + e lg +e+d+
  gi|518653169|ref|YP_008142689.1| 102 KRLMEGINKNSdFIRDYAVMLPVTVISELLGVPENDR 138
                                       6678888999999999999999999999999999985 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 4.7e-05
                           DUF1851  35 eLeydecygfvpalaLGGsekvenl 59 
                                       +L+ ++  g+v +l++GG+e++ nl
  gi|518653169|ref|YP_008142689.1| 193 PLSINQKIGYVMLLVIGGNETTTNL 217
                                       57788999**************998 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.2
                           DUF1851  19 dwlreplfeea.leklgeLeydecygfvp 46 
                                       d l++ ++ ++  ek  +L++  +ygf++
  gi|518653169|ref|YP_008142689.1| 336 DILNKFKHVKInAEKTSMLKNPMVYGFST 364
                                       55554444333157888999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.57u 0.31s 00:00:00.87 Elapsed: 00:00:00.52
# Mc/sec: 2143.93
//
Query:       gi|518653170|ref|YP_008142690.1|  [L=226]
Description: sugar fermentation stimulation protein A [Ferroplasma acidarmanus fer1]
Scores for complete 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-35  120.9   0.0    5.4e-35  120.3   0.0    1.2  1  SfsA      Sugar fermentation stimulation protein RE domain
    1.4e-15   57.2   0.0    9.3e-15   54.5   0.0    2.0  2  SfsA_N    SfsA N-terminal OB domain


Domain annotation for each model (and alignments):
>> SfsA  Sugar fermentation stimulation protein RE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0     6e-39   5.4e-35      22     130 ..     103     206 ..      85     212 .. 0.91

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 6e-39
                                       ..EEES-EETTEE-SEEEE-S.SSEEEEEEEE--EE..EEEEE-SS--HHHHHHHHHHHHHHHTT-EEEEEEEE-SS CS
                              SfsA  22 eeikrevkygnsriDfllekeeeekcyvEVKsvtleeggialfPdapteRgqkhleeLaelvkegyravvlfvvqre 98 
                                       e  +revk+gnsr+Df l++     +y+EVKs+tl+e+gia+fPdapt Rg+khle+L++l+++gy+++vlf++  e
  gi|518653170|ref|YP_008142690.1| 103 EGWQREVKVGNSRLDFRLNN-----AYIEVKSATLVENGIARFPDAPTLRGKKHLETLMDLIASGYESFVLFLIFNE 174
                                       3489*************997.....7*************************************************** PP

                                       S--EEEE-TTT-HHHHHHHHHHHHHT-EEEEE CS
                              SfsA  99 darefkpnkeidpefaealreaaeaGVevlay 130
                                       +a++f pn   dpef++a +   e+GV++  +
  gi|518653170|ref|YP_008142690.1| 175 NAKCFLPNTARDPEFSHAYYSTLEHGVKFQYL 206
                                       ****************************9765 PP

>> SfsA_N  SfsA N-terminal OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.5   0.0     1e-18   9.3e-15       1      60 [.      25      85 ..      25      87 .. 0.90
   2 ?   -0.0   0.0      0.11     1e+03      16      24 ..     177     185 ..     163     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 54.5 bits;  conditional E-value: 1e-18
                                      EEEEETTEEEEEEE.....EE----S--TTT--TT-EEEEE....ESSS-SEEEEEEEETTEE CS
                            SfsA_N  1 lrRpnRFladveldg...tvHvpntGrlkelllpGarvllsksdnpkrKtkytleavekegtw 60
                                      ++RpnRF++++ +d+    vH++++Grl+el++pG+ +l++++   + Kt+y++  +++++ w
  gi|518653170|ref|YP_008142690.1| 25 VSRPNRFMVKAMVDDkevDVHIHDPGRLEELIFPGNSILIRET--NGTKTHYSVTFCKNDDIW 85
                                      68************64444**********************64..579***********9998 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.11
                                       .EE----S- CS
                            SfsA_N  16 tvHvpntGr 24 
                                       ++++pnt r
  gi|518653170|ref|YP_008142690.1| 177 KCFLPNTAR 185
                                       69*****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       296  (0.0165096); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1470.89
//
Query:       gi|518653171|ref|YP_008142691.1|  [L=397]
Description: hypothetical protein FACI_IFERC00001G1812 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-28   99.9   0.0    1.9e-28   99.6   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    2.3e-14   53.2   0.0      4e-14   52.4   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain
      4e-07   29.9   0.0    6.1e-07   29.3   0.0    1.3  1  Peptidase_M28  Peptidase family M28
  ------ inclusion threshold ------
      0.034   13.2   0.0       0.13   11.2   0.0    1.9  2  Peptidase_M42  M42 glutamyl aminopeptidase


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.6   0.0   4.2e-32   1.9e-28       4     206 ..      84     396 ..      81     397 .] 0.81

  Alignments for each domain:
  == domain 1  score: 99.6 bits;  conditional E-value: 4.2e-32
                                       EES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THH CS
                                       xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx RF
                     Peptidase_M20   4 sHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGa 78 
                                        H+D+Vp ++ + w++ pf++t+e +++yGrG+ d+  +++++l +l+++k+e+   k ++ ++f+ dEE+g   G+
  gi|518653171|ref|YP_008142691.1|  84 CHMDTVPVGDISLWKHePFKATIEGDRIYGRGSEDNGQSIFTMLLLLKHIKREQM--KMNLNVAFVSDEETGNdYGI 158
                                       5***********************99***************************97..66***********9999*** PP

                                       HHHHH.HHH.T..................TTCESEEEEEEEESSSBTCHSTETEEEE.................... CS
                                       xxxxx.xxx.x..................xxxxxxxxxxxxxxxxxxxxxxxxxxxx.................... RF
                     Peptidase_M20  79 kalle.gle.e..................rekvdavfelhieepgileagklaigvv.................... 115
                                       k+l+  g++ +                                                                  
  gi|518653171|ref|YP_008142691.1| 159 KYLISkGIFaKddliivpdagteggfiieT--------------------------Aekstmqlkfeingiqghasm 209
                                       *****7555333344444333333333330..........................234444455556666777777 PP

                                       ............................................................................. CS
                                       ............................................................................. RF
                     Peptidase_M20 116 ............................................................................. 115
                                                                                                                    
  gi|518653171|ref|YP_008142691.1| 210 penslnafrvackfidlmdfnlhdqfgktnklfvppystfeptkheqnidnintipgrdvfywdfrilpqypadeil 286
                                       7777777777799**************************************************************** PP

                                       ..................EEEEEEEEEESHEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHH...TTTEE CS
                                       ..................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxx RF
                     Peptidase_M20 116 ..................kvevelleggapvtlndsplvkalaeaaeelfgekvelivsgpggtdarff...agipt 171
                                                         k++v ++ +++ +t + +++v +l++a+++++g++  ++    gg+ ++ f   +g   
  gi|518653171|ref|YP_008142691.1| 287 ksidgliekfsktsgakiKYTVIDRVDAPDPTPDGAEIVVLLKKAIKSVIGKDAFTVGI--GGETFASFlrgKGFSV 361
                                       ***************977777776677777777799**************966444444..5666666656555544 PP

                                       EEEEE.SSGGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                                       xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M20 172 vmifg.pgsglaHspnEyvdledlekgikvlarlle 206
                                       +++      + aH p+Ey+ ++++ + i+v++ +l 
  gi|518653171|ref|YP_008142691.1| 362 AVWSTtVI-ESAHMPDEYCLIPHILQDIEVYKYILY 396
                                       45544233.99********************98875 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0     9e-18     4e-14       2     103 ..     189     295 ..     188     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 9e-18
                                       EB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.........TCCTCCCCCEECCE-C.CCCEES CS
                         M20_dimer   2 ghkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdia....eerslprttlnvtgiegGs.aknvip 73 
                                       ++k  ++ k +++g +gH+++p++  NA++ ++++++ +  + +d+     + + +p++t+++t  e+   ++n+ip
  gi|518653171|ref|YP_008142691.1| 189 AEKSTMQLKFEINGIQGHASMPENSLNAFRVACKFIDLMDFNLHDQFgktnKLFVPPYSTFEPTKHEQNIdNINTIP 265
                                       78999999*****************************99888777669999*****************99******* PP

                                       SEEEEEEEEEHHHHHHHHHHHHHHHHHHTS CS
                         M20_dimer  74 deaeakidiRllpgedpeevleeieeilek 103
                                       ++  ++ d+R+lp+  ++e+l+ i  ++ek
  gi|518653171|ref|YP_008142691.1| 266 GRDVFYWDFRILPQYPADEILKSIDGLIEK 295
                                       *************************99997 PP

>> Peptidase_M28  Peptidase family M28
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   1.4e-10   6.1e-07       1      74 [.      68     153 ..      68     199 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 1.4e-10
                                       EEEEEESTTCESEEEEEEEE--B-TTT..............TCC..T---TTTTHHHHHHHHHHHHHCHHGGCCSSE CS
                     Peptidase_M28   1 NviatlegkatdevlllgAHyDsvgvg..............rgp..ifvGAdDnAsgvaalLelarvlaasgsrpkr 61 
                                       N++ +l g++ +++l + +H+D+v+vg              +g+     G  Dn+ ++ ++L l++ +++  ++ k+
  gi|518653171|ref|YP_008142691.1|  68 NIVLKL-GSS-SKTLWVICHMDTVPVGdislwkhepfkatiEGDriYGRGSEDNGQSIFTMLLLLKHIKR--EQMKM 140
                                       889999.666.79********************9999888866675568********************8..589** PP

                                       EEEEEEESSCSGS CS
                     Peptidase_M28  62 gvrflffdaEEag 74 
                                       ++ ++f++ EE g
  gi|518653171|ref|YP_008142691.1| 141 NLNVAFVSDEETG 153
                                       ***********96 PP

>> Peptidase_M42  M42 glutamyl aminopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.08   3.6e+02       3      25 ..      69      89 ..      68      92 .. 0.80
   2 ?   11.2   0.0     3e-05      0.13     108     169 ..      89     153 ..      85     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.08
                                      EEEEEESSTTSSEEEEEEE--B- CS
                     Peptidase_M42  3 liakkkgkekepkvmiaAHmDei 25
                                      ++ k+ +  +++ + +  HmD++
  gi|518653171|ref|YP_008142691.1| 69 IVLKLGS--SSKTLWVICHMDTV 89
                                      6666666..8999********98 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 3e-05
                                       S-TT-EEEES---..EEETTECEEETTH.HHHHHHHHHHHHHHHHCTSS-SSEEEEEEESTCTTT CS
                     Peptidase_M42 108 isvGdivvfdkef..velangkivskal.DdragvavllellkelkeeeleatvylvatvqEEvG 169
                                       + vGdi  ++ e+  +++++++i ++   D+  ++  +l llk++k+e++++++ +++   EE G
  gi|518653171|ref|YP_008142691.1|  89 VPVGDISLWKHEPfkATIEGDRIYGRGSeDNGQSIFTMLLLLKHIKREQMKMNLNVAFVSDEETG 153
                                       67888888866552234566679998543999*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); 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: 0.53u 0.29s 00:00:00.82 Elapsed: 00:00:00.48
# Mc/sec: 2508.68
//
Query:       gi|518653172|ref|YP_008142692.1|  [L=387]
Description: hypothetical protein FACI_IFERC00001G1813 [Ferroplasma acidarmanus fer1]
Scores for complete 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-62  211.6   0.1    1.8e-62  211.4   0.1    1.0  1  PALP             Pyridoxal-phosphate dependent enzyme
     0.0021   17.5   0.7     0.0049   16.4   0.7    1.6  1  TF_Zn_Ribbon     TFIIB zinc-binding
      0.004   17.1   2.1      0.009   15.9   2.1    1.5  1  PhnA_Zn_Ribbon   PhnA Zinc-Ribbon
     0.0092   15.9   1.4      0.044   13.7   0.2    2.4  2  zinc_ribbon_4    zinc-ribbon domain
  ------ inclusion threshold ------
      0.043   13.6   2.2      0.074   12.8   2.2    1.4  1  zinc_ribbon_2    zinc-ribbon domain
      0.068   13.1   0.6       0.12   12.3   0.6    1.3  1  Prok-RING_1      Prokaryotic RING finger family 1
       0.15   12.1   0.3       0.29   11.2   0.3    1.3  1  DZR              Double zinc ribbon
       0.15   12.1   0.2        0.3   11.1   0.2    1.5  1  HypA             Hydrogenase/urease nickel incorporation, met
       0.19   12.0   1.2       0.51   10.6   1.2    1.8  1  C1_4             TFIIH C1-like domain
       0.26   11.2   0.9       0.76    9.7   0.9    1.7  1  Zn_ribbon_SprT   SprT-like zinc ribbon domain
       0.33   10.6   2.2       0.22   11.2   0.3    1.7  2  Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain


Domain annotation for each model (and alignments):
>> PALP  Pyridoxal-phosphate dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4   0.1   1.1e-65   1.8e-62       1     294 []      65     365 ..      65     365 .. 0.94

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 1.1e-65
                                       GGGCSSS--EEEECCTCCCCCCE.EEEEEGGGSTTSBTTHHHHHHHHHHHHTTTTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   1 ltlgigpTPlvrlprlskelgvp.lflKlEslnptgSfKdRgaeyllarlkegtgaktvveassGNhgralAaaaal 76 
                                       +t g+g+T l r  r+s   gv+ +flK E+ nptgSfKdRg++ +++++ +       ++as+GN+ +a+A ++a 
  gi|518653172|ref|YP_008142692.1|  65 ITRGEGNTMLYRNARISNYSGVDkIFLKHEGENPTGSFKDRGMTVAVSEAVRL-NFNKTLCASTGNTSAAAASYSAF 140
                                       5789*************************************************.**********************9 PP

                                       HT-EEEEEEE.TTS-HHHHHHHHHTT-EEEEECCHHHHHHHHHHHHHHHSTTCEE--TTTSHHHHHHHHTHHHHHHH CS
                              PALP  77 lGlkvtivvp.adaspekvallrllGaevvevggdydeavaaaaelaaegegaylvsqfdnptviegygtiglEile 152
                                        G+++++ +p +++s+ k+ +  ++Ga++v ++gd+d+a++ +++++a+ +++y++++  np++ieg++ti +Ei+e
  gi|518653172|ref|YP_008142692.1| 141 GGIESYVMIPgKNVSANKLFQAIAYGANIVDIEGDFDTAMENVKKAIAKRNDFYILNSL-NPWRIEGQKTIIYEIME 216
                                       9*******883456689***************************999996777777777.9***************9 PP

                                       HTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT......-EEEEEEECTTCGGTTCCS..S.SS..B...SSS.CCST CS
                              PALP 153 qlggkpdavvvpvGgGgliaGiaaglkerrpd......vrvigvepegsdalarslragrrvtvpvs..dtiadgla 221
                                       +++  pd +  p+G+ g+ ++++++l++ r        +++++++++g++++++++ +g+++t+++   +tia++++
  gi|518653172|ref|YP_008142692.1| 217 KIK--PDFITFPAGNLGNTSAFGKALMDLRALgvidyvPKLVAIQASGASPFYDYI-NGKEDTIHPVkaETIASAIK 290
                                       995..***********************5555556799******************.888888888889******** PP

                                       CS..CGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHH.HHHHHHCCTTCEEEEEEE-B CS
                              PALP 222 vg..spselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaal.klreagelkegdrvvviltg 294
                                       +g  ++  +a ++++ + + +  v+de+++ea r+   r gi +ep+saa++a++ kl+e g +++gd+v  iltg
  gi|518653172|ref|YP_008142692.1| 291 IGnpVNYKKAKRAIEFTKGIVEKVTDEQIMEAKREID-RSGIGCEPASAASVAGVkKLKESGIISRGDTVASILTG 365
                                       **999999999**************************.************************************98 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.7     3e-06    0.0049       2      30 ..       7      32 ..       6      37 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3e-06
                                      EETTTTCEECHEETSTTCEEESSSSBEEE CS
                      TF_Zn_Ribbon  2 kCPnCgstnlveDpergelvCtdCGlVle 30
                                      kCP C+ ++     +++ ++C++CG++l+
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNAEY---TIDSNIYICGKCGNILD 32
                                      9*****975...45578*********997 PP

>> PhnA_Zn_Ribbon  PhnA Zinc-Ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   2.1   5.5e-06     0.009       4      27 ..       7      29 ..       4      29 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5.5e-06
                    PhnA_Zn_Ribbon  4 kCplCaSeytYedgallvCpeCah 27
                                      kCp C++eyt  d  +++C +C++
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNAEYT-IDSNIYICGKCGN 29
                                      9*********.5999*******85 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2   2.7e-05     0.044       4      16 ..       7      19 ..       5      21 .. 0.90
   2 ?    0.4   0.1      0.39   6.4e+02      28      34 ..      24      30 ..      23      32 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.7e-05
                     zinc_ribbon_4  4 tCpsCkakyeidd 16
                                       CpsC+a+y+id+
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNAEYTIDS 19
                                      6**********97 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.39
                     zinc_ribbon_4 28 CskCghv 34
                                      C kCg++
  gi|518653172|ref|YP_008142692.1| 24 CGKCGNI 30
                                      9***997 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   2.2   4.6e-05     0.074       1      21 [.       7      29 ..       7      31 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.6e-05
                     zinc_ribbon_2  1 fCpnCGaelq.dnakF.CpyCGt 21
                                      +Cp+C ae   d + + C +CG 
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNAEYTiDSNIYiCGKCGN 29
                                      8********8677777******6 PP

>> Prok-RING_1  Prokaryotic RING finger family 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.6   7.5e-05      0.12       6      27 ..       7      28 ..       3      37 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.5e-05
                       Prok-RING_1  6 kCpvCgkelkeedDiVvCpeCg 27
                                      kCp C+ e + ++ i +C +Cg
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNAEYTIDSNIYICGKCG 28
                                      8********************9 PP

>> DZR  Double zinc ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.3   0.00018      0.29       1      22 [.       8      31 ..       5      44 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00018
                               DZR  1 CpqCgee..lppdarfCseCgtkl 22
                                      Cp+C++e  ++++   C++Cg+ l
  gi|518653172|ref|YP_008142692.1|  8 CPSCNAEytIDSNIYICGKCGNIL 31
                                      777777744444444777777655 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 ?   11.1   0.2   0.00018       0.3      69      95 ..       4      30 ..       1      46 [. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                                      -EEEETTTS-EEECHHHHHS-TTTSSS CS
                              HypA 69 vkvrCreCgkefeleekalrCpkCgsa 95
                                       +++C +C++e++++++ + C+kCg+ 
  gi|518653172|ref|YP_008142692.1|  4 SVLKCPSCNAEYTIDSNIYICGKCGNI 30
                                      5689*********9987778****986 PP

>> C1_4  TFIIH C1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   1.2   0.00031      0.51      22      43 ..       2      23 ..       1      38 [. 0.91

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00031
                              C1_4 22 tssryrCekCkndFCiDCDvFi 43
                                      t s+ +C++C+ ++ iD  ++i
  gi|518653172|ref|YP_008142692.1|  2 THSVLKCPSCNAEYTIDSNIYI 23
                                      67899****************9 PP

>> Zn_ribbon_SprT  SprT-like zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.9   0.00047      0.76       6      35 ..       7      32 ..       5      34 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00047
                    Zn_ribbon_SprT  6 rCtgCgreythhlsirrhnYrCrrCkgtLr 35
                                      +C++C    +++  ++   Y+C++C++ L 
  gi|518653172|ref|YP_008142692.1|  7 KCPSCNA--EYTIDSNI--YICGKCGNILD 32
                                      69***95..55555555..99****98775 PP

>> Desulfoferrod_N  Desulfoferrodoxin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       6.1   9.9e+03       6      12 ..       5      11 ..       3      12 .. 0.81
   2 ?   11.2   0.3   0.00013      0.22       5      20 ..      20      35 ..      16      37 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 6.1
                                      EEE-TTT CS
                   Desulfoferrod_N  6 vYkCevC 12
                                      v kC  C
  gi|518653172|ref|YP_008142692.1|  5 VLKCPSC 11
                                      7899988 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                                      -EEE-TTT--EEEECC CS
                   Desulfoferrod_N  5 evYkCevCGniVeVle 20
                                      ++Y C  CGni  V +
  gi|518653172|ref|YP_008142692.1| 20 NIYICGKCGNILDVFH 35
                                      79************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (387 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       729  (0.0406604); expected 358.6 (0.02)
Passed bias filter:                      613  (0.0341904); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2682.58
//
Query:       gi|518653173|ref|YP_008142693.1|  [L=58]
Description: preprotein translocase subunit SecG [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.8e-13   48.2   0.1    8.8e-13   48.1   0.1    1.1  1  Sec61_beta  Sec61beta family
  ------ inclusion threshold ------
       0.15   12.1   0.0       0.16   12.0   0.0    1.0  1  Adeno_E3A   Adenovirus E3A


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 !   48.1   0.1   9.9e-17   8.8e-13       1      41 []      15      56 ..      15      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 9.9e-17
                                      XXXXXXXXXX.----SS-B-THHHHHHHHHHHHHHHHHTSS- CS
                        Sec61_beta  1 SsaGLlryye.edapgikidPkvVlvlsvafiasVilLhila 41
                                      S+aGL+ry+  e+ +g+ idPk ++++++a++++V l+++++
  gi|518653173|ref|YP_008142693.1| 15 SGAGLIRYFNeEEIKGPAIDPKLIIYIGIAMGVIVELAKVFW 56
                                      89********8889***********************99986 PP

>> Adeno_E3A  Adenovirus E3A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.8e-05      0.16      18      65 ..       8      53 ..       1      57 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.8e-05
                         Adeno_E3A 18 rrhkcfargsgefcyfelpeehiegpahgvrlttqveltrslireftk 65
                                       + + f  g+g + yf+  ee i+gpa   +l   + ++  +i e++k
  gi|518653173|ref|YP_008142693.1|  8 NQNENFQSGAGLIRYFN--EEEIKGPAIDPKLIIYIGIAMGVIVELAK 53
                                      56778999*******96..999*****************999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); 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: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 506.28
//
Query:       gi|518653174|ref|YP_008142694.1|  [L=198]
Description: hypothetical protein FACI_IFERC00001G1815 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       873  (0.0486921); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1473.89
//
Query:       gi|518653175|ref|YP_008142695.1|  [L=277]
Description: signal sequence processing protein Sec11 precursor [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   13.9   0.7      0.069   12.9   0.7    1.5  1  DUF4538   Domain of unknown function (DUF4538)
      0.038   14.3   2.6        1.1    9.5   0.1    2.4  2  DUF996    Protein of unknown function (DUF996)


Domain annotation for each model (and alignments):
>> DUF4538  Domain of unknown function (DUF4538)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.7   7.7e-06     0.069       6      36 ..      15      45 ..      10      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.7e-06
                           DUF4538  6 yvllvggvvgliglalYPiiiaPllhpeeYk 36
                                      ++ + + +++l+g+++Y+ ++ P + +e Y 
  gi|518653175|ref|YP_008142695.1| 15 IIFIAAVIIALVGITVYSGVFPPASVVESYS 45
                                      455677789********************96 PP

>> DUF996  Protein of unknown function (DUF996)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.5    0.0048        43      26      63 ..      10      46 ..       2     111 .. 0.63
   2 ?    9.5   0.1   0.00012       1.1     100     124 ..     236     260 ..     234     261 .. 0.92

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0048
                            DUF996 26 fsnaliafilsiialvvailalllvlgalatalelpgl 63
                                      ++ + i fi+++i  +v i +  +v+  + +++e++ +
  gi|518653175|ref|YP_008142695.1| 10 YRVLTIIFIAAVIIALVGITVYSGVFPPA-SVVESYSM 46
                                      44445555555554444444444444333.33444444 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00012
                            DUF996 100 krtgvklFetagllyfiGaiLtivl 124
                                        +t v  ++ agl++ i+aiLti+l
  gi|518653175|ref|YP_008142695.1| 236 YYTHVPEYSYAGLFLSIAAILTIIL 260
                                       5889999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.46
# Mc/sec: 1820.12
//
Query:       gi|518653176|ref|YP_008142696.1|  [L=322]
Description: hypothetical protein FACI_IFERC00001G1817 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
      0.069   13.1   0.5       0.15   12.0   0.0    1.8  2  EF-hand_4  Cytoskeletal-regulatory complex EF hand


Domain annotation for each model (and alignments):
>> EF-hand_4  Cytoskeletal-regulatory complex EF hand
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.1      0.27   4.8e+03      61      68 ..     173     180 ..     169     184 .. 0.83
   2 ?   12.0   0.0   8.5e-06      0.15      22      83 ..     195     260 ..     186     277 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.27
                         EF-hand_4  61 dfeefcia 68 
                                       dfe+f+i+
  gi|518653176|ref|YP_008142696.1| 173 DFEDFVIV 180
                                       9****996 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 8.5e-06
                         EF-hand_4  22 ednkltgdkvapvlknskleedklekiwdladid...edgkldfeefciamr.lifdlvngeikdv 83 
                                       ++n ++++k a  +kns+l+ ++lek+ d  di    e g+ d +e+  ++r +   ++ +e++ +
  gi|518653176|ref|YP_008142696.1| 195 HSNIINHEKYAERVKNSELRAKELEKMADSGDIKgifEAGEKDTQEYHSMLReVGVSIITDEMQRL 260
                                       57899***********************99998633368899999987777623356666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 2214.06
//
Query:       gi|518653177|ref|YP_008142697.1|  [L=281]
Description: hypothetical protein FACI_IFERC00001G1818 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-34  117.9   2.2    2.8e-08   34.1   0.1    4.2  4  CBS       CBS domain
  ------ inclusion threshold ------
      0.013   15.6   0.1        7.2    6.8   0.1    2.9  2  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.1   3.1e-12   2.8e-08       1      52 [.       5      56 ..       5      58 .. 0.95
   2 !   28.1   0.0   2.3e-10     2e-06       4      55 ..      67     117 ..      64     119 .. 0.82
   3 !   28.3   0.0     2e-10   1.8e-06      10      55 ..     135     180 ..     126     182 .. 0.84
   4 !   24.6   0.0   2.9e-09   2.6e-05       2      53 ..     226     277 ..     222     281 .] 0.85

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.1e-12
                                      HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
                               CBS  1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDll 52
                                      V+dimtrd+++ +  + ++++++ +++++++++PV d+++++ G++t+rD++
  gi|518653177|ref|YP_008142697.1|  5 VSDIMTRDPLCYTVPSAISDVIQVLIKNNITGIPVKDNQNHYQGVITRRDIF 56
                                      89********9999999*******99*********999999*********96 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 2.3e-10
                                       HSBSSCEEEETTSBHHHHHHHHH.HHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS   4 imtrdvvtvppdttleealelmr.ekgvsrlPVVdedgklvGivtlrDllral 55 
                                       +m++ + tv++++++  a++++  +k+ ++l VV++ +++ Gi+t    l+ +
  gi|518653177|ref|YP_008142697.1|  67 VMRKAP-TVNENDSINTAARQLYtQKK-RHLVVVNDKNEVTGILTPQNFLNII 117
                                       476666.**************753555.79978999999******99888776 PP

  == domain 3  score: 28.3 bits;  conditional E-value: 2e-10
                                       EEEETTSBHHHHHHHHHHHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
                               CBS  10 vtvppdttleealelmrekg.vsrlPVVdedgklvGivtlrDllral 55 
                                       v + +dt+l+ al +m +   + ++PVV+  gk+ G+vt+rD+++++
  gi|518653177|ref|YP_008142697.1| 135 VPIWEDTPLSVALLTM-NLSqIYSFPVVNRGGKFTGLVTDRDIFDKV 180
                                       6899************.655555******999***********9876 PP

  == domain 4  score: 24.6 bits;  conditional E-value: 2.9e-09
                                       HHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHH CS
                               CBS   2 gdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllr 53 
                                       + +m   + +++ +++le+a++lm ++++++lPV+ + g++ G++ +  +++
  gi|518653177|ref|YP_008142697.1| 226 KKLMVGSPKVIYLESDLEDAVKLMSSENYNQLPVLTGHGEIYGMLYDIEIMK 277
                                       5566666778999999********9999******999*******99988877 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0008       7.2       5      46 ..     151     192 ..     149     223 .. 0.72
   2 ?    5.4   0.0    0.0021        19       9      30 ..     254     275 ..     248     277 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0008
                                       CS---TT-EEEETTSSEEEEE..EEEEEETTTTEEEEEEEEETT CS
                               PRC   5 rasdliGkeVytedGeklGkV..kDvvidekegrvralvvsvgg 46 
                                        +s++   +V+++ G+  G V   D+ +d+   + + ++ s++g
  gi|518653177|ref|YP_008142697.1| 151 NLSQIYSFPVVNRGGKFTGLVtdRDI-FDK-VKMYQTIESSESG 192
                                       68999****************66666.664.6666666666664 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0021
                                       -TT-EEEETTSSEEEEEEEEEE CS
                               PRC   9 liGkeVytedGeklGkVkDvvi 30 
                                          ++V t+ Ge++G ++D+ i
  gi|518653177|ref|YP_008142697.1| 254 YNQLPVLTGHGEIYGMLYDIEI 275
                                       5679***************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.45
# Mc/sec: 1886.18
//
Query:       gi|518653178|ref|YP_008142698.1|  [L=474]
Description: hypothetical protein FACI_IFERC00001G1819 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-22   79.1   0.8    4.3e-22   78.1   0.3    1.8  2  HGTP_anticodon  Anticodon binding domain
    1.4e-08   35.0   0.1    7.1e-07   29.4   0.0    2.3  2  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
  ------ inclusion threshold ------
       0.12   12.5   0.1       0.25   11.5   0.1    1.5  1  DUF678          Protein of unknown function (DUF678)
       0.21   11.5   0.5        7.3    6.6   0.2    2.4  2  zinc_ribbon_4   zinc-ribbon domain


Domain annotation for each model (and alignments):
>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.7   7.4e+03      54      68 ..     203     218 ..     196     243 .. 0.46
   2 !   78.1   0.3   9.7e-26   4.3e-22       2      89 ..     378     463 ..     377     466 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.7
                                       SEEEEE-HHHHH.HTE CS
                    HGTP_anticodon  54 pfavvvGekele.kgt 68 
                                        + v+++++ le k  
  gi|518653178|ref|YP_008142698.1| 203 EIEVFLDPENLEfKSL 218
                                       4455555555542122 PP

  == domain 2  score: 78.1 bits;  conditional E-value: 9.7e-26
                                       EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCE CS
                    HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtre 78 
                                       ++v pl + +e+l+e a+ ++e +++++ +  ++d++++igk++++ d++g+p++++v++++le++tvtvr+rdt e
  gi|518653178|ref|YP_008142698.1| 378 FAVFPLMK-KENLKEKAEYIYENMKKQD-KYIVYDEAGTIGKRYARQDEIGTPYCITVDYQTLEDNTVTVRSRDTAE 452
                                       68999999.666****************.6777789***************************************** PP

                                       EEEEETTHHHH CS
                    HGTP_anticodon  79 qervsldelve 89 
                                       q r++++el++
  gi|518653178|ref|YP_008142698.1| 453 QKRIKIEELLD 463
                                       ********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 !   29.4   0.0   1.6e-10   7.1e-07       9      83 ..     145     221 ..     137     226 .. 0.79
   2 ?    3.2   0.0     0.018        79      84     178 ..     256     356 ..     235     357 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 1.6e-10
                                       EEEEE-SSSHHHHHHHHHHHEE..EBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHH.HHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxx RF
                      tRNA-synt_2b   9 reyiLkPtneetfvelirdevl..rskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeasld.dslrd 82 
                                        +y+L+P+  +++   ++      +  +LP+ + q +  +R+E s  + L+R+reF+q + +vf  +++l+  sl+d
  gi|518653178|ref|YP_008142698.1| 145 GDYYLRPETAQGIFVNFKLL-FnyNRGKLPMIVGQAGKGFRNEISPRQSLIRLREFNQCEIEVFLDPENLEfKSLYD 220
                                       58**********98777643.3245555****************9556*****************965543256666 PP

                                       H CS
                                       x RF
                      tRNA-synt_2b  83 l 83 
                                       +
  gi|518653178|ref|YP_008142698.1| 221 Y 221
                                       6 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.018
                                       HHHHHHHHHHTT.SCEEEEEEGTTSC...BTTSEEEEEEEEETTTSEEEEEEEEEEEET.....HHHHHTTEEEECT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxx RF
                      tRNA-synt_2b  84 ikaisriferlglefraiielmsaks...adykdkkefeavsesltkgieigtiqklgt.....rlserlgatvlde 152
                                       + ++++i+e++g+e  +++   ++ +     ++d+ + e +    +   ei+ i ++ +     ++s+  ++ + + 
  gi|518653178|ref|YP_008142698.1| 256 VLKTQNILENIGIESSKLRFRQHDPDeraHYASDSWDAEGLID--NEWFEIVGIANRTDfdlnnHQSSSGETMTTKI 330
                                       5567777788888776666553322222244556666665555..66778888877654311113444444455566 PP

                                       TSSEEEEEEEEEEEEHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxx RF
                      tRNA-synt_2b 153 nnreksvimicaaigveRllsaileq 178
                                       ++re  +++i  + g+ R+l+ +++q
  gi|518653178|ref|YP_008142698.1| 331 EEREFIPYVIEPSYGIDRILLTLMAQ 356
                                       7788899999999*****99988876 PP

>> DUF678  Protein of unknown function (DUF678)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   5.5e-05      0.25      27      74 ..      84     137 ..      76     138 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.5e-05
                            DUF678  27 TCSlCqSkLvkvsdvskvslsklkva.......vgkgntlrCaACgSsLtlLrdl 74 
                                        C  C+Sk  k+ +v   + +++ +a       +   + l+C  CgS +t++ d+
  gi|518653178|ref|YP_008142698.1|  84 ECEKCKSKF-KFESVLAFNKQDIIPAnleeakeMASDTYLKCPVCGSRITNIYDF 137
                                       689999996.55555555544444444444444488899***********99988 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.2    0.0016       7.3       4      15 ..      84      95 ..      82      98 .. 0.87
   2 ?    2.7   0.0     0.028   1.2e+02      23      35 ..     119     131 ..     109     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0016
                     zinc_ribbon_4  4 tCpsCkakyeid 15
                                      +C++Ck+k++++
  gi|518653178|ref|YP_008142698.1| 84 ECEKCKSKFKFE 95
                                      8********986 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.028
                     zinc_ribbon_4  23 gvkvrCskCghvF 35 
                                        + ++C+ Cg  +
  gi|518653178|ref|YP_008142698.1| 119 DTYLKCPVCGSRI 131
                                       56689****9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       757  (0.0422221); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); 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: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.47
# Mc/sec: 3019.59
//
Query:       gi|518653179|ref|YP_008142699.1|  [L=320]
Description: serine protease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.3e-35  120.9   0.4    1.2e-34  120.4   0.4    1.2  1  Trypsin_2      Trypsin-like peptidase domain
    2.5e-14   53.6   0.0    3.9e-14   53.0   0.0    1.3  1  Trypsin        Trypsin
    7.4e-11   42.2   0.1    1.7e-09   37.9   0.0    2.5  2  PDZ_2          PDZ domain
    1.4e-08   34.4   0.1    9.3e-08   31.8   0.0    2.3  2  PDZ_6          PDZ domain
    1.1e-06   28.9   0.3    4.9e-06   26.8   0.0    2.4  2  PDZ            PDZ domain
  ------ inclusion threshold ------
      0.014   14.1   2.5       0.71    8.4   0.1    2.1  2  Peptidase_S46  Peptidase S46
      0.046   13.4   0.5       0.24   11.1   0.0    2.3  3  LSM            LSM domain


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.4   4.7e-38   1.2e-34       1     150 []      45     182 ..      45     182 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 4.7e-38
                         Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgp 77 
                                       GsGf+++ dg+ilTn+Hv+++a+++ v         + +dgr++++++ ++dp++D+Al+k+   +++++p+++lg+
  gi|518653179|ref|YP_008142699.1|  45 GSGFIISHDGYILTNNHVIEGAETVDV---------VLNDGRKFKGEIAGTDPQTDVALVKI---PGDDFPVIELGD 109
                                       9**************************.........**************************...************ PP

                         Trypsin_2  78 sealkggepvyvvGyplggeksgsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                                       se++++g+ v ++G+ lg +++ +vs G++s+ ++   +a++  e++lqtdaa++pG+SGGpl+d +G+ vG+
  gi|518653179|ref|YP_008142699.1| 110 SEKIRVGSIVLAIGNALGLPGGHTVSMGVISAKNRPMPWADFIFEGLLQTDAAINPGNSGGPLVDLTGKAVGI 182
                                       *********************99************8888888888888************************8 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.0   0.0   1.5e-17   3.9e-14      27     219 ..      45     204 ..      18     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 53.0 bits;  conditional E-value: 1.5e-17
                                       EEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBS CS
                           Trypsin  27 CgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgd 102
                                        +G++is + ++lT++H++++a+ v+v       + ++g + k++++        +p+t   D+al+k+  +     
  gi|518653179|ref|YP_008142699.1|  45 GSGFIISHDgYILTNNHVIEGAETVDV-------VLNDGRKFKGEIAG------TDPQT---DVALVKIPGD----- 100
                                       479***9999***********777766.......66678544555555......89999...*******998..... PP

                                       SBHCCBBCSTTHTTSTTTEEEEEESSBSSTSSBSSBEEEEEEEEEEHHHHHHHTTTTSTTTEEEEESTTSSSBCTTT CS
                           Trypsin 103 tvrpiclpaassslpvgttclvsGwgrtkekgksdtlqevevpvvsretcksaykgkvtenmlcagakeggkdacqG 179
                                           i+l + s+++ vg+ +l++G       g     ++v + v+s ++    + + + e  l+++a     ++++G
  gi|518653179|ref|YP_008142699.1| 101 DFPVIELGD-SEKIRVGSIVLAIGNALGLPGG-----HTVSMGVISAKNRPMPWADFIFEGLLQTDA-----AINPG 166
                                       8899*****.6656677555555555566666.....788899999977777677778889999999.....***** PP

                                       TTTSEEEETTTEEEEEEEEESSSSCTTSEEEEEEGGGGHH CS
                           Trypsin 180 DSGGPlvcsdgelvGivswgkgcakgnrpgvytkvssyld 219
                                       +SGGPlv  +g++vGi+++    a+g  +g+ ++v+++++
  gi|518653179|ref|YP_008142699.1| 167 NSGGPLVDLTGKAVGINTAMIAQANG--IGFSIPVNTIKK 204
                                       *******************9666666..9******98875 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.15   3.9e+02      43      67 ..      70      94 ..      62      97 .. 0.90
   2 !   37.9   0.0   6.7e-13   1.7e-09       2      65 ..     219     292 ..     218     306 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.15
                                      TB--SSHHHHHHHHHTS-TT-EEEE CS
                             PDZ_2 43 gkkvksledlislllkkkpGdtVkl 67
                                      ++++++++++++++++++p+++V l
  gi|518653179|ref|YP_008142699.1| 70 DVVLNDGRKFKGEIAGTDPQTDVAL 94
                                      56789*****************987 PP

  == domain 2  score: 37.9 bits;  conditional E-value: 6.7e-13
                                       ...XX------............-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EE CS
                             PDZ_2   2 ylGvsvsdeed..........tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtV 65 
                                       y+G+s  + ++          ++gv v+ ++  +Pa +agl++gDvi+++ gk+vks +dli+ ++++k +++V
  gi|518653179|ref|YP_008142699.1| 219 YIGISGIEINEssqgrygvklENGVMVARIDRYSPAYDAGLRPGDVITEFAGKPVKSMRDLIKGVAEMKGNTDV 292
                                       56666666555566777888888**********************************************99998 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.68   1.8e+03      16      27 ..     113     124 ..     108     126 .. 0.87
   2 !   31.8   0.0   3.6e-11   9.3e-08       2      39 ..     245     280 ..     244     287 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.68
                             PDZ_6  16 lrvGDiilsvNG 27 
                                       +rvG i+l++++
  gi|518653179|ref|YP_008142699.1| 113 IRVGSIVLAIGN 124
                                       89*******986 PP

  == domain 2  score: 31.8 bits;  conditional E-value: 3.6e-11
                             PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladva 39 
                                       V  +d  sPA+ AGlr+GD+i+++ G+pv  +s+ d++
  gi|518653179|ref|YP_008142699.1| 245 VARIDRYSPAYDAGLRPGDVITEFAGKPV--KSMRDLI 280
                                       6778888**********************..9998875 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.4   6.2e+03      43      55 ..     112     124 ..     108     137 .. 0.82
   2 !   26.8   0.0   1.9e-09   4.9e-06      14      64 ..     225     279 ..     185     293 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.4
                                       TSSTTEEEEEETT CS
                               PDZ  43 glkvGDkIlsvNg 55 
                                       +++vG ++l++++
  gi|518653179|ref|YP_008142699.1| 112 KIRVGSIVLAIGN 124
                                       4999999999987 PP

  == domain 2  score: 26.8 bits;  conditional E-value: 1.9e-09
                                       EEEEEETTSS....SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHH CS
                               PDZ  14 fslkggsdqr....gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvshe 64 
                                       +++ + s  r     ++g+ v+++ + ++a  +gl++GD+I++  g++v++++++
  gi|518653179|ref|YP_008142699.1| 225 IEINESSQGRygvkLENGVMVARIDRYSPAYDAGLRPGDVITEFAGKPVKSMRDL 279
                                       33333333336666668***********************************865 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.1   0.00028      0.71      45      69 ..      41      65 ..      30      68 .. 0.87
   2 ?    5.3   0.5    0.0024       6.2     627     651 ..     159     183 ..     155     192 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00028
                                      ETTTEE-EE-STT-EEEE-HHHHHH CS
                     Peptidase_S46 45 flggCtasfVSpeGLvlTNHHCayg 69
                                      ++g  ++ ++S++G +lTN H++ g
  gi|518653179|ref|YP_008142699.1| 41 VKGAGSGFIISHDGYILTNNHVIEG 65
                                      57999****************9765 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0024
                                       ES----TT-TT-EEE-TTS-EEEEE CS
                     Peptidase_S46 627 stnDitGGNSGSPvlngkgelvGla 651
                                       +++ i  GNSG P+++  g+ vG++
  gi|518653179|ref|YP_008142699.1| 159 TDAAINPGNSGGPLVDLTGKAVGIN 183
                                       5677889****************98 PP

>> LSM  LSM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       1.3   3.2e+03       3      20 ..       4      21 ..       2      23 .. 0.77
   2 ?   11.1   0.0   9.2e-05      0.24       9      36 ..      67      94 ..      66      97 .. 0.90
   3 ?   -3.2   0.0       2.7   6.9e+03      53      59 ..     291     297 ..     283     299 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 1.3
                                      HHHTTTSEEEEEETTSEE CS
                               LSM  3 lkklinkkvtvelkngre 20
                                      +++l+n++v +  k  r 
  gi|518653179|ref|YP_008142699.1|  4 IEELNNNTVEIAEKASRA 21
                                      778999999998887775 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 9.2e-05
                                      SEEEEEETTSEEEEEEEEEEETTSEEEE CS
                               LSM  9 kkvtvelkngrelrGtLkgfDqfmNlvL 36
                                      ++v v l++gr+++G + g D++  + L
  gi|518653179|ref|YP_008142699.1| 67 ETVDVVLNDGRKFKGEIAGTDPQTDVAL 94
                                      6899******************987776 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 2.7
                                       EEEEEEG CS
                               LSM  53 glvliRG 59 
                                       + ++iRG
  gi|518653179|ref|YP_008142699.1| 291 DVIFIRG 297
                                       5689998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); 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: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2171.49
//
Query:       gi|518653180|ref|YP_008142700.1|  [L=107]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete 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   55.2   0.1    5.8e-15   54.9   0.1    1.1  1  HxlR      HxlR-like helix-turn-helix
    0.00025   21.2   0.0    0.00045   20.3   0.0    1.4  1  HTH_34    Winged helix DNA-binding domain
    0.00096   19.1   0.1     0.0012   18.7   0.1    1.2  1  PadR      Transcriptional regulator PadR-like family
     0.0027   17.7   0.1      0.018   15.0   0.1    2.0  2  HTH_45    Winged helix-turn-helix
  ------ inclusion threshold ------
       0.02   14.3   0.0      0.023   14.1   0.0    1.0  1  DUF1202   Protein of unknown function (DUF1202)
      0.027   14.3   0.0      0.039   13.8   0.0    1.2  1  DUF3116   Protein of unknown function (DUF3116)
      0.061   13.3   0.0      0.099   12.6   0.0    1.4  1  MarR      MarR family
       0.13   12.0   0.0       0.13   11.9   0.0    1.2  1  DUF4423   Domain of unknown function (DUF4423)


Domain annotation for each model (and alignments):
>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.1   2.6e-18   5.8e-15       5      83 ..      25     104 ..      22     107 .] 0.92

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2.6e-18
                                       TTHHHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE-TCGGGGHHHHHHHH CS
                              HxlR   5 kWkllilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsltekGrslepvlqelk 80 
                                        W++ i+ ++ + g+  f+++k+ + +i   +L+++L +Le+ gl+er+++p  P++v+Yslt+kG++l+++  +l+
  gi|518653180|ref|YP_008142700.1|  25 MWTVPIMLAIERhGEAGFNQIKKDVRGINSTTLSTTLGMLEKYGLLERVIIPAKPVRVKYSLTDKGKELYKISLNLA 101
                                       6999999998766**********************************************************988887 PP

                                       HHH CS
                              HxlR  81 kwg 83 
                                        ++
  gi|518653180|ref|YP_008142700.1| 102 TLI 104
                                       766 PP

>> HTH_34  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0     2e-07   0.00045       6      70 ..      31      95 ..      28     102 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2e-07
                            HTH_34  6 lsyLasvdeadfvelkeale.atdgnLsvhlkkLekagYievdkefkgkkprtllriTpeGreafk 70
                                      +       ea f+++k+ ++ +++  Ls+ l +Lek g +e+ +   +   r  +++T++G+e +k
  gi|518653180|ref|YP_008142700.1| 31 MLAIERHGEAGFNQIKKDVRgINSTTLSTTLGMLEKYGLLERVIIPAKP-VRVKYSLTDKGKELYK 95
                                      555556789******999854999****************988866655.7889********9887 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.6e-07    0.0012      10      72 ..      36      93 ..      30      96 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.6e-07
                                      EEHHHHHHHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE-STSSS-EEEEEESHCCCHH CS
                              PadR 10 syGyeiikeleelsegllelseGslYpaLkrLekeglveseweesgegpprkyYrlTdaGrre 72
                                      ++G +  +++++ + g   ++ ++l ++L  Lek gl+e+   ++  +p r  Y lTd+G++ 
  gi|518653180|ref|YP_008142700.1| 36 RHGEAGFNQIKKDVRG---INSTTLSTTLGMLEKYGLLERVIIPA--KPVRVKYSLTDKGKEL 93
                                      6777777778888666...89********************9985..9************986 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0      0.25   5.5e+02      62      75 ..      12      25 ..      10      27 .. 0.86
   2 !   15.0   0.1   8.2e-06     0.018      31      68 ..      52      96 ..      28     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.25
                            HTH_45 62 Glelleklkeleel 75
                                      G+e+l+k+ ++ ++
  gi|518653180|ref|YP_008142700.1| 12 GKEFLDKYSDIMRM 25
                                      99******999887 PP

  == domain 2  score: 15.0 bits;  conditional E-value: 8.2e-06
                            HTH_45 31 LsykllnkYLdmLvekgli.......kkskekYvlTekGlellek 68
                                      ++  +l+  L mL + gl+       k    kY+lT+kG+el++ 
  gi|518653180|ref|YP_008142700.1| 52 INSTTLSTTLGMLEKYGLLerviipaKPVRVKYSLTDKGKELYKI 96
                                      777888999999999999766678977799***********9975 PP

>> DUF1202  Protein of unknown function (DUF1202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     1e-05     0.023      23     103 ..      16      99 ..       9     104 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1e-05
                           DUF1202  23 kkqyhgilkldaitl.knldakgnqatwsaegdvs..sredlytgvgqladyellektwtkdkpvkfsamltskgtp 96 
                                         +y  i+++ ++ +   ++ +g+      + dv    +  l t +g+l  y lle+     kpv+    lt kg  
  gi|518653180|ref|YP_008142700.1|  16 LDKYSDIMRMWTVPImLAIERHGEAGFNQIKKDVRgiNSTTLSTTLGMLEKYGLLERVIIPAKPVRVKYSLTDKGKE 92 
                                       5566666666665431355666665555666666522456799********************************87 PP

                           DUF1202  97 asgwsvn 103
                                           s+n
  gi|518653180|ref|YP_008142700.1|  93 LYKISLN 99 
                                       7666666 PP

>> DUF3116  Protein of unknown function (DUF3116)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.7e-05     0.039      35      81 ..      48      95 ..      38      99 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.7e-05
                           DUF3116 35 svkkltkneLLytvYWLElkgyilRkeeka.nnkkrYelTekGellyk 81
                                       v+ ++ ++L  t+  LE +g + R    a   + +Y+lT+kG++lyk
  gi|518653180|ref|YP_008142700.1| 48 DVRGINSTTLSTTLGMLEKYGLLERVIIPAkPVRVKYSLTDKGKELYK 95
                                      446677888888889999999999987643045779***********8 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.4e-05     0.099       9      51 ..      31      74 ..      28      77 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.4e-05
                                      HHHHHHSTTEEHHHHHHHH.TS-HHHHHHHHHHHHHTTSEEEEE CS
                              MarR  9 LrilyeqgplsvseLakkl.gvskstvtrvldrLekkGlieRsk 51
                                      +  ++++g++   ++ k + g++++t++++l  Lek Gl+eR  
  gi|518653180|ref|YP_008142700.1| 31 MLAIERHGEAGFNQIKKDVrGINSTTLSTTLGMLEKYGLLERVI 74
                                      666888888888888876647*********************75 PP

>> DUF4423  Domain of unknown function (DUF4423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.9e-05      0.13      14      71 ..      18      73 ..       5      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
                           DUF4423 14 efe.yfssWyypvirellplkdfkadpeelakrlrpkisaeevekalefLlklgllkkd 71
                                      +++ +++ W  p++++ ++ + + a  ++++k +r  i+    +++l  L+k gll++ 
  gi|518653180|ref|YP_008142700.1| 18 KYSdIMRMWTVPIMLA-IERHGE-AGFNQIKKDVR-GINSTTLSTTLGMLEKYGLLERV 73
                                      344499*********8.555555.7**********.9*******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       301  (0.0167884); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 916.45
//
Query:       gi|518653181|ref|YP_008142701.1|  [L=319]
Description: hypothetical protein FACI_IFERC00001G1822 [Ferroplasma acidarmanus fer1]
Scores for complete 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-50  169.7   1.2    9.7e-50  169.4   1.2    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 !  169.4   1.2   5.4e-54   9.7e-50      11     313 ..      20     313 ..      11     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 5.4e-54
                                       HHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  11 ldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspqlylelli 87 
                                        +l  ++v++ ++++s + ++v ++l e g+iei + i+s  + + +   +  k ++  +++  +tqs+ +++++ +
  gi|518653181|ref|YP_008142701.1|  20 QHLSDKRVQHAIKVQSYIRSYVTDFLREAGYIEIAPIIISPLTDPLNHPVYDPKIHAYGGDMW-ITQSMIFHKQIAV 95 
                                       3458999***************************98888888778888888887777777888.9************ PP

                                       HCTHSEEEEEEEEE-...-S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTS CS
                                       xxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2  88 vagidrvfqiaraFR...aEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrns 161
                                          ++++f ++++ R   +E+s++ rhl EFtqi++e    + e++m+++e++i ++++++++++++++e  +r+  
  gi|518653181|ref|YP_008142701.1|  96 QE-LKKIFIMSPNVRletEEKSKSGRHLYEFTQIDVEALEKSREEMMSLAEDMIIYTISRLKKEHKEELEYFHRTLP 171
                                       *9.************5555689999************************************9999999999988876 PP

                                       EE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHHHS--SEEEEEEEBGGGSTTCBBBSTTSTTBBSEEEEEET.T CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x RF
                       tRNA-synt_2 162 kdlkkpfkrltykeaieklneigkdldkaderalvkkeknepvfvtdfPaelkpFyarkeeddkkltesyDllin.g 237
                                        d +kpf+ +t++ea +k+   gk+ +++     + ke++ pv+v+d P + + Fy r+  +++ + + +Dl+++ g
  gi|518653181|ref|YP_008142701.1| 172 -DYAKPFPVITFEEAEKKY---GKGFETP-----LSKESSTPVWVVDIPLKEREFYDREYPEKPGILRDMDLIWPeG 239
                                       .9999***********993...4555554.....5668889*********************************978 PP

                                       E.EEEEEEEB--SHHHHHHHHHHCCHHSSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                                       x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       tRNA-synt_2 238 v.ElvgGslRiedpeeleeklkskgldeeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                                       + E  +G  R+ +  +  +++++kg +   ee+f+w++e+ ++G+  ++G+g+G++R++ +++g e+I dv+ FPk+
  gi|518653181|ref|YP_008142701.1| 240 FeEASSGGEREYELSQILDRIQKKGQT---EEQFKWFIELAKQGIKYTAGFGIGIERFTRFVCGVEKIEDVTTFPKV 313
                                       89*************************...*********************************************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      678  (0.0378158); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2393.81
//
Query:       gi|518653182|ref|YP_008142702.1|  [L=147]
Description: transcriptional regulatory protein [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   41.9   0.0    9.7e-11   41.5   0.0    1.2  1  AsnC_trans_reg  Lrp/AsnC ligand binding domain
    2.4e-09   36.6   0.1    7.6e-09   35.0   0.1    1.9  2  HTH_24          Winged helix-turn-helix DNA-binding
    8.9e-07   28.6   0.1    1.9e-06   27.6   0.1    1.6  1  HTH_AsnC-type   AsnC-type helix-turn-helix domain
    6.5e-06   25.9   0.1    1.6e-05   24.7   0.0    1.7  2  TrmB            Sugar-specific transcriptional regulator TrmB
    6.1e-05   22.8   0.0     0.0001   22.1   0.0    1.4  1  HTH_5           Bacterial regulatory protein, arsR family
      7e-05   22.7   0.0    0.00016   21.5   0.0    1.5  1  MarR            MarR family
    0.00012   21.8   0.0    0.00022   21.0   0.0    1.3  1  HTH_IclR        IclR helix-turn-helix domain
    0.00046   20.2   0.1    0.00093   19.3   0.1    1.4  1  DUF2250         Uncharacterized protein conserved in archaea 
     0.0042   16.9   0.0     0.0074   16.2   0.0    1.3  1  MarR_2          MarR family
     0.0063   17.0   0.0      0.015   15.8   0.0    1.7  1  HTH_27          Winged helix DNA-binding domain
  ------ inclusion threshold ------
      0.013   15.4   0.1      0.026   14.4   0.1    1.5  1  RuvB_C          RuvB C-terminal winged helix domain
      0.018   14.8   0.0      0.046   13.5   0.0    1.7  1  HTH_DeoR        DeoR-like helix-turn-helix domain
      0.027   14.3   0.3      0.073   12.9   0.0    1.8  2  HxlR            HxlR-like helix-turn-helix
      0.035   14.3   0.0      0.079   13.2   0.0    1.6  1  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.072   13.4   0.0       0.18   12.1   0.0    1.7  2  Rrf2            Transcriptional regulator
      0.092   12.7   0.0       0.15   12.0   0.0    1.4  1  HTH_11          HTH domain
        0.1   12.1   0.2       0.16   11.6   0.2    1.2  1  DDRGK           DDRGK domain
       0.11   12.5   0.0       0.28   11.2   0.0    1.7  1  HTH_6           Helix-turn-helix domain, rpiR family
       0.15   12.1   0.0       0.26   11.3   0.0    1.4  1  PadR            Transcriptional regulator PadR-like family
       0.15   12.1   0.0       0.33   11.1   0.0    1.5  1  FeoC            FeoC like transcriptional regulator


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 !   41.5   0.0   1.1e-13   9.7e-11       2      74 ..      72     144 ..      71     145 .. 0.87

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.1e-13
                                       EEEE-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSSEEEEEEESSHHHHHHHHHHTTTTSTTEEEEEEEEEEE CS
                    AsnC_trans_reg   2 lvslepghpeqleefeealaelpeVvecyrvtGdydyllkvvvrdlealerflreklaslpgvartetsivle 74 
                                       +++ +p+++ + +++   l ++++V+++  vtGd+d++l  + +++++l++f+ e+l++++g++++ t   +e
  gi|518653182|ref|YP_008142702.1|  72 MIQYNPKASIDQRTLCLNLSKMDNVISASIVTGDWDIVLLTAQKSMRDLSKFVLEQLRTMDGIEKSVTIPLFE 144
                                       56666666667777777899*********************************************99987665 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.1   8.5e-12   7.6e-09       2      48 .]       6      52 ..       5      52 .. 0.98
   2 ?   -2.4   0.0       4.2   3.7e+03      19      26 ..     116     123 ..     112     124 .. 0.78

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 8.5e-12
                            HTH_24  2 detdrkILelLqknprisqreLAerlglSpstvnrrlkrLeeeGlIk 48
                                      d++d kI+e+L++++r  +++++ +l ++++t+ +r++rL ++G+Ik
  gi|518653182|ref|YP_008142702.1|  6 DKKDMKIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIK 52
                                      99********************************************7 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                            HTH_24  19 sqreLAer 26 
                                       s+r+L++ 
  gi|518653182|ref|YP_008142702.1| 116 SMRDLSKF 123
                                       89999986 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 !   27.6   0.1   2.1e-09   1.9e-06       1      42 []       5      46 ..       5      46 .. 0.98

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 2.1e-09
                     HTH_AsnC-type  1 LDeiDrkILeaLqedaRisyaeLAervGlSestvlrRvrrLe 42
                                      +D+ D kI+e L e +R   ++++ ++ + ++t+ +R++rL+
  gi|518653182|ref|YP_008142702.1|  5 IDKKDMKIIEYLKEHGRDKISDISNALQIPRATIFERMERLR 46
                                      69***************************************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 !   24.7   0.0   1.8e-08   1.6e-05       7      55 ..       6      54 ..       4      73 .. 0.88
   2 ?   -3.2   0.0       8.9     8e+03      42      55 ..     124     137 ..     124     141 .. 0.60

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 1.8e-08
                                      HHHCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHHHCTSEEEE CS
                              TrmB  7 seyEakvYlaLlklgpatadeiaeelgvprskvYevLrsLedkGlVere 55
                                       + ++k+  +L ++g+ ++++i+++l +pr+++ e +++L + G++++ 
  gi|518653182|ref|YP_008142702.1|  6 DKKDMKIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIKKY 54
                                      667888888999**********************************985 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8.9
                                       HHHHHHHCTSEEEE CS
                              TrmB  42 vLrsLedkGlVere 55 
                                       vL++L  ++ +e++
  gi|518653182|ref|YP_008142702.1| 124 VLEQLRTMDGIEKS 137
                                       56677666666654 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 !   22.1   0.0   1.1e-07    0.0001       5      47 .]      10      53 ..       6      53 .. 0.94

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.1e-07
                                      HHHHHHHTT.SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE CS
                             HTH_5  5 lkILklLae.gelcvcelaeelglsqstvShHLkkLreaGLVek 47
                                       kI+ +L e g  ++++++++l+++++t+ +   +Lr+ G+++k
  gi|518653182|ref|YP_008142702.1| 10 MKIIEYLKEhGRDKISDISNALQIPRATIFERMERLRKDGFIKK 53
                                      69***************************************986 PP

>> MarR  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   1.8e-07   0.00016       6      50 ..      10      54 ..       7      56 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.8e-07
                                      HHHHHHHHHSTTEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE CS
                              MarR  6 fviLrilyeqgplsvseLakklgvskstvtrvldrLekkGlieRs 50
                                      ++i++ l+e+g  ++s++ ++l++ ++t+ +   rL k+G+i+++
  gi|518653182|ref|YP_008142702.1| 10 MKIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIKKY 54
                                      578899************************************987 PP

>> HTH_IclR  IclR helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   2.4e-07   0.00022       6      49 ..      10      52 ..       8      54 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 2.4e-07
                                      HHHHCT-CTTBSS-BHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                          HTH_IclR  6 laiLdalaeapqeltlselArrtglpkStvhRlLqtLvelGyve 49
                                      + i+++l e++++ ++s++++++ +p++t +  +  L + G+++
  gi|518653182|ref|YP_008142702.1| 10 MKIIEYLKEHGRD-KISDISNALQIPRATIFERMERLRKDGFIK 52
                                      579**********.**************************9997 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 !   19.3   0.1     1e-06   0.00093       7      56 ..       6      55 ..       2      59 .. 0.94

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1e-06
                           DUF2250  7 delalkvlkhlkkanvdYaksiakeleipleevrellkkLeelGLlerve 56
                                      d++++k++++lk+ + d    i++ l+ip+  + e +++L++ G +++++
  gi|518653182|ref|YP_008142702.1|  6 DKKDMKIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIKKYT 55
                                      67789*******************************************97 PP

>> MarR_2  MarR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.2e-06    0.0074      11      54 ..      13      54 ..       8      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.2e-06
                                      HHHHHCTTTSEEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEE CS
                            MarR_2 11 LaaLgrrpgrdltvgelarrlglsksavsrilkrLvaaGLverr 54
                                      + +L  +++ d  ++++  +l+++++++  + +rL + G++ + 
  gi|518653182|ref|YP_008142702.1| 13 IEYLKEHGR-D-KISDISNALQIPRATIFERMERLRKDGFIKKY 54
                                      667777875.4.9****************************875 PP

>> HTH_27  Winged helix DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.6e-05     0.015      13      50 ..      17      53 ..       2      57 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.6e-05
                            HTH_27 13 rhrrrrkkladlcgrlnvedshisyslkkLtekGLver 50
                                      + +++r+k++d++ +l++  ++i + +++L + G++++
  gi|518653182|ref|YP_008142702.1| 17 K-EHGRDKISDISNALQIPRATIFERMERLRKDGFIKK 53
                                      3.899******************************954 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   0.1   2.9e-05     0.026       4      56 ..       5      53 ..       2      56 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.9e-05
                                      --HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEE CS
                            RuvB_C  4 LdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIer 56
                                      +d++d+k+++ lk   + g   ++ ++++l++++ ti + +E  L k g+I++
  gi|518653182|ref|YP_008142702.1|  5 IDKKDMKIIEYLK---EHGRDKISDISNALQIPRATIFERMER-LRKDGFIKK 53
                                      5888999999999...679999********************7.778888887 PP

>> HTH_DeoR  DeoR-like helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   5.1e-05     0.046       4      45 ..      11      52 ..       9      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5.1e-05
                          HTH_DeoR  4 qilellkqqgklsveelvellgvSeaTiRRDLneLeeqgllt 45
                                      +i+e+lk++g  ++ ++++ l++  aTi   ++ L ++g ++
  gi|518653182|ref|YP_008142702.1| 11 KIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIK 52
                                      8**************************966666666666655 PP

>> HxlR  HxlR-like helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   8.1e-05     0.073       8      65 ..      10      67 ..       5      70 .. 0.85
   2 ?   -2.2   0.0       4.3   3.8e+03       2      13 ..     102     113 ..     101     133 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 8.1e-05
                                      HHHHHHHTT.S-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSS-EEEEEE CS
                              HxlR  8 llilvellk.gkkRfselkralpkisqkmLaqrLreLeqdglierevypevPpkveYsl 65
                                      + i+  l + g+ + s++++al +i++ ++ +r+ +L +dg+i++ +++    k  Ys+
  gi|518653182|ref|YP_008142702.1| 10 MKIIEYLKEhGRDKISDISNAL-QIPRATIFERMERLRKDGFIKKYTVDLNYDKLGYSV 67
                                      5566667666************.**********************99988888888875 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 4.3
                                       HHSTTHHHHHHH CS
                              HxlR   2 iggkWkllilve 13 
                                       ++g W +++l++
  gi|518653182|ref|YP_008142702.1| 102 VTGDWDIVLLTA 113
                                       566677666643 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   8.9e-05     0.079      19      53 ..      18      52 ..      11      55 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 8.9e-05
                                      HHSSB-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                    Fe_dep_repress 19 ekkvvktkdlaerLnvspssVsemlkkLekdGyve 53
                                      e++  k +d++ +L++  +++ e +++L+kdG+++
  gi|518653182|ref|YP_008142702.1| 18 EHGRDKISDISNALQIPRATIFERMERLRKDGFIK 52
                                      56666789************************986 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0    0.0002      0.18      14      56 ..      13      52 ..       9      55 .. 0.87
   2 ?   -2.4   0.0       6.9   6.2e+03      43      49 ..     114     120 ..      86     138 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0002
                                      HHHHHHSSTCC-B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                              Rrf2 14 llyLakeeeeepvsseeiaerqnispsylekilakLrkaglvk 56
                                      + yL+++ +++   +++i++  +i++  +   +++Lrk g++k
  gi|518653182|ref|YP_008142702.1| 13 IEYLKEHGRDK---ISDISNALQIPRATIFERMERLRKDGFIK 52
                                      55777777776...9**************************98 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.9
                                       HHHHHHH CS
                              Rrf2  43 ekilakL 49 
                                       +k ++ L
  gi|518653182|ref|YP_008142702.1| 114 QKSMRDL 120
                                       3333333 PP

>> HTH_11  HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017      0.15       4      44 ..      11      54 ..       8      66 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                            HTH_11  4 qilelLleargpisgeeLAeeLnvSrrtvrrdIkaLeelg....v 44
                                      +i+e L+e+     +++++  L + r+t+  ++++L++ g    +
  gi|518653182|ref|YP_008142702.1| 11 KIIEYLKEHG-RDKISDISNALQIPRATIFERMERLRKDGfikkY 54
                                      89****5555.5699*************************55554 PP

>> DDRGK  DDRGK domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.2   0.00018      0.16     102     143 ..      10      51 ..       3      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00018
                                       HHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS CS
                             DDRGK 102 eefinyikekKvvlleelavkfklktqevierikeLeeqgsl 143
                                        ++i+y+ke+   ++ +++  +++    + er++ L ++g +
  gi|518653182|ref|YP_008142702.1|  10 MKIIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFI 51 
                                       589***********************************9987 PP

>> HTH_6  Helix-turn-helix domain, rpiR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00031      0.28      12      53 ..       3      40 ..       1      52 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
                                      ----HHHHHHHHHHHH-S---TT--HHHHHHHTT--HHHHHH CS
                             HTH_6 12 ekltksekkiaeyilaspdkaielsikalAkaaavSeativr 53
                                      e++ k + ki+ey++++        i+++++a+++ +ati  
  gi|518653182|ref|YP_008142702.1|  3 ENIDKKDMKIIEYLKEHGRD----KISDISNALQIPRATIFE 40
                                      678899***********976....57899*******999975 PP

>> PadR  Transcriptional regulator PadR-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00029      0.26      17      53 ..      22      57 ..       7      63 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00029
                                      HHHHCCSTT-CCTTHHHHHHHHHHHHHTTSEEEEEE- CS
                              PadR 17 keleelsegllelseGslYpaLkrLekeglvesewee 53
                                      +++++ s ++l++  ++++  ++rL+k+g+++++ ++
  gi|518653182|ref|YP_008142702.1| 22 DKISDIS-NALQIPRATIFERMERLRKDGFIKKYTVD 57
                                      4566665.458999******************99875 PP

>> FeoC  FeoC like transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00037      0.33       5      48 ..      12      55 ..       9      60 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00037
                              FeoC  5 lkeyleergrvslkeLsrhfkaspealeamLeqwvrkGrvekva 48
                                      + eyl+e+gr  ++++s ++++  +++   +e + + G ++k +
  gi|518653182|ref|YP_008142702.1| 12 IIEYLKEHGRDKISDISNALQIPRATIFERMERLRKDGFIKKYT 55
                                      569********************999988888888888777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); 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: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1080.51
//
Query:       gi|518653183|ref|YP_008142703.1|  [L=1274]
Description: hypothetical protein FACI_IFERC00001G1824 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-23   83.0   0.4    9.6e-23   80.9   0.4    2.2  1  DUF4011          Protein of unknown function (DUF4011)
    7.8e-22   77.3   0.1    2.2e-21   75.8   0.1    1.8  1  MTES_1575        REase_MTES_1575
    7.4e-20   71.4   0.1    1.9e-19   70.1   0.1    1.7  1  AAA_12           AAA domain
    3.5e-15   56.5   6.6    2.4e-07   30.8   0.0    3.3  4  AAA_11           AAA domain
      4e-07   30.0   0.0    0.00068   19.4   0.0    2.5  2  AAA_30           AAA domain
    3.6e-06   27.4   0.0     0.0002   21.7   0.0    2.4  2  AAA_19           AAA domain
      4e-05   23.5   0.0      0.072   12.8   0.0    3.3  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    0.00014   21.6   0.0     0.0017   18.1   0.0    2.4  2  IstB_IS21        IstB-like ATP binding protein
     0.0031   16.8   0.2        0.1   11.9   0.0    2.8  3  DUF2075          Uncharacterized conserved protein (DUF2075)
     0.0056   15.6   0.0      0.011   14.6   0.0    1.4  1  AAA_34           P-loop containing NTP hydrolase pore-1
      0.006   16.6   2.6      0.072   13.1   0.0    3.7  5  ResIII           Type III restriction enzyme, res subunit
     0.0085   16.0   0.0       0.31   10.9   0.0    2.6  2  Helicase_RecD    Helicase
     0.0097   15.7   0.1       0.07   13.0   0.0    2.5  2  DUF559           Protein of unknown function (DUF559)
  ------ inclusion threshold ------
      0.012   15.1   0.1       0.04   13.4   0.0    1.9  1  AAA_7            P-loop containing dynein motor region
      0.055   13.9   1.1       0.32   11.4   0.0    2.9  3  AAA              ATPase family associated with various cellul
      0.062   12.5   0.1       0.46    9.6   0.0    2.3  3  DAP3             Mitochondrial ribosomal death-associated pro
       0.11   12.9   0.0       0.28   11.5   0.0    1.7  1  AAA_16           AAA ATPase domain
       0.12   11.9   0.0        2.4    7.6   0.0    2.8  2  RNA_pol_L        RNA polymerase Rpb3/Rpb11 dimerisation domai
       0.56   10.7   2.5         13    6.4   0.0    3.4  3  CcdA             Post-segregation antitoxin CcdA
        4.8    6.6   9.8       0.13   11.8   1.9    2.3  3  UvrD-helicase    UvrD/REP helicase N-terminal domain
        5.2    7.1   7.1        9.3    6.3   0.1    4.0  3  DUF1128          Protein of unknown function (DUF1128)


Domain annotation for each model (and alignments):
>> DUF4011  Protein of unknown function (DUF4011)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.9   0.4   1.1e-25   9.6e-23       3     163 .]      17     157 ..      15     157 .. 0.89

  Alignments for each domain:
  == domain 1  score: 80.9 bits;  conditional E-value: 1.1e-25
                           DUF4011   3 LDlslRnrllnfkeskkktleiidedldelfdrLaegekklellppdeeeaakeleteeeekeerkkdkklqtllte 79 
                                       +D+s+ nrll f+ +  + l+i+++++  lfd L++++kk++++               +  ee++k+++l    ++
  gi|518653183|ref|YP_008142703.1|  17 IDTSKNNRLLYFNPE--SFLKITTPSMLFLFDDLVNKDKKMKIHL--------------SGAEENRKKDELI-FSKN 76 
                                       8************44..58**************************..............2334444555554.4567 PP

                           DUF4011  80 eelekrlrklyrkartsleEtGvniLYlalgfLewyesdksekpirAPLllvPVeLerksarsnfslkakeeeialN 156
                                       e+++k+l +l ++a  sl+E G+n+LY+ +g+L+w +++   k++   L++vPV+L+rk   +n+s+++ e +i++N
  gi|518653183|ref|YP_008142703.1|  77 EDISKSLGNLFYQANASLKEHGSNVLYISFGVLKWSDEN--GKEVETQLFFVPVTLNRK-MYNNYSIESMEGDIFFN 150
                                       89***********************************85..9999999***********.7889************* PP

                           DUF4011 157 lsLlekL 163
                                       + L+ekL
  gi|518653183|ref|YP_008142703.1| 151 PVLREKL 157
                                       *****98 PP

>> MTES_1575  REase_MTES_1575
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.1   2.6e-24   2.2e-21       4      93 ..    1164    1256 ..    1162    1258 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 2.6e-24
                         MTES_1575    4 eVaeaLrergykvkpqvgvggfriDlvvedp...gkyllaIecdgdkyhsskeardrdierqevLerlGWkilRi 75  
                                        ++a +L+++g+kv ++vg ++ +i l+++dp   ++y+l+Ie+dg+ y+s k+a +r++ r+++L   GW+++Ri
  gi|518653183|ref|YP_008142703.1| 1164 DIALKLEQEGFKVAKNVGYSRNNIPLAIIDPddqDHYILGIETDGKIYNSMKTASERERIRKKILTDRGWNLYRI 1238
                                        8999*****************************9***************************************** PP

                         MTES_1575   76 wssdwyrnpeeeleklve 93  
                                        ws d+++npe++l++l++
  gi|518653183|ref|YP_008142703.1| 1239 WSIDYMKNPEKVLHDLIN 1256
                                        **************9987 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.1   2.2e-22   1.9e-19      17     197 ..     939    1117 ..     928    1119 .. 0.86

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 2.2e-22
                            AAA_12   17 vvlLdtqYRm.hpeIsrfpsklfYkgkLkdaesvkkreleaqealeepleplvfidvekseeekekkeksyiNee 90  
                                        ++ L+  YR+ ++++  f++++fY++ L++ +s  ++++e         + + f+ ve+  ++     ks++N++
  gi|518653183|ref|YP_008142703.1|  939 KIWLKWHYRSvDDRLIAFSNRYFYDNLLETFPSSYRKSKE---------SGIQFVRVEGVYTRG----KSKTNKA 1000
                                        5679999**735689*****************99999988.........7799****9766655....589**** PP

                            AAA_12   91 EaelvvklvekllkkgseeerkkigvitpYraqvellkkklkekeeekseke.......ievntvdgfQGrekdv 158 
                                        Ea+ vv+++++   + s++  ++igv+t  ++q   ++++l++ ++++++ +       i ++  +++QG ekdv
  gi|518653183|ref|YP_008142703.1| 1001 EANEVVRVIKE---ELSNT--DSIGVVTLSESQRVAVEDTLNSYSRHDPVLAellnndtIFIKNLENVQGDEKDV 1070
                                        *****999876...55555..789******************99999888778999999**************** PP

                            AAA_12  159 iilslVRsnekk........eigflkderrlNValTRAkskliivGn 197 
                                        iils+   ++++         i     e+rlNVa+TRA++k i+v +
  gi|518653183|ref|YP_008142703.1| 1071 IILSTGYGRDENgkitmnfgPINTTGGEKRLNVAITRARKKFIVVSS 1117
                                        *****9888666566665545777889*****************986 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.0   2.8e-10   2.4e-07       3      97 ..     257     346 ..     255     435 .. 0.80
   2 ?   -2.3   1.0       3.6     3e+03     158     193 ..     562     597 ..     514     636 .. 0.50
   3 !   27.9   0.0   2.2e-09   1.8e-06     214     259 ..     866     909 ..     858     911 .. 0.91
   4 ?   -2.7   0.1       4.7     4e+03      83     114 ..     998    1029 ..     987    1068 .. 0.61

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 2.8e-10
                            AAA_11   3 ndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr... 76 
                                       ++sq+ ai+ a s s+ +++ GPPGtgK++ti+ +++            ++++ +L  ++ NaA+ ++  rl +   
  gi|518653183|ref|YP_008142703.1| 257 DSSQLMAIYAARSGSS-FILNGPPGTGKSQTIANIIADS---------MKNNKSVLFVSEKNAAIEVVKRRLEEvgl 323
                                       789************9.8*********************.........68999*************99999888766 PP

                            AAA_11  77 ..glldsegekykpkivRvgnee 97 
                                          +l+ +g++ k +i++  + +
  gi|518653183|ref|YP_008142703.1| 324 gdFILNFHGNTPKSEIIKSLHRS 346
                                       54455666777777777666666 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 3.6
                            AAA_11 158 kskskleqerrklkkerkelskeleeaeesleeevl 193
                                       + +s++++ + + kk  +e+ ++ e + ++  ee+l
  gi|518653183|ref|YP_008142703.1| 562 TYSSRWKRHSGEYKKLLNEIMENTEDKSRKQYEEIL 597
                                       222222222222222222222222222222222222 PP

  == domain 3  score: 27.9 bits;  conditional E-value: 2.2e-09
                            AAA_11 214 lakkfdvviIDEAaqavEpstliPlrlgakkvvLvGDpkQLpatvi 259
                                        a  fd++i DEA+q + p ++  l ++ k++++ GD +QLp+t++
  gi|518653183|ref|YP_008142703.1| 866 DA-SFDLLIFDEASQLTPPDAVGSLIRA-KQAIISGDTQQLPPTTF 909
                                       33.9************************.***************87 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 4.7
                            AAA_11   83 gekykpkivRvgneeeriseavksvsleekve 114 
                                         + +  ++vRv +ee + ++++  v+l+e+++
  gi|518653183|ref|YP_008142703.1|  998 NKAEANEVVRVIKEELSNTDSIGVVTLSESQR 1029
                                        44445566777777733333444444433333 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   7.9e-07   0.00068       4      67 ..     258     319 ..     255     364 .. 0.76
   2 !    7.8   0.0    0.0029       2.5      56     130 ..     824     906 ..     807     926 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 7.9e-07
                            AAA_30   4 aeQaaavealltsgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelg 67 
                                       ++Q  a+ a+ +++    +l+Gp+GtGK+ +++ + +   +++++v+ ++ +++a +v+++ l+
  gi|518653183|ref|YP_008142703.1| 258 SSQLMAIYAARSGS--SFILNGPPGTGKSQTIANIIADSMKNNKSVLFVSEKNAAIEVVKRRLE 319
                                       67888887666666..69*****************888888999***********999996443 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0029
                            AAA_30  56 gkaAkvLaeelgieastiakllkrlk...........grarlepg.tllivDEagmvdtkqlaallkaaekagakvi 120
                                       ++a k+L++ l +  s ++ +l  lk           +  + +++ +lli DEa+ +   ++   l +a++     i
  gi|518653183|ref|YP_008142703.1| 824 ENAKKRLQKPLKVLFSELKDILPGLKpcimmspdnvaAYLENDASfDLLIFDEASQLTPPDAVGSLIRAKQ----AI 896
                                       55555666666665556666665555666666666663344456679**********99988776666666....79 PP

                            AAA_30 121 lvGDerQlas 130
                                       + GD++Ql++
  gi|518653183|ref|YP_008142703.1| 897 ISGDTQQLPP 906
                                       9*******97 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   2.3e-07    0.0002       3      84 ..     262     353 ..     260     431 .. 0.83
   2 ?    2.9   0.0      0.15   1.2e+02     102     143 ..     868     906 ..     799     908 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 2.3e-07
                            AAA_19   3 eave.alkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.......... 68 
                                        a+  a + + +++ ++pGtGK++++  i+a   +++    +++l v+  + A + ++ rl+++g+           
  gi|518653183|ref|YP_008142703.1| 262 MAIYaARSGSSFILNGPPGTGKSQTIANIIADSMKNN----KSVLFVSEKNAAIEVVKRRLEEVGLGdfilnfhgnt 334
                                       566547778889999****************999999....79******************8888778877777777 PP

                            AAA_19  69 .....atTiHrlalldfddll 84 
                                            ++ +Hr   +++d+  
  gi|518653183|ref|YP_008142703.1| 335 pkseiIKSLHRS--VENDTHA 353
                                       777777777777..5555444 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.15
                            AAA_19 102 eeellivDEfqdvd..elqyrLlkallgekkklllvGDpdQliy 143
                                       + +lli DE+++++  +   +L++a      + ++ GD +Ql++
  gi|518653183|ref|YP_008142703.1| 868 SFDLLIFDEASQLTppDAVGSLIRAK-----QAIISGDTQQLPP 906
                                       23599********9733344455443.....46899*****997 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.017        14       3      32 ..     275     311 ..     273     354 .. 0.76
   2 !   12.8   0.0   8.5e-05     0.072      16     103 ..     827     907 ..     822     923 .. 0.76
   3 ?    1.3   0.0      0.29   2.5e+02     217     233 ..    1099    1115 ..     991    1116 .. 0.90

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                   Viral_helicase1   3 vhGvpGcGKStlirkllrts.......liltvnrpta 32 
                                         G pG GKS+ i +++ +s       l +++ + ++
  gi|518653183|ref|YP_008142703.1| 275 LNGPPGTGKSQTIANIIADSmknnksvLFVSEKNAAI 311
                                       5789*************99666655533333333333 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 8.5e-05
                   Viral_helicase1  16 rkllrtsliltvnrptaelltegkpklpnlsvrtvdsflmalvkstkgkililDEylllhaGyilllaalskaklvi 92 
                                       +k l++   l+v  +  +++ +g++     s  +v ++l+++     +++li+DE+ +l++   +++  l +ak++i
  gi|518653183|ref|YP_008142703.1| 827 KKRLQK--PLKVLFSELKDILPGLKPCIMMSPDNVAAYLENDAS---FDLLIFDEASQLTP--PDAVGSLIRAKQAI 896
                                       555555..455555556666666666666777788888888764...8***********98..999*********** PP

                   Viral_helicase1  93 lfGDplQipfh 103
                                       + GD++Q p  
  gi|518653183|ref|YP_008142703.1| 897 ISGDTQQLPPT 907
                                       *******9865 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.29
                   Viral_helicase1  217 enllvAlTRhrkslvil 233 
                                          l vA+TR+rk+++++
  gi|518653183|ref|YP_008142703.1| 1099 KRLNVAITRARKKFIVV 1115
                                        5677*********9875 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0     2e-06    0.0017      16      85 ..     240     308 ..     229     321 .. 0.83
   2 ?   -0.1   0.0       0.8   6.8e+02      72     120 ..     830     880 ..     825     889 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2e-06
                         IstB_IS21  16 qktledidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrved 85 
                                        k++++id++ ++ +d+   ++L++    ++  +++l Gp+G+GKs   + +  + +++++svlfv+ ++
  gi|518653183|ref|YP_008142703.1| 240 DKMPAEIDYNINTVMDA-DSSQLMAIYAARSGSSFILNGPPGTGKSQTIANIIADSMKNNKSVLFVSEKN 308
                                       57888999999966655.45667777778999***************9999**************98765 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.8
                         IstB_IS21  72 vraglsvlfvrvedLveelk..rarrdgklaralkrllkvdllilDdlgll 120
                                        ++ l+vlf  ++d++  lk  +  + +++a  l++ + +dlli D+ + l
  gi|518653183|ref|YP_008142703.1| 830 LQKPLKVLFSELKDILPGLKpcIMMSPDNVAAYLENDASFDLLIFDEASQL 880
                                       566789999999999999984456788999999*************98765 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00012       0.1       4      53 ..     273     320 ..     270     357 .. 0.86
   2 ?    1.6   0.0      0.16   1.3e+02      37     101 ..     811     881 ..     796     903 .. 0.72
   3 ?   -4.1   0.0       8.4   7.2e+03     345     360 ..    1100    1115 ..    1099    1116 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                           DUF2075   4 vlVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealak 53 
                                       ++ +G +GtGK+    n++a+    ++++++ ++s  ++ ++v++++l++
  gi|518653183|ref|YP_008142703.1| 273 FILNGPPGTGKSQTIANIIADS--MKNNKSVLFVSEKNAAIEVVKRRLEE 320
                                       7889*****************9..9********************99976 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.16
                           DUF2075  37 lsvNhplvlvlrealakkeekkkkkeafeklssfinnlsef......kkaeekkeepkedvvivDEAhrll 101
                                       ls+     +v++ + akk+ +k  k  f++l+ +   l+        + a+  +++  +d++i+DEA  l+
  gi|518653183|ref|YP_008142703.1| 811 LSRYPGSAMVIKTENAKKRLQKPLKVLFSELKDILPGLKPCimmspdNVAAYLENDASFDLLIFDEASQLT 881
                                       4455555566666666677677777777777777777776677777677777889999*********8876 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 8.4
                           DUF2075  345 ayrVLLtRGrkGlyiy 360 
                                        +++V +tR+rk ++++
  gi|518653183|ref|YP_008142703.1| 1100 RLNVAITRARKKFIVV 1115
                                        79*********99886 PP

>> AAA_34  P-loop containing NTP hydrolase pore-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.3e-05     0.011      54     119 ..     264     328 ..     236     355 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.3e-05
                            AAA_34  54 llpdgkRaGfllGDgaGvGkgrqiagiilenllqgrkkavwvsvsedLkeDaerDlkdigaseiev 119
                                       + + ++   f+l    G Gk ++ia ii++ + +++k +++vs +++ +e  +r l+++g  +  +
  gi|518653183|ref|YP_008142703.1| 264 IYAARSGSSFILNGPPGTGKSQTIANIIADSM-KNNKSVLFVSEKNAAIEVVKRRLEEVGLGDFIL 328
                                       455556677999999*************9975.67889*********************9875554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       5.5   4.7e+03      85     118 ..      45      83 ..      13     103 .. 0.69
   2 !   13.1   0.0   8.4e-05     0.072      25      78 ..     271     322 ..     232     373 .. 0.75
   3 ?   -3.3   0.4       9.2   7.8e+03      78      96 ..     571     589 ..     542     624 .. 0.52
   4 ?    0.2   0.0      0.75   6.4e+02     121     141 ..     851     877 ..     777     897 .. 0.73
   5 ?   -1.4   0.0       2.3     2e+03       4      36 ..    1024    1078 ..    1022    1079 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 5.5
                                       GEEEESSS-B--............-SEEEEEHHHHHHTH CS
                            ResIII  85 igkkvsgdkkka.....kekdstnkkilvttiqsldads 118
                                           v++dkk++      e+++++ ++++++ + +++++
  gi|518653183|ref|YP_008142703.1|  45 FDDLVNKDKKMKihlsgAEENRKKDELIFSKNEDISKSL 83 
                                       445566666666777777777788889999888888877 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 8.4e-05
                                       SEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGT CS
                            ResIII  25 krglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkfl 78 
                                         ++++ + GtGK+ ++a++i+  +k++k   +lf+  +++ +e  +++++++ 
  gi|518653183|ref|YP_008142703.1| 271 SSFILNGPPGTGKSQTIANIIADSMKNNK--SVLFVSEKNAAIEVVKRRLEEVG 322
                                       4688999*******************866..9****999987777776665544 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.2
                                       TGG....GEEEESSS-B-- CS
                            ResIII  78 lseaykeigkkvsgdkkka 96 
                                       + e++k  ++++++ ++k+
  gi|518653183|ref|YP_008142703.1| 571 SGEYKKLLNEIMENTEDKS 589
                                       3333333333333333333 PP

  == domain 4  score: 0.2 bits;  conditional E-value: 0.75
                                       ............HHHTTT-SEEEEETG CS
                            ResIII 121 e......eeeseellrdrfdviiiDEa 141
                                              + +     + +fd++i+DEa
  gi|518653183|ref|YP_008142703.1| 851 CimmspdNVAAYLENDASFDLLIFDEA 877
                                       2566665667777888999*******9 PP

  == domain 5  score: -1.4 bits;  conditional E-value: 2.3
                                        E-HHHHHHHHHHT............................TTSEEEEEESTTST CS
                            ResIII    4 lreyQeeaienlleklks......................krdkrglikmaTGtG 36  
                                        l e Q  a+e++l++++                       ++d++ +i + TG G
  gi|518653183|ref|YP_008142703.1| 1024 LSESQRVAVEDTLNSYSRhdpvlaellnndtifiknlenvQGDEKDVIILSTGYG 1078
                                        6788999999999888878888888888888888888888999999999999988 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   0.00036      0.31       2      47 ..     275     319 ..     274     355 .. 0.82
   2 ?    1.9   0.0       0.2   1.7e+02      85     117 ..     863     896 ..     821     903 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00036
                     Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegksnilvtapskenvktlfefla 47 
                                       l + +G+GKS +++ ++a  ++++k ++l ++ ++++++ + ++l+
  gi|518653183|ref|YP_008142703.1| 275 LNGPPGTGKSQTIANIIADSMKNNK-SVLFVSEKNAAIEVVKRRLE 319
                                       78899*****************988.78888888888888777664 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.2
                     Helicase_RecD  85 lklkeqadllvvDEAAai.plpllkkllekfkrv 117
                                       l+++++ dll+ DEA+++ p + + +l+++++ +
  gi|518653183|ref|YP_008142703.1| 863 LENDASFDLLIFDEASQLtPPDAVGSLIRAKQAI 896
                                       3333445*********983455777777554444 PP

>> DUF559  Protein of unknown function (DUF559)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.5   2.2e+03      63     101 ..     215     250 ..     197     256 .. 0.58
   2 !   13.0   0.0   8.3e-05      0.07      57     106 ..    1204    1256 ..    1192    1259 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.5
                                       ---------HHHHHHHHHTT-EEEEEEHHHHHH-HHHHH CS
                            DUF559  63 qhdeeeeyDaeRtelLeslGftvlRfkndevlknieevl 101
                                       +hd  +++D +R+    +  f+v++  nd++ ++i+  +
  gi|518653183|ref|YP_008142703.1| 215 NHDAIKKNDLTRAL---AGDFEVIKKLNDKMPAEIDYNI 250
                                       34444444444432...3457777777777766666555 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 8.3e-05
                                        EEEE-------...----HHHHHHHHHTT-EEEEEEHHHHHH-HHHHHHHHHH CS
                            DUF559   57 velDGaqhdee...eeyDaeRtelLeslGftvlRfkndevlknieevleeilk 106 
                                        +e DG+ +++    +e++  R+++L+  G++  R +  + +kn+e+vl+++++
  gi|518653183|ref|YP_008142703.1| 1204 IETDGKIYNSMktaSERERIRKKILTDRGWNLYRIWSIDYMKNPEKVLHDLIN 1256
                                        89999987765445789999****************************98765 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   4.7e-05      0.04      15      66 ..     251     303 ..     241     315 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 4.7e-05
                             AAA_7  15 ptvdtvrysyllel.llknkkpvllvGptGtGKtviikd.llkkldkekylslt 66 
                                       +tv  +  s l+     +++ +++l Gp GtGK+ +i + + ++++ ++ ++l+
  gi|518653183|ref|YP_008142703.1| 251 NTVMDADSSQLMAIyAARSGSSFILNGPPGTGKSQTIANiIADSMK-NNKSVLF 303
                                       5555555555555514577899*****************5555555.5554444 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   0.00038      0.32       2      25 ..     274     298 ..     273     337 .. 0.71
   2 ?   -2.6   0.1       8.1   6.9e+03      24      57 ..     545     589 ..     538     597 .. 0.67
   3 ?   -1.4   0.1       3.3   2.9e+03      21      91 ..     978    1051 ..     976    1081 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00038
                                       EEESSTTSSHH.HHHHHHHHHHTHE CS
                               AAA   2 llyGppGtGKT.llakavakelgve 25 
                                       +l GppGtGK+ ++a+ +a +++ +
  gi|518653183|ref|YP_008142703.1| 274 ILNGPPGTGKSqTIANIIADSMKNN 298
                                       799********66778888887532 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 8.1
                                       HEEEEEETTTCSSS...........STTHHHHHHHHHHHHHHHTS CS
                               AAA  24 vefleisgsellsk...........yvgesekkirelfkeakeka 57 
                                        +fl +++ +++++           + ge +k ++e++++ + k+
  gi|518653183|ref|YP_008142703.1| 545 KQFLDMNLNSIRKDmeetyssrwkrHSGEYKKLLNEIMENTEDKS 589
                                       566777777777435667777777777777788888877776655 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 3.3
                                        HHTHEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTS....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHH CS
                               AAA   21 elgvefleisgsell..skyvgesekkirelfkeakeka....kpsilfiDEidalaksrsgseseeeervvnqL 89  
                                        e+g++f++++g   +  sk+ ++ ++++  ++ke   +     +  ++ + E  ++a +++ ++ + ++ v+++L
  gi|518653183|ref|YP_008142703.1|  978 ESGIQFVRVEGVYTRgkSKTNKAEANEVVRVIKE---ELsntdSIGVVTLSESQRVAVEDTLNSYSRHDPVLAEL 1049
                                        5667777777777773222333444444444433...33334455777777777777777555555555555555 PP

                                        HH CS
                               AAA   90 lt 91  
                                        l+
  gi|518653183|ref|YP_008142703.1| 1050 LN 1051
                                        54 PP

>> DAP3  Mitochondrial ribosomal death-associated protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00054      0.46      22      59 ..     269     306 ..     259     317 .. 0.86
   2 ?   -3.9   0.0         7     6e+03     133     172 ..     825     865 ..     819     868 .. 0.79
   3 ?   -0.6   0.0      0.68   5.8e+02     218     267 ..     994    1063 ..     936    1072 .. 0.56

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00054
                                       ---EEEEE-SSSSSTTTTHHHHHHHGGGS--EEEEES- CS
                              DAP3  22 kvkrlvltGekgsGKSvlLlqalayAlekgwvvlhvpe 59 
                                           ++l+G +g+GKS +++ ++a  ++++  vl v+e
  gi|518653183|ref|YP_008142703.1| 269 SGSSFILNGPPGTGKSQTIANIIADSMKNNKSVLFVSE 306
                                       56789***********************9998888887 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7
                                       H-SSSHHHHHHHHHHHHHHHTT.SS--EEEEEE-GGGGSS- CS
                              DAP3 133 kdaksawdvfqallkeLkaqsk.grvpvlvtvDglnallkn 172
                                       + +k+  + +++l++eLk+     ++ ++++ D+++a l+n
  gi|518653183|ref|YP_008142703.1| 825 NAKKRLQKPLKVLFSELKDILPgLKPCIMMSPDNVAAYLEN 865
                                       45566667799999999998887899999999999998776 PP

  == domain 3  score: -0.6 bits;  conditional E-value: 0.68
                                        -SS--SS---HHHHHTTTTT....................GGG-S-E.................EEE---- CS
                              DAP3  218 ssntpksatlevallqeear....................pqldpYvkkydkrvaealk.gkvepievegl 267 
                                        +s+t+k+++ ev    +e+                     ++l+ Y++ +d+ +ae+l+   + + ++e++
  gi|518653183|ref|YP_008142703.1|  994 KSKTNKAEANEVVRVIKEELsntdsigvvtlsesqrvaveDTLNSYSR-HDPVLAELLNnDTIFIKNLENV 1063
                                        333333222222222222222333333333333344577799999995.6999999999744444444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00033      0.28      10      62 ..     259     310 ..     255     384 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00033
                            AAA_16  10 eqLlsalervrsgrpelvllsGesGvGKsslv.rellralekdg.giflrgkcdq 62 
                                       +qL +++  +rsg  ++ +l G++G+GKs  + + ++++++ ++ ++f+++k+  
  gi|518653183|ref|YP_008142703.1| 259 SQLMAIYA-ARSG--SSFILNGPPGTGKSQTIaNIIADSMKNNKsVLFVSEKNAA 310
                                       56666665.6666..799***********98846666677777668888887655 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 ?    0.7   0.0      0.42   3.6e+02      51      68 ..     642     659 ..     641     659 .. 0.90
   2 ?    7.6   0.0    0.0028       2.4      20      52 ..    1024    1210 ..     744    1220 .. 0.71

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.42
                                       xxxxxxxxxxxxxxxxxx RF
                         RNA_pol_L  51 slkPeealkeAlkiLkek 68 
                                       s+ Pe+alk +l+ L+++
  gi|518653183|ref|YP_008142703.1| 642 SIFPENALKDGLRELISH 659
                                       678************987 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0028
                                        xxxxxxxxxxx................................................................ RF
                         RNA_pol_L   20 lsevpgvaiea................................................................ 30  
                                        lse + va+e                                                                 
  gi|518653183|ref|YP_008142703.1| 1024 LSESQRVAVEDtlnsysrhdpvlaellnndtifiknlenvqgdekdviilstgygrdengkitmnfgpinttgge 1098
                                        445555555556777777776666666666666666665555555555555555555555555555555444444 PP

                                        ...........................xx.............................................. RF
                         RNA_pol_L   31 ...........................pv.............................................. 32  
                                                                   p                                               
  gi|518653183|ref|YP_008142703.1| 1099 krlnvaitrarkkfivvssmdpedirvPAnsgkgpdllkqymiyaknegnnehleefknndaiindialkleqeg 1173
                                        444444444444444444444444444004444444444444444455555555555555555555555555555 PP

                                        ..xxxx.................xxxxxxxxxxxxxxxx RF
                         RNA_pol_L   33 ..vkvn.................tdkdklilevetdgsl 52  
                                          v  +                 +d+d++il +etdg +
  gi|518653183|ref|YP_008142703.1| 1174 fkV--AknvgysrnniplaiidpDDQDHYILGIETDGKI 1210
                                        330..2334466666777788889*************98 PP

>> CcdA  Post-segregation antitoxin CcdA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.33   2.8e+02      10      63 ..      46      99 ..      42     100 .. 0.88
   2 ?    6.4   0.0     0.015        13      24      63 ..     284     323 ..     281     324 .. 0.96
   3 ?   -2.6   0.1       9.3   7.9e+03      31      59 ..     555     583 ..     553     585 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.33
                              CcdA 10 sdllaqAralgiNlSatleeaLaeevkeekaerwkeenreaieelNrfveehGl 63
                                       dl+++ ++++i lS++ e   ++e+   k+e+  +   +   + N+  +ehG+
  gi|518653183|ref|YP_008142703.1| 46 DDLVNKDKKMKIHLSGAEENRKKDELIFSKNEDISKSLGNLFYQANASLKEHGS 99
                                      5999***************99999999999999999888888888888888886 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.015
                              CcdA  24 SatleeaLaeevkeekaerwkeenreaieelNrfveehGl 63 
                                       S+t+   +a+ +k+ k+   + e+ +aie ++r+ ee Gl
  gi|518653183|ref|YP_008142703.1| 284 SQTIANIIADSMKNNKSVLFVSEKNAAIEVVKRRLEEVGL 323
                                       89999********************************996 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 9.3
                              CcdA  31 LaeevkeekaerwkeenreaieelNrfve 59 
                                       +++ ++e  ++rwk++  e  + lN+++e
  gi|518653183|ref|YP_008142703.1| 555 IRKDMEETYSSRWKRHSGEYKKLLNEIME 583
                                       67888999999***999888888888877 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 ?   -3.9   0.4         9   7.7e+03     151     203 ..       9      62 ..       4      97 .. 0.49
   2 ?   11.8   1.9   0.00015      0.13      11     225 ..     266     605 ..     257     643 .. 0.57
   3 ?   -3.8   0.0       8.1   6.9e+03      32      54 ..    1003    1025 ..     993    1027 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 9
                                       HHHHHHHHHHHHCCCCCH.HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS CS
                     UvrD-helicase 151 kkkleklikelsksrnik.keelslskskaeelrelvskakekqlspkelkkaf 203
                                        kk+ek++++ sk++ ++ +  +s+ k+   ++  l++++ +k+ + k   +  
  gi|518653183|ref|YP_008142703.1|   9 IKKWEKDVIDTSKNNRLLyFNPESFLKITTPSMLFLFDDLVNKDKKMKIHLSGA 62 
                                       566777777777766666533344444444444444444444333333333322 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00015
                                       S..-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHH.................. CS
                     UvrD-helicase  11 s..lggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRiee.................. 67 
                                          +g+++++   +G+GK++++a+ i+  +k++    +++l v   n+A e  k R+ee                  
  gi|518653183|ref|YP_008142703.1| 266 AarSGSSFILNGPPGTGKSQTIANIIADSMKNN----KSVLFVSEKNAAIEVVKRRLEEvglgdfilnfhgntpkse 338
                                       43356666677779*****************99....99*************************9999988766664 PP

                                       HHHHCCHHCTT-H.HHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTT.............................. CS
                     UvrD-helicase  68 alkkaeqessdde.rlrlalqnlseanisTlHsfcqkilkkeanrig.............................. 113
                                       ++k+   +s +++ + ++ l  +++   +Tl s+ + i +k  +                                 
  gi|518653183|ref|YP_008142703.1| 339 IIKSL-HRSVENDtHAQRTLVPTDRY-SGTLNSYVRAIHEKRGKLGRsiydacqielknkgnldikidrrlldltge 413
                                       22222.22222223555555554443.46777777777766666666665666666666666665544444444444 PP

                                       ........................SHTTTEEECHHHHH..HCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCC CS
                     UvrD-helicase 114 ........................ldpnfrildeedee..dlkqqellkelleksaddslnldkkkleklikelsks 164
                                                               + +nfr+ ++ +    + + +el+++ l                         
  gi|518653183|ref|YP_008142703.1| 414 eldslefqisefndyldiienygkIPENFRLDRYREDPehYYRGLELIQNAL------------------------- 465
                                       4444444444444444444444444444444333332233344444444444......................... PP

                                       CCCH......................................................................... CS
                     UvrD-helicase 165 rnik......................................................................... 168
                                          +                                                                         
  gi|518653183|ref|YP_008142703.1| 466 ---Drieeiapailtttgvdiqsmedinmlyrfvnvlnagitldeaytnpdfiketaalldsgdkirseldymmgif 539
                                       ...03333333333333333334444446677777777777777777777777777777777777777777777777 PP

                                       ..HHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSS.......TSCSHHHHHHHHHHHHHHHHHH CS
                     UvrD-helicase 169 ..keelslskskaeelrelvskakekqlspkelkkaf.......ekasdlqkkiaeflkeyqeqkk 225
                                         k+++++    ++++r+ +++  ++  + ++ + +        + +++ +k+ +e+l+++   +k
  gi|518653183|ref|YP_008142703.1| 540 lkKRKKQFLDMNLNSIRKDMEETYSSRWKRHSGEYKKllneimeNTEDKSRKQYEEILEDITFALK 605
                                       773333333333333333333333333322222222223322444445555555555555555544 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 8.1
                                        HHHHHHHHTSSSTGGGEEEEESS CS
                     UvrD-helicase   32 erilrlikeeeiepdrilvvTFT 54  
                                        + ++r ikee  + d+i vvT  
  gi|518653183|ref|YP_008142703.1| 1003 NEVVRVIKEELSNTDSIGVVTLS 1025
                                        67899999999999999999975 PP

>> DUF1128  Protein of unknown function (DUF1128)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.1     0.011       9.3      20      49 ..     468     497 ..     458     500 .. 0.83
   2 ?   -2.8   0.2       7.6   6.5e+03       4      22 ..     588     606 ..     581     619 .. 0.62
   3 ?    2.3   0.0       0.2   1.7e+02      29      50 ..     707     728 ..     699     730 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.011
                           DUF1128  20 LkmvnaavlkaedfseekyedlkdlYemVm 49 
                                        + ++ a+l+   ++ + +ed+++lY +V 
  gi|518653183|ref|YP_008142703.1| 468 IEEIAPAILTTTGVDIQSMEDINMLYRFVN 497
                                       5557789999******************95 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
                           DUF1128   4 kseenleymieeikekLkm 22 
                                       ks+++ e+++e+i+  Lk+
  gi|518653183|ref|YP_008142703.1| 588 KSRKQYEEILEDITFALKI 606
                                       4555555566665555554 PP

  == domain 3  score: 2.3 bits;  conditional E-value: 0.2
                           DUF1128  29 kaedfseekyedlkdlYemVmk 50 
                                        a++f+ ++y   ++lYe V++
  gi|518653183|ref|YP_008142703.1| 707 AASSFDIDRYVKFRELYEGVKT 728
                                       5799**************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      624  (0.0348039); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 1.05u 0.30s 00:00:01.35 Elapsed: 00:00:00.54
# Mc/sec: 7165.59
//
Query:       gi|518653184|ref|YP_008142704.1|  [L=400]
Description: hypothetical protein FACI_IFERC00001G1825 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.8e-23   81.0  33.0    7.8e-23   81.0  33.0    2.1  2  MFS_1     Major Facilitator Superfamily
    2.5e-12   46.4  27.3    4.1e-11   42.4  27.3    2.0  1  Sugar_tr  Sugar (and other) transporter


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0  33.0   8.7e-27   7.8e-23       9     339 ..       9     340 ..       1     343 [. 0.82
   2 !    2.7   7.6    0.0053        48     124     171 ..     336     383 ..     333     394 .. 0.90

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 8.7e-27
                             MFS_1   9 alarsilgpalpl.alaedlgispseigl.lltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfas 83 
                                        + ++i++++ pl a ++  g+ p+++   +l +  l+  ++++ +G l+dr+Gr++++l++++++++g++++++ s
  gi|518653184|ref|YP_008142704.1|   9 LTFWGIVATLGPLaAAGSIIGVLPHSYKVlVLLIGPLFVPFGNFTMGILTDRIGRKKIFLITMIMYGIGIVIISL-S 84 
                                       455556666666667777777777776663556699999******************************777777.5 PP

                             MFS_1  84 slw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilai 159
                                         + +l+++ +l+ +g g+    +++l+++ +p ++r++ + ++s + ++G+++ ++l  +l++s+  r+v +++a 
  gi|518653184|ref|YP_008142704.1|  85 YTFiPLIIGLMLAEFGVGGEEIPSLSLVSEDSPISQRAKWLTIISDFDNIGSAIIAGLFLVLVTSFADRVVLLLAAS 161
                                       55559************************************************************************ PP

                             MFS_1 160 vsllafvlfllllpeepperkrkspkeee.kgtgpaplvp.......awkallkdpvlwillialllfffgfsg.ll 227
                                       ++++++++    l  +++ ++ + + + e +       +        a + ++k+ +    l+ ++l+++++s+ ++
  gi|518653184|ref|YP_008142704.1| 162 FLIIVMIF--SRLSLPESFKWENIHGKVEnS-----IKTRsslyidsAGETVKKPSY---TLTLSVLMAMAISQyTT 228
                                       *****997..888888888888888888542.....222233334656667777774...55555555555555499 PP

                             MFS_1 228 tllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavlll 304
                                       + l  y+   + ++g+++  +++ ++ l++ +++++a+ l++r gr++++l +++l+++++++++l+ +  ++vl+ 
  gi|518653184|ref|YP_008142704.1| 229 FGLMAYIIGPYEFPGVFTDDMIIFVALLGASVAGFIAAPLITR-GRKKYTLYSYGLGFISTVAIFLVIPLLNNVLIF 304
                                       99999*********766666556666666666677*******9.********************************* PP

                             MFS_1 305 lvlvliGf.glgfvfpsllalasdlappeeagtasg 339
                                       ++l+++ +  + f+++s ++l  +l p++ +g  +g
  gi|518653184|ref|YP_008142704.1| 305 YPLLFFNMmMSEFAWASRTTLEPELSPTRIRGIFMG 340
                                       ********999*********************9998 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.0053
                             MFS_1 124 gllsagfslGailgpllggllasslgWravfyilaivsllafvlflll 171
                                       g++++++ l++++ ++l  +l+s+++ r+  +i+ ++ ll+f+ ++++
  gi|518653184|ref|YP_008142704.1| 336 GIFMGTVRLAPMIVYPLLVYLTSNVSIRVFIIINVGLWLLGFIAAIVW 383
                                       79999999*********************************9976666 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4  27.3   4.6e-15   4.1e-11      60     430 ..      48     377 ..      33     384 .. 0.78

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 4.6e-15
                                       HHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCH CS
                          Sugar_tr  60 iiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklR 136
                                        +G +++g+l+dr+GRkk++li+ +++ ig+v++ ++    ++  li+g +l+ +gvG++ + +  ++sE +p + R
  gi|518653184|ref|YP_008142704.1|  48 PFGNFTMGILTDRIGRKKIFLITMIMYGIGIVIISLSY---TFIPLIIGLMLAEFGVGGEEIPSLSLVSEDSPISQR 121
                                       58************************************...9*********************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHHHTT-HHHHHHHHHH CS
                          Sugar_tr 137 galvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylvekgkeeeakevlak 213
                                        +  ++   +  +G  + a++ l+l ++ + d+  +ll+ ++++ +++++ +l lPES  +  ++gk e + ++ + 
  gi|518653184|ref|YP_008142704.1| 122 AKWLTIISDFDNIGSAIIAGLFLVLVTSFA-DRVVLLLAASFLI-IVMIFSRLSLPESFKWENIHGKVENSIKTRSS 196
                                       999999988999998888888888877777.5666666666655.5899999**************99988887777 PP

                                       HHHCHHHHHHHHHHHHHHHHHHH.....HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THHH CS
                          Sugar_tr 214 lrgeedadrelaeekdsleaeqeeekaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsksl 290
                                            +  +++ e +++  ++                    l + ++++i q  t   + ++++p+ f  +  ++  
  gi|518653184|ref|YP_008142704.1| 197 -----LYIDSAGETVKKPSYT------------------LTLSVLMAMAISQYTTFGLMAYIIGPYEFPGVFTDD-- 248
                                       .....5555555555555555..................224455555555555544555556777777664444.. PP

                                       HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHHHTTT CS
                          Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialfalgw 367
                                       ++ ++      va f+a++l+ r GR++  l +   ++i +v +   +++l ++      ++  ++++ +++ ++ w
  gi|518653184|ref|YP_008142704.1| 249 MIIFVALLGASVAGFIAAPLITR-GRKKYTLYSYGLGFISTVAIF-LVIPLLNN----VLIFYPLLFFNMMMSEFAW 319
                                       57777777788999*******99.*********999999999998.99999999....5666666666677788889 PP

                                       THHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHH CS
                          Sugar_tr 368 gpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvflvfaglavlfi 430
                                       ++    l +El+p+++R++++  +  +     +++  l  ++t++++  ++ ++++gl +l++
  gi|518653184|ref|YP_008142704.1| 320 ASRT-TLEPELSPTRIRGIFMGTVRLA----PMIVYPLLVYLTSNVSIRVFIIINVGLWLLGF 377
                                       9999.788************9977654....55555566666666664455555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.59u 0.31s 00:00:00.89 Elapsed: 00:00:00.47
# Mc/sec: 2580.40
//
Query:       gi|518653185|ref|YP_008142705.1|  [L=328]
Description: transposase mutator type [Ferroplasma acidarmanus fer1]
Scores for complete 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-63  213.8   0.0    4.4e-63  213.4   0.0    1.0  1  Transposase_mut  Transposase, Mutator family
    4.2e-06   27.1   0.0    7.4e-06   26.3   0.0    1.4  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  213.4   0.0   4.9e-67   4.4e-63      23     316 ..      17     299 ..       3     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 213.4 bits;  conditional E-value: 4.9e-67
                   Transposase_mut  23 ddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtl.elriPrdRsGsFspallerykR 98 
                                       d +lk        + +++++++ +++e  +  ee+ + +nG+++r+l+T++g++ +l+iPrdR+ +F+++++e y+R
  gi|518653185|ref|YP_008142705.1|  17 DKILK--------QTIKEKIEKLMEIELNAYLEENPGVKNGKYKRDLKTKYGEIkQLNIPRDRDSNFHTQVIEPYNR 85 
                                       44444........45555555555555555567788899*************9957********************* PP

                   Transposase_mut  99 rekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeekeypllflDalylkvR 175
                                       +   +e+ ++++y +G+str+++ ++e++ g +++Sks+vS+it+ + e+v +f +R+L++  y ++flD+l   +R
  gi|518653185|ref|YP_008142705.1|  86 SI-GMEDLIVSMYSNGISTRRIAGILEDILG-NKYSKSTVSRITDLTMEEVYKFINRPLDKR-YIAVFLDGLFFYLR 159
                                       86.689*************************.66***************************9.************** PP

                   Transposase_mut 176 eegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgvelvvsDahkGLvkaisavfpeaav 252
                                         g v  ++v+ a+g++  G+ e+Lg+ ++ +Es++++++vle+L nrGlk+  l+v+D+ k L + + + +p+++ 
  gi|518653185|ref|YP_008142705.1| 160 -RGNVDKEPVIFALGIKETGEYELLGFYLTVKESHNAYKDVLEDLYNRGLKEPLLIVADGIKNLDEEVMEIYPGSEF 235
                                       .788999********************************************************************** PP

                   Transposase_mut 253 QrCrvHllrnllakvpkkkadkvaealksiykaedaeearealeefleklgkkypkvaelldea 316
                                       Q C++H++r l ++v  k+ ++++ +  +++k  + eea  ++++f  k+ +ky++   +ld+ 
  gi|518653185|ref|YP_008142705.1| 236 QLCTIHYARGLKSNVREKDIEEITIDANKMFKCDNKEEAIIRFNDFKYKWENKYSAPHLHLDTL 299
                                       *******************************************************988888764 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   8.3e-10   7.4e-06      15      94 ..     166     243 ..     149     245 .. 0.91

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 8.3e-10
                              MULE  15 lplltvvgvddngqlvplafalveseneesyewllqelleevsgqrspkviitDkekallnaleevfpeakhrlClf 91 
                                        p + ++g+++ g+  +l+f l+ +e+ + y+ +l++l ++    ++p  i+ D  k l + ++e++p+++ +lC+ 
  gi|518653185|ref|YP_008142705.1| 166 EPVIFALGIKETGEYELLGFYLTVKESHNAYKDVLEDLYNRGL--KEPLLIVADGIKNLDEEVMEIYPGSEFQLCTI 240
                                       5777899*******************************99644..6******************************* PP

                              MULE  92 Hia 94 
                                       H a
  gi|518653185|ref|YP_008142705.1| 241 HYA 243
                                       *76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2427.26
//
Query:       gi|518653186|ref|YP_008142706.1|  [L=329]
Description: cobalamin biosynthesis protein CbiG [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  105.4   0.0    2.1e-30  104.5   0.0    1.5  1  CbiG_N    Cobalamin synthesis G N-terminal
    7.6e-20   71.6   0.0    1.4e-19   70.7   0.0    1.5  1  CbiG_C    Cobalamin synthesis G C-terminus
  ------ inclusion threshold ------
      0.039   14.1   0.0      0.091   12.9   0.0    1.7  1  CbiG_mid  Cobalamin biosynthesis central region


Domain annotation for each model (and alignments):
>> CbiG_N  Cobalamin synthesis G N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.5   0.0   3.6e-34   2.1e-30       2      82 .]      51     130 ..      50     130 .. 0.98

  Alignments for each domain:
  == domain 1  score: 104.5 bits;  conditional E-value: 3.6e-34
                                       .HHHHCCC-SEEEEES-HHHHHHHHHHH---TTT--EEEEE-TT--EEEEEE-TT.TTHHHHHHHHHHHTT-EE-XX CS
                            CbiG_N   2 llrelfkeydalvfilaaGivvRliapllkdKktDpaVvvvdeagrfvisllsGhlggAnelAeeiaallgaepviT 78 
                                       +++elf+ y++++fi+a+G+vvRli p++k+K +Dp+++v+d+ g+fvi++++Gh +g nel++ ia +l+a +viT
  gi|518653186|ref|YP_008142706.1|  51 TIKELFTGYETIIFIMALGAVVRLISPYIKNKFEDPCIIVIDDGGKFVIPVIGGH-HGSNELSKGIAGILNASAVIT 126
                                       789****************************************************.********************* PP

                                       XXX. CS
                            CbiG_N  79 tatd 82 
                                       ta+d
  gi|518653186|ref|YP_008142706.1| 127 TASD 130
                                       **98 PP

>> CbiG_C  Cobalamin synthesis G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0   2.4e-23   1.4e-19       3     115 ..     211     324 ..     209     325 .. 0.96

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 2.4e-23
                                       EEEEE-SS--HHHHHHHHHHHHHHCT--GGGEEEEEESSCCSHHHHHHHHHHHCTSTEEEE-HHHHHCHHCSCT-CH CS
                            CbiG_C   3 vGiGcrrgtsaeeieeaieealeeaglseeavaalatidlKadepgllelaeklglplktfsaeeLaavevpnpsef 79 
                                       vGiG++ +++ +++++aie++++++ l  ea+++++ti++K+ +  l  la +l++ l+++++e+L++ +v ++s++
  gi|518653186|ref|YP_008142706.1| 211 VGIGFSTDATYTDMKNAIESVFRKYSLYLEAIRSISTITIKEGNTDLKVLAGDLNCMLNYYPPEKLNENSV-TRSAA 286
                                       9**********************************************************************.***** PP

                                       HHCCCSSS-HHHHHHHHHC...EECSCEEEETTEEEEE CS
                            CbiG_C  80 vkkevGvpsVaEaaAllaa..arllvpKqakggvTvAi 115
                                       v +++G +sV+ a+A + +  ++ lv+K+ +++ T+++
  gi|518653186|ref|YP_008142706.1| 287 VYRATGAYSVSNASARISSsgGKELVSKEIINNTTISV 324
                                       ****************986456899999999****997 PP

>> CbiG_mid  Cobalamin biosynthesis central region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.5e-05     0.091       1      39 [.     135     173 ..     135     227 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.5e-05
                          CbiG_mid   1 palDilgrpfGwriegegaltevsaalvngepvavlqdv 39 
                                       p+l +l++++ ++i++ ++l +vs  l++g pv+v  ++
  gi|518653186|ref|YP_008142706.1| 135 PSLEMLAKKYSMSIKNTQNLPAVSMDLIDGLPVQVTNNT 173
                                       799********************************9854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:01.66
# Mc/sec: 598.94
//
Query:       gi|518653187|ref|YP_008142707.1|  [L=453]
Description: hypothetical protein FACI_IFERC00001G1828 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-36  124.3   0.2    8.6e-36  123.4   0.1    1.5  2  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
    1.1e-18   67.6   0.4    3.1e-18   66.1   0.1    2.0  2  CbiA           CobQ/CobB/MinD/ParA nucleotide binding domain
    9.7e-16   58.2   0.5      4e-11   43.1   0.2    3.3  2  AAA_26         AAA domain
  ------ inclusion threshold ------
      0.013   15.1   0.0      0.024   14.3   0.0    1.4  1  Peptidase_S51  Peptidase family S51
      0.061   13.2   0.1       0.15   11.9   0.0    1.6  2  AAA_31         AAA domain


Domain annotation for each model (and alignments):
>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       2.8   9.9e+03      48      68 ..      66      86 ..      60      88 .. 0.81
   2 !  123.4   0.1   2.4e-39   8.6e-36       1     194 [.     250     433 ..     250     435 .. 0.92

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 2.8
                          GATase_3 48 Ggkdtiqdlallresgldeai 68
                                      G+++t++++ + +++g d +i
  gi|518653187|ref|YP_008142707.1| 66 GSNNTVKEIYYHNSEGKDISI 86
                                      899999999999998888777 PP

  == domain 2  score: 123.4 bits;  conditional E-value: 2.4e-39
                          GATase_3   1 kiavirlpaisnyt..dldpLeaepevrvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeag 75 
                                       +i++++ +a+ +y+  ++++L++ +++ ++f p+ d++l++ +d ++++Gg++++ + +l+ +s l  +ike++ +g
  gi|518653187|ref|YP_008142707.1| 250 TIGIAYNKAFTFYYpeNIELLKKFGAKIIYFDPVIDRKLPH-MDGIYIGGGYPELYAGELSGNSALLAEIKEKIDDG 325
                                       699************************************76.*********************************** PP

                          GATase_3  76 gpvlgiCGGlqmLGeeiedpegvegeageveglglLdietefekekltgqvegevel......aaegeevkGyEiHs 146
                                       +pv+++CGG+++L+e+i   +       e++++g ++++t++e    +g  +++          +ege+  G+E+H+
  gi|518653187|ref|YP_008142707.1| 326 MPVFAECGGYMYLSESINYGDA------EYPMVGAIPARTHMEG-LSLGYRKIY--PaapgeiLKEGEKAMGHEFHY 393
                                       *****************97654......8***************.666666666..24599988899********** PP

                          GATase_3 147 GrtilkekakpllkvkvggnngekdGavkksedgnvlGtYlHglfdnr 194
                                       +r + ++++++++k+    +ng+++G  +k    n+l  Y H+ f ++
  gi|518653187|ref|YP_008142707.1| 394 SRIVFNKSHSEAYKF----ENGKSEGYSSK----NILSGYAHLYFPSN 433
                                       ***************....6679*****88....*********99765 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.1   8.6e-22   3.1e-18       1     120 [.       6     186 ..       6     195 .. 0.94
   2 ?   -1.9   0.0      0.92   3.3e+03      57      86 ..     221     246 ..     198     295 .. 0.56

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 8.6e-22
                                       EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCH.HTTEB-HHHH...................... CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx...................... RF
                              CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlai.leglendiep...................... 54 
                                       ++ia+ ++G+GKTt+++++++al + gl+V++++++p+   +   ++ + n+ ++                      
  gi|518653187|ref|YP_008142707.1|   6 LMIAAPSSGTGKTTVSIGIMKALTDMGLKVQPFKVGPDYIDTGFhYFASGNESHNldsvmgsnntvkeiyyhnsegk 82 
                                       68************************************877766666666666668999999999999********* PP

                                       .......................................CCHCCCHHHHHHCHCHHHH.....EEEEEEEEESS... CS
                                       .......................................xxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxx RF
                              CbiA  55 .......................................dlkrllellealgkkkall...lkiagvvlnrvdgene 89 
                                                                              d++  +++++a++k+++++    +++gv+lnr +++ +
  gi|518653187|ref|YP_008142707.1|  83 disiiegvmglfdgkagnslkgssfeisrilgipivmviDISASGRSAAAVVKGFRDFdkrALLKGVILNRAGSDYH 159
                                       ***************************************************************************** PP

                                       -TTCHHHHHHHHHHCTS-EEEEEE--CCHCC CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  90 etllkealeelkqrygvpvlgviprdeavae 120
                                         + kea+e++    g++vlg i+r+ ++ +
  gi|518653187|ref|YP_008142707.1| 160 CSMVKEAIETTT---GIKVLGCIKRNNEL-K 186
                                       **********98...**********9988.4 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.92
                                       HCCCHHHHHHCHCHHHH..EEEEEEEEESS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA  57 krllellealgkkkalllkiagvvlnrvdg 86 
                                       ++++++ ++ +k+     k++ v+ nr ++
  gi|518653187|ref|YP_008142707.1| 221 EQIVKISSTASKP----SKYKPVIYNRREK 246
                                       4555555554444....4455555555333 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   0.2   1.1e-14     4e-11       1     194 [.       4     185 ..       4     187 .. 0.75
   2 ?    1.7   0.0     0.054   1.9e+02      19      75 ..     192     247 ..     189     278 .. 0.85

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 1.1e-14
                            AAA_26   1 rtifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspel 77 
                                       +++++++ + g GKT+vs g+++al++ g kv+ fK  + +      +++  +++              ++ ++++ 
  gi|518653187|ref|YP_008142707.1|   4 KGLMIAAPSSGTGKTTVSIGIMKALTDMGLKVQPFKV-GPDY-----IDTGFHYF--------------ASGNESHN 60 
                                       579**********************888888876663.3333.....23334444..............33444444 PP

                            AAA_26  78 aarqegedidlekivkelekdadivvVEGagglgvpitee...llnadiaknlgapvilVargglgtinqllltiea 151
                                       ++  +g   ++++i +++++ +di ++EG+ gl ++ + +    + ++i + lg+p+++V+ +  +    +++ ++ 
  gi|518653187|ref|YP_008142707.1|  61 LDSVMGSNNTVKEIYYHNSEGKDISIIEGVMGLFDGKAGNslkGSSFEISRILGIPIVMVIDISASG-RSAAAVVKG 136
                                       55555666678889899****************98866652226789***************97743.455566666 PP

                            AAA_26 152 lr..qknvrvlGvilNkvrnp....envetlekksgipvlGvvPylpdl 194
                                       +r  +k   ++GvilN+  ++       e++e+++gi+vlG++  + +l
  gi|518653187|ref|YP_008142707.1| 137 FRdfDKRALLKGVILNRAGSDyhcsMVKEAIETTTGIKVLGCIKRNNEL 185
                                       773345667********766655543999**************999887 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.054
                            AAA_26  19 lgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplsp 75 
                                       lgLv a  +++++ +y+K +++ i++  d e i ++ ++ ++++  +p++++++ ++
  gi|518653187|ref|YP_008142707.1| 192 LGLVTAA-ENQINDAYLKNLSSLIRKSIDLEQIVKISSTASKPSKYKPVIYNRREKE 247
                                       7888888.7888999999999999999999999999999999888999998877655 PP

>> Peptidase_S51  Peptidase family S51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   6.6e-06     0.024      76     163 ..     284     375 ..     262     412 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 6.6e-06
                                       HHHHHHHSSEEEE--S-HHHHHHHHHHT.THHHHHHHHHHTT-EEEEETHHHHTTSSB-GGGTTTS-GGG-S....- CS
                     Peptidase_S51  76 ieeklleadviyvgGGntfrLlkllket.gldkllreavqqglvyiGvSAGaivagesiettsysdspikap....e 147
                                       i++kl ++d+iy+gGG     + +l ++ +l + ++e++ +g++++    G +  +esi++ + ++ p +      +
  gi|518653187|ref|YP_008142707.1| 284 IDRKLPHMDGIYIGGGYPELYAGELSGNsALLAEIKEKIDDGMPVFAECGGYMYLSESINYGD-AEYPMVGAiparT 359
                                       899*************999889888876268999**************************998.4544443335778 PP

                                       --B----SSSEEETTT CS
                     Peptidase_S51 148 sfeaLgLvkfqivPHy 163
                                        +e+L L   +i P +
  gi|518653187|ref|YP_008142707.1| 360 HMEGLSLGYRKIYPAA 375
                                       8888888777777765 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   4.3e-05      0.15      12      88 ..      14      91 ..       4     102 .. 0.84
   2 ?   -2.6   0.0       1.3   4.5e+03      65      93 ..     198     223 ..     170     237 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.3e-05
                            AAA_31 12 GvGKTTtsvnlaaalaklgkkvLlvDlDpQanattglgiekneiektlyevlieeknikeaiiktk.venldlipssi 88
                                      G GKTT s+ + +al+ +g kv    + p    t    + + + +++l +v+ +++++ke++++++  +++++i + +
  gi|518653187|ref|YP_008142707.1| 14 GTGKTTVSIGIMKALTDMGLKVQPFKVGPDYIDTGFHYFASGNESHNLDSVMGSNNTVKEIYYHNSeGKDISIIEGVM 91
                                      99*********************9999999999998888899999999999889999999999777345557776655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                            AAA_31  65 eeknikeaiiktkvenl.dlipssidLaea 93 
                                        e++i++a+     +nl +li  sidL ++
  gi|518653187|ref|YP_008142707.1| 198 AENQINDAYL----KNLsSLIRKSIDLEQI 223
                                       4555555555....4555777777777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (453 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.56u 0.31s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 2934.58
//
Query:       gi|518653188|ref|YP_008142708.1|  [L=366]
Description: hypothetical protein FACI_IFERC00001G1829 [Ferroplasma acidarmanus fer1]
Scores for 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   45.6   0.2    3.7e-11   43.2   0.2    1.8  1  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophos
     0.0071   16.5   0.2      0.078   13.1   0.1    2.4  2  PglZ           PglZ domain
  ------ inclusion threshold ------
      0.069   12.5   0.0       0.13   11.6   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 !   43.2   0.2   6.1e-15   3.7e-11       4     245 ..      45     258 ..      42     265 .. 0.74

  Alignments for each domain:
  == domain 1  score: 43.2 bits;  conditional E-value: 6.1e-15
                                       EEETT-BTTHHHHHGSTSHHHHHHHHHSEEESEEE-SSS-SHHHHHHHHHHSS-HHHHS--SSSEEETTTTEEEEEE CS
                      Phosphodiest   4 islDGlradlldrlaellpnlaaLakegvsapnlrpvfPtlTfpnhaslvTGlyPgeHGivgNtfydrktgeyvvfv 80 
                                       i+lDGl +++ ++           +k+ ++++   +vfP++T  +++s+   ++Pg+HGi+g++ y +++g+ v+  
  gi|518653188|ref|YP_008142708.1|  45 ILLDGLGWNIYRQ--TGIE-----FKNEIKGT---SVFPSTTSNALSSFFLNKFPGQHGIIGYQLYIKQLGSIVNIL 111
                                       5666666666655..2222.....34444555...9************************************86665 PP

                                       TTTTGGGGGCTTS-HHHHHHHTHTTCEEEESE..TTTTSEBTTCT.SC..TBHHSBTCT.CSTTSCHHH.HHHHHHH CS
                      Phosphodiest  81 tededaprwwqgepiwdtaakarglkaaalfw..pgsevdystyyylvs.etppryleddfnakvpled.kvdkavl 153
                                        ++++           d ++ka+ + ++++++  + +  ++  y    + ++ p+++     +k ++    +++  +
  gi|518653188|ref|YP_008142708.1| 112 GYTSS------AAYMRDSMEKAYPM-SSIFNFesKVTSLNRAGY-S--TvNIIPGFI-----NKTSFSNiLYGDNTT 173
                                       55554......47777888888544.555555344444454422.1..126666666.....555555544444455 PP

                                       HHHHHCHTHSHHHHHCT.SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEE CS
                      Phosphodiest 154 qtwldaafakvvlekel.ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilv 229
                                       +t+ ++     vle++l +  d++  y  ++D++ Hk+Gp++p + ++ r++ + +  +++  +e       + +++
  gi|518653188|ref|YP_008142708.1| 174 DTYANMVHSFYVLEENLkQGRDFISYYAADVDQIAHKLGPNNPYTIENARYILQQLSMIMKKYPEY------DYVIT 244
                                       678888877777777778999*******************************************86......66*** PP

                                       ES---EEEHTTSEEEG CS
                      Phosphodiest 230 SDHGmadvsddkviel 245
                                       +DHG  +v   + i+l
  gi|518653188|ref|YP_008142708.1| 245 ADHGHVEV--GNTINL 258
                                       ******99..776665 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.097   5.8e+02       2      55 ..      41      87 ..      40      95 .. 0.60
   2 !   13.1   0.1   1.3e-05     0.078     109     170 ..     191     250 ..     165     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.097
                              PglZ  2 kvfvIisDalryeaweelkqlLnkedrfeaelsavlgvlPslTklgraallpgk 55
                                      k ++I+ D+l+++  ++      +   f+ e+ +  +v Ps T+ +  + + +k
  gi|518653188|ref|YP_008142708.1| 41 KLCFILLDGLGWNIYRQ------TGIEFKNEI-KGTSVFPSTTSNALSSFFLNK 87
                                      66777777777655443......222344455.455777888877777777665 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 1.3e-05
                              PglZ 109 lkdkevvyivhnkvDalgdkas.teqksfeaveeslkelkelvkslleengykvlltaDHGfi 170
                                        ++++ +  +   vD++++k       + e ++  l++l+ ++k+  e+     ++taDHG +
  gi|518653188|ref|YP_008142708.1| 191 KQGRDFISYYAADVDQIAHKLGpNNPYTIENARYILQQLSMIMKKYPEY---DYVITADHGHV 250
                                       467888999999*******8651566899***************99998...8899*****98 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.1e-05      0.13     123     190 ..     186     252 ..     123     258 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.1e-05
                                       HHHHH.CC.-SEEEEEE-HHHHHHHTT-HHH..HHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                     Metalloenzyme 123 aldailsgkfdlvvvniknaDmvGHtgdlea..tiaaieaaDeavkeildaieqvdgilvvtADHgnaed 190
                                       + +++++g  d++    ++ D+++H+  +++  ti+   ++ +++ +i+++  + d  +v+tADHg  e 
  gi|518653188|ref|YP_008142708.1| 186 LEENLKQG-RDFISYYAADVDQIAHKLGPNNpyTIENARYILQQLSMIMKKYPEYD--YVITADHGHVEV 252
                                       44566455.99**************9766653389999999999999999999999..********8775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2588.35
//
Query:       gi|518653189|ref|YP_008142709.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G1830 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-48  166.1  77.1    5.5e-42  143.9  48.9    2.6  2  MFS_1     Major Facilitator Superfamily
    1.4e-08   34.0  15.9    1.4e-08   34.0  15.9    4.4  3  Sugar_tr  Sugar (and other) transporter
     0.0096   14.4  20.7       0.03   12.7  20.7    1.8  1  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
        2.9    7.4   7.5          2    7.9   1.6    3.5  2  SKG6      Transmembrane alpha-helix domain


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 !  143.9  48.9   1.2e-45   5.5e-42       2     353 .]      19     411 ..      18     411 .. 0.94
   2 !   36.2  20.3   7.1e-13   3.2e-09       3     169 ..     271     468 ..     270     476 .. 0.89

  Alignments for each domain:
  == domain 1  score: 143.9 bits;  conditional E-value: 1.2e-45
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +++++l+++  +++ pa+p    + ++++ s ++++lt+y ++  v++ ++G ++d +G ++v+ll  +++ +++ +
  gi|518653189|ref|YP_008142709.1|  19 AFSGLLIIYVETMIVPAIP-VFITFFHSTYSNVSWILTAYIITGTVSAAIFGKVADIVGKKKVFLLLGIIYTIAISF 94 
                                       789999*************.66699*************************************999999999999666 PP

                             MFS_1  79 llfasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravf 154
                                       + fa++    l+++r++qG+g  +++p++ a+i d++p+e+ ++a g++sa+f++G+ +g +lg+++++ lgW++ f
  gi|518653189|ref|YP_008142709.1|  95 GGFAHT-LdELIAVRAVQGIGF-GMIPIAFAIINDVVPREKLALAQGIMSATFAIGSGIGLVLGSYITETLGWQWDF 169
                                       669555.55************7.9***************************************************** PP

                             MFS_1 155 yilaivsllafvlfllllpeepperkrkspkeee........................................... 188
                                         + +v++++++l +++++e+ ++ k k +                                               
  gi|518653189|ref|YP_008142709.1| 170 HTAIPVAIILLILTYIFIRENTVTGKQKIDFAGVsmlgaglvllifglsegehygwyshliigmfilafilfaafty 246
                                       ****************************999999******************************************* PP

                             MFS_1 189 .kgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls...glllaglllallalvgaila 261
                                        +++ + ++++  k+l+k++ +++ +++l+ ++ ++++l++++p++lq+    +   +++++gl++  + ++++++a
  gi|518653189|ref|YP_008142709.1| 247 fESHYKYAFIN-MKLLKKRNIFLSNIVGLFAMA-AMYFLFFTVPTLLQDPSPVGfgkTVFYSGLIMFPATVMNMVFA 321
                                       ***********.********9986666666665.9999*******99987666666989****************** PP

                             MFS_1 262 llagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtas 338
                                       ++a+r++++ g+r  ++++l++ ++++ +l+l  +t   + +ll  +++G g +++ + +++++  ++p+ +ag a+
  gi|518653189|ref|YP_008142709.1| 322 PVAARIIKHRGPRLSIIIGLSVDIVGFWLLYLYRAT--IPEILLDTMFVGAGISLMLVGIINVLLTSTPRANAGEAT 396
                                       ************************************..88888889999*******999999999999********* PP

                             MFS_1 339 glfntagslggalgp 353
                                       g +++++ +g++++p
  gi|518653189|ref|YP_008142709.1| 397 GMNTVFRDIGMSIAP 411
                                       *************98 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 7.1e-13
                             MFS_1   3 laaflsalarsilgpalplalaed.....lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfal 74 
                                       ++++++++a+++l++++p +l +d     +g ++   gl++   ++  +v++++++r++   G+r  +++gl + ++
  gi|518653189|ref|YP_008142709.1| 271 IVGLFAMAAMYFLFFTVP-TLLQDpspvgFGKTVFYSGLIMFPATVMNMVFAPVAARIIKHRGPRLSIIIGLSVDIV 346
                                       567899999999******.89999899999999999999999999999***************************** PP

                             MFS_1  75 glllllfa..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg 149
                                       g++ll     ++++ +l+  ++ G+g ++++ +++ ++   +p+ + g a+g+ +++  +G+ ++p++gg+l + + 
  gi|518653189|ref|YP_008142709.1| 347 GFWLLY-LyrATIPEILLDTMFVGAGISLMLVGIINVLLTSTPRANAGEATGMNTVFRDIGMSIAPAVGGALETMYT 422
                                       *66666.33599999*******************************************************9998888 PP

                             MFS_1 150 ..........................Wravfyilaivsllafvlfl 169
                                                                 + ++++i  i+ +l+f++ +
  gi|518653189|ref|YP_008142709.1| 423 lkvtvgvqiingiptkiqlpfpdstaYNYIYLIGVIFVILGFIFTA 468
                                       9999999999999999999999999888888888888888877533 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0  15.9   3.2e-12   1.4e-08      46     193 ..      48     189 ..      14     197 .. 0.84
   2 !    2.9   1.8     0.009        40     396     441 ..     205     250 ..     198     256 .. 0.76
   3 ?    1.8  10.7     0.019        85     291     435 ..     308     469 ..     294     477 .] 0.69

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 3.2e-12
                                       .HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHH CS
                          Sugar_tr  46 vlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvl 122
                                       + +++i+ ++++ +++++ ++g+++d++G+kk++l  ++++ i++   ++a+   ++  li+ R + Gig G++ + 
  gi|518653189|ref|YP_008142709.1|  48 SNVSWILTAYIITGTVSAAIFGKVADIVGKKKVFLLLGIIYTIAISFGGFAH---TLDELIAVRAVQGIGFGMIPIA 121
                                       4578************************************************...9****************99766 PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS-- CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsnadgwrillglqlvpallllill.lflPE 193
                                           i+ + p ++      l q  +++ + +++++gl+l ++++++ gw++ ++ ++  a++llil  +f++E
  gi|518653189|ref|YP_008142709.1| 122 F-AIINDVVPREK----LALAQGIMSATFAIGSGIGLVLgSYITETLGWQWDFHTAIPVAIILLILTyIFIRE 189
                                       6.55788877655....3456666666777888888888888888899************9998887466665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.009
                                       HHHHHHHHHHHHHHHCHHHT-HHHHHHHHHHHHHHHHHHHHS--ST CS
                          Sugar_tr 396 wlanflisllfpiiteaigggyvflvfaglavlfiifvfffvpetk 441
                                       +l   l+ l+f    +   g+y+ l+ +++ ++fi+f  f+++e  
  gi|518653189|ref|YP_008142709.1| 205 MLGAGLVLLIFGLSEGEHYGWYSHLIIGMFILAFILFAAFTYFESH 250
                                       45555555555555555557**********************9976 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.019
                                       HHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS........CHHHHHHHHHHHHH CS
                          Sugar_tr 291 lvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvaks.....kaasivaivfialfial 362
                                       l+ +   v+n+v+  va+ ++++ G R   ++G+++ ++ f++l     l++a+      + + ++a + ++l+  +
  gi|518653189|ref|YP_008142709.1| 308 LIMFPATVMNMVFAPVAARIIKHRGPRLSIIIGLSVDIVGFWLLY----LYRATIpeillDTMFVGAGISLMLV-GI 379
                                       45566789***********************************95....4444433344555555555555554.56 PP

                                       HHTTTTHHHHHHHHHHS..HTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH...............T-HHHHHH CS
                          Sugar_tr 363 falgwgpvpwvlvsElf..pqsvRskalaiavavnwlanflisllfpiiteaig...............ggyvflvf 422
                                        ++ ++++p   + E     + +R+++++ia av        +l  ++ ++ i+                 y++l+ 
  gi|518653189|ref|YP_008142709.1| 380 INVLLTSTPRANAGEATgmNTVFRDIGMSIAPAVGGALETMYTLKVTVGVQIINgiptkiqlpfpdstaYNYIYLIG 456
                                       67788888888888886225668999999999999888888888877777777777788888888665333444444 PP

                                       HHHHHHHHHHHHH CS
                          Sugar_tr 423 aglavlfiifvff 435
                                       +++++l++if+ f
  gi|518653189|ref|YP_008142709.1| 457 VIFVILGFIFTAF 469
                                       4444444444433 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7  20.7   6.8e-06      0.03      78     326 ..      48     281 ..       9     292 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.8e-06
                             TRI12  78 ensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagasplf 154
                                        n s + t + +  +vs  ++g+++d +g++ + +l  i+  +    g  a  ++ l+a  ++ g+  g    +  +
  gi|518653189|ref|YP_008142709.1|  48 SNVSWILTAYIITGTVSAAIFGKVADIVGKKKVFLLLGIIYTIAISFGGFAHTLDELIAVRAVQGIGFGMIPIAFAI 124
                                       567777888999999*****************99999******999******************************* PP

                             TRI12 155 vgelmsnktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavllivvwyyppsfaqlhgkkvr 231
                                       + +++      l   i+s+   + sg++  lg  ++    w+w f+  i    +a++l+++ y     + + gk+  
  gi|518653189|ref|YP_008142709.1| 125 INDVVPREKLALAQGIMSATFAIGSGIGLVLGSYITETLGWQWDFHTAIP---VAIILLILTYIFIRENTVTGKQ-- 196
                                       ******99999**********************************99875...5666777777666666677764.. PP

                             TRI12 232 kreelakldwigiilvivgvslfllgvswggkpnspwnsakviglissglgslvvfalyevygkp.vrpivppalfk 307
                                             k+d+ g+ ++ +g  l+++g+s g +    w s  +ig++       ++fa +  +    +  ++   l+k
  gi|518653189|ref|YP_008142709.1| 197 ------KIDFAGVSMLGAGLVLLIFGLSEGEH--YGWYSHLIIGMFILAF---ILFAAFTYFESHyKYAFINMKLLK 262
                                       ......9*********************9976..68********997655...555555555433034678888888 PP

                             TRI12 308 dtrgfvcillissimgamn 326
                                           f+  ++    m am 
  gi|518653189|ref|YP_008142709.1| 263 KRNIFLSNIVGLFAMAAMY 281
                                       8777777666666666665 PP

>> SKG6  Transmembrane alpha-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   1.6   0.00045         2      17      32 ..     172     187 ..     171     188 .. 0.94
   2 ?    0.0   0.4      0.13   5.8e+02      20      31 ..     455     466 ..     455     472 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00045
                              SKG6  17 aVPVaViiivLlaili 32 
                                       a+PVa+i+++L  i+i
  gi|518653189|ref|YP_008142709.1| 172 AIPVAIILLILTYIFI 187
                                       8***********9998 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.13
                              SKG6  20 VaViiivLlail 31 
                                       ++Vi ++L++i+
  gi|518653189|ref|YP_008142709.1| 455 IGVIFVILGFIF 466
                                       577777777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1006  (0.0561102); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.46
# Mc/sec: 3103.77
//
Query:       gi|518653190|ref|YP_008142710.1|  [L=471]
Description: hypothetical protein FACI_IFERC00001G1831 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  50.8    1.5e-23   83.2  50.8    1.1  1  AA_permease    Amino acid permease
    7.1e-20   71.2  57.0    1.2e-19   70.5  57.1    1.3  1  AA_permease_2  Amino acid permease
  ------ inclusion threshold ------
      0.031   14.7   1.9      0.031   14.7   1.9    3.7  3  DUF805         Protein of unknown function (DUF805)


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.2  50.8   2.5e-27   1.5e-23       3     472 ..      18     457 ..      16     463 .. 0.80

  Alignments for each domain:
  == domain 1  score: 83.2 bits;  conditional E-value: 2.5e-27
                       AA_permease   3 lvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviG 79 
                                       +++a+g +  ++    l   + +  ++++ la+ll+++ ++++m++ ++++ +++++g++yt+a + lg  +G + +
  gi|518653190|ref|YP_008142710.1|  18 VWQAMGTLSVAADAAYLLTGVVEYALGATPLALLLGVFAYLFIMNTGYQFSKHVNSAGSYYTFAGKGLGGIAGTFQA 94 
                                       7888888777888888888999999999************************************************* PP

                       AA_permease  80 lnylfswitvla.leltaasiliqfwel.vtdlpkawvtgavflvvllii.nlvgvkvygeaefilalikiiaiiaf 153
                                       +n  f+++++++ +++ +++ +i+++   ++ +   w  +a f +++++i +  g+kv+   ++      +++ +a+
  gi|518653190|ref|YP_008142710.1|  95 WNMAFYGLIGYGsFGFLGLAAFITLLDPaYKGIV-FWLPVAFFAALISFIfTHRGMKVSTDYQIA----GGVIEVAV 166
                                       **999999876538************77777777.77778888888865526689***9996654....45555555 PP

                       AA_permease 154 iivg...iillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkd 227
                                       +++g   ii++ag  ++ +                ++ +   + +ga +  ++++  +++ f  + +++++++E+ +
  gi|518653190|ref|YP_008142710.1| 167 LLIGsalIIIHAGNLNTLA---------------VFTTK---YVSGASQLLFAMIYSMILYFGTTVSITAMGEEAVS 225
                                       5555464444555444444...............22222...34445677888888899999999************ PP

                       AA_permease 228 PeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssa 304
                                       P+k+i+ka + +vi+ +i  ++++++ +++++ ++  +++ s ++  ++++f k   ++v+  l+++v+  + +++ 
  gi|518653190|ref|YP_008142710.1| 226 PQKTIKKALIGTVILSGITLIIVSYAFTIGWGPSAMASFATSPDP--GIILFRK--LNPVIYILLILVTVNSFMGYN 298
                                       ****************************************99999..6666665..578888899999999****** PP

                       AA_permease 305 nsslysasRvlyslakdglaP...kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaligli 378
                                       +s + + sR++ys+a+dg++    ++++ ++k++ P +a l+ +++sl++ ++ ++ +++ +   ++l i+a+++ +
  gi|518653190|ref|YP_008142710.1| 299 ISVSNADSRIFYSFARDGILFlpeSIGRIHKKYKTPSNAALAIFAFSLVIAIIFGVLFGPVKGGLMMLLINAYAAYV 375
                                       ******************97555************************************99**************** PP

                       AA_permease 379 vwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaay.l 454
                                        ++++++s++++++ +++ +  i       +     +i+ ++ ++i+++i+a + + + +k p+++ +   ++++ +
  gi|518653190|ref|YP_008142710.1| 376 EHIIASISLPVMMRRIHKFKV-I------EH-----LIIPVIGIVILVIIMAGTVISP-GKYPENLAVYIGISWIpI 439
                                       **********99998777777.3......22.....3444444444444444444444.456666666666666623 PP

                       AA_permease 455 ivllfliilvgvklhvkn 472
                                         +l+ i ++++ ++v+n
  gi|518653190|ref|YP_008142710.1| 440 AGILTFIEYKIHPDKVRN 457
                                       345566666666666666 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.5  57.1     2e-23   1.2e-19       8     408 ..      19     424 ..      12     446 .. 0.79

  Alignments for each domain:
  == domain 1  score: 70.5 bits;  conditional E-value: 2e-23
                     AA_permease_2   8 alvigsvig...sgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsa 81 
                                       + ++g++     ++++ +++++++  a+ l ++++v+++++++   y  +s + ++ g  y+++ ++ g  ++ + a
  gi|518653190|ref|YP_008142710.1|  19 WQAMGTLSVaadAAYLLTGVVEYALGATPLALLLGVFAYLFIMNTGYQ-FSKHVNSAGSYYTFAGKGLGGIAGTFQA 94 
                                       5555555331124555566888999999999********999999998.9988****************99999999 PP

                     AA_permease_2  82 wfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillplii 158
                                       w  +f  +++  s   +++++++++l+p + g  ++++ +a++  ++ +++++rg+k s  +q  +g++ +  + ++
  gi|518653190|ref|YP_008142710.1|  95 WNMAFYGLIGYGSFGFLGLAAFITLLDPAYKGI-VFWLPVAFFAALISFIFTHRGMKVSTDYQIAGGVIEVA-V-LL 168
                                       99888888888888899************9774.69999999999999***********************5.4.44 PP

                     AA_permease_2 159 liilglitvdgggfsslstetdtffpngwpgvllgllivlwsfdGfesaanvsee..vkkkdvpkaifigllivlvl 233
                                       +  + +i+  g+ ++ +++ t + +++ +++ +++++ ++++f+   s++ + ee   ++k+++ka++  ++++++ 
  gi|518653190|ref|YP_008142710.1| 169 IGSALIIIHAGNLNTLAVFTT-KYVSGASQLLFAMIYSMILYFGTTVSITAMGEEavSPQKTIKKALIGTVILSGIT 244
                                       554555555566776544444.5677788889***********************97778***************** PP

                     AA_permease_2 234 yllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvlP. 309
                                        + v+ af+++ +++ +a+ +++++++ ++f++++ +v  i+++++++ s +g  ++++ + sr+++++ardg+l  
  gi|518653190|ref|YP_008142710.1| 245 LIIVSYAFTIGWGPSAMASFATSPDPGIILFRKLN-PVIYILLILVTVNSFMGYNISVSNADSRIFYSFARDGILFl 320
                                       *********************************99.9999999999999************************9888 PP

                     AA_permease_2 310 .rffakvn.kfgspiraiiltaivslillllfl..lassaaynfllsvsslgliisyllliigalilrkkrphlkrp 382
                                        + + +++ k+++p++a   ++ +sl+++++f   +++ +   ++l + ++++++  ++++i++ +  ++ +++k +
  gi|518653190|ref|YP_008142710.1| 321 pESIGRIHkKYKTPSNAALAIFAFSLVIAIIFGvlFGPVKGGLMMLLINAYAAYVEHIIASISLPVMMRRIHKFKVI 397
                                       8*******9****************9999988755444344447777777777777777777766555554443443 PP

                     AA_permease_2 383 gk.ilvaiigalfllfllvalffppkg 408
                                          i+++i ++++++++  + + p+k 
  gi|518653190|ref|YP_008142710.1| 398 EHlIIPVIGIVILVIIMAGTVISPGKY 424
                                       332333333344444444444434333 PP

>> DUF805  Protein of unknown function (DUF805)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       1.6   9.6e+03      24      24 ..      52      52 ..      20      79 .. 0.57
   2 ?   -6.6   9.0         3   1.8e+04      16      16 ..     200     200 ..     123     295 .. 0.63
   3 ?   14.7   1.9   5.2e-06     0.031      16      92 ..     341     416 ..     324     428 .. 0.65

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                            DUF805 24 v 24
                                       
  gi|518653190|ref|YP_008142710.1| 52 L 52
                                      1 PP

  == domain 2  score: -6.6 bits;  conditional E-value: 3
                            DUF805  16 f 16 
                                       f
  gi|518653190|ref|YP_008142710.1| 200 F 200
                                       1 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 5.2e-06
                            DUF805  16 fvlfllllvivlallaavlaa...aavasalsvvlallllvpslavtvRRlHDtgrsgwllllllvplialllllvl 89 
                                       ++ f+l++ i++ +l+  +++   + +++a +  +  ++  +sl v++RR+H       l    ++p+i++++l+++
  gi|518653190|ref|YP_008142710.1| 341 IFAFSLVIAIIFGVLFGPVKGglmMLLINAYAAYVEHIIASISLPVMMRRIHKFKVIEHL----IIPVIGIVILVII 413
                                       3444555555555555555448887888888888888889999*********99876665....6666665555554 PP

                            DUF805  90 lll 92 
                                       ++ 
  gi|518653190|ref|YP_008142710.1| 414 MAG 416
                                       443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (471 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       893  (0.0498076); 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):               3  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.49
# Mc/sec: 2909.17
//
Query:       gi|518653191|ref|YP_008142711.1|  [L=404]
Description: multidrug efflux permease [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  179.3  82.5      1e-37  129.9  50.3    2.0  2  MFS_1        Major Facilitator Superfamily
    2.2e-07   30.0  17.8    2.2e-07   30.0  17.8    2.0  2  LacY_symp    LacY proton/sugar symporter
    5.6e-06   25.0  17.5    1.5e-05   23.6   6.8    2.3  2  MFS_3        Transmembrane secretion effector
  ------ inclusion threshold ------
       0.18   12.1   0.2       0.77   10.1   0.2    2.0  2  Flavokinase  Riboflavin kinase


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 !  129.9  50.3   2.3e-41     1e-37       2     353 .]      17     351 ..      16     351 .. 0.89
   2 !   63.2  24.2   4.4e-21     2e-17       2     170 ..     215     388 ..     214     401 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.9 bits;  conditional E-value: 2.3e-41
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalg.ll 77 
                                       +l+ ++ +l++++ +p++ ++l+   ++++  +g+++tl +l ++v+s+++G+l+d  Gr+ +l+lg ++ ++  l 
  gi|518653191|ref|YP_008142711.1|  17 SLSSMMRSLGMGASWPFMAIFLSLYIHLAVYIVGIIFTLLSLMSMVFSILGGYLADLKGRKFTLMLGSISGIFIyLS 93 
                                       6889999*******************************************************777777777777455 PP

                             MFS_1  78 lll.fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWra 152
                                       ++l f  +++ l ++l +++++ +++++p++ aliad++++e r  +++++ + +++G ++gpl g++++ s g  +
  gi|518653191|ref|YP_008142711.1|  94 IALtFLFHIYtLTIILFIFSSFSGSLVYPSASALIADVTNPESREGGYSIYRILSNVGWAVGPLMGSFIY-STGIIY 169
                                       55565567777***********************************************************.99**** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..ll 227
                                       +fy+l ++s+l  ++  +l++ ++   k+ ++++           p    l+ d++l  +++++++ff+++ +  ++
  gi|518653191|ref|YP_008142711.1| 170 IFYALVVASILQTII--ILFVKKQNVLKTGKGTRN----------P---FLVYDKYL--FIFSIATFFIILLSsqFS 229
                                       ************996..777666666666666666..........3...44555655..4444444443333356** PP

                             MFS_1 228 tllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavlll 304
                                       + lply     +++ +  +g+++a+ +lv++i++  + +l  r+g    l+ +++++l+ alg++++a++++   l+
  gi|518653191|ref|YP_008142711.1| 230 VSLPLYSEIAIKIN-VADLGYIYAINGLVVVIGQYPLIQLFARFGD---LITFIAGALFYALGYFIIAFSTNLYGLM 302
                                       ******99999999.****************************998...999******************8889999 PP

                             MFS_1 305 lvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                       + +v+i++g  +++p++++++s++ pp ++g+++g++++++s+g+a+gp
  gi|518653191|ref|YP_008142711.1| 303 FDMVIITMGENLTTPTINTVISKMSPPGKTGRYMGFNSMVNSIGRAFGP 351
                                       9***********************************************8 PP

  == domain 2  score: 63.2 bits;  conditional E-value: 4.4e-21
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       ++a+f+++l +s ++++lpl+   +  i+++ +g ++++ +l+ +++++pl  l  rfG   ++++g+l++alg ++
  gi|518653191|ref|YP_008142711.1| 215 SIATFFIILLSSQFSVSLPLYSEIAIKINVADLGYIYAINGLVVVIGQYPLIQLFARFGDLITFIAGALFYALGYFI 291
                                       688999999999999999987777889***********************************************777 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...... 149
                                       ++f+++l+ l++  v+  +g+ + +p+++++i++++p+ + gr++g+ s+ +s+G ++gp  g +++  +       
  gi|518653191|ref|YP_008142711.1| 292 IAFSTNLYGLMFDMVIITMGENLTTPTINTVISKMSPPGKTGRYMGFNSMVNSIGRAFGPSMGTYIMYTFHynglat 368
                                       77977777***********************************************************8888677766 PP

                             MFS_1 150 Wravfyilaivsllafvlfll 170
                                       W+ +  i++++s++++v+f++
  gi|518653191|ref|YP_008142711.1| 369 WS-LIAIFGVFSAIVIVIFAI 388
                                       64.368999999999887655 PP

>> LacY_symp  LacY proton/sugar symporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.0  17.8     5e-11   2.2e-07       5     189 ..       9     190 ..       5     200 .. 0.81
   2 ?    0.7  17.0     0.039   1.7e+02      10     201 ..     210     400 ..     201     404 .] 0.78

  Alignments for each domain:
  == domain 1  score: 30.0 bits;  conditional E-value: 5e-11
                         LacY_symp   5 kntnfylfalffffyffimsayfplfpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkell.wvi 80 
                                       +n++ ++ +l+ ++  + m+a +p+++++l+ +++l+   +Gi+f+ +sl+s++f  l G + d  G k  l+  +i
  gi|518653191|ref|YP_008142711.1|   9 RNRQVVIVSLSSMMRSLGMGASWPFMAIFLSLYIHLAVYIVGIIFTLLSLMSMVFSILGGYLADLKGRKFTLMlGSI 85 
                                       566666777777777777*************************************************999885269* PP

                         LacY_symp  81 slllvlfapfliyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsraskfeyGkarvfGclGyalcasl 157
                                       s +++ ++  l ++f+    l i++  +  +    lvy + +++i   ++  sr+    y   r+   +G+a++  +
  gi|518653191|ref|YP_008142711.1|  86 SGIFIYLSIALTFLFHIY-TLTIIL-FIFSSFSGSLVYPSASALIADVTNPESREGG--YSIYRILSNVGWAVGPLM 158
                                       ***999988888887643.233322.33444444589****************9986..67899************* PP

                         LacY_symp 158 aGilfsidpslvfwlasgfalilllllllskp 189
                                          ++s      f+    ++++ +++ l++k 
  gi|518653191|ref|YP_008142711.1| 159 GSFIYSTGIIYIFYALVVASILQTIIILFVKK 190
                                       ******99988888777777776666666653 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.039
                         LacY_symp  10 ylfalffffyffi.msayfpl.fpvwlkevlglsktetGivfsvislfsilfqplfGlisdklGlkkellwvislll 84 
                                       ylf ++   +f i +s  f++ +p++ +  +++  +++G +++++ l+ ++ q  +  +  ++G   +l+  i+  l
  gi|518653191|ref|YP_008142711.1| 210 YLFIFSIATFFIIlLSSQFSVsLPLYSEIAIKINVADLGYIYAINGLVVVIGQYPLIQLFARFG---DLITFIAGAL 283
                                       566666666666667777776489999999******************9998866555566777...89******** PP

                         LacY_symp  85 vlfapfliyvfepllqlnilvGalvGgvflGlvysagagaieayiekvsr..askfeyGkarvfGclGyalcasl.a 158
                                            ++i  f+  l      G++   v + ++ +  ++ i++ i k+s   ++    G   ++ ++G a++ s+ +
  gi|518653191|ref|YP_008142711.1| 284 FYALGYFIIAFSTNL-----YGLMFDMVIITMGENLTTPTINTVISKMSPpgKTGRYMGFNSMVNSIGRAFGPSMgT 355
                                       99999***9998654.....599999**********************9722444557999************9945 PP

                         LacY_symp 159 Gilfsid.pslvfw.lasgfalilllllllskpdksssakvadal 201
                                        i+++ + + l+ w l + f++  +++ +++  + ++s +   a 
  gi|518653191|ref|YP_008142711.1| 356 YIMYTFHyNGLATWsLIAIFGVFSAIVIVIFAISYNKSGNTYIAR 400
                                       699988634577775778888877777777766666666555555 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   6.8   3.4e-09   1.5e-05      36     194 ..      38     194 ..       9     204 .. 0.75
   2 !    7.8   1.7   0.00021      0.93     106     179 ..     301     377 ..     275     397 .. 0.73

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 3.4e-09
                             MFS_3  36 lmtdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavql..llalvsvlltvlaalgllspwlllalt 110
                                       l   i+ + + v ++    +L  +++sil G laD   r+  l+ + +  + +  s+ lt l ++  l+    + ++
  gi|518653191|ref|YP_008142711.1|  38 LSLYIHLAVYIVGIIFTLLSLMSMVFSILGGYLADLKGRKFTLMLGSIsgIFIYLSIALTFLFHIYTLTI---ILFI 111
                                       3335677888899999999999*************99888666655431244555666655555544443...3333 PP

                             MFS_3 111 lligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivall 187
                                        + +   +l  P+ +A + ++ + +  +    +  +  n+  +vGP +g  + ++    + +a+ + s l  i++l 
  gi|518653191|ref|YP_008142711.1| 112 -FSSFSGSLVYPSASALIADVTNPESREGGYSIYRILSNVGWAVGPLMGSFIYSTGIIYIFYALVVASILQTIIILF 187
                                       .345566899**************************************99999987778888999999999999999 PP

                             MFS_3 188 rwkrevr 194
                                         k++v 
  gi|518653191|ref|YP_008142711.1| 188 VKKQNVL 194
                                       9888875 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.00021
                             MFS_3 106 llaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGvlvaav...Gaalafavnalsy 179
                                       l+   ++i +G  l++P+ + +++ + +  +    +  ns+   i R+ GP +g  ++ ++   G a+   ++ +  
  gi|518653191|ref|YP_008142711.1| 301 LMFDMVIITMGENLTTPTINTVISKMSPPGKTGRYMGFNSMVNSIGRAFGPSMGTYIMYTFhynGLATWSLIAIFGV 377
                                       455567899**********************************************9987763324333333333333 PP

>> Flavokinase  Riboflavin kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         2   9.1e+03      70     101 ..     101     132 ..      92     134 .. 0.76
   2 ?   10.1   0.2   0.00017      0.77      17      53 ..     310     348 ..     308     367 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2
                                       --TTSEEEEEEEEEEEE----SSHHHHHHHHH CS
                       Flavokinase  70 dlygkelrvellkflRpekkFdsleaLkaqik 101
                                       ++y  ++ + + +       ++s  aL+a+++
  gi|518653191|ref|YP_008142711.1| 101 HIYTLTIILFIFSSFSGSLVYPSASALIADVT 132
                                       46777777777777888888999999999875 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00017
                                       CHTTTT--EEEEE-S-B-G..TSEEEEEEEEEEEEEEEE CS
                       Flavokinase  17 rGrelgfpTaNlelekllp..kkGVYavrvkgvaniGvr 53 
                                       +G++l  pT+N  ++k+ p  k+G Y+++ ++v +iG  
  gi|518653191|ref|YP_008142711.1| 310 MGENLTTPTINTVISKMSPpgKTGRYMGFNSMVNSIGRA 348
                                       7999********9977775579**************954 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1122  (0.0625802); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.28s 00:00:00.92 Elapsed: 00:00:00.47
# Mc/sec: 2600.58
//
Query:       gi|518653192|ref|YP_008142712.1|  [L=599]
Description: amino acid permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-41  141.4  41.7    3.5e-41  141.4  41.7    2.0  2  AA_permease_2   Amino acid permease
    2.9e-30  105.3  50.1    2.9e-30  105.3  50.1    2.1  2  AA_permease     Amino acid permease
     0.0034   16.3   2.2     0.0034   16.3   2.2    3.6  3  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
      0.025   14.6   3.0      0.049   13.7   0.5    2.9  2  DUF3593         Protein of unknown function (DUF3593)


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 !  141.4  41.7   7.9e-45   3.5e-41       2     397 ..      48     484 ..      47     491 .. 0.86
   2 ?   -1.5  11.7      0.19   8.4e+02      82     173 ..     482     580 ..     479     592 .. 0.74

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 7.9e-45
                     AA_permease_2   2 sllsafalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkv 76 
                                       + +++ +l++g++igsg +++   +a+++gpa+il+++i+  i+ l ++lvyaE+++++prsg i  y+++  g  +
  gi|518653192|ref|YP_008142712.1|  48 TSWDLYFLSLGAIIGSGWLFAEsaAAGTAGPAAILSWIIGGAIV-LVLVLVYAEIGAMIPRSGFITRYGHYSHGGIA 123
                                       5699*************99998899999***********99999.89********999******************* PP

                     AA_permease_2  77 aflsawfnwfayvpvlasilsvaasyllnalgp....dlqgn...........twltyliaiaililvalinirgik 138
                                       + +++w ++ a v++ a+ + +a+ y  + + +     + +n               +lia+a+++++ ++n++g+k
  gi|518653192|ref|YP_008142712.1| 124 GLFFGWGYFAARVAAPALEAEAAITYAGSYITKpaliYYAKNpldpsssvtllSGYGILIAAALIAGFYFLNYFGVK 200
                                       ********999988777766666666655554335533333377888888777557899****************** PP

                     AA_permease_2 139 esakiqnilgilkillpliiliilglitvdgggfsslstetdtffpn.gwpgvllglli..vlwsfdGfesaanvse 212
                                        ++k +  ++++k+++p i++i+ +++++++g f+++  + + f+p+   ++v+ ++++  +++s+ Gf    n++ 
  gi|518653192|ref|YP_008142712.1| 201 LMGKTNQGITWWKLIIPSITIILMVFLLFHAGNFNNP--ALGGFLPHnNISLVFEAISTdgIVFSYLGFRHTLNFAG 275
                                       *******************************999955..4444999955667999999999**************** PP

                     AA_permease_2 213 evkk..kdvpkaifigllivlvlyllvniaflgvvpddeianlsnlgsv................aalffeavg... 268
                                       e+k+  +d+p+a+++++l+++v+y+l+++af+ +++++ ++ +++++++                +a +++ +    
  gi|518653192|ref|YP_008142712.1| 276 EAKNpqRDIPRALIYAMLTSIVVYVLLQFAFISAINPSLLTASGGWLGLssasagtyaksidsapFAFLAKSSSlai 352
                                       *888779*********************************9999988888889888999999877666666665433 PP

                     AA_permease_2 269 gkvvaiivvilialsllgaintavigssrvlealardgvlPrffakvn.kfgspiraiiltaivslillllfllass 344
                                         v+++++++ + +s +g +n a  +++r l+ la+ g++Pr f kv+ ++g p+ ++ +++++ li+l+ +     
  gi|518653192|ref|YP_008142712.1| 353 LAVLTYLLYADAYISPAGTLNIAAGTATRSLYGLAEIGYFPRTFGKVSkRTGVPVFSLLISLVLGLIFLVPLP---- 425
                                       45888888888999**********************************99***************88865553.... PP

                     AA_permease_2 345 aaynfllsvsslgliisyllliigalilrkkrphlkrpgk.......ilvaiigalfllf 397
                                        + ++++ + s  + + y+l   ++++lr+   +lkrp k        +va+iga ++++
  gi|518653192|ref|YP_008142712.1| 426 -SWYVVVGLVSGVAGFTYILGGSTLMVLRREASDLKRPFKlpyarilSPVAFIGASLIVY 484
                                       .4788888888888889999999**************55545557666999999888876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.19
                     AA_permease_2  82 wfnwfayvpvlasilsvaasyllnalgp.......dlqgntwltyliaiaililvalinirgikesakiqnilgilk 151
                                       + +w ++  v+++ ++++a++ +++++         +++++++    + +++i +++++++g +  + i+ + + + 
  gi|518653192|ref|YP_008142712.1| 482 IVYWTGWPTVAYIAIILFAGFAVYLVFLafhhvdnIFTKENIQGGYWVPLLIIALTILSYLGESNFGGINLFPFPYD 558
                                       678888888887777666666666655444567766667788887778899999999999999999999****9999 PP

                     AA_permease_2 152 illpliiliilglitvdgggfs 173
                                       +l+++++ +i+ ++ v+ g  +
  gi|518653192|ref|YP_008142712.1| 559 FLVVMVVSLIFYFLSVKSGFRT 580
                                       9888888887777777666555 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3  50.1   6.4e-34   2.9e-30       2     377 ..      52     440 ..      51     507 .. 0.79
   2 ?   -5.1   9.8       1.9   8.5e+03      77     165 ..     485     579 ..     476     591 .. 0.67

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 6.4e-34
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfvi 78 
                                       + + +lg +iG g +++ + ++++aGp +a+l+++++g++++  +l  +ei  ++p+sg ++ y + ++g  +G + 
  gi|518653192|ref|YP_008142712.1|  52 LYFLSLGAIIGSGWLFAESAAAGTAGP-AAILSWIIGGAIVLVLVLVYAEIGAMIPRSGFITRYGHYSHGGIAGLFF 127
                                       56889**********************.888********************************************** PP

                       AA_permease  79 Glnylfswitvlaleltaasiliqfwelvtdlpkawvt.....................gavflvvlliinlvgvkv 134
                                       G+ y+   +++ ale  aa+ + +    +t+   ++++                     +a +++ + ++n++gvk+
  gi|518653192|ref|YP_008142712.1| 128 GWGYFAARVAAPALEAEAAITYAGSY--ITKPA-LIYYaknpldpsssvtllsgygiliAAALIAGFYFLNYFGVKL 201
                                       ***************77777777766..55555.4444599***************9988888888999******** PP

                       AA_permease 135 ygeaefilalikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvi..vv 209
                                        g++   +++ k+i+  ++ii+ ++ll+ +++ +           + +  +lp++       +++ ++ ++++  +v
  gi|518653192|ref|YP_008142712.1| 202 MGKTNQGITWWKLIIPSITIILMVFLLFHAGNFNN---------PA-LGGFLPHN-------NISLVFEAISTdgIV 261
                                       ****9999999999999999999666666654444.........22.45689999.......56666665554339* PP

                       AA_permease 210 faftGielvaiiagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasa.............. 272
                                       f++ G+  + + agE+k+P+++iP+a ++++++ +++Yvl+ ++ ++ ++ + l+   + + +              
  gi|518653192|ref|YP_008142712.1| 262 FSYLGFRHTLNFAGEAKNPQRDIPRALIYAMLTSIVVYVLLQFAFISAINPSLLTASGGWL-Glssasagtyaksid 337
                                       ***************************************9999999999888866655433.157778899**9999 PP

                       AA_permease 273 aspfvifikesgvsvlapl...inaviltaalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsm 345
                                       + pf    k+s +++la+l   ++a  +++  +++n +  +a+R ly la+ g++P +++k++++ gvP+ ++l+s+
  gi|518653192|ref|YP_008142712.1| 338 SAPFAFLAKSSSLAILAVLtylLYADAYISPAGTLNIAAGTATRSLYGLAEIGYFPrTFGKVSKRTGVPVFSLLISL 414
                                       999999999999888877511166678999999***********************9999999999*********** PP

                       AA_permease 346 iisllal.......llaslnlaapivfnfllaisaligl 377
                                       +++l++l       +             ++  +s+++g+
  gi|518653192|ref|YP_008142712.1| 415 VLGLIFLvplpswyV-------------VVGLVSGVAGF 440
                                       *******33333332.............33333333333 PP

  == domain 2  score: -5.1 bits;  conditional E-value: 1.9
                       AA_permease  77 viGlnylfswitvlaleltaasiliqfw...el.vtdlpkawvtgavflvvlliinlvgvkvygeaefilali..ki 147
                                        +G+ ++ + ++ l +++++   ++ f    +  ++++++  +++ +++++l+i++++g   +g + ++ +++  ++
  gi|518653192|ref|YP_008142712.1| 485 WTGWPTVAYIAIILFAGFAVYLVFLAFHhvdNIfTKENIQGGYWVPLLIIALTILSYLGESNFGGINLFPFPYdfLV 561
                                       56777666655555555555555554441112237888888889********************9999966542255 PP

                       AA_permease 148 iaiiafiivgiillaggk 165
                                       ++++++i  + ++ +g +
  gi|518653192|ref|YP_008142712.1| 562 VMVVSLIFYFLSVKSGFR 579
                                       555666655555566555 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   2.2   7.5e-07    0.0034       6      67 ..      51     112 ..      46     133 .. 0.86
   2 !    8.8   5.2   0.00014      0.63     140     233 ..     212     309 ..     181     316 .. 0.82
   3 ?   -3.0   6.6      0.56   2.5e+03     186     230 ..     496     541 ..     411     557 .. 0.57

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 7.5e-07
                    Spore_permease   6 qlfvlivsfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfpektlie 67 
                                        l +l   +++G+g l++  ++a +a+p + +s +++g i+l+lvl++ ++   +p + +i 
  gi|518653192|ref|YP_008142712.1|  51 DLYFLSLGAIIGSGWLFAESAAAGTAGPAAILSWIIGGAIVLVLVLVYAEIGAMIPRSGFIT 112
                                       567888999*****************************************999988887764 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00014
                    Spore_permease 140 flfiivilliilllillfslklaeiknlrPvlg.ngikpvlks..lkttslsflgveillllvpflkdkk.kvkkaa 212
                                         +ii+ ++iil+++llf+ + ++   l   l  n i+ v+++  +  +++s+lg+   l +    k+++ ++ +a+
  gi|518653192|ref|YP_008142712.1| 212 WKLIIPSITIILMVFLLFHAGNFNNPALGGFLPhNNISLVFEAisTDGIVFSYLGFRHTLNFAGEAKNPQrDIPRAL 288
                                       568999999**********99999999988776256888888876888************99999988752689*** PP

                    Spore_permease 213 llgvlistllyllttlivilv 233
                                       ++++l+s+++y+l+ +  i++
  gi|518653192|ref|YP_008142712.1| 289 IYAMLTSIVVYVLLQFAFISA 309
                                       *************99988876 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.56
                    Spore_permease 186 slsflgveillllvpflkdkkkvkk.aallgvlistllyllttliv 230
                                       ++ f g+ ++l+++ f    + + k  ++ g +++ l+++lt+l +
  gi|518653192|ref|YP_008142712.1| 496 IILFAGFAVYLVFLAFHHVDNIFTKeNIQGGYWVPLLIIALTILSY 541
                                       3445666666666666555444444134445555555555555444 PP

>> DUF3593  Protein of unknown function (DUF3593)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1       1.3   5.7e+03      11      20 ..     263     278 ..     261     309 .. 0.49
   2 ?   13.7   0.5   1.1e-05     0.049       5      46 ..     498     540 ..     495     552 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.3
                           DUF3593  11 pYllFLvll......k 20 
                                        Yl+F  +l      k
  gi|518653192|ref|YP_008142712.1| 263 SYLGFRHTLnfageaK 278
                                       5666655554433331 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 1.1e-05
                           DUF3593   5 falsllpYllFLvllkkske.lpkltlvGfallLlFvavtipa 46 
                                       + +   +Yl+FL + + ++  +++ +  G+++ Ll +a+ti  
  gi|518653192|ref|YP_008142712.1| 498 LFAGFAVYLVFLAFHHVDNIfTKENIQGGYWVPLLIIALTILS 540
                                       5567889*************666677789************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                        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: 0.72u 0.31s 00:00:01.03 Elapsed: 00:00:00.47
# Mc/sec: 3834.06
//
Query:       gi|518653193|ref|YP_008142713.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G1834 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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  126.5  60.8    1.6e-36  125.9  60.8    1.1  1  AA_permease    Amino acid permease
      3e-25   89.0  65.8    4.7e-25   88.3  65.7    1.4  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9  60.8   1.8e-40   1.6e-36       5     466 ..      23     454 ..      20     462 .. 0.85

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1.8e-40
                       AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGln 81 
                                       ++++ + ++g   ++   +++   +++ lay+++++ +++ +++ ++++ +++ +ggfyt+ s+  +p  G  iG++
  gi|518653193|ref|YP_008142713.1|  23 QSIAMISPLGAVAATMTGAAEFAKGSLPLAYIISIFGVLIWINTPYQFSKKINGAGGFYTFNSQGASPTYGLIIGYM 99 
                                       57788889999999999999999****************************************************** PP

                       AA_permease  82 ylfswitvlaleltaasili..qfwelvtdlpkawvt....gavflvvlliinlvgvkvygeaefilalikiiaiia 152
                                        +fs+++v+++++   s ++  + ++++ + +   +t     + f+v+l++i ++g+k + + +f +++i i  +++
  gi|518653193|ref|YP_008142713.1| 100 MWFSYFMVITNAILFTSGVFipGTISYFLHFNIGSYTwipiMTAFIVILTVIAYLGIKPSLAYSFTASVIEIALLVI 176
                                       ************87666554355555666665333335889999***************************999999 PP

                       AA_permease 153 fiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPe 229
                                       + +v i+ l ++++                   +++g    ++  f+++++++v ++f+++G ++v+++++E++ P+
  gi|518653193|ref|YP_008142713.1| 177 TSVVIIVALGSKNTYVP----------------FTAG--PADG--FAAVAVGMVLAIFSMSGSSAVVTLGEEAQQPR 233
                                       99999888888887777................4444..2233..******************************** PP

                       AA_permease 230 ksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinaviltaalssans 306
                                       k+i+ka l  +i++++++vl +++++++++ +  + +  s ++  ++++  k++g+++  +l+++ i+ +++  +++
  gi|518653193|ref|YP_008142713.1| 234 KNIKKALLISFIITGVVFVLTSYALTVGWGVSKMSTFFTSSVP--GLIVSDKYLGLPFTIVLFVF-IINSLFAGSLA 307
                                       ******************************9998877755545..99999999999988888766.5568899999* PP

                       AA_permease 307 slysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwll 382
                                        l ++sR+++s+++dgl P ++ k++  ++ P+ ai+ ++ +++++ l+a+l  +++  f +l+++s ++ ++ ++l
  gi|518653193|ref|YP_008142713.1| 308 PLNTSSRMIFSMSRDGLGPsMFSKVHPVHKTPYIAIITMAGVAYVVSLAAGLLIGPEDGFLYLVTASSAALFVGHIL 384
                                       *******************99999999****************************99******************99 PP

                       AA_permease 383 iilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllf 459
                                       +++ + +  k+lk+ ++             l+   v+ a+ +++l+ a+++++  ++ p+d + ++ + +++i  + 
  gi|518653193|ref|YP_008142713.1| 385 SNFGLGVTYKKLKEFKI-------------LTH-AVIPAIATVILAIAMFYSFVPPAYPVDYSIITAVVFIIISAIA 447
                                       99999977777666666.............333.4444444444444444444449999999999999999999999 PP

                       AA_permease 460 liilvgv 466
                                       ++i+ ++
  gi|518653193|ref|YP_008142713.1| 448 IVIYAIK 454
                                       9988765 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.3  65.7   5.2e-29   4.7e-25      17     423 ..      31     442 ..      16     450 .. 0.77

  Alignments for each domain:
  == domain 1  score: 88.3 bits;  conditional E-value: 5.2e-29
                     AA_permease_2  17 sgifvknlaas...ggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvp 90 
                                       +g ++++++++   +  +l l ++i+++ + l+ + +  ++s +++  gG y++ +++ ++  + + +++ wf+y+ 
  gi|518653193|ref|YP_008142713.1|  31 LGAVAATMTGAaefAKGSLPLAYIISIFGV-LIWINTPYQFSKKINGAGGFYTFNSQGASPTYGLIIGYMMWFSYFM 106
                                       333333333331123344566666666555.7777888899*99********************9999999888887 PP

                     AA_permease_2  91 vlas.......il.svaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillpliil 159
                                       v++        ++ +  +sy+l++         ++++ i+ a+++++++i ++gik s  + ++  ++ i l++i+ 
  gi|518653193|ref|YP_008142713.1| 107 VITNailftsgVFiPGTISYFLHFN-----IGSYTWIPIMTAFIVILTVIAYLGIKPSLAYSFTASVIEIALLVITS 178
                                       4421112211133133566666643.....3356788899999999**************99999999997665555 PP

                     AA_permease_2 160 iilglitvdgggfsslstetdtffpn...gwpgvllgllivlwsfdGfesaanvseevkk..kdvpkaifigllivl 231
                                       +++ ++++++++          f+++   g   v++g+  +++s++G ++++   ee+++  k+++ka+ i+++i++
  gi|518653193|ref|YP_008142713.1| 179 VVIIVALGSKNTYV-------PFTAGpadGFAAVAVGMVLAIFSMSGSSAVVTLGEEAQQprKNIKKALLISFIITG 248
                                       55555555555444.......345551135666899*********************6666589************* PP

                     AA_permease_2 232 vlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilialsllgaintavigssrvlealardgvl 308
                                       v+++l++ a++ + + +++++  ++  ++ ++ +++ g  ++i++ ++i+ sl+ + ++ + +ssr++++++rdg  
  gi|518653193|ref|YP_008142713.1| 249 VVFVLTSYALTVGWGVSKMSTFFTSSVPGLIVSDKYLGLPFTIVLFVFIINSLFAGSLAPLNTSSRMIFSMSRDGLG 325
                                       ******99999999999996544433379999999998899999999****************************** PP

                     AA_permease_2 309 Prffakvn.kfgspiraiiltaivslillllfl..lassaaynfllsvsslgliisyllliigalilrkkrphlkrp 382
                                       P++f+kv+  +++p+ aii+ a v+ +++l+    +++++ + +l+++ss +l++  +l  +g+ + +kk +++k  
  gi|518653193|ref|YP_008142713.1| 326 PSMFSKVHpVHKTPYIAIITMAGVAYVVSLAAGllIGPEDGFLYLVTASSAALFVGHILSNFGLGVTYKKLKEFKIL 402
                                       ********88************9998887665544566*******************************99998886 PP

                     AA_permease_2 383 gkilvaiigalfllfllvalffppkgpatqssliytiiltv 423
                                         +++ +i++++l ++++  f+pp+ p+   s+i+++++++
  gi|518653193|ref|YP_008142713.1| 403 THAVIPAIATVILAIAMFYSFVPPAYPVD-YSIITAVVFII 442
                                       66778888999999999999999988865.46676655444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1123  (0.062636); expected 358.6 (0.02)
Passed bias filter:                      327  (0.0182386); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.65u 0.35s 00:00:01.00 Elapsed: 00:00:00.51
# Mc/sec: 2818.85
//
Query:       gi|518653194|ref|YP_008142714.1|  [L=448]
Description: hypothetical protein FACI_IFERC00001G1835 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); 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:                         0  (0); expected 0.2 (1e-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 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3155.68
//
Query:       gi|518653195|ref|YP_008142715.1|  [L=131]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   13.9   0.8       0.04   13.9   0.8    2.0  2  MSA-2c    Merozoite surface antigen 2c
        4.9    7.8   8.2        1.9    9.1   1.4    2.8  2  MatP      MatP N-terminal domain


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 ?    5.6   3.8    0.0015        14      21      95 ..       9      86 ..       3      89 .. 0.80
   2 ?   13.9   0.8   4.5e-06      0.04      14      62 ..      68     116 ..      62     123 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0015
                            MSA-2c 21 ikeeapfetslfdaevleelstkddeell.kallesikgmkiileklnkflkelrknsdkleeDke..kvvkYykkhi 95
                                      ik+   +  +   ++++  l+ k d+++l +  + +++ + + ++ l +++ +   n d+ + D +  +v  Y k+h 
  gi|518653195|ref|YP_008142715.1|  9 IKNSLRITRERRKTQDVIILKLKIDNDKLnNNTIKALNTIFLEAKWLYNYVINKEFNNDIFNIDPKikNVNVYVKDHY 86
                                      7888888888888999999998866555516799999999999*********************77745666777775 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 4.5e-06
                            MSA-2c  14 Lkkvkalikeeapfetslfdaevleelstkddeellkallesikgmkii 62 
                                       + ++   ik+   +  + +++  l++ls + +ee+++  +++i+g++ +
  gi|518653195|ref|YP_008142715.1|  68 IFNIDPKIKNVNVYVKDHYETRKLNYLSSQMKEEIINRAMDNIRGLHKL 116
                                       566777899999999******************************9765 PP

>> MatP  MatP N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.6     0.055     5e+02      61      79 ..       1      19 [.       1      24 [. 0.84
   2 ?    9.1   1.4   0.00021       1.9       8      76 ..      50     113 ..      43     120 .. 0.70

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.055
                                      B-HHHHHHHHHHHHHHHHH CS
                              MatP 61 mspelenklkqairarrkr 79
                                      m +e +nk+k ++r  r r
  gi|518653195|ref|YP_008142715.1|  1 MIEEKRNKIKNSLRITRER 19
                                      5678899******999887 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00021
                                       HHHHHHHHHHHHHHHTT---BS-SSHHHHHHHHHHHHTTTT-HHHHHHHHHHHB-HHHHHHHHHHHHHH CS
                              MatP   8 leagWkwkYLvkkhregeeitryieksaaeeavqqllklenepekveeWikehmspelenklkqairar 76 
                                       lea+W ++Y+++k  + +     i+   + ++v+  +k ++  ++ +++++++m++e+ n+    ir  
  gi|518653195|ref|YP_008142715.1|  50 LEAKWLYNYVINKEFNNDIFN--IDP--KIKNVNVYVK-DHYETRKLNYLSSQMKEEIINRAMDNIRGL 113
                                       8***********987765432..222..2234444444.555556678999999999999988888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1350  (0.075297); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.31s 00:00:00.86 Elapsed: 00:00:00.52
# Mc/sec: 755.18
//
Query:       gi|518653196|ref|YP_008142716.1|  [L=287]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-21   76.3   0.0    3.8e-21   75.5   0.0    1.4  1  rve          Integrase core domain
    4.1e-06   26.5   1.1    0.00019   21.1   1.1    2.6  1  rve_3        Integrase core domain
     0.0011   19.6   0.1     0.0032   18.1   0.1    1.9  1  HTH_32       Homeodomain-like domain
     0.0072   16.1   0.2      0.019   14.8   0.2    1.7  1  HTH_23       Homeodomain-like domain
  ------ inclusion threshold ------
      0.072   13.6   4.3        0.2   12.1   4.2    1.8  2  Terminase_2  Terminase small subunit


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.5   0.0   1.1e-24   3.8e-21       2     117 ..     125     243 ..     124     244 .. 0.97

  Alignments for each domain:
  == domain 1  score: 75.5 bits;  conditional E-value: 1.1e-24
                               rve   2 trpgelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggvepervlsDngsey 78 
                                       +++++lw++D+t+++  d +    l+++ dd+sr+i+++ +  e++ ++++++le a+  +g+  pe++l+D+g+++
  gi|518653196|ref|YP_008142716.1| 125 KHSNSLWHMDWTKYS--DSE---KLIIIEDDASRFIVGMGIYGEETIDNTIEALEIAINTYGK--PEEILTDHGTQF 194
                                       699*********999..555...7***************************************..9*********** PP

                               rve  79 tsk..........afrefladlgirvsftrpgrpqdnGkvErfhrtlkd 117
                                        s+          +f+e+l + +i++ + r+ +p++nGk Er + t+k+
  gi|518653196|ref|YP_008142716.1| 195 FSNgkngipgdhnKFQEYLDNSNIKHILGRVKHPETNGKLERLNYTIKR 243
                                       ***********************************************97 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   1.1   5.3e-08   0.00019       2      63 ..     217     268 ..     216     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5.3e-08
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLg 63 
                                        i++ ++++++P +Ng+ E++n t+++   + + +          e+ + +YN+eR H sL 
  gi|518653196|ref|YP_008142716.1| 217 NIKHILGRVKHPETNGKLERLNYTIKRLRPYFSTW----------EEVVYHYNYERMHDSLS 268
                                       589999********************965554444..........799************95 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.1   8.9e-07    0.0032       3      73 .]      36     101 ..      33     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 8.9e-07
                            HTH_32   3 srwlkRyneeGlegLkdrprrgrprklsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73 
                                       +  +k+y++ G   +  r    + r l+    + +++++ e p  +p++++++l +r g+++++  +yriL
  gi|518653196|ref|YP_008142716.1|  36 NYIYKKYRDNGEYTIGKR----KHRELNSKDIEIVKKIRYEYPMSGPERIRKYL-KRKGIIIAKNNIYRIL 101
                                       556778888876666666....3335*************999*99*********.8888***********8 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   5.3e-06     0.019      10      45 ..      11      46 ..       5      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.3e-06
                            HTH_23 10 illllaeGlsvreIAreLgvsrrTvyrwlkryreeG 45
                                      i++   ++ s +eIA+e+ ++ r v  + k+yr +G
  gi|518653196|ref|YP_008142716.1| 11 IIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNG 46
                                      555556688999********************9888 PP

>> Terminase_2  Terminase small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   4.2   5.7e-05       0.2      40     111 ..       3      75 ..       1     127 [. 0.79
   2 ?   -1.6   0.0      0.93   3.3e+03      44     126 ..     217     243 ..     167     260 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.7e-05
                       Terminase_2  40 LrkpkIkkaIreakaereertiieadeVlqellkiaraeitdeve.rvklkdseevdkeilrevkegkegvkv 111
                                       L+++kIk +Ire+ + r++ +i++++++  ++++    + +d  e ++  ++++e++++ ++ vk+++ + ++
  gi|518653196|ref|YP_008142716.1|   3 LNEKKIKYIIREKNKRRSSTEIAKEMKITTRYVNYIYKKYRDNGEyTIGKRKHRELNSKDIEIVKKIRYEYPM 75 
                                       8999****************************88888888776663346678899999999999999874444 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.93
                       Terminase_2  44 kIkkaIreakaereertiieadeVlqellkiaraeitdevervklkdseevdkeilrevkegke....gvkvklkDk 116
                                       +Ik                                                                 +++++++ k
  gi|518653196|ref|YP_008142716.1| 217 NIK------------------------------------------------------------HilgrVKHPETNGK 233
                                       222............................................................13333455555555 PP

                       Terminase_2 117 lkAlellakh 126
                                       l+ l+ ++k+
  gi|518653196|ref|YP_008142716.1| 234 LERLNYTIKR 243
                                       5555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1053  (0.0587317); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2027.70
//
Query:       gi|518653197|ref|YP_008142717.1|  [L=335]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   37.7   0.1    3.7e-09   36.4   0.1    1.6  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.8e-09   35.8   4.1    1.5e-08   34.9   4.1    1.4  1  OrfB_IS605      Probable transposase
     0.0031   17.8   2.5     0.0056   17.0   2.5    1.5  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.021   14.8   0.2      0.065   13.2   0.2    1.9  1  Hormone_6       Glycoprotein hormone
      0.021   14.9   2.3      0.048   13.7   0.9    2.1  2  DUF1451         Zinc-ribbon containing domain
      0.036   13.8   5.2       0.12   12.2   5.2    1.8  1  A2L_zn_ribbon   A2L zinc ribbon domain
      0.036   14.2   0.1      0.078   13.1   0.1    1.5  1  FYVE            FYVE zinc finger
       0.06   13.3   0.2       0.12   12.4   0.2    1.4  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.22   11.1   1.5         11    5.6   0.1    2.4  2  RecR            RecR protein
       0.46   10.2   3.9       0.34   10.6   1.7    1.9  2  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.4   0.1   2.1e-12   3.7e-09      18      65 ..     213     261 ..     202     262 .. 0.88

  Alignments for each domain:
  == domain 1  score: 36.4 bits;  conditional E-value: 2.1e-12
                    OrfB_Zn_ribbon  18 kveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiN 65 
                                       ++++ +++  T k+Cs+C  k + +l++r ++C nCgf +drD+n+a+N
  gi|518653197|ref|YP_008142717.1| 213 TLILLDKFIpTTKECSNCHNKYDIKLDERIYQCHNCGFIIDRDYNSALN 261
                                       6677888888********999998***********************99 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.9   4.1   8.5e-12   1.5e-08      10     104 ..      76     175 ..      57     181 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.9 bits;  conditional E-value: 8.5e-12
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsklkkskn....ykkasrklarlh 81 
                                       +++++++k ++ DlGi+n +t+++++     ++k+++  + +++l+++ +  + ++k s+     y k ++kl +  
  gi|518653197|ref|YP_008142717.1|  76 EKPVNNQKIISFDLGIKNQLTCSNGSILNyNIPKSKKEIRLQRSLSRKARYAEGTKKLSRGqsrnYYKNKNKLNKEQ 152
                                       6788999****************998443489999999999999999888777777655445555************ PP

                        OrfB_IS605  82 rkrsrrrkhllhklathliktlk 104
                                       +k  +rrk+ ++k++++l+ +++
  gi|518653197|ref|YP_008142717.1| 153 NKTMNRRKDTINKITHYLTSNYD 175
                                       ******************99886 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   2.5   3.1e-06    0.0056       3      44 ..     209     254 ..     207     255 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.1e-06
                              C1_2   3 Hp.HpLtlskgedssesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                       H+  +L+l  ++    +++Cs C +k     d  +  Y C  C f+++ 
  gi|518653197|ref|YP_008142717.1| 209 HKaSTLILL-DKFIPTTKECSNCHNKydikLD--EriYQCHNCGFIIDR 254
                                       787789999.999999**********885443..256*********995 PP

>> Hormone_6  Glycoprotein hormone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.2   3.6e-05     0.065      11      42 ..     224     257 ..     217     269 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 3.6e-05
                                       S-BSEEEEETTTEBTTBEEEEEEEEEE..EEEEE CS
                         Hormone_6  11 ceecklkenkvfskldapiyqcvGccf..srayp 42 
                                        +ec+  +nk+  kld+ iyqc  c f   r y 
  gi|518653197|ref|YP_008142717.1| 224 TKECSNCHNKYDIKLDERIYQCHNCGFiiDRDYN 257
                                       578888899****************983346665 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.47   8.5e+02      22      73 ..     149     196 ..     116     213 .. 0.63
   2 ?   13.7   0.9   2.7e-05     0.048     112     139 ..     222     249 ..     217     251 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.47
                           DUF1451  22 keklseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldlelie 73 
                                       +++ +++ +  k+ ++++++yl      +     +++++++ w++l+ + ie
  gi|518653197|ref|YP_008142717.1| 149 NKEQNKTMNRRKDTINKITHYLTSNYDIVI----TQNDNIRGWKHLFGRKIE 196
                                       344444445556666677766655432222....222234556666666665 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 2.7e-05
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C +C+++ ++k  e+i +C++Cg
  gi|518653197|ref|YP_008142717.1| 222 PTTKECSNCHNKYDIKLDERIYQCHNCG 249
                                       67889**********************8 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   5.2   6.5e-05      0.12       4      30 ..     225     251 ..     224     252 .. 0.95

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 6.5e-05
                     A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgas 30 
                                       k+Cs+C++  ++  +  +++C +Cg++
  gi|518653197|ref|YP_008142717.1| 225 KECSNCHNKYDIKLDERIYQCHNCGFI 251
                                       78***********************97 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   4.3e-05     0.078       9      36 ..     224     253 ..     221     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 4.3e-05
                                       -SB-TTT--B--SS..S--EE-TTT--EE- CS
                              FYVE   9 vkkCeiCakkFsll..rrrhhCrlCGkvvC 36 
                                       +k+C++C++k+ +   +r + C++CG ++ 
  gi|518653197|ref|YP_008142717.1| 224 TKECSNCHNKYDIKldERIYQCHNCGFIID 253
                                       689********55434999*******9975 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.2   6.6e-05      0.12      16      44 ..     222     249 ..     213     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 6.6e-05
                     Zn_Tnp_IS1595  16 pngfvCPhCgsrkayriktrglfqCkeCr 44 
                                       p++  C +C+++  +++   + +qC  C+
  gi|518653197|ref|YP_008142717.1| 222 PTTKECSNCHNKYDIKLDE-RIYQCHNCG 249
                                       56678*****888888887.********7 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.1     0.016        28      16      24 ..     224     232 ..     217     235 .. 0.87
   2 ?    5.6   0.1    0.0064        11      12      29 ..     238     255 ..     236     256 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.016
                                       -EE-TTT-- CS
                              RecR  16 vrhCsrCgn 24 
                                        + Cs+C+n
  gi|518653197|ref|YP_008142717.1| 224 TKECSNCHN 232
                                       689*****9 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0064
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + e++ +C +Cg + ++d
  gi|518653197|ref|YP_008142717.1| 238 LDERIYQCHNCGFIIDRD 255
                                       678999*******98887 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   4.2e+03      10      19 ..     176     185 ..     174     185 .. 0.85
   2 ?   10.6   1.7   0.00019      0.34       3      25 ..     227     250 ..     226     252 .. 0.93

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
                                       ----SSS--- CS
                    DNA_RNApol_7kD  10 vslkkgdpiR 19 
                                         + ++d iR
  gi|518653197|ref|YP_008142717.1| 176 IVITQNDNIR 185
                                       6799*****9 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00019
                                       -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpi.RCkeCGh 25 
                                       C +C+++  +k  + i +C +CG+
  gi|518653197|ref|YP_008142717.1| 227 CSNCHNKYDIKLDERIyQCHNCGF 250
                                       **************9989*****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2210  (0.123264); expected 358.6 (0.02)
Passed bias filter:                      701  (0.0390987); expected 358.6 (0.02)
Passed Vit filter:                        93  (0.00518713); 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 0.25s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2374.09
//
Query:       gi|518653198|ref|YP_008142718.1|  [L=451]
Description: hypothetical protein FACI_IFERC00001G1839 [Ferroplasma acidarmanus fer1]
Scores for complete 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-50  169.5   0.1    1.4e-49  168.9   0.1    1.2  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    7.9e-19   67.9   0.0    3.6e-18   65.8   0.0    2.0  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    9.8e-15   54.6   0.1    3.4e-14   52.8   0.1    1.8  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    2.1e-14   53.8   4.6    5.4e-14   52.5   0.0    3.5  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.6e-08   32.5   2.9     0.0039   16.3   1.3    3.6  3  GIDA            Glucose inhibited division protein A
    6.2e-07   28.9   0.0     0.0078   15.4   0.0    2.7  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    8.7e-06   25.9   0.1       0.21   11.9   0.0    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    0.00049   19.4   0.9      0.011   15.0   0.1    2.4  2  Thi4            Thi4 family
    0.00052   19.2   0.4     0.0094   15.1   0.2    2.3  2  FAD_binding_2   FAD binding domain
    0.00056   19.6   2.4       0.11   12.1   0.3    3.5  4  DAO             FAD dependent oxidoreductase
    0.00084   19.0   1.2      0.027   14.0   0.0    2.9  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0017   17.7   0.2        1.5    7.9   0.1    2.7  3  FAD_binding_3   FAD binding domain
     0.0046   15.7   2.9       0.74    8.4   0.1    2.8  3  HI0933_like     HI0933-like protein
     0.0086   16.0   0.1      0.053   13.4   0.0    2.0  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
       0.01   15.2   0.1       0.98    8.7   0.0    2.2  2  FAD_oxidored    FAD dependent oxidoreductase
      0.017   14.4   0.1       0.21   10.9   0.0    2.3  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
      0.084   12.7   0.0       0.15   11.9   0.0    1.3  1  MAT1-1-2        Mating type protein 1-1-2 of unknown function
       0.09   11.8   0.1        2.2    7.2   0.0    2.3  2  Lycopene_cycl   Lycopene cyclase protein
       0.16   11.6   0.7         41    3.8   0.0    3.2  3  ApbA            Ketopantoate reductase PanE/ApbA
       0.24   10.6   0.0       0.55    9.4   0.0    1.6  2  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.9   0.1   1.6e-52   1.4e-49       1     293 [.       4     316 ..       4     317 .. 0.86

  Alignments for each domain:
  == domain 1  score: 168.9 bits;  conditional E-value: 1.6e-52
                                       CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH................ CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx................ RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias................ 57 
                                       +dvv iG+G A + aa +l++ag+ v++++      g+cl +gc++ska+ ++ + ++ +s                
  gi|518653198|ref|YP_008142718.1|   4 FDVVTIGAGGASYPAAFRLKKAGFSVIMIDdkgiMSGNCLAEGCVPSKAIIETVHTYKRISdfgdfrinyrdilkrk 80 
                                       59***************************9999999**********************999**************** PP

                                       .........HHHHCHHHH.CCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC.TTBE CS
                                       .........xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 .........evvkklnqg.ielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGvaenvg 124
                                                 + k+l++  ie l+g  v ki  ++ +v+++++    + k+ y++l++ +G+ +  ++i+G  e+++
  gi|518653198|ref|YP_008142718.1|  81 dkvqilrngLHRKELEEAgIEILKG--VAKI-IDSSTVEVKTE--AGNIKLNYKHLIIGSGAYTYMPQIKGI-EYAI 151
                                       8777777773333444333777777..6666.45547777433..4568***********************.8886 PP

                                       ECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 125 klvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealekeGvevk 201
                                       ++ + ++ + +   k lp++i+++GgGyiGvE+A++++ +g++v l+e+ dr+l  +d+e+   le  l ++ v++ 
  gi|518653198|ref|YP_008142718.1| 152 TSADLFRIDPK--IKDLPESIAIIGGGYIGVETASYMSIMGSRVELIERSDRILMDMDPEIVGKLEPLLPDMRVHFN 226
                                       66444444433..4566699***************************************************866655 PP

                                       ESCEEEEEEETTE..EEEEEETTSCE..EEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEEE CS
                                       xxxxxxxxxxxxx..xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 202 lgtsvkeidgnge..klevvledgee..idadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiya 273
                                         +sv  i+++g+  k + ++++g++  + + +v++a+G++p  +  + e++g++  +r gi v+++++tn+p+iya
  gi|518653198|ref|YP_008142718.1| 227 --NSVISIEPDGDgyKTTIIDNNGKSdsVITACVMMATGREPLIPE-GtEEAGIKF-NRKGIIVNSSMQTNIPNIYA 299
                                       ..7777*******5555599999999999**************988.55*******.999999************** PP

                                       -GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 274 iGDvaggkggpelaqaAvqq 293
                                        G v    g+  l +aA +q
  gi|518653198|ref|YP_008142718.1| 300 TGYVN---GIAPLFHAAKRQ 316
                                       **999...888888888776 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0       2.5   2.3e+03      15      40 ..      89     114 ..      83     129 .. 0.70
   2 !   65.8   0.0     4e-21   3.6e-18       1     109 [.     339     446 ..     339     447 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 2.5
                                       ES-HHHHHHHHSGEEEEEEEEECGHH CS
                     Pyr_redox_dim  15 GlteeeAkaagieikvgkfpfkangr 40 
                                       Gl  +e+++agiei  g +++ +++ 
  gi|518653198|ref|YP_008142718.1|  89 GLHRKELEEAGIEILKGVAKIIDSST 114
                                       99999999999887666666555444 PP

  == domain 2  score: 65.8 bits;  conditional E-value: 4e-21
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p +v+t p+++++G+t e+Ak+ gi++   k ++++ + a +y+e  g + l++d+ + k++G  ++G++ag +i+
  gi|518653198|ref|YP_008142718.1| 339 VPFTVYTIPNMSFTGITPEKAKELGIKYIKSKYKMADDSLAEIYNEPGGELDLIFDE-DMKIIGGYVIGNDAGNIIN 414
                                       6889*********************99999999999********************9.99***************** PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGHCH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealkea 109
                                       e+++ +++glt++d+a+  h hP  +e l+ a
  gi|518653198|ref|YP_008142718.1| 415 EISMGLSKGLTARDFAELPHQHPMTFEGLDSA 446
                                       **************************998766 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 !   52.8   0.1   3.8e-17   3.4e-14       2     305 .]       8     301 ..       7     301 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 3.8e-17
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagledylilEkg.nignsiyrypkemtfispsftsekleipdlnaiseetspafslkeek 77 
                                        iGaG a   aa  lkkag++ ++i +kg   gn + +     + i    + +   i d+  +  +        ++ 
  gi|518653198|ref|YP_008142718.1|   8 TIGAGGASYPAAFRLKKAGFSVIMIDDKGiMSGNCLAEGCVPSKAIIETVH-TYKRISDFGDFRINY-------RDI 76 
                                       599999999999999999997777777888889999998887777764433.333444444443333.......457 PP

                       Pyr_redox_3  78 lsrkealeYlrevaksfelpiklfeeVesvkk..edegfevetske..tyeAkkviiAtGefdkPnklnipGeeklv 150
                                       l+rk+ ++ lr+  +++el+    e  + v+k  ++++ ev+t+ +  +++ k++ii  G +   ++++i+G e ++
  gi|518653198|ref|YP_008142718.1|  77 LKRKDKVQILRNGLHRKELEEAGIEILKGVAKiiDSSTVEVKTEAGniKLNYKHLIIGSGAYT--YMPQIKGIE-YA 150
                                       99*****************99999999999997667889*****996778899********86..678899998.77 PP

                       Pyr_redox_3 151 khyskvkefhkya...gqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke 224
                                       + ++    +++      + +++iGg+  +v++A  +  +g++V+++ r++        + + + p i  +le l+  
  gi|518653198|ref|YP_008142718.1| 151 ITSADLFRIDPKIkdlPESIAIIGGGYIGVETASYMSIMGSRVELIERSDR-------ILMDMDPEIVGKLEPLLP- 219
                                       7777766554433123589*****************************985.......455678999999999886. PP

                       Pyr_redox_3 225 ekikvlfnaevkeikekeeeykvk..tedgkkvevkddvvla.tGykpdlsf.lkkslfeldedgrpvlteeteetn 297
                                         ++v+fn++v +i+ +   yk +   ++gk+ +v +  v++ tG +p +    ++++++ +++g++v  ++ ++tn
  gi|518653198|ref|YP_008142718.1| 220 -DMRVHFNNSVISIEPDGDGYKTTiiDNNGKSDSVITACVMMaTGREPLIPEgTEEAGIKFNRKGIIV--NSSMQTN 293
                                       .69*************999997765588888888866666666*****99772555999998888776..678**** PP

                       Pyr_redox_3 298 vpglflaG 305
                                       +p+++  G
  gi|518653198|ref|YP_008142718.1| 294 IPNIYATG 301
                                       *****988 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1       1.6   1.5e+03       2      31 ..       6      35 ..       5      41 .. 0.87
   2 ?   -0.0   0.1       1.5   1.3e+03      47      60 ..      92     105 ..      78     124 .. 0.79
   3 !   52.5   0.0     6e-17   5.4e-14       1      75 [.     169     242 ..     169     248 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 1.6
                                      EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                                      vv +G+G     +A  l++ g +V +++ +
  gi|518653198|ref|YP_008142718.1|  6 VVTIGAGGASYPAAFRLKKAGFSVIMIDDK 35
                                      899****99999999999999999998876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 1.5
                                       HHHHHHTTEEEECS CS
                         Pyr_redox  47 qeklekngievlln 60 
                                       +++le+ gie+l +
  gi|518653198|ref|YP_008142718.1|  92 RKELEEAGIEILKG 105
                                       68999999999875 PP

  == domain 3  score: 52.5 bits;  conditional E-value: 6e-17
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.ves 75 
                                       +++++GgGyig+E A++++ +g++V ++ersd++l  +D+e+   l+  l ++  +v++n++v +ie ++dg  ++
  gi|518653198|ref|YP_008142718.1| 169 SIAIIGGGYIGVETASYMSIMGSRVELIERSDRILMDMDPEIVGKLEPLLPDM--RVHFNNSVISIEPDGDGyKTT 242
                                       689********************************999999999999999998..9***************95554 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.3   4.4e-06    0.0039       1      61 [.       5      68 ..       5     150 .. 0.78
   2 !   11.6   0.0   0.00012      0.11       2      35 ..     170     202 ..     169     214 .. 0.86
   3 ?    1.2   0.0      0.18   1.6e+02     348     368 ..     287     307 ..     281     325 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.4e-06
                                      CEEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT- CS
                              GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi...thkldtiaelsCnpsiggiakgllvrEidalgg 61
                                      dv+ iG+G A + AA+ ++++G++v++i       ++++  +C ps   i   +  + i  +g 
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGFSVIMIddkGIMSGNCLAEGCVPSKAIIETVHTYKRISDFGD 68
                                      7999************************88866677888889****988777766666666665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGT CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldti 35 
                                       + +iGgG  G+e A  ++ +G +v Li ++ d+i
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGSRVELI-ERSDRI 202
                                       78************************9.444544 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.18
                                       T.TSBBSSSBTEEE-CGGGTB- CS
                              GIDA 348 n.tLetkkvkgLflAGqinGte 368
                                       n +++t+ ++++++ G +nG  
  gi|518653198|ref|YP_008142718.1| 287 NsSMQTN-IPNIYATGYVNGIA 307
                                       4499998.************85 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.98   8.7e+02       2      32 ..       3      31 ..       2      36 .. 0.78
   2 !   10.1   0.0   0.00035      0.31     134     210 ..     114     186 ..     100     208 .. 0.75
   3 !   15.4   0.0   8.7e-06    0.0078     112     179 ..     222     288 ..     217     303 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.98
                       K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalf 32
                                       +D++ iG+G ++   a +l+++   ++++ 
  gi|518653198|ref|YP_008142718.1|  3 SFDVVTIGAGGASYPAAFRLKKAG--FSVIM 31
                                      69********99998888888876..55555 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00035
                       K_oxygenase 134 tveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkee.llakkriaVvGsGqSaaeifed 209
                                       tve+k+++g + +l+ ++l++g G   ++P++   +e     + s+++ +  ++ +  +++ia++G+G  + e +  
  gi|518653198|ref|YP_008142718.1| 114 TVEVKTEAG-NIKLNYKHLIIGSGAYTYMPQIKG-IE---YAITSADLFRIDPKiKDLPESIAIIGGGYIGVETASY 185
                                       566666666.588999**************8644.44...5677777766666657889*********999998765 PP

                       K_oxygenase 210 l 210
                                       +
  gi|518653198|ref|YP_008142718.1| 186 M 186
                                       5 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 8.7e-06
                       K_oxygenase 112 qvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevlekle...gkervvHss 179
                                       +v+f+++v ++epd +     ++ +  d++g+++++ +  +++++G ep iPe +e+     +++ ++ +s
  gi|518653198|ref|YP_008142718.1| 222 RVHFNNSVISIEPDGDG----YKTTIIDNNGKSDSVITACVMMATGREPLIPEGTEEAGikfNRKGIIVNS 288
                                       69*************75....555555689***********************998765444444555555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   0.00023      0.21       2      36 ..       9      43 ..       8      63 .. 0.94
   2 !   11.2   0.0   0.00036      0.33       1      31 [.     172     202 ..     172     215 .. 0.94

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00023
                                      E--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
                     NAD_binding_8  2 vGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                                      +GaG ++  aA +L+kagf+v  ++     +G++ 
  gi|518653198|ref|YP_008142718.1|  9 IGAGGASYPAAFRLKKAGFSVIMIDDKGIMSGNCL 43
                                      8****************************999996 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00036
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       I+G+G  G  +A++++  g +v+l+e++dr+
  gi|518653198|ref|YP_008142718.1| 172 IIGGGYIGVETASYMSIMGSRVELIERSDRI 202
                                       9***************************998 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   1.3e-05     0.011      18     120 ..       4     107 ..       1     126 [. 0.85
   2 ?    2.4   0.0     0.085        76      19      50 ..     169     199 ..     159     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.3e-05
                                       EEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSEEEEET.TTHHHHHHTT---EEESSEEEE CS
                              Thi4  18 sDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsaivvrk.pakelLdelgikyedegdyvvv 93 
                                        Dvv +GaG +   aa+ l k+ ++ v++++ +  + G     G + s+ +++   + + ++++g    +++d +  
  gi|518653198|ref|YP_008142718.1|   4 FDVVTIGAGGASYPAAFRLKKA-GFSVIMIDDKGIMSGNCLAEGCVPSKAIIETvHTYKRISDFGDFRINYRDILKR 79 
                                       6******************999.********9988888888888888777776526678899999999999999999 PP

                                       SEHHHHH.HHHHHHHHTSTTEEEEESEE CS
                              Thi4  94 kdaalft.stllskvlqlanvkllnava 120
                                       kd +++    l  k l+ a++ +l++va
  gi|518653198|ref|YP_008142718.1|  80 KDKVQILrNGLHRKELEEAGIEILKGVA 107
                                       9999876256889999999999999886 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.085
                                       EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
                              Thi4  19 DvvivGaGssGLtaayylakkpdlkvailers 50 
                                        ++i+G+G  G+ +a y++   + +v ++ers
  gi|518653198|ref|YP_008142718.1| 169 SIAIIGGGYIGVETASYMSIM-GSRVELIERS 199
                                       589****************99.9999999986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   1.1e-05    0.0094       1      36 [.       5      40 ..       5      46 .. 0.90
   2 ?    1.6   0.0      0.13   1.1e+02     372     402 ..     280     304 ..     272     316 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
                                      SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGS CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgg 36
                                      Dv+ iG+G+A + AA ++++aG +v++++ ++ ++g
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGFSVIMIDDKGIMSG 40
                                      9***************************98876666 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
                                       ES-EEEBETTSBESTTEEESSBTEEE-STCE CS
                     FAD_binding_2 372 tmgGvetdengrvldadgqpipGLYAaGeva 402
                                       +  G+ ++ ++++      +ip+ YA G v 
  gi|518653198|ref|YP_008142718.1| 280 NRKGIIVNSSMQT------NIPNIYATGYVN 304
                                       5679999999999......********9876 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0       0.3   2.7e+02       1      29 [.       5      35 ..       5      42 .. 0.88
   2 ?    3.5   0.0     0.049        44     154     205 ..      93     140 ..      86     164 .. 0.71
   3 !   12.1   0.3   0.00012      0.11       2      30 ..     170     200 ..     169     203 .. 0.90
   4 ?   -1.7   0.0       1.8   1.6e+03     162     201 ..     222     263 ..     221     279 .. 0.65

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.3
                                      EEEEECTSHHHHHHHHHHHHTT..EEEEESS CS
                               DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekg 29
                                      dvv iG+G +   +A+ L ++g  V+ ++ +
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGfsVIMIDDK 35
                                      8999**************9999**9999976 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.049
                                       HHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGHH CS
                               DAO 154 raaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGawsd 205
                                       +++e++G+eil+g  v ++ +     ++ve++t+ g++   ++++++  Ga++ 
  gi|518653198|ref|YP_008142718.1|  93 KELEEAGIEILKG--VAKIID----SSTVEVKTEaGNIkLNYKHLIIGSGAYTY 140
                                       459**********..666633....4555535665776446688********85 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 0.00012
                                       EEEECTSHHHHHHHHHHHHTT..EEEEESSS CS
                               DAO   2 vviiGGGiiGlstAyeLarrg..Vtllekgd 30 
                                       ++iiGGG+iG+ tA + +  g  V l+e++d
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGsrVELIERSD 200
                                       89***************988889*****986 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 1.8
                                       EEEESECEEEEEEEETCEEEEE...EECTEEE.EEEEE.EEE--G CS
                               DAO 162 eilegtevtgleeedgkvwgve...rttpgen.daada.vVnaaG 201
                                       +++++  v ++e +dg++++     +  +g   + ++a v +a+G
  gi|518653198|ref|YP_008142718.1| 222 RVHFNNSVISIE-PDGDGYKTTiidN--NGKSdSVITAcVMMATG 263
                                       678899999995.5534333334332..34433344555888888 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.1      0.17   1.5e+02       3      30 ..       6      33 ..       4      37 .. 0.91
   2 ?   -0.6   0.0      0.92   8.2e+02     110     129 ..     102     121 ..      97     131 .. 0.78
   3 !   14.0   0.0     3e-05     0.027       2      34 ..     169     201 ..     168     226 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.17
                                      EEEE--STTHHHHHHHHHHCTSEEEEE- CS
                    UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvD 30
                                      ++ iG+G    + a  l ++g+ vi++D
  gi|518653198|ref|YP_008142718.1|  6 VVTIGAGGASYPAAFRLKKAGFSVIMID 33
                                      6789***999*****************9 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.92
                                       HHHCEEEEEE-S---TTHHH CS
                    UDPG_MGDP_dh_N 110 alkkgkvvvvkSTvpvgtae 129
                                       +lk    ++  STv v+t  
  gi|518653198|ref|YP_008142718.1| 102 ILKGVAKIIDSSTVEVKTEA 121
                                       5666677999*******986 PP

  == domain 3  score: 14.0 bits;  conditional E-value: 3e-05
                                       EEEEE--STTHHHHHHHHHHCTSEEEEE-S-HH CS
                    UDPG_MGDP_dh_N   2 kisviGlGYvGlvtaavlaeighevigvDidee 34 
                                        i++iG GY+G+ ta  ++ +g  v ++  +++
  gi|518653198|ref|YP_008142718.1| 169 SIAIIGGGYIGVETASYMSIMGSRVELIERSDR 201
                                       59********************99988776655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0044       3.9       3      32 ..       5      34 ..       3      47 .. 0.91
   2 !    7.9   0.1    0.0017       1.5       4      34 ..     170     200 ..     168     205 .. 0.92
   3 ?   -2.6   0.0       2.8   2.5e+03     120     150 ..     221     251 ..     217     261 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0044
                                      EEEEE--SHHHHHHHHHHHHTTHHEEEEES CS
                     FAD_binding_3  3 dVlIVGaGpaGlmlallLseaGvrvvlvek 32
                                      dV+ +GaG a   +a  L++aG +v++++ 
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGFSVIMIDD 34
                                      89**************************96 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0017
                                       EEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
                     FAD_binding_3   4 VlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                                       ++I+G+G  G+ +a+ +s  G rv l+e+ +
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGSRVELIERSD 200
                                       68**************************976 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.8
                                       EEETCSEEEECCEECCCCCCCEEEECCTTEE CS
                     FAD_binding_3 120 lqvrfktevesleqdeegvtaevrdketgee 150
                                       ++v+f++ v s+e d++g ++++ d++   +
  gi|518653198|ref|YP_008142718.1| 221 MRVHFNNSVISIEPDGDGYKTTIIDNNGKSD 251
                                       689999************9999998865444 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.1   0.00083      0.74       1      32 [.       4      35 ..       4      43 .. 0.93
   2 ?   -2.5   0.0       1.7   1.5e+03     118     165 ..      94     138 ..      83     144 .. 0.64
   3 !    6.7   0.1    0.0028       2.5       2      35 ..     169     202 ..     168     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00083
                                      -SEEEE--SHHHHHHHHHHHHTT--EEEE-SS CS
                       HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVllleka 32
                                      +dv+ iG+G A   aA +++k+g +V++++ +
  gi|518653198|ref|YP_008142718.1|  4 FDVVTIGAGGASYPAAFRLKKAGFSVIMIDDK 35
                                      589**************************986 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                                       HHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----S CS
                       HI0933_like 118 elkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGl 165
                                       el+eag+++   + v+++   ++++++vkt  ++ +l+ ++l++ +G  
  gi|518653198|ref|YP_008142718.1|  94 ELEEAGIEIL--KGVAKI--IDSSTVEVKTeAGNIKLNYKHLIIGSGAY 138
                                       4555555544..557777..34555777774466788888899988875 PP

  == domain 3  score: 6.7 bits;  conditional E-value: 0.0028
                                       SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
                       HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                                       ++++iGgG  G+ +A  ++  g+rV l+e+ +++
  gi|518653198|ref|YP_008142718.1| 169 SIAIIGGGYIGVETASYMSIMGSRVELIERSDRI 202
                                       589**************************99876 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.83   7.4e+02       2      30 ..       6      34 ..       5      65 .. 0.82
   2 !   13.4   0.0   5.9e-05     0.053       2      47 ..     170     215 ..     169     233 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.83
                                      EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
                           3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                                      v  iGaG      a  + +ag++V ++d 
  gi|518653198|ref|YP_008142718.1|  6 VVTIGAGGASYPAAFRLKKAGFSVIMIDD 34
                                      66799999889999999999******996 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 5.9e-05
                                       EEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHH CS
                           3HCDH_N   2 vaviGaGtmGagiaavfasagleVvlvdiseealekalekieksle 47 
                                       +a+iG G +G + a+ +   g +V l+++s+++l +   +i  +le
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGSRVELIERSDRILMDMDPEIVGKLE 215
                                       9******************************999887777666555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.0    0.0011      0.98       1      43 [.       5      47 ..       5      92 .. 0.90
   2 ?    4.4   0.1     0.021        19       2      33 ..     170     201 ..     169     202 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0011
                      FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglv 43
                                      Dvv +G+g a + AA   ++aG +v++++++g + G+  +++ 
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGFSVIMIDDKGIMSGNCLAEGC 47
                                      9******************************999998776665 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.021
                      FAD_oxidored   2 vvVvGGgpaGvaAAiaAaraGakvlLveergv 33 
                                       + ++GGg  Gv  A     +G +v L+e++++
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGSRVELIERSDR 201
                                       78**************************9986 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 ?    0.7   0.1      0.31   2.8e+02      30      59 ..       5      34 ..       2      41 .. 0.91
   2 ?   10.9   0.0   0.00023      0.21      29      69 ..     168     208 ..     161     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.31
                                      EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
                       AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDv 59
                                       v+ iG+G a   A+   k+ g +V ++D 
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRLKKAGFSVIMIDD 34
                                      5899*********************99985 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00023
                                       -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH CS
                       AlaDh_PNT_C  29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles 69 
                                         + +iGgG  G++ ++  + +g +V++++ + + l  ++ 
  gi|518653198|ref|YP_008142718.1| 168 ESIAIIGGGYIGVETASYMSIMGSRVELIERSDRILMDMDP 208
                                       5689*************************999887776665 PP

>> MAT1-1-2  Mating type protein 1-1-2 of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00016      0.15      34      98 ..     364     437 ..     341     439 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00016
                          MAT1-1-2  34 klfLrvtlslvldeaa..eeaPgkefglvqnedvkvlgGh.......vklkdegkkllvkvgeenWrsaplwHP 98 
                                        ++++++ ++++d+ a   + Pg e  l+ +ed+k++gG+         +++ +  l +  + + + + p +HP
  gi|518653198|ref|YP_008142718.1| 364 IKYIKSKYKMADDSLAeiYNEPGGELDLIFDEDMKIIGGYvigndagNIINEISMGLSKGLTARDFAELPHQHP 437
                                       468899999997777667899*******************5555554223333333334445666666666666 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0025       2.2       1      32 [.       5      34 ..       5     139 .. 0.93
   2 ?    2.5   0.0     0.068        61       2      37 ..     170     203 ..     169     207 .. 0.93

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0025
                     Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                                      Dvv iGaG A    A rl  +k+g +v++i+ 
  gi|518653198|ref|YP_008142718.1|  5 DVVTIGAGGASYPAAFRL--KKAGFSVIMIDD 34
                                      9*****************..**********63 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.068
                     Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsll 37 
                                       +++iG+G  g+  A  +  + +g +v lie s+ +l
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYM--SIMGSRVELIERSDRIL 203
                                       79***************..************99886 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0     0.045        41       2      31 ..       7      36 ..       6      66 .. 0.85
   2 ?    1.9   0.0      0.17   1.6e+02      88     123 ..      73     105 ..      68     148 .. 0.73
   3 ?    2.5   0.1      0.11     1e+02       1      32 [.     170     201 ..     170     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.045
                                      EEES-SHHHHHHHHHHHHHTHCEEEE-SCH CS
                              ApbA  2 ailGaGaiGsllaakLakagadvtlilrsr 31
                                      + +GaG+ +   a +L+kag  v++i+ + 
  gi|518653198|ref|YP_008142718.1|  7 VTIGAGGASYPAAFRLKKAGFSVIMIDDKG 36
                                      679***********************9876 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.17
                                       HGGGECTCEEEEEESSSSCHHHHHTTTSTTSEEEEE CS
                              ApbA  88 ikplldpntvvlllqNGlgheeelrealpkprvlgg 123
                                       ++++l+++ +v +l NGl  +e  ++ +   ++l g
  gi|518653198|ref|YP_008142718.1|  73 YRDILKRKDKVQILRNGLHRKELEEAGI---EILKG 105
                                       6778888888888888887666444443...44444 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.11
                                       EEEES-SHHHHHHHHHHHHHTHCEEEE-SCHH CS
                              ApbA   1 iailGaGaiGsllaakLakagadvtlilrsrr 32 
                                       iai+G G iG   a +++  g  v li rs+r
  gi|518653198|ref|YP_008142718.1| 170 IAIIGGGYIGVETASYMSIMGSRVELIERSDR 201
                                       89***************99********99984 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       5.9   5.3e+03       6      26 ..     182     202 ..     181     202 .. 0.89
   2 ?    9.4   0.0   0.00062      0.55     221     260 ..     219     257 ..     209     275 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 5.9
                                       HHHHHHHTTEEEEEEESSSSS CS
                     Amino_oxidase   6 aArqLlsaGfdVtvlEardrv 26 
                                       +A++++  G +V ++E +dr+
  gi|518653198|ref|YP_008142718.1| 182 TASYMSIMGSRVELIERSDRI 202
                                       5888889999*********97 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00062
                                       TTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S CS
                     Amino_oxidase 221 rgldirlntrVkeikregdgvtvtledgevveaDaVvvTv 260
                                       ++ ++++n+ V +i+ +gdg+++t+ d +  + D+V+ ++
  gi|518653198|ref|YP_008142718.1| 219 PDMRVHFNNSVISIEPDGDGYKTTIIDNNG-KSDSVITAC 257
                                       5668**********************9998.9*****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              20  [number of targets reported over threshold]
# CPU time: 0.60u 0.26s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3109.21
//
Query:       gi|518653199|ref|YP_008142719.1|  [L=239]
Description: resistance protein NorA [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      4e-30  104.9  17.7    4.8e-30  104.7  17.7    1.0  1  MFS_1       Major Facilitator Superfamily
      1e-06   27.9  17.9    1.7e-06   27.2  17.2    1.5  1  Sugar_tr    Sugar (and other) transporter
     0.0084   15.4  10.5     0.0062   15.9   6.7    1.9  2  MFS_4       Uncharacterised MFS-type transporter YbfB
  ------ inclusion threshold ------
      0.017   14.0  14.0       0.47    9.3   8.2    2.1  2  MFS_1_like  MFS_1 like family
       0.12   12.4   7.8      0.035   14.1   2.0    2.3  2  DUF1304     Protein of unknown function (DUF1304)
        0.3   10.0  11.4       0.15   11.0   7.3    2.0  2  PUCC        PUCC protein


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7  17.7   1.6e-33   4.8e-30       5     226 ..      14     223 ..      10     238 .. 0.88

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 1.6e-33
                             MFS_1   5 aflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll. 80 
                                        +l+al+++ ++pal  ++++++ i+  ++g l+t ++lg a++++++G l+  +G +++ l+glll++++ ++++ 
  gi|518653199|ref|YP_008142719.1|  14 RALYALNWMDIAPALK-YIKSSFDIDLIALGALVTSFYLGIAIFQVVGGLLASYIGDKKTSLTGLLLMGIF-AIISg 88 
                                       5688899999******.******************************************************.55554 PP

                             MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyil 157
                                       ++++++ l+++r+++Gl ++++f++ ++l+  + p+++ ++ ig+++++f++G  +g    ++l +++g+  +f+i+
  gi|518653199|ref|YP_008142719.1|  89 LSTNFTELIISRFFSGLSGAFFFSSTLSLLLSVIPENKSAFHIGVYNGAFAAGGGIGIFGWAILDQYIGYKIPFIIA 165
                                       856666***************************************************88888888************ PP

                             MFS_1 158 aivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..l 226
                                       +i++l  f+l+ + +++ ++ +   +  ++           ++k++l+++v+  ++ial+++++ +s   +
  gi|518653199|ref|YP_008142719.1| 166 GIITLATFILVEISFRDVRKIKTDRAALKK-----------GLKHVLTSKVI--IFIALIGIGARISEtiI 223
                                       *********999999888888888888888...........7********99..99999999665555552 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.2  17.2   5.8e-10   1.7e-06      47     188 ..      41     176 ..      27     182 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.2 bits;  conditional E-value: 5.8e-10
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHH.HHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvG.lasvl 122
                                        +g++v +f++G +i ++++gll+ ++G kk+ l++ +l+ i a+++++++   ++  li++R+++G++   ++s +
  gi|518653199|ref|YP_008142719.1|  41 ALGALVTSFYLGIAIFQVVGGLLASYIGDKKTSLTGLLLMGIFAIISGLST---NFTELIISRFFSGLSGAfFFSST 114
                                       6799***********************************************...**************755156777 PP

                                       HHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG CS
                          Sugar_tr 123 vPmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill 188
                                        ++++s + p+++  + +++y+ a ++G  ++++  ++l+++ +   ++i++ ++ +++l+ +il+
  gi|518653199|ref|YP_008142719.1| 115 LSLLLS-VIPENKSAFHIGVYNGAFAAGGGIGIFGWAILDQYIG---YKIPFIIAGIITLATFILV 176
                                       888777.669**********************998888888888...9***********9999986 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.9    0.0086        26     316     349 ..      43      79 ..      27      84 .. 0.78
   2 !   15.9   6.7   2.1e-06    0.0062      59     206 ..      71     215 ..      58     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0086
                             MFS_4 316 lglmTasf...gigQilGpllasllaeatgslalall 349
                                        +l+T  +   +i+Q++G llas + ++  sl+  ll
  gi|518653199|ref|YP_008142719.1|  43 GALVTSFYlgiAIFQVVGGLLASYIGDKKTSLTGLLL 79 
                                       4566665566699************999998876665 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 2.1e-06
                             MFS_4  59 lrllagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlahaaaarrervgal....lfaGvGlGia 131
                                        + l gll+  + ++ ++l ++f+ +++ Rf +G+++A+ +  + sl l+ + + ++++ +++    + aG G+Gi 
  gi|518653199|ref|YP_008142719.1|  71 KTSLTGLLLMGIFAIISGLSTNFTELIISRFFSGLSGAFFFSSTLSLLLSVIPENKSAFHIGVyngaFAAGGGIGIF 147
                                       335789999999999**************************999999988887777766554411114578888885 PP

                             MFS_4 132 vsgllvllllqlglsasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfG 206
                                             +++l +  + +   ++++++ ++ ++lv +  +    r+ ++++ a k+  k++ + ++++   l+G+G
  gi|518653199|ref|YP_008142719.1| 148 -----GWAILDQYIGYKIPFIIAGIITLATFILVEISFR--DVRKIKTDRAALKKGLKHVLTSKVIIFIALIGIG 215
                                       .....4666677777777788999999999888888888..3333333333333444555555555555555555 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 ?    9.3   8.2   0.00016      0.47     261     367 ..      41     146 ..      28     154 .. 0.87
   2 ?    8.9   0.4   0.00021      0.61     169     253 ..     151     231 ..     146     238 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00016
                        MFS_1_like 261 llGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaavey 337
                                        lG+lv+   ++  ++ +++  l  ++G  k  +++ll++ +  ++ ++ +n+  +++  +++g+s + ++++  + 
  gi|518653199|ref|YP_008142719.1|  41 ALGALVTSFYLGIAIFQVVGGLLASYIGDKKTSLTGLLLMGIFAIISGLSTNFTELIISRFFSGLSGAFFFSSTLSL 117
                                       677777777777667777888888999*************9988888888*************************** PP

                        MFS_1_like 338 vskiapksleatgqgllsglyfglGralGs 367
                                          ++p++  a+ +g+++g+ f +G+++G 
  gi|518653199|ref|YP_008142719.1| 118 LLSVIPENKSAFHIGVYNGA-FAAGGGIGI 146
                                       *******************9.999999995 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
                        MFS_1_like 169 idhysvnllpysallyvlaallvisllvvlilnetekesklkvtkslqvllnilknpeviifllvali.lgmswgii 244
                                       i   ++   +y+  ++++ ++ ++++++v i   +  + k++ ++ ++ l+++l   +viif++ + i   +s  ii
  gi|518653199|ref|YP_008142719.1| 151 ILDQYI---GYKIPFIIAGIITLATFILVEISFRDVRKIKTDRAALKKGLKHVLTS-KVIIFIALIGIgARISETII 223
                                       433333...46677888888888888888777777777777777766766666665.66666666655167888888 PP

                        MFS_1_like 245 enFlflYLk 253
                                       ++F+   +k
  gi|518653199|ref|YP_008142719.1| 224 GQFFVY-YK 231
                                       888655.44 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.3      0.12   3.5e+02      55      89 ..      60      94 ..      45     118 .. 0.63
   2 ?   14.1   2.0   1.2e-05     0.035      39      87 ..     125     176 ..     120     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.12
                           DUF1304 55 gliwglllgseavglalvlfflgcvvvaglygalt 89
                                      g +++ ++g+++++l+ +l++ ++ ++ gl   +t
  gi|518653199|ref|YP_008142719.1| 60 GGLLASYIGDKKTSLTGLLLMGIFAIISGLSTNFT 94
                                      33333344666666666666666666666655555 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                           DUF1304  39 kvlaanqGlYNgfLAagliwglll...gseavglalvlfflgcvvvaglyga 87 
                                       +  a+  G+YNg +Aag  +g++     ++ +g+++ +++ g++++a ++++
  gi|518653199|ref|YP_008142719.1| 125 NKSAFHIGVYNGAFAAGGGIGIFGwaiLDQYIGYKIPFIIAGIITLATFILV 176
                                       567999***********98888433568999**************9998876 PP

>> PUCC  PUCC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   7.3   5.1e-05      0.15     271     357 ..      67     150 ..      38     158 .. 0.75
   2 ?    0.8   0.1     0.062   1.9e+02      48     107 ..     159     221 ..     150     224 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 5.1e-05
                              PUCC 271 lkkarlaslgvllgllsflllilaallenvallvagvlllGlasGlfavaaltlmldlaaeeraglalGaWGaaQai 347
                                       ++ +++   g    ll  ++ i+++l +n + l+ + ++ Gl + +f  ++l+l l++ +e++++  +G++  a a 
  gi|518653199|ref|YP_008142719.1|  67 IGDKKTSLTG---LLLMGIFAIISGLSTNFTELIISRFFSGLSGAFFFSSTLSLLLSVIPENKSAFHIGVYNGAFAA 140
                                       4443333333...33344556789999999999**************************************999999 PP

                              PUCC 348 aaglavllgg 357
                                         g++++  +
  gi|518653199|ref|YP_008142719.1| 141 GGGIGIFGWA 150
                                       9999987554 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.062
                              PUCC  48 RvpyiwlGslalalglaiapla...livlsgkgeaeaaatwaglilaavaf.llvGlgvslsqT 107
                                       ++p+i+ G ++la  + ++ ++   +  +++   a ++     l   +++f +l+G+g+ +s+T
  gi|518653199|ref|YP_008142719.1| 159 KIPFIIAGIITLAT-FILVEISfrdVRKIKTDRAALKKGLKHVLTSKVIIFiALIGIGARISET 221
                                       48899999887766.4444444001444444333333333344444455552578888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.33s 00:00:00.87 Elapsed: 00:00:00.50
# Mc/sec: 1427.03
//
Query:       gi|518653200|ref|YP_008142720.1|  [L=457]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-09   37.1   0.5    5.5e-09   35.8   0.5    1.7  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    3.8e-07   30.4   6.1    1.2e-06   28.8   6.1    1.8  1  OrfB_IS605      Probable transposase
     0.0039   17.5   1.1     0.0088   16.3   1.1    1.6  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.044   13.8   0.7      0.044   13.8   0.7    2.6  4  DUF1451         Zinc-ribbon containing domain
      0.046   13.6   0.3      0.082   12.8   0.3    1.3  1  C1_1            Phorbol esters/diacylglycerol binding domain 
      0.047   13.8   0.1      0.094   12.9   0.1    1.4  1  FYVE            FYVE zinc finger
      0.092   12.9   3.9       0.41   10.8   1.8    2.4  2  COG5            Golgi transport complex subunit 5
       0.14   11.9   1.9       0.27   10.9   1.9    1.5  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.18   11.4   2.0       0.94    9.0   1.9    2.2  2  TF_Zn_Ribbon    TFIIB zinc-binding
       0.24   11.4   1.5        0.4   10.7   1.5    1.3  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
        8.6    6.4   8.0        2.5    8.1   3.1    2.6  3  zinc_ribbon_4   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 !   35.8   0.5   3.4e-12   5.5e-09      18      67 ..     354     404 ..     342     406 .. 0.84

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 3.4e-12
                    OrfB_Zn_ribbon  18 kveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                       +++ v ++  T k+C++C  k + +l++r +kC+nCg+ +drD+n+++N++
  gi|518653200|ref|YP_008142720.1| 354 NLIPVGRFIpTTKECNNCHNKYDIKLNERIYKCSNCGYIIDRDYNSSLNMI 404
                                       66667777779*******999998*************************86 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   6.1   7.2e-10   1.2e-06      10     103 ..     216     315 ..     206     321 .. 0.79

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 7.2e-10
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelq..skl...kksknykkasrklarl 80 
                                       +++ ++n+ +giD Gi++ +t++++      ++k++r  + +++l+++ +  +  +k+   ++skny k +++l r 
  gi|518653200|ref|YP_008142720.1| 216 KEERNNNRIIGIDSGIKTQLTLSNGLKLEyNIPKSKREIRLQRELSRKAKYAEgsKKKlsgEQSKNYNKNKNRLNRE 292
                                       667889999***************984334888888888888888887654441033222235777*********** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktl 103
                                        +kr+++ +++ +k++++++ ++
  gi|518653200|ref|YP_008142720.1| 293 QQKRNNKKRDVKNKIVHYITSNY 315
                                       *******************9877 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   1.1   5.4e-06    0.0088      16      44 ..     363     395 ..     353     396 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.4e-06
                              C1_2  16 sesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                         +++C+ C +k     +  +  Y+Cs C ++++ 
  gi|518653200|ref|YP_008142720.1| 363 PTTKECNNCHNKydikLN--EriYKCSNCGYIIDR 395
                                       56899*******885444..256*********995 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.9   9.7e+03      33      82 ..      89     105 ..      79     123 .. 0.53
   2 ?   -1.3   0.1       1.3   2.1e+03      43      76 ..     256     289 ..     252     295 .. 0.81
   3 ?   -1.9   0.1       1.9   3.1e+03      53      75 ..     317     339 ..     266     347 .. 0.50
   4 ?   13.8   0.7   2.7e-05     0.044     112     139 ..     363     390 ..     359     392 .. 0.92

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.9
                           DUF1451  33 keelelvaeylkrDleeaarsleeskeeleewlsldlelieesllealas 82 
                                       + +++ +++ +k+Dl                                 ++
  gi|518653200|ref|YP_008142720.1|  89 RRKINYLSAQMKQDL---------------------------------LK 105
                                       444444444444444.................................33 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.3
                           DUF1451  43 lkrDleeaarsleeskeeleewlsldlelieesl 76 
                                       l+r+l+  a++ e sk++l+ ++s +++  +++l
  gi|518653200|ref|YP_008142720.1| 256 LQRELSRKAKYAEGSKKKLSGEQSKNYNKNKNRL 289
                                       7899999999999999999888888887766665 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 1.9
                           DUF1451  53 sleeskeeleewlsldleliees 75 
                                        + +++++++ w++l+ + ie++
  gi|518653200|ref|YP_008142720.1| 317 IIITQNDNISGWQKLFGKKIENT 339
                                       22233345666777777766665 PP

  == domain 4  score: 13.8 bits;  conditional E-value: 2.7e-05
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C++C+++ ++k  e+i +C++Cg
  gi|518653200|ref|YP_008142720.1| 363 PTTKECNNCHNKYDIKLNERIYKCSNCG 390
                                       56789**********************8 PP

>> C1_1  Phorbol esters/diacylglycerol binding domain (C1 domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.3     5e-05     0.082       9      39 ..     363     394 ..     358     396 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5e-05
                                       SS--B-TTT-SB--S.SSS-EEEETTT--EE- CS
                              C1_1   9 kqptfCkhCgeflwg.kekqglkCswCkllvH 39 
                                         ++ C+ C +     ++ +++kCs+C+++++
  gi|518653200|ref|YP_008142720.1| 363 PTTKECNNCHNKYDIkLNERIYKCSNCGYIID 394
                                       67889*******9666*************986 PP

>> FYVE  FYVE zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   5.7e-05     0.094       9      36 ..     365     394 ..     363     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
                                       -SB-TTT--B-..-SSS--EE-TTT--EE- CS
                              FYVE   9 vkkCeiCakkF..sllrrrhhCrlCGkvvC 36 
                                       +k+C++C++k+  +l +r + C +CG ++ 
  gi|518653200|ref|YP_008142720.1| 365 TKECNNCHNKYdiKLNERIYKCSNCGYIID 394
                                       689********54456999*******9986 PP

>> COG5  Golgi transport complex subunit 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   1.8   0.00025      0.41       4     104 ..     185     287 ..     184     295 .. 0.86
   2 ?    2.4   0.5       0.1   1.6e+02      22      78 ..     280     337 ..     277     353 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXX CS
                              COG5   4 LepdFdpksfanallkatnnnddteldlstpl.krlnydiqeldkrlrql.itsnhleLlehlskskslssvlselk 78 
                                       L+ dF+  +f na+l  +nnn   ++ + t+  +r n  i  +d+ ++++ + sn l+L  ++ ksk +  +  el 
  gi|518653200|ref|YP_008142720.1| 185 LKYDFNNLDFGNAMLIHKNNNYYINITAYTKKeERNNNRIIGIDSGIKTQlTLSNGLKLEYNIPKSKREIRLQRELS 261
                                       678*************9999999999988876269999*********86615688999999*****99999****** PP

                                       XXXXXXXXXXXXXX-TTHHHHHHHHH CS
                              COG5  79 sslesLsasyerlkskvlepyeeaek 104
                                        + ++ + s ++l+ + ++ y++ ++
  gi|518653200|ref|YP_008142720.1| 262 RKAKYAEGSKKKLSGEQSKNYNKNKN 287
                                       *******9999999998888887655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                                       XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX CS
                              COG5  22 nnnddteldlstplkrlnydiqeldkrlrqlitsnhleLlehlskskslss.vlselk 78 
                                       +n ++++  l+ + ++ n   +++++++   itsn++ ++++ ++++  ++   ++++
  gi|518653200|ref|YP_008142720.1| 280 KNYNKNKNRLNREQQKRNNKKRDVKNKIVHYITSNYNIIITQNDNISGWQKlFGKKIE 337
                                       566777788888888999999*********************9999988887777776 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   1.9   0.00017      0.27       3      25 ..     368     391 ..     367     393 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
                                       -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpi.RCkeCGh 25 
                                       C +C+++  +k ++ i +C +CG+
  gi|518653200|ref|YP_008142720.1| 368 CNNCHNKYDIKLNERIyKCSNCGY 391
                                       99************9989*****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 ?   -1.5   0.0       1.2   1.9e+03      26      41 ..     240     255 ..     240     255 .. 0.88
   2 ?    9.0   1.9   0.00058      0.94       3      36 ..     368     400 ..     367     402 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                                       SBEEEECCCCCCCHHH CS
                      TF_Zn_Ribbon  26 GlVlednsidegpewr 41 
                                       Gl le+n+ +++ e r
  gi|518653200|ref|YP_008142720.1| 240 GLKLEYNIPKSKREIR 255
                                       899*****99998865 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00058
                                       ETTTTCEE.CHEETSTTCEEESSSSBEEEECCCCC CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDpergelvCtdCGlVlednside 36 
                                       C nC++++ + +++    + C++CG++++ +++++
  gi|518653200|ref|YP_008142720.1| 368 CNNCHNKYdIKLNER--IYKCSNCGYIIDRDYNSS 400
                                       999***986777766..778********9998875 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 ?   10.7   1.5   0.00025       0.4      18      45 ..     365     391 ..     359     392 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00025
                     Zn_Tnp_IS1595  18 gfvCPhCgsrkayriktrglfqCkeCrk 45 
                                       +  C +C+++  ++++  + ++C+ C++
  gi|518653200|ref|YP_008142720.1| 365 TKECNNCHNKYDIKLNE-RIYKCSNCGY 391
                                       567*****998899998.********97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.4   8.8e+03      14      25 ..      33      44 ..      32      45 .. 0.82
   2 ?   -3.7   0.0       7.4   1.2e+04      11      18 ..     244     251 ..     244     253 .. 0.84
   3 ?    8.1   3.1    0.0015       2.5       4      35 ..     367     393 ..     367     394 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.4
                     zinc_ribbon_4 14 iddeklpakgvk 25
                                      id++kl  ++ k
  gi|518653200|ref|YP_008142720.1| 33 IDNDKLNNNTIK 44
                                      999**9998877 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7.4
                     zinc_ribbon_4  11 kyeiddek 18 
                                       +y+i+ +k
  gi|518653200|ref|YP_008142720.1| 244 EYNIPKSK 251
                                       59999987 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0015
                     zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35 
                                       +C +C+ ky i       + +  +Cs+Cg ++
  gi|518653200|ref|YP_008142720.1| 367 ECNNCHNKYDIKL-----NERIYKCSNCGYII 393
                                       6*********987.....578899****9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2221  (0.123878); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.46
# Mc/sec: 3006.30
//
Query:       gi|518653201|ref|YP_008142721.1|  [L=54]
Description: hypothetical protein FACI_IFERC00001G1842 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); 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: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.43
# Mc/sec: 374.60
//
Query:       gi|518653202|ref|YP_008142722.1|  [L=58]
Description: hypothetical protein FACI_IFERC00001G1843 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.41
# Mc/sec: 423.02
//
Query:       gi|518653203|ref|YP_008142723.1|  [L=161]
Description: transferase [Ferroplasma acidarmanus fer1]
Scores for complete 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   21.9   0.0    0.00015   21.7   0.0    1.3  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
       0.02   15.2   0.0       0.03   14.6   0.0    1.2  1  Apocytochr_F_N   Apocytochrome F, N-terminal


Domain annotation for each model (and alignments):
>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   1.7e-08   0.00015      65     126 ..      98     160 ..      28     161 .] 0.78

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 1.7e-08
                   Acetyltransf_10  65 gqGigkaLleaveee.aekdgikleltvnaspyavpfYeklGFkav.geeqeenGirfvpMeke 126
                                       + G g  Ll+ +e++ a+  +ik ++ ++a +  +++Y +lG++++ ++    ++ + v+M k+
  gi|518653203|ref|YP_008142723.1|  98 SSGSGYDLLKVIENNvARALHIK-RIDIEAVKSLKDYYNSLGYEETgENYYDSSWKEIVNMSKS 160
                                       5799***********45444444.**********************444555678888999876 PP

>> Apocytochr_F_N  Apocytochrome F, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   3.3e-06      0.03      74     134 ..      11      77 ..       3      89 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.3e-06
                    Apocytochr_F_N  74 vlllPeGfklapedriseelkekvek......lyfqkyseekenilivgplpgdkeqeivfPvlsPd 134
                                        ++lP+Gf+l + +   +e+  + +k       yf ++s+e +ni+iv + p  k + +v+  l P+
  gi|518653203|ref|YP_008142723.1|  11 TVQLPHGFRLIKASDTGKEFISEDRKmrdykiSYFYDWSKEDNNIVIVHESPDGKLSGVVMFRLVPN 77 
                                       589*******988777666544443334456679**************9999888888877666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      430  (0.0239835); 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 0.25s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 1131.68
//
Query:       gi|518653204|ref|YP_008142724.1|  [L=489]
Description: hypothetical protein FACI_IFERC00001G1845 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-66  223.0   0.0    5.9e-66  222.5   0.0    1.2  1  FGGY_N       FGGY family of carbohydrate kinases, N-terminal 
    6.3e-44  150.1   0.6      5e-43  147.1   0.3    2.0  2  FGGY_C       FGGY family of carbohydrate kinases, C-terminal 
    0.00089   18.8   0.0     0.0016   18.0   0.0    1.5  1  BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family


Domain annotation for each model (and alignments):
>> FGGY_N  FGGY family of carbohydrate kinases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.5   0.0   9.9e-70   5.9e-66       1     245 []       5     248 ..       5     248 .. 0.98

  Alignments for each domain:
  == domain 1  score: 222.5 bits;  conditional E-value: 9.9e-70
                                       EEEEEEEESSEEEEEEEETTS-EEEEEEEE--EB-SSTT--EE-HHHHHHHHHHHHHHHHHHCT.-GCCEEEEEEEE CS
                            FGGY_N   1 lilglDcGttstkaivldekgkvvasaqaelelsspkegwaeqdpeeiwqalaeairkvleqagisekqikaIgisg 77 
                                       +il++D Gtt+ ka+++d+ g++ +++++ + +++p+egw+eq+p  i+ a+ ++i ++++ agi++ +i+  gi++
  gi|518653204|ref|YP_008142724.1|   5 YILSIDAGTTNCKAVIFDRSGEITGKSSIRMVSYYPREGWVEQNPYFIISAVKKVISQAIKIAGIDPGDIESAGITN 81 
                                       89*************************************************************************** PP

                                       -SS-EEEEETTT.EESSEEE-TT--TTHHHHHHHHHTTCHCCHHHHHSS-SSTTSHHHHHHHHHHHSCCHHCCHC.. CS
                            FGGY_N  78 qreglvllDknd.kpLynailwkdrrtaeiveklkeegnekklyektglvlstgftlsklkWlkenepevfekie.. 151
                                       qre++v++++++  p+ynai+w+drrt+++++k+++  + + + ektgl  +++f++ k++Wl++n+++++ek+   
  gi|518653204|ref|YP_008142724.1|  82 QRETTVIWNRKTgVPIYNAIVWQDRRTENVMRKMEN--YITVIEEKTGLRPDPYFSAGKIQWLLDNVEGAREKASkg 156
                                       *********9999*********************99..999**********************************99 PP

                                       ..EEEEHHHHHHHHHCT..--EEEHHHHCTTTSEETTTTEE-HHHHHHTT--GGGS-EEE-TCCEEEEEECCCCCCT CS
                            FGGY_N 152 ..kflliddyLiwrLtg..qfvtdvtnasesmlfnikklewdeellailgipeelLPklvesseiigelkpelaakl 224
                                         +f+++d++L + + g   ++td+tnas++ml+ni+klewd e+l+++ ip +lLP + +s + +g + ++     
  gi|518653204|ref|YP_008142724.1| 157 elAFGTVDSWLLFNMAGsgPHATDYTNASRTMLYNIRKLEWDSEMLELFNIPDSLLPDVEPSLNDFGSISISP---- 229
                                       999************99889***********************************************998765.... PP

                                       T.S-EEEEEEEEEHHHHHHHH CS
                            FGGY_N 225 GlkegvpvvggggDqqaaalG 245
                                       G  +++pv ++ gDqq+a++G
  gi|518653204|ref|YP_008142724.1| 230 G--KEIPVYAIIGDQQSALFG 248
                                       5..588**************9 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.053   3.2e+02      47      74 ..     136     166 ..     122     199 .. 0.68
   2 !  147.1   0.3   8.3e-47     5e-43       1     197 [.     257     442 ..     257     443 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.053
                            FGGY_C  47 agslvawlldnl.glreeirdagev....eesl 74 
                                       ag + +wlldn  g+re+ +++ge      +s+
  gi|518653204|ref|YP_008142724.1| 136 AGKI-QWLLDNVeGAREK-ASKGELafgtVDSW 166
                                       5555.******8444444.44444345554444 PP

  == domain 2  score: 147.1 bits;  conditional E-value: 8.3e-47
                            FGGY_C   1 akvslGTssflllvgtkpvisehglltpva..gedgkpeyalegsiavagslvawlldnlglreeirdageveesla 75 
                                       ak+++GT+sf+l+++ + ++++ +l +++a   e +k  ya+egsi+ ags ++w+ + l          +v +s++
  gi|518653204|ref|YP_008142724.1| 257 AKNTYGTGSFMLANTGNNIPATGSLIGTIAygLEYKKVSYAVEGSIFSAGSSIDWMKNIL----------NV-KSYD 322
                                       79***********9999*************76667***********************94..........55.8888 PP

                            FGGY_C  76 elaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekdsgkpldr 152
                                       +l++++++a + + ++vpaf+gl +pywdp argti+gl++st+  ++ar a+e+va+q+ ++l++ +k    p+++
  gi|518653204|ref|YP_008142724.1| 323 KLEEMALKAHSSNAYLVPAFTGLGSPYWDPTARGTIVGLTHSTGRNEMARMAYESVAYQTEDVLQEVKKV--TPVKE 397
                                       8999***************************************************************777..9**** PP

                            FGGY_C 153 lavdGGgskndllmqllAdilgvpVerpktaeatalGaAilAava 197
                                       l vdGG++++++lmql+ ++ g+ + ++ t+e+ta G A++A++a
  gi|518653204|ref|YP_008142724.1| 398 LKVDGGLTRSQFLMQLQSNLSGLNIIKTNTTEITATGSAYIAGLA 442
                                       *******************************************98 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   2.6e-07    0.0016       3      65 ..       9      77 ..       7     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.6e-07
                                      EEE-SSEEEEEEEETTTEEEEEEEE--.TTS-HHH..............HHHHHHHHHHT--GGGECEE CS
                       BcrAD_BadFG  3 iDgGsTttkavlmdekgevlgrgitns.anlesvrfeaa.....ekvleealtealerageeeadieet 65
                                      iD G+T +kav++d++ge+ g+      +++ +++  +       + +++++++a++ ag ++ die+ 
  gi|518653204|ref|YP_008142724.1|  9 IDAGTTNCKAVIFDRSGEITGKSSIRMvSYYPREGWVEQnpyfiISAVKKVISQAIKIAGIDPGDIESA 77
                                      9*****************988865544344443332222111115678899999999999999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (489 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3517.61
//
Query:       gi|518653205|ref|YP_008142725.1|  [L=651]
Description: hypothetical protein FACI_IFERC00001G1846 [Ferroplasma acidarmanus fer1]
Scores for complete 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-93  312.3   2.6      1e-92  311.8   2.6    1.2  1  Peptidase_M13_N  Peptidase family M13
    2.6e-66  223.2   0.0    4.6e-66  222.3   0.0    1.4  1  Peptidase_M13    Peptidase family M13
  ------ inclusion threshold ------
       0.01   15.9   0.2       0.03   14.4   0.2    1.8  1  DUF4460          Domain of unknown function (DUF4460)
      0.017   14.9   0.0      0.033   14.0   0.0    1.4  1  Peptidase_M48    Peptidase family M48


Domain annotation for each model (and alignments):
>> Peptidase_M13_N  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  311.8   2.6   2.2e-96     1e-92       1     381 [.      25     398 ..      25     399 .. 0.95

  Alignments for each domain:
  == domain 1  score: 311.8 bits;  conditional E-value: 2.2e-96
                   Peptidase_M13_N   1 PCdDFYeyaCGnWlkehpipadkssygtfeelqeelekqlreileekpsskedakavkkaktlYksCmdedaieklg 77 
                                       P +DFY y +G+Wl+e+ ip+d+s+yg+f++l e++  +l+ ile+ ++s+  ++ +k+++++Y s md+++iekl 
  gi|518653205|ref|YP_008142725.1|  25 PAKDFYGYCNGKWLEETTIPEDRSRYGAFDMLYEKNMYILKSILEDLKKSS-HNSMEKQLGDFYTSAMDTERIEKLK 100
                                       779**********************************99*****8877777.45599******************** PP

                   Peptidase_M13_N  78 lkplldllkelggldsnwkdkfdllellaklrrygidilfslgvdpdpkdpsknvlyldqpglglpdreyylkerde 154
                                       + p++  +++++++     +k++l el a+l   +++i f++g   d+k+ + ++ly++q+gl+lpdr+yyl   +e
  gi|518653205|ref|YP_008142725.1| 101 FGPIKGEMDNINNV-----TKEKLPELFAELTMKSVQIPFDIGSAEDAKNAEIYSLYIGQGGLSLPDRDYYL---NE 169
                                       ************97.....7899*********989999*********************************7...66 PP

                   Peptidase_M13_N 155 keeeileaykeylakllkllge...eaaelaeevvefekklakitldseerrdpeklynpmtlaelqklapqidwka 228
                                       + + il+ayk+++a++++l+g+   +a++ ae+vv++e++lak++ +++++rd+e+ yn+++++el + +p++ +++
  gi|518653205|ref|YP_008142725.1| 170 QMKPILDAYKKHIARMFTLYGYtqnDAENTAERVVSLETELAKFSRSKTDLRDVERAYNKYSMEELFQKFPELGFDR 246
                                       7899***************98844346779************************************9777******* PP

                   Peptidase_M13_N 229 ylsallertsssekvivtepeylkklskllaettpkrtlanYllwrlvrelapylsdefrdakfefyk.tlsgreer 304
                                       y++ + ++  + ++ i+ +pe++++  +ll++ t  + + +Yl w+++   a +l++e +d++f+f k tl g+e+ 
  gi|518653205|ref|YP_008142725.1| 247 YFKIIGSG--NMNYAIMDAPEFFEQAGALLKN-TAIENIVSYLKWKVLAGSAMFLHKEAVDENFNFFKkTLLGQEKI 320
                                       **996665..58889999************66.999********************************9******99 PP

                   Peptidase_M13_N 305 .prwkrCvsqvnsllgmalgrlyvkkyfpeeskkdveemvedikeafkerlkeldWmdeetkkkAleKldamklkig 380
                                        prw++ v++v++ +g+ lg++yv+k+f +e+ ++++ +v+dik  fkerl+++ Wm++et++kAl K ++++ kig
  gi|518653205|ref|YP_008142725.1| 321 aPRWRTVVNVVDASIGDSLGQVYVDKHFGKEAVEKITVLVNDIKAIFKERLENNPWMSKETREKALLKFSKFNAKIG 397
                                       9**************************************************************************** PP

                   Peptidase_M13_N 381 y 381
                                       y
  gi|518653205|ref|YP_008142725.1| 398 Y 398
                                       9 PP

>> Peptidase_M13  Peptidase family M13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.3   0.0     1e-69   4.6e-66       1     194 [.     451     643 ..     451     648 .. 0.98

  Alignments for each domain:
  == domain 1  score: 222.3 bits;  conditional E-value: 1e-69
                     Peptidase_M13   1 NAyYqpeensivfpaailqppffdleypeavNyggiGaviaHEltHgfddqgvqfdkegnlaswltdedaeefkeka 77 
                                       NAy++p  n+ivfpa+i+qppffd+e+++avNyggiG vi HE+tHg+ddqg +fd++gn+++w+tded++ f e+a
  gi|518653205|ref|YP_008142725.1| 451 NAYFNPMGNEIVFPAGIMQPPFFDPEMDDAVNYGGIGGVISHEITHGYDDQGSHFDENGNMVNWWTDEDKKRFDEMA 527
                                       9**************************************************************************** PP

                     Peptidase_M13  78 kclieqfsevtepektkavngaltlgEniADlggleiAyraykklksakeerlpelenltkdqlfFisyAqiwcekq 154
                                        ++++ +s v+      +vng+ltlgEniADlg++ iAy+a +k+ +a+  + +++++lt++q+fFis++q+w++k 
  gi|518653205|ref|YP_008142725.1| 528 EKVVKLYSSVEILPGL-NVNGKLTLGENIADLGAVLIAYEALQKRLKAEPAKNIKIDGLTPEQRFFISWGQVWRTKI 603
                                       **************99.************************************************************ PP

                     Peptidase_M13 155 sdeellrqllvdvHspaelRvngvlsnlpaFaeaFnckeg 194
                                       +d+e+ r +++d+Hsp+++R   +  n p+F ++F  +  
  gi|518653205|ref|YP_008142725.1| 604 RDNEARRLATIDPHSPGSVRSELPPWNHPDFCKTFGLPSS 643
                                       ***********************************98865 PP

>> DUF4460  Domain of unknown function (DUF4460)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.2   6.8e-06      0.03      36     101 ..      57     119 ..      44     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 6.8e-06
                           DUF4460  36 NeeSLklLnsyleelkkeekksikpekkkLtFyvresnseekekkgefkevsiqldentrd.vketi 101
                                        e+++ +L+s+le lkk++++s+++  +   Fy      +e ++k +f  ++ ++d n+++ +ke++
  gi|518653205|ref|YP_008142725.1|  57 YEKNMYILKSILEDLKKSSHNSMEK--QLGDFYTSA-MDTERIEKLKFGPIKGEMD-NINNvTKEKL 119
                                       599***************8766666..444788887.889999*********9996.5555245555 PP

>> Peptidase_M48  Peptidase family M48
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   7.3e-06     0.033      11      74 ..     427     496 ..     420     502 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 7.3e-06
                                       HHHHHHHTT-..-EEEEEEE-GGGT-EEEEESSS-EEEEEEHHHH.........-SSB-HHHHHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxxxxxx RF
                     Peptidase_M48  11 veelakeaglpkpltkvyvvnspkrNAFalgggknkrivltdgLl.........kqllseeelaaVlGHElGH 74 
                                       +++ +k++g +  +t+ y+   p++NA++ ++g  + iv+  g++          ++++   + +V++HE+ H
  gi|518653205|ref|YP_008142725.1| 427 LNRQLKRIGTKVDKTEWYM-TPPTVNAYFNPMG--NEIVFPAGIMqppffdpemDDAVNYGGIGGVISHEITH 496
                                       5666777777555555554.45668********..89************************************ PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (651 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       780  (0.0435049); expected 358.6 (0.02)
Passed bias filter:                      598  (0.0333538); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 4107.16
//
Query:       gi|518653206|ref|YP_008142726.1|  [L=118]
Description: DNA polymerase beta subunit [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.5e-07   31.6   0.0    1.8e-07   31.4   0.0    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
      1e-05   25.5   0.0    1.4e-05   25.1   0.0    1.2  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0061   16.7   0.0     0.0087   16.3   0.0    1.4  1  DNA_pol_B_palm  DNA polymerase beta palm
  ------ inclusion threshold ------
       0.19   11.5   0.0       0.26   11.1   0.0    1.3  1  DUF294          Putative nucleotidyltransferase DUF294


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 !   31.4   0.0   3.9e-11   1.8e-07      14      72 ..      28      84 ..       4     107 .. 0.75

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 3.9e-11
                                      TSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCCCEEECTTEEEE CS
                      NTP_transf_2 14 vakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiikfleellglevd 72
                                      +  v+l GSyarG+++  SDiD+l+++  +++  + ++ ++ + +  +++++l++ e+ 
  gi|518653206|ref|YP_008142726.1| 28 KCTVILIGSYARGDFNLWSDIDILIIGHFDAN--PLKRLKNIDFPAGYETVLLTPDEIK 84
                                      5579**********************999866..4444455555555666665555554 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   3.1e-09   1.4e-05      15      87 ..      30     104 ..      19     107 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 3.1e-09
                                       STTEEEEEE-S------EEEEEEEESS-...--HHHHHHHHHHHHHH.SSSEEEEEETTTS-HHHHHHHHHS-EEE CS
                           Polbeta  15 laylFGSrakgkareeSDiDlavllkek...ldleeelelaaelediklgkkvDlvdlneapplllyeilkegkll 87 
                                        ++l GS+a+g+++  SDiD+ ++   +   l+  + +++ a  e + l    ++ ++  +++ +++ ++++g++l
  gi|518653206|ref|YP_008142726.1|  30 TVILIGSYARGDFNLWSDIDILIIGHFDanpLKRLKNIDFPAGYETV-LLTPDEIKKMAGKNNKFIKDAFSQGIVL 104
                                       5899********************98887787777889999999999.7799999999977799999999999998 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.9e-06    0.0087      15      49 ..      19      54 ..       6     104 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.9e-06
                                      HHHHHHH-TT-EEEE-HHHHTT-SE.ESSEEEEEEB CS
                    DNA_pol_B_palm 15 kkaakeldpevevivcGSYRRgaes.sGDvDvlitk 49
                                       + ak+ld +++vi  GSY Rg  +   D+D+li  
  gi|518653206|ref|YP_008142726.1| 19 GEYAKTLDFKCTVILIGSYARGDFNlWSDIDILIIG 54
                                      467899***************9865269****9864 PP

>> DUF294  Putative nucleotidyltransferase DUF294
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.7e-05      0.26      47      74 ..      26      53 ..       4      69 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.7e-05
                            DUF294 47 pvpfallvmGSeGReEqtlktDqDnalv 74
                                      + +++++ +GS +R++  l +D D  ++
  gi|518653206|ref|YP_008142726.1| 26 DFKCTVILIGSYARGDFNLWSDIDILII 53
                                      77999*******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 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:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 929.98
//
Query:       gi|518653207|ref|YP_008142727.1|  [L=135]
Description: hypothetical protein FACI_IFERC00001G1848 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-27   95.3   0.5    3.1e-27   95.0   0.5    1.1  1  HEPN      HEPN domain


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.0   0.5   1.7e-31   3.1e-27       2     117 ..      11     127 ..      10     128 .. 0.96

  Alignments for each domain:
  == domain 1  score: 95.0 bits;  conditional E-value: 1.7e-31
                                       HHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT...-HHHHHHHH CS
                              HEPN   2 eewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelkeseelreele 78 
                                        +w+++A+++l++Ae++ ++++y++acf+aqqa e+a+KA++   g +   +h+++ Ll+++       ++l ++++
  gi|518653207|ref|YP_008142727.1|  11 ARWMSNAKYTLKSAENDKSAEFYNWACFKAQQATEYAVKAYIRGTGSD-SFGHSVSLLLNKAGF----DKNLVNIAK 82 
                                       68*********************************************9.***********9974....578****** PP

                                       HHHCCCHHCCCTSS--S......--HHHHHHHHHHHHHHHHHHHH CS
                              HEPN  79 eLekayiesrYpdakee......yteedaeealkdaeevlelvee 117
                                       +L+k+yi++rY da++e      yt ++a ea+  a  ++e ve 
  gi|518653207|ref|YP_008142727.1|  83 VLDKYYIPTRYTDAWTEgvpedyYTLDEANEAIANAGIIIEEVES 127
                                       *****************************************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (135 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.42
# Mc/sec: 957.33
//
Query:       gi|518653208|ref|YP_008142728.1|  [L=207]
Description: phosphoglycolate phosphatase [Ferroplasma acidarmanus fer1]
Scores for complete 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-31  107.2   0.3    5.3e-30  104.8   0.1    1.9  2  HAD_2            Haloacid dehalogenase-like hydrolase
    4.4e-16   59.8   0.2    1.5e-14   54.8   0.2    2.1  1  Hydrolase        haloacid dehalogenase-like hydrolase
    5.8e-08   32.7   0.0      1e-07   31.9   0.0    1.4  1  Hydrolase_like   HAD-hyrolase-like
    2.7e-05   24.7   0.0    5.9e-05   23.6   0.0    1.6  1  HAD              haloacid dehalogenase-like hydrolase
    3.5e-05   23.7   0.0    0.00016   21.5   0.0    2.2  1  Acid_PPase       Acid Phosphatase
  ------ inclusion threshold ------
      0.062   13.4   0.0       0.37   10.9   0.0    2.2  1  Hydrolase_6      Haloacid dehalogenase-like hydrolase
       0.32   10.5   1.3       0.66    9.5   0.1    1.9  2  Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosph


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 !  104.8   0.1   2.1e-33   5.3e-30       1     177 [.      10     175 ..      10     176 .. 0.93
   2 ?    0.4   0.0      0.23   5.9e+02      71      92 ..     184     205 ..     180     207 .] 0.83

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 2.1e-33
                             HAD_2   1 iiFDlDgTlldteeliiqafnelleeyglselseeelrkliglslrellrklgeseeeeekieellrkyneekkkke 77 
                                       iiFDlDgT+ ++  + i+a++ ++++yg+ + ++e +r +ig s  +l++k++ ++     ie+  + y e++    
  gi|518653208|ref|YP_008142728.1|  10 IIFDLDGTIWNSIIYRIKAWQLAFKDYGI-DTDPEVIRLMIGYSGSMLIKKMNARDP---AIEKREEMYFEKMLP-D 81 
                                       8**************************99.9***********************877...888887889999998.9 PP

                             HAD_2  78 vkpydgvkelLeeLkeagyklgivTsksreaveekleqlgiesyFdvivtsedvekkKPdpeviekaleklklkkee 154
                                       vk+y++v+ +  +L+++g+k++ivTs++r+++e+         + + ivt++dvek KPdpe+++ka++ ++ ++e+
  gi|518653208|ref|YP_008142728.1|  82 VKFYPDVEGTFSQLRNMGFKIAIVTSSRRDMIEKINV------HAEAIVTMDDVEKGKPDPEPYKKAIKIMDGTPER 152
                                       ***************************9998765433......4579****************************** PP

                             HAD_2 155 viyvGDsptDieaakkagikvia 177
                                       +i+vGD  +D+  ak +g+ ++ 
  gi|518653208|ref|YP_008142728.1| 153 TIVVGDIDNDLVPAKLLGCVAVL 175
                                       ***************99997775 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.23
                             HAD_2  71 eekkkkevkpydgvkelLeeLk 92 
                                       +e+k++e++ + ++++++e+Lk
  gi|518653208|ref|YP_008142728.1| 184 AEHKDYEISEIGDIIKIIETLK 205
                                       4666679*************97 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.2   5.9e-18   1.5e-14       3     205 ..       9     165 ..       8     170 .. 0.80

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 5.9e-18
                                       EEEEESBTTTBCHHHHHHHHHHHHCHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHETTTEHHHHTHHH..HH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xx RF
                         Hydrolase   3 tvvfDkdGTLttgepsvedvivsaalalaaaletgsehpigkalvaaakarsgaltgfatfigrgayaigkpe..wl 77 
                                        ++fD+dGT++++       i ++                 ka + a+k+ +++++         +++ig     ++
  gi|518653208|ref|YP_008142728.1|   9 SIIFDLDGTIWNSI------IYRI-----------------KAWQLAFKDYGIDTDPEVI-----RLMIGYSGsmLI 57 
                                       58999999999544......3334.................5666888888777744444.....677777762244 PP

                                       HHHHCHHHHHHHHHHHHHHCHHHHHHTTHHHHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase  78 taldippdlgaaigsaqsqgrtvallqaralavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanq 154
                                       +++                +r+ a+++ ++    ++    k +p+++ ++ +L+ +g++++++t++ + + e++  +
  gi|518653208|ref|YP_008142728.1|  58 KKM---------------NARDPAIEKREEMYFEKMLPDVKFYPDVEGTFSQLRNMGFKIAIVTSSRRDMIEKINVH 119
                                       444...............777777775555555666677799******************************99999 PP

                                       TTGGGESEEEEHHCESSTTTSHHHHHHHHHHHTSTGGGEEEEESSHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                         Hydrolase 155 lGddyfdaviasdietvakpspegkvaaireLqgkpeevamVGDgvnDaaa 205
                                       +      a+++ d+++ +kp+pe +++ai+ + g pe++++VGD  nD+  
  gi|518653208|ref|YP_008142728.1| 120 AE-----AIVTMDDVEKGKPDPEPYKKAIKIMDGTPERTIVVGDIDNDLVP 165
                                       99.....888888999********************************865 PP

>> Hydrolase_like  HAD-hyrolase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.9   0.0   4.1e-11     1e-07       3      62 ..     132     190 ..     130     201 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.9 bits;  conditional E-value: 4.1e-11
                                       STTSSHHHHHHHHHH---GGGEEEEES-TTTHHHHHHHCT-EEEEESSSSS-TTTHHHHH CS
                    Hydrolase_like   3 gKPepemydfalevlgsdpeevlmiGDrlatDiagAnnaGwksvLVltGvtrpedleepe 62 
                                       gKP pe y+ a + ++ +pe+++++GD  + D+  A+  G+  vLV  G  +++++++ e
  gi|518653208|ref|YP_008142728.1| 132 GKPDPEPYKKAIKIMDGTPERTIVVGDI-DNDLVPAKLLGCVAVLVSHGTQKRAEHKDYE 190
                                       9***************************.************************9988755 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.0   2.3e-08   5.9e-05       1     119 [.      10     117 ..      10     164 .. 0.69

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 2.3e-08
                               HAD   1 alfDfDgTLldgdslelllrfllrrgaprlwralreklllalfrellrldraglaelleallaglseelaaelerfv 77 
                                       ++fD+DgT++++     + r ++++ a   ++ +   ++  ++r +  ++ ++l + ++a   + + + + ++e+++
  gi|518653208|ref|YP_008142728.1|  10 IIFDLDGTIWNS----IIYRIKAWQLA---FKDYGIDTDPEVIRLMIGYSGSMLIKKMNARDPAIEKREEMYFEKML 79 
                                       79**********....44443444433...55666666666688888888889999999989999999999999999 PP

                               HAD  78 aevirpklldpgalellaahraaGdrvvvvSgglrplvepll 119
                                        +v+    ++p++   +++ r  G+++++v+++ r ++e + 
  gi|518653208|ref|YP_008142728.1|  80 PDVK----FYPDVEGTFSQLRNMGFKIAIVTSSRRDMIEKIN 117
                                       6666....77*9999999999******************987 PP

>> Acid_PPase  Acid Phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.3e-08   0.00016       4      71 ..       8     111 ..       5     189 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.3e-08
                                       SEEEE-STTTSSSS-TTTS...................................S-S-EEE-TTS.-EEETT--EE- CS
                        Acid_PPase   4 klivFDLDyTLWpfevdtl...................................vsaplkkeskksevvDrrgeelk 45 
                                       k i+FDLD T+W+  ++ +                                   +  p  +++++   + +    +k
  gi|518653208|ref|YP_008142728.1|   8 KSIIFDLDGTIWNSIIYRIkawqlafkdygidtdpevirlmigysgsmlikkmnARDPAIEKREE-MYFEKMLPDVK 83 
                                       679*****************************************999988888744444444444.5889999**** PP

                                       --TTHHHHHHHHHHTT--EEE..EE--S CS
                        Acid_PPase  46 lypdveeileelkskevklav..aSrtd 71 
                                       +ypdve  +++l++ + k+a+  +Sr d
  gi|518653208|ref|YP_008142728.1|  84 FYPDVEGTFSQLRNMGFKIAIvtSSRRD 111
                                       **************66665551155544 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00015      0.37       1      40 [.      10     109 ..      10     128 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                                       EEEESTTTSE............................................................ETTEE-T CS
                       Hydrolase_6   1 flfDidGvLw............................................................rgdkaip 17 
                                       ++fD+dG++w                                                             + k +p
  gi|518653208|ref|YP_008142728.1|  10 IIFDLDGTIWnsiiyrikawqlafkdygidtdpevirlmigysgsmlikkmnardpaiekreemyfekmlPDVKFYP 86 
                                       689*******99999999999999999999999999999999999999999999999999999999888779999** PP

                                       THHHHHHHHHHTT-EEEEEE--- CS
                       Hydrolase_6  18 gaaealnalraagkpvvllTNns 40 
                                        ++ ++ +lr++g +++++T + 
  gi|518653208|ref|YP_008142728.1|  87 DVEGTFSQLRNMGFKIAIVTSSR 109
                                       *******************9764 PP

>> Acid_phosphat_B  HAD superfamily, subfamily IIIB (Acid phosphatase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00026      0.66      73     101 ..       7      36 ..       1      43 [. 0.83
   2 ?   -0.4   0.2      0.27     7e+02     152     165 ..     117     130 ..      83     169 .. 0.44

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00026
                                       EEEEEE--BTTTEEHHHHHHHCH.HHTCHH CS
                   Acid_phosphat_B  73 kdavvfDiDeTvLsnspYqkyqg.lgkkkf 101
                                       ++ ++fD+D T+ +++ Y  + + l +k++
  gi|518653208|ref|YP_008142728.1|   7 NKSIIFDLDGTIWNSIIYRIKAWqLAFKDY 36 
                                       789***************999995566666 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
                                       HHHHCT-TTBSCCE CS
                   Acid_phosphat_B 152 nLkkagfsswekli 165
                                       n +++++ +++++ 
  gi|518653208|ref|YP_008142728.1| 117 NVHAEAIVTMDDVE 130
                                       33333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1427.59
//
Query:       gi|518653209|ref|YP_008142729.1|  [L=490]
Description: hypothetical protein FACI_IFERC00001G1850 [Ferroplasma acidarmanus fer1]
Scores for complete 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-55  187.3  92.1    3.4e-35  121.6  22.6    2.7  3  MFS_1        Major Facilitator Superfamily
    3.3e-08   32.8  39.2    1.5e-06   27.4   7.7    4.2  4  Sugar_tr     Sugar (and other) transporter
  ------ inclusion threshold ------
       0.69    8.7  32.0       0.14   11.0   5.6    3.3  3  MFS_1_like   MFS_1 like family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.6  22.6   5.7e-39   3.4e-35       2     239 ..      19     251 ..      18     261 .. 0.83
   2 !   50.7  27.9     2e-17   1.2e-13     129     353 .]     204     415 ..     199     415 .. 0.79
   3 !   43.1  25.5   4.2e-15   2.5e-11       5     172 ..     278     468 ..     275     489 .. 0.86

  Alignments for each domain:
  == domain 1  score: 121.6 bits;  conditional E-value: 5.7e-39
                             MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglll 78 
                                       +++++ +++  ++l+p+lp  +ae ++i++++++l+l++y l+ +++s+++G l+d +G ++++ + +l++a ++ +
  gi|518653209|ref|YP_008142729.1|  19 AMIIVAVMYVEGMLTPSLP-SIAEGFHITVDQVSLVLSTYLLTGVALSPIVGKLADLYGKKKMMSIVMLIYAGAVSV 94 
                                       56778889999********.9*****************************************************666 PP

                             MFS_1  79 llfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfy 155
                                         f++++++++++r++qG+g  +++p+g+a++++ fp++  ++a +l+s++f++G+++  +lg++++ ++gWr ++ 
  gi|518653209|ref|YP_008142729.1|  95 TGFSPNFTFMVISRAVQGVGL-TIMPLGMAMVREEFPRKMVPKAQALISGMFGVGFAVSLPLGSFISNYYGWRMTYH 170
                                       66977777************7.******************************************************* PP

                             MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeee.kgtgpaplvpawkallkdpvlwillialllfffgfsglltllp 231
                                        + ++ + +++l  l+ + e + r+++ +++   +   + pl+  + +  +    w  + +ll+ +++++g++ l+p
  gi|518653209|ref|YP_008142729.1| 171 TAIPFIVALAIL-TLWKVKESRYRRPDVKVDYVgAIALGVPLAL-IVLAMSEGSSW-GWHSLLFLGMAITGIVLLIP 244
                                       999999999996.3333344444444444444243333444444.45555555559.8889999999********** PP

                             MFS_1 232 lylqevlg 239
                                       ++    ++
  gi|518653209|ref|YP_008142729.1| 245 MF-IYERH 251
                                       *9.44444 PP

  == domain 2  score: 50.7 bits;  conditional E-value: 2e-17
                             MFS_1 129 gfslGailg.pllggllasslgWrav.fyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkal 203
                                       +++lG+ l+  +l+    ss+gW+++ f+ +ai ++++  l+ ++++e++  ++  + + +             k+l
  gi|518653209|ref|YP_008142729.1| 204 AIALGVPLAlIVLAMSEGSSWGWHSLlFLGMAITGIVL--LIPMFIYERHYYHHGGEAIFD------------MKLL 266
                                       55566655524444445588999999788888888888..557888888888888888888............8999 PP

                             MFS_1 204 lkdpvlw...illialllfffgfsglltllpl.ylqevlglsglllaglllallalvgailallagrlsdrlgrrrr 276
                                        k++vl    +l i+ +++ + +++l++ + +      +g+s  l++g+ + ++a++++++++++g+l+ r+g   +
  gi|518653209|ref|YP_008142729.1| 267 SKRNVLIaniSLTISGIGMYLSMQALSYRFETpE-PYGFGFS-ILETGISMVAFAAGMIVFSIVTGKLISRTG---I 338
                                       9999885544555555555555555555444420.4466666.8***************************88...6 PP

                             MFS_1 277 lllallllllaalglallavtssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalgp 353
                                         la+++ +++a+g+++l+++   v++l+  ++iG g++++++s+++l++ ++ ++ +g a++ ++t++++g+++g+
  gi|518653209|ref|YP_008142729.1| 339 KPLAIAGSIVSAIGFFMLSASPGLVMTLADEAIIGSGMAIMNASIINLLVLSVEARDMGLATSMNSTFRYIGSSIGA 415
                                       99999999999999999999999999999**********************************************96 PP

  == domain 3  score: 43.1 bits;  conditional E-value: 4.2e-15
                             MFS_1   5 aflsalarsilgpalplalaed.....lgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalgl 76 
                                       + +s++++++ + al+ +  e+     +g+s  e g+ ++++a+g++v+s+++G l+ r G +++ ++g +++a+g+
  gi|518653209|ref|YP_008142729.1| 278 LTISGIGMYLSMQALS-YRFETpepygFGFSILETGISMVAFAAGMIVFSIVTGKLISRTGIKPLAIAGSIVSAIGF 353
                                       4555666666666665.333335577799***********************************************6 PP

                             MFS_1  77 llllfasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg.... 149
                                       ++l+ +++l + l+  ++ G g+++++++++ l++  +  ++ g+a+++ s++  +G+ +g++++g ++s++     
  gi|518653209|ref|YP_008142729.1| 354 FMLSASPGLVMTLADEAIIGSGMAIMNASIINLLVLSVEARDMGLATSMNSTFRYIGSSIGAPIAGTVLSLYTavdv 430
                                       6666448888999999*********************************************999999998888999* PP

                             MFS_1 150 .................Wravfyilaivsllafvlfllll 172
                                                        + ++f+i a+ +++++ +  +ll
  gi|518653209|ref|YP_008142729.1| 431 vhsatgnvifsfpdataFKYAFMIGAFTFVISAFV--VLL 468
                                       *******************************9664..444 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   7.7   2.5e-10   1.5e-06      47     197 ..      49     192 ..       6     196 .. 0.86
   2 !    7.5   0.7   0.00028       1.7     146     199 ..     204     253 ..     197     275 .. 0.76
   3 !   11.5   6.9   1.7e-05       0.1      19     118 ..     283     378 ..     279     384 .. 0.88
   4 ?    1.1   4.4     0.024   1.4e+02      45      97 ..     419     470 ..     370     479 .. 0.76

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 2.5e-10
                                       HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHH CS
                          Sugar_tr  47 lsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlv 123
                                       +++l++s +l+ +++ s ++g+l+d +G+kk + i+ +++  +  ++++++   ++  ++++R + G+g+ +    +
  gi|518653209|ref|YP_008142729.1|  49 QVSLVLSTYLLTGVALSPIVGKLADLYGKKKMMSIVMLIYAGAVSVTGFSP---NFTFMVISRAVQGVGLTIMPLGM 122
                                       78999**********************************************...*********************** PP

                                       HHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHH CS
                          Sugar_tr 124 PmyisEiApkklRgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPry 197
                                        m   E+  k++ +a   l   +  +G+ v+  +g +++++ + +++ +  ++ ++ a l ++ l+ + ES ry
  gi|518653209|ref|YP_008142729.1| 123 AMVREEFPRKMVPKAQA-LISGMFGVGFAVSLPLGSFISNYYG-WRMTYHTAIPFIVA-LAILTLWKVKES-RY 192
                                       ******97777766655.5555667899999999999988888.77777777777888.777778899999.54 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00028
                                       HHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHGGGS---HHHHH CS
                          Sugar_tr 146 aitfGilvaaifglglnktsnadgwrillglqlvpallllilllflPESPrylv 199
                                       ai++G  +a i  l++++ s+ +gw+ ll+l ++++ ++l++ +f+ E    ++
  gi|518653209|ref|YP_008142729.1| 204 AIALGVPLALI-VLAMSEGSS-WGWHSLLFLGMAITGIVLLIPMFIYER--HYY 253
                                       56777777754.577777777.********************9999875..333 PP

  == domain 3  score: 11.5 bits;  conditional E-value: 1.7e-05
                                       GGGTHHHHHHHHTSTT--SHHHHHH...HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH- CS
                          Sugar_tr  19 igafltllkfaknfglsksksskeessvlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaa 95 
                                       ig +l++++  ++f   + ++    s + +g+++ +f +G i+ s+++g+l+ r G k+  +++++++ ig ++  a
  gi|518653209|ref|YP_008142729.1| 283 IGMYLSMQALSYRFETPEPYGFGF-SILETGISMVAFAAGMIVFSIVTGKLISRTGIKPLAIAGSIVSAIGFFMLSA 358
                                       788999999999999999998776.6999************************************************ PP

                                       TTTTSS-TGGGGGHHHHHHHHHH CS
                          Sugar_tr  96 akgknsvevlivgRvlvGigvGl 118
                                       ++    + + ++   ++G g+ +
  gi|518653209|ref|YP_008142729.1| 359 SP---GLVMTLADEAIIGSGMAI 378
                                       *9...677777777777776655 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.024
                                       ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TT CS
                          Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaak 97 
                                        + ++l +++ +v ++ G ++++ + d    k++++i+a+ fvi+a++  ++k
  gi|518653209|ref|YP_008142729.1| 419 GTVLSLYTAVDVVHSATGNVIFS-FPDATAFKYAFMIGAFTFVISAFVVLLSK 470
                                       55677888888899999999999.8899999*****************99998 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 ?   11.0   5.6   2.3e-05      0.14     279     379 ..      67     165 ..      16     175 .. 0.79
   2 ?    6.7  13.4   0.00046       2.8     255     381 ..     304     429 ..     199     433 .. 0.73
   3 ?   -2.1   0.2      0.22   1.3e+03     112     133 ..     448     469 ..     434     477 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 2.3e-05
                        MFS_1_like 279 faeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllwaaaveyvskiapksleatgqglls 355
                                       +  kl + +G  k++ i +l+y+   ++ ++  n+ ++++  + +g+ + ++   ++  v++ +p+++  + q+l+s
  gi|518653209|ref|YP_008142729.1|  67 IVGKLADLYGKKKMMSIVMLIYAGAVSVTGFSPNFTFMVISRAVQGVGLTIM-PLGMAMVREEFPRKMVPKAQALIS 142
                                       4579999******************************************999.899999****************** PP

                        MFS_1_like 356 glyfglGralGsliGGllwdlksa 379
                                       g+ fg+G a+   +G ++ ++++ 
  gi|518653209|ref|YP_008142729.1| 143 GM-FGVGFAVSLPLGSFISNYYGW 165
                                       98.788876544444333344444 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00046
                        MFS_1_like 255 lgasntllGslvalgvvaeiplfffaeklleklGhvklliiallayilrfllyaiienawlvlpievLhgisfgllw 331
                                        g+s    G+ ++  +++ i++ ++  kl+ ++G+  l i++ ++ ++ f+++++   ++++l  e++ g  ++++ 
  gi|518653209|ref|YP_008142729.1| 304 FGFSILETGISMVAFAAGMIVFSIVTGKLISRTGIKPLAIAGSIVSAIGFFMLSASPGLVMTLADEAIIGSGMAIMN 380
                                       5788888999999999************************************************************* PP

                        MFS_1_like 332 aaaveyvskiapksleatgqgllsglyfglGralGsliGGllwdlksaif 381
                                       a++++     +  +  +   ++ s++   +G+ +G+ i+G +  l++a++
  gi|518653209|ref|YP_008142729.1| 381 ASIINLLVLSVEARDMGLATSMNSTFR-YIGSSIGAPIAGTVLSLYTAVD 429
                                       ****99986666665555555555554.389********99988887765 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 0.22
                        MFS_1_like 112 wilfllvvlasfflaailvlld 133
                                       + +++++  ++f+++a +vll 
  gi|518653209|ref|YP_008142729.1| 448 FKYAFMIGAFTFVISAFVVLLS 469
                                       4566777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); 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:                         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: 0.69u 0.29s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 3227.33
//
Query:       gi|518653210|ref|YP_008142730.1|  [L=321]
Description: hypothetical protein FACI_IFERC00001G1851 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-87  293.0   3.0    2.8e-87  292.7   3.0    1.0  1  PdxA      Pyridoxal phosphate biosynthetic protein PdxA


Domain annotation for each model (and alignments):
>> PdxA  Pyridoxal phosphate biosynthetic protein PdxA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.7   3.0   1.6e-91   2.8e-87       6     282 .]      34     305 ..      18     305 .. 0.92

  Alignments for each domain:
  == domain 1  score: 292.7 bits;  conditional E-value: 1.6e-91
                                       EEEE-HHHHHHHHHHH..EEEEEBTTSTCETEEEEEE.S.....BTTB--HHHHHHHHHHHHHHHHHHHTTSSSEEE CS
                              PdxA   6 vvvgdkkllekaakklelkleeieeaeeaseelkvldve....veagkvsaesGaaalaslekAvelakegevdalv 78 
                                       +++gd++ ++k+++ ++l++       e++++l+ +++     ve+gkv+a++G++a++s+e+Av++a++g+vd++ 
  gi|518653210|ref|YP_008142730.1|  34 TLFGDMDNYNKTLDYCSLHM-------ENQKNLNFINTGtgepVETGKVTANAGKIAYKSIETAVQFALAGKVDVIS 103
                                       45566666666663332222.......23357888777335678********************************* PP

                                       E----HHHHHHTT---SSHHHHHHHHTTSSGSEEEEEETTEEEEESS-SS-GGGHHHH--HHHHHHHHHHHHHHHHH CS
                              PdxA  79 taPinKeaikaaglkfpGhtellaeltgtkkvvmmlaseeLrvalvTthipLkevakaitkerllevlrllakalkr 155
                                       taPinKeai +ag ++ +ht +l++lt++k +++++  ++Lr++++++h++L ++ k ++ e++ +++ +++k+lk 
  gi|518653210|ref|YP_008142730.1| 104 TAPINKEAIIKAGSPYIDHTTMLKALTNSKFTTTLFEVKKLRITFLSKHMSLMDAVKFVKYENVYNAIIDTEKSLKL 180
                                       *****************************9999999***************************************** PP

                                       TTT.SSSEEEEE-SSGGGGTTTTTSSHHHHTHHHHHHHHHHCTHEEEEEE-HHHHTSHHHHTT-SEEEESSHHHHHH CS
                              PdxA 156 dfgiekpriaVaGLNPhaGenGllGrEEeeiiepaiekaraegievegplpaDtlFtkaalkkydavvamYHDqgli 232
                                        +g+ +p iaVa+LNPhaGe+G++G EE+++i+paiekar+  ++v+gp+paD++F  a ++kydav+++YHDqg+i
  gi|518653210|ref|YP_008142730.1| 181 -LGFMEPDIAVAALNPHAGEGGMFGMEEKNEIIPAIEKARE-TMKVTGPVPADSVFYLASKGKYDAVLSLYHDQGHI 255
                                       .***************************************6.9********************************** PP

                                       HHHHHHTTTEEEEEESSSSEEEEESS-S-TTCTTTT---THHHHHHHHHH CS
                              PdxA 233 plKllafdegvnvtlGLpiirtSvDhGtafdiagkgkadekSlleAiklA 282
                                       + K+ +f ++v + +GLp++rtSvDhGtafdiagk+ ad  S++eAi +A
  gi|518653210|ref|YP_008142730.1| 256 AAKTYDFAHTVSMNIGLPFLRTSVDHGTAFDIAGKNMADYVSMKEAILTA 305
                                       ***********************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       598  (0.0333538); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2339.90
//
Query:       gi|518653211|ref|YP_008142731.1|  [L=316]
Description: hypothetical protein FACI_IFERC00001G1854 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2425.10
//
Query:       gi|518653212|ref|YP_008142732.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1855 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2237.70
//
Query:       gi|518653213|ref|YP_008142733.1|  [L=431]
Description: hypothetical protein FACI_IFERC00001G1856 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-16   59.9  22.1    7.1e-16   58.1  22.1    1.9  1  Sugar_tr       Sugar (and other) transporter
    6.6e-14   51.6  41.4    4.7e-13   48.8  16.6    2.3  2  MFS_1          Major Facilitator Superfamily
  ------ inclusion threshold ------
        1.4    8.9   9.7        1.3    9.0   0.1    3.1  2  CoA_binding_3  CoA-binding domain


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.1  22.1   1.2e-19   7.1e-16      59     419 ..      63     399 ..      20     421 .. 0.76

  Alignments for each domain:
  == domain 1  score: 58.1 bits;  conditional E-value: 1.2e-19
                                       HHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCC CS
                          Sugar_tr  59 aiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkkl 135
                                        iiG  +ag+++dr+GRk+++ i+  l+ iga+ + ++    +++++++   ++ ++ G++ +++  + +Ei p ++
  gi|518653213|ref|YP_008142733.1|  63 LIIGIGIAGPVSDRIGRKQVFYITMSLYAIGAIGITFSY---TFYLILIFLGILLFASGGEMNTIMALSQEIMPRQH 136
                                       689999*********************************...9********************************** PP

                                       HHHHHHHHHHHHHHHHHHHHHHHHHHHTSS-TTHHHHHHHCCHHHHHHHHHHG.GGS---HHHHHHTT-HHHHHHHH CS
                          Sugar_tr 136 RgalvslyqlaitfGilvaaifglglnktsnadgwrillglqlvpallllill.lflPESPrylvekgkeeeakevl 211
                                       R+  + l   +i +G lv a + +   ++s     r++++l++++ l++l++    lPES  +l +kgk e+a +  
  gi|518653213|ref|YP_008142733.1| 137 RSSTMLLELNFIPLGGLVLAAVAFSSLYSSI-YFQRLMVALTIIIVLVVLVASrRYLPESFLWLASKGKNEQAIADA 212
                                       *888888888888887775555444433333.234999999999988777665499********************* PP

                                       HHHHHCHHHHHHHHHHHHHHHHHHH......HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHH.HTTTHHHHSS- CS
                          Sugar_tr 212 aklrgeedadrelaeekdsleaeqeee.kaswkellssktvrqrlligvvlqifqqltGinaimy.ysptifenlgl 286
                                       +k  ge++  ++ ++ kd  +  + ++ +++w +++ +           ++ +f   tG   i y ++p if nl  
  gi|518653213|ref|YP_008142733.1| 213 KKYYGEAGYLERTDNTKDLSDSRDLNKtSHFWLKFFAT-----------LTTAFAGTTGFGLIAYeLGPIIFPNL-- 276
                                       ******99999999999988888666667888888877...........5566677777777777699****998.. PP

                                       THHHHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH..HHHHTTSS...CHHHHHHHHHHHHHH CS
                          Sugar_tr 287 sksllvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilgivalllvakskaasivaivfialfialf 363
                                        ++ l+ ++ +v  f++ +++ f+ ++++R+ +ll+G +g++++++i     l+++ ++  + i++ +++++  a+ 
  gi|518653213|ref|YP_008142733.1| 277 -TD-LILLVSSVAAFAMGLIG-FFGEKISRKSMLLWGNLGALAFTIITY--ELIGTWSK--YIILFWALVVILNAFV 346
                                       .56.67788888888888998.999**************9888777774..44444442..3344444444445555 PP

                                       HTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHT-HHH CS
                          Sugar_tr 364 algwgpvpwvlvsElfpqsvRskalaiavavnwlanflisllfpiiteaigggyvf 419
                                       +lg       l sE+  ++ R++ +a++ ++   + + i +++ + t +i +++ f
  gi|518653213|ref|YP_008142733.1| 347 QLGYLAED-TLKSEVWATKSRGSLTALVRFLG--IGLYIPTIYITYTYNIYQYMLF 399
                                       55544443.56677777777777777766654..3455555555555555545555 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8  16.6   7.8e-17   4.7e-13       4     226 ..      22     261 ..      18     273 .. 0.77
   2 !    7.5  17.7   0.00028       1.7      39     178 ..     281     422 ..     264     431 .] 0.73

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 7.8e-17
                             MFS_1   4 aaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll 80 
                                       + f +++ +  +++ ++++ ++   i  s   lll+   l  ++++ ++G++sdr+Gr+ v+ +++ l+a+g++ ++
  gi|518653213|ref|YP_008142733.1|  22 ISFAMGMFIESYIFGMSSIATTWVKIPDSYKALLLSRSPLWLIIGIGIAGPVSDRIGRKQVFYITMSLYAIGAIGIT 98 
                                       333333333334444443444445677777788***************************************66666 PP

                             MFS_1  81 fasslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGa.ilgpllggllasslgWravfyi 156
                                       f+ +++l+l++  +  +++g+ + +++al  ++ p+++r++ + l   ++ lG  +l++++ + l+ss+ ++ ++++
  gi|518653213|ref|YP_008142733.1|  99 FSYTFYLILIFLGILLFASGGEMNTIMALSQEIMPRQHRSSTMLLELNFIPLGGlVLAAVAFSSLYSSIYFQRLMVA 175
                                       97788866666666677779***********************99999******77779999999999999988888 PP

                             MFS_1 157 laivsllafvlfllllpeepperkrkspkeee.................kgtgpaplvpawkallkdpvlw.illia 215
                                       l+i+ +l+ vl++   + +++  +  s+ + e                   +  + l++  + l k  ++w  ++++
  gi|518653213|ref|YP_008142733.1| 176 LTIIIVLV-VLVASRRYLPESFLWLASKGKNEqaiadakkyygeagyleRTDNTKDLSD-SRDLNKTSHFWlKFFAT 250
                                       88888887.55677778888888888888887888888899999999977777777888.99999999999855555 PP

                             MFS_1 216 lllfffgfsgl 226
                                       l ++f+g++g+
  gi|518653213|ref|YP_008142733.1| 251 LTTAFAGTTGF 261
                                       55555555553 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00028
                             MFS_1  39 tlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll..fa...sslw.lllvlrvlqGlgagalfpagaal 109
                                        l++ +aa+a+ ++G+++++++r+++ll+g l+ +++ ++++  ++   s +  l+++l v+  ++  +++ a  +l
  gi|518653213|ref|YP_008142733.1| 281 LLVSSVAAFAMGLIGFFGEKISRKSMLLWGNLGALAF-TIITyeLIgtwSKYIiLFWALVVILNAFVQLGYLAEDTL 356
                                       45666789*****************************.88884533467788889999999999999********** PP

                             MFS_1 110 iadwfpkeergraigllsagfslGailgpllggllasslg...Wravfyilaivsllafvlfllllpeeppe 178
                                        +++++ + rg+ ++l+    ++G  +  +   + +  +    +  + ++++ ++++a     ++++ +++ 
  gi|518653213|ref|YP_008142733.1| 357 KSEVWATKSRGSLTALVRF-LGIGLYIPTIYITYTYNIYQymlFNILVWVIGSAGAVA-----WYILGKETG 422
                                       **************99997.44444444333333333333333444444444444444.....666666555 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00022       1.3      27      87 ..     153     213 ..     134     231 .. 0.80
   2 ?    0.6   5.2     0.083     5e+02      18      66 ..     276     321 ..     261     366 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00022
                     CoA_binding_3  27 lvllllallsfslkdafSRlwlaywavvglvllivsrllvravlrrlrrngrnerrvvavg 87 
                                       lvl+++a+ s+  + +f Rl++a  +++ lv+l++sr+ + +   +l+++g+ne ++  ++
  gi|518653213|ref|YP_008142733.1| 153 LVLAAVAFSSLYSSIYFQRLMVALTIIIVLVVLVASRRYLPESFLWLASKGKNEQAIADAK 213
                                       4555555555556788************************99999********98887444 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.083
                     CoA_binding_3  18 llrvlsawllvllllallsfslkdafSRlwlaywavvglvllivsrllv 66 
                                       l+ +++ ++ v +++++l+ ++++ +SR  ++ w  +g+++ ++   ++
  gi|518653213|ref|YP_008142733.1| 276 LTDLILLVSSVAAFAMGLIGFFGEKISRKSMLLWGNLGALAFTI---IT 321
                                       56666666777777777777888888888888887666655442...22 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (431 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); 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):               3  [number of targets reported over threshold]
# CPU time: 0.65u 0.31s 00:00:00.96 Elapsed: 00:00:00.48
# Mc/sec: 2719.78
//
Query:       gi|518653214|ref|YP_008142734.1|  [L=230]
Description: aspartate racemase [Ferroplasma acidarmanus fer1]
Scores for complete 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-53  179.6   0.0    8.5e-53  179.5   0.0    1.0  1  Asp_Glu_race    Asp/Glu/Hydantoin racemase
     0.0096   15.3   0.1      0.025   14.0   0.1    1.6  2  AroM            AroM protein
  ------ inclusion threshold ------
       0.16   11.0   0.0        6.2    5.8   0.0    2.1  2  Fungal_trans    Fungal specific transcription factor domain
       0.21   11.7   0.0       0.36   11.0   0.0    1.3  1  Integrase_H2C2  Integrase zinc binding domain


Domain annotation for each model (and alignments):
>> Asp_Glu_race  Asp/Glu/Hydantoin racemase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.5   0.0   1.9e-56   8.5e-53       1     223 [.       8     217 ..       8     218 .. 0.95

  Alignments for each domain:
  == domain 1  score: 179.5 bits;  conditional E-value: 1.9e-56
                                       EEECSCCCCHHHHHHHHHHBTTSSGGGS..EEEEE-CCS-TCHHHHHCH.T..THHHHHHHHHHHHCTTESEEEE-- CS
                      Asp_Glu_race   1 IGgmgpeatlsvlrklveatpaesdqehlplivlndsaipdrteaieeesgddpvlklleaakkLekagadaiviaC 77 
                                       IGgmgp+at ++l ++ e t a+ dqeh+++i+++d++ipdr+ a+ ++ +++pv  + +++++Le+ g++ i+i+C
  gi|518653214|ref|YP_008142734.1|   8 IGGMGPKATNQFLDRITELTDAANDQEHVRYILYSDPEIPDRIGAYFNG-TKSPVDAINKGIDFLERNGITTIAIPC 83 
                                       9*********************************************877.5569*********************** PP

                                       CHHHHHHHHHHHH-SSEEEECHHHHHHHHHHHSS-EEEEEE-HHHHHCTHHHHHHHHHGT.EEE....T-CCCHHCC CS
                      Asp_Glu_race  78 nTahavadelqkkikiPvlgiveataealkatgvkkvglLgTrgtlksglyqkeleanqgievvvpseelqssvnqa 154
                                       nTah+++ e++  + + +l++v+ t++a+   g+k+ g L+T++t+ks+ly k le+ +gi++++p++e  ++v+qa
  gi|518653214|ref|YP_008142734.1|  84 NTAHIWFSEFK--AGVNLLNMVDLTVKAILDSGYKHPGFLATTATIKSRLYIKNLEE-AGISAIIPEQE--DTVMQA 155
                                       ***********..78******************************************.6*******666..59**** PP

                                       HCHHHHTT-TTSHHHHHHHHHHHHHHTTT-SEEEE-STTHHHHHHHHHHCC-TT.SEEEEHHHHHHHHH CS
                      Asp_Glu_race 155 iyeelkaGevteearrailkllerlaergadaviLGCTelplllekaealekeksvpvidptdilaret 223
                                       ++  +k Ge+  + ++++++++++l ++g d +i++CTe+p++l+++     ++++p+id+  ila+++
  gi|518653214|ref|YP_008142734.1| 156 VK-LVKLGEISRA-KATLKPVVKELEDNGSDSIIMACTEIPVILNRE-----DTELPLIDSDRILAEKI 217
                                       **.899****999.999999999999*****************9999.....45799*********987 PP

>> AroM  AroM protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.49   2.2e+03      74     108 ..      63     100 ..      58     113 .. 0.68
   2 !   14.0   0.1   5.5e-06     0.025      37     116 ..     136     215 ..     119     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.49
                              AroM  74 rlqaaiakleeegvdlilllcTge...fpeleakapli 108
                                       ++++ i+ le++g+++i + c  +   f+e++a + l+
  gi|518653214|ref|YP_008142734.1|  63 AINKGIDFLERNGITTIAIPCNTAhiwFSEFKAGVNLL 100
                                       56777888999999999998855323366666665555 PP

  == domain 2  score: 14.0 bits;  conditional E-value: 5.5e-06
                              AroM  37 lseeeiaalapeegeavlvsrlrdGesvvlsk.ekveprlqaaiakleeegvdlilllcTg...efpeleakaplie 109
                                       l e+ i+a+ pe++++v    ++  + v+l++ ++ ++ l+ ++++le++g d i+++cT+    ++  +++ pli 
  gi|518653214|ref|YP_008142734.1| 136 LEEAGISAIIPEQEDTV----MQAVKLVKLGEiSRAKATLKPVVKELEDNGSDSIIMACTEipvILNREDTELPLID 208
                                       56666666666666644....4555678887746788899********************9664567777799**** PP

                              AroM 110 pqriles 116
                                        +ril +
  gi|518653214|ref|YP_008142734.1| 209 SDRILAE 215
                                       ***9976 PP

>> Fungal_trans  Fungal specific transcription factor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8   0.0    0.0014       6.2     182     208 ..      78     111 ..      71     160 .. 0.78
   2 ?    3.3   0.0    0.0078        35     163     193 ..     184     214 ..     183     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0014
                      Fungal_trans 182 nlpLPcddddlwesddaseetlvetk.......l 208
                                       ++++Pc+  ++w+s+++++++l++ +       l
  gi|518653214|ref|YP_008142734.1|  78 TIAIPCNTAHIWFSEFKAGVNLLNMVdltvkaiL 111
                                       6789*****************9985565554442 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.0078
                      Fungal_trans 163 DktialklGrppllddsqinlpLPcddddlw 193
                                       D +i  ++  p++l+ ++++lpL ++d+ l 
  gi|518653214|ref|YP_008142734.1| 184 DSIIMACTEIPVILNREDTELPLIDSDRILA 214
                                       889999999****************999665 PP

>> Integrase_H2C2  Integrase zinc binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   8.1e-05      0.36      11      39 ..     108     137 ..     101     139 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.1e-05
                    Integrase_H2C2  11 keaHds.agHlGiektlerlrrryyWpgmr 39 
                                       k++ ds + H+G+ +t++++++r y++++ 
  gi|518653214|ref|YP_008142734.1| 108 KAILDSgYKHPGFLATTATIKSRLYIKNLE 137
                                       555567789******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      393  (0.0219198); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1576.06
//
Query:       gi|518653215|ref|YP_008142735.1|  [L=466]
Description: hypothetical protein FACI_IFERC00001G1858 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-28   99.7   0.0    2.3e-28   99.0   0.0    1.2  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 
    8.4e-10   38.1   0.0    1.8e-09   37.0   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
    2.9e-07   30.1   0.0    4.9e-07   29.4   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.0   0.0   3.9e-32   2.3e-28      11     369 ..       4     337 ..       2     342 .. 0.86

  Alignments for each domain:
  == domain 1  score: 99.0 bits;  conditional E-value: 3.9e-32
                                       SHHSSHH.HHHHHHHHHHCTGGGS--TTSTTBHCSSH....HHHHHHHHHHHHHT-BTSSTTTSHHHHHHHHHHHHH CS
                     Pyridoxal_deC  11 aapekaesleqilediekilapgvttwhspefhkllpagnslisllgdlLadainkngftweesPaltelevvvldw 87 
                                       ++pe+  ++++i e + ++ +  ++ +    f  +++ g +    l d+  +  n ng+++++ P + +le+ v+ +
  gi|518653215|ref|YP_008142735.1|   4 QFPENGMDIQKIHETLDELGKNDIKNSRGRLFTYFYDPGIDELNKLQDIFLKFSNRNGMDYHAFPSTLKLENDVIAM 80 
                                       678888889999999999999999999988888889999999999******************************** PP

                                       HHHHTT--GGGTCCT-EEEEESSHHHHHHHHHHHHHHHHHHHHHHHTTTS.HHHHHCCEEEEEETTS-HHHHHHHHH CS
                     Pyridoxal_deC  88 laellglpeeflekegggvlqvgssestllallAartkvikemkekgkelkeaeildklvlytsdqahssvekaalv 164
                                       +a ll+      e    g++++g++es++la+ Aar +++++   +g +  e       v+     ah s  ka ++
  gi|518653215|ref|YP_008142735.1|  81 MASLLHGK----EG-SAGTFTTGGTESIILAMKAARDRFFEKH--HGVP--E-------VILP-VTAHPSFSKAVEY 140
                                       *****987....32.679*********************9864..4433..2.......3333.3489********* PP

                                       HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGG CS
                     Pyridoxal_deC 165 lgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsa 241
                                       lg+k + +p+de++   ++ ++kai e+ +    +   v  + +  +g  d +kel di  + +lwlHvDA  +G  
  gi|518653215|ref|YP_008142735.1| 141 LGLKEIRLPVDEHYLADPELMRKAITENTAM---I---VGSAPSFPYGTIDPVKELSDIALENNLWLHVDACVGG-- 209
                                       ************8877777777777777666...4...455666789****************************.. PP

                                       GGSGGGGG.......GGTTGGGESEEEEECCCCTS--SS-EEEEESSCCGCHHHH-EEECCCT.TTTTTSEECCCGS CS
                     Pyridoxal_deC 242 ficpeirh.......llkgieradSitvnphKlllvlldcsalivkdkealqqalqleaeYLehedsdvaadlgtka 311
                                       +i p+ +        +++ ++ + Si+v  hK++  + + s++++k++e  +++  ++a++ +       + + +  
  gi|518653215|ref|YP_008142735.1| 210 MILPFLKRlghnvqdFDFTLPGVSSISVDLHKYGFTPKGSSVIMYKNEELRKHQIYVNAKWPG-------YPMSNAG 279
                                       8889888777788889*********************************************99.......6777888 PP

                                       SSSSGHHT.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTEEECSTTBSSE CS
                     Pyridoxal_deC 312 iplsrrvr.ilklwfvlralGveglqnqirksvelakyleklirkderfeivaevelgl 369
                                       ++  ++    +  w ++  lG++g++    k++   k l+k i++ + +ei  ++  + 
  gi|518653215|ref|YP_008142735.1| 280 MQATKSAGpLAGTWSIMNYLGYKGYTDLASKTLSAYKTLTKGIENIG-YEITGKPDATI 337
                                       8888855416789******************************9865.56666655555 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0   0.0     3e-13   1.8e-09      51     180 ..      80     209 ..      49     307 .. 0.77

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3e-13
                                       HHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC.-TTTS...EEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBET CS
                       Aminotran_5  51 kvaelinaeseeeiiftsGtteainlvalslars.lkpgd...eivvteaehhanlvpwqelakrtgakvkviplde 123
                                         a l++ ++ +   ft G+te+i l++++++++ +++     e+++ ++ h +      ++ +  g+k   +p+de
  gi|518653215|ref|YP_008142735.1|  80 MMASLLHGKEGSAGTFTTGGTESIILAMKAARDRfFEKHHgvpEVILPVTAHPSFS----KAVEYLGLKEIRLPVDE 152
                                       567788888888889****************9997555433347888899998888....4445788888899**** PP

                                       TSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTT CS
                       Aminotran_5 124 egeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqav 180
                                       + + d++ ++k+++e+t+++  ++ s   Gti+pv+e+ ++a +++ +++vDa+ + 
  gi|518653215|ref|YP_008142735.1| 153 HYLADPELMRKAITENTAMIVGSAPSFPYGTIDPVKELSDIALENNLWLHVDACVGG 209
                                       *****************************************************8654 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.4   0.0   8.2e-11   4.9e-07      44     146 ..      96     206 ..      79     209 .. 0.88

  Alignments for each domain:
  == domain 1  score: 29.4 bits;  conditional E-value: 8.2e-11
                                       ESSHHHHHHHHHHH.....TTTTTT.-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEE CS
                   DegT_DnrJ_EryC1  44 vssGtaAlhlaLra.....lgvgpg.deVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertka 114
                                       ++ Gt+++ la++a     ++  +g  eVI p +   +  +av +lg+k + + vd + y  dp+ +++aite+t+ 
  gi|518653215|ref|YP_008142735.1|  96 TTGGTESIILAMKAardrfFEKHHGvPEVILPVTAHPSFSKAVEYLGLKEIRLPVD-EHYLADPELMRKAITENTAM 171
                                       6789**********8877633334426*****************************.8899**************** PP

                                       EE...EB-GGGB---HHHHHHHHHHCT-EEEEE-T CS
                   DegT_DnrJ_EryC1 115 Il...pVhlyGqvadmdalkaiaakhglkvieDaA 146
                                       I+   p   yG +  +++l +ia + +l++  Da+
  gi|518653215|ref|YP_008142735.1| 172 IVgsaPSFPYGTIDPVKELSDIALENNLWLHVDAC 206
                                       *94445568*************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3296.84
//
Query:       gi|518653216|ref|YP_008142736.1|  [L=317]
Description: hypothetical protein FACI_IFERC00001G1859 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-59  202.3   0.0    1.2e-59  202.1   0.0    1.0  1  PALP      Pyridoxal-phosphate dependent enzyme
  ------ inclusion threshold ------
       0.14   12.5   0.1       0.41   11.1   0.1    1.8  1  DUF4258   Domain of unknown function (DUF4258)


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 !  202.1   0.0   1.4e-63   1.2e-59       3     294 .]      10     304 ..       8     304 .. 0.88

  Alignments for each domain:
  == domain 1  score: 202.1 bits;  conditional E-value: 1.4e-63
                                       GCSSS--EEEECCTCCCCCCEEEEEEGGGSTTSBTTHHHHHHHHHHHHTT...TTTSEEEEEBSSHHHHHHHHHHHH CS
                              PALP   3 lgigpTPlvrlprlskelgvplflKlEslnptgSfKdRgaeyllarlkeg...tgaktvveassGNhgralAaaaal 76 
                                         ig+TPlv+l+r     ++++++KlE+  p+ S+KdR a  ++++++++   ++++tv+  +sGN+g++lA+a+a+
  gi|518653216|ref|YP_008142736.1|  10 STIGNTPLVKLNRTG-CRNIEIYVKLEYYSPGFSIKDRIAIGMIEDAERKgilKKGDTVIGKTSGNTGIGLAIACAV 85 
                                       679**********54.66677*************************99999************************** PP

                                       HT-EEEEEEETTS-HHHHHHHHHTT-EEEEE....CCH........HHHHHHH.HHHHHHHSTTCEE--TTTSHHHH CS
                              PALP  77 lGlkvtivvpadaspekvallrllGaevvev....ggd........ydeavaa.aaelaaegegaylvsqfdnptvi 140
                                        G+k++ v++a+ s ek  +l++lGaevv+v    g +         +eav++   el++e  +ay  +q+ np + 
  gi|518653216|ref|YP_008142736.1|  86 KGYKFITVMSAGNSMEKTVMLKALGAEVVLVpqqpG-EgpyvvsrkDNEAVEKkTDELTEE-LHAYRPNQYINPVNY 160
                                       *******************************77641.2566776667777777688*****.*************** PP

                                       HH.HHTHHHHHHHHTTTTEEEEEEE-SSSHHHHHHHHHHHHHSTT-EEEEEEECTTCGGTTCCS..S.SS..B.SSS CS
                              PALP 141 eg.ygtiglEileqlggkpdavvvpvGgGgliaGiaaglkerrpdvrvigvepegsdalarslragrrvtvpvsdti 216
                                       +    t+g Ei++q +g++da+v+ vG+Gg++ Gi+ +lk+ r d++++ vep+ +  la+         +++ + i
  gi|518653216|ref|YP_008142736.1| 161 LIhEYTTGSEIIKQSDGNIDAFVAFVGTGGTFVGISSALKKFRKDIKCYPVEPDSAQFLAGKQ------VITTRHKI 231
                                       ******************************************************888888888......33332333 PP

                                       .CCSTCSCGTTCCHHHHSEEEEEEEEEEHHHHHHHHHHHHHHHSB-B-HHHHHHHHHHHHHHHHCCTTCEEEEEEE- CS
                              PALP 217 adglavgspselafelldrlvdeivtvsdeealeamrllarregivvepssaaalaalklreagelkegdrvvvilt 293
                                         g      +++   + + lvd + +v+d+ea++++r+la++egi+++ s++a++aa+ ++ ++ +++g+ vv++l+
  gi|518653216|ref|YP_008142736.1| 232 QGG----GHAVKPPYWDESLVDGYLSVTDDEAIDTARHLASKEGIFPGFSGGANVAAA-MKLDKTMDRGSIVVTVLP 303
                                       332....3334444455666777777********************************.**********99999987 PP

                                       B CS
                              PALP 294 g 294
                                       +
  gi|518653216|ref|YP_008142736.1| 304 D 304
                                       5 PP

>> DUF4258  Domain of unknown function (DUF4258)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   4.6e-05      0.41      21      62 ..      59      94 ..      43      95 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 4.6e-05
                           DUF4258 21 evlenGeiieeyslvlgktsegrplhvvvapdedpvvviTvy 62
                                       +l++G+       v gkts+++ + +++a+  ++++ iTv+
  gi|518653216|ref|YP_008142736.1| 59 GILKKGD------TVIGKTSGNTGIGLAIACAVKGYKFITVM 94
                                      4677777......9***************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2226.13
//
Query:       gi|518653217|ref|YP_008142737.1|  [L=369]
Description: glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   0.0    2.8e-12   47.2   0.0    1.5  1  Glyco_trans_1_4  Glycosyl transferases group 1
      0.005   17.2   0.0       0.15   12.5   0.0    2.5  2  Glyco_trans_1_2  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.071   12.7   0.0       0.21   11.1   0.0    1.9  1  Glycos_transf_1  Glycosyl transferases group 1


Domain annotation for each model (and alignments):
>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   4.8e-16   2.8e-12       3     132 ..     197     325 ..     195     327 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 4.8e-16
                                       EEEEES--.-GG.GTHHHHHHHHHHHH.HHEEEEEES---..HHHHHHHTT-T.TEEEE---TH..HHHHHHH-SEE CS
                   Glyco_trans_1_4   3 vilfvGrl.eenvkgvdllleavpllrkkdvrlvivGdgprpeeleelaagleerveftGfved..laellaaadvf 76 
                                       +i+f+G++  +n+++++++l  ++ +   d++++i+G+  + + + +  +    +v+f+G v+d  +++l++++ ++
  gi|518653217|ref|YP_008142737.1| 197 DIIFIGSIyGPNIEAAEFILSLAKTMP--DFQFHIIGNV-NTHGFPH--K--PGNVKFHGLVQDaeKDNLFRNSCIA 266
                                       79******667*********9999999..79******54.4445542..2..257*******5555*********** PP

                                       EE--...---SHHHHHHHHTT-EEEE-TGGGTTT--..TTSSEE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  77 vaPs...egfglkllEamaaglpvVatdvggiaevv..gengllvppgdpealaeailrLl 132
                                       ++P+    g ++k++++ ++glpv++t++ gi+ +     +g +v  +++e + eail+L 
  gi|518653217|ref|YP_008142737.1| 267 LNPIftgGGRNVKMIDYIMHGLPVISTEI-GIRGLSqyDLSGAVVV-EKSENFREAILKLT 325
                                       ****965589*******************.9888777667786663.389********996 PP

>> Glyco_trans_1_2  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.053   3.2e+02      40      66 ..     117     145 ..      63     152 .. 0.73
   2 !   12.5   0.0   2.5e-05      0.15       9      72 ..     274     337 ..     258     342 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.053
                   Glyco_trans_1_2  40 gkevilfe..dleelaekiryllanpeer 66 
                                       ++++++++  ++e+l++k +++++  ee+
  gi|518653217|ref|YP_008142737.1| 117 ENKFVVYDahNVESLLRKGNKYHDYTEEI 145
                                       23577777778888888888888877776 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.5e-05
                   Glyco_trans_1_2   9 espnlrlfEaaacGafaltdda..egleelftpgkevilfedleelaekiryllanpeerraiaea 72 
                                        + n+++ ++ + G +++++++   gl ++   g  ++++e  e++ e+i +l  n+++ ++++ +
  gi|518653217|ref|YP_008142737.1| 274 GGRNVKMIDYIMHGLPVISTEIgiRGLSQYDLSG--AVVVEKSENFREAILKLTGNRDKLKSMSDN 337
                                       56799***************99888888887777..99999*****************99999876 PP

>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.5e-05      0.21      72     169 ..     242     338 ..     209     341 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.5e-05
                                       TCGGGEEECCHSSSHHHHHHCESEEEEEESS.BSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHH CS
                   Glycos_transf_1  72 sdnviflgevsredleellknadifvlpsis.EgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaea 147
                                         nv+f+g v + ++++l++n+ i++ p  +  g  +  + ++  glpvi++ +g  + + +   +G++v ++  e 
  gi|518653217|ref|YP_008142737.1| 242 PGNVKFHGLVQDAEKDNLFRNSCIALNPIFTgGGRNVKMIDYIMHGLPVISTEIGI-RGLSQYDLSGAVVVEK-SEN 316
                                       579******************777777755555556778*************9865.5555555579999999.9** PP

                                       HHHHHHHHHHSHHHHHHHHHHH CS
                   Glycos_transf_1 148 laeairklledeelrerlgena 169
                                       + eai kl  ++++ + ++ n+
  gi|518653217|ref|YP_008142737.1| 317 FREAILKLTGNRDKLKSMSDNT 338
                                       ************9999999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       498  (0.0277762); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); 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: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2509.82
//
Query:       gi|518653218|ref|YP_008142738.1|  [L=380]
Description: hypothetical protein FACI_IFERC00001G1861 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.7e-34  117.2   2.8      1e-33  116.7   2.8    1.3  1  ATPase       KaiC
    0.00015   20.9   0.0    0.00024   20.3   0.0    1.5  1  T2SSE        Type II/IV secretion system protein
     0.0017   18.9   0.1     0.0039   17.7   0.1    1.7  1  ABC_tran     ABC transporter
      0.002   17.7   0.2      0.015   14.8   0.2    2.0  1  AAA_25       AAA domain
      0.002   17.8   0.0     0.0047   16.6   0.0    1.6  2  SRP54        SRP54-type protein, GTPase domain
     0.0021   17.3   1.2     0.0052   16.0   1.2    1.7  1  ArsA_ATPase  Anion-transporting ATPase
     0.0064   15.8   0.0      0.012   14.9   0.0    1.4  1  Zeta_toxin   Zeta toxin
  ------ inclusion threshold ------
      0.021   14.0   0.7       0.26   10.4   0.1    2.1  2  PAXNEB       PAXNEB protein
      0.035   13.9   0.0      0.076   12.8   0.0    1.6  1  DEAD         DEAD/DEAH box helicase
      0.042   13.1   0.1      0.076   12.3   0.1    1.4  1  Rad51        Rad51
      0.046   13.5   1.1      0.068   12.9   0.2    1.7  2  AAA_29       P-loop containing region of AAA domain
      0.094   13.3   0.3       0.26   11.8   0.3    1.9  1  AAA_18       AAA domain
       0.13   12.7   3.1       0.47   11.0   0.7    2.4  2  YxiJ         YxiJ-like protein
       0.23   11.5   1.5       0.54   10.3   1.4    1.7  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
        0.4   10.7   4.8        2.1    8.4   4.3    2.3  1  DUF87        Helicase HerA, central domain
       0.77   10.2   5.8        3.7    8.0   5.9    2.2  1  AAA_23       AAA domain


Domain annotation for each model (and alignments):
>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.7   2.8   8.9e-37     1e-33       4     229 ..     118     341 ..     115     343 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.7 bits;  conditional E-value: 8.9e-37
                            ATPase   4 gIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleee 80 
                                       gI+ +D+ ++gG+  g v+li+G++G+GKt+++  Fl +ga++ ge+g+++ ++  +e++ en++++++++ +  ++
  gi|518653218|ref|YP_008142738.1| 118 GIHKIDMAISGGLRPGFVYLISGKTGSGKTTLSSIFLAEGAKN-GEKGLIILTDTFPEAFVENIRTMDINFYESYKN 193
                                       9*****************************************9.********************************* PP

                            ATPase  81 gklaiidasesaeesaee......kdkedleelieelaeaikeikakrvviDsitglayeekeavaReilrqlvrvl 151
                                       +++ i+++s +++  + e      +++e + ++i+ l+++i + ++krvviD + +l  + ++    +++  +++ l
  gi|518653218|ref|YP_008142738.1| 194 DMIEIMEISDKTKSLKLEnmknkaDYREFITKVISGLKKVIVANNIKRVVIDMVMPL-LIPDD----DYINLFINSL 265
                                       *********9998877777867777777788888999********************.77776....478999999* PP

                            ATPase 152 kklgvTailvsekssseeaaggygveefivdgvivLdlkeieeelvRtleivkmRgtkhskkehpfeIteegikvle 228
                                       ++ gv+ i++s    +++  + yg ee  v g+i+Ld+k+  + + Rt+ i km     ++  + f It++gi++++
  gi|518653218|ref|YP_008142738.1| 266 AMEGVVVIITSIL--KNSDLSVYGSEENYVAGIIKLDYKLSTKGIDRTMMIPKMPVPLNNTMPMHFAITSSGIEITS 340
                                       ***********96..5569999*****************************************************87 PP

                            ATPase 229 e 229
                                       +
  gi|518653218|ref|YP_008142738.1| 341 K 341
                                       5 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 !   20.3   0.0   2.1e-07   0.00024     116     175 ..     120     181 ..      54     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 2.1e-07
                             T2SSE 116 ekiaevlrkavrerglilvsGgTgsGKttllyallkeinks.derivtvEDpv.Eiqlegan 175
                                       +ki+ +++  +r   + l+sG TgsGKttl  + l+e +k+ ++ ++++ D+  E  +e++ 
  gi|518653218|ref|YP_008142738.1| 120 HKIDMAISGGLRPGFVYLISGKTGSGKTTLSSIFLAEGAKNgEKGLIILTDTFpEAFVENIR 181
                                       67777788888888899*******************99998778888888874255555555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.1   3.5e-06    0.0039       4      42 ..     126     166 ..     124     244 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.5e-06
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--..SEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkp..teGei 42 
                                       +s  l++g ++ i G++G+GK+tL ++++ +  +  ++G i
  gi|518653218|ref|YP_008142738.1| 126 ISGGLRPGFVYLISGKTGSGKTTLSSIFLAEGAKngEKGLI 166
                                       678899*******************9998775543466666 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   1.4e-05     0.015      22     154 ..     122     250 ..     111     257 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.4e-05
                            AAA_25  22 rrwlvkgllpagelallaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal 97 
                                        +  + g l+ g + l+ G +g+GKttl +   ++ a  G+           k l++ ++   + + + +r +  ++
  gi|518653218|ref|YP_008142738.1| 122 IDMAISGGLRPGFVYLISGKTGSGKTTLSSIFLAEGAkNGE-----------KGLIILTDTFPEAFVENIRTMDINF 187
                                       55567777778******************999999994444...........6788888888777777777777666 PP

                            AAA_25  98 ...rddarllvldlagv.eslpLfakdrggtl...ltadvdaleaaieevegvrlvviDplsra 154
                                            ++   ++ + ++ +sl L  ++++      +t ++  l ++i + ++++ vviD++  +
  gi|518653218|ref|YP_008142738.1| 188 yesYKNDMIEIMEISDKtKSLKLENMKNKADYrefITKVISGLKKVIVA-NNIKRVVIDMVMPL 250
                                       6655678889999999999999988876666567799999999999999.88999999998765 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.3     7e+03     167     187 ..      49      69 ..      45      70 .. 0.82
   2 !   16.6   0.0   4.2e-06    0.0047       3      60 ..     135     188 ..     133     219 .. 0.79

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.3
                                       TS-EEEEE-SSSTTGEEE--H CS
                             SRP54 167 klPikfigvGekiedleefdp 187
                                        +Pik+i   + ++dl  f +
  gi|518653218|ref|YP_008142738.1|  49 YIPIKIINEQDAVHDLMGFYA 69 
                                       689999999999999998875 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 4.2e-06
                                       EEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEE CS
                             SRP54   3 villvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvi 60 
                                       v+l+ G +G+GKTt  +   a   k+g+k l++ +Dtf  a ve ++t+    +++++
  gi|518653218|ref|YP_008142738.1| 135 VYLISGKTGSGKTTLSSIFLAEGAKNGEKGLIILTDTFPEAFVENIRTM----DINFY 188
                                       899***************999*****************99999877654....44444 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   1.2   4.7e-06    0.0052       5      39 ..     137     171 ..     134     240 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 4.7e-06
                                       EEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-ST CS
                       ArsA_ATPase   5 lvgGKGGVGKttvsaatavklsekgkkvllistDP 39 
                                       l++GK G GKtt+s+ + ++ +++g+k l+i tD 
  gi|518653218|ref|YP_008142738.1| 137 LISGKTGSGKTTLSSIFLAEGAKNGEKGLIILTDT 171
                                       89******************************994 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   1.1e-05     0.012      18      58 ..     135     176 ..     125     204 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.1e-05
                        Zeta_toxin  18 lillgGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                                       ++l++G +G+GK++l++ + +e + ++++ + + +D++ e +
  gi|518653218|ref|YP_008142738.1| 135 VYLISGKTGSGKTTLSSIFLAEGAkNGEKGLIILTDTFPEAF 176
                                       789*******************98666777888888887766 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00023      0.26      20      84 ..     116     179 ..     114     194 .. 0.91
   2 ?    2.1   0.1     0.077        87     159     217 ..     196     248 ..     182     281 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00023
                            PAXNEB  20 StGtpsLDklLgGGLplGsillieEdgttdfakvLlkyFlAeGvvqkhevlvlsldddpeewlre 84 
                                       S G++++D  ++GGL  G + li  + t + +++L  +FlAeG  ++ + l++  d+ pe+++++
  gi|518653218|ref|YP_008142738.1| 116 SFGIHKIDMAISGGLRPGFVYLISGK-TGSGKTTLSSIFLAEGAKNGEKGLIILTDTFPEAFVEN 179
                                       78*********************965.88999***************999999998999988765 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.077
                            PAXNEB 159 isftplddskkseeeekeslkespryssllnqiqqllkkesfsaptkknvlRivipsLl 217
                                       i+++ ++d++k  + + e++k+++ y+++++++ + lkk      ++ n+ R+vi   +
  gi|518653218|ref|YP_008142738.1| 196 IEIMEISDKTK--SLKLENMKNKADYREFITKVISGLKK---VIVAN-NIKRVVIDMVM 248
                                       44445554443..34677788888999999999999999...33333.68999997543 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.8e-05     0.076      16      98 ..     135     217 ..     122     247 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.8e-05
                                       EEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTT.....T.STSEEEEEETTSS CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....x.xxxxxxxxxxxxx RF
                              DEAD  16 dvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkk.....y.idlrvlliiggva 86 
                                         l++++TGsGKT+  +i + +       k+g k li+  t    e  ++n++++       y  d+ + + i++++
  gi|518653218|ref|YP_008142738.1| 135 VYLISGKTGSGKTTLSSIFLAEGA-----KNGEKGLIIL-TDTFPEAFVENIRTMDInfyesYkNDMIEIMEISDKT 205
                                       56899**************99776.....5666666665.3334444444444333322112123344445566666 PP

                                       HHHHHHHHHTTC CS
                                       xxxxxxxxxxxx RF
                              DEAD  87 ardqlskldngv 98 
                                       ++ +l++++n++
  gi|518653218|ref|YP_008142738.1| 206 KSLKLENMKNKA 217
                                       666666665555 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   6.8e-05     0.076      20     143 ..     116     249 ..      81     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.8e-05
                                       --S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEES..SS---GGGGHHHH.. CS
                             Rad51  20 ttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidt..egtfrperlveia.. 92 
                                       + G +k+D  ++GG++ g +  i G  +sGkt l+  +      +  ++G +g ++  dt  e+ ++  r ++i   
  gi|518653218|ref|YP_008142738.1| 116 SFGIHKIDMAISGGLRPGFVYLISGKTGSGKTTLSSIF----LAEGAKNGEKGLIILTDTfpEAFVENIRTMDINfy 188
                                       56899***************************987643....23557899999999999987888899999999899 PP

                                       HHTT--HHHHGGGEEEEE--ST..........THHHHHHHHTHHHHHHS-EEEEEEETTTG CS
                             Rad51  93 erykldkeevlenvayaRayti..........ehqeellqqaaallaedkfallivDsvta 143
                                       e yk d  e++e     +  +           e  +++++ + + ++ ++++ +++D v+ 
  gi|518653218|ref|YP_008142738.1| 189 ESYKNDMIEIMEISDKTKSLKLenmknkadyrEFITKVISGLKKVIVANNIKRVVIDMVMP 249
                                       9999999888876666666655555777777778888888999999999999999998875 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   0.2   6.1e-05     0.068      23      38 ..     133     149 ..     113     153 .. 0.82
   2 ?   -3.4   0.0       7.4   8.3e+03      37      50 ..     242     255 ..     240     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 6.1e-05
                            AAA_29  23 g.atlltGpsGsGKSTl 38 
                                       g ++l++G++GsGK+Tl
  gi|518653218|ref|YP_008142738.1| 133 GfVYLISGKTGSGKTTL 149
                                       4689************8 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 7.4
                            AAA_29  37 TllDAiqalLvpak 50 
                                        ++D ++ lL+p+ 
  gi|518653218|ref|YP_008142738.1| 242 VVIDMVMPLLIPDD 255
                                       57999999999986 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   0.00023      0.26       2      67 ..     137     208 ..     137     279 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00023
                            AAA_18   2 lltGtpGvGKttlakeLskrl.gf.......gvnlrdvakenglllevdpealdeskrldedkldklldaleen 67 
                                       l++G+ G+GKttl+     ++ ++        +     a+ +++++++ ++   es + d+   ++++d+ +  
  gi|518653218|ref|YP_008142738.1| 137 LISGKTGSGKTTLSSIFLAEGaKNgekgliiLTDTFPEAFVENIRTMDINF--YESYKNDMIEIMEISDKTKSL 208
                                       699***********9874444355677755544444445555555555555..555555555555555555544 PP

>> YxiJ  YxiJ-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.7   0.00042      0.47       2      70 ..     178     246 ..     177     250 .. 0.81
   2 ?    1.2   0.1      0.45   5.1e+02      48      70 ..     338     359 ..     331     377 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00042
                              YxiJ   2 nelkkmssllakafPsediekleedlkkdftkdd..clsaDfneyfmliagtLsyvlngkeqkipkkqikl 70 
                                       ++++ m++ +++++ +  ie +e   k +  k++    +aD+ e+++ + + L  v+  +  +i +  i++
  gi|518653218|ref|YP_008142738.1| 178 ENIRTMDINFYESYKNDMIEIMEISDKTKSLKLEnmKNKADYREFITKVISGLKKVIVAN--NIKRVVIDM 246
                                       67789**********9999999877776666666334579****************9998..787776665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.45
                              YxiJ  48 iagtLsyvlngkeqkipkkqikl 70 
                                       i++ ++yv+n+++ k++ +q++ 
  gi|518653218|ref|YP_008142738.1| 338 ITSKVNYVVNQNKLKVT-NQVNA 359
                                       78899*******77776.45554 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 ?   10.3   1.4   0.00048      0.54       3      33 ..     137     167 ..     135     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00048
                                       EEESSTTSSHHHHHHHHHHHHHHTT--EEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              CbiA   3 iastkGGvGKTtlaanLaralarrglrVllv 33 
                                       ++s+k G+GKTtl+  +++  a++g + l +
  gi|518653218|ref|YP_008142738.1| 137 LISGKTGSGKTTLSSIFLAEGAKNGEKGLII 167
                                       689***********99888888877775554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   4.3    0.0019       2.1      28      59 ..     138     170 ..     136     252 .. 0.72

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0019
                             DUF87  28 ilgsTGsGKSntvavLleelle.kkgatililD 59 
                                       i g+TGsGK+++ ++ l+e ++   ++ i++ D
  gi|518653218|ref|YP_008142738.1| 138 ISGKTGSGKTTLSSIFLAEGAKnGEKGLIILTD 170
                                       88***************9999654455566555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   5.9    0.0033       3.7      21      35 ..     135     149 ..     116     241 .. 0.85

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0033
                            AAA_23  21 ltlItGpNGaGKTTi 35 
                                       ++lI+G++G+GKTT+
  gi|518653218|ref|YP_008142738.1| 135 VYLISGKTGSGKTTL 149
                                       68************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1078  (0.0601261); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); 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: 0.59u 0.32s 00:00:00.90 Elapsed: 00:00:00.48
# Mc/sec: 2370.78
//
Query:       gi|518653219|ref|YP_008142739.1|  [L=557]
Description: cellulose synthase (UDP-forming) [Ferroplasma acidarmanus fer1]
Scores for complete 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   79.9   2.4    2.2e-22   79.9   2.4    2.5  3  Glyco_trans_2_3  Glycosyl transferase family group 2
      3e-20   72.7   0.2    5.3e-20   71.9   0.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
      2e-18   67.1   0.0    2.8e-18   66.7   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
      3e-06   26.9   2.6      5e-06   26.2   2.6    1.3  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
    0.00086   18.8   0.5     0.0015   17.9   0.3    1.4  2  Glyco_transf_49  Glycosyl-transferase for dystroglycan
  ------ inclusion threshold ------
      0.011   16.3   0.0      0.028   14.9   0.0    1.7  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 ?   -3.7   5.0         3   9.1e+03     159     191 ..      23      53 ..       2      67 .. 0.46
   2 !   79.9   2.4   7.4e-26   2.2e-22       1     196 [.     173     382 ..     173     396 .. 0.74
   3 ?   -4.2   0.5       4.5   1.4e+04     181     195 ..     463     465 ..     434     492 .. 0.47

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3
                   Glyco_trans_2_3 159 lgsllwsalplhlallllfsllalalvllllll 191
                                       ++sl  s + lh+ +++++ l++++++l  ++l
  gi|518653219|ref|YP_008142739.1|  23 IFSLGYSIIILHYKNSIITFLFSFYFWL--ATL 53 
                                       3444444444555433333333322222..111 PP

  == domain 2  score: 79.9 bits;  conditional E-value: 7.4e-26
                   Glyco_trans_2_3   1 iilllDaDtvlppdclreiaaela.spevaivqgpvlvm.nvanwleelaalf.faedhgkdilvrealgrvvpsvG 74 
                                       ++ ++D D +++ d+++e++ +l+ + ++a+vq p +++   an+l+e+a +  f  +++ +   ++++++ ++s G
  gi|518653219|ref|YP_008142739.1| 173 YVSVIDIDQMPSHDFIKEVVTLLDnNEDIAFVQVPQYYAnTDANVLAEMAQAQqF--MFYEILTEGKSISGSLFSCG 247
                                       5779********************558**********983469999999886534..56666666779********* PP

                   Glyco_trans_2_3  75 sgaflrrsalqevggwdgdessvsEDfdmglrlqrkGyrvrfvpeslvkekspltlraalrQrkRwayGc..el... 146
                                        +++ r sal +v ++d  ++++ ED+  ++++ + Gyr  +++  lv+   p t+  +++Q +Rwa G   ++   
  gi|518653219|ref|YP_008142739.1| 248 TNVIYRKSALAAVNYFD--DTNLIEDMATSINMISMGYRGLYYNKKLVYGRAPVTMEGYVNQQYRWAAGSigLIkri 322
                                       *****************..**************************************************76511345 PP

                   Glyco_trans_2_3 147 eklil............lvrllgylgsllwsalplhlallllfslla...........lalvlllllllaall 196
                                       +k+il            ++    ++ ++ w++l+++l  ++lf+++            l          +a++
  gi|518653219|ref|YP_008142739.1| 323 FKNILfkkkyslgmkidWLA-TSLWYLYGWFYLVFLL--SPLFNIFGiyvsalniyvyL----------LAWI 382
                                       44454555555544433211.1233333455555433..55665555433333322222..........2222 PP

  == domain 3  score: -4.2 bits;  conditional E-value: 4.5
                   Glyco_trans_2_3 181 alalvlllllllaal 195
                                       +            ++
  gi|518653219|ref|YP_008142739.1| 463 S------------TM 465
                                       1............11 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 !   71.9   0.2   1.8e-23   5.3e-20       2     166 ..      93     257 ..      92     260 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 1.8e-23
                                       EEEEESS-.TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-.HHHHHHHHHHH CS
                   Glycos_transf_2   2 vviptyNe.ektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenv.Gkagalnaglr 76 
                                       v +p+yNe ++++++ l ++ +    + + ++++DD+   ++ e ++e+a ++ +  +i+r+ +   kagaln++l+
  gi|518653219|ref|YP_008142739.1|  93 VLVPIYNEdKDMVARNLMAIHSS-ASQMVNLYILDDST-NNSSEAIKEIA-GRIGAVYIHRTDRSgYKAGALNNALK 166
                                       89**************9999998.77778888877765.999999****8.5899999999999989********** PP

                                       H--SS.EEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS.EEEECCHCCCCHCCCCCCS CS
                   Glycos_transf_2  77 aatgd.yilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv.generlyfkerkrslkgnl 151
                                       +   + y+ ++D D  p+ d+++++v  l++ ++d++++q+p +  +td +  ++     + ++y+  ++++   ++
  gi|518653219|ref|YP_008142739.1| 167 NFVNEeYVSVIDIDQMPSHDFIKEVVTLLDN-NEDIAFVQVPQYYANTDANVLAEMAqAQQFMFYEILTEGKSISGS 242
                                       *77777*************************.999*******************888999***************** PP

                                       TTCSTCCCEEEEHHH CS
                   Glycos_transf_2 152 sfeigsaallrreal 166
                                        f +g++ ++r++al
  gi|518653219|ref|YP_008142739.1| 243 LFSCGTNVIYRKSAL 257
                                       *************98 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.0   9.2e-22   2.8e-18       4     230 .]      91     314 ..      89     314 .. 0.82

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 9.2e-22
                   Glyco_tranf_2_3   4 lavlVptfneed.vlgevlesllaqeyprvevvvvv..desdaetlevaeelaaalpdvrvrvvvnarnlgstgksr 77 
                                       +avlVp +ne++  + + l+++ +++   v +++ +  ++++ e    ++e+a + ++v   ++++++  +s+ k+ 
  gi|518653219|ref|YP_008142739.1|  91 IAVLVPIYNEDKdMVARNLMAIHSSASQMVNLYILDdsTNNSSE---AIKEIAGRIGAV---YIHRTD--RSGYKAG 159
                                       89*********956667888888887788999999844444444...455777777765...999999..5669*** PP

                   Glyco_tranf_2_3  78 alnealra.vksdlvllvDdDtvvePdtlkrllqff.ltpkvgavgtpvflln.rstlvsalgalefaerhlrflaa 151
                                       aln+al++ v+ ++v ++D D   + d++k +++++ + +++++v++p++  n + ++++       a+ ++    +
  gi|518653219|ref|YP_008142739.1| 160 ALNNALKNfVNEEYVSVIDIDQMPSHDFIKEVVTLLdNNEDIAFVQVPQYYANtDANVLAEMAQ---AQQFMFYEIL 233
                                       *******8688**************************************887725555443322...4555533333 PP

                   Glyco_tranf_2_3 152 r..ral.gvltlnGsgslirrevlkelegldplflltdDyelglrlrragfrtayvpgaavrevfpsslkayikqrn 225
                                       +  +++ g l++ G+ + +r + l++   +d   +l +D  ++  + + g+r  y+++++v+   p + + y++q  
  gi|518653219|ref|YP_008142739.1| 234 TegKSIsGSLFSCGTNVIYRKSALAAVNYFDD-TNLIEDMATSINMISMGYRGLYYNKKLVYGRAPVTMEGYVNQQY 309
                                       3335552579999*******************.******************************************** PP

                   Glyco_tranf_2_3 226 Rwvyg 230
                                       Rw+ g
  gi|518653219|ref|YP_008142739.1| 310 RWAAG 314
                                       **975 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 !   26.2   2.6   1.7e-09     5e-06       2     183 ..      93     265 ..      92     274 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.2 bits;  conditional E-value: 1.7e-09
                   Glyco_tranf_2_2   2 vviplraseerhyieervlqkakyydeeielivvddgSsekfleevssiidlnllvylkdeddkayslaaarNrGas 78 
                                       v++p++++++   +   ++ + +   ++++l ++dd S+++  e ++ i    + vy++ +d   y  +a  N   +
  gi|518653219|ref|YP_008142739.1|  93 VLVPIYNEDKD-MVARNLMAIHSSASQMVNLYILDD-STNNSSEAIKEIAGRIGAVYIHRTDRSGYKAGALNNALKN 167
                                       88999999888.899999999888899****99998.677779**************9888888************* PP

                   Glyco_tranf_2_2  79 kaesdlvlFlDaDcfissDkfekilklitikklrenidaavvlpvvdlnkedsevlkdvedltassrvledllaaks 155
                                         + ++v+ +D D + s D ++ ++       l +n d a v    ++ + d++vl ++ +  a+  +  ++l+  +
  gi|518653219|ref|YP_008142739.1| 168 FVNEEYVSVIDIDQMPSHDFIKEVVT-----LLDNNEDIAFVQVPQYYANTDANVLAEMAQ--AQQFMFYEILTEGK 237
                                       *******************9999998.....688899989888888889999999987654..33333346777666 PP

                   Glyco_tranf_2_2 156 tlvkffapssssilinrraflevGGyDE 183
                                       ++   +   + +++ ++ a+  v  +D+
  gi|518653219|ref|YP_008142739.1| 238 SISGSLFSCGTNVIYRKSALAAVNYFDD 265
                                       6777777777888888888877777765 PP

>> Glyco_transf_49  Glycosyl-transferase for dystroglycan
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   5.1e-07    0.0015     100     176 ..     138     209 ..      85     233 .. 0.71
   2 ?   -3.9   0.0       2.2   6.5e+03     281     297 ..     483     499 ..     483     506 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 5.1e-07
                   Glyco_transf_49 100 klrsseeenykae..ellyPiNvlRNvARkaaqtefvlvlDidlvpseglvekfleflarekakkklrkektvyv.v 173
                                       +++ +  + y ++  +  y   +l N+ +++++ e+v v+Did +ps+++++++ ++l+++++         ++v v
  gi|518653219|ref|YP_008142739.1| 138 EIAGRIGAVYIHRtdRSGYKAGALNNALKNFVNEEYVSVIDIDQMPSHDFIKEVVTLLDNNED--------IAFVqV 206
                                       3322233344444469999999999*********************************97333........233325 PP

                   Glyco_transf_49 174 paF 176
                                       p +
  gi|518653219|ref|YP_008142739.1| 207 PQY 209
                                       554 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.2
                   Glyco_transf_49 281 yeFkvLsnaFlvHkGik 297
                                       y+F +L ++F+  +  k
  gi|518653219|ref|YP_008142739.1| 483 YQFVLLMPVFVLNRTSK 499
                                       99********9998666 PP

>> Glyco_tranf_2_4  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   9.4e-06     0.028      23      82 ..     123     181 ..     100     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.4e-06
                   Glyco_tranf_2_4  23 lvydndstDgtrailkel.pevkllhvdksyederrqvellkallaryaeadwvlvvDaDE 82 
                                       + + +dst ++++ +ke   ++  ++++    ++ ++  +l+++l++  ++++v v+D+D 
  gi|518653219|ref|YP_008142739.1| 123 Y-ILDDSTNNSSEAIKEIaGRIGAVYIHRTD-RSGYKAGALNNALKNFVNEEYVSVIDIDQ 181
                                       4.45778889999999973558877777655.4789999*********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (557 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       950  (0.0529868); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.63u 0.27s 00:00:00.90 Elapsed: 00:00:00.45
# Mc/sec: 3715.83
//
Query:       gi|518653220|ref|YP_008142740.1|  [L=456]
Description: hypothetical protein FACI_IFERC00001G1863 [Ferroplasma acidarmanus fer1]
Scores for complete 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-119  397.1   2.5   5.2e-119  397.1   2.5    2.0  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    1.1e-14   54.0  11.6    1.3e-08   34.1   1.3    2.7  3  tRNA-synt_1g  tRNA synthetases class I (M)
      5e-09   35.0   0.1      3e-05   22.5   0.0    2.3  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
     0.0017   17.4   0.4     0.0017   17.4   0.4    3.2  4  tRNA-synt_1f  tRNA synthetases class I (K)
  ------ inclusion threshold ------
       0.18   11.9   0.0        1.3    9.1   0.0    2.2  2  Mut7-C        Mut7-C RNAse domain


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 !  397.1   2.5  1.4e-122  5.2e-119       2     300 ..      14     312 ..      13     313 .. 0.98
   2 ?    0.3   0.8       0.1   3.6e+02      78     141 ..     365     428 ..     319     450 .. 0.70

  Alignments for each domain:
  == domain 1  score: 397.1 bits;  conditional E-value: 1.4e-122
                                       ---SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHH CS
                      tRNA-synt_1e   2 vkpleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaek 78 
                                       +kp++ ++++++vCGptvyd+sh+GhaR+ ++fD+++++l+a+gY v ++qn+tDidDkii+ra+ee+k+++e+a++
  gi|518653220|ref|YP_008142740.1|  14 FKPMHPGRINMFVCGPTVYDHSHIGHARTNIFFDVIAKYLRARGYSVFYLQNITDIDDKIINRAAEEGKKYSEVADH 90 
                                       688999*********************************************************************** PP

                                       HHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT-- CS
                      tRNA-synt_1e  79 fieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgae 155
                                       + ee+k+ + +L +   ++ +r+s ++deii+ ++k++e+gyaY++  + vyf+v+k+++Yg+ls+qn+++++++a+
  gi|518653220|ref|YP_008142740.1|  91 YFEEYKEIMGKLRIDSINYYARASLYIDEIIGQIKKIMEHGYAYETA-DGVYFNVRKFSDYGELSNQNMDQIRENAR 166
                                       **********************************************9.89*************************** PP

                                       --S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHHHHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHH CS
                      tRNA-synt_1e 156 gevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCsvmaskllgseidihsGGiDLafPhhenelaqseaa 232
                                       g ++eekk+++Df+LWk+ k+gep w+sPwgkGRPGWhie ++++++++gse dih+GG+DL+fPhhe e+aq +++
  gi|518653220|ref|YP_008142740.1| 167 GVIKEEKKSPEDFVLWKKMKPGEPFWESPWGKGRPGWHIEDTAITEAYFGSEYDIHGGGNDLIFPHHEAEIAQMRSV 243
                                       ***************************************************************************** PP

                                       SS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-TTS-EEE-HHHHHHHH CS
                      tRNA-synt_1e 233 fd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsahyrsqldfkeelleeak 300
                                        + + l++y++h+g+++i++ekmsksLknfi+ kd+lk+++p++lR+++++ +y++ +d++ +l+e++k
  gi|518653220|ref|YP_008142740.1| 244 SGkRYLARYWIHTGMVNINKEKMSKSLKNFIQTKDILKSYKPEELRFAMINSNYNTVIDYSAQLMESSK 312
                                       **55679*********************************************************99876 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.1
                                       HHHHHHHHHHHHTT----SB--BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTT CS
                      tRNA-synt_1e  78 kfieefkkdleaLnvlkptleprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgk 141
                                        fi++ +k++e++    +++  ++ e+vd+  +++ +  ++    +    d+  + +++++Y+ 
  gi|518653220|ref|YP_008142740.1| 365 AFISDANKNMENISSAAASKLIHIVEYVDSFLNIIYRKQNQESNIMDIIIDIRNHARSQKDYAI 428
                                       3677778888888888888888888888888887776555544444444566666666666665 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 !   34.1   1.3   3.5e-12   1.3e-08      12     124 ..      33     144 ..      25     154 .. 0.88
   2 !   26.7   0.2   6.3e-10   2.2e-06     313     363 ..     251     302 ..     225     324 .. 0.75
   3 ?   -1.5   0.3      0.23   8.1e+02      52     111 ..     377     440 ..     335     451 .. 0.58

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 3.5e-12
                                       S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEE CS
                      tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdky 88 
                                       ++ H+Gh+++ i  D++a+y r+rg+ v+++        +i  +A++eg + +e+++++ ee+ke++ kl i   +y
  gi|518653220|ref|YP_008142740.1|  33 DHSHIGHARTNIFFDVIAKYLRARGYSVFYLQNITDIDDKIINRAAEEGKKYSEVADHYFEEYKEIMGKLRIDSINY 109
                                       678****************************99999999*********************************98888 PP

                                       EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEET CS
                      tRNA-synt_1g  89 grttseehkelvqeifkklkekgliyekeieqlycp 124
                                       +   s    e+  +i kk+ e+g+ ye++  +++ +
  gi|518653220|ref|YP_008142740.1| 110 YARASLYIDEIIGQI-KKIMEHGYAYETADGVYFNV 144
                                       888888888888877.66777899999887777766 PP

  == domain 2  score: 26.7 bits;  conditional E-value: 6.3e-10
                                       S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHH.HS-TTS- CS
                      tRNA-synt_1g 313 kkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaa.eapekkD 363
                                       +  + +++++++ +K+SkS ++++++k++l++++++ lR+ ++  + ++  D
  gi|518653220|ref|YP_008142740.1| 251 RYWIHTGMVNINKEKMSKSLKNFIQTKDILKSYKPEELRFAMINsNYNTVID 302
                                       4556789*********************************998734444333 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.23
                                       HHHHHHHTTS-HHHHHHHHHH....HHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT CS
                      tRNA-synt_1g  52 ielkAekegvtpeelvekvhe....eikelfkklnisfdkygrttseehkelvqeifkklkekg 111
                                       i  +A+++ ++  e+v+++ +    ++++  + ++i  d  +++ s++++ ++  i kkl+e++
  gi|518653220|ref|YP_008142740.1| 377 ISSAAASKLIHIVEYVDSFLNiiyrKQNQESNIMDIIIDIRNHARSQKDYAISDYIRKKLEENN 440
                                       4444444444444444443330000333333446666677777777777777777777777665 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.0   3.8e-05      0.14      30      67 ..      27      64 ..      10     105 .. 0.84
   2 !   22.5   0.0   8.5e-09     3e-05     550     597 ..     252     299 ..     196     304 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 3.8e-05
                       tRNA-synt_1 30 gPPyvtGslHiGhalaktlkdivirykrmkGkevlyvp 67
                                        P v  + HiGha +++  d++ +y r +G++v y+ 
  gi|518653220|ref|YP_008142740.1| 27 CGPTVYDHSHIGHARTNIFFDVIAKYLRARGYSVFYLQ 64
                                      457888999************************99865 PP

  == domain 2  score: 22.5 bits;  conditional E-value: 8.5e-09
                       tRNA-synt_1 550 vlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltlilsdvgr 597
                                         +h  +++ +  KmSKsl+N i+ +d++k+y  + lR+++i+s++  
  gi|518653220|ref|YP_008142740.1| 252 YWIHTGMVNINKEKMSKSLKNFIQTKDILKSYKPEELRFAMINSNYNT 299
                                       5555555666779*****************************999875 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.025        88      29      72 ..      27      70 ..      10      74 .. 0.83
   2 ?   -1.7   0.1      0.29     1e+03     104     150 ..      84     130 ..      74     135 .. 0.77
   3 !   17.4   0.4   4.6e-07    0.0017     277     333 ..     262     316 ..     254     341 .. 0.73
   4 ?   -0.8   0.1      0.16   5.7e+02     144     170 ..     399     425 ..     353     450 .. 0.60

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.025
                      tRNA-synt_1f 29 sGispSGliHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                                       G ++  + HiG +r  +  d++a+ lr+rg +v  +  + d+D
  gi|518653220|ref|YP_008142740.1| 27 CGPTVYDHSHIGHARTNIFFDVIAKYLRARGYSVFYLQNITDID 70
                                      566666789**********************9987777666666 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.29
                      tRNA-synt_1f 104 hesyaehfnaelvesLdelgi.evefisatelYksglydeaikealen 150
                                        ++ a+h+ +e++e + +l i  ++++  ++lY +     +ik+++e+
  gi|518653220|ref|YP_008142740.1|  84 YSEVADHYFEEYKEIMGKLRIdSINYYARASLYIDEII-GQIKKIMEH 130
                                       45568899999999999999977888888999988765.456666665 PP

  == domain 3  score: 17.4 bits;  conditional E-value: 4.6e-07
                      tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYd 333
                                       + +ekms+S  n++  +d+l+ ++pe lrf +++++ ++ ++ + +  + +  d  +
  gi|518653220|ref|YP_008142740.1| 262 N-KEKMSKSLKNFIQTKDILKSYKPEELRFAMINSNYNTVIDYSAQ-LMESSKDAVE 316
                                       4.56******************************988888877766.3444444444 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.16
                      tRNA-synt_1f 144 ikealenrekikeilekyrgeereety 170
                                       i +  +++++i++i+  +r++ r+++ 
  gi|518653220|ref|YP_008142740.1| 399 IYRKQNQESNIMDIIIDIRNHARSQKD 425
                                       222334467788888888877755443 PP

>> Mut7-C  Mut7-C RNAse domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.0   0.00037       1.3      11      42 ..      48      81 ..      42      84 .. 0.85
   2 ?   -0.4   0.0       0.3   1.1e+03      54     101 ..     251     298 ..     236     326 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00037
                            Mut7-C 11 klakyLRllGydalyasdv..edeellalaakek 42
                                       +akyLR  Gy + y ++    d++++++aa+e+
  gi|518653220|ref|YP_008142740.1| 48 VIAKYLRARGYSVFYLQNItdIDDKIINRAAEEG 81
                                      58************99977446899*****9997 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.3
                            Mut7-C  54 kraklkkgvlltsrdveeqlreviarlglklslkpelsrCvaCngele 101
                                       +    +  v ++++++++ l++ i++ ++  s kpe  r  + n++ +
  gi|518653220|ref|YP_008142740.1| 251 RYWIHTGMVNINKEKMSKSLKNFIQTKDILKSYKPEELRFAMINSNYN 298
                                       443334346679999999999999999999999988888777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1120  (0.0624686); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.43
# Mc/sec: 3148.79
//
Query:       gi|518653221|ref|YP_008142741.1|  [L=180]
Description: nicotinamidase-like protein amidase [Ferroplasma acidarmanus fer1]
Scores for complete 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-35  121.4   0.0    4.8e-35  121.3   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 !  121.3   0.0   2.7e-39   4.8e-35       1     171 [.       6     170 ..       6     174 .. 0.93

  Alignments for each domain:
  == domain 1  score: 121.3 bits;  conditional E-value: 2.7e-39
                   Isochorismatase   1 talvviDmqndfveegvkeseeisavveninkllkaarkagipviftrdvheleevkgdlderkaaphfkpgttgae 77 
                                       ++++v+Dm ndfv  g   + ++ ++++ ++ +lk+ +  +ip+if +d+h     k+d++ + + +h + gt+g+e
  gi|518653221|ref|YP_008142741.1|   6 SCVLVVDMINDFV-TGKFGNSNAVESLKLAEIALKQLK-GNIPIIFAKDSHI----KNDPEFEVWGEHAIDGTWGSE 76 
                                       589**********.888888888888888888899886.99***********....********************* PP

                   Isochorismatase  78 lvpelaplegdvvvdKtrfsafagtdldeiLkelgiktivlaGiatdvCVeatardaldlGyevvvvsDAvaalspe 154
                                       +v++l+p   d+++ K++++af++tdld +L+++gi++i++ Gi+td+CVe+t+  a+ + y+v v+sD +a +++ 
  gi|518653221|ref|YP_008142741.1|  77 IVDALKPF-PDYILKKRHYDAFFDTDLDSLLRASGITNIYIFGISTDICVEHTCAGAFYRYYNVKVISDLCACIDAS 152
                                       ******97.9******************************************************************* PP

                   Isochorismatase 155 lhdaalkrlk.qafatvi 171
                                       ++  al ++k +++ t i
  gi|518653221|ref|YP_008142741.1| 153 HQISALTNIKiNYGYTSI 170
                                       ********9966655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       348  (0.0194099); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1215.49
//
Query:       gi|518653222|ref|YP_008142742.1|  [L=386]
Description: hypothetical protein FACI_IFERC00001G1865 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-20   73.8   0.0      2e-20   73.2   0.0    1.3  1  QRPTase_C        Quinolinate phosphoribosyl transferase, C-te
     0.0039   16.6   0.0     0.0065   15.9   0.0    1.3  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
     0.0097   16.3   0.0      0.018   15.5   0.0    1.4  1  NAPRTase_C       Nicotinate phosphoribosyltransferase C-termi
  ------ inclusion threshold ------
      0.028   14.1   0.0        2.8    7.6   0.0    2.3  2  Acyltransferase  Acyltransferase
      0.051   13.0   0.0      0.083   12.3   0.0    1.3  1  His_biosynth     Histidine biosynthesis protein


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 !   73.2   0.0   5.6e-24     2e-20       7     169 .]     125     303 ..     119     303 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.2 bits;  conditional E-value: 5.6e-24
                                       HHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB.......--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHH CS
                         QRPTase_C   7 rmveaaksakvrildTRkttPglrllekyAvliGGgd.......nhrlgLsdmvlikdnhiaaagsiveavksvrea 76 
                                        +++ + +    +++ R+++P++ ++  ++ +iGG++       ++ lg++   +++++   ++g+ ++a+k   ++
  gi|518653222|ref|YP_008142742.1| 125 LLKKSLGNIPFISFGIRRMHPAISPMIDRSSYIGGAAgvsgvlsSKILGIKPSGTMPHALSLILGD-HDAWKVQHDN 200
                                       5556666667788999*************************************************7.79******** PP

                                       HTTTSEEEEEESSHHHHHHHHHHT....-SEEEEES--H..HHHHHHHHHH.HHHSTT....SEEEEESS--TTTHH CS
                         QRPTase_C  77 vdkevkievevesleeleevleae....adiimLDnfsv..eelkkaveel.keknkr....vlievSGgvtlenve 142
                                       +++ v   +++  +e++ ++ +a      d i+LD++s+   ++ + + e+ +e ++r    ++i vSGg++le++ 
  gi|518653222|ref|YP_008142742.1| 201 ASFRV-FLIDTFMDEKFAAIKAADefpdIDFIRLDTPSSrrGNFPNLIREIrWELDIRghknIKIMVSGGIKLEDIP 276
                                       ****9.***********99999888888999******9877889999998889999999999*************** PP

                                       HHHCTT-SEEEECHHCHTB----EEEE CS
                         QRPTase_C 143 eyaksgvdvisvgalthsvkalDislk 169
                                       e+ + gv+ +++g+ ++s+k++D+ ++
  gi|518653222|ref|YP_008142742.1| 277 ELISAGVESFGIGTSISSAKPVDFGMD 303
                                       ************************996 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 !   15.9   0.0   1.8e-06    0.0065     153     197 ..     247     292 ..     242     293 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.8e-06
                                       HHHHHHHHHHHT.---EEEEESS--TTTCHHHHHHT--EEEESHHH CS
                    Ribul_P_3_epim 153 ikkvrklideke.ldlkievDGGvkldnieqiaeagadvlVagsav 197
                                       i+++r  +d ++ +++ki v GG+kl+ i ++++ag++ + +g+ +
  gi|518653222|ref|YP_008142742.1| 247 IREIRWELDIRGhKNIKIMVSGGIKLEDIPELISAGVESFGIGTSI 292
                                       677787777766589*************************999876 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 !   15.5   0.0   4.9e-06     0.018      42      86 ..     340     383 ..     322     385 .. 0.85

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 4.9e-06
                        NAPRTase_C  42 kkrveitpsrvekLlkkvfkdGklvyelpsleeireyvkeqlael 86 
                                       +k +    +++e++lk+++++Gk++ + +++e++r+++ +q++++
  gi|518653222|ref|YP_008142742.1| 340 TKPICHCGETMENILKPYMEKGKII-KNEDIETVRQRSLAQIENI 383
                                       55555556899************86.7789***********9986 PP

>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0098        35      82     108 ..      57      84 ..      54     104 .. 0.82
   2 ?    7.6   0.0   0.00078       2.8      29     103 ..     108     180 ..     103     207 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0098
                   Acyltransferase  82 leniselleegkl.vviFPEGtrsrege 108
                                       l+ +++lle+ ++ v+  PEGt+++++ 
  gi|518653222|ref|YP_008142742.1|  57 LNDVLSLLESHNVdVHAIPEGTVLKARD 84 
                                       56778899***************99865 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00078
                   Acyltransferase  29 lllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraagsleniselleegklvviFPEGtr 103
                                       +ll +l ++s++   +  ++kk+l +ip+++f++r+++       +++++ g+ + +s +l++ k+++i P+Gt 
  gi|518653222|ref|YP_008142742.1| 108 PLLGFLCQASGI-SSYSSLLKKSLGNIPFISFGIRRMHPAISPMIDRSSYIGGAAGVSGVLSS-KILGIKPSGTM 180
                                       567777766775.89999*****************8875544333447788888888877777.77888888876 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.3e-05     0.083      68     105 ..     256     292 ..     216     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.3e-05
                                       HHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
                      His_biosynth  68 iaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                                       i+ + +i+++v GGI+ led+ el++ag++   igt+ 
  gi|518653222|ref|YP_008142742.1| 256 IRGHKNIKIMVSGGIK-LEDIPELISAGVESFGIGTSI 292
                                       3444458999999997.566999999999999999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (386 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2807.96
//
Query:       gi|518653223|ref|YP_008142743.1|  [L=503]
Description: hypothetical protein FACI_IFERC00001G1866 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-26   93.0  62.3    2.3e-26   92.5  62.3    1.1  1  AA_permease    Amino acid permease
    4.6e-21   75.2  66.3    9.9e-21   74.0  66.3    1.4  1  AA_permease_2  Amino acid permease


Domain annotation for each model (and alignments):
>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.5  62.3   2.5e-30   2.3e-26      24     467 ..      58     492 ..      40     497 .. 0.80

  Alignments for each domain:
  == domain 1  score: 92.5 bits;  conditional E-value: 2.5e-30
                       AA_permease  24 sqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgpelGfviGlnylfswitvlaleltaasil 100
                                          G  ++ l++lla +v+ ++ +s  e++ + ++sgg+yt++++ lg+ +G +++l+y +++i+ ++   +++  +
  gi|518653223|ref|YP_008142743.1|  58 YPDGAFSIPLILLLALIVYSMMSYSSFEFSKYLSSSGGYYTFVANGLGKGFGLTTALSYISYQILSFTG--FGILGF 132
                                       55577899******************************************************9998864..688899 PP

                       AA_permease 101 iqfwelvtdlpkawvt...........gavflvvlliinlvgvkvygeaefilalikiiaiiafiivgiillaggkp 166
                                       i+f+  +  lp++ +t            ++f+++++++ + g+k + +    +  ++i++ ++f+i + ++l+g + 
  gi|518653223|ref|YP_008142743.1| 133 IGFA--YAILPSLGITvpyvnilwipvTIIFILFVSFLIYKGIKPSLK----YVTYAILIEVIFFIASSVYLIGVNH 203
                                       9999..999999999999999999999889999999999*******99....99999999********999999998 PP

                       AA_permease 167 nkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiPkailqvviri 243
                                       +k         +   f ++       + +g+f   ++++v ++ +f G +  + ia+E+k+P+k++P++i+  + ++
  gi|518653223|ref|YP_008142743.1| 204 TKI--------SIKPFTAI-------PVGGNFIILAAMMVYAIGSFVGVGGSIPIAEETKNPKKTVPRSIIASIAIL 265
                                       888........22222223.......44569*99******************************************* PP

                       AA_permease 244 tifYvlsllligllvprndlgllndsasa......aspfvifikesgvsvlaplinaviltaalssansslysasRv 314
                                       ++  +l++++ ++ +++ +  ++  + s+      +s++ + ++  g+  +a+l+++vi  + + + +s+ + asRv
  gi|518653223|ref|YP_008142743.1| 266 GVTIILAAYAEVISWGYGNMASFG-TGSGigaypvLSIYKYGFSGMGLVPFAVLLIIVIN-SFFTATVSLGTNASRV 340
                                       ****************99888877.4445789999*****************99999887.6788999********* PP

                       AA_permease 315 lyslakdglaPkvlkkvskrgvPlraillsmiisllalllaslnlaa...pivfnfllaisaliglivwlliilsyl 388
                                       ++sl+++g++P  l++ + rgvP+ ail+ +i+sl+++l++++++++    ++++ ll +s +  ++  +++++ ++
  gi|518653223|ref|YP_008142743.1| 341 IFSLSREGVIPEKLSRTNTRGVPVYAILFITIVSLVIVLATGISFELlypGKIIDALLYSSVFLLVLESPISYIVHI 417
                                       **************************************888766553111267777777777766665555555555 PP

                       AA_permease 389 rfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllfliilvg 465
                                          ++l+ + ++ +    + + ++   i+ ++++ +i+ ++ + +++++  g     ++  + +++i+++++i++  
  gi|518653223|ref|YP_008142743.1| 418 LTNTSLHMYLKKRKMKTHIFRHIIIPGISSITLVGAIIAAVYFDLSAPYIYGV----YGALVWVIVIAIVVIIMYTK 490
                                       55555554444332222333444444455555555555555555555533333....66777777777778877776 PP

                       AA_permease 466 vk 467
                                       ++
  gi|518653223|ref|YP_008142743.1| 491 YN 492
                                       65 PP

>> AA_permease_2  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.0  66.3   1.1e-24   9.9e-21      15     418 ..      50     481 ..      37     494 .. 0.69

  Alignments for each domain:
  == domain 1  score: 74.0 bits;  conditional E-value: 1.1e-24
                     AA_permease_2  15 igsgifvknlaasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkkvaflsawfnwfayvpv 91 
                                       + ++ f k  +  g  ++ l++++a +++s ++++   E+s  l++sgG y++++++ gk ++ ++a ++   ++++
  gi|518653223|ref|YP_008142743.1|  50 LLTFTFSK--YPDGAFSIPLILLLALIVYS-MMSYSSFEFSKYLSSSGGYYTFVANGLGKGFGLTTALSYISYQILS 123
                                       44555555..66677778999999999996.9*********99***************************9999999 PP

                     AA_permease_2  92 lasilsvaasyllnalgpdlqgn....twltyliaiaililvalinirgikesakiqnilgilkillpliiliilgl 164
                                       +++  ++++  +++a+ p+l  +    ++l++ + i+++++v +++++gik s k+ ++ +++ +    i++i+  +
  gi|518653223|ref|YP_008142743.1| 124 FTGFGILGFIGFAYAILPSLGITvpyvNILWIPVTIIFILFVSFLIYKGIKPSLKYVTYAILIEV----IFFIASSV 196
                                       98989999999999999988888444466666666666666666666666666666666666666....57888888 PP

                     AA_permease_2 165 itvdgggfsslstetdtffpngwpgv.llglli.vlwsfdGfesaanvseevkk..kdvpkaifigllivlvlyllv 237
                                       ++++ ++   +     t  p g +++ l+++++ ++ sf+G+ +++ ++ee k+  k+vp+ i+ +++i +v  +l 
  gi|518653223|ref|YP_008142743.1| 197 YLIGVNHTKISIKPF-TAIPVGGNFIiLAAMMVyAIGSFVGVGGSIPIAEETKNpkKTVPRSIIASIAILGVTIILA 272
                                       888777666443444.5666677775244443359****************6666489******************* PP

                     AA_permease_2 238 niaflgvvpddeianlsnlgsv.....aalffeavggkvvaiivvilial..sllgaintavigssrvlealardgv 307
                                       + a ++  + +++a+ ++  ++     ++++   + g  +  ++v+li++  s + a  ++ + +srv+++l+r+gv
  gi|518653223|ref|YP_008142743.1| 273 AYAEVISWGYGNMASFGTGSGIgaypvLSIYKYGFSGMGLVPFAVLLIIVinSFFTATVSLGTNASRVIFSLSREGV 349
                                       99988888889996665522222223245554444443333333333333347777888888889************ PP

                     AA_permease_2 308 lPrffakvnkfgspiraiiltaivslillllfl..........lassaayn........fllsvsslgliisyllli 366
                                       +P+ ++++n +g p++ai ++ ivsl+++l++           +               fll + s  ++i+ +l+ 
  gi|518653223|ref|YP_008142743.1| 350 IPEKLSRTNTRGVPVYAILFITIVSLVIVLATGisfellypgkI------IdallyssvFLLVLESPISYIVHILTN 420
                                       *************************8887777766666555552......044444555888888888899999998 PP

                     AA_permease_2 367 igalilrkkrphlkr.......pgkilvaiigalfllfllvalf.......fppkgpatqssliyt 418
                                       +++ ++ kkr+ +         p     +i ++ ++  +++a +       ++++  a    + ++
  gi|518653223|ref|YP_008142743.1| 421 TSLHMYLKKRKMKTHifrhiiiP-----GISSITLVGAIIAAVYfdlsapyIYGVYGALVWVIVIA 481
                                       88888888888665532244443.....44444444444444330000000444433333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (503 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1185  (0.066094); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.66u 0.31s 00:00:00.97 Elapsed: 00:00:00.48
# Mc/sec: 3144.27
//
Query:       gi|518653224|ref|YP_008142744.1|  [L=423]
Description: hypothetical protein FACI_IFERC00001G1867 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-48  164.1   0.0      6e-48  163.4   0.0    1.3  1  DUF4147   Domain of unknown function (DUF4147)
    5.9e-28   97.2   2.4    1.3e-27   96.1   2.4    1.6  1  MOFRL     MOFRL family


Domain annotation for each model (and alignments):
>> DUF4147  Domain of unknown function (DUF4147)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.4   0.0   6.7e-52     6e-48       5     217 ..      21     232 ..      17     249 .. 0.86

  Alignments for each domain:
  == domain 1  score: 163.4 bits;  conditional E-value: 6.7e-52
                                       HHHHHHHTTSHHHHHHTTHHHH--.......-SEEEEEESTTHHHHHHHHH.HHHG....EEEEEE.ETT-----TT CS
                           DUF4147   5 ifeaaveavdpeklvkralslkeeeldlskkkrvvvvgaGKAaaamaaaleeealk....sgvvvv.kkghaeeker 76 
                                        +++a+++++p+++++r+      ++d++k++rv+v+g+GKA+ +m + ++e+ lk     g+++   + h+e+  +
  gi|518653224|ref|YP_008142744.1|  21 KIQNAINNLHPSAAMSRNF-----NVDTEKFDRVYVIGFGKASFSMYSGIRERVLKklsyAGIIIPdDEVHNESYPE 92 
                                       5789***************.....467789*****************888874454555788888855566778889 PP

                                       -EEEEE-SSS--HHHHHHHHHHHHHHSS--TT-EEEEEE-TTHHHHS--B-TT--HHHHHHHHHHHHHCT--HHHHH CS
                           DUF4147  77 ievleaahplPdeesveaarkilelaeklkeddlvlvliSGGgSAllaaPaegitledkqaltkaLlasGasIqelN 153
                                       +evl+++hp  ++ sve+++k+l+ +++l+++dlv+vliSGGgS+l++  ++gi ++d+++++ +++++  +I  lN
  gi|518653224|ref|YP_008142744.1|  93 LEVLRGTHPYVSSLSVESSKKLLSHLDRLNQNDLVIVLISGGGSSLFEILETGIDVNDLKDISAEIMENDGDIYVLN 169
                                       ***************************************************************************** PP

                                       HHHHTTBSSTTTHHHHHHTTSEEEEEEE--STT--TTTGGG-TTS-----HHHHHHHHHHTT-- CS
                           DUF4147 154 tVRkhlsaikGGrLaraaaparvvsLilSDVvgddldvIASGPtvpdsstfadalailekykle 217
                                        +R+ lsa+k G+La++++pa+v   i+SDVv d+l++IASGP v  +   a+  ++ +ky  +
  gi|518653224|ref|YP_008142744.1| 170 RLRSSLSAVKNGKLAKYLYPASVAGYIISDVVYDNLNIIASGPLVNVPA-PANLKELAKKYIKD 232
                                       *******************************************997543.33344444444333 PP

>> MOFRL  MOFRL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.1   2.4   1.4e-31   1.3e-27       3     109 .]     314     410 ..     312     410 .. 0.92

  Alignments for each domain:
  == domain 1  score: 96.1 bits;  conditional E-value: 1.4e-31
                                       EEEEE--B----S-----HHHHHHHHHHH...HTTT-TTEEEEEEETTS--SSSS--EEEEETTHHHHHHHTT--HH CS
                             MOFRL   3 llsgGEttvtvkgkGkGGrnqelalalalelkelegaeevvllsagtDGiDGptdaaGaivdaetleraeaagldak 79 
                                       +++gGEttvtv+g+G+GGrnqela++++ +++    ++++ ++s+gtDGiDG++ aaG+ivd++t         +++
  gi|518653224|ref|YP_008142744.1| 314 FVCGGETTVTVTGNGSGGRNQELAVRIMEDIS----NNDFLFISMGTDGIDGKSIAAGGIVDNSTRI------DNLE 380
                                       799**************************555....5699**********************99964......3578 PP

                                       HHHHTT-HHHHHHHTT-EE-----S----E CS
                             MOFRL  80 eaLanndsyeffeklgallktgpTgtNVnD 109
                                       e+Lannd+y++++k++ +++tg Tg+NV+D
  gi|518653224|ref|YP_008142744.1| 381 EYLANNDTYTALSKAHGAIITGRTGNNVSD 410
                                       9***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (423 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      571  (0.0318478); 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: 0.62u 0.29s 00:00:00.90 Elapsed: 00:00:00.49
# Mc/sec: 2621.36
//
Query:       gi|518653225|ref|YP_008142745.1|  [L=53]
Description: hypothetical protein FACI_IFERC00001G1868 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       324  (0.0180713); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 411.56
//
Query:       gi|518653226|ref|YP_008142746.1|  [L=698]
Description: thermopsin precursor [Ferroplasma acidarmanus fer1]
Scores for complete 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-80  268.5  21.4    5.8e-80  268.5  21.4    3.6  5  Thermopsin  Thermopsin
    0.00082   19.8   0.1       0.23   11.9   0.0    2.7  2  DUF1214     Protein of unknown function (DUF1214)
  ------ inclusion threshold ------
       0.12   11.9   0.3         11    5.4   0.0    2.6  3  FAP         Fibronectin-attachment protein (FAP)


Domain annotation for each model (and alignments):
>> Thermopsin  Thermopsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  268.5  21.4   9.8e-84   5.8e-80       2     260 .]      67     333 ..      66     333 .. 0.96
   2 ?    0.5   0.6     0.059   3.5e+02     121     186 ..     344     423 ..     335     434 .. 0.67
   3 ?    1.3   7.2     0.034     2e+02     134     225 ..     436     532 ..     407     560 .. 0.80
   4 ?   -1.3   0.3      0.19   1.2e+03     164     218 ..     544     604 ..     512     637 .. 0.62
   5 ?   -1.7   0.1      0.27   1.6e+03     151     203 ..     610     662 ..     559     669 .. 0.51

  Alignments for each domain:
  == domain 1  score: 268.5 bits;  conditional E-value: 9.8e-84
                        Thermopsin   2 lvnvlslyssepaPmGiadyGiknns..gkltpysyntssvlGevnisslsaynsssnspesaslQLNvvlevvtgg 76 
                                       +vn+ +ly +epaP+G+adyG++ ++  g +tpy+ynt+s+lG+++i++ls+ nsss  ++++s+Q+N++l +++++
  gi|518653226|ref|YP_008142746.1|  67 SVNPENLYRNEPAPVGMADYGLGTETllGGYTPYEYNTTSFLGSAKIYNLSVANSSSG-NKCMSVQFNINLVFNNSN 142
                                       6999******************998744689************************987.99**************** PP

                        Thermopsin  77 ktysywvQnVvsfnttekqltfidNiWNftspsanlsnsaisGnGtvyasskgefYyayatey.....lelslPltl 148
                                       ++y ywvQ+V+ +nt+++++tfidNiWN+ts+ a++ ns+++G G+v++ s + +Yy++a+ +     ++l  P+t+
  gi|518653226|ref|YP_008142746.1| 143 NKYVYWVQDVAFINTSSRAITFIDNIWNMTSSGASMYNSTVNGAGKVGNYSDSGYYYSIASCTlpgndIKLPNPATI 219
                                       ***********************************************************99988999999999**** PP

                        Thermopsin 149 kLvinvsltsngvpevsFgYsid.ggvvtYDnvtinstgkasa..eilvngssltpsg.llyDaeLvlgGpgngekt 221
                                       + ++n+ +++ng+pev+ +Y+ d + ++tYD+ ++ +++++++  +++v+g++++p+g ++yDaeL+lgGpg+g++t
  gi|518653226|ref|YP_008142746.1| 220 NFMVNS-TMKNGSPEVELMYN-DgYRWMTYDSPVFIFATNVTSdqSFVVDGYNYEPDGySFYDAELILGGPGDGSST 294
                                       *****9.556***********.66**************9999999******************************** PP

                        Thermopsin 222 tfnslnatlsLyYlngtnyqpvknaydfGsdTaEtaenv 260
                                       +++s+n++l ++Y+ng+nyq+++na+++GsdTaE ++nv
  gi|518653226|ref|YP_008142746.1| 295 VDMSSNIQLGIEYWNGHNYQEITNAFNYGSDTAEIISNV 333
                                       *************************************98 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.059
                        Thermopsin 121 Gtvy......asskgefYyayateylelslPlt.lkLvinvsltsngvpevsFgYsid.......ggvvtYDnvtin 183
                                       Gt+       ++s +++Y +   + l++s+P++  ++ +n + +s  + ev+ +           +g++ Y n t+n
  gi|518653226|ref|YP_008142746.1| 344 GTIFenvtagDGSLSQVYSSADISLLNISTPFSsGSISVNGTEYSFVKHEVNLTLAPGeynlsiyNGTILYKNLTVN 420
                                       33333333334455589999999999999998636788888888777777877533224444477788888888887 PP

                        Thermopsin 184 stg 186
                                        t 
  gi|518653226|ref|YP_008142746.1| 421 LTA 423
                                       765 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.034
                        Thermopsin 134 ayateylelslPltlkLvinvsltsngvpevsFgYsid...ggvvtYDnvtinstgkasaeilvngssltps....g 203
                                       +++ +++ l   ++ +++in ++ s+  +++ F    d   ++v t D+++   +++ s  i+vng+s++       
  gi|518653226|ref|YP_008142746.1| 436 NISFTQTGLPAGTAWSVTINGKTESSDTNTIVFVLANDtytYMVETLDKIY--KAEHYSGDIIVNGYSYKSIikfsK 510
                                       455555556666788899***************999668888888888754..55566779********98766657 PP

                        Thermopsin 204 llyDaeLvlgGpgngekttfns 225
                                       + y++ ++  G  +g+  ++n 
  gi|518653226|ref|YP_008142746.1| 511 VTYEVKFIEVGLPGGSVWYVNL 532
                                       9999999999999999887764 PP

  == domain 4  score: -1.3 bits;  conditional E-value: 0.19
                        Thermopsin 164 vsFgYsidggvvtYDnvtinstgkasa...eilvngssltps...gllyDaeLvlgGpgng 218
                                        sF + + +g+ tY + + n + +       i+vng + + +     +y + +v  G   g
  gi|518653226|ref|YP_008142746.1| 544 NSFSFALINGTYTYRTSIANEPYEPVPsssGIVVNGGNISTTltfSRIYTVKFVENGLPAG 604
                                       3566666688888888888887765444568999998877663333455555555555555 PP

  == domain 5  score: -1.7 bits;  conditional E-value: 0.27
                        Thermopsin 151 vinvsltsngvpevsFgYsidggvvtYDnvtinstgkasa..eilvngssltpsg 203
                                       ++n ++  + ++++ F     +g+  Y    +n ++ + +  ++ vng+++t ++
  gi|518653226|ref|YP_008142746.1| 610 TLNGTTELSDNNTILFALH--NGTYAYTVSGVNGNKISGSsgNVDVNGKNVTVNN 662
                                       2333333333334444444..3444444444444444333345555565555555 PP

>> DUF1214  Protein of unknown function (DUF1214)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   3.8e-05      0.23      15      43 ..     428     462 ..     417     497 .. 0.74
   2 !    4.9   0.0    0.0059        35      15      54 ..     585     622 ..     580     653 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3.8e-05
                                       B-BTTSEEEEEE-SS.-S.EEEEEEEEEE......E CS
                           DUF1214  15 pldgsktYrltfpad.lPpaaafWSltly......d 43 
                                       pl+ + +Y ++f++  lP a + WS+t+       d
  gi|518653226|ref|YP_008142746.1| 428 PLNVAPKYNISFTQTgLP-AGTAWSVTINgktessD 462
                                       7888999********9*9.*********94333333 PP

  == domain 2  score: 4.9 bits;  conditional E-value: 0.0059
                                       B-BTTSEEEEEE-SS.-S.EEEEEEEEEEETTT-SB---TT CS
                           DUF1214  15 pldgsktYrltfpad.lPpaaafWSltlydaetrylvanpl 54 
                                        l+ s+ Y+++f ++ lP a + W +tl +  t  l +n+ 
  gi|518653226|ref|YP_008142746.1| 585 TLTFSRIYTVKFVENgLP-AGTTWLVTLNG--TTELSDNNT 622
                                       5777888********9*9.*********94..445666665 PP

>> FAP  Fibronectin-attachment protein (FAP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0    0.0018        11     182     245 ..     391     458 ..     382     467 .. 0.74
   2 ?    3.6   0.0    0.0065        39     220     252 ..     511     543 ..     504     554 .. 0.88
   3 ?   -2.9   0.0       0.6   3.6e+03     221     238 ..     591     608 ..     584     616 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0018
                               FAP 182 kaavrlasdmGeffmP.fPGtrinqe.tvplnanglt..GsasyyevkftdankPnGqiwagvvGepv 245
                                       k  v l+   Ge+ +  + Gt + ++ tv+l+a++     +a  y++ ft +  P+G  w+  +   +
  gi|518653226|ref|YP_008142746.1| 391 KHEVNLTLAPGEYNLSiYNGTILYKNlTVNLTAGEYLplNVAPKYNISFTQTGLPAGTAWSVTINGKT 458
                                       55666666778887754899988765489999988742379*******************98775444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.0065
                               FAP 220 syyevkftdankPnGqiwagvvGepvasgtdrG 252
                                         yevkf +   P G +w   + + v+sg+ +G
  gi|518653226|ref|YP_008142746.1| 511 VTYEVKFIEVGLPGGSVWYVNLSSTVKSGPITG 543
                                       56*****************99999999999888 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.6
                               FAP 221 yyevkftdankPnGqiwa 238
                                        y vkf ++  P+G  w 
  gi|518653226|ref|YP_008142746.1| 591 IYTVKFVENGLPAGTTWL 608
                                       699***********9995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (698 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 5094.04
//
Query:       gi|518653227|ref|YP_008142747.1|  [L=249]
Description: hypothetical protein FACI_IFERC00001G1870 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-19   69.5   0.1    7.6e-19   68.6   0.1    1.4  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.1   4.2e-23   7.6e-19       8     192 ..      32     203 ..      25     238 .. 0.77

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 4.2e-23
                            AbiEii   8 lsaladklvFkGGTaLslayglipRfSeDIDlsllrgdrkellealkealeeiaaalaeeglkvklaasigegedye 84 
                                       ++ +++ l+FkGGT L l++g + RfSeD+D+    ++++ l  +l + ++e   +l+ +g++++l+ +++   d+ 
  gi|518653227|ref|YP_008142747.1|  32 NAIYGEPLIFKGGTYLWLFHG-LRRFSEDLDF----TENSMLKGNLPDKVSE---NLKLQGINNELKIVKN---DNI 97 
                                       56899****************.**********....5777777777765554...5555555666666666...889 PP

                            AbiEii  85 glrlrypaef....ggyarqkikieigfreavppaerreippyleel..ggpafevpvysleellaeKllalldrgr 155
                                       +l++r+ +e     +  + +++ +ei+ re +    +  +   ++++    p   +  +++ e++aeK++a++    
  gi|518653227|ref|YP_008142747.1|  98 TLSFRLLSEGplytNILSMVPVYVEISRREKI---IKQAMALNFDFPeyNLPIRILSGMNVDEVAAEKVRAIY---- 167
                                       999999999888887777788999**9**888...6666666666665555667777799*************.... PP

                            AbiEii 156 drsraRDlyDlalLle.aeldaealaeallaylasrgr 192
                                        r++aRD+yDl++L+  +++  +   e+++ +l++++ 
  gi|518653227|ref|YP_008142747.1| 168 TRKKARDIYDLYYLIYfKKVIFDP--ELINMKLKFYNI 203
                                       **************9877777776..777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (249 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       541  (0.0301746); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.44
# Mc/sec: 1707.03
//
Query:       gi|518653228|ref|YP_008142748.1|  [L=191]
Description: hypothetical protein FACI_IFERC00001G1871 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1483.62
//
Query:       gi|518653229|ref|YP_008142749.1|  [L=264]
Description: hypothetical protein FACI_IFERC00001G1872 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-20   74.6   0.0    1.5e-20   74.2   0.0    1.1  1  AbiEii         Nucleotidyl transferase AbiEii toxin, Type IV 
  ------ inclusion threshold ------
      0.046   14.2   0.2      0.046   14.2   0.2    1.8  2  Phage_clamp_A  Bacteriophage clamp loader A subunit


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.0   1.6e-24   1.5e-20      14     200 ..      45     225 ..      37     256 .. 0.72

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.6e-24
                            AbiEii  14 klvFkGGTaLslayglipRfSeDIDlsllr.....gdrkellealkealeeiaaalaeeglkvklaasigegedyeg 85 
                                       +++F GGTa+s++yg +  fSeD+D+ +++        ++  +a++e+ + ++ + ++ +  + l+++++   +++ 
  gi|518653229|ref|YP_008142749.1|  45 DIIFIGGTAISKVYG-SGIFSEDLDFIFDKsydvyVVENRVKKAIDEINNFYSMEYVKSKRRDMLRYNLKI--KGPF 118
                                       689************.***********98784444444444444444444444444444444444444443..5555 PP

                            AbiEii  86 lrlrypaefggyarqkikieigfreav.ppaerreippyleelggpafevpvysleellaeKllalldrgrdrsr.. 159
                                       + +     ++ +a q+ik++i++  ++ + + ++  +++++el   ++ + +++ ee++aeK+ a++    +r++  
  gi|518653229|ref|YP_008142749.1| 119 YEM----SHSVRAIQTIKLDINLYVRPfYNPKKVLRTTIYQEL--RPYFLFTLDTEEFAAEKIKAIM----ERPTpv 185
                                       555....33888999************7777777777777777..**********************....555556 PP

                            AbiEii 160 aRDlyDlalLle.aeldaealaeallaylasrgrpgelrlap 200
                                       aRDlyDl+lL++  +++ +   ++++ +l+++ +   +++++
  gi|518653229|ref|YP_008142749.1| 186 ARDLYDLWLLITkYNVKINI--QMINYKLQKYTQVQGFNIDE 225
                                       ************88888877..77777777777755555555 PP

>> Phage_clamp_A  Bacteriophage clamp loader A subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.2   5.1e-06     0.046      19      61 ..      70     112 ..      56     119 .. 0.91
   2 ?   -2.8   0.1      0.88   7.9e+03      93     106 ..     197     211 ..     190     230 .. 0.56

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.1e-06
                                       SSSS---HHHHHHHHHTSTTTHHHHHHHHHTTTTS-HHHHHHH CS
                     Phage_clamp_A  19 iaqkdyskfmveralsqfietvvavyimdlvGsklsdeaqfdy 61 
                                       i +k y+ ++ve+ + + i+ + + y m+ v sk  d ++++ 
  gi|518653229|ref|YP_008142749.1|  70 IFDKSYDVYVVENRVKKAIDEINNFYSMEYVKSKRRDMLRYNL 112
                                       77899********************************999996 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 0.88
                                       HHCT--HH.HHHHHH CS
                     Phage_clamp_A  93 kryqvnkn.daidyk 106
                                        +y+v  n + i+yk
  gi|518653229|ref|YP_008142749.1| 197 TKYNVKINiQMINYK 211
                                       445544332345544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       844  (0.0470746); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); 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 0.23s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2085.35
//
Query:       gi|518653230|ref|YP_008142750.1|  [L=198]
Description: hypothetical protein FACI_IFERC00001G1873 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0061   16.9   0.0     0.0077   16.5   0.0    1.2  1  AbiEi_1   AbiEi antitoxin C-terminal domain


Domain annotation for each model (and alignments):
>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.3e-07    0.0077      14     110 ..      68     160 ..      56     175 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.3e-07
                           AbiEi_1  14 hlardyyagllsAawlhGaahrqpqriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeata 90 
                                        + +  y+g++sA  ++ +  +    i+v+ pk  k i+ +  r +f++ +n  ++    +  +++++ +s Pe  +
  gi|518653230|ref|YP_008142750.1|  68 NILEPSYIGISSAFSYYNLVTQIYDIIYVISPKRHKDIEIEGYRIKFITLKNT-KIYGYHI-DKNTYISISNPEKAI 142
                                       566789******************************************77776.4554555.7999*********** PP

                           AbiEi_1  91 vdlatrpsavggldnvlevL 110
                                       vd ++ ++  +++  ++e+L
  gi|518653230|ref|YP_008142750.1| 143 VDSVYLANPPISY--IEEAL 160
                                       *988766655555..55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 1492.87
//
Query:       gi|518653231|ref|YP_008142751.1|  [L=344]
Description: self-defense gene tcr3 related protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-26   93.1  39.1    1.8e-25   89.7  33.3    2.3  2  MFS_1          Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.12   12.0   1.0       0.28   10.7   1.0    1.6  1  Fzo_mitofusin  fzo-like conserved region
       0.18   11.9   3.9       0.71   10.0   0.1    2.9  2  CD225          Interferon-induced transmembrane protein


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 !   89.7  33.3   2.9e-29   1.8e-25     123     350 ..       2     268 ..       1     271 [. 0.88
   2 !    6.9   0.3   0.00044       2.6     126     181 ..     288     338 ..     277     344 .] 0.77

  Alignments for each domain:
  == domain 1  score: 89.7 bits;  conditional E-value: 2.9e-29
                             MFS_1 123 igllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepper.krkspkeee.......... 188
                                       +g+ ++g ++Ga+lg +lgg++++ +gWr++fyi+ +++++a+  ++ ++ ++ p r k + p              
  gi|518653231|ref|YP_008142751.1|   2 YGYTAVGHNVGAMLGIVLGGVITTFIGWRYIFYINVPIGIFAIYYAIKFINRSTPVRnKLDLPG--Mstlgvalisi 76 
                                       6778899***********************************8866666644444330333333..146******** PP

                             MFS_1 189 .................................kgtgpaplvpawkallkdpvlwillialllfffgfsglltllpl 232
                                                                        + ++ +pl+p +k ++ +   ++l+++++   +gf ++++ + +
  gi|518653231|ref|YP_008142751.1|  77 syagvnistsgittfnlalmgfgallillfiyiETKVAKPLLP-LKVFRIKILSYSLFASFFQS-LGFLAVVFIIIM 151
                                       ********************************99999999999.88888877333455555555.588889999999 PP

                             MFS_1 233 ylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllllvlvl 309
                                       ylq v+gls  + ++lll  ++++g +l++ +grl+dr+g+r++ +++ll ++ a + + l+ v s+  ++l+++ +
  gi|518653231|ref|YP_008142751.1| 152 YLQGVRGLS-PFDSALLLLPGYVIGSMLGPYFGRLADRIGSRIPATVGLLMMAGAIIVYSLITVNSTLYIVLVASGI 227
                                       *********.8******************************************************999999999999 PP

                             MFS_1 310 iGfglgfvfpsllalasdlappeeagtasglfntagslgga 350
                                        G+g++++fp+ +++++ + p+e  g+ sg+  t+ ++g++
  gi|518653231|ref|YP_008142751.1| 228 SGTGSSMFFPANNSAVMANSPKELYGMSSGFLRTLANIGML 268
                                       **************************************986 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00044
                             MFS_1 126 lsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkr 181
                                       + +++++G ++g +  ++++   g +++ y+  +++l+++ l   + + ++ +r+ 
  gi|518653231|ref|YP_008142751.1| 288 FEVFAGVGKLVGGVSTSFMS---GIHYSLYVSMAILLFGAFL--SFSRGKEERRSS 338
                                       78999**************9...9888888777777777554..666666665555 PP

>> Fzo_mitofusin  fzo-like conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.0   4.7e-05      0.28      21      62 ..      12      53 ..       3      57 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.7e-05
                     Fzo_mitofusin 21 tslgvlvvggvvlravgWrvialslalygllYlyErltwtnk 62
                                      +++  +v+ggv++  +gWr i    + +g++ +y  +++ n+
  gi|518653231|ref|YP_008142751.1| 12 GAMLGIVLGGVITTFIGWRYIFYINVPIGIFAIYYAIKFINR 53
                                      68899****************999998888888877776665 PP

>> CD225  Interferon-induced transmembrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.1   0.00012      0.71      14      31 ..      33      50 ..      15      62 .. 0.76
   2 ?    1.3   1.1     0.065   3.9e+02       8      27 ..     130     147 ..     126     151 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                             CD225 14 lfcclplGivAlvySvkv 31
                                      ++  +p+Gi A++y++k 
  gi|518653231|ref|YP_008142751.1| 33 FYINVPIGIFAIYYAIKF 50
                                      44789***********94 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.065
                             CD225   8 wsifntlfcclplGivAlvy 27 
                                       +s+f+ +f  l  G++A+v+
  gi|518653231|ref|YP_008142751.1| 130 YSLFASFFQSL--GFLAVVF 147
                                       79999999999..****998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (344 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      214  (0.011936); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2335.28
//
Query:       gi|518653232|ref|YP_008142752.1|  [L=463]
Description: transposase IS605 OrfB [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      7e-11   41.9   1.9    7.1e-11   41.9   0.1    1.9  2  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    2.6e-08   34.1   5.2    2.6e-08   34.1   5.2    2.0  2  OrfB_IS605      Probable transposase
    0.00061   20.1   1.1     0.0012   19.1   1.1    1.5  1  C1_2            C1 domain
  ------ inclusion threshold ------
      0.021   14.9   0.6      0.021   14.9   0.6    2.4  3  DUF1451         Zinc-ribbon containing domain
      0.075   12.6   2.4          4    7.0   3.0    2.8  2  TF_Zn_Ribbon    TFIIB zinc-binding
      0.083   12.9   0.1       0.22   11.5   0.1    1.7  1  HypA            Hydrogenase/urease nickel incorporation, meta
        0.1   12.3   1.4       0.21   11.3   1.4    1.6  1  DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
       0.28   10.8   1.6        9.5    5.9   0.0    2.5  2  RecR            RecR protein
       0.68    9.7   4.3        2.2    8.1   4.3    1.8  1  A2L_zn_ribbon   A2L zinc ribbon domain
          2    8.4   6.8          5    7.1   4.2    2.9  2  zinc_ribbon_4   zinc-ribbon domain
          6    6.7   6.6        9.6    6.1   1.1    2.5  2  zinc_ribbon_2   zinc-ribbon domain
        8.5    5.9   6.7        2.9    7.4   0.5    2.2  2  zf-ribbon_3     zinc-ribbon domain


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.2   6.3e+03       4      38 ..     243     272 ..     241     284 .. 0.51
   2 !   41.9   0.1   4.8e-14   7.1e-11      16      67 ..     339     391 ..     330     393 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.2
                    OrfB_Zn_ribbon   4 lkeqleykakeyGikveevnpayTSktCseCgskn 38 
                                       l++ l+ ka+     ++e +++  Sk+ s+  +kn
  gi|518653232|ref|YP_008142752.1| 243 LQRSLSRKAE-----YVEGSKNKLSKKQSKNYYKN 272
                                       5555555555.....44444444444444444444 PP

  == domain 2  score: 41.9 bits;  conditional E-value: 4.8e-14
                    OrfB_Zn_ribbon  16 Gikveevnpay.TSktCseCgsknkealsgrtfkCpnCgfeadrDvnAaiNil 67 
                                         ++++++++  T k+Cs+C  k + +l++r +kCpnCgf +drD+n+a+N++
  gi|518653232|ref|YP_008142752.1| 339 ASTLILIDRFIpTTKECSNCHNKYNIKLDERIYKCPNCGFIIDRDYNSALNMI 391
                                       447889999999********9999889************************86 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0       2.2   3.3e+03      51      78 ..      63      93 ..      46     115 .. 0.58
   2 !   34.1   5.2   1.7e-11   2.6e-08      10     105 ..     203     304 ..     186     312 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 2.2
                        OrfB_IS605 51 kylakeiaelqsklkkskny...kkasrkla 78
                                      k++++ i +++sk+k  + y   ++ +r+l+
  gi|518653232|ref|YP_008142752.1| 63 KEFNNDIFNIDSKIKNVNVYvkdHYETRELK 93
                                      4555555555555555544311122333333 PP

  == domain 2  score: 34.1 bits;  conditional E-value: 1.7e-11
                        OrfB_IS605  10 lpkpkgnkaagiDlGinnLatvvtedgtw.flykgrrlksdykylakeiaelqsk.....lkksknykkasrklarl 80 
                                       +++++++k ++ DlGi+n +t++++      ++k+++ k+ +++l+++   ++       +k+skny k +++l r 
  gi|518653232|ref|YP_008142752.1| 203 EKPVNNQKILSFDLGIKNQLTCSNGLILNyNIPKSKKEKRLQRSLSRKAEYVEGSknklsKKQSKNYYKNKNRLNRE 279
                                       6788999*****************974334888888888888888888776653211111456777*********** PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlke 105
                                        ++ +++rk+ ++k++++l+ +++ 
  gi|518653232|ref|YP_008142752.1| 280 QDRTKNKRKDTINKITHYLTSNYDI 304
                                       *******************999875 PP

>> C1_2  C1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   1.1   7.9e-07    0.0012       3      44 ..     337     382 ..     335     383 .. 0.83

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.9e-07
                              C1_2   3 Hp.HpLtlskgedssesfnCsaCgrk....idgff..YsCseCdfslhv 44 
                                       H+  +L+l  ++    +++Cs C +k     d  +  Y+C+ C f+++ 
  gi|518653232|ref|YP_008142752.1| 337 HKaSTLILI-DRFIPTTKECSNCHNKynikLD--EriYKCPNCGFIIDR 382
                                       777789999.999999**********885443..246*********995 PP

>> DUF1451  Zinc-ribbon containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.2      0.89   1.3e+03      43      76 ..     243     276 ..     237     308 .. 0.62
   2 ?   -0.7   0.1      0.88   1.3e+03      23      74 ..     278     325 ..     254     334 .. 0.56
   3 ?   14.9   0.6   1.4e-05     0.021     112     139 ..     350     377 ..     346     379 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.89
                           DUF1451  43 lkrDleeaarsleeskeeleewlsldlelieesl 76 
                                       l+r l+  a+++e sk++l++++s ++   +++l
  gi|518653232|ref|YP_008142752.1| 243 LQRSLSRKAEYVEGSKNKLSKKQSKNYYKNKNRL 276
                                       5666666666666666666666665555444444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.88
                           DUF1451  23 eklseaeeltkeelelvaeylkrDleeaarsleeskeeleewlsldleliee 74 
                                       ++ + +++  k+ ++++++yl        + + +++++++ w++l+ + ie+
  gi|518653232|ref|YP_008142752.1| 278 REQDRTKNKRKDTINKITHYLTSNY----DIVVTQNDNISGWQRLFGKKIES 325
                                       3334444445566666666665443....33333333455577766666665 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1.4e-05
                           DUF1451 112 lGtlvCekCgkelalkkteeippCpkCg 139
                                       + t +C +C+++ ++k  e+i +Cp+Cg
  gi|518653232|ref|YP_008142752.1| 350 PTTKECSNCHNKYNIKLDERIYKCPNCG 377
                                       66789**********************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 ?    1.2   0.0      0.17   2.6e+02      21      41 ..     223     242 ..     219     242 .. 0.84
   2 ?    7.0   3.0    0.0026         4       3      34 ..     355     385 ..     354     388 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.17
                                       EESSSSBEEEECCCCCCCHHH CS
                      TF_Zn_Ribbon  21 vCtdCGlVlednsidegpewr 41 
                                       +C++ Gl+l +n+ ++++e+r
  gi|518653232|ref|YP_008142752.1| 223 TCSN-GLILNYNIPKSKKEKR 242
                                       5555.9*************98 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0026
                                       ETTTTCEE.CHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   3 CPnCgstn.lveDpergelvCtdCGlVlednsi 34 
                                       C nC++++ + +D+    + C++CG +++ +++
  gi|518653232|ref|YP_008142752.1| 355 CSNCHNKYnIKLDER--IYKCPNCGFIIDRDYN 385
                                       999999888999977..8889999988887665 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   0.1   0.00015      0.22      67      93 ..     349     377 ..     333     382 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00015
                                       E--EEEETTTS-EEECHHH..HHS-TTTS CS
                              HypA  67 vpvkvrCreCgkefeleek..alrCpkCg 93 
                                       +p + +C++C+++++++ +   ++Cp+Cg
  gi|518653232|ref|YP_008142752.1| 349 IPTTKECSNCHNKYNIKLDerIYKCPNCG 377
                                       688899********977643578*****8 PP

>> DNA_RNApol_7kD  DNA directed RNA polymerase, 7 kDa subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.4   0.00014      0.21       3      25 ..     355     378 ..     354     380 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00014
                                       -SSS--B----SSS--.--SSS-- CS
                    DNA_RNApol_7kD   3 CgeCgaevslkkgdpi.RCkeCGh 25 
                                       C +C+++  +k  + i +C +CG+
  gi|518653232|ref|YP_008142752.1| 355 CSNCHNKYNIKLDERIyKCPNCGF 378
                                       **************9989*****8 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.3      0.04        60      16      24 ..     352     360 ..     346     361 .. 0.90
   2 ?    5.9   0.0    0.0063       9.5      12      29 ..     366     383 ..     364     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.04
                                       -EE-TTT-- CS
                              RecR  16 vrhCsrCgn 24 
                                        + Cs+C+n
  gi|518653232|ref|YP_008142752.1| 352 TKECSNCHN 360
                                       689*****9 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0063
                                       HHHH-EE-TTT--EESSS CS
                              RecR  12 akekvrhCsrCgnlteed 29 
                                       + e++  C++Cg + ++d
  gi|518653232|ref|YP_008142752.1| 366 LDERIYKCPNCGFIIDRD 383
                                       678999*******98887 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 ?    8.1   4.3    0.0014       2.2       4      30 ..     353     379 ..     352     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0014
                     A2L_zn_ribbon   4 kvCsvCggngilnseqgylvCieCgas 30 
                                       k+Cs+C++   +  +  ++ C++Cg++
  gi|518653232|ref|YP_008142752.1| 353 KECSNCHNKYNIKLDERIYKCPNCGFI 379
                                       78*******9999************97 PP

>> zinc_ribbon_4  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0         6     9e+03      14      25 ..      33      44 ..      32      45 .. 0.82
   2 ?    7.1   4.2    0.0033         5       4      35 ..     354     380 ..     354     381 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6
                     zinc_ribbon_4 14 iddeklpakgvk 25
                                      id++kl  ++ k
  gi|518653232|ref|YP_008142752.1| 33 IDNDKLNNNTIK 44
                                      999**9998877 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0033
                     zinc_ribbon_4   4 tCpsCkakyeiddeklpakgvkvrCskCghvF 35 
                                       +C +C+ ky+i  +      +  +C++Cg ++
  gi|518653232|ref|YP_008142752.1| 354 ECSNCHNKYNIKLD-----ERIYKCPNCGFII 380
                                       6**********874.....6788999999765 PP

>> zinc_ribbon_2  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   6.7     0.091   1.4e+02       2      21 ..     355     378 ..     354     380 .. 0.72
   2 ?    6.1   1.1    0.0064       9.6       1       7 [.     372     378 ..     372     385 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.091
                     zinc_ribbon_2   2 CpnCGaelq.d.nakF..CpyCGt 21 
                                       C+nC+++   + +++   Cp+CG+
  gi|518653232|ref|YP_008142752.1| 355 CSNCHNKYNiKlDERIykCPNCGF 378
                                       888888875555666678888885 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0064
                     zinc_ribbon_2   1 fCpnCGa 7  
                                       +CpnCG 
  gi|518653232|ref|YP_008142752.1| 372 KCPNCGF 378
                                       7999996 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   7.5      0.22   3.3e+02       3      23 ..     353     377 ..     351     378 .. 0.56
   2 ?    7.4   0.5    0.0019       2.9       4      14 ..     372     382 ..     369     385 .. 0.74

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.22
                       zf-ribbon_3   3 vrCPnCGa..p..lssddnvCpyCG 23 
                                       ++C+nC +  +  l+++  +Cp+CG
  gi|518653232|ref|YP_008142752.1| 353 KECSNCHNkyNikLDERIYKCPNCG 377
                                       6777774334323445555688888 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0019
                       zf-ribbon_3   4 rCPnCGaplss 14 
                                       +CPnCG +++ 
  gi|518653232|ref|YP_008142752.1| 372 KCPNCGFIIDR 382
                                       79999976565 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2309  (0.128786); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        92  (0.00513135); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3144.52
//
Query:       gi|518653233|ref|YP_008142753.1|  [L=103]
Description: multidrug efflux permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00033   19.7   4.4    0.00042   19.4   4.4    1.1  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 !   19.4   4.4   2.3e-08   0.00042       3      72 ..      12      82 ..      10      85 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 2.3e-08
                             MFS_1  3 laaflsalarsilgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllf 72
                                      l+a+l+++  s ++++l+l +++++l  + s    ++ +y l+ av++  lGrl+d + r+ +++ g+++f
  gi|518653233|ref|YP_008142753.1| 12 LLAVLMGAVDSSTIVLLSLpTITDSLKTQLSLSICIILIYLLVIAVGTTQLGRLGDILARKNIFISGIAIF 82
                                      44455555555555555555*******555555559999*******************7777******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       872  (0.0486363); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.28s 00:00:00.71 Elapsed: 00:00:00.45
# Mc/sec: 689.26
//
Query:       gi|518653234|ref|YP_008142754.1|  [L=168]
Description: transcriptional regulator [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      484  (0.0269954); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.44
# Mc/sec: 1149.03
//
Query:       gi|518653235|ref|YP_008142755.1|  [L=165]
Description: hypothetical protein FACI_IFERC00001G1878 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00034   20.6   0.0    0.00038   20.5   0.0    1.2  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.1e-08   0.00038     117     171 ..      60     109 ..      10     133 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.1e-08
                            AbiEii 117 rreippyleelggpafevpvysleellaeKllalldrgrdrsraRDlyDlalLle 171
                                       + ei+ y + + g + ++ v+s+ el+  K+ a       r  +RD+yDl+ L +
  gi|518653235|ref|YP_008142755.1|  60 ENEIRAYSRVD-GSVKTISVLSATELMSRKIEAYQ----SRGFVRDIYDLYVLTN 109
                                       34444444444.67889****************99....************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       447  (0.0249317); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.29s 00:00:00.70 Elapsed: 00:00:00.44
# Mc/sec: 1126.26
//
Query:       gi|518653236|ref|YP_008142756.1|  [L=298]
Description: TENA/THI-4 protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-38  132.3   0.9    2.7e-38  131.9   0.9    1.1  1  TENA_THI-4       TENA/THI-4/PQQC family
    6.8e-17   61.1   1.4    1.7e-16   59.8   0.0    2.4  3  zf-C2H2_9        C2H2 type zinc-finger (1 copy)
    4.6e-15   55.9   0.1    1.2e-14   54.5   0.1    1.6  2  Haem_oxygenas_2  Iron-containing redox enzyme


Domain annotation for each model (and alignments):
>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.9   0.9   4.5e-42   2.7e-38      13     206 ..      82     285 ..      70     289 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.9 bits;  conditional E-value: 4.5e-42
                                       C..SHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-S.SHHHHHHHHHHHHHHHHCH....HHHHHHH CS
                        TENA_THI-4  13 n..HpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskss.dlevrrelesrivdhdgee....ielhlrl 82 
                                       n  HpF++++++ +  +  +q+y++++y++lk++vr++++i sk++ +   ++e+e+  +++ g+     iel+l +
  gi|518653236|ref|YP_008142756.1|  82 NnpHPFIIKMQDYN--KYILQGYAVEHYFFLKQWVRSCSAIISKTDyNDVQTYEMENMVTEYFGNGkkphIELLLDM 156
                                       457*********88..9**********************77777653677789***********9999********* PP

                                       HHHTT-HHHHHCTTT--HHHHHHHHHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHH.....S-TSCHHHHH CS
                        TENA_THI-4  83 aealGlsreelsktkpspatkayvrylldlarrgslaeavaallpclfvyqeiaerlkeklr.....alegpeyyew 154
                                       ae +G+sr+++++tkp+  t+++++ + ++a+   + e++aa++++++ ++++++ ++  +      a++++  +e+
  gi|518653236|ref|YP_008142756.1| 157 AEGFGISRKKIMETKPLKNTENAINRWREIAQNNGWIEIMAAMHSLELIANSALRPYGARYDyfnlgAFDNNNVPET 233
                                       **********************************************************9999*************** PP

                                       HHHHCSHHHHHHHHHHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHHH CS
                        TENA_THI-4 155 vkeyaseefraaveeakrllerllakvsdeqleelqeiflkalefetsfltm 206
                                       vk +++e++ ++ ++ +++l+++ ++++d  +e +q+ +l +++ ++++l +
  gi|518653236|ref|YP_008142756.1| 234 VKAFLMEGYHSDNAHSIEALNIIEKYSRDYNIENIQDAYLASTYVFYNYLEA 285
                                       **************************************************54 PP

>> zf-C2H2_9  C2H2 type zinc-finger (1 copy)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.0   2.9e-20   1.7e-16       1      58 [.       1      60 [.       1      61 [. 0.94
   2 ?   -2.2   0.1      0.66   3.9e+03      36      44 ..      72      80 ..      69      82 .. 0.76
   3 ?   -3.4   0.0       1.5   9.1e+03      21      32 ..     237     248 ..     230     250 .. 0.82

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 2.9e-20
                                      --B-TTT--B-S..SHHHHHHHHHHHTSSS--HHHHHHHHHT-SS---HHHHHHHHHHHH CS
                         zf-C2H2_9  1 mplCPvCevkfn..swkdlseHilsaasksdaeHvmWLNRniskkrlskdELekklekff 58
                                      m +CPvC++kf   ++  lseH++ +a+ sd+ HvmWLNRn+ k + +k  Le  +++++
  gi|518653236|ref|YP_008142756.1|  1 MAICPVCNLKFGnnDFLALSEHFIGKAKDSDPLHVMWLNRNLTKTKADKKGLEPLFRNLY 60
                                      89*********66799**********************************9999999887 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.66
                                      HHHHT-SS- CS
                         zf-C2H2_9 36 LNRniskkr 44
                                      +NR++s+ r
  gi|518653236|ref|YP_008142756.1| 72 INRFVSEYR 80
                                      5****9865 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 1.5
                                       HHHHTSSS--HH CS
                         zf-C2H2_9  21 ilsaasksdaeH 32 
                                       +l++  +sd++H
  gi|518653236|ref|YP_008142756.1| 237 FLMEGYHSDNAH 248
                                       678888999999 PP

>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       0.5     3e+03       8      40 ..      23      61 ..      19      68 .. 0.58
   2 !   54.5   0.1     2e-18   1.2e-14       2     159 ..     101     263 ..     100     279 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.5
                   Haem_oxygenas_2  8 apyklvfgdwl..alvhsrlt....drevkrallenlsE 40
                                      ++ k ++ d+l  +++ ++lt    d +    l++nl++
  gi|518653236|ref|YP_008142756.1| 23 FIGKAKDSDPLhvMWLNRNLTktkaDKKGLEPLFRNLYD 61
                                      555566666655577777777555544445556666666 PP

  == domain 2  score: 54.5 bits;  conditional E-value: 2e-18
                   Haem_oxygenas_2   2 eflrqrapyklvfgdwlalvhsrltdrevkrallenls.EElGdgdlernHvelyrrllkalGldeeplealpelpe 77 
                                        ++ +++++ +++++  ++++s++++++v+ + +en+  E +G+g+  + H el+ ++++++G++++ +  +++l++
  gi|518653236|ref|YP_008142756.1| 101 GYAVEHYFFLKQWVRSCSAIISKTDYNDVQTYEMENMVtEYFGNGK--KPHIELLLDMAEGFGISRKKIMETKPLKN 175
                                       6999**********************************99999888..99*************************** PP

                   Haem_oxygenas_2  78 tlalinlfeavalsrrllgallGallalEllvsletlklaee........lrelgldeeapeyfdlHvtiDnaHaam 146
                                       t ++in ++++a ++ ++ ++++a++ lEl +++ ++++ +         + + +++e+   ++ +  + DnaH+ +
  gi|518653236|ref|YP_008142756.1| 176 TENAINRWREIAQNNGWI-EIMAAMHSLELIANSALRPYGARydyfnlgaFDNNNVPETVKAFLMEGYHSDNAHSIE 251
                                       ******************.479**********8888888888888998888889999999999999999******** PP

                   Haem_oxygenas_2 147 aleaviellatee 159
                                       al ++ie++  + 
  gi|518653236|ref|YP_008142756.1| 252 AL-NIIEKYSRDY 263
                                       **.9999987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      460  (0.0256568); 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: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2042.66
//
Query:       gi|518653237|ref|YP_008142757.1|  [L=70]
Description: hypothetical protein FACI_IFERC00001G1880 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-22   77.5   0.6    8.6e-22   77.4   0.6    1.0  1  Ta0938    Ta0938


Domain annotation for each model (and alignments):
>> Ta0938  Ta0938
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.6   4.8e-26   8.6e-22      36     104 ..       1      69 [.       1      70 [] 0.97

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 4.8e-26
                                       BSSS--SSSS-TTS-THHHHHHHHHHHS---EE---TTT-S--EEEE-----TT-SS-----HHHHHTT CS
                            Ta0938  36 lffccdicakefvnllnevkkrtglskideleingnyykgrnveaksgekelkfyvkfnddaeieefke 104
                                       +ffcc+ica  +  +ln+vk +tg++kid+le++gny++gr+++aksg++e+k+y +   d+ + e+k+
  gi|518653237|ref|YP_008142757.1|   1 MFFCCNICADILEGMLNKVKDETGWNKIDYLELHGNYSSGRTCTAKSGNEEFKYYYRTYGDGRVMEYKK 69 
                                       6********************************************************999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      324  (0.0180713); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 481.40
//
Query:       gi|518653238|ref|YP_008142758.1|  [L=445]
Description: hypothetical protein FACI_IFERC00001G1881 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.9e-20   73.9   1.6    3.1e-18   66.6   1.6    2.3  1  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    3.4e-14   53.4  34.0      1e-11   45.2  34.0    2.9  1  AAA_15      AAA ATPase domain
    1.4e-09   37.7   8.6    5.7e-09   35.7   3.8    2.3  2  SMC_N       RecF/RecN/SMC N terminal domain
      4e-08   34.0   6.3    7.1e-08   33.2   6.3    1.4  1  AAA_23      AAA domain
    9.2e-05   21.9   1.6      0.068   12.4   0.0    2.2  2  DUF2813     Protein of unknown function (DUF2813)
    0.00015   22.1   0.3        0.8   10.0   0.1    3.2  3  AAA_22      AAA domain
    0.00066   20.2   0.1      0.023   15.2   0.0    2.5  3  ABC_tran    ABC transporter
     0.0021   17.8   0.0     0.0062   16.2   0.0    1.8  1  AAA_29      P-loop containing region of AAA domain
  ------ inclusion threshold ------
       0.13   11.5   0.0       0.49    9.6   0.0    1.9  2  Zeta_toxin  Zeta toxin
       0.14   11.8   0.0        4.9    6.8   0.0    2.6  3  AAA_30      AAA domain


Domain annotation for each model (and alignments):
>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   1.6   1.7e-21   3.1e-18       2     302 ..      27     394 ..      26     395 .. 0.83

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.7e-21
                            AAA_21   2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqgvryryglrl 78 
                                        v++G+NgsGK+n+++a+ +    ++ ++   +++s++ +++++++l  + ++e+p+ f+++ f  +g +  y++++
  gi|518653238|ref|YP_008142758.1|  27 IVMVGKNGSGKTNIIEAINF----NKVLFKPEPIKSPFTKWWGYSNLVYNHNIEEPISFSFN-FTVDGHKLFYEYDI 98 
                                       799***************99....99************************************.99999999999999 PP

                            AAA_21  79 ersqveeklssvetllesgllldkrsleeedvfnpeargirggvsvfslkelsvsepndlqfgkaltditsrawsll 155
                                        +++                                       + +f + ++ ++++ d  ++   ++i++  + ++
  gi|518653238|ref|YP_008142758.1|  99 MDNNG--------------------------------------LPNFISEHIVIENYVDILREGSKVEIKHLDNAIE 137
                                       99998......................................3444444444444444444444444444444444 PP

                            AAA_21 156 llldglrkerigllnifadyfgfakekrllqrlvrslklveielsdlgegeeliasvderlrer............. 219
                                       +l+      ++g+ ++ +    +   k   +++++ ++++ + +s++++g+ ++a  +  +r +             
  gi|518653238|ref|YP_008142758.1| 138 KLSKT----DFGNIQYLNIDEAEIFSKIKKTQYINDISTNQSIISMTLVGSSMNAGGSGISRLNinrnmgtqnffdm 210
                                       44433....77777777777777777777777777777777777777777777777777777777777777788888 PP

                            AAA_21 220 ............................................................................. 219
                                                                                                                    
  gi|518653238|ref|YP_008142758.1| 211 knyiivaspilkpdnknmynnladfvffsglrnifnniiaagpidykaiknrvpvagpslisedgsglvrmlyqyfl 287
                                       88888888888888888888888888888889999999999999999999999999********************* PP

                            AAA_21 220 ..............................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEp 266
                                                                     +v+++++ +++ + + +l+ G+ +l  +++ l+++ +   ll+iDE+
  gi|518653238|ref|YP_008142758.1| 288 knrslpelvengiktffpgwelnfeampdgTVTLVVKYGDGYFYPPNLPLGFYKL-IMVLELIEQKP--ELLIIDEI 361
                                       *******************************************************.99999999887..9******* PP

                            AAA_21 267 EngLHPkllrrllellkelsrngaQviltTHSplll 302
                                       En+ H k+++ +l+ +   s++g++ i++THSp ++
  gi|518653238|ref|YP_008142758.1| 362 ENSFHEKMIEYILDAI---SARGIKTIISTHSPMVV 394
                                       *************999...7779*********9776 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2  34.0   5.8e-15     1e-11       3     369 .]       5     394 ..       4     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 5.8e-15
                            AAA_15   3 IkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikI 79 
                                       Ikki+ikNF+s+k++++++++ l v +GkN+sGK++i+ea++ F +                         +k+  I
  gi|518653238|ref|YP_008142758.1|   5 IKKIIIKNFKSIKNITLNIND-LIVMVGKNGSGKTNIIEAIN-FNK-----------------------VLFKPEPI 56 
                                       9********************.*******************3.333.......................23333333 PP

                            AAA_15  80 dvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkelpkekeekle 156
                                       +  f   +k+  y  + ++ +++++        s   ++  d +  +++++++d++   + + +   ++++ +  +e
  gi|518653238|ref|YP_008142758.1|  57 KSPF---TKWWGYSNLVYNHNIEEPI-------SFSFNFTVDGHKLFYEYDIMDNNGLPNFISEHIVIENYVDILRE 123
                                       3333...2222222333322222222.......3333566688888999999999999999999999999******* PP

                            AAA_15 157 kekeelkidkedlkklikkleeslkkee....elknvlksaiiklllisakRnvsdedsekkssllgklkekileea 229
                                        +k e+k+ ++ ++kl+k+   ++++      e+++++k+ ++  ++  ++  +s ++  ++ ++ g+ +++++ + 
  gi|518653238|ref|YP_008142758.1| 124 GSKVEIKHLDNAIEKLSKTDFGNIQYLNideaEIFSKIKKTQYINDISTNQSIISMTLVGSSMNAGGSGISRLNIN- 199
                                       ******************9999998888888999999999999999999999999999999999999999999998. PP

                            AAA_15 230 lqekleeelteklkeiqeklkeidkklaeelk................kilkkkidkik.kfnykgkkneeieik.. 287
                                            + + t+++ ++++ +  ++ +l+ + k                +i++++i     + ++          k  
  gi|518653238|ref|YP_008142758.1| 200 -----RNMGTQNFFDMKNYIIVASPILKPDNKnmynnladfvffsglrNIFNNIIAAGPiDYKAI---------Knr 262
                                       .....778888888888888888888888777777666666667777644444444432222222.........133 PP

                            AAA_15 288 .....................................................ddeelplnknGsGv..qrllllil 309
                                                                                            d++ + + k G+G+     l+l +
  gi|518653238|ref|YP_008142758.1| 263 vpvagpslisedgsglvrmlyqyflknrslpelvengiktffpgwelnfeampDGTVTLVVKYGDGYfyPPNLPLGF 339
                                       33344557777777777777777777777777**********99999999999999999999999973334566666 PP

                            AAA_15 310 lileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSphii 369
                                        +l +     +e+k+ +l+i+E+E++ H      +i++++++++    ++ii+THSp ++
  gi|518653238|ref|YP_008142758.1| 340 YKLIMVLE-LIEQKPELLIIDEIENSFHE----KMIEYILDAISARGIKTIISTHSPMVV 394
                                       55555555.6899***************5....679999999988888*********886 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   3.8   3.2e-12   5.7e-09       2      46 ..       5      46 ..       4      50 .. 0.94
   2 ?    4.3   0.2     0.013        23     149     218 ..     342     412 ..     336     414 .. 0.79

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 3.2e-12
                                      EEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHH CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  2 lkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilF 46
                                      +k+++i+nFks+  k+++l++++ + ++vG+NGSGK+n+++Ai F
  gi|518653238|ref|YP_008142758.1|  5 IKKIIIKNFKSI--KNITLNIND-LIVMVGKNGSGKTNIIEAINF 46
                                      89**********..799999998.8999***************99 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.013
                                       HHHHHHCCS--S.EEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-..SCEEEEEEEETTE CS
                                       xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxx RF
                             SMC_N 149 LlfAiqkvkpap.lyllDeidaaLDeknvkkvaellkeksknaQfivislreemleka..dklvgvtkvengv 218
                                       L++ ++ ++++p l ++Dei+    ek ++ + + + ++      i+ +++  ++  +  ++++ v++v+n++
  gi|518653238|ref|YP_008142758.1| 342 LIMVLELIEQKPeLLIIDEIENSFHEKMIEYILDAISARG--IKTIISTHSPMVVDLVdlKNILIVKMVNNQT 412
                                       4555555555554889*********************999..9999999999988877556777777777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   6.3     4e-11   7.1e-08       1     157 [.       7     169 ..       7     209 .. 0.62

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4e-11
                            AAA_23   1 kLkienfrsfrdqeidFskgltlItGpNGaGKTTildAikl..aLygetprlsrks.....grgfeksdve....ie 66 
                                       k+ i+nf+s+++ +++ +  l + +G+NG+GKT i++Ai +  +L+   p  s+       ++   ++ +e    ++
  gi|518653238|ref|YP_008142758.1|   7 KIIIKNFKSIKNITLNIN-DLIVMVGKNGSGKTNIIEAINFnkVLFKPEPIKSPFTkwwgySNLVYNHNIEepisFS 82 
                                       799**************9.899*******************667887555544444898873333344444332244 PP

                            AAA_23  67 se...gkvkayveltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskkiilnlilflgq 140
                                       ++   +  k ++e ++ +++g    ++    e +  ++      +++++ei+ l++ i++l + +   + +i++l  
  gi|518653238|ref|YP_008142758.1|  83 FNftvDGHKLFYEYDIMDNNGLP--NF--ISEHIVIENYVDILREGSKVEIKHLDNAIEKLSKTD---FGNIQYLNI 152
                                       44555333455777766666632..22..222222222333444556666666666666654433...333333333 PP

                            AAA_23 141 erfeefelkdkkerlee 157
                                       +++e f++ +k + +++
  gi|518653238|ref|YP_008142758.1| 153 DEAEIFSKIKKTQYIND 169
                                       33333333333333333 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0   3.8e-05     0.068       4      43 ..       6      45 ..       3      88 .. 0.90
   2 !    8.4   0.3   0.00062       1.1     286     344 ..     355     415 ..     345     427 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 3.8e-05
                           DUF2813  4 erieisGFRGinrLSlsleentvLiGENaWGKSSLldALs 43
                                      ++i i+ F+ i+ + l+++++ v++G N  GK  +++A+ 
  gi|518653238|ref|YP_008142758.1|  6 KKIIIKNFKSIKNITLNINDLIVMVGKNGSGKTNIIEAIN 45
                                      78999********************************985 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.00062
                           DUF2813 286 illlEdpearLHPtmlaiaWellellPlQkiltTNSveLlsqvplesi..rrLvResdrtq 344
                                       +l+++++e+  H +m+  + + ++   ++ i++T S   + +v+l++i   ++v ++ +++
  gi|518653238|ref|YP_008142758.1| 355 LLIIDEIENSFHEKMIEYILDAISARGIKTIISTHSPMVVDLVDLKNIliVKMVNNQTKVE 415
                                       8999******************************************972256776666665 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.073   1.3e+02       7      24 ..      26      43 ..      24      50 .. 0.85
   2 ?    5.4   0.0     0.012        21      74     130 ..     128     184 ..     104     188 .. 0.77
   3 !   10.0   0.1   0.00045       0.8      89     126 ..     351     385 ..     339     391 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.073
                            AAA_22  7 ilvvtGesGtGKTtllrr 24
                                      ++v +G  G+GKT  ++ 
  gi|518653238|ref|YP_008142758.1| 26 LIVMVGKNGSGKTNIIEA 43
                                      6899*********88765 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.012
                            AAA_22  74 sseellealeqalrarav.ielliiDEaqhlrs.eealeeLrsllnlsrkgvqliLvGt 130
                                       + ++l +a+e+ +++ +  i+ l iDEa+ + s  +  +++ +++  +++ +++ LvG 
  gi|518653238|ref|YP_008142758.1| 128 EIKHLDNAIEKLSKTDFGnIQYLNIDEAEIF-SkIKKTQYINDIST-NQSIISMTLVGS 184
                                       55677777777777777799**********9.55777777766665.699999999996 PP

  == domain 3  score: 10.0 bits;  conditional E-value: 0.00045
                            AAA_22  89 ravielliiDEaqh.lrseealeeLrsllnlsrkgvqli 126
                                       ++  elliiDE+++ + +e+++e++ +       g++ i
  gi|518653238|ref|YP_008142758.1| 351 QKP-ELLIIDEIENsF-HEKMIEYILDAIS--ARGIKTI 385
                                       344.8*********88.*******965544..5665555 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.3e-05     0.023       6      32 ..      19      45 ..      16      65 .. 0.88
   2 ?   -2.7   0.0       4.2   7.5e+03      29      37 ..     134     142 ..      71     174 .. 0.66
   3 ?    2.1   0.0      0.15   2.6e+02     111     135 ..     337     361 ..     323     363 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                                      EEEETTSEEEEEESTTSSHHHHHHHHT CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  6 lklkegekvaivGenGaGKStLlklla 32
                                      ++l+ + ++++vG+nG+GK+ +++++ 
  gi|518653238|ref|YP_008142758.1| 19 ITLNINDLIVMVGKNGSGKTNIIEAIN 45
                                      56667789***************9995 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 4.2
                                       HHHTTSS-- CS
                                       xxxxxxxxx RF
                          ABC_tran  29 kllagllkp 37 
                                       +++ +l+k 
  gi|518653238|ref|YP_008142758.1| 134 NAIEKLSKT 142
                                       233333333 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.15
                                       HHHHHHHHHHHHHHHTSSEEEEEST CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 111 gGqkqrvalarallkkpkllllDEp 135
                                        G  + +++ +++ +kp+ll++DE 
  gi|518653238|ref|YP_008142758.1| 337 LGFYKLIMVLELIEQKPELLIIDEI 361
                                       56667888999999*********95 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   3.5e-06    0.0062      12      43 ..      13      45 ..       5      59 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 3.5e-06
                            AAA_29 12 fdg.htieidlkgatlltGpsGsGKSTllDAiq 43
                                      f+  + i+++ ++ ++++G++GsGK+ ++ Ai+
  gi|518653238|ref|YP_008142758.1| 13 FKSiKNITLNINDLIVMVGKNGSGKTNIIEAIN 45
                                      555566677777999****************96 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0   0.00028      0.49      17      36 ..      25      44 ..      13      48 .. 0.89
   2 ?   -2.2   0.0       1.2   2.1e+03      61      95 ..     256     290 ..     255     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00028
                        Zeta_toxin 17 klillgGqpGAGKselaell 36
                                      +li+++G  G+GK++++e++
  gi|518653238|ref|YP_008142758.1| 25 DLIVMVGKNGSGKTNIIEAI 44
                                      689**************987 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
                        Zeta_toxin  61 yeeilkadpkkaseltqkdaselvekllqeaieng 95 
                                       y++i +  p    +l+++d s lv++l q+ ++n+
  gi|518653238|ref|YP_008142758.1| 256 YKAIKNRVPVAGPSLISEDGSGLVRMLYQYFLKNR 290
                                       77777777888889999*************99987 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0    0.0027       4.9      11      38 ..      17      44 ..      14      48 .. 0.82
   2 ?   -1.7   0.0       1.1     2e+03      64     114 ..     123     172 ..     117     184 .. 0.65
   3 ?    1.5   0.0      0.12   2.1e+02      87     120 ..     350     385 ..     335     388 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0027
                            AAA_30 11 ealltsgdrvavltGpAGtGKttalkal 38
                                      ++++ + + + v++G  G+GKt +++a+
  gi|518653238|ref|YP_008142758.1| 17 KNITLNINDLIVMVGKNGSGKTNIIEAI 44
                                      55666667799**************998 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 1.1
                            AAA_30  64 eelgieastiakllkrlkgrarlepgtllivDEagmvdtkqlaallkaaek 114
                                       e++ +e + +++ +++l + +++ + + l +DEa   +  + ++ ++ +++
  gi|518653238|ref|YP_008142758.1| 123 EGSKVEIKHLDNAIEKLSK-TDFGNIQYLNIDEAEIFSKIKKTQYINDIST 172
                                       5555555555555555554.5667778999999999888777777766665 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.12
                            AAA_30  87 epg.tllivDEagmv.dtkqlaallkaaekagakvi 120
                                       e++ +lli+DE+      k+++ +l+a++++g+k i
  gi|518653238|ref|YP_008142758.1| 350 EQKpELLIIDEIENSfHEKMIEYILDAISARGIKTI 385
                                       55669******9876477778889999998888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (445 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); 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: 0.56u 0.28s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3091.84
//
Query:       gi|518653239|ref|YP_008142759.1|  [L=114]
Description: hypothetical protein FACI_IFERC00001G1882 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.4   0.1      0.025   14.2   0.1    1.2  1  DUF4998   Domain of unknown function


Domain annotation for each model (and alignments):
>> DUF4998  Domain of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.1   1.4e-06     0.025      90     182 ..      12     105 ..       5     109 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.4e-06
                           DUF4998  90 ivtydkkgnsSlksevtgevYGdsYqasltnrslksvele..kkeltinwskveqealvkteleYtnkagkektvki 164
                                       i+ yd +gn S  ++ + ++ G++Yq++++   ++    e   ++l+i++s  +  a    ++e ++++gk ++ k+
  gi|518653239|ref|YP_008142759.1|  12 IIEYDCDGNCSRITKQIKNILGQEYQNNIYLLGIEFEIEEwiCDSLKIKYSAKRPPAKALNDFE-KEHSGKYRKDKL 87 
                                       889*************************988777643333678889999988887774334443.556677777777 PP

                           DUF4998 165 kkkeeetvledfkegtsf 182
                                       ++++++   +  ++++sf
  gi|518653239|ref|YP_008142759.1|  88 PSYSSKLDYNRLNKNKSF 105
                                       766666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 00:00:00.42
# Mc/sec: 811.72
//
Query:       gi|518653240|ref|YP_008142760.1|  [L=420]
Description: multidrug efflux permease [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-30  104.7  45.6    1.1e-19   70.6  21.8    2.1  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
       0.12   10.7  14.5     0.0061   15.0   6.3    2.3  2  MFS_3     Transmembrane secretion effector
       0.13   11.9   0.2        0.4   10.4   0.1    1.7  2  TetR      Bacterial transcriptional repressor


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6  21.8   1.8e-23   1.1e-19       1     262 [.      27     280 ..      27     285 .. 0.81
   2 !   48.0  15.8   1.4e-16   8.3e-13      16     166 ..     246     402 ..     244     416 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 1.8e-23
                             MFS_1   1 lllaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrr.vlllglllfalgl 76 
                                       l+l+ +ls+++r+ ++++l+l+l++ ++     ig ++ l ++ ++ +++++Gr++dr+Grr   l++ +l+++   
  gi|518653240|ref|YP_008142760.1|  27 LALVSLLSSATRYPVWIVLTLLLSSVYHTPFLIIGVIFFLSSAISFPFNILAGRIMDRIGRRTlSLIIPILISITY- 102
                                       5789999999*****************************************************5555555555555. PP

                             MFS_1  77 llllfa....sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg 149
                                       +ll+++     +l ++++  v +    ++ + +++a+++d++ ++er +a++l+ +++++G+ +g +++g+++ +++
  gi|518653240|ref|YP_008142760.1| 103 FLLFYTayreLQLIYIIIETVASTTLLSVQNVLINAITTDMSIDQERLSAFSLIRVAANAGVGIGLVIAGVMS-LIS 178
                                       555543353333334555556666666999999999999999999***************************9.999 PP

                             MFS_1 150 Wravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlw.illialllfffgfsg 225
                                         + f++  i+s++ f +  ++ +++++ ++  ++        +++++      ++d+ l  + +++++++ f+ ++
  gi|518653240|ref|YP_008142760.1| 179 PYVFFIVPVIASIFEFYI--FYRFVPESLNRVLEKLNT----IKKKFTV-----HRDRLLVaVSIFMAISMLFADQF 244
                                       889999999999999666..888999999999988888....6666666.....44442223355555555667777 PP

                             MFS_1 226 lltllplylqevlglsglllaglllallalvgailal 262
                                        + +lplyl + ++++  ++++l++++ alv++ l++
  gi|518653240|ref|YP_008142760.1| 245 EMPTLPLYLETYRHIT-EFYITLIYGVNALVVILLQF 280
                                       ****************.9*************998865 PP

  == domain 2  score: 48.0 bits;  conditional E-value: 1.4e-16
                             MFS_1  16 gpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslw.lllvl 91 
                                       +p+lpl+l +  +i++  i l++++ al+ +++++ l ++++rfG  + + +g+ll+a++ +l++ a++   ll+  
  gi|518653240|ref|YP_008142760.1| 246 MPTLPLYLETYRHITEFYITLIYGVNALVVILLQFRLNSIGERFGYIKSFSVGMLLYAFS-FLGFAATGNLvLLAGN 321
                                       799**9**9***************************************************.4444356666599999 PP

                             MFS_1  92 rvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllgglla.sslg.....Wravfyilaivsl 162
                                        ++  +g+++ +p   + i++++p ++rg ++g+ s+ ++  + lgpl+g +++  +++     W + f i+a +++
  gi|518653240|ref|YP_008142760.1| 322 TAMLTVGECLCNPFLSVTISRISPANKRGEYFGFSSSLIGTIFPLGPLVGTIFLtYLFNpqilmWALFFAINASLAI 398
                                       9************************************999999999999999994444599999************* PP

                             MFS_1 163 lafv 166
                                       +++v
  gi|518653240|ref|YP_008142760.1| 399 ISLV 402
                                       *966 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   6.3     1e-06    0.0061      58     192 ..      71     203 ..      13     240 .. 0.83
   2 ?    0.4   1.1     0.028   1.6e+02      88     189 ..     297     405 ..     289     417 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1e-06
                             MFS_3  58 ifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkr 134
                                        f + ilaG + D + rR + l++ +l+ ++  ll   +a+  l+ + +++ t+      ++++   +A++ ++   
  gi|518653240|ref|YP_008142760.1|  71 SFPFNILAGRIMDRIGRRTLSLIIPILISITYFLLFY-TAYRELQLIYIIIETVASTTLLSVQNVLINAITTDMSID 146
                                       46689***************99999888776665555.55555667778888999999999*************999 PP

                             MFS_3 135 rdvpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnalsylalivallrwkre 192
                                       ++  +A  L  v  n    +G  ++Gv ++++ + + f v +++ ++  +++ r  +e
  gi|518653240|ref|YP_008142760.1| 147 QERLSAFSLIRVAANAGVGIGLVIAGV-MSLISPYVFFIVPVIASIFEFYIFYRFVPE 203
                                       99999*********************7.6999*******9999988877777666555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.028
                             MFS_3  88 vsvlltvlaalgllsp...wlllaltlligiGaalndPaWqAsvgelvkrrdvpaAvaLnsvginiaRsvGPAlgGv 161
                                       v +ll  +++lg+ +    +ll + t ++ +G  l +P  + +++ + ++++  +    +s  i +    GP +g +
  gi|518653240|ref|YP_008142760.1| 297 VGMLLYAFSFLGFAATgnlVLLAGNTAMLTVGECLCNPFLSVTISRISPANKRGEYFGFSSSLIGTIFPLGPLVGTI 373
                                       55666666677666431114455667777778888888777777777777777777777777777777777777777 PP

                             MFS_3 162 lvaav.Ga...alafavnalsylalivallrw 189
                                        ++ +  +   ++a  ++  + la+i  ++r 
  gi|518653240|ref|YP_008142760.1| 374 FLTYLfNPqilMWALFFAINASLAIISLVARK 405
                                       66643122211222222222334444444333 PP

>> TetR  Bacterial transcriptional repressor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.67     4e+03     124     136 ..     169     181 ..     155     183 .. 0.83
   2 ?   10.4   0.1   6.7e-05       0.4      26      69 ..     187     230 ..     181     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.67
                                       HHHHHHHHHHCCB CS
                              TetR 124 gvyqvlsllkPyl 136
                                       +++ v+sl++Py+
  gi|518653240|ref|YP_008142760.1| 169 VIAGVMSLISPYV 181
                                       67789******96 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 6.7e-05
                                       HHHHHHHHHHHTHHHHHSHHHHHHC-HHHHHHHHHHHHHHHHHH CS
                              TetR  26 ylealfelmwrYRFlyrDlaellsrnpeLakryrqlleelqaql 69 
                                        + ++fe+   YRF  + l+ +l++  +++k+++  +++l +++
  gi|518653240|ref|YP_008142760.1| 187 VIASIFEFYIFYRFVPESLNRVLEKLNTIKKKFTVHRDRLLVAV 230
                                       56899****************************99888887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (420 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1041  (0.0580624); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.58u 0.29s 00:00:00.86 Elapsed: 00:00:00.46
# Mc/sec: 2772.39
//
Query:       gi|518653241|ref|YP_008142761.1|  [L=137]
Description: hypothetical protein FACI_IFERC00001G1884 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score 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   13.3   1.0       0.82    9.0   0.4    2.2  2  Cyt_bd_oxida_II  Cytochrome bd terminal oxidase subunit II
       0.65   10.0   5.3       0.39   10.7   2.8    1.9  2  NdhL             NADH dehydrogenase transmembrane subunit


Domain annotation for each model (and alignments):
>> 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 ?    2.9   0.0    0.0064        57      99     125 ..       7      31 ..       3      57 .. 0.63
   2 ?    9.0   0.4   9.2e-05      0.82      56      92 ..      69     108 ..      67     117 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0064
                   Cyt_bd_oxida_II  99 efrskaeskrwrklwdlaffigSllaa 125
                                       e+++++   ++r++wd++ ++gS ++ 
  gi|518653241|ref|YP_008142761.1|   7 EYKKRKL--KKRERWDIIKILGSSFTL 31 
                                       6655543..568888888888775432 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 9.2e-05
                   Cyt_bd_oxida_II  56 vWLvtaggalfaaFPlayatlfsglylpl...lliLlgli 92 
                                       v++++ g a+  +FP++  +lf++ yl     l+i+l++i
  gi|518653241|ref|YP_008142761.1|  69 VTMILLGFAMIFSFPTTEGYLFNQNYLITredLFIILAMI 108
                                       899***********************98633345555555 PP

>> NdhL  NADH dehydrogenase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   2.8   4.3e-05      0.39       5      59 ..      29      83 ..      25      90 .. 0.82
   2 ?   -1.6   0.0      0.29   2.6e+03      23      37 ..     104     118 ..      88     124 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
                              NdhL  5 leqdtllvllaylalsvlYllviPlilylwlrkRWyvaskiErlliymlvflfFP 59
                                      ++ ++++ ll ++ + +lYl viP+i++ + r    ++  + ++l+ + + + FP
  gi|518653241|ref|YP_008142761.1| 29 FTLSMIFCLLIFGHMIFLYLSVIPPIMMAFPRGEDRRKPLVTMILLGFAMIFSFP 83
                                      667788999999*****************98888777777877777666666777 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.29
                              NdhL  23 YllviPlilylwlrk 37 
                                        l +iP+ +y+  + 
  gi|518653241|ref|YP_008142761.1| 104 ILAMIPQSVYIGTNV 118
                                       456677777765555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (137 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); 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 0.30s 00:00:00.73 Elapsed: 00:00:00.45
# Mc/sec: 904.81
//
Query:       gi|518653242|ref|YP_008142762.1|  [L=441]
Description: RecQ1 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.5   2.5    1.1e-26   93.8   2.5    1.4  1  DUF3427       Domain of unknown function (DUF3427)
    1.5e-06   28.5   0.1    7.4e-06   26.3   0.0    2.2  2  Helicase_C    Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.079   12.0   0.3       0.12   11.4   0.3    1.2  1  DUF444        Protein of unknown function (DUF444)
       0.23   11.0   0.0       0.77    9.3   0.0    1.7  2  adh_short_C2  Enoyl-(Acyl carrier protein) reductase


Domain annotation for each model (and alignments):
>> DUF3427  Domain of unknown function (DUF3427)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.8   2.5   2.4e-30   1.1e-26      47     282 ..     177     434 ..     142     436 .. 0.79

  Alignments for each domain:
  == domain 1  score: 93.8 bits;  conditional E-value: 2.4e-30
                           DUF3427  47 etiesalrvLdlsffksaekkkygniplieke.ekenkeyrlseefkkllen......................... 97 
                                       +  e + + + + f    + ++y+ i++iek+ e++nk+++  +  ++ + n                         
  gi|518653242|ref|YP_008142762.1| 177 NFNEDIEKTMAGAFKRICQINSYSWISFIEKTlEENNKTWEELSATERRMVNmfyftiynsppeklnyansldalne 253
                                       44555566666666555666667777777755555555555444444444444666666677777777777777777 PP

                           DUF3427  98 ....eeFkkfledlielglarykkkyse.eryednglvlyekYsrkdvcrLlnweknevsstigGykvdkkt.tcpi 168
                                           + + ++l+dl+ + l++++  +s  +++ d +l ++++Ysr++++  l+      s + +G+k+ k++    +
  gi|518653242|ref|YP_008142762.1| 254 istyPVLFSELKDLLLYLLSTINFVESSkNINGDIPLHVHSEYSRNQILGALDIMDPA-SMR-EGVKYIKEKkIDIL 328
                                       7666889999*********99886665526677**********************999.777.*******9988899 PP

                           DUF3427 169 FvtyeK.eedisestkYeDeFideqtlswiSkskrtleskevkkiieqkeeglkihLFVkk.aksdaegkeFyYlGe 243
                                        vt +K e++ s +t+Y+D+ i+e++++w+++s  + +s+  ++++ ++ +++ki LF +  +++d   +++++lG+
  gi|518653242|ref|YP_008142762.1| 329 LVTVHKeEKSYSPTTMYKDYAINENEFHWQTQSTVSSDSDTARRYFGETGQEHKILLFTREyRENDLGASPYVFLGR 405
                                       ******7788999*****************************************************99999****** PP

                           DUF3427 244 vdavesskkettkknkkgkpvveielkLktpvredlyey 282
                                       v  v++          +g+++v+i +kL++p+  + +e+
  gi|518653242|ref|YP_008142762.1| 406 VRHVRH----------TGSNPVSIIWKLDEPILPQYLEK 434
                                       ****86..........3556***********98777666 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 !   26.3   0.0   1.7e-09   7.4e-06      66     109 ..       6      49 ..       2      50 .. 0.94
   2 ?   -2.4   0.0       1.3   5.9e+03      50      50 ..     308     308 ..     260     338 .. 0.54

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 1.7e-09
                                       SSSEEEESGGGTSSSTSTTESEEEESSSSSSHHHHHHHHTTSSS CS
                        Helicase_C  66 esdvLiatdvaerGidipkvnlVinfdlprnvtsyiqriGRtgR 109
                                       e++v+ a d   +G+dip++n+V ++ + +++t +iq+ GR  R
  gi|518653242|ref|YP_008142762.1|   6 EIKVIFAVDLYNEGVDIPEINTVLFLRPTESLTVFIQQLGRGLR 49 
                                       789**************************************988 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.3
                                       S CS
                        Helicase_C  50 l 50 
                                       +
  gi|518653242|ref|YP_008142762.1| 308 M 308
                                       2 PP

>> DUF444  Protein of unknown function (DUF444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.3   2.7e-05      0.12     329     399 ..     160     229 ..     152     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.7e-05
                            DUF444 329 YppseWNiYaaqasDgdnwseDsekavellaekilplvqyfaYveitpsaseeeqtlweeyekvaeeeenf 399
                                       Y+ +++ + +a+a+  dn++eD ek+++ + ++i++ ++ ++++   +++ ee+++ wee+++ +++  n+
  gi|518653242|ref|YP_008142762.1| 160 YSKNTFSRLCANAGVIDNFNEDIEKTMAGAFKRICQ-INSYSWISFIEKTLEENNKTWEELSATERRMVNM 229
                                       888899999999**********************75.789999999999************9998876555 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00017      0.77      72     115 ..     167     210 ..     153     257 .. 0.79
   2 ?   -1.2   0.0      0.28   1.2e+03      46      74 ..     303     329 ..     291     345 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00017
                                       EEEE-----EGCSS-GGGH-HHHHHHHHHHHTHHHHHHHHHHHH CS
                      adh_short_C2  72 ilvnnagiapklkgpfletsreefdraldvnlyslfllakaalp 115
                                        l+ nag+ ++ ++++++t    f+r++++n ys +++++  l+
  gi|518653242|ref|YP_008142762.1| 167 RLCANAGVIDNFNEDIEKTMAGAFKRICQINSYSWISFIEKTLE 210
                                       5889********************************99988776 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.28
                                       EE--TTSHHHHHHHHHHHHHHHSSEEEEE CS
                      adh_short_C2  46 lecDVtdeeqvealveevvekfgklDilv 74 
                                        ++D+ d++++++ v+ ++ek  k+Dil+
  gi|518653242|ref|YP_008142762.1| 303 GALDIMDPASMREGVKYIKEK--KIDILL 329
                                       679***************998..788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3064.38
//
Query:       gi|518653243|ref|YP_008142763.1|  [L=371]
Description: hypothetical protein FACI_IFERC00001G1886 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.9e-21   74.7   0.1    7.5e-21   73.8   0.1    1.5  1  OrfB_Zn_ribbon  Putative transposase DNA-binding domain
    7.5e-09   35.8   0.4    1.5e-08   34.9   0.2    1.6  2  OrfB_IS605      Probable transposase
     0.0015   18.0   0.3      0.003   17.0   0.3    1.5  1  TF_Zn_Ribbon    TFIIB zinc-binding
  ------ inclusion threshold ------
        0.4   10.9   1.8        0.8    9.9   1.8    1.5  1  Auto_anti-p27   Sjogren's syndrome/scleroderma autoantigen 1 
       0.61   10.1   3.4        1.4    9.0   3.4    1.6  1  Zn_Tnp_IS1595   Transposase zinc-ribbon domain
       0.98    9.5   3.1          2    8.5   0.0    2.8  3  CpXC            CpXC protein


Domain annotation for each model (and alignments):
>> OrfB_Zn_ribbon  Putative transposase DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.1   2.5e-24   7.5e-21       1      69 []     277     346 ..     277     346 .. 0.98

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.5e-24
                    OrfB_Zn_ribbon   1 frklkeqleykakeyGikveevnpayTSktCseCgsknke.alsgrtfkCpnCgfeadrDvnAaiNilkr 69 
                                       f++l+ ++eyka e+Gi+v +++p++TS +C++C  ++k+ ++++ tfkC +Cg++  +D+ A++Ni +r
  gi|518653243|ref|YP_008142763.1| 277 FYQLRLFIEYKAMEAGIPVMVIDPHNTSRECPNCHTISKKnRPERSTFKCISCGLKGEADYIASLNIRNR 346
                                       7899************************************99*************************986 PP

>> OrfB_IS605  Probable transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7   7.9e+03      49      74 ..      22      47 ..      19      58 .. 0.74
   2 !   34.9   0.2   5.1e-12   1.5e-08       5     111 ..     153     255 ..     149     262 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                        OrfB_IS605 49 dykylakeiaelqsklkksknykkas 74
                                      ++k+++++   +++++ + k+y k s
  gi|518653243|ref|YP_008142763.1| 22 TFKKFNEACNFVSRIAWDNKIYNKIS 47
                                      57778888888888888888887766 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 5.1e-12
                        OrfB_IS605   5 eveve.lpkpkgnkaagiDlGinnLatvvtedgtwflykgrrlksdykylakeiaelqsklkksknykkasrklarl 80 
                                        v+v+ +p+ ++++++g+D+Gi n+ + +t++    +y+g ++k+  +     + +lqs   ks     a+r l++l
  gi|518653243|ref|YP_008142763.1| 153 SVDVPeQPVIEPKNVIGVDMGIANISVDSTGK----YYSGEKVKEVREHNLDLRSRLQSVNTKS-----AKRHLKKL 220
                                       4444449999**********************....************************7766.....8******* PP

                        OrfB_IS605  81 hrkrsrrrkhllhklathliktlkev....gvetL 111
                                       + k  r+ ++  h ++++++++ k +    ++e+L
  gi|518653243|ref|YP_008142763.1| 221 SGKEHRFATNTNHIISKEIVNKAKGTssaiAIEDL 255
                                       ********************987655443355555 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.3     1e-06     0.003       2      34 ..     306     338 ..     305     343 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1e-06
                                       EETTTTCEECHEETSTTCEEESSSSBEEEECCC CS
                      TF_Zn_Ribbon   2 kCPnCgstnlveDpergelvCtdCGlVlednsi 34 
                                        CPnC++ +  + per ++ C +CGl  e ++i
  gi|518653243|ref|YP_008142763.1| 306 ECPNCHTISKKNRPERSTFKCISCGLKGEADYI 338
                                       5******555899*************9998888 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 ?    9.9   1.8   0.00027       0.8      15      40 .]     304     330 ..     303     330 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00027
                     Auto_anti-p27  15 aetCpvCgvPLmrdr.kggkvyCvaCd 40 
                                       +  Cp+C ++  ++r ++ +  C++C+
  gi|518653243|ref|YP_008142763.1| 304 SRECPNCHTISKKNRpERSTFKCISCG 330
                                       678************989999*****6 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   3.4   0.00046       1.4      19      44 ..     305     330 ..     300     332 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00046
                     Zn_Tnp_IS1595  19 fvCPhCgsr.kayriktrglfqCkeCr 44 
                                       + CP+C+   k  r + r  f+C +C+
  gi|518653243|ref|YP_008142763.1| 305 RECPNCHTIsKKNRPE-RSTFKCISCG 330
                                       78*****665555555.6********7 PP

>> CpXC  CpXC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   3.3e+03      84     108 ..     214     244 ..     192     252 .. 0.61
   2 ?   -0.6   0.4      0.45   1.3e+03      39      45 ..     306     312 ..     287     319 .. 0.75
   3 ?    8.5   0.0   0.00066         2       2      38 ..     325     361 ..     324     364 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                              CpXC  84 k......egytlRlvidmaelaEkilileag 108
                                       k      +g + R++++ ++++ k ++ +a+
  gi|518653243|ref|YP_008142763.1| 214 KrhlkklSGKEHRFATNTNHIISKEIVNKAK 244
                                       1122234666779999999988887776665 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.45
                              CpXC  39 tCpkCga 45 
                                       +Cp+C++
  gi|518653243|ref|YP_008142763.1| 306 ECPNCHT 312
                                       5777765 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00066
                              CpXC   2 tCpaCgkefeaeiwtsidadedpelkeklldgslfea 38 
                                       +C +Cg + ea+   s+++ ++  + + +++g++f +
  gi|518653243|ref|YP_008142763.1| 325 KCISCGLKGEADYIASLNIRNRAVANQPIVAGDFFVH 361
                                       7********************************9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       794  (0.0442858); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.43
# Mc/sec: 2605.63
//
Query:       gi|518653244|ref|YP_008142764.1|  [L=649]
Description: hypothetical protein FACI_IFERC00001G1887 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-30  106.0   0.0    6.6e-30  104.4   0.0    1.9  1  ResIII         Type III restriction enzyme, res subunit
      3e-15   56.3   1.7    8.9e-15   54.7   0.3    2.4  3  PLDc_2         PLD-like domain
      9e-09   35.3   0.0    2.9e-08   33.7   0.0    1.9  2  SWI2_SNF2      SWI2/SNF2 ATPase
    9.2e-08   31.7   0.5    9.2e-08   31.7   0.5    1.8  2  RE_NgoFVII     NgoFVII restriction endonuclease
    8.2e-05   22.4   0.0    0.00055   19.8   0.0    2.4  2  DEAD           DEAD/DEAH box helicase
  ------ inclusion threshold ------
      0.064   12.7   0.0       0.71    9.2   0.0    2.4  1  TniB           Bacterial TniB protein
      0.078   12.5   0.1        0.2   11.2   0.1    1.6  1  PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1


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 !  104.4   0.0   2.6e-33   6.6e-30       2     171 .]     331     488 ..     330     488 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 2.6e-33
                                       -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.......-EEEEESSHHHHHHHHHHGGG CS
                            ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkee..kflflvprkslleqtleefkk 76 
                                       +++++yQ +++e+l++ ++ +++ ++l++ aTGtGKT+++a   +++ ++++ +  + lf+++r+++l+q +  f++
  gi|518653244|ref|YP_008142764.1| 331 FHPYPYQSKILEELRADRQLRGNYHNLVVSATGTGKTIISAFDYKQFVREHPDSsnRLLFIAHREEILKQSIACFRN 407
                                       6789***********999999*****************************998899********************* PP

                                       GTGG....GEEEESSS-B--.......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHH CS
                            ResIII  77 flseaykeigkkvsgdkkkakekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswrei 153
                                       +l+++    g+ + g+ k        + + l+++iq++ +++      + +l+++++d+iiiDE H+++a ks+ ++
  gi|518653244|ref|YP_008142764.1| 408 VLKDPE--FGNLYVGNYKPL------SDEHLFMSIQTFESIR-----PDLQLDKHYYDFIIIDEFHHAAA-KSYANL 470
                                       ****97..899999999999......999*************.....99*********************.****** PP

                                       HHT---SEEEEEESS-S- CS
                            ResIII 154 lekfkeavllglTATper 171
                                       l++f++ ++lglTATper
  gi|518653244|ref|YP_008142764.1| 471 LNHFNPEIMLGLTATPER 488
                                       ****************86 PP

>> PLDc_2  PLD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.1   2.8e+03      93     112 ..     144     163 ..     138     165 .. 0.80
   2 !   54.7   0.3   3.5e-18   8.9e-15       6     133 .]     164     294 ..     159     294 .. 0.87
   3 ?   -1.0   0.0       0.6   1.5e+03      64      88 ..     567     593 ..     528     620 .. 0.59

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.1
                            PLDc_2  93 tvivGSsNltkrgldlnlEl 112
                                        +++GSsN  + + +l+ E+
  gi|518653244|ref|YP_008142764.1| 144 SLFTGSSNEPQFYYELQKEI 163
                                       6799****988888887776 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 3.5e-18
                            PLDc_2   6 ksAkksidiatyyf..vsdreildallkaakrgvkvrilldskkddagavdeaslkelkellleagvevrvfetllg 80 
                                       +  ++++d+ + ++     r i+++l++  ++g k+r+++      +g+ d +   el++l +++++++  ++t+++
  gi|518653244|ref|YP_008142764.1| 164 QT-SDQVDMLVSFIkwTGLRLIIKKLKEFTDNGGKLRVITTT---YMGVTDIKAIEELAKL-TNTEIKIS-YDTKNT 234
                                       44.8999999999954444557*******************9...999*9***********.99999988.466689 PP

                            PLDc_2  81 slHaKlylidgk....tvivGSsNltkrgldlnlElnvviedk...elakeleeeFerlw 133
                                       ++HaK+y++ ++    t++vGSsNl+ ++ ++ lE+n++i++    ++++++++ F+++w
  gi|518653244|ref|YP_008142764.1| 235 RMHAKTYIFLRNtgysTAYVGSSNLSGAAISSGLEWNLKITKIdmqDVFDKIDATFDSYW 294
                                       *********6555888************************98777899*********999 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.6
                            PLDc_2  64 llleagvevrvfetll....gslHaKlyl 88 
                                       + +++  ++  +++ l    +  HaK++ 
  gi|518653244|ref|YP_008142764.1| 567 V-RKYSTDINSMKA-LgfcvTKAHAKFMA 593
                                       3.444444444442.12234555666654 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       2.2   5.5e+03      51      77 ..      59      85 ..      18     102 .. 0.71
   2 !   33.7   0.0   1.1e-11   2.9e-08      20     203 ..     355     533 ..     336     549 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.2
                         SWI2_SNF2 51 kvvvvtDRkdLdkQlsktfakageekp 77
                                      k + v DR d  + l +++++ g+e++
  gi|518653244|ref|YP_008142764.1| 59 KRLPVSDRLDFVNNLLDKINSDGREST 85
                                      445577888888888888887666653 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.1e-11
                         SWI2_SNF2  20 gGviWHtqGSGKsltmvflakkllee.elknpkvvvvtDRkdLdkQlsktfakageekpkqaesrkeLkellekese 95 
                                       + ++   +G GK++ ++f  k+ ++e   ++ +++++  R+++ kQ  + f+++ ++ +   +      + l   s+
  gi|518653244|ref|YP_008142764.1| 355 HNLVVSATGTGKTIISAFDYKQFVREhPDSSNRLLFIAHREEILKQSIACFRNVLKDPE-FGNLYVGNYKPL---SD 427
                                       45666789**********99999985266999********************9987753.333333334444...67 PP

                         SWI2_SNF2  96 kiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpnaafigFTGTPilkkdkktkevFgey 172
                                       + +f  iq fe+ +     +l+++   ++++DE H    +++a+ l++ ++   ++g+T TP  ++ ++  + F++ 
  gi|518653244|ref|YP_008142764.1| 428 EHLFMSIQTFESIRP--DLQLDKHYYDFIIIDEFHHAAAKSYANLLNH-FNPEIMLGLTATPERMDGRDILKYFNNH 501
                                       889999****75332..235666666799*********9999876665.5566799******************988 PP

                         SWI2_SNF2 173 i.dkYtikeaveDgavvpilYesrlaklelke 203
                                       i ++ ++ ea++ +  +p +Y + + +++l++
  gi|518653244|ref|YP_008142764.1| 502 ItSEIRLPEAIDQHLLCPFQYFGITDSVDLEN 533
                                       835899*************9998888777765 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.2       1.2     3e+03     132     185 ..      70     123 ..      49     138 .. 0.55
   2 !   31.7   0.5   3.6e-11   9.2e-08       2     139 ..     161     297 ..     160     346 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.2
                                       HHHHHHH.HXEEGGGSXXSSXXXXXX-GGGSTT-EE-.-HHS--SSEEEEE---- CS
                        RE_NgoFVII 132 iqsllsksiskniaeveeniikeknsllsevegvekv.vdeskseesveipllae 185
                                       +++ll k i+ +  e + +  ++ n++l+++++++++  d+ +s  ++ ++++ +
  gi|518653244|ref|YP_008142764.1|  70 VNNLLDK-INSDGRESTSKEKIHINNPLDKISSKTEQnCDNIESPPKILLSAYPK 123
                                       5555555.55555555543444445555555544443033444444444444443 PP

  == domain 2  score: 31.7 bits;  conditional E-value: 3.6e-11
                                       HHHHHXSEEEEEESXXXHHHHHHHHHHHHXX..XXSEEEEEEXSHHHHXXXHHHHHHHHHHHHHHHHCTSEEEEEXS CS
                        RE_NgoFVII   2 elleksdelliisGYvspaslselikllkeq..sdikitlivGMypleglskrlheallklnkklseegigevkvsy 76 
                                       ++++ sd++++++ ++  + l   ik lke   +  k+ +i   y          +a+++l+k +      e+k+sy
  gi|518653244|ref|YP_008142764.1| 161 KEIQTSDQVDMLVSFIKWTGLRLIIKKLKEFtdNGGKLRVITTTYM----GVTDIKAIEELAKLT----NTEIKISY 229
                                       67999*************************9555556666654444....444556666666665....35699999 PP

                                       SS...XBXXXEEEEEET.TEEEEEEESXXSXXTTS..XXXSBXEEEEEE.HHHHHHHHHHHHHHHHH. CS
                        RE_NgoFVII  77 sv...kvHsKlYiwkkdgkplsAliGSANlssngl..rtrqrEtlvdldtedafkeldeyiqsllsks 139
                                        +   ++H+K Yi++++     A++GS Nls ++     + +  ++++d +d f+++d+ ++s  s +
  gi|518653244|ref|YP_008142764.1| 230 DTkntRMHAKTYIFLRNTGYSTAYVGSSNLSGAAIssGLEWNLKITKIDMQDVFDKIDATFDSYWSSE 297
                                       99999**************************9988555555666777888888888888888777763 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.1       2.1   5.3e+03      65     102 ..     186     229 ..     182     238 .. 0.50
   2 !   19.8   0.0   2.1e-07   0.00055       3     170 ..     336     487 ..     334     493 .. 0.75

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.1
                                       HHHHHHTTT.STSEEE.EEETTSSHHHHHHHH...HTT.CSEEE CS
                                       xxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxx...xxx.xxxxx RF
                              DEAD  65 nnlkkfkky.idlrvl.liiggvaardqlskl...dng.vdivv 102
                                       ++lk+f+++  +lrv   ++ gv+  + +++l    n+ ++i +
  gi|518653244|ref|YP_008142764.1| 186 KKLKEFTDNgGKLRVItTTYMGVTDIKAIEELaklTNTeIKISY 229
                                       55666666533366664444455444444444111333455554 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 2.1e-07
                                       HHHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT CS
                                       xxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD   3 iQaeaiplil......gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky 73 
                                       +Q+++++++       g+ + lv  +TG+GKT + ++   q v e + ++ ++ l+++  +e+ +q +  +++++k 
  gi|518653244|ref|YP_008142764.1| 336 YQSKILEELRadrqlrGNYHNLVVSATGTGKTIISAFDYKQFVRE-HPDSSNRLLFIAHREEILKQSIACFRNVLKD 411
                                       5666666665444443445778999*************9999976.899999************************6 PP

                                       STSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              DEAD  74 idlrvlliiggvaardqlskldngvdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlp 150
                                          +   ++ g+ +    ++    + + + t + +   l+   l+ +   f+++DE +    +++ + +n+   ++ 
  gi|518653244|ref|YP_008142764.1| 412 P--EFGNLYVGNYKPLSDEH----LFMSIQTFESIRPDLQ---LDKHYYDFIIIDEFHHAAAKSYANLLNHFNPEI- 478
                                       4..44434444333333333....4667888888887665...555789**************9999998877776. PP

                                       HHCTTSTTTSEEEEEESSBS CS
                                       xxxxxxxxxxxxxxxxxxxx RF
                              DEAD 151 qitcdgklqrqvivlSATlp 170
                                                  ++ l+AT++
  gi|518653244|ref|YP_008142764.1| 479 -----------MLGLTATPE 487
                                       ...........777777775 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00028      0.71      11     137 ..     332     468 ..     328     476 .. 0.63

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00028
                              TniB  11 igyprakeilerLeeLleypkrkrmpnlllvGdsnnGKtmi....vekFarlhppekd.....edaekv...pvlvv 75 
                                       + yp   +ile+L++  +   r    + l+v+ + +GKt i     ++F r+hp++++     +++e++    +  +
  gi|518653244|ref|YP_008142764.1| 332 HPYPYQSKILEELRADRQL--RGN-YHNLVVSATGTGKTIIsafdYKQFVREHPDSSNrllfiAHREEIlkqSIACF 405
                                       5666666666666543333..223.4568999*******99444448999999988654555444443323244444 PP

                              TniB  76 q.appkpdekrlyaaiLealgaplkararvskleqqv.lrllrelkvrvLiiDEihnllagsar 137
                                       + + + p+  +ly    + l+ ++    +++++e+      l++     +iiDE+h++ a s+ 
  gi|518653244|ref|YP_008142764.1| 406 RnVLKDPEFGNLYVGNYKPLSDEHL-FMSIQTFESIRpDLQLDKHYYDFIIIDEFHHAAAKSYA 468
                                       3367888888999998888888853.33333333332023689999999999999999877665 PP

>> PP_kinase_C_1  Polyphosphate kinase C-terminal domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   7.7e-05       0.2      52     117 ..     184     249 ..     159     263 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 7.7e-05
                                       HHHHHHHHHHTT-EEEEEES--SSS--HHHHHHHHHHHHHT-EEEE--TT--B--EEEEEEE---S CS
                     PP_kinase_C_1  52 ivkaLieAaengkqvtvlvElkArfdeenNiewakkleeagvkvvygvvglkvhaklllvvrreee 117
                                       i+k+L+e ++ng +  v+        + + ie   kl+++ +k+ y ++++++hak+ +  r+++ 
  gi|518653244|ref|YP_008142764.1| 184 IIKKLKEFTDNGGKLRVITTTYMGVTDIKAIEELAKLTNTEIKISYDTKNTRMHAKTYIFLRNTGY 249
                                       889999999999999999999999999999***************************999998754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (649 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       823  (0.0459033); expected 358.6 (0.02)
Passed bias filter:                      555  (0.0309554); 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: 0.70u 0.29s 00:00:00.99 Elapsed: 00:00:00.48
# Mc/sec: 4059.53
//
Query:       gi|518653245|ref|YP_008142765.1|  [L=217]
Description: hypothetical protein FACI_IFERC00001G1888 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.033   14.6   0.0       0.22   12.0   0.0    2.2  2  DUF2768   Protein of unknown function (DUF2768)


Domain annotation for each model (and alignments):
>> DUF2768  Protein of unknown function (DUF2768)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.12   2.2e+03      23      48 ..      13      38 ..      10      39 .. 0.82
   2 ?   12.0   0.0   1.2e-05      0.22      18      50 ..     155     187 ..     152     188 .. 0.94

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.12
                           DUF2768 23 reklknkflkiivaliAyilllvsgl 48
                                      r  +kn +++i+ +  A+  +l  g+
  gi|518653245|ref|YP_008142765.1| 13 RGNIKNDVINILNENKAFKWMLNTGV 38
                                      66799999999999999999987776 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 1.2e-05
                           DUF2768  18 liilsreklknkflkiivaliAyilllvsglii 50 
                                        i++ rek++++ ++++++++++  + vs l+i
  gi|518653245|ref|YP_008142765.1| 155 NITIDREKINEESIQTFMETLSFNYINVSQLMI 187
                                       58999************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (217 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.46
# Mc/sec: 1404.13
//
Query:       gi|518653246|ref|YP_008142766.1|  [L=252]
Description: permease [Ferroplasma acidarmanus fer1]
Scores for complete 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-40  137.6  33.8    6.5e-40  137.2  33.8    1.0  1  TauE           Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
       0.38   10.8   3.0       0.31   11.1   0.4    2.1  2  Epiglycanin_C  Mucin, catalytic, TM and cytoplasmic tail regi
       0.47   10.2   0.0       0.47   10.2   0.0    5.9  7  Adeno_E3_CR2   Adenovirus E3 region protein CR2


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  137.2  33.8   1.1e-43   6.5e-40       2     234 ..      10     247 ..       9     248 .. 0.94

  Alignments for each domain:
  == domain 1  score: 137.2 bits;  conditional E-value: 1.1e-43
                              TauE   2 llagllaGfvagllGiGggliavPlLlll...lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsli 75 
                                       +++g+++G++ g+lG  g + +vP+L+++   l p++a++tsll+ v+ts++ a+ +++rg+v+++ +++++lg++i
  gi|518653246|ref|YP_008142766.1|  10 IILGIIVGALTGVLGSSGVVAVVPALIIInseL-PQEAIGTSLLIDVITSVMVAYVYFKRGRVNIKKGIPMILGAII 85 
                                       89*************************975544.899**************************************** PP

                              TauE  76 GallGallllllpsellkllfgvlllllallmllrkkr...srak..grerrptaillvliggl.vGllsGllGiGg 146
                                       G+++G+ ++ l+p+e +k+ f+v++++++++ l+r+k+      k  +r    +++ +vli  + vGl++G+lG++g
  gi|518653246|ref|YP_008142766.1|  86 GSQIGVRIAFLIPAESVKIGFAVFIIAMGIYSLIRRKEmqnT--KdtQRLLNIKPWEIVLI-TIpVGLATGILGASG 159
                                       ********************************9988876642..24578999999988998.666************ PP

                              TauE 147 GfllvpllllllglplkkavatslllilvislagalgyalagavdwpllllllpgallGallGarlarrlsertlrr 223
                                       G++ +++ +l+l+l++k+av+ts++ +++++ +g++gy++ag++ + ++l+++  ++l +l+ +r+ + +++    +
  gi|518653246|ref|YP_008142766.1| 160 GIMFLIISILILKLDIKTAVGTSTFSMIISASSGTVGYLIAGHIMIIAALIIGSISILSGLIFSRIGNNINPLSTYK 236
                                       ************************************************************************99*** PP

                              TauE 224 lfallllvlgv 234
                                       +++++ +++g+
  gi|518653246|ref|YP_008142766.1| 237 ILGTVFIIIGI 247
                                       ********998 PP

>> Epiglycanin_C  Mucin, catalytic, TM and cytoplasmic tail region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4   5.1e-05      0.31      13      54 ..     136     179 ..     126     193 .. 0.82
   2 ?   -1.2   0.1      0.36   2.1e+03      11      38 ..     196     222 ..     187     229 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.1e-05
                     Epiglycanin_C  13 lkPWeiiLitLvavvva..vGllvgLsfCvrnllslrnladtav 54 
                                       +kPWei+Lit+   +++   G + g++f +  +l l+   +tav
  gi|518653246|ref|YP_008142766.1| 136 IKPWEIVLITIPVGLATgiLGASGGIMFLIISILILKLDIKTAV 179
                                       79********9766654336888899999999999888788877 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.36
                     Epiglycanin_C  11 GslkPWeiiLitLvavvvavGllvgLsf 38 
                                       G+l   +i++i+ + ++ ++ +l gL+f
  gi|518653246|ref|YP_008142766.1| 196 GYLIAGHIMIIA-ALIIGSISILSGLIF 222
                                       677777777665.557788999999988 PP

>> Adeno_E3_CR2  Adenovirus E3 region protein CR2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   2.2      0.61   3.6e+03       7      15 ..      13      21 ..      10      23 .. 0.62
   2 ?    2.3   1.6     0.024   1.4e+02       7      19 ..      26      38 ..      26      39 .. 0.90
   3 ?   -2.0   0.1      0.53   3.1e+03      19      27 ..      56      64 ..      50      74 .. 0.61
   4 ?   10.2   0.0   7.9e-05      0.47      12      36 ..     102     126 ..     101     129 .. 0.87
   5 ?   -4.9   5.2         3   1.8e+04       1      25 [.     146     170 ..     143     171 .. 0.73
   6 ?   -1.0   2.2      0.25   1.5e+03       6      17 ..     203     214 ..     201     218 .. 0.81
   7 ?   -4.5   3.4         3   1.8e+04      17      23 ..     241     247 ..     237     252 .] 0.49

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.61
                      Adeno_E3_CR2  7 aIivaVvvG 15
                                      +Iiv+ + G
  gi|518653246|ref|YP_008142766.1| 13 GIIVGALTG 21
                                      677776666 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.024
                      Adeno_E3_CR2  7 aIivaVvvGlaiI 19
                                      +++vaVv  l+iI
  gi|518653246|ref|YP_008142766.1| 26 SGVVAVVPALIII 38
                                      789****999998 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.53
                      Adeno_E3_CR2 19 IiicmlyYa 27
                                      I  +m+ Y+
  gi|518653246|ref|YP_008142766.1| 56 ITSVMVAYV 64
                                      334566665 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 7.9e-05
                      Adeno_E3_CR2  12 VvvGlaiIiicmlyYaCcYrkhraq 36 
                                       V +G+a+ ii m +Y   +rk   +
  gi|518653246|ref|YP_008142766.1| 102 VKIGFAVFIIAMGIYSLIRRKEMQN 126
                                       779******************8765 PP

  == domain 5  score: -4.9 bits;  conditional E-value: 3
                      Adeno_E3_CR2   1 IPsstiaIivaVvvGlaiIiicmly 25 
                                       IP  + ++i +   G++ +ii +l+
  gi|518653246|ref|YP_008142766.1| 146 IPVGLATGILGASGGIMFLIISILI 170
                                       5555667777777788888888875 PP

  == domain 6  score: -1.0 bits;  conditional E-value: 0.25
                      Adeno_E3_CR2   6 iaIivaVvvGla 17 
                                       i Ii+a ++G +
  gi|518653246|ref|YP_008142766.1| 203 IMIIAALIIGSI 214
                                       679*****9965 PP

  == domain 7  score: -4.5 bits;  conditional E-value: 3
                      Adeno_E3_CR2  17 aiIiicm 23 
                                       + Iii +
  gi|518653246|ref|YP_008142766.1| 241 VFIIIGI 247
                                       4444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1070  (0.0596798); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1729.63
//
Query:       gi|518653247|ref|YP_008142767.1|  [L=407]
Description: hypothetical protein FACI_IFERC00001G1890 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-19   68.8  48.7    3.9e-19   68.8  48.7    2.1  2  MFS_1     Major Facilitator Superfamily
      0.001   17.5   1.3      0.001   17.5   1.3    3.0  3  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8  48.7   4.4e-23   3.9e-19      10     345 ..      19     352 ..       9     357 .. 0.75
   2 !    2.0   9.8    0.0085        76      89     171 ..     311     393 ..     307     401 .. 0.73

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 4.4e-23
                             MFS_1  10 larsilgpalplalaedlg..ispseigl..lltlyalgaavaslplGrl..sdrfGrrrvlllglllfalglllll 80 
                                       l+ + l+++++ ++a +l   +  s +g+  ++ ++ +g+++++l+ + l  +d++ +r+++ ++ +++a++ +ll+
  gi|518653247|ref|YP_008142767.1|  19 LMVMSLWFSAS-TIAPELEpvWGISGLGTliVTLMVQIGFVLGALISATLglADKVNPRKLFTFSSIMSAIF-TLLF 93 
                                       44444455555.55555555555666666325555888999999999877779*******************.4444 PP

                             MFS_1  81 ..fasslw.lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailg.pllgg.llasslgWra 152
                                         +   ++ + +vl + +G+++++++p+++ +++ wfp  +rg+a+g++ ag  lG++l   +l   ++     Wra
  gi|518653247|ref|YP_008142767.1|  94 vlL-YRHFlIEMVLMLSTGIMMAGVYPVAVLIVSSWFPT-RRGLALGIVIAGLTLGTALPhIILDLpFI---TEWRA 165
                                       233.77777*****************************9.*****************999444444234...59*** PP

                             MFS_1 153 vfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsg..ll 227
                                       ++ +  ++s+l++ ++l+ l +++ + k ++ k +            +k++ k++++  +l+ + +f+ ++ +  + 
  gi|518653247|ref|YP_008142767.1| 166 LMEFSSLLSILGGAMVLFALHDDKNQIKAPKFKWD-----------TIKQIIKNKPV--MLANFGYFGHMWELyaMW 229
                                       **************988999999999999888888...........59999999999..7888888876666677** PP

                             MFS_1 228 tllplylqevlgls......glllaglllallalvgailallagrlsdrlgr..rrrlllallllllaalglallav 296
                                       t++p++l + + +        ++++ + +++++l g+ +++l+g +sdr+gr   + ++l++++++++++gl + av
  gi|518653247|ref|YP_008142767.1| 230 TWIPIFLLSSFAFYytgsrlLFITGIASFSIIGLSGVTGSVLGGVISDRIGRtlSTSIYLSISGTAAILIGLTYRAV 306
                                       ***************999973344444477777777777**********9987777777777778888888888888 PP

                             MFS_1 297 tssavllllvlvliGfglgfv....fpsllalasdlappeeagtasglfntag 345
                                       +       ++ +++G+ +g++    ++ + +++++l     +g+a+ + + +g
  gi|518653247|ref|YP_008142767.1| 307 P-------YITIILGIVWGITaiadSAQFSTAVTELSNDAIRGSALTFQMAVG 352
                                       8.......788999999999955544444444444444455666655555544 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.0085
                             MFS_1  89 lvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllaf 165
                                       ++l ++ G++a a  +   +++++++++  rg+a+ + +a   l ++    +  +l   +gW+++f +l i ++ ++
  gi|518653247|ref|YP_008142767.1| 311 IILGIVWGITAIADSAQFSTAVTELSNDAIRGSALTFQMAVGFLITVGSIYAIDILRNIVGWHWAFSFLSIGAFAGM 387
                                       778888888887777888899999999999*****7666655555544455555666999***********999999 PP

                             MFS_1 166 vlflll 171
                                       + ++ l
  gi|518653247|ref|YP_008142767.1| 388 ISMIRL 393
                                       833333 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   4.6     0.026   2.4e+02     333     383 ..      46      96 ..       8     102 .. 0.76
   2 ?   -0.4   0.6      0.03   2.7e+02     465     513 ..     104     152 ..      97     156 .. 0.74
   3 !   17.5   1.3   1.1e-07     0.001     284     379 ..     199     300 ..     181     308 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.026
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 333 nlltGvvvipgaalGillgGllvkklklsakklaklvlvvsllslllllll 383
                                       +l++ ++v +g++lG l++  l    k++++kl +++ ++s + +ll++ll
  gi|518653247|ref|YP_008142767.1|  46 TLIVTLMVQIGFVLGALISATLGLADKVNPRKLFTFSSIMSAIFTLLFVLL 96 
                                       556666666777888888888888889999999999888887777776655 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.03
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 465 illflvsflgalgrvpallvilRcVkkedksfalGlqlllirllgliPg 513
                                       ++l+l + +++ g  p  ++i+ +  +  + +alG+ ++ + l  ++P 
  gi|518653247|ref|YP_008142767.1| 104 MVLMLSTGIMMAGVYPVAVLIVSSWFPTRRGLALGIVIAGLTLGTALPH 152
                                       4455556667778889999999999999999999999988888777765 PP

  == domain 3  score: 17.5 bits;  conditional E-value: 1.1e-07
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx....xxxxxxxxxxxxxxxxx RF
                              OATP 284 pkalkrllknpifllvilssvfeillvaGfitFlpkylEtqFsl..saseAnlltG....vvvipgaalGillgGll 354
                                       + ++k+++kn+  +l  ++   ++  + +++t++p +l + F    + s+  ++tG    +++ +++++G +lgG++
  gi|518653247|ref|YP_008142767.1| 199 WDTIKQIIKNKPVMLANFGYFGHMWELYAMWTWIPIFLLSSFAFyyTGSRLLFITGiasfSIIGLSGVTGSVLGGVI 275
                                       5799************************************98862255666678895554455678899******** PP

                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                              OATP 355 vkklklsakklaklvlvvsllslll 379
                                         ++  + ++ + l++  +   l++
  gi|518653247|ref|YP_008142767.1| 276 SDRIGRTLSTSIYLSISGTAAILIG 300
                                       ***9999998888887776666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       979  (0.0546043); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         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 0.29s 00:00:00.88 Elapsed: 00:00:00.47
# Mc/sec: 2605.01
//
Query:       gi|518653248|ref|YP_008142768.1|  [L=458]
Description: hypothetical protein FACI_IFERC00001G1891 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-20   72.8   5.4    2.3e-19   70.3   5.4    2.2  1  ATPase_2         ATPase domain predominantly from Archaea
    2.5e-19   69.6   0.1    1.1e-18   67.5   0.1    2.2  1  DUF234           Archaea bacterial proteins of unknown functi
    1.7e-09   37.8   0.8    1.7e-09   37.8   0.8    2.1  2  AAA_14           AAA domain
     0.0026   18.0   0.1     0.0072   16.6   0.0    1.7  2  AAA_22           AAA domain
      0.003   17.9   0.0     0.0078   16.6   0.0    1.6  2  AAA_16           AAA ATPase domain
     0.0051   16.3   0.1       0.02   14.4   0.1    2.1  1  HTH_24           Winged helix-turn-helix DNA-binding
     0.0062   16.4   0.0      0.016   15.0   0.0    1.7  1  HTH_5            Bacterial regulatory protein, arsR family
  ------ inclusion threshold ------
      0.016   14.6   0.0      0.041   13.3   0.0    1.6  1  TniB             Bacterial TniB protein
      0.017   15.3   0.1      0.046   13.9   0.1    1.7  1  DUF4143          Domain of unknown function (DUF4143)
      0.023   14.9   0.5      0.096   12.9   0.0    2.2  2  HTH_34           Winged helix DNA-binding domain
      0.043   13.8   2.8      0.052   13.5   0.4    2.4  2  HTH_45           Winged helix-turn-helix
      0.073   13.5   0.1       0.15   12.5   0.1    1.5  1  AAA              ATPase family associated with various cellul
       0.21   12.5   5.1        1.7    9.6   0.3    3.0  2  Stap_Strp_toxin  Staphylococcal/Streptococcal toxin, OB-fold 


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.3   5.4   1.6e-22   2.3e-19       1     208 [.       8     192 ..       8     208 .. 0.84

  Alignments for each domain:
  == domain 1  score: 70.3 bits;  conditional E-value: 1.6e-22
                          ATPase_2   1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkk 77 
                                       F++R+ el+ l++ +++++ + + iYG++++GKt L+ke+i+ +     + +y     ++ +++++        k++
  gi|518653248|ref|YP_008142768.1|   8 FINRKYELNFLNKKYDEDKPQLIIIYGRRRIGKTELIKEFISGK-----KTVYHLCTADSIEENITYL------KSE 73 
                                       99***************************************998.....4566666666666666666......444 PP

                          ATPase_2  78 lekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiiiiDelqklidlglngaellvkeLlnliesltk 154
                                       ++  +g+            +   ++f  +++l+++ik++  kiii +De+ +l+   ln  +  ++ +++++++l+ 
  gi|518653248|ref|YP_008142768.1|  74 FSSITGKSYFL--------NLEVDLFTLFKYLIDEIKDE--KIIIALDEITYLV--SLN--KGILSIFQKIYDELMV 136
                                       44444333333........234788999*********99..9************..999..99************** PP

                          ATPase_2 155 ekhlcvviclsSeglfie.rvyneselegrhky.ilvddldketalnflkegfkel 208
                                       + +l++++ +sS +++ +  ++ +s+ +gr+++ +++  +d + +  f    f+++
  gi|518653248|ref|YP_008142768.1| 137 NSRLFIIFSGSSISMMEDeILNFKSPVYGRRTGsLEISGFDPNLIEYFYPGDFEDI 192
                                       *****************944566**********99*****9888888888877776 PP

>> DUF234  Archaea bacterial proteins of unknown function
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.5   0.1     8e-22   1.1e-18       1      90 [.     313     399 ..     313     408 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.5 bits;  conditional E-value: 8e-22
                            DUF234   1 wfrfvypnrseielgeseevlekikeelneyvgkvFEelvrelllelnkagklpfrftkvGrwWkkeeeiDivalde 77 
                                       +++fv pnrs++elg+ e v++ki+++ln+++g +FE+++ e++ + +    +p++  +v ++W+k+ eiD va+++
  gi|518653248|ref|YP_008142768.1| 313 YYKFVDPNRSDLELGNIESVFKKINNNLNTFYGHTFERIALEMVSRGII--PIPIHNFQVNKFWHKDVEIDGVATND 387
                                       8********************************************7766..68888999****************** PP

                            DUF234  78 eekkalfgEvKwk 90 
                                       +++ ++f+E+K+ 
  gi|518653248|ref|YP_008142768.1| 388 KND-VVFIEIKFV 399
                                       *96.*******95 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.8   1.2e-12   1.7e-09       3     110 ..      28     157 ..      26     177 .. 0.74
   2 ?   -2.9   0.1       4.6   6.4e+03      43      59 ..     239     254 ..     204     263 .. 0.41

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 1.2e-12
                            AAA_14   3 kilvitGaRrvGKTtllkqlikell.........vkkesilyinldderdkkla...dpe....kllelileklkee 63 
                                       ++++i G Rr+GKT l+k++i+ +            +e+i y++ +  + + ++   + e    +l +++ +++k+ 
  gi|518653248|ref|YP_008142768.1|  28 QLIIIYGRRRIGKTELIKEFISGKKtvyhlctadSIEENITYLKSEFSSITGKSyflNLEvdlfTLFKYLIDEIKD- 103
                                       679******************9888888999888567889998877777744332223335444666777777766. PP

                            AAA_14  64 kktylflDEiqev....pewekalkslvd....egknldvivtGSnskllskeia 110
                                       +k ++ lDEi ++    +++ ++ ++++d    + ++l +i++GS+ +++  ei 
  gi|518653248|ref|YP_008142768.1| 104 EKIIIALDEITYLvslnKGILSIFQKIYDelmvN-SRLFIIFSGSSISMMEDEIL 157
                                       9************666655555555666654423.599***********998875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.6
                            AAA_14  43 dkkladpekllelilek 59 
                                       ++++++p +++e+il++
  gi|518653248|ref|YP_008142768.1| 239 KEEFREP-RIYEMILKR 254
                                       1222222.344444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.2e-06    0.0072       4     123 ..      26     140 ..      23     150 .. 0.67
   2 ?   -3.1   0.0       6.4   8.8e+03      56      76 ..     247     269 ..     235     293 .. 0.58

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.2e-06
                            AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst...sskdllrellralglelka..erlss 75 
                                       + ++++++G   +GKT l++++ + +           ++v+  +++++   + + l +e+ +++g +      + ++
  gi|518653248|ref|YP_008142768.1|  26 KPQLIIIYGRRRIGKTELIKEFISGK-----------KTVYHLCTADSieeNITYLKSEFSSITG-KSYFlnLEVDL 90 
                                       6789********************75...........5666666666655555555555555555.34444555666 PP

                            AAA_22  76 eellealeqalraravielliiDEaqhlr..seealeeLrsllnl..srkgv 123
                                         l+++l + +++ +   ++ +DE+ +l   ++ +l+ + ++++     + +
  gi|518653248|ref|YP_008142768.1|  91 FTLFKYLIDEIKDEKI--IIALDEITYLVslNKGILSIFQKIYDElmVNSRL 140
                                       6666666666666666..*********8745477777776666644434444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 6.4
                            AAA_22  56 llrellralglelka..erlsse 76 
                                       +++++l+ + +++++  e ++  
  gi|518653248|ref|YP_008142768.1| 247 IYEMILKRISEGKNTygELQNAL 269
                                       56666666666666554333333 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   5.6e-06    0.0078       2      73 ..       8      75 ..       7     104 .. 0.76
   2 ?   -1.8   0.0       2.5   3.4e+03     117     144 ..      88     113 ..      63     127 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 5.6e-06
                            AAA_16  2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipy..sala 73
                                      ++ R+ el+ L+  ++   ++ p+l++++G + +GK+ l++e+     +++ ++  +++d+ e++i+y  s + 
  gi|518653248|ref|YP_008142768.1|  8 FINRKYELNFLNKKYD---EDKPQLIIIYGRRRIGKTELIKEFIS---GKKTVYHLCTADSIEENITYlkSEFS 75
                                      7778888877777777...77899****************99994...44467788888888888888543344 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.5
                            AAA_16 117 srllellkrllallsrderplvlvlDdl 144
                                        +l+ l+k l++ ++  e+ +++ lD++
  gi|518653248|ref|YP_008142768.1|  88 VDLFTLFKYLIDEIKD-EK-IIIALDEI 113
                                       5678888888888887.88.99999986 PP

>> HTH_24  Winged helix-turn-helix DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.5e-05      0.02       8      48 .]     247     290 ..     244     290 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.5e-05
                            HTH_24   8 ILelLqk...nprisqreLAerlglSpstvnrrlkrLeeeGlIk 48 
                                       I+e + k   +++ ++ eL  +l+l +++++r+l+ L+++ +Ik
  gi|518653248|ref|YP_008142768.1| 247 IYEMILKrisEGKNTYGELQNALHLDSGNISRYLETLISSRFIK 290
                                       666666667789**************************998886 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   1.2e-05     0.016       7      46 ..     251     290 ..     250     291 .. 0.94

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 1.2e-05
                                       HHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE CS
                             HTH_5   7 ILklLaegelcvcelaeelglsqstvShHLkkLreaGLVe 46 
                                       ILk  +eg+ + +el ++l+l  +++S++L  L  +++++
  gi|518653248|ref|YP_008142768.1| 251 ILKRISEGKNTYGELQNALHLDSGNISRYLETLISSRFIK 290
                                       99999****************************9999987 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     3e-05     0.041      22      61 ..      14      53 ..       3      73 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3e-05
                              TniB 22 rLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhpp 61
                                      +L+ L ++ ++++++ ++++G+  +GKt ++++F + ++ 
  gi|518653248|ref|YP_008142768.1| 14 ELNFLNKKYDEDKPQLIIIYGRRRIGKTELIKEFISGKKT 53
                                      577788889999*9********************988765 PP

>> DUF4143  Domain of unknown function (DUF4143)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.3e-05     0.046      64     120 ..     339     397 ..     312     398 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           DUF4143  64 edsenkGallEnlVaqeLlky...sekegakly.yyrdkngaEvDfvielkggkivpiEvK 120
                                       + ++++G+ +E + ++++++       ++ ++  ++++    E+D v +++++ +v iE+K
  gi|518653248|ref|YP_008142768.1| 339 NLNTFYGHTFERIALEMVSRGiipIPIHNFQVNkFWHK--DVEIDGVATNDKNDVVFIEIK 397
                                       33499*******99999998898855555555425555..69******************9 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 ?   12.9   0.0     7e-05     0.096      13      57 ..     258     301 ..     251     307 .. 0.86
   2 ?   -1.5   0.1       2.2     3e+03      31      54 ..     416     438 ..     406     453 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7e-05
                            HTH_34  13 deadfvelkealeatdgnLsvhlkkLekagYievdkefkgkkprt 57 
                                        + ++ el++al + +gn+s  l++L + ++i++ + +++k +r 
  gi|518653248|ref|YP_008142768.1| 258 GKNTYGELQNALHLDSGNISRYLETLISSRFIKYIIPLNQK-RRG 301
                                       567889****************************9999888.444 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2.2
                            HTH_34  31 LsvhlkkLekagYievdkefkgkk 54 
                                       Lsv++k  +k  Y  + k+fk k 
  gi|518653248|ref|YP_008142768.1| 416 LSVNIKR-NKEYYMIIAKSFKTKS 438
                                       5555554.6778999999999984 PP

>> HTH_45  Winged helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       2.4   3.3e+03      33      57 ..      91     116 ..      70     130 .. 0.63
   2 ?   13.5   0.4   3.8e-05     0.052       7      50 ..     247     297 ..     244     316 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.4
                            HTH_45  33 ykllnkYLdmLvekgli.kkskekYv 57 
                                       + l++  +d + ++++i   ++ +Y 
  gi|518653248|ref|YP_008142768.1|  91 FTLFKYLIDEIKDEKIIiALDEITYL 116
                                       22333345778888776344666665 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 3.8e-05
                            HTH_45   7 IiadILeaisegeakkTkimykanLsykllnkYLdmLvekgli.......k 50 
                                       I+  IL+ iseg+++  ++  +  L+  ++++YL++L++  +i       +
  gi|518653248|ref|YP_008142768.1| 247 IYEMILKRISEGKNTYGELQNALHLDSGNISRYLETLISSRFIkyiiplnQ 297
                                       7778**************************************955555544 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   0.00011      0.15       1     120 [.      30     157 ..      30     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                                       EEEESSTTSSHHHHHHHHHHH.......H.......THEEEEEETTTCS.SSSTTHHHHHHHHHHHH.HHHTS.TSE CS
                               AAA   1 vllyGppGtGKTllakavake.......l.......gvefleisgsell.skyvgesekkirelfke.akeka.kps 60 
                                       +++yG   +GKT l+k  ++        +       ++++l+ + s+++ ++y+ + e ++  lfk  + e + ++ 
  gi|518653248|ref|YP_008142768.1|  30 IIIYGRRRIGKTELIKEFISGkktvyhlCtadsieeNITYLKSEFSSITgKSYFLNLEVDLFTLFKYlIDEIKdEKI 106
                                       57999999********999885555554144444444667777888888666888888888888888445544666* PP

                                       EEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHH CS
                               AAA  61 ilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpall 120
                                       i+ +DEi  l++ +        + +++ + +  d++  + s++++i  + +++++++++l
  gi|518653248|ref|YP_008142768.1| 107 IIALDEITYLVSLN--------KGILSIFQKIYDELMVN-SRLFIIFSGSSISMMEDEIL 157
                                       **********9999........88899999999998885.66888888888988888877 PP

>> Stap_Strp_toxin  Staphylococcal/Streptococcal toxin, OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.3    0.0012       1.7      27      65 ..      56      94 ..      37     108 .. 0.86
   2 ?    3.5   0.7     0.093   1.3e+02      10      37 ..     394     422 ..     384     445 .. 0.71

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                   Stap_Strp_toxin 27 kykkkdkelkvillvkseleskelaqffkgkkVdiFgle 65
                                      + ++ d+  + i ++kse++s   +  f + +Vd+F+l 
  gi|518653248|ref|YP_008142768.1| 56 HLCTADSIEENITYLKSEFSSITGKSYFLNLEVDLFTLF 94
                                      568889999999*************************84 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.093
                   Stap_Strp_toxin  10 yeeteik.sid...sltshnlkykkkdkelkv 37 
                                       +e   ik  +d   ++++++lkyk  ++++k+
  gi|518653248|ref|YP_008142768.1| 394 IE---IKfVPDvdgIKIYNELKYKSLSVNIKR 422
                                       44...44444455899***********99998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (458 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.45
# Mc/sec: 3033.72
//
Query:       gi|518653249|ref|YP_008142769.1|  [L=55]
Description: hypothetical protein FACI_IFERC00001G1892 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); 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: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 398.07
//
Query:       gi|518653250|ref|YP_008142770.1|  [L=678]
Description: hypothetical protein FACI_IFERC00001G1893 [Ferroplasma acidarmanus fer1]
Scores for 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-36  124.0   1.7    1.4e-35  123.0   1.7    1.4  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 !  123.0   1.7   7.7e-40   1.4e-35       2     364 ..      75     552 ..      74     557 .. 0.87

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 7.7e-40
                                       EEESSEEEEEEEETTTTEEEEEE-TT-B-TTSSB-SHHHHHHHHHHHHTGGGHCTTHHHHHC............... CS
                         SBP_bac_5   2 vvpaLAeswwevsdDgktytfkLRkgvkFsDGtpltAeDvvfsferlldpdtasgyasllee............... 63 
                                       vvp LA+   +++ + ++y f  R g+kFs+G+ l+A  v+fs+ r + +++++ ++++                  
  gi|518653250|ref|YP_008142770.1|  75 VVPILASH--YTNINDTHYLFDMRNGAKFSNGQSLNATSVWFSLARGIVMGQGPFSSDYSGTlfnatmagitgiylp 149
                                       7999***9..679999****************************************999998*************** PP

                                       ........................................................TCTEEEEEEEETTEEEEEESS CS
                         SBP_bac_5  64 ........................................................dqdikkveavddytvrftlkk 84 
                                                                                                   ++ ++  + t+++++++
  gi|518653250|ref|YP_008142770.1| 150 vnityalvnagynipmvtyhvnstltitrynytiaatdladmlsnfnynttemkvmEYPNQALVVNTNGTFTINTEH 226
                                       *******************9999999999999999999999999999999999999777888888889999999999 PP

                                       ETT.TTTTHCHHHHHHHGC.......CHTCTCTTTTTGTTTSE-BSSSEEEEEEETTT.EEEEEE-TTST....... CS
                         SBP_bac_5  85 pna.lfltllaavpasiak.......kaaekeddkdkdtnekpvgtGPYklkefkpgq.kivlernpdYw....... 145
                                        +a l++ l    + +i++            ++ ++   ++  +g+GPY++ ++++g  +ivl++npdYw       
  gi|518653250|ref|YP_008142770.1| 227 EYAyLLSDLAGGSWGDIVEpsyvdahGGVQVNTPSSYIDANGAIGSGPYVISSVVKGFsTIVLKANPDYWvtsamvk 303
                                       9984477777888888888999999744445555566678889**********99986699**************** PP

                                       ......TTSCSSSSEEEEEE-.SHHHHHHHHHTTSSSEEESTTCCTHCHHHHHTTEEE.....EEEEEEEEEEEEEE CS
                         SBP_bac_5 146 ......gggkpkldriefkvipdsdaraaalqsGeiddvaepppsdieqlkeakglkv.....lyespgggvtylaf 211
                                             +++++ ++ +++ +  + ++r++ + +G  ++ ++ p s+   ++   +++      ++++ ++g++y+++
  gi|518653250|ref|YP_008142770.1| 304 ngsisvMAEPASIKTVVIDYGLSHADRLEDFDKGISQISTIAPSSFKSMIDGFHNKTErtgalVKSFSEAGTYYISM 380
                                       *****999****************************99999999999999888888889999*************** PP

                                       TTTSTGGGSHHHHHHHHHHS-HHHHHHHCTTTSS.EEESSS.STTTSTTC.CSCHCCCSHH......SHHHHHHHHH CS
                         SBP_bac_5 212 NtkkppfddkrvRqAlsyAiDreeivkavlegya.tpansl.lppsspga.deeykpayka......ydpekAkklL 279
                                       N + +  +++++R+Al  A+++ + +k++ ++y  tp + + l+p sp + +  y+p   +       ++++A k +
  gi|518653250|ref|YP_008142770.1| 381 NVADNYTNNTNFREALYDAMNYSAQLKIYDNNYNsTPEAYAeLGPLSPIYgHAFYNP---DnlpmpsQNITAALKNI 454
                                       ***********************9888884333323333333333333330333333...13458899999999999 PP

                                       HHTT-BCSSTSCEETC.............EEEEEEEEETTSHHHHHHHHHHHHHHHHTTEEEEEEEE.CHHHHHHHH CS
                         SBP_bac_5 280 keaGykdgdggglrek.............klkltlllasgspaekaiaeliqqqlkkiGikvevktv.dwaatyler 342
                                         aG    ++ +l++               + +++++++ ++ e+a +    +++++iG+ ++ k v d+  +++ +
  gi|518653250|ref|YP_008142770.1| 455 SIAGDAMHFYVKLSNGtrygdktgtdlstHTFTLTAISPATSIETAQLSSAISSFEQIGLAFTTKLVtDS-IADTYT 530
                                       9999888888888777888888***9997777788888889999999999*****************776.777789 PP

                                       HHCTTESEEEEEEECTTSTTHH CS
                         SBP_bac_5 343 vkdgdfdmillgwgadypdpdn 364
                                       +++ +++++   w +dypdp  
  gi|518653250|ref|YP_008142770.1| 531 TNNSTPQFYDIYWLPDYPDPIG 552
                                       *******************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (678 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       958  (0.053433); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.41
# Mc/sec: 4909.65
//
Query:       gi|518653251|ref|YP_008142771.1|  [L=128]
Description: HEPN protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.8e-19   68.6   1.5    5.3e-19   68.5   1.5    1.0  1  HEPN      HEPN domain
  ------ inclusion threshold ------
      0.037   14.0   0.0      0.051   13.6   0.0    1.3  1  NICE-3    NICE-3 protein


Domain annotation for each model (and alignments):
>> HEPN  HEPN domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.5   1.5   5.9e-23   5.3e-19       1     116 [.       6     126 ..       6     128 .] 0.92

  Alignments for each domain:
  == domain 1  score: 68.5 bits;  conditional E-value: 5.9e-23
                                       HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHTT--.SSCCHHHHHHCCHHHT.........-H CS
                              HEPN   1 aeewlrrAeedleaAellleegdydlacfhaqqaaekalKAlllkkggeppkthdlreLleelkkelke......se 71 
                                       ae +++rA+++le+  +l++ ++ydla+f+  q +e++lK+ +l+k g +  th+l+eL+++l++ + +      +e
  gi|518653251|ref|YP_008142771.1|   6 AEILKKRANDFLEEGAHLIDIKKYDLAIFNLDQYCELILKYKILTKLGFYLDTHSLKELINKLSEFDDNikdlvnNE 82 
                                       58899********************************************************8888887777787777 PP

                                       HHHHHHHHHHCCCHHCCCTSS--S--HHHHHHHHHHHHHHHHH.HH CS
                              HEPN  72 elreeleeLekayiesrYpdakeeyteedaeealkdaeevlel.ve 116
                                       +   ++ +L++ayi +rY ++++  +e++ +++ k+  ev++  v+
  gi|518653251|ref|YP_008142771.1|  83 KDLLYIGRLTDAYISARYMPFEF--DEKETKNVYKFIVEVFNRyVN 126
                                       888888****************9..***********9999987565 PP

>> NICE-3  NICE-3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   5.7e-06     0.051     146     176 ..      87     117 ..      55     122 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 5.7e-06
                            NICE-3 146 lidqlldlyehARhgpeeFgeeeylkyqell 176
                                        i +l d+y +AR+ p eF+e+e ++  + +
  gi|518653251|ref|YP_008142771.1|  87 YIGRLTDAYISARYMPFEFDEKETKNVYKFI 117
                                       5889*******************99876655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 999.94
//
Query:       gi|518653252|ref|YP_008142772.1|  [L=104]
Description: DNA polymerase beta subunit [Ferroplasma acidarmanus fer1]
Scores for complete 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-09   36.2   0.2    6.8e-09   35.9   0.2    1.3  1  NTP_transf_2    Nucleotidyltransferase domain
    1.2e-07   31.7   0.3    1.8e-07   31.2   0.2    1.4  1  Polbeta         Polymerase beta, Nucleotidyltransferase
     0.0051   17.0   0.0     0.0064   16.7   0.0    1.1  1  DNA_pol_B_palm  DNA polymerase beta palm


Domain annotation for each model (and alignments):
>> NTP_transf_2  Nucleotidyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.9   0.2   1.1e-12   6.8e-09       8      61 ..      27      77 ..      13     103 .. 0.72

  Alignments for each domain:
  == domain 1  score: 35.9 bits;  conditional E-value: 1.1e-12
                                      HHHHTTTSEEEEEHHHHCTTSCTTSSEEEEEEESTTCHHHHHHEHHHHHHHHCC CS
                      NTP_transf_2  8 lkelepvakvvlfGSyarGtalkgSDiDllvvlpeevsrekkeegleklaeiik 61
                                      +k  + +a+v++fGS+ +G ++  SDiD+lv+ ++      k+e++ k  + i+
  gi|518653252|ref|YP_008142772.1| 27 VKNIDNNARVFVFGSVLTGNTTASSDIDILVLESNKNL---KDEINIKVLKYID 77
                                      5666669*************************999965...3333333333333 PP

>> Polbeta  Polymerase beta, Nucleotidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.2   0.2   2.9e-11   1.8e-07      12      52 ..      32      71 ..      21     100 .. 0.77

  Alignments for each domain:
  == domain 1  score: 31.2 bits;  conditional E-value: 2.9e-11
                                      HHHSTTEEEEEE-S------EEEEEEEESS---HHHHHHHH CS
                           Polbeta 12 eielaylFGSrakgkareeSDiDlavllkekldleeelela 52
                                      + + +++FGS+++g+++ +SDiD+ vl ++k +l++e++++
  gi|518653252|ref|YP_008142772.1| 32 NNARVFVFGSVLTGNTTASSDIDILVLESNK-NLKDEINIK 71
                                      55679**********************9999.677766664 PP

>> DNA_pol_B_palm  DNA polymerase beta palm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   1.1e-06    0.0064      10      64 ..      19      74 ..      14      87 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 1.1e-06
                                      HHHHHHHHHHHH-TT-EEEE-HHHHTT-SE.ESSEEEEEEBTTBSTTSS--HHHHH CS
                    DNA_pol_B_palm 10 lealvkkaakeldpevevivcGSYRRgaes.sGDvDvlitkkdakseskklkklle 64
                                      + + v   +k++d++++v v GS   g+++ s D+D+l+ +++++ +++ + k+l+
  gi|518653252|ref|YP_008142772.1| 19 VCKEVYIFVKNIDNNARVFVFGSVLTGNTTaSSDIDILVLESNKNLKDEINIKVLK 74
                                      5566777899**************999865389*********99998777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (104 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); 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: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 783.37
//
Query:       gi|518653253|ref|YP_008142773.1|  [L=229]
Description: hypothetical protein FACI_IFERC00001G1896 [Ferroplasma acidarmanus fer1]
Scores for complete 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-27   94.9   0.0    7.9e-27   94.6   0.0    1.1  1  CbiZ      Adenosylcobinamide amidohydrolase


Domain annotation for each model (and alignments):
>> CbiZ  Adenosylcobinamide amidohydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.6   0.0   4.4e-31   7.9e-27       8     192 .]      43     212 ..      37     212 .. 0.90

  Alignments for each domain:
  == domain 1  score: 94.6 bits;  conditional E-value: 4.4e-31
                              CbiZ   8 vlssavlngGlrelravlnhqvpegyeredpeeyleeyleelglppektvgllTaadmenaaiaeeefedlevtavv 84 
                                       +lss++ +g  +++r +++++++e +++++ + y+++ le++gl  ++t++++T +d++++ i + e    +  ++v
  gi|518653253|ref|YP_008142773.1|  43 ALSSTISGG--GHIRSIVFNTLQEYIQEDKFDLYINKILENYGL-GANTPVFVTLVDINHMKIINTE----DYLIAV 112
                                       677775544..46999999999********999***********.8*********************....99**** PP

                              CbiZ  85 TaGvesnavragdedeeaekpGTINiivlinaaLtdaalvralitatEAKtaalqdlgvrsryseg.atGTgTDaia 160
                                       TaG+ s +++ + +    +kpGTIN++v+++++ + +a+++++ +atEAK+ a  +lg++  +     +GT +Da++
  gi|518653253|ref|YP_008142773.1| 113 TAGI-SEPASFKGN----RKPGTINVMVIVKRKPEGNAMADMFRVATEAKSMAAFALGLKFGN--IpSPGTVSDAVC 182
                                       ****.888777773....79***************************************7444..35********** PP

                              CbiZ 161 vaadkegeeeltyaGkhtklGeliaraVyeAv 192
                                       v+    gee ++y+G  t lG+ i + +y++v
  gi|518653253|ref|YP_008142773.1| 183 VVFA--GEEGIRYCGFGTALGDKIIESIYDSV 212
                                       ***9..55569******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (229 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); 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: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1599.40
//
Query:       gi|518653254|ref|YP_008142774.1|  [L=326]
Description: hypothetical protein FACI_IFERC00001G1897 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-21   75.3   0.0    6.9e-21   74.9   0.0    1.1  1  Peripla_BP_2  Periplasmic binding protein


Domain annotation for each model (and alignments):
>> Peripla_BP_2  Periplasmic binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.9   0.0   3.8e-25   6.9e-21       1     234 [.      54     273 ..      54     276 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.9 bits;  conditional E-value: 3.8e-25
                                       EEE-SHHHHHHHHHTT-GGGEEEB-GGG--GGGGGGT..TS-BSBESSSB-HHHHHHH--SEEEE-GGG...GGGHH CS
                      Peripla_BP_2   1 iaslspsvteillalGatdkvvgvdtttsdpldadkleeaivevgadgeidvEklaalkPDlvilskglgltdedee 77 
                                       i+slsp+ t++l+alG++  + +v+ +t +p+   +   +  +v  + +++  ++++lkPD vi+s+++  ++e  e
  gi|518653254|ref|YP_008142774.1|  54 IVSLSPAATGTLYALGVSSDIIAVGPCTHFPYNVTE---NLQKVTCYPDFSAQQIINLKPDAVISSSSY-KATEVQE 126
                                       9*******************************9987...899999999*********************.9999999 PP

                                       HHHHHS-EE..E----TTSHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHTS-TT.-EEEEEEEETTE..EE CS
                      Peripla_BP_2  78 llksgiptv..ivessntgeslkeqiralgellgledeaeklvaeidsklaaaksaidsekpkpvlvfggadeggyv 152
                                       ll++gi+++  +  s++t+  +++q + lg+l+g+ ++a kl ++++  l ++k+     ++k v++    ++ ++ 
  gi|518653254|ref|YP_008142774.1| 127 LLDAGINYIylDSGSGSTFHLIEKQDTLLGKLTGTMSNASKLNSWMNTSLNDFKDTGL--TNKSVFYALCIENHAPW 201
                                       ******9861155566777*******************************99998654..558898888889999** PP

                                       EE-TTSTTTHHHHTS--EESTTT--STT-EEE-HHHHHHH--SEEEEEEHHHHT-S--HHHHT-SHHHHTSHHHHTT CS
                      Peripla_BP_2 153 vagsnsyigdlldalgieniaaeskkseyeeisaEqilasdpdvifvsgraeadnktgleflkenpllaelpAvkng 229
                                        +g+n++i+ +++ + ++n+  +   s++ + s   +++++p+v++  +r       +l++ +++p+++++pA+kn 
  gi|518653254|ref|YP_008142774.1| 202 TSGNNTFINSMFNYAHLKNVMTD---SGFFQASTQVVANDSPQVLLLGTR------VNLSQ-INTPTYESTPAYKND 268
                                       ********************777...69**********************......55555.699************ PP

                                       -EEEE CS
                      Peripla_BP_2 230 rVyal 234
                                        V+ +
  gi|518653254|ref|YP_008142774.1| 269 SVFQI 273
                                       **977 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2407.27
//
Query:       gi|518653255|ref|YP_008142775.1|  [L=349]
Description: ABC-type Fe3+-siderophores transporter, permease component [Ferroplasma acidarmanus fer1]
Scores for complete 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-79  265.8  42.3    4.9e-79  265.6  42.3    1.0  1  FecCD     FecCD transport family
  ------ inclusion threshold ------
       0.22   10.4   7.0        1.1    8.1   0.0    2.5  2  DUF3488   Domain of unknown function (DUF3488)


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 !  265.6  42.3   5.5e-83   4.9e-79       2     312 .]      24     340 ..      23     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 265.6 bits;  conditional E-value: 5.5e-83
                             FecCD   2 lllllllslllgavkispsevfeallgka.......dsleaeivlelrlprvlaallvGaaLavaGallQtvtrNpL 71 
                                       +++++++sl +g+v+is++++++++l +        ++ +  i+  +r p v+a ++vGaaL+v Ga++Q+++rNp+
  gi|518653255|ref|YP_008142775.1|  24 FIIAFIVSLDTGPVHISLKNIVNIILFQIgagkltaTQGNYVIIAMIREPEVVASAAVGAALGVGGAVIQSIFRNPI 100
                                       789**********************99889999999999999*********************************** PP

                             FecCD  72 adPsilGissgaalgavlalllllgslslfalplaaflgallalllvlllarkrkgasplkliLaGiavsallsalt 148
                                        +P++ G+ssgaalgavla+++ ++ ++lf+lp++af++a+++++lv++l+ +++++ p+ l+L+Gia+s+++++l+
  gi|518653255|ref|YP_008142775.1| 101 SEPYVTGVSSGAALGAVLAIVFSITIFGLFTLPIFAFVFAIIVVSLVYMLSIRSGRTPPVILLLTGIAISLFATSLV 177
                                       ***************************************************999*********************** PP

                             FecCD 149 sllllllneealesilfwllGslsgaswskvllllvllllllllllllarkldllalgdetAkslGvnvervrllll 225
                                       +++l+   ++  ++i fw+lGslsg+ ws+  ++++l++++ ++l +++++l++l++gd  Aks G+nver +l +l
  gi|518653255|ref|YP_008142775.1| 178 AIMLYS-RPALENTIFFWFLGSLSGILWSEDEIVVPLVIVTSVILGMMYKQLNALQMGDVYAKSAGINVERSKLGAL 253
                                       ****99.999******************************************************************* PP

                             FecCD 226 llvalltavavalvGpigFvGLivPhiarllvgadhrkllplsallGallllladllarlllsptelpvgivtaliG 302
                                        l++++++++v+++G igFvGLi Ph+ rl++g ++++++p+sa+lGa++l+l++ +a+l+++ +  pvg++t +iG
  gi|518653255|ref|YP_008142775.1| 254 GLTTIAVSASVSISGLIGFVGLIFPHVSRLIFGGSNKYVIPASAILGATFLMLCNDIAHLIITGIVFPVGVITGMIG 330
                                       ***************************************************************************** PP

                             FecCD 303 apffiylllr 312
                                       +pff++l++r
  gi|518653255|ref|YP_008142775.1| 331 VPFFMILMAR 340
                                       *******986 PP

>> DUF3488  Domain of unknown function (DUF3488)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00012       1.1      84     115 ..       3      34 ..       1      61 [. 0.85
   2 ?    1.1   5.8     0.018   1.6e+02       5      74 ..     117     186 ..     111     240 .. 0.60

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00012
                           DUF3488  84 alKllElrsrRDalvllllgffllatsflfsq 115
                                       + K+ E++  RD ++ +++++f++a  + +++
  gi|518653255|ref|YP_008142775.1|   3 GNKYSEMQHHRDTMFAIAIAIFIIAFIVSLDT 34 
                                       579********************998665555 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.018
                           DUF3488   5 lllalalallplalrlplwvlllaalllvwrlllarrraplpsrwlllllallav.allllsygtllgrda 74 
                                       +l+++  + +  +  lp++ +++a++++ + ++l  r+ + p+ +ll l  ++   +++ l   +l +r a
  gi|518653255|ref|YP_008142775.1| 117 VLAIVFSITIFGLFTLPIFAFVFAIIVVSLVYMLSIRSGRTPPVILL-LTGIAISlFATSLVAIMLYSRPA 186
                                       45555555555666777777777776666556665666666662332.22222221222222223333444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (349 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1044  (0.0582297); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 2572.39
//
Query:       gi|518653256|ref|YP_008142776.1|  [L=247]
Description: ABC-type Fe3+-siderophores transporter, ATPase component [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-24   87.1   0.1      2e-24   86.6   0.1    1.2  1  ABC_tran    ABC transporter
    2.6e-06   27.4   1.2     0.0031   17.4   0.0    2.1  2  AAA_21      AAA domain, putative AbiEii toxin, Type IV TA sys
    1.3e-05   24.7   5.4     0.0014   18.2   5.4    2.1  1  SMC_N       RecF/RecN/SMC N terminal domain
     0.0012   18.6   0.3      0.002   17.9   0.3    1.6  1  AAA_15      AAA ATPase domain
  ------ inclusion threshold ------
       0.04   14.1   0.0      0.068   13.4   0.0    1.4  1  MoeA_C      MoeA C-terminal region (domain IV)
      0.077   12.8   0.1       0.14   11.9   0.1    1.4  1  AAA_29      P-loop containing region of AAA domain
        0.1   12.3   0.0       0.18   11.5   0.0    1.4  1  AAA_24      AAA domain
        0.1   12.4   0.1        5.6    6.7   0.1    2.2  2  ATP_bind_1  Conserved hypothetical ATP binding protein
       0.11   12.8   0.0       0.18   12.1   0.0    1.5  1  AAA_16      AAA ATPase domain
       0.18   12.3   4.5       0.45   11.0   4.5    1.7  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 !   86.6   0.1   1.1e-27     2e-24       4     137 .]      19     157 ..      16     157 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 1.1e-27
                                       EEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH. CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
                          ABC_tran   4 vslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren. 79 
                                       +s++l +ge++ i G+nG+GK++ l +  +  k ++Ge+++dg+++k+ ++++   +i++++qe     +ltvr+  
  gi|518653256|ref|YP_008142776.1|  19 LSFSLGRGEILSICGKNGSGKTSTLVAANNYIKLEKGEVNVDGNNIKNMKINQIATKIAYVQQEIPEPMGLTVRDIm 95 
                                       89**************************************************************99999999***9* PP

                                       ........HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                                       ........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  80 ........esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                                               +++e+i+kal+  ++ +      +++ ++LSgG+k++v++a  + ++++ +l+DEpt+
  gi|518653256|ref|YP_008142776.1|  96 eiagytreNKEEDIQKALDLCEMGDSI----DRDFATLSGGEKRMVSIASGIYQNSDYILMDEPTS 157
                                       ****96655556666666666666644....5555*****************************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 !    8.4   1.0   0.00093       1.7       4      19 ..      31      46 ..      28      69 .. 0.76
   2 !   17.4   0.0   1.7e-06    0.0031     212     283 ..     104     175 ..      60     191 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.00093
                            AAA_21  4 liGpNgsGKSnLLdal 19
                                      + G+NgsGK++ L a 
  gi|518653256|ref|YP_008142776.1| 31 ICGKNGSGKTSTLVAA 46
                                      89*********98766 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 1.7e-06
                            AAA_21 212 vderlrergvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHP...kllrrllellk 283
                                       ++e ++++ + + e+gd  +++++ lS G kr+  +++ +++     + +l DEp ++L+    +ll+ +++ lk
  gi|518653256|ref|YP_008142776.1| 104 NKEEDIQKALDLCEMGDSIDRDFATLSGGEKRMVSIASGIYQNS---DYILMDEPTSFLDIdkiHLLENIIKSLK 175
                                       3333333389999****************************999...77************66666666666664 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   5.4   7.6e-07    0.0014      26     193 ..      28     181 ..      19     207 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 7.6e-07
                                       EEEEEESTTSSHHHHHHHHHHHCT.T.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  26 ftaivGpNGSGKsnlldAilFvLG.ersakklrseklsdlihkskekasvkkaeveitfdnedkklkiekeevsisr 101
                                       + +i G+NGSGK++ l A   ++  e+   ++  ++++++     ++ ++k a+v+  + ++           +++ 
  gi|518653256|ref|YP_008142776.1|  28 ILSICGKNGSGKTSTLVAANNYIKlEKGEVNVDGNNIKNMK---INQIATKIAYVQQEIPEPMGL--------TVRD 93 
                                       56799999999988666653333303333344444444443...335556666666654444444........4444 PP

                                       EEETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N 102 rvkrkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkk 178
                                        ++  g ++   ++   +  ++ e+  s + +  +LSgGek +v++a       ++ +   l+De  + LD  +++ 
  gi|518653256|ref|YP_008142776.1|  94 IMEIAGYTRENKEEDIQKALDLCEMGDSIDRDFATLSGGEKRMVSIA----SGIYQNSDYILMDEPTSFLDIDKIHL 166
                                       44444443333333333446777777777777789*********986....567899999***************** PP

                                       HHHHHHHHCTTSEEE CS
                                       xxxxxxxxxxxxxxx RF
                             SMC_N 179 vaellkeksknaQfi 193
                                       + +++k+ +k    i
  gi|518653256|ref|YP_008142776.1| 167 LENIIKSLKKMGKGI 181
                                       ******999875444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   1.1e-06     0.002      25      78 ..      28      70 ..      19     227 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                            AAA_15 25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdik 78
                                      +  ++GkN+sGK+s l a     n       ++ik+ek ++++  n+ ++++i 
  gi|518653256|ref|YP_008142776.1| 28 ILSICGKNGSGKTSTLVAA----N-------NYIKLEKGEVNVDGNNIKNMKIN 70
                                      6789**************8....3.......34555555555555544444442 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 ?   13.4   0.0   3.8e-05     0.068      35      61 ..      33      59 ..       8      63 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.8e-05
                                      S---TT-GGGCTT--EEEEE-TT--EE CS
                            MoeA_C 35 gkqgSglLsslaeAnglivipegtegl 61
                                      gk+gSg +s+l+ An +i +++g+ ++
  gi|518653256|ref|YP_008142776.1| 33 GKNGSGKTSTLVAANNYIKLEKGEVNV 59
                                      79********************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 ?   11.9   0.1   7.8e-05      0.14      20      42 ..      24      47 ..      12      59 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 7.8e-05
                            AAA_29 20 dlkgatlltGpsGsGK.STllDAi 42
                                       + ++  + G++GsGK STl+ A 
  gi|518653256|ref|YP_008142776.1| 24 GRGEILSICGKNGSGKtSTLVAAN 47
                                      4444889*********77887665 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0    0.0001      0.18       7      48 ..      31      80 ..      26     129 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.0001
                            AAA_24  7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie...........s 48
                                      i G++g+GKT+++  + +   +i +ekG  ++d++++++++           +
  gi|518653256|ref|YP_008142776.1| 31 ICGKNGSGKTSTLVAA-N--NYIKLEKGEVNVDGNNIKNMKinqiatkiayvQ 80
                                      89*********99999.4..58999**********999886654444443330 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 ?    6.7   0.1    0.0031       5.6       1      32 [.      31      59 ..      31      70 .. 0.84
   2 ?    4.0   0.0     0.021        38      89     139 ..     144     195 ..      86     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0031
                        ATP_bind_1  1 vvGpaGsGKttfvgalseilelrgrsvavvNL 32
                                      ++G  GsGKt+   a +++++l++ +v   N 
  gi|518653256|ref|YP_008142776.1| 31 ICGKNGSGKTSTLVAANNYIKLEKGEV---NV 59
                                      68***********999*9999996554...44 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.021
                        ATP_bind_1  89 e.eddyllfDtPGQielfthseslakiveeLesefalvvvyLvDsqrltdpt 139
                                       + ++dy+l+D P           l +i+++L++ ++ + ++L D +++ + +
  gi|518653256|ref|YP_008142776.1| 144 YqNSDYILMDEPTSFLDIDKIHLLENIIKSLKKMGKGILLVLHDINIAINMS 195
                                       4366899999998877778888999*******************99876644 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   0.0    0.0001      0.18      22      88 ..      24      85 ..      19     200 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.0001
                            AAA_16 22 grpelvllsGesGvGKsslvrellralekdggif.lrgkcdqlesaipysalaqalareellrqllde 88
                                      gr+e++ + G  G+GK+s + ++ ++++ ++g + + g++ ++   +    + q++++  +++q+  e
  gi|518653256|ref|YP_008142776.1| 24 GRGEILSICGKNGSGKTSTLVAANNYIKLEKGEVnVDGNNIKN---MK---INQIATKIAYVQQEIPE 85
                                      7889****************99999999998888899998888...22...34444333555555555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   4.5   0.00025      0.45      20      75 ..      27      79 ..       7     181 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00025
                            AAA_23 20 gltlItGpNGaGKTTil.dAiklaLygetprlsrksgrgfeksdveiesegkvkayv 75
                                       +  I+G+NG+GKT+ l  A  ++  ++  ++ + +g+++++ +++  + +++ ayv
  gi|518653256|ref|YP_008142776.1| 27 EILSICGKNGSGKTSTLvAANNYIKLEK--GEVNVDGNNIKNMKIN--QIATKIAYV 79
                                      4678*********976625555555553..4444445555555544..334444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      558  (0.0311228); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 1751.10
//
Query:       gi|518653257|ref|YP_008142777.1|  [L=116]
Description: hypothetical protein FACI_IFERC00001G1900 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-34  118.2   6.5    2.4e-34  118.1   6.5    1.0  1  YbjQ_1    Putative heavy-metal-binding
  ------ inclusion threshold ------
      0.027   14.8   0.7       0.42   11.0   0.2    2.2  2  DUF4156   Domain of unknown function (DUF4156)


Domain annotation for each model (and alignments):
>> YbjQ_1  Putative heavy-metal-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   6.5   2.7e-38   2.4e-34       1     103 [.       7     108 ..       7     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 2.7e-38
                            YbjQ_1   1 mivtttesiegkeivevlgivtgetvrsrnvlkdilaglrslvGGelkayeeeleeareeAlerlkeeAeelGAnAv 77 
                                       +i++tt++++g +iv+++g+v+g +vrsr ++ +++aglrsl+GGe+k+y+ +l+ear +A+ r+k++A+elGAn v
  gi|518653257|ref|YP_008142777.1|   7 VITVTTPEVSGMTIVRTIGTVFGIVVRSRGLGGNVVAGLRSLAGGEIKEYTAMLTEARIHAVGRMKANASELGANGV 83 
                                       699************************************************************************** PP

                            YbjQ_1  78 vgvrldtseigekgmlevlayGTAVk 103
                                       v++r+d+seig+ +m+e++ayGTAV+
  gi|518653257|ref|YP_008142777.1|  84 VAMRFDSSEIGQ-TMSEIVAYGTAVV 108
                                       **********99.************8 PP

>> DUF4156  Domain of unknown function (DUF4156)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.0     0.018   1.6e+02      59      75 ..      36      52 ..      30      64 .. 0.78
   2 ?   11.0   0.2   4.6e-05      0.42      44      73 ..      62      91 ..      50     108 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.018
                           DUF4156 59 alGgntivlvtstatet 75
                                       lGgn++ ++ s a+ +
  gi|518653257|ref|YP_008142777.1| 36 GLGGNVVAGLRSLAGGE 52
                                      69*****9999886554 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.6e-05
                           DUF4156 44 elvrgaandLrneAaalGgntivlvtstat 73
                                      e  + a+  ++ +A++lG+n +v +   ++
  gi|518653257|ref|YP_008142777.1| 62 EARIHAVGRMKANASELGANGVVAMRFDSS 91
                                      566788999*************99876643 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.43
# Mc/sec: 804.30
//
Query:       gi|518653258|ref|YP_008142778.1|  [L=440]
Description: hypothetical protein FACI_IFERC00001G1901 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-42  146.4  70.2    1.4e-42  146.0  70.2    1.2  1  AA_permease_2   Amino acid permease
    7.1e-41  140.3  63.5    9.4e-41  139.9  63.5    1.2  1  AA_permease     Amino acid permease
    1.7e-09   37.0  33.2    1.7e-09   37.0  33.2    2.4  2  Spore_permease  Spore germination protein
  ------ inclusion threshold ------
       0.15   12.1   0.2       0.15   12.1   0.2    3.9  5  PilX_N          PilX N-terminal


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 !  146.0  70.2   3.2e-46   1.4e-42       5     418 ..      11     417 ..       7     427 .. 0.81

  Alignments for each domain:
  == domain 1  score: 146.0 bits;  conditional E-value: 3.2e-46
                     AA_permease_2   5 safalvigsvigsgifvkn..laasggpalilwvwiavligslavllvyaElssalprsgGi.yvytkaafgkkvaf 78 
                                        a+a+ +g++ig+gifv +   +a +g+ +++ ++++ ++  ++ +  + El+s +p+ +G+ ++y ++afg  ++f
  gi|518653258|ref|YP_008142778.1|  11 VATAVGLGAIIGAGIFVLSgtTIALAGANALIAFVLVGVLA-IIIAMELGELGSIMPHAKGAsFSYIYEAFGSEMGF 86 
                                       5899**************99978888888777777766666.67888899**9996666555278************ PP

                     AA_permease_2  79 lsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilkillp 155
                                       ++++++ f+++ ++a+i+  ++syl +++g    ++ +  +++ai+++ ++a++ni+gik+ ak+ ++l+ +k+  +
  gi|518653258|ref|YP_008142778.1|  87 ITGILLYFSFSTAIAAIALGFGSYLGSLVGL---HTGYYPIIFAIILIFVLAIVNIVGIKKAAKADFYLVMVKLA-I 159
                                       *****************************95...467778999*******************************5.7 PP

                     AA_permease_2 156 liiliilglitvdgggfsslstetdtffpngwpgvllglli....vlwsfdGfesaanvseevkk..kdvpkaifig 226
                                       l+i++i+++i++  + +     +t++f++ + + +++++++    v+++++Gf s++ +++ +k    ++ kai+++
  gi|518653258|ref|YP_008142778.1| 160 LTIFVIAAVILAYTTKSL----NTSNFVTPVAKDNISAIFAasiaVFFAYSGFQSISTFTSDIKGgaNKAAKAIILS 232
                                       788888888887555554....477777776664444443334449******************87446******** PP

                     AA_permease_2 227 llivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggk.vvaiivvilialsllgaintavigssrvleal 302
                                       +li++v+y+lv +a++  vp ++ + +++   ++a  ++ v+++    ++v i++ ++   a ++ +++ssr+l+++
  gi|518653258|ref|YP_008142778.1| 233 VLISMVFYILVVLALILMVPASKYTISAD---PLAFALKYVHAPySIYALVTIGALIATTSATLAMIMTSSRILYQI 306
                                       *************************9887...799999999999455555556666677778899999********* PP

                     AA_permease_2 303 ardgvlPrffakvn.kfgspiraiiltaivslillllfllassaaynfllsvsslgliisyllliigalilrkkrph 378
                                       +  + lP+ff+k n k+   ++++i++ ++ +++  lf+     ++++++++s++gl++syl+++++ +  r+ ++ 
  gi|518653258|ref|YP_008142778.1| 307 GDNKLLPKFFRKFNyKKDVSVNGVIISSLIGIVM--LFS----GNIYIIAAISNFGLLLSYLVASFAIIHFRRIKKF 377
                                       *************************999999443..454....579******************9877766655453 PP

                     AA_permease_2 379 l..krpgkilvaiigalfllfllvalffppkgpatqssliyt 418
                                          k+p  ++++ii+ ++ll+++++++ p + ++++  +i++
  gi|518653258|ref|YP_008142778.1| 378 GsfKTP-LYPFTIIAGIILLIVFILGM-PREALDIGVVIILL 417
                                       332333.47888888888888877766.66666666666665 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9  63.5   2.1e-44   9.4e-41       5     467 ..      15     427 ..      11     438 .. 0.84

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 2.1e-44
                       AA_permease   5 ialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngp.ksggfytyasrflgpelGfviGl 80 
                                         lg +iG+g+fv +g +++ aG  +al+a++l+gv  +++++ lge+ +++p   g+   y+ +  g+e+Gf +G+
  gi|518653258|ref|YP_008142778.1|  15 VGLGAIIGAGIFVLSGTTIALAGA-NALIAFVLVGVLAIIIAMELGELGSIMPhAKGASFSYIYEAFGSEMGFITGI 90 
                                       679********************9.999*************************76666668**************** PP

                       AA_permease  81 n.ylfswitvlaleltaasiliqfwelvtdlpkawvtgavflvvlliinlvgvkvygeaefilalikiiaiiafiiv 156
                                       + y++++ + +a++l+  s+l ++++l t +   +++++++++vl i+n+vg+k  ++a f l ++k+ ++ +f+i 
  gi|518653258|ref|YP_008142778.1|  91 LlYFSFSTAIAAIALGFGSYLGSLVGLHTGYY-PIIFAIILIFVLAIVNIVGIKKAAKADFYLVMVKLAILTIFVIA 166
                                       *5666666666666666666666677766666.8999**************************************** PP

                       AA_permease 157 giillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvivvfaftGielvaiiagEvkdPeksiP 233
                                        +il    k  +           s+f   + ++       ++++++++ ++v+fa++G+ ++ +  +++k  + +  
  gi|518653258|ref|YP_008142778.1| 167 AVILAYTTKSLNT----------SNFVTPVAKD-------NISAIFAASIAVFFAYSGFQSISTFTSDIKGGANKAA 226
                                       *988888887777..........3333333344.......8************************************ PP

                       AA_permease 234 kailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvs.vlaplinaviltaalssanssly 309
                                       kai+  v++ ++fY+l++l+++l+vp +  ++ +d      p+  ++k+   +  +  l++++ l+a++s+ +++++
  gi|518653258|ref|YP_008142778.1| 227 KAIILSVLISMVFYILVVLALILMVPASKYTISAD------PLAFALKYVHAPySIYALVTIGALIATTSATLAMIM 297
                                       *****************************999993......455566665544157899****************** PP

                       AA_permease 310 sasRvlyslakdglaPkvlkkvs.krgvPlraillsmiisllalllaslnlaapivfnfllaisaliglivwlliil 385
                                       ++sR+ly   +++l+Pk+++k++ k+ v ++++++s++i+ ++l+  +++ +         ais +  l+ +l++++
  gi|518653258|ref|YP_008142778.1| 298 TSSRILYQIGDNKLLPKFFRKFNyKKDVSVNGVIISSLIGIVMLFSGNIYII--------AAISNFGLLLSYLVASF 366
                                       ********************9987999*****************88888888........9**************** PP

                       AA_permease 386 sylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgpkdwgaasfaaaylivllflii 462
                                       +++ fR+  k+ g       fk++l+p++ i ++++li ++l +     l              + + +i+llf+++
  gi|518653258|ref|YP_008142778.1| 367 AIIHFRRI-KKFGS------FKTPLYPFTIIAGIILLIVFILGMPRE-ALD-------------IGVVIILLLFMLY 422
                                       ******99.45555......899999999888887777666554333.333.............4555555555555 PP

                       AA_permease 463 lvgvk 467
                                       ++ ++
  gi|518653258|ref|YP_008142778.1| 423 YFFIE 427
                                       55555 PP

>> Spore_permease  Spore germination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.0  33.2   3.7e-13   1.7e-09      13     278 ..      18     295 ..       7     344 .. 0.77
   2 ?   -6.8   7.8         4   1.8e+04     105     124 ..     381     400 ..     347     432 .. 0.52

  Alignments for each domain:
  == domain 1  score: 37.0 bits;  conditional E-value: 3.7e-13
                    Spore_permease  13 sfqlGvgiltlprsvaeqatpdgWisvllagiiililvllmlkllkkfp..ektliellkkilgkwLGsllsilfil 87 
                                        +++G+gi +l ++ ++ a++++ i+ +l g++++i+++ + +l + +p  +   ++++ + +g+ +G++ +il+  
  gi|518653258|ref|YP_008142778.1|  18 GAIIGAGIFVLSGTTIALAGANALIAFVLVGVLAIIIAMELGELGSIMPhaKGASFSYIYEAFGSEMGFITGILLYF 94 
                                       579************************************999987765511778999******************** PP

                    Spore_permease  88 yFlllaafelRefseliqvflledtplwiiilllllvilYlvvk..Gieslar......eflfiivilliilllill 156
                                        F + +a  +  f+  +   +  +t  + ii+ ++l++++++v+  Gi++ a+      ++ ++i+ +++i  +il 
  gi|518653258|ref|YP_008142778.1|  95 SFSTAIAAIALGFGSYLGSLVGLHTGYYPIIFAIILIFVLAIVNivGIKKAAKadfylvMVKLAILTIFVIAAVILA 171
                                       ****************************************999777*******988765444444444455555555 PP

                    Spore_permease 157 fslklaei.knlrPvlgngikpvlkslkttslsflgve.illllvpflkdkkkvkkaallgvlistllyllttlivi 231
                                         +k+ +  ++++Pv+++ i+ ++ ++  + ++++g+  i ++        +k++ka++l+vlis+++y+l++l  i
  gi|518653258|ref|YP_008142778.1| 172 YTTKSLNTsNFVTPVAKDNISAIFAASIAVFFAYSGFQsISTFTSDIKGGANKAAKAIILSVLISMVFYILVVLALI 248
                                       6666666515689************************736666666666799************************* PP

                    Spore_permease 232 lvlsveqlkkatwptlsllkvievpefierlevllivvwilvifaki 278
                                       l+  + +  ++  p+   lk ++ p  i  l  ++ ++ +      +
  gi|518653258|ref|YP_008142778.1| 249 LMVPASKYTISADPLAFALKYVHAPYSIYALVTIGALIATTSATLAM 295
                                       *******9999999999999999995565555555444332222222 PP

  == domain 2  score: -6.8 bits;  conditional E-value: 4
                    Spore_permease 105 qvflledtplwiiilllllv 124
                                       ++ l++ t ++ iill++++
  gi|518653258|ref|YP_008142778.1| 381 KTPLYPFTIIAGIILLIVFI 400
                                       44444444444444433333 PP

>> PilX_N  PilX N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.3       0.6   2.7e+03       7      20 ..     126     139 ..     120     142 .. 0.50
   2 ?   -4.0   1.0       3.5   1.6e+04       5       9 ..     163     167 ..     151     171 .. 0.44
   3 ?   -1.0   1.3       0.4   1.8e+03       4      14 ..     240     251 ..     239     254 .. 0.70
   4 ?   12.1   0.2   3.2e-05      0.15      11      42 ..     276     307 ..     275     316 .. 0.92
   5 ?   -2.9   1.1       1.5   6.9e+03       2       8 ..     392     407 ..     391     421 .. 0.37

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.6
                            PilX_N   7 vtllllavltllgv 20 
                                        +++l +vl ++++
  gi|518653258|ref|YP_008142778.1| 126 FAIILIFVLAIVNI 139
                                       44455555444443 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 3.5
                            PilX_N   5 Lvvtl 9  
                                        v+++
  gi|518653258|ref|YP_008142778.1| 163 FVIAA 167
                                       12244 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.4
                            PilX_N   4 a.Lvvtllllav 14 
                                       + Lvv++l+l+v
  gi|518653258|ref|YP_008142778.1| 240 YiLVVLALILMV 251
                                       448998888887 PP

  == domain 4  score: 12.1 bits;  conditional E-value: 3.2e-05
                            PilX_N  11 llavltllgvatiqgslleerlsandrdriqa 42 
                                       ++a++t+ ++ ++++++l++ ++++++ ++ +
  gi|518653258|ref|YP_008142778.1| 276 IYALVTIGALIATTSATLAMIMTSSRILYQIG 307
                                       799***********************998875 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1.5
                            PilX_N   2 Gia.Lvv........t 8  
                                       Gi+ L+v        +
  gi|518653258|ref|YP_008142778.1| 392 GIIlLIVfilgmpreA 407
                                       5554444333222221 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (440 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1381  (0.077026); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.91u 0.39s 00:00:01.30 Elapsed: 00:00:00.57
# Mc/sec: 2337.93
//
Query:       gi|518653259|ref|YP_008142779.1|  [L=477]
Description: hypothetical protein FACI_IFERC00001G1902 [Ferroplasma acidarmanus fer1]
Scores for complete 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-22   77.6  63.8    2.7e-21   75.9  63.8    1.7  1  AA_permease_2    Amino acid permease
    4.7e-16   58.5  58.3    7.6e-16   57.8  58.3    1.3  1  AA_permease      Amino acid permease
     0.0069   16.5   1.9      0.086   13.0   1.9    3.0  1  Pox_A9           A9 protein conserved region
  ------ inclusion threshold ------
      0.077   12.9   0.1       0.54   10.2   0.1    2.6  1  Herpes_US9       Alphaherpesvirus tegument protein US9


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 !   75.9  63.8   5.9e-25   2.7e-21       2     415 ..      11     444 ..      10     459 .. 0.72

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.9e-25
                     AA_permease_2   2 sllsafalvigsvigsgifvkn...laasggpalilwvwiavligslavllvyaElssalprsgGiyvytkaafgkk 75 
                                       +++++++ +i +++ +g f+ +   +++++g+++ l+++i+  i++lav++vy+ +s + ++ gG y y++ a+++k
  gi|518653259|ref|YP_008142779.1|  11 TFWGLVFYAIMVIAPAGPFAFTgasAMEYAGKIAPLTFLIGGAILFLAVIAVYI-YSEKVSNAGGYYKYVEVATHNK 86 
                                       589999999999955443322224589************9999999*******9.8888****************** PP

                     AA_permease_2  76 vaflsawfnwfayvpvlasilsvaasyllnalgpdlqgntwltyliaiaililvalinirgikesakiqnilgilki 152
                                         + s+ f+ ++ v++  +++s++++++l++  + ++g t ++++++ + +i+ ++  ++gi  + + q+i +++ +
  gi|518653259|ref|YP_008142779.1|  87 YLSKSVGFYYLFMVLSSIIGSSILLGWFLYIGLEVMVGYTLPFVFVVLVSFITPVIYLVVGILALNYSQKIAIVVGL 163
                                       ******************************644799999**9999999999999*********************** PP

                     AA_permease_2 153 llpliiliilglitvdgggfsslstetdtffpn..gwpgvllglli.vlwsfdGfesaanvseevkk..kdvpkaif 224
                                       +  l++++ l +++v ++  + + +   ++f++  g  g++lg+ +  + +f+G+ s+++ +ee k+  k+++kai+
  gi|518653259|ref|YP_008142779.1| 164 F-DLAFFLTLSVAIVIKSPYNVI-QYF-NIFNStnGFHGFFLGMVTgGFVAFSGYGSIVVLAEETKTpgKTIKKAIV 237
                                       6.777777777777766555533.344.34444256666777765539****************887779******* PP

                     AA_permease_2 225 igllivlvlyllvniaflgvvpddeianlsnlgsvaalffeavggkvvaiivvilial...sllgaintavigssrv 298
                                        +lli + + ++v  a +g+++++  a l+     +a+ +  + +  + +i  +++ +   s+l++   +  +++r 
  gi|518653259|ref|YP_008142779.1| 238 TSLLIMIAYDTFVIYANVGGLGPNLPAGLAY----FAPGLYVTDSYYGIYITLLAFSVflvSALISTVIFGNSAARD 310
                                       *************999999999998886554....4444444444444444443333311133333344445788** PP

                     AA_permease_2 299 lealardgvlPrffakvn.kfgspiraiiltaivslillllfllas....saaynfllsvsslgliisyllliigal 370
                                       l++lardg+lP+ f k++ k+ +p+ a+i +++v+ ++++ + l++    +   n l+++ ++ +ii   +++ + +
  gi|518653259|ref|YP_008142779.1| 311 LYSLARDGILPKTFTKIHkKYRIPYMAVIAVFVVA-VVGISLGLVPlvyyYGENNGLFDLLVINSIIGSVFTLSYHI 386
                                       ******************99**************9.55555555564444555556666666666666666666666 PP

                     AA_permease_2 371 ilrkkrphl.kr.............pgkilvaiigalfllfllvalffppkgpatqssl 415
                                       i+  + p+l  r              ++ ++  i++ ++l+ lv++    + +  +  +
  gi|518653259|ref|YP_008142779.1| 387 IVNETLPVLmHRlkqlnpvthiiapTAASVMIGIAIYYSLIGLVWPL-SAAYIFLPGLI 444
                                       66666665553322233233443321112333333444444444433.22333444444 PP

>> AA_permease  Amino acid permease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.8  58.3   1.7e-19   7.6e-16       2     474 ..      15     458 ..      13     463 .. 0.74

  Alignments for each domain:
  == domain 1  score: 57.8 bits;  conditional E-value: 1.7e-19
                       AA_permease   2 vlvialggviGtglfvglgvvlsqaGplgallayllagvviflvmlslgeiatngpksggfytyasrflgp.elGfv 77 
                                       +++ a+  + ++g f  +g  + +  +  a l +l++g+++fl++++++  + +++++gg+y+y++  ++   l+ +
  gi|518653259|ref|YP_008142779.1|  15 LVFYAIMVIAPAGPFAFTGASAMEYAGKIAPLTFLIGGAILFLAVIAVYIYSEKVSNAGGYYKYVEVATHNkYLSKS 91 
                                       5677777788888888888888877777889***********************************99998689*** PP

                       AA_permease  78 iGlnylfswitvlaleltaasiliqfwel.vtdlpkawvt.........gavflvvlliinlvgvkvygeaefilal 144
                                       +G+ ylf+ +  +    +++sil+++  +   +++   +t         + ++ v++l++ ++++ ++ +   i+++
  gi|518653259|ref|YP_008142779.1|  92 VGFYYLFMVLSSI----IGSSILLGWFLYiGLEVM-VGYTlpfvfvvlvSFITPVIYLVVGILALNYSQK---IAIV 160
                                       **99776666555....566777777755455666.4555777778777777778888888888888877...5555 PP

                       AA_permease 145 ikiiaiiafiivgiillaggkpnkgagfrflgdngsifknnlppgfakeeegafknfisvfvi.vvfaftGielvai 220
                                       + +  ++ f+ ++ + ++ + p +       ++n +    n ++g        f++f+ ++v+  ++af+G++++++
  gi|518653259|ref|YP_008142779.1| 161 VGLFDLAFFLTLS-VAIVIKSPYNV----IQYFNIF----NSTNG--------FHGFFLGMVTgGFVAFSGYGSIVV 220
                                       5555566666666.55556666666....4588888....88899........*****999983588********** PP

                       AA_permease 221 iagEvkdPeksiPkailqvviritifYvlsllligllvprndlgllndsasaaspfvifikesgvsvlaplinavil 297
                                       +a+E+k P k+i+kai   +++ +   ++++++ + +++ n +  l+  a    p  +++ +   +++  l   v l
  gi|518653259|ref|YP_008142779.1| 221 LAEETKTPGKTIKKAIVTSLLIMIAYDTFVIYANVGGLGPNLPAGLAYFA----PGLYVTDSYYGIYITLLAFSVFL 293
                                       ****************99999999988999999999*****999999555....44455555555566666666677 PP

                       AA_permease 298 taalssansslysasRvlyslakdglaP.kvlkkvskrgvPlraillsmiisllal......llaslnlaapivfnf 367
                                       ++al s + +  sa R lysla+dg++P ++ k ++k++ P++a++++++++++++      l+ ++  +    f+ 
  gi|518653259|ref|YP_008142779.1| 294 VSALISTVIFGNSAARDLYSLARDGILPkTFTKIHKKYRIPYMAVIAVFVVAVVGIslglvpLVYYYGEN-NGLFDL 369
                                       788888888999****************88999999********************99987655555554.555555 PP

                       AA_permease 368 llais...aliglivwlliilsylrfRkalkyqgrsieelgfkaallplgvilvlaaliiillilalyayltvkkgp 441
                                       l+  s    + +l+ ++++         +l +  +++++l   ++ +  ++ +v++ + i++ + +l+ +l      
  gi|518653259|ref|YP_008142779.1| 370 LVINSiigSVFTLSYHIIV-------NETLPVLMHRLKQLNPVTHIIAPTAASVMIGIAIYYSLIGLVWPLS----- 434
                                       4422200022233333333.......3444455566777777777888888888888888887777777776..... PP

                       AA_permease 442 kdwgaasfaaaylivllfliilvgvklhvknkr 474
                                                aay+ ++ ++i+ +++++  knk+
  gi|518653259|ref|YP_008142779.1| 435 ---------AAYIFLPGLIILAIIITYSRKNKV 458
                                       .........566666666666666666666665 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   1.9   1.9e-05     0.086      22      48 ..     129     155 ..     127     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.9e-05
                            Pox_A9  22 fafVvlksiisMvmyLvlGvaLlyiss 48 
                                       f fVvl s i+ v+yLv+G+  l  s+
  gi|518653259|ref|YP_008142779.1| 129 FVFVVLVSFITPVIYLVVGILALNYSQ 155
                                       89******************8877665 PP

>> Herpes_US9  Alphaherpesvirus tegument protein US9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00012      0.54      24      51 ..     326     351 ..     314     359 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00012
                        Herpes_US9  24 klrrRkkrtfCvitliivllvAvlsaaF 51 
                                       k++++ +    ++ +i+v++vAv++ + 
  gi|518653259|ref|YP_008142779.1| 326 KIHKKYR--IPYMAVIAVFVVAVVGISL 351
                                       5555555..889***********99766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (477 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1100  (0.0613531); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.32s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3342.67
//
Query:       gi|518653260|ref|YP_008142780.1|  [L=362]
Description: hypothetical protein FACI_IFERC00001G1903 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.1e-121  406.5   0.0   1.3e-121  406.4   0.0    1.0  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    1.5e-10   40.8   0.0    2.3e-10   40.2   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    1.4e-05   24.2   0.0    2.1e-05   23.7   0.0    1.1  1  Aminotran_5      Aminotransferase class-V
    0.00063   19.1   0.0     0.0011   18.3   0.0    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0061   16.5   0.0       0.16   11.9   0.0    2.9  2  DUF1967          Domain of unknown function (DUF1967)
  ------ inclusion threshold ------
      0.011   14.3   0.0      0.016   13.8   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.4   0.0  4.2e-125  1.3e-121       2     360 ..       9     356 ..       8     357 .. 0.96

  Alignments for each domain:
  == domain 1  score: 406.4 bits;  conditional E-value: 4.2e-125
                                       HHHHHHHHHHHHHTSS-SSS.SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHH CS
                   DegT_DnrJ_EryC1   2 ikeeeleaveevlksgwlts.gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvata 77 
                                       i+e+e+e+v ++++sgw++s g+++++FE +f+ ++g+k+ +++s+Gt+AlhlaL+a+g+++gdeVIvp ltF++ +
  gi|518653260|ref|YP_008142780.1|   9 IGEKEIEYVDDAVRSGWVSShGEYINRFEDNFKSFIGTKFGLTTSNGTTALHLALSAMGIKEGDEVIVPDLTFISPV 85 
                                       7899************************************************************************* PP

                                       HHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEEEEB-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EET CS
                   DegT_DnrJ_EryC1  78 navlelgakpvfvDvdpdtynidpaaieaaitertkaIlpVhlyGqvadmdalkaiaakhglkvieDaAhAlGatyk 154
                                       navl++ a+pv++D+dp+ ++id+++ie++ite+tkaI++VhlyG++a+md+l +i +k++l++ieD+A++lG++yk
  gi|518653260|ref|YP_008142780.1|  86 NAVLYNHATPVLCDIDPENWCIDAEKIEKLITEKTKAIIVVHLYGNSANMDRLMEIKEKYNLYLIEDTAESLGTEYK 162
                                       ***************************************************************************** PP

                                       TEECCCSSSEEEEE-BTTSSS-SSS-EEEEESTHHHHHHHHHHHBTTCECCTCSSCECCSS---B-B-BHHHHHHHH CS
                   DegT_DnrJ_EryC1 155 gkkvGalgdaavfSFyptKnlttGeGGavvtndeelaekarvlrnhGlkrkaekryvgevelGynyrlteiqAAigl 231
                                       gkk+G++gda++fSFy++K++ttGeGG ++tn+ee+ +++ +lr hG++   e+ry+++  +Gynyr+t++qAA+g+
  gi|518653260|ref|YP_008142780.1| 163 GKKLGSFGDAGCFSFYGNKTMTTGEGGFCTTNNEEIYRMMLLLRDHGMR--PENRYWHDY-IGYNYRMTNLQAALGV 236
                                       ***********************************************99..69*******.**************** PP

                                       HHHCTHHHHHHHHHHHHHHHHHHHHTCCCCEESCGGTTSSSEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SG CS
                   DegT_DnrJ_EryC1 232 aqLerldelvarRreiaelykeeLaelegtaelttpketkkhawhlyavlveeeaevkrdelvealkeegigtrvhy 308
                                       aqLerl+++++++r+ia+ yk++L +    +++++ k   k  ++ly +l ++++  +r++l+ +l  +gi+tr ++
  gi|518653260|ref|YP_008142780.1| 237 AQLERLNSFIEKKRHIASEYKKNLPGNV--LPHPEGKLY-KGTYWLYSILAKDKD--ERERLISFLFGKGIDTRKFF 308
                                       **********************999865..344444444.489999999999884..5******************* PP

                                       SCHGGGSCCHHHHHHCCCHC-HHHHHHHHHEEEEEGGTTGSHHHHHHHHHHH CS
                   DegT_DnrJ_EryC1 309 pnplhrqpvyaerkeeasgdlpnaerlaervlsLplypelteedvdrVveal 360
                                         p+h +p y+e +++   ++pn+ +++er ++Lp++++l+++++ ++++++
  gi|518653260|ref|YP_008142780.1| 309 -YPVHVMPPYKEFNKV---NYPNSTSISERGINLPSSVKLSDDEIGYICDCI 356
                                       .6**********9766...69****************************987 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.0   7.7e-14   2.3e-10      47     189 ..      34     154 ..      16     156 .. 0.91

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 7.7e-14
                                       HHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEESS-THHHHHHHHTTSEEEEEEBE CS
                     Aminotran_1_2  47 peleealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdptyasyknilrlsggevvryply 123
                                         +e +  +f+g        ++  +++++G++al  al ++  +  gde++vpd+t+ s  n++ +++++ v + ++
  gi|518653260|ref|YP_008142780.1|  34 NRFEDNFKSFIG--------TKFGLTTSNGTTALHLALSAMG-IKEGDEVIVPDLTFISPVNAVLYNHATPVLCDID 101
                                       567778888888........66699*****************.********************************66 PP

                                       ETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEET CS
                     Aminotran_1_2 124 seedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDea 189
                                        +e++ +d+e++e++++e      ktk i+v       G  a+ + l ++   ++kynl+l+ D a
  gi|518653260|ref|YP_008142780.1| 102 -PENWCIDAEKIEKLITE------KTKAIIVVHL---YGNSANMDRLMEI---KEKYNLYLIEDTA 154
                                       .9****************......99***98766...5999999******...********98865 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   6.9e-09   2.1e-05      45     181 ..      33     158 ..      23     167 .. 0.85

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 6.9e-09
                                       HHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEB CS
                       Aminotran_5  45 veearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaehhanlvpwqelakrtgakvkvipl 121
                                       ++  +++++ +i+++     + ts++t+a+ l++ +++  +k+gde++v ++   + +   + l +  +  +  i  
  gi|518653260|ref|YP_008142780.1|  33 INRFEDNFKSFIGTKF---GLTTSNGTTALHLALSAMG--IKEGDEVIVPDLTFISPV--NAVLYNHATPVLCDIDP 102
                                       6778899999999998...799************9995..9***************99..44455567777878887 PP

                                       ETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
                       Aminotran_5 122 deegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                                        e++ +d +++ekl++ektk++++ h     G+   ++++ ++  k++ +++ D a ++g
  gi|518653260|ref|YP_008142780.1| 103 -ENWCIDAEKIEKLITEKTKAIIVVHL---YGNSANMDRLMEIKEKYNLYLIEDTAESLG 158
                                       .89**********************97...677777777776668899999999998876 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   3.7e-07    0.0011      34     224 ..      33     226 ..      26     260 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.7e-07
                                       HHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH-.-TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT.TB CS
                   Beta_elim_lyase  34 vnrLedavaelfgkeaalfvpqGtaAnsillkill.qrgeevivtepahihfdetgaiaelagvklrdlknkea.Gk 108
                                       +nr+ed+++  +g++ +l + +Gt A +++l+++  + g+eviv +     f    +++ ++ ++++ ++++ +   
  gi|518653260|ref|YP_008142780.1|  33 INRFEDNFKSFIGTKFGLTTSNGTTALHLALSAMGiKEGDEVIVPDL---TFISPVNAVLYNHATPVLCDIDPEnWC 106
                                       799****************************99987******99876...555666777788888888886654389 PP

                                       E-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHH CS
                   Beta_elim_lyase 109 mdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkem 185
                                       +d+ek+e++i+e+ +     ++i++    n+        ++++++ +i +ky++ l+ D A         + + k++
  gi|518653260|ref|YP_008142780.1| 107 IDAEKIEKLITEKTK-----AIIVVHLYGNS--------ANMDRLMEIKEKYNLYLIEDTAES---L-GTEYKGKKL 166
                                       ************433.....55555554443........667777777789999999998733...2.445566777 PP

                                       HTTSSEEEEE..SSSTT--SS-EEEEE-HH.......................HHHHHHH CS
                   Beta_elim_lyase 186 fsyvDsvtms..lkKdllanvGgvlafrddel...................edylaerve 224
                                        s  D  ++s  + K +++  Gg++ ++++e+                   +dy+ +  +
  gi|518653260|ref|YP_008142780.1| 167 GSFGDAGCFSfyGNKTMTTGEGGFCTTNNEEIyrmmlllrdhgmrpenrywHDYIGYNYR 226
                                       777777666622467777777788888888777777777777777776666444444444 PP

>> DUF1967  Domain of unknown function (DUF1967)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.0   5.4e-05      0.16      49      68 ..      62      81 ..      58      82 .. 0.92
   2 ?    0.5   0.0       0.2   5.9e+02      10      23 ..     103     116 ..      98     120 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.4e-05
                                      HHHTTT--TT-EEEETTEEE CS
                           DUF1967 49 aLrkaGakeGdtVrIgdveF 68
                                      aL ++G+keGd+V + d++F
  gi|518653260|ref|YP_008142780.1| 62 ALSAMGIKEGDEVIVPDLTF 81
                                      799************99998 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.2
                                       TEEEEE-HHHHHHH CS
                           DUF1967  10 gvfvVeGekierlv 23 
                                       + + ++ ekie+l+
  gi|518653260|ref|YP_008142780.1| 103 ENWCIDAEKIEKLI 116
                                       56**********98 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   5.2e-06     0.016      56     142 ..      35     124 ..      31     144 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.2e-06
                                       HHHHHHHHHHT-SEEEEESSHHHHHHHHHHTT.S-TTEEEEEESTSSHH.HHHHHHHTHHHTTCEEEEEST.TSHHH CS
                   Cys_Met_Meta_PP  56 vleeriaaLeggeaalavssGmaAiaaailal.lkaGdeivvsddlYgg.tqrllkkvlkklgievkfvdt.sdlee 129
                                        +e++     g++ +l +s G++A+++a+ a+ +k+Gde++v d  + +  +++l + ++ +  +++  +   d+e+
  gi|518653260|ref|YP_008142780.1|  35 RFEDNFKSFIGTKFGLTTSNGTTALHLALSAMgIKEGDEVIVPDLTFISpVNAVLYNHATPVLCDIDPENWcIDAEK 111
                                       57888888899999***************9986899********9986516677788888888888888854799** PP

                                       HHHHCCTTEEEEE CS
                   Cys_Met_Meta_PP 130 lekaikentklvy 142
                                       +ek i+e+tk++ 
  gi|518653260|ref|YP_008142780.1| 112 IEKLITEKTKAII 124
                                       **********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (362 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); 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: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.48
# Mc/sec: 2283.72
//
Query:       gi|518653261|ref|YP_008142781.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1904 [Ferroplasma acidarmanus fer1]
Scores for 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-109  364.2   0.0   8.8e-109  363.9   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.8e-57  193.5   0.0      5e-57  193.1   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    3.5e-08   32.9   0.0    5.6e-08   32.2   0.0    1.3  1  RmlD_sub_bind    RmlD substrate binding domain
    0.00024   20.7   0.0    0.00039   20.0   0.0    1.3  1  NmrA             NmrA-like family
  ------ inclusion threshold ------
      0.025   13.7   0.0      0.036   13.2   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      0.068   12.6   0.0       0.16   11.4   0.0    1.6  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  363.9   0.0    3e-112  8.8e-109       1     332 []       5     312 ..       5     312 .. 0.97

  Alignments for each domain:
  == domain 1  score: 363.9 bits;  conditional E-value: 3e-112
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       LiTGi+G++G+yla+lLl+k+y+v+g+ rr s+ n++r+++l       + ++++l++gDl+D ss+ ++++  qpd
  gi|518653261|ref|YP_008142781.1|   5 LITGITGQDGAYLAKLLLKKNYKVYGLYRRVSTPNFWRLQALD------IYDRVNLISGDLSDLSSILNAFKASQPD 75 
                                       9****************************************96......45789*********************** PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-S.SSSB-TTS-----SHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvq.evpqtEttpfyPrsPY 153
                                       evy+LAAqs+V+ sfe+P  ta+v++l ++r+Lea++     +++++y+a+tsE++G+     p +E++pf+P sPY
  gi|518653261|ref|YP_008142781.1|  76 EVYHLAAQSFVEASFESPLSTADVTGLSVTRILEAVKLFS--NSTKVYFAGTSEMFGSSYtGEPLNENHPFNPMSPY 150
                                       ************************************9975..78**************963789************* PP

                                       HHHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHH CS
                     GDP_Man_Dehyd 154 aaaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyv 230
                                       aaaKly +wi + yre yg+++ +gilfnhesp rg +fvtrki + va+i+lg++++++lGn++a+Rdwg++ +yv
  gi|518653261|ref|YP_008142781.1| 151 AAAKLYGYWISKIYREGYGIYVASGILFNHESPLRGMEFVTRKIANEVAKINLGLEKKIHLGNINARRDWGYAPEYV 227
                                       ***************************************************************************** PP

                                       HHHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB-- CS
                     GDP_Man_Dehyd 231 eamwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlll 307
                                       eam+ mlq dk++d+viat+ethsv+efv+ af  ++++                  +++ e+d+++ rp +v +l 
  gi|518653261|ref|YP_008142781.1| 228 EAMHSMLQLDKADDFVIATNETHSVEEFVKYAFDYIKED-----------------YRDYLEIDKRFIRPLDVPALQ 287
                                       ***********************************9865.................35689**************** PP

                                       B-THHHHHHH----SS-HHHHHHHH CS
                     GDP_Man_Dehyd 308 gdaskakeeLgWkpkvsfeelvrem 332
                                       gd ska++   Wkp+++f+elv++m
  gi|518653261|ref|YP_008142781.1| 288 GDYSKAEKTFKWKPETKFRELVNMM 312
                                       **********************998 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.1   0.0   1.7e-60     5e-57       1     240 [.       4     244 ..       4     245 .. 0.96

  Alignments for each domain:
  == domain 1  score: 193.1 bits;  conditional E-value: 1.7e-60
                                       EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC......EEEE--TT-HHHHHHHHHHHT-SEEEE- CS
                         Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl......elveldltdrsalerlfkeeqpdavihl 71 
                                       +l+tG+tG++G++l+k ll+k+y+v gl r+ s+ n++rl+ l      +l+ +dl d s++ ++fk  qpd+v+hl
  gi|518653261|ref|YP_008142781.1|   4 ALITGITGQDGAYLAKLLLKKNYKVYGLYRRVSTPNFWRLQALdiydrvNLISGDLSDLSSILNAFKASQPDEVYHL 80 
                                       59*************************************************************************** PP

                                       -S---HHHHHHSHHHHHHHHTHHHHHHHHHHHHH.TCTEEEEEEEGGGGTSCSS.SSBSTCSTTS----SSHHHHHH CS
                         Epimerase  72 Aavggvaassedpadfieknlqgtlnlleaarka.gvkrllflsSsevYGkdae.qpkeettltgplkpnspYaaaK 146
                                       Aa++ v+as+e+p  +++ +   ++++lea++   +  +++f+++se++G + +  p +e+    p++p spYaaaK
  gi|518653261|ref|YP_008142781.1|  81 AAQSFVEASFESPLSTADVTGLSVTRILEAVKLFsNSTKVYFAGTSEMFGSSYTgEPLNENH---PFNPMSPYAAAK 154
                                       ********************************876888************999944788888...************ PP

                                       HHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHH CS
                         Epimerase 147 lageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeail 223
                                       l+g+++ + y++ yg+ + +++lfn+++p +g+++v+r+i+  ++ki++g ++ + lg+ +a+Rd++y+ +++ea++
  gi|518653261|ref|YP_008142781.1| 155 LYGYWISKIYREGYGIYVASGILFNHESPLRGMEFVTRKIANEVAKINLGLEKKIHLGNINARRDWGYAPEYVEAMH 231
                                       ***************************************************999999******************** PP

                                       HHHHHHTT-STTEEEEE CS
                         Epimerase 224 lvlehvdagdkgeiyni 240
                                        +l+     dk ++++i
  gi|518653261|ref|YP_008142781.1| 232 SMLQL----DKADDFVI 244
                                       ****9....55667777 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 !   32.2   0.0   1.9e-11   5.6e-08       3     132 ..       4     157 ..       1     169 [. 0.90

  Alignments for each domain:
  == domain 1  score: 32.2 bits;  conditional E-value: 1.9e-11
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT.....................T--TTSHHHHHHHHHHH--SEEEE- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre.....................eldltdaeavaellkeakpdvvvna 58 
                                        l+tG +Gq G  Lak+l +++++v++l r+                     + dl+d +++ +++k+ +pd v+++
  gi|518653261|ref|YP_008142781.1|   4 ALITGITGQDGAYLAKLLLKKNYKVYGLYRRvstpnfwrlqaldiydrvnliSGDLSDLSSILNAFKASQPDEVYHL 80 
                                       69**************************9999********************************************* PP

                                       -----HHHHHHSHHHHHHHHTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-........TTS-B-TTS----SSHHHH CS
                     RmlD_sub_bind  59 AAytavDkaEseeeaayavnaeavealAeaaaavgalLihvStDyVFdGe........kkrpYeeddetsPlnvYGr 127
                                       AA   v +  + + + + v   +v ++ ea +     L   St   F G+        + +p +e+++ +P++ Y++
  gi|518653261|ref|YP_008142781.1|  81 AAQSFVEASFESPLSTADVTGLSVTRILEAVK-----LFSNSTKVYFAGTsemfgssyTGEPLNENHPFNPMSPYAA 152
                                       ***************************99865.....5555555555555555555588899*************** PP

                                       HHHHH CS
                     RmlD_sub_bind 128 tKlaG 132
                                       +Kl G
  gi|518653261|ref|YP_008142781.1| 153 AKLYG 157
                                       **987 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   1.3e-07   0.00039       2      66 ..       5      73 ..       4      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.3e-07
                                      EESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHHHST....TEEEES-TT-HHHHHHHHTT-S CS
                              NmrA  2 lviGaTGrqGksvvrallkaghkvralvRdtkselakslkeaG....velvkgdlddkeslvealkgvd 66
                                      l++G TG+ G+++++ llk+++kv  l R +++ +   l++      v+l++gdl d +s+ +a+k ++
  gi|518653261|ref|YP_008142781.1|  5 LITGITGQDGAYLAKLLLKKNYKVYGLYRRVSTPNFWRLQALDiydrVNLISGDLSDLSSILNAFKASQ 73
                                      799****************************999999999864333399****************9875 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.036       2      97 ..       5      93 ..       4     118 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
                                      EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HH.HHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-S CS
                   Polysacc_synt_2  2 lvtGagGsiGselvrqilkkkpkkiillerdEl.klyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvd 79
                                      l+tG +G  G  l + +lkk+ k   l+ r  + + ++++  l + +++  +      + gd+ d +++ +a+++ ++d
  gi|518653261|ref|YP_008142781.1|  5 LITGITGQDGAYLAKLLLKKNYKVYGLYRRVSTpNFWRLQA-L-DIYDR--V----NLISGDLSDLSSILNAFKASQPD 75
                                      79999999999999999999999999998866514555554.4.23333..3....3457******************* PP

                                      EEEE------HHHHHHSH CS
                   Polysacc_synt_2 80 vvfhaAAlKhVPlveenp 97
                                       v+h AA   V +  e p
  gi|518653261|ref|YP_008142781.1| 76 EVYHLAAQSFVEASFESP 93
                                      *******98887665555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.3e-05      0.16       1      70 [.       2      71 ..       2      75 .. 0.89
   2 ?   -4.0   0.0       2.8   8.4e+03     142     153 ..     143     154 ..     141     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
                                      SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHH CS
                         adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvek 70
                                      k++l+tG ++  G  +ak l+k+++kv+ + r+ ++ + +  +  +  +++  i++D++d +++ +++++
  gi|518653261|ref|YP_008142781.1|  2 KTALITGITGQDGAYLAKLLLKKNYKVYGLYRRVSTPNFWRLQALDIYDRVNLISGDLSDLSSILNAFKA 71
                                      799**************************99999999766666666699*************99998876 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 2.8
                                       B-TTBHHHHHHH CS
                         adh_short 142 pvagvaaYsAsK 153
                                       p++ +++Y+A+K
  gi|518653261|ref|YP_008142781.1| 143 PFNPMSPYAAAK 154
                                       5667899****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); 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: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2471.14
//
Query:       gi|518653262|ref|YP_008142782.1|  [L=381]
Description: lipopolysaccharide N-acetylglucosaminyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-23   82.3   0.0    5.3e-23   81.4   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    5.2e-14   52.8   0.0    8.8e-14   52.1   0.0    1.3  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 !   81.4   0.0   5.9e-27   5.3e-23       9     154 ..     203     348 ..     196     363 .. 0.93

  Alignments for each domain:
  == domain 1  score: 81.4 bits;  conditional E-value: 5.9e-27
                                       TTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCH CS
                   Glycos_transf_1   9 lgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevs 82 
                                       +   ++++ i++v+r+++ Kg+d lik+f ++     p ++l i+G   + ee ++l kl++el+l++ v+f g   
  gi|518653262|ref|YP_008142782.1| 203 YDPVKRQRNIITVSRITPDKGLDILIKSFYRVSSS-YPAWNLEIIGeitDNEEYNKLIKLIDELGLGESVKFSGIFT 278
                                       555678999***********************876.*************99999*********************** PP

                                       SSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHH CS
                   Glycos_transf_1  83 redleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairk 154
                                       r +l+e ++++ if+l s  E+f+i+ lEA++ g+ vi++ ag +++ +k g    +v++ ++++l +ai++
  gi|518653262|ref|YP_008142782.1| 279 RIQLIEKYRSSAIFCLASLHESFAISRLEAISQGMYVISTTAGCAMDFLKYGL--HIVPESDIQSLGNAIKE 348
                                       *************************************************9988..57777799999999986 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 !   52.1   0.0   9.8e-18   8.8e-14       2     130 ..     210     348 ..     209     351 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 9.8e-18
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgp.rp..eeleelaa..gleerveftGfv..edlael 69 
                                       ++i++v+r+++  kg+d+l++ + ++ ++ + ++l i+G+ + ++  ++l +l++  gl e+v+f G     +l e 
  gi|518653262|ref|YP_008142782.1| 210 RNIITVSRITPD-KGLDILIKSFYRVSSSyPaWNLEIIGEITdNEeyNKLIKLIDelGLGESVKFSGIFtrIQLIEK 285
                                       6899*****655.**************88648*******655332234555555479999*******7744469999 PP

                                       HHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSS.EE--TT-HHHHHHHHHH CS
                   Glyco_trans_1_4  70 laaadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgeng.llvppgdpealaeailr 130
                                       ++++ +f++ s  e+f ++ lEa + g+ v++t++g + +++ + g  +vp+ d ++l +ai +
  gi|518653262|ref|YP_008142782.1| 286 YRSSAIFCLASlhESFAISRLEAISQGMYVISTTAGCAMDFL-KYGlHIVPESDIQSLGNAIKE 348
                                       ***********************************4334444.455247798999999999976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (381 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       433  (0.0241508); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); 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: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.47
# Mc/sec: 2455.00
//
Query:       gi|518653263|ref|YP_008142783.1|  [L=407]
Description: lipopolysaccharide N-acetylglucosaminyltransferase [Ferroplasma acidarmanus fer1]
Scores for 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   73.0   0.4    3.4e-20   72.3   0.4    1.3  1  Glycos_transf_1  Glycosyl transferases group 1
    1.4e-13   51.4   0.0    2.1e-13   50.8   0.0    1.3  1  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.038   14.4   0.1       0.07   13.6   0.1    1.4  1  RbsD_FucU        RbsD / FucU transport protein family


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.4   5.7e-24   3.4e-20      12     159 ..     225     372 ..     217     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 5.7e-24
                                       TTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES....STTHHHHHHHHHHHCTTCGGGEEECCHSSS CS
                   Glycos_transf_1  12 nekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG...ngeeekelkklaeelelsdnviflgevsred 85 
                                       +ek++ i++ +rl+++Kg+  +i  ++++ k    +v +v+aG   +  ee ++ +l  +++l++ v++ g++ +++
  gi|518653263|ref|YP_008142783.1| 225 KEKENKIIFFARLVYRKGIFDFILIVKEIVK--SLRVEVVVAGqfqHSYEERYFFELLSKYHLEKFVKYKGKLTDDE 299
                                       599**************************97..59**********8777778889999******************* PP

                                       HHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHHHHSH CS
                   Glycos_transf_1  86 leellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkllede 159
                                       l + l+ a+++v+ps+s++f i++l A+++++pv+a+++ g++ + k +    lvk+ +  a+a++ +++++ e
  gi|518653263|ref|YP_008142783.1| 300 LYSELSTAKAMVYPSHSDSFSISILQAIYLNTPVVAYDIAGISVYKKFNCV-KLVKEFDTTAIANKTIDIMNGE 372
                                       **************************************9999877665554.5556666888888888888776 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 !   50.8   0.0   3.6e-17   2.1e-13       2     132 ..     229     369 ..     228     371 .. 0.80

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 3.6e-17
                                       EEEEEES---GG.GTHHHHHHHHHHHH.H.HEEEEEES---.....HHHHHHHT..T-T.TEEEE---..THHHHHH CS
                   Glyco_trans_1_4   2 pvilfvGrleenvkgvdllleavpllrkk.dvrlvivGdgp...rpeeleelaa..gleerveftGfv..edlaell 70 
                                       ++i+f+ rl+  +kg+  ++  v+++ k+ +v++v++G+ +   +++ + el++  +le+ v++ G++  ++l + l
  gi|518653263|ref|YP_008142783.1| 229 NKIIFFARLV-YRKGIFDFILIVKEIVKSlRVEVVVAGQFQhsyEERYFFELLSkyHLEKFVKYKGKLtdDELYSEL 304
                                       689******4.56**********99997866*******64322322344445545788878*******8555***** PP

                                       HH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--.TTSS.EE--TT-HHHHHHHHHHHH CS
                   Glyco_trans_1_4  71 aaadvfvaPs..egfglkllEamaaglpvVatdvggiaevv.geng.llvppgdpealaeailrLl 132
                                       + a+ +v Ps   +f++++l+a  + +pvVa d++gi+    + n   lv++ d+ a+a++ ++++
  gi|518653263|ref|YP_008142783.1| 305 STAKAMVYPShsDSFSISILQAIYLNTPVVAYDIAGISV-YkKFNCvKLVKEFDTTAIANKTIDIM 369
                                       **********977*********************99654.33434325999999999999998876 PP

>> RbsD_FucU  RbsD / FucU transport protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.2e-05      0.07      41     130 ..     236     325 ..     226     327 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.2e-05
                                       E.-CBTTBS-HHHHHHHHHCTS-EEEEEEETCHHHHT.HHHHHHHHHHCCCCCC---EEEE-HHHHHHHGGGCSEEE CS
                         RbsD_FucU  41 dlalragvpsfldvleavlselpvekvivaeevkeen.pevleelkellakaeeekeieeveheefkerakkakavv 116
                                       +l+ r+g+ +f+ +++++++ l ve v+va +++++  ++ + el + ++ ++  k   +++ +e++ ++++aka+v
  gi|518653263|ref|YP_008142783.1| 236 RLVYRKGIFDFILIVKEIVKSLRVE-VVVAGQFQHSYeERYFFELLSKYHLEKFVKYKGKLTDDELYSELSTAKAMV 311
                                       5899*********************.9***999655535555555555554333445788999************** PP

                                       E-S--STT--EEEE CS
                         RbsD_FucU 117 rTGEttpYaniiLk 130
                                         +    ++  iL+
  gi|518653263|ref|YP_008142783.1| 312 YPSHSDSFSISILQ 325
                                       99988888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.28s 00:00:00.81 Elapsed: 00:00:00.46
# Mc/sec: 2640.85
//
Query:       gi|518653264|ref|YP_008142784.1|  [L=351]
Description: glycosyl transferase group 1 [Ferroplasma acidarmanus fer1]
Scores for complete 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-11   41.6   0.0    1.6e-10   40.8   0.0    1.4  1  Glycos_transf_1  Glycosyl transferases group 1
    7.3e-10   39.4   0.0    1.1e-09   38.9   0.0    1.2  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 !   40.8   0.0   1.8e-14   1.6e-10      13     122 ..     167     276 ..     162     319 .. 0.89

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 1.8e-14
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsredle 87 
                                       +k+  +l++  ++++Kg   ++ ++a l  +  +n+k+ + G   ++ + e+++ +++ ++ +n++++  + ++++ 
  gi|518653264|ref|YP_008142784.1| 167 NKDIDFLFLTSFTYNKGMYDFLNLVAGLSNK-YNNIKFAMGGfaTEQTLSEIRSFMKSNNI-ENIEIHPDLTEQEKY 241
                                       578899**********************877.***********888888888888888888.9************** PP

                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEE CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpvias 122
                                       +l+++a++++lps+ +g +i+ +EA  +g +v+++
  gi|518653264|ref|YP_008142784.1| 242 NLYSRAKVYILPSMEDGIPITFYEAWGYGNIVVSY 276
                                       ********************************986 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   1.2e-13   1.1e-09       3     133 ..     171     308 ..     169     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 1.2e-13
                                       EEEEES---GG.GTHHHHHHHHHHHH.H.H.EEEEEES---....HHHHHHHT..T-T.TEEEE---..THHHHHHH CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkk.d.vrlvivGdgprp..eeleelaa..gleerveftGfv..edlaella 71 
                                       ++lf+ +++ n kg+  +l+ v+ l +k + +++ + G  +++  +e+++ ++  ++ e++e++  +  +++ +l++
  gi|518653264|ref|YP_008142784.1| 171 DFLFLTSFTYN-KGMYDFLNLVAGLSNKyNnIKFAMGGFATEQtlSEIRSFMKsnNI-ENIEIHPDLteQEKYNLYS 245
                                       589*****667.**********999999746*******6643334566665545677.7********8777****** PP

                                       H-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT..-HHHHHHHHHHHHH CS
                   Glyco_trans_1_4  72 aadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppg..dpealaeailrLle 133
                                       +a+v+++Ps   g++++ +Ea  +g  vV+  +     ++ +  l+vp +  + ++l + +++++e
  gi|518653264|ref|YP_008142784.1| 246 RAKVYILPSmeDGIPITFYEAWGYGNIVVSYLLDT---YIDVKDLIVPVElrNQKQLLDSCIEIYE 308
                                       **********55*****************997733...3456667776554467888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.43
# Mc/sec: 2423.80
//
Query:       gi|518653265|ref|YP_008142785.1|  [L=528]
Description: hypothetical protein FACI_IFERC00001G1908 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-62  211.8  39.8    2.2e-62  211.4  39.8    1.2  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.4  39.8   1.2e-66   2.2e-62       7     456 .]      47     524 ..      23     524 .. 0.82

  Alignments for each domain:
  == domain 1  score: 211.4 bits;  conditional E-value: 1.2e-66
                           DUF2079   7 stayDlGifdQviwntsqGelfysslsgvlhlLgqHfapillllaplyalfPsvltLllvqalllslgglplyrlar 83 
                                       +++ D+Gi++Q++ + + G+lfys l    + L++Hf+pil++l++ y+lfPs++tL ++q++++ +++l+ly l +
  gi|518653265|ref|YP_008142785.1|  47 MSGWDMGIYMQALSSGISGHLFYSALVPG-SYLAEHFSPILFILLIPYYLFPSAYTLIVLQSFAIGFSTLVLYLLSK 122
                                       6899**********************999.*********************************************** PP

                           DUF2079  84 erlls............rrlalliallYllspvvinptlfdFhpevlaiPll.llalllalrrrkwllllvlillll 147
                                       e+l++             + +++i++ Y++sp++ +p+ fdFh +v++ Pl+ +la++ +++++ +l++++l+l+++
  gi|518653265|ref|YP_008142785.1| 123 EILQKieiiktgkwlntSTISFIISMAYIMSPLTESPVFFDFHLMVFL-PLFfFLAIYSFMKKQYILNIIFLALIVS 198
                                       **989*******************************************.66515678889***************** PP

                           DUF2079 148 lvredlslvvvilglwlilre..........rkrrkiglillllglawvilvtsvl......iPlfsstksqvfgve 208
                                       l+++++s+ ++++ + ++l +          + r  i ++++l++l+ ++++ ++l      +P+            
  gi|518653265|ref|YP_008142785.1| 199 LHSTFVSIALMAILFEIFLNRtfmitsihspV-RSSIYFFISLAILGPYFILAGILkgdiagVPASVL--------- 265
                                       ********************944433333321.22234444444444444444444333333332222......... PP

                           DUF2079 209 rysylg.sSlleillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspql 284
                                       r    g  + ++++++++t+p l+l  l+ +   kl  l+ +f+ ++fl ++  pa+ l  +P++++ ++s y++++
  gi|518653265|ref|YP_008142785.1| 266 RIHVSGsVGPTALVIDTFTNPALILHLLVQNYILKLTLLFFAFGGFAFLFVR-YPASILTFIPYIIYSMFSTYPSYY 341
                                       333333568899999*************************************.************************ PP

                           DUF2079 285 slgyqYsllvipflvlaaifglakls.ssvelrrikriwsvalvlvlvltlflnparslsflvpdsespvvylstla 360
                                       ++gyqY+++ ip+++++  +g+  l  s+  ++++k+ ++ al++ +v++l+ + +  +   + d+ s ++y s ++
  gi|518653265|ref|YP_008142785.1| 342 TIGYQYTMMFIPMVAVSGAIGIYILIkSQMHKPSFKLQLRIALSVIIVIALLGF-SIATPIVSGDTNSNSMYASVSQ 417
                                       **************9988888877765666777888888888877777777655.3333333333333355555555 PP

                           DUF2079 361 qlqas........rellklIpsdasvlatsnLaPhlan..Rayvylfpeneelydleylleevdyvlld......va 421
                                       + +++        +++++ Ip++a++++++nL+P++ n  +a   +fp   +   ++  ++ ++y++ +       +
  gi|518653265|ref|YP_008142785.1| 418 YGNNTymnqvifeHKIANSIPKNATLVTSNNLFPLFGNdlNAT--AFPFTPDV-VIN--ADYYQYLVDNqnsmwsIE 489
                                       55555556668***************************76666..55555554.344..788999999988888756 PP

                           DUF2079 422 frgwasrkdrerklidklrnsgrygviaeedgvll 456
                                       +++ + ++ + + l  + + sg+y+v+a++ gv++
  gi|518653265|ref|YP_008142785.1| 490 TANISGTSISLNMLEHEYMASGNYKVYADNYGVIV 524
                                       67788999999999999****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1202  (0.0670422); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); 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: 0.57u 0.28s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 3676.53
//
Query:       gi|518653266|ref|YP_008142786.1|  [L=460]
Description: mercuric reductase [Ferroplasma acidarmanus fer1]
Scores for 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-56  190.1   0.1    7.1e-56  189.6   0.1    1.2  1  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.5e-28   97.7   0.2    8.3e-28   96.8   0.2    1.4  1  Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase,
    6.6e-17   61.9   0.6    2.1e-16   60.2   0.1    2.1  2  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
    1.3e-12   47.6   0.6    2.9e-12   46.5   0.6    1.6  1  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    1.5e-07   30.9   0.3    2.1e-06   27.1   0.7    2.4  2  GIDA           Glucose inhibited division protein A
    0.00026   20.2   0.0     0.0048   16.1   0.0    2.2  2  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
     0.0017   17.2   3.4       0.43    9.2   0.5    4.0  5  HI0933_like    HI0933-like protein
     0.0017   18.3   0.3     0.0098   15.8   0.0    2.4  3  3HCDH_N        3-hydroxyacyl-CoA dehydrogenase, NAD binding d
     0.0075   16.8   1.1        2.4    8.8   0.0    3.6  3  F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
      0.011   15.8   0.3       0.39   10.8   0.0    2.5  2  Shikimate_DH   Shikimate / quinate 5-dehydrogenase
      0.021   15.2   0.2       0.32   11.5   0.0    2.7  3  NAD_binding_7  Putative NAD(P)-binding
      0.023   14.0   0.1        1.1    8.5   0.0    2.4  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
      0.028   13.8   1.1       0.29   10.5   0.0    2.5  3  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
      0.057   13.0   0.3        3.2    7.2   0.0    2.5  2  DAO            FAD dependent oxidoreductase
       0.23   11.7   1.6         13    6.1   0.0    2.5  2  NAD_binding_8  NAD(P)-binding Rossmann-like domain
       0.25   10.4   3.0          1    8.3   1.4    2.4  3  FAD_binding_2  FAD binding domain


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.6   0.1   6.4e-59   7.1e-56       1     293 [.       4     317 ..       4     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: 189.6 bits;  conditional E-value: 6.4e-59
                                       CSEEEE--SHHHHHHHHHHHH...HTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.............. CS
                                       xxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.............. RF
                       Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaq...agakvtlve...legtclnggcllskallgvaedaeias.............. 57 
                                       +d+++iG G+AG+aaa+++++   +++k++l++   l+gtc+n+gc++sk l ++++++++a+              
  gi|518653266|ref|YP_008142786.1|   4 YDLAIIGWGAAGFAAAIKASEltsNQMKIALIGtgeLGGTCVNVGCVPSKFLIEASKNYKEAKspayagitssatld 80 
                                       689******************9988*******8888***************************************** PP

                                       ..............HHHHCHHHHCCCCHC.CTCEEEEESCEEEEETEEECTCEEEEEESEEEE---EEE-BCTCTTC CS
                                       ..............xxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2  58 ..............evvkklnqgielllg.eevvkidpgkkkvklekkkegdeekiaydklvlAtGssprdlgipGv 119
                                                     e     +++++ +++  e +++++g +k+ ++++ + +++++++ + ++AtGs+++++ + G+
  gi|518653266|ref|YP_008142786.1|  81 fsefmeslnqfvsgE----RETKYTSVMKnFENIDLIEGLAKFIDNDTISVNNTELKATNFIIATGSRTFIPEVRGL 153
                                       *****9998876652....333433333302257777999*****99999*************************** PP

                                       .TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHT CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 120 aenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaaleealeke 196
                                               ++++s+  +k  +lp +++v+G+G +++ElA a++++g+ev++  + +r+l+++d+++  +l++al+ +
  gi|518653266|ref|YP_008142786.1| 154 -------TDYYTSDTVWKMRKLPGKLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILKGFDDDVNSQLMAALKSN 223
                                       .......4889****************************************************************** PP

                                       TEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS.HCCT-EEEETTEEE--TTSBESSTTEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 197 GvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle.eklglelderggivvdeflrtnvpgiy 272
                                       G+ ++lg ++ ei++++ k + v+ +g+  d d ++va+G+ p+ ++l+ ++ g++   ++givv++  rt+ p+iy
  gi|518653266|ref|YP_008142786.1| 224 GIVFHLGVNFYEIKNEEGKKDIVTWTGTFGDFDEIIVATGRMPNIDGLDlRAGGITA--DNGIVVNPDFRTTNPKIY 298
                                       **************9999777**********************************88..****************** PP

                                       E-GGGCTECCSS--HHHHHHH CS
                                       xxxxxxxxxxxxxxxxxxxxx RF
                       Pyr_redox_2 273 aiGDvaggkggpelaqaAvqq 293
                                       a+GD++  +++++l + A ++
  gi|518653266|ref|YP_008142786.1| 299 AAGDCV--RQSLKLETLAGKE 317
                                       ******..6666666666665 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 !   96.8   0.2   7.4e-31   8.3e-28       1     107 [.     337     442 ..     337     444 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.8 bits;  conditional E-value: 7.4e-31
                                       BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHH CS
                     Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliq 77 
                                       +p vvft+p+vasvG+te+e+k+++ie++v ++++k++ +a + +   g++K+ +  k++k+lG+h+++p a+e i 
  gi|518653266|ref|YP_008142786.1| 337 VPWVVFTEPNVASVGYTEAELKKKHIEYDVRTVELKNVVKANILNSYTGIAKI-ISGKDKKILGIHVIAPMAAEFIT 412
                                       79**************************************************9.5677******************* PP

                                       HHHHHHHTTSBHHHHHTSBSSSSSTGGGGH CS
                     Pyr_redox_dim  78 elavaikagltvedladtihihPtlsealk 107
                                       e   +ik+glt +dl+dtih+ Pt++e++k
  gi|518653266|ref|YP_008142786.1| 413 EGVYLIKNGLTYDDLIDTIHVFPTVAESIK 442
                                       ***************************987 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1       3.8   4.3e+03       2      22 ..       6      26 ..       5      35 .. 0.81
   2 !   60.2   0.1   1.9e-19   2.1e-16       1      74 [.     171     243 ..     171     250 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 3.8
                                      EEEECSSHHHHHHHHHHHHTT CS
                         Pyr_redox  2 vvvvGgGyiglElAgalaelg 22
                                      ++++G G  g  +A  ++el 
  gi|518653266|ref|YP_008142786.1|  6 LAIIGWGAAGFAAAIKASELT 26
                                      689999999999998888876 PP

  == domain 2  score: 60.2 bits;  conditional E-value: 1.9e-19
                                       EEEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTSEE CS
                         Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedgve 74 
                                       k++v+G+G ++lElA a++++g++V+++ rs+++l+++D+++ + l+  l+ ngi ++l+ +  ei+ +e + +
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILKGFDDDVNSQLMAALKSNGIVFHLGVNFYEIKNEEGK-K 243
                                       689****************************************************************76664.3 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 !   46.5   0.6   2.6e-15   2.9e-12       2     305 .]       8     301 ..       7     301 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 2.6e-15
                       Pyr_redox_3   2 IiGaGPaGlaaaielkkagled..ylilEkgnignsiyrypk..emtfispsftsekleipdlnaiseetspafs.. 72 
                                       IiG G+aG aaai++ ++  ++  +  +  g++g +  +     ++ +i  s++ ++ + p    i+ ++   fs  
  gi|518653266|ref|YP_008142786.1|   8 IIGWGAAGFAAAIKASELTSNQmkIALIGTGELGGTCVNVGCvpSKFLIEASKNYKEAKSPAYAGITSSATLDFSef 84 
                                       9*************99988865115679*******999975421455677777888888888888887776444422 PP

                       Pyr_redox_3  73 lk..eeklsrkealeYlrevaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGee 147
                                       ++  ++ +s++   +Y++ + + +++       +e ++k  ++ +++ ++ +++A++ iiAtG   +   +++ G +
  gi|518653266|ref|YP_008142786.1|  85 MEslNQFVSGERETKYTSVMKNFENI-----DLIEGLAKFIDNDTISVNNTELKATNFIIATGS--RTFIPEVRGLT 154
                                       11236677888888887777777766.....56788888889999******************9..78889999998 PP

                       Pyr_redox_3 148 klvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvke 224
                                       +    + +v +++k+   k++ViG ++ a + A+ + + g+eV+++ r++ i k           d++++l +++k+
  gi|518653266|ref|YP_008142786.1| 155 D-YYTSDTVWKMRKL-PGKLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILKG-------FDDDVNSQLMAALKS 222
                                       4.3334444444333.679******************************977665.......567888888888888 PP

                       Pyr_redox_3 225 ekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvlteeteetnvpgl 301
                                       + i ++   +  eik++e + ++ t +g ++   d++++atG  p+++ l+     +++d+ +v++++   t  p +
  gi|518653266|ref|YP_008142786.1| 223 NGIVFHLGVNFYEIKNEEGKKDIVTWTG-TFGDFDEIIVATGRMPNIDGLDLRAGGITADNGIVVNPDFRTT-NPKI 297
                                       88*********************99998.567889**************99866666678888999876655.6999 PP

                       Pyr_redox_3 302 flaG 305
                                       + aG
  gi|518653266|ref|YP_008142786.1| 298 YAAG 301
                                       9998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.7   1.9e-09   2.1e-06       1     150 [.       5     143 ..       5     167 .. 0.82
   2 ?    0.1   0.0      0.29   3.2e+02       2      29 ..     172     199 ..     171     216 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 1.9e-09
                                       CEEEE-SSHHHHHHHHHHHHT...T--EEEE..ES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEE CS
                              GIDA   1 dviViGgGhAGceAAlaaarl...GakvlLi..thkldtiaelsCnpsiggiakgllvrEidalggliikaadkagi 72 
                                       d+ +iG G AG++AA++a++l    +k++Li   +  +t+++++C ps   i +++  +E +      + ++ +a++
  gi|518653266|ref|YP_008142786.1|   5 DLAIIGWGAAGFAAAIKASELtsnQMKIALIgtGELGGTCVNVGCVPSKFLIEASKNYKEAKSP--AYAGITSSATL 79 
                                       5789*************997622267899999888999**************999999999884..45555555555 PP

                                       EEEEESTTS-CCC-EEEEEE-HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--T CS
                              GIDA  73 qfrilNrskGpavralraqvdrelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatG 149
                                        f          +++l  q    + ++++t +++n +n+++ie+ ++ ++         +  +++++ka +++iatG
  gi|518653266|ref|YP_008142786.1|  80 DFSE-------FMESL-NQFVSGERETKYTSVMKNFENIDLIEGLAKFIDN------DTISVNNTELKATNFIIATG 142
                                       4433.......46666.899999************************9965......566779999*********** PP

                                       T CS
                              GIDA 150 t 150
                                       +
  gi|518653266|ref|YP_008142786.1| 143 S 143
                                       9 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.29
                                       EEEE-SSHHHHHHHHHHHHTT--EEEEE CS
                              GIDA   2 viViGgGhAGceAAlaaarlGakvlLit 29 
                                       + ViG G   +e A+a ++ G +v ++ 
  gi|518653266|ref|YP_008142786.1| 172 LAVIGSGEVALELAYAFSNFGSEVHIFN 199
                                       67**********************9983 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0     0.096   1.1e+02       3      29 ..       4      31 ..       2      38 .. 0.82
   2 !   16.1   0.0   4.3e-06    0.0048     140     233 ..     125     209 ..      89     221 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.096
                       K_oxygenase  3 lDligiGiGpsnLsLailleevk.kelk 29
                                      +Dl++iG G++  + ai ++e   +++k
  gi|518653266|ref|YP_008142786.1|  4 YDLAIIGWGAAGFAAAIKASELTsNQMK 31
                                      9*************99999887755555 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 4.3e-06
                       K_oxygenase 140 aegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkk 216
                                        + +++el+a n ++++G++  iPev   l+   + + s+++ + +   + + ++aV+GsG  a e+++   +  + 
  gi|518653266|ref|YP_008142786.1| 125 ISVNNTELKATNFIIATGSRTFIPEVRG-LT---DYYTSDTVWKMR---KLPGKLAVIGSGEVALELAYAFSNFGS- 193
                                       4557899*****************9865.54...577777777665...68999**********999998776655. PP

                       K_oxygenase 217 velklvtrsealepldd 233
                                        e++++ rs+++ +  d
  gi|518653266|ref|YP_008142786.1| 194 -EVHIFNRSNRILKGFD 209
                                       .8888999888776555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.5   0.00038      0.43       2      29 ..       5      35 ..       4      46 .. 0.77
   2 ?   -1.5   0.0      0.71     8e+02      53      84 ..      85     114 ..      74     122 .. 0.82
   3 ?    0.3   0.0       0.2   2.2e+02     144     166 ..     124     145 ..     113     150 .. 0.83
   4 ?   -0.8   0.0      0.42   4.8e+02       3      37 ..     172     206 ..     171     209 .. 0.92
   5 ?    3.8   0.0     0.017        19     111     163 ..     212     263 ..     208     269 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
                                      SEEEE--SHHHHHHHHHH...HHTT--EEEE CS
                       HI0933_like  2 dviviGgGaAGlmaAisa...akrgkrVlll 29
                                      d+++iG GaAG+ aAi+a    +++ +++l+
  gi|518653266|ref|YP_008142786.1|  5 DLAIIGWGAAGFAAAIKAselTSNQMKIALI 35
                                      899**************94434455555555 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.71
                                       T-SGGGEEES...STTTTHHHHHHS-HHHHHH CS
                       HI0933_like  53 seepeellsrypenpkflksalsrftnedlia 84 
                                        e++++++s   e+++++ s++++f+n dli+
  gi|518653266|ref|YP_008142786.1|  85 MESLNQFVSG--ERETKYTSVMKNFENIDLIE 114
                                       5677888888..8999999********99997 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.2
                                       EEEE.TTEEEEESEEEE----SS CS
                       HI0933_like 144 rvktkseeeleadklvlAtGGlS 166
                                       ++++ +++el+a++ ++AtG+  
  gi|518653266|ref|YP_008142786.1| 124 TISV-NNTELKATNFIIATGSRT 145
                                       5677.899************865 PP

  == domain 4  score: -0.8 bits;  conditional E-value: 0.42
                                       EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS-H CS
                       HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakklgr 37 
                                       ++viG G   l  A + ++ g++V ++++ +++++
  gi|518653266|ref|YP_008142786.1| 172 LAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILK 206
                                       68***************************999876 PP

  == domain 5  score: 3.8 bits;  conditional E-value: 0.017
                                       HHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE--- CS
                       HI0933_like 111 ivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtG 163
                                       + + l+++lk++g+ ++l  +  ++++ee++k  v+  +++    d++++AtG
  gi|518653266|ref|YP_008142786.1| 212 VNSQLMAALKSNGIVFHLGVNFYEIKNEEGKKDIVTW-TGTFGDFDEIIVATG 263
                                       5667999******************888888666666.99999*********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 ?   -1.8   0.2       2.2   2.5e+03       2      17 ..      32      47 ..      31     126 .. 0.64
   2 !   15.8   0.0   8.7e-06    0.0098       1      51 [.     171     221 ..     171     235 .. 0.89
   3 ?   -2.0   0.0       2.6   2.9e+03     122     143 ..     386     408 ..     381     442 .. 0.60

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.2
                                      EEEE--SCCHHHHHHH CS
                           3HCDH_N  2 vaviGaGtmGagiaav 17
                                      +a iG+G +G    +v
  gi|518653266|ref|YP_008142786.1| 32 IALIGTGELGGTCVNV 47
                                      6777777777655444 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 8.7e-06
                                       EEEEE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTT CS
                           3HCDH_N   1 kvaviGaGtmGagiaavfasagleVvlvdiseealekalekieksleklve 51 
                                       k+aviG+G +  ++a++f + g eV+++++s+++l+   + ++++l  + +
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILKGFDDDVNSQLMAALK 221
                                       589**********************************99999997766544 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 2.6
                                       HCCCSS.SGGGEEEEEE-SSTTT CS
                           3HCDH_N 122 laealk.rperviglHFfnPppl 143
                                       +a+ ++ ++++++g+H + P   
  gi|518653266|ref|YP_008142786.1| 386 IAKIISgKDKKILGIHVIAPMAA 408
                                       55556514455999999999764 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.89   9.9e+02       2      18 ..       6      22 ..       5      29 .. 0.82
   2 ?    3.6   0.0     0.089     1e+02       1      16 [.      31      46 ..      31      87 .. 0.71
   3 !    8.8   0.0    0.0021       2.4       1      49 [.     171     215 ..     171     238 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.89
                                      EEEETTSHHHHHHHHHH CS
                     F420_oxidored  2 igiiGaGnmgealasgl 18
                                      ++iiG G  g+a a ++
  gi|518653266|ref|YP_008142786.1|  6 LAIIGWGAAGFAAAIKA 22
                                      79********9987665 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.089
                                      EEEEETTSHHHHHHHH CS
                     F420_oxidored  1 kigiiGaGnmgealas 16
                                      ki++iG+G++g + ++
  gi|518653266|ref|YP_008142786.1| 31 KIALIGTGELGGTCVN 46
                                      79********987654 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.0021
                                       EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-E CS
                     F420_oxidored   1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvk 49 
                                       k+++iG+G+++  la  +++ g   +e+ +  +r++  ++ + ++++ +
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFG---SEVHIF-NRSNRILKGFDDDVNSQ 215
                                       78********************...***977.88887777777766644 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   0.1      0.15   1.7e+02       9      28 ..      26      45 ..      17      49 .. 0.77
   2 ?   10.8   0.0   0.00035      0.39      14      56 ..     171     212 ..     164     229 .. 0.82

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.15
                                      ..TT-EEEEES-SHHHHHHH CS
                      Shikimate_DH  9 slkekkvlliGaGemaelva 28
                                      + ++ k+ liG+Ge++   +
  gi|518653266|ref|YP_008142786.1| 26 TSNQMKIALIGTGELGGTCV 45
                                      457889********997765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00035
                                       EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH CS
                      Shikimate_DH  14 kvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel 56 
                                       k  +iG Ge+a ++a ++++ g + v ++NR+ +  k + +++
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFGSE-VHIFNRSNRILKGFDDDV 212
                                       6789******************99.******987766666655 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.1      0.95   1.1e+03      18      39 ..      17      38 ..       2     141 .. 0.74
   2 ?   11.5   0.0   0.00028      0.32       9      46 ..     171     215 ..     163     271 .. 0.64
   3 ?   -2.2   0.0         5   5.6e+03      33      59 ..     400     427 ..     393     448 .. 0.73

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.95
                     NAD_binding_7 18 vAarkvrklleagakvtvvape 39
                                       Aa k++ l +++ k+ ++   
  gi|518653266|ref|YP_008142786.1| 17 AAAIKASELTSNQMKIALIGTG 38
                                      5667777777777777776544 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00028
                     NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapevkeele........e 46 
                                       k  v+G GevA++ ++ + ++g +v++      ++l+        +
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFGSEVHIFNRSN-RILKgfdddvnsQ 215
                                       568************************87773.3333333344441 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 5
                     NAD_binding_7  33 vtvvapevkeeleelvklaeeele.kdl 59 
                                       ++v+ap  +e++ e v l+++ l  +dl
  gi|518653266|ref|YP_008142786.1| 400 IHVIAPMAAEFITEGVYLIKNGLTyDDL 427
                                       7899999988888888888777642443 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 ?    2.8   0.1     0.054        61      32      52 ..       7      27 ..       2      33 .. 0.87
   2 ?    8.5   0.0   0.00097       1.1      28      81 ..     169     223 ..     162     246 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.054
                                      EEESTSHHHHHHHHHHHHTT- CS
                       AlaDh_PNT_C 32 lviGgGvaGlqAiatakglga 52
                                       +iG G aG +A+  a++l  
  gi|518653266|ref|YP_008142786.1|  7 AIIGWGAAGFAAAIKASELTS 27
                                      79*************999865 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00097
                                       --EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEEHCHH CS
                       AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvevlksq 81 
                                       p+k  viG G + l+ + + +++g +V +++ + + l+ +++ ++++ + +lks+
  gi|518653266|ref|YP_008142786.1| 169 PGKLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILKGFDDdVNSQLMAALKSN 223
                                       89***********************************999998888866666555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.2      0.93     1e+03      39      58 ..       6      25 ..       2      37 .. 0.80
   2 ?    0.6   0.5      0.28   3.1e+02      34      52 ..      27      45 ..      10     120 .. 0.79
   3 ?   10.5   0.0   0.00026      0.29      38      73 ..     171     206 ..     154     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.93
                                      EEEES-SHHHHHHHHHHHHT CS
                      2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkaf 58
                                      ++iiG G+ G a+a +++++
  gi|518653266|ref|YP_008142786.1|  6 LAIIGWGAAGFAAAIKASEL 25
                                      89********9999888766 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.28
                                      GTTSEEEEES-SHHHHHHH CS
                      2-Hacid_dh_C 34 lsgktvGiiGlGrIGqava 52
                                       +++++++iG+G++G +  
  gi|518653266|ref|YP_008142786.1| 27 SNQMKIALIGTGELGGTCV 45
                                      568899********97655 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00026
                                       EEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHH CS
                      2-Hacid_dh_C  38 tvGiiGlGrIGqavakrlkafgmkviaydrskkkee 73 
                                       ++++iG G+++ ++a  ++ fg +v +++rs++  +
  gi|518653266|ref|YP_008142786.1| 171 KLAVIGSGEVALELAYAFSNFGSEVHIFNRSNRILK 206
                                       689***************************987444 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.054        61       1      35 [.       5      42 ..       5      95 .. 0.87
   2 ?    7.2   0.0    0.0029       3.2     150     203 ..     214     265 ..     208     324 .. 0.74

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.054
                                      EEEEECTSHHHHHHHHHHHHT.T....EEEEESSSSTTSS CS
                               DAO  1 dvviiGGGiiGlstAyeLarr.g....Vtllekgdiagsg 35
                                      d++iiG G +G ++A  +++       ++l+  g ++g g
  gi|518653266|ref|YP_008142786.1|  5 DLAIIGWGAAGFAAAIKASELtSnqmkIALIGTG-ELG-G 42
                                      789***************8763246889999888.766.4 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0029
                                       HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEE.EEEEEEEE--GGG CS
                               DAO 150 aalaraaealGveilegtevtgleeedgkvwgverttpgen.daadavVnaaGaw 203
                                         l++a++++G+ +++g +  ++++e+gk   v   t g+  d +d +++a+G  
  gi|518653266|ref|YP_008142786.1| 214 SQLMAALKSNGIVFHLGVNFYEIKNEEGKKDIVT-WT-GTFgD-FDEIIVATGRM 265
                                       5689999****************99998877773.22.66644.599******44 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.9     0.068        76       1      35 [.       8      44 ..       8      48 .. 0.76
   2 ?    6.1   0.0     0.012        13       1      31 [.     174     204 ..     174     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.068
                                      EE--SHHHHHHHHHHHC...CTEEEEEE-SSSSSSGGG CS
                     NAD_binding_8  1 IvGaGlsGlvaAylLak...agfdvlllekrdrlGGra 35
                                      I+G G++G +aA  +++   ++ ++ l+ ++  lGG +
  gi|518653266|ref|YP_008142786.1|  8 IIGWGAAGFAAAIKASEltsNQMKIALIGTG-ELGGTC 44
                                      89999*****999888733258899998776.666665 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.012
                                       EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
                     NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                                       ++G+G  +l +Ay+ ++ g +v+++ +++r+
  gi|518653266|ref|YP_008142786.1| 174 VIGSGEVALELAYAFSNFGSEVHIFNRSNRI 204
                                       8*************************99986 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   1.4   0.00093         1       1      20 [.       5      24 ..       5      45 .. 0.79
   2 ?   -2.7   0.0         2   2.3e+03       3      30 ..     173     200 ..     172     203 .. 0.87
   3 ?    0.5   0.0      0.22   2.4e+02     374     403 ..     282     305 ..     251     315 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00093
                                      SEEEE--SHHHHHHHHHHHH CS
                     FAD_binding_2  1 DviViGsGlAGLaAAleaae 20
                                      D+ +iG G+AG aAA++a+e
  gi|518653266|ref|YP_008142786.1|  5 DLAIIGWGAAGFAAAIKASE 24
                                      899**************988 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2
                                       EEE--SHHHHHHHHHHHHTTT-EEEEES CS
                     FAD_binding_2   3 iViGsGlAGLaAAleaaeaGlkvavvek 30 
                                        ViGsG   L  A++ ++ G +v + + 
  gi|518653266|ref|YP_008142786.1| 173 AVIGSGEVALELAYAFSNFGSEVHIFNR 200
                                       69************99999999998775 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.22
                                       -EEEBETTSBESTTEEESSBTEEE-STCEE CS
                     FAD_binding_2 374 gGvetdengrvldadgqpipGLYAaGevaa 403
                                        G+++++++r+      + p  YAaG +  
  gi|518653266|ref|YP_008142786.1| 282 NGIVVNPDFRT------TNPKIYAAGDCVR 305
                                       59999999999......99*******9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.61u 0.31s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 3021.06
//
Query:       gi|518653267|ref|YP_008142787.1|  [L=56]
Description: copper chaperone [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-09   36.6   0.1    4.9e-09   36.5   0.1    1.1  1  HMA       Heavy-metal-associated domain


Domain annotation for each model (and alignments):
>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.1   2.7e-13   4.9e-09       2      45 ..       7      50 ..       6      55 .. 0.92

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 2.7e-13
                               HMA  2 vrvsgmhCagCaakvekvLselpgVesvkvdlatktvtVegdae 45
                                      +rv gm+C+ C ++v   L++l+gV++v+v+l  + + ++ +++
  gi|518653267|ref|YP_008142787.1|  7 LRVYGMTCDDCPKHVSTGLKNLNGVKEVSVSLTDGIAHIRATDT 50
                                      7999********************************99998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       385  (0.0214736); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 425.25
//
Query:       gi|518653268|ref|YP_008142788.1|  [L=328]
Description: mercuric reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.4e-07   29.9   2.2    7.1e-07   29.2   2.2    1.4  1  Glycos_transf_2  Glycosyl transferase family 2
  ------ inclusion threshold ------
      0.065   12.7   0.3       0.12   11.8   0.3    1.4  1  Capsule_synth    Capsule polysaccharide biosynthesis protein


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 !   29.2   2.2     8e-11   7.1e-07       1     133 [.       5     143 ..       5     179 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 8e-11
                                       EEEEEESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglra 77 
                                       svvi  y +++ ++  ++s++ +  ++++ei+v++  +  e  ++l++      ++r++++   + ++  + +++++
  gi|518653268|ref|YP_008142788.1|   5 SVVIFDYDRKNFIKDIVKSIAVNIGDKNIEILVIKSYEDPEIDNFLKDN-----NIRFFTLLDHKKQSDYIKCAVKE 76 
                                       899999**************9999**************99999999999.....9*******999************ PP

                                       --SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS...........E CS
                   Glycos_transf_2  78 atgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv...........g 133
                                       + g++++f D+Dd++ +++++ +++ + ++++ + + + + + + +++   n+++           +
  gi|518653268|ref|YP_008142788.1|  77 SLGEILMFHDDDDQFIDEKVSYVYNLFCQHEDLGYYHNNFDTIDQEGNAVYNRNYktpkfvslyikN 143
                                       *****************************99988888888877777777777666555544444441 PP

>> Capsule_synth  Capsule polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.3   1.3e-05      0.12      72     132 ..     228     289 ..     214     310 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.3e-05
                     Capsule_synth  72 apkklaqdvlp..qakldiayklialilqhklpkYkrHrilnalaelkgsilkrvaykvedre 132
                                       + +k++++++   ++ + i  +  +++ +  ++ Y++ ri n++  ++ ++lkr ++ ++  e
  gi|518653268|ref|YP_008142788.1| 228 PVTKMRNTFMRafSEGIRIFCYYSNFLENTSYSSYMKLRIINLKLAYNFWALKRKYKIMRS-E 289
                                       45667777775335778888999******************************97765553.3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.47
# Mc/sec: 2092.73
//
Query:       gi|518653269|ref|YP_008142789.1|  [L=487]
Description: heteropolysaccharide repeat-containing protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-14   52.9  72.3    5.7e-14   52.2  43.9    2.1  2  Polysacc_synt    Polysaccharide biosynthesis protein
    2.3e-12   47.2  22.3    2.3e-12   47.2  22.3    4.0  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    9.4e-11   41.5  29.0    9.4e-11   41.5  29.0    2.3  2  Polysacc_synt_3  Polysaccharide biosynthesis protein
    3.2e-06   26.0  50.2    3.2e-06   26.0  50.2    1.7  2  MurJ             Lipid II flippase MurJ
    0.00015   21.5  58.1    0.00021   21.0  21.4    3.5  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 !   52.2  43.9   1.6e-17   5.7e-14      19     273 ..       5     268 ..       2     269 .. 0.78
   2 !    6.7  20.3    0.0011       4.1      84     225 ..     284     448 ..     273     463 .. 0.80

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 1.6e-17
                     Polysacc_synt  19 afvtlvylarilgpegfGlvalalaivtllviltdlGlnaalvreiakyrek.......kelvslillnvllvllvl 88 
                                       + v+++++a +l+++ +G  +l++ai+ ++ + + lG+++ l  +i+ + ++         + ++++ ++++++  +
  gi|518653269|ref|YP_008142789.1|   5 STVFYFLIAHLLSTTLVGSISLLYAIMNIAGVAFVLGFSQGLEHFISYHISRgnyrnvrAMIRRIGIFAIISSIAAM 81 
                                       579*************************************9999999888888854554444444445555555555 PP

                     Polysacc_synt  89 vllfllllliaa..flglpelavlylilalmllllvgvasfrrglfqglermkyaavsqvveqlsrvilvliavflf 163
                                        ++++++++i a  +++   ++  ++++ +++  ++++  +++++  gl+r +  ++s +  +++   + ++++f+ 
  gi|518653269|ref|YP_008142789.1|  82 TIIYFISPFI-AitLFHSDFYVEFIRLIGIAIS-AFIFRDLFSSIILGLKRYRTYSLSYIFVNIFSYFFPILLLFYS 156
                                       5566666666.4344444445555555555555.5555555666666666666666666666666666777777777 PP

                     Polysacc_synt 164 ldivaavlgavlaalvggivslavlrkkf.r.prfvils.lklvrellsfsapltisslaillytyidsillglllg 237
                                       ++  ++++g++la lv+++++++++ +++ +  r+ +++    ++ l+ +s+pl++ s++++  +y+d+i+ +++l+
  gi|518653269|ref|YP_008142789.1| 157 GKAIYVIIGIALAGLVNAVIFIIMVLRIYlHlERTLNSEtIDPFKTLFIYSFPLFFASIMTTGANYLDRIVVSYFLN 233
                                       77888888888888888888888888888657777777779************************************ PP

                     Polysacc_synt 238 aeavGiYnaayqllvaisgllapivtaalfPvfsel 273
                                        +  GiYn+a  +++a+++++ pi +  l+P++s +
  gi|518653269|ref|YP_008142789.1| 234 LSFIGIYNFALVISSAATVFIMPISN-MLIPRLSSY 268
                                       **************************.******986 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0011
                     Polysacc_synt  84 vllvlvllfllllliaa.........flglpelavlylilalmll..llvgvasfrrglfqglermkyaavsqvveq 149
                                       +l++++l+++ + +  a         f g+ +    ++i+++m++  l+vg +++ +g+ + +++ + +++s+ +  
  gi|518653269|ref|YP_008142789.1| 284 LLNIASLVYIPAAMGIAamsritlynFAGKNYTIAYIPIIIIMIAtsLFVGSVILASGI-KSVRKTRIFLLSSGLAL 359
                                       55667777776666555577777776666666666677888888887899999998887.89*************** PP

                     Polysacc_synt 150 lsrvilvliavflfldivaavlgavlaalvggivslavlrkkfr..............prfvilslklvrellsfsa 212
                                       l+ +i++++++  f+ i +a +++++ ++v+ iv +++ rk+                   +++ l +   ++s+++
  gi|518653269|ref|YP_008142789.1| 360 LTNLIFSIVLIPRFS-IIGASIAYSSMTIVNFIVIYVYARKFNIsnydirtigkiwgsSLIMFSILFYLQSIFSYNI 435
                                       ***************.***************9999999995443678888999999965555555899999999999 PP

                     Polysacc_synt 213 pltisslaillyt 225
                                       pl i +++  ++ 
  gi|518653269|ref|YP_008142789.1| 436 PLEILYIFLGIII 448
                                       9988888876655 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 ?   -3.2  13.0       2.3   8.1e+03      46     133 ..      23     116 ..       4     118 .. 0.56
   2 ?    0.6  22.4      0.15   5.3e+02       6     132 ..     109     251 ..     104     257 .. 0.70
   3 ?   -5.1  11.2         5   1.8e+04      40     117 ..     227     314 ..     226     334 .. 0.49
   4 !   47.2  22.3   6.5e-16   2.3e-12       3     141 ..     323     456 ..     321     458 .. 0.89

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                   Polysacc_synt_C  46 nllli.plfgivGaaiatvlallvvavlnlyalrrllgiklellrrllkpllaalvmgivvylllllllglllla.. 119
                                       ++ l+   ++i G+a+   +++ +  ++ +++ r  ++    ++rr+   ++++ + ++ ++++ + ++ ++l +  
  gi|518653269|ref|YP_008142789.1|  23 SISLLyAIMNIAGVAFVLGFSQGLEHFISYHISRGNYRNVRAMIRRIGIFAIISSIAAMTIIYFISPFIAITLFHsd 99 
                                       33344256789999999999999999999888887665555457777633333333333322344444444444456 PP

                   Polysacc_synt_C 120 ...alalllavlvgalv 133
                                           ++ l+++++ a++
  gi|518653269|ref|YP_008142789.1| 100 fyvEFIRLIGIAISAFI 116
                                       65544555555555554 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.15
                   Polysacc_synt_C   6 alsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfg.....ivGaaiatvlallvvavln...l 74 
                                        ++i  + +  ++ssi+ gl+r +++ ++ ++  ++   + +ll+ + g     i+G+a+a ++  ++ +++    +
  gi|518653269|ref|YP_008142789.1| 109 GIAISAFIFRDLFSSIILGLKRYRTYSLSYIFVNIFSYFFPILLLFYSGkaiyvIIGIALAGLVNAVIFIIMVlriY 185
                                       455555556699*********************************54443333379988887765555444443336 PP

                   Polysacc_synt_C  75 yalrrllgikl.ellrrll...kpllaalvmgivvylllllllglllla......alalllavlvgal 132
                                        +l r+l+    + +++l+    pl++a +m   + +l +++++ +l+       ++al+++ ++   
  gi|518653269|ref|YP_008142789.1| 186 LHLERTLNSETiDPFKTLFiysFPLFFASIMTTGANYLDRIVVSYFLNLsfigiyNFALVISSAA--T 251
                                       67777777777*77888876888888888888888889999999998775554443344444433..3 PP

  == domain 3  score: -5.1 bits;  conditional E-value: 5
                   Polysacc_synt_C  40 lvklilnllli..plfgivGaaiatvlallvvavln.....lyalrrllgikl..ellrrllkpllaalvmgiv.vy 106
                                       +v   lnl +i  + f +v  ++atv+ + ++ +l+     ++ l  + g+k    +l ++  ++ + ++mgi+ + 
  gi|518653269|ref|YP_008142789.1| 227 VVSYFLNLSFIgiYNFALVISSAATVFIMPISNMLIprlssYFSLDDIRGFKRsiRMLLNIASLVYIPAAMGIAaMS 303
                                       78888898888445555555566666666666655544444555555555555664455555666666777777222 PP

                   Polysacc_synt_C 107 lllllllglll 117
                                        ++l+++   +
  gi|518653269|ref|YP_008142789.1| 304 RITLYNFAGKN 314
                                       22222222222 PP

  == domain 4  score: 47.2 bits;  conditional E-value: 6.5e-16
                   Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrr 79 
                                        i+++++ +++ s++l+s + ++ +++i+l+++ +++l +li++++lip+f+i+Ga+ia     +v ++++++++r+
  gi|518653269|ref|YP_008142789.1| 323 IIIMIATSLFVGSVILASGIKSVRKTRIFLLSSGLALLTNLIFSIVLIPRFSIIGASIAYSSMTIVNFIVIYVYARK 399
                                       6788888889999*********************************************************9999999 PP

                   Polysacc_synt_C  80 llgiklellrrllkpllaalvmgivvylllllllgllllaalalllavlvgalvYlllllll 141
                                           +++ +r++ k+  ++l+m+ ++++l++++   ++l+    +l +++g+++Y l l l+
  gi|518653269|ref|YP_008142789.1| 400 FNISNYD-IRTIGKIWGSSLIMFSILFYLQSIFSYNIPLE----ILYIFLGIIIYTLELKLF 456
                                       6666666.*****************998888888888776....888889999998766555 PP

>> Polysacc_synt_3  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  29.0   2.6e-14   9.4e-11       2     288 ..      12     315 ..      11     320 .. 0.75
   2 ?   -3.7   7.8       1.5   5.4e+03     102     194 ..     335     428 ..     315     435 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 2.6e-14
                   Polysacc_synt_3   2 LARLLspedFGvvaialvvislanlfvdmGlssal.......iqke..dlteedlstvftfnlvlgllialvlflla 69 
                                       +A LLs    G ++++ +++++a +   +G+s+ l       i +   ++ ++ ++++  f +++++++++++++++
  gi|518653269|ref|YP_008142789.1|  12 IAHLLSTTLVGSISLLYAIMNIAGVAFVLGFSQGLehfisyhISRGnyRNVRAMIRRIGIFAIISSIAAMTIIYFIS 88 
                                       68899999999999999999999999999998876333222232221345555899999****************** PP

                   Polysacc_synt_3  70 plias.fynqpelvtvlrvlalvlilsglssvqeallrrelkFkklfkitlvssvvgvivai.vlAllglgvwALvi 144
                                       p+ia  ++ ++  v+ +r++++ +    +  + ++++    ++ + +   ++ ++++ ++ i +l + g+ ++ ++ 
  gi|518653269|ref|YP_008142789.1|  89 PFIAItLFHSDFYVEFIRLIGIAISAFIFRDLFSSIILGLKRYRTYSLSYIFVNIFSYFFPIlLLFYSGKAIYVIIG 165
                                       ****8799***********9998655555555555555555666666666666666655544144566777776666 PP

                   Polysacc_synt_3 145 gtllssl..lslvllwlaskwrprlkfs...lkslkelfsfglklllsnllnylarnldnlliGkvlssaaLGlYsv 216
                                         l+  +  +++++++l++   ++ +++   ++ +k lf ++  l++++++ + a+ ld +++ ++l+ + +G+Y+ 
  gi|518653269|ref|YP_008142789.1| 166 IALAGLVnaVIFIIMVLRIYLHLERTLNsetIDPFKTLFIYSFPLFFASIMTTGANYLDRIVVSYFLNLSFIGIYNF 242
                                       66654430033333333333444444441125779****************************************** PP

                   Polysacc_synt_3 217 akrlaslpvaeitsviakVlfPalSrl..qddkkklrelylkvlrlialivlPiavglavvaellvkvllGsqW 288
                                       a  ++s+  + +  +i+++l+P lS+    dd + ++++++ +l++ +l+ +P+a+g+a++++  +  + G+++
  gi|518653269|ref|YP_008142789.1| 243 ALVISSA-ATVFIMPISNMLIPRLSSYfsLDDIRGFKRSIRMLLNIASLVYIPAAMGIAAMSRITLYNFAGKNY 315
                                       *977666.5667789**********97335999*****************************988777777766 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 1.5
                   Polysacc_synt_3 102 eallrrelkFkklfkitlvssvvgvivaivlAllglgvwALvigtllssllslvllwlaskwrprlkfslkslkelf 178
                                       + +l+  +k  + ++i l+ss ++++  ++  +++   ++++  ++++s + +v +++++ +  ++++s   ++ + 
  gi|518653269|ref|YP_008142789.1| 335 SVILASGIKSVRKTRIFLLSSGLALLTNLIFSIVLIPRFSIIGASIAYSSMTIVNFIVIYVYARKFNISNYDIRTIG 411
                                       55555555555666777889999999999999999999*******************************99999998 PP

                   Polysacc_synt_3 179 sf.glklllsnllnyla 194
                                       ++ g+ l+++++l yl 
  gi|518653269|ref|YP_008142789.1| 412 KIwGSSLIMFSILFYLQ 428
                                       85499999999998875 PP

>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.3      0.17   6.1e+02     101     134 ..      11      44 ..       4      50 .. 0.72
   2 !   26.0  50.2   8.9e-10   3.2e-06      64     436 ..      66     430 ..      48     444 .. 0.80

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.17
                              MurJ 101 lrillpylllvslsavfgavLnarkkFfapafsP 134
                                       l   l++ +lv+ +++++a+ n +++ f+ +fs+
  gi|518653269|ref|YP_008142789.1|  11 LIAHLLSTTLVGSISLLYAIMNIAGVAFVLGFSQ 44 
                                       5555677778888888888888888777777776 PP

  == domain 2  score: 26.0 bits;  conditional E-value: 8.9e-10
                              MurJ  64 ilvlllvtligilaapllirllatgf..deetlelavsllrillpylllvslsavfgavLnarkkFfapafsPvllN 138
                                       i  ++++++i+ +aa  +i+++++ +  +     + v+++r++   +    +  +f+++    k++   ++s +++N
  gi|518653269|ref|YP_008142789.1|  66 IRRIGIFAIISSIAAMTIIYFISPFIaiTLFHSDFYVEFIRLIGIAISAFIFRDLFSSIILGLKRYRTYSLSYIFVN 142
                                       34455566666666666666666666444444567899*****99999999************************** PP

                              MurJ 139 vsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfa..frdeglkkflklllptllgvsv 213
                                       +   ++ +ll  + g +ai++  iG+ ++g++ +++ ++++ +++l+l+ +++  ++d+ +k+++   +p ++++ +
  gi|518653269|ref|YP_008142789.1| 143 IFSYFFPILLLFYSG-KAIYV-IIGIALAGLVNAVIFIIMVLRIYLHLERTLNseTIDP-FKTLFIYSFPLFFASIM 216
                                       ********9999999.66666.8************************777665114444.67777766777777777 PP

                              MurJ 214 sqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltlllli 290
                                          + ++d ++ s++   s+  +++  +++  +  +f++ is++l+PrlS  ++ +d   +++ ++  + +  l+ i
  gi|518653269|ref|YP_008142789.1| 217 TTGANYLDRIVVSYFLNLSFIGIYNFALVISSAATVFIMPISNMLIPRLSSYFSLDDIRGFKRSIRMLLNIASLVYI 293
                                       7777899999999988888888888888999999******************************************* PP

                              MurJ 291 pvsfgllvlskpivsllferGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnil 367
                                       p+++g++++s+ i+   f  G  +++ ++++  ++ + a +L+  +   +l++   + + t+  +  s ++l +n++
  gi|518653269|ref|YP_008142789.1| 294 PAAMGIAAMSR-ITLYNF-AG--KNYTIAYIPIIIIMIATSLFVGS--VILASGIKSVRKTRIFLLSSGLALLTNLI 364
                                       *********96.544444.33..46677888889999999997655..59*************************** PP

                              MurJ 368 lsllllpplgvvglalatslsaliglvllyvllrkrlk.lteargiktflaklvvllalaavvilllssl 436
                                       +s++l+p+++ +g ++a+s   +++++++yv++rk     ++ r+i +   +     +++  ++ +l+s+
  gi|518653269|ref|YP_008142789.1| 365 FSIVLIPRFSIIGASIAYSSMTIVNFIVIYVYARKFNIsNYDIRTIGKIWGS----SLIMFSILFYLQSI 430
                                       ********************************99964434444444444444....33444444444444 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0  21.4     6e-08   0.00021      10     154 ..       2     144 ..       1     154 [. 0.80
   2 ?   -3.2  10.4       1.6   5.8e+03      83     156 ..     107     184 ..      98     188 .. 0.68
   3 !   10.8  20.4     8e-05      0.29       1     160 [.     209     367 ..     209     368 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 6e-08
                              MatE  10 sllslidtllvgrl.gskalAavsialsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsl 84 
                                       +l+s+++ +l+++l +++ ++++s+   i ++ +v f+lg+s +l+ ++++ +  +n+++++  +r++ i++++ s+
  gi|518653269|ref|YP_008142789.1|   2 FLSSTVFYFLIAHLlSTTLVGSISLLYAIMNIAGVaFVLGFSQGLEHFISYHISRGNYRNVRAMIRRIGIFAIISSI 78 
                                       57899999********************************************************************* PP

                              MatE  85 iiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                                       +++ ++++ s++i+  + +++       +++r++++ i a+++  ++s+i  g ++ ++    +++ +++
  gi|518653269|ref|YP_008142789.1|  79 AAMTIIYFISPFIAITLFHSDFY----VEFIRLIGIAISAFIFRDLFSSIILGLKRYRTYSLSYIFVNIF 144
                                       *************9988888855....5556666666666666666666665555555544444443333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
                              MatE  83 sliiallvllfseqilslftqdee..vlelakrylrililgipalalqlvlsgilrgagktkvplyislisl..lln 155
                                        + ia+ +++f++ + s++   +     +l+  +++i  ++ p+l+l+   ++i+  +g++ ++l+ ++i +  +l+
  gi|518653269|ref|YP_008142789.1| 107 LIGIAISAFIFRDLFSSIILGLKRyrTYSLSYIFVNIFSYFFPILLLFYSGKAIYVIIGIALAGLVNAVIFIimVLR 183
                                       34444555566666666666555555688999999999999999999999999999999999988755443212555 PP

                              MatE 156 i 156
                                       i
  gi|518653269|ref|YP_008142789.1| 184 I 184
                                       5 PP

  == domain 3  score: 10.8 bits;  conditional E-value: 8e-05
                              MatE   1 Pialenllesllslidtllvgrl.gskalAavsialsilsllfvfllglstalttlvgqalGaknfkrakealrqgl 76 
                                       P+++++++ +  + +d ++v+++   + ++ +++al i+s  +vf++ +s+ l ++ + ++   + +++k+++r+ l
  gi|518653269|ref|YP_008142789.1| 209 PLFFASIMTTGANYLDRIVVSYFlNLSFIGIYNFALVISSAATVFIMPISNMLIPRLSSYFSLDDIRGFKRSIRMLL 285
                                       99*************************************************************************** PP

                              MatE  77 illlllsliiallvllfseqilslftqdeevlelakrylrililgipalalqlvlsgilrgagktkvplyislisll 153
                                        ++ l+++++a+ + + s++ l+ f  ++  ++++  ++ +++ ++++   +++l++  +++ kt++ l  s ++ll
  gi|518653269|ref|YP_008142789.1| 286 NIASLVYIPAAMGIAAMSRITLYNFAGKNYTIAYIPIIIIMIATSLFVG--SVILASGIKSVRKTRIFLLSSGLALL 360
                                       *************************999977766666666666665555..99************************ PP

                              MatE 154 lniplny 160
                                        n++++ 
  gi|518653269|ref|YP_008142789.1| 361 TNLIFSI 367
                                       ***9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (487 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1072  (0.0597914); 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:                         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: 0.69u 0.33s 00:00:01.02 Elapsed: 00:00:00.50
# Mc/sec: 2906.96
//
Query:       gi|518653270|ref|YP_008142790.1|  [L=256]
Description: glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for 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-09   36.5   0.3    5.6e-09   36.0   0.3    1.3  1  Glycos_transf_2  Glycosyl transferase family 2
    6.9e-05   23.3   0.1    0.00014   22.3   0.1    1.6  1  Glyco_tranf_2_4  Glycosyl transferase family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.3   6.3e-13   5.6e-09       5     127 ..       7     130 ..       4     181 .. 0.78

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 6.3e-13
                                       EESS-TTTHHHHHHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCH.C-TTEEEEEESSS-HHHHHHHHHHHH--S CS
                   Glycos_transf_2   5 ptyNeektlletlesllaqdpypdfeiivvDDgStDetveileelak.edprvrvirreenvGkagalnaglraatg 80 
                                       ++yN  k +l++l+s++ +  + ++ +++vD+ S+D+t e+l++ ++ ++  v+  + ++++G   a+ ++ ++a+ 
  gi|518653270|ref|YP_008142790.1|   7 TVYNSRKRVLQSLNSIIGI--KIEKSVYIVDNYSSDGTFELLRKNQDkYNMVVIQAHCTRGWGRYLAIQKAEEKASN 81 
                                       58****************9..99**********************996666666677778889999*********99 PP

                                       S.EEEEEESSEEE-TTHHHHHHHHHHH...TTCEEEEEEEEEECCCCCCC CS
                   Glycos_transf_2  81 d.yilflDaDdepdpdwleklvealekd..gadvvlgqrprifgetdeie 127
                                       d  ++f+D D++++ + + +lve++ ++   + v+l ++  + + ++  +
  gi|518653270|ref|YP_008142790.1|  82 DdMFMFIDLDTIYNAE-FARLVEYAYAHidHKTVFLDNHLCYYDVNHAVP 130
                                       99*************8.556666655544355555555555555555444 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 !   22.3   0.1   1.6e-08   0.00014       6      86 ..      14      96 ..       9     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 1.6e-08
                   Glyco_tranf_2_4  6 iLpeflahhlalgfd.rilvydndstDgtrailkelpe.vkllhvdksyederrqvellkallaryaeadwvlvvDaDE 82
                                      +  + l  +  + ++  ++++dn s+Dgt ++l+++++ ++++ ++ + ++      +++++ ++++++d  +++D D 
  gi|518653270|ref|YP_008142790.1| 14 RVLQSLNSIIGIKIEkSVYIVDNYSSDGTFELLRKNQDkYNMVVIQAHCTRGWGRYLAIQKAEEKASNDDMFMFIDLDT 92
                                      555666666666665269***************8865448888888887754445668888888999***********7 PP

                   Glyco_tranf_2_4 83 flvv 86
                                      ++  
  gi|518653270|ref|YP_008142790.1| 93 IYNA 96
                                      7665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.27s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 1745.08
//
Query:       gi|518653271|ref|YP_008142791.1|  [L=272]
Description: formate dehydrogenase subunit D [Ferroplasma acidarmanus fer1]
Scores for complete 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-74  248.0   0.0    1.1e-73  247.8   0.0    1.0  1  FdhD-NarQ  FdhD/NarQ family


Domain annotation for each model (and alignments):
>> FdhD-NarQ  FdhD/NarQ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.8   0.0   6.1e-78   1.1e-73       2     236 ..      26     269 ..      25     270 .. 0.90

  Alignments for each domain:
  == domain 1  score: 247.8 bits;  conditional E-value: 6.1e-78
                                       --EEEEEEETT....EEEEEEEE-SSSHHHHHHHHHHHCTS--SGGGEEEEEEETTTEE......EE-S........ CS
                         FdhD-NarQ   2 eEepltivvng....relatlmatpadleelalGfllsegliesaediesievdedeas......vavatrakaedk 68 
                                       +Eepl+i+++       + ++m+tp d+ +la+Gfl++eg+i+ +e+i +i++ +d +       v v+ +  +++ 
  gi|518653271|ref|YP_008142791.1|  26 VEEPLEIRIDYenntYDVSVIMRTPVDDFALAAGFLFTEGIIK-PENIIDIKYPTDAGIseknniVIVSVNSFEKQL 101
                                       79*****997633336789***********************8.888999999876555666776666666655555 PP

                                       .---------------.---...--.H-----------EEGGGHHHHHHHHHTS-SHHHHHS--EEEEEEE.TTEEE CS
                         FdhD-NarQ  69 eerrtakrvvtsgCglcgkesleel.letlelpesdlklsaeallrlmdalrekqelfketggvHaaalfdadgell 144
                                         +r++  +v+s+Cg+cgk++++++ l++ +l +++ k++ ++ll+l+  ++++q++fk+tggvHaaa++d +g++l
  gi|518653271|ref|YP_008142791.1| 102 VGNRNF--YVNSSCGVCGKTNINDIfLKAEHLISQRNKIHYNQLLKLPGIMKNNQKIFKNTGGVHAAAILDYSGNIL 176
                                       678999..**************9996666666799****************************************** PP

                                       EEEEESSHHHHHHHHHHHHHT.TSS-S.SSEEEESS-B-HHHHHHHHHHT-SEEEESS-B-HHHHHHHHHHT-EEEE CS
                         FdhD-NarQ 145 avreDvGRHnAlDkviGaallegldls.dkilvvsgRlssemvqKaaragipvlvsvsaptslavelAeeagltlvg 220
                                        + eDvGRHnA+Dk+iG+++l+g++ s + +l vsgR+ +e+vqKaa+ gipv+ svsap+slavelA+e+++tlv 
  gi|518653271|ref|YP_008142791.1| 177 SMGEDVGRHNAVDKAIGKMVLKGINRSpEAVLQVSGRAGFEIVQKAAMYGIPVVSSVSAPSSLAVELADEFNMTLVS 253
                                       *************************66266889******************************************** PP

                                       EEETTEEEEEE-GGGE CS
                         FdhD-NarQ 221 fvrgkrfnvYtgaeRi 236
                                       fvrg++fn+Yt++eRi
  gi|518653271|ref|YP_008142791.1| 254 FVRGNSFNIYTHSERI 269
                                       ***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1935.06
//
Query:       gi|518653272|ref|YP_008142792.1|  [L=143]
Description: hypothetical protein FACI_IFERC00001G1915 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1100.27
//
Query:       gi|518653273|ref|YP_008142793.1|  [L=978]
Description: hypothetical protein FACI_IFERC00001G1916 [Ferroplasma acidarmanus fer1]
Scores for complete 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-83  279.9   0.1    5.5e-83  279.3   0.1    1.2  1  Molybdopterin    Molybdopterin oxidoreductase
    1.2e-22   80.1   0.0    2.3e-22   79.1   0.0    1.5  1  Molydop_binding  Molydopterin dinucleotide binding domain
    3.9e-17   62.0   0.9    3.9e-17   62.0   0.9    2.3  1  Molybdop_Fe4S4   Molybdopterin oxidoreductase Fe4S4 domain
    1.7e-12   47.2   0.0    3.7e-12   46.1   0.0    1.6  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    5.4e-11   41.8  18.0    2.8e-06   26.9   2.1    3.6  3  Fer4             4Fe-4S binding domain
    6.2e-09   35.3   1.8    2.4e-08   33.4   1.8    2.1  1  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
      2e-08   34.0  20.7    6.5e-06   26.0   2.9    3.2  2  Fer4_6           4Fe-4S binding domain
    3.8e-08   33.4   7.9    3.8e-08   33.4   7.9    3.0  2  Fer4_21          4Fe-4S dicluster domain
    1.3e-07   31.6   8.2      6e-06   26.3   2.6    3.5  3  Fer4_10          4Fe-4S dicluster domain
    2.2e-06   28.2  12.1    2.2e-06   28.2  12.1    3.8  3  Fer4_7           4Fe-4S dicluster domain
    2.9e-06   27.6   6.6    2.9e-06   27.6   6.6    2.9  3  Fer4_8           4Fe-4S dicluster domain
    1.4e-05   25.2  10.8    1.4e-05   25.2  10.8    3.8  3  Fer4_9           4Fe-4S dicluster domain
    0.00018   22.1   4.5      0.024   15.4   0.8    2.9  2  Fer4_15          4Fe-4S single cluster domain
    0.00054   20.8  18.6     0.0019   19.1   4.6    4.1  3  Fer4_16          4Fe-4S double cluster binding domain
     0.0014   19.0   0.7          3    8.3   0.0    2.8  2  zf-C2HE          C2HE / C2H2 / C2HC zinc-binding finger
     0.0015   18.5  13.8     0.0053   16.8   2.2    3.4  3  Fer4_2           4Fe-4S binding domain
  ------ inclusion threshold ------
      0.019   15.5  10.1      0.019   15.5  10.1    3.4  4  Fer4_17          4Fe-4S dicluster domain
      0.077   13.6  14.6          3    8.5   3.3    3.6  3  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
       0.23   11.7  16.8        0.2   11.9   2.8    3.1  3  Fer4_18          4Fe-4S dicluster domain
       0.49   11.3  16.3       0.32   11.9   0.7    3.3  3  Fer4_22          4Fe-4S dicluster domain
        2.1    9.1  19.1       0.52   11.0   2.3    3.2  2  Fer4_4           4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.3   0.1   6.4e-86   5.5e-83       1     431 [.     316     739 ..     316     740 .. 0.94

  Alignments for each domain:
  == domain 1  score: 279.3 bits;  conditional E-value: 6.4e-86
                                       B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BE CS
                     Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfy 77 
                                       RlkyP++R   + +GkFv++sWdeA ++ a+ lk++ +kyg+++ ++ +s++ + +e+ ++l+k+++ ++    +++
  gi|518653273|ref|YP_008142793.1| 316 RLKYPLIR---K-NGKFVQASWDEAIDFAAKGLKKVGEKYGNESLMFIASSKGT-NEESYLLQKMARQIFH--NNNV 385
                                       9*******...6.8*******************************987777777.888888*******999..5889 PP

                                       ECCGGGTTHHHH....CHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECSS CS
                     Molybdopterin  78 dwyadlppasaq....qtigsdsrsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigpr 150
                                       d+  + + a a     +t+g++         +++d+++s+l+ ++G+N +e +p+l +r+ +a++ +  k+iv + r
  gi|518653273|ref|YP_008142793.1| 386 DNSSRFCQAPATtglwRTVGYGGD-----AGSIQDIYKSELVMIVGANTAESHPVLATRVKRAHKLNHQKLIVSDLR 457
                                       999999988877666655555433.....34799******************************9999********* PP

                                       B-HCGGGCSEEEEEHTTTHHHHHHHHHHHHHHCCCCTCHHHHHHEECHHHCCCCCCCEECCSHHHHHHCCHHHHHHH CS
                     Molybdopterin 151 yaellkfadewlaikpgtdaalalamghvilqelkvdkeflrkytygkeetdmpllvtleeetgkkkevvariarel 227
                                       ++e++++ad +l ++pgtd  l+ a++++i++++++d ef++k+ +g++e+ + l+  + e+++ +++++ ++++e 
  gi|518653273|ref|YP_008142793.1| 458 KNEMAERADIYLHPSPGTDIVLLSALSKYIIDQGWHDREFIEKRVNGFDEYYKSLEPFTLENASSITGIPEKQIIET 534
                                       ***************************************************************************** PP

                                       HHHHHHHTSSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCC CS
                     Molybdopterin 228 arnaaktagksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvksl 304
                                       a+ +++ +  + i++ +g+++++ g++   a+ nL+ l+gn+g+pg+g   l+G ++++g a++ ga+p+ l+ ++ 
  gi|518653273|ref|YP_008142793.1| 535 AEMIHSVKS-MCILWAMGITQHSAGSDESTAISNLLVLTGNYGRPGTGAYPLRGHNNVQG-ASDFGAMPTYLPGYQP 609
                                       *******99.********************************************999999.9999999999999999 PP

                                       TT...HHHHHCCCTTTCSTSS--ECGGCHHHHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCSSH CS
                     Molybdopterin 305 ke...ekikfaaeqpgnlgnfprnlfversnllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrlts 378
                                        +     +kf + +  +l+ +p+++ v+ ++++ + ++k++y++g++   + +d n + + lekld+++v d++ ++
  gi|518653273|ref|YP_008142793.1| 610 IKdkeVIKKFEKAWHTELPTKPGIDNVSCIENIDNDKIKAMYVVGQEIASTGPDSNMIRDSLEKLDFLIVEDVFFSE 686
                                       997766678999999******************************9999999************************* PP

                                       HHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHHHHHHH CS
                     Molybdopterin 379 talyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIlkaLak 431
                                       ta+yaD++LPa+  +Eke+++tn+e+r+q++ q+++p    k+dw+I++ +ak
  gi|518653273|ref|YP_008142793.1| 687 TAKYADVVLPATVSLEKEGTFTNTERRIQRIYQVMEPYEQTKPDWEIIQGIAK 739
                                       *************************************************9998 PP

>> Molydop_binding  Molydopterin dinucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.1   0.0   2.7e-25   2.3e-22       1     110 [.     823     930 ..     823     931 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.1 bits;  conditional E-value: 2.7e-25
                                       EEEEEE-BTTBSTTTTTCGCCHHHHCSSS.-EEEEEHHHHHHHT--TT-EEEEEETTEEEEEEEEEESSB-TTEEEE CS
                   Molydop_binding   1 lrLitgrsldqlhsqtrtrpvlrlakpep.evveinpedAaalGikdGdlVevesrrGsvevrakvtervrpGvvfm 76 
                                       l+L++gr l+++h + +t +++  +++ p  ++ei+++ Aa++ i++Gd V+v+s++Gs+++ra +terv    ++m
  gi|518653273|ref|YP_008142793.1| 823 LHLNNGRMLEHFHEGNETFKTEGIKEKVPdTFLEISEKLAAEYKIQTGDFVRVTSKWGSIKARALITERVSGNELYM 899
                                       79*************************************************************************** PP

                                       ESSHCC.....S-GHCTS--SCSTTT--CSTT-E CS
                   Molydop_binding  77 pfgwweagekggnaNaltddatdplsgtpefksv 110
                                       p+++ +   + +++N lt++  dp s tp++k+ 
  gi|518653273|ref|YP_008142793.1| 900 PMNAAS---DDATVNLLTSYTRDPDSDTPAYKEL 930
                                       ****99...**********************986 PP

>> Molybdop_Fe4S4  Molybdopterin oxidoreductase Fe4S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.0   0.9   4.6e-20   3.9e-17       1      55 []     259     313 ..     259     313 .. 0.97

  Alignments for each domain:
  == domain 1  score: 62.0 bits;  conditional E-value: 4.6e-20
                                       SEEEEEE-SSBTT--EEEEEEETTEEEEEEE-TTSTTTTT---HHHHTCHHCCCB CS
                    Molybdop_Fe4S4   1 ekvvktaCpyCgvgCglevhvkdgkivkvegdpdhpvnegrlCvKGrtllervyn 55 
                                       +k++kt+C+yCgvgC++++++k+ ki kv++  ++p+n   +C+KG++++ +v++
  gi|518653273|ref|YP_008142793.1| 259 IKKTKTVCTYCGVGCSFTMWTKGRKILKVQPEVESPANGISTCIKGKFGWGFVNS 313
                                       589*************************************************996 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   4.4e-15   3.7e-12       6      77 ..       6      72 ..       3      77 .. 0.96

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 4.4e-15
                            Fer2_4  6 ltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepnvracstpvedGlkv 77
                                      + +DG ++  +  +t+++A+++n++d+p+ c++      l+a+ +C +C+V  +g+  vrac+t++++++kv
  gi|518653273|ref|YP_008142793.1|  6 IFIDGIPLNIKGEETILQAMMDNNIDIPHVCYN----PALGAIESCDTCIVNADGKY-VRACTTQAKNNMKV 72
                                      78*******************************....99****************98.*************9 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   3.0   7.1e-08   6.1e-05       2      18 ..     141     157 ..     140     159 .. 0.92
   2 !   26.9   2.1   3.3e-09   2.8e-06       3      23 ..     185     205 ..     183     206 .. 0.93
   3 ?    0.3   0.2      0.81   6.9e+02       6      12 ..     264     270 ..     259     271 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 7.1e-08
                                       EEETTTSSS-THHHHHS CS
                              Fer4   2 videekCigCGaCvevC 18 
                                        +d++ Ci CG+Cve+C
  gi|518653273|ref|YP_008142793.1| 141 RYDPDQCILCGRCVEAC 157
                                       68*************** PP

  == domain 2  score: 26.9 bits;  conditional E-value: 3.3e-09
                                       EETTTSSS-THHHHHSTTTEE CS
                              Fer4   3 ideekCigCGaCvevCPvgAI 23 
                                       i+ + C+ CG Cv vCPv+A+
  gi|518653273|ref|YP_008142793.1| 185 INDSSCVSCGHCVTVCPVNAL 205
                                       8999****************7 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.81
                                       TTSSS-T CS
                              Fer4   6 ekCigCG 12 
                                         C++CG
  gi|518653273|ref|YP_008142793.1| 264 TVCTYCG 270
                                       57****9 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   1.8   2.8e-11   2.4e-08       4      39 ..      86     122 ..      84     123 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2.8e-11
                   NADH-G_4Fe-4S_3   4 ilellLanHpldCltCdkn.GnCeLQdlayelgvees 39 
                                       ++  +L nH+l+C++C++n G+C L++ +  l+v+++
  gi|518653273|ref|YP_008142793.1|  86 AVNRILHNHDLYCTVCENNnGDCALHSAVDTLQVTRQ 122
                                       6889**************************9999976 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   4.2   3.3e-06    0.0028       4      19 ..     142     157 ..     141     159 .. 0.95
   2 !   26.0   2.9   7.6e-09   6.5e-06       4      24 .]     185     205 ..     184     205 .. 0.94

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.3e-06
                            Fer4_6   4 idpdkCigCgdCvrvC 19 
                                       +dpd Ci Cg+Cv +C
  gi|518653273|ref|YP_008142793.1| 142 YDPDQCILCGRCVEAC 157
                                       8*************** PP

  == domain 2  score: 26.0 bits;  conditional E-value: 7.6e-09
                            Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                                       i++++C++Cg Cv+vCP +a+
  gi|518653273|ref|YP_008142793.1| 185 INDSSCVSCGHCVTVCPVNAL 205
                                       89****************997 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   7.9   4.4e-11   3.8e-08       4      55 ..     143     204 ..     141     208 .. 0.72
   2 ?   -2.4   0.3       6.5   5.5e+03      11      18 ..     266     273 ..     249     277 .. 0.55

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 4.4e-11
                           Fer4_21   4 dedkCigCgkCliaCedtshqai..........eidaktvlkvvedeCvGCnlCssvCPved 55 
                                       d+d+Ci Cg+C+ aC+d  ++            ++  +   ++ +++Cv C  C++vCPv+ 
  gi|518653273|ref|YP_008142793.1| 143 DPDQCILCGRCVEACQDVEVNETlhidwslerpRVVWDDNKAINDSSCVSCGHCVTVCPVNA 204
                                       89***************77654334455443333333334477899**************54 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 6.5
                           Fer4_21  11 CgkCliaC 18 
                                       C+ C + C
  gi|518653273|ref|YP_008142793.1| 266 CTYCGVGC 273
                                       44444433 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.3       2.6   2.2e+03      40      51 ..      42      62 ..      38      65 .. 0.65
   2 !   17.7   0.3   3.3e-06    0.0028       3      19 ..     141     157 ..     139     175 .. 0.82
   3 !   26.3   2.6     7e-09     6e-06       3      51 ..     184     273 ..     182     274 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 2.6
                           Fer4_10 40 kkvekCtgc.........gaC 51
                                      +++e+C++c          aC
  gi|518653273|ref|YP_008142793.1| 42 GAIESCDTCivnadgkyvRAC 62
                                      568899999766664443455 PP

  == domain 2  score: 17.7 bits;  conditional E-value: 3.3e-06
                           Fer4_10   3 vidddtCirCgkCvkaC 19 
                                       ++d+d+Ci Cg+Cv+aC
  gi|518653273|ref|YP_008142793.1| 141 RYDPDQCILCGRCVEAC 157
                                       689************** PP

  == domain 3  score: 26.3 bits;  conditional E-value: 7e-09
                           Fer4_10   3 vidddtCirCgkCvkaCPadl........................................tsvgakgeaseeeavr 39 
                                        i+d++C+ Cg Cv++CP+++                                         + ++++++++ee+++
  gi|518653273|ref|YP_008142793.1| 184 AINDSSCVSCGHCVTVCPVNAlmeksmleeagyftsltrkakynliefgkdlekpvgngmiMKISNIEAKMREEQIK 260
                                       5899***************99***************************************99999************ PP

                           Fer4_10  40 kkvekCtgcg.aC 51 
                                       k    Ct cg  C
  gi|518653273|ref|YP_008142793.1| 261 KTKTVCTYCGvGC 273
                                       *********9666 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0  11.7      0.01       8.8       2      48 ..      98     157 ..      46     160 .. 0.73
   2 !   28.2  12.1   2.5e-09   2.2e-06       1      52 []     146     204 ..     146     204 .. 0.72
   3 ?    2.2   0.1      0.32   2.7e+02       4      13 ..     265     274 ..     222     303 .. 0.70

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.01
                            Fer4_7   2 CigC....gaCvaaCpvkaieldeeenek............gtekveidpekClgCgaCvavC 48 
                                       C+ C    g C+    v++++++    +k             ++ +++dp++C+ Cg+Cv++C
  gi|518653273|ref|YP_008142793.1|  98 CTVCennnGDCALHSAVDTLQVTR---QKypftskgyepdySNPFYRYDPDQCILCGRCVEAC 157
                                       444422222444444444444433...3333344443333344778***************** PP

  == domain 2  score: 28.2 bits;  conditional E-value: 2.5e-09
                            Fer4_7   1 rCigCgaCvaaCp....vkaieldeeenekgt...ekveidpekClgCgaCvavCPtga 52 
                                       +Ci Cg+Cv+aC     ++++ +d + + +++   +  +i+ ++C++Cg+Cv+vCP++a
  gi|518653273|ref|YP_008142793.1| 146 QCILCGRCVEACQdvevNETLHIDWSLERPRVvwdDNKAINDSSCVSCGHCVTVCPVNA 204
                                       6***********8655455555554433332223344489999**************97 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.32
                            Fer4_7   4 gCgaCvaaCp 13 
                                        C +C + C+
  gi|518653273|ref|YP_008142793.1| 265 VCTYCGVGCS 274
                                       3555555554 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   1.1       4.1   3.5e+03      45      56 ..      92     103 ..      45     132 .. 0.56
   2 !   27.6   6.6   3.4e-09   2.9e-06       3      64 ..     145     203 ..     143     204 .. 0.84
   3 ?   -2.0   0.1         6   5.1e+03       8      15 ..     266     273 ..     240     301 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 4.1
                            Fer4_8  45 eealwsCttcga 56 
                                       ++   +Ct c++
  gi|518653273|ref|YP_008142793.1|  92 HNHDLYCTVCEN 103
                                       444456666654 PP

  == domain 2  score: 27.6 bits;  conditional E-value: 3.4e-09
                            Fer4_8   3 ekCieCgaCqsaCpvlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                                       ++Ci Cg+C +aC  ++     + d   e+   v+++++  ++ +  sC++cg+C++vCpv+
  gi|518653273|ref|YP_008142793.1| 145 DQCILCGRCVEACQDVEVNETLHIDWSLERPR-VVWDDN--KAINDSSCVSCGHCVTVCPVN 203
                                       68************999999888888888888.555555..3567789************97 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 6
                            Fer4_8   8 CgaCqsaC 15 
                                       C +C   C
  gi|518653273|ref|YP_008142793.1| 266 CTYCGVGC 273
                                       44444444 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0  12.6     0.032        28      33      47 ..     129     158 ..      45     162 .. 0.72
   2 !   25.2  10.8   1.6e-08   1.4e-05       1      50 [.     146     204 ..     146     205 .. 0.67
   3 ?    2.0   0.3      0.28   2.4e+02       4      23 ..     265     284 ..     245     303 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.032
                            Fer4_9  33 e...............eaCigCgaCveaCp 47 
                                       +               ++Ci Cg+CveaC+
  gi|518653273|ref|YP_008142793.1| 129 KgyepdysnpfyrydpDQCILCGRCVEACQ 158
                                       133445555666666689***********8 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 1.6e-08
                            Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase..........eaCigCgaCveaCpkga 50 
                                       +C+ Cg+CveaC+   v+e       +l++ +           ++C++Cg Cv +Cp +a
  gi|518653273|ref|YP_008142793.1| 146 QCILCGRCVEACQDVEVNETLHIDW-SLERPRVvwddnkaindSSCVSCGHCVTVCPVNA 204
                                       6***********5444433333222.2222222344557899999************986 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.28
                            Fer4_9   4 gCgaCveaCpagvvvedaae 23 
                                        C++C   C ++++++ ++ 
  gi|518653273|ref|YP_008142793.1| 265 VCTYCGVGCSFTMWTKGRKI 284
                                       49999999988887776655 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.8   2.8e-05     0.024       3      29 ..     142     168 ..     141     180 .. 0.88
   2 ?    7.1   0.2     0.011       9.3       3      19 ..     185     201 ..     184     225 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.8e-05
                           Fer4_15   3 vDrdaCigcglCvaeapevfeldedgl 29 
                                       +D d+Ci cg+Cv+++++v +++  ++
  gi|518653273|ref|YP_008142793.1| 142 YDPDQCILCGRCVEACQDVEVNETLHI 168
                                       799****************99887665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.011
                           Fer4_15   3 vDrdaCigcglCvaeap 19 
                                       ++ + C +cg Cv+++p
  gi|518653273|ref|YP_008142793.1| 185 INDSSCVSCGHCVTVCP 201
                                       67789***********8 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   1.3         2   1.7e+03      33      62 ..      68     103 ..      42     104 .. 0.57
   2 !    8.6   0.2    0.0043       3.6       1      13 [.     146     158 ..     139     178 .. 0.86
   3 !   19.1   4.6   2.2e-06    0.0019       2      62 ..     190     271 ..     189     276 .. 0.52

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 2
                           Fer4_16  33 y......ntaekkdlaedeekckkqeaitgCdiCqd 62 
                                       +      n ++ k  ++++ ++  +++  +C +C++
  gi|518653273|ref|YP_008142793.1|  68 NnmkvlfNSPDVKARETEAVNRILHNHDLYCTVCEN 103
                                       122345566666666666666667889999999975 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0043
                           Fer4_16   1 rCgtCgkCaevCP 13 
                                       +C+ Cg+C+e+C 
  gi|518653273|ref|YP_008142793.1| 146 QCILCGRCVEACQ 158
                                       5999999999995 PP

  == domain 3  score: 19.1 bits;  conditional E-value: 2.2e-06
                           Fer4_16   2 CgtCgkCaevCPtnaikekkekeieare.......cisy.......................ntaekkdlaedeekc 48 
                                       C++Cg C+ vCP+na+ ek   ++e          +  +                       +     +++ + +++
  gi|518653273|ref|YP_008142793.1| 190 CVSCGHCVTVCPVNALMEK--SMLEEAGyftsltrK--AkynliefgkdlekpvgngmimkiS-----NIEAKMREE 257
                                       *****************99..455444433333332..1235566666666666654332212.....222222222 PP

                           Fer4_16  49 kkqeaitgCdiCqd 62 
                                       ++++  t C  C  
  gi|518653273|ref|YP_008142793.1| 258 QIKKTKTVCTYCGV 271
                                       22233355555544 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 !    8.1   0.1    0.0042       3.6      22      47 ..      80     105 ..      49     107 .. 0.75
   2 !    8.3   0.0    0.0036         3      21      44 ..     247     270 ..     210     276 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0042
                           zf-C2HE  22 eslseeqskelilktpLkCtrCganf 47 
                                       + +++e  ++++ +++L Ct C++n 
  gi|518653273|ref|YP_008142793.1|  80 KARETEAVNRILHNHDLYCTVCENNN 105
                                       446677888899***********765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0036
                           zf-C2HE  21 ieslseeqskelilktpLkCtrCg 44 
                                       i++++ +  +e i+kt+  Ct+Cg
  gi|518653273|ref|YP_008142793.1| 247 ISNIEAKMREEQIKKTKTVCTYCG 270
                                       3667788889999**********9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.4       9.9   8.5e+03      13      16 ..      47      50 ..      43      64 .. 0.60
   2 !   16.8   2.2   6.2e-06    0.0053       3      20 ..     140     157 ..     138     158 .. 0.92
   3 !   16.3   4.0   8.8e-06    0.0075       5      21 ..     185     201 ..     182     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.9
                            Fer4_2 13 CgaC 16
                                      C +C
  gi|518653273|ref|YP_008142793.1| 47 CDTC 50
                                      4444 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 6.2e-06
                            Fer4_2   3 vvvdtdrCigCgaCvsaC 20 
                                       + +d+d Ci Cg Cv aC
  gi|518653273|ref|YP_008142793.1| 140 YRYDPDQCILCGRCVEAC 157
                                       679*************** PP

  == domain 3  score: 16.3 bits;  conditional E-value: 8.8e-06
                            Fer4_2   5 vdtdrCigCgaCvsaCP 21 
                                       ++  +C++Cg Cv++CP
  gi|518653273|ref|YP_008142793.1| 185 INDSSCVSCGHCVTVCP 201
                                       67789************ PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   4.7    0.0043       3.7       5      57 ..      98     158 ..      96     161 .. 0.53
   2 ?   15.5  10.1   2.3e-05     0.019       1      58 [.     146     202 ..     146     204 .. 0.71
   3 ?    6.1   8.0     0.019        16       2      32 ..     190     248 ..     189     277 .. 0.54
   4 ?   -0.6   0.3       2.3     2e+03       5      20 ..     266     281 ..     264     302 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0043
                           Fer4_17   5 CgyClp...eCpsyeaydnepkkllraaklglleeaeke......ekaslCieCgeCerkCP 57 
                                       C  C++    C  + a d+  + +++++ +++++++ +          ++Ci Cg+C+++C 
  gi|518653273|ref|YP_008142793.1|  98 CTVCENnngDCALHSAVDT-LQVTRQKYPFTSKGYEPDYsnpfyrYDPDQCILCGRCVEACQ 158
                                       3333333333444444333.34444554444333332223355545789************5 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 2.3e-05
                           Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaeke...ekaslCieCgeCerkCPq 58 
                                       +Ci Cg C+++C   e +++    l  +++l++ + + ++    + s+C++Cg C+++CP 
  gi|518653273|ref|YP_008142793.1| 146 QCILCGRCVEACQDVEVNET----LHIDWSLERPRVVWDDnkaINDSSCVSCGHCVTVCPV 202
                                       5*************999887....44444444444443331114569*************6 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.019
                           Fer4_17   2 CiqCgyClpeCpsyeaydn...epk....kllraakl.....................g 32 
                                       C +Cg+C+ +Cp ++ +++   e++    +l r+ak+                     +
  gi|518653273|ref|YP_008142793.1| 190 CVSCGHCVTVCPVNALMEKsmlEEAgyftSLTRKAKYnliefgkdlekpvgngmimkiS 248
                                       99999999999987775553332223333666666665555555555444444444441 PP

  == domain 4  score: -0.6 bits;  conditional E-value: 2.3
                           Fer4_17   5 CgyClpeCpsyeaydn 20 
                                       C yC   C++ ++++ 
  gi|518653273|ref|YP_008142793.1| 266 CTYCGVGCSFTMWTKG 281
                                       9999888988887665 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   3.3    0.0035         3       2      19 ..     143     160 ..     143     162 .. 0.94
   2 ?    8.0   3.4     0.005       4.2       1      17 [.     185     201 ..     185     203 .. 0.90
   3 ?   -0.7   0.0       2.6   2.2e+03      14      38 ..     374     398 ..     373     404 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0035
                           Fer4_13   2 DrdtCiacgaCvelaPdv 19 
                                       D d+Ci cg Cve++ dv
  gi|518653273|ref|YP_008142793.1| 143 DPDQCILCGRCVEACQDV 160
                                       789************997 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.005
                           Fer4_13   1 VDrdtCiacgaCvelaP 17 
                                       ++ ++C++cg Cv ++P
  gi|518653273|ref|YP_008142793.1| 185 INDSSCVSCGHCVTVCP 201
                                       5679************9 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.6
                           Fer4_13  14 elaPdvFeeddeggasvvaeqptse 38 
                                       ++a ++F+ ++ ++ s++ + p ++
  gi|518653273|ref|YP_008142793.1| 374 KMARQIFHNNNVDNSSRFCQAPATT 398
                                       68999************99988765 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   2.5    0.0058       4.9      84      99 ..     146     161 ..     144     176 .. 0.81
   2 ?   11.9   2.8   0.00023       0.2      52      75 ..     181     204 ..     173     213 .. 0.81
   3 ?   -1.9   0.1       4.3   3.6e+03      45      66 ..     250     271 ..     239     278 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0058
                           Fer4_18  84 eciscllcidacdkvm 99 
                                       +ci c++c++ac++v 
  gi|518653273|ref|YP_008142793.1| 146 QCILCGRCVEACQDVE 161
                                       7***********9874 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00023
                           Fer4_18  52 erkekgagdcidcescvkvcPtgi 75 
                                       ++k+ +++ c++c++cv+vcP++ 
  gi|518653273|ref|YP_008142793.1| 181 DNKAINDSSCVSCGHCVTVCPVNA 204
                                       556677899************975 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 4.3
                           Fer4_18  45 kalkekeerkekgagdcidces 66 
                                        + k +ee+ +k+++ c+ c++
  gi|518653273|ref|YP_008142793.1| 250 IEAKMREEQIKKTKTVCTYCGV 271
                                       4556666777777777877764 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.1    0.0025       2.1      75      93 ..     140     158 ..     109     160 .. 0.80
   2 ?   11.9   0.7   0.00037      0.32      75      95 ..     183     203 ..     174     204 .. 0.81
   3 ?   -2.0   0.1         8   6.8e+03      71      86 ..     255     270 ..     231     283 .. 0.65

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0025
                           Fer4_22  75 ekfgesgCvGCgRCieacp 93 
                                        +++  +C+ CgRC+eac+
  gi|518653273|ref|YP_008142793.1| 140 YRYDPDQCILCGRCVEACQ 158
                                       4668899***********7 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00037
                           Fer4_22  75 ekfgesgCvGCgRCieacpvk 95 
                                       + ++ s+Cv Cg C+++cpv+
  gi|518653273|ref|YP_008142793.1| 183 KAINDSSCVSCGHCVTVCPVN 203
                                       566889999999999999975 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 8
                           Fer4_22  71 sefkekfgesgCvGCg 86 
                                       +e + k  +++C+ Cg
  gi|518653273|ref|YP_008142793.1| 255 REEQIKKTKTVCTYCG 270
                                       3333333455555555 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   3.6     0.009       7.7       2      14 ..     145     157 ..     144     160 .. 0.88
   2 ?   11.0   2.3   0.00061      0.52       3      17 .]     189     203 ..     187     206 .. 0.92

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.009
                            Fer4_4   2 erCigCgsCvaaC 14 
                                       + Ci Cg+Cv aC
  gi|518653273|ref|YP_008142793.1| 145 DQCILCGRCVEAC 157
                                       66*********** PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00061
                            Fer4_4   3 rCigCgsCvaaCPqg 17 
                                       +C+ Cg Cv +CP++
  gi|518653273|ref|YP_008142793.1| 189 SCVSCGHCVTVCPVN 203
                                       7************75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (978 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        23  (0.00128284); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              21  [number of targets reported over threshold]
# CPU time: 0.75u 0.31s 00:00:01.06 Elapsed: 00:00:00.48
# Mc/sec: 6110.64
//
Query:       gi|518653274|ref|YP_008142794.1|  [L=200]
Description: hypothetical protein FACI_IFERC00001G1917 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.021   14.7   0.8      0.068   13.1   0.7    2.0  2  Ycf9      YCF9


Domain annotation for each model (and alignments):
>> Ycf9  YCF9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.37   6.6e+03      32      45 ..      41      54 ..      39      56 .. 0.79
   2 ?   13.1   0.7   3.8e-06     0.068       6      56 ..     142     192 ..     140     194 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.37
                                      HHHHHHHHHHHHHH CS
                              Ycf9 32 qsknlifsgsalWv 45
                                      ++++ i  + +lW 
  gi|518653274|ref|YP_008142794.1| 41 ENNENINHAMGLWG 54
                                      67788999999995 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.8e-06
                                       HHHHHHHHHHHHHHHHHHHHSTSTHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
                              Ycf9   6 laaLvllSfvlVvgVPVayatpqnwsqsknlifsgsalWvaLVllvgilnf 56 
                                       +++++ll +v +  +P  +  +  w+++k l+ ++++ W++     ++lnf
  gi|518653274|ref|YP_008142794.1| 142 TILFILLALVYINDIPASLFHSPVWERGKALFQLITGTWLMYLTFAATLNF 192
                                       67899********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       619  (0.0345251); 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:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.47
# Mc/sec: 1271.43
//
Query:       gi|518653275|ref|YP_008142795.1|  [L=152]
Description: hypothetical protein FACI_IFERC00001G1918 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.7e-20   70.8   0.0    1.2e-19   70.6   0.0    1.1  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
     0.0039   17.0   0.0     0.0063   16.3   0.0    1.3  1  AAA_26    AAA domain
     0.0095   15.9   0.2      0.011   15.6   0.2    1.2  1  ATPase_2  ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.018   14.8   0.6        2.1    8.0   0.2    2.1  2  PRK       Phosphoribulokinase / Uridine kinase family
      0.059   13.4   0.2       0.15   12.1   0.2    1.7  1  AAA_14    AAA domain


Domain annotation for each model (and alignments):
>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   3.2e-23   1.2e-19       1     102 [.       3     101 ..       3     127 .. 0.89

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 3.2e-23
                              MobB   1 vlgivgksgsGKTtLleklipelkarglrvgtiKha.hhgfdvdkpgkDsyrhrkAGAkevlvaskerlalikelee 76 
                                       ++++ g s sGKTt++ ++i+el+   +++g+iK   h+++++d++ kD++++++AGA  +   +++r+  + e   
  gi|518653275|ref|YP_008142795.1|   3 IFSFFGSSSSGKTTIIANIISELSG-SMKIGYIKNIpHDNISLDTEYKDTWKMENAGAYRIYGLAPSRTYSMVE--- 75 
                                       6899*******************86.69******97255689********************999999999999... PP

                              MobB  77 aelsleellarlsevDlvlvEGfkke 102
                                       +e+s++e++++ ++vD+ ++EGfk+ 
  gi|518653275|ref|YP_008142795.1|  76 KETSTDEIIEKENDVDIFIIEGFKAF 101
                                       3689********************75 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   1.8e-06    0.0063      10     112 ..      10     103 ..       8     108 .. 0.79

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.8e-06
                            AAA_26  10 tgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarqegedi 86 
                                        ++GKT++++ +++ l +  +k+gy+K i  ++     + l +e+ ++++ +e + ++++   l+p+      +++ 
  gi|518653275|ref|YP_008142795.1|  10 SSSGKTTIIANIISEL-SGSMKIGYIKNIPHDN-----ISLDTEYKDTWK-MENAGAYRIY-GLAPSRTYSMVEKET 78 
                                       689*************.899*********8877.....466677776664.5557788885.678887777777777 PP

                            AAA_26  87 dlekivkelekdadivvVEGagglgv 112
                                         ++i  e e+d di+++EG++  ++
  gi|518653275|ref|YP_008142795.1|  79 STDEI-IEKENDVDIFIIEGFKAFDK 103
                                       78888.4668899*******987665 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 !   15.6   0.2   3.1e-06     0.011      25      83 ..       6      71 ..       1     123 [. 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.1e-06
                          ATPase_2 25 iYGpegsGKtaLlkeiienledkdkyviyyialreesiskldefieeeeekkklekal............g 83
                                       +G+ +sGKt+++ +ii++l+  + ++ y+ ++  ++is  +e+ +      k+e+a              
  gi|518653275|ref|YP_008142795.1|  6 FFGSSSSGKTTIIANIISELSG-SMKIGYIKNIPHDNISLDTEYKD----TWKMENAGayriyglapsrtY 71
                                      69******************77.55689999999999998777733....222222222333444454442 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.2   0.00059       2.1       3      29 ..       5      31 ..       3      61 .. 0.64
   2 ?    5.3   0.0    0.0041        15      89     127 ..      68     106 ..      59     111 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.00059
                               PRK  3 gvagsSGaGkttvarklekifgrekvk 29
                                      +  gsS +Gktt+ +++ + + +  + 
  gi|518653275|ref|YP_008142795.1|  5 SFFGSSSSGKTTIIANIISELSGSMKI 31
                                      5679***********999999855443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0041
                               PRK  89 kpiYsheteeaapdk.eeliegadvlviEGlhalyderva 127
                                       +++Ys +++e   d+  e+ ++ d+ +iEG   ++d++++
  gi|518653275|ref|YP_008142795.1|  68 SRTYSMVEKETSTDEiIEKENDVDIFIIEGFK-AFDKSIK 106
                                       699999999999854156777899******65.5677776 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.2   4.2e-05      0.15       6      47 ..       5      45 ..       1     132 [. 0.50

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.2e-05
                            AAA_14  6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkla 47
                                         G   +GKTt++ ++i+el   + +i yi+   +++ +l+
  gi|518653275|ref|YP_008142795.1|  5 SFFGSSSSGKTTIIANIISELS-GSMKIGYIKNIPHDNISLD 45
                                      56677889**********9999.4555555543333332222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1094.78
//
Query:       gi|518653276|ref|YP_008142796.1|  [L=181]
Description: molybdopterin-guanine dinucleotide biosynthesis protein A [Ferroplasma acidarmanus fer1]
Scores for complete 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   33.6   0.0      6e-08   33.2   0.0    1.1  1  NTP_transf_3  MobA-like NTP transferase domain
     0.0021   18.0   0.1      0.042   13.8   0.1    2.2  1  CTP_transf_3  Cytidylyltransferase
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.027   13.7   0.0    1.4  1  CofC          Guanylyl transferase CofC like
      0.019   15.2   0.7       0.03   14.5   0.7    1.3  1  Methylase_S   Type I restriction modification DNA specificity


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 !   33.2   0.0   1.3e-11     6e-08       8     156 ..       9     149 ..       3     153 .. 0.83

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 1.3e-11
                                       S-TTTTTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH CS
                      NTP_transf_3   8 rSsRmggdKallplggkpllervldalraag.vdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraa 83 
                                       +S+R+ ++K  ++l+g+ +++r+ + l++ g ++++++ +++ +++     ++  v+e++d     + s++  l++ 
  gi|518653276|ref|YP_008142796.1|   9 NSQRL-QNKHNMELCGEKMIDRISRILSETGrFSNIILFTKNFSLK-----SKFAVTEEDDTNGILFDSILYCLEKY 79 
                                       67788.8***********************779********97776.....7889999999999999*******976 PP

                                       .SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEEEECC..EEEGGGHHHHHHH..CTHTTHHHCHHH CS
                      NTP_transf_3  84 adadavlvlacDmPlltpelverllaaaaasgadvvvptyegerghpl..lfrarllsalaal..lgdqgarrllrr 156
                                            +l + +DmP+++++ +e ++++++  g++  v+  +g++ +pl  ++++++ + ++++  +g+   r+++++
  gi|518653276|ref|YP_008142796.1|  80 ---HEFLAIGGDMPYIDKKSIENIFDNYK--GNS--VAYKSGNFYQPLfaVYSRDVEQPMLKYrkEGNGSIRKFMDE 149
                                       ...79**********************86..444..455778999***77778888887777733444555877765 PP

>> CTP_transf_3  Cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   9.4e-06     0.042       2     120 ..       3     109 ..       2     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 9.4e-06
                                       EEEEE-SSSSSSTTGGGSEETTEEHHHHHHHHHHHTTTTSEEEEEES-HHHHHHHHHTTSEEEE--TTCSSHH..HH CS
                      CTP_transf_3   2 aIipARsgSkRlpgKnlldlggkpliayvleaalkskafekvivaTDseeiknvakefgasvlvtrsslesdt..er 76 
                                       aIi A  +S+Rl +K   +l g+ +i+++ + + + + f+++i+ T     kn+  +   ++ vt+++  ++   ++
  gi|518653276|ref|YP_008142796.1|   3 AIIFAK-NSQRLQNKHNMELCGEKMIDRISRILSETGRFSNIILFT-----KNFSLK--SKFAVTEEDDTNGIlfDS 71 
                                       666664.8*********************************99966.....444444..478888888888744478 PP

                                       HHHHHHHHTTT.TTSEEEEE-TT-TT--HHHHHHHHHHHHHSTT CS
                      CTP_transf_3  77 flevvkaflmseneeiivnlqGdnPllqeevikkaietlkenqe 120
                                       +l  +++++        + + Gd P +++++i+++++++k n  
  gi|518653276|ref|YP_008142796.1|  72 ILYCLEKYHEF------LAIGGDMPYIDKKSIENIFDNYKGNSV 109
                                       88888888777......888888888888888888888887755 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.9e-06     0.027      50     114 ..      38     105 ..       7     115 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.9e-06
                              CofC  50 sedeevleyald.elgvevvkekekdlntaveka..feeieekeviiipsdiPlikkedvkdllelek 114
                                       ++  +++ + ++ +l+ +  + +e d n+ +     ++  + +e + i  d+P i+k+ ++++++  k
  gi|518653276|ref|YP_008142796.1|  38 GRFSNIILFTKNfSLKSKFAVTEEDDTNGILFDSilYCLEKYHEFLAIGGDMPYIDKKSIENIFDNYK 105
                                       5566777777764788898888889****997776788788899********************9876 PP

>> Methylase_S  Type I restriction modification DNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   6.7e-06      0.03      34     132 ..       6     100 ..       2     101 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 6.7e-06
                                       EE-HH.HCCTEE-HHHHCCTT---B-.TT-EEEE-SSSTT-EEEESS-BEE-TTEEEEEEST.TT--HHHHHHHHHH CS
                       Methylase_S  34 yirag.ilnnkvvkdglgykkkyilp.kgdilissratiGkvayrdkkyylnqsvivlipkn.kkkineflylylll 107
                                       + +++ +l+n   k  ++ ++++ ++  ++il +  + ++++++++k++ l +++ v +  + ++ +  + +ly+l 
  gi|518653276|ref|YP_008142796.1|   6 FAKNSqRLQN---KHNMELCGEKMIDrISRILSE-TGRFSNIILFTKNFSLKSKFAVTEEDDtNGIL-FDSILYCLE 77 
                                       5555656666...889999999999966666666.6***********************98866666.555555554 PP

                                       CHHHHHHHCCSSTTT---HHHHCC- CS
                       Methylase_S 108 klkklkslsvgstqpkltkenlkki 132
                                         k++++l +g+++p+++k+ +++i
  gi|518653276|ref|YP_008142796.1|  78 --KYHEFLAIGGDMPYIDKKSIENI 100
                                       ..56777778*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       468  (0.026103); expected 358.6 (0.02)
Passed bias filter:                      344  (0.0191868); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1371.07
//
Query:       gi|518653277|ref|YP_008142797.1|  [L=584]
Description: hypothetical protein FACI_IFERC00001G1920 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-32  112.7   0.0    1.9e-32  112.2   0.0    1.2  1  MoeA_N         MoeA N-terminal region (domain I and II)
    1.1e-21   77.0   0.0    1.9e-21   76.2   0.0    1.4  1  MoCF_biosynth  Probable molybdopterin binding domain
     0.0016   18.6   0.0     0.0053   16.9   0.0    1.9  2  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 !  112.2   0.0   3.2e-36   1.9e-32       3     157 .]      11     174 ..       9     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 112.2 bits;  conditional E-value: 3.2e-36
                                       HHHHHHHHHHH-.HH-EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--.............. CS
                            MoeA_N   3 veealaiilaal.eleeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........s 69 
                                       +++al+i+++++ el+++e +pl  +a gr++ae + ++ ++P f +S++DGYA+ a++ +gas ++p        +
  gi|518653277|ref|YP_008142797.1|  11 FQDALEIVKNNMaELKDAEeIPL-YNATGRISAETIFSNNNLPLFSRSQVDGYAIIASDIKGASYDSPvslklageT 86 
                                       799*********99977777***.9999***********************************************96 PP

                                       .....-S---TT-.EEEE-TTSB--TT--EEEEGGGE.E....EETTE..S--STTTTEE-TTSSB-TTSEEE-TTB CS
                            MoeA_N  70 aageeperllpgg.avrimTGaplPegadaVvpvEdteeeeaketvev..kavkpgenvrraGedikaGevllragt 143
                                       + ge++ +   +g ++++ TG+++P gada vp Edt+ +e +++  +  ++v++ +    aG d+ +Ge ll +++
  gi|518653277|ref|YP_008142797.1|  87 NIGEKAVEFPGSGkCIKVPTGGVIPVGADAMVPFEDTK-QEGNAI--QffQQVNRFNELSNAGIDVTKGEKLLDSNS 160
                                       66666666666666***********************6.333332..1468999999******************** PP

                                       B--CCCHHHHHHCT CS
                            MoeA_N 144 rltpaeigllasvG 157
                                       +++p+ i++las G
  gi|518653277|ref|YP_008142797.1| 161 MIDPRNIAVLASTG 174
                                       ************98 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.2   0.0   3.3e-25   1.9e-21       1     142 [.     187     324 ..     187     326 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.2 bits;  conditional E-value: 3.3e-25
                                       EEEEE-HHHH.......TTSSGBHHHHHHHHHHHTTSE.EEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSS CS
                     MoCF_biosynth   1 avitvGdell.......sgkieDtngpllaellkelgv.evskytvvpDdeeeikeallaaleeadviittGGtGpt 69 
                                       +++++G+ell       +gki+ +n+  ++++l+++ + +v +y+++ D++++ik+a+ +++ee+dv +t+G t+++
  gi|518653277|ref|YP_008142797.1| 187 GIVSTGNELLypgtpykEGKIYESNSLSIKAELSKYPAfNVNDYGIIEDNYDKIKSAIDRSIEENDVTLTIGSTSAG 263
                                       699*******************************98777*******************9999*************** PP

                                       TT--HHHHHHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHHHGGH CS
                     MoCF_biosynth  70 pdDvtpealaklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeillpal 142
                                       + D+++++l +         +++f++++ kpgkp ++a+    +++    ++gLPG+p++++++l  +++p l
  gi|518653277|ref|YP_008142797.1| 264 DHDMVYKILGDKTP------GIIFHGIRVKPGKPAIFAMS---GEK---IMFGLPGFPVSSMMILYSLVIPNL 324
                                       ********987777......4************9998888...543...699*************99999987 PP

>> MoeA_C  MoeA C-terminal region (domain IV)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.98   5.9e+03      27      59 ..      38      70 ..      34      74 .. 0.65
   2 !   16.9   0.0   8.8e-07    0.0053       2      62 ..     339     398 ..     338     408 .. 0.88

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.98
                                      -EEEEEE-S---TT-GGGCTT--EEEEE-TT-- CS
                            MoeA_C 27 geyvaeptgkqgSglLsslaeAnglivipegte 59
                                      g++ ae + +++   L s ++ +g+++i ++ +
  gi|518653277|ref|YP_008142797.1| 38 GRISAETIFSNNNLPLFSRSQVDGYAIIASDIK 70
                                      666666665555556677777788888877765 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.8e-07
                                       EEESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE- CS
                            MoeA_C   2 arlaedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegle 62 
                                       a ++ ++  ++g +++l  +l +++  y+a+++  ++Sg +s +++A g+ +i+++t + +
  gi|518653277|ref|YP_008142797.1| 339 AITGQRFELHQGNTDLLLIKLVKHGETYKAYQV-PGNSGSISRISKATGYSIIDSKTSFMD 398
                                       5678899999***********************.********************9998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (584 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); 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:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 4256.04
//
Query:       gi|518653278|ref|YP_008142798.1|  [L=409]
Description: molybdopterin biosynthesis MoeA protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-30  104.4   0.0    6.5e-30  104.0   0.0    1.2  1  MoeA_N         MoeA N-terminal region (domain I and II)
    4.3e-16   58.9   0.1    6.9e-16   58.2   0.1    1.3  1  MoCF_biosynth  Probable molybdopterin binding domain
    4.6e-05   23.5   0.0    0.00011   22.3   0.0    1.7  1  MoeA_C         MoeA C-terminal region (domain IV)
  ------ inclusion threshold ------
      0.081   12.8   0.0        4.1    7.3   0.0    2.4  2  DeoRC          DeoR C terminal sensor domain


Domain annotation for each model (and alignments):
>> MoeA_N  MoeA N-terminal region (domain I and II)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   1.4e-33   6.5e-30      17     157 .]      30     178 ..      13     178 .. 0.87

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 1.4e-33
                                       -EEE.EEGGCG-TT-BBSS-EE-SS-BSSS-EESSSEEEEEEBTTB--...................-S---TT-.E CS
                            MoeA_N  17 eeee.vplaaealgrvlaedvvApedvPpfdnSamDGYAvraeagsgaseeep........saageeperllpgg.a 83 
                                       +++  +pl  +a g+++  +++ ++++P  ++SamDGYA++++++ +a++ +p        +aag++pe+ ++ g +
  gi|518653278|ref|YP_008142798.1|  30 PDSIqLPL-DSASGKISSGEIITTVNIPDKNKSAMDGYALKSTDTLNATPANPvklvlkgtIAAGDTPEEIVKDGtC 105
                                       44545899.8899************************************************999999999999999* PP

                                       EEE-TTSB--TT--EEEEGGGE.E....EETTE.S--STTTTEE-TTSSB-TTSEEE-TTBB--CCCHHHHHHCT CS
                            MoeA_N  84 vrimTGaplPegadaVvpvEdteeeeaketvev.kavkpgenvrraGedikaGevllragtrltpaeigllasvG 157
                                       ++i TG+ +Peg daV + E++e     + + v ++v++genv +aGed+  G+++l +++ + p+ +++l s G
  gi|518653278|ref|YP_008142798.1| 106 IEIYTGSIMPEGSDAVARAENCE--VIGNYIYVySSVNSGENVAPAGEDLNIGDTILGKNSLIYPQNLAALKSSG 178
                                       **********************5..322322336899**********************************9987 PP

>> MoCF_biosynth  Probable molybdopterin binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.2   0.1   1.5e-19   6.9e-16       1     138 [.     191     315 ..     191     321 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.2 bits;  conditional E-value: 1.5e-19
                                       EEEEE-HHHHTTSSGBHHHHHHHHHHHTTSEEEEEEEEE-SSHHHHHHHHHHHHHTSSEEEEESS-SSSTT--HHHH CS
                     MoCF_biosynth   1 avitvGdellsgkieDtngpllaellkelgvevskytvvpDdeeeikeallaaleeadviittGGtGptpdDvtpea 77 
                                       ++i +G el++++ie+++g ll    ++   e+++ ++v Dd+  i+ a+++ +e+  ++i+tGG +++++D+t +a
  gi|518653278|ref|YP_008142798.1| 191 GIINTGKELINKQIENSTGMLLRTFYTSSFTETIDGGIVDDDKPSIAVAVRSMIEKCHILIVTGGSSLGRRDMTTDA 267
                                       699**************************************************9999******************** PP

                                       HHHHHSEE-HHHHHHHHHHHHHHCCTTSHGGGGGGE.EETTEEEEE-SSHHHHHHHHHHHH CS
                     MoCF_biosynth  78 laklfekelegfeeafrrvslkpgkpvgvapgailsravgktiigLPGspkavkealeeil 138
                                       l+  ++        +f +vs kpg+ +g+  +   +++   +++ + G p+a+     +++
  gi|518653278|ref|YP_008142798.1| 268 LSGEGK-------MLFSGVSIKPGRTIGLFNI---KNR---PVLSVSGLPVAALLSSMIFV 315
                                       *****9.......6***********7776666...433...79999999999877666555 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 !   22.3   0.0   2.5e-08   0.00011       4      71 ..     335     402 ..     333     403 .. 0.92

  Alignments for each domain:
  == domain 1  score: 22.3 bits;  conditional E-value: 2.5e-08
                                       ESS-EE--SSS-EEEEEEEES-S-EEEEEE-S---TT-GGGCTT--EEEEE-TT--EE-TT-EEEEEE CS
                            MoeA_C   4 laedlksdpgrreflRvilteedgeyvaeptgkqgSglLsslaeAnglivipegtegleaGeeVevil 71 
                                       l ++++  +g ++f+ ++    dge++  p+ ++ Sg+L+++ + n +i i+e+ eg+ +G  V++++
  gi|518653278|ref|YP_008142798.1| 335 LDKSIHNRAGFTTFQIARSYAIDGELHSIPLNTKVSGNLTAIIKGNSIIKIDENLEGIPEGSRVNIYV 402
                                       66789999999999999988889*****************************************9987 PP

>> DeoRC  DeoR C terminal sensor domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0   0.00092       4.1      15      62 ..      98     145 ..      89     154 .. 0.91
   2 ?    2.9   0.0     0.021        96       4      30 ..     231     257 ..     229     260 .. 0.91

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.00092
                             DeoRC  15 eliedgdtifldaGtTtlelaraLaekknltvvTnslnvaeeLseked 62 
                                       e+++dg +i + +G+ + e  +a+a+ +n+ v+ n + v + +++ e+
  gi|518653278|ref|YP_008142798.1|  98 EIVKDGTCIEIYTGSIMPEGSDAVARAENCEVIGNYIYVYSSVNSGEN 145
                                       689************************************998877665 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.021
                             DeoRC   4 eeKrrIAkaAaeliedgdtifldaGtT 30 
                                       + K  IA a+ ++ie+ +++++ +G++
  gi|518653278|ref|YP_008142798.1| 231 DDKPSIAVAVRSMIEKCHILIVTGGSS 257
                                       57999********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (409 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       372  (0.0207485); 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:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 3072.14
//
Query:       gi|518653279|ref|YP_008142799.1|  [L=53]
Description: hypothetical protein FACI_IFERC00001G1922 [Ferroplasma acidarmanus fer1]
Scores for complete 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   47.8   0.1    1.8e-12   47.7   0.1    1.0  1  ATPase_2  ATPase domain predominantly from Archaea
    3.5e-05   23.9   0.2    9.5e-05   22.4   0.0    1.7  2  AAA_14    AAA domain
    6.9e-05   23.3   0.0    7.5e-05   23.2   0.0    1.0  1  AAA_16    AAA ATPase domain
    0.00043   19.7   0.0    0.00048   19.6   0.0    1.0  1  TniB      Bacterial TniB protein
     0.0022   18.3   0.0     0.0022   18.3   0.0    1.2  1  AAA_22    AAA domain
     0.0054   16.9   0.0     0.0074   16.5   0.0    1.2  1  Roc       Ras of Complex, Roc, domain of DAPkinase
  ------ inclusion threshold ------
      0.016   14.3   0.0      0.019   14.1   0.0    1.0  1  DAP3      Mitochondrial ribosomal death-associated protein 3
      0.036   13.3   0.0      0.038   13.2   0.0    1.0  1  NB-ARC    NB-ARC domain
      0.051   13.2   0.0      0.067   12.8   0.0    1.1  1  Ras       Ras family
      0.054   13.2   0.0       0.14   11.8   0.0    1.6  2  AAA_24    AAA domain


Domain annotation for each model (and alignments):
>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.7   0.1   9.9e-16   1.8e-12       1      45 [.       3      47 ..       3      52 .. 0.96

  Alignments for each domain:
  == domain 1  score: 47.7 bits;  conditional E-value: 9.9e-16
                          ATPase_2  1 FfdRekelkeleeilerepneiyfiYGpegsGKtaLlkeiienle 45
                                      F+dR +elk l+  ++++++e+++iYG++++GKt Llk++++n++
  gi|518653279|ref|YP_008142799.1|  3 FIDRINELKALNDRYDSGKAEFIVIYGRRRVGKTELLKQFMNNHD 47
                                      99*****************************************85 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.56     1e+03      68      80 ..       2      14 ..       1      24 [. 0.68
   2 !   22.4   0.0   5.3e-08   9.5e-05       3      27 ..      23      47 ..      21      52 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.56
                            AAA_14 68 lflDEiqevpewe 80
                                      +f+D i e++ + 
  gi|518653279|ref|YP_008142799.1|  2 IFIDRINELKALN 14
                                      7888887776554 PP

  == domain 2  score: 22.4 bits;  conditional E-value: 5.3e-08
                            AAA_14  3 kilvitGaRrvGKTtllkqlikell 27
                                      + +vi G RrvGKT llkq+++++ 
  gi|518653279|ref|YP_008142799.1| 23 EFIVIYGRRRVGKTELLKQFMNNHD 47
                                      679******************8875 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.2e-08   7.5e-05       5      47 ..       6      45 ..       3      52 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.2e-08
                            AAA_16  5 ReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellra 47
                                      R +el++L++ ++   sg  e ++++G + vGK+ l++++++ 
  gi|518653279|ref|YP_008142799.1|  6 RINELKALNDRYD---SGKAEFIVIYGRRRVGKTELLKQFMNN 45
                                      5567777777666...88889*******************974 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-07   0.00048      20      60 ..       7      47 ..       3      50 .. 0.93

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                              TniB 20 lerLeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhp 60
                                      +++L++L ++ ++ + + ++++G+  +GKt ++++F+++h 
  gi|518653279|ref|YP_008142799.1|  7 INELKALNDRYDSGKAEFIVIYGRRRVGKTELLKQFMNNHD 47
                                      578999********************************995 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   1.2e-06    0.0022       4      30 ..      21      47 ..       7      52 .. 0.91

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.2e-06
                            AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                                      +a ++v++G   +GKT ll+++++++d
  gi|518653279|ref|YP_008142799.1| 21 KAEFIVIYGRRRVGKTELLKQFMNNHD 47
                                      789********************9986 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   4.1e-06    0.0074       2      23 ..      25      46 ..      24      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 4.1e-06
                                      EEEESSTTSSHHHHHHCHCT-C CS
                               Roc  2 vvlvGdsgvGKtsllkrfvedk 23
                                      +v+ G  +vGKt llk+f++++
  gi|518653279|ref|YP_008142799.1| 25 IVIYGRRRVGKTELLKQFMNNH 46
                                      7999***************985 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 ?   14.1   0.0   1.1e-05     0.019      12      44 ..      11      43 ..       6      46 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                                      HHHTTS-SSS---EEEEE-SSSSSTTTTHHHHH CS
                              DAP3 12 kklkkadkkkkvkrlvltGekgsGKSvlLlqal 44
                                      k l++  +++k++ +v++G++ +GK+ lL q +
  gi|518653279|ref|YP_008142799.1| 11 KALNDRYDSGKAEFIVIYGRRRVGKTELLKQFM 43
                                      678888999**********************98 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.1e-05     0.038      11      47 ..      16      49 ..       5      52 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
                                      HHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCSHCCC CS
                            NB-ARC 11 kLlekdelqslvvalvGmgGvGKttlakqilnksdev 47
                                      + + +++    ++ ++G+  vGKt l+kq +n++d +
  gi|518653279|ref|YP_008142799.1| 16 RYD-SGKA--EFIVIYGRRRVGKTELLKQFMNNHDGI 49
                                      333.4444..49********************98865 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.7e-05     0.067       2      23 ..      25      46 ..      24      48 .. 0.93

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-05
                                      EEEEESTTSSHHHHHHHHHHSS CS
                               Ras  2 lvlvGdsavGKtslllrfvkdk 23
                                      +v+ G + vGKt ll +f++++
  gi|518653279|ref|YP_008142799.1| 25 IVIYGRRRVGKTELLKQFMNNH 46
                                      7999***************985 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.59   1.1e+03      69      80 ..       2      13 ..       1      20 [. 0.56
   2 ?   11.8   0.0   8.1e-05      0.14       5      22 ..      25      42 ..      21      51 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.59
                            AAA_24 69 lviDtideleel 80
                                      ++iD i+el  l
  gi|518653279|ref|YP_008142799.1|  2 IFIDRINELKAL 13
                                      566666665443 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 8.1e-05
                            AAA_24  5 iliyGpsgiGKTtlakel 22
                                      i+iyG   +GKT l+k++
  gi|518653279|ref|YP_008142799.1| 25 IVIYGRRRVGKTELLKQF 42
                                      89***************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       368  (0.0205254); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.31u 0.27s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 425.21
//
Query:       gi|518653280|ref|YP_008142800.1|  [L=57]
Description: hypothetical protein FACI_IFERC00001G1923 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       240  (0.0133861); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.38
# Mc/sec: 450.02
//
Query:       gi|518653281|ref|YP_008142801.1|  [L=251]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-60  205.2   1.8    1.5e-60  205.0   1.8    1.0  1  Transposase_mut  Transposase, Mutator family
  ------ inclusion threshold ------
      0.058   13.8   0.0       0.12   12.8   0.0    1.5  1  MULE             MULE transposase domain


Domain annotation for each model (and alignments):
>> Transposase_mut  Transposase, Mutator family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.0   1.8   1.7e-64   1.5e-60       9     228 ..       7     224 ..       1     229 [. 0.94

  Alignments for each domain:
  == domain 1  score: 205.0 bits;  conditional E-value: 1.7e-64
                   Transposase_mut   9 elealka.ieeasgkddllkellktvleelleaeldealgaeryerseersnqRnGsrerklsTragtlelriPrdR 84 
                                       +l+++k+ i+ +  + + +++l k +l++l+++e++e+++a ryer ++r+ +RnG+++r+l T+ g++ l  P+ R
  gi|518653281|ref|YP_008142801.1|   7 QLKEVKEkIKSYGLNRENMRDLKKWILNDLMNEEAEEQINASRYERNNNRKDYRNGYKQRSLLTTDGKILLDKPQFR 83 
                                       444444404456667799*********************************************************** PP

                   Transposase_mut  85 sGsFspallerykRrekaleavvielyvkGvstrkveklveelygeksvSksevSaitkeldeaveafreRsLeeke 161
                                       + sF++a++++y R ek +e+ ++e y++Gvstr v+k+v++l +  +vS+s vS+++ +ld++v++f eR ++ + 
  gi|518653281|ref|YP_008142801.1|  84 ETSFHTAVFDNYSRVEKSVESIILESYLSGVSTRSVNKVVQSLDV--QVSASYVSSLSSRLDKTVNEFLERKIDGE- 157
                                       *******************************************99..79**************************9. PP

                   Transposase_mut 162 ypllflDalylkvReegrvvskavliaigvdadGsreiLglevadsEsekfWlavlesLknrGlkgv 228
                                       y ++++D++ylk+R++gr ++ka++i +g+++dG+reiLg ++ dsE e  W+ +l++Lk+r l+g 
  gi|518653281|ref|YP_008142801.1| 158 YRFIYIDGTYLKIRDNGRYRNKAIYICVGINSDGYREILGSRIYDSETEIEWELFLDDLKKRELTGF 224
                                       **************************************************************99875 PP

>> MULE  MULE transposase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.12       2      55 ..     161     219 ..     160     224 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
                              MULE   2 vvlDgTykt...n.kyklp.lltvvgvddngqlvplafalveseneesyewllqellee 55 
                                       + +DgTy++   n +y+ +  ++ vg+++ g   +l+  + +se+e  +e +l++l+++
  gi|518653281|ref|YP_008142801.1| 161 IYIDGTYLKirdNgRYRNKaIYICVGINSDGYREILGSRIYDSETEIEWELFLDDLKKR 219
                                       789****873333467666145569*****************************98875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1372  (0.0765241); expected 358.6 (0.02)
Passed bias filter:                      758  (0.0422779); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 00:00:00.44
# Mc/sec: 1704.99
//
Query:       gi|518653282|ref|YP_008142802.1|  [L=196]
Description: hypothetical protein FACI_IFERC00001G1925 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.031   14.6   0.5      0.031   14.6   0.5    1.7  2  MapZ_C2   MapZ extracellular C-terminal domain 2


Domain annotation for each model (and alignments):
>> MapZ_C2  MapZ extracellular C-terminal domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.5   1.7e-06     0.031       9      84 ..      18      95 ..      11     101 .. 0.77
   2 ?   -3.1   0.0      0.54   9.7e+03       8      23 ..     133     148 ..     129     151 .. 0.63

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.7e-06
                           MapZ_C2  9 dvadssnpawtwapgvkekviatsierGyiveggyilervriengegyYnlyatdnkskl...glsekalplYlvtina 84
                                      + ++++ +++++++  k+k  +t   r +i++  y  +++ i+  +g Ynl +  +ks     ++ e+   +Y+  ++ 
  gi|518653282|ref|YP_008142802.1| 18 KYSEKDISTYNFSNANKNK-AETNFLRNFIQDTRYNTKKMAIKIEDGKYNLLKLMTKSLPlivQAMEQLQLIYITDLDN 95
                                      5566777889999888887.488999***************************99885424545555555667766655 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 0.54
                           MapZ_C2   8 sdvadssnpawtwapg 23 
                                       s+++ ++n+   +a+ 
  gi|518653282|ref|YP_008142802.1| 133 SKIQGVNNNKNVYADN 148
                                       5666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1075  (0.0599587); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1327.31
//
Query:       gi|518653283|ref|YP_008142803.1|  [L=403]
Description: hypothetical protein FACI_IFERC00001G1926 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.6e-31  110.4  27.5    5.6e-31  108.6  27.5    1.8  1  AAA_15           AAA ATPase domain
    5.7e-24   85.5   9.1    1.6e-22   80.7   9.1    2.3  1  AAA_21           AAA domain, putative AbiEii toxin, Type IV T
      4e-10   39.5   0.4    1.6e-07   30.9   0.0    2.5  3  DUF2813          Protein of unknown function (DUF2813)
    6.8e-05   22.4   7.1    0.00021   20.8   7.1    2.0  1  SMC_N            RecF/RecN/SMC N terminal domain
    0.00011   22.8  11.7    0.00048   20.7  11.5    2.2  1  AAA_23           AAA domain
      0.004   16.9   0.0     0.0086   15.8   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
     0.0059   16.3   0.1       0.93    9.3   0.0    2.5  2  Glyco_hydro_42C  Beta-galactosidase C-terminal domain
  ------ inclusion threshold ------
      0.014   15.5   0.1      0.044   13.9   0.1    1.9  1  PPR_3            Pentatricopeptide repeat domain
      0.016   15.7   0.1       0.13   12.8   0.0    2.3  3  ABC_tran         ABC transporter
      0.033   13.8   0.0      0.076   12.6   0.0    1.5  1  AAA_27           AAA domain


Domain annotation for each model (and alignments):
>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.6  27.5   3.1e-34   5.6e-31       1     368 [.       1     345 [.       1     346 [. 0.64

  Alignments for each domain:
  == domain 1  score: 108.6 bits;  conditional E-value: 3.1e-34
                            AAA_15   1 MkIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlFlnnkekkn.......kkvikiekedleifen 70 
                                       M Ik i ikNF+ + + ei  ++ ++vl+G+Nn+GK+silea+ +  n +  k+                 + i+ +
  gi|518653283|ref|YP_008142803.1|   1 M-IKHIAIKNFKGINSLEITPKK-FNVLVGRNNTGKTSILEAISVCTNPNLIKDllmykygP---------FFIN-Y 65 
                                       8.9*************9999999.*******************9999977444422222221.........2222.2 PP

                            AAA_15  71 iseskdikIdvefaekekakeyektlkskekkkadlllkkkesdlkktikdkklklkknelsdekisvekkkskkel 147
                                        s + +ikId               +k k+ + ++   +++ + lk+ +++  +k   n + d   +++ +k +k l
  gi|518653283|ref|YP_008142803.1|  66 SSDKASIKIDTDD------------NKVKKLNLRNPTPEQILNLLKNDLNELSIKK-DNVYVDIGRYIDVEKIIKVL 129
                                       3444444444444............2223333333344444444444444444442.23333444444444444444 PP

                            AAA_15 148 pkekeeklekekeelkidkedlkklikkleeslkkeeelknvlksaiiklllisakRnvsdedsekkssllgklkek 224
                                       +k + +++ +++  + ++ +d   ++        +++ l     s+++++++ ++++n+ + +s++   + ++    
  gi|518653283|ref|YP_008142803.1| 130 DKDSIYEASLDSIAVLVNYSDHPVILT----AERYND-LLIDTLSKLYDTYISKNEKNSATGKSNS---NRMEFR-- 196
                                       444444444444444455444444444....111222.2222333333343433333333333333...222333.. PP

                            AAA_15 225 ileealqekl.....eeelteklkeiqeklkeidkklaeelkkilkkkidkik.kfnykgkkneei.eik....... 287
                                              ++l     +  lt++ + i +k ++  ++ ++ l+ +++ k +k+  ++++ +kk++ i ++k       
  gi|518653283|ref|YP_008142803.1| 197 -------DRLnmlryRYPLTRNDSFIIDKKDNVTFINDTLLSAEFFHKSQKLAlQVENIIKKDNIIpNLKrfdfysi 266
                                       .......333333446678888888999999999888888998888777777665555555544430444889999* PP

                            AAA_15 288 ......ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkelandnktQ 358
                                              d+e+p++ +G+G+++l+ ++++++++e +        i++iEEPE++ Hp   ++li++++++an+++ Q
  gi|518653283|ref|YP_008142803.1| 267 vldteeGDQEIPVESMGDGFKSLVHILIKLYDNEGD--------IIVIEEPENYMHPGYIRELIHYIISIANNSHVQ 335
                                       ************************************........********************************* PP

                            AAA_15 359 viitTHSphi 368
                                       ++itTHS  +
  gi|518653283|ref|YP_008142803.1| 336 LFITTHSQDF 345
                                       *******876 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   9.1   8.8e-26   1.6e-22       1     299 [.      23     343 ..      23     346 .. 0.60

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 8.8e-26
                            AAA_21   1 lnvliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeie.............. 63 
                                       +nvl+G+N++GK+++L+a+++                   ++  i  ll  ++    ++++ +              
  gi|518653283|ref|YP_008142803.1|  23 FNVLVGRNNTGKTSILEAISVCT-----------------NPNLIKDLLMYKYGPFFINYSSDkasikidtddnkvk 82 
                                       8******************9986.................3333444444444444444444400000000000000 PP

                            AAA_21  64 eflsqgvryryglrlersqv...eeklssvetllesgllldkrsleeedvfnpearg..irggvsvfslkelsvsep 135
                                       +++++++  + +l+l ++++   + k+ +v  + ++++ + k ++   +++++ea+   i ++v +  ++ ++ +e 
  gi|518653283|ref|YP_008142803.1|  83 KLNLRNPTPEQILNLLKNDLnelSIKKDNVYVDIGRYIDVEKIIKVLDKDSIYEASLdsIAVLVNYSDHPVILTAER 159
                                       24445555555555555555544444444444555555555555555555554443300333333333344444444 PP

                            AAA_21 136 ndlqfgkaltditsrawsllllldglrke...rigllnifadyfgfakekrllqrlvrslklveielsdlgegeeli 209
                                        ++  +++l +++ ++ s ++ + + +k    r+ + +  +++ + +++ r  +  +++ + v +  ++l+ +e  +
  gi|518653283|ref|YP_008142803.1| 160 YNDLLIDTLSKLYDTYISKNEKNSATGKSnsnRMEFRDRLNMLRYRYPLTRNDSFIIDKKDNVTFINDTLLSAEFFH 236
                                       44444444444444444444444444444555555555555555555555555555555555555555555555555 PP

                            AAA_21 210 asvderlrer..................gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEn 268
                                       +s +++l+ +                   +v+  ++++qe+p+ +++dG+k+l  +l  l++  +  ++++i+EpEn
  gi|518653283|ref|YP_008142803.1| 237 KSQKLALQVEniikkdniipnlkrfdfySIVLDTEEGDQEIPVESMGDGFKSLVHILIKLYDNEG--DIIVIEEPEN 311
                                       5555555555999999999999999999*************************777777776665..********** PP

                            AAA_21 269 gLHPkllrrll.ellkelsrngaQviltTHSp 299
                                        +HP  +r+l+  +++++++  +Q+++tTHS 
  gi|518653283|ref|YP_008142803.1| 312 YMHPGYIRELIhYIISIANNSHVQLFITTHSQ 343
                                       ***********66668888889*********5 PP

>> DUF2813  Protein of unknown function (DUF2813)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   9.2e-11   1.6e-07       3      69 ..       2      70 ..       1      76 [. 0.88
   2 ?   -2.9   0.0       1.8   3.2e+03     207     232 ..     166     191 ..     136     209 .. 0.69
   3 !    6.1   0.0    0.0031       5.5     285     325 ..     302     346 ..     290     351 .. 0.75

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 9.2e-11
                           DUF2813  3 LerieisGFRGinrLSlsleentvLiGENaWGKSSLldALslilnve..kelyqFtlkDFhvdeseeee 69
                                      +++i i+ F+Gin L ++ ++ +vL+G N  GK S+l+A+s+  n++  k+l  ++   F++++s+++ 
  gi|518653283|ref|YP_008142803.1|  2 IKHIAIKNFKGINSLEITPKKFNVLVGRNNTGKTSILEAISVCTNPNliKDLLMYKYGPFFINYSSDKA 70
                                      689****************************************99875578888888889988887665 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.8
                           DUF2813 207 qalssllehYfleksasrkkkrkere 232
                                        +ls+l + Y++++++++++ +++ +
  gi|518653283|ref|YP_008142803.1| 166 DTLSKLYDTYISKNEKNSATGKSNSN 191
                                       56777888888876665555444433 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0031
                           DUF2813 285 PilllEdpearLHPtml....aiaWellellPlQkiltTNSveLl 325
                                        i+++E+pe+ +HP  +    + + ++ +   +Q  +tT S++ l
  gi|518653283|ref|YP_008142803.1| 302 DIIVIEEPENYMHPGYIreliHYIISIANNSHVQLFITTHSQDFL 346
                                       59************8761111445556667779999999999887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   7.1   1.2e-07   0.00021       1      81 [.       1      74 [.       1     352 [. 0.65

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 1.2e-07
                                      EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEE CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                             SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaev 79
                                      ++k++ i+nFk +  ++ ++   k+f+++vG+N  GK+++l+Ai+ +   +  k l   k+     +     s++ka++
  gi|518653283|ref|YP_008142803.1|  1 MIKHIAIKNFKGI--NSLEITP-KKFNVLVGRNNTGKTSILEAISVCTNPNLIKDLLMYKYGPFFIN----YSSDKASI 72
                                      699**********..4555555.55*******************87776666666655555554443....34555555 PP

                                      EE CS
                                      xx RF
                             SMC_N 80 ei 81
                                      +i
  gi|518653283|ref|YP_008142803.1| 73 KI 74
                                      55 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7  11.5   2.7e-07   0.00048       2      87 ..       5     109 ..       4     266 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.7e-07
                            AAA_23   2 LkienfrsfrdqeidFskgltlItGpNGaGKTTildAiklaLyget.prlsrks....grgfeksdveiesegkvka 73 
                                       + i+nf+ ++  ei  + ++++++G N +GKT+il+Ai  ++     ++l   +      ++           ++ka
  gi|518653283|ref|YP_008142803.1|   5 IAIKNFKGINSLEITPK-KFNVLVGRNNTGKTSILEAISVCTNPNLiKDLLMYKygpfFINY----------SSDKA 70 
                                       78**************9.9**********************986332333332233332233..........34444 PP

                            AAA_23  74 yveltfenkdgry.........................t 87 
                                       +++++  +++ ++                         +
  gi|518653283|ref|YP_008142803.1|  71 SIKIDTDDNKVKKlnlrnptpeqilnllkndlnelsikK 109
                                       444444444333333332222224333333333333331 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 !   15.8   0.0   4.8e-06    0.0086      11      46 ..       9      45 ..       2      51 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
                            AAA_29 11 tfdg.htieidlkgatlltGpsGsGKSTllDAiqalL 46
                                       f+g +++ei++k + +l+G++ +GK+++l Ai++  
  gi|518653283|ref|YP_008142803.1|  9 NFKGiNSLEITPKKFNVLVGRNNTGKTSILEAISVCT 45
                                      588889999**99********************9765 PP

>> Glyco_hydro_42C  Beta-galactosidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0     0.016        29      16      32 ..      61      77 ..      60      81 .. 0.88
   2 !    9.3   0.0   0.00052      0.93      17      41 ..     145     168 ..     143     171 .. 0.90

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.016
                                      EEEE-SSS-EE----TT CS
                   Glyco_hydro_42C 16 FvlNfsneevtvtlpas 32
                                      F++N+s+++ +++++++
  gi|518653283|ref|YP_008142803.1| 61 FFINYSSDKASIKIDTD 77
                                      9***********99765 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00052
                                       EEE-SSS-EE----TT-EEEES-.. CS
                   Glyco_hydro_42C  17 vlNfsneevtvtlpasagdlltgel 41 
                                       ++N+s+++v++t+ + + dll+++l
  gi|518653283|ref|YP_008142803.1| 145 LVNYSDHPVILTA-ERYNDLLIDTL 168
                                       79**********9.*******9976 PP

>> PPR_3  Pentatricopeptide repeat domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   2.5e-05     0.044      20      54 ..     228     262 ..     218     269 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                             PPR_3  20 hLLtayanagnkklalevlermkkkgikPtvvtyN 54 
                                       +LL+a +  + +klal+v + +kk+ i P++  + 
  gi|518653283|ref|YP_008142803.1| 228 TLLSAEFFHKSQKLALQVENIIKKDNIIPNLKRFD 262
                                       7*****************************97765 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   7.2e-05      0.13       5      37 ..      15      47 ..      12     134 .. 0.91
   2 ?   -0.8   0.0       1.1     2e+03      26     130 ..     288     304 ..     167     311 .. 0.66
   3 ?    0.1   0.0      0.59   1.1e+03      26      50 ..     288     311 ..     281     391 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 7.2e-05
                                      EEEEETTSEEEEEESTTSSHHHHHHHHTTSS-- CS
                                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  5 slklkegekvaivGenGaGKStLlkllagllkp 37
                                      sl++ + +  ++vG+n +GK+++l++++  ++p
  gi|518653283|ref|YP_008142803.1| 15 SLEITPKKFNVLVGRNNTGKTSILEAISVCTNP 47
                                      789999999******************977766 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.1
                                       HHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHHHHHHSTTGGTTCBGE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  26 tLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvrenesdeeiekalsklglkelkdtvv 102
                                       +L+ +l++l++++                                                                
  gi|518653283|ref|YP_008142803.1| 288 SLVHILIKLYDNEG--------------------------------------------------------------- 301
                                       34444444444322............................................................... PP

                                       STTSGGS-HHHHHHHHHHHHHHHTSSEE CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran 103 ksspssLSgGqkqrvalarallkkpkll 130
                                                                +++
  gi|518653283|ref|YP_008142803.1| 302 -------------------------DII 304
                                       .........................333 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.59
                                       HHHHHHTTSS--SEEEEEETTCEGG CS
                                       xxxxxxxxxxxxxxxxxxxxxxxxx RF
                          ABC_tran  26 tLlkllagllkpteGeilldgkdlk 50 
                                       +L+ +l++l++++ + i ++ ++ +
  gi|518653283|ref|YP_008142803.1| 288 SLVHILIKLYDNEGDIIVIE-EPEN 311
                                       78999999999765555555.2222 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   4.3e-05     0.076      21      47 ..      18      42 ..       9      44 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                            AAA_27 21 fsaeeadlhliyGpNEAGKstalrAis 47
                                      +  + +++ +++G N +GK+++l+Ais
  gi|518653283|ref|YP_008142803.1| 18 I--TPKKFNVLVGRNNTGKTSILEAIS 42
                                      3..4799******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 2936.34
//
Query:       gi|518653284|ref|YP_008142804.1|  [L=198]
Description: hypothetical protein FACI_IFERC00001G1927 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0081   16.5   0.0      0.012   15.9   0.0    1.2  1  AbiEi_1   AbiEi antitoxin C-terminal domain
  ------ inclusion threshold ------
        0.2   11.4   0.0       0.28   10.9   0.0    1.4  1  Hira      TUP1-like enhancer of split
        2.7    8.9   7.2         18    6.3   0.6    3.0  3  DUF4065   Protein of unknown function (DUF4065)


Domain annotation for each model (and alignments):
>> AbiEi_1  AbiEi antitoxin C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     2e-06     0.012      15      95 ..      69     147 ..      60     162 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2e-06
                           AbiEi_1  15 lardyyagllsAawlhGaahrqpqriqvlvpkpakkipkglarvefvvrinvaalptkdvaaeaggvpvssPeatav 91 
                                       + +  y+g++sA  ++ +  +  ++i+v+ pk  k ++ +  + +f++ +n ++     +  +++++ +s Pe  +v
  gi|518653284|ref|YP_008142804.1|  69 ILEPSYIGISSAFSYYDLVTQIYNTIYVISPKRHKDVEIEGYKIKFITLKNTKVYG-YHI-DKNTYISISDPEKAIV 143
                                       55789******************************************888876655.444.7899**********99 PP

                           AbiEi_1  92 dlat 95 
                                       d ++
  gi|518653284|ref|YP_008142804.1| 144 DSVY 147
                                       9665 PP

>> Hira  TUP1-like enhancer of split
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   4.7e-05      0.28      74     111 ..     105     142 ..      87     191 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.7e-05
                              Hira  74 asltsnGvpivtlsngdgylydkslktWlrvsdswwal 111
                                       + ++   +  +tl+n + y y+ + +t++ +sd+  a+
  gi|518653284|ref|YP_008142804.1| 105 VEIEGYKIKFITLKNTKVYGYHIDKNTYISISDPEKAI 142
                                       5666777889***********************96655 PP

>> DUF4065  Protein of unknown function (DUF4065)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0     0.055   3.3e+02      75     106 ..      13      44 ..       2      50 .. 0.76
   2 ?    6.3   0.6    0.0029        18      35      92 ..      88     147 ..      82     150 .. 0.71
   3 ?    3.1   0.2     0.028   1.7e+02       3      18 ..     173     188 ..     171     193 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.055
                           DUF4065  75 dkeae..lseeekevidkvikkykdlsaseLsel 106
                                       d   +  +   ++e+i+    +y++l a++L++ 
  gi|518653284|ref|YP_008142804.1|  13 DY--KgiFRTYDIEIIENSNIRYSSLVANRLVKH 44 
                                       22..1349999**************999999975 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0029
                           DUF4065  35 pevydeikelgskpieekeeeisdeklekkekkeveeleddkeae....lseeekevidkvi 92 
                                        ++y++i  +   p+++k+ ei+  k++    k+++ + ++  ++    +s+ ek+++d v+
  gi|518653284|ref|YP_008142804.1|  88 TQIYNTI--YVISPKRHKDVEIEGYKIKFITLKNTKVYGYHIDKNtyisISDPEKAIVDSVY 147
                                       5788877..5666777777777777776666666555555544446799**********996 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.028
                           DUF4065   3 KllYfadflhlkrtgk 18 
                                       Kll++++ +h k+t +
  gi|518653284|ref|YP_008142804.1| 173 KLLFYSEKMHSKKTYE 188
                                       9**********99866 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.43
# Mc/sec: 1372.08
//
Query:       gi|518653285|ref|YP_008142805.1|  [L=293]
Description: hypothetical protein FACI_IFERC00001G1928 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-21   77.6   0.0    1.6e-21   77.4   0.0    1.1  1  AbiEii    Nucleotidyl transferase AbiEii toxin, Type IV TA sy


Domain annotation for each model (and alignments):
>> AbiEii  Nucleotidyl transferase AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.4   0.0     9e-26   1.6e-21      13     200 ..      45     226 ..      34     266 .. 0.83

  Alignments for each domain:
  == domain 1  score: 77.4 bits;  conditional E-value: 9e-26
                            AbiEii  13 dklvFkGGTaLslayglipRfSeDIDlsllr.gdrkellealkealeeiaaalaeeglkvklaasigege..dyegl 86 
                                       ++++F GGTa+s+ yg + RfSeD+D+ +++  d+++  +++k+a++e+ ++   e  + k++  ++     +++ +
  gi|518653285|ref|YP_008142805.1|  45 EDIIFIGGTAISKIYG-SGRFSEDLDFIFDKsYDTSDVENRVKKAINEVNNFYPIEYSTLKRRDMLRYNLkiKGPFY 120
                                       6789************.***********9999999999999999999999999999888887766654334444444 PP

                            AbiEii  87 rlrypaefggyarqkikieigfreav.ppaerreippyleelggpafevpvysleellaeKllalldrgrdrsraRD 162
                                        +     ++ +a q+ik++i++  ++ + + ++  ++++ e+   ++ + ++  ee++aeK+ a++   r+++ a D
  gi|518653285|ref|YP_008142805.1| 121 EM----SHSVRAIQSIKLDINLYVRPfYNPKKVLRTTIYPEI--RPYFLFTLETEEFAAEKIKAIM--ERKNPVAWD 189
                                       44....33899999********99998888887778888888..9*********************..889999*** PP

                            AbiEii 163 lyDlalLle.aeldaealaeallaylasrgrpgelrlap 200
                                       lyDl+lL++  +++ +   e+++ +l+++ +   +++++
  gi|518653285|ref|YP_008142805.1| 190 LYDLWLLITkYNVKINM--EMINYKLQKYTQVQGFNIDE 226
                                       *********99999999..99999999988855666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-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: 2235.64
//
Query:       gi|518653286|ref|YP_008142806.1|  [L=62]
Description: hypothetical protein FACI_IFERC00001G1929 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.26s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 491.66
//
Query:       gi|518653287|ref|YP_008142807.1|  [L=131]
Description: hypothetical protein FACI_IFERC00001G1930 [Ferroplasma acidarmanus fer1]
Scores for complete 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   18.9   0.0     0.0042   17.7   0.0    1.6  1  Asp_protease_2   Aspartyl protease
  ------ inclusion threshold ------
      0.045   14.3   0.0      0.092   13.3   0.0    1.5  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease


Domain annotation for each model (and alignments):
>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   4.7e-07    0.0042       3      87 ..       8     103 ..       6     106 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 4.7e-07
                    Asp_protease_2   3 vtinG...kpv.rfllDTGasttlispelaekl.....glkvreseltvrvsgaggevka..rlvrldslklggltl 68 
                                       ++inG   kp+ ++llDTG+s +++  +l + +     g +v+ se+ + +   + e k    + +++s+ +gg+t+
  gi|518653287|ref|YP_008142807.1|   8 IQINGrrmKPIlNALLDTGSSLNVLGHQLPDGHltfeiGPEVYNSEG-TEALIPDTEEKQifGTLTFESIIIGGFTI 83 
                                       789**7776668**************999976665655777777774.44455555555522556677999****** PP

                    Asp_protease_2  69 knvpalvld.lgeeidglLG 87 
                                       ++ +++ +  ++  ++ ++G
  gi|518653287|ref|YP_008142807.1|  84 TDPRFTTFTlMKIADEAIIG 103
                                       *9999887744556667776 PP

>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0     1e-05     0.092       2      87 ..       7     104 ..       6     109 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1e-05
                                       EEEETTEEE....EEEEETT-SS-EEEHHHHH.HTTGGGGEB..TT--EE-TT...ST..T-EEEEEEEEEE.EETT CS
                   gag-asp_proteas   2 kvkingkpv....kflvDTGAsstiiseelae.rlglsrkedkgkvevktang...ev..eakrvrldsvkiggiel 68 
                                       +++ing+++    ++l+DTG s  ++  +l +  l  +  ++ +++e + a     e+    ++ +++s+ igg+++
  gi|518653287|ref|YP_008142807.1|   7 NIQINGRRMkpilNALLDTGSSLNVLGHQLPDgHLTFEIGPEVYNSEGTEALIpdtEEkqIFGTLTFESIIIGGFTI 83 
                                       689999975222369***************997445555554444333333221112211447889999*9**9999 PP

                                       EEEEEEEEEESS..SSEEEEH CS
                   gag-asp_proteas  69 rnvsavvlegel..ddlLLGl 87 
                                       ++ +++ ++ ++  d+ ++G+
  gi|518653287|ref|YP_008142807.1|  84 TDPRFTTFTLMKiaDEAIIGH 104
                                       999999988663348889887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      282  (0.0157287); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 855.51
//
Query:       gi|518653288|ref|YP_008142808.1|  [L=68]
Description: hypothetical protein FACI_IFERC00001G1931 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); 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: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 523.46
//
Query:       gi|518653289|ref|YP_008142809.1|  [L=55]
Description: hypothetical protein FACI_IFERC00001G1932 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       193  (0.0107647); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 414.85
//
Query:       gi|518653290|ref|YP_008142810.1|  [L=172]
Description: hypothetical protein FACI_IFERC00001G1933 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.18   11.2   0.9       0.22   10.9   0.9    1.1  1  Sipho_tail  Phage tail protein


Domain annotation for each model (and alignments):
>> Sipho_tail  Phage tail protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.9   1.2e-05      0.22      55     148 ..      12     110 ..       9     140 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 1.2e-05
                        Sipho_tail  55 lrraLasilnqkkpkklifsdepdkyylavlsgdidldeknni...gkgeitflvpdpyaysvetsllnetnfagnl 128
                                       +rr+L  +ln   + k+if d    ++ a   + ++++++       k  i  + p+p++ s+ ++l+n + +++++
  gi|518653290|ref|YP_008142810.1|  12 KRRKLSIFLNENIKDKIIFYDNETITISANWAEGLSVEKFPIFaitKKEKILSFLPSPIKSSIYNELDNIILLQDDT 88 
                                       799999999999999*******99**************9988888899999999*********************** PP

                        Sipho_tail 129 wgfdlnisn...kteyk.sdtvtv 148
                                        +f +n +    +  y  s++ ++
  gi|518653290|ref|YP_008142810.1|  89 IHFRMNKEShffQ--YSiSQNLKI 110
                                       *999998866432..333554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      255  (0.0142228); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1231.34
//
Query:       gi|518653291|ref|YP_008142811.1|  [L=69]
Description: hypothetical protein FACI_IFERC00001G1934 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy 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:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.42
# Mc/sec: 499.00
//
Query:       gi|518653292|ref|YP_008142812.1|  [L=211]
Description: hypothetical protein FACI_IFERC00001G1935 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (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   29.1   6.3    1.1e-06   29.1   6.3    2.5  2  SNARE_assoc      SNARE associated Golgi protein
  ------ inclusion threshold ------
       0.15   12.3   0.4       0.36   11.1   0.4    1.6  1  Glycophorin_A    Glycophorin A
        2.7    8.5   6.1         11    6.5   6.1    2.1  1  FeoB_associated  FeoB-associated Cys-rich membrane protein
        3.8    7.1   5.8         13    5.4   0.6    2.5  2  DUF3341          Protein of unknown function (DUF3341)
        7.5    4.7  15.7         11    4.1  15.7    1.3  1  DUF2070          Predicted membrane protein (DUF2070)


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 !   29.1   6.3   3.1e-10   1.1e-06       5     115 ..      38     144 ..      30     150 .. 0.82
   2 ?    1.7   0.2     0.095   3.4e+02      15      40 ..     166     191 ..     150     210 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.1e-10
                       SNARE_assoc   5 vllvaaGvlfglllgtlvtslgallGaslayllgrylgrkalrrkllsekrvkalerlverygflallllrllpivP 81 
                                       +l +a++  f++ l +l +  g ++G+ + +    y g  a+  k+  ++++ a++ lv ry ++a++++  +p  P
  gi|518653292|ref|YP_008142812.1|  38 ILFAALSGRFDPGLLILSSTGGPTIGKMVLFQSF-YSG--AAITKVKTRENLTAFQTLVSRYAWIAVFIVASTPS-P 110
                                       22244444448888999999**********9887.555..57777999**************************7.8 PP

                       SNARE_assoc  82 rdlvnyvaGltrvsfkrFflatfiGsipwalvya 115
                                       +d+v +++G++r+s  rF+ a ++G+ + + +++
  gi|518653292|ref|YP_008142812.1| 111 DDIVYVPLGIARYSRIRFLTALLAGKTVITALTV 144
                                       *************************987655554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.095
                       SNARE_assoc  15 glllgtlvtslgallGaslayllgry 40 
                                       +++  +++ ++ a+l+ +++y++ r+
  gi|518653292|ref|YP_008142812.1| 166 STIEIIIIGIIFAILAVLITYIINRI 191
                                       55667888888889999999988775 PP

>> Glycophorin_A  Glycophorin A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.4    0.0001      0.36      57      86 ..     169     192 ..     159     206 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0001
                                       -TTHHHHHHHHHHHHHHHHHHHHHHHHTHS CS
                     Glycophorin_A  57 elvitliifgvmAgvigtillisYlirRli 86 
                                       e  i++iif+++A++i      +Y+i R+ 
  gi|518653292|ref|YP_008142812.1| 169 EIIIIGIIFAILAVLI------TYIINRID 192
                                       4567888999998765......56666655 PP

>> FeoB_associated  FeoB-associated Cys-rich membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   6.1    0.0032        11       2      22 ..     169     189 ..     168     195 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0032
                   FeoB_associated   2 tiIVgliiaaavafvirrlik 22 
                                       +iI+++ii+a++a++i ++i 
  gi|518653292|ref|YP_008142812.1| 169 EIIIIGIIFAILAVLITYIIN 189
                                       79*******999999998886 PP

>> DUF3341  Protein of unknown function (DUF3341)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.6    0.0037        13      87     109 ..      24      46 ..       8      62 .. 0.88
   2 ?    4.1   0.2    0.0088        32      54      78 ..     170     194 ..     151     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.0037
                                       S-HHHHHHHHTHHHHHHHHHHHH CS
                           DUF3341  87 fslpafipitFEltvLfaalatv 109
                                        sl+ fip+ + + +Lfaal+  
  gi|518653292|ref|YP_008142812.1|  24 SSLIIFIPVPYLFVILFAALSGR 46 
                                       57899**************9865 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0088
                                       HHHHHHHHHHHHHHHHHIIIIISS- CS
                           DUF3341  54 allgGllGlalalllqvytsvvdyp 78 
                                       ++++G++ ++la+l++++++ +d++
  gi|518653292|ref|YP_008142812.1| 170 IIIIGIIFAILAVLITYIINRIDWK 194
                                       46889999****************7 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1  15.7    0.0031        11      18     178 ..      30     191 ..       5     201 .. 0.73

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0031
                           DUF2070  18 llliillalligllaflssk.lfgillfglpalvaflltlpvlrilggr.ltykrs..lflalltelivviisllai 90 
                                       + +  l+++l+++l+ ++ + l  +   g p++  ++l++ + + + ++ ++++ +  +f  l++   +++++++a+
  gi|518653292|ref|YP_008142812.1|  30 IPVPYLFVILFAALSGRFDPgLLILSSTGGPTIGKMVLFQSFYSGAAITkVKTRENltAFQTLVSRYAWIAVFIVAS 106
                                       2233344444444444444476666778889************9999888777777789999999999999888888 PP

                           DUF2070  91 llsallqalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvly......fspesflllllls 161
                                       + s    +  + ++ l++a +  +r+l  ++ +++     v+ al+ + ++il   ++       +++s++ ++++ 
  gi|518653292|ref|YP_008142812.1| 107 TPSP---D-DIVYVPLGIARYSRIRFLTALLAGKT-----VITALTVLGAGILSHSVFgslnlgEDKYSTIEIIIIG 174
                                       8774...2.33355666777777777777776666.....66677777777777777777788889999******** PP

                           DUF2070 162 lifalavylfivvvdrp 178
                                       +ifa++++l+ ++++r 
  gi|518653292|ref|YP_008142812.1| 175 IIFAILAVLITYIINRI 191
                                       **************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         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: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1425.30
//
Query:       gi|518653293|ref|YP_008142813.1|  [L=460]
Description: hypothetical protein FACI_IFERC00001G1936 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 3372.03
//
Query:       gi|518653294|ref|YP_008142814.1|  [L=411]
Description: hypothetical protein FACI_IFERC00001G1937 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.026   14.1   0.6      0.062   12.8   0.1    1.9  2  HEPN_AbiU2  AbiU2


Domain annotation for each model (and alignments):
>> HEPN_AbiU2  AbiU2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-06     0.062     148     187 ..      22      64 ..      12      73 .. 0.83
   2 ?   -2.2   0.1      0.13   2.4e+03      96     125 ..     243     272 ..     180     284 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-06
                        HEPN_AbiU2 148 akeeled...ityddieeliddaleivnklllllfgtsfdyde 187
                                       + +e+++   +ty++i ++i ++ e+++ +++ l++ s d+  
  gi|518653294|ref|YP_008142814.1|  22 DFYEIFNvpyPTYPEISKAISTLHELFENYSWYLENISKDNTR 64 
                                       4566677888************************999888765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.13
                        HEPN_AbiU2  96 eadekfpdavekefeellellrklikklkk 125
                                       ++de    a+++ + el+e l+k+i+  ++
  gi|518653294|ref|YP_008142814.1| 243 SSDEFSLRACGNHEVELSESLKKKISINEN 272
                                       444555555555555666666666665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       798  (0.0445089); expected 358.6 (0.02)
Passed bias filter:                      576  (0.0321267); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.45
# Mc/sec: 2762.25
//
Query:       gi|518653295|ref|YP_008142815.1|  [L=558]
Description: hypothetical protein FACI_IFERC00001G1938 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.4e-54  183.8  33.1    7.2e-54  183.3  33.1    1.1  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  183.3  33.1     4e-58   7.2e-54       2     448 ..      41     535 ..      40     538 .. 0.82

  Alignments for each domain:
  == domain 1  score: 183.3 bits;  conditional E-value: 4e-58
                           DUF2079   2 lasLnstayDlGifdQviwntsqGelfysslsgvlhlLgqHfapillllaplyalfPsvltLllvqalllslgglpl 78 
                                       ++sL ++a+DlG+  Q++++ ++   fy+sl g+ + L+qHf+++ ++ +ply+lfPs+ tL +++ ++++l+g  +
  gi|518653295|ref|YP_008142815.1|  41 YYSLGTSAFDLGLNAQELYSFLHTGSFYTSLMGE-NALAQHFTLFKFIEVPLYYLFPSPITLMIFEDIFIALAGYIV 116
                                       89********************************.****************************************** PP

                           DUF2079  79 yrlarerlls....rrlalliallYl....lspvvinptlfdFhpevlaiPlllla.lllalrrrkwllllvlilll 146
                                       y +    l++    ++  +l+++ +l    +sp   + + f Fh + ++ P+++l+ ++ +l +r++l ++  i+++
  gi|518653295|ref|YP_008142815.1| 117 YLISTNLLKDhiksEKILFLVSIGFLlsyeFSPFSESLVSFSFHNMAFL-PFFFLLaFYSFLAERRILHIVSIIFII 192
                                       *998777655666677766666655511116899999999*********.987665055566778888888889999 PP

                           DUF2079 147 llvredlslvvvilglwlilre..rkrrk.................iglillllglawvilvtsvliPlfsstksqv 204
                                       +l+  ++++v v l + +++    r   k                 + +++l++ l++ +++   +i+l   ++s+ 
  gi|518653295|ref|YP_008142815.1| 193 SLHANFVYIVGVLLLYEFLFLHtyR--GKkintwfvrntnsrriasVSIFILAIVLLYGYILLAGIIKLRIAGISSF 267
                                       9****************99996331..223355556666666678999******************99998888755 PP

                           DUF2079 205 fgverysylg...sSlleillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnlls 278
                                       +     + +g   +S  +++l li++p+  ++ + s+ g+k++++ ll+ + + lp++ sp +L++++P++l+++ s
  gi|518653295|ref|YP_008142815.1| 268 SILPTTGETGtpaGSPIGLILLLIEKPGEFISIISSNHGEKVFFINLLLKSNLYLPFF-SPMSLILSIPYMLYAIPS 343
                                       4444445555999****************9****************************.****************** PP

                           DUF2079 279 gyspqlslgyqYsllvipflvlaaifglakls.....................ssvelrrikriwsvalvlvlvltl 334
                                       +y ++++lgyqY+++++  + ++ai g+  l                      s ++ r+ + i+s ++vlvlv   
  gi|518653295|ref|YP_008142815.1| 344 SYASYYQLGYQYFAMLLGAIYISAIMGAYNLIrlgkymyhhskqlrlklqkilSYKPERTGIAIVSILIVLVLV--- 417
                                       *************************************************9976655555555555555555544... PP

                           DUF2079 335 flnparslsflvpdsesp......vvylstlaqlqas...rellklIpsdasvlatsnLaPhlanRayvylfpenee 402
                                       +++p+  l++l  +++ p      + +  +      +    ++  + p++a++l+++ L+P ++n   vy+ p+   
  gi|518653295|ref|YP_008142815.1| 418 ISLPYGILAPLELEQTPPgsvmndINKEIPCGS---AtylINMSGYLPKNAYILTENTLMPYFSNYLHVYVSPYTPG 491
                                       556677888888888888765443333334444...24459999*********************999999888888 PP

                           DUF2079 403 lydleylleevdyvlld.vafrgwasrkdrerklidklrnsgrygvi 448
                                       +y     l +++y++++ ++f +    + + ++ +++  ++++y++i
  gi|518653295|ref|YP_008142815.1| 492 YY-M--NLSKYQYIIIQnNSFWATYGGNYSLQNIVNDGLTNSNYTII 535
                                       73.3..379********666666667777777777777777888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.47
# Mc/sec: 3561.50
//
Query:       gi|518653296|ref|YP_008142816.1|  [L=158]
Description: hypothetical protein FACI_IFERC00001G1939 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (158 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-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: 1110.89
//
Query:       gi|518653297|ref|YP_008142817.1|  [L=307]
Description: transposase, IS4 family protein [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.6e-18   65.7   3.2    7.5e-18   65.0   3.2    1.3  1  DDE_Tnp_1    Transposase DDE domain
    3.7e-13   49.8   0.1    7.1e-12   45.6   0.0    2.2  2  DDE_Tnp_1_5  Transposase DDE domain
    1.3e-05   25.2   1.1    7.3e-05   22.8   1.1    2.0  1  DDE_Tnp_1_3  Transposase DDE domain
  ------ inclusion threshold ------
      0.018   15.0   1.0        3.1    7.7   0.1    2.2  2  DUF4252      Domain of unknown function (DUF4252)
      0.018   14.5   0.1      0.038   13.4   0.1    1.5  1  PhoH         PhoH-like protein
       0.04   14.0   0.6        0.1   12.7   0.0    2.1  2  La           La domain


Domain annotation for each model (and alignments):
>> DDE_Tnp_1  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.0   3.2   2.5e-21   7.5e-18       7     212 ..     128     297 ..     123     299 .. 0.82

  Alignments for each domain:
  == domain 1  score: 65.0 bits;  conditional E-value: 2.5e-21
                         DDE_Tnp_1   7 livDattvrvpgtkedarwgyk.ggkykygyklhiavdtrsglilsvvitpgnvhdskglkqlldelrprkgklvla 82 
                                        i+D+t  +++  +   + g+k ++k+k ++klh++++++   +ls+ it+  +hdsk+++ ll  ++  +  ++++
  gi|518653297|ref|YP_008142817.1| 128 CIIDSTGYKITIRG--DYLGHKwHKKRKGWIKLHVIISLKDVNVLSFTITDEHTHDSKAARKLLSKMKN-NILRIFG 201
                                       68999999986666..6669999999*****************************************98.******* PP

                         DDE_Tnp_1  83 DaGYasaelldtleekgvdyiirlkkntklyrkgaeskrrgrlrkhdrnkiltksqkrrnkskkekgdvyyvtntns 159
                                       D+GY+  +++  +   g++ +i+++kn+ ++++g      + + k  r+   +  +++++                 
  gi|518653297|ref|YP_008142817.1| 202 DKGYD-SKYIYNMF--GYNAVIPPRKNASTKSRG-----SSARAKIVRYIKKNSMEQWKEN---------------- 254
                                       ****9.77777777..7*************9773.....3336667777777777777777................ PP

                         DDE_Tnp_1 160 ellsaeevaelyrlRwqiErvFkwlkrkfgldrlryrglnrveaqllllllal 212
                                                + y +Rw +E  F+ lkr+++ +  ++++ + + ++l l+   +
  gi|518653297|ref|YP_008142817.1| 255 ---------NSYGKRWIVEIYFSGLKRVMS-EVIKAKKIEYIIQELALKVVNY 297
                                       .........889***************776.6666666665555555555555 PP

>> DDE_Tnp_1_5  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.6   0.0   2.4e-15   7.1e-12      19     110 ..      51     138 ..      38     140 .. 0.87
   2 ?    1.8   0.1     0.096   2.9e+02       3      31 ..     236     264 ..     234     280 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.6 bits;  conditional E-value: 2.4e-15
                       DDE_Tnp_1_5  19 kekkkngkrgrpqvysdaaiqtcltvkvlfklplRqlqGfvqsllklaglellvpdystlsrraktlevkipvkrks 95 
                                        e+k++gk g+p++ +da i  +  ++ +f++p+R l+G+++sl  ++g+  +   ys + rr ++++ ++   +++
  gi|518653297|ref|YP_008142817.1|  51 LEEKNSGKIGHPYKVPDALIMYLARLRSIFNVPFRSLEGILRSLAIITGI--KSISYSEIFRRIRRIQPELN--NTN 123
                                       356788*****************************************999..8899***********99994..444 PP

                       DDE_Tnp_1_5  96 kglhlvvdstGlkvl 110
                                         l  ++dstG k++
  gi|518653297|ref|YP_008142817.1| 124 SKLDCIIDSTGYKIT 138
                                       459*********986 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.096
                       DDE_Tnp_1_5   3 RGsltiwldeeaiaawkekkkngkrgrpq 31 
                                       R +++ ++ ++ +++wke++  gkr   +
  gi|518653297|ref|YP_008142817.1| 236 RAKIVRYIKKNSMEQWKENNSYGKRWIVE 264
                                       7888999*********9999999986655 PP

>> DDE_Tnp_1_3  Transposase DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   1.1   2.4e-08   7.3e-05      37     102 ..     150     216 ..     145     282 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 2.4e-08
                       DDE_Tnp_1_3  37 kssmGWfyGfkLhliindk.GeilavkltpgnvdDrepveelakellg...klfaDkgyiskklaeelle 102
                                       k   GW+   kLh+ii+ k  ++l++++t+  ++D + +++l +++++   ++f+Dkgy sk + +++  
  gi|518653297|ref|YP_008142817.1| 150 KKRKGWI---KLHVIISLKdVNVLSFTITDEHTHDSKAARKLLSKMKNnilRIFGDKGYDSKYIYNMFGY 216
                                       6677885...******966269*****************998887776222579*******999877644 PP

>> DUF4252  Domain of unknown function (DUF4252)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0037        11      68     100 ..     161     193 ..     147     215 .. 0.82
   2 ?    7.7   0.1    0.0011       3.1      81     129 ..     228     278 ..     221     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0037
                           DUF4252  68 lkklksikvlttenkadaeklkkevkkilkknk 100
                                       + +lk ++vl+++ +++ +  +k+++k+l+k k
  gi|518653297|ref|YP_008142817.1| 161 IISLKDVNVLSFTITDEHTHDSKAARKLLSKMK 193
                                       449**********99999999999999999977 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0011
                           DUF4252  81 nkadaeklkkevkkilkknkyeeLmrvkdkgek..vkiyvkekkdkvselv 129
                                       +k+  +  ++++ +++kkn++e++ + ++ g++  v+iy+ + k ++se++
  gi|518653297|ref|YP_008142817.1| 228 TKSRGSSARAKIVRYIKKNSMEQWKENNSYGKRwiVEIYFSGLKRVMSEVI 278
                                       4577788899********************9999********999999986 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.1   1.3e-05     0.038      76     117 ..     263     304 ..     257     306 .. 0.95

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.3e-05
                                       --TTTHHHHHHHTTTS-TTCHHHHHHTTSEEEEEGGGGTT-- CS
                              PhoH  76 vdpylrplydaLkdllgaekvekllekgkievaplaymRGrT 117
                                       v++y++ l   ++++++a+k+e+++++  ++v++ + mRG T
  gi|518653297|ref|YP_008142817.1| 263 VEIYFSGLKRVMSEVIKAKKIEYIIQELALKVVNYNIMRGMT 304
                                       789*************************************98 PP

>> La  La domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05       0.1      18      49 ..     142     173 ..     139     193 .. 0.86
   2 ?   -3.7   0.1       4.4   1.3e+04       5      10 ..     263     268 ..     263     269 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                                       HHHHHHHTTSTTS---HHHHHTSSHHHHHHSS CS
                                La  18 kFLrkkmdkdpegwVplsliasfkrmkkltkd 49 
                                       ++L  k  k+ +gw++l++i+s k ++ l+ +
  gi|518653297|ref|YP_008142817.1| 142 DYLGHKWHKKRKGWIKLHVIISLKDVNVLSFT 173
                                       689999999999**************988754 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 4.4
                                       HHHHHH CS
                                La   5 vEfYFS 10 
                                       vE YFS
  gi|518653297|ref|YP_008142817.1| 263 VEIYFS 268
                                       899**9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       809  (0.0451224); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2254.71
//
Query:       gi|518653298|ref|YP_008142818.1|  [L=171]
Description: mannosyltransferase B [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-15   55.9   0.1    1.1e-12   47.8   0.1    2.1  1  Glycos_transf_1  Glycosyl transferases group 1
    7.2e-10   39.4   0.0    9.5e-10   39.0   0.0    1.3  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 !   47.8   0.1   1.3e-16   1.1e-12       2     164 ..       4     145 ..       3     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 1.3e-16
                                       HHHHHHHTTTTTT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES.STTHHHHHHHHHHHCTTCGGGEE CS
                   Glycos_transf_1   2 kekkrkklgknekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaGngeeekelkklaeelelsdnvifl 78 
                                       ke+ rk+lg++ +kk+ilsv+  +++K++  +  +++ l    ++ +klv +G                ++d ++f 
  gi|518653298|ref|YP_008142818.1|   4 KEQLRKELGLPLDKKLILSVSSDQPRKNIPMVKSVMDNL----DSSFKLVRVG--------------IPVGDSITFN 62 
                                       68899********************************98....899*******..............6777777775 PP

                                       ECCHSSSHHHHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTHCHHCHTTTSEEEE-TT-HHHHHHHHHHH CS
                   Glycos_transf_1  79 gevsredleellknadifvlpsisEgfGivllEAmaaglpviasnaggpaevvkdgetGllvkpnnaealaeairkl 155
                                         v+  ++ ++++++d+++lp   EgfG +++EA++ glpv++sn+  ++ev + +   llv p++ ++ +e+i  +
  gi|518653298|ref|YP_008142818.1|  63 -DVDTVKINKIYNASDMLFLPTLEEGFGYPVVEAFKTGLPVLTSNIDVIKEVSNGAA--LLVNPEELKENVEGIYGI 136
                                       .555688********************************************876666..999999999999999999 PP

                                       HHSHHHHHH CS
                   Glycos_transf_1 156 ledeelrer 164
                                       +++ e +++
  gi|518653298|ref|YP_008142818.1| 137 MDNHEYYVK 145
                                       999866654 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 !   39.0   0.0   1.1e-13   9.5e-10      55     132 ..      57     137 ..      17     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 1.1e-13
                                       .TEEEE---..THHHHHHHH-SEEEE--..---SHHHHHHHHTT-EEEE-TGGGTTT--TTSSEE--TT-HHHHHHH CS
                   Glyco_trans_1_4  55 erveftGfv..edlaellaaadvfvaPs..egfglkllEamaaglpvVatdvggiaevvgengllvppgdpealaea 127
                                       ++++f   v   +++++++a+d++ +P+  egfg+ ++Ea+  glpv ++++  i+ev + ++llv+p++ ++ +e 
  gi|518653298|ref|YP_008142818.1|  57 DSITFND-VdtVKINKIYNASDMLFLPTleEGFGYPVVEAFKTGLPVLTSNIDVIKEVSNGAALLVNPEELKENVEG 132
                                       4455554.312269***************88*********************999**774467***88877777777 PP

                                       HHHHH CS
                   Glyco_trans_1_4 128 ilrLl 132
                                       i  ++
  gi|518653298|ref|YP_008142818.1| 133 IYGIM 137
                                       66665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1215.75
//
Query:       gi|518653299|ref|YP_008142819.1|  [L=351]
Description: hypothetical protein FACI_IFERC00001G1942 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-55  187.5   0.0    4.9e-55  186.8   0.0    1.3  1  NTP_transferase  Nucleotidyl transferase
    6.4e-11   42.9   0.0    8.3e-11   42.5   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    4.1e-07   29.5  11.8     0.0011   18.6   0.4    4.6  7  Hexapep          Bacterial transferase hexapeptide (six repea
  ------ inclusion threshold ------
       0.03   14.1   0.6       0.03   14.1   0.6    4.3  6  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 !  186.8   0.0   1.1e-58   4.9e-55       1     246 [.       2     235 ..       2     237 .. 0.96

  Alignments for each domain:
  == domain 1  score: 186.8 bits;  conditional E-value: 1.1e-58
                                       EEEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEE CS
                   NTP_transferase   1 kavILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevli 77 
                                       k++IL+GG+GtRL+PLt+t +k+l+p+++k ++ q++l+ l ++gi++i ++l +   + v++++++gs+f++++++
  gi|518653299|ref|YP_008142819.1|   2 KGIILHGGAGTRLRPLTHTGPKQLIPIANK-PMSQYVLEYLTDAGINDICMILGDISPEKVKDYYGDGSEFDCNIQY 77 
                                       79****************************.********************************************** PP

                                       EEESS--BGGHHHHHTHHHHTTSSE..EEEEETTEEEESTTHHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEEC CS
                   NTP_transferase  78 alepegkgtAdAvalaaelledeksdelvlvLggDhlikdayeeavkkaiekaakgtvtfgivpveeateyGviead 154
                                       + +  + g+A+Av l  ++++++k    ++v+ gD li+ +++++++k+++++   ++ +++++   ++++Gv+e+ 
  gi|518653299|ref|YP_008142819.1|  78 IDQGAPLGIANAVSLTSNFVGNDK----FVVILGDNLIEGKIKTFMDKFEKSNY--DAFIVLTKSMHPKDFGVAEFR 148
                                       *********************999....577777888888*************9..9******************** PP

                                       TTSBEEEEECS-SSHSHCSEECCSEEEEETTHHHHHHHCCHHHTTSSCHHHHHHHHHHHTTEEEEEECSTTEE-EEE CS
                   NTP_transferase 155 eegrverfvEKPkeakaselassGiYvfnsevllflakdleelkrgedeitdilpkaleegkvalaflfkdaeyWsD 231
                                       ++ + ++++EKP++++ s+++ +GiY+f++ +++++ k+l++++r e eit++++ +l++ k+  + + +++  W+D
  gi|518653299|ref|YP_008142819.1| 149 DN-KLINLIEKPENPP-SNYVLTGIYFFTPLIFDYI-KKLKPSWRNEYEITEAIQLLLKDNKNIGYDIIDGW--WKD 220
                                       96.8999*********.*******************.77*********************999999899995..*** PP

                                       XSSHHHHHHHHHHHH CS
                   NTP_transferase 232 vGtldslleanekla 246
                                       +Gt+d++l an+ ++
  gi|518653299|ref|YP_008142819.1| 221 TGTVDDILAANMLIL 235
                                       ***********9776 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0   1.9e-14   8.3e-11       1     124 [.       3     135 ..       3     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.9e-14
                                       EEEEEESS-TTTT.....TTHHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSH..CHHHHHHTTCTS-EEE-TTS.S CS
                      NTP_transf_3   1 aviLAGGrSsRmg.....gdKallplggkpllervldalraagvdevvvvggd..eevlaalarlgvrvvededp.g 69 
                                       ++iL GG+++R+      g+K+l+p+++kp+ ++vl+ l++ag+++++++ gd  +e  +++ + g ++  + ++ +
  gi|518653299|ref|YP_008142819.1|   3 GIILHGGAGTRLRplthtGPKQLIPIANKPMSQYVLEYLTDAGINDICMILGDisPEKVKDYYGDGSEFDCNIQYiD 79 
                                       79**********6554447*******************************999885555567788999999988878 PP

                                       -SHHHHHHHHHHHH....SSSCEEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESS CS
                      NTP_transf_3  70 kgplaslaaalraaa...dadavlvlacDmPlltpelverllaaaaasgadvvvptye 124
                                       +g   ++a a++  +   ++d ++v+++D     +  ++++++++++s++d++++ ++
  gi|518653299|ref|YP_008142819.1|  80 QGAPLGIANAVSLTSnfvGNDKFVVILGDNLI--EGKIKTFMDKFEKSNYDAFIVLTK 135
                                       999999999998744577************55..7899***********999887665 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.2   5.6e+03      11      19 ..      98     108 ..      95     108 .. 0.65
   2 !   18.6   0.4   2.4e-07    0.0011       4      35 ..     253     284 ..     250     285 .. 0.93
   3 !   18.5   0.1   2.7e-07    0.0012       1      22 [.     274     295 ..     274     300 .. 0.93
   4 !    8.8   0.4    0.0003       1.4       2      28 ..     287     311 ..     286     318 .. 0.70
   5 !    4.6   1.0    0.0063        28       3      28 ..     304     328 ..     301     330 .. 0.57
   6 !    4.7   0.1    0.0059        26       2      12 ..     320     330 ..     319     337 .. 0.67
   7 ?   -4.2   0.0       3.9   1.7e+04      23      28 ..     344     349 ..     342     349 .. 0.55

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.2
                                       -T..TEEEETT CS
                           Hexapep  11 gp..faviggn 19 
                                       g+  f+vi+g+
  gi|518653299|ref|YP_008142819.1|  98 GNdkFVVILGD 108
                                       55558888875 PP

  == domain 2  score: 18.6 bits;  conditional E-value: 2.4e-07
                                       EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
                           Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                                       IG+nv++   + i+g+++IGdn++I   + ig
  gi|518653299|ref|YP_008142819.1| 253 IGKNVVLSDDSLIRGPAIIGDNTVIQDKTFIG 284
                                       9************************9988887 PP

  == domain 3  score: 18.5 bits;  conditional E-value: 2.7e-07
                                       TEEEETTEEE-TTEEEETTEEE CS
                           Hexapep   1 stvIGsnvlIgpfaviggnVkI 22 
                                       +tvI ++++Igp++ ig+n++I
  gi|518653299|ref|YP_008142819.1| 274 NTVIQDKTFIGPYTSIGDNCTI 295
                                       69*******************9 PP

  == domain 4  score: 8.8 bits;  conditional E-value: 0.0003
                                       EEEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       t IG+n++I   a i +n +I dn+ I
  gi|518653299|ref|YP_008142819.1| 287 TSIGDNCTIK-KASI-ENSIIMDNSNI 311
                                       78********.5555.55555555554 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0063
                                       EEETTEEE-TTEEEETTEEE-TTEEE CS
                           Hexapep   3 vIGsnvlIgpfaviggnVkIGdnvkI 28 
                                       +I +n+ I+   +i + + IG+n++I
  gi|518653299|ref|YP_008142819.1| 304 IIMDNSNIDTENTIVDSI-IGENSVI 328
                                       566666666644444444.7777776 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.0059
                                       EEEETTEEE-T CS
                           Hexapep   2 tvIGsnvlIgp 12 
                                       ++IG+n++I++
  gi|518653299|ref|YP_008142819.1| 320 SIIGENSVIMN 330
                                       56777777773 PP

  == domain 7  score: -4.2 bits;  conditional E-value: 3.9
                                       -TTEEE CS
                           Hexapep  23 GdnvkI 28 
                                       G+n++I
  gi|518653299|ref|YP_008142819.1| 344 GENSRI 349
                                       555554 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.1      0.71   3.2e+03      18      23 ..     104     109 ..     103     111 .. 0.79
   2 ?    1.6   0.1     0.055   2.4e+02      18      26 ..     251     259 ..     245     265 .. 0.74
   3 ?    6.8   0.8    0.0012       5.5       2      27 ..     251     278 ..     250     279 .. 0.86
   4 ?   14.1   0.6   6.7e-06      0.03       1      26 [.     268     295 ..     268     296 .. 0.95
   5 ?    1.5   0.1     0.055   2.5e+02      19      26 ..     321     328 ..     315     331 .. 0.61
   6 ?   -3.3   0.0       1.8   7.9e+03      20      26 ..     343     349 ..     340     350 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 0.71
                                       EEE-TT CS
                         Hexapep_2  18 vslGdn 23 
                                       v+lGdn
  gi|518653299|ref|YP_008142819.1| 104 VILGDN 109
                                       788888 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.055
                                       EEE-TT-EE CS
                         Hexapep_2  18 vslGdncvv 26 
                                       v +G+n+v+
  gi|518653299|ref|YP_008142819.1| 251 VAIGKNVVL 259
                                       556666665 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0012
                                       EEE-TT-EE-TT-EE..SEEE-TT-EE- CS
                         Hexapep_2   2 viIGdnCliGanagi..GvslGdncvvg 27 
                                       v IG+n+++  ++ i  + ++Gdn v++
  gi|518653299|ref|YP_008142819.1| 251 VAIGKNVVLSDDSLIrgPAIIGDNTVIQ 278
                                       7899999999999999559999999985 PP

  == domain 4  score: 14.1 bits;  conditional E-value: 6.7e-06
                                       .EEE-TT-EE-TT-EES..EEE-TT-EE CS
                         Hexapep_2   1 pviIGdnCliGanagiG..vslGdncvv 26 
                                       p iIGdn++i     iG  +s+Gdnc++
  gi|518653299|ref|YP_008142819.1| 268 PAIIGDNTVIQDKTFIGpyTSIGDNCTI 295
                                       789*************99********98 PP

  == domain 5  score: 1.5 bits;  conditional E-value: 0.055
                                       EE-TT-EE CS
                         Hexapep_2  19 slGdncvv 26 
                                       ++G+n+v+
  gi|518653299|ref|YP_008142819.1| 321 IIGENSVI 328
                                       34444444 PP

  == domain 6  score: -3.3 bits;  conditional E-value: 1.8
                                       E-TT-EE CS
                         Hexapep_2  20 lGdncvv 26 
                                       lG+n+ +
  gi|518653299|ref|YP_008142819.1| 343 LGENSRI 349
                                       6777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-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: 00:00:00.47
# Mc/sec: 2244.26
//
Query:       gi|518653300|ref|YP_008142820.1|  [L=275]
Description: dTDP-4-dehydrorhamnose reductase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-54  184.0   0.0    3.4e-54  183.9   0.0    1.0  1  RmlD_sub_bind    RmlD substrate binding domain
    4.5e-14   52.5   1.0    4.5e-14   52.5   1.0    1.7  2  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-10   41.1   0.1    2.1e-10   40.5   0.1    1.3  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
    3.4e-07   29.7   0.1    2.1e-06   27.1   0.0    2.1  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
      1e-05   24.9   0.1    2.5e-05   23.6   0.1    1.6  1  NAD_binding_4    Male sterility protein
  ------ inclusion threshold ------
       0.49    9.9   4.4        4.4    6.8   0.8    2.3  2  DUF5039          Domain of unknown function (DUF5039)


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 !  183.9   0.0   1.2e-57   3.4e-54       1     284 [.       1     270 [.       1     273 [. 0.95

  Alignments for each domain:
  == domain 1  score: 183.9 bits;  conditional E-value: 1.2e-57
                                       EEEEEESTTSHHHHHHHHHCTTTSEEEEEE-TTT--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHH CS
                     RmlD_sub_bind   1 mkilvtGanGqlGseLakqlaeeglevlaltreeldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayav 77 
                                       mk l++G++GqlG++L   l++     ++l+ + +dl++ ++++++l++ + d v+n+AA t vDk+E e ++ay +
  gi|518653300|ref|YP_008142820.1|   1 MKTLIIGSGGQLGKALSSILEN----SIPLSHDVIDLRNVNNIENTLDKYSFDTVINCAAMTSVDKCEIEIDSAYYI 73 
                                       899*****************94....48************************************************* PP

                                       HTHHHHHHHHHHHHCT-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHHHHH-SSEEEEEE-SEESS CS
                     RmlD_sub_bind  78 naeavealAeaaaavgalLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqavlaagkkalivRtswvyge 154
                                       n  + + + +++++ +  LihvStDyVF+G+k + Y+edd   P+n+YG +Kl G    + + ++ li+Rts vyg+
  gi|518653300|ref|YP_008142820.1|  74 NGLSMKYIGDYCRENNKYLIHVSTDYVFNGNKGN-YTEDDISYPINYYGLSKLIGDTYAN-SYQNSLIIRTSGVYGA 148
                                       *******************************776.********************98865.88999**********9 PP

                                       SSS-HHHHHHHHHHH-SEEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS-EEHHHHHHHHHHHH CS
                     RmlD_sub_bind 155 kgknfvktmlrlakereelkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlanegetswlefArailkea 231
                                        ++nf   ++++++++  ++ + D + sP  a+ lA+ + +ll+ ++      g++ +++ + +s++efA +i++++
  gi|518653300|ref|YP_008142820.1| 149 -KNNFPLYVIDRLRNNSGINAF-DNYYSPVNANVLAHSISKLLDLKLT-----GILNVSGPR-LSRYEFALKIADKF 217
                                       .89*****************98.7899*****************9996.....******998.************** PP

                                       CHTTSEEEEE-CCCS--SS---SBE-B--HHHHHCCT----BHHHHHHHHHHH CS
                     RmlD_sub_bind 232 gadseevkpistaeyptpAkRPanSvLdtekleatfgiklrewrealkevlke 284
                                       g +++ ++ ++ +++   AkRP +S+L++ek++a   ++  +  ++l+e+ k+
  gi|518653300|ref|YP_008142820.1| 218 GLNKALINKTDYNSVKFIAKRPYDSSLNNEKAKALLKFSFDDIDYNLNEFKKN 270
                                       ***********************************999999888888887665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   1.0   1.5e-17   4.5e-14       2     188 ..       4     159 ..       3     172 .. 0.87
   2 ?   -3.3   0.0       1.7   5.1e+03      17      54 ..     222     261 ..     219     270 .. 0.65

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.5e-17
                                       EEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHCEEEE--TT-HHHHHHHHHHHT-SEEEE--S---HH CS
                         Epimerase   2 lVtGatGfiGsalvkallekgyevigldrlssasntarledlelveldltdrsalerlfkeeqpdavihlAavggva 78 
                                       l++G  G++G+al   l++     i l+++                +dl++ +++e+ ++++ +d+vi++Aa  +v+
  gi|518653300|ref|YP_008142820.1|   4 LIIGSGGQLGKALSSILENS----IPLSHD---------------VIDLRNVNNIENTLDKYSFDTVINCAAMTSVD 61 
                                       78899999999998888875....888888...............99****************************** PP

                                       HHHHSHHHHHHHHTHHHHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS--.--SSHHHHHHHHHHHHHH CS
                         Epimerase  79 assedpadfieknlqgtlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgpl.kpnspYaaaKlageklve 154
                                          ++    +++n   +  + +++r+++   l+++s++ v+  ++    +e+     + +p + Y+++Kl g+ ++ 
  gi|518653300|ref|YP_008142820.1|  62 KCEIEIDSAYYINGLSMKYIGDYCRENNK-YLIHVSTDYVFNGNKGN-YTEDD----IsYPINYYGLSKLIGDTYAN 132
                                       ****************************9.***********988884.44444....449****************9 PP

                                       HHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHH CS
                         Epimerase 155 ayaaqyglnaiilrlfnlyGprngegevsrvipa 188
                                       +y+++     +i+r + +yG+   ++++  vi +
  gi|518653300|ref|YP_008142820.1| 133 SYQNS-----LIIRTSGVYGAK--NNFPLYVIDR 159
                                       99655.....599*******99..5555555555 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
                                       HHHHCT.SE.EEEEES-STTTTCHHCHHCEEEE--TT-HH CS
                         Epimerase  17 allekg.ye.vigldrlssasntarledlelveldltdrs 54 
                                       al +k+ y+ v  +++++++s  ++++ + l +  + d +
  gi|518653300|ref|YP_008142820.1| 222 ALINKTdYNsVKFIAKRPYDSSLNNEKAKALLKFSFDDID 261
                                       5666666777888888888888888777755555555544 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 !   40.5   0.1     7e-14   2.1e-10      59     171 ..      31     138 ..       4     155 .. 0.90

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 7e-14
                                       --TT-HHHHHHHHHHHT-SEEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S CS
                     GDP_Man_Dehyd  59 gDltDssslerllaevqpdevynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGk 135
                                        Dl++ +++e+ l+++ +d+v+n AA+  Vd+   + +  + +n+l +  + + +r+ +    + ++++St+ v+  
  gi|518653300|ref|YP_008142820.1|  31 IDLRNVNNIENTLDKYSFDTVINCAAMTSVDKCEIEIDSAYYINGLSMKYIGDYCRENN----KYLIHVSTDYVFNG 103
                                       69******************************998899999**************9965....5799********54 PP

                                       -SSSSB-TTS-----SHHHHHHHHHHHHHHHHHHHH CS
                     GDP_Man_Dehyd 136 vqevpqtEttpfyPrsPYaaaKlyadwivvnyreay 171
                                         +  +tE+   yP + Y+ +Kl+ d+ + +y+++ 
  gi|518653300|ref|YP_008142820.1| 104 N-KGNYTEDDISYPINYYGLSKLIGDTYANSYQNSL 138
                                       4.5789**************************9986 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   7.2e-10   2.1e-06      58     155 ..      28     137 ..      11     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 7.2e-10
                                       ..E--TT-HHHHHHHTT..T-SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS. CS
                   Polysacc_synt_2  58 pvigdvrdkerlekaleelkvdvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkvvliStDKAvn. 133
                                         + d+r+ +++e++l++++ d+v+++AA+  V  +e ++ +a   N l+++ + + + e++ k ++ +StD   n 
  gi|518653300|ref|YP_008142820.1|  28 HDVIDLRNVNNIENTLDKYSFDTVINCAAMTSVDKCEIEIDSAYYINGLSMKYIGDYCRENN-KYLIHVSTDYVFNg 103
                                       457899****************************************************9877.89******965432 PP

                                       ............--SHHHHHHHHHHHHHHHGGG- CS
                   Polysacc_synt_2 134 ............PtnvmGatKrlaekllqalake 155
                                                   P+n +G++K++ + ++ +++++
  gi|518653300|ref|YP_008142820.1| 104 nkgnyteddisyPINYYGLSKLIGDTYANSYQNS 137
                                       2233333333339**********99999888775 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   0.1   8.3e-09   2.5e-05      87     208 ..      47     147 ..      37     178 .. 0.75

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 8.3e-09
                                       H--EEEE--SS-S.ST...TSSEEHHHHHHHHHHHHHHHTSSS--.-EEEEEEGGGTTS-TTT--SSS-H......H CS
                     NAD_binding_4  87 evdviihsaAtvnfde...pykellrvNveGtrevlelakklkklkvllhvSTayvngeregeveekvyeegekeek 160
                                       + d +i++aA +++d+   +++ ++ +N ++++ + + +++   +k l+hvST yv + ++g+              
  gi|518653300|ref|YP_008142820.1|  47 SFDTVINCAAMTSVDKceiEIDSAYYINGLSMKYIGDYCREN--NKYLIHVSTDYVFNGNKGNY------------- 108
                                       679***********998889999*****************44..558******66666666554............. PP

                                       HH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 161 ldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                           ++++     n Y  sK +++   ++++++     +i+R s ++g
  gi|518653300|ref|YP_008142820.1| 109 ----TEDDISYPINYYGLSKLIGDTYANSYQNS-----LIIRTSGVYG 147
                                       ....34445555566666666666666666622.....4666666655 PP

>> DUF5039  Domain of unknown function (DUF5039)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.8    0.0015       4.4      26      50 ..      76     101 ..      59     142 .. 0.77
   2 ?    4.3   0.1    0.0089        26     120     152 ..     238     271 ..     220     274 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0015
                           DUF5039  26 lveaya.dyceannkyisindvdylk 50 
                                       l+ +y+ dyc +nnky+     dy+ 
  gi|518653300|ref|YP_008142820.1|  76 LSMKYIgDYCRENNKYLIHVSTDYVF 101
                                       66677659*********999999975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0089
                           DUF5039 120 eayk.elyyaerktlskyriealryvleeykekk 152
                                        +y   l ++  k+l k+  + + y l+e+k++ 
  gi|518653300|ref|YP_008142820.1| 238 RPYDsSLNNEKAKALLKFSFDDIDYNLNEFKKNM 271
                                       566514777778*******************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); 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: 0.50u 0.28s 00:00:00.78 Elapsed: 00:00:00.44
# Mc/sec: 1861.73
//
Query:       gi|518653301|ref|YP_008142821.1|  [L=328]
Description: hypothetical protein FACI_IFERC00001G1944 [Ferroplasma acidarmanus fer1]
Scores for 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-64  219.1   0.0    1.2e-64  218.8   0.0    1.1  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
      9e-52  175.9   0.0    1.1e-51  175.7   0.0    1.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.7e-09   37.1   0.0    2.4e-09   36.6   0.0    1.1  1  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    1.6e-07   30.7   0.0    3.2e-06   26.5   0.0    2.1  2  Polysacc_synt_2  Polysaccharide biosynthesis protein
    1.3e-06   27.8   0.0    0.00029   20.1   0.0    2.7  2  NAD_binding_4    Male sterility protein
    2.8e-06   26.6   0.0    5.1e-06   25.8   0.0    1.5  1  RmlD_sub_bind    RmlD substrate binding domain
     0.0038   16.7   0.0       0.42   10.1   0.0    2.9  2  adh_short        short chain dehydrogenase


Domain annotation for each model (and alignments):
>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  218.8   0.0   4.8e-68   1.2e-64       1     330 [.       5     296 ..       5     298 .. 0.92

  Alignments for each domain:
  == domain 1  score: 218.8 bits;  conditional E-value: 4.8e-68
                                       EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-S CS
                     GDP_Man_Dehyd   1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpd 77 
                                       L+TG+aGfiGs+++++L ++ ye + i++++++ + +++++++ +     ++++k+++  + D   ++++++++  d
  gi|518653301|ref|YP_008142821.1|   5 LVTGGAGFIGSNFINYLHKN-YEDY-IINLDKLSYGSNLNNIEIS-----SDKYKFIRKSIGD--DITEIIDNT--D 70 
                                       9***************9887.6665.5788999899999998753.....4689*********..89******9..9 PP

                                       EEEE--S---HHHHTTSHHHHHHHHTHHHHHHHHHHHHCT..TTSEEEEEEEGGGG-S-SSSSB-TTS-----SHHH CS
                     GDP_Man_Dehyd  78 evynLAAqshVdvsfekPeytaevnvlGtlrLLeairalglekkvrfyqaStsEvYGkvqevpqtEttpfyPrsPYa 154
                                        ++n+AA+shVd+s+ +P+ ++  n+ G+l+LLe+ir+ +  ++  ++ ++t+E YG+  +  + E+  ++P sPY+
  gi|518653301|ref|YP_008142821.1|  71 YIINFAAESHVDRSIANPQSFVSENINGVLNLLECIRKSK--NDPVLINIGTDEEYGDIVNGSFIEQDMLKPSSPYS 145
                                       *************************************975..67899****************************** PP

                                       HHHHHHHHHHHHHHHHH---EEEEEE-EEESTTS-TTSCCCHHHHHHHHHHTTS-C-EECTTTT-EEEEEEHHHHHH CS
                     GDP_Man_Dehyd 155 aaKlyadwivvnyreayglfavngilfnhesprrgetfvtrkitravarialgkqevlylGnldakRdwghvkDyve 231
                                       a+K+++  ++ +y ++yg+ +++++++n+ + ++   f++++i++++ r +l++ +++ +G ++++Rdw + +D v+
  gi|518653301|ref|YP_008142821.1| 146 ASKAASSLLALSYFRTYGIKTMVTRTSNNFGKYQ---FPEKLIPKTIIRNLLNL-DIPLYGSGKNIRDWIYTEDNVR 218
                                       *********************************6...***************98.77889***************** PP

                                       HHHHHHHCSS---EEE-TT-EEECHHCHHCCHHCCCHHHHHH............TTGGCCCEECGG--SS--SB--B CS
                     GDP_Man_Dehyd 232 amwlmlqqdkpedyviatgethsvrefvelaflelgktiewegkgeeevgrakesgkvvvevdpkyfrpgevdlllg 308
                                       a+ ++l ++k        ge +++ +  el++++++++i   +            g ++ +++++ +rpg++ ++ +
  gi|518653301|ref|YP_008142821.1| 219 AILTVLFKGK-------YGEIYNISSNHELENIDIVEKIFDLM------------G-KKGNLKYVSDRPGHDVRYSI 275
                                       ********99.......7******************9987542............2.245678899*********** PP

                                       -THHHHHHH----SS-HHHHHH CS
                     GDP_Man_Dehyd 309 daskakeeLgWkpkvsfeelvr 330
                                         +k+k  LgWkp+++f + ++
  gi|518653301|ref|YP_008142821.1| 276 RSDKLK-SLGWKPEYGFPDALK 296
                                       *****9.9*********98776 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  175.7   0.0   4.3e-55   1.1e-51       2     240 ..       5     235 ..       4     236 .. 0.94

  Alignments for each domain:
  == domain 1  score: 175.7 bits;  conditional E-value: 4.3e-55
                                       EEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
                         Epimerase   2 lVtGatGfiGsalvkallekgye.vigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa 73 
                                       lVtG++GfiGs+++++l ++  + +i+ld+ls++sn +++e      ++++  + d  +++++++  + d++i++Aa
  gi|518653301|ref|YP_008142821.1|   5 LVTGGAGFIGSNFINYLHKNYEDyIINLDKLSYGSNLNNIEISsdkyKFIRKSIGD--DITEIID--NTDYIINFAA 77 
                                       8********************99***************999889977888877775..89*****..89******** PP

                                       ---HHHHHHSHHHHHHHHTHHHHHHHHHHHHHTCT.EEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHH CS
                         Epimerase  74 vggvaassedpadfieknlqgtlnlleaarkagvk.rllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlag 149
                                       +++v++s+ +p+ f+ +n++g+lnlle++rk++ +  l++++++e YG+  +    e+     lkp+spY+a+K+a+
  gi|518653301|ref|YP_008142821.1|  78 ESHVDRSIANPQSFVSENINGVLNLLECIRKSKNDpVLINIGTDEEYGDIVNGSFIEQD---MLKPSSPYSASKAAS 151
                                       ******************************9966659***********88874345555...79************* PP

                                       HHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHHHTTSSSEEEETTST-EEEEEEHHHHHHHHHHHH CS
                         Epimerase 150 eklveayaaqyglnaiilrlfnlyGprngegevsrvipalirkilegkqevtllgdgtalRdflyveDvaeaillvl 226
                                         l+ +y ++yg++++++r +n++G++   ++++++ip+ i + l++  ++ l+g+g++ Rd++y eD ++ail+vl
  gi|518653301|ref|YP_008142821.1| 152 SLLALSYFRTYGIKTMVTRTSNNFGKY---QFPEKLIPKTIIRNLLNL-DIPLYGSGKNIRDWIYTEDNVRAILTVL 224
                                       ***************************...9*****************.**************************** PP

                                       HHHTT-STTEEEEE CS
                         Epimerase 227 ehvdagdkgeiyni 240
                                        +   g+ geiyni
  gi|518653301|ref|YP_008142821.1| 225 FK---GKYGEIYNI 235
                                       **...9999****9 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.6   0.0   9.4e-13   2.4e-09       1     224 [.       5     219 ..       5     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 36.6 bits;  conditional E-value: 9.4e-13
                         3Beta_HSD   1 vvtGgaGFlGralvkeLvrleelkevrvlD.lrespelleelskvnvkkviegDvtdkdkleealegvdvvihlasl 76 
                                       +vtGgaGF+G++ ++ L +  e   +  lD l  +++l +   +++  k+i   + d  +++e +++ d +i  a+ 
  gi|518653301|ref|YP_008142821.1|   5 LVTGGAGFIGSNFINYLHKNYE-DYIINLDkLSYGSNLNNIEISSDKYKFIRKSIGD--DITEIIDNTDYIINFAAE 78 
                                       69**************999887.6677777356667776666677777788888865..89**************** PP

                         3Beta_HSD  77 vdvag.kltedeimkvnvkGTrnvleacvkagv.rvlvYtSsaevvgpnslgeeilngdEeleyeslhqdaypesKa 151
                                       + v     + +++ + n++G  n+le  +k+   +vl+   + e  g+      i+ng   ++   +++++y+ sKa
  gi|518653301|ref|YP_008142821.1|  79 SHVDRsIANPQSFVSENINGVLNLLECIRKSKNdPVLINIGTDEEYGD------IVNGSFIEQDMLKPSSPYSASKA 149
                                       **987578899***************9988765267777777666666......888999999999**********9 PP

                         3Beta_HSD 152 laEklvlkaNgrtlknggrlyTcaLRpagiyGegd..kll..vpllkqlaklglalfkigdeevlsdrvYvgNvawa 224
                                        +  l l+           + T   R +  +G ++  ++l  ++ +++l++l   +  +g+ +++ d++Y +  + a
  gi|518653301|ref|YP_008142821.1| 150 ASSLLALSYFR----TY-GIKTMVTRTSNNFGKYQfpEKLipKTIIRNLLNL--DIPLYGSGKNIRDWIYTEDNVRA 219
                                       88877776544....32.3677777999999988633333013344555554..59999***********9865544 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.5   0.0   1.3e-09   3.2e-06       2     129 ..       5     121 ..       4     127 .. 0.80
   2 ?    1.9   0.0     0.039     1e+02     201     260 ..     208     261 ..     203     276 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.5 bits;  conditional E-value: 1.3e-09
                                       EEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T- CS
                   Polysacc_synt_2   2 lvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkv 78 
                                       lvtG++G iGs++++ + k+    ii l++  +     + e+    +++k+k+   + igd      ++++++  + 
  gi|518653301|ref|YP_008142821.1|   5 LVTGGAGFIGSNFINYLHKNYEDYIINLDKLSYGSNLNNIEI----SSDKYKFI-RKSIGD-----DITEIID--NT 69 
                                       8*******************9999999998776544433333....23344333.555765.....7999***..9* PP

                                       SEEEE------HHHHHHSHHHHHHHHHHHHHHHHHHHHHTT-SEE.EEEEEG CS
                   Polysacc_synt_2  79 dvvfhaAAlKhVPlveenpleaiktNvlgtenvieaaieagvkkv.vliStD 129
                                       d++++ AA  hV     np + ++ N+ g  n++e+  +++ + v + i tD
  gi|518653301|ref|YP_008142821.1|  70 DYIINFAAESHVDRSIANPQSFVSENINGVLNLLECIRKSKNDPVlINIGTD 121
                                       ***********************************99888766542567776 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.039
                                       EEEE-HHHHHHHHHHHHHH--SS-EEEE--.-EEEHHHHHHHH..........SSSS-EE CS
                   Polysacc_synt_2 201 RyfmtieeavqLvlqalalakggeifvldmGepvkivdlakalielsgleekkeedieik 260
                                       R ++  e+ v+ +l+ l ++k gei+     + ++ +d+++++ +l+g++ +      +k
  gi|518653301|ref|YP_008142821.1| 208 RDWIYTEDNVRAILTVLFKGKYGEIYNISSNHELENIDIVEKIFDLMGKKGN------LK 261
                                       668888999*****************999999***************96543......34 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.3   0.0    0.0074        19       1      21 [.       6      26 ..       6      36 .. 0.84
   2 !   20.1   0.0   1.1e-07   0.00029      80     208 ..      61     176 ..      59     249 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0074
                                      EE-TTSHHHHHHHHHHHHHS- CS
                     NAD_binding_4  1 lTGaTGFLGkvLlekLLrttp 21
                                      +TG+ GF+G+ +++ L ++ +
  gi|518653301|ref|YP_008142821.1|  6 VTGGAGFIGSNFINYLHKNYE 26
                                      7***********998876665 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 1.1e-07
                                       HHHHHHHH--EEEE--SS-S.STTSSE...EHHHHHHHHHHHHHHHTSSS--.-EEEEEE..GGGTTS-TTT--SSS CS
                     NAD_binding_4  80 dlqelaeevdviihsaAtvnfdepyke...llrvNveGtrevlelakklkklkvllhvST..ayvngeregeveekv 151
                                       d+ e+++++d ii+ aA  ++d+++ +   +++ N++G+ ++le  +k k+  vl+ + T   y +  +        
  gi|518653301|ref|YP_008142821.1|  61 DITEIIDNTDYIINFAAESHVDRSIANpqsFVSENINGVLNLLECIRKSKNDPVLINIGTdeEYGDIVNG------- 130
                                       7899*******************98775558999*****************9999999984333333333....... PP

                                       -H......HHH--EEEETTTCCCHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE- CS
                     NAD_binding_4 152 yeegekeekldederaklkglpntYeqsKalaEklvrearrrsglpvvivRpsiitg 208
                                                  +  ++++ + +  Y+ sKa++  l  +++r  g+++++ R s+  g
  gi|518653301|ref|YP_008142821.1| 131 -----------SFIEQDMLKPSSPYSASKAASSLLALSYFRTYGIKTMVTRTSNNFG 176
                                       ...........3445666778889****************999******99997665 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 !   25.8   0.0     2e-09   5.1e-06       3     156 ..       4     179 ..       1     271 [. 0.73

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 2e-09
                                       EEEESTTSHHHHHHHHHCTTTSEEEEEE-TT..................T--TTSHHHHHHHHHHH--SEEEE---- CS
                     RmlD_sub_bind   3 ilvtGanGqlGseLakqlaeeglevlaltre..................eldltdaeavaellkeakpdvvvnaAAy 61 
                                        lvtG+ G +Gs+ ++ l+++  +++    +                   +  +  + ++e++++   d ++n AA 
  gi|518653301|ref|YP_008142821.1|   4 FLVTGGAGFIGSNFINYLHKNYEDYIINLDKlsygsnlnnieissdkykFIRKSIGDDITEIIDN--TDYIINFAAE 78 
                                       79999999999999999998766655443334888888888555552221112222344555555..789******* PP

                                       --HHHHHHSHHHHHHHHTHHHHHHHHHHHHC..T-EEEEEEEGGGS-S-TTS-B-TTS----SSHHHHHHHHHHHHH CS
                     RmlD_sub_bind  62 tavDkaEseeeaayavnaeavealAeaaaav..galLihvStDyVFdGekkrpYeeddetsPlnvYGrtKlaGEqav 136
                                         vD+   ++++    n ++v +l e  ++   + +Li + tD  +    +  + e+d  +P + Y ++K+a     
  gi|518653301|ref|YP_008142821.1|  79 SHVDRSIANPQSFVSENINGVLNLLECIRKSknDPVLINIGTDEEYGDIVNGSFIEQDMLKPSSPYSASKAASSLLA 155
                                       *************************98876511679**********999999******************9998776 PP

                                       HH....H-SSEEEEEE-SEESSSS CS
                     RmlD_sub_bind 137 la....agkkalivRtswvygekg 156
                                       l+    +g k+++ Rts  +g+++
  gi|518653301|ref|YP_008142821.1| 156 LSyfrtYGIKTMVTRTSNNFGKYQ 179
                                       6644447789999****9999853 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.1   0.0   0.00016      0.42     100     162 ..      87     157 ..       2     169 .. 0.71
   2 ?    2.7   0.0     0.029        75     116     140 ..     217     241 ..     215     247 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00016
                                       HHHHHHHHHTHHHHHHHHHHHHHHH..........HCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHH CS
                         adh_short 100 ewervievNltgvflltravlpaml..........kqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrs 162
                                       + ++ ++ N++gv++l + + +  +          +++ G+Ivn +S + +  ++  ++YsAsKaa   l+ s
  gi|518653301|ref|YP_008142821.1|  87 NPQSFVSENINGVLNLLECIRKS-KndpvlinigtDEEYGDIVN-GSFIEQDMLKPSSPYSASKAASSLLALS 157
                                       45566777777777777666655.223334477778999****9.788889999999*********9887765 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.029
                                       HHHHHHHHHHCTTEEEEEEEEGGGT CS
                         adh_short 116 travlpamlkqssGrIvnvsSvagk 140
                                       +ra+l+ + k++ G+I n+sS++ +
  gi|518653301|ref|YP_008142821.1| 217 VRAILTVLFKGKYGEIYNISSNHEL 241
                                       688999999************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); 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:                         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 0.28s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2360.77
//
Query:       gi|518653302|ref|YP_008142822.1|  [L=179]
Description: dTDP-4-dehydrorhamnose 3,5-epimerase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-51  172.8   0.0    5.8e-51  172.5   0.0    1.0  1  dTDP_sugar_isom  dTDP-4-dehydrorhamnose 3,5-epimerase
  ------ inclusion threshold ------
      0.047   13.3   0.0      0.097   12.3   0.0    1.5  1  Cupin_1          Cupin


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 !  172.5   0.0   6.4e-55   5.8e-51       4     168 ..      11     173 ..       9     174 .. 0.98

  Alignments for each domain:
  == domain 1  score: 172.5 bits;  conditional E-value: 6.4e-55
                                       STTCEEEEE-EEEETTEEEEEEEEHHHHHHHTS-----EEEEEEEETTBEEEEEEESSCS---EEEEEEESEEEEEE CS
                   dTDP_sugar_isom   4 iegvlliepkvfgDeRGfflesfneeefaeagleaefvqdnlsvskkgvlRGlHfqkepkaqaklvrvvrGevldva 80 
                                       i++v+l++ k+f D+RGff e+++e+ +++ +++++f q nls+skk+v RG+Hfq +p+ q+kl++v++G+++d  
  gi|518653302|ref|YP_008142822.1|  11 IKDVKLVNSKKFDDNRGFFEEVYREKILEDFNIQNKFSQVNLSFSKKNVFRGFHFQLNPELQGKLITVISGKIIDYG 87 
                                       89*************************************************************************** PP

                                       EE-BTTSTTTT-EEEEEEETTT--EEEE-TTEEEEEEE-SSEEEEEEEESS---GGGEEEE-TT-TTTT---.SS.B CS
                   dTDP_sugar_isom  81 VDlRkgSptfgkwvgveLsaenkrqlyipegfahGflvlsdeaevlYkvteyyapesergirwnDpelgidw.eeli 156
                                       +DlRk+S++f+ +v++e++  + +++yipegfahGfl+l+d + vlY++t+ ++++ ++gir++D+el+i+  +++i
  gi|518653302|ref|YP_008142822.1|  88 IDLRKDSKSFKCHVEYEIT--SGKMIYIPEGFAHGFLALED-SYVLYLTTNEFNQSLDSGIRYDDKELNISLpDNII 161
                                       ******************9..99****************98.899*****99*********************99** PP

                                       --HHHHT-B-HH CS
                   dTDP_sugar_isom 157 lSekDkaapsla 168
                                       +SekDk+++ l+
  gi|518653302|ref|YP_008142822.1| 162 ISEKDKKLKHLN 173
                                       ********9987 PP

>> Cupin_1  Cupin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   1.1e-05     0.097      64     116 ..      74     134 ..      60     160 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.1e-05
                                       EEEEEEEETTSS...........EEEEEE....EETTEEEEE-TT-EEEEEEESSSSEEEEEEEESS CS
                           Cupin_1  64 egrvgfvvpgng..........nrdfhkk....lreGdvfvvPaglvhfqynsgdepavaivvfdtn 116
                                       ++   +v++g+           +++f+      ++ G ++++P+g++h + + + ++   +v++ t+
  gi|518653302|ref|YP_008142822.1|  74 KLI--TVISGKIidygidlrkdSKSFKCHveyeITSGKMIYIPEGFAHGFLALE-DS---YVLYLTT 134
                                       444..5555555566666666644444444577*******************95.32...2233333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (179 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); 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: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.51
# Mc/sec: 1062.38
//
Query:       gi|518653303|ref|YP_008142823.1|  [L=356]
Description: hypothetical protein FACI_IFERC00001G1946 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-23   82.0   0.5    7.9e-21   74.3   0.0    2.2  2  Glycos_transf_1  Glycosyl transferases group 1
    2.8e-12   47.2   0.0      7e-12   45.9   0.0    1.6  2  Glyco_trans_1_4  Glycosyl transferases group 1
  ------ inclusion threshold ------
      0.029   14.4   0.0       0.12   12.4   0.0    1.8  2  Glyco_transf_4   Glycosyltransferase Family 4


Domain annotation for each model (and alignments):
>> Glycos_transf_1  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.1    0.0014       8.5      60      97 ..     108     145 ..      70     160 .. 0.90
   2 !   74.3   0.0   1.3e-24   7.9e-21      13     153 ..     186     320 ..     176     323 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0014
                                       HHHHHHHHHHCTTCGGGEEECCHSSSHHHHHHCESEEE CS
                   Glycos_transf_1  60 kelkklaeelelsdnviflgevsredleellknadifv 97 
                                         l + ++e+++ +n i++ +++++ + +l++na+ fv
  gi|518653303|ref|YP_008142823.1| 108 SFLDQIIDEYGNIKNKIIFNFIKKSGMYNLYNNANFFV 145
                                       568889****************************9988 PP

  == domain 2  score: 74.3 bits;  conditional E-value: 1.3e-24
                                       TT-EEEEEESS-TTTTTHHHHHHHHHCCCCCHCSCEEEEEES...STTHHHHHHHHHHHCTTCGGGEEECCHSSSHH CS
                   Glycos_transf_1  13 ekkkiilsvgrlekeKgvdllikafallkkqlnpnvklviaG..ngeeekelkklaeelelsdnviflgevsredle 87 
                                       ++ ++++s+gr++ +K++++l+k +++lk     n++++iaG  n  +e+++++l+++     nv++  +++++d++
  gi|518653303|ref|YP_008142823.1| 186 KDNNLVISIGRIDIRKNYEVLLKIAEKLK-----NYRFIIAGalNRGDEEYYRNLIKNKPS--NVEIKANINEHDKI 255
                                       7899**********************985.....9*******8877777888888777665..************** PP

                                       HHHHCESEEEEEESSBSS-HHHHHHHHTT--EEEETTTTH.CHHCHTTTSEEEE-TT-HHHHHHHHH CS
                   Glycos_transf_1  88 ellknadifvlpsisEgfGivllEAmaaglpviasnaggp.aevvkdgetGllvkpnnaealaeair 153
                                       ellk+a+i+ +  ++E  Gi++lEAm++gl  ++  +ggp  +++++g  G+ + ++  ++++e+i+
  gi|518653303|ref|YP_008142823.1| 256 ELLKKASIYMHMNRRENYGISILEAMSYGLVPVVPESGGPwEDIIEHGRYGYGFNSV--DDAVERIK 320
                                       **********************************99555527799999988777666..77777776 PP

>> Glyco_trans_1_4  Glycosyl transferases group 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.1   6.6e+03      62      79 ..     128     147 ..     111     155 .. 0.67
   2 !   45.9   0.0   1.2e-15     7e-12       3     129 ..     190     320 ..     188     323 .. 0.83

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.1
                                       --.TH.HHHHHHH-SEEEE- CS
                   Glyco_trans_1_4  62 fv.ed.laellaaadvfvaP 79 
                                       f+ ++ + +l+++a+ fv+ 
  gi|518653303|ref|YP_008142823.1| 128 FIkKSgMYNLYNNANFFVNS 147
                                       44222488999999999985 PP

  == domain 2  score: 45.9 bits;  conditional E-value: 1.2e-15
                                       EEEEES---GG.GTHHHHHHHHHHHH.HHEEEEEES---....HHHHHHHTT-T.TEEEE---..THHHHHHHH-SE CS
                   Glyco_trans_1_4   3 vilfvGrleenvkgvdllleavpllrkkdvrlvivGdgp..rpeeleelaagleerveftGfv..edlaellaaadv 75 
                                        ++ +Gr+ + +k+ ++ll+ +++l+  ++r++i+G  +  ++e +++l+++  ++ve+   +  +d+ ell++a++
  gi|518653303|ref|YP_008142823.1| 190 LVISIGRI-DIRKNYEVLLKIAEKLK--NYRFIIAGALNrgDEEYYRNLIKNKPSNVEIKANIneHDKIELLKKASI 263
                                       67899***.555**************..78******64433446778777755578*******9778********** PP

                                       EEE--..---SHHHHHHHHTT-EEEE-TGGGT.TT--..TTSSEE--TT-HHHHHHHHH CS
                   Glyco_trans_1_4  76 fvaPs..egfglkllEamaaglpvVatdvggi.aevv..gengllvppgdpealaeail 129
                                       +   +  e  g+++lEam++gl  V+ + gg+ ++++  g+ g+ ++  ++++ +e+i 
  gi|518653303|ref|YP_008142823.1| 264 YMHMNrrENYGISILEAMSYGLVPVVPESGGPwEDIIehGRYGYGFN--SVDDAVERIK 320
                                       *****988**************9999999985488889989998887..6777776665 PP

>> Glyco_transf_4  Glycosyltransferase Family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.9e-05      0.12      39     163 ..      48     172 ..      13     178 .. 0.73
   2 ?   -1.1   0.0      0.27   1.6e+03      53      76 ..     304     327 ..     293     337 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.9e-05
                    Glyco_transf_4  39 lvvrvprvpl..pllkrllrslaflrrlrrllkrekpDvvHahspaalgaallalrrrlgiplVltvHglyekrllk 113
                                       ++++ p++++   +l+ l++++a  +++ r+  ++++D+v  ++p  +++         +i   + + +l+   +  
  gi|518653303|ref|YP_008142823.1|  48 NIIETPYYFRenMKLPSLYYYVARTKKFLRHYIQNQFDLVFNNHPNMFLYK-------ADINALHGFSFLD--QIID 115
                                       55555555541256667778888888999999999*****99999888654.......5999999999999..5777 PP

                    Glyco_transf_4 114 arlkplsrllralerrl....lrradrviavSeatadelreryg...vppekitVip 163
                                        + + ++++++++ ++     l +   ++++S++t +  r++++   ++p+ ++ i+
  gi|518653303|ref|YP_008142823.1| 116 EYGNIKNKIIFNFIKKSgmynLYNNANFFVNSKYTLQISRKLFPllnIKPNLMRLIY 172
                                       777777777777777777777555567999999999998887775556666666665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.27
                    Glyco_transf_4  53 rllrslaflrrlrrllkrekpDvv 76 
                                       r+++ + ++ ++ +++k+ ++D+v
  gi|518653303|ref|YP_008142823.1| 304 RYGYGFNSVDDAVERIKNIDFDIV 327
                                       666777778889999********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (356 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       663  (0.0369792); expected 358.6 (0.02)
Passed bias filter:                      315  (0.0175693); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2553.73
//
Query:       gi|518653304|ref|YP_008142824.1|  [L=695]
Description: hypothetical protein FACI_IFERC00001G1947 [Ferroplasma acidarmanus fer1]
Scores for complete 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  130.4  26.3    1.3e-37  129.7  26.3    1.2  1  DUF2079   Predicted membrane protein (DUF2079)


Domain annotation for each model (and alignments):
>> DUF2079  Predicted membrane protein (DUF2079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7  26.3   7.3e-42   1.3e-37      11     403 ..      40     441 ..      30     466 .. 0.85

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 7.3e-42
                           DUF2079  11 DlGifdQviwntsqGelfysslsgvlhlLgqHfapillllaplyalfPsvltLllvqalllslgglplyrlarerll 87 
                                       D ++ +Q++ ++   ++f+ ++ g  + ++ H++ il ll+p+ a++ s   L ++q++l+  +++pl+ la+++l 
  gi|518653304|ref|YP_008142824.1|  40 DTTTSLQSLLSAFYHQPFVNTVPGG-SYFSVHASEILILLLPFFAVWHSFINLYIIQSVLIYSASIPLFLLAQKKLH 115
                                       5555678888888888888888888.*************************************************** PP

                           DUF2079  88 srrlalliallYllspvvinptlfdFhpevlaiPllllalllalrrrkwllllvlilllllvredlslvvvilglwl 164
                                       + ++++l+a+++ll+p++      +F  ++l++ ++  +++ ++ +++  ++ +  +l+l ++e+  ++  ++gl+l
  gi|518653304|ref|YP_008142824.1| 116 NDKASFLMATVFLLNPYIHDN---PFETLTLFMGFIIYSYY-FFDAKRYVAFGITFILALSTMEFNPVIGGFFGLYL 188
                                       *******************88...****************9.*********************************** PP

                           DUF2079 165 ilr...................erkrrk..........iglillllglawvilvtsvliPlfsstksqvfgverysy 212
                                       il                    e               ++ + + +++++++l++s  i +f+ +k+    + ++s+
  gi|518653304|ref|YP_008142824.1| 189 ILLflydkikissiknlikrpvE----QfkviksqlseLKNFRSYFSIGIILLIIS--IGFFYGDKY---LILYFSH 256
                                       ***77777766666655554440....04455566666677777777777777777..778888886...5567888 PP

                           DUF2079 213 lg.sSlleillnlitqpllvlqellspegdklkyllllflplgflpllsspawLlvalPllllnllsgyspqlslgy 288
                                          + ++ i ++ i++   +++ + +    k+  l++l  p++fl +l   +  l+ lP +l+  +s  sp++s+g 
  gi|518653304|ref|YP_008142824.1| 257 GShAITSNIAGSNISSFSAIIKDFKTDISSKIDSLMYLNSPFLFLSFL--SPFALLELPWFLTYSISTFSPYWSIGV 331
                                       776778889999999999999999988889*****************9..6667789******************** PP

                           DUF2079 289 qYsllvipflvlaaifglaklsssvelrrikriwsvalvlvlvltlflnparslsflvpdsespvvylstlaqlqas 365
                                       +Y  ++ipf++++ai gl k++s  e  ++k+++ ++++l+l++tl+l+ ++ ++++v + +s   +++++++   +
  gi|518653304|ref|YP_008142824.1| 332 YYDSYIIPFAAISAILGLYKIHSMLEDGDRKKVVNRIAYLALIVTLILLISNVVAPMVTNPVS---PVNSNDY---G 402
                                       *************************************************66666666654444...3444444...2 PP

                           DUF2079 366 .rellklIpsdasvlatsnLaPhlanRayvylfpeneel 403
                                         +l++lIp +a v +  n +P ++  ay + f+++e+ 
  gi|518653304|ref|YP_008142824.1| 403 vAQLASLIPGNAKVTTGVNELPIVSSYAYNTWFYGPENN 441
                                       479**********************98888888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (695 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      274  (0.0152825); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 4827.96
//
Query:       gi|518653305|ref|YP_008142825.1|  [L=62]
Description: hypothetical protein FACI_IFERC00001G1948 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (62 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      249  (0.0138881); 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 0.26s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 432.70
//
Query:       gi|518653306|ref|YP_008142826.1|  [L=246]
Description: Alpha-D-glucoside glucohydrolase 1 [Ferroplasma acidarmanus fer1]
Scores for complete 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-25   88.4   0.0    6.5e-25   87.9   0.0    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    1.8e-05   24.8   0.0    2.4e-05   24.3   0.0    1.2  1  Glyco_tranf_2_3  Glycosyltransferase like family 2
    0.00038   20.0   0.2    0.00069   19.2   0.2    1.4  1  Glyco_tranf_2_2  Glycosyltransferase like family 2
  ------ inclusion threshold ------
      0.025   14.0   0.0      0.039   13.4   0.0    1.3  1  Glyco_transf_21  Glycosyl transferase family 21


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.9   0.0   1.5e-28   6.5e-25       1     133 [.       9     144 ..       9     182 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.9 bits;  conditional E-value: 1.5e-28
                                       EEEEEESS-TTTHHHH...HHHHHHHGGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektllet...lesllaqdpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnag 74 
                                       ++v  t Ne ++l+++   ++s+l++  + ++++++vDD+S+D+t+e++ e++++++  ++i +e+++    a+ +g
  gi|518653306|ref|YP_008142826.1|   9 TIVLATLNEIDNLPRLcsdIDSILKN-AKIKYQLLFVDDNSSDGTREFIIEYCNKNKLSKYIFNEHKKSTLIARYQG 84 
                                       58999****77777765558999999.************************************************** PP

                                       HHH--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEEECCCCCCCHC-SS..E CS
                   Glycos_transf_2  75 lraatgdyilflDaDdepdpdwleklvealekdgadvvlgqrprifgetdeiernkrv..g 133
                                       + +++g+yi+++D+D++++p++l  +++ l + ++d+v+++r++++g+++++++ +++  +
  gi|518653306|ref|YP_008142826.1|  85 INHSDGKYIILMDSDLQHPPKYLVNIYNGLLE-NYDIVIASRYVKDGSSGNRKPIRGIisR 144
                                       ********************************.******************9999887552 PP

>> Glyco_tranf_2_3  Glycosyltransferase like family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   5.4e-09   2.4e-05       3     127 ..       7     128 ..       5     150 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 5.4e-09
                   Glyco_tranf_2_3   3 dlavlVptfneedvlge...vlesllaqeyprvevvvvvdesdaetlevaeelaaalpdvrv.rvvvnarnlgstgk 75 
                                       dl+++ +t+ne d l +    ++s+l+++ + +++ +v+d+s+++t+e++ e    + ++++ ++++n++    +++
  gi|518653306|ref|YP_008142826.1|   7 DLTIVLATLNEIDNLPRlcsDIDSILKNAKIKYQLLFVDDNSSDGTREFIIEY---CNKNKLsKYIFNEH-K--KST 77 
                                       5889999999999666643379*****99********************9995...55555515666666.3..455 PP

                   Glyco_tranf_2_3  76 sralnealravksdlvllvDdDtvvePdtlkrllqffltpkvgavgtpvfll 127
                                         a ++++++ ++++++l+D+D    P +l  + + +  +++++v ++++++
  gi|518653306|ref|YP_008142826.1|  78 LIARYQGINHSDGKYIILMDSDLQHPPKYLVNIYNGL-LENYDIVIASRYVK 128
                                       5566*********************999976555544.46677776666655 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 !   19.2   0.2   1.5e-07   0.00069      18      92 ..      30     100 ..      27     120 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.5e-07
                   Glyco_tranf_2_2  18 rvlqkakyydeeielivvddgSsekfleevssiidlnllv.ylkdeddkayslaaarNrGaskaesdlvlFlDaDc 92 
                                        +l++ak    + +l++vdd Ss+ + e +   +++n+l  y+ +e +k  s   ar +G++++ + +++ +D+D 
  gi|518653306|ref|YP_008142826.1|  30 SILKNAKI---KYQLLFVDDNSSDGTREFIIEYCNKNKLSkYIFNEHKK--STLIARYQGINHSDGKYIILMDSDL 100
                                       56666666...889***********************999787777554..778899*****************95 PP

>> Glyco_transf_21  Glycosyl transferase family 21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.6e-06     0.039      24      92 ..      83     150 ..      70     161 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.6e-06
                   Glyco_transf_21  24 qaleaakydllvisDsdvrvkpdyLeellaaledpkvglVtslpvgsdakglaaaleaaflntlagvlq 92 
                                       q+++    +++++ Dsd   +p+yL ++ + l + +  +V +  ++ d ++  ++  + +++ +a +++
  gi|518653306|ref|YP_008142826.1|  83 QGINHSDGKYIILMDSDLQHPPKYLVNIYNGLLE-NYDIVIASRYVKDGSSGNRKPIRGIISRGASLMA 150
                                       556667789************************7.9******999999988777766666665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       593  (0.0330749); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        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: 0.60u 0.35s 00:00:00.95 Elapsed: 00:00:00.56
# Mc/sec: 1312.21
//
Query:       gi|518653307|ref|YP_008142827.1|  [L=80]
Description: hypothetical protein FACI_IFERC00001G1950 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (80 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1118  (0.0623571); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.28s 00:00:00.72 Elapsed: 00:00:00.46
# Mc/sec: 518.49
//
Query:       gi|518653308|ref|YP_008142828.1|  [L=52]
Description: hypothetical protein FACI_IFERC00001G1951 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 353.72
//
Query:       gi|518653309|ref|YP_008142829.1|  [L=139]
Description: cell wall biosynthesis glycosyltransferase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-12   45.6   1.8    8.5e-12   45.2   1.8    1.2  1  Glycos_transf_2  Glycosyl transferase family 2
    6.1e-05   23.0   0.0    7.5e-05   22.7   0.0    1.1  1  Glyco_tranf_2_3  Glycosyltransferase like family 2


Domain annotation for each model (and alignments):
>> Glycos_transf_2  Glycosyl transferase family 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.2   1.8   9.5e-16   8.5e-12       1     119 [.      10     122 ..      10     136 .. 0.83

  Alignments for each domain:
  == domain 1  score: 45.2 bits;  conditional E-value: 9.5e-16
                                       EEEEEESS-TTTHHHHHHHHHHH.GGCCEEEEEEEEES-SSCHHHHHGGGCHC-TTEEEEEESSS-HHHHHHHHHHH CS
                   Glycos_transf_2   1 svviptyNeektlletlesllaq.dpypdfeiivvDDgStDetveileelakedprvrvirreenvGkagalnaglr 76 
                                       s++i++y +++ ll++++s+++q  ++  +eii++++    +    +++      +++ i  +e   + g l ++l 
  gi|518653309|ref|YP_008142829.1|  10 SIIITAYKRKEFLLNAIKSVINQtLDKNYYEIIIIKNFIDNRIDTYIKNN-----HITEIVSKEE-SLFGKLVEALN 80 
                                       8**********************999999*********955555555555.....5555555544.6********** PP

                                       H--SSEEEEEESSEEE-TTHHHHHHHHHHH.TTCEEEEEEEEE CS
                   Glycos_transf_2  77 aatgdyilflDaDdepdpdwleklvealekdgadvvlgqrpri 119
                                        a+g++i fl +Dd ++ ++le ++++++  ++ + +++  +i
  gi|518653309|ref|YP_008142829.1|  81 IANGEIISFLEDDDLFSNNKLEIIYNRFKY-NKNLCYYHNNHI 122
                                       ****************************99.555655555555 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 !   22.7   0.0   8.3e-09   7.5e-05       4     112 ..       9     108 ..       7     126 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 8.3e-09
                   Glyco_tranf_2_3   4 lavlVptfneedvlgevlesllaqeypr..vevvvvvdesdaetlevaeelaaalpdvrvrvvvnarnlgstgksra 78 
                                       ++++++++++ + l++ + s+++q+ +   +e++++ +  d      ++        ++++ +v ++     +   +
  gi|518653309|ref|YP_008142829.1|   9 ISIIITAYKRKEFLLNAIKSVINQTLDKnyYEIIIIKNFIDNRIDTYIKN-------NHITEIVSKE-E---SLFGK 74 
                                       89**********************974447************97777765.......4666665544.2...44456 PP

                   Glyco_tranf_2_3  79 lnealravksdlvllvDdDtvvePdtlkrllqff 112
                                       l+eal++++++++ +++dD++ + + l+ + + f
  gi|518653309|ref|YP_008142829.1|  75 LVEALNIANGEIISFLEDDDLFSNNKLEIIYNRF 108
                                       88********************999999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      296  (0.0165096); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-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: 994.67
//
Query:       gi|518653310|ref|YP_008142830.1|  [L=312]
Description: hypothetical protein FACI_IFERC00001G1953 [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.2e-19   69.3   0.1      6e-19   68.4   0.1    1.5  1  rve            Integrase core domain
    6.1e-18   64.4   0.2    1.5e-17   63.1   0.2    1.7  1  rve_3          Integrase core domain
    3.2e-11   43.2   1.2    7.2e-11   42.1   1.2    1.5  1  HTH_21         HTH-like domain
    1.3e-05   25.3   1.2      5e-05   23.4   1.2    2.1  1  rve_2          Integrase core domain
     0.0054   16.9   0.8     0.0054   16.9   0.8    1.8  2  DDE_Tnp_IS240  DDE domain
  ------ inclusion threshold ------
      0.096   13.3   0.3      0.096   13.3   0.3    1.8  2  HTH_32         Homeodomain-like domain
        0.2   11.5   0.5       0.34   10.7   0.1    1.6  2  Calici_MSP     Calicivirus minor structural protein
       0.38   11.1   3.5         15    6.0   0.1    3.6  3  NUMOD1         NUMOD1 domain
       0.54   10.5   6.3        1.7    8.8   0.1    3.1  3  Alpha_Helical  Alpha helical domain


Domain annotation for each model (and alignments):
>> rve  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.4   0.1     3e-22     6e-19       5     118 ..     113     227 ..     109     228 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.4 bits;  conditional E-value: 3e-22
                               rve   5 gelwqvDvtvvripdgggkayllvvvddfsrlilaealsdemdastvlalleravarfggve...pervlsDngsey 78 
                                       ++lw++D+ +v+  + +g +yl +v d+fs++ + +  s+  +a+++++ +e+a+a +        +++++Dng++y
  gi|518653310|ref|YP_008142830.1| 113 NQLWETDIHYVS--THNGMYYLMAVKDCFSKRWISYNFSRTCTAKDCVKPIEEAYAIRYSNSnlsNLVLRTDNGTQY 187
                                       99**********..66667*************************************999988999************ PP

                               rve  79 tskafrefladlgirvsftrpgrpqdnGkvErfhrtlkde 118
                                       ++k+f+++++ l+i++++ +++ p+dnG +E+fh  lk++
  gi|518653310|ref|YP_008142830.1| 188 IAKSFKDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTD 227
                                       *************************************975 PP

>> rve_3  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.1   0.2   7.7e-21   1.5e-17       2      67 .]     200     265 ..     199     265 .. 0.98

  Alignments for each domain:
  == domain 1  score: 63.1 bits;  conditional E-value: 7.7e-21
                             rve_3   2 gielsyiapgkPqqNglvEsfngtlrdellneelfrslaearekleawredYNteRPHssLgykTP 67 
                                        i+++yi+  +P +Ng +Esf+++l++ ++ ++  +s ++a+e++e ++ dYN+ RPHss+gy+TP
  gi|518653310|ref|YP_008142830.1| 200 NIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYAFNDYNNYRPHSSIGYLTP 265
                                       699**************************************************************9 PP

>> HTH_21  HTH-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.1   1.2   3.6e-14   7.2e-11      17      59 ..      56      97 ..      42      98 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.1 bits;  conditional E-value: 3.6e-14
                            HTH_21 17 skgrYGyrriwaeLrreggvrvnhkrVrRlMrelGLrgvqrrk 59
                                      ++ +YG+rriwa Lr+e gv++n k+VrR+ +  +L+ ++ + 
  gi|518653310|ref|YP_008142830.1| 56 KRVTYGHRRIWAVLRNE-GVKINIKTVRRIIKSRNLQLPYAKH 97
                                      346**************.789***************9998875 PP

>> rve_2  Integrase core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   1.2   2.5e-08     5e-05       1      50 [.     218     271 ..     218     272 .. 0.88

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 2.5e-08
                             rve_2   1 EsfFgsLKtElvygetfktleeleaaiedYIew.YNnkR....lkglsPvqYrnq 50 
                                       Esf  sLKt+ + +   ++ e ++ ++ +Y    YNn R    +++l+Pv++++q
  gi|518653310|ref|YP_008142830.1| 218 ESFHNSLKTDYIWQNDLESYEDAK-ELMEYAFNdYNNYRphssIGYLTPVEFEKQ 271
                                       9**************999999876.677886555*****888888********98 PP

>> DDE_Tnp_IS240  DDE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.8   2.7e-06    0.0054       4     139 ..     116     257 ..     113     258 .. 0.81
   2 ?   -3.9   0.3       7.3   1.5e+04      92     108 ..     280     296 ..     266     302 .. 0.51

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 2.7e-06
                     DDE_Tnp_IS240   4 wrvDETyvkikGkwaYlyravDkegr.ildflvskrRdtkaakaflrka..lkkek..lepeeivtDkasay.asal 74 
                                       w+ D  yv  +   +Yl ++ D  ++  + + +s    +k + + ++ a  ++ ++  l++ ++ tD    y a+ +
  gi|518653310|ref|YP_008142830.1| 116 WETDIHYVSTHNGMYYLMAVKDCFSKrWISYNFSRTCTAKDCVKPIEEAyaIRYSNsnLSNLVLRTDNGTQYiAKSF 192
                                       7777788888888889988889888879999999999999888888875224544455999*****97766636788 PP

                     DDE_Tnp_IS240  75 kelkregelfdevshvqvkylnnriEsdhrtlKkrlrptrgfkslksaaktlagfeavknlrkgh 139
                                       k   r  +  +e  + q++  n  iEs h+ lK  +  ++ ++s + a++ ++     +n +++h
  gi|518653310|ref|YP_008142830.1| 193 KDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYAFNDYNNYRPH 257
                                       888887777777788899999*****************************999877777777776 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.3
                     DDE_Tnp_IS240  92 vkylnnriEsdhrtlKk 108
                                        k l +r+ ++ r+lK 
  gi|518653310|ref|YP_008142830.1| 280 NKFLEDRMKREERRLKS 296
                                       33555555555555554 PP

>> HTH_32  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.3   4.8e-05     0.096      25      73 .]      37      85 ..      20      85 .. 0.85
   2 ?   -3.3   0.1       7.1   1.4e+04      21      22 ..     291     292 ..     274     305 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 4.8e-05
                            HTH_32 25 rpr.klsdevrariiallreeprWsprqlaarlaeregvkvShstvyriL 73
                                      +++ ++++ +  r++++  ++ +++ r++ a l + egvk+   tv+ri+
  gi|518653310|ref|YP_008142830.1| 37 HKKsRIPENTINRVLEISGKRVTYGHRRIWAVL-RNEGVKINIKTVRRII 85
                                      34449*************55559**********.9999**********96 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 7.1
                            HTH_32  21 pr 22 
                                       +r
  gi|518653310|ref|YP_008142830.1| 291 ER 292
                                       22 PP

>> Calici_MSP  Calicivirus minor structural protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00017      0.34      37     129 ..       8      98 ..       3     113 .. 0.75
   2 ?   -3.6   0.1       4.2   8.4e+03      37      54 ..     279     296 ..     273     303 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00017
                        Calici_MSP  37 qnelletllkkqealqksqleltrdlsinapaarvlsaldaGldevsarrlagsGerviwgnldrpimh..agtmds 111
                                       +n+l  + + k+  +q+s +   r ++++ +++r+  +  + ++e+s +r++  G+r iw  l    ++    t+  
  gi|518653310|ref|YP_008142830.1|   8 RNKLSVSRFSKITGIQRSYIYYNRKITVKHKKSRIPENTINRVLEISGKRVT-YGHRRIWAVLRNEGVKinIKTVRR 83 
                                       57777778899***************************************96.6999***99976544300334444 PP

                        Calici_MSP 112 irqtrhldslshslatfk 129
                                       i ++r    l    a  k
  gi|518653310|ref|YP_008142830.1|  84 IIKSRN---LQLPYAKHK 98 
                                       444444...344444444 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 4.2
                        Calici_MSP  37 qnelletllkkqealqks 54 
                                       +n+ le  +k+ e   ks
  gi|518653310|ref|YP_008142830.1| 279 RNKFLEDRMKREERRLKS 296
                                       689999999998876555 PP

>> NUMOD1  NUMOD1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1      0.04        79      18      35 ..      12      29 ..      12      29 .. 0.93
   2 ?    6.0   0.1    0.0076        15      18      35 ..     191     208 ..     190     208 .. 0.87
   3 ?   -1.8   0.1       2.1   4.3e+03      23      31 ..     296     304 ..     296     305 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.04
                            NUMOD1 18 SireAakyLgishntInk 35
                                      S+++++k+ gi +++I++
  gi|518653310|ref|YP_008142830.1| 12 SVSRFSKITGIQRSYIYY 29
                                      8999************86 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0076
                            NUMOD1  18 SireAakyLgishntInk 35 
                                       S +++ + L+i+h +I+k
  gi|518653310|ref|YP_008142830.1| 191 SFKDTVRLLNIKHEYIKK 208
                                       66788899********97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.1
                            NUMOD1  23 akyLgishn 31 
                                       +++++is++
  gi|518653310|ref|YP_008142830.1| 296 SRKINISRR 304
                                       6899***97 PP

>> Alpha_Helical  Alpha helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.047        94      18      46 ..      79     107 ..      74     116 .. 0.83
   2 ?    8.8   0.1   0.00086       1.7      18      75 ..     190     247 ..     185     251 .. 0.94
   3 ?   -0.3   0.2      0.57   1.1e+03      84     104 ..     275     295 ..     271     302 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.047
                     Alpha_Helical  18 elferivegaklrgkwnkkkalelakeme 46 
                                       ++ +ri+++++l+ ++ k+k ++ +++++
  gi|518653310|ref|YP_008142830.1|  79 KTVRRIIKSRNLQLPYAKHKNRTNKRNLT 107
                                       56789***************999999886 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.00086
                     Alpha_Helical  18 elferivegaklrgkwnkkkalelakemeselqslkysylepedLakseevkklkeka 75 
                                       + f+ +v+  +++ ++ kk++ e   ++es  +slk  y+  +dL + e++k+l e+a
  gi|518653310|ref|YP_008142830.1| 190 KSFKDTVRLLNIKHEYIKKQTPEDNGDIESFHNSLKTDYIWQNDLESYEDAKELMEYA 247
                                       57999*************************************************9875 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.57
                     Alpha_Helical  84 geewsekfleeaekeekekte 104
                                       +ee+ +kfle+  k+e+++++
  gi|518653310|ref|YP_008142830.1| 275 SEEFRNKFLEDRMKREERRLK 295
                                       68999*****99999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       994  (0.0554409); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2231.41
//
Query:       gi|518653311|ref|YP_008142831.1|  [L=91]
Description: transposase [Ferroplasma acidarmanus fer1]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.7e-11   44.3   0.0    2.5e-11   43.7   0.0    1.3  1  HTH_Tnp_1     Transposase
    9.3e-07   28.8   0.0    1.5e-06   28.1   0.0    1.4  1  HTH_29        Winged helix-turn helix
    0.00016   21.7   0.0    0.00024   21.1   0.0    1.4  1  HTH_28        Helix-turn-helix domain
      0.004   16.9   0.0     0.0064   16.3   0.0    1.4  1  HTH_23        Homeodomain-like domain
  ------ inclusion threshold ------
      0.016   15.3   0.0       0.02   15.0   0.0    1.3  1  HTH_Tnp_1_2   Helix-turn-helix of insertion element transposa
      0.067   13.7   0.0      0.075   13.6   0.0    1.2  1  LZ_Tnp_IS481  leucine-zipper of insertion element IS481


Domain annotation for each model (and alignments):
>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.0   8.5e-15   2.5e-11       6      74 ..       3      73 ..       1      74 [. 0.82

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.5e-15
                         HTH_Tnp_1  6 rwsdefKariVreslepgksvsevArrhgvspnqLykWrrqyr...egeeaspaefeltaleeenrelkrel 74
                                      ++++ +K++iV es  ++ +++e++rrhgvs +++ykWr ++    ++   +  ++   + ++en++lkr++
  gi|518653311|ref|YP_008142831.1|  3 KFTPDEKVAIVMES-FTSNNIAELCRRHGVSVASFYKWRDKFIesgKKGFYESGRSGENEYQKENEKLKRLV 73
                                      8*************.7899***********************866533333333357789999999999876 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   5.2e-10   1.5e-06      14      51 ..      21      58 ..      10      65 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 5.2e-10
                            HTH_29 14 tvsqiAkllglsrrtvyrwlkrfeegGlaalldrrrsg 51
                                      +++++++++g+s  ++y+w++ f e G ++  ++ rsg
  gi|518653311|ref|YP_008142831.1| 21 NIAELCRRHGVSVASFYKWRDKFIESGKKGFYESGRSG 58
                                      89*****************************9977777 PP

>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   8.2e-08   0.00024       5      44 ..      12      51 ..       8      58 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 8.2e-08
                            HTH_28  5 iikllaaGhsvreaArelgisrrtvyrWikryeegGiagL 44
                                      i+++    ++++e++r++g+s  + y+W+ ++ e G  g 
  gi|518653311|ref|YP_008142831.1| 12 IVMESFTSNNIAELCRRHGVSVASFYKWRDKFIESGKKGF 51
                                      55555556799***********************997765 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   2.1e-06    0.0064      20      45 ..      22      47 ..      10      52 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 2.1e-06
                            HTH_23 20 vreIAreLgvsrrTvyrwlkryreeG 45
                                      ++e +r++gvs    y+w+ ++ e+G
  gi|518653311|ref|YP_008142831.1| 22 IAELCRRHGVSVASFYKWRDKFIESG 47
                                      7899******************7676 PP

>> HTH_Tnp_1_2  Helix-turn-helix of insertion element transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   0.0   6.8e-06      0.02      20      54 ..      13      45 ..       8      84 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6.8e-06
                                      HHHHH--S-HHHHHHHHTS-HHHHHHHHH-HHHHH CS
                       HTH_Tnp_1_2 20 vendyekltldeiaeevgvsrsTlykWkkkkeFie 54
                                      v + +    ++e+++  gvs + +ykW++k  Fie
  gi|518653311|ref|YP_008142831.1| 13 VMESFTSNNIAELCRRHGVSVASFYKWRDK--FIE 45
                                      5567888899******************86..665 PP

>> LZ_Tnp_IS481  leucine-zipper of insertion element IS481
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   2.5e-05     0.075      25      59 ..      19      53 ..       5      76 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.5e-05
                      LZ_Tnp_IS481 25 rrtvaqvarelGvslrtaykwlarfraeGldGlld 59
                                         +a+ +r  Gvs  + ykw ++f   G +G+ +
  gi|518653311|ref|YP_008142831.1| 19 SNNIAELCRRHGVSVASFYKWRDKFIESGKKGFYE 53
                                      35689999*********************999865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 683.70
//
[ok]
